Multiple sequence alignment - TraesCS3A01G322400

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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 TraesCS3A01G322400 chr3A 100.000 6818 0 0 1 6818 565791895 565798712 0.000000e+00 12591.0
1 TraesCS3A01G322400 chr3A 86.204 1080 120 17 3751 4818 565794204 565795266 0.000000e+00 1142.0
2 TraesCS3A01G322400 chr3A 86.204 1080 120 17 2310 3372 565795645 565796712 0.000000e+00 1142.0
3 TraesCS3A01G322400 chr3A 89.105 257 26 2 3370 3624 565793733 565793989 1.100000e-82 318.0
4 TraesCS3A01G322400 chr3A 89.105 257 26 2 1839 2095 565795264 565795518 1.100000e-82 318.0
5 TraesCS3A01G322400 chr3A 87.347 245 31 0 1793 2037 565793242 565793486 1.450000e-71 281.0
6 TraesCS3A01G322400 chr3A 87.347 245 31 0 1348 1592 565793687 565793931 1.450000e-71 281.0
7 TraesCS3A01G322400 chr3D 92.771 6211 356 46 651 6812 423011152 423017318 0.000000e+00 8896.0
8 TraesCS3A01G322400 chr3D 86.178 1078 128 10 2310 3372 423014246 423015317 0.000000e+00 1146.0
9 TraesCS3A01G322400 chr3D 83.670 1090 139 27 3751 4818 423012795 423013867 0.000000e+00 990.0
10 TraesCS3A01G322400 chr3D 89.028 319 22 4 1 309 423010485 423010800 3.860000e-102 383.0
11 TraesCS3A01G322400 chr3D 86.127 346 37 9 3367 3706 423012352 423012692 5.030000e-96 363.0
12 TraesCS3A01G322400 chr3D 84.073 383 32 13 245 624 423010807 423011163 6.550000e-90 342.0
13 TraesCS3A01G322400 chr3D 89.961 259 23 3 1839 2097 423013865 423014120 1.420000e-86 331.0
14 TraesCS3A01G322400 chr3D 94.444 36 0 2 2724 2758 423013288 423013322 3.000000e-03 54.7
15 TraesCS3A01G322400 chr3B 92.266 3116 180 19 651 3733 553733671 553730584 0.000000e+00 4362.0
16 TraesCS3A01G322400 chr3B 92.805 2460 143 19 4382 6818 553729919 553727471 0.000000e+00 3531.0
17 TraesCS3A01G322400 chr3B 83.104 1089 143 31 3751 4818 553732013 553730945 0.000000e+00 953.0
18 TraesCS3A01G322400 chr3B 93.771 594 32 3 3732 4320 553730502 553729909 0.000000e+00 887.0
19 TraesCS3A01G322400 chr3B 91.705 434 33 1 2939 3372 553729916 553729486 3.520000e-167 599.0
20 TraesCS3A01G322400 chr3B 92.208 308 21 2 1 307 553734331 553734026 3.780000e-117 433.0
21 TraesCS3A01G322400 chr3B 83.805 389 35 13 245 630 553734017 553733654 1.820000e-90 344.0
22 TraesCS3A01G322400 chr3B 89.961 259 23 3 1839 2097 553730947 553730692 1.420000e-86 331.0
23 TraesCS3A01G322400 chr3B 86.957 253 33 0 1340 1592 553732525 553732273 1.120000e-72 285.0
24 TraesCS3A01G322400 chr3B 85.124 242 36 0 1796 2037 553732973 553732732 1.470000e-61 248.0
