Multiple sequence alignment - TraesCS3A01G354000

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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 TraesCS3A01G354000 chr3A 100.000 3173 0 0 1 3173 601542143 601545315 0 5860
1 TraesCS3A01G354000 chr3D 88.994 3262 166 62 2 3173 459480702 459477544 0 3856
2 TraesCS3A01G354000 chr3B 88.944 3229 196 50 1 3163 607409407 607406274 0 3836


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 TraesCS3A01G354000 chr3A 601542143 601545315 3172 False 5860 5860 100.000 1 3173 1 chr3A.!!$F1 3172
1 TraesCS3A01G354000 chr3D 459477544 459480702 3158 True 3856 3856 88.994 2 3173 1 chr3D.!!$R1 3171
2 TraesCS3A01G354000 chr3B 607406274 607409407 3133 True 3836 3836 88.944 1 3163 1 chr3B.!!$R1 3162

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
983 1050 0.389556 GGAAGAAAGTCCGTCCGTCC 60.39 60.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2755 2858 0.10412 TTGTCCTGTCACGTCACTGG 59.896 55.0 9.29 9.29 36.85 4.0 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
62 63 4.207891 ACGAGTAGCACCTTTCATTCAT 57.792 40.909 0.00 0.00 0.00 2.57
67 68 8.150945 ACGAGTAGCACCTTTCATTCATATATT 58.849 33.333 0.00 0.00 0.00 1.28
68 69 8.438513 CGAGTAGCACCTTTCATTCATATATTG 58.561 37.037 0.00 0.00 0.00 1.90
69 70 9.494271 GAGTAGCACCTTTCATTCATATATTGA 57.506 33.333 0.00 0.00 0.00 2.57
90 92 6.656632 TGATAGTAAATAGAGGCCAGACAG 57.343 41.667 5.01 0.00 0.00 3.51
109 111 4.017126 ACAGCCTTTTTAGGGACTATTGC 58.983 43.478 0.00 0.00 42.38 3.56
188 190 5.002464 TCTTGTAATGGTAGTCGGCTTAC 57.998 43.478 0.00 0.00 0.00 2.34
207 209 5.711976 GCTTACATGGTAGAATGGGCATAAT 59.288 40.000 0.00 0.00 31.46 1.28
239 241 5.984725 TCTCTTCACGGAATATGGCTTTTA 58.015 37.500 0.00 0.00 0.00 1.52
250 252 8.865978 CGGAATATGGCTTTTAAAGGTTTTTAC 58.134 33.333 6.84 0.00 0.00 2.01
325 350 5.764686 TCAGTCTGAATAGTTTGTGCACATT 59.235 36.000 22.39 11.67 0.00 2.71
356 381 4.484236 TCGACCATCAAAATTGTGCAATC 58.516 39.130 0.00 0.00 0.00 2.67
366 391 6.433716 TCAAAATTGTGCAATCTCATGTAGGA 59.566 34.615 0.00 0.00 0.00 2.94
409 436 0.879090 AATCAACCCGTCGCCTTTTC 59.121 50.000 0.00 0.00 0.00 2.29
410 437 0.958876 ATCAACCCGTCGCCTTTTCC 60.959 55.000 0.00 0.00 0.00 3.13
414 442 2.663196 CCGTCGCCTTTTCCCTCT 59.337 61.111 0.00 0.00 0.00 3.69
438 468 2.014033 AAAGGAGGGTTTTCCGGCCA 62.014 55.000 2.24 0.00 42.29 5.36
