Multiple sequence alignment - TraesCS3B01G065300

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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 TraesCS3B01G065300 chr3B 100.000 2555 0 0 1 2555 39142578 39140024 0.000000e+00 4719.0
1 TraesCS3B01G065300 chr3B 81.879 1043 161 10 562 1589 40848359 40847330 0.000000e+00 854.0
2 TraesCS3B01G065300 chr3B 84.058 138 18 4 1596 1731 40718670 40718535 2.060000e-26 130.0
3 TraesCS3B01G065300 chr3A 94.699 1377 71 2 1001 2376 31788690 31787315 0.000000e+00 2137.0
4 TraesCS3B01G065300 chr3A 92.974 982 56 6 1 971 31789835 31788856 0.000000e+00 1419.0
5 TraesCS3B01G065300 chr3A 94.643 168 9 0 804 971 31788858 31788691 7.010000e-66 261.0
6 TraesCS3B01G065300 chr3A 91.209 182 15 1 2375 2555 518731257 518731076 1.960000e-61 246.0
7 TraesCS3B01G065300 chr3A 94.656 131 6 1 2375 2504 31787275 31787145 4.310000e-48 202.0
8 TraesCS3B01G065300 chr3D 82.051 1053 160 10 562 1599 23145490 23144452 0.000000e+00 870.0
9 TraesCS3B01G065300 chr7A 88.382 241 22 5 2101 2341 539653896 539653662 4.160000e-73 285.0
10 TraesCS3B01G065300 chr1D 91.209 182 15 1 2375 2555 484578407 484578588 1.960000e-61 246.0
11 TraesCS3B01G065300 chr1D 86.585 164 22 0 2391 2554 382739774 382739611 5.620000e-42 182.0
12 TraesCS3B01G065300 chr1B 90.110 182 17 1 2375 2555 674841440 674841621 4.250000e-58 235.0
13 TraesCS3B01G065300 chr7B 91.667 168 14 0 2388 2555 63632106 63631939 1.530000e-57 233.0
14 TraesCS3B01G065300 chr7B 83.200 125 16 5 442 563 295510087 295510209 2.690000e-20 110.0
15 TraesCS3B01G065300 chr7B 83.607 122 15 5 442 560 609182864 609182983 2.690000e-20 110.0
16 TraesCS3B01G065300 chrUn 85.714 182 25 1 2375 2555 274279871 274280052 9.330000e-45 191.0
17 TraesCS3B01G065300 chrUn 83.815 173 28 0 2379 2551 266836753 266836925 5.660000e-37 165.0
18 TraesCS3B01G065300 chr6B 85.057 174 24 2 2379 2551 51031246 51031418 2.610000e-40 176.0
19 TraesCS3B01G065300 chr7D 83.505 194 21 6 2101 2284 109016790 109016598 1.220000e-38 171.0
20 TraesCS3B01G065300 chr1A 81.618 136 24 1 433 567 278644447 278644312 7.470000e-21 111.0
21 TraesCS3B01G065300 chr5D 96.364 55 2 0 2111 2165 24048554 24048500 9.730000e-15 91.6


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 TraesCS3B01G065300 chr3B 39140024 39142578 2554 True 4719.00 4719 100.000 1 2555 1 chr3B.!!$R1 2554
1 TraesCS3B01G065300 chr3B 40847330 40848359 1029 True 854.00 854 81.879 562 1589 1 chr3B.!!$R3 1027
