Multiple sequence alignment - TraesCS1B01G277600

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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 TraesCS1B01G277600 chr1B 100.000 2744 0 0 1 2744 485804181 485806924 0.000000e+00 5068
1 TraesCS1B01G277600 chr1A 88.550 2786 189 48 1 2728 462122861 462125574 0.000000e+00 3258
2 TraesCS1B01G277600 chr1D 91.761 1942 92 31 1 1907 362780321 362782229 0.000000e+00 2638
3 TraesCS1B01G277600 chr1D 86.528 527 66 4 2205 2727 479133064 479132539 2.370000e-160 575
4 TraesCS1B01G277600 chr3B 87.311 528 65 2 2201 2728 585028822 585029347 1.090000e-168 603
5 TraesCS1B01G277600 chr5B 86.882 526 66 3 2201 2725 577250734 577250211 1.090000e-163 586
6 TraesCS1B01G277600 chr4D 86.667 525 66 4 2203 2725 72533666 72534188 1.830000e-161 579
7 TraesCS1B01G277600 chr4D 86.011 529 67 7 2201 2726 445088744 445089268 6.640000e-156 560
8 TraesCS1B01G277600 chr6A 86.174 528 69 4 2201 2727 572592656 572593180 3.970000e-158 568
9 TraesCS1B01G277600 chr3D 86.174 528 69 4 2201 2727 512503520 512502996 3.970000e-158 568
10 TraesCS1B01G277600 chr3D 86.174 528 66 6 2201 2727 305882578 305883099 5.130000e-157 564
11 TraesCS1B01G277600 chr3D 85.878 524 72 2 2201 2724 382944731 382945252 8.580000e-155 556


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 TraesCS1B01G277600 chr1B 485804181 485806924 2743 False 5068 5068 100.000 1 2744 1 chr1B.!!$F1 2743
1 TraesCS1B01G277600 chr1A 462122861 462125574 2713 False 3258 3258 88.550 1 2728 1 chr1A.!!$F1 2727
2 TraesCS1B01G277600 chr1D 362780321 362782229 1908 False 2638 2638 91.761 1 1907 1 chr1D.!!$F1 1906
3 TraesCS1B01G277600 chr1D 479132539 479133064 525 True 575 575 86.528 2205 2727 1 chr1D.!!$R1 522
4 TraesCS1B01G277600 chr3B 585028822 585029347 525 False 603 603 87.311 2201 2728 1 chr3B.!!$F1 527
5 TraesCS1B01G277600 chr5B 577250211 577250734 523 True 586 586 86.882 2201 2725 1 chr5B.!!$R1 524
6 TraesCS1B01G277600 chr4D 72533666 72534188 522 False 579 579 86.667 2203 2725 1 chr4D.!!$F1 522
7 TraesCS1B01G277600 chr4D 445088744 445089268 524 False 560 560 86.011 2201 2726 1 chr4D.!!$F2 525
8 TraesCS1B01G277600 chr6A 572592656 572593180 524 False 568 568 86.174 2201 2727 1 chr6A.!!$F1 526
9 TraesCS1B01G277600 chr3D 512502996 512503520 524 True 568 568 86.174 2201 2727 1 chr3D.!!$R1 526
