Multiple sequence alignment - TraesCS3D01G113300

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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 TraesCS3D01G113300 chr3D 100.000 3936 0 0 1 3936 67461754 67457819 0.000000e+00 7269
1 TraesCS3D01G113300 chr3A 91.357 4015 164 71 1 3936 78720630 78716720 0.000000e+00 5323
2 TraesCS3D01G113300 chr3B 89.539 4053 226 84 4 3936 112265772 112261798 0.000000e+00 4953
3 TraesCS3D01G113300 chr1D 86.066 244 32 2 2177 2419 473857518 473857760 1.080000e-65 261
4 TraesCS3D01G113300 chr1B 85.656 244 33 2 2177 2419 658909952 658910194 5.050000e-64 255
5 TraesCS3D01G113300 chrUn 84.585 253 37 2 2177 2428 1493065 1492814 2.350000e-62 250
6 TraesCS3D01G113300 chr7D 90.741 108 10 0 2159 2266 55389130 55389237 1.140000e-30 145


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 TraesCS3D01G113300 chr3D 67457819 67461754 3935 True 7269 7269 100.000 1 3936 1 chr3D.!!$R1 3935
1 TraesCS3D01G113300 chr3A 78716720 78720630 3910 True 5323 5323 91.357 1 3936 1 chr3A.!!$R1 3935
2 TraesCS3D01G113300 chr3B 112261798 112265772 3974 True 4953 4953 89.539 4 3936 1 chr3B.!!$R1 3932

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
597 640 0.179124 CCTGCTTACCTCACTCGCTC 60.179 60.0 0.00 0.00 0.0 5.03 F
973 1034 0.392729 CAAAGCTCCCTCTCTGCAGG 60.393 60.0 15.13 4.77 0.0 4.85 F
974 1035 0.839853 AAAGCTCCCTCTCTGCAGGT 60.840 55.0 15.13 0.00 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 2310 3.631227 TGCTCATCATCAACACACAAACA 59.369 39.130 0.00 0.0 0.00 2.83 R
2661 2817 0.247736 CAAGGAGCTCTTGCCGTAGT 59.752 55.000 14.64 0.0 45.24 2.73 R
2969 3125 2.501261 GATAATCCACGGGCCTAAACC 58.499 52.381 0.84 0.0 0.00 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
59 60 3.846023 GCATGCACGTAAATCCTGAATCG 60.846 47.826 14.21 0.00 0.00 3.34
111 113 6.305693 AGCAAGGCGTTATATCAGAATTTC 57.694 37.500 0.00 0.00 0.00 2.17
180 193 0.321298 ACTCAAATTGGACCGACCGG 60.321 55.000 6.94 6.94 42.61 5.28
261 295 2.226912 CCCCAAAACGAATTCAACGCTA 59.773 45.455 6.22 0.00 0.00 4.26
312 346 4.630069 ACATACGCTAACCAAGAACACATC 59.370 41.667 0.00 0.00 0.00 3.06
313 347 3.402628 ACGCTAACCAAGAACACATCT 57.597 42.857 0.00 0.00 41.32 2.90
314 348 4.530710 ACGCTAACCAAGAACACATCTA 57.469 40.909 0.00 0.00 37.42 1.98
