Multiple sequence alignment - TraesCS7B01G426000

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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 TraesCS7B01G426000 chr7B 100.000 3047 0 0 1 3047 695315969 695312923 0.000000e+00 5627
1 TraesCS7B01G426000 chr7B 92.559 2325 130 20 285 2582 116121916 116124224 0.000000e+00 3295
2 TraesCS7B01G426000 chr7B 92.253 2259 141 17 281 2533 570271842 570274072 0.000000e+00 3171
3 TraesCS7B01G426000 chr7B 91.094 1673 138 6 916 2583 2234971 2236637 0.000000e+00 2254
4 TraesCS7B01G426000 chr7B 94.481 453 16 6 2596 3047 696079729 696080173 0.000000e+00 689
5 TraesCS7B01G426000 chr7B 89.965 289 25 3 1 286 696079447 696079734 1.330000e-98 370
6 TraesCS7B01G426000 chr2B 93.859 2231 123 12 285 2508 690224703 690222480 0.000000e+00 3349
7 TraesCS7B01G426000 chr2B 90.793 2346 157 22 285 2583 787779405 787781738 0.000000e+00 3081
8 TraesCS7B01G426000 chr2B 91.761 1675 129 5 916 2583 717646738 717645066 0.000000e+00 2320
9 TraesCS7B01G426000 chr2B 91.252 1669 137 5 916 2583 84712618 84714278 0.000000e+00 2265
10 TraesCS7B01G426000 chr6B 93.303 2165 122 9 372 2533 101927774 101925630 0.000000e+00 3173
11 TraesCS7B01G426000 chr6B 90.996 1677 140 5 916 2583 561272816 561271142 0.000000e+00 2250
12 TraesCS7B01G426000 chr6B 86.000 450 28 14 2598 3045 688129419 688129835 1.670000e-122 449
13 TraesCS7B01G426000 chr6B 84.821 448 30 18 2598 3045 688082306 688082715 1.690000e-112 416
14 TraesCS7B01G426000 chr4A 92.786 2204 135 9 399 2583 731357686 731355488 0.000000e+00 3168
15 TraesCS7B01G426000 chr4B 91.267 2313 143 29 285 2556 562423898 562421604 0.000000e+00 3097
16 TraesCS7B01G426000 chr3B 91.053 2280 151 20 282 2525 44276644 44278906 0.000000e+00 3031
17 TraesCS7B01G426000 chrUn 90.953 1669 142 5 916 2583 238884795 238883135 0.000000e+00 2237
18 TraesCS7B01G426000 chrUn 92.763 456 22 4 2593 3047 199127156 199126711 0.000000e+00 649
19 TraesCS7B01G426000 chrUn 92.763 456 22 4 2593 3047 335603464 335603019 0.000000e+00 649
20 TraesCS7B01G426000 chrUn 92.683 451 23 3 2598 3047 314127608 314127167 2.560000e-180 641
21 TraesCS7B01G426000 chr5B 93.269 1352 76 9 285 1635 421592863 421594200 0.000000e+00 1978
22 TraesCS7B01G426000 chr5D 92.763 456 22 4 2593 3047 523190971 523191416 0.000000e+00 649
23 TraesCS7B01G426000 chr5D 91.886 456 26 4 2593 3047 523318526 523318971 7.170000e-176 627
24 TraesCS7B01G426000 chr5D 89.845 453 37 4 2596 3047 545908717 545909161 9.480000e-160 573
25 TraesCS7B01G426000 chr7A 91.429 455 29 3 2594 3047 723989150 723988705 1.550000e-172 616
26 TraesCS7B01G426000 chr6D 90.728 453 27 5 2596 3047 405652389 405652827 9.410000e-165 590
27 TraesCS7B01G426000 chr2D 88.132 455 27 10 2594 3047 648516025 648515597 1.620000e-142 516
28 TraesCS7B01G426000 chr2D 88.772 285 25 4 1 281 609292390 609292671 2.910000e-90 342
29 TraesCS7B01G426000 chr2D 84.646 254 34 4 10 260 648516313 648516062 6.520000e-62 248
30 TraesCS7B01G426000 chr7D 89.362 282 26 3 1 281 25023687 25023965 4.830000e-93 351


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 TraesCS7B01G426000 chr7B 695312923 695315969 3046 True 5627.0 5627 100.000 1 3047 1 chr7B.!!$R1 3046
1 TraesCS7B01G426000 chr7B 116121916 116124224 2308 False 3295.0 3295 92.559 285 2582 1 chr7B.!!$F2 2297
2 TraesCS7B01G426000 chr7B 570271842 570274072 2230 False 3171.0 3171 92.253 281 2533 1 chr7B.!!$F3 2252
3 TraesCS7B01G426000 chr7B 2234971 2236637 1666 False 2254.0 2254 91.094 916 2583 1 chr7B.!!$F1 1667
4 TraesCS7B01G426000 chr7B 696079447 696080173 726 False 529.5 689 92.223 1 3047 2 chr7B.!!$F4 3046
5 TraesCS7B01G426000 chr2B 690222480 690224703 2223 True 3349.0 3349 93.859 285 2508 1 chr2B.!!$R1 2223
6 TraesCS7B01G426000 chr2B 787779405 787781738 2333 False 3081.0 3081 90.793 285 2583 1 chr2B.!!$F2 2298
7 TraesCS7B01G426000 chr2B 717645066 717646738 1672 True 2320.0 2320 91.761 916 2583 1 chr2B.!!$R2 1667
8 TraesCS7B01G426000 chr2B 84712618 84714278 1660 False 2265.0 2265 91.252 916 2583 1 chr2B.!!$F1 1667
9 TraesCS7B01G426000 chr6B 101925630 101927774 2144 True 3173.0 3173 93.303 372 2533 1 chr6B.!!$R1 2161
10 TraesCS7B01G426000 chr6B 561271142 561272816 1674 True 2250.0 2250 90.996 916 2583 1 chr6B.!!$R2 1667
11 TraesCS7B01G426000 chr4A 731355488 731357686 2198 True 3168.0 3168 92.786 399 2583 1 chr4A.!!$R1 2184
12 TraesCS7B01G426000 chr4B 562421604 562423898 2294 True 3097.0 3097 91.267 285 2556 1 chr4B.!!$R1 2271
13 TraesCS7B01G426000 chr3B 44276644 44278906 2262 False 3031.0 3031 91.053 282 2525 1 chr3B.!!$F1 2243
14 TraesCS7B01G426000 chrUn 238883135 238884795 1660 True 2237.0 2237 90.953 916 2583 1 chrUn.!!$R2 1667
15 TraesCS7B01G426000 chr5B 421592863 421594200 1337 False 1978.0 1978 93.269 285 1635 1 chr5B.!!$F1 1350
16 TraesCS7B01G426000 chr2D 648515597 648516313 716 True 382.0 516 86.389 10 3047 2 chr2D.!!$R1 3037

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
246 251 0.247814 CGACAATTCATGCCTGCGAC 60.248 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2098 2188 0.037232 CAGGTCGGTGTTCCTCTTCC 60.037 60.0 0.0 0.0 30.91 3.46 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
24 25 0.400213 TCTGCCGAGAACCAACCATT 59.600 50.000 0.00 0.00 0.00 3.16
