Multiple sequence alignment - TraesCS7A01G326800

Loading Multiple Alignment...

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 TraesCS7A01G326800 chr7A 100.000 3305 0 0 1 3305 474791310 474788006 0 6104
1 TraesCS7A01G326800 chr7D 94.261 2509 82 10 808 3305 413248480 413246023 0 3779
2 TraesCS7A01G326800 chr7D 92.545 778 44 9 3 771 413249251 413248479 0 1103
3 TraesCS7A01G326800 chr7B 94.783 1725 55 8 1589 3305 427711631 427709934 0 2654
4 TraesCS7A01G326800 chr7B 90.102 1566 105 27 3 1548 427713163 427711628 0 1988


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 TraesCS7A01G326800 chr7A 474788006 474791310 3304 True 6104 6104 100.0000 1 3305 1 chr7A.!!$R1 3304
1 TraesCS7A01G326800 chr7D 413246023 413249251 3228 True 2441 3779 93.4030 3 3305 2 chr7D.!!$R1 3302
2 TraesCS7A01G326800 chr7B 427709934 427713163 3229 True 2321 2654 92.4425 3 3305 2 chr7B.!!$R1 3302

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
776 796 0.038166 TCCCAACTGATGCCAAGGAC 59.962 55.0 0.0 0.0 0.0 3.85 F
777 797 0.038744 CCCAACTGATGCCAAGGACT 59.961 55.0 0.0 0.0 0.0 3.85 F
1035 1095 0.519961 ATTACCGTTGCTTCGTTGGC 59.480 50.0 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2007 2070 0.549902 TGTCCCCACCATCACCAGAT 60.550 55.000 0.0 0.0 33.87 2.90 R
2078 2141 0.905357 ACTGTACCTGTCATCCCTGC 59.095 55.000 0.0 0.0 0.00 4.85 R
2939 3010 1.623811 TCTAACTGAGGGAAGTGCCAC 59.376 52.381 0.0 0.0 38.95 5.01 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 4.220602 GCTTGATTCTAAAAGGGCAAAGGA 59.779 41.667 0.00 0.00 0.00 3.36
37 38 4.735369 TGATTCTAAAAGGGCAAAGGACA 58.265 39.130 0.00 0.00 0.00 4.02
69 70 5.360591 ACAAGAACCGTTGATCTATGATCC 58.639 41.667 5.27 0.00 0.00 3.36
77 78 2.160205 TGATCTATGATCCGACGGTCC 58.840 52.381 14.79 7.52 0.00 4.46
115 117 6.351711 GGCTGGAGTCTGCAGTATATATTGAT 60.352 42.308 21.00 0.00 38.17 2.57
178 180 3.268034 AAAGGGGAGACAGAAGAGAGT 57.732 47.619 0.00 0.00 0.00 3.24
183 185 3.020984 GGGAGACAGAAGAGAGTTCGAT 58.979 50.000 0.00 0.00 0.00 3.59
289 291 3.064134 TCAATCTCTTCGTCTAGCTGTCG 59.936 47.826 0.00 0.00 0.00 4.35
332 335 3.623510 GGTTTAGATCTGAGCTTTTCCCG 59.376 47.826 5.18 0.00 0.00 5.14
398 409 3.651562 AATTCGATCGCCGTTTGTTAG 57.348 42.857 11.09 0.00 39.75 2.34
408 419 4.152759 TCGCCGTTTGTTAGAATAGGTTTG 59.847 41.667 0.00 0.00 0.00 2.93
451 462 2.593925 AAGAAGGGGCTCTCCTTTTG 57.406 50.000 2.06 0.00 46.31 2.44
478 489 4.519730 TCAATTTCACCGGTTAATTTCCGT 59.480 37.500 17.63 0.00 45.63 4.69
480 491 1.712401 TCACCGGTTAATTTCCGTCG 58.288 50.000 2.97 9.67 45.63 5.12
481 492 1.271934 TCACCGGTTAATTTCCGTCGA 59.728 47.619 2.97 11.25 45.63 4.20
