Multiple sequence alignment - TraesCS1A01G402600

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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 TraesCS1A01G402600 chr1A 100.000 2186 0 0 1 2186 566122959 566125144 0.000000e+00 4037.0
1 TraesCS1A01G402600 chr1D 86.887 2242 151 67 1 2185 471847984 471850139 0.000000e+00 2379.0
2 TraesCS1A01G402600 chr1B 87.015 1417 102 35 812 2182 655858473 655859853 0.000000e+00 1522.0
3 TraesCS1A01G402600 chr1B 84.125 800 40 23 1 781 655857740 655858471 0.000000e+00 693.0
4 TraesCS1A01G402600 chr1B 88.235 51 6 0 1 51 655857070 655857120 6.520000e-06 62.1
5 TraesCS1A01G402600 chr2A 79.048 630 58 38 811 1411 457221460 457222044 4.430000e-97 364.0
6 TraesCS1A01G402600 chr2A 87.209 86 8 1 615 697 457221193 457221278 6.420000e-16 95.3
7 TraesCS1A01G402600 chr2B 78.155 206 22 9 615 799 410942382 410942585 2.290000e-20 110.0
8 TraesCS1A01G402600 chr2D 77.143 210 30 10 615 811 345247643 345247847 2.970000e-19 106.0


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 TraesCS1A01G402600 chr1A 566122959 566125144 2185 False 4037.000000 4037 100.000000 1 2186 1 chr1A.!!$F1 2185
1 TraesCS1A01G402600 chr1D 471847984 471850139 2155 False 2379.000000 2379 86.887000 1 2185 1 chr1D.!!$F1 2184
2 TraesCS1A01G402600 chr1B 655857070 655859853 2783 False 759.033333 1522 86.458333 1 2182 3 chr1B.!!$F1 2181
3 TraesCS1A01G402600 chr2A 457221193 457222044 851 False 229.650000 364 83.128500 615 1411 2 chr2A.!!$F1 796

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
291 978 0.109039 GACCAGAGGAAGAGTCGCAC 60.109 60.0 0.0 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 2748 0.252197 TCATCCTCCGACGACTCTGA 59.748 55.0 0.0 0.0 0.0 3.27 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
130 802 3.684788 AGGACTCGTTCATGTTTATGTGC 59.315 43.478 0.00 0.00 35.73 4.57
140 812 2.627945 TGTTTATGTGCCGTCAGATCC 58.372 47.619 0.00 0.00 0.00 3.36
182 854 1.152943 TCTCCGACCTCCGATCCAG 60.153 63.158 0.00 0.00 41.76 3.86
221 893 3.333189 CGATCAGCGGACCATGCG 61.333 66.667 0.00 0.00 37.44 4.73
223 895 1.067416 GATCAGCGGACCATGCGTA 59.933 57.895 0.00 0.00 37.44 4.42
225 897 1.676678 ATCAGCGGACCATGCGTAGT 61.677 55.000 0.00 0.00 37.44 2.73
227 899 0.870307 CAGCGGACCATGCGTAGTAC 60.870 60.000 0.00 0.00 37.44 2.73
229 901 0.179119 GCGGACCATGCGTAGTACTT 60.179 55.000 0.00 0.00 32.35 2.24
230 902 1.556564 CGGACCATGCGTAGTACTTG 58.443 55.000 0.00 0.00 0.00 3.16
231 903 1.801395 CGGACCATGCGTAGTACTTGG 60.801 57.143 0.00 4.67 38.11 3.61
232 904 1.206371 GGACCATGCGTAGTACTTGGT 59.794 52.381 14.67 14.67 45.38 3.67
237 924 3.439293 CATGCGTAGTACTTGGTCTGAG 58.561 50.000 0.00 0.00 0.00 3.35
274 961 1.656095 GACACGTAGCAAGCATCAGAC 59.344 52.381 0.00 0.00 0.00 3.51
275 962 1.002366 CACGTAGCAAGCATCAGACC 58.998 55.000 0.00 0.00 0.00 3.85
276 963 0.608130 ACGTAGCAAGCATCAGACCA 59.392 50.000 0.00 0.00 0.00 4.02
277 964 1.284657 CGTAGCAAGCATCAGACCAG 58.715 55.000 0.00 0.00 0.00 4.00
278 965 1.134995 CGTAGCAAGCATCAGACCAGA 60.135 52.381 0.00 0.00 0.00 3.86
291 978 0.109039 GACCAGAGGAAGAGTCGCAC 60.109 60.000 0.00 0.00 0.00 5.34
