Multiple sequence alignment - TraesCS4A01G088400

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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 TraesCS4A01G088400 chr4A 100.000 2732 0 0 1 2732 93899424 93896693 0.000000e+00 5046.0
1 TraesCS4A01G088400 chr4B 88.351 2807 173 63 1 2732 455614683 455617410 0.000000e+00 3230.0
2 TraesCS4A01G088400 chr4D 91.296 2183 101 27 584 2732 370530170 370532297 0.000000e+00 2896.0
3 TraesCS4A01G088400 chr4D 92.937 269 11 2 1 269 370529363 370529623 4.270000e-103 385.0
4 TraesCS4A01G088400 chr4D 89.407 236 15 4 342 571 370529765 370529996 3.440000e-74 289.0
5 TraesCS4A01G088400 chr6D 86.574 216 24 5 1132 1343 420004058 420004272 1.640000e-57 233.0
6 TraesCS4A01G088400 chr6A 86.574 216 24 5 1132 1343 563026354 563026568 1.640000e-57 233.0
7 TraesCS4A01G088400 chr6B 90.341 176 15 2 1132 1306 632954892 632955066 2.120000e-56 230.0
8 TraesCS4A01G088400 chr7A 87.952 166 18 2 1128 1292 126035209 126035045 7.720000e-46 195.0
9 TraesCS4A01G088400 chr7B 84.946 186 20 5 1128 1306 84220622 84220806 6.010000e-42 182.0
10 TraesCS4A01G088400 chr7D 84.409 186 21 4 1128 1306 123146299 123146483 2.800000e-40 176.0
11 TraesCS4A01G088400 chr2B 77.358 159 29 6 1162 1315 1695317 1695473 1.350000e-13 87.9


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 TraesCS4A01G088400 chr4A 93896693 93899424 2731 True 5046 5046 100.000000 1 2732 1 chr4A.!!$R1 2731
1 TraesCS4A01G088400 chr4B 455614683 455617410 2727 False 3230 3230 88.351000 1 2732 1 chr4B.!!$F1 2731
2 TraesCS4A01G088400 chr4D 370529363 370532297 2934 False 1190 2896 91.213333 1 2732 3 chr4D.!!$F1 2731

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
898 1219 0.246635 GAACTCCCTAGCAGCGTTCA 59.753 55.0 8.27 0.0 35.34 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2021 2370 0.17915 GCAGACAGTCTCGCTCGATT 60.179 55.0 14.37 0.0 0.0 3.34 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
178 181 2.495155 ATATATGCATGGCCGCAGAA 57.505 45.000 10.16 2.65 46.99 3.02
192 195 5.163663 TGGCCGCAGAACTTAATAAGAAATG 60.164 40.000 7.06 3.40 0.00 2.32
219 225 4.908156 GTGTACAGTACATAATACGAGGCG 59.092 45.833 16.57 0.00 41.34 5.52
221 227 7.747036 TGTACAGTACATAATACGAGGCGCG 62.747 48.000 9.51 9.63 38.88 6.86
231 237 3.918220 GAGGCGCGCAGATCAACG 61.918 66.667 34.42 0.00 0.00 4.10
242 248 3.241900 CGCAGATCAACGTCTGAAATCTG 60.242 47.826 17.64 17.64 46.77 2.90
259 265 7.633621 TGAAATCTGACGAATAATTGAGCATC 58.366 34.615 0.00 0.00 0.00 3.91
269 275 9.687210 ACGAATAATTGAGCATCGTATACTTTA 57.313 29.630 0.56 0.00 44.08 1.85
272 278 6.787085 AATTGAGCATCGTATACTTTAGGC 57.213 37.500 0.56 0.20 38.61 3.93
273 279 4.252971 TGAGCATCGTATACTTTAGGCC 57.747 45.455 0.00 0.00 38.61 5.19
