Multiple sequence alignment - TraesCS3A01G228900

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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 TraesCS3A01G228900 chr3A 100.000 2999 0 0 1 2999 428322477 428325475 0.000000e+00 5539.0
1 TraesCS3A01G228900 chr3D 93.849 2211 95 19 1 2172 308738075 308740283 0.000000e+00 3291.0
2 TraesCS3A01G228900 chr3D 92.926 311 12 5 2170 2479 308740316 308740617 7.630000e-121 444.0
3 TraesCS3A01G228900 chr3D 78.391 435 47 22 2595 2996 406788299 406787879 3.860000e-59 239.0
4 TraesCS3A01G228900 chr3B 93.160 1535 70 14 672 2172 412875136 412873603 0.000000e+00 2220.0
5 TraesCS3A01G228900 chr3B 86.957 690 67 16 1 672 412915081 412914397 0.000000e+00 754.0
6 TraesCS3A01G228900 chr3B 92.182 307 16 4 2173 2479 412873567 412873269 7.680000e-116 427.0
7 TraesCS3A01G228900 chr3B 79.147 211 27 9 2802 2996 808073795 808073586 2.430000e-26 130.0
8 TraesCS3A01G228900 chr3B 87.013 77 10 0 2797 2873 422262865 422262941 1.480000e-13 87.9
9 TraesCS3A01G228900 chr3B 86.957 69 5 4 1 65 90469229 90469161 1.150000e-09 75.0
10 TraesCS3A01G228900 chr6B 82.629 426 49 15 1 406 59113818 59113398 1.320000e-93 353.0
11 TraesCS3A01G228900 chr6B 81.884 414 46 18 10 402 165297104 165297509 3.730000e-84 322.0
12 TraesCS3A01G228900 chr2B 82.353 425 53 15 1 406 656018885 656019306 1.710000e-92 350.0
13 TraesCS3A01G228900 chr2B 77.027 222 36 8 2790 2996 793460963 793461184 2.440000e-21 113.0
14 TraesCS3A01G228900 chr1A 82.353 425 50 17 1 406 113219237 113218819 2.210000e-91 346.0
15 TraesCS3A01G228900 chr1A 81.633 441 56 19 1 424 591974908 591974476 2.860000e-90 342.0
16 TraesCS3A01G228900 chr1A 81.465 437 58 17 1 418 386382878 386382446 1.330000e-88 337.0
17 TraesCS3A01G228900 chr4D 81.176 425 55 17 1 406 37617616 37617198 4.820000e-83 318.0
18 TraesCS3A01G228900 chr4D 79.856 278 24 11 2742 2996 458390370 458390638 1.110000e-39 174.0
19 TraesCS3A01G228900 chr2A 79.727 439 54 17 1 415 723833267 723832840 4.890000e-73 285.0
20 TraesCS3A01G228900 chr4A 79.505 444 56 20 1 415 203644833 203644396 1.760000e-72 283.0
21 TraesCS3A01G228900 chr7A 79.433 423 66 16 1 406 139130662 139130244 2.280000e-71 279.0
22 TraesCS3A01G228900 chr5A 79.540 435 52 23 1 416 626444826 626444410 2.940000e-70 276.0
23 TraesCS3A01G228900 chr5A 76.866 402 69 18 2478 2864 323405219 323404827 3.920000e-49 206.0
24 TraesCS3A01G228900 chr5B 79.091 440 61 17 1 412 208527606 208527170 1.060000e-69 274.0
25 TraesCS3A01G228900 chr4B 77.320 291 48 18 2526 2805 497024213 497023930 4.000000e-34 156.0
26 TraesCS3A01G228900 chr6A 87.288 118 6 3 837 953 93422195 93422304 3.140000e-25 126.0


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 TraesCS3A01G228900 chr3A 428322477 428325475 2998 False 5539.0 5539 100.0000 1 2999 1 chr3A.!!$F1 2998
1 TraesCS3A01G228900 chr3D 308738075 308740617 2542 False 1867.5 3291 93.3875 1 2479 2 chr3D.!!$F1 2478
2 TraesCS3A01G228900 chr3B 412873269 412875136 1867 True 1323.5 2220 92.6710 672 2479 2 chr3B.!!$R4 1807
3 TraesCS3A01G228900 chr3B 412914397 412915081 684 True 754.0 754 86.9570 1 672 1 chr3B.!!$R2 671

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
633 658 0.670162 ACTTTTCAAGTGCATGCGCT 59.330 45.0 27.71 27.71 41.01 5.92 F
1074 1131 0.037790 AGAAACTCGCACAGCTCCTC 60.038 55.0 0.00 0.00 0.00 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1709 1775 0.102844 TTTGCTGTTCTTGCACTGGC 59.897 50.0 0.0 0.0 40.40 4.85 R
2826 2944 0.038526 AAGCTACGACGAGGTTGGTG 60.039 55.0 0.0 0.0 35.86 4.17 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
83 86 6.820470 TTGTTCGCATTTTTCTAAAAGTGG 57.180 33.333 11.23 3.95 36.49 4.00
221 226 2.202756 GCCTTCTCTGGCGTACGG 60.203 66.667 18.39 0.00 43.74 4.02
226 231 1.174078 TTCTCTGGCGTACGGTGACA 61.174 55.000 18.39 0.00 0.00 3.58
228 233 0.802222 CTCTGGCGTACGGTGACATG 60.802 60.000 18.39 0.00 0.00 3.21
287 304 3.560636 ATAGCTTACACCTGGCGAAAT 57.439 42.857 0.00 0.00 0.00 2.17
288 305 2.200373 AGCTTACACCTGGCGAAATT 57.800 45.000 0.00 0.00 0.00 1.82
304 321 5.863935 GGCGAAATTGAGAAGCTAAATGTTT 59.136 36.000 0.00 0.00 0.00 2.83
450 473 5.132144 AGTGGGGTATGGATTAGTTCGAATT 59.868 40.000 0.00 0.00 0.00 2.17
480 503 1.055849 TGTGTGGTGCCAGATGTACT 58.944 50.000 0.00 0.00 0.00 2.73
603 628 3.777478 CATCGTATTACACGGTTGAGGT 58.223 45.455 0.00 0.00 42.83 3.85
631 656 3.266541 TGTACTTTTCAAGTGCATGCG 57.733 42.857 14.09 0.00 46.84 4.73
633 658 0.670162 ACTTTTCAAGTGCATGCGCT 59.330 45.000 27.71 27.71 41.01 5.92
959 1016 6.176183 TCTTCTCCTCCTTGCTTTATTTCTG 58.824 40.000 0.00 0.00 0.00 3.02
974 1031 3.594603 TTTCTGTCTCCCGAGATCAAC 57.405 47.619 0.00 0.00 39.97 3.18
996 1053 2.579684 TACACACACTGCGCACACCA 62.580 55.000 5.66 0.00 0.00 4.17
1017 1074 1.750399 CATGGACGAAAGCCCCCAG 60.750 63.158 0.00 0.00 33.11 4.45
1018 1075 2.231380 ATGGACGAAAGCCCCCAGT 61.231 57.895 0.00 0.00 33.11 4.00
1074 1131 0.037790 AGAAACTCGCACAGCTCCTC 60.038 55.000 0.00 0.00 0.00 3.71
1294 1360 0.107508 CTCCGTCGACTACCCAGGTA 60.108 60.000 14.70 0.00 0.00 3.08
1376 1442 2.723010 CGAACGATGCAAAGAAGAGCAC 60.723 50.000 0.00 0.00 44.49 4.40
