Multiple sequence alignment - TraesCS3D01G405900

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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 TraesCS3D01G405900 chr3D 100.000 3251 0 0 1 3251 520192920 520189670 0.000000e+00 6004.0
1 TraesCS3D01G405900 chr3D 96.159 755 29 0 2497 3251 584758286 584757532 0.000000e+00 1234.0
2 TraesCS3D01G405900 chr3D 83.320 1283 157 30 994 2237 570559181 570560445 0.000000e+00 1131.0
3 TraesCS3D01G405900 chr3D 82.227 1266 186 29 994 2235 570393678 570394928 0.000000e+00 1055.0
4 TraesCS3D01G405900 chr3D 89.790 715 61 8 2537 3251 380279217 380278515 0.000000e+00 905.0
5 TraesCS3D01G405900 chr3D 79.658 1229 206 28 1017 2223 570496372 570495166 0.000000e+00 845.0
6 TraesCS3D01G405900 chr3D 79.123 1231 186 43 997 2202 570379584 570380768 0.000000e+00 784.0
7 TraesCS3D01G405900 chr3D 78.888 1241 180 49 994 2202 570281034 570282224 0.000000e+00 765.0
8 TraesCS3D01G405900 chr3D 95.604 455 20 0 2499 2953 40543859 40543405 0.000000e+00 730.0
9 TraesCS3D01G405900 chr3A 93.420 1535 45 18 991 2469 655637091 655635557 0.000000e+00 2224.0
10 TraesCS3D01G405900 chr3A 83.564 1229 156 26 1039 2235 703395197 703396411 0.000000e+00 1109.0
11 TraesCS3D01G405900 chr3A 83.028 1255 171 26 1017 2247 703304281 703303045 0.000000e+00 1099.0
12 TraesCS3D01G405900 chr3A 81.596 1266 194 28 994 2235 703270275 703271525 0.000000e+00 1011.0
13 TraesCS3D01G405900 chr3A 78.485 1241 184 52 994 2202 703170781 703171970 0.000000e+00 736.0
14 TraesCS3D01G405900 chr3A 91.961 311 20 4 585 891 655637450 655637141 6.440000e-117 431.0
15 TraesCS3D01G405900 chr3A 92.661 218 12 3 329 545 655638206 655637992 8.760000e-81 311.0
16 TraesCS3D01G405900 chr3A 90.533 169 16 0 4 172 655638466 655638298 1.170000e-54 224.0
17 TraesCS3D01G405900 chr3A 80.645 155 13 9 559 709 703394731 703394872 1.600000e-18 104.0
18 TraesCS3D01G405900 chr3B 95.577 1379 50 3 991 2369 685039273 685037906 0.000000e+00 2198.0
19 TraesCS3D01G405900 chr3B 83.632 1283 153 31 994 2237 757807620 757808884 0.000000e+00 1153.0
20 TraesCS3D01G405900 chr3B 82.019 1268 184 32 994 2235 757734144 757735393 0.000000e+00 1038.0
21 TraesCS3D01G405900 chr3B 89.125 754 70 8 2498 3251 47612359 47613100 0.000000e+00 928.0
22 TraesCS3D01G405900 chr3B 80.144 1254 209 28 1017 2247 757773415 757772179 0.000000e+00 900.0
23 TraesCS3D01G405900 chr3B 90.418 574 42 5 1 566 685041713 685041145 0.000000e+00 743.0
24 TraesCS3D01G405900 chr3B 77.787 1238 196 48 994 2202 757472865 757474052 0.000000e+00 689.0
