Multiple sequence alignment - TraesCS6A01G171200

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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 TraesCS6A01G171200 chr6A 100.000 3470 0 0 1 3470 181893203 181896672 0.000000e+00 6408
1 TraesCS6A01G171200 chr6B 94.942 2946 72 33 525 3455 239282781 239285664 0.000000e+00 4543
2 TraesCS6A01G171200 chr6B 88.011 367 22 15 137 495 239282265 239282617 6.930000e-112 414
3 TraesCS6A01G171200 chr6B 94.444 144 8 0 1 144 239281217 239281360 4.510000e-54 222
4 TraesCS6A01G171200 chr6D 94.578 2988 74 31 492 3470 139307688 139310596 0.000000e+00 4540
5 TraesCS6A01G171200 chr6D 88.600 500 40 12 1 495 139290109 139290596 2.980000e-165 592


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 TraesCS6A01G171200 chr6A 181893203 181896672 3469 False 6408.000000 6408 100.000000 1 3470 1 chr6A.!!$F1 3469
1 TraesCS6A01G171200 chr6B 239281217 239285664 4447 False 1726.333333 4543 92.465667 1 3455 3 chr6B.!!$F1 3454
2 TraesCS6A01G171200 chr6D 139307688 139310596 2908 False 4540.000000 4540 94.578000 492 3470 1 chr6D.!!$F2 2978

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
914 2008 0.033208 CCCTCAGCTCACCTCTCTCT 60.033 60.0 0.0 0.0 0.0 3.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 3733 0.038526 GCAGCAGCAGCAAGAATTGT 60.039 50.0 4.63 0.0 44.59 2.71 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
38 39 6.286758 ACATGCGAACTGATCTTCTATCAAT 58.713 36.000 0.00 0.00 0.00 2.57
39 40 7.436933 ACATGCGAACTGATCTTCTATCAATA 58.563 34.615 0.00 0.00 0.00 1.90
81 82 3.599343 TGAGGGATCACGAAATCACAAG 58.401 45.455 6.77 0.00 31.08 3.16
86 87 6.414732 AGGGATCACGAAATCACAAGAATAA 58.585 36.000 6.77 0.00 31.08 1.40
118 119 1.965930 GCAACGTCATGCCCACTCA 60.966 57.895 0.54 0.00 40.49 3.41
147 1060 6.528537 TGCATGAATGTATTTGCCTTAGTT 57.471 33.333 0.00 0.00 34.20 2.24
154 1067 9.255304 TGAATGTATTTGCCTTAGTTTTTGTTC 57.745 29.630 0.00 0.00 0.00 3.18
158 1071 7.806014 TGTATTTGCCTTAGTTTTTGTTCGATC 59.194 33.333 0.00 0.00 0.00 3.69
172 1086 6.784068 TTGTTCGATCGAAAAACTTGAAAC 57.216 33.333 30.61 15.94 35.75 2.78
177 1091 6.315551 TCGATCGAAAAACTTGAAACACAAA 58.684 32.000 16.99 0.00 38.08 2.83
183 1097 8.026607 TCGAAAAACTTGAAACACAAAAGAGAT 58.973 29.630 0.00 0.00 38.08 2.75
207 1124 4.705110 TCCAAGAGGTTTGAGTGAATGA 57.295 40.909 0.00 0.00 35.89 2.57
211 1128 6.379703 TCCAAGAGGTTTGAGTGAATGAAAAA 59.620 34.615 0.00 0.00 35.89 1.94
277 1194 1.854743 CTCGGCAATACAGATCACACG 59.145 52.381 0.00 0.00 0.00 4.49
282 1199 3.511699 GCAATACAGATCACACGACTGA 58.488 45.455 0.00 0.00 35.85 3.41
330 1247 3.878778 AGATCCCAATTCTCCAAAGTCG 58.121 45.455 0.00 0.00 0.00 4.18
