Multiple sequence alignment - TraesCS2D01G511100

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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 TraesCS2D01G511100 chr2D 100.000 3304 0 0 1 3304 602703074 602706377 0.000000e+00 6102
1 TraesCS2D01G511100 chr2D 85.761 1847 225 26 491 2322 601717994 601716171 0.000000e+00 1919
2 TraesCS2D01G511100 chr2D 84.062 1098 128 28 381 1451 601691746 601690669 0.000000e+00 1014
3 TraesCS2D01G511100 chr2D 97.080 137 3 1 2672 2807 420406024 420406160 2.560000e-56 230
4 TraesCS2D01G511100 chr2A 94.713 2667 129 9 18 2680 735341570 735344228 0.000000e+00 4133
5 TraesCS2D01G511100 chr2A 86.207 1508 197 10 860 2361 734894144 734892642 0.000000e+00 1622
6 TraesCS2D01G511100 chr2A 90.494 526 20 10 2807 3304 735344232 735344755 0.000000e+00 667
7 TraesCS2D01G511100 chr2A 96.377 138 4 1 2671 2807 115247949 115248086 3.320000e-55 226
8 TraesCS2D01G511100 chr2B 94.345 2688 128 16 1 2680 733071493 733074164 0.000000e+00 4100
9 TraesCS2D01G511100 chr2B 85.481 1956 218 32 714 2645 732046385 732044472 0.000000e+00 1978
10 TraesCS2D01G511100 chr2B 83.664 2014 276 35 381 2357 732019147 732017150 0.000000e+00 1847
11 TraesCS2D01G511100 chr2B 83.623 2015 275 35 381 2357 732014380 732012383 0.000000e+00 1842
12 TraesCS2D01G511100 chr2B 91.585 511 31 6 2803 3301 733074162 733074672 0.000000e+00 695
13 TraesCS2D01G511100 chrUn 84.149 2410 303 47 220 2579 258620943 258623323 0.000000e+00 2261
14 TraesCS2D01G511100 chrUn 83.965 2426 309 48 220 2594 296303357 296300961 0.000000e+00 2252
15 TraesCS2D01G511100 chr6D 97.744 133 3 0 2679 2811 435990637 435990505 2.560000e-56 230
16 TraesCS2D01G511100 chr6B 97.744 133 3 0 2676 2808 346808773 346808641 2.560000e-56 230
17 TraesCS2D01G511100 chr5D 97.080 137 3 1 2672 2807 90184285 90184421 2.560000e-56 230
18 TraesCS2D01G511100 chr3D 97.059 136 4 0 2675 2810 210622419 210622554 2.560000e-56 230
19 TraesCS2D01G511100 chr4B 95.139 144 6 1 2671 2814 158279513 158279371 3.320000e-55 226
20 TraesCS2D01G511100 chr1B 95.070 142 5 2 2672 2812 623731977 623732117 4.290000e-54 222
21 TraesCS2D01G511100 chr1D 93.289 149 9 1 2677 2825 43298888 43298741 5.550000e-53 219


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 TraesCS2D01G511100 chr2D 602703074 602706377 3303 False 6102.0 6102 100.0000 1 3304 1 chr2D.!!$F2 3303
1 TraesCS2D01G511100 chr2D 601716171 601717994 1823 True 1919.0 1919 85.7610 491 2322 1 chr2D.!!$R2 1831
2 TraesCS2D01G511100 chr2D 601690669 601691746 1077 True 1014.0 1014 84.0620 381 1451 1 chr2D.!!$R1 1070
3 TraesCS2D01G511100 chr2A 735341570 735344755 3185 False 2400.0 4133 92.6035 18 3304 2 chr2A.!!$F2 3286
