Multiple sequence alignment - TraesCS4B01G248200

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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 TraesCS4B01G248200 chr4B 100.000 8487 0 0 1 8487 513088271 513079785 0.000000e+00 15673.0
1 TraesCS4B01G248200 chr4B 87.339 387 27 13 7951 8328 512800958 512800585 2.830000e-114 424.0
2 TraesCS4B01G248200 chr4B 88.608 79 7 2 8362 8440 512800509 512800433 2.520000e-15 95.3
3 TraesCS4B01G248200 chr4B 91.803 61 4 1 8425 8485 512799132 512799073 5.460000e-12 84.2
4 TraesCS4B01G248200 chr4D 95.760 7147 186 33 1 7065 416439145 416432034 0.000000e+00 11411.0
5 TraesCS4B01G248200 chr4D 93.707 1303 39 14 7082 8356 416431595 416430308 0.000000e+00 1912.0
6 TraesCS4B01G248200 chr4D 93.407 91 5 1 8398 8487 416430213 416430123 5.340000e-27 134.0
7 TraesCS4B01G248200 chr4D 93.750 64 3 1 8357 8420 416430281 416430219 2.520000e-15 95.3
8 TraesCS4B01G248200 chr4A 96.373 6645 151 34 1 6581 47639759 47646377 0.000000e+00 10853.0
9 TraesCS4B01G248200 chr4A 93.780 1447 52 15 6937 8356 47647294 47648729 0.000000e+00 2139.0
10 TraesCS4B01G248200 chr4A 91.146 384 17 8 6577 6946 47646680 47647060 9.830000e-139 505.0
11 TraesCS4B01G248200 chr4A 90.196 102 8 2 8357 8457 47648756 47648856 1.920000e-26 132.0
12 TraesCS4B01G248200 chr4A 100.000 41 0 0 8447 8487 47649330 47649370 9.140000e-10 76.8
13 TraesCS4B01G248200 chr3D 96.250 80 3 0 677 756 48643605 48643684 1.920000e-26 132.0
14 TraesCS4B01G248200 chr5D 94.366 71 4 0 11 81 483532931 483533001 9.010000e-20 110.0
15 TraesCS4B01G248200 chr5A 90.789 76 6 1 6 81 439838182 439838108 5.420000e-17 100.0
16 TraesCS4B01G248200 chr2A 88.889 72 7 1 161 231 742699846 742699917 4.220000e-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 TraesCS4B01G248200 chr4B 513079785 513088271 8486 True 15673.000000 15673 100.000 1 8487 1 chr4B.!!$R1 8486
1 TraesCS4B01G248200 chr4B 512799073 512800958 1885 True 201.166667 424 89.250 7951 8485 3 chr4B.!!$R2 534
2 TraesCS4B01G248200 chr4D 416430123 416439145 9022 True 3388.075000 11411 94.156 1 8487 4 chr4D.!!$R1 8486
3 TraesCS4B01G248200 chr4A 47639759 47649370 9611 False 2741.160000 10853 94.299 1 8487 5 chr4A.!!$F1 8486

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
901 926 1.561076 TCATCATACCAGCAGGCAGTT 59.439 47.619 0.00 0.0 39.06 3.16 F
1905 1930 0.178961 GGGGAGCTTTGTTGAAGGGT 60.179 55.000 0.00 0.0 35.82 4.34 F
2406 2431 1.610554 ATGGCAATTGGGCTCAGCAC 61.611 55.000 7.72 0.0 43.83 4.40 F
2799 2824 1.820906 CGGTGAGCATGGTGGGATG 60.821 63.158 0.00 0.0 0.00 3.51 F
4288 4357 1.885887 GCTCACAGCCAACACCATTTA 59.114 47.619 0.00 0.0 34.48 1.40 F
4596 4668 0.324614 CACCACCTGATGTAGCCACA 59.675 55.000 0.00 0.0 39.52 4.17 F
5094 5166 3.193691 CCAATAACTCACTCAGGTCGTCT 59.806 47.826 0.00 0.0 0.00 4.18 F
5663 5735 0.698238 TGCAGGGCAGTAGTTTGGAT 59.302 50.000 0.00 0.0 33.32 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2088 2113 1.000506 TGGTCACGAGCTGGTAAAGTC 59.999 52.381 0.00 0.0 0.00 3.01 R
