Multiple sequence alignment - TraesCS1B01G422900

Loading Multiple Alignment...

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 TraesCS1B01G422900 chr1B 100.000 2670 0 0 1 2670 645573010 645570341 0.000000 4931.0
1 TraesCS1B01G422900 chr1A 88.909 2714 142 62 3 2661 560247944 560250553 0.000000 3197.0
2 TraesCS1B01G422900 chr1D 90.918 1982 108 40 3 1968 467663355 467661430 0.000000 2597.0
3 TraesCS1B01G422900 chr1D 94.872 585 14 8 2089 2670 467659705 467659134 0.000000 900.0
4 TraesCS1B01G422900 chr1D 92.683 41 1 1 1999 2039 467659744 467659706 0.000103 58.4


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 TraesCS1B01G422900 chr1B 645570341 645573010 2669 True 4931.000000 4931 100.000000 1 2670 1 chr1B.!!$R1 2669
1 TraesCS1B01G422900 chr1A 560247944 560250553 2609 False 3197.000000 3197 88.909000 3 2661 1 chr1A.!!$F1 2658
2 TraesCS1B01G422900 chr1D 467659134 467663355 4221 True 1185.133333 2597 92.824333 3 2670 3 chr1D.!!$R1 2667

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
244 245 0.456221 CTTGGGCGTGTAGAGACGAT 59.544 55.0 3.07 0.0 42.1 3.73 F
989 1005 0.830648 TGCGTTATTGAGGGAGGGAG 59.169 55.0 0.00 0.0 0.0 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1191 1207 0.032017 AGGGTACGAAGCAGGAGGAT 60.032 55.000 0.00 0.0 0.0 3.24 R
2640 4364 2.166829 TGTGCGCTATTTTCCCAACAT 58.833 42.857 9.73 0.0 0.0 2.71 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
17 18 3.690745 AGCCCTGAACAATGCAGC 58.309 55.556 0.00 0.00 32.06 5.25
64 65 2.991250 TCTCAGCCTACTTGCCATTTC 58.009 47.619 0.00 0.00 0.00 2.17
75 76 6.375455 CCTACTTGCCATTTCTAACACTCAAT 59.625 38.462 0.00 0.00 0.00 2.57
91 92 3.181466 ACTCAATGGTGGTTTGCTTTTCC 60.181 43.478 0.00 0.00 0.00 3.13
241 242 0.737715 CTGCTTGGGCGTGTAGAGAC 60.738 60.000 0.00 0.00 42.25 3.36
242 243 1.805945 GCTTGGGCGTGTAGAGACG 60.806 63.158 0.00 0.00 42.42 4.18
243 244 1.880894 CTTGGGCGTGTAGAGACGA 59.119 57.895 3.07 0.00 42.10 4.20
244 245 0.456221 CTTGGGCGTGTAGAGACGAT 59.544 55.000 3.07 0.00 42.10 3.73
327 328 1.578206 GAGGAGAAACTTGGTGCGCC 61.578 60.000 10.11 10.11 0.00 6.53
356 357 1.027357 GCACATGGTATGCTCCCAAG 58.973 55.000 0.00 0.00 40.08 3.61
366 367 1.755783 GCTCCCAAGCCCCAAGATG 60.756 63.158 0.00 0.00 43.10 2.90
465 472 2.812591 TGCAAATACGACCGGCTTTTAA 59.187 40.909 0.00 0.00 0.00 1.52
468 475 4.268522 CAAATACGACCGGCTTTTAATCG 58.731 43.478 0.00 3.67 38.71 3.34
