Multiple sequence alignment - TraesCS7D01G501800

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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 TraesCS7D01G501800 chr7D 100.000 2315 0 0 1 2315 607547604 607545290 0.000000e+00 4276.0
1 TraesCS7D01G501800 chr7D 88.308 1206 57 29 141 1320 610239754 610240901 0.000000e+00 1369.0
2 TraesCS7D01G501800 chr7D 79.108 852 67 43 391 1199 608451011 608450228 3.460000e-133 484.0
3 TraesCS7D01G501800 chr7D 76.230 854 108 49 591 1402 608488457 608487657 4.700000e-97 364.0
4 TraesCS7D01G501800 chr7D 85.616 292 26 9 1018 1300 514993748 514993464 2.250000e-75 292.0
5 TraesCS7D01G501800 chr7D 87.500 136 14 2 579 712 608443614 608443480 1.110000e-33 154.0
6 TraesCS7D01G501800 chr7D 81.622 185 21 6 1 175 608485377 608485196 8.620000e-30 141.0
7 TraesCS7D01G501800 chr7D 76.380 326 32 19 103 385 514995048 514994725 1.440000e-27 134.0
8 TraesCS7D01G501800 chr7D 85.714 105 10 3 1317 1416 610240935 610241039 3.150000e-19 106.0
9 TraesCS7D01G501800 chr7D 90.625 64 5 1 113 175 608451892 608451829 1.470000e-12 84.2
10 TraesCS7D01G501800 chr7D 100.000 28 0 0 574 601 514994096 514994069 4.000000e-03 52.8
11 TraesCS7D01G501800 chr7D 100.000 28 0 0 1361 1388 607546175 607546148 4.000000e-03 52.8
12 TraesCS7D01G501800 chr7D 100.000 28 0 0 1430 1457 607546244 607546217 4.000000e-03 52.8
13 TraesCS7D01G501800 chr7B 83.095 1189 104 62 238 1393 693198788 693197664 0.000000e+00 992.0
14 TraesCS7D01G501800 chr7B 83.908 783 59 29 590 1319 698857980 698857212 0.000000e+00 686.0
15 TraesCS7D01G501800 chr7B 86.410 493 44 8 868 1341 693792696 693792208 3.410000e-143 518.0
16 TraesCS7D01G501800 chr7B 87.555 458 31 12 428 879 696590306 696589869 7.380000e-140 507.0
17 TraesCS7D01G501800 chr7B 82.505 543 50 28 863 1381 694766887 694766366 3.530000e-118 435.0
18 TraesCS7D01G501800 chr7B 85.714 364 23 8 437 789 698853813 698853468 7.870000e-95 357.0
19 TraesCS7D01G501800 chr7B 76.578 713 108 40 648 1321 694799054 694798362 1.020000e-88 337.0
20 TraesCS7D01G501800 chr7B 81.061 396 52 12 1018 1401 696363010 696362626 6.260000e-76 294.0
21 TraesCS7D01G501800 chr7B 87.451 255 22 7 1630 1876 693197421 693197169 3.760000e-73 285.0
22 TraesCS7D01G501800 chr7B 83.828 303 22 14 590 872 693793262 693792967 1.760000e-66 263.0
23 TraesCS7D01G501800 chr7B 86.239 218 13 6 334 540 698858286 698858075 1.080000e-53 220.0
24 TraesCS7D01G501800 chr7B 83.983 231 23 7 333 560 693793545 693793326 2.330000e-50 209.0
25 TraesCS7D01G501800 chr7B 87.838 148 15 2 404 551 696363605 696363461 1.100000e-38 171.0
26 TraesCS7D01G501800 chr7B 92.208 77 6 0 333 409 696363704 696363628 2.430000e-20 110.0
27 TraesCS7D01G501800 chr7B 96.875 64 2 0 1562 1625 693197532 693197469 8.750000e-20 108.0
28 TraesCS7D01G501800 chrUn 85.714 959 65 25 483 1416 77545541 77544630 0.000000e+00 946.0
29 TraesCS7D01G501800 chr4A 85.286 768 56 26 590 1319 661973310 661974058 0.000000e+00 739.0
30 TraesCS7D01G501800 chr4A 91.781 146 12 0 2133 2278 190826819 190826674 1.080000e-48 204.0
31 TraesCS7D01G501800 chr4A 85.039 127 11 5 414 540 661973061 661973179 3.120000e-24 122.0
32 TraesCS7D01G501800 chr7A 80.437 869 80 33 590 1394 700451725 700450883 4.290000e-162 580.0
33 TraesCS7D01G501800 chr7A 76.815 785 104 46 597 1321 699766855 699766089 1.010000e-98 370.0
34 TraesCS7D01G501800 chr7A 80.769 442 41 23 590 1018 699741117 699740707 2.890000e-79 305.0
35 TraesCS7D01G501800 chr7A 87.037 270 18 9 1686 1940 699740278 699740011 2.910000e-74 289.0
36 TraesCS7D01G501800 chr7A 78.599 514 42 35 27 509 699741752 699741276 6.300000e-71 278.0
37 TraesCS7D01G501800 chr7A 90.610 213 13 5 334 540 700452063 700451852 2.270000e-70 276.0
38 TraesCS7D01G501800 chr7A 89.091 165 12 5 2142 2305 721594988 721594829 1.400000e-47 200.0
39 TraesCS7D01G501800 chr7A 87.879 165 14 5 2142 2305 721664539 721664380 3.040000e-44 189.0
40 TraesCS7D01G501800 chr3B 95.946 148 6 0 2140 2287 564031964 564032111 8.270000e-60 241.0
41 TraesCS7D01G501800 chr3B 80.000 260 32 8 2050 2305 482988974 482988731 8.500000e-40 174.0
42 TraesCS7D01G501800 chr3D 90.964 166 10 3 2142 2307 431719903 431720063 3.870000e-53 219.0
43 TraesCS7D01G501800 chr6D 89.157 166 11 6 2143 2307 248515971 248516130 1.400000e-47 200.0
44 TraesCS7D01G501800 chr4D 88.623 167 13 6 2142 2307 344120195 344120034 5.050000e-47 198.0
45 TraesCS7D01G501800 chr2D 87.574 169 13 7 2142 2309 62566060 62565899 3.040000e-44 189.0


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 TraesCS7D01G501800 chr7D 607545290 607547604 2314 True 1460.533333 4276 100.000000 1 2315 3 chr7D.!!$R3 2314
1 TraesCS7D01G501800 chr7D 610239754 610241039 1285 False 737.500000 1369 87.011000 141 1416 2 chr7D.!!$F1 1275
2 TraesCS7D01G501800 chr7D 608450228 608451892 1664 True 284.100000 484 84.866500 113 1199 2 chr7D.!!$R4 1086
3 TraesCS7D01G501800 chr7D 608485196 608488457 3261 True 252.500000 364 78.926000 1 1402 2 chr7D.!!$R5 1401
