Multiple sequence alignment - TraesCS6B01G179500

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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 TraesCS6B01G179500 chr6B 100.000 8424 0 0 1 8424 199759175 199767598 0.000000e+00 15557.0
1 TraesCS6B01G179500 chr6B 97.674 86 2 0 3691 3776 343032935 343032850 1.890000e-31 148.0
2 TraesCS6B01G179500 chr6B 95.652 92 2 2 3687 3776 694537978 694538069 6.810000e-31 147.0
3 TraesCS6B01G179500 chr6D 95.502 5024 151 28 763 5739 110878482 110883477 0.000000e+00 7956.0
4 TraesCS6B01G179500 chr6D 97.591 1702 28 8 5739 7432 110883552 110885248 0.000000e+00 2904.0
5 TraesCS6B01G179500 chr6D 90.558 932 50 14 7516 8422 110885228 110886146 0.000000e+00 1199.0
6 TraesCS6B01G179500 chr6D 97.674 86 2 0 3691 3776 36114548 36114633 1.890000e-31 148.0
7 TraesCS6B01G179500 chr6A 98.004 1904 33 2 3841 5740 135244618 135246520 0.000000e+00 3301.0
8 TraesCS6B01G179500 chr6A 96.882 1700 41 7 5739 7432 135246594 135248287 0.000000e+00 2835.0
9 TraesCS6B01G179500 chr6A 95.719 1752 52 5 2170 3902 135242871 135244618 0.000000e+00 2798.0
10 TraesCS6B01G179500 chr6A 88.184 1151 78 30 763 1888 135239548 135240665 0.000000e+00 1319.0
11 TraesCS6B01G179500 chr6A 85.237 718 78 11 2 711 472346223 472346920 0.000000e+00 713.0
12 TraesCS6B01G179500 chr6A 89.016 437 28 8 7897 8326 135248913 135249336 2.690000e-144 523.0
13 TraesCS6B01G179500 chr6A 94.237 295 14 3 1890 2184 135240906 135241197 1.670000e-121 448.0
14 TraesCS6B01G179500 chr6A 90.179 336 19 3 7519 7842 135248272 135248605 7.820000e-115 425.0
15 TraesCS6B01G179500 chr6A 89.189 74 7 1 8336 8408 135249879 135249952 3.240000e-14 91.6
16 TraesCS6B01G179500 chr6A 94.231 52 3 0 711 762 472346953 472347004 7.010000e-11 80.5
17 TraesCS6B01G179500 chr6A 95.918 49 2 0 714 762 613739044 613738996 7.010000e-11 80.5
18 TraesCS6B01G179500 chr5B 93.417 714 41 4 2 711 662010777 662010066 0.000000e+00 1053.0
19 TraesCS6B01G179500 chr5B 85.472 530 65 4 187 711 427280275 427280797 7.440000e-150 542.0
20 TraesCS6B01G179500 chr5B 98.077 52 1 0 714 765 662010030 662009979 3.240000e-14 91.6
21 TraesCS6B01G179500 chr5B 89.831 59 6 0 711 769 662012242 662012300 9.070000e-10 76.8
22 TraesCS6B01G179500 chr3B 94.318 528 27 3 185 711 605296229 605296754 0.000000e+00 806.0
23 TraesCS6B01G179500 chr3B 83.425 181 24 4 557 732 605294608 605294429 6.770000e-36 163.0
24 TraesCS6B01G179500 chr3B 94.949 99 5 0 2 100 605295898 605295996 1.130000e-33 156.0
25 TraesCS6B01G179500 chr3B 94.737 57 3 0 706 762 605296782 605296838 1.160000e-13 89.8
26 TraesCS6B01G179500 chr4A 93.110 537 35 2 171 706 648906424 648906959 0.000000e+00 785.0
27 TraesCS6B01G179500 chr4A 94.558 147 7 1 3094 3239 682754625 682754771 8.510000e-55 226.0
28 TraesCS6B01G179500 chr4A 94.643 56 3 0 711 766 648906996 648907051 4.190000e-13 87.9
29 TraesCS6B01G179500 chr4B 88.433 536 54 5 181 711 579424254 579424786 2.560000e-179 640.0
30 TraesCS6B01G179500 chr4B 84.786 585 69 12 185 760 562622759 562622186 3.410000e-158 569.0
31 TraesCS6B01G179500 chr4B 91.447 152 9 3 3094 3242 516951178 516951328 1.110000e-48 206.0
32 TraesCS6B01G179500 chr4B 96.154 52 1 1 711 762 579424819 579424869 5.420000e-12 84.2
33 TraesCS6B01G179500 chr2A 85.747 442 46 7 218 649 766295583 766295149 1.290000e-122 451.0
34 TraesCS6B01G179500 chr2A 94.444 54 3 0 706 759 770091201 770091254 5.420000e-12 84.2
35 TraesCS6B01G179500 chr2A 93.617 47 2 1 7463 7508 749969819 749969865 1.520000e-07 69.4
36 TraesCS6B01G179500 chr5D 88.509 322 25 4 323 639 371832064 371831750 6.170000e-101 379.0
37 TraesCS6B01G179500 chr5D 90.506 158 11 4 3094 3249 397941260 397941415 1.110000e-48 206.0
38 TraesCS6B01G179500 chr5D 94.118 102 6 0 2 103 371832163 371832062 1.130000e-33 156.0
39 TraesCS6B01G179500 chr5D 95.238 84 3 1 7434 7517 45632964 45632882 1.910000e-26 132.0
40 TraesCS6B01G179500 chr3D 92.517 147 10 1 3094 3239 562562316 562562462 8.570000e-50 209.0
41 TraesCS6B01G179500 chr3D 89.506 162 15 2 3090 3250 488863582 488863422 3.990000e-48 204.0
42 TraesCS6B01G179500 chr3D 97.674 86 2 0 3691 3776 498226159 498226244 1.890000e-31 148.0
43 TraesCS6B01G179500 chr3D 80.315 127 23 1 190 314 516072962 516072836 2.500000e-15 95.3
44 TraesCS6B01G179500 chr7D 90.909 154 11 3 3094 3244 464086605 464086452 3.990000e-48 204.0
45 TraesCS6B01G179500 chr7B 90.850 153 12 2 3093 3244 665284788 665284939 3.990000e-48 204.0
46 TraesCS6B01G179500 chr7B 89.189 111 10 1 3689 3797 461476085 461475975 4.100000e-28 137.0
47 TraesCS6B01G179500 chr4D 97.701 87 2 0 3691 3777 72256162 72256248 5.270000e-32 150.0
48 TraesCS6B01G179500 chr4D 90.654 107 7 2 3673 3776 437825625 437825519 1.140000e-28 139.0
49 TraesCS6B01G179500 chr4D 91.667 48 4 0 8329 8376 85394048 85394001 5.460000e-07 67.6
50 TraesCS6B01G179500 chr4D 91.667 48 4 0 8329 8376 241389418 241389465 5.460000e-07 67.6
51 TraesCS6B01G179500 chr4D 91.667 48 4 0 8329 8376 450996914 450996867 5.460000e-07 67.6
