Multiple sequence alignment - TraesCS1A01G065400

Loading Multiple Alignment...

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 TraesCS1A01G065400 chr1A 100.000 7139 0 0 1 7139 47799404 47806542 0.000000e+00 13184.0
1 TraesCS1A01G065400 chr1A 84.158 101 13 2 455 555 47789883 47789980 2.120000e-15 95.3
2 TraesCS1A01G065400 chr1D 93.565 3248 122 38 288 3509 47873226 47876412 0.000000e+00 4759.0
3 TraesCS1A01G065400 chr1D 96.429 2744 76 12 3559 6286 47876580 47879317 0.000000e+00 4505.0
4 TraesCS1A01G065400 chr1D 88.419 544 31 10 6474 7009 47879447 47879966 1.690000e-175 627.0
5 TraesCS1A01G065400 chr1D 93.857 293 13 3 1 289 47872899 47873190 3.060000e-118 436.0
6 TraesCS1A01G065400 chr1D 84.375 224 17 9 1183 1391 47873999 47874219 3.380000e-48 204.0
7 TraesCS1A01G065400 chr1D 97.183 71 2 0 7059 7129 47879980 47880050 3.500000e-23 121.0
8 TraesCS1A01G065400 chr1D 85.714 105 13 2 2722 2824 253346848 253346952 7.570000e-20 110.0
9 TraesCS1A01G065400 chr1B 93.069 2799 111 21 3506 6286 67537565 67540298 0.000000e+00 4017.0
10 TraesCS1A01G065400 chr1B 96.152 1767 55 7 1746 3509 67535611 67537367 0.000000e+00 2874.0
11 TraesCS1A01G065400 chr1B 88.510 792 54 20 1081 1870 67534855 67535611 0.000000e+00 924.0
12 TraesCS1A01G065400 chr1B 86.845 783 45 22 6373 7129 67540461 67541211 0.000000e+00 822.0
13 TraesCS1A01G065400 chr1B 90.141 568 41 6 288 849 67534054 67534612 0.000000e+00 725.0
14 TraesCS1A01G065400 chr1B 87.638 453 35 6 945 1391 67534617 67535054 2.300000e-139 507.0
15 TraesCS1A01G065400 chr1B 92.150 293 13 6 1 289 67533732 67534018 8.620000e-109 405.0
16 TraesCS1A01G065400 chr1B 87.975 158 16 1 1234 1391 67534819 67534973 4.400000e-42 183.0
17 TraesCS1A01G065400 chr5A 92.251 1368 60 25 3506 4871 456503155 456504478 0.000000e+00 1897.0
18 TraesCS1A01G065400 chr5A 93.708 890 48 7 2625 3509 456502116 456503002 0.000000e+00 1327.0
19 TraesCS1A01G065400 chr5A 95.156 640 28 2 2625 3262 474538146 474538784 0.000000e+00 1007.0
20 TraesCS1A01G065400 chr5A 92.226 656 40 6 4545 5195 474539220 474539869 0.000000e+00 918.0
21 TraesCS1A01G065400 chr5A 95.794 428 18 0 4069 4496 474538796 474539223 0.000000e+00 691.0
22 TraesCS1A01G065400 chr5A 91.724 290 21 3 5738 6026 427869712 427869999 4.010000e-107 399.0
23 TraesCS1A01G065400 chr5A 94.064 219 11 2 5200 5417 474540186 474540403 1.480000e-86 331.0
24 TraesCS1A01G065400 chr5A 94.118 102 5 1 5585 5685 474540588 474540689 3.450000e-33 154.0
25 TraesCS1A01G065400 chr5A 89.286 84 9 0 2730 2813 444560857 444560940 9.790000e-19 106.0
26 TraesCS1A01G065400 chr5A 98.182 55 0 1 5447 5501 474540403 474540456 2.120000e-15 95.3
27 TraesCS1A01G065400 chr5D 92.330 1369 49 20 3506 4871 371443511 371444826 0.000000e+00 1895.0
28 TraesCS1A01G065400 chr5D 94.582 886 43 5 2625 3508 371442475 371443357 0.000000e+00 1365.0
29 TraesCS1A01G065400 chr5D 90.608 724 39 9 5306 6026 371468131 371468828 0.000000e+00 933.0
30 TraesCS1A01G065400 chr5D 90.583 446 32 6 4873 5315 371465343 371465781 3.710000e-162 582.0
31 TraesCS1A01G065400 chr6B 83.778 450 39 15 4373 4820 711737110 711737527 5.190000e-106 396.0
32 TraesCS1A01G065400 chr6B 90.370 135 9 3 4223 4353 711736986 711737120 2.650000e-39 174.0
33 TraesCS1A01G065400 chr6B 89.583 48 3 1 3506 3553 343032816 343032771 7.730000e-05 60.2
34 TraesCS1A01G065400 chr6A 83.991 431 38 12 4392 4821 613089975 613090375 1.120000e-102 385.0
35 TraesCS1A01G065400 chr6A 89.844 128 10 2 4229 4353 613089841 613089968 2.060000e-35 161.0
36 TraesCS1A01G065400 chr6A 89.583 48 3 1 3506 3553 297641344 297641389 7.730000e-05 60.2
37 TraesCS1A01G065400 chr3A 86.735 98 12 1 2728 2824 358268439 358268342 2.720000e-19 108.0
38 TraesCS1A01G065400 chr3A 86.735 98 12 1 2728 2824 630362476 630362379 2.720000e-19 108.0
39 TraesCS1A01G065400 chr2D 93.333 45 1 1 3504 3548 153795122 153795164 1.660000e-06 65.8
40 TraesCS1A01G065400 chr2D 93.333 45 1 1 3504 3548 153800778 153800820 1.660000e-06 65.8
41 TraesCS1A01G065400 chr2A 93.333 45 1 1 3504 3548 147474737 147474695 1.660000e-06 65.8
42 TraesCS1A01G065400 chr6D 89.583 48 3 1 3506 3553 218393638 218393683 7.730000e-05 60.2


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 TraesCS1A01G065400 chr1A 47799404 47806542 7138 False 13184.000000 13184 100.000000 1 7139 1 chr1A.!!$F2 7138
1 TraesCS1A01G065400 chr1D 47872899 47880050 7151 False 1775.333333 4759 92.304667 1 7129 6 chr1D.!!$F2 7128
2 TraesCS1A01G065400 chr1B 67533732 67541211 7479 False 1307.125000 4017 90.310000 1 7129 8 chr1B.!!$F1 7128
3 TraesCS1A01G065400 chr5A 456502116 456504478 2362 False 1612.000000 1897 92.979500 2625 4871 2 chr5A.!!$F3 2246
4 TraesCS1A01G065400 chr5A 474538146 474540689 2543 False 532.716667 1007 94.923333 2625 5685 6 chr5A.!!$F4 3060
5 TraesCS1A01G065400 chr5D 371442475 371444826 2351 False 1630.000000 1895 93.456000 2625 4871 2 chr5D.!!$F1 2246
