Multiple sequence alignment - TraesCS6B01G149900

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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 TraesCS6B01G149900 chr6B 100.000 3306 0 0 1 3306 151136067 151132762 0.000000e+00 6106
1 TraesCS6B01G149900 chr6D 92.004 2689 128 35 2 2640 78273264 78270613 0.000000e+00 3694
2 TraesCS6B01G149900 chr6D 86.280 328 19 7 2783 3108 78269813 78269510 1.900000e-87 333
3 TraesCS6B01G149900 chr6A 91.508 2685 135 35 2 2640 93820644 93818007 0.000000e+00 3609
4 TraesCS6B01G149900 chr7B 90.090 111 10 1 3196 3306 720142441 720142550 3.440000e-30 143
5 TraesCS6B01G149900 chr2D 88.288 111 13 0 3196 3306 607988460 607988350 2.070000e-27 134
6 TraesCS6B01G149900 chr1A 88.496 113 9 3 3196 3306 556163404 556163294 2.070000e-27 134
7 TraesCS6B01G149900 chr4A 88.889 108 11 1 3196 3303 701630885 701630991 7.440000e-27 132
8 TraesCS6B01G149900 chr4A 88.182 110 12 1 3196 3305 698834202 698834094 2.680000e-26 130
9 TraesCS6B01G149900 chr7A 88.288 111 9 1 3196 3306 720725043 720724937 2.680000e-26 130
10 TraesCS6B01G149900 chr1D 88.288 111 10 2 3196 3306 143452172 143452065 2.680000e-26 130
11 TraesCS6B01G149900 chr2B 87.387 111 12 1 3196 3306 756948449 756948341 3.460000e-25 126
12 TraesCS6B01G149900 chr1B 87.387 111 12 1 3196 3306 32431605 32431713 3.460000e-25 126


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 TraesCS6B01G149900 chr6B 151132762 151136067 3305 True 6106.0 6106 100.000 1 3306 1 chr6B.!!$R1 3305
1 TraesCS6B01G149900 chr6D 78269510 78273264 3754 True 2013.5 3694 89.142 2 3108 2 chr6D.!!$R1 3106
2 TraesCS6B01G149900 chr6A 93818007 93820644 2637 True 3609.0 3609 91.508 2 2640 1 chr6A.!!$R1 2638

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
150 175 0.387622 TGTCCGTTCGGCGAGTTTAG 60.388 55.0 10.46 0.97 44.77 1.85 F
1050 1088 0.185901 TGGTGAAGCCCAGCTCTTTT 59.814 50.0 7.31 0.00 43.38 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1429 1467 0.250901 AGCTCGTGGAAGTTGCCAAT 60.251 50.0 0.00 0.0 40.20 3.16 R
2667 2727 0.024619 GGAGACATAACGAAACGCGC 59.975 55.0 5.73 0.0 46.04 6.86 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
49 50 4.865761 GATCCGCGCCGCTGTGTA 62.866 66.667 7.78 0.00 0.00 2.90
78 90 4.929819 TTTTCCTCCCAGCACTTTTTAC 57.070 40.909 0.00 0.00 0.00 2.01
134 154 1.456705 TTTGCCCCCTTGTGGTGTC 60.457 57.895 0.00 0.00 0.00 3.67
150 175 0.387622 TGTCCGTTCGGCGAGTTTAG 60.388 55.000 10.46 0.97 44.77 1.85
153 178 1.082117 CCGTTCGGCGAGTTTAGCAT 61.082 55.000 10.46 0.00 44.77 3.79
182 208 6.857437 ATTTTGGGTTTAGGGATCTTCTTG 57.143 37.500 0.00 0.00 0.00 3.02
183 211 5.592587 TTTGGGTTTAGGGATCTTCTTGA 57.407 39.130 0.00 0.00 0.00 3.02
212 240 0.950836 TTCTTGGTGCGTGTTGGATG 59.049 50.000 0.00 0.00 0.00 3.51
215 243 2.282180 GGTGCGTGTTGGATGGGT 60.282 61.111 0.00 0.00 0.00 4.51
265 293 6.922957 TGCCGCATAGATTTTGATTAATTTCC 59.077 34.615 0.00 0.00 0.00 3.13
365 393 7.011295 GGCATGTGATCTTTGTGAAAAAGAAAA 59.989 33.333 1.32 0.00 39.43 2.29
366 394 8.060090 GCATGTGATCTTTGTGAAAAAGAAAAG 58.940 33.333 1.32 0.00 39.43 2.27
367 395 9.304731 CATGTGATCTTTGTGAAAAAGAAAAGA 57.695 29.630 1.32 0.00 39.43 2.52
370 398 9.958285 GTGATCTTTGTGAAAAAGAAAAGAAAC 57.042 29.630 1.32 0.79 39.43 2.78
403 431 4.669206 TGTGATGCTTCCATGTTGTTTT 57.331 36.364 0.00 0.00 0.00 2.43
469 497 2.671619 AATGGTGGGTTGCGGTCG 60.672 61.111 0.00 0.00 0.00 4.79
478 506 1.134907 GGGTTGCGGTCGATCTCTTTA 60.135 52.381 0.00 0.00 0.00 1.85
486 514 5.870433 TGCGGTCGATCTCTTTAAATGTTTA 59.130 36.000 0.00 0.00 0.00 2.01
498 526 8.189119 TCTTTAAATGTTTAGGCATTTCAGGT 57.811 30.769 7.22 0.00 44.85 4.00
513 541 6.311200 GCATTTCAGGTGGAATGTTTTCATAC 59.689 38.462 11.78 0.00 39.94 2.39
515 543 6.968263 TTCAGGTGGAATGTTTTCATACAA 57.032 33.333 0.00 0.00 39.94 2.41
646 680 5.761726 AGCACATGGTATGAGATGTTATGTG 59.238 40.000 0.00 0.00 43.93 3.21
744 778 2.944129 ACCTGAAAGCTTTAGGTTGCA 58.056 42.857 23.58 12.75 41.93 4.08
764 798 3.347216 CACATTACTTGGTCAAGGGAGG 58.653 50.000 14.29 7.05 42.53 4.30
771 805 1.879575 TGGTCAAGGGAGGTGATAGG 58.120 55.000 0.00 0.00 0.00 2.57
886 920 5.554070 TGATGATATTGCTGTAGTGATGGG 58.446 41.667 0.00 0.00 0.00 4.00
994 1028 5.582689 AAGATACATTTGGTAGGCAAAGC 57.417 39.130 0.00 0.00 34.92 3.51
1050 1088 0.185901 TGGTGAAGCCCAGCTCTTTT 59.814 50.000 7.31 0.00 43.38 2.27
1053 1091 2.165998 GTGAAGCCCAGCTCTTTTGAT 58.834 47.619 0.00 0.00 38.25 2.57
1065 1103 5.231779 CAGCTCTTTTGATCTCGACATACAG 59.768 44.000 0.00 0.00 0.00 2.74
1068 1106 5.344066 TCTTTTGATCTCGACATACAGCTC 58.656 41.667 0.00 0.00 0.00 4.09
1074 1112 2.096013 TCTCGACATACAGCTCGACAAG 59.904 50.000 0.00 0.00 35.17 3.16
1272 1310 2.509786 TCGGCCGTTAACATCGCC 60.510 61.111 27.15 15.19 0.00 5.54
1429 1467 3.674410 CGAAGAGAGCTGCTGTTCATACA 60.674 47.826 7.01 0.00 44.76 2.29
1443 1481 4.022416 TGTTCATACATTGGCAACTTCCAC 60.022 41.667 0.00 0.00 35.50 4.02
1473 1511 2.912624 GCACACCCAGCAGAAGCAC 61.913 63.158 0.00 0.00 45.49 4.40
1542 1580 2.354203 GGAGAATTTCCAGCAGTCGTCT 60.354 50.000 0.00 0.00 46.01 4.18
1554 1592 3.058570 AGCAGTCGTCTGATATCATCGAC 60.059 47.826 32.54 32.54 44.76 4.20
1698 1736 3.556423 GGTGGACGTCCTGTATTTTCTGT 60.556 47.826 33.39 0.00 36.82 3.41
1813 1851 1.350193 CTTCACCATCGACGTTCCAG 58.650 55.000 0.00 0.00 0.00 3.86
