Multiple sequence alignment - TraesCS6D01G091900

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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 TraesCS6D01G091900 chr6D 100.000 4653 0 0 1 4653 57473911 57469259 0.000000e+00 8593.0
1 TraesCS6D01G091900 chr6D 87.500 72 8 1 4019 4089 420763469 420763540 1.070000e-11 82.4
2 TraesCS6D01G091900 chr6D 97.561 41 1 0 3952 3992 427966150 427966110 2.320000e-08 71.3
3 TraesCS6D01G091900 chr6B 92.200 1718 85 23 890 2585 129304835 129303145 0.000000e+00 2385.0
4 TraesCS6D01G091900 chr6B 90.133 527 29 8 3173 3699 129302426 129301923 0.000000e+00 664.0
5 TraesCS6D01G091900 chr6B 84.448 643 55 16 2239 2865 178011583 178010970 4.010000e-165 592.0
6 TraesCS6D01G091900 chr6B 80.187 641 74 17 1 626 129305487 129304885 9.250000e-117 431.0
7 TraesCS6D01G091900 chr6B 91.228 228 15 2 2582 2809 129303033 129302811 5.850000e-79 305.0
8 TraesCS6D01G091900 chr6B 89.754 244 12 6 4300 4539 129299748 129299514 2.720000e-77 300.0
9 TraesCS6D01G091900 chr6B 86.070 201 18 8 4096 4289 129300965 129300768 1.700000e-49 207.0
10 TraesCS6D01G091900 chr6B 91.304 115 3 1 3759 3873 129301490 129301383 2.900000e-32 150.0
11 TraesCS6D01G091900 chr6A 87.941 1559 118 35 68 1588 72447279 72445753 0.000000e+00 1773.0
12 TraesCS6D01G091900 chr6A 92.155 1211 75 16 1663 2865 72445661 72444463 0.000000e+00 1692.0
13 TraesCS6D01G091900 chr6A 92.691 1163 66 12 2872 4026 72444425 72443274 0.000000e+00 1659.0
14 TraesCS6D01G091900 chr6A 94.035 637 31 5 4022 4653 72443181 72442547 0.000000e+00 959.0
15 TraesCS6D01G091900 chr1D 88.542 192 12 3 669 853 246072995 246072807 1.680000e-54 224.0
16 TraesCS6D01G091900 chr1D 95.349 43 2 0 3952 3994 406814296 406814254 8.350000e-08 69.4
17 TraesCS6D01G091900 chr7D 88.172 186 19 1 666 851 602082505 602082323 7.840000e-53 219.0
18 TraesCS6D01G091900 chr7D 88.398 181 18 3 671 851 80797780 80797957 1.010000e-51 215.0
19 TraesCS6D01G091900 chr7D 91.667 60 1 3 3933 3990 205240127 205240070 3.860000e-11 80.5
20 TraesCS6D01G091900 chr7D 93.878 49 1 1 3941 3989 510616025 510615979 6.460000e-09 73.1
21 TraesCS6D01G091900 chr7D 92.000 50 2 1 3952 4001 492853638 492853685 8.350000e-08 69.4
22 TraesCS6D01G091900 chr3D 88.462 182 16 3 671 851 93254534 93254357 1.010000e-51 215.0
23 TraesCS6D01G091900 chr3D 93.878 49 3 0 3952 4000 594965133 594965181 1.800000e-09 75.0
24 TraesCS6D01G091900 chr2D 87.766 188 18 3 666 852 602170190 602170373 1.010000e-51 215.0
25 TraesCS6D01G091900 chr2A 87.701 187 19 2 666 851 24738353 24738536 1.010000e-51 215.0
26 TraesCS6D01G091900 chr2A 97.368 38 1 0 3952 3989 777082992 777083029 1.080000e-06 65.8
27 TraesCS6D01G091900 chr4D 88.043 184 17 3 669 851 369096736 369096915 3.650000e-51 213.0
28 TraesCS6D01G091900 chr5B 86.911 191 20 3 666 854 10436951 10437138 4.720000e-50 209.0
29 TraesCS6D01G091900 chr5B 75.799 219 40 11 17 230 480413125 480413335 1.070000e-16 99.0
30 TraesCS6D01G091900 chr7A 88.372 86 10 0 4565 4650 210737191 210737276 2.290000e-18 104.0
31 TraesCS6D01G091900 chr1B 93.443 61 4 0 4029 4089 406343663 406343723 1.780000e-14 91.6
32 TraesCS6D01G091900 chr1B 92.063 63 5 0 4028 4090 16176673 16176735 6.410000e-14 89.8
33 TraesCS6D01G091900 chrUn 91.935 62 5 0 4028 4089 277307533 277307472 2.310000e-13 87.9
34 TraesCS6D01G091900 chr3A 91.935 62 5 0 4028 4089 727187166 727187227 2.310000e-13 87.9
35 TraesCS6D01G091900 chr5D 90.476 63 6 0 4028 4090 267080476 267080538 2.980000e-12 84.2
36 TraesCS6D01G091900 chr2B 90.476 63 6 0 4028 4090 549512504 549512566 2.980000e-12 84.2
37 TraesCS6D01G091900 chr2B 90.476 63 6 0 4028 4090 798200926 798200988 2.980000e-12 84.2
38 TraesCS6D01G091900 chr2B 97.368 38 1 0 3952 3989 699174286 699174323 1.080000e-06 65.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G091900 chr6D 57469259 57473911 4652 True 8593.000000 8593 100.000000 1 4653 1 chr6D.!!$R1 4652
1 TraesCS6D01G091900 chr6B 129299514 129305487 5973 True 634.571429 2385 88.696571 1 4539 7 chr6B.!!$R2 4538
