Multiple sequence alignment - TraesCS7B01G242100

Loading Multiple Alignment...

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 TraesCS7B01G242100 chr7B 100.000 5519 0 0 1534 7052 450267361 450272879 0.000000e+00 10192.0
1 TraesCS7B01G242100 chr7B 100.000 1292 0 0 1 1292 450265828 450267119 0.000000e+00 2386.0
2 TraesCS7B01G242100 chr7A 93.534 4160 186 29 2234 6327 500326006 500330148 0.000000e+00 6115.0
3 TraesCS7B01G242100 chr7A 90.145 619 37 12 1534 2128 500325387 500326005 0.000000e+00 784.0
4 TraesCS7B01G242100 chr7A 91.053 570 30 7 733 1292 500324800 500325358 0.000000e+00 750.0
5 TraesCS7B01G242100 chr7A 85.240 271 29 7 3530 3800 500327767 500328026 1.170000e-67 268.0
6 TraesCS7B01G242100 chr7A 82.915 199 17 5 6495 6676 500330391 500330589 5.660000e-36 163.0
7 TraesCS7B01G242100 chr7A 89.524 105 11 0 2132 2236 371770052 371769948 4.440000e-27 134.0
8 TraesCS7B01G242100 chr7D 94.803 3906 133 25 1534 5379 432495484 432491589 0.000000e+00 6024.0
9 TraesCS7B01G242100 chr7D 97.319 1007 23 2 5321 6327 432491594 432490592 0.000000e+00 1707.0
10 TraesCS7B01G242100 chr7D 91.194 829 40 9 483 1292 432496327 432495513 0.000000e+00 1096.0
11 TraesCS7B01G242100 chr7D 84.861 469 38 13 1 464 432497280 432496840 6.490000e-120 442.0
12 TraesCS7B01G242100 chr7D 88.643 361 19 10 6339 6680 432490546 432490189 3.040000e-113 420.0
13 TraesCS7B01G242100 chr7D 90.000 310 20 9 6749 7052 432490188 432489884 2.390000e-104 390.0
14 TraesCS7B01G242100 chr7D 89.524 105 11 0 2132 2236 333690868 333690972 4.440000e-27 134.0
15 TraesCS7B01G242100 chr2B 90.741 108 10 0 2129 2236 353566029 353566136 2.050000e-30 145.0
16 TraesCS7B01G242100 chr3D 90.654 107 10 0 2130 2236 513957384 513957278 7.370000e-30 143.0
17 TraesCS7B01G242100 chr3D 90.654 107 10 0 2130 2236 579138798 579138692 7.370000e-30 143.0
18 TraesCS7B01G242100 chr2D 89.720 107 11 0 2130 2236 388818757 388818863 3.430000e-28 137.0
19 TraesCS7B01G242100 chr1A 89.189 111 11 1 2130 2240 104946164 104946055 3.430000e-28 137.0
20 TraesCS7B01G242100 chr1A 96.875 32 0 1 6666 6696 518952754 518952723 1.300000e-02 52.8
21 TraesCS7B01G242100 chr3B 87.500 112 12 2 2126 2236 157237742 157237632 2.060000e-25 128.0


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 TraesCS7B01G242100 chr7B 450265828 450272879 7051 False 6289.000000 10192 100.000000 1 7052 2 chr7B.!!$F1 7051
1 TraesCS7B01G242100 chr7A 500324800 500330589 5789 False 1616.000000 6115 88.577400 733 6676 5 chr7A.!!$F1 5943
2 TraesCS7B01G242100 chr7D 432489884 432497280 7396 True 1679.833333 6024 91.136667 1 7052 6 chr7D.!!$R1 7051

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
922 1437 0.027063 CGGTCGTCGCAAACTTGTTT 59.973 50.000 0.00 0.00 0.00 2.83 F
1806 2346 0.029834 GCAGTCTGTGTGCCTTGTTG 59.970 55.000 0.93 0.00 34.67 3.33 F
3430 4018 1.005748 GCAAACAAGGAAGGGCTGC 60.006 57.895 0.00 0.00 0.00 5.25 F
4144 4742 0.601576 TTAAGGAAAGTGCGCTGCGA 60.602 50.000 28.07 8.22 0.00 5.10 F
5221 5841 0.038310 GGGGCTATAATGGTCCTGGC 59.962 60.000 0.00 0.00 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2571 3121 0.038166 AGGTACACATGGCACCCAAG 59.962 55.000 0.00 0.00 36.95 3.61 R
3502 4090 3.308035 TCCTAGGTATCCACGTGTCAT 57.692 47.619 15.65 8.58 0.00 3.06 R
5134 5754 0.322008 GGAACCTTGCACCTCCTCTG 60.322 60.000 0.00 0.00 0.00 3.35 R
6015 6688 0.543277 CCCTACCATGAAGAGCAGCA 59.457 55.000 0.00 0.00 0.00 4.41 R
6727 7511 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40 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
49 50 7.254218 CCAGATTTTGTTCTTCAAGAAAGCAAC 60.254 37.037 0.00 0.00 35.75 4.17
79 80 5.452078 TTTTCTTTGACCTGCCAATGTAG 57.548 39.130 0.00 0.00 0.00 2.74
83 84 3.998913 TTGACCTGCCAATGTAGATCA 57.001 42.857 0.00 0.00 0.00 2.92
85 86 3.609853 TGACCTGCCAATGTAGATCAAC 58.390 45.455 0.00 0.00 0.00 3.18
96 97 7.335924 GCCAATGTAGATCAACAAACTAAGGTA 59.664 37.037 0.00 0.00 32.02 3.08
100 101 7.609056 TGTAGATCAACAAACTAAGGTACTCC 58.391 38.462 0.00 0.00 38.49 3.85
123 124 5.984926 CCTTGTTTCATGTTTGCTTGTGTAT 59.015 36.000 0.00 0.00 0.00 2.29
124 125 6.144402 CCTTGTTTCATGTTTGCTTGTGTATC 59.856 38.462 0.00 0.00 0.00 2.24
125 126 6.389830 TGTTTCATGTTTGCTTGTGTATCT 57.610 33.333 0.00 0.00 0.00 1.98
126 127 6.437928 TGTTTCATGTTTGCTTGTGTATCTC 58.562 36.000 0.00 0.00 0.00 2.75
127 128 5.627499 TTCATGTTTGCTTGTGTATCTCC 57.373 39.130 0.00 0.00 0.00 3.71
129 130 2.422597 TGTTTGCTTGTGTATCTCCGG 58.577 47.619 0.00 0.00 0.00 5.14
130 131 2.037902 TGTTTGCTTGTGTATCTCCGGA 59.962 45.455 2.93 2.93 0.00 5.14
170 171 1.896220 TGCTTGCCGACTTGATTTCT 58.104 45.000 0.00 0.00 0.00 2.52
181 182 4.849926 CGACTTGATTTCTTGCTGAACATG 59.150 41.667 0.00 0.00 33.88 3.21
182 183 5.561532 CGACTTGATTTCTTGCTGAACATGT 60.562 40.000 0.00 0.00 33.88 3.21
195 196 5.105797 TGCTGAACATGTTTGTTGAGTTCTT 60.106 36.000 13.36 0.00 45.51 2.52
222 223 7.209471 TGTTAATACAAAGCTCCGAAACAAT 57.791 32.000 0.00 0.00 0.00 2.71
240 241 8.502161 GAAACAATTTTCGTACAATGCTAAGT 57.498 30.769 0.00 0.00 32.08 2.24
241 242 8.865590 AAACAATTTTCGTACAATGCTAAGTT 57.134 26.923 0.00 0.00 0.00 2.66
242 243 8.502161 AACAATTTTCGTACAATGCTAAGTTC 57.498 30.769 0.00 0.00 0.00 3.01
