Multiple sequence alignment - TraesCS7A01G073300

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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 TraesCS7A01G073300 chr7A 100.000 3829 0 0 1 3829 38772810 38768982 0.000000e+00 7071
1 TraesCS7A01G073300 chr7A 94.107 3377 171 11 1 3374 546026731 546030082 0.000000e+00 5108
2 TraesCS7A01G073300 chr7A 94.930 355 18 0 3473 3827 546030083 546030437 1.200000e-154 556
3 TraesCS7A01G073300 chr5A 83.342 3722 558 50 1 3694 46230375 46234062 0.000000e+00 3382


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 TraesCS7A01G073300 chr7A 38768982 38772810 3828 True 7071 7071 100.0000 1 3829 1 chr7A.!!$R1 3828
1 TraesCS7A01G073300 chr7A 546026731 546030437 3706 False 2832 5108 94.5185 1 3827 2 chr7A.!!$F1 3826
2 TraesCS7A01G073300 chr5A 46230375 46234062 3687 False 3382 3382 83.3420 1 3694 1 chr5A.!!$F1 3693

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
977 980 0.325933 TCATGGCTCTTGACCCAGTG 59.674 55.0 0.00 0.00 34.01 3.66 F
1226 1230 0.320073 CACCACCAAGCAATTGCCAG 60.320 55.0 26.45 18.36 43.38 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2351 2359 0.176449 CTGCAGGGATGACATCACGA 59.824 55.000 17.08 2.78 37.89 4.35 R
3010 3027 1.141053 GCATCCAGTTTCGAGGGGTAT 59.859 52.381 0.00 0.00 0.00 2.73 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 2.191375 CACGCTGCCCTGGATGAT 59.809 61.111 0.00 0.00 0.00 2.45
141 143 1.202348 GCATCTCTCTGAAGCACGCTA 60.202 52.381 0.00 0.00 39.03 4.26
200 202 3.057245 GGCTTGTGGAAGAGATTGGTTTC 60.057 47.826 0.00 0.00 0.00 2.78
266 268 0.950116 GCAGTGCCTGGATTATGAGC 59.050 55.000 2.85 0.00 31.21 4.26
293 295 5.331098 GTTAGTGTTAGCCGTAGAGAGTTC 58.669 45.833 0.00 0.00 0.00 3.01
311 313 5.036117 AGTTCAGGCTGTCAGAAAGTAAA 57.964 39.130 15.27 0.00 0.00 2.01
329 331 4.938226 AGTAAAGTGCTCAAGTTCTATGCC 59.062 41.667 0.00 0.00 0.00 4.40
337 340 3.628008 TCAAGTTCTATGCCGAGGAGTA 58.372 45.455 0.00 0.00 0.00 2.59
390 393 1.561643 AGCGTGAAAGGGAGAGATGA 58.438 50.000 0.00 0.00 0.00 2.92
402 405 9.571816 GAAAGGGAGAGATGAAAATATCAATCT 57.428 33.333 0.00 0.00 42.54 2.40
562 565 5.187381 TGCATTTGTCATATTTGTCATGGGT 59.813 36.000 0.00 0.00 0.00 4.51
583 586 0.963856 ATGTACTCGCTCCGACCACA 60.964 55.000 0.00 0.00 32.02 4.17
612 615 5.639506 ACAACTACTCGACCATTGATTTCTG 59.360 40.000 0.00 0.00 0.00 3.02
613 616 4.759782 ACTACTCGACCATTGATTTCTGG 58.240 43.478 0.00 0.00 38.55 3.86
684 687 5.189736 TGAGTATGTCCTCCAGTATTTGCTT 59.810 40.000 0.00 0.00 0.00 3.91
