Multiple sequence alignment - TraesCS4D01G140900

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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 TraesCS4D01G140900 chr4D 100.000 2750 0 0 1 2750 124601110 124598361 0.000000e+00 5079
1 TraesCS4D01G140900 chr4B 89.572 2618 101 77 165 2708 188212616 188210097 0.000000e+00 3164
2 TraesCS4D01G140900 chr4A 90.514 2161 84 39 465 2591 446070953 446073026 0.000000e+00 2743
3 TraesCS4D01G140900 chr4A 86.036 444 27 15 1 425 446068898 446069325 6.990000e-121 444
4 TraesCS4D01G140900 chr4A 87.943 141 6 3 2610 2750 446073282 446073411 3.670000e-34 156


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 TraesCS4D01G140900 chr4D 124598361 124601110 2749 True 5079.000000 5079 100.000000 1 2750 1 chr4D.!!$R1 2749
1 TraesCS4D01G140900 chr4B 188210097 188212616 2519 True 3164.000000 3164 89.572000 165 2708 1 chr4B.!!$R1 2543
2 TraesCS4D01G140900 chr4A 446068898 446073411 4513 False 1114.333333 2743 88.164333 1 2750 3 chr4A.!!$F1 2749

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
456 1435 0.040499 AGAGGTGAGGTGAGAGTCCC 59.96 60.0 0.0 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2346 4049 0.610232 AAAGGTGGTGGCATGAGAGC 60.61 55.0 0.0 0.0 0.0 4.09 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
43 45 0.808755 CAGCTGCTGATGCACATCAA 59.191 50.000 24.88 0.42 46.10 2.57
50 52 5.079689 TGCTGATGCACATCAATGAAAAT 57.920 34.783 13.91 0.00 46.10 1.82
56 58 7.604549 TGATGCACATCAATGAAAATTGTAGT 58.395 30.769 10.82 0.00 44.14 2.73
58 60 6.157904 TGCACATCAATGAAAATTGTAGTGG 58.842 36.000 18.28 8.24 37.59 4.00
59 61 6.015603 TGCACATCAATGAAAATTGTAGTGGA 60.016 34.615 18.28 15.41 37.59 4.02
60 62 6.529125 GCACATCAATGAAAATTGTAGTGGAG 59.471 38.462 18.28 8.37 37.59 3.86
115 120 4.328712 GTCAATTTTGGCGTCAGTTTTGTT 59.671 37.500 0.00 0.00 0.00 2.83
119 124 6.763303 ATTTTGGCGTCAGTTTTGTTTATC 57.237 33.333 0.00 0.00 0.00 1.75
183 192 4.531426 ACAAGGCCGGCCACCAAA 62.531 61.111 45.13 0.00 38.92 3.28
220 229 3.308530 GTCAGAAAACAATTCCAAGGCG 58.691 45.455 0.00 0.00 0.00 5.52
272 285 5.369409 AACCCTAATTAGGTCACTAAGCC 57.631 43.478 26.38 0.00 42.13 4.35
279 292 2.674796 AGGTCACTAAGCCGATGAAC 57.325 50.000 0.00 0.00 0.00 3.18
280 293 1.899814 AGGTCACTAAGCCGATGAACA 59.100 47.619 0.00 0.00 32.20 3.18
281 294 2.501723 AGGTCACTAAGCCGATGAACAT 59.498 45.455 0.00 0.00 32.20 2.71
282 295 2.866762 GGTCACTAAGCCGATGAACATC 59.133 50.000 4.88 4.88 30.08 3.06
283 296 8.818406 TTAGGTCACTAAGCCGATGAACATCG 62.818 46.154 24.32 24.32 44.80 3.84
