Multiple sequence alignment - TraesCS2B01G287600

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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 TraesCS2B01G287600 chr2B 100.000 3095 0 0 1 3095 396955772 396958866 0.000000e+00 5716
1 TraesCS2B01G287600 chr2B 98.113 106 2 0 1 106 72134510 72134405 5.270000e-43 185
2 TraesCS2B01G287600 chr2B 99.029 103 1 0 1 103 732495182 732495080 5.270000e-43 185
3 TraesCS2B01G287600 chr2D 95.883 2453 47 15 101 2534 327622087 327624504 0.000000e+00 3921
4 TraesCS2B01G287600 chr2D 93.514 185 9 2 2904 3088 313809882 313809701 3.930000e-69 272
5 TraesCS2B01G287600 chr2D 95.266 169 8 0 2903 3071 330215230 330215062 5.090000e-68 268
6 TraesCS2B01G287600 chr2D 94.017 117 6 1 1 117 609032189 609032304 3.170000e-40 176
7 TraesCS2B01G287600 chr2A 95.533 2485 51 17 101 2543 432590763 432593229 0.000000e+00 3919
8 TraesCS2B01G287600 chr2A 89.153 295 26 4 2615 2907 432593226 432593516 2.270000e-96 363
9 TraesCS2B01G287600 chr4D 89.224 863 91 2 1140 2001 120072233 120071372 0.000000e+00 1077
10 TraesCS2B01G287600 chr4D 94.828 174 8 1 2898 3071 16666592 16666764 1.410000e-68 270
11 TraesCS2B01G287600 chr4D 92.742 124 7 2 1 123 128439236 128439114 8.820000e-41 178
12 TraesCS2B01G287600 chr4A 89.236 864 89 4 1140 2001 451595158 451594297 0.000000e+00 1077
13 TraesCS2B01G287600 chr4A 98.095 105 2 0 1 105 683963527 683963423 1.900000e-42 183
14 TraesCS2B01G287600 chr4B 89.108 863 92 2 1140 2001 183002958 183002097 0.000000e+00 1072
15 TraesCS2B01G287600 chr4B 99.029 103 1 0 1 103 14105985 14106087 5.270000e-43 185
16 TraesCS2B01G287600 chr7D 95.783 166 7 0 2905 3070 285959 285794 5.090000e-68 268
17 TraesCS2B01G287600 chr7D 95.758 165 7 0 2905 3069 184379985 184379821 1.830000e-67 267
18 TraesCS2B01G287600 chr3D 95.783 166 7 0 2904 3069 562563356 562563521 5.090000e-68 268
19 TraesCS2B01G287600 chr3D 92.350 183 10 3 2906 3088 19300389 19300211 1.100000e-64 257
20 TraesCS2B01G287600 chr3D 94.872 117 4 2 1 117 359861439 359861553 6.820000e-42 182
21 TraesCS2B01G287600 chr1B 95.783 166 7 0 2906 3071 672032773 672032608 5.090000e-68 268
22 TraesCS2B01G287600 chr1D 91.848 184 14 1 2887 3069 383724212 383724395 3.960000e-64 255
23 TraesCS2B01G287600 chr5B 99.048 105 1 0 1 105 67902020 67901916 4.070000e-44 189
24 TraesCS2B01G287600 chr3B 99.038 104 1 0 1 104 47020070 47020173 1.470000e-43 187


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 TraesCS2B01G287600 chr2B 396955772 396958866 3094 False 5716 5716 100.000 1 3095 1 chr2B.!!$F1 3094
1 TraesCS2B01G287600 chr2D 327622087 327624504 2417 False 3921 3921 95.883 101 2534 1 chr2D.!!$F1 2433
2 TraesCS2B01G287600 chr2A 432590763 432593516 2753 False 2141 3919 92.343 101 2907 2 chr2A.!!$F1 2806
3 TraesCS2B01G287600 chr4D 120071372 120072233 861 True 1077 1077 89.224 1140 2001 1 chr4D.!!$R1 861
4 TraesCS2B01G287600 chr4A 451594297 451595158 861 True 1077 1077 89.236 1140 2001 1 chr4A.!!$R1 861
5 TraesCS2B01G287600 chr4B 183002097 183002958 861 True 1072 1072 89.108 1140 2001 1 chr4B.!!$R1 861

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
172 173 0.243636 GGTTCCCGCACTCCATTTTG 59.756 55.000 0.0 0.0 0.00 2.44 F
484 507 2.177531 GTTGCTGCACTGCATCCG 59.822 61.111 0.0 0.0 42.96 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1106 1142 3.760035 CTCCAGCTGCGTACCGGT 61.760 66.667 13.98 13.98 0.00 5.28 R
2466 2518 1.250840 GCTTTTAGCCTGTGTGGGGG 61.251 60.000 0.00 0.00 34.48 5.40 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
51 52 8.691661 ATAGATTTGGTCAAACTTTGTGTAGT 57.308 30.769 1.44 0.00 32.51 2.73
52 53 7.404671 AGATTTGGTCAAACTTTGTGTAGTT 57.595 32.000 1.44 0.00 39.97 2.24
53 54 7.836842 AGATTTGGTCAAACTTTGTGTAGTTT 58.163 30.769 1.44 0.00 46.42 2.66
63 64 6.190954 ACTTTGTGTAGTTTGACTTTGACC 57.809 37.500 0.00 0.00 0.00 4.02
64 65 5.708230 ACTTTGTGTAGTTTGACTTTGACCA 59.292 36.000 0.00 0.00 0.00 4.02
65 66 6.207810 ACTTTGTGTAGTTTGACTTTGACCAA 59.792 34.615 0.00 0.00 0.00 3.67
66 67 6.576662 TTGTGTAGTTTGACTTTGACCAAA 57.423 33.333 0.00 0.00 0.00 3.28
67 68 6.767524 TGTGTAGTTTGACTTTGACCAAAT 57.232 33.333 0.00 0.00 35.14 2.32
68 69 6.791303 TGTGTAGTTTGACTTTGACCAAATC 58.209 36.000 0.00 0.00 35.14 2.17
69 70 6.601613 TGTGTAGTTTGACTTTGACCAAATCT 59.398 34.615 0.00 0.00 35.14 2.40
70 71 7.122055 TGTGTAGTTTGACTTTGACCAAATCTT 59.878 33.333 0.00 0.00 35.14 2.40
71 72 8.617809 GTGTAGTTTGACTTTGACCAAATCTTA 58.382 33.333 0.00 0.00 35.14 2.10
72 73 9.349713 TGTAGTTTGACTTTGACCAAATCTTAT 57.650 29.630 0.00 0.00 35.14 1.73
76 77 9.076596 GTTTGACTTTGACCAAATCTTATATGC 57.923 33.333 0.00 0.00 35.14 3.14
77 78 7.015226 TGACTTTGACCAAATCTTATATGCG 57.985 36.000 0.00 0.00 0.00 4.73
78 79 6.038161 TGACTTTGACCAAATCTTATATGCGG 59.962 38.462 0.00 0.00 0.00 5.69
79 80 6.119536 ACTTTGACCAAATCTTATATGCGGA 58.880 36.000 0.00 0.00 0.00 5.54
