Multiple sequence alignment - TraesCS7A01G185700

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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 TraesCS7A01G185700 chr7A 100.000 3296 0 0 1 3296 139743827 139747122 0.000000e+00 6087.0
1 TraesCS7A01G185700 chr7A 87.337 1998 176 31 485 2451 139788259 139790210 0.000000e+00 2217.0
2 TraesCS7A01G185700 chr7A 84.294 1961 196 50 470 2409 49894622 49896491 0.000000e+00 1812.0
3 TraesCS7A01G185700 chr7A 89.714 1225 111 9 1189 2399 139611779 139613002 0.000000e+00 1550.0
4 TraesCS7A01G185700 chr7A 84.060 1675 166 51 744 2404 49404463 49402876 0.000000e+00 1520.0
5 TraesCS7A01G185700 chr7A 95.019 783 34 3 2516 3296 139756330 139757109 0.000000e+00 1225.0
6 TraesCS7A01G185700 chr7A 85.036 822 59 23 371 1160 139610991 139611780 0.000000e+00 778.0
7 TraesCS7A01G185700 chr7A 91.435 432 21 7 1 430 139666388 139666805 2.210000e-161 579.0
8 TraesCS7A01G185700 chr7A 90.551 254 16 5 1 246 139787347 139787600 2.450000e-86 329.0
9 TraesCS7A01G185700 chr7A 81.250 208 27 6 470 667 49404679 49404474 1.220000e-34 158.0
10 TraesCS7A01G185700 chr7A 93.243 74 4 1 380 453 139788102 139788174 1.250000e-19 108.0
11 TraesCS7A01G185700 chr7A 85.366 82 9 3 361 440 49405140 49405060 7.580000e-12 82.4
12 TraesCS7A01G185700 chr7B 91.562 2145 117 30 357 2465 105001330 105003446 0.000000e+00 2900.0
13 TraesCS7A01G185700 chr7B 87.541 2135 178 42 380 2451 105009402 105011511 0.000000e+00 2388.0
14 TraesCS7A01G185700 chr7B 89.081 1850 143 24 639 2473 104955864 104957669 0.000000e+00 2242.0
15 TraesCS7A01G185700 chr7B 90.189 846 40 19 1 825 104999983 105000806 0.000000e+00 1062.0
16 TraesCS7A01G185700 chr7B 88.652 282 24 4 1 274 105009118 105009399 1.470000e-88 337.0
17 TraesCS7A01G185700 chr7B 88.571 70 5 3 275 342 697253165 697253233 7.580000e-12 82.4
18 TraesCS7A01G185700 chr7D 93.694 1792 85 13 575 2355 139887548 139889322 0.000000e+00 2658.0
19 TraesCS7A01G185700 chr7D 87.142 2131 165 49 380 2451 139939508 139941588 0.000000e+00 2316.0
20 TraesCS7A01G185700 chr7D 92.046 1119 86 1 1189 2304 139865575 139866693 0.000000e+00 1570.0
21 TraesCS7A01G185700 chr7D 93.194 573 25 7 1 565 139886707 139887273 0.000000e+00 830.0
22 TraesCS7A01G185700 chr7D 85.158 539 35 18 639 1160 139865066 139865576 8.160000e-141 510.0
23 TraesCS7A01G185700 chr7D 89.377 273 21 5 10 274 139939233 139939505 1.470000e-88 337.0
24 TraesCS7A01G185700 chr7D 81.404 285 25 10 1 274 139863362 139863629 1.200000e-49 207.0
