Multiple sequence alignment - TraesCS2D01G232600

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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 TraesCS2D01G232600 chr2D 100.000 6066 0 0 1 6066 205624039 205617974 0.000000e+00 11202.0
1 TraesCS2D01G232600 chr2A 92.449 5443 194 63 739 6064 277598520 277603862 0.000000e+00 7574.0
2 TraesCS2D01G232600 chr2A 88.640 669 15 17 1 659 277597785 277598402 0.000000e+00 758.0
3 TraesCS2D01G232600 chr2A 92.727 55 4 0 664 718 277598466 277598520 5.040000e-11 80.5
4 TraesCS2D01G232600 chr2A 94.872 39 2 0 637 675 277598419 277598457 1.830000e-05 62.1
5 TraesCS2D01G232600 chr2B 93.438 2545 118 17 2708 5232 259784519 259782004 0.000000e+00 3729.0
6 TraesCS2D01G232600 chr2B 86.610 2808 166 93 3 2706 259787255 259784554 0.000000e+00 2909.0
7 TraesCS2D01G232600 chr2B 95.704 838 29 3 5233 6066 259781731 259780897 0.000000e+00 1341.0


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 TraesCS2D01G232600 chr2D 205617974 205624039 6065 True 11202.000000 11202 100.000000 1 6066 1 chr2D.!!$R1 6065
1 TraesCS2D01G232600 chr2A 277597785 277603862 6077 False 2118.650000 7574 92.172000 1 6064 4 chr2A.!!$F1 6063
2 TraesCS2D01G232600 chr2B 259780897 259787255 6358 True 2659.666667 3729 91.917333 3 6066 3 chr2B.!!$R1 6063

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
963 1086 0.251341 GGTGGATTGCTGAACAGGGT 60.251 55.0 3.99 0.0 0.00 4.34 F
1201 1344 0.243365 TTTCTGCGATTTTGCGGCAT 59.757 45.0 2.28 0.0 41.12 4.40 F
1462 1636 0.671472 CAACATGTGCCGCTCAGAGA 60.671 55.0 0.00 0.0 0.00 3.10 F
1781 1964 0.737715 CCACCGAACAGCAGCTCTAC 60.738 60.0 0.00 0.0 0.00 2.59 F
2282 2486 0.912006 AGGCTGTCTTTCTCCCTCCC 60.912 60.0 0.00 0.0 0.00 4.30 F
3762 4008 0.104671 GTGGCAGAGGAGAGATCAGC 59.895 60.0 0.00 0.0 0.00 4.26 F
3805 4051 0.532573 TCGTCAATGGAGAGAGGCAC 59.467 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2962 3203 1.004979 AGCTCTAGGTCGGTCTTGTCT 59.995 52.381 0.00 0.00 0.00 3.41 R
2987 3228 0.884704 TTGGCCTTGAGCTCGACAAC 60.885 55.000 9.64 0.00 43.05 3.32 R
3220 3461 0.944386 GTTTTCTGCACTCGGCTTCA 59.056 50.000 0.00 0.00 45.15 3.02 R
3266 3507 2.497173 AATGGCGCCAAAGCACACA 61.497 52.632 36.33 6.47 39.83 3.72 R
4108 4354 0.825010 CTGCACCCTTGACCTTTGCT 60.825 55.000 0.00 0.00 34.18 3.91 R
4903 5166 1.654137 CGTTTTCAACTGCGCGCTT 60.654 52.632 33.29 16.87 0.00 4.68 R
5283 5819 2.096909 CGTGTTGCAGACGAGGTTAAAG 60.097 50.000 13.51 0.00 39.21 1.85 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
47 48 1.067071 AGCTCAGCGGTTAGTGGTTAC 60.067 52.381 0.00 0.00 0.00 2.50
84 85 1.062685 ACGACTAGCAGCACGATCG 59.937 57.895 14.88 14.88 35.74 3.69
151 152 1.954382 GAAACCAAGCCTCCGTTTCTT 59.046 47.619 8.57 0.00 41.27 2.52
