Multiple sequence alignment - TraesCS1A01G103700

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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 TraesCS1A01G103700 chr1A 100.000 3549 0 0 1 3549 99727976 99724428 0.000000e+00 6554.0
1 TraesCS1A01G103700 chr1A 96.824 850 25 2 2702 3549 493928074 493927225 0.000000e+00 1419.0
2 TraesCS1A01G103700 chr1A 96.698 848 28 0 2702 3549 105280351 105281198 0.000000e+00 1411.0
3 TraesCS1A01G103700 chr1A 84.293 834 106 12 900 1724 99640947 99641764 0.000000e+00 791.0
4 TraesCS1A01G103700 chr1A 80.440 455 50 22 459 892 99640256 99640692 9.570000e-81 311.0
5 TraesCS1A01G103700 chr1A 75.541 462 68 22 461 900 99751279 99750841 6.050000e-43 185.0
6 TraesCS1A01G103700 chr5D 93.715 2307 100 14 416 2705 11577479 11575201 0.000000e+00 3415.0
7 TraesCS1A01G103700 chr5D 82.619 1214 180 16 1122 2316 459750353 459751554 0.000000e+00 1044.0
8 TraesCS1A01G103700 chr5D 81.826 1216 185 19 1122 2316 459758480 459759680 0.000000e+00 989.0
9 TraesCS1A01G103700 chr5D 81.826 1216 185 19 1122 2316 459762941 459764141 0.000000e+00 989.0
10 TraesCS1A01G103700 chr5D 77.540 1683 259 64 898 2519 11614413 11612789 0.000000e+00 904.0
11 TraesCS1A01G103700 chr5D 77.742 1249 180 49 1499 2705 459742051 459743243 0.000000e+00 676.0
12 TraesCS1A01G103700 chr5D 81.731 832 106 19 900 1722 11420775 11421569 0.000000e+00 652.0
13 TraesCS1A01G103700 chr5D 79.639 776 97 34 1796 2519 11365565 11366331 5.290000e-138 501.0
14 TraesCS1A01G103700 chr5D 82.335 334 29 16 459 770 11419824 11420149 2.720000e-66 263.0
15 TraesCS1A01G103700 chr5D 81.737 334 33 14 461 777 11630742 11630420 1.640000e-63 254.0
16 TraesCS1A01G103700 chr5D 76.549 452 63 22 461 892 11362612 11363040 1.290000e-49 207.0
17 TraesCS1A01G103700 chr5D 94.309 123 7 0 289 411 11577646 11577524 4.680000e-44 189.0
18 TraesCS1A01G103700 chr5D 100.000 41 0 0 486 526 11577528 11577488 3.800000e-10 76.8
19 TraesCS1A01G103700 chr5B 93.103 2233 122 13 1 2207 11502164 11504390 0.000000e+00 3241.0
20 TraesCS1A01G103700 chr5B 83.862 756 114 5 982 1730 11605576 11604822 0.000000e+00 713.0
21 TraesCS1A01G103700 chr5B 89.474 513 18 17 2194 2705 11504408 11504885 1.810000e-172 616.0
22 TraesCS1A01G103700 chr5B 85.315 572 81 3 1371 1940 564457180 564457750 3.950000e-164 588.0
23 TraesCS1A01G103700 chr5B 84.817 573 83 4 1371 1940 564218602 564219173 1.110000e-159 573.0
24 TraesCS1A01G103700 chr5B 79.439 535 78 16 1812 2329 564445082 564445601 2.030000e-92 350.0