6 TraesCS1A01G065400 chr5D 371465343 371468828 3485 False 757.500000 933 90.595500 4873 6026 2 chr5D.!!$F2 1153
7 TraesCS1A01G065400 chr6B 711736986 711737527 541 False 285.000000 396 87.074000 4223 4820 2 chr6B.!!$F1 597
8 TraesCS1A01G065400 chr6A 613089841 613090375 534 False 273.000000 385 86.917500 4229 4821 2 chr6A.!!$F2 592

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
659 705 0.181824 GGGTTGGCGGGCTAGATTAA 59.818 55.0 2.38 0.0 0.00 1.40 F
775 823 0.304705 GCGTATGAGAAATGCACCCG 59.695 55.0 0.00 0.0 0.00 5.28 F
1253 1397 0.393808 GCCACGGGCTTTTCTCCATA 60.394 55.0 7.58 0.0 46.69 2.74 F
1410 1554 0.409092 ATTCATCTTGGTGTGGCCCA 59.591 50.0 0.00 0.0 36.04 5.36 F
3384 3656 0.935898 CATGAGGAGCTTCGACATGC 59.064 55.0 17.59 0.0 33.42 4.06 F
4887 5497 0.616891 ATCAGTGGAGCAGCATGACA 59.383 50.0 0.00 0.0 39.69 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2410 2676 5.687285 GTGAAAGCAACATAGAAAACAGTGG 59.313 40.000 0.00 0.0 0.00 4.00 R
2728 2994 2.930826 TATTTTGGATCGGAGGGAGC 57.069 50.000 0.00 0.0 0.00 4.70 R
2961 3230 5.527582 CACTACTGCCCATAACAAATAGACC 59.472 44.000 0.00 0.0 0.00 3.85 R
3489 3763 1.662629 GTGATCTTGACCATCACAGCG 59.337 52.381 7.74 0.0 46.48 5.18 R
5133 5747 0.723981 GCTTGAACCTGCATCGACTC 59.276 55.000 0.00 0.0 0.00 3.36 R
6185 9593 0.109342 CCAGAGCCATGGTATCACCC 59.891 60.000 14.67 0.0 37.50 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
79 80 3.268647 TTCTCCCTCCCTCCACCCC 62.269 68.421 0.00 0.00 0.00 4.95
247 252 3.150335 CGATTCGCTCGTAGGTCAG 57.850 57.895 0.00 0.00 42.56 3.51
406 450 1.325338 CGTTTTCTCGTCGGTTTGTGT 59.675 47.619 0.00 0.00 0.00 3.72
442 486 1.590698 GCACGCACCATTTTTCGTTTT 59.409 42.857 0.00 0.00 32.38 2.43
443 487 2.347200 GCACGCACCATTTTTCGTTTTC 60.347 45.455 0.00 0.00 32.38 2.29
448 492 4.085619 CGCACCATTTTTCGTTTTCTTCTG 60.086 41.667 0.00 0.00 0.00 3.02
464 508 6.961359 TTCTTCTGTACATATTGTCGTTGG 57.039 37.500 0.00 0.00 0.00 3.77
558 602 4.137116 TCTCTATGTGGTTTGATTCGGG 57.863 45.455 0.00 0.00 0.00 5.14
656 702 3.489513 GGGGTTGGCGGGCTAGAT 61.490 66.667 2.38 0.00 0.00 1.98
657 703 2.595655 GGGTTGGCGGGCTAGATT 59.404 61.111 2.38 0.00 0.00 2.40
658 704 1.702022 GGGGTTGGCGGGCTAGATTA 61.702 60.000 2.38 0.00 0.00 1.75
659 705 0.181824 GGGTTGGCGGGCTAGATTAA 59.818 55.000 2.38 0.00 0.00 1.40
660 706 1.202891 GGGTTGGCGGGCTAGATTAAT 60.203 52.381 2.38 0.00 0.00 1.40
661 707 2.152016 GGTTGGCGGGCTAGATTAATC 58.848 52.381 7.41 7.41 0.00 1.75
662 708 2.486548 GGTTGGCGGGCTAGATTAATCA 60.487 50.000 17.56 3.25 0.00 2.57
663 709 3.412386 GTTGGCGGGCTAGATTAATCAT 58.588 45.455 17.56 5.59 0.00 2.45
756 803 2.422597 TGGTTTCTGAATGTAGCACGG 58.577 47.619 0.00 0.00 0.00 4.94
775 823 0.304705 GCGTATGAGAAATGCACCCG 59.695 55.000 0.00 0.00 0.00 5.28
829 878 7.060979 CGGATGTGTTTTGTTTCAGTGAATATG 59.939 37.037 6.36 0.00 0.00 1.78
851 900 3.557228 TTGCAATTTTGGCAAGGAGTT 57.443 38.095 0.00 0.00 45.57 3.01
852 901 2.836262 TGCAATTTTGGCAAGGAGTTG 58.164 42.857 0.00 1.45 38.54 3.16
854 903 3.071312 TGCAATTTTGGCAAGGAGTTGAT 59.929 39.130 10.29 0.00 38.54 2.57
866 915 1.005037 AGTTGATCGCGTGCCTTCA 60.005 52.632 5.77 0.08 0.00 3.02
869 918 1.135689 GTTGATCGCGTGCCTTCATTT 60.136 47.619 5.77 0.00 0.00 2.32
901 950 5.120830 CCTAGCAATTAGTGTCTTGTGTGAC 59.879 44.000 0.00 0.00 37.47 3.67
905 954 5.180117 GCAATTAGTGTCTTGTGTGACTGAT 59.820 40.000 0.00 0.00 37.79 2.90
1029 1086 3.491766 TCTTCATCTTGGTCTACCCCT 57.508 47.619 0.00 0.00 34.29 4.79
1032 1089 0.753262 CATCTTGGTCTACCCCTCCG 59.247 60.000 0.00 0.00 34.29 4.63
1122 1179 2.291217 GGGCTCTTCTCCATCCTTGTTT 60.291 50.000 0.00 0.00 0.00 2.83
1177 1234 4.177026 CTCTTCTCCATACTCGTTTGGTG 58.823 47.826 6.46 4.80 34.03 4.17
1186 1243 1.270412 ACTCGTTTGGTGTAATGCCGA 60.270 47.619 0.00 0.00 0.00 5.54
1253 1397 0.393808 GCCACGGGCTTTTCTCCATA 60.394 55.000 7.58 0.00 46.69 2.74
1257 1401 1.134788 ACGGGCTTTTCTCCATACTCG 60.135 52.381 0.00 0.00 0.00 4.18
1258 1402 1.134788 CGGGCTTTTCTCCATACTCGT 60.135 52.381 0.00 0.00 0.00 4.18
1259 1403 2.677037 CGGGCTTTTCTCCATACTCGTT 60.677 50.000 0.00 0.00 0.00 3.85
1264 1408 4.933400 GCTTTTCTCCATACTCGTTTGGTA 59.067 41.667 6.46 0.00 34.03 3.25
1268 1412 6.479972 TTCTCCATACTCGTTTGGTATCAT 57.520 37.500 6.46 0.00 34.03 2.45
1273 1417 2.632377 ACTCGTTTGGTATCATGCCAG 58.368 47.619 0.00 0.00 37.31 4.85
1274 1418 1.331756 CTCGTTTGGTATCATGCCAGC 59.668 52.381 0.00 0.00 37.31 4.85
1276 1420 1.767759 GTTTGGTATCATGCCAGCCT 58.232 50.000 0.00 0.00 37.31 4.58
1289 1433 4.341783 AGCCTCTGGTGCTGCCAC 62.342 66.667 0.00 0.00 43.61 5.01
1365 1509 1.300620 CTCGTCTGGTTTCACGCCA 60.301 57.895 0.00 0.00 35.93 5.69
1410 1554 0.409092 ATTCATCTTGGTGTGGCCCA 59.591 50.000 0.00 0.00 36.04 5.36
1562 1707 8.778358 GCTATTTGGTTATCCTGAAGTAGATTG 58.222 37.037 0.00 0.00 34.23 2.67
1568 1713 6.043243 GGTTATCCTGAAGTAGATTGGATGGA 59.957 42.308 0.00 0.00 37.96 3.41
1644 1789 2.049888 TTGACTGTGCATGTGTTGGA 57.950 45.000 0.00 0.00 0.00 3.53
