Multiple sequence alignment - TraesCS5A01G151000

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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 TraesCS5A01G151000 chr5A 100.000 5011 0 0 1 5011 328719281 328714271 0.000000e+00 9254.0
1 TraesCS5A01G151000 chr5B 93.104 3901 165 34 1 3855 277638455 277634613 0.000000e+00 5618.0
2 TraesCS5A01G151000 chr5B 93.458 963 49 12 4054 5011 277632595 277631642 0.000000e+00 1417.0
3 TraesCS5A01G151000 chr5B 96.744 215 7 0 3842 4056 277632890 277632676 4.770000e-95 359.0
4 TraesCS5A01G151000 chr5D 93.631 2842 124 32 404 3233 244369631 244366835 0.000000e+00 4193.0
5 TraesCS5A01G151000 chr5D 94.670 863 37 7 4054 4914 244366580 244365725 0.000000e+00 1330.0
6 TraesCS5A01G151000 chr5D 97.949 195 3 1 3862 4056 244366843 244366650 2.230000e-88 337.0
7 TraesCS5A01G151000 chr5D 92.273 220 7 7 176 394 244369982 244369772 2.270000e-78 303.0
8 TraesCS5A01G151000 chr5D 88.776 196 4 4 1 178 244370257 244370062 1.820000e-54 224.0
9 TraesCS5A01G151000 chr1D 97.143 35 1 0 4963 4997 470344514 470344480 5.420000e-05 60.2


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 TraesCS5A01G151000 chr5A 328714271 328719281 5010 True 9254.000000 9254 100.000000 1 5011 1 chr5A.!!$R1 5010
1 TraesCS5A01G151000 chr5B 277631642 277638455 6813 True 2464.666667 5618 94.435333 1 5011 3 chr5B.!!$R1 5010
2 TraesCS5A01G151000 chr5D 244365725 244370257 4532 True 1277.400000 4193 93.459800 1 4914 5 chr5D.!!$R1 4913

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
932 1172 0.040067 CCTGAAAGCGGTTGTTGAGC 60.040 55.0 0.0 0.0 0.00 4.26 F
1375 1618 0.034863 GTCCAAAACCCTATCGCCCA 60.035 55.0 0.0 0.0 0.00 5.36 F
1446 1689 0.041238 TCTCCACCCACTCCTTCGAT 59.959 55.0 0.0 0.0 0.00 3.59 F
3241 3500 0.035056 GCAAGGGGCATACTCACACT 60.035 55.0 0.0 0.0 43.97 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 2037 2.303022 GGATGAGAAGACAACCTGGTCA 59.697 50.000 0.00 0.0 40.29 4.02 R
3241 3500 1.067425 ACAGATAACCACGCTTACGCA 60.067 47.619 0.00 0.0 45.53 5.24 R
3247 3506 1.134401 CCATGGACAGATAACCACGCT 60.134 52.381 5.56 0.0 39.06 5.07 R
4924 7025 0.107654 GGCCCACATGTCTAGTGACC 60.108 60.000 0.00 0.0 42.28 4.02 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
141 160 4.005650 CTGCCTAGATTTCAGTTTCAGCA 58.994 43.478 0.00 0.00 0.00 4.41
235 335 2.756760 CCTCTTGTGTTGGATGGATTGG 59.243 50.000 0.00 0.00 0.00 3.16
274 374 0.755327 AAGGCTGTGGTTGGGTGAAC 60.755 55.000 0.00 0.00 0.00 3.18
329 429 2.008329 GCTCTGCCATTGTTCTCTGAG 58.992 52.381 0.00 0.00 0.00 3.35
330 430 2.354503 GCTCTGCCATTGTTCTCTGAGA 60.355 50.000 2.58 2.58 0.00 3.27
331 431 3.260740 CTCTGCCATTGTTCTCTGAGAC 58.739 50.000 6.92 3.80 0.00 3.36
332 432 2.902486 TCTGCCATTGTTCTCTGAGACT 59.098 45.455 6.92 0.00 0.00 3.24
333 433 3.056250 TCTGCCATTGTTCTCTGAGACTC 60.056 47.826 6.92 4.62 0.00 3.36
334 434 2.902486 TGCCATTGTTCTCTGAGACTCT 59.098 45.455 6.92 0.00 0.00 3.24
