Multiple sequence alignment - TraesCS6A01G393100

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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 TraesCS6A01G393100 chr6A 100.000 3803 0 0 1 3803 607053914 607057716 0.000000e+00 7023.0
1 TraesCS6A01G393100 chr6B 93.778 3809 196 22 16 3803 702242539 702246327 0.000000e+00 5683.0
2 TraesCS6A01G393100 chr6B 87.912 182 20 2 2888 3067 702247924 702248105 2.980000e-51 213.0
3 TraesCS6A01G393100 chr6B 96.875 32 1 0 2917 2948 702270807 702270838 2.000000e-03 54.7
4 TraesCS6A01G393100 chr6D 89.557 3524 249 63 16 3489 460787717 460791171 0.000000e+00 4359.0
5 TraesCS6A01G393100 chr6D 90.816 294 18 8 3517 3803 460791160 460791451 5.960000e-103 385.0
6 TraesCS6A01G393100 chr6D 84.593 344 45 7 3184 3520 460792915 460793257 6.090000e-88 335.0
7 TraesCS6A01G393100 chr3B 94.247 591 32 2 2545 3135 739118322 739117734 0.000000e+00 902.0
8 TraesCS6A01G393100 chr3B 93.570 591 36 2 2545 3135 13127140 13127728 0.000000e+00 880.0
9 TraesCS6A01G393100 chr3B 95.604 91 3 1 3268 3358 739117733 739117644 1.100000e-30 145.0


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 TraesCS6A01G393100 chr6A 607053914 607057716 3802 False 7023.0 7023 100.0000 1 3803 1 chr6A.!!$F1 3802
1 TraesCS6A01G393100 chr6B 702242539 702248105 5566 False 2948.0 5683 90.8450 16 3803 2 chr6B.!!$F2 3787
2 TraesCS6A01G393100 chr6D 460787717 460793257 5540 False 1693.0 4359 88.3220 16 3803 3 chr6D.!!$F1 3787
3 TraesCS6A01G393100 chr3B 13127140 13127728 588 False 880.0 880 93.5700 2545 3135 1 chr3B.!!$F1 590
4 TraesCS6A01G393100 chr3B 739117644 739118322 678 True 523.5 902 94.9255 2545 3358 2 chr3B.!!$R1 813

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
917 952 0.037590 TATCTGGGTTGGCGTTTGCT 59.962 50.0 0.0 0.0 42.25 3.91 F
1365 1403 0.247736 CAAACTCCCACTCCCTCTCG 59.752 60.0 0.0 0.0 0.00 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1940 0.181587 TCTCGAGCTCCCTAGACCTG 59.818 60.0 7.81 0.00 0.00 4.00 R
3257 3295 0.801251 GGTCAGCTGTCAATCTGCAC 59.199 55.0 14.67 0.36 42.26 4.57 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
35 36 6.539649 TTCTTTGATAACAAACCTGAGTCG 57.460 37.500 0.00 0.00 40.47 4.18
122 123 2.557317 ACCTGGTCAGTTGTAACAACG 58.443 47.619 0.00 0.00 0.00 4.10
131 132 3.743567 GTTGTAACAACGTCACAACCA 57.256 42.857 17.68 0.00 43.92 3.67
156 157 4.261489 GCAATGCCATACCTGAATGAGAAG 60.261 45.833 0.00 0.00 0.00 2.85
159 160 3.117776 TGCCATACCTGAATGAGAAGCAT 60.118 43.478 0.00 0.00 39.43 3.79
