Multiple sequence alignment - TraesCS4B01G238800

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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 TraesCS4B01G238800 chr4B 100.000 7419 0 0 1 7419 495597795 495590377 0.000000e+00 13701
1 TraesCS4B01G238800 chr4A 92.768 5033 235 61 687 5650 58884353 58879381 0.000000e+00 7158
2 TraesCS4B01G238800 chr4A 92.170 1341 58 25 5873 7207 58879123 58877824 0.000000e+00 1851
3 TraesCS4B01G238800 chr4A 91.629 669 40 8 1 665 58884998 58884342 0.000000e+00 911
4 TraesCS4B01G238800 chr4A 93.333 210 11 1 5662 5868 58879400 58879191 2.600000e-79 307
5 TraesCS4B01G238800 chr4A 91.758 182 12 3 7238 7419 58877723 58877545 4.440000e-62 250
6 TraesCS4B01G238800 chr4D 94.422 2743 104 24 2940 5650 401088496 401085771 0.000000e+00 4172
7 TraesCS4B01G238800 chr4D 97.195 2389 51 7 2486 4861 417630743 417628358 0.000000e+00 4026
8 TraesCS4B01G238800 chr4D 90.186 2150 136 36 835 2957 401090782 401088681 0.000000e+00 2732
9 TraesCS4B01G238800 chr4D 92.553 1692 83 17 544 2213 417632510 417630840 0.000000e+00 2386
10 TraesCS4B01G238800 chr4D 94.255 1323 50 12 5891 7207 417627233 417625931 0.000000e+00 1999
11 TraesCS4B01G238800 chr4D 91.883 1232 64 16 5986 7207 401085516 401084311 0.000000e+00 1688
12 TraesCS4B01G238800 chr4D 95.541 785 30 4 4867 5650 417628269 417627489 0.000000e+00 1251
13 TraesCS4B01G238800 chr4D 92.473 558 27 7 1 552 417633439 417632891 0.000000e+00 784
14 TraesCS4B01G238800 chr4D 91.039 558 35 7 1 552 401094672 401094124 0.000000e+00 739
15 TraesCS4B01G238800 chr4D 95.652 207 9 0 5662 5868 417627508 417627302 4.290000e-87 333
16 TraesCS4B01G238800 chr4D 94.340 212 7 2 5662 5868 401085790 401085579 3.340000e-83 320
17 TraesCS4B01G238800 chr4D 94.382 178 6 3 7238 7414 401084190 401084016 3.410000e-68 270
18 TraesCS4B01G238800 chr4D 89.831 177 10 3 7238 7414 417625809 417625641 3.480000e-53 220
19 TraesCS4B01G238800 chr4D 86.190 210 12 6 628 826 401092839 401092636 2.100000e-50 211
20 TraesCS4B01G238800 chr2B 84.456 193 29 1 2363 2555 379102299 379102490 9.830000e-44 189
21 TraesCS4B01G238800 chr2A 82.629 213 36 1 2343 2555 227833254 227833465 3.530000e-43 187
22 TraesCS4B01G238800 chr7B 81.373 204 35 3 2345 2548 675993104 675993304 5.960000e-36 163


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 TraesCS4B01G238800 chr4B 495590377 495597795 7418 True 13701.000000 13701 100.000000 1 7419 1 chr4B.!!$R1 7418
1 TraesCS4B01G238800 chr4A 58877545 58884998 7453 True 2095.400000 7158 92.331600 1 7419 5 chr4A.!!$R1 7418
2 TraesCS4B01G238800 chr4D 417625641 417633439 7798 True 1571.285714 4026 93.928571 1 7414 7 chr4D.!!$R2 7413
3 TraesCS4B01G238800 chr4D 401084016 401094672 10656 True 1447.428571 4172 91.777429 1 7414 7 chr4D.!!$R1 7413

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
321 322 0.032678 CGTATGTAGGCTGGCTGGAG 59.967 60.000 14.70 0.00 0.00 3.86 F
718 1954 0.243907 CCAGTGACAGTCGTGGTAGG 59.756 60.000 12.06 0.00 0.00 3.18 F
719 1955 1.244816 CAGTGACAGTCGTGGTAGGA 58.755 55.000 0.00 0.00 0.00 2.94 F
1776 4902 0.176680 AGGTTATCACTCAGCGCCAG 59.823 55.000 2.29 2.37 0.00 4.85 F
2412 5539 1.051812 AGGATTAGGATGCCCTGTCG 58.948 55.000 0.00 0.00 44.15 4.35 F
3315 6670 2.240500 GCGCAGAAGAGGTATGCCG 61.241 63.158 0.30 0.00 40.50 5.69 F
5020 8490 1.108776 TGGTTTATCGGGAGTCCTCG 58.891 55.000 9.58 11.22 0.00 4.63 F
5381 8851 1.095228 CAGTCACCACCACACACCAC 61.095 60.000 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 4757 0.385390 CAAGTCAAACCGGCTGCTTT 59.615 50.000 0.0 0.00 0.00 3.51 R
1632 4758 0.465460 TCAAGTCAAACCGGCTGCTT 60.465 50.000 0.0 4.79 0.00 3.91 R
2614 5756 0.550914 AGGTTCCCAGTGTCAAAGCA 59.449 50.000 0.0 0.00 0.00 3.91 R
2901 6046 3.917629 TCCCAAGGAAATGTTAGGGTACA 59.082 43.478 0.0 0.00 37.56 2.90 R
3346 6701 9.431887 CTGCAACTTTACTATGTAGAAGGTAAA 57.568 33.333 0.0 0.00 34.42 2.01 R
5204 8674 2.766828 GCTACCTACCAGGACAGATGTT 59.233 50.000 0.0 0.00 37.67 2.71 R
6283 9831 0.037326 CTAGTGCTCTCGCCAAACCA 60.037 55.000 0.0 0.00 34.43 3.67 R
7048 10614 0.467290 TGCTTCCACTTTCCACACCC 60.467 55.000 0.0 0.00 0.00 4.61 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
182 183 3.857854 CTGATGCAGCACGACGCC 61.858 66.667 0.00 0.00 44.04 5.68
