Multiple sequence alignment - TraesCS4B01G243000

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 TraesCS4B01G243000 chr4B 100.000 3877 0 0 1 3877 503557345 503561221 0.000000e+00 7160.0
1 TraesCS4B01G243000 chr4B 81.600 125 21 2 126 248 554011143 554011267 6.850000e-18 102.0
2 TraesCS4B01G243000 chr4D 95.634 2565 95 12 791 3340 405304972 405307534 0.000000e+00 4100.0
3 TraesCS4B01G243000 chr4D 92.009 463 19 6 3425 3877 405321315 405321769 5.460000e-178 634.0
4 TraesCS4B01G243000 chr4D 96.721 61 2 0 3425 3485 405321250 405321310 6.850000e-18 102.0
5 TraesCS4B01G243000 chr4D 86.022 93 13 0 3763 3855 32219518 32219610 2.460000e-17 100.0
6 TraesCS4B01G243000 chr4A 93.588 2776 122 24 1134 3877 63008352 63011103 0.000000e+00 4089.0
7 TraesCS4B01G243000 chr4A 88.180 643 58 8 3 643 63005661 63006287 0.000000e+00 750.0
8 TraesCS4B01G243000 chr4A 90.437 366 27 4 665 1026 63007658 63008019 3.510000e-130 475.0
9 TraesCS4B01G243000 chr2A 75.153 978 190 31 1906 2867 147462208 147461268 1.000000e-110 411.0
10 TraesCS4B01G243000 chr2A 88.136 118 14 0 3760 3877 146786075 146786192 1.450000e-29 141.0
11 TraesCS4B01G243000 chr3B 80.126 317 46 11 381 681 715950998 715950683 1.810000e-53 220.0
12 TraesCS4B01G243000 chr3B 79.231 130 19 8 125 248 248328663 248328790 2.480000e-12 84.2
13 TraesCS4B01G243000 chr7D 92.683 123 9 0 1 123 350071796 350071918 1.110000e-40 178.0
14 TraesCS4B01G243000 chr3D 92.742 124 8 1 1 123 336010641 336010764 1.110000e-40 178.0
15 TraesCS4B01G243000 chr3D 90.323 124 11 1 1 123 102184882 102185005 1.110000e-35 161.0
16 TraesCS4B01G243000 chr2D 91.935 124 9 1 1 123 286970072 286969949 5.150000e-39 172.0
17 TraesCS4B01G243000 chr2D 88.136 118 14 0 3760 3877 154184124 154184007 1.450000e-29 141.0
18 TraesCS4B01G243000 chr2D 82.569 109 14 4 125 230 470977975 470977869 1.480000e-14 91.6
19 TraesCS4B01G243000 chr5A 91.870 123 8 2 1 121 98478247 98478369 1.850000e-38 171.0
20 TraesCS4B01G243000 chr5A 91.200 125 9 2 1 123 247570596 247570720 6.660000e-38 169.0
21 TraesCS4B01G243000 chr6D 91.057 123 11 0 1 123 329352575 329352453 2.400000e-37 167.0
22 TraesCS4B01G243000 chr1A 89.683 126 12 1 1 126 120137174 120137298 4.010000e-35 159.0
23 TraesCS4B01G243000 chr1A 86.022 93 13 0 3763 3855 535062223 535062315 2.460000e-17 100.0
24 TraesCS4B01G243000 chr2B 88.136 118 14 0 3760 3877 211626994 211626877 1.450000e-29 141.0
25 TraesCS4B01G243000 chr2B 78.906 128 23 4 125 248 140208179 140208306 2.480000e-12 84.2
26 TraesCS4B01G243000 chr6B 82.540 126 18 4 126 248 566504171 566504295 1.470000e-19 108.0
27 TraesCS4B01G243000 chr6B 83.636 110 16 2 427 534 465663569 465663678 6.850000e-18 102.0
28 TraesCS4B01G243000 chr6B 80.000 125 24 1 125 248 550976328 550976452 1.480000e-14 91.6
29 TraesCS4B01G243000 chr6B 79.688 128 23 3 124 248 216879903 216879776 5.340000e-14 89.8
30 TraesCS4B01G243000 chr6B 80.000 125 20 4 127 248 550977059 550977181 1.920000e-13 87.9