3005 3030 1.817099 GCTTGCTGACCTGATCCCG 60.817 63.158 0.00 0.0 0.00 5.14 R
4265 4334 0.819259 TGGTGTTGGCTGTGAGCTTC 60.819 55.000 0.00 0.0 41.99 3.86 R
4342 4411 1.172812 GGATATTGCTGCCCGGAACC 61.173 60.000 0.73 0.0 0.00 3.62 R
5536 5608 0.883833 CGCTTCTTTGGCCTTGTCAT 59.116 50.000 3.32 0.0 0.00 3.06 R
5642 5714 1.133637 TCCAAACTACTGCCCTGCAAA 60.134 47.619 0.00 0.0 38.41 3.68 R
6839 7240 0.037975 CATCAACAACCAAGCCCAGC 60.038 55.000 0.00 0.0 0.00 4.85 R
7628 8706 1.087202 GTGGCATATGCGACGGTTGA 61.087 55.000 24.27 0.0 39.79 3.18 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
51 52 3.834231 GTGGATGCCCATATTTAAGCCAT 59.166 43.478 0.00 0.00 45.68 4.40
52 53 4.284234 GTGGATGCCCATATTTAAGCCATT 59.716 41.667 0.00 0.00 45.68 3.16
109 110 2.817258 CCCAATTCGTTGGCTCTTAACA 59.183 45.455 1.67 0.00 40.74 2.41
158 162 5.687780 AGAGATAATCACCACAATGCATCA 58.312 37.500 0.00 0.00 0.00 3.07
241 245 5.014544 TGGAGAGAAGGGAATGATTTTGTCT 59.985 40.000 0.00 0.00 0.00 3.41
372 376 6.019801 GCGTATCTCCACTAACATACAACTTG 60.020 42.308 0.00 0.00 0.00 3.16
377 381 3.689649 CCACTAACATACAACTTGCCTCC 59.310 47.826 0.00 0.00 0.00 4.30
523 547 8.443160 TCTTGATTAGTTTTCTTATCGCTGTTG 58.557 33.333 0.00 0.00 38.38 3.33
890 915 8.725148 GTTCAGTGGAATCATATTCATCATACC 58.275 37.037 2.36 0.00 35.05 2.73
901 926 1.561076 TCATCATACCAGCAGGCAGTT 59.439 47.619 0.00 0.00 39.06 3.16
1095 1120 2.089980 CAATTGCAGGAGTTCCAGAGG 58.910 52.381 0.28 0.00 38.89 3.69
1217 1242 5.289193 CGGTGATAACAAATGAAATGCCAAG 59.711 40.000 0.00 0.00 0.00 3.61
1237 1262 1.813862 GCAATGAGGCCACGGCTTATA 60.814 52.381 5.01 0.00 38.98 0.98
1539 1564 0.248289 ATGCAATGACAAGGGCAAGC 59.752 50.000 0.00 0.00 40.02 4.01
1541 1566 0.389426 GCAATGACAAGGGCAAGCAG 60.389 55.000 0.00 0.00 0.00 4.24
1779 1804 3.290948 AGGTCAAACCAACTACAAGCA 57.709 42.857 0.00 0.00 41.95 3.91
1905 1930 0.178961 GGGGAGCTTTGTTGAAGGGT 60.179 55.000 0.00 0.00 35.82 4.34
2076 2101 4.098416 GTTTGCAGAAAACACAGACAGTC 58.902 43.478 0.00 0.00 46.30 3.51
2088 2113 3.786576 CACAGACAGTCGCTAATAACTCG 59.213 47.826 0.00 0.00 0.00 4.18
2126 2151 1.669779 CCAGAGTAAGCTTGCTGCATC 59.330 52.381 22.52 7.58 45.94 3.91
2247 2272 2.093106 AGTCCGTACGAGCAAAGAGAT 58.907 47.619 18.76 0.00 0.00 2.75
2406 2431 1.610554 ATGGCAATTGGGCTCAGCAC 61.611 55.000 7.72 0.00 43.83 4.40
2493 2518 4.142491 TGGATGTCACAACAAAACACTGTC 60.142 41.667 0.00 0.00 39.30 3.51
2518 2543 4.503910 TCACAATATCAACCAAGAGTCGG 58.496 43.478 0.00 0.00 0.00 4.79
2799 2824 1.820906 CGGTGAGCATGGTGGGATG 60.821 63.158 0.00 0.00 0.00 3.51
3005 3030 4.756135 TGCTGCAAAAGAATCCCAAAATTC 59.244 37.500 0.00 0.00 36.16 2.17
3054 3079 2.953466 ACATGTTGCAGAATCATGCC 57.047 45.000 16.99 0.00 45.91 4.40
3178 3203 2.621055 CGATTTGTCACCAACTCCCAAA 59.379 45.455 0.00 0.00 29.02 3.28
3214 3239 4.137543 GGCTTCAGTTAATGAGGTATGGG 58.862 47.826 0.00 0.00 39.68 4.00
