Multiple sequence alignment - TraesCS1D01G242200

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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 TraesCS1D01G242200 chr1D 100.000 3026 0 0 967 3992 332683217 332686242 0.000000e+00 5589.0
1 TraesCS1D01G242200 chr1D 100.000 645 0 0 1 645 332682251 332682895 0.000000e+00 1192.0
2 TraesCS1D01G242200 chr1D 80.294 680 100 12 3316 3990 236443512 236442862 2.160000e-132 483.0
3 TraesCS1D01G242200 chr1D 77.226 685 138 14 3320 3992 26645030 26644352 6.260000e-103 385.0
4 TraesCS1D01G242200 chr1D 80.272 294 43 9 3318 3607 222917690 222917972 1.450000e-49 207.0
5 TraesCS1D01G242200 chr1A 95.667 2354 76 11 967 3316 430337130 430339461 0.000000e+00 3759.0
6 TraesCS1D01G242200 chr1A 97.059 646 14 3 1 645 430336260 430336901 0.000000e+00 1083.0
7 TraesCS1D01G242200 chr1A 79.119 613 102 14 3327 3931 4667116 4666522 2.230000e-107 399.0
8 TraesCS1D01G242200 chr1B 82.556 665 104 11 3181 3838 447552954 447553613 3.460000e-160 575.0
9 TraesCS1D01G242200 chr1B 76.923 624 115 17 3313 3929 6967652 6968253 1.070000e-85 327.0
10 TraesCS1D01G242200 chr1B 76.198 626 116 19 3313 3929 6936859 6937460 2.330000e-77 300.0
11 TraesCS1D01G242200 chr2D 78.592 682 113 19 3316 3991 568794526 568795180 1.720000e-113 420.0
12 TraesCS1D01G242200 chr2D 74.157 623 129 18 3381 3992 357687732 357688333 3.100000e-56 230.0
13 TraesCS1D01G242200 chr2D 78.344 314 53 7 3586 3898 640717727 640717428 5.270000e-44 189.0
14 TraesCS1D01G242200 chr2D 85.965 114 12 4 3322 3432 571042751 571042639 7.010000e-23 119.0
15 TraesCS1D01G242200 chr2D 89.394 66 6 1 3570 3635 450939527 450939463 9.190000e-12 82.4
16 TraesCS1D01G242200 chr7B 75.948 686 140 17 3316 3987 677361744 677362418 2.970000e-86 329.0
17 TraesCS1D01G242200 chr7B 76.410 195 38 7 3436 3627 719160930 719161119 9.130000e-17 99.0
18 TraesCS1D01G242200 chr4B 77.338 631 87 31 3316 3932 645330067 645329479 4.980000e-84 322.0
19 TraesCS1D01G242200 chr4B 75.969 516 75 28 3387 3887 39312476 39312957 1.870000e-53 220.0
20 TraesCS1D01G242200 chr2A 75.393 699 83 51 3316 3990 538388923 538388290 5.120000e-64 255.0
21 TraesCS1D01G242200 chr7A 74.701 585 110 25 3316 3880 25105521 25106087 4.010000e-55 226.0
22 TraesCS1D01G242200 chr3D 73.134 536 110 21 3316 3841 360577325 360577836 1.150000e-35 161.0
23 TraesCS1D01G242200 chr2B 80.095 211 27 13 3316 3519 475634357 475634155 4.160000e-30 143.0
