Multiple sequence alignment - TraesCS2D01G539300

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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 TraesCS2D01G539300 chr2D 100.000 4739 0 0 1 4739 619712743 619708005 0.000000e+00 8752.0
1 TraesCS2D01G539300 chr2D 82.216 731 59 37 816 1493 585679389 585680101 8.900000e-157 564.0
2 TraesCS2D01G539300 chr2D 83.168 606 63 19 1620 2195 585680253 585680849 7.030000e-143 518.0
3 TraesCS2D01G539300 chr2D 74.386 1343 153 111 3047 4315 585681853 585683078 9.560000e-107 398.0
4 TraesCS2D01G539300 chr2D 76.802 444 63 31 2292 2718 585681069 585681489 3.710000e-51 213.0
5 TraesCS2D01G539300 chr2D 93.939 99 5 1 2907 3004 585681751 585681849 1.060000e-31 148.0
6 TraesCS2D01G539300 chr2D 95.556 45 0 2 210 253 13841548 13841591 2.370000e-08 71.3
7 TraesCS2D01G539300 chr2B 93.403 3911 139 52 574 4425 759451109 759447259 0.000000e+00 5683.0
8 TraesCS2D01G539300 chr2B 81.679 1441 146 78 816 2173 706724162 706725567 0.000000e+00 1090.0
9 TraesCS2D01G539300 chr2B 95.156 289 7 3 4455 4739 759447086 759446801 2.600000e-122 449.0
10 TraesCS2D01G539300 chr2B 73.992 1315 164 103 3070 4315 706726532 706727737 2.080000e-98 370.0
11 TraesCS2D01G539300 chr2B 92.308 169 12 1 38 206 759451818 759451651 6.130000e-59 239.0
12 TraesCS2D01G539300 chr2B 85.542 166 16 6 2574 2736 706725991 706726151 2.930000e-37 167.0
13 TraesCS2D01G539300 chr2B 92.308 104 7 1 2902 3004 706726406 706726509 3.820000e-31 147.0
14 TraesCS2D01G539300 chr2B 100.000 38 0 0 4422 4459 759447179 759447142 2.370000e-08 71.3
15 TraesCS2D01G539300 chr2A 93.081 3917 145 67 596 4459 751384229 751380386 0.000000e+00 5616.0
16 TraesCS2D01G539300 chr2A 80.756 1429 157 70 816 2173 719720773 719722154 0.000000e+00 1007.0
17 TraesCS2D01G539300 chr2A 85.931 462 34 12 6 441 751384921 751384465 9.290000e-127 464.0
18 TraesCS2D01G539300 chr2A 95.819 287 3 4 4455 4739 751380330 751380051 5.590000e-124 455.0
19 TraesCS2D01G539300 chr2A 74.439 1025 125 86 3047 4039 719723032 719723951 9.900000e-82 315.0
20 TraesCS2D01G539300 chr2A 82.392 301 23 14 4455 4736 751250879 751250590 7.930000e-58 235.0
21 TraesCS2D01G539300 chr2A 82.333 300 23 14 4455 4735 751273508 751273220 2.850000e-57 233.0
22 TraesCS2D01G539300 chr2A 85.366 164 12 8 2573 2732 719722518 719722673 4.910000e-35 159.0
23 TraesCS2D01G539300 chr3B 82.178 303 24 14 4452 4735 713761547 713761838 2.850000e-57 233.0
24 TraesCS2D01G539300 chr4A 93.548 62 4 0 3671 3732 249771578 249771639 5.050000e-15 93.5
25 TraesCS2D01G539300 chr4A 100.000 28 0 0 1795 1822 738972847 738972820 9.000000e-03 52.8
