Multiple sequence alignment - TraesCS6D01G245900

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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 TraesCS6D01G245900 chr6D 100.000 4310 0 0 1 4310 348038358 348034049 0.000000e+00 7960
1 TraesCS6D01G245900 chr6B 89.929 2552 109 37 3 2473 532140704 532143188 0.000000e+00 3153
2 TraesCS6D01G245900 chr6B 88.455 1845 133 41 2511 4308 532143256 532145067 0.000000e+00 2154
3 TraesCS6D01G245900 chr6A 87.747 2579 173 66 1824 4310 495458845 495461372 0.000000e+00 2880
4 TraesCS6D01G245900 chr6A 89.004 773 22 23 44 776 495457239 495457988 0.000000e+00 898
5 TraesCS6D01G245900 chr6A 86.509 593 19 25 804 1338 495457978 495458567 2.870000e-166 595
6 TraesCS6D01G245900 chr6A 87.500 200 9 9 1520 1703 495458651 495458850 2.610000e-52 217
7 TraesCS6D01G245900 chr1D 98.462 260 4 0 2944 3203 455204960 455204701 3.930000e-125 459


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 TraesCS6D01G245900 chr6D 348034049 348038358 4309 True 7960.0 7960 100.000 1 4310 1 chr6D.!!$R1 4309
1 TraesCS6D01G245900 chr6B 532140704 532145067 4363 False 2653.5 3153 89.192 3 4308 2 chr6B.!!$F1 4305
2 TraesCS6D01G245900 chr6A 495457239 495461372 4133 False 1147.5 2880 87.690 44 4310 4 chr6A.!!$F1 4266

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
24 25 0.033991 AGAGAGCCAGACTTCGCCTA 60.034 55.0 0.0 0.0 0.00 3.93 F
1539 1684 0.032813 ATCTGTGGCCCCATTTCTGG 60.033 55.0 0.0 0.0 42.73 3.86 F
2497 2778 0.036388 GCTGGATCAGTCCCGTCAAA 60.036 55.0 0.0 0.0 44.41 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2067 0.961753 GCTTTTAGCAGGTGCAGGTT 59.038 50.0 4.48 0.00 45.16 3.50 R
2639 2925 0.098376 CGCCTTCAGAGAGCAATTGC 59.902 55.0 23.05 23.05 42.49 3.56 R
4024 4366 0.251341 GGAGCTGTTTGGGGTGATGT 60.251 55.0 0.00 0.00 0.00 3.06 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 0.033991 AGAGAGCCAGACTTCGCCTA 60.034 55.000 0.00 0.00 0.00 3.93
120 142 2.065512 TGTTGTCGTGATCATTGACCG 58.934 47.619 21.42 11.27 0.00 4.79
121 143 1.393539 GTTGTCGTGATCATTGACCGG 59.606 52.381 21.42 0.00 0.00 5.28
122 144 0.739462 TGTCGTGATCATTGACCGGC 60.739 55.000 21.42 12.75 0.00 6.13
123 145 1.518352 TCGTGATCATTGACCGGCG 60.518 57.895 0.00 0.00 0.00 6.46
124 146 1.518352 CGTGATCATTGACCGGCGA 60.518 57.895 9.30 0.00 0.00 5.54
125 147 1.482621 CGTGATCATTGACCGGCGAG 61.483 60.000 9.30 0.06 0.00 5.03
127 149 2.203070 ATCATTGACCGGCGAGGC 60.203 61.111 9.30 0.17 46.52 4.70
128 150 4.812476 TCATTGACCGGCGAGGCG 62.812 66.667 9.30 12.20 46.52 5.52
129 151 4.812476 CATTGACCGGCGAGGCGA 62.812 66.667 20.49 0.00 46.52 5.54
130 152 4.814294 ATTGACCGGCGAGGCGAC 62.814 66.667 20.49 13.54 46.52 5.19
137 159 4.778143 GGCGAGGCGACACCCAAT 62.778 66.667 0.00 0.00 40.58 3.16
138 160 3.195698 GCGAGGCGACACCCAATC 61.196 66.667 0.00 0.00 40.58 2.67
139 161 2.885644 CGAGGCGACACCCAATCG 60.886 66.667 0.00 0.00 40.58 3.34
155 177 1.972198 TCGCCAACGATCTTCAGGT 59.028 52.632 0.00 0.00 45.12 4.00
220 244 2.375766 GGCGCGTCATGATCGATCC 61.376 63.158 22.31 14.60 0.00 3.36
435 481 0.896226 GGGTCGGTTGTCTAGCTCTT 59.104 55.000 0.00 0.00 0.00 2.85
437 483 2.338500 GGTCGGTTGTCTAGCTCTTTG 58.662 52.381 0.00 0.00 0.00 2.77
438 484 2.288886 GGTCGGTTGTCTAGCTCTTTGT 60.289 50.000 0.00 0.00 0.00 2.83
685 751 1.141881 CCCGGCCATATAGCTAGCG 59.858 63.158 9.55 0.00 0.00 4.26
755 825 2.551912 CCCACGCCAACTTCACACC 61.552 63.158 0.00 0.00 0.00 4.16
857 927 1.884464 CACGCACACACACAGAGCT 60.884 57.895 0.00 0.00 0.00 4.09
859 929 1.592400 CGCACACACACAGAGCTGA 60.592 57.895 4.21 0.00 0.00 4.26
862 932 0.882042 CACACACACAGAGCTGACCC 60.882 60.000 4.21 0.00 0.00 4.46
864 934 0.969149 CACACACAGAGCTGACCCTA 59.031 55.000 4.21 0.00 0.00 3.53
867 937 1.203523 CACACAGAGCTGACCCTACTC 59.796 57.143 4.21 0.00 0.00 2.59
870 940 1.076632 AGAGCTGACCCTACTCCGG 60.077 63.158 0.00 0.00 0.00 5.14
912 990 1.606668 CACGAGAGGAAGCTAGCTAGG 59.393 57.143 19.70 4.96 0.00 3.02
1159 1258 0.250513 CAGTAAGCACCACCTCCTCC 59.749 60.000 0.00 0.00 0.00 4.30
1160 1259 0.117340 AGTAAGCACCACCTCCTCCT 59.883 55.000 0.00 0.00 0.00 3.69
1161 1260 0.984995 GTAAGCACCACCTCCTCCTT 59.015 55.000 0.00 0.00 0.00 3.36