274 280 3.243336 GAGCATCGTATACTTTAGGCCG 58.757 50.000 0.00 0.00 0.00 6.13
275 281 2.029290 AGCATCGTATACTTTAGGCCGG 60.029 50.000 0.00 0.00 0.00 6.13
276 282 2.334838 CATCGTATACTTTAGGCCGGC 58.665 52.381 21.18 21.18 0.00 6.13
278 284 2.034124 TCGTATACTTTAGGCCGGCTT 58.966 47.619 28.56 23.35 0.00 4.35
279 285 3.221771 TCGTATACTTTAGGCCGGCTTA 58.778 45.455 28.56 22.00 0.00 3.09
280 286 3.828451 TCGTATACTTTAGGCCGGCTTAT 59.172 43.478 28.56 15.39 0.00 1.73
282 288 5.653769 TCGTATACTTTAGGCCGGCTTATAT 59.346 40.000 28.56 19.13 0.00 0.86
283 289 6.828273 TCGTATACTTTAGGCCGGCTTATATA 59.172 38.462 28.56 18.11 0.00 0.86
284 290 7.503566 TCGTATACTTTAGGCCGGCTTATATAT 59.496 37.037 28.56 20.56 0.00 0.86
290 296 9.392259 ACTTTAGGCCGGCTTATATATAATTTC 57.608 33.333 28.56 3.63 0.00 2.17
291 297 8.741603 TTTAGGCCGGCTTATATATAATTTCC 57.258 34.615 28.56 2.87 0.00 3.13
292 298 6.321821 AGGCCGGCTTATATATAATTTCCA 57.678 37.500 28.56 0.00 0.00 3.53
293 299 6.911308 AGGCCGGCTTATATATAATTTCCAT 58.089 36.000 28.56 0.00 0.00 3.41
314 329 1.882623 GGCAGCTAAACTCTTGCTTGT 59.117 47.619 0.00 0.00 34.51 3.16
315 330 3.074412 GGCAGCTAAACTCTTGCTTGTA 58.926 45.455 0.00 0.00 34.51 2.41
316 331 3.691609 GGCAGCTAAACTCTTGCTTGTAT 59.308 43.478 0.00 0.00 34.51 2.29
317 332 4.156739 GGCAGCTAAACTCTTGCTTGTATT 59.843 41.667 0.00 0.00 34.51 1.89
318 333 5.091431 GCAGCTAAACTCTTGCTTGTATTG 58.909 41.667 0.00 0.00 34.51 1.90
319 334 5.335191 GCAGCTAAACTCTTGCTTGTATTGT 60.335 40.000 0.00 0.00 34.51 2.71
320 335 6.128282 GCAGCTAAACTCTTGCTTGTATTGTA 60.128 38.462 0.00 0.00 34.51 2.41
321 336 7.414540 GCAGCTAAACTCTTGCTTGTATTGTAT 60.415 37.037 0.00 0.00 34.51 2.29
322 337 7.907045 CAGCTAAACTCTTGCTTGTATTGTATG 59.093 37.037 0.00 0.00 34.51 2.39
323 338 7.607991 AGCTAAACTCTTGCTTGTATTGTATGT 59.392 33.333 0.00 0.00 32.61 2.29
364 476 2.678934 GGCTTTTCCCCCGGTTCC 60.679 66.667 0.00 0.00 0.00 3.62
365 477 2.116556 GCTTTTCCCCCGGTTCCA 59.883 61.111 0.00 0.00 0.00 3.53
378 490 2.097466 CCGGTTCCATGTACTGAAATGC 59.903 50.000 0.00 0.00 0.00 3.56
404 517 1.149148 CGATGGCAGCTGATGAGATG 58.851 55.000 20.43 0.00 38.73 2.90
523 645 7.148639 GCCAGTTTTCGTTTCTTTTCTTTTCTT 60.149 33.333 0.00 0.00 0.00 2.52
524 646 8.708742 CCAGTTTTCGTTTCTTTTCTTTTCTTT 58.291 29.630 0.00 0.00 0.00 2.52
571 723 1.302511 GAAGCGTCCAGGAAGGCAA 60.303 57.895 14.61 0.00 37.29 4.52
574 726 2.747855 CGTCCAGGAAGGCAAGCC 60.748 66.667 2.02 2.02 37.29 4.35
575 727 2.436109 GTCCAGGAAGGCAAGCCA 59.564 61.111 14.40 0.00 38.92 4.75
576 728 1.973812 GTCCAGGAAGGCAAGCCAC 60.974 63.158 14.40 6.80 38.92 5.01
577 729 2.115910 CCAGGAAGGCAAGCCACA 59.884 61.111 14.40 0.00 38.92 4.17
578 730 1.531365 CCAGGAAGGCAAGCCACAA 60.531 57.895 14.40 0.00 38.92 3.33
