Multiple sequence alignment - TraesCS6B01G331400

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 TraesCS6B01G331400 chr6B 100.000 4185 0 0 1 4185 582821876 582826060 0.000000e+00 7729.0
1 TraesCS6B01G331400 chr6A 93.562 3355 144 24 853 4185 535974664 535977968 0.000000e+00 4933.0
2 TraesCS6B01G331400 chr6A 88.190 779 64 16 1 772 535973874 535974631 0.000000e+00 904.0
3 TraesCS6B01G331400 chr6D 91.398 1709 89 22 2488 4185 389582946 389584607 0.000000e+00 2289.0
4 TraesCS6B01G331400 chr6D 95.180 1224 45 3 873 2082 389581021 389582244 0.000000e+00 1921.0
5 TraesCS6B01G331400 chr6D 88.175 778 55 22 1 772 389580031 389580777 0.000000e+00 893.0
6 TraesCS6B01G331400 chr6D 89.355 310 23 7 2168 2471 389582278 389582583 8.490000e-102 381.0
7 TraesCS6B01G331400 chr5A 86.869 495 49 6 1 491 73402884 73403366 1.320000e-149 540.0
8 TraesCS6B01G331400 chr4A 88.352 455 41 5 320 772 613119421 613119865 1.710000e-148 536.0
9 TraesCS6B01G331400 chr2D 100.000 30 0 0 3658 3687 80684607 80684636 5.840000e-04 56.5
10 TraesCS6B01G331400 chr2B 100.000 30 0 0 3658 3687 132331124 132331153 5.840000e-04 56.5


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 TraesCS6B01G331400 chr6B 582821876 582826060 4184 False 7729.0 7729 100.000 1 4185 1 chr6B.!!$F1 4184
1 TraesCS6B01G331400 chr6A 535973874 535977968 4094 False 2918.5 4933 90.876 1 4185 2 chr6A.!!$F1 4184
2 TraesCS6B01G331400 chr6D 389580031 389584607 4576 False 1371.0 2289 91.027 1 4185 4 chr6D.!!$F1 4184

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
172 177 0.178068 AGGTGACACGACAGCAACTT 59.822 50.000 0.00 0.0 40.20 2.66 F
768 782 0.321021 TGTCATTGCAAATGGGGTGC 59.679 50.000 1.71 0.0 42.55 5.01 F
1143 1348 0.165079 GTTGTGCGTGGATACCGTTG 59.835 55.000 0.00 0.0 33.54 4.10 F
2091 2301 1.069906 GCTGAACTGTGTTGGTTAGCG 60.070 52.381 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1124 1329 0.165079 CAACGGTATCCACGCACAAC 59.835 55.000 0.0 0.0 34.00 3.32 R
2276 2496 1.072806 TGGAGCACATCATCCCTATGC 59.927 52.381 0.0 0.0 34.47 3.14 R
2988 3556 0.610687 CGCAGTTTCTCCCCTCTTCT 59.389 55.000 0.0 0.0 0.00 2.85 R
3538 4106 1.135083 AGTCCGGTCAATGCGAAGTAG 60.135 52.381 0.0 0.0 0.00 2.57 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 4.563184 CCTTGCTAGCTACTCGTAGTTTTG 59.437 45.833 17.23 0.00 35.65 2.44
66 67 4.778534 TGCTAGCTACTCGTAGTTTTGT 57.221 40.909 17.23 0.00 35.65 2.83
94 98 2.440409 CAGTGGGAATTTGGGAGTCTG 58.560 52.381 0.00 0.00 0.00 3.51
107 112 1.623811 GGAGTCTGGTTTGCTACTGGA 59.376 52.381 0.00 0.00 0.00 3.86
145 150 4.039973 CCTGCGGGATAACTAACTGGATAA 59.960 45.833 5.28 0.00 33.58 1.75
168 173 1.253100 TCATAGGTGACACGACAGCA 58.747 50.000 0.00 0.00 40.20 4.41
