Multiple sequence alignment - TraesCS2B01G454600

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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 TraesCS2B01G454600 chr2B 100.000 3259 0 0 1 3259 649481612 649478354 0.000000e+00 6019.0
1 TraesCS2B01G454600 chr2B 85.955 178 25 0 1438 1615 649670188 649670365 1.190000e-44 191.0
2 TraesCS2B01G454600 chr2D 91.272 2452 127 35 177 2568 543848506 543846082 0.000000e+00 3262.0
3 TraesCS2B01G454600 chr2D 84.548 1249 122 45 940 2157 544171647 544170439 0.000000e+00 1171.0
4 TraesCS2B01G454600 chr2D 85.556 180 24 2 1761 1939 544260178 544260356 1.540000e-43 187.0
5 TraesCS2B01G454600 chr2D 85.393 178 26 0 1438 1615 544259872 544260049 5.550000e-43 185.0
6 TraesCS2B01G454600 chr2A 87.667 2165 123 59 468 2568 686705275 686703191 0.000000e+00 2386.0
7 TraesCS2B01G454600 chr2A 84.215 1267 108 48 903 2152 686778270 686777079 0.000000e+00 1147.0
8 TraesCS2B01G454600 chr2A 87.295 488 43 12 1 470 686705854 686705368 1.030000e-149 540.0
9 TraesCS2B01G454600 chr2A 77.341 534 53 34 306 811 686778870 686778377 1.500000e-63 254.0
10 TraesCS2B01G454600 chr2A 85.955 178 25 0 1438 1615 686797549 686797726 1.190000e-44 191.0
11 TraesCS2B01G454600 chr2A 85.556 180 24 2 1761 1939 686797862 686798040 1.540000e-43 187.0
12 TraesCS2B01G454600 chr4A 92.211 719 26 9 2570 3259 67292365 67291648 0.000000e+00 990.0
13 TraesCS2B01G454600 chr4B 85.164 701 67 21 2574 3259 52568816 52569494 0.000000e+00 684.0
14 TraesCS2B01G454600 chr4B 84.892 695 72 17 2578 3259 52570010 52570684 0.000000e+00 671.0
15 TraesCS2B01G454600 chr4B 91.176 170 15 0 2578 2747 52569639 52569808 7.030000e-57 231.0
16 TraesCS2B01G454600 chr4B 82.474 97 17 0 3163 3259 52569053 52568957 5.790000e-13 86.1
17 TraesCS2B01G454600 chr7A 94.848 330 15 1 2722 3049 680393280 680392951 6.240000e-142 514.0
18 TraesCS2B01G454600 chr7A 93.836 146 9 0 2574 2719 680393400 680393255 1.520000e-53 220.0
19 TraesCS2B01G454600 chr7A 92.632 95 6 1 3062 3155 680392905 680392811 5.670000e-28 135.0
20 TraesCS2B01G454600 chr7A 100.000 61 0 0 3199 3259 680392816 680392756 2.660000e-21 113.0
21 TraesCS2B01G454600 chr3A 95.455 308 14 0 2577 2884 111839394 111839087 2.920000e-135 492.0
22 TraesCS2B01G454600 chr3A 95.238 189 9 0 2874 3062 111838085 111837897 1.900000e-77 300.0
23 TraesCS2B01G454600 chr3A 93.038 158 10 1 3096 3252 111837728 111837571 2.530000e-56 230.0
24 TraesCS2B01G454600 chr6D 84.000 250 39 1 1752 2001 426984491 426984739 4.200000e-59 239.0