1163 1262 0.111253 AAGCACCACCTCCTCCTTTG 59.889 55.000 0.00 0.00 0.00 2.77
1166 1265 0.984230 CACCACCTCCTCCTTTGCTA 59.016 55.000 0.00 0.00 0.00 3.49
1378 1510 1.828979 GCACAGGAATTCGGGGTTTA 58.171 50.000 0.00 0.00 0.00 2.01
1379 1511 2.164338 GCACAGGAATTCGGGGTTTAA 58.836 47.619 0.00 0.00 0.00 1.52
1385 1517 5.221362 ACAGGAATTCGGGGTTTAAACTTTG 60.221 40.000 17.50 7.87 0.00 2.77
1387 1519 5.010314 AGGAATTCGGGGTTTAAACTTTGAC 59.990 40.000 17.50 0.97 0.00 3.18
1390 1522 3.742385 TCGGGGTTTAAACTTTGACGAT 58.258 40.909 17.50 0.00 0.00 3.73
1391 1523 4.136051 TCGGGGTTTAAACTTTGACGATT 58.864 39.130 17.50 0.00 0.00 3.34
1392 1524 5.303971 TCGGGGTTTAAACTTTGACGATTA 58.696 37.500 17.50 0.00 0.00 1.75
1394 1526 6.073112 TCGGGGTTTAAACTTTGACGATTAAG 60.073 38.462 17.50 0.00 0.00 1.85
1395 1527 6.293571 CGGGGTTTAAACTTTGACGATTAAGT 60.294 38.462 17.50 0.00 36.20 2.24
1396 1528 7.095271 CGGGGTTTAAACTTTGACGATTAAGTA 60.095 37.037 17.50 0.00 33.66 2.24
1397 1529 8.733458 GGGGTTTAAACTTTGACGATTAAGTAT 58.267 33.333 17.50 0.00 33.66 2.12
1410 1546 9.132923 TGACGATTAAGTATAGAGTGAAGGATT 57.867 33.333 0.00 0.00 0.00 3.01
1536 1680 1.478105 GTTGATCTGTGGCCCCATTTC 59.522 52.381 0.00 0.00 0.00 2.17
1539 1684 0.032813 ATCTGTGGCCCCATTTCTGG 60.033 55.000 0.00 0.00 42.73 3.86
1567 1712 2.158711 TCTGTTCTGATCCATCCATGCC 60.159 50.000 0.00 0.00 0.00 4.40
1725 1892 2.174363 TCCACTCAACATCACTGCAG 57.826 50.000 13.48 13.48 0.00 4.41
1746 1913 7.455058 TGCAGACTAGTTATTCCCTACAAAAA 58.545 34.615 0.00 0.00 0.00 1.94
1791 1958 5.339611 CGTTGCTGTTTTTATTGAGTGCTAC 59.660 40.000 0.00 0.00 0.00 3.58
1792 1959 6.438763 GTTGCTGTTTTTATTGAGTGCTACT 58.561 36.000 0.00 0.00 0.00 2.57
1793 1960 7.570507 CGTTGCTGTTTTTATTGAGTGCTACTA 60.571 37.037 0.00 0.00 0.00 1.82
1794 1961 7.364522 TGCTGTTTTTATTGAGTGCTACTAG 57.635 36.000 0.00 0.00 0.00 2.57
1795 1962 6.934645 TGCTGTTTTTATTGAGTGCTACTAGT 59.065 34.615 0.00 0.00 0.00 2.57
1796 1963 8.092068 TGCTGTTTTTATTGAGTGCTACTAGTA 58.908 33.333 1.89 1.89 0.00 1.82
1809 1976 8.228035 AGTGCTACTAGTAATTCCTAACTCTG 57.772 38.462 3.76 0.00 0.00 3.35
1813 1980 8.301002 GCTACTAGTAATTCCTAACTCTGGATG 58.699 40.741 3.76 0.00 33.09 3.51
1824 1991 6.013379 TCCTAACTCTGGATGATGTCAAAACT 60.013 38.462 0.00 0.00 0.00 2.66
1900 2067 2.052468 AGAGGAGGTATGCATGCATGA 58.948 47.619 37.43 21.08 37.82 3.07
1906 2073 1.269413 GGTATGCATGCATGAACCTGC 60.269 52.381 37.43 18.27 42.62 4.85
1947 2138 6.316390 CACTTAGATTAGGGAACATGACAACC 59.684 42.308 0.00 0.00 0.00 3.77
2000 2191 4.084433 GCATTTGACGTTGATGCATTTTGT 60.084 37.500 20.03 0.00 44.18 2.83
2013 2204 4.508662 TGCATTTTGTTTTTCGTTTCCCT 58.491 34.783 0.00 0.00 0.00 4.20
2041 2234 3.087031 CTGTTCCAAATCTCACATGCCT 58.913 45.455 0.00 0.00 0.00 4.75
2092 2285 2.482142 GCAGGGTATCAGTTTCTCCTCG 60.482 54.545 0.00 0.00 0.00 4.63
2163 2356 2.235155 TCAACCTTATACCAAGAGCGCA 59.765 45.455 11.47 0.00 0.00 6.09
2185 2380 6.019479 CGCAGGTTCATGTCTAATTTCTAGTC 60.019 42.308 0.00 0.00 0.00 2.59
2448 2684 9.338291 GCATGTCTGCTAATTAATATGTTCATG 57.662 33.333 0.00 0.00 45.32 3.07
2451 2687 8.562052 TGTCTGCTAATTAATATGTTCATGCAG 58.438 33.333 0.00 0.00 43.53 4.41
2480 2761 6.751514 TTTATACCGACATCACAAAATGCT 57.248 33.333 0.00 0.00 0.00 3.79
2489 2770 4.157289 ACATCACAAAATGCTGGATCAGTC 59.843 41.667 0.00 0.00 33.43 3.51
2490 2771 3.084039 TCACAAAATGCTGGATCAGTCC 58.916 45.455 0.00 0.00 45.31 3.85
2491 2772 2.165030 CACAAAATGCTGGATCAGTCCC 59.835 50.000 0.00 0.00 44.41 4.46
2492 2773 1.402968 CAAAATGCTGGATCAGTCCCG 59.597 52.381 0.00 0.00 44.41 5.14
2493 2774 0.620556 AAATGCTGGATCAGTCCCGT 59.379 50.000 0.00 0.00 44.41 5.28
2494 2775 0.179000 AATGCTGGATCAGTCCCGTC 59.821 55.000 0.00 0.00 44.41 4.79
2495 2776 0.977627 ATGCTGGATCAGTCCCGTCA 60.978 55.000 0.00 0.00 44.41 4.35
2496 2777 1.191489 TGCTGGATCAGTCCCGTCAA 61.191 55.000 0.00 0.00 44.41 3.18
2497 2778 0.036388 GCTGGATCAGTCCCGTCAAA 60.036 55.000 0.00 0.00 44.41 2.69
2498 2779 2.009042 GCTGGATCAGTCCCGTCAAAG 61.009 57.143 0.00 0.00 44.41 2.77
2499 2780 1.550524 CTGGATCAGTCCCGTCAAAGA 59.449 52.381 0.00 0.00 44.41 2.52
2500 2781 1.974957 TGGATCAGTCCCGTCAAAGAA 59.025 47.619 0.00 0.00 44.41 2.52
