Multiple sequence alignment - TraesCS2B01G123900

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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 TraesCS2B01G123900 chr2B 100.000 3359 0 0 1 3359 91835457 91838815 0.000000e+00 6204.0
1 TraesCS2B01G123900 chr2B 92.086 139 8 2 313 448 91835722 91835860 3.420000e-45 193.0
2 TraesCS2B01G123900 chr2B 92.086 139 8 2 266 404 91835769 91835904 3.420000e-45 193.0
3 TraesCS2B01G123900 chr2B 100.000 28 0 0 3066 3093 91838494 91838521 6.000000e-03 52.8
4 TraesCS2B01G123900 chr2B 100.000 28 0 0 3038 3065 91838522 91838549 6.000000e-03 52.8
5 TraesCS2B01G123900 chr2A 92.254 3008 169 30 258 3245 59324729 59321766 0.000000e+00 4205.0
6 TraesCS2B01G123900 chr2A 86.275 459 45 11 1 448 59325034 59324583 1.810000e-132 483.0
7 TraesCS2B01G123900 chr2A 84.892 139 18 2 313 448 59324768 59324630 1.630000e-28 137.0
8 TraesCS2B01G123900 chr2A 86.364 132 8 4 3233 3359 59321749 59321623 5.850000e-28 135.0
9 TraesCS2B01G123900 chr2D 94.041 2618 107 18 313 2906 59006378 59008970 0.000000e+00 3925.0
10 TraesCS2B01G123900 chr2D 86.715 414 33 9 1 404 59006119 59006520 1.110000e-119 440.0
11 TraesCS2B01G123900 chr2D 90.076 262 22 1 3102 3359 59008991 59009252 1.490000e-88 337.0
12 TraesCS2B01G123900 chr2D 93.651 189 5 2 2877 3065 59009292 59009473 3.300000e-70 276.0
13 TraesCS2B01G123900 chr2D 85.981 214 24 2 3147 3359 59009555 59009763 1.210000e-54 224.0
14 TraesCS2B01G123900 chr2D 93.103 87 6 0 3067 3153 59009447 59009533 9.780000e-26 128.0
15 TraesCS2B01G123900 chr3D 76.013 617 142 6 1052 1665 116042501 116043114 7.000000e-82 315.0
16 TraesCS2B01G123900 chr3B 75.365 617 146 6 1052 1665 169628732 169629345 3.280000e-75 292.0
17 TraesCS2B01G123900 chr3A 75.365 617 146 6 1052 1665 112957494 112958107 3.280000e-75 292.0


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 TraesCS2B01G123900 chr2B 91835457 91838815 3358 False 1339.120000 6204 96.83440 1 3359 5 chr2B.!!$F1 3358
1 TraesCS2B01G123900 chr2A 59321623 59325034 3411 True 1240.000000 4205 87.44625 1 3359 4 chr2A.!!$R1 3358
2 TraesCS2B01G123900 chr2D 59006119 59009763 3644 False 888.333333 3925 90.59450 1 3359 6 chr2D.!!$F1 3358
3 TraesCS2B01G123900 chr3D 116042501 116043114 613 False 315.000000 315 76.01300 1052 1665 1 chr3D.!!$F1 613
4 TraesCS2B01G123900 chr3B 169628732 169629345 613 False 292.000000 292 75.36500 1052 1665 1 chr3B.!!$F1 613
5 TraesCS2B01G123900 chr3A 112957494 112958107 613 False 292.000000 292 75.36500 1052 1665 1 chr3A.!!$F1 613

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