516 529 0.461548 TCTCGTGGCTTGCCTCTATG 59.538 55.000 13.18 0.00 0.00 2.23
528 542 3.801698 TGCCTCTATGCTTGTTCTGATC 58.198 45.455 0.00 0.00 0.00 2.92
548 562 0.963962 AGTCACGGCGGAAGACTTTA 59.036 50.000 20.81 0.00 39.45 1.85
555 569 3.435671 ACGGCGGAAGACTTTATTCTTTG 59.564 43.478 13.24 0.00 35.90 2.77
557 571 4.628333 CGGCGGAAGACTTTATTCTTTGTA 59.372 41.667 0.00 0.00 35.90 2.41
558 572 5.121142 CGGCGGAAGACTTTATTCTTTGTAA 59.879 40.000 0.00 0.00 35.90 2.41
582 600 4.021102 AGTTTGTGGTGGTAGATTGAGG 57.979 45.455 0.00 0.00 0.00 3.86
600 618 5.836024 TGAGGTACAATTTGGGTAAGAGT 57.164 39.130 0.78 0.00 0.00 3.24
604 622 8.044908 TGAGGTACAATTTGGGTAAGAGTAATC 58.955 37.037 0.78 0.00 0.00 1.75
605 623 7.344134 AGGTACAATTTGGGTAAGAGTAATCC 58.656 38.462 0.78 0.00 0.00 3.01
606 624 6.544931 GGTACAATTTGGGTAAGAGTAATCCC 59.455 42.308 0.78 0.00 40.26 3.85
609 627 6.194967 CAATTTGGGTAAGAGTAATCCCCTT 58.805 40.000 4.88 0.00 39.20 3.95
610 628 5.871324 TTTGGGTAAGAGTAATCCCCTTT 57.129 39.130 4.88 0.00 39.20 3.11
611 629 6.973700 TTTGGGTAAGAGTAATCCCCTTTA 57.026 37.500 4.88 0.00 39.20 1.85
612 630 6.570654 TTGGGTAAGAGTAATCCCCTTTAG 57.429 41.667 4.88 0.00 39.20 1.85
639 659 2.618709 CAAAAGCAAGAAGAACGACCCT 59.381 45.455 0.00 0.00 0.00 4.34
640 660 1.884235 AAGCAAGAAGAACGACCCTG 58.116 50.000 0.00 0.00 0.00 4.45
682 702 9.835389 CTTCTAGGTTGTCTACTAGTACTATGT 57.165 37.037 2.33 6.64 38.24 2.29
683 703 9.829507 TTCTAGGTTGTCTACTAGTACTATGTC 57.170 37.037 2.33 0.00 38.24 3.06
707 727 3.005554 GCTAAGTGCTTCTGCTCATTCA 58.994 45.455 0.00 0.00 40.48 2.57
745 765 3.995199 TGAGATGTTCAGGCGGATAATC 58.005 45.455 0.00 0.00 0.00 1.75
769 789 4.421365 TTGCCTCCCAACTGATGC 57.579 55.556 0.00 0.00 0.00 3.91
770 790 1.304381 TTGCCTCCCAACTGATGCC 60.304 57.895 0.00 0.00 0.00 4.40
771 791 2.079088 TTGCCTCCCAACTGATGCCA 62.079 55.000 0.00 0.00 0.00 4.92
772 792 1.304381 GCCTCCCAACTGATGCCAA 60.304 57.895 0.00 0.00 0.00 4.52
773 793 1.318158 GCCTCCCAACTGATGCCAAG 61.318 60.000 0.00 0.00 0.00 3.61
774 794 0.682209 CCTCCCAACTGATGCCAAGG 60.682 60.000 0.00 0.00 0.00 3.61
775 795 0.329261 CTCCCAACTGATGCCAAGGA 59.671 55.000 0.00 0.00 0.00 3.36
776 796 0.038166 TCCCAACTGATGCCAAGGAC 59.962 55.000 0.00 0.00 0.00 3.85
777 797 0.038744 CCCAACTGATGCCAAGGACT 59.961 55.000 0.00 0.00 0.00 3.85
778 798 1.171308 CCAACTGATGCCAAGGACTG 58.829 55.000 0.00 0.00 0.00 3.51
779 799 1.271543 CCAACTGATGCCAAGGACTGA 60.272 52.381 0.00 0.00 0.00 3.41
780 800 2.507484 CAACTGATGCCAAGGACTGAA 58.493 47.619 0.00 0.00 0.00 3.02
781 801 2.486472 ACTGATGCCAAGGACTGAAG 57.514 50.000 0.00 0.00 0.00 3.02
