Multiple sequence alignment - TraesCS4B01G066700

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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 TraesCS4B01G066700 chr4B 100.000 5026 0 0 1 5026 59595666 59590641 0.000000e+00 9282
1 TraesCS4B01G066700 chr4A 93.519 5076 213 65 1 5026 559043653 559048662 0.000000e+00 7444
2 TraesCS4B01G066700 chr4D 93.391 5054 200 61 1 5026 40657890 40652943 0.000000e+00 7360
3 TraesCS4B01G066700 chr2D 77.660 282 50 9 1148 1427 449556344 449556074 5.210000e-35 159
4 TraesCS4B01G066700 chr2A 77.660 282 50 9 1148 1427 593443486 593443756 5.210000e-35 159
5 TraesCS4B01G066700 chr2B 76.512 281 55 7 1148 1427 528829625 528829895 5.250000e-30 143


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 TraesCS4B01G066700 chr4B 59590641 59595666 5025 True 9282 9282 100.000 1 5026 1 chr4B.!!$R1 5025
1 TraesCS4B01G066700 chr4A 559043653 559048662 5009 False 7444 7444 93.519 1 5026 1 chr4A.!!$F1 5025
2 TraesCS4B01G066700 chr4D 40652943 40657890 4947 True 7360 7360 93.391 1 5026 1 chr4D.!!$R1 5025

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
392 414 0.036875 CGGAGGAGGAGGCAAAAGTT 59.963 55.000 0.00 0.0 0.00 2.66 F
923 968 0.104620 AGTACCACCACCACCTTCCT 60.105 55.000 0.00 0.0 0.00 3.36 F
2211 2274 0.179089 GCTGATCATCTCGGTGCACT 60.179 55.000 17.98 0.0 32.34 4.40 F
2240 2306 0.608035 GCCGTGTCCCAGGAAATTGA 60.608 55.000 0.00 0.0 0.00 2.57 F
2575 2641 1.211212 CCCAATGGCTCTGATCAGTCA 59.789 52.381 21.92 17.7 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2279 0.178975 TTCCTGGGACACGGCAAATT 60.179 50.000 0.00 0.0 0.00 1.82 R
2218 2281 0.178975 ATTTCCTGGGACACGGCAAA 60.179 50.000 0.00 0.0 0.00 3.68 R
3241 3307 1.059264 GCATTGACGACGTACTGAAGC 59.941 52.381 0.00 0.0 0.00 3.86 R
3859 3925 2.173519 CATGGTTTCCAAGCTGATGGT 58.826 47.619 4.36 0.0 41.46 3.55 R
4419 4490 1.066858 ACTCAGGCCTACACATGTTCG 60.067 52.381 3.98 0.0 0.00 3.95 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
34 35 3.290948 AAAGCACAGGACAGTTGGTAA 57.709 42.857 0.00 0.00 0.00 2.85
48 52 7.648510 GGACAGTTGGTAATATACTTCGAAGAG 59.351 40.741 31.08 7.44 38.43 2.85
87 92 3.814268 CATTCAGGGCAACGGGCG 61.814 66.667 0.00 0.00 46.16 6.13
93 98 4.382320 GGGCAACGGGCGTCTACA 62.382 66.667 0.00 0.00 46.16 2.74
97 107 1.074872 GCAACGGGCGTCTACACTAC 61.075 60.000 0.00 0.00 0.00 2.73
191 201 2.037677 AACCAACCCTGTCCCCCT 60.038 61.111 0.00 0.00 0.00 4.79
192 202 1.137594 CAACCAACCCTGTCCCCCTA 61.138 60.000 0.00 0.00 0.00 3.53
193 203 1.138228 AACCAACCCTGTCCCCCTAC 61.138 60.000 0.00 0.00 0.00 3.18
194 204 1.540367 CCAACCCTGTCCCCCTACA 60.540 63.158 0.00 0.00 0.00 2.74