52 53 3.659092 CAACGCCTTTGCCGAGCA 61.659 61.111 0.00 0.00 36.47 4.26
92 93 4.013728 CCAATATTGGGACTCCGTGAAAA 58.986 43.478 24.61 0.00 44.70 2.29
93 94 4.096382 CCAATATTGGGACTCCGTGAAAAG 59.904 45.833 24.61 0.00 44.70 2.27
98 99 3.622630 TGGGACTCCGTGAAAAGAAAAA 58.377 40.909 0.00 0.00 35.24 1.94
171 172 0.535553 TGGCTTTCCCGTGTTGTACC 60.536 55.000 0.00 0.00 35.87 3.34
187 188 4.196626 TGTACCCTCGGTAAAGATGTTG 57.803 45.455 0.00 0.00 40.12 3.33
197 198 7.361713 CCTCGGTAAAGATGTTGAGCAAAATTA 60.362 37.037 0.00 0.00 0.00 1.40
198 199 7.877003 TCGGTAAAGATGTTGAGCAAAATTAA 58.123 30.769 0.00 0.00 0.00 1.40
199 200 8.353684 TCGGTAAAGATGTTGAGCAAAATTAAA 58.646 29.630 0.00 0.00 0.00 1.52
200 201 8.973378 CGGTAAAGATGTTGAGCAAAATTAAAA 58.027 29.630 0.00 0.00 0.00 1.52
241 246 1.369091 GGCGACGACAATTCATGCCT 61.369 55.000 0.00 0.00 38.00 4.75
246 251 0.247814 CGACAATTCATGCCTGCGAC 60.248 55.000 0.00 0.00 0.00 5.19
313 336 4.778143 GCCGCGTCCCCAACAGAT 62.778 66.667 4.92 0.00 0.00 2.90
515 545 4.856607 GTCGAGCGCCTCTTCCCG 62.857 72.222 2.29 0.00 0.00 5.14
522 552 3.125573 GCCTCTTCCCGCCGTTTC 61.126 66.667 0.00 0.00 0.00 2.78
523 553 2.663196 CCTCTTCCCGCCGTTTCT 59.337 61.111 0.00 0.00 0.00 2.52
524 554 1.003718 CCTCTTCCCGCCGTTTCTT 60.004 57.895 0.00 0.00 0.00 2.52
525 555 1.019805 CCTCTTCCCGCCGTTTCTTC 61.020 60.000 0.00 0.00 0.00 2.87
526 556 1.004200 TCTTCCCGCCGTTTCTTCC 60.004 57.895 0.00 0.00 0.00 3.46
527 557 2.032987 TTCCCGCCGTTTCTTCCC 59.967 61.111 0.00 0.00 0.00 3.97
560 604 1.874299 TTCCCTCCCATTTGCCCCTC 61.874 60.000 0.00 0.00 0.00 4.30
687 731 1.142748 CGAAGCAGAGGAAGCCGAT 59.857 57.895 0.00 0.00 0.00 4.18
1050 1103 5.105473 GCAGTACCTTCCATACAACTACTCA 60.105 44.000 0.00 0.00 0.00 3.41
1061 1114 4.430765 CTACTCACCGCCCGCGTT 62.431 66.667 4.92 0.00 37.81 4.84
1216 1271 3.733960 CCGCGGACGAGACAGTGA 61.734 66.667 24.07 0.00 43.93 3.41
1276 1331 2.341101 GGCGACGAGGAACAGGAGA 61.341 63.158 0.00 0.00 0.00 3.71
1277 1332 1.585006 GCGACGAGGAACAGGAGAA 59.415 57.895 0.00 0.00 0.00 2.87
1278 1333 0.456995 GCGACGAGGAACAGGAGAAG 60.457 60.000 0.00 0.00 0.00 2.85
1279 1334 0.456995 CGACGAGGAACAGGAGAAGC 60.457 60.000 0.00 0.00 0.00 3.86
1280 1335 0.603569 GACGAGGAACAGGAGAAGCA 59.396 55.000 0.00 0.00 0.00 3.91
1281 1336 0.605589 ACGAGGAACAGGAGAAGCAG 59.394 55.000 0.00 0.00 0.00 4.24
1290 1366 0.251832 AGGAGAAGCAGGACGAGGAA 60.252 55.000 0.00 0.00 0.00 3.36
1434 1516 2.203523 TTCCTCGACCCGACCACA 60.204 61.111 0.00 0.00 0.00 4.17
1537 1619 3.188100 GCGTCTACATGCAGCGCA 61.188 61.111 21.84 5.73 46.23 6.09
1705 1789 1.533756 CCGTTCACAAGCCAACTGTTG 60.534 52.381 13.50 13.50 0.00 3.33
1800 1890 1.421410 CCACGTCTACAAGCGCATCC 61.421 60.000 11.47 0.00 0.00 3.51
1804 1894 0.721718 GTCTACAAGCGCATCCACAC 59.278 55.000 11.47 0.00 0.00 3.82
1904 1994 2.366837 TCAGATGGGTGGCCGGAT 60.367 61.111 5.05 0.00 0.00 4.18
2018 2108 2.125106 GCCGCCCTTCGTGAAGAT 60.125 61.111 11.11 0.00 40.79 2.40
2030 2120 1.134367 CGTGAAGATAAGACCGAGGCA 59.866 52.381 0.00 0.00 0.00 4.75
2087 2177 0.251297 TCGACCTACTCCGGACCAAA 60.251 55.000 0.00 0.00 0.00 3.28
2098 2188 2.399611 GACCAAAATCGCCGCGAG 59.600 61.111 21.61 9.43 39.91 5.03
2172 2262 4.052229 CCGACGAGGCGGTCAAGT 62.052 66.667 9.61 0.00 46.07 3.16
2569 2775 1.609501 ACTGGAAGCTAGGCCGACA 60.610 57.895 0.00 0.00 37.60 4.35
2594 2800 2.579201 CCGAACGGCTGGAGATGT 59.421 61.111 0.00 0.00 0.00 3.06
2595 2801 1.079127 CCGAACGGCTGGAGATGTT 60.079 57.895 0.00 0.00 0.00 2.71
2596 2802 1.084370 CCGAACGGCTGGAGATGTTC 61.084 60.000 0.00 0.00 37.84 3.18
2597 2803 0.108615 CGAACGGCTGGAGATGTTCT 60.109 55.000 0.00 0.00 38.78 3.01
2598 2804 1.363744 GAACGGCTGGAGATGTTCTG 58.636 55.000 0.00 0.00 38.11 3.02
2599 2805 0.976641 AACGGCTGGAGATGTTCTGA 59.023 50.000 0.00 0.00 0.00 3.27
2600 2806 0.534412 ACGGCTGGAGATGTTCTGAG 59.466 55.000 0.00 0.00 0.00 3.35
2601 2807 0.809241 CGGCTGGAGATGTTCTGAGC 60.809 60.000 0.00 0.00 33.23 4.26
2602 2808 0.251354 GGCTGGAGATGTTCTGAGCA 59.749 55.000 0.00 0.00 34.71 4.26
2603 2809 1.339438 GGCTGGAGATGTTCTGAGCAA 60.339 52.381 0.00 0.00 34.71 3.91
2604 2810 2.641305 GCTGGAGATGTTCTGAGCAAT 58.359 47.619 0.00 0.00 33.81 3.56
2605 2811 2.355132 GCTGGAGATGTTCTGAGCAATG 59.645 50.000 0.00 0.00 33.81 2.82
2606 2812 2.355132 CTGGAGATGTTCTGAGCAATGC 59.645 50.000 0.00 0.00 0.00 3.56
2607 2813 1.329906 GGAGATGTTCTGAGCAATGCG 59.670 52.381 0.00 0.00 0.00 4.73
2608 2814 0.731417 AGATGTTCTGAGCAATGCGC 59.269 50.000 0.00 0.00 42.91 6.09
2617 2823 3.407657 GCAATGCGCTCTCCTCTG 58.592 61.111 9.73 0.00 37.77 3.35
2618 2824 2.821688 GCAATGCGCTCTCCTCTGC 61.822 63.158 9.73 3.09 37.77 4.26
2619 2825 2.178890 CAATGCGCTCTCCTCTGCC 61.179 63.158 9.73 0.00 0.00 4.85
2620 2826 2.663075 AATGCGCTCTCCTCTGCCA 61.663 57.895 9.73 0.00 0.00 4.92
2621 2827 2.189191 AATGCGCTCTCCTCTGCCAA 62.189 55.000 9.73 0.00 0.00 4.52
2622 2828 2.511145 GCGCTCTCCTCTGCCAAG 60.511 66.667 0.00 0.00 0.00 3.61
2623 2829 2.511145 CGCTCTCCTCTGCCAAGC 60.511 66.667 0.00 0.00 0.00 4.01
2624 2830 2.988800 GCTCTCCTCTGCCAAGCT 59.011 61.111 0.00 0.00 0.00 3.74
2625 2831 1.670949 CGCTCTCCTCTGCCAAGCTA 61.671 60.000 0.00 0.00 0.00 3.32
2626 2832 0.104671 GCTCTCCTCTGCCAAGCTAG 59.895 60.000 0.00 0.00 0.00 3.42
2627 2833 1.484038 CTCTCCTCTGCCAAGCTAGT 58.516 55.000 0.00 0.00 0.00 2.57