220 231 5.611374 CATCGTCTATTCCCCATTTGTACT 58.389 41.667 0.00 0.00 0.00 2.73
221 232 6.740401 GCATCGTCTATTCCCCATTTGTACTA 60.740 42.308 0.00 0.00 0.00 1.82
222 233 6.152932 TCGTCTATTCCCCATTTGTACTAC 57.847 41.667 0.00 0.00 0.00 2.73
417 460 2.937433 GCTTACTTCCTGGGTCTTGCTC 60.937 54.545 0.00 0.00 0.00 4.26
427 470 4.680237 TCTTGCTCCCGTGCCGTG 62.680 66.667 0.00 0.00 0.00 4.94
473 516 1.134175 CTTGCTTCTCCTCTCTCGTCC 59.866 57.143 0.00 0.00 0.00 4.79
488 531 1.002366 CGTCCATTTCTTCGCCTGAG 58.998 55.000 0.00 0.00 0.00 3.35
490 533 2.427506 GTCCATTTCTTCGCCTGAGTT 58.572 47.619 0.00 0.00 0.00 3.01
500 543 2.593956 GCCTGAGTTTCCTCCCCGT 61.594 63.158 0.00 0.00 36.86 5.28
510 553 1.192146 TCCTCCCCGTTCTTGGACTG 61.192 60.000 0.00 0.00 0.00 3.51
579 623 5.705905 AGGAGGTAGTAGTTTTGAATTGTGC 59.294 40.000 0.00 0.00 0.00 4.57
642 686 3.179048 TCAAGTGATGCAGTATTCGTCG 58.821 45.455 0.00 0.00 0.00 5.12
675 758 2.160205 TCTTAGTCGTCTGGTCTGGTG 58.840 52.381 0.00 0.00 0.00 4.17
677 760 1.991121 TAGTCGTCTGGTCTGGTGTT 58.009 50.000 0.00 0.00 0.00 3.32
678 761 1.120530 AGTCGTCTGGTCTGGTGTTT 58.879 50.000 0.00 0.00 0.00 2.83
679 762 2.313317 AGTCGTCTGGTCTGGTGTTTA 58.687 47.619 0.00 0.00 0.00 2.01
680 763 2.897969 AGTCGTCTGGTCTGGTGTTTAT 59.102 45.455 0.00 0.00 0.00 1.40
681 764 3.056749 AGTCGTCTGGTCTGGTGTTTATC 60.057 47.826 0.00 0.00 0.00 1.75
724 827 1.651737 TGTCCTTGCCTTGGCTACTA 58.348 50.000 13.18 0.00 0.00 1.82
725 828 2.196595 TGTCCTTGCCTTGGCTACTAT 58.803 47.619 13.18 0.00 0.00 2.12
726 829 3.380393 TGTCCTTGCCTTGGCTACTATA 58.620 45.455 13.18 0.00 0.00 1.31
727 830 3.134081 TGTCCTTGCCTTGGCTACTATAC 59.866 47.826 13.18 4.74 0.00 1.47
728 831 3.388350 GTCCTTGCCTTGGCTACTATACT 59.612 47.826 13.18 0.00 0.00 2.12
787 890 1.737236 TGGAATTCGCGTGATTCTTGG 59.263 47.619 25.37 0.00 0.00 3.61
811 914 5.404946 CAATTTCTTCAGAATGGACGCAAT 58.595 37.500 0.00 0.00 36.16 3.56
815 918 4.183865 TCTTCAGAATGGACGCAATACTG 58.816 43.478 0.00 0.00 36.16 2.74
816 919 3.885724 TCAGAATGGACGCAATACTGA 57.114 42.857 0.00 0.00 36.16 3.41
817 920 4.200838 TCAGAATGGACGCAATACTGAA 57.799 40.909 0.00 0.00 36.16 3.02
873 980 6.127925 TGTCTTGTCTTACATGCATTGGATTC 60.128 38.462 0.00 0.00 0.00 2.52
963 1086 0.251341 GGTGGATTGCTGAACAGGGT 60.251 55.000 3.99 0.00 0.00 4.34
987 1110 3.846023 GCATAAGCATCGTCATTCAACCG 60.846 47.826 0.00 0.00 41.58 4.44
989 1112 1.359848 AGCATCGTCATTCAACCGAC 58.640 50.000 0.00 0.00 32.86 4.79
990 1113 1.075542 GCATCGTCATTCAACCGACA 58.924 50.000 0.00 0.00 32.86 4.35
994 1135 0.439985 CGTCATTCAACCGACAGCTG 59.560 55.000 13.48 13.48 32.24 4.24
1071 1214 4.646877 GCCCCCACCGAAACCGAA 62.647 66.667 0.00 0.00 0.00 4.30
1072 1215 2.113562 CCCCCACCGAAACCGAAA 59.886 61.111 0.00 0.00 0.00 3.46
