Multiple sequence alignment - TraesCS2A01G434500

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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 TraesCS2A01G434500 chr2A 100.000 2939 0 0 1 2939 686843658 686840720 0.000000e+00 5428.0
1 TraesCS2A01G434500 chr2A 84.821 224 20 5 1123 1345 686842299 686842089 2.290000e-51 213.0
2 TraesCS2A01G434500 chr2A 84.821 224 20 5 1360 1570 686842536 686842314 2.290000e-51 213.0
3 TraesCS2A01G434500 chr2A 96.907 97 3 0 2792 2888 41474161 41474257 2.340000e-36 163.0
4 TraesCS2A01G434500 chr2D 91.816 1564 108 13 685 2242 544614350 544612801 0.000000e+00 2161.0
5 TraesCS2A01G434500 chr2D 82.280 728 80 26 2 722 544614954 544614269 4.220000e-163 584.0
6 TraesCS2A01G434500 chr2D 84.593 344 30 12 2444 2764 544612404 544612061 1.310000e-83 320.0
7 TraesCS2A01G434500 chr2D 84.375 224 21 9 1360 1570 544613916 544613694 1.070000e-49 207.0
8 TraesCS2A01G434500 chr2D 93.243 74 5 0 2350 2423 544612463 544612390 3.100000e-20 110.0
9 TraesCS2A01G434500 chr2B 94.360 851 44 3 685 1535 650169049 650168203 0.000000e+00 1303.0
10 TraesCS2A01G434500 chr2B 92.173 741 48 5 1485 2216 650168211 650167472 0.000000e+00 1038.0
11 TraesCS2A01G434500 chr2B 84.648 469 47 13 260 722 650169417 650168968 7.470000e-121 444.0
12 TraesCS2A01G434500 chr2B 82.712 295 34 8 1289 1570 650168683 650168393 2.260000e-61 246.0
13 TraesCS2A01G434500 chr2B 84.677 248 22 7 2 245 650169636 650169401 1.760000e-57 233.0
14 TraesCS2A01G434500 chr2B 84.043 188 18 5 1123 1310 650168378 650168203 1.400000e-38 171.0
15 TraesCS2A01G434500 chr2B 93.204 103 7 0 2323 2425 650166920 650166818 5.070000e-33 152.0
16 TraesCS2A01G434500 chr1A 97.959 98 1 1 2786 2883 133417555 133417459 5.040000e-38 169.0
17 TraesCS2A01G434500 chr3D 97.872 94 2 0 2795 2888 129678089 129677996 2.340000e-36 163.0
18 TraesCS2A01G434500 chr3B 94.286 105 5 1 2778 2882 15111008 15111111 3.030000e-35 159.0
19 TraesCS2A01G434500 chr7D 92.661 109 7 1 2787 2895 618321457 618321350 3.920000e-34 156.0
20 TraesCS2A01G434500 chr6A 91.964 112 7 2 2795 2904 609730977 609731088 3.920000e-34 156.0
21 TraesCS2A01G434500 chr1B 92.593 108 6 2 2791 2896 47517435 47517328 1.410000e-33 154.0
22 TraesCS2A01G434500 chr6B 89.916 119 6 6 2772 2887 639915431 639915316 6.560000e-32 148.0
23 TraesCS2A01G434500 chr4A 87.218 133 9 7 2787 2918 683881161 683881286 8.490000e-31 145.0
24 TraesCS2A01G434500 chr4A 100.000 28 0 0 189 216 717629675 717629648 5.000000e-03 52.8


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 TraesCS2A01G434500 chr2A 686840720 686843658 2938 True 1951.333333 5428 89.880667 1 2939 3 chr2A.!!$R1 2938
1 TraesCS2A01G434500 chr2D 544612061 544614954 2893 True 676.400000 2161 87.261400 2 2764 5 chr2D.!!$R1 2762
2 TraesCS2A01G434500 chr2B 650166818 650169636 2818 True 512.428571 1303 87.973857 2 2425 7 chr2B.!!$R1 2423

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
569 579 0.032403 TGACGGGGTGTTACTTCGTG 59.968 55.0 0.0 0.0 34.06 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2437 2979 0.036388 ATGCTTACCAGGTGTGTCCG 60.036 55.0 0.76 0.0 41.99 4.79 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
27 28 4.688879 TGTAAAGTTGTGAAGGATAGCACG 59.311 41.667 0.00 0.00 37.83 5.34
88 89 8.510505 AGAGAGAACATTTTAATGACTCAAAGC 58.489 33.333 22.22 14.52 41.10 3.51
99 100 4.572985 TGACTCAAAGCAGAAACAATGG 57.427 40.909 0.00 0.00 0.00 3.16
108 109 5.179452 AGCAGAAACAATGGTACCTACAT 57.821 39.130 14.36 0.00 0.00 2.29
238 243 5.633996 TTTTACGCTTGCAAGTTTCATTG 57.366 34.783 26.55 10.90 0.00 2.82
239 244 2.869233 ACGCTTGCAAGTTTCATTGT 57.131 40.000 26.55 11.47 32.56 2.71
240 245 2.462889 ACGCTTGCAAGTTTCATTGTG 58.537 42.857 26.55 8.99 32.56 3.33
241 246 2.159254 ACGCTTGCAAGTTTCATTGTGT 60.159 40.909 26.55 9.63 32.56 3.72
242 247 2.468777 CGCTTGCAAGTTTCATTGTGTC 59.531 45.455 26.55 5.38 32.56 3.67
243 248 2.468777 GCTTGCAAGTTTCATTGTGTCG 59.531 45.455 26.55 0.00 32.56 4.35
244 249 2.118228 TGCAAGTTTCATTGTGTCGC 57.882 45.000 0.00 0.00 32.56 5.19
245 250 1.675483 TGCAAGTTTCATTGTGTCGCT 59.325 42.857 0.00 0.00 32.56 4.93
246 251 2.098934 TGCAAGTTTCATTGTGTCGCTT 59.901 40.909 0.00 0.00 32.56 4.68
247 252 3.115554 GCAAGTTTCATTGTGTCGCTTT 58.884 40.909 0.00 0.00 32.56 3.51
248 253 3.180387 GCAAGTTTCATTGTGTCGCTTTC 59.820 43.478 0.00 0.00 32.56 2.62
249 254 3.626028 AGTTTCATTGTGTCGCTTTCC 57.374 42.857 0.00 0.00 0.00 3.13
250 255 2.032030 AGTTTCATTGTGTCGCTTTCCG 60.032 45.455 0.00 0.00 38.61 4.30
251 256 0.237235 TTCATTGTGTCGCTTTCCGC 59.763 50.000 0.00 0.00 36.73 5.54
252 257 0.882484 TCATTGTGTCGCTTTCCGCA 60.882 50.000 0.00 0.00 39.08 5.69
253 258 0.040514 CATTGTGTCGCTTTCCGCAA 60.041 50.000 0.00 0.00 39.08 4.85
254 259 0.665835 ATTGTGTCGCTTTCCGCAAA 59.334 45.000 0.00 0.00 39.08 3.68
255 260 0.452184 TTGTGTCGCTTTCCGCAAAA 59.548 45.000 0.00 0.00 39.08 2.44
256 261 0.452184 TGTGTCGCTTTCCGCAAAAA 59.548 45.000 0.00 0.00 39.08 1.94
282 287 2.979813 GTTTCATTGTGTCGCCATGAAC 59.020 45.455 11.36 5.24 31.85 3.18
353 360 1.129437 GTTCACCGAGCTCATTCAAGC 59.871 52.381 15.40 0.00 42.82 4.01
390 397 0.872388 CTTCCGCCTACACAAACACC 59.128 55.000 0.00 0.00 0.00 4.16
409 416 9.853555 CAAACACCTATGCATGAAATAGTTTAA 57.146 29.630 10.16 0.00 0.00 1.52
512 519 6.818142 GGTACTAAGCCCTTTCGTGTATTTAA 59.182 38.462 0.00 0.00 0.00 1.52
