Multiple sequence alignment - TraesCS2B01G104500

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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 TraesCS2B01G104500 chr2B 100.000 3218 0 0 1 3218 65061458 65058241 0.000000e+00 5943
1 TraesCS2B01G104500 chr2B 89.000 100 11 0 1593 1692 65090323 65090224 1.210000e-24 124
2 TraesCS2B01G104500 chr2A 91.032 2509 152 37 729 3218 42188899 42186445 0.000000e+00 3319
3 TraesCS2B01G104500 chr2A 79.319 1204 234 8 1073 2261 42191221 42190018 0.000000e+00 830
4 TraesCS2B01G104500 chr2A 80.581 757 135 7 1572 2319 42199726 42198973 1.000000e-159 573
5 TraesCS2B01G104500 chr2A 87.766 188 22 1 133 319 42189214 42189027 5.410000e-53 219
6 TraesCS2B01G104500 chr2A 92.806 139 5 5 1 137 42189389 42189254 2.530000e-46 196
7 TraesCS2B01G104500 chr2D 77.722 1589 268 66 863 2411 37357329 37355787 0.000000e+00 894
8 TraesCS2B01G104500 chr2D 89.296 682 46 15 176 842 37358638 37357969 0.000000e+00 830
9 TraesCS2B01G104500 chr2D 78.361 305 47 16 1582 1885 37301023 37300737 2.550000e-41 180
10 TraesCS2B01G104500 chr2D 84.496 129 17 3 2938 3063 252532361 252532233 1.210000e-24 124
11 TraesCS2B01G104500 chr2D 84.496 129 17 3 2938 3063 302052805 302052677 1.210000e-24 124
12 TraesCS2B01G104500 chr2D 95.745 47 1 1 88 133 37358782 37358736 1.240000e-09 75
13 TraesCS2B01G104500 chr7D 82.909 275 31 10 2830 3095 490906344 490906077 1.930000e-57 233
14 TraesCS2B01G104500 chr7D 84.519 239 24 7 2867 3095 295433787 295434022 1.160000e-54 224
15 TraesCS2B01G104500 chr7B 82.105 285 37 8 2823 3097 527022678 527022398 6.940000e-57 231
16 TraesCS2B01G104500 chr4B 81.985 272 36 7 2826 3086 295182852 295182583 5.410000e-53 219
17 TraesCS2B01G104500 chr5D 83.682 239 26 7 2867 3095 246436867 246437102 2.510000e-51 213
18 TraesCS2B01G104500 chr5D 84.091 132 18 3 2935 3063 470205540 470205671 1.210000e-24 124
19 TraesCS2B01G104500 chr5D 83.088 136 20 3 2935 3067 88104224 88104359 1.570000e-23 121
20 TraesCS2B01G104500 chr6B 81.455 275 31 12 2834 3095 158263306 158263039 1.170000e-49 207
21 TraesCS2B01G104500 chr7A 79.152 283 40 13 2826 3095 555708968 555709244 9.170000e-41 178
22 TraesCS2B01G104500 chr1D 79.200 250 34 11 2858 3095 34519300 34519543 1.200000e-34 158
23 TraesCS2B01G104500 chr1D 84.496 129 17 3 2938 3063 316936945 316936817 1.210000e-24 124
24 TraesCS2B01G104500 chr1D 84.496 129 17 3 2938 3063 399097161 399097033 1.210000e-24 124
25 TraesCS2B01G104500 chr3B 85.271 129 16 3 2938 3063 445113358 445113230 2.610000e-26 130


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 TraesCS2B01G104500 chr2B 65058241 65061458 3217 True 5943.000000 5943 100.000000 1 3218 1 chr2B.!!$R1 3217
1 TraesCS2B01G104500 chr2A 42186445 42191221 4776 True 1141.000000 3319 87.730750 1 3218 4 chr2A.!!$R2 3217
2 TraesCS2B01G104500 chr2A 42198973 42199726 753 True 573.000000 573 80.581000 1572 2319 1 chr2A.!!$R1 747
