Multiple sequence alignment - TraesCS5B01G549600

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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 TraesCS5B01G549600 chr5B 100.000 2654 0 0 1 2654 701391993 701394646 0.000000e+00 4902.0
1 TraesCS5B01G549600 chr4A 94.341 1449 70 6 502 1945 621428556 621429997 0.000000e+00 2211.0
2 TraesCS5B01G549600 chr4A 88.115 488 51 5 1 484 621428019 621428503 8.240000e-160 573.0
3 TraesCS5B01G549600 chr4A 96.142 337 11 2 1945 2281 621430241 621430575 1.390000e-152 549.0
4 TraesCS5B01G549600 chr4A 96.335 191 7 0 2461 2651 621430775 621430965 5.510000e-82 315.0
5 TraesCS5B01G549600 chr4A 93.985 133 8 0 2333 2465 621430571 621430703 4.480000e-48 202.0
6 TraesCS5B01G549600 chr5D 93.774 1317 69 9 485 1795 549805893 549807202 0.000000e+00 1965.0
7 TraesCS5B01G549600 chr5D 94.825 599 23 6 1868 2465 549807459 549808050 0.000000e+00 928.0
8 TraesCS5B01G549600 chr5D 86.503 489 59 3 1 484 549805359 549805845 5.030000e-147 531.0
9 TraesCS5B01G549600 chr5D 94.241 191 11 0 2461 2651 549808122 549808312 2.580000e-75 292.0
10 TraesCS5B01G549600 chr5A 85.792 183 24 2 2462 2644 659145138 659145318 2.700000e-45 193.0
11 TraesCS5B01G549600 chr7A 89.362 47 5 0 2587 2633 109260837 109260883 2.850000e-05 60.2
12 TraesCS5B01G549600 chr6B 86.538 52 7 0 2588 2639 348848340 348848289 1.030000e-04 58.4
13 TraesCS5B01G549600 chr6B 89.130 46 5 0 2588 2633 547714821 547714866 1.030000e-04 58.4


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 TraesCS5B01G549600 chr5B 701391993 701394646 2653 False 4902 4902 100.00000 1 2654 1 chr5B.!!$F1 2653
1 TraesCS5B01G549600 chr4A 621428019 621430965 2946 False 770 2211 93.78360 1 2651 5 chr4A.!!$F1 2650
2 TraesCS5B01G549600 chr5D 549805359 549808312 2953 False 929 1965 92.33575 1 2651 4 chr5D.!!$F1 2650

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
180 184 0.108662 TCTCGTCATCAACAGCGCAT 60.109 50.0 11.47 0.00 0.00 4.73 F
461 468 0.178975 ATTGACCCCAAAACGGCTCA 60.179 50.0 0.00 0.00 35.67 4.26 F
726 780 0.682209 AGATTGCTGACCATGGGTGC 60.682 55.0 18.09 16.75 35.25 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1082 1140 1.718757 AATGGATTTCTCGCTGGCGC 61.719 55.000 10.28 0.00 39.59 6.53 R
1528 1586 2.081462 AGTGGTAACCGCAGCAAATAC 58.919 47.619 0.00 0.00 36.32 1.89 R
2531 3098 0.822944 TTGTTGCTAGCTTGCTGCCA 60.823 50.000 20.64 11.38 44.23 4.92 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
