Multiple sequence alignment - TraesCS5B01G545400

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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 TraesCS5B01G545400 chr5B 100.000 4554 0 0 1 4554 697833534 697828981 0.000000e+00 8410.0
1 TraesCS5B01G545400 chr5B 85.601 1257 156 14 1293 2528 697869121 697867869 0.000000e+00 1295.0
2 TraesCS5B01G545400 chr5B 87.734 481 52 6 3014 3490 697867509 697867032 5.150000e-154 555.0
3 TraesCS5B01G545400 chr5B 75.997 1179 222 32 1293 2436 703804903 703803751 1.850000e-153 553.0
4 TraesCS5B01G545400 chr5B 75.468 1174 245 30 1293 2436 703859469 703858309 2.410000e-147 532.0
5 TraesCS5B01G545400 chr5B 74.787 1174 242 34 1293 2430 699731231 699730076 3.190000e-131 479.0
6 TraesCS5B01G545400 chr5B 74.169 1204 219 62 1306 2449 697819176 697820347 2.530000e-112 416.0
7 TraesCS5B01G545400 chr5B 76.858 471 94 12 3026 3487 698261524 698261060 7.560000e-63 252.0
8 TraesCS5B01G545400 chr5B 81.776 214 35 4 2248 2458 703893842 703893630 4.680000e-40 176.0
9 TraesCS5B01G545400 chr5D 95.660 3502 127 15 1 3492 552727710 552731196 0.000000e+00 5602.0
10 TraesCS5B01G545400 chr5D 85.191 1256 163 16 1290 2528 552683716 552684965 0.000000e+00 1267.0
11 TraesCS5B01G545400 chr5D 87.603 484 51 8 3011 3489 552685324 552685803 1.850000e-153 553.0
12 TraesCS5B01G545400 chr5D 91.940 397 25 2 4165 4554 552733797 552734193 2.390000e-152 549.0
13 TraesCS5B01G545400 chr5D 96.066 305 12 0 3791 4095 552732174 552732478 8.800000e-137 497.0
14 TraesCS5B01G545400 chr5D 95.410 305 14 0 3489 3793 552731370 552731674 1.900000e-133 486.0
15 TraesCS5B01G545400 chr5D 74.956 1146 215 45 1324 2435 552129694 552128587 1.150000e-125 460.0
16 TraesCS5B01G545400 chr5D 74.229 1199 252 36 1274 2436 542411229 542410052 2.500000e-122 449.0
17 TraesCS5B01G545400 chr5D 73.305 1180 269 35 1290 2436 552407681 552408847 4.270000e-105 392.0
18 TraesCS5B01G545400 chr5D 85.768 267 30 5 2591 2852 552685063 552685326 4.490000e-70 276.0
19 TraesCS5B01G545400 chr5D 78.641 309 54 9 3015 3316 552409269 552409572 1.290000e-45 195.0
20 TraesCS5B01G545400 chr5D 76.807 332 66 9 3011 3338 552069157 552069481 4.680000e-40 176.0
21 TraesCS5B01G545400 chr5D 93.258 89 2 1 4086 4170 552733665 552733753 1.330000e-25 128.0
22 TraesCS5B01G545400 chr5D 77.966 118 21 5 2895 3010 60471699 60471813 8.180000e-08 69.4
23 TraesCS5B01G545400 chr4A 87.717 1962 173 25 1565 3492 615375806 615373879 0.000000e+00 2226.0
