Multiple sequence alignment - TraesCS2B01G235900

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 TraesCS2B01G235900 chr2B 100.000 2842 0 0 1 2842 236102916 236100075 0.000000e+00 5249.0
1 TraesCS2B01G235900 chr2D 88.635 1663 89 48 602 2194 179286963 179285331 0.000000e+00 1932.0
2 TraesCS2B01G235900 chr2D 93.629 518 32 1 2323 2840 179283352 179282836 0.000000e+00 773.0
3 TraesCS2B01G235900 chr2D 90.534 581 31 9 1 566 179287530 179286959 0.000000e+00 747.0
4 TraesCS2B01G235900 chr2D 100.000 43 0 0 2370 2412 179283357 179283315 2.350000e-11 80.5
5 TraesCS2B01G235900 chr2D 100.000 31 0 0 2285 2315 179283368 179283338 1.100000e-04 58.4
6 TraesCS2B01G235900 chr2A 87.170 1668 95 50 581 2172 193735303 193733679 0.000000e+00 1784.0
7 TraesCS2B01G235900 chr2A 88.682 592 30 13 1 563 193735872 193735289 0.000000e+00 688.0
8 TraesCS2B01G235900 chr2A 87.686 471 49 4 2370 2840 193732635 193732174 8.960000e-150 540.0
9 TraesCS2B01G235900 chr2A 92.157 102 6 2 2228 2327 193732705 193732604 2.950000e-30 143.0
10 TraesCS2B01G235900 chr1B 81.263 475 66 18 2370 2831 109246098 109245634 2.080000e-96 363.0
11 TraesCS2B01G235900 chr1A 79.399 466 84 8 2372 2831 66338052 66337593 4.570000e-83 318.0
12 TraesCS2B01G235900 chr1D 78.270 474 80 20 2370 2831 67980603 67980141 1.670000e-72 283.0
13 TraesCS2B01G235900 chr1D 85.207 169 23 2 2449 2616 333485855 333485688 3.760000e-39 172.0
14 TraesCS2B01G235900 chr5D 89.362 47 5 0 2145 2191 399732936 399732890 3.060000e-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 TraesCS2B01G235900 chr2B 236100075 236102916 2841 True 5249.00 5249 100.00000 1 2842 1 chr2B.!!$R1 2841
1 TraesCS2B01G235900 chr2D 179282836 179287530 4694 True 718.18 1932 94.55960 1 2840 5 chr2D.!!$R1 2839
2 TraesCS2B01G235900 chr2A 193732174 193735872 3698 True 788.75 1784 88.92375 1 2840 4 chr2A.!!$R1 2839

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
919 983 0.391927 CCCAATTCCCACTCGCGTTA 60.392 55.0 5.77 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2210 5037 0.82999 TTGTAGATCGGCTGGCATCA 59.17 50.0 1.08 0.0 0.0 3.07 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
69 70 3.242248 CCGACGTATTCATCGAAAACCTC 59.758 47.826 0.00 0.00 40.86 3.85
158 174 7.531857 AGATGTTAACAAGAGTCTCTTCTCA 57.468 36.000 13.23 7.83 33.78 3.27