365 425 0.394565 GGCTAAGGGACGCATCTGAT 59.605 55.0 0.0 0.0 0.00 2.90 F
1593 1656 0.393537 CCAAGGCTGACATCTGGTCC 60.394 60.0 0.0 0.0 46.38 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 1749 0.252375 ACCAGCTGGGGCATTTGAAT 60.252 50.0 35.42 8.61 42.91 2.57 R
2847 2937 0.031616 CTGCTCCCTCCCTACTTCCT 60.032 60.0 0.00 0.00 0.00 3.36 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
97 102 2.682155 AATCGTTCTCCTTCTCCTGC 57.318 50.000 0.00 0.00 0.00 4.85
111 116 2.168621 CTGCTGTTCGTTCGTGCG 59.831 61.111 0.00 0.00 0.00 5.34
112 117 2.278923 TGCTGTTCGTTCGTGCGA 60.279 55.556 0.00 0.51 39.28 5.10
116 121 1.401530 CTGTTCGTTCGTGCGAGTTA 58.598 50.000 0.00 0.00 42.10 2.24
120 125 1.155889 TCGTTCGTGCGAGTTACCTA 58.844 50.000 0.00 0.00 35.83 3.08
121 126 1.535028 TCGTTCGTGCGAGTTACCTAA 59.465 47.619 0.00 0.00 35.83 2.69
125 130 4.634991 GTTCGTGCGAGTTACCTAATTTG 58.365 43.478 0.00 0.00 0.00 2.32
126 131 2.669434 TCGTGCGAGTTACCTAATTTGC 59.331 45.455 0.00 0.00 34.13 3.68
127 132 2.671396 CGTGCGAGTTACCTAATTTGCT 59.329 45.455 0.00 0.00 34.50 3.91
128 133 3.861113 CGTGCGAGTTACCTAATTTGCTA 59.139 43.478 0.00 0.00 34.50 3.49
130 135 4.868734 GTGCGAGTTACCTAATTTGCTACT 59.131 41.667 0.00 0.00 34.50 2.57
131 136 5.350640 GTGCGAGTTACCTAATTTGCTACTT 59.649 40.000 0.00 0.00 34.50 2.24
132 137 5.350365 TGCGAGTTACCTAATTTGCTACTTG 59.650 40.000 0.00 0.00 34.50 3.16
133 138 5.220605 GCGAGTTACCTAATTTGCTACTTGG 60.221 44.000 0.00 0.00 31.73 3.61
156 168 1.079875 GTTAGATGCGCGTTTCCGGA 61.080 55.000 8.43 0.00 33.68 5.14
208 220 2.279935 TTTGGCGTGATAGGTTGGTT 57.720 45.000 0.00 0.00 0.00 3.67
209 221 3.420300 TTTGGCGTGATAGGTTGGTTA 57.580 42.857 0.00 0.00 0.00 2.85
210 222 3.637911 TTGGCGTGATAGGTTGGTTAT 57.362 42.857 0.00 0.00 0.00 1.89
223 235 2.148916 TGGTTATTATGCGCGGAGAG 57.851 50.000 8.83 0.00 0.00 3.20
251 263 1.694150 TCCATCAGCTAGGTGCCATAC 59.306 52.381 17.20 0.00 44.23 2.39
254 266 2.988010 TCAGCTAGGTGCCATACAAG 57.012 50.000 17.20 0.00 44.23 3.16
255 267 2.187958 TCAGCTAGGTGCCATACAAGT 58.812 47.619 17.20 0.00 44.23 3.16
263 275 2.030274 GGTGCCATACAAGTTTGGACAC 60.030 50.000 18.85 18.85 37.64 3.67
309 369 5.221661 ACCACTCTTAATAATCCGGCTAAGG 60.222 44.000 0.00 0.00 0.00 2.69
331 391 2.415512 GACGCATCTGGTTGGAGTTTAC 59.584 50.000 0.00 0.00 0.00 2.01
353 413 1.605712 CGCCTCTTAATCCGGCTAAGG 60.606 57.143 17.97 10.55 41.61 2.69
356 416 2.037381 CCTCTTAATCCGGCTAAGGGAC 59.963 54.545 19.38 0.00 36.14 4.46
363 423 1.592669 CGGCTAAGGGACGCATCTG 60.593 63.158 0.00 0.00 40.63 2.90
364 424 1.823295 GGCTAAGGGACGCATCTGA 59.177 57.895 0.00 0.00 0.00 3.27