25 TraesCS3A01G322400 chr3B 94.444 36 0 2 2724 2758 553731524 553731490 3.000000e-03 54.7
26 TraesCS3A01G322400 chr6B 100.000 31 0 0 2097 2127 225541542 225541512 2.660000e-04 58.4
27 TraesCS3A01G322400 chr6B 100.000 30 0 0 2097 2126 48563216 48563187 1.000000e-03 56.5
28 TraesCS3A01G322400 chr7B 100.000 30 0 0 2097 2126 104069069 104069040 1.000000e-03 56.5
29 TraesCS3A01G322400 chr4D 96.970 33 1 0 2097 2129 482365285 482365317 1.000000e-03 56.5
30 TraesCS3A01G322400 chr2D 100.000 30 0 0 2097 2126 124878398 124878369 1.000000e-03 56.5
31 TraesCS3A01G322400 chr2B 100.000 30 0 0 2097 2126 314770570 314770599 1.000000e-03 56.5
32 TraesCS3A01G322400 chr2B 100.000 30 0 0 2097 2126 720806651 720806680 1.000000e-03 56.5
33 TraesCS3A01G322400 chr5A 92.105 38 2 1 2097 2133 339743261 339743224 1.200000e-02 52.8


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 TraesCS3A01G322400 chr3A 565791895 565798712 6817 False 12591.000000 12591 100.000 1 6818 1 chr3A.!!$F1 6817
1 TraesCS3A01G322400 chr3A 565793242 565796712 3470 False 580.333333 1142 87.552 1348 4818 6 chr3A.!!$F2 3470
2 TraesCS3A01G322400 chr3D 423010485 423017318 6833 False 3207.000000 8896 88.624 1 6812 3 chr3D.!!$F1 6811
3 TraesCS3A01G322400 chr3D 423012352 423015317 2965 False 576.940000 1146 88.076 1839 4818 5 chr3D.!!$F2 2979
4 TraesCS3A01G322400 chr3B 553727471 553734331 6860 True 1093.427273 4362 89.650 1 6818 11 chr3B.!!$R1 6817

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
260 270 0.689055 TCAGCAGCTCTCCACATGTT 59.311 50.000 0.00 0.00 0.00 2.71 F
312 322 1.000955 AGTTTCTGCGGAATCACTCGT 59.999 47.619 16.72 0.00 0.00 4.18 F
1260 1345 0.389948 CACGAACACCTAGGAGGCAC 60.390 60.000 17.98 2.76 39.63 5.01 F
1332 1417 5.483685 AACTCACCACTACAAAGCTATGA 57.516 39.130 0.00 0.00 0.00 2.15 F
4827 5037 7.675062 AGAATTCTGATGGTATACATGACTCC 58.325 38.462 7.30 0.00 40.72 3.85 F
5335 5545 0.321919 AGGCTTTGCTGCTGAATCGA 60.322 50.000 0.00 0.00 0.00 3.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1247 1332 3.071874 TGAATTTGTGCCTCCTAGGTG 57.928 47.619 9.08 6.22 37.80 4.00 R
1322 1407 5.608676 ATGAATCAGCGATCATAGCTTTG 57.391 39.130 0.00 0.00 44.06 2.77 R
4827 5037 1.067425 TGGACCATAACAAGACCGACG 60.067 52.381 0.00 0.00 0.00 5.12 R
4930 5140 3.495001 GGTGCGGCTAATTCTTCTATGAC 59.505 47.826 0.00 0.00 0.00 3.06 R
5723 5933 1.713297 AGGAGAACTAACCGTGGTGT 58.287 50.000 0.00 0.00 0.00 4.16 R
6598 6829 2.688446 TCCGACCTCTGTCACATCATAC 59.312 50.000 0.00 0.00 41.85 2.39 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
