Multiple sequence alignment - TraesCS1A01G258100

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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 TraesCS1A01G258100 chr1A 100.000 5255 0 0 1 5255 449858196 449852942 0.000000e+00 9705.0
1 TraesCS1A01G258100 chr1B 94.428 2064 81 20 550 2588 471197641 471195587 0.000000e+00 3144.0
2 TraesCS1A01G258100 chr1B 92.113 1344 78 18 3200 4531 471194702 471193375 0.000000e+00 1869.0
3 TraesCS1A01G258100 chr1B 86.747 581 34 15 1 548 471198278 471197708 1.620000e-169 606.0
4 TraesCS1A01G258100 chr1B 89.340 394 23 11 4880 5255 471193014 471192622 1.320000e-130 477.0
5 TraesCS1A01G258100 chr1B 93.778 225 14 0 2891 3115 471195021 471194797 6.520000e-89 339.0
6 TraesCS1A01G258100 chr1B 94.969 159 7 1 2739 2896 471195598 471195440 1.130000e-61 248.0
7 TraesCS1A01G258100 chr1B 83.333 228 24 4 4612 4839 471193377 471193164 1.150000e-46 198.0
8 TraesCS1A01G258100 chr1B 90.000 70 6 1 3169 3237 471194774 471194705 7.250000e-14 89.8
9 TraesCS1A01G258100 chr1D 93.696 2078 71 29 546 2588 349566493 349564441 0.000000e+00 3057.0
10 TraesCS1A01G258100 chr1D 93.413 1503 56 19 3053 4531 349564010 349562527 0.000000e+00 2187.0
11 TraesCS1A01G258100 chr1D 95.000 320 13 3 2739 3055 349564452 349564133 2.830000e-137 499.0
12 TraesCS1A01G258100 chr1D 90.936 342 14 9 4931 5255 349561203 349560862 1.340000e-120 444.0
13 TraesCS1A01G258100 chr1D 86.486 296 12 10 269 542 349566850 349566561 3.080000e-77 300.0
14 TraesCS1A01G258100 chr1D 95.758 165 7 0 2576 2740 285371172 285371008 3.120000e-67 267.0
15 TraesCS1A01G258100 chr1D 91.803 183 13 2 2558 2740 265990452 265990632 2.430000e-63 254.0
16 TraesCS1A01G258100 chr5D 95.758 165 7 0 2576 2740 48983315 48983479 3.120000e-67 267.0
17 TraesCS1A01G258100 chr3D 95.758 165 7 0 2576 2740 145972545 145972709 3.120000e-67 267.0
18 TraesCS1A01G258100 chr3D 93.750 176 9 2 2567 2741 450884632 450884458 4.040000e-66 263.0
19 TraesCS1A01G258100 chr3B 95.758 165 7 0 2576 2740 158050956 158051120 3.120000e-67 267.0
20 TraesCS1A01G258100 chr3B 97.849 93 2 0 4522 4614 18780537 18780629 1.510000e-35 161.0
21 TraesCS1A01G258100 chr3B 93.396 106 5 2 4530 4635 549759152 549759049 7.050000e-34 156.0
22 TraesCS1A01G258100 chr6D 94.706 170 9 0 2576 2745 218407210 218407379 1.120000e-66 265.0
23 TraesCS1A01G258100 chr6A 94.253 174 8 2 2569 2740 33260035 33259862 1.120000e-66 265.0
24 TraesCS1A01G258100 chr6A 94.706 170 8 1 2576 2744 458217710 458217879 4.040000e-66 263.0
25 TraesCS1A01G258100 chr6A 97.849 93 1 1 4522 4614 542602879 542602788 5.450000e-35 159.0
26 TraesCS1A01G258100 chr4A 98.925 93 1 0 4522 4614 615120959 615121051 3.260000e-37 167.0
27 TraesCS1A01G258100 chr4A 96.875 96 3 0 4520 4615 542275966 542276061 1.510000e-35 161.0
28 TraesCS1A01G258100 chr2A 97.917 96 1 1 4528 4623 597850507 597850413 1.170000e-36 165.0
29 TraesCS1A01G258100 chr6B 95.000 100 5 0 4515 4614 716607885 716607786 1.960000e-34 158.0
30 TraesCS1A01G258100 chr7A 92.727 110 5 3 4525 4633 372015625 372015518 7.050000e-34 156.0
31 TraesCS1A01G258100 chr4B 94.175 103 5 1 4520 4622 496424334 496424233 7.050000e-34 156.0


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 TraesCS1A01G258100 chr1A 449852942 449858196 5254 True 9705.00 9705 100.0000 1 5255 1 chr1A.!!$R1 5254
1 TraesCS1A01G258100 chr1B 471192622 471198278 5656 True 871.35 3144 90.5885 1 5255 8 chr1B.!!$R1 5254
2 TraesCS1A01G258100 chr1D 349560862 349566850 5988 True 1297.40 3057 91.9062 269 5255 5 chr1D.!!$R2 4986

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
981 1121 0.984995 ACCCTAGGCTGAACTGAACC 59.015 55.0 2.05 0.0 0.0 3.62 F
990 1133 1.192146 TGAACTGAACCCCTCCTCGG 61.192 60.0 0.00 0.0 0.0 4.63 F
1898 2062 1.301677 CCAGAGAACAAGAAGGCCGC 61.302 60.0 0.00 0.0 0.0 6.53 F
3825 4618 1.642037 CTGGAATGTGCAGCGAGGTG 61.642 60.0 0.00 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2062 1.819288 TGGACTTACTCTTGCTCTCCG 59.181 52.381 0.00 0.00 0.00 4.63 R
2617 2781 2.224185 TGCTTCGTATGTGGTCACTTGT 60.224 45.455 2.66 0.00 0.00 3.16 R
3838 4631 0.532115 GAATTGGTGGCAGCGGAAAT 59.468 50.000 12.58 3.58 0.00 2.17 R
4677 5470 0.736053 TGAACAAGTTTGTCACGGCC 59.264 50.000 0.00 0.00 41.31 6.13 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
34 35 2.730183 TATTAACGCAGATTGCACGC 57.270 45.000 1.69 0.00 45.36 5.34
107 108 6.128035 CCTTTTATTGTCATGACGGATGTTGA 60.128 38.462 20.54 0.00 33.29 3.18
116 117 7.011389 TGTCATGACGGATGTTGAAATAGATTC 59.989 37.037 20.54 0.00 34.61 2.52
117 118 7.225538 GTCATGACGGATGTTGAAATAGATTCT 59.774 37.037 10.69 0.00 34.86 2.40
159 160 1.225745 CAAAACTTAGAGGCGCGCG 60.226 57.895 28.44 28.44 0.00 6.86
205 206 6.260050 TGTTTCTCATGTGAACTAACTTGGAC 59.740 38.462 9.65 3.57 0.00 4.02
214 215 6.873605 TGTGAACTAACTTGGACATGATACAG 59.126 38.462 0.00 0.00 0.00 2.74
224 225 5.771469 TGGACATGATACAGCAAAACAAAG 58.229 37.500 0.00 0.00 0.00 2.77
243 244 5.994668 ACAAAGAAACAAAACAGAAAGCCAA 59.005 32.000 0.00 0.00 0.00 4.52
247 248 6.930731 AGAAACAAAACAGAAAGCCAAACTA 58.069 32.000 0.00 0.00 0.00 2.24
259 260 1.411089 CAAACTAGACGCGCGTGAC 59.589 57.895 42.90 27.10 0.00 3.67
262 263 2.874780 CTAGACGCGCGTGACCAC 60.875 66.667 42.90 25.45 0.00 4.16
277 281 3.193479 GTGACCACCCTTTCCATTTCATC 59.807 47.826 0.00 0.00 0.00 2.92
