Multiple sequence alignment - TraesCS1B01G293900

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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 TraesCS1B01G293900 chr1B 100.000 7321 0 0 1 7321 511966364 511973684 0.000000e+00 13520
1 TraesCS1B01G293900 chr1B 91.824 636 43 6 6 636 679527665 679527034 0.000000e+00 878
2 TraesCS1B01G293900 chr1B 82.087 575 50 19 6783 7319 175429793 175429234 6.740000e-120 442
3 TraesCS1B01G293900 chr1D 92.681 5397 265 71 1980 7321 381969031 381974352 0.000000e+00 7659
4 TraesCS1B01G293900 chr1D 93.849 943 42 9 637 1565 381965521 381966461 0.000000e+00 1406
5 TraesCS1B01G293900 chr1D 81.669 611 57 20 6747 7319 114366058 114365465 2.410000e-124 457
6 TraesCS1B01G293900 chr1D 95.294 85 4 0 1882 1966 381968877 381968961 1.280000e-27 135
7 TraesCS1B01G293900 chr1A 92.341 4896 226 66 2507 7318 482244184 482249014 0.000000e+00 6826
8 TraesCS1B01G293900 chr1A 84.798 842 75 36 637 1458 482242059 482242867 0.000000e+00 797
9 TraesCS1B01G293900 chr1A 81.669 611 57 22 6747 7319 124897914 124897321 2.410000e-124 457
10 TraesCS1B01G293900 chr1A 90.526 190 16 1 2231 2418 482243952 482244141 4.390000e-62 250
11 TraesCS1B01G293900 chr6B 93.661 631 38 2 6 636 73507203 73507831 0.000000e+00 942
12 TraesCS1B01G293900 chr5B 93.661 631 38 2 6 636 421159851 421159223 0.000000e+00 942
13 TraesCS1B01G293900 chr5B 91.969 635 47 3 6 640 516086718 516086088 0.000000e+00 887
14 TraesCS1B01G293900 chr2B 92.868 631 44 1 6 636 32136571 32137200 0.000000e+00 915
15 TraesCS1B01G293900 chr7B 92.540 630 45 2 7 636 550506030 550505403 0.000000e+00 902
16 TraesCS1B01G293900 chr7B 92.114 634 44 5 6 637 357927131 357927760 0.000000e+00 889
17 TraesCS1B01G293900 chr3B 92.405 632 44 3 6 636 584535989 584535361 0.000000e+00 898
18 TraesCS1B01G293900 chr4B 91.785 633 47 5 6 636 503994320 503993691 0.000000e+00 876
19 TraesCS1B01G293900 chr5D 77.500 560 77 20 6800 7317 40929133 40928581 2.580000e-74 291


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 TraesCS1B01G293900 chr1B 511966364 511973684 7320 False 13520.000000 13520 100.000000 1 7321 1 chr1B.!!$F1 7320
1 TraesCS1B01G293900 chr1B 679527034 679527665 631 True 878.000000 878 91.824000 6 636 1 chr1B.!!$R2 630
2 TraesCS1B01G293900 chr1B 175429234 175429793 559 True 442.000000 442 82.087000 6783 7319 1 chr1B.!!$R1 536
3 TraesCS1B01G293900 chr1D 381965521 381974352 8831 False 3066.666667 7659 93.941333 637 7321 3 chr1D.!!$F1 6684
4 TraesCS1B01G293900 chr1D 114365465 114366058 593 True 457.000000 457 81.669000 6747 7319 1 chr1D.!!$R1 572
5 TraesCS1B01G293900 chr1A 482242059 482249014 6955 False 2624.333333 6826 89.221667 637 7318 3 chr1A.!!$F1 6681
6 TraesCS1B01G293900 chr1A 124897321 124897914 593 True 457.000000 457 81.669000 6747 7319 1 chr1A.!!$R1 572
7 TraesCS1B01G293900 chr6B 73507203 73507831 628 False 942.000000 942 93.661000 6 636 1 chr6B.!!$F1 630
8 TraesCS1B01G293900 chr5B 421159223 421159851 628 True 942.000000 942 93.661000 6 636 1 chr5B.!!$R1 630
9 TraesCS1B01G293900 chr5B 516086088 516086718 630 True 887.000000 887 91.969000 6 640 1 chr5B.!!$R2 634
10 TraesCS1B01G293900 chr2B 32136571 32137200 629 False 915.000000 915 92.868000 6 636 1 chr2B.!!$F1 630
11 TraesCS1B01G293900 chr7B 550505403 550506030 627 True 902.000000 902 92.540000 7 636 1 chr7B.!!$R1 629
12 TraesCS1B01G293900 chr7B 357927131 357927760 629 False 889.000000 889 92.114000 6 637 1 chr7B.!!$F1 631
13 TraesCS1B01G293900 chr3B 584535361 584535989 628 True 898.000000 898 92.405000 6 636 1 chr3B.!!$R1 630
14 TraesCS1B01G293900 chr4B 503993691 503994320 629 True 876.000000 876 91.785000 6 636 1 chr4B.!!$R1 630
15 TraesCS1B01G293900 chr5D 40928581 40929133 552 True 291.000000 291 77.500000 6800 7317 1 chr5D.!!$R1 517

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
234 236 0.447801 GGCGACGCAAACTGATCAAT 59.552 50.0 23.09 0.0 0.00 2.57 F
1492 1529 0.107165 GGCCATCAGGGTTACCAGAC 60.107 60.0 2.98 0.0 40.13 3.51 F
2306 5017 0.107456 AGGCTGCGTAGATGAATGGG 59.893 55.0 4.08 0.0 0.00 4.00 F
2573 5288 0.978146 ACTGATTGAGAGGACGGGGG 60.978 60.0 0.00 0.0 0.00 5.40 F
3576 6325 0.813184 CATCGGCAGCCATTGTCTTT 59.187 50.0 13.30 0.0 0.00 2.52 F
4219 6968 0.900421 CTCTGGTCAGACAGATGGCA 59.100 55.0 2.17 0.0 45.67 4.92 F
5246 7998 0.671472 TGATCAGTGCAACCTGCTCG 60.671 55.0 0.00 0.0 45.31 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1810 4350 0.309612 CCGAAACCCAACTTTGACCG 59.690 55.000 0.00 0.00 0.00 4.79 R