52 TraesCS6B01G179500 chr4D 91.667 48 4 0 8329 8376 451004780 451004827 5.460000e-07 67.6
53 TraesCS6B01G179500 chr2D 82.031 128 20 3 190 314 35536049 35535922 1.160000e-18 106.0
54 TraesCS6B01G179500 chr2D 84.375 64 9 1 2 64 629456210 629456273 2.540000e-05 62.1
55 TraesCS6B01G179500 chr5A 87.209 86 9 2 7436 7521 573080583 573080666 6.960000e-16 97.1
56 TraesCS6B01G179500 chr7A 96.364 55 2 0 7463 7517 667744536 667744590 3.240000e-14 91.6
57 TraesCS6B01G179500 chr1D 82.979 94 15 1 2 94 481471783 481471690 5.420000e-12 84.2
58 TraesCS6B01G179500 chr1B 82.796 93 15 1 2 93 670029739 670029831 1.950000e-11 82.4
59 TraesCS6B01G179500 chrUn 91.667 48 4 0 8329 8376 182435148 182435101 5.460000e-07 67.6
60 TraesCS6B01G179500 chrUn 91.667 48 4 0 8329 8376 182464640 182464593 5.460000e-07 67.6
61 TraesCS6B01G179500 chrUn 91.667 48 4 0 8329 8376 301691232 301691279 5.460000e-07 67.6


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 TraesCS6B01G179500 chr6B 199759175 199767598 8423 False 15557.000000 15557 100.000000 1 8424 1 chr6B.!!$F1 8423
1 TraesCS6B01G179500 chr6D 110878482 110886146 7664 False 4019.666667 7956 94.550333 763 8422 3 chr6D.!!$F2 7659
2 TraesCS6B01G179500 chr6A 135239548 135249952 10404 False 1467.575000 3301 92.676250 763 8408 8 chr6A.!!$F1 7645
3 TraesCS6B01G179500 chr6A 472346223 472347004 781 False 396.750000 713 89.734000 2 762 2 chr6A.!!$F2 760
4 TraesCS6B01G179500 chr5B 662009979 662010777 798 True 572.300000 1053 95.747000 2 765 2 chr5B.!!$R1 763
5 TraesCS6B01G179500 chr5B 427280275 427280797 522 False 542.000000 542 85.472000 187 711 1 chr5B.!!$F1 524
6 TraesCS6B01G179500 chr3B 605295898 605296838 940 False 350.600000 806 94.668000 2 762 3 chr3B.!!$F1 760
7 TraesCS6B01G179500 chr4A 648906424 648907051 627 False 436.450000 785 93.876500 171 766 2 chr4A.!!$F2 595
8 TraesCS6B01G179500 chr4B 562622186 562622759 573 True 569.000000 569 84.786000 185 760 1 chr4B.!!$R1 575
9 TraesCS6B01G179500 chr4B 579424254 579424869 615 False 362.100000 640 92.293500 181 762 2 chr4B.!!$F2 581

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
692 850 0.029567 CGTGTAAGCCAAACGCCAAA 59.970 50.000 0.00 0.0 38.78 3.28 F
1327 1535 0.035725 GGAATTCGGGGAGTTTCGGT 60.036 55.000 0.00 0.0 0.00 4.69 F
1674 1887 0.033366 GCCATGGGCGTTTTGAAGTT 59.967 50.000 15.13 0.0 39.62 2.66 F
1878 2099 0.464452 GGACGCCTATGCTTACCACT 59.536 55.000 0.00 0.0 34.43 4.00 F
2843 5026 1.692411 GGAAAACTTGGTCCTGCTGT 58.308 50.000 0.00 0.0 0.00 4.40 F
4397 6648 1.404583 GGGGCTGCAATTCATGTTGTC 60.405 52.381 0.50 0.0 0.00 3.18 F
5490 7742 0.331278 TTAAGGACTGTGGGCATGGG 59.669 55.000 0.00 0.0 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 1868 0.033366 AACTTCAAAACGCCCATGGC 59.967 50.000 6.09 0.58 46.75 4.40 R
2138 2598 1.606737 GCCCAGAGATAGCGCTTTAGG 60.607 57.143 18.68 9.61 0.00 2.69 R
3084 5267 1.679898 CCCCGTCCTCTGAGCTTTT 59.320 57.895 0.00 0.00 0.00 2.27 R
3565 5750 3.072915 AGAATTGACACTGACCACATGGA 59.927 43.478 4.53 0.00 38.94 3.41 R
4445 6696 4.708421 ACAACAATATCAAGCTTGGCAGAT 59.292 37.500 25.73 14.23 32.27 2.90 R
5573 7825 0.615331 GGTGAACAGAGATCAGGGCA 59.385 55.000 0.00 0.00 0.00 5.36 R
7467 9801 0.038159 GGAGACTCGTGTTCTGGTGG 60.038 60.000 0.00 0.00 0.00 4.61 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
45 46 1.257750 CCCTCTGTCCGGTCACATCA 61.258 60.000 0.00 0.00 0.00 3.07
89 90 2.980233 GCTATGGGCCGGCATGAC 60.980 66.667 30.85 15.61 34.27 3.06
260 409 2.915659 TTCCGCGGTCTGGACAGT 60.916 61.111 27.15 0.00 34.56 3.55
291 440 0.881118 GAATGCAGAAGGTTTGCGGA 59.119 50.000 0.00 0.00 44.40 5.54
451 600 4.915158 ACGAGTAGTTATCTAAGCCACC 57.085 45.455 0.00 0.00 0.00 4.61
452 601 4.275810 ACGAGTAGTTATCTAAGCCACCA 58.724 43.478 0.00 0.00 0.00 4.17
494 643 0.527385 GCACTCAGAGAAGCTAGCGG 60.527 60.000 9.55 0.00 0.00 5.52
569 723 3.190535 GTGACCAAACGCCAAGATTATGT 59.809 43.478 0.00 0.00 0.00 2.29
590 744 1.314730 GTTTCCTCCAAACGCCAAGA 58.685 50.000 0.00 0.00 35.26 3.02
616 770 1.868997 CGTCTCGCTTTGCCATGTT 59.131 52.632 0.00 0.00 0.00 2.71
632 786 3.758554 CCATGTTAGCACCAACTAAGCTT 59.241 43.478 3.48 3.48 39.68 3.74
692 850 0.029567 CGTGTAAGCCAAACGCCAAA 59.970 50.000 0.00 0.00 38.78 3.28
766 956 2.676748 AGCAGAAAATTTGTCCACCCA 58.323 42.857 0.00 0.00 0.00 4.51
767 957 3.242011 AGCAGAAAATTTGTCCACCCAT 58.758 40.909 0.00 0.00 0.00 4.00
856 1053 9.444600 TTGGGCTTTCGGATAGAATATATTTAC 57.555 33.333 0.00 0.00 38.86 2.01
857 1054 8.598916 TGGGCTTTCGGATAGAATATATTTACA 58.401 33.333 0.00 0.00 38.86 2.41
862 1059 8.975410 TTCGGATAGAATATATTTACACCACG 57.025 34.615 0.00 0.55 33.14 4.94
863 1060 7.031372 TCGGATAGAATATATTTACACCACGC 58.969 38.462 0.00 0.00 0.00 5.34
864 1061 7.033791 CGGATAGAATATATTTACACCACGCT 58.966 38.462 0.00 0.00 0.00 5.07
887 1087 4.953868 CCGCGGACACGTCACCAA 62.954 66.667 24.07 0.00 43.45 3.67
888 1088 2.736995 CGCGGACACGTCACCAAT 60.737 61.111 0.00 0.00 43.45 3.16
890 1090 1.666553 GCGGACACGTCACCAATCA 60.667 57.895 8.05 0.00 43.45 2.57
