Multiple sequence alignment - TraesCS7D01G217000

Loading Multiple Alignment...

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 TraesCS7D01G217000 chr7D 100.000 4044 0 0 1 4044 177104206 177108249 0.000000e+00 7468.0
1 TraesCS7D01G217000 chr7D 100.000 86 0 0 2655 2740 49381898 49381983 4.180000e-35 159.0
2 TraesCS7D01G217000 chr7D 98.876 89 1 0 2651 2739 169823367 169823455 4.180000e-35 159.0
3 TraesCS7D01G217000 chr7A 92.603 1798 82 27 1 1780 180646761 180648525 0.000000e+00 2536.0
4 TraesCS7D01G217000 chr7A 95.936 812 33 0 1778 2589 180648554 180649365 0.000000e+00 1317.0
5 TraesCS7D01G217000 chr7A 94.553 716 32 5 3331 4044 180650008 180650718 0.000000e+00 1099.0
6 TraesCS7D01G217000 chr7A 93.349 436 15 10 2754 3181 180649364 180649793 2.050000e-177 632.0
7 TraesCS7D01G217000 chr7A 95.000 60 3 0 3281 3340 180649830 180649889 1.200000e-15 95.3
8 TraesCS7D01G217000 chr7B 92.714 1743 106 14 864 2589 143322756 143324494 0.000000e+00 2495.0
9 TraesCS7D01G217000 chr7B 94.737 779 30 4 3277 4044 143324991 143325769 0.000000e+00 1201.0
10 TraesCS7D01G217000 chr7B 92.570 498 23 3 1 496 143321977 143322462 0.000000e+00 702.0
11 TraesCS7D01G217000 chr7B 92.191 397 27 3 2789 3181 143324498 143324894 3.530000e-155 558.0
12 TraesCS7D01G217000 chr7B 96.875 64 2 0 3277 3340 143324921 143324984 1.540000e-19 108.0
13 TraesCS7D01G217000 chr4A 89.535 172 10 8 2588 2755 95187623 95187456 1.140000e-50 211.0
14 TraesCS7D01G217000 chr6D 98.936 94 0 1 2652 2744 17316715 17316622 2.500000e-37 167.0
15 TraesCS7D01G217000 chr6D 93.939 99 4 1 2648 2744 340997483 340997385 9.060000e-32 148.0
16 TraesCS7D01G217000 chr6D 94.937 79 4 0 2588 2666 374102389 374102467 1.530000e-24 124.0
17 TraesCS7D01G217000 chr6B 84.302 172 19 8 2588 2755 462028628 462028795 1.160000e-35 161.0
18 TraesCS7D01G217000 chr4D 94.118 102 6 0 2649 2750 3719372 3719271 5.410000e-34 156.0
19 TraesCS7D01G217000 chr4D 96.104 77 3 0 2580 2656 15085419 15085495 4.240000e-25 126.0
20 TraesCS7D01G217000 chr3D 98.851 87 1 0 2655 2741 157035739 157035653 5.410000e-34 156.0
21 TraesCS7D01G217000 chr3D 88.889 45 3 2 3107 3150 31950962 31950919 2.000000e-03 54.7
22 TraesCS7D01G217000 chr5A 97.753 89 2 0 2652 2740 505609683 505609595 1.950000e-33 154.0
23 TraesCS7D01G217000 chr3B 96.703 91 3 0 2653 2743 723452946 723452856 7.000000e-33 152.0
24 TraesCS7D01G217000 chr6A 82.558 172 23 7 2588 2755 420829928 420829760 1.170000e-30 145.0
25 TraesCS7D01G217000 chr1B 93.103 87 6 0 2588 2674 471753765 471753679 1.180000e-25 128.0
26 TraesCS7D01G217000 chr1B 100.000 28 0 0 3107 3134 565948543 565948516 7.000000e-03 52.8
27 TraesCS7D01G217000 chr5B 96.154 78 1 2 2579 2656 14288923 14288998 4.240000e-25 126.0
28 TraesCS7D01G217000 chr2A 97.297 74 2 0 2583 2656 1322501 1322428 4.240000e-25 126.0
29 TraesCS7D01G217000 chr1D 89.583 96 7 3 2564 2656 365209496 365209401 7.100000e-23 119.0


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 TraesCS7D01G217000 chr7D 177104206 177108249 4043 False 7468.00 7468 100.0000 1 4044 1 chr7D.!!$F3 4043
1 TraesCS7D01G217000 chr7A 180646761 180650718 3957 False 1135.86 2536 94.2882 1 4044 5 chr7A.!!$F1 4043
2 TraesCS7D01G217000 chr7B 143321977 143325769 3792 False 1012.80 2495 93.8174 1 4044 5 chr7B.!!$F1 4043

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
733 783 0.979665 TGGCCTCTGAACAGGAGAAG 59.020 55.0 3.32 0.00 35.20 2.85 F
1201 1258 0.033504 GGAGCTGTTCGAACACCTCA 59.966 55.0 36.45 17.27 41.31 3.86 F
2480 2580 0.033796 ATGACGAACCCCTCTACGGA 60.034 55.0 0.00 0.00 33.16 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2652 2752 0.042131 TGTGGGACGGAGGGAGTAAT 59.958 55.0 0.00 0.0 0.00 1.89 R
2654 2754 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.0 0.00 0.0 0.00 2.59 R
3774 4026 0.527113 CTTCGCCATGGCATTGTTCA 59.473 50.0 34.93 10.0 42.06 3.18 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
35 36 1.442184 CGACGACTACAAGCGCTGT 60.442 57.895 12.58 14.26 42.47 4.40
274 275 2.202932 ATCAGGATCCACGCGCAC 60.203 61.111 15.82 0.00 0.00 5.34
378 379 1.320344 CGCTGCTCTGGTAGTGGGTA 61.320 60.000 0.00 0.00 33.18 3.69
447 448 1.781025 GCGTGTGCAAGCTGTTGGTA 61.781 55.000 3.00 0.00 42.15 3.25
449 450 1.308998 GTGTGCAAGCTGTTGGTAGT 58.691 50.000 0.00 0.00 33.87 2.73
458 459 2.972713 AGCTGTTGGTAGTCTTCCAAGA 59.027 45.455 10.97 9.23 44.21 3.02
510 513 3.902881 TGTTTGATTTGTTGTGCCCTT 57.097 38.095 0.00 0.00 0.00 3.95
513 516 3.902881 TTGATTTGTTGTGCCCTTTGT 57.097 38.095 0.00 0.00 0.00 2.83