31 TraesCS4B01G243000 chr1D 86.022 93 13 0 3763 3855 438368548 438368640 2.460000e-17 100.0
32 TraesCS4B01G243000 chr1B 86.022 93 13 0 3763 3855 594138226 594138318 2.460000e-17 100.0
33 TraesCS4B01G243000 chr1B 79.688 128 20 6 125 248 116263291 116263166 1.920000e-13 87.9
34 TraesCS4B01G243000 chrUn 79.528 127 20 6 126 248 84431072 84431196 6.900000e-13 86.1


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 TraesCS4B01G243000 chr4B 503557345 503561221 3876 False 7160.000000 7160 100.000 1 3877 1 chr4B.!!$F1 3876
1 TraesCS4B01G243000 chr4D 405304972 405307534 2562 False 4100.000000 4100 95.634 791 3340 1 chr4D.!!$F2 2549
2 TraesCS4B01G243000 chr4D 405321250 405321769 519 False 368.000000 634 94.365 3425 3877 2 chr4D.!!$F3 452
3 TraesCS4B01G243000 chr4A 63005661 63011103 5442 False 1771.333333 4089 90.735 3 3877 3 chr4A.!!$F1 3874
4 TraesCS4B01G243000 chr2A 147461268 147462208 940 True 411.000000 411 75.153 1906 2867 1 chr2A.!!$R1 961

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
244 245 0.028770 CAACCAACACGTTGCACGAT 59.971 50.0 14.18 1.33 46.05 3.73 F
1602 3183 0.107848 CCCGCAACTTCTATCCCGTT 60.108 55.0 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1952 3536 0.238289 AGAATTTGTTCGCGCAGGTG 59.762 50.0 8.75 0.0 0.00 4.00 R
3541 5162 0.179094 GACGGATGGATTACACCGCA 60.179 55.0 0.00 0.0 43.16 5.69 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
40 41 3.244770 GGTCAGAACCTGGGTAAACATCA 60.245 47.826 0.00 0.00 42.80 3.07
63 64 0.981943 CCTCCGTTCCTGTTACCCTT 59.018 55.000 0.00 0.00 0.00 3.95
64 65 1.338769 CCTCCGTTCCTGTTACCCTTG 60.339 57.143 0.00 0.00 0.00 3.61
105 106 2.210711 CCCCTACCCCGAGATCTGC 61.211 68.421 0.00 0.00 0.00 4.26
107 108 2.565645 CCTACCCCGAGATCTGCCG 61.566 68.421 0.00 0.00 0.00 5.69
117 118 0.674895 AGATCTGCCGGCTTTGACAC 60.675 55.000 29.70 18.21 0.00 3.67
162 163 8.783999 TGTTTATGAAAATTTAACGAGCGAAA 57.216 26.923 0.00 0.00 0.00 3.46
164 165 8.898792 GTTTATGAAAATTTAACGAGCGAAAGT 58.101 29.630 0.00 0.00 0.00 2.66
168 169 5.668558 AAATTTAACGAGCGAAAGTGAGT 57.331 34.783 0.00 0.00 0.00 3.41
226 227 1.001924 CAATGGCAAACGCACTACACA 60.002 47.619 0.00 0.00 0.00 3.72
229 230 0.317519 GGCAAACGCACTACACAACC 60.318 55.000 0.00 0.00 0.00 3.77
230 231 0.378962 GCAAACGCACTACACAACCA 59.621 50.000 0.00 0.00 0.00 3.67
231 232 1.202200 GCAAACGCACTACACAACCAA 60.202 47.619 0.00 0.00 0.00 3.67
232 233 2.446282 CAAACGCACTACACAACCAAC 58.554 47.619 0.00 0.00 0.00 3.77
233 234 1.740297 AACGCACTACACAACCAACA 58.260 45.000 0.00 0.00 0.00 3.33
234 235 1.011333 ACGCACTACACAACCAACAC 58.989 50.000 0.00 0.00 0.00 3.32
235 236 0.042535 CGCACTACACAACCAACACG 60.043 55.000 0.00 0.00 0.00 4.49
236 237 1.011333 GCACTACACAACCAACACGT 58.989 50.000 0.00 0.00 0.00 4.49
237 238 1.399089 GCACTACACAACCAACACGTT 59.601 47.619 0.00 0.00 0.00 3.99
238 239 2.789779 GCACTACACAACCAACACGTTG 60.790 50.000 2.84 2.84 46.94 4.10