3113 5837 0.596577 CTTTCACAGCTGCAGTGCAT 59.403 50.000 20.10 0.79 38.13 3.96 R
3115 5839 0.664761 TTCTTTCACAGCTGCAGTGC 59.335 50.000 18.93 8.58 36.93 4.40 R
4393 7143 1.630369 ACACCCATGTCTGCATACACT 59.370 47.619 7.12 0.00 31.55 3.55 R
5092 7844 0.550914 ACCGTATGGGCCATCAATGT 59.449 50.000 25.07 13.31 40.62 2.71 R
5419 8171 1.072331 TGTCTTGAGCTGAAACCTCCC 59.928 52.381 0.00 0.00 0.00 4.30 R
6949 9779 1.457455 GAGGAGGAGCAGGAGGGAG 60.457 68.421 0.00 0.00 0.00 4.30 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
93 95 3.896133 GGCGTAGATCGACGGGCA 61.896 66.667 26.24 0.00 43.13 5.36
227 229 2.972505 CAGTGGGCGACGCAAACT 60.973 61.111 23.09 20.08 0.00 2.66
234 236 0.447801 GGCGACGCAAACTGATCAAT 59.552 50.000 23.09 0.00 0.00 2.57
263 265 4.440880 TCGGAAAACCAAAAAGTAGACGA 58.559 39.130 0.00 0.00 0.00 4.20
285 289 1.458064 GATCAAAGCGACCGACGAAAA 59.542 47.619 0.00 0.00 45.77 2.29
499 506 2.552093 TGTTAGAAGGGAGAGAGGGG 57.448 55.000 0.00 0.00 0.00 4.79
515 522 3.010250 AGAGGGGTTTGGTGGAATAGTTC 59.990 47.826 0.00 0.00 0.00 3.01
516 523 2.719705 AGGGGTTTGGTGGAATAGTTCA 59.280 45.455 0.00 0.00 0.00 3.18
518 525 4.542525 AGGGGTTTGGTGGAATAGTTCATA 59.457 41.667 0.00 0.00 0.00 2.15
684 703 7.031975 AGTGAACTCTCTTTTTGCAAGAAAAG 58.968 34.615 14.77 14.77 44.25 2.27
757 778 5.505173 TGTTGATTAGCTACTACGTACCC 57.495 43.478 0.00 0.00 0.00 3.69
796 817 1.536766 GCATATGGCTGCTCGCATAAA 59.463 47.619 4.56 0.00 41.67 1.40
1071 1096 1.204231 GACGAGTTTCTCCAGGTACCC 59.796 57.143 8.74 0.00 0.00 3.69
1120 1145 1.959226 CAGTTCGTGTCCAACCCCG 60.959 63.158 0.00 0.00 0.00 5.73
1466 1497 0.179086 GCTGGTGAGCTAGCTCCTTC 60.179 60.000 35.76 25.74 44.51 3.46
1481 1512 1.180029 CCTTCCACTTTGGCCATCAG 58.820 55.000 6.09 8.81 37.47 2.90
1482 1513 1.180029 CTTCCACTTTGGCCATCAGG 58.820 55.000 6.09 7.01 37.47 3.86
1484 1515 1.077265 CCACTTTGGCCATCAGGGT 59.923 57.895 6.09 0.00 39.65 4.34
1487 1524 1.818674 CACTTTGGCCATCAGGGTTAC 59.181 52.381 6.09 0.00 39.65 2.50
1490 1527 0.331278 TTGGCCATCAGGGTTACCAG 59.669 55.000 6.09 0.00 40.13 4.00
1492 1529 0.107165 GGCCATCAGGGTTACCAGAC 60.107 60.000 2.98 0.00 40.13 3.51
1494 1531 1.407437 GCCATCAGGGTTACCAGACTG 60.407 57.143 2.98 1.57 40.13 3.51
1505 1542 6.442564 AGGGTTACCAGACTGTCAATACATAA 59.557 38.462 10.88 0.00 40.13 1.90
1558 1596 4.451900 AGAATCTGTTCTGTTTTGGTCGT 58.548 39.130 0.00 0.00 42.97 4.34
1565 1603 2.285083 TCTGTTTTGGTCGTGTGGAAG 58.715 47.619 0.00 0.00 0.00 3.46
1568 1606 2.011222 GTTTTGGTCGTGTGGAAGACA 58.989 47.619 0.00 0.00 39.01 3.41
1570 1608 2.404923 TTGGTCGTGTGGAAGACAAA 57.595 45.000 0.00 0.00 39.01 2.83
1571 1609 2.631160 TGGTCGTGTGGAAGACAAAT 57.369 45.000 0.00 0.00 39.01 2.32
1573 1611 4.280436 TGGTCGTGTGGAAGACAAATAT 57.720 40.909 0.00 0.00 39.01 1.28
1574 1612 4.250464 TGGTCGTGTGGAAGACAAATATC 58.750 43.478 0.00 0.00 39.01 1.63
1577 1615 4.929808 GTCGTGTGGAAGACAAATATCACT 59.070 41.667 0.00 0.00 35.91 3.41
1578 1616 6.097356 GTCGTGTGGAAGACAAATATCACTA 58.903 40.000 0.00 0.00 35.91 2.74
1579 1617 6.757010 GTCGTGTGGAAGACAAATATCACTAT 59.243 38.462 0.00 0.00 35.91 2.12
1582 1620 9.908152 CGTGTGGAAGACAAATATCACTATATA 57.092 33.333 0.00 0.00 35.91 0.86
1622 3103 2.921126 CGAAGCAACCAACTAGCAAAG 58.079 47.619 0.00 0.00 0.00 2.77
1655 3136 6.018994 CGACTCCTTCCGTTCCAATAAATAAG 60.019 42.308 0.00 0.00 0.00 1.73
1656 3137 6.954232 ACTCCTTCCGTTCCAATAAATAAGA 58.046 36.000 0.00 0.00 0.00 2.10
1683 4223 6.665055 GCACGCTCATTTCAAAATTAAACTCG 60.665 38.462 0.00 0.00 0.00 4.18
1705 4245 8.303156 ACTCGGATCATAAATTAGACAGATCAG 58.697 37.037 0.00 0.00 34.94 2.90
1708 4248 9.085250 CGGATCATAAATTAGACAGATCAGATG 57.915 37.037 0.00 0.00 34.94 2.90
1719 4259 4.251268 ACAGATCAGATGTGTGTCATGTG 58.749 43.478 12.34 0.00 45.48 3.21
1729 4269 7.695201 CAGATGTGTGTCATGTGTGATAAAATC 59.305 37.037 0.00 0.00 41.18 2.17
1733 4273 9.883142 TGTGTGTCATGTGTGATAAAATCTATA 57.117 29.630 0.00 0.00 36.60 1.31
1754 4294 8.577296 TCTATACTCTTGAATTCCTATTGGACG 58.423 37.037 2.27 0.00 43.06 4.79
1755 4295 5.422214 ACTCTTGAATTCCTATTGGACGT 57.578 39.130 2.27 0.00 43.06 4.34
1757 4297 6.338937 ACTCTTGAATTCCTATTGGACGTAC 58.661 40.000 2.27 0.00 43.06 3.67
1758 4298 5.345702 TCTTGAATTCCTATTGGACGTACG 58.654 41.667 15.01 15.01 43.06 3.67
1765 4305 4.880759 TCCTATTGGACGTACGTTTTCAA 58.119 39.130 23.70 23.98 37.46 2.69
1766 4306 5.481105 TCCTATTGGACGTACGTTTTCAAT 58.519 37.500 29.67 29.67 37.46 2.57
1769 4309 2.836262 TGGACGTACGTTTTCAATGGT 58.164 42.857 23.70 0.00 0.00 3.55
