Multiple sequence alignment - TraesCS2D01G287800

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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 TraesCS2D01G287800 chr2D 100.000 5480 0 0 1 5480 368014109 368008630 0.000000e+00 10120.0
1 TraesCS2D01G287800 chr2A 96.316 1873 51 10 3042 4902 498106515 498104649 0.000000e+00 3061.0
2 TraesCS2D01G287800 chr2A 95.043 1735 62 14 1328 3046 498108289 498106563 0.000000e+00 2706.0
3 TraesCS2D01G287800 chr2A 92.434 793 34 12 544 1326 498109146 498108370 0.000000e+00 1109.0
4 TraesCS2D01G287800 chr2A 88.356 292 16 10 234 515 498109415 498109132 8.800000e-88 335.0
5 TraesCS2D01G287800 chr2A 95.074 203 9 1 1 202 498110652 498110450 8.860000e-83 318.0
6 TraesCS2D01G287800 chr2A 94.839 155 8 0 5326 5480 498104607 498104453 5.480000e-60 243.0
7 TraesCS2D01G287800 chr2A 100.000 30 0 0 5330 5359 745657797 745657768 7.670000e-04 56.5
8 TraesCS2D01G287800 chr2B 95.444 1734 56 11 1328 3046 437010842 437009117 0.000000e+00 2743.0
9 TraesCS2D01G287800 chr2B 93.057 1858 84 25 3042 4871 437009069 437007229 0.000000e+00 2675.0
10 TraesCS2D01G287800 chr2B 93.928 1334 57 12 1 1323 437012236 437010916 0.000000e+00 1993.0
11 TraesCS2D01G287800 chr2B 90.521 422 35 4 4904 5322 417075127 417074708 2.230000e-153 553.0
12 TraesCS2D01G287800 chr2B 91.176 102 8 1 5360 5461 437007222 437007122 2.660000e-28 137.0
13 TraesCS2D01G287800 chr4D 90.521 422 36 3 4904 5322 43327037 43326617 6.200000e-154 555.0
14 TraesCS2D01G287800 chr3B 90.071 423 38 3 4903 5322 15306015 15305594 3.730000e-151 545.0
15 TraesCS2D01G287800 chr3B 90.071 423 38 3 4903 5322 15354335 15353914 3.730000e-151 545.0
16 TraesCS2D01G287800 chr3B 90.071 423 38 3 4903 5322 15373231 15372810 3.730000e-151 545.0
17 TraesCS2D01G287800 chr3B 90.071 423 38 3 4903 5322 15409742 15409321 3.730000e-151 545.0
18 TraesCS2D01G287800 chr3B 90.071 423 38 3 4903 5322 15423585 15423164 3.730000e-151 545.0
19 TraesCS2D01G287800 chr3B 89.835 423 39 3 4903 5322 15269522 15269101 1.740000e-149 540.0
20 TraesCS2D01G287800 chr5B 90.047 422 38 3 4904 5322 290108055 290108475 1.340000e-150 544.0
21 TraesCS2D01G287800 chr5B 95.122 41 0 2 4864 4902 54455500 54455460 4.580000e-06 63.9
22 TraesCS2D01G287800 chr5B 97.297 37 1 0 4866 4902 479643533 479643569 4.580000e-06 63.9
23 TraesCS2D01G287800 chr6A 95.122 41 2 0 4862 4902 552171448 552171488 1.270000e-06 65.8
24 TraesCS2D01G287800 chr1A 95.122 41 2 0 4862 4902 593649254 593649294 1.270000e-06 65.8
25 TraesCS2D01G287800 chr1A 100.000 34 0 0 4869 4902 382550777 382550744 4.580000e-06 63.9
26 TraesCS2D01G287800 chr1A 97.297 37 0 1 4866 4902 436259647 436259682 1.650000e-05 62.1
27 TraesCS2D01G287800 chr6B 94.737 38 2 0 4865 4902 25612789 25612752 5.930000e-05 60.2
28 TraesCS2D01G287800 chr1B 94.872 39 0 2 4865 4902 477403818 477403855 5.930000e-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 TraesCS2D01G287800 chr2D 368008630 368014109 5479 True 10120.000000 10120 100.00000 1 5480 1 chr2D.!!$R1 5479
1 TraesCS2D01G287800 chr2A 498104453 498110652 6199 True 1295.333333 3061 93.67700 1 5480 6 chr2A.!!$R2 5479
2 TraesCS2D01G287800 chr2B 437007122 437012236 5114 True 1887.000000 2743 93.40125 1 5461 4 chr2B.!!$R2 5460

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
755 1780 0.320683 TGTGAGCAGTCCAATCCACG 60.321 55.0 0.00 0.00 0.00 4.94 F
982 2008 0.523072 CTGCTTACTTGGCGCATTGT 59.477 50.0 10.83 6.69 32.62 2.71 F
1126 2153 0.527565 ATTGTGCAGGTTTCCGATGC 59.472 50.0 0.00 0.00 40.40 3.91 F
1149 2176 0.535780 TGTCCAAGAACAGGCAGCTG 60.536 55.0 10.11 10.11 0.00 4.24 F
1242 2276 0.595588 TGGTATGCGGTTGCTTTGTG 59.404 50.0 0.00 0.00 43.34 3.33 F
2910 4051 0.184451 CAGCTGTGAATATGCCCCCT 59.816 55.0 5.25 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 2811 1.131883 GCATGCTCACCAAGACATGAC 59.868 52.381 11.37 0.0 39.69 3.06 R
2501 3641 2.119801 ACAGTGCTTAGCCATCAAGG 57.880 50.000 0.29 0.0 41.84 3.61 R
2782 3923 2.728690 TGTGGCAAATCAGCACATTC 57.271 45.000 0.00 0.0 35.83 2.67 R
2795 3936 3.382865 TGCACTAAACAGAAAATGTGGCA 59.617 39.130 0.00 0.0 43.00 4.92 R
3151 4345 2.014335 TGCGTGGAGACAATCTGATG 57.986 50.000 0.00 0.0 46.06 3.07 R
4683 5903 0.251922 AGTAAGGTGGCCGTCAGGTA 60.252 55.000 0.00 0.0 40.50 3.08 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
143 145 7.781693 ACATAAAGATCATAGCACCAAAATCCT 59.218 33.333 0.00 0.00 0.00 3.24
452 1472 3.727258 CGCCATTGGGGAGGGACA 61.727 66.667 14.33 0.00 40.01 4.02
453 1473 2.276740 GCCATTGGGGAGGGACAG 59.723 66.667 4.53 0.00 40.01 3.51
454 1474 2.276740 CCATTGGGGAGGGACAGC 59.723 66.667 0.00 0.00 40.01 4.40
455 1475 2.615465 CCATTGGGGAGGGACAGCA 61.615 63.158 0.00 0.00 40.01 4.41
456 1476 1.379044 CATTGGGGAGGGACAGCAC 60.379 63.158 0.00 0.00 0.00 4.40
524 1544 2.224159 GCCTCCAGGGTCCACTCAA 61.224 63.158 0.00 0.00 37.43 3.02
605 1625 4.159506 CCAACTCGAAGGATTTCTCTCTCT 59.840 45.833 0.00 0.00 0.00 3.10
644 1664 1.549203 TAACCCGCTCTACCGAACTT 58.451 50.000 0.00 0.00 0.00 2.66
721 1741 3.441572 CCTAACCTGCTTGGATTGTTCTG 59.558 47.826 3.40 0.00 39.71 3.02
755 1780 0.320683 TGTGAGCAGTCCAATCCACG 60.321 55.000 0.00 0.00 0.00 4.94