161 162 5.221986 TGCCATACCTGAATGAGAAGCATAT 60.222 40.000 0.00 0.00 35.78 1.78
232 233 3.118261 GGACAATGAGATCCAGCTTACCA 60.118 47.826 0.00 0.00 34.87 3.25
244 245 2.208527 CTTACCAAGCCCGGCTAGA 58.791 57.895 13.73 0.00 38.25 2.43
344 345 7.766278 TCTTTTCCTGCAGATATAAAGTCAGAC 59.234 37.037 17.39 0.00 0.00 3.51
345 346 6.798427 TTCCTGCAGATATAAAGTCAGACT 57.202 37.500 17.39 0.00 0.00 3.24
346 347 6.154203 TCCTGCAGATATAAAGTCAGACTG 57.846 41.667 17.39 0.00 0.00 3.51
347 348 4.749099 CCTGCAGATATAAAGTCAGACTGC 59.251 45.833 17.39 0.00 45.92 4.40
348 349 5.453057 CCTGCAGATATAAAGTCAGACTGCT 60.453 44.000 17.39 0.00 45.91 4.24
375 377 8.237267 ACATTAGCACTAACAAATCAAGCTTAC 58.763 33.333 0.00 0.00 32.49 2.34
380 385 8.143835 AGCACTAACAAATCAAGCTTACAAAAT 58.856 29.630 0.00 0.00 0.00 1.82
412 417 4.602340 AAAAGAGAGCTCGGAACTAACA 57.398 40.909 8.37 0.00 34.09 2.41
419 425 0.247736 CTCGGAACTAACAGCAGGCT 59.752 55.000 0.00 0.00 0.00 4.58
434 440 4.646492 CAGCAGGCTATTACCAGGAATTTT 59.354 41.667 0.00 0.00 0.00 1.82
482 488 2.357034 GTGCCGAGGTGCTTCGAA 60.357 61.111 5.28 0.00 43.03 3.71
521 542 5.239306 ACAGCGAAAAATTCAGACTTCATGA 59.761 36.000 0.00 0.00 0.00 3.07
533 554 1.072806 ACTTCATGAGAGTGGCAGCAA 59.927 47.619 9.00 0.00 0.00 3.91
657 678 0.913924 TTCAGCCTGCCATCAGATGA 59.086 50.000 12.41 0.00 42.95 2.92
664 685 1.136891 CTGCCATCAGATGACACCGTA 59.863 52.381 12.41 0.00 42.95 4.02
666 687 1.134818 GCCATCAGATGACACCGTACA 60.135 52.381 12.41 0.00 0.00 2.90
684 705 4.261447 CGTACATGAGACCGGAATACATGA 60.261 45.833 27.30 15.95 40.13 3.07
699 720 3.837213 ACATGAAAAATCAGTGGAGCG 57.163 42.857 0.00 0.00 0.00 5.03
720 741 4.338400 GCGGCCCAAAATCTCTACTAAAAT 59.662 41.667 0.00 0.00 0.00 1.82
723 744 7.255486 GCGGCCCAAAATCTCTACTAAAATTAT 60.255 37.037 0.00 0.00 0.00 1.28
758 779 4.803908 GGAGGAAGGGCGGGCAAG 62.804 72.222 3.27 0.00 0.00 4.01
791 812 1.367840 GAGTGTTCAGGGTGTCGCT 59.632 57.895 0.00 0.00 0.00 4.93
797 818 0.394938 TTCAGGGTGTCGCTTGCTTA 59.605 50.000 0.00 0.00 0.00 3.09
825 846 1.285280 AGTCCATGGAATCCGGTGAA 58.715 50.000 18.20 0.00 0.00 3.18
828 849 1.633432 TCCATGGAATCCGGTGAACTT 59.367 47.619 13.46 0.00 0.00 2.66
829 850 2.041081 TCCATGGAATCCGGTGAACTTT 59.959 45.455 13.46 0.00 0.00 2.66
830 851 2.423538 CCATGGAATCCGGTGAACTTTC 59.576 50.000 5.56 0.00 0.00 2.62
831 852 2.194201 TGGAATCCGGTGAACTTTCC 57.806 50.000 0.00 6.71 37.06 3.13
833 854 1.084289 GAATCCGGTGAACTTTCCCG 58.916 55.000 0.00 10.31 39.29 5.14
875 907 1.850755 GTGAGGGTTTGGGGGAGGA 60.851 63.158 0.00 0.00 0.00 3.71