3 TraesCS2B01G104500 chr2D 37355787 37358782 2995 True 599.666667 894 87.587667 88 2411 3 chr2D.!!$R4 2323

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
452 2358 0.394565 ACCAAGCTCTGTGAGTGACC 59.605 55.0 0.0 0.0 31.39 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2413 4993 0.992802 GTAGAGCGCAGAGGAAAACG 59.007 55.0 11.47 0.0 0.0 3.6 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
115 1949 7.686438 TTAGTGCATGATAGTGTTTGTGAAT 57.314 32.000 0.00 0.00 0.00 2.57
156 2033 1.338200 GGCCCTAAGATACGCCATGAG 60.338 57.143 0.00 0.00 41.25 2.90
202 2106 4.746535 AAAGAATTTTTGGAACACCGGT 57.253 36.364 0.00 0.00 39.29 5.28
289 2194 2.897326 GTTGTGGAGGGCCTATTTTTGT 59.103 45.455 5.73 0.00 34.31 2.83
310 2215 6.717903 TTGTGAGACAAATGCATACACAGCA 61.718 40.000 0.00 0.00 38.66 4.41
381 2286 1.002366 GTATGTTGGCACTGAGCTCG 58.998 55.000 9.64 6.63 44.79 5.03
422 2328 4.715713 AGGTTTGGTCCTTAACTGAAGAC 58.284 43.478 7.19 0.00 37.33 3.01
445 2351 1.151668 CCGAGAAACCAAGCTCTGTG 58.848 55.000 0.00 0.00 0.00 3.66
452 2358 0.394565 ACCAAGCTCTGTGAGTGACC 59.605 55.000 0.00 0.00 31.39 4.02
457 2363 1.203063 AGCTCTGTGAGTGACCTGGTA 60.203 52.381 0.00 0.00 31.39 3.25
473 2381 1.054978 GGTAGGAATCGCCTCCCCTT 61.055 60.000 0.00 0.00 46.97 3.95
543 2451 1.073768 GCGTCGAAAGCTCTCTGTCC 61.074 60.000 6.86 0.00 0.00 4.02
544 2452 0.523966 CGTCGAAAGCTCTCTGTCCT 59.476 55.000 0.00 0.00 0.00 3.85
547 2455 3.503891 GTCGAAAGCTCTCTGTCCTAAC 58.496 50.000 0.00 0.00 0.00 2.34
570 2483 4.742201 GCGCCTCTGCCGACTCAA 62.742 66.667 0.00 0.00 0.00 3.02
571 2484 2.048222 CGCCTCTGCCGACTCAAA 60.048 61.111 0.00 0.00 0.00 2.69
572 2485 1.448540 CGCCTCTGCCGACTCAAAT 60.449 57.895 0.00 0.00 0.00 2.32
573 2486 1.021390 CGCCTCTGCCGACTCAAATT 61.021 55.000 0.00 0.00 0.00 1.82
574 2487 0.449388 GCCTCTGCCGACTCAAATTG 59.551 55.000 0.00 0.00 0.00 2.32
575 2488 1.813513 CCTCTGCCGACTCAAATTGT 58.186 50.000 0.00 0.00 0.00 2.71
576 2489 2.935238 GCCTCTGCCGACTCAAATTGTA 60.935 50.000 0.00 0.00 0.00 2.41
577 2490 3.535561 CCTCTGCCGACTCAAATTGTAT 58.464 45.455 0.00 0.00 0.00 2.29
578 2491 4.693283 CCTCTGCCGACTCAAATTGTATA 58.307 43.478 0.00 0.00 0.00 1.47
579 2492 4.747108 CCTCTGCCGACTCAAATTGTATAG 59.253 45.833 0.00 0.00 0.00 1.31
580 2493 5.451937 CCTCTGCCGACTCAAATTGTATAGA 60.452 44.000 0.00 0.00 0.00 1.98
581 2494 6.161855 TCTGCCGACTCAAATTGTATAGAT 57.838 37.500 0.00 0.00 0.00 1.98
582 2495 6.216569 TCTGCCGACTCAAATTGTATAGATC 58.783 40.000 0.00 0.00 0.00 2.75
583 2496 5.912892 TGCCGACTCAAATTGTATAGATCA 58.087 37.500 0.00 0.00 0.00 2.92
621 2534 1.536766 TGGACTCGCTTGCTTGATTTG 59.463 47.619 0.00 0.00 0.00 2.32
638 2551 1.568504 TTGCTTCCGTGGGAGATACT 58.431 50.000 0.00 0.00 31.21 2.12
681 2598 0.674269 TGGAATAAACCACGGCGTCC 60.674 55.000 10.85 6.35 34.77 4.79
682 2599 0.674269 GGAATAAACCACGGCGTCCA 60.674 55.000 10.85 0.00 0.00 4.02