365 425 0.394565 GGCTAAGGGACGCATCTGAT 59.605 55.000 0.00 0.00 0.00 2.90
366 426 1.506493 GCTAAGGGACGCATCTGATG 58.494 55.000 13.26 13.26 0.00 3.07
444 507 2.037381 CCTCTTAATCCGGCTAAGGGAC 59.963 54.545 19.38 0.00 36.14 4.46
609 672 7.044798 AGAAGAATCTTCTAGTTTCGGAATGG 58.955 38.462 22.72 0.00 36.28 3.16
650 713 3.069586 TGCTCTATGGCTAACGTTATGCT 59.930 43.478 21.09 10.87 0.00 3.79
1542 1605 1.718757 CGCCTGCTTATGTTGCTCCC 61.719 60.000 0.00 0.00 0.00 4.30
1593 1656 0.393537 CCAAGGCTGACATCTGGTCC 60.394 60.000 0.00 0.00 46.38 4.46
1686 1749 7.402054 TGTATAAGAAGATTGGGAAAGCAGAA 58.598 34.615 0.00 0.00 0.00 3.02
1698 1761 3.264947 GAAAGCAGAATTCAAATGCCCC 58.735 45.455 12.99 1.90 40.89 5.80
1701 1764 1.741394 GCAGAATTCAAATGCCCCAGC 60.741 52.381 8.44 0.00 40.48 4.85
1719 1782 4.502950 CCCAGCTGGTTCTCTTCAGATATC 60.503 50.000 30.63 0.00 33.11 1.63
1877 1940 0.321387 CCTGCTGCTGACATGACTGT 60.321 55.000 8.20 0.00 38.67 3.55
1888 1951 4.814147 TGACATGACTGTGACTTCTGATC 58.186 43.478 0.00 0.00 35.14 2.92
1931 1994 0.111253 ACAGAGGGCAAGGAACAAGG 59.889 55.000 0.00 0.00 0.00 3.61
1938 2001 1.000171 GGCAAGGAACAAGGAGCAAAG 60.000 52.381 0.00 0.00 0.00 2.77
2088 2151 4.556233 TCGTGTCAAAGATCGAAGACATT 58.444 39.130 16.37 0.00 42.51 2.71
2187 2250 2.093890 GGTGTGATGTCCATTGATGCA 58.906 47.619 0.00 0.00 0.00 3.96
2202 2265 4.248691 TGATGCAGAGATATTCGAGGTG 57.751 45.455 0.00 0.00 0.00 4.00
2313 2376 2.114616 CTGAAGGACATAGTCTGGGCT 58.885 52.381 0.00 0.00 32.47 5.19
2391 2469 5.671742 GCCAAGTGCAACATTTTTACAAT 57.328 34.783 0.00 0.00 41.43 2.71
2392 2470 5.678921 GCCAAGTGCAACATTTTTACAATC 58.321 37.500 0.00 0.00 41.43 2.67
2393 2471 5.334028 GCCAAGTGCAACATTTTTACAATCC 60.334 40.000 0.00 0.00 41.43 3.01
2410 2488 1.224592 CCGAGGCAATTACCAGGCT 59.775 57.895 0.00 0.00 43.98 4.58
2414 2492 1.002857 AGGCAATTACCAGGCTTCCT 58.997 50.000 0.00 0.00 37.35 3.36
2493 2571 6.258727 AGTGATGTCTGTGTAAACTTCAGTTG 59.741 38.462 0.00 0.00 38.44 3.16
2501 2579 7.224753 TCTGTGTAAACTTCAGTTGTCATCTTC 59.775 37.037 0.00 0.00 38.44 2.87
2600 2678 4.155099 CAGTGCGTTTGTGTATGGGAAATA 59.845 41.667 0.00 0.00 0.00 1.40
2656 2734 8.876275 ATCTTCGTGTTGTTACTGTTTAACTA 57.124 30.769 0.00 0.00 0.00 2.24
2659 2737 7.410800 TCGTGTTGTTACTGTTTAACTATGG 57.589 36.000 0.00 0.00 0.00 2.74
2675 2753 8.584063 TTAACTATGGCATGCATCATGATTAT 57.416 30.769 21.36 0.77 43.81 1.28
2702 2780 6.655003 TCCACTATTCTTGTGATCTGAAAACC 59.345 38.462 0.00 0.00 37.60 3.27
2728 2806 9.277783 CCTAGAGGGTGACATATTTAAATCTTG 57.722 37.037 3.39 6.73 0.00 3.02