500 530 5.888982 TCCCCTGATTTCCATTACTAGAC 57.111 43.478 0.00 0.00 0.00 2.59
512 542 6.689561 TCCATTACTAGACCCCAGATAGAAA 58.310 40.000 0.00 0.00 0.00 2.52
531 562 4.892934 AGAAATTCTTACAAACCACCAGCA 59.107 37.500 0.00 0.00 0.00 4.41
568 599 5.230182 TGTATTCACATCACTCACAGTCAC 58.770 41.667 0.00 0.00 0.00 3.67
574 605 1.048601 TCACTCACAGTCACCTTCCC 58.951 55.000 0.00 0.00 0.00 3.97
628 659 1.100510 CGGATCCCTCTTCACGTACA 58.899 55.000 6.06 0.00 0.00 2.90
634 665 1.825474 CCCTCTTCACGTACACCATCT 59.175 52.381 0.00 0.00 0.00 2.90
640 671 4.893524 TCTTCACGTACACCATCTATCCAT 59.106 41.667 0.00 0.00 0.00 3.41
641 672 4.848562 TCACGTACACCATCTATCCATC 57.151 45.455 0.00 0.00 0.00 3.51
642 673 4.470602 TCACGTACACCATCTATCCATCT 58.529 43.478 0.00 0.00 0.00 2.90
664 699 1.202510 AGCCTGATGATTCGACTGCTC 60.203 52.381 0.00 0.00 0.00 4.26
688 723 1.463056 CGACTTGCCAAACATTAGCGA 59.537 47.619 0.00 0.00 0.00 4.93
694 729 4.009798 TGCCAAACATTAGCGATAAACG 57.990 40.909 0.00 0.00 45.66 3.60
710 745 1.691196 AACGGTTATCATGGGGCATG 58.309 50.000 0.00 0.00 42.60 4.06
754 820 2.218454 CGTGACCCTACCCAACCCA 61.218 63.158 0.00 0.00 0.00 4.51
765 831 2.342650 CCAACCCAACCCTGCATCG 61.343 63.158 0.00 0.00 0.00 3.84
774 840 1.156736 ACCCTGCATCGTTCTTTTCG 58.843 50.000 0.00 0.00 0.00 3.46
813 879 2.582498 CGGGCGTGCACTAGTAGC 60.582 66.667 16.19 10.23 0.00 3.58
814 880 2.893398 GGGCGTGCACTAGTAGCT 59.107 61.111 16.19 0.00 0.00 3.32
815 881 1.519455 GGGCGTGCACTAGTAGCTG 60.519 63.158 16.19 0.00 0.00 4.24
816 882 1.215647 GGCGTGCACTAGTAGCTGT 59.784 57.895 16.19 0.00 0.00 4.40
817 883 0.454600 GGCGTGCACTAGTAGCTGTA 59.545 55.000 16.19 0.00 0.00 2.74
818 884 1.534175 GGCGTGCACTAGTAGCTGTAG 60.534 57.143 16.19 0.00 0.00 2.74
819 885 1.534175 GCGTGCACTAGTAGCTGTAGG 60.534 57.143 16.19 2.40 0.00 3.18
888 955 1.338020 CACTTCAACCTCCCAGCAAAC 59.662 52.381 0.00 0.00 0.00 2.93
889 956 1.064017 ACTTCAACCTCCCAGCAAACA 60.064 47.619 0.00 0.00 0.00 2.83
890 957 1.338020 CTTCAACCTCCCAGCAAACAC 59.662 52.381 0.00 0.00 0.00 3.32
891 958 0.817634 TCAACCTCCCAGCAAACACG 60.818 55.000 0.00 0.00 0.00 4.49
892 959 2.193536 AACCTCCCAGCAAACACGC 61.194 57.895 0.00 0.00 0.00 5.34
982 1049 0.602060 AGGAAGAAAGTCCGTCCGTC 59.398 55.000 0.00 0.00 43.03 4.79
983 1050 0.389556 GGAAGAAAGTCCGTCCGTCC 60.390 60.000 0.00 0.00 0.00 4.79
