Multiple sequence alignment - TraesCS3D01G290100

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 TraesCS3D01G290100 chr3D 100.000 4074 0 0 1 4074 400314252 400310179 0.000000e+00 7524.0
1 TraesCS3D01G290100 chr3D 81.275 502 59 21 53 525 400322798 400322303 1.380000e-99 374.0
2 TraesCS3D01G290100 chr3D 75.254 295 64 8 1081 1369 304978064 304978355 9.190000e-27 132.0
3 TraesCS3D01G290100 chr3B 91.255 3602 196 53 1 3560 525993211 525989687 0.000000e+00 4796.0
4 TraesCS3D01G290100 chr3B 93.450 458 25 4 3618 4074 525989375 525988922 0.000000e+00 675.0
5 TraesCS3D01G290100 chr3B 85.282 496 58 7 4 487 525997415 525996923 7.860000e-137 497.0
6 TraesCS3D01G290100 chr3B 74.662 296 64 8 1081 1369 416809594 416809303 1.990000e-23 121.0
7 TraesCS3D01G290100 chr3B 87.912 91 11 0 5 95 526001580 526001490 1.550000e-19 108.0
8 TraesCS3D01G290100 chr3A 94.241 1337 42 17 851 2177 519246630 519245319 0.000000e+00 2010.0
9 TraesCS3D01G290100 chr3A 92.779 914 39 11 1 887 519247544 519246631 0.000000e+00 1297.0
10 TraesCS3D01G290100 chr3A 94.286 700 30 5 2635 3327 519244956 519244260 0.000000e+00 1062.0
11 TraesCS3D01G290100 chr3A 91.942 757 37 6 3322 4074 519244074 519243338 0.000000e+00 1038.0
12 TraesCS3D01G290100 chr3A 93.215 339 21 2 2232 2570 519245319 519244983 7.860000e-137 497.0
13 TraesCS3D01G290100 chr3A 83.747 443 63 6 56 492 519251119 519250680 1.050000e-110 411.0
14 TraesCS3D01G290100 chr3A 86.061 330 36 5 205 525 519254876 519254548 3.010000e-91 346.0
15 TraesCS3D01G290100 chr3A 87.500 96 9 1 4 96 519247487 519247392 1.550000e-19 108.0
16 TraesCS3D01G290100 chr1B 82.111 341 49 7 1046 1374 580622544 580622884 8.620000e-72 281.0
17 TraesCS3D01G290100 chr1B 87.671 73 9 0 2679 2751 580624125 580624197 7.260000e-13 86.1
18 TraesCS3D01G290100 chr1D 82.059 340 49 7 1046 1373 429599513 429599852 3.100000e-71 279.0
19 TraesCS3D01G290100 chr1D 89.041 73 8 0 2679 2751 429600912 429600984 1.560000e-14 91.6
20 TraesCS3D01G290100 chr4D 81.879 298 45 6 1081 1369 394967808 394968105 4.070000e-60 243.0
21 TraesCS3D01G290100 chr4A 81.879 298 45 6 1081 1369 76627426 76627723 4.070000e-60 243.0
22 TraesCS3D01G290100 chr4B 80.537 298 49 7 1081 1369 486207202 486206905 1.910000e-53 220.0
23 TraesCS3D01G290100 chr5D 74.882 211 33 9 3840 4038 123880349 123880147 1.210000e-10 78.7


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 TraesCS3D01G290100 chr3D 400310179 400314252 4073 True 7524.000000 7524 100.000000 1 4074 1 chr3D.!!$R1 4073
