Multiple sequence alignment - TraesCS7A01G344700

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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 TraesCS7A01G344700 chr7A 100.000 6780 0 0 1 6780 506824926 506818147 0.000000e+00 12521.0
1 TraesCS7A01G344700 chr7D 93.961 4935 206 37 2 4866 426728757 426733669 0.000000e+00 7378.0
2 TraesCS7A01G344700 chr7D 91.619 1050 58 18 5381 6409 426734469 426735509 0.000000e+00 1424.0
3 TraesCS7A01G344700 chr7D 95.750 400 15 2 4863 5262 426733826 426734223 1.590000e-180 643.0
4 TraesCS7A01G344700 chr7D 91.638 287 20 1 171 457 382081898 382081616 1.770000e-105 394.0
5 TraesCS7A01G344700 chr7D 91.667 288 19 2 171 457 626719095 626719378 1.770000e-105 394.0
6 TraesCS7A01G344700 chr7D 91.349 289 18 4 171 457 382078749 382078466 8.250000e-104 388.0
7 TraesCS7A01G344700 chr7D 91.163 215 19 0 6428 6642 426736196 426736410 6.650000e-75 292.0
8 TraesCS7A01G344700 chr7D 95.652 92 3 1 6690 6780 426736413 426736504 5.480000e-31 147.0
9 TraesCS7A01G344700 chr7D 81.452 124 8 9 5257 5380 426734339 426734447 3.370000e-13 87.9
10 TraesCS7A01G344700 chr7D 96.970 33 1 0 2988 3020 31433820 31433852 1.000000e-03 56.5
11 TraesCS7A01G344700 chr7B 97.495 2116 43 7 2757 4866 443739288 443741399 0.000000e+00 3605.0
12 TraesCS7A01G344700 chr7B 94.884 1075 35 3 1703 2757 443737702 443738776 0.000000e+00 1663.0
13 TraesCS7A01G344700 chr7B 92.030 1054 50 19 678 1704 443736575 443737621 0.000000e+00 1450.0
14 TraesCS7A01G344700 chr7B 83.117 1001 123 22 2404 3377 648244396 648243415 0.000000e+00 870.0
15 TraesCS7A01G344700 chr7B 92.771 581 30 9 5381 5957 443742213 443742785 0.000000e+00 830.0
16 TraesCS7A01G344700 chr7B 93.750 400 16 2 4863 5262 443741556 443741946 5.860000e-165 592.0
17 TraesCS7A01G344700 chr7B 89.286 168 17 1 1 168 115176139 115176305 6.890000e-50 209.0
18 TraesCS7A01G344700 chr6B 91.638 287 20 1 171 457 596609764 596610046 1.770000e-105 394.0
19 TraesCS7A01G344700 chr6B 91.638 287 20 1 171 457 715999240 715999522 1.770000e-105 394.0
20 TraesCS7A01G344700 chr4D 91.638 287 19 3 171 457 123393625 123393344 6.370000e-105 392.0
21 TraesCS7A01G344700 chr3D 91.289 287 21 1 171 457 501870736 501870454 8.250000e-104 388.0
22 TraesCS7A01G344700 chr2B 91.319 288 20 2 171 457 799246493 799246210 8.250000e-104 388.0
23 TraesCS7A01G344700 chrUn 90.972 288 21 2 171 457 171000380 171000097 3.840000e-102 383.0
24 TraesCS7A01G344700 chrUn 88.690 168 18 1 1 168 45125740 45125574 3.210000e-48 204.0
25 TraesCS7A01G344700 chrUn 88.690 168 18 1 1 168 86492934 86492768 3.210000e-48 204.0
26 TraesCS7A01G344700 chrUn 88.690 168 18 1 1 168 186176531 186176697 3.210000e-48 204.0
27 TraesCS7A01G344700 chr3B 89.881 168 16 1 1 168 483346935 483347101 1.480000e-51 215.0
28 TraesCS7A01G344700 chr3B 89.286 168 17 1 1 168 201575119 201574953 6.890000e-50 209.0
29 TraesCS7A01G344700 chr5D 89.286 168 17 1 1 168 562945229 562945395 6.890000e-50 209.0
30 TraesCS7A01G344700 chr5A 89.286 168 17 1 1 168 300091130 300090964 6.890000e-50 209.0
31 TraesCS7A01G344700 chr5A 89.286 168 17 1 1 168 527646222 527646388 6.890000e-50 209.0
32 TraesCS7A01G344700 chr4A 96.875 32 1 0 2989 3020 697387657 697387688 3.000000e-03 54.7


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 TraesCS7A01G344700 chr7A 506818147 506824926 6779 True 12521.000000 12521 100.0000 1 6780 1 chr7A.!!$R1 6779
1 TraesCS7A01G344700 chr7D 426728757 426736504 7747 False 1661.983333 7378 91.5995 2 6780 6 chr7D.!!$F3 6778
2 TraesCS7A01G344700 chr7D 382078466 382081898 3432 True 391.000000 394 91.4935 171 457 2 chr7D.!!$R1 286
3 TraesCS7A01G344700 chr7B 443736575 443742785 6210 False 1628.000000 3605 94.1860 678 5957 5 chr7B.!!$F2 5279
4 TraesCS7A01G344700 chr7B 648243415 648244396 981 True 870.000000 870 83.1170 2404 3377 1 chr7B.!!$R1 973

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
573 750 0.034283 ACCTCCTCGTCCACTCTACC 60.034 60.000 0.0 0.0 0.00 3.18 F
580 757 0.173708 CGTCCACTCTACCTCCTTGC 59.826 60.000 0.0 0.0 0.00 4.01 F
1045 1256 0.539986 GGCGAGAACCAATACCCTGA 59.460 55.000 0.0 0.0 0.00 3.86 F
2291 2615 0.449388 CGTTTGAGAAGCAGATGGCC 59.551 55.000 0.0 0.0 46.50 5.36 F
2867 3724 0.320771 AGCGAATCTTGAAGCGTGGT 60.321 50.000 0.0 0.0 34.34 4.16 F
4535 5500 2.159382 GCAACGAATCTTCCTTTCCCA 58.841 47.619 0.0 0.0 0.00 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1598 1819 0.592500 CGTCCACATCTCCGTCATCG 60.593 60.000 0.00 0.0 0.00 3.84 R
1782 2087 1.358152 AGGGGCTAGCAACTGTTACA 58.642 50.000 18.24 0.0 0.00 2.41 R
2593 2925 0.764226 CTTCACGCGTTTTGCTTTCG 59.236 50.000 10.22 0.0 43.27 3.46 R
3709 4571 1.542915 CAATGTCTGTCTTTGGGCCTG 59.457 52.381 4.53 0.0 0.00 4.85 R
4610 5575 1.737363 GCAGGTCGGTTAAGAGCAGAG 60.737 57.143 0.00 0.0 40.77 3.35 R
6419 8665 0.038744 CTCCTTCAATGTGGCCCAGT 59.961 55.000 0.00 0.0 0.00 4.00 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
20 21 1.535462 CAAGGGTCTAGTTGTTTGCCG 59.465 52.381 0.00 0.00 0.00 5.69
55 56 2.473984 GTGAGTTGGGTTTAGAACGTCG 59.526 50.000 0.00 0.00 0.00 5.12
57 58 3.317711 TGAGTTGGGTTTAGAACGTCGTA 59.682 43.478 0.00 0.00 0.00 3.43
75 76 5.138125 TCGTAAGACGGTTTGGTTCTTAT 57.862 39.130 0.00 0.00 45.01 1.73