18 19 2.774044 GTAGCAGCAGAAAGGGAGC 58.226 57.895 0.00 0.00 0.00 4.70
82 83 3.117701 TCCAACTCAACTGGATCCAAACA 60.118 43.478 17.00 0.00 38.07 2.83
218 227 3.454812 ACCGGTGGAATTAGATACAGCTT 59.545 43.478 6.12 0.00 0.00 3.74
260 270 0.689055 TCAGCAGCTCTCCACATGTT 59.311 50.000 0.00 0.00 0.00 2.71
273 283 4.006989 TCCACATGTTGAGGTTTTATCCG 58.993 43.478 0.00 0.00 29.78 4.18
275 285 3.440173 CACATGTTGAGGTTTTATCCGCT 59.560 43.478 0.00 0.00 0.00 5.52
276 286 3.440173 ACATGTTGAGGTTTTATCCGCTG 59.560 43.478 0.00 0.00 0.00 5.18
282 292 4.647611 TGAGGTTTTATCCGCTGAAGAAA 58.352 39.130 0.00 0.00 0.00 2.52
309 319 3.070018 CTGAAGTTTCTGCGGAATCACT 58.930 45.455 16.72 11.97 0.00 3.41
312 322 1.000955 AGTTTCTGCGGAATCACTCGT 59.999 47.619 16.72 0.00 0.00 4.18
313 323 2.230508 AGTTTCTGCGGAATCACTCGTA 59.769 45.455 16.72 0.00 0.00 3.43
314 324 3.119101 AGTTTCTGCGGAATCACTCGTAT 60.119 43.478 16.72 0.00 0.00 3.06
315 325 4.097437 AGTTTCTGCGGAATCACTCGTATA 59.903 41.667 16.72 0.00 0.00 1.47
324 407 6.365247 GCGGAATCACTCGTATACATGTTATT 59.635 38.462 2.30 4.41 0.00 1.40
325 408 7.095774 GCGGAATCACTCGTATACATGTTATTT 60.096 37.037 2.30 0.00 0.00 1.40
360 443 4.633175 GGAAAGAAACTCTTCTCTCCGTT 58.367 43.478 0.00 0.00 38.69 4.44
370 453 4.070716 TCTTCTCTCCGTTCTTCGTAAGT 58.929 43.478 0.00 0.00 37.94 2.24
391 474 3.372206 GTCGGTTCAATCCATGTCTTCAG 59.628 47.826 0.00 0.00 0.00 3.02
420 503 2.699954 TCAGGACCTGAAATCTTTCGC 58.300 47.619 22.30 0.00 37.57 4.70
421 504 1.394917 CAGGACCTGAAATCTTTCGCG 59.605 52.381 17.22 0.00 40.01 5.87
422 505 1.002087 AGGACCTGAAATCTTTCGCGT 59.998 47.619 5.77 0.00 40.01 6.01
423 506 2.232941 AGGACCTGAAATCTTTCGCGTA 59.767 45.455 5.77 0.00 40.01 4.42
424 507 2.997986 GGACCTGAAATCTTTCGCGTAA 59.002 45.455 5.77 0.76 40.01 3.18
425 508 3.181523 GGACCTGAAATCTTTCGCGTAAC 60.182 47.826 5.77 0.00 40.01 2.50
426 509 2.410730 ACCTGAAATCTTTCGCGTAACG 59.589 45.455 5.77 0.00 45.62 3.18
443 526 5.741425 CGTAACGCATCATTTCATGAGAAT 58.259 37.500 0.00 0.00 43.53 2.40
503 586 7.095355 GCGACAGAAAGAAAACTTAGAACCATA 60.095 37.037 0.00 0.00 0.00 2.74
537 620 6.484288 ACCCAATGTGACAGAAAGATTATGA 58.516 36.000 0.00 0.00 0.00 2.15
635 719 9.110617 CATGAATGATATAATTCAACTTGACGC 57.889 33.333 17.74 0.00 46.66 5.19
636 720 7.639039 TGAATGATATAATTCAACTTGACGCC 58.361 34.615 12.44 0.00 42.22 5.68
637 721 7.281999 TGAATGATATAATTCAACTTGACGCCA 59.718 33.333 12.44 0.00 42.22 5.69
638 722 6.993786 TGATATAATTCAACTTGACGCCAA 57.006 33.333 0.00 0.00 0.00 4.52