1787 4327 9.613428 TTCAATGGTATAATTTCTAGACCACAG 57.387 33.333 0.58 0.00 41.01 3.66
1789 4329 9.613428 CAATGGTATAATTTCTAGACCACAGAA 57.387 33.333 0.58 0.00 41.01 3.02
1810 4350 7.819900 ACAGAAAAGTATATTGGTCTGACTCAC 59.180 37.037 7.85 0.00 36.75 3.51
1811 4351 7.009631 CAGAAAAGTATATTGGTCTGACTCACG 59.990 40.741 7.85 0.00 35.57 4.35
1812 4352 4.920640 AGTATATTGGTCTGACTCACGG 57.079 45.455 7.85 0.00 0.00 4.94
1813 4353 4.279145 AGTATATTGGTCTGACTCACGGT 58.721 43.478 7.85 0.00 0.00 4.83
1814 4354 3.802948 ATATTGGTCTGACTCACGGTC 57.197 47.619 7.85 0.00 44.70 4.79
1827 4367 2.018515 TCACGGTCAAAGTTGGGTTTC 58.981 47.619 0.00 0.00 0.00 2.78
1843 4383 7.501892 AGTTGGGTTTCGGTTAAGTTTTGTATA 59.498 33.333 0.00 0.00 0.00 1.47
1844 4384 7.999450 TGGGTTTCGGTTAAGTTTTGTATAT 57.001 32.000 0.00 0.00 0.00 0.86
1848 4388 8.124823 GGTTTCGGTTAAGTTTTGTATATAGCC 58.875 37.037 0.00 0.00 0.00 3.93
1858 4398 6.614087 AGTTTTGTATATAGCCCTAGTGGACA 59.386 38.462 1.75 0.00 35.39 4.02
1859 4399 7.292591 AGTTTTGTATATAGCCCTAGTGGACAT 59.707 37.037 1.75 0.00 35.39 3.06
1860 4400 6.852420 TTGTATATAGCCCTAGTGGACATC 57.148 41.667 1.75 0.00 35.39 3.06
1861 4401 6.153942 TGTATATAGCCCTAGTGGACATCT 57.846 41.667 1.75 0.00 35.39 2.90
1862 4402 6.562228 TGTATATAGCCCTAGTGGACATCTT 58.438 40.000 1.75 0.00 35.39 2.40
1863 4403 7.016914 TGTATATAGCCCTAGTGGACATCTTT 58.983 38.462 1.75 0.00 35.39 2.52
1864 4404 8.174757 TGTATATAGCCCTAGTGGACATCTTTA 58.825 37.037 1.75 0.00 35.39 1.85
1865 4405 5.810080 ATAGCCCTAGTGGACATCTTTAC 57.190 43.478 1.75 0.00 35.39 2.01
1866 4406 3.450904 AGCCCTAGTGGACATCTTTACA 58.549 45.455 1.75 0.00 35.39 2.41
1873 4413 7.365652 CCCTAGTGGACATCTTTACATAAGGTT 60.366 40.741 0.00 0.00 35.39 3.50
1909 4449 2.093310 CACGTGTGAGATGATTGCTGAC 59.907 50.000 7.58 0.00 0.00 3.51
1925 4465 3.265791 GCTGACGTGGATGAGAAAAGAT 58.734 45.455 0.00 0.00 0.00 2.40
1985 4585 7.337942 AGGAAGTTGGATAAATAGAAAGTGCAG 59.662 37.037 0.00 0.00 0.00 4.41
2034 4634 1.078143 GAGCACCATGTCCACCTCC 60.078 63.158 0.00 0.00 0.00 4.30
2047 4647 4.918201 CCTCCCCGCGCCAATCTC 62.918 72.222 0.00 0.00 0.00 2.75
2075 4675 0.322726 CAGCATGACCATGTCCACCA 60.323 55.000 11.17 0.00 39.69 4.17
2104 4704 1.224592 CCTTTGATCCTCCCACCCG 59.775 63.158 0.00 0.00 0.00 5.28
2105 4705 1.224592 CTTTGATCCTCCCACCCGG 59.775 63.158 0.00 0.00 0.00 5.73
2130 4730 1.372087 CTGCAAACGCTCTCCATCCC 61.372 60.000 0.00 0.00 0.00 3.85
2136 4736 0.259065 ACGCTCTCCATCCCTGAGTA 59.741 55.000 0.00 0.00 0.00 2.59
2196 4806 4.459089 GGCGAGGCCGAGCTCTTT 62.459 66.667 21.60 0.00 39.62 2.52
2221 4840 1.137513 GGTAGGCGATATCGTTGCAC 58.862 55.000 24.99 16.80 42.22 4.57
2223 4842 1.787155 GTAGGCGATATCGTTGCACAG 59.213 52.381 24.99 0.00 42.22 3.66
2229 4938 4.793308 CGATATCGTTGCACAGCATGCC 62.793 54.545 15.66 0.00 43.54 4.40
2258 4969 3.900966 AGCTGAATAGTCACAGATGCA 57.099 42.857 4.50 0.00 36.38 3.96
2267 4978 3.982475 AGTCACAGATGCATACGTATGG 58.018 45.455 31.14 18.98 34.32 2.74
2306 5017 0.107456 AGGCTGCGTAGATGAATGGG 59.893 55.000 4.08 0.00 0.00 4.00
2400 5111 2.488952 TGCTGTTATGCTTCAACGTGA 58.511 42.857 0.00 0.00 0.00 4.35
2457 5168 7.692908 GCTTTAAGCAAAGACAACATTGTAA 57.307 32.000 12.54 0.00 43.32 2.41
2459 5170 8.268738 GCTTTAAGCAAAGACAACATTGTAAAG 58.731 33.333 12.54 3.24 43.32 1.85
2460 5171 9.301153 CTTTAAGCAAAGACAACATTGTAAAGT 57.699 29.630 0.00 0.00 43.32 2.66
2462 5173 5.043248 AGCAAAGACAACATTGTAAAGTGC 58.957 37.500 0.00 5.81 42.43 4.40
2463 5174 5.043248 GCAAAGACAACATTGTAAAGTGCT 58.957 37.500 0.00 0.00 42.43 4.40
2479 5194 4.803329 AGTGCTGGGATAAGGATGAAAT 57.197 40.909 0.00 0.00 0.00 2.17
2546 5261 1.330655 TTCGAGTGGGAGATGGGCTC 61.331 60.000 0.00 0.00 43.17 4.70
2547 5262 2.060383 CGAGTGGGAGATGGGCTCA 61.060 63.158 0.00 0.00 45.81 4.26
2556 5271 1.969240 GAGATGGGCTCAGGAGGAACT 60.969 57.143 0.00 0.00 42.92 3.01
2573 5288 0.978146 ACTGATTGAGAGGACGGGGG 60.978 60.000 0.00 0.00 0.00 5.40
2601 5316 4.365899 ACCTCTTTGTCGGAAAAACAAC 57.634 40.909 0.00 0.00 36.41 3.32
2608 5323 4.238761 TGTCGGAAAAACAACAACAACA 57.761 36.364 0.00 0.00 0.00 3.33
2609 5324 4.230657 TGTCGGAAAAACAACAACAACAG 58.769 39.130 0.00 0.00 0.00 3.16
2610 5325 3.060230 GTCGGAAAAACAACAACAACAGC 59.940 43.478 0.00 0.00 0.00 4.40
2622 5337 6.648725 ACAACAACAACAGCAAACACTAAAAT 59.351 30.769 0.00 0.00 0.00 1.82
2631 5346 9.816354 AACAGCAAACACTAAAATTAGAAACAT 57.184 25.926 7.17 0.00 34.84 2.71
2683 5398 7.902920 AAAAATCATACTGAATACCATGCCT 57.097 32.000 0.00 0.00 0.00 4.75
2694 5409 5.074929 TGAATACCATGCCTAGGGATCAATT 59.925 40.000 13.74 12.50 0.00 2.32