2501 2782 2.370519 TGGATCAGTCCCGTCAAAGAAA 59.629 45.455 0.00 0.00 44.41 2.52
2502 2783 3.181449 TGGATCAGTCCCGTCAAAGAAAA 60.181 43.478 0.00 0.00 44.41 2.29
2503 2784 3.818773 GGATCAGTCCCGTCAAAGAAAAA 59.181 43.478 0.00 0.00 38.69 1.94
2504 2785 4.459337 GGATCAGTCCCGTCAAAGAAAAAT 59.541 41.667 0.00 0.00 38.69 1.82
2505 2786 4.829064 TCAGTCCCGTCAAAGAAAAATG 57.171 40.909 0.00 0.00 0.00 2.32
2506 2787 3.004315 TCAGTCCCGTCAAAGAAAAATGC 59.996 43.478 0.00 0.00 0.00 3.56
2507 2788 3.004734 CAGTCCCGTCAAAGAAAAATGCT 59.995 43.478 0.00 0.00 0.00 3.79
2508 2789 3.004734 AGTCCCGTCAAAGAAAAATGCTG 59.995 43.478 0.00 0.00 0.00 4.41
2509 2790 2.061028 CCCGTCAAAGAAAAATGCTGC 58.939 47.619 0.00 0.00 0.00 5.25
2520 2801 6.374565 AGAAAAATGCTGCATCAGTCTATC 57.625 37.500 16.55 7.78 33.43 2.08
2586 2867 2.325583 ACATATGAAATGTCGCCGGT 57.674 45.000 10.38 0.00 0.00 5.28
2594 2875 2.225068 AATGTCGCCGGTCTGATTAG 57.775 50.000 1.90 0.00 0.00 1.73
2595 2876 1.112113 ATGTCGCCGGTCTGATTAGT 58.888 50.000 1.90 0.00 0.00 2.24
2596 2877 0.454600 TGTCGCCGGTCTGATTAGTC 59.545 55.000 1.90 0.00 0.00 2.59
2597 2878 0.739561 GTCGCCGGTCTGATTAGTCT 59.260 55.000 1.90 0.00 0.00 3.24
2598 2879 1.134560 GTCGCCGGTCTGATTAGTCTT 59.865 52.381 1.90 0.00 0.00 3.01
2601 2887 3.444742 TCGCCGGTCTGATTAGTCTTAAA 59.555 43.478 1.90 0.00 0.00 1.52
2638 2924 3.838565 TGTTTGGTGGGTTGTATGTCAT 58.161 40.909 0.00 0.00 0.00 3.06
2639 2925 3.571828 TGTTTGGTGGGTTGTATGTCATG 59.428 43.478 0.00 0.00 0.00 3.07
2645 2931 4.175516 GTGGGTTGTATGTCATGCAATTG 58.824 43.478 17.78 0.00 37.22 2.32
2646 2932 3.189285 GGGTTGTATGTCATGCAATTGC 58.811 45.455 23.69 23.69 37.22 3.56
2655 2941 3.439129 TGTCATGCAATTGCTCTCTGAAG 59.561 43.478 29.37 7.00 42.66 3.02
2693 3000 9.979578 AAATACATTCTTGAACACTTTTGCATA 57.020 25.926 0.00 0.00 0.00 3.14
2752 3059 3.502211 TCAAATCGAAGTCCAAAGGAAGC 59.498 43.478 0.00 0.00 31.38 3.86
2781 3088 6.663944 GAACAGCTCGAGGTAACAAATTAT 57.336 37.500 18.15 0.00 41.41 1.28
2782 3089 7.073342 GAACAGCTCGAGGTAACAAATTATT 57.927 36.000 18.15 0.99 41.41 1.40
2783 3090 7.448748 AACAGCTCGAGGTAACAAATTATTT 57.551 32.000 18.15 0.00 41.41 1.40
2784 3091 7.073342 ACAGCTCGAGGTAACAAATTATTTC 57.927 36.000 18.15 0.00 41.41 2.17
2785 3092 6.093633 ACAGCTCGAGGTAACAAATTATTTCC 59.906 38.462 18.15 0.00 41.41 3.13
2786 3093 6.093495 CAGCTCGAGGTAACAAATTATTTCCA 59.907 38.462 18.15 0.00 41.41 3.53
2787 3094 6.316390 AGCTCGAGGTAACAAATTATTTCCAG 59.684 38.462 16.99 0.00 41.41 3.86
2788 3095 6.315393 GCTCGAGGTAACAAATTATTTCCAGA 59.685 38.462 15.58 0.00 41.41 3.86
2789 3096 7.466050 GCTCGAGGTAACAAATTATTTCCAGAG 60.466 40.741 15.58 13.14 41.41 3.35
2790 3097 6.315393 TCGAGGTAACAAATTATTTCCAGAGC 59.685 38.462 0.00 0.00 41.41 4.09
2793 3100 7.830739 AGGTAACAAATTATTTCCAGAGCAAG 58.169 34.615 0.00 0.00 41.41 4.01
2814 3121 2.686405 GCATCATCAACATGAGCCTCAA 59.314 45.455 0.00 0.00 42.53 3.02
2816 3123 4.202121 GCATCATCAACATGAGCCTCAATT 60.202 41.667 0.00 0.00 42.53 2.32
2817 3124 5.009310 GCATCATCAACATGAGCCTCAATTA 59.991 40.000 0.00 0.00 42.53 1.40
2818 3125 6.669278 CATCATCAACATGAGCCTCAATTAG 58.331 40.000 0.00 0.00 42.53 1.73
2819 3126 5.748402 TCATCAACATGAGCCTCAATTAGT 58.252 37.500 0.00 0.00 33.80 2.24
2820 3127 5.819379 TCATCAACATGAGCCTCAATTAGTC 59.181 40.000 0.00 0.00 33.80 2.59
2821 3128 5.164620 TCAACATGAGCCTCAATTAGTCA 57.835 39.130 0.00 0.00 0.00 3.41
2822 3129 5.748402 TCAACATGAGCCTCAATTAGTCAT 58.252 37.500 0.00 0.00 0.00 3.06
2823 3130 6.182627 TCAACATGAGCCTCAATTAGTCATT 58.817 36.000 0.00 0.00 0.00 2.57
2824 3131 6.660521 TCAACATGAGCCTCAATTAGTCATTT 59.339 34.615 0.00 0.00 0.00 2.32
2826 3133 7.472334 ACATGAGCCTCAATTAGTCATTTTT 57.528 32.000 0.00 0.00 0.00 1.94
2828 3135 6.515272 TGAGCCTCAATTAGTCATTTTTCC 57.485 37.500 0.00 0.00 0.00 3.13
2834 3141 7.364144 GCCTCAATTAGTCATTTTTCCAATCCT 60.364 37.037 0.00 0.00 0.00 3.24
2843 3150 2.692709 TTTCCAATCCTTGCCTCCAA 57.307 45.000 0.00 0.00 0.00 3.53
2844 3151 1.923356 TTCCAATCCTTGCCTCCAAC 58.077 50.000 0.00 0.00 0.00 3.77
2846 3153 1.146774 TCCAATCCTTGCCTCCAACAA 59.853 47.619 0.00 0.00 0.00 2.83
2849 3156 2.564062 CAATCCTTGCCTCCAACAACAT 59.436 45.455 0.00 0.00 0.00 2.71