26 TraesCS2D01G539300 chr7D 95.556 45 2 0 210 254 423531805 423531849 6.580000e-09 73.1
27 TraesCS2D01G539300 chr7D 90.196 51 4 1 210 260 403092198 403092149 1.100000e-06 65.8
28 TraesCS2D01G539300 chr5D 95.556 45 2 0 210 254 318879373 318879417 6.580000e-09 73.1
29 TraesCS2D01G539300 chr4D 93.750 48 3 0 210 257 20437834 20437787 6.580000e-09 73.1
30 TraesCS2D01G539300 chr7B 95.455 44 2 0 213 256 244755542 244755499 2.370000e-08 71.3
31 TraesCS2D01G539300 chr7A 95.455 44 2 0 210 253 705217952 705217995 2.370000e-08 71.3
32 TraesCS2D01G539300 chr1A 93.617 47 1 2 210 255 259202217 259202262 8.510000e-08 69.4


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 TraesCS2D01G539300 chr2D 619708005 619712743 4738 True 8752.000000 8752 100.000000 1 4739 1 chr2D.!!$R1 4738
1 TraesCS2D01G539300 chr2D 585679389 585683078 3689 False 368.200000 564 82.102200 816 4315 5 chr2D.!!$F2 3499
2 TraesCS2D01G539300 chr2B 759446801 759451818 5017 True 1610.575000 5683 95.216750 38 4739 4 chr2B.!!$R1 4701
3 TraesCS2D01G539300 chr2B 706724162 706727737 3575 False 443.500000 1090 83.380250 816 4315 4 chr2B.!!$F1 3499
4 TraesCS2D01G539300 chr2A 751380051 751384921 4870 True 2178.333333 5616 91.610333 6 4739 3 chr2A.!!$R3 4733
5 TraesCS2D01G539300 chr2A 719720773 719723951 3178 False 493.666667 1007 80.187000 816 4039 3 chr2A.!!$F1 3223


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
306 357 0.250081 GCTGGGCATGTAGCTAGTCC 60.250 60.000 0.00 0.00 44.79 3.85 F
331 382 0.385974 GAATGTTGGTGTGTGAGCGC 60.386 55.000 0.00 0.00 0.00 5.92 F
799 984 0.750850 AGAGTGTTGTGTAGTGGCGT 59.249 50.000 0.00 0.00 0.00 5.68 F
940 1132 1.098129 GGCAGGCGAAATTCTCCTCC 61.098 60.000 0.83 3.57 26.97 4.30 F
1812 2129 2.123939 CACCACCACCACCAGCAA 60.124 61.111 0.00 0.00 0.00 3.91 F
3262 4009 0.744057 TGTACATCCATGGCGTGCTG 60.744 55.000 18.30 3.67 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1948 0.236711 CGCTGCTCCTGTTGAAGTTG 59.763 55.000 0.00 0.00 0.00 3.16 R
1812 2129 1.079543 GTGATCGTCCTGCTGCTGT 60.080 57.895 0.00 0.00 0.00 4.40 R
2378 2840 1.874019 CGACGGCGTCTCCATTCTG 60.874 63.158 33.90 14.79 34.01 3.02 R
2584 3148 6.028146 TGCATGCACAACTTTAATCAATCT 57.972 33.333 18.46 0.00 0.00 2.40 R
3279 4026 0.179111 CAAAGCATGCAGGAGCCATG 60.179 55.000 21.98 2.79 41.13 3.66 R
4217 5044 0.390492 TGCAGATATCCACTGGCTCG 59.610 55.000 0.00 0.00 36.09 5.03 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
121 122 1.153524 TGGTTTGGCATGGCAGAGT 59.846 52.632 22.17 0.00 0.00 3.24
209 210 1.440618 TTGGCTGGTACTCCCTTTGA 58.559 50.000 0.00 0.00 0.00 2.69