4 TraesCS7D01G501800 chr7B 693197169 693198788 1619 True 461.666667 992 89.140333 238 1876 3 chr7B.!!$R4 1638
5 TraesCS7D01G501800 chr7B 694766366 694766887 521 True 435.000000 435 82.505000 863 1381 1 chr7B.!!$R1 518
6 TraesCS7D01G501800 chr7B 698853468 698858286 4818 True 421.000000 686 85.287000 334 1319 3 chr7B.!!$R7 985
7 TraesCS7D01G501800 chr7B 694798362 694799054 692 True 337.000000 337 76.578000 648 1321 1 chr7B.!!$R2 673
8 TraesCS7D01G501800 chr7B 693792208 693793545 1337 True 330.000000 518 84.740333 333 1341 3 chr7B.!!$R5 1008
9 TraesCS7D01G501800 chrUn 77544630 77545541 911 True 946.000000 946 85.714000 483 1416 1 chrUn.!!$R1 933
10 TraesCS7D01G501800 chr4A 661973061 661974058 997 False 430.500000 739 85.162500 414 1319 2 chr4A.!!$F1 905
11 TraesCS7D01G501800 chr7A 700450883 700452063 1180 True 428.000000 580 85.523500 334 1394 2 chr7A.!!$R5 1060
12 TraesCS7D01G501800 chr7A 699766089 699766855 766 True 370.000000 370 76.815000 597 1321 1 chr7A.!!$R1 724
13 TraesCS7D01G501800 chr7A 699740011 699741752 1741 True 290.666667 305 82.135000 27 1940 3 chr7A.!!$R4 1913

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
906 2073 0.612229 CCTTCTTCTCCAGCAGCAGA 59.388 55.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2107 6352 0.865769 CCGTTGTACAGCCACACTTC 59.134 55.0 3.94 0.0 0.0 3.01 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
19 20 1.737838 TCGAAATGAGTGGATGGCAC 58.262 50.000 0.00 0.00 0.00 5.01
20 21 0.734889 CGAAATGAGTGGATGGCACC 59.265 55.000 0.00 0.00 0.00 5.01
21 22 1.838112 GAAATGAGTGGATGGCACCA 58.162 50.000 4.93 4.93 37.63 4.17
33 34 2.647297 GCACCACCAAGCAAGCTC 59.353 61.111 0.00 0.00 0.00 4.09
60 61 1.963338 ACGTGCTCAAGCCTGAAGC 60.963 57.895 0.00 0.00 41.18 3.86
73 74 2.823535 GCCTGAAGCTAGCCCTATCCTA 60.824 54.545 12.13 0.00 38.99 2.94
84 85 5.767277 AGCCCTATCCTACTCTAGTACTC 57.233 47.826 0.00 0.00 0.00 2.59
90 91 8.971073 CCCTATCCTACTCTAGTACTCTACTAC 58.029 44.444 0.00 0.00 40.14 2.73
91 92 9.759473 CCTATCCTACTCTAGTACTCTACTACT 57.241 40.741 0.00 0.00 40.14 2.57
218 501 2.154462 GACGGGGGCATGATATTTCTG 58.846 52.381 0.00 0.00 0.00 3.02
222 505 2.560105 GGGGGCATGATATTTCTGCTTC 59.440 50.000 0.00 0.59 36.18 3.86
412 1080 1.081556 CGATTCGGCCGTGTCAATGA 61.082 55.000 27.15 0.00 0.00 2.57
454 1137 4.573607 TCTGTATGATGCGAACGTAGTACT 59.426 41.667 0.00 0.00 45.00 2.73
874 2040 1.219724 TCCGCCCCTCCTATTTAGTCT 59.780 52.381 0.00 0.00 0.00 3.24
906 2073 0.612229 CCTTCTTCTCCAGCAGCAGA 59.388 55.000 0.00 0.00 0.00 4.26
907 2074 1.209990 CCTTCTTCTCCAGCAGCAGAT 59.790 52.381 0.00 0.00 0.00 2.90
908 2075 2.553086 CTTCTTCTCCAGCAGCAGATC 58.447 52.381 0.00 0.00 0.00 2.75
962 2170 2.045524 ACCCACATCCATCTCTAGCTG 58.954 52.381 0.00 0.00 0.00 4.24
992 2218 0.764890 AAGCACACTAGCACCAAGGA 59.235 50.000 0.00 0.00 36.85 3.36
1242 2518 2.125673 GCAGAGAACGCGGCCTTA 60.126 61.111 12.47 0.00 0.00 2.69
1243 2519 1.740296 GCAGAGAACGCGGCCTTAA 60.740 57.895 12.47 0.00 0.00 1.85
1250 2526 2.202974 CGCGGCCTTAAGGTACCC 60.203 66.667 22.55 14.09 37.57 3.69
1352 2715 7.468141 TTCTGTAGCTTTTGTCTCTCTGATA 57.532 36.000 0.00 0.00 0.00 2.15
1425 2810 2.202427 GTGCAAATACGGCCGTGC 60.202 61.111 40.02 32.56 37.51 5.34
1429 2814 0.457681 GCAAATACGGCCGTGCAAAT 60.458 50.000 40.02 23.11 36.97 2.32
1430 2815 1.989430 CAAATACGGCCGTGCAAATT 58.011 45.000 40.02 27.43 0.00 1.82
1431 2816 1.653114 CAAATACGGCCGTGCAAATTG 59.347 47.619 40.02 28.25 0.00 2.32
1432 2817 0.885196 AATACGGCCGTGCAAATTGT 59.115 45.000 40.02 13.03 0.00 2.71
1434 2819 1.579084 TACGGCCGTGCAAATTGTCC 61.579 55.000 40.02 0.00 0.00 4.02
1435 2820 2.126502 GGCCGTGCAAATTGTCCG 60.127 61.111 0.00 0.00 0.00 4.79
1437 2822 1.154225 GCCGTGCAAATTGTCCGAG 60.154 57.895 7.73 1.26 0.00 4.63
1438 2823 1.852067 GCCGTGCAAATTGTCCGAGT 61.852 55.000 7.73 0.00 0.00 4.18
1439 2824 0.110238 CCGTGCAAATTGTCCGAGTG 60.110 55.000 7.73 0.00 0.00 3.51
1442 2827 2.143122 GTGCAAATTGTCCGAGTGAGA 58.857 47.619 0.00 0.00 0.00 3.27
1443 2828 2.096218 GTGCAAATTGTCCGAGTGAGAC 60.096 50.000 0.00 0.00 34.72 3.36
1444 2829 2.224281 TGCAAATTGTCCGAGTGAGACT 60.224 45.455 0.00 0.00 35.21 3.24
1445 2830 2.158449 GCAAATTGTCCGAGTGAGACTG 59.842 50.000 0.00 0.00 35.21 3.51
1446 2831 3.653344 CAAATTGTCCGAGTGAGACTGA 58.347 45.455 0.00 0.00 35.21 3.41
1447 2832 4.058124 CAAATTGTCCGAGTGAGACTGAA 58.942 43.478 0.00 0.00 35.21 3.02
1448 2833 4.543590 AATTGTCCGAGTGAGACTGAAT 57.456 40.909 0.00 0.00 35.21 2.57
1449 2834 3.577649 TTGTCCGAGTGAGACTGAATC 57.422 47.619 0.00 0.00 35.21 2.52
1450 2835 2.514803 TGTCCGAGTGAGACTGAATCA 58.485 47.619 0.00 0.00 35.21 2.57
1451 2836 2.489722 TGTCCGAGTGAGACTGAATCAG 59.510 50.000 8.98 8.98 37.52 2.90
1452 2837 1.474478 TCCGAGTGAGACTGAATCAGC 59.526 52.381 10.62 3.43 34.37 4.26
1453 2838 1.476085 CCGAGTGAGACTGAATCAGCT 59.524 52.381 10.62 8.46 34.37 4.24
1454 2839 2.479389 CCGAGTGAGACTGAATCAGCTC 60.479 54.545 20.19 20.19 36.20 4.09
1455 2840 2.423185 CGAGTGAGACTGAATCAGCTCT 59.577 50.000 24.21 19.05 36.42 4.09
