Multiple sequence alignment - TraesCS3B01G273700

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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 TraesCS3B01G273700 chr3B 100.000 2605 0 0 1 2605 440676186 440678790 0.000000e+00 4811.0
1 TraesCS3B01G273700 chr3A 96.900 1645 43 6 963 2603 461153935 461152295 0.000000e+00 2748.0
2 TraesCS3B01G273700 chr3A 88.423 501 16 9 487 968 461159616 461159139 1.350000e-157 566.0
3 TraesCS3B01G273700 chr3A 87.931 406 26 13 14 411 461160003 461159613 8.500000e-125 457.0
4 TraesCS3B01G273700 chr3D 92.571 1548 75 24 492 2031 341885282 341886797 0.000000e+00 2185.0
5 TraesCS3B01G273700 chr3D 96.881 513 13 3 2094 2605 341886789 341887299 0.000000e+00 856.0
6 TraesCS3B01G273700 chr3D 88.722 399 34 7 2 393 341884878 341885272 6.520000e-131 477.0
7 TraesCS3B01G273700 chr3D 86.316 95 11 2 12 104 9761923 9761829 4.590000e-18 102.0
8 TraesCS3B01G273700 chrUn 84.466 309 26 11 1869 2155 389446205 389445897 4.240000e-73 285.0
9 TraesCS3B01G273700 chrUn 84.142 309 27 13 1869 2155 346595325 346595633 1.970000e-71 279.0
10 TraesCS3B01G273700 chrUn 83.190 232 16 14 1869 2078 444245263 444245493 9.520000e-45 191.0
11 TraesCS3B01G273700 chr5D 84.466 309 26 13 1869 2155 446174953 446174645 4.240000e-73 285.0
12 TraesCS3B01G273700 chr5D 84.466 309 26 11 1869 2155 503219387 503219079 4.240000e-73 285.0
13 TraesCS3B01G273700 chr5D 84.091 308 28 12 1869 2155 381175046 381175353 7.100000e-71 278.0
14 TraesCS3B01G273700 chr4D 84.142 309 27 11 1869 2155 30386829 30387137 1.970000e-71 279.0
15 TraesCS3B01G273700 chr1D 84.142 309 27 13 1869 2155 254396941 254397249 1.970000e-71 279.0
16 TraesCS3B01G273700 chr1D 86.022 93 11 2 12 104 236929164 236929254 5.930000e-17 99.0
17 TraesCS3B01G273700 chr1D 86.022 93 12 1 12 104 472307277 472307186 5.930000e-17 99.0
18 TraesCS3B01G273700 chr6D 84.262 305 26 11 1873 2155 168256091 168255787 7.100000e-71 278.0
19 TraesCS3B01G273700 chr6D 83.495 309 29 13 1869 2155 135463274 135463582 4.270000e-68 268.0
20 TraesCS3B01G273700 chr5A 83.819 309 28 13 1869 2155 607275568 607275260 9.180000e-70 274.0
21 TraesCS3B01G273700 chr7D 84.071 113 14 4 2 112 29257288 29257398 3.550000e-19 106.0
22 TraesCS3B01G273700 chr7D 85.714 84 8 2 412 491 606306651 606306568 4.620000e-13 86.1
23 TraesCS3B01G273700 chr7D 85.057 87 8 4 410 491 178612887 178612801 1.660000e-12 84.2
