Multiple sequence alignment - TraesCS3D01G327500

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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 TraesCS3D01G327500 chr3D 100.000 5364 0 0 1 5364 439672623 439677986 0.000000e+00 9906
1 TraesCS3D01G327500 chr3D 99.031 1651 7 2 2130 3780 141540720 141539079 0.000000e+00 2952
2 TraesCS3D01G327500 chr3D 98.486 1651 15 3 2130 3780 141546904 141545264 0.000000e+00 2902
3 TraesCS3D01G327500 chr3D 98.701 1463 15 2 2318 3780 141563697 141562239 0.000000e+00 2593
4 TraesCS3D01G327500 chr3D 98.715 778 10 0 2566 3343 567166932 567166155 0.000000e+00 1382
5 TraesCS3D01G327500 chr3D 98.734 237 3 0 1991 2227 567167165 567166929 6.420000e-114 422
6 TraesCS3D01G327500 chr3B 92.297 4375 205 55 500 4824 576445223 576449515 0.000000e+00 6091
7 TraesCS3D01G327500 chr3B 90.311 547 40 4 4823 5360 576449613 576450155 0.000000e+00 704
8 TraesCS3D01G327500 chr3B 91.049 324 16 6 62 384 576444877 576445188 4.970000e-115 425
9 TraesCS3D01G327500 chr3A 91.807 2258 98 40 651 2856 579372974 579375196 0.000000e+00 3064
10 TraesCS3D01G327500 chr3A 92.303 1832 99 20 2841 4656 579375210 579377015 0.000000e+00 2564
11 TraesCS3D01G327500 chr3A 87.719 684 33 16 1 649 579372159 579372826 0.000000e+00 750
12 TraesCS3D01G327500 chr3A 90.311 547 38 5 4823 5360 579377262 579377802 0.000000e+00 702
13 TraesCS3D01G327500 chr7D 98.854 1658 17 2 2563 4220 141532783 141534438 0.000000e+00 2955
14 TraesCS3D01G327500 chr7D 98.903 1003 10 1 3218 4220 141540658 141541659 0.000000e+00 1790
15 TraesCS3D01G327500 chr7D 99.156 237 2 0 1991 2227 596365396 596365632 1.380000e-115 427
16 TraesCS3D01G327500 chr7D 98.312 237 4 0 1991 2227 141532553 141532789 2.990000e-112 416
17 TraesCS3D01G327500 chr5D 99.418 1546 8 1 2563 4108 28019631 28021175 0.000000e+00 2804
18 TraesCS3D01G327500 chr5D 98.734 237 3 0 1991 2227 28019401 28019637 6.420000e-114 422
19 TraesCS3D01G327500 chr1D 96.673 1653 24 9 2130 3780 46647748 46646125 0.000000e+00 2719
20 TraesCS3D01G327500 chr1D 99.042 1148 10 1 2634 3780 335749814 335748667 0.000000e+00 2058
21 TraesCS3D01G327500 chr1D 99.156 237 2 0 1991 2227 288349054 288349290 1.380000e-115 427
22 TraesCS3D01G327500 chr1D 100.000 90 0 0 1991 2080 26569548 26569459 3.320000e-37 167
23 TraesCS3D01G327500 chr6D 98.312 237 4 0 1991 2227 56369200 56369436 2.990000e-112 416


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 TraesCS3D01G327500 chr3D 439672623 439677986 5363 False 9906.000000 9906 100.0000 1 5364 1 chr3D.!!$F1 5363
1 TraesCS3D01G327500 chr3D 141539079 141540720 1641 True 2952.000000 2952 99.0310 2130 3780 1 chr3D.!!$R1 1650
2 TraesCS3D01G327500 chr3D 141545264 141546904 1640 True 2902.000000 2902 98.4860 2130 3780 1 chr3D.!!$R2 1650
3 TraesCS3D01G327500 chr3D 141562239 141563697 1458 True 2593.000000 2593 98.7010 2318 3780 1 chr3D.!!$R3 1462
4 TraesCS3D01G327500 chr3D 567166155 567167165 1010 True 902.000000 1382 98.7245 1991 3343 2 chr3D.!!$R4 1352
5 TraesCS3D01G327500 chr3B 576444877 576450155 5278 False 2406.666667 6091 91.2190 62 5360 3 chr3B.!!$F1 5298
6 TraesCS3D01G327500 chr3A 579372159 579377802 5643 False 1770.000000 3064 90.5350 1 5360 4 chr3A.!!$F1 5359
7 TraesCS3D01G327500 chr7D 141540658 141541659 1001 False 1790.000000 1790 98.9030 3218 4220 1 chr7D.!!$F1 1002
8 TraesCS3D01G327500 chr7D 141532553 141534438 1885 False 1685.500000 2955 98.5830 1991 4220 2 chr7D.!!$F3 2229
9 TraesCS3D01G327500 chr5D 28019401 28021175 1774 False 1613.000000 2804 99.0760 1991 4108 2 chr5D.!!$F1 2117
10 TraesCS3D01G327500 chr1D 46646125 46647748 1623 True 2719.000000 2719 96.6730 2130 3780 1 chr1D.!!$R2 1650
11 TraesCS3D01G327500 chr1D 335748667 335749814 1147 True 2058.000000 2058 99.0420 2634 3780 1 chr1D.!!$R3 1146

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
177 191 0.106819 CTGGCTTCTGCTTGGCCTAT 60.107 55.000 3.32 0.0 45.45 2.57 F
184 198 0.109342 CTGCTTGGCCTATGGTAGGG 59.891 60.000 3.32 0.0 46.32 3.53 F
212 226 0.251341 AGTGTGCTTTGGGATGGGAC 60.251 55.000 0.00 0.0 0.00 4.46 F
442 461 0.317160 TGTAGCAGGTTCAGTGTCCG 59.683 55.000 0.00 0.0 0.00 4.79 F
1583 1796 0.389391 AGTACCGATGGGAATCTGCG 59.611 55.000 0.00 0.0 36.97 5.18 F
1703 1917 1.351017 CCTTCCTTGCTGTCCAACCTA 59.649 52.381 0.00 0.0 0.00 3.08 F