2733 2811 9.308000 AGGGTGACATATTTAAATCTTGTTTGA 57.692 29.630 3.39 0.00 0.00 2.69
2744 2822 6.759497 AAATCTTGTTTGATGGGTAGCTAC 57.241 37.500 15.88 15.88 0.00 3.58
2885 2975 6.369059 AGCAGTAGCATTATTTTACAGCTG 57.631 37.500 13.48 13.48 45.49 4.24
3026 3472 4.406648 AAAGAAAAGGCAGAAAACCCTG 57.593 40.909 0.00 0.00 37.23 4.45
3040 3486 1.680338 ACCCTGTTGCTTCACAGTTC 58.320 50.000 9.50 0.00 42.45 3.01
3041 3487 1.064758 ACCCTGTTGCTTCACAGTTCA 60.065 47.619 9.50 0.00 42.45 3.18
3042 3488 1.334869 CCCTGTTGCTTCACAGTTCAC 59.665 52.381 9.50 0.00 42.45 3.18
3043 3489 2.016318 CCTGTTGCTTCACAGTTCACA 58.984 47.619 9.50 0.00 42.45 3.58
3044 3490 2.032550 CCTGTTGCTTCACAGTTCACAG 59.967 50.000 9.50 0.00 42.45 3.66
3045 3491 2.679837 CTGTTGCTTCACAGTTCACAGT 59.320 45.455 3.79 0.00 39.59 3.55
3046 3492 3.081061 TGTTGCTTCACAGTTCACAGTT 58.919 40.909 0.00 0.00 0.00 3.16
3047 3493 4.257731 TGTTGCTTCACAGTTCACAGTTA 58.742 39.130 0.00 0.00 0.00 2.24
3048 3494 4.094294 TGTTGCTTCACAGTTCACAGTTAC 59.906 41.667 0.00 0.00 0.00 2.50
3049 3495 3.867857 TGCTTCACAGTTCACAGTTACA 58.132 40.909 0.00 0.00 0.00 2.41
3050 3496 4.257731 TGCTTCACAGTTCACAGTTACAA 58.742 39.130 0.00 0.00 0.00 2.41
3051 3497 4.881273 TGCTTCACAGTTCACAGTTACAAT 59.119 37.500 0.00 0.00 0.00 2.71
3052 3498 5.007626 TGCTTCACAGTTCACAGTTACAATC 59.992 40.000 0.00 0.00 0.00 2.67
3053 3499 5.237344 GCTTCACAGTTCACAGTTACAATCT 59.763 40.000 0.00 0.00 0.00 2.40
3054 3500 6.238484 GCTTCACAGTTCACAGTTACAATCTT 60.238 38.462 0.00 0.00 0.00 2.40
3055 3501 7.624360 TTCACAGTTCACAGTTACAATCTTT 57.376 32.000 0.00 0.00 0.00 2.52
3056 3502 8.725405 TTCACAGTTCACAGTTACAATCTTTA 57.275 30.769 0.00 0.00 0.00 1.85
3057 3503 8.902540 TCACAGTTCACAGTTACAATCTTTAT 57.097 30.769 0.00 0.00 0.00 1.40
3058 3504 8.988934 TCACAGTTCACAGTTACAATCTTTATC 58.011 33.333 0.00 0.00 0.00 1.75
3059 3505 8.773645 CACAGTTCACAGTTACAATCTTTATCA 58.226 33.333 0.00 0.00 0.00 2.15
3060 3506 9.337396 ACAGTTCACAGTTACAATCTTTATCAA 57.663 29.630 0.00 0.00 0.00 2.57
3061 3507 9.817365 CAGTTCACAGTTACAATCTTTATCAAG 57.183 33.333 0.00 0.00 0.00 3.02
3062 3508 9.003658 AGTTCACAGTTACAATCTTTATCAAGG 57.996 33.333 0.00 0.00 0.00 3.61
3063 3509 8.999431 GTTCACAGTTACAATCTTTATCAAGGA 58.001 33.333 0.00 0.00 0.00 3.36
3064 3510 8.777865 TCACAGTTACAATCTTTATCAAGGAG 57.222 34.615 0.00 0.00 0.00 3.69
3065 3511 7.824289 TCACAGTTACAATCTTTATCAAGGAGG 59.176 37.037 0.00 0.00 0.00 4.30
3066 3512 7.607991 CACAGTTACAATCTTTATCAAGGAGGT 59.392 37.037 0.00 0.00 0.00 3.85
3067 3513 8.164070 ACAGTTACAATCTTTATCAAGGAGGTT 58.836 33.333 0.00 0.00 0.00 3.50
