Multiple sequence alignment - TraesCS7A01G511400

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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 TraesCS7A01G511400 chr7A 100.000 3099 0 0 1 3099 699089814 699092912 0.000000e+00 5723.0
1 TraesCS7A01G511400 chr7A 74.864 736 167 13 1383 2108 699066830 699067557 4.990000e-83 318.0
2 TraesCS7A01G511400 chr7A 85.366 205 27 3 2878 3080 727814870 727815073 3.130000e-50 209.0
3 TraesCS7A01G511400 chr7B 90.652 1380 80 11 773 2121 691457935 691459296 0.000000e+00 1788.0
4 TraesCS7A01G511400 chr7B 94.109 696 39 2 2386 3080 733785064 733784370 0.000000e+00 1057.0
5 TraesCS7A01G511400 chr7B 91.860 258 17 1 2121 2378 691459394 691459647 1.060000e-94 357.0
6 TraesCS7A01G511400 chr7B 83.251 203 32 2 1900 2101 691275732 691275531 5.280000e-43 185.0
7 TraesCS7A01G511400 chr7B 81.604 212 23 6 2542 2747 430842207 430842408 8.890000e-36 161.0
8 TraesCS7A01G511400 chr7B 97.143 35 1 0 3065 3099 742762455 742762489 3.340000e-05 60.2
9 TraesCS7A01G511400 chr7B 97.143 35 1 0 3065 3099 742801788 742801822 3.340000e-05 60.2
10 TraesCS7A01G511400 chr4A 97.320 709 19 0 2391 3099 564699811 564700519 0.000000e+00 1205.0
11 TraesCS7A01G511400 chr4A 96.232 690 26 0 2391 3080 625074029 625073340 0.000000e+00 1131.0
12 TraesCS7A01G511400 chr4A 93.878 147 8 1 645 791 94991762 94991617 1.450000e-53 220.0
13 TraesCS7A01G511400 chr2A 95.672 670 28 1 2411 3080 58007378 58008046 0.000000e+00 1075.0
14 TraesCS7A01G511400 chr2A 95.320 641 30 0 1 641 749458995 749458355 0.000000e+00 1018.0
15 TraesCS7A01G511400 chr2A 95.171 642 29 2 1 641 560676531 560677171 0.000000e+00 1013.0
16 TraesCS7A01G511400 chr2A 93.292 641 42 1 1 641 459001125 459001764 0.000000e+00 944.0
17 TraesCS7A01G511400 chr2A 96.429 140 4 1 634 772 127160888 127160749 2.400000e-56 230.0
18 TraesCS7A01G511400 chr2A 96.377 138 4 1 634 770 560677278 560677415 3.110000e-55 226.0
19 TraesCS7A01G511400 chr2A 94.161 137 8 0 645 781 206083151 206083015 3.130000e-50 209.0
20 TraesCS7A01G511400 chr2A 92.361 144 10 1 634 776 749457902 749457759 1.460000e-48 204.0
21 TraesCS7A01G511400 chr1A 94.228 641 34 3 1 641 399819698 399820335 0.000000e+00 976.0
22 TraesCS7A01G511400 chr5A 94.072 641 36 2 1 641 482761373 482762011 0.000000e+00 972.0
23 TraesCS7A01G511400 chr5A 94.373 622 34 1 1 622 591677553 591676933 0.000000e+00 953.0
24 TraesCS7A01G511400 chr5A 95.035 141 3 4 634 772 482762125 482762263 5.200000e-53 219.0
25 TraesCS7A01G511400 chr6A 93.916 641 37 2 1 641 54974668 54975306 0.000000e+00 966.0