195 205 1.562672 CCAACCCTGTCCCCCTACAG 61.563 65.000 0.00 0.00 45.33 2.74
196 206 0.840722 CAACCCTGTCCCCCTACAGT 60.841 60.000 3.56 0.00 44.45 3.55
197 207 0.794934 AACCCTGTCCCCCTACAGTA 59.205 55.000 3.56 0.00 44.45 2.74
198 208 0.338814 ACCCTGTCCCCCTACAGTAG 59.661 60.000 0.00 0.00 44.45 2.57
199 209 0.338814 CCCTGTCCCCCTACAGTAGT 59.661 60.000 6.84 0.00 44.45 2.73
200 210 1.572415 CCCTGTCCCCCTACAGTAGTA 59.428 57.143 6.84 0.00 44.45 1.82
203 217 2.244252 CTGTCCCCCTACAGTAGTACCT 59.756 54.545 6.84 0.00 41.63 3.08
227 243 6.848562 AAACTATTATCCATTCCCCAGAGT 57.151 37.500 0.00 0.00 0.00 3.24
230 246 4.713792 ATTATCCATTCCCCAGAGTCAC 57.286 45.455 0.00 0.00 0.00 3.67
231 247 1.971149 ATCCATTCCCCAGAGTCACA 58.029 50.000 0.00 0.00 0.00 3.58
234 250 1.339438 CCATTCCCCAGAGTCACACAG 60.339 57.143 0.00 0.00 0.00 3.66
235 251 1.625315 CATTCCCCAGAGTCACACAGA 59.375 52.381 0.00 0.00 0.00 3.41
236 252 1.801242 TTCCCCAGAGTCACACAGAA 58.199 50.000 0.00 0.00 0.00 3.02
237 253 2.030027 TCCCCAGAGTCACACAGAAT 57.970 50.000 0.00 0.00 0.00 2.40
239 255 1.339438 CCCCAGAGTCACACAGAATGG 60.339 57.143 0.00 0.00 43.62 3.16
391 413 1.128188 ACGGAGGAGGAGGCAAAAGT 61.128 55.000 0.00 0.00 0.00 2.66
392 414 0.036875 CGGAGGAGGAGGCAAAAGTT 59.963 55.000 0.00 0.00 0.00 2.66
393 415 1.545651 CGGAGGAGGAGGCAAAAGTTT 60.546 52.381 0.00 0.00 0.00 2.66
394 416 2.290071 CGGAGGAGGAGGCAAAAGTTTA 60.290 50.000 0.00 0.00 0.00 2.01
395 417 3.348119 GGAGGAGGAGGCAAAAGTTTAG 58.652 50.000 0.00 0.00 0.00 1.85
405 434 3.065510 GGCAAAAGTTTAGCTAGCTAGGC 59.934 47.826 23.03 17.65 0.00 3.93
406 435 3.065510 GCAAAAGTTTAGCTAGCTAGGCC 59.934 47.826 23.03 14.93 0.00 5.19
456 485 3.265791 CCTGCGCAGTAAAATCTCTCTT 58.734 45.455 33.75 0.00 0.00 2.85
466 495 7.251994 CAGTAAAATCTCTCTTGCTACGTACT 58.748 38.462 0.00 0.00 0.00 2.73
467 496 8.396390 CAGTAAAATCTCTCTTGCTACGTACTA 58.604 37.037 0.00 0.00 0.00 1.82
468 497 8.397148 AGTAAAATCTCTCTTGCTACGTACTAC 58.603 37.037 0.00 0.00 0.00 2.73
530 559 3.014538 TGGTGCATCCCGGATGGT 61.015 61.111 25.73 0.00 40.10 3.55
568 597 3.981211 ACTGCACCAAAAGTTAATGCTG 58.019 40.909 0.00 0.00 40.05 4.41
571 600 2.327568 CACCAAAAGTTAATGCTGGCG 58.672 47.619 0.00 0.00 0.00 5.69
625 659 4.906792 GAGCCCGGCTGCTGCTAG 62.907 72.222 19.21 9.68 42.95 3.42
733 771 0.107945 CACCTAGAACCAGAGCCAGC 60.108 60.000 0.00 0.00 0.00 4.85
839 881 2.001269 CCCCCTCCCTCCGTTTCAT 61.001 63.158 0.00 0.00 0.00 2.57
922 967 1.553704 CTAGTACCACCACCACCTTCC 59.446 57.143 0.00 0.00 0.00 3.46
923 968 0.104620 AGTACCACCACCACCTTCCT 60.105 55.000 0.00 0.00 0.00 3.36
924 969 0.769247 GTACCACCACCACCTTCCTT 59.231 55.000 0.00 0.00 0.00 3.36
925 970 1.061546 TACCACCACCACCTTCCTTC 58.938 55.000 0.00 0.00 0.00 3.46