25 TraesCS7A01G185700 chr7D 90.667 150 5 6 447 592 139864813 139864957 1.210000e-44 191.0
26 TraesCS7A01G185700 chr7D 87.603 121 13 2 2358 2477 139934742 139934861 4.430000e-29 139.0
27 TraesCS7A01G185700 chr7D 95.714 70 2 1 391 460 139863904 139863972 9.670000e-21 111.0
28 TraesCS7A01G185700 chr4A 85.251 1973 195 45 467 2416 662136601 662138500 0.000000e+00 1943.0
29 TraesCS7A01G185700 chr4A 94.885 782 36 3 2519 3296 244298326 244297545 0.000000e+00 1219.0
30 TraesCS7A01G185700 chr4A 94.872 780 38 2 2519 3296 240328193 240327414 0.000000e+00 1218.0
31 TraesCS7A01G185700 chr4A 85.455 110 10 6 361 468 662136236 662136341 3.480000e-20 110.0
32 TraesCS7A01G185700 chr5A 95.006 781 36 3 2519 3296 676429467 676430247 0.000000e+00 1223.0
33 TraesCS7A01G185700 chr5A 94.663 787 36 4 2515 3296 67259007 67259792 0.000000e+00 1216.0
34 TraesCS7A01G185700 chr1A 95.000 780 37 2 2519 3296 425636042 425635263 0.000000e+00 1223.0
35 TraesCS7A01G185700 chr6A 94.784 786 36 3 2516 3296 415740814 415741599 0.000000e+00 1219.0
36 TraesCS7A01G185700 chr6A 94.885 782 35 3 2520 3296 501210301 501211082 0.000000e+00 1218.0
37 TraesCS7A01G185700 chr6A 94.865 779 38 2 2520 3296 206527544 206528322 0.000000e+00 1216.0
38 TraesCS7A01G185700 chr6A 87.671 73 5 4 273 341 111563605 111563533 7.580000e-12 82.4
39 TraesCS7A01G185700 chr2A 80.410 536 49 30 471 981 778251923 778252427 1.120000e-94 357.0
40 TraesCS7A01G185700 chr2D 94.915 59 1 2 272 329 293004778 293004721 1.260000e-14 91.6
41 TraesCS7A01G185700 chr1B 89.552 67 3 4 270 335 623736111 623736174 7.580000e-12 82.4
42 TraesCS7A01G185700 chr4D 84.524 84 8 5 269 347 49782859 49782776 9.810000e-11 78.7
43 TraesCS7A01G185700 chr4D 86.667 75 4 5 269 340 489984084 489984013 9.810000e-11 78.7
44 TraesCS7A01G185700 chr5B 84.810 79 8 3 274 348 78312008 78311930 3.530000e-10 76.8


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 TraesCS7A01G185700 chr7A 139743827 139747122 3295 False 6087.000000 6087 100.000000 1 3296 1 chr7A.!!$F3 3295
1 TraesCS7A01G185700 chr7A 49894622 49896491 1869 False 1812.000000 1812 84.294000 470 2409 1 chr7A.!!$F1 1939
2 TraesCS7A01G185700 chr7A 139756330 139757109 779 False 1225.000000 1225 95.019000 2516 3296 1 chr7A.!!$F4 780
3 TraesCS7A01G185700 chr7A 139610991 139613002 2011 False 1164.000000 1550 87.375000 371 2399 2 chr7A.!!$F5 2028
4 TraesCS7A01G185700 chr7A 139787347 139790210 2863 False 884.666667 2217 90.377000 1 2451 3 chr7A.!!$F6 2450