315 349 4.890088 ACGCTAACCAAGAACACATCTAA 58.110 39.130 0.00 0.00 37.42 2.10
316 350 4.929808 ACGCTAACCAAGAACACATCTAAG 59.070 41.667 0.00 0.00 37.42 2.18
317 351 4.201724 CGCTAACCAAGAACACATCTAAGC 60.202 45.833 0.00 0.00 37.42 3.09
318 352 4.938226 GCTAACCAAGAACACATCTAAGCT 59.062 41.667 0.00 0.00 37.42 3.74
319 353 6.106673 GCTAACCAAGAACACATCTAAGCTA 58.893 40.000 0.00 0.00 37.42 3.32
320 354 6.256757 GCTAACCAAGAACACATCTAAGCTAG 59.743 42.308 0.00 0.00 37.42 3.42
351 390 1.549620 CAAAGCCTCTCTCTCAGAGCA 59.450 52.381 0.00 0.00 46.90 4.26
355 394 2.028203 AGCCTCTCTCTCAGAGCAAAAC 60.028 50.000 0.00 0.00 46.90 2.43
369 408 2.094545 AGCAAAACGGAAGGATGATTGC 60.095 45.455 0.00 0.00 41.34 3.56
387 430 1.154413 CACAATGAAGGTCGCACGC 60.154 57.895 0.00 0.00 0.00 5.34
388 431 1.596752 ACAATGAAGGTCGCACGCA 60.597 52.632 0.00 0.00 0.00 5.24
392 435 2.429571 GAAGGTCGCACGCACGTA 60.430 61.111 0.00 0.00 0.00 3.57
427 470 4.241555 CGCATTCGGAGGGGAGGG 62.242 72.222 0.00 0.00 0.00 4.30
457 500 2.747686 GAACCAACGCTGAGGGGA 59.252 61.111 0.51 0.00 0.00 4.81
597 640 0.179124 CCTGCTTACCTCACTCGCTC 60.179 60.000 0.00 0.00 0.00 5.03
598 641 0.524392 CTGCTTACCTCACTCGCTCG 60.524 60.000 0.00 0.00 0.00 5.03
599 642 1.874466 GCTTACCTCACTCGCTCGC 60.874 63.158 0.00 0.00 0.00 5.03
600 643 1.803943 CTTACCTCACTCGCTCGCT 59.196 57.895 0.00 0.00 0.00 4.93
682 737 4.091424 GTTGACATTGTTTATGAGCTCGC 58.909 43.478 9.64 0.00 37.69 5.03
684 739 3.618594 TGACATTGTTTATGAGCTCGCTC 59.381 43.478 9.64 11.83 43.01 5.03
695 754 3.572539 CTCGCTCGCTCTCTCGCT 61.573 66.667 0.00 0.00 0.00 4.93
696 755 3.506312 CTCGCTCGCTCTCTCGCTC 62.506 68.421 0.00 0.00 0.00 5.03
697 756 4.936248 CGCTCGCTCTCTCGCTCG 62.936 72.222 0.00 0.00 0.00 5.03
699 758 3.572539 CTCGCTCTCTCGCTCGCT 61.573 66.667 0.00 0.00 0.00 4.93
700 759 3.506312 CTCGCTCTCTCGCTCGCTC 62.506 68.421 0.00 0.00 0.00 5.03
742 801 2.585247 GAGCCGCCGTGATGGTAC 60.585 66.667 0.00 0.00 41.21 3.34
759 820 1.066152 GTACGGTAGGTTAAGGAGCCG 59.934 57.143 0.00 0.00 44.10 5.52
854 915 2.628657 AGTCAGAAAGTGTAGGCTTCGT 59.371 45.455 0.00 0.00 0.00 3.85
969 1030 1.538950 GCAAACAAAGCTCCCTCTCTG 59.461 52.381 0.00 0.00 0.00 3.35
971 1032 0.767375 AACAAAGCTCCCTCTCTGCA 59.233 50.000 0.00 0.00 0.00 4.41
973 1034 0.392729 CAAAGCTCCCTCTCTGCAGG 60.393 60.000 15.13 4.77 0.00 4.85