2 TraesCS3B01G065300 chr3A 31787145 31789835 2690 True 1004.75 2137 94.243 1 2504 4 chr3A.!!$R2 2503
3 TraesCS3B01G065300 chr3D 23144452 23145490 1038 True 870.00 870 82.051 562 1599 1 chr3D.!!$R1 1037

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
972 1191 0.112218 AGTTAGCATGCACCCCAACA 59.888 50.0 21.98 0.0 0.0 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 2102 0.250727 AACGCTACTGCCATGTTGGT 60.251 50.0 0.0 0.0 40.46 3.67 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
28 29 7.094420 TGGTTTGCTCGAATTATCAATTGAAGA 60.094 33.333 13.09 4.38 0.00 2.87
157 159 1.737355 TAATAACCGGTCGAGCGGGG 61.737 60.000 46.62 30.09 41.39 5.73
184 186 4.607293 AGGTGATAATAGAGATGCGCAA 57.393 40.909 17.11 0.00 0.00 4.85
185 187 4.564041 AGGTGATAATAGAGATGCGCAAG 58.436 43.478 17.11 0.00 43.44 4.01
192 195 1.950828 AGAGATGCGCAAGAATGAGG 58.049 50.000 17.11 0.00 33.82 3.86
203 206 1.985473 AGAATGAGGCACTTGCAACA 58.015 45.000 3.15 3.01 41.55 3.33
204 207 2.522185 AGAATGAGGCACTTGCAACAT 58.478 42.857 3.15 5.21 41.55 2.71
288 291 2.837031 AATTGCTAGGTGGTGGCCCG 62.837 60.000 0.00 0.00 0.00 6.13
305 308 0.828022 CCGGTGGCTAGTGGAATACA 59.172 55.000 0.00 0.00 0.00 2.29
318 321 1.369625 GAATACACGTGCAAGGGGAG 58.630 55.000 17.22 0.00 0.00 4.30
468 471 9.783256 GAAATGTACTCAAATGTACCCATAAAC 57.217 33.333 0.00 0.00 41.34 2.01
589 592 4.391216 TGTTCATTTGCAAAACTGGTTGTG 59.609 37.500 17.19 7.37 0.00 3.33
619 622 4.965814 TCACTAGATGAATTCATGGGAGC 58.034 43.478 25.37 10.49 36.57 4.70
642 649 5.333187 GCTAGAGCACTCATTTGATCATTCG 60.333 44.000 0.00 0.00 41.59 3.34
663 670 6.078202 TCGTTCATTTATTTGGTTTGCTGA 57.922 33.333 0.00 0.00 0.00 4.26
665 672 6.585702 TCGTTCATTTATTTGGTTTGCTGATG 59.414 34.615 0.00 0.00 0.00 3.07
808 833 8.579850 TTATTCACTAGCTGGATTCACAAAAT 57.420 30.769 3.17 0.00 0.00 1.82
815 840 5.958955 AGCTGGATTCACAAAATCTAAAGC 58.041 37.500 0.00 10.13 32.76 3.51
923 948 7.037730 TGGAGATCTGAGAAGGATTTTCTCTTT 60.038 37.037 15.53 3.56 43.91 2.52
971 1190 2.122783 TAGTTAGCATGCACCCCAAC 57.877 50.000 21.98 14.38 0.00 3.77
972 1191 0.112218 AGTTAGCATGCACCCCAACA 59.888 50.000 21.98 0.00 0.00 3.33
973 1192 0.965439 GTTAGCATGCACCCCAACAA 59.035 50.000 21.98 0.00 0.00 2.83
974 1193 0.965439 TTAGCATGCACCCCAACAAC 59.035 50.000 21.98 0.00 0.00 3.32
975 1194 0.178978 TAGCATGCACCCCAACAACA 60.179 50.000 21.98 0.00 0.00 3.33
976 1195 1.300853 GCATGCACCCCAACAACAC 60.301 57.895 14.21 0.00 0.00 3.32
977 1196 2.025767 GCATGCACCCCAACAACACA 62.026 55.000 14.21 0.00 0.00 3.72