1036 1240 1.452226 TTCTCTCCCCTCACCTCCCA 61.452 60.000 0.00 0.00 0.00 4.37
1085 1289 4.547367 CCGACCCCGAATCCAGCC 62.547 72.222 0.00 0.00 38.22 4.85
1187 1395 4.208686 GGCCTCGCTCGATTCGGT 62.209 66.667 6.18 0.00 0.00 4.69
1316 1524 0.322456 TTGCCAGGTCAGGAATTCGG 60.322 55.000 0.00 0.00 0.00 4.30
1317 1525 1.452108 GCCAGGTCAGGAATTCGGG 60.452 63.158 0.00 0.00 0.00 5.14
1318 1526 1.224592 CCAGGTCAGGAATTCGGGG 59.775 63.158 0.00 0.00 0.00 5.73
1324 1532 2.357075 GTCAGGAATTCGGGGAGTTTC 58.643 52.381 0.00 0.00 0.00 2.78
1325 1533 1.066430 TCAGGAATTCGGGGAGTTTCG 60.066 52.381 0.00 0.00 0.00 3.46
1327 1535 0.035725 GGAATTCGGGGAGTTTCGGT 60.036 55.000 0.00 0.00 0.00 4.69
1328 1536 1.084289 GAATTCGGGGAGTTTCGGTG 58.916 55.000 0.00 0.00 0.00 4.94
1355 1563 5.920273 CCTTTTAAGTGCGTGATGTGATTTT 59.080 36.000 0.00 0.00 0.00 1.82
1357 1565 2.880822 AGTGCGTGATGTGATTTTCG 57.119 45.000 0.00 0.00 0.00 3.46
1369 1577 4.740268 TGTGATTTTCGTATAGTCGTGCT 58.260 39.130 0.00 0.00 0.00 4.40
1371 1579 4.796830 GTGATTTTCGTATAGTCGTGCTGA 59.203 41.667 0.00 0.00 0.00 4.26
1375 1583 3.249013 TCGTATAGTCGTGCTGATTCG 57.751 47.619 0.00 0.00 0.00 3.34
1411 1619 0.468029 CCAGTGGAGTTGCTTGGGTT 60.468 55.000 1.68 0.00 0.00 4.11
1412 1620 1.402787 CAGTGGAGTTGCTTGGGTTT 58.597 50.000 0.00 0.00 0.00 3.27
1427 1635 2.502130 TGGGTTTGTATGCTGGATCGTA 59.498 45.455 0.00 0.00 0.00 3.43
1432 1640 5.794687 TTTGTATGCTGGATCGTACAAAG 57.205 39.130 13.92 0.00 45.74 2.77
1435 1643 0.613260 TGCTGGATCGTACAAAGGCT 59.387 50.000 0.00 0.00 0.00 4.58
1444 1652 4.177165 TCGTACAAAGGCTTTCGTGATA 57.823 40.909 10.08 0.00 0.00 2.15
1453 1661 1.767289 CTTTCGTGATATAGCGCCGT 58.233 50.000 2.29 0.00 0.00 5.68
1484 1692 6.378280 GGTGCTATATAATTGGGATTTGGGAG 59.622 42.308 0.00 0.00 0.00 4.30
1487 1695 7.669722 TGCTATATAATTGGGATTTGGGAGTTC 59.330 37.037 0.00 0.00 0.00 3.01
1491 1700 3.611025 TTGGGATTTGGGAGTTCTGTT 57.389 42.857 0.00 0.00 0.00 3.16
1505 1714 5.429957 AGTTCTGTTCAGATTTGTTGCTC 57.570 39.130 3.28 0.00 0.00 4.26
1516 1725 1.514003 TTGTTGCTCGCGATTTGGTA 58.486 45.000 10.36 0.00 0.00 3.25
1620 1833 3.506455 AGTCTTCTAGTTGCTGCGTCTAA 59.494 43.478 0.00 0.00 0.00 2.10
1639 1852 7.361799 GCGTCTAACCATAACTTTGGAATTTCT 60.362 37.037 0.00 0.00 39.25 2.52
1654 1867 8.830201 TTGGAATTTCTGTTATGGTTTTGATG 57.170 30.769 0.00 0.00 0.00 3.07
1655 1868 7.385267 TGGAATTTCTGTTATGGTTTTGATGG 58.615 34.615 0.00 0.00 0.00 3.51
1674 1887 0.033366 GCCATGGGCGTTTTGAAGTT 59.967 50.000 15.13 0.00 39.62 2.66
1675 1888 1.782044 CCATGGGCGTTTTGAAGTTG 58.218 50.000 2.85 0.00 0.00 3.16
1677 1890 0.033366 ATGGGCGTTTTGAAGTTGCC 59.967 50.000 0.00 0.00 44.98 4.52
1681 1894 2.276201 GGCGTTTTGAAGTTGCCTTTT 58.724 42.857 0.00 0.00 42.44 2.27
1684 1897 3.258228 CGTTTTGAAGTTGCCTTTTGGT 58.742 40.909 0.00 0.00 42.99 3.67
1685 1898 3.061965 CGTTTTGAAGTTGCCTTTTGGTG 59.938 43.478 0.00 0.00 42.99 4.17
1686 1899 3.971245 TTTGAAGTTGCCTTTTGGTGT 57.029 38.095 0.00 0.00 42.99 4.16
1687 1900 3.971245 TTGAAGTTGCCTTTTGGTGTT 57.029 38.095 0.00 0.00 42.99 3.32
1688 1901 5.407407 TTTGAAGTTGCCTTTTGGTGTTA 57.593 34.783 0.00 0.00 42.99 2.41
1689 1902 5.606348 TTGAAGTTGCCTTTTGGTGTTAT 57.394 34.783 0.00 0.00 42.99 1.89
1692 1905 5.830991 TGAAGTTGCCTTTTGGTGTTATACT 59.169 36.000 0.00 0.00 42.99 2.12
1693 1906 5.705609 AGTTGCCTTTTGGTGTTATACTG 57.294 39.130 0.00 0.00 42.99 2.74
1694 1907 4.022329 AGTTGCCTTTTGGTGTTATACTGC 60.022 41.667 0.00 0.00 42.99 4.40
1695 1908 3.761897 TGCCTTTTGGTGTTATACTGCT 58.238 40.909 0.00 0.00 42.99 4.24
1696 1909 3.756434 TGCCTTTTGGTGTTATACTGCTC 59.244 43.478 0.00 0.00 42.99 4.26
1698 1911 4.142600 GCCTTTTGGTGTTATACTGCTCAG 60.143 45.833 0.00 0.00 42.99 3.35
1699 1912 5.003804 CCTTTTGGTGTTATACTGCTCAGT 58.996 41.667 7.73 7.73 38.97 3.41
1700 1913 6.170506 CCTTTTGGTGTTATACTGCTCAGTA 58.829 40.000 11.64 11.64 40.34 2.74
1701 1914 6.823689 CCTTTTGGTGTTATACTGCTCAGTAT 59.176 38.462 21.77 21.77 44.07 2.12
1721 1934 8.321353 TCAGTATTAGAAAGAATTTGAGCTGGA 58.679 33.333 0.00 0.00 39.27 3.86
1723 1936 8.951243 AGTATTAGAAAGAATTTGAGCTGGAAC 58.049 33.333 0.00 0.00 39.27 3.62
1726 1939 5.380043 AGAAAGAATTTGAGCTGGAACTGA 58.620 37.500 0.00 0.00 39.27 3.41
1733 1946 1.002430 TGAGCTGGAACTGATGTGACC 59.998 52.381 0.00 0.00 0.00 4.02
1743 1956 0.770499 TGATGTGACCTGCTGGGAAA 59.230 50.000 14.82 0.00 38.76 3.13
1745 1958 1.747355 GATGTGACCTGCTGGGAAATG 59.253 52.381 14.82 0.00 38.76 2.32
1766 1979 3.826157 TGGCTGAATTCTTGGTAACTTGG 59.174 43.478 7.05 0.00 37.61 3.61
1781 2002 7.790823 GGTAACTTGGTAGTTAACTGTTGAA 57.209 36.000 18.56 4.96 46.51 2.69
1792 2013 7.321745 AGTTAACTGTTGAAAGAAAGGACAG 57.678 36.000 7.48 0.00 42.48 3.51
1793 2014 4.639135 AACTGTTGAAAGAAAGGACAGC 57.361 40.909 0.00 0.00 40.95 4.40
1820 2041 6.071221 TCCGTTATAAGTAGTTTCAGGAGCAA 60.071 38.462 0.00 0.00 0.00 3.91
1821 2042 6.592607 CCGTTATAAGTAGTTTCAGGAGCAAA 59.407 38.462 0.00 0.00 0.00 3.68
1841 2062 5.163982 GCAAACTCGTGACCTTGTTATAGAC 60.164 44.000 0.00 0.00 0.00 2.59
1842 2063 5.717078 AACTCGTGACCTTGTTATAGACA 57.283 39.130 0.00 0.00 36.19 3.41