239 240 1.399089 ACTACACAACCAACACGTTGC 59.601 47.619 4.34 0.00 45.75 4.17
240 241 1.398739 CTACACAACCAACACGTTGCA 59.601 47.619 4.34 0.00 45.75 4.08
241 242 0.109504 ACACAACCAACACGTTGCAC 60.110 50.000 4.34 0.00 45.75 4.57
242 243 1.131037 CACAACCAACACGTTGCACG 61.131 55.000 4.34 7.07 45.75 5.34
243 244 1.299562 ACAACCAACACGTTGCACGA 61.300 50.000 14.18 0.00 46.05 4.35
244 245 0.028770 CAACCAACACGTTGCACGAT 59.971 50.000 14.18 1.33 46.05 3.73
251 252 0.451628 CACGTTGCACGATCAAGCTG 60.452 55.000 14.18 1.54 46.05 4.24
312 313 2.635714 CAAGCTGATACACCTCATGCA 58.364 47.619 0.00 0.00 0.00 3.96
325 326 5.782331 ACACCTCATGCATCTGGTACTATAT 59.218 40.000 16.93 0.99 0.00 0.86
329 330 5.970592 TCATGCATCTGGTACTATATGCTC 58.029 41.667 23.66 4.01 43.98 4.26
334 335 3.487372 TCTGGTACTATATGCTCGTGCT 58.513 45.455 11.19 0.00 40.48 4.40
336 337 3.977427 TGGTACTATATGCTCGTGCTTG 58.023 45.455 11.19 0.00 40.48 4.01
359 360 8.806429 TTGTAATAGAGGCTTCATTCAAATCA 57.194 30.769 0.00 0.00 0.00 2.57
365 366 2.095059 GGCTTCATTCAAATCAGTGCGT 60.095 45.455 0.00 0.00 0.00 5.24
366 367 3.166657 GCTTCATTCAAATCAGTGCGTC 58.833 45.455 0.00 0.00 0.00 5.19
402 403 1.033746 ATGCCTGAACATGCTTCCCG 61.034 55.000 0.00 0.00 0.00 5.14
409 410 2.592861 CATGCTTCCCGCCCTAGC 60.593 66.667 0.00 0.00 38.05 3.42
427 428 1.062587 AGCGCGTGCATGATAAAGTTC 59.937 47.619 24.79 0.00 46.23 3.01
434 435 9.967031 GCGCGTGCATGATAAAGTTCATCTTTA 62.967 40.741 17.66 3.16 44.68 1.85
449 450 9.998106 AGTTCATCTTTACTTACTTGAAAGCTA 57.002 29.630 0.00 0.00 31.55 3.32
453 454 9.813080 CATCTTTACTTACTTGAAAGCTAACAC 57.187 33.333 0.00 0.00 31.55 3.32
485 487 0.552363 AAACCCCCGCCCGTAATTAT 59.448 50.000 0.00 0.00 0.00 1.28
488 490 1.002990 CCCCGCCCGTAATTATCCC 60.003 63.158 0.00 0.00 0.00 3.85
497 499 5.293569 CGCCCGTAATTATCCCATAAATCTC 59.706 44.000 0.00 0.00 0.00 2.75
537 539 2.360801 TGCGAAAAGAAAGGGAAACAGG 59.639 45.455 0.00 0.00 0.00 4.00
540 542 3.253432 CGAAAAGAAAGGGAAACAGGGAG 59.747 47.826 0.00 0.00 0.00 4.30
546 548 1.606601 GGGAAACAGGGAGCCAACC 60.607 63.158 0.00 0.00 0.00 3.77
572 574 3.681593 GGTTGCCTGGTATTTGTGTCTA 58.318 45.455 0.00 0.00 0.00 2.59
577 580 5.538118 TGCCTGGTATTTGTGTCTATATCG 58.462 41.667 0.00 0.00 0.00 2.92
635 638 6.112927 TGAGGGGTAAACTACAAAACGTAT 57.887 37.500 0.00 0.00 0.00 3.06
636 639 7.238486 TGAGGGGTAAACTACAAAACGTATA 57.762 36.000 0.00 0.00 0.00 1.47
643 646 9.597999 GGTAAACTACAAAACGTATAAAACCAG 57.402 33.333 0.00 0.00 0.00 4.00
647 689 9.940166 AACTACAAAACGTATAAAACCAGAAAG 57.060 29.630 0.00 0.00 0.00 2.62
656 698 3.812156 AAAACCAGAAAGGGAAAACCG 57.188 42.857 0.00 0.00 46.96 4.44
657 699 2.740506 AACCAGAAAGGGAAAACCGA 57.259 45.000 0.00 0.00 46.96 4.69
658 700 2.740506 ACCAGAAAGGGAAAACCGAA 57.259 45.000 0.00 0.00 46.96 4.30
659 701 3.021177 ACCAGAAAGGGAAAACCGAAA 57.979 42.857 0.00 0.00 46.96 3.46
662 704 3.491964 CCAGAAAGGGAAAACCGAAAACC 60.492 47.826 0.00 0.00 46.96 3.27
663 705 3.131400 CAGAAAGGGAAAACCGAAAACCA 59.869 43.478 0.00 0.00 46.96 3.67