759 1784 2.236146 TGAGCAGTCCAATCCACGTATT 59.764 45.455 0.00 0.00 0.00 1.89
821 1846 0.804364 TCGTTTGCAGCATGGTCATC 59.196 50.000 0.00 0.00 35.86 2.92
973 1999 2.086054 AGTCCTTCGCTGCTTACTTG 57.914 50.000 0.00 0.00 0.00 3.16
982 2008 0.523072 CTGCTTACTTGGCGCATTGT 59.477 50.000 10.83 6.69 32.62 2.71
997 2023 2.555757 GCATTGTTGAGGCTGAGACTTT 59.444 45.455 0.00 0.00 30.93 2.66
1009 2035 3.019564 CTGAGACTTTTAATGGGCCAGG 58.980 50.000 13.78 0.16 0.00 4.45
1029 2055 2.633657 GTGAGTGCGCCACTGTTG 59.366 61.111 15.61 0.00 45.44 3.33
1045 2071 6.292114 GCCACTGTTGTGCTTTAACATTTTAC 60.292 38.462 0.00 0.00 42.54 2.01
1050 2077 7.324178 TGTTGTGCTTTAACATTTTACAAGGT 58.676 30.769 0.00 0.00 33.43 3.50
1053 2080 7.324178 TGTGCTTTAACATTTTACAAGGTTGT 58.676 30.769 2.08 0.24 44.86 3.32
1065 2092 2.159014 ACAAGGTTGTGTGCTCGTCTTA 60.159 45.455 0.00 0.00 40.49 2.10
1086 2113 0.600557 CTGACGACTGAGCCTGTTCT 59.399 55.000 0.00 0.00 0.00 3.01
1102 2129 2.041485 TGTTCTGATGCCCCTGAAATGA 59.959 45.455 0.00 0.00 0.00 2.57
1126 2153 0.527565 ATTGTGCAGGTTTCCGATGC 59.472 50.000 0.00 0.00 40.40 3.91
1149 2176 0.535780 TGTCCAAGAACAGGCAGCTG 60.536 55.000 10.11 10.11 0.00 4.24
1209 2236 5.007528 GCAGCATGTTGTTTTGGTTATTTGT 59.992 36.000 11.44 0.00 39.31 2.83
1216 2243 6.876257 TGTTGTTTTGGTTATTTGTTTGAGCT 59.124 30.769 0.00 0.00 0.00 4.09
1242 2276 0.595588 TGGTATGCGGTTGCTTTGTG 59.404 50.000 0.00 0.00 43.34 3.33
1263 2297 0.602562 CATTTTCTTTGCCAGGCGGA 59.397 50.000 7.03 1.98 0.00 5.54
1275 2309 2.887152 GCCAGGCGGAATCATTAAGAAT 59.113 45.455 0.00 0.00 0.00 2.40
1352 2467 5.363562 TGCTGTGTATCAAATCCAGAGAT 57.636 39.130 0.00 0.00 0.00 2.75
1462 2577 5.934625 ACAGCCAATAAGAGTGTTCTGTAAG 59.065 40.000 0.00 0.00 32.79 2.34
1467 2582 3.475566 AAGAGTGTTCTGTAAGCTGCA 57.524 42.857 1.02 0.00 32.79 4.41
1468 2583 2.760374 AGAGTGTTCTGTAAGCTGCAC 58.240 47.619 1.02 0.00 32.57 4.57
1469 2584 1.801178 GAGTGTTCTGTAAGCTGCACC 59.199 52.381 1.02 0.00 32.72 5.01
1470 2585 1.140852 AGTGTTCTGTAAGCTGCACCA 59.859 47.619 1.02 0.00 32.72 4.17
1471 2586 1.264288 GTGTTCTGTAAGCTGCACCAC 59.736 52.381 1.02 0.00 0.00 4.16
1472 2587 1.134250 TGTTCTGTAAGCTGCACCACA 60.134 47.619 1.02 1.58 0.00 4.17
1473 2588 2.154462 GTTCTGTAAGCTGCACCACAT 58.846 47.619 1.02 0.00 0.00 3.21
1474 2589 3.244387 TGTTCTGTAAGCTGCACCACATA 60.244 43.478 1.02 0.00 0.00 2.29
1480 2599 4.582656 TGTAAGCTGCACCACATAACTTTT 59.417 37.500 1.02 0.00 0.00 2.27
1553 2674 1.328279 TGTATCTGATCGGCATCGGT 58.672 50.000 0.00 0.00 36.81 4.69
1590 2711 5.538813 TGACGTATCAGGGTAATCTAGCATT 59.461 40.000 0.00 0.00 0.00 3.56
1602 2723 8.957466 GGGTAATCTAGCATTTAGTTTCTGTTT 58.043 33.333 0.00 0.00 0.00 2.83
1690 2811 2.223377 GTCTTGTGGTCTTAAGGTTGCG 59.777 50.000 1.85 0.00 0.00 4.85
1691 2812 2.158871 TCTTGTGGTCTTAAGGTTGCGT 60.159 45.455 1.85 0.00 0.00 5.24
1707 2828 0.950555 GCGTCATGTCTTGGTGAGCA 60.951 55.000 0.00 0.00 0.00 4.26
1749 2870 6.527722 CGTAATTTGCATTTAGCTTGACATGT 59.472 34.615 0.00 0.00 45.94 3.21
1750 2871 7.062138 CGTAATTTGCATTTAGCTTGACATGTT 59.938 33.333 0.00 0.00 45.94 2.71
1779 2900 8.216423 ACTCACCAATTCAAGATAAGCTATGAT 58.784 33.333 0.00 0.00 0.00 2.45
1818 2939 1.278127 GGCAACAGGAGTAGTGCCTTA 59.722 52.381 6.28 0.00 39.18 2.69
1873 3013 7.121463 ACAAGTACGAGTTCTCTCACATATCTT 59.879 37.037 0.00 0.00 40.44 2.40
1899 3039 2.814336 GTGTCAGGCTTTTAACTGGGAG 59.186 50.000 0.00 0.00 35.47 4.30
2044 3184 7.227156 AGTCATGAGTTCACCATTACTCTTTT 58.773 34.615 0.00 0.00 41.05 2.27
2227 3367 7.172868 TGTAGTTATTAACCATCGAGTTGGA 57.827 36.000 12.02 0.00 39.25 3.53
2244 3384 6.310711 CGAGTTGGAACTACTAAAGGATCAAC 59.689 42.308 0.00 0.00 39.88 3.18
2393 3533 3.264964 ACCCCCGTATAAACACAATGACT 59.735 43.478 0.00 0.00 0.00 3.41
2501 3641 7.767198 TGTACAGCCTTTTACTTATCACCATAC 59.233 37.037 0.00 0.00 0.00 2.39
2519 3659 2.119801 ACCTTGATGGCTAAGCACTG 57.880 50.000 0.00 0.00 40.22 3.66
2552 3692 6.734137 CATTACTCAACTTTGGTGCAACTTA 58.266 36.000 2.04 0.00 36.74 2.24
2782 3923 4.691685 ACTGTTGCCATATTTTGCATTGTG 59.308 37.500 0.00 0.00 37.33 3.33
2795 3936 4.260139 TGCATTGTGAATGTGCTGATTT 57.740 36.364 0.00 0.00 41.01 2.17
2910 4051 0.184451 CAGCTGTGAATATGCCCCCT 59.816 55.000 5.25 0.00 0.00 4.79
2995 4136 8.978874 ACTATGCCACAATGATGTAATTTCTA 57.021 30.769 0.00 0.00 37.82 2.10
2996 4137 9.407380 ACTATGCCACAATGATGTAATTTCTAA 57.593 29.630 0.00 0.00 37.82 2.10
3003 4144 9.912634 CACAATGATGTAATTTCTAACCAAAGT 57.087 29.630 0.00 0.00 37.82 2.66
3101 4295 3.257393 CATCTCTCTGAACCGTTCTTGG 58.743 50.000 12.43 3.59 0.00 3.61
3151 4345 3.399330 TGCAAGGCAGTTCTGTAACTAC 58.601 45.455 1.78 0.00 44.28 2.73
3347 4542 5.965033 AATGATCATGGTTCTACAGGAGT 57.035 39.130 9.46 0.00 34.39 3.85
3351 4546 6.640518 TGATCATGGTTCTACAGGAGTAAAC 58.359 40.000 0.00 0.00 34.39 2.01
3352 4547 5.068234 TCATGGTTCTACAGGAGTAAACG 57.932 43.478 0.00 0.00 0.00 3.60
3374 4571 5.465724 ACGAGTCTTTGGTGATTAGTTTGAC 59.534 40.000 0.00 0.00 0.00 3.18
3526 4723 1.065854 CAGGGTCAACTCAGGTCCATC 60.066 57.143 0.00 0.00 0.00 3.51
3656 4853 2.969950 CCATTGGCCATTTCCATCTGAT 59.030 45.455 6.09 0.00 35.77 2.90
3737 4934 4.783036 CGTTAGAAGTGAATTGCATGTTCG 59.217 41.667 0.00 0.00 31.21 3.95