76 77 5.540911 TCGTAAGACGGTTTGGTTCTTATT 58.459 37.500 0.00 0.00 45.01 1.40
78 79 7.151308 TCGTAAGACGGTTTGGTTCTTATTTA 58.849 34.615 0.00 0.00 45.01 1.40
79 80 7.116233 TCGTAAGACGGTTTGGTTCTTATTTAC 59.884 37.037 0.00 0.00 45.01 2.01
80 81 5.851047 AGACGGTTTGGTTCTTATTTACG 57.149 39.130 0.00 0.00 0.00 3.18
103 104 2.858745 TGGTGTTAAAGGGAGAACTGC 58.141 47.619 0.00 0.00 0.00 4.40
110 111 1.261238 AAGGGAGAACTGCGAGGAGG 61.261 60.000 0.00 0.00 0.00 4.30
122 123 1.413077 GCGAGGAGGCAACCTTAGTAT 59.587 52.381 4.85 0.00 40.73 2.12
128 129 3.961408 GGAGGCAACCTTAGTATGAGAGA 59.039 47.826 0.00 0.00 31.76 3.10
131 132 4.647399 AGGCAACCTTAGTATGAGAGAGAC 59.353 45.833 0.00 0.00 37.17 3.36
142 143 0.899019 GAGAGAGACTGGGTTGGGTC 59.101 60.000 0.00 0.00 0.00 4.46
156 157 4.230745 GTTGGGTCAACCTATGGTGTAT 57.769 45.455 0.00 0.00 38.30 2.29
169 170 7.857456 ACCTATGGTGTATCAGTTGTTATGAA 58.143 34.615 0.00 0.00 32.98 2.57
185 186 7.315247 TGTTATGAATTACCCGAGTCAATTG 57.685 36.000 0.00 0.00 0.00 2.32
255 256 2.292845 GCCATTTGCTGAGCTATCTTCC 59.707 50.000 5.83 0.00 36.87 3.46
268 269 7.453393 TGAGCTATCTTCCTTTTTCTTCTTCA 58.547 34.615 0.00 0.00 0.00 3.02
270 271 7.684529 AGCTATCTTCCTTTTTCTTCTTCAGA 58.315 34.615 0.00 0.00 0.00 3.27
272 273 7.389053 GCTATCTTCCTTTTTCTTCTTCAGACA 59.611 37.037 0.00 0.00 0.00 3.41
276 277 8.802267 TCTTCCTTTTTCTTCTTCAGACAAAAA 58.198 29.630 5.86 5.86 32.00 1.94
334 335 1.681780 GGTCATTTCGCCAATCTGGGA 60.682 52.381 0.00 0.00 38.19 4.37
343 344 1.339291 GCCAATCTGGGAAATAGCAGC 59.661 52.381 0.00 0.00 38.19 5.25
365 366 2.231215 AAGCAATCGATCGGAGAAGG 57.769 50.000 16.41 0.75 43.58 3.46
410 411 0.464373 TGGATTCATTCTCCAGGCGC 60.464 55.000 0.00 0.00 37.87 6.53
441 460 2.202932 CCACGGGCTTGATCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
450 469 2.933260 GGCTTGATCTCGGTTTCTTCTC 59.067 50.000 0.00 0.00 0.00 2.87
457 476 2.072298 CTCGGTTTCTTCTCAAGCTGG 58.928 52.381 0.00 0.00 0.00 4.85
460 479 2.612972 CGGTTTCTTCTCAAGCTGGCTA 60.613 50.000 0.00 0.00 0.00 3.93
463 482 3.325293 TTCTTCTCAAGCTGGCTAGTG 57.675 47.619 0.00 0.00 0.00 2.74
486 505 2.501723 AGCCTCTTTTCTTATCCGCTCA 59.498 45.455 0.00 0.00 0.00 4.26
492 511 2.988010 TTCTTATCCGCTCATGCAGT 57.012 45.000 0.00 0.00 39.64 4.40
532 709 1.192146 TCTCACCTTCCCTTCCACCG 61.192 60.000 0.00 0.00 0.00 4.94
536 713 2.677228 CTTCCCTTCCACCGCCAT 59.323 61.111 0.00 0.00 0.00 4.40
540 717 2.370445 CCCTTCCACCGCCATCTCT 61.370 63.158 0.00 0.00 0.00 3.10
542 719 0.390860 CCTTCCACCGCCATCTCTAG 59.609 60.000 0.00 0.00 0.00 2.43
550 727 1.417890 CCGCCATCTCTAGACCCATTT 59.582 52.381 0.00 0.00 0.00 2.32
555 732 4.455606 CCATCTCTAGACCCATTTTCCAC 58.544 47.826 0.00 0.00 0.00 4.02
557 734 3.803340 TCTCTAGACCCATTTTCCACCT 58.197 45.455 0.00 0.00 0.00 4.00
558 735 3.775316 TCTCTAGACCCATTTTCCACCTC 59.225 47.826 0.00 0.00 0.00 3.85
561 738 1.636003 AGACCCATTTTCCACCTCCTC 59.364 52.381 0.00 0.00 0.00 3.71
568 745 0.471211 TTTCCACCTCCTCGTCCACT 60.471 55.000 0.00 0.00 0.00 4.00
573 750 0.034283 ACCTCCTCGTCCACTCTACC 60.034 60.000 0.00 0.00 0.00 3.18
575 752 1.670791 CTCCTCGTCCACTCTACCTC 58.329 60.000 0.00 0.00 0.00 3.85
576 753 0.255318 TCCTCGTCCACTCTACCTCC 59.745 60.000 0.00 0.00 0.00 4.30
578 755 1.341187 CCTCGTCCACTCTACCTCCTT 60.341 57.143 0.00 0.00 0.00 3.36
579 756 1.746220 CTCGTCCACTCTACCTCCTTG 59.254 57.143 0.00 0.00 0.00 3.61
580 757 0.173708 CGTCCACTCTACCTCCTTGC 59.826 60.000 0.00 0.00 0.00 4.01
619 815 1.063717 AGCCAAACCCTATCACCATGG 60.064 52.381 11.19 11.19 0.00 3.66
645 841 1.334243 CCATACTTCCTCGTCGACCTC 59.666 57.143 10.58 0.00 0.00 3.85
651 847 1.095600 TCCTCGTCGACCTCAGAATG 58.904 55.000 10.58 0.00 37.54 2.67
656 852 1.067142 CGTCGACCTCAGAATGGGAAA 60.067 52.381 10.58 0.00 41.11 3.13
660 856 5.183228 GTCGACCTCAGAATGGGAAAAATA 58.817 41.667 3.51 0.00 41.11 1.40
661 857 5.064834 GTCGACCTCAGAATGGGAAAAATAC 59.935 44.000 3.51 0.00 41.11 1.89
729 926 9.665719 AAATAAGCAGAAAAGAAAAGGAAAACA 57.334 25.926 0.00 0.00 0.00 2.83
793 998 3.296854 GGAACAGAAACCAGAAAACCCT 58.703 45.455 0.00 0.00 0.00 4.34
794 999 3.704566 GGAACAGAAACCAGAAAACCCTT 59.295 43.478 0.00 0.00 0.00 3.95
868 1075 1.900545 GAGTCCTTAACTGGGCGCCT 61.901 60.000 28.56 9.11 38.74 5.52
1023 1234 2.975799 GGAACGAAGCCCAACGCA 60.976 61.111 0.00 0.00 41.38 5.24
1045 1256 0.539986 GGCGAGAACCAATACCCTGA 59.460 55.000 0.00 0.00 0.00 3.86
1053 1264 0.623324 CCAATACCCTGACCCCCAGA 60.623 60.000 0.00 0.00 45.78 3.86
1055 1266 0.988678 AATACCCTGACCCCCAGAGC 60.989 60.000 0.00 0.00 45.78 4.09
1396 1612 1.529826 GCGCGTGATTTTAGCTTCTGG 60.530 52.381 8.43 0.00 0.00 3.86
1399 1615 3.725010 CGCGTGATTTTAGCTTCTGGTTC 60.725 47.826 0.00 0.00 0.00 3.62
1431 1647 1.574428 CAACTTTGCGGGTCTTCGG 59.426 57.895 0.00 0.00 0.00 4.30
1598 1819 2.630580 AGGCGAGGATATGGAAGAAGAC 59.369 50.000 0.00 0.00 0.00 3.01
1732 2035 8.588290 AGTTATATACTCCTAGGAGATTGCTG 57.412 38.462 39.72 17.05 44.53 4.41
1739 2042 5.162925 ACTCCTAGGAGATTGCTGTACCTAT 60.163 44.000 39.72 13.65 44.53 2.57
1782 2087 7.649306 GTCACTTATGCTGAATTTCTGTGTTTT 59.351 33.333 5.36 0.00 0.00 2.43
1872 2196 7.984050 TCTCCTTGTCATGACATTCTAAAGATC 59.016 37.037 28.32 0.00 41.52 2.75
2195 2519 3.884774 AACCGGGAAGCTGCCACA 61.885 61.111 14.44 0.00 0.00 4.17