1685 1830 2.283145 ATGCCATCAAGTAGCATCCC 57.717 50.000 0.00 0.00 43.58 3.85
1819 2081 7.372451 TGTGCAAGTATTACAATTCCAGTAC 57.628 36.000 0.00 0.00 0.00 2.73
1833 2095 4.094830 TCCAGTACGATACTAGGATGCA 57.905 45.455 0.00 0.00 37.23 3.96
1834 2096 4.663334 TCCAGTACGATACTAGGATGCAT 58.337 43.478 0.00 0.00 37.23 3.96
1835 2097 5.077564 TCCAGTACGATACTAGGATGCATT 58.922 41.667 0.00 0.00 37.23 3.56
1836 2098 5.538813 TCCAGTACGATACTAGGATGCATTT 59.461 40.000 0.00 0.00 37.23 2.32
1837 2099 6.717997 TCCAGTACGATACTAGGATGCATTTA 59.282 38.462 0.00 0.00 37.23 1.40
1838 2100 7.231925 TCCAGTACGATACTAGGATGCATTTAA 59.768 37.037 0.00 0.00 37.23 1.52
1839 2101 7.542477 CCAGTACGATACTAGGATGCATTTAAG 59.458 40.741 0.00 0.93 37.23 1.85
1898 2160 6.692232 TTTGACGTTTTTGGTTAACAGTTG 57.308 33.333 8.10 0.00 0.00 3.16
2019 2282 5.366477 TGAGGCTAATCAATCCAGTATGACA 59.634 40.000 0.00 0.00 39.69 3.58
2227 2490 6.915544 TCTTCATGACATATTCACAAGAGC 57.084 37.500 0.00 0.00 36.92 4.09
2410 2676 4.970662 TCTCTGAACTATTTGGCAATGC 57.029 40.909 0.00 0.00 0.00 3.56
2473 2739 8.940397 AGATATAATCCCAAACATAACCTTGG 57.060 34.615 0.00 0.00 41.58 3.61
2728 2994 8.752254 CATTTTCAGCTGCTATCATTAAACATG 58.248 33.333 9.47 0.03 0.00 3.21
2749 3015 3.138283 TGCTCCCTCCGATCCAAAATAAT 59.862 43.478 0.00 0.00 0.00 1.28
2961 3230 6.567959 TGCAAGTCTCTACATGATCTACTTG 58.432 40.000 19.06 19.06 39.79 3.16
3148 3417 7.662669 TCAAGGTTTAGTTGACTTATTGGTACC 59.337 37.037 4.43 4.43 0.00 3.34
3384 3656 0.935898 CATGAGGAGCTTCGACATGC 59.064 55.000 17.59 0.00 33.42 4.06
3489 3763 0.671251 CTATGAGGTCTCGGCAGGTC 59.329 60.000 0.00 0.00 0.00 3.85
3539 4018 5.001874 GGCTTATATTTAGAAACGGAGGGG 58.998 45.833 0.00 0.00 0.00 4.79
3621 4218 4.080863 AGAGACCTAACCTAATGTGCAAGG 60.081 45.833 0.37 0.37 38.93 3.61
3635 4232 3.388024 TGTGCAAGGACTTGACTAGTTCT 59.612 43.478 15.76 0.00 45.12 3.01
3696 4293 1.528309 CTGGGGCCAAAGAACGTGT 60.528 57.895 4.39 0.00 0.00 4.49
3697 4294 1.795170 CTGGGGCCAAAGAACGTGTG 61.795 60.000 4.39 0.00 0.00 3.82
3836 4434 3.146847 GGTGGTTTCAACTTACAGGAGG 58.853 50.000 0.00 0.00 0.00 4.30
3899 4497 2.409870 GCCCCAGTGAATGCCTTCG 61.410 63.158 0.00 0.00 33.86 3.79
4081 4683 2.231964 GCCATCATGGTTTTCAAGCTCA 59.768 45.455 5.31 0.00 40.46 4.26
4086 4688 7.119690 CCATCATGGTTTTCAAGCTCATCTTG 61.120 42.308 0.00 0.00 42.03 3.02
4137 4739 4.553351 CGTATCCAATAACACAGCAGCATG 60.553 45.833 0.00 0.00 40.87 4.06
4179 4781 8.079211 ACATCTTCTGCTGTAAGTATTCCTAA 57.921 34.615 0.00 0.00 35.30 2.69
4617 5222 4.539870 CCAGAATTGTGTTGCACAGTAAG 58.460 43.478 1.49 0.00 45.39 2.34
4655 5262 3.548818 CCTCTTCAAACAGTTTCAAGCCG 60.549 47.826 4.82 0.00 0.00 5.52
4887 5497 0.616891 ATCAGTGGAGCAGCATGACA 59.383 50.000 0.00 0.00 39.69 3.58
4924 5534 5.916661 TCAACAGGTAGATACTCCAGAAC 57.083 43.478 0.00 0.00 0.00 3.01
4992 5602 6.761099 TGTTCTGTAGACTTCTGATAGGTC 57.239 41.667 0.00 0.00 0.00 3.85
5133 5747 5.970140 TTTCACATTGCATCACAAACTTG 57.030 34.783 0.00 0.00 42.86 3.16
5328 8613 6.776094 AGCAAAAGAATTTACTAGCATCGTC 58.224 36.000 0.00 0.00 37.28 4.20
5330 8615 6.684555 GCAAAAGAATTTACTAGCATCGTCAG 59.315 38.462 0.00 0.00 37.28 3.51
5426 8726 2.479837 TCTTCACTGGCACGTTACAAG 58.520 47.619 0.00 0.00 0.00 3.16
5685 9071 2.075566 TGGTGCCCCTGTGAGTGAA 61.076 57.895 0.00 0.00 0.00 3.18
5694 9080 2.292267 CCTGTGAGTGAAAGTGTGCTT 58.708 47.619 0.00 0.00 36.30 3.91
5733 9129 1.674962 GACTATTACACCTCGCCGTCT 59.325 52.381 0.00 0.00 0.00 4.18
5877 9273 1.002792 CTCGACATCGCTTCCATCGTA 60.003 52.381 0.00 0.00 39.60 3.43
5967 9363 0.035630 ACAAGCCTGCAGAGATCACC 60.036 55.000 17.39 0.00 0.00 4.02
5982 9378 3.588842 AGATCACCCTCCTGAATGTGAAA 59.411 43.478 0.00 0.00 40.74 2.69
6018 9414 1.890041 CGGGTTGCAGTTGACGGAA 60.890 57.895 0.00 0.00 0.00 4.30
6022 9418 0.586802 GTTGCAGTTGACGGAAGGTC 59.413 55.000 0.00 0.00 46.27 3.85
6156 9552 7.542824 CACTTTTAGTCAGTAGCTAGGTTCTTC 59.457 40.741 0.00 0.00 0.00 2.87
6160 9556 2.423892 TCAGTAGCTAGGTTCTTCGCAG 59.576 50.000 0.00 0.00 0.00 5.18
6163 9559 3.628487 AGTAGCTAGGTTCTTCGCAGTAG 59.372 47.826 0.00 0.00 0.00 2.57
6176 9572 5.185249 TCTTCGCAGTAGTAAGATTCCAGTT 59.815 40.000 0.00 0.00 0.00 3.16
6178 9574 3.865745 CGCAGTAGTAAGATTCCAGTTGG 59.134 47.826 0.00 0.00 0.00 3.77
6188 9596 3.257627 TCCAGTTGGAAGACAGGGT 57.742 52.632 0.00 0.00 42.18 4.34
6189 9597 0.764890 TCCAGTTGGAAGACAGGGTG 59.235 55.000 0.00 0.00 42.18 4.61
6204 9612 0.109342 GGGTGATACCATGGCTCTGG 59.891 60.000 13.04 5.30 41.02 3.86
6205 9613 0.536006 GGTGATACCATGGCTCTGGC 60.536 60.000 13.04 4.28 40.15 4.85
6206 9614 0.471617 GTGATACCATGGCTCTGGCT 59.528 55.000 13.04 0.00 40.15 4.75
6207 9615 1.694150 GTGATACCATGGCTCTGGCTA 59.306 52.381 13.04 0.00 40.15 3.93
6286 9704 4.524328 AGGCCTGTCAGAAACAATTTTAGG 59.476 41.667 3.11 0.00 37.45 2.69
6288 9706 5.222631 GCCTGTCAGAAACAATTTTAGGTG 58.777 41.667 0.00 0.00 37.45 4.00
6289 9707 5.772521 CCTGTCAGAAACAATTTTAGGTGG 58.227 41.667 0.00 0.00 37.45 4.61