1106 1173 4.543361 TGCCGCCGGGGGATACTA 62.543 66.667 39.60 16.92 35.78 1.82
1107 1174 3.001406 GCCGCCGGGGGATACTAT 61.001 66.667 39.60 0.00 35.78 2.12
1111 1178 1.183030 CGCCGGGGGATACTATGACA 61.183 60.000 11.42 0.00 0.00 3.58
1113 1180 0.608640 CCGGGGGATACTATGACAGC 59.391 60.000 0.00 0.00 0.00 4.40
1120 1187 2.738846 GGATACTATGACAGCGGCAATG 59.261 50.000 1.45 0.00 0.00 2.82
1121 1188 2.979814 TACTATGACAGCGGCAATGT 57.020 45.000 1.45 0.00 0.00 2.71
1122 1189 2.113860 ACTATGACAGCGGCAATGTT 57.886 45.000 1.45 0.00 0.00 2.71
1126 1193 1.948508 GACAGCGGCAATGTTGTCA 59.051 52.632 12.69 0.00 45.84 3.58
1127 1194 0.310543 GACAGCGGCAATGTTGTCAA 59.689 50.000 12.69 0.00 45.84 3.18
1131 1198 1.353609 GCGGCAATGTTGTCAATGGC 61.354 55.000 0.00 2.01 43.58 4.40
1139 1206 1.894282 TTGTCAATGGCGCGTTCCA 60.894 52.632 8.43 8.15 40.97 3.53
1196 1278 2.223595 CGTCCTACTCCTCGTCGTACTA 60.224 54.545 0.00 0.00 0.00 1.82
1197 1279 3.120041 GTCCTACTCCTCGTCGTACTAC 58.880 54.545 0.00 0.00 0.00 2.73
1198 1280 2.760650 TCCTACTCCTCGTCGTACTACA 59.239 50.000 0.00 0.00 0.00 2.74
1270 1352 4.421479 AGCTCGGCGACAACCTCG 62.421 66.667 4.99 0.00 45.97 4.63
1332 1414 1.602888 CCAGCAGCTGTCTTTGCCT 60.603 57.895 21.26 0.00 41.17 4.75
1457 1543 1.378762 GCCACAGCCCTGGAACTTA 59.621 57.895 0.00 0.00 32.30 2.24
1466 1552 2.890945 GCCCTGGAACTTACACAATTGT 59.109 45.455 4.92 4.92 40.02 2.71
1504 1590 2.751259 TGGAGATTGCAATTGAGCTGTC 59.249 45.455 14.33 0.00 34.99 3.51
1667 1754 3.378399 GAGAGGAAGGAGCGGGTGC 62.378 68.421 0.00 0.00 43.24 5.01
1696 1783 2.664851 CTGAAACGGCACCAGCGA 60.665 61.111 0.00 0.00 43.41 4.93
1806 1894 0.107017 ATCATTGGCTCTGGTTCCGG 60.107 55.000 0.00 0.00 0.00 5.14
1935 2023 0.959372 ACAGCTACGACTACTGCGGT 60.959 55.000 2.42 2.42 34.72 5.68
1944 2032 0.815734 ACTACTGCGGTTACAGCGAT 59.184 50.000 1.99 0.00 42.41 4.58
1962 2050 2.809861 ATCCCAGCAACCAGAGCACG 62.810 60.000 0.00 0.00 0.00 5.34
1993 2081 3.974835 TACCACGGCCAGCAGCATG 62.975 63.158 2.24 0.00 46.50 4.06
2127 2215 2.400402 GACGTCGACGAGGAGCTC 59.600 66.667 41.52 24.33 43.02 4.09
2232 2323 1.338655 CGTTAGTGGTTTTTGGTGGGG 59.661 52.381 0.00 0.00 0.00 4.96
2233 2324 1.689813 GTTAGTGGTTTTTGGTGGGGG 59.310 52.381 0.00 0.00 0.00 5.40
2259 2350 2.184322 CGCACCAGACGGCACTAT 59.816 61.111 0.00 0.00 34.57 2.12
2262 2353 1.538204 CGCACCAGACGGCACTATTAT 60.538 52.381 0.00 0.00 34.57 1.28