280 284 3.334881 ACCACCCTTTCCATTTCATCTCT 59.665 43.478 0.00 0.00 0.00 3.10
282 286 3.129988 CACCCTTTCCATTTCATCTCTGC 59.870 47.826 0.00 0.00 0.00 4.26
350 357 1.308998 ACGGAAAGCTCACACCAAAG 58.691 50.000 0.00 0.00 0.00 2.77
358 365 3.607741 AGCTCACACCAAAGATGATGAG 58.392 45.455 0.00 0.00 35.58 2.90
394 426 1.221021 GTAGCCTCCAAAGGACGGG 59.779 63.158 0.00 0.00 46.67 5.28
447 479 6.695278 CGCTTCTGTAAAATCTGTTGGAAAAA 59.305 34.615 0.00 0.00 0.00 1.94
488 524 9.993454 TTCATCAGAATTACTTATCCAGATCAG 57.007 33.333 0.00 0.00 0.00 2.90
503 539 1.674962 GATCAGAGCAGCCACATTTCC 59.325 52.381 0.00 0.00 0.00 3.13
539 579 1.002868 CCACCAACCAGAGCCAGAG 60.003 63.158 0.00 0.00 0.00 3.35
542 582 2.752358 CAACCAGAGCCAGAGCCA 59.248 61.111 0.00 0.00 41.25 4.75
543 583 1.376942 CAACCAGAGCCAGAGCCAG 60.377 63.158 0.00 0.00 41.25 4.85
544 584 1.537397 AACCAGAGCCAGAGCCAGA 60.537 57.895 0.00 0.00 41.25 3.86
788 897 2.125269 CGCCACGGACTAAAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
808 917 3.638592 AAGAATTCCACGGGCGGGG 62.639 63.158 0.65 0.00 40.85 5.73
867 976 4.717313 GGGCTCGTCAACACCCCC 62.717 72.222 0.00 0.00 36.24 5.40
885 994 3.371063 GACTCCGTCCACTCCGCA 61.371 66.667 0.00 0.00 0.00 5.69
886 995 3.628280 GACTCCGTCCACTCCGCAC 62.628 68.421 0.00 0.00 0.00 5.34
887 996 4.436998 CTCCGTCCACTCCGCACC 62.437 72.222 0.00 0.00 0.00 5.01
930 1039 3.064820 CCGAATTCCAAATTCCTACACCG 59.935 47.826 0.00 0.00 0.00 4.94
935 1044 1.006832 CAAATTCCTACACCGCTCCG 58.993 55.000 0.00 0.00 0.00 4.63
981 1121 0.984995 ACCCTAGGCTGAACTGAACC 59.015 55.000 2.05 0.00 0.00 3.62
990 1133 1.192146 TGAACTGAACCCCTCCTCGG 61.192 60.000 0.00 0.00 0.00 4.63
1080 1223 2.416432 CCTCTTCGACCCGGACCTC 61.416 68.421 0.73 0.00 0.00 3.85
1106 1249 2.202146 GGACGACGACGACGACAG 60.202 66.667 25.15 7.04 42.66 3.51
1107 1250 2.864248 GACGACGACGACGACAGC 60.864 66.667 25.15 8.43 42.66 4.40
1129 1272 2.817834 CGCTCGGGAATTTCGGCA 60.818 61.111 0.00 0.00 0.00 5.69
1134 1277 2.542907 CGGGAATTTCGGCATCGGG 61.543 63.158 0.00 0.00 36.95 5.14
1551 1715 2.279252 CGGCTGATACGGAACCGG 60.279 66.667 17.44 0.00 44.69 5.28
1869 2033 2.594592 GTGACCGCAACCAAGGCT 60.595 61.111 0.00 0.00 0.00 4.58
1898 2062 1.301677 CCAGAGAACAAGAAGGCCGC 61.302 60.000 0.00 0.00 0.00 6.53
1902 2066 2.358737 AACAAGAAGGCCGCGGAG 60.359 61.111 33.48 10.94 0.00 4.63
2511 2675 7.715657 AGCAGAACAATTGTTTGTCAATCTAA 58.284 30.769 24.02 0.00 45.30 2.10
2586 2750 7.989947 TTATCCAAACTATTACTCCCTCTGT 57.010 36.000 0.00 0.00 0.00 3.41
2587 2751 6.893020 ATCCAAACTATTACTCCCTCTGTT 57.107 37.500 0.00 0.00 0.00 3.16
2588 2752 6.295719 TCCAAACTATTACTCCCTCTGTTC 57.704 41.667 0.00 0.00 0.00 3.18
2589 2753 5.189145 TCCAAACTATTACTCCCTCTGTTCC 59.811 44.000 0.00 0.00 0.00 3.62
2590 2754 5.429130 CAAACTATTACTCCCTCTGTTCCC 58.571 45.833 0.00 0.00 0.00 3.97
2591 2755 4.348020 ACTATTACTCCCTCTGTTCCCA 57.652 45.455 0.00 0.00 0.00 4.37
2592 2756 4.695606 ACTATTACTCCCTCTGTTCCCAA 58.304 43.478 0.00 0.00 0.00 4.12
2593 2757 5.098663 ACTATTACTCCCTCTGTTCCCAAA 58.901 41.667 0.00 0.00 0.00 3.28
2594 2758 5.731678 ACTATTACTCCCTCTGTTCCCAAAT 59.268 40.000 0.00 0.00 0.00 2.32
2595 2759 6.906901 ACTATTACTCCCTCTGTTCCCAAATA 59.093 38.462 0.00 0.00 0.00 1.40
2596 2760 6.848562 ATTACTCCCTCTGTTCCCAAATAT 57.151 37.500 0.00 0.00 0.00 1.28
2597 2761 7.947782 ATTACTCCCTCTGTTCCCAAATATA 57.052 36.000 0.00 0.00 0.00 0.86
2598 2762 7.758820 TTACTCCCTCTGTTCCCAAATATAA 57.241 36.000 0.00 0.00 0.00 0.98
2599 2763 6.253946 ACTCCCTCTGTTCCCAAATATAAG 57.746 41.667 0.00 0.00 0.00 1.73
2600 2764 5.731678 ACTCCCTCTGTTCCCAAATATAAGT 59.268 40.000 0.00 0.00 0.00 2.24
2601 2765 6.126739 ACTCCCTCTGTTCCCAAATATAAGTC 60.127 42.308 0.00 0.00 0.00 3.01
2602 2766 5.970640 TCCCTCTGTTCCCAAATATAAGTCT 59.029 40.000 0.00 0.00 0.00 3.24
2603 2767 6.447084 TCCCTCTGTTCCCAAATATAAGTCTT 59.553 38.462 0.00 0.00 0.00 3.01
2604 2768 7.036863 TCCCTCTGTTCCCAAATATAAGTCTTT 60.037 37.037 0.00 0.00 0.00 2.52
2605 2769 7.615757 CCCTCTGTTCCCAAATATAAGTCTTTT 59.384 37.037 0.00 0.00 0.00 2.27
2606 2770 9.025041 CCTCTGTTCCCAAATATAAGTCTTTTT 57.975 33.333 0.00 0.00 0.00 1.94
2624 2788 9.832445 AGTCTTTTTAGAGATTACAACAAGTGA 57.168 29.630 0.00 0.00 0.00 3.41
2625 2789 9.865484 GTCTTTTTAGAGATTACAACAAGTGAC 57.135 33.333 0.00 0.00 0.00 3.67
2626 2790 9.052759 TCTTTTTAGAGATTACAACAAGTGACC 57.947 33.333 0.00 0.00 0.00 4.02
2627 2791 8.740123 TTTTTAGAGATTACAACAAGTGACCA 57.260 30.769 0.00 0.00 0.00 4.02
2628 2792 7.724305 TTTAGAGATTACAACAAGTGACCAC 57.276 36.000 0.00 0.00 0.00 4.16
2629 2793 5.290493 AGAGATTACAACAAGTGACCACA 57.710 39.130 2.78 0.00 0.00 4.17
2630 2794 5.869579 AGAGATTACAACAAGTGACCACAT 58.130 37.500 2.78 0.00 0.00 3.21
2631 2795 7.004555 AGAGATTACAACAAGTGACCACATA 57.995 36.000 2.78 0.00 0.00 2.29
2632 2796 6.874134 AGAGATTACAACAAGTGACCACATAC 59.126 38.462 2.78 0.00 0.00 2.39
2633 2797 5.637810 AGATTACAACAAGTGACCACATACG 59.362 40.000 2.78 0.00 0.00 3.06
2634 2798 3.462483 ACAACAAGTGACCACATACGA 57.538 42.857 2.78 0.00 0.00 3.43
2635 2799 3.799366 ACAACAAGTGACCACATACGAA 58.201 40.909 2.78 0.00 0.00 3.85
2636 2800 3.807622 ACAACAAGTGACCACATACGAAG 59.192 43.478 2.78 0.00 0.00 3.79
2637 2801 2.413837 ACAAGTGACCACATACGAAGC 58.586 47.619 2.78 0.00 0.00 3.86