687 690 4.574674 TGTCCTCCAGTATTTGCTTGAT 57.425 40.909 0.00 0.00 0.00 2.57
688 691 4.264253 TGTCCTCCAGTATTTGCTTGATG 58.736 43.478 0.00 0.00 0.00 3.07
715 718 6.975772 AGTACGAAAACTCAAGAGAGATATGC 59.024 38.462 3.73 0.00 44.98 3.14
750 753 1.303317 AACCAACCTCACCGGATGC 60.303 57.895 9.46 0.00 34.41 3.91
814 817 7.390162 AGTCATGTTTTCCACACATTTGTTTTT 59.610 29.630 0.00 0.00 38.61 1.94
821 824 4.160439 TCCACACATTTGTTTTTGCCTACA 59.840 37.500 0.00 0.00 31.66 2.74
942 945 1.548081 TGACTTCGACCCGGATACAA 58.452 50.000 0.73 0.00 0.00 2.41
977 980 0.325933 TCATGGCTCTTGACCCAGTG 59.674 55.000 0.00 0.00 34.01 3.66
1050 1053 1.843368 CTCCCCATGTGATTGCTGTT 58.157 50.000 0.00 0.00 0.00 3.16
1051 1054 2.173519 CTCCCCATGTGATTGCTGTTT 58.826 47.619 0.00 0.00 0.00 2.83
1052 1055 2.564062 CTCCCCATGTGATTGCTGTTTT 59.436 45.455 0.00 0.00 0.00 2.43
1089 1093 3.550437 ACTGGTCATATGCCTGTCTTC 57.450 47.619 17.09 0.00 33.76 2.87
1172 1176 2.095466 CCGGCGAATGTTTGTTATGTGT 60.095 45.455 9.30 0.00 0.00 3.72
1198 1202 4.821805 CACAAGGTTCAGTACACAATTCCT 59.178 41.667 0.00 0.00 0.00 3.36
1226 1230 0.320073 CACCACCAAGCAATTGCCAG 60.320 55.000 26.45 18.36 43.38 4.85
1250 1254 0.541063 TGGGACAACTCCACGCTCTA 60.541 55.000 0.00 0.00 38.52 2.43
1303 1307 0.669625 GTACTGGTTGCCGTCAGGAC 60.670 60.000 0.00 0.00 41.02 3.85
1312 1316 1.949257 CCGTCAGGACAACTTTGCC 59.051 57.895 0.00 0.00 41.02 4.52
1318 1322 0.535102 AGGACAACTTTGCCACTCCG 60.535 55.000 5.57 0.00 0.00 4.63
1348 1352 1.409241 CCACGTGTAGTAGGGCCTCTA 60.409 57.143 10.74 9.04 0.00 2.43
1368 1372 1.032014 GACCTTGCCAACTTCTTGCA 58.968 50.000 0.00 0.00 0.00 4.08
1384 1388 1.377725 GCAGCAGCAGTACCCACAT 60.378 57.895 0.00 0.00 41.58 3.21
1390 1394 0.532573 AGCAGTACCCACATCTCGTG 59.467 55.000 0.00 0.00 45.92 4.35
1466 1471 4.518970 TGCCTGTTTTTCAAGTACTCATCC 59.481 41.667 0.00 0.00 0.00 3.51
1471 1476 8.846211 CCTGTTTTTCAAGTACTCATCCTTTTA 58.154 33.333 0.00 0.00 0.00 1.52
1511 1517 8.756486 ATGAGATAACCATGATCATGAAACAA 57.244 30.769 32.71 15.55 41.20 2.83
1553 1559 2.095059 GCGTTTGACAGAAGCATCCAAT 60.095 45.455 0.00 0.00 0.00 3.16
1574 1580 2.575735 TGCCATCCAAGTGGTTCTATCA 59.424 45.455 0.00 0.00 41.47 2.15
1621 1628 7.809331 GTCAGATATGCTCAACTATTCAGAGAG 59.191 40.741 0.00 0.00 33.50 3.20
1658 1665 2.050077 GACCGTTGCCTTTGCTGC 60.050 61.111 0.00 0.00 38.71 5.25
1699 1706 5.356190 CAGAGTGTCATGCATCAGGTTTTAT 59.644 40.000 0.00 0.00 0.00 1.40