10 TraesCS1B01G277600 chr3D 305882578 305883099 521 False 564 564 86.174 2201 2727 1 chr3D.!!$F1 526
11 TraesCS1B01G277600 chr3D 382944731 382945252 521 False 556 556 85.878 2201 2724 1 chr3D.!!$F2 523

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
836 878 0.175073 GATACGTCTTCAGGGGCGTT 59.825 55.0 0.0 0.0 38.56 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2151 2224 0.034283 ACGGACTAGTCCCCTGTCTC 60.034 60.0 31.78 8.64 46.96 3.36 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
82 84 7.699391 ACATGATTCTGTGATTATTTTTCTGCG 59.301 33.333 0.00 0.00 0.00 5.18
104 106 0.743701 ATTCTCTCTTGCAGCAGCCG 60.744 55.000 0.00 0.00 41.13 5.52
105 107 2.793160 TTCTCTCTTGCAGCAGCCGG 62.793 60.000 0.00 0.00 41.13 6.13
122 124 1.610673 GGCCCTCTCACCAGTCTCA 60.611 63.158 0.00 0.00 0.00 3.27
225 233 2.444033 TCCTTTTGTTCCTCCCCCTA 57.556 50.000 0.00 0.00 0.00 3.53
274 283 1.134280 CCATTGCCCGAGTGAGATCTT 60.134 52.381 0.00 0.00 0.00 2.40
326 347 8.625651 CGTACTATATCCAAGCTATATTGCTCT 58.374 37.037 12.14 0.77 43.24 4.09
356 377 1.341080 AGGGTTGGTTCTTGGCATTG 58.659 50.000 0.00 0.00 0.00 2.82
432 465 5.479724 GGAGGTGGTACTACTAAAAGTGAGT 59.520 44.000 9.41 0.00 0.00 3.41
518 558 2.046217 GGGTTTCAGCCCGTCCTC 60.046 66.667 0.00 0.00 39.17 3.71
533 573 2.588989 CTCCTGCTTCCCTGCTCC 59.411 66.667 0.00 0.00 0.00 4.70
582 622 6.822676 AGCTTTATTCTTGACTTGATGAGAGG 59.177 38.462 0.00 0.00 0.00 3.69
683 723 1.251251 GCAGTTGCCAATTCTGGACT 58.749 50.000 0.00 0.00 46.92 3.85
686 726 1.177401 GTTGCCAATTCTGGACTCCC 58.823 55.000 0.00 0.00 46.92 4.30
692 732 1.003118 CAATTCTGGACTCCCGGTTCA 59.997 52.381 0.00 0.00 39.88 3.18
763 805 5.499004 AACAAATGCTAGAGTGGAAGGTA 57.501 39.130 0.00 0.00 0.00 3.08
789 831 3.267483 ACGTGCCGCAAGTTTCTTATAT 58.733 40.909 6.09 0.00 0.00 0.86
796 838 6.806249 TGCCGCAAGTTTCTTATATTTTTCTG 59.194 34.615 0.00 0.00 0.00 3.02
820 862 5.678871 GCCTCTTCACATGTAGAACGTGATA 60.679 44.000 0.00 0.00 39.29 2.15
836 878 0.175073 GATACGTCTTCAGGGGCGTT 59.825 55.000 0.00 0.00 38.56 4.84
861 903 2.997899 GCATGGCGAGCAGATAACT 58.002 52.632 0.00 0.00 0.00 2.24
862 904 0.864455 GCATGGCGAGCAGATAACTC 59.136 55.000 0.00 0.00 0.00 3.01
863 905 1.807755 GCATGGCGAGCAGATAACTCA 60.808 52.381 0.00 0.00 33.58 3.41
864 906 2.133553 CATGGCGAGCAGATAACTCAG 58.866 52.381 0.00 0.00 33.58 3.35