552 562 1.655099 GCGTACCGCGTAGAAAAATGA 59.345 47.619 4.92 0.00 44.55 2.57
554 564 2.284063 CGTACCGCGTAGAAAAATGACG 60.284 50.000 4.92 0.00 39.55 4.35
557 567 0.372334 CGCGTAGAAAAATGACGGGG 59.628 55.000 0.00 0.00 43.39 5.73
558 568 1.445871 GCGTAGAAAAATGACGGGGT 58.554 50.000 0.00 0.00 37.08 4.95
560 570 2.419667 CGTAGAAAAATGACGGGGTGT 58.580 47.619 0.00 0.00 33.01 4.16
562 572 3.995705 CGTAGAAAAATGACGGGGTGTTA 59.004 43.478 0.00 0.00 33.01 2.41
563 573 4.143052 CGTAGAAAAATGACGGGGTGTTAC 60.143 45.833 0.00 0.00 33.01 2.50
564 574 4.094830 AGAAAAATGACGGGGTGTTACT 57.905 40.909 0.00 0.00 0.00 2.24
565 575 4.466827 AGAAAAATGACGGGGTGTTACTT 58.533 39.130 0.00 0.00 0.00 2.24
569 579 0.032403 TGACGGGGTGTTACTTCGTG 59.968 55.000 0.00 0.00 34.06 4.35
570 580 0.032540 GACGGGGTGTTACTTCGTGT 59.967 55.000 0.00 0.00 34.06 4.49
571 581 0.032540 ACGGGGTGTTACTTCGTGTC 59.967 55.000 0.00 0.00 32.60 3.67
572 582 0.032403 CGGGGTGTTACTTCGTGTCA 59.968 55.000 0.00 0.00 0.00 3.58
573 583 1.505425 GGGGTGTTACTTCGTGTCAC 58.495 55.000 0.00 0.00 0.00 3.67
574 584 1.202557 GGGGTGTTACTTCGTGTCACA 60.203 52.381 3.42 0.00 31.12 3.58
587 597 0.531090 TGTCACACGGTGGCACTTAC 60.531 55.000 18.45 7.46 43.49 2.34
601 611 6.589907 GGTGGCACTTACCATTTGATAAAAAG 59.410 38.462 18.45 0.00 43.01 2.27
626 636 4.392940 AGTGCCCTCATGATTTATACAGC 58.607 43.478 0.00 0.00 0.00 4.40
627 637 3.187227 GTGCCCTCATGATTTATACAGCG 59.813 47.826 0.00 0.00 0.00 5.18
651 661 4.584688 GTCTTTGGACCCGTACGG 57.415 61.111 27.68 27.68 36.53 4.02
652 662 1.739196 GTCTTTGGACCCGTACGGC 60.739 63.158 29.15 15.91 36.53 5.68
653 663 2.208619 TCTTTGGACCCGTACGGCA 61.209 57.895 29.15 18.36 33.26 5.69
654 664 1.740296 CTTTGGACCCGTACGGCAG 60.740 63.158 29.15 18.37 33.26 4.85
655 665 3.887335 TTTGGACCCGTACGGCAGC 62.887 63.158 29.15 18.25 33.26 5.25
658 668 4.814294 GACCCGTACGGCAGCCTG 62.814 72.222 29.15 16.11 33.26 4.85
669 679 3.957586 CAGCCTGGCCCACACTCA 61.958 66.667 16.57 0.00 0.00 3.41
670 680 3.644606 AGCCTGGCCCACACTCAG 61.645 66.667 16.57 0.00 0.00 3.35
671 681 3.640407 GCCTGGCCCACACTCAGA 61.640 66.667 7.66 0.00 0.00 3.27
672 682 2.667418 CCTGGCCCACACTCAGAG 59.333 66.667 0.00 0.00 0.00 3.35
673 683 2.667418 CTGGCCCACACTCAGAGG 59.333 66.667 0.00 0.00 0.00 3.69
674 684 1.915266 CTGGCCCACACTCAGAGGA 60.915 63.158 0.00 0.00 0.00 3.71
675 685 1.461268 TGGCCCACACTCAGAGGAA 60.461 57.895 0.00 0.00 0.00 3.36
676 686 1.003233 GGCCCACACTCAGAGGAAC 60.003 63.158 1.53 0.00 0.00 3.62
677 687 1.374758 GCCCACACTCAGAGGAACG 60.375 63.158 1.53 0.00 0.00 3.95
678 688 1.293498 CCCACACTCAGAGGAACGG 59.707 63.158 1.53 0.00 0.00 4.44
679 689 1.293498 CCACACTCAGAGGAACGGG 59.707 63.158 1.53 0.00 0.00 5.28
680 690 1.472662 CCACACTCAGAGGAACGGGT 61.473 60.000 1.53 0.00 0.00 5.28
681 691 0.319900 CACACTCAGAGGAACGGGTG 60.320 60.000 1.53 0.00 0.00 4.61
682 692 0.469331 ACACTCAGAGGAACGGGTGA 60.469 55.000 1.53 0.00 0.00 4.02
683 693 0.244994 CACTCAGAGGAACGGGTGAG 59.755 60.000 1.53 0.00 41.88 3.51
684 694 0.178958 ACTCAGAGGAACGGGTGAGT 60.179 55.000 1.53 0.00 43.81 3.41
685 695 0.244994 CTCAGAGGAACGGGTGAGTG 59.755 60.000 0.00 0.00 33.20 3.51
686 696 1.185618 TCAGAGGAACGGGTGAGTGG 61.186 60.000 0.00 0.00 0.00 4.00
687 697 1.155390 AGAGGAACGGGTGAGTGGA 59.845 57.895 0.00 0.00 0.00 4.02
688 698 1.186267 AGAGGAACGGGTGAGTGGAC 61.186 60.000 0.00 0.00 0.00 4.02
689 699 2.168666 GAGGAACGGGTGAGTGGACC 62.169 65.000 0.00 0.00 34.96 4.46
694 704 2.976356 GGGTGAGTGGACCCGTAC 59.024 66.667 0.00 0.00 46.45 3.67
734 744 2.048503 GGAACGGGTGAGTGGACG 60.049 66.667 0.00 0.00 0.00 4.79
918 928 2.172483 ATTCTTGACCGCCACGCTCT 62.172 55.000 0.00 0.00 0.00 4.09
971 981 1.080434 GACTTCTGCGGCGTCTCTT 60.080 57.895 9.37 0.00 0.00 2.85
972 982 1.347817 GACTTCTGCGGCGTCTCTTG 61.348 60.000 9.37 0.00 0.00 3.02
973 983 2.734673 CTTCTGCGGCGTCTCTTGC 61.735 63.158 9.37 0.00 0.00 4.01
974 984 3.226429 TTCTGCGGCGTCTCTTGCT 62.226 57.895 9.37 0.00 0.00 3.91
978 988 4.821589 CGGCGTCTCTTGCTCCCC 62.822 72.222 0.00 0.00 0.00 4.81
986 996 0.827368 CTCTTGCTCCCCAGACTACC 59.173 60.000 0.00 0.00 0.00 3.18
1032 1042 4.856607 GTCTTCGGCCGCGAGAGG 62.857 72.222 25.19 9.06 0.00 3.69
1100 1110 3.188786 GCCGTCGTGCCATCAGTC 61.189 66.667 0.00 0.00 0.00 3.51
1176 1186 2.754995 GGAGTACGTCCCGTCGACC 61.755 68.421 10.58 0.00 41.54 4.79
1315 1325 1.814527 GTGGCGTCTCCGGAGTATT 59.185 57.895 30.17 0.00 37.80 1.89
1316 1326 0.248949 GTGGCGTCTCCGGAGTATTC 60.249 60.000 30.17 18.30 37.80 1.75
1499 1509 0.809636 TCGTCGTCGCCGGATTACTA 60.810 55.000 5.05 0.00 36.96 1.82
1501 1511 0.378257 GTCGTCGCCGGATTACTACA 59.622 55.000 5.05 0.00 33.95 2.74
1504 1514 1.596464 CGTCGCCGGATTACTACACTC 60.596 57.143 5.05 0.00 0.00 3.51
1611 1663 2.675772 ACCCCGTCGACACCTCTC 60.676 66.667 17.16 0.00 0.00 3.20
1623 1675 4.544689 CCTCTCGAGCAGCGACCG 62.545 72.222 7.81 0.00 45.59 4.79
1626 1678 4.103103 CTCGAGCAGCGACCGTCA 62.103 66.667 0.00 0.00 45.59 4.35
1651 1703 3.729906 GACTACGCCGCGTCGACAT 62.730 63.158 23.94 4.29 41.54 3.06
2062 2126 2.099141 TTGCTGCTAGTAGTTGCCTG 57.901 50.000 9.73 0.00 0.00 4.85
2082 2146 3.575630 TGACTTGCAATACGACTCACTC 58.424 45.455 0.00 0.00 0.00 3.51
2121 2185 4.201841 TGCTTCACATCAATAACGAGCATG 60.202 41.667 0.00 0.00 34.33 4.06
2163 2227 3.250744 CTTGCTCTTTCATGCATTGGTG 58.749 45.455 0.00 0.00 39.07 4.17
2172 2236 5.725325 TTCATGCATTGGTGAGATCAAAA 57.275 34.783 0.00 0.00 0.00 2.44