2263 2354 2.287970 CGCACCAGACGGCACTATTATA 60.288 50.000 0.00 0.00 34.57 0.98
2264 2355 3.318017 GCACCAGACGGCACTATTATAG 58.682 50.000 0.00 0.00 34.57 1.31
2265 2356 3.318017 CACCAGACGGCACTATTATAGC 58.682 50.000 0.00 0.00 34.57 2.97
2330 2428 2.439701 CAGTGCAGCCATGGAGGG 60.440 66.667 18.40 4.48 38.09 4.30
2331 2429 3.736224 AGTGCAGCCATGGAGGGG 61.736 66.667 18.40 1.64 38.09 4.79
2469 2571 3.184581 CGTGCTAGACTTTGAGAACAACC 59.815 47.826 0.00 0.00 35.63 3.77
2507 2609 3.055602 AGTTCCCGGTTACTTCCATGTAC 60.056 47.826 0.00 0.00 0.00 2.90
2542 2644 0.399949 ATTATCTGCCCCACTCCCGA 60.400 55.000 0.00 0.00 0.00 5.14
2557 2659 2.401766 CCGAGTCCAAGTGCATGCC 61.402 63.158 16.68 6.65 0.00 4.40
2573 2675 1.376037 GCCCCTCTGTCGTCCAAAG 60.376 63.158 0.00 0.00 0.00 2.77
2584 2686 0.609131 CGTCCAAAGCACCCCTGAAT 60.609 55.000 0.00 0.00 0.00 2.57
2585 2687 1.177401 GTCCAAAGCACCCCTGAATC 58.823 55.000 0.00 0.00 0.00 2.52
2586 2688 0.039618 TCCAAAGCACCCCTGAATCC 59.960 55.000 0.00 0.00 0.00 3.01
2587 2689 0.040204 CCAAAGCACCCCTGAATCCT 59.960 55.000 0.00 0.00 0.00 3.24
2588 2690 1.467920 CAAAGCACCCCTGAATCCTC 58.532 55.000 0.00 0.00 0.00 3.71
2589 2691 1.075601 AAAGCACCCCTGAATCCTCA 58.924 50.000 0.00 0.00 0.00 3.86
2590 2692 0.329596 AAGCACCCCTGAATCCTCAC 59.670 55.000 0.00 0.00 0.00 3.51
2591 2693 1.077429 GCACCCCTGAATCCTCACC 60.077 63.158 0.00 0.00 0.00 4.02
2592 2694 1.566298 GCACCCCTGAATCCTCACCT 61.566 60.000 0.00 0.00 0.00 4.00
2593 2695 0.543749 CACCCCTGAATCCTCACCTC 59.456 60.000 0.00 0.00 0.00 3.85
2594 2696 0.419459 ACCCCTGAATCCTCACCTCT 59.581 55.000 0.00 0.00 0.00 3.69
2647 2749 2.372350 CTTCCGTGCTCGTTTTGTTTC 58.628 47.619 7.47 0.00 35.01 2.78
2652 2754 1.724581 GCTCGTTTTGTTTCGCCCG 60.725 57.895 0.00 0.00 0.00 6.13
2669 2771 1.623811 CCCGTTTTCCTTCTCCTCTGA 59.376 52.381 0.00 0.00 0.00 3.27
2683 2785 3.422796 TCCTCTGAGACTACACTCAACC 58.577 50.000 6.17 0.00 44.62 3.77
2692 2794 2.049228 CTACACTCAACCGTTGTCGAC 58.951 52.381 9.11 9.11 39.71 4.20
2705 2807 3.311110 TCGACCTCCCAGTGGCAC 61.311 66.667 10.29 10.29 0.00 5.01
2735 2838 3.427243 TGTTTTTAACAAAGTCCACGCG 58.573 40.909 3.53 3.53 38.72 6.01
2781 2885 0.939577 CGTGACAGGACAAGACACGG 60.940 60.000 0.00 0.00 46.07 4.94
2861 2981 4.233558 GTTGGGTGGGGTTGGGCT 62.234 66.667 0.00 0.00 0.00 5.19