25 TraesCS2B01G454600 chr6B 83.004 253 41 2 1752 2003 642724705 642724956 9.100000e-56 228.0
26 TraesCS2B01G454600 chr6A 83.200 250 41 1 1752 2001 571683601 571683849 9.100000e-56 228.0
27 TraesCS2B01G454600 chr5B 76.536 179 34 8 2574 2748 78741414 78741588 1.250000e-14 91.6
28 TraesCS2B01G454600 chr5B 81.651 109 16 3 2 106 610005717 610005825 1.610000e-13 87.9


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 TraesCS2B01G454600 chr2B 649478354 649481612 3258 True 6019.000000 6019 100.000000 1 3259 1 chr2B.!!$R1 3258
1 TraesCS2B01G454600 chr2D 543846082 543848506 2424 True 3262.000000 3262 91.272000 177 2568 1 chr2D.!!$R1 2391
2 TraesCS2B01G454600 chr2D 544170439 544171647 1208 True 1171.000000 1171 84.548000 940 2157 1 chr2D.!!$R2 1217
3 TraesCS2B01G454600 chr2A 686703191 686705854 2663 True 1463.000000 2386 87.481000 1 2568 2 chr2A.!!$R1 2567
4 TraesCS2B01G454600 chr2A 686777079 686778870 1791 True 700.500000 1147 80.778000 306 2152 2 chr2A.!!$R2 1846
5 TraesCS2B01G454600 chr4A 67291648 67292365 717 True 990.000000 990 92.211000 2570 3259 1 chr4A.!!$R1 689
6 TraesCS2B01G454600 chr4B 52568816 52570684 1868 False 528.666667 684 87.077333 2574 3259 3 chr4B.!!$F1 685
7 TraesCS2B01G454600 chr7A 680392756 680393400 644 True 245.500000 514 95.329000 2574 3259 4 chr7A.!!$R1 685
8 TraesCS2B01G454600 chr3A 111837571 111839394 1823 True 340.666667 492 94.577000 2577 3252 3 chr3A.!!$R1 675

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
648 798 0.388294 TGATGCTCAGCTCTCCATCG 59.612 55.0 0.0 0.0 37.49 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 2785 0.249398 CCTGCTTAACCTGTAGCCGT 59.751 55.0 0.0 0.0 36.56 5.68 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
29 30 4.095782 TCAACTTGAGAAGGTTTTTCCACG 59.904 41.667 0.00 0.00 39.02 4.94
39 40 4.721132 AGGTTTTTCCACGTCAAATCCTA 58.279 39.130 10.36 0.00 39.02 2.94
41 42 5.183140 AGGTTTTTCCACGTCAAATCCTATG 59.817 40.000 10.36 0.00 39.02 2.23
54 55 7.303261 GTCAAATCCTATGTCATATGTGCATG 58.697 38.462 18.73 11.86 0.00 4.06
57 58 8.785946 CAAATCCTATGTCATATGTGCATGTTA 58.214 33.333 18.73 9.05 0.00 2.41
73 74 7.138736 GTGCATGTTATTTATGTTATTCCGCT 58.861 34.615 0.00 0.00 0.00 5.52
82 83 1.539388 TGTTATTCCGCTGCTTGTTGG 59.461 47.619 0.00 0.00 0.00 3.77
87 88 0.749818 TCCGCTGCTTGTTGGTTGAA 60.750 50.000 0.00 0.00 0.00 2.69
89 90 0.662619 CGCTGCTTGTTGGTTGAAGA 59.337 50.000 0.00 0.00 0.00 2.87
97 98 2.766313 TGTTGGTTGAAGATGTCCTCG 58.234 47.619 0.00 0.00 0.00 4.63