1816 1854 2.511600 CCATCGACGTTCCAGCCC 60.512 66.667 0.00 0.00 0.00 5.19
1821 1859 4.373116 GACGTTCCAGCCCGAGCA 62.373 66.667 0.00 0.00 43.56 4.26
2012 2050 3.206964 GCCTGTGGCTAAGAGAATTACC 58.793 50.000 0.73 0.00 46.69 2.85
2013 2051 3.118223 GCCTGTGGCTAAGAGAATTACCT 60.118 47.826 0.73 0.00 46.69 3.08
2025 2063 3.645687 GAGAATTACCTCTCTCTGGCCAT 59.354 47.826 5.51 0.00 39.08 4.40
2068 2106 4.989279 TGCTTTCAAGGATCAATAAGGC 57.011 40.909 0.00 0.00 0.00 4.35
2085 2126 0.800631 GGCGCCACTTTAACCACTAC 59.199 55.000 24.80 0.00 0.00 2.73
2086 2127 1.609841 GGCGCCACTTTAACCACTACT 60.610 52.381 24.80 0.00 0.00 2.57
2087 2128 2.354003 GGCGCCACTTTAACCACTACTA 60.354 50.000 24.80 0.00 0.00 1.82
2122 2163 8.576442 TGTCCTGAACAATTTCTTTATCCTTTC 58.424 33.333 0.00 0.00 34.03 2.62
2229 2270 1.328279 TCACTTCGGCAGTCTCTGAA 58.672 50.000 0.66 0.00 30.92 3.02
2239 2280 3.057946 GGCAGTCTCTGAAACACCATTTC 60.058 47.826 0.66 0.00 32.44 2.17
2245 2286 7.433425 CAGTCTCTGAAACACCATTTCTTTTTC 59.567 37.037 1.48 0.00 32.44 2.29
2248 2289 8.531146 TCTCTGAAACACCATTTCTTTTTCTTT 58.469 29.630 1.48 0.00 0.00 2.52
2249 2290 9.154847 CTCTGAAACACCATTTCTTTTTCTTTT 57.845 29.630 1.48 0.00 0.00 2.27
2250 2291 9.150348 TCTGAAACACCATTTCTTTTTCTTTTC 57.850 29.630 1.48 0.00 0.00 2.29
2251 2292 9.154847 CTGAAACACCATTTCTTTTTCTTTTCT 57.845 29.630 1.48 0.00 0.00 2.52
2252 2293 9.500785 TGAAACACCATTTCTTTTTCTTTTCTT 57.499 25.926 1.48 0.00 0.00 2.52
2363 2404 2.113139 CACCTCCACCGCCTGTTT 59.887 61.111 0.00 0.00 0.00 2.83
2373 2414 1.613437 ACCGCCTGTTTTCATTCCTTG 59.387 47.619 0.00 0.00 0.00 3.61
2437 2478 1.153005 GATAGCAGCAGCAGGCCTT 60.153 57.895 0.00 0.00 46.50 4.35
2438 2479 1.153005 ATAGCAGCAGCAGGCCTTC 60.153 57.895 0.00 0.00 46.50 3.46
2439 2480 2.621517 ATAGCAGCAGCAGGCCTTCC 62.622 60.000 0.00 0.00 46.50 3.46
2521 2562 8.482943 TCAGCTTTCACTACCTTATTATAGCAA 58.517 33.333 0.00 0.00 0.00 3.91
2640 2700 5.623956 TTCCTGTAGAAAGAAGGTTGTGA 57.376 39.130 0.00 0.00 32.59 3.58
2641 2701 5.825593 TCCTGTAGAAAGAAGGTTGTGAT 57.174 39.130 0.00 0.00 32.59 3.06
2642 2702 6.187727 TCCTGTAGAAAGAAGGTTGTGATT 57.812 37.500 0.00 0.00 32.59 2.57
2643 2703 6.601332 TCCTGTAGAAAGAAGGTTGTGATTT 58.399 36.000 0.00 0.00 32.59 2.17
2644 2704 6.486657 TCCTGTAGAAAGAAGGTTGTGATTTG 59.513 38.462 0.00 0.00 32.59 2.32
2645 2705 6.294176 CCTGTAGAAAGAAGGTTGTGATTTGG 60.294 42.308 0.00 0.00 0.00 3.28
2646 2706 5.534654 TGTAGAAAGAAGGTTGTGATTTGGG 59.465 40.000 0.00 0.00 0.00 4.12
2647 2707 4.803452 AGAAAGAAGGTTGTGATTTGGGA 58.197 39.130 0.00 0.00 0.00 4.37
2648 2708 5.397360 AGAAAGAAGGTTGTGATTTGGGAT 58.603 37.500 0.00 0.00 0.00 3.85
2651 2711 2.879103 AGGTTGTGATTTGGGATCGT 57.121 45.000 0.00 0.00 0.00 3.73
2652 2712 3.992943 AGGTTGTGATTTGGGATCGTA 57.007 42.857 0.00 0.00 0.00 3.43
2653 2713 4.295141 AGGTTGTGATTTGGGATCGTAA 57.705 40.909 0.00 0.00 0.00 3.18
2655 2715 3.128068 GGTTGTGATTTGGGATCGTAACC 59.872 47.826 0.00 0.00 33.08 2.85
2657 2717 1.937899 GTGATTTGGGATCGTAACCGG 59.062 52.381 0.00 0.00 33.95 5.28
2658 2718 1.555992 TGATTTGGGATCGTAACCGGT 59.444 47.619 0.00 0.00 33.95 5.28
2659 2719 2.207590 GATTTGGGATCGTAACCGGTC 58.792 52.381 8.04 0.00 43.60 4.79
2663 2723 2.279054 GATCGTAACCGGTCCGCC 60.279 66.667 18.79 10.91 38.29 6.13
2665 2725 2.674461 GATCGTAACCGGTCCGCCTC 62.674 65.000 18.79 14.30 38.29 4.70
2666 2726 3.446570 CGTAACCGGTCCGCCTCT 61.447 66.667 8.04 0.00 0.00 3.69
2667 2727 2.183555 GTAACCGGTCCGCCTCTG 59.816 66.667 8.04 0.00 0.00 3.35
2668 2728 3.766691 TAACCGGTCCGCCTCTGC 61.767 66.667 8.04 0.00 0.00 4.26
2678 2738 3.712881 GCCTCTGCGCGTTTCGTT 61.713 61.111 8.43 0.00 41.07 3.85
2681 2741 0.025001 CCTCTGCGCGTTTCGTTATG 59.975 55.000 8.43 0.00 41.07 1.90
2682 2742 0.713883 CTCTGCGCGTTTCGTTATGT 59.286 50.000 8.43 0.00 41.07 2.29
2683 2743 0.711670 TCTGCGCGTTTCGTTATGTC 59.288 50.000 8.43 0.00 41.07 3.06
2686 2746 0.024619 GCGCGTTTCGTTATGTCTCC 59.975 55.000 8.43 0.00 41.07 3.71
2688 2748 1.320555 CGCGTTTCGTTATGTCTCCTG 59.679 52.381 0.00 0.00 0.00 3.86
2689 2749 1.060698 GCGTTTCGTTATGTCTCCTGC 59.939 52.381 0.00 0.00 0.00 4.85
2691 2751 3.766151 CGTTTCGTTATGTCTCCTGCTA 58.234 45.455 0.00 0.00 0.00 3.49
2693 2753 3.795623 TTCGTTATGTCTCCTGCTACC 57.204 47.619 0.00 0.00 0.00 3.18
2694 2754 2.029623 TCGTTATGTCTCCTGCTACCC 58.970 52.381 0.00 0.00 0.00 3.69
2695 2755 1.754803 CGTTATGTCTCCTGCTACCCA 59.245 52.381 0.00 0.00 0.00 4.51
2696 2756 2.167693 CGTTATGTCTCCTGCTACCCAA 59.832 50.000 0.00 0.00 0.00 4.12
2697 2757 3.738281 CGTTATGTCTCCTGCTACCCAAG 60.738 52.174 0.00 0.00 0.00 3.61
2698 2758 2.254152 ATGTCTCCTGCTACCCAAGA 57.746 50.000 0.00 0.00 0.00 3.02
2699 2759 1.267121 TGTCTCCTGCTACCCAAGAC 58.733 55.000 0.00 0.00 37.47 3.01
2700 2760 1.203187 TGTCTCCTGCTACCCAAGACT 60.203 52.381 0.00 0.00 37.75 3.24
2701 2761 1.478916 GTCTCCTGCTACCCAAGACTC 59.521 57.143 0.00 0.00 34.80 3.36
2702 2762 1.077169 TCTCCTGCTACCCAAGACTCA 59.923 52.381 0.00 0.00 0.00 3.41
2703 2763 1.205893 CTCCTGCTACCCAAGACTCAC 59.794 57.143 0.00 0.00 0.00 3.51
2704 2764 1.203187 TCCTGCTACCCAAGACTCACT 60.203 52.381 0.00 0.00 0.00 3.41
2705 2765 1.066573 CCTGCTACCCAAGACTCACTG 60.067 57.143 0.00 0.00 0.00 3.66
2706 2766 1.895798 CTGCTACCCAAGACTCACTGA 59.104 52.381 0.00 0.00 0.00 3.41
2707 2767 2.300152 CTGCTACCCAAGACTCACTGAA 59.700 50.000 0.00 0.00 0.00 3.02