782 802 1.701847 ACTGATGCCAAGGACTGAAGT 59.298 47.619 0.00 0.00 0.00 3.01
783 803 2.289945 ACTGATGCCAAGGACTGAAGTC 60.290 50.000 1.63 1.63 44.04 3.01
784 804 1.699083 TGATGCCAAGGACTGAAGTCA 59.301 47.619 12.32 0.00 46.47 3.41
785 805 2.106338 TGATGCCAAGGACTGAAGTCAA 59.894 45.455 12.32 0.00 46.47 3.18
786 806 2.957402 TGCCAAGGACTGAAGTCAAT 57.043 45.000 12.32 0.00 46.47 2.57
787 807 2.783135 TGCCAAGGACTGAAGTCAATC 58.217 47.619 12.32 0.00 46.47 2.67
788 808 2.373169 TGCCAAGGACTGAAGTCAATCT 59.627 45.455 12.32 0.00 46.47 2.40
789 809 3.181440 TGCCAAGGACTGAAGTCAATCTT 60.181 43.478 12.32 4.14 46.47 2.40
790 810 3.190118 GCCAAGGACTGAAGTCAATCTTG 59.810 47.826 12.32 14.20 46.47 3.02
791 811 4.392940 CCAAGGACTGAAGTCAATCTTGT 58.607 43.478 18.48 0.00 46.47 3.16
792 812 4.823989 CCAAGGACTGAAGTCAATCTTGTT 59.176 41.667 18.48 0.54 46.47 2.83
793 813 5.997746 CCAAGGACTGAAGTCAATCTTGTTA 59.002 40.000 18.48 0.00 46.47 2.41
794 814 6.148480 CCAAGGACTGAAGTCAATCTTGTTAG 59.852 42.308 18.48 7.29 46.47 2.34
795 815 6.426646 AGGACTGAAGTCAATCTTGTTAGT 57.573 37.500 12.32 0.00 46.47 2.24
796 816 6.831976 AGGACTGAAGTCAATCTTGTTAGTT 58.168 36.000 12.32 0.00 46.47 2.24
797 817 7.963532 AGGACTGAAGTCAATCTTGTTAGTTA 58.036 34.615 12.32 0.00 46.47 2.24
798 818 8.091449 AGGACTGAAGTCAATCTTGTTAGTTAG 58.909 37.037 12.32 0.00 46.47 2.34
799 819 7.873505 GGACTGAAGTCAATCTTGTTAGTTAGT 59.126 37.037 12.32 0.00 46.47 2.24
800 820 9.262358 GACTGAAGTCAATCTTGTTAGTTAGTT 57.738 33.333 5.58 0.00 44.18 2.24
801 821 9.046296 ACTGAAGTCAATCTTGTTAGTTAGTTG 57.954 33.333 0.00 0.00 36.40 3.16
802 822 8.958119 TGAAGTCAATCTTGTTAGTTAGTTGT 57.042 30.769 0.00 0.00 36.40 3.32
851 909 8.985315 TGATCTGCCTTATTTTTGATGACTAT 57.015 30.769 0.00 0.00 0.00 2.12
887 945 2.835764 TGGCACTAGGTTATCCTTTCGT 59.164 45.455 0.00 0.00 42.12 3.85
918 977 5.902051 AACTCACAAACGCTAGTACTTTC 57.098 39.130 0.00 0.00 0.00 2.62
967 1027 1.152333 GCCAGGTTGAACCCCCTTT 60.152 57.895 11.41 0.00 39.75 3.11
971 1031 2.158370 CCAGGTTGAACCCCCTTTTAGT 60.158 50.000 11.41 0.00 39.75 2.24
998 1058 4.396790 TGACAGTTGTGTTTTACAGTTCCC 59.603 41.667 0.00 0.00 41.10 3.97
999 1059 4.337145 ACAGTTGTGTTTTACAGTTCCCA 58.663 39.130 0.00 0.00 41.10 4.37
1011 1071 1.669760 GTTCCCAATGTCGGACGCA 60.670 57.895 3.34 0.00 0.00 5.24
1035 1095 0.519961 ATTACCGTTGCTTCGTTGGC 59.480 50.000 0.00 0.00 0.00 4.52
1077 1137 2.775960 TGATGTGGATCTGAAGGATGCT 59.224 45.455 0.00 0.00 42.27 3.79
1107 1167 4.866508 ATTTGGTCGAGTTACTGAGACA 57.133 40.909 15.79 3.73 35.49 3.41
1115 1175 6.094603 GGTCGAGTTACTGAGACAAAGGTATA 59.905 42.308 15.79 0.00 35.49 1.47