243 244 7.871853 ACAATTTTCGTACAATGCTAAGTTCT 58.128 30.769 0.00 0.00 0.00 3.01
244 245 8.349983 ACAATTTTCGTACAATGCTAAGTTCTT 58.650 29.630 0.00 0.00 0.00 2.52
245 246 9.180678 CAATTTTCGTACAATGCTAAGTTCTTT 57.819 29.630 0.00 0.00 0.00 2.52
246 247 9.744468 AATTTTCGTACAATGCTAAGTTCTTTT 57.256 25.926 0.00 0.00 0.00 2.27
247 248 9.744468 ATTTTCGTACAATGCTAAGTTCTTTTT 57.256 25.926 0.00 0.00 0.00 1.94
251 252 9.872757 TCGTACAATGCTAAGTTCTTTTTAAAG 57.127 29.630 0.00 0.00 37.36 1.85
252 253 8.627428 CGTACAATGCTAAGTTCTTTTTAAAGC 58.373 33.333 0.00 0.00 35.99 3.51
253 254 7.946655 ACAATGCTAAGTTCTTTTTAAAGCC 57.053 32.000 0.00 0.00 35.99 4.35
254 255 7.496747 ACAATGCTAAGTTCTTTTTAAAGCCA 58.503 30.769 0.00 0.00 35.99 4.75
255 256 7.438160 ACAATGCTAAGTTCTTTTTAAAGCCAC 59.562 33.333 0.00 0.00 35.99 5.01
256 257 6.709018 TGCTAAGTTCTTTTTAAAGCCACT 57.291 33.333 0.00 0.48 35.99 4.00
262 263 3.832527 TCTTTTTAAAGCCACTGCCTCT 58.167 40.909 0.00 0.00 38.69 3.69
270 271 2.125350 CACTGCCTCTTCCGCCTC 60.125 66.667 0.00 0.00 0.00 4.70
271 272 3.394836 ACTGCCTCTTCCGCCTCC 61.395 66.667 0.00 0.00 0.00 4.30
281 282 3.854669 CCGCCTCCGCCTTGATCT 61.855 66.667 0.00 0.00 0.00 2.75
290 291 1.821332 GCCTTGATCTTGAGGGCCG 60.821 63.158 0.00 0.00 37.12 6.13
304 305 4.894784 TGAGGGCCGAATCATCTATAAAC 58.105 43.478 0.00 0.00 0.00 2.01
310 311 6.316390 GGGCCGAATCATCTATAAACAATAGG 59.684 42.308 0.00 0.00 38.53 2.57
360 361 6.516739 AATTCTTAGCCCACTTAGCTTTTC 57.483 37.500 0.00 0.00 41.83 2.29
362 363 4.579869 TCTTAGCCCACTTAGCTTTTCAG 58.420 43.478 0.00 0.00 41.83 3.02
366 367 4.923415 AGCCCACTTAGCTTTTCAGTTAT 58.077 39.130 0.00 0.00 37.24 1.89
368 369 4.096532 GCCCACTTAGCTTTTCAGTTATCC 59.903 45.833 0.00 0.00 0.00 2.59
369 370 4.332819 CCCACTTAGCTTTTCAGTTATCCG 59.667 45.833 0.00 0.00 0.00 4.18
370 371 4.935808 CCACTTAGCTTTTCAGTTATCCGT 59.064 41.667 0.00 0.00 0.00 4.69
373 374 1.732259 AGCTTTTCAGTTATCCGTGCG 59.268 47.619 0.00 0.00 0.00 5.34
374 375 1.463444 GCTTTTCAGTTATCCGTGCGT 59.537 47.619 0.00 0.00 0.00 5.24
384 385 7.201835 TCAGTTATCCGTGCGTTATGTAATAA 58.798 34.615 0.00 0.00 36.20 1.40
385 386 7.380333 TCAGTTATCCGTGCGTTATGTAATAAG 59.620 37.037 0.00 0.00 39.94 1.73
386 387 6.643770 AGTTATCCGTGCGTTATGTAATAAGG 59.356 38.462 0.00 0.00 44.97 2.69
393 399 3.811083 CGTTATGTAATAAGGCCCACCA 58.189 45.455 0.00 0.00 39.94 4.17
414 420 4.438065 CCACTCATCACACAACACGAAAAA 60.438 41.667 0.00 0.00 0.00 1.94
415 421 5.273170 CACTCATCACACAACACGAAAAAT 58.727 37.500 0.00 0.00 0.00 1.82
420 426 7.643579 TCATCACACAACACGAAAAATTATGA 58.356 30.769 0.00 0.00 0.00 2.15
464 470 4.043435 AGAGCCCCTTTGACAGATTTAACT 59.957 41.667 0.00 0.00 0.00 2.24
465 471 4.336280 AGCCCCTTTGACAGATTTAACTC 58.664 43.478 0.00 0.00 0.00 3.01
466 472 3.127030 GCCCCTTTGACAGATTTAACTCG 59.873 47.826 0.00 0.00 0.00 4.18
467 473 4.575885 CCCCTTTGACAGATTTAACTCGA 58.424 43.478 0.00 0.00 0.00 4.04
468 474 4.631813 CCCCTTTGACAGATTTAACTCGAG 59.368 45.833 11.84 11.84 0.00 4.04
469 475 4.093556 CCCTTTGACAGATTTAACTCGAGC 59.906 45.833 13.61 0.00 0.00 5.03
470 476 4.690748 CCTTTGACAGATTTAACTCGAGCA 59.309 41.667 13.61 0.00 0.00 4.26
471 477 5.179368 CCTTTGACAGATTTAACTCGAGCAA 59.821 40.000 13.61 3.94 0.00 3.91
487 515 3.242220 CGAGCAAGAGTATGTGTGATTGC 60.242 47.826 0.00 0.00 42.48 3.56
488 516 2.674852 AGCAAGAGTATGTGTGATTGCG 59.325 45.455 0.00 0.00 45.73 4.85
490 518 2.385013 AGAGTATGTGTGATTGCGCA 57.615 45.000 5.66 5.66 0.00 6.09
496 524 3.819188 TGTGATTGCGCACACACA 58.181 50.000 31.24 31.24 43.35 3.72
497 525 1.354858 TGTGATTGCGCACACACAC 59.645 52.632 31.24 25.90 43.35 3.82
498 526 1.094650 TGTGATTGCGCACACACACT 61.095 50.000 31.24 6.28 43.35 3.55
499 527 0.029300 GTGATTGCGCACACACACTT 59.971 50.000 29.00 3.80 38.63 3.16
500 528 0.737804 TGATTGCGCACACACACTTT 59.262 45.000 11.12 0.00 0.00 2.66
521 1022 0.471211 GGGTCGATCCATCCCCTACA 60.471 60.000 10.69 0.00 38.11 2.74
534 1035 2.381961 TCCCCTACAGAAGCCCAATTTT 59.618 45.455 0.00 0.00 0.00 1.82
545 1046 6.544931 CAGAAGCCCAATTTTCTCATCATCTA 59.455 38.462 0.00 0.00 31.53 1.98
558 1059 7.815840 TCTCATCATCTATTCGAGAAAGTCT 57.184 36.000 0.00 0.00 37.85 3.24
568 1069 4.855715 TCGAGAAAGTCTCACTCATGTT 57.144 40.909 6.12 0.00 43.55 2.71
647 1148 7.240674 TGAAATAACTCATACGCAATCAACAC 58.759 34.615 0.00 0.00 0.00 3.32
668 1169 9.663904 CAACACATTATCAATTATAAACCTCCG 57.336 33.333 0.00 0.00 33.76 4.63
678 1179 9.151177 TCAATTATAAACCTCCGTAGTAGGAAT 57.849 33.333 0.00 0.00 34.53 3.01
721 1233 1.003580 TCTCCTTTGAGGCGATTTGCT 59.996 47.619 0.00 0.00 45.43 3.91
722 1234 2.236146 TCTCCTTTGAGGCGATTTGCTA 59.764 45.455 0.00 0.00 45.43 3.49
723 1235 2.611292 CTCCTTTGAGGCGATTTGCTAG 59.389 50.000 0.00 0.00 45.43 3.42
724 1236 1.064654 CCTTTGAGGCGATTTGCTAGC 59.935 52.381 8.10 8.10 45.43 3.42
725 1237 1.739466 CTTTGAGGCGATTTGCTAGCA 59.261 47.619 14.93 14.93 45.43 3.49
726 1238 2.042686 TTGAGGCGATTTGCTAGCAT 57.957 45.000 20.13 3.92 45.43 3.79
755 1267 7.105588 TGAGACAAGCTTACACACATATCAAT 58.894 34.615 0.00 0.00 0.00 2.57
771 1283 1.176527 CAATGGCCAGAATCAACCGT 58.823 50.000 13.05 0.00 0.00 4.83
772 1284 2.026729 TCAATGGCCAGAATCAACCGTA 60.027 45.455 13.05 0.00 0.00 4.02
