Multiple sequence alignment - TraesCS2B01G288000

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 TraesCS2B01G288000 chr2B 100.000 4089 0 0 1 4089 397457464 397453376 0.000000e+00 7552.0
1 TraesCS2B01G288000 chr2A 93.062 2551 105 28 670 3188 434613947 434611437 0.000000e+00 3664.0
2 TraesCS2B01G288000 chr2A 89.505 505 34 10 1 492 434616570 434616072 4.490000e-174 621.0
3 TraesCS2B01G288000 chr2A 92.326 417 15 3 3689 4089 434579673 434579258 9.860000e-161 577.0
4 TraesCS2B01G288000 chr2A 90.663 332 16 10 3441 3760 434579959 434579631 1.050000e-115 427.0
5 TraesCS2B01G288000 chr2A 91.724 145 5 3 3281 3419 434611336 434611193 1.160000e-45 195.0
6 TraesCS2B01G288000 chr2A 83.036 112 17 2 412 521 746625236 746625125 2.600000e-17 100.0
7 TraesCS2B01G288000 chr2A 97.619 42 1 0 3417 3458 434580305 434580264 5.670000e-09 73.1
8 TraesCS2B01G288000 chr2D 91.246 2296 62 59 1175 3419 328372825 328370618 0.000000e+00 2998.0
9 TraesCS2B01G288000 chr2D 90.879 1195 76 17 1 1177 328374060 328372881 0.000000e+00 1572.0
10 TraesCS2B01G288000 chr2D 88.440 718 31 21 3417 4089 328370568 328369858 0.000000e+00 819.0
11 TraesCS2B01G288000 chr2D 82.911 158 22 4 404 559 602777389 602777543 1.980000e-28 137.0
12 TraesCS2B01G288000 chr4D 80.941 404 57 16 156 556 108223179 108222793 6.640000e-78 302.0
13 TraesCS2B01G288000 chr3A 75.922 461 75 19 69 521 738257847 738258279 1.930000e-48 204.0
14 TraesCS2B01G288000 chr1D 75.000 528 84 23 39 556 9039734 9039245 2.490000e-47 200.0
15 TraesCS2B01G288000 chr1D 76.879 173 30 7 389 556 420854373 420854206 5.630000e-14 89.8
16 TraesCS2B01G288000 chr7A 75.385 455 72 14 106 550 595046935 595047359 2.510000e-42 183.0
17 TraesCS2B01G288000 chr7A 78.000 200 32 11 361 550 11282871 11283068 9.290000e-22 115.0
18 TraesCS2B01G288000 chr7D 74.947 475 79 21 36 500 555185569 555186013 9.030000e-42 182.0
19 TraesCS2B01G288000 chr3D 79.532 171 23 11 359 521 608567083 608566917 1.200000e-20 111.0
20 TraesCS2B01G288000 chr3D 76.970 165 34 4 389 550 566602509 566602346 1.570000e-14 91.6
21 TraesCS2B01G288000 chr3B 80.952 105 15 5 393 495 771320501 771320400 1.220000e-10 78.7
22 TraesCS2B01G288000 chrUn 100.000 31 0 0 589 619 335430176 335430206 1.590000e-04 58.4
23 TraesCS2B01G288000 chrUn 100.000 31 0 0 589 619 451735544 451735514 1.590000e-04 58.4


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 TraesCS2B01G288000 chr2B 397453376 397457464 4088 True 7552.000000 7552 100.000000 1 4089 1 chr2B.!!$R1 4088
1 TraesCS2B01G288000 chr2A 434611193 434616570 5377 True 1493.333333 3664 91.430333 1 3419 3 chr2A.!!$R3 3418
2 TraesCS2B01G288000 chr2A 434579258 434580305 1047 True 359.033333 577 93.536000 3417 4089 3 chr2A.!!$R2 672