865 907 1.474330 TGGCGAGCAGATAACTCAGA 58.526 50.000 0.00 0.00 33.58 3.27
866 908 2.034878 TGGCGAGCAGATAACTCAGAT 58.965 47.619 0.00 0.00 33.58 2.90
871 913 4.022762 GCGAGCAGATAACTCAGATAAGGA 60.023 45.833 0.00 0.00 33.58 3.36
873 915 5.563867 CGAGCAGATAACTCAGATAAGGACC 60.564 48.000 0.00 0.00 33.58 4.46
874 916 5.463154 AGCAGATAACTCAGATAAGGACCT 58.537 41.667 0.00 0.00 0.00 3.85
876 918 5.303078 GCAGATAACTCAGATAAGGACCTGA 59.697 44.000 0.00 0.00 37.77 3.86
900 942 0.392998 CTCAGCCGTATTTGGTGCCT 60.393 55.000 0.00 0.00 0.00 4.75
932 978 3.740128 CTAGGCGGTGGAGCGCAAT 62.740 63.158 23.04 13.95 38.18 3.56
942 988 0.881118 GGAGCGCAATTGAAGAACCA 59.119 50.000 11.47 0.00 0.00 3.67
944 990 2.288152 GGAGCGCAATTGAAGAACCAAA 60.288 45.455 11.47 0.00 0.00 3.28
955 1001 4.792068 TGAAGAACCAAACCAAGATCACT 58.208 39.130 0.00 0.00 0.00 3.41
966 1013 3.834813 ACCAAGATCACTGAAGAGCTGTA 59.165 43.478 0.00 0.00 33.95 2.74
1017 1064 4.087892 ATGAGCAGCTTCGCGGGT 62.088 61.111 6.13 0.00 37.15 5.28
1191 1238 1.891933 TGTTCCTCCTCATGGCCATA 58.108 50.000 20.30 0.95 0.00 2.74
1358 1411 2.437895 GCCTCCGCCCAAGGTAAC 60.438 66.667 0.00 0.00 36.21 2.50
1393 1450 2.100631 GCTTCCGCGAGCTGCTTTA 61.101 57.895 8.23 0.00 43.27 1.85
1397 1454 0.736325 TCCGCGAGCTGCTTTACTTC 60.736 55.000 8.23 0.00 43.27 3.01
1398 1455 1.696832 CCGCGAGCTGCTTTACTTCC 61.697 60.000 8.23 0.00 43.27 3.46
1432 1494 3.632107 GCGTTCGGTTCACGTGCA 61.632 61.111 11.67 0.00 44.69 4.57
1458 1520 0.389391 CAGTGGTGACAAGAGGACGT 59.611 55.000 0.00 0.00 46.06 4.34
1590 1661 2.787249 CGTTTGCAGATGGAGGCG 59.213 61.111 0.00 0.00 0.00 5.52
1865 1937 0.171231 GCGAAGGAAAATGCTGGACC 59.829 55.000 0.00 0.00 0.00 4.46
1900 1972 3.129813 TGAGCAGCATTCAATTCATGTCC 59.870 43.478 0.00 0.00 0.00 4.02
1917 1989 1.819903 GTCCAGTTAGTCTCGCCTCTT 59.180 52.381 0.00 0.00 0.00 2.85
1929 2001 1.078143 GCCTCTTGGTCGAATGCCT 60.078 57.895 0.00 0.00 35.27 4.75
1956 2028 8.026396 TCTTCATGTTATGATCTTCCATCTGA 57.974 34.615 0.00 0.00 39.39 3.27
1987 2059 3.706698 TCGAGTGGCATTCTTCTAATCG 58.293 45.455 8.43 0.00 0.00 3.34
1989 2061 3.738281 CGAGTGGCATTCTTCTAATCGGT 60.738 47.826 8.43 0.00 0.00 4.69
1990 2062 4.192317 GAGTGGCATTCTTCTAATCGGTT 58.808 43.478 2.33 0.00 0.00 4.44
1991 2063 4.589908 AGTGGCATTCTTCTAATCGGTTT 58.410 39.130 0.00 0.00 0.00 3.27