786 1298 1.101331 ACCGTATCGTGAAGACCCTC 58.899 55.000 0.00 0.00 0.00 4.30
792 1304 1.116308 TCGTGAAGACCCTCACAACA 58.884 50.000 4.75 0.00 45.03 3.33
866 1380 4.803426 CCAGTCCGCTCGCACCTC 62.803 72.222 0.00 0.00 0.00 3.85
922 1437 0.027063 CGGTCGTCGCAAACTTGTTT 59.973 50.000 0.00 0.00 0.00 2.83
1806 2346 0.029834 GCAGTCTGTGTGCCTTGTTG 59.970 55.000 0.93 0.00 34.67 3.33
1833 2373 6.091169 TCCGTTTGGTCGTTAGATAATTCAAC 59.909 38.462 0.00 0.00 36.30 3.18
1839 2379 7.259882 TGGTCGTTAGATAATTCAACGTGTAT 58.740 34.615 6.05 0.00 44.02 2.29
1952 2493 9.535878 GTTTATCTGTTTGGGTTGTTTTGATTA 57.464 29.630 0.00 0.00 0.00 1.75
1984 2525 3.703556 TCAAGGCTTTGAACATGTTTGGA 59.296 39.130 13.36 0.00 40.26 3.53
2076 2624 9.183368 TGCATAATCATAACCAGTTTTATGTGA 57.817 29.630 11.48 0.00 39.52 3.58
2081 2629 7.624360 TCATAACCAGTTTTATGTGATGGTC 57.376 36.000 0.00 0.00 43.36 4.02
2088 2636 6.823182 CCAGTTTTATGTGATGGTCAGATACA 59.177 38.462 0.00 0.00 33.14 2.29
2128 2676 4.580167 TGCAGTCAAAGTTGCTGTAGATTT 59.420 37.500 13.35 0.00 40.87 2.17
2138 2686 4.755266 TGCTGTAGATTTTACTCCCTCC 57.245 45.455 0.00 0.00 0.00 4.30
2139 2687 4.101114 TGCTGTAGATTTTACTCCCTCCA 58.899 43.478 0.00 0.00 0.00 3.86
2157 2705 4.040461 CCTCCATCCCATATTAGTTGTCGT 59.960 45.833 0.00 0.00 0.00 4.34
2158 2706 4.956085 TCCATCCCATATTAGTTGTCGTG 58.044 43.478 0.00 0.00 0.00 4.35
2208 2756 6.814954 ATGTCTAGGTACATCCATTTCAGT 57.185 37.500 0.00 0.00 35.08 3.41
2210 2758 5.719563 TGTCTAGGTACATCCATTTCAGTGA 59.280 40.000 0.00 0.00 39.02 3.41
2247 2796 4.776308 ACGGAGGGAGTAGTTTTTCTATGT 59.224 41.667 0.00 0.00 0.00 2.29
2460 3010 7.386059 TCTGAGTGAAACAGCTAACATGATAA 58.614 34.615 0.00 0.00 41.43 1.75
2521 3071 1.150827 GCTTGGTGCAGGCATTTTTC 58.849 50.000 0.00 0.00 42.31 2.29
2538 3088 7.255416 GGCATTTTTCCATGGTAAATTGTGTTT 60.255 33.333 26.23 7.81 0.00 2.83
2807 3369 6.660521 TGAAATTTTCACCATGCAGAGAGTAT 59.339 34.615 7.74 0.00 34.08 2.12
2885 3468 9.188588 CATTTGCTCTGGCTTTTGTATATAATG 57.811 33.333 0.00 0.00 39.59 1.90
3430 4018 1.005748 GCAAACAAGGAAGGGCTGC 60.006 57.895 0.00 0.00 0.00 5.25
3502 4090 8.220755 AGCTACAAGTCTTGTTGAAATTAACA 57.779 30.769 25.27 4.72 42.22 2.41
3516 4104 7.067532 TGAAATTAACATGACACGTGGATAC 57.932 36.000 21.57 8.76 0.00 2.24
3586 4174 1.352352 CAACCTGACCAACTCCTCCAT 59.648 52.381 0.00 0.00 0.00 3.41
3685 4273 4.152402 CGTTCGTCTGACCATCTTTTCAAT 59.848 41.667 1.55 0.00 0.00 2.57
3767 4355 3.730061 GCAAGTGCAGCAGTTGATATCAC 60.730 47.826 36.95 19.65 44.73 3.06
3837 4425 1.002430 TGAGGAGTCACATCTTGCCAC 59.998 52.381 0.00 0.00 0.00 5.01
3905 4495 3.053455 CAAGGAGAGTCGTGTTGAACTC 58.947 50.000 0.00 0.00 33.94 3.01
3925 4515 1.174783 GAGGTAGTGTCGAGGAAGCA 58.825 55.000 0.00 0.00 0.00 3.91
3943 4533 1.102154 CAGTGGTCAGTGTTTTGGCA 58.898 50.000 0.00 0.00 0.00 4.92
4053 4651 9.653287 CTGATAACTTTACAATGAGTTAGGTCA 57.347 33.333 0.00 0.00 40.51 4.02
4060 4658 4.785301 ACAATGAGTTAGGTCATGGGATG 58.215 43.478 0.00 0.00 37.24 3.51
4069 4667 1.139455 GGTCATGGGATGCATTTTGGG 59.861 52.381 0.00 0.00 0.00 4.12
4100 4698 5.757886 TCATGATGTTCTTTTGACCGTTTC 58.242 37.500 0.00 0.00 0.00 2.78
4109 4707 2.074729 TTGACCGTTTCCCCAACAAT 57.925 45.000 0.00 0.00 34.68 2.71
4144 4742 0.601576 TTAAGGAAAGTGCGCTGCGA 60.602 50.000 28.07 8.22 0.00 5.10
4407 5005 7.598248 TGGTAGGAAGTAACATAGGATTCCTA 58.402 38.462 14.77 14.77 46.10 2.94
4485 5083 6.071896 GGAGGATTAGCTAAATAATGCCCAAC 60.072 42.308 10.85 3.05 34.91 3.77
4535 5133 3.050089 TGGAAGAGAAACCCCTGTGTTA 58.950 45.455 0.00 0.00 0.00 2.41
4536 5134 3.181448 TGGAAGAGAAACCCCTGTGTTAC 60.181 47.826 0.00 0.00 0.00 2.50
4537 5135 3.072622 GGAAGAGAAACCCCTGTGTTACT 59.927 47.826 0.00 0.00 0.00 2.24
4538 5136 4.445879 GGAAGAGAAACCCCTGTGTTACTT 60.446 45.833 0.00 0.00 0.00 2.24
4539 5137 4.353383 AGAGAAACCCCTGTGTTACTTC 57.647 45.455 0.00 0.00 0.00 3.01
4566 5184 2.338015 CCATTGGCGAACTGCTGCT 61.338 57.895 0.00 0.00 45.43 4.24
4626 5245 3.206150 GTTGAGAGTTCCTGACTTTGCA 58.794 45.455 0.00 0.00 39.19 4.08
4660 5279 2.875672 GCTGTTACTGGCTCACATGGAA 60.876 50.000 0.00 0.00 0.00 3.53
4688 5307 7.700022 AGCTTTTCTTAGCAGAATCTGATTT 57.300 32.000 15.38 1.11 43.68 2.17
4729 5349 7.426929 AGTCATGAACAGATAGTTGTGTTTC 57.573 36.000 0.00 0.00 39.27 2.78
4744 5364 1.148273 TTTCGGGTTGAGCAGCAGT 59.852 52.632 0.00 0.00 0.00 4.40
4948 5568 9.638239 TTCTAATGTTTATTTGGAATTGCTGTC 57.362 29.630 0.00 0.00 0.00 3.51
5130 5750 0.992695 GGTAGGGGATATGAAGGGGC 59.007 60.000 0.00 0.00 0.00 5.80
5134 5754 1.075659 GGGATATGAAGGGGCTGGC 59.924 63.158 0.00 0.00 0.00 4.85
5194 5814 1.965754 GAAGAGGAGGCAGGTCGCAT 61.966 60.000 0.00 0.00 45.17 4.73
5221 5841 0.038310 GGGGCTATAATGGTCCTGGC 59.962 60.000 0.00 0.00 0.00 4.85
5353 6026 8.056571 CAGCTTATCGTAATTACTGCACTTAAC 58.943 37.037 13.56 0.00 0.00 2.01
5366 6039 2.863704 GCACTTAACCTTGCTTGCCTTG 60.864 50.000 0.00 0.00 35.74 3.61
5808 6481 4.748798 CAGGGGAGCTGGGGGAGT 62.749 72.222 0.00 0.00 0.00 3.85
5897 6570 2.291190 GTCGACCAGACCTAGAGTATGC 59.709 54.545 3.51 0.00 43.95 3.14
6042 6715 3.649981 CTCTTCATGGTAGGGATGATGGT 59.350 47.826 0.00 0.00 29.96 3.55
6108 6781 1.339097 AGTTAAGACGGTGCAGGTCT 58.661 50.000 13.23 13.23 46.27 3.85