3 TraesCS2B01G288000 chr2D 328369858 328374060 4202 True 1796.333333 2998 90.188333 1 4089 3 chr2D.!!$R1 4088

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
166 167 0.109272 TCATGCGACGAGAACCTGTC 60.109 55.0 0.00 0.00 0.00 3.51 F
648 707 1.158007 ACAATTTGTGAGGGAGGGGT 58.842 50.0 0.15 0.00 0.00 4.95 F
1859 3899 0.107214 CCATTATGTGGGCCACTCGT 60.107 55.0 34.69 22.87 44.79 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1488 3523 0.179037 ATGTCATCCCGTCCTGCATG 60.179 55.000 0.00 0.00 0.0 4.06 R
2455 4511 0.456312 CGCCGACCAGTTACTCAGTC 60.456 60.000 2.84 2.84 0.0 3.51 R
3553 6039 1.130561 GATACGGTTCAAAGCAGCACC 59.869 52.381 0.00 0.00 0.0 5.01 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
65 66 2.356075 CGTGGACCAAACGGCGTA 60.356 61.111 15.20 0.00 37.39 4.42
66 67 1.738830 CGTGGACCAAACGGCGTAT 60.739 57.895 15.20 0.05 37.39 3.06
76 77 2.172851 AACGGCGTATGTTTCCTTCA 57.827 45.000 15.20 0.00 0.00 3.02
89 90 4.642885 TGTTTCCTTCATTCCTTGAAACGT 59.357 37.500 0.00 0.00 44.71 3.99
166 167 0.109272 TCATGCGACGAGAACCTGTC 60.109 55.000 0.00 0.00 0.00 3.51
173 174 1.741706 GACGAGAACCTGTCCGTCATA 59.258 52.381 0.00 0.00 43.57 2.15
185 186 3.867493 TGTCCGTCATACGTACAGAGTAG 59.133 47.826 0.00 0.00 35.55 2.57
189 190 2.611292 GTCATACGTACAGAGTAGGCGT 59.389 50.000 0.00 0.00 39.23 5.68
218 219 3.812262 TGTCCATCCATCTTGTGCATAG 58.188 45.455 0.00 0.00 0.00 2.23
221 222 2.511659 CATCCATCTTGTGCATAGGGG 58.488 52.381 0.00 0.00 0.00 4.79
322 328 3.588906 ACCACGTGTGCGACTCGA 61.589 61.111 15.65 0.00 42.00 4.04
467 485 4.884668 ACTAGGCACAGCAAGTTAGTTA 57.115 40.909 0.00 0.00 0.00 2.24
498 546 3.805971 AGTTACAGCGTGTGGAAGTAAAC 59.194 43.478 1.58 0.00 29.87 2.01
509 557 4.141711 TGTGGAAGTAAACTGAGAGCTTGT 60.142 41.667 0.00 0.00 0.00 3.16
521 569 3.742882 TGAGAGCTTGTGAGTTTGAATCG 59.257 43.478 0.00 0.00 0.00 3.34
527 575 4.213482 GCTTGTGAGTTTGAATCGTACCTT 59.787 41.667 0.00 0.00 0.00 3.50
528 576 5.666969 TTGTGAGTTTGAATCGTACCTTG 57.333 39.130 0.00 0.00 0.00 3.61
533 581 4.072131 AGTTTGAATCGTACCTTGTGCAT 58.928 39.130 0.00 0.00 0.00 3.96
566 625 1.343142 GGTTGGAAAACAAATCGGCCT 59.657 47.619 0.00 0.00 41.58 5.19
607 666 3.307199 CCCGGTGGGTATACATTATGGTC 60.307 52.174 5.01 0.00 38.25 4.02
631 690 9.337396 GTCAAATGACCATATTATCCTTGTACA 57.663 33.333 2.04 0.00 39.07 2.90
632 691 9.913310 TCAAATGACCATATTATCCTTGTACAA 57.087 29.630 8.28 8.28 0.00 2.41
648 707 1.158007 ACAATTTGTGAGGGAGGGGT 58.842 50.000 0.15 0.00 0.00 4.95
659 718 5.131067 GTGAGGGAGGGGTGTATTATTTTC 58.869 45.833 0.00 0.00 0.00 2.29
664 723 4.577693 GGAGGGGTGTATTATTTTCGGTTC 59.422 45.833 0.00 0.00 0.00 3.62
668 727 6.494146 AGGGGTGTATTATTTTCGGTTCAAAA 59.506 34.615 0.00 0.00 0.00 2.44
758 2723 9.095065 GAAGAAATATTCTACGTGCTTAAGGAA 57.905 33.333 4.29 0.00 39.61 3.36
794 2759 6.775629 ACAAGGGTTGATGTGTAAACTATGTT 59.224 34.615 0.00 0.00 0.00 2.71
