Multiple sequence alignment - TraesCS7B01G194600

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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 TraesCS7B01G194600 chr7B 100.000 3033 0 0 1 3033 334452887 334455919 0.000000e+00 5602
1 TraesCS7B01G194600 chr7D 86.644 1475 101 53 616 2031 189910119 189911556 0.000000e+00 1544
2 TraesCS7B01G194600 chr7D 91.496 976 63 11 2074 3033 189912428 189913399 0.000000e+00 1325
3 TraesCS7B01G194600 chr7D 89.382 631 41 16 1 605 189909451 189910081 0.000000e+00 771
4 TraesCS7B01G194600 chr7A 87.068 1330 109 30 1731 3028 194289923 194288625 0.000000e+00 1445
5 TraesCS7B01G194600 chr7A 87.660 1175 71 41 610 1725 194291152 194289993 0.000000e+00 1299
6 TraesCS7B01G194600 chr7A 85.758 653 35 26 1 607 194291862 194291222 3.300000e-179 638
7 TraesCS7B01G194600 chr4B 95.449 835 23 7 1202 2031 624107964 624107140 0.000000e+00 1317
8 TraesCS7B01G194600 chr3B 76.699 412 82 12 2606 3007 756823910 756823503 1.830000e-52 217
9 TraesCS7B01G194600 chr3B 76.156 411 85 11 2606 3007 756708778 756708372 1.430000e-48 204


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 TraesCS7B01G194600 chr7B 334452887 334455919 3032 False 5602.000000 5602 100.000000 1 3033 1 chr7B.!!$F1 3032
1 TraesCS7B01G194600 chr7D 189909451 189913399 3948 False 1213.333333 1544 89.174000 1 3033 3 chr7D.!!$F1 3032
2 TraesCS7B01G194600 chr7A 194288625 194291862 3237 True 1127.333333 1445 86.828667 1 3028 3 chr7A.!!$R1 3027
3 TraesCS7B01G194600 chr4B 624107140 624107964 824 True 1317.000000 1317 95.449000 1202 2031 1 chr4B.!!$R1 829

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
565 623 0.034767 TCGGAACCTCGCTCCTAGAA 60.035 55.0 0.0 0.0 0.0 2.10 F
954 1106 0.243907 CGACAAGAGAAAGGCGGAGA 59.756 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1703 0.823460 TGCTGCGTATCATGGACAGA 59.177 50.0 0.00 0.0 0.00 3.41 R
2758 3913 0.387929 GGATGGCGTCAACGGAGATA 59.612 55.0 9.27 0.0 40.23 1.98 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
24 26 4.869861 GCCAACACAGAAATCAACAAAACT 59.130 37.500 0.00 0.00 0.00 2.66
37 39 0.111266 CAAAACTTCGACGGACGCAG 60.111 55.000 0.00 0.00 40.71 5.18
119 138 1.380302 CCCCCAACACTCCAAGGAG 59.620 63.158 14.44 14.44 46.91 3.69