545 548 6.027749 GCTGGTAGCATGTTGTGTTAATTAC 58.972 40.000 0.00 0.00 41.89 1.89
546 549 6.128007 GCTGGTAGCATGTTGTGTTAATTACT 60.128 38.462 0.00 0.00 41.89 2.24
547 550 7.065324 GCTGGTAGCATGTTGTGTTAATTACTA 59.935 37.037 0.00 0.00 41.89 1.82
548 551 8.487313 TGGTAGCATGTTGTGTTAATTACTAG 57.513 34.615 0.00 0.00 0.00 2.57
620 664 7.328249 TGCGAATTGTGAAATTCTTGGTTATTC 59.672 33.333 8.96 0.00 37.10 1.75
718 768 8.607441 AACTCTTAATTTTCTTTTTGATGGCC 57.393 30.769 0.00 0.00 0.00 5.36
722 772 8.090214 TCTTAATTTTCTTTTTGATGGCCTCTG 58.910 33.333 3.32 0.00 0.00 3.35
723 773 6.423776 AATTTTCTTTTTGATGGCCTCTGA 57.576 33.333 3.32 0.00 0.00 3.27
725 775 4.853924 TTCTTTTTGATGGCCTCTGAAC 57.146 40.909 3.32 0.00 0.00 3.18
727 777 3.822735 TCTTTTTGATGGCCTCTGAACAG 59.177 43.478 3.32 0.00 0.00 3.16
728 778 2.205022 TTTGATGGCCTCTGAACAGG 57.795 50.000 3.32 0.00 36.50 4.00
729 779 1.361204 TTGATGGCCTCTGAACAGGA 58.639 50.000 3.32 0.00 35.20 3.86
732 782 1.556911 GATGGCCTCTGAACAGGAGAA 59.443 52.381 3.32 0.00 35.20 2.87
733 783 0.979665 TGGCCTCTGAACAGGAGAAG 59.020 55.000 3.32 0.00 35.20 2.85
734 784 1.270907 GGCCTCTGAACAGGAGAAGA 58.729 55.000 0.00 0.00 35.20 2.87
740 790 5.451798 GCCTCTGAACAGGAGAAGATTCTAG 60.452 48.000 1.93 0.00 37.73 2.43
762 812 9.790344 TCTAGTGAAGTATAGGGAGTATGTAAC 57.210 37.037 0.00 0.00 0.00 2.50
848 898 2.480759 GCATTCCGTGACCATACTACGT 60.481 50.000 0.00 0.00 36.17 3.57
850 900 3.940209 TTCCGTGACCATACTACGTTT 57.060 42.857 0.00 0.00 36.17 3.60
855 905 4.687483 CCGTGACCATACTACGTTTTTCTT 59.313 41.667 0.00 0.00 36.17 2.52
868 918 5.588240 ACGTTTTTCTTGTTGAGAATTCCC 58.412 37.500 0.65 0.00 43.65 3.97
921 971 2.083715 CCTTCTTTGGGCCCCTACA 58.916 57.895 22.27 0.00 0.00 2.74
945 995 2.364317 TGCTAGCCGCCTCTTCCT 60.364 61.111 13.29 0.00 38.05 3.36
1201 1258 0.033504 GGAGCTGTTCGAACACCTCA 59.966 55.000 36.45 17.27 41.31 3.86
1354 1411 5.968528 TGCGTTTAACATTGGTTCCTAAT 57.031 34.783 0.00 0.00 38.45 1.73
1360 1417 7.544622 GTTTAACATTGGTTCCTAATCCTTCC 58.455 38.462 0.00 0.00 38.45 3.46
1436 1494 8.934023 AAGTTTGGAGAACAATTAACTGGATA 57.066 30.769 0.00 0.00 39.21 2.59
1484 1542 1.212688 TGGGTCTGCACTTATCCATGG 59.787 52.381 4.97 4.97 0.00 3.66
1534 1601 4.864247 GGGCAAGCAGTACAACAAATTATG 59.136 41.667 0.00 0.00 0.00 1.90
1703 1770 3.116900 TCCCTGGCTGTAGACATATGGTA 60.117 47.826 7.80 0.00 29.25 3.25
1720 1787 8.893727 ACATATGGTAATTCTTGTAAGCTTGAC 58.106 33.333 9.86 4.25 0.00 3.18
1814 1913 3.454375 TCTTTCCGCCATATCGAAGTTC 58.546 45.455 0.00 0.00 0.00 3.01
1878 1977 2.555199 CTGGAGTGCAACATAGCTACC 58.445 52.381 0.00 0.00 41.43 3.18
1979 2079 1.455217 TGCTCCTCCTACCGCTACC 60.455 63.158 0.00 0.00 0.00 3.18
2187 2287 2.028130 CCTCATCCGCATTCTTGGC 58.972 57.895 0.00 0.00 0.00 4.52
2192 2292 1.406180 CATCCGCATTCTTGGCATGAA 59.594 47.619 16.87 16.87 0.00 2.57
2204 2304 1.284491 TGGCATGAATTCCCAGTGCTA 59.716 47.619 16.52 11.06 36.15 3.49
2233 2333 3.931578 TCTTGAAAGAGGTAAGAGCTGC 58.068 45.455 0.00 0.00 0.00 5.25
2246 2346 3.730761 GCTGCGCCAAGGTGACTG 61.731 66.667 4.18 0.99 42.68 3.51
2291 2391 3.319122 AGCAGAAACCAGTTGGAATTGTC 59.681 43.478 4.92 0.00 38.94 3.18
2301 2401 8.122472 ACCAGTTGGAATTGTCCTTATTTAAG 57.878 34.615 4.92 0.00 45.22 1.85
2344 2444 4.049393 GCGTTCAGCCTTCACAGT 57.951 55.556 0.00 0.00 40.81 3.55
2480 2580 0.033796 ATGACGAACCCCTCTACGGA 60.034 55.000 0.00 0.00 33.16 4.69
2552 2652 0.700564 TGAGGAAGAAGCCTGCCAAT 59.299 50.000 0.00 0.00 40.92 3.16
2589 2689 2.159226 ACTCGCCACATCTTGCTACTAC 60.159 50.000 0.00 0.00 0.00 2.73
2590 2690 2.099921 CTCGCCACATCTTGCTACTACT 59.900 50.000 0.00 0.00 0.00 2.57
2591 2691 2.496070 TCGCCACATCTTGCTACTACTT 59.504 45.455 0.00 0.00 0.00 2.24
2592 2692 2.860735 CGCCACATCTTGCTACTACTTC 59.139 50.000 0.00 0.00 0.00 3.01
2593 2693 3.198872 GCCACATCTTGCTACTACTTCC 58.801 50.000 0.00 0.00 0.00 3.46
2594 2694 3.118592 GCCACATCTTGCTACTACTTCCT 60.119 47.826 0.00 0.00 0.00 3.36
2595 2695 4.688021 CCACATCTTGCTACTACTTCCTC 58.312 47.826 0.00 0.00 0.00 3.71
2596 2696 4.442192 CCACATCTTGCTACTACTTCCTCC 60.442 50.000 0.00 0.00 0.00 4.30
2597 2697 3.381908 ACATCTTGCTACTACTTCCTCCG 59.618 47.826 0.00 0.00 0.00 4.63
2598 2698 3.083122 TCTTGCTACTACTTCCTCCGT 57.917 47.619 0.00 0.00 0.00 4.69
2599 2699 4.226427 TCTTGCTACTACTTCCTCCGTA 57.774 45.455 0.00 0.00 0.00 4.02
2600 2700 4.592942 TCTTGCTACTACTTCCTCCGTAA 58.407 43.478 0.00 0.00 0.00 3.18
2601 2701 5.012239 TCTTGCTACTACTTCCTCCGTAAA 58.988 41.667 0.00 0.00 0.00 2.01
2602 2702 4.708726 TGCTACTACTTCCTCCGTAAAC 57.291 45.455 0.00 0.00 0.00 2.01
2603 2703 4.338879 TGCTACTACTTCCTCCGTAAACT 58.661 43.478 0.00 0.00 0.00 2.66