2628 2834 1.408702 CTCTCCTCTGCCAAGCTAGTC 59.591 57.143 0.00 0.00 0.00 2.59
2629 2835 0.102120 CTCCTCTGCCAAGCTAGTCG 59.898 60.000 0.00 0.00 0.00 4.18
2630 2836 1.142748 CCTCTGCCAAGCTAGTCGG 59.857 63.158 0.00 0.00 0.00 4.79
2631 2837 1.608717 CCTCTGCCAAGCTAGTCGGT 61.609 60.000 0.00 0.00 0.00 4.69
2632 2838 0.179124 CTCTGCCAAGCTAGTCGGTC 60.179 60.000 0.00 0.00 0.00 4.79
2633 2839 1.153549 CTGCCAAGCTAGTCGGTCC 60.154 63.158 0.00 0.00 0.00 4.46
2634 2840 2.202756 GCCAAGCTAGTCGGTCCG 60.203 66.667 4.39 4.39 0.00 4.79
2635 2841 2.202756 CCAAGCTAGTCGGTCCGC 60.203 66.667 6.34 1.61 0.00 5.54
2636 2842 2.711922 CCAAGCTAGTCGGTCCGCT 61.712 63.158 6.34 9.84 0.00 5.52
2637 2843 1.517257 CAAGCTAGTCGGTCCGCTG 60.517 63.158 6.34 4.06 32.22 5.18
2638 2844 3.358076 AAGCTAGTCGGTCCGCTGC 62.358 63.158 6.34 12.58 32.22 5.25
2639 2845 3.827898 GCTAGTCGGTCCGCTGCT 61.828 66.667 6.34 7.21 0.00 4.24
2640 2846 2.885861 CTAGTCGGTCCGCTGCTT 59.114 61.111 6.34 0.00 0.00 3.91
2641 2847 2.001361 GCTAGTCGGTCCGCTGCTTA 62.001 60.000 6.34 0.00 0.00 3.09
2642 2848 0.669077 CTAGTCGGTCCGCTGCTTAT 59.331 55.000 6.34 0.00 0.00 1.73
2643 2849 0.384309 TAGTCGGTCCGCTGCTTATG 59.616 55.000 6.34 0.00 0.00 1.90
2644 2850 1.153628 GTCGGTCCGCTGCTTATGT 60.154 57.895 6.34 0.00 0.00 2.29
2645 2851 1.153647 TCGGTCCGCTGCTTATGTG 60.154 57.895 6.34 0.00 0.00 3.21
2646 2852 2.813179 CGGTCCGCTGCTTATGTGC 61.813 63.158 0.00 0.00 0.00 4.57
2647 2853 1.450312 GGTCCGCTGCTTATGTGCT 60.450 57.895 0.00 0.00 0.00 4.40
2648 2854 0.179084 GGTCCGCTGCTTATGTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
2649 2855 1.212616 GTCCGCTGCTTATGTGCTAG 58.787 55.000 0.00 0.00 0.00 3.42
2650 2856 0.530650 TCCGCTGCTTATGTGCTAGC 60.531 55.000 8.10 8.10 37.89 3.42
2651 2857 0.531532 CCGCTGCTTATGTGCTAGCT 60.532 55.000 17.23 0.00 38.22 3.32
2652 2858 1.293924 CGCTGCTTATGTGCTAGCTT 58.706 50.000 17.23 3.47 38.22 3.74
2653 2859 1.004185 CGCTGCTTATGTGCTAGCTTG 60.004 52.381 17.23 0.00 38.22 4.01
2654 2860 1.332997 GCTGCTTATGTGCTAGCTTGG 59.667 52.381 17.23 1.70 38.22 3.61
2655 2861 1.332997 CTGCTTATGTGCTAGCTTGGC 59.667 52.381 17.23 11.58 38.22 4.52
2656 2862 0.665298 GCTTATGTGCTAGCTTGGCC 59.335 55.000 17.23 0.00 34.57 5.36
2657 2863 0.940126 CTTATGTGCTAGCTTGGCCG 59.060 55.000 17.23 0.00 0.00 6.13
2658 2864 0.463654 TTATGTGCTAGCTTGGCCGG 60.464 55.000 17.23 0.00 0.00 6.13
2659 2865 1.622607 TATGTGCTAGCTTGGCCGGT 61.623 55.000 17.23 0.00 0.00 5.28
2660 2866 2.820037 GTGCTAGCTTGGCCGGTC 60.820 66.667 17.23 0.00 0.00 4.79
2661 2867 4.096003 TGCTAGCTTGGCCGGTCC 62.096 66.667 17.23 5.67 0.00 4.46
2662 2868 4.096003 GCTAGCTTGGCCGGTCCA 62.096 66.667 12.86 12.86 44.85 4.02
2663 2869 2.911143 CTAGCTTGGCCGGTCCAT 59.089 61.111 16.81 6.59 46.04 3.41
2664 2870 1.224592 CTAGCTTGGCCGGTCCATT 59.775 57.895 16.81 9.42 46.04 3.16
2665 2871 0.394352 CTAGCTTGGCCGGTCCATTT 60.394 55.000 16.81 9.13 46.04 2.32
2666 2872 0.039035 TAGCTTGGCCGGTCCATTTT 59.961 50.000 16.81 8.85 46.04 1.82
2667 2873 0.831711 AGCTTGGCCGGTCCATTTTT 60.832 50.000 16.81 3.11 46.04 1.94
2668 2874 0.670239 GCTTGGCCGGTCCATTTTTG 60.670 55.000 16.81 7.77 46.04 2.44
2669 2875 0.037419 CTTGGCCGGTCCATTTTTGG 60.037 55.000 16.81 2.68 46.04 3.28
2670 2876 2.105806 TTGGCCGGTCCATTTTTGGC 62.106 55.000 16.81 0.00 46.04 4.52
2671 2877 3.055580 GCCGGTCCATTTTTGGCA 58.944 55.556 1.90 0.00 45.06 4.92
2672 2878 1.596408 GCCGGTCCATTTTTGGCAT 59.404 52.632 1.90 0.00 45.06 4.40
2673 2879 0.740516 GCCGGTCCATTTTTGGCATG 60.741 55.000 1.90 0.00 45.06 4.06
2674 2880 0.740516 CCGGTCCATTTTTGGCATGC 60.741 55.000 9.90 9.90 0.00 4.06
2675 2881 0.740516 CGGTCCATTTTTGGCATGCC 60.741 55.000 30.54 30.54 0.00 4.40
2676 2882 0.740516 GGTCCATTTTTGGCATGCCG 60.741 55.000 30.87 15.63 39.42 5.69
2677 2883 0.740516 GTCCATTTTTGGCATGCCGG 60.741 55.000 30.87 23.65 39.42 6.13
2678 2884 0.902048 TCCATTTTTGGCATGCCGGA 60.902 50.000 30.87 25.46 39.42 5.14
2679 2885 0.460635 CCATTTTTGGCATGCCGGAG 60.461 55.000 30.87 16.61 39.42 4.63
2680 2886 0.531657 CATTTTTGGCATGCCGGAGA 59.468 50.000 30.87 17.36 39.42 3.71
2681 2887 0.819582 ATTTTTGGCATGCCGGAGAG 59.180 50.000 30.87 0.00 39.42 3.20
2682 2888 0.539438 TTTTTGGCATGCCGGAGAGT 60.539 50.000 30.87 0.00 39.42 3.24
2683 2889 1.243342 TTTTGGCATGCCGGAGAGTG 61.243 55.000 30.87 0.00 39.42 3.51
2684 2890 4.783621 TGGCATGCCGGAGAGTGC 62.784 66.667 30.87 9.05 39.42 4.40
2693 2899 4.008933 GGAGAGTGCGGGTGCTGT 62.009 66.667 0.00 0.00 43.34 4.40
2694 2900 2.031163 GAGAGTGCGGGTGCTGTT 59.969 61.111 0.00 0.00 43.34 3.16
2695 2901 2.281070 AGAGTGCGGGTGCTGTTG 60.281 61.111 0.00 0.00 43.34 3.33
2696 2902 4.030452 GAGTGCGGGTGCTGTTGC 62.030 66.667 0.00 0.00 43.34 4.17
2697 2903 4.569180 AGTGCGGGTGCTGTTGCT 62.569 61.111 0.00 0.00 43.34 3.91
2698 2904 4.030452 GTGCGGGTGCTGTTGCTC 62.030 66.667 0.00 0.00 43.34 4.26
2699 2905 4.560743 TGCGGGTGCTGTTGCTCA 62.561 61.111 0.00 0.00 43.34 4.26
2700 2906 3.730761 GCGGGTGCTGTTGCTCAG 61.731 66.667 5.37 5.37 46.12 3.35
2711 2917 2.238353 TTGCTCAGCAAGAAGACGC 58.762 52.632 8.40 0.00 43.99 5.19
2712 2918 1.560004 TTGCTCAGCAAGAAGACGCG 61.560 55.000 8.40 3.53 43.99 6.01
2713 2919 2.024319 GCTCAGCAAGAAGACGCGT 61.024 57.895 13.85 13.85 0.00 6.01
2714 2920 1.950098 GCTCAGCAAGAAGACGCGTC 61.950 60.000 31.30 31.30 0.00 5.19
