Multiple sequence alignment - TraesCS7A01G528100

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 TraesCS7A01G528100 chr7A 100.000 3953 0 0 1 3953 708712860 708708908 0.000000e+00 7300.0
1 TraesCS7A01G528100 chr7A 93.276 1859 119 6 1 1857 618109129 618110983 0.000000e+00 2736.0
2 TraesCS7A01G528100 chr7A 92.701 822 31 12 3157 3953 708783538 708784355 0.000000e+00 1158.0
3 TraesCS7A01G528100 chr5D 94.190 1859 102 6 1 1857 15725259 15727113 0.000000e+00 2830.0
4 TraesCS7A01G528100 chr5D 93.995 766 44 2 1859 2624 477880019 477880782 0.000000e+00 1158.0
5 TraesCS7A01G528100 chr5D 93.791 757 45 2 1858 2612 15727143 15727899 0.000000e+00 1136.0
6 TraesCS7A01G528100 chr5D 94.118 51 3 0 3228 3278 406199455 406199405 1.180000e-10 78.7
7 TraesCS7A01G528100 chr5B 93.384 1859 117 6 1 1857 660693619 660691765 0.000000e+00 2747.0
8 TraesCS7A01G528100 chr5B 93.617 47 3 0 3232 3278 486897345 486897299 1.970000e-08 71.3
9 TraesCS7A01G528100 chr4B 93.384 1859 117 6 1 1857 612336352 612338206 0.000000e+00 2747.0
10 TraesCS7A01G528100 chr4B 92.706 754 54 1 1858 2611 176026601 176027353 0.000000e+00 1086.0
11 TraesCS7A01G528100 chr5A 93.222 1859 119 7 1 1857 10295631 10297484 0.000000e+00 2728.0
12 TraesCS7A01G528100 chr3B 93.111 1858 124 4 1 1857 818056644 818058498 0.000000e+00 2719.0
13 TraesCS7A01G528100 chr1B 92.957 1860 119 9 1 1858 526384578 526382729 0.000000e+00 2699.0
14 TraesCS7A01G528100 chr1B 93.351 752 50 0 1858 2609 526382700 526381949 0.000000e+00 1112.0
15 TraesCS7A01G528100 chr4A 93.198 1823 117 7 38 1857 597729891 597728073 0.000000e+00 2673.0
16 TraesCS7A01G528100 chr4A 93.209 751 51 0 1858 2608 583816277 583815527 0.000000e+00 1105.0
17 TraesCS7A01G528100 chr2B 92.684 1859 129 7 1 1857 12280666 12282519 0.000000e+00 2673.0
18 TraesCS7A01G528100 chr7B 90.922 1377 76 33 2606 3953 709049989 709048633 0.000000e+00 1805.0
19 TraesCS7A01G528100 chr7B 93.758 785 35 7 3182 3953 709093912 709094695 0.000000e+00 1166.0
20 TraesCS7A01G528100 chr7B 92.686 752 53 1 1858 2609 42034207 42033458 0.000000e+00 1083.0
21 TraesCS7A01G528100 chr7D 93.995 1199 41 17 2769 3953 615943888 615942707 0.000000e+00 1786.0
22 TraesCS7A01G528100 chr7D 93.376 785 38 8 3182 3953 616008198 616008981 0.000000e+00 1149.0
23 TraesCS7A01G528100 chr7D 96.667 60 0 2 2693 2751 615943943 615943885 9.040000e-17 99.0
24 TraesCS7A01G528100 chr2D 94.695 754 40 0 1858 2611 643682967 643682214 0.000000e+00 1171.0
25 TraesCS7A01G528100 chr3A 93.883 752 46 0 1858 2609 87796452 87797203 0.000000e+00 1134.0
26 TraesCS7A01G528100 chr3A 93.484 752 47 2 1858 2609 59805558 59806307 0.000000e+00 1116.0


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 TraesCS7A01G528100 chr7A 708708908 708712860 3952 True 7300.0 7300 100.0000 1 3953 1 chr7A.!!$R1 3952