332 1249 4.164988 AGATCCCAATTCTCCAAAGTCGAT 59.835 41.667 0.00 0.00 0.00 3.59
333 1250 3.609853 TCCCAATTCTCCAAAGTCGATG 58.390 45.455 0.00 0.00 0.00 3.84
338 1255 5.048782 CCAATTCTCCAAAGTCGATGTGAAA 60.049 40.000 0.00 0.00 0.00 2.69
339 1256 6.437928 CAATTCTCCAAAGTCGATGTGAAAA 58.562 36.000 0.00 0.00 0.00 2.29
340 1257 6.824305 ATTCTCCAAAGTCGATGTGAAAAT 57.176 33.333 0.00 0.00 0.00 1.82
341 1258 5.862924 TCTCCAAAGTCGATGTGAAAATC 57.137 39.130 0.00 0.00 0.00 2.17
342 1259 4.695455 TCTCCAAAGTCGATGTGAAAATCC 59.305 41.667 0.00 0.00 0.00 3.01
343 1260 4.651778 TCCAAAGTCGATGTGAAAATCCT 58.348 39.130 0.00 0.00 0.00 3.24
348 1265 4.256920 AGTCGATGTGAAAATCCTTCCTG 58.743 43.478 0.00 0.00 0.00 3.86
350 1267 4.002982 TCGATGTGAAAATCCTTCCTGTG 58.997 43.478 0.00 0.00 0.00 3.66
368 1285 3.861840 TGTGAATGAAAGAGACCCGATC 58.138 45.455 0.00 0.00 0.00 3.69
369 1286 2.860735 GTGAATGAAAGAGACCCGATCG 59.139 50.000 8.51 8.51 0.00 3.69
370 1287 2.758423 TGAATGAAAGAGACCCGATCGA 59.242 45.455 18.66 0.00 0.00 3.59
371 1288 3.384789 TGAATGAAAGAGACCCGATCGAT 59.615 43.478 18.66 0.00 0.00 3.59
372 1289 2.871182 TGAAAGAGACCCGATCGATG 57.129 50.000 18.66 9.93 0.00 3.84
373 1290 2.100197 TGAAAGAGACCCGATCGATGT 58.900 47.619 18.66 13.43 0.00 3.06
374 1291 2.099263 TGAAAGAGACCCGATCGATGTC 59.901 50.000 18.66 21.05 0.00 3.06
375 1292 2.060050 AAGAGACCCGATCGATGTCT 57.940 50.000 28.70 28.70 41.83 3.41
376 1293 1.313772 AGAGACCCGATCGATGTCTG 58.686 55.000 31.52 11.35 39.36 3.51
377 1294 1.025812 GAGACCCGATCGATGTCTGT 58.974 55.000 31.52 17.32 39.36 3.41
387 1304 2.742774 TCGATGTCTGTTATCGCATGG 58.257 47.619 0.00 0.00 45.13 3.66
416 1333 4.261031 CCGGTTTGTTCGAAACTCTTGAAT 60.261 41.667 0.00 0.00 0.00 2.57
417 1334 4.670621 CGGTTTGTTCGAAACTCTTGAATG 59.329 41.667 0.00 0.00 0.00 2.67
418 1335 5.503357 CGGTTTGTTCGAAACTCTTGAATGA 60.503 40.000 0.00 0.00 0.00 2.57
419 1336 6.262601 GGTTTGTTCGAAACTCTTGAATGAA 58.737 36.000 0.00 0.00 0.00 2.57
490 1407 6.419116 CCACATTAGTGTCATCTCGTCTATTG 59.581 42.308 0.00 0.00 44.39 1.90
522 1578 9.121658 TGTGGTGTATTTTGTGAAGTAAATACA 57.878 29.630 13.45 13.45 42.42 2.29
543 1599 5.321927 ACAGTACTGTAATCCTTTTTGGGG 58.678 41.667 26.91 0.00 42.90 4.96
584 1640 2.425539 TCATGTCGATTTCAAGCTGCA 58.574 42.857 1.02 0.00 0.00 4.41
605 1661 0.957395 TCCGTACTCGTCCTGACACC 60.957 60.000 0.00 0.00 35.01 4.16
705 1769 0.249398 CTCCGACGGATTTTGGAGGT 59.751 55.000 18.71 0.00 41.90 3.85
721 1785 4.708177 TGGAGGTTTTGAAGAGAGACAAG 58.292 43.478 0.00 0.00 0.00 3.16
730 1794 5.682234 TGAAGAGAGACAAGCATATCCAA 57.318 39.130 0.00 0.00 0.00 3.53