233 234 1.076549 GGTGGTCATGGGCAAGGAA 59.923 57.895 0.00 0.00 0.00 3.36
239 240 2.092429 GGTCATGGGCAAGGAACTATCA 60.092 50.000 0.00 0.00 38.49 2.15
247 248 3.755378 GGCAAGGAACTATCATATGCTGG 59.245 47.826 0.00 0.00 38.49 4.85
260 261 4.802051 GCTGGCCCGGCAGATGAA 62.802 66.667 21.29 0.00 35.55 2.57
286 287 3.068165 GTGGACATGGACTCGTGATCATA 59.932 47.826 0.00 0.00 34.18 2.15
294 295 3.502595 GGACTCGTGATCATATCGGAGAA 59.497 47.826 0.00 0.00 43.58 2.87
300 301 3.829601 GTGATCATATCGGAGAAGGAGGT 59.170 47.826 0.00 0.00 43.58 3.85
302 303 1.964223 TCATATCGGAGAAGGAGGTGC 59.036 52.381 0.00 0.00 43.58 5.01
316 317 1.887707 GGTGCGTATGTAGGCTGGC 60.888 63.158 0.00 0.00 37.90 4.85
317 318 1.144057 GTGCGTATGTAGGCTGGCT 59.856 57.895 9.28 9.28 37.90 4.75
318 319 1.143838 TGCGTATGTAGGCTGGCTG 59.856 57.895 14.70 0.00 37.90 4.85
319 320 1.595382 GCGTATGTAGGCTGGCTGG 60.595 63.158 14.70 0.00 34.50 4.85
320 321 2.028125 GCGTATGTAGGCTGGCTGGA 62.028 60.000 14.70 0.00 34.50 3.86
321 322 0.032678 CGTATGTAGGCTGGCTGGAG 59.967 60.000 14.70 0.00 0.00 3.86
322 323 1.123928 GTATGTAGGCTGGCTGGAGT 58.876 55.000 14.70 0.07 0.00 3.85
323 324 1.486726 GTATGTAGGCTGGCTGGAGTT 59.513 52.381 14.70 0.00 0.00 3.01
324 325 0.543749 ATGTAGGCTGGCTGGAGTTC 59.456 55.000 14.70 0.00 0.00 3.01
325 326 1.222113 GTAGGCTGGCTGGAGTTCC 59.778 63.158 14.70 0.00 0.00 3.62
326 327 1.229496 TAGGCTGGCTGGAGTTCCA 60.229 57.895 14.70 0.18 45.30 3.53
327 328 0.840288 TAGGCTGGCTGGAGTTCCAA 60.840 55.000 14.70 0.00 46.97 3.53
328 329 1.228552 GGCTGGCTGGAGTTCCAAA 60.229 57.895 1.99 0.00 46.97 3.28
329 330 0.613012 GGCTGGCTGGAGTTCCAAAT 60.613 55.000 1.99 0.00 46.97 2.32
330 331 0.813821 GCTGGCTGGAGTTCCAAATC 59.186 55.000 1.99 0.00 46.97 2.17
346 347 7.177216 AGTTCCAAATCATCATCAGTGCTTTTA 59.823 33.333 0.00 0.00 0.00 1.52
353 354 7.977789 TCATCATCAGTGCTTTTACTTTGTA 57.022 32.000 0.00 0.00 0.00 2.41
382 383 2.538939 GCAATCGTCGGAGTTATTTGGC 60.539 50.000 0.00 0.00 0.00 4.52
397 398 7.806180 AGTTATTTGGCTGACTGGAATAGTAT 58.194 34.615 0.00 0.00 40.53 2.12
402 406 6.757897 TGGCTGACTGGAATAGTATTTTTG 57.242 37.500 0.00 0.00 40.53 2.44
407 411 7.550906 GCTGACTGGAATAGTATTTTTGACTCT 59.449 37.037 0.00 0.00 40.53 3.24
414 418 9.383519 GGAATAGTATTTTTGACTCTGTGATGA 57.616 33.333 0.00 0.00 0.00 2.92
429 433 6.594744 TCTGTGATGACCATGCAATAGTAAT 58.405 36.000 0.00 0.00 0.00 1.89
462 466 5.178061 GTGATGTAGTGATGTCCATTGTCA 58.822 41.667 0.00 0.00 0.00 3.58
475 479 4.072131 TCCATTGTCAGCTGTAAACCTTC 58.928 43.478 14.67 0.00 0.00 3.46
500 504 3.007290 AGAGACTGCAACATTGTCAGCTA 59.993 43.478 13.26 2.65 36.47 3.32
553 560 6.653273 TTTGAAAATTGAAACATGCGTCAA 57.347 29.167 12.58 12.58 38.09 3.18
571 976 4.666655 CGTCAATCTTTTTCTGGTGCTACG 60.667 45.833 0.00 0.00 0.00 3.51
657 1891 2.539688 GCGGAGTTGGAAAAAGCAAAAG 59.460 45.455 0.00 0.00 0.00 2.27
682 1916 7.567571 GCATTCTTGCCTTTTTAAAGAAGAAC 58.432 34.615 15.53 6.40 43.38 3.01
710 1946 1.202580 ACACTCTTGCCAGTGACAGTC 60.203 52.381 13.03 0.00 45.92 3.51
713 1949 0.249447 TCTTGCCAGTGACAGTCGTG 60.249 55.000 0.00 0.00 0.00 4.35
715 1951 1.966901 TTGCCAGTGACAGTCGTGGT 61.967 55.000 18.75 0.00 32.20 4.16
716 1952 1.110518 TGCCAGTGACAGTCGTGGTA 61.111 55.000 18.75 13.75 32.20 3.25
717 1953 0.388649 GCCAGTGACAGTCGTGGTAG 60.389 60.000 18.75 0.00 32.20 3.18
718 1954 0.243907 CCAGTGACAGTCGTGGTAGG 59.756 60.000 12.06 0.00 0.00 3.18
719 1955 1.244816 CAGTGACAGTCGTGGTAGGA 58.755 55.000 0.00 0.00 0.00 2.94
720 1956 1.611977 CAGTGACAGTCGTGGTAGGAA 59.388 52.381 0.00 0.00 0.00 3.36
873 3967 1.316266 CTCACCTCCCCCAGATCCT 59.684 63.158 0.00 0.00 0.00 3.24
1303 4399 5.358922 CCTGATTGCTTGTTTTCCTTTTCA 58.641 37.500 0.00 0.00 0.00 2.69
1428 4524 1.751351 GCCTGGAAATGGAACCTTAGC 59.249 52.381 0.00 0.00 0.00 3.09
1431 4527 3.445096 CCTGGAAATGGAACCTTAGCTTG 59.555 47.826 0.00 0.00 0.00 4.01
1457 4556 6.985188 TTCTGATATTTGCACTAGGTTCAC 57.015 37.500 0.00 0.00 0.00 3.18
1485 4584 5.388599 ACCTGTAGATTTAGGGGAATTGG 57.611 43.478 0.00 0.00 38.42 3.16
1494 4593 2.917713 AGGGGAATTGGCACATTGTA 57.082 45.000 0.00 0.00 39.30 2.41
1509 4608 6.202570 GGCACATTGTATGAACACATGTTTTT 59.797 34.615 0.00 0.00 38.56 1.94
1542 4668 3.060602 GTGAGTTGTAGAACCTGCAGTC 58.939 50.000 13.81 4.44 31.81 3.51