1073 1216 2.263021 CCCCCACCGAAACCGAAAC 61.263 63.158 0.00 0.00 0.00 2.78
1074 1217 2.263021 CCCCACCGAAACCGAAACC 61.263 63.158 0.00 0.00 0.00 3.27
1075 1218 2.609759 CCCACCGAAACCGAAACCG 61.610 63.158 0.00 0.00 0.00 4.44
1076 1219 1.594836 CCACCGAAACCGAAACCGA 60.595 57.895 0.00 0.00 0.00 4.69
1102 1245 3.554342 CCTCCTGCCCATCCGAGG 61.554 72.222 0.00 0.00 36.23 4.63
1137 1280 4.078639 ACAGGTGAGAGGAGAAACAAAG 57.921 45.455 0.00 0.00 0.00 2.77
1164 1307 5.441718 TCTTGTTATCCTTCTTCCTGCAT 57.558 39.130 0.00 0.00 0.00 3.96
1201 1344 0.243365 TTTCTGCGATTTTGCGGCAT 59.757 45.000 2.28 0.00 41.12 4.40
1264 1411 1.268079 GGTCAGAGGAGCAACAAAAGC 59.732 52.381 0.00 0.00 41.19 3.51
1364 1523 7.264373 TGTTCAGACATCTTCCTTTTCTTTC 57.736 36.000 0.00 0.00 0.00 2.62
1365 1524 7.056635 TGTTCAGACATCTTCCTTTTCTTTCT 58.943 34.615 0.00 0.00 0.00 2.52
1366 1525 7.557719 TGTTCAGACATCTTCCTTTTCTTTCTT 59.442 33.333 0.00 0.00 0.00 2.52
1367 1526 8.409371 GTTCAGACATCTTCCTTTTCTTTCTTT 58.591 33.333 0.00 0.00 0.00 2.52
1368 1527 8.159344 TCAGACATCTTCCTTTTCTTTCTTTC 57.841 34.615 0.00 0.00 0.00 2.62
1369 1528 7.995488 TCAGACATCTTCCTTTTCTTTCTTTCT 59.005 33.333 0.00 0.00 0.00 2.52
1370 1529 8.628280 CAGACATCTTCCTTTTCTTTCTTTCTT 58.372 33.333 0.00 0.00 0.00 2.52
1371 1530 9.194972 AGACATCTTCCTTTTCTTTCTTTCTTT 57.805 29.630 0.00 0.00 0.00 2.52
1377 1536 4.025730 CCTTTTCTTTCTTTCTTTTGCGGC 60.026 41.667 0.00 0.00 0.00 6.53
1389 1548 4.735132 TGCGGCGGAGGAAGTTCG 62.735 66.667 9.78 0.00 0.00 3.95
1462 1636 0.671472 CAACATGTGCCGCTCAGAGA 60.671 55.000 0.00 0.00 0.00 3.10
1773 1956 1.445582 CCGTAGACCACCGAACAGC 60.446 63.158 0.00 0.00 0.00 4.40
1779 1962 2.345244 CCACCGAACAGCAGCTCT 59.655 61.111 0.00 0.00 0.00 4.09
1780 1963 1.185618 ACCACCGAACAGCAGCTCTA 61.186 55.000 0.00 0.00 0.00 2.43
1781 1964 0.737715 CCACCGAACAGCAGCTCTAC 60.738 60.000 0.00 0.00 0.00 2.59
1782 1965 0.737715 CACCGAACAGCAGCTCTACC 60.738 60.000 0.00 0.00 0.00 3.18
1783 1966 1.185618 ACCGAACAGCAGCTCTACCA 61.186 55.000 0.00 0.00 0.00 3.25
1789 1972 1.482593 ACAGCAGCTCTACCATACCAC 59.517 52.381 0.00 0.00 0.00 4.16
1790 1973 1.123928 AGCAGCTCTACCATACCACC 58.876 55.000 0.00 0.00 0.00 4.61
1797 1982 5.009811 CAGCTCTACCATACCACCTTAGTAC 59.990 48.000 0.00 0.00 0.00 2.73
1969 2154 2.116238 TCCTATTGTCCCTGTACCAGC 58.884 52.381 0.00 0.00 0.00 4.85
2175 2366 2.677875 TGCTGGCGCAGAGAGAGA 60.678 61.111 10.83 0.00 42.25 3.10
2176 2367 2.104729 GCTGGCGCAGAGAGAGAG 59.895 66.667 10.83 0.00 32.44 3.20
2177 2368 2.413963 GCTGGCGCAGAGAGAGAGA 61.414 63.158 10.83 0.00 32.44 3.10
2280 2484 1.339535 CCAAGGCTGTCTTTCTCCCTC 60.340 57.143 0.00 0.00 32.41 4.30
2281 2485 0.988063 AAGGCTGTCTTTCTCCCTCC 59.012 55.000 0.00 0.00 29.99 4.30
2282 2486 0.912006 AGGCTGTCTTTCTCCCTCCC 60.912 60.000 0.00 0.00 0.00 4.30
