Multiple sequence alignment - TraesCS4B01G062500

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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 TraesCS4B01G062500 chr4B 100.000 4957 0 0 1 4957 54141882 54136926 0.000000e+00 9154
1 TraesCS4B01G062500 chr4B 85.919 1186 125 25 2857 4020 54347342 54346177 0.000000e+00 1227
2 TraesCS4B01G062500 chr4B 84.837 1075 132 22 1572 2628 54349404 54348343 0.000000e+00 1053
3 TraesCS4B01G062500 chr4B 89.202 426 31 11 3520 3931 54037054 54036630 7.360000e-143 518
4 TraesCS4B01G062500 chr4D 88.506 2932 187 59 2 2862 37139089 37136237 0.000000e+00 3410
5 TraesCS4B01G062500 chr4D 96.526 1756 59 2 2857 4611 37136067 37134313 0.000000e+00 2904
6 TraesCS4B01G062500 chr4D 85.582 1186 124 26 2857 4020 37254244 37253084 0.000000e+00 1199
7 TraesCS4B01G062500 chr4D 86.131 685 84 7 1696 2371 37262445 37261763 0.000000e+00 728
8 TraesCS4B01G062500 chr4D 85.882 425 44 11 3520 3931 37049758 37049337 5.890000e-119 438
9 TraesCS4B01G062500 chr4D 87.805 369 21 9 4612 4957 37131275 37130908 1.280000e-110 411
10 TraesCS4B01G062500 chr4D 86.813 182 18 3 898 1078 37263411 37263235 1.090000e-46 198
11 TraesCS4B01G062500 chr4A 93.081 2139 87 12 2857 4957 565042505 565044620 0.000000e+00 3073
12 TraesCS4B01G062500 chr4A 89.388 1649 116 33 1225 2859 565040729 565042332 0.000000e+00 2021
13 TraesCS4B01G062500 chr4A 86.065 1263 92 36 1 1189 565039471 565040723 0.000000e+00 1280
14 TraesCS4B01G062500 chr4A 84.790 1190 129 32 2857 4020 564973395 564974558 0.000000e+00 1147
15 TraesCS4B01G062500 chr4A 82.123 1404 170 37 1504 2859 564971699 564973069 0.000000e+00 1127
16 TraesCS4B01G062500 chr4A 84.892 417 48 12 3521 3931 565305165 565305572 1.660000e-109 407
17 TraesCS4B01G062500 chr4A 85.024 207 25 4 2245 2451 191358317 191358517 6.500000e-49 206
18 TraesCS4B01G062500 chr4A 80.663 181 22 8 898 1078 564971187 564971354 1.450000e-25 128
19 TraesCS4B01G062500 chr1B 87.179 234 28 2 2245 2478 196869138 196868907 1.060000e-66 265
20 TraesCS4B01G062500 chr7D 86.473 207 24 3 2245 2451 61277116 61276914 1.800000e-54 224


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 TraesCS4B01G062500 chr4B 54136926 54141882 4956 True 9154.000000 9154 100.000000 1 4957 1 chr4B.!!$R2 4956
1 TraesCS4B01G062500 chr4B 54346177 54349404 3227 True 1140.000000 1227 85.378000 1572 4020 2 chr4B.!!$R3 2448