145 170 1.485124 TGCAGTCGAGGTCATACCAT 58.515 50.000 0.00 0.00 41.95 3.55
149 174 3.367498 GCAGTCGAGGTCATACCATATCC 60.367 52.174 0.00 0.00 41.95 2.59
184 219 3.543665 GATCAGATCAGCAGGAAAAGCT 58.456 45.455 5.44 0.00 44.62 3.74
186 221 4.767578 TCAGATCAGCAGGAAAAGCTAT 57.232 40.909 0.00 0.00 41.14 2.97
400 444 1.318158 CCACTCCATCCTGGCTTTGC 61.318 60.000 0.00 0.00 37.47 3.68
401 445 0.609957 CACTCCATCCTGGCTTTGCA 60.610 55.000 0.00 0.00 37.47 4.08
410 454 3.530535 TCCTGGCTTTGCAAAACTTTTC 58.469 40.909 13.84 0.00 0.00 2.29
445 490 3.181476 GCCAAAGTGAAAGCAGAAAAGGA 60.181 43.478 0.00 0.00 0.00 3.36
552 602 0.721718 CATTTCGTCCTGCTCGGAAC 59.278 55.000 0.00 0.00 45.32 3.62
560 618 3.708220 CTGCTCGGAACCTCGCTCC 62.708 68.421 0.00 0.00 0.00 4.70
565 623 0.034767 TCGGAACCTCGCTCCTAGAA 60.035 55.000 0.00 0.00 0.00 2.10
584 642 2.411628 AGCGGGCATTGTTATGTGTA 57.588 45.000 0.00 0.00 34.12 2.90
598 656 3.068881 TGTAGCTGACACCAGGGC 58.931 61.111 0.00 0.00 40.72 5.19
612 738 2.140792 AGGGCCCGCTCGTTATGAT 61.141 57.895 18.44 0.00 0.00 2.45
653 780 9.986833 GAAATCTTTAAAATGTGTTTGTGCTTT 57.013 25.926 0.00 0.00 0.00 3.51
669 796 1.067669 GCTTTAGCATAGCCTTTGGCC 59.932 52.381 4.82 0.00 45.29 5.36
684 811 2.561478 TGGCCGTAAGAAAGAGCTTT 57.439 45.000 0.00 0.00 43.02 3.51
687 814 2.585845 GCCGTAAGAAAGAGCTTTTGC 58.414 47.619 0.00 0.00 44.12 3.68
705 832 8.220618 GCTTTTGCTTGATTTTACTAGTTGAG 57.779 34.615 0.00 0.00 43.35 3.02
715 855 6.870971 TTTTACTAGTTGAGGAAAACGCAT 57.129 33.333 0.00 0.00 42.14 4.73
716 856 7.966246 TTTTACTAGTTGAGGAAAACGCATA 57.034 32.000 0.00 0.00 42.14 3.14
718 858 7.534085 TTACTAGTTGAGGAAAACGCATATG 57.466 36.000 0.00 0.00 35.13 1.78
724 864 4.380531 TGAGGAAAACGCATATGGATCTC 58.619 43.478 4.56 0.00 0.00 2.75
739 879 4.767478 TGGATCTCTTGCAAGAATCTCAG 58.233 43.478 29.70 20.37 34.03 3.35
798 938 6.725246 CAGAAAAATGGTCAAGTAAAGTCGT 58.275 36.000 0.00 0.00 0.00 4.34
890 1030 2.283821 GCCAGGCCCATCAAACCA 60.284 61.111 0.00 0.00 0.00 3.67
892 1032 1.984026 CCAGGCCCATCAAACCACC 60.984 63.158 0.00 0.00 0.00 4.61
899 1039 1.204467 CCCATCAAACCACCCGAATTG 59.796 52.381 0.00 0.00 0.00 2.32
906 1058 1.913778 ACCACCCGAATTGTTAACCC 58.086 50.000 2.48 0.00 0.00 4.11
907 1059 0.806241 CCACCCGAATTGTTAACCCG 59.194 55.000 2.48 1.87 0.00 5.28