80 81 6.260936 ACTTTGACCAAATCTTATATGCGGAG 59.739 38.462 0.00 0.00 0.00 4.63
81 82 5.290493 TGACCAAATCTTATATGCGGAGT 57.710 39.130 0.00 0.00 0.00 3.85
82 83 6.413783 TGACCAAATCTTATATGCGGAGTA 57.586 37.500 0.00 0.00 0.00 2.59
83 84 6.822442 TGACCAAATCTTATATGCGGAGTAA 58.178 36.000 0.00 0.00 0.00 2.24
84 85 7.276658 TGACCAAATCTTATATGCGGAGTAAA 58.723 34.615 0.00 0.00 0.00 2.01
85 86 7.771361 TGACCAAATCTTATATGCGGAGTAAAA 59.229 33.333 0.00 0.00 0.00 1.52
86 87 8.514330 ACCAAATCTTATATGCGGAGTAAAAA 57.486 30.769 0.00 0.00 0.00 1.94
87 88 8.621286 ACCAAATCTTATATGCGGAGTAAAAAG 58.379 33.333 0.00 0.00 0.00 2.27
88 89 8.836413 CCAAATCTTATATGCGGAGTAAAAAGA 58.164 33.333 0.00 0.00 0.00 2.52
92 93 7.902032 TCTTATATGCGGAGTAAAAAGAAACG 58.098 34.615 0.00 0.00 0.00 3.60
93 94 3.824414 ATGCGGAGTAAAAAGAAACGG 57.176 42.857 0.00 0.00 0.00 4.44
94 95 2.836262 TGCGGAGTAAAAAGAAACGGA 58.164 42.857 0.00 0.00 0.00 4.69
95 96 2.803956 TGCGGAGTAAAAAGAAACGGAG 59.196 45.455 0.00 0.00 0.00 4.63
96 97 2.159037 GCGGAGTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
97 98 2.740447 CGGAGTAAAAAGAAACGGAGGG 59.260 50.000 0.00 0.00 0.00 4.30
98 99 3.555586 CGGAGTAAAAAGAAACGGAGGGA 60.556 47.826 0.00 0.00 0.00 4.20
99 100 4.001652 GGAGTAAAAAGAAACGGAGGGAG 58.998 47.826 0.00 0.00 0.00 4.30
160 161 1.404315 CCTCTTCTCGAAAGGTTCCCG 60.404 57.143 7.27 0.00 0.00 5.14
172 173 0.243636 GGTTCCCGCACTCCATTTTG 59.756 55.000 0.00 0.00 0.00 2.44
240 244 2.500098 TGTATTGCCACAGACCCTACTC 59.500 50.000 0.00 0.00 0.00 2.59
248 252 3.635373 CCACAGACCCTACTCGCTAATAA 59.365 47.826 0.00 0.00 0.00 1.40
482 505 2.270257 TGGGTTGCTGCACTGCATC 61.270 57.895 0.00 0.34 42.96 3.91
483 506 2.570181 GGTTGCTGCACTGCATCC 59.430 61.111 0.00 11.11 42.96 3.51
484 507 2.177531 GTTGCTGCACTGCATCCG 59.822 61.111 0.00 0.00 42.96 4.18
485 508 3.740397 TTGCTGCACTGCATCCGC 61.740 61.111 0.00 5.48 42.96 5.54
514 537 3.279434 GTGAAGTGAACTTGTTGGAGGT 58.721 45.455 0.00 0.00 36.11 3.85
593 616 2.240612 GATGGAGACGTTGTTGCCGC 62.241 60.000 0.00 0.00 0.00 6.53
774 810 4.455877 AGGCGAAGAAAAAGAATGTACCAG 59.544 41.667 0.00 0.00 0.00 4.00
775 811 4.215613 GGCGAAGAAAAAGAATGTACCAGT 59.784 41.667 0.00 0.00 0.00 4.00
776 812 5.410439 GGCGAAGAAAAAGAATGTACCAGTA 59.590 40.000 0.00 0.00 0.00 2.74
777 813 6.304882 GCGAAGAAAAAGAATGTACCAGTAC 58.695 40.000 0.86 0.86 36.63 2.73
778 814 6.620089 GCGAAGAAAAAGAATGTACCAGTACC 60.620 42.308 5.53 0.00 35.26 3.34
779 815 6.425721 CGAAGAAAAAGAATGTACCAGTACCA 59.574 38.462 5.53 0.00 35.26 3.25
986 1022 4.343323 CGCATCCCACACACCCCA 62.343 66.667 0.00 0.00 0.00 4.96
987 1023 2.676471 GCATCCCACACACCCCAC 60.676 66.667 0.00 0.00 0.00 4.61
992 1028 4.596585 CCACACACCCCACCCCAC 62.597 72.222 0.00 0.00 0.00 4.61
2028 2064 1.476488 GTTGGCCACCATCAATACCAC 59.524 52.381 3.88 0.00 31.53 4.16
2151 2187 5.601662 TCTAGCTCCGATAACAATTCAAGG 58.398 41.667 0.00 0.00 0.00 3.61
2281 2322 8.107196 AGTTAAGTATCCATCCATCCTTTTCT 57.893 34.615 0.00 0.00 0.00 2.52
2373 2425 1.342819 TGTTGTTGCCAATTGCTACCC 59.657 47.619 0.00 0.00 43.88 3.69
2374 2426 1.342819 GTTGTTGCCAATTGCTACCCA 59.657 47.619 0.00 0.00 43.88 4.51
2386 2438 2.571212 TGCTACCCACAACAACTCAAG 58.429 47.619 0.00 0.00 0.00 3.02
2420 2472 5.720202 TGGTACTGTAGTTGATTAGCACTG 58.280 41.667 0.00 0.00 0.00 3.66
2424 2476 5.473931 ACTGTAGTTGATTAGCACTGACTG 58.526 41.667 0.00 0.00 0.00 3.51
2457 2509 0.312102 GAAATTAGGCAGCCCATCGC 59.688 55.000 8.22 0.00 37.98 4.58
2502 2557 2.993853 CCAGAAGGCAGGGGACTC 59.006 66.667 0.00 0.00 40.21 3.36
2524 2579 6.028146 TCGTACAATACAAGGTGCTTAGAA 57.972 37.500 0.00 0.00 0.00 2.10
2534 2589 6.183347 ACAAGGTGCTTAGAAAGATGCTTAT 58.817 36.000 0.00 0.00 0.00 1.73
2540 2595 9.326413 GGTGCTTAGAAAGATGCTTATAGTAAA 57.674 33.333 0.00 0.00 0.00 2.01
2565 2620 7.763172 ATGAACTAAGCTCTTTTAGACATCG 57.237 36.000 0.00 0.00 35.20 3.84
2566 2621 6.920817 TGAACTAAGCTCTTTTAGACATCGA 58.079 36.000 0.00 0.00 35.20 3.59
2567 2622 7.548097 TGAACTAAGCTCTTTTAGACATCGAT 58.452 34.615 0.00 0.00 35.20 3.59
2568 2623 7.489435 TGAACTAAGCTCTTTTAGACATCGATG 59.511 37.037 23.68 23.68 35.20 3.84
2569 2624 5.751028 ACTAAGCTCTTTTAGACATCGATGC 59.249 40.000 25.11 17.04 35.20 3.91
2570 2625 4.399004 AGCTCTTTTAGACATCGATGCT 57.601 40.909 25.11 22.52 0.00 3.79
2571 2626 4.764172 AGCTCTTTTAGACATCGATGCTT 58.236 39.130 25.11 15.41 0.00 3.91
2572 2627 5.907207 AGCTCTTTTAGACATCGATGCTTA 58.093 37.500 25.11 14.40 0.00 3.09
2573 2628 6.520272 AGCTCTTTTAGACATCGATGCTTAT 58.480 36.000 25.11 10.89 0.00 1.73
2574 2629 6.989169 AGCTCTTTTAGACATCGATGCTTATT 59.011 34.615 25.11 5.15 0.00 1.40
2575 2630 7.497249 AGCTCTTTTAGACATCGATGCTTATTT 59.503 33.333 25.11 4.34 0.00 1.40
2576 2631 7.796197 GCTCTTTTAGACATCGATGCTTATTTC 59.204 37.037 25.11 13.63 0.00 2.17
2577 2632 8.948631 TCTTTTAGACATCGATGCTTATTTCT 57.051 30.769 25.11 19.60 0.00 2.52
2580 2635 9.594478 TTTTAGACATCGATGCTTATTTCTACA 57.406 29.630 25.11 12.93 0.00 2.74