211 212 1.351017 TGGCTGGTACTCCCTTTGAAG 59.649 52.381 0.00 0.00 0.00 3.02
212 213 1.351350 GGCTGGTACTCCCTTTGAAGT 59.649 52.381 0.00 0.00 0.00 3.01
213 214 2.570302 GGCTGGTACTCCCTTTGAAGTA 59.430 50.000 0.00 0.00 0.00 2.24
214 215 3.369576 GGCTGGTACTCCCTTTGAAGTAG 60.370 52.174 0.00 0.00 0.00 2.57
215 216 3.261137 GCTGGTACTCCCTTTGAAGTAGT 59.739 47.826 0.00 0.00 0.00 2.73
216 217 4.822026 CTGGTACTCCCTTTGAAGTAGTG 58.178 47.826 0.00 0.00 0.00 2.74
306 357 0.250081 GCTGGGCATGTAGCTAGTCC 60.250 60.000 0.00 0.00 44.79 3.85
311 362 1.576356 GCATGTAGCTAGTCCTGCAC 58.424 55.000 0.00 0.00 41.15 4.57
313 364 1.405463 CATGTAGCTAGTCCTGCACGA 59.595 52.381 0.00 0.00 30.27 4.35
331 382 0.385974 GAATGTTGGTGTGTGAGCGC 60.386 55.000 0.00 0.00 0.00 5.92
345 396 1.977594 GAGCGCGTGGTGTATTTGGG 61.978 60.000 4.91 0.00 0.00 4.12
354 405 3.008049 GTGGTGTATTTGGGAGTGAGAGT 59.992 47.826 0.00 0.00 0.00 3.24
369 420 2.573462 TGAGAGTAGCAGCCCAGAAAAT 59.427 45.455 0.00 0.00 0.00 1.82
410 461 3.412237 AGTTTAGCTAGGCGGTTTGAA 57.588 42.857 0.00 0.00 0.00 2.69
415 466 2.973945 AGCTAGGCGGTTTGAACTTAG 58.026 47.619 0.00 0.00 0.00 2.18
427 478 5.803461 GGTTTGAACTTAGTGTGTTGGTTTC 59.197 40.000 0.00 0.00 0.00 2.78
508 627 7.463961 TTTCCTTATAAACAGAGTCTCTCGT 57.536 36.000 0.00 0.00 35.36 4.18
510 629 7.463961 TCCTTATAAACAGAGTCTCTCGTTT 57.536 36.000 22.63 22.63 39.00 3.60
512 631 9.017509 TCCTTATAAACAGAGTCTCTCGTTTTA 57.982 33.333 23.49 16.67 37.84 1.52
531 650 8.079809 TCGTTTTATTCTCCATTCAAGGTTTTC 58.920 33.333 0.00 0.00 0.00 2.29
532 651 8.082242 CGTTTTATTCTCCATTCAAGGTTTTCT 58.918 33.333 0.00 0.00 0.00 2.52
585 761 2.460918 AGATGACGCTAATTTCGGACG 58.539 47.619 5.09 0.00 0.00 4.79
586 762 1.521423 GATGACGCTAATTTCGGACGG 59.479 52.381 5.09 0.00 0.00 4.79
710 887 5.616204 GCATACGTCAAAACCCTAAGACAAC 60.616 44.000 0.00 0.00 0.00 3.32
730 910 6.412214 ACAACAAGAGGTTACTGTTACAACT 58.588 36.000 0.00 0.00 37.72 3.16
731 911 7.558604 ACAACAAGAGGTTACTGTTACAACTA 58.441 34.615 0.00 0.00 37.72 2.24
732 912 7.493645 ACAACAAGAGGTTACTGTTACAACTAC 59.506 37.037 0.00 0.00 37.72 2.73
796 981 2.795175 ACGAGAGTGTTGTGTAGTGG 57.205 50.000 0.00 0.00 46.97 4.00
797 982 1.269621 ACGAGAGTGTTGTGTAGTGGC 60.270 52.381 0.00 0.00 46.97 5.01
798 983 1.419374 GAGAGTGTTGTGTAGTGGCG 58.581 55.000 0.00 0.00 0.00 5.69
799 984 0.750850 AGAGTGTTGTGTAGTGGCGT 59.249 50.000 0.00 0.00 0.00 5.68
865 1053 3.002791 TCTGTTGCACCAGATCGATTTC 58.997 45.455 10.27 0.00 36.57 2.17
940 1132 1.098129 GGCAGGCGAAATTCTCCTCC 61.098 60.000 0.83 3.57 26.97 4.30
1329 1574 3.642778 CTGGTGGCTACGACGTGGG 62.643 68.421 11.56 4.59 0.00 4.61