2851 3158 3.737559 TCCTTGCCTCCAACAACATAT 57.262 42.857 0.00 0.00 0.00 1.78
2852 3159 4.046286 TCCTTGCCTCCAACAACATATT 57.954 40.909 0.00 0.00 0.00 1.28
2853 3160 4.415596 TCCTTGCCTCCAACAACATATTT 58.584 39.130 0.00 0.00 0.00 1.40
2855 3162 5.306678 TCCTTGCCTCCAACAACATATTTTT 59.693 36.000 0.00 0.00 0.00 1.94
2859 3166 5.988561 TGCCTCCAACAACATATTTTTGTTC 59.011 36.000 8.61 1.07 43.71 3.18
2860 3167 5.988561 GCCTCCAACAACATATTTTTGTTCA 59.011 36.000 8.61 0.87 43.71 3.18
2863 3170 7.042119 CCTCCAACAACATATTTTTGTTCAACC 60.042 37.037 8.61 0.00 43.71 3.77
2864 3171 6.763610 TCCAACAACATATTTTTGTTCAACCC 59.236 34.615 8.61 0.00 43.71 4.11
2866 3173 7.281999 CCAACAACATATTTTTGTTCAACCCTT 59.718 33.333 8.61 0.00 43.71 3.95
2867 3174 7.784633 ACAACATATTTTTGTTCAACCCTTG 57.215 32.000 0.00 0.00 37.73 3.61
2868 3175 7.560368 ACAACATATTTTTGTTCAACCCTTGA 58.440 30.769 0.00 0.00 37.73 3.02
2869 3176 7.710475 ACAACATATTTTTGTTCAACCCTTGAG 59.290 33.333 0.00 0.00 41.38 3.02
2871 3178 7.209475 ACATATTTTTGTTCAACCCTTGAGTG 58.791 34.615 0.00 0.00 41.38 3.51
2872 3179 5.675684 ATTTTTGTTCAACCCTTGAGTGT 57.324 34.783 0.00 0.00 41.38 3.55
2873 3180 5.476091 TTTTTGTTCAACCCTTGAGTGTT 57.524 34.783 0.00 0.00 41.38 3.32
2875 3182 3.644966 TGTTCAACCCTTGAGTGTTCT 57.355 42.857 0.00 0.00 41.38 3.01
2876 3183 3.541632 TGTTCAACCCTTGAGTGTTCTC 58.458 45.455 0.00 0.00 41.38 2.87
2982 3295 0.912006 AGGCCCAGAAGAACCTCTCC 60.912 60.000 0.00 0.00 0.00 3.71
2991 3304 1.476477 AGAACCTCTCCTACGAAGCC 58.524 55.000 0.00 0.00 0.00 4.35
3015 3328 1.465794 GAGACGCAACCCTAGAGACT 58.534 55.000 0.00 0.00 0.00 3.24
3048 3361 0.606604 TCACCGACTTCAACCTAGCC 59.393 55.000 0.00 0.00 0.00 3.93
3174 3496 4.849329 CTCTACCACGGCGGCGAC 62.849 72.222 38.93 7.01 39.03 5.19
3192 3514 2.175811 GACGTGAAATGCGCCACC 59.824 61.111 4.18 0.00 0.00 4.61
3231 3553 2.553028 GCTGGACCTGAACATCAAAGGA 60.553 50.000 1.91 0.00 34.97 3.36
3385 3707 3.369471 CCCTACGAGAGATTCTTTTGGCA 60.369 47.826 0.00 0.00 0.00 4.92
3436 3764 6.373216 TGGTTACACTTTATACGTACGTACCT 59.627 38.462 28.99 17.34 33.01 3.08
3557 3885 6.608002 ACCTCCTAAAATTCTGATCGACTACT 59.392 38.462 0.00 0.00 0.00 2.57
3558 3886 7.778853 ACCTCCTAAAATTCTGATCGACTACTA 59.221 37.037 0.00 0.00 0.00 1.82
3559 3887 8.293867 CCTCCTAAAATTCTGATCGACTACTAG 58.706 40.741 0.00 0.00 0.00 2.57
3571 3902 6.710744 TGATCGACTACTAGAACATAGCATCA 59.289 38.462 0.00 0.00 0.00 3.07
3610 3941 3.819337 CTGTTGAGGGATGGCATTATGAG 59.181 47.826 0.00 0.00 0.00 2.90
3752 4087 7.282585 AGTAAGCAGATCACATTATTGGCTTA 58.717 34.615 0.00 0.00 40.45 3.09
3759 4094 5.261209 TCACATTATTGGCTTATTGTGGC 57.739 39.130 16.01 0.00 35.59 5.01
3786 4121 0.827507 AAGTCAATGGTGGGTGGTGC 60.828 55.000 0.00 0.00 0.00 5.01
3807 4142 4.023792 TGCTTTGCATGTCTTGACTAACTG 60.024 41.667 2.35 0.00 31.71 3.16
3826 4161 3.840666 ACTGGTAGAAGAGGAGCAATTGA 59.159 43.478 10.34 0.00 0.00 2.57
3849 4184 4.525912 AATTCAAATTTTCGAGCCTGCT 57.474 36.364 0.00 0.00 0.00 4.24
3874 4209 5.679734 TGAAAGTGCACTTCTGAATTCTC 57.320 39.130 31.20 21.53 34.61 2.87
3903 4238 2.139917 TGTCAACACACGTATCCTTGC 58.860 47.619 0.00 0.00 0.00 4.01
3905 4240 2.412089 GTCAACACACGTATCCTTGCTC 59.588 50.000 0.00 0.00 0.00 4.26
3906 4241 1.732259 CAACACACGTATCCTTGCTCC 59.268 52.381 0.00 0.00 0.00 4.70
3926 4263 3.809832 TCCTTCTTCGAAAAAGCACTCAG 59.190 43.478 5.67 0.00 0.00 3.35
3954 4291 2.610374 TGTCCAAACGAGTAGTGCAAAC 59.390 45.455 0.00 0.00 0.00 2.93
4014 4356 5.333581 TGACCTTCTTCTTCCTCTCATACA 58.666 41.667 0.00 0.00 0.00 2.29
4017 4359 4.442753 CCTTCTTCTTCCTCTCATACAGCC 60.443 50.000 0.00 0.00 0.00 4.85
4163 4505 4.383118 CCGAAAGAGCCTTAGATCCAAGAA 60.383 45.833 2.11 0.00 0.00 2.52
4281 4623 1.514014 CCGCCGCTGCATTACAAAC 60.514 57.895 0.00 0.00 37.32 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.478879 GCGAAGTCTGGCTCTCTTAGTC 60.479 54.545 0.00 0.00 0.00 2.59
1 2 1.474879 GCGAAGTCTGGCTCTCTTAGT 59.525 52.381 0.00 0.00 0.00 2.24
5 6 0.033991 TAGGCGAAGTCTGGCTCTCT 60.034 55.000 0.00 0.00 46.61 3.10
12 13 2.767505 ACCAAAACTAGGCGAAGTCTG 58.232 47.619 0.00 0.00 46.61 3.51
15 16 4.814771 GCATATACCAAAACTAGGCGAAGT 59.185 41.667 0.00 0.00 0.00 3.01
19 20 2.478894 CCGCATATACCAAAACTAGGCG 59.521 50.000 0.00 0.00 43.07 5.52
