Multiple sequence alignment - TraesCS2D01G380400

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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 TraesCS2D01G380400 chr2D 100.000 5965 0 0 1 5965 484851818 484857782 0.000000e+00 11016
1 TraesCS2D01G380400 chr2D 94.200 500 17 1 499 986 397963570 397964069 0.000000e+00 752
2 TraesCS2D01G380400 chr2D 94.000 500 15 7 498 986 6219498 6219993 0.000000e+00 743
3 TraesCS2D01G380400 chr2A 96.974 3404 63 14 2571 5965 628734418 628737790 0.000000e+00 5679
4 TraesCS2D01G380400 chr2A 97.482 1549 34 4 987 2532 628730513 628732059 0.000000e+00 2639
5 TraesCS2D01G380400 chr2A 92.368 511 27 3 1 500 628730010 628730519 0.000000e+00 717
6 TraesCS2D01G380400 chr2A 91.195 477 41 1 508 984 191972393 191971918 0.000000e+00 647
7 TraesCS2D01G380400 chr2B 92.843 1956 101 20 4014 5965 569498184 569500104 0.000000e+00 2800
8 TraesCS2D01G380400 chr2B 98.673 226 3 0 3798 4023 569497443 569497668 9.310000e-108 401
9 TraesCS2D01G380400 chr5D 96.192 499 8 3 499 986 11172007 11172505 0.000000e+00 806
10 TraesCS2D01G380400 chr5D 94.200 500 18 1 498 986 401034411 401034910 0.000000e+00 752
11 TraesCS2D01G380400 chr5D 94.355 496 17 1 502 986 529172861 529173356 0.000000e+00 750
12 TraesCS2D01G380400 chr6D 95.372 497 12 3 501 986 305074224 305074720 0.000000e+00 780
13 TraesCS2D01G380400 chr3D 94.779 498 15 1 500 986 533412852 533413349 0.000000e+00 765
14 TraesCS2D01G380400 chr3D 93.750 496 19 7 502 986 596278581 596279075 0.000000e+00 734
15 TraesCS2D01G380400 chr3D 91.734 496 29 7 502 986 612613101 612612607 0.000000e+00 678
16 TraesCS2D01G380400 chr7D 94.212 501 18 1 500 989 500789271 500788771 0.000000e+00 754
17 TraesCS2D01G380400 chr1D 93.988 499 18 1 500 986 75927935 75927437 0.000000e+00 745
18 TraesCS2D01G380400 chr3A 92.540 496 26 1 502 986 187438710 187438215 0.000000e+00 701
19 TraesCS2D01G380400 chr6B 94.667 75 3 1 500 574 13832028 13831955 1.360000e-21 115


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 TraesCS2D01G380400 chr2D 484851818 484857782 5964 False 11016.000000 11016 100.000 1 5965 1 chr2D.!!$F3 5964
1 TraesCS2D01G380400 chr2A 628730010 628737790 7780 False 3011.666667 5679 95.608 1 5965 3 chr2A.!!$F1 5964
2 TraesCS2D01G380400 chr2B 569497443 569500104 2661 False 1600.500000 2800 95.758 3798 5965 2 chr2B.!!$F1 2167
3 TraesCS2D01G380400 chr7D 500788771 500789271 500 True 754.000000 754 94.212 500 989 1 chr7D.!!$R1 489

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
205 206 0.846693 AGGGGCCATCATGTACCTTC 59.153 55.000 4.39 0.0 0.00 3.46 F
1004 1027 0.462759 GTGGCTGACCCTAGCATGAC 60.463 60.000 0.00 0.0 45.46 3.06 F