2708 2768 2.906389 TGCTACCCAAGACTCACTGAAT 59.094 45.455 0.00 0.00 0.00 2.57
2709 2769 3.055819 TGCTACCCAAGACTCACTGAATC 60.056 47.826 0.00 0.00 0.00 2.52
2710 2770 3.680196 GCTACCCAAGACTCACTGAATCC 60.680 52.174 0.00 0.00 0.00 3.01
2711 2771 2.338809 ACCCAAGACTCACTGAATCCA 58.661 47.619 0.00 0.00 0.00 3.41
2712 2772 2.304180 ACCCAAGACTCACTGAATCCAG 59.696 50.000 0.00 0.00 45.76 3.86
2721 2781 2.918571 CTGAATCCAGTGTGCACGT 58.081 52.632 13.13 0.00 35.70 4.49
2722 2782 2.078849 CTGAATCCAGTGTGCACGTA 57.921 50.000 13.13 0.00 35.70 3.57
2723 2783 1.726791 CTGAATCCAGTGTGCACGTAC 59.273 52.381 13.13 5.72 35.70 3.67
2724 2784 1.069358 TGAATCCAGTGTGCACGTACA 59.931 47.619 13.13 1.17 36.20 2.90
2725 2785 2.289382 TGAATCCAGTGTGCACGTACAT 60.289 45.455 13.13 0.00 36.20 2.29
2726 2786 2.472695 ATCCAGTGTGCACGTACATT 57.527 45.000 13.13 0.00 36.20 2.71
2727 2787 2.248280 TCCAGTGTGCACGTACATTT 57.752 45.000 13.13 0.00 36.20 2.32
2728 2788 2.566913 TCCAGTGTGCACGTACATTTT 58.433 42.857 13.13 0.00 36.20 1.82
2729 2789 3.729966 TCCAGTGTGCACGTACATTTTA 58.270 40.909 13.13 0.00 36.20 1.52
2730 2790 3.495377 TCCAGTGTGCACGTACATTTTAC 59.505 43.478 13.13 0.92 36.20 2.01
2731 2791 3.364565 CCAGTGTGCACGTACATTTTACC 60.365 47.826 13.13 0.00 36.20 2.85
2732 2792 2.477375 AGTGTGCACGTACATTTTACCG 59.523 45.455 13.13 0.00 36.20 4.02
2733 2793 2.221517 GTGTGCACGTACATTTTACCGT 59.778 45.455 13.13 0.00 32.43 4.83
2734 2794 2.475864 TGTGCACGTACATTTTACCGTC 59.524 45.455 13.13 0.00 0.00 4.79
2735 2795 2.475864 GTGCACGTACATTTTACCGTCA 59.524 45.455 0.00 0.00 0.00 4.35
2736 2796 3.123959 GTGCACGTACATTTTACCGTCAT 59.876 43.478 0.00 0.00 0.00 3.06
2737 2797 3.747010 TGCACGTACATTTTACCGTCATT 59.253 39.130 0.00 0.00 0.00 2.57
2738 2798 4.085884 GCACGTACATTTTACCGTCATTG 58.914 43.478 0.00 0.00 0.00 2.82
2739 2799 4.377635 GCACGTACATTTTACCGTCATTGT 60.378 41.667 0.00 0.00 0.00 2.71
2740 2800 5.681880 CACGTACATTTTACCGTCATTGTT 58.318 37.500 0.00 0.00 0.00 2.83
2741 2801 5.786574 CACGTACATTTTACCGTCATTGTTC 59.213 40.000 0.00 0.00 0.00 3.18
2742 2802 5.010749 CGTACATTTTACCGTCATTGTTCG 58.989 41.667 0.00 0.00 0.00 3.95
2743 2803 5.388682 CGTACATTTTACCGTCATTGTTCGT 60.389 40.000 0.00 0.00 0.00 3.85
2744 2804 5.025986 ACATTTTACCGTCATTGTTCGTC 57.974 39.130 0.00 0.00 0.00 4.20
2745 2805 4.512198 ACATTTTACCGTCATTGTTCGTCA 59.488 37.500 0.00 0.00 0.00 4.35
2748 2808 0.677288 ACCGTCATTGTTCGTCAGGA 59.323 50.000 0.00 0.00 0.00 3.86
2771 2831 1.967494 GGCCTTGCCGTCCGTTTTA 60.967 57.895 0.00 0.00 39.62 1.52
2773 2833 1.371595 GCCTTGCCGTCCGTTTTATA 58.628 50.000 0.00 0.00 0.00 0.98
2774 2834 1.329599 GCCTTGCCGTCCGTTTTATAG 59.670 52.381 0.00 0.00 0.00 1.31
2776 2836 2.624636 CTTGCCGTCCGTTTTATAGGT 58.375 47.619 0.00 0.00 0.00 3.08
2778 2838 2.348660 TGCCGTCCGTTTTATAGGTTG 58.651 47.619 0.00 0.00 0.00 3.77
2780 2840 2.348660 CCGTCCGTTTTATAGGTTGCA 58.651 47.619 0.00 0.00 0.00 4.08
2791 3558 9.274065 CGTTTTATAGGTTGCATCTTTCTTTAC 57.726 33.333 0.00 0.00 0.00 2.01
2838 3605 0.310543 TAACTTGCTTGCACGGCTTG 59.689 50.000 11.39 7.09 0.00 4.01
2868 3635 2.282887 GGCCACGGAACCATGGTT 60.283 61.111 30.23 30.23 41.54 3.67
2869 3636 1.906333 GGCCACGGAACCATGGTTT 60.906 57.895 30.33 13.04 38.60 3.27
2870 3637 0.609681 GGCCACGGAACCATGGTTTA 60.610 55.000 30.33 0.00 38.60 2.01
2871 3638 0.524414 GCCACGGAACCATGGTTTAC 59.476 55.000 30.33 23.48 38.60 2.01
2872 3639 1.898902 CCACGGAACCATGGTTTACA 58.101 50.000 30.33 0.00 38.60 2.41
2873 3640 2.442413 CCACGGAACCATGGTTTACAT 58.558 47.619 30.33 13.28 41.57 2.29
2874 3641 3.611970 CCACGGAACCATGGTTTACATA 58.388 45.455 30.33 0.00 37.84 2.29
2875 3642 3.625764 CCACGGAACCATGGTTTACATAG 59.374 47.826 30.33 18.77 37.84 2.23
2876 3643 4.258543 CACGGAACCATGGTTTACATAGT 58.741 43.478 30.33 19.34 37.84 2.12
2877 3644 5.421277 CACGGAACCATGGTTTACATAGTA 58.579 41.667 30.33 0.00 37.84 1.82
2878 3645 5.875910 CACGGAACCATGGTTTACATAGTAA 59.124 40.000 30.33 0.00 37.84 2.24
2879 3646 6.540914 CACGGAACCATGGTTTACATAGTAAT 59.459 38.462 30.33 4.10 37.84 1.89
2880 3647 7.711772 CACGGAACCATGGTTTACATAGTAATA 59.288 37.037 30.33 0.00 37.84 0.98
2881 3648 7.712205 ACGGAACCATGGTTTACATAGTAATAC 59.288 37.037 30.33 12.81 37.84 1.89
2882 3649 7.929785 CGGAACCATGGTTTACATAGTAATACT 59.070 37.037 30.33 2.65 37.84 2.12
2942 3709 3.440872 TGTTGTTTTCAGTAAACCACGCT 59.559 39.130 0.60 0.00 44.49 5.07
2963 3730 3.474904 CGCCACGCAATTCGACGA 61.475 61.111 0.00 0.00 41.67 4.20
2966 3733 0.859232 GCCACGCAATTCGACGATAT 59.141 50.000 0.00 0.00 41.67 1.63
3002 3769 1.541670 GGGTTCCTAACTGTTCACGCA 60.542 52.381 0.00 0.00 0.00 5.24
3004 3771 2.614983 GGTTCCTAACTGTTCACGCAAA 59.385 45.455 0.00 0.00 0.00 3.68
3005 3772 3.065648 GGTTCCTAACTGTTCACGCAAAA 59.934 43.478 0.00 0.00 0.00 2.44
3006 3773 4.279659 GTTCCTAACTGTTCACGCAAAAG 58.720 43.478 0.00 0.00 0.00 2.27
3007 3774 2.289547 TCCTAACTGTTCACGCAAAAGC 59.710 45.455 0.00 0.00 0.00 3.51
3008 3775 2.032799 CCTAACTGTTCACGCAAAAGCA 59.967 45.455 0.00 0.00 0.00 3.91
3009 3776 2.645730 AACTGTTCACGCAAAAGCAA 57.354 40.000 0.00 0.00 0.00 3.91
3010 3777 1.908065 ACTGTTCACGCAAAAGCAAC 58.092 45.000 0.00 0.00 0.00 4.17
3011 3778 1.472480 ACTGTTCACGCAAAAGCAACT 59.528 42.857 0.00 0.00 0.00 3.16
3013 3780 3.035942 CTGTTCACGCAAAAGCAACTAC 58.964 45.455 0.00 0.00 0.00 2.73