3216 3241 5.193679 GCTTCAGTTAATGAGGTATGGGTT 58.806 41.667 0.00 0.00 39.68 4.11
3254 3279 7.810766 AGCGTTATGATTTACACATTTTTGG 57.189 32.000 0.00 0.00 0.00 3.28
3264 3289 9.959749 GATTTACACATTTTTGGTCTCTTGTAA 57.040 29.630 0.00 0.00 0.00 2.41
3451 3486 9.372369 CCTCCTTTTCATTTGTAACTACTCTAG 57.628 37.037 0.00 0.00 0.00 2.43
3762 3831 7.125659 TGGAGAATCATGTACTGAAATGGTCTA 59.874 37.037 0.00 0.00 37.44 2.59
3895 3964 7.391554 TCTTTTGTCATGATTAGTCCTTCCAAG 59.608 37.037 0.00 0.00 0.00 3.61
4265 4334 2.492019 TATTCGTCACCTGCTCATCG 57.508 50.000 0.00 0.00 0.00 3.84
4288 4357 1.885887 GCTCACAGCCAACACCATTTA 59.114 47.619 0.00 0.00 34.48 1.40
4342 4411 2.094675 CTGCACATTTCCCCCAGTTAG 58.905 52.381 0.00 0.00 0.00 2.34
4372 4441 1.561076 AGCAATATCCTGTGCCAGACA 59.439 47.619 4.00 0.00 41.88 3.41
4416 4485 0.603172 CTCAGCAAGACAGCACAGCT 60.603 55.000 0.00 0.00 40.77 4.24
4515 4587 7.605691 CCCAATATTCTCCAGTCTATGATGTTC 59.394 40.741 0.00 0.00 0.00 3.18
4520 4592 4.892345 TCTCCAGTCTATGATGTTCTCCAG 59.108 45.833 0.00 0.00 0.00 3.86
4571 4643 0.680061 GACGACCAAGGACAGAAGGT 59.320 55.000 0.00 0.00 37.00 3.50
4596 4668 0.324614 CACCACCTGATGTAGCCACA 59.675 55.000 0.00 0.00 39.52 4.17
4903 4975 3.934457 GGTTACATGGAAACCCAACAG 57.066 47.619 17.31 0.00 40.49 3.16
5094 5166 3.193691 CCAATAACTCACTCAGGTCGTCT 59.806 47.826 0.00 0.00 0.00 4.18
5280 5352 5.104941 TCAAAGTCAAGTTCAGTCTCTTGGA 60.105 40.000 0.00 0.00 40.67 3.53
5536 5608 5.586243 GTGCCTAATATGAAGACAGCTTTGA 59.414 40.000 0.00 0.00 33.61 2.69
5642 5714 4.731313 AGACAAGGTGAATTTTCTCCCT 57.269 40.909 7.59 2.93 40.75 4.20
5661 5733 1.270550 CTTTGCAGGGCAGTAGTTTGG 59.729 52.381 0.00 0.00 40.61 3.28
5663 5735 0.698238 TGCAGGGCAGTAGTTTGGAT 59.302 50.000 0.00 0.00 33.32 3.41
5665 5737 2.171003 GCAGGGCAGTAGTTTGGATTT 58.829 47.619 0.00 0.00 0.00 2.17
5703 5776 5.979288 TTCTGTCCTCTTACTGTTACTCC 57.021 43.478 0.00 0.00 0.00 3.85
5704 5777 5.258216 TCTGTCCTCTTACTGTTACTCCT 57.742 43.478 0.00 0.00 0.00 3.69
5705 5778 5.254901 TCTGTCCTCTTACTGTTACTCCTC 58.745 45.833 0.00 0.00 0.00 3.71
5706 5779 5.014333 TCTGTCCTCTTACTGTTACTCCTCT 59.986 44.000 0.00 0.00 0.00 3.69
5707 5780 5.642165 TGTCCTCTTACTGTTACTCCTCTT 58.358 41.667 0.00 0.00 0.00 2.85
5708 5781 6.787170 TGTCCTCTTACTGTTACTCCTCTTA 58.213 40.000 0.00 0.00 0.00 2.10
5709 5782 6.658391 TGTCCTCTTACTGTTACTCCTCTTAC 59.342 42.308 0.00 0.00 0.00 2.34
5710 5783 6.885918 GTCCTCTTACTGTTACTCCTCTTACT 59.114 42.308 0.00 0.00 0.00 2.24
5711 5784 6.885376 TCCTCTTACTGTTACTCCTCTTACTG 59.115 42.308 0.00 0.00 0.00 2.74
5712 5785 6.660094 CCTCTTACTGTTACTCCTCTTACTGT 59.340 42.308 0.00 0.00 0.00 3.55
5713 5786 7.177041 CCTCTTACTGTTACTCCTCTTACTGTT 59.823 40.741 0.00 0.00 0.00 3.16
5714 5787 9.228949 CTCTTACTGTTACTCCTCTTACTGTTA 57.771 37.037 0.00 0.00 0.00 2.41
5715 5788 9.007901 TCTTACTGTTACTCCTCTTACTGTTAC 57.992 37.037 0.00 0.00 0.00 2.50
5716 5789 8.930846 TTACTGTTACTCCTCTTACTGTTACT 57.069 34.615 0.00 0.00 0.00 2.24
