Multiple sequence alignment - TraesCS1A01G226500

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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 TraesCS1A01G226500 chr1A 100.000 4083 0 0 3098 7180 396466166 396462084 0.000000e+00 7540.0
1 TraesCS1A01G226500 chr1A 100.000 2610 0 0 1 2610 396469263 396466654 0.000000e+00 4820.0
2 TraesCS1A01G226500 chr1D 95.245 3428 116 23 3098 6501 316021667 316018263 0.000000e+00 5384.0
3 TraesCS1A01G226500 chr1D 96.086 2606 83 9 1 2596 316024498 316021902 0.000000e+00 4229.0
4 TraesCS1A01G226500 chr1D 94.563 515 15 3 6667 7180 316017987 316017485 0.000000e+00 784.0
5 TraesCS1A01G226500 chr1D 87.970 133 13 3 294 425 316024257 316024127 3.470000e-33 154.0
6 TraesCS1A01G226500 chr1B 93.146 3443 175 30 3098 6512 428114318 428110909 0.000000e+00 4994.0
7 TraesCS1A01G226500 chr1B 95.367 2547 94 13 1 2533 428117236 428114700 0.000000e+00 4028.0
8 TraesCS1A01G226500 chr3A 83.607 183 20 6 551 732 519234124 519233951 5.760000e-36 163.0
9 TraesCS1A01G226500 chr3D 81.967 183 23 6 551 732 400282101 400281928 5.800000e-31 147.0
10 TraesCS1A01G226500 chr3B 76.471 187 27 10 551 736 525987869 525987699 1.280000e-12 86.1


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 TraesCS1A01G226500 chr1A 396462084 396469263 7179 True 6180.00 7540 100.0000 1 7180 2 chr1A.!!$R1 7179
1 TraesCS1A01G226500 chr1D 316017485 316024498 7013 True 2637.75 5384 93.4660 1 7180 4 chr1D.!!$R1 7179
2 TraesCS1A01G226500 chr1B 428110909 428117236 6327 True 4511.00 4994 94.2565 1 6512 2 chr1B.!!$R1 6511

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
118 120 0.185416 TTCTAGGTCCTAGGGGCTCG 59.815 60.000 23.3 0.0 35.03 5.03 F
1022 1036 0.250513 GGTCGTCTCAAGGCAAGGAT 59.749 55.000 0.0 0.0 0.00 3.24 F
1266 1282 1.066002 CCTGCCACAACTTGTTCTGTG 59.934 52.381 0.0 0.0 42.14 3.66 F
2023 2040 2.109126 GGCCCTGATGACACGCTTC 61.109 63.158 0.0 0.0 0.00 3.86 F
2586 2603 0.698238 TGAAGTGGGTGGGAGAATGG 59.302 55.000 0.0 0.0 0.00 3.16 F
2592 2609 1.786441 TGGGTGGGAGAATGGTTTTCT 59.214 47.619 0.0 0.0 0.00 2.52 F
4408 4436 1.131126 CGCCTCTATGTTTGCTTGGTG 59.869 52.381 0.0 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1626 1643 0.259938 GAATGGGCCTGGTTGAGGAT 59.740 55.000 4.53 0.00 46.33 3.24 R
2069 2086 2.091541 TGCTGCCTTGTATTGCTTACC 58.908 47.619 0.00 0.00 0.00 2.85 R
2586 2603 4.742659 ACACACACACACAAAACAGAAAAC 59.257 37.500 0.00 0.00 0.00 2.43 R
3272 3289 2.271944 AGGTGTGCTTACCCAAAGAC 57.728 50.000 6.37 0.00 41.83 3.01 R
4408 4436 4.262249 GGGAGAGCATGGTCATACTAGAAC 60.262 50.000 25.71 5.66 0.00 3.01 R
4556 4586 4.860907 GTGAAAGCATGAGCCACTAAATTG 59.139 41.667 0.00 0.00 43.56 2.32 R
6235 6282 1.211190 GGTGCTTGCTTGTAGCTGC 59.789 57.895 0.00 0.00 42.97 5.25 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
54 55 4.389374 TGAAGATGGTTGAGAACTCCAAC 58.611 43.478 0.00 0.00 42.18 3.77
55 56 4.141505 TGAAGATGGTTGAGAACTCCAACA 60.142 41.667 0.00 7.46 44.07 3.33
58 59 3.194005 TGGTTGAGAACTCCAACAGAC 57.806 47.619 0.00 0.00 44.07 3.51
113 115 4.817286 AGTGGTAATTCTAGGTCCTAGGG 58.183 47.826 23.30 2.61 35.03 3.53
118 120 0.185416 TTCTAGGTCCTAGGGGCTCG 59.815 60.000 23.30 0.00 35.03 5.03
180 182 0.336392 TCTGCTGGGAGCTAGGAAGA 59.664 55.000 0.00 0.00 42.97 2.87
199 201 6.049149 GGAAGATCTGAAACCGATAACATGA 58.951 40.000 0.00 0.00 0.00 3.07
236 238 6.611381 TCCGTTTTGCTTAAGATGATCTTTG 58.389 36.000 13.54 8.07 37.89 2.77
249 251 6.243900 AGATGATCTTTGTCCTGTTTCACAT 58.756 36.000 0.00 0.00 0.00 3.21
287 289 6.181190 GGCAGGGGATCTAAATTAGTATTCC 58.819 44.000 0.00 5.62 0.00 3.01
291 293 7.937394 CAGGGGATCTAAATTAGTATTCCGTTT 59.063 37.037 0.00 0.00 0.00 3.60
324 332 7.296150 TGATATTAAGGCAGGGGGTCTAAAATA 59.704 37.037 0.00 0.00 0.00 1.40
368 376 7.407033 TGATATCAAGGCAGGGGATCTAAATAT 59.593 37.037 1.98 0.00 0.00 1.28
416 424 6.954352 AGGTGGGGGATCTAAAATAGTATC 57.046 41.667 0.00 0.00 0.00 2.24
465 473 3.286751 GCCAACGCTTGCACCAGA 61.287 61.111 0.00 0.00 0.00 3.86
504 512 6.604795 CCCTGGACTTGAATATTTCACATTCT 59.395 38.462 0.00 0.00 39.87 2.40
868 879 1.373570 CATTCTCAAGTTCGAGGGGC 58.626 55.000 0.00 0.00 33.59 5.80
874 885 0.537371 CAAGTTCGAGGGGCCAAGTT 60.537 55.000 4.39 0.00 0.00 2.66
1021 1035 1.671742 GGTCGTCTCAAGGCAAGGA 59.328 57.895 0.00 0.00 0.00 3.36
1022 1036 0.250513 GGTCGTCTCAAGGCAAGGAT 59.749 55.000 0.00 0.00 0.00 3.24
1203 1219 5.355071 TCCATGAATGTGATGCTTCTGTAAC 59.645 40.000 0.00 0.00 0.00 2.50
1205 1221 6.127814 CCATGAATGTGATGCTTCTGTAACTT 60.128 38.462 0.00 0.00 0.00 2.66
1266 1282 1.066002 CCTGCCACAACTTGTTCTGTG 59.934 52.381 0.00 0.00 42.14 3.66
1275 1291 6.205464 CCACAACTTGTTCTGTGAACTATGAT 59.795 38.462 11.06 0.00 44.68 2.45
1349 1365 4.641989 GTGCAATCTGTAATTGGGATGAGT 59.358 41.667 0.00 0.00 0.00 3.41
1380 1396 2.285220 CCATCATAATATAGCGCACGGC 59.715 50.000 11.47 0.00 44.05 5.68
1424 1441 9.167311 CCAAACTCTTTGTATTTATGAGTAGCT 57.833 33.333 0.00 0.00 38.98 3.32
1447 1464 7.561722 AGCTGAATTCTGTAGTTATCTACTCCA 59.438 37.037 13.17 0.00 44.74 3.86
1576 1593 3.306472 TTAGGAACCCACAAAGCAACT 57.694 42.857 0.00 0.00 0.00 3.16