580 732 1.905354 AGGAAGGCAAGCCACAAGC 60.905 57.895 14.40 0.00 44.25 4.01
607 921 2.030717 CGTACATTCTCCCGAGATCTGG 60.031 54.545 0.00 0.00 37.29 3.86
625 939 1.957177 TGGCTATACGCTCCTTCTCAG 59.043 52.381 0.00 0.00 39.13 3.35
653 967 1.598701 GGCTAGGCAAGGGCAAAGTG 61.599 60.000 12.16 0.00 43.71 3.16
672 987 0.533491 GGGTACATCACACGTAGGCA 59.467 55.000 0.00 0.00 0.00 4.75
676 991 2.225068 ACATCACACGTAGGCATAGC 57.775 50.000 0.00 0.00 0.00 2.97
708 1023 1.069978 GATCTAGCCAGCCTTGGTCTC 59.930 57.143 0.00 0.00 46.80 3.36
716 1031 1.122019 AGCCTTGGTCTCGGTCACTT 61.122 55.000 0.00 0.00 0.00 3.16
717 1032 0.670854 GCCTTGGTCTCGGTCACTTC 60.671 60.000 0.00 0.00 0.00 3.01
767 1088 1.941325 AAGCAGTGTAGAATAGCGCC 58.059 50.000 2.29 0.00 0.00 6.53
769 1090 1.202463 AGCAGTGTAGAATAGCGCCAG 60.202 52.381 2.29 0.00 0.00 4.85
787 1108 2.432510 CCAGCCCTTTCTCCACTACTAG 59.567 54.545 0.00 0.00 0.00 2.57
788 1109 3.366396 CAGCCCTTTCTCCACTACTAGA 58.634 50.000 0.00 0.00 0.00 2.43
789 1110 3.383185 CAGCCCTTTCTCCACTACTAGAG 59.617 52.174 0.00 0.00 0.00 2.43
790 1111 3.011934 AGCCCTTTCTCCACTACTAGAGT 59.988 47.826 0.00 0.00 39.82 3.24
791 1112 3.382227 GCCCTTTCTCCACTACTAGAGTC 59.618 52.174 0.00 0.00 35.64 3.36
792 1113 4.862371 CCCTTTCTCCACTACTAGAGTCT 58.138 47.826 0.00 0.00 35.64 3.24
802 1123 3.774216 ACTACTAGAGTCTAGGACCACGT 59.226 47.826 27.07 12.91 29.95 4.49
811 1132 4.119862 GTCTAGGACCACGTACGTACATA 58.880 47.826 22.34 15.25 0.00 2.29
885 1206 1.641577 CTTTCCCACGATCGAACTCC 58.358 55.000 24.34 0.00 0.00 3.85
894 1215 0.318275 GATCGAACTCCCTAGCAGCG 60.318 60.000 0.00 0.00 0.00 5.18
895 1216 1.038130 ATCGAACTCCCTAGCAGCGT 61.038 55.000 0.00 0.00 0.00 5.07
896 1217 1.215647 CGAACTCCCTAGCAGCGTT 59.784 57.895 0.00 0.00 0.00 4.84
897 1218 0.802607 CGAACTCCCTAGCAGCGTTC 60.803 60.000 4.59 4.59 0.00 3.95
898 1219 0.246635 GAACTCCCTAGCAGCGTTCA 59.753 55.000 8.27 0.00 35.34 3.18
899 1220 0.247736 AACTCCCTAGCAGCGTTCAG 59.752 55.000 0.00 0.00 0.00 3.02
911 1232 2.235016 CGTTCAGCCGTTCACACGT 61.235 57.895 0.00 0.00 45.62 4.49
934 1255 2.557490 GCCTCCCTCACTATAAGTACGG 59.443 54.545 0.00 0.00 0.00 4.02
935 1256 3.749954 GCCTCCCTCACTATAAGTACGGA 60.750 52.174 0.00 0.00 0.00 4.69
938 1273 5.121380 TCCCTCACTATAAGTACGGAACT 57.879 43.478 0.00 0.00 41.49 3.01
1021 1356 4.323477 TCAAGAACCACCCGGGCG 62.323 66.667 24.08 12.24 42.05 6.13
1380 1715 4.039357 CACGCCGACGACCTGTCT 62.039 66.667 0.00 0.00 45.87 3.41
1515 1850 1.179174 CCTCGGTCTCAGTGTCCACA 61.179 60.000 0.00 0.00 0.00 4.17
1751 2095 1.733399 GTGAAGCGTCCACCGTCTC 60.733 63.158 0.00 0.00 39.32 3.36
1752 2096 2.504244 GAAGCGTCCACCGTCTCG 60.504 66.667 0.00 0.00 39.32 4.04
1791 2135 0.394192 GGGCATCCATGAGTCGATCA 59.606 55.000 0.00 0.00 43.70 2.92