298 985 1.141053 AGGAAGAGTCGCACAAACCTT 59.859 47.619 0.00 0.00 0.00 3.50
308 995 2.348218 CGCACAAACCTTCACTAACGTC 60.348 50.000 0.00 0.00 0.00 4.34
309 996 2.610374 GCACAAACCTTCACTAACGTCA 59.390 45.455 0.00 0.00 0.00 4.35
324 1012 1.888512 ACGTCAAAGGAATGCATGCTT 59.111 42.857 20.33 10.16 42.14 3.91
326 1014 3.243839 ACGTCAAAGGAATGCATGCTTTT 60.244 39.130 20.33 8.94 46.25 2.27
327 1015 3.122278 CGTCAAAGGAATGCATGCTTTTG 59.878 43.478 28.24 28.24 46.25 2.44
328 1016 4.309099 GTCAAAGGAATGCATGCTTTTGA 58.691 39.130 31.11 31.11 46.25 2.69
329 1017 4.751098 GTCAAAGGAATGCATGCTTTTGAA 59.249 37.500 34.43 21.43 46.25 2.69
330 1018 4.992319 TCAAAGGAATGCATGCTTTTGAAG 59.008 37.500 32.11 14.71 46.25 3.02
348 1036 5.514274 TGAAGTTTGAACCCTGAATTCAC 57.486 39.130 3.38 0.00 35.82 3.18
355 1043 3.948473 TGAACCCTGAATTCACGTCAAAA 59.052 39.130 3.38 0.00 31.11 2.44
357 1045 2.884639 ACCCTGAATTCACGTCAAAAGG 59.115 45.455 3.38 1.53 0.00 3.11
360 1048 4.320494 CCCTGAATTCACGTCAAAAGGAAG 60.320 45.833 3.38 0.00 0.00 3.46
361 1049 4.222114 CTGAATTCACGTCAAAAGGAAGC 58.778 43.478 3.38 0.00 0.00 3.86
370 1064 2.610374 GTCAAAAGGAAGCACACGTACA 59.390 45.455 0.00 0.00 0.00 2.90
384 1078 8.667987 AGCACACGTACAAATATTATTTGTTG 57.332 30.769 29.87 24.82 42.10 3.33
395 1089 7.961326 AATATTATTTGTTGGACAGGAAGCT 57.039 32.000 0.00 0.00 0.00 3.74
396 1090 5.649782 ATTATTTGTTGGACAGGAAGCTG 57.350 39.130 0.00 0.00 0.00 4.24
397 1091 1.691196 TTTGTTGGACAGGAAGCTGG 58.309 50.000 0.00 0.00 0.00 4.85
398 1092 0.843309 TTGTTGGACAGGAAGCTGGA 59.157 50.000 0.00 0.00 0.00 3.86
399 1093 0.843309 TGTTGGACAGGAAGCTGGAA 59.157 50.000 0.00 0.00 0.00 3.53
400 1094 1.425066 TGTTGGACAGGAAGCTGGAAT 59.575 47.619 0.00 0.00 0.00 3.01
401 1095 2.158475 TGTTGGACAGGAAGCTGGAATT 60.158 45.455 0.00 0.00 0.00 2.17
402 1096 2.489722 GTTGGACAGGAAGCTGGAATTC 59.510 50.000 0.00 0.00 0.00 2.17
403 1097 1.004745 TGGACAGGAAGCTGGAATTCC 59.995 52.381 18.17 18.17 45.56 3.01
408 1102 1.946745 GGAAGCTGGAATTCCTCGAG 58.053 55.000 24.73 15.01 42.52 4.04
409 1103 1.208293 GGAAGCTGGAATTCCTCGAGT 59.792 52.381 24.73 6.97 42.52 4.18
410 1104 2.431057 GGAAGCTGGAATTCCTCGAGTA 59.569 50.000 24.73 2.90 42.52 2.59
411 1105 3.449632 GAAGCTGGAATTCCTCGAGTAC 58.550 50.000 24.73 7.33 36.82 2.73
412 1106 2.457598 AGCTGGAATTCCTCGAGTACA 58.542 47.619 24.73 0.00 36.82 2.90
413 1107 2.832129 AGCTGGAATTCCTCGAGTACAA 59.168 45.455 24.73 1.32 36.82 2.41
414 1108 3.118956 AGCTGGAATTCCTCGAGTACAAG 60.119 47.826 24.73 11.53 36.82 3.16
429 1123 2.936032 AAGGGGCTGGTCCTGGTC 60.936 66.667 0.00 0.00 34.34 4.02
432 1126 4.394712 GGGCTGGTCCTGGTCGTG 62.395 72.222 0.00 0.00 34.39 4.35
457 1159 4.267349 AGCGTCCTTGTTAATGTAGTGT 57.733 40.909 0.00 0.00 0.00 3.55
458 1160 5.395682 AGCGTCCTTGTTAATGTAGTGTA 57.604 39.130 0.00 0.00 0.00 2.90
459 1161 5.408356 AGCGTCCTTGTTAATGTAGTGTAG 58.592 41.667 0.00 0.00 0.00 2.74
460 1162 4.032558 GCGTCCTTGTTAATGTAGTGTAGC 59.967 45.833 0.00 0.00 0.00 3.58
461 1163 4.565564 CGTCCTTGTTAATGTAGTGTAGCC 59.434 45.833 0.00 0.00 0.00 3.93
495 1197 2.946990 TCATCGATCACTTGCCGTACTA 59.053 45.455 0.00 0.00 0.00 1.82