2862 2982 4.232061 TTGGGTGGGGTTGGGCTG 62.232 66.667 0.00 0.00 0.00 4.85
2910 3030 0.954449 TCGTCGCGGGGAGATAGATC 60.954 60.000 6.13 0.00 0.00 2.75
2912 3032 1.674651 TCGCGGGGAGATAGATCGG 60.675 63.158 6.13 0.00 0.00 4.18
2917 3037 1.166989 GGGGAGATAGATCGGTCGAC 58.833 60.000 7.13 7.13 0.00 4.20
3137 3278 0.438830 CGAGTTGGTTAGCTGTTCGC 59.561 55.000 0.00 0.00 39.57 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 5.011125 GCTGTCTGGCCTCTATTTACTATCA 59.989 44.000 3.32 0.00 0.00 2.15
68 69 5.474825 GCTGTCTGGCCTCTATTTACTATC 58.525 45.833 3.32 0.00 0.00 2.08
69 70 5.476091 GCTGTCTGGCCTCTATTTACTAT 57.524 43.478 3.32 0.00 0.00 2.12
70 71 4.939052 GCTGTCTGGCCTCTATTTACTA 57.061 45.455 3.32 0.00 0.00 1.82
90 92 3.632333 AGGCAATAGTCCCTAAAAAGGC 58.368 45.455 0.00 0.00 0.00 4.35
109 111 2.093890 TGCTGAATTGTGTGCCATAGG 58.906 47.619 0.00 0.00 0.00 2.57
188 190 4.322198 GCCAATTATGCCCATTCTACCATG 60.322 45.833 0.00 0.00 0.00 3.66
207 209 0.318441 CCGTGAAGAGAGAGTGCCAA 59.682 55.000 0.00 0.00 0.00 4.52
239 241 8.049721 TGTGGAAATTTGATGGTAAAAACCTTT 58.950 29.630 0.00 0.00 0.00 3.11
325 350 3.973206 TTTGATGGTCGAGCTTCCTTA 57.027 42.857 22.93 9.55 0.00 2.69
356 381 5.707298 ACCAACAAAGAACATCCTACATGAG 59.293 40.000 0.00 0.00 0.00 2.90
366 391 1.953686 CACCGGACCAACAAAGAACAT 59.046 47.619 9.46 0.00 0.00 2.71
410 437 2.861147 AACCCTCCTTTTCGAAGAGG 57.139 50.000 25.14 25.14 45.72 3.69
414 442 2.223745 CGGAAAACCCTCCTTTTCGAA 58.776 47.619 0.00 0.00 39.92 3.71
500 530 6.889722 TGGTTTGTAAGAATTTCTATCTGGGG 59.110 38.462 0.00 0.00 0.00 4.96
512 542 5.321102 TGTATGCTGGTGGTTTGTAAGAAT 58.679 37.500 0.00 0.00 0.00 2.40
531 562 5.252547 TGTGAATACATGCACCAACTGTAT 58.747 37.500 4.43 4.43 37.62 2.29
568 599 1.068121 AGAGTGGAAGGTTGGGAAGG 58.932 55.000 0.00 0.00 0.00 3.46
574 605 2.938956 ACTGGAAGAGTGGAAGGTTG 57.061 50.000 0.00 0.00 37.43 3.77
596 627 1.447643 GATCCGTCACATCCCCCTG 59.552 63.158 0.00 0.00 0.00 4.45
628 659 4.756564 TCAGGCTTAGATGGATAGATGGT 58.243 43.478 0.00 0.00 0.00 3.55
634 665 5.716703 TCGAATCATCAGGCTTAGATGGATA 59.283 40.000 13.15 0.00 42.38 2.59
640 671 3.491619 GCAGTCGAATCATCAGGCTTAGA 60.492 47.826 0.00 0.00 0.00 2.10
641 672 2.799412 GCAGTCGAATCATCAGGCTTAG 59.201 50.000 0.00 0.00 0.00 2.18
642 673 2.432146 AGCAGTCGAATCATCAGGCTTA 59.568 45.455 0.00 0.00 0.00 3.09
688 723 3.586470 TGCCCCATGATAACCGTTTAT 57.414 42.857 0.00 0.00 0.00 1.40