1928 2272 9.671521 CTTTCGTTCATTTAGTAAGAACATACG 57.328 33.333 12.80 0.00 41.17 3.06
1929 2273 8.746922 TTCGTTCATTTAGTAAGAACATACGT 57.253 30.769 12.80 0.00 41.17 3.57
1930 2274 9.838975 TTCGTTCATTTAGTAAGAACATACGTA 57.161 29.630 12.80 0.00 41.17 3.57
1973 2322 5.041951 ACTATGTGTGTGTTTATTTGGCG 57.958 39.130 0.00 0.00 0.00 5.69
1980 2329 2.873472 TGTGTTTATTTGGCGAGACGTT 59.127 40.909 0.00 0.00 0.00 3.99
1989 2338 3.698029 TGGCGAGACGTTAGTAATACC 57.302 47.619 0.00 0.00 0.00 2.73
1990 2339 3.016031 TGGCGAGACGTTAGTAATACCA 58.984 45.455 0.00 0.00 0.00 3.25
1993 2342 4.033684 GCGAGACGTTAGTAATACCACTG 58.966 47.826 0.00 0.00 0.00 3.66
2009 2358 3.447586 ACCACTGCTACTACACTGTATGG 59.552 47.826 2.46 2.46 0.00 2.74
2010 2359 3.181475 CCACTGCTACTACACTGTATGGG 60.181 52.174 0.00 0.00 0.00 4.00
2012 2361 4.081642 CACTGCTACTACACTGTATGGGTT 60.082 45.833 0.00 0.00 32.50 4.11
2013 2362 4.159879 ACTGCTACTACACTGTATGGGTTC 59.840 45.833 0.00 0.00 32.50 3.62
2017 2366 5.163447 GCTACTACACTGTATGGGTTCATGA 60.163 44.000 0.00 0.00 34.96 3.07
2020 2369 3.942829 ACACTGTATGGGTTCATGAGTG 58.057 45.455 13.82 13.82 43.48 3.51
2021 2370 3.582647 ACACTGTATGGGTTCATGAGTGA 59.417 43.478 18.64 0.00 42.11 3.41
2024 2373 5.295292 CACTGTATGGGTTCATGAGTGAATC 59.705 44.000 0.00 0.00 45.46 2.52
2025 2374 4.441792 TGTATGGGTTCATGAGTGAATCG 58.558 43.478 0.00 0.00 44.71 3.34
2026 2375 3.912496 ATGGGTTCATGAGTGAATCGA 57.088 42.857 0.00 0.00 44.71 3.59
2027 2376 3.251479 TGGGTTCATGAGTGAATCGAG 57.749 47.619 0.00 0.00 44.71 4.04
2028 2377 1.936547 GGGTTCATGAGTGAATCGAGC 59.063 52.381 0.00 0.00 44.71 5.03
2036 2385 1.131504 GAGTGAATCGAGCGAGACTGT 59.868 52.381 0.00 0.00 0.00 3.55
2076 2425 3.057019 GGATTTGTTCCGTTTTGCTTCC 58.943 45.455 0.00 0.00 33.93 3.46
2078 2427 3.810310 TTTGTTCCGTTTTGCTTCCAT 57.190 38.095 0.00 0.00 0.00 3.41
2081 2430 4.130286 TGTTCCGTTTTGCTTCCATTTT 57.870 36.364 0.00 0.00 0.00 1.82
2083 2432 4.568760 TGTTCCGTTTTGCTTCCATTTTTC 59.431 37.500 0.00 0.00 0.00 2.29
2085 2434 4.367450 TCCGTTTTGCTTCCATTTTTCTG 58.633 39.130 0.00 0.00 0.00 3.02
2130 2484 3.344515 AGTTTAATCGGAAAGTGCTCCC 58.655 45.455 0.00 0.00 31.03 4.30
2145 2499 3.788766 CCCGAGAACGCGCTTTGG 61.789 66.667 5.73 5.11 38.29 3.28
2204 2558 0.805322 CTCGCAGGAGCTAAGCTGTG 60.805 60.000 0.00 0.00 39.88 3.66
2216 2570 1.784525 AAGCTGTGCTCGTCTGTAAC 58.215 50.000 0.00 0.00 38.25 2.50
2230 2584 2.965831 TCTGTAACTCTGCAACTCTGGT 59.034 45.455 0.00 0.00 0.00 4.00
2264 2618 9.846248 GTATTGTAAAGATGATAATCCAATGCC 57.154 33.333 3.65 0.00 0.00 4.40
2265 2619 6.899393 TGTAAAGATGATAATCCAATGCCC 57.101 37.500 0.00 0.00 0.00 5.36
2290 2644 7.170658 CCTCGATCTAGCTAAGATTCCTTTTTG 59.829 40.741 0.00 0.00 45.35 2.44
2291 2645 7.782049 TCGATCTAGCTAAGATTCCTTTTTGA 58.218 34.615 0.00 0.00 45.35 2.69