1626 1643 7.984617 GCAGGTTAAAAGGGCATTAAATAATGA 59.015 33.333 15.53 0.00 44.40 2.57
1633 1650 8.551682 AAAGGGCATTAAATAATGATCCTCAA 57.448 30.769 19.45 0.00 44.40 3.02
2023 2040 2.109126 GGCCCTGATGACACGCTTC 61.109 63.158 0.00 0.00 0.00 3.86
2069 2086 8.954350 AGTCATTTCTCATAAAACTGATTGGAG 58.046 33.333 0.00 0.00 0.00 3.86
2227 2244 7.676572 GCAGAAGAGTTTCCGGATGTTAATTAC 60.677 40.741 4.15 0.00 33.64 1.89
2275 2292 5.076182 TGTTGCTCAATGGGAAGTGATTAA 58.924 37.500 0.00 0.00 0.00 1.40
2586 2603 0.698238 TGAAGTGGGTGGGAGAATGG 59.302 55.000 0.00 0.00 0.00 3.16
2591 2608 1.893137 GTGGGTGGGAGAATGGTTTTC 59.107 52.381 0.00 0.00 0.00 2.29
2592 2609 1.786441 TGGGTGGGAGAATGGTTTTCT 59.214 47.619 0.00 0.00 0.00 2.52
2593 2610 2.171003 GGGTGGGAGAATGGTTTTCTG 58.829 52.381 0.00 0.00 0.00 3.02
2594 2611 2.490902 GGGTGGGAGAATGGTTTTCTGT 60.491 50.000 0.00 0.00 0.00 3.41
2597 2614 4.100963 GGTGGGAGAATGGTTTTCTGTTTT 59.899 41.667 0.00 0.00 0.00 2.43
2598 2615 5.049828 GTGGGAGAATGGTTTTCTGTTTTG 58.950 41.667 0.00 0.00 0.00 2.44
2599 2616 4.714308 TGGGAGAATGGTTTTCTGTTTTGT 59.286 37.500 0.00 0.00 0.00 2.83
2600 2617 5.049828 GGGAGAATGGTTTTCTGTTTTGTG 58.950 41.667 0.00 0.00 0.00 3.33
2601 2618 5.395214 GGGAGAATGGTTTTCTGTTTTGTGT 60.395 40.000 0.00 0.00 0.00 3.72
2602 2619 5.519927 GGAGAATGGTTTTCTGTTTTGTGTG 59.480 40.000 0.00 0.00 0.00 3.82
2603 2620 6.036577 AGAATGGTTTTCTGTTTTGTGTGT 57.963 33.333 0.00 0.00 0.00 3.72
2604 2621 5.868801 AGAATGGTTTTCTGTTTTGTGTGTG 59.131 36.000 0.00 0.00 0.00 3.82
2605 2622 4.592485 TGGTTTTCTGTTTTGTGTGTGT 57.408 36.364 0.00 0.00 0.00 3.72
2606 2623 4.302455 TGGTTTTCTGTTTTGTGTGTGTG 58.698 39.130 0.00 0.00 0.00 3.82
2607 2624 4.202161 TGGTTTTCTGTTTTGTGTGTGTGT 60.202 37.500 0.00 0.00 0.00 3.72
2608 2625 4.149747 GGTTTTCTGTTTTGTGTGTGTGTG 59.850 41.667 0.00 0.00 0.00 3.82
2609 2626 4.576216 TTTCTGTTTTGTGTGTGTGTGT 57.424 36.364 0.00 0.00 0.00 3.72
3302 3319 5.701290 GGGTAAGCACACCTATGATGTTATC 59.299 44.000 6.69 0.00 38.73 1.75
3580 3600 8.138712 ACATTTCCGCAAAACTACAGATTTAAA 58.861 29.630 0.00 0.00 0.00 1.52
3798 3818 4.079558 AGCATCACCAACCCTGAAGATAAT 60.080 41.667 0.00 0.00 0.00 1.28
3829 3849 2.361104 GCCGGGTGGATGCAAAGA 60.361 61.111 2.18 0.00 37.49 2.52
3870 3890 2.763448 AGGAGGGCGATATAATCTCTGC 59.237 50.000 0.00 0.00 0.00 4.26
3878 3898 7.831193 AGGGCGATATAATCTCTGCATTTTATT 59.169 33.333 0.00 0.00 0.00 1.40
3921 3941 5.068636 ACTTTCTCATGGATCATGGCATAC 58.931 41.667 0.00 0.00 41.66 2.39
3961 3982 2.561419 GTCAACTGGTAGTAGTGAGCCA 59.439 50.000 0.00 0.00 0.00 4.75
3981 4002 5.359009 AGCCATTCAATTCAGTTGATCGAAT 59.641 36.000 0.00 0.00 45.77 3.34
4057 4079 3.720002 TCACCCCCTCACCCTAATTTATC 59.280 47.826 0.00 0.00 0.00 1.75
4408 4436 1.131126 CGCCTCTATGTTTGCTTGGTG 59.869 52.381 0.00 0.00 0.00 4.17
4425 4453 4.137116 TGGTGTTCTAGTATGACCATGC 57.863 45.455 0.00 0.00 31.64 4.06
4456 4484 8.027189 CCTAATATAGTGTAAGCTTACGATGCA 58.973 37.037 27.07 14.97 36.45 3.96
4602 4632 6.478016 CACTTCATCATCTGTCGTGACAATAT 59.522 38.462 4.03 0.00 41.33 1.28
4671 4707 6.623979 TGGGCCTACTATGTTACTGTTAAA 57.376 37.500 4.53 0.00 0.00 1.52
4676 4712 9.169592 GGCCTACTATGTTACTGTTAAATTTCA 57.830 33.333 0.00 0.00 0.00 2.69
4765 4801 5.882000 CCATTGACAGGTTTCATCTGTATGA 59.118 40.000 0.00 0.00 44.51 2.15
4832 4868 8.654230 TCATCTTTGATCTGATTAAGCTGTAC 57.346 34.615 12.70 0.00 0.00 2.90
4886 4922 2.679336 CAGGCGAATCATGTGTTCATCA 59.321 45.455 11.97 0.00 31.15 3.07
4972 5008 6.762702 TTTCCTTGTAAGAACGTTTCCTTT 57.237 33.333 0.46 0.00 0.00 3.11
5132 5168 2.739379 GCTGTTCAAAGAGACTACTGGC 59.261 50.000 0.00 0.00 0.00 4.85
5334 5370 3.368190 CTGGGAGCAGCGACCTCTG 62.368 68.421 9.46 0.00 37.15 3.35
5358 5394 3.557595 GCCAGAATCAGGTCTGTTATTCG 59.442 47.826 1.84 0.00 43.02 3.34
5544 5581 1.065126 GTGTTTAGGATGAGCTGGCCT 60.065 52.381 3.32 0.00 35.82 5.19
5586 5623 6.274157 TGACTAATCTCTCTCTTGTCAACC 57.726 41.667 0.00 0.00 31.30 3.77
5701 5738 2.841442 ACACTCAACTCAAGGGTAGC 57.159 50.000 0.00 0.00 0.00 3.58
5706 5745 4.021016 CACTCAACTCAAGGGTAGCTAGTT 60.021 45.833 0.00 0.00 0.00 2.24
5712 5751 4.264262 ACTCAAGGGTAGCTAGTTCAGGTA 60.264 45.833 0.00 0.00 36.15 3.08
5763 5802 5.848921 AGTGGAATCTGAAGGCTAATAGGAT 59.151 40.000 0.00 0.00 0.00 3.24
5807 5846 3.861840 TCCTGGAAAAATGAGCTACTCG 58.138 45.455 0.00 0.00 32.35 4.18
5863 5903 4.757149 ACTCAAACTAGGTCAAATGTGCTC 59.243 41.667 0.00 0.00 0.00 4.26
5965 6008 1.237285 ATGCTGCGGTCCTTGTTCAC 61.237 55.000 0.00 0.00 0.00 3.18
6019 6062 0.600782 GTGTAAACGAGGGACGCCAA 60.601 55.000 0.00 0.00 46.94 4.52
6053 6096 7.492994 GGAAGTCTCATATTGTAAGTTCTCACC 59.507 40.741 0.00 0.00 0.00 4.02
6189 6236 4.439837 CCTTACGGTTCTAGAACTACCAGC 60.440 50.000 29.66 14.46 40.94 4.85
6235 6282 4.342862 TGAAGTTCCTCTTGAGTTCTGG 57.657 45.455 0.00 0.00 36.40 3.86
6327 6374 0.323999 TTCTCGCACCCTAGCTGGTA 60.324 55.000 0.00 0.00 36.67 3.25
6390 6439 9.638300 CTTGTAAATATTACATGCTTTCGAGTC 57.362 33.333 3.98 0.00 0.00 3.36
6447 6501 2.328099 CGCTGCCACCTGAAACCTC 61.328 63.158 0.00 0.00 0.00 3.85