2 TraesCS6D01G091900 chr6B 178010970 178011583 613 True 592.000000 592 84.448000 2239 2865 1 chr6B.!!$R1 626
3 TraesCS6D01G091900 chr6A 72442547 72447279 4732 True 1520.750000 1773 91.705500 68 4653 4 chr6A.!!$R1 4585

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
646 665 0.103572 TTATGGGCTCGGTCGCTAAC 59.896 55.0 0.0 0.0 0.00 2.34 F
951 990 0.179045 CCTCCCAAGCCGTTCCATAG 60.179 60.0 0.0 0.0 0.00 2.23 F
1700 1798 0.110056 GAGCACAGCAAACACATCCG 60.110 55.0 0.0 0.0 0.00 4.18 F
3376 3794 0.037232 AGGGAGCAGCGAAGTTGTAC 60.037 55.0 0.0 0.0 42.08 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1456 1513 0.034198 TCCATTTGGTTGTCTCGCGA 59.966 50.0 9.26 9.26 36.34 5.87 R
2226 2329 1.086634 GTGCCTGCCTTCTAAGAGCG 61.087 60.0 0.00 0.00 0.00 5.03 R
3453 3871 0.104855 TGGCATGATCGGTCAGTAGC 59.895 55.0 3.97 8.23 37.87 3.58 R
4349 6600 0.109342 ATGTTCGAGCCCATCATCCC 59.891 55.0 0.00 0.00 0.00 3.85 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
108 113 8.359060 TGTGGAAAAATGTTTGTGTATTAAGC 57.641 30.769 0.00 0.00 0.00 3.09
112 117 9.862585 GGAAAAATGTTTGTGTATTAAGCAAAG 57.137 29.630 0.00 0.00 33.50 2.77
168 174 5.808540 CGGCAATGTTCATGATTTCTGAAAT 59.191 36.000 15.09 15.09 34.59 2.17
283 289 8.075593 AGAAAAACAATGTTCATGAATTTCCG 57.924 30.769 12.12 2.65 32.04 4.30
289 295 6.527722 ACAATGTTCATGAATTTCCGAAATCG 59.472 34.615 12.12 0.00 39.44 3.34
303 309 6.328641 TCCGAAATCGTTTCCCAATTTTAA 57.671 33.333 1.79 0.00 36.30 1.52
315 322 9.008965 GTTTCCCAATTTTAATAATGTTTGCCT 57.991 29.630 0.00 0.00 0.00 4.75
334 341 6.154203 TGCCTATTCACAAAATTGTTCACA 57.846 33.333 0.00 0.00 39.91 3.58
391 401 6.607735 ATGCTCACAAATTGGAAAAAGTTG 57.392 33.333 0.00 0.00 0.00 3.16
515 526 8.683550 AAAAAGGAAGTAGAAACGAAAACTTG 57.316 30.769 0.00 0.00 32.51 3.16
516 527 7.619964 AAAGGAAGTAGAAACGAAAACTTGA 57.380 32.000 0.00 0.00 32.51 3.02
617 636 1.336755 CGGCCCAAAATGTACATAGCC 59.663 52.381 9.21 14.54 35.78 3.93
619 638 2.666317 GCCCAAAATGTACATAGCCCT 58.334 47.619 9.21 0.00 0.00 5.19
646 665 0.103572 TTATGGGCTCGGTCGCTAAC 59.896 55.000 0.00 0.00 0.00 2.34
651 670 1.359475 GCTCGGTCGCTAACTAGGG 59.641 63.158 0.00 0.00 37.58 3.53
668 687 5.008980 ACTAGGGACCTATATGCGTCTAAC 58.991 45.833 0.00 0.00 0.00 2.34
684 718 5.638783 CGTCTAACGAAGTCTTTGGAGTAT 58.361 41.667 4.81 0.00 45.00 2.12
687 721 7.201333 CGTCTAACGAAGTCTTTGGAGTATTTC 60.201 40.741 4.81 0.00 45.00 2.17
710 744 1.071239 CGAGCAAAGATTGATACCGCG 60.071 52.381 0.00 0.00 0.00 6.46
734 768 7.692705 GCGAATAAGGTGTTTACAAGAGATTTC 59.307 37.037 0.00 0.00 0.00 2.17
870 904 6.980051 AAAAAGCGTTCGAATAGGACTATT 57.020 33.333 0.00 4.34 38.38 1.73
872 906 8.483307 AAAAAGCGTTCGAATAGGACTATTAA 57.517 30.769 0.00 0.00 36.02 1.40
873 907 8.658499 AAAAGCGTTCGAATAGGACTATTAAT 57.342 30.769 0.00 0.00 36.02 1.40
874 908 9.754382 AAAAGCGTTCGAATAGGACTATTAATA 57.246 29.630 0.00 0.00 36.02 0.98
875 909 9.754382 AAAGCGTTCGAATAGGACTATTAATAA 57.246 29.630 0.00 0.00 36.02 1.40
887 921 8.544687 AGGACTATTAATAAAGTTACGGAGGT 57.455 34.615 0.00 0.00 0.00 3.85
949 988 2.231380 ACCTCCCAAGCCGTTCCAT 61.231 57.895 0.00 0.00 0.00 3.41
950 989 0.912487 ACCTCCCAAGCCGTTCCATA 60.912 55.000 0.00 0.00 0.00 2.74
951 990 0.179045 CCTCCCAAGCCGTTCCATAG 60.179 60.000 0.00 0.00 0.00 2.23
952 991 0.541863 CTCCCAAGCCGTTCCATAGT 59.458 55.000 0.00 0.00 0.00 2.12
954 993 1.483415 TCCCAAGCCGTTCCATAGTAC 59.517 52.381 0.00 0.00 0.00 2.73
955 994 1.485066 CCCAAGCCGTTCCATAGTACT 59.515 52.381 0.00 0.00 0.00 2.73
956 995 2.550978 CCAAGCCGTTCCATAGTACTG 58.449 52.381 5.39 0.00 0.00 2.74
957 996 2.167693 CCAAGCCGTTCCATAGTACTGA 59.832 50.000 5.39 0.00 0.00 3.41
958 997 3.369052 CCAAGCCGTTCCATAGTACTGAA 60.369 47.826 5.39 0.00 0.00 3.02
959 998 4.250464 CAAGCCGTTCCATAGTACTGAAA 58.750 43.478 5.39 0.00 0.00 2.69
960 999 3.858247 AGCCGTTCCATAGTACTGAAAC 58.142 45.455 5.39 3.84 0.00 2.78
961 1000 3.514309 AGCCGTTCCATAGTACTGAAACT 59.486 43.478 5.39 0.00 0.00 2.66
