Multiple sequence alignment - TraesCS6B01G382000

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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 TraesCS6B01G382000 chr6B 100.000 6781 0 0 1 6781 657002563 656995783 0.000000e+00 12523.0
1 TraesCS6B01G382000 chr6B 83.951 1134 153 23 3125 4252 656547070 656545960 0.000000e+00 1059.0
2 TraesCS6B01G382000 chr6B 84.729 406 52 6 4252 4647 656544617 656544212 1.370000e-106 398.0
3 TraesCS6B01G382000 chr6A 94.453 4002 155 23 1533 5488 580537564 580533584 0.000000e+00 6098.0
4 TraesCS6B01G382000 chr6A 86.034 2907 281 61 3131 6008 580319023 580316213 0.000000e+00 3003.0
5 TraesCS6B01G382000 chr6A 90.518 791 50 12 5478 6252 580533561 580532780 0.000000e+00 1022.0
6 TraesCS6B01G382000 chr6A 89.110 753 57 15 458 1200 580538478 580537741 0.000000e+00 913.0
7 TraesCS6B01G382000 chr6A 86.825 630 73 6 2027 2650 580320264 580319639 0.000000e+00 695.0
8 TraesCS6B01G382000 chr6A 91.549 355 25 3 6269 6619 580532792 580532439 1.020000e-132 484.0
9 TraesCS6B01G382000 chr6A 83.188 458 41 9 6358 6781 580315740 580315285 2.970000e-103 387.0
10 TraesCS6B01G382000 chr6A 81.470 313 44 9 60 370 135571491 135571791 1.890000e-60 244.0
11 TraesCS6B01G382000 chr6A 91.176 102 9 0 1006 1107 580321415 580321314 9.170000e-29 139.0
12 TraesCS6B01G382000 chr6A 90.099 101 8 2 6269 6367 580315864 580315764 5.520000e-26 130.0
13 TraesCS6B01G382000 chr6A 93.878 49 3 0 5924 5972 580314828 580314780 2.620000e-09 75.0
14 TraesCS6B01G382000 chr6D 94.327 3314 134 29 2723 6014 434256023 434252742 0.000000e+00 5029.0
15 TraesCS6B01G382000 chr6D 86.880 2904 271 53 3130 6008 434171949 434169131 0.000000e+00 3151.0
16 TraesCS6B01G382000 chr6D 87.154 2818 218 72 1 2742 434258785 434256036 0.000000e+00 3066.0
17 TraesCS6B01G382000 chr6D 86.142 635 78 6 2025 2653 434173188 434172558 0.000000e+00 676.0
18 TraesCS6B01G382000 chr6D 88.337 523 44 11 6269 6781 434252332 434251817 4.500000e-171 612.0
19 TraesCS6B01G382000 chr6D 94.262 122 7 0 6131 6252 434252441 434252320 3.230000e-43 187.0
20 TraesCS6B01G382000 chr6D 89.815 108 11 0 1006 1113 434174815 434174708 9.170000e-29 139.0
21 TraesCS6B01G382000 chr6D 88.660 97 8 2 6104 6197 434169138 434169042 1.550000e-21 115.0
22 TraesCS6B01G382000 chr6D 89.286 56 6 0 5924 5979 434167011 434166956 3.390000e-08 71.3
23 TraesCS6B01G382000 chr7D 94.406 1877 78 15 2723 4579 86842074 86843943 0.000000e+00 2859.0
24 TraesCS6B01G382000 chr7D 91.608 429 24 9 2319 2739 86841634 86842058 3.520000e-162 582.0
25 TraesCS6B01G382000 chr5A 81.572 407 63 11 52 455 641392785 641392388 6.560000e-85 326.0
26 TraesCS6B01G382000 chr5D 81.055 417 50 15 57 456 374652184 374652588 8.540000e-79 305.0
27 TraesCS6B01G382000 chr5D 80.048 421 61 12 52 455 513521093 513520679 2.390000e-74 291.0
28 TraesCS6B01G382000 chr5D 77.559 254 39 12 6497 6746 345976274 345976035 3.300000e-28 137.0
29 TraesCS6B01G382000 chr3A 86.758 219 23 5 53 269 214120936 214121150 8.790000e-59 239.0
30 TraesCS6B01G382000 chr3A 83.429 175 22 7 49 222 729436414 729436582 9.110000e-34 156.0
31 TraesCS6B01G382000 chr2D 78.947 209 26 14 65 269 11028019 11027825 7.140000e-25 126.0
32 TraesCS6B01G382000 chrUn 78.571 168 27 8 70 235 110998632 110998792 1.200000e-17 102.0


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 TraesCS6B01G382000 chr6B 656995783 657002563 6780 True 12523.000000 12523 100.000000 1 6781 1 chr6B.!!$R1 6780
1 TraesCS6B01G382000 chr6B 656544212 656547070 2858 True 728.500000 1059 84.340000 3125 4647 2 chr6B.!!$R2 1522
2 TraesCS6B01G382000 chr6A 580532439 580538478 6039 True 2129.250000 6098 91.407500 458 6619 4 chr6A.!!$R2 6161
3 TraesCS6B01G382000 chr6A 580314780 580321415 6635 True 738.166667 3003 88.533333 1006 6781 6 chr6A.!!$R1 5775
4 TraesCS6B01G382000 chr6D 434251817 434258785 6968 True 2223.500000 5029 91.020000 1 6781 4 chr6D.!!$R2 6780
5 TraesCS6B01G382000 chr6D 434166956 434174815 7859 True 830.460000 3151 88.156600 1006 6197 5 chr6D.!!$R1 5191
6 TraesCS6B01G382000 chr7D 86841634 86843943 2309 False 1720.500000 2859 93.007000 2319 4579 2 chr7D.!!$F1 2260

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
221 223 0.179078 GACATCTGAGCAGCTCCCAG 60.179 60.000 20.16 12.10 0.00 4.45 F
884 906 0.534203 TATTTCATCCCCGCCGCTTC 60.534 55.000 0.00 0.00 0.00 3.86 F
1458 1513 0.039978 AGTGAAGTGAGACGCGTCTG 60.040 55.000 43.61 0.00 40.61 3.51 F
1490 1559 0.835941 CATCTGGGGAGCTAGCTGTT 59.164 55.000 24.99 0.00 0.00 3.16 F
2077 3029 1.340502 TGCAGGGAAACAACTGACACA 60.341 47.619 0.00 0.00 36.86 3.72 F
2371 3328 2.503356 CAGGGGATGCTCAGTAACTTCT 59.497 50.000 0.00 0.00 0.00 2.85 F
3776 4930 0.337082 TAGGGTTCCATCAGACCGGA 59.663 55.000 9.46 0.00 36.78 5.14 F
3782 4936 0.324738 TCCATCAGACCGGAGAAGCT 60.325 55.000 9.46 0.00 0.00 3.74 F