6458 6512 3.074390 ACCTGAAACCTCCATCATGTTGA 59.926 43.478 5.30 0.00 0.00 3.18
6477 6531 5.822519 TGTTGATGGTGAGTATGGAAATAGC 59.177 40.000 0.00 0.00 0.00 2.97
6527 6581 0.033796 GGGGGTAGGTTAAACTGGGC 60.034 60.000 2.38 0.00 0.00 5.36
6528 6582 0.997363 GGGGTAGGTTAAACTGGGCT 59.003 55.000 2.38 0.00 0.00 5.19
6529 6583 2.199208 GGGGTAGGTTAAACTGGGCTA 58.801 52.381 2.38 0.00 0.00 3.93
6530 6584 2.172082 GGGGTAGGTTAAACTGGGCTAG 59.828 54.545 2.38 0.00 0.00 3.42
6531 6585 2.842496 GGGTAGGTTAAACTGGGCTAGT 59.158 50.000 2.38 0.00 42.89 2.57
6532 6586 3.370209 GGGTAGGTTAAACTGGGCTAGTG 60.370 52.174 3.59 0.00 40.26 2.74
6533 6587 3.516700 GGTAGGTTAAACTGGGCTAGTGA 59.483 47.826 3.59 0.00 40.26 3.41
6534 6588 4.163649 GGTAGGTTAAACTGGGCTAGTGAT 59.836 45.833 3.59 0.00 40.26 3.06
6535 6589 4.222124 AGGTTAAACTGGGCTAGTGATG 57.778 45.455 3.59 0.00 40.26 3.07
6536 6590 3.587506 AGGTTAAACTGGGCTAGTGATGT 59.412 43.478 3.59 0.00 40.26 3.06
6537 6591 4.042934 AGGTTAAACTGGGCTAGTGATGTT 59.957 41.667 3.59 0.00 40.26 2.71
6538 6592 4.765339 GGTTAAACTGGGCTAGTGATGTTT 59.235 41.667 3.59 0.00 40.26 2.83
6539 6593 5.243060 GGTTAAACTGGGCTAGTGATGTTTT 59.757 40.000 3.59 0.00 40.26 2.43
6540 6594 6.239204 GGTTAAACTGGGCTAGTGATGTTTTT 60.239 38.462 3.59 0.00 40.26 1.94
6541 6595 7.040271 GGTTAAACTGGGCTAGTGATGTTTTTA 60.040 37.037 3.59 0.00 40.26 1.52
6542 6596 8.520351 GTTAAACTGGGCTAGTGATGTTTTTAT 58.480 33.333 3.59 0.00 40.26 1.40
6543 6597 6.759497 AACTGGGCTAGTGATGTTTTTATC 57.241 37.500 3.59 0.00 40.26 1.75
6544 6598 6.067217 ACTGGGCTAGTGATGTTTTTATCT 57.933 37.500 1.44 0.00 38.49 1.98
6545 6599 5.882557 ACTGGGCTAGTGATGTTTTTATCTG 59.117 40.000 1.44 0.00 38.49 2.90
6546 6600 6.061022 TGGGCTAGTGATGTTTTTATCTGA 57.939 37.500 0.00 0.00 0.00 3.27
6547 6601 5.880332 TGGGCTAGTGATGTTTTTATCTGAC 59.120 40.000 0.00 0.00 0.00 3.51
6548 6602 5.006746 GGGCTAGTGATGTTTTTATCTGACG 59.993 44.000 0.00 0.00 0.00 4.35
6549 6603 5.810587 GGCTAGTGATGTTTTTATCTGACGA 59.189 40.000 0.00 0.00 0.00 4.20
6550 6604 6.312918 GGCTAGTGATGTTTTTATCTGACGAA 59.687 38.462 0.00 0.00 0.00 3.85
6551 6605 7.174082 GCTAGTGATGTTTTTATCTGACGAAC 58.826 38.462 0.00 0.00 0.00 3.95
6552 6606 7.148639 GCTAGTGATGTTTTTATCTGACGAACA 60.149 37.037 0.00 0.00 35.04 3.18
6553 6607 6.888430 AGTGATGTTTTTATCTGACGAACAC 58.112 36.000 0.00 0.00 33.58 3.32
6554 6608 6.073222 AGTGATGTTTTTATCTGACGAACACC 60.073 38.462 0.00 0.00 33.58 4.16
6555 6609 4.718858 TGTTTTTATCTGACGAACACCG 57.281 40.909 0.00 0.00 45.44 4.94
6556 6610 3.059461 TGTTTTTATCTGACGAACACCGC 60.059 43.478 0.00 0.00 43.32 5.68
6557 6611 2.442212 TTTATCTGACGAACACCGCA 57.558 45.000 0.00 0.00 43.32 5.69
6558 6612 1.990799 TTATCTGACGAACACCGCAG 58.009 50.000 0.00 0.00 43.32 5.18
6559 6613 0.885879 TATCTGACGAACACCGCAGT 59.114 50.000 0.00 0.00 43.32 4.40
6560 6614 0.033504 ATCTGACGAACACCGCAGTT 59.966 50.000 0.00 0.00 43.32 3.16
6561 6615 0.179094 TCTGACGAACACCGCAGTTT 60.179 50.000 0.00 0.00 43.32 2.66
6562 6616 0.655733 CTGACGAACACCGCAGTTTT 59.344 50.000 0.00 0.00 43.32 2.43
6563 6617 1.063469 CTGACGAACACCGCAGTTTTT 59.937 47.619 0.00 0.00 43.32 1.94
6564 6618 2.277969 TGACGAACACCGCAGTTTTTA 58.722 42.857 0.00 0.00 43.32 1.52
6565 6619 2.873472 TGACGAACACCGCAGTTTTTAT 59.127 40.909 0.00 0.00 43.32 1.40
6566 6620 3.312973 TGACGAACACCGCAGTTTTTATT 59.687 39.130 0.00 0.00 43.32 1.40
6567 6621 3.623863 ACGAACACCGCAGTTTTTATTG 58.376 40.909 0.00 0.00 43.32 1.90
6568 6622 2.403698 CGAACACCGCAGTTTTTATTGC 59.596 45.455 0.00 0.00 36.97 3.56
6569 6623 3.376540 GAACACCGCAGTTTTTATTGCA 58.623 40.909 0.00 0.00 40.28 4.08
6570 6624 3.658757 ACACCGCAGTTTTTATTGCAT 57.341 38.095 0.00 0.00 40.28 3.96
6571 6625 3.574614 ACACCGCAGTTTTTATTGCATC 58.425 40.909 0.00 0.00 40.28 3.91
6572 6626 3.005261 ACACCGCAGTTTTTATTGCATCA 59.995 39.130 0.00 0.00 40.28 3.07
6573 6627 4.175516 CACCGCAGTTTTTATTGCATCAT 58.824 39.130 0.00 0.00 40.28 2.45
6574 6628 5.105957 ACACCGCAGTTTTTATTGCATCATA 60.106 36.000 0.00 0.00 40.28 2.15
6575 6629 5.229887 CACCGCAGTTTTTATTGCATCATAC 59.770 40.000 0.00 0.00 40.28 2.39
6576 6630 5.125417 ACCGCAGTTTTTATTGCATCATACT 59.875 36.000 0.00 0.00 40.28 2.12
6577 6631 6.317642 ACCGCAGTTTTTATTGCATCATACTA 59.682 34.615 0.00 0.00 40.28 1.82
6578 6632 6.632834 CCGCAGTTTTTATTGCATCATACTAC 59.367 38.462 0.00 0.00 40.28 2.73
6579 6633 6.632834 CGCAGTTTTTATTGCATCATACTACC 59.367 38.462 0.00 0.00 40.28 3.18
6580 6634 7.479980 GCAGTTTTTATTGCATCATACTACCA 58.520 34.615 0.00 0.00 40.02 3.25
6581 6635 7.973388 GCAGTTTTTATTGCATCATACTACCAA 59.027 33.333 0.00 0.00 40.02 3.67
6582 6636 9.507280 CAGTTTTTATTGCATCATACTACCAAG 57.493 33.333 0.00 0.00 0.00 3.61
6583 6637 9.243105 AGTTTTTATTGCATCATACTACCAAGT 57.757 29.630 0.00 0.00 39.91 3.16
6584 6638 9.503427 GTTTTTATTGCATCATACTACCAAGTC 57.497 33.333 0.00 0.00 37.15 3.01
6585 6639 9.461312 TTTTTATTGCATCATACTACCAAGTCT 57.539 29.630 0.00 0.00 37.15 3.24
6587 6641 9.542462 TTTATTGCATCATACTACCAAGTCTAC 57.458 33.333 0.00 0.00 37.15 2.59
6588 6642 6.538945 TTGCATCATACTACCAAGTCTACA 57.461 37.500 0.00 0.00 37.15 2.74