6226 6899 6.491745 TGGTATTATTTTGGTTCAGTGAGCAA 59.508 34.615 9.35 6.26 35.43 3.91
6247 6920 2.890945 ACTGGGTTGTTATGTCAAAGCC 59.109 45.455 0.00 0.00 0.00 4.35
6293 6966 2.817844 GTTGCTTCTCGGTTGGGTTATT 59.182 45.455 0.00 0.00 0.00 1.40
6294 6967 3.985019 TGCTTCTCGGTTGGGTTATTA 57.015 42.857 0.00 0.00 0.00 0.98
6295 6968 4.497291 TGCTTCTCGGTTGGGTTATTAT 57.503 40.909 0.00 0.00 0.00 1.28
6322 6995 3.015312 GCCTGGTCGGGTGGAGTAC 62.015 68.421 0.00 0.00 0.00 2.73
6332 7027 0.905357 GGTGGAGTACATGCTCTGGT 59.095 55.000 0.00 0.00 35.89 4.00
6358 7074 2.430367 GTCGGCCCTTGTGGTCTT 59.570 61.111 0.00 0.00 36.18 3.01
6380 7096 3.517901 TGGAGTTGTGGGTATAACCAGAG 59.482 47.826 10.63 0.00 42.20 3.35
6433 7149 1.904287 TGGAACCCACTACATTGCAC 58.096 50.000 0.00 0.00 0.00 4.57
6451 7167 0.107214 ACGATGGCCCGAAACATCAT 60.107 50.000 8.49 0.00 42.72 2.45
6467 7183 8.581263 CGAAACATCATTGAAAAAGTCATCATC 58.419 33.333 0.00 0.00 35.70 2.92
6496 7237 3.243201 GCTGGAAGAAACACAAGTTCTGG 60.243 47.826 0.00 0.00 36.84 3.86
6529 7290 2.561478 ATTTAGGACGTTGCACTGGT 57.439 45.000 0.00 0.00 0.00 4.00
6568 7336 4.574759 CCATACGCTTCGATTTGTGTTAC 58.425 43.478 5.39 0.00 0.00 2.50
6651 7435 5.738693 CACAAATAATGTTGCACATAGGACG 59.261 40.000 0.00 0.00 41.46 4.79
6680 7464 8.251750 TGTAAGCAAAGTGTTCACATATACTC 57.748 34.615 5.74 0.00 0.00 2.59
6681 7465 6.743575 AAGCAAAGTGTTCACATATACTCC 57.256 37.500 5.74 0.00 0.00 3.85
6682 7466 5.186198 AGCAAAGTGTTCACATATACTCCC 58.814 41.667 5.74 0.00 0.00 4.30
6683 7467 5.045578 AGCAAAGTGTTCACATATACTCCCT 60.046 40.000 5.74 0.00 0.00 4.20
6684 7468 5.294552 GCAAAGTGTTCACATATACTCCCTC 59.705 44.000 5.74 0.00 0.00 4.30
6685 7469 5.615925 AAGTGTTCACATATACTCCCTCC 57.384 43.478 5.74 0.00 0.00 4.30
6686 7470 3.637229 AGTGTTCACATATACTCCCTCCG 59.363 47.826 5.74 0.00 0.00 4.63
6687 7471 2.364324 TGTTCACATATACTCCCTCCGC 59.636 50.000 0.00 0.00 0.00 5.54
6688 7472 1.629043 TCACATATACTCCCTCCGCC 58.371 55.000 0.00 0.00 0.00 6.13
6689 7473 0.608640 CACATATACTCCCTCCGCCC 59.391 60.000 0.00 0.00 0.00 6.13
6690 7474 0.544595 ACATATACTCCCTCCGCCCC 60.545 60.000 0.00 0.00 0.00 5.80
6691 7475 0.544357 CATATACTCCCTCCGCCCCA 60.544 60.000 0.00 0.00 0.00 4.96
6692 7476 0.192566 ATATACTCCCTCCGCCCCAA 59.807 55.000 0.00 0.00 0.00 4.12
6693 7477 0.030909 TATACTCCCTCCGCCCCAAA 60.031 55.000 0.00 0.00 0.00 3.28
6694 7478 0.917333 ATACTCCCTCCGCCCCAAAA 60.917 55.000 0.00 0.00 0.00 2.44
6695 7479 0.917333 TACTCCCTCCGCCCCAAAAT 60.917 55.000 0.00 0.00 0.00 1.82
6696 7480 1.754234 CTCCCTCCGCCCCAAAATG 60.754 63.158 0.00 0.00 0.00 2.32
6697 7481 2.037208 CCCTCCGCCCCAAAATGT 59.963 61.111 0.00 0.00 0.00 2.71
6698 7482 1.208844 TCCCTCCGCCCCAAAATGTA 61.209 55.000 0.00 0.00 0.00 2.29
6699 7483 0.106217 CCCTCCGCCCCAAAATGTAT 60.106 55.000 0.00 0.00 0.00 2.29
6700 7484 1.032014 CCTCCGCCCCAAAATGTATG 58.968 55.000 0.00 0.00 0.00 2.39
6701 7485 1.409521 CCTCCGCCCCAAAATGTATGA 60.410 52.381 0.00 0.00 0.00 2.15
6702 7486 1.676006 CTCCGCCCCAAAATGTATGAC 59.324 52.381 0.00 0.00 0.00 3.06
6703 7487 1.283613 TCCGCCCCAAAATGTATGACT 59.716 47.619 0.00 0.00 0.00 3.41
6704 7488 2.099405 CCGCCCCAAAATGTATGACTT 58.901 47.619 0.00 0.00 0.00 3.01
6705 7489 2.495669 CCGCCCCAAAATGTATGACTTT 59.504 45.455 0.00 0.00 0.00 2.66
6706 7490 3.056179 CCGCCCCAAAATGTATGACTTTT 60.056 43.478 0.00 0.00 0.00 2.27
6707 7491 4.562552 CCGCCCCAAAATGTATGACTTTTT 60.563 41.667 0.00 0.00 36.34 1.94
6738 7522 9.349145 AAAAGAAACATTTTATATTTCGGGACG 57.651 29.630 0.00 0.00 41.32 4.79
6754 7538 2.037381 GGGACGGAGGGAGTATCATTTC 59.963 54.545 0.00 0.00 36.25 2.17
6761 7545 4.054671 GAGGGAGTATCATTTCTCTTGCG 58.945 47.826 0.00 0.00 36.25 4.85
6771 7555 4.451096 TCATTTCTCTTGCGTGGTAGTTTC 59.549 41.667 0.00 0.00 0.00 2.78
6785 7569 7.007995 GCGTGGTAGTTTCATTATTAAAACTGC 59.992 37.037 9.99 8.61 43.58 4.40
6786 7570 8.018520 CGTGGTAGTTTCATTATTAAAACTGCA 58.981 33.333 14.81 0.00 44.72 4.41
6787 7571 9.124807 GTGGTAGTTTCATTATTAAAACTGCAC 57.875 33.333 14.81 9.18 44.72 4.57
6817 7602 0.752009 TGTGCCTTTTACCACCGCAA 60.752 50.000 0.00 0.00 0.00 4.85
6821 7606 0.312729 CCTTTTACCACCGCAACCAC 59.687 55.000 0.00 0.00 0.00 4.16
6833 7618 2.159627 CCGCAACCACTAGTCAAATCAC 59.840 50.000 0.00 0.00 0.00 3.06
6834 7619 2.805671 CGCAACCACTAGTCAAATCACA 59.194 45.455 0.00 0.00 0.00 3.58
6835 7620 3.120546 CGCAACCACTAGTCAAATCACAG 60.121 47.826 0.00 0.00 0.00 3.66
6843 7628 5.419155 CACTAGTCAAATCACAGGACCTAGA 59.581 44.000 0.00 0.00 31.99 2.43
6852 7637 3.205507 TCACAGGACCTAGAGCCTCTAAT 59.794 47.826 2.55 0.00 30.41 1.73
6859 7644 4.279145 ACCTAGAGCCTCTAATCGTTGAA 58.721 43.478 2.55 0.00 0.00 2.69
6914 7699 8.246871 AGCTTCCAAGAAATTAATCTTAGTTGC 58.753 33.333 0.00 0.00 37.56 4.17
6926 7711 2.756760 TCTTAGTTGCGTTCTCGGGTAT 59.243 45.455 0.00 0.00 37.56 2.73
6936 7721 5.474532 TGCGTTCTCGGGTATTATACACTAT 59.525 40.000 2.98 0.00 37.56 2.12
6946 7731 7.183460 GGGTATTATACACTATCTCTCCCTGT 58.817 42.308 4.67 0.00 0.00 4.00
6952 7737 3.910627 ACACTATCTCTCCCTGTTTGGTT 59.089 43.478 0.00 0.00 0.00 3.67
6960 7745 3.971305 TCTCCCTGTTTGGTTCAAGACTA 59.029 43.478 0.00 0.00 0.00 2.59