185 201 3.261897 CCAACATGAACTCTGTAGAGGGT 59.738 47.826 13.08 0.00 46.13 4.34
197 217 5.957798 TCTGTAGAGGGTTTAACATGTACG 58.042 41.667 0.00 0.00 0.00 3.67
198 218 5.477984 TCTGTAGAGGGTTTAACATGTACGT 59.522 40.000 0.00 0.00 0.00 3.57
199 219 6.658816 TCTGTAGAGGGTTTAACATGTACGTA 59.341 38.462 0.00 0.00 0.00 3.57
200 220 6.620678 TGTAGAGGGTTTAACATGTACGTAC 58.379 40.000 18.90 18.90 0.00 3.67
210 230 9.443283 GTTTAACATGTACGTACAGAGGTATAG 57.557 37.037 30.15 15.37 39.92 1.31
259 280 1.529010 CCTTGCCAACTGTCCAGCA 60.529 57.895 0.00 0.00 0.00 4.41
317 346 4.779993 ATTTTCATCACTAGGGACTCCC 57.220 45.455 5.90 5.90 45.90 4.30
350 379 0.538287 AGCAAAACTCCACTCTGGCC 60.538 55.000 0.00 0.00 37.47 5.36
366 395 1.202758 TGGCCGGCAGGTAAATATCTG 60.203 52.381 30.85 0.00 40.50 2.90
368 397 2.572290 GCCGGCAGGTAAATATCTGTT 58.428 47.619 24.80 0.00 36.79 3.16
438 473 7.912250 GCCAACTTCAATCTGAATACAATACAG 59.088 37.037 0.00 0.00 35.59 2.74
520 555 1.054348 CGCAAACACAATCACGCGAG 61.054 55.000 15.93 4.59 45.17 5.03
563 598 2.093973 CGGCCTCAGTCACTGAAACTAT 60.094 50.000 9.30 0.00 40.18 2.12
564 599 3.617531 CGGCCTCAGTCACTGAAACTATT 60.618 47.826 9.30 0.00 40.18 1.73
565 600 4.327680 GGCCTCAGTCACTGAAACTATTT 58.672 43.478 9.30 0.00 40.18 1.40
566 601 4.762251 GGCCTCAGTCACTGAAACTATTTT 59.238 41.667 9.30 0.00 40.18 1.82
567 602 5.241728 GGCCTCAGTCACTGAAACTATTTTT 59.758 40.000 9.30 0.00 40.18 1.94
587 622 4.503714 TTTTTCTTGAGGGACAGTGACT 57.496 40.909 0.00 0.00 0.00 3.41
588 623 3.475566 TTTCTTGAGGGACAGTGACTG 57.524 47.619 11.70 11.70 37.52 3.51
589 624 2.381752 TCTTGAGGGACAGTGACTGA 57.618 50.000 20.97 0.00 35.18 3.41
590 625 2.677914 TCTTGAGGGACAGTGACTGAA 58.322 47.619 20.97 0.54 35.18 3.02
591 626 3.038280 TCTTGAGGGACAGTGACTGAAA 58.962 45.455 20.97 3.02 35.18 2.69
592 627 2.910688 TGAGGGACAGTGACTGAAAC 57.089 50.000 20.97 9.77 35.18 2.78
593 628 2.398588 TGAGGGACAGTGACTGAAACT 58.601 47.619 20.97 12.92 35.18 2.66
594 629 3.572642 TGAGGGACAGTGACTGAAACTA 58.427 45.455 20.97 0.00 35.18 2.24
595 630 3.964688 TGAGGGACAGTGACTGAAACTAA 59.035 43.478 20.97 4.00 35.18 2.24
596 631 4.593206 TGAGGGACAGTGACTGAAACTAAT 59.407 41.667 20.97 0.00 35.18 1.73
718 756 4.530857 CGGCCGGGACCATCAGAC 62.531 72.222 20.10 0.00 0.00 3.51