1700 1707 5.356190 AGAGTGTCATGCATCAGGTTTTATG 59.644 40.000 0.00 0.00 0.00 1.90
1711 1718 6.149973 GCATCAGGTTTTATGCATGCTCTATA 59.850 38.462 20.33 5.65 46.19 1.31
1767 1774 9.573166 TTTTTCTTTCCAATCTCTGATGACTAA 57.427 29.630 0.00 0.00 0.00 2.24
1775 1782 7.663081 TCCAATCTCTGATGACTAATATTTGGC 59.337 37.037 0.00 0.00 0.00 4.52
1790 1797 4.607293 ATTTGGCCTTTCTGTTCTTTCC 57.393 40.909 3.32 0.00 0.00 3.13
1808 1815 7.804843 TCTTTCCGTTTTTATTTAGGTGTCA 57.195 32.000 0.00 0.00 0.00 3.58
1900 1908 2.046217 GGAGAAGGTTCGGGCCAC 60.046 66.667 4.39 0.00 0.00 5.01
2018 2026 1.869754 CGCAGCTATGTCACCGCTTAT 60.870 52.381 0.00 0.00 0.00 1.73
2202 2210 2.122636 TTTGGCCAAACCCAGGGG 60.123 61.111 27.13 6.87 37.83 4.79
2209 2217 1.801242 CCAAACCCAGGGGAAACTTT 58.199 50.000 11.37 0.00 38.96 2.66
2260 2268 2.307496 TGCAACAAATCCATGGGAGT 57.693 45.000 13.02 2.62 34.05 3.85
2297 2305 2.281484 ACCGCACGCTGAAACCAT 60.281 55.556 0.00 0.00 0.00 3.55
2314 2322 8.607441 TGAAACCATAGATATGATAGTTGCAC 57.393 34.615 1.32 0.00 35.75 4.57
2334 2342 4.757149 GCACACTTCTCCAACTTAACTGAT 59.243 41.667 0.00 0.00 0.00 2.90
2337 2345 6.091441 CACACTTCTCCAACTTAACTGATAGC 59.909 42.308 0.00 0.00 0.00 2.97
2351 2359 3.957497 ACTGATAGCGATCTTCAGAGGTT 59.043 43.478 17.40 0.00 39.36 3.50
2370 2382 0.176449 TCGTGATGTCATCCCTGCAG 59.824 55.000 6.78 6.78 0.00 4.41
2371 2383 0.812811 CGTGATGTCATCCCTGCAGG 60.813 60.000 26.87 26.87 0.00 4.85
2373 2385 0.994247 TGATGTCATCCCTGCAGGTT 59.006 50.000 30.63 15.54 36.75 3.50
2382 2394 1.992557 TCCCTGCAGGTTTTAGGACAT 59.007 47.619 30.63 0.00 36.75 3.06
2513 2529 1.005394 CTTGTCCGCGTTACAGGGT 60.005 57.895 4.92 0.00 0.00 4.34
2515 2531 0.179051 TTGTCCGCGTTACAGGGTTT 60.179 50.000 4.92 0.00 0.00 3.27
2545 2561 0.538584 ATCAGCTCATTGGCAGTCGA 59.461 50.000 0.00 0.00 34.17 4.20
2597 2613 7.956328 ATATGTAGAAGGTACACTCAGTCAA 57.044 36.000 0.00 0.00 0.00 3.18
2678 2694 0.840617 TGCGGTAATGCCCCTTCATA 59.159 50.000 0.00 0.00 0.00 2.15
2685 2701 0.255890 ATGCCCCTTCATACGCACTT 59.744 50.000 0.00 0.00 33.31 3.16
2713 2729 7.582435 TCGAAAGCTCTGAAGTTATTTACTG 57.418 36.000 0.00 0.00 37.12 2.74
2889 2906 7.060383 ACCTCATCTCAGATGGTATTAACAG 57.940 40.000 14.96 2.06 0.00 3.16
2992 3009 7.662604 AAATGATTTCCTTTTTGCATCTGTC 57.337 32.000 0.00 0.00 0.00 3.51
3022 3039 0.254747 CCTGCCAATACCCCTCGAAA 59.745 55.000 0.00 0.00 0.00 3.46
3030 3047 0.539986 TACCCCTCGAAACTGGATGC 59.460 55.000 0.00 0.00 0.00 3.91
3165 3182 2.477863 GCTTCACCATGCGTTATTCCAC 60.478 50.000 0.00 0.00 0.00 4.02