2698 5413 3.571401 CCATGCCTAGGGATCAATTGTTC 59.429 47.826 13.74 6.65 0.00 3.18
2699 5414 4.209538 CATGCCTAGGGATCAATTGTTCA 58.790 43.478 13.74 0.00 0.00 3.18
2744 5460 6.079336 TCCATATGGCTCCATGATTTTGAAT 58.921 36.000 17.58 0.00 37.82 2.57
2929 5652 1.186200 ATGAGTCTGCTAGTTCGGCA 58.814 50.000 0.00 0.00 38.10 5.69
2965 5688 3.244976 GGTCAATCAAAACAGCAATCCG 58.755 45.455 0.00 0.00 0.00 4.18
3070 5793 3.362706 TCCAGTCTCCAGTATACACACC 58.637 50.000 5.50 0.00 0.00 4.16
3074 5797 3.769844 AGTCTCCAGTATACACACCAAGG 59.230 47.826 5.50 0.00 0.00 3.61
3192 5941 3.869832 CAGGTATGATGCAGACAGTCTTG 59.130 47.826 0.00 0.00 0.00 3.02
3295 6044 4.853007 ACAAGCTCTCATTAAGCCAAGAT 58.147 39.130 0.00 0.00 40.75 2.40
3301 6050 5.108187 TCTCATTAAGCCAAGATGAAGCT 57.892 39.130 0.00 0.00 38.88 3.74
3316 6065 6.882656 AGATGAAGCTACTGAATACACACAT 58.117 36.000 0.00 0.00 0.00 3.21
3331 6080 8.954950 AATACACACATTTGATCCTAGAAGAG 57.045 34.615 0.00 0.00 0.00 2.85
3576 6325 0.813184 CATCGGCAGCCATTGTCTTT 59.187 50.000 13.30 0.00 0.00 2.52
3881 6630 8.005192 TCTATTGCCAAATGTAATGTGCATTA 57.995 30.769 0.00 0.90 35.73 1.90
3913 6662 4.161565 TCGCTTGTATACTCCAATTGGTCT 59.838 41.667 23.76 12.36 36.34 3.85
4219 6968 0.900421 CTCTGGTCAGACAGATGGCA 59.100 55.000 2.17 0.00 45.67 4.92
4393 7143 7.180229 TCCCTGTTATCTCATACTGTCTCAAAA 59.820 37.037 0.00 0.00 0.00 2.44
4440 7190 4.964897 TGGTGATTCCTGTGATGATCTACT 59.035 41.667 0.00 0.00 37.07 2.57
4454 7204 5.344743 TGATCTACTTTGGAGAGCGAATT 57.655 39.130 0.00 0.00 31.85 2.17
4568 7320 1.710013 ATGCACGTCCTCTTGTAACG 58.290 50.000 0.00 0.00 41.93 3.18
4687 7439 5.105797 TGGAATGTATGTCTTTGTCCAATGC 60.106 40.000 0.00 0.00 0.00 3.56
4779 7531 4.948608 TCAGTTTCGTTACTGTTTTGCA 57.051 36.364 15.64 0.00 44.62 4.08
4810 7562 1.440353 CGCGTGCAAGTTTGTAGCC 60.440 57.895 0.00 0.00 0.00 3.93
5092 7844 2.835764 ACCTCGACCTGCCAAAAGTATA 59.164 45.455 0.00 0.00 0.00 1.47
5132 7884 1.669779 GCAGCATCACAAGATCACTCC 59.330 52.381 0.00 0.00 30.20 3.85
5171 7923 3.330701 TGCTAATAGGGCTTGGAATAGGG 59.669 47.826 0.00 0.00 0.00 3.53
5246 7998 0.671472 TGATCAGTGCAACCTGCTCG 60.671 55.000 0.00 0.00 45.31 5.03
5251 8003 1.601903 CAGTGCAACCTGCTCGTAAAA 59.398 47.619 0.00 0.00 45.31 1.52
5253 8005 2.884639 AGTGCAACCTGCTCGTAAAATT 59.115 40.909 0.00 0.00 45.31 1.82
5257 8009 5.688176 GTGCAACCTGCTCGTAAAATTTAAA 59.312 36.000 0.00 0.00 45.31 1.52
5419 8171 4.080919 TGAGTGGTTTAGGGACATCATGAG 60.081 45.833 0.09 0.00 0.00 2.90
5434 8186 1.280133 CATGAGGGAGGTTTCAGCTCA 59.720 52.381 5.39 0.00 44.10 4.26
5470 8222 7.065803 ACAGGTTACGATTTAATGACCATTCTG 59.934 37.037 0.00 0.00 32.50 3.02
5510 8262 2.767394 CCAGATGGGCATTTTCCATGAA 59.233 45.455 0.00 0.00 44.34 2.57
5514 8266 5.883673 CAGATGGGCATTTTCCATGAAAATT 59.116 36.000 11.10 0.00 46.07 1.82
5561 8313 0.951558 GTTGTGCTTGTAGGGTGTGG 59.048 55.000 0.00 0.00 0.00 4.17
5626 8378 0.898320 AGCGGTCAGTGCTGATAAGT 59.102 50.000 5.11 0.00 42.14 2.24
5674 8426 4.014406 GCCATGGCATTGATATCATCTCA 58.986 43.478 32.08 3.91 41.49 3.27
5714 8466 6.706270 TCTTTCTCCTAAACAGCTACACAAAG 59.294 38.462 0.00 0.00 0.00 2.77
5770 8522 0.392336 TGGTGCACTGCAATTTTCCC 59.608 50.000 17.98 2.13 41.47 3.97
5783 8535 4.381079 GCAATTTTCCCGTGCTAATTACCA 60.381 41.667 0.00 0.00 35.36 3.25
5784 8536 5.681179 GCAATTTTCCCGTGCTAATTACCAT 60.681 40.000 0.00 0.00 35.36 3.55
5788 8540 3.804036 TCCCGTGCTAATTACCATGAAG 58.196 45.455 0.00 0.00 0.00 3.02
5862 8616 2.828877 CAGGTCCGTACACACTTTTCA 58.171 47.619 0.00 0.00 0.00 2.69
6033 8789 4.163552 TGTCAGTCAAATCATCGTACGAC 58.836 43.478 22.14 5.69 0.00 4.34
6081 8837 2.171003 GATGTGTCAAAAGGGGGAAGG 58.829 52.381 0.00 0.00 0.00 3.46
6176 8936 8.782533 AATTTCAGTTTCAAGTTCACGTATTC 57.217 30.769 0.00 0.00 0.00 1.75
6292 9052 9.681692 CAAAATGAACATGAGAACATTCACTAA 57.318 29.630 0.00 0.00 34.15 2.24
6372 9140 8.328146 GTGACTTTCCTGTTTCTTTATTTTTGC 58.672 33.333 0.00 0.00 0.00 3.68
6373 9141 8.257306 TGACTTTCCTGTTTCTTTATTTTTGCT 58.743 29.630 0.00 0.00 0.00 3.91
6408 9183 8.936864 AGAACATGAGCTTGTGTTTACTAATAC 58.063 33.333 15.91 4.48 38.57 1.89
6410 9185 7.165485 ACATGAGCTTGTGTTTACTAATACCA 58.835 34.615 0.00 0.00 0.00 3.25
6428 9204 7.896383 AATACCAAAATGCAGGCTCTAATTA 57.104 32.000 0.00 0.00 0.00 1.40
6481 9257 7.338196 TCTTGTAAAATGACACTTTGGACAAGA 59.662 33.333 17.48 17.48 42.41 3.02
6587 9381 9.929722 GGAATATTTTTGTTTTTGAGACAAACC 57.070 29.630 2.24 0.00 44.16 3.27
6598 9392 6.877611 TTTGAGACAAACCTTGAGGAATAC 57.122 37.500 3.59 0.00 38.94 1.89