978 1197 0.463204 CATGCACCCCAACAACACAA 59.537 50.000 0.00 0.00 0.00 3.33
979 1198 0.463620 ATGCACCCCAACAACACAAC 59.536 50.000 0.00 0.00 0.00 3.32
980 1199 0.900182 TGCACCCCAACAACACAACA 60.900 50.000 0.00 0.00 0.00 3.33
981 1200 0.247736 GCACCCCAACAACACAACAA 59.752 50.000 0.00 0.00 0.00 2.83
982 1201 1.134551 GCACCCCAACAACACAACAAT 60.135 47.619 0.00 0.00 0.00 2.71
983 1202 2.101582 GCACCCCAACAACACAACAATA 59.898 45.455 0.00 0.00 0.00 1.90
984 1203 3.712187 CACCCCAACAACACAACAATAC 58.288 45.455 0.00 0.00 0.00 1.89
985 1204 2.696187 ACCCCAACAACACAACAATACC 59.304 45.455 0.00 0.00 0.00 2.73
986 1205 2.695666 CCCCAACAACACAACAATACCA 59.304 45.455 0.00 0.00 0.00 3.25
987 1206 3.133003 CCCCAACAACACAACAATACCAA 59.867 43.478 0.00 0.00 0.00 3.67
988 1207 4.367450 CCCAACAACACAACAATACCAAG 58.633 43.478 0.00 0.00 0.00 3.61
989 1208 3.801594 CCAACAACACAACAATACCAAGC 59.198 43.478 0.00 0.00 0.00 4.01
990 1209 4.441356 CCAACAACACAACAATACCAAGCT 60.441 41.667 0.00 0.00 0.00 3.74
991 1210 5.221145 CCAACAACACAACAATACCAAGCTA 60.221 40.000 0.00 0.00 0.00 3.32
992 1211 5.689383 ACAACACAACAATACCAAGCTAG 57.311 39.130 0.00 0.00 0.00 3.42
993 1212 4.518970 ACAACACAACAATACCAAGCTAGG 59.481 41.667 0.00 0.00 0.00 3.02
994 1213 4.367039 ACACAACAATACCAAGCTAGGT 57.633 40.909 0.00 0.00 45.72 3.08
995 1214 4.072131 ACACAACAATACCAAGCTAGGTG 58.928 43.478 0.00 0.00 43.14 4.00
996 1215 4.202419 ACACAACAATACCAAGCTAGGTGA 60.202 41.667 0.00 0.00 43.14 4.02
997 1216 4.759693 CACAACAATACCAAGCTAGGTGAA 59.240 41.667 0.00 0.00 43.14 3.18
998 1217 5.240623 CACAACAATACCAAGCTAGGTGAAA 59.759 40.000 0.00 0.00 43.14 2.69
999 1218 5.473504 ACAACAATACCAAGCTAGGTGAAAG 59.526 40.000 0.00 0.00 43.14 2.62
1206 1425 1.217511 CACTGAGCATGACCTCGCT 59.782 57.895 0.00 0.00 42.42 4.93
1233 1452 1.933853 GCGTTGAAGATCGCCACTAAT 59.066 47.619 0.00 0.00 45.54 1.73
1293 1512 0.546122 AGAACAACCAGAGCACACCA 59.454 50.000 0.00 0.00 0.00 4.17
1344 1563 2.003301 GCTTACACTGAAGCCACTAGC 58.997 52.381 0.00 0.00 45.08 3.42
1366 1585 3.580731 GCTCTAGAGATTTATGCCGACC 58.419 50.000 24.24 0.00 0.00 4.79
1374 1593 7.304497 AGAGATTTATGCCGACCTATACTTT 57.696 36.000 0.00 0.00 0.00 2.66
1386 1605 6.171213 CGACCTATACTTTGAAAGAGGGTTT 58.829 40.000 12.53 0.00 0.00 3.27
1390 1609 8.666821 ACCTATACTTTGAAAGAGGGTTTTACT 58.333 33.333 12.53 0.00 0.00 2.24
1393 1612 6.944234 ACTTTGAAAGAGGGTTTTACTCTG 57.056 37.500 12.53 0.00 44.17 3.35
1394 1613 6.659824 ACTTTGAAAGAGGGTTTTACTCTGA 58.340 36.000 12.53 0.00 44.17 3.27