496 1198 2.838386 TCGATCACTTGCCGTACTAC 57.162 50.000 0.00 0.00 0.00 2.73
497 1199 2.362736 TCGATCACTTGCCGTACTACT 58.637 47.619 0.00 0.00 0.00 2.57
562 1264 7.987458 TCCTGTGTATAGAATTCCAATCAGAAC 59.013 37.037 0.65 0.00 0.00 3.01
581 1283 5.239744 CAGAACACATATACTAGAGGTCGCT 59.760 44.000 0.00 0.00 0.00 4.93
582 1284 5.239744 AGAACACATATACTAGAGGTCGCTG 59.760 44.000 0.00 0.00 0.00 5.18
616 1318 1.717194 TCGTCCTTGTTAACCGATGC 58.283 50.000 2.48 0.00 0.00 3.91
781 1516 2.895372 CCATTCTACACGGCCGGC 60.895 66.667 31.76 21.18 0.00 6.13
783 1518 3.395702 ATTCTACACGGCCGGCCA 61.396 61.111 42.78 24.32 35.37 5.36
784 1519 2.961893 ATTCTACACGGCCGGCCAA 61.962 57.895 42.78 29.01 35.37 4.52
786 1521 3.202001 CTACACGGCCGGCCAATG 61.202 66.667 42.78 38.16 35.37 2.82
803 1538 3.118454 GCACCACACGTATGCGCT 61.118 61.111 9.73 0.00 42.83 5.92
820 1604 5.342806 TGCGCTTGCATGTCTATATAAAC 57.657 39.130 9.73 0.00 45.56 2.01
826 1610 5.147330 TGCATGTCTATATAAACCCGAGG 57.853 43.478 0.00 0.00 0.00 4.63
839 1623 1.529948 CCGAGGCCCATCATGCAAT 60.530 57.895 0.00 0.00 0.00 3.56
858 1643 5.721000 TGCAATTCTACCCATCTCCATTTTT 59.279 36.000 0.00 0.00 0.00 1.94
861 1646 7.428826 CAATTCTACCCATCTCCATTTTTAGC 58.571 38.462 0.00 0.00 0.00 3.09
863 1648 5.684704 TCTACCCATCTCCATTTTTAGCAG 58.315 41.667 0.00 0.00 0.00 4.24
866 1653 5.332743 ACCCATCTCCATTTTTAGCAGAAA 58.667 37.500 0.00 0.00 0.00 2.52
883 1670 3.629398 CAGAAACAAACCAAGCTCTCACT 59.371 43.478 0.00 0.00 0.00 3.41
884 1671 4.096984 CAGAAACAAACCAAGCTCTCACTT 59.903 41.667 0.00 0.00 0.00 3.16
885 1672 5.296780 CAGAAACAAACCAAGCTCTCACTTA 59.703 40.000 0.00 0.00 0.00 2.24
886 1673 5.529060 AGAAACAAACCAAGCTCTCACTTAG 59.471 40.000 0.00 0.00 0.00 2.18
887 1674 4.689612 ACAAACCAAGCTCTCACTTAGA 57.310 40.909 0.00 0.00 0.00 2.10
888 1675 5.234466 ACAAACCAAGCTCTCACTTAGAT 57.766 39.130 0.00 0.00 32.41 1.98
889 1676 5.241662 ACAAACCAAGCTCTCACTTAGATC 58.758 41.667 0.00 0.00 32.41 2.75
890 1677 5.221722 ACAAACCAAGCTCTCACTTAGATCA 60.222 40.000 0.00 0.00 32.41 2.92
891 1678 4.734398 ACCAAGCTCTCACTTAGATCAG 57.266 45.455 0.00 0.00 32.41 2.90
892 1679 4.348486 ACCAAGCTCTCACTTAGATCAGA 58.652 43.478 0.00 0.00 32.41 3.27
893 1680 4.774726 ACCAAGCTCTCACTTAGATCAGAA 59.225 41.667 0.00 0.00 32.41 3.02
920 1707 1.003233 AAGCTCGGAACCTGAAGCC 60.003 57.895 0.00 0.00 0.00 4.35
971 1765 4.275443 CCTTCCTAGATCAAAATCTGCTGC 59.725 45.833 0.00 0.00 42.36 5.25
981 1775 1.548357 AATCTGCTGCACGTCTCCCT 61.548 55.000 0.00 0.00 0.00 4.20
994 1793 2.032528 TCCCTTCTGGCGCAACAG 59.967 61.111 10.83 8.74 39.84 3.16
1060 1871 1.154599 GTGCACATGTTCAGCGTCG 60.155 57.895 13.17 0.00 0.00 5.12
1141 1952 3.112205 ATGGTGGCGGAGATGCTCC 62.112 63.158 3.36 3.36 46.44 4.70
1216 2028 2.269978 GCAACACCATGCATCACCT 58.730 52.632 0.00 0.00 45.70 4.00
1217 2029 0.171903 GCAACACCATGCATCACCTC 59.828 55.000 0.00 0.00 45.70 3.85
1219 2031 0.700564 AACACCATGCATCACCTCCT 59.299 50.000 0.00 0.00 0.00 3.69
1220 2032 0.254178 ACACCATGCATCACCTCCTC 59.746 55.000 0.00 0.00 0.00 3.71
1221 2033 0.253894 CACCATGCATCACCTCCTCA 59.746 55.000 0.00 0.00 0.00 3.86