26 TraesCS7A01G511400 chr6A 93.760 641 39 1 1 641 22756828 22757467 0.000000e+00 961.0
27 TraesCS7A01G511400 chr6A 95.714 140 5 1 634 772 22757575 22757714 1.120000e-54 224.0
28 TraesCS7A01G511400 chr6A 95.000 140 6 1 634 772 54975413 54975552 5.200000e-53 219.0
29 TraesCS7A01G511400 chr6A 92.517 147 7 4 645 790 103976411 103976268 1.130000e-49 207.0
30 TraesCS7A01G511400 chr3B 93.281 640 41 2 2 641 708795528 708796165 0.000000e+00 942.0
31 TraesCS7A01G511400 chr3B 74.038 1117 244 37 1018 2113 555156081 555154990 6.180000e-112 414.0
32 TraesCS7A01G511400 chr3B 96.212 132 5 0 645 776 64548255 64548124 1.870000e-52 217.0
33 TraesCS7A01G511400 chr3B 76.562 384 44 25 2386 2753 90739424 90739071 5.310000e-38 169.0
34 TraesCS7A01G511400 chr1B 81.831 699 114 9 2391 3080 209564368 209565062 2.680000e-160 575.0
35 TraesCS7A01G511400 chr1B 96.992 133 4 0 645 777 581115126 581115258 1.120000e-54 224.0
36 TraesCS7A01G511400 chr2B 92.333 300 23 0 2781 3080 778832238 778831939 7.940000e-116 427.0
37 TraesCS7A01G511400 chr3A 80.274 583 78 22 2474 3037 700757908 700757344 3.720000e-109 405.0
38 TraesCS7A01G511400 chr3A 78.727 550 101 10 1569 2115 563395108 563395644 1.370000e-93 353.0
39 TraesCS7A01G511400 chr7D 79.318 440 51 20 2391 2812 638269451 638269034 3.940000e-69 272.0
40 TraesCS7A01G511400 chr7D 100.000 35 0 0 3065 3099 82466992 82466958 7.170000e-07 65.8
41 TraesCS7A01G511400 chr4B 94.928 138 6 1 634 770 1738519 1738382 6.730000e-52 215.0
42 TraesCS7A01G511400 chr4B 93.151 146 9 1 645 789 11437328 11437183 2.420000e-51 213.0
43 TraesCS7A01G511400 chr5B 93.056 144 9 1 634 776 360408745 360408602 3.130000e-50 209.0
44 TraesCS7A01G511400 chr5B 93.571 140 8 1 634 772 44136461 44136600 1.130000e-49 207.0
45 TraesCS7A01G511400 chr3D 77.657 367 41 25 2391 2743 160722832 160723171 5.280000e-43 185.0
46 TraesCS7A01G511400 chr3D 97.143 35 1 0 3065 3099 454669735 454669701 3.340000e-05 60.2
47 TraesCS7A01G511400 chr6D 95.238 42 2 0 2706 2747 414095571 414095612 1.990000e-07 67.6
48 TraesCS7A01G511400 chrUn 100.000 32 0 0 3068 3099 334693055 334693024 3.340000e-05 60.2
49 TraesCS7A01G511400 chrUn 97.143 35 1 0 3065 3099 335123900 335123934 3.340000e-05 60.2


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 TraesCS7A01G511400 chr7A 699089814 699092912 3098 False 5723.0 5723 100.0000 1 3099 1 chr7A.!!$F2 3098
1 TraesCS7A01G511400 chr7A 699066830 699067557 727 False 318.0 318 74.8640 1383 2108 1 chr7A.!!$F1 725
2 TraesCS7A01G511400 chr7B 691457935 691459647 1712 False 1072.5 1788 91.2560 773 2378 2 chr7B.!!$F4 1605