26 27 1.410517 TGCGACCTGAATCTCCTCATC 59.589 52.381 0.00 0.00 0.00 2.92
27 28 1.410517 GCGACCTGAATCTCCTCATCA 59.589 52.381 0.00 0.00 0.00 3.07
37 38 5.308759 TGAATCTCCTCATCAATGATGGCTA 59.691 40.000 21.58 7.57 40.15 3.93
55 56 2.093764 GCTACAGTCAGCCTCACATTCT 60.094 50.000 0.00 0.00 35.40 2.40
68 69 5.114780 CCTCACATTCTTCTCATTCGTGAT 58.885 41.667 0.00 0.00 32.02 3.06
72 73 4.696877 ACATTCTTCTCATTCGTGATTGCA 59.303 37.500 0.00 0.00 0.00 4.08
93 96 0.669619 TGTCAATGTGTTGCAGCAGG 59.330 50.000 2.40 0.00 35.26 4.85
98 101 0.819259 ATGTGTTGCAGCAGGTCGTT 60.819 50.000 2.40 0.00 0.00 3.85
109 112 0.970937 CAGGTCGTTGGCTCCCTCTA 60.971 60.000 0.00 0.00 0.00 2.43
110 113 0.252103 AGGTCGTTGGCTCCCTCTAA 60.252 55.000 0.00 0.00 0.00 2.10
117 121 0.976073 TGGCTCCCTCTAAACCCTCG 60.976 60.000 0.00 0.00 0.00 4.63
121 125 0.682209 TCCCTCTAAACCCTCGGACG 60.682 60.000 0.00 0.00 0.00 4.79
153 157 6.509418 TTGGTATAAAACTCAGTTGCCATC 57.491 37.500 0.00 0.00 0.00 3.51
165 169 2.969238 GCCATCACCCGCATCTCG 60.969 66.667 0.00 0.00 38.08 4.04
172 176 0.460109 CACCCGCATCTCGTCATCAA 60.460 55.000 0.00 0.00 36.19 2.57
180 184 0.108662 TCTCGTCATCAACAGCGCAT 60.109 50.000 11.47 0.00 0.00 4.73
184 188 1.362768 GTCATCAACAGCGCATCTCA 58.637 50.000 11.47 0.00 0.00 3.27
210 214 5.759273 CCCATTCTCTCTCATTAAAGCTCAG 59.241 44.000 0.00 0.00 0.00 3.35
212 216 7.218614 CCATTCTCTCTCATTAAAGCTCAGAT 58.781 38.462 0.00 0.00 0.00 2.90
223 227 6.560253 TTAAAGCTCAGATGGTGTTCTTTC 57.440 37.500 0.00 0.00 33.76 2.62
229 233 6.772716 AGCTCAGATGGTGTTCTTTCTTTTTA 59.227 34.615 0.00 0.00 0.00 1.52
230 234 7.449704 AGCTCAGATGGTGTTCTTTCTTTTTAT 59.550 33.333 0.00 0.00 0.00 1.40
255 259 5.123979 GTGAGAAGCTCGGTTTTGGAAATAT 59.876 40.000 0.00 0.00 32.35 1.28
264 268 4.673320 CGGTTTTGGAAATATCGGGTGTTC 60.673 45.833 0.00 0.00 0.00 3.18
265 269 4.461431 GGTTTTGGAAATATCGGGTGTTCT 59.539 41.667 0.00 0.00 0.00 3.01
287 291 0.674581 TCGTCTGCCTTGAGCCATTG 60.675 55.000 0.00 0.00 42.71 2.82
294 301 1.680207 GCCTTGAGCCATTGAATCCTC 59.320 52.381 0.00 0.00 34.35 3.71
317 324 1.665679 CCGCTGCCTACACATAACTTG 59.334 52.381 0.00 0.00 0.00 3.16
339 346 1.082117 CGCGCTCATAAACTTCCCGT 61.082 55.000 5.56 0.00 0.00 5.28
348 355 2.295253 AAACTTCCCGTAGATGCTCG 57.705 50.000 0.00 0.00 0.00 5.03
371 378 7.594714 TCGTCTATGTCCTTTATCTATGCTTC 58.405 38.462 0.00 0.00 0.00 3.86