2715 2921 0.387878 CTCAGCAAGAAGACGCGTCT 60.388 55.000 34.98 34.98 42.75 4.18
2716 2922 0.879090 TCAGCAAGAAGACGCGTCTA 59.121 50.000 39.33 20.30 39.39 2.59
2717 2923 1.472878 TCAGCAAGAAGACGCGTCTAT 59.527 47.619 39.33 28.13 39.39 1.98
2718 2924 1.585668 CAGCAAGAAGACGCGTCTATG 59.414 52.381 39.33 33.74 39.39 2.23
2719 2925 0.299003 GCAAGAAGACGCGTCTATGC 59.701 55.000 36.59 36.59 39.39 3.14
2728 2934 3.099524 GCGTCTATGCGAGATGAGG 57.900 57.895 10.95 0.00 43.06 3.86
2729 2935 1.006314 GCGTCTATGCGAGATGAGGC 61.006 60.000 10.95 3.61 43.06 4.70
2730 2936 0.595588 CGTCTATGCGAGATGAGGCT 59.404 55.000 2.19 0.00 43.06 4.58
2731 2937 1.665448 CGTCTATGCGAGATGAGGCTG 60.665 57.143 0.00 0.00 43.06 4.85
2732 2938 0.964700 TCTATGCGAGATGAGGCTGG 59.035 55.000 0.00 0.00 0.00 4.85
2733 2939 0.669932 CTATGCGAGATGAGGCTGGC 60.670 60.000 0.00 0.00 39.67 4.85
2734 2940 1.117749 TATGCGAGATGAGGCTGGCT 61.118 55.000 2.24 2.24 39.89 4.75
2735 2941 2.588314 GCGAGATGAGGCTGGCTG 60.588 66.667 9.06 0.00 36.78 4.85
2736 2942 2.898738 CGAGATGAGGCTGGCTGT 59.101 61.111 9.06 0.00 0.00 4.40
2737 2943 1.227205 CGAGATGAGGCTGGCTGTC 60.227 63.158 9.06 6.78 0.00 3.51
2738 2944 1.227205 GAGATGAGGCTGGCTGTCG 60.227 63.158 9.06 0.00 0.00 4.35
2739 2945 2.894387 GATGAGGCTGGCTGTCGC 60.894 66.667 9.06 0.00 0.00 5.19
2740 2946 3.382803 GATGAGGCTGGCTGTCGCT 62.383 63.158 9.06 0.00 36.09 4.93
2741 2947 3.382803 ATGAGGCTGGCTGTCGCTC 62.383 63.158 9.06 0.00 36.09 5.03
2742 2948 3.768922 GAGGCTGGCTGTCGCTCT 61.769 66.667 9.06 0.00 36.09 4.09
2743 2949 3.308014 GAGGCTGGCTGTCGCTCTT 62.308 63.158 9.06 0.00 36.09 2.85
2744 2950 3.123620 GGCTGGCTGTCGCTCTTG 61.124 66.667 0.00 0.00 36.09 3.02
2745 2951 3.123620 GCTGGCTGTCGCTCTTGG 61.124 66.667 0.00 0.00 36.09 3.61
2746 2952 2.345244 CTGGCTGTCGCTCTTGGT 59.655 61.111 0.00 0.00 36.09 3.67
2747 2953 1.591703 CTGGCTGTCGCTCTTGGTA 59.408 57.895 0.00 0.00 36.09 3.25
2748 2954 0.459237 CTGGCTGTCGCTCTTGGTAG 60.459 60.000 0.00 0.00 36.09 3.18
2749 2955 1.811679 GGCTGTCGCTCTTGGTAGC 60.812 63.158 0.00 0.00 39.21 3.58
2755 2961 2.434359 GCTCTTGGTAGCGCCGTT 60.434 61.111 2.29 0.00 41.21 4.44
2756 2962 2.740714 GCTCTTGGTAGCGCCGTTG 61.741 63.158 2.29 0.00 41.21 4.10
2757 2963 1.080093 CTCTTGGTAGCGCCGTTGA 60.080 57.895 2.29 0.00 41.21 3.18
2758 2964 1.352156 CTCTTGGTAGCGCCGTTGAC 61.352 60.000 2.29 0.00 41.21 3.18
2759 2965 2.726691 CTTGGTAGCGCCGTTGACG 61.727 63.158 2.29 0.00 41.21 4.35
2760 2966 3.210223 TTGGTAGCGCCGTTGACGA 62.210 57.895 2.29 0.00 43.02 4.20
2761 2967 3.177249 GGTAGCGCCGTTGACGAC 61.177 66.667 2.29 0.00 43.02 4.34
2769 2975 2.469847 CGTTGACGACGCATGTGG 59.530 61.111 11.65 0.00 45.86 4.17
2770 2976 2.173382 GTTGACGACGCATGTGGC 59.827 61.111 11.65 6.63 39.90 5.01
2771 2977 2.280457 TTGACGACGCATGTGGCA 60.280 55.556 13.61 1.22 45.17 4.92
2772 2978 2.603247 TTGACGACGCATGTGGCAC 61.603 57.895 13.61 11.55 45.17 5.01
2773 2979 4.134187 GACGACGCATGTGGCACG 62.134 66.667 13.61 15.46 45.17 5.34
2774 2980 4.961511 ACGACGCATGTGGCACGT 62.962 61.111 13.61 16.07 45.42 4.49
2775 2981 4.428922 CGACGCATGTGGCACGTG 62.429 66.667 30.68 30.68 45.17 4.49
2776 2982 4.088762 GACGCATGTGGCACGTGG 62.089 66.667 33.93 26.42 45.17 4.94
2788 2994 4.619227 ACGTGGCCTCCGTGGTTG 62.619 66.667 18.24 0.00 37.12 3.77
2789 2995 4.619227 CGTGGCCTCCGTGGTTGT 62.619 66.667 3.32 0.00 38.35 3.32
2790 2996 2.203294 GTGGCCTCCGTGGTTGTT 60.203 61.111 3.32 0.00 38.35 2.83
2791 2997 2.203280 TGGCCTCCGTGGTTGTTG 60.203 61.111 3.32 0.00 38.35 3.33
2792 2998 3.670377 GGCCTCCGTGGTTGTTGC 61.670 66.667 0.00 0.00 38.35 4.17
2793 2999 3.670377 GCCTCCGTGGTTGTTGCC 61.670 66.667 0.00 0.00 38.35 4.52
2794 3000 2.113139 CCTCCGTGGTTGTTGCCT 59.887 61.111 0.00 0.00 0.00 4.75
2795 3001 1.528309 CCTCCGTGGTTGTTGCCTT 60.528 57.895 0.00 0.00 0.00 4.35
2796 3002 1.654220 CTCCGTGGTTGTTGCCTTG 59.346 57.895 0.00 0.00 0.00 3.61
2797 3003 1.077357 TCCGTGGTTGTTGCCTTGT 60.077 52.632 0.00 0.00 0.00 3.16
2798 3004 0.681564 TCCGTGGTTGTTGCCTTGTT 60.682 50.000 0.00 0.00 0.00 2.83
2799 3005 0.527385 CCGTGGTTGTTGCCTTGTTG 60.527 55.000 0.00 0.00 0.00 3.33
2800 3006 0.527385 CGTGGTTGTTGCCTTGTTGG 60.527 55.000 0.00 0.00 39.35 3.77
2826 3032 3.803082 CTCGCCGGCATGTGGTTG 61.803 66.667 28.98 7.38 0.00 3.77
2829 3035 4.054825 GCCGGCATGTGGTTGGTG 62.055 66.667 24.80 0.00 0.00 4.17
2830 3036 2.282110 CCGGCATGTGGTTGGTGA 60.282 61.111 0.00 0.00 0.00 4.02
2831 3037 2.334946 CCGGCATGTGGTTGGTGAG 61.335 63.158 0.00 0.00 0.00 3.51
2832 3038 2.964978 GGCATGTGGTTGGTGAGC 59.035 61.111 0.00 0.00 0.00 4.26
2833 3039 1.604593 GGCATGTGGTTGGTGAGCT 60.605 57.895 0.00 0.00 0.00 4.09
2834 3040 1.582968 GCATGTGGTTGGTGAGCTG 59.417 57.895 0.00 0.00 0.00 4.24
2835 3041 1.582968 CATGTGGTTGGTGAGCTGC 59.417 57.895 0.00 0.00 0.00 5.25
2836 3042 0.892358 CATGTGGTTGGTGAGCTGCT 60.892 55.000 0.00 0.00 0.00 4.24
2837 3043 0.892358 ATGTGGTTGGTGAGCTGCTG 60.892 55.000 7.01 0.00 0.00 4.41
2838 3044 2.595463 TGGTTGGTGAGCTGCTGC 60.595 61.111 7.01 7.62 40.05 5.25
2839 3045 3.368571 GGTTGGTGAGCTGCTGCC 61.369 66.667 7.01 9.97 40.80 4.85
2840 3046 2.282040 GTTGGTGAGCTGCTGCCT 60.282 61.111 7.01 0.00 40.80 4.75
2841 3047 1.900498 GTTGGTGAGCTGCTGCCTT 60.900 57.895 7.01 0.00 40.80 4.35
2842 3048 1.601759 TTGGTGAGCTGCTGCCTTC 60.602 57.895 7.01 4.94 40.80 3.46