24 TraesCS3B01G273700 chr7D 85.333 75 8 1 422 493 19944127 19944053 1.000000e-09 75.0
25 TraesCS3B01G273700 chr4A 87.097 93 9 2 12 104 712444334 712444245 4.590000e-18 102.0
26 TraesCS3B01G273700 chr2A 86.170 94 12 1 12 104 11648578 11648485 1.650000e-17 100.0
27 TraesCS3B01G273700 chr2A 85.417 96 10 3 12 104 11646311 11646217 2.130000e-16 97.1
28 TraesCS3B01G273700 chr5B 92.683 41 2 1 450 490 476009238 476009277 1.010000e-04 58.4


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 TraesCS3B01G273700 chr3B 440676186 440678790 2604 False 4811.000000 4811 100.000000 1 2605 1 chr3B.!!$F1 2604
1 TraesCS3B01G273700 chr3A 461152295 461153935 1640 True 2748.000000 2748 96.900000 963 2603 1 chr3A.!!$R1 1640
2 TraesCS3B01G273700 chr3A 461159139 461160003 864 True 511.500000 566 88.177000 14 968 2 chr3A.!!$R2 954
3 TraesCS3B01G273700 chr3D 341884878 341887299 2421 False 1172.666667 2185 92.724667 2 2605 3 chr3D.!!$F1 2603

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
756 791 0.181114 ACAGAGAAACAGCAGCACCA 59.819 50.0 0.0 0.0 0.0 4.17 F
1570 1632 0.111639 GTTAGCTTCCCAACCACCCA 59.888 55.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1582 1645 0.248843 CTGTGGAGAGACTGGGAAGC 59.751 60.000 0.0 0.0 0.00 3.86 R
2570 2634 4.816925 AGTGAGAGAGTTTTGCTACCAAAC 59.183 41.667 0.0 0.0 40.45 2.93 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
38 39 5.505173 ACATAATTAAGATGCACACAGCC 57.495 39.130 0.00 0.00 44.83 4.85
70 71 3.236816 CACACAAAAAGATCATGTCGGC 58.763 45.455 0.00 0.00 0.00 5.54
157 159 2.044252 AGCCTCTTGCCTGCCATG 60.044 61.111 0.00 0.00 42.71 3.66
160 162 4.237445 CTCTTGCCTGCCATGAGG 57.763 61.111 0.00 0.00 40.32 3.86
173 178 2.689983 GCCATGAGGGGAAATGTAAGTG 59.310 50.000 0.00 0.00 37.04 3.16
209 216 0.610174 CAGCAACTCTAGCAGGTCCA 59.390 55.000 0.00 0.00 0.00 4.02
234 241 8.028354 CACAAAAGCACATGAACTCCATAATAA 58.972 33.333 0.00 0.00 33.31 1.40
242 249 6.995686 ACATGAACTCCATAATAACGCCAATA 59.004 34.615 0.00 0.00 33.31 1.90
244 251 7.667043 TGAACTCCATAATAACGCCAATATC 57.333 36.000 0.00 0.00 0.00 1.63
259 266 3.428999 CCAATATCGATGCTACGGGGTAG 60.429 52.174 8.54 0.00 38.97 3.18
283 292 7.619050 AGAAAGAACATTCTAGCAGATTCTCA 58.381 34.615 0.00 0.00 37.88 3.27
305 314 1.043673 ATACAGGGTGCTCGAGTCCC 61.044 60.000 28.35 28.35 41.36 4.46
344 357 5.137412 TCCAGAGAAAAAGGAAAAGGGAA 57.863 39.130 0.00 0.00 0.00 3.97