377 384 7.373617 TGTCCTTTATCTATGCTTCATACCA 57.626 36.000 0.00 0.00 0.00 3.25
378 385 7.977818 TGTCCTTTATCTATGCTTCATACCAT 58.022 34.615 0.00 0.00 0.00 3.55
381 388 9.100197 TCCTTTATCTATGCTTCATACCATGTA 57.900 33.333 0.00 0.00 0.00 2.29
407 414 0.179189 GCCCGTTCTTTTGCATCTCG 60.179 55.000 0.00 0.00 0.00 4.04
408 415 0.447801 CCCGTTCTTTTGCATCTCGG 59.552 55.000 0.00 0.00 36.85 4.63
421 428 2.287909 GCATCTCGGAGTTATTCTCGCT 60.288 50.000 4.69 0.00 43.60 4.93
431 438 5.446073 GGAGTTATTCTCGCTGTTTTGCTAC 60.446 44.000 0.00 0.00 43.60 3.58
441 448 2.684881 CTGTTTTGCTACCTGCCTATGG 59.315 50.000 0.00 0.00 42.00 2.74
456 463 2.687935 CCTATGGATTGACCCCAAAACG 59.312 50.000 0.00 0.00 37.22 3.60
461 468 0.178975 ATTGACCCCAAAACGGCTCA 60.179 50.000 0.00 0.00 35.67 4.26
495 549 4.171005 GCATGTCCAGTCATGTTGAAATG 58.829 43.478 6.72 0.00 44.68 2.32
511 565 5.598416 TGAAATGGACGATGTAGATCAGT 57.402 39.130 0.29 0.00 0.00 3.41
533 587 1.136147 GCGTCTTGAGCCATGCTTG 59.864 57.895 0.00 0.00 39.88 4.01
538 592 3.486375 CGTCTTGAGCCATGCTTGTTATG 60.486 47.826 0.00 0.00 39.88 1.90
542 596 2.945008 TGAGCCATGCTTGTTATGCTAC 59.055 45.455 0.00 0.00 39.88 3.58
567 621 2.031245 CACATGGTAGCTTTTTGCACGA 60.031 45.455 0.00 0.00 45.94 4.35
584 638 2.405357 CACGAGCATATGCGCTAGTAAC 59.595 50.000 25.78 9.49 44.70 2.50
598 652 6.252015 TGCGCTAGTAACTATAAAAACACTCG 59.748 38.462 9.73 0.00 0.00 4.18
658 712 6.043327 GTTTGCAAATTTACAAACCAGGAC 57.957 37.500 26.46 9.68 46.29 3.85
665 719 6.723298 AATTTACAAACCAGGACATCACAA 57.277 33.333 0.00 0.00 0.00 3.33
688 742 4.452455 AGCTAGTAAGACATGCACACAAAC 59.548 41.667 0.00 0.00 0.00 2.93
698 752 1.002576 TGCACACAAACTCAATCGCAG 60.003 47.619 0.00 0.00 0.00 5.18
713 767 1.806542 TCGCAGAACCAGAAAGATTGC 59.193 47.619 0.00 0.00 0.00 3.56
716 770 2.816087 GCAGAACCAGAAAGATTGCTGA 59.184 45.455 1.87 0.00 34.06 4.26
720 774 3.446442 ACCAGAAAGATTGCTGACCAT 57.554 42.857 1.87 0.00 34.06 3.55
721 775 3.087031 ACCAGAAAGATTGCTGACCATG 58.913 45.455 1.87 0.00 34.06 3.66
722 776 2.426024 CCAGAAAGATTGCTGACCATGG 59.574 50.000 11.19 11.19 34.06 3.66
723 777 2.426024 CAGAAAGATTGCTGACCATGGG 59.574 50.000 18.09 0.00 34.06 4.00
726 780 0.682209 AGATTGCTGACCATGGGTGC 60.682 55.000 18.09 16.75 35.25 5.01
727 781 0.966875 GATTGCTGACCATGGGTGCA 60.967 55.000 18.09 19.13 35.25 4.57
731 789 1.742880 CTGACCATGGGTGCACTCG 60.743 63.158 18.09 2.22 35.25 4.18
736 794 1.577328 CCATGGGTGCACTCGTGAAC 61.577 60.000 35.45 9.41 38.43 3.18