671 2023 3.446310 AAACCGAAAACCAACCACATC 57.554 42.857 0.00 0.00 0.00 3.06
682 2034 1.303317 ACCACATCGGCTGGTTTCC 60.303 57.895 0.00 0.00 39.07 3.13
686 2038 1.299648 CATCGGCTGGTTTCCCTCA 59.700 57.895 0.00 0.00 0.00 3.86
689 2041 1.750399 CGGCTGGTTTCCCTCATGG 60.750 63.158 0.00 0.00 0.00 3.66
700 2052 2.496341 CTCATGGGAGCTTCGCGA 59.504 61.111 3.71 3.71 33.67 5.87
701 2053 1.153568 CTCATGGGAGCTTCGCGAA 60.154 57.895 22.01 22.01 33.67 4.70
717 2069 0.927537 CGAACGAGAAGTGTTGTGCA 59.072 50.000 0.00 0.00 0.00 4.57
735 2087 4.778143 CGGAGGGCTCCCAAACCG 62.778 72.222 18.07 18.07 46.96 4.44
742 2094 0.243636 GGCTCCCAAACCGTTCATTG 59.756 55.000 0.00 0.00 0.00 2.82
772 2125 1.080434 AAGAAGTGCTCGCCGACTC 60.080 57.895 0.00 0.00 0.00 3.36
774 2127 3.612371 GAAGTGCTCGCCGACTCGT 62.612 63.158 0.00 0.00 0.00 4.18
780 2133 3.329688 CTCGCCGACTCGTTGCTCT 62.330 63.158 0.00 0.00 0.00 4.09
783 2136 2.962569 CCGACTCGTTGCTCTCCA 59.037 61.111 0.00 0.00 0.00 3.86
828 2181 1.003580 CCATGTATTGCGGATAGGGCT 59.996 52.381 0.00 0.00 0.00 5.19
881 2234 3.057174 AGAAAAGTAGAGCGACTGACCAG 60.057 47.826 0.00 0.00 0.00 4.00
902 2255 2.191400 CAGATCCCCTCCACTCAAAGA 58.809 52.381 0.00 0.00 0.00 2.52
969 2322 1.693083 GAACACGCCGAAATCCCTCG 61.693 60.000 0.00 0.00 38.58 4.63
1092 2448 3.095347 GCCGCCTTCGAATCCTCCT 62.095 63.158 0.00 0.00 38.10 3.69
1241 2822 0.657659 CACGCGATCGCCTACTACAG 60.658 60.000 32.63 18.72 39.84 2.74
1401 2982 3.691342 CTCTCCGTGCCCGTGGAA 61.691 66.667 0.00 0.00 32.89 3.53
1596 3177 1.449601 CACCGCCCGCAACTTCTAT 60.450 57.895 0.00 0.00 0.00 1.98
1602 3183 0.107848 CCCGCAACTTCTATCCCGTT 60.108 55.000 0.00 0.00 0.00 4.44
1770 3351 2.908940 ACCGACAAGGACGTCCGT 60.909 61.111 28.26 23.34 45.00 4.69
1844 3425 2.026262 ACATGCCCGGTGAGTAAGAAAT 60.026 45.455 0.00 0.00 0.00 2.17
1850 3431 3.592059 CCGGTGAGTAAGAAATTCCGAA 58.408 45.455 0.00 0.00 38.96 4.30
1851 3432 4.189231 CCGGTGAGTAAGAAATTCCGAAT 58.811 43.478 0.00 0.00 38.96 3.34
1854 3435 5.350365 CGGTGAGTAAGAAATTCCGAATTCA 59.650 40.000 6.82 0.00 38.96 2.57
1860 3441 7.569240 AGTAAGAAATTCCGAATTCATCCTCT 58.431 34.615 6.82 3.47 0.00 3.69
1874 3455 0.627451 TCCTCTCTGCATTTGGCCAT 59.373 50.000 6.09 0.00 43.89 4.40
1878 3459 1.659622 CTCTGCATTTGGCCATCGCA 61.660 55.000 19.58 19.58 43.89 5.10
1879 3460 1.215912 CTGCATTTGGCCATCGCAA 59.784 52.632 20.69 7.76 43.89 4.85
1880 3461 1.079875 CTGCATTTGGCCATCGCAAC 61.080 55.000 20.69 5.16 43.89 4.17
1881 3462 1.810853 GCATTTGGCCATCGCAACC 60.811 57.895 6.09 0.00 36.38 3.77
1892 3473 1.469703 CATCGCAACCTCTTCAATGCA 59.530 47.619 0.00 0.00 38.69 3.96
1917 3501 4.817063 CGCGCATTTCAGGGCACG 62.817 66.667 8.75 0.00 46.59 5.34
1952 3536 0.516439 GATCGTACCCGGAGATCGTC 59.484 60.000 0.73 0.00 37.11 4.20
1967 3551 2.876879 CGTCACCTGCGCGAACAAA 61.877 57.895 12.10 0.00 0.00 2.83
2101 3694 2.681064 CCTGTTCCCGGACCCGTA 60.681 66.667 0.73 0.00 37.81 4.02
2222 3815 2.582265 GCTGTTCGTGAACGCGACA 61.582 57.895 15.93 10.17 43.94 4.35