5750 5823 7.962918 CCAGTAATTTATGTGACTTGCAGTTAC 59.037 37.037 4.87 4.87 35.53 2.50
5933 6006 5.146010 TGCATATTGGTTCAAAGGGTTTC 57.854 39.130 0.00 0.00 0.00 2.78
5977 6050 4.339530 TCTTAACAGTCTGAGGATGATCCG 59.660 45.833 6.91 0.00 42.75 4.18
6157 6230 6.777580 TGTTCACTCTAGGAGATACATGCATA 59.222 38.462 0.00 0.00 33.32 3.14
6323 6396 2.228059 CTGTCATTGATCAGCCCATCC 58.772 52.381 0.00 0.00 0.00 3.51
6397 6470 5.532406 TGGAAGTCTTTGTTGGAAGAATCAG 59.468 40.000 0.00 0.00 37.40 2.90
6417 6490 8.801882 AATCAGGAAAATGGAAAACGACTATA 57.198 30.769 0.00 0.00 0.00 1.31
6438 6511 1.946475 GAGGTACGAGCACCCTCCAC 61.946 65.000 0.00 0.00 39.62 4.02
6439 6512 2.577593 GTACGAGCACCCTCCACC 59.422 66.667 0.00 0.00 34.49 4.61
6526 6599 5.139727 TCATTTATTTATGGGCTCCTGTGG 58.860 41.667 0.00 0.00 0.00 4.17
6680 7060 1.276138 CCAGAAGGGAAACATTTGGGC 59.724 52.381 0.00 0.00 40.01 5.36
6682 7062 1.149923 AGAAGGGAAACATTTGGGCCT 59.850 47.619 4.53 0.00 32.27 5.19
6684 7064 1.644509 AGGGAAACATTTGGGCCTTC 58.355 50.000 4.53 0.00 0.00 3.46
6685 7065 1.149923 AGGGAAACATTTGGGCCTTCT 59.850 47.619 4.53 0.00 0.00 2.85
6686 7066 1.276138 GGGAAACATTTGGGCCTTCTG 59.724 52.381 4.53 1.37 0.00 3.02
6712 7105 4.467438 CCAGTCAATTTTGAGGGGCTTATT 59.533 41.667 0.00 0.00 37.98 1.40
6752 7145 8.410912 GCTTGGTTCTTCCTTTCTTTTACTTAA 58.589 33.333 0.00 0.00 37.07 1.85
6797 7198 5.275695 CCGTTTATATTGCGTTTTCATGTGC 60.276 40.000 0.00 0.00 0.00 4.57
6807 7208 7.824704 TGCGTTTTCATGTGCAAAATAATAT 57.175 28.000 0.00 0.00 33.80 1.28
6809 7210 8.715998 TGCGTTTTCATGTGCAAAATAATATTT 58.284 25.926 0.00 0.00 33.80 1.40
6931 7333 4.814234 TGGTAGGAATGAACGTTGATATGC 59.186 41.667 5.00 0.00 0.00 3.14
6943 7588 6.545504 ACGTTGATATGCTGAATCATAACC 57.454 37.500 0.00 0.00 33.52 2.85
6958 7603 8.081633 TGAATCATAACCAAATGAACAGTGAAC 58.918 33.333 0.00 0.00 39.25 3.18
7069 7874 9.394767 TCATATGCGTGGCAATAATCTAATAAT 57.605 29.630 0.00 0.00 43.62 1.28
7076 7881 7.535258 CGTGGCAATAATCTAATAATCAACAGC 59.465 37.037 0.00 0.00 0.00 4.40
7130 8197 7.023575 CGCATTTCTGAAAACATTAACTAGCT 58.976 34.615 6.95 0.00 0.00 3.32
7198 8265 9.191995 CCAATTCCATTTTACTACTTTGTTGTC 57.808 33.333 0.00 0.00 0.00 3.18
7381 8450 3.695606 GCTGGTGTCGAGGCCTCA 61.696 66.667 31.67 16.40 0.00 3.86
7429 8498 6.767902 GCAGAATTTTCCCTGATAGACATGTA 59.232 38.462 0.00 0.00 32.37 2.29
7513 8590 4.071423 TCGATTTCTTGCATTGTTCCTCA 58.929 39.130 0.00 0.00 0.00 3.86
7565 8643 2.450476 AGTGTGATTTCCAATGCTCCC 58.550 47.619 0.00 0.00 0.00 4.30
7583 8661 1.000171 CCCTTTTCTCCTGCAAAGCAC 60.000 52.381 0.00 0.00 33.79 4.40
7628 8706 1.203174 CCAGGGGTGGTTTGGAAATCT 60.203 52.381 0.00 0.00 33.76 2.40
7640 8718 1.338674 TGGAAATCTCAACCGTCGCAT 60.339 47.619 0.00 0.00 0.00 4.73
7652 8730 1.217585 CGTCGCATATGCCACAGAGG 61.218 60.000 22.67 14.99 41.84 3.69
7671 8749 2.438434 GCCCAAGGGATGTGTCCG 60.438 66.667 9.92 0.00 46.09 4.79
7681 8759 1.429148 GATGTGTCCGGCCGATCAAC 61.429 60.000 30.73 19.09 0.00 3.18