1222 2034 0.254178 ACCATGCATCACCTCCTCAC 59.746 55.000 0.00 0.00 0.00 3.51
1223 2035 0.253894 CCATGCATCACCTCCTCACA 59.746 55.000 0.00 0.00 0.00 3.58
1291 2105 2.514205 TTCTTTTGCCTCTTTGCTGC 57.486 45.000 0.00 0.00 0.00 5.25
1319 2137 8.592809 CAGGTCTATAGCTAGGATCATTCTTTT 58.407 37.037 0.00 0.00 0.00 2.27
1332 2151 9.525826 AGGATCATTCTTTTGTTTTACAGATCT 57.474 29.630 0.00 0.00 0.00 2.75
1344 2163 5.957771 TTTACAGATCTATCAACTGGCCT 57.042 39.130 3.32 0.00 36.17 5.19
1415 2238 6.015265 TGTCCATTCTTTCAAGCAATCAATCA 60.015 34.615 0.00 0.00 0.00 2.57
1444 2267 2.095768 AGTGTGTGCGTACATGAATTGC 60.096 45.455 10.21 0.00 39.39 3.56
1461 2284 2.825836 CGTCTGCAGCCCCCATTC 60.826 66.667 9.47 0.00 0.00 2.67
1482 2305 5.055642 TCGGGTATATTTAGCTCACATCG 57.944 43.478 0.00 0.00 0.00 3.84
1497 2320 3.642778 ATCGTCGGGCCACTGTTCG 62.643 63.158 4.39 0.00 0.00 3.95
1509 2332 2.035832 CCACTGTTCGGCCAATCTTTTT 59.964 45.455 2.24 0.00 0.00 1.94
1568 2392 8.904099 AACTACCATAGTTGCATTATAGGTTC 57.096 34.615 6.06 0.00 46.58 3.62
1569 2393 8.029782 ACTACCATAGTTGCATTATAGGTTCA 57.970 34.615 6.06 0.00 34.86 3.18
1634 2489 6.956202 ATACTACCACTTCGCACTAGTTAT 57.044 37.500 0.00 0.00 0.00 1.89
1637 2492 3.596214 ACCACTTCGCACTAGTTATTGG 58.404 45.455 0.00 0.00 0.00 3.16
1684 2539 2.753849 GCCTGGCCCGCATGTAAA 60.754 61.111 7.66 0.00 0.00 2.01
1702 2557 6.548441 TGTAAACACTAACATGGCACTAAC 57.452 37.500 0.00 0.00 0.00 2.34
1723 2578 5.479716 ACTTGTTTGACCGTTAAGTTGAG 57.520 39.130 0.00 0.00 0.00 3.02
1735 2590 3.070576 GTTGAGCATGGGGCCCAC 61.071 66.667 31.54 17.27 46.50 4.61
1777 2632 5.047731 CCTCCCTTTTGACCAATTTTCTCTC 60.048 44.000 0.00 0.00 0.00 3.20
1778 2633 5.454062 TCCCTTTTGACCAATTTTCTCTCA 58.546 37.500 0.00 0.00 0.00 3.27
1780 2635 5.536161 CCCTTTTGACCAATTTTCTCTCAGA 59.464 40.000 0.00 0.00 0.00 3.27
1845 2700 1.276421 GCCTGTAGTTCTTGGAGCTGA 59.724 52.381 0.00 0.00 0.00 4.26
1886 2741 3.672295 GAGGGAGGCAAGCTGGTCG 62.672 68.421 0.00 0.00 0.00 4.79
1889 2744 2.032681 GAGGCAAGCTGGTCGGTT 59.967 61.111 0.00 0.00 0.00 4.44
1893 2748 2.113139 CAAGCTGGTCGGTTGGGT 59.887 61.111 0.00 0.00 45.09 4.51
1895 2750 2.448582 AAGCTGGTCGGTTGGGTCA 61.449 57.895 0.00 0.00 30.87 4.02
1902 2757 1.529948 TCGGTTGGGTCAGAGTCGT 60.530 57.895 0.00 0.00 0.00 4.34
1904 2766 1.080705 GGTTGGGTCAGAGTCGTCG 60.081 63.158 0.00 0.00 0.00 5.12
1924 2786 1.422531 GAGGATGACCAGAGCCTCAT 58.577 55.000 0.00 0.00 44.91 2.90
1968 2830 3.933332 GGTAGAGAAGGAATTCGTTGGTG 59.067 47.826 17.58 0.00 0.00 4.17
2036 2898 3.505790 AACATGGGCGCCAACCTCA 62.506 57.895 30.85 17.34 36.95 3.86
2049 2911 0.472734 AACCTCACCTGGAGCTCTGT 60.473 55.000 14.64 5.98 42.62 3.41
2050 2912 0.472734 ACCTCACCTGGAGCTCTGTT 60.473 55.000 14.64 0.00 42.62 3.16
2066 2928 0.872451 TGTTTTCTTGAGCGTCGCGA 60.872 50.000 12.30 3.71 0.00 5.87
2079 2941 2.131067 TCGCGACATGGGAGCCATA 61.131 57.895 3.71 0.00 43.15 2.74
2092 2954 3.455910 GGGAGCCATACATATATGCTGGA 59.544 47.826 27.33 8.71 37.46 3.86
2093 2955 4.446371 GGAGCCATACATATATGCTGGAC 58.554 47.826 27.33 21.02 37.46 4.02
2117 2979 2.361992 TGCTCTCCGGGCTCGTTA 60.362 61.111 4.71 0.00 33.95 3.18