2283 2487 0.912006 GGCTGTCTTTCTCCCTCCCT 60.912 60.000 0.00 0.00 0.00 4.20
2314 2518 3.996150 AATGCAACAGTGAGGAACAAG 57.004 42.857 0.00 0.00 0.00 3.16
2369 2573 7.415541 GCATTAAACATTCTCCATACAAGCTGA 60.416 37.037 0.00 0.00 0.00 4.26
2370 2574 7.994425 TTAAACATTCTCCATACAAGCTGAA 57.006 32.000 0.00 0.00 0.00 3.02
2410 2614 6.319141 AGTCTAACCAATGTTTGCTTCTTC 57.681 37.500 0.00 0.00 35.87 2.87
2422 2626 1.270839 TGCTTCTTCTTTCTGTCGGGG 60.271 52.381 0.00 0.00 0.00 5.73
2445 2649 4.567959 GCAACAATTTTGACTCTGCTTGTT 59.432 37.500 0.00 0.00 37.31 2.83
2589 2793 2.288579 TGTGGTATCGGATATTCGTGCC 60.289 50.000 2.72 4.92 0.00 5.01
2651 2855 4.223923 AGAAGCTGTTCTAGGTATGCAGTT 59.776 41.667 0.00 0.00 41.54 3.16
2652 2856 5.422331 AGAAGCTGTTCTAGGTATGCAGTTA 59.578 40.000 0.00 0.00 41.54 2.24
2654 2858 6.049955 AGCTGTTCTAGGTATGCAGTTAAA 57.950 37.500 0.00 0.00 34.81 1.52
2685 2889 6.304356 TGACTGAACAAGAACATTAAGCAG 57.696 37.500 0.00 0.00 0.00 4.24
2695 2899 5.846203 AGAACATTAAGCAGCACACAAAAT 58.154 33.333 0.00 0.00 0.00 1.82
2697 2901 7.432869 AGAACATTAAGCAGCACACAAAATTA 58.567 30.769 0.00 0.00 0.00 1.40
2698 2902 7.382218 AGAACATTAAGCAGCACACAAAATTAC 59.618 33.333 0.00 0.00 0.00 1.89
2699 2903 6.748132 ACATTAAGCAGCACACAAAATTACT 58.252 32.000 0.00 0.00 0.00 2.24
2700 2904 7.881142 ACATTAAGCAGCACACAAAATTACTA 58.119 30.769 0.00 0.00 0.00 1.82
2701 2905 8.023128 ACATTAAGCAGCACACAAAATTACTAG 58.977 33.333 0.00 0.00 0.00 2.57
2703 2907 4.398319 AGCAGCACACAAAATTACTAGGT 58.602 39.130 0.00 0.00 0.00 3.08
2704 2908 5.556915 AGCAGCACACAAAATTACTAGGTA 58.443 37.500 0.00 0.00 0.00 3.08
2705 2909 6.180472 AGCAGCACACAAAATTACTAGGTAT 58.820 36.000 0.00 0.00 0.00 2.73
2706 2910 6.094048 AGCAGCACACAAAATTACTAGGTATG 59.906 38.462 0.00 0.00 0.00 2.39
2845 3086 2.544277 GCTGAATGCTGCAACTGTCAAA 60.544 45.455 6.36 0.00 38.66 2.69
2849 3090 1.906757 TGCTGCAACTGTCAAAAACG 58.093 45.000 0.00 0.00 0.00 3.60
2920 3161 2.958355 CAAGGAAGAGCAGGACCAAAAA 59.042 45.455 0.00 0.00 0.00 1.94
2962 3203 2.117423 TCTCGGCAGTGGGAGTCA 59.883 61.111 0.00 0.00 0.00 3.41
2987 3228 3.905678 CCGACCTAGAGCTGCGGG 61.906 72.222 0.00 0.00 38.40 6.13
3169 3410 4.020617 CTCAACAGGAGGGCGGCA 62.021 66.667 12.47 0.00 40.13 5.69
3220 3461 3.971702 AGGAAGGCGGCCAAGCTT 61.972 61.111 23.09 6.34 37.29 3.74
3266 3507 4.003648 GGTGATCACATCCTTCGTTCTTT 58.996 43.478 26.47 0.00 0.00 2.52
3398 3644 1.881903 CTCCTTCAGCAGCGACCTCA 61.882 60.000 0.00 0.00 0.00 3.86
3422 3668 0.394488 CACTCCGAGCTCCCTCTGTA 60.394 60.000 8.47 0.00 35.90 2.74
3553 3799 1.202256 GCAGTCGACATCGGTGTGATA 60.202 52.381 19.50 0.00 39.09 2.15
3682 3928 4.021925 AGGAAGCTGGTGGCCGAC 62.022 66.667 0.00 0.00 43.05 4.79