699 2616 3.249189 AGTCCGGCCCAAGCTTGA 61.249 61.111 28.05 3.34 39.73 3.02
761 2691 8.194433 TCTGTGCTATAGTATATACTACGTGC 57.806 38.462 22.07 22.67 41.18 5.34
765 2695 6.813152 TGCTATAGTATATACTACGTGCACGA 59.187 38.462 42.94 25.37 41.18 4.35
792 2722 7.251321 AGATCTCCACTTGTAAACTCAGATT 57.749 36.000 0.00 0.00 0.00 2.40
794 2724 6.419484 TCTCCACTTGTAAACTCAGATTGA 57.581 37.500 0.00 0.00 0.00 2.57
796 2726 7.453393 TCTCCACTTGTAAACTCAGATTGATT 58.547 34.615 0.00 0.00 0.00 2.57
811 2741 4.872691 AGATTGATTCTGTTGACATCCGAC 59.127 41.667 0.00 0.00 31.79 4.79
838 2768 1.400737 AGGAAAGTATACTCGCGGCT 58.599 50.000 6.13 0.00 0.00 5.52
860 2801 2.286872 CGTCGTATGGTCAGGACTAGT 58.713 52.381 0.00 0.00 32.45 2.57
879 3429 2.158667 AGTGGACTACCCCAACAAGTTG 60.159 50.000 0.00 0.00 38.06 3.16
1081 3631 1.607801 CCTGCATCGTCTCCCTGTCA 61.608 60.000 0.00 0.00 0.00 3.58
1135 3685 2.746277 GGCACGACACCATCACCC 60.746 66.667 0.00 0.00 0.00 4.61
1183 3733 2.280797 GCCTCCAACAGACGTGCA 60.281 61.111 0.00 0.00 0.00 4.57
1208 3758 0.874607 ATCGCGCCGTGGATAAGAAC 60.875 55.000 0.00 0.00 0.00 3.01
1284 3837 2.669133 CCGGTGGGAGATGAGCCAA 61.669 63.158 0.00 0.00 34.06 4.52
1377 3930 0.530650 ACTGTGACGGTCTTGTGCTG 60.531 55.000 9.88 2.22 0.00 4.41
1419 3972 2.237392 GTGGGTTCTCAATCCAGCTACT 59.763 50.000 0.00 0.00 0.00 2.57
1433 3986 2.675423 TACTCGCCACGTCCTGCT 60.675 61.111 0.00 0.00 0.00 4.24
1434 3987 2.214181 CTACTCGCCACGTCCTGCTT 62.214 60.000 0.00 0.00 0.00 3.91
1450 4003 1.295746 CTTCTGCCTCAGAGCTGCA 59.704 57.895 1.02 0.00 41.75 4.41
1482 4035 1.679032 GGGCTTCGTAGGTGCTTTGAT 60.679 52.381 0.00 0.00 0.00 2.57
1491 4050 3.063704 TGCTTTGATGGGGCGCTG 61.064 61.111 7.64 0.00 0.00 5.18
1497 4056 4.115199 GATGGGGCGCTGGGTCTT 62.115 66.667 7.64 0.00 0.00 3.01
1794 4353 5.411977 CAGCTTGAATGATGAGTCTTTCAGT 59.588 40.000 6.78 0.00 44.40 3.41
1803 4362 4.174411 TGAGTCTTTCAGTGTCATACCG 57.826 45.455 0.00 0.00 0.00 4.02
1897 4456 0.187117 TCATGAAGGGCCCAAACACA 59.813 50.000 27.56 16.08 0.00 3.72
1947 4515 1.744522 TGCAATGATGTGGATGGTTCG 59.255 47.619 0.00 0.00 0.00 3.95
1958 4526 1.339631 GGATGGTTCGAATCCACCACA 60.340 52.381 17.86 3.77 46.01 4.17
2180 4748 8.771766 CACATCAGAAATTGTCTATGACTATGG 58.228 37.037 0.00 0.00 33.56 2.74
2206 4774 1.078426 CCCTACGTTCCAAGCCTGG 60.078 63.158 0.00 0.00 45.08 4.45
2209 4777 0.034896 CTACGTTCCAAGCCTGGTGT 59.965 55.000 0.15 1.89 43.97 4.16
2234 4809 6.535150 TCAATCTAGTTGGACGCTAGAAAATG 59.465 38.462 6.20 6.51 45.29 2.32
2256 4831 4.236935 GAGGTACAATTGCATTTGTGTGG 58.763 43.478 28.50 5.82 40.00 4.17
2272 4847 3.820467 TGTGTGGCAAGGCAATATATAGC 59.180 43.478 0.00 0.00 0.00 2.97
2283 4858 5.420421 AGGCAATATATAGCAGACGATGAGT 59.580 40.000 0.00 0.00 0.00 3.41
2304 4879 5.831997 AGTACCAATTTTTCAAGTGCTGAC 58.168 37.500 0.00 0.00 32.21 3.51
2334 4914 8.850156 GGCATCAGTTTATAATCATTGTAACCT 58.150 33.333 0.00 0.00 0.00 3.50