962 1001 4.708421 AGCCGTTCCATAGTACTGAAACTA 59.292 41.667 5.39 0.00 36.44 2.24
979 1018 3.498927 ACTATGTCCCTAAACGTGACG 57.501 47.619 2.24 2.24 0.00 4.35
1021 1065 2.918802 TTCCACACCTACGGCCGT 60.919 61.111 36.01 36.01 0.00 5.68
1214 1258 2.360165 TCTTAACGCTCCCGATTCTACC 59.640 50.000 0.00 0.00 38.29 3.18
1218 1267 2.526432 ACGCTCCCGATTCTACCATAT 58.474 47.619 0.00 0.00 38.29 1.78
1219 1268 2.231478 ACGCTCCCGATTCTACCATATG 59.769 50.000 0.00 0.00 38.29 1.78
1229 1280 6.166279 CGATTCTACCATATGTATGCCACTT 58.834 40.000 1.24 0.00 32.40 3.16
1237 1288 5.124457 CCATATGTATGCCACTTTGATAGCC 59.876 44.000 1.24 0.00 32.40 3.93
1250 1301 0.778815 GATAGCCTCGCGTCGATTTG 59.221 55.000 5.77 0.00 34.61 2.32
1251 1302 1.215655 ATAGCCTCGCGTCGATTTGC 61.216 55.000 5.77 6.47 34.61 3.68
1363 1420 3.818787 CGCACCTGGATGCCAAGC 61.819 66.667 0.00 0.00 42.99 4.01
1449 1506 2.255770 TTCTTTGGGGTTTGGGTTGT 57.744 45.000 0.00 0.00 0.00 3.32
1450 1507 1.490574 TCTTTGGGGTTTGGGTTGTG 58.509 50.000 0.00 0.00 0.00 3.33
1451 1508 0.179059 CTTTGGGGTTTGGGTTGTGC 60.179 55.000 0.00 0.00 0.00 4.57
1454 1511 1.456705 GGGGTTTGGGTTGTGCTGA 60.457 57.895 0.00 0.00 0.00 4.26
1455 1512 1.739667 GGGTTTGGGTTGTGCTGAC 59.260 57.895 0.00 0.00 0.00 3.51
1456 1513 0.755327 GGGTTTGGGTTGTGCTGACT 60.755 55.000 0.00 0.00 0.00 3.41
1457 1514 0.668535 GGTTTGGGTTGTGCTGACTC 59.331 55.000 0.00 0.00 0.00 3.36
1458 1515 0.307760 GTTTGGGTTGTGCTGACTCG 59.692 55.000 0.00 0.00 0.00 4.18
1459 1516 1.444119 TTTGGGTTGTGCTGACTCGC 61.444 55.000 0.00 0.00 0.00 5.03
1460 1517 3.414700 GGGTTGTGCTGACTCGCG 61.415 66.667 0.00 0.00 0.00 5.87
1495 1554 5.003160 TGGATTCTGTCATGGTGTAAACTG 58.997 41.667 0.00 0.00 0.00 3.16
1527 1586 1.686052 GTTGGTGAACTGATGCCCAAA 59.314 47.619 0.00 0.00 36.96 3.28
1554 1613 4.795278 CCAAATAGAGCATTGCGTTTCTTC 59.205 41.667 2.38 0.00 0.00 2.87
1555 1614 3.933155 ATAGAGCATTGCGTTTCTTCG 57.067 42.857 2.38 0.00 0.00 3.79
1556 1615 1.512926 AGAGCATTGCGTTTCTTCGT 58.487 45.000 2.38 0.00 0.00 3.85
1557 1616 2.683968 AGAGCATTGCGTTTCTTCGTA 58.316 42.857 2.38 0.00 0.00 3.43
1558 1617 3.064207 AGAGCATTGCGTTTCTTCGTAA 58.936 40.909 2.38 0.00 39.35 3.18
1559 1618 3.123621 AGAGCATTGCGTTTCTTCGTAAG 59.876 43.478 2.38 0.00 38.57 2.34
1621 1709 5.326069 ACTACGATTAGCATAGAGGGATGT 58.674 41.667 0.00 0.00 0.00 3.06
1644 1732 8.433421 TGTCTTCTAAAGTAGACAAAGTTTGG 57.567 34.615 19.45 2.42 45.27 3.28
1645 1733 7.497909 TGTCTTCTAAAGTAGACAAAGTTTGGG 59.502 37.037 19.45 0.00 45.27 4.12
1646 1734 6.996282 TCTTCTAAAGTAGACAAAGTTTGGGG 59.004 38.462 19.45 0.00 33.84 4.96
1647 1735 5.627135 TCTAAAGTAGACAAAGTTTGGGGG 58.373 41.667 19.45 0.00 34.12 5.40
1649 1737 3.790089 AGTAGACAAAGTTTGGGGGAG 57.210 47.619 19.45 0.00 34.12 4.30
1650 1738 3.323775 AGTAGACAAAGTTTGGGGGAGA 58.676 45.455 19.45 0.00 34.12 3.71
1690 1788 3.855503 CTTGCCTGGGAGCACAGCA 62.856 63.158 0.00 0.00 43.97 4.41
1697 1795 0.467844 TGGGAGCACAGCAAACACAT 60.468 50.000 0.00 0.00 0.00 3.21
1700 1798 0.110056 GAGCACAGCAAACACATCCG 60.110 55.000 0.00 0.00 0.00 4.18
1704 1802 0.944386 ACAGCAAACACATCCGTCAC 59.056 50.000 0.00 0.00 0.00 3.67
1724 1822 7.168972 CCGTCACATTTTGAAGCAATTTTTAGA 59.831 33.333 0.00 0.00 35.39 2.10
1744 1842 4.826556 AGAGGTAGCATTTCAAGAGTGAC 58.173 43.478 0.00 0.00 31.90 3.67
1749 1847 4.077300 AGCATTTCAAGAGTGACTCACA 57.923 40.909 15.86 0.00 36.74 3.58
2082 2185 7.316640 CCACAGGCATAACTGATAGTATCTAC 58.683 42.308 11.40 0.00 40.97 2.59
2084 2187 9.232473 CACAGGCATAACTGATAGTATCTACTA 57.768 37.037 11.40 0.00 40.85 1.82
2110 2213 8.525290 TCATGTATAGTTGATGAAGAGAGACA 57.475 34.615 0.00 0.00 0.00 3.41
2226 2329 6.761714 ACAATCAACTCCGTCAGATTAATACC 59.238 38.462 0.00 0.00 0.00 2.73
2306 2409 1.064832 AGGGAGAGCAGGAGAAATTGC 60.065 52.381 0.00 0.00 0.00 3.56
2346 2455 3.865700 GCAGCAGTTGGTGGTAAAC 57.134 52.632 12.65 0.00 43.24 2.01
2382 2491 8.386264 GGGAAGAATTATATGAGGAATCAGGAA 58.614 37.037 0.00 0.00 0.00 3.36
2473 2582 1.960994 GAAGAAAGCTGCGCGAGGAC 61.961 60.000 12.10 0.00 0.00 3.85
2504 2613 6.830324 TCATTTCTTCCTGTTCCTGATAATGG 59.170 38.462 0.00 0.00 0.00 3.16