1 TraesCS3D01G290100 chr3B 525988922 525997415 8493 True 1989.333333 4796 89.995667 1 4074 3 chr3B.!!$R3 4073
2 TraesCS3D01G290100 chr3A 519243338 519254876 11538 True 846.125000 2010 90.471375 1 4074 8 chr3A.!!$R1 4073

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
763 9639 0.382515 CCCACGTACTAGAGCTGCTC 59.617 60.0 21.72 21.72 0.00 4.26 F
1786 10735 0.034198 TGTCGCTTTCGGTTCATCCA 59.966 50.0 0.00 0.00 36.13 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 11337 0.179189 GCTTTGCCTGTTCGGAATCG 60.179 55.0 0.00 0.00 37.82 3.34 R
3290 12258 0.171455 GGACGAGAGCATGTTCGAGT 59.829 55.0 18.59 15.14 39.93 4.18 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
74 8925 2.283173 CCTCCACCAAGGCCAACC 60.283 66.667 5.01 0.00 37.29 3.77
131 8985 2.067932 CTCCACCAAGGCCAACTCCA 62.068 60.000 5.01 0.00 37.29 3.86
185 9039 2.365635 CCGTCATCCCCACCTCCT 60.366 66.667 0.00 0.00 0.00 3.69
392 9246 1.004560 CTCTTCAAGCAGCGGGACA 60.005 57.895 0.00 0.00 0.00 4.02
612 9476 2.286772 CGATCATGTGACGTCGTCCATA 60.287 50.000 22.05 9.08 0.00 2.74
614 9478 1.200483 CATGTGACGTCGTCCATAGC 58.800 55.000 22.05 8.16 0.00 2.97
763 9639 0.382515 CCCACGTACTAGAGCTGCTC 59.617 60.000 21.72 21.72 0.00 4.26
845 9724 5.794894 TCCATCTAGAAACTGAACAACTCC 58.205 41.667 0.00 0.00 0.00 3.85
904 9821 2.157085 GGTGAACTGACCGATCGTTTTC 59.843 50.000 15.09 7.94 0.00 2.29
906 9823 3.057019 TGAACTGACCGATCGTTTTCTG 58.943 45.455 15.09 12.84 0.00 3.02
1431 10352 1.609072 GTTTTGGAAGTGCTGGGACTC 59.391 52.381 0.00 0.00 0.00 3.36
1444 10385 1.267121 GGGACTCACACAAGAGGCTA 58.733 55.000 0.00 0.00 43.43 3.93
1554 10495 2.147150 GGACTGTGAGTTCTTCTTGCC 58.853 52.381 0.00 0.00 0.00 4.52
1558 10499 5.234466 ACTGTGAGTTCTTCTTGCCTTAT 57.766 39.130 0.00 0.00 0.00 1.73
1603 10544 1.821216 ACGGATTTTGTCGCCTGAAT 58.179 45.000 0.00 0.00 0.00 2.57
1705 10646 3.133003 CCAACATCCTCCTCGACTACAAT 59.867 47.826 0.00 0.00 0.00 2.71
1729 10670 4.919774 TGAGCCCAAGGTAAGTAAATCA 57.080 40.909 0.00 0.00 0.00 2.57
1735 10676 6.897413 AGCCCAAGGTAAGTAAATCATCAAAT 59.103 34.615 0.00 0.00 0.00 2.32
1740 10681 8.917088 CAAGGTAAGTAAATCATCAAATCCCAT 58.083 33.333 0.00 0.00 0.00 4.00
1746 10687 7.775120 AGTAAATCATCAAATCCCATCAACAC 58.225 34.615 0.00 0.00 0.00 3.32
1747 10688 4.906065 ATCATCAAATCCCATCAACACG 57.094 40.909 0.00 0.00 0.00 4.49
1748 10689 3.949132 TCATCAAATCCCATCAACACGA 58.051 40.909 0.00 0.00 0.00 4.35
1749 10690 4.525996 TCATCAAATCCCATCAACACGAT 58.474 39.130 0.00 0.00 33.27 3.73