2344 4924 8.986477 ATAATCATTGTAACCTTTTTGCACTC 57.014 30.769 0.00 0.00 0.00 3.51
2369 4949 8.726988 TCCTTTTTCATTAGTTTTCATAGACGG 58.273 33.333 0.00 0.00 0.00 4.79
2375 4955 8.697846 TCATTAGTTTTCATAGACGGTGTTAG 57.302 34.615 0.00 0.00 0.00 2.34
2413 4993 3.004002 GGCCGCTTGTTATGGTATTTACC 59.996 47.826 0.00 0.00 46.62 2.85
2426 5006 3.063045 GGTATTTACCGTTTTCCTCTGCG 59.937 47.826 0.00 0.00 36.50 5.18
2453 5033 8.645814 TCTACTTGTATGGAAGAGTTAACTGA 57.354 34.615 14.14 0.00 0.00 3.41
2464 5044 7.338196 TGGAAGAGTTAACTGAACAAAACATCA 59.662 33.333 14.14 0.00 40.86 3.07
2480 5060 8.415553 ACAAAACATCAAATCTTGAGAACATCA 58.584 29.630 0.00 0.00 43.98 3.07
2483 5063 7.698506 ACATCAAATCTTGAGAACATCATGT 57.301 32.000 0.00 0.00 43.98 3.21
2492 5072 4.392047 TGAGAACATCATGTCACAAAGCT 58.608 39.130 0.00 0.00 31.12 3.74
2495 5075 4.389992 AGAACATCATGTCACAAAGCTACG 59.610 41.667 0.00 0.00 0.00 3.51
2505 5085 5.690409 TGTCACAAAGCTACGACTTTAAGAG 59.310 40.000 0.00 0.00 37.78 2.85
2520 5100 6.116126 ACTTTAAGAGAACTGAGCAAAGTGT 58.884 36.000 0.00 0.00 34.44 3.55
2521 5101 6.599638 ACTTTAAGAGAACTGAGCAAAGTGTT 59.400 34.615 0.00 0.00 34.44 3.32
2522 5102 7.121315 ACTTTAAGAGAACTGAGCAAAGTGTTT 59.879 33.333 0.00 0.00 34.44 2.83
2523 5103 4.889832 AGAGAACTGAGCAAAGTGTTTG 57.110 40.909 0.00 0.00 43.44 2.93
2524 5104 3.629398 AGAGAACTGAGCAAAGTGTTTGG 59.371 43.478 1.80 0.00 40.94 3.28
2577 5157 1.793258 CGAAGCTGGAGCATCATAGG 58.207 55.000 0.65 0.00 45.16 2.57
2578 5158 1.069823 CGAAGCTGGAGCATCATAGGT 59.930 52.381 0.65 0.00 45.16 3.08
2579 5159 2.492012 GAAGCTGGAGCATCATAGGTG 58.508 52.381 0.65 0.00 45.16 4.00
2582 5162 2.104451 AGCTGGAGCATCATAGGTGAAG 59.896 50.000 0.65 0.00 45.16 3.02
2605 5185 2.476619 AGTCGATCACGCAAAGAAACAG 59.523 45.455 0.00 0.00 39.58 3.16
2642 5228 3.530149 AGAGAAGTAGGGGTAGAGCTCTT 59.470 47.826 23.84 5.74 0.00 2.85
2689 5275 9.209048 TGTACATACAAAGTGAGGGTAGATTAT 57.791 33.333 0.00 0.00 32.40 1.28
2715 5301 2.195922 CAAAAAGCACCAGCAACTGTC 58.804 47.619 0.00 0.00 45.49 3.51
2717 5303 1.696063 AAAGCACCAGCAACTGTCAT 58.304 45.000 0.00 0.00 45.49 3.06
2719 5305 2.566833 AGCACCAGCAACTGTCATTA 57.433 45.000 0.00 0.00 45.49 1.90
2720 5306 2.862541 AGCACCAGCAACTGTCATTAA 58.137 42.857 0.00 0.00 45.49 1.40
2721 5307 3.424703 AGCACCAGCAACTGTCATTAAT 58.575 40.909 0.00 0.00 45.49 1.40
2722 5308 3.828451 AGCACCAGCAACTGTCATTAATT 59.172 39.130 0.00 0.00 45.49 1.40
2723 5309 5.009631 AGCACCAGCAACTGTCATTAATTA 58.990 37.500 0.00 0.00 45.49 1.40
2744 5335 1.898863 AGGGAGGGTAGCATGTCATT 58.101 50.000 0.00 0.00 0.00 2.57
2771 5362 4.130118 CGATATGAGCAACCCTTTTAGCT 58.870 43.478 0.00 0.00 40.60 3.32
2810 5401 9.578439 CATTAAAAATCTCCTTTGTCCTTGATC 57.422 33.333 0.00 0.00 0.00 2.92
2820 5411 9.672673 CTCCTTTGTCCTTGATCTTCTAATTTA 57.327 33.333 0.00 0.00 0.00 1.40
2828 5419 8.211629 TCCTTGATCTTCTAATTTACTAAGGGC 58.788 37.037 0.00 0.00 33.54 5.19