795 2760 7.940137 ACAAGGGTTGATGTGTAAACTATGTTA 59.060 33.333 0.00 0.00 0.00 2.41
910 2875 1.996898 TCGAAAATGACCCGATCGTTG 59.003 47.619 15.09 7.36 36.62 4.10
941 2907 3.283259 AAAAGAAGATGGATCGGGGAC 57.717 47.619 0.00 0.00 0.00 4.46
962 2928 5.220491 GGACAGAAGAATGTAGATTTCACGC 60.220 44.000 0.00 0.00 32.25 5.34
987 2953 2.873133 AAGCCGATCGGTAGAAGAAG 57.127 50.000 33.33 6.93 37.65 2.85
1014 2984 1.602377 GTGCGTATGGCCAGATTAACC 59.398 52.381 13.05 0.00 42.61 2.85
1183 3153 6.183360 CGAGGAACACACGGTACTAATTACTA 60.183 42.308 0.00 0.00 0.00 1.82
1185 3155 6.660949 AGGAACACACGGTACTAATTACTACT 59.339 38.462 0.00 0.00 0.00 2.57
1186 3156 6.969473 GGAACACACGGTACTAATTACTACTC 59.031 42.308 0.00 0.00 0.00 2.59
1189 3159 7.338710 ACACACGGTACTAATTACTACTCCTA 58.661 38.462 0.00 0.00 0.00 2.94
1190 3160 7.281100 ACACACGGTACTAATTACTACTCCTAC 59.719 40.741 0.00 0.00 0.00 3.18
1227 3252 3.242220 GCGTGTGTTCATCTCATCATGTC 60.242 47.826 0.00 0.00 0.00 3.06
1292 3317 1.407979 GTGACGACCCAAGACGGATAT 59.592 52.381 0.00 0.00 36.56 1.63
1401 3426 4.081642 ACGGCCTCATGATGGTATACATAC 60.082 45.833 0.00 0.00 40.72 2.39
1471 3506 3.678289 AGCAAGTGCAAGTGATGACATA 58.322 40.909 6.00 0.00 45.16 2.29
1483 3518 5.713025 AGTGATGACATATGTTTTGTTGGC 58.287 37.500 10.30 0.00 0.00 4.52
1484 3519 5.243507 AGTGATGACATATGTTTTGTTGGCA 59.756 36.000 10.30 0.84 0.00 4.92
1485 3520 6.071221 AGTGATGACATATGTTTTGTTGGCAT 60.071 34.615 10.30 5.99 40.47 4.40
1486 3521 6.035220 GTGATGACATATGTTTTGTTGGCATG 59.965 38.462 10.30 0.00 37.93 4.06
1487 3522 4.244066 TGACATATGTTTTGTTGGCATGC 58.756 39.130 9.90 9.90 0.00 4.06
1488 3523 3.598299 ACATATGTTTTGTTGGCATGCC 58.402 40.909 30.54 30.54 0.00 4.40
1708 3744 8.364894 TGCACTCTCTTCTTTGTTGTACTATAA 58.635 33.333 0.00 0.00 0.00 0.98
1709 3745 8.865001 GCACTCTCTTCTTTGTTGTACTATAAG 58.135 37.037 0.00 0.00 0.00 1.73
1710 3746 9.915629 CACTCTCTTCTTTGTTGTACTATAAGT 57.084 33.333 0.00 0.00 0.00 2.24
1840 3880 1.376553 GTCAGGCCAGCAGAAGGTC 60.377 63.158 5.01 0.00 0.00 3.85
1859 3899 0.107214 CCATTATGTGGGCCACTCGT 60.107 55.000 34.69 22.87 44.79 4.18
1876 3916 3.307782 ACTCGTTGGTAAGTCACAAAACG 59.692 43.478 0.00 0.00 44.11 3.60
1887 3927 8.525876 GGTAAGTCACAAAACGAAACAAAATAC 58.474 33.333 0.00 0.00 0.00 1.89
1890 3932 6.249682 AGTCACAAAACGAAACAAAATACGTG 59.750 34.615 0.00 0.00 38.92 4.49
1898 3940 4.612712 CGAAACAAAATACGTGCTCACCAT 60.613 41.667 0.00 0.00 0.00 3.55
1931 3973 2.014857 GGGCATCCCGAGTAAGAAAAC 58.985 52.381 0.00 0.00 32.13 2.43
1932 3974 2.014857 GGCATCCCGAGTAAGAAAACC 58.985 52.381 0.00 0.00 0.00 3.27
1933 3975 2.355818 GGCATCCCGAGTAAGAAAACCT 60.356 50.000 0.00 0.00 0.00 3.50
1934 3976 2.678336 GCATCCCGAGTAAGAAAACCTG 59.322 50.000 0.00 0.00 0.00 4.00
