Multiple sequence alignment - TraesCS1D01G407000

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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 TraesCS1D01G407000 chr1D 100.000 2840 0 0 1 2840 470313000 470310161 0.000000e+00 5245
1 TraesCS1D01G407000 chr1D 84.551 1424 110 67 503 1853 470340071 470338685 0.000000e+00 1310
2 TraesCS1D01G407000 chr1D 82.996 247 21 13 133 367 470340853 470340616 1.330000e-48 204
3 TraesCS1D01G407000 chr1B 87.816 1699 116 41 544 2198 652926288 652924637 0.000000e+00 1906
4 TraesCS1D01G407000 chr1B 84.483 1044 100 27 1017 2005 653039779 653038743 0.000000e+00 974
5 TraesCS1D01G407000 chr1B 89.817 491 19 7 1 484 652926842 652926376 4.050000e-168 601
6 TraesCS1D01G407000 chr1B 87.115 520 51 16 2322 2840 652924600 652924096 2.450000e-160 575
7 TraesCS1D01G407000 chr1B 82.353 323 17 5 632 923 653040207 653039894 7.860000e-61 244
8 TraesCS1D01G407000 chr1A 82.921 1616 132 64 503 2005 564041357 564039773 0.000000e+00 1323
9 TraesCS1D01G407000 chr1A 87.549 1012 76 20 1348 2317 563989677 563988674 0.000000e+00 1125
10 TraesCS1D01G407000 chr1A 90.068 292 23 5 110 398 563989989 563989701 9.610000e-100 374
11 TraesCS1D01G407000 chr1A 88.462 260 27 1 2584 2840 563988187 563987928 7.640000e-81 311
12 TraesCS1D01G407000 chr1A 81.749 263 24 14 133 379 564042118 564041864 6.210000e-47 198
13 TraesCS1D01G407000 chr5A 84.012 344 48 5 2398 2740 619338388 619338725 9.810000e-85 324
14 TraesCS1D01G407000 chr3D 83.626 342 48 7 2402 2740 514372243 514371907 5.910000e-82 315
15 TraesCS1D01G407000 chr3D 84.270 267 39 3 2473 2738 364266388 364266124 1.010000e-64 257
16 TraesCS1D01G407000 chr6D 83.587 329 47 3 2413 2741 367138506 367138185 4.600000e-78 302
17 TraesCS1D01G407000 chr2A 81.921 354 54 7 2393 2740 177705794 177706143 9.950000e-75 291
18 TraesCS1D01G407000 chr2B 82.635 334 50 6 2410 2740 117751828 117752156 3.580000e-74 289
19 TraesCS1D01G407000 chr3B 85.240 271 36 3 2471 2740 474411996 474411729 2.790000e-70 276
20 TraesCS1D01G407000 chr5B 83.913 230 19 15 133 356 3901493 3901276 1.330000e-48 204
21 TraesCS1D01G407000 chr6B 86.010 193 17 9 139 325 502022550 502022362 6.210000e-47 198
22 TraesCS1D01G407000 chr7B 84.925 199 19 10 133 325 710079735 710079542 1.040000e-44 191


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 TraesCS1D01G407000 chr1D 470310161 470313000 2839 True 5245.000000 5245 100.000000 1 2840 1 chr1D.!!$R1 2839
1 TraesCS1D01G407000 chr1D 470338685 470340853 2168 True 757.000000 1310 83.773500 133 1853 2 chr1D.!!$R2 1720
2 TraesCS1D01G407000 chr1B 652924096 652926842 2746 True 1027.333333 1906 88.249333 1 2840 3 chr1B.!!$R1 2839
3 TraesCS1D01G407000 chr1B 653038743 653040207 1464 True 609.000000 974 83.418000 632 2005 2 chr1B.!!$R2 1373
4 TraesCS1D01G407000 chr1A 564039773 564042118 2345 True 760.500000 1323 82.335000 133 2005 2 chr1A.!!$R2 1872
