Multiple sequence alignment - TraesCS5D01G059800

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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 TraesCS5D01G059800 chr5D 100.000 6149 0 0 1 6149 56471704 56465556 0.000000e+00 11356.0
1 TraesCS5D01G059800 chr5D 100.000 3024 0 0 6467 9490 56465238 56462215 0.000000e+00 5585.0
2 TraesCS5D01G059800 chr5B 96.580 5321 112 32 860 6148 59181078 59175796 0.000000e+00 8754.0
3 TraesCS5D01G059800 chr5B 96.050 2329 68 9 6467 8783 59175769 59173453 0.000000e+00 3770.0
4 TraesCS5D01G059800 chr5B 95.258 717 25 6 8782 9490 59173493 59172778 0.000000e+00 1127.0
5 TraesCS5D01G059800 chr5B 84.888 536 36 18 334 842 59181706 59181189 5.120000e-137 499.0
6 TraesCS5D01G059800 chr5B 92.885 253 16 2 1 252 59181966 59181715 5.420000e-97 366.0
7 TraesCS5D01G059800 chr5A 94.675 3042 104 21 6492 9490 44995434 44992408 0.000000e+00 4667.0
8 TraesCS5D01G059800 chr5A 90.000 1020 79 10 2704 3707 44999178 44998166 0.000000e+00 1297.0
9 TraesCS5D01G059800 chr5A 86.439 1202 51 46 558 1696 45001020 44999868 0.000000e+00 1214.0
10 TraesCS5D01G059800 chr5A 95.070 710 22 4 4904 5601 44996791 44996083 0.000000e+00 1105.0
11 TraesCS5D01G059800 chr5A 89.620 684 55 9 1983 2663 44999852 44999182 0.000000e+00 856.0
12 TraesCS5D01G059800 chr5A 95.294 425 20 0 5725 6149 44996085 44995661 0.000000e+00 675.0
13 TraesCS5D01G059800 chr5A 87.716 521 49 12 4098 4608 44997767 44997252 2.280000e-165 593.0
14 TraesCS5D01G059800 chr5A 84.277 318 42 6 4610 4926 44997127 44996817 4.310000e-78 303.0
15 TraesCS5D01G059800 chr5A 85.075 201 9 7 360 546 45001359 45001166 1.630000e-42 185.0
16 TraesCS5D01G059800 chr1A 84.435 469 52 11 8756 9208 538406024 538405561 8.750000e-120 442.0
17 TraesCS5D01G059800 chr1A 91.129 124 10 1 5598 5720 22387464 22387587 5.890000e-37 167.0
18 TraesCS5D01G059800 chr7B 94.488 127 7 0 5593 5719 431680487 431680361 7.520000e-46 196.0
19 TraesCS5D01G059800 chr7B 85.714 56 6 2 5564 5617 643348860 643348915 3.700000e-04 58.4
20 TraesCS5D01G059800 chr7D 93.860 114 7 0 5594 5707 593265177 593265064 1.270000e-38 172.0
21 TraesCS5D01G059800 chr6D 91.270 126 11 0 5594 5719 178859039 178858914 1.270000e-38 172.0
22 TraesCS5D01G059800 chr7A 90.551 127 11 1 5593 5719 556654827 556654702 5.890000e-37 167.0
23 TraesCS5D01G059800 chr7A 89.844 128 13 0 5593 5720 222941907 222942034 2.120000e-36 165.0
24 TraesCS5D01G059800 chr1D 89.474 133 13 1 5588 5720 23328067 23328198 5.890000e-37 167.0
25 TraesCS5D01G059800 chr4D 89.474 133 10 4 5580 5708 409217 409349 2.120000e-36 165.0
26 TraesCS5D01G059800 chr4D 96.703 91 2 1 4020 4110 449455694 449455605 5.940000e-32 150.0
27 TraesCS5D01G059800 chrUn 93.814 97 4 2 4011 4106 23900941 23900846 2.760000e-30 145.0
28 TraesCS5D01G059800 chr2B 93.814 97 4 2 4011 4106 799161143 799161048 2.760000e-30 145.0
29 TraesCS5D01G059800 chr2B 93.814 97 4 2 4011 4106 799214299 799214204 2.760000e-30 145.0
30 TraesCS5D01G059800 chr2B 92.157 102 4 3 4020 4121 782178763 782178860 3.570000e-29 141.0
31 TraesCS5D01G059800 chr2B 90.000 110 6 5 3992 4099 41129599 41129493 4.620000e-28 137.0
32 TraesCS5D01G059800 chr4A 98.765 81 0 1 4020 4100 614251508 614251429 9.930000e-30 143.0
33 TraesCS5D01G059800 chr3B 90.741 108 5 5 3996 4101 3660753 3660857 1.290000e-28 139.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G059800 chr5D 56462215 56471704 9489 True 8470.500000 11356 100.000000 1 9490 2 chr5D.!!$R1 9489
1 TraesCS5D01G059800 chr5B 59172778 59181966 9188 True 2903.200000 8754 93.132200 1 9490 5 chr5B.!!$R1 9489
2 TraesCS5D01G059800 chr5A 44992408 45001359 8951 True 1210.555556 4667 89.796222 360 9490 9 chr5A.!!$R1 9130

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
364 366 0.108186 TCGGATGGCAGCAAGTACAG 60.108 55.000 4.64 0.00 0.00 2.74 F
812 991 0.323451 GGTACCCAGCCCTTTTCAGG 60.323 60.000 0.00 0.00 40.45 3.86 F
983 1259 0.388134 GCTGTGCTAGTTTCGTCCGA 60.388 55.000 0.00 0.00 0.00 4.55 F
1233 1518 0.834687 TGGAGGCACGTTTAGGGTCT 60.835 55.000 0.00 0.00 43.80 3.85 F
1293 1591 1.078918 CTGGCGGATCTTGCTGACA 60.079 57.895 9.73 0.00 0.00 3.58 F
1306 1604 1.137282 TGCTGACACGTTTGAGGTGTA 59.863 47.619 6.42 0.00 45.85 2.90 F
1411 1709 1.378250 GAGCCTGCTCATGTTGCCT 60.378 57.895 14.07 2.09 42.31 4.75 F
2672 2985 3.049206 TGCAATTAGAAAGCACAAACGC 58.951 40.909 0.00 0.00 32.55 4.84 F
3440 3756 2.683211 AGTGTGGCCTTTTCTCCATT 57.317 45.000 3.32 0.00 34.47 3.16 F
4402 4822 4.273235 TGCCACTTATATGCATGTTCTTCG 59.727 41.667 10.16 0.00 0.00 3.79 F
4708 5257 0.648441 GTGCGTGTCTCGTTTGAACA 59.352 50.000 0.00 0.00 42.13 3.18 F