2638 2802 2.224185 ACAAGTGACCACATACGAAGCA 60.224 45.455 2.78 0.00 0.00 3.91
2639 2803 2.805671 CAAGTGACCACATACGAAGCAA 59.194 45.455 2.78 0.00 0.00 3.91
2640 2804 3.120321 AGTGACCACATACGAAGCAAA 57.880 42.857 2.78 0.00 0.00 3.68
2641 2805 3.472652 AGTGACCACATACGAAGCAAAA 58.527 40.909 2.78 0.00 0.00 2.44
2642 2806 4.072131 AGTGACCACATACGAAGCAAAAT 58.928 39.130 2.78 0.00 0.00 1.82
2643 2807 4.083324 AGTGACCACATACGAAGCAAAATG 60.083 41.667 2.78 0.00 0.00 2.32
2644 2808 4.068599 TGACCACATACGAAGCAAAATGA 58.931 39.130 0.00 0.00 0.00 2.57
2645 2809 4.154015 TGACCACATACGAAGCAAAATGAG 59.846 41.667 0.00 0.00 0.00 2.90
2646 2810 4.072131 ACCACATACGAAGCAAAATGAGT 58.928 39.130 0.00 0.00 0.00 3.41
2647 2811 4.083324 ACCACATACGAAGCAAAATGAGTG 60.083 41.667 0.00 0.00 0.00 3.51
2648 2812 4.154015 CCACATACGAAGCAAAATGAGTGA 59.846 41.667 0.00 0.00 0.00 3.41
2649 2813 5.334802 CCACATACGAAGCAAAATGAGTGAA 60.335 40.000 0.00 0.00 0.00 3.18
2650 2814 6.317088 CACATACGAAGCAAAATGAGTGAAT 58.683 36.000 0.00 0.00 0.00 2.57
2651 2815 6.467047 CACATACGAAGCAAAATGAGTGAATC 59.533 38.462 0.00 0.00 0.00 2.52
2652 2816 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
2653 2817 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
2654 2818 6.170675 ACGAAGCAAAATGAGTGAATCTAC 57.829 37.500 0.00 0.00 0.00 2.59
2655 2819 5.163953 ACGAAGCAAAATGAGTGAATCTACG 60.164 40.000 0.00 0.00 0.00 3.51
2656 2820 4.606457 AGCAAAATGAGTGAATCTACGC 57.394 40.909 0.00 0.00 0.00 4.42
2657 2821 4.256920 AGCAAAATGAGTGAATCTACGCT 58.743 39.130 0.00 0.00 0.00 5.07
2658 2822 4.331168 AGCAAAATGAGTGAATCTACGCTC 59.669 41.667 0.00 0.00 44.55 5.03
2659 2823 4.331168 GCAAAATGAGTGAATCTACGCTCT 59.669 41.667 0.00 0.00 44.58 4.09
2660 2824 5.520288 GCAAAATGAGTGAATCTACGCTCTA 59.480 40.000 0.00 0.00 44.58 2.43
2661 2825 6.036083 GCAAAATGAGTGAATCTACGCTCTAA 59.964 38.462 0.00 0.00 44.58 2.10
2662 2826 7.413000 GCAAAATGAGTGAATCTACGCTCTAAA 60.413 37.037 0.00 0.00 44.58 1.85
2663 2827 8.443160 CAAAATGAGTGAATCTACGCTCTAAAA 58.557 33.333 0.00 0.00 44.58 1.52
2664 2828 8.723942 AAATGAGTGAATCTACGCTCTAAAAT 57.276 30.769 0.00 0.00 44.58 1.82
2665 2829 9.817809 AAATGAGTGAATCTACGCTCTAAAATA 57.182 29.630 0.00 0.00 44.58 1.40
2666 2830 9.988815 AATGAGTGAATCTACGCTCTAAAATAT 57.011 29.630 0.00 0.00 44.58 1.28
2667 2831 8.803201 TGAGTGAATCTACGCTCTAAAATATG 57.197 34.615 0.00 0.00 44.58 1.78
2668 2832 8.414003 TGAGTGAATCTACGCTCTAAAATATGT 58.586 33.333 0.00 0.00 44.58 2.29
2669 2833 8.581057 AGTGAATCTACGCTCTAAAATATGTG 57.419 34.615 0.00 0.00 0.00 3.21
2670 2834 8.198109 AGTGAATCTACGCTCTAAAATATGTGT 58.802 33.333 0.00 0.00 0.00 3.72
2671 2835 9.459640 GTGAATCTACGCTCTAAAATATGTGTA 57.540 33.333 0.00 0.00 0.00 2.90
2672 2836 9.459640 TGAATCTACGCTCTAAAATATGTGTAC 57.540 33.333 0.00 0.00 0.00 2.90
2673 2837 9.459640 GAATCTACGCTCTAAAATATGTGTACA 57.540 33.333 0.00 0.00 0.00 2.90
2674 2838 9.982651 AATCTACGCTCTAAAATATGTGTACAT 57.017 29.630 0.00 2.75 40.22 2.29
2676 2840 9.888878 TCTACGCTCTAAAATATGTGTACATAC 57.111 33.333 6.85 0.00 41.15 2.39
2677 2841 9.673454 CTACGCTCTAAAATATGTGTACATACA 57.327 33.333 6.85 0.00 41.15 2.29
2679 2843 9.193133 ACGCTCTAAAATATGTGTACATACATC 57.807 33.333 6.85 0.00 41.15 3.06
2680 2844 9.411801 CGCTCTAAAATATGTGTACATACATCT 57.588 33.333 6.85 0.00 41.15 2.90
2699 2863 7.615582 ACATCTGTATGTTGTAGTCCATTTG 57.384 36.000 0.00 0.00 44.07 2.32
2700 2864 7.394016 ACATCTGTATGTTGTAGTCCATTTGA 58.606 34.615 0.00 0.00 44.07 2.69
2701 2865 7.882791 ACATCTGTATGTTGTAGTCCATTTGAA 59.117 33.333 0.00 0.00 44.07 2.69
2702 2866 8.729756 CATCTGTATGTTGTAGTCCATTTGAAA 58.270 33.333 0.00 0.00 0.00 2.69
2703 2867 8.862325 TCTGTATGTTGTAGTCCATTTGAAAT 57.138 30.769 0.00 0.00 0.00 2.17
2704 2868 8.729756 TCTGTATGTTGTAGTCCATTTGAAATG 58.270 33.333 10.84 10.84 0.00 2.32
2705 2869 8.402798 TGTATGTTGTAGTCCATTTGAAATGT 57.597 30.769 15.93 1.43 0.00 2.71
2706 2870 8.511321 TGTATGTTGTAGTCCATTTGAAATGTC 58.489 33.333 15.93 9.10 0.00 3.06
2707 2871 7.765695 ATGTTGTAGTCCATTTGAAATGTCT 57.234 32.000 15.93 14.81 0.00 3.41
2708 2872 8.862325 ATGTTGTAGTCCATTTGAAATGTCTA 57.138 30.769 15.93 13.97 0.00 2.59
2709 2873 8.322906 TGTTGTAGTCCATTTGAAATGTCTAG 57.677 34.615 15.93 1.90 0.00 2.43
2710 2874 8.154203 TGTTGTAGTCCATTTGAAATGTCTAGA 58.846 33.333 15.93 12.79 0.00 2.43
2711 2875 8.999431 GTTGTAGTCCATTTGAAATGTCTAGAA 58.001 33.333 15.93 16.70 0.00 2.10
2712 2876 9.567776 TTGTAGTCCATTTGAAATGTCTAGAAA 57.432 29.630 15.93 11.59 0.00 2.52
2713 2877 9.219603 TGTAGTCCATTTGAAATGTCTAGAAAG 57.780 33.333 15.93 0.00 0.00 2.62
2714 2878 9.436957 GTAGTCCATTTGAAATGTCTAGAAAGA 57.563 33.333 15.93 1.84 0.00 2.52
2734 2898 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
2735 2899 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
2736 2900 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
2737 2901 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
2738 2902 6.141790 ACTTATATTTAGGAACGGAGGGAGT 58.858 40.000 0.00 0.00 0.00 3.85
2739 2903 7.300658 ACTTATATTTAGGAACGGAGGGAGTA 58.699 38.462 0.00 0.00 0.00 2.59
2794 2958 6.770785 TGATATTTTAATCAAGAAGGTCCCCG 59.229 38.462 0.00 0.00 32.97 5.73
2816 2981 5.694006 CCGCATTATCTTACTTCAAGAGAGG 59.306 44.000 0.00 0.00 46.37 3.69
2895 3486 7.046652 ACTGATTGTCCATGAGTCATTAAGAG 58.953 38.462 1.86 0.00 0.00 2.85