1485 1551 1.739562 CAGCTGCTCTTCGTCCACC 60.740 63.158 0.00 0.00 0.00 4.61
1565 1631 0.392729 TTCTCCTCCGACTCGACCTC 60.393 60.000 0.00 0.00 0.00 3.85
1612 1678 2.993853 CCTCCAGGAAGAGCCACC 59.006 66.667 0.00 0.00 40.02 4.61
1680 1746 2.676121 CCACCCGATGCCTTGCAA 60.676 61.111 0.00 0.00 43.62 4.08
1709 1775 3.777925 CTTGGCGACGAAGCACCG 61.778 66.667 0.00 0.00 39.27 4.94
1731 1797 2.099592 CCAGTGCAAGAACAGCAAAAGA 59.900 45.455 0.00 0.00 44.64 2.52
1762 1828 2.901209 CGAATGCGATCAAGAAGATGC 58.099 47.619 0.00 0.00 40.82 3.91
1779 1845 2.033194 GCTCGTGGAAGAAACCGGG 61.033 63.158 6.32 0.00 0.00 5.73
1821 1887 0.108186 TGGTGAAGCGATCGAGCAAT 60.108 50.000 21.57 0.00 40.15 3.56
1869 1935 2.711922 GGAGATGGTCGTGGAGCGT 61.712 63.158 0.00 0.00 42.13 5.07
2077 2143 2.023181 GATCGTACGCGCGGTGTA 59.977 61.111 35.22 15.11 38.14 2.90
2098 2165 2.681344 AGTTGTGGTTTTCAGTTCGTCC 59.319 45.455 0.00 0.00 0.00 4.79
2106 2174 4.626172 GGTTTTCAGTTCGTCCTAGCTTAG 59.374 45.833 0.00 0.00 0.00 2.18
2130 2213 1.800586 GCAGATGTATGTACATGCCCG 59.199 52.381 18.81 6.62 46.20 6.13
2131 2214 2.547855 GCAGATGTATGTACATGCCCGA 60.548 50.000 18.81 1.74 46.20 5.14
2188 2306 1.970640 TGCCTGTCTCTAGTTGAGCAA 59.029 47.619 0.00 0.00 42.38 3.91
2195 2313 5.858381 TGTCTCTAGTTGAGCAATTTGAGT 58.142 37.500 13.51 0.00 42.38 3.41
2241 2359 8.911247 ATTTTGAGTTAGTTTTTGTGTCAGAC 57.089 30.769 0.00 0.00 0.00 3.51
2276 2394 4.516321 TGTTTGATGCTCGGATATGAATGG 59.484 41.667 0.00 0.00 0.00 3.16
2443 2561 2.007608 GTCCGGCTATTGAAACAGGAC 58.992 52.381 0.00 0.00 39.63 3.85
2465 2583 0.661020 ACAAGTACCAACAAGTGCGC 59.339 50.000 0.00 0.00 0.00 6.09
2483 2601 3.677002 CTAGCTGAGCAGTAAGGCC 57.323 57.895 7.39 0.00 0.00 5.19
2484 2602 0.826715 CTAGCTGAGCAGTAAGGCCA 59.173 55.000 7.39 0.00 0.00 5.36
2485 2603 1.208052 CTAGCTGAGCAGTAAGGCCAA 59.792 52.381 7.39 0.00 0.00 4.52
2486 2604 0.322008 AGCTGAGCAGTAAGGCCAAC 60.322 55.000 7.39 2.07 0.00 3.77
2487 2605 0.322008 GCTGAGCAGTAAGGCCAACT 60.322 55.000 5.01 5.00 0.00 3.16
2488 2606 1.731720 CTGAGCAGTAAGGCCAACTC 58.268 55.000 5.01 2.54 0.00 3.01
2489 2607 0.037326 TGAGCAGTAAGGCCAACTCG 60.037 55.000 5.01 4.62 0.00 4.18
2490 2608 0.246635 GAGCAGTAAGGCCAACTCGA 59.753 55.000 5.01 0.00 0.00 4.04
2491 2609 0.685097 AGCAGTAAGGCCAACTCGAA 59.315 50.000 5.01 0.00 0.00 3.71
2492 2610 0.796927 GCAGTAAGGCCAACTCGAAC 59.203 55.000 5.01 0.00 0.00 3.95
2493 2611 1.068474 CAGTAAGGCCAACTCGAACG 58.932 55.000 5.01 0.00 0.00 3.95
2494 2612 0.669625 AGTAAGGCCAACTCGAACGC 60.670 55.000 5.01 0.00 0.00 4.84
2495 2613 1.735198 TAAGGCCAACTCGAACGCG 60.735 57.895 5.01 3.53 39.35 6.01
2498 2616 4.430423 GCCAACTCGAACGCGCAG 62.430 66.667 5.73 2.42 37.46 5.18
2499 2617 3.036084 CCAACTCGAACGCGCAGT 61.036 61.111 5.73 3.19 37.46 4.40
2500 2618 2.465920 CAACTCGAACGCGCAGTC 59.534 61.111 5.73 2.15 37.46 3.51
2501 2619 2.733593 AACTCGAACGCGCAGTCC 60.734 61.111 5.73 0.00 37.46 3.85
2502 2620 4.719369 ACTCGAACGCGCAGTCCC 62.719 66.667 5.73 1.85 37.46 4.46
2503 2621 4.717629 CTCGAACGCGCAGTCCCA 62.718 66.667 5.73 0.00 37.46 4.37
2504 2622 4.287781 TCGAACGCGCAGTCCCAA 62.288 61.111 5.73 0.00 37.46 4.12
2505 2623 3.342627 CGAACGCGCAGTCCCAAA 61.343 61.111 5.73 0.00 0.00 3.28
2506 2624 2.251371 GAACGCGCAGTCCCAAAC 59.749 61.111 5.73 0.00 0.00 2.93
2507 2625 3.573489 GAACGCGCAGTCCCAAACG 62.573 63.158 5.73 0.00 0.00 3.60
2524 2642 2.010145 ACGGACATCTGTTTGATCCG 57.990 50.000 9.32 9.32 43.80 4.18
2525 2643 1.290203 CGGACATCTGTTTGATCCGG 58.710 55.000 0.00 0.00 38.28 5.14
2526 2644 1.134818 CGGACATCTGTTTGATCCGGA 60.135 52.381 6.61 6.61 38.28 5.14
2527 2645 2.483714 CGGACATCTGTTTGATCCGGAT 60.484 50.000 19.21 19.21 38.28 4.18
2528 2646 3.545703 GGACATCTGTTTGATCCGGATT 58.454 45.455 20.22 1.69 32.05 3.01
2529 2647 3.947834 GGACATCTGTTTGATCCGGATTT 59.052 43.478 20.22 0.00 32.05 2.17
2530 2648 4.201950 GGACATCTGTTTGATCCGGATTTG 60.202 45.833 20.22 8.80 32.05 2.32
2531 2649 3.129287 ACATCTGTTTGATCCGGATTTGC 59.871 43.478 20.22 6.53 32.05 3.68
2532 2650 3.071874 TCTGTTTGATCCGGATTTGCT 57.928 42.857 20.22 0.00 0.00 3.91
2533 2651 3.009723 TCTGTTTGATCCGGATTTGCTC 58.990 45.455 20.22 6.74 0.00 4.26
2534 2652 2.091541 TGTTTGATCCGGATTTGCTCC 58.908 47.619 20.22 4.90 41.07 4.70
2535 2653 2.091541 GTTTGATCCGGATTTGCTCCA 58.908 47.619 20.22 7.85 45.24 3.86
2536 2654 2.689983 GTTTGATCCGGATTTGCTCCAT 59.310 45.455 20.22 0.00 45.24 3.41
2537 2655 3.855255 TTGATCCGGATTTGCTCCATA 57.145 42.857 20.22 0.00 45.24 2.74
2538 2656 4.371624 TTGATCCGGATTTGCTCCATAT 57.628 40.909 20.22 0.00 45.24 1.78
2539 2657 3.678289 TGATCCGGATTTGCTCCATATG 58.322 45.455 20.22 0.00 45.24 1.78
2540 2658 2.566833 TCCGGATTTGCTCCATATGG 57.433 50.000 16.25 16.25 45.24 2.74
2541 2659 1.073763 TCCGGATTTGCTCCATATGGG 59.926 52.381 21.78 13.13 45.24 4.00
2542 2660 1.073763 CCGGATTTGCTCCATATGGGA 59.926 52.381 21.78 7.71 45.24 4.37
2553 2671 4.740154 TCCATATGGGATGGGTAAAAGG 57.260 45.455 21.78 0.00 42.15 3.11
2554 2672 4.320398 TCCATATGGGATGGGTAAAAGGA 58.680 43.478 21.78 0.00 42.15 3.36
2555 2673 4.105697 TCCATATGGGATGGGTAAAAGGAC 59.894 45.833 21.78 0.00 42.15 3.85
2556 2674 4.106341 CCATATGGGATGGGTAAAAGGACT 59.894 45.833 14.52 0.00 40.01 3.85