25 TraesCS3D01G405900 chr3B 94.667 300 8 4 564 857 685039648 685039351 2.960000e-125 459.0
26 TraesCS3D01G405900 chr3B 81.818 110 14 3 559 668 757807222 757807325 1.610000e-13 87.9
27 TraesCS3D01G405900 chr3B 76.687 163 31 5 159 319 104323483 104323640 2.080000e-12 84.2
28 TraesCS3D01G405900 chr1D 97.128 766 19 3 2488 3251 404197457 404198221 0.000000e+00 1290.0
29 TraesCS3D01G405900 chr1D 96.154 754 29 0 2498 3251 33576626 33575873 0.000000e+00 1232.0
30 TraesCS3D01G405900 chr5D 96.817 754 24 0 2498 3251 520994841 520994088 0.000000e+00 1260.0
31 TraesCS3D01G405900 chr5D 89.965 568 44 9 2684 3251 481174369 481174923 0.000000e+00 721.0
32 TraesCS3D01G405900 chr5D 89.726 146 15 0 2496 2641 481174220 481174365 1.540000e-43 187.0
33 TraesCS3D01G405900 chr7B 88.845 753 68 6 2498 3250 653890986 653890250 0.000000e+00 911.0
34 TraesCS3D01G405900 chr7B 79.861 144 27 2 167 309 86632613 86632755 1.600000e-18 104.0
35 TraesCS3D01G405900 chr2A 75.032 773 153 22 2495 3244 673995255 673994500 4.050000e-84 322.0
36 TraesCS3D01G405900 chr7D 89.401 217 23 0 1471 1687 565060544 565060328 1.150000e-69 274.0
37 TraesCS3D01G405900 chr7D 75.000 204 45 6 212 412 25896273 25896473 4.470000e-14 89.8
38 TraesCS3D01G405900 chr5B 80.342 117 20 3 202 317 162768564 162768678 5.780000e-13 86.1
39 TraesCS3D01G405900 chr6A 92.157 51 2 2 214 263 595028074 595028025 1.620000e-08 71.3


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 TraesCS3D01G405900 chr3D 520189670 520192920 3250 True 6004.000000 6004 100.00000 1 3251 1 chr3D.!!$R3 3250
1 TraesCS3D01G405900 chr3D 584757532 584758286 754 True 1234.000000 1234 96.15900 2497 3251 1 chr3D.!!$R5 754
2 TraesCS3D01G405900 chr3D 570559181 570560445 1264 False 1131.000000 1131 83.32000 994 2237 1 chr3D.!!$F4 1243
3 TraesCS3D01G405900 chr3D 570393678 570394928 1250 False 1055.000000 1055 82.22700 994 2235 1 chr3D.!!$F3 1241
4 TraesCS3D01G405900 chr3D 380278515 380279217 702 True 905.000000 905 89.79000 2537 3251 1 chr3D.!!$R2 714
5 TraesCS3D01G405900 chr3D 570495166 570496372 1206 True 845.000000 845 79.65800 1017 2223 1 chr3D.!!$R4 1206
6 TraesCS3D01G405900 chr3D 570379584 570380768 1184 False 784.000000 784 79.12300 997 2202 1 chr3D.!!$F2 1205
7 TraesCS3D01G405900 chr3D 570281034 570282224 1190 False 765.000000 765 78.88800 994 2202 1 chr3D.!!$F1 1208
8 TraesCS3D01G405900 chr3A 703303045 703304281 1236 True 1099.000000 1099 83.02800 1017 2247 1 chr3A.!!$R1 1230
9 TraesCS3D01G405900 chr3A 703270275 703271525 1250 False 1011.000000 1011 81.59600 994 2235 1 chr3A.!!$F2 1241