719 757 3.399181 GGCCGGGACCATCAGACA 61.399 66.667 2.18 0.00 0.00 3.41
720 758 2.187946 GCCGGGACCATCAGACAG 59.812 66.667 2.18 0.00 0.00 3.51
721 759 2.359169 GCCGGGACCATCAGACAGA 61.359 63.158 2.18 0.00 0.00 3.41
741 789 3.622826 CCGTCCGGTCAACCCACT 61.623 66.667 0.00 0.00 0.00 4.00
813 867 0.741915 GCGTCCAACAAAGTCCCAAA 59.258 50.000 0.00 0.00 0.00 3.28
814 868 1.535226 GCGTCCAACAAAGTCCCAAAC 60.535 52.381 0.00 0.00 0.00 2.93
815 869 2.021457 CGTCCAACAAAGTCCCAAACT 58.979 47.619 0.00 0.00 41.10 2.66
816 870 2.032924 CGTCCAACAAAGTCCCAAACTC 59.967 50.000 0.00 0.00 37.17 3.01
817 871 2.032924 GTCCAACAAAGTCCCAAACTCG 59.967 50.000 0.00 0.00 37.17 4.18
898 962 2.048503 CTTCGCCTTCCGTCCGTT 60.049 61.111 0.00 0.00 38.35 4.44
899 963 1.666872 CTTCGCCTTCCGTCCGTTT 60.667 57.895 0.00 0.00 38.35 3.60
900 964 1.623973 CTTCGCCTTCCGTCCGTTTC 61.624 60.000 0.00 0.00 38.35 2.78
901 965 3.116531 CGCCTTCCGTCCGTTTCC 61.117 66.667 0.00 0.00 0.00 3.13
902 966 2.745100 GCCTTCCGTCCGTTTCCC 60.745 66.667 0.00 0.00 0.00 3.97
903 967 2.745037 CCTTCCGTCCGTTTCCCA 59.255 61.111 0.00 0.00 0.00 4.37
904 968 1.071814 CCTTCCGTCCGTTTCCCAA 59.928 57.895 0.00 0.00 0.00 4.12
917 981 2.046314 CCCAATTCCCACTCGCGT 60.046 61.111 5.77 0.00 0.00 6.01
919 983 0.391927 CCCAATTCCCACTCGCGTTA 60.392 55.000 5.77 0.00 0.00 3.18
935 1000 2.836262 CGTTACACCAACCAACCACTA 58.164 47.619 0.00 0.00 33.19 2.74
1009 1080 1.080974 CGCCCGCCCGTATAAGTAG 60.081 63.158 0.00 0.00 0.00 2.57
1042 1113 0.741221 GGACACGGAGCATCAGAACC 60.741 60.000 0.00 0.00 36.25 3.62
1044 1115 1.215382 CACGGAGCATCAGAACCGA 59.785 57.895 11.27 0.00 46.94 4.69
1068 1139 4.072088 CCGACGCGACAAGCCAAC 62.072 66.667 15.93 0.00 44.76 3.77
1069 1140 3.334751 CGACGCGACAAGCCAACA 61.335 61.111 15.93 0.00 44.76 3.33
1071 1142 3.579626 GACGCGACAAGCCAACAGC 62.580 63.158 15.93 0.00 44.76 4.40
1073 1144 2.980233 GCGACAAGCCAACAGCCT 60.980 61.111 0.00 0.00 45.47 4.58
1075 1146 2.328099 CGACAAGCCAACAGCCTCC 61.328 63.158 0.00 0.00 45.47 4.30
1077 1148 2.677875 CAAGCCAACAGCCTCCCC 60.678 66.667 0.00 0.00 45.47 4.81
1078 1149 2.860971 AAGCCAACAGCCTCCCCT 60.861 61.111 0.00 0.00 45.47 4.79
1079 1150 1.541368 AAGCCAACAGCCTCCCCTA 60.541 57.895 0.00 0.00 45.47 3.53
1080 1151 1.566298 AAGCCAACAGCCTCCCCTAG 61.566 60.000 0.00 0.00 45.47 3.02