5 TraesCS7A01G185700 chr7A 49402876 49405140 2264 True 586.800000 1520 83.558667 361 2404 3 chr7A.!!$R1 2043
6 TraesCS7A01G185700 chr7B 104955864 104957669 1805 False 2242.000000 2242 89.081000 639 2473 1 chr7B.!!$F1 1834
7 TraesCS7A01G185700 chr7B 104999983 105003446 3463 False 1981.000000 2900 90.875500 1 2465 2 chr7B.!!$F3 2464
8 TraesCS7A01G185700 chr7B 105009118 105011511 2393 False 1362.500000 2388 88.096500 1 2451 2 chr7B.!!$F4 2450
9 TraesCS7A01G185700 chr7D 139886707 139889322 2615 False 1744.000000 2658 93.444000 1 2355 2 chr7D.!!$F3 2354
10 TraesCS7A01G185700 chr7D 139939233 139941588 2355 False 1326.500000 2316 88.259500 10 2451 2 chr7D.!!$F4 2441
11 TraesCS7A01G185700 chr7D 139863362 139866693 3331 False 517.800000 1570 88.997800 1 2304 5 chr7D.!!$F2 2303
12 TraesCS7A01G185700 chr4A 244297545 244298326 781 True 1219.000000 1219 94.885000 2519 3296 1 chr4A.!!$R2 777
13 TraesCS7A01G185700 chr4A 240327414 240328193 779 True 1218.000000 1218 94.872000 2519 3296 1 chr4A.!!$R1 777
14 TraesCS7A01G185700 chr4A 662136236 662138500 2264 False 1026.500000 1943 85.353000 361 2416 2 chr4A.!!$F1 2055
15 TraesCS7A01G185700 chr5A 676429467 676430247 780 False 1223.000000 1223 95.006000 2519 3296 1 chr5A.!!$F2 777
16 TraesCS7A01G185700 chr5A 67259007 67259792 785 False 1216.000000 1216 94.663000 2515 3296 1 chr5A.!!$F1 781
17 TraesCS7A01G185700 chr1A 425635263 425636042 779 True 1223.000000 1223 95.000000 2519 3296 1 chr1A.!!$R1 777
18 TraesCS7A01G185700 chr6A 415740814 415741599 785 False 1219.000000 1219 94.784000 2516 3296 1 chr6A.!!$F2 780
19 TraesCS7A01G185700 chr6A 501210301 501211082 781 False 1218.000000 1218 94.885000 2520 3296 1 chr6A.!!$F3 776
20 TraesCS7A01G185700 chr6A 206527544 206528322 778 False 1216.000000 1216 94.865000 2520 3296 1 chr6A.!!$F1 776
21 TraesCS7A01G185700 chr2A 778251923 778252427 504 False 357.000000 357 80.410000 471 981 1 chr2A.!!$F1 510

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
926 4282 0.460284 CTCCACATCCACAGGTACGC 60.46 60.0 0.0 0.0 0.0 4.42 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2482 5908 0.164217 GCGCGAACGTTTGGAATACA 59.836 50.0 12.1 0.0 42.83 2.29 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
23 24 2.731572 CCAGCCAAAGGAAGATCATGT 58.268 47.619 0.00 0.00 0.00 3.21
160 172 8.767085 CAAATGTGCAAACTCTGAATAAACATT 58.233 29.630 0.00 0.00 37.33 2.71
161 173 7.878477 ATGTGCAAACTCTGAATAAACATTG 57.122 32.000 0.00 0.00 0.00 2.82