1456 2841 3.731565 CGAGTGAGACTGAATCAGCTCTG 60.732 52.174 24.21 13.92 36.42 3.35
1457 2842 3.429492 AGTGAGACTGAATCAGCTCTGA 58.571 45.455 24.21 13.61 44.59 3.27
1458 2843 3.831333 AGTGAGACTGAATCAGCTCTGAA 59.169 43.478 24.21 10.53 43.58 3.02
1459 2844 4.467082 AGTGAGACTGAATCAGCTCTGAAT 59.533 41.667 24.21 13.02 43.58 2.57
1460 2845 4.805192 GTGAGACTGAATCAGCTCTGAATC 59.195 45.833 24.21 5.89 43.58 2.52
1461 2846 4.465305 TGAGACTGAATCAGCTCTGAATCA 59.535 41.667 24.21 14.72 44.53 2.57
1465 2850 3.794717 TGAATCAGCTCTGAATCAGCTC 58.205 45.455 12.25 0.00 44.25 4.09
1468 2853 5.128335 TGAATCAGCTCTGAATCAGCTCTAA 59.872 40.000 12.25 0.00 44.25 2.10
1471 2856 6.083098 TCAGCTCTGAATCAGCTCTAATAC 57.917 41.667 5.18 0.00 44.25 1.89
1477 2862 4.697514 TGAATCAGCTCTAATACCAGTGC 58.302 43.478 0.00 0.00 35.71 4.40
1496 2881 3.249320 GTGCACCAGTAGCATCATGTATG 59.751 47.826 5.22 0.00 44.79 2.39
1515 2922 8.517056 CATGTATGCATATAGGAAGCAATCAAA 58.483 33.333 10.16 0.00 42.15 2.69
1539 3021 8.842358 AACAATTTTCTCAATGCAAGATGAAT 57.158 26.923 0.00 0.00 0.00 2.57
1540 3022 8.842358 ACAATTTTCTCAATGCAAGATGAATT 57.158 26.923 0.00 0.00 0.00 2.17
1542 3024 8.931775 CAATTTTCTCAATGCAAGATGAATTCA 58.068 29.630 11.26 11.26 0.00 2.57
1592 3138 1.826720 CCCTTGGTTGGTGGAATCATG 59.173 52.381 0.00 0.00 0.00 3.07
1625 3187 0.880278 CACCGTGTGGACTGAACAGG 60.880 60.000 6.76 0.00 39.21 4.00
1633 3609 3.233355 GACTGAACAGGCCGTCAAT 57.767 52.632 0.00 0.00 0.00 2.57
1647 3623 0.179265 GTCAATCATGCGCGCTATCG 60.179 55.000 33.29 17.24 39.07 2.92
1724 3715 3.181507 CGTGACATGACATGTTGGGATTC 60.182 47.826 21.66 8.18 45.03 2.52
1779 5374 2.398554 TGCTCTGCGGCGGATTTTC 61.399 57.895 12.67 3.11 34.52 2.29
1780 5375 2.703409 CTCTGCGGCGGATTTTCG 59.297 61.111 12.67 0.00 0.00 3.46
1781 5376 1.809619 CTCTGCGGCGGATTTTCGA 60.810 57.895 12.67 0.00 0.00 3.71
1783 5378 2.813179 CTGCGGCGGATTTTCGAGG 61.813 63.158 9.78 0.00 0.00 4.63
1784 5379 2.510691 GCGGCGGATTTTCGAGGA 60.511 61.111 9.78 0.00 0.00 3.71
1785 5380 1.887707 GCGGCGGATTTTCGAGGAT 60.888 57.895 9.78 0.00 0.00 3.24
1790 5385 1.531578 GCGGATTTTCGAGGATAAGCC 59.468 52.381 0.00 0.00 0.00 4.35
1792 5387 3.202906 CGGATTTTCGAGGATAAGCCAA 58.797 45.455 4.48 0.00 40.02 4.52
1878 5490 3.277142 ACCACACGGAAAGTTTCTTCT 57.723 42.857 15.05 0.00 35.59 2.85
1881 5493 5.187687 ACCACACGGAAAGTTTCTTCTTTA 58.812 37.500 15.05 0.00 37.70 1.85
1897 5509 5.927689 TCTTCTTTATAAAGCGACACGGAAA 59.072 36.000 18.68 5.45 35.99 3.13
1898 5510 5.520022 TCTTTATAAAGCGACACGGAAAC 57.480 39.130 18.68 0.00 35.99 2.78
1910 5534 3.740115 ACACGGAAACTTGCTGAGTATT 58.260 40.909 0.00 0.00 37.72 1.89
1942 5566 9.981114 AATCCCATTATTTTCGGAAATGTTATC 57.019 29.630 12.12 0.00 36.22 1.75
1944 5568 7.561722 TCCCATTATTTTCGGAAATGTTATCCA 59.438 33.333 12.12 0.00 36.22 3.41
1946 5570 8.194104 CCATTATTTTCGGAAATGTTATCCACA 58.806 33.333 12.12 0.00 40.71 4.17
1970 6215 9.747898 ACAAGGATAGGTAAAATTGTCATGTAA 57.252 29.630 0.00 0.00 0.00 2.41
1976 6221 9.855021 ATAGGTAAAATTGTCATGTAAGCAAAC 57.145 29.630 0.00 0.00 0.00 2.93
1977 6222 7.951591 AGGTAAAATTGTCATGTAAGCAAACT 58.048 30.769 0.00 0.00 0.00 2.66
1985 6230 5.588648 TGTCATGTAAGCAAACTATAAGCCC 59.411 40.000 0.00 0.00 0.00 5.19
1987 6232 5.588648 TCATGTAAGCAAACTATAAGCCCAC 59.411 40.000 0.00 0.00 0.00 4.61
1989 6234 2.038387 AGCAAACTATAAGCCCACCG 57.962 50.000 0.00 0.00 0.00 4.94
1991 6236 2.089201 GCAAACTATAAGCCCACCGTT 58.911 47.619 0.00 0.00 0.00 4.44
1993 6238 3.078837 CAAACTATAAGCCCACCGTTGT 58.921 45.455 0.00 0.00 0.00 3.32
1995 6240 3.531934 ACTATAAGCCCACCGTTGTAC 57.468 47.619 0.00 0.00 0.00 2.90
1996 6241 3.102204 ACTATAAGCCCACCGTTGTACT 58.898 45.455 0.00 0.00 0.00 2.73
1998 6243 2.172851 TAAGCCCACCGTTGTACTTG 57.827 50.000 0.00 0.00 0.00 3.16
2001 6246 1.574702 GCCCACCGTTGTACTTGCTC 61.575 60.000 0.00 0.00 0.00 4.26
2002 6247 0.034896 CCCACCGTTGTACTTGCTCT 59.965 55.000 0.00 0.00 0.00 4.09
2003 6248 1.274167 CCCACCGTTGTACTTGCTCTA 59.726 52.381 0.00 0.00 0.00 2.43
2006 6251 3.192001 CCACCGTTGTACTTGCTCTACTA 59.808 47.826 0.00 0.00 0.00 1.82
2027 6272 3.823716 GCAGTTTTTGTTGCTTCGAAG 57.176 42.857 21.02 21.02 37.35 3.79
2029 6274 3.857093 GCAGTTTTTGTTGCTTCGAAGAA 59.143 39.130 28.95 16.67 45.90 2.52
2031 6276 5.331902 CAGTTTTTGTTGCTTCGAAGAAGA 58.668 37.500 28.95 14.69 45.90 2.87
2033 6278 5.354234 AGTTTTTGTTGCTTCGAAGAAGAGA 59.646 36.000 28.95 10.64 45.90 3.10
2034 6279 5.811399 TTTTGTTGCTTCGAAGAAGAGAA 57.189 34.783 28.95 15.21 45.90 2.87
2035 6280 5.409643 TTTGTTGCTTCGAAGAAGAGAAG 57.590 39.130 28.95 0.10 45.90 2.85
2037 6282 3.804325 TGTTGCTTCGAAGAAGAGAAGTG 59.196 43.478 28.95 0.00 45.90 3.16
2038 6283 2.408050 TGCTTCGAAGAAGAGAAGTGC 58.592 47.619 28.95 10.37 45.90 4.40
2039 6284 2.224042 TGCTTCGAAGAAGAGAAGTGCA 60.224 45.455 28.95 12.95 45.90 4.57
2040 6285 2.802816 GCTTCGAAGAAGAGAAGTGCAA 59.197 45.455 28.95 0.00 45.90 4.08
2041 6286 3.363477 GCTTCGAAGAAGAGAAGTGCAAC 60.363 47.826 28.95 1.67 45.90 4.17
2059 6304 7.734924 GTGCAACTCCAATAGATTGATATGA 57.265 36.000 3.76 0.00 40.14 2.15