2 TraesCS4B01G062500 chr4D 37130908 37139089 8181 True 2241.666667 3410 90.945667 2 4957 3 chr4D.!!$R3 4955
3 TraesCS4B01G062500 chr4D 37253084 37254244 1160 True 1199.000000 1199 85.582000 2857 4020 1 chr4D.!!$R2 1163
4 TraesCS4B01G062500 chr4D 37261763 37263411 1648 True 463.000000 728 86.472000 898 2371 2 chr4D.!!$R4 1473
5 TraesCS4B01G062500 chr4A 565039471 565044620 5149 False 2124.666667 3073 89.511333 1 4957 3 chr4A.!!$F4 4956
6 TraesCS4B01G062500 chr4A 564971187 564974558 3371 False 800.666667 1147 82.525333 898 4020 3 chr4A.!!$F3 3122

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
963 1034 0.177604 CTTGCAGCTACCCTCCTCTG 59.822 60.000 0.00 0.00 0.00 3.35 F
1128 1220 0.035881 CCACCTCTGCTCTTTGCTCA 59.964 55.000 0.00 0.00 43.37 4.26 F
1132 1224 1.270732 CCTCTGCTCTTTGCTCACAGT 60.271 52.381 0.00 0.00 43.37 3.55 F
1253 1345 1.588824 TTGGCAAGCTGCGGAGATTG 61.589 55.000 27.77 27.77 46.21 2.67 F
1347 1456 1.672356 CCAAGGGGTTGCGACAGAG 60.672 63.158 6.39 0.00 0.00 3.35 F
1954 2630 1.745489 CTCCAGGTTTACGGGCTGC 60.745 63.158 0.00 0.00 34.03 5.25 F
2238 2923 2.221055 CCACGAGTGCTTACTGAACAAC 59.779 50.000 0.00 0.00 0.00 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2206 2891 1.661112 GCACTCGTGGAGCTAACAATC 59.339 52.381 0.00 0.00 32.04 2.67 R
3117 4655 2.576191 AGCAACTTCTACAGGGCCATTA 59.424 45.455 6.18 0.00 0.00 1.90 R
3192 4731 2.548493 CCAACATTTTGACAGCCTTGGG 60.548 50.000 0.00 0.00 34.24 4.12 R
3294 4833 9.788960 GTCATGTTCTTTCTATGGTTTTATTCC 57.211 33.333 0.00 0.00 0.00 3.01 R
3373 4920 8.969267 AGCTCGAAAGATAATAACAGTATTTCG 58.031 33.333 10.05 10.05 45.22 3.46 R
3610 5167 1.123077 AATCCTCGCCAGCATCACTA 58.877 50.000 0.00 0.00 0.00 2.74 R
4270 5838 1.263217 GGCGCAATATTTAGTCCCACG 59.737 52.381 10.83 0.00 0.00 4.94 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
32 33 8.529102 CAGATTGTATCATTTTGAATTCTTGCG 58.471 33.333 7.05 0.00 0.00 4.85
41 42 7.918033 TCATTTTGAATTCTTGCGTGTTCTTTA 59.082 29.630 7.05 0.00 0.00 1.85
42 43 8.538856 CATTTTGAATTCTTGCGTGTTCTTTAA 58.461 29.630 7.05 0.00 0.00 1.52
74 75 6.369005 CGTGGATTGATCTTCATGATTAAGC 58.631 40.000 0.00 0.00 36.65 3.09
99 100 3.865477 TGTTTCCAACACCGTCAGT 57.135 47.368 0.00 0.00 36.25 3.41
109 110 1.888018 ACCGTCAGTGACCATACCG 59.112 57.895 17.57 4.69 0.00 4.02
110 111 1.141019 CCGTCAGTGACCATACCGG 59.859 63.158 17.57 10.24 42.50 5.28
189 194 2.160171 CACCCTCCTCCCACCCAAA 61.160 63.158 0.00 0.00 0.00 3.28