2174 2238 7.407393 TTCATGCATTGGTGAGATCAAAATA 57.593 32.000 0.00 0.00 0.00 1.40
2179 2243 6.183360 TGCATTGGTGAGATCAAAATATGACC 60.183 38.462 0.00 0.00 41.93 4.02
2199 2263 5.049060 TGACCGAATTTAATGTGGACACAAG 60.049 40.000 9.42 0.00 45.41 3.16
2213 2277 9.712305 ATGTGGACACAAGCTATATTTATCTAC 57.288 33.333 9.42 0.00 45.41 2.59
2216 2280 9.764363 TGGACACAAGCTATATTTATCTACTTG 57.236 33.333 0.00 0.00 39.09 3.16
2217 2281 9.209175 GGACACAAGCTATATTTATCTACTTGG 57.791 37.037 0.00 0.00 37.84 3.61
2218 2282 9.209175 GACACAAGCTATATTTATCTACTTGGG 57.791 37.037 0.00 0.00 41.62 4.12
2219 2283 7.661847 ACACAAGCTATATTTATCTACTTGGGC 59.338 37.037 0.00 0.00 39.98 5.36
2220 2284 7.119846 CACAAGCTATATTTATCTACTTGGGCC 59.880 40.741 0.00 0.00 37.84 5.80
2223 2297 7.625469 AGCTATATTTATCTACTTGGGCCTTC 58.375 38.462 4.53 0.00 0.00 3.46
2244 2318 6.128117 CCTTCCAAATGGCAAATTTCTGATTG 60.128 38.462 0.00 0.00 34.44 2.67
2245 2319 5.247084 TCCAAATGGCAAATTTCTGATTGG 58.753 37.500 0.00 10.73 36.89 3.16
2252 2326 6.866480 TGGCAAATTTCTGATTGGTAAGATC 58.134 36.000 0.00 0.00 0.00 2.75
2253 2327 6.436847 TGGCAAATTTCTGATTGGTAAGATCA 59.563 34.615 0.00 0.00 32.87 2.92
2256 2330 9.206870 GCAAATTTCTGATTGGTAAGATCAAAA 57.793 29.630 0.00 0.00 33.45 2.44
2262 2336 9.912634 TTCTGATTGGTAAGATCAAAATTTGAC 57.087 29.630 10.91 5.52 43.48 3.18
2264 2338 9.350357 CTGATTGGTAAGATCAAAATTTGACAG 57.650 33.333 10.91 6.00 43.48 3.51
2265 2339 9.076781 TGATTGGTAAGATCAAAATTTGACAGA 57.923 29.630 10.91 0.00 43.48 3.41
2266 2340 9.912634 GATTGGTAAGATCAAAATTTGACAGAA 57.087 29.630 10.91 0.00 43.48 3.02
2269 2343 9.912634 TGGTAAGATCAAAATTTGACAGAATTC 57.087 29.630 10.91 3.78 43.48 2.17
2270 2344 9.912634 GGTAAGATCAAAATTTGACAGAATTCA 57.087 29.630 10.91 0.00 43.48 2.57
2283 2357 3.338249 CAGAATTCAATCTGTCGGTGGT 58.662 45.455 8.44 0.00 41.54 4.16
2285 2359 4.568359 CAGAATTCAATCTGTCGGTGGTAG 59.432 45.833 8.44 0.00 41.54 3.18
2286 2360 3.543680 ATTCAATCTGTCGGTGGTAGG 57.456 47.619 0.00 0.00 0.00 3.18
2288 2362 2.253610 TCAATCTGTCGGTGGTAGGTT 58.746 47.619 0.00 0.00 0.00 3.50
2290 2364 1.640917 ATCTGTCGGTGGTAGGTTGT 58.359 50.000 0.00 0.00 0.00 3.32
2291 2365 2.291209 TCTGTCGGTGGTAGGTTGTA 57.709 50.000 0.00 0.00 0.00 2.41
2292 2366 2.811410 TCTGTCGGTGGTAGGTTGTAT 58.189 47.619 0.00 0.00 0.00 2.29
2293 2367 3.167485 TCTGTCGGTGGTAGGTTGTATT 58.833 45.455 0.00 0.00 0.00 1.89
2294 2368 3.579586 TCTGTCGGTGGTAGGTTGTATTT 59.420 43.478 0.00 0.00 0.00 1.40
2296 2370 5.075858 TGTCGGTGGTAGGTTGTATTTAG 57.924 43.478 0.00 0.00 0.00 1.85
2298 2372 3.451902 TCGGTGGTAGGTTGTATTTAGGG 59.548 47.826 0.00 0.00 0.00 3.53
2299 2373 3.451902 CGGTGGTAGGTTGTATTTAGGGA 59.548 47.826 0.00 0.00 0.00 4.20
2301 2375 5.618236 GGTGGTAGGTTGTATTTAGGGATC 58.382 45.833 0.00 0.00 0.00 3.36
2302 2376 5.368816 GGTGGTAGGTTGTATTTAGGGATCT 59.631 44.000 0.00 0.00 0.00 2.75
2304 2378 7.071572 GGTGGTAGGTTGTATTTAGGGATCTTA 59.928 40.741 0.00 0.00 0.00 2.10
2305 2379 8.657712 GTGGTAGGTTGTATTTAGGGATCTTAT 58.342 37.037 0.00 0.00 0.00 1.73
2307 2381 9.102453 GGTAGGTTGTATTTAGGGATCTTATCT 57.898 37.037 0.00 0.00 0.00 1.98
2333 2846 2.734276 TTTTGCGGCAATTTAGGGAC 57.266 45.000 17.19 0.00 0.00 4.46
2348 2861 9.807649 CAATTTAGGGACCTTATCAAAATTCAG 57.192 33.333 0.00 0.00 29.84 3.02
2425 2967 2.795329 CTCCACCTGGTAAGCATGTTT 58.205 47.619 0.00 0.00 36.34 2.83
2426 2968 3.157087 CTCCACCTGGTAAGCATGTTTT 58.843 45.455 0.00 0.00 36.34 2.43
2427 2969 3.571590 TCCACCTGGTAAGCATGTTTTT 58.428 40.909 0.00 0.00 36.34 1.94
2449 2991 2.111162 TTTTTGCGGACACACCTGG 58.889 52.632 0.00 0.00 36.31 4.45
2450 2992 0.681564 TTTTTGCGGACACACCTGGT 60.682 50.000 0.00 0.00 36.31 4.00
2451 2993 0.180642 TTTTGCGGACACACCTGGTA 59.819 50.000 0.00 0.00 36.31 3.25
2452 2994 0.180642 TTTGCGGACACACCTGGTAA 59.819 50.000 0.00 0.00 36.31 2.85
2453 2995 0.250124 TTGCGGACACACCTGGTAAG 60.250 55.000 0.00 0.00 36.31 2.34
2454 2996 2.033194 GCGGACACACCTGGTAAGC 61.033 63.158 0.00 0.00 36.31 3.09
2455 2997 1.369692 CGGACACACCTGGTAAGCA 59.630 57.895 0.00 0.00 36.31 3.91
2456 2998 0.036388 CGGACACACCTGGTAAGCAT 60.036 55.000 0.00 0.00 36.31 3.79
2457 2999 1.453155 GGACACACCTGGTAAGCATG 58.547 55.000 0.00 0.00 35.41 4.06
2458 3000 1.271379 GGACACACCTGGTAAGCATGT 60.271 52.381 0.00 0.00 35.41 3.21
2462 3004 2.226437 CACACCTGGTAAGCATGTTGAC 59.774 50.000 0.00 0.00 0.00 3.18
2479 3021 2.244281 GACGTCGGTCAACACTAGAG 57.756 55.000 0.00 0.00 42.91 2.43
2480 3022 1.802960 GACGTCGGTCAACACTAGAGA 59.197 52.381 0.00 0.00 42.91 3.10
2481 3023 2.419324 GACGTCGGTCAACACTAGAGAT 59.581 50.000 0.00 0.00 42.91 2.75
2482 3024 2.818432 ACGTCGGTCAACACTAGAGATT 59.182 45.455 0.00 0.00 0.00 2.40
2483 3025 3.119919 ACGTCGGTCAACACTAGAGATTC 60.120 47.826 0.00 0.00 0.00 2.52
2485 3027 4.416620 GTCGGTCAACACTAGAGATTCAG 58.583 47.826 0.00 0.00 0.00 3.02
2486 3028 4.156190 GTCGGTCAACACTAGAGATTCAGA 59.844 45.833 0.00 0.00 0.00 3.27
2487 3029 4.950475 TCGGTCAACACTAGAGATTCAGAT 59.050 41.667 0.00 0.00 0.00 2.90
2489 3031 5.393569 CGGTCAACACTAGAGATTCAGATGT 60.394 44.000 0.00 0.00 0.00 3.06
2492 3034 8.200792 GGTCAACACTAGAGATTCAGATGTATT 58.799 37.037 0.00 0.00 0.00 1.89
2493 3035 9.029243 GTCAACACTAGAGATTCAGATGTATTG 57.971 37.037 0.00 0.00 0.00 1.90
2494 3036 8.753133 TCAACACTAGAGATTCAGATGTATTGT 58.247 33.333 0.00 0.00 0.00 2.71
2495 3037 9.376075 CAACACTAGAGATTCAGATGTATTGTT 57.624 33.333 0.00 0.00 0.00 2.83