2604 2704 5.500234 TGCTACTACTTCCTCCGTAAACTA 58.500 41.667 0.00 0.00 0.00 2.24
2605 2705 5.945784 TGCTACTACTTCCTCCGTAAACTAA 59.054 40.000 0.00 0.00 0.00 2.24
2606 2706 6.604795 TGCTACTACTTCCTCCGTAAACTAAT 59.395 38.462 0.00 0.00 0.00 1.73
2607 2707 7.775093 TGCTACTACTTCCTCCGTAAACTAATA 59.225 37.037 0.00 0.00 0.00 0.98
2608 2708 8.791675 GCTACTACTTCCTCCGTAAACTAATAT 58.208 37.037 0.00 0.00 0.00 1.28
2614 2714 9.418839 ACTTCCTCCGTAAACTAATATAAGAGT 57.581 33.333 0.00 0.00 0.00 3.24
2615 2715 9.680315 CTTCCTCCGTAAACTAATATAAGAGTG 57.320 37.037 0.00 0.00 0.00 3.51
2616 2716 8.757982 TCCTCCGTAAACTAATATAAGAGTGT 57.242 34.615 0.00 0.00 0.00 3.55
2617 2717 9.193806 TCCTCCGTAAACTAATATAAGAGTGTT 57.806 33.333 0.00 0.00 0.00 3.32
2618 2718 9.813446 CCTCCGTAAACTAATATAAGAGTGTTT 57.187 33.333 0.00 0.00 0.00 2.83
2645 2745 9.733219 AGATCACTACTTTAGTAATCTAAACGC 57.267 33.333 0.00 0.00 40.05 4.84
2646 2746 9.733219 GATCACTACTTTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 40.05 5.07
2647 2747 9.733219 ATCACTACTTTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
2648 2748 8.954350 TCACTACTTTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 40.05 4.09
2649 2749 9.570488 CACTACTTTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 40.05 2.85
2661 2761 8.653036 ATCTAAACGCTCTTATATTACTCCCT 57.347 34.615 0.00 0.00 0.00 4.20
2662 2762 8.108551 TCTAAACGCTCTTATATTACTCCCTC 57.891 38.462 0.00 0.00 0.00 4.30
2663 2763 5.725325 AACGCTCTTATATTACTCCCTCC 57.275 43.478 0.00 0.00 0.00 4.30
2664 2764 3.757493 ACGCTCTTATATTACTCCCTCCG 59.243 47.826 0.00 0.00 0.00 4.63
2665 2765 3.757493 CGCTCTTATATTACTCCCTCCGT 59.243 47.826 0.00 0.00 0.00 4.69
2666 2766 4.142643 CGCTCTTATATTACTCCCTCCGTC 60.143 50.000 0.00 0.00 0.00 4.79
2667 2767 4.158209 GCTCTTATATTACTCCCTCCGTCC 59.842 50.000 0.00 0.00 0.00 4.79
2668 2768 4.670765 TCTTATATTACTCCCTCCGTCCC 58.329 47.826 0.00 0.00 0.00 4.46
2669 2769 4.106825 TCTTATATTACTCCCTCCGTCCCA 59.893 45.833 0.00 0.00 0.00 4.37
2670 2770 2.077687 TATTACTCCCTCCGTCCCAC 57.922 55.000 0.00 0.00 0.00 4.61
2671 2771 0.042131 ATTACTCCCTCCGTCCCACA 59.958 55.000 0.00 0.00 0.00 4.17
2672 2772 0.178926 TTACTCCCTCCGTCCCACAA 60.179 55.000 0.00 0.00 0.00 3.33
2673 2773 0.042131 TACTCCCTCCGTCCCACAAT 59.958 55.000 0.00 0.00 0.00 2.71
2674 2774 0.042131 ACTCCCTCCGTCCCACAATA 59.958 55.000 0.00 0.00 0.00 1.90
2675 2775 1.344087 ACTCCCTCCGTCCCACAATAT 60.344 52.381 0.00 0.00 0.00 1.28
2676 2776 2.090943 ACTCCCTCCGTCCCACAATATA 60.091 50.000 0.00 0.00 0.00 0.86
2677 2777 2.969950 CTCCCTCCGTCCCACAATATAA 59.030 50.000 0.00 0.00 0.00 0.98
2678 2778 2.969950 TCCCTCCGTCCCACAATATAAG 59.030 50.000 0.00 0.00 0.00 1.73
2679 2779 2.969950 CCCTCCGTCCCACAATATAAGA 59.030 50.000 0.00 0.00 0.00 2.10
2680 2780 3.006967 CCCTCCGTCCCACAATATAAGAG 59.993 52.174 0.00 0.00 0.00 2.85
2681 2781 3.555168 CCTCCGTCCCACAATATAAGAGC 60.555 52.174 0.00 0.00 0.00 4.09
2682 2782 2.035449 TCCGTCCCACAATATAAGAGCG 59.965 50.000 0.00 0.00 0.00 5.03
2683 2783 2.223971 CCGTCCCACAATATAAGAGCGT 60.224 50.000 0.00 0.00 0.00 5.07
2684 2784 3.454375 CGTCCCACAATATAAGAGCGTT 58.546 45.455 0.00 0.00 0.00 4.84
2685 2785 3.869246 CGTCCCACAATATAAGAGCGTTT 59.131 43.478 0.00 0.00 0.00 3.60
2686 2786 4.331717 CGTCCCACAATATAAGAGCGTTTT 59.668 41.667 0.00 0.00 0.00 2.43
2687 2787 5.163794 CGTCCCACAATATAAGAGCGTTTTT 60.164 40.000 0.00 0.00 0.00 1.94
2688 2788 6.027749 GTCCCACAATATAAGAGCGTTTTTG 58.972 40.000 0.00 0.00 0.00 2.44
2689 2789 5.941058 TCCCACAATATAAGAGCGTTTTTGA 59.059 36.000 0.00 0.00 0.00 2.69
2690 2790 6.027749 CCCACAATATAAGAGCGTTTTTGAC 58.972 40.000 0.00 0.00 0.00 3.18
2691 2791 6.348950 CCCACAATATAAGAGCGTTTTTGACA 60.349 38.462 0.00 0.00 0.00 3.58
2692 2792 6.523201 CCACAATATAAGAGCGTTTTTGACAC 59.477 38.462 0.00 0.00 0.00 3.67
2693 2793 7.298122 CACAATATAAGAGCGTTTTTGACACT 58.702 34.615 0.00 0.00 0.00 3.55
2694 2794 8.440059 CACAATATAAGAGCGTTTTTGACACTA 58.560 33.333 0.00 0.00 0.00 2.74
2695 2795 8.995220 ACAATATAAGAGCGTTTTTGACACTAA 58.005 29.630 0.00 0.00 0.00 2.24
2696 2796 9.988350 CAATATAAGAGCGTTTTTGACACTAAT 57.012 29.630 0.00 0.00 0.00 1.73
2697 2797 9.988350 AATATAAGAGCGTTTTTGACACTAATG 57.012 29.630 0.00 0.00 0.00 1.90
2698 2798 5.751243 AAGAGCGTTTTTGACACTAATGT 57.249 34.783 0.00 0.00 43.71 2.71
2699 2799 6.854496 AAGAGCGTTTTTGACACTAATGTA 57.146 33.333 0.00 0.00 39.95 2.29
2700 2800 6.467723 AGAGCGTTTTTGACACTAATGTAG 57.532 37.500 0.00 0.00 39.95 2.74
2701 2801 5.989777 AGAGCGTTTTTGACACTAATGTAGT 59.010 36.000 0.00 0.00 39.95 2.73