6589 6643 6.149129 TGCATCATACTACCAAGTCTACAG 57.851 41.667 0.00 0.00 37.15 2.74
6590 6644 5.069119 TGCATCATACTACCAAGTCTACAGG 59.931 44.000 0.00 0.00 37.15 4.00
6591 6645 5.509840 GCATCATACTACCAAGTCTACAGGG 60.510 48.000 0.00 0.00 37.15 4.45
6592 6646 5.461516 TCATACTACCAAGTCTACAGGGA 57.538 43.478 0.00 0.00 37.15 4.20
6593 6647 6.027025 TCATACTACCAAGTCTACAGGGAT 57.973 41.667 0.00 0.00 37.15 3.85
6594 6648 7.157947 TCATACTACCAAGTCTACAGGGATA 57.842 40.000 0.00 0.00 37.15 2.59
6595 6649 7.002879 TCATACTACCAAGTCTACAGGGATAC 58.997 42.308 0.00 0.00 37.15 2.24
6596 6650 5.202746 ACTACCAAGTCTACAGGGATACA 57.797 43.478 0.00 0.00 39.74 2.29
6597 6651 5.778542 ACTACCAAGTCTACAGGGATACAT 58.221 41.667 0.00 0.00 39.74 2.29
6598 6652 6.203072 ACTACCAAGTCTACAGGGATACATT 58.797 40.000 0.00 0.00 39.74 2.71
6599 6653 5.359194 ACCAAGTCTACAGGGATACATTG 57.641 43.478 0.00 0.00 39.74 2.82
6600 6654 5.030147 ACCAAGTCTACAGGGATACATTGA 58.970 41.667 0.00 0.00 39.74 2.57
6601 6655 5.667626 ACCAAGTCTACAGGGATACATTGAT 59.332 40.000 0.00 0.00 39.74 2.57
6602 6656 6.158695 ACCAAGTCTACAGGGATACATTGATT 59.841 38.462 0.00 0.00 39.74 2.57
6603 6657 7.056635 CCAAGTCTACAGGGATACATTGATTT 58.943 38.462 0.00 0.00 39.74 2.17
6604 6658 7.557719 CCAAGTCTACAGGGATACATTGATTTT 59.442 37.037 0.00 0.00 39.74 1.82
6605 6659 8.616076 CAAGTCTACAGGGATACATTGATTTTC 58.384 37.037 0.00 0.00 39.74 2.29
6606 6660 7.861629 AGTCTACAGGGATACATTGATTTTCA 58.138 34.615 0.00 0.00 39.74 2.69
6607 6661 7.989741 AGTCTACAGGGATACATTGATTTTCAG 59.010 37.037 0.00 0.00 39.74 3.02
6608 6662 7.227512 GTCTACAGGGATACATTGATTTTCAGG 59.772 40.741 0.00 0.00 39.74 3.86
6609 6663 5.203528 ACAGGGATACATTGATTTTCAGGG 58.796 41.667 0.00 0.00 39.74 4.45
6610 6664 4.586001 CAGGGATACATTGATTTTCAGGGG 59.414 45.833 0.00 0.00 39.74 4.79
6611 6665 3.897505 GGGATACATTGATTTTCAGGGGG 59.102 47.826 0.00 0.00 39.74 5.40
6612 6666 4.387437 GGGATACATTGATTTTCAGGGGGA 60.387 45.833 0.00 0.00 39.74 4.81
6613 6667 5.208121 GGATACATTGATTTTCAGGGGGAA 58.792 41.667 0.00 0.00 0.00 3.97
6614 6668 5.660864 GGATACATTGATTTTCAGGGGGAAA 59.339 40.000 0.00 0.00 43.59 3.13
6615 6669 6.327365 GGATACATTGATTTTCAGGGGGAAAT 59.673 38.462 0.00 0.00 44.59 2.17
6616 6670 7.147497 GGATACATTGATTTTCAGGGGGAAATT 60.147 37.037 0.00 0.00 44.59 1.82
6617 6671 6.452757 ACATTGATTTTCAGGGGGAAATTT 57.547 33.333 0.00 0.00 44.59 1.82
6618 6672 7.566658 ACATTGATTTTCAGGGGGAAATTTA 57.433 32.000 0.00 0.00 44.59 1.40
6619 6673 7.623630 ACATTGATTTTCAGGGGGAAATTTAG 58.376 34.615 0.00 0.00 44.59 1.85
6620 6674 5.675684 TGATTTTCAGGGGGAAATTTAGC 57.324 39.130 0.00 0.00 44.59 3.09
6621 6675 4.469586 TGATTTTCAGGGGGAAATTTAGCC 59.530 41.667 0.00 0.00 44.59 3.93
6622 6676 3.551635 TTTCAGGGGGAAATTTAGCCA 57.448 42.857 0.00 0.00 40.51 4.75
6623 6677 3.774842 TTCAGGGGGAAATTTAGCCAT 57.225 42.857 0.00 0.00 30.98 4.40
6624 6678 4.890499 TTCAGGGGGAAATTTAGCCATA 57.110 40.909 0.00 0.00 30.98 2.74
6625 6679 4.178956 TCAGGGGGAAATTTAGCCATAC 57.821 45.455 0.00 0.00 0.00 2.39
6626 6680 3.529734 TCAGGGGGAAATTTAGCCATACA 59.470 43.478 0.00 0.00 0.00 2.29
6627 6681 4.169856 TCAGGGGGAAATTTAGCCATACAT 59.830 41.667 0.00 0.00 0.00 2.29
6628 6682 5.374154 TCAGGGGGAAATTTAGCCATACATA 59.626 40.000 0.00 0.00 0.00 2.29
6629 6683 6.046643 TCAGGGGGAAATTTAGCCATACATAT 59.953 38.462 0.00 0.00 0.00 1.78
6630 6684 6.378280 CAGGGGGAAATTTAGCCATACATATC 59.622 42.308 0.00 0.00 0.00 1.63
6631 6685 5.357032 GGGGGAAATTTAGCCATACATATCG 59.643 44.000 0.00 0.00 0.00 2.92
6632 6686 5.944007 GGGGAAATTTAGCCATACATATCGT 59.056 40.000 0.00 0.00 0.00 3.73
6633 6687 6.093633 GGGGAAATTTAGCCATACATATCGTC 59.906 42.308 0.00 0.00 0.00 4.20
6634 6688 6.093633 GGGAAATTTAGCCATACATATCGTCC 59.906 42.308 0.00 0.00 0.00 4.79
6635 6689 6.093633 GGAAATTTAGCCATACATATCGTCCC 59.906 42.308 0.00 0.00 0.00 4.46
6636 6690 5.755409 ATTTAGCCATACATATCGTCCCA 57.245 39.130 0.00 0.00 0.00 4.37
6637 6691 5.755409 TTTAGCCATACATATCGTCCCAT 57.245 39.130 0.00 0.00 0.00 4.00
6638 6692 3.616956 AGCCATACATATCGTCCCATG 57.383 47.619 0.00 0.00 0.00 3.66
6639 6693 2.906389 AGCCATACATATCGTCCCATGT 59.094 45.455 0.00 0.00 38.81 3.21
6640 6694 3.055819 AGCCATACATATCGTCCCATGTC 60.056 47.826 0.00 0.00 36.74 3.06
6641 6695 3.306710 GCCATACATATCGTCCCATGTCA 60.307 47.826 0.00 0.00 36.74 3.58
6642 6696 4.802583 GCCATACATATCGTCCCATGTCAA 60.803 45.833 0.00 0.00 36.74 3.18
6643 6697 4.931601 CCATACATATCGTCCCATGTCAAG 59.068 45.833 0.00 0.00 36.74 3.02
6644 6698 2.838736 ACATATCGTCCCATGTCAAGC 58.161 47.619 0.00 0.00 29.34 4.01
6645 6699 1.794701 CATATCGTCCCATGTCAAGCG 59.205 52.381 0.00 0.00 0.00 4.68
6646 6700 1.107945 TATCGTCCCATGTCAAGCGA 58.892 50.000 0.00 0.00 0.00 4.93
6647 6701 0.179100 ATCGTCCCATGTCAAGCGAG 60.179 55.000 0.00 0.00 0.00 5.03
6648 6702 1.811266 CGTCCCATGTCAAGCGAGG 60.811 63.158 0.00 0.00 0.00 4.63
6649 6703 1.596934 GTCCCATGTCAAGCGAGGA 59.403 57.895 0.00 0.00 0.00 3.71
6650 6704 0.741221 GTCCCATGTCAAGCGAGGAC 60.741 60.000 0.00 0.00 37.25 3.85
6651 6705 1.811266 CCCATGTCAAGCGAGGACG 60.811 63.158 0.00 0.00 38.10 4.79