3015 3782 3.035942 GTTCACGCAAAAGCAACTACTG 58.964 45.455 0.00 0.00 0.00 2.74
3029 3796 1.492176 ACTACTGGCATCCAATCAGGG 59.508 52.381 0.00 0.00 38.24 4.45
3034 3801 1.831286 GCATCCAATCAGGGGCTGG 60.831 63.158 0.00 0.00 38.24 4.85
3038 3805 0.039618 TCCAATCAGGGGCTGGAAAC 59.960 55.000 0.00 0.00 36.30 2.78
3047 3814 2.570284 GGCTGGAAACGGGGGTTTG 61.570 63.158 0.00 0.00 37.13 2.93
3087 3854 3.439857 TCATTCTTCCCAGAAACCAGG 57.560 47.619 0.00 0.00 42.53 4.45
3090 3857 1.064825 TCTTCCCAGAAACCAGGTCC 58.935 55.000 0.00 0.00 0.00 4.46
3095 3862 1.620822 CCAGAAACCAGGTCCCAAAG 58.379 55.000 0.00 0.00 0.00 2.77
3108 3875 2.689983 GTCCCAAAGTGGCATCATAAGG 59.310 50.000 0.00 0.00 35.79 2.69
3109 3876 2.034124 CCCAAAGTGGCATCATAAGGG 58.966 52.381 0.00 0.00 35.79 3.95
3110 3877 2.358090 CCCAAAGTGGCATCATAAGGGA 60.358 50.000 6.81 0.00 35.79 4.20
3111 3878 3.569491 CCAAAGTGGCATCATAAGGGAT 58.431 45.455 0.00 0.00 0.00 3.85
3112 3879 3.571401 CCAAAGTGGCATCATAAGGGATC 59.429 47.826 0.00 0.00 0.00 3.36
3113 3880 3.515602 AAGTGGCATCATAAGGGATCC 57.484 47.619 1.92 1.92 0.00 3.36
3114 3881 1.349026 AGTGGCATCATAAGGGATCCG 59.651 52.381 5.45 0.00 0.00 4.18
3115 3882 0.692476 TGGCATCATAAGGGATCCGG 59.308 55.000 5.45 0.00 0.00 5.14
3116 3883 0.678048 GGCATCATAAGGGATCCGGC 60.678 60.000 5.45 0.00 0.00 6.13
3117 3884 0.326264 GCATCATAAGGGATCCGGCT 59.674 55.000 5.45 0.00 0.00 5.52
3118 3885 1.677217 GCATCATAAGGGATCCGGCTC 60.677 57.143 5.45 0.00 0.00 4.70
3119 3886 1.065854 CATCATAAGGGATCCGGCTCC 60.066 57.143 16.35 16.35 34.31 4.70
3141 3908 3.936203 GGGCCCACGTGTCAGTGA 61.936 66.667 19.95 0.00 44.43 3.41
3142 3909 2.357517 GGCCCACGTGTCAGTGAG 60.358 66.667 15.65 0.00 44.43 3.51
3143 3910 2.357517 GCCCACGTGTCAGTGAGG 60.358 66.667 15.65 7.60 44.43 3.86
3144 3911 2.343758 CCCACGTGTCAGTGAGGG 59.656 66.667 15.65 1.34 44.43 4.30
3145 3912 2.207229 CCCACGTGTCAGTGAGGGA 61.207 63.158 15.65 0.00 44.43 4.20
3146 3913 1.745890 CCACGTGTCAGTGAGGGAA 59.254 57.895 15.65 0.00 44.43 3.97
3147 3914 0.600255 CCACGTGTCAGTGAGGGAAC 60.600 60.000 15.65 0.00 44.43 3.62
3150 3917 0.389391 CGTGTCAGTGAGGGAACTGT 59.611 55.000 0.00 0.00 46.33 3.55
3151 3918 1.611977 CGTGTCAGTGAGGGAACTGTA 59.388 52.381 0.00 0.00 46.33 2.74
3152 3919 2.351835 CGTGTCAGTGAGGGAACTGTAG 60.352 54.545 0.00 0.00 46.33 2.74
3153 3920 2.028930 GTGTCAGTGAGGGAACTGTAGG 60.029 54.545 0.00 0.00 46.33 3.18
3154 3921 1.550976 GTCAGTGAGGGAACTGTAGGG 59.449 57.143 0.00 0.00 46.33 3.53
3155 3922 1.149288 TCAGTGAGGGAACTGTAGGGT 59.851 52.381 4.41 0.00 46.33 4.34
3156 3923 1.276421 CAGTGAGGGAACTGTAGGGTG 59.724 57.143 0.00 0.00 44.43 4.61
3157 3924 0.036294 GTGAGGGAACTGTAGGGTGC 60.036 60.000 0.00 0.00 44.43 5.01
3158 3925 1.198759 TGAGGGAACTGTAGGGTGCC 61.199 60.000 0.00 0.00 44.08 5.01
3159 3926 2.267961 GGGAACTGTAGGGTGCCG 59.732 66.667 0.00 0.00 35.76 5.69
3160 3927 2.590114 GGGAACTGTAGGGTGCCGT 61.590 63.158 0.00 0.00 35.76 5.68
3161 3928 1.259840 GGGAACTGTAGGGTGCCGTA 61.260 60.000 0.00 0.00 35.76 4.02
3162 3929 0.108472 GGAACTGTAGGGTGCCGTAC 60.108 60.000 12.61 12.61 37.68 3.67
3163 3930 0.457337 GAACTGTAGGGTGCCGTACG 60.457 60.000 8.69 8.69 39.36 3.67
3164 3931 1.880819 AACTGTAGGGTGCCGTACGG 61.881 60.000 30.06 30.06 44.52 4.02
3174 3941 2.838225 CCGTACGGCAGGGATCCT 60.838 66.667 23.44 0.00 33.75 3.24
3175 3942 2.728817 CGTACGGCAGGGATCCTC 59.271 66.667 12.58 1.55 0.00 3.71
3176 3943 2.728817 GTACGGCAGGGATCCTCG 59.271 66.667 12.58 12.81 0.00 4.63
3177 3944 2.125961 GTACGGCAGGGATCCTCGT 61.126 63.158 12.58 17.45 37.70 4.18
3178 3945 1.826921 TACGGCAGGGATCCTCGTC 60.827 63.158 19.85 9.95 35.99 4.20
3179 3946 3.917760 CGGCAGGGATCCTCGTCC 61.918 72.222 12.58 7.20 37.56 4.79
3188 3955 3.601443 GGATCCTCGTCCCATCATAAG 57.399 52.381 3.84 0.00 31.82 1.73
3189 3956 2.900546 GGATCCTCGTCCCATCATAAGT 59.099 50.000 3.84 0.00 31.82 2.24
3190 3957 4.087182 GGATCCTCGTCCCATCATAAGTA 58.913 47.826 3.84 0.00 31.82 2.24
3191 3958 4.712337 GGATCCTCGTCCCATCATAAGTAT 59.288 45.833 3.84 0.00 31.82 2.12
3192 3959 5.394663 GGATCCTCGTCCCATCATAAGTATG 60.395 48.000 3.84 0.00 32.18 2.39
3193 3960 4.480115 TCCTCGTCCCATCATAAGTATGT 58.520 43.478 0.00 0.00 35.26 2.29
3194 3961 5.637127 TCCTCGTCCCATCATAAGTATGTA 58.363 41.667 0.00 0.00 35.26 2.29
3195 3962 5.475909 TCCTCGTCCCATCATAAGTATGTAC 59.524 44.000 0.00 0.00 35.26 2.90
3196 3963 5.243060 CCTCGTCCCATCATAAGTATGTACA 59.757 44.000 0.00 0.00 35.26 2.90
3197 3964 6.239204 CCTCGTCCCATCATAAGTATGTACAA 60.239 42.308 0.00 0.00 35.26 2.41
3198 3965 7.114866 TCGTCCCATCATAAGTATGTACAAA 57.885 36.000 0.00 0.00 35.26 2.83
3199 3966 7.557724 TCGTCCCATCATAAGTATGTACAAAA 58.442 34.615 0.00 0.00 35.26 2.44
3200 3967 7.709182 TCGTCCCATCATAAGTATGTACAAAAG 59.291 37.037 0.00 0.00 35.26 2.27
3201 3968 7.042051 CGTCCCATCATAAGTATGTACAAAAGG 60.042 40.741 0.00 0.00 35.26 3.11
3202 3969 7.228706 GTCCCATCATAAGTATGTACAAAAGGG 59.771 40.741 0.00 0.00 35.26 3.95
3203 3970 6.016276 CCCATCATAAGTATGTACAAAAGGGC 60.016 42.308 0.00 0.00 35.26 5.19
3204 3971 6.016276 CCATCATAAGTATGTACAAAAGGGCC 60.016 42.308 0.00 0.00 35.26 5.80
3205 3972 5.442391 TCATAAGTATGTACAAAAGGGCCC 58.558 41.667 16.46 16.46 35.26 5.80
3206 3973 2.413310 AGTATGTACAAAAGGGCCCG 57.587 50.000 18.44 4.09 0.00 6.13
3207 3974 1.631898 AGTATGTACAAAAGGGCCCGT 59.368 47.619 18.44 11.44 0.00 5.28