803 861 1.956170 GCGGTGGCTCATACATCCG 60.956 63.158 0.00 0.00 40.72 4.18
804 862 1.441729 CGGTGGCTCATACATCCGT 59.558 57.895 0.00 0.00 34.38 4.69
809 867 3.059884 GTGGCTCATACATCCGTACATG 58.940 50.000 0.00 0.00 0.00 3.21
810 868 2.069273 GGCTCATACATCCGTACATGC 58.931 52.381 0.00 0.00 0.00 4.06
838 896 0.879839 AACCAATTTTGCAGCACCGC 60.880 50.000 0.00 0.00 0.00 5.68
870 928 3.386237 GCTCTCCTGGCCTCACGT 61.386 66.667 3.32 0.00 0.00 4.49
885 943 1.538512 TCACGTCCTCTTTAGACACCG 59.461 52.381 0.00 0.00 33.70 4.94
902 960 3.259876 ACACCGTCTCCTATTTTAGTGCA 59.740 43.478 0.00 0.00 0.00 4.57
906 964 4.260784 CCGTCTCCTATTTTAGTGCAATGC 60.261 45.833 0.00 0.00 0.00 3.56
918 976 2.034124 GTGCAATGCCCACCTTCATAT 58.966 47.619 1.53 0.00 0.00 1.78
981 1039 4.226427 TCTTGAATCATCCCTCAACCAG 57.774 45.455 0.00 0.00 0.00 4.00
991 1049 3.589641 TCCCTCAACCAGTTGTTAGGTA 58.410 45.455 14.03 0.23 41.16 3.08
1004 1062 7.446013 CCAGTTGTTAGGTAAACTTACAATGGA 59.554 37.037 14.90 0.00 46.57 3.41
1040 1098 1.687660 TGCATGCACATTGTTCCTTGT 59.312 42.857 18.46 0.00 0.00 3.16
1106 1164 2.357009 CCAGCGAGAAATCCATTGAAGG 59.643 50.000 0.00 0.00 0.00 3.46
1185 1243 4.041567 TCCAAAAGGTCTGCAGTAGAATCA 59.958 41.667 14.67 0.00 37.12 2.57
1209 1267 1.131420 GCTCAAGCAGAAAGTCGCG 59.869 57.895 0.00 0.00 41.59 5.87
1247 1305 0.972883 GAGGCCGCTGGAGATAAGAT 59.027 55.000 0.00 0.00 0.00 2.40
1269 1327 7.373493 AGATGAAAGTTGATGAAATTGTCACC 58.627 34.615 0.00 0.00 39.72 4.02
1319 1377 3.186047 CGCTAAACCCGCCGACAG 61.186 66.667 0.00 0.00 0.00 3.51
1393 1451 2.126071 CCGTCGACGCATTGGAGT 60.126 61.111 31.73 0.00 38.18 3.85
1499 1557 3.334751 CGTCGTCGCTGCCAACAA 61.335 61.111 0.00 0.00 0.00 2.83
1528 1586 2.551459 CAGTCTGCAAAGGACAAGAAGG 59.449 50.000 7.27 0.00 36.29 3.46
1548 1606 2.081462 GTATTTGCTGCGGTTACCACT 58.919 47.619 1.13 0.00 0.00 4.00
1572 1630 0.111061 ACAAGGTGGCTTCTGATGCA 59.889 50.000 16.12 0.00 0.00 3.96
1665 1723 2.265739 GCATGAGTGGCACCTCGA 59.734 61.111 15.27 0.00 34.04 4.04
1945 2435 9.202273 GATTTCTGATGGCATAAAGACTACTAG 57.798 37.037 10.93 0.00 0.00 2.57
1946 2436 7.661536 TTCTGATGGCATAAAGACTACTAGT 57.338 36.000 10.93 0.00 0.00 2.57
1947 2437 8.762481 TTCTGATGGCATAAAGACTACTAGTA 57.238 34.615 10.93 1.89 0.00 1.82
1948 2438 8.167605 TCTGATGGCATAAAGACTACTAGTAC 57.832 38.462 0.00 0.00 0.00 2.73
1949 2439 7.999545 TCTGATGGCATAAAGACTACTAGTACT 59.000 37.037 0.00 0.00 0.00 2.73