169 174 1.616374 TCATAGGTGACACGACAGCAA 59.384 47.619 0.00 0.00 40.20 3.91
171 176 1.037493 TAGGTGACACGACAGCAACT 58.963 50.000 0.00 0.00 40.20 3.16
172 177 0.178068 AGGTGACACGACAGCAACTT 59.822 50.000 0.00 0.00 40.20 2.66
175 180 1.663643 GTGACACGACAGCAACTTCAA 59.336 47.619 0.00 0.00 0.00 2.69
176 181 1.933181 TGACACGACAGCAACTTCAAG 59.067 47.619 0.00 0.00 0.00 3.02
178 183 2.802816 GACACGACAGCAACTTCAAGAT 59.197 45.455 0.00 0.00 0.00 2.40
179 184 2.802816 ACACGACAGCAACTTCAAGATC 59.197 45.455 0.00 0.00 0.00 2.75
180 185 3.062763 CACGACAGCAACTTCAAGATCT 58.937 45.455 0.00 0.00 0.00 2.75
181 186 3.122613 CACGACAGCAACTTCAAGATCTC 59.877 47.826 0.00 0.00 0.00 2.75
182 187 2.670414 CGACAGCAACTTCAAGATCTCC 59.330 50.000 0.00 0.00 0.00 3.71
183 188 3.616076 CGACAGCAACTTCAAGATCTCCT 60.616 47.826 0.00 0.00 0.00 3.69
184 189 4.380973 CGACAGCAACTTCAAGATCTCCTA 60.381 45.833 0.00 0.00 0.00 2.94
185 190 5.083533 ACAGCAACTTCAAGATCTCCTAG 57.916 43.478 0.00 0.00 0.00 3.02
186 191 4.530161 ACAGCAACTTCAAGATCTCCTAGT 59.470 41.667 0.00 0.00 0.00 2.57
228 238 9.874205 CATTGTATCCTTGTCCATTATGTTTTT 57.126 29.630 0.00 0.00 0.00 1.94
230 240 8.877864 TGTATCCTTGTCCATTATGTTTTTCT 57.122 30.769 0.00 0.00 0.00 2.52
231 241 8.739039 TGTATCCTTGTCCATTATGTTTTTCTG 58.261 33.333 0.00 0.00 0.00 3.02
232 242 7.781324 ATCCTTGTCCATTATGTTTTTCTGT 57.219 32.000 0.00 0.00 0.00 3.41
233 243 8.877864 ATCCTTGTCCATTATGTTTTTCTGTA 57.122 30.769 0.00 0.00 0.00 2.74
234 244 8.877864 TCCTTGTCCATTATGTTTTTCTGTAT 57.122 30.769 0.00 0.00 0.00 2.29
235 245 9.308000 TCCTTGTCCATTATGTTTTTCTGTATT 57.692 29.630 0.00 0.00 0.00 1.89
236 246 9.573133 CCTTGTCCATTATGTTTTTCTGTATTC 57.427 33.333 0.00 0.00 0.00 1.75
264 274 1.668419 CTTGGTCATCGGGTTGGATC 58.332 55.000 0.00 0.00 0.00 3.36
266 276 0.541392 TGGTCATCGGGTTGGATCAG 59.459 55.000 0.00 0.00 0.00 2.90
281 291 3.265791 GGATCAGCACACAAGTAGAAGG 58.734 50.000 0.00 0.00 0.00 3.46
294 304 4.974368 AGTAGAAGGTGAAGACGATCTG 57.026 45.455 0.00 0.00 0.00 2.90
304 314 5.336213 GGTGAAGACGATCTGTGTAGGTTTA 60.336 44.000 0.00 0.00 0.00 2.01
306 316 6.812160 GTGAAGACGATCTGTGTAGGTTTAAT 59.188 38.462 0.00 0.00 0.00 1.40
307 317 7.331193 GTGAAGACGATCTGTGTAGGTTTAATT 59.669 37.037 0.00 0.00 0.00 1.40
310 321 8.873215 AGACGATCTGTGTAGGTTTAATTATG 57.127 34.615 0.00 0.00 0.00 1.90
414 425 8.429641 TCATTCTTTCAGTTACTGGTCTACTTT 58.570 33.333 12.79 0.00 31.51 2.66
431 442 7.275123 GGTCTACTTTTACAGACTATTGAACCG 59.725 40.741 2.13 0.00 40.83 4.44
483 494 3.060873 GCGTCGATGAACTCTTATGCTTC 60.061 47.826 9.31 0.00 0.00 3.86
519 532 5.707066 ACAGAATGCTCTATTTCCCTCTT 57.293 39.130 0.00 0.00 42.53 2.85
546 559 4.993705 TTCACTTCACCCAATCCTTACT 57.006 40.909 0.00 0.00 0.00 2.24