2853 5444 4.888326 ATGCATTTTTGCCCTTAGTCAA 57.112 36.364 0.00 0.00 0.00 3.18
2860 5451 1.989706 TGCCCTTAGTCAAAACCACC 58.010 50.000 0.00 0.00 0.00 4.61
2866 5457 4.324267 CCTTAGTCAAAACCACCCTACAG 58.676 47.826 0.00 0.00 0.00 2.74
2892 5483 1.732809 GTCCTTACTTTTCGGCTCTGC 59.267 52.381 0.00 0.00 0.00 4.26
2917 5508 5.335976 CCAGTTTTGCCCTTAGATTTGTCTC 60.336 44.000 0.00 0.00 0.00 3.36
2924 5515 4.682050 GCCCTTAGATTTGTCTCTGAGGTC 60.682 50.000 4.59 0.00 43.94 3.85
2936 5527 0.951040 CTGAGGTCGTTTGAGTGCCC 60.951 60.000 0.00 0.00 0.00 5.36
2937 5528 1.371558 GAGGTCGTTTGAGTGCCCT 59.628 57.895 0.00 0.00 0.00 5.19
2943 5534 1.021202 CGTTTGAGTGCCCTTTGACA 58.979 50.000 0.00 0.00 0.00 3.58
3079 5672 8.515695 AAGGTATTGTTTATAACTACCCAAGC 57.484 34.615 8.21 0.00 35.66 4.01
3080 5673 7.868974 AGGTATTGTTTATAACTACCCAAGCT 58.131 34.615 8.21 0.00 34.93 3.74
3081 5674 8.333984 AGGTATTGTTTATAACTACCCAAGCTT 58.666 33.333 0.00 0.00 34.93 3.74
3082 5675 9.617523 GGTATTGTTTATAACTACCCAAGCTTA 57.382 33.333 0.00 0.00 0.00 3.09
3099 5692 7.047891 CCAAGCTTATTACACTGTTATCAGGA 58.952 38.462 0.00 0.00 45.14 3.86
3155 5748 7.834881 TTAATGTCTTATGACCTCGGATAGT 57.165 36.000 6.32 0.00 42.28 2.12
3160 5753 8.070034 TGTCTTATGACCTCGGATAGTTTAAA 57.930 34.615 6.32 0.00 42.28 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 1857 4.335037 GCAACTCTCCATCCAAAGATCTTC 59.665 45.833 8.78 0.00 0.00 2.87
29 1863 3.942829 TGTAGCAACTCTCCATCCAAAG 58.057 45.455 0.00 0.00 0.00 2.77
55 1889 2.227865 TGTTCTTTTTAGTGGCCATCGC 59.772 45.455 9.72 0.00 0.00 4.58
115 1949 0.774276 TGCATCCCTGGTACCACAAA 59.226 50.000 11.60 0.00 0.00 2.83
156 2033 4.717280 CCTATGGTAGATCCCATACTTCCC 59.283 50.000 6.61 0.00 43.48 3.97
185 2089 4.208746 TCACTACCGGTGTTCCAAAAATT 58.791 39.130 19.93 0.00 45.50 1.82
202 2106 3.599343 CAGTACTTGCAGCCAATCACTA 58.401 45.455 0.00 0.00 0.00 2.74
289 2194 3.410508 TGCTGTGTATGCATTTGTCTCA 58.589 40.909 3.54 0.58 35.31 3.27
310 2215 0.104304 ACTGTCGTCTCTTTGCCGTT 59.896 50.000 0.00 0.00 0.00 4.44
381 2286 4.336280 ACCTTTTGCCTCTATCACTTTCC 58.664 43.478 0.00 0.00 0.00 3.13
422 2328 2.031682 CAGAGCTTGGTTTCTCGGTTTG 60.032 50.000 0.00 0.00 34.66 2.93
445 2351 1.202428 GCGATTCCTACCAGGTCACTC 60.202 57.143 0.00 0.00 36.53 3.51
473 2381 2.989253 TTCTGACCGCTCGCTCCA 60.989 61.111 0.00 0.00 0.00 3.86
477 2385 2.508891 CGATGTTCTGACCGCTCGC 61.509 63.158 0.00 0.00 0.00 5.03
543 2451 4.148825 AGAGGCGCCGGCTGTTAG 62.149 66.667 26.68 9.69 38.98 2.34
544 2452 4.451150 CAGAGGCGCCGGCTGTTA 62.451 66.667 31.64 0.00 38.98 2.41
568 2481 8.620416 TCGGGAATTTGTGATCTATACAATTTG 58.380 33.333 8.44 0.00 37.81 2.32
569 2482 8.746052 TCGGGAATTTGTGATCTATACAATTT 57.254 30.769 0.00 0.00 37.81 1.82
570 2483 8.786898 CATCGGGAATTTGTGATCTATACAATT 58.213 33.333 0.00 0.00 37.81 2.32
571 2484 7.391554 CCATCGGGAATTTGTGATCTATACAAT 59.608 37.037 0.00 0.00 35.60 2.71
572 2485 6.710295 CCATCGGGAATTTGTGATCTATACAA 59.290 38.462 0.00 0.00 34.52 2.41