3762 4008 0.104671 GTGGCAGAGGAGAGATCAGC 59.895 60.000 0.00 0.00 0.00 4.26
3805 4051 0.532573 TCGTCAATGGAGAGAGGCAC 59.467 55.000 0.00 0.00 0.00 5.01
3857 4103 2.104170 GGAAGAGGAACGATCTGGAGT 58.896 52.381 0.00 0.00 0.00 3.85
4012 4258 2.472049 GAGACGAAACAGCTGCGC 59.528 61.111 15.27 0.00 0.00 6.09
4099 4345 2.666862 AAATGCCGTGCCGTCGAA 60.667 55.556 0.00 0.00 0.00 3.71
4108 4354 2.261671 GCCGTCGAAGCTCTGGAA 59.738 61.111 0.00 0.00 0.00 3.53
4184 4430 3.745799 TCATTCCAAAAGAAGGTGCGTA 58.254 40.909 0.00 0.00 38.07 4.42
4291 4537 2.109774 CTCAGATCTCAACTCCAGGCT 58.890 52.381 0.00 0.00 0.00 4.58
4356 4602 3.924918 TGAAGAGACTCTGGAGAAACG 57.075 47.619 5.55 0.00 0.00 3.60
4359 4605 3.426787 AGAGACTCTGGAGAAACGAGA 57.573 47.619 3.56 0.00 32.70 4.04
4360 4606 3.757270 AGAGACTCTGGAGAAACGAGAA 58.243 45.455 3.56 0.00 33.26 2.87
4459 4705 5.010922 CCAGTTGGAAATGAAATTGGAGACA 59.989 40.000 0.00 0.00 36.10 3.41
4530 4776 3.502211 GCCCAGAAGAAGAAAATGACGAA 59.498 43.478 0.00 0.00 0.00 3.85
4533 4779 4.515191 CCAGAAGAAGAAAATGACGAACCA 59.485 41.667 0.00 0.00 0.00 3.67
4660 4906 2.507484 TGCCATGACTTGAAACAGGAG 58.493 47.619 0.00 0.00 0.00 3.69
4680 4926 2.048419 TTGTGCAGCAGAGCTCCAGT 62.048 55.000 10.93 0.00 36.40 4.00
4706 4952 1.070601 AGCCAAAACCAATGGAAGTGC 59.929 47.619 6.16 1.77 40.56 4.40
4903 5166 3.682858 GCCAGAAAACAATAGCGTCACTA 59.317 43.478 0.00 0.00 34.64 2.74
5157 5420 4.539293 CCTTCCCTGATTCCATATGGAGAT 59.461 45.833 23.35 18.68 46.36 2.75
5212 5476 5.620738 AGGCTCATATGAGAAAAGCACTA 57.379 39.130 32.38 0.00 44.74 2.74
5275 5811 7.665145 TGGTCAACTTGTCTCATGAAATTATCA 59.335 33.333 0.00 0.00 43.67 2.15
5283 5819 9.859427 TTGTCTCATGAAATTATCAAAATGGTC 57.141 29.630 0.00 0.00 42.54 4.02
5311 5847 2.355837 TCTGCAACACGACTCCGC 60.356 61.111 0.00 0.00 39.95 5.54
5619 6157 7.830739 ACAGCAGGTAATATTTCAAGGAAAAG 58.169 34.615 0.00 0.00 35.11 2.27
5620 6158 7.451566 ACAGCAGGTAATATTTCAAGGAAAAGT 59.548 33.333 0.00 0.00 35.11 2.66
5702 6241 2.584835 ATTCACTAAGGCAAGCACCA 57.415 45.000 0.00 0.00 0.00 4.17
6060 6620 3.498661 GGTCCACCATTTGAGTTCCTTCT 60.499 47.826 0.00 0.00 35.64 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 5.050091 CCGCTGAGCTTAATTCGATTACAAT 60.050 40.000 1.78 0.00 0.00 2.71
47 48 0.374758 TGCTAACGACTAGTACGCCG 59.625 55.000 12.63 7.26 0.00 6.46
84 85 4.828939 TCTTGTGATAATGGCAATGGGATC 59.171 41.667 0.00 0.00 0.00 3.36
473 516 3.077359 AGGAAACTCAGGCGAAGAAATG 58.923 45.455 0.00 0.00 32.90 2.32
488 531 0.399075 TCCAAGAACGGGGAGGAAAC 59.601 55.000 0.00 0.00 0.00 2.78
490 533 0.473117 AGTCCAAGAACGGGGAGGAA 60.473 55.000 0.00 0.00 32.85 3.36
500 543 2.158310 TGGAGAGAGGACAGTCCAAGAA 60.158 50.000 22.31 0.00 39.61 2.52
510 553 1.028905 CACCGAGATGGAGAGAGGAC 58.971 60.000 0.00 0.00 42.00 3.85