907 942 0.824759 GAGTGGCGTCTATCTGGGTT 59.175 55.000 0.00 0.00 0.00 4.11
908 943 0.537188 AGTGGCGTCTATCTGGGTTG 59.463 55.000 0.00 0.00 0.00 3.77
909 944 0.462047 GTGGCGTCTATCTGGGTTGG 60.462 60.000 0.00 0.00 0.00 3.77
910 945 1.523938 GGCGTCTATCTGGGTTGGC 60.524 63.158 0.00 0.00 0.00 4.52
912 947 1.515954 CGTCTATCTGGGTTGGCGT 59.484 57.895 0.00 0.00 0.00 5.68
913 948 0.108329 CGTCTATCTGGGTTGGCGTT 60.108 55.000 0.00 0.00 0.00 4.84
916 951 0.451783 CTATCTGGGTTGGCGTTTGC 59.548 55.000 0.00 0.00 41.71 3.68
917 952 0.037590 TATCTGGGTTGGCGTTTGCT 59.962 50.000 0.00 0.00 42.25 3.91
1197 1232 2.837291 CAGCTCCTCCTCCTCGGG 60.837 72.222 0.00 0.00 0.00 5.14
1303 1338 3.255379 GAATCCTGCGCGACCGTC 61.255 66.667 12.10 0.00 36.67 4.79
1304 1339 4.814294 AATCCTGCGCGACCGTCC 62.814 66.667 12.10 0.00 36.67 4.79
1311 1346 3.110178 CGCGACCGTCCCAAACTC 61.110 66.667 0.00 0.00 0.00 3.01
1313 1348 2.431942 CGACCGTCCCAAACTCCG 60.432 66.667 0.00 0.00 0.00 4.63
1314 1349 2.739132 GACCGTCCCAAACTCCGT 59.261 61.111 0.00 0.00 0.00 4.69
1315 1350 1.373873 GACCGTCCCAAACTCCGTC 60.374 63.158 0.00 0.00 0.00 4.79
1316 1351 2.431942 CCGTCCCAAACTCCGTCG 60.432 66.667 0.00 0.00 0.00 5.12
1322 1360 2.657237 CAAACTCCGTCGCTCCCT 59.343 61.111 0.00 0.00 0.00 4.20
1330 1368 4.500116 GTCGCTCCCTGGAGACGC 62.500 72.222 17.38 11.32 44.53 5.19
1333 1371 4.154347 GCTCCCTGGAGACGCAGG 62.154 72.222 17.38 0.00 44.53 4.85
1365 1403 0.247736 CAAACTCCCACTCCCTCTCG 59.752 60.000 0.00 0.00 0.00 4.04
1488 1526 2.503356 CAACTCCCTGCTCCACTTCTAT 59.497 50.000 0.00 0.00 0.00 1.98
1515 1553 0.543410 TCGGTTTACCCTCTCTGGCA 60.543 55.000 0.00 0.00 0.00 4.92
1539 1577 0.810648 GGCTGTTCGATGAAATGCCA 59.189 50.000 14.91 0.00 39.87 4.92
1557 1595 1.379443 AGCGAGGGACACCGTATCA 60.379 57.895 0.00 0.00 43.47 2.15
1575 1613 3.961480 TCATTCAACACTCTGATCGGT 57.039 42.857 0.42 0.00 0.00 4.69
1583 1621 3.722147 ACACTCTGATCGGTTCATATGC 58.278 45.455 0.42 0.00 32.72 3.14
1587 1625 3.381045 TCTGATCGGTTCATATGCGAAC 58.619 45.455 7.79 6.34 43.75 3.95
1588 1626 3.068165 TCTGATCGGTTCATATGCGAACT 59.932 43.478 7.79 0.00 43.92 3.01
1590 1628 1.835121 TCGGTTCATATGCGAACTCG 58.165 50.000 0.00 5.15 43.92 4.18
1635 1673 5.368989 GGAGTATTCAAGGTTATGGTGGAG 58.631 45.833 0.00 0.00 0.00 3.86
1636 1674 5.368989 GAGTATTCAAGGTTATGGTGGAGG 58.631 45.833 0.00 0.00 0.00 4.30
1639 1677 2.638325 TCAAGGTTATGGTGGAGGGAA 58.362 47.619 0.00 0.00 0.00 3.97
1677 1715 1.666553 GACCATCACGGCGTTGTCA 60.667 57.895 11.19 0.00 39.03 3.58
1692 1730 4.720902 TCAGGCGCATGTGTGGGG 62.721 66.667 22.69 0.00 38.61 4.96