941 1093 2.657296 ACGGTCACGCACGACAAG 60.657 61.111 0.00 1.41 46.04 3.16
945 1097 0.596600 GGTCACGCACGACAAGAGAA 60.597 55.000 0.00 0.00 37.66 2.87
947 1099 1.190323 GTCACGCACGACAAGAGAAAG 59.810 52.381 0.00 0.00 35.88 2.62
948 1100 0.508641 CACGCACGACAAGAGAAAGG 59.491 55.000 0.00 0.00 0.00 3.11
949 1101 1.222115 ACGCACGACAAGAGAAAGGC 61.222 55.000 0.00 0.00 0.00 4.35
954 1106 0.243907 CGACAAGAGAAAGGCGGAGA 59.756 55.000 0.00 0.00 0.00 3.71
963 1115 5.805728 AGAGAAAGGCGGAGAAGAAAAATA 58.194 37.500 0.00 0.00 0.00 1.40
965 1117 6.372937 AGAGAAAGGCGGAGAAGAAAAATAAG 59.627 38.462 0.00 0.00 0.00 1.73
972 1124 6.371825 GGCGGAGAAGAAAAATAAGAGAAAGA 59.628 38.462 0.00 0.00 0.00 2.52
979 1131 7.710766 AGAAAAATAAGAGAAAGACGACGTT 57.289 32.000 0.13 0.00 0.00 3.99
981 1133 5.840940 AAATAAGAGAAAGACGACGTTGG 57.159 39.130 7.90 0.00 0.00 3.77
1008 1160 2.496111 CCGCTTAACCGCCCATATAAA 58.504 47.619 0.00 0.00 0.00 1.40
1010 1162 2.224784 CGCTTAACCGCCCATATAAACC 59.775 50.000 0.00 0.00 0.00 3.27
1012 1164 3.749632 GCTTAACCGCCCATATAAACCCT 60.750 47.826 0.00 0.00 0.00 4.34
1015 1167 1.234615 CCGCCCATATAAACCCTGCG 61.235 60.000 0.00 0.00 40.17 5.18
1066 1218 3.667087 CGTAGCAAGCCAAGCCAA 58.333 55.556 0.00 0.00 0.00 4.52
1067 1219 1.503542 CGTAGCAAGCCAAGCCAAG 59.496 57.895 0.00 0.00 0.00 3.61
1068 1220 1.237285 CGTAGCAAGCCAAGCCAAGT 61.237 55.000 0.00 0.00 0.00 3.16
1069 1221 1.821216 GTAGCAAGCCAAGCCAAGTA 58.179 50.000 0.00 0.00 0.00 2.24
1070 1222 1.740025 GTAGCAAGCCAAGCCAAGTAG 59.260 52.381 0.00 0.00 0.00 2.57
1071 1223 1.213799 GCAAGCCAAGCCAAGTAGC 59.786 57.895 0.00 0.00 0.00 3.58
1072 1224 1.885871 CAAGCCAAGCCAAGTAGCC 59.114 57.895 0.00 0.00 0.00 3.93
1077 1229 0.895100 CCAAGCCAAGTAGCCAAGCA 60.895 55.000 0.00 0.00 0.00 3.91
1263 1433 1.596895 GACGAGAAGAAGGGCGAGGT 61.597 60.000 0.00 0.00 0.00 3.85
1495 1675 4.889856 TCCATGTGATCGCCGCCG 62.890 66.667 3.31 0.00 0.00 6.46
1523 1703 1.595382 GGTTCAGCTGCTCGTGTGT 60.595 57.895 9.47 0.00 0.00 3.72
1813 2087 6.128445 GCGAGATATGTGTATTTCTTGGGATG 60.128 42.308 0.00 0.00 30.62 3.51
1946 2228 8.779354 AGATACATAAGACTTTTGACTGGAAC 57.221 34.615 11.97 0.00 0.00 3.62
1999 2299 6.707440 AGAGTACCAGATGTCATCACTAAG 57.293 41.667 15.20 1.59 0.00 2.18
2061 3198 2.582052 TGGAAACGATTGCTTCTGGTT 58.418 42.857 0.00 0.00 0.00 3.67