2292 2646 7.923344 TCGATCTAGCTAAGATTCCTTTTTGAG 59.077 37.037 0.00 0.00 45.35 3.02
2293 2647 7.170658 CGATCTAGCTAAGATTCCTTTTTGAGG 59.829 40.741 0.00 0.00 45.35 3.86
2294 2648 8.095452 ATCTAGCTAAGATTCCTTTTTGAGGA 57.905 34.615 0.00 0.00 44.65 3.71
2295 2649 8.722422 ATCTAGCTAAGATTCCTTTTTGAGGAT 58.278 33.333 0.00 0.00 44.65 3.24
2362 2716 0.462759 AGCGCTCCCATTAGCTGTTC 60.463 55.000 2.64 0.00 40.49 3.18
2386 2740 2.616510 CCTTTCCCACTTACTCCAGCTG 60.617 54.545 6.78 6.78 0.00 4.24
2407 2761 3.003480 GGTCATCCAGTGTTAAGTCTGC 58.997 50.000 0.00 0.00 0.00 4.26
2410 2764 2.724977 TCCAGTGTTAAGTCTGCTCG 57.275 50.000 0.00 0.00 0.00 5.03
2428 2782 2.826702 GTGTTCACACCCTCCCGT 59.173 61.111 0.00 0.00 40.85 5.28
2430 2784 1.458777 TGTTCACACCCTCCCGTCT 60.459 57.895 0.00 0.00 0.00 4.18
2432 2786 0.320508 GTTCACACCCTCCCGTCTTC 60.321 60.000 0.00 0.00 0.00 2.87
2488 2842 0.531200 AAGCAGTACTACGCAGGTCC 59.469 55.000 7.83 0.00 0.00 4.46
2566 2921 1.129437 GGCTCGAATTTCTGTGCACTC 59.871 52.381 19.41 4.87 0.00 3.51
2617 2977 3.207265 TGCACCTGAGTTTTGCTAAGA 57.793 42.857 0.00 0.00 37.16 2.10
2707 3067 0.394352 ATCACCGGCCACCAGAATTC 60.394 55.000 0.00 0.00 0.00 2.17
2719 3079 2.169352 ACCAGAATTCAGGATCAGGACG 59.831 50.000 22.56 0.00 0.00 4.79
2720 3080 2.208431 CAGAATTCAGGATCAGGACGC 58.792 52.381 8.44 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 108 4.648651 TCATGGGCATGACAGATTATCTG 58.351 43.478 19.49 19.49 42.42 2.90
129 132 1.066605 GTACGTACGTCATGGGCTCAT 59.933 52.381 26.53 0.00 0.00 2.90
130 133 0.452987 GTACGTACGTCATGGGCTCA 59.547 55.000 26.53 0.00 0.00 4.26
131 134 0.590732 CGTACGTACGTCATGGGCTC 60.591 60.000 33.95 5.60 44.13 4.70
132 135 1.430632 CGTACGTACGTCATGGGCT 59.569 57.895 33.95 0.00 44.13 5.19
133 136 3.987187 CGTACGTACGTCATGGGC 58.013 61.111 33.95 8.35 44.13 5.36
156 159 3.270027 TCTGCGGCCATGCATATATAAC 58.730 45.455 2.24 0.00 45.26 1.89
178 181 6.174760 TGTACACGGGCATTTCTTATTAAGT 58.825 36.000 3.45 0.00 0.00 2.24
192 195 3.976942 CGTATTATGTACTGTACACGGGC 59.023 47.826 21.84 10.84 42.23 6.13
219 225 0.790207 TTTCAGACGTTGATCTGCGC 59.210 50.000 0.00 0.00 44.94 6.09
221 227 3.928992 TCAGATTTCAGACGTTGATCTGC 59.071 43.478 17.39 0.62 44.94 4.26
231 237 7.122550 GCTCAATTATTCGTCAGATTTCAGAC 58.877 38.462 0.00 0.00 0.00 3.51
242 248 7.798486 AGTATACGATGCTCAATTATTCGTC 57.202 36.000 0.00 0.00 34.20 4.20
259 265 2.521105 AAGCCGGCCTAAAGTATACG 57.479 50.000 26.15 0.00 0.00 3.06
269 275 6.321821 TGGAAATTATATATAAGCCGGCCT 57.678 37.500 26.15 14.38 0.00 5.19
270 276 6.016276 CCATGGAAATTATATATAAGCCGGCC 60.016 42.308 26.15 5.07 0.00 6.13
272 278 6.545666 TGCCATGGAAATTATATATAAGCCGG 59.454 38.462 18.40 0.00 0.00 6.13
273 279 7.566760 TGCCATGGAAATTATATATAAGCCG 57.433 36.000 18.40 2.64 0.00 5.52