1935 3977 3.868754 GCATCCCGAGTAAGAAAACCTGT 60.869 47.826 0.00 0.00 0.00 4.00
1939 3981 2.737252 CCGAGTAAGAAAACCTGTCTGC 59.263 50.000 0.00 0.00 0.00 4.26
2007 4061 2.230940 GCACGTATCGATGCTGCGT 61.231 57.895 17.02 14.29 38.84 5.24
2112 4166 3.877508 CCGAGGTAATCAAGTTTGATCCC 59.122 47.826 7.74 10.43 46.60 3.85
2136 4190 1.202533 CCGAGGGTATCACATCACACC 60.203 57.143 0.00 0.00 0.00 4.16
2137 4191 1.480545 CGAGGGTATCACATCACACCA 59.519 52.381 0.00 0.00 32.42 4.17
2138 4192 2.738643 CGAGGGTATCACATCACACCAC 60.739 54.545 0.00 0.00 32.42 4.16
2139 4193 2.236146 GAGGGTATCACATCACACCACA 59.764 50.000 0.00 0.00 32.42 4.17
2140 4194 2.846206 AGGGTATCACATCACACCACAT 59.154 45.455 0.00 0.00 32.42 3.21
2141 4195 2.945008 GGGTATCACATCACACCACATG 59.055 50.000 0.00 0.00 32.42 3.21
2142 4196 3.370421 GGGTATCACATCACACCACATGA 60.370 47.826 0.00 0.00 32.42 3.07
2144 4198 4.883585 GGTATCACATCACACCACATGAAT 59.116 41.667 0.00 0.00 0.00 2.57
2145 4199 5.008019 GGTATCACATCACACCACATGAATC 59.992 44.000 0.00 0.00 0.00 2.52
2152 4208 5.632244 TCACACCACATGAATCAATCAAG 57.368 39.130 0.00 0.00 42.54 3.02
2225 4281 4.120589 GAGTTCGATCCAACAGGGTAATC 58.879 47.826 5.98 0.00 38.11 1.75
2232 4288 4.216411 TCCAACAGGGTAATCTAAGCAC 57.784 45.455 0.00 0.00 38.11 4.40
2233 4289 3.585289 TCCAACAGGGTAATCTAAGCACA 59.415 43.478 0.00 0.00 38.11 4.57
2234 4290 3.689649 CCAACAGGGTAATCTAAGCACAC 59.310 47.826 0.00 0.00 0.00 3.82
2235 4291 3.247006 ACAGGGTAATCTAAGCACACG 57.753 47.619 0.00 0.00 0.00 4.49
2236 4292 2.565834 ACAGGGTAATCTAAGCACACGT 59.434 45.455 0.00 0.00 0.00 4.49
2237 4293 3.007614 ACAGGGTAATCTAAGCACACGTT 59.992 43.478 0.00 0.00 0.00 3.99
2238 4294 3.617263 CAGGGTAATCTAAGCACACGTTC 59.383 47.826 0.00 0.00 0.00 3.95
2239 4295 3.514309 AGGGTAATCTAAGCACACGTTCT 59.486 43.478 0.00 0.00 0.00 3.01
2240 4296 3.617263 GGGTAATCTAAGCACACGTTCTG 59.383 47.826 0.00 0.00 0.00 3.02
2241 4297 4.243270 GGTAATCTAAGCACACGTTCTGT 58.757 43.478 0.00 0.00 0.00 3.41
2286 4342 3.675698 TGAGGTTTCGTTTGTTTTGCAAC 59.324 39.130 0.00 0.00 36.72 4.17
2287 4343 3.920446 AGGTTTCGTTTGTTTTGCAACT 58.080 36.364 0.00 0.00 36.72 3.16
2288 4344 3.924073 AGGTTTCGTTTGTTTTGCAACTC 59.076 39.130 0.00 0.00 36.72 3.01
2289 4345 3.061563 GGTTTCGTTTGTTTTGCAACTCC 59.938 43.478 0.00 0.00 36.72 3.85
2321 4377 2.439507 ACGATGGCTGGGAACTAATGAT 59.560 45.455 0.00 0.00 0.00 2.45
2322 4378 3.070018 CGATGGCTGGGAACTAATGATC 58.930 50.000 0.00 0.00 0.00 2.92
2323 4379 3.244353 CGATGGCTGGGAACTAATGATCT 60.244 47.826 0.00 0.00 0.00 2.75
2324 4380 3.845781 TGGCTGGGAACTAATGATCTC 57.154 47.619 0.00 0.00 0.00 2.75
2326 4382 4.556697 TGGCTGGGAACTAATGATCTCTA 58.443 43.478 0.00 0.00 0.00 2.43
2421 4477 6.096282 TCTCATGTCATCGTTTACAGGTATCA 59.904 38.462 0.00 0.00 0.00 2.15
2447 4503 8.643324 AGCTTCTATCTCTCCGTTTGTTATTAT 58.357 33.333 0.00 0.00 0.00 1.28