2729 2829 6.780706 AAAACGCTCTTATATTATGGGACG 57.219 37.500 0.00 0.00 0.00 4.79
2730 2830 4.451629 ACGCTCTTATATTATGGGACGG 57.548 45.455 0.00 0.00 0.00 4.79
2731 2831 4.084287 ACGCTCTTATATTATGGGACGGA 58.916 43.478 0.00 0.00 0.00 4.69
2732 2832 4.158025 ACGCTCTTATATTATGGGACGGAG 59.842 45.833 0.00 0.00 0.00 4.63
2733 2833 4.440250 CGCTCTTATATTATGGGACGGAGG 60.440 50.000 0.00 0.00 0.00 4.30
2734 2834 4.141914 GCTCTTATATTATGGGACGGAGGG 60.142 50.000 0.00 0.00 0.00 4.30
2735 2835 5.269991 CTCTTATATTATGGGACGGAGGGA 58.730 45.833 0.00 0.00 0.00 4.20
2736 2836 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2737 2837 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2738 2838 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2739 2839 2.376695 TTATGGGACGGAGGGAGTAG 57.623 55.000 0.00 0.00 0.00 2.57
2740 2840 1.229131 TATGGGACGGAGGGAGTAGT 58.771 55.000 0.00 0.00 0.00 2.73
2741 2841 0.338814 ATGGGACGGAGGGAGTAGTT 59.661 55.000 0.00 0.00 0.00 2.24
2742 2842 0.115745 TGGGACGGAGGGAGTAGTTT 59.884 55.000 0.00 0.00 0.00 2.66
2743 2843 1.358787 TGGGACGGAGGGAGTAGTTTA 59.641 52.381 0.00 0.00 0.00 2.01
2744 2844 1.753649 GGGACGGAGGGAGTAGTTTAC 59.246 57.143 0.00 0.00 0.00 2.01
2745 2845 2.450476 GGACGGAGGGAGTAGTTTACA 58.550 52.381 0.00 0.00 0.00 2.41
2746 2846 2.426381 GGACGGAGGGAGTAGTTTACAG 59.574 54.545 0.00 0.00 0.00 2.74
2747 2847 3.350833 GACGGAGGGAGTAGTTTACAGA 58.649 50.000 0.00 0.00 0.00 3.41
2748 2848 3.354467 ACGGAGGGAGTAGTTTACAGAG 58.646 50.000 0.00 0.00 0.00 3.35
2749 2849 2.688958 CGGAGGGAGTAGTTTACAGAGG 59.311 54.545 0.00 0.00 0.00 3.69
2750 2850 3.032459 GGAGGGAGTAGTTTACAGAGGG 58.968 54.545 0.00 0.00 0.00 4.30
2751 2851 3.309701 GGAGGGAGTAGTTTACAGAGGGA 60.310 52.174 0.00 0.00 0.00 4.20
2752 2852 3.955551 GAGGGAGTAGTTTACAGAGGGAG 59.044 52.174 0.00 0.00 0.00 4.30
2753 2853 3.337301 AGGGAGTAGTTTACAGAGGGAGT 59.663 47.826 0.00 0.00 0.00 3.85
2754 2854 4.543337 AGGGAGTAGTTTACAGAGGGAGTA 59.457 45.833 0.00 0.00 0.00 2.59
2772 2872 4.819630 GGAGTAGATGAGAGCTATATCCCG 59.180 50.000 0.00 0.00 0.00 5.14
2774 2874 5.433526 AGTAGATGAGAGCTATATCCCGTC 58.566 45.833 0.00 0.00 0.00 4.79
2775 2875 3.626930 AGATGAGAGCTATATCCCGTCC 58.373 50.000 0.00 0.00 0.00 4.79
2874 2975 0.748367 GAATCTGGGGAAACGGCTCC 60.748 60.000 0.00 0.00 34.41 4.70
3047 3148 1.917273 GCATGTGTTGCCATGATCAC 58.083 50.000 0.00 0.00 46.15 3.06
3080 3181 0.110486 GGTCTCCCTCCAGTTTTGCA 59.890 55.000 0.00 0.00 0.00 4.08
3082 3183 1.140312 TCTCCCTCCAGTTTTGCACT 58.860 50.000 0.00 0.00 35.35 4.40
3119 3220 1.420138 AGTGTGTAGTGGGTTTCCTGG 59.580 52.381 0.00 0.00 0.00 4.45
3121 3222 1.142060 TGTGTAGTGGGTTTCCTGGTG 59.858 52.381 0.00 0.00 0.00 4.17
3169 3272 5.715921 TCCCACCTCATGTAATCTCTATCA 58.284 41.667 0.00 0.00 0.00 2.15
3174 3277 7.989741 CCACCTCATGTAATCTCTATCAAACTT 59.010 37.037 0.00 0.00 0.00 2.66
3199 3313 9.771534 TTTGTTTTAAAGTAATGGAAATGGGAG 57.228 29.630 0.00 0.00 0.00 4.30
3200 3314 7.382898 TGTTTTAAAGTAATGGAAATGGGAGC 58.617 34.615 0.00 0.00 0.00 4.70
3201 3315 7.015682 TGTTTTAAAGTAATGGAAATGGGAGCA 59.984 33.333 0.00 0.00 0.00 4.26
3202 3316 6.773976 TTAAAGTAATGGAAATGGGAGCAG 57.226 37.500 0.00 0.00 0.00 4.24
3203 3317 2.659428 AGTAATGGAAATGGGAGCAGC 58.341 47.619 0.00 0.00 0.00 5.25
3213 3327 2.282180 GGAGCAGCCCGGTTCAAA 60.282 61.111 0.00 0.00 0.00 2.69
3214 3328 1.901464 GGAGCAGCCCGGTTCAAAA 60.901 57.895 0.00 0.00 0.00 2.44
3215 3329 1.460273 GGAGCAGCCCGGTTCAAAAA 61.460 55.000 0.00 0.00 0.00 1.94
3251 3365 3.243128 GCACCGGCAAAAATGTGC 58.757 55.556 0.00 0.00 46.09 4.57
3252 3366 4.746361 CACCGGCAAAAATGTGCA 57.254 50.000 0.00 0.00 46.81 4.57
3253 3367 2.983433 CACCGGCAAAAATGTGCAA 58.017 47.368 0.00 0.00 46.81 4.08
3254 3368 0.581053 CACCGGCAAAAATGTGCAAC 59.419 50.000 0.00 0.00 46.81 4.17
3255 3369 0.531753 ACCGGCAAAAATGTGCAACC 60.532 50.000 0.00 0.00 46.81 3.77
3256 3370 0.249826 CCGGCAAAAATGTGCAACCT 60.250 50.000 0.00 0.00 46.81 3.50
3257 3371 0.860533 CGGCAAAAATGTGCAACCTG 59.139 50.000 0.00 0.00 46.81 4.00
3258 3372 0.587768 GGCAAAAATGTGCAACCTGC 59.412 50.000 0.00 0.00 46.81 4.85
3259 3373 1.585297 GCAAAAATGTGCAACCTGCT 58.415 45.000 0.00 0.00 45.31 4.24
3260 3374 2.547642 GGCAAAAATGTGCAACCTGCTA 60.548 45.455 0.00 0.00 46.81 3.49
3261 3375 2.476241 GCAAAAATGTGCAACCTGCTAC 59.524 45.455 0.00 0.00 45.31 3.58
3262 3376 3.715495 CAAAAATGTGCAACCTGCTACA 58.285 40.909 0.00 3.74 45.31 2.74
3263 3377 4.309099 CAAAAATGTGCAACCTGCTACAT 58.691 39.130 0.00 9.45 45.31 2.29
3264 3378 4.605640 AAAATGTGCAACCTGCTACATT 57.394 36.364 16.62 16.62 46.49 2.71