1151 1211 1.228510 GGGCCTGGAATGCTTAGCT 59.771 57.895 5.60 0.00 0.00 3.32
1175 1235 4.522114 TGTGTGGTGGAATATACACATGG 58.478 43.478 11.28 0.00 45.83 3.66
1255 1315 7.302350 ACAATTTTGCCACTAAAAACTTGTC 57.698 32.000 0.00 0.00 33.67 3.18
1270 1330 8.862325 AAAAACTTGTCATGGTGAGATATGTA 57.138 30.769 0.00 0.00 0.00 2.29
1293 1353 9.757227 TGTAAACAACTGGAATAATTTCTTTGG 57.243 29.630 0.00 0.00 32.16 3.28
1332 1393 7.884877 TCATTCTGTCTATTTGGTGAATCTGTT 59.115 33.333 0.00 0.00 0.00 3.16
1398 1460 5.772393 TGATTCCTTGGTATGGTAGTTGT 57.228 39.130 0.00 0.00 0.00 3.32
1400 1462 6.548321 TGATTCCTTGGTATGGTAGTTGTTT 58.452 36.000 0.00 0.00 0.00 2.83
1407 1469 7.063780 CCTTGGTATGGTAGTTGTTTAAGTACG 59.936 40.741 0.00 0.00 41.55 3.67
1456 1518 5.352284 GTGGTGTAGTACAATCAGGATCTG 58.648 45.833 4.11 0.00 0.00 2.90
1561 1624 6.992715 GCTACTGATTTGTACCCTACATCAAT 59.007 38.462 0.00 0.00 38.68 2.57
1574 1637 6.879458 ACCCTACATCAATAGTTGTTGTCTTC 59.121 38.462 9.04 0.00 41.33 2.87
1578 1641 2.734606 TCAATAGTTGTTGTCTTCGCCG 59.265 45.455 0.00 0.00 0.00 6.46
1609 1672 1.948104 TGCAAGTCGGTGGTATATGC 58.052 50.000 0.00 0.00 0.00 3.14
1656 1719 4.702612 TGTTTTCTCTGGCTTGTTAACACA 59.297 37.500 8.07 2.41 0.00 3.72
2052 2115 1.413077 GGTAGCAGGGATGACAGGTAC 59.587 57.143 0.00 0.00 35.01 3.34
2073 2136 2.101582 CAGTAGCAGGGATGACAGGTAC 59.898 54.545 0.00 0.00 35.74 3.34
2074 2137 2.108168 GTAGCAGGGATGACAGGTACA 58.892 52.381 0.00 0.00 35.63 2.90
2075 2138 1.198713 AGCAGGGATGACAGGTACAG 58.801 55.000 0.00 0.00 0.00 2.74
2076 2139 0.905357 GCAGGGATGACAGGTACAGT 59.095 55.000 0.00 0.00 0.00 3.55
2077 2140 2.108168 GCAGGGATGACAGGTACAGTA 58.892 52.381 0.00 0.00 0.00 2.74
2078 2141 2.101582 GCAGGGATGACAGGTACAGTAG 59.898 54.545 0.00 0.00 0.00 2.57
2079 2142 2.101582 CAGGGATGACAGGTACAGTAGC 59.898 54.545 1.13 1.13 0.00 3.58
2080 2143 2.108168 GGGATGACAGGTACAGTAGCA 58.892 52.381 12.31 0.00 0.00 3.49
2081 2144 2.101582 GGGATGACAGGTACAGTAGCAG 59.898 54.545 12.31 6.59 0.00 4.24
2082 2145 2.101582 GGATGACAGGTACAGTAGCAGG 59.898 54.545 12.31 6.28 0.00 4.85
2083 2146 1.557099 TGACAGGTACAGTAGCAGGG 58.443 55.000 12.31 3.95 0.00 4.45
2084 2147 1.076513 TGACAGGTACAGTAGCAGGGA 59.923 52.381 12.31 0.00 0.00 4.20
2085 2148 2.292257 TGACAGGTACAGTAGCAGGGAT 60.292 50.000 12.31 0.00 0.00 3.85
2086 2149 2.101582 GACAGGTACAGTAGCAGGGATG 59.898 54.545 12.31 3.82 0.00 3.51
2087 2150 2.292257 ACAGGTACAGTAGCAGGGATGA 60.292 50.000 12.31 0.00 0.00 2.92
2088 2151 2.101582 CAGGTACAGTAGCAGGGATGAC 59.898 54.545 12.31 0.00 0.00 3.06
2089 2152 2.108168 GGTACAGTAGCAGGGATGACA 58.892 52.381 4.82 0.00 0.00 3.58