579 623 3.070018 AGCCGAGTTCATCAAGAAACAG 58.930 45.455 0.00 0.00 38.13 3.16
638 682 5.691815 ACTAAGAAGAAGAAGAAGACGACG 58.308 41.667 0.00 0.00 0.00 5.12
642 686 6.799925 CAGACGACTAAGAAGAAGAAGAAGAC 59.200 42.308 0.00 0.00 0.00 3.01
724 827 6.205464 ACACGCAACCACGTATAGTATAGTAT 59.795 38.462 5.43 5.43 46.34 2.12
725 828 5.527214 ACACGCAACCACGTATAGTATAGTA 59.473 40.000 0.00 0.00 46.34 1.82
726 829 4.336433 ACACGCAACCACGTATAGTATAGT 59.664 41.667 0.00 0.00 46.34 2.12
727 830 4.852138 ACACGCAACCACGTATAGTATAG 58.148 43.478 0.00 0.00 46.34 1.31
728 831 4.898829 ACACGCAACCACGTATAGTATA 57.101 40.909 0.00 0.00 46.34 1.47
777 880 6.017400 TCTGAAGAAATTGCCAAGAATCAC 57.983 37.500 0.00 0.00 0.00 3.06
787 890 3.174375 GCGTCCATTCTGAAGAAATTGC 58.826 45.455 0.00 0.00 37.61 3.56
811 914 5.594725 AGCTCGATTAGGATGTTCTTCAGTA 59.405 40.000 0.00 0.00 0.00 2.74
815 918 4.938080 TCAGCTCGATTAGGATGTTCTTC 58.062 43.478 0.00 0.00 0.00 2.87
816 919 5.543507 ATCAGCTCGATTAGGATGTTCTT 57.456 39.130 0.00 0.00 0.00 2.52
817 920 6.629128 CATATCAGCTCGATTAGGATGTTCT 58.371 40.000 4.35 0.00 35.39 3.01
963 1086 2.820330 TGAATGACGATGCTTATGCGA 58.180 42.857 0.00 0.00 43.34 5.10
987 1110 0.396060 GATCCATCCCTCCAGCTGTC 59.604 60.000 13.81 0.00 0.00 3.51
989 1112 1.370437 CGATCCATCCCTCCAGCTG 59.630 63.158 6.78 6.78 0.00 4.24
990 1113 2.515071 GCGATCCATCCCTCCAGCT 61.515 63.158 0.00 0.00 0.00 4.24
994 1135 4.008933 CCGGCGATCCATCCCTCC 62.009 72.222 9.30 0.00 0.00 4.30
1102 1245 4.997395 TCTCACCTGTTCATCAGTTAAAGC 59.003 41.667 0.00 0.00 42.19 3.51
1137 1280 5.825151 CAGGAAGAAGGATAACAAGAATCCC 59.175 44.000 0.00 0.00 43.44 3.85
1164 1307 6.397272 GCAGAAATGGAAACCATCAATGTAA 58.603 36.000 3.69 0.00 44.40 2.41
1201 1344 1.333619 GCAAGGCGAACAGTGAGAAAA 59.666 47.619 0.00 0.00 0.00 2.29
1296 1447 6.035975 TGACACTACACATGCATTATTCTTCG 59.964 38.462 0.00 0.00 0.00 3.79
1297 1448 7.307493 TGACACTACACATGCATTATTCTTC 57.693 36.000 0.00 0.00 0.00 2.87
1364 1523 1.210155 CCTCCGCCGCAAAAGAAAG 59.790 57.895 0.00 0.00 0.00 2.62
1365 1524 0.820074 TTCCTCCGCCGCAAAAGAAA 60.820 50.000 0.00 0.00 0.00 2.52
1366 1525 1.228003 TTCCTCCGCCGCAAAAGAA 60.228 52.632 0.00 0.00 0.00 2.52
1367 1526 1.671054 CTTCCTCCGCCGCAAAAGA 60.671 57.895 0.00 0.00 0.00 2.52
1368 1527 1.515521 AACTTCCTCCGCCGCAAAAG 61.516 55.000 0.00 0.00 0.00 2.27
1369 1528 1.512156 GAACTTCCTCCGCCGCAAAA 61.512 55.000 0.00 0.00 0.00 2.44
1370 1529 1.964373 GAACTTCCTCCGCCGCAAA 60.964 57.895 0.00 0.00 0.00 3.68
1371 1530 2.358247 GAACTTCCTCCGCCGCAA 60.358 61.111 0.00 0.00 0.00 4.85
1377 1536 0.246635 ACATGTCCGAACTTCCTCCG 59.753 55.000 0.00 0.00 0.00 4.63
1389 1548 7.440523 ACTCTCAAAGTCAATAAACATGTCC 57.559 36.000 0.00 0.00 30.02 4.02
1456 1630 4.371624 TGGCCTTCTCATTTTTCTCTGA 57.628 40.909 3.32 0.00 0.00 3.27