192 197 0.413434 CCCTCCTCCCACCCAAAAAT 59.587 55.000 0.00 0.00 0.00 1.82
202 213 7.904022 TCCTCCCACCCAAAAATAATAATCTTT 59.096 33.333 0.00 0.00 0.00 2.52
219 230 4.126520 TCTTTAAATGTTTCCAGGGCCT 57.873 40.909 0.00 0.00 0.00 5.19
368 390 3.254657 CCTCTAACAAATGCCCGTTTCAA 59.745 43.478 0.00 0.00 0.00 2.69
393 434 5.473066 AATAAATATGCAGGCAACCCATC 57.527 39.130 0.00 0.00 32.13 3.51
470 516 2.710377 CAACCCATGGACGAATCAAGA 58.290 47.619 15.22 0.00 0.00 3.02
489 535 5.070446 TCAAGACGATATGCAACCCTCTATT 59.930 40.000 0.00 0.00 0.00 1.73
490 536 5.552870 AGACGATATGCAACCCTCTATTT 57.447 39.130 0.00 0.00 0.00 1.40
559 609 2.291282 ACCCCTCACAAATAATCCGCAA 60.291 45.455 0.00 0.00 0.00 4.85
588 638 4.549298 CGCGCTTATAAATGTCTTGCGTTA 60.549 41.667 5.56 0.00 43.16 3.18
603 661 6.018994 GTCTTGCGTTACAATAATGGAGTAGG 60.019 42.308 0.00 0.00 37.72 3.18
619 677 5.935789 TGGAGTAGGAGTACAAATTTTTCCG 59.064 40.000 0.00 0.00 33.16 4.30
793 852 2.358247 GCCAGGAACGGAAAGCGA 60.358 61.111 0.00 0.00 0.00 4.93
817 876 2.743928 GCGTCACTCCCAAGGCTG 60.744 66.667 0.00 0.00 0.00 4.85
853 912 3.120979 CTCCATCGTACCGCGCTCA 62.121 63.158 5.56 0.00 41.07 4.26
957 1028 2.673523 CAGGCTTGCAGCTACCCT 59.326 61.111 7.85 0.00 41.99 4.34
960 1031 2.674220 GGCTTGCAGCTACCCTCCT 61.674 63.158 7.85 0.00 41.99 3.69
961 1032 1.153269 GCTTGCAGCTACCCTCCTC 60.153 63.158 0.00 0.00 38.45 3.71
963 1034 0.177604 CTTGCAGCTACCCTCCTCTG 59.822 60.000 0.00 0.00 0.00 3.35
964 1035 2.503546 GCAGCTACCCTCCTCTGC 59.496 66.667 0.00 0.00 43.95 4.26
966 1037 1.621672 GCAGCTACCCTCCTCTGCTT 61.622 60.000 5.89 0.00 46.00 3.91
1078 1170 1.587054 CAGGTTCGGCTCTTCTCGT 59.413 57.895 0.00 0.00 0.00 4.18
1080 1172 1.153804 GGTTCGGCTCTTCTCGTCC 60.154 63.158 0.00 0.00 0.00 4.79
1081 1173 1.514443 GTTCGGCTCTTCTCGTCCG 60.514 63.158 0.00 0.00 42.96 4.79
1083 1175 1.673337 TCGGCTCTTCTCGTCCGAA 60.673 57.895 0.00 0.00 46.59 4.30
1091 1183 0.450583 TTCTCGTCCGAACTCCGATG 59.549 55.000 0.00 0.00 41.76 3.84
1128 1220 0.035881 CCACCTCTGCTCTTTGCTCA 59.964 55.000 0.00 0.00 43.37 4.26
1132 1224 1.270732 CCTCTGCTCTTTGCTCACAGT 60.271 52.381 0.00 0.00 43.37 3.55
1134 1226 2.479656 CTCTGCTCTTTGCTCACAGTTC 59.520 50.000 0.00 0.00 43.37 3.01
1144 1236 1.590932 CTCACAGTTCACAGCTGCTT 58.409 50.000 15.27 0.00 37.47 3.91
1189 1281 2.724690 CTCGCGTATCCGAATTTGGTAG 59.275 50.000 11.68 3.42 36.72 3.18