1843 2064 5.916661 ACTCGTGACCTTGTTATAGACAT 57.083 39.130 0.00 0.00 38.26 3.06
1844 2065 5.892568 ACTCGTGACCTTGTTATAGACATC 58.107 41.667 0.00 0.00 38.26 3.06
1845 2066 5.417894 ACTCGTGACCTTGTTATAGACATCA 59.582 40.000 0.00 0.00 38.26 3.07
1846 2067 6.071560 ACTCGTGACCTTGTTATAGACATCAA 60.072 38.462 0.00 0.00 38.26 2.57
1847 2068 6.330278 TCGTGACCTTGTTATAGACATCAAG 58.670 40.000 0.00 0.00 38.26 3.02
1877 2098 0.532196 GGGACGCCTATGCTTACCAC 60.532 60.000 0.00 0.00 39.56 4.16
1878 2099 0.464452 GGACGCCTATGCTTACCACT 59.536 55.000 0.00 0.00 34.43 4.00
1888 2109 6.572314 GCCTATGCTTACCACTGAAAACAATT 60.572 38.462 0.00 0.00 33.53 2.32
1931 2391 3.138304 TCCAGCACACATACAGACAAAC 58.862 45.455 0.00 0.00 0.00 2.93
1968 2428 5.181009 CAGGCTTGTCATTCACTCTATTCA 58.819 41.667 0.00 0.00 0.00 2.57
1972 2432 7.395489 AGGCTTGTCATTCACTCTATTCATTTT 59.605 33.333 0.00 0.00 0.00 1.82
2007 2467 8.856153 TTTAACCTCATGCACATAAGTTAAGA 57.144 30.769 0.00 0.00 31.90 2.10
2047 2507 5.336372 GCACTCTGGCCATGTTAAAATTGTA 60.336 40.000 5.51 0.00 0.00 2.41
2171 2631 4.322080 TCTCTGGGCGTCATGTTTATAG 57.678 45.455 0.00 0.00 0.00 1.31
2178 4325 4.700213 GGGCGTCATGTTTATAGGCATAAT 59.300 41.667 0.00 0.00 0.00 1.28
2241 4388 7.749126 GCTTAACATTGTTTAGTGTGACCATAC 59.251 37.037 14.90 0.00 0.00 2.39
2242 4389 8.678593 TTAACATTGTTTAGTGTGACCATACA 57.321 30.769 7.45 0.00 0.00 2.29
2255 4402 7.665559 AGTGTGACCATACAAACATATGAAAGT 59.334 33.333 10.38 6.80 34.94 2.66
2267 4414 4.826733 ACATATGAAAGTGTTTCCAGTGCA 59.173 37.500 10.38 0.00 38.90 4.57
2344 4492 5.487153 ACTTAGATGTGCTACAGACTACG 57.513 43.478 0.00 0.00 0.00 3.51
2403 4551 6.327279 ACCATCTTTTAGTAACCAGTTTGC 57.673 37.500 0.00 0.00 0.00 3.68
2462 4610 9.973450 TCTATATCAAAATGCTAGAAGACTGTC 57.027 33.333 0.00 0.00 0.00 3.51
2843 5026 1.692411 GGAAAACTTGGTCCTGCTGT 58.308 50.000 0.00 0.00 0.00 4.40
2965 5148 2.099098 CGTTTGTTTGGTGCTTTCTCCT 59.901 45.455 0.00 0.00 0.00 3.69
2970 5153 3.130340 TGTTTGGTGCTTTCTCCTTGTTC 59.870 43.478 0.00 0.00 0.00 3.18
2987 5170 5.394224 CCTTGTTCTGATACGTACCTGACAT 60.394 44.000 0.00 0.00 0.00 3.06
3056 5239 9.461312 TTCTTGAAATATTTAGGCACACTGTAT 57.539 29.630 0.00 0.00 0.00 2.29
3084 5267 3.040965 CAGCCCTCTGCCAGAAAAA 57.959 52.632 0.00 0.00 42.71 1.94
3489 5674 4.042187 ACTTCAGGACTGCAATAAGGAAGT 59.958 41.667 13.74 13.74 38.96 3.01
3565 5750 9.474313 TGGCTTATTATGTTTTACTTGGAGATT 57.526 29.630 0.00 0.00 0.00 2.40
3931 6177 1.541588 GGGAAGTGCAAACATCAGGAC 59.458 52.381 0.00 0.00 0.00 3.85
3959 6205 5.975693 AACTAGCTCTATCTGCTATGACC 57.024 43.478 0.00 0.00 41.45 4.02
3973 6220 2.649531 ATGACCTTGTTGACGGGAAA 57.350 45.000 0.00 0.00 0.00 3.13
4397 6648 1.404583 GGGGCTGCAATTCATGTTGTC 60.405 52.381 0.50 0.00 0.00 3.18
4445 6696 2.042464 GTATCATCTGGGCTGGAGTCA 58.958 52.381 0.00 0.00 0.00 3.41
5196 7448 2.675348 GAACAGAACTGCTGGTGCTATC 59.325 50.000 1.46 0.00 46.92 2.08
5367 7619 8.776376 ATGTTGTTCCCATTCATTTTAACATC 57.224 30.769 0.00 0.00 32.59 3.06
5449 7701 3.777522 CTCTCTGTTCCCAATTCTAGGGT 59.222 47.826 0.00 0.00 46.82 4.34
5490 7742 0.331278 TTAAGGACTGTGGGCATGGG 59.669 55.000 0.00 0.00 0.00 4.00
5491 7743 0.844661 TAAGGACTGTGGGCATGGGT 60.845 55.000 0.00 0.00 0.00 4.51
5573 7825 3.341823 CAGAGTCTGCATACCTTTGCTT 58.658 45.455 7.33 0.00 43.18 3.91
5587 7839 0.694771 TTGCTTGCCCTGATCTCTGT 59.305 50.000 0.00 0.00 0.00 3.41
5597 7849 4.445448 GCCCTGATCTCTGTTCACCAATAT 60.445 45.833 0.00 0.00 0.00 1.28
5648 7900 5.504853 GAAGGAGATGTCCCAGAGATTTTT 58.495 41.667 5.02 0.00 45.26 1.94
5719 7971 5.127519 TGTTAGCGCTTTTACTATGGTAGGA 59.872 40.000 18.68 0.00 0.00 2.94
5853 8181 6.368805 TGGCCATGGATAATGTGTATTAACA 58.631 36.000 18.40 0.00 34.11 2.41
6007 8335 6.815641 CAGTAATTTCTGAGATGTGCTACACT 59.184 38.462 6.22 0.00 37.61 3.55
6008 8336 7.009999 CAGTAATTTCTGAGATGTGCTACACTC 59.990 40.741 6.22 0.00 37.61 3.51
6506 8835 6.318648 GCAAAGGGTGTATGAGATGTATGAAA 59.681 38.462 0.00 0.00 0.00 2.69
6533 8862 6.796785 TTCATGATGTCACTCTGGAATAGA 57.203 37.500 0.00 0.00 0.00 1.98
6621 8950 1.745087 CAACCAGACAGCAACACAGTT 59.255 47.619 0.00 0.00 0.00 3.16
6725 9054 2.420687 GGGTCTAATCAGGGAACAGCAG 60.421 54.545 0.00 0.00 0.00 4.24
6764 9093 2.741985 TCGGCCAGTTGCATCACG 60.742 61.111 2.24 0.00 43.89 4.35
6800 9129 3.370103 CCATCCAATTCAGCCAGCAAATT 60.370 43.478 0.00 0.00 0.00 1.82
6881 9210 0.454957 CATTCGCCTGAAAAGCCACG 60.455 55.000 0.00 0.00 37.71 4.94
7006 9338 1.001181 CCATTGCCAAACCCAGACTTG 59.999 52.381 0.00 0.00 0.00 3.16
7250 9584 1.802069 TTCGTCGTGATTGCCATTGA 58.198 45.000 0.00 0.00 0.00 2.57
7334 9668 6.291849 CGACTCGCTTCCTTGTATAATTTCAG 60.292 42.308 0.00 0.00 0.00 3.02
7415 9749 5.547465 AGAAGACGGTGTGAATTGATGTTA 58.453 37.500 0.00 0.00 0.00 2.41
7416 9750 5.995282 AGAAGACGGTGTGAATTGATGTTAA 59.005 36.000 0.00 0.00 0.00 2.01
7417 9751 5.607119 AGACGGTGTGAATTGATGTTAAC 57.393 39.130 0.00 0.00 0.00 2.01
7418 9752 5.060506 AGACGGTGTGAATTGATGTTAACA 58.939 37.500 11.41 11.41 0.00 2.41