3068 3514 8.669243 CAGTTACAATCTTTATCAAGGAGGTTC 58.331 37.037 0.00 0.00 0.00 3.62
3069 3515 8.383175 AGTTACAATCTTTATCAAGGAGGTTCA 58.617 33.333 0.00 0.00 0.00 3.18
3070 3516 8.451748 GTTACAATCTTTATCAAGGAGGTTCAC 58.548 37.037 0.00 0.00 0.00 3.18
3071 3517 6.542821 ACAATCTTTATCAAGGAGGTTCACA 58.457 36.000 0.00 0.00 0.00 3.58
3072 3518 6.656693 ACAATCTTTATCAAGGAGGTTCACAG 59.343 38.462 0.00 0.00 0.00 3.66
3073 3519 5.825593 TCTTTATCAAGGAGGTTCACAGT 57.174 39.130 0.00 0.00 0.00 3.55
3143 3589 5.057149 TCACAGTTACAAAGAGGAAAGCTC 58.943 41.667 0.00 0.00 0.00 4.09
3146 3592 5.529060 ACAGTTACAAAGAGGAAAGCTCAAG 59.471 40.000 0.00 0.00 0.00 3.02
3171 3645 5.390991 GCAGTAGTTTTCATACTCTGCCAAC 60.391 44.000 12.81 0.00 40.02 3.77
3257 3761 6.660722 GCAAGATGCTGAATAAGATTCAGAG 58.339 40.000 26.02 8.26 46.57 3.35
3260 3764 9.491675 CAAGATGCTGAATAAGATTCAGAGTAT 57.508 33.333 26.02 17.75 46.57 2.12
3312 3820 2.615912 CTGAGGCAAAGATTCGGGAATC 59.384 50.000 12.40 12.40 45.66 2.52
3328 3836 3.130693 GGGAATCGCTGTAGACTGTAGTT 59.869 47.826 0.00 0.00 0.00 2.24
3330 3838 4.380655 GGAATCGCTGTAGACTGTAGTTGT 60.381 45.833 0.00 0.00 0.00 3.32
3331 3839 4.785511 ATCGCTGTAGACTGTAGTTGTT 57.214 40.909 0.00 0.00 0.00 2.83
3332 3840 4.579454 TCGCTGTAGACTGTAGTTGTTT 57.421 40.909 0.00 0.00 0.00 2.83
3333 3841 4.295870 TCGCTGTAGACTGTAGTTGTTTG 58.704 43.478 0.00 0.00 0.00 2.93
3334 3842 4.037089 TCGCTGTAGACTGTAGTTGTTTGA 59.963 41.667 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
79 84 1.480137 CAGCAGGAGAAGGAGAACGAT 59.520 52.381 0.00 0.00 0.00 3.73
97 102 1.121967 GTAACTCGCACGAACGAACAG 59.878 52.381 0.14 0.00 42.39 3.16
116 121 4.736473 ACCAACCAAGTAGCAAATTAGGT 58.264 39.130 0.00 0.00 0.00 3.08
120 125 6.572314 GCATCTAACCAACCAAGTAGCAAATT 60.572 38.462 0.00 0.00 0.00 1.82
121 126 5.105756 GCATCTAACCAACCAAGTAGCAAAT 60.106 40.000 0.00 0.00 0.00 2.32
125 130 2.351726 CGCATCTAACCAACCAAGTAGC 59.648 50.000 0.00 0.00 0.00 3.58
126 131 2.351726 GCGCATCTAACCAACCAAGTAG 59.648 50.000 0.30 0.00 0.00 2.57
127 132 2.352388 GCGCATCTAACCAACCAAGTA 58.648 47.619 0.30 0.00 0.00 2.24
128 133 1.165270 GCGCATCTAACCAACCAAGT 58.835 50.000 0.30 0.00 0.00 3.16
130 135 0.604243 ACGCGCATCTAACCAACCAA 60.604 50.000 5.73 0.00 0.00 3.67
131 136 0.604243 AACGCGCATCTAACCAACCA 60.604 50.000 5.73 0.00 0.00 3.67
132 137 0.519961 AAACGCGCATCTAACCAACC 59.480 50.000 5.73 0.00 0.00 3.77
133 138 1.465187 GGAAACGCGCATCTAACCAAC 60.465 52.381 5.73 0.00 0.00 3.77
156 168 2.555757 GCCAAAACAGAAGAGACAGCAT 59.444 45.455 0.00 0.00 0.00 3.79
208 220 3.067601 TCTGTTTCTCTCCGCGCATAATA 59.932 43.478 8.75 0.00 0.00 0.98