3265 3379 3.581024 AATGTGCAACCTGCTACATTG 57.419 42.857 19.35 0.00 44.80 2.82
3266 3380 0.597568 TGTGCAACCTGCTACATTGC 59.402 50.000 0.00 1.30 45.31 3.56
3269 3383 1.986698 GCAACCTGCTACATTGCAAG 58.013 50.000 4.94 0.00 46.37 4.01
3270 3384 1.986698 CAACCTGCTACATTGCAAGC 58.013 50.000 4.94 2.77 42.83 4.01
3271 3385 0.523072 AACCTGCTACATTGCAAGCG 59.477 50.000 4.94 0.64 42.83 4.68
3272 3386 1.226491 CCTGCTACATTGCAAGCGC 60.226 57.895 4.94 0.00 42.83 5.92
3547 3791 5.480422 TCTCTTTAGCACAGTATGAAGTCCA 59.520 40.000 0.00 0.00 39.69 4.02
3548 3792 5.479306 TCTTTAGCACAGTATGAAGTCCAC 58.521 41.667 0.00 0.00 39.69 4.02
3605 3857 6.940298 TCAAAATCTGTTTCTTCGAATAGGGT 59.060 34.615 0.00 0.00 0.00 4.34
3613 3865 2.504175 TCTTCGAATAGGGTCCCAAAGG 59.496 50.000 11.55 0.00 0.00 3.11
3688 3940 9.419297 GTTGTACAACATCTCTACATGAGTTTA 57.581 33.333 29.46 0.00 40.87 2.01
3774 4026 0.249322 CGAGGATTCGTACGCCCATT 60.249 55.000 11.24 0.00 41.84 3.16
3823 4075 6.963049 ACAAGTTCTAGCACCTAAATAACG 57.037 37.500 0.00 0.00 0.00 3.18
3917 4169 0.165295 CATCACAACTGTCAGCTGCG 59.835 55.000 9.47 2.20 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
362 363 0.968901 CGGTACCCACTACCAGAGCA 60.969 60.000 6.25 0.00 45.11 4.26
370 371 3.762247 GCACGGCGGTACCCACTA 61.762 66.667 13.24 0.00 33.26 2.74
378 379 4.250305 AAAGACCAGCACGGCGGT 62.250 61.111 13.24 0.00 39.03 5.68
447 448 4.337145 ACTGTCTACGATCTTGGAAGACT 58.663 43.478 0.00 0.00 37.98 3.24
449 450 4.590918 AGACTGTCTACGATCTTGGAAGA 58.409 43.478 8.91 0.00 39.78 2.87
458 459 6.920758 GCAAATGATTCTAGACTGTCTACGAT 59.079 38.462 13.34 9.97 0.00 3.73
510 513 0.323629 GCTACCAGCCTACCACACAA 59.676 55.000 0.00 0.00 34.48 3.33
513 516 0.541392 CATGCTACCAGCCTACCACA 59.459 55.000 0.00 0.00 41.51 4.17
552 555 8.673711 ACGTCCAAACTAGTACGTATGTAATAA 58.326 33.333 17.57 0.00 45.85 1.40
553 556 8.208718 ACGTCCAAACTAGTACGTATGTAATA 57.791 34.615 17.57 0.00 45.85 0.98
554 557 7.088589 ACGTCCAAACTAGTACGTATGTAAT 57.911 36.000 17.57 0.18 45.85 1.89
555 558 6.494893 ACGTCCAAACTAGTACGTATGTAA 57.505 37.500 17.57 0.00 45.85 2.41
557 560 6.494893 TTACGTCCAAACTAGTACGTATGT 57.505 37.500 22.63 11.84 46.49 2.29
558 561 7.975866 AATTACGTCCAAACTAGTACGTATG 57.024 36.000 22.63 7.46 46.49 2.39
559 562 8.028938 ACAAATTACGTCCAAACTAGTACGTAT 58.971 33.333 22.63 11.19 46.49 3.06
560 563 7.367285 ACAAATTACGTCCAAACTAGTACGTA 58.633 34.615 19.70 19.70 45.85 3.57
562 565 6.695292 ACAAATTACGTCCAAACTAGTACG 57.305 37.500 13.06 13.06 40.99 3.67
563 566 9.797473 GTTAACAAATTACGTCCAAACTAGTAC 57.203 33.333 0.00 0.00 0.00 2.73
564 567 9.762933 AGTTAACAAATTACGTCCAAACTAGTA 57.237 29.630 8.61 0.00 0.00 1.82
565 568 8.667076 AGTTAACAAATTACGTCCAAACTAGT 57.333 30.769 8.61 0.00 0.00 2.57
566 569 9.590088 GAAGTTAACAAATTACGTCCAAACTAG 57.410 33.333 8.61 0.00 0.00 2.57
681 731 8.299570 AGAAAATTAAGAGTTTCGTCATTGCAT 58.700 29.630 0.00 0.00 42.85 3.96
718 768 6.376864 TCACTAGAATCTTCTCCTGTTCAGAG 59.623 42.308 0.00 0.00 38.70 3.35
722 772 6.930731 ACTTCACTAGAATCTTCTCCTGTTC 58.069 40.000 0.00 0.00 38.70 3.18
723 773 6.926630 ACTTCACTAGAATCTTCTCCTGTT 57.073 37.500 0.00 0.00 38.70 3.16
725 775 8.792633 CCTATACTTCACTAGAATCTTCTCCTG 58.207 40.741 0.00 0.00 38.70 3.86
727 777 7.945664 TCCCTATACTTCACTAGAATCTTCTCC 59.054 40.741 0.00 0.00 38.70 3.71
728 778 8.927675 TCCCTATACTTCACTAGAATCTTCTC 57.072 38.462 0.00 0.00 38.70 2.87
729 779 8.507761 ACTCCCTATACTTCACTAGAATCTTCT 58.492 37.037 0.00 0.00 41.24 2.85
732 782 9.747898 CATACTCCCTATACTTCACTAGAATCT 57.252 37.037 0.00 0.00 32.31 2.40
733 783 9.523168 ACATACTCCCTATACTTCACTAGAATC 57.477 37.037 0.00 0.00 32.31 2.52
762 812 6.024049 CGTTGCTTATAAGAAGCCAGAAAAG 58.976 40.000 16.85 0.00 42.36 2.27
769 819 4.083484 ACAACACGTTGCTTATAAGAAGCC 60.083 41.667 16.85 0.00 44.03 4.35
819 869 1.078918 TCACGGAATGCAGCTCCAG 60.079 57.895 15.88 11.30 32.77 3.86
848 898 6.183360 GGACAGGGAATTCTCAACAAGAAAAA 60.183 38.462 8.33 0.00 46.85 1.94
850 900 4.827284 GGACAGGGAATTCTCAACAAGAAA 59.173 41.667 8.33 0.00 46.85 2.52
855 905 4.536090 AGTATGGACAGGGAATTCTCAACA 59.464 41.667 8.33 1.01 0.00 3.33
893 943 1.256812 CCAAAGAAGGCGGGTTTCAT 58.743 50.000 0.00 0.00 0.00 2.57
1201 1258 3.055719 CCACGGGATGCGCTTGTT 61.056 61.111 9.73 0.00 0.00 2.83
1424 1482 9.936329 ACCTACCATTTCAATATCCAGTTAATT 57.064 29.630 0.00 0.00 0.00 1.40
1436 1494 8.497745 ACTGATGATCTAACCTACCATTTCAAT 58.502 33.333 0.00 0.00 0.00 2.57
1452 1510 3.070734 GTGCAGACCCATACTGATGATCT 59.929 47.826 0.00 0.00 37.54 2.75
1484 1542 0.314935 CACACATTCACCACCCAAGC 59.685 55.000 0.00 0.00 0.00 4.01
