Multiple sequence alignment - TraesCS4D01G033900

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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 TraesCS4D01G033900 chr4D 100.000 3131 0 0 1 3131 15516048 15519178 0.000000e+00 5782.0
1 TraesCS4D01G033900 chr4A 90.127 1104 77 13 1285 2366 585101110 585100017 0.000000e+00 1406.0
2 TraesCS4D01G033900 chr4A 84.778 1281 89 31 12 1275 585102347 585101156 0.000000e+00 1188.0
3 TraesCS4D01G033900 chr4A 90.483 704 31 15 2385 3057 585099911 585099213 0.000000e+00 896.0
4 TraesCS4D01G033900 chr4B 90.254 985 62 17 1292 2263 25950794 25951757 0.000000e+00 1256.0
5 TraesCS4D01G033900 chr4B 84.288 1292 117 36 9 1280 25949527 25950752 0.000000e+00 1182.0
6 TraesCS4D01G033900 chr4B 91.880 665 38 9 2480 3131 25951997 25952658 0.000000e+00 915.0
7 TraesCS4D01G033900 chr3B 85.294 408 44 6 1452 1846 420433330 420432926 1.050000e-109 407.0
8 TraesCS4D01G033900 chr7A 79.545 132 22 4 160 289 58974862 58974734 4.300000e-14 89.8
9 TraesCS4D01G033900 chr7D 76.374 182 31 12 113 289 427007025 427007199 1.550000e-13 87.9
10 TraesCS4D01G033900 chr7D 87.500 56 5 2 236 289 333757557 333757612 2.610000e-06 63.9
11 TraesCS4D01G033900 chr7B 85.714 70 7 2 222 289 442258031 442258099 1.560000e-08 71.3
12 TraesCS4D01G033900 chr5A 97.143 35 1 0 253 287 666465294 666465260 3.370000e-05 60.2


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 TraesCS4D01G033900 chr4D 15516048 15519178 3130 False 5782.000000 5782 100.000000 1 3131 1 chr4D.!!$F1 3130
1 TraesCS4D01G033900 chr4A 585099213 585102347 3134 True 1163.333333 1406 88.462667 12 3057 3 chr4A.!!$R1 3045
2 TraesCS4D01G033900 chr4B 25949527 25952658 3131 False 1117.666667 1256 88.807333 9 3131 3 chr4B.!!$F1 3122

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
961 993 0.179 CAAACTAGGGCTCGCTCCAT 59.821 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2483 2704 1.067213 GTGGTCTCTCTCTTCACTGCC 60.067 57.143 0.0 0.0 0.0 4.85 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
146 147 3.340814 GAAGTCTTGCTTCCTGGATCA 57.659 47.619 0.00 0.00 45.95 2.92
206 207 8.295569 GGAAATACCGAGTAGCTTATGTAAAG 57.704 38.462 0.00 0.00 0.00 1.85
208 209 8.868635 AAATACCGAGTAGCTTATGTAAAGAC 57.131 34.615 0.00 0.00 0.00 3.01
230 232 8.136057 AGACAGATTATGCTTGAATTAAGTCG 57.864 34.615 0.00 0.00 38.70 4.18
231 233 7.225538 AGACAGATTATGCTTGAATTAAGTCGG 59.774 37.037 0.00 0.00 38.70 4.79
234 236 7.441157 CAGATTATGCTTGAATTAAGTCGGGTA 59.559 37.037 0.00 0.00 38.70 3.69
276 278 9.830975 ACTTGGTCTTAAAATTAATTTGTGCTT 57.169 25.926 14.04 1.13 32.27 3.91
282 284 7.535940 TCTTAAAATTAATTTGTGCTTCCGTCG 59.464 33.333 14.04 0.00 32.27 5.12
284 286 5.866335 AATTAATTTGTGCTTCCGTCGTA 57.134 34.783 0.00 0.00 0.00 3.43
286 288 2.450609 ATTTGTGCTTCCGTCGTACT 57.549 45.000 0.00 0.00 0.00 2.73
305 307 6.314400 TCGTACTTTTATAATTTTCTGCGCCT 59.686 34.615 4.18 0.00 0.00 5.52
317 319 0.370273 CTGCGCCTGAATTCGTGTAC 59.630 55.000 4.18 0.00 0.00 2.90