2581 2636 8.803201 TTAGACATCGATGCTTATTTCTACAG 57.197 34.615 25.11 0.00 0.00 2.74
2582 2637 7.043961 AGACATCGATGCTTATTTCTACAGA 57.956 36.000 25.11 0.00 0.00 3.41
2583 2638 7.492524 AGACATCGATGCTTATTTCTACAGAA 58.507 34.615 25.11 0.00 0.00 3.02
2584 2639 7.981789 AGACATCGATGCTTATTTCTACAGAAA 59.018 33.333 25.11 6.85 46.60 2.52
2585 2640 8.492673 ACATCGATGCTTATTTCTACAGAAAA 57.507 30.769 25.11 0.00 45.81 2.29
2586 2641 8.946085 ACATCGATGCTTATTTCTACAGAAAAA 58.054 29.630 25.11 4.51 45.81 1.94
2608 2663 7.500720 AAAATGTTTAGTTAAGTGTACGCCT 57.499 32.000 1.98 0.00 0.00 5.52
2609 2664 7.500720 AAATGTTTAGTTAAGTGTACGCCTT 57.499 32.000 1.98 2.86 0.00 4.35
2610 2665 7.500720 AATGTTTAGTTAAGTGTACGCCTTT 57.499 32.000 1.98 0.00 0.00 3.11
2611 2666 6.923928 TGTTTAGTTAAGTGTACGCCTTTT 57.076 33.333 1.98 0.00 0.00 2.27
2612 2667 8.606040 ATGTTTAGTTAAGTGTACGCCTTTTA 57.394 30.769 1.98 0.00 0.00 1.52
2613 2668 8.606040 TGTTTAGTTAAGTGTACGCCTTTTAT 57.394 30.769 1.98 0.00 0.00 1.40
2614 2669 9.703892 TGTTTAGTTAAGTGTACGCCTTTTATA 57.296 29.630 1.98 0.00 0.00 0.98
2626 2681 5.997385 ACGCCTTTTATAAATAAGCATCGG 58.003 37.500 0.00 0.00 0.00 4.18
2629 2684 6.512741 CGCCTTTTATAAATAAGCATCGGTGT 60.513 38.462 0.00 0.00 0.00 4.16
2644 2699 2.029649 TCGGTGTTTAGAGAAAGACGGG 60.030 50.000 5.74 0.00 39.22 5.28
2652 2707 8.347771 GTGTTTAGAGAAAGACGGGTTTATTTT 58.652 33.333 0.00 0.00 30.10 1.82
2654 2709 9.390795 GTTTAGAGAAAGACGGGTTTATTTTTC 57.609 33.333 0.00 0.00 0.00 2.29
2696 2751 2.099831 GTGACGCTCCCTCGTACG 59.900 66.667 9.53 9.53 43.42 3.67
2713 2768 6.803320 CCTCGTACGTTCAGTAAAATAAGTGA 59.197 38.462 16.05 0.00 37.02 3.41
2744 2799 1.300620 CGTCTGGGCAGAACGTTGA 60.301 57.895 5.00 0.00 39.48 3.18
2745 2800 0.670546 CGTCTGGGCAGAACGTTGAT 60.671 55.000 5.00 0.00 39.48 2.57
2754 2809 4.130118 GGCAGAACGTTGATGGAATAGAT 58.870 43.478 5.00 0.00 0.00 1.98
2755 2810 4.212214 GGCAGAACGTTGATGGAATAGATC 59.788 45.833 5.00 0.00 0.00 2.75
2756 2811 4.084849 GCAGAACGTTGATGGAATAGATCG 60.085 45.833 5.00 0.00 0.00 3.69
2757 2812 4.051922 AGAACGTTGATGGAATAGATCGC 58.948 43.478 5.00 0.00 0.00 4.58
2758 2813 3.452755 ACGTTGATGGAATAGATCGCA 57.547 42.857 0.00 0.00 0.00 5.10
2759 2814 3.123804 ACGTTGATGGAATAGATCGCAC 58.876 45.455 0.00 0.00 0.00 5.34
2760 2815 2.153817 CGTTGATGGAATAGATCGCACG 59.846 50.000 0.00 0.00 0.00 5.34
2775 2830 5.460419 AGATCGCACGAAACAGATCTTAATC 59.540 40.000 0.00 0.00 45.10 1.75
2782 2837 0.527600 ACAGATCTTAATCGCGCGCA 60.528 50.000 32.61 18.69 36.97 6.09
2803 2858 0.527565 GCACATGCACTTTAGGGGTG 59.472 55.000 0.00 0.00 41.59 4.61
2804 2859 1.909700 CACATGCACTTTAGGGGTGT 58.090 50.000 0.00 0.00 37.07 4.16
2805 2860 2.238521 CACATGCACTTTAGGGGTGTT 58.761 47.619 0.00 0.00 37.07 3.32
2806 2861 3.417101 CACATGCACTTTAGGGGTGTTA 58.583 45.455 0.00 0.00 37.07 2.41
2826 2881 7.281549 GGTGTTAACATTTACCGATAAGACCAT 59.718 37.037 12.26 0.00 38.84 3.55
2837 2892 5.932303 ACCGATAAGACCATATGTAATGCAC 59.068 40.000 1.24 0.00 0.00 4.57
2845 2900 5.304778 ACCATATGTAATGCACGATGCTTA 58.695 37.500 1.24 5.26 45.31 3.09
2907 2962 5.207768 CACATGTGTTTGCTTCTGAACTAC 58.792 41.667 18.03 0.00 0.00 2.73
2908 2963 5.008019 CACATGTGTTTGCTTCTGAACTACT 59.992 40.000 18.03 0.00 0.00 2.57
2909 2964 5.237344 ACATGTGTTTGCTTCTGAACTACTC 59.763 40.000 0.00 0.00 0.00 2.59
2910 2965 4.127171 TGTGTTTGCTTCTGAACTACTCC 58.873 43.478 0.00 0.00 0.00 3.85
2911 2966 3.498777 GTGTTTGCTTCTGAACTACTCCC 59.501 47.826 0.00 0.00 0.00 4.30
2912 2967 3.391296 TGTTTGCTTCTGAACTACTCCCT 59.609 43.478 0.00 0.00 0.00 4.20
2913 2968 3.963428 TTGCTTCTGAACTACTCCCTC 57.037 47.619 0.00 0.00 0.00 4.30
2914 2969 2.180276 TGCTTCTGAACTACTCCCTCC 58.820 52.381 0.00 0.00 0.00 4.30
2915 2970 1.135333 GCTTCTGAACTACTCCCTCCG 59.865 57.143 0.00 0.00 0.00 4.63
2916 2971 2.448453 CTTCTGAACTACTCCCTCCGT 58.552 52.381 0.00 0.00 0.00 4.69
2917 2972 2.599408 TCTGAACTACTCCCTCCGTT 57.401 50.000 0.00 0.00 0.00 4.44
2918 2973 2.444421 TCTGAACTACTCCCTCCGTTC 58.556 52.381 0.00 0.00 37.02 3.95
2919 2974 1.477295 CTGAACTACTCCCTCCGTTCC 59.523 57.143 0.00 0.00 35.97 3.62
2920 2975 1.076677 TGAACTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 35.97 3.36
2921 2976 2.309755 TGAACTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 35.97 2.94
2922 2977 3.245371 TGAACTACTCCCTCCGTTCCTAA 60.245 47.826 0.00 0.00 35.97 2.69
2923 2978 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2924 2979 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2925 2980 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2926 2981 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2927 2982 6.141790 ACTACTCCCTCCGTTCCTAAATATT 58.858 40.000 0.00 0.00 0.00 1.28
2928 2983 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
2929 2984 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
2930 2985 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
2931 2986 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