24 TraesCS5B01G545400 chr4A 84.615 1261 170 13 1289 2528 615457348 615456091 0.000000e+00 1232.0
25 TraesCS5B01G545400 chr4A 89.383 697 56 7 3489 4170 615372792 615372099 0.000000e+00 861.0
26 TraesCS5B01G545400 chr4A 85.921 483 59 6 3014 3490 615455733 615455254 1.460000e-139 507.0
27 TraesCS5B01G545400 chr4A 74.222 1125 247 26 1337 2434 632615771 632616879 9.050000e-117 431.0
28 TraesCS5B01G545400 chr4A 85.870 368 39 6 1209 1576 615376182 615375828 3.330000e-101 379.0
29 TraesCS5B01G545400 chr4A 93.506 154 9 1 4175 4328 615372058 615371906 1.270000e-55 228.0
30 TraesCS5B01G545400 chr4A 88.235 153 6 9 354 502 615429447 615429303 6.060000e-39 172.0
31 TraesCS5B01G545400 chr4A 81.818 121 11 7 2894 3013 240371293 240371403 1.740000e-14 91.6
32 TraesCS5B01G545400 chr4A 93.750 48 2 1 1165 1212 615376333 615376287 2.270000e-08 71.3
33 TraesCS5B01G545400 chr2D 75.320 1171 234 37 1297 2430 651431730 651432882 1.130000e-140 510.0
34 TraesCS5B01G545400 chr2B 75.000 1172 247 34 1297 2433 780875181 780874021 2.450000e-137 499.0
35 TraesCS5B01G545400 chr2B 80.800 125 15 4 2887 3011 166470783 166470898 6.280000e-14 89.8
36 TraesCS5B01G545400 chr6D 74.555 1179 240 41 1297 2433 69108726 69107566 1.150000e-125 460.0
37 TraesCS5B01G545400 chr6D 75.926 756 165 8 1340 2091 459064392 459063650 5.560000e-99 372.0
38 TraesCS5B01G545400 chr2A 76.866 804 156 22 1297 2091 776212928 776213710 1.170000e-115 427.0
39 TraesCS5B01G545400 chr2A 83.553 152 23 2 1 151 706330849 706330699 1.710000e-29 141.0
40 TraesCS5B01G545400 chr7B 78.831 496 85 12 3012 3490 577282396 577281904 2.640000e-82 316.0
41 TraesCS5B01G545400 chr7D 78.499 493 89 13 3012 3490 535551210 535550721 1.590000e-79 307.0
42 TraesCS5B01G545400 chr7D 81.395 172 32 0 1319 1490 180985442 180985271 1.710000e-29 141.0
43 TraesCS5B01G545400 chr7A 78.234 487 86 13 3012 3481 618177508 618177991 1.240000e-75 294.0
44 TraesCS5B01G545400 chr7A 88.776 98 9 2 178 273 564250695 564250792 8.000000e-23 119.0
45 TraesCS5B01G545400 chr3B 80.508 118 13 5 2899 3016 556538482 556538589 1.050000e-11 82.4
46 TraesCS5B01G545400 chr3B 85.135 74 9 2 2955 3027 355442228 355442156 1.760000e-09 75.0
47 TraesCS5B01G545400 chr3D 89.655 58 6 0 2955 3012 5879429 5879372 1.760000e-09 75.0
48 TraesCS5B01G545400 chr3A 89.474 57 6 0 2955 3011 215955029 215955085 6.320000e-09 73.1