694 729 1.187567 GGCCATGCCCCATGATAACC 61.188 60.000 0.00 0.19 43.81 2.85
754 820 1.535462 CGAAAAGAACGATGCAGGGTT 59.465 47.619 4.97 4.97 0.00 4.11
765 831 2.450160 CTGTTGTGCACCGAAAAGAAC 58.550 47.619 15.69 10.53 0.00 3.01
813 879 1.531264 CGCGTACACTACAGCCTACAG 60.531 57.143 0.00 0.00 0.00 2.74
814 880 0.448990 CGCGTACACTACAGCCTACA 59.551 55.000 0.00 0.00 0.00 2.74
815 881 0.864797 GCGCGTACACTACAGCCTAC 60.865 60.000 8.43 0.00 0.00 3.18
816 882 1.430632 GCGCGTACACTACAGCCTA 59.569 57.895 8.43 0.00 0.00 3.93
817 883 2.181021 GCGCGTACACTACAGCCT 59.819 61.111 8.43 0.00 0.00 4.58
818 884 2.884207 GGCGCGTACACTACAGCC 60.884 66.667 8.43 0.00 42.19 4.85
819 885 1.683790 CTTGGCGCGTACACTACAGC 61.684 60.000 8.43 0.00 0.00 4.40
892 959 3.858989 TGTGCGTGTGTGCGTGTG 61.859 61.111 0.00 0.00 37.81 3.82
897 964 2.324477 GACTGTGTGCGTGTGTGC 59.676 61.111 0.00 0.00 0.00 4.57
948 1015 0.248289 TTCCTCCGGACGTGGAAATC 59.752 55.000 18.68 0.00 37.64 2.17
1068 1135 3.164269 CGAGGGATCTGGGTGGGG 61.164 72.222 0.00 0.00 0.00 4.96
1071 1138 1.760086 AGAGCGAGGGATCTGGGTG 60.760 63.158 0.00 0.00 37.56 4.61
1076 1143 3.222855 CGGCAGAGCGAGGGATCT 61.223 66.667 0.00 0.00 40.15 2.75
1106 1173 0.523072 GACAACATTGCCGCTGTCAT 59.477 50.000 5.15 0.00 38.43 3.06
1107 1174 0.817229 TGACAACATTGCCGCTGTCA 60.817 50.000 8.00 8.00 44.38 3.58
1111 1178 0.244450 CCATTGACAACATTGCCGCT 59.756 50.000 0.00 0.00 0.00 5.52
1113 1180 1.072116 CGCCATTGACAACATTGCCG 61.072 55.000 0.00 0.00 0.00 5.69
1120 1187 1.442017 GGAACGCGCCATTGACAAC 60.442 57.895 5.73 0.00 0.00 3.32
1121 1188 1.240641 ATGGAACGCGCCATTGACAA 61.241 50.000 11.92 0.00 46.29 3.18
1122 1189 1.673993 ATGGAACGCGCCATTGACA 60.674 52.632 11.92 0.00 46.29 3.58
1131 1198 3.564027 GCGAAGGGATGGAACGCG 61.564 66.667 3.53 3.53 39.90 6.01
1196 1278 3.719268 TGCTCCTATGGATGTTGTTGT 57.281 42.857 0.00 0.00 0.00 3.32
1197 1279 4.201657 TGATGCTCCTATGGATGTTGTTG 58.798 43.478 0.00 0.00 0.00 3.33
1198 1280 4.458397 CTGATGCTCCTATGGATGTTGTT 58.542 43.478 0.00 0.00 0.00 2.83
1332 1414 2.372688 GGGGAGGAGGACATGGGA 59.627 66.667 0.00 0.00 0.00 4.37
1445 1531 2.890945 ACAATTGTGTAAGTTCCAGGGC 59.109 45.455 11.07 0.00 35.72 5.19
1449 1535 5.301555 TCGATCACAATTGTGTAAGTTCCA 58.698 37.500 31.99 15.08 45.76 3.53
1451 1537 6.178507 CGATCGATCACAATTGTGTAAGTTC 58.821 40.000 31.99 24.13 45.76 3.01