324 326 2.412870 CTGAATTCGTGTACTGTGCCA 58.587 47.619 0.04 0.00 0.00 4.92
335 337 2.638480 ACTGTGCCAGTTAGCTTTCA 57.362 45.000 0.00 0.00 42.59 2.69
351 353 2.613026 TTCAGCTTCAACCTTGTCGA 57.387 45.000 0.00 0.00 0.00 4.20
354 356 1.528586 CAGCTTCAACCTTGTCGACAG 59.471 52.381 19.11 10.82 0.00 3.51
360 362 3.804036 TCAACCTTGTCGACAGTCAATT 58.196 40.909 19.11 7.48 0.00 2.32
370 372 3.441222 TCGACAGTCAATTAGGCGAACTA 59.559 43.478 0.41 0.00 0.00 2.24
376 379 3.309954 GTCAATTAGGCGAACTAAGGCTG 59.690 47.826 2.47 4.36 44.43 4.85
453 456 5.353123 ACGAGTCAAAGCTGAAAAACTTACA 59.647 36.000 0.00 0.00 31.88 2.41
455 458 6.358030 CGAGTCAAAGCTGAAAAACTTACATG 59.642 38.462 0.00 0.00 31.88 3.21
467 470 1.336440 ACTTACATGTTTGCTTGCGCA 59.664 42.857 5.66 5.66 46.24 6.09
518 521 9.346725 CTGAATTTTGATTTCAGTAAAGTAGGC 57.653 33.333 5.48 0.00 43.23 3.93
519 522 8.855110 TGAATTTTGATTTCAGTAAAGTAGGCA 58.145 29.630 0.00 0.00 0.00 4.75
520 523 9.346725 GAATTTTGATTTCAGTAAAGTAGGCAG 57.653 33.333 0.00 0.00 0.00 4.85
521 524 7.817418 TTTTGATTTCAGTAAAGTAGGCAGT 57.183 32.000 0.00 0.00 0.00 4.40
522 525 7.435068 TTTGATTTCAGTAAAGTAGGCAGTC 57.565 36.000 0.00 0.00 0.00 3.51
523 526 5.488341 TGATTTCAGTAAAGTAGGCAGTCC 58.512 41.667 0.00 0.00 0.00 3.85
524 527 4.967084 TTTCAGTAAAGTAGGCAGTCCA 57.033 40.909 0.00 0.00 33.74 4.02
525 528 5.499004 TTTCAGTAAAGTAGGCAGTCCAT 57.501 39.130 0.00 0.00 33.74 3.41
526 529 5.499004 TTCAGTAAAGTAGGCAGTCCATT 57.501 39.130 0.00 0.00 33.74 3.16
527 530 5.086104 TCAGTAAAGTAGGCAGTCCATTC 57.914 43.478 0.00 0.00 33.74 2.67
528 531 4.777896 TCAGTAAAGTAGGCAGTCCATTCT 59.222 41.667 0.00 0.00 33.74 2.40
529 532 5.955959 TCAGTAAAGTAGGCAGTCCATTCTA 59.044 40.000 0.00 0.00 33.74 2.10
530 533 6.439375 TCAGTAAAGTAGGCAGTCCATTCTAA 59.561 38.462 0.00 0.00 33.74 2.10
531 534 7.125811 TCAGTAAAGTAGGCAGTCCATTCTAAT 59.874 37.037 0.00 0.00 33.74 1.73
532 535 7.770897 CAGTAAAGTAGGCAGTCCATTCTAATT 59.229 37.037 0.00 0.00 33.74 1.40
533 536 8.329502 AGTAAAGTAGGCAGTCCATTCTAATTT 58.670 33.333 0.00 0.00 35.28 1.82
534 537 8.957466 GTAAAGTAGGCAGTCCATTCTAATTTT 58.043 33.333 0.00 0.00 33.80 1.82
535 538 7.396540 AAGTAGGCAGTCCATTCTAATTTTG 57.603 36.000 0.00 0.00 33.74 2.44
536 539 6.721318 AGTAGGCAGTCCATTCTAATTTTGA 58.279 36.000 0.00 0.00 33.74 2.69
537 540 7.349598 AGTAGGCAGTCCATTCTAATTTTGAT 58.650 34.615 0.00 0.00 33.74 2.57
538 541 7.836183 AGTAGGCAGTCCATTCTAATTTTGATT 59.164 33.333 0.00 0.00 33.74 2.57
539 542 7.486407 AGGCAGTCCATTCTAATTTTGATTT 57.514 32.000 0.00 0.00 33.74 2.17
540 543 7.550712 AGGCAGTCCATTCTAATTTTGATTTC 58.449 34.615 0.00 0.00 33.74 2.17
541 544 7.178983 AGGCAGTCCATTCTAATTTTGATTTCA 59.821 33.333 0.00 0.00 33.74 2.69
542 545 7.490402 GGCAGTCCATTCTAATTTTGATTTCAG 59.510 37.037 0.00 0.00 0.00 3.02
543 546 8.031277 GCAGTCCATTCTAATTTTGATTTCAGT 58.969 33.333 0.00 0.00 0.00 3.41
552 555 9.174166 TCTAATTTTGATTTCAGTAAGGTAGGC 57.826 33.333 0.00 0.00 0.00 3.93
553 556 7.775053 AATTTTGATTTCAGTAAGGTAGGCA 57.225 32.000 0.00 0.00 0.00 4.75
565 568 3.636153 AGGTAGGCAGTCCATTCTTTC 57.364 47.619 0.00 0.00 33.74 2.62