3250 3267 4.501071 GGTAGTAGCCGAAGAAACATTCA 58.499 43.478 0.00 0.00 0.00 2.57
3264 3281 8.862325 AAGAAACATTCATCAGGTATGTACAA 57.138 30.769 0.00 0.00 36.89 2.41
3265 3282 8.268850 AGAAACATTCATCAGGTATGTACAAC 57.731 34.615 0.00 0.00 36.89 3.32
3304 3323 8.945481 CCATGCAAATGGTTCATAATTTCTTA 57.055 30.769 0.00 0.00 36.95 2.10
3331 3350 7.987750 TTAACACATAAATCCACAGTTGCTA 57.012 32.000 0.00 0.00 0.00 3.49
3345 3364 6.016276 CCACAGTTGCTAAAATATATCCACCC 60.016 42.308 0.00 0.00 0.00 4.61
3388 3407 0.178990 AAACAGGGGCTTGTGTCCTC 60.179 55.000 0.00 0.00 38.23 3.71
3391 3410 2.034221 GGGGCTTGTGTCCTCCAC 59.966 66.667 0.00 0.00 44.78 4.02
3400 3419 1.305802 TGTCCTCCACATAGCCCGT 60.306 57.895 0.00 0.00 0.00 5.28
3403 3422 1.144057 CCTCCACATAGCCCGTCAC 59.856 63.158 0.00 0.00 0.00 3.67
3430 3449 4.453480 TGGAACAAAACTGAAGATCCCT 57.547 40.909 0.00 0.00 31.92 4.20
3436 3455 4.103153 ACAAAACTGAAGATCCCTCTCACA 59.897 41.667 0.00 0.00 0.00 3.58
3444 3463 3.108376 AGATCCCTCTCACAAAGGTACC 58.892 50.000 2.73 2.73 31.51 3.34
3446 3465 3.839323 TCCCTCTCACAAAGGTACCTA 57.161 47.619 16.67 0.00 31.51 3.08
3447 3466 4.348020 TCCCTCTCACAAAGGTACCTAT 57.652 45.455 16.67 2.59 31.51 2.57
3448 3467 4.030913 TCCCTCTCACAAAGGTACCTATG 58.969 47.826 16.67 14.11 31.51 2.23
3451 3470 4.223032 CCTCTCACAAAGGTACCTATGTGT 59.777 45.833 16.67 16.49 42.80 3.72
3455 3474 6.042781 TCTCACAAAGGTACCTATGTGTTCTT 59.957 38.462 16.67 0.00 42.80 2.52
3460 3479 6.877611 AAGGTACCTATGTGTTCTTTGTTG 57.122 37.500 16.67 0.00 0.00 3.33
3461 3480 4.760204 AGGTACCTATGTGTTCTTTGTTGC 59.240 41.667 14.41 0.00 0.00 4.17
3463 3482 5.935789 GGTACCTATGTGTTCTTTGTTGCTA 59.064 40.000 4.06 0.00 0.00 3.49
3465 3484 7.120726 GGTACCTATGTGTTCTTTGTTGCTATT 59.879 37.037 4.06 0.00 0.00 1.73
3466 3485 7.145932 ACCTATGTGTTCTTTGTTGCTATTC 57.854 36.000 0.00 0.00 0.00 1.75
3468 3487 7.119846 ACCTATGTGTTCTTTGTTGCTATTCTC 59.880 37.037 0.00 0.00 0.00 2.87
3469 3488 5.342806 TGTGTTCTTTGTTGCTATTCTCG 57.657 39.130 0.00 0.00 0.00 4.04
3470 3489 4.151798 GTGTTCTTTGTTGCTATTCTCGC 58.848 43.478 0.00 0.00 0.00 5.03
3471 3490 3.120683 TGTTCTTTGTTGCTATTCTCGCG 60.121 43.478 0.00 0.00 0.00 5.87
3486 3507 5.696260 TTCTCGCGTGTGTTTATCTAATG 57.304 39.130 5.77 0.00 0.00 1.90
3614 3635 2.224769 TGAGTGCCTTAAACTTCAGGGG 60.225 50.000 0.00 0.00 0.00 4.79
3668 3689 1.768077 GGCTCTAGCACCCCCAGAT 60.768 63.158 4.07 0.00 44.36 2.90
3723 3744 1.837439 TCGGCTAGTTGATGGTTGGAT 59.163 47.619 0.00 0.00 0.00 3.41