10 TraesCS3D01G405900 chr3A 655635557 655638466 2909 True 797.500000 2224 92.14375 4 2469 4 chr3A.!!$R2 2465
11 TraesCS3D01G405900 chr3A 703170781 703171970 1189 False 736.000000 736 78.48500 994 2202 1 chr3A.!!$F1 1208
12 TraesCS3D01G405900 chr3A 703394731 703396411 1680 False 606.500000 1109 82.10450 559 2235 2 chr3A.!!$F3 1676
13 TraesCS3D01G405900 chr3B 685037906 685041713 3807 True 1133.333333 2198 93.55400 1 2369 3 chr3B.!!$R2 2368
14 TraesCS3D01G405900 chr3B 757734144 757735393 1249 False 1038.000000 1038 82.01900 994 2235 1 chr3B.!!$F4 1241
15 TraesCS3D01G405900 chr3B 47612359 47613100 741 False 928.000000 928 89.12500 2498 3251 1 chr3B.!!$F1 753
16 TraesCS3D01G405900 chr3B 757772179 757773415 1236 True 900.000000 900 80.14400 1017 2247 1 chr3B.!!$R1 1230
17 TraesCS3D01G405900 chr3B 757472865 757474052 1187 False 689.000000 689 77.78700 994 2202 1 chr3B.!!$F3 1208
18 TraesCS3D01G405900 chr3B 757807222 757808884 1662 False 620.450000 1153 82.72500 559 2237 2 chr3B.!!$F5 1678
19 TraesCS3D01G405900 chr1D 404197457 404198221 764 False 1290.000000 1290 97.12800 2488 3251 1 chr1D.!!$F1 763
20 TraesCS3D01G405900 chr1D 33575873 33576626 753 True 1232.000000 1232 96.15400 2498 3251 1 chr1D.!!$R1 753
21 TraesCS3D01G405900 chr5D 520994088 520994841 753 True 1260.000000 1260 96.81700 2498 3251 1 chr5D.!!$R1 753
22 TraesCS3D01G405900 chr5D 481174220 481174923 703 False 454.000000 721 89.84550 2496 3251 2 chr5D.!!$F1 755
23 TraesCS3D01G405900 chr7B 653890250 653890986 736 True 911.000000 911 88.84500 2498 3250 1 chr7B.!!$R1 752
24 TraesCS3D01G405900 chr2A 673994500 673995255 755 True 322.000000 322 75.03200 2495 3244 1 chr2A.!!$R1 749

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
275 276 0.105408 ACGAAGTAACCACAGCCGTT 59.895 50.0 0.0 0.0 41.94 4.44 F
756 2431 0.325860 ATACCTTCCCCAGTACGCCA 60.326 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2130 3896 0.99192 TGTTCTCCATCTGGAACCCC 59.008 55.0 0.0 0.0 44.91 4.95 R
2483 4305 0.03582 GCGTCCATGGAACTTGGGTA 60.036 55.0 18.2 0.0 34.85 3.69 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
54 55 0.463654 TGGGTGCATCTACGGAATGC 60.464 55.000 10.80 10.80 41.35 3.56
87 88 3.529734 TGGAGGCCATTATTCCTAAACCA 59.470 43.478 5.01 0.00 31.71 3.67
96 97 3.801307 ATTCCTAAACCAGGGAACGTT 57.199 42.857 0.00 0.00 45.58 3.99
140 141 3.128938 AGACACGAGACTCCCTAAAATCG 59.871 47.826 0.00 0.00 36.32 3.34
156 157 2.327200 ATCGGCCTAAACCAAGCTAC 57.673 50.000 0.00 0.00 0.00 3.58
184 185 5.243060 CGTCATTATACACTCACCCCTATGA 59.757 44.000 0.00 0.00 0.00 2.15