2140 3002 3.755628 GTCGGTGGTGAGCGGCTA 61.756 66.667 0.60 0.00 44.27 3.93
2154 3016 1.568612 CGGCTATAGGCATTGCACGG 61.569 60.000 24.43 3.42 44.01 4.94
2185 3047 3.341629 CCAGGTGGCATGGAGGGT 61.342 66.667 0.60 0.00 40.51 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 711 1.152777 CCAAGGCCACTGGACACAA 60.153 57.895 17.11 0.00 29.21 3.33
84 756 3.612860 CACAAATTCTCCGTACTTCTCCG 59.387 47.826 0.00 0.00 0.00 4.63
130 802 0.324943 AAGTGTTGGGGATCTGACGG 59.675 55.000 0.00 0.00 0.00 4.79
182 854 2.281276 AGACCAAAACCCCGCGTC 60.281 61.111 4.92 0.00 0.00 5.19
221 893 4.379290 GGAACGACTCAGACCAAGTACTAC 60.379 50.000 0.00 0.00 0.00 2.73
223 895 2.557490 GGAACGACTCAGACCAAGTACT 59.443 50.000 0.00 0.00 0.00 2.73
225 897 2.557056 CTGGAACGACTCAGACCAAGTA 59.443 50.000 0.00 0.00 33.11 2.24
227 899 1.937108 GCTGGAACGACTCAGACCAAG 60.937 57.143 0.00 0.00 33.11 3.61
229 901 0.827925 AGCTGGAACGACTCAGACCA 60.828 55.000 0.00 0.00 33.11 4.02
230 902 0.318762 AAGCTGGAACGACTCAGACC 59.681 55.000 0.00 0.00 33.11 3.85
231 903 1.269831 ACAAGCTGGAACGACTCAGAC 60.270 52.381 0.00 0.00 33.11 3.51
232 904 1.040646 ACAAGCTGGAACGACTCAGA 58.959 50.000 0.00 0.00 33.11 3.27
237 924 3.000815 TCCAACAAGCTGGAACGAC 57.999 52.632 0.00 0.00 42.69 4.34
274 961 0.318441 TTGTGCGACTCTTCCTCTGG 59.682 55.000 0.00 0.00 0.00 3.86
275 962 1.795286 GTTTGTGCGACTCTTCCTCTG 59.205 52.381 0.00 0.00 0.00 3.35
276 963 1.270358 GGTTTGTGCGACTCTTCCTCT 60.270 52.381 0.00 0.00 0.00 3.69
277 964 1.149148 GGTTTGTGCGACTCTTCCTC 58.851 55.000 0.00 0.00 0.00 3.71
278 965 0.759346 AGGTTTGTGCGACTCTTCCT 59.241 50.000 0.00 0.00 0.00 3.36
291 978 4.573201 TCCTTTGACGTTAGTGAAGGTTTG 59.427 41.667 8.61 0.00 39.46 2.93
298 985 3.734463 TGCATTCCTTTGACGTTAGTGA 58.266 40.909 0.00 0.00 0.00 3.41
308 995 4.753107 ACTTCAAAAGCATGCATTCCTTTG 59.247 37.500 21.98 18.47 0.00 2.77
309 996 4.964593 ACTTCAAAAGCATGCATTCCTTT 58.035 34.783 21.98 13.65 0.00 3.11
324 1012 6.337356 GTGAATTCAGGGTTCAAACTTCAAA 58.663 36.000 8.80 0.00 37.34 2.69
325 1013 5.449862 CGTGAATTCAGGGTTCAAACTTCAA 60.450 40.000 18.34 0.00 37.34 2.69
326 1014 4.036262 CGTGAATTCAGGGTTCAAACTTCA 59.964 41.667 18.34 0.00 37.34 3.02
327 1015 4.036380 ACGTGAATTCAGGGTTCAAACTTC 59.964 41.667 26.86 3.89 37.34 3.01
328 1016 3.951680 ACGTGAATTCAGGGTTCAAACTT 59.048 39.130 26.86 5.00 37.34 2.66
329 1017 3.551846 ACGTGAATTCAGGGTTCAAACT 58.448 40.909 26.86 5.63 37.34 2.66
330 1018 3.314080 TGACGTGAATTCAGGGTTCAAAC 59.686 43.478 26.86 9.61 37.34 2.93
348 1036 0.655733 ACGTGTGCTTCCTTTTGACG 59.344 50.000 0.00 0.00 0.00 4.35
355 1043 7.859325 AATAATATTTGTACGTGTGCTTCCT 57.141 32.000 0.00 0.00 0.00 3.36
357 1045 8.889849 ACAAATAATATTTGTACGTGTGCTTC 57.110 30.769 24.85 0.00 40.47 3.86
360 1048 7.751348 TCCAACAAATAATATTTGTACGTGTGC 59.249 33.333 25.89 0.00 41.30 4.57
361 1049 9.057365 GTCCAACAAATAATATTTGTACGTGTG 57.943 33.333 25.89 20.09 41.30 3.82
370 1064 8.253113 CAGCTTCCTGTCCAACAAATAATATTT 58.747 33.333 0.00 0.00 34.31 1.40
384 1078 1.756430 GGAATTCCAGCTTCCTGTCC 58.244 55.000 20.04 0.00 39.30 4.02
393 1087 2.961526 TGTACTCGAGGAATTCCAGC 57.038 50.000 26.22 16.02 38.89 4.85