2228 2552 9.883142 TTTGAAAATGATTTGAACTTAGGTGTT 57.117 25.926 0.00 0.00 0.00 3.32
2273 2597 3.674753 GCAAATTTGAACCAAGGTCATCG 59.325 43.478 22.31 0.00 0.00 3.84
2291 2615 0.449388 CGTTTGAGAAGCAGATGGCC 59.551 55.000 0.00 0.00 46.50 5.36
2292 2616 1.538047 GTTTGAGAAGCAGATGGCCA 58.462 50.000 8.56 8.56 46.50 5.36
2369 2693 6.759497 ATCTTGGAACTTAACAAGGTATGC 57.241 37.500 0.00 0.00 43.20 3.14
2392 2716 6.127225 TGCTGCTTTATCTCACTTCACTAGAT 60.127 38.462 0.00 0.00 34.44 1.98
2406 2730 7.971168 CACTTCACTAGATCAGTTAGGTACTTG 59.029 40.741 0.00 0.00 35.70 3.16
2457 2784 7.361542 GCTGACTGGGCATATTTAGTGATAATG 60.362 40.741 0.00 0.00 0.00 1.90
2546 2874 1.067250 GGAGGATGTGAGAGAGCGC 59.933 63.158 0.00 0.00 0.00 5.92
2606 2938 2.786578 TCATGAAACGAAAGCAAAACGC 59.213 40.909 0.00 0.00 42.91 4.84
2678 3016 0.473755 TGAAGGCAGCAGACTTGGAA 59.526 50.000 0.03 0.00 45.23 3.53
2867 3724 0.320771 AGCGAATCTTGAAGCGTGGT 60.321 50.000 0.00 0.00 34.34 4.16
2921 3778 5.940192 CTATTACAGCACAACTCCAACAA 57.060 39.130 0.00 0.00 0.00 2.83
3579 4441 2.807045 GGACTGCACTGCTCGACG 60.807 66.667 1.98 0.00 0.00 5.12
3646 4508 8.677300 CCTTTACACTTTTGCAGTATCATATGT 58.323 33.333 1.90 0.00 32.76 2.29
3709 4571 5.393135 GCTTTGATGGTACTAGAAAAAGCCC 60.393 44.000 17.82 1.54 41.19 5.19
3746 4608 4.957971 ACATTGAAGTTCGAATGTTAGCG 58.042 39.130 19.39 0.00 39.27 4.26
4141 5003 4.927978 AGCTGATCTTATACGTCAAGCT 57.072 40.909 0.00 0.00 0.00 3.74
4173 5035 4.823442 TGATGATGTTGAAGCTGAGTTTGT 59.177 37.500 0.00 0.00 0.00 2.83
4175 5037 4.198530 TGATGTTGAAGCTGAGTTTGTGA 58.801 39.130 0.00 0.00 0.00 3.58
4177 5039 5.125257 TGATGTTGAAGCTGAGTTTGTGAAA 59.875 36.000 0.00 0.00 0.00 2.69
4180 5042 5.357878 TGTTGAAGCTGAGTTTGTGAAAGAT 59.642 36.000 0.00 0.00 0.00 2.40
4187 5049 6.016777 AGCTGAGTTTGTGAAAGATAAAGTGG 60.017 38.462 0.00 0.00 0.00 4.00
4535 5500 2.159382 GCAACGAATCTTCCTTTCCCA 58.841 47.619 0.00 0.00 0.00 4.37
4610 5575 5.357878 TGATTTCAACCCAGCAATATCACTC 59.642 40.000 0.00 0.00 0.00 3.51
4645 5610 3.252701 CGACCTGCGGTAAGTACATCTAT 59.747 47.826 0.00 0.00 35.25 1.98
4667 5632 2.835027 TCTAGCTGATGCATGAAGCTG 58.165 47.619 30.50 22.83 46.47 4.24
4770 5735 7.367285 TGCATGTACAGTGAAAGTTTATTTCC 58.633 34.615 0.33 0.00 0.00 3.13
4806 5772 6.327279 ACCAAGGTGTTTGTTTATAAGCTC 57.673 37.500 0.83 0.00 34.87 4.09
4926 6054 6.790285 TCTTTTCCGTGAATAGTAAACCAC 57.210 37.500 0.00 0.00 0.00 4.16
4987 6115 9.310449 TCTCTTACCAGAATAGTAAAACACTCT 57.690 33.333 0.00 0.00 38.80 3.24
5009 6137 8.157476 ACTCTTGACTTGGAAATACTTGTACAT 58.843 33.333 0.00 0.00 0.00 2.29
5021 6149 9.570488 GAAATACTTGTACATCGTCTTAAGTCT 57.430 33.333 1.63 0.00 31.55 3.24
5048 6176 7.769044 CCAGGCTCTAATTTTGTACTTAGCTAA 59.231 37.037 5.94 5.94 0.00 3.09
5075 6203 8.938906 GTTTAACTATAATTCTCGACAACCCAA 58.061 33.333 0.00 0.00 0.00 4.12
5092 6220 1.570813 CAACAGACACGCAGACTGAA 58.429 50.000 6.65 0.00 35.85 3.02
5190 6318 7.737869 TCCTGAAGCATTTATTACGGGTATAA 58.262 34.615 0.00 0.00 0.00 0.98
5274 6664 7.239763 TGGCCGATCTATCAGTGATATTTTA 57.760 36.000 13.22 0.98 0.00 1.52
5275 6665 7.851228 TGGCCGATCTATCAGTGATATTTTAT 58.149 34.615 13.22 5.45 0.00 1.40
5276 6666 7.981789 TGGCCGATCTATCAGTGATATTTTATC 59.018 37.037 13.22 12.04 0.00 1.75
5277 6667 8.200792 GGCCGATCTATCAGTGATATTTTATCT 58.799 37.037 13.22 0.00 0.00 1.98
5278 6668 9.243637 GCCGATCTATCAGTGATATTTTATCTC 57.756 37.037 13.22 6.06 0.00 2.75
5317 6707 6.838382 TCAAGCTAAGGGGTATCTTATTTCC 58.162 40.000 0.00 0.00 0.00 3.13
5322 6712 7.725844 AGCTAAGGGGTATCTTATTTCCAATTG 59.274 37.037 0.00 0.00 0.00 2.32
5326 6716 7.825709 AGGGGTATCTTATTTCCAATTGATCA 58.174 34.615 7.12 0.00 0.00 2.92
5327 6717 7.725844 AGGGGTATCTTATTTCCAATTGATCAC 59.274 37.037 7.12 0.00 0.00 3.06
5328 6718 7.039714 GGGGTATCTTATTTCCAATTGATCACC 60.040 40.741 7.12 0.00 0.00 4.02
5329 6719 7.725844 GGGTATCTTATTTCCAATTGATCACCT 59.274 37.037 7.12 0.00 0.00 4.00
5462 7691 8.971073 CCTTGATTCCCTTGATACAGTTATTTT 58.029 33.333 0.00 0.00 0.00 1.82
5480 7709 9.136323 AGTTATTTTGAAACAAGAATCTGAGGT 57.864 29.630 0.00 0.00 0.00 3.85
5492 7721 6.126863 AGAATCTGAGGTTGTGGACAATTA 57.873 37.500 0.00 0.00 38.24 1.40
5504 7733 6.012658 TGTGGACAATTATCTTGAAGCAAC 57.987 37.500 0.00 0.00 0.00 4.17
5540 7770 6.155393 ACATTAACTTTTTGTCAACCCCTTGA 59.845 34.615 0.00 0.00 33.76 3.02
5541 7771 6.800072 TTAACTTTTTGTCAACCCCTTGAT 57.200 33.333 0.00 0.00 38.69 2.57
5542 7772 5.692115 AACTTTTTGTCAACCCCTTGATT 57.308 34.783 0.00 0.00 38.69 2.57
5543 7773 5.276461 ACTTTTTGTCAACCCCTTGATTC 57.724 39.130 0.00 0.00 38.69 2.52
5544 7774 4.100963 ACTTTTTGTCAACCCCTTGATTCC 59.899 41.667 0.00 0.00 38.69 3.01
5545 7775 3.611025 TTTGTCAACCCCTTGATTCCT 57.389 42.857 0.00 0.00 38.69 3.36
5546 7776 3.611025 TTGTCAACCCCTTGATTCCTT 57.389 42.857 0.00 0.00 38.69 3.36
5547 7777 4.733077 TTGTCAACCCCTTGATTCCTTA 57.267 40.909 0.00 0.00 38.69 2.69
5548 7778 4.733077 TGTCAACCCCTTGATTCCTTAA 57.267 40.909 0.00 0.00 38.69 1.85
5549 7779 5.269554 TGTCAACCCCTTGATTCCTTAAT 57.730 39.130 0.00 0.00 38.69 1.40
5566 7796 7.377766 TCCTTAATGCAGTTGATTAAGACAC 57.622 36.000 15.24 0.00 42.39 3.67
5656 7886 1.575419 AGCCAATACAGTACGGGGAA 58.425 50.000 0.00 0.00 0.00 3.97
5683 7913 1.660167 CGCATGAGAAGCCTGATGAA 58.340 50.000 0.00 0.00 36.31 2.57