1576 1643 5.118664 CGTCCTACATAATTTAGCATCGGTG 59.881 44.000 0.00 0.00 0.00 4.94
1703 1770 6.017605 CAGTGTCAGTCAAGCTTACAAGAATT 60.018 38.462 0.00 0.00 33.61 2.17
1720 1787 7.178712 AGTCTAATTTTCGTTTCAGTGTCAG 57.821 36.000 0.00 0.00 0.00 3.51
1814 1913 4.391216 CCAGCAATTATCTTCGGCTATCAG 59.609 45.833 0.00 0.00 32.71 2.90
1878 1977 9.720667 CAATGGTTAACTGACATTGTATACATG 57.279 33.333 19.68 9.60 43.83 3.21
1979 2079 0.179073 CCAATGGGGCTAGACGACTG 60.179 60.000 0.00 0.00 0.00 3.51
2088 2188 4.079787 TCTGGGCTGTAGGATAGCAAAAAT 60.080 41.667 0.00 0.00 42.88 1.82
2099 2199 1.967066 CAGGTATCTCTGGGCTGTAGG 59.033 57.143 0.00 0.00 0.00 3.18
2133 2233 3.956744 ACCTCAAATCTGTTAGCCCTTC 58.043 45.455 0.00 0.00 0.00 3.46
2175 2275 2.466846 GAATTCATGCCAAGAATGCGG 58.533 47.619 0.00 0.00 35.96 5.69
2187 2287 4.272489 TCCTTTAGCACTGGGAATTCATG 58.728 43.478 7.93 1.13 0.00 3.07
2192 2292 6.101734 TCAAGATATCCTTTAGCACTGGGAAT 59.898 38.462 0.00 0.00 31.42 3.01
2204 2304 7.990314 GCTCTTACCTCTTTCAAGATATCCTTT 59.010 37.037 0.00 0.00 33.93 3.11
2233 2333 2.949106 CAAGCAGTCACCTTGGCG 59.051 61.111 0.00 0.00 36.82 5.69
2246 2346 1.750193 TACAGGGTAGCAATGCAAGC 58.250 50.000 8.35 6.40 0.00 4.01
2291 2391 8.705594 TCTCCAGATGTTACCTCTTAAATAAGG 58.294 37.037 0.62 0.00 38.70 2.69
2301 2401 6.547880 TGAGAATACTCTCCAGATGTTACCTC 59.452 42.308 0.00 0.00 46.67 3.85
2450 2550 3.657448 TTCGTCATCGGCGTGCCAT 62.657 57.895 12.06 0.99 37.69 4.40
2480 2580 2.521224 GCGATCTCCGGGGTAGGT 60.521 66.667 0.00 0.00 39.04 3.08
2552 2652 3.998341 GGCGAGTACCTTGTGATTTTGTA 59.002 43.478 0.00 0.00 0.00 2.41
2589 2689 9.680315 CACTCTTATATTAGTTTACGGAGGAAG 57.320 37.037 0.00 0.00 0.00 3.46
2590 2690 9.193806 ACACTCTTATATTAGTTTACGGAGGAA 57.806 33.333 0.00 0.00 0.00 3.36
2591 2691 8.757982 ACACTCTTATATTAGTTTACGGAGGA 57.242 34.615 0.00 0.00 0.00 3.71
2592 2692 9.813446 AAACACTCTTATATTAGTTTACGGAGG 57.187 33.333 0.00 0.00 0.00 4.30
2620 2720 9.733219 AGCGTTTAGATTACTAAAGTAGTGATC 57.267 33.333 10.62 10.62 46.38 2.92
2621 2721 9.733219 GAGCGTTTAGATTACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
2622 2722 8.954350 AGAGCGTTTAGATTACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
2623 2723 9.570488 AAGAGCGTTTAGATTACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
2635 2735 9.091220 AGGGAGTAATATAAGAGCGTTTAGATT 57.909 33.333 7.79 7.79 31.52 2.40
2636 2736 8.653036 AGGGAGTAATATAAGAGCGTTTAGAT 57.347 34.615 0.00 0.00 0.00 1.98
2637 2737 7.176340 GGAGGGAGTAATATAAGAGCGTTTAGA 59.824 40.741 0.00 0.00 0.00 2.10
2638 2738 7.314393 GGAGGGAGTAATATAAGAGCGTTTAG 58.686 42.308 0.00 0.00 0.00 1.85
2639 2739 6.072286 CGGAGGGAGTAATATAAGAGCGTTTA 60.072 42.308 0.00 0.00 0.00 2.01
2640 2740 5.278858 CGGAGGGAGTAATATAAGAGCGTTT 60.279 44.000 0.00 0.00 0.00 3.60
2641 2741 4.217983 CGGAGGGAGTAATATAAGAGCGTT 59.782 45.833 0.00 0.00 0.00 4.84
2642 2742 3.757493 CGGAGGGAGTAATATAAGAGCGT 59.243 47.826 0.00 0.00 0.00 5.07
2643 2743 3.757493 ACGGAGGGAGTAATATAAGAGCG 59.243 47.826 0.00 0.00 0.00 5.03
2644 2744 4.158209 GGACGGAGGGAGTAATATAAGAGC 59.842 50.000 0.00 0.00 0.00 4.09
2645 2745 4.705991 GGGACGGAGGGAGTAATATAAGAG 59.294 50.000 0.00 0.00 0.00 2.85
2646 2746 4.106825 TGGGACGGAGGGAGTAATATAAGA 59.893 45.833 0.00 0.00 0.00 2.10
2647 2747 4.220163 GTGGGACGGAGGGAGTAATATAAG 59.780 50.000 0.00 0.00 0.00 1.73
2648 2748 4.154942 GTGGGACGGAGGGAGTAATATAA 58.845 47.826 0.00 0.00 0.00 0.98
2649 2749 3.140707 TGTGGGACGGAGGGAGTAATATA 59.859 47.826 0.00 0.00 0.00 0.86
2650 2750 2.090943 TGTGGGACGGAGGGAGTAATAT 60.091 50.000 0.00 0.00 0.00 1.28
2651 2751 1.288633 TGTGGGACGGAGGGAGTAATA 59.711 52.381 0.00 0.00 0.00 0.98
2652 2752 0.042131 TGTGGGACGGAGGGAGTAAT 59.958 55.000 0.00 0.00 0.00 1.89
2653 2753 0.178926 TTGTGGGACGGAGGGAGTAA 60.179 55.000 0.00 0.00 0.00 2.24
2654 2754 0.042131 ATTGTGGGACGGAGGGAGTA 59.958 55.000 0.00 0.00 0.00 2.59
2655 2755 0.042131 TATTGTGGGACGGAGGGAGT 59.958 55.000 0.00 0.00 0.00 3.85
2656 2756 1.424638 ATATTGTGGGACGGAGGGAG 58.575 55.000 0.00 0.00 0.00 4.30
2657 2757 2.779429 TATATTGTGGGACGGAGGGA 57.221 50.000 0.00 0.00 0.00 4.20
2658 2758 2.969950 TCTTATATTGTGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
2659 2759 3.555168 GCTCTTATATTGTGGGACGGAGG 60.555 52.174 0.00 0.00 0.00 4.30
2660 2760 3.654414 GCTCTTATATTGTGGGACGGAG 58.346 50.000 0.00 0.00 0.00 4.63
2661 2761 2.035449 CGCTCTTATATTGTGGGACGGA 59.965 50.000 0.00 0.00 0.00 4.69
2662 2762 2.223971 ACGCTCTTATATTGTGGGACGG 60.224 50.000 0.00 0.00 0.00 4.79
2663 2763 3.093717 ACGCTCTTATATTGTGGGACG 57.906 47.619 0.00 0.00 0.00 4.79