2330 3923 2.125912 CTGCCCAAGGAGACGACG 60.126 66.667 0.00 0.00 0.00 5.12
2597 4190 4.457496 ATCCTGCACGGGCTGACG 62.457 66.667 19.12 2.00 41.06 4.35
2600 4193 4.680237 CTGCACGGGCTGACGGAA 62.680 66.667 12.74 0.00 41.06 4.30
2881 4474 0.900647 AACCTCTCGCAGTAGCCAGT 60.901 55.000 0.00 0.00 37.52 4.00
2916 4510 4.223125 TGGCCCCTGCTTTGCTGT 62.223 61.111 0.00 0.00 37.74 4.40
2978 4572 0.678950 TCACAGATCGAACTGGCACA 59.321 50.000 24.36 4.65 41.59 4.57
3055 4652 1.940613 GAATACCAGCGGATGACCAAC 59.059 52.381 0.00 0.00 35.59 3.77
3110 4708 1.609320 GCTTCCACCTCTCAACAGTCC 60.609 57.143 0.00 0.00 0.00 3.85
3128 4728 0.391263 CCTGGTTCTTGCGGTAGGAC 60.391 60.000 0.00 0.00 0.00 3.85
3152 4760 1.006825 GTGATGTGCGTCAGTGCGTA 61.007 55.000 8.39 1.99 37.81 4.42
3246 4863 6.516718 AGTTAGCTATTCGATTAGTGCACAT 58.483 36.000 21.04 4.18 0.00 3.21
3267 4884 1.028905 AGAGTCCTATCGTGAGCAGC 58.971 55.000 0.00 0.00 0.00 5.25
3331 4949 0.107456 ATCAAGATAGGCAGCACCCG 59.893 55.000 0.00 0.00 40.58 5.28
3335 4953 0.397254 AGATAGGCAGCACCCGTACT 60.397 55.000 0.00 0.00 40.58 2.73
3400 5020 1.226603 GTCTTACGACGGCAGCGAT 60.227 57.895 0.00 0.00 0.00 4.58
3401 5021 1.226575 TCTTACGACGGCAGCGATG 60.227 57.895 0.00 0.00 0.00 3.84
3511 5131 2.356135 CCAGTGATTTTGTCCCTACGG 58.644 52.381 0.00 0.00 0.00 4.02
3535 5156 3.110178 GCTTTCCGTCCGACGTGG 61.110 66.667 19.13 5.58 40.58 4.94
3536 5157 2.431942 CTTTCCGTCCGACGTGGG 60.432 66.667 19.13 10.85 40.58 4.61
3537 5158 3.216944 CTTTCCGTCCGACGTGGGT 62.217 63.158 19.13 0.00 40.58 4.51
3538 5159 3.502990 TTTCCGTCCGACGTGGGTG 62.503 63.158 19.13 10.19 40.58 4.61
3558 5183 1.487452 CGTGCGGTGTAATCCATCCG 61.487 60.000 0.00 0.00 44.86 4.18
3578 5203 1.446099 CGCTTTCCGCTAGCTCACA 60.446 57.895 13.93 0.00 36.49 3.58
3691 5317 3.642778 TTCCTCGCGCAGGTGCTAC 62.643 63.158 20.54 0.00 43.95 3.58
3722 5351 4.385405 AGGCGACAGAGCTGCACC 62.385 66.667 1.02 0.00 37.29 5.01
3741 5374 0.458889 CAGAGCAGAGCAGAGCAGAC 60.459 60.000 0.00 0.00 0.00 3.51
3742 5375 0.899253 AGAGCAGAGCAGAGCAGACA 60.899 55.000 0.00 0.00 0.00 3.41
3743 5376 0.737019 GAGCAGAGCAGAGCAGACAC 60.737 60.000 0.00 0.00 0.00 3.67
3746 5379 1.015085 CAGAGCAGAGCAGACACAGC 61.015 60.000 0.00 0.00 0.00 4.40
3747 5380 1.186917 AGAGCAGAGCAGACACAGCT 61.187 55.000 0.00 0.00 46.82 4.24
3748 5381 1.004799 AGCAGAGCAGACACAGCTG 60.005 57.895 13.48 13.48 43.58 4.24
3749 5382 1.005275 GCAGAGCAGACACAGCTGA 60.005 57.895 23.35 0.00 43.58 4.26
3750 5383 0.391395 GCAGAGCAGACACAGCTGAT 60.391 55.000 23.35 7.98 43.58 2.90
3755 5388 1.832366 AGCAGACACAGCTGATCAGAT 59.168 47.619 27.04 18.40 41.61 2.90
3756 5389 2.236644 AGCAGACACAGCTGATCAGATT 59.763 45.455 27.04 10.54 41.61 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.536090 AGATGATGTTTACCCAGGTTCTGA 59.464 41.667 0.00 0.00 32.44 3.27
22 23 4.080299 GGAGATGATGTTTACCCAGGTTCT 60.080 45.833 0.00 0.00 0.00 3.01
40 41 2.108970 GGTAACAGGAACGGAGGAGAT 58.891 52.381 0.00 0.00 0.00 2.75