5 TraesCS1D01G407000 chr1A 563987928 563989989 2061 True 603.333333 1125 88.693000 110 2840 3 chr1A.!!$R1 2730

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
487 855 0.035176 TACGGCCAACAGGTACCAAC 59.965 55.0 15.94 0.0 0.00 3.77 F
1332 1937 0.037326 CGTTGCCCAAGAGCTACAGA 60.037 55.0 0.00 0.0 38.23 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1661 2275 0.242286 CTGATCGGAGCCTCCATACG 59.758 60.0 12.13 0.0 35.91 3.06 R
2746 3705 0.111253 CCTTATGGGCCCATCTGTCC 59.889 60.0 40.77 1.7 37.82 4.02 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
26 27 1.204146 GATGGGAGCAAGTGGGTCTA 58.796 55.000 0.00 0.00 43.58 2.59
32 33 0.602905 AGCAAGTGGGTCTACGTTGC 60.603 55.000 0.00 0.00 43.11 4.17
36 37 0.685097 AGTGGGTCTACGTTGCATGT 59.315 50.000 0.00 0.00 0.00 3.21
101 103 7.951347 ATCAAGCAACTGGATTTTTCTAGAT 57.049 32.000 0.00 0.00 0.00 1.98
152 156 5.796424 AGTCAAGCAACTGGATTCAATTT 57.204 34.783 0.00 0.00 0.00 1.82
307 325 4.103153 AGAATCGATGGGGATGTTGTATGT 59.897 41.667 0.00 0.00 0.00 2.29
310 328 3.133691 CGATGGGGATGTTGTATGTGAG 58.866 50.000 0.00 0.00 0.00 3.51
318 336 7.092623 TGGGGATGTTGTATGTGAGTACTAATT 60.093 37.037 0.00 0.00 0.00 1.40
352 376 7.431376 CGTAACTAGTACAACATACATGACTGG 59.569 40.741 0.00 0.00 32.45 4.00
398 423 7.280428 CAGCAGTCAGTCAAATTCTCTTCATAT 59.720 37.037 0.00 0.00 0.00 1.78
399 424 8.481314 AGCAGTCAGTCAAATTCTCTTCATATA 58.519 33.333 0.00 0.00 0.00 0.86
400 425 9.270640 GCAGTCAGTCAAATTCTCTTCATATAT 57.729 33.333 0.00 0.00 0.00 0.86
433 801 3.068873 TGACTAAACCACACCAAATTGCC 59.931 43.478 0.00 0.00 0.00 4.52
438 806 2.114616 ACCACACCAAATTGCCTCAAA 58.885 42.857 0.00 0.00 0.00 2.69
472 840 6.755461 CTGAAAGTATGCAACTCTATACGG 57.245 41.667 0.00 0.00 37.50 4.02
487 855 0.035176 TACGGCCAACAGGTACCAAC 59.965 55.000 15.94 0.00 0.00 3.77
488 856 1.072505 CGGCCAACAGGTACCAACT 59.927 57.895 15.94 0.00 0.00 3.16
490 858 0.400594 GGCCAACAGGTACCAACTCT 59.599 55.000 15.94 0.00 0.00 3.24
491 859 1.626825 GGCCAACAGGTACCAACTCTA 59.373 52.381 15.94 0.00 0.00 2.43
519 1020 9.918630 ACTACTAGAACAAATACAATTGTACGT 57.081 29.630 20.26 14.37 42.49 3.57
522 1023 9.918630 ACTAGAACAAATACAATTGTACGTAGT 57.081 29.630 20.26 13.88 42.49 2.73
540 1041 1.346395 AGTAGGTCAAATGTGCGTGGA 59.654 47.619 0.00 0.00 0.00 4.02
583 1084 1.139654 TGAGCTGACCTATGCATCACC 59.860 52.381 0.19 0.00 0.00 4.02
584 1085 0.105593 AGCTGACCTATGCATCACCG 59.894 55.000 0.19 0.00 0.00 4.94
585 1086 0.179073 GCTGACCTATGCATCACCGT 60.179 55.000 0.19 0.00 0.00 4.83
586 1087 1.743772 GCTGACCTATGCATCACCGTT 60.744 52.381 0.19 0.00 0.00 4.44
587 1088 1.935873 CTGACCTATGCATCACCGTTG 59.064 52.381 0.19 0.00 0.00 4.10
588 1089 0.657840 GACCTATGCATCACCGTTGC 59.342 55.000 0.19 0.00 40.55 4.17
601 1111 3.006940 CACCGTTGCATACATGGTTACT 58.993 45.455 0.00 0.00 33.81 2.24
602 1112 3.063452 CACCGTTGCATACATGGTTACTC 59.937 47.826 0.00 0.00 33.81 2.59