335 435 3.260740 GCCATTGTTCTCTGAGACTCTG 58.739 50.000 6.92 3.34 0.00 3.35
336 436 3.056250 GCCATTGTTCTCTGAGACTCTGA 60.056 47.826 6.92 11.15 0.00 3.27
344 444 2.259875 CTGAGACTCTGACCGACCGC 62.260 65.000 3.68 0.00 0.00 5.68
350 450 2.434359 CTGACCGACCGCCTTTCC 60.434 66.667 0.00 0.00 0.00 3.13
426 661 1.326852 GCTGCTGATGATGAGTGAACG 59.673 52.381 0.00 0.00 0.00 3.95
476 711 3.833070 GGTCCTCTCTTTGTCCTTGTCTA 59.167 47.826 0.00 0.00 0.00 2.59
516 751 0.782384 CTGAACCGAGAAAACCGTCG 59.218 55.000 0.00 0.00 35.91 5.12
573 809 4.754372 TCTTAATTGACAGTGCAGCAAG 57.246 40.909 0.00 0.00 0.00 4.01
638 874 7.169308 ACGAACTATATGGACGAACATTTGATC 59.831 37.037 14.16 0.00 32.39 2.92
654 890 2.710377 TGATCTGTTGCCGTATGCTTT 58.290 42.857 0.00 0.00 42.00 3.51
655 891 3.081061 TGATCTGTTGCCGTATGCTTTT 58.919 40.909 0.00 0.00 42.00 2.27
656 892 2.987413 TCTGTTGCCGTATGCTTTTG 57.013 45.000 0.00 0.00 42.00 2.44
688 924 0.590230 TTTTTCGCTGTCGTTTGCCG 60.590 50.000 0.00 0.00 36.96 5.69
744 980 0.590195 CACAGCAAGAGAACACCAGC 59.410 55.000 0.00 0.00 0.00 4.85
760 996 1.407437 CCAGCGTTTAGATTCAGGCCT 60.407 52.381 0.00 0.00 0.00 5.19
787 1023 2.814805 AACCCTGACATGATCCTTGG 57.185 50.000 0.00 0.00 0.00 3.61
794 1030 4.082026 CCTGACATGATCCTTGGTTTTTCC 60.082 45.833 0.00 0.00 0.00 3.13
813 1049 7.495135 TTTTCCAAAATTTCTTGAAGATGGC 57.505 32.000 6.85 0.00 0.00 4.40
845 1082 9.706846 GATCTTTTTGTTTGCCATATTTTATGC 57.293 29.630 0.00 0.00 0.00 3.14
847 1084 8.719648 TCTTTTTGTTTGCCATATTTTATGCAG 58.280 29.630 0.00 0.00 34.81 4.41
848 1085 6.981762 TTTGTTTGCCATATTTTATGCAGG 57.018 33.333 0.00 0.00 34.81 4.85
849 1086 5.929058 TGTTTGCCATATTTTATGCAGGA 57.071 34.783 0.00 0.00 34.81 3.86
850 1087 5.904941 TGTTTGCCATATTTTATGCAGGAG 58.095 37.500 0.00 0.00 34.81 3.69
852 1089 6.605194 TGTTTGCCATATTTTATGCAGGAGTA 59.395 34.615 0.00 0.00 34.81 2.59
853 1090 6.633500 TTGCCATATTTTATGCAGGAGTAC 57.367 37.500 0.00 0.00 34.81 2.73
858 1098 9.014297 GCCATATTTTATGCAGGAGTACTTTAT 57.986 33.333 0.00 0.00 0.00 1.40
898 1138 4.802918 GCAGAACTGTAGAAGTAGGGCAAA 60.803 45.833 3.77 0.00 38.56 3.68
899 1139 5.491982 CAGAACTGTAGAAGTAGGGCAAAT 58.508 41.667 0.00 0.00 38.56 2.32
900 1140 6.640518 CAGAACTGTAGAAGTAGGGCAAATA 58.359 40.000 0.00 0.00 38.56 1.40
901 1141 7.275920 CAGAACTGTAGAAGTAGGGCAAATAT 58.724 38.462 0.00 0.00 38.56 1.28
902 1142 7.225538 CAGAACTGTAGAAGTAGGGCAAATATG 59.774 40.741 0.00 0.00 38.56 1.78
903 1143 5.930135 ACTGTAGAAGTAGGGCAAATATGG 58.070 41.667 0.00 0.00 37.36 2.74
904 1144 5.428783 ACTGTAGAAGTAGGGCAAATATGGT 59.571 40.000 0.00 0.00 37.36 3.55
905 1145 5.680619 TGTAGAAGTAGGGCAAATATGGTG 58.319 41.667 0.00 0.00 0.00 4.17
906 1146 4.862641 AGAAGTAGGGCAAATATGGTGT 57.137 40.909 0.00 0.00 0.00 4.16
907 1147 4.526970 AGAAGTAGGGCAAATATGGTGTG 58.473 43.478 0.00 0.00 0.00 3.82
908 1148 2.654863 AGTAGGGCAAATATGGTGTGC 58.345 47.619 0.00 0.00 37.55 4.57
909 1149 2.242196 AGTAGGGCAAATATGGTGTGCT 59.758 45.455 0.00 0.00 38.36 4.40