25 TraesCS1A01G103700 chr5B 81.962 316 42 4 1958 2264 564510208 564510517 1.640000e-63 254.0
26 TraesCS1A01G103700 chr5B 80.833 120 14 5 2400 2519 564186600 564186710 6.310000e-13 86.1
27 TraesCS1A01G103700 chr2A 96.816 848 26 1 2702 3549 497980402 497981248 0.000000e+00 1415.0
28 TraesCS1A01G103700 chr2A 96.454 846 30 0 2704 3549 772451493 772452338 0.000000e+00 1397.0
29 TraesCS1A01G103700 chr3A 96.588 850 27 1 2702 3549 708642374 708643223 0.000000e+00 1408.0
30 TraesCS1A01G103700 chr7A 96.572 846 27 2 2704 3549 37844208 37843365 0.000000e+00 1400.0
31 TraesCS1A01G103700 chr7A 96.353 850 30 1 2701 3549 36142352 36141503 0.000000e+00 1397.0
32 TraesCS1A01G103700 chr5A 96.344 848 31 0 2702 3549 631637884 631638731 0.000000e+00 1395.0
33 TraesCS1A01G103700 chr5A 83.004 1112 153 19 1230 2316 579844238 579843138 0.000000e+00 974.0
34 TraesCS1A01G103700 chr5A 87.218 399 44 2 1684 2076 579849935 579849538 6.990000e-122 448.0
35 TraesCS1A01G103700 chr5A 76.352 647 100 28 1900 2519 579893820 579894440 7.450000e-77 298.0
36 TraesCS1A01G103700 chr5A 75.371 337 40 27 2185 2519 579193792 579193497 4.810000e-24 122.0
37 TraesCS1A01G103700 chr5A 88.158 76 8 1 2381 2456 580185649 580185723 4.880000e-14 89.8
38 TraesCS1A01G103700 chr1B 96.019 854 34 0 2696 3549 328146989 328146136 0.000000e+00 1389.0


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 TraesCS1A01G103700 chr1A 99724428 99727976 3548 True 6554.000000 6554 100.0000 1 3549 1 chr1A.!!$R1 3548
1 TraesCS1A01G103700 chr1A 493927225 493928074 849 True 1419.000000 1419 96.8240 2702 3549 1 chr1A.!!$R3 847
2 TraesCS1A01G103700 chr1A 105280351 105281198 847 False 1411.000000 1411 96.6980 2702 3549 1 chr1A.!!$F1 847
3 TraesCS1A01G103700 chr1A 99640256 99641764 1508 False 551.000000 791 82.3665 459 1724 2 chr1A.!!$F2 1265
4 TraesCS1A01G103700 chr5D 11575201 11577646 2445 True 1226.933333 3415 96.0080 289 2705 3 chr5D.!!$R3 2416
5 TraesCS1A01G103700 chr5D 459750353 459751554 1201 False 1044.000000 1044 82.6190 1122 2316 1 chr5D.!!$F2 1194
6 TraesCS1A01G103700 chr5D 459758480 459764141 5661 False 989.000000 989 81.8260 1122 2316 2 chr5D.!!$F5 1194
7 TraesCS1A01G103700 chr5D 11612789 11614413 1624 True 904.000000 904 77.5400 898 2519 1 chr5D.!!$R1 1621
8 TraesCS1A01G103700 chr5D 459742051 459743243 1192 False 676.000000 676 77.7420 1499 2705 1 chr5D.!!$F1 1206
9 TraesCS1A01G103700 chr5D 11419824 11421569 1745 False 457.500000 652 82.0330 459 1722 2 chr5D.!!$F4 1263
10 TraesCS1A01G103700 chr5D 11362612 11366331 3719 False 354.000000 501 78.0940 461 2519 2 chr5D.!!$F3 2058