2843 3049 2.749441 GGTGAGCTGCTGCCTTCC 60.749 66.667 7.01 8.19 40.80 3.46
2844 3050 2.749441 GTGAGCTGCTGCCTTCCC 60.749 66.667 7.01 0.00 40.80 3.97
2845 3051 4.399395 TGAGCTGCTGCCTTCCCG 62.399 66.667 7.01 0.00 40.80 5.14
2852 3058 4.077184 CTGCCTTCCCGCCGTGTA 62.077 66.667 0.00 0.00 0.00 2.90
2853 3059 4.382320 TGCCTTCCCGCCGTGTAC 62.382 66.667 0.00 0.00 0.00 2.90
2854 3060 4.382320 GCCTTCCCGCCGTGTACA 62.382 66.667 0.00 0.00 0.00 2.90
2855 3061 2.582436 CCTTCCCGCCGTGTACAT 59.418 61.111 0.00 0.00 0.00 2.29
2856 3062 1.813753 CCTTCCCGCCGTGTACATG 60.814 63.158 8.18 8.18 0.00 3.21
2857 3063 1.079405 CTTCCCGCCGTGTACATGT 60.079 57.895 13.91 2.69 0.00 3.21
2858 3064 1.358725 CTTCCCGCCGTGTACATGTG 61.359 60.000 9.11 7.94 0.00 3.21
2859 3065 3.496131 CCCGCCGTGTACATGTGC 61.496 66.667 9.11 8.01 0.00 4.57
2860 3066 2.434185 CCGCCGTGTACATGTGCT 60.434 61.111 15.25 0.00 0.00 4.40
2861 3067 2.739704 CCGCCGTGTACATGTGCTG 61.740 63.158 15.25 13.07 0.00 4.41
2862 3068 2.480555 GCCGTGTACATGTGCTGC 59.519 61.111 15.25 10.93 0.00 5.25
2863 3069 3.039202 GCCGTGTACATGTGCTGCC 62.039 63.158 15.25 2.61 0.00 4.85
2864 3070 2.739704 CCGTGTACATGTGCTGCCG 61.740 63.158 15.25 13.26 0.00 5.69
2865 3071 2.480555 GTGTACATGTGCTGCCGC 59.519 61.111 15.25 0.00 0.00 6.53
2866 3072 2.034879 GTGTACATGTGCTGCCGCT 61.035 57.895 15.25 0.00 36.97 5.52
2867 3073 2.034317 TGTACATGTGCTGCCGCTG 61.034 57.895 15.25 0.00 36.97 5.18
2868 3074 3.126879 TACATGTGCTGCCGCTGC 61.127 61.111 14.83 14.83 36.97 5.25
2888 3094 3.132139 CTTGCAGCTGCCTCGCAT 61.132 61.111 34.64 0.00 38.13 4.73
2889 3095 3.109612 CTTGCAGCTGCCTCGCATC 62.110 63.158 34.64 6.50 38.13 3.91
2890 3096 3.617143 TTGCAGCTGCCTCGCATCT 62.617 57.895 34.64 0.00 38.13 2.90
2892 3098 3.574445 CAGCTGCCTCGCATCTGC 61.574 66.667 0.00 0.00 43.85 4.26
2893 3099 3.783580 AGCTGCCTCGCATCTGCT 61.784 61.111 0.00 0.00 38.13 4.24
2894 3100 3.574445 GCTGCCTCGCATCTGCTG 61.574 66.667 0.09 0.00 38.13 4.41
2909 3115 3.075998 CTGCTTCGCTGCTACGTG 58.924 61.111 0.00 0.00 0.00 4.49
2910 3116 3.076296 CTGCTTCGCTGCTACGTGC 62.076 63.158 0.00 0.00 43.25 5.34
2919 3125 4.427394 GCTACGTGCATGAGGGAG 57.573 61.111 14.17 5.33 42.31 4.30
2920 3126 1.884926 GCTACGTGCATGAGGGAGC 60.885 63.158 14.17 11.41 39.21 4.70
2921 3127 1.819229 CTACGTGCATGAGGGAGCT 59.181 57.895 14.17 0.00 0.00 4.09
2922 3128 0.176680 CTACGTGCATGAGGGAGCTT 59.823 55.000 14.17 0.00 0.00 3.74
2923 3129 0.108186 TACGTGCATGAGGGAGCTTG 60.108 55.000 14.17 0.00 0.00 4.01
2924 3130 2.110967 CGTGCATGAGGGAGCTTGG 61.111 63.158 0.00 0.00 0.00 3.61
2925 3131 1.001641 GTGCATGAGGGAGCTTGGT 60.002 57.895 0.00 0.00 0.00 3.67
2926 3132 1.001764 TGCATGAGGGAGCTTGGTG 60.002 57.895 0.00 0.00 0.00 4.17
2927 3133 1.751927 GCATGAGGGAGCTTGGTGG 60.752 63.158 0.00 0.00 0.00 4.61
2928 3134 1.751927 CATGAGGGAGCTTGGTGGC 60.752 63.158 0.00 0.00 0.00 5.01
2929 3135 2.988839 ATGAGGGAGCTTGGTGGCC 61.989 63.158 0.00 0.00 0.00 5.36
2930 3136 4.785453 GAGGGAGCTTGGTGGCCG 62.785 72.222 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.523072 CAATGGTTGGTTCTCGGCAG 59.477 55.000 0.00 0.00 0.00 4.85
24 25 2.916502 AAGGCGTTGTCGAGTGTGCA 62.917 55.000 0.00 0.00 39.71 4.57
71 72 4.941263 TCTTTTCACGGAGTCCCAATATTG 59.059 41.667 8.58 8.58 41.61 1.90
85 86 6.343616 CGTTGTCCGTTATTTTTCTTTTCACG 60.344 38.462 0.00 0.00 0.00 4.35
92 93 5.678047 CGTTTTCGTTGTCCGTTATTTTTCT 59.322 36.000 0.00 0.00 38.65 2.52
93 94 5.108668 CCGTTTTCGTTGTCCGTTATTTTTC 60.109 40.000 0.00 0.00 42.35 2.29
98 99 1.195222 GCCGTTTTCGTTGTCCGTTAT 59.805 47.619 0.00 0.00 42.35 1.89
107 108 2.263945 CCAACTTTTGCCGTTTTCGTT 58.736 42.857 0.00 0.00 42.35 3.85
171 172 2.972625 TGCTCAACATCTTTACCGAGG 58.027 47.619 0.00 0.00 0.00 4.63
246 251 0.179000 CTAGCTGGGGCCACTGTAAG 59.821 60.000 14.05 7.42 39.73 2.34
362 386 2.306715 AAAACGGGCTTCTGGGGGTT 62.307 55.000 0.00 0.00 0.00 4.11
363 388 2.306715 AAAAACGGGCTTCTGGGGGT 62.307 55.000 0.00 0.00 0.00 4.95
515 545 0.386858 GAAAAGCGGGAAGAAACGGC 60.387 55.000 0.00 0.00 34.78 5.68
516 546 0.240145 GGAAAAGCGGGAAGAAACGG 59.760 55.000 0.00 0.00 0.00 4.44
517 547 0.240145 GGGAAAAGCGGGAAGAAACG 59.760 55.000 0.00 0.00 0.00 3.60
518 548 0.601558 GGGGAAAAGCGGGAAGAAAC 59.398 55.000 0.00 0.00 0.00 2.78
519 549 0.541063 GGGGGAAAAGCGGGAAGAAA 60.541 55.000 0.00 0.00 0.00 2.52
520 550 1.076014 GGGGGAAAAGCGGGAAGAA 59.924 57.895 0.00 0.00 0.00 2.52
521 551 2.157452 TGGGGGAAAAGCGGGAAGA 61.157 57.895 0.00 0.00 0.00 2.87
522 552 1.977009 GTGGGGGAAAAGCGGGAAG 60.977 63.158 0.00 0.00 0.00 3.46
523 553 2.014033 AAGTGGGGGAAAAGCGGGAA 62.014 55.000 0.00 0.00 0.00 3.97
524 554 2.420466 GAAGTGGGGGAAAAGCGGGA 62.420 60.000 0.00 0.00 0.00 5.14
525 555 1.977009 GAAGTGGGGGAAAAGCGGG 60.977 63.158 0.00 0.00 0.00 6.13
526 556 1.977009 GGAAGTGGGGGAAAAGCGG 60.977 63.158 0.00 0.00 0.00 5.52
527 557 1.977009 GGGAAGTGGGGGAAAAGCG 60.977 63.158 0.00 0.00 0.00 4.68
560 604 2.812619 GGGAGAATGGCGGGAGGAG 61.813 68.421 0.00 0.00 0.00 3.69
608 652 2.180017 GGCGTACTTCTTCGGCGA 59.820 61.111 4.99 4.99 42.00 5.54
662 706 3.710722 CCTCTGCTTCGGCTGGGT 61.711 66.667 0.00 0.00 42.37 4.51
1034 1087 2.093869 GGCGGTGAGTAGTTGTATGGAA 60.094 50.000 0.00 0.00 0.00 3.53
1101 1156 1.985116 GCCGAGGTGAGAGAAGGGT 60.985 63.158 0.00 0.00 0.00 4.34