1461 1680 3.614870 GCAAGGAAGCGTTCAAATGGATT 60.615 43.478 0.00 0.00 0.00 3.01
1477 1696 5.796502 ATGGATTAAGAAGAAGTCCCCAA 57.203 39.130 0.00 0.00 0.00 4.12
1495 1714 4.322049 CCCCAATGTCCTACATAGATCGTC 60.322 50.000 0.00 0.00 37.97 4.20
1518 1737 2.831685 TGACGGAGCATTGTAGTGTT 57.168 45.000 0.00 0.00 0.00 3.32
1562 1781 1.098050 GTCCCCAAGTGATGACATGC 58.902 55.000 0.00 0.00 0.00 4.06
1628 1847 9.309516 GTCGACTGTATCTAAAAATGTTATGGA 57.690 33.333 8.70 0.00 0.00 3.41
1699 1918 7.846823 AGATGAACCCTAGGAATACCATATAGG 59.153 40.741 11.48 0.00 45.67 2.57
1824 2043 9.862371 AACAAAATCAATAAAAGTACACACACA 57.138 25.926 0.00 0.00 0.00 3.72
1845 2064 5.412904 CACAAGGAGAAATCCTACTGTTTCC 59.587 44.000 0.00 0.00 39.65 3.13
1882 2102 5.338632 TGGGAAGTAACCTATGAGTGAAGA 58.661 41.667 0.00 0.00 0.00 2.87
1884 2104 5.395435 GGGAAGTAACCTATGAGTGAAGACC 60.395 48.000 0.00 0.00 0.00 3.85
1892 2112 1.896220 TGAGTGAAGACCAACATGGC 58.104 50.000 0.00 0.00 42.67 4.40
1899 2119 0.391661 AGACCAACATGGCAGTAGCG 60.392 55.000 0.00 0.00 42.67 4.26
1929 2149 0.037877 ATGCAGCCAAGAAGCAGAGT 59.962 50.000 0.00 0.00 42.14 3.24
1985 2205 7.469260 TCTAAGACAAAGTTTTTGAACGAAGG 58.531 34.615 8.41 0.00 0.00 3.46
2109 2329 9.204570 GAACATTAGCTACAAAGTGTAAAGAGA 57.795 33.333 0.00 0.00 31.67 3.10
2167 2387 6.875726 CCCGCATGTATATATTGATAGGATGG 59.124 42.308 0.00 0.00 0.00 3.51
2185 2405 1.004277 TGGTCAATGGGTACAAGCCTC 59.996 52.381 0.00 0.00 36.53 4.70
2189 2409 0.035439 AATGGGTACAAGCCTCGGTG 60.035 55.000 0.00 0.00 36.53 4.94
2203 2423 3.070018 CCTCGGTGGAGATTGCATAATC 58.930 50.000 0.00 0.00 43.27 1.75
2219 2439 2.510768 AATCGAGAGCGGTGGTTATC 57.489 50.000 0.00 0.00 38.28 1.75
2292 2512 4.373156 ACAACCTCAACAGAAAGCCTAT 57.627 40.909 0.00 0.00 0.00 2.57
2309 2529 3.004944 GCCTATGCTAGAGTAGTCACCAC 59.995 52.174 0.00 0.00 33.53 4.16
2318 2538 0.728466 GTAGTCACCACGTCGAGCAC 60.728 60.000 0.00 0.00 0.00 4.40
2365 2585 1.683365 GCCCATGCCAGGTGTCAAT 60.683 57.895 0.00 0.00 0.00 2.57
2376 2596 2.559785 GTGTCAATGGCACCTCCTG 58.440 57.895 6.73 0.00 35.26 3.86
2402 2664 6.369065 ACTTCTCAGCTTAAGATTACGTTTGG 59.631 38.462 6.67 0.00 0.00 3.28
2447 2709 4.709397 CCAAGGCATTTGTAAACCCATCTA 59.291 41.667 0.00 0.00 34.87 1.98
2466 2728 6.263168 CCATCTACAACTTGGTCTTTTGAAGT 59.737 38.462 0.00 0.00 0.00 3.01
2504 2766 1.043022 CTCCTTGCTTGCAACCCTTT 58.957 50.000 3.70 0.00 0.00 3.11
2505 2767 1.000171 CTCCTTGCTTGCAACCCTTTC 60.000 52.381 3.70 0.00 0.00 2.62