6290 9708 5.278957 CCTGTCAGAAACAATTTTAGGTGGG 60.279 44.000 0.00 0.00 37.45 4.61
6291 9709 4.586841 TGTCAGAAACAATTTTAGGTGGGG 59.413 41.667 0.00 0.00 34.03 4.96
6292 9710 4.830600 GTCAGAAACAATTTTAGGTGGGGA 59.169 41.667 0.00 0.00 0.00 4.81
6293 9711 5.480422 GTCAGAAACAATTTTAGGTGGGGAT 59.520 40.000 0.00 0.00 0.00 3.85
6294 9712 6.014584 GTCAGAAACAATTTTAGGTGGGGATT 60.015 38.462 0.00 0.00 0.00 3.01
6295 9713 6.556874 TCAGAAACAATTTTAGGTGGGGATTT 59.443 34.615 0.00 0.00 0.00 2.17
6296 9714 6.873605 CAGAAACAATTTTAGGTGGGGATTTC 59.126 38.462 0.00 0.00 0.00 2.17
6297 9715 5.400066 AACAATTTTAGGTGGGGATTTCG 57.600 39.130 0.00 0.00 0.00 3.46
6298 9716 4.668636 ACAATTTTAGGTGGGGATTTCGA 58.331 39.130 0.00 0.00 0.00 3.71
6299 9717 4.705023 ACAATTTTAGGTGGGGATTTCGAG 59.295 41.667 0.00 0.00 0.00 4.04
6300 9718 2.413310 TTTAGGTGGGGATTTCGAGC 57.587 50.000 0.00 0.00 0.00 5.03
6301 9719 1.580059 TTAGGTGGGGATTTCGAGCT 58.420 50.000 0.00 0.00 0.00 4.09
6302 9720 2.464796 TAGGTGGGGATTTCGAGCTA 57.535 50.000 0.00 0.00 0.00 3.32
6303 9721 1.807814 AGGTGGGGATTTCGAGCTAT 58.192 50.000 0.00 0.00 0.00 2.97
6304 9722 1.694696 AGGTGGGGATTTCGAGCTATC 59.305 52.381 0.00 0.00 0.00 2.08
6305 9723 1.416401 GGTGGGGATTTCGAGCTATCA 59.584 52.381 0.00 0.00 0.00 2.15
6306 9724 2.548920 GGTGGGGATTTCGAGCTATCAG 60.549 54.545 0.00 0.00 0.00 2.90
6307 9725 2.365617 GTGGGGATTTCGAGCTATCAGA 59.634 50.000 0.00 0.00 0.00 3.27
6308 9726 3.007398 GTGGGGATTTCGAGCTATCAGAT 59.993 47.826 0.00 0.00 0.00 2.90
6309 9727 4.220821 GTGGGGATTTCGAGCTATCAGATA 59.779 45.833 0.00 0.00 0.00 1.98
6310 9728 4.838423 TGGGGATTTCGAGCTATCAGATAA 59.162 41.667 0.00 0.00 0.00 1.75
6320 9738 3.963374 AGCTATCAGATAACTGTGGCTGA 59.037 43.478 10.67 9.09 43.81 4.26
6337 9864 7.537715 TGTGGCTGAAGTATATTTGATTGTTG 58.462 34.615 0.00 0.00 0.00 3.33
6346 9873 8.330466 AGTATATTTGATTGTTGGTCGTTGAA 57.670 30.769 0.00 0.00 0.00 2.69
6347 9874 8.788806 AGTATATTTGATTGTTGGTCGTTGAAA 58.211 29.630 0.00 0.00 0.00 2.69
6348 9875 9.567848 GTATATTTGATTGTTGGTCGTTGAAAT 57.432 29.630 0.00 0.00 0.00 2.17
6352 9879 7.865875 TTGATTGTTGGTCGTTGAAATATTG 57.134 32.000 0.00 0.00 0.00 1.90
6353 9880 6.385843 TGATTGTTGGTCGTTGAAATATTGG 58.614 36.000 0.00 0.00 0.00 3.16
6357 9884 3.417101 TGGTCGTTGAAATATTGGCACT 58.583 40.909 0.00 0.00 0.00 4.40
6359 9886 5.189928 TGGTCGTTGAAATATTGGCACTAT 58.810 37.500 0.00 0.00 0.00 2.12
6361 9888 5.971202 GGTCGTTGAAATATTGGCACTATTG 59.029 40.000 10.41 0.00 0.00 1.90
6362 9889 6.183360 GGTCGTTGAAATATTGGCACTATTGA 60.183 38.462 10.41 1.69 0.00 2.57
6364 9891 6.821160 TCGTTGAAATATTGGCACTATTGAGA 59.179 34.615 10.41 4.50 0.00 3.27
6365 9892 6.907212 CGTTGAAATATTGGCACTATTGAGAC 59.093 38.462 10.41 8.42 0.00 3.36
6366 9893 7.413988 CGTTGAAATATTGGCACTATTGAGACA 60.414 37.037 10.41 6.82 0.00 3.41
6368 9895 7.988737 TGAAATATTGGCACTATTGAGACAAG 58.011 34.615 10.41 0.00 0.00 3.16
6375 9902 4.082571 GGCACTATTGAGACAAGCAAACAT 60.083 41.667 0.00 0.00 0.00 2.71
6377 9904 6.024049 GCACTATTGAGACAAGCAAACATAC 58.976 40.000 0.00 0.00 0.00 2.39
6378 9905 6.128172 GCACTATTGAGACAAGCAAACATACT 60.128 38.462 0.00 0.00 0.00 2.12
6379 9906 7.064609 GCACTATTGAGACAAGCAAACATACTA 59.935 37.037 0.00 0.00 0.00 1.82
6380 9907 8.598924 CACTATTGAGACAAGCAAACATACTAG 58.401 37.037 0.00 0.00 0.00 2.57
6381 9908 5.862924 TTGAGACAAGCAAACATACTAGC 57.137 39.130 0.00 0.00 0.00 3.42
6382 9909 4.893608 TGAGACAAGCAAACATACTAGCA 58.106 39.130 0.00 0.00 0.00 3.49
6383 9910 5.491070 TGAGACAAGCAAACATACTAGCAT 58.509 37.500 0.00 0.00 0.00 3.79
6423 9954 8.954950 TTGAGGAAATATTGAGAGAAGCTAAG 57.045 34.615 0.00 0.00 0.00 2.18
6428 9959 9.691362 GGAAATATTGAGAGAAGCTAAGACTAG 57.309 37.037 0.00 0.00 0.00 2.57
6432 9963 6.503589 TTGAGAGAAGCTAAGACTAGTCAC 57.496 41.667 24.44 10.79 0.00 3.67
6433 9964 5.561679 TGAGAGAAGCTAAGACTAGTCACA 58.438 41.667 24.44 10.55 0.00 3.58
6452 9986 5.957796 GTCACAAACACAAACTAAACTCTCG 59.042 40.000 0.00 0.00 0.00 4.04
6481 10020 2.224621 CCTCTTGTGGCCTGAAGAGAAA 60.225 50.000 30.83 8.73 45.51 2.52
6484 10023 3.117888 TCTTGTGGCCTGAAGAGAAAACT 60.118 43.478 3.32 0.00 0.00 2.66
6509 10048 2.686835 AGCCAGCCTCACCTCTCC 60.687 66.667 0.00 0.00 0.00 3.71
6597 10142 2.755836 TGAGTCGCAGTTTTTCTTGC 57.244 45.000 0.00 0.00 0.00 4.01
6632 10177 5.470368 TCTTCACCGATACTCTTGTTCTTG 58.530 41.667 0.00 0.00 0.00 3.02
6633 10178 4.866508 TCACCGATACTCTTGTTCTTGT 57.133 40.909 0.00 0.00 0.00 3.16
6634 10179 5.209818 TCACCGATACTCTTGTTCTTGTT 57.790 39.130 0.00 0.00 0.00 2.83
6635 10180 5.227908 TCACCGATACTCTTGTTCTTGTTC 58.772 41.667 0.00 0.00 0.00 3.18
6636 10181 5.010719 TCACCGATACTCTTGTTCTTGTTCT 59.989 40.000 0.00 0.00 0.00 3.01
6637 10182 5.696724 CACCGATACTCTTGTTCTTGTTCTT 59.303 40.000 0.00 0.00 0.00 2.52
6639 10184 5.926542 CCGATACTCTTGTTCTTGTTCTTCA 59.073 40.000 0.00 0.00 0.00 3.02
6640 10185 6.128795 CCGATACTCTTGTTCTTGTTCTTCAC 60.129 42.308 0.00 0.00 0.00 3.18