1216 1271 1.452651 CCATGCCGCTGGTGAGATT 60.453 57.895 0.00 0.00 0.00 2.40
1252 1307 1.028330 TGTTCCTCGTCGCCGTAGAT 61.028 55.000 0.00 0.00 35.01 1.98
1276 1331 0.894184 TCGTCTTCCTCGTCCTGCTT 60.894 55.000 0.00 0.00 0.00 3.91
1277 1332 1.303398 TCGTCTTCCTCGTCCTGCT 60.303 57.895 0.00 0.00 0.00 4.24
1278 1333 1.137825 CTCGTCTTCCTCGTCCTGC 59.862 63.158 0.00 0.00 0.00 4.85
1279 1334 0.677098 TCCTCGTCTTCCTCGTCCTG 60.677 60.000 0.00 0.00 0.00 3.86
1280 1335 0.393267 CTCCTCGTCTTCCTCGTCCT 60.393 60.000 0.00 0.00 0.00 3.85
1281 1336 1.378124 CCTCCTCGTCTTCCTCGTCC 61.378 65.000 0.00 0.00 0.00 4.79
1290 1366 1.222387 CTCCTCGTCCTCCTCGTCT 59.778 63.158 0.00 0.00 0.00 4.18
1667 1750 1.811679 GCGAAAAGAGGCGGGAGAG 60.812 63.158 0.00 0.00 0.00 3.20
1800 1890 2.625906 CCACTTGTCGCACGTGTG 59.374 61.111 22.93 22.93 32.79 3.82
2018 2108 1.290955 CCAACGTGCCTCGGTCTTA 59.709 57.895 0.00 0.00 44.69 2.10
2030 2120 2.029964 ATCAACGCCGACCAACGT 59.970 55.556 0.00 0.00 46.07 3.99
2087 2177 2.105128 CTCTTCCTCGCGGCGATT 59.895 61.111 26.60 0.00 34.61 3.34
2098 2188 0.037232 CAGGTCGGTGTTCCTCTTCC 60.037 60.000 0.00 0.00 30.91 3.46
2172 2262 3.387091 ATGCGCCCTGTACCACGA 61.387 61.111 4.18 0.00 0.00 4.35
2279 2437 4.819761 GTCTCGGCGGCATCAGCA 62.820 66.667 10.53 0.00 44.61 4.41
2550 2756 1.153549 GTCGGCCTAGCTTCCAGTG 60.154 63.158 0.00 0.00 0.00 3.66
2556 2762 2.660064 CCTGGTGTCGGCCTAGCTT 61.660 63.158 0.00 0.00 0.00 3.74
2583 2789 0.251354 TGCTCAGAACATCTCCAGCC 59.749 55.000 5.72 0.00 31.46 4.85
2584 2790 2.105006 TTGCTCAGAACATCTCCAGC 57.895 50.000 2.27 2.27 32.56 4.85
2585 2791 2.355132 GCATTGCTCAGAACATCTCCAG 59.645 50.000 0.16 0.00 0.00 3.86
2586 2792 2.362736 GCATTGCTCAGAACATCTCCA 58.637 47.619 0.16 0.00 0.00 3.86
2587 2793 1.329906 CGCATTGCTCAGAACATCTCC 59.670 52.381 7.12 0.00 0.00 3.71
2588 2794 1.267932 GCGCATTGCTCAGAACATCTC 60.268 52.381 0.30 0.00 41.73 2.75
2589 2795 0.731417 GCGCATTGCTCAGAACATCT 59.269 50.000 0.30 0.00 41.73 2.90
2590 2796 3.231222 GCGCATTGCTCAGAACATC 57.769 52.632 0.30 0.00 41.73 3.06
2600 2806 2.821688 GCAGAGGAGAGCGCATTGC 61.822 63.158 11.47 1.63 46.98 3.56
2601 2807 2.178890 GGCAGAGGAGAGCGCATTG 61.179 63.158 11.47 0.00 0.00 2.82
2602 2808 2.188994 GGCAGAGGAGAGCGCATT 59.811 61.111 11.47 0.00 0.00 3.56
2603 2809 2.590391 CTTGGCAGAGGAGAGCGCAT 62.590 60.000 11.47 0.00 0.00 4.73
2604 2810 3.306595 CTTGGCAGAGGAGAGCGCA 62.307 63.158 11.47 0.00 0.00 6.09
2605 2811 2.511145 CTTGGCAGAGGAGAGCGC 60.511 66.667 0.00 0.00 0.00 5.92
2606 2812 1.670949 TAGCTTGGCAGAGGAGAGCG 61.671 60.000 0.00 0.00 38.34 5.03
2607 2813 0.104671 CTAGCTTGGCAGAGGAGAGC 59.895 60.000 0.00 0.00 0.00 4.09
2608 2814 1.408702 GACTAGCTTGGCAGAGGAGAG 59.591 57.143 0.00 0.00 0.00 3.20
2609 2815 1.479709 GACTAGCTTGGCAGAGGAGA 58.520 55.000 0.00 0.00 0.00 3.71
2610 2816 0.102120 CGACTAGCTTGGCAGAGGAG 59.898 60.000 0.96 0.00 0.00 3.69
2611 2817 1.323271 CCGACTAGCTTGGCAGAGGA 61.323 60.000 0.96 0.00 0.00 3.71
2612 2818 1.142748 CCGACTAGCTTGGCAGAGG 59.857 63.158 0.96 0.00 0.00 3.69
2613 2819 0.179124 GACCGACTAGCTTGGCAGAG 60.179 60.000 0.96 0.00 0.00 3.35
2614 2820 1.605058 GGACCGACTAGCTTGGCAGA 61.605 60.000 0.96 0.00 0.00 4.26
2615 2821 1.153549 GGACCGACTAGCTTGGCAG 60.154 63.158 0.96 0.00 0.00 4.85
2616 2822 2.978824 GGACCGACTAGCTTGGCA 59.021 61.111 0.96 0.00 0.00 4.92
2617 2823 2.202756 CGGACCGACTAGCTTGGC 60.203 66.667 8.64 0.00 0.00 4.52
2618 2824 2.202756 GCGGACCGACTAGCTTGG 60.203 66.667 20.50 0.00 0.00 3.61
2619 2825 1.517257 CAGCGGACCGACTAGCTTG 60.517 63.158 20.50 0.00 37.94 4.01
2620 2826 2.885861 CAGCGGACCGACTAGCTT 59.114 61.111 20.50 0.00 37.94 3.74
2621 2827 3.827898 GCAGCGGACCGACTAGCT 61.828 66.667 20.50 0.63 41.07 3.32
2622 2828 2.001361 TAAGCAGCGGACCGACTAGC 62.001 60.000 20.50 17.92 0.00 3.42
2623 2829 0.669077 ATAAGCAGCGGACCGACTAG 59.331 55.000 20.50 10.01 0.00 2.57
2624 2830 0.384309 CATAAGCAGCGGACCGACTA 59.616 55.000 20.50 0.61 0.00 2.59
2625 2831 1.141881 CATAAGCAGCGGACCGACT 59.858 57.895 20.50 11.68 0.00 4.18
2626 2832 1.153628 ACATAAGCAGCGGACCGAC 60.154 57.895 20.50 9.27 0.00 4.79
2627 2833 1.153647 CACATAAGCAGCGGACCGA 60.154 57.895 20.50 0.00 0.00 4.69
2628 2834 2.813179 GCACATAAGCAGCGGACCG 61.813 63.158 10.29 10.29 0.00 4.79
2629 2835 0.179084 TAGCACATAAGCAGCGGACC 60.179 55.000 0.00 0.00 36.85 4.46
2630 2836 1.212616 CTAGCACATAAGCAGCGGAC 58.787 55.000 0.00 0.00 36.85 4.79
2631 2837 0.530650 GCTAGCACATAAGCAGCGGA 60.531 55.000 10.63 0.00 38.63 5.54
2632 2838 0.531532 AGCTAGCACATAAGCAGCGG 60.532 55.000 18.83 0.00 41.32 5.52
2633 2839 1.004185 CAAGCTAGCACATAAGCAGCG 60.004 52.381 18.83 0.00 41.32 5.18
2634 2840 1.332997 CCAAGCTAGCACATAAGCAGC 59.667 52.381 18.83 0.00 41.32 5.25
2635 2841 1.332997 GCCAAGCTAGCACATAAGCAG 59.667 52.381 18.83 0.00 41.32 4.24
2636 2842 1.382522 GCCAAGCTAGCACATAAGCA 58.617 50.000 18.83 0.00 41.32 3.91
2637 2843 0.665298 GGCCAAGCTAGCACATAAGC 59.335 55.000 18.83 10.26 39.08 3.09
2638 2844 0.940126 CGGCCAAGCTAGCACATAAG 59.060 55.000 18.83 0.00 0.00 1.73
2639 2845 0.463654 CCGGCCAAGCTAGCACATAA 60.464 55.000 18.83 0.00 0.00 1.90
2640 2846 1.146041 CCGGCCAAGCTAGCACATA 59.854 57.895 18.83 0.00 0.00 2.29
2641 2847 2.124570 CCGGCCAAGCTAGCACAT 60.125 61.111 18.83 0.00 0.00 3.21
2642 2848 3.605749 GACCGGCCAAGCTAGCACA 62.606 63.158 18.83 0.00 0.00 4.57