4 TraesCS2D01G511100 chr2A 734892642 734894144 1502 True 1622.0 1622 86.2070 860 2361 1 chr2A.!!$R1 1501
5 TraesCS2D01G511100 chr2B 733071493 733074672 3179 False 2397.5 4100 92.9650 1 3301 2 chr2B.!!$F1 3300
6 TraesCS2D01G511100 chr2B 732044472 732046385 1913 True 1978.0 1978 85.4810 714 2645 1 chr2B.!!$R1 1931
7 TraesCS2D01G511100 chr2B 732012383 732019147 6764 True 1844.5 1847 83.6435 381 2357 2 chr2B.!!$R2 1976
8 TraesCS2D01G511100 chrUn 258620943 258623323 2380 False 2261.0 2261 84.1490 220 2579 1 chrUn.!!$F1 2359
9 TraesCS2D01G511100 chrUn 296300961 296303357 2396 True 2252.0 2252 83.9650 220 2594 1 chrUn.!!$R1 2374

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
272 278 0.107643 TTGGCAACGAGGACATGTCA 59.892 50.000 26.47 0.93 42.51 3.58 F
577 601 1.338337 AGATATCAACGAGTGCCTCCG 59.662 52.381 5.32 0.00 0.00 4.63 F
582 606 2.504274 AACGAGTGCCTCCGACCAA 61.504 57.895 0.00 0.00 0.00 3.67 F
848 896 2.551270 AGGACCTAGTTGCTTGATCCA 58.449 47.619 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1467 0.605319 ATGGCCACGACACGTTGATT 60.605 50.000 8.16 0.0 38.32 2.57 R
2229 2301 1.077169 AGTTCCTTCCCCACCATTTCC 59.923 52.381 0.00 0.0 0.00 3.13 R
2231 2303 3.265489 TCTAGTTCCTTCCCCACCATTT 58.735 45.455 0.00 0.0 0.00 2.32 R
2783 5105 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.0 0.00 2.17 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
29 30 4.819761 GACGATGCAGCCTCGCCA 62.820 66.667 18.78 0.00 39.71 5.69
48 49 3.373110 GCCAGAGTTGGGAGGGAAAATAT 60.373 47.826 0.00 0.00 45.16 1.28
74 75 1.448540 CTGCCTAGTCACTTGCCGG 60.449 63.158 0.00 0.00 0.00 6.13
112 114 4.270566 GCTTGTGTCATCTGAGCTAGAATG 59.729 45.833 0.00 0.00 39.30 2.67
133 135 1.472480 GGCGAAACTAATGGTGCATGT 59.528 47.619 0.00 0.00 0.00 3.21
272 278 0.107643 TTGGCAACGAGGACATGTCA 59.892 50.000 26.47 0.93 42.51 3.58
278 284 3.066380 CAACGAGGACATGTCAACATCA 58.934 45.455 26.47 0.00 33.61 3.07
300 307 3.644966 TTGTCGGCCCAAATCTTCTAT 57.355 42.857 0.00 0.00 0.00 1.98
386 394 5.706447 TGGTGTAGCTGTTCTCTAGGATAT 58.294 41.667 0.00 0.00 0.00 1.63
437 446 6.704937 GGTGCCAAGTTATATGTTAGTAGGTC 59.295 42.308 0.00 0.00 0.00 3.85
532 554 6.096001 CCATTTGATATATAAAGCCTCCTGCC 59.904 42.308 0.00 0.00 42.71 4.85
575 599 3.717400 TCAGATATCAACGAGTGCCTC 57.283 47.619 5.32 0.00 0.00 4.70
577 601 1.338337 AGATATCAACGAGTGCCTCCG 59.662 52.381 5.32 0.00 0.00 4.63
582 606 2.504274 AACGAGTGCCTCCGACCAA 61.504 57.895 0.00 0.00 0.00 3.67
630 654 5.931724 TGTATCAATATGCAAGGGACATACG 59.068 40.000 0.00 0.00 33.03 3.06
848 896 2.551270 AGGACCTAGTTGCTTGATCCA 58.449 47.619 0.00 0.00 0.00 3.41
858 910 5.564550 AGTTGCTTGATCCATCAGTTTACT 58.435 37.500 0.00 0.00 38.19 2.24
869 921 9.906660 GATCCATCAGTTTACTGTTATCTCTAG 57.093 37.037 9.53 0.00 44.12 2.43