2557 2675 5.400189 CCATATGGGATGGGTAAAAGGACTT 60.400 44.000 14.52 0.00 40.01 3.01
2558 2676 3.732048 TGGGATGGGTAAAAGGACTTC 57.268 47.619 0.00 0.00 0.00 3.01
2559 2677 2.310647 TGGGATGGGTAAAAGGACTTCC 59.689 50.000 0.00 0.00 0.00 3.46
2560 2678 2.310647 GGGATGGGTAAAAGGACTTCCA 59.689 50.000 0.00 0.00 38.89 3.53
2561 2679 3.052869 GGGATGGGTAAAAGGACTTCCAT 60.053 47.826 0.00 3.48 38.89 3.41
2562 2680 3.954258 GGATGGGTAAAAGGACTTCCATG 59.046 47.826 7.50 0.00 38.89 3.66
2563 2681 4.569865 GGATGGGTAAAAGGACTTCCATGT 60.570 45.833 7.50 0.00 38.89 3.21
2564 2682 4.028993 TGGGTAAAAGGACTTCCATGTC 57.971 45.455 0.00 0.00 38.89 3.06
2570 2688 3.644861 GGACTTCCATGTCCGGTTT 57.355 52.632 0.00 0.00 45.69 3.27
2571 2689 1.165270 GGACTTCCATGTCCGGTTTG 58.835 55.000 0.00 0.00 45.69 2.93
2572 2690 1.271163 GGACTTCCATGTCCGGTTTGA 60.271 52.381 0.00 0.00 45.69 2.69
2573 2691 2.076863 GACTTCCATGTCCGGTTTGAG 58.923 52.381 0.00 0.00 0.00 3.02
2574 2692 0.804989 CTTCCATGTCCGGTTTGAGC 59.195 55.000 0.00 0.00 0.00 4.26
2575 2693 0.608035 TTCCATGTCCGGTTTGAGCC 60.608 55.000 0.00 0.00 0.00 4.70
2583 2701 2.597510 GGTTTGAGCCGGCCTTGT 60.598 61.111 26.15 3.43 0.00 3.16
2584 2702 2.644992 GTTTGAGCCGGCCTTGTG 59.355 61.111 26.15 0.00 0.00 3.33
2585 2703 2.193536 GTTTGAGCCGGCCTTGTGT 61.194 57.895 26.15 1.92 0.00 3.72
2586 2704 1.896660 TTTGAGCCGGCCTTGTGTC 60.897 57.895 26.15 13.99 0.00 3.67
2587 2705 4.680237 TGAGCCGGCCTTGTGTCG 62.680 66.667 26.15 0.00 0.00 4.35
2588 2706 4.373116 GAGCCGGCCTTGTGTCGA 62.373 66.667 26.15 0.00 0.00 4.20
2589 2707 4.379243 AGCCGGCCTTGTGTCGAG 62.379 66.667 26.15 0.00 0.00 4.04
2595 2713 2.358737 CCTTGTGTCGAGGCACCC 60.359 66.667 5.32 0.00 38.52 4.61
2596 2714 2.425592 CTTGTGTCGAGGCACCCA 59.574 61.111 5.32 0.00 38.52 4.51
2597 2715 1.227823 CTTGTGTCGAGGCACCCAA 60.228 57.895 5.32 0.00 38.52 4.12
2598 2716 1.507141 CTTGTGTCGAGGCACCCAAC 61.507 60.000 5.32 0.00 38.52 3.77
2599 2717 3.041940 GTGTCGAGGCACCCAACG 61.042 66.667 0.00 0.00 33.53 4.10
2600 2718 4.980805 TGTCGAGGCACCCAACGC 62.981 66.667 0.00 0.00 0.00 4.84
2620 2738 3.138128 GGCCGCGCCCTAATTTGT 61.138 61.111 0.00 0.00 44.06 2.83
2621 2739 2.706834 GGCCGCGCCCTAATTTGTT 61.707 57.895 0.00 0.00 44.06 2.83
2622 2740 1.226575 GCCGCGCCCTAATTTGTTC 60.227 57.895 0.00 0.00 0.00 3.18
2623 2741 1.061887 CCGCGCCCTAATTTGTTCG 59.938 57.895 0.00 0.00 0.00 3.95
2624 2742 1.641123 CCGCGCCCTAATTTGTTCGT 61.641 55.000 0.00 0.00 0.00 3.85
2625 2743 0.520412 CGCGCCCTAATTTGTTCGTG 60.520 55.000 0.00 0.00 0.00 4.35
2626 2744 0.796870 GCGCCCTAATTTGTTCGTGC 60.797 55.000 0.00 0.00 0.00 5.34
2627 2745 0.520412 CGCCCTAATTTGTTCGTGCG 60.520 55.000 0.00 0.00 34.52 5.34
2628 2746 0.179174 GCCCTAATTTGTTCGTGCGG 60.179 55.000 0.00 0.00 0.00 5.69
2629 2747 0.450184 CCCTAATTTGTTCGTGCGGG 59.550 55.000 0.00 0.00 0.00 6.13
2630 2748 1.444836 CCTAATTTGTTCGTGCGGGA 58.555 50.000 0.00 0.00 0.00 5.14
2631 2749 1.129811 CCTAATTTGTTCGTGCGGGAC 59.870 52.381 0.00 0.00 0.00 4.46
2632 2750 1.801771 CTAATTTGTTCGTGCGGGACA 59.198 47.619 0.00 0.00 0.00 4.02
2633 2751 1.243902 AATTTGTTCGTGCGGGACAT 58.756 45.000 0.00 0.00 0.00 3.06
2634 2752 2.102070 ATTTGTTCGTGCGGGACATA 57.898 45.000 0.00 0.75 0.00 2.29
2635 2753 1.880271 TTTGTTCGTGCGGGACATAA 58.120 45.000 0.00 0.00 0.00 1.90
2636 2754 1.880271 TTGTTCGTGCGGGACATAAA 58.120 45.000 0.00 0.00 0.00 1.40
2637 2755 1.880271 TGTTCGTGCGGGACATAAAA 58.120 45.000 0.00 0.00 0.00 1.52
2638 2756 2.219458 TGTTCGTGCGGGACATAAAAA 58.781 42.857 0.00 0.00 0.00 1.94
2656 2774 3.810310 AAAAACCGACAAAAGGCATGA 57.190 38.095 0.00 0.00 0.00 3.07
2657 2775 3.810310 AAAACCGACAAAAGGCATGAA 57.190 38.095 0.00 0.00 0.00 2.57
2658 2776 3.810310 AAACCGACAAAAGGCATGAAA 57.190 38.095 0.00 0.00 0.00 2.69
2659 2777 3.810310 AACCGACAAAAGGCATGAAAA 57.190 38.095 0.00 0.00 0.00 2.29
2660 2778 3.810310 ACCGACAAAAGGCATGAAAAA 57.190 38.095 0.00 0.00 0.00 1.94
2722 2840 8.974060 AAATATAATTACAAGTCCACCATCGT 57.026 30.769 0.00 0.00 0.00 3.73
2723 2841 8.603242 AATATAATTACAAGTCCACCATCGTC 57.397 34.615 0.00 0.00 0.00 4.20
2724 2842 3.973206 ATTACAAGTCCACCATCGTCA 57.027 42.857 0.00 0.00 0.00 4.35
2725 2843 2.736144 TACAAGTCCACCATCGTCAC 57.264 50.000 0.00 0.00 0.00 3.67
2726 2844 0.319555 ACAAGTCCACCATCGTCACG 60.320 55.000 0.00 0.00 0.00 4.35
2727 2845 1.014044 CAAGTCCACCATCGTCACGG 61.014 60.000 0.00 0.00 0.00 4.94
2728 2846 2.781595 AAGTCCACCATCGTCACGGC 62.782 60.000 0.00 0.00 0.00 5.68
2729 2847 4.077184 TCCACCATCGTCACGGCC 62.077 66.667 0.00 0.00 0.00 6.13
2730 2848 4.386951 CCACCATCGTCACGGCCA 62.387 66.667 2.24 0.00 0.00 5.36
2731 2849 2.358125 CACCATCGTCACGGCCAA 60.358 61.111 2.24 0.00 0.00 4.52
2732 2850 1.745115 CACCATCGTCACGGCCAAT 60.745 57.895 2.24 0.00 0.00 3.16
2733 2851 1.745115 ACCATCGTCACGGCCAATG 60.745 57.895 2.24 0.00 0.00 2.82
2734 2852 1.745115 CCATCGTCACGGCCAATGT 60.745 57.895 2.24 0.00 0.00 2.71
2735 2853 0.461163 CCATCGTCACGGCCAATGTA 60.461 55.000 2.24 0.00 0.00 2.29
2736 2854 0.930310 CATCGTCACGGCCAATGTAG 59.070 55.000 2.24 0.00 0.00 2.74
2737 2855 0.821517 ATCGTCACGGCCAATGTAGA 59.178 50.000 2.24 5.20 0.00 2.59
2738 2856 0.172578 TCGTCACGGCCAATGTAGAG 59.827 55.000 2.24 0.00 0.00 2.43