1840 1863 1.597937 GCTTTTGTCCAGAAGTGCGTG 60.598 52.381 0.33 0.0 0.00 5.34 F
2541 2567 0.036164 ATAAGCACGTCACCAGGCAA 59.964 50.000 0.00 0.0 0.00 4.52 F
2546 2572 0.036388 CACGTCACCAGGCAACCTAT 60.036 55.000 0.00 0.0 29.64 2.57 F
2548 2574 0.249120 CGTCACCAGGCAACCTATCA 59.751 55.000 0.00 0.0 29.64 2.15 F
3647 5993 0.932955 AGAGGGCTCCATCAGAGAGA 59.067 55.000 3.28 0.0 46.50 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1368 1.160137 ATCTCAAGAACACGCTTGCC 58.840 50.000 0.00 0.00 43.78 4.52 R
2453 2479 1.452110 TGTTCATTGCCGGACTGATG 58.548 50.000 5.05 2.81 0.00 3.07 R
3647 5993 0.179009 TTCTTGCTGCTTGCCACTCT 60.179 50.000 0.00 0.00 42.00 3.24 R
4520 7391 2.373169 ACTCTTGCTTTCCACCTCATCA 59.627 45.455 0.00 0.00 0.00 3.07 R
4523 7394 2.806745 CGAACTCTTGCTTTCCACCTCA 60.807 50.000 0.00 0.00 0.00 3.86 R
4559 7430 2.361757 CCTCCTGCATCTCTGAGTACTG 59.638 54.545 0.00 2.90 0.00 2.74 R
5559 8439 0.178992 CTTCCTTGGGAGGTGTTGCA 60.179 55.000 0.00 0.00 43.97 4.08 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
90 91 6.552445 AGTAGCATCTTCTGTTGACCTAAT 57.448 37.500 0.00 0.00 0.00 1.73
106 107 9.413048 GTTGACCTAATGTATTGATACTCTAGC 57.587 37.037 3.11 0.00 34.41 3.42
124 125 7.200455 ACTCTAGCAACGTTTTAAAGCATTTT 58.800 30.769 0.00 0.00 40.09 1.82
153 154 8.889717 CGAAGGTTATACATAAACACCAGAAAT 58.110 33.333 0.17 0.00 32.42 2.17
205 206 0.846693 AGGGGCCATCATGTACCTTC 59.153 55.000 4.39 0.00 0.00 3.46
212 217 4.142381 GGCCATCATGTACCTTCAAAGAAC 60.142 45.833 0.00 0.00 0.00 3.01
241 246 3.334691 CTGTGCTCCGTTCTAATCCAAA 58.665 45.455 0.00 0.00 0.00 3.28
246 251 2.939103 CTCCGTTCTAATCCAAAGCCAG 59.061 50.000 0.00 0.00 0.00 4.85
274 279 4.020617 CCAGGAAGCTGCACGGGA 62.021 66.667 1.02 0.00 0.00 5.14
314 326 1.629043 CCCGTCATAGCTTAGCCCTA 58.371 55.000 0.00 0.00 0.00 3.53
392 404 6.015772 GTGGAAGTACAAGAGAGAGAAAGAGT 60.016 42.308 0.00 0.00 0.00 3.24
417 429 9.326413 GTGTTTTGTACTATATGTTCCATAGCT 57.674 33.333 0.00 0.00 30.45 3.32
418 430 9.542462 TGTTTTGTACTATATGTTCCATAGCTC 57.458 33.333 0.00 0.00 30.45 4.09
421 433 9.982651 TTTGTACTATATGTTCCATAGCTCTTC 57.017 33.333 0.00 0.00 30.45 2.87
430 442 5.707298 TGTTCCATAGCTCTTCTTTTCCTTG 59.293 40.000 0.00 0.00 0.00 3.61
454 466 4.412796 TGAACTATTGAGCTGGATCCTG 57.587 45.455 14.23 14.14 0.00 3.86
476 488 9.337714 TCCTGATATCCATATAATTCCTCACAA 57.662 33.333 0.00 0.00 0.00 3.33
579 602 8.433421 ACACAAGTTATAGCGTGCTATATTTT 57.567 30.769 19.27 14.20 40.09 1.82
654 677 4.985538 ACCTTAAGACACCATCGTAGAG 57.014 45.455 3.36 0.00 43.63 2.43
671 694 5.935206 TCGTAGAGAGACATAATCTAGCCAG 59.065 44.000 0.00 0.00 38.00 4.85
679 702 8.121833 AGAGACATAATCTAGCCAGATAGGAAT 58.878 37.037 0.00 0.00 40.81 3.01