603 610 7.340999 AGAACACACCTAGTTGTTAACCAAAAT 59.659 33.333 2.48 0.00 34.07 1.82
604 611 7.412853 ACACACCTAGTTGTTAACCAAAATT 57.587 32.000 2.48 0.00 34.07 1.82
605 612 8.522542 ACACACCTAGTTGTTAACCAAAATTA 57.477 30.769 2.48 0.00 34.07 1.40
639 646 2.526304 TGGTACACTTGTCAGACAGC 57.474 50.000 2.82 0.00 0.00 4.40
640 647 1.760029 TGGTACACTTGTCAGACAGCA 59.240 47.619 2.82 0.00 0.00 4.41
641 648 2.224042 TGGTACACTTGTCAGACAGCAG 60.224 50.000 2.82 1.93 0.00 4.24
642 649 2.224066 GGTACACTTGTCAGACAGCAGT 60.224 50.000 2.82 2.61 0.00 4.40
643 650 2.231215 ACACTTGTCAGACAGCAGTC 57.769 50.000 2.82 0.05 45.31 3.51
658 665 2.575694 CAGTCACTGCCTGCTACTAG 57.424 55.000 0.00 0.00 0.00 2.57
755 767 4.344865 TGCCGGCCCTCCACTTTC 62.345 66.667 26.77 0.00 0.00 2.62
775 787 2.026520 CCGCGGGCAAAACAAATGG 61.027 57.895 20.10 0.00 0.00 3.16
890 902 8.039538 GGTTGCCTAACTACCCAGTTATATATC 58.960 40.741 0.00 0.00 44.35 1.63
902 914 7.956315 ACCCAGTTATATATCCTGCTTTCTAGA 59.044 37.037 6.75 0.00 0.00 2.43
926 938 1.304617 CAAAGGGAGGAAGAGGCCC 59.695 63.158 0.00 0.00 42.37 5.80
979 995 3.532138 CGCCTTCCATGCGTTATTG 57.468 52.632 0.00 0.00 46.59 1.90
980 996 1.013596 CGCCTTCCATGCGTTATTGA 58.986 50.000 0.00 0.00 46.59 2.57
981 997 1.003545 CGCCTTCCATGCGTTATTGAG 60.004 52.381 0.00 0.00 46.59 3.02
983 999 1.949525 CCTTCCATGCGTTATTGAGGG 59.050 52.381 0.00 0.00 0.00 4.30
984 1000 2.421388 CCTTCCATGCGTTATTGAGGGA 60.421 50.000 0.00 0.00 31.46 4.20
987 1003 1.597742 CATGCGTTATTGAGGGAGGG 58.402 55.000 0.00 0.00 0.00 4.30
988 1004 1.140852 CATGCGTTATTGAGGGAGGGA 59.859 52.381 0.00 0.00 0.00 4.20
989 1005 0.830648 TGCGTTATTGAGGGAGGGAG 59.169 55.000 0.00 0.00 0.00 4.30
990 1006 1.120530 GCGTTATTGAGGGAGGGAGA 58.879 55.000 0.00 0.00 0.00 3.71
1089 1105 4.792804 GCCCTGCTGCTCTCCACC 62.793 72.222 0.00 0.00 0.00 4.61
1105 1121 3.003173 CCTCCCTGGCAGGTTCGA 61.003 66.667 30.68 19.86 31.93 3.71
1106 1122 2.370445 CCTCCCTGGCAGGTTCGAT 61.370 63.158 30.68 0.00 31.93 3.59
1107 1123 1.144936 CTCCCTGGCAGGTTCGATC 59.855 63.158 30.68 0.00 31.93 3.69
1108 1124 2.202932 CCCTGGCAGGTTCGATCG 60.203 66.667 30.68 9.36 31.93 3.69
1113 1129 2.740714 GGCAGGTTCGATCGTGTGC 61.741 63.158 15.94 17.67 0.00 4.57
1135 1151 3.246619 CTGTCTTGTCCTTCGTTCTAGC 58.753 50.000 0.00 0.00 0.00 3.42
1140 1156 2.724454 TGTCCTTCGTTCTAGCTAGCT 58.276 47.619 23.12 23.12 0.00 3.32