910 1150 1.477553 AGGGCAAATATGGTGTGCTG 58.522 50.000 0.00 0.00 38.36 4.41
911 1151 1.005805 AGGGCAAATATGGTGTGCTGA 59.994 47.619 0.00 0.00 38.36 4.26
912 1152 1.824230 GGGCAAATATGGTGTGCTGAA 59.176 47.619 0.00 0.00 38.36 3.02
913 1153 2.417243 GGGCAAATATGGTGTGCTGAAC 60.417 50.000 0.00 0.00 38.36 3.18
914 1154 2.417243 GGCAAATATGGTGTGCTGAACC 60.417 50.000 0.00 0.00 38.36 3.62
915 1155 2.493278 GCAAATATGGTGTGCTGAACCT 59.507 45.455 4.94 0.00 38.60 3.50
932 1172 0.040067 CCTGAAAGCGGTTGTTGAGC 60.040 55.000 0.00 0.00 0.00 4.26
939 1179 3.611766 AGCGGTTGTTGAGCTAGTAAT 57.388 42.857 0.00 0.00 39.74 1.89
940 1180 3.939066 AGCGGTTGTTGAGCTAGTAATT 58.061 40.909 0.00 0.00 39.74 1.40
941 1181 3.684788 AGCGGTTGTTGAGCTAGTAATTG 59.315 43.478 0.00 0.00 39.74 2.32
942 1182 3.682858 GCGGTTGTTGAGCTAGTAATTGA 59.317 43.478 0.00 0.00 0.00 2.57
943 1183 4.153475 GCGGTTGTTGAGCTAGTAATTGAA 59.847 41.667 0.00 0.00 0.00 2.69
945 1185 6.307155 CGGTTGTTGAGCTAGTAATTGAAAG 58.693 40.000 0.00 0.00 0.00 2.62
946 1186 6.147164 CGGTTGTTGAGCTAGTAATTGAAAGA 59.853 38.462 0.00 0.00 0.00 2.52
947 1187 7.522374 GGTTGTTGAGCTAGTAATTGAAAGAG 58.478 38.462 0.00 0.00 0.00 2.85
949 1189 7.004555 TGTTGAGCTAGTAATTGAAAGAGGA 57.995 36.000 0.00 0.00 0.00 3.71
950 1190 6.874134 TGTTGAGCTAGTAATTGAAAGAGGAC 59.126 38.462 0.00 0.00 0.00 3.85
952 1192 5.185249 TGAGCTAGTAATTGAAAGAGGACGT 59.815 40.000 0.00 0.00 0.00 4.34
953 1193 5.411781 AGCTAGTAATTGAAAGAGGACGTG 58.588 41.667 0.00 0.00 0.00 4.49
985 1227 1.679898 GTCCCCATCGATCCCATCC 59.320 63.158 0.00 0.00 0.00 3.51
988 1230 1.376466 CCCATCGATCCCATCCCAC 59.624 63.158 0.00 0.00 0.00 4.61
1041 1284 4.637489 CTCTCCATCTCCGGCGCG 62.637 72.222 0.00 0.00 0.00 6.86
1162 1405 0.518636 CTCCGACTACGACGACCAAA 59.481 55.000 0.00 0.00 42.66 3.28
1375 1618 0.034863 GTCCAAAACCCTATCGCCCA 60.035 55.000 0.00 0.00 0.00 5.36
1378 1621 0.944386 CAAAACCCTATCGCCCATCG 59.056 55.000 0.00 0.00 40.15 3.84
1446 1689 0.041238 TCTCCACCCACTCCTTCGAT 59.959 55.000 0.00 0.00 0.00 3.59
1653 1896 1.149174 GGTGGATGCGATGGTGGAT 59.851 57.895 0.00 0.00 0.00 3.41
1686 1929 4.711949 AGGCTGCAAGGGCTCGTG 62.712 66.667 0.50 0.00 41.91 4.35
1794 2037 2.669569 AGCAATCACCGCGTGCTT 60.670 55.556 14.60 3.99 46.25 3.91
1852 2095 5.582269 TGTTCTTAGAGTGATTACATGCAGC 59.418 40.000 0.00 0.00 0.00 5.25
1938 2181 8.506437 TCTTGCAATTTAGTCAGTAATTCAGTG 58.494 33.333 0.00 0.00 0.00 3.66
1966 2209 4.261994 GGTTTGGAGCTACATCTTGCAAAA 60.262 41.667 0.00 0.00 34.65 2.44
2001 2244 2.564553 ATCAGCTCGGAGCAACGGTC 62.565 60.000 29.88 0.61 45.56 4.79
2080 2324 7.509546 CAAGGGTGGTAGTTATTCATGTCTAT 58.490 38.462 0.00 0.00 0.00 1.98
2091 2335 9.355916 AGTTATTCATGTCTATGCAGAGTAGTA 57.644 33.333 8.44 0.00 34.21 1.82
2151 2400 5.863965 TCATTCATCACAACAGGTTCACTA 58.136 37.500 0.00 0.00 0.00 2.74
2172 2421 6.592994 CACTAGTGTAGATTATGCATGGGATG 59.407 42.308 15.06 0.00 0.00 3.51
2209 2459 7.288810 TCCTTTCAAGAGTGCATTGTTTATT 57.711 32.000 0.00 0.00 0.00 1.40