1719 1757 0.318120 ATTTGAGGGTGGCAAAAGCG 59.682 50.000 0.00 0.00 38.57 4.68
1802 1840 1.675714 CGTGCTGGTGGACATGTATGT 60.676 52.381 0.00 0.00 45.16 2.29
1820 1858 3.971702 GAAGTGCAGGGGGCTGGT 61.972 66.667 0.00 0.00 45.15 4.00
1902 1940 0.546122 TGATGGTGTCAGGGTATGCC 59.454 55.000 0.00 0.00 31.80 4.40
1938 1976 3.318275 TCGAGATGGCTAGAGCGTTATTT 59.682 43.478 0.00 0.00 43.26 1.40
1986 2024 0.947244 CATGGACGGCTCTTATTGGC 59.053 55.000 0.00 0.00 0.00 4.52
1992 2030 2.882170 GGCTCTTATTGGCGGGTTT 58.118 52.632 0.00 0.00 0.00 3.27
2121 2159 2.483877 TCAGTACCGTACGTTCGATGTT 59.516 45.455 16.59 0.17 0.00 2.71
2208 2246 3.278574 TGCCTTAGTTGACATGTATGCC 58.721 45.455 0.00 0.00 0.00 4.40
2232 2270 2.292267 CATGGGTTCATACAGACAGCC 58.708 52.381 0.00 0.00 31.33 4.85
2246 2284 2.559668 AGACAGCCATGGATGTGTTTTG 59.440 45.455 38.71 10.18 45.31 2.44
2261 2299 3.068024 GTGTTTTGTGGTGTGGATGACAT 59.932 43.478 0.00 0.00 36.78 3.06
2397 2435 3.325870 TAAGATCACTTTCACGGCAGTG 58.674 45.455 11.07 11.07 41.91 3.66
2454 2492 8.749354 ACACAAGGGTTTGAGATATTTAATTCC 58.251 33.333 0.00 0.00 37.73 3.01
2486 2524 6.258068 GGCAAGTATGGTGTAGAACAAGATAC 59.742 42.308 0.00 0.00 30.40 2.24
2621 2659 5.770919 TCTTAGGAGAGAATGTGAGATCCA 58.229 41.667 0.00 0.00 0.00 3.41
2628 2666 5.435291 AGAGAATGTGAGATCCATGGAAAC 58.565 41.667 20.67 15.80 0.00 2.78
2661 2699 4.505039 GGAAAACTTGCAGAGGAGGAACTA 60.505 45.833 0.00 0.00 41.55 2.24
2693 2731 3.895232 TCCTAGCTACAAGCCTGAAAG 57.105 47.619 0.00 0.00 43.77 2.62
2746 2784 4.829492 CAGATGGAAGGAAACAGAAAAGGT 59.171 41.667 0.00 0.00 0.00 3.50
2811 2849 2.921754 GCGTACAAAGTAGCAGTGTAGG 59.078 50.000 0.00 0.00 36.93 3.18
2847 2885 1.059584 TGAGTGGGGGAAAGACTGCA 61.060 55.000 0.00 0.00 0.00 4.41
3068 3106 0.182299 TGCATGGACAACTGGTGACA 59.818 50.000 0.00 0.00 39.59 3.58
3257 3295 8.647143 ATCAAAACCAACAACTCACAATTTAG 57.353 30.769 0.00 0.00 0.00 1.85
3325 3363 3.960102 ACTCCATGGTCAATGTGTTGTTT 59.040 39.130 12.58 0.00 36.69 2.83
3408 3448 9.216117 GGCAAACTACTGACTTTTCTTAATCTA 57.784 33.333 0.00 0.00 0.00 1.98
3629 3681 2.223711 GGTGATGACCAACCACAACAAC 60.224 50.000 0.00 0.00 42.59 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.230849 TGTTATCAAAGAAAGCACCATTCAT 57.769 32.000 0.00 0.00 0.00 2.57
1 2 6.647334 TGTTATCAAAGAAAGCACCATTCA 57.353 33.333 0.00 0.00 0.00 2.57
2 3 7.095649 GGTTTGTTATCAAAGAAAGCACCATTC 60.096 37.037 0.00 0.00 42.66 2.67
3 4 6.705825 GGTTTGTTATCAAAGAAAGCACCATT 59.294 34.615 0.00 0.00 42.66 3.16