731 1795 6.244552 TGAAGAGAGACAAGCATATCCAAT 57.755 37.500 0.00 0.00 0.00 3.16
732 1796 6.286758 TGAAGAGAGACAAGCATATCCAATC 58.713 40.000 0.00 0.00 0.00 2.67
733 1797 5.226194 AGAGAGACAAGCATATCCAATCC 57.774 43.478 0.00 0.00 0.00 3.01
734 1798 4.657504 AGAGAGACAAGCATATCCAATCCA 59.342 41.667 0.00 0.00 0.00 3.41
735 1799 4.970711 AGAGACAAGCATATCCAATCCAG 58.029 43.478 0.00 0.00 0.00 3.86
739 1803 3.202818 ACAAGCATATCCAATCCAGTCCA 59.797 43.478 0.00 0.00 0.00 4.02
874 1938 4.626081 GACGGCAGGCAGTGGTGT 62.626 66.667 0.88 0.00 0.00 4.16
877 1941 4.586235 GGCAGGCAGTGGTGTGGT 62.586 66.667 0.00 0.00 0.00 4.16
878 1942 3.289834 GCAGGCAGTGGTGTGGTG 61.290 66.667 0.00 0.00 0.00 4.17
879 1943 2.595463 CAGGCAGTGGTGTGGTGG 60.595 66.667 0.00 0.00 0.00 4.61
881 1945 4.586235 GGCAGTGGTGTGGTGGCT 62.586 66.667 0.00 0.00 34.08 4.75
884 1950 3.570212 AGTGGTGTGGTGGCTCCC 61.570 66.667 2.66 0.00 34.77 4.30
905 1999 3.385384 CACTCCGCCCTCAGCTCA 61.385 66.667 0.00 0.00 40.39 4.26
906 2000 3.386237 ACTCCGCCCTCAGCTCAC 61.386 66.667 0.00 0.00 40.39 3.51
907 2001 4.154347 CTCCGCCCTCAGCTCACC 62.154 72.222 0.00 0.00 40.39 4.02
908 2002 4.704103 TCCGCCCTCAGCTCACCT 62.704 66.667 0.00 0.00 40.39 4.00
909 2003 4.154347 CCGCCCTCAGCTCACCTC 62.154 72.222 0.00 0.00 40.39 3.85
910 2004 3.073735 CGCCCTCAGCTCACCTCT 61.074 66.667 0.00 0.00 40.39 3.69
911 2005 2.899505 GCCCTCAGCTCACCTCTC 59.100 66.667 0.00 0.00 38.99 3.20
912 2006 1.685421 GCCCTCAGCTCACCTCTCT 60.685 63.158 0.00 0.00 38.99 3.10
913 2007 1.675720 GCCCTCAGCTCACCTCTCTC 61.676 65.000 0.00 0.00 38.99 3.20
914 2008 0.033208 CCCTCAGCTCACCTCTCTCT 60.033 60.000 0.00 0.00 0.00 3.10
915 2009 1.392589 CCTCAGCTCACCTCTCTCTC 58.607 60.000 0.00 0.00 0.00 3.20
916 2010 1.392589 CTCAGCTCACCTCTCTCTCC 58.607 60.000 0.00 0.00 0.00 3.71
917 2011 0.033601 TCAGCTCACCTCTCTCTCCC 60.034 60.000 0.00 0.00 0.00 4.30
918 2012 0.033208 CAGCTCACCTCTCTCTCCCT 60.033 60.000 0.00 0.00 0.00 4.20
919 2013 0.258774 AGCTCACCTCTCTCTCCCTC 59.741 60.000 0.00 0.00 0.00 4.30
920 2014 1.101049 GCTCACCTCTCTCTCCCTCG 61.101 65.000 0.00 0.00 0.00 4.63
921 2015 1.077357 TCACCTCTCTCTCCCTCGC 60.077 63.158 0.00 0.00 0.00 5.03
922 2016 2.124693 CACCTCTCTCTCCCTCGCC 61.125 68.421 0.00 0.00 0.00 5.54
923 2017 2.520741 CCTCTCTCTCCCTCGCCC 60.521 72.222 0.00 0.00 0.00 6.13
924 2018 2.520741 CTCTCTCTCCCTCGCCCC 60.521 72.222 0.00 0.00 0.00 5.80
925 2019 4.507916 TCTCTCTCCCTCGCCCCG 62.508 72.222 0.00 0.00 0.00 5.73
1785 2879 2.582436 GGGTCCGCGATCAAGGAA 59.418 61.111 8.23 0.00 38.41 3.36
1942 3036 1.031571 GCACCTGGGAATTCGCATCA 61.032 55.000 23.68 7.32 38.16 3.07