101 102 1.550976 GGTTGAAGATGTCCTCGGAGT 59.449 52.381 4.02 0.00 0.00 3.85
107 108 2.248248 AGATGTCCTCGGAGTTCACAA 58.752 47.619 4.02 0.00 0.00 3.33
175 195 2.504367 CCCAACACTAACTTCACCAGG 58.496 52.381 0.00 0.00 0.00 4.45
218 238 4.523558 AGCGAAGTGTCCTTACTAAACTCT 59.476 41.667 0.00 0.00 0.00 3.24
223 243 3.995048 GTGTCCTTACTAAACTCTGGTGC 59.005 47.826 0.00 0.00 0.00 5.01
251 271 5.553123 TCCGTTCATTTAGGAGCAAGTTTA 58.447 37.500 0.00 0.00 0.00 2.01
427 456 4.638421 TCACCACACCAGTAAAAGTCAAAG 59.362 41.667 0.00 0.00 0.00 2.77
497 622 3.127030 GTGCCAACACTAAACTATGAGCC 59.873 47.826 0.00 0.00 43.85 4.70
511 636 4.721776 ACTATGAGCCCTCCACTTAATTCA 59.278 41.667 0.00 0.00 0.00 2.57
567 715 1.676678 GAGGATAGGTCAGCGTGCCA 61.677 60.000 0.00 0.00 0.00 4.92
579 727 3.132111 TCAGCGTGCCACTGATAAGATAA 59.868 43.478 0.00 0.00 39.21 1.75
648 798 0.388294 TGATGCTCAGCTCTCCATCG 59.612 55.000 0.00 0.00 37.49 3.84
737 907 2.985139 GACGCTTATATACGAGCAACCC 59.015 50.000 7.11 0.00 38.81 4.11
745 915 3.741476 CGAGCAACCCAGCAAGCC 61.741 66.667 0.00 0.00 36.85 4.35
758 928 1.203100 AGCAAGCCTGTCTTCCCAAAT 60.203 47.619 0.00 0.00 31.27 2.32
783 953 4.083862 AGGTTCGCCCTCGCTTCC 62.084 66.667 0.00 0.00 40.71 3.46
790 960 4.082523 CCCTCGCTTCCGCCTTCA 62.083 66.667 0.00 0.00 0.00 3.02
808 978 2.042831 AGCAAGGCTGGCATTCGAC 61.043 57.895 17.80 0.00 37.57 4.20
812 982 2.859273 AAGGCTGGCATTCGACTCCG 62.859 60.000 3.38 0.00 37.07 4.63
814 984 2.185350 CTGGCATTCGACTCCGCT 59.815 61.111 0.00 0.00 35.37 5.52
842 1012 1.821332 CCGCCCTCCTCAGCAAATC 60.821 63.158 0.00 0.00 0.00 2.17
856 1038 1.134946 GCAAATCCCTCCACCATTTCG 59.865 52.381 0.00 0.00 0.00 3.46
858 1040 2.825532 CAAATCCCTCCACCATTTCGTT 59.174 45.455 0.00 0.00 0.00 3.85
859 1041 2.128771 ATCCCTCCACCATTTCGTTG 57.871 50.000 0.00 0.00 0.00 4.10
888 1079 7.147880 ACCTTCGTCTCCAATATATATACAGGC 60.148 40.741 0.00 0.00 0.00 4.85
889 1080 6.710597 TCGTCTCCAATATATATACAGGCC 57.289 41.667 0.00 0.00 0.00 5.19
890 1081 5.298527 TCGTCTCCAATATATATACAGGCCG 59.701 44.000 0.00 0.00 0.00 6.13
891 1082 5.507482 CGTCTCCAATATATATACAGGCCGG 60.507 48.000 0.00 0.00 0.00 6.13
892 1083 5.597182 GTCTCCAATATATATACAGGCCGGA 59.403 44.000 10.86 0.00 0.00 5.14
995 1232 1.195442 GGGACAGGGGATAGCTAGCC 61.195 65.000 20.11 20.11 0.00 3.93
1073 1310 3.415087 CCTGGCCTTCCTCCTGGG 61.415 72.222 3.32 0.00 38.57 4.45
1312 1549 5.159925 CCGTCTACGTAAGATCTCGATCTA 58.840 45.833 10.50 0.00 41.45 1.98
1313 1550 5.286797 CCGTCTACGTAAGATCTCGATCTAG 59.713 48.000 10.50 7.40 41.45 2.43