2529 2638 4.994220 TCATGCATCACATTGTTTTTGC 57.006 36.364 0.00 7.92 36.64 3.68
2570 2679 8.225603 AGTGCATTTAGTTAATATTGACCCTG 57.774 34.615 6.74 1.94 0.00 4.45
2689 2918 9.180678 GTGTAATGTTTGATTTCGTTTCATCTT 57.819 29.630 0.00 0.00 0.00 2.40
2692 2921 8.970691 AATGTTTGATTTCGTTTCATCTTAGG 57.029 30.769 0.00 0.00 0.00 2.69
2694 2923 7.936584 TGTTTGATTTCGTTTCATCTTAGGTT 58.063 30.769 0.00 0.00 0.00 3.50
2695 2924 7.860373 TGTTTGATTTCGTTTCATCTTAGGTTG 59.140 33.333 0.00 0.00 0.00 3.77
2696 2925 5.938322 TGATTTCGTTTCATCTTAGGTTGC 58.062 37.500 0.00 0.00 0.00 4.17
2697 2926 5.471797 TGATTTCGTTTCATCTTAGGTTGCA 59.528 36.000 0.00 0.00 0.00 4.08
2698 2927 5.759506 TTTCGTTTCATCTTAGGTTGCAA 57.240 34.783 0.00 0.00 0.00 4.08
2699 2928 5.957842 TTCGTTTCATCTTAGGTTGCAAT 57.042 34.783 0.59 0.00 0.00 3.56
2700 2929 5.957842 TCGTTTCATCTTAGGTTGCAATT 57.042 34.783 0.59 0.00 0.00 2.32
2701 2930 6.325919 TCGTTTCATCTTAGGTTGCAATTT 57.674 33.333 0.59 0.00 0.00 1.82
2728 2957 9.816787 TTTTACCCATCCTTACATTTAAGTTCT 57.183 29.630 0.00 0.00 33.92 3.01
2779 3010 7.839705 TCCCTACTTGAATAGATTCTGTAGTGT 59.160 37.037 20.89 9.28 39.66 3.55
2828 3185 9.615295 TCAAATAATTAAGCGGAAGTAAAACAC 57.385 29.630 0.00 0.00 0.00 3.32
2837 3194 4.272748 GCGGAAGTAAAACACCATCCTATC 59.727 45.833 0.00 0.00 33.43 2.08
2838 3195 4.814771 CGGAAGTAAAACACCATCCTATCC 59.185 45.833 0.00 0.00 33.43 2.59
2850 3207 6.176183 CACCATCCTATCCATTCCAATAGAC 58.824 44.000 0.00 0.00 0.00 2.59
2851 3208 5.851693 ACCATCCTATCCATTCCAATAGACA 59.148 40.000 0.00 0.00 0.00 3.41
2918 3306 5.067674 GGCATTCACTTTTGCATATACCAGA 59.932 40.000 0.00 0.00 40.66 3.86
2948 3336 8.974060 ACTTTTAAGGAAGTAGTGATTTGACA 57.026 30.769 0.00 0.00 38.06 3.58
3006 3422 9.391006 TGATGTATTCTCCAGTTTTATACAACC 57.609 33.333 0.00 0.00 35.88 3.77
3007 3423 9.391006 GATGTATTCTCCAGTTTTATACAACCA 57.609 33.333 0.00 0.00 35.88 3.67
3015 3431 8.371770 TCCAGTTTTATACAACCAAAAATTGC 57.628 30.769 0.00 0.00 31.96 3.56
3018 3434 8.825745 CAGTTTTATACAACCAAAAATTGCTGT 58.174 29.630 0.00 0.00 0.00 4.40
3040 3456 6.520272 TGTCCTTGGAAAACATTACCATTTG 58.480 36.000 0.00 0.00 33.56 2.32
3062 3478 2.040278 TCTGTCCCCTTTGAACATCTGG 59.960 50.000 0.00 0.00 0.00 3.86
3097 3513 4.527509 TTCCATGTGTGTGTGTTTGTTT 57.472 36.364 0.00 0.00 0.00 2.83
3129 3545 4.156556 GCCATGTGCTTCATTTAGAGACAA 59.843 41.667 0.00 0.00 36.87 3.18
3130 3546 5.634896 CCATGTGCTTCATTTAGAGACAAC 58.365 41.667 0.00 0.00 34.09 3.32
3131 3547 5.413833 CCATGTGCTTCATTTAGAGACAACT 59.586 40.000 0.00 0.00 34.09 3.16
3136 3552 5.049198 TGCTTCATTTAGAGACAACTGCTTG 60.049 40.000 0.00 0.00 0.00 4.01
3137 3553 5.180117 GCTTCATTTAGAGACAACTGCTTGA 59.820 40.000 0.00 0.00 0.00 3.02
3154 3570 7.425606 ACTGCTTGAACTAACCTTAATTGTTG 58.574 34.615 0.00 0.00 0.00 3.33
3157 3573 7.502895 TGCTTGAACTAACCTTAATTGTTGGTA 59.497 33.333 7.23 0.00 36.55 3.25
3158 3574 8.354426 GCTTGAACTAACCTTAATTGTTGGTAA 58.646 33.333 7.23 1.06 36.55 2.85
3192 3610 3.755905 TGTGATGCCTAATTTCGCTTGAA 59.244 39.130 0.00 0.00 0.00 2.69
3265 3683 4.035675 GCAATGAGCTGGTATTACAAGGTC 59.964 45.833 19.29 19.29 41.15 3.85
3286 3704 0.179111 TGGCGCTATCAAAGGAGACG 60.179 55.000 7.64 0.00 0.00 4.18
3371 3789 1.768684 TTTGGAGGGAGCAGCGAAGT 61.769 55.000 0.00 0.00 0.00 3.01
3376 3794 0.037232 AGGGAGCAGCGAAGTTGTAC 60.037 55.000 0.00 0.00 42.08 2.90
3405 3823 0.630673 ATATCAAGGTTGCAGCCCCA 59.369 50.000 16.95 0.10 0.00 4.96
3446 3864 4.319046 CGTTGTTGGAGATCAAACACTCAG 60.319 45.833 2.19 0.00 37.08 3.35
3453 3871 4.153835 GGAGATCAAACACTCAGCTTCTTG 59.846 45.833 0.00 0.00 35.17 3.02
3527 3945 0.322726 TGCTTGCTTGCTATCTGGCA 60.323 50.000 3.47 0.00 40.74 4.92
3538 3956 2.898705 CTATCTGGCAGAAAACGAGCT 58.101 47.619 22.84 4.66 0.00 4.09
3585 4003 3.499338 TGGAGCACTTGAATTGTCCATT 58.501 40.909 3.87 0.00 0.00 3.16
3591 4009 4.096984 GCACTTGAATTGTCCATTAGGAGG 59.903 45.833 0.00 0.00 46.92 4.30
3596 4014 0.918983 TTGTCCATTAGGAGGCCCTG 59.081 55.000 0.00 0.00 46.92 4.45