3802 5002 6.278363 ACGCCAGTTAAATAATGATCGTAGT 58.722 36.000 0.00 0.00 0.00 2.73
3803 5003 6.759827 ACGCCAGTTAAATAATGATCGTAGTT 59.240 34.615 0.00 0.00 0.00 2.24
3997 5203 9.088512 GGAACTAGTATAGAAGTGAATTGTGTG 57.911 37.037 0.00 0.00 42.77 3.82
4528 5738 6.933521 GCCATATTTCTGCTGAAGAGAAGATA 59.066 38.462 6.13 1.62 33.43 1.98
4529 5739 7.607223 GCCATATTTCTGCTGAAGAGAAGATAT 59.393 37.037 6.13 3.73 33.43 1.63
4683 5903 1.645710 AGGTTCGAGTTCTGGGACAT 58.354 50.000 0.00 0.00 38.20 3.06
4715 5935 4.380550 GCCACCTTACTTTATTCAAGTGCC 60.381 45.833 0.00 0.00 45.98 5.01
4883 6108 6.377712 GCTTGATTATATAGTACTCCCTCCGT 59.622 42.308 0.00 0.00 0.00 4.69
4886 6111 3.735720 ATATAGTACTCCCTCCGTCCC 57.264 52.381 0.00 0.00 0.00 4.46
4898 6123 3.583086 CCCTCCGTCCCACAATATAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
4902 6127 5.607477 TCCGTCCCACAATATAAGATGTTC 58.393 41.667 0.00 0.00 0.00 3.18
4903 6128 4.755123 CCGTCCCACAATATAAGATGTTCC 59.245 45.833 0.00 0.00 0.00 3.62
4904 6129 5.364778 CGTCCCACAATATAAGATGTTCCA 58.635 41.667 0.00 0.00 0.00 3.53
4905 6130 5.820423 CGTCCCACAATATAAGATGTTCCAA 59.180 40.000 0.00 0.00 0.00 3.53
4906 6131 6.317642 CGTCCCACAATATAAGATGTTCCAAA 59.682 38.462 0.00 0.00 0.00 3.28
4907 6132 7.148154 CGTCCCACAATATAAGATGTTCCAAAA 60.148 37.037 0.00 0.00 0.00 2.44
4908 6133 8.527810 GTCCCACAATATAAGATGTTCCAAAAA 58.472 33.333 0.00 0.00 0.00 1.94
4909 6134 8.748412 TCCCACAATATAAGATGTTCCAAAAAG 58.252 33.333 0.00 0.00 0.00 2.27
4910 6135 8.531146 CCCACAATATAAGATGTTCCAAAAAGT 58.469 33.333 0.00 0.00 0.00 2.66
4911 6136 9.573133 CCACAATATAAGATGTTCCAAAAAGTC 57.427 33.333 0.00 0.00 0.00 3.01
4923 6148 3.780902 CCAAAAAGTCACTTTGGTGGAC 58.219 45.455 21.46 0.68 45.21 4.02
4924 6149 3.434637 CAAAAAGTCACTTTGGTGGACG 58.565 45.455 2.78 0.00 43.17 4.79
4925 6150 1.675552 AAAGTCACTTTGGTGGACGG 58.324 50.000 0.68 0.00 43.17 4.79
4926 6151 0.179029 AAGTCACTTTGGTGGACGGG 60.179 55.000 0.00 0.00 43.17 5.28
4927 6152 1.147600 GTCACTTTGGTGGACGGGT 59.852 57.895 0.00 0.00 43.17 5.28
4928 6153 1.147376 TCACTTTGGTGGACGGGTG 59.853 57.895 0.00 0.00 43.17 4.61
4929 6154 2.203294 ACTTTGGTGGACGGGTGC 60.203 61.111 0.00 0.00 0.00 5.01
4930 6155 2.203280 CTTTGGTGGACGGGTGCA 60.203 61.111 0.00 0.00 0.00 4.57
4931 6156 1.603455 CTTTGGTGGACGGGTGCAT 60.603 57.895 0.00 0.00 32.40 3.96
4932 6157 1.152652 TTTGGTGGACGGGTGCATT 60.153 52.632 0.00 0.00 32.40 3.56
4933 6158 1.459455 TTTGGTGGACGGGTGCATTG 61.459 55.000 0.00 0.00 32.40 2.82
4934 6159 3.061848 GGTGGACGGGTGCATTGG 61.062 66.667 0.00 0.00 32.40 3.16
4935 6160 2.033448 GTGGACGGGTGCATTGGA 59.967 61.111 0.00 0.00 32.40 3.53
4936 6161 2.040544 GTGGACGGGTGCATTGGAG 61.041 63.158 0.00 0.00 32.40 3.86
4937 6162 3.134127 GGACGGGTGCATTGGAGC 61.134 66.667 0.00 0.00 0.00 4.70
4938 6163 3.134127 GACGGGTGCATTGGAGCC 61.134 66.667 15.66 15.66 0.00 4.70
4939 6164 4.740822 ACGGGTGCATTGGAGCCC 62.741 66.667 19.11 12.02 37.79 5.19
4940 6165 4.431131 CGGGTGCATTGGAGCCCT 62.431 66.667 19.11 0.00 38.97 5.19
4941 6166 3.006677 GGGTGCATTGGAGCCCTA 58.993 61.111 14.84 0.00 38.12 3.53
4942 6167 1.538666 GGGTGCATTGGAGCCCTAT 59.461 57.895 14.84 0.00 38.12 2.57
4943 6168 0.771127 GGGTGCATTGGAGCCCTATA 59.229 55.000 14.84 0.00 38.12 1.31
4944 6169 1.355720 GGGTGCATTGGAGCCCTATAT 59.644 52.381 14.84 0.00 38.12 0.86
4945 6170 2.225117 GGGTGCATTGGAGCCCTATATT 60.225 50.000 14.84 0.00 38.12 1.28
4946 6171 3.500343 GGTGCATTGGAGCCCTATATTT 58.500 45.455 0.00 0.00 0.00 1.40
4947 6172 3.897505 GGTGCATTGGAGCCCTATATTTT 59.102 43.478 0.00 0.00 0.00 1.82
4948 6173 4.262164 GGTGCATTGGAGCCCTATATTTTG 60.262 45.833 0.00 0.00 0.00 2.44
4949 6174 4.584325 GTGCATTGGAGCCCTATATTTTGA 59.416 41.667 0.00 0.00 0.00 2.69
4950 6175 5.068987 GTGCATTGGAGCCCTATATTTTGAA 59.931 40.000 0.00 0.00 0.00 2.69
4951 6176 5.840149 TGCATTGGAGCCCTATATTTTGAAT 59.160 36.000 0.00 0.00 0.00 2.57
4952 6177 7.009550 TGCATTGGAGCCCTATATTTTGAATA 58.990 34.615 0.00 0.00 0.00 1.75
4953 6178 7.177216 TGCATTGGAGCCCTATATTTTGAATAG 59.823 37.037 0.00 0.00 0.00 1.73
4954 6179 7.177392 GCATTGGAGCCCTATATTTTGAATAGT 59.823 37.037 0.00 0.00 0.00 2.12
4955 6180 8.517878 CATTGGAGCCCTATATTTTGAATAGTG 58.482 37.037 0.00 0.00 0.00 2.74
4956 6181 7.149202 TGGAGCCCTATATTTTGAATAGTGT 57.851 36.000 0.00 0.00 0.00 3.55
4957 6182 7.224297 TGGAGCCCTATATTTTGAATAGTGTC 58.776 38.462 0.00 0.00 0.00 3.67
4958 6183 7.147391 TGGAGCCCTATATTTTGAATAGTGTCA 60.147 37.037 0.00 0.00 0.00 3.58
4959 6184 7.719633 GGAGCCCTATATTTTGAATAGTGTCAA 59.280 37.037 0.00 0.00 35.72 3.18
4960 6185 9.120538 GAGCCCTATATTTTGAATAGTGTCAAA 57.879 33.333 0.00 0.00 43.92 2.69
5034 6259 9.330063 ACATATTGATGTATGTTACACAAGAGG 57.670 33.333 0.00 0.00 44.77 3.69
5035 6260 9.546428 CATATTGATGTATGTTACACAAGAGGA 57.454 33.333 0.00 0.00 42.23 3.71
5037 6262 8.862325 ATTGATGTATGTTACACAAGAGGAAA 57.138 30.769 0.00 0.00 42.23 3.13
5038 6263 8.862325 TTGATGTATGTTACACAAGAGGAAAT 57.138 30.769 0.00 0.00 42.23 2.17
5039 6264 8.862325 TGATGTATGTTACACAAGAGGAAATT 57.138 30.769 0.00 0.00 42.23 1.82
5040 6265 8.946085 TGATGTATGTTACACAAGAGGAAATTC 58.054 33.333 0.00 0.00 42.23 2.17
5041 6266 9.167311 GATGTATGTTACACAAGAGGAAATTCT 57.833 33.333 0.00 0.00 42.23 2.40