1191 1283 2.861935 CGCGTATCCGAATTTGGTAGTT 59.138 45.455 11.68 0.00 35.63 2.24
1192 1284 3.302221 CGCGTATCCGAATTTGGTAGTTG 60.302 47.826 11.68 1.28 35.63 3.16
1193 1285 3.001939 GCGTATCCGAATTTGGTAGTTGG 59.998 47.826 11.68 0.00 35.63 3.77
1194 1286 4.186159 CGTATCCGAATTTGGTAGTTGGT 58.814 43.478 11.68 0.00 35.63 3.67
1195 1287 5.350633 CGTATCCGAATTTGGTAGTTGGTA 58.649 41.667 11.68 0.00 35.63 3.25
1196 1288 5.232838 CGTATCCGAATTTGGTAGTTGGTAC 59.767 44.000 11.68 4.63 35.63 3.34
1197 1289 7.661921 CGTATCCGAATTTGGTAGTTGGTACC 61.662 46.154 11.68 4.43 43.67 3.34
1253 1345 1.588824 TTGGCAAGCTGCGGAGATTG 61.589 55.000 27.77 27.77 46.21 2.67
1303 1412 2.174360 GGAAGTACTGTAACCCGTCCT 58.826 52.381 0.00 0.00 0.00 3.85
1346 1455 2.429930 CCAAGGGGTTGCGACAGA 59.570 61.111 6.39 0.00 0.00 3.41
1347 1456 1.672356 CCAAGGGGTTGCGACAGAG 60.672 63.158 6.39 0.00 0.00 3.35
1348 1457 2.032681 AAGGGGTTGCGACAGAGC 59.967 61.111 6.39 0.00 37.71 4.09
1349 1458 3.553095 AAGGGGTTGCGACAGAGCC 62.553 63.158 6.39 0.00 36.02 4.70
1397 1528 4.416533 GTGCTGGAGCTCGATGAG 57.583 61.111 7.83 2.08 42.66 2.90
1438 1569 5.682234 TCCTCTGATGCTAAACTTGATGA 57.318 39.130 0.00 0.00 0.00 2.92
1440 1571 4.269603 CCTCTGATGCTAAACTTGATGACG 59.730 45.833 0.00 0.00 0.00 4.35
1441 1572 4.820897 TCTGATGCTAAACTTGATGACGT 58.179 39.130 0.00 0.00 0.00 4.34
1547 1785 6.436261 CAATTGGCTGAATCACATCTATGTC 58.564 40.000 0.00 0.00 39.39 3.06
1566 1805 8.341903 TCTATGTCTGTTTAACATGTGTTTGTG 58.658 33.333 0.00 0.00 37.86 3.33
1570 1809 5.574830 TCTGTTTAACATGTGTTTGTGCAAC 59.425 36.000 0.00 1.98 39.31 4.17
1599 1838 3.573772 CTCGTCGGTGCAGCAAGGA 62.574 63.158 17.33 7.95 0.00 3.36
1728 2399 7.744087 TTGTATTGTACTGTTGCAGAAAGAT 57.256 32.000 2.91 0.00 35.18 2.40
1737 2408 9.098355 GTACTGTTGCAGAAAGATATCATACAA 57.902 33.333 5.32 0.00 35.18 2.41
1821 2492 5.609533 ACACTGTACATATAACACCCTCC 57.390 43.478 0.00 0.00 0.00 4.30
1823 2494 6.437755 ACACTGTACATATAACACCCTCCTA 58.562 40.000 0.00 0.00 0.00 2.94
1837 2511 5.487488 ACACCCTCCTAATCTTGTTGTCATA 59.513 40.000 0.00 0.00 0.00 2.15
1851 2527 8.352201 TCTTGTTGTCATAGAAGAACCATTTTG 58.648 33.333 0.00 0.00 0.00 2.44
1870 2546 3.777106 TGTTCTCCTCTGTTTGCTGAT 57.223 42.857 0.00 0.00 0.00 2.90
1954 2630 1.745489 CTCCAGGTTTACGGGCTGC 60.745 63.158 0.00 0.00 34.03 5.25
2058 2740 7.666623 CACAATTGGGAAAATACTTGGTAAGT 58.333 34.615 10.83 0.00 45.40 2.24