2090 2153 2.101582 GGTACAGTAGCAGGGATGACAG 59.898 54.545 4.82 0.00 0.00 3.51
2091 2154 1.198713 ACAGTAGCAGGGATGACAGG 58.801 55.000 0.00 0.00 0.00 4.00
2092 2155 1.198713 CAGTAGCAGGGATGACAGGT 58.801 55.000 0.00 0.00 0.00 4.00
2093 2156 2.292257 ACAGTAGCAGGGATGACAGGTA 60.292 50.000 0.00 0.00 0.00 3.08
2094 2157 2.101582 CAGTAGCAGGGATGACAGGTAC 59.898 54.545 0.00 0.00 35.74 3.34
2132 2195 2.283143 TATGGTGGCAGGGATGGTGC 62.283 60.000 0.00 0.00 40.42 5.01
2230 2293 2.892425 GTGATGGAGGAAGCCGCG 60.892 66.667 0.00 0.00 0.00 6.46
2595 2658 5.505181 AAAAGTCCTGTCATGATACTGGT 57.495 39.130 0.00 0.00 39.01 4.00
2690 2753 8.910351 AGAACAACAGCTCTTTATTTAGTCTT 57.090 30.769 0.00 0.00 0.00 3.01
2725 2788 4.703897 AGGAAAGAATCAACGTTCTGTGA 58.296 39.130 0.00 0.00 38.41 3.58
2736 2799 2.370849 ACGTTCTGTGATTGGGGTAACT 59.629 45.455 0.00 0.00 0.00 2.24
2892 2963 3.502211 TCTGCTTGGCTTAGTGCTAAAAC 59.498 43.478 0.00 0.00 41.55 2.43
2939 3010 4.179926 TGCTTGCTCTAGTACTGTTCTG 57.820 45.455 5.39 0.00 0.00 3.02
3030 3101 2.390696 TGGGCTCCTAGTATAACGCAA 58.609 47.619 0.00 0.00 0.00 4.85
3041 3112 3.627577 AGTATAACGCAATGCTTCCTTGG 59.372 43.478 2.94 0.00 0.00 3.61
3103 3174 3.840666 TCTCTTACCTTCATTCCTGCTGT 59.159 43.478 0.00 0.00 0.00 4.40
3114 3185 1.729586 TCCTGCTGTAACCCAAGTCT 58.270 50.000 0.00 0.00 0.00 3.24
3180 3251 9.490663 GTTGATCCTTTATTAATGTGTTTCTCG 57.509 33.333 0.00 0.00 0.00 4.04
3194 3265 0.685097 TTCTCGAAGGGGGAACTGTG 59.315 55.000 0.00 0.00 0.00 3.66
3239 3310 6.228258 CCTACACTTGCTTCTGGTTAACTTA 58.772 40.000 5.42 0.00 0.00 2.24
3246 3317 1.705256 TCTGGTTAACTTACGCAGCG 58.295 50.000 14.82 14.82 0.00 5.18
3266 3337 4.872691 AGCGAGAAGGTGTAGATGAAAATG 59.127 41.667 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 1.864711 CGGTTCTTGTTGATCGTGTGT 59.135 47.619 0.00 0.00 0.00 3.72
37 38 2.234300 ACGGTTCTTGTTGATCGTGT 57.766 45.000 0.00 0.00 35.05 4.49
69 70 2.531206 GATCTGAGAAAAGGACCGTCG 58.469 52.381 0.00 0.00 0.00 5.12
77 78 2.093764 ACTCCAGCCGATCTGAGAAAAG 60.094 50.000 6.27 0.00 45.72 2.27
131 133 2.035321 GACGAAGAGATAAGGCCTGGAG 59.965 54.545 5.69 0.00 0.00 3.86
183 185 2.611224 GGCGAGAGGTTTTAGTCGGAAA 60.611 50.000 0.00 0.00 32.99 3.13
332 335 3.589881 GCACATGGATCTGCCGCC 61.590 66.667 0.00 0.00 40.66 6.13
398 409 4.319177 AGCATCGCTATCCAAACCTATTC 58.681 43.478 0.00 0.00 36.99 1.75
408 419 1.202580 ACCAGTTGAGCATCGCTATCC 60.203 52.381 0.00 0.00 39.88 2.59
451 462 6.146510 GGAAATTAACCGGTGAAATTGAAACC 59.853 38.462 22.27 18.74 0.00 3.27
480 491 5.277058 CCACGAGAAATCCAGATCGAAAATC 60.277 44.000 0.00 0.00 38.50 2.17
481 492 4.572389 CCACGAGAAATCCAGATCGAAAAT 59.428 41.667 0.00 0.00 38.50 1.82