2932 2987 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
2933 2988 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
2934 2989 6.260271 CCCTCCGTTCCTAAATATTTGTCTTC 59.740 42.308 11.05 0.00 0.00 2.87
2935 2990 7.048512 CCTCCGTTCCTAAATATTTGTCTTCT 58.951 38.462 11.05 0.00 0.00 2.85
2936 2991 7.553044 CCTCCGTTCCTAAATATTTGTCTTCTT 59.447 37.037 11.05 0.00 0.00 2.52
2937 2992 9.595823 CTCCGTTCCTAAATATTTGTCTTCTTA 57.404 33.333 11.05 0.00 0.00 2.10
2938 2993 9.595823 TCCGTTCCTAAATATTTGTCTTCTTAG 57.404 33.333 11.05 0.00 0.00 2.18
2939 2994 9.595823 CCGTTCCTAAATATTTGTCTTCTTAGA 57.404 33.333 11.05 0.00 0.00 2.10
2956 3011 9.877178 TCTTCTTAGAGATTTCAAATAGTCACC 57.123 33.333 0.00 0.00 0.00 4.02
2957 3012 9.658799 CTTCTTAGAGATTTCAAATAGTCACCA 57.341 33.333 0.00 0.00 0.00 4.17
2958 3013 9.436957 TTCTTAGAGATTTCAAATAGTCACCAC 57.563 33.333 0.00 0.00 0.00 4.16
2959 3014 8.593679 TCTTAGAGATTTCAAATAGTCACCACA 58.406 33.333 0.00 0.00 0.00 4.17
2960 3015 9.388506 CTTAGAGATTTCAAATAGTCACCACAT 57.611 33.333 0.00 0.00 0.00 3.21
2963 3018 9.334947 AGAGATTTCAAATAGTCACCACATATG 57.665 33.333 0.00 0.00 0.00 1.78
3011 3066 7.576236 AGTGTAGATTCACTCATTTTGTTTCG 58.424 34.615 0.00 0.00 44.07 3.46
3012 3067 7.226720 AGTGTAGATTCACTCATTTTGTTTCGT 59.773 33.333 0.00 0.00 44.07 3.85
3013 3068 8.492748 GTGTAGATTCACTCATTTTGTTTCGTA 58.507 33.333 0.00 0.00 35.68 3.43
3014 3069 9.214957 TGTAGATTCACTCATTTTGTTTCGTAT 57.785 29.630 0.00 0.00 0.00 3.06
3015 3070 9.478019 GTAGATTCACTCATTTTGTTTCGTATG 57.522 33.333 0.00 0.00 0.00 2.39
3016 3071 8.099364 AGATTCACTCATTTTGTTTCGTATGT 57.901 30.769 0.00 0.00 0.00 2.29
3017 3072 9.214957 AGATTCACTCATTTTGTTTCGTATGTA 57.785 29.630 0.00 0.00 0.00 2.29
3018 3073 9.478019 GATTCACTCATTTTGTTTCGTATGTAG 57.522 33.333 0.00 0.00 0.00 2.74
3019 3074 7.956420 TCACTCATTTTGTTTCGTATGTAGT 57.044 32.000 0.00 0.00 0.00 2.73
3020 3075 8.014322 TCACTCATTTTGTTTCGTATGTAGTC 57.986 34.615 0.00 0.00 0.00 2.59
3021 3076 7.654116 TCACTCATTTTGTTTCGTATGTAGTCA 59.346 33.333 0.00 0.00 0.00 3.41
3022 3077 8.443160 CACTCATTTTGTTTCGTATGTAGTCAT 58.557 33.333 0.00 0.00 38.00 3.06
3023 3078 8.656849 ACTCATTTTGTTTCGTATGTAGTCATC 58.343 33.333 0.00 0.00 35.70 2.92
3024 3079 8.541133 TCATTTTGTTTCGTATGTAGTCATCA 57.459 30.769 0.00 0.00 35.70 3.07
3025 3080 9.161629 TCATTTTGTTTCGTATGTAGTCATCAT 57.838 29.630 0.00 0.00 35.70 2.45
3026 3081 9.773328 CATTTTGTTTCGTATGTAGTCATCATT 57.227 29.630 0.00 0.00 35.70 2.57
3028 3083 9.605955 TTTTGTTTCGTATGTAGTCATCATTTG 57.394 29.630 0.00 0.00 35.70 2.32
3029 3084 8.541133 TTGTTTCGTATGTAGTCATCATTTGA 57.459 30.769 0.00 0.00 35.70 2.69
3030 3085 8.541133 TGTTTCGTATGTAGTCATCATTTGAA 57.459 30.769 0.00 0.00 35.70 2.69
3031 3086 8.994170 TGTTTCGTATGTAGTCATCATTTGAAA 58.006 29.630 0.00 0.00 35.70 2.69
3032 3087 9.262472 GTTTCGTATGTAGTCATCATTTGAAAC 57.738 33.333 13.84 13.84 38.83 2.78
3033 3088 7.534085 TCGTATGTAGTCATCATTTGAAACC 57.466 36.000 0.00 0.00 35.70 3.27
3034 3089 7.327975 TCGTATGTAGTCATCATTTGAAACCT 58.672 34.615 0.00 0.00 35.70 3.50
3035 3090 7.491372 TCGTATGTAGTCATCATTTGAAACCTC 59.509 37.037 0.00 0.00 35.70 3.85
3036 3091 7.492669 CGTATGTAGTCATCATTTGAAACCTCT 59.507 37.037 0.00 0.00 35.70 3.69
3037 3092 9.817809 GTATGTAGTCATCATTTGAAACCTCTA 57.182 33.333 0.00 0.00 35.70 2.43
3039 3094 9.739276 ATGTAGTCATCATTTGAAACCTCTAAA 57.261 29.630 0.00 0.00 35.70 1.85
3040 3095 9.567776 TGTAGTCATCATTTGAAACCTCTAAAA 57.432 29.630 0.00 0.00 35.70 1.52
3043 3098 9.354673 AGTCATCATTTGAAACCTCTAAAAAGA 57.645 29.630 0.00 0.00 35.70 2.52
3044 3099 9.399403 GTCATCATTTGAAACCTCTAAAAAGAC 57.601 33.333 0.00 0.00 35.70 3.01
3045 3100 9.130661 TCATCATTTGAAACCTCTAAAAAGACA 57.869 29.630 0.00 0.00 0.00 3.41
3046 3101 9.748708 CATCATTTGAAACCTCTAAAAAGACAA 57.251 29.630 0.00 0.00 0.00 3.18
3063 3118 9.855021 AAAAAGACAAATATTTAGGAACGGATG 57.145 29.630 0.00 0.00 0.00 3.51
3064 3119 7.568199 AAGACAAATATTTAGGAACGGATGG 57.432 36.000 0.00 0.00 0.00 3.51
3065 3120 6.895782 AGACAAATATTTAGGAACGGATGGA 58.104 36.000 0.00 0.00 0.00 3.41
3066 3121 6.992715 AGACAAATATTTAGGAACGGATGGAG 59.007 38.462 0.00 0.00 0.00 3.86
3067 3122 6.659824 ACAAATATTTAGGAACGGATGGAGT 58.340 36.000 0.00 0.00 0.00 3.85
3068 3123 7.798071 ACAAATATTTAGGAACGGATGGAGTA 58.202 34.615 0.00 0.00 0.00 2.59
3069 3124 7.931948 ACAAATATTTAGGAACGGATGGAGTAG 59.068 37.037 0.00 0.00 0.00 2.57
3070 3125 7.850935 AATATTTAGGAACGGATGGAGTAGA 57.149 36.000 0.00 0.00 0.00 2.59
3071 3126 5.793030 ATTTAGGAACGGATGGAGTAGAG 57.207 43.478 0.00 0.00 0.00 2.43
3072 3127 4.515028 TTAGGAACGGATGGAGTAGAGA 57.485 45.455 0.00 0.00 0.00 3.10
3073 3128 3.603965 AGGAACGGATGGAGTAGAGAT 57.396 47.619 0.00 0.00 0.00 2.75
3074 3129 3.226777 AGGAACGGATGGAGTAGAGATG 58.773 50.000 0.00 0.00 0.00 2.90
3075 3130 3.117474 AGGAACGGATGGAGTAGAGATGA 60.117 47.826 0.00 0.00 0.00 2.92
3076 3131 3.254657 GGAACGGATGGAGTAGAGATGAG 59.745 52.174 0.00 0.00 0.00 2.90