2739 2857 0.108804 CGTCACGGCCAATGTAGAGT 60.109 55.000 2.24 0.00 0.00 3.24
2740 2858 1.133598 CGTCACGGCCAATGTAGAGTA 59.866 52.381 2.24 0.00 0.00 2.59
2741 2859 2.537401 GTCACGGCCAATGTAGAGTAC 58.463 52.381 2.24 0.00 0.00 2.73
2742 2860 2.165845 GTCACGGCCAATGTAGAGTACT 59.834 50.000 2.24 0.00 0.00 2.73
2743 2861 2.829720 TCACGGCCAATGTAGAGTACTT 59.170 45.455 2.24 0.00 0.00 2.24
2744 2862 4.018490 TCACGGCCAATGTAGAGTACTTA 58.982 43.478 2.24 0.00 0.00 2.24
2745 2863 4.463539 TCACGGCCAATGTAGAGTACTTAA 59.536 41.667 2.24 0.00 0.00 1.85
2746 2864 4.804139 CACGGCCAATGTAGAGTACTTAAG 59.196 45.833 2.24 0.00 0.00 1.85
2747 2865 4.708421 ACGGCCAATGTAGAGTACTTAAGA 59.292 41.667 10.09 0.00 0.00 2.10
2748 2866 5.363005 ACGGCCAATGTAGAGTACTTAAGAT 59.637 40.000 10.09 0.00 0.00 2.40
2749 2867 6.548622 ACGGCCAATGTAGAGTACTTAAGATA 59.451 38.462 10.09 0.00 0.00 1.98
2750 2868 7.069085 ACGGCCAATGTAGAGTACTTAAGATAA 59.931 37.037 10.09 0.00 0.00 1.75
2751 2869 7.924412 CGGCCAATGTAGAGTACTTAAGATAAA 59.076 37.037 10.09 0.00 0.00 1.40
2752 2870 9.609346 GGCCAATGTAGAGTACTTAAGATAAAA 57.391 33.333 10.09 0.00 0.00 1.52
2781 2899 5.607119 AACTTATAAAGATAATGCGGCCG 57.393 39.130 24.05 24.05 0.00 6.13
2782 2900 3.435671 ACTTATAAAGATAATGCGGCCGC 59.564 43.478 42.35 42.35 42.35 6.53
2783 2901 1.165270 ATAAAGATAATGCGGCCGCC 58.835 50.000 44.42 29.47 41.09 6.13
2784 2902 0.887387 TAAAGATAATGCGGCCGCCC 60.887 55.000 44.42 27.23 41.09 6.13
2785 2903 4.643387 AGATAATGCGGCCGCCCC 62.643 66.667 44.42 27.57 41.09 5.80
2830 2948 4.680237 CGTCTTCAGGCGCCACCA 62.680 66.667 31.54 8.82 43.14 4.17
2831 2949 2.281484 GTCTTCAGGCGCCACCAA 60.281 61.111 31.54 16.59 43.14 3.67
2832 2950 2.281484 TCTTCAGGCGCCACCAAC 60.281 61.111 31.54 0.00 43.14 3.77
2833 2951 3.365265 CTTCAGGCGCCACCAACC 61.365 66.667 31.54 0.00 43.14 3.77
2834 2952 3.850098 CTTCAGGCGCCACCAACCT 62.850 63.158 31.54 1.71 43.14 3.50
2835 2953 3.842925 TTCAGGCGCCACCAACCTC 62.843 63.158 31.54 0.00 43.14 3.85
2840 2958 4.657824 CGCCACCAACCTCGTCGT 62.658 66.667 0.00 0.00 0.00 4.34
2841 2959 2.652530 GCCACCAACCTCGTCGTA 59.347 61.111 0.00 0.00 0.00 3.43
2842 2960 1.445582 GCCACCAACCTCGTCGTAG 60.446 63.158 0.00 0.00 0.00 3.51
2843 2961 1.445582 CCACCAACCTCGTCGTAGC 60.446 63.158 0.00 0.00 0.00 3.58
2844 2962 1.585006 CACCAACCTCGTCGTAGCT 59.415 57.895 0.00 0.00 0.00 3.32
2845 2963 0.038526 CACCAACCTCGTCGTAGCTT 60.039 55.000 0.00 0.00 0.00 3.74
2846 2964 0.038526 ACCAACCTCGTCGTAGCTTG 60.039 55.000 0.00 0.00 0.00 4.01
2847 2965 0.038526 CCAACCTCGTCGTAGCTTGT 60.039 55.000 0.00 0.00 0.00 3.16
2848 2966 1.337821 CAACCTCGTCGTAGCTTGTC 58.662 55.000 0.00 0.00 0.00 3.18
2849 2967 0.956633 AACCTCGTCGTAGCTTGTCA 59.043 50.000 0.00 0.00 0.00 3.58
2850 2968 0.522180 ACCTCGTCGTAGCTTGTCAG 59.478 55.000 0.00 0.00 0.00 3.51
2851 2969 0.179161 CCTCGTCGTAGCTTGTCAGG 60.179 60.000 0.00 0.00 0.00 3.86
2852 2970 0.522180 CTCGTCGTAGCTTGTCAGGT 59.478 55.000 0.00 0.00 34.24 4.00
2853 2971 0.520404 TCGTCGTAGCTTGTCAGGTC 59.480 55.000 0.00 0.00 31.45 3.85
2854 2972 0.793478 CGTCGTAGCTTGTCAGGTCG 60.793 60.000 0.00 0.00 31.45 4.79
2855 2973 0.520404 GTCGTAGCTTGTCAGGTCGA 59.480 55.000 0.00 0.00 31.81 4.20
2856 2974 1.132643 GTCGTAGCTTGTCAGGTCGAT 59.867 52.381 0.00 0.00 34.70 3.59
2857 2975 1.132453 TCGTAGCTTGTCAGGTCGATG 59.868 52.381 0.00 0.00 30.36 3.84
2858 2976 1.135373 CGTAGCTTGTCAGGTCGATGT 60.135 52.381 0.00 0.00 31.45 3.06
2859 2977 2.096980 CGTAGCTTGTCAGGTCGATGTA 59.903 50.000 0.00 0.00 31.45 2.29
2860 2978 2.656560 AGCTTGTCAGGTCGATGTAC 57.343 50.000 0.00 0.00 0.00 2.90
2861 2979 1.135373 AGCTTGTCAGGTCGATGTACG 60.135 52.381 0.00 0.00 44.09 3.67
2862 2980 1.909376 CTTGTCAGGTCGATGTACGG 58.091 55.000 0.00 0.00 42.82 4.02
2863 2981 1.201647 CTTGTCAGGTCGATGTACGGT 59.798 52.381 0.00 0.00 42.82 4.83
2864 2982 0.524414 TGTCAGGTCGATGTACGGTG 59.476 55.000 0.00 0.00 42.82 4.94
2865 2983 0.179145 GTCAGGTCGATGTACGGTGG 60.179 60.000 0.00 0.00 42.82 4.61
2866 2984 1.141019 CAGGTCGATGTACGGTGGG 59.859 63.158 0.00 0.00 42.82 4.61
2867 2985 2.056223 AGGTCGATGTACGGTGGGG 61.056 63.158 0.00 0.00 42.82 4.96
2868 2986 2.497770 GTCGATGTACGGTGGGGG 59.502 66.667 0.00 0.00 42.82 5.40
2869 2987 3.463585 TCGATGTACGGTGGGGGC 61.464 66.667 0.00 0.00 42.82 5.80
2870 2988 4.884257 CGATGTACGGTGGGGGCG 62.884 72.222 0.00 0.00 38.46 6.13
2871 2989 3.777910 GATGTACGGTGGGGGCGT 61.778 66.667 0.00 0.00 0.00 5.68
2872 2990 3.728279 GATGTACGGTGGGGGCGTC 62.728 68.421 0.00 0.00 0.00 5.19
2883 3001 4.382320 GGGCGTCGGGCAACAGTA 62.382 66.667 0.00 0.00 46.16 2.74
2884 3002 3.116531 GGCGTCGGGCAACAGTAC 61.117 66.667 0.00 0.00 46.16 2.73
2885 3003 3.475774 GCGTCGGGCAACAGTACG 61.476 66.667 0.00 0.00 42.87 3.67
2886 3004 2.807895 CGTCGGGCAACAGTACGG 60.808 66.667 0.00 0.00 34.02 4.02
2887 3005 2.433664 GTCGGGCAACAGTACGGG 60.434 66.667 0.00 0.00 39.74 5.28
2888 3006 4.382320 TCGGGCAACAGTACGGGC 62.382 66.667 0.00 0.00 39.74 6.13
2946 3064 4.248842 CGGTGTGGCTGGTGGTGA 62.249 66.667 0.00 0.00 0.00 4.02
2947 3065 2.594592 GGTGTGGCTGGTGGTGAC 60.595 66.667 0.00 0.00 0.00 3.67
2948 3066 2.594592 GTGTGGCTGGTGGTGACC 60.595 66.667 0.00 0.00 43.48 4.02