209 221 2.159099 TCTGTTTCTCTCCGCGCATAAT 60.159 45.455 8.75 0.00 0.00 1.28
210 222 1.203758 TCTGTTTCTCTCCGCGCATAA 59.796 47.619 8.75 0.00 0.00 1.90
223 235 4.125703 CACCTAGCTGATGGATCTGTTTC 58.874 47.826 0.00 0.00 0.00 2.78
251 263 0.240945 GATGCGGGTGTCCAAACTTG 59.759 55.000 0.00 0.00 0.00 3.16
254 266 1.586154 CCAGATGCGGGTGTCCAAAC 61.586 60.000 0.00 0.00 0.00 2.93
255 267 1.303236 CCAGATGCGGGTGTCCAAA 60.303 57.895 0.00 0.00 0.00 3.28
309 369 0.321653 AACTCCAACCAGATGCGTCC 60.322 55.000 1.23 0.00 0.00 4.79
331 391 3.719214 GCCGGATTAAGAGGCGTG 58.281 61.111 5.05 0.00 41.53 5.34
353 413 0.745845 AACTGCCATCAGATGCGTCC 60.746 55.000 4.68 0.00 42.95 4.79
356 416 2.286294 GTCTAAACTGCCATCAGATGCG 59.714 50.000 4.68 0.00 42.95 4.73
363 423 1.840635 AGAGGGGTCTAAACTGCCATC 59.159 52.381 0.00 0.00 0.00 3.51
364 424 1.972588 AGAGGGGTCTAAACTGCCAT 58.027 50.000 0.00 0.00 0.00 4.40
365 425 1.742308 AAGAGGGGTCTAAACTGCCA 58.258 50.000 0.00 0.00 0.00 4.92
366 426 3.994931 TTAAGAGGGGTCTAAACTGCC 57.005 47.619 0.00 0.00 0.00 4.85
609 672 5.698545 AGAGCAATCTGTAGTGAAGACAAAC 59.301 40.000 0.00 0.00 0.00 2.93
650 713 8.974060 AGGTACTGTCAATCAAGAAAGTAAAA 57.026 30.769 0.00 0.00 39.41 1.52
776 839 5.125097 GTCATCAAGGTCAATCAAAGCAGAT 59.875 40.000 0.00 0.00 0.00 2.90
1005 1068 3.392616 TCAGAATATTCCCCTTCTGCTCC 59.607 47.826 11.92 0.00 45.12 4.70
1212 1275 6.595326 TGACCTCATACATCTGAACAATGTTC 59.405 38.462 18.42 18.42 38.31 3.18
1365 1428 2.684881 CCTGCTGTGACAAAAGTCAACT 59.315 45.455 0.00 0.00 34.88 3.16
1542 1605 4.446371 AGCCTTTCCTATTGATCACTTCG 58.554 43.478 0.00 0.00 0.00 3.79
1593 1656 1.352352 ACAAAGAGGATCACCCCACAG 59.648 52.381 0.00 0.00 37.82 3.66
1635 1698 9.956640 ATATTCATCAGATTCTTATCCTGGAAC 57.043 33.333 0.00 0.00 0.00 3.62
1686 1749 0.252375 ACCAGCTGGGGCATTTGAAT 60.252 50.000 35.42 8.61 42.91 2.57
1698 1761 4.630111 GGATATCTGAAGAGAACCAGCTG 58.370 47.826 6.78 6.78 0.00 4.24
1701 1764 5.521906 TTCGGATATCTGAAGAGAACCAG 57.478 43.478 20.83 0.00 36.40 4.00
1719 1782 0.537188 TCCTTAGCAGAAGCCTTCGG 59.463 55.000 0.00 0.00 43.56 4.30
1877 1940 2.235650 CAGCTCAAGGGATCAGAAGTCA 59.764 50.000 0.00 0.00 0.00 3.41
1888 1951 1.584380 GAGTTGCTGCAGCTCAAGGG 61.584 60.000 36.61 0.00 40.56 3.95
1938 2001 3.080319 AGCATTCAAGTTGGAGAGCTTC 58.920 45.455 7.83 0.00 0.00 3.86
2187 2250 2.599677 GGGGTCACCTCGAATATCTCT 58.400 52.381 0.00 0.00 36.80 3.10
2202 2265 0.461961 CGAGATGGAAGTCAGGGGTC 59.538 60.000 0.00 0.00 0.00 4.46
2229 2292 6.530534 CGATAGTATCACCGTTTGTCTTCTTT 59.469 38.462 10.71 0.00 0.00 2.52