1335 1580 3.066190 CTACGACGTGGGGGCTGA 61.066 66.667 11.56 0.00 0.00 4.26
1336 1581 3.352338 CTACGACGTGGGGGCTGAC 62.352 68.421 11.56 0.00 0.00 3.51
1420 1668 3.687125 CTCCCTAACCTTCCAAGAAACC 58.313 50.000 0.00 0.00 0.00 3.27
1501 1749 3.139077 AGTTGTTCGTTCCCACTTGATC 58.861 45.455 0.00 0.00 0.00 2.92
1522 1770 2.247358 CCACACCTGCCCTTAATTTGT 58.753 47.619 0.00 0.00 0.00 2.83
1653 1948 7.253783 CGAAATCTACATGTGTATGTGTGTCTC 60.254 40.741 9.11 0.00 46.63 3.36
1812 2129 2.123939 CACCACCACCACCAGCAA 60.124 61.111 0.00 0.00 0.00 3.91
2204 2534 8.846211 GCTTGGGCTAATGATTAAGTATTTACA 58.154 33.333 0.00 0.00 35.22 2.41
2237 2668 8.873215 TGCTCTACTAGTAGTTGCAAATATTC 57.127 34.615 31.15 14.20 39.03 1.75
2243 2674 7.573710 ACTAGTAGTTGCAAATATTCCATGGA 58.426 34.615 11.44 11.44 0.00 3.41
2244 2675 8.052748 ACTAGTAGTTGCAAATATTCCATGGAA 58.947 33.333 28.92 28.92 38.59 3.53
2245 2676 7.338800 AGTAGTTGCAAATATTCCATGGAAG 57.661 36.000 29.98 17.97 37.56 3.46
2378 2840 2.951458 CCGGCGTTCAAGAAACCC 59.049 61.111 6.01 0.00 34.11 4.11
2508 3026 4.402155 GGTTAAATCATGCCACTTGGATCA 59.598 41.667 0.00 0.00 37.39 2.92
2584 3148 3.134623 ACCCAGATCGATGCATCTTTACA 59.865 43.478 23.73 3.67 30.07 2.41
2854 3564 0.969894 CCCCGCCTTTCGAGATCTAT 59.030 55.000 0.00 0.00 41.67 1.98
2865 3575 8.559536 GCCTTTCGAGATCTATCTATCATCTAG 58.440 40.741 0.00 0.00 37.25 2.43
2866 3576 9.830975 CCTTTCGAGATCTATCTATCATCTAGA 57.169 37.037 0.00 0.00 37.25 2.43
3262 4009 0.744057 TGTACATCCATGGCGTGCTG 60.744 55.000 18.30 3.67 0.00 4.41
3277 4024 3.429141 CTGGCCAGTCTGCGCTTG 61.429 66.667 25.53 1.08 0.00 4.01
3278 4025 4.254709 TGGCCAGTCTGCGCTTGT 62.255 61.111 9.73 0.00 0.00 3.16
3279 4026 3.426568 GGCCAGTCTGCGCTTGTC 61.427 66.667 9.73 0.00 0.00 3.18
3280 4027 2.666190 GCCAGTCTGCGCTTGTCA 60.666 61.111 9.73 0.00 0.00 3.58
3281 4028 2.037136 GCCAGTCTGCGCTTGTCAT 61.037 57.895 9.73 0.00 0.00 3.06
3282 4029 1.792301 CCAGTCTGCGCTTGTCATG 59.208 57.895 9.73 0.00 0.00 3.07
3283 4030 1.642037 CCAGTCTGCGCTTGTCATGG 61.642 60.000 9.73 5.74 0.00 3.66
3284 4031 2.037136 AGTCTGCGCTTGTCATGGC 61.037 57.895 9.73 0.00 0.00 4.40
3285 4032 2.037136 GTCTGCGCTTGTCATGGCT 61.037 57.895 9.73 0.00 0.00 4.75
3286 4033 1.742880 TCTGCGCTTGTCATGGCTC 60.743 57.895 9.73 0.00 0.00 4.70
3317 4064 3.606595 TGCTCTCTCTCACTTTCCATG 57.393 47.619 0.00 0.00 0.00 3.66
3319 4066 2.499289 GCTCTCTCTCACTTTCCATGGA 59.501 50.000 11.44 11.44 0.00 3.41
3320 4067 3.134442 GCTCTCTCTCACTTTCCATGGAT 59.866 47.826 17.06 0.00 0.00 3.41
3323 4070 5.523588 TCTCTCTCACTTTCCATGGATACT 58.476 41.667 17.06 0.00 37.61 2.12