1 TraesCS7A01G528100 chr7A 618109129 618110983 1854 False 2736.0 2736 93.2760 1 1857 1 chr7A.!!$F1 1856
2 TraesCS7A01G528100 chr7A 708783538 708784355 817 False 1158.0 1158 92.7010 3157 3953 1 chr7A.!!$F2 796
3 TraesCS7A01G528100 chr5D 15725259 15727899 2640 False 1983.0 2830 93.9905 1 2612 2 chr5D.!!$F2 2611
4 TraesCS7A01G528100 chr5D 477880019 477880782 763 False 1158.0 1158 93.9950 1859 2624 1 chr5D.!!$F1 765
5 TraesCS7A01G528100 chr5B 660691765 660693619 1854 True 2747.0 2747 93.3840 1 1857 1 chr5B.!!$R2 1856
6 TraesCS7A01G528100 chr4B 612336352 612338206 1854 False 2747.0 2747 93.3840 1 1857 1 chr4B.!!$F2 1856
7 TraesCS7A01G528100 chr4B 176026601 176027353 752 False 1086.0 1086 92.7060 1858 2611 1 chr4B.!!$F1 753
8 TraesCS7A01G528100 chr5A 10295631 10297484 1853 False 2728.0 2728 93.2220 1 1857 1 chr5A.!!$F1 1856
9 TraesCS7A01G528100 chr3B 818056644 818058498 1854 False 2719.0 2719 93.1110 1 1857 1 chr3B.!!$F1 1856
10 TraesCS7A01G528100 chr1B 526381949 526384578 2629 True 1905.5 2699 93.1540 1 2609 2 chr1B.!!$R1 2608
11 TraesCS7A01G528100 chr4A 597728073 597729891 1818 True 2673.0 2673 93.1980 38 1857 1 chr4A.!!$R2 1819
12 TraesCS7A01G528100 chr4A 583815527 583816277 750 True 1105.0 1105 93.2090 1858 2608 1 chr4A.!!$R1 750
13 TraesCS7A01G528100 chr2B 12280666 12282519 1853 False 2673.0 2673 92.6840 1 1857 1 chr2B.!!$F1 1856
14 TraesCS7A01G528100 chr7B 709048633 709049989 1356 True 1805.0 1805 90.9220 2606 3953 1 chr7B.!!$R2 1347
15 TraesCS7A01G528100 chr7B 709093912 709094695 783 False 1166.0 1166 93.7580 3182 3953 1 chr7B.!!$F1 771
16 TraesCS7A01G528100 chr7B 42033458 42034207 749 True 1083.0 1083 92.6860 1858 2609 1 chr7B.!!$R1 751
17 TraesCS7A01G528100 chr7D 616008198 616008981 783 False 1149.0 1149 93.3760 3182 3953 1 chr7D.!!$F1 771
18 TraesCS7A01G528100 chr7D 615942707 615943943 1236 True 942.5 1786 95.3310 2693 3953 2 chr7D.!!$R1 1260
19 TraesCS7A01G528100 chr2D 643682214 643682967 753 True 1171.0 1171 94.6950 1858 2611 1 chr2D.!!$R1 753
20 TraesCS7A01G528100 chr3A 87796452 87797203 751 False 1134.0 1134 93.8830 1858 2609 1 chr3A.!!$F2 751
21 TraesCS7A01G528100 chr3A 59805558 59806307 749 False 1116.0 1116 93.4840 1858 2609 1 chr3A.!!$F1 751

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
243 245 0.539051 ACCTTGAAGGGCGATGAGAG 59.461 55.0 16.78 0.0 40.58 3.20 F
1066 1071 0.033991 ACGAGGCTCTCCTTGCTAGA 60.034 55.0 13.50 0.0 46.10 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1312 1318 0.034896 GAGTTCGGGAGCTTGTTGGA 59.965 55.0 0.0 0.0 0.00 3.53 R
2961 3021 0.039165 GGTGGCTGCTAACACTTTGC 60.039 55.0 0.0 0.0 37.72 3.68 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
60 61 3.021695 ACCACTGCTCCATGATTTGATG 58.978 45.455 0.00 0.00 0.00 3.07
81 82 1.441311 CCCAACGCAAAGTGCCTTT 59.559 52.632 0.00 0.00 41.12 3.11
88 89 2.625790 ACGCAAAGTGCCTTTATTCCAA 59.374 40.909 0.63 0.00 41.12 3.53