1873 2092 2.105006 TCAGTTCATCAGGCTTCTGC 57.895 50.000 0.00 0.0 38.36 4.26 F
3972 4258 0.324614 TCGCAAAGGAGCAATCCTCA 59.675 50.000 0.00 0.0 42.62 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 1724 0.244994 CTAGCAGTGTCAGTTCGCCT 59.755 55.000 0.00 0.00 0.00 5.52 R
1686 1899 0.324943 GCTAGGTTGGACAGCAAGGA 59.675 55.000 0.00 0.00 35.35 3.36 R
1776 1995 3.700539 CACCTGGCATGACATATTTTCCA 59.299 43.478 0.00 0.00 0.00 3.53 R
1845 2064 4.900652 AGCCTGATGAACTGATGATAGACT 59.099 41.667 0.00 0.00 0.00 3.24 R
2968 3247 1.677576 TGACCTGCAAAGTTTGAGCTG 59.322 47.619 19.82 8.55 0.00 4.24 R
3428 3711 5.507985 GCTGCATAGGAACAAAGAACAGTTT 60.508 40.000 0.00 0.00 0.00 2.66 R
4277 4563 0.105224 TTGTCAAGGCCGTCGAAGAA 59.895 50.000 0.00 0.00 39.69 2.52 R
4878 5303 0.320771 GCCTGACGAGGTGACATGTT 60.321 55.000 0.00 0.00 42.15 2.71 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
50 51 3.603532 TCCAGTCTGAAGAATGTGATGC 58.396 45.455 0.00 0.00 38.35 3.91
177 191 0.106819 CTGGCTTCTGCTTGGCCTAT 60.107 55.000 3.32 0.00 45.45 2.57
181 195 1.134098 GCTTCTGCTTGGCCTATGGTA 60.134 52.381 3.32 0.00 36.03 3.25
184 198 0.109342 CTGCTTGGCCTATGGTAGGG 59.891 60.000 3.32 0.00 46.32 3.53
185 199 0.327095 TGCTTGGCCTATGGTAGGGA 60.327 55.000 3.32 0.00 46.32 4.20
186 200 1.068121 GCTTGGCCTATGGTAGGGAT 58.932 55.000 3.32 0.00 46.32 3.85
187 201 1.003696 GCTTGGCCTATGGTAGGGATC 59.996 57.143 3.32 0.00 46.32 3.36
206 220 1.071542 TCGATCAAGTGTGCTTTGGGA 59.928 47.619 0.00 0.00 31.49 4.37
208 222 2.159476 CGATCAAGTGTGCTTTGGGATG 60.159 50.000 0.00 0.00 31.49 3.51
209 223 1.619654 TCAAGTGTGCTTTGGGATGG 58.380 50.000 0.00 0.00 31.49 3.51
210 224 0.604578 CAAGTGTGCTTTGGGATGGG 59.395 55.000 0.00 0.00 31.49 4.00
211 225 0.482446 AAGTGTGCTTTGGGATGGGA 59.518 50.000 0.00 0.00 0.00 4.37
212 226 0.251341 AGTGTGCTTTGGGATGGGAC 60.251 55.000 0.00 0.00 0.00 4.46
264 278 5.486735 TCATTGGCATGTTTGGAATCTTT 57.513 34.783 0.00 0.00 0.00 2.52
305 323 2.362736 TGCCAAGAAGAGCTGCTATTG 58.637 47.619 15.02 11.06 0.00 1.90
335 353 2.684001 TGAGGTTACGCCAAGGTATG 57.316 50.000 0.00 0.00 40.61 2.39
346 364 3.470645 CCAAGGTATGGTGCTACTACC 57.529 52.381 0.00 0.00 44.85 3.18
374 393 2.087646 GGATCTTGTCTGGCACCTTTC 58.912 52.381 0.00 0.00 0.00 2.62
422 441 3.467803 ACTGAGAAAGTTCTTCAACGGG 58.532 45.455 0.00 0.00 37.73 5.28
425 444 3.203716 GAGAAAGTTCTTCAACGGGTGT 58.796 45.455 0.00 0.00 37.73 4.16
442 461 0.317160 TGTAGCAGGTTCAGTGTCCG 59.683 55.000 0.00 0.00 0.00 4.79
469 488 3.071575 GCATTTTGCTGCCCCCTT 58.928 55.556 0.00 0.00 40.96 3.95
472 491 0.397564 CATTTTGCTGCCCCCTTGTT 59.602 50.000 0.00 0.00 0.00 2.83
473 492 0.397564 ATTTTGCTGCCCCCTTGTTG 59.602 50.000 0.00 0.00 0.00 3.33
621 657 0.471022 TGTGTCCTGTCTGCCCACTA 60.471 55.000 0.00 0.00 0.00 2.74
627 663 2.269241 GTCTGCCCACTAGCCACC 59.731 66.667 0.00 0.00 0.00 4.61
649 686 4.322801 CCCGATGGATACTCCCTGATAAAC 60.323 50.000 0.00 0.00 35.03 2.01
651 688 5.046304 CCGATGGATACTCCCTGATAAACAT 60.046 44.000 0.00 0.00 35.03 2.71
653 690 7.310423 CCGATGGATACTCCCTGATAAACATTA 60.310 40.741 0.00 0.00 35.03 1.90
654 691 8.260818 CGATGGATACTCCCTGATAAACATTAT 58.739 37.037 0.00 0.00 35.03 1.28
655 692 9.965902 GATGGATACTCCCTGATAAACATTATT 57.034 33.333 0.00 0.00 35.03 1.40
699 882 1.610522 GCACATGCAGGACTTTGTTCT 59.389 47.619 4.84 0.00 41.59 3.01
703 886 2.928801 TGCAGGACTTTGTTCTAGCA 57.071 45.000 0.00 0.00 0.00 3.49
704 887 3.423539 TGCAGGACTTTGTTCTAGCAT 57.576 42.857 0.00 0.00 0.00 3.79
706 889 3.077359 GCAGGACTTTGTTCTAGCATGT 58.923 45.455 0.00 0.00 0.00 3.21
728 916 4.785301 TGGAGAATCAATCCACAGAATCC 58.215 43.478 0.00 0.00 41.96 3.01
732 920 4.406972 AGAATCAATCCACAGAATCCTCGA 59.593 41.667 0.00 0.00 0.00 4.04
763 951 1.604604 CACACCGTGAAAATGACCCT 58.395 50.000 5.28 0.00 35.23 4.34
812 1000 2.113139 AAGTCAACAGCCCGTGGG 59.887 61.111 0.00 0.00 38.57 4.61
841 1030 3.567397 AGATTATCCGGATAGATCGGGG 58.433 50.000 22.88 4.54 46.78 5.73
849 1038 2.377628 GATAGATCGGGGCGCACCAA 62.378 60.000 31.47 12.33 42.91 3.67
871 1060 2.095059 CCAATCCGGAGCTTTTCTGTTG 60.095 50.000 11.34 5.96 36.56 3.33
995 1189 4.211330 TTGGAAAGTGGCGGCCCA 62.211 61.111 17.97 2.62 39.32 5.36
1103 1309 2.815647 CGCCCCGCTTCTTCTCAC 60.816 66.667 0.00 0.00 0.00 3.51
1108 1314 0.790814 CCCGCTTCTTCTCACGTTTC 59.209 55.000 0.00 0.00 0.00 2.78