5734 7964 1.734163 ACCCGAACATAAAGAAGGCG 58.266 50.000 0.00 0.00 0.00 5.52
5775 8005 0.247736 ACAGCTTCACATCGGAGGAC 59.752 55.000 0.00 0.00 0.00 3.85
5776 8006 0.534412 CAGCTTCACATCGGAGGACT 59.466 55.000 0.00 0.00 0.00 3.85
5792 8022 5.194432 GGAGGACTTGATGAGACAGTAGTA 58.806 45.833 0.00 0.00 0.00 1.82
5793 8023 5.066764 GGAGGACTTGATGAGACAGTAGTAC 59.933 48.000 0.00 0.00 0.00 2.73
5794 8024 4.951094 AGGACTTGATGAGACAGTAGTACC 59.049 45.833 0.00 0.00 0.00 3.34
5795 8025 4.098196 GGACTTGATGAGACAGTAGTACCC 59.902 50.000 0.00 0.00 0.00 3.69
5797 8027 4.707448 ACTTGATGAGACAGTAGTACCCAG 59.293 45.833 0.00 0.00 0.00 4.45
5798 8028 4.317530 TGATGAGACAGTAGTACCCAGT 57.682 45.455 0.00 0.00 0.00 4.00
5801 8031 6.250711 TGATGAGACAGTAGTACCCAGTTAA 58.749 40.000 0.00 0.00 0.00 2.01
5802 8032 6.895756 TGATGAGACAGTAGTACCCAGTTAAT 59.104 38.462 0.00 0.00 0.00 1.40
5803 8033 6.525578 TGAGACAGTAGTACCCAGTTAATG 57.474 41.667 0.00 0.00 0.00 1.90
5897 8130 9.829507 AGAAGTATACAAAGATTCTTCTCATGG 57.170 33.333 5.50 0.00 38.48 3.66
5920 8153 2.851824 GTCAAACGACAGCTTTGGTTTG 59.148 45.455 25.69 25.69 46.43 2.93
5937 8170 2.203351 GGCTATTGGAAGCGGGGG 60.203 66.667 0.00 0.00 43.74 5.40
5941 8174 1.102978 CTATTGGAAGCGGGGGTTTG 58.897 55.000 0.00 0.00 0.00 2.93
6029 8262 2.940410 AGGGCCGAAATATGTTTGTACG 59.060 45.455 0.00 0.00 0.00 3.67
6033 8266 2.285950 CCGAAATATGTTTGTACGCGGG 60.286 50.000 12.47 0.00 30.42 6.13
6103 8337 3.317993 AGCACAAAATTAAAGAGCACCGT 59.682 39.130 0.00 0.00 0.00 4.83
6138 8372 3.129462 TCGTCTGCTCCTAGATTCAACAG 59.871 47.826 0.00 0.00 0.00 3.16
6144 8378 4.287067 TGCTCCTAGATTCAACAGGTCTTT 59.713 41.667 0.00 0.00 0.00 2.52
6146 8380 5.569630 GCTCCTAGATTCAACAGGTCTTTCA 60.570 44.000 0.00 0.00 0.00 2.69
6148 8382 7.633772 GCTCCTAGATTCAACAGGTCTTTCATA 60.634 40.741 0.00 0.00 0.00 2.15
6182 8417 9.496873 TTCTCAAATCTTAAAGTTCGAATACCA 57.503 29.630 0.00 0.00 0.00 3.25
6315 8560 3.731652 TCGGTCCGAAACACTTTTAGA 57.268 42.857 12.68 0.00 31.06 2.10
6319 8564 4.132336 GGTCCGAAACACTTTTAGACCTT 58.868 43.478 9.84 0.00 41.25 3.50
6320 8565 4.212847 GGTCCGAAACACTTTTAGACCTTC 59.787 45.833 9.84 0.00 41.25 3.46
6321 8566 4.053295 TCCGAAACACTTTTAGACCTTCG 58.947 43.478 0.00 0.00 35.25 3.79
6331 8576 1.940883 TAGACCTTCGACGCGGCAAT 61.941 55.000 14.85 0.00 0.00 3.56
6347 8592 2.560105 GGCAATCCATTTAGGCCAGATC 59.440 50.000 5.01 0.00 44.01 2.75
6348 8593 3.225104 GCAATCCATTTAGGCCAGATCA 58.775 45.455 5.01 0.00 37.29 2.92
6369 8614 2.882301 GTACGTTAGCCACCGCCG 60.882 66.667 0.00 0.00 34.57 6.46
6384 8630 2.447887 GCCGAGTGCGTCATGTGAG 61.448 63.158 0.00 0.00 35.23 3.51
6387 8633 0.388520 CGAGTGCGTCATGTGAGGAA 60.389 55.000 6.87 0.00 32.08 3.36
6388 8634 1.737029 CGAGTGCGTCATGTGAGGAAT 60.737 52.381 6.87 0.00 32.08 3.01
6394 8640 4.210120 GTGCGTCATGTGAGGAATCTATTC 59.790 45.833 6.87 0.00 36.08 1.75
6409 8655 5.912149 ATCTATTCTGGATACCAAAGCCA 57.088 39.130 0.00 0.00 30.80 4.75
6412 8658 1.367346 TCTGGATACCAAAGCCACCA 58.633 50.000 0.00 0.00 30.80 4.17
6413 8659 1.004277 TCTGGATACCAAAGCCACCAC 59.996 52.381 0.00 0.00 30.80 4.16
6416 8662 1.173913 GATACCAAAGCCACCACACC 58.826 55.000 0.00 0.00 0.00 4.16
6417 8663 0.608035 ATACCAAAGCCACCACACCG 60.608 55.000 0.00 0.00 0.00 4.94
6418 8664 3.977244 CCAAAGCCACCACACCGC 61.977 66.667 0.00 0.00 0.00 5.68
6419 8665 3.215568 CAAAGCCACCACACCGCA 61.216 61.111 0.00 0.00 0.00 5.69
6421 8667 3.714487 AAAGCCACCACACCGCACT 62.714 57.895 0.00 0.00 0.00 4.40
6422 8668 4.935495 AGCCACCACACCGCACTG 62.935 66.667 0.00 0.00 0.00 3.66
6432 8678 3.751246 CCGCACTGGGCCACATTG 61.751 66.667 0.00 6.14 40.31 2.82
6444 9358 1.213926 GCCACATTGAAGGAGGAGGAT 59.786 52.381 0.00 0.00 0.00 3.24
6447 9361 3.054139 CCACATTGAAGGAGGAGGATCAA 60.054 47.826 0.00 0.00 36.25 2.57
6457 9371 2.163211 GAGGAGGATCAACTTTTGCTGC 59.837 50.000 0.00 0.00 36.25 5.25
6461 9375 1.670967 GGATCAACTTTTGCTGCTGGC 60.671 52.381 0.00 0.00 42.22 4.85
6481 9395 1.903877 CGGGCTTGTCATGTCCCTCT 61.904 60.000 3.89 0.00 36.61 3.69
6483 9397 1.457346 GGCTTGTCATGTCCCTCTTG 58.543 55.000 0.00 0.00 0.00 3.02
6547 9461 2.687436 CCGATCAAACGTCGCGTC 59.313 61.111 5.77 0.00 39.99 5.19
6559 9473 0.737715 GTCGCGTCAAGAAGGAGCAT 60.738 55.000 5.77 0.00 0.00 3.79
6595 9509 2.066340 CCAGCCCAACACCTAGTGA 58.934 57.895 0.96 0.00 36.96 3.41
6596 9510 0.620556 CCAGCCCAACACCTAGTGAT 59.379 55.000 0.96 0.00 36.96 3.06
6598 9512 2.158900 CCAGCCCAACACCTAGTGATAG 60.159 54.545 0.96 0.00 36.96 2.08
6603 9517 2.501723 CCAACACCTAGTGATAGCTGGT 59.498 50.000 0.00 0.00 36.96 4.00
6642 9556 2.668632 GCCCTTCCCATCGTGTCA 59.331 61.111 0.00 0.00 0.00 3.58
6643 9557 1.224592 GCCCTTCCCATCGTGTCAT 59.775 57.895 0.00 0.00 0.00 3.06
6644 9558 0.815615 GCCCTTCCCATCGTGTCATC 60.816 60.000 0.00 0.00 0.00 2.92
6645 9559 0.530650 CCCTTCCCATCGTGTCATCG 60.531 60.000 0.00 0.00 0.00 3.84
6646 9560 1.154205 CCTTCCCATCGTGTCATCGC 61.154 60.000 0.00 0.00 0.00 4.58
6647 9561 1.153449 TTCCCATCGTGTCATCGCC 60.153 57.895 0.00 0.00 0.00 5.54
6648 9562 1.613317 TTCCCATCGTGTCATCGCCT 61.613 55.000 0.00 0.00 0.00 5.52
6649 9563 1.884464 CCCATCGTGTCATCGCCTG 60.884 63.158 0.00 0.00 0.00 4.85
6650 9564 1.153568 CCATCGTGTCATCGCCTGT 60.154 57.895 0.00 0.00 0.00 4.00