2448 4504 8.917655 GCTTCTATCTCTCCGTTTGTTATTATC 58.082 37.037 0.00 0.00 0.00 1.75
2449 4505 9.967346 CTTCTATCTCTCCGTTTGTTATTATCA 57.033 33.333 0.00 0.00 0.00 2.15
2455 4511 7.706607 TCTCTCCGTTTGTTATTATCATCACTG 59.293 37.037 0.00 0.00 0.00 3.66
2668 4728 0.460284 CCCAGCCACAGTCGATACAC 60.460 60.000 0.00 0.00 0.00 2.90
2725 4790 7.592051 AGAAAGAGATGAAACAAGATTTCTGC 58.408 34.615 0.00 0.00 35.17 4.26
2733 4798 7.333528 TGAAACAAGATTTCTGCTGTTAACT 57.666 32.000 7.22 0.00 29.59 2.24
2734 4799 8.445275 TGAAACAAGATTTCTGCTGTTAACTA 57.555 30.769 7.22 0.00 29.59 2.24
2735 4800 8.898761 TGAAACAAGATTTCTGCTGTTAACTAA 58.101 29.630 7.22 0.00 29.59 2.24
2736 4801 9.387123 GAAACAAGATTTCTGCTGTTAACTAAG 57.613 33.333 7.22 0.00 29.59 2.18
3096 5161 2.644299 TCCAGGACAAATGACATGGACT 59.356 45.455 13.64 0.00 43.32 3.85
3161 5227 6.474751 GGATACGAGTGGTCATACTTGTAAAC 59.525 42.308 9.37 7.35 45.71 2.01
3163 5229 3.611113 CGAGTGGTCATACTTGTAAACCG 59.389 47.826 9.58 0.00 32.50 4.44
3301 5401 5.483685 TGTAAACTGCATACTGGACTCTT 57.516 39.130 0.00 0.00 0.00 2.85
3331 5432 5.760743 TGAGAAGAGTACATCTGGATACGAG 59.239 44.000 0.00 0.00 38.67 4.18
3422 5580 6.830114 GCATAAGCTTCTATCAAACTACGT 57.170 37.500 0.00 0.00 37.91 3.57
3491 5971 2.034532 CATCCTGCCAGTGTGCCA 59.965 61.111 0.00 0.00 0.00 4.92
3553 6039 2.665649 TTGCCTACACACCATCGTAG 57.334 50.000 0.00 0.00 35.82 3.51
3592 6078 3.498927 TCTAACCTACTTGTACGCAGC 57.501 47.619 0.00 0.00 0.00 5.25
3599 6085 3.099619 CTTGTACGCAGCGGGCATG 62.100 63.158 21.15 14.70 45.17 4.06
4058 6592 3.047877 GCGCGCCTGGTGTAGTTT 61.048 61.111 23.24 0.00 0.00 2.66
4064 6598 3.371591 CGCGCCTGGTGTAGTTTATAAAA 59.628 43.478 9.31 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 7.231519 AGCTGCCTACACTCTTTTCTTTTAATT 59.768 33.333 0.00 0.00 0.00 1.40
27 28 2.061773 CGTGGTTTCAGTGACTAGCTG 58.938 52.381 0.00 0.00 35.43 4.24
56 57 2.496111 TGAAGGAAACATACGCCGTTT 58.504 42.857 0.00 0.00 39.23 3.60
57 58 2.172851 TGAAGGAAACATACGCCGTT 57.827 45.000 0.00 0.00 0.00 4.44
76 77 6.391227 AAAATGAGTCACGTTTCAAGGAAT 57.609 33.333 0.00 0.00 36.80 3.01
123 124 1.407437 GCCATGTCGGTCCTCAATCTT 60.407 52.381 0.00 0.00 36.97 2.40
125 126 1.154205 CGCCATGTCGGTCCTCAATC 61.154 60.000 0.00 0.00 36.97 2.67
173 174 3.273434 TCATTACGCCTACTCTGTACGT 58.727 45.455 0.00 0.00 40.53 3.57
185 186 2.948979 TGGATGGACAATTCATTACGCC 59.051 45.455 0.00 0.00 0.00 5.68
189 190 6.183360 GCACAAGATGGATGGACAATTCATTA 60.183 38.462 0.00 0.00 34.32 1.90
218 219 4.465632 AAATAAATGAAGGAAACGCCCC 57.534 40.909 0.00 0.00 37.37 5.80
221 222 8.635983 GTTTCAGTAAATAAATGAAGGAAACGC 58.364 33.333 0.00 0.00 34.64 4.84
322 328 2.498481 TCTCGTCCCCGTGATAACAAAT 59.502 45.455 0.00 0.00 32.17 2.32
370 386 8.360390 GTTTTGTTTGACCCTTCTATTCTTCAT 58.640 33.333 0.00 0.00 0.00 2.57