7419 9753 5.179368 AGACGGTGTGAATTGATGTTAACAG 59.821 40.000 14.65 0.00 0.00 3.16
7420 9754 4.819630 ACGGTGTGAATTGATGTTAACAGT 59.180 37.500 14.65 2.50 0.00 3.55
7421 9755 5.992829 ACGGTGTGAATTGATGTTAACAGTA 59.007 36.000 14.65 2.49 0.00 2.74
7422 9756 6.653320 ACGGTGTGAATTGATGTTAACAGTAT 59.347 34.615 14.65 4.47 0.00 2.12
7423 9757 7.174253 ACGGTGTGAATTGATGTTAACAGTATT 59.826 33.333 14.65 12.24 0.00 1.89
7424 9758 8.661257 CGGTGTGAATTGATGTTAACAGTATTA 58.339 33.333 14.65 0.00 0.00 0.98
7458 9792 3.078560 GCTAAGTGCACGTACCGC 58.921 61.111 12.01 9.61 42.31 5.68
7460 9794 2.785105 CTAAGTGCACGTACCGCGC 61.785 63.158 12.01 0.00 46.11 6.86
7461 9795 3.554989 TAAGTGCACGTACCGCGCA 62.555 57.895 12.01 3.13 42.53 6.09
7475 9809 4.308458 CGCACGGGACCACCAGAA 62.308 66.667 0.00 0.00 40.22 3.02
7476 9810 2.668550 GCACGGGACCACCAGAAC 60.669 66.667 0.00 0.00 40.22 3.01
7477 9811 2.825982 CACGGGACCACCAGAACA 59.174 61.111 0.00 0.00 40.22 3.18
7478 9812 1.597027 CACGGGACCACCAGAACAC 60.597 63.158 0.00 0.00 40.22 3.32
7479 9813 2.357034 CGGGACCACCAGAACACG 60.357 66.667 0.00 0.00 40.22 4.49
7480 9814 2.863346 CGGGACCACCAGAACACGA 61.863 63.158 0.00 0.00 40.22 4.35
7481 9815 1.004918 GGGACCACCAGAACACGAG 60.005 63.158 0.00 0.00 39.85 4.18
7482 9816 1.746517 GGACCACCAGAACACGAGT 59.253 57.895 0.00 0.00 35.97 4.18
7483 9817 0.319641 GGACCACCAGAACACGAGTC 60.320 60.000 0.00 0.00 35.97 3.36
7484 9818 0.674534 GACCACCAGAACACGAGTCT 59.325 55.000 0.00 0.00 0.00 3.24
7485 9819 0.674534 ACCACCAGAACACGAGTCTC 59.325 55.000 0.00 0.00 0.00 3.36
7486 9820 0.038159 CCACCAGAACACGAGTCTCC 60.038 60.000 0.00 0.00 0.00 3.71
7487 9821 0.962489 CACCAGAACACGAGTCTCCT 59.038 55.000 0.00 0.00 0.00 3.69
7488 9822 1.068194 CACCAGAACACGAGTCTCCTC 60.068 57.143 0.00 0.00 0.00 3.71
7496 9830 2.795297 GAGTCTCCTCGTGCTCGG 59.205 66.667 8.49 0.00 37.69 4.63
7497 9831 2.752238 AGTCTCCTCGTGCTCGGG 60.752 66.667 8.49 4.42 37.69 5.14
7509 9843 3.402681 CTCGGGGTGTGCCTCCAT 61.403 66.667 0.00 0.00 34.45 3.41
7510 9844 2.933287 TCGGGGTGTGCCTCCATT 60.933 61.111 0.00 0.00 34.45 3.16
7511 9845 2.438434 CGGGGTGTGCCTCCATTC 60.438 66.667 0.00 0.00 34.45 2.67
7512 9846 2.438434 GGGGTGTGCCTCCATTCG 60.438 66.667 0.00 0.00 34.45 3.34
7513 9847 2.438434 GGGTGTGCCTCCATTCGG 60.438 66.667 0.00 0.00 34.45 4.30
7583 9922 3.377172 ACTTCTGGGAGAACGTTTTTGTG 59.623 43.478 0.46 0.00 29.89 3.33
7590 9929 4.156008 GGGAGAACGTTTTTGTGATGCTAT 59.844 41.667 0.46 0.00 0.00 2.97
7591 9930 5.353123 GGGAGAACGTTTTTGTGATGCTATA 59.647 40.000 0.46 0.00 0.00 1.31
7742 10084 1.757118 TCTAGTCGAATGGAGGGCAAG 59.243 52.381 0.00 0.00 0.00 4.01
7850 10207 3.926821 ACGTGTCCACACTTTTTGTTT 57.073 38.095 8.19 0.00 44.34 2.83
7851 10208 4.245845 ACGTGTCCACACTTTTTGTTTT 57.754 36.364 8.19 0.00 44.34 2.43
7852 10209 3.984633 ACGTGTCCACACTTTTTGTTTTG 59.015 39.130 8.19 0.00 44.34 2.44
7853 10210 4.230657 CGTGTCCACACTTTTTGTTTTGA 58.769 39.130 8.19 0.00 44.34 2.69
7876 10233 0.319555 CAGGTACGTGTCCACACCTG 60.320 60.000 16.34 16.34 44.03 4.00
7917 10559 7.255942 CCCTTGATTTTTCTTCTAAGCCTTCAA 60.256 37.037 0.00 0.00 0.00 2.69
7959 10601 6.860034 TCCTCCCTAATTAGTAGATGTAGCA 58.140 40.000 11.50 0.00 30.50 3.49
7963 10605 8.582657 TCCCTAATTAGTAGATGTAGCATCTC 57.417 38.462 14.05 7.43 30.50 2.75
7964 10606 8.394822 TCCCTAATTAGTAGATGTAGCATCTCT 58.605 37.037 14.05 12.94 30.50 3.10
7965 10607 9.030452 CCCTAATTAGTAGATGTAGCATCTCTT 57.970 37.037 14.05 7.47 30.50 2.85
7966 10608 9.853555 CCTAATTAGTAGATGTAGCATCTCTTG 57.146 37.037 14.05 0.57 30.50 3.02
7971 10613 7.840342 AGTAGATGTAGCATCTCTTGTTTTG 57.160 36.000 14.05 0.00 0.00 2.44
7976 10618 8.416329 AGATGTAGCATCTCTTGTTTTGTTTTT 58.584 29.630 5.86 0.00 0.00 1.94
8020 10669 3.770263 TGATGTTTCAAGCTGCTATGC 57.230 42.857 0.90 0.00 0.00 3.14
8024 10673 2.096335 TGTTTCAAGCTGCTATGCATCG 59.904 45.455 0.19 0.00 38.13 3.84
8042 10691 1.203052 TCGTATTCGAGGTGGTTGACC 59.797 52.381 0.00 0.00 41.35 4.02
8118 10767 2.586079 CGCAGATGGCTACACCGG 60.586 66.667 0.00 0.00 43.94 5.28
8122 10771 0.392998 CAGATGGCTACACCGGCTTT 60.393 55.000 0.00 0.00 43.94 3.51
8218 10867 6.386284 ACTATGAGGGCTAGAGAGGTAAAAT 58.614 40.000 0.00 0.00 0.00 1.82
8244 10893 5.783111 GGAACCTTGTTCAGCATGTTTTAT 58.217 37.500 9.01 0.00 37.40 1.40
8247 10896 5.954335 ACCTTGTTCAGCATGTTTTATAGC 58.046 37.500 0.00 0.00 37.40 2.97
8273 10922 4.329801 TGAAGCTCACACGCTACATAATTG 59.670 41.667 0.00 0.00 39.86 2.32
8408 11590 7.288810 TCCAAAATAGCATCAACTTTGTTCT 57.711 32.000 0.00 0.00 0.00 3.01
8416 11598 7.195839 AGCATCAACTTTGTTCTCTTAGTTC 57.804 36.000 0.00 0.00 0.00 3.01
8422 11604 4.985409 ACTTTGTTCTCTTAGTTCTGAGCG 59.015 41.667 0.00 0.00 0.00 5.03
8423 11605 4.585955 TTGTTCTCTTAGTTCTGAGCGT 57.414 40.909 0.00 0.00 0.00 5.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.195002 CCGACATTGATGCCGCGT 61.195 61.111 4.92 0.00 32.14 6.01
89 90 3.463505 CTGCTTACCGTGTCGCAG 58.536 61.111 11.10 11.10 43.10 5.18
94 95 1.372997 CACGCTCTGCTTACCGTGT 60.373 57.895 10.75 0.00 44.15 4.49
152 155 4.511246 CTGACCGCCATGGCCCAT 62.511 66.667 30.79 16.35 43.94 4.00