2970 3088 3.055719 CGCCCATGCACGTTCCTT 61.056 61.111 0.00 0.00 37.32 3.36
2971 3089 2.877691 GCCCATGCACGTTCCTTC 59.122 61.111 0.00 0.00 37.47 3.46
2972 3090 3.039202 GCCCATGCACGTTCCTTCG 62.039 63.158 0.00 0.00 37.47 3.79
2973 3091 1.671054 CCCATGCACGTTCCTTCGT 60.671 57.895 0.00 0.00 45.10 3.85
2980 3098 1.664306 ACGTTCCTTCGTGGACTCC 59.336 57.895 0.00 0.00 46.14 3.85
2981 3099 0.826672 ACGTTCCTTCGTGGACTCCT 60.827 55.000 0.00 0.00 46.14 3.69
2982 3100 0.109226 CGTTCCTTCGTGGACTCCTC 60.109 60.000 0.00 0.00 46.14 3.71
2983 3101 0.246910 GTTCCTTCGTGGACTCCTCC 59.753 60.000 0.00 0.00 46.14 4.30
2984 3102 0.114560 TTCCTTCGTGGACTCCTCCT 59.885 55.000 0.00 0.00 46.14 3.69
2985 3103 0.114560 TCCTTCGTGGACTCCTCCTT 59.885 55.000 0.00 0.00 40.56 3.36
2986 3104 0.247736 CCTTCGTGGACTCCTCCTTG 59.752 60.000 0.00 0.00 37.48 3.61
2987 3105 1.257743 CTTCGTGGACTCCTCCTTGA 58.742 55.000 0.00 0.00 37.48 3.02
2988 3106 0.966920 TTCGTGGACTCCTCCTTGAC 59.033 55.000 0.00 0.00 37.48 3.18
2989 3107 0.898789 TCGTGGACTCCTCCTTGACC 60.899 60.000 0.00 0.00 37.48 4.02
2990 3108 0.900647 CGTGGACTCCTCCTTGACCT 60.901 60.000 0.00 0.00 37.48 3.85
2991 3109 0.899019 GTGGACTCCTCCTTGACCTC 59.101 60.000 0.00 0.00 37.48 3.85
2992 3110 0.252284 TGGACTCCTCCTTGACCTCC 60.252 60.000 0.00 0.00 37.48 4.30
2993 3111 0.041982 GGACTCCTCCTTGACCTCCT 59.958 60.000 0.00 0.00 33.07 3.69
2994 3112 1.190643 GACTCCTCCTTGACCTCCTG 58.809 60.000 0.00 0.00 0.00 3.86
2995 3113 0.907230 ACTCCTCCTTGACCTCCTGC 60.907 60.000 0.00 0.00 0.00 4.85
2996 3114 0.906756 CTCCTCCTTGACCTCCTGCA 60.907 60.000 0.00 0.00 0.00 4.41
2997 3115 1.194781 TCCTCCTTGACCTCCTGCAC 61.195 60.000 0.00 0.00 0.00 4.57
2998 3116 1.079543 CTCCTTGACCTCCTGCACG 60.080 63.158 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 44 9.305110 GCGAACAAAATTTGATAAAAGAACATG 57.695 29.630 13.19 0.00 0.00 3.21
104 107 9.039165 ACATGAACCATTCTTTAAATCCTGAAT 57.961 29.630 0.00 0.00 0.00 2.57
152 155 8.225603 TCAATCAAGGAGATTTTAAGGTATGC 57.774 34.615 0.00 0.00 44.48 3.14
205 210 1.153823 CACCGTACGCCAGAGAAGG 60.154 63.158 10.49 0.00 0.00 3.46
221 226 8.352942 AGGAATTTAAGAGTTTTGTCATGTCAC 58.647 33.333 0.00 0.00 0.00 3.67
226 231 8.391075 TCGAAGGAATTTAAGAGTTTTGTCAT 57.609 30.769 0.00 0.00 0.00 3.06
228 233 8.504005 TGATCGAAGGAATTTAAGAGTTTTGTC 58.496 33.333 0.00 0.00 0.00 3.18
272 277 3.410631 TCTCAATTTCGCCAGGTGTAA 57.589 42.857 0.00 0.00 0.00 2.41
273 278 3.334691 CTTCTCAATTTCGCCAGGTGTA 58.665 45.455 0.00 0.00 0.00 2.90
287 304 8.188139 ACGAAAAAGAAACATTTAGCTTCTCAA 58.812 29.630 0.00 0.00 31.63 3.02
288 305 7.643764 CACGAAAAAGAAACATTTAGCTTCTCA 59.356 33.333 0.00 0.00 31.63 3.27
304 321 5.508200 AAACCTTATGTGCACGAAAAAGA 57.492 34.783 13.13 0.00 0.00 2.52
426 449 3.649843 TCGAACTAATCCATACCCCACT 58.350 45.455 0.00 0.00 0.00 4.00
450 473 3.258372 TGGCACCACACACTTGTTTAAAA 59.742 39.130 0.00 0.00 31.66 1.52
506 529 4.648651 ACCATTAACTCTACCGCAAAGTT 58.351 39.130 0.00 0.00 37.10 2.66
631 656 3.163594 CTGCACGCATGTTTACTTTAGC 58.836 45.455 0.00 0.00 0.00 3.09
633 658 2.550180 TGCTGCACGCATGTTTACTTTA 59.450 40.909 0.00 0.00 45.47 1.85
695 722 4.093998 GTCACGTTCTCCATTCTAGTCGTA 59.906 45.833 0.00 0.00 0.00 3.43
712 739 2.273557 ACGTAAGCAAGTTTGTCACGT 58.726 42.857 11.85 11.85 45.62 4.49
959 1016 2.693591 TGTATGGTTGATCTCGGGAGAC 59.306 50.000 0.00 0.00 40.75 3.36
974 1031 1.227342 TGTGCGCAGTGTGTGTATGG 61.227 55.000 12.22 0.00 0.00 2.74
996 1053 0.395724 GGGGGCTTTCGTCCATGAAT 60.396 55.000 0.00 0.00 36.31 2.57
1074 1131 0.512518 TGATGCAAGAAGAACGCACG 59.487 50.000 0.00 0.00 38.73 5.34
1153 1210 1.530655 CTTGGTGGGGGTTGGTGTC 60.531 63.158 0.00 0.00 0.00 3.67
1376 1442 3.701604 GACCTAGAGCGTGCACCCG 62.702 68.421 12.15 0.97 0.00 5.28
1417 1483 1.179814 AGACGCCGACAAGAGGAGTT 61.180 55.000 0.00 0.00 41.79 3.01
1464 1530 0.966179 TGGACGAAGAGCAGCTGTAA 59.034 50.000 16.64 0.00 0.00 2.41
1485 1551 3.521220 CTTTCGTCGTCGGTCGCG 61.521 66.667 0.00 0.00 39.67 5.87
1565 1631 2.289547 CTGTTGGTGTGGTAAAACTCGG 59.710 50.000 0.00 0.00 0.00 4.63
1588 1654 0.750911 CTCTTCCTGGAGGCATTGGC 60.751 60.000 1.17 1.17 40.13 4.52
1589 1655 0.750911 GCTCTTCCTGGAGGCATTGG 60.751 60.000 0.04 0.00 34.21 3.16
1680 1746 2.670592 GCCAAGTTAACCCGCGGT 60.671 61.111 26.12 9.29 37.65 5.68
1709 1775 0.102844 TTTGCTGTTCTTGCACTGGC 59.897 50.000 0.00 0.00 40.40 4.85
1713 1779 3.549625 CCTCTCTTTTGCTGTTCTTGCAC 60.550 47.826 0.00 0.00 40.40 4.57
1731 1797 1.068753 CGCATTCGCATCCTCCTCT 59.931 57.895 0.00 0.00 38.40 3.69
1762 1828 1.375523 CCCCGGTTTCTTCCACGAG 60.376 63.158 0.00 0.00 0.00 4.18
1821 1887 0.681887 TCCGGAAGTCTGCGTATGGA 60.682 55.000 0.00 0.00 34.01 3.41
1869 1935 4.201679 CCCACGCTGGCGATACGA 62.202 66.667 21.77 0.00 42.83 3.43
2077 2143 2.681344 GGACGAACTGAAAACCACAACT 59.319 45.455 0.00 0.00 0.00 3.16
2098 2165 7.706607 TGTACATACATCTGCAAACTAAGCTAG 59.293 37.037 0.00 0.00 0.00 3.42
2106 2174 4.498009 GGGCATGTACATACATCTGCAAAC 60.498 45.833 16.37 4.98 44.57 2.93
2130 2213 4.895224 TTCTGCATGAGAATTCTGCATC 57.105 40.909 14.00 10.18 44.25 3.91
2158 2241 3.558411 GACAGGCACGAGCGATGC 61.558 66.667 8.25 3.08 43.41 3.91