931 976 0.969894 CACCACCTTCCTTCGTCTCT 59.030 55.000 0.00 0.00 0.00 3.10
940 985 0.257616 CCTTCGTCTCTCCCCTCTCT 59.742 60.000 0.00 0.00 0.00 3.10
941 986 1.388547 CTTCGTCTCTCCCCTCTCTG 58.611 60.000 0.00 0.00 0.00 3.35
975 1024 1.066114 GAGAAACAGCTCCGTCGTCG 61.066 60.000 0.00 0.00 0.00 5.12
976 1025 1.371389 GAAACAGCTCCGTCGTCGT 60.371 57.895 0.71 0.00 35.01 4.34
977 1026 1.335697 GAAACAGCTCCGTCGTCGTC 61.336 60.000 0.71 0.00 35.01 4.20
1447 1505 7.557719 TGTGAGTTTTTCCATCTTCTTCTTCTT 59.442 33.333 0.00 0.00 0.00 2.52
1448 1506 8.073167 GTGAGTTTTTCCATCTTCTTCTTCTTC 58.927 37.037 0.00 0.00 0.00 2.87
1449 1507 7.995488 TGAGTTTTTCCATCTTCTTCTTCTTCT 59.005 33.333 0.00 0.00 0.00 2.85
1450 1508 8.759481 AGTTTTTCCATCTTCTTCTTCTTCTT 57.241 30.769 0.00 0.00 0.00 2.52
1451 1509 8.845227 AGTTTTTCCATCTTCTTCTTCTTCTTC 58.155 33.333 0.00 0.00 0.00 2.87
1452 1510 8.845227 GTTTTTCCATCTTCTTCTTCTTCTTCT 58.155 33.333 0.00 0.00 0.00 2.85
1453 1511 8.986929 TTTTCCATCTTCTTCTTCTTCTTCTT 57.013 30.769 0.00 0.00 0.00 2.52
1454 1512 8.614469 TTTCCATCTTCTTCTTCTTCTTCTTC 57.386 34.615 0.00 0.00 0.00 2.87
1455 1513 7.552050 TCCATCTTCTTCTTCTTCTTCTTCT 57.448 36.000 0.00 0.00 0.00 2.85
1456 1514 7.972301 TCCATCTTCTTCTTCTTCTTCTTCTT 58.028 34.615 0.00 0.00 0.00 2.52
1457 1515 8.093927 TCCATCTTCTTCTTCTTCTTCTTCTTC 58.906 37.037 0.00 0.00 0.00 2.87
1458 1516 8.096414 CCATCTTCTTCTTCTTCTTCTTCTTCT 58.904 37.037 0.00 0.00 0.00 2.85
1459 1517 9.492973 CATCTTCTTCTTCTTCTTCTTCTTCTT 57.507 33.333 0.00 0.00 0.00 2.52
1460 1518 9.710900 ATCTTCTTCTTCTTCTTCTTCTTCTTC 57.289 33.333 0.00 0.00 0.00 2.87
1539 1600 0.251634 CCTTTCCTCTCCCTGCACTC 59.748 60.000 0.00 0.00 0.00 3.51
1651 1713 2.435059 GCCTTCTCGCCACCTCAC 60.435 66.667 0.00 0.00 0.00 3.51
1658 1720 3.314331 CGCCACCTCACCCTGTCT 61.314 66.667 0.00 0.00 0.00 3.41
1778 1841 8.136165 ACTATTGTCTCCATACGTATCTGAAAC 58.864 37.037 4.74 3.35 0.00 2.78
1819 1882 8.082852 GGAACTATCTATTCATACGAGAGCAAA 58.917 37.037 0.00 0.00 0.00 3.68
1870 1933 2.217750 TGTGTCGTGGTCTGAAATTGG 58.782 47.619 0.00 0.00 0.00 3.16
1875 1938 0.244721 GTGGTCTGAAATTGGCAGCC 59.755 55.000 3.66 3.66 33.45 4.85
2207 2270 0.749049 TGAGGCTGATCATCTCGGTG 59.251 55.000 16.49 0.00 32.34 4.94
2208 2271 0.599728 GAGGCTGATCATCTCGGTGC 60.600 60.000 0.00 0.00 32.34 5.01
2209 2272 1.144716 GGCTGATCATCTCGGTGCA 59.855 57.895 0.00 0.00 32.34 4.57
2210 2273 1.156645 GGCTGATCATCTCGGTGCAC 61.157 60.000 8.80 8.80 32.34 4.57
2211 2274 0.179089 GCTGATCATCTCGGTGCACT 60.179 55.000 17.98 0.00 32.34 4.40
2212 2275 1.568606 CTGATCATCTCGGTGCACTG 58.431 55.000 20.12 20.12 0.00 3.66