144 145 8.396390 GCATTTGAATGTATCTATAGCATCCAG 58.604 37.037 5.68 0.00 38.65 3.86
243 245 0.539051 ACCTTGAAGGGCGATGAGAG 59.461 55.000 16.78 0.00 40.58 3.20
260 262 5.441718 TGAGAGGATTAGGTTTTGCAGAT 57.558 39.130 0.00 0.00 0.00 2.90
310 312 8.725405 TGTGTGAAAACAGTAAAATACTCTGA 57.275 30.769 0.00 0.00 36.76 3.27
365 367 2.132762 CCTACGTGTGGTTTGAGACAC 58.867 52.381 0.00 0.00 39.31 3.67
385 387 2.092375 ACGGAGATCCAATTTCCCCTTC 60.092 50.000 0.00 0.00 35.14 3.46
395 397 5.790618 TCCAATTTCCCCTTCTCTCTTTCTA 59.209 40.000 0.00 0.00 0.00 2.10
459 461 3.558533 GGAAACGGGTGAATTACAGGAGT 60.559 47.826 0.00 0.00 0.00 3.85
500 502 3.323691 GCCCTGGTATTTCACACCTTTTT 59.676 43.478 0.00 0.00 36.96 1.94
501 503 4.560716 GCCCTGGTATTTCACACCTTTTTC 60.561 45.833 0.00 0.00 36.96 2.29
524 526 1.269569 CGCGGATGACAGCCTGTTATA 60.270 52.381 8.35 0.00 33.92 0.98
537 539 8.757164 ACAGCCTGTTATATTTTAAAGCAAAC 57.243 30.769 0.00 0.00 0.00 2.93
539 541 9.369904 CAGCCTGTTATATTTTAAAGCAAACAT 57.630 29.630 7.49 0.00 0.00 2.71
582 584 5.762179 AGAACATCCTGGACAACTATGAA 57.238 39.130 0.00 0.00 0.00 2.57
656 658 6.395426 AAACAAATGCTCACAAGAAGATGA 57.605 33.333 0.00 0.00 0.00 2.92
691 693 4.801330 AATGTCCTGAATGTAGTGACGA 57.199 40.909 0.00 0.00 0.00 4.20
699 701 5.289675 CCTGAATGTAGTGACGATGACTTTC 59.710 44.000 0.00 0.00 0.00 2.62
702 704 4.492791 TGTAGTGACGATGACTTTCGAA 57.507 40.909 0.00 0.00 41.62 3.71
714 716 7.148120 ACGATGACTTTCGAAGAGAAATACCTA 60.148 37.037 12.35 0.00 46.60 3.08
766 769 3.369546 AAAGGGAAATTCAAGCACACG 57.630 42.857 0.00 0.00 0.00 4.49
786 789 5.237779 ACACGAAAGATAAAGCGAGGAAAAA 59.762 36.000 0.00 0.00 0.00 1.94
826 829 5.654209 AGAAAAATATTCTTCCAGTGGAGCC 59.346 40.000 12.67 0.00 31.21 4.70
859 862 2.300956 TTAAATCAGTGGCCCAAGCA 57.699 45.000 0.00 0.00 42.56 3.91
880 883 0.968405 TCCCCACTTTTGCAATGAGC 59.032 50.000 0.00 0.00 45.96 4.26
940 943 3.141398 GCACATGACCAGAGACTTTTGA 58.859 45.455 0.00 0.00 0.00 2.69
955 958 6.599445 AGACTTTTGATGGGGAGATGATAAG 58.401 40.000 0.00 0.00 0.00 1.73
1022 1025 5.450818 ACATAAAAGCCAAGGAGGTATGA 57.549 39.130 0.00 0.00 40.61 2.15
1066 1071 0.033991 ACGAGGCTCTCCTTGCTAGA 60.034 55.000 13.50 0.00 46.10 2.43
1098 1103 3.684305 CGACTTATTGCACATCCTGACAA 59.316 43.478 0.00 0.00 0.00 3.18
1115 1120 0.710567 CAACTTGTGCGCGAGAGTAG 59.289 55.000 21.46 1.82 0.00 2.57
1130 1135 5.006455 GCGAGAGTAGTTAAGGCAAAATACC 59.994 44.000 6.60 0.00 31.87 2.73
1159 1164 0.457443 CTGATCTGCTAGACACGGCA 59.543 55.000 0.00 0.00 36.94 5.69
1166 1171 4.513442 TCTGCTAGACACGGCATTTATTT 58.487 39.130 0.00 0.00 37.83 1.40
1183 1188 0.878416 TTTATAATGCATCGCCGGGC 59.122 50.000 9.54 9.54 0.00 6.13
1199 1204 1.533711 GGCTGGCAGGGTATCATGT 59.466 57.895 17.64 0.00 0.00 3.21
1210 1215 5.065914 CAGGGTATCATGTATGGTTTGGAG 58.934 45.833 0.00 0.00 0.00 3.86