2643 2849 2.820037 GACCGGCCAAGCTAGCAC 60.820 66.667 18.83 2.90 0.00 4.40
2644 2850 4.096003 GGACCGGCCAAGCTAGCA 62.096 66.667 18.83 0.00 36.34 3.49
2645 2851 4.096003 TGGACCGGCCAAGCTAGC 62.096 66.667 14.27 6.62 45.87 3.42
2653 2859 1.898330 ATGCCAAAAATGGACCGGCC 61.898 55.000 0.00 4.32 42.27 6.13
2654 2860 0.740516 CATGCCAAAAATGGACCGGC 60.741 55.000 0.00 0.00 43.28 6.13
2655 2861 0.740516 GCATGCCAAAAATGGACCGG 60.741 55.000 6.36 0.00 0.00 5.28
2656 2862 0.740516 GGCATGCCAAAAATGGACCG 60.741 55.000 32.08 0.00 35.81 4.79
2657 2863 0.740516 CGGCATGCCAAAAATGGACC 60.741 55.000 34.93 4.81 35.37 4.46
2658 2864 0.740516 CCGGCATGCCAAAAATGGAC 60.741 55.000 34.93 5.36 35.37 4.02
2659 2865 0.902048 TCCGGCATGCCAAAAATGGA 60.902 50.000 34.93 27.43 35.37 3.41
2660 2866 0.460635 CTCCGGCATGCCAAAAATGG 60.461 55.000 34.93 25.68 35.37 3.16
2661 2867 0.531657 TCTCCGGCATGCCAAAAATG 59.468 50.000 34.93 17.95 35.37 2.32
2662 2868 0.819582 CTCTCCGGCATGCCAAAAAT 59.180 50.000 34.93 0.00 35.37 1.82
2663 2869 0.539438 ACTCTCCGGCATGCCAAAAA 60.539 50.000 34.93 16.88 35.37 1.94
2664 2870 1.074775 ACTCTCCGGCATGCCAAAA 59.925 52.632 34.93 18.66 35.37 2.44
2665 2871 1.675310 CACTCTCCGGCATGCCAAA 60.675 57.895 34.93 21.19 35.37 3.28
2666 2872 2.046023 CACTCTCCGGCATGCCAA 60.046 61.111 34.93 21.55 35.37 4.52
2667 2873 4.783621 GCACTCTCCGGCATGCCA 62.784 66.667 34.93 16.95 35.37 4.92
2676 2882 3.537206 AACAGCACCCGCACTCTCC 62.537 63.158 0.00 0.00 42.27 3.71
2677 2883 2.031163 AACAGCACCCGCACTCTC 59.969 61.111 0.00 0.00 42.27 3.20
2678 2884 2.281070 CAACAGCACCCGCACTCT 60.281 61.111 0.00 0.00 42.27 3.24
2679 2885 4.030452 GCAACAGCACCCGCACTC 62.030 66.667 0.00 0.00 42.27 3.51
2680 2886 4.569180 AGCAACAGCACCCGCACT 62.569 61.111 0.00 0.00 42.27 4.40
2681 2887 4.030452 GAGCAACAGCACCCGCAC 62.030 66.667 0.00 0.00 42.27 5.34
2682 2888 4.560743 TGAGCAACAGCACCCGCA 62.561 61.111 0.00 0.00 42.27 5.69
2683 2889 3.730761 CTGAGCAACAGCACCCGC 61.731 66.667 0.00 0.00 39.86 6.13
2690 2896 1.194098 CGTCTTCTTGCTGAGCAACAG 59.806 52.381 17.04 14.69 43.99 3.16
2691 2897 1.220529 CGTCTTCTTGCTGAGCAACA 58.779 50.000 17.04 2.75 43.99 3.33
2692 2898 0.110464 GCGTCTTCTTGCTGAGCAAC 60.110 55.000 17.04 5.92 43.99 4.17
2693 2899 1.560004 CGCGTCTTCTTGCTGAGCAA 61.560 55.000 19.84 19.84 46.80 3.91
2694 2900 2.023771 CGCGTCTTCTTGCTGAGCA 61.024 57.895 1.40 1.40 36.47 4.26
2695 2901 1.950098 GACGCGTCTTCTTGCTGAGC 61.950 60.000 31.12 0.00 0.00 4.26
2696 2902 0.387878 AGACGCGTCTTCTTGCTGAG 60.388 55.000 34.98 0.00 36.31 3.35
2697 2903 0.879090 TAGACGCGTCTTCTTGCTGA 59.121 50.000 42.90 22.40 40.93 4.26
2698 2904 1.585668 CATAGACGCGTCTTCTTGCTG 59.414 52.381 42.90 25.49 40.93 4.41
2699 2905 1.914634 CATAGACGCGTCTTCTTGCT 58.085 50.000 42.90 22.19 40.93 3.91
2700 2906 0.299003 GCATAGACGCGTCTTCTTGC 59.701 55.000 42.90 37.85 40.93 4.01
2710 2916 1.006314 GCCTCATCTCGCATAGACGC 61.006 60.000 0.00 0.00 36.93 5.19
2711 2917 0.595588 AGCCTCATCTCGCATAGACG 59.404 55.000 0.00 0.00 36.93 4.18
2712 2918 1.336702 CCAGCCTCATCTCGCATAGAC 60.337 57.143 0.00 0.00 36.93 2.59
2713 2919 0.964700 CCAGCCTCATCTCGCATAGA 59.035 55.000 0.00 0.00 39.02 1.98
2714 2920 0.669932 GCCAGCCTCATCTCGCATAG 60.670 60.000 0.00 0.00 0.00 2.23
2715 2921 1.117749 AGCCAGCCTCATCTCGCATA 61.118 55.000 0.00 0.00 0.00 3.14
2716 2922 2.110627 GCCAGCCTCATCTCGCAT 59.889 61.111 0.00 0.00 0.00 4.73
2717 2923 3.079478 AGCCAGCCTCATCTCGCA 61.079 61.111 0.00 0.00 0.00 5.10
2718 2924 2.588314 CAGCCAGCCTCATCTCGC 60.588 66.667 0.00 0.00 0.00 5.03
2719 2925 1.227205 GACAGCCAGCCTCATCTCG 60.227 63.158 0.00 0.00 0.00 4.04
2720 2926 1.227205 CGACAGCCAGCCTCATCTC 60.227 63.158 0.00 0.00 0.00 2.75
2721 2927 2.898738 CGACAGCCAGCCTCATCT 59.101 61.111 0.00 0.00 0.00 2.90
2722 2928 2.894387 GCGACAGCCAGCCTCATC 60.894 66.667 0.00 0.00 37.42 2.92
2723 2929 3.382803 GAGCGACAGCCAGCCTCAT 62.383 63.158 0.00 0.00 46.67 2.90
2724 2930 4.074526 GAGCGACAGCCAGCCTCA 62.075 66.667 0.00 0.00 46.67 3.86
2725 2931 3.308014 AAGAGCGACAGCCAGCCTC 62.308 63.158 0.00 0.00 46.67 4.70
2726 2932 3.317571 AAGAGCGACAGCCAGCCT 61.318 61.111 0.00 0.00 46.67 4.58
2727 2933 3.123620 CAAGAGCGACAGCCAGCC 61.124 66.667 0.00 0.00 46.67 4.85
2728 2934 2.507110 TACCAAGAGCGACAGCCAGC 62.507 60.000 0.00 0.00 46.67 4.85
2729 2935 0.459237 CTACCAAGAGCGACAGCCAG 60.459 60.000 0.00 0.00 46.67 4.85
2730 2936 1.591703 CTACCAAGAGCGACAGCCA 59.408 57.895 0.00 0.00 46.67 4.75
2731 2937 1.811679 GCTACCAAGAGCGACAGCC 60.812 63.158 0.00 0.00 46.67 4.85
2732 2938 3.787458 GCTACCAAGAGCGACAGC 58.213 61.111 0.00 0.00 45.58 4.40
2738 2944 2.434359 AACGGCGCTACCAAGAGC 60.434 61.111 6.90 0.00 46.72 4.09
2739 2945 1.080093 TCAACGGCGCTACCAAGAG 60.080 57.895 6.90 0.00 39.03 2.85
2740 2946 1.373748 GTCAACGGCGCTACCAAGA 60.374 57.895 6.90 0.00 39.03 3.02
2741 2947 2.726691 CGTCAACGGCGCTACCAAG 61.727 63.158 6.90 0.00 39.03 3.61
2742 2948 2.735478 CGTCAACGGCGCTACCAA 60.735 61.111 6.90 0.00 39.03 3.67
2743 2949 3.672447 TCGTCAACGGCGCTACCA 61.672 61.111 6.90 0.00 39.03 3.25
2744 2950 3.177249 GTCGTCAACGGCGCTACC 61.177 66.667 6.90 0.00 40.29 3.18
2753 2959 2.173382 GCCACATGCGTCGTCAAC 59.827 61.111 0.00 0.00 0.00 3.18
2754 2960 2.280457 TGCCACATGCGTCGTCAA 60.280 55.556 0.00 0.00 45.60 3.18