5702 8260 0.592637 TTCAGGTGATTGCAAGCGTG 59.407 50.000 10.55 11.52 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1277 0.185175 TAGAGCGGGGCAGTGAGATA 59.815 55.000 0.00 0.00 0.00 1.98 R
1904 2845 0.323087 TGAGTACGGCCAGCTACTGA 60.323 55.000 2.24 0.00 32.44 3.41 R
2663 3704 3.462021 GAAGACACAGCCTTATAGCCAG 58.538 50.000 0.00 0.00 0.00 4.85 R
3465 4618 4.633126 ACGTCAGGAAAGATTGATGTCATG 59.367 41.667 0.00 0.00 38.79 3.07 R
3756 4910 1.062428 TCCGGTCTGATGGAACCCTAT 60.062 52.381 0.00 0.00 0.00 2.57 R
3782 4936 1.533625 GCATGCCACTCCACTTTACA 58.466 50.000 6.36 0.00 0.00 2.41 R
5744 8302 0.106167 TGCTAGCCACCGAGGAGTAT 60.106 55.000 13.29 0.00 41.22 2.12 R
5779 8337 5.707298 TCGAAGAGATTGCTTTGGAAGAATT 59.293 36.000 0.00 0.00 31.49 2.17 R
6628 10060 0.177604 TGTTGTTTGCTTGCAAGGGG 59.822 50.000 27.10 4.07 0.00 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
25 27 3.305398 AGTGTGTTGTCTCTTCGGATC 57.695 47.619 0.00 0.00 0.00 3.36
58 60 1.586422 CCATGTATGTTGGAGAGCGG 58.414 55.000 0.00 0.00 36.26 5.52
59 61 0.940126 CATGTATGTTGGAGAGCGGC 59.060 55.000 0.00 0.00 0.00 6.53
72 74 2.124320 GCGGCTAAATGGCTCCCA 60.124 61.111 0.00 0.00 39.32 4.37
191 193 3.112580 CGTGAGGTTCGTGCAAAATTTT 58.887 40.909 0.00 0.00 0.00 1.82
207 209 7.118101 TGCAAAATTTTAGCTCATTTGGACATC 59.882 33.333 19.20 0.00 32.91 3.06
218 220 0.251354 TTGGACATCTGAGCAGCTCC 59.749 55.000 20.16 3.72 0.00 4.70
221 223 0.179078 GACATCTGAGCAGCTCCCAG 60.179 60.000 20.16 12.10 0.00 4.45
279 281 3.440872 AGTTTACGGTTTTGCACTGTTCA 59.559 39.130 0.00 0.00 43.05 3.18
323 325 0.534412 AGAGCAGTTCGGATGTCCAG 59.466 55.000 0.00 0.00 35.14 3.86
326 328 2.362397 GAGCAGTTCGGATGTCCAGATA 59.638 50.000 0.00 0.00 35.14 1.98
345 347 6.072175 CCAGATAAGTTGAAATTTTGGACGGA 60.072 38.462 0.00 0.00 0.00 4.69
364 366 5.416947 ACGGACCTCACACACTAAAATATC 58.583 41.667 0.00 0.00 0.00 1.63
366 368 6.379133 ACGGACCTCACACACTAAAATATCTA 59.621 38.462 0.00 0.00 0.00 1.98
405 410 8.926710 TCTGAATTTTCTCGAACTTGTTAGATC 58.073 33.333 0.00 0.00 0.00 2.75
418 423 6.157211 ACTTGTTAGATCTTACTGTTCACCG 58.843 40.000 12.72 0.00 0.00 4.94
424 429 4.950475 AGATCTTACTGTTCACCGAGATCA 59.050 41.667 12.15 0.00 41.04 2.92
433 438 2.382882 TCACCGAGATCAGATGAGCTT 58.617 47.619 1.62 0.00 41.40 3.74
435 440 2.864946 CACCGAGATCAGATGAGCTTTG 59.135 50.000 1.62 0.00 41.40 2.77
438 443 3.382855 CGAGATCAGATGAGCTTTGGAG 58.617 50.000 1.62 0.00 41.40 3.86
497 503 9.907229 ATATGGTACTTCTCCTAAAAAGAAAGG 57.093 33.333 0.00 0.00 32.60 3.11
518 524 1.140452 CAGGCCTAGTCATGCTCATGT 59.860 52.381 3.98 0.00 39.72 3.21
519 525 2.366590 CAGGCCTAGTCATGCTCATGTA 59.633 50.000 3.98 0.00 39.72 2.29
520 526 2.632028 AGGCCTAGTCATGCTCATGTAG 59.368 50.000 1.29 5.45 39.72 2.74
521 527 2.366916 GGCCTAGTCATGCTCATGTAGT 59.633 50.000 9.41 3.33 39.72 2.73
577 583 7.807977 AATAATTCAGGCAAGTCATTATCGT 57.192 32.000 0.00 0.00 0.00 3.73
593 599 2.507854 CGTGGTCCCACAGGTCAGT 61.508 63.158 16.27 0.00 46.47 3.41
595 601 1.383943 TGGTCCCACAGGTCAGTGT 60.384 57.895 0.00 0.00 37.82 3.55
709 719 1.447838 CACACCCTCCAATCGACCG 60.448 63.158 0.00 0.00 0.00 4.79
720 730 1.065701 CAATCGACCGACTACCTCCAG 59.934 57.143 0.00 0.00 0.00 3.86
748 758 2.923035 CCTCCCCTCACACGTGGT 60.923 66.667 21.57 2.37 0.00 4.16
768 778 3.941188 CCTGGCCCACACGTCAGT 61.941 66.667 0.00 0.00 0.00 3.41
781 791 2.050077 TCAGTGACGCTGCAGACG 60.050 61.111 20.43 22.03 44.66 4.18
782 792 3.108289 CAGTGACGCTGCAGACGG 61.108 66.667 26.36 14.63 38.52 4.79
808 818 2.656055 CGTCCCGGTTCCCGTAAA 59.344 61.111 0.00 0.00 46.80 2.01
884 906 0.534203 TATTTCATCCCCGCCGCTTC 60.534 55.000 0.00 0.00 0.00 3.86
951 980 2.876645 CTCTGGAAGCGTCGCGTC 60.877 66.667 22.64 22.64 36.39 5.19
988 1017 2.126502 CACGCAACCCGGCATTTC 60.127 61.111 0.00 0.00 42.52 2.17
1226 1258 2.107141 CGGTCGCATTCTCTCCCC 59.893 66.667 0.00 0.00 0.00 4.81
1232 1264 2.419198 CATTCTCTCCCCGCTCGG 59.581 66.667 0.48 0.48 0.00 4.63
1244 1276 4.200283 GCTCGGTCGCCTCCTCTG 62.200 72.222 0.00 0.00 0.00 3.35
1245 1277 2.752238 CTCGGTCGCCTCCTCTGT 60.752 66.667 0.00 0.00 0.00 3.41
1248 1280 0.818445 TCGGTCGCCTCCTCTGTATC 60.818 60.000 0.00 0.00 0.00 2.24
1249 1281 0.820074 CGGTCGCCTCCTCTGTATCT 60.820 60.000 0.00 0.00 0.00 1.98
1251 1283 1.681538 GTCGCCTCCTCTGTATCTCA 58.318 55.000 0.00 0.00 0.00 3.27
1263 1312 1.075970 TATCTCACTGCCCCGCTCT 60.076 57.895 0.00 0.00 0.00 4.09
1269 1318 1.000019 ACTGCCCCGCTCTACTGTA 60.000 57.895 0.00 0.00 0.00 2.74
1271 1320 1.000019 TGCCCCGCTCTACTGTACT 60.000 57.895 0.00 0.00 0.00 2.73
1272 1321 1.320344 TGCCCCGCTCTACTGTACTG 61.320 60.000 0.00 0.00 0.00 2.74
1273 1322 1.321074 GCCCCGCTCTACTGTACTGT 61.321 60.000 10.46 10.46 0.00 3.55
1274 1323 1.183549 CCCCGCTCTACTGTACTGTT 58.816 55.000 10.89 0.00 0.00 3.16
1275 1324 1.549170 CCCCGCTCTACTGTACTGTTT 59.451 52.381 10.89 0.00 0.00 2.83