6600 9394 6.187727 TGAGACAAACCTTGAGGAATACTT 57.812 37.500 3.59 0.00 38.94 2.24
6601 9395 6.601332 TGAGACAAACCTTGAGGAATACTTT 58.399 36.000 3.59 0.00 38.94 2.66
6657 9451 5.744666 TTTTAGGACAACTTTGAGGAACG 57.255 39.130 0.00 0.00 0.00 3.95
6659 9453 1.766496 AGGACAACTTTGAGGAACGGA 59.234 47.619 0.00 0.00 0.00 4.69
6712 9513 2.210116 AGCATACTCCGGTTAATTGCG 58.790 47.619 0.00 0.00 33.99 4.85
6735 9536 3.359523 GGCCCACGTTCCGAAACC 61.360 66.667 0.00 0.00 31.27 3.27
6736 9537 3.359523 GCCCACGTTCCGAAACCC 61.360 66.667 0.00 0.00 31.27 4.11
6737 9538 2.670592 CCCACGTTCCGAAACCCC 60.671 66.667 0.00 0.00 31.27 4.95
6738 9539 2.670592 CCACGTTCCGAAACCCCC 60.671 66.667 0.00 0.00 31.27 5.40
6739 9540 2.111460 CACGTTCCGAAACCCCCA 59.889 61.111 0.00 0.00 31.27 4.96
6740 9541 2.111669 ACGTTCCGAAACCCCCAC 59.888 61.111 0.00 0.00 31.27 4.61
6741 9542 3.045492 CGTTCCGAAACCCCCACG 61.045 66.667 0.00 0.00 31.27 4.94
6742 9543 3.359523 GTTCCGAAACCCCCACGC 61.360 66.667 0.00 0.00 0.00 5.34
6743 9544 3.875023 TTCCGAAACCCCCACGCA 61.875 61.111 0.00 0.00 0.00 5.24
6744 9545 3.417167 TTCCGAAACCCCCACGCAA 62.417 57.895 0.00 0.00 0.00 4.85
6767 9579 3.723348 GTCGCCGTTTCAGCCCAC 61.723 66.667 0.00 0.00 0.00 4.61
6773 9585 2.398554 CGTTTCAGCCCACCATCCG 61.399 63.158 0.00 0.00 0.00 4.18
6780 9592 2.448582 GCCCACCATCCGTATCCCA 61.449 63.158 0.00 0.00 0.00 4.37
6781 9593 1.990160 GCCCACCATCCGTATCCCAA 61.990 60.000 0.00 0.00 0.00 4.12
6795 9608 4.504461 CGTATCCCAAAAATCAGTCTCTCG 59.496 45.833 0.00 0.00 0.00 4.04
6808 9626 1.152839 CTCTCGGTCTCTCCTCCCC 60.153 68.421 0.00 0.00 0.00 4.81
6949 9779 4.452733 CGTTGCGACCCTCCCCTC 62.453 72.222 0.00 0.00 0.00 4.30
6954 9784 3.756783 CGACCCTCCCCTCTCCCT 61.757 72.222 0.00 0.00 0.00 4.20
6974 9816 1.826054 CTGCTCCTCCTCCGACGAT 60.826 63.158 0.00 0.00 0.00 3.73
6979 9821 0.835276 TCCTCCTCCGACGATGACTA 59.165 55.000 0.00 0.00 0.00 2.59
6981 9823 2.636403 TCCTCCTCCGACGATGACTATA 59.364 50.000 0.00 0.00 0.00 1.31
7055 9903 3.667282 CAGCACCAGCACCAGCAC 61.667 66.667 0.00 0.00 45.49 4.40
7058 9906 2.981909 CACCAGCACCAGCACCAG 60.982 66.667 0.00 0.00 45.49 4.00
7059 9907 4.962836 ACCAGCACCAGCACCAGC 62.963 66.667 0.00 0.00 45.49 4.85
7060 9908 4.960866 CCAGCACCAGCACCAGCA 62.961 66.667 0.00 0.00 45.49 4.41
7061 9909 3.362797 CAGCACCAGCACCAGCAG 61.363 66.667 0.00 0.00 45.49 4.24
7298 10170 2.047274 CCCAATGCGTCGTCCTGT 60.047 61.111 0.00 0.00 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 180 2.203167 TCGCGCCTCTACTCCGAT 60.203 61.111 0.00 0.00 0.00 4.18
227 229 7.695480 TGGTTTTCCGATCTTTTATTGATCA 57.305 32.000 0.00 0.00 44.36 2.92
234 236 9.122779 TCTACTTTTTGGTTTTCCGATCTTTTA 57.877 29.630 0.00 0.00 44.36 1.52
295 299 1.200519 TTCGATCCTTTGATCCGGGT 58.799 50.000 0.00 0.00 43.82 5.28
499 506 8.850156 AGCAATATATGAACTATTCCACCAAAC 58.150 33.333 0.00 0.00 0.00 2.93
515 522 3.434641 CCACGAGGCTCAAGCAATATATG 59.565 47.826 15.95 0.00 44.36 1.78
516 523 3.557898 CCCACGAGGCTCAAGCAATATAT 60.558 47.826 15.95 0.00 44.36 0.86
518 525 1.475751 CCCACGAGGCTCAAGCAATAT 60.476 52.381 15.95 0.00 44.36 1.28
562 576 5.626142 TGGCTTGTCTTGTACTCCAAATAA 58.374 37.500 0.00 0.00 31.20 1.40
684 703 4.141620 TGGGAGCATACCATCTTCTCTTTC 60.142 45.833 0.00 0.00 31.83 2.62
757 778 1.072678 ATGAGCGGCATCATCTGGG 59.927 57.895 1.45 0.00 34.84 4.45
796 817 0.892755 TCGGTTGGCTCATCGTAAGT 59.107 50.000 0.00 0.00 39.48 2.24
1071 1096 2.428530 TGGACTCTCCGAACAGATGATG 59.571 50.000 0.00 0.00 40.17 3.07
1242 1267 2.108157 AACGTCGTGCAGAAGCCA 59.892 55.556 0.00 0.00 41.13 4.75
1247 1272 2.661537 CTGGCAACGTCGTGCAGA 60.662 61.111 13.82 0.00 46.81 4.26
1466 1497 0.542702 AACCCTGATGGCCAAAGTGG 60.543 55.000 10.96 15.66 41.55 4.00
1481 1512 4.546829 TGTATTGACAGTCTGGTAACCC 57.453 45.455 4.53 0.00 0.00 4.11
1482 1513 8.732746 ATTTATGTATTGACAGTCTGGTAACC 57.267 34.615 4.53 0.00 39.50 2.85
1487 1524 8.514594 ACACAAATTTATGTATTGACAGTCTGG 58.485 33.333 0.00 0.00 39.50 3.86
1492 1529 9.897744 ACAGAACACAAATTTATGTATTGACAG 57.102 29.630 15.90 2.17 39.50 3.51
1534 1572 5.357032 ACGACCAAAACAGAACAGATTCTTT 59.643 36.000 0.00 0.00 42.91 2.52
1539 1577 3.312421 CACACGACCAAAACAGAACAGAT 59.688 43.478 0.00 0.00 0.00 2.90
1582 1620 6.238759 GCTTCGCCTTTTCCAATATTAGTCAT 60.239 38.462 0.00 0.00 0.00 3.06
1583 1621 5.065988 GCTTCGCCTTTTCCAATATTAGTCA 59.934 40.000 0.00 0.00 0.00 3.41
1585 1623 4.947388 TGCTTCGCCTTTTCCAATATTAGT 59.053 37.500 0.00 0.00 0.00 2.24
1589 1627 3.119137 GGTTGCTTCGCCTTTTCCAATAT 60.119 43.478 0.00 0.00 0.00 1.28