3728 3749 4.503296 GGCTAGTTGATGGTTGGATCGTAT 60.503 45.833 0.00 0.00 0.00 3.06
3730 3751 5.864474 GCTAGTTGATGGTTGGATCGTATAG 59.136 44.000 0.00 0.00 0.00 1.31
3756 3777 4.355543 TTTCAAATCAGCTATCGGTTGC 57.644 40.909 0.00 0.00 0.00 4.17
3764 3785 0.804989 GCTATCGGTTGCTTGTTGCT 59.195 50.000 0.00 0.00 43.37 3.91
3794 3815 4.245660 ACTTGGATTCGTGTGTCATGTAG 58.754 43.478 0.00 0.00 0.00 2.74
3804 3825 5.400188 TCGTGTGTCATGTAGTTTAAGAACG 59.600 40.000 0.00 0.00 40.75 3.95
3809 3830 7.592533 TGTGTCATGTAGTTTAAGAACGTCTAC 59.407 37.037 0.00 0.00 40.75 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 1.003355 CCTGGCGCTGGAAGAAGAA 60.003 57.895 7.64 0.00 34.07 2.52
107 109 3.039202 GATGCGTGAAGTTGGGGCG 62.039 63.158 0.00 0.00 0.00 6.13
200 202 0.249657 GGAGCTTGAGCATACCTCCG 60.250 60.000 5.70 0.00 45.16 4.63
266 268 2.756760 TCTACGGCTAACACTAACCCTG 59.243 50.000 0.00 0.00 0.00 4.45
293 295 3.058639 GCACTTTACTTTCTGACAGCCTG 60.059 47.826 0.00 0.00 0.00 4.85
311 313 1.550524 TCGGCATAGAACTTGAGCACT 59.449 47.619 0.00 0.00 0.00 4.40
329 331 4.571176 GCCAAAGACCTTAAATACTCCTCG 59.429 45.833 0.00 0.00 0.00 4.63
337 340 4.337264 AGGGATGCCAAAGACCTTAAAT 57.663 40.909 5.86 0.00 0.00 1.40
390 393 9.638176 AGTGGATTGCTTCTAGATTGATATTTT 57.362 29.630 0.00 0.00 0.00 1.82
402 405 5.809001 ACTTGATGAAGTGGATTGCTTCTA 58.191 37.500 0.00 0.00 41.12 2.10
440 443 4.599047 AGCTATGCACTCCTGTCTTATC 57.401 45.455 0.00 0.00 0.00 1.75
471 474 4.200838 TCACGCATCAGGAATTGTTCTA 57.799 40.909 0.00 0.00 0.00 2.10
562 565 0.678684 TGGTCGGAGCGAGTACATGA 60.679 55.000 0.00 0.00 36.23 3.07
583 586 2.902705 TGGTCGAGTAGTTGTGCTTT 57.097 45.000 0.00 0.00 0.00 3.51
684 687 4.627058 TCTTGAGTTTTCGTACTGCATCA 58.373 39.130 0.00 0.00 0.00 3.07
687 690 4.037565 TCTCTCTTGAGTTTTCGTACTGCA 59.962 41.667 0.00 0.00 40.98 4.41
688 691 4.547532 TCTCTCTTGAGTTTTCGTACTGC 58.452 43.478 0.00 0.00 40.98 4.40
715 718 5.865552 GGTTGGTTGAATGATTGTTCATCAG 59.134 40.000 0.00 0.00 45.52 2.90
750 753 5.238583 ACGTCTACCTGAAAGAAGAAATGG 58.761 41.667 0.00 0.00 34.07 3.16
942 945 6.097839 AGAGCCATGATGAGCATTTTGTTTAT 59.902 34.615 8.26 0.00 34.15 1.40
977 980 5.869579 TGGGAATATGACATAGCTCCTTTC 58.130 41.667 18.95 9.65 0.00 2.62
1032 1035 2.307496 AAACAGCAATCACATGGGGA 57.693 45.000 0.00 0.00 0.00 4.81
1056 1059 9.672673 GGCATATGACCAGTACAAATAGATATT 57.327 33.333 6.97 0.00 0.00 1.28
1057 1060 9.051259 AGGCATATGACCAGTACAAATAGATAT 57.949 33.333 4.47 0.00 0.00 1.63