3077 3132 3.586470 ACGGATGGAGTAGAGATGAGT 57.414 47.619 0.00 0.00 0.00 3.41
3078 3133 4.708576 ACGGATGGAGTAGAGATGAGTA 57.291 45.455 0.00 0.00 0.00 2.59
3079 3134 5.050126 ACGGATGGAGTAGAGATGAGTAA 57.950 43.478 0.00 0.00 0.00 2.24
3080 3135 5.067273 ACGGATGGAGTAGAGATGAGTAAG 58.933 45.833 0.00 0.00 0.00 2.34
3081 3136 5.067273 CGGATGGAGTAGAGATGAGTAAGT 58.933 45.833 0.00 0.00 0.00 2.24
3082 3137 6.183361 ACGGATGGAGTAGAGATGAGTAAGTA 60.183 42.308 0.00 0.00 0.00 2.24
3083 3138 6.370442 CGGATGGAGTAGAGATGAGTAAGTAG 59.630 46.154 0.00 0.00 0.00 2.57
3084 3139 6.150474 GGATGGAGTAGAGATGAGTAAGTAGC 59.850 46.154 0.00 0.00 0.00 3.58
3085 3140 6.002653 TGGAGTAGAGATGAGTAAGTAGCA 57.997 41.667 0.00 0.00 0.00 3.49
3086 3141 6.606069 TGGAGTAGAGATGAGTAAGTAGCAT 58.394 40.000 0.00 0.00 0.00 3.79
3087 3142 7.063593 TGGAGTAGAGATGAGTAAGTAGCATT 58.936 38.462 0.00 0.00 0.00 3.56
3088 3143 7.013750 TGGAGTAGAGATGAGTAAGTAGCATTG 59.986 40.741 0.00 0.00 0.00 2.82
3089 3144 7.283625 AGTAGAGATGAGTAAGTAGCATTGG 57.716 40.000 0.00 0.00 0.00 3.16
3090 3145 6.836527 AGTAGAGATGAGTAAGTAGCATTGGT 59.163 38.462 0.00 0.00 0.00 3.67
3091 3146 5.911752 AGAGATGAGTAAGTAGCATTGGTG 58.088 41.667 0.00 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 9.787435 ACTACACAAAGTTTGACCAAATCTATA 57.213 29.630 22.23 0.00 32.36 1.31
26 27 8.691661 ACTACACAAAGTTTGACCAAATCTAT 57.308 30.769 22.23 0.00 32.36 1.98
27 28 8.514330 AACTACACAAAGTTTGACCAAATCTA 57.486 30.769 22.23 0.00 36.26 1.98
28 29 7.404671 AACTACACAAAGTTTGACCAAATCT 57.595 32.000 22.23 0.00 36.26 2.40
39 40 6.207810 TGGTCAAAGTCAAACTACACAAAGTT 59.792 34.615 0.00 0.00 41.46 2.66
40 41 5.708230 TGGTCAAAGTCAAACTACACAAAGT 59.292 36.000 0.00 0.00 0.00 2.66
41 42 6.189677 TGGTCAAAGTCAAACTACACAAAG 57.810 37.500 0.00 0.00 0.00 2.77
42 43 6.576662 TTGGTCAAAGTCAAACTACACAAA 57.423 33.333 0.00 0.00 0.00 2.83
43 44 6.576662 TTTGGTCAAAGTCAAACTACACAA 57.423 33.333 0.00 0.00 0.00 3.33
44 45 6.601613 AGATTTGGTCAAAGTCAAACTACACA 59.398 34.615 2.55 0.00 35.97 3.72
45 46 7.027778 AGATTTGGTCAAAGTCAAACTACAC 57.972 36.000 2.55 0.00 35.97 2.90
46 47 7.639113 AAGATTTGGTCAAAGTCAAACTACA 57.361 32.000 2.55 0.00 35.97 2.74
50 51 9.076596 GCATATAAGATTTGGTCAAAGTCAAAC 57.923 33.333 2.55 0.00 35.97 2.93
51 52 7.967854 CGCATATAAGATTTGGTCAAAGTCAAA 59.032 33.333 2.55 0.00 37.29 2.69
52 53 7.415095 CCGCATATAAGATTTGGTCAAAGTCAA 60.415 37.037 2.55 0.00 33.32 3.18
53 54 6.038161 CCGCATATAAGATTTGGTCAAAGTCA 59.962 38.462 2.55 0.00 33.32 3.41
54 55 6.260050 TCCGCATATAAGATTTGGTCAAAGTC 59.740 38.462 2.55 1.51 33.32 3.01
55 56 6.119536 TCCGCATATAAGATTTGGTCAAAGT 58.880 36.000 2.55 0.00 33.32 2.66
56 57 6.260936 ACTCCGCATATAAGATTTGGTCAAAG 59.739 38.462 2.55 0.00 33.32 2.77
57 58 6.119536 ACTCCGCATATAAGATTTGGTCAAA 58.880 36.000 0.00 0.00 34.46 2.69
58 59 5.680619 ACTCCGCATATAAGATTTGGTCAA 58.319 37.500 0.00 0.00 0.00 3.18
59 60 5.290493 ACTCCGCATATAAGATTTGGTCA 57.710 39.130 0.00 0.00 0.00 4.02
60 61 7.724305 TTTACTCCGCATATAAGATTTGGTC 57.276 36.000 0.00 0.00 0.00 4.02
61 62 8.514330 TTTTTACTCCGCATATAAGATTTGGT 57.486 30.769 0.00 0.00 0.00 3.67
62 63 8.836413 TCTTTTTACTCCGCATATAAGATTTGG 58.164 33.333 0.00 0.00 0.00 3.28
66 67 8.548721 CGTTTCTTTTTACTCCGCATATAAGAT 58.451 33.333 0.00 0.00 0.00 2.40
67 68 7.010738 CCGTTTCTTTTTACTCCGCATATAAGA 59.989 37.037 0.00 0.00 0.00 2.10
68 69 7.010738 TCCGTTTCTTTTTACTCCGCATATAAG 59.989 37.037 0.00 0.00 0.00 1.73
69 70 6.817641 TCCGTTTCTTTTTACTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
70 71 6.339730 TCCGTTTCTTTTTACTCCGCATATA 58.660 36.000 0.00 0.00 0.00 0.86
71 72 5.180271 TCCGTTTCTTTTTACTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
72 73 4.567971 TCCGTTTCTTTTTACTCCGCATA 58.432 39.130 0.00 0.00 0.00 3.14
73 74 3.404899 TCCGTTTCTTTTTACTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
74 75 2.803956 CTCCGTTTCTTTTTACTCCGCA 59.196 45.455 0.00 0.00 0.00 5.69
75 76 2.159037 CCTCCGTTTCTTTTTACTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
76 77 2.740447 CCCTCCGTTTCTTTTTACTCCG 59.260 50.000 0.00 0.00 0.00 4.63
77 78 4.001652 CTCCCTCCGTTTCTTTTTACTCC 58.998 47.826 0.00 0.00 0.00 3.85
78 79 4.639334 ACTCCCTCCGTTTCTTTTTACTC 58.361 43.478 0.00 0.00 0.00 2.59
79 80 4.701651 ACTCCCTCCGTTTCTTTTTACT 57.298 40.909 0.00 0.00 0.00 2.24
80 81 5.545588 AGTACTCCCTCCGTTTCTTTTTAC 58.454 41.667 0.00 0.00 0.00 2.01
81 82 5.813513 AGTACTCCCTCCGTTTCTTTTTA 57.186 39.130 0.00 0.00 0.00 1.52
82 83 4.701651 AGTACTCCCTCCGTTTCTTTTT 57.298 40.909 0.00 0.00 0.00 1.94
83 84 4.837298 AGTAGTACTCCCTCCGTTTCTTTT 59.163 41.667 0.00 0.00 0.00 2.27
84 85 4.414677 AGTAGTACTCCCTCCGTTTCTTT 58.585 43.478 0.00 0.00 0.00 2.52
85 86 4.044946 AGTAGTACTCCCTCCGTTTCTT 57.955 45.455 0.00 0.00 0.00 2.52
86 87 3.735720 AGTAGTACTCCCTCCGTTTCT 57.264 47.619 0.00 0.00 0.00 2.52
87 88 3.119209 CCAAGTAGTACTCCCTCCGTTTC 60.119 52.174 2.58 0.00 0.00 2.78