164 176 8.143193 TGTGCAAACTCTGAATAAACATTGAAT 58.857 29.630 0.00 0.00 0.00 2.57
253 741 3.350219 ACATTTCCTACCATGTCGCTT 57.650 42.857 0.00 0.00 0.00 4.68
265 753 0.819259 TGTCGCTTGAGGCTTGCTTT 60.819 50.000 0.00 0.00 39.13 3.51
530 2487 3.186409 CAGTGAACGTACATGACAAAGGG 59.814 47.826 0.00 0.00 0.00 3.95
621 2892 3.288290 ATCGGCGGCTCTACCTCG 61.288 66.667 7.21 0.00 35.61 4.63
644 2960 6.099125 TCGTCCTTGGTATAATCTTCCATTCA 59.901 38.462 0.00 0.00 0.00 2.57
648 2964 7.939039 TCCTTGGTATAATCTTCCATTCACATC 59.061 37.037 0.00 0.00 0.00 3.06
675 3003 2.069273 GATTGTTCAGTCAGTCCCACG 58.931 52.381 0.00 0.00 0.00 4.94
682 3010 3.959293 TCAGTCAGTCCCACGTAGATTA 58.041 45.455 0.00 0.00 0.00 1.75
696 3025 5.944049 CGTAGATTATTGTACGTGTGCTT 57.056 39.130 0.00 0.00 39.51 3.91
697 3026 5.714272 CGTAGATTATTGTACGTGTGCTTG 58.286 41.667 0.00 0.00 39.51 4.01
698 3027 5.276207 CGTAGATTATTGTACGTGTGCTTGG 60.276 44.000 0.00 0.00 39.51 3.61
699 3028 4.575885 AGATTATTGTACGTGTGCTTGGT 58.424 39.130 0.00 0.00 0.00 3.67
700 3029 4.391830 AGATTATTGTACGTGTGCTTGGTG 59.608 41.667 0.00 0.00 0.00 4.17
749 3084 1.203013 ACTGGGTTAAAAGCCCTGGTC 60.203 52.381 8.39 0.00 45.80 4.02
776 3119 4.783227 ACTAACTTCCAATGGCTTCTCCTA 59.217 41.667 0.00 0.00 35.26 2.94
815 3158 1.376609 CCTGGTCGTATTTGGCAGCC 61.377 60.000 3.66 3.66 0.00 4.85
887 4241 2.554032 GTGTCAACCAGGTCATTTGAGG 59.446 50.000 0.00 0.00 29.97 3.86
926 4282 0.460284 CTCCACATCCACAGGTACGC 60.460 60.000 0.00 0.00 0.00 4.42
969 4357 9.858247 GCATAATTTTCGACGTTAATCAATCTA 57.142 29.630 0.00 0.00 0.00 1.98
1017 4409 4.058124 CTCGGATGTTTCTTTCAGTGACA 58.942 43.478 0.00 0.00 0.00 3.58
1167 4563 2.783609 ACATCATGAGCAGAGCACTT 57.216 45.000 0.09 0.00 0.00 3.16
1386 4782 0.824109 CCACCGACTGCTATCCTCAA 59.176 55.000 0.00 0.00 0.00 3.02
1440 4836 2.064581 GTACGCTCCCATCCCCTGT 61.065 63.158 0.00 0.00 0.00 4.00
1450 4846 3.924013 ATCCCCTGTGGCTCCGACA 62.924 63.158 0.00 0.00 0.00 4.35
1475 4874 0.961358 AAGAGACTCCAGTCCGACCG 60.961 60.000 2.96 0.00 45.85 4.79
1554 4953 1.334243 GTCGAGTACGGAGGAGGATTG 59.666 57.143 0.00 0.00 40.21 2.67
1569 4968 1.646189 GATTGAAGACCAGAGGCGTC 58.354 55.000 0.00 0.00 0.00 5.19
1827 5226 2.665603 GGCTTCTCCTTCACGCCT 59.334 61.111 0.00 0.00 37.76 5.52
1903 5302 2.604686 TCGGTGGGAAGCAGCTCT 60.605 61.111 0.00 0.00 0.00 4.09
2136 5535 2.579787 GGCGTCACGATCGACCTG 60.580 66.667 24.34 10.18 31.91 4.00
2258 5657 2.293955 TGGAGATGTTGTACGACGTCAA 59.706 45.455 29.13 16.10 37.89 3.18