751 774 4.672587 TTAACTCTGAACACTGAGCACT 57.327 40.909 0.00 0.00 34.47 4.40
793 816 6.703607 TGCAATAACCACAAAATAAACCTGTG 59.296 34.615 0.00 0.00 40.13 3.66
892 915 3.073022 CGCTAATTACGTGAATAGCGC 57.927 47.619 29.00 0.00 39.01 5.92
932 955 7.478520 TGCTAAAATATAGCGTTTCCTTCTC 57.521 36.000 3.31 0.00 43.13 2.87
946 969 6.344780 CGTTTCCTTCTCAATACGCTATAACG 60.345 42.308 0.00 0.00 39.50 3.18
969 992 3.114693 GCTATAGCGTCGTTATAGCGT 57.885 47.619 31.83 5.17 42.23 5.07
1004 1027 0.462759 GTGGCTGACCCTAGCATGAC 60.463 60.000 0.00 0.00 45.46 3.06
1056 1079 2.036958 TCATCAATAACACAGGGGCG 57.963 50.000 0.00 0.00 0.00 6.13
1059 1082 2.437716 AATAACACAGGGGCGCCG 60.438 61.111 22.54 9.65 0.00 6.46
1088 1111 4.130118 ACTGCAAGACGTTTCTCATCTTT 58.870 39.130 0.00 0.00 37.43 2.52
1233 1256 2.432146 AGTCGAATTATGGCTGAGCAGA 59.568 45.455 6.82 0.00 0.00 4.26
1236 1259 3.118629 TCGAATTATGGCTGAGCAGAGTT 60.119 43.478 6.82 0.00 0.00 3.01
1251 1274 2.232452 CAGAGTTGATGGAGTCCTCGTT 59.768 50.000 11.33 0.00 0.00 3.85
1516 1539 3.253188 TCTCTGGGAATTTTTCAACAGCG 59.747 43.478 6.40 2.45 36.64 5.18
1638 1661 9.784680 GATTACCAGGTACATAACTATGATACG 57.215 37.037 0.00 0.00 37.15 3.06
1684 1707 8.618702 ATGAGATTTGTTATATGCTTCCAGAG 57.381 34.615 0.00 0.00 0.00 3.35
1703 1726 8.287439 TCCAGAGAAACTTAAAATGAACACAA 57.713 30.769 0.00 0.00 0.00 3.33
1725 1748 5.830000 ATAAGAAAAGTTAATGGACGCCC 57.170 39.130 0.00 0.00 0.00 6.13
1840 1863 1.597937 GCTTTTGTCCAGAAGTGCGTG 60.598 52.381 0.33 0.00 0.00 5.34
1857 1880 4.483977 GCGTGTGCATTTGCTATAAAAC 57.516 40.909 3.94 0.00 42.66 2.43
1858 1881 3.917380 GCGTGTGCATTTGCTATAAAACA 59.083 39.130 3.94 0.00 42.66 2.83
2293 2318 3.320541 TCACAATGTTTTACCTTGCCTGG 59.679 43.478 0.00 0.00 28.56 4.45
2330 2355 7.516785 CGCGTGCATATTTCTGAAGTTACTATT 60.517 37.037 0.00 0.00 0.00 1.73
2505 2531 5.614308 TGAGTGAACATTCTCTCACAATGT 58.386 37.500 18.00 0.00 46.68 2.71
2514 2540 4.687901 TCTCTCACAATGTGAACAGGAA 57.312 40.909 17.41 0.00 42.26 3.36
2532 2558 2.541762 GGAATGAGAGCATAAGCACGTC 59.458 50.000 0.00 0.00 45.49 4.34
2533 2559 2.967599 ATGAGAGCATAAGCACGTCA 57.032 45.000 0.00 0.00 45.49 4.35
2534 2560 1.996292 TGAGAGCATAAGCACGTCAC 58.004 50.000 0.00 0.00 45.49 3.67
2535 2561 1.281899 GAGAGCATAAGCACGTCACC 58.718 55.000 0.00 0.00 45.49 4.02
2536 2562 0.608130 AGAGCATAAGCACGTCACCA 59.392 50.000 0.00 0.00 45.49 4.17
2537 2563 1.002366 GAGCATAAGCACGTCACCAG 58.998 55.000 0.00 0.00 45.49 4.00
2538 2564 0.391661 AGCATAAGCACGTCACCAGG 60.392 55.000 0.00 0.00 45.49 4.45
2539 2565 1.982073 GCATAAGCACGTCACCAGGC 61.982 60.000 0.00 0.00 41.58 4.85
2540 2566 0.673333 CATAAGCACGTCACCAGGCA 60.673 55.000 0.00 0.00 0.00 4.75
2541 2567 0.036164 ATAAGCACGTCACCAGGCAA 59.964 50.000 0.00 0.00 0.00 4.52