1316 1553 6.862608 GTCTACGTAAGATCTCGATCTAGTCA 59.137 42.308 10.50 0.85 46.75 3.41
1317 1554 7.061441 GTCTACGTAAGATCTCGATCTAGTCAG 59.939 44.444 10.50 5.02 46.75 3.51
1319 1556 5.693104 ACGTAAGATCTCGATCTAGTCAGTC 59.307 44.000 10.50 0.00 46.75 3.51
1321 1558 6.128929 CGTAAGATCTCGATCTAGTCAGTCTG 60.129 46.154 9.66 0.00 46.75 3.51
1323 1560 5.297547 AGATCTCGATCTAGTCAGTCTGTC 58.702 45.833 7.62 0.00 45.69 3.51
1324 1561 3.449632 TCTCGATCTAGTCAGTCTGTCG 58.550 50.000 0.00 0.94 0.00 4.35
1326 1563 3.597255 TCGATCTAGTCAGTCTGTCGTT 58.403 45.455 0.00 0.00 32.73 3.85
1328 1565 4.454847 TCGATCTAGTCAGTCTGTCGTTTT 59.545 41.667 0.00 0.00 32.73 2.43
1329 1566 4.789119 CGATCTAGTCAGTCTGTCGTTTTC 59.211 45.833 0.00 0.00 0.00 2.29
1330 1567 5.617087 CGATCTAGTCAGTCTGTCGTTTTCA 60.617 44.000 0.00 0.00 0.00 2.69
1331 1568 5.109662 TCTAGTCAGTCTGTCGTTTTCAG 57.890 43.478 0.00 0.00 0.00 3.02
1332 1569 3.802948 AGTCAGTCTGTCGTTTTCAGT 57.197 42.857 0.00 0.00 34.86 3.41
1334 1571 4.861210 AGTCAGTCTGTCGTTTTCAGTAG 58.139 43.478 0.00 0.00 34.86 2.57
1336 1573 3.887110 TCAGTCTGTCGTTTTCAGTAGGA 59.113 43.478 0.00 0.00 34.86 2.94
1340 1581 4.989168 GTCTGTCGTTTTCAGTAGGATTGT 59.011 41.667 0.00 0.00 34.86 2.71
1344 1585 7.876068 TCTGTCGTTTTCAGTAGGATTGTATTT 59.124 33.333 0.00 0.00 34.86 1.40
1346 1587 7.094975 TGTCGTTTTCAGTAGGATTGTATTTGG 60.095 37.037 0.00 0.00 0.00 3.28
1347 1588 6.938030 TCGTTTTCAGTAGGATTGTATTTGGT 59.062 34.615 0.00 0.00 0.00 3.67
1348 1589 7.021196 CGTTTTCAGTAGGATTGTATTTGGTG 58.979 38.462 0.00 0.00 0.00 4.17
1351 1592 5.185454 TCAGTAGGATTGTATTTGGTGCAG 58.815 41.667 0.00 0.00 0.00 4.41
1352 1593 3.947834 AGTAGGATTGTATTTGGTGCAGC 59.052 43.478 9.47 9.47 0.00 5.25
1402 1652 7.329471 TCGAGTTGACTTTTGAGTGAATATCTG 59.671 37.037 0.00 0.00 0.00 2.90
1499 1759 3.636231 CTGGGCAACTCCACCGGA 61.636 66.667 9.46 0.00 36.21 5.14
1652 1920 6.314400 TCACGTAAATAACCTAGCACATTTCC 59.686 38.462 0.00 0.00 0.00 3.13
1679 1947 7.168302 CGATCTCTTTTCTTGCGTGATAAGTAT 59.832 37.037 8.11 5.04 0.00 2.12
1683 1951 8.181487 TCTTTTCTTGCGTGATAAGTATGTAC 57.819 34.615 8.11 0.00 0.00 2.90
1684 1952 6.563398 TTTCTTGCGTGATAAGTATGTACG 57.437 37.500 0.00 0.00 37.77 3.67
1685 1953 5.239359 TCTTGCGTGATAAGTATGTACGT 57.761 39.130 0.00 0.00 37.12 3.57
1687 1955 5.513849 TCTTGCGTGATAAGTATGTACGTTG 59.486 40.000 0.00 0.00 37.12 4.10
1688 1956 4.984205 TGCGTGATAAGTATGTACGTTGA 58.016 39.130 0.00 0.00 37.12 3.18