587 603 0.961753 GCAAACCCTGGTTCTCAAGG 59.038 55.000 1.29 0.00 37.35 3.61
591 607 2.538141 CCCTGGTTCTCAAGGCCCA 61.538 63.158 0.00 0.00 0.00 5.36
603 619 2.356278 GGCCCACCTGCTCAATCA 59.644 61.111 0.00 0.00 0.00 2.57
616 632 4.264253 TGCTCAATCACTCGGAAATGATT 58.736 39.130 10.04 10.04 44.52 2.57
644 660 7.764695 TGGATAAGATGTACGTACATGTTTG 57.235 36.000 39.34 0.00 44.62 2.93
645 661 7.324935 TGGATAAGATGTACGTACATGTTTGT 58.675 34.615 39.34 31.08 44.62 2.83
646 662 8.468399 TGGATAAGATGTACGTACATGTTTGTA 58.532 33.333 39.34 28.35 44.62 2.41
662 681 8.896744 ACATGTTTGTAGTCATAGAAATGGATG 58.103 33.333 0.00 0.00 33.16 3.51
780 803 1.202533 ACCGTGTCAAAGACAGACAGG 60.203 52.381 0.00 8.55 45.77 4.00
781 804 0.861837 CGTGTCAAAGACAGACAGGC 59.138 55.000 0.00 0.00 45.77 4.85
782 805 1.539065 CGTGTCAAAGACAGACAGGCT 60.539 52.381 0.00 0.00 45.77 4.58
867 891 1.261938 TACCGTACCCAGCACAGCAT 61.262 55.000 0.00 0.00 0.00 3.79
917 949 4.039357 CGATCGGCGCGACCCTAT 62.039 66.667 12.10 0.00 39.18 2.57
918 950 2.338984 GATCGGCGCGACCCTATT 59.661 61.111 12.10 0.00 39.18 1.73
919 951 1.733399 GATCGGCGCGACCCTATTC 60.733 63.158 12.10 0.00 39.18 1.75
920 952 3.222354 ATCGGCGCGACCCTATTCC 62.222 63.158 12.10 0.00 39.18 3.01
959 991 1.815840 GCAAACTAGGGCTCGCTCC 60.816 63.158 0.00 0.00 0.00 4.70
961 993 0.179000 CAAACTAGGGCTCGCTCCAT 59.821 55.000 0.00 0.00 0.00 3.41
1192 1239 1.592669 GCGACCGAGGATGGTGATG 60.593 63.158 0.00 0.00 44.01 3.07
1193 1240 1.068083 CGACCGAGGATGGTGATGG 59.932 63.158 0.00 0.00 44.01 3.51
1269 1322 1.109920 AGATGCTACTGGCCGACGAT 61.110 55.000 0.00 0.00 40.92 3.73
1275 1328 2.561467 TACTGGCCGACGATCCTCCA 62.561 60.000 0.00 0.00 0.00 3.86
1280 1333 3.518998 CGACGATCCTCCAGCGGT 61.519 66.667 0.00 0.00 0.00 5.68
1463 1570 4.057428 GGACGTGACGGCAGAGCT 62.057 66.667 14.80 0.00 36.10 4.09
1597 1704 0.401738 CAGGAAGAAGGCCAAGGACA 59.598 55.000 5.01 0.00 0.00 4.02
1650 1757 1.678635 CGGTGGTGGCAATGGTGAT 60.679 57.895 0.00 0.00 0.00 3.06
1663 1770 2.809601 GTGATCGCGGCGTGAAGT 60.810 61.111 27.92 12.19 0.00 3.01
1727 1834 4.003788 CGAGGACAAGGCCACGGT 62.004 66.667 5.01 0.00 38.18 4.83
1728 1835 2.642254 CGAGGACAAGGCCACGGTA 61.642 63.158 5.01 0.00 38.18 4.02
1752 1859 0.818040 ACAAGACGGTGGACTTTGCC 60.818 55.000 0.00 0.00 0.00 4.52
1787 1894 0.033504 GTCGACACCAGAAGCTTCCA 59.966 55.000 22.81 0.00 0.00 3.53
1801 1908 3.834013 TTCCACGGGCGCAATGTGA 62.834 57.895 22.39 5.87 35.66 3.58
1880 1990 3.991536 GAGTTGTCGAGGAGGCCGC 62.992 68.421 0.00 0.00 0.00 6.53
2148 2265 7.039882 GGATTTGATCGGTGTAGTCTAGAAAA 58.960 38.462 0.00 0.00 0.00 2.29
2174 2291 6.696411 AGAATCTTCAGAACTCAATCGTCTT 58.304 36.000 0.00 0.00 0.00 3.01
2197 2314 2.094734 GCTGCTTGCAAATTGTAATGGC 59.905 45.455 0.00 0.00 42.31 4.40
2228 2345 7.547019 TGTGTTGCAAGATTTTGTGTCATTTTA 59.453 29.630 0.00 0.00 36.65 1.52
2242 2359 9.826574 TTGTGTCATTTTAGTTAGTTACTCTGT 57.173 29.630 0.00 0.00 38.33 3.41
2280 2402 9.520204 AAATCATATTTTAACTTGCGATGGAAG 57.480 29.630 0.00 0.00 0.00 3.46