395 1089 2.500098 CCCTTGTACTCGAGGAATTCCA 59.500 50.000 26.22 5.01 45.72 3.53
396 1090 2.158943 CCCCTTGTACTCGAGGAATTCC 60.159 54.545 17.31 17.31 45.72 3.01
397 1091 2.742204 GCCCCTTGTACTCGAGGAATTC 60.742 54.545 18.41 0.00 45.72 2.17
398 1092 1.209747 GCCCCTTGTACTCGAGGAATT 59.790 52.381 18.41 0.00 45.72 2.17
399 1093 0.831307 GCCCCTTGTACTCGAGGAAT 59.169 55.000 18.41 0.00 45.72 3.01
400 1094 0.252103 AGCCCCTTGTACTCGAGGAA 60.252 55.000 18.41 5.54 45.72 3.36
401 1095 0.970937 CAGCCCCTTGTACTCGAGGA 60.971 60.000 18.41 4.89 45.72 3.71
402 1096 1.517832 CAGCCCCTTGTACTCGAGG 59.482 63.158 18.41 0.00 43.21 4.63
403 1097 1.258445 ACCAGCCCCTTGTACTCGAG 61.258 60.000 11.84 11.84 0.00 4.04
404 1098 1.229082 ACCAGCCCCTTGTACTCGA 60.229 57.895 0.00 0.00 0.00 4.04
405 1099 1.218316 GACCAGCCCCTTGTACTCG 59.782 63.158 0.00 0.00 0.00 4.18
406 1100 0.910088 AGGACCAGCCCCTTGTACTC 60.910 60.000 0.00 0.00 37.37 2.59
407 1101 1.161113 AGGACCAGCCCCTTGTACT 59.839 57.895 0.00 0.00 37.37 2.73
408 1102 1.299976 CAGGACCAGCCCCTTGTAC 59.700 63.158 0.00 0.00 37.37 2.90
409 1103 1.923395 CCAGGACCAGCCCCTTGTA 60.923 63.158 0.00 0.00 37.37 2.41
410 1104 3.260100 CCAGGACCAGCCCCTTGT 61.260 66.667 0.00 0.00 37.37 3.16
411 1105 3.260100 ACCAGGACCAGCCCCTTG 61.260 66.667 0.00 0.00 37.37 3.61
412 1106 2.936032 GACCAGGACCAGCCCCTT 60.936 66.667 0.00 0.00 37.37 3.95
429 1123 0.730155 TAACAAGGACGCTACGCACG 60.730 55.000 0.00 0.00 0.00 5.34
430 1124 1.421382 TTAACAAGGACGCTACGCAC 58.579 50.000 0.00 0.00 0.00 5.34
431 1125 1.996898 CATTAACAAGGACGCTACGCA 59.003 47.619 0.00 0.00 0.00 5.24
432 1126 1.997606 ACATTAACAAGGACGCTACGC 59.002 47.619 0.00 0.00 0.00 4.42
457 1159 0.759959 TGAACTGTTCCCGTTGGCTA 59.240 50.000 17.26 0.00 0.00 3.93
458 1160 0.110486 ATGAACTGTTCCCGTTGGCT 59.890 50.000 17.26 0.00 0.00 4.75
459 1161 0.521735 GATGAACTGTTCCCGTTGGC 59.478 55.000 17.26 0.00 0.00 4.52
460 1162 0.796312 CGATGAACTGTTCCCGTTGG 59.204 55.000 17.26 0.00 0.00 3.77
461 1163 1.790755 TCGATGAACTGTTCCCGTTG 58.209 50.000 22.46 12.45 0.00 4.10
495 1197 6.665680 TCAGAGGAGCTATTTCTTGACTAAGT 59.334 38.462 0.00 0.00 35.38 2.24
496 1198 7.106439 TCAGAGGAGCTATTTCTTGACTAAG 57.894 40.000 0.00 0.00 35.16 2.18
497 1199 7.179338 AGTTCAGAGGAGCTATTTCTTGACTAA 59.821 37.037 0.00 0.00 32.27 2.24
562 1264 3.366476 GCCAGCGACCTCTAGTATATGTG 60.366 52.174 0.00 0.00 0.00 3.21
616 1318 2.679837 CACGGTCAATCTTTCTCATGGG 59.320 50.000 0.00 0.00 0.00 4.00
781 1516 0.179166 GCATACGTGTGGTGCATTGG 60.179 55.000 14.49 0.00 38.68 3.16
783 1518 1.793581 CGCATACGTGTGGTGCATT 59.206 52.632 14.49 0.00 38.75 3.56
784 1519 2.749865 GCGCATACGTGTGGTGCAT 61.750 57.895 14.49 0.00 42.83 3.96
786 1521 2.677003 AAGCGCATACGTGTGGTGC 61.677 57.895 11.47 12.99 45.06 5.01
787 1522 1.132436 CAAGCGCATACGTGTGGTG 59.868 57.895 11.47 3.44 45.06 4.17
789 1524 2.098298 GCAAGCGCATACGTGTGG 59.902 61.111 11.47 5.52 42.83 4.17
803 1538 5.547465 CCTCGGGTTTATATAGACATGCAA 58.453 41.667 5.83 0.00 0.00 4.08
820 1604 2.989173 ATTGCATGATGGGCCTCGGG 62.989 60.000 4.53 0.00 0.00 5.14
826 1610 1.615392 GGGTAGAATTGCATGATGGGC 59.385 52.381 0.00 0.00 0.00 5.36