1750 10691 4.949238 TCATCAAATCCCATCAACACGATT 59.051 37.500 0.00 0.00 29.21 3.34
1751 10692 4.700268 TCAAATCCCATCAACACGATTG 57.300 40.909 0.00 0.00 29.21 2.67
1753 10694 4.764308 TCAAATCCCATCAACACGATTGAA 59.236 37.500 10.18 0.00 29.21 2.69
1754 10695 4.970662 AATCCCATCAACACGATTGAAG 57.029 40.909 10.18 6.68 29.21 3.02
1755 10696 2.083774 TCCCATCAACACGATTGAAGC 58.916 47.619 10.18 0.00 29.21 3.86
1756 10697 1.811965 CCCATCAACACGATTGAAGCA 59.188 47.619 10.18 0.00 29.21 3.91
1772 10721 1.154338 GCATGTCTGCTTGTGTCGC 60.154 57.895 0.00 0.00 45.32 5.19
1773 10722 1.572085 GCATGTCTGCTTGTGTCGCT 61.572 55.000 0.00 0.00 45.32 4.93
1774 10723 0.870393 CATGTCTGCTTGTGTCGCTT 59.130 50.000 0.00 0.00 0.00 4.68
1777 10726 0.111089 GTCTGCTTGTGTCGCTTTCG 60.111 55.000 0.00 0.00 0.00 3.46
1778 10727 1.205064 CTGCTTGTGTCGCTTTCGG 59.795 57.895 0.00 0.00 36.13 4.30
1779 10728 1.498865 CTGCTTGTGTCGCTTTCGGT 61.499 55.000 0.00 0.00 36.13 4.69
1780 10729 1.092921 TGCTTGTGTCGCTTTCGGTT 61.093 50.000 0.00 0.00 36.13 4.44
1781 10730 0.384353 GCTTGTGTCGCTTTCGGTTC 60.384 55.000 0.00 0.00 36.13 3.62
1782 10731 0.934496 CTTGTGTCGCTTTCGGTTCA 59.066 50.000 0.00 0.00 36.13 3.18
1783 10732 1.531149 CTTGTGTCGCTTTCGGTTCAT 59.469 47.619 0.00 0.00 36.13 2.57
1784 10733 1.144969 TGTGTCGCTTTCGGTTCATC 58.855 50.000 0.00 0.00 36.13 2.92
1785 10734 0.442699 GTGTCGCTTTCGGTTCATCC 59.557 55.000 0.00 0.00 36.13 3.51
1786 10735 0.034198 TGTCGCTTTCGGTTCATCCA 59.966 50.000 0.00 0.00 36.13 3.41
1787 10736 1.153353 GTCGCTTTCGGTTCATCCAA 58.847 50.000 0.00 0.00 36.13 3.53
1788 10737 1.136057 GTCGCTTTCGGTTCATCCAAC 60.136 52.381 0.00 0.00 36.13 3.77
1789 10738 1.156736 CGCTTTCGGTTCATCCAACT 58.843 50.000 0.00 0.00 35.06 3.16
1790 10739 1.128692 CGCTTTCGGTTCATCCAACTC 59.871 52.381 0.00 0.00 35.06 3.01
1791 10740 2.427506 GCTTTCGGTTCATCCAACTCT 58.572 47.619 0.00 0.00 35.06 3.24
1792 10741 2.814336 GCTTTCGGTTCATCCAACTCTT 59.186 45.455 0.00 0.00 35.06 2.85
1793 10742 3.120165 GCTTTCGGTTCATCCAACTCTTC 60.120 47.826 0.00 0.00 35.06 2.87
1794 10743 2.762535 TCGGTTCATCCAACTCTTCC 57.237 50.000 0.00 0.00 35.06 3.46
1795 10744 2.257207 TCGGTTCATCCAACTCTTCCT 58.743 47.619 0.00 0.00 35.06 3.36
1796 10745 2.637872 TCGGTTCATCCAACTCTTCCTT 59.362 45.455 0.00 0.00 35.06 3.36
1797 10746 2.744202 CGGTTCATCCAACTCTTCCTTG 59.256 50.000 0.00 0.00 35.06 3.61
1798 10747 3.084786 GGTTCATCCAACTCTTCCTTGG 58.915 50.000 0.00 0.00 39.79 3.61
1830 10779 1.829523 TTGCAGATTTTGGGCTGGCC 61.830 55.000 14.23 14.23 32.83 5.36