88 89 2.830321 CCAAGTAGTACTCCCTCCGTTT 59.170 50.000 2.58 0.00 0.00 3.60
89 90 2.454538 CCAAGTAGTACTCCCTCCGTT 58.545 52.381 2.58 0.00 0.00 4.44
90 91 1.959028 GCCAAGTAGTACTCCCTCCGT 60.959 57.143 2.58 0.00 0.00 4.69
91 92 0.745468 GCCAAGTAGTACTCCCTCCG 59.255 60.000 2.58 0.00 0.00 4.63
92 93 1.757699 CTGCCAAGTAGTACTCCCTCC 59.242 57.143 2.58 0.00 0.00 4.30
93 94 2.458620 ACTGCCAAGTAGTACTCCCTC 58.541 52.381 2.58 0.00 33.79 4.30
94 95 2.625282 ACTGCCAAGTAGTACTCCCT 57.375 50.000 2.58 0.00 33.79 4.20
160 161 5.756195 TCAGCATATACAAAATGGAGTGC 57.244 39.130 0.00 0.00 0.00 4.40
172 173 7.385267 AGGAGATGACATTCTTCAGCATATAC 58.615 38.462 0.00 0.00 34.19 1.47
303 314 4.750098 CCAAGTAGCCGTACCTTATCAATG 59.250 45.833 0.00 0.00 0.00 2.82
411 424 4.068599 GGTCCATACTACCTACGACTACC 58.931 52.174 0.00 0.00 33.97 3.18
482 505 2.047274 ACTTCACGGACCATGCGG 60.047 61.111 0.00 0.00 34.75 5.69
483 506 0.948623 TTCACTTCACGGACCATGCG 60.949 55.000 0.00 0.00 37.19 4.73
484 507 0.517316 GTTCACTTCACGGACCATGC 59.483 55.000 0.00 0.00 0.00 4.06
485 508 2.169832 AGTTCACTTCACGGACCATG 57.830 50.000 0.00 0.00 0.00 3.66
486 509 2.158813 ACAAGTTCACTTCACGGACCAT 60.159 45.455 0.00 0.00 33.11 3.55
487 510 1.208535 ACAAGTTCACTTCACGGACCA 59.791 47.619 0.00 0.00 33.11 4.02
514 537 2.214216 ACCGTGCTTGGCTCAGGTA 61.214 57.895 0.00 0.00 31.51 3.08
593 616 1.026718 GGTTGCCTCATGGTTCTCGG 61.027 60.000 0.00 0.00 35.27 4.63
723 759 0.383590 ATCTCTCGTCACTCGCATGG 59.616 55.000 0.00 0.00 39.67 3.66
779 815 3.371097 CTCTACCCGCACGCATGGT 62.371 63.158 5.65 5.65 36.15 3.55
1106 1142 3.760035 CTCCAGCTGCGTACCGGT 61.760 66.667 13.98 13.98 0.00 5.28
2028 2064 5.952387 TCCATGGAGTATTATTTTGGGAGG 58.048 41.667 11.44 0.00 0.00 4.30
2281 2322 4.439700 GCATAGTAGCAAGAGTACACGGAA 60.440 45.833 0.00 0.00 0.00 4.30
2373 2425 3.065786 ACTGCATCACTTGAGTTGTTGTG 59.934 43.478 0.00 0.00 0.00 3.33
2374 2426 3.282021 ACTGCATCACTTGAGTTGTTGT 58.718 40.909 0.00 0.00 0.00 3.32
2407 2459 4.787598 CCAAACAGTCAGTGCTAATCAAC 58.212 43.478 0.00 0.00 0.00 3.18
2420 2472 8.451748 CCTAATTTCTACTTTAGCCAAACAGTC 58.548 37.037 0.00 0.00 0.00 3.51
2424 2476 7.153217 TGCCTAATTTCTACTTTAGCCAAAC 57.847 36.000 0.00 0.00 0.00 2.93
2466 2518 1.250840 GCTTTTAGCCTGTGTGGGGG 61.251 60.000 0.00 0.00 34.48 5.40
2496 2549 3.518590 CACCTTGTATTGTACGAGTCCC 58.481 50.000 0.00 0.00 38.31 4.46
2498 2551 3.846360 AGCACCTTGTATTGTACGAGTC 58.154 45.455 0.00 0.00 38.31 3.36
2502 2557 6.588756 TCTTTCTAAGCACCTTGTATTGTACG 59.411 38.462 0.00 0.00 0.00 3.67
2540 2595 8.035394 TCGATGTCTAAAAGAGCTTAGTTCATT 58.965 33.333 0.00 0.00 31.61 2.57
2541 2596 7.548097 TCGATGTCTAAAAGAGCTTAGTTCAT 58.452 34.615 0.00 0.00 32.76 2.57
2542 2597 6.920817 TCGATGTCTAAAAGAGCTTAGTTCA 58.079 36.000 0.00 0.00 31.86 3.18
2543 2598 7.515998 GCATCGATGTCTAAAAGAGCTTAGTTC 60.516 40.741 25.47 0.00 31.86 3.01
2544 2599 6.256757 GCATCGATGTCTAAAAGAGCTTAGTT 59.743 38.462 25.47 0.00 31.86 2.24
2545 2600 5.751028 GCATCGATGTCTAAAAGAGCTTAGT 59.249 40.000 25.47 0.00 31.86 2.24
2546 2601 5.982516 AGCATCGATGTCTAAAAGAGCTTAG 59.017 40.000 25.47 0.00 0.00 2.18
2547 2602 5.907207 AGCATCGATGTCTAAAAGAGCTTA 58.093 37.500 25.47 0.00 0.00 3.09
2548 2603 4.764172 AGCATCGATGTCTAAAAGAGCTT 58.236 39.130 25.47 0.00 0.00 3.74
2549 2604 4.399004 AGCATCGATGTCTAAAAGAGCT 57.601 40.909 25.47 10.20 0.00 4.09
2550 2605 6.777526 ATAAGCATCGATGTCTAAAAGAGC 57.222 37.500 25.47 8.01 0.00 4.09
2551 2606 9.039870 AGAAATAAGCATCGATGTCTAAAAGAG 57.960 33.333 25.47 0.00 0.00 2.85
2552 2607 8.948631 AGAAATAAGCATCGATGTCTAAAAGA 57.051 30.769 25.47 8.38 0.00 2.52
2554 2609 9.594478 TGTAGAAATAAGCATCGATGTCTAAAA 57.406 29.630 25.47 12.20 0.00 1.52
2555 2610 9.249457 CTGTAGAAATAAGCATCGATGTCTAAA 57.751 33.333 25.47 16.38 0.00 1.85
2556 2611 8.630037 TCTGTAGAAATAAGCATCGATGTCTAA 58.370 33.333 25.47 10.26 0.00 2.10
2557 2612 8.166422 TCTGTAGAAATAAGCATCGATGTCTA 57.834 34.615 25.47 19.02 0.00 2.59
2558 2613 7.043961 TCTGTAGAAATAAGCATCGATGTCT 57.956 36.000 25.47 19.95 0.00 3.41
2559 2614 7.700322 TTCTGTAGAAATAAGCATCGATGTC 57.300 36.000 25.47 17.50 0.00 3.06
2560 2615 8.492673 TTTTCTGTAGAAATAAGCATCGATGT 57.507 30.769 25.47 10.33 42.83 3.06
2583 2638 7.933396 AGGCGTACACTTAACTAAACATTTTT 58.067 30.769 0.00 0.00 0.00 1.94
2584 2639 7.500720 AGGCGTACACTTAACTAAACATTTT 57.499 32.000 0.00 0.00 0.00 1.82
2585 2640 7.500720 AAGGCGTACACTTAACTAAACATTT 57.499 32.000 0.00 0.00 0.00 2.32
2586 2641 7.500720 AAAGGCGTACACTTAACTAAACATT 57.499 32.000 0.74 0.00 0.00 2.71
2587 2642 7.500720 AAAAGGCGTACACTTAACTAAACAT 57.499 32.000 0.74 0.00 0.00 2.71
2588 2643 6.923928 AAAAGGCGTACACTTAACTAAACA 57.076 33.333 0.74 0.00 0.00 2.83
2596 2651 9.381033 TGCTTATTTATAAAAGGCGTACACTTA 57.619 29.630 1.21 0.00 0.00 2.24
2597 2652 8.271312 TGCTTATTTATAAAAGGCGTACACTT 57.729 30.769 1.21 0.00 0.00 3.16
2598 2653 7.852971 TGCTTATTTATAAAAGGCGTACACT 57.147 32.000 1.21 0.00 0.00 3.55