639 723 7.384439 TGATATAATTCAACTTGACGCCAAA 57.616 32.000 0.00 0.00 0.00 3.28
640 724 7.821652 TGATATAATTCAACTTGACGCCAAAA 58.178 30.769 0.00 0.00 0.00 2.44
641 725 8.300286 TGATATAATTCAACTTGACGCCAAAAA 58.700 29.630 0.00 0.00 0.00 1.94
670 754 8.622157 AGAAGAGAATGATGCAATTCAACTATG 58.378 33.333 12.48 0.00 38.74 2.23
702 786 6.409704 CATCTGACCAGATCTCCAACTTTAA 58.590 40.000 9.40 0.00 45.78 1.52
706 790 7.944554 TCTGACCAGATCTCCAACTTTAATTTT 59.055 33.333 0.00 0.00 31.41 1.82
713 797 9.354673 AGATCTCCAACTTTAATTTTCTTGACA 57.645 29.630 0.00 0.00 0.00 3.58
748 832 3.441500 AAGAGAGGAAACAATGACCCC 57.558 47.619 0.00 0.00 0.00 4.95
749 833 1.636003 AGAGAGGAAACAATGACCCCC 59.364 52.381 0.00 0.00 0.00 5.40
754 838 3.388913 AGGAAACAATGACCCCCAAAAA 58.611 40.909 0.00 0.00 0.00 1.94
823 907 4.757149 ACAGGAAAATTGTGCTGTCTAGTC 59.243 41.667 16.46 0.00 46.00 2.59
824 908 4.756642 CAGGAAAATTGTGCTGTCTAGTCA 59.243 41.667 8.92 0.00 32.67 3.41
835 919 3.244249 GCTGTCTAGTCACACCCTTTCTT 60.244 47.826 0.00 0.00 0.00 2.52
960 1044 5.008118 GCTTGAGCTGAGTTAAAGACTGTTT 59.992 40.000 0.00 0.00 37.05 2.83
1190 1274 5.049612 CGCAGATTATTCACATGAGCTCAAT 60.050 40.000 22.50 11.79 0.00 2.57
1215 1299 7.687941 AACATAAATGGTGAGAAAGGTACTG 57.312 36.000 0.00 0.00 40.86 2.74
1247 1332 4.083537 TCACAATATTTGTCCTGCACGAAC 60.084 41.667 0.00 0.00 43.23 3.95
1260 1345 0.389948 CACGAACACCTAGGAGGCAC 60.390 60.000 17.98 2.76 39.63 5.01
1322 1407 6.072064 TGCTCTTACTAGAAACTCACCACTAC 60.072 42.308 0.00 0.00 0.00 2.73
1332 1417 5.483685 AACTCACCACTACAAAGCTATGA 57.516 39.130 0.00 0.00 0.00 2.15
4818 5028 8.605947 CAAGGGGATAAGAATTCTGATGGTATA 58.394 37.037 10.26 0.00 0.00 1.47
4827 5037 7.675062 AGAATTCTGATGGTATACATGACTCC 58.325 38.462 7.30 0.00 40.72 3.85
4930 5140 6.423905 TGAAGAAAAGGTACATGAAGAAGTCG 59.576 38.462 0.00 0.00 0.00 4.18
4947 5157 6.508777 AGAAGTCGTCATAGAAGAATTAGCC 58.491 40.000 0.00 0.00 29.95 3.93
4964 5174 1.659233 CCGCACCAATGACTGCAAA 59.341 52.632 0.00 0.00 32.57 3.68
4998 5208 8.017946 GCTCTTAAACCAGTAGAAGATTTTGTG 58.982 37.037 0.00 0.00 0.00 3.33
5088 5298 9.372369 GCAAAGACTATAGATACACAAGAAACT 57.628 33.333 6.78 0.00 0.00 2.66
5103 5313 7.498900 ACACAAGAAACTATGAACATCTCACAA 59.501 33.333 0.00 0.00 36.69 3.33
5122 5332 2.414994 ATGTGATCAGCCTCAACAGG 57.585 50.000 0.00 0.00 43.82 4.00
5151 5361 5.393027 GCTTGAAGAACCTGAAGTTGTCAAA 60.393 40.000 0.00 0.00 39.40 2.69
5178 5388 1.993956 ACAGTGAGACTCTGAGCACT 58.006 50.000 4.19 7.53 41.90 4.40