2188 2306 7.855375 TCATCATAGAACTCCAAGACTCAAAT 58.145 34.615 0.00 0.00 0.00 2.32
2240 2358 3.609175 GCATCAAACATACAACGCTGTGT 60.609 43.478 0.71 0.00 36.96 3.72
2241 2359 2.910482 GCATCAAACATACAACGCTGTG 59.090 45.455 0.71 0.00 36.96 3.66
2276 2394 1.210155 GCACGCATGTCTTTGGACC 59.790 57.895 0.00 0.00 41.47 4.46
2340 2458 5.529430 TGATTTGAAACACATAGAACGTGGT 59.471 36.000 0.00 0.00 38.74 4.16
2399 2517 2.447244 AGTAGTTGTCAGCACTCAGC 57.553 50.000 0.00 0.00 46.19 4.26
2400 2518 5.105957 ACATCTAGTAGTTGTCAGCACTCAG 60.106 44.000 7.88 0.00 0.00 3.35
2401 2519 4.767409 ACATCTAGTAGTTGTCAGCACTCA 59.233 41.667 7.88 0.00 0.00 3.41
2402 2520 5.317733 ACATCTAGTAGTTGTCAGCACTC 57.682 43.478 7.88 0.00 0.00 3.51
2403 2521 4.158764 GGACATCTAGTAGTTGTCAGCACT 59.841 45.833 29.53 4.87 43.34 4.40
2404 2522 4.425520 GGACATCTAGTAGTTGTCAGCAC 58.574 47.826 29.53 16.32 43.34 4.40
2443 2561 2.540769 CGCACTTGTTGGTACTTGTTGG 60.541 50.000 0.00 0.00 0.00 3.77
2465 2583 0.826715 TGGCCTTACTGCTCAGCTAG 59.173 55.000 3.32 0.00 0.00 3.42
2474 2592 1.068474 CGTTCGAGTTGGCCTTACTG 58.932 55.000 14.68 8.20 0.00 2.74
2481 2599 4.430423 CTGCGCGTTCGAGTTGGC 62.430 66.667 8.43 0.00 38.10 4.52
2482 2600 3.000080 GACTGCGCGTTCGAGTTGG 62.000 63.158 8.43 0.00 38.10 3.77
2483 2601 2.465920 GACTGCGCGTTCGAGTTG 59.534 61.111 8.43 0.00 38.10 3.16
2484 2602 2.733593 GGACTGCGCGTTCGAGTT 60.734 61.111 8.43 0.00 38.10 3.01
2485 2603 4.719369 GGGACTGCGCGTTCGAGT 62.719 66.667 8.43 4.87 38.10 4.18
2486 2604 4.717629 TGGGACTGCGCGTTCGAG 62.718 66.667 8.43 1.22 38.10 4.04
2487 2605 3.793775 TTTGGGACTGCGCGTTCGA 62.794 57.895 8.43 0.00 38.10 3.71
2488 2606 3.342627 TTTGGGACTGCGCGTTCG 61.343 61.111 8.43 0.00 39.07 3.95
2489 2607 2.251371 GTTTGGGACTGCGCGTTC 59.749 61.111 8.43 2.11 0.00 3.95
2490 2608 3.645975 CGTTTGGGACTGCGCGTT 61.646 61.111 8.43 0.00 0.00 4.84
2499 2617 2.226330 CAAACAGATGTCCGTTTGGGA 58.774 47.619 12.02 0.00 45.23 4.37
2500 2618 2.704725 CAAACAGATGTCCGTTTGGG 57.295 50.000 12.02 0.00 45.23 4.12
2503 2621 2.742053 CGGATCAAACAGATGTCCGTTT 59.258 45.455 4.09 0.00 38.58 3.60
2504 2622 2.346803 CGGATCAAACAGATGTCCGTT 58.653 47.619 4.09 0.00 38.58 4.44
2505 2623 1.405526 CCGGATCAAACAGATGTCCGT 60.406 52.381 0.00 0.00 40.61 4.69
2506 2624 1.134818 TCCGGATCAAACAGATGTCCG 60.135 52.381 0.00 5.21 41.41 4.79
2507 2625 2.691409 TCCGGATCAAACAGATGTCC 57.309 50.000 0.00 0.00 37.00 4.02
2508 2626 4.731773 GCAAATCCGGATCAAACAGATGTC 60.732 45.833 19.43 1.19 37.00 3.06
2509 2627 3.129287 GCAAATCCGGATCAAACAGATGT 59.871 43.478 19.43 0.00 37.00 3.06
2510 2628 3.379372 AGCAAATCCGGATCAAACAGATG 59.621 43.478 19.43 8.02 37.00 2.90
2511 2629 3.624777 AGCAAATCCGGATCAAACAGAT 58.375 40.909 19.43 0.00 40.48 2.90
2512 2630 3.009723 GAGCAAATCCGGATCAAACAGA 58.990 45.455 19.43 0.00 0.00 3.41
2513 2631 2.098117 GGAGCAAATCCGGATCAAACAG 59.902 50.000 19.43 5.46 38.67 3.16
2514 2632 2.091541 GGAGCAAATCCGGATCAAACA 58.908 47.619 19.43 0.00 38.67 2.83
2515 2633 2.851805 GGAGCAAATCCGGATCAAAC 57.148 50.000 19.43 7.99 38.67 2.93
2533 2651 4.106341 AGTCCTTTTACCCATCCCATATGG 59.894 45.833 15.41 15.41 38.88 2.74
2534 2652 5.324832 AGTCCTTTTACCCATCCCATATG 57.675 43.478 0.00 0.00 0.00 1.78
2535 2653 5.162980 GGAAGTCCTTTTACCCATCCCATAT 60.163 44.000 0.00 0.00 0.00 1.78
2536 2654 4.167307 GGAAGTCCTTTTACCCATCCCATA 59.833 45.833 0.00 0.00 0.00 2.74
2537 2655 3.052869 GGAAGTCCTTTTACCCATCCCAT 60.053 47.826 0.00 0.00 0.00 4.00
2538 2656 2.310647 GGAAGTCCTTTTACCCATCCCA 59.689 50.000 0.00 0.00 0.00 4.37
2539 2657 2.310647 TGGAAGTCCTTTTACCCATCCC 59.689 50.000 0.00 0.00 36.82 3.85
2540 2658 3.732048 TGGAAGTCCTTTTACCCATCC 57.268 47.619 0.00 0.00 36.82 3.51
2541 2659 4.600062 ACATGGAAGTCCTTTTACCCATC 58.400 43.478 0.00 0.00 36.82 3.51
2542 2660 4.600062 GACATGGAAGTCCTTTTACCCAT 58.400 43.478 0.00 0.00 36.82 4.00
2543 2661 4.028993 GACATGGAAGTCCTTTTACCCA 57.971 45.455 0.00 0.00 36.82 4.51
2553 2671 2.076863 CTCAAACCGGACATGGAAGTC 58.923 52.381 9.46 0.00 37.80 3.01
2554 2672 1.882352 GCTCAAACCGGACATGGAAGT 60.882 52.381 9.46 0.00 0.00 3.01
2555 2673 0.804989 GCTCAAACCGGACATGGAAG 59.195 55.000 9.46 0.00 0.00 3.46
2556 2674 0.608035 GGCTCAAACCGGACATGGAA 60.608 55.000 9.46 0.00 0.00 3.53
2557 2675 1.002624 GGCTCAAACCGGACATGGA 60.003 57.895 9.46 0.00 0.00 3.41
2558 2676 3.590824 GGCTCAAACCGGACATGG 58.409 61.111 9.46 0.00 0.00 3.66
2566 2684 2.597510 ACAAGGCCGGCTCAAACC 60.598 61.111 28.56 8.41 0.00 3.27
2567 2685 2.130073 GACACAAGGCCGGCTCAAAC 62.130 60.000 28.56 9.28 0.00 2.93
2568 2686 1.896660 GACACAAGGCCGGCTCAAA 60.897 57.895 28.56 0.00 0.00 2.69
2569 2687 2.281484 GACACAAGGCCGGCTCAA 60.281 61.111 28.56 0.00 0.00 3.02
2570 2688 4.680237 CGACACAAGGCCGGCTCA 62.680 66.667 28.56 0.00 0.00 4.26
2571 2689 4.373116 TCGACACAAGGCCGGCTC 62.373 66.667 28.56 16.85 0.00 4.70
2572 2690 4.379243 CTCGACACAAGGCCGGCT 62.379 66.667 28.56 9.77 0.00 5.52
2578 2696 2.358737 GGGTGCCTCGACACAAGG 60.359 66.667 8.27 0.00 42.55 3.61
2579 2697 1.227823 TTGGGTGCCTCGACACAAG 60.228 57.895 8.27 0.00 42.55 3.16
2580 2698 1.525077 GTTGGGTGCCTCGACACAA 60.525 57.895 8.27 0.00 42.55 3.33
2581 2699 2.110213 GTTGGGTGCCTCGACACA 59.890 61.111 8.27 0.00 42.55 3.72