603 1113 3.055385 ACCGTTGCATACATGGTTACTCT 60.055 43.478 0.00 0.00 32.55 3.24
604 1114 4.160814 ACCGTTGCATACATGGTTACTCTA 59.839 41.667 0.00 0.00 32.55 2.43
605 1115 4.506654 CCGTTGCATACATGGTTACTCTAC 59.493 45.833 0.00 0.00 0.00 2.59
606 1116 5.348986 CGTTGCATACATGGTTACTCTACT 58.651 41.667 0.00 0.00 0.00 2.57
624 1141 3.895232 ACTCATGCGATTAGTCAACCT 57.105 42.857 0.00 0.00 0.00 3.50
704 1221 0.442310 ATGCATGCACACGTACGAAC 59.558 50.000 25.37 8.37 0.00 3.95
770 1319 3.255725 CGGTTGAATTTCTGCATTGCAT 58.744 40.909 12.53 0.00 38.13 3.96
771 1320 3.061563 CGGTTGAATTTCTGCATTGCATG 59.938 43.478 12.53 6.76 38.13 4.06
867 1416 3.508840 GGGAATCGCCAACTGCCG 61.509 66.667 0.00 0.00 38.95 5.69
907 1460 0.312102 CACGAGCTCGGCAGATCATA 59.688 55.000 36.93 0.00 44.95 2.15
976 1548 9.844257 AGGGAGAATTAATTCAGAGATTGTTAG 57.156 33.333 26.02 0.00 39.23 2.34
986 1558 5.972935 TCAGAGATTGTTAGTATTCGGCAA 58.027 37.500 0.00 0.00 0.00 4.52
1075 1665 2.415608 ATCATGACCGAGACGCCGT 61.416 57.895 0.00 0.00 0.00 5.68
1077 1667 4.175489 ATGACCGAGACGCCGTCG 62.175 66.667 12.13 0.94 37.67 5.12
1332 1937 0.037326 CGTTGCCCAAGAGCTACAGA 60.037 55.000 0.00 0.00 38.23 3.41
1669 2289 1.878522 GTCACTGCGGCGTATGGAG 60.879 63.158 9.37 0.00 0.00 3.86
1758 2384 1.006220 TGTGATGAGCGCTGACGTT 60.006 52.632 18.48 0.00 42.83 3.99
1771 2397 1.374758 GACGTTGGAGGAGCTGTGG 60.375 63.158 0.00 0.00 0.00 4.17
1856 2496 4.214971 GCTATGATGGTGGTGATGATCAAC 59.785 45.833 2.92 2.92 33.88 3.18
1867 2535 8.085296 GGTGGTGATGATCAACTAGTTAGATAG 58.915 40.741 12.25 0.00 34.53 2.08
1936 2604 2.227388 GAGAAAGCAAAGCTAGCTGCAA 59.773 45.455 25.52 0.00 42.53 4.08
1937 2605 2.030451 AGAAAGCAAAGCTAGCTGCAAC 60.030 45.455 25.52 17.04 42.53 4.17
2000 2669 9.177304 GTATGCACAAAGATATGATTGATTGTG 57.823 33.333 11.04 11.04 46.28 3.33
2034 2703 6.377996 ACATGTATGTGCAATTGATTAGGTGT 59.622 34.615 10.34 1.19 40.03 4.16
2139 2817 5.096443 AGAGGAAGGTGATCTAAAAGCTG 57.904 43.478 0.00 0.00 0.00 4.24
2144 2822 4.640771 AGGTGATCTAAAAGCTGGACAA 57.359 40.909 0.00 0.00 0.00 3.18
2162 2841 0.178961 AACCTTGACCTTCCCTTGGC 60.179 55.000 0.00 0.00 0.00 4.52
2165 2844 0.674895 CTTGACCTTCCCTTGGCGAG 60.675 60.000 0.00 0.00 0.00 5.03
2203 2882 1.264020 CAACAGTTGGGATCACACGTG 59.736 52.381 15.48 15.48 0.00 4.49
2204 2883 0.250295 ACAGTTGGGATCACACGTGG 60.250 55.000 21.57 9.11 0.00 4.94
2206 2885 0.762418 AGTTGGGATCACACGTGGAA 59.238 50.000 21.57 7.61 0.00 3.53
2208 2887 1.950909 GTTGGGATCACACGTGGAAAA 59.049 47.619 21.57 2.02 0.00 2.29
2230 2926 0.443869 ATGCTCAATTCACACGTCGC 59.556 50.000 0.00 0.00 0.00 5.19
2231 2927 1.132640 GCTCAATTCACACGTCGCC 59.867 57.895 0.00 0.00 0.00 5.54
2232 2928 1.565156 GCTCAATTCACACGTCGCCA 61.565 55.000 0.00 0.00 0.00 5.69
2237 2933 1.298157 ATTCACACGTCGCCATGTGG 61.298 55.000 8.58 0.00 45.16 4.17
2238 2934 3.422303 CACACGTCGCCATGTGGG 61.422 66.667 8.58 0.00 43.07 4.61