189 190 2.253610 ACACTCACCCCTATGAACGAA 58.746 47.619 0.00 0.00 0.00 3.85
201 202 5.291128 CCCTATGAACGAACTTACACACATC 59.709 44.000 0.00 0.00 0.00 3.06
205 206 5.224888 TGAACGAACTTACACACATCCTAC 58.775 41.667 0.00 0.00 0.00 3.18
207 208 3.056322 ACGAACTTACACACATCCTACCC 60.056 47.826 0.00 0.00 0.00 3.69
208 209 3.677976 CGAACTTACACACATCCTACCCC 60.678 52.174 0.00 0.00 0.00 4.95
237 238 1.072489 ACCTCAGAGATATCGAGCCGA 59.928 52.381 0.00 0.00 41.13 5.54
246 247 4.987832 AGATATCGAGCCGACACAATATC 58.012 43.478 0.00 4.01 39.18 1.63
275 276 0.105408 ACGAAGTAACCACAGCCGTT 59.895 50.000 0.00 0.00 41.94 4.44
278 279 2.490991 GAAGTAACCACAGCCGTTTCT 58.509 47.619 0.00 0.00 0.00 2.52
297 298 2.168521 TCTTGGTCGATGGGAATGTCTC 59.831 50.000 0.00 0.00 0.00 3.36
327 328 6.201044 CACTGAATAAGTATCACCGGATTCAC 59.799 42.308 9.46 0.00 36.83 3.18
345 346 2.526304 ACGAAAGTGCAAGCAGTAGA 57.474 45.000 2.36 0.00 46.97 2.59
396 397 1.472480 CGGTTCCATCACAATGAACCC 59.528 52.381 13.39 0.00 38.50 4.11
414 423 2.169352 ACCCACACATCTGAGCTACATC 59.831 50.000 0.00 0.00 0.00 3.06
462 471 7.716799 ATTTCATAAGTTGCCAATCAAGGTA 57.283 32.000 0.00 0.00 34.91 3.08
535 544 1.518133 GCAGCTCACTACTCGGCAG 60.518 63.158 0.00 0.00 0.00 4.85
677 2328 1.774217 AAGCACCTTCCCCACAGGA 60.774 57.895 0.00 0.00 45.68 3.86
756 2431 0.325860 ATACCTTCCCCAGTACGCCA 60.326 55.000 0.00 0.00 0.00 5.69
771 2446 2.573869 CCACAGCACGATCCGACT 59.426 61.111 0.00 0.00 0.00 4.18
840 2529 0.661020 CGCCATTAATTCCGGTGTCC 59.339 55.000 0.00 0.00 0.00 4.02
858 2563 1.063341 TCCAGAGATCTCACCTCCAGG 60.063 57.143 24.39 13.11 42.17 4.45
864 2569 0.690411 ATCTCACCTCCAGGCTCCAG 60.690 60.000 0.00 0.00 39.32 3.86
865 2570 1.611851 CTCACCTCCAGGCTCCAGT 60.612 63.158 0.00 0.00 39.32 4.00
876 2581 6.071278 CCTCCAGGCTCCAGTAGTATATAAAC 60.071 46.154 0.00 0.00 0.00 2.01
881 2586 6.270231 AGGCTCCAGTAGTATATAAACAAGGG 59.730 42.308 0.00 0.00 0.00 3.95
905 2610 2.390599 CCACCGACTGAATGCCACG 61.391 63.158 0.00 0.00 0.00 4.94
923 2628 2.651361 CTCCACTCGGCAAGTCGT 59.349 61.111 0.00 0.00 35.45 4.34
924 2629 1.444553 CTCCACTCGGCAAGTCGTC 60.445 63.158 0.00 0.00 35.45 4.20
926 2633 0.607217 TCCACTCGGCAAGTCGTCTA 60.607 55.000 0.00 0.00 35.45 2.59
941 2659 4.056050 GTCGTCTAACACTTCAACACCAT 58.944 43.478 0.00 0.00 0.00 3.55
944 2662 5.010314 TCGTCTAACACTTCAACACCATACT 59.990 40.000 0.00 0.00 0.00 2.12
949 2667 5.552870 ACACTTCAACACCATACTTCTCT 57.447 39.130 0.00 0.00 0.00 3.10
955 2673 1.279271 ACACCATACTTCTCTGGCCAC 59.721 52.381 0.00 0.00 35.88 5.01
956 2674 1.556911 CACCATACTTCTCTGGCCACT 59.443 52.381 0.00 0.00 35.88 4.00