4999 5596 1.786937 TTGGAAGGCAAGGAAAAGCA 58.213 45.000 0.00 0.00 0.00 3.91 F
5623 6230 1.904287 TTCCACAATGTAGTGTGCCC 58.096 50.000 6.92 0.00 46.24 5.36 F
6621 7228 0.947244 AAGGAAGTGCAGTTGAAGCG 59.053 50.000 12.53 0.00 33.85 4.68 F
8239 8879 0.458543 CGTCGTGGCAGCTCAATAGT 60.459 55.000 0.00 0.00 0.00 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1819 0.188342 AACTTGGCCAATGGTCCTGT 59.812 50.000 20.85 8.67 0.00 4.00 R
1660 1958 0.897863 CCCGGCCAAAAACCATGAGA 60.898 55.000 2.24 0.00 0.00 3.27 R
1964 2274 2.288666 AGATGACAAAACGTGTGTGCT 58.711 42.857 9.69 2.63 41.96 4.40 R
2995 3311 5.534407 TCTGCACGAGTATTTGTAACAGAA 58.466 37.500 7.62 0.00 33.45 3.02 R
3102 3418 6.835914 AGCGATTTGTAGAAACAGAAATCAG 58.164 36.000 0.00 0.00 34.54 2.90 R
3408 3724 2.095853 GGCCACACTACATCAATTCACG 59.904 50.000 0.00 0.00 0.00 4.35 R
3440 3756 9.602568 AAAATGAATATGCAGCATTTTATGTGA 57.397 25.926 14.58 0.00 45.27 3.58 R
3586 3903 1.195115 GGCAGGTGTCTGTATCCTCA 58.805 55.000 0.00 0.00 42.78 3.86 R
4631 5180 3.057734 GGAGTAAGTTCACTGTTGTCCG 58.942 50.000 0.00 0.00 0.00 4.79 R
5623 6230 0.577269 CTTAAATCTCGGGAAGCGCG 59.423 55.000 0.00 0.00 41.10 6.86 R
5999 6606 3.571590 AGCATGCTACTTAGTCTAGCCT 58.428 45.455 21.21 0.00 36.54 4.58 R
6621 7228 5.335976 GGGATCAAACAGAGGAAACAATGAC 60.336 44.000 0.00 0.00 0.00 3.06 R
7531 8156 0.613260 GGCAGGGGGTGAATTTTTCC 59.387 55.000 0.00 0.00 0.00 3.13 R
8329 8970 0.103572 AAGCAGCCAGTTGTTGCAAG 59.896 50.000 0.00 0.00 40.22 4.01 R
9131 9819 0.255604 AATGTGCCGTGGATCCATCA 59.744 50.000 19.62 13.48 0.00 3.07 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
52 53 7.560991 TCAAGGTAATATCAAATTGCTCCACAT 59.439 33.333 0.00 0.00 0.00 3.21
65 66 2.295909 GCTCCACATGCCTGTTTGTAAA 59.704 45.455 0.00 0.00 31.62 2.01
86 87 0.676466 AATTCATCTTGGCGTGCCGA 60.676 50.000 6.37 3.16 39.42 5.54
100 101 1.212751 GCCGAGCCATTTGTGGTTC 59.787 57.895 1.70 1.70 36.08 3.62
108 109 2.538037 GCCATTTGTGGTTCGTTGTTTC 59.462 45.455 0.00 0.00 0.00 2.78
127 128 1.099689 CCGTCAACCACAACCACTTT 58.900 50.000 0.00 0.00 0.00 2.66
133 134 3.829601 TCAACCACAACCACTTTCAACTT 59.170 39.130 0.00 0.00 0.00 2.66
154 156 6.836242 ACTTTTCATGATCCCCTAATCTCTC 58.164 40.000 0.00 0.00 0.00 3.20
158 160 3.551635 TGATCCCCTAATCTCTCTCCC 57.448 52.381 0.00 0.00 0.00 4.30
164 166 2.225267 CCCTAATCTCTCTCCCTCTCCC 60.225 59.091 0.00 0.00 0.00 4.30
171 173 3.078305 TCTCTCTCCCTCTCCCTCTTTTT 59.922 47.826 0.00 0.00 0.00 1.94
186 188 4.214971 CCTCTTTTTAGCATCATGATCCCG 59.785 45.833 4.86 0.00 0.00 5.14
214 216 4.377021 TCACCATAAGGATACACATTCGC 58.623 43.478 0.00 0.00 38.69 4.70
224 226 4.327898 GGATACACATTCGCGTAGACAAAA 59.672 41.667 5.77 0.00 0.00 2.44
252 254 2.285544 GCATCCAAACGCAACACAAAAC 60.286 45.455 0.00 0.00 0.00 2.43
253 255 1.997669 TCCAAACGCAACACAAAACC 58.002 45.000 0.00 0.00 0.00 3.27
254 256 1.546476 TCCAAACGCAACACAAAACCT 59.454 42.857 0.00 0.00 0.00 3.50
255 257 2.028930 TCCAAACGCAACACAAAACCTT 60.029 40.909 0.00 0.00 0.00 3.50
257 259 3.187432 CCAAACGCAACACAAAACCTTTT 59.813 39.130 0.00 0.00 0.00 2.27
258 260 4.319839 CCAAACGCAACACAAAACCTTTTT 60.320 37.500 0.00 0.00 0.00 1.94
279 281 6.578163 TTTTTAACACCCCTTGTAGCATAC 57.422 37.500 0.00 0.00 43.42 2.39
280 282 5.508280 TTTAACACCCCTTGTAGCATACT 57.492 39.130 0.00 0.00 43.54 2.12
281 283 6.623979 TTTAACACCCCTTGTAGCATACTA 57.376 37.500 0.00 0.00 43.54 1.82
294 296 6.712179 GTAGCATACTACTCCCTTTAGTGT 57.288 41.667 0.00 0.00 44.61 3.55
295 297 7.110043 GTAGCATACTACTCCCTTTAGTGTT 57.890 40.000 0.00 0.00 44.61 3.32
296 298 8.230472 GTAGCATACTACTCCCTTTAGTGTTA 57.770 38.462 0.00 0.00 44.61 2.41
297 299 7.729124 AGCATACTACTCCCTTTAGTGTTAA 57.271 36.000 0.00 0.00 31.99 2.01
298 300 8.142485 AGCATACTACTCCCTTTAGTGTTAAA 57.858 34.615 0.00 0.00 31.99 1.52
299 301 8.599792 AGCATACTACTCCCTTTAGTGTTAAAA 58.400 33.333 0.00 0.00 31.99 1.52
300 302 9.223099 GCATACTACTCCCTTTAGTGTTAAAAA 57.777 33.333 0.00 0.00 31.99 1.94
324 326 9.893305 AAAACATTTTACATTACGAGAAGAAGG 57.107 29.630 0.00 0.00 0.00 3.46
325 327 7.611213 ACATTTTACATTACGAGAAGAAGGG 57.389 36.000 0.00 0.00 0.00 3.95
326 328 7.391620 ACATTTTACATTACGAGAAGAAGGGA 58.608 34.615 0.00 0.00 0.00 4.20
327 329 7.549488 ACATTTTACATTACGAGAAGAAGGGAG 59.451 37.037 0.00 0.00 0.00 4.30
328 330 6.600882 TTTACATTACGAGAAGAAGGGAGT 57.399 37.500 0.00 0.00 0.00 3.85
329 331 7.707624 TTTACATTACGAGAAGAAGGGAGTA 57.292 36.000 0.00 0.00 0.00 2.59
330 332 7.893124 TTACATTACGAGAAGAAGGGAGTAT 57.107 36.000 0.00 0.00 0.00 2.12
331 333 6.793505 ACATTACGAGAAGAAGGGAGTATT 57.206 37.500 0.00 0.00 0.00 1.89
332 334 7.893124 ACATTACGAGAAGAAGGGAGTATTA 57.107 36.000 0.00 0.00 0.00 0.98
364 366 0.108186 TCGGATGGCAGCAAGTACAG 60.108 55.000 4.64 0.00 0.00 2.74