2388 3482 3.947841 GCGCACGCTTCCAACACA 61.948 61.111 7.96 0.00 38.26 3.72
2391 3485 1.154413 GCACGCTTCCAACACATCG 60.154 57.895 0.00 0.00 0.00 3.84
2521 3615 7.520776 GCATTTCTCATCTCAAGATCTTCATGG 60.521 40.741 4.57 0.00 31.21 3.66
2548 3642 6.091305 GGTCTTTGATTTTGGCATAGCTTTTC 59.909 38.462 0.00 0.00 0.00 2.29
2549 3643 6.870439 GTCTTTGATTTTGGCATAGCTTTTCT 59.130 34.615 0.00 0.00 0.00 2.52
2550 3644 7.062722 GTCTTTGATTTTGGCATAGCTTTTCTC 59.937 37.037 0.00 0.00 0.00 2.87
2551 3645 5.981088 TGATTTTGGCATAGCTTTTCTCA 57.019 34.783 0.00 0.00 0.00 3.27
2554 3648 7.388437 TGATTTTGGCATAGCTTTTCTCAAAT 58.612 30.769 0.00 0.00 0.00 2.32
2555 3649 7.332430 TGATTTTGGCATAGCTTTTCTCAAATG 59.668 33.333 0.00 0.00 0.00 2.32
2556 3650 5.726980 TTGGCATAGCTTTTCTCAAATGT 57.273 34.783 0.00 0.00 0.00 2.71
2557 3651 6.832520 TTGGCATAGCTTTTCTCAAATGTA 57.167 33.333 0.00 0.00 0.00 2.29
2558 3652 6.194796 TGGCATAGCTTTTCTCAAATGTAC 57.805 37.500 0.00 0.00 0.00 2.90
2572 3666 7.090808 TCTCAAATGTACGTATCTATGATGGC 58.909 38.462 0.00 0.00 0.00 4.40
2573 3667 6.754193 TCAAATGTACGTATCTATGATGGCA 58.246 36.000 0.00 0.00 0.00 4.92
2576 3670 7.658179 AATGTACGTATCTATGATGGCAAAG 57.342 36.000 0.00 0.00 0.00 2.77
2577 3671 6.399639 TGTACGTATCTATGATGGCAAAGA 57.600 37.500 0.00 0.00 0.00 2.52
2578 3672 6.447162 TGTACGTATCTATGATGGCAAAGAG 58.553 40.000 0.00 0.00 0.00 2.85
2639 3733 5.598830 GGACCTCCAGAGAGATGTAACAATA 59.401 44.000 0.00 0.00 43.39 1.90
2640 3734 6.461788 GGACCTCCAGAGAGATGTAACAATAC 60.462 46.154 0.00 0.00 43.39 1.89
2641 3735 5.958380 ACCTCCAGAGAGATGTAACAATACA 59.042 40.000 0.00 0.00 43.39 2.29
2642 3736 6.440647 ACCTCCAGAGAGATGTAACAATACAA 59.559 38.462 0.00 0.00 43.39 2.41
2643 3737 7.126421 ACCTCCAGAGAGATGTAACAATACAAT 59.874 37.037 0.00 0.00 43.39 2.71
2657 3751 3.777465 ATACAATTCTTGCTGCTGCTG 57.223 42.857 17.00 7.82 40.48 4.41
2661 3755 0.674581 ATTCTTGCTGCTGCTGCGTA 60.675 50.000 23.38 14.41 43.34 4.42
2662 3756 1.568612 TTCTTGCTGCTGCTGCGTAC 61.569 55.000 23.38 3.41 43.34 3.67
2663 3757 3.358667 CTTGCTGCTGCTGCGTACG 62.359 63.158 23.38 11.84 43.34 3.67
2702 3796 6.004574 AGTTCATATACTGAGGTATCGCTCA 58.995 40.000 0.00 0.00 39.19 4.26
2830 3930 3.270027 CATGAAGTAGGATGGAACGCAA 58.730 45.455 0.00 0.00 0.00 4.85
2838 3938 0.179129 GATGGAACGCAATGCCAAGG 60.179 55.000 0.00 0.00 34.95 3.61
2869 3969 5.749596 TGTACTTGTTTGACATCCAACAG 57.250 39.130 0.00 0.00 33.85 3.16
2926 4026 1.917955 CCGACTAACATGCTGTACACG 59.082 52.381 0.00 0.00 0.00 4.49
2979 4079 4.263018 AGTAGACTACCCCGAACAAAAC 57.737 45.455 9.06 0.00 0.00 2.43
3060 4160 2.743636 TGATCCTCAACCGTCTGAAC 57.256 50.000 0.00 0.00 0.00 3.18