1258 1264 3.364621 GCATTTGCAACGGAAATAGTGTG 59.635 43.478 0.00 0.00 41.59 3.82
1267 1273 2.159585 CGGAAATAGTGTGCGCATTTGA 60.160 45.455 15.91 0.00 0.00 2.69
1278 1284 4.215185 TGTGCGCATTTGAAGAGACAATTA 59.785 37.500 15.91 0.00 0.00 1.40
1282 1288 6.538381 TGCGCATTTGAAGAGACAATTAGATA 59.462 34.615 5.66 0.00 0.00 1.98
1333 1339 0.600255 CAACAAGCTCCCGAACTCGT 60.600 55.000 0.00 0.00 37.74 4.18
1378 1384 1.000955 GAGAGTCACGCTTGGAAGGAA 59.999 52.381 0.00 0.00 0.00 3.36
1382 1388 1.734465 GTCACGCTTGGAAGGAAGATG 59.266 52.381 0.00 0.00 0.00 2.90
1405 1411 5.980715 TGACATCATGCGTATATTTACACGT 59.019 36.000 0.00 0.00 40.25 4.49
1457 1467 6.700081 CCGATTACCAAATTATGACGAAGAGA 59.300 38.462 0.00 0.00 0.00 3.10
1571 1581 0.258774 GGTCCAGCCACAATACCCAT 59.741 55.000 0.00 0.00 37.17 4.00
1574 1584 0.033208 CCAGCCACAATACCCATGGT 60.033 55.000 11.73 1.30 40.16 3.55
1641 1651 7.062488 CCCCAAAAAGTACGTATTTTTACATGC 59.938 37.037 23.73 0.00 37.67 4.06
1685 1695 5.941058 TGGCGGTTCAAACTAATAGATTTCA 59.059 36.000 0.00 0.00 0.00 2.69
1808 1819 3.775316 ACGAACTCAAGGAGGTATGGAAT 59.225 43.478 0.00 0.00 33.35 3.01
1909 1949 4.022416 GTGTTTGGCACCATAGAAATGACA 60.022 41.667 0.00 0.00 42.10 3.58
1931 1971 4.062991 ACGATCTTCGCAAAAGGTAAAGT 58.937 39.130 0.00 0.00 45.12 2.66
2059 2099 2.349701 TTGCCATCCGTGCAACAAT 58.650 47.368 0.00 0.00 43.36 2.71
2061 2101 1.093972 TGCCATCCGTGCAACAATAG 58.906 50.000 0.00 0.00 35.74 1.73
2115 2155 0.983378 AGCTCGGATGGGCTAAGGTT 60.983 55.000 0.00 0.00 37.00 3.50
2137 2177 6.347644 GGTTAATGTTGATGGAAGCTTTTTGC 60.348 38.462 0.00 0.00 43.29 3.68
2153 2193 4.431416 TTTTGCAGGAAAGTAGGAGTGA 57.569 40.909 0.00 0.00 0.00 3.41
2209 2249 7.805163 TGGAAGAATTATCTTATCAGCTTGGA 58.195 34.615 0.00 0.00 45.91 3.53
2231 2271 3.388345 TTATATACCGCGGTGCAATGA 57.612 42.857 40.02 22.44 0.00 2.57
2236 2276 2.553770 CGCGGTGCAATGAAACGA 59.446 55.556 1.25 0.00 0.00 3.85
2245 2285 0.110867 CAATGAAACGAACTGCGCGA 60.111 50.000 12.10 0.00 46.04 5.87
2325 2366 0.817654 TCATCGAGACGGATTGCAGT 59.182 50.000 0.00 0.00 0.00 4.40
2328 2369 0.601057 TCGAGACGGATTGCAGTTCA 59.399 50.000 0.00 0.00 0.00 3.18
2329 2370 1.000394 TCGAGACGGATTGCAGTTCAA 60.000 47.619 0.00 0.00 39.32 2.69
2344 2385 0.516877 TTCAATGACAAAGGCGCTCG 59.483 50.000 7.64 0.00 0.00 5.03
2368 2409 5.870433 GTCCTCTCGTCTATTGATAGATCGA 59.130 44.000 16.89 16.89 41.09 3.59
2499 2541 1.211969 GCGTAGAGAGTTGCGTGGA 59.788 57.895 0.00 0.00 0.00 4.02
2551 2593 1.746615 TTGAGCGAGGCCTTGCATC 60.747 57.895 40.11 32.01 42.40 3.91
2565 2607 4.494199 GCCTTGCATCATTGTACGAACTAC 60.494 45.833 0.00 0.00 0.00 2.73
2639 2681 1.064060 ACTGTTCGAGTTTGCTTGTGC 59.936 47.619 0.00 0.00 40.20 4.57
2667 2709 1.417890 CCATCGGTCCTGCTTAGGATT 59.582 52.381 0.00 0.00 40.51 3.01
2671 2713 3.101437 TCGGTCCTGCTTAGGATTGTTA 58.899 45.455 0.00 0.00 40.51 2.41
2767 2810 2.471103 CGACCACGGAAATAACGAAACG 60.471 50.000 0.00 0.00 35.72 3.60