2240 2936 4.697756 CACGTCGCCATGTGGGGT 62.698 66.667 14.74 0.00 46.93 4.95
2245 2941 3.520862 CGCCATGTGGGGTGATGC 61.521 66.667 7.86 0.00 42.54 3.91
2291 2991 2.605837 TGACTTGTGTGTAAGCCGAA 57.394 45.000 0.00 0.00 0.00 4.30
2292 2992 3.120321 TGACTTGTGTGTAAGCCGAAT 57.880 42.857 0.00 0.00 0.00 3.34
2317 3017 5.365314 AGGAAATAAAGAACCCACAGCAAAA 59.635 36.000 0.00 0.00 0.00 2.44
2318 3018 6.052360 GGAAATAAAGAACCCACAGCAAAAA 58.948 36.000 0.00 0.00 0.00 1.94
2347 3306 1.148157 CCAGCTCGACTTACATGGCG 61.148 60.000 0.00 0.00 0.00 5.69
2363 3322 2.564975 CGGTAAGGCGAGACGTGT 59.435 61.111 0.00 0.00 0.00 4.49
2400 3359 6.314648 TCTCTGCTTATACAAAATGCTCACAG 59.685 38.462 0.00 0.00 0.00 3.66
2418 3377 4.471747 TCACAGTGGTAATGCCCATAGTTA 59.528 41.667 0.00 0.00 36.74 2.24
2425 3384 4.022329 GGTAATGCCCATAGTTATGCCAAC 60.022 45.833 0.00 0.00 32.40 3.77
2429 3388 4.861196 TGCCCATAGTTATGCCAACTTTA 58.139 39.130 6.16 0.00 32.40 1.85
2431 3390 4.278419 GCCCATAGTTATGCCAACTTTAGG 59.722 45.833 6.16 3.33 32.40 2.69
2440 3399 9.695155 AGTTATGCCAACTTTAGGTATGTTATT 57.305 29.630 0.00 0.00 33.35 1.40
2446 3405 9.297037 GCCAACTTTAGGTATGTTATTATGGAT 57.703 33.333 0.00 0.00 0.00 3.41
2452 3411 8.630054 TTAGGTATGTTATTATGGATTGTGCC 57.370 34.615 0.00 0.00 0.00 5.01
2453 3412 6.609876 AGGTATGTTATTATGGATTGTGCCA 58.390 36.000 0.00 0.00 43.23 4.92
2462 3421 2.377073 TGGATTGTGCCATGTATGTGG 58.623 47.619 0.00 0.00 42.35 4.17
2463 3422 2.291475 TGGATTGTGCCATGTATGTGGT 60.291 45.455 0.00 0.00 41.47 4.16
2464 3423 2.358898 GGATTGTGCCATGTATGTGGTC 59.641 50.000 0.00 0.00 41.47 4.02
2465 3424 2.575805 TTGTGCCATGTATGTGGTCA 57.424 45.000 0.00 0.00 41.47 4.02
2474 3433 5.593968 CCATGTATGTGGTCAATTTCCATG 58.406 41.667 2.93 0.00 37.30 3.66
2500 3459 1.250328 TGCCTTGAACTCCATGCAAG 58.750 50.000 0.00 0.00 38.90 4.01
2516 3475 7.801104 TCCATGCAAGTTCATACTAAATAGGA 58.199 34.615 0.00 0.00 33.17 2.94
2608 3567 5.597806 CACATAAGATGGCTCAATGCAAAT 58.402 37.500 0.00 0.00 45.15 2.32
2627 3586 5.220719 GCAAATGCATTCCTATTTTTGAGGC 60.221 40.000 13.38 0.00 41.59 4.70
2628 3587 5.945144 AATGCATTCCTATTTTTGAGGCT 57.055 34.783 5.99 0.00 33.73 4.58
2688 3647 2.880443 ACTTGCAATGTGGACCATTCT 58.120 42.857 0.00 0.00 41.93 2.40
2746 3705 1.302431 TTCATGCACCACTCACCCG 60.302 57.895 0.00 0.00 0.00 5.28
2791 3750 3.258372 GTCCCACACATCAGTAACTGAGA 59.742 47.826 0.00 0.00 44.08 3.27
2801 3760 1.817447 AGTAACTGAGACCACCTACGC 59.183 52.381 0.00 0.00 0.00 4.42
2825 3787 2.033448 TGCCGCTAACAAGGGGTG 59.967 61.111 9.85 0.00 43.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.900122 GCAAGTCATACATGCAACGT 57.100 45.000 0.00 0.00 41.89 3.99
46 47 0.899019 TCACAAGCCATGCATGCAAT 59.101 45.000 26.68 10.65 29.81 3.56
68 69 4.873817 TCCAGTTGCTTGATTGTGATTTG 58.126 39.130 0.00 0.00 0.00 2.32
74 75 6.165700 AGAAAAATCCAGTTGCTTGATTGT 57.834 33.333 0.00 0.00 28.47 2.71