1462 1636 3.967332 CCACATGGCCTTCTCATTTTT 57.033 42.857 3.32 0.00 0.00 1.94
1489 1664 4.154918 GGATGAAACCTCACTCACATGTTC 59.845 45.833 0.00 0.00 33.30 3.18
1773 1956 3.961408 ACTAAGGTGGTATGGTAGAGCTG 59.039 47.826 0.00 0.00 0.00 4.24
1779 1962 3.962718 GCCTGTACTAAGGTGGTATGGTA 59.037 47.826 1.52 0.00 39.75 3.25
1780 1963 2.770232 GCCTGTACTAAGGTGGTATGGT 59.230 50.000 1.52 0.00 39.75 3.55
1781 1964 2.769663 TGCCTGTACTAAGGTGGTATGG 59.230 50.000 1.52 0.00 39.75 2.74
1782 1965 3.196901 TGTGCCTGTACTAAGGTGGTATG 59.803 47.826 1.52 0.00 39.75 2.39
1783 1966 3.197116 GTGTGCCTGTACTAAGGTGGTAT 59.803 47.826 1.52 0.00 39.75 2.73
1789 1972 4.323417 TGAATTGTGTGCCTGTACTAAGG 58.677 43.478 0.00 0.00 40.63 2.69
1790 1973 5.877012 AGATGAATTGTGTGCCTGTACTAAG 59.123 40.000 0.00 0.00 0.00 2.18
1797 1982 2.159421 GCTGAGATGAATTGTGTGCCTG 60.159 50.000 0.00 0.00 0.00 4.85
1969 2154 2.162716 GCTTGTCCTGTTAGCCACG 58.837 57.895 0.00 0.00 0.00 4.94
2172 2363 5.021033 TGGAATCTTGATTGCTCTCTCTC 57.979 43.478 14.20 0.00 0.00 3.20
2173 2364 4.683942 GCTGGAATCTTGATTGCTCTCTCT 60.684 45.833 14.20 0.00 0.00 3.10
2174 2365 3.560896 GCTGGAATCTTGATTGCTCTCTC 59.439 47.826 14.20 0.00 0.00 3.20
2175 2366 3.200385 AGCTGGAATCTTGATTGCTCTCT 59.800 43.478 14.20 7.13 0.00 3.10
2176 2367 3.543665 AGCTGGAATCTTGATTGCTCTC 58.456 45.455 14.20 5.42 0.00 3.20
2177 2368 3.543665 GAGCTGGAATCTTGATTGCTCT 58.456 45.455 18.64 13.91 41.26 4.09
2280 2484 4.780815 TGTTGCATTAGAGTATTGGAGGG 58.219 43.478 0.00 0.00 0.00 4.30
2281 2485 5.295292 CACTGTTGCATTAGAGTATTGGAGG 59.705 44.000 4.88 0.00 0.00 4.30
2282 2486 6.108687 TCACTGTTGCATTAGAGTATTGGAG 58.891 40.000 4.88 0.00 0.00 3.86
2283 2487 6.048732 TCACTGTTGCATTAGAGTATTGGA 57.951 37.500 4.88 0.00 0.00 3.53
2410 2614 1.247567 ATTGTTGCCCCGACAGAAAG 58.752 50.000 0.00 0.00 0.00 2.62
2422 2626 4.114794 ACAAGCAGAGTCAAAATTGTTGC 58.885 39.130 0.00 0.00 0.00 4.17
2589 2793 3.242349 GCTGCTTCACGAGATCATCTTTG 60.242 47.826 0.00 0.00 0.00 2.77
2673 2877 6.529463 AATTTTGTGTGCTGCTTAATGTTC 57.471 33.333 0.00 0.00 0.00 3.18
2676 2880 7.485913 CCTAGTAATTTTGTGTGCTGCTTAATG 59.514 37.037 0.00 0.00 0.00 1.90
2685 2889 6.128007 ACTGCATACCTAGTAATTTTGTGTGC 60.128 38.462 7.49 7.49 42.23 4.57
2706 2910 3.001414 CCATAGAGATGCATGCTACTGC 58.999 50.000 20.33 11.24 42.62 4.40
2719 2957 5.178096 TGTTCAATCAAAGGCCATAGAGA 57.822 39.130 5.01 0.00 0.00 3.10
2773 3014 1.565390 CCTTCTCCCATCCTGGTGCA 61.565 60.000 0.00 0.00 35.17 4.57
2775 3016 1.225704 GCCTTCTCCCATCCTGGTG 59.774 63.158 0.00 0.00 35.17 4.17
2845 3086 2.953821 CCATCCAGCGTTGCGTTT 59.046 55.556 0.00 0.00 0.00 3.60
2962 3203 1.004979 AGCTCTAGGTCGGTCTTGTCT 59.995 52.381 0.00 0.00 0.00 3.41