1689 1957 5.032220 TGCGTGATAAGTATGTACGTTGAG 58.968 41.667 0.00 0.00 37.12 3.02
1693 1961 7.149176 GCGTGATAAGTATGTACGTTGAGTATG 60.149 40.741 0.00 0.00 37.69 2.39
1696 1964 8.132995 TGATAAGTATGTACGTTGAGTATGTGG 58.867 37.037 0.00 0.00 37.69 4.17
1697 1965 5.909621 AGTATGTACGTTGAGTATGTGGT 57.090 39.130 0.00 0.00 37.69 4.16
2173 2484 3.956199 TGAGGAATTTGATCTCATTGGGC 59.044 43.478 0.00 0.00 33.21 5.36
2176 2487 4.404715 AGGAATTTGATCTCATTGGGCTTG 59.595 41.667 0.00 0.00 0.00 4.01
2178 2489 2.905415 TTGATCTCATTGGGCTTGGT 57.095 45.000 0.00 0.00 0.00 3.67
2179 2490 2.905415 TGATCTCATTGGGCTTGGTT 57.095 45.000 0.00 0.00 0.00 3.67
2183 2499 1.425066 TCTCATTGGGCTTGGTTGAGT 59.575 47.619 0.00 0.00 36.17 3.41
2199 2515 0.820871 GAGTGAGAGGGTTGAGCGAT 59.179 55.000 0.00 0.00 0.00 4.58
2366 2685 5.291858 ACATTTATATGACACACACAGAGCG 59.708 40.000 0.00 0.00 35.65 5.03
2368 2687 3.808466 ATATGACACACACAGAGCGAT 57.192 42.857 0.00 0.00 0.00 4.58
2369 2688 2.462456 ATGACACACACAGAGCGATT 57.538 45.000 0.00 0.00 0.00 3.34
2462 2785 6.146021 CAGCGTCTGTATATGCATGAATTACA 59.854 38.462 10.16 10.68 33.64 2.41
2568 2894 6.994496 TCCTGTATTATATACGCTACGCCTAT 59.006 38.462 0.00 0.00 0.00 2.57
2569 2895 7.500227 TCCTGTATTATATACGCTACGCCTATT 59.500 37.037 0.00 0.00 0.00 1.73
2570 2896 8.133627 CCTGTATTATATACGCTACGCCTATTT 58.866 37.037 0.00 0.00 0.00 1.40
2571 2897 8.845942 TGTATTATATACGCTACGCCTATTTG 57.154 34.615 0.00 0.00 0.00 2.32
2572 2898 6.823678 ATTATATACGCTACGCCTATTTGC 57.176 37.500 0.00 0.00 0.00 3.68
2687 3015 1.737355 GCAAGTCTGGCAGCCAACAA 61.737 55.000 17.03 0.61 30.80 2.83
2768 3096 0.690192 TCGGCTCCAACAGATTTCCA 59.310 50.000 0.00 0.00 0.00 3.53
2771 3099 1.672881 GGCTCCAACAGATTTCCATCG 59.327 52.381 0.00 0.00 34.17 3.84
2778 3106 1.134401 ACAGATTTCCATCGGACGCAT 60.134 47.619 0.00 0.00 34.17 4.73
2975 5505 2.426522 CCAAGTCTGAGGCAAATTCGA 58.573 47.619 0.00 0.00 0.00 3.71
3005 5535 3.113322 GGTTCCTTCGTTGCAAAGTTTC 58.887 45.455 12.18 0.00 0.00 2.78
3137 5816 4.891992 ACTACAGCAGAAAAAGGAGCTA 57.108 40.909 0.00 0.00 35.19 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.582550 GTGGAAAAACCTTCTCAAGTTGAG 58.417 41.667 24.37 24.37 41.58 3.02
10 11 3.625764 TGACGTGGAAAAACCTTCTCAAG 59.374 43.478 0.00 0.00 39.86 3.02
23 24 4.545208 TGACATAGGATTTGACGTGGAA 57.455 40.909 0.00 0.00 0.00 3.53
29 30 6.866010 TGCACATATGACATAGGATTTGAC 57.134 37.500 13.77 0.55 0.00 3.18
54 55 7.193595 ACAAGCAGCGGAATAACATAAATAAC 58.806 34.615 0.00 0.00 0.00 1.89
57 58 5.835113 ACAAGCAGCGGAATAACATAAAT 57.165 34.783 0.00 0.00 0.00 1.40