75 76 7.596494 TCTAGAAAAATCCAGTTGCTTGATTG 58.404 34.615 0.00 0.00 28.47 2.67
76 77 7.765695 TCTAGAAAAATCCAGTTGCTTGATT 57.234 32.000 0.00 0.00 28.94 2.57
152 156 6.127423 CCGTAGAGGTCTGATTTTCTTCCTTA 60.127 42.308 0.00 0.00 34.51 2.69
211 222 1.362237 TCCCTTCATGGCCAAGGAAAT 59.638 47.619 21.63 0.00 42.94 2.17
318 336 9.825972 GTATGTTGTACTAGTTACGACTAAACA 57.174 33.333 0.00 1.57 43.36 2.83
334 354 5.720202 TCTGACCAGTCATGTATGTTGTAC 58.280 41.667 0.04 0.00 39.13 2.90
335 355 5.714806 TCTCTGACCAGTCATGTATGTTGTA 59.285 40.000 0.04 0.00 39.13 2.41
336 356 4.528206 TCTCTGACCAGTCATGTATGTTGT 59.472 41.667 0.04 0.00 39.13 3.32
337 357 5.077134 TCTCTGACCAGTCATGTATGTTG 57.923 43.478 0.04 0.00 39.13 3.33
338 358 5.012046 TGTTCTCTGACCAGTCATGTATGTT 59.988 40.000 0.04 0.00 39.13 2.71
339 359 4.528206 TGTTCTCTGACCAGTCATGTATGT 59.472 41.667 0.04 0.00 39.13 2.29
340 360 4.867047 GTGTTCTCTGACCAGTCATGTATG 59.133 45.833 0.04 0.00 39.13 2.39
352 376 7.547370 ACTGCTGATATTTTAGTGTTCTCTGAC 59.453 37.037 0.00 0.00 0.00 3.51
398 423 7.654520 GTGTGGTTTAGTCACAACTGAACTATA 59.345 37.037 11.45 3.51 46.12 1.31
399 424 6.482308 GTGTGGTTTAGTCACAACTGAACTAT 59.518 38.462 11.45 0.00 46.12 2.12
400 425 5.813672 GTGTGGTTTAGTCACAACTGAACTA 59.186 40.000 11.45 4.68 46.12 2.24
401 426 4.634443 GTGTGGTTTAGTCACAACTGAACT 59.366 41.667 11.45 0.49 46.12 3.01
472 840 3.629142 ATAGAGTTGGTACCTGTTGGC 57.371 47.619 14.36 0.00 36.63 4.52
508 1009 7.117236 CACATTTGACCTACTACGTACAATTGT 59.883 37.037 16.68 16.68 34.53 2.71
509 1010 7.453034 CACATTTGACCTACTACGTACAATTG 58.547 38.462 3.24 3.24 0.00 2.32
510 1011 6.091713 GCACATTTGACCTACTACGTACAATT 59.908 38.462 0.00 0.00 0.00 2.32
511 1012 5.579511 GCACATTTGACCTACTACGTACAAT 59.420 40.000 0.00 0.00 0.00 2.71
512 1013 4.925054 GCACATTTGACCTACTACGTACAA 59.075 41.667 0.00 0.00 0.00 2.41
513 1014 4.487948 GCACATTTGACCTACTACGTACA 58.512 43.478 0.00 0.00 0.00 2.90
514 1015 3.545078 CGCACATTTGACCTACTACGTAC 59.455 47.826 0.00 0.00 0.00 3.67
515 1016 3.191162 ACGCACATTTGACCTACTACGTA 59.809 43.478 0.00 0.00 0.00 3.57
516 1017 2.029649 ACGCACATTTGACCTACTACGT 60.030 45.455 0.00 0.00 0.00 3.57
517 1018 2.344441 CACGCACATTTGACCTACTACG 59.656 50.000 0.00 0.00 0.00 3.51
518 1019 2.671396 CCACGCACATTTGACCTACTAC 59.329 50.000 0.00 0.00 0.00 2.73
519 1020 2.563620 TCCACGCACATTTGACCTACTA 59.436 45.455 0.00 0.00 0.00 1.82
520 1021 1.346395 TCCACGCACATTTGACCTACT 59.654 47.619 0.00 0.00 0.00 2.57
521 1022 1.803334 TCCACGCACATTTGACCTAC 58.197 50.000 0.00 0.00 0.00 3.18
522 1023 2.779755 ATCCACGCACATTTGACCTA 57.220 45.000 0.00 0.00 0.00 3.08
523 1024 2.290008 TGTATCCACGCACATTTGACCT 60.290 45.455 0.00 0.00 0.00 3.85
524 1025 2.080693 TGTATCCACGCACATTTGACC 58.919 47.619 0.00 0.00 0.00 4.02
525 1026 3.000041 TCTGTATCCACGCACATTTGAC 59.000 45.455 0.00 0.00 0.00 3.18
526 1027 3.261580 CTCTGTATCCACGCACATTTGA 58.738 45.455 0.00 0.00 0.00 2.69