2599 2654 7.529519 CGATGCTTATTTATAAAAGGCGTACAC 59.470 37.037 1.21 0.00 0.00 2.90
2600 2655 7.307514 CCGATGCTTATTTATAAAAGGCGTACA 60.308 37.037 1.21 0.00 0.00 2.90
2601 2656 7.013529 CCGATGCTTATTTATAAAAGGCGTAC 58.986 38.462 1.21 2.97 0.00 3.67
2602 2657 6.707161 ACCGATGCTTATTTATAAAAGGCGTA 59.293 34.615 1.21 0.00 0.00 4.42
2603 2658 5.529800 ACCGATGCTTATTTATAAAAGGCGT 59.470 36.000 1.21 8.12 0.00 5.68
2604 2659 5.851177 CACCGATGCTTATTTATAAAAGGCG 59.149 40.000 1.21 0.61 0.00 5.52
2605 2660 6.735130 ACACCGATGCTTATTTATAAAAGGC 58.265 36.000 1.21 7.55 0.00 4.35
2612 2667 8.958119 TTCTCTAAACACCGATGCTTATTTAT 57.042 30.769 0.00 0.00 0.00 1.40
2613 2668 8.780846 TTTCTCTAAACACCGATGCTTATTTA 57.219 30.769 0.00 0.00 0.00 1.40
2614 2669 7.606456 TCTTTCTCTAAACACCGATGCTTATTT 59.394 33.333 0.00 0.00 0.00 1.40
2626 2681 7.430992 AATAAACCCGTCTTTCTCTAAACAC 57.569 36.000 0.00 0.00 0.00 3.32
2629 2684 9.346005 AGAAAAATAAACCCGTCTTTCTCTAAA 57.654 29.630 0.00 0.00 29.39 1.85
2652 2707 4.501071 GTGCTTACGGGAGATGTTTAGAA 58.499 43.478 0.00 0.00 0.00 2.10
2654 2709 2.858344 CGTGCTTACGGGAGATGTTTAG 59.142 50.000 0.00 0.00 0.00 1.85
2656 2711 1.722011 CGTGCTTACGGGAGATGTTT 58.278 50.000 0.00 0.00 0.00 2.83
2678 2733 2.099831 GTACGAGGGAGCGTCACG 59.900 66.667 0.00 0.00 44.39 4.35
2688 2743 6.803320 TCACTTATTTTACTGAACGTACGAGG 59.197 38.462 24.41 10.69 0.00 4.63
2696 2751 7.320560 GCTTGACGTTCACTTATTTTACTGAAC 59.679 37.037 0.00 0.00 39.33 3.18
2713 2768 4.295119 AGACGCCCGCTTGACGTT 62.295 61.111 0.00 0.00 40.69 3.99
2744 2799 3.792401 TGTTTCGTGCGATCTATTCCAT 58.208 40.909 0.00 0.00 0.00 3.41
2745 2800 3.119280 TCTGTTTCGTGCGATCTATTCCA 60.119 43.478 0.00 0.00 0.00 3.53
2754 2809 3.546271 CGATTAAGATCTGTTTCGTGCGA 59.454 43.478 0.00 0.00 0.00 5.10
2755 2810 3.837838 GCGATTAAGATCTGTTTCGTGCG 60.838 47.826 17.50 7.24 0.00 5.34
2756 2811 3.598330 GCGATTAAGATCTGTTTCGTGC 58.402 45.455 17.50 5.48 0.00 5.34
2757 2812 3.837838 GCGCGATTAAGATCTGTTTCGTG 60.838 47.826 12.10 21.34 39.37 4.35
2758 2813 2.281762 GCGCGATTAAGATCTGTTTCGT 59.718 45.455 12.10 0.00 0.00 3.85
2759 2814 2.654003 CGCGCGATTAAGATCTGTTTCG 60.654 50.000 28.94 13.97 0.00 3.46
2760 2815 2.880456 CGCGCGATTAAGATCTGTTTC 58.120 47.619 28.94 0.00 0.00 2.78
2800 2855 6.594937 TGGTCTTATCGGTAAATGTTAACACC 59.405 38.462 11.22 6.67 0.00 4.16
2837 2892 1.267261 CGAGTACCTCCCTAAGCATCG 59.733 57.143 0.00 0.00 0.00 3.84
2845 2900 2.575279 TCTCTTACACGAGTACCTCCCT 59.425 50.000 0.00 0.00 32.83 4.20
2888 2943 4.127171 GGAGTAGTTCAGAAGCAAACACA 58.873 43.478 0.00 0.00 0.00 3.72
2891 2946 3.997681 GAGGGAGTAGTTCAGAAGCAAAC 59.002 47.826 0.00 0.00 0.00 2.93
2899 2954 1.477295 GGAACGGAGGGAGTAGTTCAG 59.523 57.143 9.01 0.00 43.24 3.02
2907 2962 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
2908 2963 5.427481 AGACAAATATTTAGGAACGGAGGGA 59.573 40.000 0.00 0.00 0.00 4.20
2909 2964 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
2910 2965 7.048512 AGAAGACAAATATTTAGGAACGGAGG 58.951 38.462 0.00 0.00 0.00 4.30
2911 2966 8.494016 AAGAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
2912 2967 9.595823 CTAAGAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
2913 2968 9.595823 TCTAAGAAGACAAATATTTAGGAACGG 57.404 33.333 0.00 0.00 0.00 4.44
2930 2985 9.877178 GGTGACTATTTGAAATCTCTAAGAAGA 57.123 33.333 0.00 0.00 0.00 2.87
2931 2986 9.658799 TGGTGACTATTTGAAATCTCTAAGAAG 57.341 33.333 0.00 0.00 0.00 2.85
2932 2987 9.436957 GTGGTGACTATTTGAAATCTCTAAGAA 57.563 33.333 0.00 0.00 0.00 2.52
2933 2988 8.593679 TGTGGTGACTATTTGAAATCTCTAAGA 58.406 33.333 0.00 0.00 0.00 2.10
2934 2989 8.777865 TGTGGTGACTATTTGAAATCTCTAAG 57.222 34.615 0.00 0.00 0.00 2.18
2937 2992 9.334947 CATATGTGGTGACTATTTGAAATCTCT 57.665 33.333 0.00 0.00 0.00 3.10
2938 2993 8.562892 CCATATGTGGTGACTATTTGAAATCTC 58.437 37.037 0.00 0.00 40.83 2.75
2939 2994 8.274322 TCCATATGTGGTGACTATTTGAAATCT 58.726 33.333 8.51 0.00 46.16 2.40
2940 2995 8.450578 TCCATATGTGGTGACTATTTGAAATC 57.549 34.615 8.51 0.00 46.16 2.17
2941 2996 8.853126 CATCCATATGTGGTGACTATTTGAAAT 58.147 33.333 8.51 0.00 46.16 2.17
2942 2997 7.833682 ACATCCATATGTGGTGACTATTTGAAA 59.166 33.333 8.51 0.00 44.79 2.69
2943 2998 7.345691 ACATCCATATGTGGTGACTATTTGAA 58.654 34.615 8.51 0.00 44.79 2.69
2944 2999 6.899089 ACATCCATATGTGGTGACTATTTGA 58.101 36.000 8.51 0.00 44.79 2.69
2945 3000 8.853077 ATACATCCATATGTGGTGACTATTTG 57.147 34.615 8.51 0.00 45.99 2.32
2950 3005 8.972127 GTCTATATACATCCATATGTGGTGACT 58.028 37.037 8.51 3.01 45.99 3.41
2951 3006 8.749354 TGTCTATATACATCCATATGTGGTGAC 58.251 37.037 8.51 5.34 45.99 3.67
2952 3007 8.893563 TGTCTATATACATCCATATGTGGTGA 57.106 34.615 8.51 0.00 45.99 4.02
2987 3042 7.352739 ACGAAACAAAATGAGTGAATCTACAC 58.647 34.615 0.00 0.00 40.60 2.90
2988 3043 7.490962 ACGAAACAAAATGAGTGAATCTACA 57.509 32.000 0.00 0.00 0.00 2.74
2989 3044 9.478019 CATACGAAACAAAATGAGTGAATCTAC 57.522 33.333 0.00 0.00 0.00 2.59