371 387 7.340743 TGTTTTGTTTGACCCTTCTATTCTTCA 59.659 33.333 0.00 0.00 0.00 3.02
380 396 6.546972 TTGTTTTGTTTTGTTTGACCCTTC 57.453 33.333 0.00 0.00 0.00 3.46
386 402 8.860128 GTTTGGTTTTTGTTTTGTTTTGTTTGA 58.140 25.926 0.00 0.00 0.00 2.69
467 485 4.142227 CCACACGCTGTAACTAACTAGGAT 60.142 45.833 0.00 0.00 0.00 3.24
498 546 4.143158 CGATTCAAACTCACAAGCTCTCAG 60.143 45.833 0.00 0.00 0.00 3.35
509 557 3.496884 GCACAAGGTACGATTCAAACTCA 59.503 43.478 0.00 0.00 0.00 3.41
550 598 3.425758 CGTCTTAGGCCGATTTGTTTTCC 60.426 47.826 0.00 0.00 0.00 3.13
551 599 3.425758 CCGTCTTAGGCCGATTTGTTTTC 60.426 47.826 0.00 0.00 0.00 2.29
556 604 1.571919 CTCCGTCTTAGGCCGATTTG 58.428 55.000 0.00 0.00 0.00 2.32
557 605 0.464452 CCTCCGTCTTAGGCCGATTT 59.536 55.000 0.00 0.00 0.00 2.17
560 608 2.441532 CCCTCCGTCTTAGGCCGA 60.442 66.667 0.00 0.00 32.34 5.54
566 625 1.675219 GCACAACCCCTCCGTCTTA 59.325 57.895 0.00 0.00 0.00 2.10
587 646 4.610605 TGACCATAATGTATACCCACCG 57.389 45.455 0.00 0.00 0.00 4.94
622 681 4.506625 CCTCCCTCACAAATTGTACAAGGA 60.507 45.833 14.65 10.95 29.97 3.36
627 686 2.041216 ACCCCTCCCTCACAAATTGTAC 59.959 50.000 0.00 0.00 0.00 2.90
631 690 1.158007 ACACCCCTCCCTCACAAATT 58.842 50.000 0.00 0.00 0.00 1.82
632 691 2.053747 TACACCCCTCCCTCACAAAT 57.946 50.000 0.00 0.00 0.00 2.32
686 2651 6.458888 GCATTTTACTTCAGTTCCTGCCTATC 60.459 42.308 0.00 0.00 0.00 2.08
689 2654 3.507622 GCATTTTACTTCAGTTCCTGCCT 59.492 43.478 0.00 0.00 0.00 4.75
744 2709 1.670674 CGCAGGTTCCTTAAGCACGTA 60.671 52.381 0.00 0.00 35.49 3.57
758 2723 2.906897 CCCTTGTTGCACGCAGGT 60.907 61.111 0.00 0.00 0.00 4.00
910 2875 8.704234 CGATCCATCTTCTTTTATACTAGTTGC 58.296 37.037 0.00 0.00 0.00 4.17
941 2907 4.259970 CGGCGTGAAATCTACATTCTTCTG 60.260 45.833 0.00 0.00 0.00 3.02
987 2953 0.878416 TGGCCATACGCACAAGTTTC 59.122 50.000 0.00 0.00 40.31 2.78
1014 2984 2.113433 GCTGCTGCCTCTCCACATG 61.113 63.158 3.85 0.00 0.00 3.21
1183 3153 3.363627 GCCTGGTTACTGTAGTAGGAGT 58.636 50.000 14.43 0.00 0.00 3.85
1185 3155 2.372264 CGCCTGGTTACTGTAGTAGGA 58.628 52.381 14.43 0.00 0.00 2.94
1186 3156 1.202382 GCGCCTGGTTACTGTAGTAGG 60.202 57.143 0.00 8.75 0.00 3.18
1189 3159 1.214589 CGCGCCTGGTTACTGTAGT 59.785 57.895 0.00 0.00 0.00 2.73
1190 3160 1.076533 CACGCGCCTGGTTACTGTAG 61.077 60.000 5.73 0.00 0.00 2.74
1227 3252 9.708222 CAAATTAATCTTCCGTCAGTTAATCAG 57.292 33.333 0.00 0.00 0.00 2.90
1292 3317 1.119684 TTCGCTGCAGGCTTAGGATA 58.880 50.000 17.12 0.00 39.13 2.59
1483 3518 2.971095 ATCCCGTCCTGCATGGCATG 62.971 60.000 22.99 22.99 38.13 4.06
1484 3519 2.760378 ATCCCGTCCTGCATGGCAT 61.760 57.895 0.00 0.00 38.13 4.40
1485 3520 3.410628 ATCCCGTCCTGCATGGCA 61.411 61.111 0.00 0.00 36.92 4.92
1486 3521 2.903855 CATCCCGTCCTGCATGGC 60.904 66.667 0.00 0.00 35.26 4.40