7682 8760 1.899437 ATGTGTCCGGCCGATCAACT 61.899 55.000 30.73 12.26 0.00 3.16
7683 8761 1.810030 GTGTCCGGCCGATCAACTC 60.810 63.158 30.73 15.38 0.00 3.01
7748 8827 7.128883 AGGTCCCTGTATATTGTGGAAAGTATT 59.871 37.037 0.00 0.00 0.00 1.89
7749 8828 7.778382 GGTCCCTGTATATTGTGGAAAGTATTT 59.222 37.037 0.00 0.00 43.98 1.40
7797 8900 5.407387 GGTGTTAGCTTCACAATTCGTTAGA 59.593 40.000 18.66 0.00 37.52 2.10
7836 8939 5.189659 AGCTTTAGTACATCTAGCGGAAG 57.810 43.478 0.00 0.00 34.12 3.46
7984 9087 1.429825 CTAGCGGTGTCCAGAGTCG 59.570 63.158 0.00 0.00 0.00 4.18
7987 9090 1.733399 GCGGTGTCCAGAGTCGAAC 60.733 63.158 0.00 0.00 0.00 3.95
7988 9091 1.957562 CGGTGTCCAGAGTCGAACT 59.042 57.895 0.00 0.00 0.00 3.01
7989 9092 0.387367 CGGTGTCCAGAGTCGAACTG 60.387 60.000 12.19 12.19 35.43 3.16
7990 9093 0.959553 GGTGTCCAGAGTCGAACTGA 59.040 55.000 18.43 5.94 37.54 3.41
8044 9147 4.752101 AGTCAGCAGTTGATTACTTGTGTC 59.248 41.667 0.00 0.00 38.29 3.67
8205 9308 4.377431 CGAGGCCGTTTTATCATATTCTGC 60.377 45.833 0.00 0.00 0.00 4.26
8291 9403 7.334421 TGATCCTATATTCGGCTTAATTGCTTC 59.666 37.037 0.00 0.00 0.00 3.86
8341 9453 2.223805 GGTTTTTGCTGAACCAGGAGTG 60.224 50.000 10.33 0.00 44.71 3.51
8420 9605 1.584724 TCAGGTGGGGATTTCTCTCC 58.415 55.000 0.00 0.00 43.10 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 2.575532 CATCCACAACCTCAAGTGTGT 58.424 47.619 3.38 0.00 33.99 3.72
51 52 8.579850 AAGCATGGTTGATTAATTAGTGAGAA 57.420 30.769 9.83 0.00 27.45 2.87
52 53 8.049117 AGAAGCATGGTTGATTAATTAGTGAGA 58.951 33.333 16.18 0.00 29.99 3.27
241 245 1.072806 GGCCAGTGGAGCATGATATCA 59.927 52.381 15.20 8.10 0.00 2.15
372 376 7.066404 CACTTTATTTAAAGAAGAGAGGGAGGC 59.934 40.741 15.19 0.00 44.07 4.70
377 381 7.362142 GGTGGCACTTTATTTAAAGAAGAGAGG 60.362 40.741 18.45 8.04 44.07 3.69
468 474 3.243267 GCAACTGAAAACAACCGGTGTAT 60.243 43.478 8.52 1.48 40.60 2.29
749 774 3.666797 GCCCATTTTGAAGAACGTTTACG 59.333 43.478 0.46 0.00 46.33 3.18
890 915 1.339438 ACCAGATACAACTGCCTGCTG 60.339 52.381 0.00 0.00 36.67 4.41
901 926 6.635755 TCAAATGACAATACGACCAGATACA 58.364 36.000 0.00 0.00 0.00 2.29
996 1021 4.096382 GTGTGGTGAAACTGTGACATTTCT 59.904 41.667 15.93 0.00 36.09 2.52
1095 1120 1.740296 CTGCTGGGCATTTTGCTGC 60.740 57.895 0.00 0.00 44.28 5.25
1191 1216 4.381505 GGCATTTCATTTGTTATCACCGGT 60.382 41.667 0.00 0.00 0.00 5.28
1217 1242 1.103398 ATAAGCCGTGGCCTCATTGC 61.103 55.000 7.39 3.43 43.17 3.56
1237 1262 1.134551 AGCAAAATTTTGTGGCCACGT 60.135 42.857 30.07 13.72 40.24 4.49
1506 1531 3.118000 TCATTGCATTCTGGAGATCAGCT 60.118 43.478 0.00 0.00 43.06 4.24
1541 1566 4.517285 TGATACCTTTTCAGGCTGATGAC 58.483 43.478 19.50 5.23 45.56 3.06
1590 1615 0.179097 CTTTCTCCTGCGGACTAGGC 60.179 60.000 0.00 0.00 35.23 3.93
1779 1804 2.165998 GTTGATTTCTCTTGCAGGCCT 58.834 47.619 0.00 0.00 0.00 5.19
1905 1930 6.128035 CCAAAGAATTACCATGATCGTTGTCA 60.128 38.462 0.00 0.00 31.97 3.58