1111 1317 2.096713 CCGCTTCTTCTCACGTTTCTTG 60.097 50.000 0.00 0.00 0.00 3.02
1112 1318 2.540101 CGCTTCTTCTCACGTTTCTTGT 59.460 45.455 0.00 0.00 0.00 3.16
1114 1320 4.494199 CGCTTCTTCTCACGTTTCTTGTTT 60.494 41.667 0.00 0.00 0.00 2.83
1116 1322 5.447279 GCTTCTTCTCACGTTTCTTGTTTGA 60.447 40.000 0.00 0.00 0.00 2.69
1119 1325 7.780008 TCTTCTCACGTTTCTTGTTTGATTA 57.220 32.000 0.00 0.00 0.00 1.75
1120 1326 7.627340 TCTTCTCACGTTTCTTGTTTGATTAC 58.373 34.615 0.00 0.00 0.00 1.89
1121 1327 5.969741 TCTCACGTTTCTTGTTTGATTACG 58.030 37.500 0.00 0.00 33.57 3.18
1122 1328 4.520078 TCACGTTTCTTGTTTGATTACGC 58.480 39.130 0.00 0.00 31.86 4.42
1157 1368 1.538075 CTTACGCGGTTGGATTTTGGT 59.462 47.619 12.47 0.00 0.00 3.67
1158 1369 1.606903 TACGCGGTTGGATTTTGGTT 58.393 45.000 12.47 0.00 0.00 3.67
1455 1666 3.777925 GCTGCGCACACCTGTACG 61.778 66.667 5.66 0.00 37.82 3.67
1456 1667 2.049526 CTGCGCACACCTGTACGA 60.050 61.111 5.66 0.00 36.98 3.43
1457 1668 2.049526 TGCGCACACCTGTACGAG 60.050 61.111 5.66 0.00 36.98 4.18
1458 1669 3.479269 GCGCACACCTGTACGAGC 61.479 66.667 0.30 0.00 36.98 5.03
1459 1670 2.258591 CGCACACCTGTACGAGCT 59.741 61.111 0.00 0.00 36.98 4.09
1460 1671 1.504900 CGCACACCTGTACGAGCTA 59.495 57.895 0.00 0.00 36.98 3.32
1461 1672 0.797249 CGCACACCTGTACGAGCTAC 60.797 60.000 0.00 0.00 36.98 3.58
1513 1724 1.815613 TGCTGCCGCTGCTTATTTTAA 59.184 42.857 21.13 0.00 38.71 1.52
1536 1747 1.623359 GAACTGACACTGCTAGCTCG 58.377 55.000 17.23 9.58 0.00 5.03
1583 1796 0.389391 AGTACCGATGGGAATCTGCG 59.611 55.000 0.00 0.00 36.97 5.18
1613 1826 7.811713 ACAGTAAACGGTAGATTTAGACTGTTC 59.188 37.037 0.00 0.00 42.89 3.18
1666 1879 2.997986 CCTTTGGCATGAAGTGAAATGC 59.002 45.455 0.00 0.00 46.80 3.56
1703 1917 1.351017 CCTTCCTTGCTGTCCAACCTA 59.649 52.381 0.00 0.00 0.00 3.08
1715 1929 5.592688 GCTGTCCAACCTAGCCAATTAATTA 59.407 40.000 0.00 0.00 0.00 1.40
1720 1934 8.568794 GTCCAACCTAGCCAATTAATTATCTTC 58.431 37.037 0.00 0.00 0.00 2.87
1725 1939 9.700831 ACCTAGCCAATTAATTATCTTCTGTTT 57.299 29.630 0.00 0.00 0.00 2.83
1776 1995 4.011966 TGTCAGAGTGATTGATGCAACT 57.988 40.909 0.00 0.00 0.00 3.16
1820 2039 7.395489 AGGTGATTTCTTGCAATAGTTCTGAAT 59.605 33.333 0.00 0.00 0.00 2.57
1821 2040 8.677300 GGTGATTTCTTGCAATAGTTCTGAATA 58.323 33.333 0.00 0.00 0.00 1.75
1822 2041 9.495754 GTGATTTCTTGCAATAGTTCTGAATAC 57.504 33.333 0.00 0.00 0.00 1.89
1873 2092 2.105006 TCAGTTCATCAGGCTTCTGC 57.895 50.000 0.00 0.00 38.36 4.26
2193 2412 5.111989 TCTTCTGCATTCTTGGACTATTCG 58.888 41.667 0.00 0.00 0.00 3.34
3428 3711 3.737559 ACATCCCTTGAATAAGCACCA 57.262 42.857 0.00 0.00 32.40 4.17
3972 4258 0.324614 TCGCAAAGGAGCAATCCTCA 59.675 50.000 0.00 0.00 42.62 3.86
4361 4647 2.672307 GTGAGGCTGCTGCTGCTT 60.672 61.111 26.79 21.66 40.48 3.91
4362 4648 1.376424 GTGAGGCTGCTGCTGCTTA 60.376 57.895 26.79 13.28 40.48 3.09
4363 4649 0.957395 GTGAGGCTGCTGCTGCTTAA 60.957 55.000 26.79 13.39 40.48 1.85
4364 4650 0.957395 TGAGGCTGCTGCTGCTTAAC 60.957 55.000 26.79 16.81 40.48 2.01
4365 4651 0.676151 GAGGCTGCTGCTGCTTAACT 60.676 55.000 26.79 17.10 40.48 2.24
4391 4685 2.191375 CGGCTGGTCTCATGGCAT 59.809 61.111 0.00 0.00 0.00 4.40
4394 4688 1.225426 GCTGGTCTCATGGCATCCA 59.775 57.895 0.00 0.61 38.19 3.41
4505 4800 5.680619 ACAATCTGCCTCGTTTATATCCAA 58.319 37.500 0.00 0.00 0.00 3.53
4511 4806 5.361427 TGCCTCGTTTATATCCAAATTCGA 58.639 37.500 0.00 0.00 0.00 3.71
4617 4912 1.919918 GGGAAATTGCAAATTCGCTCG 59.080 47.619 27.81 0.00 36.07 5.03
4620 4915 3.492313 GAAATTGCAAATTCGCTCGAGT 58.508 40.909 15.13 0.00 0.00 4.18
4623 4918 2.594529 TGCAAATTCGCTCGAGTTTC 57.405 45.000 15.13 0.00 32.90 2.78
4626 4921 1.126846 CAAATTCGCTCGAGTTTCGCT 59.873 47.619 15.13 0.00 40.21 4.93
4627 4922 0.716108 AATTCGCTCGAGTTTCGCTG 59.284 50.000 15.13 0.00 40.21 5.18
4629 4924 1.275471 TTCGCTCGAGTTTCGCTGTG 61.275 55.000 15.13 0.00 40.21 3.66
4632 4927 1.618640 GCTCGAGTTTCGCTGTGTCC 61.619 60.000 15.13 0.00 40.21 4.02
4647 4942 4.697352 GCTGTGTCCTGATGTCAAATAAGT 59.303 41.667 0.00 0.00 0.00 2.24
4650 4945 6.969366 TGTGTCCTGATGTCAAATAAGTTTG 58.031 36.000 0.00 0.00 44.81 2.93
4653 4948 5.710099 GTCCTGATGTCAAATAAGTTTGGGA 59.290 40.000 1.55 0.00 43.85 4.37
4654 4949 5.945784 TCCTGATGTCAAATAAGTTTGGGAG 59.054 40.000 1.55 0.00 43.85 4.30