2555 3107 4.971939 TGTGAATCTCATGAACACCTCAA 58.028 39.130 14.71 0.57 37.67 3.02
2561 3113 5.499139 TCTCATGAACACCTCAAAAACAC 57.501 39.130 0.00 0.00 37.67 3.32
2563 3115 3.383185 TCATGAACACCTCAAAAACACCC 59.617 43.478 0.00 0.00 37.67 4.61
2577 3131 5.878406 AAAACACCCATAATCAACAACCA 57.122 34.783 0.00 0.00 0.00 3.67
2583 3137 5.530915 CACCCATAATCAACAACCATCGTAT 59.469 40.000 0.00 0.00 0.00 3.06
2585 3139 6.605594 ACCCATAATCAACAACCATCGTATTT 59.394 34.615 0.00 0.00 0.00 1.40
2586 3140 7.776030 ACCCATAATCAACAACCATCGTATTTA 59.224 33.333 0.00 0.00 0.00 1.40
2587 3141 8.792633 CCCATAATCAACAACCATCGTATTTAT 58.207 33.333 0.00 0.00 0.00 1.40
2630 3195 5.450171 AGTTCGATATTTCCTCGATACGTG 58.550 41.667 0.00 0.00 43.93 4.49
2636 3201 3.804786 TTTCCTCGATACGTGGCAATA 57.195 42.857 0.00 0.00 39.87 1.90
2645 3210 2.373540 ACGTGGCAATAAAGTAGCGA 57.626 45.000 0.00 0.00 0.00 4.93
2691 3256 5.630121 TGTGGATGTGTTTTCAATACTCCT 58.370 37.500 0.00 0.00 0.00 3.69
2697 3262 7.970614 GGATGTGTTTTCAATACTCCTTTGATC 59.029 37.037 0.00 0.00 33.37 2.92
2699 3264 7.004086 TGTGTTTTCAATACTCCTTTGATCCT 58.996 34.615 0.00 0.00 33.37 3.24
2749 3314 0.387239 GATGTTGCGGTTTGGCTGTC 60.387 55.000 0.00 0.00 0.00 3.51
2755 3320 0.237498 GCGGTTTGGCTGTCAGTTAC 59.763 55.000 0.93 0.00 0.00 2.50
2757 3322 1.531149 CGGTTTGGCTGTCAGTTACTG 59.469 52.381 5.94 5.94 0.00 2.74
2764 3329 2.030805 GGCTGTCAGTTACTGGCTTTTG 60.031 50.000 18.11 6.94 45.58 2.44
2765 3330 2.878406 GCTGTCAGTTACTGGCTTTTGA 59.122 45.455 18.11 0.00 36.97 2.69
2766 3331 3.503748 GCTGTCAGTTACTGGCTTTTGAT 59.496 43.478 18.11 0.00 36.97 2.57
2767 3332 4.695455 GCTGTCAGTTACTGGCTTTTGATA 59.305 41.667 18.11 0.00 36.97 2.15
2768 3333 5.355350 GCTGTCAGTTACTGGCTTTTGATAT 59.645 40.000 18.11 0.00 36.97 1.63
2769 3334 6.538742 GCTGTCAGTTACTGGCTTTTGATATA 59.461 38.462 18.11 0.00 36.97 0.86
2770 3335 7.065803 GCTGTCAGTTACTGGCTTTTGATATAA 59.934 37.037 18.11 0.00 36.97 0.98
2771 3336 8.492673 TGTCAGTTACTGGCTTTTGATATAAG 57.507 34.615 18.11 0.00 36.97 1.73
2772 3337 8.318412 TGTCAGTTACTGGCTTTTGATATAAGA 58.682 33.333 18.11 0.00 36.97 2.10
2773 3338 8.821894 GTCAGTTACTGGCTTTTGATATAAGAG 58.178 37.037 9.99 0.00 32.76 2.85
2774 3339 8.758829 TCAGTTACTGGCTTTTGATATAAGAGA 58.241 33.333 12.79 0.00 31.51 3.10
2775 3340 9.383519 CAGTTACTGGCTTTTGATATAAGAGAA 57.616 33.333 4.14 0.00 0.00 2.87
2780 3345 8.897752 ACTGGCTTTTGATATAAGAGAATGAAC 58.102 33.333 0.00 0.00 0.00 3.18
2781 3346 8.225603 TGGCTTTTGATATAAGAGAATGAACC 57.774 34.615 0.00 0.00 0.00 3.62
2782 3347 7.833682 TGGCTTTTGATATAAGAGAATGAACCA 59.166 33.333 0.00 0.00 0.00 3.67
2783 3348 8.131731 GGCTTTTGATATAAGAGAATGAACCAC 58.868 37.037 0.00 0.00 0.00 4.16
2784 3349 8.677300 GCTTTTGATATAAGAGAATGAACCACA 58.323 33.333 0.00 0.00 0.00 4.17
2785 3350 9.994432 CTTTTGATATAAGAGAATGAACCACAC 57.006 33.333 0.00 0.00 0.00 3.82
2786 3351 9.513906 TTTTGATATAAGAGAATGAACCACACA 57.486 29.630 0.00 0.00 0.00 3.72
2787 3352 9.513906 TTTGATATAAGAGAATGAACCACACAA 57.486 29.630 0.00 0.00 0.00 3.33
2788 3353 9.513906 TTGATATAAGAGAATGAACCACACAAA 57.486 29.630 0.00 0.00 0.00 2.83
2789 3354 8.946085 TGATATAAGAGAATGAACCACACAAAC 58.054 33.333 0.00 0.00 0.00 2.93
2790 3355 9.167311 GATATAAGAGAATGAACCACACAAACT 57.833 33.333 0.00 0.00 0.00 2.66
2792 3357 8.918202 ATAAGAGAATGAACCACACAAACTAA 57.082 30.769 0.00 0.00 0.00 2.24
2793 3358 7.639113 AAGAGAATGAACCACACAAACTAAA 57.361 32.000 0.00 0.00 0.00 1.85
2794 3359 7.823745 AGAGAATGAACCACACAAACTAAAT 57.176 32.000 0.00 0.00 0.00 1.40
2795 3360 8.918202 AGAGAATGAACCACACAAACTAAATA 57.082 30.769 0.00 0.00 0.00 1.40
2796 3361 8.784043 AGAGAATGAACCACACAAACTAAATAC 58.216 33.333 0.00 0.00 0.00 1.89
2797 3362 8.691661 AGAATGAACCACACAAACTAAATACT 57.308 30.769 0.00 0.00 0.00 2.12
2798 3363 8.784043 AGAATGAACCACACAAACTAAATACTC 58.216 33.333 0.00 0.00 0.00 2.59
2799 3364 6.870971 TGAACCACACAAACTAAATACTCC 57.129 37.500 0.00 0.00 0.00 3.85
2800 3365 5.766174 TGAACCACACAAACTAAATACTCCC 59.234 40.000 0.00 0.00 0.00 4.30
2801 3366 5.578157 ACCACACAAACTAAATACTCCCT 57.422 39.130 0.00 0.00 0.00 4.20
2802 3367 5.557866 ACCACACAAACTAAATACTCCCTC 58.442 41.667 0.00 0.00 0.00 4.30
2803 3368 5.309806 ACCACACAAACTAAATACTCCCTCT 59.690 40.000 0.00 0.00 0.00 3.69
2804 3369 5.643777 CCACACAAACTAAATACTCCCTCTG 59.356 44.000 0.00 0.00 0.00 3.35
2805 3370 6.231211 CACACAAACTAAATACTCCCTCTGT 58.769 40.000 0.00 0.00 0.00 3.41
2806 3371 7.383687 CACACAAACTAAATACTCCCTCTGTA 58.616 38.462 0.00 0.00 0.00 2.74
2807 3372 7.876068 CACACAAACTAAATACTCCCTCTGTAA 59.124 37.037 0.00 0.00 0.00 2.41
2808 3373 8.434392 ACACAAACTAAATACTCCCTCTGTAAA 58.566 33.333 0.00 0.00 0.00 2.01
2809 3374 8.718734 CACAAACTAAATACTCCCTCTGTAAAC 58.281 37.037 0.00 0.00 0.00 2.01
2810 3375 8.657712 ACAAACTAAATACTCCCTCTGTAAACT 58.342 33.333 0.00 0.00 0.00 2.66
2821 3386 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
2822 3387 7.883217 TCCCTCTGTAAACTAATATAAGAGCG 58.117 38.462 0.00 0.00 0.00 5.03
2823 3388 7.504911 TCCCTCTGTAAACTAATATAAGAGCGT 59.495 37.037 0.00 0.00 0.00 5.07
2824 3389 8.142551 CCCTCTGTAAACTAATATAAGAGCGTT 58.857 37.037 0.00 0.00 0.00 4.84
2825 3390 9.530633 CCTCTGTAAACTAATATAAGAGCGTTT 57.469 33.333 0.00 0.00 0.00 3.60
2840 3405 9.953697 ATAAGAGCGTTTAGATCACTAAAGTAG 57.046 33.333 0.00 0.00 45.42 2.57
2841 3406 7.393841 AGAGCGTTTAGATCACTAAAGTAGT 57.606 36.000 0.00 0.00 45.42 2.73