6961 7746 4.065789 CTCCCTGTTTGGTTCAAGACTAC 58.934 47.826 0.00 0.00 0.00 2.73
6973 7758 2.158219 TCAAGACTACTGGGAAGGGTCA 60.158 50.000 0.00 0.00 0.00 4.02
6981 7769 7.841729 AGACTACTGGGAAGGGTCATATATATG 59.158 40.741 15.47 15.47 35.04 1.78
7009 7797 1.002868 GATGAGGATGGGCGATGGG 60.003 63.158 0.00 0.00 0.00 4.00
7023 7811 0.631212 GATGGGGAAGAATGGGTGGT 59.369 55.000 0.00 0.00 0.00 4.16
7029 7817 0.521735 GAAGAATGGGTGGTTGCGTC 59.478 55.000 0.00 0.00 0.00 5.19
7049 7837 3.205338 TCGACAACCGACGATCCTTATA 58.795 45.455 0.00 0.00 43.23 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 5.299279 TGAAGAACAAAATCTGGGTGAGAAC 59.701 40.000 0.00 0.00 33.12 3.01
56 57 4.751767 ACATTGGCAGGTCAAAGAAAAA 57.248 36.364 0.00 0.00 0.00 1.94
96 97 4.160252 ACAAGCAAACATGAAACAAGGAGT 59.840 37.500 0.00 0.00 0.00 3.85
100 101 6.919662 AGATACACAAGCAAACATGAAACAAG 59.080 34.615 0.00 0.00 0.00 3.16
106 107 3.684305 CGGAGATACACAAGCAAACATGA 59.316 43.478 0.00 0.00 0.00 3.07
123 124 3.090037 CTGGAAAAGTACTCTCCGGAGA 58.910 50.000 31.67 31.67 41.86 3.71
124 125 3.090037 TCTGGAAAAGTACTCTCCGGAG 58.910 50.000 26.32 26.32 39.28 4.63
125 126 3.165087 TCTGGAAAAGTACTCTCCGGA 57.835 47.619 22.92 22.92 41.41 5.14
126 127 4.473477 AATCTGGAAAAGTACTCTCCGG 57.527 45.455 20.05 20.05 37.02 5.14
127 128 5.725362 AGAAATCTGGAAAAGTACTCTCCG 58.275 41.667 15.69 11.74 31.37 4.63
129 130 6.652900 AGCAAGAAATCTGGAAAAGTACTCTC 59.347 38.462 0.00 0.00 0.00 3.20
130 131 6.538263 AGCAAGAAATCTGGAAAAGTACTCT 58.462 36.000 0.00 0.00 0.00 3.24
170 171 4.717233 ACTCAACAAACATGTTCAGCAA 57.283 36.364 12.39 0.00 0.00 3.91
181 182 9.944663 TGTATTAACATGAAGAACTCAACAAAC 57.055 29.630 0.00 0.00 37.67 2.93
195 196 6.428465 TGTTTCGGAGCTTTGTATTAACATGA 59.572 34.615 0.00 0.00 34.97 3.07
231 232 7.653311 CAGTGGCTTTAAAAAGAACTTAGCATT 59.347 33.333 6.64 0.00 38.28 3.56
232 233 7.147976 CAGTGGCTTTAAAAAGAACTTAGCAT 58.852 34.615 6.64 0.00 38.28 3.79
233 234 6.503524 CAGTGGCTTTAAAAAGAACTTAGCA 58.496 36.000 6.64 0.00 38.28 3.49
234 235 5.402568 GCAGTGGCTTTAAAAAGAACTTAGC 59.597 40.000 6.64 6.13 38.28 3.09
235 236 5.920840 GGCAGTGGCTTTAAAAAGAACTTAG 59.079 40.000 9.90 0.94 40.87 2.18
236 237 5.596772 AGGCAGTGGCTTTAAAAAGAACTTA 59.403 36.000 14.51 0.00 40.87 2.24
237 238 4.405680 AGGCAGTGGCTTTAAAAAGAACTT 59.594 37.500 14.51 0.00 40.87 2.66
238 239 3.960755 AGGCAGTGGCTTTAAAAAGAACT 59.039 39.130 14.51 6.13 40.87 3.01
239 240 4.038042 AGAGGCAGTGGCTTTAAAAAGAAC 59.962 41.667 21.55 3.63 38.98 3.01
240 241 4.215109 AGAGGCAGTGGCTTTAAAAAGAA 58.785 39.130 21.55 0.00 38.98 2.52
241 242 3.832527 AGAGGCAGTGGCTTTAAAAAGA 58.167 40.909 21.55 0.00 38.98 2.52
242 243 4.550422 GAAGAGGCAGTGGCTTTAAAAAG 58.450 43.478 21.55 0.00 38.98 2.27
243 244 3.320826 GGAAGAGGCAGTGGCTTTAAAAA 59.679 43.478 21.55 0.00 38.98 1.94
244 245 2.890945 GGAAGAGGCAGTGGCTTTAAAA 59.109 45.455 21.55 0.00 38.98 1.52
245 246 2.514803 GGAAGAGGCAGTGGCTTTAAA 58.485 47.619 21.55 0.00 38.98 1.52
246 247 1.610624 CGGAAGAGGCAGTGGCTTTAA 60.611 52.381 21.55 0.00 38.98 1.52
247 248 0.036388 CGGAAGAGGCAGTGGCTTTA 60.036 55.000 21.55 0.00 38.98 1.85
248 249 1.302832 CGGAAGAGGCAGTGGCTTT 60.303 57.895 21.55 12.78 38.98 3.51
249 250 2.348998 CGGAAGAGGCAGTGGCTT 59.651 61.111 21.55 5.50 38.98 4.35
250 251 4.400961 GCGGAAGAGGCAGTGGCT 62.401 66.667 20.74 20.74 42.48 4.75
252 253 3.672295 GAGGCGGAAGAGGCAGTGG 62.672 68.421 0.00 0.00 39.37 4.00
253 254 2.125350 GAGGCGGAAGAGGCAGTG 60.125 66.667 0.00 0.00 39.37 3.66
254 255 3.394836 GGAGGCGGAAGAGGCAGT 61.395 66.667 0.00 0.00 39.37 4.40
255 256 4.521062 CGGAGGCGGAAGAGGCAG 62.521 72.222 0.00 0.00 39.37 4.85
270 271 1.821332 GCCCTCAAGATCAAGGCGG 60.821 63.158 0.00 0.00 33.18 6.13
271 272 1.821332 GGCCCTCAAGATCAAGGCG 60.821 63.158 0.00 0.00 44.82 5.52
281 282 5.163248 TGTTTATAGATGATTCGGCCCTCAA 60.163 40.000 0.00 0.00 0.00 3.02
290 291 8.223769 CACGCACCTATTGTTTATAGATGATTC 58.776 37.037 0.00 0.00 38.86 2.52
304 305 1.078497 TCCTGCCACGCACCTATTG 60.078 57.895 0.00 0.00 33.79 1.90
360 361 5.900339 ATTACATAACGCACGGATAACTG 57.100 39.130 0.00 0.00 0.00 3.16
362 363 6.617105 GCCTTATTACATAACGCACGGATAAC 60.617 42.308 0.00 0.00 30.42 1.89
366 367 3.125316 GCCTTATTACATAACGCACGGA 58.875 45.455 0.00 0.00 30.42 4.69
368 369 2.222445 GGGCCTTATTACATAACGCACG 59.778 50.000 0.84 0.00 31.24 5.34
369 370 3.002965 GTGGGCCTTATTACATAACGCAC 59.997 47.826 4.53 0.00 32.88 5.34
370 371 3.207778 GTGGGCCTTATTACATAACGCA 58.792 45.455 4.53 0.00 31.24 5.24
373 374 4.788679 AGTGGTGGGCCTTATTACATAAC 58.211 43.478 4.53 0.00 35.27 1.89
374 375 4.475381 TGAGTGGTGGGCCTTATTACATAA 59.525 41.667 4.53 0.00 35.27 1.90
384 385 1.847506 TGTGATGAGTGGTGGGCCT 60.848 57.895 4.53 0.00 35.27 5.19
385 386 1.675641 GTGTGATGAGTGGTGGGCC 60.676 63.158 0.00 0.00 0.00 5.80
386 387 0.537143 TTGTGTGATGAGTGGTGGGC 60.537 55.000 0.00 0.00 0.00 5.36
387 388 1.238439 GTTGTGTGATGAGTGGTGGG 58.762 55.000 0.00 0.00 0.00 4.61
388 389 1.603802 GTGTTGTGTGATGAGTGGTGG 59.396 52.381 0.00 0.00 0.00 4.61
393 399 4.955925 TTTTTCGTGTTGTGTGATGAGT 57.044 36.364 0.00 0.00 0.00 3.41
414 420 1.271054 GCGGCCCTCTGTCATCATAAT 60.271 52.381 0.00 0.00 0.00 1.28