2061 6306 8.235226 GTGCAACTCCAATAGATTGATATGATG 58.765 37.037 3.76 0.00 40.14 3.07
2062 6307 7.094506 TGCAACTCCAATAGATTGATATGATGC 60.095 37.037 3.76 7.11 40.14 3.91
2063 6308 7.094506 GCAACTCCAATAGATTGATATGATGCA 60.095 37.037 3.76 0.00 40.14 3.96
2064 6309 7.918536 ACTCCAATAGATTGATATGATGCAC 57.081 36.000 3.76 0.00 40.14 4.57
2065 6310 6.592994 ACTCCAATAGATTGATATGATGCACG 59.407 38.462 3.76 0.00 40.14 5.34
2066 6311 6.466812 TCCAATAGATTGATATGATGCACGT 58.533 36.000 3.76 0.00 40.14 4.49
2068 6313 7.445096 TCCAATAGATTGATATGATGCACGTTT 59.555 33.333 3.76 0.00 40.14 3.60
2069 6314 7.536281 CCAATAGATTGATATGATGCACGTTTG 59.464 37.037 3.76 0.00 40.14 2.93
2071 6316 6.441093 AGATTGATATGATGCACGTTTGTT 57.559 33.333 0.00 0.00 0.00 2.83
2072 6317 6.260377 AGATTGATATGATGCACGTTTGTTG 58.740 36.000 0.00 0.00 0.00 3.33
2073 6318 4.354071 TGATATGATGCACGTTTGTTGG 57.646 40.909 0.00 0.00 0.00 3.77
2074 6319 3.755905 TGATATGATGCACGTTTGTTGGT 59.244 39.130 0.00 0.00 0.00 3.67
2075 6320 4.938226 TGATATGATGCACGTTTGTTGGTA 59.062 37.500 0.00 0.00 0.00 3.25
2076 6321 3.829886 ATGATGCACGTTTGTTGGTAG 57.170 42.857 0.00 0.00 0.00 3.18
2077 6322 2.839975 TGATGCACGTTTGTTGGTAGA 58.160 42.857 0.00 0.00 0.00 2.59
2078 6323 3.206964 TGATGCACGTTTGTTGGTAGAA 58.793 40.909 0.00 0.00 0.00 2.10
2080 6325 4.277174 TGATGCACGTTTGTTGGTAGAAAT 59.723 37.500 0.00 0.00 0.00 2.17
2081 6326 4.217754 TGCACGTTTGTTGGTAGAAATC 57.782 40.909 0.00 0.00 0.00 2.17
2082 6327 3.880490 TGCACGTTTGTTGGTAGAAATCT 59.120 39.130 0.00 0.00 0.00 2.40
2083 6328 4.219033 GCACGTTTGTTGGTAGAAATCTG 58.781 43.478 0.00 0.00 0.00 2.90
2084 6329 4.024387 GCACGTTTGTTGGTAGAAATCTGA 60.024 41.667 0.00 0.00 0.00 3.27
2085 6330 5.504994 GCACGTTTGTTGGTAGAAATCTGAA 60.505 40.000 0.00 0.00 0.00 3.02
2086 6331 6.668323 CACGTTTGTTGGTAGAAATCTGAAT 58.332 36.000 0.00 0.00 0.00 2.57
2087 6332 7.138736 CACGTTTGTTGGTAGAAATCTGAATT 58.861 34.615 0.00 0.00 0.00 2.17
2088 6333 7.113404 CACGTTTGTTGGTAGAAATCTGAATTG 59.887 37.037 0.00 0.00 0.00 2.32
2089 6334 7.138736 CGTTTGTTGGTAGAAATCTGAATTGT 58.861 34.615 0.00 0.00 0.00 2.71
2090 6335 8.286800 CGTTTGTTGGTAGAAATCTGAATTGTA 58.713 33.333 0.00 0.00 0.00 2.41
2094 6339 8.243426 TGTTGGTAGAAATCTGAATTGTATTGC 58.757 33.333 0.00 0.00 0.00 3.56
2095 6340 8.462016 GTTGGTAGAAATCTGAATTGTATTGCT 58.538 33.333 0.00 0.00 0.00 3.91
2096 6341 9.679661 TTGGTAGAAATCTGAATTGTATTGCTA 57.320 29.630 0.00 0.00 0.00 3.49
2097 6342 9.851686 TGGTAGAAATCTGAATTGTATTGCTAT 57.148 29.630 0.00 0.00 0.00 2.97
2112 6357 8.969121 TGTATTGCTATTTGAATGTTGAAGTG 57.031 30.769 0.00 0.00 0.00 3.16
2113 6358 8.575589 TGTATTGCTATTTGAATGTTGAAGTGT 58.424 29.630 0.00 0.00 0.00 3.55
2114 6359 7.878477 ATTGCTATTTGAATGTTGAAGTGTG 57.122 32.000 0.00 0.00 0.00 3.82
2116 6361 4.622740 GCTATTTGAATGTTGAAGTGTGGC 59.377 41.667 0.00 0.00 0.00 5.01
2117 6362 4.942761 ATTTGAATGTTGAAGTGTGGCT 57.057 36.364 0.00 0.00 0.00 4.75
2119 6364 2.653726 TGAATGTTGAAGTGTGGCTGT 58.346 42.857 0.00 0.00 0.00 4.40
2120 6365 3.814625 TGAATGTTGAAGTGTGGCTGTA 58.185 40.909 0.00 0.00 0.00 2.74
2121 6366 3.563808 TGAATGTTGAAGTGTGGCTGTAC 59.436 43.478 0.00 0.00 0.00 2.90
2122 6367 2.700722 TGTTGAAGTGTGGCTGTACA 57.299 45.000 0.00 0.00 0.00 2.90
2123 6368 2.992593 TGTTGAAGTGTGGCTGTACAA 58.007 42.857 0.00 0.00 31.36 2.41
2124 6369 2.680841 TGTTGAAGTGTGGCTGTACAAC 59.319 45.455 0.00 0.00 37.23 3.32
2125 6370 1.577468 TGAAGTGTGGCTGTACAACG 58.423 50.000 0.00 0.00 31.36 4.10
2126 6371 0.865769 GAAGTGTGGCTGTACAACGG 59.134 55.000 0.00 0.00 31.36 4.44
2133 6378 2.860293 CTGTACAACGGCCTTGCG 59.140 61.111 13.00 0.00 32.41 4.85
2134 6379 1.959226 CTGTACAACGGCCTTGCGT 60.959 57.895 13.00 2.89 32.41 5.24
2136 6381 1.666872 GTACAACGGCCTTGCGTCT 60.667 57.895 13.00 0.00 32.41 4.18
2137 6382 1.666553 TACAACGGCCTTGCGTCTG 60.667 57.895 13.00 4.96 32.41 3.51
2138 6383 2.372040 TACAACGGCCTTGCGTCTGT 62.372 55.000 13.00 9.33 32.41 3.41
2142 6387 4.681978 GGCCTTGCGTCTGTCGGT 62.682 66.667 0.00 0.00 40.26 4.69
2152 6669 2.344741 GCGTCTGTCGGTTTTACATCTC 59.655 50.000 0.00 0.00 40.26 2.75
2153 6670 2.921754 CGTCTGTCGGTTTTACATCTCC 59.078 50.000 0.00 0.00 35.71 3.71
2158 6675 6.001460 TCTGTCGGTTTTACATCTCCATTTT 58.999 36.000 0.00 0.00 0.00 1.82
2159 6676 6.007936 TGTCGGTTTTACATCTCCATTTTG 57.992 37.500 0.00 0.00 0.00 2.44
2163 6680 5.516339 CGGTTTTACATCTCCATTTTGCATC 59.484 40.000 0.00 0.00 0.00 3.91
2164 6681 6.397272 GGTTTTACATCTCCATTTTGCATCA 58.603 36.000 0.00 0.00 0.00 3.07
2165 6682 7.043565 GGTTTTACATCTCCATTTTGCATCAT 58.956 34.615 0.00 0.00 0.00 2.45
2166 6683 7.223387 GGTTTTACATCTCCATTTTGCATCATC 59.777 37.037 0.00 0.00 0.00 2.92
2167 6684 7.649533 TTTACATCTCCATTTTGCATCATCT 57.350 32.000 0.00 0.00 0.00 2.90
2168 6685 8.750515 TTTACATCTCCATTTTGCATCATCTA 57.249 30.769 0.00 0.00 0.00 1.98
2169 6686 8.929260 TTACATCTCCATTTTGCATCATCTAT 57.071 30.769 0.00 0.00 0.00 1.98
2170 6687 7.834881 ACATCTCCATTTTGCATCATCTATT 57.165 32.000 0.00 0.00 0.00 1.73
2171 6688 7.658261 ACATCTCCATTTTGCATCATCTATTG 58.342 34.615 0.00 0.00 0.00 1.90