2542 2568 0.882927 TAAGCACGTCACCAGGCAAC 60.883 55.000 0.00 0.00 0.00 4.17
2544 2570 2.111043 CACGTCACCAGGCAACCT 59.889 61.111 0.00 0.00 37.17 3.50
2545 2571 1.369692 CACGTCACCAGGCAACCTA 59.630 57.895 0.00 0.00 29.64 3.08
2546 2572 0.036388 CACGTCACCAGGCAACCTAT 60.036 55.000 0.00 0.00 29.64 2.57
2547 2573 0.249398 ACGTCACCAGGCAACCTATC 59.751 55.000 0.00 0.00 29.64 2.08
2548 2574 0.249120 CGTCACCAGGCAACCTATCA 59.751 55.000 0.00 0.00 29.64 2.15
2549 2575 1.338674 CGTCACCAGGCAACCTATCAA 60.339 52.381 0.00 0.00 29.64 2.57
2550 2576 2.680805 CGTCACCAGGCAACCTATCAAT 60.681 50.000 0.00 0.00 29.64 2.57
2551 2577 3.356290 GTCACCAGGCAACCTATCAATT 58.644 45.455 0.00 0.00 29.64 2.32
2552 2578 3.763897 GTCACCAGGCAACCTATCAATTT 59.236 43.478 0.00 0.00 29.64 1.82
2553 2579 3.763360 TCACCAGGCAACCTATCAATTTG 59.237 43.478 0.00 0.00 29.64 2.32
2555 2581 4.403432 CACCAGGCAACCTATCAATTTGAT 59.597 41.667 15.78 15.78 37.98 2.57
2556 2582 5.025453 ACCAGGCAACCTATCAATTTGATT 58.975 37.500 16.62 0.00 36.17 2.57
2557 2583 5.484998 ACCAGGCAACCTATCAATTTGATTT 59.515 36.000 16.62 3.42 36.17 2.17
2558 2584 5.813672 CCAGGCAACCTATCAATTTGATTTG 59.186 40.000 16.62 15.11 36.17 2.32
2559 2585 6.351202 CCAGGCAACCTATCAATTTGATTTGA 60.351 38.462 16.62 0.00 36.17 2.69
2560 2586 7.270047 CAGGCAACCTATCAATTTGATTTGAT 58.730 34.615 16.62 6.08 42.71 2.57
2561 2587 7.767198 CAGGCAACCTATCAATTTGATTTGATT 59.233 33.333 16.62 2.22 41.33 2.57
2562 2588 8.323567 AGGCAACCTATCAATTTGATTTGATTT 58.676 29.630 16.62 2.39 41.33 2.17
2563 2589 8.949177 GGCAACCTATCAATTTGATTTGATTTT 58.051 29.630 16.62 1.18 42.29 1.82
2613 4959 6.475596 TTAACTTACCTATACTCCCACTGC 57.524 41.667 0.00 0.00 0.00 4.40
2619 4965 3.329520 ACCTATACTCCCACTGCAACAAA 59.670 43.478 0.00 0.00 0.00 2.83
2624 4970 6.909550 ATACTCCCACTGCAACAAATTTTA 57.090 33.333 0.00 0.00 0.00 1.52
2676 5022 2.004733 CAGAAGATTGACTGCATGCGA 58.995 47.619 14.09 1.21 0.00 5.10
2720 5066 8.958119 TTCATACATGTTTACTGGATCCTTAC 57.042 34.615 14.23 4.53 0.00 2.34
2848 5194 1.188863 GGCTTGCCTTGGAATGACAT 58.811 50.000 4.11 0.00 0.00 3.06
2964 5310 1.879575 AGAAGATGTCGGGATCCCAA 58.120 50.000 30.42 10.17 35.37 4.12
3481 5827 1.000896 ACCCCAAGAAAGGCCATCG 60.001 57.895 5.01 0.00 0.00 3.84
3540 5886 3.070018 AGTTGCAAATCTGACTCTTCGG 58.930 45.455 0.00 0.00 0.00 4.30
3647 5993 0.932955 AGAGGGCTCCATCAGAGAGA 59.067 55.000 3.28 0.00 46.50 3.10
4055 6926 3.627577 GCAACTATGGGATTCGTGATGTT 59.372 43.478 0.00 0.00 0.00 2.71
4115 6986 6.891908 AGTTCCTTGGTATCACAATTTATGCT 59.108 34.615 0.00 0.00 0.00 3.79
4559 7430 0.526211 GTTCGGGAATTGAACAGGGC 59.474 55.000 1.26 0.00 44.00 5.19