6734 6899 1.332997 CCAAATGAGATGCTCCGCTTC 59.667 52.381 0.00 0.00 33.70 3.86
6770 6935 0.837691 TCATGCAGTGACCTCCCAGT 60.838 55.000 0.00 0.00 0.00 4.00
6817 6983 3.490590 CGACCCTCAGACATTCAGATGAG 60.491 52.174 0.00 0.00 39.10 2.90
6818 6984 3.703556 GACCCTCAGACATTCAGATGAGA 59.296 47.826 2.72 0.00 41.35 3.27
6856 7022 2.275318 CTCATCTCTTCGCCCAAAGAC 58.725 52.381 0.00 0.00 32.03 3.01
6867 7033 2.032550 CGCCCAAAGACATAGCTTCATG 59.967 50.000 0.00 0.00 0.00 3.07
6923 7089 0.179121 TCCGTTATACGCCACTGCTG 60.179 55.000 0.00 0.00 40.91 4.41
6924 7090 0.179121 CCGTTATACGCCACTGCTGA 60.179 55.000 0.00 0.00 40.91 4.26
6925 7091 1.538204 CCGTTATACGCCACTGCTGAT 60.538 52.381 0.00 0.00 40.91 2.90
6926 7092 1.522676 CGTTATACGCCACTGCTGATG 59.477 52.381 0.00 0.00 33.65 3.07
6927 7093 1.261619 GTTATACGCCACTGCTGATGC 59.738 52.381 0.00 0.00 40.20 3.91
6928 7094 0.249868 TATACGCCACTGCTGATGCC 60.250 55.000 0.00 0.00 38.71 4.40
6929 7095 2.947938 ATACGCCACTGCTGATGCCC 62.948 60.000 0.00 0.00 38.71 5.36
6931 7097 4.437587 GCCACTGCTGATGCCCCT 62.438 66.667 0.00 0.00 38.71 4.79
6956 7122 0.533755 CCTTCCATCCCGTGCTCATC 60.534 60.000 0.00 0.00 0.00 2.92
7028 7194 4.885907 ACCATTGACATTCAGCTTCCTATG 59.114 41.667 0.00 0.00 0.00 2.23
7052 7218 4.101448 GGGGAGCCATCACTGCGT 62.101 66.667 0.00 0.00 0.00 5.24
7083 7249 1.694856 GGCCTTGGTCCCCACATAA 59.305 57.895 0.00 0.00 30.78 1.90
7113 7279 6.931838 TGGTTAGAGATTTCGTCAATGTACT 58.068 36.000 0.00 0.00 0.00 2.73
7114 7280 8.058667 TGGTTAGAGATTTCGTCAATGTACTA 57.941 34.615 0.00 0.00 0.00 1.82
7115 7281 7.972277 TGGTTAGAGATTTCGTCAATGTACTAC 59.028 37.037 0.00 0.00 0.00 2.73
7141 7307 5.468746 TGTTATGAGCAAGTGAGTTTGGTAC 59.531 40.000 0.00 0.00 38.76 3.34
7156 7322 3.827008 TGGTACTCATGCTCTTGGATC 57.173 47.619 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.930251 TCCTCTCTGTTCCCAGTCTG 58.070 55.000 0.00 0.00 39.82 3.51
55 56 2.635427 GTTTCCTCTCTGTTCCCAGTCT 59.365 50.000 0.00 0.00 39.82 3.24
58 59 3.341823 CATGTTTCCTCTCTGTTCCCAG 58.658 50.000 0.00 0.00 40.25 4.45
76 77 6.817765 ATTACCACTACAACAGAAACCATG 57.182 37.500 0.00 0.00 0.00 3.66
180 182 7.275183 TGAAGATCATGTTATCGGTTTCAGAT 58.725 34.615 0.00 0.00 0.00 2.90
213 215 6.381801 ACAAAGATCATCTTAAGCAAAACGG 58.618 36.000 0.00 0.00 35.27 4.44
214 216 6.524586 GGACAAAGATCATCTTAAGCAAAACG 59.475 38.462 0.00 0.00 35.27 3.60
249 251 6.508920 AGATCCCCTGCCCTAATATCAAAATA 59.491 38.462 0.00 0.00 0.00 1.40
262 264 5.780958 ATACTAATTTAGATCCCCTGCCC 57.219 43.478 10.39 0.00 0.00 5.36
287 289 7.222611 CCCTGCCTTAATATCAAAATCAAAACG 59.777 37.037 0.00 0.00 0.00 3.60
291 293 5.602145 CCCCCTGCCTTAATATCAAAATCAA 59.398 40.000 0.00 0.00 0.00 2.57
348 356 8.112183 AGAATAATATTTAGATCCCCTGCCTTG 58.888 37.037 0.00 0.00 0.00 3.61
416 424 0.381801 AACAAGAAGCGCACAACAGG 59.618 50.000 11.47 0.00 0.00 4.00
465 473 1.077265 CAGGGGCCCAAGTGACATT 59.923 57.895 27.72 0.00 0.00 2.71
504 512 2.440253 ACCCAGTTGTACAGGCTTAACA 59.560 45.455 0.00 0.00 0.00 2.41
868 879 1.240641 TGCACGGCCATGTAACTTGG 61.241 55.000 2.24 0.00 37.31 3.61
874 885 3.255888 TGTTTAATTTGCACGGCCATGTA 59.744 39.130 2.24 0.00 0.00 2.29
1021 1035 1.972872 CTTTCATAGGCTTCCCGCAT 58.027 50.000 0.00 0.00 41.67 4.73
1022 1036 0.748005 GCTTTCATAGGCTTCCCGCA 60.748 55.000 0.00 0.00 41.67 5.69
1034 1048 8.842358 ATGTTCATTCTTTTGATTGCTTTCAT 57.158 26.923 0.00 0.00 31.81 2.57
1349 1365 8.020819 GCGCTATATTATGATGGCAAAGTTTAA 58.979 33.333 0.00 0.00 33.15 1.52
1380 1396 4.605640 TTGGAAAGCAAAGGATTCAAGG 57.394 40.909 0.00 0.00 0.00 3.61
1576 1593 3.415212 CTGAAGGATCCTGAACTTTGCA 58.585 45.455 17.02 0.00 0.00 4.08
1626 1643 0.259938 GAATGGGCCTGGTTGAGGAT 59.740 55.000 4.53 0.00 46.33 3.24
1633 1650 0.998928 TGTATGTGAATGGGCCTGGT 59.001 50.000 4.53 0.00 0.00 4.00
2023 2040 2.879026 CTCATCACAGCATTGGATGGAG 59.121 50.000 0.00 0.00 39.07 3.86
2069 2086 2.091541 TGCTGCCTTGTATTGCTTACC 58.908 47.619 0.00 0.00 0.00 2.85
2173 2190 6.032094 GTCATATTGTTTCACCAGCTCATTG 58.968 40.000 0.00 0.00 0.00 2.82
2227 2244 7.547370 CAGGAAAGTCACCTCTCTTTATACAAG 59.453 40.741 0.00 0.00 35.35 3.16
2275 2292 9.777008 TCCAAATAACCCTAAACAAATATCCTT 57.223 29.630 0.00 0.00 0.00 3.36
2586 2603 4.742659 ACACACACACACAAAACAGAAAAC 59.257 37.500 0.00 0.00 0.00 2.43
3272 3289 2.271944 AGGTGTGCTTACCCAAAGAC 57.728 50.000 6.37 0.00 41.83 3.01
3302 3319 3.702330 TCTGTAGCGTAATGTTGGATCG 58.298 45.455 0.00 0.00 0.00 3.69
3829 3849 6.350780 CCTCCTTTCGGTAACTTGTATACTGT 60.351 42.308 4.17 0.55 32.58 3.55
4408 4436 4.262249 GGGAGAGCATGGTCATACTAGAAC 60.262 50.000 25.71 5.66 0.00 3.01
4425 4453 8.452534 CGTAAGCTTACACTATATTAGGGAGAG 58.547 40.741 30.63 9.05 33.28 3.20
4456 4484 7.253983 CCGCATATACTACATCGCGATAAATTT 60.254 37.037 23.22 7.90 45.17 1.82
4550 4580 7.592885 AGCATGAGCCACTAAATTGATTAAT 57.407 32.000 0.00 0.00 43.56 1.40
4551 4581 7.408756 AAGCATGAGCCACTAAATTGATTAA 57.591 32.000 0.00 0.00 43.56 1.40
4552 4582 7.122501 TGAAAGCATGAGCCACTAAATTGATTA 59.877 33.333 0.00 0.00 43.56 1.75