415 421 0.106708 GCGGCCCTCTGTCATCATAA 59.893 55.000 0.00 0.00 0.00 1.90
420 426 3.011517 AAGGCGGCCCTCTGTCAT 61.012 61.111 17.02 0.00 41.90 3.06
464 470 4.176271 CAATCACACATACTCTTGCTCGA 58.824 43.478 0.00 0.00 0.00 4.04
465 471 3.242220 GCAATCACACATACTCTTGCTCG 60.242 47.826 0.00 0.00 36.83 5.03
466 472 3.242220 CGCAATCACACATACTCTTGCTC 60.242 47.826 0.00 0.00 37.44 4.26
467 473 2.674852 CGCAATCACACATACTCTTGCT 59.325 45.455 0.00 0.00 37.44 3.91
468 474 2.789092 GCGCAATCACACATACTCTTGC 60.789 50.000 0.30 0.00 36.52 4.01
469 475 2.416202 TGCGCAATCACACATACTCTTG 59.584 45.455 8.16 0.00 0.00 3.02
470 476 2.416547 GTGCGCAATCACACATACTCTT 59.583 45.455 14.00 0.00 36.77 2.85
471 477 2.002586 GTGCGCAATCACACATACTCT 58.997 47.619 14.00 0.00 36.77 3.24
487 515 0.865769 GACCCTAAAGTGTGTGTGCG 59.134 55.000 0.00 0.00 0.00 5.34
488 516 0.865769 CGACCCTAAAGTGTGTGTGC 59.134 55.000 0.00 0.00 0.00 4.57
490 518 2.028385 GGATCGACCCTAAAGTGTGTGT 60.028 50.000 0.00 0.00 0.00 3.72
491 519 2.028476 TGGATCGACCCTAAAGTGTGTG 60.028 50.000 0.00 0.00 38.00 3.82
492 520 2.253610 TGGATCGACCCTAAAGTGTGT 58.746 47.619 0.00 0.00 38.00 3.72
493 521 3.458189 GATGGATCGACCCTAAAGTGTG 58.542 50.000 0.00 0.00 38.00 3.82
494 522 2.434702 GGATGGATCGACCCTAAAGTGT 59.565 50.000 0.00 0.00 38.00 3.55
495 523 2.224305 GGGATGGATCGACCCTAAAGTG 60.224 54.545 0.00 0.00 40.39 3.16
496 524 2.047830 GGGATGGATCGACCCTAAAGT 58.952 52.381 0.00 0.00 40.39 2.66
497 525 1.348036 GGGGATGGATCGACCCTAAAG 59.652 57.143 16.34 0.00 42.86 1.85
498 526 1.430992 GGGGATGGATCGACCCTAAA 58.569 55.000 16.34 0.00 42.86 1.85
499 527 3.159141 GGGGATGGATCGACCCTAA 57.841 57.895 16.34 0.00 42.86 2.69
500 528 4.968553 GGGGATGGATCGACCCTA 57.031 61.111 16.34 0.00 42.86 3.53
521 1022 5.516984 AGATGATGAGAAAATTGGGCTTCT 58.483 37.500 0.00 0.00 34.58 2.85
534 1035 7.500559 TGAGACTTTCTCGAATAGATGATGAGA 59.499 37.037 0.00 0.00 46.25 3.27
545 1046 5.398603 ACATGAGTGAGACTTTCTCGAAT 57.601 39.130 0.00 0.00 46.25 3.34
558 1059 3.433274 GCGATCAAAGTGAACATGAGTGA 59.567 43.478 0.00 0.00 0.00 3.41
568 1069 2.677836 GGTTATGCAGCGATCAAAGTGA 59.322 45.455 0.00 0.00 0.00 3.41
668 1169 8.074972 CGGACAATTAGAGTGTATTCCTACTAC 58.925 40.741 0.00 0.00 0.00 2.73
678 1179 8.234136 AGATAATGTCGGACAATTAGAGTGTA 57.766 34.615 15.72 0.00 0.00 2.90
679 1180 7.113658 AGATAATGTCGGACAATTAGAGTGT 57.886 36.000 15.72 0.00 0.00 3.55
721 1233 5.639506 GTGTAAGCTTGTCTCAAAGATGCTA 59.360 40.000 9.86 0.00 31.55 3.49
722 1234 4.453819 GTGTAAGCTTGTCTCAAAGATGCT 59.546 41.667 9.86 0.00 32.53 3.79
723 1235 4.214119 TGTGTAAGCTTGTCTCAAAGATGC 59.786 41.667 9.86 0.00 0.00 3.91
724 1236 5.237127 TGTGTGTAAGCTTGTCTCAAAGATG 59.763 40.000 9.86 0.00 0.00 2.90
725 1237 5.368145 TGTGTGTAAGCTTGTCTCAAAGAT 58.632 37.500 9.86 0.00 0.00 2.40
726 1238 4.765273 TGTGTGTAAGCTTGTCTCAAAGA 58.235 39.130 9.86 0.00 0.00 2.52
755 1267 1.472552 CGATACGGTTGATTCTGGCCA 60.473 52.381 4.71 4.71 0.00 5.36
786 1298 1.247567 GTTGGATGAGGGGTGTTGTG 58.752 55.000 0.00 0.00 0.00 3.33
792 1304 3.077907 CACCGTTGGATGAGGGGT 58.922 61.111 0.00 0.00 0.00 4.95
818 1330 1.066908 CAATGTGGTTTTCAGTGGCGT 59.933 47.619 0.00 0.00 0.00 5.68
873 1388 1.009389 GTCAAGCCGTCAAGGACTCG 61.009 60.000 0.00 0.00 45.00 4.18
922 1437 0.252103 AGGAGAGAGGTTGCGGGTAA 60.252 55.000 0.00 0.00 0.00 2.85
1020 1541 2.031616 TCGTCGTCAGGGTCGTCT 59.968 61.111 0.00 0.00 0.00 4.18
1078 1599 4.161295 TTCGGGCTCGGCATCCTG 62.161 66.667 5.94 0.00 36.95 3.86
1079 1600 3.854669 CTTCGGGCTCGGCATCCT 61.855 66.667 5.94 0.00 36.95 3.24
1806 2346 6.477688 TGAATTATCTAACGACCAAACGGATC 59.522 38.462 0.00 0.00 37.61 3.36
1833 2373 5.516696 GGAATCGTCCATCATGATATACACG 59.483 44.000 8.15 13.39 44.26 4.49
1848 2388 2.003301 GCTGAAGACAAGGAATCGTCC 58.997 52.381 0.00 0.00 45.35 4.79
1952 2493 5.104982 TGTTCAAAGCCTTGATCAACCTTTT 60.105 36.000 19.35 11.30 41.22 2.27
2076 2624 3.895232 AGCGAAAGTGTATCTGACCAT 57.105 42.857 0.00 0.00 0.00 3.55
2081 2629 8.947940 GCAAATAATTAAGCGAAAGTGTATCTG 58.052 33.333 0.00 0.00 0.00 2.90
2088 2636 6.908825 TGACTGCAAATAATTAAGCGAAAGT 58.091 32.000 0.00 0.00 0.00 2.66
2128 2676 5.989717 ACTAATATGGGATGGAGGGAGTAA 58.010 41.667 0.00 0.00 0.00 2.24
2138 2686 4.126437 TGCACGACAACTAATATGGGATG 58.874 43.478 0.00 0.00 0.00 3.51
2139 2687 4.415881 TGCACGACAACTAATATGGGAT 57.584 40.909 0.00 0.00 0.00 3.85
2157 2705 4.818005 CAGTGCTAGATACATCCATTTGCA 59.182 41.667 0.00 0.00 0.00 4.08
2158 2706 5.059161 TCAGTGCTAGATACATCCATTTGC 58.941 41.667 0.00 0.00 0.00 3.68
2208 2756 6.131264 TCCCTCCGTCTTATATTAGTTGTCA 58.869 40.000 0.00 0.00 0.00 3.58
2210 2758 6.134754 ACTCCCTCCGTCTTATATTAGTTGT 58.865 40.000 0.00 0.00 0.00 3.32
2221 2769 3.902467 AGAAAAACTACTCCCTCCGTCTT 59.098 43.478 0.00 0.00 0.00 3.01
2367 2917 4.735369 AGGTGTAGATCCTCTGATAGGTG 58.265 47.826 0.00 0.00 46.62 4.00
2489 3039 3.575256 TGCACCAAGCTCAAGATGAAAAT 59.425 39.130 0.00 0.00 45.94 1.82
2490 3040 2.957680 TGCACCAAGCTCAAGATGAAAA 59.042 40.909 0.00 0.00 45.94 2.29
2571 3121 0.038166 AGGTACACATGGCACCCAAG 59.962 55.000 0.00 0.00 36.95 3.61
2734 3287 3.696051 TCTGAAGCCCACTAATGCAATTC 59.304 43.478 0.00 0.00 37.87 2.17
2745 3298 4.525912 AATGTTCAAATCTGAAGCCCAC 57.474 40.909 0.00 0.00 42.27 4.61