2066 3203 3.126001 ACGATTGCTTCTGGTTCTGAA 57.874 42.857 0.00 0.00 0.00 3.02
2067 3204 2.808543 ACGATTGCTTCTGGTTCTGAAC 59.191 45.455 12.05 12.05 0.00 3.18
2101 3238 3.553917 CGGTTGAACAAATTCACCAAACC 59.446 43.478 0.00 0.00 44.66 3.27
2134 3271 1.595794 TCGCCGACTGAAAACAAAGAC 59.404 47.619 0.00 0.00 0.00 3.01
2135 3272 1.656429 CGCCGACTGAAAACAAAGACG 60.656 52.381 0.00 0.00 0.00 4.18
2144 3281 0.598065 AAACAAAGACGGGCTCATGC 59.402 50.000 0.00 0.00 38.76 4.06
2224 3361 2.487934 CTCGATTGGCTGGACCTAATG 58.512 52.381 0.00 0.00 40.22 1.90
2247 3384 6.563422 TGGTGATTGAAAAGAAAGAACAGTG 58.437 36.000 0.00 0.00 0.00 3.66
2252 3389 9.173021 TGATTGAAAAGAAAGAACAGTGTTCTA 57.827 29.630 33.12 17.84 31.41 2.10
2285 3423 7.010183 GGGGAAAAGAAAAGAAAAGAAAGAACG 59.990 37.037 0.00 0.00 0.00 3.95
2290 3428 5.417894 AGAAAAGAAAAGAAAGAACGGTGGT 59.582 36.000 0.00 0.00 0.00 4.16
2390 3532 3.706594 CCCAGAGACTTTACCAGCATCTA 59.293 47.826 0.00 0.00 0.00 1.98
2394 3536 3.983741 AGACTTTACCAGCATCTATCGC 58.016 45.455 0.00 0.00 0.00 4.58
2407 3549 3.944055 TCTATCGCCTTCCTAATCTGC 57.056 47.619 0.00 0.00 0.00 4.26
2426 3568 1.807755 GCATCTTGCAGGCGTGAGATA 60.808 52.381 11.29 0.00 44.26 1.98
2540 3682 2.762887 CCAGTCTGCAGGTATCTTCTCA 59.237 50.000 15.13 0.00 0.00 3.27
2564 3706 0.592637 TTGCTTGATTCACAGCCGTG 59.407 50.000 14.24 0.00 45.08 4.94
2573 3728 2.594592 ACAGCCGTGCTTGTTCCC 60.595 61.111 0.00 0.00 36.40 3.97
2604 3759 3.627395 TTCACCTAGCTGTTACCATGG 57.373 47.619 11.19 11.19 0.00 3.66
2610 3765 3.197766 CCTAGCTGTTACCATGGAACTCA 59.802 47.826 21.47 10.69 0.00 3.41
2631 3786 0.947660 TTGCAGAACGCTGAGCAGAG 60.948 55.000 4.88 0.14 45.17 3.35
2675 3830 1.080434 GCCATCGCCGATCTACTCC 60.080 63.158 0.00 0.00 0.00 3.85
2677 3832 1.235281 CCATCGCCGATCTACTCCGA 61.235 60.000 0.00 0.00 0.00 4.55
2717 3872 4.760047 GCATGGTGGTCGCGGACT 62.760 66.667 6.13 0.00 32.47 3.85
2758 3913 2.653702 GCGCTCACTCTGGTGTCT 59.346 61.111 0.00 0.00 43.41 3.41
2799 3954 0.391597 GGTCAGTGTCTTCGTTCCCA 59.608 55.000 0.00 0.00 0.00 4.37
2806 3961 2.032528 CTTCGTTCCCAGCAGCCA 59.967 61.111 0.00 0.00 0.00 4.75
2851 4006 3.056821 TCAACGATCTTCCAGACAACGAT 60.057 43.478 0.00 0.00 0.00 3.73
2894 4049 2.518112 TGGCGTTCCAGCAAAGCA 60.518 55.556 0.00 0.00 40.97 3.91