3598 4016 1.009060 TGTCCATTAGGAGGCCCTGTA 59.991 52.381 0.00 0.00 46.92 2.74
3603 4021 3.515901 CCATTAGGAGGCCCTGTATACTC 59.484 52.174 0.00 0.00 44.15 2.59
3610 4028 3.297736 AGGCCCTGTATACTCTGTGTAC 58.702 50.000 0.00 0.00 33.45 2.90
3651 4069 1.237285 GCATGTGCGGGTTCAGAGTT 61.237 55.000 0.00 0.00 0.00 3.01
3652 4070 0.798776 CATGTGCGGGTTCAGAGTTC 59.201 55.000 0.00 0.00 0.00 3.01
3653 4071 0.687354 ATGTGCGGGTTCAGAGTTCT 59.313 50.000 0.00 0.00 0.00 3.01
3717 4138 2.031012 TGTGCGGCTTCAGGACTG 59.969 61.111 0.00 0.00 0.00 3.51
3718 4139 2.031163 GTGCGGCTTCAGGACTGT 59.969 61.111 0.00 0.00 0.00 3.55
3886 4681 6.458206 GCCATCGAGACATTTATAAGTGCAAA 60.458 38.462 7.82 0.00 0.00 3.68
3906 5045 8.621286 GTGCAAATACAGTATAAAGTTGGCTAT 58.379 33.333 0.00 0.00 0.00 2.97
3975 5114 6.607689 TGTCAAAAAGCGTCTTACATTATGG 58.392 36.000 0.00 0.00 0.00 2.74
3982 5121 3.554337 GCGTCTTACATTATGGGACGGAT 60.554 47.826 25.20 0.00 46.26 4.18
3989 5128 4.168101 ACATTATGGGACGGATGGAGTAT 58.832 43.478 0.00 0.00 0.00 2.12
3991 5130 5.422331 ACATTATGGGACGGATGGAGTATAG 59.578 44.000 0.00 0.00 0.00 1.31
4004 5144 7.868415 CGGATGGAGTATAGGTCTTTTTAGAAG 59.132 40.741 0.00 0.00 0.00 2.85
4010 5150 9.939802 GAGTATAGGTCTTTTTAGAAGTTCCAA 57.060 33.333 0.00 0.00 0.00 3.53
4202 5442 1.136695 TGAGCCAAACCAGCAAAACAG 59.863 47.619 0.00 0.00 0.00 3.16
4276 5517 1.103398 AGCTGGTTCGTTTTGCAGCT 61.103 50.000 0.00 0.00 36.91 4.24
4505 6758 1.171308 GCTGTGTGCTCCATGTGATT 58.829 50.000 0.00 0.00 38.95 2.57
4576 6829 5.560724 TCCTTTTTCTCGAGTGAATTCCAT 58.439 37.500 13.13 0.00 0.00 3.41
4580 6833 7.327032 CCTTTTTCTCGAGTGAATTCCATTTTC 59.673 37.037 13.13 0.00 0.00 2.29
4614 6867 8.331730 AGTTGTACATTTGGGACACTAATTAC 57.668 34.615 0.00 0.00 39.29 1.89
4633 6886 3.328382 ACCCGATCGAGTGAAAATTCA 57.672 42.857 18.66 0.00 34.20 2.57
4646 6899 8.936864 CGAGTGAAAATTCATCTATAATACCCC 58.063 37.037 0.00 0.00 39.73 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 36 7.793427 CCAAACATTTTTGTCAAAATCGTGATC 59.207 33.333 11.44 0.00 40.09 2.92
39 41 6.595772 TCCCAAACATTTTTGTCAAAATCG 57.404 33.333 11.44 8.28 40.09 3.34
79 84 8.954950 AATACACAAACATTTTTCCACAATCA 57.045 26.923 0.00 0.00 0.00 2.57
84 89 8.359060 TGCTTAATACACAAACATTTTTCCAC 57.641 30.769 0.00 0.00 0.00 4.02
289 295 9.008965 AGGCAAACATTATTAAAATTGGGAAAC 57.991 29.630 0.00 0.00 0.00 2.78
303 309 9.723601 ACAATTTTGTGAATAGGCAAACATTAT 57.276 25.926 0.00 0.00 40.49 1.28
315 322 9.645059 TGAAAACTGTGAACAATTTTGTGAATA 57.355 25.926 7.29 0.00 41.31 1.75
370 378 6.479660 TCATCAACTTTTTCCAATTTGTGAGC 59.520 34.615 0.00 0.00 0.00 4.26
619 638 1.747367 CGAGCCCATAAACCCGCAA 60.747 57.895 0.00 0.00 0.00 4.85
632 651 1.359475 CCTAGTTAGCGACCGAGCC 59.641 63.158 0.00 0.00 38.01 4.70
646 665 4.094590 CGTTAGACGCATATAGGTCCCTAG 59.905 50.000 0.00 0.00 33.65 3.02
651 670 5.049543 AGACTTCGTTAGACGCATATAGGTC 60.050 44.000 0.00 0.00 42.21 3.85
668 687 6.083925 CGAAGAAATACTCCAAAGACTTCG 57.916 41.667 0.00 0.00 45.11 3.79
684 718 5.063438 CGGTATCAATCTTTGCTCGAAGAAA 59.937 40.000 3.87 0.00 38.98 2.52
687 721 3.302740 GCGGTATCAATCTTTGCTCGAAG 60.303 47.826 0.00 0.00 0.00 3.79
871 905 8.897752 CAGTACTACTACCTCCGTAACTTTATT 58.102 37.037 0.00 0.00 0.00 1.40
872 906 8.267894 TCAGTACTACTACCTCCGTAACTTTAT 58.732 37.037 0.00 0.00 0.00 1.40
873 907 7.620880 TCAGTACTACTACCTCCGTAACTTTA 58.379 38.462 0.00 0.00 0.00 1.85
874 908 6.476378 TCAGTACTACTACCTCCGTAACTTT 58.524 40.000 0.00 0.00 0.00 2.66
875 909 6.054860 TCAGTACTACTACCTCCGTAACTT 57.945 41.667 0.00 0.00 0.00 2.66
879 913 6.054860 AGTTTCAGTACTACTACCTCCGTA 57.945 41.667 0.00 0.00 0.00 4.02
881 915 6.541641 ACATAGTTTCAGTACTACTACCTCCG 59.458 42.308 6.21 0.00 33.69 4.63
882 916 7.681543 GCACATAGTTTCAGTACTACTACCTCC 60.682 44.444 6.21 0.00 33.69 4.30
883 917 7.194962 GCACATAGTTTCAGTACTACTACCTC 58.805 42.308 6.21 0.00 33.69 3.85
885 919 6.127535 TGGCACATAGTTTCAGTACTACTACC 60.128 42.308 6.21 4.61 33.69 3.18
886 920 6.750963 GTGGCACATAGTTTCAGTACTACTAC 59.249 42.308 13.86 0.31 44.52 2.73