552 565 5.104485 ACTTCACCCAATCCTTACTACCATC 60.104 44.000 0.00 0.00 0.00 3.51
563 576 7.496346 TCCTTACTACCATCTTCTCAATTGT 57.504 36.000 5.13 0.00 0.00 2.71
568 581 6.299141 ACTACCATCTTCTCAATTGTTGTGT 58.701 36.000 5.13 0.00 0.00 3.72
592 605 4.319177 AGGCACACTCAAGAATACAAGAC 58.681 43.478 0.00 0.00 0.00 3.01
635 648 6.220201 CCTCCATAAGTTTCTTAGCTAGCTC 58.780 44.000 23.26 5.53 0.00 4.09
638 651 7.067421 TCCATAAGTTTCTTAGCTAGCTCCTA 58.933 38.462 23.26 7.23 0.00 2.94
651 664 5.721000 AGCTAGCTCCTAAATATCATCTGCT 59.279 40.000 12.68 0.00 0.00 4.24
682 695 5.303078 ACCAGCGAGATTAGACTGTATGAAT 59.697 40.000 0.00 0.00 0.00 2.57
684 697 6.364706 CCAGCGAGATTAGACTGTATGAATTC 59.635 42.308 0.00 0.00 0.00 2.17
685 698 6.920210 CAGCGAGATTAGACTGTATGAATTCA 59.080 38.462 11.26 11.26 0.00 2.57
686 699 7.598118 CAGCGAGATTAGACTGTATGAATTCAT 59.402 37.037 23.75 23.75 40.22 2.57
687 700 8.147058 AGCGAGATTAGACTGTATGAATTCATT 58.853 33.333 25.26 8.14 37.76 2.57
688 701 8.219769 GCGAGATTAGACTGTATGAATTCATTG 58.780 37.037 25.26 17.23 37.76 2.82
689 702 9.468532 CGAGATTAGACTGTATGAATTCATTGA 57.531 33.333 25.26 11.72 37.76 2.57
736 750 4.849235 TGAGTGGTGGGGAATATATATGCA 59.151 41.667 3.03 0.00 0.00 3.96
739 753 5.253798 AGTGGTGGGGAATATATATGCATGT 59.746 40.000 10.16 5.06 0.00 3.21
740 754 5.951747 GTGGTGGGGAATATATATGCATGTT 59.048 40.000 10.16 0.00 0.00 2.71
764 778 3.992643 TGAGTTTGTCATTGCAAATGGG 58.007 40.909 1.71 0.00 40.01 4.00
765 779 3.244146 TGAGTTTGTCATTGCAAATGGGG 60.244 43.478 1.71 0.00 40.01 4.96
766 780 2.705127 AGTTTGTCATTGCAAATGGGGT 59.295 40.909 1.71 0.00 40.01 4.95
767 781 2.807392 GTTTGTCATTGCAAATGGGGTG 59.193 45.455 1.71 0.00 40.01 4.61
768 782 0.321021 TGTCATTGCAAATGGGGTGC 59.679 50.000 1.71 0.00 42.55 5.01
777 791 4.319139 GCAAATGGGGTGCAAAATTTTT 57.681 36.364 0.00 0.00 41.80 1.94
892 1079 8.812513 TTTTGTTTCATCATACCATCTCTCAT 57.187 30.769 0.00 0.00 0.00 2.90
958 1145 6.846325 ACTCAGTTTACAGTTCTTACAAGC 57.154 37.500 0.00 0.00 0.00 4.01
988 1175 9.967451 TTGTGTTGTTTTATGATAGGGAATAGA 57.033 29.630 0.00 0.00 0.00 1.98
1014 1201 4.036518 ACAGAATTATGAGCTCAGGGAGT 58.963 43.478 22.96 9.37 31.39 3.85
1080 1267 0.617413 AGCTGTCCAAGGTGATCCAG 59.383 55.000 0.00 0.00 34.56 3.86
1099 1304 7.933577 TGATCCAGTATCACCTATTTTGCTTAG 59.066 37.037 0.00 0.00 39.77 2.18
1124 1329 6.757897 TGCAACTCATTATTCTTTACCCTG 57.242 37.500 0.00 0.00 0.00 4.45
1132 1337 2.335316 TTCTTTACCCTGTTGTGCGT 57.665 45.000 0.00 0.00 0.00 5.24
1139 1344 1.024579 CCCTGTTGTGCGTGGATACC 61.025 60.000 0.00 0.00 0.00 2.73
1143 1348 0.165079 GTTGTGCGTGGATACCGTTG 59.835 55.000 0.00 0.00 33.54 4.10
1147 1352 1.136169 GTGCGTGGATACCGTTGTTTC 60.136 52.381 0.00 0.00 33.54 2.78
1158 1363 8.479689 TGGATACCGTTGTTTCTATTTCTCATA 58.520 33.333 0.00 0.00 0.00 2.15