1205 1277 4.196193 TCAAGAAACGAAGAGCCAAGAAA 58.804 39.130 0.00 0.00 0.00 2.52
1340 1412 3.530535 AGCAACCAACAAATTTGACCAC 58.469 40.909 24.64 7.09 0.00 4.16
1395 1467 7.375834 CACGGTGTATAAAGGCATCTTATCTA 58.624 38.462 0.00 0.00 32.01 1.98
1434 1506 4.262549 CCATCAAGAAGGCCAAAAATGTCA 60.263 41.667 5.01 0.00 0.00 3.58
1451 1523 3.972133 TGTCATGCAGAGGGAAATTGAT 58.028 40.909 0.00 0.00 0.00 2.57
1484 1556 7.581213 AAATGAGGTTGTCATACTTTCACAA 57.419 32.000 0.00 0.00 45.89 3.33
1700 1772 4.932200 GCTGCTTCCATATCAGTATACCAC 59.068 45.833 0.00 0.00 0.00 4.16
1782 1854 3.973206 TTGGAGCTTCGAGGTCAATTA 57.027 42.857 13.47 0.00 44.10 1.40
2006 2078 7.809546 ATCACTAATGAGAGACAATCGTCTA 57.190 36.000 0.00 0.00 44.06 2.59
2114 2186 4.141018 AGCTTAAAAGGGGAAGAAAGACCA 60.141 41.667 0.00 0.00 0.00 4.02
2402 2484 8.258007 TGCTATAAGCCTATAACCATATGTGTC 58.742 37.037 1.24 0.00 41.51 3.67
2427 2528 6.896021 TTCCTATGCTAGTAGGTGATGTAC 57.104 41.667 6.37 0.00 41.65 2.90
2482 2587 3.623060 CAGCTGCAATTTATACCTGACGT 59.377 43.478 0.00 0.00 0.00 4.34
2483 2588 4.808895 CAGCTGCAATTTATACCTGACGTA 59.191 41.667 0.00 0.00 0.00 3.57
2484 2589 5.466728 CAGCTGCAATTTATACCTGACGTAT 59.533 40.000 0.00 0.00 40.84 3.06
2485 2590 6.645003 CAGCTGCAATTTATACCTGACGTATA 59.355 38.462 0.00 0.00 38.64 1.47
2486 2591 6.868864 AGCTGCAATTTATACCTGACGTATAG 59.131 38.462 1.02 0.00 40.29 1.31
2558 2666 4.530553 ACAGGTCCATGAATGTACACACTA 59.469 41.667 0.00 0.00 0.00 2.74
2682 5004 5.118203 ACGCTTTGTCGAAATACTTGTACTC 59.882 40.000 0.00 0.00 0.00 2.59
2684 5006 5.163884 GCTTTGTCGAAATACTTGTACTCCC 60.164 44.000 0.00 0.00 0.00 4.30
2685 5007 5.733620 TTGTCGAAATACTTGTACTCCCT 57.266 39.130 0.00 0.00 0.00 4.20
2686 5008 5.320549 TGTCGAAATACTTGTACTCCCTC 57.679 43.478 0.00 0.00 0.00 4.30
2687 5009 4.159135 TGTCGAAATACTTGTACTCCCTCC 59.841 45.833 0.00 0.00 0.00 4.30
2688 5010 3.379372 TCGAAATACTTGTACTCCCTCCG 59.621 47.826 0.00 0.00 0.00 4.63
2689 5011 3.129988 CGAAATACTTGTACTCCCTCCGT 59.870 47.826 0.00 0.00 0.00 4.69
2690 5012 4.680702 GAAATACTTGTACTCCCTCCGTC 58.319 47.826 0.00 0.00 0.00 4.79
2691 5013 2.134789 TACTTGTACTCCCTCCGTCC 57.865 55.000 0.00 0.00 0.00 4.79
2692 5014 0.614134 ACTTGTACTCCCTCCGTCCC 60.614 60.000 0.00 0.00 0.00 4.46
2693 5015 0.613853 CTTGTACTCCCTCCGTCCCA 60.614 60.000 0.00 0.00 0.00 4.37
2695 5017 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2696 5018 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2697 5019 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2699 5021 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2700 5022 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2701 5023 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2702 5024 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2703 