5042 6267 8.322906 TGTATGTTACACAAGAGGAAATTCTG 57.677 34.615 0.00 0.00 32.89 3.02
5043 6268 8.154203 TGTATGTTACACAAGAGGAAATTCTGA 58.846 33.333 0.00 0.00 32.89 3.27
5044 6269 9.167311 GTATGTTACACAAGAGGAAATTCTGAT 57.833 33.333 0.00 0.00 0.00 2.90
5045 6270 7.439157 TGTTACACAAGAGGAAATTCTGATG 57.561 36.000 0.00 0.00 0.00 3.07
5046 6271 7.223584 TGTTACACAAGAGGAAATTCTGATGA 58.776 34.615 0.00 0.00 0.00 2.92
5047 6272 7.884877 TGTTACACAAGAGGAAATTCTGATGAT 59.115 33.333 0.00 0.00 0.00 2.45
5048 6273 6.754702 ACACAAGAGGAAATTCTGATGATG 57.245 37.500 0.00 0.00 0.00 3.07
5049 6274 6.479006 ACACAAGAGGAAATTCTGATGATGA 58.521 36.000 0.00 0.00 0.00 2.92
5050 6275 6.944290 ACACAAGAGGAAATTCTGATGATGAA 59.056 34.615 0.00 0.00 0.00 2.57
5051 6276 7.449395 ACACAAGAGGAAATTCTGATGATGAAA 59.551 33.333 0.00 0.00 0.00 2.69
5052 6277 8.467598 CACAAGAGGAAATTCTGATGATGAAAT 58.532 33.333 0.00 0.00 0.00 2.17
5053 6278 9.690913 ACAAGAGGAAATTCTGATGATGAAATA 57.309 29.630 0.00 0.00 0.00 1.40
5056 6281 9.917887 AGAGGAAATTCTGATGATGAAATAAGT 57.082 29.630 0.00 0.00 0.00 2.24
5064 6289 9.739276 TTCTGATGATGAAATAAGTAACCAAGT 57.261 29.630 0.00 0.00 0.00 3.16
5065 6290 9.166173 TCTGATGATGAAATAAGTAACCAAGTG 57.834 33.333 0.00 0.00 0.00 3.16
5066 6291 9.166173 CTGATGATGAAATAAGTAACCAAGTGA 57.834 33.333 0.00 0.00 0.00 3.41
5067 6292 9.166173 TGATGATGAAATAAGTAACCAAGTGAG 57.834 33.333 0.00 0.00 0.00 3.51
5068 6293 9.167311 GATGATGAAATAAGTAACCAAGTGAGT 57.833 33.333 0.00 0.00 0.00 3.41
5069 6294 8.918202 TGATGAAATAAGTAACCAAGTGAGTT 57.082 30.769 0.00 0.00 0.00 3.01
5089 6314 6.909895 TGAGTTACACACAAATGACAAAATCG 59.090 34.615 0.00 0.00 0.00 3.34
5090 6315 6.791303 AGTTACACACAAATGACAAAATCGT 58.209 32.000 0.00 0.00 0.00 3.73
5091 6316 6.690957 AGTTACACACAAATGACAAAATCGTG 59.309 34.615 0.00 0.00 0.00 4.35
5092 6317 5.242069 ACACACAAATGACAAAATCGTGA 57.758 34.783 0.00 0.00 0.00 4.35
5093 6318 5.830912 ACACACAAATGACAAAATCGTGAT 58.169 33.333 0.00 0.00 0.00 3.06
5094 6319 6.272318 ACACACAAATGACAAAATCGTGATT 58.728 32.000 0.00 0.00 0.00 2.57
5095 6320 6.756074 ACACACAAATGACAAAATCGTGATTT 59.244 30.769 2.04 2.04 42.35 2.17
5110 6335 9.793252 AAATCGTGATTTTGGAAAGATGAATAG 57.207 29.630 2.04 0.00 37.74 1.73
5111 6336 7.921786 TCGTGATTTTGGAAAGATGAATAGT 57.078 32.000 0.00 0.00 0.00 2.12
5112 6337 7.751732 TCGTGATTTTGGAAAGATGAATAGTG 58.248 34.615 0.00 0.00 0.00 2.74
5113 6338 6.470235 CGTGATTTTGGAAAGATGAATAGTGC 59.530 38.462 0.00 0.00 0.00 4.40
5114 6339 7.315142 GTGATTTTGGAAAGATGAATAGTGCA 58.685 34.615 0.00 0.00 0.00 4.57
5115 6340 7.977853 GTGATTTTGGAAAGATGAATAGTGCAT 59.022 33.333 0.00 0.00 0.00 3.96
5116 6341 7.977293 TGATTTTGGAAAGATGAATAGTGCATG 59.023 33.333 0.00 0.00 0.00 4.06
5117 6342 6.839124 TTTGGAAAGATGAATAGTGCATGT 57.161 33.333 0.00 0.00 0.00 3.21
5118 6343 7.936496 TTTGGAAAGATGAATAGTGCATGTA 57.064 32.000 0.00 0.00 0.00 2.29
5119 6344 8.523915 TTTGGAAAGATGAATAGTGCATGTAT 57.476 30.769 0.00 0.00 0.00 2.29
5120 6345 8.523915 TTGGAAAGATGAATAGTGCATGTATT 57.476 30.769 4.41 4.41 0.00 1.89
5121 6346 9.625747 TTGGAAAGATGAATAGTGCATGTATTA 57.374 29.630 0.00 0.00 0.00 0.98
5122 6347 9.797642 TGGAAAGATGAATAGTGCATGTATTAT 57.202 29.630 0.00 0.00 0.00 1.28
5174 6399 9.787532 TCATTTTTACATAGCTCAAATGCTTAC 57.212 29.630 0.00 0.00 43.74 2.34
5175 6400 9.793252 CATTTTTACATAGCTCAAATGCTTACT 57.207 29.630 0.00 0.00 43.74 2.24
5186 6411 7.857885 AGCTCAAATGCTTACTTATTTTATCGC 59.142 33.333 0.00 0.00 40.93 4.58
5187 6412 7.113544 GCTCAAATGCTTACTTATTTTATCGCC 59.886 37.037 0.00 0.00 0.00 5.54
5188 6413 7.990917 TCAAATGCTTACTTATTTTATCGCCA 58.009 30.769 0.00 0.00 0.00 5.69
5189 6414 8.462811 TCAAATGCTTACTTATTTTATCGCCAA 58.537 29.630 0.00 0.00 0.00 4.52
5190 6415 9.081997 CAAATGCTTACTTATTTTATCGCCAAA 57.918 29.630 0.00 0.00 0.00 3.28
5191 6416 8.628882 AATGCTTACTTATTTTATCGCCAAAC 57.371 30.769 0.00 0.00 0.00 2.93
5192 6417 7.385778 TGCTTACTTATTTTATCGCCAAACT 57.614 32.000 0.00 0.00 0.00 2.66
5193 6418 7.822658 TGCTTACTTATTTTATCGCCAAACTT 58.177 30.769 0.00 0.00 0.00 2.66
5194 6419 8.301002 TGCTTACTTATTTTATCGCCAAACTTT 58.699 29.630 0.00 0.00 0.00 2.66
5195 6420 9.777575 GCTTACTTATTTTATCGCCAAACTTTA 57.222 29.630 0.00 0.00 0.00 1.85
5198 6423 8.959734 ACTTATTTTATCGCCAAACTTTACAC 57.040 30.769 0.00 0.00 0.00 2.90
5199 6424 8.569641 ACTTATTTTATCGCCAAACTTTACACA 58.430 29.630 0.00 0.00 0.00 3.72
5200 6425 9.567848 CTTATTTTATCGCCAAACTTTACACAT 57.432 29.630 0.00 0.00 0.00 3.21
5201 6426 7.810766 ATTTTATCGCCAAACTTTACACATG 57.189 32.000 0.00 0.00 0.00 3.21
5202 6427 5.950758 TTATCGCCAAACTTTACACATGT 57.049 34.783 0.00 0.00 0.00 3.21
5203 6428 3.617540 TCGCCAAACTTTACACATGTG 57.382 42.857 24.25 24.25 0.00 3.21
5204 6429 2.946329 TCGCCAAACTTTACACATGTGT 59.054 40.909 32.47 32.47 46.87 3.72
5205 6430 4.127907 TCGCCAAACTTTACACATGTGTA 58.872 39.130 30.31 30.31 44.42 2.90
5220 6445 8.797350 ACACATGTGTAATATCCATCCATATG 57.203 34.615 29.66 0.00 42.90 1.78
5221 6446 8.605065 ACACATGTGTAATATCCATCCATATGA 58.395 33.333 29.66 0.00 42.90 2.15
5222 6447 9.623000 CACATGTGTAATATCCATCCATATGAT 57.377 33.333 18.03 0.00 34.84 2.45
5223 6448 9.842775 ACATGTGTAATATCCATCCATATGATC 57.157 33.333 3.65 0.00 34.84 2.92