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 TraesCS5B01G545400 chr5B 697828981 697833534 4553 True 8410.000000 8410 100.000000 1 4554 1 chr5B.!!$R1 4553
1 TraesCS5B01G545400 chr5B 697867032 697869121 2089 True 925.000000 1295 86.667500 1293 3490 2 chr5B.!!$R7 2197
2 TraesCS5B01G545400 chr5B 703803751 703804903 1152 True 553.000000 553 75.997000 1293 2436 1 chr5B.!!$R4 1143
3 TraesCS5B01G545400 chr5B 703858309 703859469 1160 True 532.000000 532 75.468000 1293 2436 1 chr5B.!!$R5 1143
4 TraesCS5B01G545400 chr5B 699730076 699731231 1155 True 479.000000 479 74.787000 1293 2430 1 chr5B.!!$R3 1137
5 TraesCS5B01G545400 chr5B 697819176 697820347 1171 False 416.000000 416 74.169000 1306 2449 1 chr5B.!!$F1 1143
6 TraesCS5B01G545400 chr5D 552727710 552734193 6483 False 1452.400000 5602 94.466800 1 4554 5 chr5D.!!$F5 4553
7 TraesCS5B01G545400 chr5D 552683716 552685803 2087 False 698.666667 1267 86.187333 1290 3489 3 chr5D.!!$F4 2199
8 TraesCS5B01G545400 chr5D 552128587 552129694 1107 True 460.000000 460 74.956000 1324 2435 1 chr5D.!!$R2 1111
9 TraesCS5B01G545400 chr5D 542410052 542411229 1177 True 449.000000 449 74.229000 1274 2436 1 chr5D.!!$R1 1162
10 TraesCS5B01G545400 chr5D 552407681 552409572 1891 False 293.500000 392 75.973000 1290 3316 2 chr5D.!!$F3 2026
11 TraesCS5B01G545400 chr4A 615455254 615457348 2094 True 869.500000 1232 85.268000 1289 3490 2 chr4A.!!$R3 2201
12 TraesCS5B01G545400 chr4A 615371906 615376333 4427 True 753.060000 2226 90.045200 1165 4328 5 chr4A.!!$R2 3163
13 TraesCS5B01G545400 chr4A 632615771 632616879 1108 False 431.000000 431 74.222000 1337 2434 1 chr4A.!!$F2 1097
14 TraesCS5B01G545400 chr2D 651431730 651432882 1152 False 510.000000 510 75.320000 1297 2430 1 chr2D.!!$F1 1133
15 TraesCS5B01G545400 chr2B 780874021 780875181 1160 True 499.000000 499 75.000000 1297 2433 1 chr2B.!!$R1 1136
16 TraesCS5B01G545400 chr6D 69107566 69108726 1160 True 460.000000 460 74.555000 1297 2433 1 chr6D.!!$R1 1136
17 TraesCS5B01G545400 chr6D 459063650 459064392 742 True 372.000000 372 75.926000 1340 2091 1 chr6D.!!$R2 751
18 TraesCS5B01G545400 chr2A 776212928 776213710 782 False 427.000000 427 76.866000 1297 2091 1 chr2A.!!$F1 794

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
425 440 0.324943 ACGTGGAGGGAGGACAAATG 59.675 55.000 0.00 0.00 0.00 2.32 F
729 744 0.531974 CCGGCCAATACACGTGCTAT 60.532 55.000 17.22 9.92 0.00 2.97 F
730 745 0.581529 CGGCCAATACACGTGCTATG 59.418 55.000 17.22 11.57 0.00 2.23 F