2905 4060 0.751643 AGCAAAGCAACAGGTCGGTT 60.752 50.000 0.00 0.00 0.00 4.44
2970 4125 1.078848 GTGGCTCCTTGCATCTCGT 60.079 57.895 0.00 0.00 45.15 4.18
3016 4174 3.561725 GGCTCTCCGAGGTATGAATTTTG 59.438 47.826 0.00 0.00 0.00 2.44
3028 4186 0.237235 GAATTTTGCACGGCTCGACA 59.763 50.000 1.50 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 5.263185 CGTCGAAGTTTTGTTGATTTCTGT 58.737 37.500 0.00 0.00 0.00 3.41
14 15 1.589320 CGTCCGTCGAAGTTTTGTTGA 59.411 47.619 0.00 0.00 42.86 3.18
184 219 6.996180 ATTTAATCAGGACTCTTCGGGATA 57.004 37.500 0.00 0.00 0.00 2.59
186 221 5.693769 AATTTAATCAGGACTCTTCGGGA 57.306 39.130 0.00 0.00 0.00 5.14
400 444 0.599991 GCGGGCCAGGAAAAGTTTTG 60.600 55.000 4.39 0.00 0.00 2.44
401 445 1.745890 GCGGGCCAGGAAAAGTTTT 59.254 52.632 4.39 0.00 0.00 2.43
445 490 4.210331 GTTAGGCCATTGATCCACATTCT 58.790 43.478 5.01 0.00 0.00 2.40
519 569 1.467374 CGAAATGGGTTCATTCACCGC 60.467 52.381 0.00 0.00 42.29 5.68
560 618 3.002656 CACATAACAATGCCCGCTTCTAG 59.997 47.826 0.00 0.00 0.00 2.43
565 623 2.288666 CTACACATAACAATGCCCGCT 58.711 47.619 0.00 0.00 0.00 5.52
570 628 4.944962 TGTCAGCTACACATAACAATGC 57.055 40.909 0.00 0.00 31.43 3.56
592 650 3.861797 ATAACGAGCGGGCCCTGG 61.862 66.667 22.43 6.20 0.00 4.45
593 651 2.383245 ATCATAACGAGCGGGCCCTG 62.383 60.000 22.43 14.92 0.00 4.45
594 652 2.140792 ATCATAACGAGCGGGCCCT 61.141 57.895 22.43 0.00 0.00 5.19
598 656 2.732412 ATCTCATCATAACGAGCGGG 57.268 50.000 0.00 0.00 0.00 6.13
601 659 4.476862 TCGCTAATCTCATCATAACGAGC 58.523 43.478 0.00 0.00 0.00 5.03
602 660 5.004251 GCATCGCTAATCTCATCATAACGAG 59.996 44.000 0.00 0.00 0.00 4.18
603 661 4.859245 GCATCGCTAATCTCATCATAACGA 59.141 41.667 0.00 0.00 0.00 3.85
604 662 4.259174 CGCATCGCTAATCTCATCATAACG 60.259 45.833 0.00 0.00 0.00 3.18
605 663 4.859245 TCGCATCGCTAATCTCATCATAAC 59.141 41.667 0.00 0.00 0.00 1.89
606 664 5.059404 TCGCATCGCTAATCTCATCATAA 57.941 39.130 0.00 0.00 0.00 1.90
608 666 3.582714 TCGCATCGCTAATCTCATCAT 57.417 42.857 0.00 0.00 0.00 2.45
612 738 3.982475 AGATTTCGCATCGCTAATCTCA 58.018 40.909 7.13 0.00 35.09 3.27
669 796 5.095691 TCAAGCAAAAGCTCTTTCTTACG 57.904 39.130 0.00 0.00 31.45 3.18
684 811 8.458573 TTTCCTCAACTAGTAAAATCAAGCAA 57.541 30.769 0.00 0.00 0.00 3.91