2172 6689 6.644248 TCTCCATTTTGCATCATCTATTGG 57.356 37.500 0.00 0.00 0.00 3.16
2173 6690 6.367161 TCTCCATTTTGCATCATCTATTGGA 58.633 36.000 0.00 0.00 0.00 3.53
2174 6691 6.489022 TCTCCATTTTGCATCATCTATTGGAG 59.511 38.462 8.49 8.49 45.79 3.86
2175 6692 6.131264 TCCATTTTGCATCATCTATTGGAGT 58.869 36.000 0.00 0.00 0.00 3.85
2176 6693 6.608405 TCCATTTTGCATCATCTATTGGAGTT 59.392 34.615 0.00 0.00 0.00 3.01
2177 6694 6.700081 CCATTTTGCATCATCTATTGGAGTTG 59.300 38.462 0.00 0.00 0.00 3.16
2178 6695 4.906065 TTGCATCATCTATTGGAGTTGC 57.094 40.909 0.00 0.00 0.00 4.17
2179 6696 3.888583 TGCATCATCTATTGGAGTTGCA 58.111 40.909 0.00 0.00 35.86 4.08
2180 6697 3.628942 TGCATCATCTATTGGAGTTGCAC 59.371 43.478 0.00 0.00 34.43 4.57
2181 6698 3.881688 GCATCATCTATTGGAGTTGCACT 59.118 43.478 0.00 0.00 31.58 4.40
2182 6699 4.337555 GCATCATCTATTGGAGTTGCACTT 59.662 41.667 0.00 0.00 31.58 3.16
2183 6700 5.163581 GCATCATCTATTGGAGTTGCACTTT 60.164 40.000 0.00 0.00 31.58 2.66
2184 6701 6.626623 GCATCATCTATTGGAGTTGCACTTTT 60.627 38.462 0.00 0.00 31.58 2.27
2185 6702 7.415541 GCATCATCTATTGGAGTTGCACTTTTA 60.416 37.037 0.00 0.00 31.58 1.52
2186 6703 7.377766 TCATCTATTGGAGTTGCACTTTTAC 57.622 36.000 0.00 0.00 0.00 2.01
2187 6704 6.939730 TCATCTATTGGAGTTGCACTTTTACA 59.060 34.615 0.00 0.00 0.00 2.41
2188 6705 7.611467 TCATCTATTGGAGTTGCACTTTTACAT 59.389 33.333 0.00 0.00 0.00 2.29
2189 6706 7.377766 TCTATTGGAGTTGCACTTTTACATC 57.622 36.000 0.00 0.00 0.00 3.06
2190 6707 6.939730 TCTATTGGAGTTGCACTTTTACATCA 59.060 34.615 0.00 0.00 0.00 3.07
2191 6708 6.594788 ATTGGAGTTGCACTTTTACATCAT 57.405 33.333 0.00 0.00 0.00 2.45
2192 6709 5.627499 TGGAGTTGCACTTTTACATCATC 57.373 39.130 0.00 0.00 0.00 2.92
2193 6710 5.069318 TGGAGTTGCACTTTTACATCATCA 58.931 37.500 0.00 0.00 0.00 3.07
2194 6711 5.534278 TGGAGTTGCACTTTTACATCATCAA 59.466 36.000 0.00 0.00 0.00 2.57
2195 6712 6.209192 TGGAGTTGCACTTTTACATCATCAAT 59.791 34.615 0.00 0.00 0.00 2.57
2196 6713 7.392953 TGGAGTTGCACTTTTACATCATCAATA 59.607 33.333 0.00 0.00 0.00 1.90
2197 6714 8.408601 GGAGTTGCACTTTTACATCATCAATAT 58.591 33.333 0.00 0.00 0.00 1.28
2217 6734 9.481340 TCAATATACATCATCTGTTAGAGTTGC 57.519 33.333 0.00 0.00 39.39 4.17
2218 6735 8.715998 CAATATACATCATCTGTTAGAGTTGCC 58.284 37.037 0.00 0.00 39.39 4.52
2220 6737 4.764172 ACATCATCTGTTAGAGTTGCCTC 58.236 43.478 0.00 0.00 32.90 4.70
2223 6740 5.489792 TCATCTGTTAGAGTTGCCTCTTT 57.510 39.130 0.00 0.00 46.08 2.52
2280 6797 9.770097 TGTAAAATTTACATCTCCAAATTTGCA 57.230 25.926 13.93 0.00 41.26 4.08
2283 6800 9.504708 AAAATTTACATCTCCAAATTTGCATCA 57.495 25.926 12.92 0.00 41.26 3.07
2284 6801 9.675464 AAATTTACATCTCCAAATTTGCATCAT 57.325 25.926 12.92 0.00 40.83 2.45
2286 6803 7.649533 TTACATCTCCAAATTTGCATCATCT 57.350 32.000 12.92 0.00 0.00 2.90
2288 6805 7.834881 ACATCTCCAAATTTGCATCATCTAT 57.165 32.000 12.92 0.00 0.00 1.98
2290 6807 7.724506 ACATCTCCAAATTTGCATCATCTATCT 59.275 33.333 12.92 0.00 0.00 1.98
2291 6808 9.227777 CATCTCCAAATTTGCATCATCTATCTA 57.772 33.333 12.92 0.00 0.00 1.98
2294 6811 8.260270 TCCAAATTTGCATCATCTATCTATCG 57.740 34.615 12.92 0.00 0.00 2.92
2295 6812 8.096414 TCCAAATTTGCATCATCTATCTATCGA 58.904 33.333 12.92 0.00 0.00 3.59
2297 6814 9.756461 CAAATTTGCATCATCTATCTATCGAAG 57.244 33.333 5.01 0.00 0.00 3.79
2298 6815 9.716531 AAATTTGCATCATCTATCTATCGAAGA 57.283 29.630 0.00 0.00 45.75 2.87
2300 6817 8.699283 TTTGCATCATCTATCTATCGAAGATG 57.301 34.615 15.06 15.06 44.95 2.90
2301 6818 6.752335 GCATCATCTATCTATCGAAGATGC 57.248 41.667 16.01 14.74 44.95 3.91
2305 6822 7.936496 TCATCTATCTATCGAAGATGCTCTT 57.064 36.000 16.01 0.00 44.95 2.85
2306 6823 9.625747 ATCATCTATCTATCGAAGATGCTCTTA 57.374 33.333 16.01 3.07 44.95 2.10
2308 6825 9.502145 CATCTATCTATCGAAGATGCTCTTAAC 57.498 37.037 10.29 0.00 44.95 2.01
2309 6826 8.856153 TCTATCTATCGAAGATGCTCTTAACT 57.144 34.615 15.84 0.00 44.95 2.24
2310 6827 9.945904 TCTATCTATCGAAGATGCTCTTAACTA 57.054 33.333 15.84 0.00 44.95 2.24
2313 6830 8.046294 TCTATCGAAGATGCTCTTAACTATCC 57.954 38.462 0.00 0.00 45.12 2.59
2314 6831 5.455056 TCGAAGATGCTCTTAACTATCCC 57.545 43.478 0.00 0.00 36.73 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.678728 GGTGCCATCCACTCATTTCGA 60.679 52.381 0.00 0.00 44.08 3.71
15 16 2.914097 AGCTTGCTTGGTGGTGCC 60.914 61.111 0.00 0.00 37.90 5.01
16 17 1.737355 TTGAGCTTGCTTGGTGGTGC 61.737 55.000 0.00 0.00 0.00 5.01
17 18 0.746063 TTTGAGCTTGCTTGGTGGTG 59.254 50.000 0.00 0.00 0.00 4.17
18 19 0.746659 GTTTGAGCTTGCTTGGTGGT 59.253 50.000 0.00 0.00 0.00 4.16
19 20 0.746063 TGTTTGAGCTTGCTTGGTGG 59.254 50.000 0.00 0.00 0.00 4.61
20 21 2.806608 ATGTTTGAGCTTGCTTGGTG 57.193 45.000 0.00 0.00 0.00 4.17
21 22 2.694628 TGAATGTTTGAGCTTGCTTGGT 59.305 40.909 0.00 0.00 0.00 3.67
22 23 3.054878 GTGAATGTTTGAGCTTGCTTGG 58.945 45.455 0.00 0.00 0.00 3.61
23 24 2.722629 CGTGAATGTTTGAGCTTGCTTG 59.277 45.455 0.00 0.00 0.00 4.01
24 25 2.358898 ACGTGAATGTTTGAGCTTGCTT 59.641 40.909 0.00 0.00 0.00 3.91
25 26 1.949525 ACGTGAATGTTTGAGCTTGCT 59.050 42.857 0.00 0.00 0.00 3.91