2002 2027 9.877178 ATTATCTTTACTGGTTGAAGACTGTAG 57.123 33.333 0.00 0.00 32.73 2.74
2076 2101 4.206609 GCTGGTAAAGTCGAGTTATTAGCG 59.793 45.833 5.80 4.27 0.00 4.26
2088 2113 1.000506 TGGTCACGAGCTGGTAAAGTC 59.999 52.381 0.00 0.00 0.00 3.01
2126 2151 2.002586 CATTCTGTAGTCCACCGCTTG 58.997 52.381 0.00 0.00 0.00 4.01
2247 2272 4.935205 CGAGGAGATTCATGTGGTGTTTTA 59.065 41.667 0.00 0.00 0.00 1.52
2406 2431 5.287035 GCTATTTCTTGGCGTTTCAGATTTG 59.713 40.000 0.00 0.00 0.00 2.32
2493 2518 5.051441 CGACTCTTGGTTGATATTGTGATCG 60.051 44.000 0.00 0.00 0.00 3.69
2541 2566 2.677875 CCAAGGGGGCTGTTGCTC 60.678 66.667 0.00 0.00 39.42 4.26
2799 2824 3.875134 CCCTACGTCCAATGTTATGGTTC 59.125 47.826 0.00 0.00 41.46 3.62
3005 3030 1.817099 GCTTGCTGACCTGATCCCG 60.817 63.158 0.00 0.00 0.00 5.14
3054 3079 2.556622 GTTTACCCCTGTGTTGTCCATG 59.443 50.000 0.00 0.00 0.00 3.66
3238 3263 9.959749 TTACAAGAGACCAAAAATGTGTAAATC 57.040 29.630 0.00 0.00 29.76 2.17
3762 3831 8.392479 AGAATCTTACGATACCCTTATCCTACT 58.608 37.037 0.00 0.00 31.70 2.57
3796 3865 2.736144 TGTTGTCAGTGTCCCGATAC 57.264 50.000 0.00 0.00 0.00 2.24
3918 3987 9.337396 TGTCAGTTATCATAAAGAACAACAAGT 57.663 29.630 0.00 0.00 0.00 3.16
3975 4044 4.157289 ACCTTATGAAGAAGTTGCAGCATG 59.843 41.667 2.55 0.00 40.87 4.06
4265 4334 0.819259 TGGTGTTGGCTGTGAGCTTC 60.819 55.000 0.00 0.00 41.99 3.86
4288 4357 3.169512 ACCACCCATTTCCGAAGAATT 57.830 42.857 0.00 0.00 0.00 2.17
4342 4411 1.172812 GGATATTGCTGCCCGGAACC 61.173 60.000 0.73 0.00 0.00 3.62
4416 4485 7.160547 TGTCCATACGTTCTTGAATACTGTA 57.839 36.000 0.00 0.00 0.00 2.74
4515 4587 2.094675 CATAAGTTGGGGTTGCTGGAG 58.905 52.381 0.00 0.00 0.00 3.86
4571 4643 3.146066 GCTACATCAGGTGGTGTTGAAA 58.854 45.455 8.73 0.00 31.26 2.69
4596 4668 6.839124 TGATTATGTGAATTGGCAGAACTT 57.161 33.333 0.00 0.00 0.00 2.66
4903 4975 2.297701 TGTCTGTTGGAGGTTTGAAGC 58.702 47.619 0.00 0.00 0.00 3.86
5094 5166 9.363401 ACACTAGTACTGCCAATGTTATCTATA 57.637 33.333 5.39 0.00 0.00 1.31
5387 5459 4.997395 TCTGAGCATTAAACACAGAAGGAC 59.003 41.667 6.55 0.00 35.20 3.85
5536 5608 0.883833 CGCTTCTTTGGCCTTGTCAT 59.116 50.000 3.32 0.00 0.00 3.06
5642 5714 1.133637 TCCAAACTACTGCCCTGCAAA 60.134 47.619 0.00 0.00 38.41 3.68
5661 5733 8.524870 ACAGAAAATATGCTTCAACACAAATC 57.475 30.769 1.77 0.00 0.00 2.17
5663 5735 6.922957 GGACAGAAAATATGCTTCAACACAAA 59.077 34.615 1.77 0.00 0.00 2.83
5665 5737 5.769662 AGGACAGAAAATATGCTTCAACACA 59.230 36.000 1.77 0.00 0.00 3.72
5702 5775 4.238514 GTGCTGACAGTAACAGTAAGAGG 58.761 47.826 3.99 0.00 37.64 3.69
5703 5776 4.238514 GGTGCTGACAGTAACAGTAAGAG 58.761 47.826 3.42 0.00 37.64 2.85
5704 5777 3.639561 TGGTGCTGACAGTAACAGTAAGA 59.360 43.478 7.24 0.00 37.64 2.10
5705 5778 3.990092 TGGTGCTGACAGTAACAGTAAG 58.010 45.455 7.24 0.00 37.64 2.34
5706 5779 3.990092 CTGGTGCTGACAGTAACAGTAA 58.010 45.455 25.52 0.00 40.21 2.24
5707 5780 3.660501 CTGGTGCTGACAGTAACAGTA 57.339 47.619 25.52 0.00 40.21 2.74