2279 5678 1.481871 GGTGGTAGACTCGGATTCCA 58.518 55.000 3.09 0.00 0.00 3.53
2385 5807 0.326264 GATTGCTCCAGAGTGGGTGT 59.674 55.000 0.00 0.00 38.32 4.16
2411 5836 5.452496 CGTCTGATCATCCCTTCACTGTTAT 60.452 44.000 0.00 0.00 0.00 1.89
2420 5845 4.517453 TCCCTTCACTGTTATTTTTCCGTG 59.483 41.667 0.00 0.00 0.00 4.94
2432 5858 4.373348 TTTTTCCGTGTTTGTCCGATTT 57.627 36.364 0.00 0.00 0.00 2.17
2490 5916 4.955811 ATAAGGACAGCGATGTATTCCA 57.044 40.909 6.16 0.00 0.00 3.53
2491 5917 3.627395 AAGGACAGCGATGTATTCCAA 57.373 42.857 6.16 0.00 0.00 3.53
2492 5918 3.627395 AGGACAGCGATGTATTCCAAA 57.373 42.857 6.16 0.00 0.00 3.28
2493 5919 3.270877 AGGACAGCGATGTATTCCAAAC 58.729 45.455 6.16 0.00 0.00 2.93
2494 5920 2.030457 GGACAGCGATGTATTCCAAACG 59.970 50.000 6.16 0.00 0.00 3.60
2495 5921 2.671396 GACAGCGATGTATTCCAAACGT 59.329 45.455 6.16 0.00 32.28 3.99
2496 5922 3.071479 ACAGCGATGTATTCCAAACGTT 58.929 40.909 3.50 0.00 32.28 3.99
2497 5923 3.124636 ACAGCGATGTATTCCAAACGTTC 59.875 43.478 3.50 0.00 32.28 3.95
2498 5924 2.347452 AGCGATGTATTCCAAACGTTCG 59.653 45.455 0.00 0.00 32.28 3.95
2499 5925 2.689635 CGATGTATTCCAAACGTTCGC 58.310 47.619 0.00 0.00 0.00 4.70
2501 5927 0.164217 TGTATTCCAAACGTTCGCGC 59.836 50.000 0.00 0.00 46.04 6.86
2502 5928 0.519792 GTATTCCAAACGTTCGCGCC 60.520 55.000 0.00 0.00 46.04 6.53
2503 5929 0.671163 TATTCCAAACGTTCGCGCCT 60.671 50.000 0.00 0.00 46.04 5.52
2504 5930 0.671163 ATTCCAAACGTTCGCGCCTA 60.671 50.000 0.00 0.00 46.04 3.93
2505 5931 0.671163 TTCCAAACGTTCGCGCCTAT 60.671 50.000 0.00 0.00 46.04 2.57
2506 5932 0.173029 TCCAAACGTTCGCGCCTATA 59.827 50.000 0.00 0.00 46.04 1.31
2507 5933 1.202440 TCCAAACGTTCGCGCCTATAT 60.202 47.619 0.00 0.00 46.04 0.86
2508 5934 1.070843 CCAAACGTTCGCGCCTATATG 60.071 52.381 0.00 0.00 46.04 1.78
2509 5935 1.855978 CAAACGTTCGCGCCTATATGA 59.144 47.619 0.00 0.00 46.04 2.15
2510 5936 2.433868 AACGTTCGCGCCTATATGAT 57.566 45.000 0.00 0.00 46.04 2.45
2511 5937 3.564235 AACGTTCGCGCCTATATGATA 57.436 42.857 0.00 0.00 46.04 2.15
2512 5938 2.860062 ACGTTCGCGCCTATATGATAC 58.140 47.619 0.00 0.00 46.04 2.24
2513 5939 2.486982 ACGTTCGCGCCTATATGATACT 59.513 45.455 0.00 0.00 46.04 2.12
2529 5955 4.533815 TGATACTCCTTCTGTCGGTGTAT 58.466 43.478 10.26 10.26 41.42 2.29
2683 6117 1.946768 CCAAGACCACGAAGAGCAAAA 59.053 47.619 0.00 0.00 0.00 2.44
2685 6119 2.872245 CAAGACCACGAAGAGCAAAAGA 59.128 45.455 0.00 0.00 0.00 2.52
2799 6234 1.205893 GAGCGAATCACCCTTGAGTCT 59.794 52.381 1.17 0.00 43.36 3.24