2091 2345 0.960364 GGCGATGTTCCCAAGCTTCA 60.960 55.000 0.00 0.00 0.00 3.02 F
2161 2415 1.004440 GAGCGACTGCCTTCCAAGT 60.004 57.895 0.00 0.00 44.31 3.16 F
3326 3851 1.133181 TCCTGGAACATGCTGTGGGA 61.133 55.000 0.00 0.00 38.20 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1228 1351 0.614697 TCCTGAGATGCGACCTTGGA 60.615 55.000 0.00 0.00 0.0 3.53 R
1553 1694 1.939838 GCACTCGTCGAAAGGAACCAT 60.940 52.381 0.00 0.00 0.0 3.55 R
2161 2415 2.133281 TCGACAGATTCCCGGAACTA 57.867 50.000 0.73 0.00 0.0 2.24 R
2983 3486 1.062002 CAATAAAGCCGTGCACTACCG 59.938 52.381 16.19 0.67 0.0 4.02 R
3339 3864 1.078143 GGTCCTCGCCATGAAGCTT 60.078 57.895 0.00 0.00 0.0 3.74 R
4172 7548 2.703536 TCTTCAGCCAACACCTCTTACA 59.296 45.455 0.00 0.00 0.0 2.41 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
110 111 5.893687 TGATGTACAATTCATTGATGTGCC 58.106 37.500 0.00 0.00 40.14 5.01
121 122 1.327303 TGATGTGCCTTTGGTTGACC 58.673 50.000 0.00 0.00 0.00 4.02
132 133 1.222300 TGGTTGACCGTTTGATGTCG 58.778 50.000 0.00 0.00 39.43 4.35
175 177 4.377839 TTTTTCCGAAAGTCATTGTGCA 57.622 36.364 0.00 0.00 0.00 4.57
212 214 3.193691 AGAGTAGCTCTACGTTGCATGTT 59.806 43.478 0.00 0.00 39.28 2.71
218 220 7.926555 AGTAGCTCTACGTTGCATGTTTAATAT 59.073 33.333 0.00 0.00 40.80 1.28
220 222 6.761242 AGCTCTACGTTGCATGTTTAATATCA 59.239 34.615 0.00 0.00 0.00 2.15
333 335 0.817634 TTGAGTGGTCGGGTTTGCTG 60.818 55.000 0.00 0.00 0.00 4.41
358 373 1.890489 TGGCTGTAGACGCTCTAAACA 59.110 47.619 0.00 0.00 29.58 2.83
422 437 0.544357 ATCACGTGGAGGGAGGACAA 60.544 55.000 17.00 0.00 34.57 3.18
425 440 0.324943 ACGTGGAGGGAGGACAAATG 59.675 55.000 0.00 0.00 0.00 2.32
660 675 2.436646 CACGGAGTCCATGCACCC 60.437 66.667 10.49 0.00 41.61 4.61
691 706 7.054124 ACAACTGGAATCAAGTCTTACAAAGA 58.946 34.615 0.00 0.00 34.51 2.52
729 744 0.531974 CCGGCCAATACACGTGCTAT 60.532 55.000 17.22 9.92 0.00 2.97
730 745 0.581529 CGGCCAATACACGTGCTATG 59.418 55.000 17.22 11.57 0.00 2.23
750 765 1.901591 CTATTTCGCATCCAGCCCAT 58.098 50.000 0.00 0.00 41.38 4.00
785 800 8.621532 TGAGCTTCAATAACTAGTGAATGTTT 57.378 30.769 0.00 0.00 39.22 2.83
790 805 7.447374 TCAATAACTAGTGAATGTTTGGTGG 57.553 36.000 0.00 0.00 0.00 4.61
885 900 6.313519 TGGTAATTGCTTCCTAGAGATTGT 57.686 37.500 0.00 0.00 0.00 2.71
930 945 2.298163 CCATCCGCCCGTTAGTATTACT 59.702 50.000 1.30 1.30 0.00 2.24
968 983 2.621526 GGTGGGTTTTGTCTGGTAGTTG 59.378 50.000 0.00 0.00 0.00 3.16