433 435 2.647299 TGTCACAATCTAACCACCCCAT 59.353 45.455 0.00 0.00 0.00 4.00
434 436 3.016736 GTCACAATCTAACCACCCCATG 58.983 50.000 0.00 0.00 0.00 3.66
435 437 2.916269 TCACAATCTAACCACCCCATGA 59.084 45.455 0.00 0.00 0.00 3.07
436 438 3.527253 TCACAATCTAACCACCCCATGAT 59.473 43.478 0.00 0.00 0.00 2.45
437 439 3.633525 CACAATCTAACCACCCCATGATG 59.366 47.826 0.00 0.00 0.00 3.07
463 479 1.899814 CACCCCAGCTACTAGTTCACA 59.100 52.381 0.00 0.00 0.00 3.58
464 480 2.093973 CACCCCAGCTACTAGTTCACAG 60.094 54.545 0.00 0.00 0.00 3.66
465 481 2.180276 CCCCAGCTACTAGTTCACAGT 58.820 52.381 0.00 0.00 0.00 3.55
466 482 2.567615 CCCCAGCTACTAGTTCACAGTT 59.432 50.000 0.00 0.00 0.00 3.16
467 483 3.368531 CCCCAGCTACTAGTTCACAGTTC 60.369 52.174 0.00 0.00 0.00 3.01
468 484 3.258372 CCCAGCTACTAGTTCACAGTTCA 59.742 47.826 0.00 0.00 0.00 3.18
469 485 4.081420 CCCAGCTACTAGTTCACAGTTCAT 60.081 45.833 0.00 0.00 0.00 2.57
470 486 5.127194 CCCAGCTACTAGTTCACAGTTCATA 59.873 44.000 0.00 0.00 0.00 2.15
479 500 6.377327 AGTTCACAGTTCATACACAAAAGG 57.623 37.500 0.00 0.00 0.00 3.11
525 546 2.305927 TCCAAAACCAAACAAAAGGGCA 59.694 40.909 0.00 0.00 0.00 5.36
546 567 4.579869 CACATCTGCCTAAACTACCACTT 58.420 43.478 0.00 0.00 0.00 3.16
556 583 6.271566 CCTAAACTACCACTTCGAGGAATAC 58.728 44.000 0.00 0.00 0.00 1.89
566 721 9.978044 ACCACTTCGAGGAATACTATAAAATAC 57.022 33.333 0.00 0.00 0.00 1.89
567 722 9.420551 CCACTTCGAGGAATACTATAAAATACC 57.579 37.037 0.00 0.00 0.00 2.73
635 807 2.058595 CCCTGTTCCCGGAGATCGT 61.059 63.158 0.73 0.00 37.11 3.73
670 842 1.587876 GACGGCGATGCGACATGTA 60.588 57.895 16.62 0.00 32.52 2.29
688 860 1.358725 TAATGCGACCTGCTGCGTTC 61.359 55.000 0.00 0.00 46.63 3.95
707 879 2.960819 TCTCGCTAGGCTGTTTTTCTC 58.039 47.619 0.00 0.00 0.00 2.87
771 950 1.785951 GTCGGCAGCTTTTACGTCC 59.214 57.895 0.00 0.00 0.00 4.79
808 987 1.377612 GTCGGTACCCAGCCCTTTT 59.622 57.895 6.25 0.00 0.00 2.27
809 988 0.675837 GTCGGTACCCAGCCCTTTTC 60.676 60.000 6.25 0.00 0.00 2.29
810 989 1.128809 TCGGTACCCAGCCCTTTTCA 61.129 55.000 6.25 0.00 0.00 2.69
811 990 0.676782 CGGTACCCAGCCCTTTTCAG 60.677 60.000 6.25 0.00 0.00 3.02
812 991 0.323451 GGTACCCAGCCCTTTTCAGG 60.323 60.000 0.00 0.00 40.45 3.86
866 1139 3.614698 ACGTCCCGCCGTTGGTTA 61.615 61.111 0.00 0.00 37.96 2.85
900 1173 2.600769 AGCGACCCGTGTTCTCCT 60.601 61.111 0.00 0.00 0.00 3.69
901 1174 2.432628 GCGACCCGTGTTCTCCTG 60.433 66.667 0.00 0.00 0.00 3.86
902 1175 3.048602 CGACCCGTGTTCTCCTGT 58.951 61.111 0.00 0.00 0.00 4.00
904 1177 1.080705 GACCCGTGTTCTCCTGTCG 60.081 63.158 0.00 0.00 0.00 4.35
979 1255 1.597663 GTTGTGCTGTGCTAGTTTCGT 59.402 47.619 0.00 0.00 0.00 3.85
982 1258 0.666274 TGCTGTGCTAGTTTCGTCCG 60.666 55.000 0.00 0.00 0.00 4.79
983 1259 0.388134 GCTGTGCTAGTTTCGTCCGA 60.388 55.000 0.00 0.00 0.00 4.55
1098 1377 2.840102 ATCGCCTCCTTCCTCGGG 60.840 66.667 0.00 0.00 0.00 5.14
1165 1448 1.768077 CACTCCCCTCCCCATCTCC 60.768 68.421 0.00 0.00 0.00 3.71
1171 1454 1.532794 CCTCCCCATCTCCCTCTCG 60.533 68.421 0.00 0.00 0.00 4.04
1233 1518 0.834687 TGGAGGCACGTTTAGGGTCT 60.835 55.000 0.00 0.00 43.80 3.85
1278 1563 1.610554 CCCCTCCATTTTGCTGCTGG 61.611 60.000 0.00 0.00 0.00 4.85
1279 1564 1.217244 CCTCCATTTTGCTGCTGGC 59.783 57.895 0.00 0.00 42.22 4.85
1281 1566 2.125832 CCATTTTGCTGCTGGCGG 60.126 61.111 0.00 0.00 45.43 6.13
1293 1591 1.078918 CTGGCGGATCTTGCTGACA 60.079 57.895 9.73 0.00 0.00 3.58
1306 1604 1.137282 TGCTGACACGTTTGAGGTGTA 59.863 47.619 6.42 0.00 45.85 2.90
1322 1620 3.086282 GGTGTATGGTTTTGGATTCGGT 58.914 45.455 0.00 0.00 0.00 4.69
1354 1652 1.639635 GGCTGTGGGAGATGGTGGAT 61.640 60.000 0.00 0.00 0.00 3.41
1411 1709 1.378250 GAGCCTGCTCATGTTGCCT 60.378 57.895 14.07 2.09 42.31 4.75
1642 1940 4.466015 TGCACCTATCAGATCAAGTGTGTA 59.534 41.667 0.00 0.00 0.00 2.90
1643 1941 5.129320 TGCACCTATCAGATCAAGTGTGTAT 59.871 40.000 0.00 0.00 0.00 2.29
1644 1942 6.051717 GCACCTATCAGATCAAGTGTGTATT 58.948 40.000 0.00 0.00 0.00 1.89
1645 1943 7.147742 TGCACCTATCAGATCAAGTGTGTATTA 60.148 37.037 0.00 0.00 0.00 0.98
1646 1944 7.169982 GCACCTATCAGATCAAGTGTGTATTAC 59.830 40.741 0.00 0.00 0.00 1.89
1647 1945 8.417106 CACCTATCAGATCAAGTGTGTATTACT 58.583 37.037 0.00 0.00 0.00 2.24
1648 1946 8.634444 ACCTATCAGATCAAGTGTGTATTACTC 58.366 37.037 0.00 0.00 0.00 2.59
1649 1947 8.633561 CCTATCAGATCAAGTGTGTATTACTCA 58.366 37.037 0.00 0.00 0.00 3.41
1651 1949 8.883954 ATCAGATCAAGTGTGTATTACTCATG 57.116 34.615 0.00 0.00 0.00 3.07
1652 1950 6.758416 TCAGATCAAGTGTGTATTACTCATGC 59.242 38.462 0.00 0.00 0.00 4.06
1653 1951 6.760298 CAGATCAAGTGTGTATTACTCATGCT 59.240 38.462 0.00 0.00 0.00 3.79