2862 6297 5.826208 TGATAGCATGCAGATCTTTGTGAAT 59.174 36.000 24.68 3.46 0.00 2.57
2922 6357 2.833582 GCGGGATCCCAGTCGAGA 60.834 66.667 30.42 0.00 35.37 4.04
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.201652 GGAGAACAAGCCTTTACTTACATGATC 60.202 40.741 0.00 0.00 0.00 2.92
23 24 5.307196 AGACAGGAGAACAAGCCTTTACTTA 59.693 40.000 0.00 0.00 30.41 2.24
253 741 1.993956 TAAAGCCAAAGCAAGCCTCA 58.006 45.000 0.00 0.00 43.56 3.86
279 767 2.290464 TCTTTTGCCTTCGTTTCGGAA 58.710 42.857 0.00 0.00 0.00 4.30
280 768 1.956297 TCTTTTGCCTTCGTTTCGGA 58.044 45.000 0.00 0.00 0.00 4.55
281 769 2.989422 ATCTTTTGCCTTCGTTTCGG 57.011 45.000 0.00 0.00 0.00 4.30
530 2487 1.447314 CCTCGAGTTAACCCGCACC 60.447 63.158 12.31 0.00 0.00 5.01
621 2892 7.054124 TGTGAATGGAAGATTATACCAAGGAC 58.946 38.462 0.00 0.00 37.24 3.85
644 2960 5.056480 TGACTGAACAATCACGAAAGATGT 58.944 37.500 0.00 0.00 0.00 3.06
648 2964 4.084328 GGACTGACTGAACAATCACGAAAG 60.084 45.833 0.00 0.00 0.00 2.62
675 3003 5.579511 ACCAAGCACACGTACAATAATCTAC 59.420 40.000 0.00 0.00 0.00 2.59
682 3010 2.143122 CTCACCAAGCACACGTACAAT 58.857 47.619 0.00 0.00 0.00 2.71
693 3022 5.897377 ATTTATACACCAACTCACCAAGC 57.103 39.130 0.00 0.00 0.00 4.01
694 3023 7.067008 CCCTAATTTATACACCAACTCACCAAG 59.933 40.741 0.00 0.00 0.00 3.61
695 3024 6.887545 CCCTAATTTATACACCAACTCACCAA 59.112 38.462 0.00 0.00 0.00 3.67
696 3025 6.419791 CCCTAATTTATACACCAACTCACCA 58.580 40.000 0.00 0.00 0.00 4.17
697 3026 5.298527 GCCCTAATTTATACACCAACTCACC 59.701 44.000 0.00 0.00 0.00 4.02
698 3027 5.007332 CGCCCTAATTTATACACCAACTCAC 59.993 44.000 0.00 0.00 0.00 3.51
699 3028 5.120399 CGCCCTAATTTATACACCAACTCA 58.880 41.667 0.00 0.00 0.00 3.41
700 3029 5.121105 ACGCCCTAATTTATACACCAACTC 58.879 41.667 0.00 0.00 0.00 3.01
749 3084 6.931840 GGAGAAGCCATTGGAAGTTAGTATAG 59.068 42.308 6.95 0.00 36.34 1.31
776 3119 2.887152 GGAGGATGCACAAGAACAAGTT 59.113 45.455 0.00 0.00 0.00 2.66
815 3158 2.029649 CAGCAGAAATGGTGGAAAGGTG 60.030 50.000 0.00 0.00 34.04 4.00
884 4238 1.367659 GAGCAGACATCTTGTGCCTC 58.632 55.000 0.00 0.00 37.98 4.70
887 4241 0.801251 GTGGAGCAGACATCTTGTGC 59.199 55.000 0.00 0.00 37.48 4.57
926 4282 2.951457 TGCCATGCTCAATTCATGTG 57.049 45.000 5.25 0.00 39.60 3.21
1167 4563 4.752594 GTGGTGCCCCTCCCCCTA 62.753 72.222 0.00 0.00 0.00 3.53
1210 4606 1.504275 ATGCTCACCTTGCCCTCCTT 61.504 55.000 0.00 0.00 0.00 3.36
1311 4707 2.187946 CCGGTGTCCATGAGGAGC 59.812 66.667 0.00 0.00 46.92 4.70
1386 4782 1.004394 GGGTCGAACAAGGGATCCTTT 59.996 52.381 12.58 7.66 41.69 3.11