527 1028 2.223112 GCTCTGTATCCACGCACATTTG 60.223 50.000 0.00 0.00 0.00 2.32
528 1029 2.009774 GCTCTGTATCCACGCACATTT 58.990 47.619 0.00 0.00 0.00 2.32
529 1030 1.066215 TGCTCTGTATCCACGCACATT 60.066 47.619 0.00 0.00 0.00 2.71
530 1031 0.536724 TGCTCTGTATCCACGCACAT 59.463 50.000 0.00 0.00 0.00 3.21
531 1032 1.971418 TGCTCTGTATCCACGCACA 59.029 52.632 0.00 0.00 0.00 4.57
532 1033 2.373938 GTGCTCTGTATCCACGCAC 58.626 57.895 0.00 0.00 43.22 5.34
533 1034 0.320050 TTGTGCTCTGTATCCACGCA 59.680 50.000 0.00 0.00 32.32 5.24
534 1035 1.438651 TTTGTGCTCTGTATCCACGC 58.561 50.000 0.00 0.00 32.32 5.34
535 1036 2.223112 GCATTTGTGCTCTGTATCCACG 60.223 50.000 0.00 0.00 32.32 4.94
540 1041 2.794103 TGTGGCATTTGTGCTCTGTAT 58.206 42.857 0.00 0.00 34.73 2.29
550 1051 2.089201 TCAGCTCAGATGTGGCATTTG 58.911 47.619 0.00 0.00 0.00 2.32
558 1059 2.113807 TGCATAGGTCAGCTCAGATGT 58.886 47.619 0.00 0.00 0.00 3.06
561 1062 2.102084 GTGATGCATAGGTCAGCTCAGA 59.898 50.000 0.00 0.00 0.00 3.27
583 1084 5.348986 AGTAGAGTAACCATGTATGCAACG 58.651 41.667 0.00 0.00 0.00 4.10
584 1085 6.338146 TGAGTAGAGTAACCATGTATGCAAC 58.662 40.000 0.00 0.00 0.00 4.17
585 1086 6.538945 TGAGTAGAGTAACCATGTATGCAA 57.461 37.500 0.00 0.00 0.00 4.08
586 1087 6.515832 CATGAGTAGAGTAACCATGTATGCA 58.484 40.000 0.00 0.00 32.34 3.96
587 1088 5.406780 GCATGAGTAGAGTAACCATGTATGC 59.593 44.000 0.00 0.00 37.51 3.14
588 1089 5.631096 CGCATGAGTAGAGTAACCATGTATG 59.369 44.000 0.00 0.00 37.51 2.39
591 1092 3.699538 TCGCATGAGTAGAGTAACCATGT 59.300 43.478 0.00 0.00 37.51 3.21
601 1111 4.645136 AGGTTGACTAATCGCATGAGTAGA 59.355 41.667 6.75 0.00 43.71 2.59
602 1112 4.938080 AGGTTGACTAATCGCATGAGTAG 58.062 43.478 0.00 0.00 45.81 2.57
603 1113 5.339008 AAGGTTGACTAATCGCATGAGTA 57.661 39.130 0.00 0.00 0.00 2.59
604 1114 3.895232 AGGTTGACTAATCGCATGAGT 57.105 42.857 0.00 0.00 0.00 3.41
605 1115 5.233050 CAGTAAGGTTGACTAATCGCATGAG 59.767 44.000 0.00 0.00 0.00 2.90
606 1116 5.109210 CAGTAAGGTTGACTAATCGCATGA 58.891 41.667 0.00 0.00 0.00 3.07
624 1141 6.379988 GGGATATGCTTTCTTTTTCCCAGTAA 59.620 38.462 0.00 0.00 40.87 2.24
690 1207 1.065436 TTCGGTTCGTACGTGTGCA 59.935 52.632 16.05 0.00 0.00 4.57
691 1208 1.208009 TGTTCGGTTCGTACGTGTGC 61.208 55.000 16.05 4.07 30.11 4.57
692 1209 1.384409 GATGTTCGGTTCGTACGTGTG 59.616 52.381 16.05 4.30 30.11 3.82
693 1210 1.666888 GGATGTTCGGTTCGTACGTGT 60.667 52.381 16.05 0.00 30.11 4.49
704 1221 2.292267 CAGGAATTCAGGGATGTTCGG 58.708 52.381 7.93 0.00 0.00 4.30
934 1487 2.100031 CCTGTGATAACGCTGCGCA 61.100 57.895 23.51 10.98 0.00 6.09
976 1548 0.739813 AGCACTCCGTTGCCGAATAC 60.740 55.000 0.00 0.00 44.14 1.89
986 1558 2.903357 CCATGGCTAGCACTCCGT 59.097 61.111 18.24 0.00 0.00 4.69
992 1564 2.029518 CGATCGCCATGGCTAGCA 59.970 61.111 33.07 15.31 39.32 3.49
1274 1876 2.511145 CGCTCTGCTGCCCTTCTC 60.511 66.667 0.00 0.00 0.00 2.87
1275 1877 4.774503 GCGCTCTGCTGCCCTTCT 62.775 66.667 0.00 0.00 41.73 2.85