2900 3491 7.009179 TGTCCATGAGTCATTAAGAGAAGTT 57.991 36.000 1.86 0.00 0.00 2.66
3151 3867 9.076781 TGAAAAGATTGTCCATGAGTCATTAAA 57.923 29.630 1.86 0.00 0.00 1.52
3152 3868 9.912634 GAAAAGATTGTCCATGAGTCATTAAAA 57.087 29.630 1.86 0.00 0.00 1.52
3153 3869 9.918630 AAAAGATTGTCCATGAGTCATTAAAAG 57.081 29.630 1.86 0.00 0.00 2.27
3154 3870 8.641498 AAGATTGTCCATGAGTCATTAAAAGT 57.359 30.769 1.86 0.00 0.00 2.66
3155 3871 9.739276 AAGATTGTCCATGAGTCATTAAAAGTA 57.261 29.630 1.86 0.00 0.00 2.24
3156 3872 9.739276 AGATTGTCCATGAGTCATTAAAAGTAA 57.261 29.630 1.86 0.00 0.00 2.24
3311 4070 6.978080 GGAAGTTTCACACTTTTAGCAATCAA 59.022 34.615 0.00 0.00 46.53 2.57
3396 4156 7.652524 ACAGTGATTATCATGTAGACTCTGT 57.347 36.000 0.00 1.88 0.00 3.41
3526 4316 7.830739 ACTGATTATTTCACAACTTCAATCCC 58.169 34.615 0.00 0.00 0.00 3.85
3527 4317 6.851609 TGATTATTTCACAACTTCAATCCCG 58.148 36.000 0.00 0.00 0.00 5.14
3528 4318 6.432783 TGATTATTTCACAACTTCAATCCCGT 59.567 34.615 0.00 0.00 0.00 5.28
3529 4319 6.642707 TTATTTCACAACTTCAATCCCGTT 57.357 33.333 0.00 0.00 0.00 4.44
3530 4320 4.993029 TTTCACAACTTCAATCCCGTTT 57.007 36.364 0.00 0.00 0.00 3.60
3543 4333 6.791303 TCAATCCCGTTTTTGCTGTATATTC 58.209 36.000 0.00 0.00 0.00 1.75
3694 4484 6.454795 TGGAATAATTGTTCTTTGGTCTTGC 58.545 36.000 13.76 0.00 0.00 4.01
3825 4618 1.642037 CTGGAATGTGCAGCGAGGTG 61.642 60.000 0.00 0.00 0.00 4.00
3838 4631 1.668751 GCGAGGTGTTTCAGTTTGACA 59.331 47.619 0.00 0.00 0.00 3.58
4051 4844 2.292845 AGAACTTCTGAAAGCAGCAAGC 59.707 45.455 0.00 0.00 42.01 4.01
4077 4870 2.432146 TGATAAGAAGCCAGCATCGTCT 59.568 45.455 0.00 0.00 0.00 4.18
4113 4906 1.966148 TAGCTGATCCCAGGGAGGCT 61.966 60.000 26.70 26.70 40.72 4.58
4119 4912 2.574195 ATCCCAGGGAGGCTGGTGAT 62.574 60.000 15.44 0.00 40.23 3.06
4215 5008 4.898265 AGATATGTCACATACTCCTGCACT 59.102 41.667 0.00 0.00 0.00 4.40
4236 5029 0.555769 TTCCTTTCAAGGGTGCCAGT 59.444 50.000 5.73 0.00 46.47 4.00
4256 5049 6.464222 CCAGTCCTCATCTTGTAAACTAACA 58.536 40.000 0.00 0.00 0.00 2.41
4272 5065 7.806680 AAACTAACAAATAATCATGGGGGTT 57.193 32.000 0.00 0.00 0.00 4.11
4275 5068 5.675684 AACAAATAATCATGGGGGTTGAC 57.324 39.130 0.00 0.00 0.00 3.18
4460 5253 1.168714 GGTTCTGCAGGTTTAGGCTG 58.831 55.000 15.13 0.00 0.00 4.85
4523 5316 8.357290 TCTTATGCTGTACTCTAACCTTGTTA 57.643 34.615 0.00 0.00 0.00 2.41
4528 5321 8.942338 TGCTGTACTCTAACCTTGTTATAATG 57.058 34.615 0.00 0.00 0.00 1.90
4529 5322 8.537016 TGCTGTACTCTAACCTTGTTATAATGT 58.463 33.333 0.00 0.00 0.00 2.71
4535 5328 8.702819 ACTCTAACCTTGTTATAATGTACTCCC 58.297 37.037 0.00 0.00 0.00 4.30
4536 5329 8.849543 TCTAACCTTGTTATAATGTACTCCCT 57.150 34.615 0.00 0.00 0.00 4.20
4537 5330 8.921205 TCTAACCTTGTTATAATGTACTCCCTC 58.079 37.037 0.00 0.00 0.00 4.30
4538 5331 6.496144 ACCTTGTTATAATGTACTCCCTCC 57.504 41.667 0.00 0.00 0.00 4.30
4539 5332 5.070047 ACCTTGTTATAATGTACTCCCTCCG 59.930 44.000 0.00 0.00 0.00 4.63
4540 5333 5.070047 CCTTGTTATAATGTACTCCCTCCGT 59.930 44.000 0.00 0.00 0.00 4.69
4541 5334 6.266103 CCTTGTTATAATGTACTCCCTCCGTA 59.734 42.308 0.00 0.00 0.00 4.02
4542 5335 7.201938 CCTTGTTATAATGTACTCCCTCCGTAA 60.202 40.741 0.00 0.00 0.00 3.18
4543 5336 7.658525 TGTTATAATGTACTCCCTCCGTAAA 57.341 36.000 0.00 0.00 0.00 2.01
4544 5337 7.491682 TGTTATAATGTACTCCCTCCGTAAAC 58.508 38.462 0.00 0.00 0.00 2.01
4545 5338 7.342799 TGTTATAATGTACTCCCTCCGTAAACT 59.657 37.037 0.00 0.00 0.00 2.66
4546 5339 8.850156 GTTATAATGTACTCCCTCCGTAAACTA 58.150 37.037 0.00 0.00 0.00 2.24
4547 5340 7.902920 ATAATGTACTCCCTCCGTAAACTAA 57.097 36.000 0.00 0.00 0.00 2.24
4548 5341 6.803366 AATGTACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
4549 5342 7.902920 AATGTACTCCCTCCGTAAACTAATA 57.097 36.000 0.00 0.00 0.00 0.98
4550 5343 8.488308 AATGTACTCCCTCCGTAAACTAATAT 57.512 34.615 0.00 0.00 0.00 1.28
4551 5344 9.592196 AATGTACTCCCTCCGTAAACTAATATA 57.408 33.333 0.00 0.00 0.00 0.86
4552 5345 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
4553 5346 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
4554 5347 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
4555 5348 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
4556 5349 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
4557 5350 7.008941 TCCCTCCGTAAACTAATATAAGAGCT 58.991 38.462 0.00 0.00 0.00 4.09
4558 5351 7.508296 TCCCTCCGTAAACTAATATAAGAGCTT 59.492 37.037 0.00 0.00 0.00 3.74
4559 5352 8.148999 CCCTCCGTAAACTAATATAAGAGCTTT 58.851 37.037 0.00 0.00 0.00 3.51
4560 5353 9.543783 CCTCCGTAAACTAATATAAGAGCTTTT 57.456 33.333 0.00 0.00 0.00 2.27
4587 5380 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
4588 5381 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
4589 5382 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
4590 5383 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
4591 5384 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
4592 5385 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
4593 5386 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
4608 5401 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
4609 5402 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
4610 5403 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
4623 5416 9.317827 AGTTTACAGAGGGAGTAATACTGTTTA 57.682 33.333 0.00 0.00 41.17 2.01