385 401 2.996691 GCTTTGTTTTTGGTGAAGCG 57.003 45.000 0.00 0.00 34.18 4.68
410 426 1.649390 CCGAGTCTCTCCCTCACACG 61.649 65.000 0.00 0.00 0.00 4.49
442 1421 3.541224 ACACACAGTGAGGAGAGGT 57.459 52.632 7.81 0.00 36.96 3.85
447 1426 0.485099 ACAGTGAGGAGAGGTGAGGT 59.515 55.000 0.00 0.00 0.00 3.85
451 1430 1.076438 TGAGGAGAGGTGAGGTGAGA 58.924 55.000 0.00 0.00 0.00 3.27
452 1431 1.005332 TGAGGAGAGGTGAGGTGAGAG 59.995 57.143 0.00 0.00 0.00 3.20
453 1432 1.005450 GAGGAGAGGTGAGGTGAGAGT 59.995 57.143 0.00 0.00 0.00 3.24
454 1433 1.005450 AGGAGAGGTGAGGTGAGAGTC 59.995 57.143 0.00 0.00 0.00 3.36
455 1434 1.470051 GAGAGGTGAGGTGAGAGTCC 58.530 60.000 0.00 0.00 0.00 3.85
456 1435 0.040499 AGAGGTGAGGTGAGAGTCCC 59.960 60.000 0.00 0.00 0.00 4.46
458 1437 0.040499 AGGTGAGGTGAGAGTCCCTC 59.960 60.000 6.91 6.91 46.20 4.30
459 1438 0.040499 GGTGAGGTGAGAGTCCCTCT 59.960 60.000 13.23 0.00 46.17 3.69
509 2131 0.729116 CCATGTGATGTGAAGGCGTC 59.271 55.000 0.00 0.00 0.00 5.19
529 2151 0.927767 TGTCTCCTACCTCCTCCCTC 59.072 60.000 0.00 0.00 0.00 4.30
564 2191 1.676967 GCTTTCCCCACTGCCTCTG 60.677 63.158 0.00 0.00 0.00 3.35
565 2192 1.676967 CTTTCCCCACTGCCTCTGC 60.677 63.158 0.00 0.00 38.26 4.26
568 2195 4.106925 CCCCACTGCCTCTGCCTC 62.107 72.222 0.00 0.00 36.33 4.70
569 2196 3.007920 CCCACTGCCTCTGCCTCT 61.008 66.667 0.00 0.00 36.33 3.69
570 2197 2.268280 CCACTGCCTCTGCCTCTG 59.732 66.667 0.00 0.00 36.33 3.35
571 2198 2.436292 CACTGCCTCTGCCTCTGC 60.436 66.667 0.00 0.00 36.33 4.26
572 2199 3.715097 ACTGCCTCTGCCTCTGCC 61.715 66.667 0.00 0.00 36.33 4.85
573 2200 3.400928 CTGCCTCTGCCTCTGCCT 61.401 66.667 0.00 0.00 36.33 4.75
574 2201 3.388703 CTGCCTCTGCCTCTGCCTC 62.389 68.421 0.00 0.00 36.33 4.70
575 2202 3.082701 GCCTCTGCCTCTGCCTCT 61.083 66.667 0.00 0.00 36.33 3.69
576 2203 2.901813 CCTCTGCCTCTGCCTCTG 59.098 66.667 0.00 0.00 36.33 3.35
577 2204 2.187424 CTCTGCCTCTGCCTCTGC 59.813 66.667 0.00 0.00 36.33 4.26
578 2205 3.388703 CTCTGCCTCTGCCTCTGCC 62.389 68.421 0.00 0.00 36.33 4.85
579 2206 3.400928 CTGCCTCTGCCTCTGCCT 61.401 66.667 0.00 0.00 36.33 4.75
602 2229 3.282021 GCCTTATCATCACCACACATGT 58.718 45.455 0.00 0.00 0.00 3.21
670 2302 3.416351 CCCCCTCCCCTTCAGTTC 58.584 66.667 0.00 0.00 0.00 3.01
672 2304 2.670148 CCCCTCCCCTTCAGTTCGG 61.670 68.421 0.00 0.00 0.00 4.30
673 2305 1.612442 CCCTCCCCTTCAGTTCGGA 60.612 63.158 0.00 0.00 0.00 4.55
674 2306 1.597461 CCTCCCCTTCAGTTCGGAC 59.403 63.158 0.00 0.00 0.00 4.79
675 2307 1.597461 CTCCCCTTCAGTTCGGACC 59.403 63.158 0.00 0.00 0.00 4.46