1253 1458 2.516906 TGCTCAGATGGTTCAATTGCA 58.483 42.857 0.00 0.00 0.00 4.08
1271 1476 2.837591 TGCAAGGTACCTGATAGCAAGA 59.162 45.455 17.14 0.00 33.40 3.02
1306 1511 4.017126 AGGAAGGCTACCAAAATGCTTAC 58.983 43.478 0.00 0.00 0.00 2.34
1307 1512 3.761752 GGAAGGCTACCAAAATGCTTACA 59.238 43.478 0.00 0.00 0.00 2.41
1328 1533 4.119136 CAAAAACCTTGAAATGGCGTTCT 58.881 39.130 0.00 0.00 33.71 3.01
1580 1788 5.899299 TCGTGATATAGGACGAGATATCGA 58.101 41.667 17.95 0.00 39.59 3.59
1741 1949 6.032775 GCACATTAGATTGTGTCATTTTGTCG 59.967 38.462 6.46 0.00 46.93 4.35
1795 2003 1.283321 AGAAGTCCAAAGGGCAGATCC 59.717 52.381 0.00 0.00 0.00 3.36
2091 2301 1.069906 GCTGAACTGTGTTGGTTAGCG 60.070 52.381 0.00 0.00 0.00 4.26
2102 2312 3.128242 TGTTGGTTAGCGAAACGGAAAAA 59.872 39.130 0.00 0.00 39.13 1.94
2110 2320 3.810941 AGCGAAACGGAAAAATACACAGA 59.189 39.130 0.00 0.00 0.00 3.41
2276 2496 5.063944 ACATGCAGCGTTACTTAATCAGAAG 59.936 40.000 0.00 0.00 0.00 2.85
2292 2512 2.812591 CAGAAGCATAGGGATGATGTGC 59.187 50.000 0.00 0.00 34.73 4.57
2330 2550 6.385467 ACCTAAGCATATCTTTGTTCTCCTCT 59.615 38.462 0.00 0.00 36.25 3.69
2473 2694 9.653287 TTTCTGTCAATGAGTAACAGTTATAGG 57.347 33.333 0.00 0.00 40.94 2.57
2742 3310 3.802862 ATGCTGCAAGGATGAGAGG 57.197 52.632 6.36 0.00 46.20 3.69
2785 3353 1.684049 CTGGAGCCCCGAGAACTCT 60.684 63.158 0.41 0.00 34.29 3.24
2786 3354 1.229209 TGGAGCCCCGAGAACTCTT 60.229 57.895 0.41 0.00 34.29 2.85
2864 3432 4.311606 GGGTTTGAAGACTGAAGAGACTC 58.688 47.826 0.00 0.00 0.00 3.36
2986 3554 3.020984 GGAAGAGACCGAGACTTCATCT 58.979 50.000 0.00 0.00 40.89 2.90
2988 3556 3.358111 AGAGACCGAGACTTCATCTGA 57.642 47.619 0.00 0.00 38.00 3.27
3003 3571 3.772025 TCATCTGAGAAGAGGGGAGAAAC 59.228 47.826 0.00 0.00 0.00 2.78
3036 3604 4.642429 TCTGTAAAGGAGGAAGAAACTGC 58.358 43.478 0.00 0.00 0.00 4.40
3040 3608 1.343069 AGGAGGAAGAAACTGCGACT 58.657 50.000 0.00 0.00 0.00 4.18
3055 3623 4.034510 ACTGCGACTGTTTCTGAAAAGAAG 59.965 41.667 4.09 5.91 0.00 2.85
3057 3625 3.304057 GCGACTGTTTCTGAAAAGAAGGG 60.304 47.826 4.09 2.26 0.00 3.95
3163 3731 4.180496 GCATCAGCAGGCAAAAGC 57.820 55.556 0.00 0.00 41.58 3.51
3214 3782 4.033358 CAGCACGAGAAGTACATTCCAATC 59.967 45.833 0.00 0.00 38.84 2.67
3253 3821 2.892852 CACAGTGAATTCCCACCAACAT 59.107 45.455 2.27 0.00 37.76 2.71
3326 3894 3.682858 TGCCTGACTTATTTTGTAGTCGC 59.317 43.478 0.00 0.00 42.88 5.19
3478 4046 5.615289 TGCTATATCCTGCTCTCCTTTTTC 58.385 41.667 0.00 0.00 0.00 2.29
3495 4063 9.109393 CTCCTTTTTCGGTAAATCTGAATATCA 57.891 33.333 0.00 0.00 40.58 2.15
3597 4165 8.974060 TCAACCTTTGACTGAAAAATACTACT 57.026 30.769 0.00 0.00 34.08 2.57
3598 4166 9.403583 TCAACCTTTGACTGAAAAATACTACTT 57.596 29.630 0.00 0.00 34.08 2.24