2281 2403 7.857734 TCATATTTTAACTTGCGATGGAAGA 57.142 32.000 5.03 0.00 0.00 2.87
2282 2404 8.450578 TCATATTTTAACTTGCGATGGAAGAT 57.549 30.769 5.03 0.00 0.00 2.40
2283 2405 8.344831 TCATATTTTAACTTGCGATGGAAGATG 58.655 33.333 5.03 0.00 0.00 2.90
2284 2406 4.963276 TTTAACTTGCGATGGAAGATGG 57.037 40.909 5.03 0.00 0.00 3.51
2285 2407 1.755179 AACTTGCGATGGAAGATGGG 58.245 50.000 5.03 0.00 0.00 4.00
2286 2408 0.911769 ACTTGCGATGGAAGATGGGA 59.088 50.000 5.03 0.00 0.00 4.37
2287 2409 1.134280 ACTTGCGATGGAAGATGGGAG 60.134 52.381 5.03 0.00 0.00 4.30
2397 2606 3.947196 TCAAGGATGCAGCAAAATATCGT 59.053 39.130 3.51 0.00 0.00 3.73
2401 2610 5.308014 AGGATGCAGCAAAATATCGTATCA 58.692 37.500 3.51 0.00 0.00 2.15
2406 2615 5.207768 GCAGCAAAATATCGTATCAACAGG 58.792 41.667 0.00 0.00 0.00 4.00
2407 2616 5.007626 GCAGCAAAATATCGTATCAACAGGA 59.992 40.000 0.00 0.00 0.00 3.86
2411 2620 7.653713 AGCAAAATATCGTATCAACAGGACTAG 59.346 37.037 0.00 0.00 0.00 2.57
2412 2621 7.569591 GCAAAATATCGTATCAACAGGACTAGC 60.570 40.741 0.00 0.00 0.00 3.42
2413 2622 6.650427 AATATCGTATCAACAGGACTAGCA 57.350 37.500 0.00 0.00 0.00 3.49
2417 2626 4.096532 TCGTATCAACAGGACTAGCAAGAG 59.903 45.833 0.00 0.00 0.00 2.85
2419 2628 5.393135 CGTATCAACAGGACTAGCAAGAGAA 60.393 44.000 0.00 0.00 0.00 2.87
2420 2629 4.955811 TCAACAGGACTAGCAAGAGAAA 57.044 40.909 0.00 0.00 0.00 2.52
2422 2631 5.869579 TCAACAGGACTAGCAAGAGAAATT 58.130 37.500 0.00 0.00 0.00 1.82
2423 2632 6.299141 TCAACAGGACTAGCAAGAGAAATTT 58.701 36.000 0.00 0.00 0.00 1.82
2424 2633 6.205464 TCAACAGGACTAGCAAGAGAAATTTG 59.795 38.462 0.00 0.00 0.00 2.32
2447 2656 7.376435 TGCTATTTTGATCAGACGAATTTCA 57.624 32.000 0.00 0.00 0.00 2.69
2463 2672 7.015289 ACGAATTTCACACTTATCGATGTTTG 58.985 34.615 8.54 1.90 34.62 2.93
2465 2674 7.904977 CGAATTTCACACTTATCGATGTTTGAT 59.095 33.333 8.54 0.00 32.38 2.57
2466 2675 9.214953 GAATTTCACACTTATCGATGTTTGATC 57.785 33.333 8.54 0.00 0.00 2.92
2467 2676 7.665561 TTTCACACTTATCGATGTTTGATCA 57.334 32.000 8.54 0.00 0.00 2.92
2468 2677 7.848223 TTCACACTTATCGATGTTTGATCAT 57.152 32.000 8.54 0.00 0.00 2.45
2469 2678 7.848223 TCACACTTATCGATGTTTGATCATT 57.152 32.000 8.54 0.00 0.00 2.57
2470 2679 7.909267 TCACACTTATCGATGTTTGATCATTC 58.091 34.615 8.54 0.00 0.00 2.67
2477 2698 7.980742 ATCGATGTTTGATCATTCACAAATG 57.019 32.000 0.00 0.00 43.10 2.32
2478 2699 6.912082 TCGATGTTTGATCATTCACAAATGT 58.088 32.000 0.00 0.00 42.46 2.71
2483 2704 8.800231 TGTTTGATCATTCACAAATGTAACAG 57.200 30.769 0.00 0.00 42.46 3.16
2494 2715 4.516698 ACAAATGTAACAGGCAGTGAAGAG 59.483 41.667 0.00 0.00 0.00 2.85
2495 2716 4.623932 AATGTAACAGGCAGTGAAGAGA 57.376 40.909 0.00 0.00 0.00 3.10
2498 2719 3.256879 TGTAACAGGCAGTGAAGAGAGAG 59.743 47.826 0.00 0.00 0.00 3.20
2500 2721 1.892474 ACAGGCAGTGAAGAGAGAGAC 59.108 52.381 0.00 0.00 0.00 3.36
2585 2806 9.707957 TTTATCCACCTACCAAAATGAACATAT 57.292 29.630 0.00 0.00 0.00 1.78
2617 2847 8.146053 TCAAAACTGTCATCTTCTATAGGGAA 57.854 34.615 0.00 0.00 0.00 3.97