370 383 0.400213 TGACAAGTGGGTCCCATGAC 59.600 55.000 15.49 10.32 40.98 3.06
408 421 1.556451 GCTACCCCCTCGGTAAAGAAA 59.444 52.381 0.00 0.00 46.85 2.52
411 424 3.920231 ACCCCCTCGGTAAAGAAATAC 57.080 47.619 0.00 0.00 45.97 1.89
412 425 3.457836 ACCCCCTCGGTAAAGAAATACT 58.542 45.455 0.00 0.00 45.97 2.12
413 426 3.453717 ACCCCCTCGGTAAAGAAATACTC 59.546 47.826 0.00 0.00 45.97 2.59
414 427 3.181457 CCCCCTCGGTAAAGAAATACTCC 60.181 52.174 0.00 0.00 0.00 3.85
415 428 3.181457 CCCCTCGGTAAAGAAATACTCCC 60.181 52.174 0.00 0.00 0.00 4.30
416 429 3.710165 CCCTCGGTAAAGAAATACTCCCT 59.290 47.826 0.00 0.00 0.00 4.20
417 430 4.202233 CCCTCGGTAAAGAAATACTCCCTC 60.202 50.000 0.00 0.00 0.00 4.30
418 431 4.650131 CCTCGGTAAAGAAATACTCCCTCT 59.350 45.833 0.00 0.00 0.00 3.69
419 432 5.452077 CCTCGGTAAAGAAATACTCCCTCTG 60.452 48.000 0.00 0.00 0.00 3.35
420 433 5.021458 TCGGTAAAGAAATACTCCCTCTGT 58.979 41.667 0.00 0.00 0.00 3.41
421 434 5.126707 TCGGTAAAGAAATACTCCCTCTGTC 59.873 44.000 0.00 0.00 0.00 3.51
422 435 5.672503 GGTAAAGAAATACTCCCTCTGTCC 58.327 45.833 0.00 0.00 0.00 4.02
423 436 5.189145 GGTAAAGAAATACTCCCTCTGTCCA 59.811 44.000 0.00 0.00 0.00 4.02
424 437 6.126739 GGTAAAGAAATACTCCCTCTGTCCAT 60.127 42.308 0.00 0.00 0.00 3.41
425 438 7.070821 GGTAAAGAAATACTCCCTCTGTCCATA 59.929 40.741 0.00 0.00 0.00 2.74
426 439 7.510675 AAAGAAATACTCCCTCTGTCCATAA 57.489 36.000 0.00 0.00 0.00 1.90
427 440 7.698163 AAGAAATACTCCCTCTGTCCATAAT 57.302 36.000 0.00 0.00 0.00 1.28
428 441 8.798975 AAGAAATACTCCCTCTGTCCATAATA 57.201 34.615 0.00 0.00 0.00 0.98
429 442 8.980832 AGAAATACTCCCTCTGTCCATAATAT 57.019 34.615 0.00 0.00 0.00 1.28
433 446 9.845214 AATACTCCCTCTGTCCATAATATAAGT 57.155 33.333 0.00 0.00 0.00 2.24
434 447 7.546250 ACTCCCTCTGTCCATAATATAAGTG 57.454 40.000 0.00 0.00 0.00 3.16
435 448 6.014156 ACTCCCTCTGTCCATAATATAAGTGC 60.014 42.308 0.00 0.00 0.00 4.40
436 449 5.047306 TCCCTCTGTCCATAATATAAGTGCG 60.047 44.000 0.00 0.00 0.00 5.34
437 450 5.279506 CCCTCTGTCCATAATATAAGTGCGT 60.280 44.000 0.00 0.00 0.00 5.24
438 451 6.223852 CCTCTGTCCATAATATAAGTGCGTT 58.776 40.000 0.00 0.00 0.00 4.84
439 452 6.706270 CCTCTGTCCATAATATAAGTGCGTTT 59.294 38.462 0.00 0.00 0.00 3.60
440 453 7.226720 CCTCTGTCCATAATATAAGTGCGTTTT 59.773 37.037 0.00 0.00 0.00 2.43
441 454 8.500753 TCTGTCCATAATATAAGTGCGTTTTT 57.499 30.769 0.00 0.00 0.00 1.94
442 455 9.602568 TCTGTCCATAATATAAGTGCGTTTTTA 57.397 29.630 0.00 0.00 0.00 1.52