4 5 6.041979 AGGTTTGTTATCAAAGAAAGCACCAT 59.958 34.615 11.03 0.00 44.45 3.55
5 6 5.362430 AGGTTTGTTATCAAAGAAAGCACCA 59.638 36.000 11.03 0.00 44.45 4.17
6 7 5.691754 CAGGTTTGTTATCAAAGAAAGCACC 59.308 40.000 11.03 0.00 44.45 5.01
7 8 6.503524 TCAGGTTTGTTATCAAAGAAAGCAC 58.496 36.000 11.03 0.00 44.45 4.40
8 9 6.321181 ACTCAGGTTTGTTATCAAAGAAAGCA 59.679 34.615 11.03 0.00 44.45 3.91
9 10 6.739112 ACTCAGGTTTGTTATCAAAGAAAGC 58.261 36.000 0.00 2.76 43.15 3.51
10 11 7.072030 CGACTCAGGTTTGTTATCAAAGAAAG 58.928 38.462 0.00 0.00 43.04 2.62
11 12 6.017440 CCGACTCAGGTTTGTTATCAAAGAAA 60.017 38.462 0.00 0.00 43.04 2.52
12 13 5.468746 CCGACTCAGGTTTGTTATCAAAGAA 59.531 40.000 0.00 0.00 43.04 2.52
13 14 4.994852 CCGACTCAGGTTTGTTATCAAAGA 59.005 41.667 0.00 0.00 43.04 2.52
14 15 4.154195 CCCGACTCAGGTTTGTTATCAAAG 59.846 45.833 0.00 0.00 43.04 2.77
35 36 1.230324 GGATTGCGCAGTCTAATCCC 58.770 55.000 28.72 11.18 42.47 3.85
122 123 0.388659 TGGCATTGCTTGGTTGTGAC 59.611 50.000 8.82 0.00 0.00 3.67
131 132 3.634504 TCATTCAGGTATGGCATTGCTT 58.365 40.909 4.78 0.00 0.00 3.91
161 162 8.053355 GGAGGTTTTCTCTCAAGGGAAATAATA 58.947 37.037 5.92 0.00 42.10 0.98
180 181 8.814931 CAGAGATATCTATGATCTTGGAGGTTT 58.185 37.037 20.45 0.00 37.37 3.27
232 233 2.221299 TTGTGGTCTAGCCGGGCTT 61.221 57.895 29.02 11.52 40.44 4.35
244 245 1.348036 GAGTTAGGAGCTGGTTGTGGT 59.652 52.381 0.00 0.00 0.00 4.16
347 348 7.978982 AGCTTGATTTGTTAGTGCTAATGTAG 58.021 34.615 0.00 0.00 0.00 2.74
348 349 7.921786 AGCTTGATTTGTTAGTGCTAATGTA 57.078 32.000 0.00 0.00 0.00 2.29
361 362 6.514947 TCTGCATTTTGTAAGCTTGATTTGT 58.485 32.000 9.86 0.00 0.00 2.83
375 377 6.361748 GCTCTCTTTTACAGTTCTGCATTTTG 59.638 38.462 0.00 0.00 0.00 2.44
380 385 4.310769 GAGCTCTCTTTTACAGTTCTGCA 58.689 43.478 6.43 0.00 0.00 4.41
412 417 4.526438 AAATTCCTGGTAATAGCCTGCT 57.474 40.909 0.00 0.00 0.00 4.24
419 425 5.106078 GGTGTTCGCAAAATTCCTGGTAATA 60.106 40.000 0.00 0.00 0.00 0.98
434 440 3.109547 GCGTCGATGGTGTTCGCA 61.110 61.111 6.79 0.00 45.01 5.10
482 488 1.687612 CTGTCTGCAGGACCCCAAT 59.312 57.895 15.13 0.00 43.89 3.16
521 542 2.502295 CTTCTTCTTTGCTGCCACTCT 58.498 47.619 0.00 0.00 0.00 3.24
559 580 1.805945 GGTCGTCATGCTCCGTGAC 60.806 63.158 7.36 7.36 44.25 3.67
592 613 3.134127 GAACTGATGGGCCACCGC 61.134 66.667 9.28 1.39 40.75 5.68
657 678 0.609957 TCCGGTCTCATGTACGGTGT 60.610 55.000 0.00 0.00 46.06 4.16
664 685 4.753516 TTCATGTATTCCGGTCTCATGT 57.246 40.909 20.90 0.00 37.64 3.21
666 687 6.828273 TGATTTTTCATGTATTCCGGTCTCAT 59.172 34.615 0.00 0.00 0.00 2.90