4655 4950 5.711976 CCTGATGTCAAATAAGTTTGGGAGT 59.288 40.000 1.55 0.00 43.85 3.85
4656 4951 6.127897 CCTGATGTCAAATAAGTTTGGGAGTC 60.128 42.308 1.55 0.00 43.85 3.36
4658 4953 6.430925 TGATGTCAAATAAGTTTGGGAGTCTG 59.569 38.462 1.55 0.00 43.85 3.51
4659 4954 5.070001 TGTCAAATAAGTTTGGGAGTCTGG 58.930 41.667 1.55 0.00 43.85 3.86
4660 4955 4.079253 TCAAATAAGTTTGGGAGTCTGGC 58.921 43.478 1.55 0.00 43.85 4.85
4661 4956 3.806949 AATAAGTTTGGGAGTCTGGCA 57.193 42.857 0.00 0.00 0.00 4.92
4664 4959 0.550914 AGTTTGGGAGTCTGGCACAA 59.449 50.000 0.00 0.00 38.70 3.33
4665 4960 0.668535 GTTTGGGAGTCTGGCACAAC 59.331 55.000 0.00 0.00 38.70 3.32
4667 4962 0.550914 TTGGGAGTCTGGCACAACTT 59.449 50.000 0.00 0.00 38.70 2.66
4668 4963 0.108585 TGGGAGTCTGGCACAACTTC 59.891 55.000 0.00 0.00 38.70 3.01
4670 4965 0.108585 GGAGTCTGGCACAACTTCCA 59.891 55.000 0.00 0.00 38.70 3.53
4674 4969 3.658398 CTGGCACAACTTCCAGGAT 57.342 52.632 0.00 0.00 44.64 3.24
4675 4970 1.457346 CTGGCACAACTTCCAGGATC 58.543 55.000 0.00 0.00 44.64 3.36
4677 4972 1.355381 TGGCACAACTTCCAGGATCAT 59.645 47.619 0.00 0.00 31.92 2.45
4678 4973 2.575735 TGGCACAACTTCCAGGATCATA 59.424 45.455 0.00 0.00 31.92 2.15
4679 4974 3.209410 GGCACAACTTCCAGGATCATAG 58.791 50.000 0.00 0.00 0.00 2.23
4681 4976 4.265073 GCACAACTTCCAGGATCATAGTT 58.735 43.478 0.00 0.00 0.00 2.24
4683 4978 6.058183 GCACAACTTCCAGGATCATAGTTAT 58.942 40.000 4.23 0.00 0.00 1.89
4684 4979 7.217200 GCACAACTTCCAGGATCATAGTTATA 58.783 38.462 4.23 0.00 0.00 0.98
4685 4980 7.171678 GCACAACTTCCAGGATCATAGTTATAC 59.828 40.741 4.23 0.00 0.00 1.47
4686 4981 7.657761 CACAACTTCCAGGATCATAGTTATACC 59.342 40.741 4.23 0.00 0.00 2.73
4687 4982 7.347222 ACAACTTCCAGGATCATAGTTATACCA 59.653 37.037 4.23 0.00 0.00 3.25
4688 4983 7.546250 ACTTCCAGGATCATAGTTATACCAG 57.454 40.000 0.00 0.00 0.00 4.00
4691 4986 7.782897 TCCAGGATCATAGTTATACCAGAAG 57.217 40.000 0.00 0.00 0.00 2.85
4692 4987 6.211584 TCCAGGATCATAGTTATACCAGAAGC 59.788 42.308 0.00 0.00 0.00 3.86
4693 4988 6.014242 CCAGGATCATAGTTATACCAGAAGCA 60.014 42.308 0.00 0.00 0.00 3.91
4694 4989 6.870965 CAGGATCATAGTTATACCAGAAGCAC 59.129 42.308 0.00 0.00 0.00 4.40
4695 4990 6.554982 AGGATCATAGTTATACCAGAAGCACA 59.445 38.462 0.00 0.00 0.00 4.57
4697 4992 5.588240 TCATAGTTATACCAGAAGCACACG 58.412 41.667 0.00 0.00 0.00 4.49
4698 4993 3.955650 AGTTATACCAGAAGCACACGT 57.044 42.857 0.00 0.00 0.00 4.49
4699 4994 4.267349 AGTTATACCAGAAGCACACGTT 57.733 40.909 0.00 0.00 0.00 3.99
4700 4995 5.395682 AGTTATACCAGAAGCACACGTTA 57.604 39.130 0.00 0.00 0.00 3.18
4701 4996 5.974108 AGTTATACCAGAAGCACACGTTAT 58.026 37.500 0.00 0.00 0.00 1.89
4702 4997 7.104043 AGTTATACCAGAAGCACACGTTATA 57.896 36.000 0.00 0.00 0.00 0.98
4703 4998 7.549839 AGTTATACCAGAAGCACACGTTATAA 58.450 34.615 0.00 0.00 0.00 0.98
4704 4999 7.490402 AGTTATACCAGAAGCACACGTTATAAC 59.510 37.037 5.47 5.47 0.00 1.89
4705 5000 3.997762 ACCAGAAGCACACGTTATAACA 58.002 40.909 15.67 0.00 0.00 2.41
4706 5001 3.994392 ACCAGAAGCACACGTTATAACAG 59.006 43.478 15.67 9.51 0.00 3.16
4707 5002 3.370978 CCAGAAGCACACGTTATAACAGG 59.629 47.826 15.67 8.85 0.00 4.00
4708 5003 3.000727 AGAAGCACACGTTATAACAGGC 58.999 45.455 15.67 11.77 0.00 4.85
4709 5004 2.465860 AGCACACGTTATAACAGGCA 57.534 45.000 15.67 0.00 0.00 4.75
4710 5005 2.073816 AGCACACGTTATAACAGGCAC 58.926 47.619 15.67 2.19 0.00 5.01
4711 5006 1.801771 GCACACGTTATAACAGGCACA 59.198 47.619 15.67 0.00 0.00 4.57
4712 5007 2.159707 GCACACGTTATAACAGGCACAG 60.160 50.000 15.67 0.21 0.00 3.66
4713 5008 3.064207 CACACGTTATAACAGGCACAGT 58.936 45.455 15.67 0.81 0.00 3.55
4714 5009 3.496884 CACACGTTATAACAGGCACAGTT 59.503 43.478 15.67 0.00 41.93 3.16
4723 5018 6.861065 ATAACAGGCACAGTTATAATTCGG 57.139 37.500 7.83 0.00 46.59 4.30
4737 5032 1.239296 ATTCGGATGATGCATGCCCG 61.239 55.000 21.80 21.80 41.36 6.13
4756 5051 3.555966 CCGCTAAAAAGGGAATGAGGAT 58.444 45.455 0.00 0.00 0.00 3.24
4773 5068 6.564709 TGAGGATGATCACACTTCTTTTTG 57.435 37.500 0.00 0.00 0.00 2.44
4774 5069 6.064060 TGAGGATGATCACACTTCTTTTTGT 58.936 36.000 0.00 0.00 0.00 2.83
4775 5070 6.016860 TGAGGATGATCACACTTCTTTTTGTG 60.017 38.462 0.00 0.00 43.82 3.33
4830 5253 1.742761 CGTGATCCATGAACTTGGCT 58.257 50.000 0.00 0.00 36.66 4.75
4838 5261 4.214310 TCCATGAACTTGGCTTTTCTTCA 58.786 39.130 0.00 0.00 36.66 3.02