1276 1325 2.756760 CCCCGCTCTACTGTACTGTTTA 59.243 50.000 10.89 0.00 0.00 2.01
1277 1326 3.181489 CCCCGCTCTACTGTACTGTTTAG 60.181 52.174 10.89 9.62 0.00 1.85
1283 1332 8.400947 CCGCTCTACTGTACTGTTTAGTATTAA 58.599 37.037 10.89 0.00 41.22 1.40
1300 1349 9.709495 TTAGTATTAATGGTTAAGTGTTCGTGT 57.291 29.630 0.00 0.00 0.00 4.49
1301 1350 8.611654 AGTATTAATGGTTAAGTGTTCGTGTT 57.388 30.769 0.00 0.00 0.00 3.32
1302 1351 9.709495 AGTATTAATGGTTAAGTGTTCGTGTTA 57.291 29.630 0.00 0.00 0.00 2.41
1305 1359 5.934935 ATGGTTAAGTGTTCGTGTTAAGG 57.065 39.130 0.00 0.00 0.00 2.69
1322 1376 0.678048 AGGTTGCTCTGCCGATTTCC 60.678 55.000 0.00 0.00 0.00 3.13
1335 1390 2.036733 CCGATTTCCCCGCTATTCAGTA 59.963 50.000 0.00 0.00 0.00 2.74
1336 1391 3.318017 CGATTTCCCCGCTATTCAGTAG 58.682 50.000 0.00 0.00 0.00 2.57
1341 1396 4.174704 TCCCCGCTATTCAGTAGTAAGA 57.825 45.455 0.00 0.00 32.72 2.10
1342 1397 4.737578 TCCCCGCTATTCAGTAGTAAGAT 58.262 43.478 0.00 0.00 32.72 2.40
1344 1399 5.601313 TCCCCGCTATTCAGTAGTAAGATTT 59.399 40.000 0.00 0.00 32.72 2.17
1345 1400 6.779049 TCCCCGCTATTCAGTAGTAAGATTTA 59.221 38.462 0.00 0.00 32.72 1.40
1346 1401 7.453752 TCCCCGCTATTCAGTAGTAAGATTTAT 59.546 37.037 0.00 0.00 32.72 1.40
1347 1402 7.760340 CCCCGCTATTCAGTAGTAAGATTTATC 59.240 40.741 0.00 0.00 32.72 1.75
1349 1404 9.347934 CCGCTATTCAGTAGTAAGATTTATCTG 57.652 37.037 0.00 0.00 33.41 2.90
1350 1405 9.900710 CGCTATTCAGTAGTAAGATTTATCTGT 57.099 33.333 0.00 0.00 33.41 3.41
1356 1411 9.952188 TCAGTAGTAAGATTTATCTGTTGATCG 57.048 33.333 0.00 0.00 37.19 3.69
1361 1416 9.132923 AGTAAGATTTATCTGTTGATCGGAGTA 57.867 33.333 0.00 0.00 37.19 2.59
1377 1432 4.282449 TCGGAGTAGATTTGGTTGACTTCA 59.718 41.667 0.00 0.00 0.00 3.02
1383 1438 6.876257 AGTAGATTTGGTTGACTTCAGTGATC 59.124 38.462 0.00 0.00 0.00 2.92
1395 1450 0.530650 CAGTGATCGGGAATGGACGG 60.531 60.000 0.00 0.00 0.00 4.79
1397 1452 2.661866 GATCGGGAATGGACGGCG 60.662 66.667 4.80 4.80 0.00 6.46
1419 1474 3.516615 GAGCGCTAGTCTGTTCTGAATT 58.483 45.455 11.50 0.00 0.00 2.17
1427 1482 5.869753 AGTCTGTTCTGAATTTGGATTCG 57.130 39.130 0.00 0.00 43.75 3.34
1432 1487 2.368439 TCTGAATTTGGATTCGCTGGG 58.632 47.619 0.00 0.00 43.75 4.45
1433 1488 0.817013 TGAATTTGGATTCGCTGGGC 59.183 50.000 0.00 0.00 43.75 5.36
1448 1503 1.053835 TGGGCTGACCAGTGAAGTGA 61.054 55.000 0.00 0.00 46.80 3.41
1458 1513 0.039978 AGTGAAGTGAGACGCGTCTG 60.040 55.000 43.61 0.00 40.61 3.51
1460 1515 1.444553 GAAGTGAGACGCGTCTGGG 60.445 63.158 43.61 0.00 40.61 4.45
1468 1523 3.436001 ACGCGTCTGGGTCTAATTG 57.564 52.632 5.58 0.00 36.35 2.32
1470 1525 1.274167 ACGCGTCTGGGTCTAATTGAA 59.726 47.619 5.58 0.00 36.35 2.69
1472 1527 2.695359 GCGTCTGGGTCTAATTGAACA 58.305 47.619 0.00 0.00 33.02 3.18
1474 1529 3.309954 GCGTCTGGGTCTAATTGAACATC 59.690 47.826 0.00 0.00 33.02 3.06
1476 1531 4.568359 CGTCTGGGTCTAATTGAACATCTG 59.432 45.833 0.00 0.00 33.02 2.90
1477 1532 4.878397 GTCTGGGTCTAATTGAACATCTGG 59.122 45.833 0.00 0.00 33.02 3.86
1480 1549 3.202151 GGGTCTAATTGAACATCTGGGGA 59.798 47.826 0.00 0.00 33.02 4.81
1490 1559 0.835941 CATCTGGGGAGCTAGCTGTT 59.164 55.000 24.99 0.00 0.00 3.16
1497 1566 2.284190 GGGAGCTAGCTGTTCATGTTC 58.716 52.381 24.99 3.92 0.00 3.18
1508 1577 6.449698 AGCTGTTCATGTTCAATCGATTTTT 58.550 32.000 8.21 0.00 0.00 1.94
1509 1578 7.592938 AGCTGTTCATGTTCAATCGATTTTTA 58.407 30.769 8.21 0.00 0.00 1.52
1513 1582 8.020819 TGTTCATGTTCAATCGATTTTTAGGAC 58.979 33.333 8.21 2.77 0.00 3.85
1514 1583 6.771076 TCATGTTCAATCGATTTTTAGGACG 58.229 36.000 8.21 0.00 0.00 4.79
1524 1599 5.125900 TCGATTTTTAGGACGACACCTGATA 59.874 40.000 9.87 0.00 40.81 2.15
1528 1603 4.445452 TTAGGACGACACCTGATACAAC 57.555 45.455 9.87 0.00 40.81 3.32
1562 1637 2.398588 AGAGTTCACTGACACTTGGGA 58.601 47.619 0.00 0.00 0.00 4.37
1564 1639 3.134458 GAGTTCACTGACACTTGGGAAG 58.866 50.000 0.00 0.00 0.00 3.46
1583 1977 3.516981 AGTGGTCTGATCTGTTCGATG 57.483 47.619 0.00 0.00 30.84 3.84
1588 1982 4.037327 TGGTCTGATCTGTTCGATGAGATC 59.963 45.833 20.03 20.03 42.93 2.75
1591 1985 3.957468 TGATCTGTTCGATGAGATCACG 58.043 45.455 23.39 0.00 46.22 4.35
1621 2015 4.813027 ACTGAAACCATTGACAATGATGC 58.187 39.130 26.36 15.02 41.46 3.91
1635 2029 1.555967 TGATGCAAAAAGGGGTAGGC 58.444 50.000 0.00 0.00 0.00 3.93
1643 2037 4.349365 CAAAAAGGGGTAGGCAATAGGAA 58.651 43.478 0.00 0.00 0.00 3.36
1647 2041 2.158460 AGGGGTAGGCAATAGGAAATGC 60.158 50.000 0.00 0.00 41.82 3.56
1677 2071 5.132985 TCTGGCTTCTCCTAGTATCAGTACT 59.867 44.000 0.00 0.00 43.45 2.73
1687 2081 8.637196 TCCTAGTATCAGTACTACAATGATGG 57.363 38.462 0.00 0.00 41.35 3.51
1689 2083 8.735315 CCTAGTATCAGTACTACAATGATGGAG 58.265 40.741 0.00 0.00 43.75 3.86
1690 2084 6.987386 AGTATCAGTACTACAATGATGGAGC 58.013 40.000 0.00 0.00 41.66 4.70
1692 2086 5.268118 TCAGTACTACAATGATGGAGCAG 57.732 43.478 0.00 0.00 41.66 4.24
1693 2087 4.711846 TCAGTACTACAATGATGGAGCAGT 59.288 41.667 0.00 0.00 41.66 4.40