24 TraesCS1D01G242200 chr2B 74.426 305 67 9 3575 3872 184390356 184390656 1.950000e-23 121.0


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 TraesCS1D01G242200 chr1D 332682251 332686242 3991 False 3390.5 5589 100.000 1 3992 2 chr1D.!!$F2 3991
1 TraesCS1D01G242200 chr1D 236442862 236443512 650 True 483.0 483 80.294 3316 3990 1 chr1D.!!$R2 674
2 TraesCS1D01G242200 chr1D 26644352 26645030 678 True 385.0 385 77.226 3320 3992 1 chr1D.!!$R1 672
3 TraesCS1D01G242200 chr1A 430336260 430339461 3201 False 2421.0 3759 96.363 1 3316 2 chr1A.!!$F1 3315
4 TraesCS1D01G242200 chr1A 4666522 4667116 594 True 399.0 399 79.119 3327 3931 1 chr1A.!!$R1 604
5 TraesCS1D01G242200 chr1B 447552954 447553613 659 False 575.0 575 82.556 3181 3838 1 chr1B.!!$F3 657
6 TraesCS1D01G242200 chr1B 6967652 6968253 601 False 327.0 327 76.923 3313 3929 1 chr1B.!!$F2 616
7 TraesCS1D01G242200 chr1B 6936859 6937460 601 False 300.0 300 76.198 3313 3929 1 chr1B.!!$F1 616
8 TraesCS1D01G242200 chr2D 568794526 568795180 654 False 420.0 420 78.592 3316 3991 1 chr2D.!!$F2 675
9 TraesCS1D01G242200 chr2D 357687732 357688333 601 False 230.0 230 74.157 3381 3992 1 chr2D.!!$F1 611
10 TraesCS1D01G242200 chr7B 677361744 677362418 674 False 329.0 329 75.948 3316 3987 1 chr7B.!!$F1 671
11 TraesCS1D01G242200 chr4B 645329479 645330067 588 True 322.0 322 77.338 3316 3932 1 chr4B.!!$R1 616
12 TraesCS1D01G242200 chr2A 538388290 538388923 633 True 255.0 255 75.393 3316 3990 1 chr2A.!!$R1 674
13 TraesCS1D01G242200 chr7A 25105521 25106087 566 False 226.0 226 74.701 3316 3880 1 chr7A.!!$F1 564

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
23 24 1.985473 TGCAGGTCAGCAATTCACTT 58.015 45.0 0.0 0.0 42.46 3.16 F
1926 1928 0.040157 CCAGTGTTGATGTTGTGCCG 60.040 55.0 0.0 0.0 0.00 5.69 F
2527 2529 0.108138 CCCTAAGCTGACGAACCTGG 60.108 60.0 0.0 0.0 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 1980 0.322816 CACCAGTCCCCAACCATCTG 60.323 60.0 0.0 0.0 0.00 2.90 R
2940 2942 0.323629 TAGCGAGGTTTTGTGGGAGG 59.676 55.0 0.0 0.0 0.00 4.30 R
3559 3591 0.392706 ATGGTAATCGATGCTGGCGA 59.607 50.0 0.0 0.0 42.48 5.54 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
23 24 1.985473 TGCAGGTCAGCAATTCACTT 58.015 45.000 0.00 0.00 42.46 3.16
85 87 2.927553 AAAAGGCGCACATCTGATTC 57.072 45.000 10.83 0.00 0.00 2.52
154 156 6.667007 AACTTGCCTTTCTGTTTTCATTTG 57.333 33.333 0.00 0.00 0.00 2.32