1457 1543 2.279741 CCCGATCGATCACAATTGTGT 58.720 47.619 31.99 21.66 45.76 3.72
1466 1552 1.735973 CAGACAGCCCGATCGATCA 59.264 57.895 24.40 0.00 0.00 2.92
1504 1590 1.676006 AGGCAAGGAAAACAACAGTCG 59.324 47.619 0.00 0.00 0.00 4.18
1679 1766 1.781025 TTTCGCTGGTGCCGTTTCAG 61.781 55.000 0.00 0.00 35.36 3.02
1687 1774 1.282875 GGTGAAGTTTCGCTGGTGC 59.717 57.895 5.51 0.00 37.80 5.01
1721 1808 1.202582 GATGGAGATCGGGATGGTACG 59.797 57.143 0.00 0.00 0.00 3.67
1760 1848 1.352156 CGTTAGTGGCAAGAGACGGC 61.352 60.000 0.00 0.00 0.00 5.68
1806 1894 2.730672 CTTCCTGCACGCGTACTGC 61.731 63.158 13.44 13.02 41.47 4.40
1935 2023 0.392461 GGTTGCTGGGATCGCTGTAA 60.392 55.000 14.11 14.11 0.00 2.41
1944 2032 2.431683 GTGCTCTGGTTGCTGGGA 59.568 61.111 0.00 0.00 0.00 4.37
1962 2050 3.712907 TGGTAGCGGCTGTTCCCC 61.713 66.667 13.86 5.25 0.00 4.81
2040 2128 2.819595 CCATTGTCACCGGCTCCG 60.820 66.667 0.00 0.48 39.44 4.63
2049 2137 1.302431 CCACCAGTCGCCATTGTCA 60.302 57.895 0.00 0.00 0.00 3.58
2256 2347 4.156922 CCTGACCTGACCGAGCTATAATAG 59.843 50.000 0.00 0.00 0.00 1.73
2257 2348 4.079970 CCTGACCTGACCGAGCTATAATA 58.920 47.826 0.00 0.00 0.00 0.98
2259 2350 2.307768 CCTGACCTGACCGAGCTATAA 58.692 52.381 0.00 0.00 0.00 0.98
2262 2353 1.379977 CCCTGACCTGACCGAGCTA 60.380 63.158 0.00 0.00 0.00 3.32
2263 2354 2.681778 CCCTGACCTGACCGAGCT 60.682 66.667 0.00 0.00 0.00 4.09
2264 2355 2.997897 ACCCTGACCTGACCGAGC 60.998 66.667 0.00 0.00 0.00 5.03
2265 2356 2.650116 CCACCCTGACCTGACCGAG 61.650 68.421 0.00 0.00 0.00 4.63
2330 2428 4.803426 CGCCACTCTGACCTCGCC 62.803 72.222 0.00 0.00 0.00 5.54
2332 2430 4.803426 GGCGCCACTCTGACCTCG 62.803 72.222 24.80 0.00 0.00 4.63
2333 2431 4.459089 GGGCGCCACTCTGACCTC 62.459 72.222 30.85 1.84 0.00 3.85
2336 2434 4.681978 AACGGGCGCCACTCTGAC 62.682 66.667 30.85 7.76 0.00 3.51
2423 2521 0.534203 AGGCGATCGGTCTCTCTCTC 60.534 60.000 18.30 0.00 0.00 3.20
2424 2522 0.106918 AAGGCGATCGGTCTCTCTCT 60.107 55.000 18.30 0.00 0.00 3.10
2425 2523 0.309612 GAAGGCGATCGGTCTCTCTC 59.690 60.000 18.30 0.00 0.00 3.20
2426 2524 1.104577 GGAAGGCGATCGGTCTCTCT 61.105 60.000 18.30 0.00 0.00 3.10
2469 2571 1.593006 GAACTCACGGAACACACACAG 59.407 52.381 0.00 0.00 0.00 3.66
2542 2644 2.036256 GGGGCATGCACTTGGACT 59.964 61.111 21.47 0.00 0.00 3.85
2557 2659 0.951040 GTGCTTTGGACGACAGAGGG 60.951 60.000 0.00 0.00 32.18 4.30