4857 5280 6.411376 TCTTCAAAAGAACAGAACTGGTGTA 58.589 36.000 6.76 0.00 33.83 2.90
4878 5303 9.383519 GGTGTAGAGATGTTTATGAATCTGAAA 57.616 33.333 0.00 0.00 33.26 2.69
4891 5316 4.452114 TGAATCTGAAAACATGTCACCTCG 59.548 41.667 0.00 0.00 0.00 4.63
4898 5323 1.807165 CATGTCACCTCGTCAGGCG 60.807 63.158 0.00 0.00 45.05 5.52
4904 5329 1.379443 ACCTCGTCAGGCGGTATGA 60.379 57.895 0.00 0.00 45.05 2.15
4932 5357 5.601583 TTAGGCGATTATACACCACAAGA 57.398 39.130 0.00 0.00 0.00 3.02
4946 5379 5.645067 ACACCACAAGAACATCACATCATAG 59.355 40.000 0.00 0.00 0.00 2.23
4955 5388 7.799081 AGAACATCACATCATAGGATCTCAAA 58.201 34.615 0.00 0.00 0.00 2.69
4971 5404 9.638176 AGGATCTCAAATTATTCTGCAAGTATT 57.362 29.630 0.00 0.00 33.76 1.89
4996 5430 4.761227 ACATCCCCATGTTTTCAAAAATGC 59.239 37.500 0.00 0.00 40.66 3.56
5010 5444 6.125327 TCAAAAATGCTACGAACTTGTTCA 57.875 33.333 13.05 0.00 0.00 3.18
5018 5452 5.178623 TGCTACGAACTTGTTCAATAGTTGG 59.821 40.000 13.05 0.00 34.88 3.77
5023 5457 8.161699 ACGAACTTGTTCAATAGTTGGTAATT 57.838 30.769 13.05 0.00 40.16 1.40
5061 5495 4.498682 GGCAGCAATATCCACTGAACATTC 60.499 45.833 0.00 0.00 33.10 2.67
5062 5496 4.096833 GCAGCAATATCCACTGAACATTCA 59.903 41.667 4.29 0.00 33.10 2.57
5070 5504 4.647611 TCCACTGAACATTCACCGTAAAT 58.352 39.130 0.00 0.00 32.90 1.40
5071 5505 4.454161 TCCACTGAACATTCACCGTAAATG 59.546 41.667 0.00 0.00 39.50 2.32
5098 5532 5.066117 CCTGACATGATTCTGATCCAAACTG 59.934 44.000 0.00 0.00 0.00 3.16
5105 5539 1.699656 CTGATCCAAACTGCTCGCCG 61.700 60.000 0.00 0.00 0.00 6.46
5119 5553 3.120792 GCTCGCCGATACAAGAACATTA 58.879 45.455 0.00 0.00 0.00 1.90
5169 5603 1.366319 ATTCCTATGGGGCTGGCTAG 58.634 55.000 0.00 0.00 34.39 3.42
5171 5605 0.864659 TCCTATGGGGCTGGCTAGTA 59.135 55.000 0.00 0.00 34.39 1.82
5185 5619 5.394224 GCTGGCTAGTACAACACTCAAGATA 60.394 44.000 0.00 0.00 38.80 1.98
5189 5623 5.517054 GCTAGTACAACACTCAAGATACAGC 59.483 44.000 0.00 0.00 38.80 4.40
5200 5634 8.924303 ACACTCAAGATACAGCACCTAATATTA 58.076 33.333 0.00 0.00 0.00 0.98
5201 5635 9.935241 CACTCAAGATACAGCACCTAATATTAT 57.065 33.333 0.00 0.00 0.00 1.28
5318 5752 0.740164 CAAGCAGAGCTCGTGCAGAT 60.740 55.000 28.21 17.02 43.82 2.90
5360 5794 0.108945 GCATCTGCTGAAGGGTTTGC 60.109 55.000 0.00 0.00 38.21 3.68
5361 5795 1.250328 CATCTGCTGAAGGGTTTGCA 58.750 50.000 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 4.622457 GCATCACATTCTTCAGACTGGAGA 60.622 45.833 9.58 9.58 0.00 3.71
33 34 3.126514 CACAGGCATCACATTCTTCAGAC 59.873 47.826 0.00 0.00 0.00 3.51
50 51 2.069273 CTTCGTTGGTAGCTTCACAGG 58.931 52.381 0.00 0.00 0.00 4.00
177 191 2.430694 CACACTTGATCGATCCCTACCA 59.569 50.000 22.31 0.19 0.00 3.25
181 195 1.198713 AGCACACTTGATCGATCCCT 58.801 50.000 22.31 1.94 0.00 4.20
184 198 2.096496 CCCAAAGCACACTTGATCGATC 59.904 50.000 18.72 18.72 35.85 3.69
185 199 2.086869 CCCAAAGCACACTTGATCGAT 58.913 47.619 0.00 0.00 35.85 3.59
186 200 1.071542 TCCCAAAGCACACTTGATCGA 59.928 47.619 0.00 0.00 35.85 3.59
187 201 1.522668 TCCCAAAGCACACTTGATCG 58.477 50.000 0.00 0.00 35.85 3.69
206 220 0.987294 CAAGTCAGGAGTGGTCCCAT 59.013 55.000 0.00 0.00 45.26 4.00
208 222 1.679898 CCAAGTCAGGAGTGGTCCC 59.320 63.158 0.00 0.00 45.26 4.46
209 223 1.003233 GCCAAGTCAGGAGTGGTCC 60.003 63.158 0.00 0.00 44.33 4.46
210 224 0.108585 TTGCCAAGTCAGGAGTGGTC 59.891 55.000 0.00 0.00 0.00 4.02
211 225 0.179018 GTTGCCAAGTCAGGAGTGGT 60.179 55.000 0.00 0.00 0.00 4.16
212 226 0.179020 TGTTGCCAAGTCAGGAGTGG 60.179 55.000 0.00 0.00 0.00 4.00
283 301 2.795231 TAGCAGCTCTTCTTGGCATT 57.205 45.000 0.00 0.00 0.00 3.56
335 353 3.097614 TCCTTCTTCTGGTAGTAGCACC 58.902 50.000 0.00 0.00 39.20 5.01
337 355 4.873010 AGATCCTTCTTCTGGTAGTAGCA 58.127 43.478 1.44 1.44 0.00 3.49
338 356 5.128008 ACAAGATCCTTCTTCTGGTAGTAGC 59.872 44.000 0.00 0.00 40.28 3.58
339 357 6.605594 AGACAAGATCCTTCTTCTGGTAGTAG 59.394 42.308 0.00 0.00 40.28 2.57
346 364 3.269178 GCCAGACAAGATCCTTCTTCTG 58.731 50.000 0.00 0.00 40.28 3.02
393 412 0.959553 AACTTTCTCAGTCGCCTCGA 59.040 50.000 0.00 0.00 32.94 4.04
394 413 1.068194 AGAACTTTCTCAGTCGCCTCG 60.068 52.381 0.00 0.00 32.94 4.63
422 441 1.797025 GGACACTGAACCTGCTACAC 58.203 55.000 0.00 0.00 0.00 2.90
425 444 1.292223 GCGGACACTGAACCTGCTA 59.708 57.895 0.00 0.00 0.00 3.49
442 461 1.153958 GCAAAATGCCTGGAGACGC 60.154 57.895 0.00 0.00 37.42 5.19