2822 2865 4.761235 AGACATTTCTGCAACACATGAG 57.239 40.909 0.00 0.00 0.00 2.90
2824 2867 2.029649 ACATTTCTGCAACACATGAGGC 60.030 45.455 0.00 0.00 0.00 4.70
2825 2868 1.689984 TTTCTGCAACACATGAGGCA 58.310 45.000 0.00 2.41 34.66 4.75
2826 2869 1.913778 TTCTGCAACACATGAGGCAT 58.086 45.000 0.00 0.00 35.45 4.40
2828 2871 2.635714 TCTGCAACACATGAGGCATAG 58.364 47.619 0.00 0.00 35.45 2.23
2835 2878 5.771469 CAACACATGAGGCATAGTTTCAAA 58.229 37.500 0.00 0.00 0.00 2.69
2884 2943 4.398549 TTTAAGACGAAAATGAGCACCG 57.601 40.909 0.00 0.00 0.00 4.94
2888 2947 1.798813 GACGAAAATGAGCACCGAACT 59.201 47.619 0.00 0.00 0.00 3.01
2889 2948 2.991190 GACGAAAATGAGCACCGAACTA 59.009 45.455 0.00 0.00 0.00 2.24
2891 2950 4.000988 ACGAAAATGAGCACCGAACTAAT 58.999 39.130 0.00 0.00 0.00 1.73
2892 2951 4.454504 ACGAAAATGAGCACCGAACTAATT 59.545 37.500 0.00 0.00 0.00 1.40
2893 2952 5.022021 CGAAAATGAGCACCGAACTAATTC 58.978 41.667 0.00 0.00 0.00 2.17
2895 2954 3.627395 ATGAGCACCGAACTAATTCCA 57.373 42.857 0.00 0.00 0.00 3.53
2897 2956 2.037902 TGAGCACCGAACTAATTCCACA 59.962 45.455 0.00 0.00 0.00 4.17
2898 2957 2.415512 GAGCACCGAACTAATTCCACAC 59.584 50.000 0.00 0.00 0.00 3.82
2899 2958 2.147958 GCACCGAACTAATTCCACACA 58.852 47.619 0.00 0.00 0.00 3.72
2901 2960 2.482721 CACCGAACTAATTCCACACACC 59.517 50.000 0.00 0.00 0.00 4.16
2902 2961 2.370849 ACCGAACTAATTCCACACACCT 59.629 45.455 0.00 0.00 0.00 4.00
2908 2967 1.901591 AATTCCACACACCTGAGCAG 58.098 50.000 0.00 0.00 0.00 4.24
2909 2968 0.767375 ATTCCACACACCTGAGCAGT 59.233 50.000 0.00 0.00 0.00 4.40
2910 2969 1.419381 TTCCACACACCTGAGCAGTA 58.581 50.000 0.00 0.00 0.00 2.74
2911 2970 1.419381 TCCACACACCTGAGCAGTAA 58.581 50.000 0.00 0.00 0.00 2.24
2912 2971 1.977854 TCCACACACCTGAGCAGTAAT 59.022 47.619 0.00 0.00 0.00 1.89
2913 2972 2.028112 TCCACACACCTGAGCAGTAATC 60.028 50.000 0.00 0.00 0.00 1.75
2914 2973 2.027745 CCACACACCTGAGCAGTAATCT 60.028 50.000 0.00 0.00 0.00 2.40
2915 2974 3.195610 CCACACACCTGAGCAGTAATCTA 59.804 47.826 0.00 0.00 0.00 1.98
2921 2980 3.311871 ACCTGAGCAGTAATCTACGTACG 59.688 47.826 15.01 15.01 0.00 3.67
2938 2997 2.074547 ACGTATGAACACAAGACCCG 57.925 50.000 0.00 0.00 0.00 5.28
3000 3060 2.434761 CTACGTACGTGGCTTCGTAAG 58.565 52.381 30.25 12.55 45.55 2.34
3070 3138 4.688879 CGTTCTTCCAATACAGTTAGCACA 59.311 41.667 0.00 0.00 0.00 4.57
3074 3142 1.665679 CCAATACAGTTAGCACAGCCG 59.334 52.381 0.00 0.00 0.00 5.52
3122 3193 0.320421 ACAACCGACCGACCAATCAG 60.320 55.000 0.00 0.00 0.00 2.90
3669 3773 4.295119 GTGTCCGTGTCCGTGGCT 62.295 66.667 0.00 0.00 0.00 4.75
3696 3800 1.004918 GGCCGTGTAGTTGAGCTGT 60.005 57.895 0.00 0.00 0.00 4.40
3880 3984 4.083862 GGAAGAGGCCGCGGTTCT 62.084 66.667 28.70 25.42 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 4.662961 GCACTTTGCGTTGGGGCC 62.663 66.667 0.00 0.00 31.71 5.80