5224 6449 9.841295 CATGTGTAATATCCATCCATATGATCA 57.159 33.333 3.65 0.00 34.84 2.92
5226 6451 9.841295 TGTGTAATATCCATCCATATGATCATG 57.159 33.333 18.72 3.77 34.84 3.07
5227 6452 9.842775 GTGTAATATCCATCCATATGATCATGT 57.157 33.333 18.72 8.98 34.84 3.21
5233 6458 7.803487 TCCATCCATATGATCATGTAGAACT 57.197 36.000 18.72 0.00 34.84 3.01
5234 6459 7.845037 TCCATCCATATGATCATGTAGAACTC 58.155 38.462 18.72 0.00 34.84 3.01
5235 6460 7.677319 TCCATCCATATGATCATGTAGAACTCT 59.323 37.037 18.72 0.00 34.84 3.24
5236 6461 8.319881 CCATCCATATGATCATGTAGAACTCTT 58.680 37.037 18.72 0.00 34.84 2.85
5237 6462 9.722184 CATCCATATGATCATGTAGAACTCTTT 57.278 33.333 18.72 0.00 34.84 2.52
5239 6464 9.770097 TCCATATGATCATGTAGAACTCTTTTC 57.230 33.333 18.72 0.00 0.00 2.29
5240 6465 9.775854 CCATATGATCATGTAGAACTCTTTTCT 57.224 33.333 18.72 0.00 0.00 2.52
5300 6525 7.817418 TTATAATAAAGTCCTCCAATGCACC 57.183 36.000 0.00 0.00 0.00 5.01
5301 6526 2.507407 TAAAGTCCTCCAATGCACCC 57.493 50.000 0.00 0.00 0.00 4.61
5302 6527 0.482446 AAAGTCCTCCAATGCACCCA 59.518 50.000 0.00 0.00 0.00 4.51
5303 6528 0.706433 AAGTCCTCCAATGCACCCAT 59.294 50.000 0.00 0.00 0.00 4.00
5304 6529 0.033796 AGTCCTCCAATGCACCCATG 60.034 55.000 0.00 0.00 0.00 3.66
5305 6530 0.323725 GTCCTCCAATGCACCCATGT 60.324 55.000 0.00 0.00 0.00 3.21
5306 6531 0.409092 TCCTCCAATGCACCCATGTT 59.591 50.000 0.00 0.00 0.00 2.71
5307 6532 0.819582 CCTCCAATGCACCCATGTTC 59.180 55.000 0.00 0.00 0.00 3.18
5308 6533 0.819582 CTCCAATGCACCCATGTTCC 59.180 55.000 0.00 0.00 0.00 3.62
5309 6534 0.113972 TCCAATGCACCCATGTTCCA 59.886 50.000 0.00 0.00 0.00 3.53
5310 6535 0.975135 CCAATGCACCCATGTTCCAA 59.025 50.000 0.00 0.00 0.00 3.53
5311 6536 1.347050 CCAATGCACCCATGTTCCAAA 59.653 47.619 0.00 0.00 0.00 3.28
5312 6537 2.224475 CCAATGCACCCATGTTCCAAAA 60.224 45.455 0.00 0.00 0.00 2.44
5313 6538 3.474600 CAATGCACCCATGTTCCAAAAA 58.525 40.909 0.00 0.00 0.00 1.94
5314 6539 4.073549 CAATGCACCCATGTTCCAAAAAT 58.926 39.130 0.00 0.00 0.00 1.82
5315 6540 3.399440 TGCACCCATGTTCCAAAAATC 57.601 42.857 0.00 0.00 0.00 2.17
5316 6541 2.038295 TGCACCCATGTTCCAAAAATCC 59.962 45.455 0.00 0.00 0.00 3.01
5317 6542 2.038295 GCACCCATGTTCCAAAAATCCA 59.962 45.455 0.00 0.00 0.00 3.41
5318 6543 3.663025 CACCCATGTTCCAAAAATCCAC 58.337 45.455 0.00 0.00 0.00 4.02
5319 6544 3.324556 CACCCATGTTCCAAAAATCCACT 59.675 43.478 0.00 0.00 0.00 4.00
5320 6545 3.578282 ACCCATGTTCCAAAAATCCACTC 59.422 43.478 0.00 0.00 0.00 3.51
5321 6546 3.834231 CCCATGTTCCAAAAATCCACTCT 59.166 43.478 0.00 0.00 0.00 3.24
5322 6547 4.284234 CCCATGTTCCAAAAATCCACTCTT 59.716 41.667 0.00 0.00 0.00 2.85
5323 6548 5.480073 CCCATGTTCCAAAAATCCACTCTTA 59.520 40.000 0.00 0.00 0.00 2.10
5324 6549 6.014669 CCCATGTTCCAAAAATCCACTCTTAA 60.015 38.462 0.00 0.00 0.00 1.85
5446 6671 3.243367 TGAGGCAATTTTCAAAGGTCGTG 60.243 43.478 0.00 0.00 0.00 4.35
5454 6679 0.318699 TCAAAGGTCGTGTGCTCTCG 60.319 55.000 3.99 3.99 0.00 4.04
5477 6702 2.144730 GCATTTTGCCTGTTTGCATCA 58.855 42.857 0.00 0.00 41.70 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 81 4.074970 GGACCCATGTGGCAATATTCTAG 58.925 47.826 0.00 0.00 37.83 2.43
143 145 9.671279 ATGACATATATAATTGCGAATTGAGGA 57.329 29.630 0.00 0.00 32.38 3.71
261 1266 7.874940 TGTAACTGAAAATCACTTTCTCATGG 58.125 34.615 0.00 0.00 43.42 3.66
454 1474 2.771763 AAGAGGAACAGCGCTCCGTG 62.772 60.000 7.13 0.00 38.08 4.94
455 1475 2.493907 GAAGAGGAACAGCGCTCCGT 62.494 60.000 7.13 0.00 38.08 4.69
456 1476 1.807573 GAAGAGGAACAGCGCTCCG 60.808 63.158 7.13 0.00 38.08 4.63
605 1625 1.682740 TGTGGATGGCGACGACTATA 58.317 50.000 0.65 0.00 0.00 1.31
644 1664 0.183971 GTGGATCTCCTCTCCTCGGA 59.816 60.000 0.00 0.00 36.82 4.55
755 1780 5.634020 CGATATCAGTCCCGGAAAGAAATAC 59.366 44.000 0.73 0.00 0.00 1.89
759 1784 3.067742 GTCGATATCAGTCCCGGAAAGAA 59.932 47.826 0.73 0.00 0.00 2.52
821 1846 2.440539 ACTGCAGTTAGAACTCCACG 57.559 50.000 15.25 0.00 37.08 4.94
953 1979 2.094182 CCAAGTAAGCAGCGAAGGACTA 60.094 50.000 0.00 0.00 0.00 2.59
973 1999 2.180017 CAGCCTCAACAATGCGCC 59.820 61.111 4.18 0.00 0.00 6.53
982 2008 4.335416 CCCATTAAAAGTCTCAGCCTCAA 58.665 43.478 0.00 0.00 0.00 3.02
997 2023 0.331278 CTCACCACCTGGCCCATTAA 59.669 55.000 0.00 0.00 39.32 1.40
1029 2055 7.276878 ACACAACCTTGTAAAATGTTAAAGCAC 59.723 33.333 0.00 0.00 39.91 4.40
1045 2071 1.299541 AAGACGAGCACACAACCTTG 58.700 50.000 0.00 0.00 0.00 3.61
1050 2077 3.575630 GTCAGATAAGACGAGCACACAA 58.424 45.455 0.00 0.00 0.00 3.33
1065 2092 1.203523 GAACAGGCTCAGTCGTCAGAT 59.796 52.381 0.00 0.00 0.00 2.90
1086 2113 0.617935 TCGTCATTTCAGGGGCATCA 59.382 50.000 0.00 0.00 0.00 3.07
1102 2129 1.001815 CGGAAACCTGCACAATTTCGT 60.002 47.619 6.52 0.00 33.91 3.85
1149 2176 1.365699 ACGTCGTGATTACCATTGCC 58.634 50.000 0.00 0.00 0.00 4.52
1209 2236 3.282021 GCATACCAATCAGGAGCTCAAA 58.718 45.455 17.19 0.00 41.22 2.69
1216 2243 2.016604 GCAACCGCATACCAATCAGGA 61.017 52.381 0.00 0.00 38.46 3.86
1263 2297 6.784473 GGATTTCCCTCCCATTCTTAATGATT 59.216 38.462 1.23 0.00 41.46 2.57
1275 2309 2.175499 CTGCAATAGGATTTCCCTCCCA 59.825 50.000 0.00 0.00 43.31 4.37
1326 2362 5.687780 TCTGGATTTGATACACAGCATGAT 58.312 37.500 0.00 0.00 39.69 2.45