676 2308 0.905337 CTCCCCTTCAGTTCGGACCT 60.905 60.000 0.00 0.00 0.00 3.85
734 2373 2.354259 CTTCCACTGTTGCTCATCCTC 58.646 52.381 0.00 0.00 0.00 3.71
735 2374 1.649321 TCCACTGTTGCTCATCCTCT 58.351 50.000 0.00 0.00 0.00 3.69
736 2375 1.552337 TCCACTGTTGCTCATCCTCTC 59.448 52.381 0.00 0.00 0.00 3.20
739 2378 2.027377 CACTGTTGCTCATCCTCTCCTT 60.027 50.000 0.00 0.00 0.00 3.36
748 2387 4.202151 GCTCATCCTCTCCTTCTTCTTCTC 60.202 50.000 0.00 0.00 0.00 2.87
760 2405 2.952978 TCTTCTTCTCCTCTCCGTATGC 59.047 50.000 0.00 0.00 0.00 3.14
785 2430 1.211457 GTGTCTCCTGCCCTGATTGAT 59.789 52.381 0.00 0.00 0.00 2.57
854 2514 0.250513 AGGTTCCTCTGTTCATCGGC 59.749 55.000 0.00 0.00 0.00 5.54
855 2515 1.084370 GGTTCCTCTGTTCATCGGCG 61.084 60.000 0.00 0.00 0.00 6.46
857 2517 2.852495 TTCCTCTGTTCATCGGCGCC 62.852 60.000 19.07 19.07 0.00 6.53
877 2537 4.154918 CGCCAGCTTTCTAGATTCAACTTT 59.845 41.667 0.00 0.00 0.00 2.66
885 2545 5.745312 TCTAGATTCAACTTTGCCTCTGA 57.255 39.130 0.00 0.00 0.00 3.27
886 2546 6.114187 TCTAGATTCAACTTTGCCTCTGAA 57.886 37.500 0.00 0.00 32.67 3.02
894 2554 2.005451 CTTTGCCTCTGAATCGTCTGG 58.995 52.381 0.00 0.00 0.00 3.86
918 2578 2.548920 GGGAGGAGTATCGATGCTTTGG 60.549 54.545 17.46 0.00 34.37 3.28
959 2627 2.005971 ATCCGACTTAGTTTGCCGTC 57.994 50.000 0.00 0.00 0.00 4.79
971 2639 1.223187 TTGCCGTCGAAGAAAGGAAC 58.777 50.000 0.00 0.00 39.69 3.62
981 2649 2.640316 AGAAAGGAACAGAAACCGCT 57.360 45.000 0.00 0.00 0.00 5.52
1515 3196 2.027625 CAACCCGCTGTTCGAGTCC 61.028 63.158 0.00 0.00 41.67 3.85
1951 3646 8.967918 ACTAGTAGTTCTATTTGTGCTATGTGA 58.032 33.333 0.00 0.00 0.00 3.58
1952 3647 9.239002 CTAGTAGTTCTATTTGTGCTATGTGAC 57.761 37.037 0.00 0.00 0.00 3.67
1953 3648 7.611770 AGTAGTTCTATTTGTGCTATGTGACA 58.388 34.615 0.00 0.00 0.00 3.58
2032 3727 5.857268 AGGCAAAACATTTGCACTCTTATT 58.143 33.333 24.22 2.37 46.58 1.40
2033 3728 6.290605 AGGCAAAACATTTGCACTCTTATTT 58.709 32.000 24.22 1.55 46.58 1.40
2034 3729 6.203338 AGGCAAAACATTTGCACTCTTATTTG 59.797 34.615 24.22 0.00 46.58 2.32
2035 3730 5.847515 GCAAAACATTTGCACTCTTATTTGC 59.152 36.000 19.73 14.99 44.34 3.68
2036 3731 6.365050 CAAAACATTTGCACTCTTATTTGCC 58.635 36.000 0.00 0.00 38.00 4.52
2037 3732 5.473066 AACATTTGCACTCTTATTTGCCT 57.527 34.783 0.00 0.00 38.00 4.75
2049 3744 8.338259 CACTCTTATTTGCCTGTTATGTATGAC 58.662 37.037 0.00 0.00 0.00 3.06
2077 3777 7.400439 ACATAAATGGACTATCATCCCAGATG 58.600 38.462 0.00 0.00 38.06 2.90
2080 3780 5.954153 ATGGACTATCATCCCAGATGATC 57.046 43.478 20.35 9.87 39.30 2.92