2638 2868 6.410540 GGAAGTGTACATTCAAGGAAGATCT 58.589 40.000 0.00 0.00 0.00 2.75
2675 2906 5.097529 GGTTGATATGCCGAATAATGCATG 58.902 41.667 0.00 0.00 46.99 4.06
2712 2943 4.024725 TGTTACGCCAAATGCCGTATATTC 60.025 41.667 0.00 0.00 36.24 1.75
2759 2994 8.728088 ATTTCGCATTTACACTAGTCAAAAAG 57.272 30.769 0.00 0.00 0.00 2.27
2768 3003 4.449068 ACACTAGTCAAAAAGCTGTCGATG 59.551 41.667 0.00 0.00 0.00 3.84
2778 3013 1.433471 CTGTCGATGTGCCGAGCTA 59.567 57.895 0.00 0.00 39.43 3.32
2994 3235 2.225117 ACCCTCCAACCTTCAAATCAGG 60.225 50.000 0.00 0.00 37.45 3.86
3070 3314 5.073691 CCCCCTCCATCATGTACTTTAGAAT 59.926 44.000 0.00 0.00 0.00 2.40
3071 3315 6.000219 CCCCTCCATCATGTACTTTAGAATG 59.000 44.000 0.00 0.00 0.00 2.67
3073 3317 6.183361 CCCTCCATCATGTACTTTAGAATGGA 60.183 42.308 6.75 6.75 34.84 3.41
3093 3337 4.379339 GAGTAGTCTCCAAGATGTGACC 57.621 50.000 0.00 0.00 34.87 4.02
3097 3341 1.819288 GTCTCCAAGATGTGACCTCGA 59.181 52.381 0.00 0.00 0.00 4.04
3099 3343 2.428530 TCTCCAAGATGTGACCTCGATG 59.571 50.000 0.00 0.00 0.00 3.84
3104 3348 1.827344 AGATGTGACCTCGATGCTCAA 59.173 47.619 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.214208 TCCTGAAGAAGATTTTGATCCTCAGA 59.786 38.462 2.95 0.00 0.00 3.27
140 141 7.148086 GCTAACCTGTTATGTGATTTTGATCCA 60.148 37.037 0.00 0.00 0.00 3.41
146 147 6.490040 ACACTGCTAACCTGTTATGTGATTTT 59.510 34.615 17.04 2.02 31.54 1.82
192 193 9.482627 AGCATAATCTGTCTTTACATAAGCTAC 57.517 33.333 0.00 0.00 34.37 3.58
206 207 7.348201 CCGACTTAATTCAAGCATAATCTGTC 58.652 38.462 0.00 0.00 37.83 3.51
208 209 6.260936 ACCCGACTTAATTCAAGCATAATCTG 59.739 38.462 0.00 0.00 37.83 2.90
230 232 3.260632 AGTCAATTGGCACCAAAATACCC 59.739 43.478 13.47 0.00 39.55 3.69
231 233 4.535526 AGTCAATTGGCACCAAAATACC 57.464 40.909 13.47 0.00 39.55 2.73
276 278 7.463119 CGCAGAAAATTATAAAAGTACGACGGA 60.463 37.037 0.00 0.00 0.00 4.69
282 284 7.469260 TCAGGCGCAGAAAATTATAAAAGTAC 58.531 34.615 10.83 0.00 0.00 2.73
284 286 6.509418 TCAGGCGCAGAAAATTATAAAAGT 57.491 33.333 10.83 0.00 0.00 2.66
286 288 7.219917 CGAATTCAGGCGCAGAAAATTATAAAA 59.780 33.333 16.75 0.00 0.00 1.52
305 307 2.535012 TGGCACAGTACACGAATTCA 57.465 45.000 6.22 0.00 0.00 2.57
335 337 1.139058 ACTGTCGACAAGGTTGAAGCT 59.861 47.619 20.49 0.00 0.00 3.74
346 348 1.542472 TCGCCTAATTGACTGTCGACA 59.458 47.619 18.88 18.88 0.00 4.35
347 349 2.273370 TCGCCTAATTGACTGTCGAC 57.727 50.000 9.11 9.11 0.00 4.20
351 353 4.504858 CCTTAGTTCGCCTAATTGACTGT 58.495 43.478 0.00 0.00 35.14 3.55
354 356 3.309954 CAGCCTTAGTTCGCCTAATTGAC 59.690 47.826 0.00 0.00 35.14 3.18
360 362 0.611200 TTGCAGCCTTAGTTCGCCTA 59.389 50.000 0.00 0.00 0.00 3.93
370 372 1.035139 CACTCCTTTGTTGCAGCCTT 58.965 50.000 0.00 0.00 0.00 4.35
376 379 3.626028 ACGAAATCACTCCTTTGTTGC 57.374 42.857 0.00 0.00 0.00 4.17
467 470 8.197439 AGTTTCAAACTTTTTGTAGCATTAGCT 58.803 29.630 0.00 0.00 46.98 3.32
510 513 7.669722 TCAAAATTAGAATGGACTGCCTACTTT 59.330 33.333 0.00 0.00 34.31 2.66
511 514 7.175104 TCAAAATTAGAATGGACTGCCTACTT 58.825 34.615 0.00 0.00 34.31 2.24