71 72 2.035066 ACATCTTCAACCAACAAGCAGC 59.965 45.455 0.00 0.00 0.00 5.25
73 74 2.622942 GGACATCTTCAACCAACAAGCA 59.377 45.455 0.00 0.00 0.00 3.91
82 83 3.254892 GAACTCCGAGGACATCTTCAAC 58.745 50.000 0.00 0.00 0.00 3.18
87 88 1.924731 TGTGAACTCCGAGGACATCT 58.075 50.000 0.00 0.00 0.00 2.90
89 90 1.691976 TGTTGTGAACTCCGAGGACAT 59.308 47.619 0.00 0.00 0.00 3.06
107 108 2.512476 ACTAAACAACCCCTCCACTTGT 59.488 45.455 0.00 0.00 0.00 3.16
150 170 3.072211 GTGAAGTTAGTGTTGGGGCTAC 58.928 50.000 0.00 0.00 0.00 3.58
151 171 2.039348 GGTGAAGTTAGTGTTGGGGCTA 59.961 50.000 0.00 0.00 0.00 3.93
152 172 1.202891 GGTGAAGTTAGTGTTGGGGCT 60.203 52.381 0.00 0.00 0.00 5.19
154 174 2.504367 CTGGTGAAGTTAGTGTTGGGG 58.496 52.381 0.00 0.00 0.00 4.96
155 175 2.105821 TCCTGGTGAAGTTAGTGTTGGG 59.894 50.000 0.00 0.00 0.00 4.12
156 176 3.139077 GTCCTGGTGAAGTTAGTGTTGG 58.861 50.000 0.00 0.00 0.00 3.77
157 177 3.560068 GTGTCCTGGTGAAGTTAGTGTTG 59.440 47.826 0.00 0.00 0.00 3.33
158 178 3.454812 AGTGTCCTGGTGAAGTTAGTGTT 59.545 43.478 0.00 0.00 0.00 3.32
218 238 0.249120 AATGAACGGAGATCGCACCA 59.751 50.000 0.00 0.00 43.89 4.17
223 243 3.053455 GCTCCTAAATGAACGGAGATCG 58.947 50.000 8.63 0.00 45.67 3.69
298 322 2.296073 TTTCCAATTGGGCGTTACCT 57.704 45.000 24.29 0.00 39.10 3.08
349 378 3.587797 CTTGCCAAGATGTTCAAGCAT 57.412 42.857 0.00 0.00 31.02 3.79
402 431 2.548480 GACTTTTACTGGTGTGGTGAGC 59.452 50.000 0.00 0.00 0.00 4.26
406 435 3.380320 GCTTTGACTTTTACTGGTGTGGT 59.620 43.478 0.00 0.00 0.00 4.16
407 436 3.380004 TGCTTTGACTTTTACTGGTGTGG 59.620 43.478 0.00 0.00 0.00 4.17
427 456 0.454600 TACGGTCGATCTGGAACTGC 59.545 55.000 0.00 0.00 0.00 4.40
497 622 7.219484 AGTTGTCAAATGAATTAAGTGGAGG 57.781 36.000 0.00 0.00 0.00 4.30
511 636 5.482908 ACTCAGATTCGCTAGTTGTCAAAT 58.517 37.500 0.00 0.00 0.00 2.32
579 727 4.142049 GCTGGCTAGATCTCAGTAAACTGT 60.142 45.833 0.00 0.00 44.12 3.55
648 798 1.989430 CACGAGAGGTCTCTTTGCTC 58.011 55.000 5.48 0.00 40.61 4.26
714 869 3.913163 GGTTGCTCGTATATAAGCGTCTC 59.087 47.826 2.73 0.00 41.51 3.36
716 871 2.985139 GGGTTGCTCGTATATAAGCGTC 59.015 50.000 2.73 0.00 41.51 5.19
737 907 0.538057 TTGGGAAGACAGGCTTGCTG 60.538 55.000 7.56 0.00 43.70 4.41
745 915 1.471684 GCTGCTGATTTGGGAAGACAG 59.528 52.381 0.00 0.00 0.00 3.51
758 928 4.704833 GGGCGAACCTGCTGCTGA 62.705 66.667 8.20 0.00 35.85 4.26
790 960 2.042831 GTCGAATGCCAGCCTTGCT 61.043 57.895 0.00 0.00 40.77 3.91
808 978 3.130160 GGCAAGGCAAGAGCGGAG 61.130 66.667 0.00 0.00 43.41 4.63
