Multiple sequence alignment - TraesCS3D01G533700

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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 TraesCS3D01G533700 chr3D 100.000 5095 0 0 1 5095 609089471 609084377 0.000000e+00 9409.0
1 TraesCS3D01G533700 chr3B 90.865 3886 162 66 14 3820 819792495 819788724 0.000000e+00 5031.0
2 TraesCS3D01G533700 chr3B 92.165 3076 130 35 2066 5075 819790488 819787458 0.000000e+00 4242.0
3 TraesCS3D01G533700 chr3A 91.229 2839 137 54 87 2898 742444031 742441278 0.000000e+00 3760.0
4 TraesCS3D01G533700 chr3A 92.339 2232 116 26 2900 5087 742441207 742438987 0.000000e+00 3123.0
5 TraesCS3D01G533700 chr2D 87.891 256 16 9 4756 4999 623474984 623474732 2.320000e-73 287.0
6 TraesCS3D01G533700 chr2D 85.069 288 28 9 3501 3784 623496454 623496178 3.880000e-71 279.0
7 TraesCS3D01G533700 chr2D 77.841 176 21 12 4793 4961 642203691 642203527 5.430000e-15 93.5
8 TraesCS3D01G533700 chr2D 77.536 138 24 5 4926 5062 598308983 598308852 5.470000e-10 76.8
9 TraesCS3D01G533700 chr2B 87.963 216 17 6 4061 4275 765484586 765484379 3.940000e-61 246.0
10 TraesCS3D01G533700 chr2B 77.113 284 46 14 4793 5071 799614132 799614401 4.110000e-31 147.0
11 TraesCS3D01G533700 chr2A 83.550 231 27 3 4679 4907 754707353 754707132 6.690000e-49 206.0
12 TraesCS3D01G533700 chr2A 75.540 278 49 14 4802 5074 766919414 766919151 8.960000e-23 119.0
13 TraesCS3D01G533700 chr2A 78.448 116 23 2 4880 4994 766973813 766973699 1.970000e-09 75.0
14 TraesCS3D01G533700 chr7B 81.250 208 15 13 394 598 354697015 354696829 4.110000e-31 147.0
15 TraesCS3D01G533700 chr7B 80.769 208 19 12 394 598 207959627 207959438 5.320000e-30 143.0
16 TraesCS3D01G533700 chr1B 79.808 208 21 12 394 598 488600569 488600380 1.150000e-26 132.0
17 TraesCS3D01G533700 chr6D 73.668 319 66 14 1667 1979 460649431 460649737 1.940000e-19 108.0
18 TraesCS3D01G533700 chr6D 82.353 102 17 1 2561 2661 460650570 460650671 2.530000e-13 87.9
19 TraesCS3D01G533700 chr6B 76.630 184 38 4 1797 1979 701863983 701864162 4.200000e-16 97.1
20 TraesCS3D01G533700 chr6B 82.353 102 17 1 2561 2661 701864907 701865008 2.530000e-13 87.9
21 TraesCS3D01G533700 chr6A 72.871 317 72 11 1667 1979 606962440 606962746 4.200000e-16 97.1


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 TraesCS3D01G533700 chr3D 609084377 609089471 5094 True 9409.0 9409 100.000 1 5095 1 chr3D.!!$R1 5094
1 TraesCS3D01G533700 chr3B 819787458 819792495 5037 True 4636.5 5031 91.515 14 5075 2 chr3B.!!$R1 5061
2 TraesCS3D01G533700 chr3A 742438987 742444031 5044 True 3441.5 3760 91.784 87 5087 2 chr3A.!!$R1 5000