1631 3112 7.046033 TCTTATTTATTGGAACGGAAGGAGTC 58.954 38.462 0.00 0.00 0.00 3.36
1655 3136 6.630676 TTAATTTTGAAATGAGCGTGCATC 57.369 33.333 0.00 0.00 0.00 3.91
1656 3137 6.646240 AGTTTAATTTTGAAATGAGCGTGCAT 59.354 30.769 0.00 0.00 0.00 3.96
1683 4223 9.941325 ACATCTGATCTGTCTAATTTATGATCC 57.059 33.333 0.00 0.00 32.00 3.36
1699 4239 4.020839 TCACACATGACACACATCTGATCT 60.021 41.667 0.00 0.00 37.07 2.75
1700 4240 4.248058 TCACACATGACACACATCTGATC 58.752 43.478 0.00 0.00 37.07 2.92
1705 4245 7.755591 AGATTTTATCACACATGACACACATC 58.244 34.615 0.00 0.00 37.79 3.06
1745 4285 5.121142 ACCATTGAAAACGTACGTCCAATAG 59.879 40.000 27.51 24.66 0.00 1.73
1750 4290 6.645700 TTATACCATTGAAAACGTACGTCC 57.354 37.500 23.05 14.13 0.00 4.79
1751 4291 9.202545 GAAATTATACCATTGAAAACGTACGTC 57.797 33.333 23.05 10.10 0.00 4.34
1757 4297 9.931210 GGTCTAGAAATTATACCATTGAAAACG 57.069 33.333 0.00 0.00 0.00 3.60
1766 4306 9.667107 CTTTTCTGTGGTCTAGAAATTATACCA 57.333 33.333 0.00 0.00 42.03 3.25
1781 4321 6.879458 GTCAGACCAATATACTTTTCTGTGGT 59.121 38.462 0.00 0.00 40.53 4.16
1782 4322 7.106239 AGTCAGACCAATATACTTTTCTGTGG 58.894 38.462 0.00 0.00 33.63 4.17
1785 4325 7.009631 CGTGAGTCAGACCAATATACTTTTCTG 59.990 40.741 0.00 0.00 33.26 3.02
1787 4327 6.255887 CCGTGAGTCAGACCAATATACTTTTC 59.744 42.308 0.00 0.00 0.00 2.29
1789 4329 5.187186 ACCGTGAGTCAGACCAATATACTTT 59.813 40.000 0.00 0.00 0.00 2.66
1791 4331 4.279145 ACCGTGAGTCAGACCAATATACT 58.721 43.478 0.00 0.00 0.00 2.12
1810 4350 0.309612 CCGAAACCCAACTTTGACCG 59.690 55.000 0.00 0.00 0.00 4.79
1811 4351 1.395635 ACCGAAACCCAACTTTGACC 58.604 50.000 0.00 0.00 0.00 4.02
1812 4352 4.096833 ACTTAACCGAAACCCAACTTTGAC 59.903 41.667 0.00 0.00 0.00 3.18
1813 4353 4.271661 ACTTAACCGAAACCCAACTTTGA 58.728 39.130 0.00 0.00 0.00 2.69
1814 4354 4.642445 ACTTAACCGAAACCCAACTTTG 57.358 40.909 0.00 0.00 0.00 2.77
1815 4355 5.664294 AAACTTAACCGAAACCCAACTTT 57.336 34.783 0.00 0.00 0.00 2.66
1816 4356 5.047164 ACAAAACTTAACCGAAACCCAACTT 60.047 36.000 0.00 0.00 0.00 2.66
1817 4357 4.463539 ACAAAACTTAACCGAAACCCAACT 59.536 37.500 0.00 0.00 0.00 3.16
1818 4358 4.746729 ACAAAACTTAACCGAAACCCAAC 58.253 39.130 0.00 0.00 0.00 3.77
1819 4359 6.712179 ATACAAAACTTAACCGAAACCCAA 57.288 33.333 0.00 0.00 0.00 4.12
1827 4367 8.146412 ACTAGGGCTATATACAAAACTTAACCG 58.854 37.037 0.00 0.00 0.00 4.44
1843 4383 5.216622 TGTAAAGATGTCCACTAGGGCTAT 58.783 41.667 0.00 0.00 41.31 2.97
1844 4384 4.616553 TGTAAAGATGTCCACTAGGGCTA 58.383 43.478 0.00 0.00 41.31 3.93
1848 4388 7.125792 ACCTTATGTAAAGATGTCCACTAGG 57.874 40.000 0.00 0.00 0.00 3.02
1863 4403 9.742144 TGGCAAGATTAAAAGTAACCTTATGTA 57.258 29.630 0.00 0.00 0.00 2.29
1864 4404 8.520351 GTGGCAAGATTAAAAGTAACCTTATGT 58.480 33.333 0.00 0.00 0.00 2.29
1865 4405 7.696453 CGTGGCAAGATTAAAAGTAACCTTATG 59.304 37.037 0.00 0.00 0.00 1.90
1866 4406 7.392393 ACGTGGCAAGATTAAAAGTAACCTTAT 59.608 33.333 7.60 0.00 0.00 1.73
1873 4413 5.057819 TCACACGTGGCAAGATTAAAAGTA 58.942 37.500 21.57 0.00 0.00 2.24
1909 4449 7.806690 TGTTTTTCTATCTTTTCTCATCCACG 58.193 34.615 0.00 0.00 0.00 4.94
1974 4574 2.526304 ACGTTCTGCTGCACTTTCTA 57.474 45.000 0.00 0.00 0.00 2.10
1985 4585 3.166657 GCATCTTTCATCAACGTTCTGC 58.833 45.455 0.00 0.00 0.00 4.26
2034 4634 3.976701 AAGTGGAGATTGGCGCGGG 62.977 63.158 8.83 0.00 0.00 6.13
2042 4642 2.842496 TCATGCTGGAGAAGTGGAGATT 59.158 45.455 0.00 0.00 0.00 2.40
2047 4647 0.325933 TGGTCATGCTGGAGAAGTGG 59.674 55.000 0.00 0.00 0.00 4.00
2105 4705 4.410743 GAGCGTTTGCAGGCTGGC 62.411 66.667 17.64 10.61 44.32 4.85
2113 4713 1.078143 AGGGATGGAGAGCGTTTGC 60.078 57.895 0.00 0.00 43.24 3.68
2116 4716 0.616111 ACTCAGGGATGGAGAGCGTT 60.616 55.000 0.00 0.00 36.26 4.84
2130 4730 0.965866 TCGGCAGGTCAGGTACTCAG 60.966 60.000 0.00 0.00 34.60 3.35
2136 4736 2.997897 GGAGTCGGCAGGTCAGGT 60.998 66.667 0.00 0.00 0.00 4.00
2196 4806 2.771089 ACGATATCGCCTACCTTCGTA 58.229 47.619 24.59 0.00 44.43 3.43
2223 4842 2.156917 TCAGCTAGCAATATGGCATGC 58.843 47.619 18.83 9.90 42.87 4.06
2229 4938 7.150640 TCTGTGACTATTCAGCTAGCAATATG 58.849 38.462 18.83 6.41 30.10 1.78
2267 4978 7.466590 GCAGCCTGAATCTAAAGAAAGTACATC 60.467 40.741 0.00 0.00 0.00 3.06
2325 5036 2.232452 ACAAAGAGCTGATAGCACGACT 59.768 45.455 0.00 0.00 45.56 4.18
2336 5047 2.985406 GCTCCAGAAACAAAGAGCTG 57.015 50.000 0.00 0.00 46.50 4.24
2341 5052 2.925306 GCTGCATGCTCCAGAAACAAAG 60.925 50.000 20.33 4.03 38.95 2.77
2400 5111 1.242076 CCAGCACTTTAAGCACAGCT 58.758 50.000 0.00 0.00 42.56 4.24