63 64 1.035923 GAGCTGTGGATCTCGGATCA 58.964 55.000 13.59 1.17 0.00 2.92
64 65 0.039617 CGAGCTGTGGATCTCGGATC 60.040 60.000 0.00 5.59 45.89 3.36
107 108 1.652563 GGTTGTCGGTGTCAAAGCC 59.347 57.895 0.00 0.00 0.00 4.35
109 110 1.170290 GGGGGTTGTCGGTGTCAAAG 61.170 60.000 0.00 0.00 0.00 2.77
154 155 1.738350 TCTCCTACTCACTTTCGCTCG 59.262 52.381 0.00 0.00 0.00 5.03
162 163 1.178276 CAAGGCGTCTCCTACTCACT 58.822 55.000 0.00 0.00 46.94 3.41
164 165 1.890894 GCAAGGCGTCTCCTACTCA 59.109 57.895 0.00 0.00 46.94 3.41
217 218 1.011333 ACGTGTTGGTTGTGTAGTGC 58.989 50.000 0.00 0.00 0.00 4.40
235 236 5.261370 CTATATCAGCTTGATCGTGCAAC 57.739 43.478 11.45 0.00 38.26 4.17
251 252 4.677378 CACAGTCGTGTAGCTTGCTATATC 59.323 45.833 5.59 0.00 38.41 1.63
267 268 2.486636 TTAGACCAGCGGCACAGTCG 62.487 60.000 1.45 0.00 34.41 4.18
312 313 4.082845 AGCACGAGCATATAGTACCAGAT 58.917 43.478 7.77 0.00 45.49 2.90
325 326 2.738643 GCCTCTATTACAAGCACGAGCA 60.739 50.000 7.77 0.00 45.49 4.26
329 330 3.521560 TGAAGCCTCTATTACAAGCACG 58.478 45.455 0.00 0.00 0.00 5.34
334 335 8.806429 TGATTTGAATGAAGCCTCTATTACAA 57.194 30.769 0.00 0.00 0.00 2.41
336 337 8.341173 CACTGATTTGAATGAAGCCTCTATTAC 58.659 37.037 0.00 0.00 0.00 1.89
365 366 2.987547 GGGTGTCGACCGTCCAGA 60.988 66.667 14.12 0.00 44.23 3.86
366 367 2.646175 ATGGGTGTCGACCGTCCAG 61.646 63.158 20.72 0.00 44.23 3.86
409 410 2.804421 TGAACTTTATCATGCACGCG 57.196 45.000 3.53 3.53 0.00 6.01
427 428 9.813080 GTGTTAGCTTTCAAGTAAGTAAAGATG 57.187 33.333 0.00 0.00 33.05 2.90
434 435 4.952460 TCGGTGTTAGCTTTCAAGTAAGT 58.048 39.130 0.00 0.00 0.00 2.24
453 454 1.680860 GGGGGTTTCCAACACTATCGG 60.681 57.143 0.00 0.00 37.22 4.18
485 487 4.167113 TCCGGAAAATGGAGATTTATGGGA 59.833 41.667 0.00 0.00 31.18 4.37
497 499 6.007936 TCGCATTATATTTCCGGAAAATGG 57.992 37.500 32.03 21.36 38.08 3.16
503 505 6.928979 TTCTTTTCGCATTATATTTCCGGA 57.071 33.333 0.00 0.00 0.00 5.14
505 507 6.636850 CCCTTTCTTTTCGCATTATATTTCCG 59.363 38.462 0.00 0.00 0.00 4.30
554 556 5.538118 CGATATAGACACAAATACCAGGCA 58.462 41.667 0.00 0.00 0.00 4.75
559 561 3.059044 CGCGCGATATAGACACAAATACC 59.941 47.826 28.94 0.00 0.00 2.73
572 574 3.750639 TTTTTCCTTTTCGCGCGATAT 57.249 38.095 35.21 0.00 0.00 1.63
612 615 4.420522 ACGTTTTGTAGTTTACCCCTCA 57.579 40.909 0.00 0.00 0.00 3.86
621 624 9.940166 CTTTCTGGTTTTATACGTTTTGTAGTT 57.060 29.630 0.00 0.00 36.25 2.24
625 628 6.546772 TCCCTTTCTGGTTTTATACGTTTTGT 59.453 34.615 0.00 0.00 0.00 2.83
635 638 4.534797 TCGGTTTTCCCTTTCTGGTTTTA 58.465 39.130 0.00 0.00 36.42 1.52
636 639 3.367321 TCGGTTTTCCCTTTCTGGTTTT 58.633 40.909 0.00 0.00 36.42 2.43
643 646 3.804786 TGGTTTTCGGTTTTCCCTTTC 57.195 42.857 0.00 0.00 36.42 2.62
647 689 1.481363 TGGTTGGTTTTCGGTTTTCCC 59.519 47.619 0.00 0.00 36.42 3.97
656 698 0.958822 AGCCGATGTGGTTGGTTTTC 59.041 50.000 0.00 0.00 41.21 2.29
657 699 0.673437 CAGCCGATGTGGTTGGTTTT 59.327 50.000 0.00 0.00 44.69 2.43
658 700 2.340427 CAGCCGATGTGGTTGGTTT 58.660 52.632 0.00 0.00 44.69 3.27