5184 5394 2.270047 GAGACTCTGAGCACTTGCATC 58.730 52.381 4.19 0.00 45.16 3.91
5185 5395 1.066286 AGACTCTGAGCACTTGCATCC 60.066 52.381 4.19 0.00 45.16 3.51
5217 5427 5.810587 GGAATACAGTTCAGCGACAGAATTA 59.189 40.000 0.00 0.00 0.00 1.40
5227 5437 4.272018 CAGCGACAGAATTAATCTTCCCTG 59.728 45.833 0.00 0.00 35.73 4.45
5248 5458 6.047870 CCTGATGTATTCAACAAGGAGAGAG 58.952 44.000 0.00 0.00 42.70 3.20
5276 5486 5.337554 CACATCTGATAAAGCCACATGTTG 58.662 41.667 0.00 0.00 0.00 3.33
5335 5545 0.321919 AGGCTTTGCTGCTGAATCGA 60.322 50.000 0.00 0.00 0.00 3.59
5340 5550 3.631144 CTTTGCTGCTGAATCGAAACAA 58.369 40.909 0.00 0.00 0.00 2.83
5365 5575 9.709495 AAAAGAAAGTTATTGCAAATGCTGATA 57.291 25.926 1.71 2.98 42.66 2.15
5386 5596 7.907389 TGATAATTCTAGTGAGGAACAGTGTT 58.093 34.615 8.61 8.61 33.78 3.32
5429 5639 2.503356 GGACAGATGTGGGTGAAGAGAT 59.497 50.000 0.00 0.00 0.00 2.75
5433 5643 2.169352 AGATGTGGGTGAAGAGATTCCG 59.831 50.000 0.00 0.00 0.00 4.30
5550 5760 0.604578 TGCAAGCCAAAGATGAAGCC 59.395 50.000 0.00 0.00 0.00 4.35
5578 5788 3.195396 AGAATCTGAGAAGAGTCCACTGC 59.805 47.826 0.00 0.00 33.87 4.40
5628 5838 0.737367 TCAGAGCGCCAAATCACTCG 60.737 55.000 2.29 0.00 34.31 4.18
5630 5840 2.436646 AGCGCCAAATCACTCGGG 60.437 61.111 2.29 0.00 0.00 5.14
5690 5900 1.885850 GTGTTGGAACGTGGTCGCT 60.886 57.895 0.00 0.00 41.18 4.93
5691 5901 1.885388 TGTTGGAACGTGGTCGCTG 60.885 57.895 0.00 0.00 41.18 5.18
6050 6270 5.163426 TGTCTGTAAAGGGTTGTCGAGTTAA 60.163 40.000 0.00 0.00 0.00 2.01
6070 6290 8.161699 AGTTAAAAACATCCTTTGTGTACGAT 57.838 30.769 0.00 0.00 38.99 3.73
6174 6401 7.008021 ACATGCCAAAAACTTCCAATTATCT 57.992 32.000 0.00 0.00 0.00 1.98
6175 6402 7.452562 ACATGCCAAAAACTTCCAATTATCTT 58.547 30.769 0.00 0.00 0.00 2.40
6516 6747 7.934855 ATTATTGACAATTCTGCTTCAGACT 57.065 32.000 5.89 0.00 40.46 3.24
6522 6753 9.453572 TTGACAATTCTGCTTCAGACTATTATT 57.546 29.630 0.00 0.00 40.46 1.40
6598 6829 5.551760 AAGAAAATCAGTAATGCTCACGG 57.448 39.130 0.00 0.00 0.00 4.94
6599 6830 4.579869 AGAAAATCAGTAATGCTCACGGT 58.420 39.130 0.00 0.00 0.00 4.83
6702 6936 6.070481 TCAGGTATACATAGACTTGTTGCCAA 60.070 38.462 5.01 0.00 0.00 4.52
6730 6964 8.124823 CAGTGCAAATATCAGACGAACAATATT 58.875 33.333 0.00 0.00 0.00 1.28
6785 7021 8.565416 ACTAGTAAAATCACAGTAAGTTTTGCC 58.435 33.333 0.00 0.00 29.95 4.52
6813 7049 2.452813 CGCAGACATACCACGCACC 61.453 63.158 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 1.210234 TGGTGTCATGATGGCCTACAG 59.790 52.381 3.32 0.00 0.00 2.74
121 122 2.265589 TGTCTCCCGGTTTTTCCTTC 57.734 50.000 0.00 0.00 0.00 3.46