2430 5141 6.201425 ACAATGTTGTCTTTGCTTAAAGCATG 59.799 34.615 0.00 0.00 44.20 4.06
2447 5158 4.789012 ATCCCAGCACTTTACAATGTTG 57.211 40.909 0.00 0.00 0.00 3.33
2454 5165 5.036117 TCATCCTTATCCCAGCACTTTAC 57.964 43.478 0.00 0.00 0.00 2.01
2456 5167 4.591321 TTCATCCTTATCCCAGCACTTT 57.409 40.909 0.00 0.00 0.00 2.66
2457 5168 4.591321 TTTCATCCTTATCCCAGCACTT 57.409 40.909 0.00 0.00 0.00 3.16
2459 5170 4.464008 TCATTTCATCCTTATCCCAGCAC 58.536 43.478 0.00 0.00 0.00 4.40
2460 5171 4.413189 TCTCATTTCATCCTTATCCCAGCA 59.587 41.667 0.00 0.00 0.00 4.41
2462 5173 8.600668 TCTATTCTCATTTCATCCTTATCCCAG 58.399 37.037 0.00 0.00 0.00 4.45
2463 5174 8.510358 TCTATTCTCATTTCATCCTTATCCCA 57.490 34.615 0.00 0.00 0.00 4.37
2506 5221 1.294780 CTGGACTCTGCACCACTCC 59.705 63.158 0.00 0.00 32.44 3.85
2546 5261 3.102972 TCCTCTCAATCAGTTCCTCCTG 58.897 50.000 0.00 0.00 0.00 3.86
2547 5262 3.103742 GTCCTCTCAATCAGTTCCTCCT 58.896 50.000 0.00 0.00 0.00 3.69
2556 5271 1.080354 ACCCCCGTCCTCTCAATCA 59.920 57.895 0.00 0.00 0.00 2.57
2573 5288 5.488645 TTTCCGACAAAGAGGTTAAACAC 57.511 39.130 0.00 0.00 0.00 3.32
2601 5316 8.627487 TCTAATTTTAGTGTTTGCTGTTGTTG 57.373 30.769 0.00 0.00 32.61 3.33
2608 5323 9.816354 ACAATGTTTCTAATTTTAGTGTTTGCT 57.184 25.926 0.00 0.00 32.61 3.91
2631 5346 7.071572 AGGTAAACCTTACAGAAACTAGGACAA 59.928 37.037 0.00 0.00 46.09 3.18
2665 5380 4.532126 TCCCTAGGCATGGTATTCAGTATG 59.468 45.833 2.05 0.00 37.54 2.39
2683 5398 9.177608 CTTACAAAGATGAACAATTGATCCCTA 57.822 33.333 13.59 0.00 0.00 3.53
2694 5409 6.993079 TGTAGAGAGCTTACAAAGATGAACA 58.007 36.000 0.00 0.00 0.00 3.18
2698 5413 7.044181 TGGAATGTAGAGAGCTTACAAAGATG 58.956 38.462 1.03 0.00 0.00 2.90
2699 5414 7.187824 TGGAATGTAGAGAGCTTACAAAGAT 57.812 36.000 1.03 0.00 0.00 2.40
2744 5460 7.931578 AATACCACGATCTTCATTTTAACCA 57.068 32.000 0.00 0.00 0.00 3.67
2807 5526 6.808704 GCTATTTTCTTGAGAACCCATTCAAC 59.191 38.462 0.00 0.00 37.29 3.18
2867 5588 7.006865 AGTATGAGCTCATAAGAGATGCAAT 57.993 36.000 32.72 10.76 41.38 3.56
2929 5652 4.405358 TGATTGACCAAAACAGGCTCTTTT 59.595 37.500 0.00 0.00 0.00 2.27
2965 5688 5.872070 AGAAGAACGACTGATGGATCTTTTC 59.128 40.000 0.00 0.00 0.00 2.29
3113 5837 0.596577 CTTTCACAGCTGCAGTGCAT 59.403 50.000 20.10 0.79 38.13 3.96
3115 5839 0.664761 TTCTTTCACAGCTGCAGTGC 59.335 50.000 18.93 8.58 36.93 4.40
3116 5840 2.357009 AGTTTCTTTCACAGCTGCAGTG 59.643 45.455 17.84 17.84 38.32 3.66
3117 5841 2.615912 GAGTTTCTTTCACAGCTGCAGT 59.384 45.455 15.27 0.00 0.00 4.40
3295 6044 6.934083 TCAAATGTGTGTATTCAGTAGCTTCA 59.066 34.615 0.00 0.00 0.00 3.02
3301 6050 8.977412 TCTAGGATCAAATGTGTGTATTCAGTA 58.023 33.333 0.00 0.00 0.00 2.74
3316 6065 7.257790 TGTTTGGATCTCTTCTAGGATCAAA 57.742 36.000 8.42 2.02 39.82 2.69
3331 6080 0.681243 GTCCCTGGCCTGTTTGGATC 60.681 60.000 3.32 0.00 38.35 3.36
3445 6194 8.938906 CAGCTGCATGTTTTAGGATTTTATTTT 58.061 29.630 0.00 0.00 0.00 1.82
3446 6195 8.313292 TCAGCTGCATGTTTTAGGATTTTATTT 58.687 29.630 9.47 0.00 0.00 1.40
3447 6196 7.839907 TCAGCTGCATGTTTTAGGATTTTATT 58.160 30.769 9.47 0.00 0.00 1.40
3448 6197 7.408756 TCAGCTGCATGTTTTAGGATTTTAT 57.591 32.000 9.47 0.00 0.00 1.40
3576 6325 1.865865 GTCTCCAGTGAGCACGAAAA 58.134 50.000 0.00 0.00 38.58 2.29
3881 6630 3.871594 GAGTATACAAGCGAGGCAAATGT 59.128 43.478 5.50 0.00 0.00 2.71
4219 6968 5.184892 AGTACCAGAAAGCATTGAATCCT 57.815 39.130 0.00 0.00 0.00 3.24
4363 7113 6.041409 AGACAGTATGAGATAACAGGGACATG 59.959 42.308 0.00 0.00 39.69 3.21
4393 7143 1.630369 ACACCCATGTCTGCATACACT 59.370 47.619 7.12 0.00 31.55 3.55
4440 7190 3.750371 TCCTGAAAATTCGCTCTCCAAA 58.250 40.909 0.00 0.00 0.00 3.28
4454 7204 4.202398 GCCATAGATCTGACCATCCTGAAA 60.202 45.833 5.18 0.00 0.00 2.69
4600 7352 5.189934 AGAAAGTACCTTCCCTGGATAAGTG 59.810 44.000 0.43 0.00 0.00 3.16
4687 7439 5.391950 CCATTCAAACTTCGATACTTGTGGG 60.392 44.000 0.00 0.00 0.00 4.61
4779 7531 1.068474 GCACGCGATAAAGTGACAGT 58.932 50.000 15.93 0.00 40.56 3.55
4845 7597 2.014010 AATGGGTGCCTGAAACACAT 57.986 45.000 0.00 0.00 43.52 3.21
5036 7788 3.735746 GTGCCTACAAAAATGTCAACTGC 59.264 43.478 0.00 0.00 0.00 4.40
5039 7791 3.735746 GCAGTGCCTACAAAAATGTCAAC 59.264 43.478 2.85 0.00 0.00 3.18
5050 7802 2.110006 TGCAACGCAGTGCCTACA 59.890 55.556 10.11 0.00 45.00 2.74
5092 7844 0.550914 ACCGTATGGGCCATCAATGT 59.449 50.000 25.07 13.31 40.62 2.71
5171 7923 1.877443 ACACTTATGAACGGTGTTGCC 59.123 47.619 0.00 0.00 40.68 4.52
5419 8171 1.072331 TGTCTTGAGCTGAAACCTCCC 59.928 52.381 0.00 0.00 0.00 4.30