6651 9565 1.423721 CCATCGTGTCATCGCCTGTG 61.424 60.000 0.00 0.00 0.00 3.66
6652 9566 1.153568 ATCGTGTCATCGCCTGTGG 60.154 57.895 0.00 0.00 0.00 4.17
6653 9567 3.490759 CGTGTCATCGCCTGTGGC 61.491 66.667 0.00 0.00 46.75 5.01
6669 9583 3.053291 GCGCCCGACCATTGTGAA 61.053 61.111 0.00 0.00 0.00 3.18
6670 9584 3.039202 GCGCCCGACCATTGTGAAG 62.039 63.158 0.00 0.00 0.00 3.02
6671 9585 2.398554 CGCCCGACCATTGTGAAGG 61.399 63.158 0.00 0.00 0.00 3.46
6672 9586 1.002624 GCCCGACCATTGTGAAGGA 60.003 57.895 0.00 0.00 0.00 3.36
6673 9587 1.026718 GCCCGACCATTGTGAAGGAG 61.027 60.000 0.00 0.00 0.00 3.69
6674 9588 0.392998 CCCGACCATTGTGAAGGAGG 60.393 60.000 0.00 0.00 0.00 4.30
6675 9589 0.613260 CCGACCATTGTGAAGGAGGA 59.387 55.000 0.00 0.00 0.00 3.71
6676 9590 1.406069 CCGACCATTGTGAAGGAGGAG 60.406 57.143 0.00 0.00 0.00 3.69
6677 9591 1.743996 GACCATTGTGAAGGAGGAGC 58.256 55.000 0.00 0.00 0.00 4.70
6678 9592 0.036010 ACCATTGTGAAGGAGGAGCG 60.036 55.000 0.00 0.00 0.00 5.03
6679 9593 0.745845 CCATTGTGAAGGAGGAGCGG 60.746 60.000 0.00 0.00 0.00 5.52
6680 9594 1.078143 ATTGTGAAGGAGGAGCGGC 60.078 57.895 0.00 0.00 0.00 6.53
6681 9595 1.841302 ATTGTGAAGGAGGAGCGGCA 61.841 55.000 1.45 0.00 0.00 5.69
6682 9596 2.050836 TTGTGAAGGAGGAGCGGCAA 62.051 55.000 1.45 0.00 0.00 4.52
6683 9597 2.035442 GTGAAGGAGGAGCGGCAAC 61.035 63.158 1.45 0.00 0.00 4.17
6684 9598 2.436824 GAAGGAGGAGCGGCAACC 60.437 66.667 1.45 5.38 0.00 3.77
6769 9684 1.529713 CCTCCTCGTCTAGGGGCTC 60.530 68.421 0.00 0.00 45.79 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.252215 CCACTTTCATCGGCAAACAACTA 59.748 43.478 0.00 0.00 0.00 2.24
9 10 2.034558 CCACTTTCATCGGCAAACAACT 59.965 45.455 0.00 0.00 0.00 3.16
17 18 2.325082 ACGTGCCACTTTCATCGGC 61.325 57.895 0.00 0.00 46.43 5.54
19 20 0.439985 CTCACGTGCCACTTTCATCG 59.560 55.000 11.67 0.00 0.00 3.84
20 21 1.512926 ACTCACGTGCCACTTTCATC 58.487 50.000 11.67 0.00 0.00 2.92
31 32 2.220133 CGTTCTAAACCCAACTCACGTG 59.780 50.000 9.94 9.94 0.00 4.49
55 56 7.229530 CGTAAATAAGAACCAAACCGTCTTAC 58.770 38.462 0.00 0.00 0.00 2.34
57 58 5.179929 CCGTAAATAAGAACCAAACCGTCTT 59.820 40.000 0.00 0.00 0.00 3.01
62 63 5.009911 ACCAACCGTAAATAAGAACCAAACC 59.990 40.000 0.00 0.00 0.00 3.27
66 67 4.716794 ACACCAACCGTAAATAAGAACCA 58.283 39.130 0.00 0.00 0.00 3.67
67 68 5.694231 AACACCAACCGTAAATAAGAACC 57.306 39.130 0.00 0.00 0.00 3.62
72 73 6.302269 TCCCTTTAACACCAACCGTAAATAA 58.698 36.000 0.00 0.00 0.00 1.40
75 76 4.136051 CTCCCTTTAACACCAACCGTAAA 58.864 43.478 0.00 0.00 0.00 2.01
76 77 3.390639 TCTCCCTTTAACACCAACCGTAA 59.609 43.478 0.00 0.00 0.00 3.18
78 79 1.770061 TCTCCCTTTAACACCAACCGT 59.230 47.619 0.00 0.00 0.00 4.83
79 80 2.551032 GTTCTCCCTTTAACACCAACCG 59.449 50.000 0.00 0.00 0.00 4.44
80 81 3.568430 CAGTTCTCCCTTTAACACCAACC 59.432 47.826 0.00 0.00 0.00 3.77
103 104 2.693591 TCATACTAAGGTTGCCTCCTCG 59.306 50.000 0.00 0.00 36.74 4.63
110 111 5.451242 CCAGTCTCTCTCATACTAAGGTTGC 60.451 48.000 0.00 0.00 0.00 4.17
122 123 0.191064 ACCCAACCCAGTCTCTCTCA 59.809 55.000 0.00 0.00 0.00 3.27
142 143 7.768582 TCATAACAACTGATACACCATAGGTTG 59.231 37.037 0.00 0.00 36.28 3.77
156 157 6.045072 ACTCGGGTAATTCATAACAACTGA 57.955 37.500 0.00 0.00 0.00 3.41
169 170 4.918588 AGGAAACAATTGACTCGGGTAAT 58.081 39.130 13.59 0.00 0.00 1.89
185 186 2.747446 TGCTTTCGCATAGGAAGGAAAC 59.253 45.455 0.00 0.00 42.25 2.78
255 256 8.519492 TGTGTTTTTGTCTGAAGAAGAAAAAG 57.481 30.769 9.75 0.00 42.03 2.27
294 295 4.394729 ACCTTTCGTCTTGCTTCCATAAA 58.605 39.130 0.00 0.00 0.00 1.40
295 296 4.000988 GACCTTTCGTCTTGCTTCCATAA 58.999 43.478 0.00 0.00 38.57 1.90
296 297 3.007506 TGACCTTTCGTCTTGCTTCCATA 59.992 43.478 0.00 0.00 42.49 2.74
297 298 2.224523 TGACCTTTCGTCTTGCTTCCAT 60.225 45.455 0.00 0.00 42.49 3.41
298 299 1.140052 TGACCTTTCGTCTTGCTTCCA 59.860 47.619 0.00 0.00 42.49 3.53
334 335 2.677836 TCGATTGCTTTCGCTGCTATTT 59.322 40.909 0.00 0.00 38.97 1.40
343 344 1.840181 TCTCCGATCGATTGCTTTCG 58.160 50.000 18.66 1.85 40.46 3.46
365 366 2.106511 TGCATTCTCAATACTAGGGGGC 59.893 50.000 0.00 0.00 0.00 5.80
410 411 1.011242 CGTGGAAAGCACACACACG 60.011 57.895 0.00 0.00 46.82 4.49
432 451 3.997021 GCTTGAGAAGAAACCGAGATCAA 59.003 43.478 0.00 0.00 0.00 2.57
441 460 3.434984 CACTAGCCAGCTTGAGAAGAAAC 59.565 47.826 8.09 0.00 0.00 2.78
450 469 4.215349 GCTCCACTAGCCAGCTTG 57.785 61.111 0.00 0.00 46.25 4.01
460 479 3.118592 CGGATAAGAAAAGAGGCTCCACT 60.119 47.826 11.71 2.79 0.00 4.00
463 482 2.158885 AGCGGATAAGAAAAGAGGCTCC 60.159 50.000 11.71 0.00 0.00 4.70
492 511 1.290431 AGGAGAAGATGAGAGGCAGGA 59.710 52.381 0.00 0.00 0.00 3.86
532 709 3.117888 TGGAAAATGGGTCTAGAGATGGC 60.118 47.826 0.00 0.00 0.00 4.40
536 713 3.775316 GAGGTGGAAAATGGGTCTAGAGA 59.225 47.826 0.00 0.00 0.00 3.10
540 717 2.844348 GAGGAGGTGGAAAATGGGTCTA 59.156 50.000 0.00 0.00 0.00 2.59
542 719 1.679032 CGAGGAGGTGGAAAATGGGTC 60.679 57.143 0.00 0.00 0.00 4.46
550 727 0.898789 GAGTGGACGAGGAGGTGGAA 60.899 60.000 0.00 0.00 0.00 3.53
555 732 0.256464 AGGTAGAGTGGACGAGGAGG 59.744 60.000 0.00 0.00 0.00 4.30
557 734 0.255318 GGAGGTAGAGTGGACGAGGA 59.745 60.000 0.00 0.00 0.00 3.71
558 735 0.256464 AGGAGGTAGAGTGGACGAGG 59.744 60.000 0.00 0.00 0.00 4.63
561 738 0.173708 GCAAGGAGGTAGAGTGGACG 59.826 60.000 0.00 0.00 0.00 4.79