291 440 4.101741 GGTAAGGGCATCTCTAACACTGAT 59.898 45.833 0.00 0.00 0.00 2.90
451 600 1.933181 CACGTATACATGCACCCTGTG 59.067 52.381 3.32 0.00 36.51 3.66
452 601 1.742411 GCACGTATACATGCACCCTGT 60.742 52.381 18.47 0.00 41.65 4.00
473 622 0.172352 GCTAGCTTCTCTGAGTGCGT 59.828 55.000 7.70 9.45 0.00 5.24
601 755 0.804364 TGCTAACATGGCAAAGCGAG 59.196 50.000 0.00 0.00 37.80 5.03
613 767 4.394920 GCATAAGCTTAGTTGGTGCTAACA 59.605 41.667 17.72 0.00 35.85 2.41
616 770 4.081142 TCTGCATAAGCTTAGTTGGTGCTA 60.081 41.667 22.79 12.66 42.74 3.49
632 786 2.298610 CGTCTGGACCTAGTCTGCATA 58.701 52.381 0.00 0.00 32.47 3.14
692 850 3.627395 TCTTGGTTCACGCCAATATCT 57.373 42.857 0.00 0.00 46.22 1.98
706 864 9.918630 CTAACAAATTTCAGAATTGATCTTGGT 57.081 29.630 3.88 0.00 35.73 3.67
766 956 0.753111 GGATCTTTTCGCTGGGGCAT 60.753 55.000 0.00 0.00 38.60 4.40
767 957 1.378514 GGATCTTTTCGCTGGGGCA 60.379 57.895 0.00 0.00 38.60 5.36
886 1086 4.063967 TGACGTCGCCGCCTGATT 62.064 61.111 11.62 0.00 37.70 2.57
887 1087 4.796231 GTGACGTCGCCGCCTGAT 62.796 66.667 18.36 0.00 37.70 2.90
1036 1240 3.200887 GATCGCGGCGATGAGGTCT 62.201 63.158 38.86 17.29 47.00 3.85
1327 1535 0.179015 TCACGCACTTAAAAGGGGCA 60.179 50.000 8.65 0.00 32.75 5.36
1328 1536 1.135402 CATCACGCACTTAAAAGGGGC 60.135 52.381 0.00 0.00 0.00 5.80
1355 1563 2.032290 CCGAATCAGCACGACTATACGA 60.032 50.000 0.00 0.00 37.03 3.43
1357 1565 2.052157 GCCGAATCAGCACGACTATAC 58.948 52.381 0.00 0.00 0.00 1.47
1411 1619 4.188462 CCTTTGTACGATCCAGCATACAA 58.812 43.478 0.00 0.00 36.11 2.41
1412 1620 3.792401 CCTTTGTACGATCCAGCATACA 58.208 45.455 0.00 0.00 0.00 2.29
1427 1635 3.555956 CGCTATATCACGAAAGCCTTTGT 59.444 43.478 0.00 0.00 0.00 2.83
1432 1640 0.790814 GGCGCTATATCACGAAAGCC 59.209 55.000 7.64 0.00 36.32 4.35
1435 1643 1.335810 AGACGGCGCTATATCACGAAA 59.664 47.619 6.90 0.00 0.00 3.46
1453 1661 6.921486 TCCCAATTATATAGCACCGTAAGA 57.079 37.500 0.00 0.00 43.02 2.10
1462 1670 7.890655 AGAACTCCCAAATCCCAATTATATAGC 59.109 37.037 0.00 0.00 0.00 2.97
1465 1673 7.595488 ACAGAACTCCCAAATCCCAATTATAT 58.405 34.615 0.00 0.00 0.00 0.86
1469 1677 4.132122 ACAGAACTCCCAAATCCCAATT 57.868 40.909 0.00 0.00 0.00 2.32
1484 1692 4.214437 CGAGCAACAAATCTGAACAGAAC 58.786 43.478 8.59 0.00 41.36 3.01
1487 1695 2.578495 GCGAGCAACAAATCTGAACAG 58.422 47.619 0.00 0.00 0.00 3.16
1491 1700 1.725641 ATCGCGAGCAACAAATCTGA 58.274 45.000 16.66 0.00 0.00 3.27
1505 1714 1.418342 CCAGACGGTACCAAATCGCG 61.418 60.000 13.54 0.00 0.00 5.87
1516 1725 1.347707 TCAGATTTTCAGCCAGACGGT 59.652 47.619 0.00 0.00 33.28 4.83
1639 1852 3.197333 CCATGGCCATCAAAACCATAACA 59.803 43.478 17.61 0.00 42.31 2.41
1655 1868 0.033366 AACTTCAAAACGCCCATGGC 59.967 50.000 6.09 0.58 46.75 4.40
1674 1887 3.756434 GAGCAGTATAACACCAAAAGGCA 59.244 43.478 0.00 0.00 0.00 4.75
1675 1888 3.756434 TGAGCAGTATAACACCAAAAGGC 59.244 43.478 0.00 0.00 0.00 4.35
1692 1905 7.826252 AGCTCAAATTCTTTCTAATACTGAGCA 59.174 33.333 22.45 0.00 45.85 4.26
1693 1906 8.121708 CAGCTCAAATTCTTTCTAATACTGAGC 58.878 37.037 17.47 17.47 44.98 4.26
1694 1907 8.610896 CCAGCTCAAATTCTTTCTAATACTGAG 58.389 37.037 0.00 0.00 34.78 3.35
1695 1908 8.321353 TCCAGCTCAAATTCTTTCTAATACTGA 58.679 33.333 0.00 0.00 0.00 3.41
1696 1909 8.498054 TCCAGCTCAAATTCTTTCTAATACTG 57.502 34.615 0.00 0.00 0.00 2.74
1698 1911 8.951243 AGTTCCAGCTCAAATTCTTTCTAATAC 58.049 33.333 0.00 0.00 0.00 1.89
1699 1912 8.950210 CAGTTCCAGCTCAAATTCTTTCTAATA 58.050 33.333 0.00 0.00 0.00 0.98
1700 1913 7.667219 TCAGTTCCAGCTCAAATTCTTTCTAAT 59.333 33.333 0.00 0.00 0.00 1.73
1701 1914 6.998074 TCAGTTCCAGCTCAAATTCTTTCTAA 59.002 34.615 0.00 0.00 0.00 2.10
1705 1918 5.537674 ACATCAGTTCCAGCTCAAATTCTTT 59.462 36.000 0.00 0.00 0.00 2.52
1721 1934 0.037303 CCCAGCAGGTCACATCAGTT 59.963 55.000 0.00 0.00 0.00 3.16
1723 1936 0.325933 TTCCCAGCAGGTCACATCAG 59.674 55.000 0.00 0.00 36.75 2.90
1726 1939 1.617804 CCATTTCCCAGCAGGTCACAT 60.618 52.381 0.00 0.00 36.75 3.21
1733 1946 1.481871 ATTCAGCCATTTCCCAGCAG 58.518 50.000 0.00 0.00 0.00 4.24
1743 1956 4.463891 CCAAGTTACCAAGAATTCAGCCAT 59.536 41.667 8.44 0.00 0.00 4.40
1745 1958 3.826729 ACCAAGTTACCAAGAATTCAGCC 59.173 43.478 8.44 0.00 0.00 4.85
1766 1979 8.205131 TGTCCTTTCTTTCAACAGTTAACTAC 57.795 34.615 8.04 0.00 0.00 2.73
1781 2002 2.568623 AACGGATGCTGTCCTTTCTT 57.431 45.000 7.06 0.00 45.46 2.52
1792 2013 6.278363 TCCTGAAACTACTTATAACGGATGC 58.722 40.000 0.00 0.00 0.00 3.91
1793 2014 6.421202 GCTCCTGAAACTACTTATAACGGATG 59.579 42.308 0.00 0.00 0.00 3.51
1820 2041 5.717078 TGTCTATAACAAGGTCACGAGTT 57.283 39.130 0.00 0.00 34.03 3.01
1821 2042 5.417894 TGATGTCTATAACAAGGTCACGAGT 59.582 40.000 0.00 0.00 42.37 4.18
1841 2062 3.535561 GTCCCTGTGTACATCCTTGATG 58.464 50.000 0.00 2.62 44.71 3.07
1842 2063 2.168521 CGTCCCTGTGTACATCCTTGAT 59.831 50.000 0.00 0.00 0.00 2.57
1843 2064 1.548719 CGTCCCTGTGTACATCCTTGA 59.451 52.381 0.00 0.00 0.00 3.02
1844 2065 2.007049 GCGTCCCTGTGTACATCCTTG 61.007 57.143 0.00 0.00 0.00 3.61