4553 4583 5.927281 AAGCATGAGCCACTAAATTGATT 57.073 34.783 0.00 0.00 43.56 2.57
4556 4586 4.860907 GTGAAAGCATGAGCCACTAAATTG 59.139 41.667 0.00 0.00 43.56 2.32
4602 4632 1.620323 CCCAGATGATCGCCTATGACA 59.380 52.381 0.00 0.00 0.00 3.58
4671 4707 8.526147 CAGGGAAACTCAAAATATCACTGAAAT 58.474 33.333 0.00 0.00 42.74 2.17
4676 4712 5.324409 TGCAGGGAAACTCAAAATATCACT 58.676 37.500 0.00 0.00 0.00 3.41
4765 4801 3.737559 TTTGGATGATAGCAACCTGGT 57.262 42.857 8.85 0.00 37.80 4.00
4832 4868 5.049818 GTCCAATGCTTTAGGATCATCTTCG 60.050 44.000 0.00 0.00 33.33 3.79
4886 4922 7.858498 ACATAGTACCCAGCTTTAGTATGTTT 58.142 34.615 15.51 2.53 39.94 2.83
4930 4966 6.245408 AGGAAAACAGGCATATGTTAGACAA 58.755 36.000 4.29 0.00 42.49 3.18
4937 4973 6.245408 TCTTACAAGGAAAACAGGCATATGT 58.755 36.000 4.29 0.00 33.96 2.29
4972 5008 8.715191 AAATGTTAGTTCTTTTCATGCACAAA 57.285 26.923 0.00 0.00 0.00 2.83
5132 5168 3.257393 CTTTGACAATCCAGAGAGACCG 58.743 50.000 0.00 0.00 0.00 4.79
5257 5293 8.836413 TCCTAATATTTTCTGGCAGTATTTTCG 58.164 33.333 15.27 5.05 0.00 3.46
5334 5370 2.777832 AACAGACCTGATTCTGGCTC 57.222 50.000 9.34 6.74 46.38 4.70
5470 5507 6.956497 AGCTCTGAGGATTCTAAAACTTGAT 58.044 36.000 6.83 0.00 0.00 2.57
5483 5520 4.534103 ACAAAGTAGGAAAGCTCTGAGGAT 59.466 41.667 6.83 0.00 0.00 3.24
5490 5527 6.131544 TGACAAAACAAAGTAGGAAAGCTC 57.868 37.500 0.00 0.00 0.00 4.09
5571 5608 2.376808 ATGCGGTTGACAAGAGAGAG 57.623 50.000 0.00 0.00 0.00 3.20
5582 5619 3.945285 AGTTATTCCCACTAATGCGGTTG 59.055 43.478 0.00 0.00 0.00 3.77
5586 5623 6.861065 AATGTAGTTATTCCCACTAATGCG 57.139 37.500 0.00 0.00 0.00 4.73
5658 5695 9.787435 TGTATTCGGTGCTTTTCCTATTATTAT 57.213 29.630 0.00 0.00 0.00 1.28
5733 5772 4.583871 AGCCTTCAGATTCCACTAACTTG 58.416 43.478 0.00 0.00 0.00 3.16
5769 5808 8.830915 TTTCCAGGAAATGTGGCTTATATAAA 57.169 30.769 10.90 0.00 34.77 1.40
5771 5810 8.830915 TTTTTCCAGGAAATGTGGCTTATATA 57.169 30.769 15.75 0.00 34.77 0.86
5863 5903 8.932791 ACTTTACATCCTTGATAAACAACGTAG 58.067 33.333 0.00 0.00 34.56 3.51
5965 6008 3.693807 CCCCCTGACATGATGGAATATG 58.306 50.000 0.00 0.00 0.00 1.78
6019 6062 6.319048 ACAATATGAGACTTCCATTCCACT 57.681 37.500 0.00 0.00 0.00 4.00
6053 6096 7.733402 AAAAATCAGTCCATTGATGTTTTGG 57.267 32.000 0.00 0.00 40.45 3.28
6099 6146 6.773976 AATTGTACCACATAATGTCCAAGG 57.226 37.500 0.00 0.00 0.00 3.61
6235 6282 1.211190 GGTGCTTGCTTGTAGCTGC 59.789 57.895 0.00 0.00 42.97 5.25
6327 6374 2.359107 CACACGCCAGCCACTGAT 60.359 61.111 0.00 0.00 32.44 2.90
6390 6439 3.465403 CAGAGGGGAGAGTGCCGG 61.465 72.222 0.00 0.00 0.00 6.13
6458 6512 6.998673 GGTTTAGCTATTTCCATACTCACCAT 59.001 38.462 0.00 0.00 0.00 3.55
6510 6564 2.842496 ACTAGCCCAGTTTAACCTACCC 59.158 50.000 0.00 0.00 31.59 3.69
6511 6565 3.516700 TCACTAGCCCAGTTTAACCTACC 59.483 47.826 0.00 0.00 34.26 3.18
6512 6566 4.813750 TCACTAGCCCAGTTTAACCTAC 57.186 45.455 0.00 0.00 34.26 3.18
6513 6567 4.781087 ACATCACTAGCCCAGTTTAACCTA 59.219 41.667 0.00 0.00 34.26 3.08
6514 6568 3.587506 ACATCACTAGCCCAGTTTAACCT 59.412 43.478 0.00 0.00 34.26 3.50
6515 6569 3.951663 ACATCACTAGCCCAGTTTAACC 58.048 45.455 0.00 0.00 34.26 2.85
6516 6570 5.959618 AAACATCACTAGCCCAGTTTAAC 57.040 39.130 0.00 0.00 34.26 2.01
6517 6571 6.969993 AAAAACATCACTAGCCCAGTTTAA 57.030 33.333 0.00 0.00 34.26 1.52
6518 6572 8.107095 AGATAAAAACATCACTAGCCCAGTTTA 58.893 33.333 0.00 0.00 34.26 2.01
6519 6573 6.948309 AGATAAAAACATCACTAGCCCAGTTT 59.052 34.615 0.00 0.00 34.26 2.66
6520 6574 6.375455 CAGATAAAAACATCACTAGCCCAGTT 59.625 38.462 0.00 0.00 34.26 3.16
6521 6575 5.882557 CAGATAAAAACATCACTAGCCCAGT 59.117 40.000 0.00 0.00 38.32 4.00
6522 6576 6.037610 GTCAGATAAAAACATCACTAGCCCAG 59.962 42.308 0.00 0.00 0.00 4.45
6523 6577 5.880332 GTCAGATAAAAACATCACTAGCCCA 59.120 40.000 0.00 0.00 0.00 5.36
6524 6578 5.006746 CGTCAGATAAAAACATCACTAGCCC 59.993 44.000 0.00 0.00 0.00 5.19
6525 6579 5.810587 TCGTCAGATAAAAACATCACTAGCC 59.189 40.000 0.00 0.00 0.00 3.93
6526 6580 6.887376 TCGTCAGATAAAAACATCACTAGC 57.113 37.500 0.00 0.00 0.00 3.42
6527 6581 8.162880 GTGTTCGTCAGATAAAAACATCACTAG 58.837 37.037 0.00 0.00 32.95 2.57
6528 6582 7.117236 GGTGTTCGTCAGATAAAAACATCACTA 59.883 37.037 0.00 0.00 32.52 2.74
6529 6583 6.073222 GGTGTTCGTCAGATAAAAACATCACT 60.073 38.462 0.00 0.00 32.52 3.41
6530 6584 6.077838 GGTGTTCGTCAGATAAAAACATCAC 58.922 40.000 0.00 0.00 32.52 3.06
6531 6585 5.107259 CGGTGTTCGTCAGATAAAAACATCA 60.107 40.000 0.00 0.00 31.89 3.07
6532 6586 5.313623 CGGTGTTCGTCAGATAAAAACATC 58.686 41.667 0.00 0.00 32.95 3.06
6533 6587 4.378046 GCGGTGTTCGTCAGATAAAAACAT 60.378 41.667 0.00 0.00 41.72 2.71
6534 6588 3.059461 GCGGTGTTCGTCAGATAAAAACA 60.059 43.478 0.00 0.00 41.72 2.83
6535 6589 3.059461 TGCGGTGTTCGTCAGATAAAAAC 60.059 43.478 0.00 0.00 41.72 2.43
6536 6590 3.132160 TGCGGTGTTCGTCAGATAAAAA 58.868 40.909 0.00 0.00 41.72 1.94
6537 6591 2.734606 CTGCGGTGTTCGTCAGATAAAA 59.265 45.455 0.00 0.00 41.80 1.52
6538 6592 2.288579 ACTGCGGTGTTCGTCAGATAAA 60.289 45.455 0.00 0.00 41.80 1.40
6539 6593 1.271379 ACTGCGGTGTTCGTCAGATAA 59.729 47.619 0.00 0.00 41.80 1.75