3 TraesCS7A01G511400 chr7B 733784370 733785064 694 True 1057.0 1057 94.1090 2386 3080 1 chr7B.!!$R2 694
4 TraesCS7A01G511400 chr4A 564699811 564700519 708 False 1205.0 1205 97.3200 2391 3099 1 chr4A.!!$F1 708
5 TraesCS7A01G511400 chr4A 625073340 625074029 689 True 1131.0 1131 96.2320 2391 3080 1 chr4A.!!$R2 689
6 TraesCS7A01G511400 chr2A 58007378 58008046 668 False 1075.0 1075 95.6720 2411 3080 1 chr2A.!!$F1 669
7 TraesCS7A01G511400 chr2A 459001125 459001764 639 False 944.0 944 93.2920 1 641 1 chr2A.!!$F2 640
8 TraesCS7A01G511400 chr2A 560676531 560677415 884 False 619.5 1013 95.7740 1 770 2 chr2A.!!$F3 769
9 TraesCS7A01G511400 chr2A 749457759 749458995 1236 True 611.0 1018 93.8405 1 776 2 chr2A.!!$R3 775
10 TraesCS7A01G511400 chr1A 399819698 399820335 637 False 976.0 976 94.2280 1 641 1 chr1A.!!$F1 640
11 TraesCS7A01G511400 chr5A 591676933 591677553 620 True 953.0 953 94.3730 1 622 1 chr5A.!!$R1 621
12 TraesCS7A01G511400 chr5A 482761373 482762263 890 False 595.5 972 94.5535 1 772 2 chr5A.!!$F1 771
13 TraesCS7A01G511400 chr6A 22756828 22757714 886 False 592.5 961 94.7370 1 772 2 chr6A.!!$F1 771
14 TraesCS7A01G511400 chr6A 54974668 54975552 884 False 592.5 966 94.4580 1 772 2 chr6A.!!$F2 771
15 TraesCS7A01G511400 chr3B 708795528 708796165 637 False 942.0 942 93.2810 2 641 1 chr3B.!!$F1 639
16 TraesCS7A01G511400 chr3B 555154990 555156081 1091 True 414.0 414 74.0380 1018 2113 1 chr3B.!!$R3 1095
17 TraesCS7A01G511400 chr1B 209564368 209565062 694 False 575.0 575 81.8310 2391 3080 1 chr1B.!!$F1 689
18 TraesCS7A01G511400 chr3A 700757344 700757908 564 True 405.0 405 80.2740 2474 3037 1 chr3A.!!$R1 563
19 TraesCS7A01G511400 chr3A 563395108 563395644 536 False 353.0 353 78.7270 1569 2115 1 chr3A.!!$F1 546


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
819 1289 0.107945 AAGAATCCCGCAGAGACAGC 60.108 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2996 0.870393 CGCATAGCAGTGCCCATAAG 59.13 55.0 12.58 0.0 42.06 1.73 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
30 31 2.091541 CCACCACGTTTGCCTTCATAT 58.908 47.619 0.00 0.00 0.00 1.78
111 112 5.784390 TGAAATTCATCCCCAAAATTCTCCA 59.216 36.000 0.00 0.00 0.00 3.86
220 221 1.903877 CTCCGGACAGGCAGAACCAT 61.904 60.000 0.00 0.00 43.14 3.55
222 223 0.469917 CCGGACAGGCAGAACCATAT 59.530 55.000 0.00 0.00 43.14 1.78
223 224 1.691976 CCGGACAGGCAGAACCATATA 59.308 52.381 0.00 0.00 43.14 0.86
294 295 1.144936 GCAAGCATAGGACTCCGCT 59.855 57.895 0.00 0.00 35.90 5.52