1083 1175 1.627297 CCAACAGCCTCCCCTAGTCC 61.627 65.000 0.00 0.00 0.00 3.85
1105 1197 2.936912 GCGCCGCTCCAGATATCCT 61.937 63.158 0.00 0.00 0.00 3.24
1119 1211 4.081972 CAGATATCCTTCTATCCACACCCG 60.082 50.000 0.00 0.00 0.00 5.28
1126 1228 0.250038 CTATCCACACCCGCCATGAG 60.250 60.000 0.00 0.00 0.00 2.90
1277 1388 1.215382 CAAGAGGATCACGTCGCCA 59.785 57.895 0.00 0.00 37.82 5.69
1347 1464 2.804090 GGAAGTCGTCGTCCGTGC 60.804 66.667 0.00 0.00 37.94 5.34
1393 1510 4.500116 GTCGCTGGACTCGGCCTC 62.500 72.222 0.00 0.00 42.12 4.70
1400 1517 3.213402 GACTCGGCCTCCTCCTCG 61.213 72.222 0.00 0.00 0.00 4.63
1783 1913 3.583086 TCCATCTTCCGACTTCTCCTTTT 59.417 43.478 0.00 0.00 0.00 2.27
1809 1939 9.456147 TTTATTTAGCACAGCAGTTCCTTTATA 57.544 29.630 0.00 0.00 0.00 0.98
1810 1940 6.737254 TTTAGCACAGCAGTTCCTTTATAC 57.263 37.500 0.00 0.00 0.00 1.47
1812 1942 4.256920 AGCACAGCAGTTCCTTTATACTG 58.743 43.478 0.00 0.00 43.58 2.74
1870 2006 9.715121 AAATTCGGATTAAGACTTACACTAACA 57.285 29.630 0.00 0.00 0.00 2.41
1961 2100 4.367023 TGCCGGCCACACGTACTC 62.367 66.667 26.77 0.00 0.00 2.59
1981 2120 4.629200 ACTCTTCTCGCACAAAATCATCTC 59.371 41.667 0.00 0.00 0.00 2.75
1982 2121 4.825422 TCTTCTCGCACAAAATCATCTCT 58.175 39.130 0.00 0.00 0.00 3.10
2071 2212 6.150318 CGATGGTGCGAGTATTTCTATACTT 58.850 40.000 0.00 0.00 45.43 2.24
2080 2221 6.328641 AGTATTTCTATACTTGCGGACGAT 57.671 37.500 0.00 0.00 43.48 3.73
2136 2277 1.003696 GGGCTTTCTGGCTTGTAGTCT 59.996 52.381 0.00 0.00 41.48 3.24
2191 2333 6.877668 TCCATAGTAACAGGGTTACAATCA 57.122 37.500 18.32 4.44 0.00 2.57
2194 2336 7.181305 TCCATAGTAACAGGGTTACAATCAAGA 59.819 37.037 18.32 7.12 0.00 3.02
2196 2338 8.830580 CATAGTAACAGGGTTACAATCAAGATG 58.169 37.037 18.32 8.19 0.00 2.90
2226 5053 2.232208 CTGTATGATGCCAGCCGATCTA 59.768 50.000 0.00 0.00 0.00 1.98
2281 5110 7.175816 TCGGAATAACTTCTCTCTCTATCATGG 59.824 40.741 0.00 0.00 0.00 3.66
2315 5208 9.553064 GATTTCAGATACAAGATGGTCATAAGT 57.447 33.333 0.00 0.00 0.00 2.24
2330 5223 5.844004 GTCATAAGTCGACCTCAATATGGT 58.156 41.667 13.01 0.00 41.07 3.55
2340 5233 5.894298 ACCTCAATATGGTCATAAGCTGA 57.106 39.130 0.00 0.00 31.03 4.26
2341 5234 6.445451 ACCTCAATATGGTCATAAGCTGAT 57.555 37.500 0.00 0.00 35.97 2.90
2342 5235 6.471146 ACCTCAATATGGTCATAAGCTGATC 58.529 40.000 0.00 0.00 35.97 2.92