3743 4314 4.686091 GCTAGGCATGAAAGTTGAAAAACC 59.314 41.667 0.00 0.00 0.00 3.27
3753 4324 1.070134 GTTGAAAAACCTTCAGCCCCC 59.930 52.381 0.00 0.00 0.00 5.40
3782 4355 7.615757 TCTCACTAGACATTTCTGATCCTTGTA 59.384 37.037 0.00 0.00 32.75 2.41
3783 4356 8.134202 TCACTAGACATTTCTGATCCTTGTAA 57.866 34.615 0.00 0.00 32.75 2.41
3784 4357 8.035394 TCACTAGACATTTCTGATCCTTGTAAC 58.965 37.037 0.00 0.00 32.75 2.50
3785 4358 7.278868 CACTAGACATTTCTGATCCTTGTAACC 59.721 40.741 0.00 0.00 32.75 2.85
3786 4359 6.380079 AGACATTTCTGATCCTTGTAACCT 57.620 37.500 0.00 0.00 0.00 3.50
3787 4360 7.496346 AGACATTTCTGATCCTTGTAACCTA 57.504 36.000 0.00 0.00 0.00 3.08
3790 4363 9.482627 GACATTTCTGATCCTTGTAACCTATAG 57.517 37.037 0.00 0.00 0.00 1.31
3791 4364 9.213777 ACATTTCTGATCCTTGTAACCTATAGA 57.786 33.333 0.00 0.00 0.00 1.98
3892 4465 1.026718 CGCAATGAACCCTGGAGTCC 61.027 60.000 0.73 0.73 0.00 3.85
4063 4636 1.450134 GCACCTGCATCGACATGGA 60.450 57.895 0.00 0.00 41.59 3.41
4064 4637 1.434622 GCACCTGCATCGACATGGAG 61.435 60.000 0.00 0.87 45.76 3.86
4069 4642 2.905075 CTGCATCGACATGGAGGTAAA 58.095 47.619 0.00 0.00 43.17 2.01
4073 4650 3.181469 GCATCGACATGGAGGTAAAGGTA 60.181 47.826 0.00 0.00 0.00 3.08
4107 4684 3.381590 AGAGTTTGGCAAAGACCTGAAAC 59.618 43.478 13.94 0.00 0.00 2.78
4108 4685 2.430694 AGTTTGGCAAAGACCTGAAACC 59.569 45.455 13.94 0.00 29.88 3.27
4110 4687 1.981256 TGGCAAAGACCTGAAACCTC 58.019 50.000 0.00 0.00 0.00 3.85
4139 4716 1.149148 GGTCCAGCGACAGTTCTTTC 58.851 55.000 0.00 0.00 41.13 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.815817 AATTCCCACTGCCGGCAAAC 61.816 55.000 32.09 0.00 0.00 2.93
66 67 1.118356 AAATTCCCACTGCCGGCAAA 61.118 50.000 32.09 21.77 0.00 3.68
94 98 2.808543 CAGAACAGTCCAGTAGCAAACC 59.191 50.000 0.00 0.00 0.00 3.27
107 112 1.374190 CAGGAGGCAGCAGAACAGT 59.626 57.895 0.00 0.00 0.00 3.55
145 150 3.849911 CTGTCGTGTCACCTATGAACAT 58.150 45.455 0.00 0.00 36.31 2.71
155 160 1.286501 TGAAGTTGCTGTCGTGTCAC 58.713 50.000 0.00 0.00 0.00 3.67
168 173 5.396213 GCCATCACTAGGAGATCTTGAAGTT 60.396 44.000 0.00 0.00 0.00 2.66
169 174 4.100808 GCCATCACTAGGAGATCTTGAAGT 59.899 45.833 0.00 0.00 0.00 3.01
171 176 4.100653 CAGCCATCACTAGGAGATCTTGAA 59.899 45.833 0.00 0.00 0.00 2.69
172 177 3.640498 CAGCCATCACTAGGAGATCTTGA 59.360 47.826 0.00 0.00 0.00 3.02
175 180 3.609256 TCAGCCATCACTAGGAGATCT 57.391 47.619 0.00 0.00 0.00 2.75
176 181 3.577848 ACATCAGCCATCACTAGGAGATC 59.422 47.826 0.00 0.00 0.00 2.75
178 183 2.697229 CACATCAGCCATCACTAGGAGA 59.303 50.000 0.00 0.00 0.00 3.71
179 184 2.697229 TCACATCAGCCATCACTAGGAG 59.303 50.000 0.00 0.00 0.00 3.69
180 185 2.750814 TCACATCAGCCATCACTAGGA 58.249 47.619 0.00 0.00 0.00 2.94