2842 3407 8.503458 AGAGCGTTTAGATCACTAAAGTAGTA 57.497 34.615 0.00 0.00 45.42 1.82
2843 3408 8.954350 AGAGCGTTTAGATCACTAAAGTAGTAA 58.046 33.333 0.00 0.00 45.42 2.24
2844 3409 9.733219 GAGCGTTTAGATCACTAAAGTAGTAAT 57.267 33.333 0.00 0.00 45.42 1.89
2845 3410 9.733219 AGCGTTTAGATCACTAAAGTAGTAATC 57.267 33.333 0.00 0.00 45.42 1.75
2846 3411 9.733219 GCGTTTAGATCACTAAAGTAGTAATCT 57.267 33.333 6.37 6.37 44.17 2.40
2852 3417 9.733219 AGATCACTAAAGTAGTAATCTAAACGC 57.267 33.333 0.03 0.00 41.03 4.84
2853 3418 9.733219 GATCACTAAAGTAGTAATCTAAACGCT 57.267 33.333 0.00 0.00 37.23 5.07
2854 3419 9.733219 ATCACTAAAGTAGTAATCTAAACGCTC 57.267 33.333 0.00 0.00 37.23 5.03
2855 3420 8.954350 TCACTAAAGTAGTAATCTAAACGCTCT 58.046 33.333 0.00 0.00 37.23 4.09
2856 3421 9.570488 CACTAAAGTAGTAATCTAAACGCTCTT 57.430 33.333 0.00 0.00 37.23 2.85
2870 3435 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
2871 3436 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
2872 3437 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
2873 3438 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
2874 3439 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
2875 3440 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
2876 3441 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
2877 3442 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2878 3443 9.512588 CTCTTATATTAGTTTACGGAGGGAGTA 57.487 37.037 0.00 0.00 0.00 2.59
2879 3444 9.289782 TCTTATATTAGTTTACGGAGGGAGTAC 57.710 37.037 0.00 0.00 0.00 2.73
2880 3445 8.995027 TTATATTAGTTTACGGAGGGAGTACA 57.005 34.615 0.00 0.00 0.00 2.90
2881 3446 9.592196 TTATATTAGTTTACGGAGGGAGTACAT 57.408 33.333 0.00 0.00 0.00 2.29
2883 3448 6.699575 TTAGTTTACGGAGGGAGTACATAC 57.300 41.667 0.00 0.00 0.00 2.39
2884 3449 4.864726 AGTTTACGGAGGGAGTACATACT 58.135 43.478 0.00 0.00 39.71 2.12
2885 3450 6.006275 AGTTTACGGAGGGAGTACATACTA 57.994 41.667 0.00 0.00 36.50 1.82
2886 3451 6.426587 AGTTTACGGAGGGAGTACATACTAA 58.573 40.000 0.00 0.00 36.50 2.24
2887 3452 6.891908 AGTTTACGGAGGGAGTACATACTAAA 59.108 38.462 0.00 0.00 36.50 1.85
2888 3453 6.699575 TTACGGAGGGAGTACATACTAAAC 57.300 41.667 0.00 0.00 36.50 2.01
2889 3454 4.603131 ACGGAGGGAGTACATACTAAACA 58.397 43.478 0.00 0.00 36.50 2.83
2890 3455 4.643784 ACGGAGGGAGTACATACTAAACAG 59.356 45.833 0.00 0.00 36.50 3.16
2891 3456 4.643784 CGGAGGGAGTACATACTAAACAGT 59.356 45.833 0.00 0.00 36.50 3.55
2892 3457 5.126707 CGGAGGGAGTACATACTAAACAGTT 59.873 44.000 0.00 0.00 36.50 3.16
2893 3458 6.350780 CGGAGGGAGTACATACTAAACAGTTT 60.351 42.308 3.49 3.49 36.50 2.66
2894 3459 6.817140 GGAGGGAGTACATACTAAACAGTTTG 59.183 42.308 8.93 1.82 36.50 2.93
2895 3460 7.310237 GGAGGGAGTACATACTAAACAGTTTGA 60.310 40.741 8.93 0.00 36.50 2.69
2896 3461 8.147244 AGGGAGTACATACTAAACAGTTTGAT 57.853 34.615 8.93 0.00 36.50 2.57
2897 3462 8.041323 AGGGAGTACATACTAAACAGTTTGATG 58.959 37.037 8.93 11.16 36.50 3.07
2898 3463 7.201617 GGGAGTACATACTAAACAGTTTGATGC 60.202 40.741 8.93 0.00 36.50 3.91
2899 3464 7.549488 GGAGTACATACTAAACAGTTTGATGCT 59.451 37.037 8.93 3.83 36.50 3.79
2900 3465 8.848474 AGTACATACTAAACAGTTTGATGCTT 57.152 30.769 8.93 0.00 34.13 3.91
2901 3466 9.938280 AGTACATACTAAACAGTTTGATGCTTA 57.062 29.630 8.93 0.00 34.13 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.119846 GTGCTATCCTTCACAACTTTACATCTT 59.880 37.037 0.00 0.00 33.63 2.40
69 70 8.196771 TGTTTCTGCTTTGAGTCATTAAAATGT 58.803 29.630 0.00 0.00 37.65 2.71
72 73 9.033481 CATTGTTTCTGCTTTGAGTCATTAAAA 57.967 29.630 0.00 0.00 0.00 1.52
88 89 7.335627 TCCTTATGTAGGTACCATTGTTTCTG 58.664 38.462 15.94 0.00 45.03 3.02
99 100 9.668497 AGAAACTTCATTTCCTTATGTAGGTAC 57.332 33.333 0.00 0.00 46.94 3.34
108 109 7.383687 TCGAGCTAAGAAACTTCATTTCCTTA 58.616 34.615 0.00 0.00 46.94 2.69
141 142 4.782252 TTTTTACTGTTCAACGACCTCG 57.218 40.909 0.00 0.00 46.33 4.63
228 233 3.548014 CGGAAAGCGACACAATGAAACTT 60.548 43.478 0.00 0.00 0.00 2.66
229 234 2.032030 CGGAAAGCGACACAATGAAACT 60.032 45.455 0.00 0.00 0.00 2.66
230 235 2.307049 CGGAAAGCGACACAATGAAAC 58.693 47.619 0.00 0.00 0.00 2.78
231 236 1.334599 GCGGAAAGCGACACAATGAAA 60.335 47.619 0.00 0.00 35.41 2.69
232 237 0.237235 GCGGAAAGCGACACAATGAA 59.763 50.000 0.00 0.00 35.41 2.57
233 238 1.866237 GCGGAAAGCGACACAATGA 59.134 52.632 0.00 0.00 35.41 2.57
234 239 4.440214 GCGGAAAGCGACACAATG 57.560 55.556 0.00 0.00 35.41 2.82
256 261 4.116747 TGGCGACACAATGAAACTTTTT 57.883 36.364 0.00 0.00 33.40 1.94
257 262 3.791973 TGGCGACACAATGAAACTTTT 57.208 38.095 0.00 0.00 33.40 2.27
273 278 3.063997 GGACATTTGTAGAGTTCATGGCG 59.936 47.826 0.00 0.00 0.00 5.69
282 287 3.942829 TGAGCTTGGGACATTTGTAGAG 58.057 45.455 0.00 0.00 39.30 2.43
327 332 3.678056 ATGAGCTCGGTGAACAGTAAA 57.322 42.857 9.64 0.00 0.00 2.01
353 360 3.377798 GGAAGTACTCTTCTAGTCCCACG 59.622 52.174 0.00 0.00 46.47 4.94
354 361 3.377798 CGGAAGTACTCTTCTAGTCCCAC 59.622 52.174 0.00 0.00 46.47 4.61
374 381 2.006888 CATAGGTGTTTGTGTAGGCGG 58.993 52.381 0.00 0.00 0.00 6.13
428 435 5.473846 AGCCTTTTGTAACTAAGCTTCCTTC 59.526 40.000 0.00 0.00 32.47 3.46
476 483 6.135819 AGGGCTTAGTACCAACTTGTATTT 57.864 37.500 0.00 0.00 37.15 1.40
477 484 5.774102 AGGGCTTAGTACCAACTTGTATT 57.226 39.130 0.00 0.00 37.15 1.89
478 485 5.774102 AAGGGCTTAGTACCAACTTGTAT 57.226 39.130 0.00 0.00 37.15 2.29
481 488 3.435671 CGAAAGGGCTTAGTACCAACTTG 59.564 47.826 0.00 0.00 37.15 3.16