2140 2825 6.313658 ACCAACTTCATTTGCTCTTTGTTTTC 59.686 34.615 0.00 0.00 0.00 2.29
2206 2891 7.336161 AGTAAGTCTATGCACACTACCTTAG 57.664 40.000 0.00 0.00 0.00 2.18
2238 2923 2.221055 CCACGAGTGCTTACTGAACAAC 59.779 50.000 0.00 0.00 0.00 3.32
2383 3068 5.048153 GCATATGCACGATCTGTCTACTA 57.952 43.478 22.84 0.00 41.59 1.82
2393 3078 6.876789 CACGATCTGTCTACTATCTGGTCTAT 59.123 42.308 0.00 0.00 0.00 1.98
2430 3118 8.244113 GGAATGTTTGGTCCTTTCTTACATAAG 58.756 37.037 0.00 0.00 34.65 1.73
2741 3470 9.374711 TGGGTATTACTGAATCTGTCATATACA 57.625 33.333 15.08 8.39 35.07 2.29
3117 4655 3.457380 ACATCATGGCAGAGGTCTACAAT 59.543 43.478 0.00 0.00 0.00 2.71
3192 4731 5.004345 CCTTTGATGTTTGACGTGTGTTTTC 59.996 40.000 0.00 0.00 0.00 2.29
3305 4844 6.394025 AAGCTGTAAAACGGAATAAAACCA 57.606 33.333 0.00 0.00 0.00 3.67
3417 4964 3.484407 AGCTCTGAATTTGCTCAACAGT 58.516 40.909 0.00 0.00 30.41 3.55
3470 5027 8.552296 ACTAAGATTCTACCATCAAAGGTGAAT 58.448 33.333 0.00 0.00 43.14 2.57
3610 5167 2.965147 CAAGTTGATTGGTTGGGGAACT 59.035 45.455 0.00 0.00 35.08 3.01
3974 5542 1.332195 AAAGTTTGAGCTGCCCCTTC 58.668 50.000 0.00 0.00 0.00 3.46
4008 5576 5.394553 GCTGTTGGAATTAGCTATTTGCCTT 60.395 40.000 14.77 0.00 44.23 4.35
4026 5594 2.351738 CCTTTCAAGTTTAAGCGGGCAG 60.352 50.000 0.00 0.00 0.00 4.85
4049 5617 4.853468 TTAGCATTGATGGTACCAGGAA 57.147 40.909 21.41 15.07 40.12 3.36
4091 5659 6.354130 AGCTATTAATGTGTCCGTTAATGGT 58.646 36.000 13.49 0.00 40.99 3.55
4244 5812 3.443681 AGAAAAACAACCCCTCATATGCG 59.556 43.478 0.00 0.00 0.00 4.73
4270 5838 3.721706 CACCCCCTCTGCTCCCAC 61.722 72.222 0.00 0.00 0.00 4.61
4317 5885 6.186957 TGTCATGCAATACTAATGGACCTTT 58.813 36.000 0.00 0.00 0.00 3.11
4375 5943 3.826729 AGCCCCATAAACTTCAACAGAAC 59.173 43.478 0.00 0.00 0.00 3.01
4518 6087 8.277918 AGGTATAGGAGAATTTTGCTCATCTTT 58.722 33.333 0.00 0.00 34.07 2.52
4529 6098 7.686438 TTTTGCTCATCTTTGATAGCTTACA 57.314 32.000 0.00 0.00 0.00 2.41
4649 9256 3.496884 TGAAAACGTTGCTCACATACTCC 59.503 43.478 0.00 0.00 0.00 3.85
4686 9295 7.337938 AGTCACAAATTTTGGGATTCAAGTTT 58.662 30.769 16.65 0.00 46.25 2.66
4717 9331 5.575157 AGATAGGTCTCTCACAAGACAAGA 58.425 41.667 6.40 0.00 46.15 3.02
4746 9366 7.283625 ACAAAACCAACAAGCATAGTTCATA 57.716 32.000 0.00 0.00 0.00 2.15
4859 9500 2.658285 CATGTATGTGCCCTTGGATGT 58.342 47.619 0.00 0.00 0.00 3.06
4883 9524 8.128582 TGTCAAAACTTGATCACACATAAACTC 58.871 33.333 0.00 0.00 42.47 3.01