122 123 2.583143 CTTGTCTCCCGGTTTTTCCTT 58.417 47.619 0.00 0.00 0.00 3.36
198 207 5.177696 GCTAAAGCTGTATCTAATTCCACCG 59.822 44.000 0.00 0.00 38.21 4.94
260 270 3.973206 TCTTCAGCGGATAAAACCTCA 57.027 42.857 0.00 0.00 0.00 3.86
282 292 3.541632 TCCGCAGAAACTTCAGACTTTT 58.458 40.909 0.00 0.00 0.00 2.27
289 299 3.067106 GAGTGATTCCGCAGAAACTTCA 58.933 45.455 0.00 0.00 35.09 3.02
300 310 7.869016 AATAACATGTATACGAGTGATTCCG 57.131 36.000 0.00 0.00 0.00 4.30
324 407 9.862149 AGAGTTTCTTTCCACTTTTTCCTATAA 57.138 29.630 0.00 0.00 0.00 0.98
325 408 9.862149 AAGAGTTTCTTTCCACTTTTTCCTATA 57.138 29.630 0.00 0.00 31.57 1.31
330 413 7.990917 AGAGAAGAGTTTCTTTCCACTTTTTC 58.009 34.615 0.00 0.00 43.63 2.29
360 443 3.256383 TGGATTGAACCGACTTACGAAGA 59.744 43.478 0.00 0.00 45.77 2.87
370 453 3.599343 CTGAAGACATGGATTGAACCGA 58.401 45.455 0.00 0.00 0.00 4.69
391 474 2.479566 TCAGGTCCTGAAGTCATTGC 57.520 50.000 19.75 0.00 37.57 3.56
453 536 7.935338 CATTGGTTGCATCATCTAATTAACC 57.065 36.000 0.00 0.00 37.27 2.85
537 620 6.309389 ACCTGAAACCTTCTATACGGAAAT 57.691 37.500 0.00 0.00 0.00 2.17
571 654 1.779569 AGCGTACACTGTACTGCAAC 58.220 50.000 24.82 10.02 0.00 4.17
615 699 6.993786 TTGGCGTCAAGTTGAATTATATCA 57.006 33.333 7.25 0.00 0.00 2.15
640 724 8.985805 GTTGAATTGCATCATTCTCTTCTTTTT 58.014 29.630 11.43 0.00 0.00 1.94
641 725 8.365647 AGTTGAATTGCATCATTCTCTTCTTTT 58.634 29.630 11.43 0.00 0.00 2.27
642 726 7.893658 AGTTGAATTGCATCATTCTCTTCTTT 58.106 30.769 11.43 0.00 0.00 2.52
643 727 7.463961 AGTTGAATTGCATCATTCTCTTCTT 57.536 32.000 11.43 0.00 0.00 2.52
644 728 8.622157 CATAGTTGAATTGCATCATTCTCTTCT 58.378 33.333 11.43 7.47 0.00 2.85
645 729 8.618677 TCATAGTTGAATTGCATCATTCTCTTC 58.381 33.333 11.43 1.92 0.00 2.87
646 730 8.515695 TCATAGTTGAATTGCATCATTCTCTT 57.484 30.769 11.43 1.67 0.00 2.85
647 731 8.693120 ATCATAGTTGAATTGCATCATTCTCT 57.307 30.769 11.43 11.32 34.96 3.10
648 732 9.181805 CAATCATAGTTGAATTGCATCATTCTC 57.818 33.333 11.43 5.97 34.96 2.87
649 733 8.141909 CCAATCATAGTTGAATTGCATCATTCT 58.858 33.333 11.43 6.69 34.96 2.40
650 734 7.384115 CCCAATCATAGTTGAATTGCATCATTC 59.616 37.037 4.46 4.46 34.96 2.67
651 735 7.214381 CCCAATCATAGTTGAATTGCATCATT 58.786 34.615 0.00 0.00 34.96 2.57
652 736 6.740401 GCCCAATCATAGTTGAATTGCATCAT 60.740 38.462 0.00 0.00 34.96 2.45
653 737 5.452216 GCCCAATCATAGTTGAATTGCATCA 60.452 40.000 0.00 0.00 34.96 3.07
654 738 4.986659 GCCCAATCATAGTTGAATTGCATC 59.013 41.667 0.00 0.00 34.96 3.91
655 739 4.202284 GGCCCAATCATAGTTGAATTGCAT 60.202 41.667 0.00 0.00 34.96 3.96