1352 2467 5.304357 TCCAGTCGCATTTCTAAGATCCATA 59.696 40.000 0.00 0.00 0.00 2.74
1406 2521 4.346127 AGCAAGTGAGCACATATCCTGATA 59.654 41.667 3.19 0.00 36.85 2.15
1543 2664 1.669760 GTTTCCACACCGATGCCGA 60.670 57.895 0.00 0.00 38.22 5.54
1553 2674 4.888917 TGATACGTCATTGAGTTTCCACA 58.111 39.130 0.00 0.00 0.00 4.17
1602 2723 7.648142 CACAAGGAGCAAAATAACTCAAACTA 58.352 34.615 0.00 0.00 34.48 2.24
1690 2811 1.131883 GCATGCTCACCAAGACATGAC 59.868 52.381 11.37 0.00 39.69 3.06
1691 2812 1.271488 TGCATGCTCACCAAGACATGA 60.271 47.619 20.33 0.00 39.69 3.07
1749 2870 6.716628 AGCTTATCTTGAATTGGTGAGTGAAA 59.283 34.615 0.00 0.00 0.00 2.69
1750 2871 6.240894 AGCTTATCTTGAATTGGTGAGTGAA 58.759 36.000 0.00 0.00 0.00 3.18
1779 2900 8.774546 TGTTGCCATTATCATAAGGGAAATAA 57.225 30.769 12.46 0.00 33.18 1.40
1788 2909 6.992123 CACTACTCCTGTTGCCATTATCATAA 59.008 38.462 0.00 0.00 0.00 1.90
1794 2915 2.355716 GGCACTACTCCTGTTGCCATTA 60.356 50.000 6.58 0.00 41.63 1.90
1873 3013 4.142271 CCAGTTAAAAGCCTGACACACAAA 60.142 41.667 0.00 0.00 0.00 2.83
1899 3039 3.829601 TCCACCAATTGTGTTTATGGGAC 59.170 43.478 4.43 0.00 43.85 4.46
2081 3221 2.355108 GCAGATAGCCTGTGGAGAAACA 60.355 50.000 0.00 0.00 44.71 2.83
2227 3367 6.215636 ACATCCCAGTTGATCCTTTAGTAGTT 59.784 38.462 0.00 0.00 0.00 2.24
2244 3384 7.331026 ACCATCATAACGATTATACATCCCAG 58.669 38.462 0.00 0.00 29.21 4.45
2353 3493 5.394333 CGGGGGTTTCTTTTTGTTCTTTGTA 60.394 40.000 0.00 0.00 0.00 2.41
2393 3533 3.051581 ACTCCAGGTCGATAGTACCCTA 58.948 50.000 0.00 0.00 37.77 3.53
2403 3543 4.019501 AGTCTAAGTAGAACTCCAGGTCGA 60.020 45.833 0.00 0.00 33.47 4.20
2478 3618 6.069615 AGGTATGGTGATAAGTAAAAGGCTGT 60.070 38.462 0.00 0.00 0.00 4.40
2501 3641 2.119801 ACAGTGCTTAGCCATCAAGG 57.880 50.000 0.29 0.00 41.84 3.61
2519 3659 9.341899 CACCAAAGTTGAGTAATGCTTAATAAC 57.658 33.333 0.00 0.00 0.00 1.89
2552 3692 6.663523 CCAGTACTTTTGTTCCCCTGATAAAT 59.336 38.462 0.00 0.00 0.00 1.40
2782 3923 2.728690 TGTGGCAAATCAGCACATTC 57.271 45.000 0.00 0.00 35.83 2.67
2795 3936 3.382865 TGCACTAAACAGAAAATGTGGCA 59.617 39.130 0.00 0.00 43.00 4.92
2995 4136 6.940867 GGATTGGTCTTAAGAGTACTTTGGTT 59.059 38.462 5.12 0.00 37.53 3.67
2996 4137 6.473758 GGATTGGTCTTAAGAGTACTTTGGT 58.526 40.000 5.12 0.00 37.53 3.67
3003 4144 6.023603 AGTCAAGGGATTGGTCTTAAGAGTA 58.976 40.000 5.12 0.00 0.00 2.59
3101 4295 8.333186 CGTAGTAGTAAATTAAACCTTCCATGC 58.667 37.037 0.00 0.00 0.00 4.06
3151 4345 2.014335 TGCGTGGAGACAATCTGATG 57.986 50.000 0.00 0.00 46.06 3.07
3226 4420 9.717942 GATAATTCTCTGCCTATGTTTATCTGT 57.282 33.333 0.00 0.00 0.00 3.41
3347 4542 7.711772 TCAAACTAATCACCAAAGACTCGTTTA 59.288 33.333 0.00 0.00 0.00 2.01
3351 4546 5.107065 GGTCAAACTAATCACCAAAGACTCG 60.107 44.000 0.00 0.00 0.00 4.18
3352 4547 5.763204 TGGTCAAACTAATCACCAAAGACTC 59.237 40.000 0.00 0.00 35.93 3.36
3656 4853 2.126057 TGGCATACCTCCATGACATGA 58.874 47.619 17.24 2.55 39.06 3.07
3737 4934 7.837505 TCATCATCGTTGTATAAATTGACGTC 58.162 34.615 9.11 9.11 35.42 4.34
3803 5003 9.658475 CTTAATGTGACGAACAACTTTTTGATA 57.342 29.630 0.00 0.00 43.61 2.15
3922 5127 7.011482 GTCACATCTTGAAACAGACTAACAGTT 59.989 37.037 0.00 0.00 35.39 3.16
4240 5447 3.712016 TTAGGGCAAACAGCTGTCATA 57.288 42.857 21.95 6.69 44.79 2.15
4278 5485 4.223953 TCCTAATCTCCATCTGGGTACAC 58.776 47.826 0.00 0.00 38.11 2.90
4528 5738 5.338137 GGTGTACTTCAGTTACCAGGCTAAT 60.338 44.000 0.00 0.00 35.47 1.73
4529 5739 4.020839 GGTGTACTTCAGTTACCAGGCTAA 60.021 45.833 0.00 0.00 35.47 3.09
4659 5879 1.132643 CCCAGAACTCGAACCTAGACG 59.867 57.143 0.00 0.00 0.00 4.18
4661 5881 2.224942 TGTCCCAGAACTCGAACCTAGA 60.225 50.000 0.00 0.00 0.00 2.43
4683 5903 0.251922 AGTAAGGTGGCCGTCAGGTA 60.252 55.000 0.00 0.00 40.50 3.08
4786 6006 6.962311 ACATAAAGAGATAGGATGATGCCCTA 59.038 38.462 0.00 0.00 40.27 3.53
4831 6056 7.824289 AGCTGTGTGTAGTTGTCACATTATAAT 59.176 33.333 2.23 0.00 45.43 1.28
4883 6108 8.657387 TTTTTGGAACATCTTATATTGTGGGA 57.343 30.769 0.00 0.00 39.30 4.37
4911 6136 2.551912 GCACCCGTCCACCAAAGTG 61.552 63.158 0.00 0.00 44.12 3.16
4912 6137 2.203294 GCACCCGTCCACCAAAGT 60.203 61.111 0.00 0.00 0.00 2.66
4913 6138 1.178534 AATGCACCCGTCCACCAAAG 61.179 55.000 0.00 0.00 0.00 2.77
4914 6139 1.152652 AATGCACCCGTCCACCAAA 60.153 52.632 0.00 0.00 0.00 3.28
4915 6140 1.900981 CAATGCACCCGTCCACCAA 60.901 57.895 0.00 0.00 0.00 3.67
4916 6141 2.282110 CAATGCACCCGTCCACCA 60.282 61.111 0.00 0.00 0.00 4.17
4917 6142 3.061848 CCAATGCACCCGTCCACC 61.062 66.667 0.00 0.00 0.00 4.61
4918 6143 2.033448 TCCAATGCACCCGTCCAC 59.967 61.111 0.00 0.00 0.00 4.02
4919 6144 2.350895 CTCCAATGCACCCGTCCA 59.649 61.111 0.00 0.00 0.00 4.02
4920 6145 3.134127 GCTCCAATGCACCCGTCC 61.134 66.667 0.00 0.00 0.00 4.79
4921 6146 3.134127 GGCTCCAATGCACCCGTC 61.134 66.667 0.00 0.00 34.04 4.79
4922 6147 4.740822 GGGCTCCAATGCACCCGT 62.741 66.667 0.00 0.00 31.32 5.28
4924 6149 0.771127 TATAGGGCTCCAATGCACCC 59.229 55.000 0.00 0.00 43.17 4.61
4925 6150 2.887151 ATATAGGGCTCCAATGCACC 57.113 50.000 0.00 0.00 36.97 5.01
4926 6151 4.584325 TCAAAATATAGGGCTCCAATGCAC 59.416 41.667 0.00 0.00 36.44 4.57
4927 6152 4.802307 TCAAAATATAGGGCTCCAATGCA 58.198 39.130 0.00 0.00 34.04 3.96