4902 9543 4.287552 ACTCGAAATAGGCTCTTCCCTTA 58.712 43.478 0.00 0.00 36.41 2.69
4907 9548 5.221742 CGAAATAGGCTCTTCCCTTAGGATT 60.222 44.000 0.00 0.00 43.54 3.01
4914 9555 2.131023 CTTCCCTTAGGATTGAGGCCT 58.869 52.381 3.86 3.86 43.54 5.19
4929 9570 5.901413 TGAGGCCTTCTAGATTCATGAAT 57.099 39.130 20.85 20.85 0.00 2.57
4950 9591 8.165239 TGAATGTAAGCTTTTTCTCTTGCTTA 57.835 30.769 3.20 0.00 44.08 3.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 3.364621 CCACGCATGCAATTAAAGAACAC 59.635 43.478 19.57 0.00 0.00 3.32
41 42 2.691526 AGATCAATCCACGCATGCAATT 59.308 40.909 19.57 8.49 0.00 2.32
42 43 2.304092 AGATCAATCCACGCATGCAAT 58.696 42.857 19.57 1.32 0.00 3.56
98 99 0.686769 ACTCCCTCCGGTATGGTCAC 60.687 60.000 0.00 0.00 39.52 3.67
99 100 0.928505 TACTCCCTCCGGTATGGTCA 59.071 55.000 0.00 0.00 39.52 4.02
109 110 8.635765 TGCATATTTTGATAATTACTCCCTCC 57.364 34.615 0.00 0.00 0.00 4.30
110 111 9.899226 GTTGCATATTTTGATAATTACTCCCTC 57.101 33.333 0.00 0.00 0.00 4.30
192 197 8.700973 GGCCCTGGAAACATTTAAAGATTATTA 58.299 33.333 0.00 0.00 41.51 0.98
202 213 3.430453 CAAGAGGCCCTGGAAACATTTA 58.570 45.455 0.00 0.00 41.51 1.40
217 228 1.838112 TATGCCAACTTGCCAAGAGG 58.162 50.000 12.25 13.19 38.23 3.69
219 230 2.378038 GGATATGCCAACTTGCCAAGA 58.622 47.619 12.25 0.00 36.34 3.02
246 262 0.886563 CTACCTCGACCTCACGGTTT 59.113 55.000 0.00 0.00 45.73 3.27
249 265 0.170561 CAACTACCTCGACCTCACGG 59.829 60.000 0.00 0.00 0.00 4.94
256 272 6.618811 TCTACAATCTTTCAACTACCTCGAC 58.381 40.000 0.00 0.00 0.00 4.20
260 277 6.702329 CCACTCTACAATCTTTCAACTACCT 58.298 40.000 0.00 0.00 0.00 3.08
346 368 2.817258 TGAAACGGGCATTTGTTAGAGG 59.183 45.455 0.00 0.00 0.00 3.69
368 390 6.059787 TGGGTTGCCTGCATATTTATTTTT 57.940 33.333 0.00 0.00 0.00 1.94
409 450 5.180117 TCTTCTTGCGAGAATCTTTTTGGAG 59.820 40.000 16.86 1.48 40.93 3.86
459 504 4.318121 GGTTGCATATCGTCTTGATTCGTC 60.318 45.833 0.00 0.00 38.57 4.20
588 638 9.975218 AAATTTGTACTCCTACTCCATTATTGT 57.025 29.630 0.00 0.00 0.00 2.71
603 661 5.980715 TCCTTTTGCGGAAAAATTTGTACTC 59.019 36.000 15.86 0.00 37.14 2.59
619 677 1.812571 TCCTTGCGAGAATCCTTTTGC 59.187 47.619 1.22 0.00 0.00 3.68
696 754 8.494016 AATCAACAACCCGTTTTTAATTCAAA 57.506 26.923 0.00 0.00 34.86 2.69
825 884 1.105167 TACGATGGAGACCGCCGATT 61.105 55.000 0.00 0.00 0.00 3.34
957 1028 1.002274 GGAGGGAGGAAGCAGAGGA 59.998 63.158 0.00 0.00 0.00 3.71
960 1031 2.041265 GGGGAGGGAGGAAGCAGA 59.959 66.667 0.00 0.00 0.00 4.26