636 673 9.753674 TTCTGAAAATAATGTTTATCAGGGAGT 57.246 29.630 11.41 0.00 35.99 3.85
649 686 8.571336 AGACCAAGTTCACTTCTGAAAATAATG 58.429 33.333 0.00 0.00 38.17 1.90
651 688 9.621629 TTAGACCAAGTTCACTTCTGAAAATAA 57.378 29.630 0.00 0.00 38.17 1.40
653 690 8.519799 TTTAGACCAAGTTCACTTCTGAAAAT 57.480 30.769 0.00 0.00 38.17 1.82
654 691 7.415206 GCTTTAGACCAAGTTCACTTCTGAAAA 60.415 37.037 0.00 0.00 38.17 2.29
655 692 6.038271 GCTTTAGACCAAGTTCACTTCTGAAA 59.962 38.462 0.00 0.00 38.17 2.69
657 694 5.057149 GCTTTAGACCAAGTTCACTTCTGA 58.943 41.667 0.00 0.00 33.11 3.27
658 695 4.816385 TGCTTTAGACCAAGTTCACTTCTG 59.184 41.667 0.00 0.00 33.11 3.02
659 696 4.816925 GTGCTTTAGACCAAGTTCACTTCT 59.183 41.667 0.00 0.00 33.11 2.85
660 697 4.574828 TGTGCTTTAGACCAAGTTCACTTC 59.425 41.667 0.00 0.00 33.11 3.01
699 882 4.776435 TGGATTGATTCTCCACATGCTA 57.224 40.909 0.00 0.00 37.87 3.49
706 889 4.476113 AGGATTCTGTGGATTGATTCTCCA 59.524 41.667 0.00 0.00 40.49 3.86
728 916 0.803117 TGTGCCGTAAGAGAGTCGAG 59.197 55.000 0.00 0.00 43.02 4.04
763 951 1.752498 GCACCAATGGCAGATTCATCA 59.248 47.619 0.00 0.00 0.00 3.07
788 976 1.239968 GGGCTGTTGACTTGCAGAGG 61.240 60.000 0.00 0.00 34.87 3.69
812 1000 2.011122 TCCGGATAATCTCCTCCACC 57.989 55.000 0.00 0.00 42.47 4.61
841 1030 4.114997 CCGGATTGGTTGGTGCGC 62.115 66.667 0.00 0.00 0.00 6.09
849 1038 1.073923 ACAGAAAAGCTCCGGATTGGT 59.926 47.619 3.57 0.00 39.52 3.67
882 1071 2.479389 CGGCTTCTCTCTCTGTTAGCAG 60.479 54.545 0.00 0.00 43.87 4.24
883 1072 1.474478 CGGCTTCTCTCTCTGTTAGCA 59.526 52.381 0.00 0.00 0.00 3.49
884 1073 1.474879 ACGGCTTCTCTCTCTGTTAGC 59.525 52.381 0.00 0.00 0.00 3.09
886 1075 2.791655 TCACGGCTTCTCTCTCTGTTA 58.208 47.619 0.00 0.00 0.00 2.41
887 1076 1.621992 TCACGGCTTCTCTCTCTGTT 58.378 50.000 0.00 0.00 0.00 3.16
888 1077 1.621992 TTCACGGCTTCTCTCTCTGT 58.378 50.000 0.00 0.00 0.00 3.41
889 1078 2.288457 TGTTTCACGGCTTCTCTCTCTG 60.288 50.000 0.00 0.00 0.00 3.35
894 1088 1.947456 GGTTTGTTTCACGGCTTCTCT 59.053 47.619 0.00 0.00 0.00 3.10
901 1095 3.580731 AGTTTGTTGGTTTGTTTCACGG 58.419 40.909 0.00 0.00 0.00 4.94
1097 1303 6.415702 CGTAATCAAACAAGAAACGTGAGAA 58.584 36.000 0.00 0.00 0.00 2.87
1103 1309 3.906008 CCAGCGTAATCAAACAAGAAACG 59.094 43.478 0.00 0.00 35.41 3.60
1108 1314 3.004315 ACCAACCAGCGTAATCAAACAAG 59.996 43.478 0.00 0.00 0.00 3.16
1111 1317 3.636282 AACCAACCAGCGTAATCAAAC 57.364 42.857 0.00 0.00 0.00 2.93
1112 1318 4.339814 AGAAAACCAACCAGCGTAATCAAA 59.660 37.500 0.00 0.00 0.00 2.69
1114 1320 3.482436 AGAAAACCAACCAGCGTAATCA 58.518 40.909 0.00 0.00 0.00 2.57
1116 1322 4.142038 AGAAGAAAACCAACCAGCGTAAT 58.858 39.130 0.00 0.00 0.00 1.89
1119 1325 2.052782 AGAAGAAAACCAACCAGCGT 57.947 45.000 0.00 0.00 0.00 5.07
1120 1326 3.606153 CGTAAGAAGAAAACCAACCAGCG 60.606 47.826 0.00 0.00 43.02 5.18
1121 1327 3.852205 GCGTAAGAAGAAAACCAACCAGC 60.852 47.826 0.00 0.00 43.02 4.85
1122 1328 3.606153 CGCGTAAGAAGAAAACCAACCAG 60.606 47.826 0.00 0.00 43.02 4.00
1157 1368 3.500368 GAACTTCACGCGCGCACAA 62.500 57.895 32.58 18.66 0.00 3.33
1158 1369 3.995669 GAACTTCACGCGCGCACA 61.996 61.111 32.58 11.31 0.00 4.57
1292 1503 1.288350 CGTCCTCGATGTAGACGTCT 58.712 55.000 23.66 23.66 46.23 4.18
1455 1666 3.129871 ACTGGTATCGTACTCGTAGCTC 58.870 50.000 0.00 0.00 38.33 4.09
1456 1667 3.191078 ACTGGTATCGTACTCGTAGCT 57.809 47.619 0.00 0.00 38.33 3.32
1457 1668 3.959573 AACTGGTATCGTACTCGTAGC 57.040 47.619 0.00 0.00 38.33 3.58
1458 1669 4.497006 CCCAAACTGGTATCGTACTCGTAG 60.497 50.000 0.00 0.00 35.17 3.51
1459 1670 3.378112 CCCAAACTGGTATCGTACTCGTA 59.622 47.826 0.00 0.00 35.17 3.43
1460 1671 2.165030 CCCAAACTGGTATCGTACTCGT 59.835 50.000 0.00 0.00 35.17 4.18
1461 1672 2.165030 ACCCAAACTGGTATCGTACTCG 59.835 50.000 0.00 0.00 36.67 4.18
1513 1724 0.244994 CTAGCAGTGTCAGTTCGCCT 59.755 55.000 0.00 0.00 0.00 5.52
1536 1747 3.252458 AGTTTACCGTGAGATTTTGTGGC 59.748 43.478 0.00 0.00 0.00 5.01
1583 1796 3.900966 AATCTACCGTTTACTGTCCCC 57.099 47.619 0.00 0.00 0.00 4.81
1640 1853 6.662865 TTTCACTTCATGCCAAAGGAAATA 57.337 33.333 0.00 0.00 0.00 1.40
1666 1879 5.682659 AGGAAGGACATGATTTCATCAGAG 58.317 41.667 0.00 0.00 43.53 3.35
1686 1899 0.324943 GCTAGGTTGGACAGCAAGGA 59.675 55.000 0.00 0.00 35.35 3.36
1720 1934 8.141268 ACCAACCTAAATGTAACATGAAAACAG 58.859 33.333 0.00 0.00 0.00 3.16