1546 4672 3.895656 AGTTGTAGAACCTGCAGTCAGTA 59.104 43.478 13.81 0.00 38.66 2.74
1560 4686 8.131100 CCTGCAGTCAGTATTTTATTATTGGTG 58.869 37.037 13.81 0.00 38.66 4.17
1561 4687 7.479980 TGCAGTCAGTATTTTATTATTGGTGC 58.520 34.615 0.00 0.00 0.00 5.01
1562 4688 7.121907 TGCAGTCAGTATTTTATTATTGGTGCA 59.878 33.333 0.00 0.00 32.31 4.57
1563 4689 8.137437 GCAGTCAGTATTTTATTATTGGTGCAT 58.863 33.333 0.00 0.00 0.00 3.96
1564 4690 9.454585 CAGTCAGTATTTTATTATTGGTGCATG 57.545 33.333 0.00 0.00 0.00 4.06
1565 4691 8.632679 AGTCAGTATTTTATTATTGGTGCATGG 58.367 33.333 0.00 0.00 0.00 3.66
1566 4692 8.413229 GTCAGTATTTTATTATTGGTGCATGGT 58.587 33.333 0.00 0.00 0.00 3.55
1567 4693 8.412456 TCAGTATTTTATTATTGGTGCATGGTG 58.588 33.333 0.00 0.00 0.00 4.17
1582 4708 5.009631 TGCATGGTGCTAACTAAGACATTT 58.990 37.500 3.41 0.00 45.31 2.32
1629 4755 7.112779 AGCTGTATATGCAAAAGGTTTCTACT 58.887 34.615 0.00 0.00 0.00 2.57
1631 4757 8.889717 GCTGTATATGCAAAAGGTTTCTACTAA 58.110 33.333 0.00 0.00 0.00 2.24
1776 4902 0.176680 AGGTTATCACTCAGCGCCAG 59.823 55.000 2.29 2.37 0.00 4.85
1884 5010 3.193267 TGATTCTTTGGTTGCTATGGTGC 59.807 43.478 0.00 0.00 0.00 5.01
1897 5023 3.499737 GGTGCGATGTCTTGCCCG 61.500 66.667 0.00 0.00 0.00 6.13
1922 5048 2.401766 GGCACGGCAATCTGGAGTG 61.402 63.158 0.00 0.00 36.05 3.51
1924 5050 1.237285 GCACGGCAATCTGGAGTGTT 61.237 55.000 0.25 0.00 35.46 3.32
2089 5215 7.976175 ACTTTCACTTTGTCCTTGAGATTTTTC 59.024 33.333 0.00 0.00 0.00 2.29
2098 5224 4.524328 TCCTTGAGATTTTTCCTTGCCTTC 59.476 41.667 0.00 0.00 0.00 3.46
2106 5232 7.512130 AGATTTTTCCTTGCCTTCATTTTCTT 58.488 30.769 0.00 0.00 0.00 2.52
2109 5235 5.458041 TTCCTTGCCTTCATTTTCTTGAG 57.542 39.130 0.00 0.00 0.00 3.02
2133 5259 5.050837 GCACAACAACATCAACATTTTCTCC 60.051 40.000 0.00 0.00 0.00 3.71
2199 5326 6.156949 TGTCTGTCATAAATAGGCTCTTCCTT 59.843 38.462 0.00 0.00 44.75 3.36
2244 5371 8.680903 ACATTCCTAGAATGAAAGCAGTTAATG 58.319 33.333 20.97 0.00 0.00 1.90
2247 5374 5.888161 CCTAGAATGAAAGCAGTTAATGGGT 59.112 40.000 0.00 0.00 0.00 4.51
2298 5425 8.208718 TGTATTTTCGGAAATATGGAGTTCTG 57.791 34.615 12.00 0.00 39.29 3.02
2318 5445 8.052748 AGTTCTGTTAATCCATTTACTGGCATA 58.947 33.333 0.00 0.00 45.52 3.14
2323 5450 9.634021 TGTTAATCCATTTACTGGCATATACAA 57.366 29.630 0.00 0.00 45.52 2.41
2412 5539 1.051812 AGGATTAGGATGCCCTGTCG 58.948 55.000 0.00 0.00 44.15 4.35
2433 5560 6.594159 TGTCGACTCCAATCTTTAGGAATTTC 59.406 38.462 17.92 0.00 32.57 2.17
2435 5562 5.880332 CGACTCCAATCTTTAGGAATTTCCA 59.120 40.000 17.57 1.22 39.61 3.53
2467 5594 7.712639 GTCTCACATAATGCTAAGAATCCTCAA 59.287 37.037 0.00 0.00 0.00 3.02
2526 5653 4.015872 AGTTGCTCCGTTCCTATGAAAA 57.984 40.909 0.00 0.00 30.79 2.29
2614 5756 5.131142 CCCTACATTCCACCAAGAACTAGAT 59.869 44.000 0.00 0.00 0.00 1.98
2821 5966 4.605183 TGTTCCTTTTCCTTTCACTGGAA 58.395 39.130 0.00 0.00 41.33 3.53
2901 6046 7.921786 TGCTTTTACTGCTACTGACAATATT 57.078 32.000 0.00 0.00 0.00 1.28
3087 6437 3.243035 TGTTGAATGAACTGTTGCCGAAG 60.243 43.478 0.00 0.00 35.37 3.79
3315 6670 2.240500 GCGCAGAAGAGGTATGCCG 61.241 63.158 0.30 0.00 40.50 5.69
3745 7104 1.542492 AGGCACTTGCATCTGAAAGG 58.458 50.000 3.15 0.00 44.36 3.11
4434 7793 4.032104 GCAAGCTGAAAATTTATTGCTCGG 59.968 41.667 10.67 2.70 39.82 4.63
4447 7806 6.903883 TTATTGCTCGGTCTGACTAATTTC 57.096 37.500 7.85 0.00 0.00 2.17
4569 7928 9.136323 TCTATGTCTACAGTGATGTTATGTGAT 57.864 33.333 0.00 0.00 0.00 3.06
4698 8070 8.691661 AATTATGTGTTTTAGTGTCACTTCCT 57.308 30.769 11.54 0.00 33.82 3.36
4832 8219 8.709646 ACGTTTTACTCATTTTGATCAGTACTC 58.290 33.333 0.00 0.00 0.00 2.59
5020 8490 1.108776 TGGTTTATCGGGAGTCCTCG 58.891 55.000 9.58 11.22 0.00 4.63
5219 8689 5.698741 AATCATCAACATCTGTCCTGGTA 57.301 39.130 0.00 0.00 0.00 3.25
5220 8690 4.743057 TCATCAACATCTGTCCTGGTAG 57.257 45.455 0.00 0.00 0.00 3.18
5338 8808 8.604890 GGTCATGAACTGAACTAGTAAAATAGC 58.395 37.037 2.64 0.00 38.64 2.97
5344 8814 5.189934 ACTGAACTAGTAAAATAGCCAGCCT 59.810 40.000 0.00 0.00 38.04 4.58
5381 8851 1.095228 CAGTCACCACCACACACCAC 61.095 60.000 0.00 0.00 0.00 4.16
5397 8867 7.097192 CACACACCACACAGTTATTAGACTAT 58.903 38.462 0.00 0.00 0.00 2.12
5511 8982 3.746045 AAAAGTGGAGACAACTAGCGA 57.254 42.857 0.00 0.00 46.06 4.93
5584 9063 7.065803 CACTATTCGACATGGGAAACACTTATT 59.934 37.037 0.00 0.00 0.00 1.40