1654 1952 7.922811 CAGATCAAGTGTGTATTACTCATGCTA 59.077 37.037 0.00 0.00 0.00 3.49
1655 1953 8.140628 AGATCAAGTGTGTATTACTCATGCTAG 58.859 37.037 0.00 0.00 0.00 3.42
1656 1954 6.042777 TCAAGTGTGTATTACTCATGCTAGC 58.957 40.000 8.10 8.10 0.00 3.42
1660 1958 7.050377 AGTGTGTATTACTCATGCTAGCATTT 58.950 34.615 27.59 16.52 33.90 2.32
1672 1975 5.726980 TGCTAGCATTTCTCATGGTTTTT 57.273 34.783 14.93 0.00 0.00 1.94
1696 1999 4.212716 GCCGGGTTTCCCTTAATTATCTT 58.787 43.478 2.18 0.00 42.67 2.40
1697 2000 5.379187 GCCGGGTTTCCCTTAATTATCTTA 58.621 41.667 2.18 0.00 42.67 2.10
1699 2002 7.170277 GCCGGGTTTCCCTTAATTATCTTATA 58.830 38.462 2.18 0.00 42.67 0.98
1700 2003 7.832685 GCCGGGTTTCCCTTAATTATCTTATAT 59.167 37.037 2.18 0.00 42.67 0.86
1701 2004 9.749340 CCGGGTTTCCCTTAATTATCTTATATT 57.251 33.333 0.00 0.00 42.67 1.28
1784 2094 6.772233 TCATGCTAGCATTTTATTAGGAAGCA 59.228 34.615 27.59 0.00 41.22 3.91
1949 2259 6.713762 TTACATGTGGAAATTGGGATGATC 57.286 37.500 9.11 0.00 0.00 2.92
1950 2260 4.875389 ACATGTGGAAATTGGGATGATCT 58.125 39.130 0.00 0.00 0.00 2.75
1951 2261 4.647853 ACATGTGGAAATTGGGATGATCTG 59.352 41.667 0.00 0.00 0.00 2.90
1964 2274 7.773489 TGGGATGATCTGTTCAATGTAAAAA 57.227 32.000 0.00 0.00 38.03 1.94
2672 2985 3.049206 TGCAATTAGAAAGCACAAACGC 58.951 40.909 0.00 0.00 32.55 4.84
2833 3147 4.967084 TTACACTGTGGGAACTGTACAT 57.033 40.909 13.09 0.00 0.00 2.29
2834 3148 3.857157 ACACTGTGGGAACTGTACATT 57.143 42.857 13.09 0.00 0.00 2.71
2995 3311 3.821748 AGATGCTTCATCACATCATGCT 58.178 40.909 9.19 0.00 44.16 3.79
3102 3418 3.314541 TTACCTTGACTTCTTCCGAGC 57.685 47.619 0.00 0.00 0.00 5.03
3440 3756 2.683211 AGTGTGGCCTTTTCTCCATT 57.317 45.000 3.32 0.00 34.47 3.16
3505 3822 5.772393 ATGTCCTTCCAACATGGTAACTA 57.228 39.130 0.00 0.00 39.03 2.24
3586 3903 4.275936 GGATGCTGTTACAACTTGTTGTCT 59.724 41.667 20.47 2.60 36.44 3.41
3643 3972 5.105834 GCAAGGCTGCTAAATCATCTAAG 57.894 43.478 0.00 0.00 45.74 2.18
3757 4168 8.208224 TGGTAAAAAGTCAAGACATAGACAAGA 58.792 33.333 2.72 0.00 37.23 3.02
4173 4591 4.747810 CCAAATTGGTAGTCTTGAATGCC 58.252 43.478 3.34 0.00 31.35 4.40
4382 4802 5.416083 ACTTTTTGGTAGTCTTGTTTTGCC 58.584 37.500 0.00 0.00 0.00 4.52
4402 4822 4.273235 TGCCACTTATATGCATGTTCTTCG 59.727 41.667 10.16 0.00 0.00 3.79
4631 5180 7.926018 AGACCAACCTGATGTTTAAAATGTTTC 59.074 33.333 0.00 0.00 34.00 2.78
4708 5257 0.648441 GTGCGTGTCTCGTTTGAACA 59.352 50.000 0.00 0.00 42.13 3.18
4833 5382 8.621532 TTACATAACAGCTTTTGAGTTCTGAT 57.378 30.769 6.34 0.00 0.00 2.90
4834 5383 9.719355 TTACATAACAGCTTTTGAGTTCTGATA 57.281 29.630 6.34 0.00 0.00 2.15
4835 5384 8.261492 ACATAACAGCTTTTGAGTTCTGATAG 57.739 34.615 6.34 0.00 0.00 2.08
4836 5385 8.097038 ACATAACAGCTTTTGAGTTCTGATAGA 58.903 33.333 6.34 0.00 0.00 1.98
4873 5422 4.241681 TGTTTTGTTGGACAAGAAGTTGC 58.758 39.130 0.00 0.00 39.53 4.17
4999 5596 1.786937 TTGGAAGGCAAGGAAAAGCA 58.213 45.000 0.00 0.00 0.00 3.91
5090 5687 4.636206 CCTATCCTAACTGCAAGGAACAAC 59.364 45.833 9.64 0.00 46.06 3.32
5359 5966 5.300034 TCTTGATGAATGTTGCAAGTTCACT 59.700 36.000 22.47 14.67 38.95 3.41
5619 6226 3.308402 CCCTCCATTCCACAATGTAGTGT 60.308 47.826 0.00 0.00 38.22 3.55
5622 6229 2.164219 CCATTCCACAATGTAGTGTGCC 59.836 50.000 6.92 0.00 46.24 5.01
5623 6230 1.904287 TTCCACAATGTAGTGTGCCC 58.096 50.000 6.92 0.00 46.24 5.36
5665 6272 7.589958 AGTTTGACCATACATTTAACCAACA 57.410 32.000 0.00 0.00 0.00 3.33
6621 7228 0.947244 AAGGAAGTGCAGTTGAAGCG 59.053 50.000 12.53 0.00 33.85 4.68
7309 7931 3.163630 TGCTTGCCTGTTTCTTTGAAC 57.836 42.857 0.00 0.00 0.00 3.18
7349 7971 6.158598 ACAAGTTGCTGTTGCCTTTTATATG 58.841 36.000 1.81 0.00 38.71 1.78
7362 7984 5.413499 CCTTTTATATGGCCTGCAATATGC 58.587 41.667 3.32 0.00 45.29 3.14
7378 8000 6.158598 GCAATATGCATGTAGTTATTTGGGG 58.841 40.000 10.16 0.00 44.26 4.96
7427 8049 4.599047 TTTTTGTTGATGCACCCCTTAG 57.401 40.909 0.00 0.00 0.00 2.18
7428 8050 2.969821 TTGTTGATGCACCCCTTAGT 57.030 45.000 0.00 0.00 0.00 2.24
7435 8057 5.968676 TGATGCACCCCTTAGTAAATAGT 57.031 39.130 0.00 0.00 0.00 2.12
7489 8114 2.029290 GTGGAACAGTCGTACCATCACT 60.029 50.000 0.00 0.00 41.80 3.41
7631 8264 5.543405 ACTGATCATTTAGGCTGAGCTAGAT 59.457 40.000 3.72 0.00 30.52 1.98
7684 8317 5.099042 ACCATACTGACCATTTGTCTACC 57.901 43.478 0.00 0.00 44.75 3.18
7711 8344 8.336498 AGTTACGTGTCGTCTCATAAAATATG 57.664 34.615 0.00 0.00 41.54 1.78
7857 8490 7.068716 GGTTTCAGGTTTTGCCATATCTTATCT 59.931 37.037 0.00 0.00 40.61 1.98
7862 8495 5.389516 GGTTTTGCCATATCTTATCTACGCG 60.390 44.000 3.53 3.53 37.17 6.01
7867 8500 3.119459 CCATATCTTATCTACGCGTGCCT 60.119 47.826 24.59 8.30 0.00 4.75
7941 8575 5.709164 ACTGATCTTGCTTGTATGAGCTTTT 59.291 36.000 0.00 0.00 43.11 2.27