378 380 1.229853 AACACCGAGGGAAGGGGAT 60.230 57.895 0.00 0.00 35.74 3.85
520 522 4.436998 CTCCGCCGTCGCCTTCTT 62.437 66.667 0.00 0.00 0.00 2.52
530 532 1.139947 CGCCTTCTTCCCTCGTCTC 59.860 63.158 0.00 0.00 0.00 3.36
635 637 0.738063 AGTGCGTGACGTGTTTGACA 60.738 50.000 6.91 0.00 0.00 3.58
748 1218 1.153369 CGAGATGGTCAACGCCCAT 60.153 57.895 0.00 0.00 45.37 4.00
751 1221 0.908910 AGATGGTCAACGCCCATACA 59.091 50.000 0.00 0.00 42.76 2.29
815 1285 2.834549 AGAGAAAAGAATCCCGCAGAGA 59.165 45.455 0.00 0.00 0.00 3.10
816 1286 2.933260 GAGAAAAGAATCCCGCAGAGAC 59.067 50.000 0.00 0.00 0.00 3.36
817 1287 2.303022 AGAAAAGAATCCCGCAGAGACA 59.697 45.455 0.00 0.00 0.00 3.41
818 1288 2.393271 AAAGAATCCCGCAGAGACAG 57.607 50.000 0.00 0.00 0.00 3.51
819 1289 0.107945 AAGAATCCCGCAGAGACAGC 60.108 55.000 0.00 0.00 0.00 4.40
820 1290 1.219124 GAATCCCGCAGAGACAGCA 59.781 57.895 0.00 0.00 0.00 4.41
821 1291 0.391661 GAATCCCGCAGAGACAGCAA 60.392 55.000 0.00 0.00 0.00 3.91
822 1292 0.674895 AATCCCGCAGAGACAGCAAC 60.675 55.000 0.00 0.00 0.00 4.17
823 1293 1.830587 ATCCCGCAGAGACAGCAACA 61.831 55.000 0.00 0.00 0.00 3.33
824 1294 2.031516 CCCGCAGAGACAGCAACAG 61.032 63.158 0.00 0.00 0.00 3.16
825 1295 1.301244 CCGCAGAGACAGCAACAGT 60.301 57.895 0.00 0.00 0.00 3.55
829 1299 2.093310 CGCAGAGACAGCAACAGTAATG 59.907 50.000 0.00 0.00 0.00 1.90
831 1301 3.005554 CAGAGACAGCAACAGTAATGGG 58.994 50.000 0.00 0.00 0.00 4.00
896 1383 1.656818 CCCTGCCAATAGTTGCGTGG 61.657 60.000 0.00 0.00 35.39 4.94
943 1430 2.048127 GCCGTCGTCTTGCCTTCT 60.048 61.111 0.00 0.00 0.00 2.85
976 1463 0.319900 CCCATACCAGAATCGCCTCG 60.320 60.000 0.00 0.00 0.00 4.63
996 1497 1.176619 TCGTTCTCCTTCGCAGTGGA 61.177 55.000 0.00 0.00 0.00 4.02
1012 1513 2.719979 GAGCAATGCTGGCATCCG 59.280 61.111 14.48 4.81 39.88 4.18
1013 1514 1.820906 GAGCAATGCTGGCATCCGA 60.821 57.895 14.48 0.00 39.88 4.55
1014 1515 1.783031 GAGCAATGCTGGCATCCGAG 61.783 60.000 14.48 1.62 39.88 4.63
1046 1547 4.796231 GACGTCGTCGGCCTGCAT 62.796 66.667 10.05 0.00 39.49 3.96
1087 1588 2.286950 GCGCACTTGTTCAAGATCAACA 60.287 45.455 17.75 0.00 31.76 3.33
1134 1635 1.874019 CGGCAGGTTGATCGAGTCG 60.874 63.158 6.09 6.09 0.00 4.18
1172 1673 2.943978 GCTACCACTGGTGCGTCCT 61.944 63.158 11.32 0.00 36.19 3.85
1205 1706 4.028490 TCACACGGGGGCATCCAC 62.028 66.667 0.00 0.00 37.22 4.02
1220 1721 1.896220 TCCACAGACCATGTTTCAGC 58.104 50.000 0.00 0.00 41.41 4.26
1254 1755 0.755327 AAACCAAGAACGCCAAGGCT 60.755 50.000 9.73 0.00 39.32 4.58
1285 1786 1.139256 TCGATCTGAGGCTAGTCGACT 59.861 52.381 23.66 23.66 36.52 4.18
1294 1795 0.386858 GCTAGTCGACTGTCGCACAA 60.387 55.000 28.12 5.25 40.21 3.33