2237 2487 4.241590 TGGTTGTCAGCATTCATGAAAC 57.758 40.909 13.09 7.96 0.00 2.78
2397 2650 8.489489 TCCTTCAATCTTCTCTATGCAACTAAT 58.511 33.333 0.00 0.00 0.00 1.73
2404 2657 5.620738 TCTCTATGCAACTAATCTGCCTT 57.379 39.130 0.00 0.00 39.13 4.35
2415 2668 3.446442 AATCTGCCTTCACCAAGATGT 57.554 42.857 0.00 0.00 0.00 3.06
2523 2776 1.336755 GTTCAAGGCAAGAAAAGGCGA 59.663 47.619 0.00 0.00 36.55 5.54
2535 2788 3.437049 AGAAAAGGCGAAACATACTGAGC 59.563 43.478 0.00 0.00 0.00 4.26
2539 2792 1.009829 GCGAAACATACTGAGCTGGG 58.990 55.000 0.00 0.00 0.00 4.45
2917 3171 9.612620 GGCGGAAAATAATAATGAGAATACAAG 57.387 33.333 0.00 0.00 0.00 3.16
2937 3191 7.530426 ACAAGATCTGAAAAAGCCTTTACAT 57.470 32.000 0.00 0.00 0.00 2.29
2990 3248 1.091771 GCTATCAGTGTGCCATGCGT 61.092 55.000 0.00 0.00 0.00 5.24
3014 3272 6.267496 AGTTTTCGTATTTAGCTGGCAAAT 57.733 33.333 0.00 0.00 0.00 2.32
3059 3318 7.123997 TGTGTATTATCATGGTTTTGCCTTCAT 59.876 33.333 0.00 0.00 38.35 2.57
3093 3352 2.417933 GCTCATACACACAGAAAGCCAG 59.582 50.000 0.00 0.00 0.00 4.85
3103 3362 5.240623 CACACAGAAAGCCAGTTATAAACCA 59.759 40.000 0.00 0.00 0.00 3.67
3185 3444 3.572632 ACCTGCTATCTACTACACCGA 57.427 47.619 0.00 0.00 0.00 4.69
3241 3500 0.035056 GCAAGGGGCATACTCACACT 60.035 55.000 0.00 0.00 43.97 3.55
3247 3506 1.404986 GGGCATACTCACACTGCGTAA 60.405 52.381 0.00 0.00 36.76 3.18
3364 3623 5.505324 CCAGTTAGTACAGACTACATACGGC 60.505 48.000 0.00 0.00 37.91 5.68
3492 3760 1.135803 CCGCACCTAAACATTTGGTCG 60.136 52.381 0.00 2.30 30.72 4.79
3493 3761 1.801771 CGCACCTAAACATTTGGTCGA 59.198 47.619 8.56 0.00 31.30 4.20
3494 3762 2.412325 CGCACCTAAACATTTGGTCGAC 60.412 50.000 7.13 7.13 31.30 4.20
3495 3763 2.550606 GCACCTAAACATTTGGTCGACA 59.449 45.455 18.91 0.27 30.72 4.35
3496 3764 3.364964 GCACCTAAACATTTGGTCGACAG 60.365 47.826 18.91 2.22 30.72 3.51
3497 3765 3.188460 CACCTAAACATTTGGTCGACAGG 59.812 47.826 18.91 13.97 30.72 4.00
3498 3766 2.161609 CCTAAACATTTGGTCGACAGGC 59.838 50.000 18.91 0.00 0.00 4.85
3531 3799 2.327325 TCTGGGTCCAGAGCTAGTTT 57.673 50.000 15.14 0.00 46.80 2.66
3587 3855 3.256631 ACATGAGGTGAGAACAAAATGGC 59.743 43.478 0.00 0.00 0.00 4.40
3654 3928 2.960819 AGGCGCTACTGTTCTTACTTG 58.039 47.619 7.64 0.00 0.00 3.16
3687 3961 0.382515 GTACTAGAGGTGCAGGCGAG 59.617 60.000 0.00 0.00 0.00 5.03
3724 3998 4.706476 CAGAACAATGGGAATTTAGCCTCA 59.294 41.667 0.00 0.00 0.00 3.86
3726 4000 4.322057 ACAATGGGAATTTAGCCTCACT 57.678 40.909 0.00 0.00 0.00 3.41
3745 4019 3.951680 CACTAAGGTGGTGGTCTTTTGTT 59.048 43.478 0.00 0.00 39.59 2.83
3766 4040 6.096695 TGTTGTTTGAGGTCTTAAAAACTGC 58.903 36.000 0.00 0.00 34.39 4.40
3814 4088 3.228188 TGTTGTTGGAATGCCTTCTCT 57.772 42.857 1.62 0.00 34.31 3.10
3818 4092 2.290514 TGTTGGAATGCCTTCTCTCTGG 60.291 50.000 1.62 0.00 34.31 3.86
3823 4097 3.136260 GGAATGCCTTCTCTCTGGAAGAT 59.864 47.826 5.89 0.00 45.62 2.40
3860 5870 5.733937 GCGTCAAAAAGTTTAAGCCTTGGTA 60.734 40.000 0.00 0.00 0.00 3.25