11 TraesCS1A01G103700 chr5B 11502164 11504885 2721 False 1928.500000 3241 91.2885 1 2705 2 chr5B.!!$F6 2704
12 TraesCS1A01G103700 chr5B 11604822 11605576 754 True 713.000000 713 83.8620 982 1730 1 chr5B.!!$R1 748
13 TraesCS1A01G103700 chr5B 564457180 564457750 570 False 588.000000 588 85.3150 1371 1940 1 chr5B.!!$F4 569
14 TraesCS1A01G103700 chr5B 564218602 564219173 571 False 573.000000 573 84.8170 1371 1940 1 chr5B.!!$F2 569
15 TraesCS1A01G103700 chr5B 564445082 564445601 519 False 350.000000 350 79.4390 1812 2329 1 chr5B.!!$F3 517
16 TraesCS1A01G103700 chr2A 497980402 497981248 846 False 1415.000000 1415 96.8160 2702 3549 1 chr2A.!!$F1 847
17 TraesCS1A01G103700 chr2A 772451493 772452338 845 False 1397.000000 1397 96.4540 2704 3549 1 chr2A.!!$F2 845
18 TraesCS1A01G103700 chr3A 708642374 708643223 849 False 1408.000000 1408 96.5880 2702 3549 1 chr3A.!!$F1 847
19 TraesCS1A01G103700 chr7A 37843365 37844208 843 True 1400.000000 1400 96.5720 2704 3549 1 chr7A.!!$R2 845
20 TraesCS1A01G103700 chr7A 36141503 36142352 849 True 1397.000000 1397 96.3530 2701 3549 1 chr7A.!!$R1 848
21 TraesCS1A01G103700 chr5A 631637884 631638731 847 False 1395.000000 1395 96.3440 2702 3549 1 chr5A.!!$F3 847
22 TraesCS1A01G103700 chr5A 579843138 579844238 1100 True 974.000000 974 83.0040 1230 2316 1 chr5A.!!$R2 1086
23 TraesCS1A01G103700 chr5A 579893820 579894440 620 False 298.000000 298 76.3520 1900 2519 1 chr5A.!!$F1 619
24 TraesCS1A01G103700 chr1B 328146136 328146989 853 True 1389.000000 1389 96.0190 2696 3549 1 chr1B.!!$R1 853

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
209 210 0.255033 GTAAGGGGCGAGGGAAACAT 59.745 55.0 0.0 0.0 0.0 2.71 F
237 238 0.327924 AGATCATCAAACCACCGCCA 59.672 50.0 0.0 0.0 0.0 5.69 F
1043 3121 0.978146 ATCCCCTTCACTCTCACCCG 60.978 60.0 0.0 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1648 3753 0.250338 AAGTCAGGTCTTGGGCGTTC 60.250 55.000 0.0 0.00 0.00 3.95 R
1699 3804 0.820871 AGCAGAAGAGGTCGTCATCC 59.179 55.000 0.0 0.00 0.00 3.51 R
2819 5600 1.070445 CTGCAAAGTGGGCCAATTTCA 59.930 47.619 27.5 23.82 29.07 2.69 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
19 20 2.170012 GACTAGGGATGTGTGGGGTA 57.830 55.000 0.00 0.00 0.00 3.69
23 24 1.213296 AGGGATGTGTGGGGTATGAC 58.787 55.000 0.00 0.00 0.00 3.06
25 26 2.022428 AGGGATGTGTGGGGTATGACTA 60.022 50.000 0.00 0.00 0.00 2.59
28 29 3.431766 GGATGTGTGGGGTATGACTACAC 60.432 52.174 5.30 5.30 41.36 2.90
37 38 1.066605 GTATGACTACACGCCGTCCAT 59.933 52.381 0.00 0.00 0.00 3.41