573 2486 6.183361 ACCATCGGGAATTTGTGATCTATACA 60.183 38.462 0.00 0.00 38.05 2.29
574 2487 6.231211 ACCATCGGGAATTTGTGATCTATAC 58.769 40.000 0.00 0.00 38.05 1.47
575 2488 6.042666 TGACCATCGGGAATTTGTGATCTATA 59.957 38.462 0.00 0.00 38.05 1.31
576 2489 5.163205 TGACCATCGGGAATTTGTGATCTAT 60.163 40.000 0.00 0.00 38.05 1.98
577 2490 4.163268 TGACCATCGGGAATTTGTGATCTA 59.837 41.667 0.00 0.00 38.05 1.98
578 2491 3.054434 TGACCATCGGGAATTTGTGATCT 60.054 43.478 0.00 0.00 38.05 2.75
579 2492 3.278574 TGACCATCGGGAATTTGTGATC 58.721 45.455 0.00 0.00 38.05 2.92
580 2493 3.364460 TGACCATCGGGAATTTGTGAT 57.636 42.857 0.00 0.00 38.05 3.06
581 2494 2.869101 TGACCATCGGGAATTTGTGA 57.131 45.000 0.00 0.00 38.05 3.58
582 2495 2.099592 CCATGACCATCGGGAATTTGTG 59.900 50.000 0.00 0.00 38.05 3.33
583 2496 2.025416 TCCATGACCATCGGGAATTTGT 60.025 45.455 0.00 0.00 38.05 2.83
621 2534 1.067821 CTCAGTATCTCCCACGGAAGC 59.932 57.143 0.00 0.00 0.00 3.86
638 2551 3.057526 CACACGTAACTGACTCCATCTCA 60.058 47.826 0.00 0.00 0.00 3.27
655 2568 2.350007 CCGTGGTTTATTCCAACACACG 60.350 50.000 14.99 14.99 43.47 4.49
681 2598 3.058160 CAAGCTTGGGCCGGACTG 61.058 66.667 19.14 0.00 39.73 3.51
682 2599 2.351924 TTTCAAGCTTGGGCCGGACT 62.352 55.000 25.73 0.00 39.73 3.85
757 2687 0.733150 TGGAGATCTACTCGTGCACG 59.267 55.000 32.76 32.76 45.76 5.34
761 2691 5.562506 TTACAAGTGGAGATCTACTCGTG 57.437 43.478 17.92 17.92 45.76 4.35
765 2695 6.948886 TCTGAGTTTACAAGTGGAGATCTACT 59.051 38.462 6.49 0.00 39.47 2.57
792 2722 2.673893 CGGTCGGATGTCAACAGAATCA 60.674 50.000 0.00 0.00 0.00 2.57
794 2724 1.405526 CCGGTCGGATGTCAACAGAAT 60.406 52.381 2.83 0.00 37.50 2.40
796 2726 1.183030 ACCGGTCGGATGTCAACAGA 61.183 55.000 16.90 0.00 38.96 3.41
811 2741 3.195661 GAGTATACTTTCCTTGCACCGG 58.804 50.000 6.88 0.00 0.00 5.28
838 2768 0.963856 AGTCCTGACCATACGACGCA 60.964 55.000 0.00 0.00 0.00 5.24
860 2801 2.128535 TCAACTTGTTGGGGTAGTCCA 58.871 47.619 12.75 0.00 37.22 4.02
879 3429 3.366739 ATCGAAGGCGGGGTCGTTC 62.367 63.158 0.00 0.00 38.41 3.95
1032 3582 2.202797 AGCTCGTGCGGCACATAG 60.203 61.111 30.23 25.54 45.42 2.23
1067 3617 0.811915 CGACTTGACAGGGAGACGAT 59.188 55.000 0.00 0.00 33.97 3.73
1208 3758 2.895372 GATGGCCGCCGTAGTTGG 60.895 66.667 3.42 0.00 0.00 3.77
1419 3972 3.303135 AGAAGCAGGACGTGGCGA 61.303 61.111 0.00 0.00 34.54 5.54
1433 3986 1.197812 TATGCAGCTCTGAGGCAGAA 58.802 50.000 12.86 3.26 40.18 3.02
1434 3987 1.134580 GTTATGCAGCTCTGAGGCAGA 60.135 52.381 12.86 6.88 41.40 4.26
1794 4353 3.845259 GGAGGCGCCGGTATGACA 61.845 66.667 23.20 0.00 0.00 3.58
1827 4386 1.226101 GTTGGACGTCGCGTATCGA 60.226 57.895 21.82 7.61 46.29 3.59
1897 4456 2.863809 ACAAGCCGACCTGAAAGATTT 58.136 42.857 0.00 0.00 34.07 2.17
1947 4515 2.524306 TGAACCCATTGTGGTGGATTC 58.476 47.619 0.00 0.00 41.44 2.52
1958 4526 2.857483 TGACATGACGTTGAACCCATT 58.143 42.857 0.00 0.00 0.00 3.16