2095 3795 8.319881 TCCCAGATGATCAGAATATCATTCTTC 58.680 37.037 0.09 0.00 44.69 2.87
2135 3836 5.989477 TCCTAATGTAATGAAGTGTGAGGG 58.011 41.667 0.00 0.00 0.00 4.30
2169 3870 4.715534 TCCTCTTTTGATGGGTTGTACA 57.284 40.909 0.00 0.00 0.00 2.90
2346 4049 3.382546 CCAAGCATATTGACCCCTTTCTG 59.617 47.826 0.00 0.00 0.00 3.02
2507 4210 8.845227 TGTTCATACTGCTTTAGAACAATGAAA 58.155 29.630 0.00 0.00 43.71 2.69
2508 4211 9.846248 GTTCATACTGCTTTAGAACAATGAAAT 57.154 29.630 0.00 0.00 38.66 2.17
2593 4297 5.855045 TCTAAGTCCAACTCAAAAGTCTCC 58.145 41.667 0.00 0.00 33.48 3.71
2600 4304 5.357032 TCCAACTCAAAAGTCTCCAGTTTTC 59.643 40.000 0.00 0.00 33.55 2.29
2603 4307 7.315890 CAACTCAAAAGTCTCCAGTTTTCTTT 58.684 34.615 0.00 0.00 33.55 2.52
2604 4308 7.468141 ACTCAAAAGTCTCCAGTTTTCTTTT 57.532 32.000 0.00 0.00 38.36 2.27
2642 4583 6.170675 GCGAAAGGCGATTGATATATTCTT 57.829 37.500 0.00 0.00 44.57 2.52
2645 4586 8.391106 GCGAAAGGCGATTGATATATTCTTATT 58.609 33.333 0.00 0.00 44.57 1.40
2646 4587 9.694520 CGAAAGGCGATTGATATATTCTTATTG 57.305 33.333 0.00 0.00 44.57 1.90
2647 4588 9.495754 GAAAGGCGATTGATATATTCTTATTGC 57.504 33.333 0.00 0.00 0.00 3.56
2648 4589 8.798859 AAGGCGATTGATATATTCTTATTGCT 57.201 30.769 0.00 0.00 32.01 3.91
2649 4590 8.206325 AGGCGATTGATATATTCTTATTGCTG 57.794 34.615 0.00 0.00 32.01 4.41
2650 4591 6.909357 GGCGATTGATATATTCTTATTGCTGC 59.091 38.462 0.00 0.00 32.01 5.25
2651 4592 6.626488 GCGATTGATATATTCTTATTGCTGCG 59.374 38.462 0.00 0.00 0.00 5.18
2652 4593 7.464577 GCGATTGATATATTCTTATTGCTGCGA 60.465 37.037 0.00 0.00 0.00 5.10
2653 4594 8.546244 CGATTGATATATTCTTATTGCTGCGAT 58.454 33.333 7.65 7.65 0.00 4.58
2655 4596 9.999009 ATTGATATATTCTTATTGCTGCGATTG 57.001 29.630 7.84 2.27 0.00 2.67
2659 4600 2.358957 TCTTATTGCTGCGATTGTGCT 58.641 42.857 7.84 0.00 35.36 4.40
2732 4675 5.636123 TCCTGCCTTTGTCCACTTTAATTA 58.364 37.500 0.00 0.00 0.00 1.40
2741 4684 9.590088 CTTTGTCCACTTTAATTACGTTTAGTC 57.410 33.333 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 14 0.835276 AGCAGCTGATGATGTGGCTA 59.165 50.000 20.43 0.00 33.43 3.93
34 36 6.015603 TCCACTACAATTTTCATTGATGTGCA 60.016 34.615 1.97 0.00 42.35 4.57
77 82 7.148490 GCCAAAATTGACTTACGCCATTTATTT 60.148 33.333 0.00 0.00 0.00 1.40
81 86 3.993736 GCCAAAATTGACTTACGCCATTT 59.006 39.130 0.00 0.00 0.00 2.32
82 87 3.584834 GCCAAAATTGACTTACGCCATT 58.415 40.909 0.00 0.00 0.00 3.16
83 88 2.415357 CGCCAAAATTGACTTACGCCAT 60.415 45.455 0.00 0.00 0.00 4.40
84 89 1.068885 CGCCAAAATTGACTTACGCCA 60.069 47.619 0.00 0.00 0.00 5.69