2213 2276 1.135721 CTGATCATCTCGGTGCACTGA 59.864 52.381 26.32 26.32 0.00 3.41
2214 2277 1.758862 TGATCATCTCGGTGCACTGAT 59.241 47.619 28.01 21.47 0.00 2.90
2216 2279 3.384467 TGATCATCTCGGTGCACTGATTA 59.616 43.478 28.01 19.21 0.00 1.75
2217 2280 3.885724 TCATCTCGGTGCACTGATTAA 57.114 42.857 28.01 16.79 0.00 1.40
2218 2281 4.406648 TCATCTCGGTGCACTGATTAAT 57.593 40.909 28.01 18.16 0.00 1.40
2221 2284 4.944962 TCTCGGTGCACTGATTAATTTG 57.055 40.909 28.01 14.76 0.00 2.32
2222 2285 3.126858 TCTCGGTGCACTGATTAATTTGC 59.873 43.478 28.01 9.55 35.45 3.68
2231 2297 2.752354 CTGATTAATTTGCCGTGTCCCA 59.248 45.455 0.00 0.00 0.00 4.37
2240 2306 0.608035 GCCGTGTCCCAGGAAATTGA 60.608 55.000 0.00 0.00 0.00 2.57
2260 2326 2.941720 GAGCACCAGATCCACTCAATTC 59.058 50.000 0.00 0.00 0.00 2.17
2298 2364 7.682824 GTTCACTGATGTCATATGAACTTCTG 58.317 38.462 21.33 13.84 42.49 3.02
2380 2446 4.590647 TGGATGAGACCAGAGGATATTGAC 59.409 45.833 0.00 0.00 34.77 3.18
2383 2449 6.667414 GGATGAGACCAGAGGATATTGACTAT 59.333 42.308 0.00 0.00 0.00 2.12
2575 2641 1.211212 CCCAATGGCTCTGATCAGTCA 59.789 52.381 21.92 17.70 0.00 3.41
2576 2642 2.158652 CCCAATGGCTCTGATCAGTCAT 60.159 50.000 21.92 18.93 32.98 3.06
2683 2749 2.685017 ATCGCCACAGCTCCAGGA 60.685 61.111 0.00 0.00 36.60 3.86
2882 2948 8.037382 TGACAGCATCTAAATGAGAAGAAAAG 57.963 34.615 0.00 0.00 37.85 2.27
3133 3199 2.107378 TCACTAAAGGTTGGTGATGCCA 59.893 45.455 3.37 0.00 44.69 4.92
3169 3235 1.275291 TGCCTCTCTAAACCCACTTCG 59.725 52.381 0.00 0.00 0.00 3.79
3241 3307 2.124570 CATGGAGGGCCTCAACCG 60.125 66.667 33.27 14.88 34.31 4.44
3304 3370 1.863454 GCTGATTATCTGGACACTGCG 59.137 52.381 1.49 0.00 0.00 5.18
3465 3531 5.598005 TCAATTGACACTCAAAACCCTTCAT 59.402 36.000 3.38 0.00 40.12 2.57
3610 3676 1.534729 ACGGATGCAAAGGAGGTTTC 58.465 50.000 0.00 0.00 0.00 2.78
3652 3718 4.772886 AGCAAACCCTAATATCCTCGTT 57.227 40.909 0.00 0.00 0.00 3.85
4039 4105 7.147976 TGACGGATCAGTATAAATCATCTGTG 58.852 38.462 0.00 0.00 33.99 3.66
4085 4151 7.489435 TGTGCGATTTGTGAAACTAATTTTTGA 59.511 29.630 0.00 0.00 42.17 2.69
4099 4166 7.489160 ACTAATTTTTGAGGTCCTTGTTGTTC 58.511 34.615 0.00 0.00 0.00 3.18
4101 4168 5.993748 TTTTTGAGGTCCTTGTTGTTCTT 57.006 34.783 0.00 0.00 0.00 2.52
4104 4171 4.229304 TGAGGTCCTTGTTGTTCTTCAA 57.771 40.909 0.00 0.00 0.00 2.69
4110 4177 5.163457 GGTCCTTGTTGTTCTTCAAATTCCA 60.163 40.000 0.00 0.00 37.81 3.53
4117 4184 6.811170 TGTTGTTCTTCAAATTCCAAGTTCAC 59.189 34.615 0.00 0.00 37.81 3.18
4158 4225 6.869913 TGTAGAAATGGTACCTTTGTAAGTCG 59.130 38.462 14.36 0.00 0.00 4.18
4214 4281 8.103305 ACAGTAAAGAATGTGTGACCTTCATAT 58.897 33.333 0.00 0.00 0.00 1.78
4272 4339 1.921887 CATGCGCATGTTCACCAAATC 59.078 47.619 36.45 0.00 34.23 2.17