4679 5472 6.477053 TTATCTCTCCAGAGCATATATGGC 57.523 41.667 14.51 6.90 40.35 4.40
4682 5475 1.552337 CTCCAGAGCATATATGGCCGT 59.448 52.381 14.51 1.35 40.35 5.68
4706 5499 3.064820 ACAAACTTGTTCATGTGTCGTCC 59.935 43.478 0.00 0.00 38.47 4.79
4708 5501 1.067974 ACTTGTTCATGTGTCGTCCGA 59.932 47.619 0.00 0.00 0.00 4.55
4720 5513 0.876399 TCGTCCGAGACAAATCGACA 59.124 50.000 0.00 0.00 45.56 4.35
4744 5537 8.867112 CATCTGGTTGATGGAAATTATTTCTG 57.133 34.615 16.02 0.41 46.55 3.02
4745 5538 8.472413 CATCTGGTTGATGGAAATTATTTCTGT 58.528 33.333 16.02 6.40 46.55 3.41
4746 5539 8.055279 TCTGGTTGATGGAAATTATTTCTGTC 57.945 34.615 16.02 13.93 39.59 3.51
4747 5540 7.669304 TCTGGTTGATGGAAATTATTTCTGTCA 59.331 33.333 16.02 15.85 39.59 3.58
4748 5541 7.829725 TGGTTGATGGAAATTATTTCTGTCAG 58.170 34.615 16.02 0.00 39.59 3.51
4749 5542 6.753744 GGTTGATGGAAATTATTTCTGTCAGC 59.246 38.462 16.02 18.26 39.59 4.26
4750 5543 7.363268 GGTTGATGGAAATTATTTCTGTCAGCT 60.363 37.037 23.07 0.00 39.59 4.24
4751 5544 7.707624 TGATGGAAATTATTTCTGTCAGCTT 57.292 32.000 16.02 0.00 39.59 3.74
4752 5545 8.125978 TGATGGAAATTATTTCTGTCAGCTTT 57.874 30.769 16.02 0.00 39.59 3.51
4768 5561 8.635765 TGTCAGCTTTAATCTGGATAAACTTT 57.364 30.769 0.00 0.00 32.63 2.66
4821 5619 7.948278 AATCCGATAAGCATAGTACTGAAAC 57.052 36.000 5.39 0.00 0.00 2.78
4835 5633 7.918536 AGTACTGAAACTGTAACGATCTCTA 57.081 36.000 0.00 0.00 0.00 2.43
4840 5638 7.924412 ACTGAAACTGTAACGATCTCTACAAAA 59.076 33.333 0.00 0.00 0.00 2.44
4841 5639 8.827177 TGAAACTGTAACGATCTCTACAAAAT 57.173 30.769 0.00 0.00 0.00 1.82
4842 5640 9.268268 TGAAACTGTAACGATCTCTACAAAATT 57.732 29.630 0.00 2.35 0.00 1.82
4862 5660 9.918630 CAAAATTAGTTGGTTCTGAATTCTGAT 57.081 29.630 14.89 3.08 0.00 2.90
4867 5665 5.709164 AGTTGGTTCTGAATTCTGATTGGAG 59.291 40.000 14.89 0.00 0.00 3.86
4868 5666 5.246981 TGGTTCTGAATTCTGATTGGAGT 57.753 39.130 14.89 0.00 0.00 3.85
4869 5667 5.634118 TGGTTCTGAATTCTGATTGGAGTT 58.366 37.500 14.89 0.00 0.00 3.01
4870 5668 6.070656 TGGTTCTGAATTCTGATTGGAGTTT 58.929 36.000 14.89 0.00 0.00 2.66
4873 5671 7.255590 GGTTCTGAATTCTGATTGGAGTTTGAA 60.256 37.037 14.89 0.00 0.00 2.69
4874 5672 8.302438 GTTCTGAATTCTGATTGGAGTTTGAAT 58.698 33.333 14.89 0.00 0.00 2.57
4875 5673 8.413309 TCTGAATTCTGATTGGAGTTTGAATT 57.587 30.769 10.68 0.00 37.00 2.17
4877 5675 9.485206 CTGAATTCTGATTGGAGTTTGAATTTT 57.515 29.630 7.05 0.00 35.24 1.82
4878 5676 9.835389 TGAATTCTGATTGGAGTTTGAATTTTT 57.165 25.926 7.05 0.00 35.24 1.94
4916 5862 4.921470 AGACGTTACACATGAAAATCCG 57.079 40.909 0.00 0.00 0.00 4.18
5058 6942 1.523258 CTCAGGCATCAAGCTCCCG 60.523 63.158 0.00 0.00 44.79 5.14
5067 6951 2.284995 AAGCTCCCGCCCTTCTCT 60.285 61.111 0.00 0.00 36.60 3.10
5069 6953 3.855853 GCTCCCGCCCTTCTCTCC 61.856 72.222 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 9.247126 TGTTGATTCTTGATTGTTAATTGTGTG 57.753 29.630 0.00 0.00 0.00 3.82
65 66 1.376037 GGAACACCAGAAGCGAGGG 60.376 63.158 0.00 0.00 0.00 4.30
133 134 4.192317 CGCCTCTAAGTTTTGGCTATCTT 58.808 43.478 10.36 0.00 42.90 2.40
159 160 4.580580 ACAAAGGTCCTGAATTCTGTTGTC 59.419 41.667 7.05 0.00 0.00 3.18
205 206 7.697352 TGTTTCTTTGTTTTGCTGTATCATG 57.303 32.000 0.00 0.00 0.00 3.07
214 215 7.149144 GCTTTCTGTTTTGTTTCTTTGTTTTGC 60.149 33.333 0.00 0.00 0.00 3.68
224 225 7.009265 GTCTAGTTTGGCTTTCTGTTTTGTTTC 59.991 37.037 0.00 0.00 0.00 2.78
243 244 2.126580 GGTCACGCGCGTCTAGTT 60.127 61.111 35.61 7.71 0.00 2.24
259 260 3.698040 CAGAGATGAAATGGAAAGGGTGG 59.302 47.826 0.00 0.00 0.00 4.61
262 263 3.629087 AGCAGAGATGAAATGGAAAGGG 58.371 45.455 0.00 0.00 0.00 3.95
266 267 4.408270 AGCTAGAGCAGAGATGAAATGGAA 59.592 41.667 4.01 0.00 45.16 3.53
277 281 4.852962 GCCCAAGCTAGAGCAGAG 57.147 61.111 4.01 0.00 45.16 3.35
350 357 0.531532 CAGGACGTGCCCTCATCATC 60.532 60.000 2.38 0.00 37.37 2.92
358 365 1.043673 ACTAGGATCAGGACGTGCCC 61.044 60.000 2.38 0.00 37.37 5.36
394 426 5.405571 TCTCGTGTTTGCTTATTTCTCAGAC 59.594 40.000 0.00 0.00 0.00 3.51
447 479 5.258841 TCTGATGAATGAATGTGCTTTCCT 58.741 37.500 0.00 0.00 0.00 3.36
484 520 1.684248 GGGAAATGTGGCTGCTCTGAT 60.684 52.381 0.00 0.00 0.00 2.90
485 521 0.322816 GGGAAATGTGGCTGCTCTGA 60.323 55.000 0.00 0.00 0.00 3.27
486 522 0.323178 AGGGAAATGTGGCTGCTCTG 60.323 55.000 0.00 0.00 0.00 3.35
487 523 0.323178 CAGGGAAATGTGGCTGCTCT 60.323 55.000 0.00 0.00 0.00 4.09
488 524 1.941999 GCAGGGAAATGTGGCTGCTC 61.942 60.000 0.00 0.00 35.26 4.26
503 539 1.302033 GGTCAGTGAGTGGTGCAGG 60.302 63.158 0.00 0.00 0.00 4.85
542 582 3.385749 CTATGCCCGGTGCGGTTCT 62.386 63.158 0.00 0.00 46.80 3.01
543 583 2.895372 CTATGCCCGGTGCGGTTC 60.895 66.667 0.00 0.00 46.80 3.62
808 917 0.744771 GGTGCGGATCCAGTTTCTCC 60.745 60.000 13.41 1.94 0.00 3.71
811 920 2.750888 GCGGTGCGGATCCAGTTTC 61.751 63.158 13.41 0.00 0.00 2.78
814 923 4.760047 GTGCGGTGCGGATCCAGT 62.760 66.667 13.41 0.00 0.00 4.00
896 1005 4.789123 ATTCGGAAACCCGGGGCG 62.789 66.667 27.92 8.86 46.72 6.13
897 1006 2.361992 AATTCGGAAACCCGGGGC 60.362 61.111 27.92 13.83 46.72 5.80
898 1007 1.751544 GGAATTCGGAAACCCGGGG 60.752 63.158 27.92 12.73 46.72 5.73
903 1012 4.801330 AGGAATTTGGAATTCGGAAACC 57.199 40.909 0.00 9.41 0.00 3.27
938 1047 2.111878 CGGCATCCATGGAGGGAC 59.888 66.667 26.71 18.77 40.44 4.46
945 1085 1.153588 GTTTTGGGCGGCATCCATG 60.154 57.895 12.47 0.00 33.82 3.66