1694 2088 5.891551 TCAGTACTACAATGATGGAGCAGTA 59.108 40.000 0.00 0.00 41.66 2.74
1695 2089 5.980116 CAGTACTACAATGATGGAGCAGTAC 59.020 44.000 0.00 0.00 41.66 2.73
1696 2090 4.046938 ACTACAATGATGGAGCAGTACG 57.953 45.455 0.00 0.00 41.66 3.67
1698 2092 4.643334 ACTACAATGATGGAGCAGTACGTA 59.357 41.667 0.00 0.00 41.66 3.57
1699 2093 4.046938 ACAATGATGGAGCAGTACGTAG 57.953 45.455 0.00 0.00 0.00 3.51
1710 2615 8.830201 TGGAGCAGTACGTAGTTTTATTAAAA 57.170 30.769 0.00 0.00 37.78 1.52
1711 2616 9.270640 TGGAGCAGTACGTAGTTTTATTAAAAA 57.729 29.630 0.00 0.00 37.78 1.94
1846 2786 1.541379 ATGGCTCCCGTTTTTGTACC 58.459 50.000 0.00 0.00 0.00 3.34
1914 2856 3.829026 TGGCATACTATCTCAGTAGCTGG 59.171 47.826 0.00 0.00 43.01 4.85
1978 2920 2.266554 TGCAGTTTTCCTTTTTGTGCG 58.733 42.857 0.00 0.00 31.99 5.34
2005 2948 2.508526 ACAGATGGCAGTTTTCCTGTC 58.491 47.619 0.00 0.00 46.41 3.51
2013 2956 3.467803 GCAGTTTTCCTGTCTGTGTACT 58.532 45.455 0.00 0.00 43.55 2.73
2014 2957 4.502604 GGCAGTTTTCCTGTCTGTGTACTA 60.503 45.833 0.00 0.00 42.76 1.82
2016 2959 5.050295 GCAGTTTTCCTGTCTGTGTACTAAC 60.050 44.000 0.00 0.00 43.55 2.34
2034 2978 4.703575 ACTAACTACAGATACAGACGGCAA 59.296 41.667 0.00 0.00 0.00 4.52
2077 3029 1.340502 TGCAGGGAAACAACTGACACA 60.341 47.619 0.00 0.00 36.86 3.72
2248 3200 6.459923 ACATCTTCTTGGTTCAGTTAGAGAC 58.540 40.000 0.00 0.00 0.00 3.36
2330 3283 4.687948 CACAGACAGTCTTCAATGGTACTG 59.312 45.833 0.00 0.00 43.90 2.74
2371 3328 2.503356 CAGGGGATGCTCAGTAACTTCT 59.497 50.000 0.00 0.00 0.00 2.85
2675 3716 2.990066 ACTGTGTCTGGCTATAAGGC 57.010 50.000 0.00 0.00 41.77 4.35
2757 3830 8.373048 TGGTATTATTCGCTTTGTTGGTATAG 57.627 34.615 0.00 0.00 0.00 1.31
2763 3836 6.811253 TTCGCTTTGTTGGTATAGACAAAT 57.189 33.333 8.57 0.00 42.76 2.32
2908 3983 5.668471 TGCCACATCTGAAAAATTCACAAA 58.332 33.333 0.00 0.00 35.46 2.83
3189 4332 8.199449 CCCATTTGTCTTAACTTCATGCATAAT 58.801 33.333 0.00 0.00 0.00 1.28
3316 4462 7.815549 ACGTGACTTGTATTTTCCAAAGTTTTT 59.184 29.630 0.00 0.00 0.00 1.94
3492 4645 4.452455 ACATCAATCTTTCCTGACGTCAAC 59.548 41.667 20.49 0.00 0.00 3.18
3756 4910 5.355350 GCTTTAGTCGGTACTACTGAAGGTA 59.645 44.000 22.57 1.45 44.14 3.08
3776 4930 0.337082 TAGGGTTCCATCAGACCGGA 59.663 55.000 9.46 0.00 36.78 5.14
3782 4936 0.324738 TCCATCAGACCGGAGAAGCT 60.325 55.000 9.46 0.00 0.00 3.74
3854 5008 1.133915 TCTGGGCATTCGGTATTTCCC 60.134 52.381 0.00 0.00 0.00 3.97
3921 5075 6.093219 GGCACTCTTTATATGGTATGCATGAG 59.907 42.308 10.16 5.65 33.48 2.90
3952 5106 1.098050 CCCTGGCTAGTTTGATGTGC 58.902 55.000 0.00 0.00 0.00 4.57
3960 5114 3.441572 GCTAGTTTGATGTGCAATGGTCT 59.558 43.478 0.00 0.00 36.15 3.85
3962 5116 5.297776 GCTAGTTTGATGTGCAATGGTCTAT 59.702 40.000 0.00 0.00 36.15 1.98
3973 5128 6.211184 TGTGCAATGGTCTATTTCCTCAATTT 59.789 34.615 0.00 0.00 0.00 1.82
4403 6911 0.803117 GTTTAGAAGAGTTGCGCCCC 59.197 55.000 4.18 0.00 0.00 5.80
4733 7255 3.104519 ACTTTGGAATGATGGATGGCA 57.895 42.857 0.00 0.00 0.00 4.92
4788 7310 2.629617 ACAGCTAAATGCAAAGTGGCTT 59.370 40.909 0.00 0.00 45.94 4.35
5154 7677 1.412710 TGGCGACTCACAGAAGACTTT 59.587 47.619 0.00 0.00 0.00 2.66
5288 7811 4.017037 TGCCATTCTTTCCCCCACTTAATA 60.017 41.667 0.00 0.00 0.00 0.98
5566 8124 1.135689 CACAGAATAAAGCCACACGCC 60.136 52.381 0.00 0.00 38.78 5.68
5592 8150 8.186178 CGCAGGTAAGATATAATTCACCATAC 57.814 38.462 0.00 0.00 0.00 2.39
5593 8151 7.277981 CGCAGGTAAGATATAATTCACCATACC 59.722 40.741 0.00 0.00 0.00 2.73
5594 8152 8.100791 GCAGGTAAGATATAATTCACCATACCA 58.899 37.037 0.00 0.00 34.19 3.25
5599 8157 8.868522 AAGATATAATTCACCATACCATGTGG 57.131 34.615 0.00 0.00 42.55 4.17
5616 8174 7.639113 CCATGTGGTTATTTAAGCTTCCTTA 57.361 36.000 0.00 0.00 34.93 2.69
5619 8177 9.125026 CATGTGGTTATTTAAGCTTCCTTATCT 57.875 33.333 0.00 0.00 33.75 1.98
5702 8260 0.592637 TTCAGGTGATTGCAAGCGTG 59.407 50.000 10.55 11.52 0.00 5.34
5744 8302 3.241530 AGTGCTGCCCTCGGAACA 61.242 61.111 0.00 0.00 28.86 3.18
5759 8317 0.824759 GAACATACTCCTCGGTGGCT 59.175 55.000 0.00 0.00 35.26 4.75
5779 8337 6.318144 GTGGCTAGCATAATCGGATACTACTA 59.682 42.308 18.24 0.00 0.00 1.82
5828 8386 2.160205 TCTCAGTACCGTCACTCTTGG 58.840 52.381 0.00 0.00 0.00 3.61
6009 8603 3.243401 CCCTGCGGTTTAAATATTGCCTC 60.243 47.826 0.00 0.00 0.00 4.70
6013 8607 6.031751 TGCGGTTTAAATATTGCCTCTTTT 57.968 33.333 0.00 0.00 0.00 2.27
6015 8609 7.603651 TGCGGTTTAAATATTGCCTCTTTTTA 58.396 30.769 0.00 0.00 0.00 1.52
6016 8610 7.757624 TGCGGTTTAAATATTGCCTCTTTTTAG 59.242 33.333 0.00 0.00 0.00 1.85
6018 8612 7.704899 CGGTTTAAATATTGCCTCTTTTTAGGG 59.295 37.037 0.00 0.00 37.11 3.53
6019 8613 7.494625 GGTTTAAATATTGCCTCTTTTTAGGGC 59.505 37.037 0.00 0.00 45.45 5.19
6020 8614 7.971368 TTAAATATTGCCTCTTTTTAGGGCT 57.029 32.000 0.00 0.00 45.45 5.19
6024 8622 7.971368 ATATTGCCTCTTTTTAGGGCTAAAA 57.029 32.000 0.00 0.00 45.45 1.52