2030 2520 1.303091 TGTCGTCGCTGATCTTCCGA 61.303 55.000 0.00 0.00 0.00 4.55
2162 2653 7.548075 AGGTGGTTACTATCGTACAATTTCAAG 59.452 37.037 0.00 0.00 0.00 3.02
2261 2752 7.908082 CGCACTATTAGCATATCTACTTCTCTC 59.092 40.741 0.00 0.00 0.00 3.20
2344 2835 1.887198 GTCGACAACTCTCCCTCTCAA 59.113 52.381 11.55 0.00 0.00 3.02
2353 2844 1.138568 CTCCCTCTCAAGGCATCCAT 58.861 55.000 0.00 0.00 41.85 3.41
2390 2881 1.474330 CCTTTAAAGCCGCCTCCAAT 58.526 50.000 9.86 0.00 0.00 3.16
2550 3117 0.822944 TGGCAGCAAGCTAGCAACAA 60.823 50.000 18.83 0.00 44.79 2.83
2621 3188 4.118584 GCTGGGTTGCCTCCAAAT 57.881 55.556 0.00 0.00 33.36 2.32
2651 3218 2.833943 TGCTCTCAGATAGCCACAAAGA 59.166 45.455 5.38 0.00 39.30 2.52
2652 3219 3.453717 TGCTCTCAGATAGCCACAAAGAT 59.546 43.478 5.38 0.00 39.30 2.40
2653 3220 4.080695 TGCTCTCAGATAGCCACAAAGATT 60.081 41.667 5.38 0.00 39.30 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.653868 AGCCATCATTGATGAGGAGATTC 58.346 43.478 24.93 6.25 42.09 2.52
37 38 2.636893 AGAAGAATGTGAGGCTGACTGT 59.363 45.455 5.53 0.00 0.00 3.55
55 56 4.455190 TGACAATGCAATCACGAATGAGAA 59.545 37.500 0.00 0.00 38.57 2.87
68 69 3.124560 CTGCAACACATTGACAATGCAA 58.875 40.909 24.85 6.50 42.53 4.08
72 73 2.288579 CCTGCTGCAACACATTGACAAT 60.289 45.455 3.02 0.00 38.15 2.71
93 96 1.675116 GGTTTAGAGGGAGCCAACGAC 60.675 57.143 0.00 0.00 0.00 4.34
98 101 0.976073 CGAGGGTTTAGAGGGAGCCA 60.976 60.000 0.00 0.00 35.91 4.75
109 112 1.589803 CTTTTCACGTCCGAGGGTTT 58.410 50.000 0.00 0.00 0.00 3.27
110 113 0.883370 GCTTTTCACGTCCGAGGGTT 60.883 55.000 0.00 0.00 0.00 4.11
117 121 5.616488 TTTATACCAAGCTTTTCACGTCC 57.384 39.130 0.00 0.00 0.00 4.79
121 125 7.649057 ACTGAGTTTTATACCAAGCTTTTCAC 58.351 34.615 0.00 0.00 0.00 3.18
153 157 0.460109 TTGATGACGAGATGCGGGTG 60.460 55.000 0.00 0.00 46.49 4.61
165 169 1.362768 TGAGATGCGCTGTTGATGAC 58.637 50.000 9.73 0.00 0.00 3.06
172 176 0.182061 AATGGGATGAGATGCGCTGT 59.818 50.000 9.73 0.00 0.00 4.40
180 184 7.681259 TTTAATGAGAGAGAATGGGATGAGA 57.319 36.000 0.00 0.00 0.00 3.27
184 188 6.100859 TGAGCTTTAATGAGAGAGAATGGGAT 59.899 38.462 0.00 0.00 0.00 3.85
210 214 8.567948 TCTCACATAAAAAGAAAGAACACCATC 58.432 33.333 0.00 0.00 0.00 3.51
212 216 7.873719 TCTCACATAAAAAGAAAGAACACCA 57.126 32.000 0.00 0.00 0.00 4.17
223 227 5.613358 AACCGAGCTTCTCACATAAAAAG 57.387 39.130 0.00 0.00 0.00 2.27
229 233 2.154462 CCAAAACCGAGCTTCTCACAT 58.846 47.619 0.00 0.00 0.00 3.21