4086 6183 6.015603 ACCTACTTCTGTTACAGTAGTTGACC 60.016 42.308 25.12 0.00 38.59 4.02
4116 6213 4.163441 TCTGAGACATCCAGAGTCTAGG 57.837 50.000 0.00 0.00 45.79 3.02
4206 6304 3.063180 GTCTCGAGATTCCAGCACATTTG 59.937 47.826 19.90 0.00 0.00 2.32
4215 6313 1.739466 CCAGCACATTTGATAGCGTGT 59.261 47.619 0.00 0.00 0.00 4.49
4320 6419 3.741344 GGCGCTTGTGTATTCTCGATTAT 59.259 43.478 7.64 0.00 0.00 1.28
4321 6420 4.376413 GGCGCTTGTGTATTCTCGATTATG 60.376 45.833 7.64 0.00 0.00 1.90
4569 6669 0.383491 CAAAGTGCAGCGTTGAGTCG 60.383 55.000 2.38 0.00 38.55 4.18
4603 6703 3.557595 GTGATGCTCCTCCTATTCGTTTG 59.442 47.826 0.00 0.00 0.00 2.93
4606 6707 2.194271 GCTCCTCCTATTCGTTTGTCG 58.806 52.381 0.00 0.00 41.41 4.35
4615 6716 0.931702 TTCGTTTGTCGTGCGATTGT 59.068 45.000 0.00 0.00 40.80 2.71
4618 6719 0.316607 GTTTGTCGTGCGATTGTGCA 60.317 50.000 0.00 0.00 43.95 4.57
4707 6808 6.206395 TGTGATGGCGATTATGATTTGTTT 57.794 33.333 0.00 0.00 0.00 2.83
4754 6855 6.756074 TGATGATTTGTTGACTTGTGGTTTTC 59.244 34.615 0.00 0.00 0.00 2.29
4780 6881 1.801178 CACCGTTTCCTTCTTCAGAGC 59.199 52.381 0.00 0.00 0.00 4.09
4788 6889 0.327591 CTTCTTCAGAGCTGGCCCTT 59.672 55.000 0.00 0.00 0.00 3.95
4836 6937 0.036765 GTAATGACGTGGTGGCCTCA 60.037 55.000 3.32 0.00 0.00 3.86
4924 7025 9.807386 CTGACTTTAAACGTAAGATAACTTTGG 57.193 33.333 3.62 0.00 43.62 3.28
4931 7032 6.594788 ACGTAAGATAACTTTGGGTCACTA 57.405 37.500 0.00 0.00 43.62 2.74
4950 7051 0.612732 AGACATGTGGGCCCAACATG 60.613 55.000 38.53 38.53 44.71 3.21
4951 7052 2.229690 GACATGTGGGCCCAACATGC 62.230 60.000 39.30 32.36 43.45 4.06
4978 7079 0.815615 CCTAAGGGCATCTCCAACGC 60.816 60.000 0.00 0.00 36.21 4.84
4981 7082 2.825836 GGGCATCTCCAACGCTGG 60.826 66.667 0.00 0.00 45.08 4.85
4984 7085 2.270205 CATCTCCAACGCTGGCCT 59.730 61.111 3.32 0.00 43.17 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 109 5.527582 CAGTAATGTAGGTTGGATGTTAGCC 59.472 44.000 0.00 0.00 0.00 3.93
141 160 7.041098 ACAGCGAGAAAATCAAGTGATAAAACT 60.041 33.333 0.00 0.00 33.73 2.66
235 335 2.047274 TTGTAGCGCTCCACCTGC 60.047 61.111 16.34 0.00 0.00 4.85
274 374 2.283298 CCGATTGACTTCATCCCTGTG 58.717 52.381 0.00 0.00 0.00 3.66
329 429 2.156051 AAAGGCGGTCGGTCAGAGTC 62.156 60.000 0.00 0.00 0.00 3.36
330 430 2.156051 GAAAGGCGGTCGGTCAGAGT 62.156 60.000 0.00 0.00 0.00 3.24
331 431 1.446272 GAAAGGCGGTCGGTCAGAG 60.446 63.158 0.00 0.00 0.00 3.35
332 432 2.654877 GAAAGGCGGTCGGTCAGA 59.345 61.111 0.00 0.00 0.00 3.27
333 433 2.434359 GGAAAGGCGGTCGGTCAG 60.434 66.667 0.00 0.00 0.00 3.51
334 434 4.011517 GGGAAAGGCGGTCGGTCA 62.012 66.667 0.00 0.00 0.00 4.02
335 435 4.772687 GGGGAAAGGCGGTCGGTC 62.773 72.222 0.00 0.00 0.00 4.79
344 444 2.500098 TGTCAAGTAGATCGGGGAAAGG 59.500 50.000 0.00 0.00 0.00 3.11
350 450 1.065701 CGGAGTGTCAAGTAGATCGGG 59.934 57.143 0.00 0.00 0.00 5.14
413 648 1.470098 GCTTTGCCGTTCACTCATCAT 59.530 47.619 0.00 0.00 0.00 2.45
426 661 3.381045 GGTCTTAACAGTTTGCTTTGCC 58.619 45.455 0.00 0.00 0.00 4.52