33 34 2.046313 GCTTGAGCACGTGAATGTTTG 58.954 47.619 22.23 3.47 41.59 2.93
60 61 6.670902 AGAGTACTAGAGTAGGATAGGGCTAG 59.329 46.154 0.00 0.00 33.41 3.42
62 63 5.417755 AGAGTACTAGAGTAGGATAGGGCT 58.582 45.833 0.00 0.00 0.00 5.19
73 74 9.920946 ACAGTAGTAGTAGTAGAGTACTAGAGT 57.079 37.037 0.00 0.00 44.01 3.24
84 85 8.714179 GCACATCTCATACAGTAGTAGTAGTAG 58.286 40.741 0.00 0.00 32.86 2.57
90 91 7.168804 CACAATGCACATCTCATACAGTAGTAG 59.831 40.741 0.00 0.00 32.86 2.57
91 92 6.980397 CACAATGCACATCTCATACAGTAGTA 59.020 38.462 0.00 0.00 34.10 1.82
92 93 5.814188 CACAATGCACATCTCATACAGTAGT 59.186 40.000 0.00 0.00 0.00 2.73
93 94 5.277202 GCACAATGCACATCTCATACAGTAG 60.277 44.000 0.00 0.00 44.26 2.57
94 95 4.571984 GCACAATGCACATCTCATACAGTA 59.428 41.667 0.00 0.00 44.26 2.74
95 96 3.376234 GCACAATGCACATCTCATACAGT 59.624 43.478 0.00 0.00 44.26 3.55
96 97 3.545426 CGCACAATGCACATCTCATACAG 60.545 47.826 1.20 0.00 45.36 2.74
119 120 2.104111 AGACATCCTTTCGTGTTCCACA 59.896 45.455 0.00 0.00 33.40 4.17
130 131 0.033504 ACACGCACGAGACATCCTTT 59.966 50.000 0.00 0.00 0.00 3.11
132 133 0.667487 CAACACGCACGAGACATCCT 60.667 55.000 0.00 0.00 0.00 3.24
139 142 1.011242 CCAACACAACACGCACGAG 60.011 57.895 0.00 0.00 0.00 4.18
176 179 3.532155 TGCACCGTTGGTTTGGCC 61.532 61.111 0.00 0.00 31.02 5.36
197 218 1.073923 AGAAATATCATGCCCCCGTCC 59.926 52.381 0.00 0.00 0.00 4.79
454 1137 3.403322 ACCCTATGCCTCCTCCATTTAA 58.597 45.455 0.00 0.00 0.00 1.52
906 2073 0.389025 TGTGTGACAGTGTGCTCGAT 59.611 50.000 0.00 0.00 0.00 3.59
907 2074 0.527600 GTGTGTGACAGTGTGCTCGA 60.528 55.000 0.00 0.00 0.00 4.04
908 2075 1.490693 GGTGTGTGACAGTGTGCTCG 61.491 60.000 0.00 0.00 0.00 5.03
962 2170 0.321122 AGTGTGCTTCAGCTGGTAGC 60.321 55.000 25.54 25.54 42.84 3.58
1218 2491 3.491652 GCGTTCTCTGCTTCCGCC 61.492 66.667 0.00 0.00 38.52 6.13
1231 2507 1.078918 GGTACCTTAAGGCCGCGTT 60.079 57.895 21.92 3.26 39.32 4.84
1352 2715 4.282195 AGTCTCACTCGGACAAGAAGAAAT 59.718 41.667 0.00 0.00 36.29 2.17
1362 2725 2.733858 GCTGATTCAGTCTCACTCGGAC 60.734 54.545 14.90 0.00 33.43 4.79
1425 2810 3.653344 TCAGTCTCACTCGGACAATTTG 58.347 45.455 0.00 0.00 36.29 2.32
1429 2814 2.890945 TGATTCAGTCTCACTCGGACAA 59.109 45.455 0.00 0.00 36.29 3.18
1430 2815 2.489722 CTGATTCAGTCTCACTCGGACA 59.510 50.000 5.46 0.00 36.29 4.02
1431 2816 2.733858 GCTGATTCAGTCTCACTCGGAC 60.734 54.545 14.90 0.00 33.43 4.79
1432 2817 1.474478 GCTGATTCAGTCTCACTCGGA 59.526 52.381 14.90 0.00 33.43 4.55
1434 2819 2.423185 AGAGCTGATTCAGTCTCACTCG 59.577 50.000 25.97 1.65 37.22 4.18
1435 2820 3.443329 TCAGAGCTGATTCAGTCTCACTC 59.557 47.826 25.97 18.51 37.22 3.51
1437 2822 3.865011 TCAGAGCTGATTCAGTCTCAC 57.135 47.619 25.97 9.39 37.22 3.51
1438 2823 4.465305 TGATTCAGAGCTGATTCAGTCTCA 59.535 41.667 25.97 15.08 41.92 3.27
1439 2824 5.008619 TGATTCAGAGCTGATTCAGTCTC 57.991 43.478 20.96 20.96 41.92 3.36
1444 2829 3.908643 AGCTGATTCAGAGCTGATTCA 57.091 42.857 17.87 18.56 45.28 2.57
1451 2836 5.207110 TGGTATTAGAGCTGATTCAGAGC 57.793 43.478 17.87 7.84 36.65 4.09
1452 2837 6.215121 CACTGGTATTAGAGCTGATTCAGAG 58.785 44.000 17.87 4.28 32.44 3.35
1453 2838 5.452496 GCACTGGTATTAGAGCTGATTCAGA 60.452 44.000 17.87 0.00 32.44 3.27
1454 2839 4.749099 GCACTGGTATTAGAGCTGATTCAG 59.251 45.833 9.40 9.40 32.50 3.02
1455 2840 4.162131 TGCACTGGTATTAGAGCTGATTCA 59.838 41.667 0.00 0.00 35.64 2.57
1456 2841 4.509600 GTGCACTGGTATTAGAGCTGATTC 59.490 45.833 10.32 0.00 35.64 2.52
1457 2842 4.446371 GTGCACTGGTATTAGAGCTGATT 58.554 43.478 10.32 0.00 35.64 2.57
1458 2843 3.181461 GGTGCACTGGTATTAGAGCTGAT 60.181 47.826 17.98 0.00 35.64 2.90
1459 2844 2.168521 GGTGCACTGGTATTAGAGCTGA 59.831 50.000 17.98 0.00 35.64 4.26
1460 2845 2.093500 TGGTGCACTGGTATTAGAGCTG 60.093 50.000 17.98 0.00 35.64 4.24
1461 2846 2.169352 CTGGTGCACTGGTATTAGAGCT 59.831 50.000 17.98 0.00 35.64 4.09
1462 2847 2.093447 ACTGGTGCACTGGTATTAGAGC 60.093 50.000 17.98 0.00 35.26 4.09
1463 2848 3.895232 ACTGGTGCACTGGTATTAGAG 57.105 47.619 17.98 1.98 0.00 2.43
1464 2849 3.132289 GCTACTGGTGCACTGGTATTAGA 59.868 47.826 17.98 0.10 0.00 2.10
1465 2850 3.118775 TGCTACTGGTGCACTGGTATTAG 60.119 47.826 17.98 10.75 35.31 1.73
1468 2853 1.275666 TGCTACTGGTGCACTGGTAT 58.724 50.000 17.98 0.91 35.31 2.73
1471 2856 0.036105 TGATGCTACTGGTGCACTGG 60.036 55.000 17.98 12.05 43.59 4.00
1496 2881 8.652810 AAATTGTTTGATTGCTTCCTATATGC 57.347 30.769 0.00 0.00 0.00 3.14
1507 2914 6.660722 TGCATTGAGAAAATTGTTTGATTGC 58.339 32.000 0.00 0.00 0.00 3.56
1515 2922 8.842358 AATTCATCTTGCATTGAGAAAATTGT 57.158 26.923 8.61 0.00 29.17 2.71
1539 3021 8.140628 TCGTTTCATCATCCAAAAGAAAATGAA 58.859 29.630 0.00 0.00 37.54 2.57
1540 3022 7.656412 TCGTTTCATCATCCAAAAGAAAATGA 58.344 30.769 0.00 0.00 31.26 2.57
1542 3024 7.092716 CCTCGTTTCATCATCCAAAAGAAAAT 58.907 34.615 0.00 0.00 30.91 1.82
1627 3189 0.179265 GATAGCGCGCATGATTGACG 60.179 55.000 35.10 0.00 0.00 4.35
1628 3190 0.179265 CGATAGCGCGCATGATTGAC 60.179 55.000 35.10 13.53 0.00 3.18
1642 3618 1.300233 GGAACAGCGGAGGCGATAG 60.300 63.158 0.00 0.00 46.35 2.08