181 186 3.201290 GTTCACATCAGCCATCACTAGG 58.799 50.000 0.00 0.00 0.00 3.02
182 187 3.865446 TGTTCACATCAGCCATCACTAG 58.135 45.455 0.00 0.00 0.00 2.57
183 188 3.979101 TGTTCACATCAGCCATCACTA 57.021 42.857 0.00 0.00 0.00 2.74
184 189 2.865119 TGTTCACATCAGCCATCACT 57.135 45.000 0.00 0.00 0.00 3.41
185 190 3.192001 ACAATGTTCACATCAGCCATCAC 59.808 43.478 0.00 0.00 35.10 3.06
186 191 3.423749 ACAATGTTCACATCAGCCATCA 58.576 40.909 0.00 0.00 35.10 3.07
228 238 6.728411 TGACCAAGGAGTACTAGAATACAGA 58.272 40.000 0.00 0.00 0.00 3.41
229 239 7.520776 CGATGACCAAGGAGTACTAGAATACAG 60.521 44.444 0.00 0.00 0.00 2.74
230 240 6.262496 CGATGACCAAGGAGTACTAGAATACA 59.738 42.308 0.00 0.00 0.00 2.29
231 241 6.294065 CCGATGACCAAGGAGTACTAGAATAC 60.294 46.154 0.00 0.00 0.00 1.89
232 242 5.768662 CCGATGACCAAGGAGTACTAGAATA 59.231 44.000 0.00 0.00 0.00 1.75
233 243 4.585162 CCGATGACCAAGGAGTACTAGAAT 59.415 45.833 0.00 0.00 0.00 2.40
234 244 3.952323 CCGATGACCAAGGAGTACTAGAA 59.048 47.826 0.00 0.00 0.00 2.10
235 245 3.552875 CCGATGACCAAGGAGTACTAGA 58.447 50.000 0.00 0.00 0.00 2.43
236 246 2.623889 CCCGATGACCAAGGAGTACTAG 59.376 54.545 0.00 0.00 0.00 2.57
239 249 1.192428 ACCCGATGACCAAGGAGTAC 58.808 55.000 0.00 0.00 0.00 2.73
264 274 3.111853 TCACCTTCTACTTGTGTGCTG 57.888 47.619 0.00 0.00 0.00 4.41
266 276 3.495001 GTCTTCACCTTCTACTTGTGTGC 59.505 47.826 0.00 0.00 0.00 4.57
281 291 3.851976 ACCTACACAGATCGTCTTCAC 57.148 47.619 0.00 0.00 0.00 3.18
294 304 8.980143 ATTTGTGTGCATAATTAAACCTACAC 57.020 30.769 0.00 0.00 38.06 2.90
304 314 6.876155 TGGAGCAATATTTGTGTGCATAATT 58.124 32.000 0.00 0.00 40.83 1.40
306 316 5.911378 TGGAGCAATATTTGTGTGCATAA 57.089 34.783 0.00 0.00 40.83 1.90
307 317 6.772233 AGTATGGAGCAATATTTGTGTGCATA 59.228 34.615 0.00 0.00 40.83 3.14
310 321 5.505173 AGTATGGAGCAATATTTGTGTGC 57.495 39.130 0.00 0.00 38.59 4.57
345 356 9.076596 GGAGCATGTTTTCTTGTGTATAAAATC 57.923 33.333 0.00 0.00 0.00 2.17
404 415 8.092687 GGTTCAATAGTCTGTAAAAGTAGACCA 58.907 37.037 0.00 0.00 43.32 4.02
449 460 1.198867 CATCGACGCCAACCAATTCAA 59.801 47.619 0.00 0.00 0.00 2.69
453 464 0.802494 GTTCATCGACGCCAACCAAT 59.198 50.000 0.00 0.00 0.00 3.16
483 494 5.366460 AGCATTCTGTTGGTGATCTCTATG 58.634 41.667 0.00 0.00 0.00 2.23
519 532 3.888930 GGATTGGGTGAAGTGAAAGTGAA 59.111 43.478 0.00 0.00 0.00 3.18
546 559 7.390440 CCTTACACAACAATTGAGAAGATGGTA 59.610 37.037 13.59 1.19 0.00 3.25
552 565 5.437289 TGCCTTACACAACAATTGAGAAG 57.563 39.130 13.59 5.77 0.00 2.85
568 581 5.932303 GTCTTGTATTCTTGAGTGTGCCTTA 59.068 40.000 0.00 0.00 0.00 2.69
592 605 2.439701 CCATGCAGCAGGAGGTGG 60.440 66.667 9.10 2.69 43.34 4.61
651 664 8.405418 ACAGTCTAATCTCGCTGGTAATTATA 57.595 34.615 0.00 0.00 33.62 0.98