5619 9098 8.491045 TTGATGAAGTGATCCTACATATACCA 57.509 34.615 0.00 0.00 0.00 3.25
5638 9117 3.712733 ACCAATAGGCATGCAATTCCAAT 59.287 39.130 21.36 0.00 39.06 3.16
5639 9118 4.164604 ACCAATAGGCATGCAATTCCAATT 59.835 37.500 21.36 4.95 39.06 2.32
5640 9119 4.753107 CCAATAGGCATGCAATTCCAATTC 59.247 41.667 21.36 0.00 0.00 2.17
5641 9120 5.361427 CAATAGGCATGCAATTCCAATTCA 58.639 37.500 21.36 0.00 0.00 2.57
5642 9121 3.255969 AGGCATGCAATTCCAATTCAC 57.744 42.857 21.36 0.00 0.00 3.18
5643 9122 2.568062 AGGCATGCAATTCCAATTCACA 59.432 40.909 21.36 0.00 0.00 3.58
5644 9123 3.199071 AGGCATGCAATTCCAATTCACAT 59.801 39.130 21.36 0.00 0.00 3.21
5645 9124 3.942748 GGCATGCAATTCCAATTCACATT 59.057 39.130 21.36 0.00 0.00 2.71
5646 9125 4.034742 GGCATGCAATTCCAATTCACATTC 59.965 41.667 21.36 0.00 0.00 2.67
5647 9126 4.034742 GCATGCAATTCCAATTCACATTCC 59.965 41.667 14.21 0.00 0.00 3.01
5648 9127 5.424757 CATGCAATTCCAATTCACATTCCT 58.575 37.500 0.00 0.00 0.00 3.36
5649 9128 5.486735 TGCAATTCCAATTCACATTCCTT 57.513 34.783 0.00 0.00 0.00 3.36
5650 9129 5.481105 TGCAATTCCAATTCACATTCCTTC 58.519 37.500 0.00 0.00 0.00 3.46
5651 9130 5.246656 TGCAATTCCAATTCACATTCCTTCT 59.753 36.000 0.00 0.00 0.00 2.85
5652 9131 5.809051 GCAATTCCAATTCACATTCCTTCTC 59.191 40.000 0.00 0.00 0.00 2.87
5653 9132 6.572898 GCAATTCCAATTCACATTCCTTCTCA 60.573 38.462 0.00 0.00 0.00 3.27
5654 9133 7.380536 CAATTCCAATTCACATTCCTTCTCAA 58.619 34.615 0.00 0.00 0.00 3.02
5655 9134 6.975196 TTCCAATTCACATTCCTTCTCAAA 57.025 33.333 0.00 0.00 0.00 2.69
5656 9135 6.975196 TCCAATTCACATTCCTTCTCAAAA 57.025 33.333 0.00 0.00 0.00 2.44
5657 9136 7.358770 TCCAATTCACATTCCTTCTCAAAAA 57.641 32.000 0.00 0.00 0.00 1.94
5859 9343 7.494298 CAGAAACCTTTTTGCTTTAAGCCTTTA 59.506 33.333 14.80 0.00 41.51 1.85
5868 9352 5.386924 TGCTTTAAGCCTTTAACTGGGTAA 58.613 37.500 14.80 0.00 41.51 2.85
5869 9353 6.014012 TGCTTTAAGCCTTTAACTGGGTAAT 58.986 36.000 14.80 0.00 41.51 1.89
5870 9354 7.176490 TGCTTTAAGCCTTTAACTGGGTAATA 58.824 34.615 14.80 0.00 41.51 0.98
5995 9543 2.939103 GGAGGTTGCTACAAGCTATGTG 59.061 50.000 11.63 0.00 43.77 3.21
6070 9618 6.514947 AGAAGCTGATAGCATTCTCAGTAAG 58.485 40.000 3.43 0.00 45.56 2.34
6100 9648 6.682423 TTGTCAAGTAAGATGCCATACATG 57.318 37.500 0.00 0.00 39.84 3.21
6193 9741 2.346766 TGCTTCTGGAGTGCTTGAAA 57.653 45.000 0.00 0.00 0.00 2.69
6403 9951 0.103208 CGCCGGAGCAGATAAGAACT 59.897 55.000 5.05 0.00 39.83 3.01
6425 9973 6.146760 ACTATACTGGAAATCTGAGGTCCAT 58.853 40.000 11.33 6.24 40.61 3.41
6441 9989 3.951680 GGTCCATACACCATACCTTTTGG 59.048 47.826 0.00 0.00 40.05 3.28
6491 10039 9.671279 TGTTCAGAATCACACTGATGTATATTT 57.329 29.630 0.00 0.00 42.68 1.40
6504 10054 9.289782 ACTGATGTATATTTCCTGCTAAAATCC 57.710 33.333 0.00 0.00 0.00 3.01
6519 10069 2.919666 AATCCGAGGTTGCAATTTCG 57.080 45.000 21.56 21.56 0.00 3.46
6522 10072 1.156736 CCGAGGTTGCAATTTCGTCT 58.843 50.000 24.45 9.01 0.00 4.18
6547 10097 7.962964 TGAAGAAATACTGAAGTGGTTACAG 57.037 36.000 0.00 0.00 37.62 2.74
6583 10133 9.561270 AACTGTTATATCATATCTCGATTGTCG 57.439 33.333 0.00 0.00 42.10 4.35
6677 10227 5.001232 CCAGAGAAGAAAAACATTCCGGTA 58.999 41.667 0.00 0.00 0.00 4.02
6678 10228 5.106673 CCAGAGAAGAAAAACATTCCGGTAC 60.107 44.000 0.00 0.00 0.00 3.34
6679 10229 5.001874 AGAGAAGAAAAACATTCCGGTACC 58.998 41.667 0.16 0.16 0.00 3.34
6718 10276 6.394345 AGAAACCAGATTCCAGTATTTCCT 57.606 37.500 0.00 0.00 0.00 3.36
6749 10308 2.037902 TGTGTAGGGTTGAAAGCGATGA 59.962 45.455 0.00 0.00 0.00 2.92
6874 10433 1.598601 GTAACCTTCCGCAAAACGTCA 59.401 47.619 0.00 0.00 41.42 4.35
6875 10434 0.379316 AACCTTCCGCAAAACGTCAC 59.621 50.000 0.00 0.00 41.42 3.67
7048 10614 0.512952 CGGAACTCTGAACTTTGGCG 59.487 55.000 0.00 0.00 0.00 5.69
7090 10656 1.071385 CGCTAATCAGGATCCAAGGCT 59.929 52.381 15.82 0.00 0.00 4.58
7104 10670 0.178961 AAGGCTGTTTCTTGGGGGAC 60.179 55.000 0.00 0.00 0.00 4.46
7114 10680 3.899052 TCTTGGGGGACAACTAATACG 57.101 47.619 0.00 0.00 34.76 3.06
7116 10682 3.839490 TCTTGGGGGACAACTAATACGAA 59.161 43.478 0.00 0.00 34.76 3.85
7117 10683 4.472108 TCTTGGGGGACAACTAATACGAAT 59.528 41.667 0.00 0.00 34.76 3.34
7119 10685 5.280654 TGGGGGACAACTAATACGAATAC 57.719 43.478 0.00 0.00 0.00 1.89
7120 10686 4.964262 TGGGGGACAACTAATACGAATACT 59.036 41.667 0.00 0.00 0.00 2.12