274 276 4.084287 ACTCGTCTCATGGGTGTACTTTA 58.916 43.478 0.00 0.00 0.00 1.85
385 387 7.076842 TGCTCTCTTTTCCTTTTCGATATTG 57.923 36.000 0.00 0.00 0.00 1.90
409 411 8.177119 TGGAAAAGCATGTGATTACTTTTAGT 57.823 30.769 6.50 0.00 35.42 2.24
410 412 8.637986 TGGAAAAGCATGTGATTACTTTTAGTT 58.362 29.630 6.50 0.00 35.42 2.24
411 413 9.476202 GGAAAAGCATGTGATTACTTTTAGTTT 57.524 29.630 6.50 0.00 35.42 2.66
592 594 8.506168 TGAGATTTCGCTAGTTGGAAATTATT 57.494 30.769 15.11 8.14 41.55 1.40
1284 1286 3.378427 GCATGTGGATTAGTGAAGGGTTC 59.622 47.826 0.00 0.00 0.00 3.62
1395 1397 1.133407 CTAGAGACCAACGAGTCAGCC 59.867 57.143 0.00 0.00 39.34 4.85
1491 1493 1.346068 GTGGTTCTCAAGGAGCAGACT 59.654 52.381 0.00 0.00 0.00 3.24
1762 1764 4.181578 CCTACGGTATTTGTCCTTCACTG 58.818 47.826 0.00 0.00 0.00 3.66
1764 1766 3.660865 ACGGTATTTGTCCTTCACTGAC 58.339 45.455 0.00 0.00 0.00 3.51
1926 1928 0.040157 CCAGTGTTGATGTTGTGCCG 60.040 55.000 0.00 0.00 0.00 5.69
1978 1980 0.252197 AGTCTATGGGTTTCCGGCAC 59.748 55.000 0.00 0.00 35.24 5.01
2022 2024 6.120507 ACTTTAGAAGAACTGGAGCATCTT 57.879 37.500 0.00 0.00 36.17 2.40
2024 2026 6.652900 ACTTTAGAAGAACTGGAGCATCTTTC 59.347 38.462 0.00 0.00 33.73 2.62
2043 2045 9.130661 CATCTTTCTCATCTTAGGACTCTTAGA 57.869 37.037 0.00 0.00 33.82 2.10
2076 2078 0.673437 AAAATGTGCCTGGTGGTTCG 59.327 50.000 0.00 0.00 35.27 3.95
2079 2081 2.203294 GTGCCTGGTGGTTCGGTT 60.203 61.111 0.00 0.00 35.27 4.44
2081 2083 2.203294 GCCTGGTGGTTCGGTTGT 60.203 61.111 0.00 0.00 35.27 3.32
2238 2240 3.849951 CTCTGCCCACCGCCGTAT 61.850 66.667 0.00 0.00 36.24 3.06
2257 2259 4.279420 CGTATCTGGAGGATCTGTTCATGA 59.721 45.833 0.00 0.00 35.98 3.07
2278 2280 1.067582 GGATACTTCGGCTGTCGGG 59.932 63.158 0.30 0.00 39.77 5.14
2371 2373 2.410322 CTGTTGCACCCAGCTACCCA 62.410 60.000 0.00 0.00 46.43 4.51
2373 2375 0.611896 GTTGCACCCAGCTACCCAAT 60.612 55.000 0.00 0.00 45.94 3.16
2385 2387 0.329931 TACCCAATGGATTGTGCGGT 59.670 50.000 0.00 2.26 36.06 5.68
2389 2391 1.269206 CCAATGGATTGTGCGGTATGC 60.269 52.381 0.00 0.00 38.35 3.14
2413 2415 3.855630 CTGGAAGGTCTAGCGATCG 57.144 57.895 11.69 11.69 0.00 3.69
2415 2417 1.265635 CTGGAAGGTCTAGCGATCGAG 59.734 57.143 21.57 8.54 0.00 4.04
2424 2426 2.904178 TAGCGATCGAGTGGGCTCCA 62.904 60.000 21.57 0.00 38.49 3.86
2436 2438 4.333417 GCTCCAGCCATCAAGCTT 57.667 55.556 0.00 0.00 42.61 3.74
2470 2472 0.610232 CCAAGCCCTTCCAAGTGGAG 60.610 60.000 0.00 0.00 46.36 3.86