2987 3228 0.884704 TTGGCCTTGAGCTCGACAAC 60.885 55.000 9.64 0.00 43.05 3.32
3220 3461 0.944386 GTTTTCTGCACTCGGCTTCA 59.056 50.000 0.00 0.00 45.15 3.02
3250 3491 3.849645 GCACACAAAGAACGAAGGATGTG 60.850 47.826 11.69 11.69 42.78 3.21
3266 3507 2.497173 AATGGCGCCAAAGCACACA 61.497 52.632 36.33 6.47 39.83 3.72
3553 3799 4.618635 TCTCCATCTCAAGGAAGTCATCT 58.381 43.478 0.00 0.00 34.08 2.90
3857 4103 0.835971 TGGGCCAGCTCAAGTCTACA 60.836 55.000 0.00 0.00 0.00 2.74
4108 4354 0.825010 CTGCACCCTTGACCTTTGCT 60.825 55.000 0.00 0.00 34.18 3.91
4115 4361 2.354259 CTCAATCTCTGCACCCTTGAC 58.646 52.381 0.00 0.00 0.00 3.18
4162 4408 2.554032 ACGCACCTTCTTTTGGAATGAG 59.446 45.455 0.00 0.00 33.01 2.90
4184 4430 0.914644 TTATCTTGCTGCTCCAGGCT 59.085 50.000 0.00 0.00 42.39 4.58
4291 4537 2.231964 GGCAAAGACATCTGAATTGGCA 59.768 45.455 11.46 0.00 43.57 4.92
4356 4602 4.378459 CCAGTTCTGCAATAAACGGTTCTC 60.378 45.833 0.00 0.00 0.00 2.87
4359 4605 3.482436 TCCAGTTCTGCAATAAACGGTT 58.518 40.909 0.00 0.00 0.00 4.44
4360 4606 3.134574 TCCAGTTCTGCAATAAACGGT 57.865 42.857 0.00 0.00 0.00 4.83
4366 4612 5.809001 AGTTGAGATTCCAGTTCTGCAATA 58.191 37.500 0.00 0.00 0.00 1.90
4373 4619 4.387256 CGACTTGAGTTGAGATTCCAGTTC 59.613 45.833 0.00 0.00 0.00 3.01
4459 4705 3.072184 AGGCTGATGACAAGTTCTTCTGT 59.928 43.478 0.00 0.00 32.75 3.41
4504 4750 4.764308 GTCATTTTCTTCTTCTGGGCTTCT 59.236 41.667 0.00 0.00 0.00 2.85
4530 4776 1.964223 TCTCTTTGAGCTCGAACTGGT 59.036 47.619 12.62 0.00 0.00 4.00
4533 4779 4.592485 TCTTTCTCTTTGAGCTCGAACT 57.408 40.909 12.62 0.00 0.00 3.01
4615 4861 1.877165 GGCGAACTCCGACGATTCC 60.877 63.158 0.00 0.00 41.76 3.01
4660 4906 3.261933 GGAGCTCTGCTGCACAAC 58.738 61.111 14.64 0.00 46.16 3.32
4680 4926 3.237746 TCCATTGGTTTTGGCTGATGAA 58.762 40.909 1.86 0.00 34.06 2.57
4706 4952 3.055094 AGGTCTGTACTTGCCATAGGTTG 60.055 47.826 0.00 0.00 0.00 3.77
4816 5068 6.295349 CCTGTAGAAACCAGTTACTCATCAGT 60.295 42.308 0.00 0.00 36.55 3.41
4835 5098 3.003275 CGAGCTAGCTCTTTCTCCTGTAG 59.997 52.174 35.36 16.19 40.69 2.74
4903 5166 1.654137 CGTTTTCAACTGCGCGCTT 60.654 52.632 33.29 16.87 0.00 4.68
5202 5466 8.719648 CATCTCTCCATATGAATAGTGCTTTTC 58.280 37.037 3.65 0.00 0.00 2.29
5283 5819 2.096909 CGTGTTGCAGACGAGGTTAAAG 60.097 50.000 13.51 0.00 39.21 1.85
5311 5847 7.475015 CAAGTGTTGGGTGAACATATAAGATG 58.525 38.462 0.00 0.00 46.34 2.90
5357 5893 2.953284 AGGATCTCTGCCAATGGATG 57.047 50.000 2.05 0.00 0.00 3.51
5361 5897 3.548745 TGTGTAGGATCTCTGCCAATG 57.451 47.619 0.00 0.00 0.00 2.82
5467 6003 3.865745 CCGAAGTAGCAATGGTCTAGTTG 59.134 47.826 0.00 0.00 31.75 3.16
5702 6241 5.097742 TGGAATTATTGACGTCTGACCAT 57.902 39.130 17.92 3.85 0.00 3.55


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

AutoCloner maintained by Alex Coulton.