4273 4340 1.246649 TGCGCATGTTCACCAAATCT 58.753 45.000 5.66 0.00 0.00 2.40
4295 4363 8.902540 ATCTCAAACATTATATAGCAACGGAA 57.097 30.769 0.00 0.00 0.00 4.30
4319 4389 9.530633 GAAAATACCGACTTCTAACATATCTGT 57.469 33.333 0.00 0.00 37.12 3.41
4346 4416 3.754323 ACATTGATGCCATTGCCAAAAAG 59.246 39.130 0.00 0.00 36.33 2.27
4392 4462 5.931146 TGCACAGAAAACACAAAATTTCACT 59.069 32.000 0.00 0.00 37.87 3.41
4395 4465 8.439286 GCACAGAAAACACAAAATTTCACTAAA 58.561 29.630 0.00 0.00 37.87 1.85
4419 4490 5.453567 AATTTCTGCAACTCTGGTAAACC 57.546 39.130 0.00 0.00 0.00 3.27
4437 4508 0.249120 CCGAACATGTGTAGGCCTGA 59.751 55.000 17.99 0.00 0.00 3.86
4444 4515 1.550327 TGTGTAGGCCTGAGTGAGAG 58.450 55.000 17.99 0.00 0.00 3.20
4618 4689 3.181487 ACAGCAATTATTCCCGCATCAAC 60.181 43.478 0.00 0.00 0.00 3.18
4727 4799 1.047801 GGTGGTGTTTTGGGCTTCAT 58.952 50.000 0.00 0.00 0.00 2.57
4741 4813 5.266788 TGGGCTTCATTCTCATTTTCATCT 58.733 37.500 0.00 0.00 0.00 2.90
4744 4816 6.769822 GGGCTTCATTCTCATTTTCATCTAGA 59.230 38.462 0.00 0.00 0.00 2.43
4755 4827 7.062957 TCATTTTCATCTAGAGATTTTCCCCC 58.937 38.462 0.00 0.00 31.21 5.40
4881 4953 4.386088 CCCCTTGGACATCTCAATCAAGAT 60.386 45.833 0.00 0.00 37.57 2.40
4931 5003 3.181505 TGTGTTAAGTTTGCACAACCTCG 60.182 43.478 8.98 0.00 39.76 4.63
4951 5023 6.098679 CCTCGATGTTGATCCTGATTATCTC 58.901 44.000 0.00 0.00 0.00 2.75
4987 5059 2.779755 TGGGTTTCATACGCATGACT 57.220 45.000 0.00 0.00 43.90 3.41
5011 5083 2.232208 CTGAAACCTTTCCTTGATGCCC 59.768 50.000 0.00 0.00 36.36 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 92 2.480419 ACCACGTACGTGTAGTGTAGAC 59.520 50.000 37.86 0.00 44.02 2.59
93 98 2.031157 GGTACAACCACGTACGTGTAGT 60.031 50.000 37.86 32.42 44.02 2.73
97 107 2.138596 AAGGTACAACCACGTACGTG 57.861 50.000 35.57 35.57 41.95 4.49
196 206 9.330220 GGGGAATGGATAATAGTTTAGGTACTA 57.670 37.037 0.00 0.00 41.75 1.82
197 207 7.797617 TGGGGAATGGATAATAGTTTAGGTACT 59.202 37.037 0.00 0.00 46.37 2.73
198 208 7.981142 TGGGGAATGGATAATAGTTTAGGTAC 58.019 38.462 0.00 0.00 0.00 3.34
199 209 8.020253 TCTGGGGAATGGATAATAGTTTAGGTA 58.980 37.037 0.00 0.00 0.00 3.08
200 210 6.855061 TCTGGGGAATGGATAATAGTTTAGGT 59.145 38.462 0.00 0.00 0.00 3.08
203 217 7.570982 TGACTCTGGGGAATGGATAATAGTTTA 59.429 37.037 0.00 0.00 0.00 2.01
221 237 3.407424 TTCCATTCTGTGTGACTCTGG 57.593 47.619 0.00 0.00 0.00 3.86
292 314 3.585990 CCATGCGATTCGGGTGCC 61.586 66.667 8.34 0.00 0.00 5.01
391 413 2.838202 ACAGTTGGCCTAGCTAGCTAAA 59.162 45.455 24.20 13.38 32.14 1.85
392 414 2.431057 GACAGTTGGCCTAGCTAGCTAA 59.569 50.000 24.20 9.27 28.95 3.09
393 415 2.032620 GACAGTTGGCCTAGCTAGCTA 58.967 52.381 22.85 22.85 28.95 3.32