5025 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2704 5026 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2705 5027 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2706 5028 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2707 5029 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2708 5030 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2709 5031 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2710 5032 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2711 5033 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2712 5034 7.335924 CCGTCCCAAAATTCTTGTCTTAGATTA 59.664 37.037 0.00 0.00 0.00 1.75
2713 5035 8.391106 CGTCCCAAAATTCTTGTCTTAGATTAG 58.609 37.037 0.00 0.00 0.00 1.73
2714 5036 9.232473 GTCCCAAAATTCTTGTCTTAGATTAGT 57.768 33.333 0.00 0.00 0.00 2.24
2715 5037 9.449719 TCCCAAAATTCTTGTCTTAGATTAGTC 57.550 33.333 0.00 0.00 0.00 2.59
2716 5038 9.454859 CCCAAAATTCTTGTCTTAGATTAGTCT 57.545 33.333 0.00 0.00 38.52 3.24
2724 5046 9.491675 TCTTGTCTTAGATTAGTCTAGATACGG 57.508 37.037 0.00 0.00 38.17 4.02
2725 5047 9.491675 CTTGTCTTAGATTAGTCTAGATACGGA 57.508 37.037 0.00 0.00 38.17 4.69
2727 5049 9.438228 TGTCTTAGATTAGTCTAGATACGGATG 57.562 37.037 0.00 0.00 38.17 3.51
2728 5050 9.439500 GTCTTAGATTAGTCTAGATACGGATGT 57.561 37.037 0.00 0.00 38.17 3.06
2759 5081 6.743575 ACTAAAATGTGACTTGCTACATCC 57.256 37.500 0.00 0.00 36.56 3.51
2760 5082 4.685169 AAAATGTGACTTGCTACATCCG 57.315 40.909 0.00 0.00 36.56 4.18
2761 5083 3.334583 AATGTGACTTGCTACATCCGT 57.665 42.857 0.00 0.00 36.56 4.69
2762 5084 4.465632 AATGTGACTTGCTACATCCGTA 57.534 40.909 0.00 0.00 36.56 4.02
2763 5085 4.672587 ATGTGACTTGCTACATCCGTAT 57.327 40.909 0.00 0.00 32.32 3.06
2764 5086 4.465632 TGTGACTTGCTACATCCGTATT 57.534 40.909 0.00 0.00 0.00 1.89
2765 5087 4.827692 TGTGACTTGCTACATCCGTATTT 58.172 39.130 0.00 0.00 0.00 1.40
2766 5088 5.968254 TGTGACTTGCTACATCCGTATTTA 58.032 37.500 0.00 0.00 0.00 1.40
2767 5089 6.040247 TGTGACTTGCTACATCCGTATTTAG 58.960 40.000 0.00 0.00 0.00 1.85
2768 5090 6.127563 TGTGACTTGCTACATCCGTATTTAGA 60.128 38.462 0.00 0.00 0.00 2.10
2769 5091 6.198591 GTGACTTGCTACATCCGTATTTAGAC 59.801 42.308 0.00 0.00 0.00 2.59
2770 5092 6.127563 TGACTTGCTACATCCGTATTTAGACA 60.128 38.462 0.00 0.00 0.00 3.41
2771 5093 6.636705 ACTTGCTACATCCGTATTTAGACAA 58.363 36.000 0.00 0.00 0.00 3.18
2772 5094 7.101054 ACTTGCTACATCCGTATTTAGACAAA 58.899 34.615 0.00 0.00 0.00 2.83
2773 5095 7.769044 ACTTGCTACATCCGTATTTAGACAAAT 59.231 33.333 0.00 0.00 38.02 2.32
2774 5096 7.709269 TGCTACATCCGTATTTAGACAAATC 57.291 36.000 0.00 0.00 35.88 2.17
2775 5097 7.497595 TGCTACATCCGTATTTAGACAAATCT 58.502 34.615 0.00 0.00 35.88 2.40
2776 5098 8.635328 TGCTACATCCGTATTTAGACAAATCTA 58.365 33.333 0.00 0.00 35.88 1.98