2582 2700 3.041940 CGTTGGGTGCCTCGACAC 61.042 66.667 0.00 0.00 39.94 3.67
2583 2701 4.980805 GCGTTGGGTGCCTCGACA 62.981 66.667 0.00 0.00 0.00 4.35
2604 2722 1.226575 GAACAAATTAGGGCGCGGC 60.227 57.895 26.39 26.39 0.00 6.53
2605 2723 1.061887 CGAACAAATTAGGGCGCGG 59.938 57.895 8.83 0.00 0.00 6.46
2606 2724 0.520412 CACGAACAAATTAGGGCGCG 60.520 55.000 0.00 0.00 0.00 6.86
2607 2725 0.796870 GCACGAACAAATTAGGGCGC 60.797 55.000 0.00 0.00 29.71 6.53
2608 2726 3.306206 GCACGAACAAATTAGGGCG 57.694 52.632 0.00 0.00 29.71 6.13
2609 2727 0.179174 CCGCACGAACAAATTAGGGC 60.179 55.000 0.00 0.00 36.56 5.19
2610 2728 0.450184 CCCGCACGAACAAATTAGGG 59.550 55.000 0.00 0.00 0.00 3.53
2611 2729 1.129811 GTCCCGCACGAACAAATTAGG 59.870 52.381 0.00 0.00 0.00 2.69
2612 2730 1.801771 TGTCCCGCACGAACAAATTAG 59.198 47.619 0.00 0.00 0.00 1.73
2613 2731 1.880271 TGTCCCGCACGAACAAATTA 58.120 45.000 0.00 0.00 0.00 1.40
2614 2732 1.243902 ATGTCCCGCACGAACAAATT 58.756 45.000 0.00 0.00 0.00 1.82
2615 2733 2.102070 TATGTCCCGCACGAACAAAT 57.898 45.000 0.00 0.00 0.00 2.32
2616 2734 1.880271 TTATGTCCCGCACGAACAAA 58.120 45.000 0.00 0.00 0.00 2.83
2617 2735 1.880271 TTTATGTCCCGCACGAACAA 58.120 45.000 0.00 0.00 0.00 2.83
2618 2736 1.880271 TTTTATGTCCCGCACGAACA 58.120 45.000 0.00 0.00 0.00 3.18
2619 2737 2.973419 TTTTTATGTCCCGCACGAAC 57.027 45.000 0.00 0.00 0.00 3.95
2636 2754 3.810310 TCATGCCTTTTGTCGGTTTTT 57.190 38.095 0.00 0.00 0.00 1.94
2637 2755 3.810310 TTCATGCCTTTTGTCGGTTTT 57.190 38.095 0.00 0.00 0.00 2.43
2638 2756 3.810310 TTTCATGCCTTTTGTCGGTTT 57.190 38.095 0.00 0.00 0.00 3.27
2639 2757 3.810310 TTTTCATGCCTTTTGTCGGTT 57.190 38.095 0.00 0.00 0.00 4.44
2640 2758 3.810310 TTTTTCATGCCTTTTGTCGGT 57.190 38.095 0.00 0.00 0.00 4.69
2696 2814 9.403583 ACGATGGTGGACTTGTAATTATATTTT 57.596 29.630 0.00 0.00 0.00 1.82
2697 2815 8.974060 ACGATGGTGGACTTGTAATTATATTT 57.026 30.769 0.00 0.00 0.00 1.40
2698 2816 8.208224 TGACGATGGTGGACTTGTAATTATATT 58.792 33.333 0.00 0.00 0.00 1.28
2699 2817 7.656137 GTGACGATGGTGGACTTGTAATTATAT 59.344 37.037 0.00 0.00 0.00 0.86
2700 2818 6.982141 GTGACGATGGTGGACTTGTAATTATA 59.018 38.462 0.00 0.00 0.00 0.98
2701 2819 5.815740 GTGACGATGGTGGACTTGTAATTAT 59.184 40.000 0.00 0.00 0.00 1.28
2702 2820 5.172934 GTGACGATGGTGGACTTGTAATTA 58.827 41.667 0.00 0.00 0.00 1.40
2703 2821 4.000988 GTGACGATGGTGGACTTGTAATT 58.999 43.478 0.00 0.00 0.00 1.40
2704 2822 3.596214 GTGACGATGGTGGACTTGTAAT 58.404 45.455 0.00 0.00 0.00 1.89
2705 2823 2.608506 CGTGACGATGGTGGACTTGTAA 60.609 50.000 0.00 0.00 0.00 2.41
2706 2824 1.068125 CGTGACGATGGTGGACTTGTA 60.068 52.381 0.00 0.00 0.00 2.41
2707 2825 0.319555 CGTGACGATGGTGGACTTGT 60.320 55.000 0.00 0.00 0.00 3.16
2708 2826 1.014044 CCGTGACGATGGTGGACTTG 61.014 60.000 6.54 0.00 0.00 3.16
2709 2827 1.292223 CCGTGACGATGGTGGACTT 59.708 57.895 6.54 0.00 0.00 3.01
2710 2828 2.970639 CCGTGACGATGGTGGACT 59.029 61.111 6.54 0.00 0.00 3.85
2711 2829 2.813908 GCCGTGACGATGGTGGAC 60.814 66.667 6.54 0.00 0.00 4.02
2712 2830 4.077184 GGCCGTGACGATGGTGGA 62.077 66.667 6.54 0.00 0.00 4.02
2713 2831 3.892740 TTGGCCGTGACGATGGTGG 62.893 63.158 6.54 0.00 0.00 4.61
2714 2832 1.745115 ATTGGCCGTGACGATGGTG 60.745 57.895 6.54 0.00 0.00 4.17
2715 2833 1.745115 CATTGGCCGTGACGATGGT 60.745 57.895 6.54 0.00 29.10 3.55
2716 2834 0.461163 TACATTGGCCGTGACGATGG 60.461 55.000 6.54 0.00 36.79 3.51
2717 2835 0.930310 CTACATTGGCCGTGACGATG 59.070 55.000 6.54 4.56 38.37 3.84
2718 2836 0.821517 TCTACATTGGCCGTGACGAT 59.178 50.000 6.54 0.00 0.00 3.73
2719 2837 0.172578 CTCTACATTGGCCGTGACGA 59.827 55.000 6.54 8.70 0.00 4.20
2720 2838 0.108804 ACTCTACATTGGCCGTGACG 60.109 55.000 14.26 0.00 0.00 4.35
2721 2839 2.165845 AGTACTCTACATTGGCCGTGAC 59.834 50.000 14.26 1.81 0.00 3.67
2722 2840 2.453521 AGTACTCTACATTGGCCGTGA 58.546 47.619 14.26 0.00 0.00 4.35
2723 2841 2.961526 AGTACTCTACATTGGCCGTG 57.038 50.000 0.00 1.64 0.00 4.94
2724 2842 4.708421 TCTTAAGTACTCTACATTGGCCGT 59.292 41.667 1.63 0.00 0.00 5.68
2725 2843 5.258456 TCTTAAGTACTCTACATTGGCCG 57.742 43.478 1.63 0.00 0.00 6.13
2726 2844 9.609346 TTTTATCTTAAGTACTCTACATTGGCC 57.391 33.333 0.00 0.00 0.00 5.36
2756 2874 6.915843 CGGCCGCATTATCTTTATAAGTTTTT 59.084 34.615 14.67 0.00 31.18 1.94
2757 2875 6.435428 CGGCCGCATTATCTTTATAAGTTTT 58.565 36.000 14.67 0.00 31.18 2.43
2758 2876 5.562113 GCGGCCGCATTATCTTTATAAGTTT 60.562 40.000 43.55 0.00 41.49 2.66
2759 2877 4.083484 GCGGCCGCATTATCTTTATAAGTT 60.083 41.667 43.55 0.00 41.49 2.66
2760 2878 3.435671 GCGGCCGCATTATCTTTATAAGT 59.564 43.478 43.55 0.00 41.49 2.24
2761 2879 3.181510 GGCGGCCGCATTATCTTTATAAG 60.182 47.826 46.88 5.10 44.11 1.73
2762 2880 2.745281 GGCGGCCGCATTATCTTTATAA 59.255 45.455 46.88 0.00 44.11 0.98
2763 2881 2.352388 GGCGGCCGCATTATCTTTATA 58.648 47.619 46.88 0.00 44.11 0.98
2764 2882 1.165270 GGCGGCCGCATTATCTTTAT 58.835 50.000 46.88 0.00 44.11 1.40
2765 2883 0.887387 GGGCGGCCGCATTATCTTTA 60.887 55.000 46.88 0.00 44.11 1.85
2766 2884 2.193536 GGGCGGCCGCATTATCTTT 61.194 57.895 46.88 0.00 44.11 2.52
2767 2885 2.594592 GGGCGGCCGCATTATCTT 60.595 61.111 46.88 0.00 44.11 2.40
2768 2886 4.643387 GGGGCGGCCGCATTATCT 62.643 66.667 46.88 0.00 44.11 1.98