4928 6153 5.789643 TTCAAAATATAGGGCTCCAATGC 57.210 39.130 0.00 0.00 0.00 3.56
4929 6154 8.517878 CACTATTCAAAATATAGGGCTCCAATG 58.482 37.037 0.00 0.00 31.30 2.82
4930 6155 8.227507 ACACTATTCAAAATATAGGGCTCCAAT 58.772 33.333 0.00 0.00 33.22 3.16
4931 6156 7.582719 ACACTATTCAAAATATAGGGCTCCAA 58.417 34.615 0.00 0.00 33.22 3.53
4932 6157 7.147391 TGACACTATTCAAAATATAGGGCTCCA 60.147 37.037 0.00 0.00 33.22 3.86
4933 6158 7.224297 TGACACTATTCAAAATATAGGGCTCC 58.776 38.462 0.00 0.00 33.22 4.70
4934 6159 8.677148 TTGACACTATTCAAAATATAGGGCTC 57.323 34.615 0.00 0.00 33.22 4.70
4935 6160 9.474313 TTTTGACACTATTCAAAATATAGGGCT 57.526 29.630 6.88 0.00 45.99 5.19
5022 6247 7.672983 TCATCAGAATTTCCTCTTGTGTAAC 57.327 36.000 0.00 0.00 37.35 2.50
5023 6248 8.102676 TCATCATCAGAATTTCCTCTTGTGTAA 58.897 33.333 0.00 0.00 0.00 2.41
5024 6249 7.623630 TCATCATCAGAATTTCCTCTTGTGTA 58.376 34.615 0.00 0.00 0.00 2.90
5025 6250 6.479006 TCATCATCAGAATTTCCTCTTGTGT 58.521 36.000 0.00 0.00 0.00 3.72
5026 6251 6.997239 TCATCATCAGAATTTCCTCTTGTG 57.003 37.500 0.00 0.00 0.00 3.33
5027 6252 8.591114 ATTTCATCATCAGAATTTCCTCTTGT 57.409 30.769 0.00 0.00 0.00 3.16
5030 6255 9.917887 ACTTATTTCATCATCAGAATTTCCTCT 57.082 29.630 0.00 0.00 0.00 3.69
5038 6263 9.739276 ACTTGGTTACTTATTTCATCATCAGAA 57.261 29.630 0.00 0.00 0.00 3.02
5039 6264 9.166173 CACTTGGTTACTTATTTCATCATCAGA 57.834 33.333 0.00 0.00 0.00 3.27
5040 6265 9.166173 TCACTTGGTTACTTATTTCATCATCAG 57.834 33.333 0.00 0.00 0.00 2.90
5041 6266 9.166173 CTCACTTGGTTACTTATTTCATCATCA 57.834 33.333 0.00 0.00 0.00 3.07
5042 6267 9.167311 ACTCACTTGGTTACTTATTTCATCATC 57.833 33.333 0.00 0.00 0.00 2.92
5043 6268 9.520515 AACTCACTTGGTTACTTATTTCATCAT 57.479 29.630 0.00 0.00 0.00 2.45
5044 6269 8.918202 AACTCACTTGGTTACTTATTTCATCA 57.082 30.769 0.00 0.00 0.00 3.07
5046 6271 9.787435 TGTAACTCACTTGGTTACTTATTTCAT 57.213 29.630 14.80 0.00 45.19 2.57
5047 6272 9.048446 GTGTAACTCACTTGGTTACTTATTTCA 57.952 33.333 14.80 0.00 45.19 2.69
5048 6273 9.048446 TGTGTAACTCACTTGGTTACTTATTTC 57.952 33.333 14.80 3.74 45.19 2.17
5049 6274 8.833493 GTGTGTAACTCACTTGGTTACTTATTT 58.167 33.333 14.80 0.00 45.19 1.40
5050 6275 7.988599 TGTGTGTAACTCACTTGGTTACTTATT 59.011 33.333 14.80 0.00 45.19 1.40
5051 6276 7.502696 TGTGTGTAACTCACTTGGTTACTTAT 58.497 34.615 14.80 0.00 45.19 1.73
5052 6277 6.876155 TGTGTGTAACTCACTTGGTTACTTA 58.124 36.000 14.80 4.70 45.19 2.24
5053 6278 5.736813 TGTGTGTAACTCACTTGGTTACTT 58.263 37.500 14.80 0.00 45.19 2.24
5054 6279 5.347620 TGTGTGTAACTCACTTGGTTACT 57.652 39.130 14.80 0.00 45.19 2.24
5055 6280 6.425577 TTTGTGTGTAACTCACTTGGTTAC 57.574 37.500 9.06 9.06 46.27 2.50
5056 6281 6.824196 TCATTTGTGTGTAACTCACTTGGTTA 59.176 34.615 6.18 0.00 46.27 2.85
5057 6282 5.650266 TCATTTGTGTGTAACTCACTTGGTT 59.350 36.000 6.18 0.00 46.27 3.67
5058 6283 5.065988 GTCATTTGTGTGTAACTCACTTGGT 59.934 40.000 6.18 0.00 46.27 3.67
5059 6284 5.065859 TGTCATTTGTGTGTAACTCACTTGG 59.934 40.000 6.18 0.00 46.27 3.61
5060 6285 6.117911 TGTCATTTGTGTGTAACTCACTTG 57.882 37.500 6.18 1.62 46.27 3.16
5061 6286 6.751514 TTGTCATTTGTGTGTAACTCACTT 57.248 33.333 6.18 0.00 46.27 3.16
5062 6287 6.751514 TTTGTCATTTGTGTGTAACTCACT 57.248 33.333 6.18 0.00 46.27 3.41
5063 6288 7.097047 CGATTTTGTCATTTGTGTGTAACTCAC 60.097 37.037 0.00 0.00 40.43 3.51
5064 6289 6.909895 CGATTTTGTCATTTGTGTGTAACTCA 59.090 34.615 0.00 0.00 38.75 3.41
5065 6290 6.910433 ACGATTTTGTCATTTGTGTGTAACTC 59.090 34.615 0.00 0.00 38.04 3.01
5066 6291 6.690957 CACGATTTTGTCATTTGTGTGTAACT 59.309 34.615 0.00 0.00 38.04 2.24
5067 6292 6.689241 TCACGATTTTGTCATTTGTGTGTAAC 59.311 34.615 0.00 0.00 37.35 2.50
5068 6293 6.786207 TCACGATTTTGTCATTTGTGTGTAA 58.214 32.000 0.00 0.00 0.00 2.41
5069 6294 6.364945 TCACGATTTTGTCATTTGTGTGTA 57.635 33.333 0.00 0.00 0.00 2.90
5070 6295 5.242069 TCACGATTTTGTCATTTGTGTGT 57.758 34.783 0.00 0.00 0.00 3.72
5071 6296 6.752335 AATCACGATTTTGTCATTTGTGTG 57.248 33.333 0.00 0.00 0.00 3.82
5072 6297 7.769272 AAAATCACGATTTTGTCATTTGTGT 57.231 28.000 15.19 0.00 45.99 3.72
5084 6309 9.793252 CTATTCATCTTTCCAAAATCACGATTT 57.207 29.630 0.00 0.00 42.35 2.17
5085 6310 8.960591 ACTATTCATCTTTCCAAAATCACGATT 58.039 29.630 0.00 0.00 0.00 3.34
5086 6311 8.400947 CACTATTCATCTTTCCAAAATCACGAT 58.599 33.333 0.00 0.00 0.00 3.73
5087 6312 7.626240 GCACTATTCATCTTTCCAAAATCACGA 60.626 37.037 0.00 0.00 0.00 4.35
5088 6313 6.470235 GCACTATTCATCTTTCCAAAATCACG 59.530 38.462 0.00 0.00 0.00 4.35
5089 6314 7.315142 TGCACTATTCATCTTTCCAAAATCAC 58.685 34.615 0.00 0.00 0.00 3.06
5090 6315 7.465353 TGCACTATTCATCTTTCCAAAATCA 57.535 32.000 0.00 0.00 0.00 2.57
5091 6316 7.977853 ACATGCACTATTCATCTTTCCAAAATC 59.022 33.333 0.00 0.00 0.00 2.17
5092 6317 7.844009 ACATGCACTATTCATCTTTCCAAAAT 58.156 30.769 0.00 0.00 0.00 1.82
5093 6318 7.230849 ACATGCACTATTCATCTTTCCAAAA 57.769 32.000 0.00 0.00 0.00 2.44
5094 6319 6.839124 ACATGCACTATTCATCTTTCCAAA 57.161 33.333 0.00 0.00 0.00 3.28
5095 6320 8.523915 AATACATGCACTATTCATCTTTCCAA 57.476 30.769 0.00 0.00 0.00 3.53
5096 6321 9.797642 ATAATACATGCACTATTCATCTTTCCA 57.202 29.630 0.00 0.00 0.00 3.53
5148 6373 9.787532 GTAAGCATTTGAGCTATGTAAAAATGA 57.212 29.630 9.87 0.00 45.89 2.57