3061 4161 1.967779 TGATCCTCAACCGTCTGAACA 59.032 47.619 0.00 0.00 0.00 3.18
3062 4162 2.367241 TGATCCTCAACCGTCTGAACAA 59.633 45.455 0.00 0.00 0.00 2.83
3063 4163 2.234300 TCCTCAACCGTCTGAACAAC 57.766 50.000 0.00 0.00 0.00 3.32
3064 4164 1.760613 TCCTCAACCGTCTGAACAACT 59.239 47.619 0.00 0.00 0.00 3.16
3065 4165 1.867233 CCTCAACCGTCTGAACAACTG 59.133 52.381 0.00 0.00 0.00 3.16
3066 4166 2.483013 CCTCAACCGTCTGAACAACTGA 60.483 50.000 0.00 0.00 0.00 3.41
3067 4167 3.194861 CTCAACCGTCTGAACAACTGAA 58.805 45.455 0.00 0.00 0.00 3.02
3089 4189 6.372381 TGAACAACTCATGTATCCAGTTCATG 59.628 38.462 13.12 0.00 42.99 3.07
3115 4215 5.278957 GCAGTCACCCAATTCTTGTATTTGT 60.279 40.000 0.00 0.00 0.00 2.83
3127 4230 4.223032 TCTTGTATTTGTCCCTCAGACCTC 59.777 45.833 0.00 0.00 45.68 3.85
3128 4231 2.838202 TGTATTTGTCCCTCAGACCTCC 59.162 50.000 0.00 0.00 45.68 4.30
3129 4232 2.350863 ATTTGTCCCTCAGACCTCCT 57.649 50.000 0.00 0.00 45.68 3.69
3146 4249 4.202253 ACCTCCTTTTCACTTTTGCCATTC 60.202 41.667 0.00 0.00 0.00 2.67
3177 4280 3.186119 CTCAGAAGGAAATGTCTCTCGC 58.814 50.000 0.00 0.00 0.00 5.03
3187 4290 0.735471 TGTCTCTCGCATCTCCTTCG 59.265 55.000 0.00 0.00 0.00 3.79
3214 4317 2.708861 TGGAGCTCTGTAAGAAAACCCA 59.291 45.455 14.64 0.00 46.34 4.51
3250 4353 0.318762 GCCGCCTTACTATGCTAGCT 59.681 55.000 17.23 4.07 0.00 3.32
3423 4526 7.830099 ATAAATTCTAAGAAATGAGCCAGGG 57.170 36.000 0.00 0.00 0.00 4.45
3430 4533 4.388577 AGAAATGAGCCAGGGTAACTTT 57.611 40.909 0.00 0.00 0.00 2.66
3441 4544 4.096382 CCAGGGTAACTTTATGACACATGC 59.904 45.833 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.288015 AGAAGATCAGTTCGCATGTATCAG 58.712 41.667 0.00 0.00 0.00 2.90
12 13 6.986250 TGATAGAAGATCAGTTCGCATGTAT 58.014 36.000 0.00 0.00 0.00 2.29
17 18 7.043961 ACTATTGATAGAAGATCAGTTCGCA 57.956 36.000 5.08 0.00 34.50 5.10
38 39 6.539173 TCAAATCAAAGAGCCCAAAGTACTA 58.461 36.000 0.00 0.00 0.00 1.82
39 40 5.385198 TCAAATCAAAGAGCCCAAAGTACT 58.615 37.500 0.00 0.00 0.00 2.73
118 119 8.967664 AAGGCAAATACATTCATGCAATATTT 57.032 26.923 0.00 0.00 40.51 1.40
147 1060 7.326305 TGTTTCAAGTTTTTCGATCGAACAAAA 59.674 29.630 29.15 23.31 33.41 2.44
154 1067 6.547493 TTTGTGTTTCAAGTTTTTCGATCG 57.453 33.333 9.36 9.36 37.35 3.69
158 1071 7.561237 TCTCTTTTGTGTTTCAAGTTTTTCG 57.439 32.000 0.00 0.00 37.35 3.46
172 1086 6.396829 ACCTCTTGGAAAATCTCTTTTGTG 57.603 37.500 0.00 0.00 34.73 3.33
177 1091 6.264067 CACTCAAACCTCTTGGAAAATCTCTT 59.736 38.462 0.00 0.00 37.04 2.85
183 1097 5.890985 TCATTCACTCAAACCTCTTGGAAAA 59.109 36.000 0.00 0.00 37.04 2.29
187 1101 5.772825 TTTCATTCACTCAAACCTCTTGG 57.227 39.130 0.00 0.00 39.83 3.61