3208 3975 1.741145 GTATGTACAAAAGGGCCCGTG 59.259 52.381 18.44 18.47 0.00 4.94
3209 3976 1.248101 ATGTACAAAAGGGCCCGTGC 61.248 55.000 18.44 12.51 0.00 5.34
3210 3977 2.670251 TACAAAAGGGCCCGTGCG 60.670 61.111 18.44 10.77 38.85 5.34
3211 3978 3.479127 TACAAAAGGGCCCGTGCGT 62.479 57.895 18.44 16.41 38.85 5.24
3212 3979 2.962142 TACAAAAGGGCCCGTGCGTT 62.962 55.000 18.44 0.59 38.85 4.84
3213 3980 2.113562 AAAAGGGCCCGTGCGTTA 59.886 55.556 18.44 0.00 38.85 3.18
3214 3981 2.263021 AAAAGGGCCCGTGCGTTAC 61.263 57.895 18.44 0.00 38.85 2.50
3215 3982 2.962142 AAAAGGGCCCGTGCGTTACA 62.962 55.000 18.44 0.00 38.85 2.41
3216 3983 2.962142 AAAGGGCCCGTGCGTTACAA 62.962 55.000 18.44 0.00 38.85 2.41
3217 3984 3.729698 GGGCCCGTGCGTTACAAC 61.730 66.667 5.69 0.00 38.85 3.32
3284 4051 9.547753 TGTTCTATAATCTGAGATTTTGTAGCC 57.452 33.333 13.54 8.10 0.00 3.93
3285 4052 9.547753 GTTCTATAATCTGAGATTTTGTAGCCA 57.452 33.333 13.54 0.00 0.00 4.75
3290 4057 7.951347 AATCTGAGATTTTGTAGCCATTTCT 57.049 32.000 0.97 0.00 0.00 2.52
3291 4058 7.951347 ATCTGAGATTTTGTAGCCATTTCTT 57.049 32.000 0.00 0.00 0.00 2.52
3292 4059 9.466497 AATCTGAGATTTTGTAGCCATTTCTTA 57.534 29.630 0.97 0.00 0.00 2.10
3293 4060 8.862325 TCTGAGATTTTGTAGCCATTTCTTAA 57.138 30.769 0.00 0.00 0.00 1.85
3294 4061 9.295825 TCTGAGATTTTGTAGCCATTTCTTAAA 57.704 29.630 0.00 0.00 0.00 1.52
3304 4071 9.679661 TGTAGCCATTTCTTAAATACATGAAGA 57.320 29.630 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.615325 GCCAAATCTTCAAAATTGCCGAAAG 60.615 40.000 0.00 0.00 0.00 2.62
8 9 3.065655 TGCCAAATCTTCAAAATTGCCG 58.934 40.909 0.00 0.00 0.00 5.69
10 11 4.696402 TCCATGCCAAATCTTCAAAATTGC 59.304 37.500 0.00 0.00 0.00 3.56
11 12 6.037830 GGATCCATGCCAAATCTTCAAAATTG 59.962 38.462 6.95 0.00 0.00 2.32
56 57 4.959839 AGTAAAAAGTGCTGGGAGGAAAAA 59.040 37.500 0.00 0.00 0.00 1.94
58 59 4.178956 AGTAAAAAGTGCTGGGAGGAAA 57.821 40.909 0.00 0.00 0.00 3.13
59 60 3.876309 AGTAAAAAGTGCTGGGAGGAA 57.124 42.857 0.00 0.00 0.00 3.36
60 61 3.751518 GAAGTAAAAAGTGCTGGGAGGA 58.248 45.455 0.00 0.00 0.00 3.71
134 154 1.082117 ATGCTAAACTCGCCGAACGG 61.082 55.000 9.00 9.00 43.89 4.44
150 175 7.412853 TCCCTAAACCCAAAATTAGTTATGC 57.587 36.000 0.00 0.00 0.00 3.14
153 178 9.470399 GAAGATCCCTAAACCCAAAATTAGTTA 57.530 33.333 0.00 0.00 0.00 2.24
182 208 5.147162 CACGCACCAAGAAAAAGAGTAATC 58.853 41.667 0.00 0.00 0.00 1.75
183 211 4.578928 ACACGCACCAAGAAAAAGAGTAAT 59.421 37.500 0.00 0.00 0.00 1.89
198 226 1.460273 AAACCCATCCAACACGCACC 61.460 55.000 0.00 0.00 0.00 5.01
212 240 2.607038 CGAAAGGCAGCAAGTTAAACCC 60.607 50.000 0.00 0.00 0.00 4.11
265 293 1.078918 TGGAGCAGATTCCGCACAG 60.079 57.895 0.00 0.00 40.27 3.66
365 393 1.342174 CACATGCCCTGCTTTGTTTCT 59.658 47.619 0.00 0.00 0.00 2.52
366 394 1.340889 TCACATGCCCTGCTTTGTTTC 59.659 47.619 0.00 0.00 0.00 2.78
367 395 1.412079 TCACATGCCCTGCTTTGTTT 58.588 45.000 0.00 0.00 0.00 2.83
370 398 3.733236 CATCACATGCCCTGCTTTG 57.267 52.632 0.00 0.00 0.00 2.77
486 514 2.610438 ACATTCCACCTGAAATGCCT 57.390 45.000 0.00 0.00 36.33 4.75
498 526 8.363390 TGCTACAAATTGTATGAAAACATTCCA 58.637 29.630 6.27 0.00 31.66 3.53
744 778 2.986728 ACCTCCCTTGACCAAGTAATGT 59.013 45.455 8.72 0.00 36.72 2.71
764 798 6.699575 ATTAATTTGCCTCACACCTATCAC 57.300 37.500 0.00 0.00 0.00 3.06
771 805 5.351458 GGATCCAATTAATTTGCCTCACAC 58.649 41.667 6.95 0.00 33.73 3.82
873 907 0.181114 TGCATCCCCATCACTACAGC 59.819 55.000 0.00 0.00 0.00 4.40
878 912 0.835941 GACTCTGCATCCCCATCACT 59.164 55.000 0.00 0.00 0.00 3.41
994 1028 2.205022 TTTCCTGAACCCATGCTGAG 57.795 50.000 0.00 0.00 0.00 3.35
1050 1088 2.288186 GTCGAGCTGTATGTCGAGATCA 59.712 50.000 0.00 0.00 45.41 2.92
1053 1091 1.734163 TGTCGAGCTGTATGTCGAGA 58.266 50.000 0.00 0.00 45.41 4.04
1065 1103 1.009389 CCGTCCAACTCTTGTCGAGC 61.009 60.000 0.00 0.00 43.85 5.03
1068 1106 0.388649 CCTCCGTCCAACTCTTGTCG 60.389 60.000 0.00 0.00 0.00 4.35
1272 1310 2.556840 AATGGATGCTGTCACGGGGG 62.557 60.000 0.00 0.00 0.00 5.40
1377 1415 1.131638 TCTTCTGGTTGAGGTGCTGT 58.868 50.000 0.00 0.00 0.00 4.40
1386 1424 3.572584 GCAGCATCTTTTCTTCTGGTTG 58.427 45.455 0.00 0.00 0.00 3.77
1429 1467 0.250901 AGCTCGTGGAAGTTGCCAAT 60.251 50.000 0.00 0.00 40.20 3.16
1542 1580 3.315191 TGCTCAAGACGTCGATGATATCA 59.685 43.478 21.90 8.10 0.00 2.15
1554 1592 0.907837 CGTGTATCGTGCTCAAGACG 59.092 55.000 0.00 0.00 38.20 4.18
1698 1736 1.466167 CTCGAAGACCCGAACGACTTA 59.534 52.381 0.00 0.00 38.17 2.24
1813 1851 1.009829 CTTATGTCAACTGCTCGGGC 58.990 55.000 0.00 0.00 39.26 6.13
1816 1854 2.672961 TCCCTTATGTCAACTGCTCG 57.327 50.000 0.00 0.00 0.00 5.03
1821 1859 7.890127 TCAAATCTGATTTCCCTTATGTCAACT 59.110 33.333 12.50 0.00 0.00 3.16
1863 1901 3.891366 GCATTGCCCCTGTAACAAGATAT 59.109 43.478 0.00 0.00 0.00 1.63
1965 2003 2.295070 GACAGAAAGCGGCCCTTTTAAA 59.705 45.455 17.12 0.00 43.64 1.52
1966 2004 1.883926 GACAGAAAGCGGCCCTTTTAA 59.116 47.619 17.12 0.00 43.64 1.52
2012 2050 1.337703 CTCTTCGATGGCCAGAGAGAG 59.662 57.143 23.54 20.88 36.88 3.20
2013 2051 1.341482 ACTCTTCGATGGCCAGAGAGA 60.341 52.381 29.77 20.74 37.97 3.10
2025 2063 8.997621 AGCATAAAAATGTTACTACTCTTCGA 57.002 30.769 0.00 0.00 0.00 3.71
2048 2086 3.793465 GCGCCTTATTGATCCTTGAAAGC 60.793 47.826 0.00 0.00 0.00 3.51
2068 2106 4.445452 TCTAGTAGTGGTTAAAGTGGCG 57.555 45.455 0.00 0.00 0.00 5.69