1058 1061 8.314021 CAGGCATATGACCAGTACAAATAGATA 58.686 37.037 4.47 0.00 0.00 1.98
1059 1062 7.164122 CAGGCATATGACCAGTACAAATAGAT 58.836 38.462 4.47 0.00 0.00 1.98
1063 1066 5.104360 AGACAGGCATATGACCAGTACAAAT 60.104 40.000 4.47 0.00 0.00 2.32
1172 1176 3.897141 TGTGTACTGAACCTTGTGTCA 57.103 42.857 0.00 0.00 0.00 3.58
1198 1202 0.534203 GCTTGGTGGTGGAAGACGAA 60.534 55.000 0.00 0.00 0.00 3.85
1226 1230 3.256960 TGGAGTTGTCCCAGCCCC 61.257 66.667 0.00 0.00 43.15 5.80
1237 1241 2.035576 AGTTTTCGTAGAGCGTGGAGTT 59.964 45.455 0.00 0.00 42.13 3.01
1250 1254 2.702592 TCTGTTGTGGGAGTTTTCGT 57.297 45.000 0.00 0.00 0.00 3.85
1303 1307 1.021202 TGTTCGGAGTGGCAAAGTTG 58.979 50.000 0.00 0.00 0.00 3.16
1312 1316 0.238289 GTGGCATTGTGTTCGGAGTG 59.762 55.000 0.00 0.00 0.00 3.51
1318 1322 1.871039 ACTACACGTGGCATTGTGTTC 59.129 47.619 26.29 0.00 46.61 3.18
1348 1352 1.322442 GCAAGAAGTTGGCAAGGTCT 58.678 50.000 0.00 3.22 33.87 3.85
1368 1372 0.539051 GAGATGTGGGTACTGCTGCT 59.461 55.000 0.00 0.00 0.00 4.24
1404 1408 3.580458 AGTACTCTGAATGCCAGACAGTT 59.420 43.478 0.00 0.00 46.38 3.16
1466 1471 6.149973 TCTCATCAGTCACCTGCAATTAAAAG 59.850 38.462 0.00 0.00 38.66 2.27
1471 1476 3.708403 TCTCATCAGTCACCTGCAATT 57.292 42.857 0.00 0.00 38.66 2.32
1472 1477 3.928005 ATCTCATCAGTCACCTGCAAT 57.072 42.857 0.00 0.00 38.66 3.56
1511 1517 4.133078 GCCTAATTGAGCTAGCATTCTGT 58.867 43.478 18.83 0.00 0.00 3.41
1553 1559 2.575735 TGATAGAACCACTTGGATGGCA 59.424 45.455 1.14 0.00 44.33 4.92
1642 1649 3.605664 GGCAGCAAAGGCAACGGT 61.606 61.111 0.00 0.00 44.61 4.83
1646 1653 2.612567 CGTACGGCAGCAAAGGCAA 61.613 57.895 7.57 0.00 44.61 4.52
1751 1758 7.664731 AGGCCAAATATTAGTCATCAGAGATTG 59.335 37.037 5.01 0.00 0.00 2.67
1767 1774 5.105756 CGGAAAGAACAGAAAGGCCAAATAT 60.106 40.000 5.01 0.00 0.00 1.28
1770 1777 2.360801 CGGAAAGAACAGAAAGGCCAAA 59.639 45.455 5.01 0.00 0.00 3.28
1775 1782 8.642908 AAATAAAAACGGAAAGAACAGAAAGG 57.357 30.769 0.00 0.00 0.00 3.11
1790 1797 7.013529 GCAGTAGTGACACCTAAATAAAAACG 58.986 38.462 0.42 0.00 0.00 3.60
1808 1815 3.955650 ACGTACATTCTTGGCAGTAGT 57.044 42.857 0.00 0.00 0.00 2.73
1900 1908 3.009143 GCAGTTATACAATAGGGAGGGGG 59.991 52.174 0.00 0.00 0.00 5.40
1906 1914 2.290071 CGGGGGCAGTTATACAATAGGG 60.290 54.545 0.00 0.00 0.00 3.53
1911 1919 0.542805 GGACGGGGGCAGTTATACAA 59.457 55.000 0.00 0.00 0.00 2.41
2202 2210 9.803315 AAAATGTACTTCCTCTTTGAAAGTTTC 57.197 29.630 8.75 8.75 0.00 2.78
2209 2217 6.545666 TGCTGAAAAATGTACTTCCTCTTTGA 59.454 34.615 0.00 0.00 0.00 2.69