85 90 1.068816 ACGCCAAAATTGACTTACGCC 60.069 47.619 0.00 0.00 0.00 5.68
86 91 2.239201 GACGCCAAAATTGACTTACGC 58.761 47.619 0.00 0.00 0.00 4.42
87 92 3.059188 ACTGACGCCAAAATTGACTTACG 60.059 43.478 0.00 0.00 0.00 3.18
92 97 3.862845 ACAAAACTGACGCCAAAATTGAC 59.137 39.130 0.00 0.00 0.00 3.18
115 120 4.030913 AGGTCCAAGATTCTCACCGATAA 58.969 43.478 0.00 0.00 31.92 1.75
119 124 1.134670 GGAGGTCCAAGATTCTCACCG 60.135 57.143 0.00 0.00 35.64 4.94
272 285 1.349627 GCACAGGCGATGTTCATCG 59.650 57.895 24.77 24.77 41.41 3.84
283 296 2.814183 GATTGCAGCACAGCACAGGC 62.814 60.000 0.00 0.00 45.61 4.85
284 297 1.211969 GATTGCAGCACAGCACAGG 59.788 57.895 0.00 0.00 45.61 4.00
285 298 1.211969 GGATTGCAGCACAGCACAG 59.788 57.895 0.00 0.00 45.61 3.66
286 299 1.108132 TTGGATTGCAGCACAGCACA 61.108 50.000 0.00 0.00 45.61 4.57
287 300 0.245539 ATTGGATTGCAGCACAGCAC 59.754 50.000 0.00 0.00 45.61 4.40
288 301 0.528924 GATTGGATTGCAGCACAGCA 59.471 50.000 0.00 0.00 43.99 4.41
289 302 0.179119 GGATTGGATTGCAGCACAGC 60.179 55.000 0.00 0.00 0.00 4.40
290 303 1.135199 GTGGATTGGATTGCAGCACAG 60.135 52.381 0.00 0.00 0.00 3.66
385 401 0.968393 AGGGAGAGACTCGGCTGTTC 60.968 60.000 0.00 0.00 0.00 3.18
452 1431 1.304217 TCGTGGAGTGGAGAGGGAC 60.304 63.158 0.00 0.00 0.00 4.46
453 1432 1.000771 CTCGTGGAGTGGAGAGGGA 60.001 63.158 0.00 0.00 31.90 4.20
454 1433 0.612174 TTCTCGTGGAGTGGAGAGGG 60.612 60.000 0.00 0.00 40.17 4.30
455 1434 0.528470 GTTCTCGTGGAGTGGAGAGG 59.472 60.000 0.00 0.00 40.17 3.69
456 1435 0.528470 GGTTCTCGTGGAGTGGAGAG 59.472 60.000 0.00 0.00 40.17 3.20
458 1437 0.528470 GAGGTTCTCGTGGAGTGGAG 59.472 60.000 0.00 0.00 0.00 3.86
459 1438 0.112606 AGAGGTTCTCGTGGAGTGGA 59.887 55.000 0.00 0.00 35.36 4.02
460 1439 0.528470 GAGAGGTTCTCGTGGAGTGG 59.472 60.000 0.00 0.00 33.35 4.00
461 1440 0.528470 GGAGAGGTTCTCGTGGAGTG 59.472 60.000 0.41 0.00 44.28 3.51
509 2131 0.930726 AGGGAGGAGGTAGGAGACAG 59.069 60.000 0.00 0.00 0.00 3.51
555 2182 3.715097 GGCAGAGGCAGAGGCAGT 61.715 66.667 0.00 0.00 43.71 4.40
564 2191 4.527583 CGAGGCAGAGGCAGAGGC 62.528 72.222 0.00 0.00 43.71 4.70
565 2192 4.527583 GCGAGGCAGAGGCAGAGG 62.528 72.222 0.00 0.00 43.71 3.69
568 2195 2.037620 ATAAGGCGAGGCAGAGGCAG 62.038 60.000 0.00 0.00 43.71 4.85
569 2196 2.032860 GATAAGGCGAGGCAGAGGCA 62.033 60.000 0.00 0.00 43.71 4.75
570 2197 1.301322 GATAAGGCGAGGCAGAGGC 60.301 63.158 0.00 0.00 40.13 4.70
571 2198 0.683973 ATGATAAGGCGAGGCAGAGG 59.316 55.000 0.00 0.00 0.00 3.69
572 2199 1.342496 TGATGATAAGGCGAGGCAGAG 59.658 52.381 0.00 0.00 0.00 3.35