512 519 7.224167 GGTACGCTTAAATAAGATGCTAAGTGT 59.776 37.037 10.62 10.62 43.70 3.55
544 553 4.612033 CGAAGTAACACCCCGTCATTTTTC 60.612 45.833 0.00 0.00 0.00 2.29
552 562 0.032540 GACACGAAGTAACACCCCGT 59.967 55.000 0.00 0.00 41.61 5.28
554 564 1.202557 TGTGACACGAAGTAACACCCC 60.203 52.381 0.22 0.00 41.61 4.95
569 579 1.226030 GGTAAGTGCCACCGTGTGAC 61.226 60.000 5.71 0.00 35.23 3.67
570 580 1.070105 GGTAAGTGCCACCGTGTGA 59.930 57.895 5.71 0.00 35.23 3.58
571 581 0.605319 ATGGTAAGTGCCACCGTGTG 60.605 55.000 0.00 0.00 41.94 3.82
572 582 0.109723 AATGGTAAGTGCCACCGTGT 59.890 50.000 0.00 0.00 41.94 4.49
573 583 1.068610 CAAATGGTAAGTGCCACCGTG 60.069 52.381 0.00 0.00 41.94 4.94
574 584 1.202830 TCAAATGGTAAGTGCCACCGT 60.203 47.619 0.00 0.00 41.94 4.83
575 585 1.529226 TCAAATGGTAAGTGCCACCG 58.471 50.000 0.00 0.00 41.94 4.94
576 586 5.652994 TTTATCAAATGGTAAGTGCCACC 57.347 39.130 0.00 0.00 41.94 4.61
587 597 6.466812 AGGGCACTTTCTTTTTATCAAATGG 58.533 36.000 0.00 0.00 0.00 3.16
601 611 6.514048 GCTGTATAAATCATGAGGGCACTTTC 60.514 42.308 0.09 0.00 0.00 2.62
626 636 4.285851 GTCCAAAGACCAGGCTCG 57.714 61.111 0.00 0.00 37.00 5.03
652 662 3.914579 CTGAGTGTGGGCCAGGCTG 62.915 68.421 6.40 7.75 0.00 4.85
653 663 3.644606 CTGAGTGTGGGCCAGGCT 61.645 66.667 6.40 8.19 0.00 4.58
654 664 3.618780 CTCTGAGTGTGGGCCAGGC 62.619 68.421 6.40 1.26 0.00 4.85
655 665 2.667418 CTCTGAGTGTGGGCCAGG 59.333 66.667 6.40 0.00 0.00 4.45
656 666 1.483595 TTCCTCTGAGTGTGGGCCAG 61.484 60.000 6.40 0.00 0.00 4.85
657 667 1.461268 TTCCTCTGAGTGTGGGCCA 60.461 57.895 0.00 0.00 0.00 5.36
658 668 1.003233 GTTCCTCTGAGTGTGGGCC 60.003 63.158 0.00 0.00 0.00 5.80
659 669 1.374758 CGTTCCTCTGAGTGTGGGC 60.375 63.158 3.66 0.00 0.00 5.36
660 670 1.293498 CCGTTCCTCTGAGTGTGGG 59.707 63.158 3.66 0.00 0.00 4.61
661 671 1.293498 CCCGTTCCTCTGAGTGTGG 59.707 63.158 3.66 0.23 0.00 4.17
662 672 0.319900 CACCCGTTCCTCTGAGTGTG 60.320 60.000 3.66 0.00 0.00 3.82
663 673 0.469331 TCACCCGTTCCTCTGAGTGT 60.469 55.000 3.66 0.00 0.00 3.55
664 674 0.244994 CTCACCCGTTCCTCTGAGTG 59.755 60.000 3.66 0.00 0.00 3.51
665 675 0.178958 ACTCACCCGTTCCTCTGAGT 60.179 55.000 3.66 0.00 38.82 3.41
666 676 0.244994 CACTCACCCGTTCCTCTGAG 59.755 60.000 0.00 0.00 36.90 3.35
667 677 1.185618 CCACTCACCCGTTCCTCTGA 61.186 60.000 0.00 0.00 0.00 3.27
668 678 1.185618 TCCACTCACCCGTTCCTCTG 61.186 60.000 0.00 0.00 0.00 3.35
669 679 1.155390 TCCACTCACCCGTTCCTCT 59.845 57.895 0.00 0.00 0.00 3.69
670 680 1.292541 GTCCACTCACCCGTTCCTC 59.707 63.158 0.00 0.00 0.00 3.71
671 681 2.214920 GGTCCACTCACCCGTTCCT 61.215 63.158 0.00 0.00 0.00 3.36
672 682 2.346365 GGTCCACTCACCCGTTCC 59.654 66.667 0.00 0.00 0.00 3.62
678 688 2.570181 CGTACGGGTCCACTCACC 59.430 66.667 7.57 0.00 35.42 4.02
679 689 2.570181 CCGTACGGGTCCACTCAC 59.430 66.667 27.00 0.00 0.00 3.51
680 690 3.376078 GCCGTACGGGTCCACTCA 61.376 66.667 33.98 0.00 38.44 3.41
681 691 3.352338 CTGCCGTACGGGTCCACTC 62.352 68.421 33.98 16.70 38.44 3.51
682 692 3.379445 CTGCCGTACGGGTCCACT 61.379 66.667 33.98 0.00 38.44 4.00
686 696 4.814294 CAGGCTGCCGTACGGGTC 62.814 72.222 33.98 20.64 38.44 4.46
800 810 3.668226 GCCTCGAGTTTAAAAGCTTGCTC 60.668 47.826 12.31 2.71 0.00 4.26
918 928 0.904865 ATCCAGAGAGGGTTGCGTGA 60.905 55.000 0.00 0.00 38.24 4.35
923 933 1.826024 CCGGATCCAGAGAGGGTTG 59.174 63.158 13.41 0.00 38.24 3.77
971 981 1.612442 GTGGGTAGTCTGGGGAGCA 60.612 63.158 0.00 0.00 0.00 4.26
972 982 2.368011 GGTGGGTAGTCTGGGGAGC 61.368 68.421 0.00 0.00 0.00 4.70
973 983 1.689582 GGGTGGGTAGTCTGGGGAG 60.690 68.421 0.00 0.00 0.00 4.30
974 984 2.453054 GGGTGGGTAGTCTGGGGA 59.547 66.667 0.00 0.00 0.00 4.81
978 988 1.272554 GGGAAGGGGTGGGTAGTCTG 61.273 65.000 0.00 0.00 0.00 3.51
986 996 3.809013 CCATCGGGGAAGGGGTGG 61.809 72.222 0.00 0.00 40.01 4.61
1346 1356 2.567049 GCGCGTACTCTGGTGACT 59.433 61.111 8.43 0.00 0.00 3.41
1470 1480 4.104417 GACGACGAGCTCTGCCGT 62.104 66.667 19.68 19.68 37.92 5.68
1499 1509 2.035312 ACGGCGAGGTAGGAGTGT 59.965 61.111 16.62 0.00 0.00 3.55
1501 1511 3.450115 GCACGGCGAGGTAGGAGT 61.450 66.667 16.62 0.00 0.00 3.85
1611 1663 2.951745 GATGACGGTCGCTGCTCG 60.952 66.667 3.34 1.74 40.15 5.03
1623 1675 1.298190 GGCGTAGTCCGACGATGAC 60.298 63.158 5.14 0.00 45.82 3.06
1875 1936 1.518572 CTGGTACGGACGATGGCAC 60.519 63.158 0.00 0.00 36.31 5.01
1879 1940 0.663688 CTCCTCTGGTACGGACGATG 59.336 60.000 0.00 0.00 39.80 3.84
1883 1944 2.772691 CCGCTCCTCTGGTACGGAC 61.773 68.421 12.26 0.00 39.80 4.79
2016 2080 4.914983 TGCATGAGGAATCCAATATCTCC 58.085 43.478 0.61 0.00 0.00 3.71
2062 2126 2.924290 GGAGTGAGTCGTATTGCAAGTC 59.076 50.000 4.94 0.00 0.00 3.01
2074 2138 2.550180 GCAAACAGGAAAGGAGTGAGTC 59.450 50.000 0.00 0.00 0.00 3.36
2082 2146 1.007387 GCACGGCAAACAGGAAAGG 60.007 57.895 0.00 0.00 0.00 3.11
2172 2236 6.826231 TGTGTCCACATTAAATTCGGTCATAT 59.174 34.615 0.00 0.00 36.21 1.78
2174 2238 5.007034 TGTGTCCACATTAAATTCGGTCAT 58.993 37.500 0.00 0.00 36.21 3.06
2179 2243 5.046910 AGCTTGTGTCCACATTAAATTCG 57.953 39.130 0.20 0.00 41.52 3.34
2199 2263 6.824196 GGAAGGCCCAAGTAGATAAATATAGC 59.176 42.308 0.00 0.00 34.14 2.97
2219 2283 4.897140 TCAGAAATTTGCCATTTGGAAGG 58.103 39.130 0.00 0.00 37.39 3.46
2220 2284 6.128117 CCAATCAGAAATTTGCCATTTGGAAG 60.128 38.462 0.00 0.00 37.39 3.46
2223 2297 5.005094 ACCAATCAGAAATTTGCCATTTGG 58.995 37.500 0.00 5.33 37.64 3.28