394 416 0.827368 GACAGTTGGCCTAGCTAGCT 59.173 55.000 23.12 23.12 30.11 3.32
395 417 0.528684 CGACAGTTGGCCTAGCTAGC 60.529 60.000 15.74 6.62 0.00 3.42
405 434 1.856265 GCAAAGAGGGCGACAGTTGG 61.856 60.000 0.00 0.00 0.00 3.77
406 435 1.165907 TGCAAAGAGGGCGACAGTTG 61.166 55.000 0.00 0.00 0.00 3.16
466 495 1.208358 CTCGAACTGCGTCCACGTA 59.792 57.895 0.36 0.00 42.22 3.57
467 496 2.050351 CTCGAACTGCGTCCACGT 60.050 61.111 0.36 0.00 42.22 4.49
468 497 1.337817 CTTCTCGAACTGCGTCCACG 61.338 60.000 0.00 0.00 41.80 4.94
519 548 0.608640 GATCGCTAACCATCCGGGAT 59.391 55.000 2.97 2.97 41.15 3.85
520 549 1.469335 GGATCGCTAACCATCCGGGA 61.469 60.000 0.00 0.00 41.15 5.14
524 553 1.048601 TCTGGGATCGCTAACCATCC 58.951 55.000 11.46 0.00 38.34 3.51
530 559 2.558795 GCAGTAGATCTGGGATCGCTAA 59.441 50.000 11.46 0.00 43.78 3.09
579 608 2.983907 TTTGTTACTGTCCGTGTCCA 57.016 45.000 0.00 0.00 0.00 4.02
580 609 3.058501 CCATTTTGTTACTGTCCGTGTCC 60.059 47.826 0.00 0.00 0.00 4.02
581 610 3.608474 GCCATTTTGTTACTGTCCGTGTC 60.608 47.826 0.00 0.00 0.00 3.67
582 611 2.292292 GCCATTTTGTTACTGTCCGTGT 59.708 45.455 0.00 0.00 0.00 4.49
583 612 2.664424 CGCCATTTTGTTACTGTCCGTG 60.664 50.000 0.00 0.00 0.00 4.94
584 613 1.533731 CGCCATTTTGTTACTGTCCGT 59.466 47.619 0.00 0.00 0.00 4.69
614 648 4.906792 CTCCCGCTAGCAGCAGCC 62.907 72.222 16.45 0.00 42.58 4.85
645 679 1.112950 GCCTCTGTAGTCTGTACCCC 58.887 60.000 0.00 0.00 0.00 4.95
689 723 0.670546 CTTACAGTGGAGGCCGTGTG 60.671 60.000 0.00 0.00 0.00 3.82
690 724 1.671742 CTTACAGTGGAGGCCGTGT 59.328 57.895 0.00 0.00 0.00 4.49
733 771 2.731691 CTATCGGGGATGGGTTGGCG 62.732 65.000 0.00 0.00 0.00 5.69
824 866 2.489938 TGAAATGAAACGGAGGGAGG 57.510 50.000 0.00 0.00 0.00 4.30
839 881 3.247411 CACGGCGCTATGTTATGATGAAA 59.753 43.478 6.90 0.00 0.00 2.69
922 967 1.388547 CAGAGAGGGGAGAGACGAAG 58.611 60.000 0.00 0.00 0.00 3.79
923 968 0.681564 GCAGAGAGGGGAGAGACGAA 60.682 60.000 0.00 0.00 0.00 3.85
924 969 1.077357 GCAGAGAGGGGAGAGACGA 60.077 63.158 0.00 0.00 0.00 4.20
925 970 2.124693 GGCAGAGAGGGGAGAGACG 61.125 68.421 0.00 0.00 0.00 4.18
931 976 2.607750 GTGTGGGCAGAGAGGGGA 60.608 66.667 0.00 0.00 0.00 4.81
940 985 0.770499 TCTCAATTGGAGTGTGGGCA 59.230 50.000 5.42 0.00 44.40 5.36
941 986 1.909700 TTCTCAATTGGAGTGTGGGC 58.090 50.000 5.42 0.00 44.40 5.36
1396 1445 0.804989 GGGCGTTGAAGAACATGAGG 59.195 55.000 0.00 0.00 31.78 3.86
1651 1713 4.487714 TGCTAAATGTAGGAAGACAGGG 57.512 45.455 0.00 0.00 31.51 4.45
1658 1720 4.473196 TCCCAGACATGCTAAATGTAGGAA 59.527 41.667 9.71 0.00 30.64 3.36
1819 1882 0.314935 CACAAGGTGCGCTCCATTTT 59.685 50.000 28.68 12.91 0.00 1.82