1148 1164 6.461788 CCTTCGTTCTAGCTAGCTAGGAAATT 60.462 42.308 38.82 12.32 44.45 1.82
1153 1169 6.658188 TCTAGCTAGCTAGGAAATTCCTTC 57.342 41.667 38.82 12.24 46.91 3.46
1155 1171 5.545063 AGCTAGCTAGGAAATTCCTTCTC 57.455 43.478 20.79 9.46 46.91 2.87
1175 1191 6.109320 TCTCGACGAAGAATCTAAGAAGTC 57.891 41.667 0.00 0.00 0.00 3.01
1204 1220 7.717436 TGATCTAGTATATATCCTCCTGCTTCG 59.283 40.741 0.00 0.00 0.00 3.79
1205 1221 6.959904 TCTAGTATATATCCTCCTGCTTCGT 58.040 40.000 0.00 0.00 0.00 3.85
1220 1236 2.460918 CTTCGTACCCTTGCATCTACG 58.539 52.381 0.00 0.00 34.59 3.51
1222 1238 1.133598 TCGTACCCTTGCATCTACGTG 59.866 52.381 0.00 0.00 34.82 4.49
1223 1239 1.135199 CGTACCCTTGCATCTACGTGT 60.135 52.381 0.00 0.00 0.00 4.49
1224 1240 2.268298 GTACCCTTGCATCTACGTGTG 58.732 52.381 0.00 0.00 0.00 3.82
1225 1241 0.673644 ACCCTTGCATCTACGTGTGC 60.674 55.000 13.38 13.38 41.61 4.57
1229 1245 2.826277 TGCATCTACGTGTGCACAG 58.174 52.632 22.40 16.54 45.60 3.66
1230 1246 0.670239 TGCATCTACGTGTGCACAGG 60.670 55.000 32.01 32.01 45.60 4.00
1231 1247 0.670546 GCATCTACGTGTGCACAGGT 60.671 55.000 37.96 37.96 45.53 4.00
1232 1248 1.403647 GCATCTACGTGTGCACAGGTA 60.404 52.381 36.54 36.54 43.64 3.08
1237 1253 2.941453 ACGTGTGCACAGGTAGATAG 57.059 50.000 36.41 15.89 42.38 2.08
1238 1254 1.476891 ACGTGTGCACAGGTAGATAGG 59.523 52.381 36.41 14.29 42.38 2.57
1239 1255 1.202417 CGTGTGCACAGGTAGATAGGG 60.202 57.143 27.22 2.07 0.00 3.53
1240 1256 1.831736 GTGTGCACAGGTAGATAGGGT 59.168 52.381 22.40 0.00 0.00 4.34
1241 1257 2.108168 TGTGCACAGGTAGATAGGGTC 58.892 52.381 17.42 0.00 0.00 4.46
1253 1269 3.899726 AGATAGGGTCGTGATGTAGTGT 58.100 45.455 0.00 0.00 0.00 3.55
1288 1315 0.176680 AGTTCCTAGCTCACATGGCG 59.823 55.000 0.00 0.00 34.52 5.69
1292 1319 2.202743 TAGCTCACATGGCGACGC 60.203 61.111 12.43 12.43 34.52 5.19
1307 1335 2.440501 CGACGCCATGTATTTTGCTTC 58.559 47.619 0.00 0.00 0.00 3.86
1311 1339 3.181397 CGCCATGTATTTTGCTTCCTTG 58.819 45.455 0.00 0.00 0.00 3.61
1343 1371 3.359033 TGCATCAAGAGATTTGAAGGGG 58.641 45.455 0.00 0.00 30.20 4.79
1353 1385 5.003096 AGATTTGAAGGGGACAAGATGTT 57.997 39.130 0.00 0.00 0.00 2.71
1354 1386 6.012508 AGAGATTTGAAGGGGACAAGATGTTA 60.013 38.462 0.00 0.00 0.00 2.41
1383 1419 2.221055 GCTTAATTAGGTGATCCACGCG 59.779 50.000 3.53 3.53 34.83 6.01
1422 1464 6.211515 GTCATGAGAAAACAGATGCACTTTT 58.788 36.000 0.00 0.00 0.00 2.27
1423 1465 6.698766 GTCATGAGAAAACAGATGCACTTTTT 59.301 34.615 0.00 0.00 30.93 1.94