1992 2064 5.010282 AGTGGCATTCTTCTAATCGGTTTT 58.990 37.500 0.00 0.00 0.00 2.43
1993 2065 5.123979 AGTGGCATTCTTCTAATCGGTTTTC 59.876 40.000 0.00 0.00 0.00 2.29
1994 2066 4.398044 TGGCATTCTTCTAATCGGTTTTCC 59.602 41.667 0.00 0.00 0.00 3.13
1995 2067 4.640647 GGCATTCTTCTAATCGGTTTTCCT 59.359 41.667 0.00 0.00 37.95 3.36
1996 2068 5.125578 GGCATTCTTCTAATCGGTTTTCCTT 59.874 40.000 0.00 0.00 37.95 3.36
1997 2069 6.350194 GGCATTCTTCTAATCGGTTTTCCTTT 60.350 38.462 0.00 0.00 37.95 3.11
1998 2070 7.090808 GCATTCTTCTAATCGGTTTTCCTTTT 58.909 34.615 0.00 0.00 37.95 2.27
2030 2102 5.586339 TCTGCGAGTTCTTCTAATCTGATG 58.414 41.667 0.00 0.00 0.00 3.07
2038 2110 4.433615 TCTTCTAATCTGATGAACGGTGC 58.566 43.478 0.00 0.00 0.00 5.01
2089 2162 6.371825 AGGAATTAAAGAAAGTGGAGCTAACG 59.628 38.462 0.00 0.00 0.00 3.18
2117 2190 4.530875 CTCAAACTTAGGGCATCTCCAAT 58.469 43.478 0.00 0.00 36.21 3.16
2118 2191 4.272489 TCAAACTTAGGGCATCTCCAATG 58.728 43.478 0.00 0.00 36.21 2.82
2119 2192 4.018506 TCAAACTTAGGGCATCTCCAATGA 60.019 41.667 0.00 0.00 36.21 2.57
2120 2193 4.803329 AACTTAGGGCATCTCCAATGAT 57.197 40.909 0.00 0.00 36.21 2.45
2123 2196 2.875094 AGGGCATCTCCAATGATAGC 57.125 50.000 0.00 0.00 36.21 2.97
2127 2200 1.446907 CATCTCCAATGATAGCCCGC 58.553 55.000 0.00 0.00 0.00 6.13
2130 2203 1.211703 TCTCCAATGATAGCCCGCAAA 59.788 47.619 0.00 0.00 0.00 3.68
2140 2213 0.243636 AGCCCGCAAATTTTCTTCCG 59.756 50.000 0.00 0.00 0.00 4.30
2142 2215 1.070471 CCCGCAAATTTTCTTCCGCG 61.070 55.000 10.39 10.39 42.21 6.46
2146 2219 1.335506 GCAAATTTTCTTCCGCGTCCA 60.336 47.619 4.92 0.00 0.00 4.02
2150 2223 1.438651 TTTTCTTCCGCGTCCATCAG 58.561 50.000 4.92 0.00 0.00 2.90
2151 2224 0.391130 TTTCTTCCGCGTCCATCAGG 60.391 55.000 4.92 0.00 0.00 3.86
2152 2225 1.254975 TTCTTCCGCGTCCATCAGGA 61.255 55.000 4.92 0.00 43.21 3.86
2162 2235 0.325671 TCCATCAGGAGACAGGGGAC 60.326 60.000 0.00 0.00 39.61 4.46
2163 2236 0.326048 CCATCAGGAGACAGGGGACT 60.326 60.000 0.00 0.00 38.30 3.85
2180 2253 1.199558 GACTAGTCCGTGGACACAGAC 59.800 57.143 20.51 10.10 46.76 3.51
2182 2255 0.535780 TAGTCCGTGGACACAGACGT 60.536 55.000 20.51 0.00 46.76 4.34
2187 2260 0.594602 CGTGGACACAGACGTAGGAA 59.405 55.000 3.12 0.00 0.00 3.36
2191 2264 1.884579 GGACACAGACGTAGGAAGACA 59.115 52.381 0.00 0.00 0.00 3.41
2192 2265 2.095161 GGACACAGACGTAGGAAGACAG 60.095 54.545 0.00 0.00 0.00 3.51