1027 1170 2.579738 GAGGTCGAAGTGGGAGGC 59.420 66.667 0.00 0.00 0.00 4.70
1107 1250 2.438434 AAATTCCCGAGCGGCAGG 60.438 61.111 1.45 5.05 0.00 4.85
1416 1580 4.215742 CCGGATCGGCGGCACTTA 62.216 66.667 10.53 0.00 41.17 2.24
1869 2033 6.542370 CCTTCTTGTTCTCTGGTTTCTTTGTA 59.458 38.462 0.00 0.00 0.00 2.41
1898 2062 1.819288 TGGACTTACTCTTGCTCTCCG 59.181 52.381 0.00 0.00 0.00 4.63
1902 2066 3.006967 TGGTCTTGGACTTACTCTTGCTC 59.993 47.826 0.00 0.00 32.47 4.26
2031 2195 5.627499 TCCTAAACATTGCATTGTCACTC 57.373 39.130 14.21 0.00 0.00 3.51
2221 2385 2.923605 GCACATACAACAAAGCAGGCAG 60.924 50.000 0.00 0.00 0.00 4.85
2577 2741 6.100424 AGACTTATATTTGGGAACAGAGGGAG 59.900 42.308 0.00 0.00 44.54 4.30
2578 2742 5.970640 AGACTTATATTTGGGAACAGAGGGA 59.029 40.000 0.00 0.00 44.54 4.20
2579 2743 6.253946 AGACTTATATTTGGGAACAGAGGG 57.746 41.667 0.00 0.00 44.54 4.30
2580 2744 8.581253 AAAAGACTTATATTTGGGAACAGAGG 57.419 34.615 0.00 0.00 44.54 3.69
2598 2762 9.832445 TCACTTGTTGTAATCTCTAAAAAGACT 57.168 29.630 0.00 0.00 0.00 3.24
2599 2763 9.865484 GTCACTTGTTGTAATCTCTAAAAAGAC 57.135 33.333 0.00 0.00 0.00 3.01
2600 2764 9.052759 GGTCACTTGTTGTAATCTCTAAAAAGA 57.947 33.333 0.00 0.00 0.00 2.52
2601 2765 8.836413 TGGTCACTTGTTGTAATCTCTAAAAAG 58.164 33.333 0.00 0.00 0.00 2.27
2602 2766 8.617809 GTGGTCACTTGTTGTAATCTCTAAAAA 58.382 33.333 0.00 0.00 0.00 1.94
2603 2767 7.771361 TGTGGTCACTTGTTGTAATCTCTAAAA 59.229 33.333 2.66 0.00 0.00 1.52
2604 2768 7.276658 TGTGGTCACTTGTTGTAATCTCTAAA 58.723 34.615 2.66 0.00 0.00 1.85
2605 2769 6.822442 TGTGGTCACTTGTTGTAATCTCTAA 58.178 36.000 2.66 0.00 0.00 2.10
2606 2770 6.413783 TGTGGTCACTTGTTGTAATCTCTA 57.586 37.500 2.66 0.00 0.00 2.43
2607 2771 5.290493 TGTGGTCACTTGTTGTAATCTCT 57.710 39.130 2.66 0.00 0.00 3.10
2608 2772 6.183360 CGTATGTGGTCACTTGTTGTAATCTC 60.183 42.308 2.66 0.00 0.00 2.75
2609 2773 5.637810 CGTATGTGGTCACTTGTTGTAATCT 59.362 40.000 2.66 0.00 0.00 2.40
2610 2774 5.636121 TCGTATGTGGTCACTTGTTGTAATC 59.364 40.000 2.66 0.00 0.00 1.75
2611 2775 5.543714 TCGTATGTGGTCACTTGTTGTAAT 58.456 37.500 2.66 0.00 0.00 1.89
2612 2776 4.946445 TCGTATGTGGTCACTTGTTGTAA 58.054 39.130 2.66 0.00 0.00 2.41
2613 2777 4.587584 TCGTATGTGGTCACTTGTTGTA 57.412 40.909 2.66 0.00 0.00 2.41
2614 2778 3.462483 TCGTATGTGGTCACTTGTTGT 57.538 42.857 2.66 0.00 0.00 3.32
2615 2779 3.363970 GCTTCGTATGTGGTCACTTGTTG 60.364 47.826 2.66 0.00 0.00 3.33
2616 2780 2.806244 GCTTCGTATGTGGTCACTTGTT 59.194 45.455 2.66 0.00 0.00 2.83
2617 2781 2.224185 TGCTTCGTATGTGGTCACTTGT 60.224 45.455 2.66 0.00 0.00 3.16
2618 2782 2.412870 TGCTTCGTATGTGGTCACTTG 58.587 47.619 2.66 0.00 0.00 3.16
2619 2783 2.831685 TGCTTCGTATGTGGTCACTT 57.168 45.000 2.66 0.00 0.00 3.16
2620 2784 2.831685 TTGCTTCGTATGTGGTCACT 57.168 45.000 2.66 0.00 0.00 3.41
2621 2785 3.889196 TTTTGCTTCGTATGTGGTCAC 57.111 42.857 0.00 0.00 0.00 3.67
2622 2786 4.068599 TCATTTTGCTTCGTATGTGGTCA 58.931 39.130 0.00 0.00 0.00 4.02
2623 2787 4.154195 ACTCATTTTGCTTCGTATGTGGTC 59.846 41.667 0.00 0.00 0.00 4.02
2624 2788 4.072131 ACTCATTTTGCTTCGTATGTGGT 58.928 39.130 0.00 0.00 0.00 4.16
2625 2789 4.154015 TCACTCATTTTGCTTCGTATGTGG 59.846 41.667 0.00 0.00 0.00 4.17
2626 2790 5.281693 TCACTCATTTTGCTTCGTATGTG 57.718 39.130 0.00 0.00 0.00 3.21
2627 2791 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
2628 2792 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
2629 2793 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
2630 2794 6.034577 CGTAGATTCACTCATTTTGCTTCGTA 59.965 38.462 0.00 0.00 0.00 3.43
2631 2795 5.163953 CGTAGATTCACTCATTTTGCTTCGT 60.164 40.000 0.00 0.00 0.00 3.85
2632 2796 5.251081 CGTAGATTCACTCATTTTGCTTCG 58.749 41.667 0.00 0.00 0.00 3.79
2633 2797 5.024555 GCGTAGATTCACTCATTTTGCTTC 58.975 41.667 0.00 0.00 0.00 3.86
2634 2798 4.697352 AGCGTAGATTCACTCATTTTGCTT 59.303 37.500 0.00 0.00 0.00 3.91
2635 2799 4.256920 AGCGTAGATTCACTCATTTTGCT 58.743 39.130 0.00 0.00 0.00 3.91
2636 2800 4.331168 AGAGCGTAGATTCACTCATTTTGC 59.669 41.667 0.00 0.00 0.00 3.68
2637 2801 7.525688 TTAGAGCGTAGATTCACTCATTTTG 57.474 36.000 0.00 0.00 0.00 2.44
2638 2802 8.547967 TTTTAGAGCGTAGATTCACTCATTTT 57.452 30.769 0.00 0.00 0.00 1.82
2639 2803 8.723942 ATTTTAGAGCGTAGATTCACTCATTT 57.276 30.769 0.00 0.00 0.00 2.32
2640 2804 9.988815 ATATTTTAGAGCGTAGATTCACTCATT 57.011 29.630 0.00 0.00 0.00 2.57
2641 2805 9.416794 CATATTTTAGAGCGTAGATTCACTCAT 57.583 33.333 0.00 0.00 0.00 2.90
2642 2806 8.414003 ACATATTTTAGAGCGTAGATTCACTCA 58.586 33.333 0.00 0.00 0.00 3.41
2643 2807 8.695284 CACATATTTTAGAGCGTAGATTCACTC 58.305 37.037 0.00 0.00 0.00 3.51
2644 2808 8.198109 ACACATATTTTAGAGCGTAGATTCACT 58.802 33.333 0.00 0.00 0.00 3.41
2645 2809 8.354011 ACACATATTTTAGAGCGTAGATTCAC 57.646 34.615 0.00 0.00 0.00 3.18
2646 2810 9.459640 GTACACATATTTTAGAGCGTAGATTCA 57.540 33.333 0.00 0.00 0.00 2.57
2647 2811 9.459640 TGTACACATATTTTAGAGCGTAGATTC 57.540 33.333 0.00 0.00 0.00 2.52
2648 2812 9.982651 ATGTACACATATTTTAGAGCGTAGATT 57.017 29.630 0.00 0.00 34.26 2.40
2650 2814 9.888878 GTATGTACACATATTTTAGAGCGTAGA 57.111 33.333 0.00 0.00 40.53 2.59
2651 2815 9.673454 TGTATGTACACATATTTTAGAGCGTAG 57.327 33.333 0.00 0.00 40.53 3.51
2653 2817 9.193133 GATGTATGTACACATATTTTAGAGCGT 57.807 33.333 0.00 0.00 40.53 5.07
2654 2818 9.411801 AGATGTATGTACACATATTTTAGAGCG 57.588 33.333 0.00 0.00 40.53 5.03