480 493 5.470047 AAACGCTCTTATACTATGGGAGG 57.530 43.478 0.00 0.00 0.00 4.30
481 494 3.432378 ACGCTCTTATACTATGGGAGGG 58.568 50.000 0.00 0.00 40.93 4.30
482 495 3.075582 ACGCTCTTATACTATGGGAGGGA 59.924 47.826 16.60 0.00 39.28 4.20
483 496 3.697045 CGCTCTTATACTATGGGAGGGAG 59.303 52.174 0.00 0.00 38.62 4.30
484 497 4.027437 GCTCTTATACTATGGGAGGGAGG 58.973 52.174 0.00 0.00 0.00 4.30
485 498 4.615513 CTCTTATACTATGGGAGGGAGGG 58.384 52.174 0.00 0.00 0.00 4.30
486 499 4.265605 TCTTATACTATGGGAGGGAGGGA 58.734 47.826 0.00 0.00 0.00 4.20
487 500 4.295238 TCTTATACTATGGGAGGGAGGGAG 59.705 50.000 0.00 0.00 0.00 4.30
488 501 1.937098 TACTATGGGAGGGAGGGAGT 58.063 55.000 0.00 0.00 0.00 3.85
489 502 1.937098 ACTATGGGAGGGAGGGAGTA 58.063 55.000 0.00 0.00 0.00 2.59
490 503 1.504221 ACTATGGGAGGGAGGGAGTAC 59.496 57.143 0.00 0.00 0.00 2.73
534 547 2.362077 GACTGCTTTTGAGCCTCCAAAA 59.638 45.455 8.38 8.38 41.92 2.44
572 587 2.359900 CAATCCGTTTTAGAGGCTGCT 58.640 47.619 0.00 0.00 0.00 4.24
613 629 1.068954 GTTGCTTGCTCTTAGGCACAC 60.069 52.381 0.00 0.00 42.27 3.82
614 630 0.606401 TGCTTGCTCTTAGGCACACC 60.606 55.000 0.00 0.00 42.27 4.16
666 699 0.672401 ACCACAAGGCATAACGGACG 60.672 55.000 0.00 0.00 39.06 4.79
712 747 5.899631 TGGTTCCTTCTGTTACCTAAACT 57.100 39.130 0.00 0.00 38.99 2.66
734 769 5.588648 ACTTGCTTTTACAACAGCTAGAACA 59.411 36.000 15.27 0.00 40.17 3.18
735 770 5.418310 TGCTTTTACAACAGCTAGAACAC 57.582 39.130 0.00 0.00 36.92 3.32
736 771 4.878971 TGCTTTTACAACAGCTAGAACACA 59.121 37.500 0.00 0.00 36.92 3.72
737 772 5.355630 TGCTTTTACAACAGCTAGAACACAA 59.644 36.000 0.00 0.00 36.92 3.33
738 773 5.681543 GCTTTTACAACAGCTAGAACACAAC 59.318 40.000 0.00 0.00 32.87 3.32
739 774 6.676943 GCTTTTACAACAGCTAGAACACAACA 60.677 38.462 0.00 0.00 32.87 3.33
740 775 5.984233 TTACAACAGCTAGAACACAACAG 57.016 39.130 0.00 0.00 0.00 3.16
741 776 4.137116 ACAACAGCTAGAACACAACAGA 57.863 40.909 0.00 0.00 0.00 3.41
742 777 4.122776 ACAACAGCTAGAACACAACAGAG 58.877 43.478 0.00 0.00 0.00 3.35
743 778 4.141937 ACAACAGCTAGAACACAACAGAGA 60.142 41.667 0.00 0.00 0.00 3.10
744 779 4.672587 ACAGCTAGAACACAACAGAGAA 57.327 40.909 0.00 0.00 0.00 2.87
745 780 5.023533 ACAGCTAGAACACAACAGAGAAA 57.976 39.130 0.00 0.00 0.00 2.52
746 781 4.811557 ACAGCTAGAACACAACAGAGAAAC 59.188 41.667 0.00 0.00 0.00 2.78
747 782 4.811024 CAGCTAGAACACAACAGAGAAACA 59.189 41.667 0.00 0.00 0.00 2.83