4580 7451 2.361757 CAGTACTCAGAGATGCAGGAGG 59.638 54.545 3.79 0.00 0.00 4.30
4974 7845 3.990469 AGACAAAGACTAGCACAATCACG 59.010 43.478 0.00 0.00 0.00 4.35
4994 7865 3.005684 ACGGCAACATGATGAAACAACAT 59.994 39.130 7.22 0.00 0.00 2.71
5110 7981 3.063510 TGCTTCCTCAATCAACCTCTG 57.936 47.619 0.00 0.00 0.00 3.35
5462 8341 0.034960 TGCCTACGCCCAAATAGCAA 60.035 50.000 0.00 0.00 0.00 3.91
5559 8439 1.962807 TGCACTTGCTTAGTTTGCCAT 59.037 42.857 2.33 0.00 42.66 4.40
5620 8500 8.044574 TCCAGATTCCACCATATATTCTTTCA 57.955 34.615 0.00 0.00 0.00 2.69
5675 8556 5.698089 CGGCTTCAAGAAGATGATTGCTATA 59.302 40.000 13.70 0.00 40.79 1.31
5676 8557 6.370994 CGGCTTCAAGAAGATGATTGCTATAT 59.629 38.462 13.70 0.00 40.79 0.86
5677 8558 7.412781 CGGCTTCAAGAAGATGATTGCTATATC 60.413 40.741 13.70 0.00 40.79 1.63
5678 8559 7.148272 GGCTTCAAGAAGATGATTGCTATATCC 60.148 40.741 13.70 0.00 40.79 2.59
5679 8560 7.607223 GCTTCAAGAAGATGATTGCTATATCCT 59.393 37.037 13.70 0.00 40.79 3.24
5762 8643 0.036388 TCCCTGCCGTTGAGAACATC 60.036 55.000 0.00 0.00 0.00 3.06
5794 8675 1.196581 CACGCATTTCATCGAACACCA 59.803 47.619 0.00 0.00 0.00 4.17
5796 8677 3.063316 CACGCATTTCATCGAACACCATA 59.937 43.478 0.00 0.00 0.00 2.74
5837 8718 5.418676 GAGATCAGTTCTTTCTCCTGGAAG 58.581 45.833 0.00 0.00 33.74 3.46
5874 8755 2.026262 GCCCAGAAACCCTGAATACTCA 60.026 50.000 0.00 0.00 45.78 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.588252 GATGGCATGTACACGCATCC 59.412 55.000 16.66 5.15 0.00 3.51
90 91 9.642327 TTAAAACGTTGCTAGAGTATCAATACA 57.358 29.630 0.00 0.00 37.82 2.29
124 125 8.095792 TCTGGTGTTTATGTATAACCTTCGAAA 58.904 33.333 0.00 0.00 0.00 3.46
144 145 5.452078 TGTAAGCTTCCAAATTTCTGGTG 57.548 39.130 0.00 0.00 37.74 4.17
146 147 4.619160 GCCTGTAAGCTTCCAAATTTCTGG 60.619 45.833 0.00 0.00 37.87 3.86
153 154 1.202927 AGCAGCCTGTAAGCTTCCAAA 60.203 47.619 0.00 0.00 42.61 3.28
205 206 1.826385 CACAGGGGCTAGGTTCTTTG 58.174 55.000 0.00 0.00 0.00 2.77
212 217 3.854669 CGGAGCACAGGGGCTAGG 61.855 72.222 0.00 0.00 45.99 3.02
241 246 3.928754 TCCTGGAATCTACATACTGGCT 58.071 45.455 0.00 0.00 0.00 4.75
246 251 4.061596 GCAGCTTCCTGGAATCTACATAC 58.938 47.826 12.13 0.00 39.54 2.39
274 279 5.063880 GGGGCATAATGTAGAAAAGATCGT 58.936 41.667 0.00 0.00 0.00 3.73
277 282 5.048846 ACGGGGCATAATGTAGAAAAGAT 57.951 39.130 0.00 0.00 0.00 2.40
314 326 7.466804 TCCAGTTTGGACACTTCCTATTTAAT 58.533 34.615 0.00 0.00 42.67 1.40
350 362 7.654022 ACTTCCACAAACTTCCTATTTTCAA 57.346 32.000 0.00 0.00 0.00 2.69
351 363 7.776030 TGTACTTCCACAAACTTCCTATTTTCA 59.224 33.333 0.00 0.00 0.00 2.69
367 379 6.015772 ACTCTTTCTCTCTCTTGTACTTCCAC 60.016 42.308 0.00 0.00 0.00 4.02
417 429 7.502226 TCAATAGTTCAAGCAAGGAAAAGAAGA 59.498 33.333 0.00 0.00 0.00 2.87