6540 6594 0.885879 ACTGCGGTGTTCGTCAGATA 59.114 50.000 0.00 0.00 41.80 1.98
6541 6595 0.033504 AACTGCGGTGTTCGTCAGAT 59.966 50.000 0.00 3.23 41.80 2.90
6542 6596 0.179094 AAACTGCGGTGTTCGTCAGA 60.179 50.000 0.00 0.00 41.80 3.27
6543 6597 0.655733 AAAACTGCGGTGTTCGTCAG 59.344 50.000 0.00 0.00 43.44 3.51
6544 6598 1.088306 AAAAACTGCGGTGTTCGTCA 58.912 45.000 0.36 0.00 41.72 4.35
6545 6599 3.531262 ATAAAAACTGCGGTGTTCGTC 57.469 42.857 0.36 0.00 41.72 4.20
6546 6600 3.623863 CAATAAAAACTGCGGTGTTCGT 58.376 40.909 0.36 0.00 41.72 3.85
6547 6601 2.403698 GCAATAAAAACTGCGGTGTTCG 59.596 45.455 0.36 0.00 42.76 3.95
6548 6602 3.376540 TGCAATAAAAACTGCGGTGTTC 58.623 40.909 0.36 0.00 41.63 3.18
6549 6603 3.444703 TGCAATAAAAACTGCGGTGTT 57.555 38.095 0.00 0.00 41.63 3.32
6550 6604 3.005261 TGATGCAATAAAAACTGCGGTGT 59.995 39.130 0.00 0.00 41.63 4.16
6551 6605 3.573598 TGATGCAATAAAAACTGCGGTG 58.426 40.909 0.00 0.00 41.63 4.94
6552 6606 3.932545 TGATGCAATAAAAACTGCGGT 57.067 38.095 0.00 0.00 41.63 5.68
6553 6607 5.581605 AGTATGATGCAATAAAAACTGCGG 58.418 37.500 0.00 0.00 41.63 5.69
6554 6608 6.632834 GGTAGTATGATGCAATAAAAACTGCG 59.367 38.462 0.00 0.00 41.63 5.18
6555 6609 7.479980 TGGTAGTATGATGCAATAAAAACTGC 58.520 34.615 0.00 0.00 39.09 4.40
6556 6610 9.507280 CTTGGTAGTATGATGCAATAAAAACTG 57.493 33.333 0.00 0.00 0.00 3.16
6557 6611 9.243105 ACTTGGTAGTATGATGCAATAAAAACT 57.757 29.630 0.00 0.00 31.21 2.66
6558 6612 9.503427 GACTTGGTAGTATGATGCAATAAAAAC 57.497 33.333 0.00 0.00 33.84 2.43
6559 6613 9.461312 AGACTTGGTAGTATGATGCAATAAAAA 57.539 29.630 0.00 0.00 33.84 1.94
6561 6615 9.542462 GTAGACTTGGTAGTATGATGCAATAAA 57.458 33.333 0.00 0.00 33.84 1.40
6562 6616 8.700973 TGTAGACTTGGTAGTATGATGCAATAA 58.299 33.333 0.00 0.00 33.84 1.40
6563 6617 8.245195 TGTAGACTTGGTAGTATGATGCAATA 57.755 34.615 0.00 0.00 33.84 1.90
6564 6618 7.124573 TGTAGACTTGGTAGTATGATGCAAT 57.875 36.000 0.00 0.00 33.84 3.56
6565 6619 6.406961 CCTGTAGACTTGGTAGTATGATGCAA 60.407 42.308 0.00 0.00 33.84 4.08
6566 6620 5.069119 CCTGTAGACTTGGTAGTATGATGCA 59.931 44.000 0.00 0.00 33.84 3.96
6567 6621 5.509840 CCCTGTAGACTTGGTAGTATGATGC 60.510 48.000 0.00 0.00 33.84 3.91
6568 6622 5.833667 TCCCTGTAGACTTGGTAGTATGATG 59.166 44.000 0.00 0.00 33.84 3.07
6569 6623 6.027025 TCCCTGTAGACTTGGTAGTATGAT 57.973 41.667 0.00 0.00 33.84 2.45
6570 6624 5.461516 TCCCTGTAGACTTGGTAGTATGA 57.538 43.478 0.00 0.00 33.84 2.15
6571 6625 6.776116 TGTATCCCTGTAGACTTGGTAGTATG 59.224 42.308 0.00 0.00 33.84 2.39
6572 6626 6.919158 TGTATCCCTGTAGACTTGGTAGTAT 58.081 40.000 0.00 0.00 33.84 2.12
6573 6627 6.331577 TGTATCCCTGTAGACTTGGTAGTA 57.668 41.667 0.00 0.00 33.84 1.82
6574 6628 5.202746 TGTATCCCTGTAGACTTGGTAGT 57.797 43.478 0.00 0.00 37.31 2.73
6575 6629 6.323996 TCAATGTATCCCTGTAGACTTGGTAG 59.676 42.308 0.00 0.00 0.00 3.18
6576 6630 6.199376 TCAATGTATCCCTGTAGACTTGGTA 58.801 40.000 0.00 0.00 0.00 3.25
6577 6631 5.030147 TCAATGTATCCCTGTAGACTTGGT 58.970 41.667 0.00 0.00 0.00 3.67
6578 6632 5.614324 TCAATGTATCCCTGTAGACTTGG 57.386 43.478 0.00 0.00 0.00 3.61
6579 6633 8.511604 AAAATCAATGTATCCCTGTAGACTTG 57.488 34.615 0.00 0.00 0.00 3.16
6580 6634 8.328758 TGAAAATCAATGTATCCCTGTAGACTT 58.671 33.333 0.00 0.00 0.00 3.01
6581 6635 7.861629 TGAAAATCAATGTATCCCTGTAGACT 58.138 34.615 0.00 0.00 0.00 3.24
6582 6636 7.227512 CCTGAAAATCAATGTATCCCTGTAGAC 59.772 40.741 0.00 0.00 0.00 2.59
6583 6637 7.282585 CCTGAAAATCAATGTATCCCTGTAGA 58.717 38.462 0.00 0.00 0.00 2.59
6584 6638 6.488006 CCCTGAAAATCAATGTATCCCTGTAG 59.512 42.308 0.00 0.00 0.00 2.74
6585 6639 6.364701 CCCTGAAAATCAATGTATCCCTGTA 58.635 40.000 0.00 0.00 0.00 2.74
6586 6640 5.203528 CCCTGAAAATCAATGTATCCCTGT 58.796 41.667 0.00 0.00 0.00 4.00
6587 6641 4.586001 CCCCTGAAAATCAATGTATCCCTG 59.414 45.833 0.00 0.00 0.00 4.45
6588 6642 4.387891 CCCCCTGAAAATCAATGTATCCCT 60.388 45.833 0.00 0.00 0.00 4.20
6589 6643 3.897505 CCCCCTGAAAATCAATGTATCCC 59.102 47.826 0.00 0.00 0.00 3.85
6590 6644 4.803452 TCCCCCTGAAAATCAATGTATCC 58.197 43.478 0.00 0.00 0.00 2.59
6591 6645 6.790232 TTTCCCCCTGAAAATCAATGTATC 57.210 37.500 0.00 0.00 39.98 2.24
6592 6646 7.754091 AATTTCCCCCTGAAAATCAATGTAT 57.246 32.000 0.00 0.00 45.67 2.29
6593 6647 7.566658 AAATTTCCCCCTGAAAATCAATGTA 57.433 32.000 0.00 0.00 45.67 2.29
6594 6648 6.452757 AAATTTCCCCCTGAAAATCAATGT 57.547 33.333 0.00 0.00 45.67 2.71
6595 6649 6.539826 GCTAAATTTCCCCCTGAAAATCAATG 59.460 38.462 0.00 0.00 45.67 2.82
6596 6650 6.352996 GGCTAAATTTCCCCCTGAAAATCAAT 60.353 38.462 0.00 0.00 45.67 2.57
6597 6651 5.045942 GGCTAAATTTCCCCCTGAAAATCAA 60.046 40.000 0.00 0.00 45.67 2.57
6598 6652 4.469586 GGCTAAATTTCCCCCTGAAAATCA 59.530 41.667 0.00 0.00 45.67 2.57
6599 6653 4.469586 TGGCTAAATTTCCCCCTGAAAATC 59.530 41.667 0.00 0.00 45.67 2.17
6600 6654 4.434195 TGGCTAAATTTCCCCCTGAAAAT 58.566 39.130 0.00 0.00 45.67 1.82
6601 6655 3.863086 TGGCTAAATTTCCCCCTGAAAA 58.137 40.909 0.00 0.00 45.67 2.29
6602 6656 3.551635 TGGCTAAATTTCCCCCTGAAA 57.448 42.857 0.00 0.00 46.54 2.69
6603 6657 3.774842 ATGGCTAAATTTCCCCCTGAA 57.225 42.857 0.00 0.00 0.00 3.02