2777 5099 9.472361 GCTACATCCGTATTTAGACAAATCTAA 57.528 33.333 0.00 0.00 44.17 2.10
2780 5102 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
2781 5103 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
2783 5105 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
2784 5106 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
2792 5114 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2793 5115 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2794 5116 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2795 5117 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2796 5118 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2797 5119 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2798 5120 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2799 5121 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2800 5122 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2801 5123 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2802 5124 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2803 5125 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2804 5126 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2805 5127 1.961133 TTTTGGGACGGAGGGAGTAT 58.039 50.000 0.00 0.00 0.00 2.12
2818 5140 5.183522 CGGAGGGAGTATTAACTTAGCTAGG 59.816 48.000 0.48 0.48 35.56 3.02
2822 5144 8.800515 AGGGAGTATTAACTTAGCTAGGAATT 57.199 34.615 10.24 0.00 35.56 2.17
3070 5411 7.328737 GCATAGGGTGTAAATTAGTACATCGAG 59.671 40.741 0.00 0.00 36.17 4.04
3075 5416 7.434602 GGGTGTAAATTAGTACATCGAGTTCTC 59.565 40.741 0.00 0.00 36.17 2.87
3110 5918 2.258726 GGACAACAACTCCGGGTGC 61.259 63.158 0.00 0.00 0.00 5.01
3116 5924 1.674322 CAACTCCGGGTGCGGAAAT 60.674 57.895 0.00 0.00 37.63 2.17
3159 5967 3.059352 ACCAGCGAGCACTAAAATCTT 57.941 42.857 0.00 0.00 0.00 2.40
3231 6609 6.713450 TGTTGTCCCTTGTTTAATAAGTCTCC 59.287 38.462 1.10 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 5.548573 TCCTATATTTTCCCTCCCAACTCT 58.451 41.667 0.00 0.00 0.00 3.24
48 49 4.383118 GCAAGTGACTAGGCAGATTTCCTA 60.383 45.833 0.00 0.00 35.21 2.94
74 75 9.584839 GATGACACAAGCATTTAATTTTGTTTC 57.415 29.630 9.45 9.45 33.24 2.78
112 114 1.102978 ATGCACCATTAGTTTCGCCC 58.897 50.000 0.00 0.00 0.00 6.13
133 135 7.737972 TTCCATTTAATGAAACTTGACGAGA 57.262 32.000 6.50 0.00 0.00 4.04
272 278 1.626686 TTGGGCCGACAAATGATGTT 58.373 45.000 0.00 0.00 44.12 2.71
300 307 9.421806 CATTGTTCAAGCTTAAACATCCAAATA 57.578 29.630 15.90 0.00 35.46 1.40
386 394 3.072915 CAGTGATATATGGGTTGCCCTCA 59.927 47.826 5.73 0.00 45.70 3.86
401 410 1.915489 ACTTGGCACCCATCAGTGATA 59.085 47.619 5.03 0.00 40.34 2.15
532 554 6.040391 TGAAGGGAAAAATACACTGTTGGAAG 59.960 38.462 0.00 0.00 0.00 3.46