418 430 7.651808 TCAATAGTTCAAGCAAGGAAAAGAAG 58.348 34.615 0.00 0.00 0.00 2.85
421 433 5.860716 GCTCAATAGTTCAAGCAAGGAAAAG 59.139 40.000 0.00 0.00 34.86 2.27
430 442 3.563390 GGATCCAGCTCAATAGTTCAAGC 59.437 47.826 6.95 0.00 34.95 4.01
464 476 3.117093 TGGGGGTGTTTTGTGAGGAATTA 60.117 43.478 0.00 0.00 0.00 1.40
476 488 1.905894 GCCATGTAAATGGGGGTGTTT 59.094 47.619 14.08 0.00 41.94 2.83
654 677 7.710676 TTCCTATCTGGCTAGATTATGTCTC 57.289 40.000 18.48 0.00 40.79 3.36
734 757 2.992543 GCTAAGTGCTCAGTGTTCAGAG 59.007 50.000 0.00 0.00 38.95 3.35
751 774 5.995565 ATTGCACGGTAGATATAGGCTAA 57.004 39.130 0.00 0.00 0.00 3.09
759 782 4.739587 TGTGGTTATTGCACGGTAGATA 57.260 40.909 0.00 0.00 0.00 1.98
831 854 4.101942 CGTTGTAGCGGGTAACGTTATAA 58.898 43.478 11.86 0.00 46.52 0.98
839 862 4.101942 CGTTATAACGTTGTAGCGGGTAA 58.898 43.478 25.83 2.36 46.63 2.85
892 915 1.027357 AGCAAATTCAGCCGCTATGG 58.973 50.000 0.00 0.00 42.50 2.74
989 1012 2.868583 CAAATCGTCATGCTAGGGTCAG 59.131 50.000 0.00 0.00 0.00 3.51
990 1013 2.236146 ACAAATCGTCATGCTAGGGTCA 59.764 45.455 0.00 0.00 0.00 4.02
991 1014 2.609459 CACAAATCGTCATGCTAGGGTC 59.391 50.000 0.00 0.00 0.00 4.46
992 1015 2.632377 CACAAATCGTCATGCTAGGGT 58.368 47.619 0.00 0.00 0.00 4.34
993 1016 1.331756 GCACAAATCGTCATGCTAGGG 59.668 52.381 0.00 0.00 35.16 3.53
1088 1111 3.338674 TGCGCTTGATGCAAACGA 58.661 50.000 9.73 0.00 43.06 3.85
1233 1256 1.550976 GGAACGAGGACTCCATCAACT 59.449 52.381 0.00 0.00 0.00 3.16
1236 1259 1.639722 TTGGAACGAGGACTCCATCA 58.360 50.000 0.00 0.00 41.36 3.07
1251 1274 2.720915 TGTTCGATGGCATCAATTGGA 58.279 42.857 25.88 12.41 0.00 3.53
1345 1368 1.160137 ATCTCAAGAACACGCTTGCC 58.840 50.000 0.00 0.00 43.78 4.52
1516 1539 3.372795 CAATGATGCCCACATTGCC 57.627 52.632 12.23 0.00 44.67 4.52
1638 1661 7.712639 TCTCATCTAAATGTTCATCTAGGCAAC 59.287 37.037 0.00 0.00 34.32 4.17
1703 1726 5.506708 AGGGCGTCCATTAACTTTTCTTAT 58.493 37.500 9.71 0.00 34.83 1.73
1707 1730 3.504520 TCAAGGGCGTCCATTAACTTTTC 59.495 43.478 9.71 0.00 34.83 2.29
1719 1742 3.528597 AGAAATAGACTCAAGGGCGTC 57.471 47.619 0.00 0.00 0.00 5.19
1787 1810 8.638685 GTACACTTGTACTTGAAGTTTAGTCA 57.361 34.615 1.97 0.00 45.47 3.41
1804 1827 5.510671 ACAAAAGCTCGATTTGTACACTTG 58.489 37.500 12.26 2.31 46.21 3.16
1840 1863 7.593273 TGTTGTAGTGTTTTATAGCAAATGCAC 59.407 33.333 8.28 0.00 45.16 4.57
1857 1880 8.344831 TGAACTGAGAAATTTGATGTTGTAGTG 58.655 33.333 0.00 0.00 0.00 2.74
1858 1881 8.345565 GTGAACTGAGAAATTTGATGTTGTAGT 58.654 33.333 0.00 0.00 0.00 2.73
2172 2197 4.323945 GGGTTCTGGAAAAAGGGTGTTTTT 60.324 41.667 0.00 0.00 34.64 1.94
2293 2318 2.575262 GCACGCGAGAAATGCAGC 60.575 61.111 15.93 0.00 39.23 5.25