2479 2481 2.046023 CAAGTGGAGATGGCGGCA 60.046 61.111 16.34 16.34 0.00 5.69
2480 2482 2.110967 CAAGTGGAGATGGCGGCAG 61.111 63.158 19.29 0.00 0.00 4.85
2481 2483 3.984193 AAGTGGAGATGGCGGCAGC 62.984 63.158 20.74 20.74 44.18 5.25
2502 2504 1.136565 CGGCGCCATTGTTACAAGG 59.863 57.895 28.98 3.05 0.00 3.61
2505 2507 1.872197 GCGCCATTGTTACAAGGCCA 61.872 55.000 22.86 0.00 44.18 5.36
2519 2521 0.548510 AGGCCATTCCCTAAGCTGAC 59.451 55.000 5.01 0.00 32.11 3.51
2527 2529 0.108138 CCCTAAGCTGACGAACCTGG 60.108 60.000 0.00 0.00 0.00 4.45
2611 2613 3.138798 CCATGCCTGCACTGGAGC 61.139 66.667 12.42 0.00 31.12 4.70
2668 2670 2.512515 CGGGACTTGCTAGCAGCC 60.513 66.667 18.45 19.04 41.51 4.85
2669 2671 2.512515 GGGACTTGCTAGCAGCCG 60.513 66.667 18.45 12.70 41.51 5.52
2698 2700 1.137825 CTGAGAACGCTCGACCTCC 59.862 63.158 0.00 0.00 44.33 4.30
2721 2723 3.052620 GCTCAGCGTCCTAGCGTCA 62.053 63.158 0.00 0.00 43.00 4.35
2739 2741 3.557054 CGTCACTGGAGAATTTCCCTTCA 60.557 47.826 0.00 0.00 46.19 3.02
2754 2756 1.470632 CCTTCAGTCATGGAGCTCGAC 60.471 57.143 7.83 9.78 29.58 4.20
2787 2789 2.015587 CCCAAGCTCAAGAAGATCAGC 58.984 52.381 0.00 0.00 0.00 4.26
2793 2795 2.354259 CTCAAGAAGATCAGCGGCTTT 58.646 47.619 0.00 0.00 0.00 3.51
2898 2900 3.244805 TGAATGATGAGCCATGGGAGATC 60.245 47.826 15.13 0.00 0.00 2.75
2899 2901 1.810455 TGATGAGCCATGGGAGATCA 58.190 50.000 15.13 1.99 0.00 2.92
2901 2903 2.714793 TGATGAGCCATGGGAGATCATT 59.285 45.455 15.13 0.00 30.98 2.57
2956 2958 0.107831 TCACCTCCCACAAAACCTCG 59.892 55.000 0.00 0.00 0.00 4.63
2958 2960 1.073199 CCTCCCACAAAACCTCGCT 59.927 57.895 0.00 0.00 0.00 4.93
2963 2965 4.451900 CTCCCACAAAACCTCGCTATTAT 58.548 43.478 0.00 0.00 0.00 1.28
3000 3003 3.376546 TCAGAGATGACTGACGTCTGATG 59.623 47.826 26.71 12.09 43.93 3.07
3008 3011 3.084786 ACTGACGTCTGATGTCTGATGA 58.915 45.455 31.09 13.13 36.80 2.92
3009 3012 3.119673 ACTGACGTCTGATGTCTGATGAC 60.120 47.826 31.09 9.09 43.20 3.06
3010 3013 7.327443 GACTGACGTCTGATGTCTGATGACA 62.327 48.000 31.09 12.47 45.10 3.58
3146 3149 4.008074 TCTCCTTCGACTTTGAGCATTT 57.992 40.909 0.00 0.00 0.00 2.32
3151 3154 4.142816 CCTTCGACTTTGAGCATTTACCTG 60.143 45.833 0.00 0.00 0.00 4.00
3154 3157 3.941483 CGACTTTGAGCATTTACCTGGAT 59.059 43.478 0.00 0.00 0.00 3.41
3253 3258 7.595819 AATTTTGTCAGGTTTCCTTACATGA 57.404 32.000 0.00 0.00 37.55 3.07
3354 3359 2.866515 TCCCCTAAAAGGCCATAAGGA 58.133 47.619 5.01 0.00 36.29 3.36