516 529 1.728971 CCGTGACTGATCAGAACAAGC 59.271 52.381 29.27 14.74 34.75 4.01
528 542 0.600255 AAAGTCTTCCGCCGTGACTG 60.600 55.000 5.64 0.00 40.44 3.51
548 562 8.245195 ACCACCACAAACTAATTACAAAGAAT 57.755 30.769 0.00 0.00 0.00 2.40
555 569 8.556213 TCAATCTACCACCACAAACTAATTAC 57.444 34.615 0.00 0.00 0.00 1.89
557 571 6.659242 CCTCAATCTACCACCACAAACTAATT 59.341 38.462 0.00 0.00 0.00 1.40
558 572 6.180472 CCTCAATCTACCACCACAAACTAAT 58.820 40.000 0.00 0.00 0.00 1.73
567 585 5.772393 AATTGTACCTCAATCTACCACCA 57.228 39.130 0.00 0.00 44.85 4.17
582 600 6.544931 GGGGATTACTCTTACCCAAATTGTAC 59.455 42.308 0.00 0.00 43.67 2.90
599 617 6.264744 GCTTTTGGTATCCTAAAGGGGATTAC 59.735 42.308 18.52 0.00 43.14 1.89
600 618 6.068735 TGCTTTTGGTATCCTAAAGGGGATTA 60.069 38.462 18.52 0.00 43.14 1.75
604 622 3.976015 TGCTTTTGGTATCCTAAAGGGG 58.024 45.455 18.52 2.24 43.14 4.79
605 623 5.261216 TCTTGCTTTTGGTATCCTAAAGGG 58.739 41.667 18.52 2.77 43.14 3.95
606 624 6.659242 TCTTCTTGCTTTTGGTATCCTAAAGG 59.341 38.462 18.52 7.52 43.14 3.11
609 627 6.148811 CGTTCTTCTTGCTTTTGGTATCCTAA 59.851 38.462 0.00 0.00 0.00 2.69
610 628 5.642063 CGTTCTTCTTGCTTTTGGTATCCTA 59.358 40.000 0.00 0.00 0.00 2.94
611 629 4.455877 CGTTCTTCTTGCTTTTGGTATCCT 59.544 41.667 0.00 0.00 0.00 3.24
612 630 4.454504 TCGTTCTTCTTGCTTTTGGTATCC 59.545 41.667 0.00 0.00 0.00 2.59
639 659 4.982241 AGAAGAATCTTGTCCTGGAACA 57.018 40.909 0.00 0.00 29.15 3.18
640 660 5.046231 ACCTAGAAGAATCTTGTCCTGGAAC 60.046 44.000 0.00 0.00 37.10 3.62
647 667 7.832769 AGTAGACAACCTAGAAGAATCTTGTC 58.167 38.462 0.00 0.33 37.32 3.18
703 723 7.999679 TCTCAAGTTGACAACTGATTTTGAAT 58.000 30.769 21.24 0.00 41.91 2.57
707 727 7.338800 ACATCTCAAGTTGACAACTGATTTT 57.661 32.000 21.24 2.58 41.91 1.82
745 765 0.698818 AGTTGGGAGGCAACCTAAGG 59.301 55.000 0.00 0.00 31.76 2.69
769 789 4.392940 ACAAGATTGACTTCAGTCCTTGG 58.607 43.478 19.87 9.08 41.68 3.61
770 790 6.708054 ACTAACAAGATTGACTTCAGTCCTTG 59.292 38.462 16.65 16.65 44.15 3.61
771 791 6.831976 ACTAACAAGATTGACTTCAGTCCTT 58.168 36.000 4.48 0.00 44.15 3.36
772 792 6.426646 ACTAACAAGATTGACTTCAGTCCT 57.573 37.500 4.48 0.00 44.15 3.85
773 793 7.873505 ACTAACTAACAAGATTGACTTCAGTCC 59.126 37.037 4.48 0.00 44.15 3.85
774 794 8.819643 ACTAACTAACAAGATTGACTTCAGTC 57.180 34.615 0.00 0.00 44.97 3.51
775 795 9.046296 CAACTAACTAACAAGATTGACTTCAGT 57.954 33.333 0.00 0.00 36.61 3.41
776 796 9.046296 ACAACTAACTAACAAGATTGACTTCAG 57.954 33.333 0.00 0.00 36.61 3.02
777 797 8.958119 ACAACTAACTAACAAGATTGACTTCA 57.042 30.769 0.00 0.00 36.61 3.02
851 909 2.354729 CCAGCACCCCGGATTGAA 59.645 61.111 0.73 0.00 0.00 2.69