2036 4604 6.239430 GCACATGAGATTGTAAGATCCTCCTA 60.239 42.308 0.00 0.00 0.00 2.94
2180 4748 3.528532 CTTGGAACGTAGGGGATTACAC 58.471 50.000 0.00 0.00 0.00 2.90
2206 4774 2.960819 AGCGTCCAACTAGATTGACAC 58.039 47.619 0.00 0.00 41.23 3.67
2209 4777 5.654603 TTTCTAGCGTCCAACTAGATTGA 57.345 39.130 0.00 0.00 44.19 2.57
2234 4809 4.236935 CCACACAAATGCAATTGTACCTC 58.763 43.478 19.35 0.00 41.44 3.85
2256 4831 4.245660 TCGTCTGCTATATATTGCCTTGC 58.754 43.478 15.19 4.13 0.00 4.01
2272 4847 6.480524 TGAAAAATTGGTACTCATCGTCTG 57.519 37.500 0.00 0.00 0.00 3.51
2283 4858 4.261405 CCGTCAGCACTTGAAAAATTGGTA 60.261 41.667 0.00 0.00 37.61 3.25
2304 4879 5.947228 ATGATTATAAACTGATGCCACCG 57.053 39.130 0.00 0.00 0.00 4.94
2334 4914 8.785329 AAACTAATGAAAAAGGAGTGCAAAAA 57.215 26.923 0.00 0.00 0.00 1.94
2337 4917 7.551585 TGAAAACTAATGAAAAAGGAGTGCAA 58.448 30.769 0.00 0.00 0.00 4.08
2344 4924 8.512138 ACCGTCTATGAAAACTAATGAAAAAGG 58.488 33.333 0.00 0.00 0.00 3.11
2369 4949 5.397240 GCCGAAACAACAAATACACTAACAC 59.603 40.000 0.00 0.00 0.00 3.32
2375 4955 2.312348 CGGCCGAAACAACAAATACAC 58.688 47.619 24.07 0.00 0.00 2.90
2413 4993 0.992802 GTAGAGCGCAGAGGAAAACG 59.007 55.000 11.47 0.00 0.00 3.60
2423 5003 2.758423 TCTTCCATACAAGTAGAGCGCA 59.242 45.455 11.47 0.00 0.00 6.09
2424 5004 3.181485 ACTCTTCCATACAAGTAGAGCGC 60.181 47.826 0.00 0.00 36.63 5.92
2426 5006 7.489757 CAGTTAACTCTTCCATACAAGTAGAGC 59.510 40.741 4.77 0.00 36.63 4.09
2453 5033 9.252962 GATGTTCTCAAGATTTGATGTTTTGTT 57.747 29.630 0.00 0.00 39.30 2.83
2464 5044 7.514784 TTGTGACATGATGTTCTCAAGATTT 57.485 32.000 0.00 0.00 37.44 2.17
2480 5060 6.220930 TCTTAAAGTCGTAGCTTTGTGACAT 58.779 36.000 0.00 0.00 38.89 3.06
2483 5063 6.080648 TCTCTTAAAGTCGTAGCTTTGTGA 57.919 37.500 0.00 8.38 38.89 3.58
2492 5072 5.700722 TGCTCAGTTCTCTTAAAGTCGTA 57.299 39.130 0.00 0.00 0.00 3.43
2495 5075 6.258947 ACACTTTGCTCAGTTCTCTTAAAGTC 59.741 38.462 0.00 0.00 35.44 3.01
2505 5085 2.159254 TGCCAAACACTTTGCTCAGTTC 60.159 45.455 0.00 0.00 39.31 3.01
2564 5144 4.290093 ACTACTTCACCTATGATGCTCCA 58.710 43.478 0.00 0.00 33.85 3.86
2570 5150 5.049336 CGTGATCGACTACTTCACCTATGAT 60.049 44.000 9.82 0.00 37.13 2.45
2577 5157 2.257974 TGCGTGATCGACTACTTCAC 57.742 50.000 6.11 6.11 39.71 3.18
2578 5158 3.057806 TCTTTGCGTGATCGACTACTTCA 60.058 43.478 0.00 0.00 39.71 3.02
2579 5159 3.499048 TCTTTGCGTGATCGACTACTTC 58.501 45.455 0.00 0.00 39.71 3.01
2582 5162 3.427528 TGTTTCTTTGCGTGATCGACTAC 59.572 43.478 0.00 0.00 39.71 2.73
2605 5185 9.152595 CCCTACTTCTCTGTGTAATTTACTTTC 57.847 37.037 7.99 0.57 0.00 2.62
2662 5248 6.921486 TCTACCCTCACTTTGTATGTACAA 57.079 37.500 0.00 1.62 43.80 2.41
2689 5275 2.237643 TGCTGGTGCTTTTTGCTATCA 58.762 42.857 0.00 0.00 43.37 2.15
2707 5293 6.405842 CCCTCCCTTTAATTAATGACAGTTGC 60.406 42.308 11.61 0.00 0.00 4.17
2711 5297 6.486993 GCTACCCTCCCTTTAATTAATGACAG 59.513 42.308 11.61 7.23 0.00 3.51