1725 1939 6.072948 CGTCACCAACCTAAATGTAACATGAA 60.073 38.462 0.00 0.00 0.00 2.57
1730 1944 7.599630 TTATCGTCACCAACCTAAATGTAAC 57.400 36.000 0.00 0.00 0.00 2.50
1732 1946 7.332557 ACATTATCGTCACCAACCTAAATGTA 58.667 34.615 0.00 0.00 0.00 2.29
1734 1948 6.315144 TGACATTATCGTCACCAACCTAAATG 59.685 38.462 0.00 0.00 40.94 2.32
1737 1951 5.186215 TCTGACATTATCGTCACCAACCTAA 59.814 40.000 0.00 0.00 40.94 2.69
1767 1986 6.566141 CATGACATATTTTCCAGTTGCATCA 58.434 36.000 0.00 0.00 0.00 3.07
1776 1995 3.700539 CACCTGGCATGACATATTTTCCA 59.299 43.478 0.00 0.00 0.00 3.53
1840 2059 8.511321 CCTGATGAACTGATGATAGACTAGTAC 58.489 40.741 0.00 0.00 0.00 2.73
1845 2064 4.900652 AGCCTGATGAACTGATGATAGACT 59.099 41.667 0.00 0.00 0.00 3.24
1848 2067 5.697178 CAGAAGCCTGATGAACTGATGATAG 59.303 44.000 0.00 0.00 43.02 2.08
1873 2092 5.220854 GGTCAATTCCACCTGTGATATTTCG 60.221 44.000 0.00 0.00 0.00 3.46
2475 2708 6.929625 TCAAGGACTTGAATTTTGTCAACAA 58.070 32.000 12.04 0.00 45.56 2.83
2476 2709 6.522625 TCAAGGACTTGAATTTTGTCAACA 57.477 33.333 12.04 0.00 45.56 3.33
2968 3247 1.677576 TGACCTGCAAAGTTTGAGCTG 59.322 47.619 19.82 8.55 0.00 4.24
3428 3711 5.507985 GCTGCATAGGAACAAAGAACAGTTT 60.508 40.000 0.00 0.00 0.00 2.66
4277 4563 0.105224 TTGTCAAGGCCGTCGAAGAA 59.895 50.000 0.00 0.00 39.69 2.52
4391 4685 4.265856 AGGATAGTGGTACAGTCATGGA 57.734 45.455 0.00 0.00 43.36 3.41
4394 4688 6.013379 CCAGATAGGATAGTGGTACAGTCAT 58.987 44.000 0.00 0.00 40.28 3.06
4524 4819 9.450807 GCCTTGTATGCATAATTAACTTTACAG 57.549 33.333 8.28 0.00 0.00 2.74
4617 4912 1.728971 CATCAGGACACAGCGAAACTC 59.271 52.381 0.00 0.00 0.00 3.01
4620 4915 1.069978 TGACATCAGGACACAGCGAAA 59.930 47.619 0.00 0.00 0.00 3.46
4623 4918 1.511850 TTTGACATCAGGACACAGCG 58.488 50.000 0.00 0.00 0.00 5.18
4647 4942 0.550914 AGTTGTGCCAGACTCCCAAA 59.449 50.000 0.00 0.00 0.00 3.28
4650 4945 0.606673 GGAAGTTGTGCCAGACTCCC 60.607 60.000 0.00 0.00 0.00 4.30
4658 4953 2.134789 ATGATCCTGGAAGTTGTGCC 57.865 50.000 0.00 0.00 0.00 5.01
4659 4954 3.878778 ACTATGATCCTGGAAGTTGTGC 58.121 45.455 0.00 0.00 0.00 4.57
4660 4955 7.657761 GGTATAACTATGATCCTGGAAGTTGTG 59.342 40.741 17.65 3.86 32.85 3.33
4661 4956 7.347222 TGGTATAACTATGATCCTGGAAGTTGT 59.653 37.037 17.65 14.46 32.85 3.32
4664 4959 7.306013 TCTGGTATAACTATGATCCTGGAAGT 58.694 38.462 0.00 0.00 0.00 3.01
4665 4960 7.782897 TCTGGTATAACTATGATCCTGGAAG 57.217 40.000 0.00 0.00 0.00 3.46
4667 4962 6.211584 GCTTCTGGTATAACTATGATCCTGGA 59.788 42.308 0.00 0.00 0.00 3.86
4668 4963 6.014242 TGCTTCTGGTATAACTATGATCCTGG 60.014 42.308 0.00 0.00 0.00 4.45
4670 4965 6.554982 TGTGCTTCTGGTATAACTATGATCCT 59.445 38.462 0.00 0.00 0.00 3.24
4671 4966 6.647067 GTGTGCTTCTGGTATAACTATGATCC 59.353 42.308 0.00 0.00 0.00 3.36
4672 4967 6.363626 CGTGTGCTTCTGGTATAACTATGATC 59.636 42.308 0.00 0.00 0.00 2.92
4673 4968 6.183360 ACGTGTGCTTCTGGTATAACTATGAT 60.183 38.462 0.00 0.00 0.00 2.45
4674 4969 5.126545 ACGTGTGCTTCTGGTATAACTATGA 59.873 40.000 0.00 0.00 0.00 2.15
4675 4970 5.348986 ACGTGTGCTTCTGGTATAACTATG 58.651 41.667 0.00 0.00 0.00 2.23
4677 4972 5.395682 AACGTGTGCTTCTGGTATAACTA 57.604 39.130 0.00 0.00 0.00 2.24
4678 4973 3.955650 ACGTGTGCTTCTGGTATAACT 57.044 42.857 0.00 0.00 0.00 2.24
4679 4974 7.276218 TGTTATAACGTGTGCTTCTGGTATAAC 59.724 37.037 10.92 14.86 0.00 1.89
4681 4976 6.865411 TGTTATAACGTGTGCTTCTGGTATA 58.135 36.000 10.92 0.00 0.00 1.47
4683 4978 5.136816 TGTTATAACGTGTGCTTCTGGTA 57.863 39.130 10.92 0.00 0.00 3.25
4684 4979 3.994392 CTGTTATAACGTGTGCTTCTGGT 59.006 43.478 10.92 0.00 0.00 4.00
4685 4980 3.370978 CCTGTTATAACGTGTGCTTCTGG 59.629 47.826 10.92 0.00 0.00 3.86
4686 4981 3.181520 GCCTGTTATAACGTGTGCTTCTG 60.182 47.826 10.92 0.00 0.00 3.02
4687 4982 3.000727 GCCTGTTATAACGTGTGCTTCT 58.999 45.455 10.92 0.00 0.00 2.85
4688 4983 2.739913 TGCCTGTTATAACGTGTGCTTC 59.260 45.455 10.92 0.00 0.00 3.86
4691 4986 1.801771 TGTGCCTGTTATAACGTGTGC 59.198 47.619 10.92 10.37 0.00 4.57
4692 4987 3.064207 ACTGTGCCTGTTATAACGTGTG 58.936 45.455 10.92 0.95 0.00 3.82
4693 4988 3.396260 ACTGTGCCTGTTATAACGTGT 57.604 42.857 10.92 0.01 0.00 4.49
4694 4989 7.528481 TTATAACTGTGCCTGTTATAACGTG 57.472 36.000 20.55 5.60 41.33 4.49
4695 4990 8.726870 AATTATAACTGTGCCTGTTATAACGT 57.273 30.769 23.53 17.33 44.80 3.99
4697 4992 8.280497 CCGAATTATAACTGTGCCTGTTATAAC 58.720 37.037 23.53 8.75 44.80 1.89