2343 5236 6.271857 ACCTCAATATGGTCATAAGCTGATCT 59.728 38.462 0.00 0.00 35.86 2.75
2344 5237 6.817641 CCTCAATATGGTCATAAGCTGATCTC 59.182 42.308 0.00 0.00 35.86 2.75
2345 5238 7.307131 TCAATATGGTCATAAGCTGATCTCA 57.693 36.000 0.00 0.00 35.86 3.27
2357 5250 4.043596 AGCTGATCTCAATAAACCCTCCT 58.956 43.478 0.00 0.00 0.00 3.69
2360 5253 4.030913 TGATCTCAATAAACCCTCCTCGT 58.969 43.478 0.00 0.00 0.00 4.18
2431 5324 1.165270 GACAATGTAGCCAACGCCTT 58.835 50.000 0.00 0.00 34.57 4.35
2464 5357 2.204029 TACCACCCCCGGCTCTTT 60.204 61.111 0.00 0.00 0.00 2.52
2502 5395 0.977108 GGCCATGCCCTCCATCAAAA 60.977 55.000 0.00 0.00 44.06 2.44
2511 5404 3.673323 GCCCTCCATCAAAACGTGAATTC 60.673 47.826 0.00 0.00 40.50 2.17
2596 5489 3.951680 TCCGGCCTTCTTAAAATCATTCC 59.048 43.478 0.00 0.00 0.00 3.01
2803 5696 1.909302 GGAATTCCACTGAGACCTCCA 59.091 52.381 20.04 0.00 35.64 3.86
2840 5733 2.909662 TCCCATGTACAACATCTGACCA 59.090 45.455 0.00 0.00 36.53 4.02
2841 5734 3.329225 TCCCATGTACAACATCTGACCAA 59.671 43.478 0.00 0.00 36.53 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.338809 TGAGGGTCCAATCACTGAAGT 58.661 47.619 0.00 0.00 0.00 3.01
128 144 9.523168 AAGAGACTCTTGTTAACATCTACTACT 57.477 33.333 17.02 3.89 34.98 2.57
129 145 9.777575 GAAGAGACTCTTGTTAACATCTACTAC 57.222 37.037 22.39 0.00 36.73 2.73
152 168 7.551974 ACAGAGTTCATGTTGGAATATGAGAAG 59.448 37.037 0.00 0.00 37.73 2.85
158 174 7.419518 CCCTCTACAGAGTTCATGTTGGAATAT 60.420 40.741 5.56 0.00 40.48 1.28
185 201 9.177608 ACTATACCTCTGTACGTACATGTTAAA 57.822 33.333 27.50 12.82 35.36 1.52
197 217 3.749226 ACGGGCTACTATACCTCTGTAC 58.251 50.000 0.00 0.00 0.00 2.90
198 218 5.513788 CCTTACGGGCTACTATACCTCTGTA 60.514 48.000 0.00 0.00 0.00 2.74
199 219 4.396522 CTTACGGGCTACTATACCTCTGT 58.603 47.826 0.00 0.00 0.00 3.41
200 220 3.757493 CCTTACGGGCTACTATACCTCTG 59.243 52.174 0.00 0.00 0.00 3.35
210 230 5.302823 TCCTACTAAAATCCTTACGGGCTAC 59.697 44.000 0.00 0.00 34.39 3.58
229 249 4.580580 CAGTTGGCAAGGGAAATATCCTAC 59.419 45.833 0.00 0.00 45.77 3.18
291 312 6.987404 GGAGTCCCTAGTGATGAAAATAGAAC 59.013 42.308 0.00 0.00 0.00 3.01
325 354 4.498682 CCAGAGTGGAGTTTTGCTTTCAAG 60.499 45.833 0.00 0.00 40.96 3.02
350 379 4.273480 CCTTCAACAGATATTTACCTGCCG 59.727 45.833 0.00 0.00 33.90 5.69