656 740 3.132646 GGCCCAATCATAGTTGAATTGCA 59.867 43.478 0.00 0.00 34.96 4.08
657 741 3.132646 TGGCCCAATCATAGTTGAATTGC 59.867 43.478 0.00 0.00 34.96 3.56
658 742 5.303589 AGATGGCCCAATCATAGTTGAATTG 59.696 40.000 0.00 0.00 34.96 2.32
659 743 5.303589 CAGATGGCCCAATCATAGTTGAATT 59.696 40.000 0.00 0.00 34.96 2.17
660 744 4.831155 CAGATGGCCCAATCATAGTTGAAT 59.169 41.667 0.00 0.00 34.96 2.57
661 745 4.079844 TCAGATGGCCCAATCATAGTTGAA 60.080 41.667 0.00 0.00 34.96 2.69
662 746 3.459227 TCAGATGGCCCAATCATAGTTGA 59.541 43.478 0.00 0.00 36.00 3.18
670 754 0.548031 TCTGGTCAGATGGCCCAATC 59.452 55.000 0.00 0.00 39.61 2.67
730 814 1.354368 TGGGGGTCATTGTTTCCTCTC 59.646 52.381 0.00 0.00 0.00 3.20
754 838 2.107204 GGGAGCACATCATAGGGACATT 59.893 50.000 0.00 0.00 0.00 2.71
823 907 4.761739 TCAAGATTAGCAAGAAAGGGTGTG 59.238 41.667 0.00 0.00 0.00 3.82
824 908 4.985538 TCAAGATTAGCAAGAAAGGGTGT 58.014 39.130 0.00 0.00 0.00 4.16
835 919 0.991146 TGGCCACCTCAAGATTAGCA 59.009 50.000 0.00 0.00 0.00 3.49
857 941 1.134280 AGCACTACAGACCATGATGGC 60.134 52.381 12.25 4.53 42.67 4.40
1190 1274 7.335924 GCAGTACCTTTCTCACCATTTATGTTA 59.664 37.037 0.00 0.00 0.00 2.41
1247 1332 3.071874 TGAATTTGTGCCTCCTAGGTG 57.928 47.619 9.08 6.22 37.80 4.00
1322 1407 5.608676 ATGAATCAGCGATCATAGCTTTG 57.391 39.130 0.00 0.00 44.06 2.77
1332 1417 5.633830 AAACAGAACAATGAATCAGCGAT 57.366 34.783 0.00 0.00 0.00 4.58
4827 5037 1.067425 TGGACCATAACAAGACCGACG 60.067 52.381 0.00 0.00 0.00 5.12
4930 5140 3.495001 GGTGCGGCTAATTCTTCTATGAC 59.505 47.826 0.00 0.00 0.00 3.06
4947 5157 1.987770 GATTTTGCAGTCATTGGTGCG 59.012 47.619 7.22 0.00 42.96 5.34
4964 5174 8.635765 TTCTACTGGTTTAAGAGCAAATGATT 57.364 30.769 0.00 0.00 34.90 2.57
4978 5188 7.060421 TCCTTCACAAAATCTTCTACTGGTTT 58.940 34.615 0.00 0.00 0.00 3.27
4998 5208 9.430623 GAGCTATCAGGTTTAATATCTTCCTTC 57.569 37.037 0.00 0.00 0.00 3.46
5088 5298 6.259387 GCTGATCACATTGTGAGATGTTCATA 59.741 38.462 22.82 2.43 46.04 2.15
5096 5306 2.568509 TGAGGCTGATCACATTGTGAGA 59.431 45.455 22.82 12.12 46.04 3.27
5103 5313 1.632409 ACCTGTTGAGGCTGATCACAT 59.368 47.619 0.00 0.00 44.33 3.21
5122 5332 4.381411 ACTTCAGGTTCTTCAAGCAGTAC 58.619 43.478 0.00 0.00 31.93 2.73
5151 5361 5.238214 GCTCAGAGTCTCACTGTTTTCAAAT 59.762 40.000 1.94 0.00 36.81 2.32
5178 5388 3.169378 TCCACCAGCTGGATGCAA 58.831 55.556 39.19 18.79 44.99 4.08
5184 5394 2.290260 TGAACTGTATTCCACCAGCTGG 60.290 50.000 31.60 31.60 42.29 4.85
5185 5395 3.005554 CTGAACTGTATTCCACCAGCTG 58.994 50.000 6.78 6.78 31.76 4.24