476 711 2.174360 GAGGCAAGGGCTTCTGAATTT 58.826 47.619 0.00 0.00 42.43 1.82
516 751 2.673833 ACGAGAAATTGGACAGTCGTC 58.326 47.619 0.00 0.00 35.89 4.20
573 809 6.005583 TCAGTTCAGTTTCAAATCAGATGC 57.994 37.500 0.00 0.00 0.00 3.91
654 890 5.341993 CAGCGAAAAACGATCATAAAAGCAA 59.658 36.000 0.00 0.00 45.77 3.91
655 891 4.851014 CAGCGAAAAACGATCATAAAAGCA 59.149 37.500 0.00 0.00 45.77 3.91
656 892 4.851558 ACAGCGAAAAACGATCATAAAAGC 59.148 37.500 0.00 0.00 45.77 3.51
657 893 5.223094 CGACAGCGAAAAACGATCATAAAAG 59.777 40.000 0.00 0.00 45.77 2.27
658 894 5.076765 CGACAGCGAAAAACGATCATAAAA 58.923 37.500 0.00 0.00 45.77 1.52
659 895 4.150980 ACGACAGCGAAAAACGATCATAAA 59.849 37.500 0.00 0.00 45.77 1.40
660 896 3.676172 ACGACAGCGAAAAACGATCATAA 59.324 39.130 0.00 0.00 45.77 1.90
661 897 3.247442 ACGACAGCGAAAAACGATCATA 58.753 40.909 0.00 0.00 45.77 2.15
688 924 4.335594 AGTTGCTTCAGTAAACAACAGGAC 59.664 41.667 7.39 0.00 43.74 3.85
744 980 1.017387 GCCAGGCCTGAATCTAAACG 58.983 55.000 34.91 14.69 0.00 3.60
769 1005 1.673767 ACCAAGGATCATGTCAGGGT 58.326 50.000 0.00 0.00 0.00 4.34
787 1023 7.857389 GCCATCTTCAAGAAATTTTGGAAAAAC 59.143 33.333 8.01 0.00 0.00 2.43
813 1049 8.767478 ATATGGCAAACAAAAAGATCTTGAAG 57.233 30.769 9.17 4.32 0.00 3.02
819 1055 9.706846 GCATAAAATATGGCAAACAAAAAGATC 57.293 29.630 0.00 0.00 0.00 2.75
821 1057 8.613060 TGCATAAAATATGGCAAACAAAAAGA 57.387 26.923 0.00 0.00 32.54 2.52
822 1058 7.964011 CCTGCATAAAATATGGCAAACAAAAAG 59.036 33.333 0.00 0.00 35.59 2.27
828 1065 5.906073 ACTCCTGCATAAAATATGGCAAAC 58.094 37.500 0.00 0.00 35.59 2.93
858 1098 8.614346 ACAGTTCTGCTACAATTTTACGTTTTA 58.386 29.630 0.00 0.00 0.00 1.52
875 1115 2.233922 TGCCCTACTTCTACAGTTCTGC 59.766 50.000 0.00 0.00 36.88 4.26
876 1116 4.537135 TTGCCCTACTTCTACAGTTCTG 57.463 45.455 0.00 0.00 36.88 3.02
898 1138 3.719268 TTCAGGTTCAGCACACCATAT 57.281 42.857 2.20 0.00 36.67 1.78
899 1139 3.411446 CTTTCAGGTTCAGCACACCATA 58.589 45.455 2.20 0.00 36.67 2.74
900 1140 2.233271 CTTTCAGGTTCAGCACACCAT 58.767 47.619 2.20 0.00 36.67 3.55
901 1141 1.679139 CTTTCAGGTTCAGCACACCA 58.321 50.000 2.20 0.00 36.67 4.17
902 1142 0.312102 GCTTTCAGGTTCAGCACACC 59.688 55.000 0.00 0.00 33.45 4.16
903 1143 0.040958 CGCTTTCAGGTTCAGCACAC 60.041 55.000 0.00 0.00 32.71 3.82
904 1144 1.165907 CCGCTTTCAGGTTCAGCACA 61.166 55.000 0.00 0.00 32.71 4.57
905 1145 1.166531 ACCGCTTTCAGGTTCAGCAC 61.167 55.000 0.00 0.00 39.29 4.40
906 1146 1.148273 ACCGCTTTCAGGTTCAGCA 59.852 52.632 0.00 0.00 39.29 4.41
907 1147 4.065110 ACCGCTTTCAGGTTCAGC 57.935 55.556 0.00 0.00 39.29 4.26
912 1152 1.308998 CTCAACAACCGCTTTCAGGT 58.691 50.000 0.00 0.00 45.29 4.00
913 1153 0.040067 GCTCAACAACCGCTTTCAGG 60.040 55.000 0.00 0.00 0.00 3.86
914 1154 0.947244 AGCTCAACAACCGCTTTCAG 59.053 50.000 0.00 0.00 0.00 3.02
915 1155 2.143122 CTAGCTCAACAACCGCTTTCA 58.857 47.619 0.00 0.00 35.33 2.69
932 1172 5.289675 CAGCACGTCCTCTTTCAATTACTAG 59.710 44.000 0.00 0.00 0.00 2.57