513 516 7.573968 ATCAAAATTAGAATGGACTGCCTAC 57.426 36.000 0.00 0.00 34.31 3.18
514 517 8.593945 AAATCAAAATTAGAATGGACTGCCTA 57.406 30.769 0.00 0.00 34.31 3.93
515 518 7.178983 TGAAATCAAAATTAGAATGGACTGCCT 59.821 33.333 0.00 0.00 34.31 4.75
516 519 7.322664 TGAAATCAAAATTAGAATGGACTGCC 58.677 34.615 0.00 0.00 0.00 4.85
517 520 8.031277 ACTGAAATCAAAATTAGAATGGACTGC 58.969 33.333 0.00 0.00 0.00 4.40
526 529 9.174166 GCCTACCTTACTGAAATCAAAATTAGA 57.826 33.333 0.00 0.00 0.00 2.10
527 530 8.956426 TGCCTACCTTACTGAAATCAAAATTAG 58.044 33.333 0.00 0.00 0.00 1.73
528 531 8.871629 TGCCTACCTTACTGAAATCAAAATTA 57.128 30.769 0.00 0.00 0.00 1.40
529 532 7.451566 ACTGCCTACCTTACTGAAATCAAAATT 59.548 33.333 0.00 0.00 0.00 1.82
530 533 6.948309 ACTGCCTACCTTACTGAAATCAAAAT 59.052 34.615 0.00 0.00 0.00 1.82
531 534 6.303839 ACTGCCTACCTTACTGAAATCAAAA 58.696 36.000 0.00 0.00 0.00 2.44
532 535 5.876357 ACTGCCTACCTTACTGAAATCAAA 58.124 37.500 0.00 0.00 0.00 2.69
533 536 5.488341 GACTGCCTACCTTACTGAAATCAA 58.512 41.667 0.00 0.00 0.00 2.57
534 537 4.081087 GGACTGCCTACCTTACTGAAATCA 60.081 45.833 0.00 0.00 0.00 2.57
535 538 4.081087 TGGACTGCCTACCTTACTGAAATC 60.081 45.833 0.00 0.00 34.31 2.17
536 539 3.844211 TGGACTGCCTACCTTACTGAAAT 59.156 43.478 0.00 0.00 34.31 2.17
537 540 3.244582 TGGACTGCCTACCTTACTGAAA 58.755 45.455 0.00 0.00 34.31 2.69
538 541 2.897350 TGGACTGCCTACCTTACTGAA 58.103 47.619 0.00 0.00 34.31 3.02
539 542 2.615986 TGGACTGCCTACCTTACTGA 57.384 50.000 0.00 0.00 34.31 3.41
540 543 3.452627 AGAATGGACTGCCTACCTTACTG 59.547 47.826 0.00 0.00 34.31 2.74
541 544 3.725634 AGAATGGACTGCCTACCTTACT 58.274 45.455 0.00 0.00 34.31 2.24
542 545 4.489306 AAGAATGGACTGCCTACCTTAC 57.511 45.455 0.00 0.00 34.31 2.34
543 546 4.534500 TGAAAGAATGGACTGCCTACCTTA 59.466 41.667 0.00 0.00 34.31 2.69
544 547 3.330701 TGAAAGAATGGACTGCCTACCTT 59.669 43.478 0.00 0.00 34.31 3.50
545 548 2.912956 TGAAAGAATGGACTGCCTACCT 59.087 45.455 0.00 0.00 34.31 3.08
546 549 3.350219 TGAAAGAATGGACTGCCTACC 57.650 47.619 0.00 0.00 34.31 3.18
547 550 3.127721 GCTTGAAAGAATGGACTGCCTAC 59.872 47.826 0.00 0.00 34.31 3.18
552 555 4.301628 GGTTTGCTTGAAAGAATGGACTG 58.698 43.478 0.00 0.00 0.00 3.51
553 556 3.321968 GGGTTTGCTTGAAAGAATGGACT 59.678 43.478 0.00 0.00 0.00 3.85
565 568 1.691196 TGAGAACCAGGGTTTGCTTG 58.309 50.000 4.99 0.00 38.60 4.01
587 603 1.001641 AGTGATTGAGCAGGTGGGC 60.002 57.895 0.00 0.00 0.00 5.36
591 607 0.976641 TTCCGAGTGATTGAGCAGGT 59.023 50.000 0.00 0.00 0.00 4.00
632 648 8.869897 CATTTCTATGACTACAAACATGTACGT 58.130 33.333 0.00 1.61 33.37 3.57
636 652 8.896744 CATCCATTTCTATGACTACAAACATGT 58.103 33.333 0.00 0.00 33.37 3.21
637 653 8.896744 ACATCCATTTCTATGACTACAAACATG 58.103 33.333 0.00 0.00 33.37 3.21
644 660 7.657354 TGCACATACATCCATTTCTATGACTAC 59.343 37.037 0.00 0.00 33.37 2.73
645 661 7.734942 TGCACATACATCCATTTCTATGACTA 58.265 34.615 0.00 0.00 33.37 2.59
646 662 6.594744 TGCACATACATCCATTTCTATGACT 58.405 36.000 0.00 0.00 33.37 3.41
662 681 5.061435 CAGATGCTCGTATACATGCACATAC 59.939 44.000 18.13 11.72 38.29 2.39