1893 10842 5.123344 CGTAATGGGAACTTTTGGGTAAGAG 59.877 44.000 0.00 0.00 0.00 2.85
1910 10863 6.814146 GGGTAAGAGAAGACAGTTGATTAGTG 59.186 42.308 0.00 0.00 0.00 2.74
1975 10929 5.072741 AGCATGTGGACTAATCTTGTGTTT 58.927 37.500 0.00 0.00 0.00 2.83
2095 11050 1.079405 GCTCATCACCGGACGGAAA 60.079 57.895 18.80 5.03 38.96 3.13
2151 11106 2.561478 TTGGCTACTTGGGTGAGTTC 57.439 50.000 0.00 0.00 0.00 3.01
2202 11157 2.808543 CAGGGAACAACTGTTAGTGAGC 59.191 50.000 0.00 0.00 38.56 4.26
2203 11158 2.438021 AGGGAACAACTGTTAGTGAGCA 59.562 45.455 0.00 0.00 38.56 4.26
2204 11159 2.548480 GGGAACAACTGTTAGTGAGCAC 59.452 50.000 0.00 0.00 38.56 4.40
2205 11160 3.467803 GGAACAACTGTTAGTGAGCACT 58.532 45.455 8.35 8.35 45.02 4.40
2206 11161 3.248602 GGAACAACTGTTAGTGAGCACTG 59.751 47.826 13.12 0.00 42.52 3.66
2207 11162 3.819564 ACAACTGTTAGTGAGCACTGA 57.180 42.857 13.12 2.08 42.52 3.41
2208 11163 3.458189 ACAACTGTTAGTGAGCACTGAC 58.542 45.455 15.99 15.99 45.02 3.51
2223 11180 3.306364 GCACTGACTACTGAGATGGTTGT 60.306 47.826 0.00 0.00 0.00 3.32
2230 11187 1.271597 ACTGAGATGGTTGTGCCCTTC 60.272 52.381 0.00 0.00 36.04 3.46
2247 11204 4.455606 CCCTTCTAATTCCTTCTCGCAAT 58.544 43.478 0.00 0.00 0.00 3.56
2251 11208 7.315890 CCTTCTAATTCCTTCTCGCAATTTTT 58.684 34.615 0.00 0.00 0.00 1.94
2292 11252 8.689061 TGTTTGAACTAGAACTGTGTAGAGTAA 58.311 33.333 0.00 0.00 0.00 2.24
2294 11254 8.687292 TTGAACTAGAACTGTGTAGAGTAAGA 57.313 34.615 0.00 0.00 0.00 2.10
2298 11258 9.523168 AACTAGAACTGTGTAGAGTAAGAATCT 57.477 33.333 0.00 0.00 0.00 2.40
2324 11284 2.103094 TGATCCCACTTGATCATCCGAC 59.897 50.000 0.00 0.00 44.65 4.79
2337 11297 2.163509 CATCCGACGTCTATCTCCCAT 58.836 52.381 14.70 0.00 0.00 4.00
2363 11323 2.631418 TGCAGCGAGTAGTAACAGAC 57.369 50.000 0.00 0.00 0.00 3.51
2372 11332 4.731720 GAGTAGTAACAGACTCGTTTCCC 58.268 47.826 0.00 0.00 39.81 3.97
2373 11333 4.405548 AGTAGTAACAGACTCGTTTCCCT 58.594 43.478 0.00 0.00 39.81 4.20
2377 11337 3.320673 AACAGACTCGTTTCCCTGATC 57.679 47.619 0.00 0.00 0.00 2.92
2379 11339 1.472878 CAGACTCGTTTCCCTGATCGA 59.527 52.381 0.00 0.00 0.00 3.59
2579 11539 1.749033 GAATCCCCTCGCCTACAGG 59.251 63.158 0.00 0.00 38.53 4.00
3092 12060 4.568359 GGTGACGAGACGTACTGAATACTA 59.432 45.833 0.00 0.00 41.37 1.82
3093 12061 5.236047 GGTGACGAGACGTACTGAATACTAT 59.764 44.000 0.00 0.00 41.37 2.12
3094 12062 6.354080 GTGACGAGACGTACTGAATACTATC 58.646 44.000 0.00 0.00 41.37 2.08
3141 12109 3.066203 TCGCTCGTGTACATATGTGATGT 59.934 43.478 18.81 0.00 36.13 3.06
3152 12120 2.168326 ATGTGATGTTGTCGCTGTGA 57.832 45.000 0.00 0.00 38.20 3.58