2244 2318 9.912634 TGAATTCTGTCAAATTTTGATCTTACC 57.087 29.630 14.54 2.28 42.47 2.85
2262 2336 3.338249 ACCACCGACAGATTGAATTCTG 58.662 45.455 7.05 0.00 46.94 3.02
2264 2338 3.871594 CCTACCACCGACAGATTGAATTC 59.128 47.826 0.00 0.00 0.00 2.17
2265 2339 3.263425 ACCTACCACCGACAGATTGAATT 59.737 43.478 0.00 0.00 0.00 2.17
2266 2340 2.838202 ACCTACCACCGACAGATTGAAT 59.162 45.455 0.00 0.00 0.00 2.57
2267 2341 2.253610 ACCTACCACCGACAGATTGAA 58.746 47.619 0.00 0.00 0.00 2.69
2268 2342 1.933021 ACCTACCACCGACAGATTGA 58.067 50.000 0.00 0.00 0.00 2.57
2269 2343 2.289444 ACAACCTACCACCGACAGATTG 60.289 50.000 0.00 0.00 0.00 2.67
2270 2344 1.975680 ACAACCTACCACCGACAGATT 59.024 47.619 0.00 0.00 0.00 2.40
2271 2345 1.640917 ACAACCTACCACCGACAGAT 58.359 50.000 0.00 0.00 0.00 2.90
2272 2346 2.291209 TACAACCTACCACCGACAGA 57.709 50.000 0.00 0.00 0.00 3.41
2273 2347 3.604875 AATACAACCTACCACCGACAG 57.395 47.619 0.00 0.00 0.00 3.51
2274 2348 4.081531 CCTAAATACAACCTACCACCGACA 60.082 45.833 0.00 0.00 0.00 4.35
2276 2350 3.451902 CCCTAAATACAACCTACCACCGA 59.548 47.826 0.00 0.00 0.00 4.69
2277 2351 3.451902 TCCCTAAATACAACCTACCACCG 59.548 47.826 0.00 0.00 0.00 4.94
2278 2352 5.368816 AGATCCCTAAATACAACCTACCACC 59.631 44.000 0.00 0.00 0.00 4.61
2279 2353 6.496144 AGATCCCTAAATACAACCTACCAC 57.504 41.667 0.00 0.00 0.00 4.16
2281 2355 9.102453 AGATAAGATCCCTAAATACAACCTACC 57.898 37.037 0.00 0.00 0.00 3.18
2314 2388 1.273886 GGTCCCTAAATTGCCGCAAAA 59.726 47.619 10.42 0.00 0.00 2.44
2315 2389 0.892063 GGTCCCTAAATTGCCGCAAA 59.108 50.000 10.42 0.00 0.00 3.68
2316 2390 0.039035 AGGTCCCTAAATTGCCGCAA 59.961 50.000 8.55 8.55 0.00 4.85
2320 2394 6.538945 TTTTGATAAGGTCCCTAAATTGCC 57.461 37.500 0.00 0.00 0.00 4.52
2321 2395 8.257306 TGAATTTTGATAAGGTCCCTAAATTGC 58.743 33.333 7.97 3.16 29.31 3.56
2326 2839 7.928873 AGTCTGAATTTTGATAAGGTCCCTAA 58.071 34.615 0.00 0.00 0.00 2.69
2331 2844 9.871238 TGTAGTAGTCTGAATTTTGATAAGGTC 57.129 33.333 0.00 0.00 0.00 3.85
2348 2861 8.450180 GGTAAGTACTCTGAACTTGTAGTAGTC 58.550 40.741 0.00 0.00 37.71 2.59
2431 2973 0.681564 ACCAGGTGTGTCCGCAAAAA 60.682 50.000 0.00 0.00 41.99 1.94
2432 2974 0.180642 TACCAGGTGTGTCCGCAAAA 59.819 50.000 0.76 0.00 41.99 2.44
2433 2975 0.180642 TTACCAGGTGTGTCCGCAAA 59.819 50.000 0.76 0.00 41.99 3.68
2434 2976 0.250124 CTTACCAGGTGTGTCCGCAA 60.250 55.000 0.76 0.00 41.99 4.85
2435 2977 1.369692 CTTACCAGGTGTGTCCGCA 59.630 57.895 0.76 0.00 41.99 5.69
2436 2978 2.033194 GCTTACCAGGTGTGTCCGC 61.033 63.158 0.76 0.00 41.99 5.54
2437 2979 0.036388 ATGCTTACCAGGTGTGTCCG 60.036 55.000 0.76 0.00 41.99 4.79
2438 2980 1.271379 ACATGCTTACCAGGTGTGTCC 60.271 52.381 0.76 0.00 37.03 4.02
2439 2981 2.185004 ACATGCTTACCAGGTGTGTC 57.815 50.000 0.76 0.00 37.03 3.67
2440 2982 2.158682 TCAACATGCTTACCAGGTGTGT 60.159 45.455 0.76 0.00 38.67 3.72
2441 2983 2.226437 GTCAACATGCTTACCAGGTGTG 59.774 50.000 0.76 0.00 38.67 3.82
2442 2984 2.504367 GTCAACATGCTTACCAGGTGT 58.496 47.619 0.76 0.00 38.67 4.16
2443 2985 1.464608 CGTCAACATGCTTACCAGGTG 59.535 52.381 0.76 0.00 38.67 4.00
2444 2986 1.071699 ACGTCAACATGCTTACCAGGT 59.928 47.619 0.00 0.00 40.78 4.00
2445 2987 1.732259 GACGTCAACATGCTTACCAGG 59.268 52.381 11.55 0.00 0.00 4.45
2446 2988 1.390123 CGACGTCAACATGCTTACCAG 59.610 52.381 17.16 0.00 0.00 4.00
2447 2989 1.424403 CGACGTCAACATGCTTACCA 58.576 50.000 17.16 0.00 0.00 3.25
2448 2990 0.719465 CCGACGTCAACATGCTTACC 59.281 55.000 17.16 0.00 0.00 2.85
2449 2991 1.389106 GACCGACGTCAACATGCTTAC 59.611 52.381 17.16 0.00 38.99 2.34
2450 2992 1.000052 TGACCGACGTCAACATGCTTA 60.000 47.619 17.16 0.00 46.09 3.09
2451 2993 0.249699 TGACCGACGTCAACATGCTT 60.250 50.000 17.16 0.00 46.09 3.91
2452 2994 1.365999 TGACCGACGTCAACATGCT 59.634 52.632 17.16 0.00 46.09 3.79
2453 2995 3.945436 TGACCGACGTCAACATGC 58.055 55.556 17.16 0.00 46.09 4.06
2462 3004 3.119955 TGAATCTCTAGTGTTGACCGACG 60.120 47.826 0.00 0.00 0.00 5.12
2493 3035 9.612620 CCAAGAAATGAACTACAAGTATTCAAC 57.387 33.333 8.23 0.00 36.03 3.18
2494 3036 9.349713 ACCAAGAAATGAACTACAAGTATTCAA 57.650 29.630 8.23 0.00 36.03 2.69
2495 3037 8.918202 ACCAAGAAATGAACTACAAGTATTCA 57.082 30.769 0.00 0.00 36.81 2.57
2532 3084 5.169992 TGAGGTGTTCATGAGATTCACAT 57.830 39.130 17.42 13.28 33.57 3.21
2534 3086 5.947228 TTTGAGGTGTTCATGAGATTCAC 57.053 39.130 0.00 4.90 35.27 3.18
2537 3089 6.461509 GGTGTTTTTGAGGTGTTCATGAGATT 60.462 38.462 0.00 0.00 35.27 2.40
2555 3107 5.878406 TGGTTGTTGATTATGGGTGTTTT 57.122 34.783 0.00 0.00 0.00 2.43
2561 3113 6.633500 AATACGATGGTTGTTGATTATGGG 57.367 37.500 0.00 0.00 0.00 4.00
2617 3182 3.804786 TTATTGCCACGTATCGAGGAA 57.195 42.857 9.50 0.00 39.84 3.36
2630 3195 7.852945 GCATATATTCATCGCTACTTTATTGCC 59.147 37.037 0.00 0.00 0.00 4.52
2671 3236 7.214467 TCAAAGGAGTATTGAAAACACATCC 57.786 36.000 0.00 0.00 34.04 3.51
2673 3238 7.671398 AGGATCAAAGGAGTATTGAAAACACAT 59.329 33.333 0.00 0.00 39.98 3.21
2676 3241 7.176690 GGAAGGATCAAAGGAGTATTGAAAACA 59.823 37.037 0.00 0.00 39.98 2.83
2691 3256 4.469945 AGGTCGTATCAAGGAAGGATCAAA 59.530 41.667 0.00 0.00 0.00 2.69
2697 3262 2.959707 AGCTAGGTCGTATCAAGGAAGG 59.040 50.000 0.00 0.00 0.00 3.46
2699 3264 3.628008 TGAGCTAGGTCGTATCAAGGAA 58.372 45.455 16.71 0.00 0.00 3.36
2749 3314 8.948631 TCTCTTATATCAAAAGCCAGTAACTG 57.051 34.615 0.00 0.00 0.00 3.16
2755 3320 8.348507 GGTTCATTCTCTTATATCAAAAGCCAG 58.651 37.037 0.00 0.00 0.00 4.85