833 1003 1.002069 ATGGTGGAGGGATTTGCTGA 58.998 50.000 0.00 0.00 0.00 4.26
842 1012 1.595093 GGCAACGAAATGGTGGAGGG 61.595 60.000 0.00 0.00 0.00 4.30
856 1038 0.534203 TTGGAGACGAAGGTGGCAAC 60.534 55.000 0.00 0.00 0.00 4.17
858 1040 1.271856 TATTGGAGACGAAGGTGGCA 58.728 50.000 0.00 0.00 0.00 4.92
859 1041 2.622064 ATATTGGAGACGAAGGTGGC 57.378 50.000 0.00 0.00 0.00 5.01
889 1080 4.200283 GAGAGGTCAGCGGCTCCG 62.200 72.222 0.00 3.56 43.09 4.63
890 1081 2.757917 AGAGAGGTCAGCGGCTCC 60.758 66.667 0.00 0.00 0.00 4.70
891 1082 1.724582 GAGAGAGAGGTCAGCGGCTC 61.725 65.000 0.00 0.00 0.00 4.70
892 1083 1.752694 GAGAGAGAGGTCAGCGGCT 60.753 63.158 0.00 0.00 0.00 5.52
946 1182 4.927782 GTGCAGTGCCGGGACACA 62.928 66.667 28.90 22.04 43.23 3.72
1312 1549 3.802948 ACTGAAAACGACAGACTGACT 57.197 42.857 10.08 0.00 38.55 3.41
1313 1550 3.982058 CCTACTGAAAACGACAGACTGAC 59.018 47.826 10.08 1.49 38.55 3.51
1316 1553 5.221461 ACAATCCTACTGAAAACGACAGACT 60.221 40.000 0.00 0.00 38.55 3.24
1317 1554 4.989168 ACAATCCTACTGAAAACGACAGAC 59.011 41.667 0.00 0.00 38.55 3.51
1319 1556 7.596749 AATACAATCCTACTGAAAACGACAG 57.403 36.000 0.00 0.00 40.68 3.51
1321 1558 7.094933 ACCAAATACAATCCTACTGAAAACGAC 60.095 37.037 0.00 0.00 0.00 4.34
1323 1560 7.021196 CACCAAATACAATCCTACTGAAAACG 58.979 38.462 0.00 0.00 0.00 3.60
1324 1561 6.806739 GCACCAAATACAATCCTACTGAAAAC 59.193 38.462 0.00 0.00 0.00 2.43
1326 1563 6.007076 TGCACCAAATACAATCCTACTGAAA 58.993 36.000 0.00 0.00 0.00 2.69
1328 1565 5.172687 TGCACCAAATACAATCCTACTGA 57.827 39.130 0.00 0.00 0.00 3.41
1329 1566 4.201950 GCTGCACCAAATACAATCCTACTG 60.202 45.833 0.00 0.00 0.00 2.74
1330 1567 3.947834 GCTGCACCAAATACAATCCTACT 59.052 43.478 0.00 0.00 0.00 2.57
1331 1568 3.947834 AGCTGCACCAAATACAATCCTAC 59.052 43.478 1.02 0.00 0.00 3.18
1332 1569 4.235079 AGCTGCACCAAATACAATCCTA 57.765 40.909 1.02 0.00 0.00 2.94
1334 1571 3.243201 GCTAGCTGCACCAAATACAATCC 60.243 47.826 7.70 0.00 42.31 3.01
1336 1573 2.355756 CGCTAGCTGCACCAAATACAAT 59.644 45.455 13.93 0.00 43.06 2.71
1340 1581 1.428370 CGCGCTAGCTGCACCAAATA 61.428 55.000 24.19 0.00 43.06 1.40
1499 1759 1.306226 GTGGAGGGTGTAGGGCTCT 60.306 63.158 0.00 0.00 0.00 4.09
1652 1920 2.337583 TCACGCAAGAAAAGAGATCGG 58.662 47.619 0.00 0.00 43.62 4.18
1679 1947 2.629137 ACCACCACATACTCAACGTACA 59.371 45.455 0.00 0.00 0.00 2.90
1683 1951 1.068125 TCGACCACCACATACTCAACG 60.068 52.381 0.00 0.00 0.00 4.10
1684 1952 2.736144 TCGACCACCACATACTCAAC 57.264 50.000 0.00 0.00 0.00 3.18