655 668 6.490381 TCATACAGTCTAATCTCGCTGGTAAT 59.510 38.462 0.00 0.00 33.62 1.89
682 695 6.989169 CCACCCAAAAAGTACAATTCAATGAA 59.011 34.615 0.00 0.00 0.00 2.57
684 697 5.700373 CCCACCCAAAAAGTACAATTCAATG 59.300 40.000 0.00 0.00 0.00 2.82
685 698 5.368230 ACCCACCCAAAAAGTACAATTCAAT 59.632 36.000 0.00 0.00 0.00 2.57
686 699 4.717280 ACCCACCCAAAAAGTACAATTCAA 59.283 37.500 0.00 0.00 0.00 2.69
687 700 4.100189 CACCCACCCAAAAAGTACAATTCA 59.900 41.667 0.00 0.00 0.00 2.57
688 701 4.100344 ACACCCACCCAAAAAGTACAATTC 59.900 41.667 0.00 0.00 0.00 2.17
689 702 4.034410 ACACCCACCCAAAAAGTACAATT 58.966 39.130 0.00 0.00 0.00 2.32
690 703 3.386402 CACACCCACCCAAAAAGTACAAT 59.614 43.478 0.00 0.00 0.00 2.71
691 704 2.761208 CACACCCACCCAAAAAGTACAA 59.239 45.455 0.00 0.00 0.00 2.41
692 705 2.291670 ACACACCCACCCAAAAAGTACA 60.292 45.455 0.00 0.00 0.00 2.90
693 706 2.100087 CACACACCCACCCAAAAAGTAC 59.900 50.000 0.00 0.00 0.00 2.73
694 707 2.025226 TCACACACCCACCCAAAAAGTA 60.025 45.455 0.00 0.00 0.00 2.24
695 708 1.190643 CACACACCCACCCAAAAAGT 58.809 50.000 0.00 0.00 0.00 2.66
696 709 1.408702 CTCACACACCCACCCAAAAAG 59.591 52.381 0.00 0.00 0.00 2.27
736 750 8.714179 CATTTGCAATGACAAACTCATTAACAT 58.286 29.630 0.00 0.00 46.27 2.71
739 753 6.649973 CCCATTTGCAATGACAAACTCATTAA 59.350 34.615 0.00 0.00 46.27 1.40
740 754 6.164876 CCCATTTGCAATGACAAACTCATTA 58.835 36.000 0.00 0.00 46.27 1.90
786 800 2.703007 TGCTAGTTTGCACCCCATTTTT 59.297 40.909 0.00 0.00 38.12 1.94
787 801 2.324541 TGCTAGTTTGCACCCCATTTT 58.675 42.857 0.00 0.00 38.12 1.82
811 825 8.638685 ATCACAATTATGCTTAAAGATTGCAC 57.361 30.769 0.00 0.00 39.63 4.57
826 840 8.054152 TGCACAACATAAGTGATCACAATTAT 57.946 30.769 27.02 18.78 44.45 1.28
871 888 9.887629 ATGATATGAGAGATGGTATGATGAAAC 57.112 33.333 0.00 0.00 0.00 2.78
907 1094 4.220821 TCGAGTTAGACCAAAGAGAATGCT 59.779 41.667 0.00 0.00 0.00 3.79
958 1145 7.757526 TCCCTATCATAAAACAACACAAATCG 58.242 34.615 0.00 0.00 0.00 3.34
988 1175 6.248433 TCCCTGAGCTCATAATTCTGTTTTT 58.752 36.000 18.63 0.00 0.00 1.94
1014 1201 1.134461 GCATGGCCATTATTTGCACCA 60.134 47.619 17.92 0.00 35.31 4.17
1080 1267 7.496529 TGCATCTAAGCAAAATAGGTGATAC 57.503 36.000 0.00 0.00 42.46 2.24
1099 1304 7.067494 ACAGGGTAAAGAATAATGAGTTGCATC 59.933 37.037 0.00 0.00 35.78 3.91
1124 1329 0.165079 CAACGGTATCCACGCACAAC 59.835 55.000 0.00 0.00 34.00 3.32
1132 1337 6.703319 TGAGAAATAGAAACAACGGTATCCA 58.297 36.000 0.00 0.00 0.00 3.41
1253 1458 5.491982 CAGTTTCTTGCTATCAGGTACCTT 58.508 41.667 13.15 0.54 0.00 3.50
1271 1476 0.396811 CCTTCCTCACGTCCCAGTTT 59.603 55.000 0.00 0.00 0.00 2.66
1306 1511 4.025813 CAGAACGCCATTTCAAGGTTTTTG 60.026 41.667 0.00 0.00 0.00 2.44
1307 1512 4.119136 CAGAACGCCATTTCAAGGTTTTT 58.881 39.130 0.00 0.00 0.00 1.94