2664 2764 5.813080 AAAACGCTCTTATATTGTGGGAC 57.187 39.130 0.00 0.00 0.00 4.46
2665 2765 5.941058 TCAAAAACGCTCTTATATTGTGGGA 59.059 36.000 0.00 0.00 0.00 4.37
2666 2766 6.027749 GTCAAAAACGCTCTTATATTGTGGG 58.972 40.000 0.00 0.00 0.00 4.61
2667 2767 6.523201 GTGTCAAAAACGCTCTTATATTGTGG 59.477 38.462 0.00 0.00 35.42 4.17
2668 2768 7.298122 AGTGTCAAAAACGCTCTTATATTGTG 58.702 34.615 0.00 0.00 45.69 3.33
2669 2769 7.435068 AGTGTCAAAAACGCTCTTATATTGT 57.565 32.000 0.00 0.00 45.69 2.71
2670 2770 9.988350 ATTAGTGTCAAAAACGCTCTTATATTG 57.012 29.630 0.00 0.00 45.69 1.90
2671 2771 9.988350 CATTAGTGTCAAAAACGCTCTTATATT 57.012 29.630 0.00 0.00 45.69 1.28
2672 2772 9.162764 ACATTAGTGTCAAAAACGCTCTTATAT 57.837 29.630 0.00 0.00 45.69 0.86
2673 2773 8.542497 ACATTAGTGTCAAAAACGCTCTTATA 57.458 30.769 0.00 0.00 45.69 0.98
2674 2774 7.435068 ACATTAGTGTCAAAAACGCTCTTAT 57.565 32.000 0.00 0.00 45.69 1.73
2675 2775 6.854496 ACATTAGTGTCAAAAACGCTCTTA 57.146 33.333 0.00 0.00 45.69 2.10
2676 2776 5.751243 ACATTAGTGTCAAAAACGCTCTT 57.249 34.783 0.00 0.00 45.69 2.85
2677 2777 5.989777 ACTACATTAGTGTCAAAAACGCTCT 59.010 36.000 0.00 0.00 45.69 4.09
2678 2778 6.071463 CACTACATTAGTGTCAAAAACGCTC 58.929 40.000 5.34 0.00 45.69 5.03
2705 2805 6.204108 CCGTCCCATAATATAAGAGCGTTTTT 59.796 38.462 0.00 0.00 0.00 1.94
2706 2806 5.699458 CCGTCCCATAATATAAGAGCGTTTT 59.301 40.000 0.00 0.00 0.00 2.43
2707 2807 5.011329 TCCGTCCCATAATATAAGAGCGTTT 59.989 40.000 0.00 0.00 0.00 3.60
2708 2808 4.525487 TCCGTCCCATAATATAAGAGCGTT 59.475 41.667 0.00 0.00 0.00 4.84
2709 2809 4.084287 TCCGTCCCATAATATAAGAGCGT 58.916 43.478 0.00 0.00 0.00 5.07
2710 2810 4.440250 CCTCCGTCCCATAATATAAGAGCG 60.440 50.000 0.00 0.00 0.00 5.03
2711 2811 4.141914 CCCTCCGTCCCATAATATAAGAGC 60.142 50.000 0.00 0.00 0.00 4.09
2712 2812 5.269991 TCCCTCCGTCCCATAATATAAGAG 58.730 45.833 0.00 0.00 0.00 2.85
2713 2813 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2714 2814 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2715 2815 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2716 2816 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2717 2817 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2718 2818 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2719 2819 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2720 2820 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2721 2821 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2722 2822 0.338814 AACTACTCCCTCCGTCCCAT 59.661 55.000 0.00 0.00 0.00 4.00
2723 2823 0.115745 AAACTACTCCCTCCGTCCCA 59.884 55.000 0.00 0.00 0.00 4.37
2724 2824 1.753649 GTAAACTACTCCCTCCGTCCC 59.246 57.143 0.00 0.00 0.00 4.46
2725 2825 2.426381 CTGTAAACTACTCCCTCCGTCC 59.574 54.545 0.00 0.00 0.00 4.79
2726 2826 3.350833 TCTGTAAACTACTCCCTCCGTC 58.649 50.000 0.00 0.00 0.00 4.79
2727 2827 3.354467 CTCTGTAAACTACTCCCTCCGT 58.646 50.000 0.00 0.00 0.00 4.69
2728 2828 2.688958 CCTCTGTAAACTACTCCCTCCG 59.311 54.545 0.00 0.00 0.00 4.63
2729 2829 3.032459 CCCTCTGTAAACTACTCCCTCC 58.968 54.545 0.00 0.00 0.00 4.30
2730 2830 3.955551 CTCCCTCTGTAAACTACTCCCTC 59.044 52.174 0.00 0.00 0.00 4.30
2731 2831 3.337301 ACTCCCTCTGTAAACTACTCCCT 59.663 47.826 0.00 0.00 0.00 4.20
2732 2832 3.710724 ACTCCCTCTGTAAACTACTCCC 58.289 50.000 0.00 0.00 0.00 4.30
2733 2833 5.753716 TCTACTCCCTCTGTAAACTACTCC 58.246 45.833 0.00 0.00 0.00 3.85
2734 2834 7.055378 TCATCTACTCCCTCTGTAAACTACTC 58.945 42.308 0.00 0.00 0.00 2.59
2735 2835 6.971340 TCATCTACTCCCTCTGTAAACTACT 58.029 40.000 0.00 0.00 0.00 2.57
2736 2836 7.055378 TCTCATCTACTCCCTCTGTAAACTAC 58.945 42.308 0.00 0.00 0.00 2.73
2737 2837 7.209340 TCTCATCTACTCCCTCTGTAAACTA 57.791 40.000 0.00 0.00 0.00 2.24
2738 2838 6.080969 TCTCATCTACTCCCTCTGTAAACT 57.919 41.667 0.00 0.00 0.00 2.66
2739 2839 5.221165 GCTCTCATCTACTCCCTCTGTAAAC 60.221 48.000 0.00 0.00 0.00 2.01
2740 2840 4.890581 GCTCTCATCTACTCCCTCTGTAAA 59.109 45.833 0.00 0.00 0.00 2.01
2741 2841 4.167113 AGCTCTCATCTACTCCCTCTGTAA 59.833 45.833 0.00 0.00 0.00 2.41
2742 2842 3.719479 AGCTCTCATCTACTCCCTCTGTA 59.281 47.826 0.00 0.00 0.00 2.74
2743 2843 2.513738 AGCTCTCATCTACTCCCTCTGT 59.486 50.000 0.00 0.00 0.00 3.41
2744 2844 3.228188 AGCTCTCATCTACTCCCTCTG 57.772 52.381 0.00 0.00 0.00 3.35
2745 2845 6.126478 GGATATAGCTCTCATCTACTCCCTCT 60.126 46.154 0.00 0.00 0.00 3.69
2746 2846 6.062095 GGATATAGCTCTCATCTACTCCCTC 58.938 48.000 0.00 0.00 0.00 4.30
2747 2847 5.103686 GGGATATAGCTCTCATCTACTCCCT 60.104 48.000 0.00 0.00 37.84 4.20