88 89 8.951243 GGAAGGGCTCTATATGAAAACATATTC 58.049 37.037 7.80 0.00 0.00 1.75
113 114 8.887393 TCTAGAGTTTTAAGGGAATTAGGTTGT 58.113 33.333 0.00 0.00 0.00 3.32
126 127 0.393077 AGGTTGTTCAGGGTGACTCG 59.607 55.000 0.00 0.00 0.00 4.18
133 134 3.146847 GTTCAGGGTGACTCGGAAAAAT 58.853 45.455 0.00 0.00 0.00 1.82
139 140 3.146847 GGTGACTCGGAAAAATGACCTT 58.853 45.455 0.00 0.00 0.00 3.50
143 144 4.274950 TGACTCGGAAAAATGACCTTGAAC 59.725 41.667 0.00 0.00 0.00 3.18
146 147 4.211920 TCGGAAAAATGACCTTGAACCTT 58.788 39.130 0.00 0.00 0.00 3.50
160 161 2.125512 CCTTGAGTCGAAGCGGGG 60.126 66.667 0.00 0.00 0.00 5.73
209 210 0.255033 GTAAGGGGCGAGGGAAACAT 59.745 55.000 0.00 0.00 0.00 2.71
216 217 1.523154 GCGAGGGAAACATGTGGCAA 61.523 55.000 0.00 0.00 0.00 4.52
217 218 0.958091 CGAGGGAAACATGTGGCAAA 59.042 50.000 0.00 0.00 0.00 3.68
225 226 4.866486 GGAAACATGTGGCAAAAGATCATC 59.134 41.667 0.00 0.00 0.00 2.92
226 227 5.471556 AAACATGTGGCAAAAGATCATCA 57.528 34.783 0.00 0.00 0.00 3.07
236 237 1.463674 AAGATCATCAAACCACCGCC 58.536 50.000 0.00 0.00 0.00 6.13
237 238 0.327924 AGATCATCAAACCACCGCCA 59.672 50.000 0.00 0.00 0.00 5.69
248 249 1.538075 ACCACCGCCAAAAATAAGTCG 59.462 47.619 0.00 0.00 0.00 4.18
251 252 2.224549 CACCGCCAAAAATAAGTCGTCA 59.775 45.455 0.00 0.00 0.00 4.35
258 259 4.513692 CCAAAAATAAGTCGTCACCAGACA 59.486 41.667 0.00 0.00 45.23 3.41
263 264 2.684001 AGTCGTCACCAGACAAAACA 57.316 45.000 0.00 0.00 45.23 2.83
264 265 3.194005 AGTCGTCACCAGACAAAACAT 57.806 42.857 0.00 0.00 45.23 2.71
274 275 3.551454 CCAGACAAAACATGAGTTGCCAG 60.551 47.826 0.00 0.00 38.17 4.85
534 577 9.240159 TGATTAATTTTGATGCTTTCATGATCG 57.760 29.630 0.00 0.00 33.34 3.69
535 578 9.454585 GATTAATTTTGATGCTTTCATGATCGA 57.545 29.630 0.00 0.00 33.34 3.59
706 777 4.588951 TCTTCTCTAGTTTCAGTGCCTTCA 59.411 41.667 0.00 0.00 0.00 3.02
721 792 4.516321 GTGCCTTCAAATTTGCCAGAAATT 59.484 37.500 13.54 0.00 0.00 1.82
722 793 5.008911 GTGCCTTCAAATTTGCCAGAAATTT 59.991 36.000 13.54 0.00 39.60 1.82
723 794 5.593502 TGCCTTCAAATTTGCCAGAAATTTT 59.406 32.000 13.54 0.00 37.64 1.82
810 1189 5.237344 GCATAAGGAAGATGTATGTGGTCAC 59.763 44.000 0.00 0.00 0.00 3.67
822 1201 2.360844 TGTGGTCACGCAAAAAGAGAA 58.639 42.857 0.00 0.00 33.42 2.87
828 1207 2.806244 TCACGCAAAAAGAGAACTAGGC 59.194 45.455 0.00 0.00 0.00 3.93
1043 3121 0.978146 ATCCCCTTCACTCTCACCCG 60.978 60.000 0.00 0.00 0.00 5.28
1087 3173 5.480422 GTCCAAACATCCTACCCTTTTGAAT 59.520 40.000 0.00 0.00 30.23 2.57
1088 3174 5.714806 TCCAAACATCCTACCCTTTTGAATC 59.285 40.000 0.00 0.00 30.23 2.52