3359 3374 5.458595 CCCTAAAAGGCCATAAGGAAGAAT 58.541 41.667 5.01 0.00 36.29 2.40
3422 3440 5.696724 CCTATCCGGCTTAGTGAAGTAATTG 59.303 44.000 0.00 0.00 34.90 2.32
3426 3444 6.465948 TCCGGCTTAGTGAAGTAATTGTTTA 58.534 36.000 0.00 0.00 34.90 2.01
3454 3475 4.242336 ACTCCTCAAATCTCCCCAAATC 57.758 45.455 0.00 0.00 0.00 2.17
3459 3480 4.325658 CCTCAAATCTCCCCAAATCCTCTT 60.326 45.833 0.00 0.00 0.00 2.85
3500 3526 1.669760 CCGAGTAAAACTGGCGCCA 60.670 57.895 30.59 30.59 0.00 5.69
3523 3553 1.265454 CCTTTCTCCTACCCCACGCT 61.265 60.000 0.00 0.00 0.00 5.07
3539 3569 3.710722 CTGCCCTGTCTCCCGCTT 61.711 66.667 0.00 0.00 0.00 4.68
3573 3615 0.602106 CCTCATCGCCAGCATCGATT 60.602 55.000 0.00 0.00 43.27 3.34
3620 3662 2.125225 GGACCCTTCCCTCACCCT 59.875 66.667 0.00 0.00 35.57 4.34
3758 3809 3.350163 AATGGCCTCTGGGGTGGG 61.350 66.667 3.32 0.00 37.43 4.61
3820 3882 2.258726 GCCGGAGCCAAACGAGTTT 61.259 57.895 5.05 0.00 0.00 2.66
3953 4018 2.282674 TACGACCACTGCTCCGGT 60.283 61.111 0.00 0.00 38.56 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 87 5.360591 AGCTGGAGTAGATTAAAATGGTCG 58.639 41.667 0.00 0.00 0.00 4.79
327 329 9.039870 CCTCAACTATTGCTAGAGTTTAGATTG 57.960 37.037 15.40 2.09 33.70 2.67
385 387 9.476202 AAACTAAAAGTAATCACATGCTTTTCC 57.524 29.630 9.00 0.00 40.34 3.13
550 552 5.661056 ATCTCAGAATCTACAAACGTGGA 57.339 39.130 0.00 0.00 0.00 4.02
592 594 2.962421 GACAATCCCCAAAACAACAGGA 59.038 45.455 0.00 0.00 0.00 3.86
1270 1272 3.868754 GCCTGAACGAACCCTTCACTAAT 60.869 47.826 0.00 0.00 0.00 1.73
1284 1286 2.202492 CTCTCGTCGGCCTGAACG 60.202 66.667 13.99 13.99 0.00 3.95
1395 1397 1.365633 GTAGGCCCATCTGCTCTCG 59.634 63.158 0.00 0.00 0.00 4.04
1402 1404 1.142936 TGCATGATGTAGGCCCATCT 58.857 50.000 19.09 6.04 41.47 2.90
1491 1493 5.620206 TGTGAAAGAAGGCTTCTAATGTCA 58.380 37.500 28.78 23.57 39.61 3.58
1762 1764 2.608261 GCAGCCTAGATACATCCGTGTC 60.608 54.545 0.00 0.00 39.77 3.67
1764 1766 1.337260 GGCAGCCTAGATACATCCGTG 60.337 57.143 3.29 0.00 0.00 4.94
1978 1980 0.322816 CACCAGTCCCCAACCATCTG 60.323 60.000 0.00 0.00 0.00 2.90
2022 2024 9.922477 TGTATTCTAAGAGTCCTAAGATGAGAA 57.078 33.333 0.00 0.00 0.00 2.87
2043 2045 4.160252 GGCACATTTTCCAGACCATGTATT 59.840 41.667 0.00 0.00 0.00 1.89
2098 2100 1.740297 CTGAGATGCTTCTTGCTGCT 58.260 50.000 3.29 0.00 43.37 4.24
2238 2240 3.444029 TGTCATGAACAGATCCTCCAGA 58.556 45.455 0.00 0.00 32.81 3.86
2257 2259 0.456221 CGACAGCCGAAGTATCCTGT 59.544 55.000 0.00 0.00 40.92 4.00