274 280 7.286316 AGCTGCCATGGAAATTATATATAAGCC 59.714 37.037 18.40 11.42 0.00 4.35
275 281 8.230472 AGCTGCCATGGAAATTATATATAAGC 57.770 34.615 18.40 0.00 0.00 3.09
279 285 9.759473 AGTTTAGCTGCCATGGAAATTATATAT 57.241 29.630 18.40 0.00 0.00 0.86
280 286 9.231297 GAGTTTAGCTGCCATGGAAATTATATA 57.769 33.333 18.40 0.00 0.00 0.86
282 288 7.290061 AGAGTTTAGCTGCCATGGAAATTATA 58.710 34.615 18.40 0.00 0.00 0.98
283 289 6.131961 AGAGTTTAGCTGCCATGGAAATTAT 58.868 36.000 18.40 0.00 0.00 1.28
284 290 5.509498 AGAGTTTAGCTGCCATGGAAATTA 58.491 37.500 18.40 0.00 0.00 1.40
286 292 3.973425 AGAGTTTAGCTGCCATGGAAAT 58.027 40.909 18.40 0.00 0.00 2.17
287 293 3.439857 AGAGTTTAGCTGCCATGGAAA 57.560 42.857 18.40 3.36 0.00 3.13
288 294 3.084039 CAAGAGTTTAGCTGCCATGGAA 58.916 45.455 18.40 3.09 0.00 3.53
289 295 2.715046 CAAGAGTTTAGCTGCCATGGA 58.285 47.619 18.40 0.00 0.00 3.41
290 296 1.133790 GCAAGAGTTTAGCTGCCATGG 59.866 52.381 7.63 7.63 0.00 3.66
291 297 2.089980 AGCAAGAGTTTAGCTGCCATG 58.910 47.619 0.00 0.00 37.20 3.66
292 298 2.490903 CAAGCAAGAGTTTAGCTGCCAT 59.509 45.455 0.00 0.00 38.86 4.40
293 299 1.881973 CAAGCAAGAGTTTAGCTGCCA 59.118 47.619 0.00 0.00 38.86 4.92
358 470 2.746904 TGCATTTCAGTACATGGAACCG 59.253 45.455 0.00 0.00 0.00 4.44
359 471 4.675510 CATGCATTTCAGTACATGGAACC 58.324 43.478 0.00 0.00 36.98 3.62
364 476 3.441163 GTGCCATGCATTTCAGTACATG 58.559 45.455 0.00 0.00 41.91 3.21
365 477 2.097954 CGTGCCATGCATTTCAGTACAT 59.902 45.455 0.00 0.00 41.91 2.29
378 490 2.827190 AGCTGCCATCGTGCCATG 60.827 61.111 0.00 0.00 0.00 3.66
404 517 5.003804 TGAAAGAGCTGTAAAACCAGATCC 58.996 41.667 0.00 0.00 46.48 3.36
523 645 8.322828 TGTACTAGTATTAATTGTGGCCAGAAA 58.677 33.333 20.52 11.47 0.00 2.52
524 646 7.853299 TGTACTAGTATTAATTGTGGCCAGAA 58.147 34.615 18.87 18.87 0.00 3.02
525 647 7.426606 TGTACTAGTATTAATTGTGGCCAGA 57.573 36.000 5.11 0.00 0.00 3.86
526 648 6.202954 GCTGTACTAGTATTAATTGTGGCCAG 59.797 42.308 5.11 5.30 0.00 4.85
527 649 6.053005 GCTGTACTAGTATTAATTGTGGCCA 58.947 40.000 0.00 0.00 0.00 5.36
528 650 5.469084 GGCTGTACTAGTATTAATTGTGGCC 59.531 44.000 5.75 0.00 0.00 5.36
574 726 3.585862 AGAATGTACGGTGTAGCTTGTG 58.414 45.455 0.00 0.00 0.00 3.33
575 727 3.368116 GGAGAATGTACGGTGTAGCTTGT 60.368 47.826 0.00 0.00 0.00 3.16
576 728 3.187700 GGAGAATGTACGGTGTAGCTTG 58.812 50.000 0.00 0.00 0.00 4.01
577 729 2.167900 GGGAGAATGTACGGTGTAGCTT 59.832 50.000 0.00 0.00 0.00 3.74
578 730 1.755380 GGGAGAATGTACGGTGTAGCT 59.245 52.381 0.00 0.00 0.00 3.32
580 732 2.019249 TCGGGAGAATGTACGGTGTAG 58.981 52.381 0.00 0.00 34.75 2.74
581 733 2.019249 CTCGGGAGAATGTACGGTGTA 58.981 52.381 0.00 0.00 39.18 2.90
582 734 0.815734 CTCGGGAGAATGTACGGTGT 59.184 55.000 0.00 0.00 39.18 4.16