4698 4993 8.205512 TCCGAATTATAACTGTGCCTGTTATAA 58.794 33.333 23.41 23.41 45.39 0.98
4699 4994 7.728148 TCCGAATTATAACTGTGCCTGTTATA 58.272 34.615 14.72 14.72 38.65 0.98
4700 4995 6.588204 TCCGAATTATAACTGTGCCTGTTAT 58.412 36.000 16.05 16.05 40.08 1.89
4701 4996 5.979993 TCCGAATTATAACTGTGCCTGTTA 58.020 37.500 6.98 6.98 33.64 2.41
4702 4997 4.839121 TCCGAATTATAACTGTGCCTGTT 58.161 39.130 0.00 3.69 0.00 3.16
4703 4998 4.481368 TCCGAATTATAACTGTGCCTGT 57.519 40.909 0.00 0.00 0.00 4.00
4704 4999 5.056480 TCATCCGAATTATAACTGTGCCTG 58.944 41.667 0.00 0.00 0.00 4.85
4705 5000 5.290493 TCATCCGAATTATAACTGTGCCT 57.710 39.130 0.00 0.00 0.00 4.75
4706 5001 5.617751 GCATCATCCGAATTATAACTGTGCC 60.618 44.000 0.00 0.00 0.00 5.01
4707 5002 5.049474 TGCATCATCCGAATTATAACTGTGC 60.049 40.000 0.00 0.00 0.00 4.57
4708 5003 6.544038 TGCATCATCCGAATTATAACTGTG 57.456 37.500 0.00 0.00 0.00 3.66
4709 5004 6.348786 GCATGCATCATCCGAATTATAACTGT 60.349 38.462 14.21 0.00 0.00 3.55
4710 5005 6.025896 GCATGCATCATCCGAATTATAACTG 58.974 40.000 14.21 0.00 0.00 3.16
4711 5006 5.124457 GGCATGCATCATCCGAATTATAACT 59.876 40.000 21.36 0.00 0.00 2.24
4712 5007 5.335127 GGCATGCATCATCCGAATTATAAC 58.665 41.667 21.36 0.00 0.00 1.89
4713 5008 4.398988 GGGCATGCATCATCCGAATTATAA 59.601 41.667 21.36 0.00 0.00 0.98
4714 5009 3.947196 GGGCATGCATCATCCGAATTATA 59.053 43.478 21.36 0.00 0.00 0.98
4720 5015 2.281002 CGGGCATGCATCATCCGA 60.281 61.111 22.95 0.00 42.94 4.55
4721 5016 4.034258 GCGGGCATGCATCATCCG 62.034 66.667 23.01 23.01 43.13 4.18
4723 5018 0.953727 TTTAGCGGGCATGCATCATC 59.046 50.000 21.36 0.49 37.31 2.92
4737 5032 5.829924 TGATCATCCTCATTCCCTTTTTAGC 59.170 40.000 0.00 0.00 0.00 3.09
4791 5086 7.324354 TCACGCTTCATACACTAATACTGTA 57.676 36.000 0.00 0.00 0.00 2.74
4792 5087 6.203808 TCACGCTTCATACACTAATACTGT 57.796 37.500 0.00 0.00 0.00 3.55
4793 5088 6.363626 GGATCACGCTTCATACACTAATACTG 59.636 42.308 0.00 0.00 0.00 2.74
4794 5089 6.040504 TGGATCACGCTTCATACACTAATACT 59.959 38.462 0.00 0.00 0.00 2.12
4795 5090 6.213677 TGGATCACGCTTCATACACTAATAC 58.786 40.000 0.00 0.00 0.00 1.89
4796 5091 6.399639 TGGATCACGCTTCATACACTAATA 57.600 37.500 0.00 0.00 0.00 0.98
4812 5107 4.219288 AGAAAAGCCAAGTTCATGGATCAC 59.781 41.667 0.00 0.00 43.54 3.06
4838 5261 6.235231 TCTCTACACCAGTTCTGTTCTTTT 57.765 37.500 0.00 0.00 0.00 2.27
4851 5274 8.078060 TCAGATTCATAAACATCTCTACACCA 57.922 34.615 0.00 0.00 0.00 4.17
4878 5303 0.320771 GCCTGACGAGGTGACATGTT 60.321 55.000 0.00 0.00 42.15 2.71
4879 5304 1.293498 GCCTGACGAGGTGACATGT 59.707 57.895 0.00 0.00 42.15 3.21
4891 5316 5.106673 GCCTAAATAAATCATACCGCCTGAC 60.107 44.000 0.00 0.00 0.00 3.51
4904 5329 8.911918 TGTGGTGTATAATCGCCTAAATAAAT 57.088 30.769 0.00 0.00 38.63 1.40
4932 5357 8.991783 AATTTGAGATCCTATGATGTGATGTT 57.008 30.769 0.00 0.00 0.00 2.71
4955 5388 8.004215 TGGGGATGTAAATACTTGCAGAATAAT 58.996 33.333 0.00 0.00 30.13 1.28
4971 5404 6.429385 GCATTTTTGAAAACATGGGGATGTAA 59.571 34.615 0.00 0.00 33.81 2.41
4996 5430 6.780706 ACCAACTATTGAACAAGTTCGTAG 57.219 37.500 16.78 16.78 42.28 3.51
5018 5452 6.512415 GCTGCCTGTAGATGACATCAAATTAC 60.512 42.308 17.57 10.99 37.45 1.89
5023 5457 2.236893 TGCTGCCTGTAGATGACATCAA 59.763 45.455 17.57 2.21 37.45 2.57
5061 5495 4.000325 TCATGTCAGGAACATTTACGGTG 59.000 43.478 0.00 0.00 46.73 4.94
5062 5496 4.280436 TCATGTCAGGAACATTTACGGT 57.720 40.909 0.00 0.00 46.73 4.83
5070 5504 4.225717 TGGATCAGAATCATGTCAGGAACA 59.774 41.667 0.00 0.00 43.51 3.18
5071 5505 4.774124 TGGATCAGAATCATGTCAGGAAC 58.226 43.478 0.00 0.00 33.21 3.62
5075 5509 5.448768 GCAGTTTGGATCAGAATCATGTCAG 60.449 44.000 0.00 0.00 33.21 3.51
5077 5511 4.639310 AGCAGTTTGGATCAGAATCATGTC 59.361 41.667 0.00 0.00 33.21 3.06
5098 5532 1.571919 ATGTTCTTGTATCGGCGAGC 58.428 50.000 17.22 11.50 0.00 5.03
5119 5553 5.688220 TCCCTACTCCCTAGATTCTTCAT 57.312 43.478 0.00 0.00 0.00 2.57
5169 5603 4.389077 GGTGCTGTATCTTGAGTGTTGTAC 59.611 45.833 0.00 0.00 0.00 2.90
5171 5605 3.071602 AGGTGCTGTATCTTGAGTGTTGT 59.928 43.478 0.00 0.00 0.00 3.32
5222 5656 4.261031 CGTCCACGGGAATAAATTGAATCC 60.261 45.833 0.00 0.00 31.38 3.01
5249 5683 2.735823 GCTTTGAGTTCACTTTGGCTG 58.264 47.619 0.00 0.00 0.00 4.85
5318 5752 1.937223 CGCATATTAACCACTCGCCAA 59.063 47.619 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.