975 990 5.121105 GTTTTGTCTGGTAGTTGTAGTGGT 58.879 41.667 0.00 0.00 0.00 4.16
1019 1034 6.610741 AATCCAATAAGAATGAAGTCTCGC 57.389 37.500 0.00 0.00 0.00 5.03
1078 1093 0.995024 CTCCTGGGGGAAAGTGACAT 59.005 55.000 0.00 0.00 41.69 3.06
1134 1149 1.685765 CCCACCGTGGAGAGATCCA 60.686 63.158 19.81 0.00 40.96 3.41
1272 1395 9.232473 GATTCTAGGGTTTCAATCAGTTAACTT 57.768 33.333 5.07 0.00 0.00 2.66
2091 2345 0.960364 GGCGATGTTCCCAAGCTTCA 60.960 55.000 0.00 0.00 0.00 3.02
2122 2376 2.228822 CCTCGGTTATTATGCCAATGCC 59.771 50.000 0.00 0.00 36.33 4.40
2161 2415 1.004440 GAGCGACTGCCTTCCAAGT 60.004 57.895 0.00 0.00 44.31 3.16
2274 2569 5.054477 TCTTTACCAAGTTCAGCTGTGTAC 58.946 41.667 14.67 10.57 0.00 2.90
2276 2571 1.202770 ACCAAGTTCAGCTGTGTACCC 60.203 52.381 14.67 0.00 0.00 3.69
2289 2589 3.512496 TGTGTACCCTGTGTCCTTCATA 58.488 45.455 0.00 0.00 0.00 2.15
2528 2894 6.530534 GCAGGAAGTTGATCTGATTTTCAATG 59.469 38.462 0.00 0.38 34.60 2.82
2551 2917 5.419155 TGACTCACCAAATCTAGTCTACCAG 59.581 44.000 0.00 0.00 39.27 4.00
2571 2937 5.175859 CCAGGAAAGATAAAAGTAGTGCGA 58.824 41.667 0.00 0.00 0.00 5.10
2663 3157 7.699878 AGGAGGAAAGATACACATACCTTTTT 58.300 34.615 0.00 0.00 0.00 1.94
2664 3158 7.611855 AGGAGGAAAGATACACATACCTTTTTG 59.388 37.037 0.00 0.00 0.00 2.44
2734 3233 2.501723 ACGTGAGCAACATAGGAGGATT 59.498 45.455 0.00 0.00 0.00 3.01
2940 3443 5.420409 GGACCATGACTTAGTTTCGAGATT 58.580 41.667 0.00 0.00 0.00 2.40
2954 3457 7.134815 AGTTTCGAGATTTGATGTGTTTCAAG 58.865 34.615 0.00 0.00 36.97 3.02
2983 3486 2.570302 TCTAGCCTACCCCAACTTGTTC 59.430 50.000 0.00 0.00 0.00 3.18
2993 3496 1.263217 CCAACTTGTTCGGTAGTGCAC 59.737 52.381 9.40 9.40 0.00 4.57
3043 3561 7.275560 ACTGAGTGTGTTGCAACTTTTTAAATC 59.724 33.333 28.61 15.92 0.00 2.17
3191 3716 2.472695 AAAAGCCTGACGATACTGCA 57.527 45.000 0.00 0.00 0.00 4.41
3326 3851 1.133181 TCCTGGAACATGCTGTGGGA 61.133 55.000 0.00 0.00 38.20 4.37
3339 3864 3.009363 TGCTGTGGGATTGAAGAGAATCA 59.991 43.478 0.00 0.00 37.82 2.57
3350 3875 3.693085 TGAAGAGAATCAAGCTTCATGGC 59.307 43.478 0.00 0.00 42.03 4.40
3400 3925 3.866582 CCCGGTGAGATCCCAGGC 61.867 72.222 0.00 0.00 0.00 4.85
3534 5149 4.526438 AATAGCCTTATTGGTGGAGCTT 57.474 40.909 0.00 0.00 38.35 3.74
3553 5168 7.448161 TGGAGCTTTGACTTTTCATCATTTAGA 59.552 33.333 0.00 0.00 0.00 2.10
3588 5203 7.716799 TTCCCATGATTGCTTTTATACTTGT 57.283 32.000 0.00 0.00 0.00 3.16
3633 5255 5.556915 TGAAGGGTTGTACAATCTTACAGG 58.443 41.667 18.07 0.00 33.50 4.00