3324 4071 5.362143 TCTCTCTCACTTTCCATGGATACTG 59.638 44.000 17.06 10.14 37.61 2.74
3325 4072 4.125703 CTCTCACTTTCCATGGATACTGC 58.874 47.826 17.06 0.00 37.61 4.40
3360 4118 2.745821 TCTCAAAGTGCATGTCTGATGC 59.254 45.455 0.00 0.00 44.76 3.91
3377 4135 4.985413 TGATGCTAGCTTTTTACATGTGC 58.015 39.130 17.23 2.37 0.00 4.57
3571 4332 6.875972 TTTAGGTAGAGGAAGAAGAAGCAT 57.124 37.500 0.00 0.00 0.00 3.79
3577 4338 4.577875 AGAGGAAGAAGAAGCATCACAAG 58.422 43.478 0.00 0.00 0.00 3.16
3594 4355 0.584876 AAGGCTTGTTGAACGTACGC 59.415 50.000 16.72 0.00 0.00 4.42
3597 4358 1.226030 GCTTGTTGAACGTACGCCCT 61.226 55.000 16.72 0.00 0.00 5.19
3653 4426 1.536149 CGACAACGTTCCTCGATCTC 58.464 55.000 16.45 0.00 42.86 2.75
3795 4583 2.611292 GGCTCATTCTTCAGGTTCATCG 59.389 50.000 0.00 0.00 0.00 3.84
4157 4981 0.313672 TTCCAGAATTTGTGCGTGCC 59.686 50.000 0.00 0.00 0.00 5.01
4217 5044 5.888982 TCAGGTTAGACTATCCCATTTCC 57.111 43.478 6.04 0.00 0.00 3.13
4233 5061 2.088104 TTCCGAGCCAGTGGATATCT 57.912 50.000 15.20 0.00 33.42 1.98
4262 5102 5.388890 GCGTGTATAGCATATTCTTCTGTGC 60.389 44.000 0.00 0.00 37.84 4.57
4265 5105 5.920840 TGTATAGCATATTCTTCTGTGCGTC 59.079 40.000 0.00 0.00 42.18 5.19
4386 5226 8.850156 AGAAAATTCAGTTGCATAACAAGTAGT 58.150 29.630 0.00 0.00 40.04 2.73
4394 5234 8.033038 CAGTTGCATAACAAGTAGTAGGAGTAA 58.967 37.037 0.00 0.00 40.04 2.24
4395 5235 8.591072 AGTTGCATAACAAGTAGTAGGAGTAAA 58.409 33.333 0.00 0.00 40.25 2.01
4396 5236 9.211485 GTTGCATAACAAGTAGTAGGAGTAAAA 57.789 33.333 0.00 0.00 39.50 1.52
4397 5237 9.781633 TTGCATAACAAGTAGTAGGAGTAAAAA 57.218 29.630 0.00 0.00 33.24 1.94
4459 5382 3.340814 AGCGATGAAACTCACCTGAAT 57.659 42.857 0.00 0.00 0.00 2.57
4460 5383 3.265791 AGCGATGAAACTCACCTGAATC 58.734 45.455 0.00 0.00 0.00 2.52
4462 5385 3.308323 GCGATGAAACTCACCTGAATCTC 59.692 47.826 0.00 0.00 0.00 2.75
4464 5387 4.931601 CGATGAAACTCACCTGAATCTCAA 59.068 41.667 0.00 0.00 0.00 3.02
4465 5388 5.163913 CGATGAAACTCACCTGAATCTCAAC 60.164 44.000 0.00 0.00 0.00 3.18
4466 5389 5.296151 TGAAACTCACCTGAATCTCAACT 57.704 39.130 0.00 0.00 0.00 3.16
4468 5391 4.963318 AACTCACCTGAATCTCAACTGA 57.037 40.909 0.00 0.00 0.00 3.41
4469 5392 5.495926 AACTCACCTGAATCTCAACTGAT 57.504 39.130 0.00 0.00 0.00 2.90
4470 5393 6.611613 AACTCACCTGAATCTCAACTGATA 57.388 37.500 0.00 0.00 0.00 2.15
4554 5539 4.850193 CACCCCATTTCCTGTGCT 57.150 55.556 0.00 0.00 0.00 4.40
4555 5540 3.056213 CACCCCATTTCCTGTGCTT 57.944 52.632 0.00 0.00 0.00 3.91
4556 5541 1.341080 CACCCCATTTCCTGTGCTTT 58.659 50.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.472029 ACCTAGAGTCCATTGACCCTG 58.528 52.381 0.00 0.00 42.81 4.45