6034 8632 8.635328 TCTTTTTAGGGCTAAAACCAACTTTAG 58.365 33.333 0.00 0.00 42.61 1.85
6040 8638 5.047802 GGGCTAAAACCAACTTTAGTAACCC 60.048 44.000 5.32 4.17 39.88 4.11
6050 8648 7.666804 ACCAACTTTAGTAACCCGAAATATTGT 59.333 33.333 0.00 0.00 0.00 2.71
6062 8660 7.033185 ACCCGAAATATTGTTTGTTGCTATTC 58.967 34.615 0.00 0.00 0.00 1.75
6064 8662 7.706179 CCCGAAATATTGTTTGTTGCTATTCAT 59.294 33.333 0.00 0.00 0.00 2.57
6065 8663 9.086336 CCGAAATATTGTTTGTTGCTATTCATT 57.914 29.630 0.00 0.00 0.00 2.57
6097 8847 8.866970 TTAGGGGAAACGTCAACTTTATTAAT 57.133 30.769 0.00 0.00 0.00 1.40
6116 8866 6.767524 TTAATCCGAAATATTGCCTGTTGT 57.232 33.333 0.00 0.00 0.00 3.32
6164 9175 0.605589 GTCCCACTAGTTTTGCGGCT 60.606 55.000 0.00 0.00 0.00 5.52
6249 9465 0.709992 TGGGCTGGAATTTAGGGCTT 59.290 50.000 0.00 0.00 0.00 4.35
6250 9466 1.114627 GGGCTGGAATTTAGGGCTTG 58.885 55.000 0.00 0.00 0.00 4.01
6251 9467 0.461548 GGCTGGAATTTAGGGCTTGC 59.538 55.000 0.00 0.00 0.00 4.01
6252 9468 1.185315 GCTGGAATTTAGGGCTTGCA 58.815 50.000 0.00 0.00 0.00 4.08
6253 9469 1.758862 GCTGGAATTTAGGGCTTGCAT 59.241 47.619 0.00 0.00 0.00 3.96
6254 9470 2.169144 GCTGGAATTTAGGGCTTGCATT 59.831 45.455 0.00 0.00 0.00 3.56
6255 9471 3.739209 GCTGGAATTTAGGGCTTGCATTC 60.739 47.826 0.00 0.00 0.00 2.67
6256 9472 3.703052 CTGGAATTTAGGGCTTGCATTCT 59.297 43.478 0.00 0.00 0.00 2.40
6257 9473 4.865905 TGGAATTTAGGGCTTGCATTCTA 58.134 39.130 0.00 0.00 0.00 2.10
6258 9474 5.268387 TGGAATTTAGGGCTTGCATTCTAA 58.732 37.500 0.00 0.00 0.00 2.10
6259 9475 5.719085 TGGAATTTAGGGCTTGCATTCTAAA 59.281 36.000 13.08 13.08 36.52 1.85
6260 9476 6.212388 TGGAATTTAGGGCTTGCATTCTAAAA 59.788 34.615 14.00 1.20 35.96 1.52
6261 9477 7.102993 GGAATTTAGGGCTTGCATTCTAAAAA 58.897 34.615 14.00 1.60 35.96 1.94
6345 9563 0.535780 TGCCTCCTGTGCACTTTGAG 60.536 55.000 19.41 18.63 32.85 3.02
6356 9607 0.040958 CACTTTGAGCAACCAGTCGC 60.041 55.000 0.00 0.00 0.00 5.19
6391 9642 6.485313 TCTGATTTCCGAGTTTCTAAAAAGCA 59.515 34.615 0.00 0.00 0.00 3.91
6483 9911 3.131046 AGGAGTTTGTTGGTTTGCTTCTG 59.869 43.478 0.00 0.00 0.00 3.02
6502 9931 5.964958 TCTGTCCCTCTAAGCAATTTTTG 57.035 39.130 0.00 0.00 0.00 2.44
6512 9941 7.254421 CCTCTAAGCAATTTTTGTTCAAACCAC 60.254 37.037 0.00 0.00 0.00 4.16
6525 9955 1.073177 AAACCACGCGATAACTTCCG 58.927 50.000 15.93 0.00 0.00 4.30
6619 10051 8.606040 AACAGAAATCAAATAAACCACCAATG 57.394 30.769 0.00 0.00 0.00 2.82
6628 10060 7.708752 TCAAATAAACCACCAATGACAAGAAAC 59.291 33.333 0.00 0.00 0.00 2.78
6649 10108 1.935199 CCCTTGCAAGCAAACAACAAG 59.065 47.619 21.43 3.08 37.94 3.16
6659 10118 7.042590 TGCAAGCAAACAACAAGATAAAATGAG 60.043 33.333 0.00 0.00 0.00 2.90
6724 10183 9.620259 ATCTTTCCTTATCTTTTGACTATGGAC 57.380 33.333 0.00 0.00 0.00 4.02
6739 10201 1.048601 TGGACTCCTCCTCACAACAC 58.951 55.000 0.00 0.00 37.48 3.32
6754 10216 5.614308 TCACAACACATCTCAATCTCAGTT 58.386 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.305398 AGATCCGAAGAGACAACACAC 57.695 47.619 0.00 0.00 0.00 3.82
21 22 3.721087 TGGGTTCTCTTTGGAAGATCC 57.279 47.619 0.00 0.00 36.82 3.36
25 27 5.256474 ACATACATGGGTTCTCTTTGGAAG 58.744 41.667 0.00 0.00 0.00 3.46
72 74 1.153409 CGCAGGAGCAGATGAGCTT 60.153 57.895 0.00 0.00 46.75 3.74
135 137 8.948145 CATCTTCCATGCAAAAATAATTTGGAA 58.052 29.630 11.13 11.13 33.62 3.53
137 139 7.337436 ACCATCTTCCATGCAAAAATAATTTGG 59.663 33.333 0.00 0.00 0.00 3.28
144 146 5.954150 ACTAGACCATCTTCCATGCAAAAAT 59.046 36.000 0.00 0.00 0.00 1.82
264 266 1.748493 TGTCCTGAACAGTGCAAAACC 59.252 47.619 0.00 0.00 32.81 3.27
279 281 7.725251 TCAGCAAAAATAACAAAATCTGTCCT 58.275 30.769 0.00 0.00 37.23 3.85
311 313 5.414789 TTCAACTTATCTGGACATCCGAA 57.585 39.130 0.00 0.00 39.43 4.30
323 325 6.072119 AGGTCCGTCCAAAATTTCAACTTATC 60.072 38.462 0.00 0.00 39.02 1.75
326 328 3.958147 AGGTCCGTCCAAAATTTCAACTT 59.042 39.130 0.00 0.00 39.02 2.66
345 347 8.758829 TGTGATAGATATTTTAGTGTGTGAGGT 58.241 33.333 0.00 0.00 0.00 3.85
378 380 8.657074 TCTAACAAGTTCGAGAAAATTCAGAA 57.343 30.769 0.00 0.00 0.00 3.02
379 381 8.833231 ATCTAACAAGTTCGAGAAAATTCAGA 57.167 30.769 0.00 0.00 0.00 3.27
380 382 8.930760 AGATCTAACAAGTTCGAGAAAATTCAG 58.069 33.333 0.00 0.00 0.00 3.02
381 383 8.833231 AGATCTAACAAGTTCGAGAAAATTCA 57.167 30.769 0.00 0.00 0.00 2.57
385 387 9.193133 CAGTAAGATCTAACAAGTTCGAGAAAA 57.807 33.333 0.00 0.00 0.00 2.29
386 388 8.358148 ACAGTAAGATCTAACAAGTTCGAGAAA 58.642 33.333 0.00 0.00 0.00 2.52
389 391 7.808381 TGAACAGTAAGATCTAACAAGTTCGAG 59.192 37.037 16.41 0.00 36.50 4.04
390 392 7.594015 GTGAACAGTAAGATCTAACAAGTTCGA 59.406 37.037 16.41 0.00 36.50 3.71
391 393 7.148787 GGTGAACAGTAAGATCTAACAAGTTCG 60.149 40.741 16.41 0.00 36.50 3.95
392 394 7.148787 CGGTGAACAGTAAGATCTAACAAGTTC 60.149 40.741 15.43 15.43 35.37 3.01
393 395 6.645415 CGGTGAACAGTAAGATCTAACAAGTT 59.355 38.462 0.00 0.00 0.00 2.66