236 1153 7.522374 CCGAGTCCTAAAGATTTTCTTCAAAG 58.478 38.462 0.00 0.00 35.27 2.77
296 1213 9.108284 GAGAATTGGGATCTTTAGAAGAAGAAG 57.892 37.037 0.00 0.00 41.63 2.85
297 1214 8.049721 GGAGAATTGGGATCTTTAGAAGAAGAA 58.950 37.037 0.00 0.00 41.63 2.52
308 1225 4.019321 TCGACTTTGGAGAATTGGGATCTT 60.019 41.667 0.00 0.00 0.00 2.40
313 1230 3.127548 CACATCGACTTTGGAGAATTGGG 59.872 47.826 0.00 0.00 0.00 4.12
330 1247 5.964958 TTCACAGGAAGGATTTTCACATC 57.035 39.130 0.00 0.00 0.00 3.06
332 1249 5.384336 TCATTCACAGGAAGGATTTTCACA 58.616 37.500 0.00 0.00 38.77 3.58
333 1250 5.964958 TCATTCACAGGAAGGATTTTCAC 57.035 39.130 0.00 0.00 38.77 3.18
338 1255 5.942826 GTCTCTTTCATTCACAGGAAGGATT 59.057 40.000 0.00 0.00 42.72 3.01
339 1256 5.495640 GTCTCTTTCATTCACAGGAAGGAT 58.504 41.667 0.00 0.00 42.72 3.24
340 1257 4.263068 GGTCTCTTTCATTCACAGGAAGGA 60.263 45.833 0.00 0.00 41.64 3.36
341 1258 4.006319 GGTCTCTTTCATTCACAGGAAGG 58.994 47.826 0.00 0.00 36.25 3.46
342 1259 4.006319 GGGTCTCTTTCATTCACAGGAAG 58.994 47.826 0.00 0.00 36.25 3.46
343 1260 3.557054 CGGGTCTCTTTCATTCACAGGAA 60.557 47.826 0.00 0.00 37.45 3.36
348 1265 2.860735 CGATCGGGTCTCTTTCATTCAC 59.139 50.000 7.38 0.00 0.00 3.18
350 1267 3.438297 TCGATCGGGTCTCTTTCATTC 57.562 47.619 16.41 0.00 0.00 2.67
368 1285 2.742774 TCCATGCGATAACAGACATCG 58.257 47.619 0.55 0.55 46.25 3.84
369 1286 3.366121 CGATCCATGCGATAACAGACATC 59.634 47.826 0.00 0.00 0.00 3.06
370 1287 3.320626 CGATCCATGCGATAACAGACAT 58.679 45.455 0.00 0.00 0.00 3.06
371 1288 2.545742 CCGATCCATGCGATAACAGACA 60.546 50.000 0.00 0.00 0.00 3.41
372 1289 2.061773 CCGATCCATGCGATAACAGAC 58.938 52.381 0.00 0.00 0.00 3.51
373 1290 1.605457 GCCGATCCATGCGATAACAGA 60.605 52.381 0.00 0.00 0.00 3.41
374 1291 0.792640 GCCGATCCATGCGATAACAG 59.207 55.000 0.00 0.00 0.00 3.16
375 1292 0.602638 GGCCGATCCATGCGATAACA 60.603 55.000 0.00 0.00 34.01 2.41
376 1293 1.626654 CGGCCGATCCATGCGATAAC 61.627 60.000 24.07 0.00 34.01 1.89
377 1294 1.374125 CGGCCGATCCATGCGATAA 60.374 57.895 24.07 0.00 34.01 1.75
387 1304 1.293267 TTCGAACAAACCGGCCGATC 61.293 55.000 30.73 13.24 0.00 3.69
439 1356 9.722184 GTATCTAGTAAAAGGGAAACAGAAGTT 57.278 33.333 0.00 0.00 40.40 2.66
441 1358 8.319146 TGGTATCTAGTAAAAGGGAAACAGAAG 58.681 37.037 0.00 0.00 0.00 2.85
450 1367 8.888579 CACTAATGTGGTATCTAGTAAAAGGG 57.111 38.462 0.00 0.00 40.33 3.95
490 1407 7.145323 ACTTCACAAAATACACCACATTTAGC 58.855 34.615 0.00 0.00 0.00 3.09
522 1578 4.930696 CCCCCAAAAAGGATTACAGTACT 58.069 43.478 0.00 0.00 41.22 2.73
541 1597 0.179054 GCCGTAGTGAATTCTCCCCC 60.179 60.000 7.05 0.00 0.00 5.40
542 1598 0.179054 GGCCGTAGTGAATTCTCCCC 60.179 60.000 7.05 0.00 0.00 4.81