2821 3383 9.931210 GAATAAACCTCTTAACATATTTGACGG 57.069 33.333 0.00 0.00 0.00 4.79
3086 3670 3.760151 CAGGAGATTTTGCACTTCCATCA 59.240 43.478 0.00 0.00 0.00 3.07
3089 3673 3.507162 TCAGGAGATTTTGCACTTCCA 57.493 42.857 0.00 0.00 0.00 3.53
3325 3909 4.904241 TCCACATTAAATGCCAAAAAGGG 58.096 39.130 0.00 0.00 38.09 3.95
3430 4018 3.627123 TGCATCAATACAATTCAGGTCCG 59.373 43.478 0.00 0.00 0.00 4.79
3502 4090 3.308035 TCCTAGGTATCCACGTGTCAT 57.692 47.619 15.65 8.58 0.00 3.06
3685 4273 6.778821 TCTCAACCAAATCTCCATCAACTTA 58.221 36.000 0.00 0.00 0.00 2.24
3767 4355 3.347216 CTGAAGTCCCTGTACCAATTGG 58.653 50.000 23.31 23.31 42.17 3.16
3837 4425 2.420022 GGTCAGGTCCAACAATTGATCG 59.580 50.000 13.59 0.00 0.00 3.69
3884 4472 3.053455 GAGTTCAACACGACTCTCCTTG 58.947 50.000 0.00 0.00 39.30 3.61
3905 4495 0.099082 GCTTCCTCGACACTACCTCG 59.901 60.000 0.00 0.00 0.00 4.63
3925 4515 1.102978 GTGCCAAAACACTGACCACT 58.897 50.000 0.00 0.00 37.58 4.00
3943 4533 0.846693 ACTCCAAAACCTCAGGCAGT 59.153 50.000 0.00 0.00 0.00 4.40
3953 4543 7.875971 ACTCAGATTCATGTTAACTCCAAAAC 58.124 34.615 7.22 0.00 0.00 2.43
4045 4643 4.441913 CCAAAATGCATCCCATGACCTAAC 60.442 45.833 0.00 0.00 33.49 2.34
4049 4647 1.139455 CCCAAAATGCATCCCATGACC 59.861 52.381 0.00 0.00 33.49 4.02
4053 4651 2.555732 ACTCCCAAAATGCATCCCAT 57.444 45.000 0.00 0.00 35.06 4.00
4060 4658 3.633525 TCATGATGCTACTCCCAAAATGC 59.366 43.478 0.00 0.00 0.00 3.56
4069 4667 7.185453 GTCAAAAGAACATCATGATGCTACTC 58.815 38.462 31.17 21.99 42.39 2.59
4109 4707 7.447238 ACTTTCCTTAATCGAATCTCCAACAAA 59.553 33.333 0.00 0.00 0.00 2.83
4124 4722 0.447801 CGCAGCGCACTTTCCTTAAT 59.552 50.000 11.47 0.00 0.00 1.40
4144 4742 4.262808 GCTGATGGACTCTATGCTGGTATT 60.263 45.833 0.00 0.00 0.00 1.89
4485 5083 5.279708 CCTCCATATAAGGCTAGTCACCTTG 60.280 48.000 9.66 0.00 46.99 3.61
4535 5133 2.683742 CGCCAATGGTATCTTGGGAAGT 60.684 50.000 0.00 0.00 42.84 3.01
4536 5134 1.949525 CGCCAATGGTATCTTGGGAAG 59.050 52.381 0.00 0.00 42.84 3.46
4537 5135 1.562008 TCGCCAATGGTATCTTGGGAA 59.438 47.619 0.00 0.00 42.84 3.97
4538 5136 1.208706 TCGCCAATGGTATCTTGGGA 58.791 50.000 0.00 0.00 42.84 4.37
4539 5137 1.676006 GTTCGCCAATGGTATCTTGGG 59.324 52.381 0.00 0.00 42.84 4.12
4626 5245 4.526970 CAGTAACAGCCCCATAACTTCAT 58.473 43.478 0.00 0.00 0.00 2.57
4660 5279 8.798859 TCAGATTCTGCTAAGAAAAGCTTATT 57.201 30.769 8.89 0.00 45.44 1.40
4688 5307 9.317936 GTTCATGACTACACATTCAGATATTGA 57.682 33.333 0.00 0.00 0.00 2.57
4729 5349 1.165907 TGAAACTGCTGCTCAACCCG 61.166 55.000 0.00 0.00 0.00 5.28
4744 5364 5.860611 TCTGAGAAGGAAATACCGTTGAAA 58.139 37.500 0.00 0.00 44.74 2.69
4904 5524 8.873830 ACATTAGAAGACACGAAACATGAATAG 58.126 33.333 0.00 0.00 0.00 1.73
4948 5568 3.444742 TGCCATATCCTGCAAAGAAAGTG 59.555 43.478 0.00 0.00 33.87 3.16
5130 5750 1.376942 CTTGCACCTCCTCTGCCAG 60.377 63.158 0.00 0.00 33.36 4.85
5134 5754 0.322008 GGAACCTTGCACCTCCTCTG 60.322 60.000 0.00 0.00 0.00 3.35
5221 5841 7.772292 TCTCCATCAATTAGAATGAACTCCTTG 59.228 37.037 0.00 0.00 0.00 3.61
5353 6026 3.256631 ACATTAAGTCAAGGCAAGCAAGG 59.743 43.478 0.00 0.00 0.00 3.61
5533 6206 2.876368 CTTGGAGGGGCACGATCACC 62.876 65.000 0.00 0.00 0.00 4.02
5808 6481 0.829990 TGCTTCTGTCCCGCATATCA 59.170 50.000 0.00 0.00 0.00 2.15
5859 6532 1.301677 GACCTCTGCCCAAGAAAGCG 61.302 60.000 0.00 0.00 33.37 4.68
5897 6570 2.289072 CCTCGGCCTACATATGAACCAG 60.289 54.545 10.38 0.97 0.00 4.00
5961 6634 0.673644 CACCTCCTGGCCTGTAAACG 60.674 60.000 3.32 0.00 36.63 3.60
6015 6688 0.543277 CCCTACCATGAAGAGCAGCA 59.457 55.000 0.00 0.00 0.00 4.41
6042 6715 3.972133 TCCAAGGATGAACTAGTACCGA 58.028 45.455 0.00 0.00 0.00 4.69
6108 6781 7.601705 ACGGGTAGTTTAATATTACAGGCTA 57.398 36.000 0.00 0.00 0.00 3.93
6226 6899 2.890945 GGCTTTGACATAACAACCCAGT 59.109 45.455 0.00 0.00 0.00 4.00
6247 6920 6.974622 CCCAAAAGAACCAAATAATCAGATCG 59.025 38.462 0.00 0.00 0.00 3.69
6293 6966 1.410004 CGACCAGGCTTGAGGGTATA 58.590 55.000 0.00 0.00 34.39 1.47
6294 6967 1.338136 CCGACCAGGCTTGAGGGTAT 61.338 60.000 0.00 0.00 34.39 2.73
6295 6968 1.987855 CCGACCAGGCTTGAGGGTA 60.988 63.158 0.00 0.00 34.39 3.69
6332 7027 2.221299 AAGGGCCGACCAACAGCTA 61.221 57.895 0.00 0.00 43.89 3.32
6358 7074 3.517901 CTCTGGTTATACCCACAACTCCA 59.482 47.826 0.00 0.00 37.50 3.86
6380 7096 4.090588 TCGTGATGGCGGAACCCC 62.091 66.667 0.00 0.00 37.83 4.95
6433 7149 1.024271 AATGATGTTTCGGGCCATCG 58.976 50.000 4.39 0.00 40.25 3.84
6451 7167 4.071423 TCTGCCGATGATGACTTTTTCAA 58.929 39.130 0.00 0.00 37.92 2.69
6467 7183 0.603707 TGTTTCTTCCAGCTCTGCCG 60.604 55.000 0.00 0.00 0.00 5.69
6496 7237 3.945921 GTCCTAAATAGGCCTTGGTGAAC 59.054 47.826 12.58 0.00 43.31 3.18
6529 7290 3.443045 GCGACCCGTCTCCCGTTA 61.443 66.667 0.00 0.00 33.66 3.18
6547 7308 4.030865 TCGTAACACAAATCGAAGCGTATG 59.969 41.667 0.00 0.00 0.00 2.39
6548 7309 4.168014 TCGTAACACAAATCGAAGCGTAT 58.832 39.130 0.00 0.00 0.00 3.06
6568 7336 4.811024 ACCAGCACAAGATATACACATTCG 59.189 41.667 0.00 0.00 0.00 3.34
6637 7411 5.539582 TTACAATTCGTCCTATGTGCAAC 57.460 39.130 0.00 0.00 37.35 4.17
6651 7435 8.970691 ATATGTGAACACTTTGCTTACAATTC 57.029 30.769 6.51 0.00 35.21 2.17