2573 2675 1.077429 GGTGAGGATTCAGGGGTGC 60.077 63.158 0.00 0.00 32.98 5.01
2584 2686 1.930251 CACTGAGGAAGAGGTGAGGA 58.070 55.000 0.00 0.00 32.12 3.71
2585 2687 0.248843 GCACTGAGGAAGAGGTGAGG 59.751 60.000 0.00 0.00 32.12 3.86
2586 2688 1.067000 CAGCACTGAGGAAGAGGTGAG 60.067 57.143 0.00 0.00 44.77 3.51
2587 2689 0.972134 CAGCACTGAGGAAGAGGTGA 59.028 55.000 0.00 0.00 44.77 4.02
2588 2690 0.673022 GCAGCACTGAGGAAGAGGTG 60.673 60.000 0.81 0.00 44.77 4.00
2589 2691 1.676384 GCAGCACTGAGGAAGAGGT 59.324 57.895 0.81 0.00 0.00 3.85
2590 2692 1.078567 GGCAGCACTGAGGAAGAGG 60.079 63.158 0.81 0.00 0.00 3.69
2591 2693 0.391395 CAGGCAGCACTGAGGAAGAG 60.391 60.000 0.81 0.00 40.97 2.85
2592 2694 1.675801 CAGGCAGCACTGAGGAAGA 59.324 57.895 0.81 0.00 40.97 2.87
2593 2695 2.039405 GCAGGCAGCACTGAGGAAG 61.039 63.158 13.41 0.00 44.79 3.46
2594 2696 2.033141 GCAGGCAGCACTGAGGAA 59.967 61.111 13.41 0.00 44.79 3.36
2624 2726 0.234884 CAAAACGAGCACGGAAGGTC 59.765 55.000 8.74 0.00 44.46 3.85
2647 2749 1.003718 AGGAGAAGGAAAACGGGCG 60.004 57.895 0.00 0.00 0.00 6.13
2669 2771 2.287427 CGACAACGGTTGAGTGTAGTCT 60.287 50.000 26.39 1.17 35.72 3.24
2683 2785 1.372997 CACTGGGAGGTCGACAACG 60.373 63.158 18.91 1.63 41.26 4.10
2705 2807 1.033574 TGTTAAAAACAGGTGCCCCG 58.966 50.000 0.00 0.00 36.25 5.73
2719 2822 1.794116 GTAGCGCGTGGACTTTGTTAA 59.206 47.619 8.43 0.00 0.00 2.01
2755 2858 0.104120 TTGTCCTGTCACGTCACTGG 59.896 55.000 9.29 9.29 36.85 4.00
2781 2885 1.652329 GCATGCATAAGCGTCGTGC 60.652 57.895 14.21 0.00 46.23 5.34
2792 2896 4.525576 CGCGCGAACTGCATGCAT 62.526 61.111 28.94 7.28 46.97 3.96
2861 2981 4.680237 CGACGGAACAGCCAGCCA 62.680 66.667 0.00 0.00 35.94 4.75
2891 3011 0.954449 GATCTATCTCCCCGCGACGA 60.954 60.000 8.23 0.32 0.00 4.20
2892 3012 1.502640 GATCTATCTCCCCGCGACG 59.497 63.158 8.23 0.00 0.00 5.12
2894 3014 1.674651 CCGATCTATCTCCCCGCGA 60.675 63.158 8.23 0.00 0.00 5.87
2895 3015 1.924320 GACCGATCTATCTCCCCGCG 61.924 65.000 0.00 0.00 0.00 6.46
2896 3016 1.884444 GACCGATCTATCTCCCCGC 59.116 63.158 0.00 0.00 0.00 6.13
2897 3017 0.321387 TCGACCGATCTATCTCCCCG 60.321 60.000 0.00 0.00 0.00 5.73
2898 3018 1.166989 GTCGACCGATCTATCTCCCC 58.833 60.000 3.51 0.00 0.00 4.81
2899 3019 1.166989 GGTCGACCGATCTATCTCCC 58.833 60.000 20.85 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.