2193 2266 2.553172 GACACAGACGTAGGAAGACAGT 59.447 50.000 0.00 0.00 0.00 3.55
2195 2268 3.752222 ACACAGACGTAGGAAGACAGTAG 59.248 47.826 0.00 0.00 0.00 2.57
2196 2269 2.748532 ACAGACGTAGGAAGACAGTAGC 59.251 50.000 0.00 0.00 0.00 3.58
2197 2270 2.097791 CAGACGTAGGAAGACAGTAGCC 59.902 54.545 0.00 0.00 0.00 3.93
2198 2271 1.063764 GACGTAGGAAGACAGTAGCCG 59.936 57.143 0.00 0.00 0.00 5.52
2199 2272 1.339438 ACGTAGGAAGACAGTAGCCGA 60.339 52.381 0.00 0.00 0.00 5.54
2212 2285 0.444651 TAGCCGAATTTCAAACCGCG 59.555 50.000 0.00 0.00 0.00 6.46
2230 2303 3.969981 CCGCGTTTTAACTAACCAAACAG 59.030 43.478 4.92 0.00 31.81 3.16
2283 2357 6.961554 CGAAGTTTGGATAGAAAATAGCACAC 59.038 38.462 0.00 0.00 0.00 3.82
2301 2375 6.762333 AGCACACATCATCTATACATAGCAA 58.238 36.000 0.00 0.00 0.00 3.91
2439 2520 2.766970 GTGTGTGCACGTAAATGGTT 57.233 45.000 13.13 0.00 35.75 3.67
2442 2523 1.784283 GTGTGCACGTAAATGGTTTGC 59.216 47.619 13.13 0.00 0.00 3.68
2444 2525 0.039978 TGCACGTAAATGGTTTGCCG 60.040 50.000 0.00 0.00 37.67 5.69
2456 2537 1.291132 GTTTGCCGCTCTGTCCTATC 58.709 55.000 0.00 0.00 0.00 2.08
2493 2574 4.055360 TGCGTGTGGACTACATATAATGC 58.945 43.478 0.00 0.00 42.24 3.56
2551 2632 4.822350 AGTTGAGCAAGAGGAAGTAAAACC 59.178 41.667 0.00 0.00 0.00 3.27
2624 2706 9.332502 TGACTAACTAAGTTGCAAAACTTGATA 57.667 29.630 13.00 4.08 42.47 2.15
2634 2716 4.098416 GCAAAACTTGATAACGCTGATCC 58.902 43.478 0.00 0.00 0.00 3.36
2649 2731 0.753262 GATCCGGATAGTGTGCCAGT 59.247 55.000 19.15 0.00 0.00 4.00
2651 2733 1.399714 TCCGGATAGTGTGCCAGTAG 58.600 55.000 0.00 0.00 0.00 2.57
2652 2734 0.249489 CCGGATAGTGTGCCAGTAGC 60.249 60.000 0.00 0.00 44.14 3.58
2663 2745 1.344942 GCCAGTAGCACGACAACGAG 61.345 60.000 0.00 0.00 42.97 4.18
2728 2810 1.721133 GCTTTCGTGCGTGAAACCG 60.721 57.895 0.00 0.00 34.34 4.44
2736 2818 3.022287 CGTGAAACCGCACTTGCT 58.978 55.556 0.00 0.00 39.32 3.91
2737 2819 1.082756 CGTGAAACCGCACTTGCTC 60.083 57.895 0.00 0.00 39.32 4.26
2738 2820 1.082756 GTGAAACCGCACTTGCTCG 60.083 57.895 0.00 0.00 39.32 5.03
2739 2821 2.127232 GAAACCGCACTTGCTCGC 60.127 61.111 0.00 0.00 39.32 5.03
2740 2822 2.892334 GAAACCGCACTTGCTCGCA 61.892 57.895 0.00 0.00 39.32 5.10
2741 2823 2.770587 GAAACCGCACTTGCTCGCAG 62.771 60.000 0.00 0.00 39.32 5.18
2742 2824 3.807631 AACCGCACTTGCTCGCAGA 62.808 57.895 0.00 0.00 39.32 4.26