887 921 6.434965 TGTGGCACATAGTTTCAGTACTACTA 59.565 38.462 17.96 6.49 44.52 1.82
949 988 7.394359 ACGTTTAGGGACATAGTTTCAGTACTA 59.606 37.037 0.00 0.00 35.25 1.82
950 989 6.210185 ACGTTTAGGGACATAGTTTCAGTACT 59.790 38.462 0.00 0.00 0.00 2.73
951 990 6.309737 CACGTTTAGGGACATAGTTTCAGTAC 59.690 42.308 0.00 0.00 0.00 2.73
952 991 6.209192 TCACGTTTAGGGACATAGTTTCAGTA 59.791 38.462 0.00 0.00 0.00 2.74
954 993 5.475719 TCACGTTTAGGGACATAGTTTCAG 58.524 41.667 0.00 0.00 0.00 3.02
955 994 5.471556 TCACGTTTAGGGACATAGTTTCA 57.528 39.130 0.00 0.00 0.00 2.69
967 1006 1.301087 TGGTGGCGTCACGTTTAGG 60.301 57.895 14.98 0.00 44.50 2.69
968 1007 1.562575 GGTGGTGGCGTCACGTTTAG 61.563 60.000 14.98 0.00 44.50 1.85
969 1008 1.594836 GGTGGTGGCGTCACGTTTA 60.595 57.895 14.98 0.00 44.50 2.01
970 1009 2.898343 GGTGGTGGCGTCACGTTT 60.898 61.111 14.98 0.00 44.50 3.60
971 1010 4.922026 GGGTGGTGGCGTCACGTT 62.922 66.667 14.98 0.00 44.50 3.99
1125 1169 1.343580 GGTAGAAGAAGAGAGGGGCCT 60.344 57.143 0.84 0.00 0.00 5.19
1128 1172 1.342175 ACGGGTAGAAGAAGAGAGGGG 60.342 57.143 0.00 0.00 0.00 4.79
1214 1258 5.942236 AGGCTATCAAAGTGGCATACATATG 59.058 40.000 0.00 0.00 36.78 1.78
1218 1267 3.741075 CGAGGCTATCAAAGTGGCATACA 60.741 47.826 0.00 0.00 0.00 2.29
1219 1268 2.802816 CGAGGCTATCAAAGTGGCATAC 59.197 50.000 0.00 0.00 0.00 2.39
1229 1280 0.384309 AATCGACGCGAGGCTATCAA 59.616 50.000 15.93 0.00 39.91 2.57
1237 1288 0.043566 CATGAGCAAATCGACGCGAG 60.044 55.000 15.93 6.55 39.91 5.03
1251 1302 3.451556 ATGGAGACGCCGGCATGAG 62.452 63.158 28.98 12.87 40.66 2.90
1363 1420 3.129502 CTGCCACGCCTCACCATG 61.130 66.667 0.00 0.00 0.00 3.66
1368 1425 4.687215 GTCAGCTGCCACGCCTCA 62.687 66.667 9.47 0.00 0.00 3.86
1449 1506 1.371758 GTTGTCTCGCGAGTCAGCA 60.372 57.895 32.69 24.57 36.85 4.41
1450 1507 2.089349 GGTTGTCTCGCGAGTCAGC 61.089 63.158 30.99 30.99 0.00 4.26
1451 1508 0.318699 TTGGTTGTCTCGCGAGTCAG 60.319 55.000 33.33 11.53 0.00 3.51
1454 1511 1.148310 CATTTGGTTGTCTCGCGAGT 58.852 50.000 33.33 10.14 0.00 4.18
1455 1512 0.443869 CCATTTGGTTGTCTCGCGAG 59.556 55.000 30.03 30.03 0.00 5.03
1456 1513 0.034198 TCCATTTGGTTGTCTCGCGA 59.966 50.000 9.26 9.26 36.34 5.87
1457 1514 1.086696 ATCCATTTGGTTGTCTCGCG 58.913 50.000 0.00 0.00 36.34 5.87
1458 1515 2.749621 AGAATCCATTTGGTTGTCTCGC 59.250 45.455 0.00 0.00 36.34 5.03
1459 1516 3.753272 ACAGAATCCATTTGGTTGTCTCG 59.247 43.478 0.00 0.00 36.34 4.04
1460 1517 4.761739 TGACAGAATCCATTTGGTTGTCTC 59.238 41.667 17.91 4.20 35.99 3.36
1495 1554 5.241064 TCAGTTCACCAACTCTACAGTCTAC 59.759 44.000 0.00 0.00 41.24 2.59
1527 1586 1.745087 CGCAATGCTCTATTTGGGTGT 59.255 47.619 2.94 0.00 0.00 4.16
1554 1613 2.002586 CCATGTTCACAGCCTCTTACG 58.997 52.381 0.00 0.00 0.00 3.18
1555 1614 1.740025 GCCATGTTCACAGCCTCTTAC 59.260 52.381 0.00 0.00 0.00 2.34
1556 1615 1.630369 AGCCATGTTCACAGCCTCTTA 59.370 47.619 0.00 0.00 0.00 2.10
1557 1616 0.403271 AGCCATGTTCACAGCCTCTT 59.597 50.000 0.00 0.00 0.00 2.85
1558 1617 0.322277 CAGCCATGTTCACAGCCTCT 60.322 55.000 0.00 0.00 0.00 3.69
1559 1618 0.607489 ACAGCCATGTTCACAGCCTC 60.607 55.000 0.00 0.00 35.63 4.70
1560 1619 0.892358 CACAGCCATGTTCACAGCCT 60.892 55.000 0.00 0.00 37.65 4.58
1561 1620 1.582968 CACAGCCATGTTCACAGCC 59.417 57.895 0.00 0.00 37.65 4.85
1562 1621 0.890542 TCCACAGCCATGTTCACAGC 60.891 55.000 0.00 0.00 37.65 4.40
1563 1622 0.877071 GTCCACAGCCATGTTCACAG 59.123 55.000 0.00 0.00 37.65 3.66
1564 1623 0.473755 AGTCCACAGCCATGTTCACA 59.526 50.000 0.00 0.00 37.65 3.58
1621 1709 6.996282 CCCCAAACTTTGTCTACTTTAGAAGA 59.004 38.462 0.88 0.00 36.40 2.87
1643 1731 0.688087 CAGGACAGTAGGTCTCCCCC 60.688 65.000 0.00 0.00 46.16 5.40
1644 1732 1.331399 GCAGGACAGTAGGTCTCCCC 61.331 65.000 0.00 0.00 46.16 4.81
1645 1733 1.668101 CGCAGGACAGTAGGTCTCCC 61.668 65.000 0.00 0.00 46.16 4.30
1646 1734 1.810532 CGCAGGACAGTAGGTCTCC 59.189 63.158 0.00 0.00 46.16 3.71
1647 1735 1.139947 GCGCAGGACAGTAGGTCTC 59.860 63.158 0.30 0.00 46.16 3.36
1649 1737 1.961180 ATGGCGCAGGACAGTAGGTC 61.961 60.000 10.83 0.00 46.20 3.85