1299 1901 4.947147 AACGCGGCCTTGCTTCCA 62.947 61.111 12.47 0.00 0.00 3.53
1651 2265 1.878522 CTCCATACGCCGCAGTGAC 60.879 63.158 0.00 0.00 0.00 3.67
1656 2270 4.221422 GAGCCTCCATACGCCGCA 62.221 66.667 0.00 0.00 0.00 5.69
1661 2275 0.242286 CTGATCGGAGCCTCCATACG 59.758 60.000 12.13 0.00 35.91 3.06
1669 2289 0.249657 GACACCATCTGATCGGAGCC 60.250 60.000 10.61 0.00 0.00 4.70
1758 2384 1.000359 TCGATCCACAGCTCCTCCA 60.000 57.895 0.00 0.00 0.00 3.86
1867 2535 8.208903 ACATACTCCAATATAACCACACCTAAC 58.791 37.037 0.00 0.00 0.00 2.34
1936 2604 5.069648 TGAAATTAGATCAGCAGGAGATCGT 59.930 40.000 0.00 0.00 45.05 3.73
1937 2605 5.536260 TGAAATTAGATCAGCAGGAGATCG 58.464 41.667 0.00 0.00 45.05 3.69
2139 2817 0.771755 AGGGAAGGTCAAGGTTGTCC 59.228 55.000 0.00 0.00 36.76 4.02
2144 2822 1.460699 GCCAAGGGAAGGTCAAGGT 59.539 57.895 0.00 0.00 0.00 3.50
2162 2841 1.800681 GGTTCCCGCAATTTCCTCG 59.199 57.895 0.00 0.00 0.00 4.63
2188 2867 1.600023 TTTCCACGTGTGATCCCAAC 58.400 50.000 15.65 0.00 0.00 3.77
2208 2887 3.554524 CGACGTGTGAATTGAGCATTTT 58.445 40.909 0.00 0.00 0.00 1.82
2210 2889 1.135972 GCGACGTGTGAATTGAGCATT 60.136 47.619 0.00 0.00 0.00 3.56
2211 2890 0.443869 GCGACGTGTGAATTGAGCAT 59.556 50.000 0.00 0.00 0.00 3.79
2212 2891 1.565156 GGCGACGTGTGAATTGAGCA 61.565 55.000 0.00 0.00 0.00 4.26
2213 2892 1.132640 GGCGACGTGTGAATTGAGC 59.867 57.895 0.00 0.00 0.00 4.26
2216 2895 3.294908 CATGGCGACGTGTGAATTG 57.705 52.632 1.00 0.00 42.59 2.32
2228 2924 3.520862 GCATCACCCCACATGGCG 61.521 66.667 0.00 0.00 0.00 5.69
2230 2926 2.409055 CGTGCATCACCCCACATGG 61.409 63.158 0.00 0.00 32.37 3.66
2231 2927 3.055080 GCGTGCATCACCCCACATG 62.055 63.158 0.00 0.00 32.37 3.21
2232 2928 2.751436 GCGTGCATCACCCCACAT 60.751 61.111 0.00 0.00 32.37 3.21
2237 2933 4.760047 ACTCGGCGTGCATCACCC 62.760 66.667 6.85 0.00 0.00 4.61
2238 2934 3.490759 CACTCGGCGTGCATCACC 61.491 66.667 6.85 0.00 36.72 4.02
2257 2953 5.331902 CACAAGTCAAGTACCTGTGTTTTG 58.668 41.667 0.00 0.00 42.99 2.44
2265 2961 4.377897 GCTTACACACAAGTCAAGTACCT 58.622 43.478 0.00 0.00 0.00 3.08
2274 2970 3.259876 TCCTATTCGGCTTACACACAAGT 59.740 43.478 0.00 0.00 0.00 3.16
2291 2991 5.826643 TGCTGTGGGTTCTTTATTTCCTAT 58.173 37.500 0.00 0.00 0.00 2.57
2292 2992 5.249780 TGCTGTGGGTTCTTTATTTCCTA 57.750 39.130 0.00 0.00 0.00 2.94
2317 3017 8.556213 TGTAAGTCGAGCTGGTTTATTTATTT 57.444 30.769 0.00 0.00 0.00 1.40
2318 3018 8.612619 CATGTAAGTCGAGCTGGTTTATTTATT 58.387 33.333 0.00 0.00 0.00 1.40
2319 3019 7.226720 CCATGTAAGTCGAGCTGGTTTATTTAT 59.773 37.037 0.00 0.00 0.00 1.40
2320 3020 6.537301 CCATGTAAGTCGAGCTGGTTTATTTA 59.463 38.462 0.00 0.00 0.00 1.40
2321 3021 5.354234 CCATGTAAGTCGAGCTGGTTTATTT 59.646 40.000 0.00 0.00 0.00 1.40
2322 3022 4.876107 CCATGTAAGTCGAGCTGGTTTATT 59.124 41.667 0.00 0.00 0.00 1.40
2323 3023 4.442706 CCATGTAAGTCGAGCTGGTTTAT 58.557 43.478 0.00 0.00 0.00 1.40