2743 2825 3.043713 CCGCACTTGCTCGCAGAA 61.044 61.111 0.00 0.00 39.32 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
82 84 0.733729 CTGCTGCAAGAGAGAATGGC 59.266 55.000 3.02 0.00 34.07 4.40
104 106 0.980231 ATGAGACTGGTGAGAGGGCC 60.980 60.000 0.00 0.00 0.00 5.80
105 107 0.177604 CATGAGACTGGTGAGAGGGC 59.822 60.000 0.00 0.00 0.00 5.19
116 118 1.769465 AGCCTGATGATGCATGAGACT 59.231 47.619 2.46 0.00 26.55 3.24
122 124 2.430248 TCAACAGCCTGATGATGCAT 57.570 45.000 0.00 0.00 0.00 3.96
225 233 0.621862 GGAGGGGAGGAGTGGTCAAT 60.622 60.000 0.00 0.00 0.00 2.57
274 283 8.434392 GTCTCTCTCTATCTACTTAAAGGGAGA 58.566 40.741 2.89 2.89 42.04 3.71
326 347 1.426751 ACCAACCCTACAAGACGGAA 58.573 50.000 0.00 0.00 0.00 4.30
356 377 2.818132 CATCCAGTCCTCGAGCCC 59.182 66.667 6.99 0.00 0.00 5.19
398 431 4.421515 CCACCTCCCTGCAGCTGG 62.422 72.222 17.12 11.43 0.00 4.85
432 465 3.626670 CACCAAATTGCAGGCAAAAGAAA 59.373 39.130 11.10 0.00 39.55 2.52
518 558 1.970352 GAGAGGAGCAGGGAAGCAGG 61.970 65.000 0.00 0.00 36.85 4.85
533 573 7.206981 TGAAAAGCATACAGAAAAAGGAGAG 57.793 36.000 0.00 0.00 0.00 3.20
582 622 5.932303 TGTAGAGTATCCTGTTTGTTTCTGC 59.068 40.000 0.00 0.00 33.66 4.26
683 723 1.002624 GTGGCAATCTGAACCGGGA 60.003 57.895 6.32 0.00 0.00 5.14
686 726 0.888736 TGGTGTGGCAATCTGAACCG 60.889 55.000 0.00 0.00 0.00 4.44
692 732 0.607489 GCACTCTGGTGTGGCAATCT 60.607 55.000 0.00 0.00 44.65 2.40
789 831 5.620206 TCTACATGTGAAGAGGCAGAAAAA 58.380 37.500 9.11 0.00 0.00 1.94
796 838 2.668457 CACGTTCTACATGTGAAGAGGC 59.332 50.000 9.11 1.02 44.34 4.70
820 862 1.291272 GTAACGCCCCTGAAGACGT 59.709 57.895 0.00 0.00 41.16 4.34
860 902 5.362143 TGAGTTCATCAGGTCCTTATCTGAG 59.638 44.000 0.00 0.00 45.96 3.35
861 903 5.272402 TGAGTTCATCAGGTCCTTATCTGA 58.728 41.667 0.00 0.00 46.79 3.27
862 904 5.604758 TGAGTTCATCAGGTCCTTATCTG 57.395 43.478 0.00 0.00 34.92 2.90
874 916 3.270027 CCAAATACGGCTGAGTTCATCA 58.730 45.455 0.00 0.00 36.21 3.07
876 918 3.009723 CACCAAATACGGCTGAGTTCAT 58.990 45.455 0.00 0.00 0.00 2.57
890 932 0.614812 GGGAAATGCAGGCACCAAAT 59.385 50.000 0.00 0.00 0.00 2.32
900 942 1.614711 CCTAGGCAGGGGAAATGCA 59.385 57.895 0.00 0.00 45.68 3.96
928 970 4.692228 TCTTGGTTTGGTTCTTCAATTGC 58.308 39.130 0.00 0.00 0.00 3.56
932 978 5.067674 CAGTGATCTTGGTTTGGTTCTTCAA 59.932 40.000 0.00 0.00 0.00 2.69