1 2 2.840651 CAACCTAGAGTCCATTGACCCT 59.159 50.000 0.00 0.00 42.81 4.34
2 3 2.092914 CCAACCTAGAGTCCATTGACCC 60.093 54.545 0.00 0.00 42.81 4.46
3 4 2.681097 GCCAACCTAGAGTCCATTGACC 60.681 54.545 0.00 0.00 42.81 4.02
4 5 2.633488 GCCAACCTAGAGTCCATTGAC 58.367 52.381 0.00 0.00 42.09 3.18
121 122 4.383444 CCCTTCTAGCACAAGATCATCACA 60.383 45.833 0.00 0.00 0.00 3.58
168 169 1.269517 CCAACCCCGTTTGATTGTGTG 60.270 52.381 0.00 0.00 0.00 3.82
246 297 3.684788 GCATGTCGTTCCATTGTACTTCT 59.315 43.478 0.00 0.00 0.00 2.85
255 306 1.089481 ATTCGCGCATGTCGTTCCAT 61.089 50.000 8.75 0.00 41.07 3.41
269 320 0.939106 GCCAACACACCAACATTCGC 60.939 55.000 0.00 0.00 0.00 4.70
306 357 0.662619 ACACACCAACATTCGTGCAG 59.337 50.000 0.00 0.00 33.09 4.41
311 362 0.110688 CGCTCACACACCAACATTCG 60.111 55.000 0.00 0.00 0.00 3.34
313 364 1.654220 GCGCTCACACACCAACATT 59.346 52.632 0.00 0.00 0.00 2.71
331 382 2.028476 TCTCACTCCCAAATACACCACG 60.028 50.000 0.00 0.00 0.00 4.94
345 396 0.459489 CTGGGCTGCTACTCTCACTC 59.541 60.000 0.00 0.00 0.00 3.51
354 405 5.329035 GAAATCAATTTTCTGGGCTGCTA 57.671 39.130 0.00 0.00 40.54 3.49
369 420 3.616956 AGATCTGCCACGAGAAATCAA 57.383 42.857 0.00 0.00 0.00 2.57
410 461 8.403236 GTGAATAAAGAAACCAACACACTAAGT 58.597 33.333 0.00 0.00 0.00 2.24
415 466 9.744468 AATAAGTGAATAAAGAAACCAACACAC 57.256 29.630 0.00 0.00 0.00 3.82
444 563 2.235016 GCTGACTACTCCATCCGATCT 58.765 52.381 0.00 0.00 0.00 2.75
452 571 1.273267 ACCCTCATGCTGACTACTCCA 60.273 52.381 0.00 0.00 0.00 3.86
471 590 2.831685 AAGGAAAAATGGGCCGAAAC 57.168 45.000 0.00 0.00 0.00 2.78
482 601 8.365647 ACGAGAGACTCTGTTTATAAGGAAAAA 58.634 33.333 10.44 0.00 0.00 1.94
533 652 7.934120 CGGATGGAGGAAGTATTTCTTTATTCT 59.066 37.037 0.00 0.00 36.40 2.40
537 656 6.801718 TCGGATGGAGGAAGTATTTCTTTA 57.198 37.500 0.00 0.00 36.40 1.85
549 668 4.262036 CGTCATCTAATTTCGGATGGAGGA 60.262 45.833 12.52 0.00 39.57 3.71
550 669 3.990469 CGTCATCTAATTTCGGATGGAGG 59.010 47.826 12.52 0.00 39.57 4.30
710 887 8.355169 TGTAGTAGTTGTAACAGTAACCTCTTG 58.645 37.037 0.00 0.00 0.00 3.02
730 910 8.557592 TTAACTCTCGATCTTGTCTTGTAGTA 57.442 34.615 0.00 0.00 0.00 1.82
731 911 5.968528 AACTCTCGATCTTGTCTTGTAGT 57.031 39.130 0.00 0.00 0.00 2.73
732 912 8.744008 TTTTAACTCTCGATCTTGTCTTGTAG 57.256 34.615 0.00 0.00 0.00 2.74
796 981 3.489398 CCCACATCACTAGAGTAGAACGC 60.489 52.174 0.00 0.00 0.00 4.84
797 982 3.695060 ACCCACATCACTAGAGTAGAACG 59.305 47.826 0.00 0.00 0.00 3.95
798 983 5.047235 ACAACCCACATCACTAGAGTAGAAC 60.047 44.000 0.00 0.00 0.00 3.01
799 984 5.084519 ACAACCCACATCACTAGAGTAGAA 58.915 41.667 0.00 0.00 0.00 2.10