5708 5781 2.533266 CTGGTGCTGACAGTAACAGT 57.467 50.000 25.52 0.00 40.21 3.55
5713 5786 6.593770 CACATAAATTACTGGTGCTGACAGTA 59.406 38.462 3.99 10.33 46.62 2.74
5715 5788 5.643348 TCACATAAATTACTGGTGCTGACAG 59.357 40.000 0.00 0.00 41.64 3.51
5716 5789 5.411361 GTCACATAAATTACTGGTGCTGACA 59.589 40.000 0.00 0.00 0.00 3.58
5977 6050 1.683319 GGGGCATCTTCCAGACTTTCC 60.683 57.143 0.00 0.00 0.00 3.13
6013 6086 4.638865 GTGGTCATAATTAGCCTTTTCCGT 59.361 41.667 0.00 0.00 0.00 4.69
6016 6089 7.602753 ACTTTGTGGTCATAATTAGCCTTTTC 58.397 34.615 0.00 0.00 0.00 2.29
6157 6230 4.793071 CGCGAGAGTTATCTGATGAGATT 58.207 43.478 0.00 0.00 39.76 2.40
6230 6303 5.423015 TCATGACCACAAGAGAGAATAAGC 58.577 41.667 0.00 0.00 0.00 3.09
6231 6304 7.605691 ACTTTCATGACCACAAGAGAGAATAAG 59.394 37.037 11.03 2.32 32.72 1.73
6233 6306 7.009179 ACTTTCATGACCACAAGAGAGAATA 57.991 36.000 11.03 0.00 32.72 1.75
6234 6307 5.874093 ACTTTCATGACCACAAGAGAGAAT 58.126 37.500 11.03 0.00 32.72 2.40
6236 6309 4.963318 ACTTTCATGACCACAAGAGAGA 57.037 40.909 11.03 0.00 32.72 3.10
6237 6310 7.496529 TTTTACTTTCATGACCACAAGAGAG 57.503 36.000 11.03 0.00 33.95 3.20
6238 6311 8.463930 AATTTTACTTTCATGACCACAAGAGA 57.536 30.769 11.03 0.00 0.00 3.10
6240 6313 9.959749 GTAAATTTTACTTTCATGACCACAAGA 57.040 29.630 11.03 0.00 0.00 3.02
6241 6314 9.965824 AGTAAATTTTACTTTCATGACCACAAG 57.034 29.630 14.66 0.00 0.00 3.16
6323 6396 2.842208 TGGCACTTGTTCTTTGTTCG 57.158 45.000 0.00 0.00 0.00 3.95
6397 6470 7.282450 ACCTCATATAGTCGTTTTCCATTTTCC 59.718 37.037 0.00 0.00 0.00 3.13
6417 6490 4.787735 AGGGTGCTCGTACCTCAT 57.212 55.556 4.22 0.00 40.66 2.90
6497 6570 7.495606 CAGGAGCCCATAAATAAATGAAAAACC 59.504 37.037 0.00 0.00 0.00 3.27
6503 6576 5.139727 CCACAGGAGCCCATAAATAAATGA 58.860 41.667 0.00 0.00 0.00 2.57
6630 7010 9.371136 TCTTTTATCTTTCTAGCACAGTGTATG 57.629 33.333 1.61 0.00 0.00 2.39
6633 7013 8.725148 CAATCTTTTATCTTTCTAGCACAGTGT 58.275 33.333 1.61 0.00 0.00 3.55
6680 7060 4.144297 TCAAAATTGACTGGTCCAGAAGG 58.856 43.478 26.18 0.00 35.18 3.46
6682 7062 4.144297 CCTCAAAATTGACTGGTCCAGAA 58.856 43.478 26.18 10.64 35.18 3.02
6684 7064 2.821969 CCCTCAAAATTGACTGGTCCAG 59.178 50.000 17.88 17.88 37.52 3.86
6685 7065 2.490718 CCCCTCAAAATTGACTGGTCCA 60.491 50.000 0.00 0.00 32.90 4.02
6686 7066 2.171003 CCCCTCAAAATTGACTGGTCC 58.829 52.381 0.00 0.00 32.90 4.46
6712 7105 1.630369 ACCAAGCCAGCTAACATCTCA 59.370 47.619 0.00 0.00 0.00 3.27
6752 7145 7.923414 ACGGAAGTTAAGATCTTAGCAAAAT 57.077 32.000 25.48 12.31 46.40 1.82
6775 7176 6.624710 TGCACATGAAAACGCAATATAAAC 57.375 33.333 0.00 0.00 0.00 2.01
6809 7210 9.995003 AAAAATGTTATGATGAAGTAGCCAAAA 57.005 25.926 0.00 0.00 0.00 2.44
6838 7239 0.178953 ATCAACAACCAAGCCCAGCT 60.179 50.000 0.00 0.00 42.56 4.24
6839 7240 0.037975 CATCAACAACCAAGCCCAGC 60.038 55.000 0.00 0.00 0.00 4.85
6873 7275 5.949952 GTCAAAAAGAATTAGGGCCCTAGAA 59.050 40.000 30.23 20.25 0.00 2.10
6931 7333 7.819644 TCACTGTTCATTTGGTTATGATTCAG 58.180 34.615 0.00 0.00 39.69 3.02