957 2675 1.556911 ACCATACTTCTCTGGCCACTG 59.443 52.381 0.00 0.00 35.88 3.66
958 2676 1.661341 CATACTTCTCTGGCCACTGC 58.339 55.000 0.00 0.00 0.00 4.40
982 2700 2.211353 CGGAAGCTAGAACCTACTGC 57.789 55.000 0.00 0.00 0.00 4.40
983 2701 1.476891 CGGAAGCTAGAACCTACTGCA 59.523 52.381 0.00 0.00 0.00 4.41
984 2702 2.480416 CGGAAGCTAGAACCTACTGCAG 60.480 54.545 13.48 13.48 0.00 4.41
985 2703 2.498078 GGAAGCTAGAACCTACTGCAGT 59.502 50.000 25.12 25.12 0.00 4.40
986 2704 3.700038 GGAAGCTAGAACCTACTGCAGTA 59.300 47.826 24.63 24.63 0.00 2.74
987 2705 4.202070 GGAAGCTAGAACCTACTGCAGTAG 60.202 50.000 36.75 36.75 45.68 2.57
989 2707 2.691011 GCTAGAACCTACTGCAGTAGCT 59.309 50.000 37.82 31.29 44.97 3.32
1842 3605 3.751246 TACCGCCCGTTCGTGGAG 61.751 66.667 1.43 1.66 36.85 3.86
2272 4044 3.393800 GCCTTTTCCTGCCTTTTCTTTC 58.606 45.455 0.00 0.00 0.00 2.62
2413 4235 6.820152 TGTGTGATATGGATTCAGAGTTTCAG 59.180 38.462 0.00 0.00 0.00 3.02
2438 4260 5.227569 TCAGAGCAAAACCATTCACTCTA 57.772 39.130 0.00 0.00 32.45 2.43
2440 4262 4.756642 CAGAGCAAAACCATTCACTCTACA 59.243 41.667 0.00 0.00 32.45 2.74
2455 4277 7.342769 TCACTCTACAAGACAAGAAGTACAA 57.657 36.000 0.00 0.00 0.00 2.41
2469 4291 1.026584 GTACAAGGGTTGGCACGTTT 58.973 50.000 0.00 0.00 34.12 3.60
2470 4292 1.406180 GTACAAGGGTTGGCACGTTTT 59.594 47.619 0.00 0.00 34.12 2.43
2471 4293 1.765230 ACAAGGGTTGGCACGTTTTA 58.235 45.000 0.00 0.00 34.12 1.52
2472 4294 1.679153 ACAAGGGTTGGCACGTTTTAG 59.321 47.619 0.00 0.00 34.12 1.85
2473 4295 0.671796 AAGGGTTGGCACGTTTTAGC 59.328 50.000 0.00 0.00 0.00 3.09
2474 4296 0.179001 AGGGTTGGCACGTTTTAGCT 60.179 50.000 0.00 0.00 0.00 3.32
2475 4297 0.240145 GGGTTGGCACGTTTTAGCTC 59.760 55.000 0.00 0.00 0.00 4.09
2476 4298 0.110373 GGTTGGCACGTTTTAGCTCG 60.110 55.000 0.00 0.00 0.00 5.03
2477 4299 0.584876 GTTGGCACGTTTTAGCTCGT 59.415 50.000 0.00 0.00 40.99 4.18
2487 4309 5.523369 ACGTTTTAGCTCGTGTATATACCC 58.477 41.667 10.38 0.00 38.85 3.69
2488 4310 5.067674 ACGTTTTAGCTCGTGTATATACCCA 59.932 40.000 10.38 0.00 38.85 4.51
2489 4311 5.978919 CGTTTTAGCTCGTGTATATACCCAA 59.021 40.000 10.38 0.00 0.00 4.12
2490 4312 6.143438 CGTTTTAGCTCGTGTATATACCCAAG 59.857 42.308 10.38 5.91 0.00 3.61
2491 4313 6.720112 TTTAGCTCGTGTATATACCCAAGT 57.280 37.500 10.38 0.00 0.00 3.16
2492 4314 6.720112 TTAGCTCGTGTATATACCCAAGTT 57.280 37.500 10.38 5.52 0.00 2.66
2493 4315 5.197682 AGCTCGTGTATATACCCAAGTTC 57.802 43.478 10.38 0.00 0.00 3.01
2494 4316 4.038883 AGCTCGTGTATATACCCAAGTTCC 59.961 45.833 10.38 0.00 0.00 3.62
2544 4366 0.387202 CAGGAGCTCGGTATCAGGTG 59.613 60.000 7.83 0.00 0.00 4.00