1685 1953 2.159296 CGATCGACCACCACATACTCAA 60.159 50.000 10.26 0.00 0.00 3.02
1687 1955 1.404391 ACGATCGACCACCACATACTC 59.596 52.381 24.34 0.00 0.00 2.59
1688 1956 1.471119 ACGATCGACCACCACATACT 58.529 50.000 24.34 0.00 0.00 2.12
1689 1957 2.542411 GGTACGATCGACCACCACATAC 60.542 54.545 24.34 9.98 36.91 2.39
1693 1961 4.800355 GGTACGATCGACCACCAC 57.200 61.111 24.34 8.85 36.91 4.16
2157 2455 3.716431 ACCAAGCCCAATGAGATCAAAT 58.284 40.909 0.00 0.00 0.00 2.32
2165 2476 1.144708 TCACTCAACCAAGCCCAATGA 59.855 47.619 0.00 0.00 0.00 2.57
2166 2477 1.542915 CTCACTCAACCAAGCCCAATG 59.457 52.381 0.00 0.00 0.00 2.82
2167 2478 1.425066 TCTCACTCAACCAAGCCCAAT 59.575 47.619 0.00 0.00 0.00 3.16
2168 2479 0.843309 TCTCACTCAACCAAGCCCAA 59.157 50.000 0.00 0.00 0.00 4.12
2170 2481 0.322008 CCTCTCACTCAACCAAGCCC 60.322 60.000 0.00 0.00 0.00 5.19
2173 2484 2.104792 TCAACCCTCTCACTCAACCAAG 59.895 50.000 0.00 0.00 0.00 3.61
2176 2487 1.609320 GCTCAACCCTCTCACTCAACC 60.609 57.143 0.00 0.00 0.00 3.77
2178 2489 0.318441 CGCTCAACCCTCTCACTCAA 59.682 55.000 0.00 0.00 0.00 3.02
2179 2490 0.539669 TCGCTCAACCCTCTCACTCA 60.540 55.000 0.00 0.00 0.00 3.41
2183 2499 0.679960 TCGATCGCTCAACCCTCTCA 60.680 55.000 11.09 0.00 0.00 3.27
2199 2515 3.403968 TCGAACCCAAACAATGAATCGA 58.596 40.909 0.00 0.00 35.96 3.59
2430 2753 6.272822 TGCATATACAGACGCTGAGATAAT 57.727 37.500 12.77 2.87 35.18 1.28
2431 2754 5.705609 TGCATATACAGACGCTGAGATAA 57.294 39.130 12.77 0.00 35.18 1.75
2432 2755 5.415701 TCATGCATATACAGACGCTGAGATA 59.584 40.000 12.77 9.85 35.18 1.98
2433 2756 4.219288 TCATGCATATACAGACGCTGAGAT 59.781 41.667 12.77 8.36 35.18 2.75
2462 2785 0.249398 CCTGCTTAACCTGTAGCCGT 59.751 55.000 0.00 0.00 36.56 5.68
2662 2990 4.349503 TGCCAGACTTGCCGCCAT 62.350 61.111 0.00 0.00 0.00 4.40
2671 2999 0.820891 CACTTGTTGGCTGCCAGACT 60.821 55.000 22.17 5.18 33.81 3.24
2768 3096 2.328289 CGAGTCGATGCGTCCGAT 59.672 61.111 6.73 0.00 38.38 4.18
2771 3099 2.506217 TTGCGAGTCGATGCGTCC 60.506 61.111 18.61 0.00 0.00 4.79
2778 3106 1.721664 CCTATCCCGTTGCGAGTCGA 61.722 60.000 18.61 0.00 0.00 4.20
2975 5505 1.981256 ACGAAGGAACCAACATGCTT 58.019 45.000 0.00 0.00 0.00 3.91
3005 5535 8.467598 ACAGTAAATACTAGTATGTGTGTGGAG 58.532 37.037 16.11 3.91 34.13 3.86
3087 5656 5.163237 TGGCGCTAATTCCTACTTTCCTATT 60.163 40.000 7.64 0.00 0.00 1.73
3137 5816 3.807368 GCCTATCCCTATGGCGGT 58.193 61.111 0.00 0.00 37.11 5.68


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

AutoCloner maintained by Alex Coulton.