7023 7668 3.625313 TGAAACATGCGAGTTCAAGAACA 59.375 39.130 14.69 0.00 43.47 3.18
7051 7696 8.571336 AGCTGTTGATTATTAGATTATTGCCAC 58.429 33.333 0.00 0.00 0.00 5.01
7069 7874 7.646548 ATCTCTGTACATAGTAAGCTGTTGA 57.353 36.000 8.01 0.00 0.00 3.18
7076 7881 8.812329 GCAACTGAAATCTCTGTACATAGTAAG 58.188 37.037 8.01 3.59 33.71 2.34
7130 8197 7.984050 TGCACAAGGAATTAAAGATCAACAAAA 59.016 29.630 0.00 0.00 0.00 2.44
7381 8450 3.760684 GAGAAACCATTTGTGAGCCAGAT 59.239 43.478 0.00 0.00 0.00 2.90
7492 8569 4.424061 TGAGGAACAATGCAAGAAATCG 57.576 40.909 0.00 0.00 0.00 3.34
7493 8570 5.406477 GGTTTGAGGAACAATGCAAGAAATC 59.594 40.000 0.00 0.00 40.13 2.17
7494 8571 5.070847 AGGTTTGAGGAACAATGCAAGAAAT 59.929 36.000 0.00 0.00 40.13 2.17
7495 8572 4.405358 AGGTTTGAGGAACAATGCAAGAAA 59.595 37.500 0.00 0.00 40.13 2.52
7496 8573 3.960102 AGGTTTGAGGAACAATGCAAGAA 59.040 39.130 0.00 0.00 40.13 2.52
7497 8574 3.565307 AGGTTTGAGGAACAATGCAAGA 58.435 40.909 0.00 0.00 40.13 3.02
7498 8575 3.571401 AGAGGTTTGAGGAACAATGCAAG 59.429 43.478 0.00 0.00 40.13 4.01
7499 8576 3.565307 AGAGGTTTGAGGAACAATGCAA 58.435 40.909 0.00 0.00 40.13 4.08
7513 8590 3.103742 GAGGTGATCTGAGGAGAGGTTT 58.896 50.000 0.00 0.00 0.00 3.27
7565 8643 1.335324 CCGTGCTTTGCAGGAGAAAAG 60.335 52.381 12.88 0.00 45.68 2.27
7583 8661 1.585214 GACCGTTCTGTATAAACGCCG 59.415 52.381 3.04 0.00 46.09 6.46
7628 8706 1.087202 GTGGCATATGCGACGGTTGA 61.087 55.000 24.27 0.00 39.79 3.18
7652 8730 3.134127 GACACATCCCTTGGGCGC 61.134 66.667 0.00 0.00 28.72 6.53
7655 8733 2.272146 CCGGACACATCCCTTGGG 59.728 66.667 0.00 0.00 42.83 4.12
7671 8749 2.456119 CGCACTGAGTTGATCGGCC 61.456 63.158 0.00 0.00 37.90 6.13
7681 8759 0.602638 TAACAACAGCCCGCACTGAG 60.603 55.000 9.59 4.77 40.25 3.35
7682 8760 0.036164 ATAACAACAGCCCGCACTGA 59.964 50.000 9.59 0.00 40.25 3.41
7683 8761 0.881118 AATAACAACAGCCCGCACTG 59.119 50.000 1.74 1.74 43.59 3.66
7759 8862 3.307762 GCTAACACCCTTCCTTCATCAGT 60.308 47.826 0.00 0.00 0.00 3.41
7836 8939 5.358298 AAAAGATGACAAGTAGCGGAAAC 57.642 39.130 0.00 0.00 0.00 2.78
7984 9087 1.487300 GGGGAGAGGTAGGTCAGTTC 58.513 60.000 0.00 0.00 0.00 3.01
7987 9090 0.340208 AAGGGGGAGAGGTAGGTCAG 59.660 60.000 0.00 0.00 0.00 3.51
7988 9091 0.797579 AAAGGGGGAGAGGTAGGTCA 59.202 55.000 0.00 0.00 0.00 4.02
7989 9092 1.205055 CAAAGGGGGAGAGGTAGGTC 58.795 60.000 0.00 0.00 0.00 3.85
7990 9093 0.496841 ACAAAGGGGGAGAGGTAGGT 59.503 55.000 0.00 0.00 0.00 3.08
7991 9094 1.282157 CAACAAAGGGGGAGAGGTAGG 59.718 57.143 0.00 0.00 0.00 3.18
7993 9096 2.127651 ACAACAAAGGGGGAGAGGTA 57.872 50.000 0.00 0.00 0.00 3.08
8205 9308 1.572085 CTCCACGCCAACTTCTGCTG 61.572 60.000 0.00 0.00 0.00 4.41
8291 9403 6.183360 CCCAAAACCAAACTACAAAACATGTG 60.183 38.462 0.00 0.00 43.77 3.21
8341 9453 1.446272 CAGGCTCTTCGAACGACCC 60.446 63.158 0.00 0.00 0.00 4.46


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

AutoCloner maintained by Alex Coulton.