1478 1520 5.475273 TTGATCGATGATTCTGCTGTTTC 57.525 39.130 0.54 0.00 0.00 2.78
1521 1566 5.183140 GCTTCATAGTAGATCAGGAGTCTCC 59.817 48.000 11.31 11.31 36.58 3.71
1543 1588 0.036858 GTCAGCAAGGAGAGGTCCAC 60.037 60.000 0.00 0.00 46.80 4.02
1544 1589 1.194781 TCAGCAAGGAGAGGTCCACC 61.195 60.000 0.00 0.00 46.80 4.61
1545 1590 2.266055 GCAAGGAGAGGTCCACCG 59.734 66.667 0.00 0.00 46.80 4.94
1546 1591 2.982130 CAAGGAGAGGTCCACCGG 59.018 66.667 0.00 0.00 46.80 5.28
1592 1637 1.612146 TCCCGGATGCTCAAGGACA 60.612 57.895 0.73 0.00 0.00 4.02
1594 1639 0.816825 CCCGGATGCTCAAGGACATG 60.817 60.000 0.73 0.00 0.00 3.21
1597 1642 1.293924 GGATGCTCAAGGACATGACG 58.706 55.000 0.00 0.00 0.00 4.35
1633 1678 2.203611 TACGACCCAACCCCGTCA 60.204 61.111 0.00 0.00 37.69 4.35
1719 1766 9.508642 TGATCCATCTATATATCTACGTCCATC 57.491 37.037 0.00 0.00 0.00 3.51
1732 1779 6.621613 TCTACGTCCATCTGAATGTATATGC 58.378 40.000 0.00 0.00 0.00 3.14
1813 1866 6.964741 TTTGTAAGTTGTTGTAGACGTGAA 57.035 33.333 0.00 0.00 0.00 3.18
1814 1867 5.954434 TGTAAGTTGTTGTAGACGTGAAC 57.046 39.130 0.00 0.00 0.00 3.18
2039 3750 1.187087 GTCTCCGACCTCCACATCTT 58.813 55.000 0.00 0.00 0.00 2.40
2051 3764 2.679336 TCCACATCTTGATGCACGATTG 59.321 45.455 10.20 1.13 0.00 2.67
2129 3850 5.470098 ACACTGTGCTGGAATTAAAGTGTAG 59.530 40.000 7.90 0.00 43.53 2.74
2367 4090 5.243954 CACCATAGATATCCGACCTGAAAGA 59.756 44.000 0.00 0.00 34.07 2.52
2368 4091 5.839063 ACCATAGATATCCGACCTGAAAGAA 59.161 40.000 0.00 0.00 34.07 2.52
2369 4092 6.326583 ACCATAGATATCCGACCTGAAAGAAA 59.673 38.462 0.00 0.00 34.07 2.52
2370 4093 7.016661 ACCATAGATATCCGACCTGAAAGAAAT 59.983 37.037 0.00 0.00 34.07 2.17
2371 4094 7.880195 CCATAGATATCCGACCTGAAAGAAATT 59.120 37.037 0.00 0.00 34.07 1.82
2424 4147 7.589395 TGTTTTTGCGTACAATAACTCATGAT 58.411 30.769 0.00 0.00 43.78 2.45
2432 4155 9.289303 GCGTACAATAACTCATGATTCAAATTT 57.711 29.630 0.00 0.00 0.00 1.82
2536 4259 4.576879 AGGACTTTAATCCGGTTTCAGTC 58.423 43.478 20.07 20.07 44.22 3.51
2613 4337 2.101415 CCAACCTCGACATCTAGATGCA 59.899 50.000 28.86 14.35 42.39 3.96
2633 4357 6.951256 TGCACACGATTATAATCTATCTGC 57.049 37.500 20.47 19.17 33.24 4.26
2634 4358 6.454795 TGCACACGATTATAATCTATCTGCA 58.545 36.000 20.47 20.89 32.14 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.228644 TGCTGCATTGTTCAGGGCT 60.229 52.632 0.00 0.00 32.41 5.19