81 82 4.062293 CCGTAATCATTCGCCTTGGAATA 58.938 43.478 0.00 0.00 34.96 1.75
88 89 2.277084 GTTGTCCGTAATCATTCGCCT 58.723 47.619 0.00 0.00 0.00 5.52
144 145 4.287238 TCCTTTTGCGTCAGAACTTTTC 57.713 40.909 0.00 0.00 0.00 2.29
243 245 7.346751 TCCATTTATCTGCAAAACCTAATCC 57.653 36.000 0.00 0.00 0.00 3.01
260 262 9.070179 CAAGTCATGATCCATTGTATCCATTTA 57.930 33.333 0.00 0.00 0.00 1.40
365 367 2.173569 AGAAGGGGAAATTGGATCTCCG 59.826 50.000 0.00 0.00 42.62 4.63
385 387 5.233902 CCATCAGCGACAAATAGAAAGAGAG 59.766 44.000 0.00 0.00 0.00 3.20
395 397 0.254178 AGAGCCCATCAGCGACAAAT 59.746 50.000 0.00 0.00 38.01 2.32
459 461 6.279882 CAGGGCTTTGTCTACAAATTTTCAA 58.720 36.000 8.62 0.00 43.92 2.69
500 502 2.184322 GGCTGTCATCCGCGAAGA 59.816 61.111 8.23 0.00 0.00 2.87
501 503 2.169789 CAGGCTGTCATCCGCGAAG 61.170 63.158 8.23 0.00 0.00 3.79
524 526 5.807011 GCCTGATCGATGTTTGCTTTAAAAT 59.193 36.000 0.54 0.00 0.00 1.82
537 539 3.131709 ACCTTATTGGCCTGATCGATG 57.868 47.619 0.54 0.00 40.22 3.84
539 541 4.407621 TCTTTACCTTATTGGCCTGATCGA 59.592 41.667 3.32 0.00 40.22 3.59
582 584 1.352083 TTAGCTGTCCAGTGGCTCTT 58.648 50.000 3.51 0.00 37.50 2.85
656 658 7.915293 TTCAGGACATTTATTACGTCATGTT 57.085 32.000 0.00 0.00 41.06 2.71
673 675 4.106197 GTCATCGTCACTACATTCAGGAC 58.894 47.826 0.00 0.00 0.00 3.85
691 693 7.982354 CCTTAGGTATTTCTCTTCGAAAGTCAT 59.018 37.037 0.00 0.74 44.29 3.06
699 701 5.064834 GGCAAACCTTAGGTATTTCTCTTCG 59.935 44.000 3.55 0.00 33.12 3.79
702 704 4.514401 CGGCAAACCTTAGGTATTTCTCT 58.486 43.478 3.55 0.00 33.12 3.10
714 716 0.106419 TTCTGGAACCGGCAAACCTT 60.106 50.000 0.00 0.00 0.00 3.50
826 829 7.414540 GCCACTGATTTAATTAGTGTCTCCTTG 60.415 40.741 22.41 10.66 43.17 3.61
859 862 2.027837 GCTCATTGCAAAAGTGGGGATT 60.028 45.455 1.71 0.00 42.31 3.01
880 883 3.363178 GGTTGCTGAGAACTTGAAAACG 58.637 45.455 0.00 0.00 0.00 3.60
940 943 3.772025 GACGATCCTTATCATCTCCCCAT 59.228 47.826 0.00 0.00 31.93 4.00
955 958 2.724690 CCAATGAATACGTCGACGATCC 59.275 50.000 41.52 25.65 43.02 3.36
1049 1052 1.479709 TGTCTAGCAAGGAGAGCCTC 58.520 55.000 0.00 0.00 46.28 4.70
1066 1071 1.453155 CAATAAGTCGCCAGGCTTGT 58.547 50.000 10.54 0.00 43.07 3.16
1098 1103 0.314302 AACTACTCTCGCGCACAAGT 59.686 50.000 8.75 9.53 0.00 3.16
1115 1120 4.382577 CCCATGGTGGTATTTTGCCTTAAC 60.383 45.833 11.73 0.00 35.17 2.01
1130 1135 1.826921 GCAGATCAGCCCCATGGTG 60.827 63.158 11.73 0.00 43.96 4.17
1159 1164 5.678616 GCCCGGCGATGCATTATAAATAAAT 60.679 40.000 9.30 0.00 0.00 1.40
1166 1171 0.673333 CAGCCCGGCGATGCATTATA 60.673 55.000 20.38 0.00 0.00 0.98
1183 1188 2.373169 ACCATACATGATACCCTGCCAG 59.627 50.000 0.00 0.00 0.00 4.85
1192 1197 4.660303 AGGAGCTCCAAACCATACATGATA 59.340 41.667 33.90 0.00 38.89 2.15
1228 1234 0.179245 CGTTGCAAATGCGCCAAATG 60.179 50.000 4.18 0.00 45.83 2.32
1258 1264 5.221891 TCTAATTGTCTCTTCAAATGCGC 57.778 39.130 0.00 0.00 0.00 6.09