366 395 3.300667 CTCGTGCGCTGCCTTCAAC 62.301 63.158 9.73 0.00 0.00 3.18
368 397 3.300934 ATCTCGTGCGCTGCCTTCA 62.301 57.895 9.73 0.00 0.00 3.02
453 488 2.542595 ACGGATCTTTGTGTCGTGTTTC 59.457 45.455 0.00 0.00 32.60 2.78
534 569 1.227853 GACTGAGGCCGTGTGGTTT 60.228 57.895 0.00 0.00 37.67 3.27
535 570 2.426023 GACTGAGGCCGTGTGGTT 59.574 61.111 0.00 0.00 37.67 3.67
566 601 4.080582 TCAGTCACTGTCCCTCAAGAAAAA 60.081 41.667 4.28 0.00 32.61 1.94
567 602 3.454447 TCAGTCACTGTCCCTCAAGAAAA 59.546 43.478 4.28 0.00 32.61 2.29
568 603 3.038280 TCAGTCACTGTCCCTCAAGAAA 58.962 45.455 4.28 0.00 32.61 2.52
569 604 2.677914 TCAGTCACTGTCCCTCAAGAA 58.322 47.619 4.28 0.00 32.61 2.52
570 605 2.381752 TCAGTCACTGTCCCTCAAGA 57.618 50.000 4.28 0.00 32.61 3.02
571 606 3.134458 GTTTCAGTCACTGTCCCTCAAG 58.866 50.000 4.28 0.00 32.61 3.02
572 607 2.771943 AGTTTCAGTCACTGTCCCTCAA 59.228 45.455 4.28 0.00 32.61 3.02
573 608 2.398588 AGTTTCAGTCACTGTCCCTCA 58.601 47.619 4.28 0.00 32.61 3.86
574 609 4.602340 TTAGTTTCAGTCACTGTCCCTC 57.398 45.455 4.28 0.00 32.61 4.30
575 610 5.568620 AATTAGTTTCAGTCACTGTCCCT 57.431 39.130 4.28 1.66 32.61 4.20
576 611 7.923414 ATTAATTAGTTTCAGTCACTGTCCC 57.077 36.000 4.28 0.00 32.61 4.46
718 756 1.080705 GTTGACCGGACGGACTCTG 60.081 63.158 18.80 0.00 38.96 3.35
719 757 2.273912 GGTTGACCGGACGGACTCT 61.274 63.158 18.80 0.00 38.96 3.24
720 758 2.260743 GGTTGACCGGACGGACTC 59.739 66.667 18.80 6.08 38.96 3.36
721 759 3.308705 GGGTTGACCGGACGGACT 61.309 66.667 18.80 0.00 38.96 3.85
761 809 0.307760 CGTGTGGTGAGGCTTTTGTC 59.692 55.000 0.00 0.00 0.00 3.18
898 962 1.376683 CGCGAGTGGGAATTGGGAA 60.377 57.895 0.00 0.00 0.00 3.97
899 963 2.267642 CGCGAGTGGGAATTGGGA 59.732 61.111 0.00 0.00 0.00 4.37
900 964 2.046314 ACGCGAGTGGGAATTGGG 60.046 61.111 15.93 0.00 46.97 4.12
917 981 2.807472 CGCTAGTGGTTGGTTGGTGTAA 60.807 50.000 0.00 0.00 0.00 2.41
919 983 0.534203 CGCTAGTGGTTGGTTGGTGT 60.534 55.000 0.00 0.00 0.00 4.16
990 1061 3.211564 TACTTATACGGGCGGGCGC 62.212 63.158 0.00 0.00 41.06 6.53
991 1062 1.080974 CTACTTATACGGGCGGGCG 60.081 63.158 0.00 0.00 0.00 6.13
992 1063 1.373873 GCTACTTATACGGGCGGGC 60.374 63.158 0.00 0.00 0.00 6.13
993 1064 1.080974 CGCTACTTATACGGGCGGG 60.081 63.158 9.69 0.00 41.77 6.13
994 1065 1.731969 GCGCTACTTATACGGGCGG 60.732 63.158 16.02 0.00 44.92 6.13