7121 10687 6.135454 TGGGGGACAACTAATACGAATACTA 58.865 40.000 0.00 0.00 0.00 1.82
7122 10688 6.783977 TGGGGGACAACTAATACGAATACTAT 59.216 38.462 0.00 0.00 0.00 2.12
7123 10689 7.039504 TGGGGGACAACTAATACGAATACTATC 60.040 40.741 0.00 0.00 0.00 2.08
7124 10690 7.039504 GGGGGACAACTAATACGAATACTATCA 60.040 40.741 0.00 0.00 0.00 2.15
7125 10691 8.027771 GGGGACAACTAATACGAATACTATCAG 58.972 40.741 0.00 0.00 0.00 2.90
7126 10692 8.027771 GGGACAACTAATACGAATACTATCAGG 58.972 40.741 0.00 0.00 0.00 3.86
7127 10693 8.027771 GGACAACTAATACGAATACTATCAGGG 58.972 40.741 0.00 0.00 0.00 4.45
7128 10694 8.701908 ACAACTAATACGAATACTATCAGGGA 57.298 34.615 0.00 0.00 0.00 4.20
7129 10695 8.574737 ACAACTAATACGAATACTATCAGGGAC 58.425 37.037 0.00 0.00 0.00 4.46
7180 10746 1.159713 TCAAGCTTGTCGGCAGTGTG 61.160 55.000 25.19 0.00 34.17 3.82
7181 10747 1.893808 AAGCTTGTCGGCAGTGTGG 60.894 57.895 0.00 0.00 34.17 4.17
7200 10766 5.748630 GTGTGGATTTGTTTGTTTTCCTCTC 59.251 40.000 0.00 0.00 0.00 3.20
7211 10827 6.920569 TTGTTTTCCTCTCTACTTTGTGAC 57.079 37.500 0.00 0.00 0.00 3.67
7214 10830 5.825593 TTTCCTCTCTACTTTGTGACCAT 57.174 39.130 0.00 0.00 0.00 3.55
7215 10831 5.825593 TTCCTCTCTACTTTGTGACCATT 57.174 39.130 0.00 0.00 0.00 3.16
7236 10852 2.969821 TTTCTCCTTTTGGGCAGCTA 57.030 45.000 0.00 0.00 40.87 3.32
7239 10855 3.456380 TCTCCTTTTGGGCAGCTAAAT 57.544 42.857 0.00 0.00 40.87 1.40
7240 10856 3.778265 TCTCCTTTTGGGCAGCTAAATT 58.222 40.909 0.00 0.00 40.87 1.82
7241 10857 4.159557 TCTCCTTTTGGGCAGCTAAATTT 58.840 39.130 0.00 0.00 40.87 1.82
7242 10858 5.329399 TCTCCTTTTGGGCAGCTAAATTTA 58.671 37.500 0.00 0.00 40.87 1.40
7243 10859 5.957774 TCTCCTTTTGGGCAGCTAAATTTAT 59.042 36.000 0.00 0.00 40.87 1.40
7252 10907 8.719645 TGGGCAGCTAAATTTATAATTATGGT 57.280 30.769 8.28 0.00 0.00 3.55
7282 10937 3.629398 GGCTTGTAATAGCAGCATCAACT 59.371 43.478 0.00 0.00 43.02 3.16
7284 10939 5.032863 GCTTGTAATAGCAGCATCAACTTG 58.967 41.667 0.00 0.00 40.89 3.16
7372 11027 9.470399 AATTAATTAGTTCCCCTACGAACAAAT 57.530 29.630 0.00 0.00 43.82 2.32
7374 11029 9.956640 TTAATTAGTTCCCCTACGAACAAATTA 57.043 29.630 4.46 0.00 43.82 1.40
7377 11032 8.866970 TTAGTTCCCCTACGAACAAATTAAAT 57.133 30.769 4.46 0.00 43.82 1.40
7378 11033 9.956640 TTAGTTCCCCTACGAACAAATTAAATA 57.043 29.630 4.46 0.00 43.82 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 147 1.827399 GCACCTCCTCCACCGAGAAA 61.827 60.000 0.00 0.00 38.52 2.52
233 234 0.615331 CCGGGCCAGCATATGATAGT 59.385 55.000 6.97 0.00 0.00 2.12
239 240 2.532532 ATCTGCCGGGCCAGCATAT 61.533 57.895 16.10 11.01 40.04 1.78
247 248 2.825836 CAGGTTCATCTGCCGGGC 60.826 66.667 13.32 13.32 0.00 6.13
260 261 0.832135 ACGAGTCCATGTCCACAGGT 60.832 55.000 0.00 0.00 0.00 4.00
286 287 0.395311 TACGCACCTCCTTCTCCGAT 60.395 55.000 0.00 0.00 0.00 4.18
294 295 0.397254 AGCCTACATACGCACCTCCT 60.397 55.000 0.00 0.00 0.00 3.69
300 301 1.143838 CAGCCAGCCTACATACGCA 59.856 57.895 0.00 0.00 0.00 5.24
302 303 0.032678 CTCCAGCCAGCCTACATACG 59.967 60.000 0.00 0.00 0.00 3.06
317 318 4.945543 CACTGATGATGATTTGGAACTCCA 59.054 41.667 0.00 0.00 45.94 3.86
318 319 4.201990 GCACTGATGATGATTTGGAACTCC 60.202 45.833 0.00 0.00 0.00 3.85
319 320 4.639310 AGCACTGATGATGATTTGGAACTC 59.361 41.667 0.00 0.00 0.00 3.01
320 321 4.597004 AGCACTGATGATGATTTGGAACT 58.403 39.130 0.00 0.00 0.00 3.01
321 322 4.978083 AGCACTGATGATGATTTGGAAC 57.022 40.909 0.00 0.00 0.00 3.62
322 323 5.988310 AAAGCACTGATGATGATTTGGAA 57.012 34.783 0.00 0.00 34.53 3.53
323 324 5.988310 AAAAGCACTGATGATGATTTGGA 57.012 34.783 0.00 0.00 35.91 3.53
324 325 6.860080 AGTAAAAGCACTGATGATGATTTGG 58.140 36.000 0.00 0.00 35.91 3.28
325 326 8.644619 CAAAGTAAAAGCACTGATGATGATTTG 58.355 33.333 0.00 0.00 35.91 2.32
326 327 8.362639 ACAAAGTAAAAGCACTGATGATGATTT 58.637 29.630 0.00 0.00 37.27 2.17
327 328 7.889469 ACAAAGTAAAAGCACTGATGATGATT 58.111 30.769 0.00 0.00 0.00 2.57
328 329 7.458409 ACAAAGTAAAAGCACTGATGATGAT 57.542 32.000 0.00 0.00 0.00 2.45
329 330 6.882610 ACAAAGTAAAAGCACTGATGATGA 57.117 33.333 0.00 0.00 0.00 2.92
330 331 7.699391 CCATACAAAGTAAAAGCACTGATGATG 59.301 37.037 0.00 0.00 0.00 3.07
346 347 2.099592 CGATTGCATGGCCATACAAAGT 59.900 45.455 30.44 18.09 28.88 2.66
353 354 2.188829 CCGACGATTGCATGGCCAT 61.189 57.895 14.09 14.09 0.00 4.40