395 397 6.387465 TCGGTGAACAGTAAGATCTAACAAG 58.613 40.000 0.00 0.00 0.00 3.16
405 410 4.703645 TCTGATCTCGGTGAACAGTAAG 57.296 45.455 14.34 0.00 43.43 2.34
409 414 3.704512 CTCATCTGATCTCGGTGAACAG 58.295 50.000 10.09 10.09 44.06 3.16
418 423 3.132925 GCTCCAAAGCTCATCTGATCTC 58.867 50.000 0.00 0.00 45.55 2.75
433 438 6.112734 ACACGAATATACATTTCAGCTCCAA 58.887 36.000 0.00 0.00 0.00 3.53
435 440 7.598869 TCATACACGAATATACATTTCAGCTCC 59.401 37.037 0.00 0.00 0.00 4.70
438 443 9.533983 CATTCATACACGAATATACATTTCAGC 57.466 33.333 0.00 0.00 33.82 4.26
497 503 0.108207 ATGAGCATGACTAGGCCTGC 59.892 55.000 17.99 17.39 33.16 4.85
518 524 3.557185 CGTGTACTGCCTATCACGTACTA 59.443 47.826 8.11 0.00 45.26 1.82
519 525 2.353889 CGTGTACTGCCTATCACGTACT 59.646 50.000 8.11 0.00 45.26 2.73
520 526 2.713011 CGTGTACTGCCTATCACGTAC 58.287 52.381 8.11 0.00 45.26 3.67
576 582 1.071471 CACTGACCTGTGGGACCAC 59.929 63.158 14.45 14.45 46.33 4.16
577 583 1.383943 ACACTGACCTGTGGGACCA 60.384 57.895 10.90 0.00 41.84 4.02
593 599 1.008881 GTGCACGTCTCGTCTCACA 60.009 57.895 0.00 1.58 38.32 3.58
595 601 2.643272 GGTGCACGTCTCGTCTCA 59.357 61.111 11.45 0.00 38.32 3.27
709 719 2.368011 GGTGGGGCTGGAGGTAGTC 61.368 68.421 0.00 0.00 0.00 2.59
752 762 2.666190 CACTGACGTGTGGGCCAG 60.666 66.667 6.40 0.00 36.39 4.85
753 763 3.157949 TCACTGACGTGTGGGCCA 61.158 61.111 0.00 0.00 41.89 5.36
844 854 2.028778 GGAGATGATGCGCTCGCT 59.971 61.111 9.73 5.45 42.51 4.93
851 861 5.182760 GGGATGAAATAGTTGGAGATGATGC 59.817 44.000 0.00 0.00 0.00 3.91
884 906 1.281656 GCGTGGTTTTTGGACGAGG 59.718 57.895 0.00 0.00 35.05 4.63
951 980 0.463833 GCGGATTTGGGTAGGACCAG 60.464 60.000 0.00 0.00 42.47 4.00
1232 1264 1.335496 GTGAGATACAGAGGAGGCGAC 59.665 57.143 0.00 0.00 0.00 5.19
1244 1276 1.068250 GAGCGGGGCAGTGAGATAC 59.932 63.158 0.00 0.00 0.00 2.24
1245 1277 0.185175 TAGAGCGGGGCAGTGAGATA 59.815 55.000 0.00 0.00 0.00 1.98
1248 1280 2.055042 AGTAGAGCGGGGCAGTGAG 61.055 63.158 0.00 0.00 0.00 3.51
1249 1281 2.037367 AGTAGAGCGGGGCAGTGA 59.963 61.111 0.00 0.00 0.00 3.41
1251 1283 1.000019 TACAGTAGAGCGGGGCAGT 60.000 57.895 0.00 0.00 0.00 4.40
1274 1323 9.709495 ACACGAACACTTAACCATTAATACTAA 57.291 29.630 0.00 0.00 0.00 2.24
1275 1324 9.709495 AACACGAACACTTAACCATTAATACTA 57.291 29.630 0.00 0.00 0.00 1.82
1276 1325 8.611654 AACACGAACACTTAACCATTAATACT 57.388 30.769 0.00 0.00 0.00 2.12
1283 1332 5.370679 ACCTTAACACGAACACTTAACCAT 58.629 37.500 0.00 0.00 0.00 3.55
1298 1347 0.394938 TCGGCAGAGCAACCTTAACA 59.605 50.000 0.00 0.00 0.00 2.41
1299 1348 1.739067 ATCGGCAGAGCAACCTTAAC 58.261 50.000 0.00 0.00 0.00 2.01
1300 1349 2.489938 AATCGGCAGAGCAACCTTAA 57.510 45.000 0.00 0.00 0.00 1.85
1301 1350 2.356135 GAAATCGGCAGAGCAACCTTA 58.644 47.619 0.00 0.00 0.00 2.69
1302 1351 1.168714 GAAATCGGCAGAGCAACCTT 58.831 50.000 0.00 0.00 0.00 3.50
1303 1352 0.678048 GGAAATCGGCAGAGCAACCT 60.678 55.000 0.00 0.00 0.00 3.50
1305 1359 1.657751 GGGGAAATCGGCAGAGCAAC 61.658 60.000 0.00 0.00 0.00 4.17
1322 1376 8.524487 AGATAAATCTTACTACTGAATAGCGGG 58.476 37.037 0.00 0.00 31.22 6.13
1335 1390 8.012957 ACTCCGATCAACAGATAAATCTTACT 57.987 34.615 0.00 0.00 34.22 2.24
1336 1391 9.400638 CTACTCCGATCAACAGATAAATCTTAC 57.599 37.037 0.00 0.00 34.22 2.34
1341 1396 9.265901 CAAATCTACTCCGATCAACAGATAAAT 57.734 33.333 0.00 0.00 0.00 1.40
1342 1397 7.710907 CCAAATCTACTCCGATCAACAGATAAA 59.289 37.037 0.00 0.00 0.00 1.40
1344 1399 6.323996 ACCAAATCTACTCCGATCAACAGATA 59.676 38.462 0.00 0.00 0.00 1.98
1345 1400 5.129485 ACCAAATCTACTCCGATCAACAGAT 59.871 40.000 0.00 0.00 0.00 2.90
1346 1401 4.466370 ACCAAATCTACTCCGATCAACAGA 59.534 41.667 0.00 0.00 0.00 3.41
1347 1402 4.759782 ACCAAATCTACTCCGATCAACAG 58.240 43.478 0.00 0.00 0.00 3.16
1349 1404 5.063564 GTCAACCAAATCTACTCCGATCAAC 59.936 44.000 0.00 0.00 0.00 3.18
1350 1405 5.046591 AGTCAACCAAATCTACTCCGATCAA 60.047 40.000 0.00 0.00 0.00 2.57
1356 1411 5.409826 CACTGAAGTCAACCAAATCTACTCC 59.590 44.000 0.00 0.00 0.00 3.85
1361 1416 4.692625 CGATCACTGAAGTCAACCAAATCT 59.307 41.667 0.00 0.00 0.00 2.40
1377 1432 1.823295 CCGTCCATTCCCGATCACT 59.177 57.895 0.00 0.00 0.00 3.41
1383 1438 4.891727 CTCCGCCGTCCATTCCCG 62.892 72.222 0.00 0.00 0.00 5.14
1397 1452 0.811915 TCAGAACAGACTAGCGCTCC 59.188 55.000 16.34 4.45 0.00 4.70
1402 1457 6.456181 CGAATCCAAATTCAGAACAGACTAGC 60.456 42.308 0.00 0.00 41.22 3.42
1408 1463 4.409570 CAGCGAATCCAAATTCAGAACAG 58.590 43.478 0.00 0.00 41.22 3.16
1419 1474 1.377202 GTCAGCCCAGCGAATCCAA 60.377 57.895 0.00 0.00 0.00 3.53
1432 1487 1.789506 GTCTCACTTCACTGGTCAGC 58.210 55.000 0.00 0.00 0.00 4.26
1433 1488 1.932604 GCGTCTCACTTCACTGGTCAG 60.933 57.143 0.00 0.00 0.00 3.51
1440 1495 1.004277 CCAGACGCGTCTCACTTCAC 61.004 60.000 37.41 9.90 37.98 3.18
1444 1499 2.597805 ACCCAGACGCGTCTCACT 60.598 61.111 37.41 19.60 37.98 3.41