5434 8186 3.188159 TCGTAACCTGTTTGCTGTCTT 57.812 42.857 0.00 0.00 0.00 3.01
5470 8222 8.519526 CCATCTGGAAGTAGATATAGACACTTC 58.480 40.741 11.80 11.80 43.91 3.01
5514 8266 8.144478 AGAGATTTATAAGAGCGCAAGACATTA 58.856 33.333 11.47 0.00 43.02 1.90
5561 8313 9.453325 GCTTGTTAGATAGTTGTACATCTCTAC 57.547 37.037 9.72 6.19 33.58 2.59
5626 8378 4.449743 GCAAAATGAAGAGCTTGAATTGCA 59.550 37.500 14.06 0.00 0.00 4.08
5674 8426 6.901300 AGGAGAAAGACTTACTGGAGTTTTT 58.099 36.000 0.00 2.97 36.87 1.94
5770 8522 3.206150 AGGCTTCATGGTAATTAGCACG 58.794 45.455 19.03 11.83 36.42 5.34
5784 8536 2.275134 TGCACAGAATGAAGGCTTCA 57.725 45.000 30.29 30.29 45.01 3.02
5788 8540 2.229543 TGACATTGCACAGAATGAAGGC 59.770 45.455 3.15 0.00 39.69 4.35
5798 8550 5.462729 GTGATTGACAATTTGACATTGCACA 59.537 36.000 2.79 0.00 32.55 4.57
5988 8742 9.677567 GACAGTGCATCTTCTAAATTAAACAAA 57.322 29.630 0.00 0.00 0.00 2.83
5991 8745 8.507249 ACTGACAGTGCATCTTCTAAATTAAAC 58.493 33.333 7.47 0.00 0.00 2.01
6033 8789 6.095440 ACAAGAAACTGGGGATCATTATTTCG 59.905 38.462 0.00 0.00 31.96 3.46
6081 8837 5.746990 AGTAGGGTCATATATCTGCAACC 57.253 43.478 0.00 0.00 0.00 3.77
6146 8905 7.759433 ACGTGAACTTGAAACTGAAATTTCATT 59.241 29.630 20.76 13.01 45.55 2.57
6176 8936 6.905076 CGTTCCATTTCCATGTAAGAATAACG 59.095 38.462 0.00 0.00 0.00 3.18
6186 8946 2.094078 CCATTGCGTTCCATTTCCATGT 60.094 45.455 0.00 0.00 0.00 3.21
6333 9093 6.322201 ACAGGAAAGTCACATTTCATTTCACT 59.678 34.615 2.05 0.00 40.29 3.41
6372 9140 5.361285 ACAAGCTCATGTTCTACCCTAGTAG 59.639 44.000 0.00 0.00 46.34 2.57
6373 9141 5.127194 CACAAGCTCATGTTCTACCCTAGTA 59.873 44.000 0.00 0.00 0.00 1.82
6407 9182 9.759473 ATATATAATTAGAGCCTGCATTTTGGT 57.241 29.630 0.00 0.00 0.00 3.67
6428 9204 8.893563 TTTTCAACAGTGGGAGGAAAATATAT 57.106 30.769 0.00 0.00 33.83 0.86
6502 9278 4.855340 ACTCCCTCACAAGAAAAACAGAA 58.145 39.130 0.00 0.00 0.00 3.02
6567 9361 7.172361 CCTCAAGGTTTGTCTCAAAAACAAAAA 59.828 33.333 3.24 0.00 45.35 1.94
6568 9362 6.648725 CCTCAAGGTTTGTCTCAAAAACAAAA 59.351 34.615 3.24 0.00 45.35 2.44
6572 9366 5.576447 TCCTCAAGGTTTGTCTCAAAAAC 57.424 39.130 0.00 0.00 36.90 2.43
6578 9372 7.511959 AAAAGTATTCCTCAAGGTTTGTCTC 57.488 36.000 0.00 0.00 36.34 3.36
6579 9373 7.898014 AAAAAGTATTCCTCAAGGTTTGTCT 57.102 32.000 0.00 0.00 36.34 3.41
6608 9402 4.993705 TCCATTCCTCAAAGTTACACCT 57.006 40.909 0.00 0.00 0.00 4.00
6609 9403 6.590234 AAATCCATTCCTCAAAGTTACACC 57.410 37.500 0.00 0.00 0.00 4.16
6639 9433 1.766496 TCCGTTCCTCAAAGTTGTCCT 59.234 47.619 0.00 0.00 0.00 3.85
6642 9436 3.689649 GCATATCCGTTCCTCAAAGTTGT 59.310 43.478 0.00 0.00 0.00 3.32
6644 9438 4.080863 AGAGCATATCCGTTCCTCAAAGTT 60.081 41.667 0.00 0.00 0.00 2.66
6645 9439 3.452627 AGAGCATATCCGTTCCTCAAAGT 59.547 43.478 0.00 0.00 0.00 2.66
6646 9440 3.806521 CAGAGCATATCCGTTCCTCAAAG 59.193 47.826 0.00 0.00 0.00 2.77
6647 9441 3.197766 ACAGAGCATATCCGTTCCTCAAA 59.802 43.478 0.00 0.00 0.00 2.69
6652 9446 4.508124 CAGTTAACAGAGCATATCCGTTCC 59.492 45.833 8.61 0.00 0.00 3.62
6653 9447 4.508124 CCAGTTAACAGAGCATATCCGTTC 59.492 45.833 8.61 0.00 0.00 3.95
6654 9448 4.081087 ACCAGTTAACAGAGCATATCCGTT 60.081 41.667 8.61 0.00 0.00 4.44
6655 9449 3.451178 ACCAGTTAACAGAGCATATCCGT 59.549 43.478 8.61 0.00 0.00 4.69
6656 9450 3.804325 CACCAGTTAACAGAGCATATCCG 59.196 47.826 8.61 0.00 0.00 4.18
6657 9451 3.561725 GCACCAGTTAACAGAGCATATCC 59.438 47.826 8.61 0.00 0.00 2.59
6659 9453 4.194640 CAGCACCAGTTAACAGAGCATAT 58.805 43.478 16.34 0.00 0.00 1.78
6730 9531 2.732016 GGTTTGCGTGGGGGTTTC 59.268 61.111 0.00 0.00 0.00 2.78
6767 9579 4.207165 ACTGATTTTTGGGATACGGATGG 58.793 43.478 0.00 0.00 37.60 3.51
6769 9581 5.131142 AGAGACTGATTTTTGGGATACGGAT 59.869 40.000 0.00 0.00 37.60 4.18
6773 9585 4.811557 CCGAGAGACTGATTTTTGGGATAC 59.188 45.833 0.00 0.00 0.00 2.24
6780 9592 4.081917 GGAGAGACCGAGAGACTGATTTTT 60.082 45.833 0.00 0.00 0.00 1.94
6781 9593 3.445805 GGAGAGACCGAGAGACTGATTTT 59.554 47.826 0.00 0.00 0.00 1.82
6949 9779 1.457455 GAGGAGGAGCAGGAGGGAG 60.457 68.421 0.00 0.00 0.00 4.30
6954 9784 2.043852 GTCGGAGGAGGAGCAGGA 60.044 66.667 0.00 0.00 0.00 3.86
6974 9816 1.470285 GGCTTGGCGTCGTTATAGTCA 60.470 52.381 0.00 0.00 0.00 3.41
6979 9821 2.124860 GGGGCTTGGCGTCGTTAT 60.125 61.111 0.00 0.00 0.00 1.89
6981 9823 4.699522 GAGGGGCTTGGCGTCGTT 62.700 66.667 0.00 0.00 0.00 3.85
7169 10020 4.599500 AGCACACTGGGGGTCCCT 62.599 66.667 8.15 0.00 45.70 4.20
7298 10170 3.008375 AGTGCAGCTTGAGAAGGATGTTA 59.992 43.478 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.