1307 1814 4.006989 TGTCGCACAAAGCCTTATACATT 58.993 39.130 0.00 0.00 41.38 2.71
1344 1851 2.314071 TAGACCCCTCGGAGTTTGAA 57.686 50.000 4.02 0.00 0.00 2.69
1379 1886 1.227823 CGACCTGCTGTGGTTTCCA 60.228 57.895 0.00 0.00 41.00 3.53
1545 2052 3.828451 ACTTGCTGCACAATCTTGGTAAT 59.172 39.130 0.00 0.00 37.72 1.89
1551 2058 5.622007 GCTGCACAATCTTGGTAATTTGCTA 60.622 40.000 0.00 0.00 0.00 3.49
1563 2070 7.575414 TGGTAATTTGCTAGAAACACAAGAA 57.425 32.000 0.00 0.00 0.00 2.52
1590 2097 3.254060 CGATGTGTCTTTCAAGGTCGAT 58.746 45.455 0.00 0.00 32.29 3.59
1592 2099 2.143122 TGTGTCTTTCAAGGTCGATGC 58.857 47.619 0.00 0.00 0.00 3.91
1593 2100 2.143122 GTGTCTTTCAAGGTCGATGCA 58.857 47.619 0.00 0.00 0.00 3.96
1633 2146 2.523245 AGATCATCCTCGCTATGCAGA 58.477 47.619 0.00 0.00 0.00 4.26
1660 2173 2.167398 CTCCGGTCTTCAAGGCGGAA 62.167 60.000 0.00 0.00 0.00 4.30
1685 2198 0.527565 CGGGCCAATGAAGAACAAGG 59.472 55.000 4.39 0.00 0.00 3.61
1694 2207 4.978083 ATGAAGAACAAGGCTAAGCATG 57.022 40.909 0.00 0.00 0.00 4.06
1697 2210 2.716217 AGAACAAGGCTAAGCATGGTC 58.284 47.619 0.00 0.00 35.06 4.02
1799 2312 0.528017 TGACCTCAGTGATGACGAGC 59.472 55.000 2.09 0.00 0.00 5.03
1947 2460 5.077564 TCTAGCCGACCAGTATCATTGTAT 58.922 41.667 0.00 0.00 0.00 2.29
1969 2482 3.018856 CCAGCTCAAAGATGGTTGCATA 58.981 45.455 3.08 0.00 46.23 3.14
1982 2495 8.523915 AGATGGTTGCATAGAATTTATCAACA 57.476 30.769 0.00 0.00 36.48 3.33
2036 2549 2.789409 AGGGTATGAGCACCTCAAAC 57.211 50.000 0.00 0.00 44.04 2.93
2132 2743 8.587608 ACCATAGATGAATTTTGTGAAATGTGT 58.412 29.630 0.00 0.00 35.69 3.72
2149 2760 9.809096 TGAAATGTGTTGAAACTTTAGCAAATA 57.191 25.926 0.00 0.00 0.00 1.40
2196 2807 4.895668 AAATGATTGATTGGTGCCAACT 57.104 36.364 5.72 0.00 38.88 3.16
2209 2820 4.826733 TGGTGCCAACTATTTATGCTATGG 59.173 41.667 0.00 0.00 0.00 2.74
2234 2845 9.780186 GGAGATGCTAGGTAATTATACAAAACT 57.220 33.333 0.00 0.00 33.45 2.66
2244 2855 9.855021 GGTAATTATACAAAACTTGTGCAGATT 57.145 29.630 2.30 1.55 45.03 2.40
2249 2860 9.979578 TTATACAAAACTTGTGCAGATTCAAAT 57.020 25.926 2.30 0.00 45.03 2.32
2269 2880 8.514330 TCAAATACCAGTTTTGTTTAGTCAGT 57.486 30.769 0.00 0.00 35.90 3.41
2270 2881 8.617809 TCAAATACCAGTTTTGTTTAGTCAGTC 58.382 33.333 0.00 0.00 35.90 3.51
2271 2882 8.402472 CAAATACCAGTTTTGTTTAGTCAGTCA 58.598 33.333 0.00 0.00 31.05 3.41
2272 2883 7.730364 ATACCAGTTTTGTTTAGTCAGTCAG 57.270 36.000 0.00 0.00 0.00 3.51
2371 2982 5.403897 TTTCACTTGCTAAGTTGTTCGAG 57.596 39.130 0.00 0.00 40.46 4.04
2378 2989 2.855370 GCTAAGTTGTTCGAGAGCTAGC 59.145 50.000 6.62 6.62 0.00 3.42