3180 12148 3.924073 GGTTTGCGTTTCTTTGTTTCAGT 59.076 39.130 0.00 0.00 0.00 3.41
3253 12221 4.955925 TGTGCGTCCATTAATTAACCAG 57.044 40.909 0.00 0.00 0.00 4.00
3293 12261 9.995003 ACATAAAGAGATGATGGAGAATTACTC 57.005 33.333 0.00 0.00 44.24 2.59
3305 12273 4.742659 GGAGAATTACTCGAACATGCTCTC 59.257 45.833 0.00 4.58 45.76 3.20
3310 12278 0.453793 CTCGAACATGCTCTCGTCCT 59.546 55.000 10.98 0.00 36.46 3.85
3363 12522 2.438021 ACAAGGCTACAAGGTGTTGAGA 59.562 45.455 0.00 0.00 37.10 3.27
3374 12533 4.351874 AGGTGTTGAGAAAATCCTCGAA 57.648 40.909 0.00 0.00 35.99 3.71
3388 12547 6.917217 AATCCTCGAAAGCTGATAGAAAAG 57.083 37.500 0.00 0.00 0.00 2.27
3416 12575 5.105392 ACATGACAAAACACACCAAAGATGT 60.105 36.000 0.00 0.00 0.00 3.06
3534 12693 1.076265 TCATCGACGATGACCCCCT 60.076 57.895 31.37 0.00 43.11 4.79
3536 12695 1.833049 ATCGACGATGACCCCCTCC 60.833 63.158 10.09 0.00 0.00 4.30
3578 12737 3.093278 CCATGCGCCGAAGAAGAC 58.907 61.111 4.18 0.00 0.00 3.01
3589 12749 3.432252 GCCGAAGAAGACGAAGATTTTCA 59.568 43.478 0.00 0.00 32.67 2.69
3595 12755 1.621814 AGACGAAGATTTTCACCCCGA 59.378 47.619 0.00 0.00 32.67 5.14
3623 13036 1.392534 GGGAGGGAGAGGACCAAGA 59.607 63.158 0.00 0.00 0.00 3.02
3789 13203 8.490311 TGTGATGTGTTCCCTTCATATTATGTA 58.510 33.333 3.67 0.00 0.00 2.29
3970 13384 5.919755 TGGTGTTGTCATAGTGTACTTTCA 58.080 37.500 0.00 0.00 0.00 2.69
4060 13476 1.289160 CAAGATGGACCCCTCCTTCA 58.711 55.000 5.67 0.00 41.39 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 8939 2.622962 GGTGTTACTGGCGTTGGGC 61.623 63.158 0.00 0.00 42.51 5.36
131 8985 2.898343 GGCGTCGGTGTTGGTGTT 60.898 61.111 0.00 0.00 0.00 3.32
233 9087 1.530013 GGACGTCTTCGGAAGGTGGA 61.530 60.000 16.46 0.00 41.85 4.02
240 9094 0.815734 GAAGATGGGACGTCTTCGGA 59.184 55.000 16.46 0.00 41.33 4.55
449 9303 2.541762 GGACACGAAGCAGAATATCAGC 59.458 50.000 0.00 0.00 0.00 4.26
592 9456 2.209838 ATGGACGACGTCACATGATC 57.790 50.000 27.77 10.33 33.68 2.92
763 9639 1.631072 CACTAATCAAGTCGGCGCG 59.369 57.895 0.00 0.00 35.76 6.86
904 9821 0.962356 AAGAAATCCGCTGGCACCAG 60.962 55.000 12.54 12.54 46.15 4.00
906 9823 0.678048 AGAAGAAATCCGCTGGCACC 60.678 55.000 0.00 0.00 0.00 5.01
1077 9997 4.509737 GCCAGCTCGTCGTACCCC 62.510 72.222 0.00 0.00 0.00 4.95
1378 10298 0.389296 CAGTTCGATGGGTGTGCGTA 60.389 55.000 0.00 0.00 0.00 4.42
1383 10303 0.036952 CAGAGCAGTTCGATGGGTGT 60.037 55.000 0.00 0.00 0.00 4.16
1384 10304 1.364626 GCAGAGCAGTTCGATGGGTG 61.365 60.000 0.00 0.00 0.00 4.61