24 25 7.633193 TCAAAATACCGCATATACCAAAACT 57.367 32.000 0.00 0.00 0.00 2.66
120 142 4.778143 ATTGGGTGTCGCCTCGCC 62.778 66.667 1.66 0.00 37.43 5.54
121 143 3.195698 GATTGGGTGTCGCCTCGC 61.196 66.667 1.66 0.00 37.43 5.03
122 144 2.885644 CGATTGGGTGTCGCCTCG 60.886 66.667 1.66 0.12 37.43 4.63
127 149 2.867472 GTTGGCGATTGGGTGTCG 59.133 61.111 0.00 0.00 41.77 4.35
128 150 1.669760 TCGTTGGCGATTGGGTGTC 60.670 57.895 0.00 0.00 42.81 3.67
129 151 2.428187 TCGTTGGCGATTGGGTGT 59.572 55.556 0.00 0.00 42.81 4.16
138 160 2.004583 TTACCTGAAGATCGTTGGCG 57.995 50.000 2.54 0.00 39.92 5.69
139 161 4.636206 AGATTTTACCTGAAGATCGTTGGC 59.364 41.667 2.54 0.00 34.53 4.52
140 162 6.018669 GCTAGATTTTACCTGAAGATCGTTGG 60.019 42.308 0.00 0.00 34.53 3.77
151 173 4.937620 TGCTCACTTGCTAGATTTTACCTG 59.062 41.667 1.04 0.00 0.00 4.00
155 177 7.553760 TGATCATTGCTCACTTGCTAGATTTTA 59.446 33.333 1.04 0.00 0.00 1.52
200 222 1.612469 GATCGATCATGACGCGCCTG 61.612 60.000 20.52 0.55 0.00 4.85
201 223 1.372251 GATCGATCATGACGCGCCT 60.372 57.895 20.52 0.00 0.00 5.52
202 224 2.375766 GGATCGATCATGACGCGCC 61.376 63.158 25.93 0.00 0.00 6.53
220 244 1.498865 AAGGCGCTGTCTGTTGTTCG 61.499 55.000 7.64 0.00 0.00 3.95
416 462 0.896226 AAGAGCTAGACAACCGACCC 59.104 55.000 0.00 0.00 0.00 4.46
435 481 3.526534 GCTAGGGTGCAAAACAAAACAA 58.473 40.909 0.00 0.00 0.00 2.83
437 483 2.124122 CGCTAGGGTGCAAAACAAAAC 58.876 47.619 0.00 0.00 0.00 2.43
438 484 1.537135 GCGCTAGGGTGCAAAACAAAA 60.537 47.619 8.77 0.00 46.98 2.44
685 751 1.505353 GAATGTGTGCTGCTGGCTC 59.495 57.895 0.00 1.52 42.39 4.70
851 921 1.388065 CCGGAGTAGGGTCAGCTCTG 61.388 65.000 0.00 0.00 35.88 3.35
852 922 1.076632 CCGGAGTAGGGTCAGCTCT 60.077 63.158 0.00 0.00 0.00 4.09
853 923 2.128507 CCCGGAGTAGGGTCAGCTC 61.129 68.421 0.73 0.00 46.38 4.09
862 932 4.304048 ACTGGTATATCTCCCGGAGTAG 57.696 50.000 14.36 0.00 0.00 2.57
864 934 3.117246 TCAACTGGTATATCTCCCGGAGT 60.117 47.826 14.36 4.74 0.00 3.85
867 937 3.119459 CGATCAACTGGTATATCTCCCGG 60.119 52.174 0.00 0.00 0.00 5.73
870 940 3.368531 GGCCGATCAACTGGTATATCTCC 60.369 52.174 0.00 0.00 0.00 3.71
871 941 3.258372 TGGCCGATCAACTGGTATATCTC 59.742 47.826 0.00 0.00 0.00 2.75
872 942 3.006967 GTGGCCGATCAACTGGTATATCT 59.993 47.826 0.00 0.00 0.00 1.98
874 944 2.288825 CGTGGCCGATCAACTGGTATAT 60.289 50.000 0.00 0.00 35.63 0.86
875 945 1.067974 CGTGGCCGATCAACTGGTATA 59.932 52.381 0.00 0.00 35.63 1.47
876 946 0.179084 CGTGGCCGATCAACTGGTAT 60.179 55.000 0.00 0.00 35.63 2.73
877 947 1.216977 CGTGGCCGATCAACTGGTA 59.783 57.895 0.00 0.00 35.63 3.25
912 990 2.317530 CCTCCTAGTTGGCAAGCTAC 57.682 55.000 0.00 0.00 35.26 3.58
921 1007 1.153349 GCCCTTCGCCTCCTAGTTG 60.153 63.158 0.00 0.00 0.00 3.16
1159 1258 2.012673 GCATGGAGTGGAGTAGCAAAG 58.987 52.381 0.00 0.00 0.00 2.77
1160 1259 1.350684 TGCATGGAGTGGAGTAGCAAA 59.649 47.619 0.00 0.00 0.00 3.68
1161 1260 0.983467 TGCATGGAGTGGAGTAGCAA 59.017 50.000 0.00 0.00 0.00 3.91
1163 1262 2.103094 TGTATGCATGGAGTGGAGTAGC 59.897 50.000 10.16 0.00 0.00 3.58
1166 1265 3.204306 CATGTATGCATGGAGTGGAGT 57.796 47.619 15.36 0.00 46.47 3.85
1214 1326 4.463879 CTGGAGCAGACCGGCTGG 62.464 72.222 22.05 11.02 45.99 4.85
1338 1470 1.400629 GCACACATGACATGCTGACAC 60.401 52.381 15.49 5.15 36.40 3.67
1341 1473 1.914531 GCGCACACATGACATGCTGA 61.915 55.000 15.49 0.00 37.20 4.26
1342 1474 1.513373 GCGCACACATGACATGCTG 60.513 57.895 15.49 14.14 37.20 4.41
1343 1475 1.967494 TGCGCACACATGACATGCT 60.967 52.632 15.49 0.24 37.20 3.79
1364 1496 5.224888 GTCAAAGTTTAAACCCCGAATTCC 58.775 41.667 14.72 0.00 0.00 3.01
1366 1498 4.579753 TCGTCAAAGTTTAAACCCCGAATT 59.420 37.500 14.72 0.00 0.00 2.17
1387 1519 9.843334 GGTAATCCTTCACTCTATACTTAATCG 57.157 37.037 0.00 0.00 0.00 3.34
1390 1522 8.000709 TCCGGTAATCCTTCACTCTATACTTAA 58.999 37.037 0.00 0.00 0.00 1.85
1391 1523 7.520798 TCCGGTAATCCTTCACTCTATACTTA 58.479 38.462 0.00 0.00 0.00 2.24
1392 1524 6.371278 TCCGGTAATCCTTCACTCTATACTT 58.629 40.000 0.00 0.00 0.00 2.24
1394 1526 5.183522 CCTCCGGTAATCCTTCACTCTATAC 59.816 48.000 0.00 0.00 0.00 1.47
1395 1527 5.322754 CCTCCGGTAATCCTTCACTCTATA 58.677 45.833 0.00 0.00 0.00 1.31