839 1623 6.069673 TCTGCTAAAAATGGAGATGGGTAGAA 60.070 38.462 0.00 0.00 0.00 2.10
858 1643 3.815401 GAGAGCTTGGTTTGTTTCTGCTA 59.185 43.478 0.00 0.00 0.00 3.49
861 1646 3.629398 AGTGAGAGCTTGGTTTGTTTCTG 59.371 43.478 0.00 0.00 0.00 3.02
863 1648 4.639135 AAGTGAGAGCTTGGTTTGTTTC 57.361 40.909 0.00 0.00 0.00 2.78
866 1653 4.689612 TCTAAGTGAGAGCTTGGTTTGT 57.310 40.909 0.00 0.00 0.00 2.83
883 1670 3.369892 GCTTCAGCAGGGTTCTGATCTAA 60.370 47.826 0.00 0.00 43.49 2.10
884 1671 2.169352 GCTTCAGCAGGGTTCTGATCTA 59.831 50.000 0.00 0.00 43.49 1.98
885 1672 1.065564 GCTTCAGCAGGGTTCTGATCT 60.066 52.381 0.00 0.00 43.49 2.75
886 1673 1.065564 AGCTTCAGCAGGGTTCTGATC 60.066 52.381 0.75 0.00 43.49 2.92
887 1674 0.990374 AGCTTCAGCAGGGTTCTGAT 59.010 50.000 0.75 0.00 43.49 2.90
888 1675 0.322975 GAGCTTCAGCAGGGTTCTGA 59.677 55.000 0.75 0.00 43.49 3.27
889 1676 1.018226 CGAGCTTCAGCAGGGTTCTG 61.018 60.000 0.75 0.00 45.16 3.02
890 1677 1.294780 CGAGCTTCAGCAGGGTTCT 59.705 57.895 0.75 0.00 45.16 3.01
891 1678 1.743252 CCGAGCTTCAGCAGGGTTC 60.743 63.158 0.75 0.00 45.16 3.62
892 1679 1.768684 TTCCGAGCTTCAGCAGGGTT 61.769 55.000 11.82 0.00 45.16 4.11
893 1680 2.217038 TTCCGAGCTTCAGCAGGGT 61.217 57.895 11.82 0.00 45.16 4.34
920 1707 1.864862 CCTTGCTTCGTGCTCAGTG 59.135 57.895 5.00 0.00 43.37 3.66
950 1742 4.637534 GTGCAGCAGATTTTGATCTAGGAA 59.362 41.667 0.00 0.00 0.00 3.36
971 1765 2.125912 CGCCAGAAGGGAGACGTG 60.126 66.667 0.00 0.00 39.08 4.49
981 1775 3.663176 GCTGCTGTTGCGCCAGAA 61.663 61.111 16.59 6.04 43.34 3.02
1141 1952 1.079127 ACCCTGATTTGAGGTCGCG 60.079 57.895 0.00 0.00 0.00 5.87
1211 2023 1.332195 CTGTGAGTGTGAGGAGGTGA 58.668 55.000 0.00 0.00 0.00 4.02
1212 2024 1.043816 ACTGTGAGTGTGAGGAGGTG 58.956 55.000 0.00 0.00 0.00 4.00
1213 2025 1.794714 AACTGTGAGTGTGAGGAGGT 58.205 50.000 0.00 0.00 0.00 3.85
1214 2026 2.918712 AAACTGTGAGTGTGAGGAGG 57.081 50.000 0.00 0.00 0.00 4.30
1216 2028 4.487714 AGAAAAACTGTGAGTGTGAGGA 57.512 40.909 0.00 0.00 0.00 3.71
1217 2029 4.260375 CGAAGAAAAACTGTGAGTGTGAGG 60.260 45.833 0.00 0.00 0.00 3.86
1219 2031 3.621268 CCGAAGAAAAACTGTGAGTGTGA 59.379 43.478 0.00 0.00 0.00 3.58
1220 2032 3.374058 ACCGAAGAAAAACTGTGAGTGTG 59.626 43.478 0.00 0.00 0.00 3.82
1221 2033 3.606687 ACCGAAGAAAAACTGTGAGTGT 58.393 40.909 0.00 0.00 0.00 3.55
1222 2034 4.616181 AACCGAAGAAAAACTGTGAGTG 57.384 40.909 0.00 0.00 0.00 3.51
1223 2035 5.180271 TGTAACCGAAGAAAAACTGTGAGT 58.820 37.500 0.00 0.00 0.00 3.41
1291 2105 6.663093 AGAATGATCCTAGCTATAGACCTGTG 59.337 42.308 3.21 0.00 0.00 3.66
1319 2137 5.880332 GGCCAGTTGATAGATCTGTAAAACA 59.120 40.000 5.18 0.00 0.00 2.83
1326 2144 4.774124 TGAAAGGCCAGTTGATAGATCTG 58.226 43.478 5.01 0.00 0.00 2.90
1332 2151 5.452078 CTTTGTTGAAAGGCCAGTTGATA 57.548 39.130 5.01 0.00 35.78 2.15
1333 2152 4.326504 CTTTGTTGAAAGGCCAGTTGAT 57.673 40.909 5.01 0.00 35.78 2.57
1334 2153 3.799281 CTTTGTTGAAAGGCCAGTTGA 57.201 42.857 5.01 0.00 35.78 3.18
1358 2177 8.919145 TGTATTCAAAAGACATGGTTAAGGTTT 58.081 29.630 0.00 0.00 0.00 3.27
1415 2238 3.920446 TGTACGCACACACTATCATTGT 58.080 40.909 0.00 0.00 0.00 2.71