7942 8576 5.946298 TGATCTTGCTTGTATGAGCTTTTG 58.054 37.500 0.00 0.00 43.11 2.44
7943 8577 5.706833 TGATCTTGCTTGTATGAGCTTTTGA 59.293 36.000 0.00 0.00 43.11 2.69
7944 8578 6.207221 TGATCTTGCTTGTATGAGCTTTTGAA 59.793 34.615 0.00 0.00 43.11 2.69
7945 8579 5.762045 TCTTGCTTGTATGAGCTTTTGAAC 58.238 37.500 0.00 0.00 43.11 3.18
7946 8580 5.532406 TCTTGCTTGTATGAGCTTTTGAACT 59.468 36.000 0.00 0.00 43.11 3.01
7947 8581 5.362556 TGCTTGTATGAGCTTTTGAACTC 57.637 39.130 0.00 0.00 43.11 3.01
7948 8582 4.821260 TGCTTGTATGAGCTTTTGAACTCA 59.179 37.500 0.00 0.00 46.34 3.41
7958 8592 7.436118 TGAGCTTTTGAACTCATTGCTTTAAT 58.564 30.769 0.00 0.00 37.99 1.40
7967 8601 7.652909 TGAACTCATTGCTTTAATGGACTTTTG 59.347 33.333 0.00 0.00 45.05 2.44
8061 8695 3.290948 TTGGCTTGGTTACAGTTCTGT 57.709 42.857 10.33 10.33 0.00 3.41
8149 8788 7.643528 AGTGATCACAAGTGTATTATATGCG 57.356 36.000 27.02 0.00 0.00 4.73
8155 8794 6.478673 TCACAAGTGTATTATATGCGAAGTGG 59.521 38.462 0.00 0.00 0.00 4.00
8239 8879 0.458543 CGTCGTGGCAGCTCAATAGT 60.459 55.000 0.00 0.00 0.00 2.12
8329 8970 1.892474 TCTGTTTTGGCTGCATTACCC 59.108 47.619 0.50 0.00 0.00 3.69
8346 8987 1.300388 CCTTGCAACAACTGGCTGC 60.300 57.895 0.00 0.00 36.60 5.25
8625 9266 2.282887 AAGGCCGCCGGTCAATTT 60.283 55.556 11.73 0.00 0.00 1.82
8755 9396 2.938451 CAAGATCTTTGGTATCGCTGCA 59.062 45.455 4.86 0.00 0.00 4.41
8756 9397 3.266510 AGATCTTTGGTATCGCTGCAA 57.733 42.857 0.00 0.00 0.00 4.08
8757 9398 2.939103 AGATCTTTGGTATCGCTGCAAC 59.061 45.455 0.00 0.00 0.00 4.17
8758 9399 2.177394 TCTTTGGTATCGCTGCAACA 57.823 45.000 0.00 0.00 0.00 3.33
8759 9400 1.804151 TCTTTGGTATCGCTGCAACAC 59.196 47.619 0.00 0.00 0.00 3.32
8760 9401 1.806542 CTTTGGTATCGCTGCAACACT 59.193 47.619 0.00 0.00 0.00 3.55
8761 9402 1.155889 TTGGTATCGCTGCAACACTG 58.844 50.000 0.00 0.00 0.00 3.66
8762 9403 0.320050 TGGTATCGCTGCAACACTGA 59.680 50.000 0.00 0.00 0.00 3.41
8763 9404 0.721718 GGTATCGCTGCAACACTGAC 59.278 55.000 0.00 0.00 0.00 3.51
8764 9405 0.721718 GTATCGCTGCAACACTGACC 59.278 55.000 0.00 0.00 0.00 4.02
8765 9406 0.735978 TATCGCTGCAACACTGACCG 60.736 55.000 0.00 0.00 0.00 4.79
8766 9407 3.716006 CGCTGCAACACTGACCGG 61.716 66.667 0.00 0.00 0.00 5.28
8767 9408 2.591715 GCTGCAACACTGACCGGT 60.592 61.111 6.92 6.92 0.00 5.28
8768 9409 2.896801 GCTGCAACACTGACCGGTG 61.897 63.158 14.63 0.00 42.34 4.94
8769 9410 2.203139 TGCAACACTGACCGGTGG 60.203 61.111 14.63 7.31 41.09 4.61
8770 9411 2.978010 GCAACACTGACCGGTGGG 60.978 66.667 14.63 0.71 41.09 4.61
8771 9412 2.978010 CAACACTGACCGGTGGGC 60.978 66.667 14.63 0.00 41.09 5.36
8772 9413 4.619227 AACACTGACCGGTGGGCG 62.619 66.667 14.63 0.00 41.09 6.13
8788 9429 4.104143 CGGACCGCTGTTGGTATC 57.896 61.111 0.00 0.00 44.01 2.24
8789 9430 1.876714 CGGACCGCTGTTGGTATCG 60.877 63.158 0.00 0.00 44.01 2.92
8790 9431 2.171725 GGACCGCTGTTGGTATCGC 61.172 63.158 0.00 0.00 44.01 4.58
8791 9432 1.153628 GACCGCTGTTGGTATCGCT 60.154 57.895 0.00 0.00 44.01 4.93
8792 9433 1.421410 GACCGCTGTTGGTATCGCTG 61.421 60.000 0.00 0.00 44.01 5.18
8793 9434 1.447838 CCGCTGTTGGTATCGCTGT 60.448 57.895 0.00 0.00 0.00 4.40
9131 9819 4.581868 AGCATTTTGCCTTGTTGCATATT 58.418 34.783 0.00 0.00 46.52 1.28
9191 9879 1.741706 CTGGATGCCATCTTGTCACAC 59.258 52.381 4.41 0.00 30.82 3.82
9213 9901 2.294512 CCTTTTGACAGGCTTGACTTCC 59.705 50.000 1.40 0.00 0.00 3.46
9364 10055 0.385751 TGGGAAGATCATCGCTCGAC 59.614 55.000 14.94 0.00 33.72 4.20
9367 10058 0.317436 GAAGATCATCGCTCGACGCT 60.317 55.000 0.00 0.00 43.23 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 2.368655 GGCACGCCAAGATGAATTTT 57.631 45.000 2.36 0.00 35.81 1.82
89 90 2.786578 CGGAAACAACGAACCACAAATG 59.213 45.455 0.00 0.00 0.00 2.32
90 91 2.424246 ACGGAAACAACGAACCACAAAT 59.576 40.909 0.00 0.00 34.93 2.32
100 101 0.727970 TGTGGTTGACGGAAACAACG 59.272 50.000 0.00 0.00 45.56 4.10
108 109 1.064952 GAAAGTGGTTGTGGTTGACGG 59.935 52.381 0.00 0.00 0.00 4.79
127 128 6.973642 AGATTAGGGGATCATGAAAAGTTGA 58.026 36.000 0.00 0.00 0.00 3.18
133 134 5.545723 GGAGAGAGATTAGGGGATCATGAAA 59.454 44.000 0.00 0.00 0.00 2.69
154 156 2.840651 TGCTAAAAAGAGGGAGAGGGAG 59.159 50.000 0.00 0.00 0.00 4.30
158 160 5.678583 TCATGATGCTAAAAAGAGGGAGAG 58.321 41.667 0.00 0.00 0.00 3.20
164 166 4.818546 ACGGGATCATGATGCTAAAAAGAG 59.181 41.667 24.25 9.85 0.00 2.85
171 173 4.772100 TGAGATTACGGGATCATGATGCTA 59.228 41.667 24.25 9.27 0.00 3.49
186 188 9.209175 GAATGTGTATCCTTATGGTGAGATTAC 57.791 37.037 0.00 0.00 34.23 1.89
214 216 7.490962 TTGGATGCCTATTATTTTGTCTACG 57.509 36.000 0.00 0.00 0.00 3.51
224 226 3.951037 TGTTGCGTTTGGATGCCTATTAT 59.049 39.130 0.00 0.00 36.96 1.28
257 259 5.883180 AGTATGCTACAAGGGGTGTTAAAA 58.117 37.500 0.00 0.00 41.98 1.52