5149 6374 9.793252 AGTAAGCATTTGAGCTATGTAAAAATG 57.207 29.630 0.00 0.00 45.89 2.32
5164 6389 8.627487 TTGGCGATAAAATAAGTAAGCATTTG 57.373 30.769 0.00 0.00 0.00 2.32
5165 6390 9.083080 GTTTGGCGATAAAATAAGTAAGCATTT 57.917 29.630 0.00 0.00 0.00 2.32
5166 6391 8.466798 AGTTTGGCGATAAAATAAGTAAGCATT 58.533 29.630 0.00 0.00 0.00 3.56
5167 6392 7.996385 AGTTTGGCGATAAAATAAGTAAGCAT 58.004 30.769 0.00 0.00 0.00 3.79
5168 6393 7.385778 AGTTTGGCGATAAAATAAGTAAGCA 57.614 32.000 0.00 0.00 0.00 3.91
5169 6394 8.683550 AAAGTTTGGCGATAAAATAAGTAAGC 57.316 30.769 0.00 0.00 0.00 3.09
5173 6398 8.569641 TGTGTAAAGTTTGGCGATAAAATAAGT 58.430 29.630 0.00 0.00 0.00 2.24
5174 6399 8.958175 TGTGTAAAGTTTGGCGATAAAATAAG 57.042 30.769 0.00 0.00 0.00 1.73
5175 6400 9.347934 CATGTGTAAAGTTTGGCGATAAAATAA 57.652 29.630 0.00 0.00 0.00 1.40
5176 6401 8.516234 ACATGTGTAAAGTTTGGCGATAAAATA 58.484 29.630 0.00 0.00 0.00 1.40
5177 6402 7.328249 CACATGTGTAAAGTTTGGCGATAAAAT 59.672 33.333 18.03 0.00 0.00 1.82
5178 6403 6.638873 CACATGTGTAAAGTTTGGCGATAAAA 59.361 34.615 18.03 0.00 0.00 1.52
5179 6404 6.146216 CACATGTGTAAAGTTTGGCGATAAA 58.854 36.000 18.03 0.00 0.00 1.40
5180 6405 5.239744 ACACATGTGTAAAGTTTGGCGATAA 59.760 36.000 29.66 0.00 42.90 1.75
5181 6406 4.757657 ACACATGTGTAAAGTTTGGCGATA 59.242 37.500 29.66 0.00 42.90 2.92
5182 6407 3.568007 ACACATGTGTAAAGTTTGGCGAT 59.432 39.130 29.66 0.00 42.90 4.58
5183 6408 2.946329 ACACATGTGTAAAGTTTGGCGA 59.054 40.909 29.66 0.00 42.90 5.54
5184 6409 3.347958 ACACATGTGTAAAGTTTGGCG 57.652 42.857 29.66 0.00 42.90 5.69
5194 6419 9.889128 CATATGGATGGATATTACACATGTGTA 57.111 33.333 30.31 30.31 44.42 2.90
5195 6420 8.605065 TCATATGGATGGATATTACACATGTGT 58.395 33.333 32.47 32.47 39.31 3.72
5196 6421 9.623000 ATCATATGGATGGATATTACACATGTG 57.377 33.333 24.25 24.25 34.06 3.21
5197 6422 9.842775 GATCATATGGATGGATATTACACATGT 57.157 33.333 2.13 0.00 36.00 3.21
5198 6423 9.841295 TGATCATATGGATGGATATTACACATG 57.159 33.333 2.13 0.00 36.00 3.21
5200 6425 9.841295 CATGATCATATGGATGGATATTACACA 57.159 33.333 8.15 0.00 36.00 3.72
5201 6426 9.842775 ACATGATCATATGGATGGATATTACAC 57.157 33.333 8.15 0.00 36.00 2.90
5207 6432 9.498039 AGTTCTACATGATCATATGGATGGATA 57.502 33.333 8.15 0.00 36.00 2.59
5208 6433 8.389979 AGTTCTACATGATCATATGGATGGAT 57.610 34.615 8.15 0.00 36.00 3.41
5209 6434 7.677319 AGAGTTCTACATGATCATATGGATGGA 59.323 37.037 8.15 0.00 36.00 3.41
5210 6435 7.849160 AGAGTTCTACATGATCATATGGATGG 58.151 38.462 8.15 0.00 36.00 3.51
5211 6436 9.722184 AAAGAGTTCTACATGATCATATGGATG 57.278 33.333 8.15 0.00 36.00 3.51
5213 6438 9.770097 GAAAAGAGTTCTACATGATCATATGGA 57.230 33.333 8.15 1.09 32.32 3.41
5214 6439 9.775854 AGAAAAGAGTTCTACATGATCATATGG 57.224 33.333 8.15 0.00 32.32 2.74
5274 6499 8.860088 GGTGCATTGGAGGACTTTATTATAAAT 58.140 33.333 0.00 0.00 0.00 1.40
5275 6500 7.286775 GGGTGCATTGGAGGACTTTATTATAAA 59.713 37.037 0.00 0.00 0.00 1.40
5276 6501 6.775629 GGGTGCATTGGAGGACTTTATTATAA 59.224 38.462 0.00 0.00 0.00 0.98
5277 6502 6.126332 TGGGTGCATTGGAGGACTTTATTATA 60.126 38.462 0.00 0.00 0.00 0.98
5278 6503 5.140454 GGGTGCATTGGAGGACTTTATTAT 58.860 41.667 0.00 0.00 0.00 1.28
5279 6504 4.017958 TGGGTGCATTGGAGGACTTTATTA 60.018 41.667 0.00 0.00 0.00 0.98
5280 6505 3.245586 TGGGTGCATTGGAGGACTTTATT 60.246 43.478 0.00 0.00 0.00 1.40
5281 6506 2.311542 TGGGTGCATTGGAGGACTTTAT 59.688 45.455 0.00 0.00 0.00 1.40
5282 6507 1.707989 TGGGTGCATTGGAGGACTTTA 59.292 47.619 0.00 0.00 0.00 1.85
5283 6508 0.482446 TGGGTGCATTGGAGGACTTT 59.518 50.000 0.00 0.00 0.00 2.66
5284 6509 0.706433 ATGGGTGCATTGGAGGACTT 59.294 50.000 0.00 0.00 0.00 3.01
5285 6510 0.033796 CATGGGTGCATTGGAGGACT 60.034 55.000 0.00 0.00 0.00 3.85
5286 6511 0.323725 ACATGGGTGCATTGGAGGAC 60.324 55.000 0.00 0.00 0.00 3.85
5287 6512 0.409092 AACATGGGTGCATTGGAGGA 59.591 50.000 0.00 0.00 0.00 3.71
5288 6513 0.819582 GAACATGGGTGCATTGGAGG 59.180 55.000 0.00 0.00 0.00 4.30
5289 6514 0.819582 GGAACATGGGTGCATTGGAG 59.180 55.000 0.00 0.00 0.00 3.86
5290 6515 0.113972 TGGAACATGGGTGCATTGGA 59.886 50.000 0.00 0.00 0.00 3.53
5291 6516 0.975135 TTGGAACATGGGTGCATTGG 59.025 50.000 0.00 0.00 39.30 3.16
5292 6517 2.835580 TTTGGAACATGGGTGCATTG 57.164 45.000 0.00 0.00 39.30 2.82
5293 6518 3.853355 TTTTTGGAACATGGGTGCATT 57.147 38.095 0.00 0.00 39.30 3.56
5294 6519 3.307621 GGATTTTTGGAACATGGGTGCAT 60.308 43.478 0.00 0.00 39.30 3.96
5295 6520 2.038295 GGATTTTTGGAACATGGGTGCA 59.962 45.455 0.00 0.00 39.30 4.57
5296 6521 2.038295 TGGATTTTTGGAACATGGGTGC 59.962 45.455 0.00 0.00 39.30 5.01
5297 6522 3.324556 AGTGGATTTTTGGAACATGGGTG 59.675 43.478 0.00 0.00 39.30 4.61
5298 6523 3.578282 GAGTGGATTTTTGGAACATGGGT 59.422 43.478 0.00 0.00 39.30 4.51
5299 6524 3.834231 AGAGTGGATTTTTGGAACATGGG 59.166 43.478 0.00 0.00 39.30 4.00
5300 6525 5.473066 AAGAGTGGATTTTTGGAACATGG 57.527 39.130 0.00 0.00 39.30 3.66
5301 6526 8.885494 TTTTAAGAGTGGATTTTTGGAACATG 57.115 30.769 0.00 0.00 39.30 3.21
5331 6556 3.583086 CCCTCGGTCCCACAATATAAGAT 59.417 47.826 0.00 0.00 0.00 2.40
5454 6679 0.236449 GCAAACAGGCAAAATGCTGC 59.764 50.000 2.00 0.00 44.28 5.25


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

AutoCloner maintained by Alex Coulton.