6641 10186 6.399039 CGATACTCTTGTTCTTGTTCTTCACG 60.399 42.308 0.00 0.00 0.00 4.35
6642 10187 3.871594 ACTCTTGTTCTTGTTCTTCACGG 59.128 43.478 0.00 0.00 0.00 4.94
6643 10188 3.869065 TCTTGTTCTTGTTCTTCACGGT 58.131 40.909 0.00 0.00 0.00 4.83
6644 10189 3.869246 TCTTGTTCTTGTTCTTCACGGTC 59.131 43.478 0.00 0.00 0.00 4.79
6645 10190 2.198406 TGTTCTTGTTCTTCACGGTCG 58.802 47.619 0.00 0.00 0.00 4.79
6646 10191 2.159212 TGTTCTTGTTCTTCACGGTCGA 60.159 45.455 0.00 0.00 0.00 4.20
6647 10192 2.417339 TCTTGTTCTTCACGGTCGAG 57.583 50.000 0.00 0.00 0.00 4.04
6660 10205 2.357034 TCGAGTTGTTGGCGGCTC 60.357 61.111 11.43 4.06 0.00 4.70
6706 10251 0.391130 TTCTCCTGCCGCACATGTAC 60.391 55.000 0.00 0.00 0.00 2.90
6794 10340 4.479786 AGCTACCTTCCTCTTTAAGCAG 57.520 45.455 0.00 0.00 0.00 4.24
6814 10361 5.012046 AGCAGGATATAATTGGATCGTGTGA 59.988 40.000 17.94 0.00 39.20 3.58
6815 10362 5.349817 GCAGGATATAATTGGATCGTGTGAG 59.650 44.000 17.94 2.65 39.20 3.51
6816 10363 6.691508 CAGGATATAATTGGATCGTGTGAGA 58.308 40.000 12.48 0.00 34.67 3.27
6817 10364 7.326454 CAGGATATAATTGGATCGTGTGAGAT 58.674 38.462 12.48 0.00 34.67 2.75
6818 10365 7.277319 CAGGATATAATTGGATCGTGTGAGATG 59.723 40.741 12.48 0.00 34.67 2.90
6819 10366 7.038729 AGGATATAATTGGATCGTGTGAGATGT 60.039 37.037 0.00 0.00 0.00 3.06
6822 10369 2.947448 TGGATCGTGTGAGATGTCTG 57.053 50.000 0.00 0.00 0.00 3.51
6846 10393 4.987912 TGTGTGTGCATACATATGGATACG 59.012 41.667 19.74 0.00 44.76 3.06
6853 10400 1.449601 CATATGGATACGGCCGGGC 60.450 63.158 31.76 20.04 42.51 6.13
6867 10414 1.999048 CCGGGCGTATTTATATGCGA 58.001 50.000 7.76 0.00 44.26 5.10
6931 10479 1.933021 TCCGGTGTGGACTTATCTGT 58.067 50.000 0.00 0.00 43.74 3.41
6932 10480 2.253610 TCCGGTGTGGACTTATCTGTT 58.746 47.619 0.00 0.00 43.74 3.16
6933 10481 3.433343 TCCGGTGTGGACTTATCTGTTA 58.567 45.455 0.00 0.00 43.74 2.41
6934 10482 3.446161 TCCGGTGTGGACTTATCTGTTAG 59.554 47.826 0.00 0.00 43.74 2.34
6935 10483 3.430374 CCGGTGTGGACTTATCTGTTAGG 60.430 52.174 0.00 0.00 42.00 2.69
6936 10484 3.446161 CGGTGTGGACTTATCTGTTAGGA 59.554 47.826 0.00 0.00 0.00 2.94
6937 10485 4.440250 CGGTGTGGACTTATCTGTTAGGAG 60.440 50.000 0.00 0.00 0.00 3.69
6938 10486 4.466726 GGTGTGGACTTATCTGTTAGGAGT 59.533 45.833 0.00 0.00 0.00 3.85
6939 10487 5.655532 GGTGTGGACTTATCTGTTAGGAGTA 59.344 44.000 0.00 0.00 0.00 2.59
6983 10531 0.415429 AGGTGTCACCAGAGGGAGAT 59.585 55.000 24.02 0.00 41.95 2.75
7009 10558 1.055338 GAAGCAATCACAAACAGCGC 58.945 50.000 0.00 0.00 0.00 5.92
7019 10568 0.530431 CAAACAGCGCCTGCCTTTTT 60.530 50.000 2.29 0.00 44.31 1.94
7020 10569 0.249447 AAACAGCGCCTGCCTTTTTC 60.249 50.000 2.29 0.00 44.31 2.29
7021 10570 1.391157 AACAGCGCCTGCCTTTTTCA 61.391 50.000 2.29 0.00 44.31 2.69
7022 10571 1.181098 ACAGCGCCTGCCTTTTTCAT 61.181 50.000 2.29 0.00 44.31 2.57
7098 10654 0.322816 CTACCTGTGGGCACAAGCAT 60.323 55.000 0.00 0.00 44.61 3.79
7124 10680 2.282462 GTGTTCCTGGTGGGCTGG 60.282 66.667 0.00 0.00 34.39 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 2.454941 GGGTGGAGGGAGGGAGAA 59.545 66.667 0.00 0.00 0.00 2.87
196 197 2.046700 GGGTTCCGGTCGCATTGA 60.047 61.111 0.00 0.00 0.00 2.57
442 486 6.275494 TCCAACGACAATATGTACAGAAGA 57.725 37.500 0.33 0.00 0.00 2.87
443 487 6.756542 TCATCCAACGACAATATGTACAGAAG 59.243 38.462 0.33 0.00 0.00 2.85
448 492 7.477144 TCATTCATCCAACGACAATATGTAC 57.523 36.000 0.00 0.00 0.00 2.90
464 508 0.659957 GCCCAGTTCGCTCATTCATC 59.340 55.000 0.00 0.00 0.00 2.92
535 579 4.941263 CCCGAATCAAACCACATAGAGAAA 59.059 41.667 0.00 0.00 0.00 2.52
537 581 3.118408 CCCCGAATCAAACCACATAGAGA 60.118 47.826 0.00 0.00 0.00 3.10
538 582 3.206150 CCCCGAATCAAACCACATAGAG 58.794 50.000 0.00 0.00 0.00 2.43
558 602 0.825410 AAACCCAACAAACGAACCCC 59.175 50.000 0.00 0.00 0.00 4.95
660 706 9.667107 CTTACTGACTTCCCATTAGTTTAATGA 57.333 33.333 9.73 0.00 46.52 2.57
661 707 9.667107 TCTTACTGACTTCCCATTAGTTTAATG 57.333 33.333 2.56 2.56 43.94 1.90
662 708 9.892130 CTCTTACTGACTTCCCATTAGTTTAAT 57.108 33.333 0.00 0.00 0.00 1.40
663 709 8.877195 ACTCTTACTGACTTCCCATTAGTTTAA 58.123 33.333 0.00 0.00 0.00 1.52
680 727 7.750903 GCCTGCTAAATTTGTTAACTCTTACTG 59.249 37.037 7.22 0.00 0.00 2.74
682 729 7.027760 GGCCTGCTAAATTTGTTAACTCTTAC 58.972 38.462 7.22 0.00 0.00 2.34
756 803 0.304705 CGGGTGCATTTCTCATACGC 59.695 55.000 0.00 0.00 0.00 4.42
775 823 3.812053 CCTGGCAGTTATATTCACTGAGC 59.188 47.826 14.43 4.48 43.90 4.26
851 900 1.130373 GAAAATGAAGGCACGCGATCA 59.870 47.619 15.93 9.40 0.00 2.92
852 901 1.398390 AGAAAATGAAGGCACGCGATC 59.602 47.619 15.93 2.95 0.00 3.69
854 903 0.516877 CAGAAAATGAAGGCACGCGA 59.483 50.000 15.93 0.00 0.00 5.87
866 915 7.402862 ACACTAATTGCTAGGTACCAGAAAAT 58.597 34.615 15.94 6.31 31.14 1.82
869 918 5.720041 AGACACTAATTGCTAGGTACCAGAA 59.280 40.000 15.94 0.99 31.14 3.02
901 950 5.067413 AGCATGGAAGATAAAACTGCATCAG 59.933 40.000 0.00 0.00 37.52 2.90
905 954 5.357878 CCTAAGCATGGAAGATAAAACTGCA 59.642 40.000 0.00 0.00 0.00 4.41