2379 2990 3.673594 GCTAAGTTGTTCGAGAGCTAGCA 60.674 47.826 18.83 0.00 0.00 3.49
2380 2991 2.355717 AGTTGTTCGAGAGCTAGCAC 57.644 50.000 18.83 11.32 0.00 4.40
2381 2992 1.889829 AGTTGTTCGAGAGCTAGCACT 59.110 47.619 18.83 16.86 0.00 4.40
2382 2993 2.297597 AGTTGTTCGAGAGCTAGCACTT 59.702 45.455 18.83 0.84 0.00 3.16
2383 2994 2.638556 TGTTCGAGAGCTAGCACTTC 57.361 50.000 18.83 10.04 0.00 3.01
2384 2995 1.886542 TGTTCGAGAGCTAGCACTTCA 59.113 47.619 18.83 10.96 0.00 3.02
2385 2996 2.255316 GTTCGAGAGCTAGCACTTCAC 58.745 52.381 18.83 10.05 0.00 3.18
2386 2997 1.827681 TCGAGAGCTAGCACTTCACT 58.172 50.000 18.83 5.93 0.00 3.41
2387 2998 2.163509 TCGAGAGCTAGCACTTCACTT 58.836 47.619 18.83 0.00 0.00 3.16
2388 2999 3.344515 TCGAGAGCTAGCACTTCACTTA 58.655 45.455 18.83 0.00 0.00 2.24
2389 3000 3.948473 TCGAGAGCTAGCACTTCACTTAT 59.052 43.478 18.83 0.00 0.00 1.73
2432 3043 3.430862 GGCGCAACGATTCAGCCA 61.431 61.111 10.83 0.00 46.48 4.75
2601 3217 2.812499 GCCGTAATCTCCCGCAGA 59.188 61.111 0.00 0.00 34.78 4.26
2639 3255 3.385384 CTGCAGACCCCGAGCTCA 61.385 66.667 15.40 0.00 0.00 4.26
2845 3477 4.521062 AGGTCGCAGCTCGCCATC 62.521 66.667 15.41 1.63 37.01 3.51
3053 3686 1.831106 TCAGCCGTGGATGAATGTAGT 59.169 47.619 4.00 0.00 37.61 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.954788 AGTTAGTTGTTTTTCAAAACTGCAA 57.045 28.000 14.63 5.03 46.37 4.08
378 380 4.282957 TCACAATCCTTGCCTGCATTTTTA 59.717 37.500 0.00 0.00 0.00 1.52
402 404 0.811616 GGTAATGCTCGCTCCCACTG 60.812 60.000 0.00 0.00 0.00 3.66
520 522 1.506907 TTGGAGGAGGAGACGAGGGA 61.507 60.000 0.00 0.00 0.00 4.20
530 532 3.201290 CATTTCAGACGATTGGAGGAGG 58.799 50.000 0.00 0.00 0.00 4.30
635 637 0.687354 AGGACAAGGCGACTGTTGAT 59.313 50.000 0.00 0.00 42.68 2.57
748 1218 3.440872 GGAAATGTTAACGCCCACATGTA 59.559 43.478 0.00 0.00 33.76 2.29
751 1221 1.470890 CGGAAATGTTAACGCCCACAT 59.529 47.619 0.26 0.00 35.00 3.21
783 1253 6.040955 GGGATTCTTTTCTCTGTGTTTTTCCT 59.959 38.462 0.00 0.00 0.00 3.36
794 1264 2.834549 TCTCTGCGGGATTCTTTTCTCT 59.165 45.455 0.00 0.00 0.00 3.10
815 1285 0.112218 TGGCCCATTACTGTTGCTGT 59.888 50.000 0.00 0.00 0.00 4.40
816 1286 0.813184 CTGGCCCATTACTGTTGCTG 59.187 55.000 0.00 0.00 0.00 4.41
817 1287 0.967380 GCTGGCCCATTACTGTTGCT 60.967 55.000 0.00 0.00 0.00 3.91
818 1288 1.512694 GCTGGCCCATTACTGTTGC 59.487 57.895 0.00 0.00 0.00 4.17
819 1289 2.192605 GGCTGGCCCATTACTGTTG 58.807 57.895 0.00 0.00 0.00 3.33
820 1290 4.764143 GGCTGGCCCATTACTGTT 57.236 55.556 0.00 0.00 0.00 3.16
863 1335 1.856265 GCAGGGTTTTCTCCACGCAG 61.856 60.000 0.00 0.00 0.00 5.18