2673 2837 9.330063 CAAATGGACTACAACATACAGATGTAT 57.670 33.333 0.00 0.00 45.93 2.29
2674 2838 8.536175 TCAAATGGACTACAACATACAGATGTA 58.464 33.333 0.00 0.00 45.93 2.29
2676 2840 7.848223 TCAAATGGACTACAACATACAGATG 57.152 36.000 0.00 0.00 39.16 2.90
2677 2841 8.862325 TTTCAAATGGACTACAACATACAGAT 57.138 30.769 0.00 0.00 0.00 2.90
2678 2842 8.729756 CATTTCAAATGGACTACAACATACAGA 58.270 33.333 1.73 0.00 0.00 3.41
2679 2843 8.514594 ACATTTCAAATGGACTACAACATACAG 58.485 33.333 14.70 0.00 0.00 2.74
2680 2844 8.402798 ACATTTCAAATGGACTACAACATACA 57.597 30.769 14.70 0.00 0.00 2.29
2681 2845 8.730680 AGACATTTCAAATGGACTACAACATAC 58.269 33.333 14.70 0.00 0.00 2.39
2682 2846 8.862325 AGACATTTCAAATGGACTACAACATA 57.138 30.769 14.70 0.00 0.00 2.29
2683 2847 7.765695 AGACATTTCAAATGGACTACAACAT 57.234 32.000 14.70 0.00 0.00 2.71
2684 2848 8.154203 TCTAGACATTTCAAATGGACTACAACA 58.846 33.333 14.70 0.00 0.00 3.33
2685 2849 8.547967 TCTAGACATTTCAAATGGACTACAAC 57.452 34.615 14.70 0.00 0.00 3.32
2686 2850 9.567776 TTTCTAGACATTTCAAATGGACTACAA 57.432 29.630 14.70 8.52 0.00 2.41
2687 2851 9.219603 CTTTCTAGACATTTCAAATGGACTACA 57.780 33.333 14.70 3.48 0.00 2.74
2688 2852 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
2708 2872 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
2709 2873 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
2710 2874 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
2711 2875 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
2712 2876 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
2713 2877 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
2714 2878 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2715 2879 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2716 2880 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
2717 2881 8.731591 AAATACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
2718 2882 7.513091 AGAAATACTCCCTCCGTTCCTAAATAT 59.487 37.037 0.00 0.00 0.00 1.28
2719 2883 6.842807 AGAAATACTCCCTCCGTTCCTAAATA 59.157 38.462 0.00 0.00 0.00 1.40
2720 2884 5.666265 AGAAATACTCCCTCCGTTCCTAAAT 59.334 40.000 0.00 0.00 0.00 1.40
2721 2885 5.028131 AGAAATACTCCCTCCGTTCCTAAA 58.972 41.667 0.00 0.00 0.00 1.85
2722 2886 4.617593 AGAAATACTCCCTCCGTTCCTAA 58.382 43.478 0.00 0.00 0.00 2.69
2723 2887 4.079327 AGAGAAATACTCCCTCCGTTCCTA 60.079 45.833 0.00 0.00 45.96 2.94
2724 2888 3.032459 GAGAAATACTCCCTCCGTTCCT 58.968 50.000 0.00 0.00 39.53 3.36
2725 2889 3.032459 AGAGAAATACTCCCTCCGTTCC 58.968 50.000 0.00 0.00 45.96 3.62
2726 2890 3.447944 ACAGAGAAATACTCCCTCCGTTC 59.552 47.826 0.00 0.00 45.96 3.95
2727 2891 3.442076 ACAGAGAAATACTCCCTCCGTT 58.558 45.455 0.00 0.00 45.96 4.44
2728 2892 3.103080 ACAGAGAAATACTCCCTCCGT 57.897 47.619 0.00 0.00 45.96 4.69
2729 2893 3.786635 CAACAGAGAAATACTCCCTCCG 58.213 50.000 0.00 0.00 45.96 4.63
2730 2894 3.055094 TGCAACAGAGAAATACTCCCTCC 60.055 47.826 0.00 0.00 45.96 4.30
2731 2895 4.207891 TGCAACAGAGAAATACTCCCTC 57.792 45.455 0.00 0.00 45.96 4.30
2732 2896 4.851639 ATGCAACAGAGAAATACTCCCT 57.148 40.909 0.00 0.00 45.96 4.20
2733 2897 4.943705 TCAATGCAACAGAGAAATACTCCC 59.056 41.667 0.00 0.00 45.96 4.30
2734 2898 5.412594 TGTCAATGCAACAGAGAAATACTCC 59.587 40.000 0.00 0.00 45.96 3.85
2735 2899 6.073058 TGTGTCAATGCAACAGAGAAATACTC 60.073 38.462 0.00 0.00 45.22 2.59
2736 2900 5.764686 TGTGTCAATGCAACAGAGAAATACT 59.235 36.000 0.00 0.00 0.00 2.12
2737 2901 6.000891 TGTGTCAATGCAACAGAGAAATAC 57.999 37.500 0.00 0.00 0.00 1.89
2738 2902 6.430616 TGATGTGTCAATGCAACAGAGAAATA 59.569 34.615 0.00 0.00 0.00 1.40
2739 2903 5.242171 TGATGTGTCAATGCAACAGAGAAAT 59.758 36.000 0.00 0.00 0.00 2.17
2790 2954 4.703897 TCTTGAAGTAAGATAATGCGGGG 58.296 43.478 0.00 0.00 40.43 5.73
2794 2958 5.468409 GGCCTCTCTTGAAGTAAGATAATGC 59.532 44.000 0.00 0.00 44.12 3.56
2970 3561 5.590259 AGTGTGAGACTTACTTGTTTGCAAT 59.410 36.000 0.00 0.00 33.65 3.56
2985 3576 3.437049 GCTGGATGGTTAAAGTGTGAGAC 59.563 47.826 0.00 0.00 0.00 3.36
3376 4136 7.062957 TCAGGACAGAGTCTACATGATAATCA 58.937 38.462 0.00 0.00 32.47 2.57
3396 4156 2.774234 CAGGGATTAAGGCTCTTCAGGA 59.226 50.000 0.00 0.00 0.00 3.86
3524 4314 4.974368 TGGAATATACAGCAAAAACGGG 57.026 40.909 0.00 0.00 0.00 5.28
3525 4315 5.949735 ACTTGGAATATACAGCAAAAACGG 58.050 37.500 0.00 0.00 0.00 4.44
3526 4316 7.748847 AGTACTTGGAATATACAGCAAAAACG 58.251 34.615 0.00 0.00 0.00 3.60
3527 4317 9.908152 AAAGTACTTGGAATATACAGCAAAAAC 57.092 29.630 9.34 0.00 0.00 2.43
3694 4484 6.696411 AGTTTTCTGTAGGAGACTTCATCAG 58.304 40.000 0.45 0.45 43.67 2.90
3748 4541 7.062839 CAGAATTAGAGTAAGAGACAGTGCAAC 59.937 40.741 0.00 0.00 0.00 4.17
3825 4618 3.730715 CAGCGGAAATGTCAAACTGAAAC 59.269 43.478 0.00 0.00 0.00 2.78
3838 4631 0.532115 GAATTGGTGGCAGCGGAAAT 59.468 50.000 12.58 3.58 0.00 2.17
4051 4844 3.827008 TGCTGGCTTCTTATCAGGTAG 57.173 47.619 0.00 0.00 0.00 3.18
4077 4870 4.058124 CAGCTAGCACAGAAACAACTACA 58.942 43.478 18.83 0.00 0.00 2.74
4113 4906 2.906182 GATCGCTGTCGCCATCACCA 62.906 60.000 0.00 0.00 34.41 4.17
4119 4912 2.125552 CTTGGATCGCTGTCGCCA 60.126 61.111 0.00 0.00 35.26 5.69
4228 5021 0.326264 ACAAGATGAGGACTGGCACC 59.674 55.000 0.00 0.00 0.00 5.01
4256 5049 2.693074 GCGTCAACCCCCATGATTATTT 59.307 45.455 0.00 0.00 0.00 1.40