1650 1738 1.990060 ATGGCGCAGGACAGTAGGT 60.990 57.895 10.83 0.00 32.06 3.08
1690 1788 4.909696 TCAAAATGTGACGGATGTGTTT 57.090 36.364 0.00 0.00 0.00 2.83
1697 1795 4.582701 AATTGCTTCAAAATGTGACGGA 57.417 36.364 0.00 0.00 35.39 4.69
1700 1798 8.490355 CCTCTAAAAATTGCTTCAAAATGTGAC 58.510 33.333 0.00 0.00 35.39 3.67
1704 1802 8.650714 GCTACCTCTAAAAATTGCTTCAAAATG 58.349 33.333 0.00 0.00 0.00 2.32
1724 1822 4.284490 TGAGTCACTCTTGAAATGCTACCT 59.716 41.667 6.33 0.00 31.90 3.08
1744 1842 7.864686 TGTACATTCTGAACAAGATTTGTGAG 58.135 34.615 0.00 0.00 44.59 3.51
2084 2187 9.140874 TGTCTCTCTTCATCAACTATACATGAT 57.859 33.333 0.00 0.00 36.74 2.45
2085 2188 8.525290 TGTCTCTCTTCATCAACTATACATGA 57.475 34.615 0.00 0.00 0.00 3.07
2086 2189 9.761504 AATGTCTCTCTTCATCAACTATACATG 57.238 33.333 0.00 0.00 0.00 3.21
2110 2213 4.870363 ACAAAATTAGCACAGCGTGAAAT 58.130 34.783 11.94 7.89 35.23 2.17
2211 2314 3.644884 AGAGCGGTATTAATCTGACGG 57.355 47.619 0.00 0.00 0.00 4.79
2226 2329 1.086634 GTGCCTGCCTTCTAAGAGCG 61.087 60.000 0.00 0.00 0.00 5.03
2306 2409 3.275617 TCCTGGGATCAACAATAACCG 57.724 47.619 0.00 0.00 0.00 4.44
2382 2491 5.700402 ACTCCATTACTGCCTTATCAAGT 57.300 39.130 0.00 0.00 0.00 3.16
2473 2582 5.645497 CAGGAACAGGAAGAAATGAACCTAG 59.355 44.000 0.00 0.00 0.00 3.02
2529 2638 7.935338 AAATGCACTTTTGTTTATCAGTGAG 57.065 32.000 0.00 0.00 0.00 3.51
2570 2679 7.499232 ACCAGAGAATTATACTTACAATGGTGC 59.501 37.037 0.00 0.00 34.98 5.01
2679 2908 7.406799 AAAAATTGCAACCTAAGATGAAACG 57.593 32.000 0.00 0.00 0.00 3.60
2706 2935 6.890268 GGAAGAACTTAAATGTAAGGATGGGT 59.110 38.462 7.58 0.00 41.03 4.51
2718 2947 5.789643 TTGCTTGCAGGAAGAACTTAAAT 57.210 34.783 5.73 0.00 32.82 1.40
2727 2956 6.032094 CAGTAATACAATTGCTTGCAGGAAG 58.968 40.000 5.05 0.00 35.69 3.46
2728 2957 5.622007 GCAGTAATACAATTGCTTGCAGGAA 60.622 40.000 5.05 0.00 35.69 3.36
2779 3010 4.082625 ACAATTGCTCATTCTGATTTCGCA 60.083 37.500 5.05 0.00 0.00 5.10
2806 3037 7.690952 TGGTGTTTTACTTCCGCTTAATTAT 57.309 32.000 0.00 0.00 0.00 1.28
2809 3040 5.124936 GGATGGTGTTTTACTTCCGCTTAAT 59.875 40.000 0.00 0.00 0.00 1.40
2811 3042 4.004982 GGATGGTGTTTTACTTCCGCTTA 58.995 43.478 0.00 0.00 0.00 3.09
2812 3043 2.817844 GGATGGTGTTTTACTTCCGCTT 59.182 45.455 0.00 0.00 0.00 4.68
2813 3044 2.039879 AGGATGGTGTTTTACTTCCGCT 59.960 45.455 0.00 0.00 36.94 5.52
2814 3045 2.433436 AGGATGGTGTTTTACTTCCGC 58.567 47.619 0.00 0.00 36.94 5.54
2828 3185 6.378661 TGTCTATTGGAATGGATAGGATGG 57.621 41.667 0.00 0.00 0.00 3.51
2837 3194 5.068636 CAGAATCCCTGTCTATTGGAATGG 58.931 45.833 0.00 0.00 38.10 3.16
2838 3195 4.518211 GCAGAATCCCTGTCTATTGGAATG 59.482 45.833 0.00 0.00 44.71 2.67
2850 3207 3.502211 ACGTTTTTAGTGCAGAATCCCTG 59.498 43.478 0.00 0.00 45.67 4.45
2851 3208 3.751518 ACGTTTTTAGTGCAGAATCCCT 58.248 40.909 0.00 0.00 0.00 4.20
2868 3225 7.330700 CCCAAATTATGAAAGCAAACATACGTT 59.669 33.333 0.00 0.00 36.73 3.99
2869 3226 6.811170 CCCAAATTATGAAAGCAAACATACGT 59.189 34.615 0.00 0.00 0.00 3.57
2870 3227 6.255453 CCCCAAATTATGAAAGCAAACATACG 59.745 38.462 0.00 0.00 0.00 3.06
2932 3320 9.967346 TGCTACTATATGTCAAATCACTACTTC 57.033 33.333 0.00 0.00 0.00 3.01
3002 3418 3.560896 CCAAGGACAGCAATTTTTGGTTG 59.439 43.478 0.00 0.00 39.79 3.77
3006 3422 5.353678 TGTTTTCCAAGGACAGCAATTTTTG 59.646 36.000 0.00 0.00 0.00 2.44
3007 3423 5.495640 TGTTTTCCAAGGACAGCAATTTTT 58.504 33.333 0.00 0.00 0.00 1.94
3011 3427 4.961438 AATGTTTTCCAAGGACAGCAAT 57.039 36.364 0.00 0.00 0.00 3.56
3013 3429 3.572255 GGTAATGTTTTCCAAGGACAGCA 59.428 43.478 0.00 0.00 0.00 4.41
3015 3431 5.982890 ATGGTAATGTTTTCCAAGGACAG 57.017 39.130 0.00 0.00 34.80 3.51
3018 3434 6.553100 AGACAAATGGTAATGTTTTCCAAGGA 59.447 34.615 0.00 0.00 34.80 3.36
3040 3456 3.077359 CAGATGTTCAAAGGGGACAGAC 58.923 50.000 0.00 0.00 0.00 3.51
3062 3478 5.354234 CACACATGGAAAAGGTAGGTACATC 59.646 44.000 0.00 0.00 0.00 3.06
3129 3545 7.425606 CAACAATTAAGGTTAGTTCAAGCAGT 58.574 34.615 0.00 0.00 37.09 4.40
3130 3546 6.863126 CCAACAATTAAGGTTAGTTCAAGCAG 59.137 38.462 0.00 0.00 37.09 4.24