2313 2376 4.953010 TGCTGCTCGCCTTGCCAA 62.953 61.111 0.00 0.00 38.05 4.52
2337 2412 4.260355 CATGATTGCTGCGGCGGG 62.260 66.667 13.96 0.00 42.25 6.13
2342 2417 4.604843 TCTTCTTAACATGATTGCTGCG 57.395 40.909 0.00 0.00 0.00 5.18
2350 2425 4.713553 TGGCACAGTTCTTCTTAACATGA 58.286 39.130 0.00 0.00 0.00 3.07
2391 2469 1.223487 GCCTGGTAATTGCCTCGGA 59.777 57.895 20.04 0.00 0.00 4.55
2392 2470 0.394352 AAGCCTGGTAATTGCCTCGG 60.394 55.000 14.11 14.16 0.00 4.63
2393 2471 1.017387 GAAGCCTGGTAATTGCCTCG 58.983 55.000 14.11 4.77 0.00 4.63
2501 2579 8.971321 CCATGCTTTTAAATAAATCTTCATCGG 58.029 33.333 0.00 0.00 0.00 4.18
2600 2678 6.335471 TGAGCAAAAGATGATGTGAACAAT 57.665 33.333 0.00 0.00 0.00 2.71
2638 2716 7.589395 CATGCCATAGTTAAACAGTAACAACA 58.411 34.615 0.00 0.00 0.00 3.33
2639 2717 6.526674 GCATGCCATAGTTAAACAGTAACAAC 59.473 38.462 6.36 0.00 0.00 3.32
2656 2734 6.040504 GTGGATATAATCATGATGCATGCCAT 59.959 38.462 16.68 9.52 41.18 4.40
2659 2737 6.694877 AGTGGATATAATCATGATGCATGC 57.305 37.500 11.82 11.82 41.18 4.06
2675 2753 9.383519 GTTTTCAGATCACAAGAATAGTGGATA 57.616 33.333 0.00 0.00 37.58 2.59
2702 2780 9.277783 CAAGATTTAAATATGTCACCCTCTAGG 57.722 37.037 0.00 0.00 43.78 3.02
2720 2798 6.826741 GGTAGCTACCCATCAAACAAGATTTA 59.173 38.462 29.68 0.00 40.53 1.40
2728 2806 1.483415 TCCGGTAGCTACCCATCAAAC 59.517 52.381 32.51 9.52 43.51 2.93
2733 2811 1.875488 AAAGTCCGGTAGCTACCCAT 58.125 50.000 32.51 15.88 43.51 4.00
2744 2822 2.034104 GGCCTTTAGGTAAAGTCCGG 57.966 55.000 0.00 0.00 40.73 5.14
2847 2937 0.031616 CTGCTCCCTCCCTACTTCCT 60.032 60.000 0.00 0.00 0.00 3.36
3026 3472 3.764885 AACTGTGAACTGTGAAGCAAC 57.235 42.857 0.00 0.00 0.00 4.17
3040 3486 7.607991 ACCTCCTTGATAAAGATTGTAACTGTG 59.392 37.037 0.00 0.00 0.00 3.66
3041 3487 7.690256 ACCTCCTTGATAAAGATTGTAACTGT 58.310 34.615 0.00 0.00 0.00 3.55
3042 3488 8.567285 AACCTCCTTGATAAAGATTGTAACTG 57.433 34.615 0.00 0.00 0.00 3.16
3043 3489 8.383175 TGAACCTCCTTGATAAAGATTGTAACT 58.617 33.333 0.00 0.00 0.00 2.24
3044 3490 8.451748 GTGAACCTCCTTGATAAAGATTGTAAC 58.548 37.037 0.00 0.00 0.00 2.50
3045 3491 8.160765 TGTGAACCTCCTTGATAAAGATTGTAA 58.839 33.333 0.00 0.00 0.00 2.41
3046 3492 7.685481 TGTGAACCTCCTTGATAAAGATTGTA 58.315 34.615 0.00 0.00 0.00 2.41
3047 3493 6.542821 TGTGAACCTCCTTGATAAAGATTGT 58.457 36.000 0.00 0.00 0.00 2.71
3048 3494 6.656693 ACTGTGAACCTCCTTGATAAAGATTG 59.343 38.462 0.00 0.00 0.00 2.67
3049 3495 6.784031 ACTGTGAACCTCCTTGATAAAGATT 58.216 36.000 0.00 0.00 0.00 2.40
3050 3496 6.380079 ACTGTGAACCTCCTTGATAAAGAT 57.620 37.500 0.00 0.00 0.00 2.40