1487 3522 1.524621 GTCATCCCGTCCTGCATGG 60.525 63.158 0.00 0.00 37.10 3.66
1488 3523 0.179037 ATGTCATCCCGTCCTGCATG 60.179 55.000 0.00 0.00 0.00 4.06
1676 3712 2.866156 CAAAGAAGAGAGTGCACGTCAA 59.134 45.455 20.29 0.00 0.00 3.18
1680 3716 2.609459 ACAACAAAGAAGAGAGTGCACG 59.391 45.455 12.01 0.00 0.00 5.34
1713 3749 9.982651 GTTCTCATCCAGCATTAGTATTAGTAA 57.017 33.333 0.00 0.00 0.00 2.24
1716 3752 6.876257 GGGTTCTCATCCAGCATTAGTATTAG 59.124 42.308 0.00 0.00 0.00 1.73
1859 3899 5.624344 TGTTTCGTTTTGTGACTTACCAA 57.376 34.783 0.00 0.00 0.00 3.67
1876 3916 4.217754 TGGTGAGCACGTATTTTGTTTC 57.782 40.909 0.00 0.00 0.00 2.78
1887 3927 2.133553 GATGAGATCATGGTGAGCACG 58.866 52.381 0.00 0.00 34.77 5.34
1890 3932 3.555377 CCTGAGATGAGATCATGGTGAGC 60.555 52.174 0.00 0.00 36.57 4.26
1898 3940 1.976404 GGATGCCCTGAGATGAGATCA 59.024 52.381 0.00 0.00 0.00 2.92
1925 3967 1.537202 GCATTCGCAGACAGGTTTTCT 59.463 47.619 0.00 0.00 38.36 2.52
1926 3968 1.266718 TGCATTCGCAGACAGGTTTTC 59.733 47.619 0.00 0.00 45.36 2.29
1927 3969 1.317613 TGCATTCGCAGACAGGTTTT 58.682 45.000 0.00 0.00 45.36 2.43
1928 3970 3.019964 TGCATTCGCAGACAGGTTT 57.980 47.368 0.00 0.00 45.36 3.27
1939 3981 0.744414 ATCAACGTCCCCTGCATTCG 60.744 55.000 0.00 0.00 0.00 3.34
2007 4061 4.399395 CTGAGCAGGCCAGCCGAA 62.399 66.667 17.68 1.45 41.95 4.30
2100 4154 2.684881 CCTCGGAATGGGATCAAACTTG 59.315 50.000 0.00 0.00 0.00 3.16
2102 4156 2.717639 CCTCGGAATGGGATCAAACT 57.282 50.000 0.00 0.00 0.00 2.66
2112 4166 3.181466 TGTGATGTGATACCCTCGGAATG 60.181 47.826 0.00 0.00 0.00 2.67
2136 4190 9.499585 GAGTGTTATTCTTGATTGATTCATGTG 57.500 33.333 0.00 0.00 33.34 3.21
2137 4191 9.234827 TGAGTGTTATTCTTGATTGATTCATGT 57.765 29.630 0.00 0.00 33.34 3.21
2140 4194 9.234827 ACATGAGTGTTATTCTTGATTGATTCA 57.765 29.630 0.00 0.00 34.01 2.57
2225 4281 2.223377 GGGAAACAGAACGTGTGCTTAG 59.777 50.000 0.00 0.00 40.26 2.18
2232 4288 2.139917 TGAATCGGGAAACAGAACGTG 58.860 47.619 0.00 0.00 38.30 4.49
2233 4289 2.536761 TGAATCGGGAAACAGAACGT 57.463 45.000 0.00 0.00 38.30 3.99
2234 4290 3.684788 AGAATGAATCGGGAAACAGAACG 59.315 43.478 0.00 0.00 38.30 3.95
2235 4291 4.938226 AGAGAATGAATCGGGAAACAGAAC 59.062 41.667 0.00 0.00 38.30 3.01
2236 4292 5.165961 AGAGAATGAATCGGGAAACAGAA 57.834 39.130 0.00 0.00 38.30 3.02
2237 4293 4.826274 AGAGAATGAATCGGGAAACAGA 57.174 40.909 0.00 0.00 39.42 3.41
2238 4294 5.181748 AGAAGAGAATGAATCGGGAAACAG 58.818 41.667 0.00 0.00 0.00 3.16
2239 4295 5.165961 AGAAGAGAATGAATCGGGAAACA 57.834 39.130 0.00 0.00 0.00 2.83
2240 4296 5.877564 AGAAGAAGAGAATGAATCGGGAAAC 59.122 40.000 0.00 0.00 0.00 2.78
2241 4297 5.877012 CAGAAGAAGAGAATGAATCGGGAAA 59.123 40.000 0.00 0.00 0.00 3.13
2286 4342 2.341257 CCATCGTCAGTTGAGTTGGAG 58.659 52.381 0.00 0.00 0.00 3.86