230 234 1.140052 TCCAAAACCGAGCTTCTCACA 59.860 47.619 0.00 0.00 0.00 3.58
255 259 0.526211 CAGACGATCAGAACACCCGA 59.474 55.000 0.00 0.00 0.00 5.14
264 268 0.809241 GGCTCAAGGCAGACGATCAG 60.809 60.000 0.00 0.00 44.01 2.90
265 269 1.219124 GGCTCAAGGCAGACGATCA 59.781 57.895 0.00 0.00 44.01 2.92
287 291 1.735376 TAGGCAGCGGTCGAGGATTC 61.735 60.000 0.00 0.00 0.00 2.52
294 301 0.179121 TTATGTGTAGGCAGCGGTCG 60.179 55.000 0.00 0.00 0.00 4.79
317 324 1.062148 GGGAAGTTTATGAGCGCGAAC 59.938 52.381 12.10 3.72 0.00 3.95
339 346 6.943146 AGATAAAGGACATAGACGAGCATCTA 59.057 38.462 0.00 0.00 35.67 1.98
371 378 0.588252 GGCGCTTGCTACATGGTATG 59.412 55.000 7.64 0.00 39.13 2.39
377 384 2.046314 AACGGGCGCTTGCTACAT 60.046 55.556 7.64 0.00 39.13 2.29
378 385 2.725203 AAGAACGGGCGCTTGCTACA 62.725 55.000 7.64 0.00 39.13 2.74
381 388 2.193536 AAAAGAACGGGCGCTTGCT 61.194 52.632 7.64 0.00 39.13 3.91
407 414 3.437049 AGCAAAACAGCGAGAATAACTCC 59.563 43.478 0.00 0.00 42.18 3.85
408 415 4.670227 AGCAAAACAGCGAGAATAACTC 57.330 40.909 0.00 0.00 41.79 3.01
431 438 0.111253 GGGGTCAATCCATAGGCAGG 59.889 60.000 0.00 0.00 38.11 4.85
441 448 2.653557 AGCCGTTTTGGGGTCAATC 58.346 52.632 0.00 0.00 38.63 2.67
456 463 1.153469 GCAGTAGTGGAGCTGAGCC 60.153 63.158 0.00 0.00 34.87 4.70
461 468 0.539051 GGACATGCAGTAGTGGAGCT 59.461 55.000 0.00 0.00 0.00 4.09
495 549 3.120477 CGCTCTACTGATCTACATCGTCC 60.120 52.174 0.00 0.00 0.00 4.79
511 565 0.179100 GCATGGCTCAAGACGCTCTA 60.179 55.000 0.00 0.00 0.00 2.43
533 587 5.637104 CTACCATGTGTTCGTAGCATAAC 57.363 43.478 0.00 0.00 0.00 1.89
542 596 2.979813 GCAAAAAGCTACCATGTGTTCG 59.020 45.455 0.00 0.00 41.15 3.95
575 629 7.165483 CCTCGAGTGTTTTTATAGTTACTAGCG 59.835 40.741 12.31 0.00 0.00 4.26
598 652 1.401670 CGGTTCCATCGATCGATCCTC 60.402 57.143 27.20 16.55 31.62 3.71
609 663 2.289195 TGTAGTGTTGGTCGGTTCCATC 60.289 50.000 0.00 0.00 37.33 3.51
647 701 1.956477 GCTTGTGATGTCCTGGTTTGT 59.044 47.619 0.00 0.00 0.00 2.83
655 709 5.073311 TGTCTTACTAGCTTGTGATGTCC 57.927 43.478 11.27 0.00 0.00 4.02
658 712 4.872124 TGCATGTCTTACTAGCTTGTGATG 59.128 41.667 11.27 6.44 0.00 3.07
665 719 3.961480 TGTGTGCATGTCTTACTAGCT 57.039 42.857 0.00 0.00 0.00 3.32
688 742 3.329386 TCTTTCTGGTTCTGCGATTGAG 58.671 45.455 0.00 0.00 0.00 3.02
698 752 3.149196 TGGTCAGCAATCTTTCTGGTTC 58.851 45.455 0.00 0.00 0.00 3.62
713 767 1.742880 CGAGTGCACCCATGGTCAG 60.743 63.158 14.63 0.66 31.02 3.51