2506 2768 1.043022 CCTTGCTTGCAACCCTTTCT 58.957 50.000 3.70 0.00 0.00 2.52
2507 2769 1.000171 CCTTGCTTGCAACCCTTTCTC 60.000 52.381 3.70 0.00 0.00 2.87
2508 2770 1.959282 CTTGCTTGCAACCCTTTCTCT 59.041 47.619 3.70 0.00 0.00 3.10
2509 2771 2.949177 TGCTTGCAACCCTTTCTCTA 57.051 45.000 0.00 0.00 0.00 2.43
2510 2772 3.222173 TGCTTGCAACCCTTTCTCTAA 57.778 42.857 0.00 0.00 0.00 2.10
2511 2773 3.766545 TGCTTGCAACCCTTTCTCTAAT 58.233 40.909 0.00 0.00 0.00 1.73
2512 2774 4.917385 TGCTTGCAACCCTTTCTCTAATA 58.083 39.130 0.00 0.00 0.00 0.98
2513 2775 5.321102 TGCTTGCAACCCTTTCTCTAATAA 58.679 37.500 0.00 0.00 0.00 1.40
2514 2776 5.772672 TGCTTGCAACCCTTTCTCTAATAAA 59.227 36.000 0.00 0.00 0.00 1.40
2515 2777 6.266558 TGCTTGCAACCCTTTCTCTAATAAAA 59.733 34.615 0.00 0.00 0.00 1.52
2516 2778 7.039082 TGCTTGCAACCCTTTCTCTAATAAAAT 60.039 33.333 0.00 0.00 0.00 1.82
2517 2779 7.276438 GCTTGCAACCCTTTCTCTAATAAAATG 59.724 37.037 0.00 0.00 0.00 2.32
2518 2780 8.415950 TTGCAACCCTTTCTCTAATAAAATGA 57.584 30.769 0.00 0.00 0.00 2.57
2519 2781 8.593945 TGCAACCCTTTCTCTAATAAAATGAT 57.406 30.769 0.00 0.00 0.00 2.45
2520 2782 9.693739 TGCAACCCTTTCTCTAATAAAATGATA 57.306 29.630 0.00 0.00 0.00 2.15
2544 2806 9.911788 ATAATCAATCTCAATGTGTTTAGTCCT 57.088 29.630 0.00 0.00 0.00 3.85
2545 2807 8.641498 AATCAATCTCAATGTGTTTAGTCCTT 57.359 30.769 0.00 0.00 0.00 3.36
2546 2808 7.672983 TCAATCTCAATGTGTTTAGTCCTTC 57.327 36.000 0.00 0.00 0.00 3.46
2547 2809 6.655003 TCAATCTCAATGTGTTTAGTCCTTCC 59.345 38.462 0.00 0.00 0.00 3.46
2548 2810 5.560722 TCTCAATGTGTTTAGTCCTTCCA 57.439 39.130 0.00 0.00 0.00 3.53
2549 2811 6.126863 TCTCAATGTGTTTAGTCCTTCCAT 57.873 37.500 0.00 0.00 0.00 3.41
2550 2812 5.939883 TCTCAATGTGTTTAGTCCTTCCATG 59.060 40.000 0.00 0.00 0.00 3.66
2551 2813 5.875224 TCAATGTGTTTAGTCCTTCCATGA 58.125 37.500 0.00 0.00 0.00 3.07
2552 2814 6.303054 TCAATGTGTTTAGTCCTTCCATGAA 58.697 36.000 0.00 0.00 0.00 2.57
2553 2815 6.775142 TCAATGTGTTTAGTCCTTCCATGAAA 59.225 34.615 0.00 0.00 0.00 2.69
2554 2816 6.575162 ATGTGTTTAGTCCTTCCATGAAAC 57.425 37.500 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.389091 TCGTATGCAAATGCTTTTCTTCAAT 58.611 32.000 6.97 0.00 42.66 2.57
28 29 3.441572 AGAGCTCGTATGCAAATGCTTTT 59.558 39.130 8.37 0.00 42.66 2.27
110 111 4.112634 TCAGTGAGCCCCTATTGTTTTT 57.887 40.909 0.00 0.00 0.00 1.94
111 112 3.806949 TCAGTGAGCCCCTATTGTTTT 57.193 42.857 0.00 0.00 0.00 2.43
114 115 4.322057 AATTTCAGTGAGCCCCTATTGT 57.678 40.909 0.00 0.00 0.00 2.71