1396 1528 4.153411 CCTCCGGTAATCCTTCACTCTAT 58.847 47.826 0.00 0.00 0.00 1.98
1397 1529 3.563223 CCTCCGGTAATCCTTCACTCTA 58.437 50.000 0.00 0.00 0.00 2.43
1410 1546 1.284198 AGAGAGTTGTAGCCTCCGGTA 59.716 52.381 0.00 0.00 0.00 4.02
1446 1582 4.639135 TCATAACACACGGATCTCTCTG 57.361 45.455 0.00 0.00 0.00 3.35
1489 1625 5.405571 CGTCTCAAAGAAAAAGGAAGATCGA 59.594 40.000 0.00 0.00 0.00 3.59
1536 1680 4.580167 TGGATCAGAACAGAAAACAACCAG 59.420 41.667 0.00 0.00 0.00 4.00
1539 1684 5.241506 TGGATGGATCAGAACAGAAAACAAC 59.758 40.000 0.00 0.00 0.00 3.32
1567 1712 9.750125 TCAAATCAGTACTTGCATATACTACAG 57.250 33.333 9.43 0.00 30.36 2.74
1746 1913 7.148573 GCAACGATATACTATGCATAGCTGTTT 60.149 37.037 29.60 14.87 37.00 2.83
1754 1921 7.496529 AAAACAGCAACGATATACTATGCAT 57.503 32.000 3.79 3.79 39.42 3.96
1756 1923 9.878599 AATAAAAACAGCAACGATATACTATGC 57.121 29.630 0.00 0.00 37.28 3.14
1760 1927 9.162764 ACTCAATAAAAACAGCAACGATATACT 57.837 29.630 0.00 0.00 0.00 2.12
1761 1928 9.210426 CACTCAATAAAAACAGCAACGATATAC 57.790 33.333 0.00 0.00 0.00 1.47
1791 1958 8.865090 ACATCATCCAGAGTTAGGAATTACTAG 58.135 37.037 0.00 0.00 38.93 2.57
1792 1959 8.783660 ACATCATCCAGAGTTAGGAATTACTA 57.216 34.615 0.00 0.00 38.93 1.82
1793 1960 7.345653 TGACATCATCCAGAGTTAGGAATTACT 59.654 37.037 0.00 0.00 38.93 2.24
1794 1961 7.500992 TGACATCATCCAGAGTTAGGAATTAC 58.499 38.462 0.00 0.00 38.93 1.89
1795 1962 7.675161 TGACATCATCCAGAGTTAGGAATTA 57.325 36.000 0.00 0.00 38.93 1.40
1796 1963 6.566079 TGACATCATCCAGAGTTAGGAATT 57.434 37.500 0.00 0.00 38.93 2.17
1809 1976 8.514594 TGTATTTCTGAAGTTTTGACATCATCC 58.485 33.333 0.00 0.00 0.00 3.51
1813 1980 8.099364 TCCTGTATTTCTGAAGTTTTGACATC 57.901 34.615 0.00 0.00 0.00 3.06
1815 1982 7.040478 CCATCCTGTATTTCTGAAGTTTTGACA 60.040 37.037 0.00 0.00 0.00 3.58
1824 1991 4.949856 GCTTTCCCATCCTGTATTTCTGAA 59.050 41.667 0.00 0.00 0.00 3.02
1900 2067 0.961753 GCTTTTAGCAGGTGCAGGTT 59.038 50.000 4.48 0.00 45.16 3.50
2000 2191 4.223255 ACAGGGAAAAAGGGAAACGAAAAA 59.777 37.500 0.00 0.00 0.00 1.94
2013 2204 4.959210 TGTGAGATTTGGAACAGGGAAAAA 59.041 37.500 0.00 0.00 42.39 1.94
2041 2234 2.358898 GGCTGTGCAAAGAGAAGTTGAA 59.641 45.455 8.49 0.00 0.00 2.69
2071 2264 2.482142 CGAGGAGAAACTGATACCCTGC 60.482 54.545 0.00 0.00 0.00 4.85
2077 2270 0.744874 CCGCCGAGGAGAAACTGATA 59.255 55.000 0.00 0.00 45.00 2.15
2122 2315 1.331214 CTCACCCCATGTTGCTGTTT 58.669 50.000 0.00 0.00 0.00 2.83
2127 2320 0.598065 GTTGACTCACCCCATGTTGC 59.402 55.000 0.00 0.00 0.00 4.17
2185 2380 5.466728 CGTCCTGGTCATCATGGTTAATTAG 59.533 44.000 0.00 0.00 0.00 1.73
2304 2499 9.772973 ACAATCAAGTAAGTGTATTCTTGTGTA 57.227 29.630 0.00 0.00 38.53 2.90
2305 2500 8.559536 CACAATCAAGTAAGTGTATTCTTGTGT 58.440 33.333 0.00 0.00 38.53 3.72
2306 2501 8.773645 TCACAATCAAGTAAGTGTATTCTTGTG 58.226 33.333 0.00 0.00 40.45 3.33
2307 2502 8.902540 TCACAATCAAGTAAGTGTATTCTTGT 57.097 30.769 0.00 0.00 38.53 3.16
2308 2503 9.764870 CATCACAATCAAGTAAGTGTATTCTTG 57.235 33.333 0.00 0.00 38.69 3.02
2309 2504 8.950210 CCATCACAATCAAGTAAGTGTATTCTT 58.050 33.333 0.00 0.00 33.84 2.52
2310 2505 8.321353 TCCATCACAATCAAGTAAGTGTATTCT 58.679 33.333 0.00 0.00 33.84 2.40
2311 2506 8.391106 GTCCATCACAATCAAGTAAGTGTATTC 58.609 37.037 0.00 0.00 33.84 1.75
2312 2507 8.103305 AGTCCATCACAATCAAGTAAGTGTATT 58.897 33.333 0.00 0.00 33.84 1.89
2313 2508 7.624549 AGTCCATCACAATCAAGTAAGTGTAT 58.375 34.615 0.00 0.00 33.84 2.29
2314 2509 7.004555 AGTCCATCACAATCAAGTAAGTGTA 57.995 36.000 0.00 0.00 33.84 2.90
2315 2510 5.869579 AGTCCATCACAATCAAGTAAGTGT 58.130 37.500 0.00 0.00 33.84 3.55
2316 2511 6.808008 AAGTCCATCACAATCAAGTAAGTG 57.192 37.500 0.00 0.00 0.00 3.16
2317 2512 6.998074 TGAAAGTCCATCACAATCAAGTAAGT 59.002 34.615 0.00 0.00 0.00 2.24
2318 2513 7.439157 TGAAAGTCCATCACAATCAAGTAAG 57.561 36.000 0.00 0.00 0.00 2.34
2319 2514 7.815840 TTGAAAGTCCATCACAATCAAGTAA 57.184 32.000 0.00 0.00 31.67 2.24
2389 2604 6.956435 AGGTCATCTATATGCCTGAATAGTCA 59.044 38.462 0.00 0.00 37.87 3.41
2390 2605 7.416964 AGGTCATCTATATGCCTGAATAGTC 57.583 40.000 4.14 0.00 37.87 2.59
2392 2607 9.761504 CATAAGGTCATCTATATGCCTGAATAG 57.238 37.037 5.32 0.00 38.69 1.73
2394 2609 7.052873 GCATAAGGTCATCTATATGCCTGAAT 58.947 38.462 5.52 1.88 42.92 2.57