961 1032 3.093172 GGGGGAGGGAGGAAGCAG 61.093 72.222 0.00 0.00 0.00 4.24
1091 1183 1.287503 GCGATGGGATCTCGACTCC 59.712 63.158 7.00 1.31 38.38 3.85
1128 1220 1.945394 CTCAAAGCAGCTGTGAACTGT 59.055 47.619 16.47 0.00 37.47 3.55
1132 1224 2.874701 GACTTCTCAAAGCAGCTGTGAA 59.125 45.455 16.47 7.68 35.81 3.18
1134 1226 2.216046 TGACTTCTCAAAGCAGCTGTG 58.784 47.619 16.64 6.19 35.81 3.66
1189 1281 2.347731 GAAGCTGCTACTGGTACCAAC 58.652 52.381 17.11 6.50 0.00 3.77
1191 1283 0.902531 GGAAGCTGCTACTGGTACCA 59.097 55.000 15.39 15.39 0.00 3.25
1192 1284 0.179108 CGGAAGCTGCTACTGGTACC 60.179 60.000 4.43 4.43 0.00 3.34
1193 1285 0.531200 ACGGAAGCTGCTACTGGTAC 59.469 55.000 0.90 0.00 0.00 3.34
1194 1286 1.263356 AACGGAAGCTGCTACTGGTA 58.737 50.000 0.90 0.00 0.00 3.25
1195 1287 1.263356 TAACGGAAGCTGCTACTGGT 58.737 50.000 0.90 0.00 0.00 4.00
1196 1288 2.101582 AGATAACGGAAGCTGCTACTGG 59.898 50.000 0.90 0.00 0.00 4.00
1197 1289 3.444703 AGATAACGGAAGCTGCTACTG 57.555 47.619 0.90 0.00 0.00 2.74
1203 1295 7.596749 TTCTTTCTAAAGATAACGGAAGCTG 57.403 36.000 6.01 0.00 43.92 4.24
1238 1330 3.201290 ACTAATCAATCTCCGCAGCTTG 58.799 45.455 0.00 0.00 0.00 4.01
1253 1345 7.244166 TCGCAGAACTACAGTACTACTAATC 57.756 40.000 0.00 0.00 0.00 1.75
1438 1569 4.318546 GCTGTTCGATTTTCAGTGTTACGT 60.319 41.667 0.00 0.00 0.00 3.57
1440 1571 5.177696 AGAGCTGTTCGATTTTCAGTGTTAC 59.822 40.000 0.00 0.00 0.00 2.50
1441 1572 5.177511 CAGAGCTGTTCGATTTTCAGTGTTA 59.822 40.000 0.00 0.00 0.00 2.41
1547 1785 5.498384 CGTTGCACAAACACATGTTAAACAG 60.498 40.000 0.00 0.00 38.84 3.16
1570 1809 2.152699 CCGACGAGCTGCAAGTACG 61.153 63.158 1.02 7.25 39.53 3.67
1681 2352 9.988815 ACAATGATGATTAGTACTCTGTAATCC 57.011 33.333 0.00 0.00 35.57 3.01
1728 2399 5.866335 GGTTGTTGACCGTTTGTATGATA 57.134 39.130 0.00 0.00 39.00 2.15
1821 2492 8.777865 TGGTTCTTCTATGACAACAAGATTAG 57.222 34.615 0.00 0.00 0.00 1.73
1823 2494 8.641498 AATGGTTCTTCTATGACAACAAGATT 57.359 30.769 0.00 0.00 0.00 2.40
1851 2527 3.932089 GAGATCAGCAAACAGAGGAGAAC 59.068 47.826 0.00 0.00 0.00 3.01
1856 2532 5.182570 TGATTTTGAGATCAGCAAACAGAGG 59.817 40.000 11.78 0.00 35.20 3.69
1870 2546 4.507710 CACGGAAGAGGATGATTTTGAGA 58.492 43.478 0.00 0.00 0.00 3.27
1954 2630 3.243035 TGAATGAGTTTTGGTGCGAACAG 60.243 43.478 0.00 0.00 0.00 3.16
2084 2769 3.678915 AAAACAACGTAGAACCGGTTG 57.321 42.857 27.87 13.08 0.00 3.77