684 705 1.250840 GGGCCGCTCCACTGATTTTT 61.251 55.000 0.00 0.00 36.21 1.94
720 741 2.230508 CCGTTCCGGCATCTAGCTATAA 59.769 50.000 0.00 0.00 41.17 0.98
723 744 1.461091 CCCGTTCCGGCATCTAGCTA 61.461 60.000 0.00 0.00 46.86 3.32
734 755 4.468689 GCCCTTCCTCCCGTTCCG 62.469 72.222 0.00 0.00 0.00 4.30
756 777 1.229209 TCCCCTCCTCTCGCAACTT 60.229 57.895 0.00 0.00 0.00 2.66
757 778 1.684049 CTCCCCTCCTCTCGCAACT 60.684 63.158 0.00 0.00 0.00 3.16
758 779 1.985116 ACTCCCCTCCTCTCGCAAC 60.985 63.158 0.00 0.00 0.00 4.17
791 812 2.241160 TGGACTACGACAGGTAAGCAA 58.759 47.619 0.00 0.00 0.00 3.91
797 818 1.933021 TTCCATGGACTACGACAGGT 58.067 50.000 15.91 0.00 0.00 4.00
849 881 4.572571 AAACCCTCACCGCCGCAA 62.573 61.111 0.00 0.00 0.00 4.85
858 890 1.850755 GTCCTCCCCCAAACCCTCA 60.851 63.158 0.00 0.00 0.00 3.86
875 907 2.681778 CACTCTGCCTCCTCCGGT 60.682 66.667 0.00 0.00 0.00 5.28
900 935 1.896660 GAGCAAACGCCAACCCAGA 60.897 57.895 0.00 0.00 0.00 3.86
916 951 2.701163 GAAGTATGGGCCTCCGCGAG 62.701 65.000 8.23 2.69 35.02 5.03
917 952 2.762459 AAGTATGGGCCTCCGCGA 60.762 61.111 8.23 0.00 35.02 5.87
985 1020 1.739466 GCTCATCTGGCGTTTGAATCA 59.261 47.619 0.00 0.00 0.00 2.57
1310 1345 4.043100 TCTCCAGGGAGCGACGGA 62.043 66.667 10.55 0.00 41.71 4.69
1311 1346 3.827898 GTCTCCAGGGAGCGACGG 61.828 72.222 10.55 0.00 41.71 4.79
1313 1348 4.500116 GCGTCTCCAGGGAGCGAC 62.500 72.222 25.53 14.12 41.01 5.19
1315 1350 4.504916 CTGCGTCTCCAGGGAGCG 62.505 72.222 20.38 20.38 41.71 5.03
1316 1351 4.154347 CCTGCGTCTCCAGGGAGC 62.154 72.222 10.55 5.25 46.93 4.70
1347 1385 2.672414 CGAGAGGGAGTGGGAGTTT 58.328 57.895 0.00 0.00 0.00 2.66
1463 1501 3.706373 GGAGCAGGGAGTTGGCGA 61.706 66.667 0.00 0.00 0.00 5.54
1515 1553 0.602638 TTTCATCGAACAGCCTGCGT 60.603 50.000 0.00 0.00 0.00 5.24
1539 1577 0.755698 ATGATACGGTGTCCCTCGCT 60.756 55.000 2.29 0.00 0.00 4.93
1557 1595 4.271696 TGAACCGATCAGAGTGTTGAAT 57.728 40.909 0.00 0.00 33.04 2.57
1575 1613 1.926510 CAGCACGAGTTCGCATATGAA 59.073 47.619 6.97 0.00 44.43 2.57
1583 1621 1.564622 CCAACACAGCACGAGTTCG 59.435 57.895 0.00 0.00 46.33 3.95
1587 1625 2.029288 ATCGCCAACACAGCACGAG 61.029 57.895 0.00 0.00 36.05 4.18
1588 1626 2.030412 ATCGCCAACACAGCACGA 59.970 55.556 0.00 0.00 37.15 4.35
1590 1628 2.126734 GCATCGCCAACACAGCAC 60.127 61.111 0.00 0.00 0.00 4.40
1635 1673 3.774599 ATCCGGCCGCAATCTTCCC 62.775 63.158 22.85 0.00 0.00 3.97
1636 1674 2.203209 ATCCGGCCGCAATCTTCC 60.203 61.111 22.85 0.00 0.00 3.46
1639 1677 4.569180 CCCATCCGGCCGCAATCT 62.569 66.667 22.85 0.00 0.00 2.40