1267 1273 6.366340 TCCTCTCGGTATCTAATTGTCTCTT 58.634 40.000 0.00 0.00 0.00 2.85
1278 1284 5.677319 TTTCATGTTTCCTCTCGGTATCT 57.323 39.130 0.00 0.00 0.00 1.98
1282 1288 6.488683 TGTTTATTTTCATGTTTCCTCTCGGT 59.511 34.615 0.00 0.00 0.00 4.69
1312 1318 0.034896 GAGTTCGGGAGCTTGTTGGA 59.965 55.000 0.00 0.00 0.00 3.53
1378 1384 7.062255 CGTGTAAATATACGCATGATGTCATCT 59.938 37.037 13.90 0.00 41.60 2.90
1382 1388 6.143278 TCACGTGTAAATATACGCATGATGTC 59.857 38.462 16.51 0.00 39.14 3.06
1428 1434 9.151471 CTTCGTCATAATTTGGTAATCGGATAT 57.849 33.333 0.00 0.00 0.00 1.63
1450 1460 6.304356 TGCCAAGCAATATAATTCTCTTCG 57.696 37.500 0.00 0.00 34.76 3.79
1496 1506 3.243941 ACCGGTATGCGCTATGAACATTA 60.244 43.478 4.49 0.00 0.00 1.90
1498 1508 1.070134 ACCGGTATGCGCTATGAACAT 59.930 47.619 4.49 0.00 0.00 2.71
1504 1514 0.037605 GGCTAACCGGTATGCGCTAT 60.038 55.000 20.63 3.00 0.00 2.97
1571 1581 4.746535 TTCCAAATACTGCGATCTACCA 57.253 40.909 0.00 0.00 0.00 3.25
1641 1651 1.542030 AGTGACTCCGTTGCTAGTCTG 59.458 52.381 0.00 0.00 42.17 3.51
1685 1695 2.081161 GGTGAGGCCTGGGATGGAT 61.081 63.158 12.00 0.00 0.00 3.41
1776 1787 1.978455 TTGAGTTCGTGCCACAGGGT 61.978 55.000 0.00 0.00 36.17 4.34
1808 1819 1.499913 TTTCATGCTCAGGGGGCAGA 61.500 55.000 0.00 0.00 43.15 4.26
1909 1949 4.062991 ACTTTACCTTTTGCGAAGATCGT 58.937 39.130 1.45 0.00 42.81 3.73
1931 1971 2.813754 CGAGCAGAGTGGGAAATTTTCA 59.186 45.455 11.09 0.00 0.00 2.69
1996 2036 7.417342 CCCTTTTCGATCTATCTCAGAAGTTCT 60.417 40.741 0.00 0.00 36.67 3.01
2059 2099 7.717875 CCATCCTTTTTCCGTTGTATTATCCTA 59.282 37.037 0.00 0.00 0.00 2.94
2061 2101 6.544564 TCCATCCTTTTTCCGTTGTATTATCC 59.455 38.462 0.00 0.00 0.00 2.59
2115 2155 5.851720 TGCAAAAAGCTTCCATCAACATTA 58.148 33.333 0.00 0.00 45.94 1.90
2137 2177 2.569404 AGGCTTCACTCCTACTTTCCTG 59.431 50.000 0.00 0.00 30.79 3.86
2153 2193 1.504275 AATCACAGCTCCCCAGGCTT 61.504 55.000 0.00 0.00 38.03 4.35
2209 2249 4.320023 TCATTGCACCGCGGTATATAATT 58.680 39.130 33.70 9.45 0.00 1.40
2231 2271 1.368850 GCTTTCGCGCAGTTCGTTT 60.369 52.632 8.75 0.00 41.07 3.60
2236 2276 4.012895 CACGGCTTTCGCGCAGTT 62.013 61.111 8.75 0.00 43.89 3.16
2251 2291 0.615850 AGTCCTTCTAGGCAAGCCAC 59.384 55.000 14.40 0.51 38.92 5.01
2325 2366 0.516877 CGAGCGCCTTTGTCATTGAA 59.483 50.000 2.29 0.00 0.00 2.69
2328 2369 1.298859 GGACGAGCGCCTTTGTCATT 61.299 55.000 16.38 0.00 33.04 2.57
2329 2370 1.741770 GGACGAGCGCCTTTGTCAT 60.742 57.895 16.38 0.00 33.04 3.06
2344 2385 5.870433 TCGATCTATCAATAGACGAGAGGAC 59.130 44.000 14.81 0.00 41.77 3.85
2368 2409 3.454082 TCCTTTGCAATTGTTCCAACCTT 59.546 39.130 7.40 0.00 0.00 3.50
2499 2541 0.323725 CTGTGCCTTGCATAACCCCT 60.324 55.000 0.00 0.00 41.91 4.79
2524 2566 2.320587 CCTCGCTCAACACACAGGC 61.321 63.158 0.00 0.00 0.00 4.85
2529 2571 1.597854 CAAGGCCTCGCTCAACACA 60.598 57.895 5.23 0.00 0.00 3.72