2395 2610 6.013466 TGCATAAGGTCATCTATATGCCTGAA 60.013 38.462 12.50 0.00 46.28 3.02
2396 2611 5.484998 TGCATAAGGTCATCTATATGCCTGA 59.515 40.000 12.50 0.18 46.28 3.86
2397 2612 5.737860 TGCATAAGGTCATCTATATGCCTG 58.262 41.667 12.50 0.00 46.28 4.85
2398 2613 6.354938 CATGCATAAGGTCATCTATATGCCT 58.645 40.000 0.00 2.28 46.28 4.75
2399 2614 5.008415 GCATGCATAAGGTCATCTATATGCC 59.992 44.000 14.21 0.00 46.28 4.40
2448 2684 6.183360 TGTGATGTCGGTATAAAATTTCCTGC 60.183 38.462 0.00 0.00 0.00 4.85
2451 2687 8.973835 TTTTGTGATGTCGGTATAAAATTTCC 57.026 30.769 0.00 0.00 0.00 3.13
2489 2770 2.061028 GCAGCATTTTTCTTTGACGGG 58.939 47.619 0.00 0.00 0.00 5.28
2490 2771 2.741612 TGCAGCATTTTTCTTTGACGG 58.258 42.857 0.00 0.00 0.00 4.79
2491 2772 3.982701 TGATGCAGCATTTTTCTTTGACG 59.017 39.130 9.90 0.00 0.00 4.35
2492 2773 4.986659 ACTGATGCAGCATTTTTCTTTGAC 59.013 37.500 9.90 0.00 34.37 3.18
2493 2774 5.010314 AGACTGATGCAGCATTTTTCTTTGA 59.990 36.000 9.90 0.00 34.37 2.69
2494 2775 5.227908 AGACTGATGCAGCATTTTTCTTTG 58.772 37.500 9.90 0.00 34.37 2.77
2495 2776 5.464030 AGACTGATGCAGCATTTTTCTTT 57.536 34.783 9.90 0.00 34.37 2.52
2496 2777 6.602406 AGATAGACTGATGCAGCATTTTTCTT 59.398 34.615 9.90 3.24 34.37 2.52
2497 2778 6.120905 AGATAGACTGATGCAGCATTTTTCT 58.879 36.000 9.90 12.98 34.37 2.52
2498 2779 6.374565 AGATAGACTGATGCAGCATTTTTC 57.625 37.500 9.90 6.18 34.37 2.29
2499 2780 8.997323 GTATAGATAGACTGATGCAGCATTTTT 58.003 33.333 9.90 0.00 34.37 1.94
2500 2781 7.605691 GGTATAGATAGACTGATGCAGCATTTT 59.394 37.037 9.90 0.00 34.37 1.82
2501 2782 7.102346 GGTATAGATAGACTGATGCAGCATTT 58.898 38.462 9.90 0.00 34.37 2.32
2502 2783 6.626844 CGGTATAGATAGACTGATGCAGCATT 60.627 42.308 9.90 0.00 34.37 3.56
2503 2784 5.163571 CGGTATAGATAGACTGATGCAGCAT 60.164 44.000 7.91 7.91 34.37 3.79
2504 2785 4.156739 CGGTATAGATAGACTGATGCAGCA 59.843 45.833 3.82 3.82 34.37 4.41
2505 2786 4.396478 TCGGTATAGATAGACTGATGCAGC 59.604 45.833 0.00 0.00 34.37 5.25
2506 2787 6.502136 TTCGGTATAGATAGACTGATGCAG 57.498 41.667 0.00 0.00 33.33 4.41
2507 2788 6.659242 TGATTCGGTATAGATAGACTGATGCA 59.341 38.462 0.00 0.00 33.33 3.96
2508 2789 7.089770 TGATTCGGTATAGATAGACTGATGC 57.910 40.000 0.00 0.00 33.33 3.91
2509 2790 8.275015 ACTGATTCGGTATAGATAGACTGATG 57.725 38.462 0.00 0.00 33.33 3.07
2601 2887 9.012161 CCCACCAAACATAATTGATTTCAAAAT 57.988 29.630 0.00 0.00 39.55 1.82
2625 2911 3.119029 AGCAATTGCATGACATACAACCC 60.119 43.478 30.89 0.00 45.16 4.11
2638 2924 1.171308 GCCTTCAGAGAGCAATTGCA 58.829 50.000 30.89 7.52 45.16 4.08
2639 2925 0.098376 CGCCTTCAGAGAGCAATTGC 59.902 55.000 23.05 23.05 42.49 3.56
2645 2931 2.817396 GCACCGCCTTCAGAGAGC 60.817 66.667 0.00 0.00 0.00 4.09
2646 2932 2.125350 GGCACCGCCTTCAGAGAG 60.125 66.667 0.00 0.00 46.69 3.20
2693 3000 2.607187 CGAGTGGCGTTTCTCTGTTAT 58.393 47.619 0.00 0.00 34.64 1.89
2694 3001 1.933500 GCGAGTGGCGTTTCTCTGTTA 60.934 52.381 0.00 0.00 43.41 2.41
2718 3025 7.768582 TGGACTTCGATTTGATATCTTAAAGCA 59.231 33.333 3.98 0.00 0.00 3.91
2766 3073 6.093495 TGCTCTGGAAATAATTTGTTACCTCG 59.907 38.462 0.00 0.00 0.00 4.63
2776 3083 6.322969 TGATGATGCTTGCTCTGGAAATAATT 59.677 34.615 0.00 0.00 0.00 1.40
2777 3084 5.831525 TGATGATGCTTGCTCTGGAAATAAT 59.168 36.000 0.00 0.00 0.00 1.28
2779 3086 4.784177 TGATGATGCTTGCTCTGGAAATA 58.216 39.130 0.00 0.00 0.00 1.40
2780 3087 3.628008 TGATGATGCTTGCTCTGGAAAT 58.372 40.909 0.00 0.00 0.00 2.17
2781 3088 3.076079 TGATGATGCTTGCTCTGGAAA 57.924 42.857 0.00 0.00 0.00 3.13
2782 3089 2.751259 GTTGATGATGCTTGCTCTGGAA 59.249 45.455 0.00 0.00 0.00 3.53
2783 3090 2.290450 TGTTGATGATGCTTGCTCTGGA 60.290 45.455 0.00 0.00 0.00 3.86
2784 3091 2.089201 TGTTGATGATGCTTGCTCTGG 58.911 47.619 0.00 0.00 0.00 3.86
2785 3092 3.377172 TCATGTTGATGATGCTTGCTCTG 59.623 43.478 0.00 0.00 33.40 3.35
2786 3093 3.617284 TCATGTTGATGATGCTTGCTCT 58.383 40.909 0.00 0.00 33.40 4.09
2787 3094 3.792459 GCTCATGTTGATGATGCTTGCTC 60.792 47.826 0.00 0.00 37.97 4.26
2788 3095 2.099263 GCTCATGTTGATGATGCTTGCT 59.901 45.455 0.00 0.00 37.97 3.91
2789 3096 2.460918 GCTCATGTTGATGATGCTTGC 58.539 47.619 0.00 0.00 37.97 4.01