382 383 8.877779 CAGAGTCAAAAATACTATTCCAGTCAG 58.122 37.037 0.00 0.00 38.80 3.51
397 398 4.022935 GCATGGTCATCACAGAGTCAAAAA 60.023 41.667 0.00 0.00 0.00 1.94
402 406 2.391616 TGCATGGTCATCACAGAGTC 57.608 50.000 0.00 0.00 0.00 3.36
407 411 7.643569 AAATTACTATTGCATGGTCATCACA 57.356 32.000 0.00 0.00 0.00 3.58
414 418 9.243105 ACAGAGTAAAAATTACTATTGCATGGT 57.757 29.630 2.93 0.00 0.00 3.55
429 433 7.602644 GGACATCACTACATCACAGAGTAAAAA 59.397 37.037 0.00 0.00 0.00 1.94
443 447 3.261643 AGCTGACAATGGACATCACTACA 59.738 43.478 0.00 0.00 0.00 2.74
444 448 3.620374 CAGCTGACAATGGACATCACTAC 59.380 47.826 8.42 0.00 0.00 2.73
447 451 2.430465 ACAGCTGACAATGGACATCAC 58.570 47.619 23.35 0.00 0.00 3.06
462 466 4.080687 AGTCTCTACGAAGGTTTACAGCT 58.919 43.478 0.00 0.00 0.00 4.24
475 479 3.317150 TGACAATGTTGCAGTCTCTACG 58.683 45.455 4.86 0.00 33.56 3.51
500 504 5.703876 CTCGAGCTAAAAGAAAAAGGCAAT 58.296 37.500 0.00 0.00 0.00 3.56
553 560 6.575162 AAAATCGTAGCACCAGAAAAAGAT 57.425 33.333 0.00 0.00 0.00 2.40
698 1934 0.388649 CTACCACGACTGTCACTGGC 60.389 60.000 17.37 0.00 0.00 4.85
710 1946 2.747446 CCCACATTTTCTTCCTACCACG 59.253 50.000 0.00 0.00 0.00 4.94
713 1949 3.762288 GGTTCCCACATTTTCTTCCTACC 59.238 47.826 0.00 0.00 0.00 3.18
715 1951 3.328343 TCGGTTCCCACATTTTCTTCCTA 59.672 43.478 0.00 0.00 0.00 2.94
716 1952 2.107552 TCGGTTCCCACATTTTCTTCCT 59.892 45.455 0.00 0.00 0.00 3.36
717 1953 2.488153 CTCGGTTCCCACATTTTCTTCC 59.512 50.000 0.00 0.00 0.00 3.46
718 1954 3.408634 TCTCGGTTCCCACATTTTCTTC 58.591 45.455 0.00 0.00 0.00 2.87
719 1955 3.502123 TCTCGGTTCCCACATTTTCTT 57.498 42.857 0.00 0.00 0.00 2.52
720 1956 3.502123 TTCTCGGTTCCCACATTTTCT 57.498 42.857 0.00 0.00 0.00 2.52
873 3967 2.232941 GGAGTTTGGTGATGACCGTCTA 59.767 50.000 0.00 0.00 46.62 2.59
1273 4369 0.675633 ACAAGCAATCAGGCACCAAC 59.324 50.000 0.00 0.00 35.83 3.77
1428 4524 7.820648 ACCTAGTGCAAATATCAGAAAACAAG 58.179 34.615 0.00 0.00 0.00 3.16
1431 4527 7.750903 GTGAACCTAGTGCAAATATCAGAAAAC 59.249 37.037 0.00 0.00 0.00 2.43
1457 4556 4.473559 TCCCCTAAATCTACAGGTTTGAGG 59.526 45.833 0.00 0.00 0.00 3.86
1485 4584 6.768029 AAAACATGTGTTCATACAATGTGC 57.232 33.333 0.00 0.00 36.75 4.57
1542 4668 7.169645 GCACCATGCACCAATAATAAAATACTG 59.830 37.037 0.00 0.00 44.26 2.74
1560 4686 5.123820 TCAAATGTCTTAGTTAGCACCATGC 59.876 40.000 0.00 0.00 45.46 4.06
1561 4687 6.372659 ACTCAAATGTCTTAGTTAGCACCATG 59.627 38.462 0.00 0.00 0.00 3.66
1562 4688 6.476378 ACTCAAATGTCTTAGTTAGCACCAT 58.524 36.000 0.00 0.00 0.00 3.55
1563 4689 5.865085 ACTCAAATGTCTTAGTTAGCACCA 58.135 37.500 0.00 0.00 0.00 4.17
1564 4690 7.900782 TTACTCAAATGTCTTAGTTAGCACC 57.099 36.000 0.00 0.00 0.00 5.01
1611 4737 8.172352 TGCTTTTAGTAGAAACCTTTTGCATA 57.828 30.769 0.00 0.00 0.00 3.14
1629 4755 1.975660 AGTCAAACCGGCTGCTTTTA 58.024 45.000 0.00 0.00 0.00 1.52
1631 4757 0.385390 CAAGTCAAACCGGCTGCTTT 59.615 50.000 0.00 0.00 0.00 3.51
1632 4758 0.465460 TCAAGTCAAACCGGCTGCTT 60.465 50.000 0.00 4.79 0.00 3.91
1634 4760 0.598065 ATTCAAGTCAAACCGGCTGC 59.402 50.000 0.00 0.00 0.00 5.25
1884 5010 1.393539 CACTAAACGGGCAAGACATCG 59.606 52.381 0.00 0.00 0.00 3.84
1897 5023 1.135689 CAGATTGCCGTGCCACTAAAC 60.136 52.381 0.00 0.00 0.00 2.01
2089 5215 3.006110 TGCTCAAGAAAATGAAGGCAAGG 59.994 43.478 0.00 0.00 30.40 3.61
2098 5224 5.749588 TGATGTTGTTGTGCTCAAGAAAATG 59.250 36.000 16.26 0.00 35.70 2.32
2106 5232 4.652421 AATGTTGATGTTGTTGTGCTCA 57.348 36.364 0.00 0.00 0.00 4.26
2109 5235 5.050837 GGAGAAAATGTTGATGTTGTTGTGC 60.051 40.000 0.00 0.00 0.00 4.57
2133 5259 4.843220 AATTGAGTTGAAAGACTGGCAG 57.157 40.909 14.16 14.16 0.00 4.85
2213 5340 6.349300 TGCTTTCATTCTAGGAATGTAGTCC 58.651 40.000 16.52 0.00 38.03 3.85
2214 5341 7.044798 ACTGCTTTCATTCTAGGAATGTAGTC 58.955 38.462 16.52 12.19 39.41 2.59
2215 5342 6.951971 ACTGCTTTCATTCTAGGAATGTAGT 58.048 36.000 16.52 10.63 39.08 2.73
2219 5346 8.133627 CCATTAACTGCTTTCATTCTAGGAATG 58.866 37.037 12.44 12.44 0.00 2.67
2221 5348 6.603201 CCCATTAACTGCTTTCATTCTAGGAA 59.397 38.462 0.00 0.00 0.00 3.36
2222 5349 6.122277 CCCATTAACTGCTTTCATTCTAGGA 58.878 40.000 0.00 0.00 0.00 2.94
2223 5350 5.888161 ACCCATTAACTGCTTTCATTCTAGG 59.112 40.000 0.00 0.00 0.00 3.02