568 745 0.905357 GAAGCAGGCAAGGAGGTAGA 59.095 55.000 0.00 0.00 0.00 2.59
573 750 0.107459 GTAGGGAAGCAGGCAAGGAG 60.107 60.000 0.00 0.00 0.00 3.69
575 752 0.107459 GAGTAGGGAAGCAGGCAAGG 60.107 60.000 0.00 0.00 0.00 3.61
576 753 0.908198 AGAGTAGGGAAGCAGGCAAG 59.092 55.000 0.00 0.00 0.00 4.01
578 755 0.905357 GAAGAGTAGGGAAGCAGGCA 59.095 55.000 0.00 0.00 0.00 4.75
579 756 1.199615 AGAAGAGTAGGGAAGCAGGC 58.800 55.000 0.00 0.00 0.00 4.85
580 757 2.364002 GCTAGAAGAGTAGGGAAGCAGG 59.636 54.545 0.00 0.00 0.00 4.85
619 815 0.674534 ACGAGGAAGTATGGATCGGC 59.325 55.000 0.00 0.00 37.69 5.54
628 824 1.277273 TCTGAGGTCGACGAGGAAGTA 59.723 52.381 9.92 0.00 0.00 2.24
669 865 5.349543 CAGCTTTCTGTTTTCTTGCAAGTTT 59.650 36.000 25.19 0.00 35.61 2.66
706 903 7.759433 CACTGTTTTCCTTTTCTTTTCTGCTTA 59.241 33.333 0.00 0.00 0.00 3.09
709 906 6.099341 TCACTGTTTTCCTTTTCTTTTCTGC 58.901 36.000 0.00 0.00 0.00 4.26
710 907 7.276438 CCTTCACTGTTTTCCTTTTCTTTTCTG 59.724 37.037 0.00 0.00 0.00 3.02
712 909 7.320399 TCCTTCACTGTTTTCCTTTTCTTTTC 58.680 34.615 0.00 0.00 0.00 2.29
714 911 6.850752 TCCTTCACTGTTTTCCTTTTCTTT 57.149 33.333 0.00 0.00 0.00 2.52
716 913 6.663523 TCTTTCCTTCACTGTTTTCCTTTTCT 59.336 34.615 0.00 0.00 0.00 2.52
717 914 6.863275 TCTTTCCTTCACTGTTTTCCTTTTC 58.137 36.000 0.00 0.00 0.00 2.29
721 918 5.755849 TCTTCTTTCCTTCACTGTTTTCCT 58.244 37.500 0.00 0.00 0.00 3.36
722 919 6.451064 TTCTTCTTTCCTTCACTGTTTTCC 57.549 37.500 0.00 0.00 0.00 3.13
723 920 7.812669 TGTTTTCTTCTTTCCTTCACTGTTTTC 59.187 33.333 0.00 0.00 0.00 2.29
729 926 7.703058 TTTCTGTTTTCTTCTTTCCTTCACT 57.297 32.000 0.00 0.00 0.00 3.41
757 954 3.004315 TCTGTTCCGATTTTGCCAGTTTC 59.996 43.478 0.00 0.00 0.00 2.78
850 1057 1.489560 AAGGCGCCCAGTTAAGGACT 61.490 55.000 26.15 0.00 39.89 3.85
889 1097 0.930726 GGAGGAGGAGAGAAGAGGGA 59.069 60.000 0.00 0.00 0.00 4.20
1021 1232 1.132453 GGTATTGGTTCTCGCCTTTGC 59.868 52.381 0.00 0.00 0.00 3.68
1023 1234 1.633945 AGGGTATTGGTTCTCGCCTTT 59.366 47.619 0.00 0.00 0.00 3.11
1045 1256 4.101448 GCGTGATGCTCTGGGGGT 62.101 66.667 0.00 0.00 41.73 4.95
1350 1561 2.356553 GAAGTGGCACGTACCGCA 60.357 61.111 20.21 0.00 42.97 5.69
1364 1575 4.379243 ACGCGCACAGGGGAGAAG 62.379 66.667 5.73 0.00 37.07 2.85
1396 1612 2.484264 AGTTGCATCTTTACCGCTGAAC 59.516 45.455 0.00 0.00 0.00 3.18
1399 1615 3.236816 CAAAGTTGCATCTTTACCGCTG 58.763 45.455 19.67 6.39 36.12 5.18
1431 1647 2.426522 TCTACAATGCACACCAAGAGC 58.573 47.619 0.00 0.00 0.00 4.09
1598 1819 0.592500 CGTCCACATCTCCGTCATCG 60.593 60.000 0.00 0.00 0.00 3.84
1712 2015 6.045695 AGGTACAGCAATCTCCTAGGAGTATA 59.954 42.308 33.14 18.41 42.49 1.47
1732 2035 6.379988 ACCCAATTTTGTTCCATGATAGGTAC 59.620 38.462 0.00 0.00 0.00 3.34
1739 2042 4.222336 AGTGACCCAATTTTGTTCCATGA 58.778 39.130 0.00 0.00 0.00 3.07
1782 2087 1.358152 AGGGGCTAGCAACTGTTACA 58.642 50.000 18.24 0.00 0.00 2.41
1847 2153 7.767659 TGATCTTTAGAATGTCATGACAAGGAG 59.232 37.037 31.00 20.68 45.41 3.69
1897 2221 8.443176 TCTTCCTATTGCCTATTCAAGAATGAT 58.557 33.333 5.59 0.00 34.96 2.45
1906 2230 6.831976 TCCTTCTTCTTCCTATTGCCTATTC 58.168 40.000 0.00 0.00 0.00 1.75
2195 2519 6.980397 AGTTCAAATCATTTTCAAAGCGAAGT 59.020 30.769 0.00 0.00 34.32 3.01
2228 2552 1.824230 GCAATTGCCCCAACAGTATCA 59.176 47.619 20.06 0.00 34.31 2.15
2273 2597 1.471684 CTGGCCATCTGCTTCTCAAAC 59.528 52.381 5.51 0.00 40.92 2.93
2369 2693 7.487484 TGATCTAGTGAAGTGAGATAAAGCAG 58.513 38.462 0.00 0.00 30.01 4.24
2392 2716 6.665992 AACACTCATCAAGTACCTAACTGA 57.334 37.500 0.00 0.00 38.88 3.41
2406 2730 7.009540 GCAAACCAATAAGCATTAACACTCATC 59.990 37.037 0.00 0.00 32.17 2.92
2546 2874 4.030529 CGCATTTTAGCAAGACGATTTTGG 59.969 41.667 0.00 0.00 0.00 3.28
2593 2925 0.764226 CTTCACGCGTTTTGCTTTCG 59.236 50.000 10.22 0.00 43.27 3.46
2606 2938 4.865365 GTCCTGGACTTAATCTTCTTCACG 59.135 45.833 19.53 0.00 0.00 4.35
2632 2964 1.476110 CCTTCTTCAACAACCGGTGGA 60.476 52.381 18.24 5.11 0.00 4.02
2678 3016 4.959399 GCAGCTTCAGGATCTGCT 57.041 55.556 13.42 0.00 46.93 4.24
2769 3619 7.988028 AGATTAGCAAAGTTAACAGGGAGATAC 59.012 37.037 8.61 0.00 0.00 2.24
2921 3778 9.507329 TTCATTTTTCTAGTAAGAAGAGCATGT 57.493 29.630 0.00 0.00 42.60 3.21
3533 4395 4.883585 TGGACATCATCTGCCTTGTTATTC 59.116 41.667 0.00 0.00 0.00 1.75
3579 4441 8.581057 ACGTATAGATCATTCTGTTGTTCATC 57.419 34.615 0.00 0.00 33.17 2.92
3668 4530 7.335422 CCATCAAAGCTCTACATGGGATTATAC 59.665 40.741 0.00 0.00 31.85 1.47
3709 4571 1.542915 CAATGTCTGTCTTTGGGCCTG 59.457 52.381 4.53 0.00 0.00 4.85
3746 4608 5.915175 AGTACCTTCTTCCACGAATTATCC 58.085 41.667 0.00 0.00 0.00 2.59
3904 4766 2.026449 AGAAGGGATCTGCACTTTGGAG 60.026 50.000 0.00 0.00 41.32 3.86
3959 4821 3.022607 AGAAAGTAGGAACCAACGTCG 57.977 47.619 0.00 0.00 0.00 5.12
4033 4895 7.769507 TCTTCCTCAGAATCTGAATCAGAATTG 59.230 37.037 17.59 14.61 44.04 2.32
4141 5003 4.796946 GCTTCAACATCATCACCAGCAAAA 60.797 41.667 0.00 0.00 0.00 2.44
4173 5035 9.912634 CATTTAAAGCTTCCACTTTATCTTTCA 57.087 29.630 0.00 0.00 40.75 2.69
4177 5039 9.520515 TCTTCATTTAAAGCTTCCACTTTATCT 57.479 29.630 0.00 0.00 40.75 1.98
4187 5049 9.696917 TTCAGGATTTTCTTCATTTAAAGCTTC 57.303 29.630 0.00 0.00 0.00 3.86
4204 5066 4.401925 CAGGTTCTTCAGGTTCAGGATTT 58.598 43.478 0.00 0.00 0.00 2.17