1845 2066 0.249398 GCGTCCCTGTGTACATCCTT 59.751 55.000 0.00 0.00 0.00 3.36
1846 2067 1.614241 GGCGTCCCTGTGTACATCCT 61.614 60.000 0.00 0.00 0.00 3.24
1847 2068 1.153429 GGCGTCCCTGTGTACATCC 60.153 63.158 0.00 0.00 0.00 3.51
1848 2069 1.108776 TAGGCGTCCCTGTGTACATC 58.891 55.000 0.00 0.00 42.90 3.06
1849 2070 1.412710 CATAGGCGTCCCTGTGTACAT 59.587 52.381 0.00 0.00 43.28 2.29
1850 2071 0.821517 CATAGGCGTCCCTGTGTACA 59.178 55.000 0.00 0.00 43.28 2.90
1851 2072 3.661745 CATAGGCGTCCCTGTGTAC 57.338 57.895 0.00 0.00 43.28 2.90
1888 2109 9.613428 CTGGATGATGTATACCACTTTTCTTAA 57.387 33.333 0.00 0.00 0.00 1.85
1904 2364 3.198417 TCTGTATGTGTGCTGGATGATGT 59.802 43.478 0.00 0.00 0.00 3.06
1931 2391 5.241506 TGACAAGCCTGGAGTTAAATTTGAG 59.758 40.000 0.00 0.00 0.00 3.02
2007 2467 8.197439 GGCCAGAGTGCTAATTTTATGTATTTT 58.803 33.333 0.00 0.00 0.00 1.82
2016 2476 3.434309 ACATGGCCAGAGTGCTAATTTT 58.566 40.909 13.05 0.00 0.00 1.82
2047 2507 8.668510 ACAAGTTCGATGAGATAGCAAATAAT 57.331 30.769 0.00 0.00 0.00 1.28
2138 2598 1.606737 GCCCAGAGATAGCGCTTTAGG 60.607 57.143 18.68 9.61 0.00 2.69
2171 2631 6.012745 AGGAAAATGGTATGGAGATTATGCC 58.987 40.000 0.00 0.00 0.00 4.40
2241 4388 6.144402 GCACTGGAAACACTTTCATATGTTTG 59.856 38.462 7.06 0.00 46.40 2.93
2255 4402 3.984838 GCCAAATGCACTGGAAACA 57.015 47.368 18.75 0.00 40.77 2.83
2267 4414 1.903860 AGAATGTGCCATGTGCCAAAT 59.096 42.857 4.07 0.00 40.16 2.32
2389 4537 4.277423 GCAAAAGAGGCAAACTGGTTACTA 59.723 41.667 0.00 0.00 0.00 1.82
2391 4539 3.068165 AGCAAAAGAGGCAAACTGGTTAC 59.932 43.478 0.00 0.00 0.00 2.50
2396 4544 3.784338 TGAAAGCAAAAGAGGCAAACTG 58.216 40.909 0.00 0.00 0.00 3.16
2400 4548 5.477984 AGATACATGAAAGCAAAAGAGGCAA 59.522 36.000 0.00 0.00 0.00 4.52
2403 4551 6.506500 ACAGATACATGAAAGCAAAAGAGG 57.493 37.500 0.00 0.00 0.00 3.69
2441 4589 6.939163 ACTTGACAGTCTTCTAGCATTTTGAT 59.061 34.615 1.31 0.00 0.00 2.57
2591 4774 7.013274 AGTGCTTCAACAATAACACTGTACAAT 59.987 33.333 0.00 0.00 37.02 2.71
2724 4907 8.530311 TGACAATATACATTTTGCAACTCCATT 58.470 29.630 0.00 0.00 0.00 3.16
2843 5026 5.215845 TGATGTCATACCTCCCAGTGATTA 58.784 41.667 0.00 0.00 0.00 1.75
2926 5109 5.009610 ACAAACGGTTCAGTGCATCTTAAAT 59.990 36.000 0.00 0.00 0.00 1.40
2965 5148 5.407502 CATGTCAGGTACGTATCAGAACAA 58.592 41.667 8.86 0.00 0.00 2.83
2970 5153 4.855715 ATCCATGTCAGGTACGTATCAG 57.144 45.455 8.86 0.00 0.00 2.90
2987 5170 3.716353 ACATACCACAGAAGGCATATCCA 59.284 43.478 0.00 0.00 37.29 3.41
3045 5228 2.744202 GCATAGCCATATACAGTGTGCC 59.256 50.000 5.88 0.00 0.00 5.01
3084 5267 1.679898 CCCCGTCCTCTGAGCTTTT 59.320 57.895 0.00 0.00 0.00 2.27
3136 5319 3.637273 GAACTCGGGTGGGCTGGT 61.637 66.667 0.00 0.00 0.00 4.00
3439 5624 8.768501 AGGTGTAACATGAGTCTATAGATTGA 57.231 34.615 5.57 0.00 39.98 2.57
3489 5674 7.579339 GCAAATCAACCATAAGAAAAGATCCCA 60.579 37.037 0.00 0.00 0.00 4.37
3565 5750 3.072915 AGAATTGACACTGACCACATGGA 59.927 43.478 4.53 0.00 38.94 3.41
3779 5964 7.744678 AGGTATAAGGAAAAACTAGGCTACA 57.255 36.000 0.00 0.00 0.00 2.74
3931 6177 5.682943 AGCAGATAGAGCTAGTTAACTCG 57.317 43.478 12.39 7.12 41.32 4.18
4445 6696 4.708421 ACAACAATATCAAGCTTGGCAGAT 59.292 37.500 25.73 14.23 32.27 2.90
5196 7448 4.269603 CAGAATGCATAGAGGTCGTTGAAG 59.730 45.833 0.00 0.00 0.00 3.02
5367 7619 1.691976 TGCATTATCTAGGACGGGTGG 59.308 52.381 0.00 0.00 0.00 4.61
5449 7701 1.681538 TTGACGCCCAAACTAAAGCA 58.318 45.000 0.00 0.00 0.00 3.91
5490 7742 4.386049 CGACCAACTCTCAACTAATCACAC 59.614 45.833 0.00 0.00 0.00 3.82
5491 7743 4.279922 TCGACCAACTCTCAACTAATCACA 59.720 41.667 0.00 0.00 0.00 3.58
5573 7825 0.615331 GGTGAACAGAGATCAGGGCA 59.385 55.000 0.00 0.00 0.00 5.36
5587 7839 2.506231 TGGTAGGCGGAATATTGGTGAA 59.494 45.455 0.00 0.00 0.00 3.18
5597 7849 1.339631 CCTGTTCAATGGTAGGCGGAA 60.340 52.381 0.00 0.00 0.00 4.30
5663 7915 4.760204 AGTTCCAAAATCTAAACGTCCCAG 59.240 41.667 0.00 0.00 0.00 4.45
5664 7916 4.721132 AGTTCCAAAATCTAAACGTCCCA 58.279 39.130 0.00 0.00 0.00 4.37
5719 7971 2.861360 GCTTACGTGACGTTCCTGTTCT 60.861 50.000 18.28 0.00 41.54 3.01
5853 8181 9.933723 ACTGTACCAGAAATTTAATACGTAGTT 57.066 29.630 0.00 0.00 37.28 2.24
6007 8335 9.595823 GATTACTTAAACACACCTAAGCATAGA 57.404 33.333 0.00 0.00 0.00 1.98
6008 8336 9.601217 AGATTACTTAAACACACCTAAGCATAG 57.399 33.333 0.00 0.00 0.00 2.23
6427 8755 8.558973 AAATCAATGTTTCAGTTTTTCCAACA 57.441 26.923 0.00 0.00 0.00 3.33
6506 8835 9.722184 CTATTCCAGAGTGACATCATGAAATAT 57.278 33.333 0.00 0.00 0.00 1.28
6621 8950 4.965814 AGATGAACTCTGAAGCTGAACAA 58.034 39.130 0.00 0.00 31.12 2.83
6725 9054 1.454479 CCAGACCCATGCCATCACC 60.454 63.158 0.00 0.00 0.00 4.02
6764 9093 1.826720 TGGATGGCCTTGAGAAATTGC 59.173 47.619 3.32 0.00 34.31 3.56
6881 9210 1.444553 CGTCACCCTCGAGCAGTTC 60.445 63.158 6.99 1.96 0.00 3.01
7006 9338 4.785453 CGGCTGGGCTCACCTTCC 62.785 72.222 4.07 0.00 41.11 3.46
7303 9637 2.069273 CAAGGAAGCGAGTCGACATTT 58.931 47.619 18.61 5.96 0.00 2.32
7334 9668 8.435430 GGAAACAAGCTAAACAAGAATTTATGC 58.565 33.333 0.00 0.00 0.00 3.14