6604 6658 3.529734 TGTATGGCTAAATTTCCCCCTGA 59.470 43.478 0.00 0.00 0.00 3.86
6605 6659 3.909732 TGTATGGCTAAATTTCCCCCTG 58.090 45.455 0.00 0.00 0.00 4.45
6606 6660 4.832560 ATGTATGGCTAAATTTCCCCCT 57.167 40.909 0.00 0.00 0.00 4.79
6607 6661 5.357032 CGATATGTATGGCTAAATTTCCCCC 59.643 44.000 0.00 0.00 0.00 5.40
6608 6662 5.944007 ACGATATGTATGGCTAAATTTCCCC 59.056 40.000 0.00 0.00 0.00 4.81
6609 6663 6.093633 GGACGATATGTATGGCTAAATTTCCC 59.906 42.308 0.00 0.00 0.00 3.97
6610 6664 6.093633 GGGACGATATGTATGGCTAAATTTCC 59.906 42.308 0.00 0.00 0.00 3.13
6611 6665 6.653320 TGGGACGATATGTATGGCTAAATTTC 59.347 38.462 0.00 0.00 0.00 2.17
6612 6666 6.539173 TGGGACGATATGTATGGCTAAATTT 58.461 36.000 0.00 0.00 0.00 1.82
6613 6667 6.121776 TGGGACGATATGTATGGCTAAATT 57.878 37.500 0.00 0.00 0.00 1.82
6614 6668 5.755409 TGGGACGATATGTATGGCTAAAT 57.245 39.130 0.00 0.00 0.00 1.40
6615 6669 5.012664 ACATGGGACGATATGTATGGCTAAA 59.987 40.000 0.00 0.00 35.86 1.85
6616 6670 4.530553 ACATGGGACGATATGTATGGCTAA 59.469 41.667 0.00 0.00 35.86 3.09
6617 6671 4.093743 ACATGGGACGATATGTATGGCTA 58.906 43.478 0.00 0.00 35.86 3.93
6618 6672 2.906389 ACATGGGACGATATGTATGGCT 59.094 45.455 0.00 0.00 35.86 4.75
6619 6673 3.262420 GACATGGGACGATATGTATGGC 58.738 50.000 0.00 0.00 37.63 4.40
6620 6674 4.535526 TGACATGGGACGATATGTATGG 57.464 45.455 0.00 0.00 37.63 2.74
6621 6675 4.389992 GCTTGACATGGGACGATATGTATG 59.610 45.833 0.00 0.00 37.63 2.39
6622 6676 4.569943 GCTTGACATGGGACGATATGTAT 58.430 43.478 0.00 0.00 37.63 2.29
6623 6677 3.552068 CGCTTGACATGGGACGATATGTA 60.552 47.826 0.00 0.00 37.63 2.29
6624 6678 2.803133 CGCTTGACATGGGACGATATGT 60.803 50.000 0.00 0.00 40.04 2.29
6625 6679 1.794701 CGCTTGACATGGGACGATATG 59.205 52.381 0.00 0.00 0.00 1.78
6626 6680 1.686587 TCGCTTGACATGGGACGATAT 59.313 47.619 0.00 0.00 0.00 1.63
6627 6681 1.067060 CTCGCTTGACATGGGACGATA 59.933 52.381 0.00 0.00 0.00 2.92
6628 6682 0.179100 CTCGCTTGACATGGGACGAT 60.179 55.000 0.00 0.00 0.00 3.73
6629 6683 1.215382 CTCGCTTGACATGGGACGA 59.785 57.895 0.00 0.00 0.00 4.20
6630 6684 1.811266 CCTCGCTTGACATGGGACG 60.811 63.158 0.00 0.00 0.00 4.79
6631 6685 0.741221 GTCCTCGCTTGACATGGGAC 60.741 60.000 0.00 0.00 36.83 4.46
6632 6686 1.596934 GTCCTCGCTTGACATGGGA 59.403 57.895 7.70 7.70 32.91 4.37
6633 6687 1.811266 CGTCCTCGCTTGACATGGG 60.811 63.158 0.00 0.00 32.91 4.00
6634 6688 3.786101 CGTCCTCGCTTGACATGG 58.214 61.111 0.00 0.00 32.91 3.66
6648 6702 7.371300 CTCGTAGATTAGCTAGGATGGCGTC 62.371 52.000 0.37 0.00 42.97 5.19
6649 6703 5.632725 CTCGTAGATTAGCTAGGATGGCGT 61.633 50.000 0.37 0.00 42.97 5.68
6650 6704 3.181505 CTCGTAGATTAGCTAGGATGGCG 60.182 52.174 0.37 0.00 42.97 5.69
6651 6705 3.428316 GCTCGTAGATTAGCTAGGATGGC 60.428 52.174 0.37 0.00 41.61 4.40
6652 6706 4.364415 GCTCGTAGATTAGCTAGGATGG 57.636 50.000 0.37 0.00 41.61 3.51
6660 6714 1.202533 TGGCCAAGCTCGTAGATTAGC 60.203 52.381 0.61 0.00 39.08 3.09
6661 6715 2.890808 TGGCCAAGCTCGTAGATTAG 57.109 50.000 0.61 0.00 33.89 1.73
6662 6716 3.118408 ACAATGGCCAAGCTCGTAGATTA 60.118 43.478 10.96 0.00 33.89 1.75
6663 6717 2.292267 CAATGGCCAAGCTCGTAGATT 58.708 47.619 10.96 0.00 33.89 2.40
6664 6718 1.210478 ACAATGGCCAAGCTCGTAGAT 59.790 47.619 10.96 0.00 33.89 1.98
6665 6719 0.613260 ACAATGGCCAAGCTCGTAGA 59.387 50.000 10.96 0.00 0.00 2.59
6770 6935 5.365605 TCTGGGAACTCAAGTCTACAAGAAA 59.634 40.000 0.00 0.00 0.00 2.52
6817 6983 3.071602 TGAGCCTTGGGAAGCTATACATC 59.928 47.826 0.00 0.00 40.11 3.06
6818 6984 3.048600 TGAGCCTTGGGAAGCTATACAT 58.951 45.455 0.00 0.00 40.11 2.29
6856 7022 4.554919 GCTCTTGCATGTCATGAAGCTATG 60.555 45.833 17.24 10.39 39.41 2.23
6867 7033 0.747283 CCTGGAGGCTCTTGCATGTC 60.747 60.000 15.23 0.00 41.91 3.06
6891 7057 5.345202 GCGTATAACGGAATCACTAATCCTG 59.655 44.000 1.25 0.00 42.82 3.86
6923 7089 1.186200 GGAAGGTTTCAAGGGGCATC 58.814 55.000 0.00 0.00 0.00 3.91
6924 7090 0.486879 TGGAAGGTTTCAAGGGGCAT 59.513 50.000 0.00 0.00 0.00 4.40
6925 7091 0.486879 ATGGAAGGTTTCAAGGGGCA 59.513 50.000 0.00 0.00 0.00 5.36
6926 7092 1.186200 GATGGAAGGTTTCAAGGGGC 58.814 55.000 0.00 0.00 0.00 5.80
6927 7093 1.619704 GGGATGGAAGGTTTCAAGGGG 60.620 57.143 0.00 0.00 0.00 4.79
6928 7094 1.852633 GGGATGGAAGGTTTCAAGGG 58.147 55.000 0.00 0.00 0.00 3.95
6929 7095 1.271926 ACGGGATGGAAGGTTTCAAGG 60.272 52.381 0.00 0.00 0.00 3.61
6930 7096 1.812571 CACGGGATGGAAGGTTTCAAG 59.187 52.381 0.00 0.00 0.00 3.02
6931 7097 1.904287 CACGGGATGGAAGGTTTCAA 58.096 50.000 0.00 0.00 0.00 2.69
6956 7122 2.896801 GCTGGTGTTGTCTGCCGTG 61.897 63.158 0.00 0.00 0.00 4.94
7083 7249 7.921786 TTGACGAAATCTCTAACCATGATTT 57.078 32.000 0.00 0.00 41.37 2.17
7113 7279 5.483685 AACTCACTTGCTCATAACAGGTA 57.516 39.130 0.00 0.00 0.00 3.08
7114 7280 4.357918 AACTCACTTGCTCATAACAGGT 57.642 40.909 0.00 0.00 0.00 4.00
7115 7281 4.083110 CCAAACTCACTTGCTCATAACAGG 60.083 45.833 0.00 0.00 0.00 4.00
7141 7307 0.883814 GGGCGATCCAAGAGCATGAG 60.884 60.000 0.00 0.00 35.00 2.90


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

AutoCloner maintained by Alex Coulton.