1444 2267 2.825836 GAATGGGGGCTGCAGACG 60.826 66.667 20.43 0.00 0.00 4.18
1461 2284 4.806330 ACGATGTGAGCTAAATATACCCG 58.194 43.478 0.00 0.00 0.00 5.28
1465 2288 4.617530 GCCCGACGATGTGAGCTAAATATA 60.618 45.833 0.00 0.00 0.00 0.86
1478 2301 2.047274 AACAGTGGCCCGACGATG 60.047 61.111 0.00 0.00 0.00 3.84
1497 2320 5.984695 AGAAGAACCTAAAAAGATTGGCC 57.015 39.130 0.00 0.00 0.00 5.36
1605 2460 4.929808 AGTGCGAAGTGGTAGTATTTCTTG 59.070 41.667 0.00 0.00 0.00 3.02
1606 2461 5.148651 AGTGCGAAGTGGTAGTATTTCTT 57.851 39.130 0.00 0.00 0.00 2.52
1608 2463 5.648572 ACTAGTGCGAAGTGGTAGTATTTC 58.351 41.667 0.00 0.00 0.00 2.17
1634 2489 4.524714 TCAGGATTAATTTTGCCGAACCAA 59.475 37.500 0.00 0.00 0.00 3.67
1637 2492 8.134895 TCATAATCAGGATTAATTTTGCCGAAC 58.865 33.333 5.88 0.00 36.90 3.95
1684 2539 4.714632 ACAAGTTAGTGCCATGTTAGTGT 58.285 39.130 0.00 0.00 0.00 3.55
1702 2557 4.201871 TGCTCAACTTAACGGTCAAACAAG 60.202 41.667 0.00 0.00 0.00 3.16
1735 2590 2.436173 GAGGAGGGTTGACTCTAATGGG 59.564 54.545 0.00 0.00 37.63 4.00
1740 2595 1.394532 AGGGAGGAGGGTTGACTCTA 58.605 55.000 0.00 0.00 37.63 2.43
1777 2632 9.199982 AGCTCAAAATGTTTGATAAAATGTCTG 57.800 29.630 4.01 0.00 0.00 3.51
1778 2633 9.415544 GAGCTCAAAATGTTTGATAAAATGTCT 57.584 29.630 9.40 0.00 0.00 3.41
1780 2635 9.415544 GAGAGCTCAAAATGTTTGATAAAATGT 57.584 29.630 17.77 0.00 0.00 2.71
1830 2685 2.488545 GTCGTCTCAGCTCCAAGAACTA 59.511 50.000 0.00 0.00 0.00 2.24
1845 2700 1.035139 AGGTTACAACACGGTCGTCT 58.965 50.000 0.00 0.00 0.00 4.18
1877 2732 2.397413 CTGACCCAACCGACCAGCTT 62.397 60.000 0.00 0.00 0.00 3.74
1886 2741 1.080705 CGACGACTCTGACCCAACC 60.081 63.158 0.00 0.00 0.00 3.77
1889 2744 1.674651 CTCCGACGACTCTGACCCA 60.675 63.158 0.00 0.00 0.00 4.51
1893 2748 0.252197 TCATCCTCCGACGACTCTGA 59.748 55.000 0.00 0.00 0.00 3.27
1895 2750 0.748729 GGTCATCCTCCGACGACTCT 60.749 60.000 0.00 0.00 34.04 3.24
1902 2757 1.758514 GGCTCTGGTCATCCTCCGA 60.759 63.158 0.00 0.00 34.23 4.55
1904 2766 0.689080 TGAGGCTCTGGTCATCCTCC 60.689 60.000 16.72 0.00 43.33 4.30
1950 2812 2.416893 GCTCACCAACGAATTCCTTCTC 59.583 50.000 0.00 0.00 0.00 2.87
1988 2850 0.398696 TTAAACAGAGGAGGCGCCAA 59.601 50.000 31.54 6.84 40.02 4.52
2026 2888 2.046892 CTCCAGGTGAGGTTGGCG 60.047 66.667 0.00 0.00 37.45 5.69
2036 2898 2.439507 TCAAGAAAACAGAGCTCCAGGT 59.560 45.455 10.93 3.57 0.00 4.00
2049 2911 0.872451 TGTCGCGACGCTCAAGAAAA 60.872 50.000 31.88 9.58 0.00 2.29
2050 2912 0.666274 ATGTCGCGACGCTCAAGAAA 60.666 50.000 31.88 13.38 0.00 2.52
2066 2928 4.476113 AGCATATATGTATGGCTCCCATGT 59.524 41.667 14.14 0.00 44.84 3.21
2079 2941 2.434336 ACACCACGTCCAGCATATATGT 59.566 45.455 14.14 0.00 0.00 2.29
2092 2954 3.991051 CCGGAGAGCACACCACGT 61.991 66.667 0.00 0.00 0.00 4.49
2093 2955 4.742201 CCCGGAGAGCACACCACG 62.742 72.222 0.73 0.00 0.00 4.94
2117 2979 3.068881 CTCACCACCGACCACCAT 58.931 61.111 0.00 0.00 0.00 3.55
2140 3002 0.758734 TCTAGCCGTGCAATGCCTAT 59.241 50.000 1.53 0.00 0.00 2.57
2154 3016 2.336809 CTGGTCGCCCGATCTAGC 59.663 66.667 2.42 0.00 0.00 3.42


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

AutoCloner maintained by Alex Coulton.