2297 2305 7.287696 TGGAGAAGTGTGCAACTATCATATCTA 59.712 37.037 0.00 0.00 38.56 1.98
2314 2322 5.289675 CGCTATCAGTTAAGTTGGAGAAGTG 59.710 44.000 0.00 0.00 0.00 3.16
2334 2342 2.097629 CACGAACCTCTGAAGATCGCTA 59.902 50.000 5.94 0.00 36.02 4.26
2337 2345 2.921634 TCACGAACCTCTGAAGATCG 57.078 50.000 4.64 4.64 37.54 3.69
2351 2359 0.176449 CTGCAGGGATGACATCACGA 59.824 55.000 17.08 2.78 37.89 4.35
2452 2468 2.083167 AATGCCTGCAAAAACCATCG 57.917 45.000 0.00 0.00 0.00 3.84
2456 2472 5.523552 GGATAACATAATGCCTGCAAAAACC 59.476 40.000 0.00 0.00 0.00 3.27
2513 2529 6.327154 CAATGAGCTGATGAAACATAGCAAA 58.673 36.000 0.00 0.00 38.59 3.68
2515 2531 4.337274 CCAATGAGCTGATGAAACATAGCA 59.663 41.667 0.00 0.00 38.59 3.49
2545 2561 2.029828 AGCAAGTTCGTGATCGAGACTT 60.030 45.455 0.00 10.06 46.81 3.01
2597 2613 5.969086 ACATTCCCTATTGGCTTCCATATT 58.031 37.500 0.00 0.00 31.53 1.28
2709 2725 8.630054 AACTTCATTGGCAAGTATAAACAGTA 57.370 30.769 5.96 0.00 32.71 2.74
2713 2729 9.946165 GGTATAACTTCATTGGCAAGTATAAAC 57.054 33.333 5.96 0.00 32.71 2.01
2826 2843 2.094182 CCTTGCCGACTAGTTGCTTCTA 60.094 50.000 16.39 1.36 0.00 2.10
2947 2964 5.623956 TTTTTGAGTTAGGGACACAGAGA 57.376 39.130 0.00 0.00 30.44 3.10
3010 3027 1.141053 GCATCCAGTTTCGAGGGGTAT 59.859 52.381 0.00 0.00 0.00 2.73
3022 3039 4.756642 CCACATCAATATAACGCATCCAGT 59.243 41.667 0.00 0.00 0.00 4.00
3030 3047 6.427853 ACATCATGTCCCACATCAATATAACG 59.572 38.462 0.00 0.00 36.53 3.18
3081 3098 2.744352 GGCCATTCCCTCTGATCTTT 57.256 50.000 0.00 0.00 0.00 2.52
3165 3182 4.454847 CCAGCATAATACTCATTCAGGCAG 59.545 45.833 0.00 0.00 0.00 4.85
3228 3245 4.501071 TGAATGTTTCTTCGGCTACTACC 58.499 43.478 0.00 0.00 0.00 3.18
3250 3267 7.067008 GCTAAATGTTGGTTGTACATACCTGAT 59.933 37.037 20.63 11.40 35.26 2.90
3264 3281 1.472480 GCATGGTCGCTAAATGTTGGT 59.528 47.619 0.00 0.00 0.00 3.67
3265 3282 1.472082 TGCATGGTCGCTAAATGTTGG 59.528 47.619 0.00 0.00 0.00 3.77
3304 3323 8.367156 AGCAACTGTGGATTTATGTGTTAAAAT 58.633 29.630 0.00 0.00 33.60 1.82
3345 3364 6.728200 TCTTCACTGCACAAATAAGTTTGAG 58.272 36.000 7.79 1.54 46.03 3.02
3388 3407 1.686587 TCATAGTGACGGGCTATGTGG 59.313 52.381 16.87 0.61 43.62 4.17
3391 3410 2.562738 TCCATCATAGTGACGGGCTATG 59.437 50.000 13.46 13.46 44.19 2.23
3400 3419 7.223584 TCTTCAGTTTTGTTCCATCATAGTGA 58.776 34.615 0.00 0.00 0.00 3.41
3403 3422 7.201767 GGGATCTTCAGTTTTGTTCCATCATAG 60.202 40.741 0.00 0.00 0.00 2.23