2657 2699 7.545265 GCATGAAAACAATAACAATCCTAAGCA 59.455 33.333 0.00 0.00 0.00 3.91
2667 2709 5.512232 GGAAAGGGGCATGAAAACAATAACA 60.512 40.000 0.00 0.00 0.00 2.41
2671 2713 2.028203 CGGAAAGGGGCATGAAAACAAT 60.028 45.455 0.00 0.00 0.00 2.71
2788 2831 4.065789 AGAAATGTCTTTTGAGTCGTCCC 58.934 43.478 0.00 0.00 0.00 4.46
2854 2897 7.628366 GCTCATTTTCGTCTTAAATGGATGGAA 60.628 37.037 0.00 0.00 41.24 3.53
2860 2903 5.095490 GGTGCTCATTTTCGTCTTAAATGG 58.905 41.667 0.00 0.00 41.24 3.16
2884 2943 3.437049 GCTCAGGTGTGTGGAATTAGTTC 59.563 47.826 0.00 0.00 0.00 3.01
2888 2947 2.371841 ACTGCTCAGGTGTGTGGAATTA 59.628 45.455 1.66 0.00 0.00 1.40
2889 2948 1.143684 ACTGCTCAGGTGTGTGGAATT 59.856 47.619 1.66 0.00 0.00 2.17
2891 2950 1.419381 TACTGCTCAGGTGTGTGGAA 58.581 50.000 1.66 0.00 0.00 3.53
2892 2951 1.419381 TTACTGCTCAGGTGTGTGGA 58.581 50.000 1.66 0.00 0.00 4.02
2893 2952 2.027745 AGATTACTGCTCAGGTGTGTGG 60.028 50.000 1.66 0.00 0.00 4.17
2895 2954 3.119459 CGTAGATTACTGCTCAGGTGTGT 60.119 47.826 1.66 0.00 0.00 3.72
2897 2956 3.090037 ACGTAGATTACTGCTCAGGTGT 58.910 45.455 1.66 0.00 0.00 4.16
2898 2957 3.784701 ACGTAGATTACTGCTCAGGTG 57.215 47.619 1.66 0.00 0.00 4.00
2899 2958 3.311871 CGTACGTAGATTACTGCTCAGGT 59.688 47.826 7.22 0.00 0.00 4.00
2901 2960 4.533225 ACGTACGTAGATTACTGCTCAG 57.467 45.455 21.41 0.00 0.00 3.35
2902 2961 5.754890 TCATACGTACGTAGATTACTGCTCA 59.245 40.000 29.65 7.64 33.77 4.26
2908 2967 7.904977 TCTTGTGTTCATACGTACGTAGATTAC 59.095 37.037 29.65 22.99 33.77 1.89
2909 2968 7.904977 GTCTTGTGTTCATACGTACGTAGATTA 59.095 37.037 29.65 12.05 33.77 1.75
2910 2969 6.744537 GTCTTGTGTTCATACGTACGTAGATT 59.255 38.462 29.65 13.55 33.77 2.40
2911 2970 6.253746 GTCTTGTGTTCATACGTACGTAGAT 58.746 40.000 29.65 15.26 33.77 1.98
2912 2971 5.390885 GGTCTTGTGTTCATACGTACGTAGA 60.391 44.000 29.65 23.03 33.77 2.59
2913 2972 4.790140 GGTCTTGTGTTCATACGTACGTAG 59.210 45.833 29.65 21.45 33.77 3.51
2914 2973 4.379394 GGGTCTTGTGTTCATACGTACGTA 60.379 45.833 28.62 28.62 34.87 3.57
2915 2974 3.568538 GGTCTTGTGTTCATACGTACGT 58.431 45.455 25.98 25.98 0.00 3.57
2921 2980 3.660865 ACTTCGGGTCTTGTGTTCATAC 58.339 45.455 0.00 0.00 0.00 2.39
2961 3021 0.039165 GGTGGCTGCTAACACTTTGC 60.039 55.000 0.00 0.00 37.72 3.68
3000 3060 0.674269 TGGCACCGGGTTTTCGTATC 60.674 55.000 6.32 0.00 0.00 2.24
3081 3149 3.054434 TGCTCCACGTACTTAGGTAGGTA 60.054 47.826 9.66 0.00 42.71 3.08
3082 3150 2.291153 TGCTCCACGTACTTAGGTAGGT 60.291 50.000 4.67 4.67 44.57 3.08
3091 3159 1.006571 CGGTTGTGCTCCACGTACT 60.007 57.895 0.00 0.00 37.14 2.73
3122 3193 6.182039 TCCATTTTGACTGATTGATTCGAC 57.818 37.500 0.00 0.00 0.00 4.20
3128 3199 8.469200 GTCCATTATTCCATTTTGACTGATTGA 58.531 33.333 0.00 0.00 0.00 2.57
3723 3827 0.462759 GGAGCAAGGTCATCTTCGGG 60.463 60.000 1.42 0.00 32.41 5.14


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

AutoCloner maintained by Alex Coulton.