963 1020 9.781633 AACAAAGATCAAATTGAATTGGATGAA 57.218 25.926 12.31 0.00 33.11 2.57
969 1026 9.377383 GCAGAAAACAAAGATCAAATTGAATTG 57.623 29.630 0.00 8.57 0.00 2.32
975 1032 9.768662 ATAACTGCAGAAAACAAAGATCAAATT 57.231 25.926 23.35 0.00 0.00 1.82
1045 1102 1.280133 TGATGAAGAGCCCTTGACTGG 59.720 52.381 0.00 0.00 31.62 4.00
1052 1109 3.947612 ACAATGATGATGAAGAGCCCT 57.052 42.857 0.00 0.00 0.00 5.19
1122 1179 1.599518 AGATGCCGGCGTGAAACAA 60.600 52.632 29.48 2.80 35.74 2.83
1177 1234 1.090052 GCACCAGAGGTCGGCATTAC 61.090 60.000 0.00 0.00 31.02 1.89
1210 1267 1.084370 GGCGTGAACGAGGATGAAGG 61.084 60.000 7.10 0.00 43.02 3.46
1247 1391 4.449068 GCATGATACCAAACGAGTATGGAG 59.551 45.833 0.00 0.00 39.12 3.86
1253 1397 2.632377 CTGGCATGATACCAAACGAGT 58.368 47.619 0.00 0.00 36.56 4.18
1257 1401 1.678101 GAGGCTGGCATGATACCAAAC 59.322 52.381 3.38 0.00 36.56 2.93
1258 1402 1.565759 AGAGGCTGGCATGATACCAAA 59.434 47.619 3.38 0.00 36.56 3.28
1259 1403 1.134007 CAGAGGCTGGCATGATACCAA 60.134 52.381 3.38 0.00 36.56 3.67
1289 1433 1.147153 GAGGATGAAGAAGGGCCCG 59.853 63.158 18.44 0.00 0.00 6.13
1293 1437 2.290323 ACCAAACGAGGATGAAGAAGGG 60.290 50.000 0.00 0.00 0.00 3.95
1294 1438 3.059352 ACCAAACGAGGATGAAGAAGG 57.941 47.619 0.00 0.00 0.00 3.46
1295 1439 3.437049 GGAACCAAACGAGGATGAAGAAG 59.563 47.826 0.00 0.00 0.00 2.85
1296 1440 3.181449 TGGAACCAAACGAGGATGAAGAA 60.181 43.478 0.00 0.00 0.00 2.52
1297 1441 2.370519 TGGAACCAAACGAGGATGAAGA 59.629 45.455 0.00 0.00 0.00 2.87
1298 1442 2.484264 GTGGAACCAAACGAGGATGAAG 59.516 50.000 0.00 0.00 0.00 3.02
1299 1443 2.500229 GTGGAACCAAACGAGGATGAA 58.500 47.619 0.00 0.00 0.00 2.57
1300 1444 1.606994 CGTGGAACCAAACGAGGATGA 60.607 52.381 0.00 0.00 42.32 2.92
1301 1445 0.796312 CGTGGAACCAAACGAGGATG 59.204 55.000 0.00 0.00 42.32 3.51
1391 1535 0.409092 TGGGCCACACCAAGATGAAT 59.591 50.000 0.00 0.00 42.05 2.57
1562 1707 7.352079 ACCATTGTATTGAAAGAATCCATCC 57.648 36.000 0.00 0.00 0.00 3.51
1568 1713 9.685276 TCACATCTACCATTGTATTGAAAGAAT 57.315 29.630 0.00 0.00 0.00 2.40
1644 1789 5.957842 TCGCCAGAAATTTTACTGTTCAT 57.042 34.783 6.24 0.00 32.93 2.57
1685 1830 7.812309 TTCACGTATTCATGAACTTACTCAG 57.188 36.000 11.07 3.78 29.89 3.35
1711 1856 9.733556 ATTGTGTTCTCAGTTACACCATAAATA 57.266 29.630 9.39 0.00 43.04 1.40
1805 2067 8.573885 CATCCTAGTATCGTACTGGAATTGTAA 58.426 37.037 9.12 0.00 39.36 2.41
1835 2097 9.640963 GCTTCAGTAGTCAGAGTTAAATCTTAA 57.359 33.333 1.94 0.00 0.00 1.85
1836 2098 8.803235 TGCTTCAGTAGTCAGAGTTAAATCTTA 58.197 33.333 1.94 0.00 0.00 2.10
1837 2099 7.600752 GTGCTTCAGTAGTCAGAGTTAAATCTT 59.399 37.037 1.94 0.00 0.00 2.40
1838 2100 7.093992 GTGCTTCAGTAGTCAGAGTTAAATCT 58.906 38.462 0.00 0.00 0.00 2.40
1839 2101 6.311690 GGTGCTTCAGTAGTCAGAGTTAAATC 59.688 42.308 0.00 0.00 0.00 2.17
1898 2160 6.546972 AAGTCACGAGGAAAGAAAAAGATC 57.453 37.500 0.00 0.00 0.00 2.75
2019 2282 5.948842 ACTGGTTTGGTTGACCTTATTACT 58.051 37.500 1.34 0.00 38.04 2.24
2046 2309 7.384477 ACTTACAAAAGACCCTGTAGTATCAC 58.616 38.462 0.00 0.00 36.50 3.06
2091 2354 8.129496 TGTTTATATAGCGTCCATCTCCATTA 57.871 34.615 0.00 0.00 0.00 1.90
2227 2490 7.060383 AGAATATTCCTGTAGACTGTCATGG 57.940 40.000 11.92 6.35 0.00 3.66
2410 2676 5.687285 GTGAAAGCAACATAGAAAACAGTGG 59.313 40.000 0.00 0.00 0.00 4.00
2473 2739 9.148104 ACTTATGAGTAATGAAACCGTAGAAAC 57.852 33.333 0.00 0.00 33.32 2.78
2686 2952 5.551233 TGAAAATGTAAGAGACTGGGTCAG 58.449 41.667 0.52 0.00 34.60 3.51
2728 2994 2.930826 TATTTTGGATCGGAGGGAGC 57.069 50.000 0.00 0.00 0.00 4.70
2889 3158 6.183360 GCATCACGTTTTGAGTCAATAGATCA 60.183 38.462 6.36 0.00 37.77 2.92
2961 3230 5.527582 CACTACTGCCCATAACAAATAGACC 59.472 44.000 0.00 0.00 0.00 3.85
3489 3763 1.662629 GTGATCTTGACCATCACAGCG 59.337 52.381 7.74 0.00 46.48 5.18
3621 4218 9.204570 TGTTGCTTTAATAGAACTAGTCAAGTC 57.795 33.333 0.00 0.00 37.50 3.01
3635 4232 4.571919 AGCAGTACCGTGTTGCTTTAATA 58.428 39.130 0.95 0.00 45.28 0.98
3696 4293 7.292356 ACCATCAGTTATCATATAAGGTCCACA 59.708 37.037 0.00 0.00 0.00 4.17
3697 4294 7.680730 ACCATCAGTTATCATATAAGGTCCAC 58.319 38.462 0.00 0.00 0.00 4.02
3836 4434 0.328258 TAAGCCCAAGGAACTCTGCC 59.672 55.000 0.00 0.00 38.49 4.85
3881 4479 2.409870 CGAAGGCATTCACTGGGGC 61.410 63.158 12.16 0.00 34.94 5.80
3899 4497 1.820519 TGATGGCTTGACAGGATTTGC 59.179 47.619 0.00 0.00 0.00 3.68
4081 4683 5.104776 ACATGTAGTAGATGGTGCACAAGAT 60.105 40.000 20.43 7.08 0.00 2.40
4086 4688 3.623060 CCAACATGTAGTAGATGGTGCAC 59.377 47.826 17.77 8.80 37.22 4.57
4137 4739 3.320541 AGATGTATCTGCAGGAGCTGTAC 59.679 47.826 15.13 8.28 42.74 2.90
4617 5222 5.248640 TGAAGAGGTCCACAAGATTTCATC 58.751 41.667 0.00 0.00 0.00 2.92
4655 5262 2.031683 GCCCAAACGTGTGAGCATATAC 59.968 50.000 7.44 0.00 0.00 1.47
4887 5497 4.351111 ACCTGTTGAACTAGATGGTTTCCT 59.649 41.667 0.00 0.00 0.00 3.36
4924 5534 8.353684 AGAAACTGATACGATACCACTGATAAG 58.646 37.037 0.00 0.00 0.00 1.73
4992 5602 8.594881 AGTCTAGGAAAAATAATGTAGCATCG 57.405 34.615 0.00 0.00 0.00 3.84