659 701 4.079446 CAGCCGATGTGGTTGGTT 57.921 55.556 0.00 0.00 44.69 3.67
708 2060 3.660111 GCCCTCCGTGCACAACAC 61.660 66.667 18.64 0.00 46.45 3.32
723 2075 0.243636 CAATGAACGGTTTGGGAGCC 59.756 55.000 0.00 0.00 0.00 4.70
730 2082 3.566742 GGAGTGTTACCAATGAACGGTTT 59.433 43.478 0.00 0.00 37.99 3.27
735 2087 4.394729 TCTTGGGAGTGTTACCAATGAAC 58.605 43.478 0.00 0.00 45.03 3.18
742 2094 2.152016 GCACTTCTTGGGAGTGTTACC 58.848 52.381 7.66 0.00 36.09 2.85
753 2106 1.347817 GAGTCGGCGAGCACTTCTTG 61.348 60.000 11.20 0.00 0.00 3.02
759 2112 3.470567 CAACGAGTCGGCGAGCAC 61.471 66.667 18.30 0.00 34.83 4.40
772 2125 0.534412 AGGTGAGATGGAGAGCAACG 59.466 55.000 0.00 0.00 0.00 4.10
774 2127 1.552337 GTGAGGTGAGATGGAGAGCAA 59.448 52.381 0.00 0.00 0.00 3.91
780 2133 4.034246 CCGGTGAGGTGAGATGGA 57.966 61.111 0.00 0.00 34.51 3.41
881 2234 0.620556 TTTGAGTGGAGGGGATCTGC 59.379 55.000 0.00 0.00 0.00 4.26
969 2322 2.170817 GGGTTTAGGAGGAGTGGATGAC 59.829 54.545 0.00 0.00 0.00 3.06
1083 2439 3.798954 CTGCGGCGGAGGAGGATTC 62.799 68.421 21.44 0.00 0.00 2.52
1596 3177 3.060020 GAGGATGTCGCGAACGGGA 62.060 63.158 12.06 9.69 40.63 5.14
1602 3183 2.571757 GTGTGGAGGATGTCGCGA 59.428 61.111 3.71 3.71 0.00 5.87
1806 3387 0.395173 TGTCGATCTCGGGGATGACA 60.395 55.000 14.88 14.88 38.66 3.58
1844 3425 2.501316 TGCAGAGAGGATGAATTCGGAA 59.499 45.455 0.04 0.00 0.00 4.30
1850 3431 2.957006 GCCAAATGCAGAGAGGATGAAT 59.043 45.455 0.00 0.00 40.77 2.57
1851 3432 2.372264 GCCAAATGCAGAGAGGATGAA 58.628 47.619 0.00 0.00 40.77 2.57
1854 3435 0.627451 TGGCCAAATGCAGAGAGGAT 59.373 50.000 0.61 0.00 43.89 3.24
1860 3441 1.249469 TTGCGATGGCCAAATGCAGA 61.249 50.000 23.46 14.97 43.89 4.26
1874 3455 1.603456 TTGCATTGAAGAGGTTGCGA 58.397 45.000 0.00 0.00 37.92 5.10
1878 3459 3.921677 CAGCAATTGCATTGAAGAGGTT 58.078 40.909 30.89 3.86 42.83 3.50
1879 3460 3.587797 CAGCAATTGCATTGAAGAGGT 57.412 42.857 30.89 4.40 42.83 3.85
1903 3484 4.481112 CCGCGTGCCCTGAAATGC 62.481 66.667 4.92 0.00 0.00 3.56
1935 3519 1.091771 GTGACGATCTCCGGGTACGA 61.092 60.000 0.00 0.00 44.60 3.43
1952 3536 0.238289 AGAATTTGTTCGCGCAGGTG 59.762 50.000 8.75 0.00 0.00 4.00
2222 3815 4.634703 TGCACCATGAACGGCCGT 62.635 61.111 28.70 28.70 0.00 5.68
2330 3923 2.280797 TTCCACGTCTGCAGCACC 60.281 61.111 9.47 0.00 0.00 5.01
2597 4190 1.301293 CAGGTTGGCCTCCTCTTCC 59.699 63.158 15.40 2.94 44.97 3.46
2600 4193 2.208349 ACCAGGTTGGCCTCCTCT 59.792 61.111 15.40 3.52 44.97 3.69
2881 4474 2.214216 AGGCTTCACCGGTGTGCTA 61.214 57.895 34.93 18.99 46.52 3.49
2978 4572 2.372172 ACGTTCCAAATTCTCTGTCCCT 59.628 45.455 0.00 0.00 0.00 4.20
3013 4607 0.458260 CATGTCGATCCACGGGTACA 59.542 55.000 0.00 0.00 42.82 2.90
3017 4611 1.521457 CACCATGTCGATCCACGGG 60.521 63.158 0.00 0.43 42.82 5.28
3055 4652 4.497473 TGGTTTATTTGCAGTTTCTCGG 57.503 40.909 0.00 0.00 0.00 4.63
3057 4654 8.063630 CACAAAATGGTTTATTTGCAGTTTCTC 58.936 33.333 0.00 0.00 38.93 2.87