1 2 1.080298 GTGCTGCATTGTTCAGGGC 60.080 57.895 5.27 0.00 32.41 5.19
64 65 3.569701 AGCAAACCACCATTGAGTGTTAG 59.430 43.478 0.00 0.00 35.93 2.34
75 76 1.484240 CCAAGGAAAAGCAAACCACCA 59.516 47.619 0.00 0.00 0.00 4.17
110 111 7.355778 GGGAATCATACGAGATAAAAAGCAAG 58.644 38.462 0.00 0.00 0.00 4.01
147 148 1.127701 CGCCAACATTTTTGTCGTGG 58.872 50.000 0.00 0.00 0.00 4.94
241 242 3.159353 TGACACACCCTAAATCGATCG 57.841 47.619 9.36 9.36 0.00 3.69
242 243 3.809832 CCATGACACACCCTAAATCGATC 59.190 47.826 0.00 0.00 0.00 3.69
243 244 3.199946 ACCATGACACACCCTAAATCGAT 59.800 43.478 0.00 0.00 0.00 3.59
244 245 2.569853 ACCATGACACACCCTAAATCGA 59.430 45.455 0.00 0.00 0.00 3.59
293 294 1.153005 CCTCAGATCCAGCAAGCCC 60.153 63.158 0.00 0.00 0.00 5.19
353 354 2.369394 GGTAACTCATCTTGGGGCTTG 58.631 52.381 0.00 0.00 0.00 4.01
356 357 0.106669 GGGGTAACTCATCTTGGGGC 60.107 60.000 0.00 0.00 36.63 5.80
366 367 2.289257 ACGTTGCTACTTGGGGTAACTC 60.289 50.000 0.00 0.00 37.88 3.01
394 401 0.786581 CGATCGGCTTTCATCCATCG 59.213 55.000 7.38 0.00 32.67 3.84
442 449 1.644786 AAGCCGGTCGTATTTGCAGC 61.645 55.000 1.90 0.00 0.00 5.25
465 472 2.668212 CACCGGTGGTTGCACGAT 60.668 61.111 27.57 0.00 31.02 3.73
489 496 1.835927 AAGTGGTCTCTGGCTCTGGC 61.836 60.000 0.00 0.00 37.82 4.85
592 599 8.028540 CCAAATGGCTTCTAATTTTGGTTAAC 57.971 34.615 0.00 0.00 40.77 2.01
624 631 1.482182 TGACTGCTGTCTGACAAGTGT 59.518 47.619 22.31 12.63 43.29 3.55
639 646 1.821753 ACTAGTAGCAGGCAGTGACTG 59.178 52.381 22.48 22.48 42.51 3.51
640 647 2.223803 ACTAGTAGCAGGCAGTGACT 57.776 50.000 0.00 0.00 0.00 3.41
641 648 3.429135 GGTTACTAGTAGCAGGCAGTGAC 60.429 52.174 17.27 0.00 0.00 3.67
642 649 2.758979 GGTTACTAGTAGCAGGCAGTGA 59.241 50.000 17.27 0.00 0.00 3.41
643 650 2.496070 TGGTTACTAGTAGCAGGCAGTG 59.504 50.000 17.27 0.00 0.00 3.66
644 651 2.496470 GTGGTTACTAGTAGCAGGCAGT 59.504 50.000 17.27 0.00 0.00 4.40
658 665 5.062308 CGTTTTCAGCTCTGATAGTGGTTAC 59.938 44.000 0.00 0.00 39.64 2.50
761 773 4.319405 CGATGTTTTCCATTTGTTTTGCCC 60.319 41.667 0.00 0.00 32.56 5.36
775 787 6.194796 TGATGGAGGAATTTCGATGTTTTC 57.805 37.500 0.00 0.00 0.00 2.29
809 821 1.004080 TCACTGCCTCTGAGCAAGC 60.004 57.895 0.00 0.00 43.52 4.01
864 876 2.873094 AACTGGGTAGTTAGGCAACC 57.127 50.000 0.00 0.00 45.07 3.77
890 902 4.397417 CCTTTGTTCCATCTAGAAAGCAGG 59.603 45.833 0.00 0.00 0.00 4.85
902 914 2.310052 CCTCTTCCTCCCTTTGTTCCAT 59.690 50.000 0.00 0.00 0.00 3.41