748 783 5.050499 CAGCTAGAACACAACAGAGAAACAG 60.050 44.000 0.00 0.00 0.00 3.16
749 784 4.319118 GCTAGAACACAACAGAGAAACAGC 60.319 45.833 0.00 0.00 0.00 4.40
750 785 3.609853 AGAACACAACAGAGAAACAGCA 58.390 40.909 0.00 0.00 0.00 4.41
751 786 3.624861 AGAACACAACAGAGAAACAGCAG 59.375 43.478 0.00 0.00 0.00 4.24
752 787 1.672881 ACACAACAGAGAAACAGCAGC 59.327 47.619 0.00 0.00 0.00 5.25
753 788 1.672363 CACAACAGAGAAACAGCAGCA 59.328 47.619 0.00 0.00 0.00 4.41
754 789 1.672881 ACAACAGAGAAACAGCAGCAC 59.327 47.619 0.00 0.00 0.00 4.40
755 790 1.002033 CAACAGAGAAACAGCAGCACC 60.002 52.381 0.00 0.00 0.00 5.01
756 791 0.181114 ACAGAGAAACAGCAGCACCA 59.819 50.000 0.00 0.00 0.00 4.17
907 967 1.143073 CAAATCCCTACTACAGGCCCC 59.857 57.143 0.00 0.00 43.98 5.80
922 982 1.133945 GGCCCCATCTTCTCTTTCCTC 60.134 57.143 0.00 0.00 0.00 3.71
971 1032 0.385390 AAGCAAACAAAGAGGGCACG 59.615 50.000 0.00 0.00 0.00 5.34
1023 1084 2.617774 GGAATTGCAGAAGGATCAGAGC 59.382 50.000 0.00 0.00 0.00 4.09
1029 1090 1.047002 AGAAGGATCAGAGCCATCCG 58.953 55.000 7.64 0.00 44.24 4.18
1247 1308 4.663444 GCTCTGTGCACTCTCGTT 57.337 55.556 19.41 0.00 42.31 3.85
1300 1361 2.712057 TGAGAACGGAAAGGTACGAC 57.288 50.000 0.00 0.00 0.00 4.34
1330 1391 0.240945 CACGTTCAAGGGATTGTGGC 59.759 55.000 0.00 0.00 0.00 5.01
1570 1632 0.111639 GTTAGCTTCCCAACCACCCA 59.888 55.000 0.00 0.00 0.00 4.51
1582 1645 2.360767 CCACCCACCATGGCATTGG 61.361 63.158 13.04 12.47 42.82 3.16
1625 1688 3.575687 AGCTGGGTCTTCAAAAGATTTGG 59.424 43.478 3.25 0.00 40.18 3.28
1673 1736 3.390311 ACAGAGTCGAAAACCCCTTAAGT 59.610 43.478 0.97 0.00 0.00 2.24
1787 1851 2.034939 CAGAAATGAACAGTGCTGGCAA 59.965 45.455 2.70 0.00 34.19 4.52
1988 2052 1.112113 TGGCTCTCTATCCACGGAAC 58.888 55.000 0.00 0.00 0.00 3.62
2008 2072 6.881065 CGGAACCTCATCCATCATGTATATTT 59.119 38.462 0.00 0.00 39.61 1.40
2039 2103 9.261180 CATAACATAGGAACAATATGAACTCGT 57.739 33.333 0.24 0.00 35.15 4.18
2115 2179 0.819259 ATCAAATACGCGGCAGGCAT 60.819 50.000 12.47 0.00 43.84 4.40
2254 2318 9.981114 AGTTTTTCCAAAATTAACATGTCTAGG 57.019 29.630 0.00 0.00 0.00 3.02
2259 2323 8.348285 TCCAAAATTAACATGTCTAGGAAAGG 57.652 34.615 0.00 0.00 0.00 3.11
2324 2388 1.525197 CACGCAGCTTTTAAGTCGTCA 59.475 47.619 0.00 0.00 30.72 4.35
2354 2418 3.181480 ACCCTGAACAAACATTTTGGTCG 60.181 43.478 11.13 6.81 38.90 4.79
2570 2634 2.437413 GAAGCACTGGAGTTTAAGGGG 58.563 52.381 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 7.710907 TGTGTGCATCTTAATTATGTAGAGGAC 59.289 37.037 0.00 2.51 0.00 3.85