583 735 1.100510 TCTCGGGAGAATGTACGGTG 58.899 55.000 0.00 0.00 39.18 4.94
584 736 1.955080 GATCTCGGGAGAATGTACGGT 59.045 52.381 2.00 0.00 41.36 4.83
585 737 2.030717 CAGATCTCGGGAGAATGTACGG 60.031 54.545 2.00 0.00 41.36 4.02
586 738 2.030717 CCAGATCTCGGGAGAATGTACG 60.031 54.545 2.00 0.00 41.36 3.67
587 739 2.288518 GCCAGATCTCGGGAGAATGTAC 60.289 54.545 2.00 0.00 41.36 2.90
653 967 0.533491 TGCCTACGTGTGATGTACCC 59.467 55.000 0.00 0.00 0.00 3.69
676 991 1.003116 GGCTAGATCGCAGCAAATGTG 60.003 52.381 19.80 0.00 40.95 3.21
716 1031 2.297880 TGGAAGACTCCGTTTTCGATGA 59.702 45.455 0.00 0.00 45.85 2.92
717 1032 2.683968 TGGAAGACTCCGTTTTCGATG 58.316 47.619 0.00 0.00 45.85 3.84
767 1088 3.366396 TCTAGTAGTGGAGAAAGGGCTG 58.634 50.000 0.00 0.00 0.00 4.85
769 1090 3.367321 ACTCTAGTAGTGGAGAAAGGGC 58.633 50.000 17.10 0.00 36.93 5.19
787 1108 1.731720 ACGTACGTGGTCCTAGACTC 58.268 55.000 22.14 0.00 32.47 3.36
788 1109 2.028112 TGTACGTACGTGGTCCTAGACT 60.028 50.000 30.25 1.29 32.47 3.24
789 1110 2.346803 TGTACGTACGTGGTCCTAGAC 58.653 52.381 30.25 17.61 0.00 2.59
790 1111 2.760634 TGTACGTACGTGGTCCTAGA 57.239 50.000 30.25 5.20 0.00 2.43
791 1112 4.122776 AGTATGTACGTACGTGGTCCTAG 58.877 47.826 30.25 0.00 0.00 3.02
792 1113 4.119862 GAGTATGTACGTACGTGGTCCTA 58.880 47.826 30.25 14.03 0.00 2.94
823 1144 1.717645 CGCAAAGTCACCACGTACTAC 59.282 52.381 0.00 0.00 0.00 2.73
824 1145 1.337703 ACGCAAAGTCACCACGTACTA 59.662 47.619 0.00 0.00 34.79 1.82
825 1146 0.103572 ACGCAAAGTCACCACGTACT 59.896 50.000 0.00 0.00 34.79 2.73
885 1206 2.887568 CGGCTGAACGCTGCTAGG 60.888 66.667 0.00 0.00 38.36 3.02
894 1215 1.563173 GACGTGTGAACGGCTGAAC 59.437 57.895 0.00 0.00 38.28 3.18
895 1216 1.947146 CGACGTGTGAACGGCTGAA 60.947 57.895 0.00 0.00 39.34 3.02
896 1217 2.354188 CGACGTGTGAACGGCTGA 60.354 61.111 0.00 0.00 39.34 4.26
897 1218 4.059459 GCGACGTGTGAACGGCTG 62.059 66.667 0.00 0.00 39.34 4.85
901 1222 3.103911 GGAGGCGACGTGTGAACG 61.104 66.667 0.00 0.00 39.31 3.95
911 1232 2.750141 ACTTATAGTGAGGGAGGCGA 57.250 50.000 0.00 0.00 0.00 5.54
915 1236 5.131784 AGTTCCGTACTTATAGTGAGGGAG 58.868 45.833 0.00 0.00 31.29 4.30
987 1322 1.134694 GACCATTTTCCACGCGCTC 59.865 57.895 5.73 0.00 0.00 5.03
1136 1471 4.740822 GCATCCGCACCCCCTTGT 62.741 66.667 0.00 0.00 38.36 3.16
1357 1692 3.248171 GTCGTCGGCGTGCTGATC 61.248 66.667 10.18 0.51 39.49 2.92
1380 1715 3.147595 CGCTGGATGGACCTCGGA 61.148 66.667 0.00 0.00 39.86 4.55
1671 2015 3.462678 GGCTCCTCCCAGGTCGAC 61.463 72.222 7.13 7.13 36.53 4.20
1767 2111 1.800805 GACTCATGGATGCCCGTATG 58.199 55.000 0.00 0.00 34.29 2.39
1771 2115 0.668706 GATCGACTCATGGATGCCCG 60.669 60.000 0.00 0.00 34.29 6.13
1773 2117 1.506493 GTGATCGACTCATGGATGCC 58.494 55.000 0.00 0.00 35.97 4.40