2724 4557 4.458829 TCGCCGGGGTCCTGATCT 62.459 66.667 19.13 0.00 0.00 2.75
2862 4696 0.616111 GAGGCTGAGAGAGTGGGGAA 60.616 60.000 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.082140 TCCGTAGATGCACCCAGTAT 57.918 50.000 0.00 0.00 0.00 2.12
32 33 1.855295 TTCCGTAGATGCACCCAGTA 58.145 50.000 0.00 0.00 0.00 2.74
37 38 1.498865 CCGCATTCCGTAGATGCACC 61.499 60.000 13.11 0.00 41.05 5.01
54 55 0.758734 TGGCCTCCATGTCTTATCCG 59.241 55.000 3.32 0.00 0.00 4.18
87 88 2.430367 GAGGTGGCAACGTTCCCT 59.570 61.111 10.19 7.38 42.51 4.20
140 141 0.330267 TGGGTAGCTTGGTTTAGGCC 59.670 55.000 0.00 0.00 30.33 5.19
156 157 3.454375 GGTGAGTGTATAATGACGTGGG 58.546 50.000 0.00 0.00 0.00 4.61
184 185 4.562143 GGGTAGGATGTGTGTAAGTTCGTT 60.562 45.833 0.00 0.00 0.00 3.85
189 190 2.193993 GGGGGTAGGATGTGTGTAAGT 58.806 52.381 0.00 0.00 0.00 2.24
201 202 1.227383 GGTGCTCATTGGGGGTAGG 59.773 63.158 0.00 0.00 0.00 3.18
205 206 1.077212 CTGAGGTGCTCATTGGGGG 60.077 63.158 0.00 0.00 39.92 5.40
207 208 0.907486 TCTCTGAGGTGCTCATTGGG 59.093 55.000 4.59 0.00 39.92 4.12
208 209 4.567971 GATATCTCTGAGGTGCTCATTGG 58.432 47.826 4.59 0.00 39.92 3.16
246 247 6.401153 GCTGTGGTTACTTCGTTAATCTCAAG 60.401 42.308 0.00 0.00 0.00 3.02
275 276 2.571653 AGACATTCCCATCGACCAAGAA 59.428 45.455 0.00 0.00 0.00 2.52
278 279 1.134818 CGAGACATTCCCATCGACCAA 60.135 52.381 0.00 0.00 37.35 3.67
297 298 4.369182 GGTGATACTTATTCAGTGGGACG 58.631 47.826 0.00 0.00 35.97 4.79
327 328 2.408050 ACTCTACTGCTTGCACTTTCG 58.592 47.619 0.00 0.00 0.00 3.46
396 397 3.455327 CTGGATGTAGCTCAGATGTGTG 58.545 50.000 0.00 0.00 0.00 3.82
462 471 2.905085 TGCATGGGTGGAAATGTTTCAT 59.095 40.909 7.69 0.00 38.92 2.57
535 544 1.138266 TGTTTGCGGTATAGGAGGAGC 59.862 52.381 0.00 0.00 0.00 4.70
677 2328 6.385443 TGTTCTATCTATCTGTCCATTCCCT 58.615 40.000 0.00 0.00 0.00 4.20
678 2329 6.672266 TGTTCTATCTATCTGTCCATTCCC 57.328 41.667 0.00 0.00 0.00 3.97
756 2431 1.508545 CAGAGTCGGATCGTGCTGT 59.491 57.895 0.00 0.00 0.00 4.40
789 2464 4.095483 TCGACGGTGAGGACTAGTTAAATC 59.905 45.833 0.00 0.00 0.00 2.17
840 2529 0.752054 GCCTGGAGGTGAGATCTCTG 59.248 60.000 22.95 0.94 37.57 3.35
858 2563 5.932883 GCCCTTGTTTATATACTACTGGAGC 59.067 44.000 0.00 0.00 0.00 4.70
864 2569 4.450080 GGTGCGCCCTTGTTTATATACTAC 59.550 45.833 4.45 0.00 0.00 2.73
865 2570 4.634199 GGTGCGCCCTTGTTTATATACTA 58.366 43.478 4.45 0.00 0.00 1.82
881 2586 4.980805 TTCAGTCGGTGGGTGCGC 62.981 66.667 0.00 0.00 0.00 6.09
895 2600 1.375908 GAGTGGAGCGTGGCATTCA 60.376 57.895 0.00 0.00 0.00 2.57
905 2610 2.811317 CGACTTGCCGAGTGGAGC 60.811 66.667 0.00 0.00 39.19 4.70