4610 5575 1.737363 GCAGGTCGGTTAAGAGCAGAG 60.737 57.143 0.00 0.00 40.77 3.35
4645 5610 4.040095 ACAGCTTCATGCATCAGCTAGATA 59.960 41.667 23.59 0.00 42.15 1.98
4886 6014 7.878127 ACGGAAAAGAAGTCTTATCATCAAGAA 59.122 33.333 0.00 0.00 36.34 2.52
4893 6021 8.311836 ACTATTCACGGAAAAGAAGTCTTATCA 58.688 33.333 0.00 0.00 34.61 2.15
4910 6038 7.747888 TCATCAAATGTGGTTTACTATTCACG 58.252 34.615 0.00 0.00 33.25 4.35
4987 6115 6.932400 ACGATGTACAAGTATTTCCAAGTCAA 59.068 34.615 0.00 0.00 0.00 3.18
5009 6137 2.093106 GAGCCTGGAGACTTAAGACGA 58.907 52.381 10.09 0.00 0.00 4.20
5021 6149 6.070194 AGCTAAGTACAAAATTAGAGCCTGGA 60.070 38.462 0.00 0.00 31.87 3.86
5048 6176 8.316214 TGGGTTGTCGAGAATTATAGTTAAACT 58.684 33.333 0.00 0.00 0.00 2.66
5053 6181 6.469410 TGTTGGGTTGTCGAGAATTATAGTT 58.531 36.000 0.00 0.00 0.00 2.24
5063 6191 1.217882 GTGTCTGTTGGGTTGTCGAG 58.782 55.000 0.00 0.00 0.00 4.04
5075 6203 2.309528 TTTTCAGTCTGCGTGTCTGT 57.690 45.000 0.00 0.00 34.30 3.41
5092 6220 7.154656 GGTCATTTCTTAGAATTGGTGCTTTT 58.845 34.615 14.39 0.00 0.00 2.27
5190 6318 5.854745 CACGAACCCTAGTTCATGACAGATT 60.855 44.000 0.00 0.00 46.57 2.40
5274 6664 6.850555 GCTTGAGCTTAAGACAATTTGAGAT 58.149 36.000 21.52 0.00 38.21 2.75
5275 6665 6.246420 GCTTGAGCTTAAGACAATTTGAGA 57.754 37.500 21.52 0.00 38.21 3.27
5365 6755 7.053498 TGCCACTATGCTTCATTTGTTATCTA 58.947 34.615 0.00 0.00 0.00 1.98
5422 7650 5.359860 GGGAATCAAGGGTATAGTTGTTTGG 59.640 44.000 0.00 0.00 0.00 3.28
5462 7691 4.580167 CCACAACCTCAGATTCTTGTTTCA 59.420 41.667 0.00 0.00 0.00 2.69
5467 7696 3.743521 TGTCCACAACCTCAGATTCTTG 58.256 45.455 0.00 0.00 0.00 3.02
5480 7709 6.040278 TGTTGCTTCAAGATAATTGTCCACAA 59.960 34.615 0.00 0.00 40.51 3.33
5492 7721 5.733620 ATTGGTCATTGTTGCTTCAAGAT 57.266 34.783 0.00 0.00 0.00 2.40
5540 7770 8.462016 GTGTCTTAATCAACTGCATTAAGGAAT 58.538 33.333 13.95 0.00 41.37 3.01
5541 7771 7.360861 CGTGTCTTAATCAACTGCATTAAGGAA 60.361 37.037 13.95 3.77 41.37 3.36
5542 7772 6.092122 CGTGTCTTAATCAACTGCATTAAGGA 59.908 38.462 13.95 2.71 41.37 3.36
5543 7773 6.250819 CGTGTCTTAATCAACTGCATTAAGG 58.749 40.000 13.95 0.00 41.37 2.69
5544 7774 5.734498 GCGTGTCTTAATCAACTGCATTAAG 59.266 40.000 9.52 9.52 41.97 1.85
5545 7775 5.411361 AGCGTGTCTTAATCAACTGCATTAA 59.589 36.000 0.00 0.00 0.00 1.40
5546 7776 4.935205 AGCGTGTCTTAATCAACTGCATTA 59.065 37.500 0.00 0.00 0.00 1.90
5547 7777 3.753272 AGCGTGTCTTAATCAACTGCATT 59.247 39.130 0.00 0.00 0.00 3.56
5548 7778 3.338249 AGCGTGTCTTAATCAACTGCAT 58.662 40.909 0.00 0.00 0.00 3.96
5549 7779 2.766313 AGCGTGTCTTAATCAACTGCA 58.234 42.857 0.00 0.00 0.00 4.41
5566 7796 4.572389 ACAGCAATTAGAACCATAGAAGCG 59.428 41.667 0.00 0.00 0.00 4.68
5656 7886 1.952296 GGCTTCTCATGCGGATCAATT 59.048 47.619 0.00 0.00 0.00 2.32
5683 7913 0.976641 TCTGAATGACCCGCTTGAGT 59.023 50.000 0.00 0.00 0.00 3.41
5734 7964 0.859232 TCTTCGCTTGTTTCGCAGAC 59.141 50.000 0.00 0.00 34.32 3.51
5775 8005 4.707448 ACTGGGTACTACTGTCTCATCAAG 59.293 45.833 0.00 0.00 0.00 3.02
5776 8006 4.673968 ACTGGGTACTACTGTCTCATCAA 58.326 43.478 0.00 0.00 0.00 2.57
5792 8022 3.248024 TCTCTCACCACATTAACTGGGT 58.752 45.455 6.07 0.00 32.45 4.51
5793 8023 3.981071 TCTCTCACCACATTAACTGGG 57.019 47.619 6.07 0.00 32.45 4.45
5794 8024 3.624861 GCATCTCTCACCACATTAACTGG 59.375 47.826 0.22 0.22 34.62 4.00
5795 8025 3.308053 CGCATCTCTCACCACATTAACTG 59.692 47.826 0.00 0.00 0.00 3.16
5797 8027 2.030946 GCGCATCTCTCACCACATTAAC 59.969 50.000 0.30 0.00 0.00 2.01
5798 8028 2.279741 GCGCATCTCTCACCACATTAA 58.720 47.619 0.30 0.00 0.00 1.40
5801 8031 0.179702 ATGCGCATCTCTCACCACAT 59.820 50.000 19.28 0.00 0.00 3.21
5802 8032 0.823460 TATGCGCATCTCTCACCACA 59.177 50.000 29.11 1.32 0.00 4.17
5803 8033 1.594862 GTTATGCGCATCTCTCACCAC 59.405 52.381 29.11 8.00 0.00 4.16
5897 8130 1.940613 ACCAAAGCTGTCGTTTGACTC 59.059 47.619 0.00 0.00 45.70 3.36
5920 8153 2.203351 CCCCCGCTTCCAATAGCC 60.203 66.667 0.00 0.00 37.90 3.93
5941 8174 1.532794 TGTGAACAATGGCACCCCC 60.533 57.895 0.00 0.00 34.19 5.40
5976 8209 4.964593 ACCAGCTGCAAAATTTCAAATCT 58.035 34.783 8.66 0.00 0.00 2.40
6033 8266 4.296690 ACACTACACTAACTTGCGACTTC 58.703 43.478 0.00 0.00 0.00 3.01
6065 8299 9.845740 AATTTTGTGCTACATATAGATACCACA 57.154 29.630 0.00 0.00 30.43 4.17
6103 8337 1.930817 GCAGACGAGACGAGAAGCAAA 60.931 52.381 0.00 0.00 0.00 3.68
6205 8440 8.844244 AGTTTATACATGAATGGCTCAGAATTC 58.156 33.333 0.00 0.00 37.52 2.17
6270 8505 9.160496 GAACATATGTGAGACTTTGATTTCTCT 57.840 33.333 9.63 0.00 39.30 3.10
6272 8507 7.065085 CCGAACATATGTGAGACTTTGATTTCT 59.935 37.037 9.63 0.00 0.00 2.52
6273 8508 7.148407 ACCGAACATATGTGAGACTTTGATTTC 60.148 37.037 9.63 0.00 0.00 2.17
6274 8509 6.655003 ACCGAACATATGTGAGACTTTGATTT 59.345 34.615 9.63 0.00 0.00 2.17
6275 8510 6.173339 ACCGAACATATGTGAGACTTTGATT 58.827 36.000 9.63 0.00 0.00 2.57
6277 8512 5.147330 ACCGAACATATGTGAGACTTTGA 57.853 39.130 9.63 0.00 0.00 2.69
6278 8513 4.330074 GGACCGAACATATGTGAGACTTTG 59.670 45.833 9.63 0.00 0.00 2.77
6279 8514 4.504858 GGACCGAACATATGTGAGACTTT 58.495 43.478 9.63 0.00 0.00 2.66
6280 8515 3.428999 CGGACCGAACATATGTGAGACTT 60.429 47.826 8.64 0.00 0.00 3.01
6281 8516 2.099263 CGGACCGAACATATGTGAGACT 59.901 50.000 8.64 0.00 0.00 3.24
6284 8519 2.863401 TCGGACCGAACATATGTGAG 57.137 50.000 15.79 6.49 31.06 3.51