865 1053 2.987413 TGCGTCAGCTGGTAAATTTG 57.013 45.000 15.13 0.00 45.42 2.32
1110 1333 2.165301 CGATCACCGCTCCGTTTCC 61.165 63.158 0.00 0.00 0.00 3.13
1201 1440 1.812922 CATGCCGTGAGAGACTGCC 60.813 63.158 0.00 0.00 34.02 4.85
1329 1574 4.475135 GCTTCCCTCCGTCAGCCC 62.475 72.222 0.00 0.00 0.00 5.19
1333 1578 3.706373 GCCTGCTTCCCTCCGTCA 61.706 66.667 0.00 0.00 0.00 4.35
1336 1581 3.984193 CTTGGCCTGCTTCCCTCCG 62.984 68.421 3.32 0.00 0.00 4.63
1338 1583 1.077858 CTCTTGGCCTGCTTCCCTC 60.078 63.158 3.32 0.00 0.00 4.30
1339 1584 3.085223 CTCTTGGCCTGCTTCCCT 58.915 61.111 3.32 0.00 0.00 4.20
1420 1668 3.499737 GGGTCGTTGATGCTGGCG 61.500 66.667 0.00 0.00 0.00 5.69
1501 1749 1.550072 CAAATTAAGGGCAGGTGTGGG 59.450 52.381 0.00 0.00 0.00 4.61
1653 1948 0.236711 CGCTGCTCCTGTTGAAGTTG 59.763 55.000 0.00 0.00 0.00 3.16
1812 2129 1.079543 GTGATCGTCCTGCTGCTGT 60.080 57.895 0.00 0.00 0.00 4.40
2204 2534 7.093902 TGCAACTACTAGTAGAGCATTGTAGTT 60.094 37.037 31.75 17.56 45.88 2.24
2213 2543 7.926555 TGGAATATTTGCAACTACTAGTAGAGC 59.073 37.037 31.93 30.12 37.82 4.09
2237 2668 2.002586 CTGTACGTGCTTCTTCCATGG 58.997 52.381 4.97 4.97 0.00 3.66
2243 2674 4.785511 ACTACATCTGTACGTGCTTCTT 57.214 40.909 4.97 0.00 0.00 2.52
2244 2675 4.335874 CCTACTACATCTGTACGTGCTTCT 59.664 45.833 4.97 0.00 0.00 2.85
2245 2676 4.096081 ACCTACTACATCTGTACGTGCTTC 59.904 45.833 4.97 0.00 0.00 3.86
2378 2840 1.874019 CGACGGCGTCTCCATTCTG 60.874 63.158 33.90 14.79 34.01 3.02
2448 2964 8.974060 TCCATGATTTAAAGGTAAGGTATGAC 57.026 34.615 0.00 0.00 0.00 3.06
2471 2987 7.255486 GCATGATTTAACCTAACCTAACCATCC 60.255 40.741 0.00 0.00 0.00 3.51
2508 3026 8.415950 TCAAATAATGTCCATGGTGTTTAAGT 57.584 30.769 12.58 0.00 0.00 2.24
2584 3148 6.028146 TGCATGCACAACTTTAATCAATCT 57.972 33.333 18.46 0.00 0.00 2.40
3262 4009 3.426568 GACAAGCGCAGACTGGCC 61.427 66.667 11.47 0.00 0.00 5.36
3269 4016 2.758089 GGAGCCATGACAAGCGCAG 61.758 63.158 11.47 3.78 0.00 5.18
3270 4017 2.747460 GGAGCCATGACAAGCGCA 60.747 61.111 11.47 0.00 0.00 6.09
3271 4018 2.437359 AGGAGCCATGACAAGCGC 60.437 61.111 0.00 0.00 0.00 5.92
3272 4019 2.758089 GCAGGAGCCATGACAAGCG 61.758 63.158 0.00 0.00 33.58 4.68
3273 4020 1.035932 ATGCAGGAGCCATGACAAGC 61.036 55.000 0.00 0.00 41.13 4.01
3274 4021 0.738975 CATGCAGGAGCCATGACAAG 59.261 55.000 0.00 0.00 41.13 3.16
3276 4023 1.751544 GCATGCAGGAGCCATGACA 60.752 57.895 14.21 0.00 41.13 3.58
3277 4024 1.035932 AAGCATGCAGGAGCCATGAC 61.036 55.000 21.98 0.00 41.13 3.06
3278 4025 0.323999 AAAGCATGCAGGAGCCATGA 60.324 50.000 21.98 0.00 41.13 3.07
3279 4026 0.179111 CAAAGCATGCAGGAGCCATG 60.179 55.000 21.98 2.79 41.13 3.66