115 116 4.952335 AGAAATTTCAGTGAGCCCCTATTG 59.048 41.667 19.99 0.00 0.00 1.90
116 117 5.198602 AGAAATTTCAGTGAGCCCCTATT 57.801 39.130 19.99 0.00 0.00 1.73
172 174 2.804572 GCCTCATTCTTGCGCATCTCTA 60.805 50.000 12.75 0.00 0.00 2.43
177 179 0.679002 AGTGCCTCATTCTTGCGCAT 60.679 50.000 12.75 0.00 37.95 4.73
178 180 0.890542 AAGTGCCTCATTCTTGCGCA 60.891 50.000 5.66 5.66 37.95 6.09
184 186 1.985473 TGTTGCAAGTGCCTCATTCT 58.015 45.000 0.00 0.00 41.18 2.40
185 187 2.229543 TCATGTTGCAAGTGCCTCATTC 59.770 45.455 0.00 0.00 41.18 2.67
192 195 6.587226 TGAATCTAAAATCATGTTGCAAGTGC 59.413 34.615 0.00 0.00 42.50 4.40
288 291 1.206371 ACGTGTATTCCACTAGCCACC 59.794 52.381 0.00 0.00 42.20 4.61
299 302 1.369625 CTCCCCTTGCACGTGTATTC 58.630 55.000 18.38 0.09 0.00 1.75
300 303 0.035439 CCTCCCCTTGCACGTGTATT 60.035 55.000 18.38 0.00 0.00 1.89
305 308 0.834687 TAAGACCTCCCCTTGCACGT 60.835 55.000 0.00 0.00 0.00 4.49
423 426 1.028868 CCCTTAACTCTGCAGCCAGC 61.029 60.000 9.47 0.00 45.96 4.85
426 429 2.200373 TTTCCCTTAACTCTGCAGCC 57.800 50.000 9.47 0.00 0.00 4.85
468 471 1.688197 ACAAATCAGCCCCACAACTTG 59.312 47.619 0.00 0.00 0.00 3.16
619 622 5.752472 ACGAATGATCAAATGAGTGCTCTAG 59.248 40.000 0.00 0.00 0.00 2.43
642 649 6.536688 GCATCAGCAAACCAAATAAATGAAC 58.463 36.000 0.00 0.00 41.58 3.18
663 670 3.788937 GCTTTTGCTACATGGATTGCAT 58.211 40.909 0.00 0.00 43.35 3.96
754 775 9.687717 GTACAAACAATTTCACAAATCAAACAG 57.312 29.630 0.00 0.00 0.00 3.16
849 874 8.327941 GCTTTTGCTACATAGAATATGATGGA 57.672 34.615 3.87 0.00 43.35 3.41
956 1146 0.178978 TGTTGTTGGGGTGCATGCTA 60.179 50.000 20.33 2.15 0.00 3.49
971 1190 4.518970 ACCTAGCTTGGTATTGTTGTGTTG 59.481 41.667 18.82 0.00 38.79 3.33
972 1191 4.518970 CACCTAGCTTGGTATTGTTGTGTT 59.481 41.667 19.78 0.00 38.45 3.32
973 1192 4.072131 CACCTAGCTTGGTATTGTTGTGT 58.928 43.478 19.78 0.00 38.45 3.72
974 1193 4.323417 TCACCTAGCTTGGTATTGTTGTG 58.677 43.478 19.78 5.26 38.45 3.33
975 1194 4.634012 TCACCTAGCTTGGTATTGTTGT 57.366 40.909 19.78 0.00 38.45 3.32
976 1195 5.705441 TCTTTCACCTAGCTTGGTATTGTTG 59.295 40.000 19.78 6.71 38.45 3.33
977 1196 5.876357 TCTTTCACCTAGCTTGGTATTGTT 58.124 37.500 19.78 0.00 38.45 2.83
978 1197 5.499004 TCTTTCACCTAGCTTGGTATTGT 57.501 39.130 19.78 0.00 38.45 2.71
979 1198 5.220931 GCATCTTTCACCTAGCTTGGTATTG 60.221 44.000 19.78 8.17 38.45 1.90
980 1199 4.884164 GCATCTTTCACCTAGCTTGGTATT 59.116 41.667 19.78 0.00 38.45 1.89
981 1200 4.080356 TGCATCTTTCACCTAGCTTGGTAT 60.080 41.667 19.78 6.63 38.45 2.73