2790 3097 2.688446 AGGCTCATGTTGATGATGCTTG 59.312 45.455 0.00 0.00 37.97 4.01
2793 3100 2.294979 TGAGGCTCATGTTGATGATGC 58.705 47.619 14.43 0.00 37.97 3.91
2834 3141 5.923204 ACAAAAATATGTTGTTGGAGGCAA 58.077 33.333 9.62 0.00 36.95 4.52
2843 3150 7.560368 TCAAGGGTTGAACAAAAATATGTTGT 58.440 30.769 0.00 0.27 43.31 3.32
2844 3151 7.710475 ACTCAAGGGTTGAACAAAAATATGTTG 59.290 33.333 0.00 0.00 43.31 3.33
2846 3153 7.147742 ACACTCAAGGGTTGAACAAAAATATGT 60.148 33.333 0.00 0.00 39.58 2.29
2849 3156 6.783708 ACACTCAAGGGTTGAACAAAAATA 57.216 33.333 0.00 0.00 39.58 1.40
2851 3158 5.245075 AGAACACTCAAGGGTTGAACAAAAA 59.755 36.000 1.60 0.00 39.58 1.94
2852 3159 4.770010 AGAACACTCAAGGGTTGAACAAAA 59.230 37.500 1.60 0.00 39.58 2.44
2853 3160 4.340617 AGAACACTCAAGGGTTGAACAAA 58.659 39.130 1.60 0.00 39.58 2.83
2855 3162 3.054728 TGAGAACACTCAAGGGTTGAACA 60.055 43.478 1.60 0.00 39.58 3.18
2859 3166 4.452455 GTGTATGAGAACACTCAAGGGTTG 59.548 45.833 1.60 0.00 45.12 3.77
2860 3167 4.642429 GTGTATGAGAACACTCAAGGGTT 58.358 43.478 0.00 0.00 45.12 4.11
2871 3178 4.878439 TGTGTGGTGTAGTGTATGAGAAC 58.122 43.478 0.00 0.00 0.00 3.01
2872 3179 5.478407 CATGTGTGGTGTAGTGTATGAGAA 58.522 41.667 0.00 0.00 0.00 2.87
2873 3180 4.620567 GCATGTGTGGTGTAGTGTATGAGA 60.621 45.833 0.00 0.00 0.00 3.27
2875 3182 3.007398 TGCATGTGTGGTGTAGTGTATGA 59.993 43.478 0.00 0.00 0.00 2.15
2876 3183 3.333804 TGCATGTGTGGTGTAGTGTATG 58.666 45.455 0.00 0.00 0.00 2.39
2877 3184 3.599343 CTGCATGTGTGGTGTAGTGTAT 58.401 45.455 0.00 0.00 0.00 2.29
2878 3185 2.289382 CCTGCATGTGTGGTGTAGTGTA 60.289 50.000 0.00 0.00 0.00 2.90
2880 3187 1.159285 CCTGCATGTGTGGTGTAGTG 58.841 55.000 0.00 0.00 0.00 2.74
2881 3188 0.764890 ACCTGCATGTGTGGTGTAGT 59.235 50.000 0.00 0.00 32.16 2.73
2882 3189 1.806542 GAACCTGCATGTGTGGTGTAG 59.193 52.381 0.00 0.00 33.89 2.74
2884 3191 0.106769 TGAACCTGCATGTGTGGTGT 60.107 50.000 0.00 0.10 33.89 4.16
2886 3193 0.473755 TCTGAACCTGCATGTGTGGT 59.526 50.000 0.00 0.00 35.29 4.16
2982 3295 3.515286 TCTCCGCCGGCTTCGTAG 61.515 66.667 26.68 13.85 0.00 3.51
3015 3328 2.646175 GGTGAGCTGCGACCTGGTA 61.646 63.158 14.45 0.00 0.00 3.25
3174 3496 2.202171 GTGGCGCATTTCACGTCG 60.202 61.111 10.83 0.00 38.15 5.12
3231 3553 2.043248 AGCCGGTGATCGTACCCT 60.043 61.111 1.90 0.00 37.44 4.34
3310 3632 2.817844 GCCCTTCTACCGAAACACATTT 59.182 45.455 0.00 0.00 0.00 2.32
3385 3707 0.693049 AAACAAGCATCCTCGGGACT 59.307 50.000 0.00 0.00 32.98 3.85
3436 3764 7.936496 TTTCCACAGATTTTACATCAGCATA 57.064 32.000 0.00 0.00 0.00 3.14
3557 3885 5.876651 ACACTCCATGATGCTATGTTCTA 57.123 39.130 0.00 0.00 0.00 2.10
3558 3886 4.767578 ACACTCCATGATGCTATGTTCT 57.232 40.909 0.00 0.00 0.00 3.01
3559 3887 5.824904 AAACACTCCATGATGCTATGTTC 57.175 39.130 0.00 0.00 0.00 3.18
3571 3902 2.034124 ACAGCAGCAAAAACACTCCAT 58.966 42.857 0.00 0.00 0.00 3.41
3712 4047 4.744570 TGCTTACTCGACAAGACATTAGG 58.255 43.478 6.26 0.00 0.00 2.69
3752 4087 0.321653 GACTTCCACCTCGCCACAAT 60.322 55.000 0.00 0.00 0.00 2.71
3759 4094 1.442769 CACCATTGACTTCCACCTCG 58.557 55.000 0.00 0.00 0.00 4.63
3786 4121 4.516698 ACCAGTTAGTCAAGACATGCAAAG 59.483 41.667 2.72 0.00 0.00 2.77
3807 4142 6.765915 ATTTTCAATTGCTCCTCTTCTACC 57.234 37.500 0.00 0.00 0.00 3.18
3840 4175 1.354040 CACTTTCAGTAGCAGGCTCG 58.646 55.000 0.00 0.00 0.00 5.03
3849 4184 6.291377 AGAATTCAGAAGTGCACTTTCAGTA 58.709 36.000 31.58 18.08 36.11 2.74
3874 4209 2.032054 ACGTGTGTTGACATTCTGCTTG 59.968 45.455 0.00 0.00 33.63 4.01
3903 4238 3.809832 TGAGTGCTTTTTCGAAGAAGGAG 59.190 43.478 24.81 6.12 45.90 3.69
3905 4240 3.809832 TCTGAGTGCTTTTTCGAAGAAGG 59.190 43.478 24.81 12.27 45.90 3.46
3906 4241 5.407995 AGATCTGAGTGCTTTTTCGAAGAAG 59.592 40.000 20.90 20.90 45.90 2.85
3926 4263 4.386049 CACTACTCGTTTGGACAACAGATC 59.614 45.833 0.00 0.00 0.00 2.75
4017 4359 0.964860 TTTGGGGTGATGTGCCATCG 60.965 55.000 9.65 0.00 0.00 3.84
4024 4366 0.251341 GGAGCTGTTTGGGGTGATGT 60.251 55.000 0.00 0.00 0.00 3.06
4163 4505 6.100424 CCTTTGAGATCTAATAGAGGTTGGGT 59.900 42.308 0.00 0.00 0.00 4.51
4249 4591 3.279875 GCGGCGGCATCCCTTTAG 61.280 66.667 9.78 0.00 39.62 1.85
4281 4623 2.301296 CAGTGATGCTAGGGTCATAGGG 59.699 54.545 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.