2715 5301 6.777580 ACATGCTACCCTCCCTTTAATTAATG 59.222 38.462 0.00 1.47 0.00 1.90
2717 5303 6.069323 TGACATGCTACCCTCCCTTTAATTAA 60.069 38.462 0.00 0.00 0.00 1.40
2719 5305 4.229582 TGACATGCTACCCTCCCTTTAATT 59.770 41.667 0.00 0.00 0.00 1.40
2720 5306 3.785887 TGACATGCTACCCTCCCTTTAAT 59.214 43.478 0.00 0.00 0.00 1.40
2721 5307 3.186283 TGACATGCTACCCTCCCTTTAA 58.814 45.455 0.00 0.00 0.00 1.52
2722 5308 2.840511 TGACATGCTACCCTCCCTTTA 58.159 47.619 0.00 0.00 0.00 1.85
2723 5309 1.668826 TGACATGCTACCCTCCCTTT 58.331 50.000 0.00 0.00 0.00 3.11
2744 5335 2.039418 AGGGTTGCTCATATCGTAGCA 58.961 47.619 0.00 0.00 46.59 3.49
2748 5339 3.877508 GCTAAAAGGGTTGCTCATATCGT 59.122 43.478 0.00 0.00 0.00 3.73
2749 5340 4.130118 AGCTAAAAGGGTTGCTCATATCG 58.870 43.478 0.00 0.00 0.00 2.92
2753 5344 6.857437 ATTTAAGCTAAAAGGGTTGCTCAT 57.143 33.333 0.00 0.00 34.38 2.90
2755 5346 8.689251 CTTTATTTAAGCTAAAAGGGTTGCTC 57.311 34.615 0.00 0.00 34.38 4.26
2785 5376 9.539194 AGATCAAGGACAAAGGAGATTTTTAAT 57.461 29.630 0.00 0.00 0.00 1.40
2788 5379 7.727634 AGAAGATCAAGGACAAAGGAGATTTTT 59.272 33.333 0.00 0.00 0.00 1.94
2810 5401 7.147915 TGCATTTGGCCCTTAGTAAATTAGAAG 60.148 37.037 0.00 0.00 43.89 2.85
2820 5411 4.325972 CAAAAATGCATTTGGCCCTTAGT 58.674 39.130 24.74 3.46 43.89 2.24
2823 5414 1.887854 GCAAAAATGCATTTGGCCCTT 59.112 42.857 26.68 15.74 41.37 3.95
2828 5419 4.325972 ACTAAGGGCAAAAATGCATTTGG 58.674 39.130 24.74 19.72 39.99 3.28
2860 5451 6.293244 CGAAAAGTAAGGACAAAACCTGTAGG 60.293 42.308 0.00 0.00 38.84 3.18
2866 5457 3.317149 AGCCGAAAAGTAAGGACAAAACC 59.683 43.478 0.00 0.00 0.00 3.27
2872 5463 1.732809 GCAGAGCCGAAAAGTAAGGAC 59.267 52.381 0.00 0.00 0.00 3.85
2873 5464 1.338769 GGCAGAGCCGAAAAGTAAGGA 60.339 52.381 0.00 0.00 39.62 3.36
2892 5483 3.578282 ACAAATCTAAGGGCAAAACTGGG 59.422 43.478 0.00 0.00 0.00 4.45
2896 5487 5.473504 TCAGAGACAAATCTAAGGGCAAAAC 59.526 40.000 0.00 0.00 34.34 2.43
2917 5508 0.951040 GGGCACTCAAACGACCTCAG 60.951 60.000 0.00 0.00 0.00 3.35
2924 5515 1.021202 TGTCAAAGGGCACTCAAACG 58.979 50.000 0.00 0.00 0.00 3.60
3005 5596 9.985730 ACACAAAGATCATGTATTTTGAACATT 57.014 25.926 18.41 1.68 35.39 2.71
3016 5608 5.002516 TGACATGCACACAAAGATCATGTA 58.997 37.500 6.20 0.00 45.16 2.29
3023 5615 3.382855 GCAAATGACATGCACACAAAGA 58.617 40.909 0.00 0.00 43.29 2.52
3070 5663 7.985184 TGATAACAGTGTAATAAGCTTGGGTAG 59.015 37.037 9.86 0.00 0.00 3.18
3076 5669 9.515226 TTTTCCTGATAACAGTGTAATAAGCTT 57.485 29.630 3.48 3.48 42.05 3.74
3077 5670 9.515226 TTTTTCCTGATAACAGTGTAATAAGCT 57.485 29.630 0.00 0.00 42.05 3.74
3124 5717 7.599245 CCGAGGTCATAAGACATTAATAACCTC 59.401 40.741 7.49 7.49 46.80 3.85
3182 5776 1.409790 TGCCTTTATGTGCATGCCATC 59.590 47.619 20.47 10.39 31.31 3.51
3186 5780 6.607735 AAAATATTGCCTTTATGTGCATGC 57.392 33.333 11.82 11.82 37.33 4.06


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

AutoCloner maintained by Alex Coulton.