982 1201 3.263170 TGCATCTTTCACCTAGCTTGGTA 59.737 43.478 19.78 4.32 38.45 3.25
983 1202 2.040278 TGCATCTTTCACCTAGCTTGGT 59.960 45.455 14.58 14.58 41.77 3.67
984 1203 2.715046 TGCATCTTTCACCTAGCTTGG 58.285 47.619 13.05 13.05 0.00 3.61
985 1204 4.771590 TTTGCATCTTTCACCTAGCTTG 57.228 40.909 0.00 0.00 0.00 4.01
986 1205 5.717119 CATTTTGCATCTTTCACCTAGCTT 58.283 37.500 0.00 0.00 0.00 3.74
987 1206 4.381292 GCATTTTGCATCTTTCACCTAGCT 60.381 41.667 0.00 0.00 44.26 3.32
988 1207 3.861689 GCATTTTGCATCTTTCACCTAGC 59.138 43.478 0.00 0.00 44.26 3.42
1233 1452 1.968704 TGACATTGTGTTTGGCGGTA 58.031 45.000 0.00 0.00 0.00 4.02
1293 1512 1.290009 GGCAATTGCAAACGCCTCT 59.710 52.632 30.32 0.00 42.77 3.69
1344 1563 3.238441 GTCGGCATAAATCTCTAGAGCG 58.762 50.000 15.35 9.97 0.00 5.03
1347 1566 7.403671 AGTATAGGTCGGCATAAATCTCTAGA 58.596 38.462 0.00 0.00 0.00 2.43
1350 1569 6.919775 AAGTATAGGTCGGCATAAATCTCT 57.080 37.500 0.00 0.00 0.00 3.10
1366 1585 9.945904 AGAGTAAAACCCTCTTTCAAAGTATAG 57.054 33.333 0.00 0.00 35.80 1.31
1374 1593 6.014840 ACGTATCAGAGTAAAACCCTCTTTCA 60.015 38.462 0.00 0.00 37.18 2.69
1461 1680 4.175962 AGGACATTGGGGACTTCTTCTTA 58.824 43.478 0.00 0.00 0.00 2.10
1477 1696 6.150307 GTCATCTGACGATCTATGTAGGACAT 59.850 42.308 0.00 0.00 37.68 3.06
1495 1714 2.862536 CACTACAATGCTCCGTCATCTG 59.137 50.000 0.00 0.00 0.00 2.90
1518 1737 0.895100 GGTTGATGAGGTTGCTGGCA 60.895 55.000 0.00 0.00 0.00 4.92
1562 1781 1.884579 GCATACATGAGCCAGGAATGG 59.115 52.381 0.00 0.00 0.00 3.16
1603 1822 9.529325 CTCCATAACATTTTTAGATACAGTCGA 57.471 33.333 0.00 0.00 0.00 4.20
1615 1834 5.999205 TGCATGACCTCCATAACATTTTT 57.001 34.783 0.00 0.00 33.31 1.94
1628 1847 6.992123 TCGATAACTCATAAATTGCATGACCT 59.008 34.615 0.00 0.00 0.00 3.85
1699 1918 8.726988 TGTGGTTAGAATTAATAGAGTTGCAAC 58.273 33.333 22.17 22.17 0.00 4.17
1872 2092 2.224843 TGCCATGTTGGTCTTCACTCAT 60.225 45.455 0.00 0.00 40.46 2.90
1882 2102 0.250727 AACGCTACTGCCATGTTGGT 60.251 50.000 0.00 0.00 40.46 3.67
1884 2104 1.135689 GGAAACGCTACTGCCATGTTG 60.136 52.381 0.00 0.00 35.36 3.33
1892 2112 0.541863 ATGGGAGGGAAACGCTACTG 59.458 55.000 0.00 0.00 0.00 2.74
1899 2119 2.054453 GGCTGCATGGGAGGGAAAC 61.054 63.158 0.50 0.00 0.00 2.78
1995 2215 6.886459 TGCTTTGCCTCATTTTCTTATCTACT 59.114 34.615 0.00 0.00 0.00 2.57
2009 2229 2.436109 GAGGGGTGCTTTGCCTCA 59.564 61.111 0.00 0.00 0.00 3.86
2012 2232 2.037847 ATGGAGGGGTGCTTTGCC 59.962 61.111 0.00 0.00 0.00 4.52