2813 2931 4.680237 TGGTGGCGCCTGAAGACG 62.680 66.667 29.70 0.00 38.35 4.18
2814 2932 2.281484 TTGGTGGCGCCTGAAGAC 60.281 61.111 29.70 17.00 38.35 3.01
2815 2933 2.281484 GTTGGTGGCGCCTGAAGA 60.281 61.111 29.70 2.88 38.35 2.87
2816 2934 3.365265 GGTTGGTGGCGCCTGAAG 61.365 66.667 29.70 0.00 38.35 3.02
2817 2935 3.842925 GAGGTTGGTGGCGCCTGAA 62.843 63.158 29.70 14.49 38.35 3.02
2818 2936 4.329545 GAGGTTGGTGGCGCCTGA 62.330 66.667 29.70 4.80 38.35 3.86
2823 2941 3.271706 TACGACGAGGTTGGTGGCG 62.272 63.158 0.00 0.00 0.00 5.69
2824 2942 1.445582 CTACGACGAGGTTGGTGGC 60.446 63.158 0.00 0.00 0.00 5.01
2825 2943 1.445582 GCTACGACGAGGTTGGTGG 60.446 63.158 0.00 0.00 0.00 4.61
2826 2944 0.038526 AAGCTACGACGAGGTTGGTG 60.039 55.000 0.00 0.00 35.86 4.17
2827 2945 0.038526 CAAGCTACGACGAGGTTGGT 60.039 55.000 21.22 0.00 46.45 3.67
2828 2946 2.738147 CAAGCTACGACGAGGTTGG 58.262 57.895 21.22 10.26 46.45 3.77
2830 2948 0.956633 TGACAAGCTACGACGAGGTT 59.043 50.000 0.00 3.91 37.65 3.50
2831 2949 0.522180 CTGACAAGCTACGACGAGGT 59.478 55.000 0.00 0.00 0.00 3.85
2832 2950 0.179161 CCTGACAAGCTACGACGAGG 60.179 60.000 0.00 0.00 0.00 4.63
2833 2951 0.522180 ACCTGACAAGCTACGACGAG 59.478 55.000 0.00 0.00 0.00 4.18
2834 2952 0.520404 GACCTGACAAGCTACGACGA 59.480 55.000 0.00 0.00 0.00 4.20
2835 2953 0.793478 CGACCTGACAAGCTACGACG 60.793 60.000 0.00 0.00 0.00 5.12
2836 2954 0.520404 TCGACCTGACAAGCTACGAC 59.480 55.000 0.00 0.00 0.00 4.34
2837 2955 1.132453 CATCGACCTGACAAGCTACGA 59.868 52.381 0.00 0.00 0.00 3.43
2838 2956 1.135373 ACATCGACCTGACAAGCTACG 60.135 52.381 0.00 0.00 0.00 3.51
2839 2957 2.656560 ACATCGACCTGACAAGCTAC 57.343 50.000 0.00 0.00 0.00 3.58
2840 2958 2.096980 CGTACATCGACCTGACAAGCTA 59.903 50.000 0.00 0.00 42.86 3.32
2841 2959 1.135373 CGTACATCGACCTGACAAGCT 60.135 52.381 0.00 0.00 42.86 3.74
2842 2960 1.269166 CGTACATCGACCTGACAAGC 58.731 55.000 0.00 0.00 42.86 4.01
2843 2961 1.201647 ACCGTACATCGACCTGACAAG 59.798 52.381 0.00 0.00 42.86 3.16
2844 2962 1.068125 CACCGTACATCGACCTGACAA 60.068 52.381 0.00 0.00 42.86 3.18
2845 2963 0.524414 CACCGTACATCGACCTGACA 59.476 55.000 0.00 0.00 42.86 3.58
2846 2964 0.179145 CCACCGTACATCGACCTGAC 60.179 60.000 0.00 0.00 42.86 3.51
2847 2965 1.317431 CCCACCGTACATCGACCTGA 61.317 60.000 0.00 0.00 42.86 3.86
2848 2966 1.141019 CCCACCGTACATCGACCTG 59.859 63.158 0.00 0.00 42.86 4.00
2849 2967 2.056223 CCCCACCGTACATCGACCT 61.056 63.158 0.00 0.00 42.86 3.85
2850 2968 2.497770 CCCCACCGTACATCGACC 59.502 66.667 0.00 0.00 42.86 4.79
2851 2969 2.497770 CCCCCACCGTACATCGAC 59.502 66.667 0.00 0.00 42.86 4.20
2852 2970 3.463585 GCCCCCACCGTACATCGA 61.464 66.667 0.00 0.00 42.86 3.59
2853 2971 4.884257 CGCCCCCACCGTACATCG 62.884 72.222 0.00 0.00 39.52 3.84
2854 2972 3.728279 GACGCCCCCACCGTACATC 62.728 68.421 0.00 0.00 39.30 3.06
2855 2973 3.777910 GACGCCCCCACCGTACAT 61.778 66.667 0.00 0.00 39.30 2.29
2866 2984 4.382320 TACTGTTGCCCGACGCCC 62.382 66.667 0.00 0.00 36.24 6.13
2867 2985 3.116531 GTACTGTTGCCCGACGCC 61.117 66.667 0.00 0.00 36.24 5.68
2868 2986 3.475774 CGTACTGTTGCCCGACGC 61.476 66.667 0.00 0.00 38.31 5.19
2869 2987 2.807895 CCGTACTGTTGCCCGACG 60.808 66.667 0.00 0.00 0.00 5.12
2870 2988 2.433664 CCCGTACTGTTGCCCGAC 60.434 66.667 0.00 0.00 0.00 4.79
2871 2989 4.382320 GCCCGTACTGTTGCCCGA 62.382 66.667 0.00 0.00 0.00 5.14
2929 3047 4.248842 TCACCACCAGCCACACCG 62.249 66.667 0.00 0.00 0.00 4.94
2930 3048 2.594592 GTCACCACCAGCCACACC 60.595 66.667 0.00 0.00 0.00 4.16
2931 3049 2.594592 GGTCACCACCAGCCACAC 60.595 66.667 0.00 0.00 43.17 3.82
2953 3071 3.039202 GAAGGAACGTGCATGGGCG 62.039 63.158 11.36 1.34 45.35 6.13
2954 3072 2.877691 GAAGGAACGTGCATGGGC 59.122 61.111 11.36 1.14 41.68 5.36
2955 3073 1.671054 ACGAAGGAACGTGCATGGG 60.671 57.895 11.36 0.00 44.84 4.00
2956 3074 3.966215 ACGAAGGAACGTGCATGG 58.034 55.556 11.36 0.00 44.84 3.66
2966 3084 0.114560 AAGGAGGAGTCCACGAAGGA 59.885 55.000 12.86 0.00 46.80 3.36
2967 3085 0.247736 CAAGGAGGAGTCCACGAAGG 59.752 60.000 12.86 0.00 46.80 3.46
2968 3086 1.067495 GTCAAGGAGGAGTCCACGAAG 60.067 57.143 12.86 0.00 46.80 3.79
2969 3087 0.966920 GTCAAGGAGGAGTCCACGAA 59.033 55.000 12.86 0.00 46.80 3.85
2970 3088 0.898789 GGTCAAGGAGGAGTCCACGA 60.899 60.000 12.86 0.00 46.80 4.35
2971 3089 0.900647 AGGTCAAGGAGGAGTCCACG 60.901 60.000 12.86 0.00 46.80 4.94
2972 3090 0.899019 GAGGTCAAGGAGGAGTCCAC 59.101 60.000 12.86 4.72 46.80 4.02
2973 3091 0.252284 GGAGGTCAAGGAGGAGTCCA 60.252 60.000 12.86 0.00 46.80 4.02
2974 3092 0.041982 AGGAGGTCAAGGAGGAGTCC 59.958 60.000 0.00 0.00 44.33 3.85
2975 3093 1.190643 CAGGAGGTCAAGGAGGAGTC 58.809 60.000 0.00 0.00 0.00 3.36
2976 3094 0.907230 GCAGGAGGTCAAGGAGGAGT 60.907 60.000 0.00 0.00 0.00 3.85
2977 3095 0.906756 TGCAGGAGGTCAAGGAGGAG 60.907 60.000 0.00 0.00 0.00 3.69
2978 3096 1.158466 TGCAGGAGGTCAAGGAGGA 59.842 57.895 0.00 0.00 0.00 3.71
2979 3097 1.298014 GTGCAGGAGGTCAAGGAGG 59.702 63.158 0.00 0.00 0.00 4.30
2980 3098 1.079543 CGTGCAGGAGGTCAAGGAG 60.080 63.158 0.00 0.00 0.00 3.69
2981 3099 3.059982 CGTGCAGGAGGTCAAGGA 58.940 61.111 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.