908 920 1.304617 GGGCCTCTTCCTCCCTTTG 59.695 63.158 0.84 0.00 37.08 2.77
909 921 1.931180 GGGGCCTCTTCCTCCCTTT 60.931 63.158 0.84 0.00 39.95 3.11
910 922 2.286502 GGGGCCTCTTCCTCCCTT 60.287 66.667 0.84 0.00 39.95 3.95
911 923 3.296737 AGGGGCCTCTTCCTCCCT 61.297 66.667 0.00 0.00 44.43 4.20
912 924 3.093172 CAGGGGCCTCTTCCTCCC 61.093 72.222 0.00 0.00 39.67 4.30
916 928 2.273776 GAAGCAGGGGCCTCTTCC 59.726 66.667 0.00 0.00 42.56 3.46
926 938 0.671781 CGAGGTGAAGGTGAAGCAGG 60.672 60.000 0.00 0.00 0.00 4.85
977 993 0.633921 CTCTCCTCTCCCTCCCTCAA 59.366 60.000 0.00 0.00 0.00 3.02
979 995 1.152546 GCTCTCCTCTCCCTCCCTC 60.153 68.421 0.00 0.00 0.00 4.30
980 996 3.024217 GCTCTCCTCTCCCTCCCT 58.976 66.667 0.00 0.00 0.00 4.20
981 997 2.520741 CGCTCTCCTCTCCCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
983 999 1.832167 ATGCGCTCTCCTCTCCCTC 60.832 63.158 9.73 0.00 0.00 4.30
984 1000 2.132996 CATGCGCTCTCCTCTCCCT 61.133 63.158 9.73 0.00 0.00 4.20
987 1003 0.945265 GATGCATGCGCTCTCCTCTC 60.945 60.000 14.09 0.00 39.64 3.20
988 1004 1.069427 GATGCATGCGCTCTCCTCT 59.931 57.895 14.09 0.00 39.64 3.69
989 1005 2.308769 CGATGCATGCGCTCTCCTC 61.309 63.158 14.09 0.00 39.64 3.71
990 1006 2.279985 CGATGCATGCGCTCTCCT 60.280 61.111 14.09 0.00 39.64 3.69
1038 1054 1.395826 CGAAGAGGGAGGCGGATCTT 61.396 60.000 0.00 0.00 34.78 2.40
1089 1105 1.144936 GATCGAACCTGCCAGGGAG 59.855 63.158 16.70 0.00 40.58 4.30
1105 1121 0.320771 GGACAAGACAGGCACACGAT 60.321 55.000 0.00 0.00 0.00 3.73
1106 1122 1.069090 GGACAAGACAGGCACACGA 59.931 57.895 0.00 0.00 0.00 4.35
1107 1123 0.532862 AAGGACAAGACAGGCACACG 60.533 55.000 0.00 0.00 0.00 4.49
1108 1124 1.230324 GAAGGACAAGACAGGCACAC 58.770 55.000 0.00 0.00 0.00 3.82
1113 1129 2.821991 AGAACGAAGGACAAGACAGG 57.178 50.000 0.00 0.00 0.00 4.00
1153 1169 5.065474 AGGACTTCTTAGATTCTTCGTCGAG 59.935 44.000 0.00 0.00 0.00 4.04
1155 1171 5.238006 AGGACTTCTTAGATTCTTCGTCG 57.762 43.478 0.00 0.00 0.00 5.12
1175 1191 8.004215 AGCAGGAGGATATATACTAGATCAAGG 58.996 40.741 0.00 0.00 0.00 3.61
1187 1203 4.024670 GGGTACGAAGCAGGAGGATATAT 58.975 47.826 0.00 0.00 0.00 0.86
1188 1204 3.075582 AGGGTACGAAGCAGGAGGATATA 59.924 47.826 0.00 0.00 0.00 0.86
1189 1205 2.158295 AGGGTACGAAGCAGGAGGATAT 60.158 50.000 0.00 0.00 0.00 1.63
1190 1206 1.217183 AGGGTACGAAGCAGGAGGATA 59.783 52.381 0.00 0.00 0.00 2.59
1191 1207 0.032017 AGGGTACGAAGCAGGAGGAT 60.032 55.000 0.00 0.00 0.00 3.24