2178 2241 0.976641 ATCAGCCTCAACGAACCTGA 59.023 50.000 0.00 0.00 37.01 3.86
2207 2270 3.171277 GACACGGCAAATTAATCAGTGC 58.829 45.455 9.23 9.23 36.24 4.40
2208 2271 3.427503 GGGACACGGCAAATTAATCAGTG 60.428 47.826 4.95 4.95 0.00 3.66
2209 2272 2.752903 GGGACACGGCAAATTAATCAGT 59.247 45.455 0.00 0.00 0.00 3.41
2210 2273 2.752354 TGGGACACGGCAAATTAATCAG 59.248 45.455 0.00 0.00 0.00 2.90
2211 2274 2.752354 CTGGGACACGGCAAATTAATCA 59.248 45.455 0.00 0.00 0.00 2.57
2212 2275 2.099098 CCTGGGACACGGCAAATTAATC 59.901 50.000 0.00 0.00 0.00 1.75
2213 2276 2.099405 CCTGGGACACGGCAAATTAAT 58.901 47.619 0.00 0.00 0.00 1.40
2214 2277 1.074084 TCCTGGGACACGGCAAATTAA 59.926 47.619 0.00 0.00 0.00 1.40
2216 2279 0.178975 TTCCTGGGACACGGCAAATT 60.179 50.000 0.00 0.00 0.00 1.82
2217 2280 0.178975 TTTCCTGGGACACGGCAAAT 60.179 50.000 0.00 0.00 0.00 2.32
2218 2281 0.178975 ATTTCCTGGGACACGGCAAA 60.179 50.000 0.00 0.00 0.00 3.68
2221 2284 0.608035 TCAATTTCCTGGGACACGGC 60.608 55.000 0.00 0.00 0.00 5.68
2222 2285 1.453155 CTCAATTTCCTGGGACACGG 58.547 55.000 0.00 0.00 0.00 4.94
2231 2297 2.309755 TGGATCTGGTGCTCAATTTCCT 59.690 45.455 0.00 0.00 0.00 3.36
2240 2306 2.306805 TGAATTGAGTGGATCTGGTGCT 59.693 45.455 0.00 0.00 0.00 4.40
2317 2383 1.221021 GGGGCCTTTAGAGGTGTCG 59.779 63.158 0.84 0.00 45.44 4.35
2374 2440 6.071896 CGATGACAGGCCTCTTATAGTCAATA 60.072 42.308 21.24 3.21 39.17 1.90
2380 2446 3.823873 ACTCGATGACAGGCCTCTTATAG 59.176 47.826 0.00 0.00 0.00 1.31
2383 2449 1.751351 CACTCGATGACAGGCCTCTTA 59.249 52.381 0.00 0.00 0.00 2.10
2452 2518 2.673368 GTCCTTGAACACTATGGAAGCG 59.327 50.000 0.00 0.00 0.00 4.68
2576 2642 4.098914 AGCTGGTGGAATTGTAGAACAA 57.901 40.909 0.00 0.00 42.95 2.83
2683 2749 2.652530 CCTGCGTGCTTTGCCATT 59.347 55.556 0.00 0.00 0.00 3.16
2823 2889 8.861086 TGTTTGTTATTCCTTTGGTGCTAAATA 58.139 29.630 0.00 0.00 0.00 1.40
2882 2948 8.880878 TCCTTTTAAAGCACTTTTAATGTTCC 57.119 30.769 0.20 0.00 40.08 3.62
2893 2959 9.466497 TGATATTCTGATTCCTTTTAAAGCACT 57.534 29.630 0.00 0.00 0.00 4.40
2894 2960 9.727627 CTGATATTCTGATTCCTTTTAAAGCAC 57.272 33.333 0.00 0.00 0.00 4.40
2926 2992 9.227777 CATTCTTCATTAGCATTGATCATCCTA 57.772 33.333 0.00 0.00 0.00 2.94
2928 2994 8.107399 TCATTCTTCATTAGCATTGATCATCC 57.893 34.615 0.00 0.00 0.00 3.51
3133 3199 3.893813 AGAGGCAGTGAAAAGCAAAGAAT 59.106 39.130 0.00 0.00 0.00 2.40
3141 3207 3.753797 GGGTTTAGAGAGGCAGTGAAAAG 59.246 47.826 0.00 0.00 0.00 2.27
3169 3235 5.291971 TCGGTTACTTAACTTTCCAGTGTC 58.708 41.667 0.00 0.00 36.47 3.67
3241 3307 1.059264 GCATTGACGACGTACTGAAGC 59.941 52.381 0.00 0.00 0.00 3.86
3413 3479 7.387673 TGATGCCTGCTAACATACATTATACAC 59.612 37.037 0.00 0.00 0.00 2.90