1089 3175 5.393027 CCAAACATCCTACCCTTTTGAATCG 60.393 44.000 0.00 0.00 30.23 3.34
1090 3176 3.279434 ACATCCTACCCTTTTGAATCGC 58.721 45.455 0.00 0.00 0.00 4.58
1091 3177 2.018542 TCCTACCCTTTTGAATCGCG 57.981 50.000 0.00 0.00 0.00 5.87
1092 3178 1.014352 CCTACCCTTTTGAATCGCGG 58.986 55.000 6.13 0.00 0.00 6.46
1147 3240 1.827969 CTCCATGAAGACCTTCTCCGT 59.172 52.381 10.67 0.00 40.14 4.69
1207 3300 3.641986 GCGTCGGCCGTCAACAAA 61.642 61.111 27.15 0.00 39.32 2.83
1211 3304 2.052590 CGGCCGTCAACAAACACG 60.053 61.111 19.50 0.00 35.72 4.49
1218 3311 3.591835 CAACAAACACGGGCGCCT 61.592 61.111 28.56 3.74 0.00 5.52
1261 3354 2.580815 CTGCCATGCCTCGTCAGA 59.419 61.111 0.00 0.00 0.00 3.27
1271 3364 2.203379 TCGTCAGACCGTCCACCA 60.203 61.111 0.00 0.00 0.00 4.17
1275 3368 2.923035 CAGACCGTCCACCACCCT 60.923 66.667 0.00 0.00 0.00 4.34
1307 3400 1.589196 CGGATCTTCGGTCGCTTCC 60.589 63.158 0.00 0.00 0.00 3.46
1699 3804 3.744719 TTCTGGGCCGTCGACTCG 61.745 66.667 14.70 4.52 0.00 4.18
1831 3955 4.392166 TCCCGCTACCTCCTGCCA 62.392 66.667 0.00 0.00 0.00 4.92
1925 4049 3.594134 CAAGTCTTCAGGCTACAGAAGG 58.406 50.000 11.75 0.00 39.78 3.46
2017 4147 1.527433 GCTCCAAGGCCTTTGACACC 61.527 60.000 17.61 3.43 39.21 4.16
2090 4229 3.050275 GTCCGCACCAGCAGAACC 61.050 66.667 0.00 0.00 42.27 3.62
2301 4506 4.022416 TGTCTGTTGTTTGTGTTTGCTCTT 60.022 37.500 0.00 0.00 0.00 2.85
2362 4598 1.064758 TCCAGTTTGTTGTGTGCTCCT 60.065 47.619 0.00 0.00 0.00 3.69
2465 5095 6.631016 TGTCAACTATTTAGACTGCTACTGG 58.369 40.000 0.00 0.00 33.56 4.00
2467 5097 4.674281 ACTATTTAGACTGCTACTGGGC 57.326 45.455 0.00 0.00 0.00 5.36
2468 5098 4.290942 ACTATTTAGACTGCTACTGGGCT 58.709 43.478 0.00 0.00 0.00 5.19
2469 5099 5.455872 ACTATTTAGACTGCTACTGGGCTA 58.544 41.667 0.00 0.00 0.00 3.93
2470 5100 4.674281 ATTTAGACTGCTACTGGGCTAC 57.326 45.455 0.00 0.00 0.00 3.58
2482 5118 2.011122 TGGGCTACCAGCTACCTATC 57.989 55.000 0.00 0.00 43.37 2.08
2493 5243 6.583562 ACCAGCTACCTATCTATGTTGTTTC 58.416 40.000 0.00 0.00 0.00 2.78
2520 5289 7.558161 TTATCTGTATGATTTTCTGCTGTGG 57.442 36.000 0.00 0.00 36.65 4.17
2542 5311 5.034797 GGTATTTTCCGCAGTATTTCAAGC 58.965 41.667 0.00 0.00 0.00 4.01
2550 5319 2.440409 CAGTATTTCAAGCAGGGCACT 58.560 47.619 0.00 0.00 0.00 4.40
2804 5585 3.039134 CGGTTTTGTGCCCAGTCC 58.961 61.111 0.00 0.00 0.00 3.85
2902 5684 2.618241 GCTCATATTCGGCATGGTTTCA 59.382 45.455 0.00 0.00 0.00 2.69
3367 6412 0.758310 TGAAGCACACCAAATGCCCA 60.758 50.000 0.00 0.00 44.53 5.36
3449 7072 2.427506 GCAGGGTTTGAGATCGTCTTT 58.572 47.619 0.00 0.00 0.00 2.52