6680 7464 0.106217 ATACATTTTGGGGCGGAGGG 60.106 55.000 0.00 0.00 0.00 4.30
6681 7465 1.032014 CATACATTTTGGGGCGGAGG 58.968 55.000 0.00 0.00 0.00 4.30
6682 7466 1.676006 GTCATACATTTTGGGGCGGAG 59.324 52.381 0.00 0.00 0.00 4.63
6683 7467 1.283613 AGTCATACATTTTGGGGCGGA 59.716 47.619 0.00 0.00 0.00 5.54
6684 7468 1.762708 AGTCATACATTTTGGGGCGG 58.237 50.000 0.00 0.00 0.00 6.13
6685 7469 3.866883 AAAGTCATACATTTTGGGGCG 57.133 42.857 0.00 0.00 0.00 6.13
6712 7496 9.349145 CGTCCCGAAATATAAAATGTTTCTTTT 57.651 29.630 7.30 0.00 37.97 2.27
6713 7497 7.971722 CCGTCCCGAAATATAAAATGTTTCTTT 59.028 33.333 7.30 0.00 37.97 2.52
6714 7498 7.337436 TCCGTCCCGAAATATAAAATGTTTCTT 59.663 33.333 7.30 0.00 37.97 2.52
6715 7499 6.824704 TCCGTCCCGAAATATAAAATGTTTCT 59.175 34.615 7.30 0.00 37.97 2.52
6716 7500 7.018635 TCCGTCCCGAAATATAAAATGTTTC 57.981 36.000 0.00 0.54 37.12 2.78
6717 7501 6.038936 CCTCCGTCCCGAAATATAAAATGTTT 59.961 38.462 0.00 0.00 0.00 2.83
6718 7502 5.529800 CCTCCGTCCCGAAATATAAAATGTT 59.470 40.000 0.00 0.00 0.00 2.71
6719 7503 5.061179 CCTCCGTCCCGAAATATAAAATGT 58.939 41.667 0.00 0.00 0.00 2.71
6720 7504 4.454504 CCCTCCGTCCCGAAATATAAAATG 59.545 45.833 0.00 0.00 0.00 2.32
6721 7505 4.348754 TCCCTCCGTCCCGAAATATAAAAT 59.651 41.667 0.00 0.00 0.00 1.82
6722 7506 3.710677 TCCCTCCGTCCCGAAATATAAAA 59.289 43.478 0.00 0.00 0.00 1.52
6723 7507 3.307506 TCCCTCCGTCCCGAAATATAAA 58.692 45.455 0.00 0.00 0.00 1.40
6724 7508 2.895404 CTCCCTCCGTCCCGAAATATAA 59.105 50.000 0.00 0.00 0.00 0.98
6725 7509 2.158415 ACTCCCTCCGTCCCGAAATATA 60.158 50.000 0.00 0.00 0.00 0.86
6726 7510 1.339097 CTCCCTCCGTCCCGAAATAT 58.661 55.000 0.00 0.00 0.00 1.28
6727 7511 0.032813 ACTCCCTCCGTCCCGAAATA 60.033 55.000 0.00 0.00 0.00 1.40
6728 7512 0.032813 TACTCCCTCCGTCCCGAAAT 60.033 55.000 0.00 0.00 0.00 2.17
6729 7513 0.032813 ATACTCCCTCCGTCCCGAAA 60.033 55.000 0.00 0.00 0.00 3.46
6730 7514 0.466922 GATACTCCCTCCGTCCCGAA 60.467 60.000 0.00 0.00 0.00 4.30
6731 7515 1.150081 GATACTCCCTCCGTCCCGA 59.850 63.158 0.00 0.00 0.00 5.14
6732 7516 0.539901 ATGATACTCCCTCCGTCCCG 60.540 60.000 0.00 0.00 0.00 5.14
6733 7517 1.718280 AATGATACTCCCTCCGTCCC 58.282 55.000 0.00 0.00 0.00 4.46
6734 7518 2.966516 AGAAATGATACTCCCTCCGTCC 59.033 50.000 0.00 0.00 0.00 4.79
6735 7519 3.892588 AGAGAAATGATACTCCCTCCGTC 59.107 47.826 0.00 0.00 34.13 4.79
6736 7520 3.917300 AGAGAAATGATACTCCCTCCGT 58.083 45.455 0.00 0.00 34.13 4.69
6737 7521 4.626042 CAAGAGAAATGATACTCCCTCCG 58.374 47.826 0.00 0.00 34.13 4.63
6738 7522 4.384940 GCAAGAGAAATGATACTCCCTCC 58.615 47.826 0.00 0.00 34.13 4.30
6739 7523 4.054671 CGCAAGAGAAATGATACTCCCTC 58.945 47.826 0.00 0.00 43.02 4.30
6740 7524 3.452627 ACGCAAGAGAAATGATACTCCCT 59.547 43.478 0.00 0.00 43.62 4.20
6741 7525 3.557595 CACGCAAGAGAAATGATACTCCC 59.442 47.826 0.00 0.00 43.62 4.30
6742 7526 3.557595 CCACGCAAGAGAAATGATACTCC 59.442 47.826 0.00 0.00 43.62 3.85
6743 7527 4.184629 ACCACGCAAGAGAAATGATACTC 58.815 43.478 0.00 0.00 43.62 2.59
6744 7528 4.207891 ACCACGCAAGAGAAATGATACT 57.792 40.909 0.00 0.00 43.62 2.12
6745 7529 5.109903 ACTACCACGCAAGAGAAATGATAC 58.890 41.667 0.00 0.00 43.62 2.24
6746 7530 5.339008 ACTACCACGCAAGAGAAATGATA 57.661 39.130 0.00 0.00 43.62 2.15
6747 7531 4.207891 ACTACCACGCAAGAGAAATGAT 57.792 40.909 0.00 0.00 43.62 2.45
6754 7538 6.422776 AATAATGAAACTACCACGCAAGAG 57.577 37.500 0.00 0.00 43.62 2.85
6761 7545 9.124807 GTGCAGTTTTAATAATGAAACTACCAC 57.875 33.333 11.74 11.74 41.78 4.16
6785 7569 5.376854 AAAAGGCACACTTAGCATTAGTG 57.623 39.130 10.26 10.26 46.56 2.74
6786 7570 5.414765 GGTAAAAGGCACACTTAGCATTAGT 59.585 40.000 0.00 0.00 38.85 2.24
6787 7571 5.414454 TGGTAAAAGGCACACTTAGCATTAG 59.586 40.000 0.00 0.00 38.85 1.73
6817 7602 3.008049 GGTCCTGTGATTTGACTAGTGGT 59.992 47.826 0.00 0.00 0.00 4.16
6821 7606 5.451242 GCTCTAGGTCCTGTGATTTGACTAG 60.451 48.000 0.00 0.00 0.00 2.57
6833 7618 2.817258 CGATTAGAGGCTCTAGGTCCTG 59.183 54.545 22.47 10.53 31.71 3.86
6834 7619 2.444010 ACGATTAGAGGCTCTAGGTCCT 59.556 50.000 22.47 12.53 34.90 3.85
6835 7620 2.866351 ACGATTAGAGGCTCTAGGTCC 58.134 52.381 22.47 12.58 29.56 4.46
6843 7628 7.933577 TGATGATTATTTCAACGATTAGAGGCT 59.066 33.333 0.00 0.00 38.03 4.58
6914 7699 7.333921 AGAGATAGTGTATAATACCCGAGAACG 59.666 40.741 0.00 0.00 39.43 3.95
6926 7711 6.901300 ACCAAACAGGGAGAGATAGTGTATAA 59.099 38.462 0.00 0.00 43.89 0.98
6936 7721 3.045634 TCTTGAACCAAACAGGGAGAGA 58.954 45.455 0.00 0.00 43.89 3.10
6946 7731 4.445735 CCTTCCCAGTAGTCTTGAACCAAA 60.446 45.833 0.00 0.00 0.00 3.28
6952 7737 2.158219 TGACCCTTCCCAGTAGTCTTGA 60.158 50.000 0.00 0.00 0.00 3.02
6960 7745 7.025620 AGTTCATATATATGACCCTTCCCAGT 58.974 38.462 22.38 7.82 42.00 4.00
6961 7746 7.502060 AGTTCATATATATGACCCTTCCCAG 57.498 40.000 22.38 0.00 42.00 4.45
6981 7769 3.549794 CCCATCCTCATCCTTGAAGTTC 58.450 50.000 0.00 0.00 0.00 3.01
6997 7785 0.111253 ATTCTTCCCCATCGCCCATC 59.889 55.000 0.00 0.00 0.00 3.51
7009 7797 0.893727 ACGCAACCACCCATTCTTCC 60.894 55.000 0.00 0.00 0.00 3.46
7029 7817 2.486951 ATAAGGATCGTCGGTTGTCG 57.513 50.000 0.00 0.00 40.90 4.35


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

AutoCloner maintained by Alex Coulton.