1647 3623 2.202756 CTACGGAACAGCGGAGGC 60.203 66.667 0.00 0.00 40.37 4.70
1724 3715 3.052081 CGGGGCCTCTCTAATCCG 58.948 66.667 0.00 0.00 0.00 4.18
1774 5369 3.065371 CGCTTTGGCTTATCCTCGAAAAT 59.935 43.478 0.00 0.00 36.09 1.82
1779 5374 1.089481 TGCGCTTTGGCTTATCCTCG 61.089 55.000 9.73 0.00 36.09 4.63
1780 5375 1.094785 TTGCGCTTTGGCTTATCCTC 58.905 50.000 9.73 0.00 36.09 3.71
1781 5376 1.474077 CTTTGCGCTTTGGCTTATCCT 59.526 47.619 9.73 0.00 36.09 3.24
1783 5378 1.472480 TCCTTTGCGCTTTGGCTTATC 59.528 47.619 9.73 0.00 36.09 1.75
1784 5379 1.544724 TCCTTTGCGCTTTGGCTTAT 58.455 45.000 9.73 0.00 36.09 1.73
1785 5380 1.472480 GATCCTTTGCGCTTTGGCTTA 59.528 47.619 9.73 0.00 36.09 3.09
1790 5385 1.078709 TCTCGATCCTTTGCGCTTTG 58.921 50.000 9.73 0.00 0.00 2.77
1792 5387 1.078759 CGTCTCGATCCTTTGCGCTT 61.079 55.000 9.73 0.00 0.00 4.68
1837 5449 3.889196 TCAATTTTCCCTTTGTCGTCG 57.111 42.857 0.00 0.00 0.00 5.12
1878 5490 5.681880 CAAGTTTCCGTGTCGCTTTATAAA 58.318 37.500 0.00 0.00 0.00 1.40
1881 5493 2.095919 GCAAGTTTCCGTGTCGCTTTAT 60.096 45.455 0.00 0.00 0.00 1.40
1910 5534 5.441500 TCCGAAAATAATGGGATTGCTACA 58.558 37.500 0.00 0.00 0.00 2.74
1920 5544 8.194104 TGTGGATAACATTTCCGAAAATAATGG 58.806 33.333 0.00 0.00 35.94 3.16
1942 5566 7.122650 ACATGACAATTTTACCTATCCTTGTGG 59.877 37.037 0.00 0.00 0.00 4.17
1944 5568 9.747898 TTACATGACAATTTTACCTATCCTTGT 57.252 29.630 0.00 0.00 0.00 3.16
1946 5570 8.903820 GCTTACATGACAATTTTACCTATCCTT 58.096 33.333 0.00 0.00 0.00 3.36
1962 6207 5.588648 TGGGCTTATAGTTTGCTTACATGAC 59.411 40.000 0.00 0.00 0.00 3.06
1970 6215 1.280998 ACGGTGGGCTTATAGTTTGCT 59.719 47.619 0.00 0.00 0.00 3.91
1976 6221 3.814005 AGTACAACGGTGGGCTTATAG 57.186 47.619 4.97 0.00 0.00 1.31
1977 6222 3.864243 CAAGTACAACGGTGGGCTTATA 58.136 45.455 4.97 0.00 0.00 0.98
1981 6226 1.599797 GCAAGTACAACGGTGGGCT 60.600 57.895 4.97 0.00 0.00 5.19
1985 6230 3.299340 AGTAGAGCAAGTACAACGGTG 57.701 47.619 0.00 0.00 0.00 4.94
2008 6253 5.331902 TCTTCTTCGAAGCAACAAAAACTG 58.668 37.500 20.56 0.00 0.00 3.16
2010 6255 5.569413 TCTCTTCTTCGAAGCAACAAAAAC 58.431 37.500 20.56 0.00 0.00 2.43
2015 6260 3.804325 CACTTCTCTTCTTCGAAGCAACA 59.196 43.478 20.56 0.00 40.12 3.33
2018 6263 2.224042 TGCACTTCTCTTCTTCGAAGCA 60.224 45.455 20.56 8.99 40.12 3.91
2019 6264 2.408050 TGCACTTCTCTTCTTCGAAGC 58.592 47.619 20.56 6.04 40.12 3.86
2020 6265 4.054671 AGTTGCACTTCTCTTCTTCGAAG 58.945 43.478 19.35 19.35 41.74 3.79
2023 6268 2.734079 GGAGTTGCACTTCTCTTCTTCG 59.266 50.000 10.98 0.00 0.00 3.79
2024 6269 3.733337 TGGAGTTGCACTTCTCTTCTTC 58.267 45.455 10.98 0.00 0.00 2.87
2025 6270 3.845781 TGGAGTTGCACTTCTCTTCTT 57.154 42.857 10.98 0.00 0.00 2.52
2027 6272 5.482908 TCTATTGGAGTTGCACTTCTCTTC 58.517 41.667 10.98 0.00 0.00 2.87
2029 6274 5.690464 ATCTATTGGAGTTGCACTTCTCT 57.310 39.130 10.98 0.00 0.00 3.10
2031 6276 5.809001 TCAATCTATTGGAGTTGCACTTCT 58.191 37.500 3.00 0.00 38.30 2.85
2033 6278 7.994911 TCATATCAATCTATTGGAGTTGCACTT 59.005 33.333 3.00 0.00 38.30 3.16
2034 6279 7.512130 TCATATCAATCTATTGGAGTTGCACT 58.488 34.615 3.00 0.00 38.30 4.40
2035 6280 7.734924 TCATATCAATCTATTGGAGTTGCAC 57.265 36.000 3.00 0.00 38.30 4.57
2037 6282 7.094506 TGCATCATATCAATCTATTGGAGTTGC 60.095 37.037 3.00 7.73 38.30 4.17
2038 6283 8.235226 GTGCATCATATCAATCTATTGGAGTTG 58.765 37.037 3.00 0.00 38.30 3.16
2039 6284 7.118825 CGTGCATCATATCAATCTATTGGAGTT 59.881 37.037 3.00 0.00 38.30 3.01
2040 6285 6.592994 CGTGCATCATATCAATCTATTGGAGT 59.407 38.462 3.00 0.00 38.30 3.85
2041 6286 6.592994 ACGTGCATCATATCAATCTATTGGAG 59.407 38.462 3.00 0.00 38.30 3.86
2044 6289 8.071967 ACAAACGTGCATCATATCAATCTATTG 58.928 33.333 0.00 0.00 39.10 1.90
2045 6290 8.158169 ACAAACGTGCATCATATCAATCTATT 57.842 30.769 0.00 0.00 0.00 1.73
2046 6291 7.734924 ACAAACGTGCATCATATCAATCTAT 57.265 32.000 0.00 0.00 0.00 1.98
2047 6292 7.408910 CAACAAACGTGCATCATATCAATCTA 58.591 34.615 0.00 0.00 0.00 1.98
2048 6293 6.260377 CAACAAACGTGCATCATATCAATCT 58.740 36.000 0.00 0.00 0.00 2.40
2049 6294 5.456497 CCAACAAACGTGCATCATATCAATC 59.544 40.000 0.00 0.00 0.00 2.67
2053 6298 4.355543 ACCAACAAACGTGCATCATATC 57.644 40.909 0.00 0.00 0.00 1.63
2054 6299 5.182487 TCTACCAACAAACGTGCATCATAT 58.818 37.500 0.00 0.00 0.00 1.78
2055 6300 4.570930 TCTACCAACAAACGTGCATCATA 58.429 39.130 0.00 0.00 0.00 2.15
2056 6301 3.407698 TCTACCAACAAACGTGCATCAT 58.592 40.909 0.00 0.00 0.00 2.45
2058 6303 3.889196 TTCTACCAACAAACGTGCATC 57.111 42.857 0.00 0.00 0.00 3.91
2059 6304 4.518970 AGATTTCTACCAACAAACGTGCAT 59.481 37.500 0.00 0.00 0.00 3.96
2061 6306 4.024387 TCAGATTTCTACCAACAAACGTGC 60.024 41.667 0.00 0.00 0.00 5.34
2062 6307 5.666969 TCAGATTTCTACCAACAAACGTG 57.333 39.130 0.00 0.00 0.00 4.49
2063 6308 6.877611 ATTCAGATTTCTACCAACAAACGT 57.122 33.333 0.00 0.00 0.00 3.99
2064 6309 7.138736 ACAATTCAGATTTCTACCAACAAACG 58.861 34.615 0.00 0.00 0.00 3.60
2068 6313 8.243426 GCAATACAATTCAGATTTCTACCAACA 58.757 33.333 0.00 0.00 0.00 3.33
2069 6314 8.462016 AGCAATACAATTCAGATTTCTACCAAC 58.538 33.333 0.00 0.00 0.00 3.77