974 1035 0.839853 AAAGCTCCCTCTCTGCAGGT 60.840 55.000 15.13 0.00 0.00 4.00
975 1036 0.839853 AAGCTCCCTCTCTGCAGGTT 60.840 55.000 15.13 0.00 0.00 3.50
1077 1146 4.380531 CCATGGAGGTATGTACACACATC 58.619 47.826 10.38 10.38 44.42 3.06
1078 1147 4.380531 CATGGAGGTATGTACACACATCC 58.619 47.826 26.91 26.91 44.42 3.51
1168 1280 4.806247 CCTACATGTTCGTTCTTGAGATCC 59.194 45.833 2.30 0.00 0.00 3.36
1189 1301 4.697352 TCCAGCTGAAACTGAATTAGCTTC 59.303 41.667 17.39 0.00 42.38 3.86
1194 1306 7.272948 CAGCTGAAACTGAATTAGCTTCAATTC 59.727 37.037 8.42 13.01 43.20 2.17
1290 1402 1.609208 CCAGCAAGGTACTGCAAACT 58.391 50.000 9.50 0.00 40.86 2.66
1291 1403 2.778299 CCAGCAAGGTACTGCAAACTA 58.222 47.619 9.50 0.00 40.86 2.24
1292 1404 2.484264 CCAGCAAGGTACTGCAAACTAC 59.516 50.000 9.50 0.00 40.86 2.73
1293 1405 3.403038 CAGCAAGGTACTGCAAACTACT 58.597 45.455 9.50 0.00 40.86 2.57
1295 1407 2.742589 GCAAGGTACTGCAAACTACTCC 59.257 50.000 2.40 0.00 40.86 3.85
1296 1408 2.993899 CAAGGTACTGCAAACTACTCCG 59.006 50.000 0.00 0.00 40.86 4.63
1325 1439 4.758674 TCTGAAAGTCAAATTGAGAGCTGG 59.241 41.667 0.00 0.00 33.76 4.85
1338 1452 7.676683 ATTGAGAGCTGGTTAATTAGGAGTA 57.323 36.000 0.00 0.00 0.00 2.59
1340 1454 5.363005 TGAGAGCTGGTTAATTAGGAGTACC 59.637 44.000 0.00 0.00 0.00 3.34
1394 1525 7.328249 TGAATTGCACCAAATTAAAGATCGAAC 59.672 33.333 0.00 0.00 29.89 3.95
1401 1532 6.208599 ACCAAATTAAAGATCGAACCATGTGT 59.791 34.615 0.00 0.00 0.00 3.72
1403 1534 6.817765 AATTAAAGATCGAACCATGTGTGT 57.182 33.333 0.00 0.00 0.00 3.72
1406 1537 7.731882 TTAAAGATCGAACCATGTGTGTTTA 57.268 32.000 0.00 0.00 0.00 2.01
1407 1538 6.817765 AAAGATCGAACCATGTGTGTTTAT 57.182 33.333 0.00 0.00 0.00 1.40
1412 1543 8.956426 AGATCGAACCATGTGTGTTTATTTTAT 58.044 29.630 0.00 0.00 0.00 1.40
1424 1555 9.000018 GTGTGTTTATTTTATGAAGAATCGCTC 58.000 33.333 0.00 0.00 0.00 5.03
2072 2221 4.075997 GGTACGTTCGCGCATACA 57.924 55.556 8.75 0.00 46.04 2.29
2076 2225 1.322338 GTACGTTCGCGCATACAACAT 59.678 47.619 8.75 0.00 46.04 2.71
2077 2226 1.631284 ACGTTCGCGCATACAACATA 58.369 45.000 8.75 0.00 46.04 2.29
2078 2227 1.322338 ACGTTCGCGCATACAACATAC 59.678 47.619 8.75 0.00 46.04 2.39
2079 2228 1.322040 CGTTCGCGCATACAACATACA 59.678 47.619 8.75 0.00 0.00 2.29
2080 2229 2.034086 CGTTCGCGCATACAACATACAT 60.034 45.455 8.75 0.00 0.00 2.29