2287 4343 1.608025 GCCATCGTCAGTTGAGTTGGA 60.608 52.381 8.37 0.00 0.00 3.53
2288 4344 0.798776 GCCATCGTCAGTTGAGTTGG 59.201 55.000 0.00 0.00 0.00 3.77
2289 4345 1.462283 CAGCCATCGTCAGTTGAGTTG 59.538 52.381 0.00 0.00 0.00 3.16
2421 4477 4.810191 AACAAACGGAGAGATAGAAGCT 57.190 40.909 0.00 0.00 0.00 3.74
2447 4503 4.152647 ACCAGTTACTCAGTCAGTGATGA 58.847 43.478 0.00 0.76 36.43 2.92
2448 4504 4.489810 GACCAGTTACTCAGTCAGTGATG 58.510 47.826 0.00 0.00 36.43 3.07
2449 4505 3.191581 CGACCAGTTACTCAGTCAGTGAT 59.808 47.826 11.20 0.00 36.43 3.06
2455 4511 0.456312 CGCCGACCAGTTACTCAGTC 60.456 60.000 2.84 2.84 0.00 3.51
2725 4790 4.072131 ACATGTGCCACCTTAGTTAACAG 58.928 43.478 8.61 0.00 0.00 3.16
2733 4798 4.461081 GGTCAAATTACATGTGCCACCTTA 59.539 41.667 9.11 0.00 0.00 2.69
2734 4799 3.258123 GGTCAAATTACATGTGCCACCTT 59.742 43.478 9.11 0.00 0.00 3.50
2735 4800 2.825532 GGTCAAATTACATGTGCCACCT 59.174 45.455 9.11 0.00 0.00 4.00
2736 4801 2.094234 GGGTCAAATTACATGTGCCACC 60.094 50.000 9.11 5.73 0.00 4.61
3096 5161 2.363306 AAAGTGCAATCAGGTGGTGA 57.637 45.000 0.00 0.00 40.38 4.02
3135 5200 3.383825 ACAAGTATGACCACTCGTATCCC 59.616 47.826 0.00 0.00 0.00 3.85
3141 5206 3.611113 CGGTTTACAAGTATGACCACTCG 59.389 47.826 11.44 0.00 0.00 4.18
3161 5227 7.997107 TTAGTTATTTGCTAGTATCACACGG 57.003 36.000 0.00 0.00 0.00 4.94
3248 5314 9.802039 TTTCCTAAGGTACATAAACTTGTTCAT 57.198 29.630 0.00 0.00 0.00 2.57
3251 5317 9.802039 TCATTTCCTAAGGTACATAAACTTGTT 57.198 29.630 0.00 0.00 0.00 2.83
3252 5318 9.975218 ATCATTTCCTAAGGTACATAAACTTGT 57.025 29.630 0.00 0.00 0.00 3.16
3260 5326 9.975218 AGTTTACAATCATTTCCTAAGGTACAT 57.025 29.630 0.00 0.00 0.00 2.29
3262 5328 8.182227 GCAGTTTACAATCATTTCCTAAGGTAC 58.818 37.037 0.00 0.00 0.00 3.34
3263 5329 7.885922 TGCAGTTTACAATCATTTCCTAAGGTA 59.114 33.333 0.00 0.00 0.00 3.08
3264 5330 6.719370 TGCAGTTTACAATCATTTCCTAAGGT 59.281 34.615 0.00 0.00 0.00 3.50
3271 5363 7.698130 GTCCAGTATGCAGTTTACAATCATTTC 59.302 37.037 0.00 0.00 31.97 2.17
3279 5371 5.011635 TGAAGAGTCCAGTATGCAGTTTACA 59.988 40.000 0.00 0.00 31.97 2.41
3301 5401 5.775195 TCCAGATGTACTCTTCTCAAGTTGA 59.225 40.000 5.25 5.25 29.16 3.18
3331 5432 3.683365 ATTTCAAAGGCCACCACATTC 57.317 42.857 5.01 0.00 0.00 2.67
3422 5580 2.362736 ACTGCTCAGTATCGTTCGGTA 58.637 47.619 0.00 0.00 40.43 4.02
3491 5971 7.414540 GCTGTCAAATCGAAATTACCAAGAGAT 60.415 37.037 0.00 0.00 0.00 2.75
3553 6039 1.130561 GATACGGTTCAAAGCAGCACC 59.869 52.381 0.00 0.00 0.00 5.01
3592 6078 2.563050 TTCGCTCTGACTCATGCCCG 62.563 60.000 0.00 0.00 0.00 6.13
3599 6085 3.990469 TGATTCTTGTTTCGCTCTGACTC 59.010 43.478 0.00 0.00 0.00 3.36
3879 6413 0.319040 GTCGACAACAGCAGAGCTCA 60.319 55.000 17.77 0.00 36.40 4.26


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

AutoCloner maintained by Alex Coulton.