2109 2150 6.071952 AGCGCTGAATTTGAAAGGATAAAGAA 60.072 34.615 10.39 0.00 0.00 2.52
2122 2163 3.546815 GGCATACACTAGCGCTGAATTTG 60.547 47.826 22.90 11.76 0.00 2.32
2184 2225 5.355350 ACATGAGCAGCTAGGATTTGTTAAC 59.645 40.000 0.00 0.00 0.00 2.01
2185 2226 5.500234 ACATGAGCAGCTAGGATTTGTTAA 58.500 37.500 0.00 0.00 0.00 2.01
2253 2294 4.264759 TGGGATCCCTGGATTGATCAAAAA 60.265 41.667 31.05 2.00 39.30 1.94
2254 2295 3.271755 TGGGATCCCTGGATTGATCAAAA 59.728 43.478 31.05 2.72 39.30 2.44
2255 2296 2.858133 TGGGATCCCTGGATTGATCAAA 59.142 45.455 31.05 3.21 39.30 2.69
2256 2297 2.444388 CTGGGATCCCTGGATTGATCAA 59.556 50.000 31.05 11.26 39.30 2.57
2257 2298 2.060275 CTGGGATCCCTGGATTGATCA 58.940 52.381 31.05 6.14 39.30 2.92
2258 2299 2.875094 CTGGGATCCCTGGATTGATC 57.125 55.000 31.05 1.16 37.29 2.92
2363 2404 5.046735 CAGAGAGAAGAGGACAAGGAATGAA 60.047 44.000 0.00 0.00 0.00 2.57
2373 2414 3.561143 TGGATAGCAGAGAGAAGAGGAC 58.439 50.000 0.00 0.00 0.00 3.85
2437 2478 1.003812 CCTGTGAACAATAACGGGGGA 59.996 52.381 0.00 0.00 38.90 4.81
2438 2479 1.271707 ACCTGTGAACAATAACGGGGG 60.272 52.381 5.70 0.00 45.61 5.40
2439 2480 2.081462 GACCTGTGAACAATAACGGGG 58.919 52.381 5.70 0.00 45.61 5.73
2440 2481 3.000727 GAGACCTGTGAACAATAACGGG 58.999 50.000 0.00 0.00 46.56 5.28
2494 2535 8.482943 TGCTATAATAAGGTAGTGAAAGCTGAA 58.517 33.333 0.00 0.00 0.00 3.02
2496 2537 8.662781 TTGCTATAATAAGGTAGTGAAAGCTG 57.337 34.615 0.00 0.00 0.00 4.24
2586 2646 1.056660 TCCAAAGCCTTTCTCCGACT 58.943 50.000 0.00 0.00 0.00 4.18
2640 2700 2.320745 GACCGGTTACGATCCCAAAT 57.679 50.000 9.42 0.00 44.60 2.32
2641 2701 3.838795 GACCGGTTACGATCCCAAA 57.161 52.632 9.42 0.00 44.60 3.28
2646 2706 2.279054 GGCGGACCGGTTACGATC 60.279 66.667 29.26 18.65 44.60 3.69
2647 2707 2.757099 AGGCGGACCGGTTACGAT 60.757 61.111 29.26 17.18 44.60 3.73
2648 2708 3.443045 GAGGCGGACCGGTTACGA 61.443 66.667 29.26 0.00 44.60 3.43
2651 2711 3.766691 GCAGAGGCGGACCGGTTA 61.767 66.667 17.22 0.00 42.76 2.85
2661 2721 1.693083 ATAACGAAACGCGCAGAGGC 61.693 55.000 5.73 0.00 46.04 4.70
2662 2722 0.025001 CATAACGAAACGCGCAGAGG 59.975 55.000 5.73 0.00 46.04 3.69
2663 2723 0.713883 ACATAACGAAACGCGCAGAG 59.286 50.000 5.73 0.00 46.04 3.35
2665 2725 0.713883 AGACATAACGAAACGCGCAG 59.286 50.000 5.73 2.42 46.04 5.18
2666 2726 0.711670 GAGACATAACGAAACGCGCA 59.288 50.000 5.73 0.00 46.04 6.09
2667 2727 0.024619 GGAGACATAACGAAACGCGC 59.975 55.000 5.73 0.00 46.04 6.86
2669 2729 1.060698 GCAGGAGACATAACGAAACGC 59.939 52.381 0.00 0.00 0.00 4.84
2670 2730 2.607187 AGCAGGAGACATAACGAAACG 58.393 47.619 0.00 0.00 0.00 3.60
2673 2733 2.429610 GGGTAGCAGGAGACATAACGAA 59.570 50.000 0.00 0.00 0.00 3.85
2676 2736 3.451178 TCTTGGGTAGCAGGAGACATAAC 59.549 47.826 0.00 0.00 0.00 1.89
2677 2737 3.451178 GTCTTGGGTAGCAGGAGACATAA 59.549 47.826 13.38 0.00 37.33 1.90
2678 2738 3.031736 GTCTTGGGTAGCAGGAGACATA 58.968 50.000 13.38 0.00 37.33 2.29
2681 2741 1.478916 GAGTCTTGGGTAGCAGGAGAC 59.521 57.143 11.38 11.38 37.57 3.36
2682 2742 1.077169 TGAGTCTTGGGTAGCAGGAGA 59.923 52.381 0.00 0.00 0.00 3.71
2683 2743 1.205893 GTGAGTCTTGGGTAGCAGGAG 59.794 57.143 0.00 0.00 0.00 3.69
2686 2746 1.895798 TCAGTGAGTCTTGGGTAGCAG 59.104 52.381 0.00 0.00 0.00 4.24
2688 2748 3.526534 GATTCAGTGAGTCTTGGGTAGC 58.473 50.000 8.32 0.00 0.00 3.58
2689 2749 3.515502 TGGATTCAGTGAGTCTTGGGTAG 59.484 47.826 14.54 0.00 0.00 3.18
2691 2751 2.304180 CTGGATTCAGTGAGTCTTGGGT 59.696 50.000 14.54 0.00 36.30 4.51
2703 2763 1.726791 GTACGTGCACACTGGATTCAG 59.273 52.381 18.64 0.00 46.10 3.02
2704 2764 1.069358 TGTACGTGCACACTGGATTCA 59.931 47.619 18.64 1.39 0.00 2.57
2705 2765 1.790755 TGTACGTGCACACTGGATTC 58.209 50.000 18.64 0.00 0.00 2.52
2706 2766 2.472695 ATGTACGTGCACACTGGATT 57.527 45.000 18.64 0.00 0.00 3.01
2707 2767 2.472695 AATGTACGTGCACACTGGAT 57.527 45.000 18.64 0.00 0.00 3.41
2708 2768 2.248280 AAATGTACGTGCACACTGGA 57.752 45.000 18.64 0.00 0.00 3.86
2709 2769 3.364565 GGTAAAATGTACGTGCACACTGG 60.365 47.826 18.64 2.44 0.00 4.00
2710 2770 3.663233 CGGTAAAATGTACGTGCACACTG 60.663 47.826 18.64 6.25 0.00 3.66
2711 2771 2.477375 CGGTAAAATGTACGTGCACACT 59.523 45.455 18.64 3.22 0.00 3.55
2712 2772 2.221517 ACGGTAAAATGTACGTGCACAC 59.778 45.455 18.64 9.09 38.24 3.82
2713 2773 2.475864 GACGGTAAAATGTACGTGCACA 59.524 45.455 18.64 0.00 39.95 4.57
2714 2774 2.475864 TGACGGTAAAATGTACGTGCAC 59.524 45.455 8.99 6.82 39.95 4.57
2715 2775 2.752121 TGACGGTAAAATGTACGTGCA 58.248 42.857 9.28 9.28 39.95 4.57
2716 2776 4.085884 CAATGACGGTAAAATGTACGTGC 58.914 43.478 0.00 0.00 39.95 5.34
2717 2777 5.272167 ACAATGACGGTAAAATGTACGTG 57.728 39.130 0.00 0.00 39.95 4.49
2718 2778 5.388682 CGAACAATGACGGTAAAATGTACGT 60.389 40.000 0.00 0.00 42.88 3.57
2719 2779 5.010749 CGAACAATGACGGTAAAATGTACG 58.989 41.667 0.00 0.00 0.00 3.67
2720 2780 5.919196 ACGAACAATGACGGTAAAATGTAC 58.081 37.500 0.00 0.00 0.00 2.90
2721 2781 5.695363 TGACGAACAATGACGGTAAAATGTA 59.305 36.000 0.00 0.00 0.00 2.29
2722 2782 4.512198 TGACGAACAATGACGGTAAAATGT 59.488 37.500 0.00 0.00 0.00 2.71
2723 2783 5.024768 TGACGAACAATGACGGTAAAATG 57.975 39.130 0.00 0.00 0.00 2.32
2724 2784 4.153475 CCTGACGAACAATGACGGTAAAAT 59.847 41.667 0.00 0.00 0.00 1.82
2725 2785 3.495377 CCTGACGAACAATGACGGTAAAA 59.505 43.478 0.00 0.00 0.00 1.52
2726 2786 3.061322 CCTGACGAACAATGACGGTAAA 58.939 45.455 0.00 0.00 0.00 2.01