16 17 4.949238 TGGCTGTGTGCATCTTAATTATGT 59.051 37.500 0.00 0.00 45.15 2.29
38 39 4.302455 TCTTTTTGTGTGTGTTGGTGTTG 58.698 39.130 0.00 0.00 0.00 3.33
70 71 5.504665 CGGTCTTATATGGCTTTGCTCTTTG 60.505 44.000 0.00 0.00 0.00 2.77
157 159 7.939784 ATAGTTTTCACTTACATTTCCCCTC 57.060 36.000 0.00 0.00 34.06 4.30
160 162 6.811665 GGCAATAGTTTTCACTTACATTTCCC 59.188 38.462 0.00 0.00 34.06 3.97
173 178 2.819608 TGCTGAGTGGGCAATAGTTTTC 59.180 45.455 0.00 0.00 36.71 2.29
209 216 6.594788 ATTATGGAGTTCATGTGCTTTTGT 57.405 33.333 0.00 0.00 37.30 2.83
234 241 1.668919 CCGTAGCATCGATATTGGCGT 60.669 52.381 0.00 0.00 0.00 5.68
242 249 1.991121 TTCTACCCCGTAGCATCGAT 58.009 50.000 0.00 0.00 36.22 3.59
244 251 1.679680 TCTTTCTACCCCGTAGCATCG 59.320 52.381 0.00 0.00 36.22 3.84
259 266 7.548780 AGTGAGAATCTGCTAGAATGTTCTTTC 59.451 37.037 0.00 0.00 35.76 2.62
283 292 2.299521 GACTCGAGCACCCTGTATAGT 58.700 52.381 13.61 0.00 0.00 2.12
323 336 5.047021 GGATTCCCTTTTCCTTTTTCTCTGG 60.047 44.000 0.00 0.00 0.00 3.86
350 363 0.400213 TCATGGGACCCACTTGTCAC 59.600 55.000 17.78 0.00 39.19 3.67
370 383 6.038714 GGGGTAGCTTCTAAAATTCTGTCATG 59.961 42.308 0.00 0.00 0.00 3.07
408 421 9.261035 CACTTATATTATGGACAGAGGGAGTAT 57.739 37.037 0.00 0.00 0.00 2.12
411 424 6.402222 GCACTTATATTATGGACAGAGGGAG 58.598 44.000 0.00 0.00 0.00 4.30
412 425 5.047306 CGCACTTATATTATGGACAGAGGGA 60.047 44.000 0.00 0.00 0.00 4.20
413 426 5.171476 CGCACTTATATTATGGACAGAGGG 58.829 45.833 0.00 0.00 0.00 4.30
414 427 5.784177 ACGCACTTATATTATGGACAGAGG 58.216 41.667 0.00 0.00 0.00 3.69
415 428 7.715265 AAACGCACTTATATTATGGACAGAG 57.285 36.000 0.00 0.00 0.00 3.35
416 429 8.500753 AAAAACGCACTTATATTATGGACAGA 57.499 30.769 0.00 0.00 0.00 3.41
456 469 6.289064 CCTCCCATAGTATAAGAGCGTTTTT 58.711 40.000 3.93 0.00 0.00 1.94
457 470 5.221661 CCCTCCCATAGTATAAGAGCGTTTT 60.222 44.000 3.93 0.00 0.00 2.43
458 471 4.283722 CCCTCCCATAGTATAAGAGCGTTT 59.716 45.833 3.93 0.00 0.00 3.60
459 472 3.833070 CCCTCCCATAGTATAAGAGCGTT 59.167 47.826 3.93 0.00 0.00 4.84
460 473 3.075582 TCCCTCCCATAGTATAAGAGCGT 59.924 47.826 3.93 0.00 0.00 5.07
461 474 3.697045 CTCCCTCCCATAGTATAAGAGCG 59.303 52.174 3.93 0.00 0.00 5.03
462 475 4.027437 CCTCCCTCCCATAGTATAAGAGC 58.973 52.174 3.93 0.00 0.00 4.09
463 476 4.295238 TCCCTCCCTCCCATAGTATAAGAG 59.705 50.000 2.81 2.81 0.00 2.85