923 2628 7.015292 AGAGAAGTATGGTGTTGAAGTGTTAGA 59.985 37.037 0.00 0.00 0.00 2.10
924 2629 7.116948 CAGAGAAGTATGGTGTTGAAGTGTTAG 59.883 40.741 0.00 0.00 0.00 2.34
926 2633 5.760253 CAGAGAAGTATGGTGTTGAAGTGTT 59.240 40.000 0.00 0.00 0.00 3.32
958 2676 3.255379 GTTCTAGCTTCCGCGCGG 61.255 66.667 42.13 42.13 42.32 6.46
959 2677 2.332362 TAGGTTCTAGCTTCCGCGCG 62.332 60.000 25.67 25.67 42.32 6.86
960 2678 0.870735 GTAGGTTCTAGCTTCCGCGC 60.871 60.000 0.00 0.00 42.32 6.86
961 2679 0.739561 AGTAGGTTCTAGCTTCCGCG 59.260 55.000 0.00 0.00 42.32 6.46
962 2680 1.803252 GCAGTAGGTTCTAGCTTCCGC 60.803 57.143 0.00 0.00 0.00 5.54
963 2681 1.476891 TGCAGTAGGTTCTAGCTTCCG 59.523 52.381 0.00 0.00 0.00 4.30
964 2682 2.498078 ACTGCAGTAGGTTCTAGCTTCC 59.502 50.000 20.16 0.00 0.00 3.46
965 2683 3.878160 ACTGCAGTAGGTTCTAGCTTC 57.122 47.619 20.16 0.00 0.00 3.86
966 2684 3.131400 GCTACTGCAGTAGGTTCTAGCTT 59.869 47.826 40.83 12.14 46.07 3.74
967 2685 2.691011 GCTACTGCAGTAGGTTCTAGCT 59.309 50.000 40.83 12.33 46.07 3.32
968 2686 3.086818 GCTACTGCAGTAGGTTCTAGC 57.913 52.381 40.83 29.87 46.07 3.42
975 2693 5.584253 TTCTTTCTAGCTACTGCAGTAGG 57.416 43.478 40.83 29.39 46.07 3.18
977 2695 6.835819 TCTTTCTTTCTAGCTACTGCAGTA 57.164 37.500 24.63 24.63 42.74 2.74
978 2696 5.730296 TCTTTCTTTCTAGCTACTGCAGT 57.270 39.130 25.12 25.12 42.74 4.40
979 2697 5.523188 CCATCTTTCTTTCTAGCTACTGCAG 59.477 44.000 13.48 13.48 42.74 4.41
980 2698 5.423015 CCATCTTTCTTTCTAGCTACTGCA 58.577 41.667 0.00 0.00 42.74 4.41
981 2699 4.272261 GCCATCTTTCTTTCTAGCTACTGC 59.728 45.833 0.00 0.00 40.05 4.40
982 2700 5.293079 GTGCCATCTTTCTTTCTAGCTACTG 59.707 44.000 0.00 0.00 0.00 2.74
983 2701 5.046304 TGTGCCATCTTTCTTTCTAGCTACT 60.046 40.000 0.00 0.00 0.00 2.57
984 2702 5.178797 TGTGCCATCTTTCTTTCTAGCTAC 58.821 41.667 0.00 0.00 0.00 3.58
985 2703 5.420725 TGTGCCATCTTTCTTTCTAGCTA 57.579 39.130 0.00 0.00 0.00 3.32
986 2704 4.260170 CTGTGCCATCTTTCTTTCTAGCT 58.740 43.478 0.00 0.00 0.00 3.32
987 2705 3.181502 GCTGTGCCATCTTTCTTTCTAGC 60.182 47.826 0.00 0.00 0.00 3.42
989 2707 4.256920 GAGCTGTGCCATCTTTCTTTCTA 58.743 43.478 0.00 0.00 0.00 2.10
1007 2728 4.150454 CGAGGAGGGGGAGGAGCT 62.150 72.222 0.00 0.00 0.00 4.09
2130 3896 0.991920 TGTTCTCCATCTGGAACCCC 59.008 55.000 0.00 0.00 44.91 4.95
2369 4160 4.031028 CACACGAAAGAAGAGCAACTTTG 58.969 43.478 0.00 0.00 39.13 2.77
2383 4201 5.729510 TCTGAATCCATATCACACACGAAA 58.270 37.500 0.00 0.00 0.00 3.46
2384 4202 5.105351 ACTCTGAATCCATATCACACACGAA 60.105 40.000 0.00 0.00 0.00 3.85
2413 4235 5.182760 AGAGTGAATGGTTTTGCTCTGAATC 59.817 40.000 0.00 0.00 32.79 2.52