2083 2232 2.722116 TCGCGCATACAACATACATACG 59.278 45.455 8.75 0.00 0.00 3.06
2156 2310 7.649533 TTCAAAATCATGATGAGCTAACCAT 57.350 32.000 9.46 0.00 0.00 3.55
2465 2621 2.035783 GGCACCACCTCCCTTTCC 59.964 66.667 0.00 0.00 34.51 3.13
2969 3125 2.908626 GCGCCGTGTAGATTTCTTTTTG 59.091 45.455 0.00 0.00 0.00 2.44
2975 3131 6.581166 GCCGTGTAGATTTCTTTTTGGTTTAG 59.419 38.462 0.00 0.00 0.00 1.85
2976 3132 7.081976 CCGTGTAGATTTCTTTTTGGTTTAGG 58.918 38.462 0.00 0.00 0.00 2.69
2977 3133 6.581166 CGTGTAGATTTCTTTTTGGTTTAGGC 59.419 38.462 0.00 0.00 0.00 3.93
2978 3134 6.866770 GTGTAGATTTCTTTTTGGTTTAGGCC 59.133 38.462 0.00 0.00 0.00 5.19
2979 3135 5.483685 AGATTTCTTTTTGGTTTAGGCCC 57.516 39.130 0.00 0.00 0.00 5.80
2980 3136 3.737032 TTTCTTTTTGGTTTAGGCCCG 57.263 42.857 0.00 0.00 0.00 6.13
2981 3137 2.368311 TCTTTTTGGTTTAGGCCCGT 57.632 45.000 0.00 0.00 0.00 5.28
2983 3139 1.000394 CTTTTTGGTTTAGGCCCGTGG 60.000 52.381 0.00 0.00 0.00 4.94
2984 3140 0.185416 TTTTGGTTTAGGCCCGTGGA 59.815 50.000 0.00 0.00 0.00 4.02
3007 3166 7.870954 TGGATTATCCTTGTATACGCAGTTAAG 59.129 37.037 12.91 0.00 38.84 1.85
3030 3189 6.203647 AGTTTACTTCGTTTTGGTGTTATGC 58.796 36.000 0.00 0.00 0.00 3.14
3235 3394 8.668510 ACTTGTTTATGCTCTCATATACCAAG 57.331 34.615 0.00 0.00 36.74 3.61
3292 3451 0.536233 TTGTGGCGTTATGGTGTGCT 60.536 50.000 0.00 0.00 0.00 4.40
3317 3476 4.420168 ACTTGGTGTTTTGTTGACATTCG 58.580 39.130 0.00 0.00 0.00 3.34
3351 3510 2.176247 TAGGGTTCCTCCATCTCACC 57.824 55.000 0.00 0.00 38.11 4.02
3396 3555 4.162888 ACATAGAGGCACAAGACATCATCA 59.837 41.667 0.00 0.00 0.00 3.07
3432 3591 7.246674 TCAATAACGTAGGAATGATTGAAGC 57.753 36.000 0.00 0.00 32.03 3.86
3472 3631 6.778069 TCCACAATTGGTTTAGGATTACAACA 59.222 34.615 10.83 0.00 44.35 3.33
3495 3654 3.331889 AGATGGATGGAAGAGTTGGTGTT 59.668 43.478 0.00 0.00 0.00 3.32
3506 3665 0.247185 GTTGGTGTTGATGGCATGGG 59.753 55.000 3.81 0.00 0.00 4.00
3526 3685 3.197333 GGGTGATGATGATGGAGATCGAT 59.803 47.826 0.00 0.00 0.00 3.59
3553 3712 5.523552 CGTGGTCTATGTGATTGAAGCAATA 59.476 40.000 0.00 0.00 33.90 1.90
3559 3718 7.493971 GTCTATGTGATTGAAGCAATAGTGAGT 59.506 37.037 0.00 0.00 33.90 3.41
3573 3732 6.183360 GCAATAGTGAGTTGGAGACCCTTATA 60.183 42.308 0.00 0.00 0.00 0.98
3583 3742 5.486332 TGGAGACCCTTATATTGATTCCCT 58.514 41.667 0.00 0.00 0.00 4.20