942 988 4.070716 CAGCTCTTCAGTGATCTTGGTTT 58.929 43.478 0.00 0.00 0.00 3.27
944 990 2.636893 ACAGCTCTTCAGTGATCTTGGT 59.363 45.455 0.00 0.00 0.00 3.67
966 1013 3.735029 GACCGACCACTCGCTCGT 61.735 66.667 0.00 0.00 38.70 4.18
975 1022 2.407428 CGAGCTAGCTGACCGACCA 61.407 63.158 24.99 0.00 0.00 4.02
977 1024 0.040781 GATCGAGCTAGCTGACCGAC 60.041 60.000 24.99 14.72 31.85 4.79
984 1031 1.175347 TCATGGCGATCGAGCTAGCT 61.175 55.000 19.45 19.45 37.29 3.32
1017 1064 2.031012 CACGGCCTTGACTGCTGA 59.969 61.111 2.29 0.00 38.49 4.26
1191 1238 1.661341 GCTTGATGAGGTGCTCGAAT 58.339 50.000 0.00 0.00 32.35 3.34
1494 1560 1.209898 CCCGTACGCACGTAGTCAA 59.790 57.895 10.49 0.00 46.96 3.18
1711 1782 2.280186 GGGACGGCGATGGTCATC 60.280 66.667 16.62 0.00 36.12 2.92
1725 1796 2.045045 CATGGCGGCAGAAAGGGA 60.045 61.111 19.29 0.00 0.00 4.20
1865 1937 2.294512 TGCTGCTCATCTACTACCATCG 59.705 50.000 0.00 0.00 0.00 3.84
1900 1972 1.546476 ACCAAGAGGCGAGACTAACTG 59.454 52.381 0.00 0.00 39.06 3.16
1917 1989 2.559698 TGAAGAAAGGCATTCGACCA 57.440 45.000 0.00 0.00 43.15 4.02
1929 2001 9.117183 CAGATGGAAGATCATAACATGAAGAAA 57.883 33.333 0.00 0.00 43.50 2.52
1956 2028 0.904649 TGCCACTCGATCCACTCATT 59.095 50.000 0.00 0.00 0.00 2.57
1998 2070 6.436843 AGAAGAACTCGCAGAAAAGAAAAA 57.563 33.333 0.00 0.00 34.09 1.94
2003 2075 6.587990 TCAGATTAGAAGAACTCGCAGAAAAG 59.412 38.462 0.00 0.00 34.09 2.27
2008 2080 5.586339 TCATCAGATTAGAAGAACTCGCAG 58.414 41.667 0.00 0.00 0.00 5.18
2030 2102 1.001706 GAACCTTTTGAGGCACCGTTC 60.002 52.381 0.00 0.00 0.00 3.95
2062 2134 4.460731 AGCTCCACTTTCTTTAATTCCTGC 59.539 41.667 0.00 0.00 0.00 4.85
2089 2162 3.366052 TGCCCTAAGTTTGAGGATTCC 57.634 47.619 0.00 0.00 35.99 3.01
2117 2190 3.130340 GGAAGAAAATTTGCGGGCTATCA 59.870 43.478 0.00 0.00 0.00 2.15
2118 2191 3.706698 GGAAGAAAATTTGCGGGCTATC 58.293 45.455 0.00 0.00 0.00 2.08
2119 2192 2.099098 CGGAAGAAAATTTGCGGGCTAT 59.901 45.455 0.00 0.00 38.10 2.97
2120 2193 1.470890 CGGAAGAAAATTTGCGGGCTA 59.529 47.619 0.00 0.00 38.10 3.93
2123 2196 1.070471 CGCGGAAGAAAATTTGCGGG 61.070 55.000 9.69 2.83 45.03 6.13
2127 2200 2.697431 TGGACGCGGAAGAAAATTTG 57.303 45.000 12.47 0.00 0.00 2.32
2130 2203 2.009774 CTGATGGACGCGGAAGAAAAT 58.990 47.619 12.47 0.00 0.00 1.82
2140 2213 1.142748 CCTGTCTCCTGATGGACGC 59.857 63.158 0.00 0.00 37.46 5.19
2142 2215 0.325671 TCCCCTGTCTCCTGATGGAC 60.326 60.000 0.00 0.00 37.46 4.02