3425 3491 2.857186 TTGACTGATGCCTGCTAACA 57.143 45.000 0.00 0.00 0.00 2.41
3465 3531 6.625740 GCCTAGAATGTAATCAAGCTGCAAAA 60.626 38.462 1.02 0.00 0.00 2.44
3610 3676 6.169094 TGCTTTCTTAGACTCTCTCCATTTG 58.831 40.000 0.00 0.00 0.00 2.32
3694 3760 7.589954 GTGTAATTGTAATTTGTGCGGATATCC 59.410 37.037 12.14 12.14 0.00 2.59
3859 3925 2.173519 CATGGTTTCCAAGCTGATGGT 58.826 47.619 4.36 0.00 41.46 3.55
4064 4130 8.978539 GGACCTCAAAAATTAGTTTCACAAATC 58.021 33.333 0.00 0.00 0.00 2.17
4085 4151 5.069119 GGAATTTGAAGAACAACAAGGACCT 59.931 40.000 0.00 0.00 38.29 3.85
4099 4166 4.734854 CACACGTGAACTTGGAATTTGAAG 59.265 41.667 25.01 0.00 0.00 3.02
4101 4168 3.942115 TCACACGTGAACTTGGAATTTGA 59.058 39.130 25.01 7.79 36.53 2.69
4104 4171 3.945285 ACTTCACACGTGAACTTGGAATT 59.055 39.130 25.01 7.11 43.90 2.17
4110 4177 5.622770 AAAAGAACTTCACACGTGAACTT 57.377 34.783 25.01 12.40 43.90 2.66
4117 4184 7.165812 CCATTTCTACAAAAAGAACTTCACACG 59.834 37.037 0.00 0.00 35.25 4.49
4233 4300 5.402568 CGCATGAAGTGTATAGTGTATGTCC 59.597 44.000 0.00 0.00 0.00 4.02
4272 4339 9.950680 ATTTTCCGTTGCTATATAATGTTTGAG 57.049 29.630 0.00 0.00 0.00 3.02
4299 4367 9.962783 GTTATTACAGATATGTTAGAAGTCGGT 57.037 33.333 0.00 0.00 0.00 4.69
4315 4385 6.461370 GGCAATGGCATCAATGTTATTACAGA 60.461 38.462 0.00 0.00 43.71 3.41
4316 4386 5.693104 GGCAATGGCATCAATGTTATTACAG 59.307 40.000 0.00 0.00 43.71 2.74
4319 4389 5.866159 TGGCAATGGCATCAATGTTATTA 57.134 34.783 5.05 0.00 43.71 0.98
4323 4393 3.420300 TTTGGCAATGGCATCAATGTT 57.580 38.095 11.08 0.00 43.71 2.71
4324 4394 3.420300 TTTTGGCAATGGCATCAATGT 57.580 38.095 11.08 0.00 43.71 2.71
4327 4397 3.488778 ACTTTTTGGCAATGGCATCAA 57.511 38.095 11.08 4.04 43.71 2.57
4395 4465 6.280643 GGTTTACCAGAGTTGCAGAAATTTT 58.719 36.000 0.00 0.00 35.64 1.82
4398 4468 3.502211 CGGTTTACCAGAGTTGCAGAAAT 59.498 43.478 0.00 0.00 35.14 2.17
4401 4471 1.689813 TCGGTTTACCAGAGTTGCAGA 59.310 47.619 0.00 0.00 35.14 4.26
4408 4479 3.399330 ACACATGTTCGGTTTACCAGAG 58.601 45.455 0.00 0.00 35.14 3.35
4419 4490 1.066858 ACTCAGGCCTACACATGTTCG 60.067 52.381 3.98 0.00 0.00 3.95
4483 4554 9.734620 CATGACCATCATAAATTTGTATTTCGT 57.265 29.630 0.00 0.00 34.28 3.85
4727 4799 9.401058 GGGAAAATCTCTAGATGAAAATGAGAA 57.599 33.333 0.00 0.00 37.34 2.87
4755 4827 5.459536 TTTGAGAGTAGATGATGATCCCG 57.540 43.478 0.00 0.00 0.00 5.14
4931 5003 6.364706 GTGACGAGATAATCAGGATCAACATC 59.635 42.308 0.00 0.00 0.00 3.06
4951 5023 0.930310 CCATAATGCGACCAGTGACG 59.070 55.000 0.00 0.00 0.00 4.35
4987 5059 3.243839 GCATCAAGGAAAGGTTTCAGCAA 60.244 43.478 4.89 0.00 38.92 3.91


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

AutoCloner maintained by Alex Coulton.