1692 1730 1.467920 CCACCCTCAAATCCTTCAGC 58.532 55.000 0.00 0.00 0.00 4.26
1719 1757 4.341502 ATGGCAACCGCGTGCAAC 62.342 61.111 21.27 7.39 46.81 4.17
1727 1765 3.869272 GCGCTCTCATGGCAACCG 61.869 66.667 0.00 0.00 0.00 4.44
1754 1792 1.003545 CCTGTTGTGACTGAAACGCTG 60.004 52.381 0.00 0.00 0.00 5.18
1802 1840 3.970410 CCAGCCCCCTGCACTTCA 61.970 66.667 0.00 0.00 44.83 3.02
1820 1858 0.396974 AAACACCTTCCTGGCAAGCA 60.397 50.000 0.00 0.00 40.22 3.91
1902 1940 0.181587 TCTCGAGCTCCCTAGACCTG 59.818 60.000 7.81 0.00 0.00 4.00
1938 1976 5.901413 AATCCTTCTCTGGCATCTCATTA 57.099 39.130 0.00 0.00 0.00 1.90
1986 2024 1.591327 GCCAAACTGCACAAACCCG 60.591 57.895 0.00 0.00 0.00 5.28
1989 2027 2.035066 AGATCTGCCAAACTGCACAAAC 59.965 45.455 0.00 0.00 36.04 2.93
1992 2030 2.857186 TAGATCTGCCAAACTGCACA 57.143 45.000 5.18 0.00 36.04 4.57
2121 2159 2.011947 CGATGATGAAGCCTCTTTGCA 58.988 47.619 0.00 0.00 0.00 4.08
2208 2246 3.346315 TGTCTGTATGAACCCATGCTTG 58.654 45.455 0.00 0.00 36.51 4.01
2214 2252 1.357137 TGGCTGTCTGTATGAACCCA 58.643 50.000 0.00 0.00 0.00 4.51
2218 2256 3.200605 ACATCCATGGCTGTCTGTATGAA 59.799 43.478 15.53 0.00 0.00 2.57
2232 2270 3.382855 CACACCACAAAACACATCCATG 58.617 45.455 0.00 0.00 0.00 3.66
2246 2284 6.038271 GGTCTTAAATATGTCATCCACACCAC 59.962 42.308 0.00 0.00 38.04 4.16
2261 2299 5.856156 TGAACAACTCCACGGTCTTAAATA 58.144 37.500 0.00 0.00 0.00 1.40
2397 2435 2.429571 CGGCTGCATGCACACAAC 60.430 61.111 18.46 3.83 45.15 3.32
2420 2458 3.815401 CTCAAACCCTTGTGTCACTAAGG 59.185 47.826 19.41 19.41 42.46 2.69
2454 2492 1.105457 CACCATACTTGCCCACCATG 58.895 55.000 0.00 0.00 0.00 3.66
2621 2659 5.781818 AGTTTTCCAATCCTCATGTTTCCAT 59.218 36.000 0.00 0.00 0.00 3.41
2628 2666 4.219070 TCTGCAAGTTTTCCAATCCTCATG 59.781 41.667 0.00 0.00 33.76 3.07
2661 2699 3.767673 TGTAGCTAGGATCAAACCGAAGT 59.232 43.478 0.00 0.00 34.73 3.01
2746 2784 2.957402 ACCTTTCTCACCATTGCAGA 57.043 45.000 0.00 0.00 0.00 4.26
2811 2849 6.381801 CCCACTCATATTGTGTCTGAAAAAC 58.618 40.000 5.28 0.00 33.92 2.43
2847 2885 4.289672 AGAAACCATCTCACTATGTTGGGT 59.710 41.667 0.00 0.00 30.46 4.51
3068 3106 8.353423 AGTTTGTCCAGAATATTTGCATTAGT 57.647 30.769 0.00 0.00 0.00 2.24
3257 3295 0.801251 GGTCAGCTGTCAATCTGCAC 59.199 55.000 14.67 0.36 42.26 4.57
3302 3340 3.149196 ACAACACATTGACCATGGAGTC 58.851 45.455 21.47 7.13 39.30 3.36
3340 3378 5.824624 TGAGCTTCTCTCTGTGTTTTCATTT 59.175 36.000 0.00 0.00 42.38 2.32
3629 3681 2.290641 AGCACAAACGAAAAGGTAGCTG 59.709 45.455 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.