1448 1503 1.135083 CAATTAGACCCAGACGCGTCT 60.135 52.381 34.98 34.98 42.03 4.18
1458 1513 3.202151 TCCCCAGATGTTCAATTAGACCC 59.798 47.826 0.00 0.00 0.00 4.46
1460 1515 3.879892 GCTCCCCAGATGTTCAATTAGAC 59.120 47.826 0.00 0.00 0.00 2.59
1463 1518 4.444876 GCTAGCTCCCCAGATGTTCAATTA 60.445 45.833 7.70 0.00 0.00 1.40
1465 1520 2.158696 GCTAGCTCCCCAGATGTTCAAT 60.159 50.000 7.70 0.00 0.00 2.57
1466 1521 1.210478 GCTAGCTCCCCAGATGTTCAA 59.790 52.381 7.70 0.00 0.00 2.69
1467 1522 0.833287 GCTAGCTCCCCAGATGTTCA 59.167 55.000 7.70 0.00 0.00 3.18
1468 1523 1.127343 AGCTAGCTCCCCAGATGTTC 58.873 55.000 12.68 0.00 0.00 3.18
1470 1525 0.326048 ACAGCTAGCTCCCCAGATGT 60.326 55.000 16.15 5.11 36.62 3.06
1472 1527 1.127343 GAACAGCTAGCTCCCCAGAT 58.873 55.000 16.15 0.00 0.00 2.90
1474 1529 0.835941 ATGAACAGCTAGCTCCCCAG 59.164 55.000 16.15 5.80 0.00 4.45
1476 1531 0.543749 ACATGAACAGCTAGCTCCCC 59.456 55.000 16.15 7.04 0.00 4.81
1477 1532 2.284190 GAACATGAACAGCTAGCTCCC 58.716 52.381 16.15 7.42 0.00 4.30
1480 1549 3.620374 CGATTGAACATGAACAGCTAGCT 59.380 43.478 12.68 12.68 0.00 3.32
1490 1559 6.592220 TCGTCCTAAAAATCGATTGAACATGA 59.408 34.615 12.25 2.18 0.00 3.07
1497 1566 4.630069 AGGTGTCGTCCTAAAAATCGATTG 59.370 41.667 12.25 0.00 35.87 2.67
1508 1577 2.756760 GGTTGTATCAGGTGTCGTCCTA 59.243 50.000 0.00 0.00 35.87 2.94
1509 1578 1.549170 GGTTGTATCAGGTGTCGTCCT 59.451 52.381 0.00 0.00 38.51 3.85
1513 1582 1.469251 CCGAGGTTGTATCAGGTGTCG 60.469 57.143 0.00 0.00 0.00 4.35
1514 1583 1.822990 TCCGAGGTTGTATCAGGTGTC 59.177 52.381 0.00 0.00 0.00 3.67
1524 1599 1.229082 TAGGCCACTCCGAGGTTGT 60.229 57.895 5.01 0.00 40.77 3.32
1528 1603 0.684805 AACTCTAGGCCACTCCGAGG 60.685 60.000 5.01 0.00 38.05 4.63
1562 1637 3.511540 TCATCGAACAGATCAGACCACTT 59.488 43.478 0.00 0.00 37.52 3.16
1564 1639 3.129462 TCTCATCGAACAGATCAGACCAC 59.871 47.826 0.00 0.00 31.21 4.16
1583 1977 3.577649 TCAGTCAACCTTCGTGATCTC 57.422 47.619 0.00 0.00 0.00 2.75
1588 1982 2.285083 TGGTTTCAGTCAACCTTCGTG 58.715 47.619 4.32 0.00 45.87 4.35
1591 1985 4.338118 TGTCAATGGTTTCAGTCAACCTTC 59.662 41.667 4.32 0.00 45.87 3.46
1609 2003 3.390639 ACCCCTTTTTGCATCATTGTCAA 59.609 39.130 0.00 0.00 0.00 3.18
1621 2015 3.976015 TCCTATTGCCTACCCCTTTTTG 58.024 45.455 0.00 0.00 0.00 2.44
1656 2050 6.297582 TGTAGTACTGATACTAGGAGAAGCC 58.702 44.000 5.39 0.00 43.19 4.35
1668 2062 6.551227 ACTGCTCCATCATTGTAGTACTGATA 59.449 38.462 5.39 0.00 0.00 2.15
1677 2071 4.643334 ACTACGTACTGCTCCATCATTGTA 59.357 41.667 0.00 0.00 0.00 2.41
1846 2786 7.081349 TGCTTTATTTCTTGTTACACCAATCG 58.919 34.615 0.00 0.00 0.00 3.34
1899 2840 1.323412 ACGGCCAGCTACTGAGATAG 58.677 55.000 2.24 0.00 32.44 2.08
1900 2841 2.158652 AGTACGGCCAGCTACTGAGATA 60.159 50.000 2.24 0.00 32.44 1.98
1901 2842 1.033574 GTACGGCCAGCTACTGAGAT 58.966 55.000 2.24 0.00 32.44 2.75
1903 2844 0.382515 GAGTACGGCCAGCTACTGAG 59.617 60.000 2.24 0.00 32.44 3.35
1904 2845 0.323087 TGAGTACGGCCAGCTACTGA 60.323 55.000 2.24 0.00 32.44 3.41
1905 2846 0.530744 TTGAGTACGGCCAGCTACTG 59.469 55.000 2.24 0.00 0.00 2.74
1914 2856 1.009829 CTGGCATTCTTGAGTACGGC 58.990 55.000 0.00 0.00 0.00 5.68
2005 2948 7.400301 CGTCTGTATCTGTAGTTAGTACACAG 58.600 42.308 8.41 8.41 36.67 3.66
2013 2956 4.945543 TCTTGCCGTCTGTATCTGTAGTTA 59.054 41.667 0.00 0.00 0.00 2.24
2014 2957 3.762288 TCTTGCCGTCTGTATCTGTAGTT 59.238 43.478 0.00 0.00 0.00 2.24
2016 2959 3.489398 GGTCTTGCCGTCTGTATCTGTAG 60.489 52.174 0.00 0.00 0.00 2.74
2077 3029 2.954318 GGGAGATGCAGCAATTGTGTAT 59.046 45.455 4.07 8.95 0.00 2.29
2128 3080 3.064207 GCCGCCATCGATTGAGTATTTA 58.936 45.455 0.00 0.00 38.10 1.40
2330 3283 6.430451 CCCTGTTCTACATTTCGATATTTGC 58.570 40.000 0.00 0.00 0.00 3.68
2401 3361 7.965107 CGAGTACGTTAATACCTACAGAAAAGT 59.035 37.037 0.00 0.00 34.56 2.66
2519 3479 8.877779 CAATGTTTGAGAAGAACTCCAGTATAG 58.122 37.037 0.00 0.00 44.34 1.31
2663 3704 3.462021 GAAGACACAGCCTTATAGCCAG 58.538 50.000 0.00 0.00 0.00 4.85
2675 3716 4.973051 GTCAGTATAGCATCGAAGACACAG 59.027 45.833 0.00 0.00 42.51 3.66
2732 3773 8.205512 TCTATACCAACAAAGCGAATAATACCA 58.794 33.333 0.00 0.00 0.00 3.25
2908 3983 5.325239 AGCAAGGAAAAGGTTTATGCTAGT 58.675 37.500 0.00 0.00 40.56 2.57
3093 4206 8.763601 AGTTAATACTGAAAATAGACAGAGGCT 58.236 33.333 0.00 0.00 37.54 4.58
3316 4462 9.783081 TTGCTCAATAATCAAGCTATTAGATGA 57.217 29.630 0.00 0.00 36.96 2.92
3465 4618 4.633126 ACGTCAGGAAAGATTGATGTCATG 59.367 41.667 0.00 0.00 38.79 3.07
3492 4645 7.758980 TCGACATGAATCCCAAACAAATTAATG 59.241 33.333 0.00 0.00 30.56 1.90
3756 4910 1.062428 TCCGGTCTGATGGAACCCTAT 60.062 52.381 0.00 0.00 0.00 2.57
3776 4930 2.551071 GCCACTCCACTTTACAGCTTCT 60.551 50.000 0.00 0.00 0.00 2.85
3782 4936 1.533625 GCATGCCACTCCACTTTACA 58.466 50.000 6.36 0.00 0.00 2.41
3809 4963 6.882678 AGTAGCAGAAACCGTAAATACCAATT 59.117 34.615 0.00 0.00 0.00 2.32