2224 5351 7.396540 AACCCATTAACTGCTTTCATTCTAG 57.603 36.000 0.00 0.00 0.00 2.43
2225 5352 9.120538 GATAACCCATTAACTGCTTTCATTCTA 57.879 33.333 0.00 0.00 0.00 2.10
2227 5354 8.000780 AGATAACCCATTAACTGCTTTCATTC 57.999 34.615 0.00 0.00 0.00 2.67
2228 5355 7.961326 AGATAACCCATTAACTGCTTTCATT 57.039 32.000 0.00 0.00 0.00 2.57
2229 5356 7.961326 AAGATAACCCATTAACTGCTTTCAT 57.039 32.000 0.00 0.00 0.00 2.57
2318 5445 7.716998 CCTACATAATTTGAGCAGACCTTGTAT 59.283 37.037 0.00 0.00 0.00 2.29
2323 5450 4.687219 GCCCTACATAATTTGAGCAGACCT 60.687 45.833 0.00 0.00 0.00 3.85
2412 5539 7.703058 TTGGAAATTCCTAAAGATTGGAGTC 57.297 36.000 13.78 0.00 37.46 3.36
2433 5560 4.458397 AGCATTATGTGAGACCTCATTGG 58.542 43.478 2.78 0.00 42.18 3.16
2435 5562 7.129457 TCTTAGCATTATGTGAGACCTCATT 57.871 36.000 2.78 0.00 42.18 2.57
2467 5594 5.387113 TGTGTCCATATTGGCCTAATTCT 57.613 39.130 3.32 0.00 37.47 2.40
2556 5683 3.732212 GGGCTCATTCAGTTTGCTTTTT 58.268 40.909 0.00 0.00 0.00 1.94
2557 5684 2.288395 CGGGCTCATTCAGTTTGCTTTT 60.288 45.455 0.00 0.00 0.00 2.27
2558 5685 1.270550 CGGGCTCATTCAGTTTGCTTT 59.729 47.619 0.00 0.00 0.00 3.51
2567 5709 1.860641 TCTCCTTACGGGCTCATTCA 58.139 50.000 0.00 0.00 34.39 2.57
2597 5739 4.640771 AAGCATCTAGTTCTTGGTGGAA 57.359 40.909 0.00 0.00 0.00 3.53
2614 5756 0.550914 AGGTTCCCAGTGTCAAAGCA 59.449 50.000 0.00 0.00 0.00 3.91
2840 5985 7.064728 GGTGAGCGGAAATATATCTCCAATTAC 59.935 40.741 5.92 0.56 0.00 1.89
2901 6046 3.917629 TCCCAAGGAAATGTTAGGGTACA 59.082 43.478 0.00 0.00 37.56 2.90
3087 6437 5.346822 CACAATAGCAAATTTGAGCAAGGTC 59.653 40.000 22.31 1.35 0.00 3.85
3345 6700 9.781633 TGCAACTTTACTATGTAGAAGGTAAAA 57.218 29.630 0.00 0.00 34.94 1.52
3346 6701 9.431887 CTGCAACTTTACTATGTAGAAGGTAAA 57.568 33.333 0.00 0.00 34.42 2.01
4434 7793 5.875359 CACCAAGGGTAGAAATTAGTCAGAC 59.125 44.000 0.00 0.00 32.11 3.51
4447 7806 4.599047 TTCAAAATTGCACCAAGGGTAG 57.401 40.909 0.00 0.00 32.11 3.18
4577 7936 6.992715 ACAGACACTGAAATACTGCTAGTTTT 59.007 34.615 5.76 0.00 35.18 2.43
4779 8152 6.202762 CACACTTGTTACTTGTGCAATCTAGA 59.797 38.462 0.00 0.00 34.64 2.43
4986 8456 5.965334 CGATAAACCACAATGCAGATAACAC 59.035 40.000 0.00 0.00 0.00 3.32
5020 8490 5.699458 AGCACTAACAGTACCACATGTAAAC 59.301 40.000 0.00 0.00 0.00 2.01
5161 8631 9.486497 GAATAGCATCAACTGAGATTGAATCTA 57.514 33.333 7.82 0.00 41.78 1.98
5204 8674 2.766828 GCTACCTACCAGGACAGATGTT 59.233 50.000 0.00 0.00 37.67 2.71
5219 8689 9.084533 TGGTAAACAAAAAGAATTATGCTACCT 57.915 29.630 0.00 0.00 33.12 3.08
5220 8690 9.869757 ATGGTAAACAAAAAGAATTATGCTACC 57.130 29.630 0.00 0.00 32.85 3.18
5419 8889 9.599866 CTACAGGGAACTTTTTGAAATTTCTTT 57.400 29.630 18.64 3.29 40.21 2.52
5511 8982 5.131642 TGTTTGATCTTATCCATCTCTGCCT 59.868 40.000 0.00 0.00 0.00 4.75
5602 9081 7.182817 TGCCTATTGGTATATGTAGGATCAC 57.817 40.000 0.00 0.00 36.62 3.06
5619 9098 5.104859 TGTGAATTGGAATTGCATGCCTATT 60.105 36.000 16.68 14.62 31.46 1.73
5662 9141 8.840321 CGAGTATTAAGGAATGTGAATTGGAAT 58.160 33.333 0.00 0.00 0.00 3.01
5663 9142 7.201696 GCGAGTATTAAGGAATGTGAATTGGAA 60.202 37.037 0.00 0.00 0.00 3.53
5664 9143 6.260050 GCGAGTATTAAGGAATGTGAATTGGA 59.740 38.462 0.00 0.00 0.00 3.53
5665 9144 6.260936 AGCGAGTATTAAGGAATGTGAATTGG 59.739 38.462 0.00 0.00 0.00 3.16
5666 9145 7.251704 AGCGAGTATTAAGGAATGTGAATTG 57.748 36.000 0.00 0.00 0.00 2.32
5667 9146 7.865706 AAGCGAGTATTAAGGAATGTGAATT 57.134 32.000 0.00 0.00 0.00 2.17
5668 9147 7.865706 AAAGCGAGTATTAAGGAATGTGAAT 57.134 32.000 0.00 0.00 0.00 2.57
5723 9202 1.069022 CAACACCGGCTGTTTCTCATG 60.069 52.381 16.56 5.24 41.50 3.07
5827 9311 2.029918 AGCAAAAAGGTTTCTGATCCGC 60.030 45.455 0.00 0.00 0.00 5.54
5859 9343 9.762381 TCATGTAAGGAAAAATATTACCCAGTT 57.238 29.630 0.00 0.00 0.00 3.16
5995 9543 5.071955 CGATCATAGAGCGAAGGTTTTTC 57.928 43.478 0.00 0.00 44.55 2.29
6070 9618 4.142600 GGCATCTTACTTGACAATCCACAC 60.143 45.833 0.00 0.00 0.00 3.82
6100 9648 4.437659 CCGTCAGTAGAGCTGTAGTTCTTC 60.438 50.000 3.58 0.00 45.23 2.87
6193 9741 5.189736 TCCAGTCACAATACCATAGAAAGCT 59.810 40.000 0.00 0.00 0.00 3.74
6196 9744 6.774673 TGTTCCAGTCACAATACCATAGAAA 58.225 36.000 0.00 0.00 0.00 2.52
6283 9831 0.037326 CTAGTGCTCTCGCCAAACCA 60.037 55.000 0.00 0.00 34.43 3.67
6403 9951 7.015292 GTGTATGGACCTCAGATTTCCAGTATA 59.985 40.741 6.36 0.00 42.72 1.47