716 770 2.032528 CACGAGTGCACCCATGGT 59.967 61.111 14.63 0.00 35.62 3.55
720 774 2.279851 CGTTCACGAGTGCACCCA 60.280 61.111 14.63 0.00 43.02 4.51
721 775 2.028484 TCGTTCACGAGTGCACCC 59.972 61.111 14.63 0.00 44.22 4.61
731 789 1.068541 GGCCACCAATCTTTCGTTCAC 60.069 52.381 0.00 0.00 0.00 3.18
809 867 1.460359 CAAAATTGGTTGCATGACCGC 59.540 47.619 0.00 0.00 42.83 5.68
838 896 4.379243 AGCTTCGCGGGTGTCCTG 62.379 66.667 6.13 0.00 0.00 3.86
870 928 2.041350 AGGAGACGGTGTCTAAAGAGGA 59.959 50.000 5.21 0.00 43.53 3.71
885 943 4.036852 GGGCATTGCACTAAAATAGGAGAC 59.963 45.833 11.39 0.00 0.00 3.36
902 960 6.062095 GTGTAAGTATATGAAGGTGGGCATT 58.938 40.000 0.00 0.00 0.00 3.56
906 964 4.628074 CCGTGTAAGTATATGAAGGTGGG 58.372 47.826 0.00 0.00 0.00 4.61
918 976 1.727880 GATGTTTGCGCCGTGTAAGTA 59.272 47.619 4.18 0.00 0.00 2.24
981 1039 8.156994 TGTCCATTGTAAGTTTACCTAACAAC 57.843 34.615 0.00 0.00 39.30 3.32
991 1049 6.068010 TCTTGACCATGTCCATTGTAAGTTT 58.932 36.000 0.00 0.00 0.00 2.66
1004 1062 4.182693 CATGCAATGTTCTTGACCATGT 57.817 40.909 0.00 0.00 40.20 3.21
1082 1140 1.718757 AATGGATTTCTCGCTGGCGC 61.719 55.000 10.28 0.00 39.59 6.53
1247 1305 5.518812 CGGTGACAATTTCATCAACTTTCA 58.481 37.500 0.00 0.00 34.61 2.69
1319 1377 6.131544 AGGTTTTGTCAAATACGGCATATC 57.868 37.500 0.00 0.00 0.00 1.63
1393 1451 3.373001 CCAATGGCCTCCTTGAAGGAATA 60.373 47.826 15.79 2.37 45.28 1.75
1499 1557 2.517414 TTGCAGACTGGGCAAGCT 59.483 55.556 4.26 0.00 45.57 3.74
1528 1586 2.081462 AGTGGTAACCGCAGCAAATAC 58.919 47.619 0.00 0.00 36.32 1.89
1665 1723 2.417516 CATCGAAGGCCGGACGAT 59.582 61.111 21.98 21.98 45.44 3.73
2030 2520 6.291377 AGATAGTGTCAAACTGTCAATGTGT 58.709 36.000 0.00 0.00 46.58 3.72
2104 2595 5.500645 AGTGTTTAAAGCTGGTTCTTGAC 57.499 39.130 0.00 0.00 0.00 3.18
2162 2653 5.037015 TGTTGTAATTCCATTGTACGTGC 57.963 39.130 0.00 0.00 0.00 5.34
2261 2752 6.910536 ATCTGCGAGAATTTAAACTACAGG 57.089 37.500 0.00 0.00 0.00 4.00
2344 2835 4.411540 AGATTTCTCACACTATGGATGCCT 59.588 41.667 0.00 0.00 0.00 4.75
2353 2844 5.489792 AAAGGCAGAGATTTCTCACACTA 57.510 39.130 10.07 0.00 45.21 2.74
2503 3070 4.059773 TGGAGCCCACCTTATGAATTTT 57.940 40.909 0.00 0.00 0.00 1.82
2531 3098 0.822944 TTGTTGCTAGCTTGCTGCCA 60.823 50.000 20.64 11.38 44.23 4.92
2557 3124 9.586435 GCTGCCTCTAAATTTTATGTAAAATGT 57.414 29.630 10.54 8.33 43.06 2.71


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

AutoCloner maintained by Alex Coulton.