1204 1220 2.268298 CACACGTAGATGCAAGGGTAC 58.732 52.381 0.00 0.00 0.00 3.34
1205 1221 1.404986 GCACACGTAGATGCAAGGGTA 60.405 52.381 12.35 0.00 41.39 3.69
1220 1236 1.831736 ACCCTATCTACCTGTGCACAC 59.168 52.381 17.42 0.00 0.00 3.82
1222 1238 1.067212 CGACCCTATCTACCTGTGCAC 59.933 57.143 10.75 10.75 0.00 4.57
1223 1239 1.341679 ACGACCCTATCTACCTGTGCA 60.342 52.381 0.00 0.00 0.00 4.57
1224 1240 1.067212 CACGACCCTATCTACCTGTGC 59.933 57.143 0.00 0.00 0.00 4.57
1225 1241 2.651455 TCACGACCCTATCTACCTGTG 58.349 52.381 0.00 0.00 0.00 3.66
1226 1242 3.223435 CATCACGACCCTATCTACCTGT 58.777 50.000 0.00 0.00 0.00 4.00
1227 1243 3.223435 ACATCACGACCCTATCTACCTG 58.777 50.000 0.00 0.00 0.00 4.00
1228 1244 3.596940 ACATCACGACCCTATCTACCT 57.403 47.619 0.00 0.00 0.00 3.08
1229 1245 4.215827 CACTACATCACGACCCTATCTACC 59.784 50.000 0.00 0.00 0.00 3.18
1230 1246 4.820716 ACACTACATCACGACCCTATCTAC 59.179 45.833 0.00 0.00 0.00 2.59
1231 1247 5.045012 ACACTACATCACGACCCTATCTA 57.955 43.478 0.00 0.00 0.00 1.98
1232 1248 3.899726 ACACTACATCACGACCCTATCT 58.100 45.455 0.00 0.00 0.00 1.98
1233 1249 4.820716 ACTACACTACATCACGACCCTATC 59.179 45.833 0.00 0.00 0.00 2.08
1234 1250 4.789807 ACTACACTACATCACGACCCTAT 58.210 43.478 0.00 0.00 0.00 2.57
1235 1251 4.226427 ACTACACTACATCACGACCCTA 57.774 45.455 0.00 0.00 0.00 3.53
1236 1252 3.083122 ACTACACTACATCACGACCCT 57.917 47.619 0.00 0.00 0.00 4.34
1237 1253 5.762218 ACTATACTACACTACATCACGACCC 59.238 44.000 0.00 0.00 0.00 4.46
1238 1254 6.656945 CACTATACTACACTACATCACGACC 58.343 44.000 0.00 0.00 0.00 4.79
1239 1255 6.134730 GCACTATACTACACTACATCACGAC 58.865 44.000 0.00 0.00 0.00 4.34
1240 1256 5.818857 TGCACTATACTACACTACATCACGA 59.181 40.000 0.00 0.00 0.00 4.35
1241 1257 6.056428 TGCACTATACTACACTACATCACG 57.944 41.667 0.00 0.00 0.00 4.35
1253 1269 4.023980 AGGAACTGCACTGCACTATACTA 58.976 43.478 0.00 0.00 37.18 1.82
1288 1315 2.423538 AGGAAGCAAAATACATGGCGTC 59.576 45.455 0.00 0.00 34.66 5.19
1292 1319 4.178540 CAGCAAGGAAGCAAAATACATGG 58.821 43.478 0.00 0.00 36.85 3.66
1307 1335 4.177165 TGATGCATTTGTAACAGCAAGG 57.823 40.909 0.00 0.00 40.76 3.61
1311 1339 5.300969 TCTCTTGATGCATTTGTAACAGC 57.699 39.130 0.00 0.00 0.00 4.40
1343 1371 1.202076 GCCGCAGCTTAACATCTTGTC 60.202 52.381 0.00 0.00 35.50 3.18
1383 1419 2.032681 GACCCAGACCCACAGCAC 59.967 66.667 0.00 0.00 0.00 4.40