543 1599 0.831307 AGGCCGTAGTGAATTCTCCC 59.169 55.000 7.05 0.00 0.00 4.30
584 1640 0.035881 TGTCAGGACGAGTACGGACT 59.964 55.000 17.15 0.00 44.46 3.85
705 1769 6.475504 TGGATATGCTTGTCTCTCTTCAAAA 58.524 36.000 0.00 0.00 0.00 2.44
721 1785 3.504906 CACATGGACTGGATTGGATATGC 59.495 47.826 0.00 0.00 0.00 3.14
730 1794 4.158394 GCACAAAATACACATGGACTGGAT 59.842 41.667 0.00 0.00 0.00 3.41
731 1795 3.505680 GCACAAAATACACATGGACTGGA 59.494 43.478 0.00 0.00 0.00 3.86
732 1796 3.507233 AGCACAAAATACACATGGACTGG 59.493 43.478 0.00 0.00 0.00 4.00
733 1797 4.478699 CAGCACAAAATACACATGGACTG 58.521 43.478 0.00 0.00 0.00 3.51
734 1798 3.507233 CCAGCACAAAATACACATGGACT 59.493 43.478 0.00 0.00 0.00 3.85
735 1799 3.836949 CCAGCACAAAATACACATGGAC 58.163 45.455 0.00 0.00 0.00 4.02
739 1803 1.202114 CCGCCAGCACAAAATACACAT 59.798 47.619 0.00 0.00 0.00 3.21
884 1950 4.087892 CTGAGGGCGGAGTGGTGG 62.088 72.222 0.00 0.00 0.00 4.61
905 1999 2.277404 GGCGAGGGAGAGAGAGGT 59.723 66.667 0.00 0.00 0.00 3.85
906 2000 2.520741 GGGCGAGGGAGAGAGAGG 60.521 72.222 0.00 0.00 0.00 3.69
907 2001 2.520741 GGGGCGAGGGAGAGAGAG 60.521 72.222 0.00 0.00 0.00 3.20
908 2002 4.507916 CGGGGCGAGGGAGAGAGA 62.508 72.222 0.00 0.00 0.00 3.10
922 2016 1.052124 TATTGTAGAGTGGGGGCGGG 61.052 60.000 0.00 0.00 0.00 6.13
923 2017 0.834612 TTATTGTAGAGTGGGGGCGG 59.165 55.000 0.00 0.00 0.00 6.13
924 2018 1.485066 ACTTATTGTAGAGTGGGGGCG 59.515 52.381 0.00 0.00 0.00 6.13
954 2048 0.249398 GTGGCCGTGTAATCCTGAGT 59.751 55.000 0.00 0.00 0.00 3.41
1421 2515 2.435059 GGAGCGACTTGGAGGTGC 60.435 66.667 0.00 0.00 0.00 5.01
1942 3036 2.438795 GTCCTCCTCGACGCTCCT 60.439 66.667 0.00 0.00 0.00 3.69
2049 3143 3.861341 CACCATGTACCCTGTGGAG 57.139 57.895 9.74 0.42 36.82 3.86
2340 3434 1.424493 GCCCGAACATCAAGAGCTCG 61.424 60.000 8.37 0.00 0.00 5.03
2388 3482 1.270732 GCCATGATCTCCAGCTTCGAT 60.271 52.381 0.00 0.00 0.00 3.59
2391 3485 0.182061 TGGCCATGATCTCCAGCTTC 59.818 55.000 0.00 0.00 0.00 3.86
2521 3615 3.430790 GCTATGCCAAAATCAAAGACCCC 60.431 47.826 0.00 0.00 0.00 4.95
2548 3642 6.868339 TGCCATCATAGATACGTACATTTGAG 59.132 38.462 0.00 0.00 0.00 3.02
2549 3643 6.754193 TGCCATCATAGATACGTACATTTGA 58.246 36.000 0.00 1.00 0.00 2.69
2550 3644 7.420184 TTGCCATCATAGATACGTACATTTG 57.580 36.000 0.00 0.00 0.00 2.32
2551 3645 7.931407 TCTTTGCCATCATAGATACGTACATTT 59.069 33.333 0.00 0.00 0.00 2.32
2554 3648 6.399639 TCTTTGCCATCATAGATACGTACA 57.600 37.500 0.00 0.00 0.00 2.90
2555 3649 5.864474 CCTCTTTGCCATCATAGATACGTAC 59.136 44.000 0.00 0.00 31.49 3.67
2556 3650 5.773176 TCCTCTTTGCCATCATAGATACGTA 59.227 40.000 0.00 0.00 31.49 3.57