464 477 4.265605 TCCCTCCCTCCCATAGTATAAGA 58.734 47.826 0.00 0.00 0.00 2.10
465 478 4.046103 ACTCCCTCCCTCCCATAGTATAAG 59.954 50.000 0.00 0.00 0.00 1.73
466 479 4.002050 ACTCCCTCCCTCCCATAGTATAA 58.998 47.826 0.00 0.00 0.00 0.98
467 480 3.632488 ACTCCCTCCCTCCCATAGTATA 58.368 50.000 0.00 0.00 0.00 1.47
468 481 2.455064 ACTCCCTCCCTCCCATAGTAT 58.545 52.381 0.00 0.00 0.00 2.12
469 482 1.937098 ACTCCCTCCCTCCCATAGTA 58.063 55.000 0.00 0.00 0.00 1.82
470 483 1.504221 GTACTCCCTCCCTCCCATAGT 59.496 57.143 0.00 0.00 0.00 2.12
471 484 1.790157 AGTACTCCCTCCCTCCCATAG 59.210 57.143 0.00 0.00 0.00 2.23
472 485 1.937098 AGTACTCCCTCCCTCCCATA 58.063 55.000 0.00 0.00 0.00 2.74
473 486 1.027815 AAGTACTCCCTCCCTCCCAT 58.972 55.000 0.00 0.00 0.00 4.00
474 487 0.797579 AAAGTACTCCCTCCCTCCCA 59.202 55.000 0.00 0.00 0.00 4.37
475 488 2.292719 TGTAAAGTACTCCCTCCCTCCC 60.293 54.545 0.00 0.00 0.00 4.30
476 489 3.111741 TGTAAAGTACTCCCTCCCTCC 57.888 52.381 0.00 0.00 0.00 4.30
477 490 6.783482 AGATATTGTAAAGTACTCCCTCCCTC 59.217 42.308 0.00 0.00 0.00 4.30
478 491 6.694611 AGATATTGTAAAGTACTCCCTCCCT 58.305 40.000 0.00 0.00 0.00 4.20
479 492 6.997942 AGATATTGTAAAGTACTCCCTCCC 57.002 41.667 0.00 0.00 0.00 4.30
489 502 9.769093 GTCGTGCAAATTTAGATATTGTAAAGT 57.231 29.630 0.00 0.00 0.00 2.66
490 503 9.988350 AGTCGTGCAAATTTAGATATTGTAAAG 57.012 29.630 0.00 0.00 0.00 1.85
555 568 2.561478 AAAGCAGCCTCTAAAACGGA 57.439 45.000 0.00 0.00 0.00 4.69
613 629 2.939103 GCATGCTGTTACTAACCAGAGG 59.061 50.000 11.37 0.00 0.00 3.69
614 630 3.372206 GTGCATGCTGTTACTAACCAGAG 59.628 47.826 20.33 0.00 0.00 3.35
615 631 3.007940 AGTGCATGCTGTTACTAACCAGA 59.992 43.478 20.33 0.00 0.00 3.86
712 747 5.355630 TGTGTTCTAGCTGTTGTAAAAGCAA 59.644 36.000 9.30 0.00 42.06 3.91
734 769 1.672881 GTGCTGCTGTTTCTCTGTTGT 59.327 47.619 0.00 0.00 0.00 3.32
735 770 1.002033 GGTGCTGCTGTTTCTCTGTTG 60.002 52.381 0.00 0.00 0.00 3.33
736 771 1.312815 GGTGCTGCTGTTTCTCTGTT 58.687 50.000 0.00 0.00 0.00 3.16
737 772 0.181114 TGGTGCTGCTGTTTCTCTGT 59.819 50.000 0.00 0.00 0.00 3.41
738 773 0.590195 GTGGTGCTGCTGTTTCTCTG 59.410 55.000 0.00 0.00 0.00 3.35
739 774 0.536006 GGTGGTGCTGCTGTTTCTCT 60.536 55.000 0.00 0.00 0.00 3.10
740 775 0.819259 TGGTGGTGCTGCTGTTTCTC 60.819 55.000 0.00 0.00 0.00 2.87
741 776 0.395586 TTGGTGGTGCTGCTGTTTCT 60.396 50.000 0.00 0.00 0.00 2.52
742 777 0.249031 GTTGGTGGTGCTGCTGTTTC 60.249 55.000 0.00 0.00 0.00 2.78