258 260 5.508280 AGTATGCTACAAGGGGTGTTAAA 57.492 39.130 0.00 0.00 41.98 1.52
259 261 5.981174 GTAGTATGCTACAAGGGGTGTTAA 58.019 41.667 15.27 0.00 45.18 2.01
260 262 5.603170 GTAGTATGCTACAAGGGGTGTTA 57.397 43.478 15.27 0.00 45.18 2.41
261 263 4.482952 GTAGTATGCTACAAGGGGTGTT 57.517 45.455 15.27 0.00 45.18 3.32
271 273 6.712179 ACACTAAAGGGAGTAGTATGCTAC 57.288 41.667 12.62 12.62 45.96 3.58
272 274 8.827832 TTAACACTAAAGGGAGTAGTATGCTA 57.172 34.615 0.00 0.00 30.54 3.49
273 275 7.729124 TTAACACTAAAGGGAGTAGTATGCT 57.271 36.000 0.00 0.00 30.54 3.79
274 276 8.782339 TTTTAACACTAAAGGGAGTAGTATGC 57.218 34.615 0.00 0.00 30.54 3.14
298 300 9.893305 CCTTCTTCTCGTAATGTAAAATGTTTT 57.107 29.630 0.00 0.00 0.00 2.43
299 301 8.512138 CCCTTCTTCTCGTAATGTAAAATGTTT 58.488 33.333 0.00 0.00 0.00 2.83
300 302 7.881232 TCCCTTCTTCTCGTAATGTAAAATGTT 59.119 33.333 0.00 0.00 0.00 2.71
301 303 7.391620 TCCCTTCTTCTCGTAATGTAAAATGT 58.608 34.615 0.00 0.00 0.00 2.71
302 304 7.549488 ACTCCCTTCTTCTCGTAATGTAAAATG 59.451 37.037 0.00 0.00 0.00 2.32
303 305 7.621796 ACTCCCTTCTTCTCGTAATGTAAAAT 58.378 34.615 0.00 0.00 0.00 1.82
304 306 7.001099 ACTCCCTTCTTCTCGTAATGTAAAA 57.999 36.000 0.00 0.00 0.00 1.52
305 307 6.600882 ACTCCCTTCTTCTCGTAATGTAAA 57.399 37.500 0.00 0.00 0.00 2.01
306 308 7.893124 ATACTCCCTTCTTCTCGTAATGTAA 57.107 36.000 0.00 0.00 0.00 2.41
307 309 7.893124 AATACTCCCTTCTTCTCGTAATGTA 57.107 36.000 0.00 0.00 0.00 2.29
308 310 6.793505 AATACTCCCTTCTTCTCGTAATGT 57.206 37.500 0.00 0.00 0.00 2.71
313 315 9.810870 ACTAATATAATACTCCCTTCTTCTCGT 57.189 33.333 0.00 0.00 0.00 4.18
330 332 8.195436 GCTGCCATCCGAATAGTACTAATATAA 58.805 37.037 6.70 0.00 0.00 0.98
331 333 7.340999 TGCTGCCATCCGAATAGTACTAATATA 59.659 37.037 6.70 0.00 0.00 0.86
332 334 6.154534 TGCTGCCATCCGAATAGTACTAATAT 59.845 38.462 6.70 0.00 0.00 1.28
341 343 1.959042 ACTTGCTGCCATCCGAATAG 58.041 50.000 0.00 0.00 0.00 1.73
348 350 5.303971 AGATATTCTGTACTTGCTGCCATC 58.696 41.667 0.00 0.00 0.00 3.51
364 366 5.238214 GTCAAGCATCAACCAGGAGATATTC 59.762 44.000 0.00 0.00 0.00 1.75
433 435 1.227102 GCTGGGGTGGTATGCATCA 59.773 57.895 0.19 0.00 0.00 3.07
434 436 0.764890 TAGCTGGGGTGGTATGCATC 59.235 55.000 0.19 0.00 0.00 3.91
435 437 0.474184 GTAGCTGGGGTGGTATGCAT 59.526 55.000 3.79 3.79 0.00 3.96
436 438 0.620410 AGTAGCTGGGGTGGTATGCA 60.620 55.000 0.00 0.00 0.00 3.96
437 439 1.344763 CTAGTAGCTGGGGTGGTATGC 59.655 57.143 0.00 0.00 0.00 3.14
463 479 9.349713 TCTTGTTTATCCTTTTGTGTATGAACT 57.650 29.630 0.00 0.00 0.00 3.01
466 482 9.513906 TCATCTTGTTTATCCTTTTGTGTATGA 57.486 29.630 0.00 0.00 0.00 2.15
469 485 8.296713 GCTTCATCTTGTTTATCCTTTTGTGTA 58.703 33.333 0.00 0.00 0.00 2.90
470 486 7.147976 GCTTCATCTTGTTTATCCTTTTGTGT 58.852 34.615 0.00 0.00 0.00 3.72
479 500 8.922058 ATCATGTTTGCTTCATCTTGTTTATC 57.078 30.769 0.00 0.00 0.00 1.75
491 512 4.630111 TGGTTTTGGATCATGTTTGCTTC 58.370 39.130 0.00 0.00 0.00 3.86
525 546 4.620803 CGAAGTGGTAGTTTAGGCAGATGT 60.621 45.833 0.00 0.00 0.00 3.06
542 563 9.976511 TGGTATTTTATAGTATTCCTCGAAGTG 57.023 33.333 0.00 0.00 0.00 3.16
556 583 8.627403 TCTTCTCCGTGTAGTGGTATTTTATAG 58.373 37.037 0.00 0.00 0.00 1.31
565 720 2.161030 GTCTCTTCTCCGTGTAGTGGT 58.839 52.381 0.00 0.00 0.00 4.16
566 721 1.473278 GGTCTCTTCTCCGTGTAGTGG 59.527 57.143 0.00 0.00 0.00 4.00
567 722 2.160205 TGGTCTCTTCTCCGTGTAGTG 58.840 52.381 0.00 0.00 0.00 2.74
635 807 2.159240 CCGTCAGATCTCATCAACCGAA 60.159 50.000 0.00 0.00 0.00 4.30
670 842 2.669569 AACGCAGCAGGTCGCATT 60.670 55.556 0.00 0.00 46.13 3.56
688 860 2.003301 GGAGAAAAACAGCCTAGCGAG 58.997 52.381 0.00 0.00 0.00 5.03
707 879 1.226916 CTCGCACTAGCAGCAGAGG 60.227 63.158 15.32 0.47 42.27 3.69
852 1031 4.376176 CGGTAACCAACGGCGGGA 62.376 66.667 13.24 0.00 0.00 5.14
856 1035 2.356194 ACGTCGGTAACCAACGGC 60.356 61.111 7.51 0.00 44.12 5.68
857 1036 2.660612 GCACGTCGGTAACCAACGG 61.661 63.158 7.51 0.00 44.12 4.44
858 1037 2.848310 GCACGTCGGTAACCAACG 59.152 61.111 0.88 0.88 45.02 4.10
859 1038 2.848310 CGCACGTCGGTAACCAAC 59.152 61.111 0.00 0.00 33.78 3.77
889 1162 1.444553 GAGCGACAGGAGAACACGG 60.445 63.158 0.00 0.00 0.00 4.94
900 1173 4.373116 GTTCTGGGCCGAGCGACA 62.373 66.667 10.42 0.00 0.00 4.35
979 1255 1.677966 CGAGGGGAGAAGTGTCGGA 60.678 63.158 0.00 0.00 0.00 4.55
982 1258 1.668101 ATCGCGAGGGGAGAAGTGTC 61.668 60.000 16.66 0.00 0.00 3.67
983 1259 1.682684 ATCGCGAGGGGAGAAGTGT 60.683 57.895 16.66 0.00 0.00 3.55
1165 1448 3.115556 CTTCGGGAGAGCGAGAGG 58.884 66.667 0.00 0.00 41.75 3.69
1218 1503 2.388232 CGCAGACCCTAAACGTGCC 61.388 63.158 0.00 0.00 0.00 5.01
1260 1545 1.895238 CCAGCAGCAAAATGGAGGG 59.105 57.895 0.00 0.00 36.09 4.30