3596 3755 1.301913 ATTCCCTCTCCGGACCCCTA 61.302 60.000 0.00 0.00 33.16 3.53
3607 3766 0.979187 GGACCCCTACCGATGGTGAA 60.979 60.000 0.00 0.00 36.19 3.18
3611 3770 1.280998 CCCCTACCGATGGTGAAGTTT 59.719 52.381 0.00 0.00 36.19 2.66
3619 3778 7.713507 CCTACCGATGGTGAAGTTTTGATATTA 59.286 37.037 0.00 0.00 36.19 0.98
3662 3821 2.483877 TGTTTGTCAGATCCGATTGCAC 59.516 45.455 0.00 0.00 0.00 4.57
3664 3823 0.530288 TGTCAGATCCGATTGCACGA 59.470 50.000 0.00 0.00 35.09 4.35
3693 3852 1.975407 GTCGACCCAAGGGAGACGA 60.975 63.158 13.15 15.68 37.01 4.20
3714 3873 2.508439 CGTGCCGTATGACCGCTT 60.508 61.111 0.00 0.00 0.00 4.68
3747 3906 0.388006 TGCTCGTACCACACATCGTG 60.388 55.000 0.00 0.00 45.92 4.35
3751 3910 1.337387 TCGTACCACACATCGTGTTCA 59.663 47.619 0.00 0.00 45.08 3.18
3778 3938 1.555075 AGAGCCGAATGCAGTTTCCTA 59.445 47.619 0.00 0.00 44.83 2.94
3821 3981 4.405358 GGAAGGTTTTATGGCATCCAATCA 59.595 41.667 1.65 0.00 36.95 2.57
3828 3989 8.584157 GGTTTTATGGCATCCAATCAACATATA 58.416 33.333 1.65 0.00 36.95 0.86
3880 4041 2.304470 TGTTCCCAATCTCGTGATTCCA 59.696 45.455 9.67 0.73 40.61 3.53
3908 4069 7.279758 GGATCTTGGTGAAATCAAACAAAAACA 59.720 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.169733 GTCAAACGTAGTAAGAGCGAGG 58.830 50.000 0.00 0.00 45.00 4.63
17 18 2.412089 GCAGCAGGTCAAACGTAGTAAG 59.588 50.000 0.00 0.00 45.00 2.34
59 60 4.372235 ACGCACGCACGTAGTATC 57.628 55.556 0.96 0.00 46.19 2.24
184 197 1.177256 AGAAGCAAGCAACTGGCCAG 61.177 55.000 31.60 31.60 46.50 4.85
317 351 4.340950 AGAGGCTTTGACTTAGCTAGCTAG 59.659 45.833 23.03 16.84 38.67 3.42
318 352 4.282496 AGAGGCTTTGACTTAGCTAGCTA 58.718 43.478 20.67 20.67 38.67 3.32
319 353 3.103742 AGAGGCTTTGACTTAGCTAGCT 58.896 45.455 23.12 23.12 38.67 3.32
320 354 3.132111 AGAGAGGCTTTGACTTAGCTAGC 59.868 47.826 6.62 6.62 38.67 3.42
351 390 2.890311 TGTGCAATCATCCTTCCGTTTT 59.110 40.909 0.00 0.00 0.00 2.43
355 394 2.684374 TCATTGTGCAATCATCCTTCCG 59.316 45.455 0.00 0.00 0.00 4.30
369 408 1.154413 GCGTGCGACCTTCATTGTG 60.154 57.895 0.00 0.00 0.00 3.33
597 640 1.001158 GGTCTACCAAGCTAGCTAGCG 60.001 57.143 34.01 24.34 44.21 4.26
598 641 2.035321 CAGGTCTACCAAGCTAGCTAGC 59.965 54.545 33.96 33.96 43.48 3.42
599 642 2.035321 GCAGGTCTACCAAGCTAGCTAG 59.965 54.545 19.70 16.84 38.89 3.42