743 778 1.675720 GGTTGGTGGTGCTGCTGTTT 61.676 55.000 0.00 0.00 0.00 2.83
744 779 2.127232 GGTTGGTGGTGCTGCTGTT 61.127 57.895 0.00 0.00 0.00 3.16
745 780 2.519302 GGTTGGTGGTGCTGCTGT 60.519 61.111 0.00 0.00 0.00 4.40
746 781 3.297620 GGGTTGGTGGTGCTGCTG 61.298 66.667 0.00 0.00 0.00 4.41
747 782 4.603535 GGGGTTGGTGGTGCTGCT 62.604 66.667 0.00 0.00 0.00 4.24
749 784 3.528217 ATGGGGGTTGGTGGTGCTG 62.528 63.158 0.00 0.00 0.00 4.41
750 785 3.192630 ATGGGGGTTGGTGGTGCT 61.193 61.111 0.00 0.00 0.00 4.40
751 786 2.996734 CATGGGGGTTGGTGGTGC 60.997 66.667 0.00 0.00 0.00 5.01
752 787 0.762461 AAACATGGGGGTTGGTGGTG 60.762 55.000 0.00 0.00 0.00 4.17
753 788 0.030603 AAAACATGGGGGTTGGTGGT 60.031 50.000 0.00 0.00 0.00 4.16
754 789 1.071542 GAAAAACATGGGGGTTGGTGG 59.928 52.381 0.00 0.00 0.00 4.61
755 790 2.037121 GAGAAAAACATGGGGGTTGGTG 59.963 50.000 0.00 0.00 0.00 4.17
756 791 2.325484 GAGAAAAACATGGGGGTTGGT 58.675 47.619 0.00 0.00 0.00 3.67
907 967 8.087750 GGATGTAGTATGAGGAAAGAGAAGATG 58.912 40.741 0.00 0.00 0.00 2.90
922 982 6.227298 ACAGGTCTTTGAGGATGTAGTATG 57.773 41.667 0.00 0.00 0.00 2.39
1023 1084 0.958091 TGTTGGACAAAAGCGGATGG 59.042 50.000 0.00 0.00 0.00 3.51
1029 1090 4.293415 CATCAGTTCTGTTGGACAAAAGC 58.707 43.478 0.00 0.00 0.00 3.51
1247 1308 6.426937 GCTATCTGTGAAGGTAACAACAAAGA 59.573 38.462 0.72 0.72 40.58 2.52
1300 1361 1.994507 TTGAACGTGGCAAACCCGTG 61.995 55.000 1.48 0.00 40.52 4.94
1570 1632 1.686800 GGGAAGCCAATGCCATGGT 60.687 57.895 14.67 0.00 42.75 3.55
1582 1645 0.248843 CTGTGGAGAGACTGGGAAGC 59.751 60.000 0.00 0.00 0.00 3.86
1625 1688 6.500684 TTGATCAACAGGAATTAGAGCAAC 57.499 37.500 3.38 0.00 30.69 4.17
1673 1736 6.211584 GGTGCTGTATATTTCTCTCTATCCCA 59.788 42.308 0.00 0.00 0.00 4.37
1787 1851 8.392631 TGTATCCAATATATTATCCTGCCAGT 57.607 34.615 0.00 0.00 0.00 4.00
1812 1876 5.743636 AAATTGTGGTATGTGCCAAAGAT 57.256 34.783 0.00 0.00 40.68 2.40
2102 2166 3.613877 TTTCCATGCCTGCCGCGTA 62.614 57.895 4.92 0.00 42.08 4.42
2287 2351 5.079689 TGCGTGGTATGACTTCAAGAATA 57.920 39.130 0.00 0.00 0.00 1.75
2324 2388 5.743636 ATGTTTGTTCAGGGTTATTGCAT 57.256 34.783 0.00 0.00 0.00 3.96
2354 2418 6.202188 TGTGTCTTCTGTTTCCTTATTTCGTC 59.798 38.462 0.00 0.00 0.00 4.20
2570 2634 4.816925 AGTGAGAGAGTTTTGCTACCAAAC 59.183 41.667 0.00 0.00 40.45 2.93


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

AutoCloner maintained by Alex Coulton.