2272 2274 0.843309 ATCCAATATGGCACCCGACA 59.157 50.000 0.00 0.00 37.47 4.35
2278 2280 1.959085 CCCGCATCCAATATGGCAC 59.041 57.895 0.00 0.00 37.47 5.01
2309 2311 4.701663 TCAAGCTCTTGAAGGCCG 57.298 55.556 9.66 0.00 45.56 6.13
2352 2354 1.675641 GGGTAGCTGGGTGCAACAG 60.676 63.158 3.06 9.80 45.94 3.16
2371 2373 1.949525 GAGCATACCGCACAATCCATT 59.050 47.619 0.00 0.00 46.13 3.16
2373 2375 0.251634 TGAGCATACCGCACAATCCA 59.748 50.000 0.00 0.00 46.13 3.41
2385 2387 0.833287 GACCTTCCAGGCTGAGCATA 59.167 55.000 17.94 0.00 39.63 3.14
2389 2391 0.463620 GCTAGACCTTCCAGGCTGAG 59.536 60.000 17.94 6.12 39.63 3.35
2403 2405 1.152943 AGCCCACTCGATCGCTAGA 60.153 57.895 11.09 0.00 0.00 2.43
2406 2408 3.532155 GGAGCCCACTCGATCGCT 61.532 66.667 11.09 0.00 44.48 4.93
2424 2426 1.377725 CCCGACAAGCTTGATGGCT 60.378 57.895 32.50 10.03 45.30 4.75
2480 2482 3.809775 TAACAATGGCGCCGCTGC 61.810 61.111 23.90 0.00 0.00 5.25
2481 2483 2.100216 GTAACAATGGCGCCGCTG 59.900 61.111 23.90 22.96 0.00 5.18
2482 2484 1.922135 CTTGTAACAATGGCGCCGCT 61.922 55.000 23.90 9.04 0.00 5.52
2484 2486 1.136565 CCTTGTAACAATGGCGCCG 59.863 57.895 23.90 10.49 0.00 6.46
2486 2488 1.153842 GGCCTTGTAACAATGGCGC 60.154 57.895 0.00 0.00 45.75 6.53
2488 2490 2.418609 GGAATGGCCTTGTAACAATGGC 60.419 50.000 3.32 8.30 44.22 4.40
2489 2491 2.168313 GGGAATGGCCTTGTAACAATGG 59.832 50.000 3.32 0.00 36.66 3.16
2491 2493 3.473113 AGGGAATGGCCTTGTAACAAT 57.527 42.857 3.32 0.00 36.66 2.71
2493 2495 3.876156 GCTTAGGGAATGGCCTTGTAACA 60.876 47.826 3.32 0.00 36.66 2.41
2496 2498 2.092429 CAGCTTAGGGAATGGCCTTGTA 60.092 50.000 3.32 0.00 36.66 2.41
2502 2504 0.178068 TCGTCAGCTTAGGGAATGGC 59.822 55.000 0.00 0.00 0.00 4.40
2505 2507 2.093447 CAGGTTCGTCAGCTTAGGGAAT 60.093 50.000 0.00 0.00 0.00 3.01
2519 2521 1.597854 TTGTGCAGCTCCAGGTTCG 60.598 57.895 0.00 0.00 0.00 3.95
2527 2529 1.499056 CCGTCATGTTGTGCAGCTC 59.501 57.895 0.00 0.00 0.00 4.09
2611 2613 2.884639 TGCAATGGATGATGCTGAGATG 59.115 45.455 0.00 0.00 42.97 2.90
2711 2713 2.145397 ATTCTCCAGTGACGCTAGGA 57.855 50.000 0.00 6.91 0.00 2.94
2739 2741 1.508545 CACGTCGAGCTCCATGACT 59.491 57.895 8.47 0.00 0.00 3.41
2754 2756 1.448540 CTTGGGGCAGTAGAGCACG 60.449 63.158 0.00 0.00 39.34 5.34
2787 2789 4.228097 CGGAGCATCGCAAAGCCG 62.228 66.667 0.00 0.00 34.37 5.52
2793 2795 1.227350 CATCCTTCGGAGCATCGCA 60.227 57.895 0.00 0.00 34.05 5.10
2815 2817 2.109126 GCTCCGGGCAATCAGTGAC 61.109 63.158 0.00 0.00 41.35 3.67