1278 1563 1.291877 AACGTGTCAGCAAGATCCGC 61.292 55.000 0.00 0.00 0.00 5.54
1279 1564 1.136252 CAAACGTGTCAGCAAGATCCG 60.136 52.381 0.00 0.00 0.00 4.18
1281 1566 2.158449 CCTCAAACGTGTCAGCAAGATC 59.842 50.000 0.00 0.00 0.00 2.75
1293 1591 3.316868 CCAAAACCATACACCTCAAACGT 59.683 43.478 0.00 0.00 0.00 3.99
1354 1652 2.981302 CACTCCATCCAGTCGGCA 59.019 61.111 0.00 0.00 0.00 5.69
1521 1819 0.188342 AACTTGGCCAATGGTCCTGT 59.812 50.000 20.85 8.67 0.00 4.00
1642 1940 6.430308 CCATGAGAAATGCTAGCATGAGTAAT 59.570 38.462 30.19 17.86 38.82 1.89
1643 1941 5.761726 CCATGAGAAATGCTAGCATGAGTAA 59.238 40.000 30.19 16.47 38.82 2.24
1644 1942 5.163269 ACCATGAGAAATGCTAGCATGAGTA 60.163 40.000 30.19 15.96 38.82 2.59
1645 1943 4.135306 CCATGAGAAATGCTAGCATGAGT 58.865 43.478 30.19 18.35 38.82 3.41
1646 1944 4.135306 ACCATGAGAAATGCTAGCATGAG 58.865 43.478 30.19 14.48 38.82 2.90
1647 1945 4.160642 ACCATGAGAAATGCTAGCATGA 57.839 40.909 30.19 12.60 38.82 3.07
1648 1946 4.913335 AACCATGAGAAATGCTAGCATG 57.087 40.909 30.19 17.10 36.68 4.06
1649 1947 5.927281 AAAACCATGAGAAATGCTAGCAT 57.073 34.783 24.67 24.67 38.46 3.79
1650 1948 5.472148 CAAAAACCATGAGAAATGCTAGCA 58.528 37.500 21.85 21.85 0.00 3.49
1651 1949 4.866486 CCAAAAACCATGAGAAATGCTAGC 59.134 41.667 8.10 8.10 0.00 3.42
1652 1950 4.866486 GCCAAAAACCATGAGAAATGCTAG 59.134 41.667 0.00 0.00 0.00 3.42
1653 1951 4.322650 GGCCAAAAACCATGAGAAATGCTA 60.323 41.667 0.00 0.00 0.00 3.49
1654 1952 3.557686 GGCCAAAAACCATGAGAAATGCT 60.558 43.478 0.00 0.00 0.00 3.79
1655 1953 2.743664 GGCCAAAAACCATGAGAAATGC 59.256 45.455 0.00 0.00 0.00 3.56
1656 1954 2.995258 CGGCCAAAAACCATGAGAAATG 59.005 45.455 2.24 0.00 0.00 2.32
1660 1958 0.897863 CCCGGCCAAAAACCATGAGA 60.898 55.000 2.24 0.00 0.00 3.27
1697 2000 9.343539 GGTCTTAGGCTTAACAAAGATGAATAT 57.656 33.333 0.00 0.00 31.16 1.28
1699 2002 7.406104 AGGTCTTAGGCTTAACAAAGATGAAT 58.594 34.615 0.00 0.00 31.16 2.57
1700 2003 6.779860 AGGTCTTAGGCTTAACAAAGATGAA 58.220 36.000 0.00 0.00 31.16 2.57
1701 2004 6.374417 AGGTCTTAGGCTTAACAAAGATGA 57.626 37.500 0.00 0.00 31.16 2.92
1702 2005 5.586643 GGAGGTCTTAGGCTTAACAAAGATG 59.413 44.000 0.00 0.00 31.16 2.90
1704 2007 4.844655 AGGAGGTCTTAGGCTTAACAAAGA 59.155 41.667 0.00 0.00 0.00 2.52
1705 2008 5.167303 AGGAGGTCTTAGGCTTAACAAAG 57.833 43.478 0.00 0.00 0.00 2.77
1722 2032 1.425448 ACTCACCAAAAGGGAAGGAGG 59.575 52.381 0.00 0.00 41.15 4.30
1784 2094 5.116084 TCAAACTCCCTGCTAATATTGCT 57.884 39.130 0.00 0.00 0.00 3.91
1949 2259 5.052436 CGTGTGTGCTTTTTACATTGAACAG 60.052 40.000 0.00 0.00 0.00 3.16
1950 2260 4.795795 CGTGTGTGCTTTTTACATTGAACA 59.204 37.500 0.00 0.00 0.00 3.18
1951 2261 4.796312 ACGTGTGTGCTTTTTACATTGAAC 59.204 37.500 0.00 0.00 0.00 3.18
1964 2274 2.288666 AGATGACAAAACGTGTGTGCT 58.711 42.857 9.69 2.63 41.96 4.40
2442 2755 8.292444 TGGCTAATACATAAGTTTGATGCTTT 57.708 30.769 0.00 0.00 0.00 3.51
2672 2985 6.831976 AGGCCAAGTAAGAAGGTAGAATATG 58.168 40.000 5.01 0.00 0.00 1.78
2995 3311 5.534407 TCTGCACGAGTATTTGTAACAGAA 58.466 37.500 7.62 0.00 33.45 3.02
3102 3418 6.835914 AGCGATTTGTAGAAACAGAAATCAG 58.164 36.000 0.00 0.00 34.54 2.90
3408 3724 2.095853 GGCCACACTACATCAATTCACG 59.904 50.000 0.00 0.00 0.00 4.35
3440 3756 9.602568 AAAATGAATATGCAGCATTTTATGTGA 57.397 25.926 14.58 0.00 45.27 3.58
3586 3903 1.195115 GGCAGGTGTCTGTATCCTCA 58.805 55.000 0.00 0.00 42.78 3.86
3643 3972 1.957695 GCTTTTGCCAAGCACCAGC 60.958 57.895 11.85 4.01 42.56 4.85
3757 4168 8.118976 TGTAACTTGCTACTATGTCTTGTACT 57.881 34.615 0.00 0.00 0.00 2.73
3806 4219 1.203137 ACTAAAGGAAAACTGGGGGCC 60.203 52.381 0.00 0.00 0.00 5.80
3920 4338 7.656137 TGAATAAGTTCTGCTAGAAAAAGACGT 59.344 33.333 0.00 0.00 35.75 4.34
4382 4802 8.526218 AGTATCGAAGAACATGCATATAAGTG 57.474 34.615 0.00 0.00 43.58 3.16
4402 4822 6.987386 ACATGCCTAGTCATCAAGTAGTATC 58.013 40.000 0.00 0.00 0.00 2.24
4525 4950 6.894828 ACGTGAACATTAAAGGTGATTACAC 58.105 36.000 0.00 0.00 45.27 2.90
4631 5180 3.057734 GGAGTAAGTTCACTGTTGTCCG 58.942 50.000 0.00 0.00 0.00 4.79
4833 5382 6.099269 ACAAAACAGTGAAACCTCTACCTCTA 59.901 38.462 0.00 0.00 37.80 2.43
4834 5383 5.104485 ACAAAACAGTGAAACCTCTACCTCT 60.104 40.000 0.00 0.00 37.80 3.69
4835 5384 5.123936 ACAAAACAGTGAAACCTCTACCTC 58.876 41.667 0.00 0.00 37.80 3.85
4836 5385 5.112129 ACAAAACAGTGAAACCTCTACCT 57.888 39.130 0.00 0.00 37.80 3.08
4873 5422 5.581126 TGCTTTAATCATAAGCCAACAGG 57.419 39.130 0.00 0.00 45.73 4.00
5090 5687 5.975344 GCAATGAACCATCTGTATTCATGTG 59.025 40.000 0.00 3.02 41.17 3.21
5622 6229 0.808453 TTAAATCTCGGGAAGCGCGG 60.808 55.000 8.83 0.00 40.17 6.46
5623 6230 0.577269 CTTAAATCTCGGGAAGCGCG 59.423 55.000 0.00 0.00 41.10 6.86