687 814 7.534239 GCGTTTTCCTCAACTAGTAAAATCAAG 59.466 37.037 0.00 0.00 0.00 3.02
702 829 4.101585 AGAGATCCATATGCGTTTTCCTCA 59.898 41.667 0.00 0.00 0.00 3.86
703 830 4.636249 AGAGATCCATATGCGTTTTCCTC 58.364 43.478 0.00 0.00 0.00 3.71
704 831 4.696479 AGAGATCCATATGCGTTTTCCT 57.304 40.909 0.00 0.00 0.00 3.36
705 832 4.555511 GCAAGAGATCCATATGCGTTTTCC 60.556 45.833 0.00 0.00 0.00 3.13
711 851 3.396560 TCTTGCAAGAGATCCATATGCG 58.603 45.455 25.16 0.00 39.81 4.73
715 855 6.490241 TGAGATTCTTGCAAGAGATCCATA 57.510 37.500 28.68 17.55 36.22 2.74
716 856 5.369409 TGAGATTCTTGCAAGAGATCCAT 57.631 39.130 28.68 21.43 36.22 3.41
718 858 3.560896 GCTGAGATTCTTGCAAGAGATCC 59.439 47.826 28.68 23.58 36.22 3.36
724 864 2.475852 GCTTCGCTGAGATTCTTGCAAG 60.476 50.000 20.81 20.81 0.00 4.01
739 879 3.181507 TGCTATTCAATTCTGTGCTTCGC 60.182 43.478 0.00 0.00 0.00 4.70
749 889 7.975616 TGCTCCTAAACAAATGCTATTCAATTC 59.024 33.333 0.00 0.00 0.00 2.17
752 892 6.658816 TCTGCTCCTAAACAAATGCTATTCAA 59.341 34.615 0.00 0.00 0.00 2.69
798 938 3.998672 GGCAACCACTCGGACGGA 61.999 66.667 0.00 0.00 35.59 4.69
848 988 4.499696 CGGAGGTGTTTTTCAATGCTTTCT 60.500 41.667 0.00 0.00 0.00 2.52
890 1030 0.037160 AGCGGGTTAACAATTCGGGT 59.963 50.000 8.10 0.00 0.00 5.28
892 1032 0.372334 CGAGCGGGTTAACAATTCGG 59.628 55.000 8.10 0.00 0.00 4.30
899 1039 3.122971 GTGGGCGAGCGGGTTAAC 61.123 66.667 0.00 0.00 0.00 2.01
927 1079 1.190323 CTTTCTCTTGTCGTGCGTGAC 59.810 52.381 1.43 1.43 39.37 3.67
928 1080 1.487482 CTTTCTCTTGTCGTGCGTGA 58.513 50.000 0.00 0.00 0.00 4.35
929 1081 0.508641 CCTTTCTCTTGTCGTGCGTG 59.491 55.000 0.00 0.00 0.00 5.34
930 1082 1.222115 GCCTTTCTCTTGTCGTGCGT 61.222 55.000 0.00 0.00 0.00 5.24
931 1083 1.493311 GCCTTTCTCTTGTCGTGCG 59.507 57.895 0.00 0.00 0.00 5.34
932 1084 1.493311 CGCCTTTCTCTTGTCGTGC 59.507 57.895 0.00 0.00 0.00 5.34
941 1093 6.371825 TCTTATTTTTCTTCTCCGCCTTTCTC 59.628 38.462 0.00 0.00 0.00 2.87
945 1097 5.805728 TCTCTTATTTTTCTTCTCCGCCTT 58.194 37.500 0.00 0.00 0.00 4.35
947 1099 6.371825 TCTTTCTCTTATTTTTCTTCTCCGCC 59.628 38.462 0.00 0.00 0.00 6.13
948 1100 7.237871 GTCTTTCTCTTATTTTTCTTCTCCGC 58.762 38.462 0.00 0.00 0.00 5.54
949 1101 7.328737 TCGTCTTTCTCTTATTTTTCTTCTCCG 59.671 37.037 0.00 0.00 0.00 4.63