1440 4836 0.250684 TCTTGCAAATGTCGGAGCCA 60.251 50.000 0.00 0.00 0.00 4.75
1450 4846 2.613977 CGGACTGGAGTCTCTTGCAAAT 60.614 50.000 0.00 0.00 44.20 2.32
1475 4874 1.136147 CTGCAGCCATTGTCGAAGC 59.864 57.895 0.00 0.00 0.00 3.86
1554 4953 1.133407 CTGTAGACGCCTCTGGTCTTC 59.867 57.143 0.00 0.00 41.83 2.87
1569 4968 2.125912 AGCGCCTCGTTGCTGTAG 60.126 61.111 2.29 0.00 40.62 2.74
1698 5097 2.722201 GGTCTGAACCGGGAGCGAT 61.722 63.158 6.32 0.00 35.36 4.58
1827 5226 3.326588 CGTAATCCATGAAGGGGGTCATA 59.673 47.826 0.00 0.00 36.04 2.15
1890 5289 0.833287 GGATACAGAGCTGCTTCCCA 59.167 55.000 2.53 0.00 32.09 4.37
1903 5302 1.546589 AACACCTTCGGCGGGATACA 61.547 55.000 7.21 0.00 39.74 2.29
2258 5657 1.688627 GGAATCCGAGTCTACCACCCT 60.689 57.143 0.00 0.00 0.00 4.34
2296 5698 3.069586 CGATTGTGGTATAGCTTGAGGGA 59.930 47.826 3.20 0.00 0.00 4.20
2368 5788 1.754745 GACACCCACTCTGGAGCAA 59.245 57.895 0.00 0.00 40.96 3.91
2385 5807 1.757118 GTGAAGGGATGATCAGACGGA 59.243 52.381 0.09 0.00 0.00 4.69
2411 5836 4.373348 AAATCGGACAAACACGGAAAAA 57.627 36.364 0.00 0.00 0.00 1.94
2420 5845 3.242188 CGACGGGATAAAATCGGACAAAC 60.242 47.826 0.00 0.00 0.00 2.93
2432 5858 3.596310 TCACAAATGACGACGGGATAA 57.404 42.857 0.00 0.00 0.00 1.75
2473 5899 2.030457 CGTTTGGAATACATCGCTGTCC 59.970 50.000 0.00 0.00 36.79 4.02
2474 5900 2.671396 ACGTTTGGAATACATCGCTGTC 59.329 45.455 0.00 0.00 36.79 3.51
2475 5901 2.695359 ACGTTTGGAATACATCGCTGT 58.305 42.857 0.00 0.00 39.49 4.40
2476 5902 3.670203 GAACGTTTGGAATACATCGCTG 58.330 45.455 0.46 0.00 32.65 5.18
2477 5903 2.347452 CGAACGTTTGGAATACATCGCT 59.653 45.455 7.72 0.00 32.65 4.93
2478 5904 2.689635 CGAACGTTTGGAATACATCGC 58.310 47.619 7.72 0.00 32.65 4.58
2479 5905 2.689635 GCGAACGTTTGGAATACATCG 58.310 47.619 17.16 6.15 34.55 3.84
2480 5906 2.689635 CGCGAACGTTTGGAATACATC 58.310 47.619 17.16 0.00 33.53 3.06
2481 5907 1.201987 GCGCGAACGTTTGGAATACAT 60.202 47.619 12.10 0.00 42.83 2.29
2482 5908 0.164217 GCGCGAACGTTTGGAATACA 59.836 50.000 12.10 0.00 42.83 2.29
2483 5909 0.519792 GGCGCGAACGTTTGGAATAC 60.520 55.000 12.10 0.00 42.83 1.89
2484 5910 0.671163 AGGCGCGAACGTTTGGAATA 60.671 50.000 12.10 0.00 42.83 1.75
2485 5911 0.671163 TAGGCGCGAACGTTTGGAAT 60.671 50.000 12.10 0.00 42.83 3.01
2486 5912 0.671163 ATAGGCGCGAACGTTTGGAA 60.671 50.000 12.10 0.00 42.83 3.53
2487 5913 0.173029 TATAGGCGCGAACGTTTGGA 59.827 50.000 12.10 0.00 42.83 3.53
2488 5914 1.070843 CATATAGGCGCGAACGTTTGG 60.071 52.381 12.10 8.40 42.83 3.28