2748 2848 5.137551 GGGATATAGCTCTCATCTACTCCC 58.862 50.000 0.00 0.00 35.73 4.30
2749 2849 4.819630 CGGGATATAGCTCTCATCTACTCC 59.180 50.000 0.00 0.00 0.00 3.85
2750 2850 5.433526 ACGGGATATAGCTCTCATCTACTC 58.566 45.833 0.00 0.00 0.00 2.59
2751 2851 5.433526 GACGGGATATAGCTCTCATCTACT 58.566 45.833 0.00 0.00 0.00 2.57
2752 2852 4.577283 GGACGGGATATAGCTCTCATCTAC 59.423 50.000 0.00 0.00 0.00 2.59
2753 2853 4.227527 TGGACGGGATATAGCTCTCATCTA 59.772 45.833 0.00 0.00 0.00 1.98
2754 2854 3.010696 TGGACGGGATATAGCTCTCATCT 59.989 47.826 0.00 0.00 0.00 2.90
2874 2975 2.048222 TGACCTTGAGCCGCTTCG 60.048 61.111 0.00 0.00 0.00 3.79
3080 3181 3.041701 CACGCAATGGGCACAAGT 58.958 55.556 0.00 0.00 45.17 3.16
3082 3183 3.210223 CTGCACGCAATGGGCACAA 62.210 57.895 0.00 0.00 45.17 3.33
3119 3220 4.336713 GGGGATAAGAGTTCAAAGCATCAC 59.663 45.833 0.00 0.00 0.00 3.06
3121 3222 3.885901 GGGGGATAAGAGTTCAAAGCATC 59.114 47.826 0.00 0.00 0.00 3.91
3174 3277 7.875554 GCTCCCATTTCCATTACTTTAAAACAA 59.124 33.333 0.00 0.00 0.00 2.83
3178 3281 6.350949 GCTGCTCCCATTTCCATTACTTTAAA 60.351 38.462 0.00 0.00 0.00 1.52
3213 3327 3.983344 GCACTTGCGTGATCTTCATTTTT 59.017 39.130 0.00 0.00 43.97 1.94
3214 3328 3.004629 TGCACTTGCGTGATCTTCATTTT 59.995 39.130 0.00 0.00 43.97 1.82
3215 3329 2.553602 TGCACTTGCGTGATCTTCATTT 59.446 40.909 0.00 0.00 43.97 2.32
3216 3330 2.095567 GTGCACTTGCGTGATCTTCATT 60.096 45.455 10.32 0.00 43.97 2.57
3217 3331 1.466167 GTGCACTTGCGTGATCTTCAT 59.534 47.619 10.32 0.00 43.97 2.57
3218 3332 0.867746 GTGCACTTGCGTGATCTTCA 59.132 50.000 10.32 0.00 43.97 3.02
3219 3333 0.166814 GGTGCACTTGCGTGATCTTC 59.833 55.000 17.98 0.00 43.97 2.87
3220 3334 1.568612 CGGTGCACTTGCGTGATCTT 61.569 55.000 17.98 0.00 43.97 2.40
3221 3335 2.029288 CGGTGCACTTGCGTGATCT 61.029 57.895 17.98 0.00 43.97 2.75
3222 3336 2.476051 CGGTGCACTTGCGTGATC 59.524 61.111 17.98 0.00 43.97 2.92
3223 3337 3.049674 CCGGTGCACTTGCGTGAT 61.050 61.111 17.98 0.00 43.97 3.06
3235 3349 0.581053 GTTGCACATTTTTGCCGGTG 59.419 50.000 1.90 0.00 42.25 4.94
3236 3350 0.531753 GGTTGCACATTTTTGCCGGT 60.532 50.000 1.90 0.00 42.25 5.28
3237 3351 0.249826 AGGTTGCACATTTTTGCCGG 60.250 50.000 0.00 0.00 42.25 6.13
3238 3352 0.860533 CAGGTTGCACATTTTTGCCG 59.139 50.000 0.00 0.00 42.25 5.69
3239 3353 0.587768 GCAGGTTGCACATTTTTGCC 59.412 50.000 0.00 0.00 44.26 4.52
3250 3364 1.986698 CTTGCAATGTAGCAGGTTGC 58.013 50.000 0.00 8.56 46.54 4.17
3251 3365 1.730121 CGCTTGCAATGTAGCAGGTTG 60.730 52.381 0.00 0.00 46.54 3.77
3252 3366 0.523072 CGCTTGCAATGTAGCAGGTT 59.477 50.000 0.00 0.00 46.54 3.50
3253 3367 1.926511 GCGCTTGCAATGTAGCAGGT 61.927 55.000 0.00 0.00 46.54 4.00
3254 3368 1.226491 GCGCTTGCAATGTAGCAGG 60.226 57.895 0.00 0.00 46.54 4.85
3255 3369 4.372235 GCGCTTGCAATGTAGCAG 57.628 55.556 0.00 0.00 46.54 4.24
3265 3379 0.939106 ATTTTTGTCGGTGCGCTTGC 60.939 50.000 9.73 0.00 39.78 4.01
3266 3380 0.777631 CATTTTTGTCGGTGCGCTTG 59.222 50.000 9.73 0.00 0.00 4.01
3267 3381 0.383949 ACATTTTTGTCGGTGCGCTT 59.616 45.000 9.73 0.00 0.00 4.68
3268 3382 0.317770 CACATTTTTGTCGGTGCGCT 60.318 50.000 9.73 0.00 0.00 5.92
3269 3383 1.875419 GCACATTTTTGTCGGTGCGC 61.875 55.000 0.00 0.00 45.84 6.09
3270 3384 2.132402 GCACATTTTTGTCGGTGCG 58.868 52.632 0.00 0.00 45.84 5.34
3272 3386 1.857837 GGTTGCACATTTTTGTCGGTG 59.142 47.619 0.00 0.00 0.00 4.94
3273 3387 1.754226 AGGTTGCACATTTTTGTCGGT 59.246 42.857 0.00 0.00 0.00 4.69
3274 3388 2.126467 CAGGTTGCACATTTTTGTCGG 58.874 47.619 0.00 0.00 0.00 4.79
3275 3389 1.522258 GCAGGTTGCACATTTTTGTCG 59.478 47.619 0.00 0.00 44.26 4.35
3450 3693 9.548208 GAGAATGCTTGATTAAGTTTCTAACAC 57.452 33.333 13.65 3.47 37.99 3.32
3455 3698 7.672983 TTCGAGAATGCTTGATTAAGTTTCT 57.327 32.000 13.59 13.59 39.26 2.52
3506 3750 7.854916 GCTAAAGAGATCATGTTGTAATTCTGC 59.145 37.037 0.00 0.00 0.00 4.26
3547 3791 4.655963 AGATGCACTAGTTGTTTGGATGT 58.344 39.130 0.00 0.00 0.00 3.06
3548 3792 4.201753 CGAGATGCACTAGTTGTTTGGATG 60.202 45.833 0.00 0.00 0.00 3.51
3622 3874 3.568007 GGATTGTTTTGCTACCAGTGTGA 59.432 43.478 0.00 0.00 0.00 3.58
3688 3940 3.008049 AGGAGATAGCAACCGTGTCTTTT 59.992 43.478 0.00 0.00 0.00 2.27
3764 4016 1.469079 GGCATTGTTCAATGGGCGTAC 60.469 52.381 21.74 8.23 0.00 3.67
3774 4026 0.527113 CTTCGCCATGGCATTGTTCA 59.473 50.000 34.93 10.00 42.06 3.18
3796 4048 2.938956 AGGTGCTAGAACTTGTTGCT 57.061 45.000 0.00 0.00 0.00 3.91
3823 4075 6.377146 TGGATAGGAAGGATTTGCTTTGTAAC 59.623 38.462 0.00 0.00 36.32 2.50
3917 4169 8.787852 GTGGATATCTCATTAATTTGACCCTTC 58.212 37.037 2.05 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.