954 1106 7.710766 ACGTCGTCTTTCTCTTATTTTTCTT 57.289 32.000 0.00 0.00 0.00 2.52
963 1115 1.499049 GCCAACGTCGTCTTTCTCTT 58.501 50.000 0.00 0.00 0.00 2.85
965 1117 1.773496 CGCCAACGTCGTCTTTCTC 59.227 57.895 0.00 0.00 33.53 2.87
1015 1167 3.799755 GCCCACAATGCGGTCGAC 61.800 66.667 7.13 7.13 0.00 4.20
1039 1191 4.735132 TTGCTACGCCGCTCGCTT 62.735 61.111 0.00 0.00 43.23 4.68
1051 1203 1.950484 GCTACTTGGCTTGGCTTGCTA 60.950 52.381 2.77 0.00 0.00 3.49
1064 1216 2.474526 CGATCGTTTGCTTGGCTACTTG 60.475 50.000 7.03 0.00 0.00 3.16
1065 1217 1.732259 CGATCGTTTGCTTGGCTACTT 59.268 47.619 7.03 0.00 0.00 2.24
1066 1218 1.359848 CGATCGTTTGCTTGGCTACT 58.640 50.000 7.03 0.00 0.00 2.57
1067 1219 0.247695 GCGATCGTTTGCTTGGCTAC 60.248 55.000 17.81 0.00 0.00 3.58
1068 1220 1.366111 GGCGATCGTTTGCTTGGCTA 61.366 55.000 17.81 0.00 32.36 3.93
1069 1221 2.690778 GGCGATCGTTTGCTTGGCT 61.691 57.895 17.81 0.00 32.36 4.75
1070 1222 2.202479 GGCGATCGTTTGCTTGGC 60.202 61.111 17.81 0.00 32.36 4.52
1071 1223 2.098298 CGGCGATCGTTTGCTTGG 59.902 61.111 17.81 0.00 32.36 3.61
1072 1224 2.574212 GCGGCGATCGTTTGCTTG 60.574 61.111 17.81 0.39 41.72 4.01
1077 1229 0.455972 CATTTTGGCGGCGATCGTTT 60.456 50.000 17.81 0.00 41.72 3.60
1253 1423 3.003763 GTCCTCCACCTCGCCCTT 61.004 66.667 0.00 0.00 0.00 3.95
1263 1433 2.745100 CCTCGTCGTCGTCCTCCA 60.745 66.667 1.33 0.00 38.33 3.86
1310 1483 4.335647 CACCTGCCGCTTCCACCT 62.336 66.667 0.00 0.00 0.00 4.00
1504 1684 2.356313 ACACGAGCAGCTGAACCG 60.356 61.111 20.43 18.43 0.00 4.44
1523 1703 0.823460 TGCTGCGTATCATGGACAGA 59.177 50.000 0.00 0.00 0.00 3.41
1813 2087 6.410540 ACAATTTACTCAGGGTCATCTTCTC 58.589 40.000 0.00 0.00 0.00 2.87
1871 2145 4.515191 GGAAATCACAACAGCAGTTCTACA 59.485 41.667 0.00 0.00 35.28 2.74
1946 2228 2.287608 TGTTATACGATGAGCAGCGGAG 60.288 50.000 12.89 0.00 45.50 4.63
1999 2299 7.095102 GGATACCGACTTCTCTTCTAGTGTATC 60.095 44.444 0.00 0.00 33.67 2.24
2031 2331 9.271828 AGAAGCAATCGTTTCCAAATTTTAATT 57.728 25.926 0.00 0.00 33.11 1.40
2061 3198 2.171027 ACCGTTGGTTACTTGGTTCAGA 59.829 45.455 0.00 0.00 27.29 3.27
2066 3203 2.684374 GTTCAACCGTTGGTTACTTGGT 59.316 45.455 11.35 0.00 45.01 3.67
2067 3204 2.683867 TGTTCAACCGTTGGTTACTTGG 59.316 45.455 11.35 0.00 45.01 3.61
2068 3205 4.358494 TTGTTCAACCGTTGGTTACTTG 57.642 40.909 11.35 0.00 45.01 3.16