3795 5920 0.323725 AGCCATTTGTGCTACCAGGG 60.324 55.000 0.00 0.00 37.28 4.45
3802 5927 1.002134 GTGCTACCAGGGTGCACAT 60.002 57.895 26.54 3.17 44.45 3.21
3873 6000 1.067295 AACTCCTGATGTGAAGCCCA 58.933 50.000 0.00 0.00 0.00 5.36
3940 6067 4.524802 AGGCATGAAAACCATAGGATGA 57.475 40.909 0.00 0.00 33.31 2.92
3970 6097 4.797604 GCGCCTATCATCTCTGAGCTTTTA 60.798 45.833 0.00 0.00 34.12 1.52
3993 6120 6.663944 AAAGAAATGCGTCAACTATACCTC 57.336 37.500 0.00 0.00 0.00 3.85
4020 6147 2.166459 TCACGCATGAGAGAAGTTAGGG 59.834 50.000 2.50 0.00 0.00 3.53
4329 7713 7.398618 TCACATGATAAGAAATGGCCCTTTTTA 59.601 33.333 7.49 8.47 0.00 1.52
4352 7736 2.304751 ACGTGTTTCGGTTTCTCACT 57.695 45.000 0.00 0.00 44.69 3.41
4359 7743 4.331717 TGTTTCGGTTTCTCACTTGTTCTC 59.668 41.667 0.00 0.00 0.00 2.87
4370 7754 4.671377 TCACTTGTTCTCAAACATTGTGC 58.329 39.130 14.53 0.00 44.59 4.57
4371 7755 4.398988 TCACTTGTTCTCAAACATTGTGCT 59.601 37.500 14.53 0.00 44.59 4.40
4390 7774 7.680442 TGTGCTGCTACATATTTGAACTTTA 57.320 32.000 0.00 0.00 0.00 1.85
4434 7818 9.357161 AGTCGAATAGTTTTATAGACAGGATCT 57.643 33.333 0.00 0.00 41.95 2.75
4461 7845 9.679661 TTTCCTAGTTATGTTAAGATGATGCAA 57.320 29.630 0.00 0.00 0.00 4.08
4480 7864 4.830600 TGCAATCCTCATCAATATGTGCAT 59.169 37.500 0.00 0.00 36.03 3.96
4483 7867 7.177744 TGCAATCCTCATCAATATGTGCATAAT 59.822 33.333 0.00 0.00 36.03 1.28
4484 7868 7.488150 GCAATCCTCATCAATATGTGCATAATG 59.512 37.037 0.00 1.85 32.91 1.90
4511 7895 7.860918 TCATCATCAGTTACTACTACTTCGT 57.139 36.000 0.00 0.00 31.96 3.85
4540 7924 9.023962 TCAATTATAGACACAATTTTCCAAGCT 57.976 29.630 0.00 0.00 0.00 3.74
4547 7931 2.435437 ACAATTTTCCAAGCTTGTGCCT 59.565 40.909 24.35 3.09 40.80 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 3.628017 GACATCAAACGGTCAACCAAAG 58.372 45.455 0.00 0.00 34.22 2.77
121 122 4.029418 GCACAATGAAATCGACATCAAACG 59.971 41.667 6.11 0.00 0.00 3.60
159 161 1.603802 ACAGTGCACAATGACTTTCGG 59.396 47.619 21.04 0.00 0.00 4.30
175 177 4.459685 AGCTACTCTACGTGATCAAACAGT 59.540 41.667 0.00 0.00 0.00 3.55
218 220 8.275187 ACCTCATATTCAACACCCTATATTGA 57.725 34.615 0.00 0.00 0.00 2.57
220 222 8.311836 CGTACCTCATATTCAACACCCTATATT 58.688 37.037 0.00 0.00 0.00 1.28
234 236 2.288825 CCACATCCGCGTACCTCATATT 60.289 50.000 4.92 0.00 0.00 1.28
312 314 0.030235 GCAAACCCGACCACTCAAAC 59.970 55.000 0.00 0.00 0.00 2.93
319 321 2.112297 GGACAGCAAACCCGACCA 59.888 61.111 0.00 0.00 0.00 4.02