939 1179 1.540363 GGTCAGCACGTCCTCTTTCAA 60.540 52.381 0.00 0.00 0.00 2.69
940 1180 0.033504 GGTCAGCACGTCCTCTTTCA 59.966 55.000 0.00 0.00 0.00 2.69
941 1181 0.318762 AGGTCAGCACGTCCTCTTTC 59.681 55.000 0.00 0.00 0.00 2.62
942 1182 0.759346 AAGGTCAGCACGTCCTCTTT 59.241 50.000 0.00 0.00 31.16 2.52
943 1183 0.759346 AAAGGTCAGCACGTCCTCTT 59.241 50.000 0.00 0.00 31.16 2.85
945 1185 1.000506 TGTAAAGGTCAGCACGTCCTC 59.999 52.381 0.00 0.00 31.16 3.71
946 1186 1.045407 TGTAAAGGTCAGCACGTCCT 58.955 50.000 0.00 0.00 34.21 3.85
947 1187 1.145803 GTGTAAAGGTCAGCACGTCC 58.854 55.000 0.00 0.00 0.00 4.79
949 1189 2.895039 CGTGTAAAGGTCAGCACGT 58.105 52.632 7.63 0.00 46.30 4.49
952 1192 0.034337 GGGACGTGTAAAGGTCAGCA 59.966 55.000 7.98 0.00 34.87 4.41
953 1193 0.672711 GGGGACGTGTAAAGGTCAGC 60.673 60.000 7.98 0.00 34.87 4.26
985 1227 2.359850 CATCGGTGGGTGTGGTGG 60.360 66.667 0.00 0.00 0.00 4.61
1378 1621 4.475135 GAAGAGGAGCGGGTGGGC 62.475 72.222 0.00 0.00 0.00 5.36
1446 1689 1.217244 GAGGAGGAAAGCGCGGTAA 59.783 57.895 12.91 0.00 0.00 2.85
1479 1722 3.371063 GTGAGCGAGGTCGGGACA 61.371 66.667 0.89 0.00 40.23 4.02
1638 1881 1.601759 CCCATCCACCATCGCATCC 60.602 63.158 0.00 0.00 0.00 3.51
1653 1896 3.589542 CTCCCCAGCCCAAACCCA 61.590 66.667 0.00 0.00 0.00 4.51
1794 2037 2.303022 GGATGAGAAGACAACCTGGTCA 59.697 50.000 0.00 0.00 40.29 4.02
1852 2095 3.220773 CGCAATAGCTCGTAAATGCATG 58.779 45.455 0.00 0.00 39.10 4.06
1938 2181 3.412386 AGATGTAGCTCCAAACCAACAC 58.588 45.455 0.00 0.00 0.00 3.32
1966 2209 7.012327 TCCGAGCTGATCATTTTCGATTAAAAT 59.988 33.333 19.20 0.00 46.48 1.82
2080 2324 7.566569 ACTAGTTCTCTACATACTACTCTGCA 58.433 38.462 0.00 0.00 0.00 4.41
2091 2335 6.892456 TGACCAGAATGACTAGTTCTCTACAT 59.108 38.462 0.00 0.00 39.69 2.29
2151 2400 5.072193 TCACATCCCATGCATAATCTACACT 59.928 40.000 0.00 0.00 0.00 3.55
2209 2459 4.143543 TGAATGCTGACAACCAATTGAGA 58.856 39.130 7.12 0.00 39.30 3.27
2237 2487 9.897744 TTACATGAAAAATACTCTTGAAAGCTG 57.102 29.630 0.00 0.00 0.00 4.24
2351 2601 4.169856 AGGAGATAGACTGAGGGAGTGATT 59.830 45.833 0.00 0.00 33.83 2.57
2397 2650 2.886523 CAAACATCTTGGTGAAGGCAGA 59.113 45.455 0.00 0.00 0.00 4.26
2404 2657 5.323581 TCATGGAATCAAACATCTTGGTGA 58.676 37.500 0.00 0.00 0.00 4.02
2523 2776 3.562176 CCTTTCCCCAGCTCAGTATGTTT 60.562 47.826 0.00 0.00 37.40 2.83
2535 2788 3.704566 GGCTTTATAAACCCTTTCCCCAG 59.295 47.826 2.73 0.00 0.00 4.45
2539 2792 3.704566 CCCTGGCTTTATAAACCCTTTCC 59.295 47.826 10.28 0.12 0.00 3.13
2884 3138 7.771361 TCTCATTATTATTTTCCGCCACAAGTA 59.229 33.333 0.00 0.00 0.00 2.24
2917 3171 7.329471 GGTTTCATGTAAAGGCTTTTTCAGATC 59.671 37.037 18.93 8.05 28.95 2.75
2937 3191 9.296400 CTTTCTTCATTTTACTTTTCGGTTTCA 57.704 29.630 0.00 0.00 0.00 2.69
2990 3248 6.804770 TTTGCCAGCTAAATACGAAAACTA 57.195 33.333 0.00 0.00 0.00 2.24
3014 3272 1.635487 CATCCTCTCTTTGGGGGTGAA 59.365 52.381 0.00 0.00 33.39 3.18
3185 3444 3.055819 TCGCTCAATCTTGGACTAAAGCT 60.056 43.478 0.00 0.00 0.00 3.74