4275 5068 0.865111 TTGAGAACCATGACAACGCG 59.135 50.000 3.53 3.53 0.00 6.01
4313 5106 1.800586 CTATCGGCCATCACATTTCGG 59.199 52.381 2.24 0.00 0.00 4.30
4318 5111 5.179368 CGTTTTAATCTATCGGCCATCACAT 59.821 40.000 2.24 0.00 0.00 3.21
4319 5112 4.509970 CGTTTTAATCTATCGGCCATCACA 59.490 41.667 2.24 0.00 0.00 3.58
4320 5113 4.748102 TCGTTTTAATCTATCGGCCATCAC 59.252 41.667 2.24 0.00 0.00 3.06
4460 5253 2.187707 CAGCACAAAAACTGCACTCAC 58.812 47.619 0.00 0.00 37.08 3.51
4523 5316 7.902920 TTAGTTTACGGAGGGAGTACATTAT 57.097 36.000 0.00 0.00 0.00 1.28
4525 5318 6.803366 ATTAGTTTACGGAGGGAGTACATT 57.197 37.500 0.00 0.00 0.00 2.71
4528 5321 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
4529 5322 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
4530 5323 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
4531 5324 7.177041 AGCTCTTATATTAGTTTACGGAGGGAG 59.823 40.741 0.00 0.00 0.00 4.30
4532 5325 7.008941 AGCTCTTATATTAGTTTACGGAGGGA 58.991 38.462 0.00 0.00 0.00 4.20
4533 5326 7.229581 AGCTCTTATATTAGTTTACGGAGGG 57.770 40.000 0.00 0.00 0.00 4.30
4534 5327 9.543783 AAAAGCTCTTATATTAGTTTACGGAGG 57.456 33.333 0.00 0.00 0.00 4.30
4561 5354 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
4562 5355 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
4563 5356 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
4564 5357 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
4565 5358 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
4566 5359 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
4567 5360 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
4582 5375 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
4583 5376 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
4584 5377 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
4585 5378 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
4586 5379 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4594 5387 9.490083 ACAGTATTACTCCCTCTGTAAACTAAT 57.510 33.333 0.00 0.00 37.55 1.73
4595 5388 8.890410 ACAGTATTACTCCCTCTGTAAACTAA 57.110 34.615 0.00 0.00 37.55 2.24
4596 5389 8.890410 AACAGTATTACTCCCTCTGTAAACTA 57.110 34.615 0.00 0.00 38.21 2.24
4597 5390 7.793948 AACAGTATTACTCCCTCTGTAAACT 57.206 36.000 0.00 0.00 38.21 2.66
4598 5391 9.933723 TTAAACAGTATTACTCCCTCTGTAAAC 57.066 33.333 0.00 0.00 38.21 2.01
4600 5393 8.755977 CCTTAAACAGTATTACTCCCTCTGTAA 58.244 37.037 0.00 0.00 38.21 2.41
4601 5394 8.117956 TCCTTAAACAGTATTACTCCCTCTGTA 58.882 37.037 0.00 0.00 38.21 2.74
4602 5395 6.958192 TCCTTAAACAGTATTACTCCCTCTGT 59.042 38.462 0.00 0.00 40.40 3.41
4603 5396 7.419711 TCCTTAAACAGTATTACTCCCTCTG 57.580 40.000 0.00 0.00 0.00 3.35
4604 5397 7.679025 AGTTCCTTAAACAGTATTACTCCCTCT 59.321 37.037 0.00 0.00 40.56 3.69
4605 5398 7.849160 AGTTCCTTAAACAGTATTACTCCCTC 58.151 38.462 0.00 0.00 40.56 4.30
4606 5399 7.809880 AGTTCCTTAAACAGTATTACTCCCT 57.190 36.000 0.00 0.00 40.56 4.20
4607 5400 8.859236 AAAGTTCCTTAAACAGTATTACTCCC 57.141 34.615 0.00 0.00 40.56 4.30
4648 5441 6.605471 TGCTCTGGAGAGATAAAACTACAA 57.395 37.500 7.89 0.00 44.74 2.41
4669 5462 2.878406 AGTTTGTCACGGCCATATATGC 59.122 45.455 2.24 3.21 0.00 3.14
4677 5470 0.736053 TGAACAAGTTTGTCACGGCC 59.264 50.000 0.00 0.00 41.31 6.13
4679 5472 3.181501 ACACATGAACAAGTTTGTCACGG 60.182 43.478 0.00 0.00 41.31 4.94
4682 5475 3.687212 ACGACACATGAACAAGTTTGTCA 59.313 39.130 0.00 0.00 41.31 3.58
4706 5499 2.881074 ACCAGATGTCGATTTGTCTCG 58.119 47.619 0.00 0.00 39.99 4.04
4708 5501 4.271696 TCAACCAGATGTCGATTTGTCT 57.728 40.909 0.00 0.00 0.00 3.41
4720 5513 8.599624 ACAGAAATAATTTCCATCAACCAGAT 57.400 30.769 0.00 0.00 40.54 2.90
4743 5536 8.635765 AAAGTTTATCCAGATTAAAGCTGACA 57.364 30.769 9.55 0.00 35.39 3.58
4751 5544 9.120538 GCACCTGATAAAGTTTATCCAGATTAA 57.879 33.333 25.76 10.07 0.00 1.40
4752 5545 8.271458 TGCACCTGATAAAGTTTATCCAGATTA 58.729 33.333 25.76 10.65 0.00 1.75
4768 5561 6.587206 TTCATTTGAAATGTGCACCTGATA 57.413 33.333 15.69 0.00 0.00 2.15
4795 5593 9.472361 GTTTCAGTACTATGCTTATCGGATTAA 57.528 33.333 0.00 0.00 0.00 1.40
4797 5595 7.653713 CAGTTTCAGTACTATGCTTATCGGATT 59.346 37.037 0.00 0.00 0.00 3.01
4798 5596 7.148641 CAGTTTCAGTACTATGCTTATCGGAT 58.851 38.462 0.00 0.00 0.00 4.18
4799 5597 6.096423 ACAGTTTCAGTACTATGCTTATCGGA 59.904 38.462 0.00 0.00 0.00 4.55
4800 5598 6.273825 ACAGTTTCAGTACTATGCTTATCGG 58.726 40.000 0.00 0.00 0.00 4.18
4812 5610 7.524912 TGTAGAGATCGTTACAGTTTCAGTAC 58.475 38.462 7.89 0.00 0.00 2.73
4835 5633 8.912988 TCAGAATTCAGAACCAACTAATTTTGT 58.087 29.630 8.44 0.00 0.00 2.83
4840 5638 7.890127 TCCAATCAGAATTCAGAACCAACTAAT 59.110 33.333 8.44 0.00 0.00 1.73
4841 5639 7.230747 TCCAATCAGAATTCAGAACCAACTAA 58.769 34.615 8.44 0.00 0.00 2.24
4842 5640 6.778821 TCCAATCAGAATTCAGAACCAACTA 58.221 36.000 8.44 0.00 0.00 2.24
4888 5834 8.782533 ATTTTCATGTGTAACGTCTTCTTTTC 57.217 30.769 0.00 0.00 42.39 2.29
4994 6875 4.740822 CTGGGAGGCGGGGGTTTG 62.741 72.222 0.00 0.00 0.00 2.93
5004 6885 3.813724 GTGGATGGGGCTGGGAGG 61.814 72.222 0.00 0.00 0.00 4.30
5006 6887 3.988151 ATGGTGGATGGGGCTGGGA 62.988 63.158 0.00 0.00 0.00 4.37
5007 6888 3.432335 ATGGTGGATGGGGCTGGG 61.432 66.667 0.00 0.00 0.00 4.45
5020 6904 1.968017 CAGTGTGAAGCGCCATGGT 60.968 57.895 14.67 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.