2090 2310 8.079211 TCCATATCTCTTTACACTTTGTAGCT 57.921 34.615 0.00 0.00 33.92 3.32
2091 2311 8.718102 TTCCATATCTCTTTACACTTTGTAGC 57.282 34.615 0.00 0.00 33.92 3.58
2109 2329 3.718434 TGAGGGTTGAGATGCTTCCATAT 59.282 43.478 0.00 0.00 0.00 1.78
2167 2387 1.369625 CGAGGCTTGTACCCATTGAC 58.630 55.000 0.00 0.00 0.00 3.18
2185 2405 2.733552 CTCGATTATGCAATCTCCACCG 59.266 50.000 0.00 0.00 38.77 4.94
2189 2409 2.665537 CGCTCTCGATTATGCAATCTCC 59.334 50.000 0.00 0.00 38.77 3.71
2203 2423 0.317103 CTCGATAACCACCGCTCTCG 60.317 60.000 0.00 0.00 0.00 4.04
2219 2439 8.615878 TTCTATCTCTTCCTCTAATTCTCTCG 57.384 38.462 0.00 0.00 0.00 4.04
2292 2512 2.082231 GACGTGGTGACTACTCTAGCA 58.918 52.381 0.00 0.00 0.00 3.49
2318 2538 3.041940 GTGGTCGCACCCTTGACG 61.042 66.667 3.33 0.00 37.50 4.35
2365 2585 0.471780 TGAGAAGTCAGGAGGTGCCA 60.472 55.000 0.00 0.00 40.02 4.92
2376 2596 7.412020 CCAAACGTAATCTTAAGCTGAGAAGTC 60.412 40.741 0.00 0.00 0.00 3.01
2402 2664 5.470098 TGGCTACAAGACAATTTGAAGAGTC 59.530 40.000 2.79 0.00 23.92 3.36
2431 2693 6.780522 ACCAAGTTGTAGATGGGTTTACAAAT 59.219 34.615 1.45 0.00 40.35 2.32
2466 2728 8.686334 GCAAGGAGTTGGAGATTCAATTTATTA 58.314 33.333 0.00 0.00 33.87 0.98
2474 2736 3.415212 CAAGCAAGGAGTTGGAGATTCA 58.585 45.455 0.00 0.00 33.87 2.57
2475 2737 2.163211 GCAAGCAAGGAGTTGGAGATTC 59.837 50.000 0.00 0.00 33.87 2.52
2518 2780 9.911788 AGGACTAAACACATTGAGATTGATTAT 57.088 29.630 0.00 0.00 0.00 1.28
2519 2781 9.739276 AAGGACTAAACACATTGAGATTGATTA 57.261 29.630 0.00 0.00 0.00 1.75
2520 2782 8.641498 AAGGACTAAACACATTGAGATTGATT 57.359 30.769 0.00 0.00 0.00 2.57
2521 2783 7.337942 GGAAGGACTAAACACATTGAGATTGAT 59.662 37.037 0.00 0.00 0.00 2.57
2522 2784 6.655003 GGAAGGACTAAACACATTGAGATTGA 59.345 38.462 0.00 0.00 0.00 2.57
2523 2785 6.430925 TGGAAGGACTAAACACATTGAGATTG 59.569 38.462 0.00 0.00 0.00 2.67
2524 2786 6.542821 TGGAAGGACTAAACACATTGAGATT 58.457 36.000 0.00 0.00 0.00 2.40
2525 2787 6.126863 TGGAAGGACTAAACACATTGAGAT 57.873 37.500 0.00 0.00 0.00 2.75
2526 2788 5.560722 TGGAAGGACTAAACACATTGAGA 57.439 39.130 0.00 0.00 0.00 3.27
2527 2789 5.939883 TCATGGAAGGACTAAACACATTGAG 59.060 40.000 0.00 0.00 0.00 3.02
2528 2790 5.875224 TCATGGAAGGACTAAACACATTGA 58.125 37.500 0.00 0.00 0.00 2.57
2529 2791 6.573664 TTCATGGAAGGACTAAACACATTG 57.426 37.500 0.00 0.00 0.00 2.82
2530 2792 6.981722 GTTTCATGGAAGGACTAAACACATT 58.018 36.000 0.00 0.00 0.00 2.71
2531 2793 6.575162 GTTTCATGGAAGGACTAAACACAT 57.425 37.500 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.