1431 10352 2.094286 CCTGAGACTAGCCTCTTGTGTG 60.094 54.545 7.62 0.00 34.38 3.82
1554 10495 6.949352 ATGAAATGAAGTACTGCCCATAAG 57.051 37.500 0.00 0.00 0.00 1.73
1558 10499 5.538053 TCAAAATGAAATGAAGTACTGCCCA 59.462 36.000 0.00 0.00 0.00 5.36
1603 10544 7.517614 TTTAAACATTCAGTGCCAGAACATA 57.482 32.000 0.00 0.00 0.00 2.29
1705 10646 6.964464 TGATTTACTTACCTTGGGCTCATAA 58.036 36.000 0.00 0.00 0.00 1.90
1729 10670 4.949238 TCAATCGTGTTGATGGGATTTGAT 59.051 37.500 2.63 0.00 37.39 2.57
1735 10676 2.083774 GCTTCAATCGTGTTGATGGGA 58.916 47.619 15.34 0.97 37.39 4.37
1740 10681 3.187022 CAGACATGCTTCAATCGTGTTGA 59.813 43.478 0.00 2.63 34.15 3.18
1755 10696 0.870393 AAGCGACACAAGCAGACATG 59.130 50.000 0.00 0.00 37.01 3.21
1756 10697 1.532868 GAAAGCGACACAAGCAGACAT 59.467 47.619 0.00 0.00 37.01 3.06
1768 10717 1.136057 GTTGGATGAACCGAAAGCGAC 60.136 52.381 0.00 0.00 42.61 5.19
1771 10720 2.427506 AGAGTTGGATGAACCGAAAGC 58.572 47.619 0.00 0.00 42.61 3.51
1772 10721 3.437049 GGAAGAGTTGGATGAACCGAAAG 59.563 47.826 0.00 0.00 42.61 2.62
1773 10722 3.072476 AGGAAGAGTTGGATGAACCGAAA 59.928 43.478 0.00 0.00 42.61 3.46
1774 10723 2.637872 AGGAAGAGTTGGATGAACCGAA 59.362 45.455 0.00 0.00 42.61 4.30
1777 10726 3.084786 CCAAGGAAGAGTTGGATGAACC 58.915 50.000 0.00 0.00 46.53 3.62
1778 10727 4.021102 TCCAAGGAAGAGTTGGATGAAC 57.979 45.455 0.29 0.00 46.96 3.18
1784 10733 1.878102 CGTGGTCCAAGGAAGAGTTGG 60.878 57.143 0.00 0.00 45.18 3.77
1785 10734 1.202651 ACGTGGTCCAAGGAAGAGTTG 60.203 52.381 9.75 0.00 0.00 3.16
1786 10735 1.129058 ACGTGGTCCAAGGAAGAGTT 58.871 50.000 9.75 0.00 0.00 3.01
1787 10736 0.393077 CACGTGGTCCAAGGAAGAGT 59.607 55.000 7.95 0.00 0.00 3.24
1788 10737 0.951040 GCACGTGGTCCAAGGAAGAG 60.951 60.000 18.88 0.00 0.00 2.85
1789 10738 1.070786 GCACGTGGTCCAAGGAAGA 59.929 57.895 18.88 0.00 0.00 2.87
1790 10739 1.227823 TGCACGTGGTCCAAGGAAG 60.228 57.895 18.88 0.36 0.00 3.46
1791 10740 1.227823 CTGCACGTGGTCCAAGGAA 60.228 57.895 18.88 0.00 0.00 3.36
1792 10741 2.425592 CTGCACGTGGTCCAAGGA 59.574 61.111 18.88 0.00 0.00 3.36
1793 10742 2.669569 CCTGCACGTGGTCCAAGG 60.670 66.667 18.88 0.84 0.00 3.61
1794 10743 1.525995 AACCTGCACGTGGTCCAAG 60.526 57.895 18.88 2.91 36.69 3.61
1795 10744 1.821759 CAACCTGCACGTGGTCCAA 60.822 57.895 18.88 0.00 36.69 3.53
1796 10745 2.203139 CAACCTGCACGTGGTCCA 60.203 61.111 18.88 5.91 36.69 4.02
1797 10746 3.660111 GCAACCTGCACGTGGTCC 61.660 66.667 18.88 0.59 44.26 4.46
1830 10779 3.374220 TGTTCTGCTTCTTGGCATTTG 57.626 42.857 0.00 0.00 41.63 2.32