573 2200 1.069204 GTGATGATAAGGCGAGGCAGA 59.931 52.381 0.00 0.00 0.00 4.26
574 2201 1.506493 GTGATGATAAGGCGAGGCAG 58.494 55.000 0.00 0.00 0.00 4.85
575 2202 0.106708 GGTGATGATAAGGCGAGGCA 59.893 55.000 0.00 0.00 0.00 4.75
576 2203 0.106708 TGGTGATGATAAGGCGAGGC 59.893 55.000 0.00 0.00 0.00 4.70
577 2204 1.138859 TGTGGTGATGATAAGGCGAGG 59.861 52.381 0.00 0.00 0.00 4.63
578 2205 2.205074 GTGTGGTGATGATAAGGCGAG 58.795 52.381 0.00 0.00 0.00 5.03
579 2206 1.552792 TGTGTGGTGATGATAAGGCGA 59.447 47.619 0.00 0.00 0.00 5.54
670 2302 1.215647 CGAACTGAAGGGAGGTCCG 59.784 63.158 0.00 0.00 41.52 4.79
672 2304 1.202817 GACTCGAACTGAAGGGAGGTC 59.797 57.143 0.00 0.00 0.00 3.85
673 2305 1.203075 AGACTCGAACTGAAGGGAGGT 60.203 52.381 0.00 0.00 0.00 3.85
674 2306 1.474879 GAGACTCGAACTGAAGGGAGG 59.525 57.143 0.00 0.00 0.00 4.30
675 2307 1.474879 GGAGACTCGAACTGAAGGGAG 59.525 57.143 0.00 0.00 0.00 4.30
676 2308 1.075698 AGGAGACTCGAACTGAAGGGA 59.924 52.381 0.00 0.00 32.90 4.20
734 2373 2.687935 CGGAGAGGAGAAGAAGAAGGAG 59.312 54.545 0.00 0.00 0.00 3.69
735 2374 2.041891 ACGGAGAGGAGAAGAAGAAGGA 59.958 50.000 0.00 0.00 0.00 3.36
736 2375 2.452505 ACGGAGAGGAGAAGAAGAAGG 58.547 52.381 0.00 0.00 0.00 3.46
739 2378 2.952978 GCATACGGAGAGGAGAAGAAGA 59.047 50.000 0.00 0.00 0.00 2.87
748 2387 0.250038 CACATGGGCATACGGAGAGG 60.250 60.000 0.00 0.00 0.00 3.69
760 2405 2.273449 GGGCAGGAGACACATGGG 59.727 66.667 0.00 0.00 0.00 4.00
785 2430 2.630098 CCAAGAACAGTGAGTGAGGAGA 59.370 50.000 0.00 0.00 0.00 3.71
854 2514 3.265791 AGTTGAATCTAGAAAGCTGGCG 58.734 45.455 0.00 0.00 0.00 5.69
855 2515 5.397326 CAAAGTTGAATCTAGAAAGCTGGC 58.603 41.667 0.00 0.00 0.00 4.85
857 2517 5.182760 AGGCAAAGTTGAATCTAGAAAGCTG 59.817 40.000 0.00 0.00 0.00 4.24
877 2537 0.904865 ACCCAGACGATTCAGAGGCA 60.905 55.000 0.00 0.00 0.00 4.75
885 2545 0.978146 CTCCTCCCACCCAGACGATT 60.978 60.000 0.00 0.00 0.00 3.34
886 2546 1.381872 CTCCTCCCACCCAGACGAT 60.382 63.158 0.00 0.00 0.00 3.73
894 2554 0.318762 GCATCGATACTCCTCCCACC 59.681 60.000 0.00 0.00 0.00 4.61
959 2627 2.349532 GCGGTTTCTGTTCCTTTCTTCG 60.350 50.000 0.00 0.00 0.00 3.79
971 2639 2.629656 CCCTTGCCAGCGGTTTCTG 61.630 63.158 0.00 0.00 0.00 3.02
981 2649 0.856982 TCTTTTTCTCCCCCTTGCCA 59.143 50.000 0.00 0.00 0.00 4.92
1263 2944 3.403249 CTCGTCGTCGTCGTCCTCG 62.403 68.421 11.41 4.14 38.33 4.63
1266 2947 2.095469 GTCTCGTCGTCGTCGTCC 59.905 66.667 11.41 0.00 38.33 4.79
1951 3646 4.013728 TGCACCTTAAAGTCACAAGTTGT 58.986 39.130 1.64 1.64 0.00 3.32