2347 2372 3.202097 GAGCAAGGGAAGCAGTTCTATC 58.798 50.000 0.00 0.00 32.72 2.08
2446 2472 2.851263 TGCCGGACTGATGTAAAAGT 57.149 45.000 5.05 0.00 0.00 2.66
2453 2479 1.452110 TGTTCATTGCCGGACTGATG 58.548 50.000 5.05 2.81 0.00 3.07
2505 2531 4.194640 GCTTATGCTCTCATTCCTGTTCA 58.805 43.478 0.00 0.00 34.22 3.18
2514 2540 2.544685 GTGACGTGCTTATGCTCTCAT 58.455 47.619 0.00 0.00 40.48 2.90
2532 2558 3.763360 TCAAATTGATAGGTTGCCTGGTG 59.237 43.478 0.00 0.00 34.61 4.17
2533 2559 4.046286 TCAAATTGATAGGTTGCCTGGT 57.954 40.909 0.00 0.00 34.61 4.00
2534 2560 5.603170 AATCAAATTGATAGGTTGCCTGG 57.397 39.130 9.09 0.00 35.76 4.45
2535 2561 6.632909 TCAAATCAAATTGATAGGTTGCCTG 58.367 36.000 9.09 0.00 35.76 4.85
2536 2562 6.855763 TCAAATCAAATTGATAGGTTGCCT 57.144 33.333 9.09 0.00 35.76 4.75
2537 2563 8.496707 AAATCAAATCAAATTGATAGGTTGCC 57.503 30.769 9.09 0.00 46.57 4.52
2544 2570 8.871862 CGCTCCAAAAATCAAATCAAATTGATA 58.128 29.630 9.09 0.00 46.57 2.15
2546 2572 6.705381 ACGCTCCAAAAATCAAATCAAATTGA 59.295 30.769 0.00 0.00 43.03 2.57
2547 2573 6.890558 ACGCTCCAAAAATCAAATCAAATTG 58.109 32.000 0.00 0.00 0.00 2.32
2548 2574 7.495135 AACGCTCCAAAAATCAAATCAAATT 57.505 28.000 0.00 0.00 0.00 1.82
2549 2575 7.495135 AAACGCTCCAAAAATCAAATCAAAT 57.505 28.000 0.00 0.00 0.00 2.32
2550 2576 6.917217 AAACGCTCCAAAAATCAAATCAAA 57.083 29.167 0.00 0.00 0.00 2.69
2551 2577 6.145371 GCTAAACGCTCCAAAAATCAAATCAA 59.855 34.615 0.00 0.00 35.14 2.57
2552 2578 5.633182 GCTAAACGCTCCAAAAATCAAATCA 59.367 36.000 0.00 0.00 35.14 2.57
2553 2579 5.633182 TGCTAAACGCTCCAAAAATCAAATC 59.367 36.000 0.00 0.00 40.11 2.17
2555 2581 4.938080 TGCTAAACGCTCCAAAAATCAAA 58.062 34.783 0.00 0.00 40.11 2.69
2556 2582 4.037446 ACTGCTAAACGCTCCAAAAATCAA 59.963 37.500 0.00 0.00 40.11 2.57
2557 2583 3.568007 ACTGCTAAACGCTCCAAAAATCA 59.432 39.130 0.00 0.00 40.11 2.57
2558 2584 4.159120 GACTGCTAAACGCTCCAAAAATC 58.841 43.478 0.00 0.00 40.11 2.17
2559 2585 3.568007 TGACTGCTAAACGCTCCAAAAAT 59.432 39.130 0.00 0.00 40.11 1.82
2560 2586 2.946329 TGACTGCTAAACGCTCCAAAAA 59.054 40.909 0.00 0.00 40.11 1.94
2561 2587 2.566913 TGACTGCTAAACGCTCCAAAA 58.433 42.857 0.00 0.00 40.11 2.44
2562 2588 2.248280 TGACTGCTAAACGCTCCAAA 57.752 45.000 0.00 0.00 40.11 3.28
2563 2589 2.472695 ATGACTGCTAAACGCTCCAA 57.527 45.000 0.00 0.00 40.11 3.53
2564 2590 2.758423 TCTATGACTGCTAAACGCTCCA 59.242 45.455 0.00 0.00 40.11 3.86
2565 2591 3.438297 TCTATGACTGCTAAACGCTCC 57.562 47.619 0.00 0.00 40.11 4.70
2566 2592 5.043903 TCATTCTATGACTGCTAAACGCTC 58.956 41.667 0.00 0.00 35.22 5.03
2568 2594 5.914085 ATCATTCTATGACTGCTAAACGC 57.086 39.130 0.00 0.00 43.01 4.84
2569 2595 9.035607 AGTTAATCATTCTATGACTGCTAAACG 57.964 33.333 0.00 0.00 43.01 3.60