3497 8296 2.756919 GCCATCTGCTAGGTAGTACCCT 60.757 54.545 16.05 6.16 36.42 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 0.248784 GGACGGCGTGTAGTCATACC 60.249 60.000 21.19 4.80 39.01 2.73
19 20 0.179111 CATGGACGGCGTGTAGTCAT 60.179 55.000 21.19 10.23 39.01 3.06
23 24 0.390603 TTTCCATGGACGGCGTGTAG 60.391 55.000 21.19 4.12 0.00 2.74
25 26 1.964373 GTTTCCATGGACGGCGTGT 60.964 57.895 21.19 0.00 0.00 4.49
28 29 1.024046 TCATGTTTCCATGGACGGCG 61.024 55.000 15.91 4.80 46.96 6.46
37 38 5.716228 ACTCCATAAGCATTTCATGTTTCCA 59.284 36.000 0.00 0.00 35.31 3.53
88 89 9.516546 AACAACCTAATTCCCTTAAAACTCTAG 57.483 33.333 0.00 0.00 0.00 2.43
97 98 4.604490 ACCCTGAACAACCTAATTCCCTTA 59.396 41.667 0.00 0.00 0.00 2.69
113 114 3.146066 CATTTTTCCGAGTCACCCTGAA 58.854 45.455 0.00 0.00 0.00 3.02
126 127 5.069119 ACTCAAGGTTCAAGGTCATTTTTCC 59.931 40.000 0.00 0.00 0.00 3.13
133 134 2.036387 TCGACTCAAGGTTCAAGGTCA 58.964 47.619 0.00 0.00 0.00 4.02
139 140 0.319555 CCGCTTCGACTCAAGGTTCA 60.320 55.000 0.00 0.00 0.00 3.18
143 144 2.125512 CCCCGCTTCGACTCAAGG 60.126 66.667 0.00 0.00 0.00 3.61
146 147 3.691342 CCACCCCGCTTCGACTCA 61.691 66.667 0.00 0.00 0.00 3.41
160 161 1.966451 CTTCGCAACTCCCACCCAC 60.966 63.158 0.00 0.00 0.00 4.61
209 210 3.640498 TGGTTTGATGATCTTTTGCCACA 59.360 39.130 0.00 0.00 0.00 4.17
216 217 1.818674 GGCGGTGGTTTGATGATCTTT 59.181 47.619 0.00 0.00 0.00 2.52
217 218 1.271871 TGGCGGTGGTTTGATGATCTT 60.272 47.619 0.00 0.00 0.00 2.40
225 226 3.723260 ACTTATTTTTGGCGGTGGTTTG 58.277 40.909 0.00 0.00 0.00 2.93
226 227 3.551250 CGACTTATTTTTGGCGGTGGTTT 60.551 43.478 0.00 0.00 0.00 3.27
236 237 5.666969 TGTCTGGTGACGACTTATTTTTG 57.333 39.130 0.00 0.00 45.70 2.44
237 238 6.687081 TTTGTCTGGTGACGACTTATTTTT 57.313 33.333 0.00 0.00 45.70 1.94
248 249 4.601019 CAACTCATGTTTTGTCTGGTGAC 58.399 43.478 0.00 0.00 37.74 3.67
251 252 2.362077 GGCAACTCATGTTTTGTCTGGT 59.638 45.455 9.72 0.00 33.52 4.00
258 259 2.380064 TCCCTGGCAACTCATGTTTT 57.620 45.000 0.00 0.00 33.52 2.43
263 264 0.112995 TGCTTTCCCTGGCAACTCAT 59.887 50.000 0.00 0.00 35.40 2.90
264 265 0.112995 ATGCTTTCCCTGGCAACTCA 59.887 50.000 0.00 0.00 41.90 3.41
274 275 0.466372 GTCCTGCCCTATGCTTTCCC 60.466 60.000 0.00 0.00 42.00 3.97
401 403 4.033251 ATGGGACGGGAGGGGGAA 62.033 66.667 0.00 0.00 0.00 3.97
532 575 5.067413 CCTAGCTAGTAGATTTGGTGTTCGA 59.933 44.000 19.31 0.00 0.00 3.71
533 576 5.163540 ACCTAGCTAGTAGATTTGGTGTTCG 60.164 44.000 19.31 0.97 0.00 3.95
534 577 6.043411 CACCTAGCTAGTAGATTTGGTGTTC 58.957 44.000 21.96 0.00 34.59 3.18