2069 3206 5.585820 ATTTGTTCAACCGTTGGTTACTT 57.414 34.783 11.35 0.00 45.01 2.24
2070 3207 5.125739 TGAATTTGTTCAACCGTTGGTTACT 59.874 36.000 11.35 0.00 45.01 2.24
2071 3208 5.230516 GTGAATTTGTTCAACCGTTGGTTAC 59.769 40.000 11.35 7.95 45.01 2.50
2072 3209 5.341617 GTGAATTTGTTCAACCGTTGGTTA 58.658 37.500 11.35 0.00 45.01 2.85
2117 3254 1.263217 CCCGTCTTTGTTTTCAGTCGG 59.737 52.381 0.00 0.00 37.04 4.79
2119 3256 1.947456 AGCCCGTCTTTGTTTTCAGTC 59.053 47.619 0.00 0.00 0.00 3.51
2135 3272 2.747460 TTGTCAGCGCATGAGCCC 60.747 61.111 18.40 7.08 39.07 5.19
2144 3281 2.341257 AGCACTATGAAGTTGTCAGCG 58.659 47.619 0.00 0.00 40.43 5.18
2224 3361 6.564328 ACACTGTTCTTTCTTTTCAATCACC 58.436 36.000 0.00 0.00 0.00 4.02
2259 3397 7.010183 CGTTCTTTCTTTTCTTTTCTTTTCCCC 59.990 37.037 0.00 0.00 0.00 4.81
2262 3400 8.373256 CACCGTTCTTTCTTTTCTTTTCTTTTC 58.627 33.333 0.00 0.00 0.00 2.29
2263 3401 7.330946 CCACCGTTCTTTCTTTTCTTTTCTTTT 59.669 33.333 0.00 0.00 0.00 2.27
2264 3402 6.811665 CCACCGTTCTTTCTTTTCTTTTCTTT 59.188 34.615 0.00 0.00 0.00 2.52
2265 3403 6.071560 ACCACCGTTCTTTCTTTTCTTTTCTT 60.072 34.615 0.00 0.00 0.00 2.52
2266 3404 5.417894 ACCACCGTTCTTTCTTTTCTTTTCT 59.582 36.000 0.00 0.00 0.00 2.52
2285 3423 3.626930 TGGCACCAATAATTAGACCACC 58.373 45.455 0.00 0.00 0.00 4.61
2390 3532 2.636893 AGATGCAGATTAGGAAGGCGAT 59.363 45.455 0.00 0.00 0.00 4.58
2407 3549 2.133553 CTATCTCACGCCTGCAAGATG 58.866 52.381 6.59 0.00 34.07 2.90
2420 3562 2.037901 CAGGCTGAGCTTCCTATCTCA 58.962 52.381 9.42 0.00 37.70 3.27
2540 3682 3.015327 GGCTGTGAATCAAGCAAGAGAT 58.985 45.455 15.44 0.00 0.00 2.75
2573 3728 2.503356 AGCTAGGTGAATCAGTTCTGGG 59.497 50.000 0.00 0.00 35.33 4.45
2604 3759 3.736581 GCGTTCTGCAAGTGAGTTC 57.263 52.632 0.00 0.00 45.45 3.01
2631 3786 3.092511 TGAGGGGCCTCATCCTGC 61.093 66.667 4.79 0.00 46.80 4.85
2758 3913 0.387929 GGATGGCGTCAACGGAGATA 59.612 55.000 9.27 0.00 40.23 1.98
2806 3961 3.222354 GACGCAGACTTCCACCGGT 62.222 63.158 0.00 0.00 0.00 5.28
2851 4006 2.622942 GCTCTTCACCACCATGTTGAAA 59.377 45.455 0.00 0.00 0.00 2.69
2894 4049 1.487558 ACCTGTAACAACCGACCTGTT 59.512 47.619 0.00 0.00 40.13 3.16


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

AutoCloner maintained by Alex Coulton.