6441 9989 8.147058 ACATGAATCTCCTCTCATTACATGTAC 58.853 37.037 4.68 0.00 42.09 2.90
6478 10026 9.289782 GGATTTTAGCAGGAAATATACATCAGT 57.710 33.333 0.00 0.00 0.00 3.41
6479 10027 8.446273 CGGATTTTAGCAGGAAATATACATCAG 58.554 37.037 0.00 0.00 0.00 2.90
6491 10039 2.939640 GCAACCTCGGATTTTAGCAGGA 60.940 50.000 0.00 0.00 0.00 3.86
6504 10054 2.223144 TCAAGACGAAATTGCAACCTCG 59.777 45.455 23.40 23.40 37.33 4.63
6519 10069 7.497925 AACCACTTCAGTATTTCTTCAAGAC 57.502 36.000 0.00 0.00 0.00 3.01
6522 10072 7.041372 GCTGTAACCACTTCAGTATTTCTTCAA 60.041 37.037 0.00 0.00 0.00 2.69
6579 10129 3.997762 AGCAAACCTGTAATACACGACA 58.002 40.909 0.00 0.00 0.00 4.35
6619 10169 6.089551 GGTATCATTAATCCGACAATGACTCG 59.910 42.308 8.66 0.00 42.33 4.18
6677 10227 6.887545 TGGTTTCTCCAAATATACAATTCGGT 59.112 34.615 0.00 0.00 44.12 4.69
6678 10228 7.282224 TCTGGTTTCTCCAAATATACAATTCGG 59.718 37.037 0.00 0.00 46.59 4.30
6679 10229 8.208718 TCTGGTTTCTCCAAATATACAATTCG 57.791 34.615 0.00 0.00 46.59 3.34
6718 10276 2.948979 CAACCCTACACAAGCAAGAACA 59.051 45.455 0.00 0.00 0.00 3.18
6749 10308 3.119849 GCAAGTTGGATGCAGTTATTCGT 60.120 43.478 4.75 0.00 43.29 3.85
6874 10433 7.466746 ACACAGTAAGGATGCAATTAATTGT 57.533 32.000 25.15 10.05 39.88 2.71
6875 10434 9.289303 GTAACACAGTAAGGATGCAATTAATTG 57.711 33.333 21.54 21.54 40.66 2.32
7037 10603 1.826054 CCACACCCGCCAAAGTTCA 60.826 57.895 0.00 0.00 0.00 3.18
7048 10614 0.467290 TGCTTCCACTTTCCACACCC 60.467 55.000 0.00 0.00 0.00 4.61
7090 10656 3.955524 TTAGTTGTCCCCCAAGAAACA 57.044 42.857 0.00 0.00 32.51 2.83
7104 10670 8.573885 TGTCCCTGATAGTATTCGTATTAGTTG 58.426 37.037 0.00 0.00 0.00 3.16
7114 10680 5.615925 AACCTGTGTCCCTGATAGTATTC 57.384 43.478 0.00 0.00 0.00 1.75
7116 10682 5.780793 GGATAACCTGTGTCCCTGATAGTAT 59.219 44.000 0.00 0.00 0.00 2.12
7117 10683 5.145564 GGATAACCTGTGTCCCTGATAGTA 58.854 45.833 0.00 0.00 0.00 1.82
7119 10685 3.967326 TGGATAACCTGTGTCCCTGATAG 59.033 47.826 0.00 0.00 37.04 2.08
7120 10686 3.967326 CTGGATAACCTGTGTCCCTGATA 59.033 47.826 0.00 0.00 37.04 2.15
7121 10687 2.774234 CTGGATAACCTGTGTCCCTGAT 59.226 50.000 0.00 0.00 37.04 2.90
7122 10688 2.187958 CTGGATAACCTGTGTCCCTGA 58.812 52.381 0.00 0.00 37.04 3.86
7123 10689 1.210478 CCTGGATAACCTGTGTCCCTG 59.790 57.143 0.00 0.00 37.04 4.45
7124 10690 1.203440 ACCTGGATAACCTGTGTCCCT 60.203 52.381 0.00 0.00 37.04 4.20
7125 10691 1.286248 ACCTGGATAACCTGTGTCCC 58.714 55.000 0.00 0.00 37.04 4.46
7126 10692 3.181454 CCATACCTGGATAACCTGTGTCC 60.181 52.174 0.00 0.00 46.37 4.02
7127 10693 3.454812 ACCATACCTGGATAACCTGTGTC 59.545 47.826 0.00 0.00 46.37 3.67
7128 10694 3.460825 ACCATACCTGGATAACCTGTGT 58.539 45.455 0.00 0.00 46.37 3.72
7129 10695 4.080582 TCAACCATACCTGGATAACCTGTG 60.081 45.833 0.00 0.00 46.37 3.66
7180 10746 7.511959 AGTAGAGAGGAAAACAAACAAATCC 57.488 36.000 0.00 0.00 0.00 3.01
7181 10747 9.237846 CAAAGTAGAGAGGAAAACAAACAAATC 57.762 33.333 0.00 0.00 0.00 2.17
7215 10831 2.397597 AGCTGCCCAAAAGGAGAAAAA 58.602 42.857 0.00 0.00 38.24 1.94
7225 10841 9.995003 CCATAATTATAAATTTAGCTGCCCAAA 57.005 29.630 3.94 0.00 0.00 3.28
7228 10844 8.585018 ACACCATAATTATAAATTTAGCTGCCC 58.415 33.333 3.94 0.00 0.00 5.36
7236 10852 8.079809 GCCACGCTACACCATAATTATAAATTT 58.920 33.333 0.00 0.00 0.00 1.82
7239 10855 6.292923 AGCCACGCTACACCATAATTATAAA 58.707 36.000 0.00 0.00 36.99 1.40
7240 10856 5.860611 AGCCACGCTACACCATAATTATAA 58.139 37.500 0.00 0.00 36.99 0.98
7241 10857 5.477607 AGCCACGCTACACCATAATTATA 57.522 39.130 0.00 0.00 36.99 0.98
7242 10858 4.351874 AGCCACGCTACACCATAATTAT 57.648 40.909 0.00 0.00 36.99 1.28
7243 10859 3.830744 AGCCACGCTACACCATAATTA 57.169 42.857 0.00 0.00 36.99 1.40
7252 10907 2.093921 TGCTATTACAAGCCACGCTACA 60.094 45.455 0.00 0.00 42.05 2.74
7282 10937 2.235016 GGGTGTGCAGTATTCAACCAA 58.765 47.619 3.55 0.00 38.64 3.67
7284 10939 1.173913 GGGGTGTGCAGTATTCAACC 58.826 55.000 0.00 0.00 38.13 3.77
7377 11032 8.466798 TGCGACTATCTGCTTAATAATGCTATA 58.533 33.333 0.00 0.00 0.00 1.31
7378 11033 7.323420 TGCGACTATCTGCTTAATAATGCTAT 58.677 34.615 0.00 0.00 0.00 2.97
7379 11034 6.687604 TGCGACTATCTGCTTAATAATGCTA 58.312 36.000 0.00 0.00 0.00 3.49
7400 11055 1.002624 ACACCCACCTAACCATGCG 60.003 57.895 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.