2727 2787 2.296752 TCCTGACGAACAATGACGGTAA 59.703 45.455 0.00 0.00 0.00 2.85
2728 2788 1.887854 TCCTGACGAACAATGACGGTA 59.112 47.619 0.00 0.00 0.00 4.02
2729 2789 0.677288 TCCTGACGAACAATGACGGT 59.323 50.000 0.00 0.00 0.00 4.83
2730 2790 1.790755 TTCCTGACGAACAATGACGG 58.209 50.000 0.00 0.00 0.00 4.79
2731 2791 2.542178 TGTTTCCTGACGAACAATGACG 59.458 45.455 0.00 0.00 33.19 4.35
2732 2792 3.058914 CCTGTTTCCTGACGAACAATGAC 60.059 47.826 0.00 0.00 35.54 3.06
2733 2793 3.138304 CCTGTTTCCTGACGAACAATGA 58.862 45.455 0.00 0.00 35.54 2.57
2734 2794 2.350772 GCCTGTTTCCTGACGAACAATG 60.351 50.000 0.00 0.00 35.54 2.82
2735 2795 1.880027 GCCTGTTTCCTGACGAACAAT 59.120 47.619 0.00 0.00 35.54 2.71
2736 2796 1.305201 GCCTGTTTCCTGACGAACAA 58.695 50.000 0.00 0.00 35.54 2.83
2737 2797 0.534203 GGCCTGTTTCCTGACGAACA 60.534 55.000 0.00 0.00 34.80 3.18
2738 2798 0.250338 AGGCCTGTTTCCTGACGAAC 60.250 55.000 3.11 0.00 31.53 3.95
2739 2799 0.472471 AAGGCCTGTTTCCTGACGAA 59.528 50.000 5.69 0.00 33.43 3.85
2740 2800 0.250295 CAAGGCCTGTTTCCTGACGA 60.250 55.000 5.69 0.00 33.43 4.20
2741 2801 1.856265 GCAAGGCCTGTTTCCTGACG 61.856 60.000 5.69 0.00 33.43 4.35
2742 2802 1.527433 GGCAAGGCCTGTTTCCTGAC 61.527 60.000 5.69 0.00 46.69 3.51
2743 2803 1.228552 GGCAAGGCCTGTTTCCTGA 60.229 57.895 5.69 0.00 46.69 3.86
2744 2804 3.369921 GGCAAGGCCTGTTTCCTG 58.630 61.111 5.69 0.00 46.69 3.86
2762 2822 5.813080 AAGATGCAACCTATAAAACGGAC 57.187 39.130 0.00 0.00 0.00 4.79
2765 2825 9.274065 GTAAAGAAAGATGCAACCTATAAAACG 57.726 33.333 0.00 0.00 0.00 3.60
2780 2840 6.208204 AGCTGTTGCATCTTGTAAAGAAAGAT 59.792 34.615 0.00 0.00 46.79 2.40
2791 3558 3.695816 CATCATCAGCTGTTGCATCTTG 58.304 45.455 18.21 8.01 42.74 3.02
2816 3583 0.310854 GCCGTGCAAGCAAGTTAACT 59.689 50.000 1.12 1.12 0.00 2.24
2849 3616 3.061848 CCATGGTTCCGTGGCCAC 61.062 66.667 26.78 26.78 37.62 5.01
2873 3640 9.197306 ACCATGACATGACAAGTAGTATTACTA 57.803 33.333 17.24 0.00 39.20 1.82
2874 3641 8.079211 ACCATGACATGACAAGTAGTATTACT 57.921 34.615 17.24 1.30 41.91 2.24
2875 3642 8.604035 CAACCATGACATGACAAGTAGTATTAC 58.396 37.037 17.24 0.00 0.00 1.89
2876 3643 7.279981 GCAACCATGACATGACAAGTAGTATTA 59.720 37.037 17.24 0.00 0.00 0.98
2877 3644 6.094048 GCAACCATGACATGACAAGTAGTATT 59.906 38.462 17.24 0.00 0.00 1.89
2878 3645 5.586243 GCAACCATGACATGACAAGTAGTAT 59.414 40.000 17.24 0.00 0.00 2.12
2879 3646 4.935205 GCAACCATGACATGACAAGTAGTA 59.065 41.667 17.24 0.00 0.00 1.82
2880 3647 3.753272 GCAACCATGACATGACAAGTAGT 59.247 43.478 17.24 1.37 0.00 2.73
2881 3648 3.752747 TGCAACCATGACATGACAAGTAG 59.247 43.478 17.24 0.72 0.00 2.57
2882 3649 3.749226 TGCAACCATGACATGACAAGTA 58.251 40.909 17.24 1.05 0.00 2.24
2883 3650 2.555325 CTGCAACCATGACATGACAAGT 59.445 45.455 17.24 3.20 0.00 3.16
2884 3651 2.670229 GCTGCAACCATGACATGACAAG 60.670 50.000 17.24 7.84 0.00 3.16
2885 3652 1.270274 GCTGCAACCATGACATGACAA 59.730 47.619 17.24 0.00 0.00 3.18
2886 3653 0.883153 GCTGCAACCATGACATGACA 59.117 50.000 17.24 0.00 0.00 3.58
2887 3654 0.883153 TGCTGCAACCATGACATGAC 59.117 50.000 17.24 4.19 0.00 3.06
2888 3655 1.170442 CTGCTGCAACCATGACATGA 58.830 50.000 17.24 0.00 0.00 3.07
2889 3656 0.457853 GCTGCTGCAACCATGACATG 60.458 55.000 11.11 8.56 39.41 3.21
2890 3657 1.888018 GCTGCTGCAACCATGACAT 59.112 52.632 11.11 0.00 39.41 3.06
2949 3716 2.708962 GCAAATATCGTCGAATTGCGTG 59.291 45.455 20.53 8.20 41.80 5.34
3002 3769 2.875296 TGGATGCCAGTAGTTGCTTTT 58.125 42.857 0.00 0.00 0.00 2.27
3004 3771 2.584835 TTGGATGCCAGTAGTTGCTT 57.415 45.000 0.00 0.00 33.81 3.91
3005 3772 2.025981 TGATTGGATGCCAGTAGTTGCT 60.026 45.455 0.00 0.00 33.81 3.91
3006 3773 2.357009 CTGATTGGATGCCAGTAGTTGC 59.643 50.000 0.00 0.00 33.81 4.17
3007 3774 2.947652 CCTGATTGGATGCCAGTAGTTG 59.052 50.000 0.00 0.00 38.35 3.16
3008 3775 2.092212 CCCTGATTGGATGCCAGTAGTT 60.092 50.000 0.00 0.00 38.35 2.24
3009 3776 1.492176 CCCTGATTGGATGCCAGTAGT 59.508 52.381 0.00 0.00 38.35 2.73
3010 3777 1.202855 CCCCTGATTGGATGCCAGTAG 60.203 57.143 0.00 0.00 38.35 2.57
3011 3778 0.846015 CCCCTGATTGGATGCCAGTA 59.154 55.000 0.00 0.00 38.35 2.74
3013 3780 1.831286 GCCCCTGATTGGATGCCAG 60.831 63.158 0.00 0.00 38.35 4.85
3015 3782 1.831286 CAGCCCCTGATTGGATGCC 60.831 63.158 0.00 0.00 38.35 4.40
3029 3796 2.203582 AAACCCCCGTTTCCAGCC 60.204 61.111 0.00 0.00 37.69 4.85
3034 3801 1.538512 GCTCTAACAAACCCCCGTTTC 59.461 52.381 0.00 0.00 40.28 2.78
3038 3805 0.676782 CCAGCTCTAACAAACCCCCG 60.677 60.000 0.00 0.00 0.00 5.73
3043 3810 2.427506 CTCCCACCAGCTCTAACAAAC 58.572 52.381 0.00 0.00 0.00 2.93
3047 3814 4.943822 GCTCCCACCAGCTCTAAC 57.056 61.111 0.00 0.00 36.38 2.34
3087 3854 2.689983 CCTTATGATGCCACTTTGGGAC 59.310 50.000 0.00 0.00 41.95 4.46
3090 3857 3.017048 TCCCTTATGATGCCACTTTGG 57.983 47.619 0.00 0.00 41.55 3.28
3095 3862 1.611673 CCGGATCCCTTATGATGCCAC 60.612 57.143 6.06 0.00 30.04 5.01
3124 3891 3.883744 CTCACTGACACGTGGGCCC 62.884 68.421 21.57 17.59 35.63 5.80
3125 3892 2.357517 CTCACTGACACGTGGGCC 60.358 66.667 21.57 9.12 35.63 5.80
3126 3893 2.357517 CCTCACTGACACGTGGGC 60.358 66.667 21.57 12.05 34.01 5.36
3127 3894 1.754380 TTCCCTCACTGACACGTGGG 61.754 60.000 21.57 8.84 37.29 4.61
3128 3895 0.600255 GTTCCCTCACTGACACGTGG 60.600 60.000 21.57 4.47 35.63 4.94
3129 3896 0.389391 AGTTCCCTCACTGACACGTG 59.611 55.000 15.48 15.48 36.25 4.49