5133 5747 0.723981 GCTTGAACCTGCATCGACTC 59.276 55.000 0.00 0.00 0.00 3.36
5198 5816 6.318648 TGACAGTGGATCCATTTTATAGCAAC 59.681 38.462 19.62 0.00 0.00 4.17
5328 8613 7.595819 AATACTCCTAGGAATCTTCACTCTG 57.404 40.000 13.77 0.00 0.00 3.35
5402 8694 3.880490 TGTAACGTGCCAGTGAAGAATTT 59.120 39.130 0.00 0.00 0.00 1.82
5426 8726 3.546724 GGTTTGCTCCTAGGATTCTTCC 58.453 50.000 13.12 9.08 42.96 3.46
5685 9071 1.004440 GAGCCGAGGAAGCACACTT 60.004 57.895 0.00 0.00 39.43 3.16
5694 9080 1.145119 TCTGCCTTATAGAGCCGAGGA 59.855 52.381 0.00 0.00 0.00 3.71
5844 9240 1.256812 TGTCGAGCTTCCTCACATCA 58.743 50.000 0.00 0.00 38.00 3.07
5877 9273 0.894184 TCTCGCGGTCCTTGAACTCT 60.894 55.000 6.13 0.00 0.00 3.24
5967 9363 2.086869 ACGCATTTCACATTCAGGAGG 58.913 47.619 0.00 0.00 0.00 4.30
5982 9378 1.269102 CCGGTCTTCTTATCGACGCAT 60.269 52.381 0.00 0.00 0.00 4.73
6018 9414 0.178958 ACCTGTCGACTTCTGGACCT 60.179 55.000 17.92 0.00 32.19 3.85
6022 9418 3.952323 TCCTTATACCTGTCGACTTCTGG 59.048 47.826 17.92 15.01 0.00 3.86
6156 9552 3.865745 CCAACTGGAATCTTACTACTGCG 59.134 47.826 0.00 0.00 37.39 5.18
6176 9572 2.335681 TGGTATCACCCTGTCTTCCA 57.664 50.000 0.00 0.00 37.50 3.53
6178 9574 2.746472 GCCATGGTATCACCCTGTCTTC 60.746 54.545 14.67 0.00 37.50 2.87
6181 9589 0.839946 AGCCATGGTATCACCCTGTC 59.160 55.000 14.67 0.00 37.50 3.51
6182 9590 0.839946 GAGCCATGGTATCACCCTGT 59.160 55.000 14.67 0.00 37.50 4.00
6183 9591 1.135094 AGAGCCATGGTATCACCCTG 58.865 55.000 14.67 0.00 37.50 4.45
6184 9592 1.135094 CAGAGCCATGGTATCACCCT 58.865 55.000 14.67 0.00 37.50 4.34
6185 9593 0.109342 CCAGAGCCATGGTATCACCC 59.891 60.000 14.67 0.00 37.50 4.61
6186 9594 0.536006 GCCAGAGCCATGGTATCACC 60.536 60.000 14.67 0.00 42.75 4.02
6187 9595 0.471617 AGCCAGAGCCATGGTATCAC 59.528 55.000 14.67 6.21 42.75 3.06
6188 9596 2.101640 TAGCCAGAGCCATGGTATCA 57.898 50.000 14.67 0.00 42.75 2.15
6189 9597 2.304180 ACATAGCCAGAGCCATGGTATC 59.696 50.000 14.67 12.10 41.80 2.24
6204 9612 6.538742 TGCAGGACAGAGTATTTTTACATAGC 59.461 38.462 0.00 0.00 0.00 2.97
6205 9613 8.668510 ATGCAGGACAGAGTATTTTTACATAG 57.331 34.615 0.00 0.00 0.00 2.23
6206 9614 8.486210 AGATGCAGGACAGAGTATTTTTACATA 58.514 33.333 0.00 0.00 0.00 2.29
6207 9615 7.341805 AGATGCAGGACAGAGTATTTTTACAT 58.658 34.615 0.00 0.00 0.00 2.29
6209 9617 7.550906 AGAAGATGCAGGACAGAGTATTTTTAC 59.449 37.037 0.00 0.00 0.00 2.01
6286 9704 2.365617 TCTGATAGCTCGAAATCCCCAC 59.634 50.000 0.00 0.00 0.00 4.61
6288 9706 3.971245 ATCTGATAGCTCGAAATCCCC 57.029 47.619 0.00 0.00 0.00 4.81
6289 9707 5.866633 CAGTTATCTGATAGCTCGAAATCCC 59.133 44.000 10.62 0.00 43.76 3.85
6290 9708 6.364706 CACAGTTATCTGATAGCTCGAAATCC 59.635 42.308 10.62 0.00 43.76 3.01
6291 9709 6.364706 CCACAGTTATCTGATAGCTCGAAATC 59.635 42.308 10.62 0.00 43.76 2.17
6292 9710 6.219473 CCACAGTTATCTGATAGCTCGAAAT 58.781 40.000 10.62 0.00 43.76 2.17
6293 9711 5.592054 CCACAGTTATCTGATAGCTCGAAA 58.408 41.667 10.62 0.00 43.76 3.46
6294 9712 4.499865 GCCACAGTTATCTGATAGCTCGAA 60.500 45.833 10.62 0.00 43.76 3.71
6295 9713 3.004839 GCCACAGTTATCTGATAGCTCGA 59.995 47.826 10.62 0.00 43.76 4.04
6296 9714 3.005261 AGCCACAGTTATCTGATAGCTCG 59.995 47.826 10.62 9.28 43.76 5.03
6297 9715 4.038522 TCAGCCACAGTTATCTGATAGCTC 59.961 45.833 10.62 1.45 43.76 4.09
6298 9716 3.963374 TCAGCCACAGTTATCTGATAGCT 59.037 43.478 8.07 8.07 43.76 3.32
6299 9717 4.327982 TCAGCCACAGTTATCTGATAGC 57.672 45.455 7.81 3.59 43.76 2.97
6300 9718 5.911752 ACTTCAGCCACAGTTATCTGATAG 58.088 41.667 7.81 0.00 43.76 2.08
6301 9719 5.939764 ACTTCAGCCACAGTTATCTGATA 57.060 39.130 7.81 0.00 43.76 2.15
6302 9720 4.833478 ACTTCAGCCACAGTTATCTGAT 57.167 40.909 7.81 0.00 43.76 2.90
6303 9721 5.939764 ATACTTCAGCCACAGTTATCTGA 57.060 39.130 7.81 0.00 43.76 3.27
6304 9722 8.554528 CAAATATACTTCAGCCACAGTTATCTG 58.445 37.037 0.00 0.00 46.18 2.90
6305 9723 8.486210 TCAAATATACTTCAGCCACAGTTATCT 58.514 33.333 0.00 0.00 0.00 1.98
6306 9724 8.662781 TCAAATATACTTCAGCCACAGTTATC 57.337 34.615 0.00 0.00 0.00 1.75
6307 9725 9.632638 AATCAAATATACTTCAGCCACAGTTAT 57.367 29.630 0.00 0.00 0.00 1.89
6308 9726 8.892723 CAATCAAATATACTTCAGCCACAGTTA 58.107 33.333 0.00 0.00 0.00 2.24
6309 9727 7.394359 ACAATCAAATATACTTCAGCCACAGTT 59.606 33.333 0.00 0.00 0.00 3.16
6310 9728 6.886459 ACAATCAAATATACTTCAGCCACAGT 59.114 34.615 0.00 0.00 0.00 3.55
6320 9738 8.330466 TCAACGACCAACAATCAAATATACTT 57.670 30.769 0.00 0.00 0.00 2.24
6337 9864 5.751243 ATAGTGCCAATATTTCAACGACC 57.249 39.130 0.00 0.00 0.00 4.79
6346 9873 5.887598 TGCTTGTCTCAATAGTGCCAATATT 59.112 36.000 0.00 0.00 0.00 1.28
6347 9874 5.439721 TGCTTGTCTCAATAGTGCCAATAT 58.560 37.500 0.00 0.00 0.00 1.28
6348 9875 4.842574 TGCTTGTCTCAATAGTGCCAATA 58.157 39.130 0.00 0.00 0.00 1.90
6351 9878 2.857186 TGCTTGTCTCAATAGTGCCA 57.143 45.000 0.00 0.00 0.00 4.92
6352 9879 3.253188 TGTTTGCTTGTCTCAATAGTGCC 59.747 43.478 0.00 0.00 0.00 5.01