3131 3547 6.322712 ACCAACAATTAAGGTTAGTTCAAGCA 59.677 34.615 0.00 0.00 37.09 3.91
3164 3580 3.627123 CGAAATTAGGCATCACATGGTGA 59.373 43.478 1.05 1.05 46.90 4.02
3165 3581 3.793129 GCGAAATTAGGCATCACATGGTG 60.793 47.826 0.00 0.00 34.45 4.17
3167 3583 2.620115 AGCGAAATTAGGCATCACATGG 59.380 45.455 0.00 0.00 0.00 3.66
3169 3585 3.947196 TCAAGCGAAATTAGGCATCACAT 59.053 39.130 3.80 0.00 0.00 3.21
3185 3603 4.382754 GCCTAAGACAACAAATTTCAAGCG 59.617 41.667 0.00 0.00 0.00 4.68
3192 3610 3.505680 TGATGCGCCTAAGACAACAAATT 59.494 39.130 4.18 0.00 0.00 1.82
3256 3674 1.138266 GATAGCGCCAGGACCTTGTAA 59.862 52.381 2.29 0.00 0.00 2.41
3265 3683 0.465705 TCTCCTTTGATAGCGCCAGG 59.534 55.000 2.29 0.00 0.00 4.45
3286 3704 2.203126 CAGCCAGAATCCTCGCCC 60.203 66.667 0.00 0.00 0.00 6.13
3376 3794 3.486108 GCAACCTTGATATGTACTCGTCG 59.514 47.826 0.00 0.00 0.00 5.12
3395 3813 1.675310 CTCAATCGTGGGGCTGCAA 60.675 57.895 0.50 0.00 0.00 4.08
3405 3823 2.202623 GTCCGAGCGCTCAATCGT 60.203 61.111 34.69 0.00 37.23 3.73
3446 3864 2.197577 GATCGGTCAGTAGCAAGAAGC 58.802 52.381 0.00 0.00 46.19 3.86
3453 3871 0.104855 TGGCATGATCGGTCAGTAGC 59.895 55.000 3.97 8.23 37.87 3.58
3462 3880 2.664185 CGGGCTCTGGCATGATCG 60.664 66.667 0.00 0.00 40.87 3.69
3527 3945 4.202050 ACAAGCAAAATCAGCTCGTTTTCT 60.202 37.500 3.27 2.64 42.53 2.52
3538 3956 7.327214 ACCAAGTTAAAAGACAAGCAAAATCA 58.673 30.769 0.00 0.00 0.00 2.57
3585 4003 2.789992 ACAGAGTATACAGGGCCTCCTA 59.210 50.000 0.95 0.00 42.67 2.94
3591 4009 4.939052 ATGTACACAGAGTATACAGGGC 57.061 45.455 5.50 0.00 34.67 5.19
3596 4014 8.570096 TCGCAATTTATGTACACAGAGTATAC 57.430 34.615 0.00 0.00 34.67 1.47
3598 4016 7.171508 CCATCGCAATTTATGTACACAGAGTAT 59.828 37.037 0.00 0.00 34.67 2.12
3603 4021 5.265477 CACCATCGCAATTTATGTACACAG 58.735 41.667 0.00 0.00 0.00 3.66
3610 4028 4.478699 CCATAGCACCATCGCAATTTATG 58.521 43.478 0.00 0.00 0.00 1.90
3717 4138 4.700692 TCAGGATATGATACTCTGCGGTAC 59.299 45.833 0.00 0.00 31.12 3.34
3718 4139 4.700692 GTCAGGATATGATACTCTGCGGTA 59.299 45.833 0.00 0.00 40.92 4.02
3886 4681 7.534723 TCGGATAGCCAACTTTATACTGTAT 57.465 36.000 5.53 5.53 0.00 2.29
3898 5037 1.278238 CTCGTGTTCGGATAGCCAAC 58.722 55.000 0.00 1.63 37.69 3.77
3906 5045 0.109272 GAGTGATGCTCGTGTTCGGA 60.109 55.000 0.00 0.00 37.69 4.55
3960 5099 2.132762 CCGTCCCATAATGTAAGACGC 58.867 52.381 5.39 0.00 46.66 5.19
3975 5114 3.157750 AGACCTATACTCCATCCGTCC 57.842 52.381 0.00 0.00 0.00 4.79
3982 5121 8.537858 GGAACTTCTAAAAAGACCTATACTCCA 58.462 37.037 0.00 0.00 0.00 3.86
3991 5130 9.459640 GTTTGTATTGGAACTTCTAAAAAGACC 57.540 33.333 0.00 0.00 0.00 3.85
4004 5144 7.585286 TGACGTATGTAGTTTGTATTGGAAC 57.415 36.000 0.00 0.00 0.00 3.62
4036 5272 9.367444 CGGAGTAAAATGAGTAAATCTACACTT 57.633 33.333 0.00 0.00 0.00 3.16
4157 5397 8.393366 CAGTAACAATTGTGTCATGATAGGAAG 58.607 37.037 12.82 0.00 36.80 3.46
4164 5404 4.455533 GGCTCAGTAACAATTGTGTCATGA 59.544 41.667 12.82 12.70 36.80 3.07
4202 5442 1.509703 AAAGTTCGGCTCGGTTCTTC 58.490 50.000 0.00 0.00 0.00 2.87
4276 5517 3.177884 ACCTGCCCAGCTCACCAA 61.178 61.111 0.00 0.00 0.00 3.67
4289 5530 1.404717 CGGTGTCATTCAGAGGACCTG 60.405 57.143 0.00 0.00 44.27 4.00
4294 6545 1.364626 GCTGCGGTGTCATTCAGAGG 61.365 60.000 0.00 0.00 0.00 3.69
4296 6547 0.671472 CTGCTGCGGTGTCATTCAGA 60.671 55.000 0.00 0.00 0.00 3.27
4319 6570 7.015195 TCCTATCTGCACATACAAGCATAACTA 59.985 37.037 0.00 0.00 40.42 2.24
4328 6579 4.384098 CCCTTGTCCTATCTGCACATACAA 60.384 45.833 0.00 0.00 0.00 2.41
4349 6600 0.109342 ATGTTCGAGCCCATCATCCC 59.891 55.000 0.00 0.00 0.00 3.85
4505 6758 0.682532 TACCCCCATGTACGTACGCA 60.683 55.000 20.18 6.61 0.00 5.24
4576 6829 8.842280 CCAAATGTACAACTACAAGGTAGAAAA 58.158 33.333 10.17 0.00 36.43 2.29
4580 6833 6.370718 GTCCCAAATGTACAACTACAAGGTAG 59.629 42.308 0.00 2.00 36.43 3.18
4614 6867 4.122776 AGATGAATTTTCACTCGATCGGG 58.877 43.478 14.88 14.88 40.49 5.14


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

AutoCloner maintained by Alex Coulton.