996 1067 3.838468 CGCGCTACTTATACGGGC 58.162 61.111 5.56 0.00 33.01 6.13
997 1068 0.728466 GAGCGCGCTACTTATACGGG 60.728 60.000 36.69 0.00 41.97 5.28
1067 1138 2.369001 GGGACTAGGGGAGGCTGT 59.631 66.667 0.00 0.00 31.44 4.40
1068 1139 2.446802 GGGGACTAGGGGAGGCTG 60.447 72.222 0.00 0.00 31.44 4.85
1069 1140 2.625431 AGGGGACTAGGGGAGGCT 60.625 66.667 0.00 0.00 40.61 4.58
1071 1142 2.446802 GCAGGGGACTAGGGGAGG 60.447 72.222 0.00 0.00 40.21 4.30
1105 1197 0.180171 CATGGCGGGTGTGGATAGAA 59.820 55.000 0.00 0.00 0.00 2.10
1119 1211 4.166011 GCACGCGAACCTCATGGC 62.166 66.667 15.93 0.00 36.63 4.40
1177 1279 3.417224 TCCGGTGAGTCGTCGTCG 61.417 66.667 0.00 0.00 38.55 5.12
1178 1280 2.175322 GTCCGGTGAGTCGTCGTC 59.825 66.667 0.00 0.00 0.00 4.20
1179 1281 2.281345 AGTCCGGTGAGTCGTCGT 60.281 61.111 0.00 0.00 0.00 4.34
1259 1370 0.803768 CTGGCGACGTGATCCTCTTG 60.804 60.000 0.00 0.00 0.00 3.02
1393 1510 1.152839 GAGGAGGAGGACGAGGAGG 60.153 68.421 0.00 0.00 0.00 4.30
1400 1517 2.835895 GAGCGGGAGGAGGAGGAC 60.836 72.222 0.00 0.00 0.00 3.85
1567 1684 3.947459 TGGTAAGCAGCGTGGCCA 61.947 61.111 0.00 0.00 0.00 5.36
1680 1800 2.979197 CTTGTCTCCTCGACGCCGT 61.979 63.158 0.00 0.00 45.87 5.68
1699 1819 1.469940 CCTTGGTCTTGATCGTCTCCG 60.470 57.143 0.00 0.00 0.00 4.63
1715 1835 0.106719 ACCCATCCATAACCGCCTTG 60.107 55.000 0.00 0.00 0.00 3.61
1783 1913 6.648879 AAAGGAACTGCTGTGCTAAATAAA 57.351 33.333 1.26 0.00 40.86 1.40
1868 2004 9.939802 AGTAGAGAAAATAAAGGTCGTATTTGT 57.060 29.630 0.00 0.00 32.71 2.83
1870 2006 9.939802 ACAGTAGAGAAAATAAAGGTCGTATTT 57.060 29.630 0.00 0.00 33.55 1.40
1876 2015 8.834749 AACTCACAGTAGAGAAAATAAAGGTC 57.165 34.615 6.93 0.00 38.98 3.85
1918 2057 1.052124 TCTTTCCCCATATCCGCCGT 61.052 55.000 0.00 0.00 0.00 5.68
1961 2100 6.841443 ATAGAGATGATTTTGTGCGAGAAG 57.159 37.500 0.00 0.00 0.00 2.85
2071 2212 5.461078 GCTATCTAAAAGTTAATCGTCCGCA 59.539 40.000 0.00 0.00 0.00 5.69
2104 2245 1.917336 GAAAGCCCCCACGACCCATA 61.917 60.000 0.00 0.00 0.00 2.74
2162 2303 9.452287 TTGTAACCCTGTTACTATGGAATAAAC 57.548 33.333 15.74 0.00 0.00 2.01
2178 2320 4.264253 TCTGCATCTTGATTGTAACCCTG 58.736 43.478 0.00 0.00 0.00 4.45
2210 5037 0.829990 TTGTAGATCGGCTGGCATCA 59.170 50.000 1.08 0.00 0.00 3.07
2213 5040 1.220749 GGTTGTAGATCGGCTGGCA 59.779 57.895 1.08 0.00 0.00 4.92