2720 5066 9.270576 CGAAGTCAATTTGAATCAGTAGAAATG 57.729 33.333 0.00 0.00 0.00 2.32
2848 5194 2.862530 GCACGAGTTTGCACTGTCTCTA 60.863 50.000 0.00 0.00 42.49 2.43
2964 5310 4.221482 GCTTTTGATTTCAGAATCTGGGGT 59.779 41.667 10.71 0.00 41.80 4.95
3481 5827 4.940463 TGACAACAGGCTACGGATTATAC 58.060 43.478 0.00 0.00 0.00 1.47
3540 5886 3.665745 AATGTGGTGCATTTTGACCTC 57.334 42.857 0.00 0.00 44.82 3.85
3647 5993 0.179009 TTCTTGCTGCTTGCCACTCT 60.179 50.000 0.00 0.00 42.00 3.24
3956 6302 3.009805 TCTCTTTAAGGGCCTTGGTAACC 59.990 47.826 28.88 0.00 0.00 2.85
4055 6926 9.919416 TTTAGGGAATCAATGTTCAGATCATTA 57.081 29.630 6.42 0.00 34.34 1.90
4115 6986 5.763204 GGTCAACTTCTTTAACACATCCTCA 59.237 40.000 0.00 0.00 0.00 3.86
4520 7391 2.373169 ACTCTTGCTTTCCACCTCATCA 59.627 45.455 0.00 0.00 0.00 3.07
4523 7394 2.806745 CGAACTCTTGCTTTCCACCTCA 60.807 50.000 0.00 0.00 0.00 3.86
4559 7430 2.361757 CCTCCTGCATCTCTGAGTACTG 59.638 54.545 0.00 2.90 0.00 2.74
4580 7451 8.190784 TCTTGTTCTTCAGAGAAACCATTTTTC 58.809 33.333 0.00 0.00 43.21 2.29
4660 7531 0.251916 CCGCCCACTCTTGGTCATAA 59.748 55.000 0.00 0.00 42.10 1.90
4796 7667 3.721706 GGGCAGTCCTCCACCCTG 61.722 72.222 0.00 0.00 39.42 4.45
4974 7845 3.123959 GCATGTTGTTTCATCATGTTGCC 59.876 43.478 16.70 3.27 41.14 4.52
4994 7865 9.519191 AGGTAAACATAATATATCAGCAATGCA 57.481 29.630 8.35 0.00 0.00 3.96
5321 8192 4.963953 GTCACTTGTTTGTGAATCTGAACG 59.036 41.667 0.00 0.00 46.77 3.95
5462 8341 7.288852 AGTCAATCAGGTATGAGCTAACTGTAT 59.711 37.037 0.07 0.00 44.29 2.29
5559 8439 0.178992 CTTCCTTGGGAGGTGTTGCA 60.179 55.000 0.00 0.00 43.97 4.08
5620 8500 4.799564 TGAGCCTTGTGACTTTTTGTTT 57.200 36.364 0.00 0.00 0.00 2.83
5675 8556 4.997395 CCTGTTTTGCTACGCATATAGGAT 59.003 41.667 7.86 0.00 38.76 3.24
5676 8557 4.141801 ACCTGTTTTGCTACGCATATAGGA 60.142 41.667 15.78 0.00 38.76 2.94
5677 8558 4.127171 ACCTGTTTTGCTACGCATATAGG 58.873 43.478 10.51 10.51 38.76 2.57
5678 8559 4.808895 TGACCTGTTTTGCTACGCATATAG 59.191 41.667 0.00 0.00 38.76 1.31
5679 8560 4.760878 TGACCTGTTTTGCTACGCATATA 58.239 39.130 0.00 0.00 38.76 0.86
5680 8561 3.605634 TGACCTGTTTTGCTACGCATAT 58.394 40.909 0.00 0.00 38.76 1.78
5681 8562 3.046968 TGACCTGTTTTGCTACGCATA 57.953 42.857 0.00 0.00 38.76 3.14
5696 8577 2.542907 CCGTTGCACGCTTTGACCT 61.543 57.895 0.00 0.00 40.91 3.85
5794 8675 1.153168 GCCATGTCTGCGGGTGTAT 60.153 57.895 0.00 0.00 0.00 2.29
5846 8727 1.376812 GGGTTTCTGGGCTGTACCG 60.377 63.158 0.00 0.00 40.62 4.02
5874 8755 2.599597 GTCAGATGGGGCCTGCAT 59.400 61.111 0.84 0.00 0.00 3.96
5938 8819 1.368579 GCAATGCACTTTGCCTGGT 59.631 52.632 13.01 0.00 44.94 4.00


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

AutoCloner maintained by Alex Coulton.