600 643 2.032620 GCAGGTCTACCAAGCTAGCTA 58.967 52.381 19.70 0.34 38.89 3.32
682 737 3.506312 GAGCGAGCGAGAGAGCGAG 62.506 68.421 0.00 0.00 43.00 5.03
684 739 3.572539 AGAGCGAGCGAGAGAGCG 61.573 66.667 0.00 0.00 43.00 5.03
689 744 2.045829 AGACCAGAGCGAGCGAGA 60.046 61.111 0.00 0.00 0.00 4.04
694 753 2.487428 CGTCCAGACCAGAGCGAG 59.513 66.667 0.00 0.00 0.00 5.03
695 754 3.062466 CCGTCCAGACCAGAGCGA 61.062 66.667 0.00 0.00 0.00 4.93
696 755 4.135153 CCCGTCCAGACCAGAGCG 62.135 72.222 0.00 0.00 0.00 5.03
697 756 2.283529 TTCCCGTCCAGACCAGAGC 61.284 63.158 0.00 0.00 0.00 4.09
698 757 1.592223 GTTCCCGTCCAGACCAGAG 59.408 63.158 0.00 0.00 0.00 3.35
699 758 1.911766 GGTTCCCGTCCAGACCAGA 60.912 63.158 0.00 0.00 32.41 3.86
700 759 2.214216 TGGTTCCCGTCCAGACCAG 61.214 63.158 0.00 0.00 37.26 4.00
742 801 1.440476 CCGGCTCCTTAACCTACCG 59.560 63.158 0.00 0.00 40.30 4.02
759 820 2.149973 AATCTCAAATCCCAGTGCCC 57.850 50.000 0.00 0.00 0.00 5.36
807 868 5.771165 GCCGGGGATTAAACTAATGGATAAA 59.229 40.000 2.18 0.00 0.00 1.40
854 915 1.073216 GACGACGACGACTAGGACGA 61.073 60.000 15.32 0.00 42.66 4.20
915 976 3.542629 GACGCCTTGTGGTTGCAGC 62.543 63.158 0.00 0.00 35.27 5.25
969 1030 2.125512 ACGAGATGGCGAACCTGC 60.126 61.111 0.00 0.00 36.63 4.85
971 1032 1.215647 GTCACGAGATGGCGAACCT 59.784 57.895 0.00 0.00 36.63 3.50
973 1034 0.109272 TCAGTCACGAGATGGCGAAC 60.109 55.000 0.00 0.00 38.28 3.95
974 1035 0.817654 ATCAGTCACGAGATGGCGAA 59.182 50.000 0.00 0.00 38.28 4.70
975 1036 0.382158 GATCAGTCACGAGATGGCGA 59.618 55.000 0.00 0.00 38.28 5.54
1077 1146 6.640518 TGCATCTAGTAGACAACTTAAAGGG 58.359 40.000 0.85 0.00 39.80 3.95
1078 1147 7.766278 ACATGCATCTAGTAGACAACTTAAAGG 59.234 37.037 0.85 0.00 39.80 3.11
1168 1280 5.618056 TGAAGCTAATTCAGTTTCAGCTG 57.382 39.130 7.63 7.63 46.05 4.24
1189 1301 2.479049 CGATCTGCAGGCCAAAGAATTG 60.479 50.000 15.13 0.00 36.25 2.32
1194 1306 2.796651 GCGATCTGCAGGCCAAAG 59.203 61.111 15.13 0.00 45.45 2.77
1292 1404 7.278646 TCAATTTGACTTTCAGATCATACGGAG 59.721 37.037 0.00 0.00 0.00 4.63
1293 1405 7.102993 TCAATTTGACTTTCAGATCATACGGA 58.897 34.615 0.00 0.00 0.00 4.69
1295 1407 8.189709 TCTCAATTTGACTTTCAGATCATACG 57.810 34.615 0.00 0.00 0.00 3.06
1296 1408 8.121708 GCTCTCAATTTGACTTTCAGATCATAC 58.878 37.037 0.00 0.00 0.00 2.39
1338 1452 7.665559 TCAACTTGCTTCTATTTCTTACATGGT 59.334 33.333 0.00 0.00 0.00 3.55