934 1421 1.741770 CGGTCGGGAAGAAGGCAAG 60.742 63.158 0.00 0.00 0.00 4.01
996 1497 1.822613 CTCGGATGCCAGCATTGCT 60.823 57.895 5.03 5.03 40.77 3.91
1005 1506 2.105128 CGTGGTCTCTCGGATGCC 59.895 66.667 0.00 0.00 0.00 4.40
1012 1513 0.099082 GTCATCGTCCGTGGTCTCTC 59.901 60.000 0.00 0.00 0.00 3.20
1013 1514 1.645704 CGTCATCGTCCGTGGTCTCT 61.646 60.000 0.00 0.00 0.00 3.10
1014 1515 1.226323 CGTCATCGTCCGTGGTCTC 60.226 63.158 0.00 0.00 0.00 3.36
1199 1700 2.163010 GCTGAAACATGGTCTGTGGATG 59.837 50.000 0.00 0.00 38.39 3.51
1201 1702 1.421268 AGCTGAAACATGGTCTGTGGA 59.579 47.619 0.00 0.00 38.39 4.02
1205 1706 2.549754 ACGAAAGCTGAAACATGGTCTG 59.450 45.455 0.00 0.00 0.00 3.51
1220 1721 1.946768 TGGTTTTGAGCTCCACGAAAG 59.053 47.619 12.15 0.00 0.00 2.62
1254 1755 0.106868 TCAGATCGAAGACCGCCCTA 60.107 55.000 0.00 0.00 42.51 3.53
1285 1786 3.046968 TGTATAAGGCTTTGTGCGACA 57.953 42.857 4.45 0.00 44.05 4.35
1294 1795 3.450817 GGGTTTGGCAATGTATAAGGCTT 59.549 43.478 4.58 4.58 0.00 4.35
1307 1814 1.412710 CTATCTCGCTAGGGTTTGGCA 59.587 52.381 6.70 0.00 0.00 4.92
1358 1865 0.951040 GAAACCACAGCAGGTCGAGG 60.951 60.000 0.00 0.00 42.25 4.63
1379 1886 2.231478 TCGCTCTTCTTCAGGAAATCGT 59.769 45.455 0.00 0.00 33.07 3.73
1387 1894 0.449786 TCGAGCTCGCTCTTCTTCAG 59.550 55.000 30.97 0.54 40.69 3.02
1464 1971 0.767375 TCTGCACCTCTGCCTTCTTT 59.233 50.000 0.00 0.00 43.51 2.52
1545 2052 3.888930 CCCCTTCTTGTGTTTCTAGCAAA 59.111 43.478 0.00 0.00 0.00 3.68
1551 2058 0.537371 CGGCCCCTTCTTGTGTTTCT 60.537 55.000 0.00 0.00 0.00 2.52
1563 2070 1.299976 GAAAGACACATCGGCCCCT 59.700 57.895 0.00 0.00 0.00 4.79
1590 2097 0.250901 GAGCTGGGAAAACCTCTGCA 60.251 55.000 0.00 0.00 41.11 4.41
1592 2099 2.503895 ATGAGCTGGGAAAACCTCTG 57.496 50.000 0.00 0.00 41.11 3.35
1593 2100 3.846588 TCTTATGAGCTGGGAAAACCTCT 59.153 43.478 0.00 0.00 41.11 3.69
1633 2146 0.976641 TGAAGACCGGAGACTGCATT 59.023 50.000 9.46 0.00 0.00 3.56
1638 2151 1.878656 CGCCTTGAAGACCGGAGACT 61.879 60.000 9.46 0.87 0.00 3.24
1642 2155 1.550130 ATTCCGCCTTGAAGACCGGA 61.550 55.000 18.38 18.38 46.94 5.14
1660 2173 3.279434 GTTCTTCATTGGCCCGTAGAAT 58.721 45.455 0.00 0.00 0.00 2.40
1694 2207 6.318648 TGCATGTCTTCAATAATGGTTAGACC 59.681 38.462 0.00 0.00 39.22 3.85
1697 2210 6.204359 GCTGCATGTCTTCAATAATGGTTAG 58.796 40.000 0.00 0.00 0.00 2.34
1799 2312 7.046652 AGTAGATGTTTGACCATCTCTTCATG 58.953 38.462 6.93 0.00 46.70 3.07
1947 2460 1.202915 TGCAACCATCTTTGAGCTGGA 60.203 47.619 4.94 0.00 35.18 3.86
1982 2495 7.984050 CACCACATCACTCATTCTATTAGAAGT 59.016 37.037 11.56 2.11 37.69 3.01