575 599 2.163613 GCAGGGATAAACTTTTGGTCGG 59.836 50.000 0.00 0.00 0.00 4.79
577 601 4.864704 TTGCAGGGATAAACTTTTGGTC 57.135 40.909 0.00 0.00 0.00 4.02
582 606 4.709886 GGTACCATTGCAGGGATAAACTTT 59.290 41.667 7.15 0.00 0.00 2.66
630 654 3.981211 TGTTTTTCTTTGCTGAGCATCC 58.019 40.909 8.44 0.00 38.76 3.51
810 842 4.096984 GGTCCTAGCAGTAGTAGCGTTAAA 59.903 45.833 0.00 0.00 37.01 1.52
815 863 1.970092 AGGTCCTAGCAGTAGTAGCG 58.030 55.000 0.00 0.00 37.01 4.26
816 864 4.089408 ACTAGGTCCTAGCAGTAGTAGC 57.911 50.000 23.70 0.00 37.57 3.58
848 896 8.299990 AGCACTAGAGATAACAGTAAACTGAT 57.700 34.615 16.74 7.58 46.59 2.90
858 910 7.036220 GCTTTGAGTTAGCACTAGAGATAACA 58.964 38.462 23.95 7.49 38.51 2.41
902 961 9.699410 ATTTCCTTTGTTATCCATGTCTGAATA 57.301 29.630 0.00 0.00 0.00 1.75
995 1064 7.178983 TCAAACTTCTCAAATAGGCCATGAAAT 59.821 33.333 5.01 0.00 0.00 2.17
1037 1106 5.218139 GTTCACTTCAAGAAATCAAGCTGG 58.782 41.667 0.00 0.00 0.00 4.85
1340 1412 1.439353 CGCCACCAAGGATCCGATTG 61.439 60.000 5.98 6.43 41.22 2.67
1395 1467 0.605319 ATGGCCACGACACGTTGATT 60.605 50.000 8.16 0.00 38.32 2.57
1434 1506 4.246712 ACTCATCAATTTCCCTCTGCAT 57.753 40.909 0.00 0.00 0.00 3.96
1700 1772 9.445878 AGTATATTGGCACATTTGATATCTCTG 57.554 33.333 3.98 1.71 39.30 3.35
1760 1832 2.169832 TTGACCTCGAAGCTCCAAAG 57.830 50.000 0.00 0.00 0.00 2.77
1782 1854 8.308931 TGTAAGTATTCCTGTTTCGTCTATTGT 58.691 33.333 0.00 0.00 0.00 2.71
2114 2186 3.554934 TGTCTCAACTTGCCTCATTGTT 58.445 40.909 0.00 0.00 0.00 2.83
2229 2301 1.077169 AGTTCCTTCCCCACCATTTCC 59.923 52.381 0.00 0.00 0.00 3.13
2231 2303 3.265489 TCTAGTTCCTTCCCCACCATTT 58.735 45.455 0.00 0.00 0.00 2.32
2240 2312 7.670559 TCCAAGCTATATACTCTAGTTCCTTCC 59.329 40.741 0.00 0.00 0.00 3.46
2402 2484 6.412362 ACATCACCTACTAGCATAGGAAAG 57.588 41.667 12.28 3.72 44.97 2.62
2558 2666 6.194235 TGGTGCTTGAATGGGAACTATTTAT 58.806 36.000 0.00 0.00 0.00 1.40
2603 2712 5.486735 TTTCATTTTCAATGGCATCAGGT 57.513 34.783 0.00 0.00 0.00 4.00
2605 2714 6.647481 TGTCTTTTCATTTTCAATGGCATCAG 59.353 34.615 0.00 0.00 0.00 2.90
2606 2715 6.522946 TGTCTTTTCATTTTCAATGGCATCA 58.477 32.000 0.00 0.00 0.00 3.07
2607 2716 7.424227 TTGTCTTTTCATTTTCAATGGCATC 57.576 32.000 0.00 0.00 0.00 3.91
2682 5004 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2684 5006 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2685 5007 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2686 5008 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2687 5009 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2688 5010 9.232473 ACTAATCTAAGACAAGAATTTTGGGAC 57.768 33.333 5.68 0.00 0.00 4.46
2689 5011 9.449719 GACTAATCTAAGACAAGAATTTTGGGA 57.550 33.333 5.68 0.00 0.00 4.37
2690 5012 9.454859 AGACTAATCTAAGACAAGAATTTTGGG 57.545 33.333 5.68 0.00 31.46 4.12