2940 2942 0.323629 TAGCGAGGTTTTGTGGGAGG 59.676 55.000 0.00 0.00 0.00 4.30
3008 3011 2.622436 GATAGCGCCTTCTGTTTCTGT 58.378 47.619 2.29 0.00 0.00 3.41
3009 3012 1.590238 CGATAGCGCCTTCTGTTTCTG 59.410 52.381 2.29 0.00 0.00 3.02
3010 3013 1.471676 CCGATAGCGCCTTCTGTTTCT 60.472 52.381 2.29 0.00 35.83 2.52
3011 3014 0.931005 CCGATAGCGCCTTCTGTTTC 59.069 55.000 2.29 0.00 35.83 2.78
3012 3015 1.090052 GCCGATAGCGCCTTCTGTTT 61.090 55.000 2.29 0.00 35.83 2.83
3013 3016 1.521681 GCCGATAGCGCCTTCTGTT 60.522 57.895 2.29 0.00 35.83 3.16
3073 3076 9.335891 CAGTCACTCGCTATATTCTTACATTAG 57.664 37.037 0.00 0.00 0.00 1.73
3086 3089 7.382110 AGAAATATATTGCAGTCACTCGCTAT 58.618 34.615 6.21 2.31 0.00 2.97
3146 3149 7.393234 CCTGAAAACTAATTGTTGATCCAGGTA 59.607 37.037 0.00 0.00 39.13 3.08
3151 3154 6.272822 AGCCTGAAAACTAATTGTTGATCC 57.727 37.500 0.00 0.00 39.13 3.36
3154 3157 5.738783 GCCAAGCCTGAAAACTAATTGTTGA 60.739 40.000 0.00 0.00 39.13 3.18
3183 3186 3.197549 TCCACGATTCAGTCATCCATTCA 59.802 43.478 0.00 0.00 0.00 2.57
3184 3187 3.797039 TCCACGATTCAGTCATCCATTC 58.203 45.455 0.00 0.00 0.00 2.67
3253 3258 2.396955 CGTGGCTCCGTCTACGACT 61.397 63.158 3.65 0.00 42.40 4.18
3263 3268 2.443390 TAGGTAGGCCGTGGCTCC 60.443 66.667 11.25 10.84 39.70 4.70
3359 3374 5.929992 CGCCATAAGGGAGTAATCGAATTTA 59.070 40.000 0.00 0.00 40.01 1.40
3422 3440 6.149640 GGAGATTTGAGGAGTTGGAGTTAAAC 59.850 42.308 0.00 0.00 0.00 2.01
3426 3444 3.009584 GGGAGATTTGAGGAGTTGGAGTT 59.990 47.826 0.00 0.00 0.00 3.01
3454 3475 5.292101 CCGCAAGAGTGAGTAAAATAAGAGG 59.708 44.000 0.00 0.00 43.02 3.69
3459 3480 4.250464 CCACCGCAAGAGTGAGTAAAATA 58.750 43.478 0.00 0.00 39.78 1.40
3500 3526 0.797579 TGGGGTAGGAGAAAGGGAGT 59.202 55.000 0.00 0.00 0.00 3.85
3523 3553 3.706373 GAAGCGGGAGACAGGGCA 61.706 66.667 0.00 0.00 0.00 5.36
3559 3591 0.392706 ATGGTAATCGATGCTGGCGA 59.607 50.000 0.00 0.00 42.48 5.54
3565 3607 1.298859 GGCCGGATGGTAATCGATGC 61.299 60.000 5.05 0.00 37.67 3.91
3679 3725 2.986019 TCATCCCCAAACTCTTCTTGGA 59.014 45.455 3.15 0.00 45.31 3.53
3681 3727 5.789643 TTTTCATCCCCAAACTCTTCTTG 57.210 39.130 0.00 0.00 0.00 3.02
3728 3779 3.068064 CCATTGGGGCGGTTGGAC 61.068 66.667 0.00 0.00 0.00 4.02
3857 3922 5.623368 GCCTTCTTCATCTTCTTCTTCTCGA 60.623 44.000 0.00 0.00 0.00 4.04
3860 3925 4.288105 TGGCCTTCTTCATCTTCTTCTTCT 59.712 41.667 3.32 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.