967 1027 8.774890 TGTAAAACACAACTGTCAGTAACTAA 57.225 30.769 5.77 0.00 32.95 2.24
971 1031 7.148373 GGAACTGTAAAACACAACTGTCAGTAA 60.148 37.037 5.77 0.00 36.48 2.24
998 1058 1.575244 ATCATCTGCGTCCGACATTG 58.425 50.000 0.00 0.00 0.00 2.82
999 1059 2.315925 AATCATCTGCGTCCGACATT 57.684 45.000 0.00 0.00 0.00 2.71
1011 1071 3.247006 ACGAAGCAACGGTAATCATCT 57.753 42.857 7.39 0.00 37.61 2.90
1035 1095 3.249320 CAGTTGTGTTCCATGACAGACTG 59.751 47.826 0.00 0.00 37.96 3.51
1077 1137 5.595133 AGTAACTCGACCAAATTTCCCAAAA 59.405 36.000 0.00 0.00 0.00 2.44
1115 1175 6.408869 CAGGCCCATATGAAAAGAACAAAAT 58.591 36.000 3.65 0.00 0.00 1.82
1120 1180 3.631250 TCCAGGCCCATATGAAAAGAAC 58.369 45.455 3.65 0.00 0.00 3.01
1175 1235 9.175060 GAAAGAAGATTGCTTGACTAAGAAAAC 57.825 33.333 0.00 0.00 35.12 2.43
1215 1275 6.538381 GCAAAATTGTAATTATTGGTGAGGGG 59.462 38.462 0.00 0.00 0.00 4.79
1248 1308 7.882791 TGTTTACATATCTCACCATGACAAGTT 59.117 33.333 0.00 0.00 0.00 2.66
1255 1315 6.823182 TCCAGTTGTTTACATATCTCACCATG 59.177 38.462 0.00 0.00 0.00 3.66
1344 1405 4.760530 AGTGCAGATTCATACCTTAGCA 57.239 40.909 0.00 0.00 0.00 3.49
1348 1409 5.700402 AACCTAGTGCAGATTCATACCTT 57.300 39.130 0.00 0.00 0.00 3.50
1350 1411 5.066505 CCAAAACCTAGTGCAGATTCATACC 59.933 44.000 0.00 0.00 0.00 2.73
1358 1420 4.574674 ATCATCCAAAACCTAGTGCAGA 57.425 40.909 0.00 0.00 0.00 4.26
1425 1487 6.636705 TGATTGTACTACACCACCATAAGAC 58.363 40.000 0.00 0.00 0.00 3.01
1550 1613 6.036083 CGAAGACAACAACTATTGATGTAGGG 59.964 42.308 4.67 0.00 45.12 3.53
1561 1624 2.228138 AACGGCGAAGACAACAACTA 57.772 45.000 16.62 0.00 27.25 2.24
1574 1637 2.392933 TGCAAAAGTTAGAAACGGCG 57.607 45.000 4.80 4.80 36.23 6.46
1578 1641 4.733405 CACCGACTTGCAAAAGTTAGAAAC 59.267 41.667 0.00 0.00 32.22 2.78
1609 1672 3.408634 AGGAAAGTGGTGTATCAAACCG 58.591 45.455 0.00 0.00 40.86 4.44
1656 1719 5.508489 GCATATAAAGCATGGCAGACAACAT 60.508 40.000 0.00 0.00 0.00 2.71
2007 2070 0.549902 TGTCCCCACCATCACCAGAT 60.550 55.000 0.00 0.00 33.87 2.90
2052 2115 1.198713 ACCTGTCATCCCTGCTACTG 58.801 55.000 0.00 0.00 0.00 2.74
2073 2136 1.198713 ACCTGTCATCCCTGCTACTG 58.801 55.000 0.00 0.00 0.00 2.74
2074 2137 2.292257 TGTACCTGTCATCCCTGCTACT 60.292 50.000 0.00 0.00 0.00 2.57
2075 2138 2.101582 CTGTACCTGTCATCCCTGCTAC 59.898 54.545 0.00 0.00 0.00 3.58
2076 2139 2.292257 ACTGTACCTGTCATCCCTGCTA 60.292 50.000 0.00 0.00 0.00 3.49
2077 2140 1.198713 CTGTACCTGTCATCCCTGCT 58.801 55.000 0.00 0.00 0.00 4.24
2078 2141 0.905357 ACTGTACCTGTCATCCCTGC 59.095 55.000 0.00 0.00 0.00 4.85
2079 2142 3.366396 ACTACTGTACCTGTCATCCCTG 58.634 50.000 0.00 0.00 0.00 4.45