3051 3497 5.825593 ACTGTGAACCTCCTTGATAAAGA 57.174 39.130 0.00 0.00 0.00 2.52
3052 3498 6.934645 TGTAACTGTGAACCTCCTTGATAAAG 59.065 38.462 0.00 0.00 0.00 1.85
3053 3499 6.833041 TGTAACTGTGAACCTCCTTGATAAA 58.167 36.000 0.00 0.00 0.00 1.40
3054 3500 6.428083 TGTAACTGTGAACCTCCTTGATAA 57.572 37.500 0.00 0.00 0.00 1.75
3055 3501 6.428083 TTGTAACTGTGAACCTCCTTGATA 57.572 37.500 0.00 0.00 0.00 2.15
3056 3502 4.974645 TGTAACTGTGAACCTCCTTGAT 57.025 40.909 0.00 0.00 0.00 2.57
3057 3503 4.764050 TTGTAACTGTGAACCTCCTTGA 57.236 40.909 0.00 0.00 0.00 3.02
3058 3504 5.308825 AGATTGTAACTGTGAACCTCCTTG 58.691 41.667 0.00 0.00 0.00 3.61
3059 3505 5.568620 AGATTGTAACTGTGAACCTCCTT 57.431 39.130 0.00 0.00 0.00 3.36
3060 3506 5.568620 AAGATTGTAACTGTGAACCTCCT 57.431 39.130 0.00 0.00 0.00 3.69
3061 3507 7.606456 TGATAAAGATTGTAACTGTGAACCTCC 59.394 37.037 0.00 0.00 0.00 4.30
3062 3508 8.547967 TGATAAAGATTGTAACTGTGAACCTC 57.452 34.615 0.00 0.00 0.00 3.85
3063 3509 8.918202 TTGATAAAGATTGTAACTGTGAACCT 57.082 30.769 0.00 0.00 0.00 3.50
3064 3510 8.237267 CCTTGATAAAGATTGTAACTGTGAACC 58.763 37.037 0.00 0.00 0.00 3.62
3065 3511 8.999431 TCCTTGATAAAGATTGTAACTGTGAAC 58.001 33.333 0.00 0.00 0.00 3.18
3066 3512 9.219603 CTCCTTGATAAAGATTGTAACTGTGAA 57.780 33.333 0.00 0.00 0.00 3.18
3067 3513 8.593679 TCTCCTTGATAAAGATTGTAACTGTGA 58.406 33.333 0.00 0.00 0.00 3.58
3068 3514 8.777865 TCTCCTTGATAAAGATTGTAACTGTG 57.222 34.615 0.00 0.00 0.00 3.66
3069 3515 9.793259 TTTCTCCTTGATAAAGATTGTAACTGT 57.207 29.630 0.00 0.00 0.00 3.55
3143 3589 5.163814 GCAGAGTATGAAAACTACTGCCTTG 60.164 44.000 0.00 0.00 40.67 3.61
3146 3592 4.866682 GCAGAGTATGAAAACTACTGCC 57.133 45.455 0.00 0.00 40.67 4.85
3199 3673 3.737972 GCTGTAAAATAATGCCACCTGCC 60.738 47.826 0.00 0.00 40.16 4.85
3257 3761 4.985409 GCAGCAATCTGTACCAGTCTATAC 59.015 45.833 0.00 0.00 42.29 1.47
3260 3764 2.159240 CGCAGCAATCTGTACCAGTCTA 60.159 50.000 0.00 0.00 42.29 2.59
3263 3767 3.143675 CGCAGCAATCTGTACCAGT 57.856 52.632 0.00 0.00 42.29 4.00
3312 3820 4.295870 TCAAACAACTACAGTCTACAGCG 58.704 43.478 0.00 0.00 0.00 5.18
3328 3836 6.232581 ACAAATGGAGGAAACAATCAAACA 57.767 33.333 0.00 0.00 0.00 2.83
3330 3838 7.255801 GGACTACAAATGGAGGAAACAATCAAA 60.256 37.037 0.00 0.00 0.00 2.69
3331 3839 6.208599 GGACTACAAATGGAGGAAACAATCAA 59.791 38.462 0.00 0.00 0.00 2.57
3332 3840 5.710099 GGACTACAAATGGAGGAAACAATCA 59.290 40.000 0.00 0.00 0.00 2.57
3333 3841 5.710099 TGGACTACAAATGGAGGAAACAATC 59.290 40.000 0.00 0.00 0.00 2.67
3334 3842 5.640147 TGGACTACAAATGGAGGAAACAAT 58.360 37.500 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.