3110 4708 0.391263 GGTCCTACCGCAAGAACCAG 60.391 60.000 0.00 0.00 43.02 4.00
3128 4728 1.069703 CACTGACGCACATCACTTTGG 60.070 52.381 0.00 0.00 0.00 3.28
3152 4760 4.881273 TGTTCAGTGTCAAATACAGCAACT 59.119 37.500 0.00 0.00 39.29 3.16
3220 4837 7.658261 TGTGCACTAATCGAATAGCTAACTAT 58.342 34.615 19.41 0.00 41.01 2.12
3224 4841 6.512297 TGATGTGCACTAATCGAATAGCTAA 58.488 36.000 19.41 0.00 0.00 3.09
3246 4863 2.293170 CTGCTCACGATAGGACTCTGA 58.707 52.381 0.00 0.00 43.77 3.27
3322 4940 1.664151 GTTCAATAGTACGGGTGCTGC 59.336 52.381 0.00 0.00 0.00 5.25
3331 4949 5.220416 GCCGTTCACATGAGTTCAATAGTAC 60.220 44.000 0.00 0.00 0.00 2.73
3335 4953 2.670905 CGCCGTTCACATGAGTTCAATA 59.329 45.455 0.00 0.00 0.00 1.90
3366 4986 0.388649 AGACCGCAACAAGACGCTAG 60.389 55.000 0.00 0.00 0.00 3.42
3400 5020 4.467084 GGCGAAGGGACGATGCCA 62.467 66.667 0.00 0.00 45.06 4.92
3401 5021 3.757248 ATGGCGAAGGGACGATGCC 62.757 63.158 0.00 0.00 45.91 4.40
3427 5047 0.687354 AACCGAATGCTCTCACCACT 59.313 50.000 0.00 0.00 0.00 4.00
3428 5048 1.197721 CAAACCGAATGCTCTCACCAC 59.802 52.381 0.00 0.00 0.00 4.16
3464 5084 1.595993 CGACCTGGACCATGTCTCGT 61.596 60.000 22.72 2.16 32.47 4.18
3535 5156 2.746803 GGATTACACCGCACGCACC 61.747 63.158 0.00 0.00 0.00 5.01
3536 5157 1.366111 ATGGATTACACCGCACGCAC 61.366 55.000 0.00 0.00 0.00 5.34
3537 5158 1.078778 ATGGATTACACCGCACGCA 60.079 52.632 0.00 0.00 0.00 5.24
3538 5159 1.641677 GATGGATTACACCGCACGC 59.358 57.895 0.00 0.00 0.00 5.34
3539 5160 1.487452 CGGATGGATTACACCGCACG 61.487 60.000 0.00 0.00 37.11 5.34
3540 5161 0.461339 ACGGATGGATTACACCGCAC 60.461 55.000 0.00 0.00 43.16 5.34
3541 5162 0.179094 GACGGATGGATTACACCGCA 60.179 55.000 0.00 0.00 43.16 5.69
3542 5163 1.213094 CGACGGATGGATTACACCGC 61.213 60.000 0.00 0.00 43.16 5.68
3608 5233 1.557371 GGTTGGAGGAGAGAAGAAGGG 59.443 57.143 0.00 0.00 0.00 3.95
3691 5317 1.518133 CGCCTCGGAAGCTCAGAAG 60.518 63.158 0.00 0.00 0.00 2.85
3722 5351 0.458889 GTCTGCTCTGCTCTGCTCTG 60.459 60.000 0.00 0.00 0.00 3.35
3741 5374 4.388378 TCTCTCAATCTGATCAGCTGTG 57.612 45.455 18.36 16.42 0.00 3.66
3742 5375 4.650131 TCATCTCTCAATCTGATCAGCTGT 59.350 41.667 18.36 3.64 0.00 4.40
3743 5376 5.203060 TCATCTCTCAATCTGATCAGCTG 57.797 43.478 18.36 16.42 0.00 4.24
3746 5379 4.833938 TCCCTCATCTCTCAATCTGATCAG 59.166 45.833 17.07 17.07 0.00 2.90
3747 5380 4.812653 TCCCTCATCTCTCAATCTGATCA 58.187 43.478 0.00 0.00 0.00 2.92
3748 5381 5.078949 TCTCCCTCATCTCTCAATCTGATC 58.921 45.833 0.00 0.00 0.00 2.92
3749 5382 5.077369 TCTCCCTCATCTCTCAATCTGAT 57.923 43.478 0.00 0.00 0.00 2.90
3750 5383 4.533001 TCTCCCTCATCTCTCAATCTGA 57.467 45.455 0.00 0.00 0.00 3.27
3751 5384 4.833938 TGATCTCCCTCATCTCTCAATCTG 59.166 45.833 0.00 0.00 0.00 2.90
3755 5388 5.245751 GCTTATGATCTCCCTCATCTCTCAA 59.754 44.000 0.00 0.00 37.13 3.02
3756 5389 4.771577 GCTTATGATCTCCCTCATCTCTCA 59.228 45.833 0.00 0.00 37.13 3.27


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

AutoCloner maintained by Alex Coulton.