2036 2549 2.872245 CAACAATAGTAGGGCATGTCCG 59.128 50.000 11.52 0.00 34.94 4.79
2115 2628 9.824534 AAAGTTTCAACACATTTCACAAAATTC 57.175 25.926 0.00 0.00 32.69 2.17
2132 2743 8.160521 TGTACTGCTATTTGCTAAAGTTTCAA 57.839 30.769 0.00 0.00 43.37 2.69
2149 2760 6.701340 TCAGAATAACTTGACATGTACTGCT 58.299 36.000 0.00 0.00 0.00 4.24
2196 2807 7.739995 ACCTAGCATCTCCATAGCATAAATA 57.260 36.000 0.00 0.00 0.00 1.40
2234 2845 6.403866 AAACTGGTATTTGAATCTGCACAA 57.596 33.333 0.00 0.00 0.00 3.33
2244 2855 8.514330 ACTGACTAAACAAAACTGGTATTTGA 57.486 30.769 6.05 0.00 39.56 2.69
2246 2857 8.514330 TGACTGACTAAACAAAACTGGTATTT 57.486 30.769 0.00 0.00 0.00 1.40
2249 2860 5.526111 GCTGACTGACTAAACAAAACTGGTA 59.474 40.000 0.00 0.00 0.00 3.25
2271 2882 4.142160 GGAAAAACAAAGAACAGTGAGGCT 60.142 41.667 0.00 0.00 0.00 4.58
2272 2883 4.112634 GGAAAAACAAAGAACAGTGAGGC 58.887 43.478 0.00 0.00 0.00 4.70
2284 2895 8.754991 TGTCCTACTTGATAAGGAAAAACAAA 57.245 30.769 0.00 0.00 43.44 2.83
2316 2927 7.465989 TCTCTACGTTGTTTGGTTTAACAAAG 58.534 34.615 11.65 11.65 46.27 2.77
2317 2928 7.333921 TCTCTCTACGTTGTTTGGTTTAACAAA 59.666 33.333 0.00 0.00 46.27 2.83
2324 2935 4.117685 GTGTCTCTCTACGTTGTTTGGTT 58.882 43.478 0.00 0.00 0.00 3.67
2338 2949 7.093992 ACTTAGCAAGTGAAATAGTGTCTCTC 58.906 38.462 1.44 0.00 41.01 3.20
2371 2982 3.462021 CCCATAAGTGAAGTGCTAGCTC 58.538 50.000 17.23 12.88 0.00 4.09
2378 2989 1.470098 GCAGTGCCCATAAGTGAAGTG 59.530 52.381 2.85 0.00 0.00 3.16
2379 2990 1.352352 AGCAGTGCCCATAAGTGAAGT 59.648 47.619 12.58 0.00 0.00 3.01
2380 2991 2.119801 AGCAGTGCCCATAAGTGAAG 57.880 50.000 12.58 0.00 0.00 3.02
2381 2992 3.544684 CATAGCAGTGCCCATAAGTGAA 58.455 45.455 12.58 0.00 0.00 3.18
2382 2993 2.746142 GCATAGCAGTGCCCATAAGTGA 60.746 50.000 12.58 0.00 39.18 3.41
2383 2994 1.605710 GCATAGCAGTGCCCATAAGTG 59.394 52.381 12.58 1.82 39.18 3.16
2384 2995 1.811558 CGCATAGCAGTGCCCATAAGT 60.812 52.381 12.58 0.00 42.06 2.24
2385 2996 0.870393 CGCATAGCAGTGCCCATAAG 59.130 55.000 12.58 0.00 42.06 1.73
2386 2997 3.005205 CGCATAGCAGTGCCCATAA 57.995 52.632 12.58 0.00 42.06 1.90
2387 2998 4.777384 CGCATAGCAGTGCCCATA 57.223 55.556 12.58 0.00 42.06 2.74
2601 3217 2.981909 TGCTTCGGACTCGGTCGT 60.982 61.111 0.00 0.00 36.95 4.34
2845 3477 5.331902 CCATACTTTTTGCTACGTCCATTG 58.668 41.667 0.00 0.00 0.00 2.82
2863 3495 2.018542 TTTGCTACGACTGGCCATAC 57.981 50.000 5.51 2.00 0.00 2.39
2984 3617 4.338012 AGATTCTGTTGCAACCATCATGA 58.662 39.130 26.14 11.65 0.00 3.07



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

AutoCloner maintained by Alex Coulton.