3854 5008 8.654215 CGATCAGACATTGATTGGTAGATATTG 58.346 37.037 0.00 0.00 46.51 1.90
3921 5075 4.017126 ACTAGCCAGGGTAAGAAATTTGC 58.983 43.478 0.00 0.00 0.00 3.68
3952 5106 7.839907 TCCAAAATTGAGGAAATAGACCATTG 58.160 34.615 0.00 0.00 0.00 2.82
3973 5128 6.449635 AAGCTGCACGATAAAATTATCCAA 57.550 33.333 1.02 0.00 36.95 3.53
4403 6911 6.397480 CGATTGTTTCGTTCAAAAATCCTTCG 60.397 38.462 0.00 0.00 43.01 3.79
4568 7088 4.124238 TGGTAAGTACGCATTCTATTGGC 58.876 43.478 0.00 0.00 0.00 4.52
4569 7089 5.408604 GGATGGTAAGTACGCATTCTATTGG 59.591 44.000 0.00 0.00 0.00 3.16
4733 7255 7.168469 GGAAACAATTGCGTGTAAAGTTTATGT 59.832 33.333 5.05 0.00 0.00 2.29
4811 7333 8.029522 TCTAGATGCTGTTTTCAACTACTAGTG 58.970 37.037 5.39 0.00 31.69 2.74
4813 7335 9.593134 AATCTAGATGCTGTTTTCAACTACTAG 57.407 33.333 5.86 0.00 31.37 2.57
5339 7863 5.448926 AAAATGTTGTTTGACGACTTTGC 57.551 34.783 0.00 0.00 32.29 3.68
5523 8081 1.609208 TCTTCAAGAAGCACAAGGCC 58.391 50.000 0.00 0.00 46.50 5.19
5566 8124 5.547465 TGGTGAATTATATCTTACCTGCGG 58.453 41.667 0.00 0.00 0.00 5.69
5592 8150 6.530019 AAGGAAGCTTAAATAACCACATGG 57.470 37.500 0.00 0.00 42.17 3.66
5593 8151 9.125026 AGATAAGGAAGCTTAAATAACCACATG 57.875 33.333 0.00 0.00 0.00 3.21
5594 8152 9.700831 AAGATAAGGAAGCTTAAATAACCACAT 57.299 29.630 0.00 0.00 0.00 3.21
5596 8154 9.397280 AGAAGATAAGGAAGCTTAAATAACCAC 57.603 33.333 0.00 0.00 0.00 4.16
5601 8159 9.838339 CCAGAAGAAGATAAGGAAGCTTAAATA 57.162 33.333 0.00 0.00 0.00 1.40
5602 8160 8.552296 TCCAGAAGAAGATAAGGAAGCTTAAAT 58.448 33.333 0.00 0.00 0.00 1.40
5603 8161 7.918076 TCCAGAAGAAGATAAGGAAGCTTAAA 58.082 34.615 0.00 0.00 0.00 1.52
5604 8162 7.400339 TCTCCAGAAGAAGATAAGGAAGCTTAA 59.600 37.037 0.00 0.00 0.00 1.85
5605 8163 6.897966 TCTCCAGAAGAAGATAAGGAAGCTTA 59.102 38.462 0.00 0.00 0.00 3.09
5616 8174 7.434927 TCAGAAATCATCTCCAGAAGAAGAT 57.565 36.000 0.00 0.00 42.74 2.40
5619 8177 6.652481 GTGTTCAGAAATCATCTCCAGAAGAA 59.348 38.462 0.00 0.00 37.61 2.52
5702 8260 5.546621 TGACTCCAACCACTATTATAGCC 57.453 43.478 0.00 0.00 0.00 3.93
5744 8302 0.106167 TGCTAGCCACCGAGGAGTAT 60.106 55.000 13.29 0.00 41.22 2.12
5779 8337 5.707298 TCGAAGAGATTGCTTTGGAAGAATT 59.293 36.000 0.00 0.00 31.49 2.17
5931 8521 4.034510 GCAGCAGCTAAATGGTAACAGTAG 59.965 45.833 0.00 0.00 45.16 2.57
6009 8603 8.418662 ACTAAAGTTGGTTTTAGCCCTAAAAAG 58.581 33.333 13.16 8.23 43.89 2.27
6013 8607 7.448161 GGTTACTAAAGTTGGTTTTAGCCCTAA 59.552 37.037 5.65 0.00 41.96 2.69
6015 8609 5.771666 GGTTACTAAAGTTGGTTTTAGCCCT 59.228 40.000 5.65 0.00 41.96 5.19
6016 8610 5.047802 GGGTTACTAAAGTTGGTTTTAGCCC 60.048 44.000 5.65 5.21 41.96 5.19
6018 8612 5.469760 TCGGGTTACTAAAGTTGGTTTTAGC 59.530 40.000 5.65 0.00 41.96 3.09
6019 8613 7.495135 TTCGGGTTACTAAAGTTGGTTTTAG 57.505 36.000 4.46 4.46 43.21 1.85
6020 8614 7.872113 TTTCGGGTTACTAAAGTTGGTTTTA 57.128 32.000 0.00 0.00 0.00 1.52
6024 8622 7.666804 ACAATATTTCGGGTTACTAAAGTTGGT 59.333 33.333 0.00 0.00 0.00 3.67
6034 8632 6.153756 AGCAACAAACAATATTTCGGGTTAC 58.846 36.000 0.00 0.00 0.00 2.50
6084 8834 9.959749 GGCAATATTTCGGATTAATAAAGTTGA 57.040 29.630 10.92 0.00 0.00 3.18
6097 8847 3.442273 GGAACAACAGGCAATATTTCGGA 59.558 43.478 0.00 0.00 0.00 4.55
6146 8924 0.605319 CAGCCGCAAAACTAGTGGGA 60.605 55.000 0.00 0.00 37.14 4.37
6147 8925 0.605319 TCAGCCGCAAAACTAGTGGG 60.605 55.000 0.00 0.00 37.14 4.61
6164 9175 4.021544 GCCCATTTTACTGTGTCCATTTCA 60.022 41.667 0.00 0.00 0.00 2.69
6260 9476 2.233676 CGCAAGCCCTAAATCCCTTTTT 59.766 45.455 0.00 0.00 0.00 1.94
6261 9477 1.824852 CGCAAGCCCTAAATCCCTTTT 59.175 47.619 0.00 0.00 0.00 2.27
6262 9478 1.474330 CGCAAGCCCTAAATCCCTTT 58.526 50.000 0.00 0.00 0.00 3.11
6263 9479 3.191182 CGCAAGCCCTAAATCCCTT 57.809 52.632 0.00 0.00 0.00 3.95
6264 9480 4.986467 CGCAAGCCCTAAATCCCT 57.014 55.556 0.00 0.00 0.00 4.20
6276 9492 0.816825 ATATCACCAGCTGGCGCAAG 60.817 55.000 33.06 16.87 39.32 4.01
6277 9493 0.815213 GATATCACCAGCTGGCGCAA 60.815 55.000 33.06 16.40 39.32 4.85
6345 9563 4.077188 GTCTGCGCGACTGGTTGC 62.077 66.667 12.10 3.05 39.61 4.17
6483 9911 6.084326 TGAACAAAAATTGCTTAGAGGGAC 57.916 37.500 0.00 0.00 0.00 4.46
6502 9931 3.476181 GAAGTTATCGCGTGGTTTGAAC 58.524 45.455 5.77 1.49 0.00 3.18
6549 9980 0.916809 CCCCGGAAATAAGGAGGTGT 59.083 55.000 0.73 0.00 0.00 4.16
6592 10024 6.754193 TGGTGGTTTATTTGATTTCTGTTCC 58.246 36.000 0.00 0.00 0.00 3.62
6593 10025 8.711457 CATTGGTGGTTTATTTGATTTCTGTTC 58.289 33.333 0.00 0.00 0.00 3.18
6619 10051 1.269778 GCTTGCAAGGGGTTTCTTGTC 60.270 52.381 27.10 2.68 44.26 3.18
6628 10060 0.177604 TGTTGTTTGCTTGCAAGGGG 59.822 50.000 27.10 4.07 0.00 4.79
6649 10108 8.269424 CGTACAACTATGTGAGCTCATTTTATC 58.731 37.037 21.47 6.23 40.84 1.75
6720 10179 1.048601 GTGTTGTGAGGAGGAGTCCA 58.951 55.000 12.86 0.00 46.80 4.02
6724 10183 2.564504 TGAGATGTGTTGTGAGGAGGAG 59.435 50.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.