6285 8520 3.255725 GTTTCGGACCGAACATATGTGA 58.744 45.455 28.45 9.03 45.64 3.58
6286 8521 2.997303 TGTTTCGGACCGAACATATGTG 59.003 45.455 28.45 0.00 45.64 3.21
6287 8522 2.997986 GTGTTTCGGACCGAACATATGT 59.002 45.455 28.45 1.41 45.64 2.29
6315 8560 2.813908 GATTGCCGCGTCGAAGGT 60.814 61.111 4.92 0.00 0.00 3.50
6319 8564 0.460459 TAAATGGATTGCCGCGTCGA 60.460 50.000 4.92 0.00 36.79 4.20
6320 8565 0.042188 CTAAATGGATTGCCGCGTCG 60.042 55.000 4.92 0.00 36.79 5.12
6321 8566 0.307760 CCTAAATGGATTGCCGCGTC 59.692 55.000 4.92 0.00 38.35 5.19
6331 8576 2.103094 CGTCTGATCTGGCCTAAATGGA 59.897 50.000 3.32 0.00 38.35 3.41
6347 8592 0.795735 CGGTGGCTAACGTACGTCTG 60.796 60.000 23.05 17.59 0.00 3.51
6348 8593 1.503542 CGGTGGCTAACGTACGTCT 59.496 57.895 23.05 14.07 0.00 4.18
6369 8614 1.929836 GATTCCTCACATGACGCACTC 59.070 52.381 0.00 0.00 0.00 3.51
6377 8623 7.102346 GGTATCCAGAATAGATTCCTCACATG 58.898 42.308 0.00 0.00 37.51 3.21
6378 8624 6.789457 TGGTATCCAGAATAGATTCCTCACAT 59.211 38.462 0.00 0.00 37.51 3.21
6380 8626 6.672266 TGGTATCCAGAATAGATTCCTCAC 57.328 41.667 0.00 0.00 37.51 3.51
6384 8630 5.707764 GGCTTTGGTATCCAGAATAGATTCC 59.292 44.000 0.00 0.00 37.51 3.01
6387 8633 5.456763 GGTGGCTTTGGTATCCAGAATAGAT 60.457 44.000 0.00 0.00 33.81 1.98
6388 8634 4.141482 GGTGGCTTTGGTATCCAGAATAGA 60.141 45.833 0.00 0.00 33.81 1.98
6394 8640 1.271871 TGTGGTGGCTTTGGTATCCAG 60.272 52.381 0.00 0.00 33.81 3.86
6416 8662 2.203972 CTTCAATGTGGCCCAGTGCG 62.204 60.000 14.47 6.60 42.61 5.34
6417 8663 1.588082 CTTCAATGTGGCCCAGTGC 59.412 57.895 14.47 0.00 38.99 4.40
6418 8664 0.251297 TCCTTCAATGTGGCCCAGTG 60.251 55.000 13.45 13.45 40.47 3.66
6419 8665 0.038744 CTCCTTCAATGTGGCCCAGT 59.961 55.000 0.00 0.00 0.00 4.00
6421 8667 1.139498 TCCTCCTTCAATGTGGCCCA 61.139 55.000 0.00 0.00 0.00 5.36
6422 8668 0.394899 CTCCTCCTTCAATGTGGCCC 60.395 60.000 0.00 0.00 0.00 5.80
6423 8669 0.394899 CCTCCTCCTTCAATGTGGCC 60.395 60.000 0.00 0.00 0.00 5.36
6424 8670 0.620556 TCCTCCTCCTTCAATGTGGC 59.379 55.000 0.00 0.00 0.00 5.01
6425 8671 2.507058 TGATCCTCCTCCTTCAATGTGG 59.493 50.000 0.00 0.00 0.00 4.17
6426 8672 3.920231 TGATCCTCCTCCTTCAATGTG 57.080 47.619 0.00 0.00 0.00 3.21
6429 8675 5.527026 AAAGTTGATCCTCCTCCTTCAAT 57.473 39.130 0.00 0.00 31.39 2.57
6432 8678 3.441922 GCAAAAGTTGATCCTCCTCCTTC 59.558 47.826 0.00 0.00 0.00 3.46
6444 9358 1.741525 GGCCAGCAGCAAAAGTTGA 59.258 52.632 0.00 0.00 46.50 3.18
6447 9361 3.297620 CCGGCCAGCAGCAAAAGT 61.298 61.111 2.24 0.00 46.50 2.66
6457 9371 3.136123 CATGACAAGCCCGGCCAG 61.136 66.667 5.55 0.88 0.00 4.85
6461 9375 2.438434 GGGACATGACAAGCCCGG 60.438 66.667 0.00 0.00 0.00 5.73
6481 9395 1.971167 GTTGCACCGGCTCATCCAA 60.971 57.895 0.00 0.00 41.91 3.53
6483 9397 3.134127 GGTTGCACCGGCTCATCC 61.134 66.667 0.00 4.53 41.91 3.51
6531 9445 0.246374 CTTGACGCGACGTTTGATCG 60.246 55.000 15.93 0.00 41.37 3.69
6536 9450 0.249155 TCCTTCTTGACGCGACGTTT 60.249 50.000 15.93 0.00 41.37 3.60
6547 9461 2.101700 GGGCGAATGCTCCTTCTTG 58.898 57.895 0.00 0.00 42.25 3.02
6603 9517 2.738521 GCTTCTGCTTGACGGCGA 60.739 61.111 16.62 0.00 36.03 5.54
6652 9566 3.039202 CTTCACAATGGTCGGGCGC 62.039 63.158 0.00 0.00 0.00 6.53
6653 9567 2.398554 CCTTCACAATGGTCGGGCG 61.399 63.158 0.00 0.00 0.00 6.13
6654 9568 1.002624 TCCTTCACAATGGTCGGGC 60.003 57.895 0.00 0.00 0.00 6.13
6655 9569 0.392998 CCTCCTTCACAATGGTCGGG 60.393 60.000 0.00 0.00 0.00 5.14
6656 9570 0.613260 TCCTCCTTCACAATGGTCGG 59.387 55.000 0.00 0.00 0.00 4.79
6657 9571 2.009042 GCTCCTCCTTCACAATGGTCG 61.009 57.143 0.00 0.00 0.00 4.79
6658 9572 1.743996 GCTCCTCCTTCACAATGGTC 58.256 55.000 0.00 0.00 0.00 4.02
6659 9573 0.036010 CGCTCCTCCTTCACAATGGT 60.036 55.000 0.00 0.00 0.00 3.55
6660 9574 0.745845 CCGCTCCTCCTTCACAATGG 60.746 60.000 0.00 0.00 0.00 3.16
6661 9575 1.372087 GCCGCTCCTCCTTCACAATG 61.372 60.000 0.00 0.00 0.00 2.82
6662 9576 1.078143 GCCGCTCCTCCTTCACAAT 60.078 57.895 0.00 0.00 0.00 2.71
6663 9577 2.050836 TTGCCGCTCCTCCTTCACAA 62.051 55.000 0.00 0.00 0.00 3.33
6664 9578 2.515979 TTGCCGCTCCTCCTTCACA 61.516 57.895 0.00 0.00 0.00 3.58
6665 9579 2.035442 GTTGCCGCTCCTCCTTCAC 61.035 63.158 0.00 0.00 0.00 3.18
6666 9580 2.347490 GTTGCCGCTCCTCCTTCA 59.653 61.111 0.00 0.00 0.00 3.02
6667 9581 2.436824 GGTTGCCGCTCCTCCTTC 60.437 66.667 0.00 0.00 0.00 3.46
6668 9582 4.394712 CGGTTGCCGCTCCTCCTT 62.395 66.667 0.00 0.00 41.17 3.36
6679 9593 3.712881 GTGTGGCGAGACGGTTGC 61.713 66.667 0.00 0.00 34.28 4.17
6680 9594 3.041940 GGTGTGGCGAGACGGTTG 61.042 66.667 0.00 0.00 0.00 3.77
6681 9595 3.231736 AGGTGTGGCGAGACGGTT 61.232 61.111 0.00 0.00 0.00 4.44
6682 9596 3.991051 CAGGTGTGGCGAGACGGT 61.991 66.667 0.00 0.00 0.00 4.83
6684 9598 4.662961 TGCAGGTGTGGCGAGACG 62.663 66.667 0.00 0.00 0.00 4.18
6685 9599 3.044305 GTGCAGGTGTGGCGAGAC 61.044 66.667 0.00 0.00 0.00 3.36
6686 9600 3.545574 TGTGCAGGTGTGGCGAGA 61.546 61.111 0.00 0.00 0.00 4.04
6687 9601 3.349006 GTGTGCAGGTGTGGCGAG 61.349 66.667 0.00 0.00 0.00 5.03
6688 9602 4.927782 GGTGTGCAGGTGTGGCGA 62.928 66.667 0.00 0.00 0.00 5.54
6755 9670 0.382515 CTTTCGAGCCCCTAGACGAG 59.617 60.000 0.00 0.00 36.22 4.18


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

AutoCloner maintained by Alex Coulton.