2489 5915 1.855978 TCATATAGGCGCGAACGTTTG 59.144 47.619 12.10 11.39 42.83 2.93
2490 5916 2.212869 TCATATAGGCGCGAACGTTT 57.787 45.000 12.10 0.00 42.83 3.60
2491 5917 2.433868 ATCATATAGGCGCGAACGTT 57.566 45.000 12.10 0.00 42.83 3.99
2492 5918 2.486982 AGTATCATATAGGCGCGAACGT 59.513 45.455 12.10 0.00 42.83 3.99
2493 5919 3.099362 GAGTATCATATAGGCGCGAACG 58.901 50.000 12.10 0.00 37.45 3.95
2494 5920 3.128938 AGGAGTATCATATAGGCGCGAAC 59.871 47.826 12.10 0.36 36.25 3.95
2495 5921 3.353557 AGGAGTATCATATAGGCGCGAA 58.646 45.455 12.10 0.00 36.25 4.70
2496 5922 3.000684 AGGAGTATCATATAGGCGCGA 57.999 47.619 12.10 0.00 36.25 5.87
2497 5923 3.378742 AGAAGGAGTATCATATAGGCGCG 59.621 47.826 0.00 0.00 36.25 6.86
2498 5924 4.158764 ACAGAAGGAGTATCATATAGGCGC 59.841 45.833 0.00 0.00 36.25 6.53
2499 5925 5.447954 CGACAGAAGGAGTATCATATAGGCG 60.448 48.000 0.00 0.00 36.25 5.52
2500 5926 5.163602 CCGACAGAAGGAGTATCATATAGGC 60.164 48.000 0.00 0.00 36.25 3.93
2501 5927 5.946972 ACCGACAGAAGGAGTATCATATAGG 59.053 44.000 0.00 0.00 36.25 2.57
2502 5928 6.431543 ACACCGACAGAAGGAGTATCATATAG 59.568 42.308 0.00 0.00 36.25 1.31
2503 5929 6.304624 ACACCGACAGAAGGAGTATCATATA 58.695 40.000 0.00 0.00 36.25 0.86
2504 5930 5.141182 ACACCGACAGAAGGAGTATCATAT 58.859 41.667 0.00 0.00 36.25 1.78
2505 5931 4.533815 ACACCGACAGAAGGAGTATCATA 58.466 43.478 0.00 0.00 36.25 2.15
2506 5932 3.366396 ACACCGACAGAAGGAGTATCAT 58.634 45.455 0.00 0.00 36.25 2.45
2507 5933 2.803956 ACACCGACAGAAGGAGTATCA 58.196 47.619 0.00 0.00 36.25 2.15
2508 5934 6.630444 TTATACACCGACAGAAGGAGTATC 57.370 41.667 8.23 0.00 42.03 2.24
2509 5935 7.414222 TTTTATACACCGACAGAAGGAGTAT 57.586 36.000 9.53 9.53 44.07 2.12
2510 5936 6.839124 TTTTATACACCGACAGAAGGAGTA 57.161 37.500 0.00 0.00 38.73 2.59
2511 5937 5.733620 TTTTATACACCGACAGAAGGAGT 57.266 39.130 0.00 0.00 36.56 3.85
2512 5938 6.395629 TCTTTTTATACACCGACAGAAGGAG 58.604 40.000 0.00 0.00 0.00 3.69
2513 5939 6.349243 TCTTTTTATACACCGACAGAAGGA 57.651 37.500 0.00 0.00 0.00 3.36
2683 6117 2.047443 GGGAGTCCGCTTCGTCTCT 61.047 63.158 2.26 0.00 0.00 3.10
2685 6119 3.069318 GGGGAGTCCGCTTCGTCT 61.069 66.667 18.68 0.00 33.42 4.18
2708 6143 0.325296 ACTGTCTCCCGGCAAGGATA 60.325 55.000 0.00 0.00 45.00 2.59
2774 6209 0.899720 AAGGGTGATTCGCTCCGTAA 59.100 50.000 0.00 0.00 38.40 3.18
2862 6297 6.149129 AGTGCGTATCTGATCTTGAATGTA 57.851 37.500 0.00 0.00 0.00 2.29
2922 6357 1.000896 CGGGGGCCTTGTGATCTTT 60.001 57.895 0.84 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.