2206 2891 1.661112 GCACTCGTGGAGCTAACAATC 59.339 52.381 0.00 0.00 32.04 2.67
2238 2923 4.114073 CAGACTAGCTTGAGCATCTTCAG 58.886 47.826 1.04 0.00 45.16 3.02
2540 3228 4.685447 ACGAAGTATTGCCACGCA 57.315 50.000 0.00 0.00 41.94 5.24
2838 3568 4.878397 AGAGCCAAATGATACAAGCACTAC 59.122 41.667 0.00 0.00 0.00 2.73
3117 4655 2.576191 AGCAACTTCTACAGGGCCATTA 59.424 45.455 6.18 0.00 0.00 1.90
3192 4731 2.548493 CCAACATTTTGACAGCCTTGGG 60.548 50.000 0.00 0.00 34.24 4.12
3294 4833 9.788960 GTCATGTTCTTTCTATGGTTTTATTCC 57.211 33.333 0.00 0.00 0.00 3.01
3373 4920 8.969267 AGCTCGAAAGATAATAACAGTATTTCG 58.031 33.333 10.05 10.05 45.22 3.46
3456 5013 8.042515 ACAAATATTTCCATTCACCTTTGATGG 58.957 33.333 0.00 0.00 34.32 3.51
3470 5027 5.391523 GCACAGCGAGTAACAAATATTTCCA 60.392 40.000 0.00 0.00 0.00 3.53
3610 5167 1.123077 AATCCTCGCCAGCATCACTA 58.877 50.000 0.00 0.00 0.00 2.74
3803 5371 7.177041 ACCAAAACTTATTAATTAGCCCAACGA 59.823 33.333 1.40 0.00 0.00 3.85
3974 5542 2.775911 TTCCAACAGCATCAGAGGAG 57.224 50.000 0.00 0.00 0.00 3.69
4008 5576 2.264005 TCTGCCCGCTTAAACTTGAA 57.736 45.000 0.00 0.00 0.00 2.69
4026 5594 4.973168 TCCTGGTACCATCAATGCTAATC 58.027 43.478 16.75 0.00 0.00 1.75
4049 5617 6.662865 ATAGCTAGTGCACAGAATACAGAT 57.337 37.500 21.04 5.34 42.74 2.90
4119 5687 8.805175 TGAAATGGATAATTGTTTGTCACTCAT 58.195 29.630 0.00 0.00 0.00 2.90
4270 5838 1.263217 GGCGCAATATTTAGTCCCACG 59.737 52.381 10.83 0.00 0.00 4.94
4487 6056 8.494433 TGAGCAAAATTCTCCTATACCTAATGT 58.506 33.333 0.00 0.00 0.00 2.71
4571 6140 7.308109 CCTTTATTTGCTTGAAATGTGCACAAT 60.308 33.333 25.72 13.73 35.74 2.71
4633 9240 3.780902 TGTATGGAGTATGTGAGCAACG 58.219 45.455 0.00 0.00 0.00 4.10
4649 9256 9.866936 CCAAAATTTGTGACTTTGAAATGTATG 57.133 29.630 4.92 0.00 32.87 2.39
4686 9295 7.619698 TCTTGTGAGAGACCTATCTTTTGGATA 59.380 37.037 0.00 0.00 34.34 2.59
4717 9331 3.902881 TGCTTGTTGGTTTTGTTGGAT 57.097 38.095 0.00 0.00 0.00 3.41
4746 9366 1.078214 CGGTGGGAGTGCATGATGT 60.078 57.895 0.00 0.00 0.00 3.06
4815 9435 0.755686 TCATGGGTGGTTTTGGTTGC 59.244 50.000 0.00 0.00 0.00 4.17
4859 9500 7.225734 TCGAGTTTATGTGTGATCAAGTTTTGA 59.774 33.333 0.00 0.00 45.01 2.69
4883 9524 3.641906 TCCTAAGGGAAGAGCCTATTTCG 59.358 47.826 0.00 0.00 38.93 3.46
4902 9543 4.302067 TGAATCTAGAAGGCCTCAATCCT 58.698 43.478 5.23 1.02 34.90 3.24
4907 9548 5.131642 ACATTCATGAATCTAGAAGGCCTCA 59.868 40.000 18.16 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.