2699 5021 9.491675 TCCGTATCTAGACTAATCTAAGACAAG 57.508 37.037 0.00 0.00 36.98 3.16
2701 5023 9.438228 CATCCGTATCTAGACTAATCTAAGACA 57.562 37.037 0.00 0.00 36.98 3.41
2702 5024 9.439500 ACATCCGTATCTAGACTAATCTAAGAC 57.561 37.037 0.00 0.00 36.98 3.01
2733 5055 8.893727 GGATGTAGCAAGTCACATTTTAGTATT 58.106 33.333 0.00 0.00 35.55 1.89
2734 5056 7.224753 CGGATGTAGCAAGTCACATTTTAGTAT 59.775 37.037 0.00 0.00 35.55 2.12
2735 5057 6.533723 CGGATGTAGCAAGTCACATTTTAGTA 59.466 38.462 0.00 0.00 35.55 1.82
2736 5058 5.351465 CGGATGTAGCAAGTCACATTTTAGT 59.649 40.000 0.00 0.00 35.55 2.24
2737 5059 5.351465 ACGGATGTAGCAAGTCACATTTTAG 59.649 40.000 0.00 0.00 35.55 1.85
2738 5060 5.242434 ACGGATGTAGCAAGTCACATTTTA 58.758 37.500 0.00 0.00 35.55 1.52
2739 5061 4.072131 ACGGATGTAGCAAGTCACATTTT 58.928 39.130 0.00 0.00 35.55 1.82
2740 5062 3.674997 ACGGATGTAGCAAGTCACATTT 58.325 40.909 0.00 0.00 35.55 2.32
2741 5063 3.334583 ACGGATGTAGCAAGTCACATT 57.665 42.857 0.00 0.00 35.55 2.71
2742 5064 4.672587 ATACGGATGTAGCAAGTCACAT 57.327 40.909 0.00 0.00 38.08 3.21
2743 5065 4.465632 AATACGGATGTAGCAAGTCACA 57.534 40.909 0.00 0.00 33.17 3.58
2744 5066 6.198591 GTCTAAATACGGATGTAGCAAGTCAC 59.801 42.308 0.00 0.00 33.17 3.67
2745 5067 6.127563 TGTCTAAATACGGATGTAGCAAGTCA 60.128 38.462 0.00 0.00 33.17 3.41
2746 5068 6.270815 TGTCTAAATACGGATGTAGCAAGTC 58.729 40.000 0.00 0.00 33.17 3.01
2747 5069 6.216801 TGTCTAAATACGGATGTAGCAAGT 57.783 37.500 0.00 0.00 33.17 3.16
2748 5070 7.534085 TTTGTCTAAATACGGATGTAGCAAG 57.466 36.000 11.89 0.00 33.17 4.01
2749 5071 7.985184 AGATTTGTCTAAATACGGATGTAGCAA 59.015 33.333 0.00 5.47 36.66 3.91
2750 5072 7.497595 AGATTTGTCTAAATACGGATGTAGCA 58.502 34.615 0.00 0.00 36.66 3.49
2751 5073 7.948278 AGATTTGTCTAAATACGGATGTAGC 57.052 36.000 0.00 0.00 36.66 3.58
2754 5076 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
2755 5077 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
2757 5079 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
2758 5080 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
2766 5088 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2767 5089 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2768 5090 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2769 5091 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2770 5092 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2771 5093 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2772 5094 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2773 5095 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2774 5096 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2775 5097 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2776 