7458 9792 4.308458 TTCTGGTGGTCCCGTGCG 62.308 66.667 0.00 0.00 35.15 5.34
7459 9793 2.668550 GTTCTGGTGGTCCCGTGC 60.669 66.667 0.00 0.00 35.15 5.34
7460 9794 1.597027 GTGTTCTGGTGGTCCCGTG 60.597 63.158 0.00 0.00 35.15 4.94
7461 9795 2.826702 GTGTTCTGGTGGTCCCGT 59.173 61.111 0.00 0.00 35.15 5.28
7462 9796 2.357034 CGTGTTCTGGTGGTCCCG 60.357 66.667 0.00 0.00 35.15 5.14
7463 9797 1.004918 CTCGTGTTCTGGTGGTCCC 60.005 63.158 0.00 0.00 0.00 4.46
7464 9798 0.319641 GACTCGTGTTCTGGTGGTCC 60.320 60.000 0.00 0.00 0.00 4.46
7465 9799 0.674534 AGACTCGTGTTCTGGTGGTC 59.325 55.000 0.00 0.00 0.00 4.02
7466 9800 0.674534 GAGACTCGTGTTCTGGTGGT 59.325 55.000 0.00 0.00 0.00 4.16
7467 9801 0.038159 GGAGACTCGTGTTCTGGTGG 60.038 60.000 0.00 0.00 0.00 4.61
7468 9802 0.962489 AGGAGACTCGTGTTCTGGTG 59.038 55.000 0.00 0.00 32.90 4.17
7469 9803 3.441241 AGGAGACTCGTGTTCTGGT 57.559 52.632 0.00 0.00 32.90 4.00
7481 9815 3.827898 CCCCGAGCACGAGGAGAC 61.828 72.222 4.70 0.00 39.79 3.36
7482 9816 4.361971 ACCCCGAGCACGAGGAGA 62.362 66.667 11.67 0.00 39.79 3.71
7483 9817 4.135153 CACCCCGAGCACGAGGAG 62.135 72.222 11.67 0.00 39.79 3.69
7484 9818 4.988716 ACACCCCGAGCACGAGGA 62.989 66.667 11.67 0.00 39.79 3.71
7485 9819 4.742201 CACACCCCGAGCACGAGG 62.742 72.222 4.70 3.22 43.03 4.63
7492 9826 2.876368 GAATGGAGGCACACCCCGAG 62.876 65.000 0.00 0.00 38.71 4.63
7493 9827 2.933287 AATGGAGGCACACCCCGA 60.933 61.111 0.00 0.00 38.71 5.14
7494 9828 2.438434 GAATGGAGGCACACCCCG 60.438 66.667 0.00 0.00 38.71 5.73
7495 9829 2.438434 CGAATGGAGGCACACCCC 60.438 66.667 0.00 0.00 38.71 4.95
7496 9830 2.438434 CCGAATGGAGGCACACCC 60.438 66.667 0.00 0.00 38.71 4.61
7503 9837 0.606401 ACTGTTGTGCCGAATGGAGG 60.606 55.000 0.00 0.00 37.49 4.30
7504 9838 2.093306 TACTGTTGTGCCGAATGGAG 57.907 50.000 0.00 0.00 37.49 3.86
7505 9839 2.779755 ATACTGTTGTGCCGAATGGA 57.220 45.000 0.00 0.00 37.49 3.41
7506 9840 4.789481 GCATAATACTGTTGTGCCGAATGG 60.789 45.833 0.00 0.00 38.77 3.16
7507 9841 4.035558 AGCATAATACTGTTGTGCCGAATG 59.964 41.667 4.02 0.00 37.26 2.67
7508 9842 4.199310 AGCATAATACTGTTGTGCCGAAT 58.801 39.130 4.02 0.00 37.26 3.34
7509 9843 3.605634 AGCATAATACTGTTGTGCCGAA 58.394 40.909 4.02 0.00 37.26 4.30
7510 9844 3.260475 AGCATAATACTGTTGTGCCGA 57.740 42.857 4.02 0.00 37.26 5.54
7511 9845 4.355543 AAAGCATAATACTGTTGTGCCG 57.644 40.909 4.02 0.00 37.26 5.69
7512 9846 5.469479 ACAAAAGCATAATACTGTTGTGCC 58.531 37.500 4.02 0.00 42.63 5.01
7515 9849 5.243730 AGCCACAAAAGCATAATACTGTTGT 59.756 36.000 0.00 0.00 44.60 3.32
7516 9850 5.713025 AGCCACAAAAGCATAATACTGTTG 58.287 37.500 0.00 0.00 38.18 3.33
7517 9851 5.982890 AGCCACAAAAGCATAATACTGTT 57.017 34.783 0.00 0.00 0.00 3.16
7583 9922 7.064490 CACCCCAACAAAACAATTTATAGCATC 59.936 37.037 0.00 0.00 0.00 3.91
7590 9929 5.424252 TGTACCACCCCAACAAAACAATTTA 59.576 36.000 0.00 0.00 0.00 1.40
7591 9930 4.225267 TGTACCACCCCAACAAAACAATTT 59.775 37.500 0.00 0.00 0.00 1.82
7615 9955 2.228822 GAGGCCAATAACATAATGCCGG 59.771 50.000 5.01 0.00 43.56 6.13
7742 10084 6.101332 TGATATTTTTGAAATGTGCTCCAGC 58.899 36.000 0.00 0.00 42.50 4.85
7781 10138 6.266168 TGGCATTCGTTGATTACATTTTCT 57.734 33.333 0.00 0.00 0.00 2.52
7850 10207 1.964933 TGGACACGTACCTGATGTCAA 59.035 47.619 11.33 3.07 43.73 3.18
7851 10208 1.271379 GTGGACACGTACCTGATGTCA 59.729 52.381 11.33 0.00 43.73 3.58
7852 10209 1.271379 TGTGGACACGTACCTGATGTC 59.729 52.381 11.33 2.84 41.68 3.06
7853 10210 1.000506 GTGTGGACACGTACCTGATGT 59.999 52.381 11.33 0.00 37.10 3.06
7917 10559 2.108970 GGAAAGGTATCGGACTGAGGT 58.891 52.381 0.00 0.00 0.00 3.85
8001 10643 3.770263 TGCATAGCAGCTTGAAACATC 57.230 42.857 0.00 0.00 33.32 3.06
8002 10644 3.242969 CGATGCATAGCAGCTTGAAACAT 60.243 43.478 0.00 0.00 43.23 2.71
8003 10645 2.096335 CGATGCATAGCAGCTTGAAACA 59.904 45.455 0.00 0.00 43.23 2.83
8004 10646 2.096496 ACGATGCATAGCAGCTTGAAAC 59.904 45.455 0.00 0.00 43.23 2.78
8008 10657 3.422732 CGAATACGATGCATAGCAGCTTG 60.423 47.826 0.00 0.00 43.23 4.01
8020 10669 4.283432 GGTCAACCACCTCGAATACGATG 61.283 52.174 0.00 0.00 42.84 3.84
8024 10673 1.553704 AGGGTCAACCACCTCGAATAC 59.446 52.381 0.89 0.00 45.95 1.89
8042 10691 3.785505 GCGTCAACGAGAATGCATAAAGG 60.786 47.826 6.75 0.00 43.02 3.11
8046 10695 1.286501 GGCGTCAACGAGAATGCATA 58.713 50.000 6.75 0.00 43.02 3.14
8118 10767 3.921119 TTGTGATCATGGTGTGAAAGC 57.079 42.857 0.00 0.00 40.97 3.51
8122 10771 4.019950 ACAGAGATTGTGATCATGGTGTGA 60.020 41.667 0.00 0.00 38.99 3.58
8218 10867 1.962807 CATGCTGAACAAGGTTCCCAA 59.037 47.619 6.64 0.00 0.00 4.12
8233 10882 3.065371 GCTTCACCGCTATAAAACATGCT 59.935 43.478 0.00 0.00 0.00 3.79
8238 10887 3.682858 TGTGAGCTTCACCGCTATAAAAC 59.317 43.478 11.99 0.00 46.40 2.43
8244 10893 1.080772 CGTGTGAGCTTCACCGCTA 60.081 57.895 14.39 0.00 46.40 4.26
8247 10896 1.080772 TAGCGTGTGAGCTTCACCG 60.081 57.895 14.39 15.08 46.40 4.94
8326 10975 8.721478 CAATCCAGAATCCTATTTTGTATACGG 58.279 37.037 0.00 0.00 0.00 4.02
8328 10977 9.289782 AGCAATCCAGAATCCTATTTTGTATAC 57.710 33.333 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.