2755 2961 3.041351 GTGCCACATGCGTCGTCA 61.041 61.111 0.00 0.00 45.60 4.35
2756 2962 4.134187 CGTGCCACATGCGTCGTC 62.134 66.667 0.00 0.00 45.60 4.20
2757 2963 4.961511 ACGTGCCACATGCGTCGT 62.962 61.111 0.00 0.00 45.60 4.34
2758 2964 4.428922 CACGTGCCACATGCGTCG 62.429 66.667 0.82 0.00 45.60 5.12
2759 2965 4.088762 CCACGTGCCACATGCGTC 62.089 66.667 10.91 0.00 45.60 5.19
2771 2977 4.619227 CAACCACGGAGGCCACGT 62.619 66.667 18.29 18.29 46.82 4.49
2772 2978 4.619227 ACAACCACGGAGGCCACG 62.619 66.667 16.99 16.99 43.14 4.94
2773 2979 2.203294 AACAACCACGGAGGCCAC 60.203 61.111 5.01 0.00 43.14 5.01
2774 2980 2.203280 CAACAACCACGGAGGCCA 60.203 61.111 5.01 0.00 43.14 5.36
2775 2981 3.670377 GCAACAACCACGGAGGCC 61.670 66.667 0.00 0.00 43.14 5.19
2776 2982 3.670377 GGCAACAACCACGGAGGC 61.670 66.667 0.00 0.00 43.14 4.70
2777 2983 1.528309 AAGGCAACAACCACGGAGG 60.528 57.895 0.00 0.00 41.83 4.30
2778 2984 1.101049 ACAAGGCAACAACCACGGAG 61.101 55.000 0.00 0.00 41.41 4.63
2779 2985 0.681564 AACAAGGCAACAACCACGGA 60.682 50.000 0.00 0.00 41.41 4.69
2780 2986 0.527385 CAACAAGGCAACAACCACGG 60.527 55.000 0.00 0.00 41.41 4.94
2781 2987 0.527385 CCAACAAGGCAACAACCACG 60.527 55.000 0.00 0.00 41.41 4.94
2782 2988 3.360886 CCAACAAGGCAACAACCAC 57.639 52.632 0.00 0.00 41.41 4.16
2809 3015 3.803082 CAACCACATGCCGGCGAG 61.803 66.667 23.90 19.27 0.00 5.03
2812 3018 4.054825 CACCAACCACATGCCGGC 62.055 66.667 22.73 22.73 0.00 6.13
2813 3019 2.282110 TCACCAACCACATGCCGG 60.282 61.111 0.00 0.00 0.00 6.13
2814 3020 2.981560 GCTCACCAACCACATGCCG 61.982 63.158 0.00 0.00 0.00 5.69
2815 3021 1.604593 AGCTCACCAACCACATGCC 60.605 57.895 0.00 0.00 0.00 4.40
2816 3022 1.582968 CAGCTCACCAACCACATGC 59.417 57.895 0.00 0.00 0.00 4.06
2817 3023 0.892358 AGCAGCTCACCAACCACATG 60.892 55.000 0.00 0.00 0.00 3.21
2818 3024 0.892358 CAGCAGCTCACCAACCACAT 60.892 55.000 0.00 0.00 0.00 3.21
2819 3025 1.526686 CAGCAGCTCACCAACCACA 60.527 57.895 0.00 0.00 0.00 4.17
2820 3026 2.912624 GCAGCAGCTCACCAACCAC 61.913 63.158 0.00 0.00 37.91 4.16
2821 3027 2.595463 GCAGCAGCTCACCAACCA 60.595 61.111 0.00 0.00 37.91 3.67
2822 3028 3.368571 GGCAGCAGCTCACCAACC 61.369 66.667 0.00 0.00 41.70 3.77
2823 3029 1.860484 GAAGGCAGCAGCTCACCAAC 61.860 60.000 12.66 3.53 41.70 3.77
2824 3030 1.601759 GAAGGCAGCAGCTCACCAA 60.602 57.895 12.66 0.00 41.70 3.67
2825 3031 2.033141 GAAGGCAGCAGCTCACCA 59.967 61.111 12.66 0.00 41.70 4.17
2826 3032 2.749441 GGAAGGCAGCAGCTCACC 60.749 66.667 0.00 0.00 41.70 4.02
2827 3033 2.749441 GGGAAGGCAGCAGCTCAC 60.749 66.667 0.00 0.00 41.70 3.51
2828 3034 4.399395 CGGGAAGGCAGCAGCTCA 62.399 66.667 0.00 0.00 41.70 4.26
2837 3043 3.675619 ATGTACACGGCGGGAAGGC 62.676 63.158 19.75 2.84 42.76 4.35
2838 3044 1.813753 CATGTACACGGCGGGAAGG 60.814 63.158 19.75 0.00 0.00 3.46
2839 3045 1.079405 ACATGTACACGGCGGGAAG 60.079 57.895 19.75 2.20 0.00 3.46
2840 3046 1.374885 CACATGTACACGGCGGGAA 60.375 57.895 19.75 0.11 0.00 3.97
2841 3047 2.263227 CACATGTACACGGCGGGA 59.737 61.111 19.75 0.00 0.00 5.14
2842 3048 3.496131 GCACATGTACACGGCGGG 61.496 66.667 8.04 8.04 0.00 6.13
2843 3049 2.434185 AGCACATGTACACGGCGG 60.434 61.111 13.24 2.35 0.00 6.13
2844 3050 2.778026 CAGCACATGTACACGGCG 59.222 61.111 4.80 4.80 0.00 6.46
2845 3051 2.480555 GCAGCACATGTACACGGC 59.519 61.111 0.00 2.04 0.00 5.68
2846 3052 2.739704 CGGCAGCACATGTACACGG 61.740 63.158 0.00 0.00 0.00 4.94
2847 3053 2.778026 CGGCAGCACATGTACACG 59.222 61.111 0.00 0.00 0.00 4.49
2848 3054 2.480555 GCGGCAGCACATGTACAC 59.519 61.111 3.18 0.00 44.35 2.90
2871 3077 3.109612 GATGCGAGGCAGCTGCAAG 62.110 63.158 37.63 27.39 43.65 4.01
2872 3078 3.129502 GATGCGAGGCAGCTGCAA 61.130 61.111 37.63 18.68 43.65 4.08
2877 3083 3.574445 CAGCAGATGCGAGGCAGC 61.574 66.667 0.00 0.00 45.98 5.25
2878 3084 3.574445 GCAGCAGATGCGAGGCAG 61.574 66.667 0.00 0.00 46.99 4.85
2902 3108 1.884926 GCTCCCTCATGCACGTAGC 60.885 63.158 0.00 0.00 45.96 3.58
2903 3109 0.176680 AAGCTCCCTCATGCACGTAG 59.823 55.000 0.00 0.00 0.00 3.51
2904 3110 0.108186 CAAGCTCCCTCATGCACGTA 60.108 55.000 0.00 0.00 0.00 3.57
2905 3111 1.376424 CAAGCTCCCTCATGCACGT 60.376 57.895 0.00 0.00 0.00 4.49
2906 3112 2.110967 CCAAGCTCCCTCATGCACG 61.111 63.158 0.00 0.00 0.00 5.34
2907 3113 1.001641 ACCAAGCTCCCTCATGCAC 60.002 57.895 0.00 0.00 0.00 4.57
2908 3114 1.001764 CACCAAGCTCCCTCATGCA 60.002 57.895 0.00 0.00 0.00 3.96
2909 3115 1.751927 CCACCAAGCTCCCTCATGC 60.752 63.158 0.00 0.00 0.00 4.06
2910 3116 1.751927 GCCACCAAGCTCCCTCATG 60.752 63.158 0.00 0.00 0.00 3.07
2911 3117 2.679716 GCCACCAAGCTCCCTCAT 59.320 61.111 0.00 0.00 0.00 2.90
2912 3118 3.650950 GGCCACCAAGCTCCCTCA 61.651 66.667 0.00 0.00 0.00 3.86
2913 3119 4.785453 CGGCCACCAAGCTCCCTC 62.785 72.222 2.24 0.00 0.00 4.30
2935 3141 4.485834 TAGCAGCACGTACGCCGG 62.486 66.667 16.72 8.68 42.24 6.13
2936 3142 2.949678 CTAGCAGCACGTACGCCG 60.950 66.667 16.72 8.14 44.03 6.46
2937 3143 3.255379 GCTAGCAGCACGTACGCC 61.255 66.667 16.72 6.81 41.89 5.68
2938 3144 2.202623 AGCTAGCAGCACGTACGC 60.203 61.111 18.83 0.00 45.56 4.42
2939 3145 2.508891 GCAGCTAGCAGCACGTACG 61.509 63.158 25.43 15.01 45.56 3.67
2940 3146 3.389206 GCAGCTAGCAGCACGTAC 58.611 61.111 25.43 0.00 45.56 3.67


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

AutoCloner maintained by Alex Coulton.