1453 1495 6.446781 AACAGCAGAATCATCGATCAAATT 57.553 33.333 0.00 0.00 0.00 1.82
1454 1496 6.446781 AAACAGCAGAATCATCGATCAAAT 57.553 33.333 0.00 0.00 0.00 2.32
1455 1497 5.163723 GGAAACAGCAGAATCATCGATCAAA 60.164 40.000 0.00 0.00 0.00 2.69
1456 1498 4.333649 GGAAACAGCAGAATCATCGATCAA 59.666 41.667 0.00 0.00 0.00 2.57
1521 1566 0.248843 GACCTCTCCTTGCTGACCAG 59.751 60.000 0.00 0.00 0.00 4.00
1543 1588 2.280186 GCCATAGCTTCGTCCCGG 60.280 66.667 0.00 0.00 35.50 5.73
1544 1589 1.883084 GTGCCATAGCTTCGTCCCG 60.883 63.158 0.00 0.00 40.80 5.14
1545 1590 0.811616 CTGTGCCATAGCTTCGTCCC 60.812 60.000 0.00 0.00 40.80 4.46
1546 1591 1.432270 GCTGTGCCATAGCTTCGTCC 61.432 60.000 6.15 0.00 40.80 4.79
1592 1637 0.809385 CCGTAGTCACTGGTCGTCAT 59.191 55.000 0.00 0.00 0.00 3.06
1594 1639 1.154073 GCCGTAGTCACTGGTCGTC 60.154 63.158 0.00 0.00 0.00 4.20
1597 1642 1.080025 GGTGCCGTAGTCACTGGTC 60.080 63.158 0.00 0.00 36.25 4.02
1760 1807 8.797438 CAGTTATCACATTAGCCAGACTAGATA 58.203 37.037 0.00 0.00 30.79 1.98
1762 1809 6.833933 TCAGTTATCACATTAGCCAGACTAGA 59.166 38.462 0.00 0.00 30.79 2.43
1800 1853 3.904824 CGTACTCAGTTCACGTCTACAAC 59.095 47.826 0.00 0.00 0.00 3.32
1813 1866 3.561310 TCTTTGTCACGTACGTACTCAGT 59.439 43.478 22.34 11.09 0.00 3.41
1814 1867 4.137849 TCTTTGTCACGTACGTACTCAG 57.862 45.455 22.34 16.59 0.00 3.35
2039 3750 5.643348 ACAGAAAGATTACAATCGTGCATCA 59.357 36.000 0.00 0.00 40.35 3.07
2051 3764 9.482627 CCCAACATAGATAGACAGAAAGATTAC 57.517 37.037 0.00 0.00 0.00 1.89
2371 4094 8.883731 GCAAATCACTTCTCTATTGCTACTTTA 58.116 33.333 0.00 0.00 39.87 1.85
2387 4110 3.870419 ACGCAAAAACATGCAAATCACTT 59.130 34.783 0.00 0.00 46.76 3.16
2432 4155 9.616156 ACCGATAATGGTTGTTGTACAATTATA 57.384 29.630 12.26 0.00 40.59 0.98
2590 4314 3.181475 GCATCTAGATGTCGAGGTTGGAA 60.181 47.826 28.92 0.00 40.80 3.53
2591 4315 2.362397 GCATCTAGATGTCGAGGTTGGA 59.638 50.000 28.92 0.00 40.80 3.53
2600 4324 8.694975 ATTATAATCGTGTGCATCTAGATGTC 57.305 34.615 28.92 21.91 40.80 3.06
2633 4357 6.149308 TGCGCTATTTTCCCAACATAGATATG 59.851 38.462 9.73 0.00 39.55 1.78
2634 4358 6.149474 GTGCGCTATTTTCCCAACATAGATAT 59.851 38.462 9.73 0.00 0.00 1.63
2638 4362 3.376859 TGTGCGCTATTTTCCCAACATAG 59.623 43.478 9.73 0.00 0.00 2.23
2639 4363 3.348119 TGTGCGCTATTTTCCCAACATA 58.652 40.909 9.73 0.00 0.00 2.29
2640 4364 2.166829 TGTGCGCTATTTTCCCAACAT 58.833 42.857 9.73 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.