3241 3500 1.067425 ACAGATAACCACGCTTACGCA 60.067 47.619 0.00 0.00 45.53 5.24
3247 3506 1.134401 CCATGGACAGATAACCACGCT 60.134 52.381 5.56 0.00 39.06 5.07
3587 3855 5.057149 CCCATAATTGTCTCTTAACCTCCG 58.943 45.833 0.00 0.00 0.00 4.63
3654 3928 1.751924 CTAGTACTGACTCCCACCAGC 59.248 57.143 5.39 0.00 37.10 4.85
3687 3961 4.320608 TTGTTCTGCTCAATGGAAAACC 57.679 40.909 0.00 0.00 0.00 3.27
3724 3998 3.945640 ACAAAAGACCACCACCTTAGT 57.054 42.857 0.00 0.00 0.00 2.24
3726 4000 3.970842 ACAACAAAAGACCACCACCTTA 58.029 40.909 0.00 0.00 0.00 2.69
3737 4011 9.198837 GTTTTTAAGACCTCAAACAACAAAAGA 57.801 29.630 0.00 0.00 0.00 2.52
3745 4019 4.707448 TGGCAGTTTTTAAGACCTCAAACA 59.293 37.500 0.00 0.00 32.52 2.83
3766 4040 4.713824 ATGAAAGATCATGCACTTGTGG 57.286 40.909 2.81 0.00 44.63 4.17
3814 4088 4.624843 GCAACAGAGGATTGATCTTCCAGA 60.625 45.833 15.06 0.00 33.81 3.86
3818 4092 3.265791 ACGCAACAGAGGATTGATCTTC 58.734 45.455 0.00 0.00 33.54 2.87
3823 4097 2.542020 TTGACGCAACAGAGGATTGA 57.458 45.000 0.00 0.00 0.00 2.57
3860 5870 3.245407 CCAAATCCTCTCACTTCCCCTTT 60.245 47.826 0.00 0.00 0.00 3.11
3975 5985 1.376424 CCGCTGTCTTGCACCTCAT 60.376 57.895 0.00 0.00 0.00 2.90
4086 6183 2.169978 TGGATGTCTCAGAGCAGAATGG 59.830 50.000 0.00 0.00 35.86 3.16
4110 6207 4.654262 TCATCAATTAGTCACCCCCTAGAC 59.346 45.833 0.00 0.00 35.02 2.59
4115 6212 4.713792 AGATCATCAATTAGTCACCCCC 57.286 45.455 0.00 0.00 0.00 5.40
4116 6213 5.684704 TCAAGATCATCAATTAGTCACCCC 58.315 41.667 0.00 0.00 0.00 4.95
4206 6304 3.927142 AGTTGCAGAACTAACACGCTATC 59.073 43.478 0.00 0.00 40.85 2.08
4215 6313 8.564574 CAAAGTACCAAATAGTTGCAGAACTAA 58.435 33.333 2.47 0.00 45.69 2.24
4320 6419 6.247229 AGGCTGGTTGATATGTTATACACA 57.753 37.500 0.00 0.00 40.71 3.72
4321 6420 7.878127 ACATAGGCTGGTTGATATGTTATACAC 59.122 37.037 0.00 0.00 35.81 2.90
4448 6547 4.627611 CATTACTCCAATGGCTGAACTG 57.372 45.455 0.00 0.00 40.41 3.16
4528 6627 2.227388 CCAGCACCATCAGTTTCTGAAC 59.773 50.000 3.58 0.00 44.04 3.18
4569 6669 0.944311 AGCATCACAACGACGACCAC 60.944 55.000 0.00 0.00 0.00 4.16
4603 6703 1.130613 GTCTGCACAATCGCACGAC 59.869 57.895 0.00 0.00 36.86 4.34
4606 6707 0.441533 CTCAGTCTGCACAATCGCAC 59.558 55.000 0.00 0.00 36.86 5.34
4615 6716 4.983671 ATACATTACGACTCAGTCTGCA 57.016 40.909 2.61 0.00 0.00 4.41
4618 6719 7.827701 TGAAGAAATACATTACGACTCAGTCT 58.172 34.615 2.61 0.00 0.00 3.24
4754 6855 0.977395 AGAAGGAAACGGTGGAGAGG 59.023 55.000 0.00 0.00 0.00 3.69
4795 6896 4.957954 ACATTATCACCATCAATTGCCTGT 59.042 37.500 0.00 0.00 0.00 4.00
4836 6937 0.811616 GAGCGAGATTGCCCGTGAAT 60.812 55.000 0.00 0.00 34.65 2.57
4909 7010 6.750963 GTCTAGTGACCCAAAGTTATCTTACG 59.249 42.308 0.00 0.00 37.24 3.18
4924 7025 0.107654 GGCCCACATGTCTAGTGACC 60.108 60.000 0.00 0.00 42.28 4.02
4931 7032 0.612732 CATGTTGGGCCCACATGTCT 60.613 55.000 35.49 19.09 37.17 3.41


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

AutoCloner maintained by Alex Coulton.