2071 6316 9.851686 ATAGCAATACAATTCAGATTTCTACCA 57.148 29.630 0.00 0.00 0.00 3.25
2086 6331 9.409312 CACTTCAACATTCAAATAGCAATACAA 57.591 29.630 0.00 0.00 0.00 2.41
2087 6332 8.575589 ACACTTCAACATTCAAATAGCAATACA 58.424 29.630 0.00 0.00 0.00 2.29
2088 6333 8.853345 CACACTTCAACATTCAAATAGCAATAC 58.147 33.333 0.00 0.00 0.00 1.89
2089 6334 8.028354 CCACACTTCAACATTCAAATAGCAATA 58.972 33.333 0.00 0.00 0.00 1.90
2090 6335 6.869913 CCACACTTCAACATTCAAATAGCAAT 59.130 34.615 0.00 0.00 0.00 3.56
2091 6336 6.215121 CCACACTTCAACATTCAAATAGCAA 58.785 36.000 0.00 0.00 0.00 3.91
2092 6337 5.771469 CCACACTTCAACATTCAAATAGCA 58.229 37.500 0.00 0.00 0.00 3.49
2093 6338 4.622740 GCCACACTTCAACATTCAAATAGC 59.377 41.667 0.00 0.00 0.00 2.97
2094 6339 5.860182 CAGCCACACTTCAACATTCAAATAG 59.140 40.000 0.00 0.00 0.00 1.73
2095 6340 5.301551 ACAGCCACACTTCAACATTCAAATA 59.698 36.000 0.00 0.00 0.00 1.40
2096 6341 4.099881 ACAGCCACACTTCAACATTCAAAT 59.900 37.500 0.00 0.00 0.00 2.32
2097 6342 3.446873 ACAGCCACACTTCAACATTCAAA 59.553 39.130 0.00 0.00 0.00 2.69
2098 6343 3.023119 ACAGCCACACTTCAACATTCAA 58.977 40.909 0.00 0.00 0.00 2.69
2099 6344 2.653726 ACAGCCACACTTCAACATTCA 58.346 42.857 0.00 0.00 0.00 2.57
2100 6345 3.563808 TGTACAGCCACACTTCAACATTC 59.436 43.478 0.00 0.00 0.00 2.67
2101 6346 3.550820 TGTACAGCCACACTTCAACATT 58.449 40.909 0.00 0.00 0.00 2.71
2102 6347 3.207265 TGTACAGCCACACTTCAACAT 57.793 42.857 0.00 0.00 0.00 2.71
2103 6348 2.680841 GTTGTACAGCCACACTTCAACA 59.319 45.455 0.00 0.00 34.63 3.33
2105 6350 1.937223 CGTTGTACAGCCACACTTCAA 59.063 47.619 3.94 0.00 0.00 2.69
2107 6352 0.865769 CCGTTGTACAGCCACACTTC 59.134 55.000 3.94 0.00 0.00 3.01
2108 6353 1.164041 GCCGTTGTACAGCCACACTT 61.164 55.000 3.94 0.00 0.00 3.16
2110 6355 2.613506 GGCCGTTGTACAGCCACAC 61.614 63.158 17.35 2.48 41.28 3.82
2111 6356 2.281208 GGCCGTTGTACAGCCACA 60.281 61.111 17.35 0.00 41.28 4.17
2112 6357 1.599797 AAGGCCGTTGTACAGCCAC 60.600 57.895 22.51 6.73 44.03 5.01
2113 6358 1.599518 CAAGGCCGTTGTACAGCCA 60.600 57.895 22.51 0.00 44.03 4.75
2114 6359 2.978018 GCAAGGCCGTTGTACAGCC 61.978 63.158 15.09 15.09 41.94 4.85
2116 6361 1.897398 GACGCAAGGCCGTTGTACAG 61.897 60.000 14.04 7.87 42.36 2.74
2117 6362 1.957186 GACGCAAGGCCGTTGTACA 60.957 57.895 14.04 0.00 42.36 2.90
2127 6372 1.193874 GTAAAACCGACAGACGCAAGG 59.806 52.381 0.00 0.00 46.39 3.61
2128 6373 1.862201 TGTAAAACCGACAGACGCAAG 59.138 47.619 0.00 0.00 41.07 4.01
2129 6374 1.937278 TGTAAAACCGACAGACGCAA 58.063 45.000 0.00 0.00 41.07 4.85
2130 6375 2.063266 GATGTAAAACCGACAGACGCA 58.937 47.619 0.00 0.00 41.07 5.24
2131 6376 2.334838 AGATGTAAAACCGACAGACGC 58.665 47.619 0.00 0.00 41.07 5.19
2133 6378 3.921677 TGGAGATGTAAAACCGACAGAC 58.078 45.455 0.00 0.00 0.00 3.51
2134 6379 4.819105 ATGGAGATGTAAAACCGACAGA 57.181 40.909 0.00 0.00 0.00 3.41
2136 6381 5.563867 GCAAAATGGAGATGTAAAACCGACA 60.564 40.000 0.00 0.00 0.00 4.35
2137 6382 4.857037 GCAAAATGGAGATGTAAAACCGAC 59.143 41.667 0.00 0.00 0.00 4.79
2138 6383 4.520874 TGCAAAATGGAGATGTAAAACCGA 59.479 37.500 0.00 0.00 0.00 4.69
2140 6385 6.397272 TGATGCAAAATGGAGATGTAAAACC 58.603 36.000 0.00 0.00 0.00 3.27
2141 6386 7.977853 AGATGATGCAAAATGGAGATGTAAAAC 59.022 33.333 0.00 0.00 0.00 2.43
2142 6387 8.070034 AGATGATGCAAAATGGAGATGTAAAA 57.930 30.769 0.00 0.00 0.00 1.52
2152 6669 6.401047 ACTCCAATAGATGATGCAAAATGG 57.599 37.500 0.00 0.00 0.00 3.16
2153 6670 6.200286 GCAACTCCAATAGATGATGCAAAATG 59.800 38.462 0.00 0.00 29.65 2.32
2158 6675 3.628942 GTGCAACTCCAATAGATGATGCA 59.371 43.478 0.00 0.00 29.65 3.96
2159 6676 4.220533 GTGCAACTCCAATAGATGATGC 57.779 45.455 0.00 0.00 29.65 3.91
2191 6708 9.481340 GCAACTCTAACAGATGATGTATATTGA 57.519 33.333 0.00 0.00 43.00 2.57
2192 6709 8.715998 GGCAACTCTAACAGATGATGTATATTG 58.284 37.037 0.00 0.00 43.00 1.90
2193 6710 8.839310 GGCAACTCTAACAGATGATGTATATT 57.161 34.615 0.00 0.00 43.00 1.28
2254 6771 9.770097 TGCAAATTTGGAGATGTAAATTTTACA 57.230 25.926 20.94 20.94 41.80 2.41
2258 6775 9.675464 ATGATGCAAATTTGGAGATGTAAATTT 57.325 25.926 19.47 0.00 43.46 1.82
2259 6776 9.321562 GATGATGCAAATTTGGAGATGTAAATT 57.678 29.630 19.47 0.00 37.92 1.82
2260 6777 8.701895 AGATGATGCAAATTTGGAGATGTAAAT 58.298 29.630 19.47 0.00 30.13 1.40
2262 6779 7.649533 AGATGATGCAAATTTGGAGATGTAA 57.350 32.000 19.47 0.00 30.13 2.41
2263 6780 8.929260 ATAGATGATGCAAATTTGGAGATGTA 57.071 30.769 19.47 14.57 30.13 2.29
2264 6781 7.724506 AGATAGATGATGCAAATTTGGAGATGT 59.275 33.333 19.47 13.08 30.13 3.06
2265 6782 8.112016 AGATAGATGATGCAAATTTGGAGATG 57.888 34.615 19.47 0.00 30.13 2.90
2266 6783 9.976776 ATAGATAGATGATGCAAATTTGGAGAT 57.023 29.630 19.47 12.52 30.13 2.75
2268 6785 8.388853 CGATAGATAGATGATGCAAATTTGGAG 58.611 37.037 19.47 0.00 39.76 3.86
2269 6786 8.096414 TCGATAGATAGATGATGCAAATTTGGA 58.904 33.333 19.47 17.40 42.67 3.53
2270 6787 8.260270 TCGATAGATAGATGATGCAAATTTGG 57.740 34.615 19.47 2.11 42.67 3.28


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

AutoCloner maintained by Alex Coulton.