2214 5041 1.523938 GGGTTGTAGATCGGCTGGC 60.524 63.158 0.00 0.00 0.00 4.85
2281 5110 9.994432 CCATCTTGTATCTGAAATCAAGTTAAC 57.006 33.333 0.00 0.00 38.53 2.01
2325 5218 9.494271 GTTTATTGAGATCAGCTTATGACCATA 57.506 33.333 0.00 0.00 41.91 2.74
2326 5219 7.446625 GGTTTATTGAGATCAGCTTATGACCAT 59.553 37.037 0.00 0.00 41.91 3.55
2327 5220 6.767902 GGTTTATTGAGATCAGCTTATGACCA 59.232 38.462 0.00 0.00 41.91 4.02
2328 5221 6.205658 GGGTTTATTGAGATCAGCTTATGACC 59.794 42.308 0.00 0.00 41.91 4.02
2329 5222 6.995091 AGGGTTTATTGAGATCAGCTTATGAC 59.005 38.462 0.00 0.00 41.91 3.06
2330 5223 7.141758 AGGGTTTATTGAGATCAGCTTATGA 57.858 36.000 0.00 0.00 43.70 2.15
2331 5224 6.429385 GGAGGGTTTATTGAGATCAGCTTATG 59.571 42.308 0.00 0.00 0.00 1.90
2332 5225 6.331307 AGGAGGGTTTATTGAGATCAGCTTAT 59.669 38.462 0.00 0.00 0.00 1.73
2333 5226 5.667626 AGGAGGGTTTATTGAGATCAGCTTA 59.332 40.000 0.00 0.00 0.00 3.09
2334 5227 4.476479 AGGAGGGTTTATTGAGATCAGCTT 59.524 41.667 0.00 0.00 0.00 3.74
2335 5228 4.043596 AGGAGGGTTTATTGAGATCAGCT 58.956 43.478 0.00 0.00 0.00 4.24
2336 5229 4.384940 GAGGAGGGTTTATTGAGATCAGC 58.615 47.826 0.00 0.00 0.00 4.26
2337 5230 4.100189 ACGAGGAGGGTTTATTGAGATCAG 59.900 45.833 0.00 0.00 0.00 2.90
2338 5231 4.030913 ACGAGGAGGGTTTATTGAGATCA 58.969 43.478 0.00 0.00 0.00 2.92
2339 5232 4.674281 ACGAGGAGGGTTTATTGAGATC 57.326 45.455 0.00 0.00 0.00 2.75
2340 5233 6.555463 TTTACGAGGAGGGTTTATTGAGAT 57.445 37.500 0.00 0.00 0.00 2.75
2341 5234 6.363167 TTTTACGAGGAGGGTTTATTGAGA 57.637 37.500 0.00 0.00 0.00 3.27
2367 5260 5.406780 CGGCTTATGACCATCTTGTATCTTC 59.593 44.000 0.00 0.00 0.00 2.87
2431 5324 3.285484 GTGGTACAATCGGACTCCTCTA 58.715 50.000 0.00 0.00 44.16 2.43
2464 5357 3.699038 GGCCTTGGCAATACAACATTCTA 59.301 43.478 14.04 0.00 0.00 2.10
2494 5387 4.870363 AGTTGGAATTCACGTTTTGATGG 58.130 39.130 7.93 0.00 32.84 3.51
2553 5446 5.106555 CGGATGAAAGTGTTATCTTTGCTGT 60.107 40.000 0.00 0.00 37.70 4.40
2657 5550 6.599638 GGAAGTTAAAGCACATGAACCTATCT 59.400 38.462 0.00 0.00 0.00 1.98
2768 5661 4.832266 TGGAATTCCTGCAAAACTATGTGT 59.168 37.500 24.73 0.00 36.82 3.72
2803 5696 2.593956 GGAAGGAAGCCCCGTCACT 61.594 63.158 10.02 0.00 44.03 3.41


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

AutoCloner maintained by Alex Coulton.