689 708 4.191544 TCTCTCAAGAAACACAACACAGG 58.808 43.478 0.00 0.00 0.00 4.00
753 776 0.248296 TCTTTGACACGGTTTTGCGC 60.248 50.000 0.00 0.00 0.00 6.09
780 803 1.472376 CGGATCCTCTTCTCACCAAGC 60.472 57.143 10.75 0.00 0.00 4.01
781 804 1.472376 GCGGATCCTCTTCTCACCAAG 60.472 57.143 10.75 0.00 0.00 3.61
782 805 0.537188 GCGGATCCTCTTCTCACCAA 59.463 55.000 10.75 0.00 0.00 3.67
867 891 3.785859 GCCTCGCCTGGATGTGGA 61.786 66.667 0.00 0.00 0.00 4.02
915 947 8.627403 CGCGTATATATAAGGAAGGAAGGAATA 58.373 37.037 0.00 0.00 0.00 1.75
916 948 7.490000 CGCGTATATATAAGGAAGGAAGGAAT 58.510 38.462 0.00 0.00 0.00 3.01
917 949 6.626623 GCGCGTATATATAAGGAAGGAAGGAA 60.627 42.308 8.43 0.00 0.00 3.36
918 950 5.163581 GCGCGTATATATAAGGAAGGAAGGA 60.164 44.000 8.43 0.00 0.00 3.36
919 951 5.041940 GCGCGTATATATAAGGAAGGAAGG 58.958 45.833 8.43 0.00 0.00 3.46
920 952 5.647589 TGCGCGTATATATAAGGAAGGAAG 58.352 41.667 8.43 0.00 0.00 3.46
1091 1129 4.592936 CCGAGACGTAGCGCTCCG 62.593 72.222 21.47 21.47 30.64 4.63
1178 1225 0.390860 GTCTCCATCACCATCCTCGG 59.609 60.000 0.00 0.00 0.00 4.63
1182 1229 1.592669 CGCGTCTCCATCACCATCC 60.593 63.158 0.00 0.00 0.00 3.51
1280 1333 4.067512 AGGAGGCTCCTCGCTCCA 62.068 66.667 30.46 0.00 45.66 3.86
1329 1418 2.511600 CGCTCCGGGGAACACATC 60.512 66.667 4.80 0.00 0.00 3.06
1330 1419 4.096003 CCGCTCCGGGGAACACAT 62.096 66.667 4.80 0.00 44.15 3.21
1350 1442 3.657727 TCTTCTTCCCCAGATCAAAACCT 59.342 43.478 0.00 0.00 0.00 3.50
1352 1444 4.827284 TGTTCTTCTTCCCCAGATCAAAAC 59.173 41.667 0.00 0.00 0.00 2.43
1723 1830 0.829182 ACCGTCTTGTTCCCTACCGT 60.829 55.000 0.00 0.00 0.00 4.83
1727 1834 0.971386 GTCCACCGTCTTGTTCCCTA 59.029 55.000 0.00 0.00 0.00 3.53
1728 1835 0.763223 AGTCCACCGTCTTGTTCCCT 60.763 55.000 0.00 0.00 0.00 4.20
1752 1859 1.474648 CGACGTCCTGATGATGTGCG 61.475 60.000 10.58 0.00 43.35 5.34
1801 1908 2.625737 CATCTCCTCGTTGATGTTGCT 58.374 47.619 0.00 0.00 36.32 3.91
1880 1990 4.137872 CCAAGCTGCCATTGCCGG 62.138 66.667 0.00 0.00 36.33 6.13
2148 2265 7.158021 AGACGATTGAGTTCTGAAGATTCTTT 58.842 34.615 0.00 0.00 0.00 2.52
2197 2314 6.544622 ACACAAAATCTTGCAACACAATTTG 58.455 32.000 0.00 6.03 39.78 2.32
2266 2388 1.281867 TCCCATCTTCCATCGCAAGTT 59.718 47.619 0.00 0.00 39.48 2.66
2271 2393 2.332063 TTTCTCCCATCTTCCATCGC 57.668 50.000 0.00 0.00 0.00 4.58
2280 2402 4.262506 CGGAGGTACCTTATTTCTCCCATC 60.263 50.000 17.53 0.00 40.50 3.51
2281 2403 3.646637 CGGAGGTACCTTATTTCTCCCAT 59.353 47.826 17.53 0.00 40.50 4.00
2282 2404 3.036091 CGGAGGTACCTTATTTCTCCCA 58.964 50.000 17.53 0.00 40.50 4.37
2283 2405 3.036819 ACGGAGGTACCTTATTTCTCCC 58.963 50.000 17.53 8.91 40.50 4.30
2284 2406 3.069300 GGACGGAGGTACCTTATTTCTCC 59.931 52.174 17.53 9.94 40.28 3.71
2285 2407 3.703052 TGGACGGAGGTACCTTATTTCTC 59.297 47.826 17.53 0.67 36.31 2.87
2286 2408 3.716431 TGGACGGAGGTACCTTATTTCT 58.284 45.455 17.53 0.00 36.31 2.52
2287 2409 4.476628 TTGGACGGAGGTACCTTATTTC 57.523 45.455 17.53 10.19 36.31 2.17
2363 2485 4.784177 TGCATCCTTGAGCTTGATGATAA 58.216 39.130 16.11 3.39 38.49 1.75