3280 4027 2.199117 CAAAGCATGCAGGAGCCAT 58.801 52.632 21.98 0.00 41.13 4.40
3281 4028 3.689414 CAAAGCATGCAGGAGCCA 58.311 55.556 21.98 0.00 41.13 4.75
3317 4064 3.382546 ACTTGAAATGGCATGCAGTATCC 59.617 43.478 21.36 0.64 0.00 2.59
3319 4066 4.275810 AGACTTGAAATGGCATGCAGTAT 58.724 39.130 21.36 6.71 0.00 2.12
3320 4067 3.689347 AGACTTGAAATGGCATGCAGTA 58.311 40.909 21.36 5.44 0.00 2.74
3323 4070 2.516906 TGAGACTTGAAATGGCATGCA 58.483 42.857 21.36 6.13 0.00 3.96
3324 4071 3.581024 TTGAGACTTGAAATGGCATGC 57.419 42.857 9.90 9.90 0.00 4.06
3325 4072 4.921515 CACTTTGAGACTTGAAATGGCATG 59.078 41.667 0.00 0.00 0.00 4.06
3360 4118 3.728864 CGCAGGCACATGTAAAAAGCTAG 60.729 47.826 0.00 0.00 0.00 3.42
3377 4135 4.662961 TGACCAGACACGCGCAGG 62.663 66.667 5.73 3.38 0.00 4.85
3571 4332 1.745232 ACGTTCAACAAGCCTTGTGA 58.255 45.000 11.51 8.10 44.59 3.58
3577 4338 1.205820 GGCGTACGTTCAACAAGCC 59.794 57.895 17.90 1.77 36.08 4.35
3583 4344 0.457166 CGATCAGGGCGTACGTTCAA 60.457 55.000 17.90 0.00 0.00 2.69
3597 4358 3.553715 GCATGGTAGCTTCTGATCGATCA 60.554 47.826 25.80 25.80 35.16 2.92
3612 4379 0.317160 GGATCGATCCGTGCATGGTA 59.683 55.000 27.93 11.75 37.19 3.25
3653 4426 5.808030 TGATCATAGACTAGATAGCTCGTCG 59.192 44.000 6.97 0.00 40.63 5.12
3795 4583 5.074515 TCCCTTGGTCAATAGATTATTCCCC 59.925 44.000 0.00 0.00 0.00 4.81
3853 4646 0.111398 CGAATGATCAGCGCGACATG 60.111 55.000 12.10 4.97 0.00 3.21
3977 4784 7.339976 TGCTTTGATCCATCATCACTGAATTAA 59.660 33.333 0.00 0.00 41.56 1.40
3978 4785 6.829811 TGCTTTGATCCATCATCACTGAATTA 59.170 34.615 0.00 0.00 41.56 1.40
3987 4794 5.064558 ACAGATCTGCTTTGATCCATCATC 58.935 41.667 22.83 0.00 42.68 2.92
4157 4981 6.088085 GGCAATATTCAAGAAAAAGACACACG 59.912 38.462 0.00 0.00 0.00 4.49
4217 5044 0.390492 TGCAGATATCCACTGGCTCG 59.610 55.000 0.00 0.00 36.09 5.03
4233 5061 4.568956 AGAATATGCTATACACGCATGCA 58.431 39.130 19.57 0.00 46.69 3.96
4262 5102 4.096311 CGTAGACCACACAATAAGAGACG 58.904 47.826 0.00 0.00 0.00 4.18
4265 5105 4.091509 GCAACGTAGACCACACAATAAGAG 59.908 45.833 0.00 0.00 0.00 2.85
4464 5387 3.339253 TCAGTGCTGCAACATATCAGT 57.661 42.857 2.77 0.00 33.09 3.41
4465 5388 3.487042 GCTTCAGTGCTGCAACATATCAG 60.487 47.826 2.77 0.00 0.00 2.90
4466 5389 2.421073 GCTTCAGTGCTGCAACATATCA 59.579 45.455 2.77 0.00 0.00 2.15
4468 5391 2.719739 AGCTTCAGTGCTGCAACATAT 58.280 42.857 2.77 0.00 42.33 1.78
4469 5392 2.189594 AGCTTCAGTGCTGCAACATA 57.810 45.000 2.77 0.00 42.33 2.29
4470 5393 1.000607 CAAGCTTCAGTGCTGCAACAT 60.001 47.619 2.77 0.00 43.24 2.71



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

AutoCloner maintained by Alex Coulton.