333 335 2.506438 GCGTCTACAGCCACGGAC 60.506 66.667 0.00 0.00 36.50 4.79
444 459 4.327982 TTCATGCTATACTCTCCTGCAC 57.672 45.455 0.00 0.00 36.44 4.57
660 675 5.243981 AGACTTGATTCCAGTTGTCATCTG 58.756 41.667 4.19 4.19 0.00 2.90
691 706 2.544903 CGGGAAAGGTTGCGTGAAAAAT 60.545 45.455 0.00 0.00 0.00 1.82
730 745 0.819259 TGGGCTGGATGCGAAATAGC 60.819 55.000 0.00 0.00 44.05 2.97
741 756 4.099881 GCTCAAATTTTATGATGGGCTGGA 59.900 41.667 0.00 0.00 36.36 3.86
785 800 0.971959 GCAAATGCCATCCTCCACCA 60.972 55.000 0.00 0.00 34.31 4.17
790 805 0.248215 CGTTCGCAAATGCCATCCTC 60.248 55.000 0.00 0.00 37.91 3.71
885 900 4.405680 TCACAGAGAAGAAACTCCAAGACA 59.594 41.667 0.00 0.00 37.60 3.41
930 945 5.568392 ACCCACCGGTACAAATATTTTACA 58.432 37.500 6.87 0.00 42.18 2.41
960 975 4.650588 ACTGTACAACCACTACAACTACCA 59.349 41.667 0.00 0.00 0.00 3.25
968 983 6.548441 TTGCAAATACTGTACAACCACTAC 57.452 37.500 0.00 0.00 0.00 2.73
996 1011 5.529060 GGCGAGACTTCATTCTTATTGGATT 59.471 40.000 0.00 0.00 0.00 3.01
997 1012 5.059833 GGCGAGACTTCATTCTTATTGGAT 58.940 41.667 0.00 0.00 0.00 3.41
1053 1068 3.142028 TCACTTTCCCCCAGGAGATTTTT 59.858 43.478 0.00 0.00 45.19 1.94
1078 1093 0.459585 GAATAAGCCTCGTGCCGTGA 60.460 55.000 0.00 0.00 42.71 4.35
1134 1149 5.018539 TCGTCGAACTATTGGATTGGATT 57.981 39.130 0.00 0.00 0.00 3.01
1228 1351 0.614697 TCCTGAGATGCGACCTTGGA 60.615 55.000 0.00 0.00 0.00 3.53
1272 1395 3.515502 CGGAATCCAGAGCCCTATTGATA 59.484 47.826 0.00 0.00 0.00 2.15
1553 1694 1.939838 GCACTCGTCGAAAGGAACCAT 60.940 52.381 0.00 0.00 0.00 3.55
1727 1945 4.269523 AGCAAGCAGTGGGGCGAA 62.270 61.111 0.00 0.00 39.27 4.70
2122 2376 4.415150 ATGAGTGGGGCGTGCCAG 62.415 66.667 13.76 0.00 37.98 4.85
2161 2415 2.133281 TCGACAGATTCCCGGAACTA 57.867 50.000 0.73 0.00 0.00 2.24
2220 2480 6.271857 AGCAGATGATAGGTAAATGGACAGAT 59.728 38.462 0.00 0.00 0.00 2.90
2274 2569 5.614324 TCTGTAATATGAAGGACACAGGG 57.386 43.478 0.00 0.00 35.29 4.45
2276 2571 7.770433 TCCAAATCTGTAATATGAAGGACACAG 59.230 37.037 0.00 0.00 35.76 3.66
2289 2589 3.885297 CCGGCTGAATCCAAATCTGTAAT 59.115 43.478 0.00 0.00 0.00 1.89
2437 2737 7.046652 AGAATGAGTCACATCCATACTTTGAG 58.953 38.462 0.00 0.00 38.38 3.02
2528 2894 5.163499 CCTGGTAGACTAGATTTGGTGAGTC 60.163 48.000 0.00 0.00 38.89 3.36
2551 2917 6.147328 ACTGTTCGCACTACTTTTATCTTTCC 59.853 38.462 0.00 0.00 0.00 3.13
2940 3443 7.156876 AGAGTTGAAACTTGAAACACATCAA 57.843 32.000 0.00 0.00 39.88 2.57
2954 3457 2.570302 TGGGGTAGGCTAGAGTTGAAAC 59.430 50.000 0.00 0.00 0.00 2.78