2080 2143 3.759815 ACTACTGTACCTGTCATCCCT 57.240 47.619 0.00 0.00 0.00 4.20
2081 2144 3.890147 CCTACTACTGTACCTGTCATCCC 59.110 52.174 0.00 0.00 0.00 3.85
2082 2145 3.890147 CCCTACTACTGTACCTGTCATCC 59.110 52.174 0.00 0.00 0.00 3.51
2083 2146 4.789807 TCCCTACTACTGTACCTGTCATC 58.210 47.826 0.00 0.00 0.00 2.92
2084 2147 4.875578 TCCCTACTACTGTACCTGTCAT 57.124 45.455 0.00 0.00 0.00 3.06
2085 2148 4.228895 TCATCCCTACTACTGTACCTGTCA 59.771 45.833 0.00 0.00 0.00 3.58
2086 2149 4.579753 GTCATCCCTACTACTGTACCTGTC 59.420 50.000 0.00 0.00 0.00 3.51
2087 2150 4.017775 TGTCATCCCTACTACTGTACCTGT 60.018 45.833 0.00 0.00 0.00 4.00
2088 2151 4.533815 TGTCATCCCTACTACTGTACCTG 58.466 47.826 0.00 0.00 0.00 4.00
2089 2152 4.386536 CCTGTCATCCCTACTACTGTACCT 60.387 50.000 0.00 0.00 0.00 3.08
2090 2153 3.890147 CCTGTCATCCCTACTACTGTACC 59.110 52.174 0.00 0.00 0.00 3.34
2091 2154 4.534797 ACCTGTCATCCCTACTACTGTAC 58.465 47.826 0.00 0.00 0.00 2.90
2092 2155 4.875578 ACCTGTCATCCCTACTACTGTA 57.124 45.455 0.00 0.00 0.00 2.74
2093 2156 3.759815 ACCTGTCATCCCTACTACTGT 57.240 47.619 0.00 0.00 0.00 3.55
2094 2157 4.524714 CCATACCTGTCATCCCTACTACTG 59.475 50.000 0.00 0.00 0.00 2.74
2132 2195 3.282021 CCACCATACTTGTCATCCCTTG 58.718 50.000 0.00 0.00 0.00 3.61
2230 2293 4.722700 ATCACCGCCACCACTGCC 62.723 66.667 0.00 0.00 0.00 4.85
2354 2417 6.892658 TGTGATAAAGCAAACATACCACTT 57.107 33.333 0.00 0.00 0.00 3.16
2595 2658 4.261572 GCAATACAAGAACAGCACCAAAGA 60.262 41.667 0.00 0.00 0.00 2.52
2690 2753 3.924114 TCTTTCCTCAAGACCACAACA 57.076 42.857 0.00 0.00 36.51 3.33
2752 2823 3.502595 TGTTTCGTTGGTCACAAGTTTCA 59.497 39.130 0.00 0.00 37.25 2.69
2758 2829 3.193691 ACCATTTGTTTCGTTGGTCACAA 59.806 39.130 0.00 0.00 38.00 3.33
2892 2963 1.688197 ACCCATGGTTGAACAGCAAAG 59.312 47.619 11.73 0.00 38.44 2.77
2939 3010 1.623811 TCTAACTGAGGGAAGTGCCAC 59.376 52.381 0.00 0.00 38.95 5.01
3041 3112 2.278332 AGCAACTCTTTCCAGGTTCC 57.722 50.000 0.00 0.00 0.00 3.62
3103 3174 1.205460 GGGCCCTCAGACTTGGGTTA 61.205 60.000 17.04 0.00 45.06 2.85
3114 3185 2.986728 AGAACTTTCTTAAGGGCCCTCA 59.013 45.455 28.84 8.16 35.61 3.86
3168 3239 1.702957 TCCCCCTTCGAGAAACACATT 59.297 47.619 0.00 0.00 0.00 2.71
3169 3240 1.358152 TCCCCCTTCGAGAAACACAT 58.642 50.000 0.00 0.00 0.00 3.21
3180 3251 2.067365 AACAACACAGTTCCCCCTTC 57.933 50.000 0.00 0.00 0.00 3.46
3194 3265 1.192534 CGACCTTCGCTGAGAAACAAC 59.807 52.381 0.00 0.00 38.57 3.32
3239 3310 1.213013 CTACACCTTCTCGCTGCGT 59.787 57.895 22.48 2.11 0.00 5.24
3266 3337 4.999311 AGACACCGAACCCTACAAATAAAC 59.001 41.667 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.