6353 9880 4.488126 TGTTTGCTTGTCTCAATAGTGC 57.512 40.909 0.00 0.00 0.00 4.40
6357 9884 7.102993 TGCTAGTATGTTTGCTTGTCTCAATA 58.897 34.615 0.00 0.00 0.00 1.90
6359 9886 5.304778 TGCTAGTATGTTTGCTTGTCTCAA 58.695 37.500 0.00 0.00 0.00 3.02
6361 9888 6.535150 TGTATGCTAGTATGTTTGCTTGTCTC 59.465 38.462 3.24 0.00 0.00 3.36
6362 9889 6.406370 TGTATGCTAGTATGTTTGCTTGTCT 58.594 36.000 3.24 0.00 0.00 3.41
6364 9891 7.050377 AGATGTATGCTAGTATGTTTGCTTGT 58.950 34.615 3.24 0.00 0.00 3.16
6365 9892 7.488187 AGATGTATGCTAGTATGTTTGCTTG 57.512 36.000 3.24 0.00 0.00 4.01
6366 9893 8.511604 AAAGATGTATGCTAGTATGTTTGCTT 57.488 30.769 3.24 0.00 0.00 3.91
6375 9902 9.154632 TCAAGGGAATAAAGATGTATGCTAGTA 57.845 33.333 0.00 0.00 0.00 1.82
6377 9904 7.605691 CCTCAAGGGAATAAAGATGTATGCTAG 59.394 40.741 0.00 0.00 37.23 3.42
6378 9905 7.292356 TCCTCAAGGGAATAAAGATGTATGCTA 59.708 37.037 0.00 0.00 41.91 3.49
6379 9906 6.101734 TCCTCAAGGGAATAAAGATGTATGCT 59.898 38.462 0.00 0.00 41.91 3.79
6380 9907 6.299141 TCCTCAAGGGAATAAAGATGTATGC 58.701 40.000 0.00 0.00 41.91 3.14
6395 9926 5.530543 GCTTCTCTCAATATTTCCTCAAGGG 59.469 44.000 0.00 0.00 35.41 3.95
6408 9939 6.661377 TGTGACTAGTCTTAGCTTCTCTCAAT 59.339 38.462 23.01 0.00 0.00 2.57
6415 9946 5.983720 TGTGTTTGTGACTAGTCTTAGCTTC 59.016 40.000 23.01 9.93 0.00 3.86
6423 9954 7.971455 AGTTTAGTTTGTGTTTGTGACTAGTC 58.029 34.615 16.32 16.32 0.00 2.59
6428 9959 5.957796 CGAGAGTTTAGTTTGTGTTTGTGAC 59.042 40.000 0.00 0.00 0.00 3.67
6432 9963 7.406553 TGATTCGAGAGTTTAGTTTGTGTTTG 58.593 34.615 0.00 0.00 0.00 2.93
6433 9964 7.548196 TGATTCGAGAGTTTAGTTTGTGTTT 57.452 32.000 0.00 0.00 0.00 2.83
6481 10020 2.437359 GCTGGCTGGCGATGAGTT 60.437 61.111 0.00 0.00 0.00 3.01
6484 10023 4.166888 GAGGCTGGCTGGCGATGA 62.167 66.667 9.06 0.00 46.88 2.92
6574 10119 2.154462 AGAAAAACTGCGACTCATGGG 58.846 47.619 0.00 0.00 0.00 4.00
6597 10142 4.179926 TCGGTGAAGAAGACAAGATCAG 57.820 45.455 0.00 0.00 0.00 2.90
6632 10177 1.849097 ACAACTCGACCGTGAAGAAC 58.151 50.000 0.00 0.00 0.00 3.01
6633 10178 2.198406 CAACAACTCGACCGTGAAGAA 58.802 47.619 0.00 0.00 0.00 2.52
6634 10179 1.537348 CCAACAACTCGACCGTGAAGA 60.537 52.381 0.00 0.00 0.00 2.87
6635 10180 0.859232 CCAACAACTCGACCGTGAAG 59.141 55.000 0.00 0.00 0.00 3.02
6636 10181 1.155424 GCCAACAACTCGACCGTGAA 61.155 55.000 0.00 0.00 0.00 3.18
6637 10182 1.593209 GCCAACAACTCGACCGTGA 60.593 57.895 0.00 0.00 0.00 4.35
6639 10184 2.660552 CGCCAACAACTCGACCGT 60.661 61.111 0.00 0.00 0.00 4.83
6640 10185 3.411351 CCGCCAACAACTCGACCG 61.411 66.667 0.00 0.00 0.00 4.79
6641 10186 3.723348 GCCGCCAACAACTCGACC 61.723 66.667 0.00 0.00 0.00 4.79
6642 10187 2.665185 AGCCGCCAACAACTCGAC 60.665 61.111 0.00 0.00 0.00 4.20
6643 10188 2.357034 GAGCCGCCAACAACTCGA 60.357 61.111 0.00 0.00 0.00 4.04
6644 10189 3.423154 GGAGCCGCCAACAACTCG 61.423 66.667 0.00 0.00 36.34 4.18
6645 10190 1.600916 AAGGAGCCGCCAACAACTC 60.601 57.895 0.00 0.00 40.02 3.01
6646 10191 1.898574 CAAGGAGCCGCCAACAACT 60.899 57.895 0.00 0.00 40.02 3.16
6647 10192 1.734388 AACAAGGAGCCGCCAACAAC 61.734 55.000 0.00 0.00 40.02 3.32
6660 10205 1.747709 CAGAGGATCAGCCAACAAGG 58.252 55.000 0.00 0.00 40.02 3.61
6669 10214 1.333636 AAGGTCCGGCAGAGGATCAG 61.334 60.000 0.00 0.00 43.79 2.90
6706 10251 1.166531 GGGGTTTAGCTATGCGCAGG 61.167 60.000 18.32 12.65 42.61 4.85
6766 10311 3.518992 AGAGGAAGGTAGCTAGCTAGG 57.481 52.381 24.78 4.48 33.01 3.02
6794 10340 7.099764 ACATCTCACACGATCCAATTATATCC 58.900 38.462 0.00 0.00 0.00 2.59
6814 10361 2.556144 ATGCACACACACAGACATCT 57.444 45.000 0.00 0.00 0.00 2.90
6815 10362 3.066380 TGTATGCACACACACAGACATC 58.934 45.455 0.00 0.00 33.39 3.06
6816 10363 3.124578 TGTATGCACACACACAGACAT 57.875 42.857 0.00 0.00 33.39 3.06
6817 10364 2.611225 TGTATGCACACACACAGACA 57.389 45.000 0.00 0.00 35.78 3.41
6818 10365 4.034394 CCATATGTATGCACACACACAGAC 59.966 45.833 0.00 0.00 37.54 3.51
6819 10366 4.081198 TCCATATGTATGCACACACACAGA 60.081 41.667 0.00 0.00 37.54 3.41
6822 10369 5.107491 CGTATCCATATGTATGCACACACAC 60.107 44.000 0.00 0.00 37.54 3.82
6846 10393 0.730840 GCATATAAATACGCCCGGCC 59.269 55.000 3.10 0.00 0.00 6.13
6853 10400 2.348666 GCAGCCCTCGCATATAAATACG 59.651 50.000 0.00 0.00 37.52 3.06
6867 10414 0.398948 CCCCCAATAATTGCAGCCCT 60.399 55.000 0.00 0.00 0.00 5.19
6935 10483 2.035632 CCACCACCAGAGGAGATACTC 58.964 57.143 0.00 0.00 37.77 2.59
6936 10484 1.362932 ACCACCACCAGAGGAGATACT 59.637 52.381 0.00 0.00 0.00 2.12
6937 10485 1.867363 ACCACCACCAGAGGAGATAC 58.133 55.000 0.00 0.00 0.00 2.24
6938 10486 2.091278 CCTACCACCACCAGAGGAGATA 60.091 54.545 0.00 0.00 0.00 1.98
6939 10487 1.343478 CCTACCACCACCAGAGGAGAT 60.343 57.143 0.00 0.00 0.00 2.75
6983 10531 3.567585 TGTTTGTGATTGCTTCCGAATCA 59.432 39.130 0.00 0.00 37.46 2.57
7009 10558 2.094026 GCAACCCTATGAAAAAGGCAGG 60.094 50.000 0.00 0.00 32.34 4.85
7098 10654 2.290464 CACCAGGAACACAAAACCGTA 58.710 47.619 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.