2983 3486 1.062002 CAATAAAGCCGTGCACTACCG 59.938 52.381 16.19 0.67 0.00 4.02
2993 3496 6.476243 ACTACTACAACAACAATAAAGCCG 57.524 37.500 0.00 0.00 0.00 5.52
3043 3561 9.757859 ACAATTGCAATTAAAAATATCTTTGCG 57.242 25.926 23.69 8.59 41.67 4.85
3326 3851 5.163540 GCCATGAAGCTTGATTCTCTTCAAT 60.164 40.000 2.10 6.74 46.08 2.57
3339 3864 1.078143 GGTCCTCGCCATGAAGCTT 60.078 57.895 0.00 0.00 0.00 3.74
3350 3875 1.153289 CTCCTTGCATGGGTCCTCG 60.153 63.158 17.95 0.00 0.00 4.63
3377 3902 1.343580 TGGGATCTCACCGGGTCAATA 60.344 52.381 6.32 0.00 0.00 1.90
3400 3925 1.144716 TGCCTGCTAGCTTCATCCG 59.855 57.895 17.23 0.00 0.00 4.18
3499 5114 9.774742 CAATAAGGCTATTTCAACTAACAGTTC 57.225 33.333 0.00 0.00 36.03 3.01
3588 5203 6.840527 TCAGATTTGTGCATCCATAATAGGA 58.159 36.000 0.00 0.00 43.01 2.94
3652 5274 8.866970 AGAGAGTACCTAATATACTAGCCAAC 57.133 38.462 0.00 0.00 32.93 3.77
3795 5920 3.182967 GCTACTACTCAGTCATGTGCAC 58.817 50.000 10.75 10.75 36.14 4.57
3802 5927 3.708451 TGGAATGGCTACTACTCAGTCA 58.292 45.455 0.00 0.00 36.14 3.41
3873 6000 2.079925 GAGGCTGATTTGCTCGAAGTT 58.920 47.619 0.00 0.00 0.00 2.66
3929 6056 1.410517 CGCTGTGACTCATCCTATGGT 59.589 52.381 0.00 0.00 0.00 3.55
3940 6067 1.339610 GAGATGATAGGCGCTGTGACT 59.660 52.381 7.64 0.65 40.99 3.41
3970 6097 6.170506 TGAGGTATAGTTGACGCATTTCTTT 58.829 36.000 0.00 0.00 0.00 2.52
3993 6120 3.931468 ACTTCTCTCATGCGTGAAATCTG 59.069 43.478 10.41 3.55 33.05 2.90
4020 6147 2.602257 AAACTTTTGGACCAAGCTGC 57.398 45.000 7.07 0.00 0.00 5.25
4172 7548 2.703536 TCTTCAGCCAACACCTCTTACA 59.296 45.455 0.00 0.00 0.00 2.41
4257 7641 9.681692 CACAATATTTCAGAACATGTGAGAAAA 57.318 29.630 18.52 10.39 39.10 2.29
4329 7713 3.985925 GTGAGAAACCGAAACACGTAGAT 59.014 43.478 0.00 0.00 40.78 1.98
4359 7743 6.807720 TCAAATATGTAGCAGCACAATGTTTG 59.192 34.615 13.00 13.00 33.76 2.93
4406 7790 8.289939 TCCTGTCTATAAAACTATTCGACTGT 57.710 34.615 0.00 0.00 0.00 3.55
4434 7818 9.679661 TGCATCATCTTAACATAACTAGGAAAA 57.320 29.630 0.00 0.00 0.00 2.29
4461 7845 8.873186 TTCATTATGCACATATTGATGAGGAT 57.127 30.769 13.23 0.00 38.11 3.24
4472 7856 8.857694 ACTGATGATGATTCATTATGCACATA 57.142 30.769 8.51 0.00 42.73 2.29
4476 7860 8.913487 AGTAACTGATGATGATTCATTATGCA 57.087 30.769 8.51 0.00 42.73 3.96
4484 7868 9.388346 CGAAGTAGTAGTAACTGATGATGATTC 57.612 37.037 0.00 0.00 36.36 2.52


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

AutoCloner maintained by Alex Coulton.