535 578 5.484290 ACACCTAGCTAGTAGATTTGGTGTT 59.516 40.000 26.45 17.06 42.83 3.32
681 752 4.888917 AGGCACTGAAACTAGAGAAGAAC 58.111 43.478 0.00 0.00 37.18 3.01
810 1189 2.427506 AGGCCTAGTTCTCTTTTTGCG 58.572 47.619 1.29 0.00 0.00 4.85
822 1201 2.073101 GCCCCAAGCTAGGCCTAGT 61.073 63.158 34.85 21.62 43.76 2.57
828 1207 3.241520 GGTAGGCCCCAAGCTAGG 58.758 66.667 0.00 0.00 43.05 3.02
1043 3121 1.200020 CAATTGGACTGGAAACGAGGC 59.800 52.381 0.00 0.00 0.00 4.70
1147 3240 2.552743 CGTTAGCAGGAGGATGATACGA 59.447 50.000 0.00 0.00 0.00 3.43
1218 3311 4.373116 GGTTCTGGAGCGCGACCA 62.373 66.667 23.28 23.28 35.96 4.02
1261 3354 3.239253 GTCAGGGTGGTGGACGGT 61.239 66.667 0.00 0.00 0.00 4.83
1271 3364 1.380112 GGTAGCTCTCCGTCAGGGT 60.380 63.158 0.00 0.00 38.33 4.34
1275 3368 0.818445 GATCCGGTAGCTCTCCGTCA 60.818 60.000 22.63 12.95 45.63 4.35
1279 3372 0.594110 CGAAGATCCGGTAGCTCTCC 59.406 60.000 0.00 0.00 0.00 3.71
1462 3555 0.816825 CGGAGTTGATGGGGATGCAG 60.817 60.000 0.00 0.00 0.00 4.41
1522 3621 4.821589 GAAGACGGGGCGGCAGAG 62.822 72.222 12.47 3.43 37.34 3.35
1648 3753 0.250338 AAGTCAGGTCTTGGGCGTTC 60.250 55.000 0.00 0.00 0.00 3.95
1699 3804 0.820871 AGCAGAAGAGGTCGTCATCC 59.179 55.000 0.00 0.00 0.00 3.51
2090 4229 1.945394 GGCATCAGCACAAGGATACTG 59.055 52.381 0.00 0.00 47.00 2.74
2301 4506 3.823873 ACCACAACAAAGAAACACTGACA 59.176 39.130 0.00 0.00 0.00 3.58
2362 4598 8.001881 ACAACAAATACAACAAATACAGACCA 57.998 30.769 0.00 0.00 0.00 4.02
2391 4635 3.221771 ACAGCCTGCAAATTAACTGACA 58.778 40.909 0.00 0.00 0.00 3.58
2465 5095 4.345854 ACATAGATAGGTAGCTGGTAGCC 58.654 47.826 11.98 5.19 43.77 3.93
2467 5097 6.902771 ACAACATAGATAGGTAGCTGGTAG 57.097 41.667 4.27 0.00 0.00 3.18
2468 5098 7.343574 TGAAACAACATAGATAGGTAGCTGGTA 59.656 37.037 4.27 0.00 0.00 3.25
2469 5099 6.156256 TGAAACAACATAGATAGGTAGCTGGT 59.844 38.462 4.27 0.00 0.00 4.00
2470 5100 6.582636 TGAAACAACATAGATAGGTAGCTGG 58.417 40.000 4.27 0.00 0.00 4.85
2493 5243 9.447040 CACAGCAGAAAATCATACAGATAATTG 57.553 33.333 0.00 0.00 35.39 2.32
2500 5250 6.932356 ATACCACAGCAGAAAATCATACAG 57.068 37.500 0.00 0.00 0.00 2.74
2520 5289 5.636837 TGCTTGAAATACTGCGGAAAATAC 58.363 37.500 0.00 0.00 0.00 1.89
2542 5311 5.649782 ACAATCAGAAATTTAGTGCCCTG 57.350 39.130 0.00 0.00 0.00 4.45
2819 5600 1.070445 CTGCAAAGTGGGCCAATTTCA 59.930 47.619 27.50 23.82 29.07 2.69
2872 5654 3.578282 TGCCGAATATGAGCCTATTCTCA 59.422 43.478 8.70 0.00 45.97 3.27
3367 6412 0.976641 TTGCAGGAAGGATGTCGAGT 59.023 50.000 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.