1340 1454 8.939929 TCTCAACTTGCTTCTATTTCTTACATG 58.060 33.333 0.00 0.00 0.00 3.21
1351 1465 6.207221 TGCAATTCATTCTCAACTTGCTTCTA 59.793 34.615 6.62 0.00 39.64 2.10
1401 1532 7.970384 ACGAGCGATTCTTCATAAAATAAACA 58.030 30.769 0.00 0.00 0.00 2.83
1403 1534 9.089601 TGTACGAGCGATTCTTCATAAAATAAA 57.910 29.630 0.00 0.00 0.00 1.40
1406 1537 7.438160 TGATGTACGAGCGATTCTTCATAAAAT 59.562 33.333 0.00 0.00 0.00 1.82
1407 1538 6.754675 TGATGTACGAGCGATTCTTCATAAAA 59.245 34.615 0.00 0.00 0.00 1.52
1412 1543 3.775661 TGATGTACGAGCGATTCTTCA 57.224 42.857 0.00 0.00 0.00 3.02
1716 1865 4.785453 CTCTGGTGGGCGCCCTTC 62.785 72.222 43.34 33.50 36.94 3.46
1812 1961 3.792047 CTGTCGTCGCCGTCCGTA 61.792 66.667 0.00 0.00 38.35 4.02
2071 2220 8.851960 ATCTTGTACTGTACGTATGTATGTTG 57.148 34.615 12.87 0.00 32.11 3.33
2072 2221 9.512435 GAATCTTGTACTGTACGTATGTATGTT 57.488 33.333 12.87 0.00 32.11 2.71
2076 2225 8.272545 ACAGAATCTTGTACTGTACGTATGTA 57.727 34.615 12.87 2.97 42.01 2.29
2077 2226 7.154435 ACAGAATCTTGTACTGTACGTATGT 57.846 36.000 12.87 4.00 42.01 2.29
2156 2310 3.631227 TGCTCATCATCAACACACAAACA 59.369 39.130 0.00 0.00 0.00 2.83
2661 2817 0.247736 CAAGGAGCTCTTGCCGTAGT 59.752 55.000 14.64 0.00 45.24 2.73
2969 3125 2.501261 GATAATCCACGGGCCTAAACC 58.499 52.381 0.84 0.00 0.00 3.27
2975 3131 0.182775 ACAAGGATAATCCACGGGCC 59.817 55.000 0.00 0.00 39.61 5.80
2976 3132 2.922740 TACAAGGATAATCCACGGGC 57.077 50.000 0.00 0.00 39.61 6.13
2977 3133 4.491676 CGTATACAAGGATAATCCACGGG 58.508 47.826 3.32 0.00 39.61 5.28
2978 3134 3.924686 GCGTATACAAGGATAATCCACGG 59.075 47.826 3.32 0.00 39.61 4.94
2979 3135 4.552355 TGCGTATACAAGGATAATCCACG 58.448 43.478 3.32 0.00 39.61 4.94
2980 3136 5.539048 ACTGCGTATACAAGGATAATCCAC 58.461 41.667 3.32 0.00 39.61 4.02
2981 3137 5.801531 ACTGCGTATACAAGGATAATCCA 57.198 39.130 3.32 0.00 39.61 3.41
2983 3139 8.813643 ACTTAACTGCGTATACAAGGATAATC 57.186 34.615 3.32 0.00 0.00 1.75
2984 3140 9.609346 AAACTTAACTGCGTATACAAGGATAAT 57.391 29.630 3.32 0.00 0.00 1.28
3007 3166 6.141685 CAGCATAACACCAAAACGAAGTAAAC 59.858 38.462 0.00 0.00 45.00 2.01
3030 3189 1.945394 CGATCTCCCAAGCCAATTCAG 59.055 52.381 0.00 0.00 0.00 3.02
3235 3394 3.808174 GCGTATGGAACCCTAAGATCAAC 59.192 47.826 0.00 0.00 0.00 3.18