1952 3647 4.630894 TGCACCTTAAAGTCACAAGTTG 57.369 40.909 0.00 0.00 0.00 3.16
1953 3648 4.705023 ACTTGCACCTTAAAGTCACAAGTT 59.295 37.500 13.02 3.07 39.44 2.66
2002 3697 3.005684 TGCAAATGTTTTGCCTCCTACAG 59.994 43.478 19.09 0.00 44.32 2.74
2032 3727 4.570930 TGTTCGTCATACATAACAGGCAA 58.429 39.130 0.00 0.00 0.00 4.52
2033 3728 4.195225 TGTTCGTCATACATAACAGGCA 57.805 40.909 0.00 0.00 0.00 4.75
2034 3729 6.838198 TTATGTTCGTCATACATAACAGGC 57.162 37.500 0.00 0.00 41.24 4.85
2035 3730 8.282592 CCATTTATGTTCGTCATACATAACAGG 58.717 37.037 7.68 8.66 44.06 4.00
2036 3731 9.040939 TCCATTTATGTTCGTCATACATAACAG 57.959 33.333 7.68 4.61 44.06 3.16
2037 3732 8.822855 GTCCATTTATGTTCGTCATACATAACA 58.177 33.333 7.68 0.00 44.06 2.41
2049 3744 6.230472 TGGGATGATAGTCCATTTATGTTCG 58.770 40.000 0.00 0.00 40.17 3.95
2127 3828 1.415659 AGAGAGCATATGCCCTCACAC 59.584 52.381 32.79 13.39 46.66 3.82
2135 3836 5.121811 TCAAAAGAGGAAGAGAGCATATGC 58.878 41.667 20.36 20.36 42.49 3.14
2346 4049 0.610232 AAAGGTGGTGGCATGAGAGC 60.610 55.000 0.00 0.00 0.00 4.09
2507 4210 3.370840 TGCATTTGTTCCTCCTGCTAT 57.629 42.857 0.00 0.00 34.02 2.97
2508 4211 2.877097 TGCATTTGTTCCTCCTGCTA 57.123 45.000 0.00 0.00 34.02 3.49
2593 4297 6.148264 GCAGAGAGAATGGAAAAGAAAACTG 58.852 40.000 0.00 0.00 0.00 3.16
2600 4304 2.095532 CGCTGCAGAGAGAATGGAAAAG 59.904 50.000 20.43 0.00 0.00 2.27
2603 4307 0.897621 TCGCTGCAGAGAGAATGGAA 59.102 50.000 20.43 0.00 0.00 3.53
2604 4308 0.897621 TTCGCTGCAGAGAGAATGGA 59.102 50.000 20.43 0.00 33.53 3.41
2642 4583 2.749076 AGAAAGCACAATCGCAGCAATA 59.251 40.909 0.00 0.00 0.00 1.90
2645 4586 0.953727 AAGAAAGCACAATCGCAGCA 59.046 45.000 0.00 0.00 0.00 4.41
2646 4587 1.069022 TGAAGAAAGCACAATCGCAGC 60.069 47.619 0.00 0.00 0.00 5.25
2647 4588 2.975410 TGAAGAAAGCACAATCGCAG 57.025 45.000 0.00 0.00 0.00 5.18
2648 4589 2.553602 ACATGAAGAAAGCACAATCGCA 59.446 40.909 0.00 0.00 0.00 5.10
2649 4590 2.912967 CACATGAAGAAAGCACAATCGC 59.087 45.455 0.00 0.00 0.00 4.58
2650 4591 3.495193 CCACATGAAGAAAGCACAATCG 58.505 45.455 0.00 0.00 0.00 3.34
2651 4592 3.367703 CCCCACATGAAGAAAGCACAATC 60.368 47.826 0.00 0.00 0.00 2.67
2652 4593 2.564062 CCCCACATGAAGAAAGCACAAT 59.436 45.455 0.00 0.00 0.00 2.71
2653 4594 1.962807 CCCCACATGAAGAAAGCACAA 59.037 47.619 0.00 0.00 0.00 3.33
2654 4595 1.133513 ACCCCACATGAAGAAAGCACA 60.134 47.619 0.00 0.00 0.00 4.57
2655 4596 1.270550 CACCCCACATGAAGAAAGCAC 59.729 52.381 0.00 0.00 0.00 4.40
2659 4600 4.649267 TGTATCACCCCACATGAAGAAA 57.351 40.909 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.