2146 2219 1.933765 ACTAGTCCCCTGTCTCCTGAT 59.066 52.381 0.00 0.00 0.00 2.90
2150 2223 0.752376 CGGACTAGTCCCCTGTCTCC 60.752 65.000 31.78 8.69 46.96 3.71
2151 2224 0.034283 ACGGACTAGTCCCCTGTCTC 60.034 60.000 31.78 8.64 46.96 3.36
2152 2225 0.323542 CACGGACTAGTCCCCTGTCT 60.324 60.000 31.78 8.37 46.96 3.41
2175 2248 2.748532 GCTACTGTCTTCCTACGTCTGT 59.251 50.000 0.00 0.00 0.00 3.41
2180 2253 1.376543 TCGGCTACTGTCTTCCTACG 58.623 55.000 0.00 0.00 0.00 3.51
2182 2255 4.464951 TGAAATTCGGCTACTGTCTTCCTA 59.535 41.667 0.00 0.00 0.00 2.94
2187 2260 3.751698 GGTTTGAAATTCGGCTACTGTCT 59.248 43.478 0.00 0.00 0.00 3.41
2191 2264 1.467342 GCGGTTTGAAATTCGGCTACT 59.533 47.619 5.96 0.00 0.00 2.57
2192 2265 1.789054 CGCGGTTTGAAATTCGGCTAC 60.789 52.381 0.00 0.00 0.00 3.58
2193 2266 0.444651 CGCGGTTTGAAATTCGGCTA 59.555 50.000 0.00 0.00 0.00 3.93
2195 2268 0.662077 AACGCGGTTTGAAATTCGGC 60.662 50.000 12.47 0.00 0.00 5.54
2196 2269 1.761206 AAACGCGGTTTGAAATTCGG 58.239 45.000 12.47 0.62 34.23 4.30
2197 2270 4.438471 AGTTAAAACGCGGTTTGAAATTCG 59.562 37.500 31.24 0.53 35.80 3.34
2198 2271 5.876576 AGTTAAAACGCGGTTTGAAATTC 57.123 34.783 31.24 11.66 35.80 2.17
2199 2272 6.198778 GGTTAGTTAAAACGCGGTTTGAAATT 59.801 34.615 31.24 17.32 35.80 1.82
2230 2303 1.135315 TCAGCCGCTTTGCATGAATTC 60.135 47.619 0.00 0.00 0.00 2.17
2301 2375 8.846211 ACATTGTTGTACTACACTTAATTTGCT 58.154 29.630 9.75 0.00 33.16 3.91
2313 2387 8.796278 GTCGAATTAGAGACATTGTTGTACTAC 58.204 37.037 0.05 0.05 35.79 2.73
2438 2519 0.179111 CGATAGGACAGAGCGGCAAA 60.179 55.000 1.45 0.00 0.00 3.68
2439 2520 1.320344 ACGATAGGACAGAGCGGCAA 61.320 55.000 1.45 0.00 43.77 4.52
2471 2552 4.055360 GCATTATATGTAGTCCACACGCA 58.945 43.478 0.00 0.00 40.86 5.24
2493 2574 4.929211 TCATTCACTCAATGTTGGTCTACG 59.071 41.667 0.00 0.00 42.47 3.51
2526 2607 6.431278 GTTTTACTTCCTCTTGCTCAACTTC 58.569 40.000 0.00 0.00 0.00 3.01
2551 2632 6.837591 ATGCGGACATGAACGAGATCGTAG 62.838 50.000 8.50 2.39 43.20 3.51
2624 2706 1.112113 ACACTATCCGGATCAGCGTT 58.888 50.000 23.08 0.00 0.00 4.84
2634 2716 3.274393 GCTACTGGCACACTATCCG 57.726 57.895 0.00 0.00 41.35 4.18
2652 2734 1.657487 ACGTGAGCTCGTTGTCGTG 60.657 57.895 9.64 0.00 41.37 4.35


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

AutoCloner maintained by Alex Coulton.