3292 3451 3.157881 TGTCAACAAAACACCAAGTCCA 58.842 40.909 0.00 0.00 0.00 4.02
3317 3476 9.682465 GGAGGAACCCTATTATTTATATGAACC 57.318 37.037 0.00 0.00 31.76 3.62
3331 3490 2.695585 GGTGAGATGGAGGAACCCTAT 58.304 52.381 0.00 0.00 38.00 2.57
3332 3491 1.688311 CGGTGAGATGGAGGAACCCTA 60.688 57.143 0.00 0.00 38.00 3.53
3351 3510 5.765677 TGTCTGAGTAGATCCCTATTTCTCG 59.234 44.000 0.00 0.00 34.94 4.04
3396 3555 7.844009 TCCTACGTTATTGATAAGAACACCTT 58.156 34.615 0.00 0.00 38.87 3.50
3428 3587 4.268884 GTGGATTCATAAGTGTCTCGCTTC 59.731 45.833 0.00 0.00 35.69 3.86
3432 3591 6.481134 CAATTGTGGATTCATAAGTGTCTCG 58.519 40.000 3.00 0.00 36.05 4.04
3472 3631 3.331889 ACACCAACTCTTCCATCCATCTT 59.668 43.478 0.00 0.00 0.00 2.40
3495 3654 1.495574 TCATCATCACCCATGCCATCA 59.504 47.619 0.00 0.00 31.70 3.07
3506 3665 4.818642 ACATCGATCTCCATCATCATCAC 58.181 43.478 0.00 0.00 0.00 3.06
3526 3685 4.494484 CTTCAATCACATAGACCACGACA 58.506 43.478 0.00 0.00 0.00 4.35
3553 3712 5.964477 TCAATATAAGGGTCTCCAACTCACT 59.036 40.000 0.00 0.00 34.83 3.41
3559 3718 5.917087 AGGGAATCAATATAAGGGTCTCCAA 59.083 40.000 0.00 0.00 34.83 3.53
3573 3732 1.132500 GGTCCGGAGAGGGAATCAAT 58.868 55.000 3.06 0.00 41.52 2.57
3583 3742 2.389449 ATCGGTAGGGGTCCGGAGA 61.389 63.158 3.06 0.00 46.82 3.71
3596 3755 8.519799 AATAATATCAAAACTTCACCATCGGT 57.480 30.769 0.00 0.00 35.62 4.69
3619 3778 9.449719 AAACAAAGAGATTCTACCATACGAAAT 57.550 29.630 0.00 0.00 0.00 2.17
3631 3790 5.641209 CGGATCTGACAAACAAAGAGATTCT 59.359 40.000 0.00 0.00 0.00 2.40
3640 3799 3.058293 GTGCAATCGGATCTGACAAACAA 60.058 43.478 6.33 0.00 0.00 2.83
3662 3821 1.334243 GGGTCGACTACTTCCATCTCG 59.666 57.143 16.46 0.00 0.00 4.04
3664 3823 2.526888 TGGGTCGACTACTTCCATCT 57.473 50.000 16.46 0.00 0.00 2.90
3702 3861 1.329906 ACTCGTAGAAGCGGTCATACG 59.670 52.381 19.56 19.56 41.69 3.06
3747 3906 2.386661 TTCGGCTCTCCAGAATGAAC 57.613 50.000 0.00 0.00 39.69 3.18
3751 3910 0.543277 TGCATTCGGCTCTCCAGAAT 59.457 50.000 0.00 0.00 45.15 2.40
3778 3938 5.598416 TCCATACGATGAGAAGATGTGTT 57.402 39.130 0.00 0.00 0.00 3.32
3828 3989 9.793259 TTAGAGAACACTCATTTTTGGTAGAAT 57.207 29.630 0.00 0.00 33.55 2.40
3880 4041 4.739793 TGTTTGATTTCACCAAGATCCCT 58.260 39.130 0.00 0.00 0.00 4.20
3908 4069 1.803334 TTTACTGCGATCGTTTGCCT 58.197 45.000 17.81 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.