2438 4260 4.772886 ACCCTTGTACTTCTTGTCTTGT 57.227 40.909 0.00 0.00 0.00 3.16
2440 4262 4.461198 CCAACCCTTGTACTTCTTGTCTT 58.539 43.478 0.00 0.00 0.00 3.01
2455 4277 0.179001 AGCTAAAACGTGCCAACCCT 60.179 50.000 0.00 0.00 0.00 4.34
2469 4291 6.239120 GGAACTTGGGTATATACACGAGCTAA 60.239 42.308 26.25 8.15 43.50 3.09
2470 4292 5.242393 GGAACTTGGGTATATACACGAGCTA 59.758 44.000 26.25 0.50 43.50 3.32
2471 4293 4.038883 GGAACTTGGGTATATACACGAGCT 59.961 45.833 26.25 17.78 43.50 4.09
2472 4294 4.202182 TGGAACTTGGGTATATACACGAGC 60.202 45.833 26.25 14.37 43.50 5.03
2473 4295 5.524971 TGGAACTTGGGTATATACACGAG 57.475 43.478 25.15 25.15 44.88 4.18
2474 4296 5.221561 CCATGGAACTTGGGTATATACACGA 60.222 44.000 5.56 9.90 30.45 4.35
2475 4297 4.994852 CCATGGAACTTGGGTATATACACG 59.005 45.833 5.56 2.12 30.45 4.49
2476 4298 5.995897 GTCCATGGAACTTGGGTATATACAC 59.004 44.000 18.20 11.68 34.85 2.90
2477 4299 5.221561 CGTCCATGGAACTTGGGTATATACA 60.222 44.000 18.20 0.00 34.85 2.29
2478 4300 5.235516 CGTCCATGGAACTTGGGTATATAC 58.764 45.833 18.20 4.14 34.85 1.47
2479 4301 4.262721 GCGTCCATGGAACTTGGGTATATA 60.263 45.833 18.20 0.00 34.85 0.86
2480 4302 3.496160 GCGTCCATGGAACTTGGGTATAT 60.496 47.826 18.20 0.00 34.85 0.86
2481 4303 2.158871 GCGTCCATGGAACTTGGGTATA 60.159 50.000 18.20 0.00 34.85 1.47
2482 4304 1.408266 GCGTCCATGGAACTTGGGTAT 60.408 52.381 18.20 0.00 34.85 2.73
2483 4305 0.035820 GCGTCCATGGAACTTGGGTA 60.036 55.000 18.20 0.00 34.85 3.69
2484 4306 1.303317 GCGTCCATGGAACTTGGGT 60.303 57.895 18.20 0.00 34.85 4.51
2485 4307 2.398554 CGCGTCCATGGAACTTGGG 61.399 63.158 18.20 11.23 34.85 4.12
2486 4308 2.398554 CCGCGTCCATGGAACTTGG 61.399 63.158 18.20 12.39 35.45 3.61
2487 4309 1.361668 CTCCGCGTCCATGGAACTTG 61.362 60.000 18.20 8.09 32.89 3.16
2488 4310 1.079127 CTCCGCGTCCATGGAACTT 60.079 57.895 18.20 0.00 32.89 2.66
2489 4311 0.968901 TACTCCGCGTCCATGGAACT 60.969 55.000 18.20 0.00 32.89 3.01
2490 4312 0.104304 ATACTCCGCGTCCATGGAAC 59.896 55.000 18.20 11.11 32.89 3.62
2491 4313 0.104120 CATACTCCGCGTCCATGGAA 59.896 55.000 18.20 0.00 32.89 3.53
2492 4314 1.040893 ACATACTCCGCGTCCATGGA 61.041 55.000 11.44 11.44 0.00 3.41
2493 4315 0.875908 CACATACTCCGCGTCCATGG 60.876 60.000 4.97 4.97 0.00 3.66
2494 4316 0.102300 TCACATACTCCGCGTCCATG 59.898 55.000 4.92 5.54 0.00 3.66
2544 4366 2.732366 TCTCATAGCAATTCTCGACGC 58.268 47.619 0.00 0.00 0.00 5.19
2724 4557 0.613260 GCCACTGTACCTGATCCACA 59.387 55.000 0.00 0.00 0.00 4.17
2862 4696 3.267900 CGTCGCCGGAGTCAATTAT 57.732 52.632 5.05 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.