2990 3045 9.214957 ACATACGAAACAAAATGAGTGAATCTA 57.785 29.630 0.00 0.00 0.00 1.98
2991 3046 8.099364 ACATACGAAACAAAATGAGTGAATCT 57.901 30.769 0.00 0.00 0.00 2.40
2992 3047 9.478019 CTACATACGAAACAAAATGAGTGAATC 57.522 33.333 0.00 0.00 0.00 2.52
2993 3048 8.999431 ACTACATACGAAACAAAATGAGTGAAT 58.001 29.630 0.00 0.00 0.00 2.57
2994 3049 8.373048 ACTACATACGAAACAAAATGAGTGAA 57.627 30.769 0.00 0.00 0.00 3.18
2995 3050 7.654116 TGACTACATACGAAACAAAATGAGTGA 59.346 33.333 0.00 0.00 0.00 3.41
2996 3051 7.792925 TGACTACATACGAAACAAAATGAGTG 58.207 34.615 0.00 0.00 0.00 3.51
2997 3052 7.956420 TGACTACATACGAAACAAAATGAGT 57.044 32.000 0.00 0.00 0.00 3.41
2998 3053 8.655970 TGATGACTACATACGAAACAAAATGAG 58.344 33.333 0.00 0.00 36.82 2.90
2999 3054 8.541133 TGATGACTACATACGAAACAAAATGA 57.459 30.769 0.00 0.00 36.82 2.57
3000 3055 9.773328 AATGATGACTACATACGAAACAAAATG 57.227 29.630 0.00 0.00 36.82 2.32
3002 3057 9.605955 CAAATGATGACTACATACGAAACAAAA 57.394 29.630 0.00 0.00 36.82 2.44
3003 3058 8.994170 TCAAATGATGACTACATACGAAACAAA 58.006 29.630 0.00 0.00 36.82 2.83
3004 3059 8.541133 TCAAATGATGACTACATACGAAACAA 57.459 30.769 0.00 0.00 36.82 2.83
3005 3060 8.541133 TTCAAATGATGACTACATACGAAACA 57.459 30.769 0.00 0.00 37.92 2.83
3006 3061 9.262472 GTTTCAAATGATGACTACATACGAAAC 57.738 33.333 1.67 1.67 39.20 2.78
3007 3062 8.447833 GGTTTCAAATGATGACTACATACGAAA 58.552 33.333 0.00 0.00 37.92 3.46
3008 3063 7.822334 AGGTTTCAAATGATGACTACATACGAA 59.178 33.333 0.00 0.00 37.92 3.85
3009 3064 7.327975 AGGTTTCAAATGATGACTACATACGA 58.672 34.615 0.00 0.00 37.92 3.43
3010 3065 7.492669 AGAGGTTTCAAATGATGACTACATACG 59.507 37.037 0.00 0.00 37.92 3.06
3011 3066 8.723942 AGAGGTTTCAAATGATGACTACATAC 57.276 34.615 0.00 0.00 37.92 2.39
3013 3068 9.739276 TTTAGAGGTTTCAAATGATGACTACAT 57.261 29.630 0.00 0.00 37.92 2.29
3014 3069 9.567776 TTTTAGAGGTTTCAAATGATGACTACA 57.432 29.630 0.00 0.00 37.92 2.74
3017 3072 9.354673 TCTTTTTAGAGGTTTCAAATGATGACT 57.645 29.630 0.00 0.00 37.92 3.41
3018 3073 9.399403 GTCTTTTTAGAGGTTTCAAATGATGAC 57.601 33.333 0.00 0.00 37.92 3.06
3019 3074 9.130661 TGTCTTTTTAGAGGTTTCAAATGATGA 57.869 29.630 0.00 0.00 35.85 2.92
3020 3075 9.748708 TTGTCTTTTTAGAGGTTTCAAATGATG 57.251 29.630 0.00 0.00 0.00 3.07
3037 3092 9.855021 CATCCGTTCCTAAATATTTGTCTTTTT 57.145 29.630 11.05 0.00 0.00 1.94
3038 3093 8.466798 CCATCCGTTCCTAAATATTTGTCTTTT 58.533 33.333 11.05 0.00 0.00 2.27
3039 3094 7.832187 TCCATCCGTTCCTAAATATTTGTCTTT 59.168 33.333 11.05 0.00 0.00 2.52
3040 3095 7.343357 TCCATCCGTTCCTAAATATTTGTCTT 58.657 34.615 11.05 0.00 0.00 3.01
3041 3096 6.895782 TCCATCCGTTCCTAAATATTTGTCT 58.104 36.000 11.05 0.00 0.00 3.41
3042 3097 6.766467 ACTCCATCCGTTCCTAAATATTTGTC 59.234 38.462 11.05 0.00 0.00 3.18
3043 3098 6.659824 ACTCCATCCGTTCCTAAATATTTGT 58.340 36.000 11.05 0.00 0.00 2.83
3044 3099 8.148351 TCTACTCCATCCGTTCCTAAATATTTG 58.852 37.037 11.05 1.40 0.00 2.32
3045 3100 8.258850 TCTACTCCATCCGTTCCTAAATATTT 57.741 34.615 5.89 5.89 0.00 1.40
3046 3101 7.728981 TCTCTACTCCATCCGTTCCTAAATATT 59.271 37.037 0.00 0.00 0.00 1.28
3047 3102 7.239438 TCTCTACTCCATCCGTTCCTAAATAT 58.761 38.462 0.00 0.00 0.00 1.28
3048 3103 6.607970 TCTCTACTCCATCCGTTCCTAAATA 58.392 40.000 0.00 0.00 0.00 1.40
3049 3104 5.455872 TCTCTACTCCATCCGTTCCTAAAT 58.544 41.667 0.00 0.00 0.00 1.40
3050 3105 4.863548 TCTCTACTCCATCCGTTCCTAAA 58.136 43.478 0.00 0.00 0.00 1.85
3051 3106 4.515028 TCTCTACTCCATCCGTTCCTAA 57.485 45.455 0.00 0.00 0.00 2.69
3052 3107 4.104261 TCATCTCTACTCCATCCGTTCCTA 59.896 45.833 0.00 0.00 0.00 2.94
3053 3108 3.117474 TCATCTCTACTCCATCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
3054 3109 3.223435 TCATCTCTACTCCATCCGTTCC 58.777 50.000 0.00 0.00 0.00 3.62
3055 3110 3.886505 ACTCATCTCTACTCCATCCGTTC 59.113 47.826 0.00 0.00 0.00 3.95
3056 3111 3.904717 ACTCATCTCTACTCCATCCGTT 58.095 45.455 0.00 0.00 0.00 4.44
3057 3112 3.586470 ACTCATCTCTACTCCATCCGT 57.414 47.619 0.00 0.00 0.00 4.69
3058 3113 5.067273 ACTTACTCATCTCTACTCCATCCG 58.933 45.833 0.00 0.00 0.00 4.18
3059 3114 6.150474 GCTACTTACTCATCTCTACTCCATCC 59.850 46.154 0.00 0.00 0.00 3.51
3060 3115 6.712998 TGCTACTTACTCATCTCTACTCCATC 59.287 42.308 0.00 0.00 0.00 3.51
3061 3116 6.606069 TGCTACTTACTCATCTCTACTCCAT 58.394 40.000 0.00 0.00 0.00 3.41
3062 3117 6.002653 TGCTACTTACTCATCTCTACTCCA 57.997 41.667 0.00 0.00 0.00 3.86
3063 3118 7.367285 CAATGCTACTTACTCATCTCTACTCC 58.633 42.308 0.00 0.00 0.00 3.85
3064 3119 7.013846 ACCAATGCTACTTACTCATCTCTACTC 59.986 40.741 0.00 0.00 0.00 2.59
3065 3120 6.836527 ACCAATGCTACTTACTCATCTCTACT 59.163 38.462 0.00 0.00 0.00 2.57
3066 3121 6.920758 CACCAATGCTACTTACTCATCTCTAC 59.079 42.308 0.00 0.00 0.00 2.59
3067 3122 7.043961 CACCAATGCTACTTACTCATCTCTA 57.956 40.000 0.00 0.00 0.00 2.43
3068 3123 5.911752 CACCAATGCTACTTACTCATCTCT 58.088 41.667 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.