5098 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2777 5099 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2778 5100 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2779 5101 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2780 5102 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2781 5103 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2782 5104 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2783 5105 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2784 5106 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2785 5107 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
2786 5108 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
2787 5109 1.961133 AATACTCCCTCCGTCCCAAA 58.039 50.000 0.00 0.00 0.00 3.28
2788 5110 2.767960 GTTAATACTCCCTCCGTCCCAA 59.232 50.000 0.00 0.00 0.00 4.12
2789 5111 2.023695 AGTTAATACTCCCTCCGTCCCA 60.024 50.000 0.00 0.00 0.00 4.37
2790 5112 2.675583 AGTTAATACTCCCTCCGTCCC 58.324 52.381 0.00 0.00 0.00 4.46
2791 5113 4.261952 GCTAAGTTAATACTCCCTCCGTCC 60.262 50.000 0.00 0.00 31.99 4.79
2792 5114 4.583907 AGCTAAGTTAATACTCCCTCCGTC 59.416 45.833 0.00 0.00 31.99 4.79
2793 5115 4.544683 AGCTAAGTTAATACTCCCTCCGT 58.455 43.478 0.00 0.00 31.99 4.69
2794 5116 5.183522 CCTAGCTAAGTTAATACTCCCTCCG 59.816 48.000 0.00 0.00 31.99 4.63
2795 5117 6.313324 TCCTAGCTAAGTTAATACTCCCTCC 58.687 44.000 0.00 0.00 31.99 4.30
2796 5118 7.836479 TTCCTAGCTAAGTTAATACTCCCTC 57.164 40.000 0.00 0.00 31.99 4.30
2797 5119 8.800515 AATTCCTAGCTAAGTTAATACTCCCT 57.199 34.615 0.00 0.00 31.99 4.20
2798 5120 8.648693 TGAATTCCTAGCTAAGTTAATACTCCC 58.351 37.037 2.27 0.00 31.99 4.30
2799 5121 9.478768 GTGAATTCCTAGCTAAGTTAATACTCC 57.521 37.037 2.27 0.00 31.99 3.85
2800 5122 9.478768 GGTGAATTCCTAGCTAAGTTAATACTC 57.521 37.037 2.27 0.00 31.99 2.59
2801 5123 8.989131 TGGTGAATTCCTAGCTAAGTTAATACT 58.011 33.333 2.27 0.00 35.68 2.12
2802 5124 9.262358 CTGGTGAATTCCTAGCTAAGTTAATAC 57.738 37.037 2.27 0.00 0.00 1.89
2803 5125 8.429641 CCTGGTGAATTCCTAGCTAAGTTAATA 58.570 37.037 2.27 0.00 0.00 0.98
2804 5126 7.283329 CCTGGTGAATTCCTAGCTAAGTTAAT 58.717 38.462 2.27 0.00 0.00 1.40
2805 5127 6.650120 CCTGGTGAATTCCTAGCTAAGTTAA 58.350 40.000 2.27 0.00 0.00 2.01
2818 5140 1.317613 TGTGTGTGCCTGGTGAATTC 58.682 50.000 0.00 0.00 0.00 2.17
2822 5144 2.877097 ATATTGTGTGTGCCTGGTGA 57.123 45.000 0.00 0.00 0.00 4.02
3110 5918 9.797473 GCTAAATTTTCTCTTTCAAAATTTCCG 57.203 29.630 15.57 11.06 44.52 4.30
3116 5924 8.043710 TGGTTGGCTAAATTTTCTCTTTCAAAA 58.956 29.630 0.00 0.00 0.00 2.44
3159 5967 7.051623 ACAGTAATTAATCGGCTCAATTGGTA 58.948 34.615 5.42 0.00 0.00 3.25


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

AutoCloner maintained by Alex Coulton.