1956 2300 3.551551 GTCTCGCCAAATAAACACACAC 58.448 45.455 0.00 0.00 0.00 3.82
1973 2322 5.246145 AGCAGTGGTATTACTAACGTCTC 57.754 43.478 0.00 0.00 0.00 3.36
1980 2329 7.114754 ACAGTGTAGTAGCAGTGGTATTACTA 58.885 38.462 25.83 14.96 42.43 1.82
1989 2338 3.447586 ACCCATACAGTGTAGTAGCAGTG 59.552 47.826 9.25 0.27 43.43 3.66
1990 2339 3.709587 ACCCATACAGTGTAGTAGCAGT 58.290 45.455 9.25 0.00 0.00 4.40
1993 2342 4.730949 TGAACCCATACAGTGTAGTAGC 57.269 45.455 9.25 0.00 0.00 3.58
2012 2361 2.017049 TCTCGCTCGATTCACTCATGA 58.983 47.619 0.00 0.00 0.00 3.07
2013 2362 2.115595 GTCTCGCTCGATTCACTCATG 58.884 52.381 0.00 0.00 0.00 3.07
2017 2366 1.131504 GACAGTCTCGCTCGATTCACT 59.868 52.381 0.00 0.00 0.00 3.41
2020 2369 1.821336 CAGACAGTCTCGCTCGATTC 58.179 55.000 0.00 0.00 0.00 2.52
2021 2370 0.179150 GCAGACAGTCTCGCTCGATT 60.179 55.000 14.37 0.00 0.00 3.34
2024 2373 0.457509 AATGCAGACAGTCTCGCTCG 60.458 55.000 19.45 4.13 0.00 5.03
2025 2374 0.997932 CAATGCAGACAGTCTCGCTC 59.002 55.000 19.45 4.78 0.00 5.03
2026 2375 0.390866 CCAATGCAGACAGTCTCGCT 60.391 55.000 19.45 8.05 0.00 4.93
2027 2376 0.390340 TCCAATGCAGACAGTCTCGC 60.390 55.000 14.63 14.63 0.00 5.03
2028 2377 2.306341 ATCCAATGCAGACAGTCTCG 57.694 50.000 0.00 0.00 0.00 4.04
2036 2385 2.575735 TCCAACAGGTATCCAATGCAGA 59.424 45.455 0.00 0.00 0.00 4.26
2130 2484 3.011760 GACCCAAAGCGCGTTCTCG 62.012 63.158 8.43 0.00 40.37 4.04
2145 2499 4.070552 AAGCCTCCGCACGAGACC 62.071 66.667 0.00 0.00 41.63 3.85
2165 2519 1.989165 GTGAGCTGTTCTGCTTAGACG 59.011 52.381 0.00 0.00 44.17 4.18
2168 2522 2.257894 CGAGTGAGCTGTTCTGCTTAG 58.742 52.381 0.00 0.00 44.17 2.18
2204 2558 1.721926 GTTGCAGAGTTACAGACGAGC 59.278 52.381 0.00 0.00 0.00 5.03
2207 2561 2.983136 CAGAGTTGCAGAGTTACAGACG 59.017 50.000 0.00 0.00 0.00 4.18
2264 2618 5.975693 AAGGAATCTTAGCTAGATCGAGG 57.024 43.478 4.92 0.00 42.90 4.63
2265 2619 7.923344 TCAAAAAGGAATCTTAGCTAGATCGAG 59.077 37.037 0.00 0.00 42.90 4.04
2307 2661 8.734386 GCTAGATCATCCTCAAAAAGAAGAAAA 58.266 33.333 0.00 0.00 0.00 2.29
2311 2665 8.954950 TTAGCTAGATCATCCTCAAAAAGAAG 57.045 34.615 0.00 0.00 0.00 2.85
2362 2716 2.237392 CTGGAGTAAGTGGGAAAGGGAG 59.763 54.545 0.00 0.00 0.00 4.30
2386 2740 3.003480 GCAGACTTAACACTGGATGACC 58.997 50.000 0.00 0.00 35.05 4.02
2425 2779 1.269778 TGTCACTCTGCTTGAAGACGG 60.270 52.381 0.00 0.00 34.47 4.79
2428 2782 1.269778 CCGTGTCACTCTGCTTGAAGA 60.270 52.381 0.00 0.00 0.00 2.87
2430 2784 0.880278 GCCGTGTCACTCTGCTTGAA 60.880 55.000 0.65 0.00 0.00 2.69
2432 2786 0.952497 ATGCCGTGTCACTCTGCTTG 60.952 55.000 0.65 0.00 0.00 4.01
2617 2977 6.350612 GCTGTTTCTTAGACACCTACATCTCT 60.351 42.308 0.00 0.00 0.00 3.10
2707 3067 3.461773 ACCGGCGTCCTGATCCTG 61.462 66.667 6.01 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.