3412 3431 5.066593 GTGAGAGGGATCTTCAGTTTTGTT 58.933 41.667 0.00 0.00 0.00 2.83
3415 3434 4.982241 TGTGAGAGGGATCTTCAGTTTT 57.018 40.909 0.00 0.00 0.00 2.43
3421 3440 3.990959 ACCTTTGTGAGAGGGATCTTC 57.009 47.619 0.00 0.00 38.65 2.87
3436 3455 6.238925 GCAACAAAGAACACATAGGTACCTTT 60.239 38.462 22.11 9.84 0.00 3.11
3444 3463 7.176075 CGAGAATAGCAACAAAGAACACATAG 58.824 38.462 0.00 0.00 0.00 2.23
3446 3465 5.617751 GCGAGAATAGCAACAAAGAACACAT 60.618 40.000 0.00 0.00 36.44 3.21
3447 3466 4.319477 GCGAGAATAGCAACAAAGAACACA 60.319 41.667 0.00 0.00 36.44 3.72
3448 3467 4.151798 GCGAGAATAGCAACAAAGAACAC 58.848 43.478 0.00 0.00 36.44 3.32
3451 3470 3.064207 ACGCGAGAATAGCAACAAAGAA 58.936 40.909 15.93 0.00 36.06 2.52
3455 3474 1.459209 CACACGCGAGAATAGCAACAA 59.541 47.619 15.93 0.00 36.06 2.83
3460 3479 3.797256 AGATAAACACACGCGAGAATAGC 59.203 43.478 15.93 0.64 0.00 2.97
3461 3480 7.167635 ACATTAGATAAACACACGCGAGAATAG 59.832 37.037 15.93 0.53 0.00 1.73
3463 3482 5.810587 ACATTAGATAAACACACGCGAGAAT 59.189 36.000 15.93 0.00 0.00 2.40
3465 3484 4.740268 ACATTAGATAAACACACGCGAGA 58.260 39.130 15.93 0.00 0.00 4.04
3466 3485 5.742453 ACTACATTAGATAAACACACGCGAG 59.258 40.000 15.93 7.88 0.00 5.03
3468 3487 5.944049 ACTACATTAGATAAACACACGCG 57.056 39.130 3.53 3.53 0.00 6.01
3469 3488 6.034256 ACGAACTACATTAGATAAACACACGC 59.966 38.462 0.00 0.00 0.00 5.34
3470 3489 7.502177 ACGAACTACATTAGATAAACACACG 57.498 36.000 0.00 0.00 0.00 4.49
3486 3507 6.806120 AACAAATGCTCAAAAACGAACTAC 57.194 33.333 0.00 0.00 0.00 2.73
3599 3620 4.158579 GCAGAATTCCCCTGAAGTTTAAGG 59.841 45.833 0.65 0.00 33.05 2.69
3614 3635 0.375106 GCGCCACACTAGCAGAATTC 59.625 55.000 0.00 0.00 0.00 2.17
3668 3689 4.265893 ACTGATTCGAGCTGAAGAGACTA 58.734 43.478 0.00 0.00 40.65 2.59
3708 3729 7.450323 TGATCTATACGATCCAACCATCAACTA 59.550 37.037 0.00 0.00 46.52 2.24
3728 3749 7.445121 ACCGATAGCTGATTTGAAATGATCTA 58.555 34.615 0.00 0.00 0.00 1.98
3730 3751 6.551385 ACCGATAGCTGATTTGAAATGATC 57.449 37.500 0.00 0.00 0.00 2.92
3737 3758 3.266510 AGCAACCGATAGCTGATTTGA 57.733 42.857 0.00 0.00 40.13 2.69
3756 3777 6.932356 ATCCAAGTACATGATAGCAACAAG 57.068 37.500 0.00 0.00 0.00 3.16
3764 3785 5.972935 ACACACGAATCCAAGTACATGATA 58.027 37.500 0.00 0.00 0.00 2.15
3794 3815 4.492611 CTGGGAGGTAGACGTTCTTAAAC 58.507 47.826 0.00 0.00 0.00 2.01
3804 3825 2.768769 GGGCCCTGGGAGGTAGAC 60.769 72.222 19.27 0.00 31.93 2.59


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

AutoCloner maintained by Alex Coulton.