2373 2562 2.667473 ATTTTGCTGCATCCTTGAGC 57.333 45.000 1.84 0.00 0.00 4.26
2397 2606 6.605471 TTTCTCTTGCTAGTCCTGTTGATA 57.395 37.500 0.00 0.00 0.00 2.15
2401 2610 5.048434 GCAAATTTCTCTTGCTAGTCCTGTT 60.048 40.000 0.41 0.00 44.66 3.16
2412 2621 9.850628 TCTGATCAAAATAGCAAATTTCTCTTG 57.149 29.630 0.00 0.00 0.00 3.02
2413 2622 9.852091 GTCTGATCAAAATAGCAAATTTCTCTT 57.148 29.630 0.00 0.00 0.00 2.85
2417 2626 8.673626 TTCGTCTGATCAAAATAGCAAATTTC 57.326 30.769 0.00 0.00 0.00 2.17
2419 2628 9.643693 AAATTCGTCTGATCAAAATAGCAAATT 57.356 25.926 0.00 0.00 0.00 1.82
2420 2629 9.294030 GAAATTCGTCTGATCAAAATAGCAAAT 57.706 29.630 0.00 0.00 0.00 2.32
2422 2631 7.750458 GTGAAATTCGTCTGATCAAAATAGCAA 59.250 33.333 0.00 0.00 0.00 3.91
2423 2632 7.094848 TGTGAAATTCGTCTGATCAAAATAGCA 60.095 33.333 0.00 0.00 0.00 3.49
2424 2633 7.217070 GTGTGAAATTCGTCTGATCAAAATAGC 59.783 37.037 0.00 0.00 0.00 2.97
2447 2656 7.334171 TGTGAATGATCAAACATCGATAAGTGT 59.666 33.333 0.00 0.00 37.30 3.55
2463 2672 5.953183 TGCCTGTTACATTTGTGAATGATC 58.047 37.500 6.17 0.00 44.37 2.92
2465 2674 4.826733 ACTGCCTGTTACATTTGTGAATGA 59.173 37.500 6.17 0.00 44.37 2.57
2466 2675 4.919168 CACTGCCTGTTACATTTGTGAATG 59.081 41.667 0.00 0.00 46.47 2.67
2467 2676 4.826733 TCACTGCCTGTTACATTTGTGAAT 59.173 37.500 7.67 0.00 31.49 2.57
2468 2677 4.203226 TCACTGCCTGTTACATTTGTGAA 58.797 39.130 7.67 0.00 31.49 3.18
2469 2678 3.814625 TCACTGCCTGTTACATTTGTGA 58.185 40.909 6.55 6.55 0.00 3.58
2470 2679 4.275689 TCTTCACTGCCTGTTACATTTGTG 59.724 41.667 0.00 0.00 0.00 3.33
2477 2698 3.508012 TCTCTCTCTTCACTGCCTGTTAC 59.492 47.826 0.00 0.00 0.00 2.50
2478 2699 3.508012 GTCTCTCTCTTCACTGCCTGTTA 59.492 47.826 0.00 0.00 0.00 2.41
2483 2704 1.067213 GTGGTCTCTCTCTTCACTGCC 60.067 57.143 0.00 0.00 0.00 4.85
2498 2719 7.684111 TCAAACTCTTGTTCCATGATGTGGTC 61.684 42.308 0.00 0.00 40.11 4.02
2500 2721 4.520111 TCAAACTCTTGTTCCATGATGTGG 59.480 41.667 0.00 0.00 40.34 4.17
2585 2806 6.705302 AGAAGATGACAGTTTTGAGATAGCA 58.295 36.000 0.00 0.00 0.00 3.49
2617 2847 8.816894 TCTTAAGATCTTCCTTGAATGTACACT 58.183 33.333 12.24 0.00 0.00 3.55
2638 2868 7.094677 CGGCATATCAACCATGATTGATCTTAA 60.095 37.037 18.88 1.88 44.30 1.85
2675 2906 4.369167 GCGTAACATTGCCTTGTTTTTC 57.631 40.909 6.67 0.00 40.25 2.29
2712 2943 2.702478 TGGCATCTAGTTCCATGAGAGG 59.298 50.000 0.00 0.00 0.00 3.69
2759 2994 2.613739 TAGCTCGGCACATCGACAGC 62.614 60.000 0.00 0.00 35.18 4.40
2768 3003 1.338389 TGGGTAAAAGTAGCTCGGCAC 60.338 52.381 0.00 0.00 0.00 5.01
2778 3013 3.646736 GGATACTGGCTGGGTAAAAGT 57.353 47.619 0.00 0.00 0.00 2.66
2994 3235 0.802494 CCGCACCCATTAACAGTGAC 59.198 55.000 0.00 0.00 33.21 3.67
3047 3291 5.630415 TTCTAAAGTACATGATGGAGGGG 57.370 43.478 0.00 0.00 0.00 4.79
3073 3317 4.020543 GAGGTCACATCTTGGAGACTACT 58.979 47.826 0.00 0.00 30.60 2.57
3082 3326 2.200067 GAGCATCGAGGTCACATCTTG 58.800 52.381 0.00 0.00 44.14 3.02


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

AutoCloner maintained by Alex Coulton.