2757 3322 8.131731 GTGGTTCATTCTCTTATATCAAAAGCC 58.868 37.037 0.00 0.00 0.00 4.35
2764 3329 9.167311 AGTTTGTGTGGTTCATTCTCTTATATC 57.833 33.333 0.00 0.00 0.00 1.63
2767 3332 8.918202 TTAGTTTGTGTGGTTCATTCTCTTAT 57.082 30.769 0.00 0.00 0.00 1.73
2768 3333 8.740123 TTTAGTTTGTGTGGTTCATTCTCTTA 57.260 30.769 0.00 0.00 0.00 2.10
2769 3334 7.639113 TTTAGTTTGTGTGGTTCATTCTCTT 57.361 32.000 0.00 0.00 0.00 2.85
2770 3335 7.823745 ATTTAGTTTGTGTGGTTCATTCTCT 57.176 32.000 0.00 0.00 0.00 3.10
2771 3336 8.784043 AGTATTTAGTTTGTGTGGTTCATTCTC 58.216 33.333 0.00 0.00 0.00 2.87
2772 3337 8.691661 AGTATTTAGTTTGTGTGGTTCATTCT 57.308 30.769 0.00 0.00 0.00 2.40
2773 3338 8.021396 GGAGTATTTAGTTTGTGTGGTTCATTC 58.979 37.037 0.00 0.00 0.00 2.67
2774 3339 7.039993 GGGAGTATTTAGTTTGTGTGGTTCATT 60.040 37.037 0.00 0.00 0.00 2.57
2775 3340 6.433093 GGGAGTATTTAGTTTGTGTGGTTCAT 59.567 38.462 0.00 0.00 0.00 2.57
2776 3341 5.766174 GGGAGTATTTAGTTTGTGTGGTTCA 59.234 40.000 0.00 0.00 0.00 3.18
2777 3342 6.002082 AGGGAGTATTTAGTTTGTGTGGTTC 58.998 40.000 0.00 0.00 0.00 3.62
2778 3343 5.948842 AGGGAGTATTTAGTTTGTGTGGTT 58.051 37.500 0.00 0.00 0.00 3.67
2779 3344 5.309806 AGAGGGAGTATTTAGTTTGTGTGGT 59.690 40.000 0.00 0.00 0.00 4.16
2780 3345 5.643777 CAGAGGGAGTATTTAGTTTGTGTGG 59.356 44.000 0.00 0.00 0.00 4.17
2781 3346 6.231211 ACAGAGGGAGTATTTAGTTTGTGTG 58.769 40.000 0.00 0.00 0.00 3.82
2782 3347 6.435292 ACAGAGGGAGTATTTAGTTTGTGT 57.565 37.500 0.00 0.00 0.00 3.72
2783 3348 8.718734 GTTTACAGAGGGAGTATTTAGTTTGTG 58.281 37.037 0.00 0.00 0.00 3.33
2784 3349 8.657712 AGTTTACAGAGGGAGTATTTAGTTTGT 58.342 33.333 0.00 0.00 0.00 2.83
2795 3360 8.862085 GCTCTTATATTAGTTTACAGAGGGAGT 58.138 37.037 0.00 0.00 0.00 3.85
2796 3361 8.024285 CGCTCTTATATTAGTTTACAGAGGGAG 58.976 40.741 4.76 0.00 40.49 4.30
2797 3362 7.504911 ACGCTCTTATATTAGTTTACAGAGGGA 59.495 37.037 14.96 0.00 40.49 4.20
2798 3363 7.659186 ACGCTCTTATATTAGTTTACAGAGGG 58.341 38.462 8.36 8.36 42.53 4.30
2799 3364 9.530633 AAACGCTCTTATATTAGTTTACAGAGG 57.469 33.333 0.00 0.00 31.14 3.69
2814 3379 9.953697 CTACTTTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 40.05 1.73
2815 3380 8.954350 ACTACTTTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 40.05 2.10
2816 3381 7.828712 ACTACTTTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 40.05 2.85
2817 3382 7.393841 ACTACTTTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 40.05 4.09
2818 3383 9.733219 ATTACTACTTTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 40.05 5.03
2819 3384 9.733219 GATTACTACTTTAGTGATCTAAACGCT 57.267 33.333 9.68 0.00 44.10 5.07
2827 3392 9.733219 AGCGTTTAGATTACTACTTTAGTGATC 57.267 33.333 9.14 9.14 46.38 2.92
2828 3393 9.733219 GAGCGTTTAGATTACTACTTTAGTGAT 57.267 33.333 0.00 0.00 39.81 3.06
2829 3394 8.954350 AGAGCGTTTAGATTACTACTTTAGTGA 58.046 33.333 0.00 0.00 39.81 3.41
2830 3395 9.570488 AAGAGCGTTTAGATTACTACTTTAGTG 57.430 33.333 0.00 0.00 39.81 2.74
2844 3409 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
2845 3410 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
2846 3411 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
2847 3412 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
2848 3413 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
2849 3414 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
2850 3415 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
2851 3416 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
2852 3417 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
2853 3418 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
2854 3419 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
2855 3420 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
2857 3422 9.018582 GTATGTACTCCCTCCGTAAACTAATAT 57.981 37.037 0.00 0.00 0.00 1.28
2858 3423 8.220559 AGTATGTACTCCCTCCGTAAACTAATA 58.779 37.037 0.00 0.00 0.00 0.98
2859 3424 7.065504 AGTATGTACTCCCTCCGTAAACTAAT 58.934 38.462 0.00 0.00 0.00 1.73
2860 3425 6.426587 AGTATGTACTCCCTCCGTAAACTAA 58.573 40.000 0.00 0.00 0.00 2.24
2861 3426 6.006275 AGTATGTACTCCCTCCGTAAACTA 57.994 41.667 0.00 0.00 0.00 2.24
2862 3427 4.864726 AGTATGTACTCCCTCCGTAAACT 58.135 43.478 0.00 0.00 0.00 2.66
2863 3428 6.699575 TTAGTATGTACTCCCTCCGTAAAC 57.300 41.667 0.00 0.00 37.73 2.01
2864 3429 6.663093 TGTTTAGTATGTACTCCCTCCGTAAA 59.337 38.462 0.00 0.00 37.73 2.01
2865 3430 6.186957 TGTTTAGTATGTACTCCCTCCGTAA 58.813 40.000 0.00 0.00 37.73 3.18
2866 3431 5.754782 TGTTTAGTATGTACTCCCTCCGTA 58.245 41.667 0.00 0.00 37.73 4.02
2867 3432 4.603131 TGTTTAGTATGTACTCCCTCCGT 58.397 43.478 0.00 0.00 37.73 4.69
2868 3433 4.643784 ACTGTTTAGTATGTACTCCCTCCG 59.356 45.833 0.00 0.00 37.73 4.63
2869 3434 6.541934 AACTGTTTAGTATGTACTCCCTCC 57.458 41.667 0.00 0.00 35.69 4.30
2870 3435 7.609056 TCAAACTGTTTAGTATGTACTCCCTC 58.391 38.462 5.31 0.00 35.69 4.30
2871 3436 7.549147 TCAAACTGTTTAGTATGTACTCCCT 57.451 36.000 5.31 0.00 35.69 4.20
2872 3437 7.201617 GCATCAAACTGTTTAGTATGTACTCCC 60.202 40.741 5.31 0.00 35.69 4.30
2873 3438 7.549488 AGCATCAAACTGTTTAGTATGTACTCC 59.451 37.037 5.31 0.00 35.69 3.85
2874 3439 8.480643 AGCATCAAACTGTTTAGTATGTACTC 57.519 34.615 5.31 0.00 35.69 2.59
2875 3440 8.848474 AAGCATCAAACTGTTTAGTATGTACT 57.152 30.769 5.31 0.00 35.69 2.73


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

AutoCloner maintained by Alex Coulton.