3130 3897 0.389391 CAGTTCCCTCACTGACACGT 59.611 55.000 0.00 0.00 46.29 4.49
3131 3898 0.389391 ACAGTTCCCTCACTGACACG 59.611 55.000 7.82 0.00 46.29 4.49
3132 3899 2.028930 CCTACAGTTCCCTCACTGACAC 60.029 54.545 7.82 0.00 46.29 3.67
3133 3900 2.248248 CCTACAGTTCCCTCACTGACA 58.752 52.381 7.82 0.00 46.29 3.58
3134 3901 1.550976 CCCTACAGTTCCCTCACTGAC 59.449 57.143 7.82 0.00 46.29 3.51
3135 3902 1.149288 ACCCTACAGTTCCCTCACTGA 59.851 52.381 7.82 0.00 46.29 3.41
3137 3904 1.645710 CACCCTACAGTTCCCTCACT 58.354 55.000 0.00 0.00 0.00 3.41
3138 3905 0.036294 GCACCCTACAGTTCCCTCAC 60.036 60.000 0.00 0.00 0.00 3.51
3139 3906 1.198759 GGCACCCTACAGTTCCCTCA 61.199 60.000 0.00 0.00 0.00 3.86
3140 3907 1.602771 GGCACCCTACAGTTCCCTC 59.397 63.158 0.00 0.00 0.00 4.30
3141 3908 2.291043 CGGCACCCTACAGTTCCCT 61.291 63.158 0.00 0.00 0.00 4.20
3142 3909 1.259840 TACGGCACCCTACAGTTCCC 61.260 60.000 0.00 0.00 0.00 3.97
3143 3910 0.108472 GTACGGCACCCTACAGTTCC 60.108 60.000 0.00 0.00 0.00 3.62
3144 3911 0.457337 CGTACGGCACCCTACAGTTC 60.457 60.000 7.57 0.00 0.00 3.01
3145 3912 1.588082 CGTACGGCACCCTACAGTT 59.412 57.895 7.57 0.00 0.00 3.16
3146 3913 2.345760 CCGTACGGCACCCTACAGT 61.346 63.158 23.44 0.00 0.00 3.55
3147 3914 2.493030 CCGTACGGCACCCTACAG 59.507 66.667 23.44 0.00 0.00 2.74
3157 3924 2.838225 AGGATCCCTGCCGTACGG 60.838 66.667 30.06 30.06 38.57 4.02
3158 3925 2.728817 GAGGATCCCTGCCGTACG 59.271 66.667 8.55 8.69 31.76 3.67
3159 3926 2.073037 GACGAGGATCCCTGCCGTAC 62.073 65.000 8.55 4.65 34.89 3.67
3160 3927 1.826921 GACGAGGATCCCTGCCGTA 60.827 63.158 8.55 0.00 34.89 4.02
3161 3928 3.148279 GACGAGGATCCCTGCCGT 61.148 66.667 8.55 13.10 36.91 5.68
3162 3929 3.917760 GGACGAGGATCCCTGCCG 61.918 72.222 8.55 9.85 31.76 5.69
3167 3934 8.303659 CATACTTATGATGGGACGAGGATCCC 62.304 50.000 8.55 3.73 45.93 3.85
3168 3935 2.900546 ACTTATGATGGGACGAGGATCC 59.099 50.000 2.48 2.48 38.13 3.36
3169 3936 5.186021 ACATACTTATGATGGGACGAGGATC 59.814 44.000 3.19 0.00 37.15 3.36
3170 3937 5.087323 ACATACTTATGATGGGACGAGGAT 58.913 41.667 3.19 0.00 37.15 3.24
3171 3938 4.480115 ACATACTTATGATGGGACGAGGA 58.520 43.478 3.19 0.00 37.15 3.71
3172 3939 4.873746 ACATACTTATGATGGGACGAGG 57.126 45.455 3.19 0.00 37.15 4.63
3173 3940 6.327279 TGTACATACTTATGATGGGACGAG 57.673 41.667 3.19 0.00 37.15 4.18
3174 3941 6.718522 TTGTACATACTTATGATGGGACGA 57.281 37.500 0.00 0.00 37.15 4.20
3175 3942 7.042051 CCTTTTGTACATACTTATGATGGGACG 60.042 40.741 0.00 0.00 37.15 4.79
3176 3943 7.228706 CCCTTTTGTACATACTTATGATGGGAC 59.771 40.741 0.00 0.00 37.15 4.46
3177 3944 7.287061 CCCTTTTGTACATACTTATGATGGGA 58.713 38.462 0.00 0.00 37.15 4.37
3178 3945 6.016276 GCCCTTTTGTACATACTTATGATGGG 60.016 42.308 0.00 0.00 37.15 4.00
3179 3946 6.016276 GGCCCTTTTGTACATACTTATGATGG 60.016 42.308 0.00 0.00 37.15 3.51
3180 3947 6.016276 GGGCCCTTTTGTACATACTTATGATG 60.016 42.308 17.04 0.00 37.15 3.07
3181 3948 6.068670 GGGCCCTTTTGTACATACTTATGAT 58.931 40.000 17.04 0.00 37.15 2.45
3182 3949 5.442391 GGGCCCTTTTGTACATACTTATGA 58.558 41.667 17.04 0.00 37.15 2.15
3183 3950 4.274950 CGGGCCCTTTTGTACATACTTATG 59.725 45.833 22.43 0.00 39.55 1.90
3184 3951 4.080186 ACGGGCCCTTTTGTACATACTTAT 60.080 41.667 22.43 0.00 0.00 1.73
3185 3952 3.263937 ACGGGCCCTTTTGTACATACTTA 59.736 43.478 22.43 0.00 0.00 2.24
3186 3953 2.040679 ACGGGCCCTTTTGTACATACTT 59.959 45.455 22.43 0.00 0.00 2.24
3187 3954 1.631898 ACGGGCCCTTTTGTACATACT 59.368 47.619 22.43 0.00 0.00 2.12
3188 3955 1.741145 CACGGGCCCTTTTGTACATAC 59.259 52.381 22.43 0.00 0.00 2.39
3189 3956 1.951424 GCACGGGCCCTTTTGTACATA 60.951 52.381 22.43 0.00 0.00 2.29
3190 3957 1.248101 GCACGGGCCCTTTTGTACAT 61.248 55.000 22.43 0.00 0.00 2.29
3191 3958 1.899534 GCACGGGCCCTTTTGTACA 60.900 57.895 22.43 0.00 0.00 2.90
3192 3959 2.959372 GCACGGGCCCTTTTGTAC 59.041 61.111 22.43 0.33 0.00 2.90
3193 3960 2.670251 CGCACGGGCCCTTTTGTA 60.670 61.111 22.43 0.00 36.38 2.41
3194 3961 2.962142 TAACGCACGGGCCCTTTTGT 62.962 55.000 22.43 10.63 36.38 2.83
3195 3962 2.262303 TAACGCACGGGCCCTTTTG 61.262 57.895 22.43 15.24 36.38 2.44
3196 3963 2.113562 TAACGCACGGGCCCTTTT 59.886 55.556 22.43 4.37 36.38 2.27
3197 3964 2.670592 GTAACGCACGGGCCCTTT 60.671 61.111 22.43 2.91 36.38 3.11
3198 3965 3.479127 TTGTAACGCACGGGCCCTT 62.479 57.895 22.43 7.92 36.38 3.95
3199 3966 3.943691 TTGTAACGCACGGGCCCT 61.944 61.111 22.43 3.67 36.38 5.19
3200 3967 3.729698 GTTGTAACGCACGGGCCC 61.730 66.667 13.57 13.57 36.38 5.80
3201 3968 4.079748 CGTTGTAACGCACGGGCC 62.080 66.667 2.82 0.00 46.06 5.80
3258 4025 9.547753 GGCTACAAAATCTCAGATTATAGAACA 57.452 33.333 13.75 0.00 0.00 3.18
3259 4026 9.547753 TGGCTACAAAATCTCAGATTATAGAAC 57.452 33.333 13.75 8.33 0.00 3.01
3264 4031 9.638176 AGAAATGGCTACAAAATCTCAGATTAT 57.362 29.630 0.00 0.00 0.00 1.28
3265 4032 9.466497 AAGAAATGGCTACAAAATCTCAGATTA 57.534 29.630 0.00 0.00 0.00 1.75
3266 4033 7.951347 AGAAATGGCTACAAAATCTCAGATT 57.049 32.000 0.00 0.00 0.00 2.40
3267 4034 7.951347 AAGAAATGGCTACAAAATCTCAGAT 57.049 32.000 0.00 0.00 0.00 2.90
3268 4035 8.862325 TTAAGAAATGGCTACAAAATCTCAGA 57.138 30.769 0.00 0.00 0.00 3.27
3278 4045 9.679661 TCTTCATGTATTTAAGAAATGGCTACA 57.320 29.630 0.00 0.00 32.38 2.74


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

AutoCloner maintained by Alex Coulton.