5198 5408 5.482908 AGATTAATTCTGTCGCTGAACTGT 58.517 37.500 0.00 0.00 31.79 3.55
5217 5427 6.604795 CCTTGTTGAATACATCAGGGAAGATT 59.395 38.462 0.00 0.00 42.06 2.40
5227 5437 6.760770 CCTTCTCTCTCCTTGTTGAATACATC 59.239 42.308 0.00 0.00 36.44 3.06
5248 5458 3.065925 GTGGCTTTATCAGATGTGCCTTC 59.934 47.826 18.10 11.01 40.82 3.46
5276 5486 6.227298 TCTCCTGATTGGATTCAGAAGTAC 57.773 41.667 3.10 0.00 44.88 2.73
5335 5545 8.676401 AGCATTTGCAATAACTTTCTTTTGTTT 58.324 25.926 0.00 0.00 45.16 2.83
5340 5550 9.709495 TTATCAGCATTTGCAATAACTTTCTTT 57.291 25.926 0.00 0.00 45.16 2.52
5365 5575 5.239525 GCAAACACTGTTCCTCACTAGAATT 59.760 40.000 0.00 0.00 0.00 2.17
5494 5704 3.459828 TCATGGGGATGTCCTTGACTAA 58.540 45.455 0.00 0.00 36.46 2.24
5550 5760 4.420168 GACTCTTCTCAGATTCTTCCACG 58.580 47.826 0.00 0.00 0.00 4.94
5578 5788 1.461075 ATGGCTCCCTAGGGCTCAG 60.461 63.158 24.42 16.52 34.68 3.35
5628 5838 5.009310 ACGAAGTGGTTTATTGTTTCTTCCC 59.991 40.000 0.00 0.00 42.51 3.97
5630 5840 6.795593 GCTACGAAGTGGTTTATTGTTTCTTC 59.204 38.462 0.00 0.00 45.73 2.87
5673 5883 1.885388 CAGCGACCACGTTCCAACA 60.885 57.895 0.00 0.00 41.98 3.33
5690 5900 2.294074 CCGGTTCTTGTTCCTTCAACA 58.706 47.619 0.00 0.00 43.68 3.33
5691 5901 2.294979 ACCGGTTCTTGTTCCTTCAAC 58.705 47.619 0.00 0.00 35.28 3.18
5715 5925 3.200483 ACTAACCGTGGTGTTGTTCTTC 58.800 45.455 0.00 0.00 0.00 2.87
5723 5933 1.713297 AGGAGAACTAACCGTGGTGT 58.287 50.000 0.00 0.00 0.00 4.16
5985 6205 6.459298 GCATTCATTCTCCAAACCAGATACAG 60.459 42.308 0.00 0.00 0.00 2.74
6050 6270 5.927689 TCGTATCGTACACAAAGGATGTTTT 59.072 36.000 0.00 0.00 41.46 2.43
6372 6602 5.713025 TGCTTTTGAATAAGATGGTCTTGC 58.287 37.500 2.60 0.00 37.29 4.01
6513 6744 9.798885 GTGTGAATTCGAGCATTAATAATAGTC 57.201 33.333 0.04 0.00 0.00 2.59
6522 6753 6.493449 TTCAATGTGTGAATTCGAGCATTA 57.507 33.333 15.78 4.85 41.47 1.90
6523 6754 5.375417 TTCAATGTGTGAATTCGAGCATT 57.625 34.783 12.42 12.42 41.47 3.56
6598 6829 2.688446 TCCGACCTCTGTCACATCATAC 59.312 50.000 0.00 0.00 41.85 2.39
6599 6830 2.952310 CTCCGACCTCTGTCACATCATA 59.048 50.000 0.00 0.00 41.85 2.15
6619 6850 4.623932 TGTTTGCATCTTCTCCAGTACT 57.376 40.909 0.00 0.00 0.00 2.73
6702 6936 4.754618 TGTTCGTCTGATATTTGCACTGTT 59.245 37.500 0.00 0.00 0.00 3.16
6730 6964 9.113838 GAAATCTGGAATTGCTCTAATCAGTAA 57.886 33.333 0.00 0.00 0.00 2.24
6785 7021 5.432157 GTGGTATGTCTGCGATTATTTTCG 58.568 41.667 0.00 0.00 41.99 3.46


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

AutoCloner maintained by Alex Coulton.