5708 6315 8.773645 TGCTTATCAGTACCAATATTTTCGATG 58.226 33.333 0.00 0.00 0.00 3.84
5999 6606 3.571590 AGCATGCTACTTAGTCTAGCCT 58.428 45.455 21.21 0.00 36.54 4.58
6621 7228 5.335976 GGGATCAAACAGAGGAAACAATGAC 60.336 44.000 0.00 0.00 0.00 3.06
7309 7931 5.696822 CAACTTGTCTGGTGATCATTTCAG 58.303 41.667 0.00 7.92 34.17 3.02
7362 7984 6.316390 GTCAGTCTTCCCCAAATAACTACATG 59.684 42.308 0.00 0.00 0.00 3.21
7418 8040 5.126545 GGGCAAAACTATTTACTAAGGGGTG 59.873 44.000 0.00 0.00 0.00 4.61
7471 8093 3.921021 CAGAAGTGATGGTACGACTGTTC 59.079 47.826 0.00 0.00 0.00 3.18
7478 8103 1.204704 TCAGGCAGAAGTGATGGTACG 59.795 52.381 0.00 0.00 0.00 3.67
7483 8108 6.748333 TCTTATTTTCAGGCAGAAGTGATG 57.252 37.500 0.00 0.00 37.57 3.07
7489 8114 9.466497 ACTTGATAATCTTATTTTCAGGCAGAA 57.534 29.630 0.00 0.00 0.00 3.02
7531 8156 0.613260 GGCAGGGGGTGAATTTTTCC 59.387 55.000 0.00 0.00 0.00 3.13
7584 8209 8.462811 CAGTCATTTAGCCTACGTATCTATGAT 58.537 37.037 0.00 0.00 0.00 2.45
7631 8264 8.984764 CAACCTACAGCGTATAATGCTTATTTA 58.015 33.333 0.00 0.00 38.65 1.40
7684 8317 6.442487 TTTTATGAGACGACACGTAACTTG 57.558 37.500 0.00 0.00 41.37 3.16
7857 8490 2.355363 GACACACAGGCACGCGTA 60.355 61.111 13.44 0.00 0.00 4.42
7867 8500 1.446516 GCACACATGCCAGACACACA 61.447 55.000 0.00 0.00 46.97 3.72
7941 8575 6.899393 AAGTCCATTAAAGCAATGAGTTCA 57.101 33.333 0.00 0.00 45.99 3.18
7942 8576 7.867403 TCAAAAGTCCATTAAAGCAATGAGTTC 59.133 33.333 0.00 0.00 45.99 3.01
7943 8577 7.725251 TCAAAAGTCCATTAAAGCAATGAGTT 58.275 30.769 0.00 0.00 45.99 3.01
7944 8578 7.288810 TCAAAAGTCCATTAAAGCAATGAGT 57.711 32.000 0.00 0.00 45.99 3.41
7945 8579 7.869429 AGTTCAAAAGTCCATTAAAGCAATGAG 59.131 33.333 0.00 0.00 45.99 2.90
7946 8580 7.725251 AGTTCAAAAGTCCATTAAAGCAATGA 58.275 30.769 0.00 0.00 45.99 2.57
7947 8581 7.652909 TGAGTTCAAAAGTCCATTAAAGCAATG 59.347 33.333 0.00 0.00 43.23 2.82
7948 8582 7.725251 TGAGTTCAAAAGTCCATTAAAGCAAT 58.275 30.769 0.00 0.00 0.00 3.56
7949 8583 7.106439 TGAGTTCAAAAGTCCATTAAAGCAA 57.894 32.000 0.00 0.00 0.00 3.91
7950 8584 6.707440 TGAGTTCAAAAGTCCATTAAAGCA 57.293 33.333 0.00 0.00 0.00 3.91
7951 8585 7.867403 TCAATGAGTTCAAAAGTCCATTAAAGC 59.133 33.333 0.00 0.00 0.00 3.51
7952 8586 9.748708 TTCAATGAGTTCAAAAGTCCATTAAAG 57.251 29.630 0.00 0.00 0.00 1.85
8160 8799 1.681264 GTGACCAGGGGTTGTTTTCAG 59.319 52.381 0.00 0.00 35.25 3.02
8329 8970 0.103572 AAGCAGCCAGTTGTTGCAAG 59.896 50.000 0.00 0.00 40.22 4.01
8346 8987 7.115378 GCTTGAATTGACACATGGAAGTAAAAG 59.885 37.037 0.00 0.00 0.00 2.27
8607 9248 2.635443 AAATTGACCGGCGGCCTTG 61.635 57.895 28.71 10.61 0.00 3.61
8755 9396 4.619227 CGCCCACCGGTCAGTGTT 62.619 66.667 2.59 0.00 35.93 3.32
8771 9412 1.876714 CGATACCAACAGCGGTCCG 60.877 63.158 6.99 6.99 40.67 4.79
8772 9413 2.171725 GCGATACCAACAGCGGTCC 61.172 63.158 0.00 0.00 40.67 4.46
8773 9414 1.153628 AGCGATACCAACAGCGGTC 60.154 57.895 0.00 0.00 40.67 4.79
8774 9415 1.447838 CAGCGATACCAACAGCGGT 60.448 57.895 0.00 0.00 43.46 5.68
8775 9416 0.179121 TACAGCGATACCAACAGCGG 60.179 55.000 0.00 0.00 34.34 5.52
8776 9417 1.323534 GTTACAGCGATACCAACAGCG 59.676 52.381 0.00 0.00 34.34 5.18
8777 9418 2.093783 GTGTTACAGCGATACCAACAGC 59.906 50.000 0.00 0.00 30.28 4.40
8778 9419 3.367932 CAGTGTTACAGCGATACCAACAG 59.632 47.826 0.00 0.00 30.28 3.16
8779 9420 3.006003 TCAGTGTTACAGCGATACCAACA 59.994 43.478 0.00 0.00 0.00 3.33
8780 9421 3.367025 GTCAGTGTTACAGCGATACCAAC 59.633 47.826 0.00 0.00 0.00 3.77
8781 9422 3.581755 GTCAGTGTTACAGCGATACCAA 58.418 45.455 0.00 0.00 0.00 3.67
8782 9423 2.094390 GGTCAGTGTTACAGCGATACCA 60.094 50.000 0.00 0.00 0.00 3.25
8783 9424 2.537401 GGTCAGTGTTACAGCGATACC 58.463 52.381 0.00 0.00 0.00 2.73
8784 9425 2.182825 CGGTCAGTGTTACAGCGATAC 58.817 52.381 0.00 0.00 32.84 2.24
8785 9426 1.133598 CCGGTCAGTGTTACAGCGATA 59.866 52.381 0.00 0.00 32.84 2.92
8786 9427 0.108804 CCGGTCAGTGTTACAGCGAT 60.109 55.000 0.00 0.00 32.84 4.58
8787 9428 1.287815 CCGGTCAGTGTTACAGCGA 59.712 57.895 0.00 0.00 32.84 4.93
8788 9429 1.006571 ACCGGTCAGTGTTACAGCG 60.007 57.895 0.00 0.00 0.00 5.18
8789 9430 0.949105 CCACCGGTCAGTGTTACAGC 60.949 60.000 2.59 0.00 35.93 4.40
8790 9431 0.320421 CCCACCGGTCAGTGTTACAG 60.320 60.000 2.59 0.00 35.93 2.74
8791 9432 1.749665 CCCACCGGTCAGTGTTACA 59.250 57.895 2.59 0.00 35.93 2.41
8792 9433 1.670083 GCCCACCGGTCAGTGTTAC 60.670 63.158 2.59 0.00 35.93 2.50
8793 9434 2.745037 GCCCACCGGTCAGTGTTA 59.255 61.111 2.59 0.00 35.93 2.41
9131 9819 0.255604 AATGTGCCGTGGATCCATCA 59.744 50.000 19.62 13.48 0.00 3.07
9191 9879 1.986882 AGTCAAGCCTGTCAAAAGGG 58.013 50.000 0.00 0.00 37.84 3.95


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

AutoCloner maintained by Alex Coulton.