2324 3024 3.857052 CCATGTAAGTCGAGCTGGTTTA 58.143 45.455 0.00 0.00 0.00 2.01
2325 3025 2.699954 CCATGTAAGTCGAGCTGGTTT 58.300 47.619 0.00 0.00 0.00 3.27
2326 3026 1.676014 GCCATGTAAGTCGAGCTGGTT 60.676 52.381 0.00 0.00 0.00 3.67
2329 3288 1.148157 CCGCCATGTAAGTCGAGCTG 61.148 60.000 0.00 0.00 0.00 4.24
2336 3295 0.461339 CGCCTTACCGCCATGTAAGT 60.461 55.000 12.03 0.00 43.97 2.24
2347 3306 2.352503 TTTACACGTCTCGCCTTACC 57.647 50.000 0.00 0.00 0.00 2.85
2400 3359 3.506067 GGCATAACTATGGGCATTACCAC 59.494 47.826 0.00 0.00 44.72 4.16
2418 3377 9.077885 CCATAATAACATACCTAAAGTTGGCAT 57.922 33.333 0.00 0.00 0.00 4.40
2429 3388 6.609876 TGGCACAATCCATAATAACATACCT 58.390 36.000 0.00 0.00 31.92 3.08
2451 3410 5.127519 ACATGGAAATTGACCACATACATGG 59.872 40.000 6.75 0.00 46.10 3.66
2452 3411 6.037726 CACATGGAAATTGACCACATACATG 58.962 40.000 6.75 0.00 40.36 3.21
2453 3412 5.394443 GCACATGGAAATTGACCACATACAT 60.394 40.000 6.75 0.00 40.36 2.29
2454 3413 4.082300 GCACATGGAAATTGACCACATACA 60.082 41.667 6.75 0.00 40.36 2.29
2455 3414 4.082300 TGCACATGGAAATTGACCACATAC 60.082 41.667 6.75 0.41 40.36 2.39
2456 3415 4.085009 TGCACATGGAAATTGACCACATA 58.915 39.130 6.75 0.00 40.36 2.29
2457 3416 2.898612 TGCACATGGAAATTGACCACAT 59.101 40.909 6.75 0.00 40.36 3.21
2458 3417 2.314246 TGCACATGGAAATTGACCACA 58.686 42.857 6.75 0.00 40.36 4.17
2459 3418 3.598019 ATGCACATGGAAATTGACCAC 57.402 42.857 6.75 0.00 40.36 4.16
2460 3419 4.441773 GCATATGCACATGGAAATTGACCA 60.442 41.667 22.84 7.01 41.59 4.02
2461 3420 4.053295 GCATATGCACATGGAAATTGACC 58.947 43.478 22.84 0.00 41.59 4.02
2462 3421 4.053295 GGCATATGCACATGGAAATTGAC 58.947 43.478 28.07 2.71 44.36 3.18
2463 3422 3.962063 AGGCATATGCACATGGAAATTGA 59.038 39.130 28.07 0.00 44.36 2.57
2464 3423 4.330944 AGGCATATGCACATGGAAATTG 57.669 40.909 28.07 0.00 44.36 2.32
2465 3424 4.406326 TCAAGGCATATGCACATGGAAATT 59.594 37.500 28.07 6.34 44.36 1.82
2474 3433 2.368439 TGGAGTTCAAGGCATATGCAC 58.632 47.619 28.07 17.11 44.36 4.57
2555 3514 8.485578 AGTTGGTGGGAAAAATCATAAACTTA 57.514 30.769 0.00 0.00 0.00 2.24
2564 3523 3.572255 TGCACTAGTTGGTGGGAAAAATC 59.428 43.478 0.00 0.00 37.65 2.17
2565 3524 3.320826 GTGCACTAGTTGGTGGGAAAAAT 59.679 43.478 10.32 0.00 37.65 1.82
2571 3530 2.779755 TATGTGCACTAGTTGGTGGG 57.220 50.000 19.41 0.00 37.65 4.61
2608 3567 5.743636 AAAGCCTCAAAAATAGGAATGCA 57.256 34.783 0.00 0.00 36.08 3.96
2655 3614 5.697633 CACATTGCAAGTTTGAGCCTATTTT 59.302 36.000 4.94 0.00 0.00 1.82
2661 3620 1.340889 TCCACATTGCAAGTTTGAGCC 59.659 47.619 4.94 0.00 0.00 4.70
2663 3622 2.361757 TGGTCCACATTGCAAGTTTGAG 59.638 45.455 4.94 0.00 0.00 3.02
2746 3705 0.111253 CCTTATGGGCCCATCTGTCC 59.889 60.000 40.77 1.70 37.82 4.02
2778 3737 3.695060 CGTAGGTGGTCTCAGTTACTGAT 59.305 47.826 15.91 1.63 39.92 2.90
2807 3766 2.040544 CACCCCTTGTTAGCGGCAG 61.041 63.158 1.45 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.