2557 3651 4.588951 TCCTCTTTGCCATCATAGATACGT 59.411 41.667 0.00 0.00 31.49 3.57
2558 3652 5.139435 TCCTCTTTGCCATCATAGATACG 57.861 43.478 0.00 0.00 31.49 3.06
2570 3664 5.594317 TGCTATTTAAATCCTCCTCTTTGCC 59.406 40.000 3.39 0.00 0.00 4.52
2572 3666 7.680588 GCAGTGCTATTTAAATCCTCCTCTTTG 60.681 40.741 8.18 0.00 0.00 2.77
2573 3667 6.319911 GCAGTGCTATTTAAATCCTCCTCTTT 59.680 38.462 8.18 0.00 0.00 2.52
2576 3670 5.372373 AGCAGTGCTATTTAAATCCTCCTC 58.628 41.667 18.11 0.00 36.99 3.71
2577 3671 5.379706 AGCAGTGCTATTTAAATCCTCCT 57.620 39.130 18.11 0.00 36.99 3.69
2578 3672 5.180304 GCTAGCAGTGCTATTTAAATCCTCC 59.820 44.000 24.66 0.00 40.54 4.30
2639 3733 0.038526 GCAGCAGCAGCAAGAATTGT 60.039 50.000 4.63 0.00 44.59 2.71
2640 3734 1.071019 CGCAGCAGCAGCAAGAATTG 61.071 55.000 10.77 0.00 45.84 2.32
2641 3735 1.211969 CGCAGCAGCAGCAAGAATT 59.788 52.632 10.77 0.00 45.49 2.17
2642 3736 0.674581 TACGCAGCAGCAGCAAGAAT 60.675 50.000 10.77 0.00 45.49 2.40
2643 3737 1.301637 TACGCAGCAGCAGCAAGAA 60.302 52.632 10.77 0.00 45.49 2.52
2657 3751 5.629097 ACTATACATCTCAATAGCGTACGC 58.371 41.667 32.17 32.17 42.33 4.42
2830 3930 5.193099 AGTACATACCTTTTCCTTGGCAT 57.807 39.130 0.00 0.00 0.00 4.40
2838 3938 8.021396 GGATGTCAAACAAGTACATACCTTTTC 58.979 37.037 0.00 0.00 34.09 2.29
2926 4026 2.887152 ACTGTGTTCTCAAATCAAGGGC 59.113 45.455 0.00 0.00 0.00 5.19
2979 4079 7.474398 TCAATTATGCTCATTCTTCTCTTCG 57.526 36.000 0.00 0.00 0.00 3.79
3089 4189 2.712057 CAAGAATTGGGTGACTGCAC 57.288 50.000 0.00 0.00 43.94 4.57
3115 4215 1.978580 GTGAAAAGGAGGTCTGAGGGA 59.021 52.381 0.00 0.00 0.00 4.20
3127 4230 5.358922 TCTTGAATGGCAAAAGTGAAAAGG 58.641 37.500 0.00 0.00 35.74 3.11
3128 4231 6.907206 TTCTTGAATGGCAAAAGTGAAAAG 57.093 33.333 0.00 0.00 35.74 2.27
3129 4232 7.678947 TTTTCTTGAATGGCAAAAGTGAAAA 57.321 28.000 13.18 13.18 35.94 2.29
3146 4249 6.453092 ACATTTCCTTCTGAGCATTTTCTTG 58.547 36.000 0.00 0.00 0.00 3.02
3177 4280 0.173481 TCCAGAACGCGAAGGAGATG 59.827 55.000 15.93 0.99 0.00 2.90
3187 4290 1.202582 TCTTACAGAGCTCCAGAACGC 59.797 52.381 10.93 0.00 0.00 4.84
3214 4317 0.678048 GGCAATCAGGCGAGGAACTT 60.678 55.000 0.00 0.00 41.55 2.66
3250 4353 2.125391 GTGCGCCTGATGCAGAGA 60.125 61.111 4.18 0.00 44.21 3.10
3406 4509 5.104259 AGTTACCCTGGCTCATTTCTTAG 57.896 43.478 0.00 0.00 0.00 2.18
3412 4515 5.193679 GTCATAAAGTTACCCTGGCTCATT 58.806 41.667 0.00 0.00 0.00 2.57
3423 4526 6.808212 AGCAAATGCATGTGTCATAAAGTTAC 59.192 34.615 18.15 0.00 45.16 2.50
3430 4533 5.136816 ACAAAGCAAATGCATGTGTCATA 57.863 34.783 18.15 0.00 45.16 2.15


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

AutoCloner maintained by Alex Coulton.