1328 1533 4.460731 CGGATCTCATCTGGCTTATACTCA 59.539 45.833 0.00 0.00 31.92 3.41
1570 1778 3.057946 TCATGGCTTCACTCGATATCTCG 60.058 47.826 0.34 0.00 46.41 4.04
1741 1949 9.185192 CTGAAAATGAGTCACCAAAATTAGAAC 57.815 33.333 0.00 0.00 0.00 3.01
1795 2003 7.223260 TCTCCATACAGTATACCAAATACCG 57.777 40.000 0.00 0.00 0.00 4.02
2276 2496 1.072806 TGGAGCACATCATCCCTATGC 59.927 52.381 0.00 0.00 34.47 3.14
2292 2512 9.860650 AGATATGCTTAGGTACTAGATATGGAG 57.139 37.037 0.00 0.00 44.25 3.86
2330 2550 9.733556 TCTTATATTGGAAGTCTACAAGCAAAA 57.266 29.630 0.00 0.00 0.00 2.44
2390 2610 8.013378 ACAAATACGAGGTGTTTCGAATTTAAG 58.987 33.333 0.00 0.00 43.03 1.85
2435 2655 2.821546 TGACAGAAACTCCACAAGACG 58.178 47.619 0.00 0.00 0.00 4.18
2524 3091 2.019807 TAGTTCCGGAAACAGGTCCT 57.980 50.000 20.79 12.36 40.56 3.85
2537 3105 7.265673 TGCATTCAGATGTAGTACTTAGTTCC 58.734 38.462 0.00 0.00 35.63 3.62
2864 3432 3.301794 TTCCCCAATCATGTCAGATGG 57.698 47.619 0.00 0.00 0.00 3.51
2986 3554 1.625818 GCAGTTTCTCCCCTCTTCTCA 59.374 52.381 0.00 0.00 0.00 3.27
2988 3556 0.610687 CGCAGTTTCTCCCCTCTTCT 59.389 55.000 0.00 0.00 0.00 2.85
3003 3571 3.849911 TCCTTTACAGATTCAGTCGCAG 58.150 45.455 0.00 0.00 0.00 5.18
3036 3604 4.127171 TCCCTTCTTTTCAGAAACAGTCG 58.873 43.478 0.00 0.00 38.63 4.18
3040 3608 6.451064 GTTTCTCCCTTCTTTTCAGAAACA 57.549 37.500 14.89 0.00 46.48 2.83
3055 3623 1.276705 GACCCAGTCTCTGTTTCTCCC 59.723 57.143 0.00 0.00 0.00 4.30
3057 3625 2.894126 TCAGACCCAGTCTCTGTTTCTC 59.106 50.000 0.00 0.00 41.37 2.87
3163 3731 2.598045 CGGATCAGATGAACTGCCG 58.402 57.895 0.00 0.00 45.38 5.69
3214 3782 2.171237 TGTGGTGGGAGCTCATATCAAG 59.829 50.000 17.19 0.00 0.00 3.02
3298 3866 5.438761 ACAAAATAAGTCAGGCAACACTC 57.561 39.130 0.00 0.00 41.41 3.51
3478 4046 6.073765 CGGAAAGGTGATATTCAGATTTACCG 60.074 42.308 0.00 0.00 30.15 4.02
3495 4063 3.763057 AGTTAAGAAATGGCGGAAAGGT 58.237 40.909 0.00 0.00 0.00 3.50
3538 4106 1.135083 AGTCCGGTCAATGCGAAGTAG 60.135 52.381 0.00 0.00 0.00 2.57
3753 4324 5.221422 GGATCAGAAATGTCTAGTGAGAGGG 60.221 48.000 0.00 0.00 30.85 4.30
3790 4363 9.308318 GTGATCCTCTTTTGTCTATACTTCTTC 57.692 37.037 0.00 0.00 0.00 2.87
3791 4364 9.041354 AGTGATCCTCTTTTGTCTATACTTCTT 57.959 33.333 0.00 0.00 0.00 2.52
4073 4650 2.876550 GCCAAACTCTGACGTAAGGTTT 59.123 45.455 11.60 11.60 46.39 3.27
4107 4684 0.254178 CTGGACCTGAACCATGGAGG 59.746 60.000 21.47 17.64 45.67 4.30
4108 4685 0.393537 GCTGGACCTGAACCATGGAG 60.394 60.000 21.47 5.19 36.79 3.86
4110 4687 1.746615 CGCTGGACCTGAACCATGG 60.747 63.158 11.19 11.19 36.79 3.66
4121 4698 2.156343 AGAAAGAACTGTCGCTGGAC 57.844 50.000 0.00 0.00 43.71 4.02


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

AutoCloner maintained by Alex Coulton.