1893 10842 7.715265 TTCTGAACACTAATCAACTGTCTTC 57.285 36.000 0.00 0.00 0.00 2.87
1910 10863 3.186909 GCAGTTTGTTGGGTTTCTGAAC 58.813 45.455 0.00 0.00 34.96 3.18
1996 10951 0.470766 AATATTCCGGCGCCAGGTAA 59.529 50.000 28.98 21.33 0.00 2.85
2095 11050 2.981921 TCTGAGGATGCCATGATAGGT 58.018 47.619 0.00 0.00 0.00 3.08
2151 11106 2.408835 GCGATGGATGGTTTGGCG 59.591 61.111 0.00 0.00 0.00 5.69
2183 11138 2.548480 GTGCTCACTAACAGTTGTTCCC 59.452 50.000 0.00 0.00 39.31 3.97
2188 11143 3.722147 AGTCAGTGCTCACTAACAGTTG 58.278 45.455 6.13 0.00 40.20 3.16
2202 11157 4.240888 CACAACCATCTCAGTAGTCAGTG 58.759 47.826 0.00 0.00 0.00 3.66
2203 11158 3.306364 GCACAACCATCTCAGTAGTCAGT 60.306 47.826 0.00 0.00 0.00 3.41
2204 11159 3.257393 GCACAACCATCTCAGTAGTCAG 58.743 50.000 0.00 0.00 0.00 3.51
2205 11160 2.028112 GGCACAACCATCTCAGTAGTCA 60.028 50.000 0.00 0.00 38.86 3.41
2206 11161 2.622436 GGCACAACCATCTCAGTAGTC 58.378 52.381 0.00 0.00 38.86 2.59
2207 11162 1.279271 GGGCACAACCATCTCAGTAGT 59.721 52.381 0.00 0.00 42.05 2.73
2208 11163 1.556911 AGGGCACAACCATCTCAGTAG 59.443 52.381 0.00 0.00 42.05 2.57
2223 11180 2.420129 GCGAGAAGGAATTAGAAGGGCA 60.420 50.000 0.00 0.00 0.00 5.36
2251 11208 7.090953 AGTTCAAACACGAGTAATTTGGAAA 57.909 32.000 10.37 0.00 34.70 3.13
2252 11209 6.687081 AGTTCAAACACGAGTAATTTGGAA 57.313 33.333 10.37 0.00 34.70 3.53
2292 11252 5.634118 TCAAGTGGGATCAAACAAGATTCT 58.366 37.500 0.00 0.00 0.00 2.40
2294 11254 6.521151 GATCAAGTGGGATCAAACAAGATT 57.479 37.500 0.00 0.00 42.58 2.40
2324 11284 2.509052 TTTGCGATGGGAGATAGACG 57.491 50.000 0.00 0.00 0.00 4.18
2363 11323 2.474816 GGAATCGATCAGGGAAACGAG 58.525 52.381 0.00 0.00 38.12 4.18
2373 11333 0.534873 TGCCTGTTCGGAATCGATCA 59.465 50.000 0.00 0.00 45.51 2.92
2377 11337 0.179189 GCTTTGCCTGTTCGGAATCG 60.179 55.000 0.00 0.00 37.82 3.34
2379 11339 2.267045 GGCTTTGCCTGTTCGGAAT 58.733 52.632 0.73 0.00 46.69 3.01
2561 11521 1.749033 CCTGTAGGCGAGGGGATTC 59.251 63.158 0.00 0.00 0.00 2.52
2579 11539 1.355066 CGCGGGAGAGAAAAGACAGC 61.355 60.000 0.00 0.00 0.00 4.40
2624 11584 4.119862 GCTTGTTAATGATCTACAGCGGA 58.880 43.478 0.00 0.00 0.00 5.54
2633 11593 4.091424 GCGTCACTTGCTTGTTAATGATC 58.909 43.478 0.00 0.00 0.00 2.92
2669 11630 2.554462 ACCGGACGATCTGATCACATAG 59.446 50.000 9.46 5.64 0.00 2.23
2877 11838 4.549516 GCCCGTACTCGCTCGTCC 62.550 72.222 0.00 0.00 35.54 4.79
3016 11977 0.178926 TGAACCCCTCCGTAGTTCCA 60.179 55.000 0.00 0.00 39.30 3.53
3022 11983 1.987855 CCTGCTGAACCCCTCCGTA 60.988 63.158 0.00 0.00 0.00 4.02
3092 12060 1.338337 CTTGATCACCCGCTCGTAGAT 59.662 52.381 0.00 0.00 33.89 1.98
3093 12061 0.738975 CTTGATCACCCGCTCGTAGA 59.261 55.000 0.00 0.00 0.00 2.59
3094 12062 0.249073 CCTTGATCACCCGCTCGTAG 60.249 60.000 0.00 0.00 0.00 3.51
3141 12109 2.254546 ACCAAATCTCACAGCGACAA 57.745 45.000 0.00 0.00 0.00 3.18
3152 12120 4.754322 ACAAAGAAACGCAAACCAAATCT 58.246 34.783 0.00 0.00 0.00 2.40
3180 12148 3.651803 AAAATCGCATGAACCCGAAAA 57.348 38.095 0.00 0.00 37.00 2.29
3270 12238 8.465273 TCGAGTAATTCTCCATCATCTCTTTA 57.535 34.615 0.00 0.00 39.84 1.85
3290 12258 0.171455 GGACGAGAGCATGTTCGAGT 59.829 55.000 18.59 15.14 39.93 4.18
3293 12261 1.416813 GCAGGACGAGAGCATGTTCG 61.417 60.000 3.72 9.02 42.26 3.95
3348 12507 5.120830 CGAGGATTTTCTCAACACCTTGTAG 59.879 44.000 0.00 0.00 33.59 2.74
3363 12522 7.607991 TCTTTTCTATCAGCTTTCGAGGATTTT 59.392 33.333 0.00 0.00 0.00 1.82
3374 12533 8.169977 TGTCATGTTTTCTTTTCTATCAGCTT 57.830 30.769 0.00 0.00 0.00 3.74
3388 12547 6.367422 TCTTTGGTGTGTTTTGTCATGTTTTC 59.633 34.615 0.00 0.00 0.00 2.29
3428 12587 0.387565 TGCTAGTTCACTCGTGTGCA 59.612 50.000 12.66 3.52 43.49 4.57
3434 12593 0.438830 GGCGTTTGCTAGTTCACTCG 59.561 55.000 0.00 0.00 42.25 4.18
3491 12650 0.618458 GGTGGTTATCACTCCTGGCA 59.382 55.000 0.00 0.00 45.38 4.92
3574 12733 2.038033 TCGGGGTGAAAATCTTCGTCTT 59.962 45.455 0.00 0.00 33.94 3.01
3576 12735 2.000447 CTCGGGGTGAAAATCTTCGTC 59.000 52.381 0.00 0.00 33.94 4.20
3578 12737 2.094762 ACTCGGGGTGAAAATCTTCG 57.905 50.000 0.00 0.00 33.94 3.79
3595 12755 3.940506 CTCCCTCCCCGTCGACACT 62.941 68.421 17.16 0.00 0.00 3.55
3599 12759 4.124943 CCTCTCCCTCCCCGTCGA 62.125 72.222 0.00 0.00 0.00 4.20
3603 12763 3.618855 TTGGTCCTCTCCCTCCCCG 62.619 68.421 0.00 0.00 0.00 5.73
3623 13036 4.115199 GTCCCCTTGGAGCGCCAT 62.115 66.667 10.98 0.00 45.46 4.40
3712 13125 6.539826 TGATCACAATAAAGATCGCAACTCAT 59.460 34.615 0.00 0.00 42.72 2.90
3789 13203 6.839124 TGAGCAAGATTTAATTCACCACAT 57.161 33.333 0.56 0.00 0.00 3.21
3830 13244 9.802039 ACTACCAAAGGATTCAAGTAAACATAA 57.198 29.630 0.00 0.00 0.00 1.90
3832 13246 8.706322 AACTACCAAAGGATTCAAGTAAACAT 57.294 30.769 0.00 0.00 0.00 2.71
3833 13247 9.629878 TTAACTACCAAAGGATTCAAGTAAACA 57.370 29.630 0.00 0.00 0.00 2.83
3837 13251 9.667107 CTCATTAACTACCAAAGGATTCAAGTA 57.333 33.333 0.00 0.00 0.00 2.24
3838 13252 8.383175 TCTCATTAACTACCAAAGGATTCAAGT 58.617 33.333 0.00 0.00 0.00 3.16
3839 13253 8.792830 TCTCATTAACTACCAAAGGATTCAAG 57.207 34.615 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.