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
278 288 0.250234 TTGCTCCTCAATCGGGACTG 59.750 55.000 0.0 0.0 0.00 3.51 F
1122 1174 0.468648 GTACTACCTGCCATGACCCC 59.531 60.000 0.0 0.0 0.00 4.95 F
1765 1823 1.133025 CATCCATGAAAAGGACCGCAC 59.867 52.381 0.0 0.0 38.13 5.34 F
2023 2081 1.538950 CTTTTGCTTCTCCACAGGCTC 59.461 52.381 0.0 0.0 0.00 4.70 F
3657 3808 0.534203 GGAACAGGAAGGTTCGTGCA 60.534 55.000 11.4 0.0 46.34 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1452 0.107214 CACACACACCACCAGAACCT 60.107 55.000 0.00 0.0 0.00 3.50 R
2007 2065 1.203441 ATGGAGCCTGTGGAGAAGCA 61.203 55.000 0.00 0.0 0.00 3.91 R
3532 3683 0.100325 TTGACTTGCAAACAGGCACG 59.900 50.000 0.00 0.0 44.86 5.34 R
3679 3830 3.004629 TGTTTGCAGCAATGACCTTAGTG 59.995 43.478 9.12 0.0 0.00 2.74 R
4734 4940 0.035343 GGGGCAGAGGAGTGGTAAAC 60.035 60.000 0.00 0.0 0.00 2.01 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
41 42 0.451783 ATGCTCCGCGATTTGGTTTC 59.548 50.000 8.23 0.00 0.00 2.78
42 43 0.605319 TGCTCCGCGATTTGGTTTCT 60.605 50.000 8.23 0.00 0.00 2.52
54 55 1.304962 GGTTTCTTGGGGCCCGATT 60.305 57.895 19.83 0.00 0.00 3.34
55 56 1.320344 GGTTTCTTGGGGCCCGATTC 61.320 60.000 19.83 1.35 0.00 2.52
56 57 1.000145 TTTCTTGGGGCCCGATTCC 60.000 57.895 19.83 0.88 0.00 3.01
57 58 2.508407 TTTCTTGGGGCCCGATTCCC 62.508 60.000 19.83 0.00 43.42 3.97
58 59 3.420482 CTTGGGGCCCGATTCCCT 61.420 66.667 19.83 0.00 43.51 4.20
59 60 2.944390 TTGGGGCCCGATTCCCTT 60.944 61.111 19.83 0.00 43.51 3.95
60 61 2.911221 CTTGGGGCCCGATTCCCTTC 62.911 65.000 19.83 0.00 43.51 3.46
61 62 4.205484 GGGGCCCGATTCCCTTCC 62.205 72.222 17.79 0.00 43.41 3.46
187 188 2.231235 CCCATTTCAGACTTTTTCCCCG 59.769 50.000 0.00 0.00 0.00 5.73
202 204 1.654023 CCCCGGAGTTGAATTTCGCC 61.654 60.000 0.73 0.00 0.00 5.54
203 205 0.958382 CCCGGAGTTGAATTTCGCCA 60.958 55.000 0.73 0.00 0.00 5.69
220 222 2.450476 GCCATGTTCTTGGATGTTCCT 58.550 47.619 8.59 0.00 39.25 3.36
236 238 2.646175 CCTTGGTCGCCTCTCCGAA 61.646 63.158 0.00 0.00 39.17 4.30
278 288 0.250234 TTGCTCCTCAATCGGGACTG 59.750 55.000 0.00 0.00 0.00 3.51
279 289 1.522580 GCTCCTCAATCGGGACTGC 60.523 63.158 0.00 0.00 0.00 4.40
290 300 2.558313 GGACTGCGTTCAAGCTGC 59.442 61.111 0.00 0.00 39.28 5.25
291 301 2.253758 GGACTGCGTTCAAGCTGCA 61.254 57.895 1.02 0.00 39.28 4.41
294 304 2.203195 TGCGTTCAAGCTGCAGGT 60.203 55.556 13.85 13.85 38.13 4.00
295 305 2.253452 GCGTTCAAGCTGCAGGTG 59.747 61.111 20.97 13.54 0.00 4.00
296 306 2.546494 GCGTTCAAGCTGCAGGTGT 61.546 57.895 20.97 6.98 0.00 4.16
297 307 1.280746 CGTTCAAGCTGCAGGTGTG 59.719 57.895 20.97 18.38 0.00 3.82
298 308 1.656441 GTTCAAGCTGCAGGTGTGG 59.344 57.895 20.97 12.37 0.00 4.17
299 309 2.195567 TTCAAGCTGCAGGTGTGGC 61.196 57.895 20.97 1.44 0.00 5.01
319 329 2.046314 CCCCTTGTTCGATGCGGT 60.046 61.111 0.00 0.00 0.00 5.68
322 332 0.953471 CCCTTGTTCGATGCGGTTGA 60.953 55.000 0.00 0.00 0.00 3.18
329 341 3.252215 TGTTCGATGCGGTTGAGATTTTT 59.748 39.130 0.00 0.00 0.00 1.94
333 345 0.965439 TGCGGTTGAGATTTTTGGGG 59.035 50.000 0.00 0.00 0.00 4.96
413 430 1.340405 ACTTGCCTTGCCGATTCAGAT 60.340 47.619 0.00 0.00 0.00 2.90
421 438 1.473677 TGCCGATTCAGATTTTGGCTG 59.526 47.619 11.67 0.00 42.87 4.85
463 480 9.241317 CAGCCAAAGAATTTTACTGCATAATAG 57.759 33.333 0.00 0.00 35.03 1.73
532 549 2.260844 TGTGCTTCCTCTGTCTTTGG 57.739 50.000 0.00 0.00 0.00 3.28
536 553 4.134563 GTGCTTCCTCTGTCTTTGGTTTA 58.865 43.478 0.00 0.00 0.00 2.01
538 555 5.241728 GTGCTTCCTCTGTCTTTGGTTTATT 59.758 40.000 0.00 0.00 0.00 1.40
677 708 2.770232 CCGTTTCTTCCCCTACTATGGT 59.230 50.000 0.00 0.00 0.00 3.55
803 844 4.981806 TTATTTCTTTGCTGGGATTCGG 57.018 40.909 0.00 0.00 0.00 4.30
899 951 3.081061 TGCCGTTTGAGCAATCATTAGT 58.919 40.909 0.00 0.00 37.28 2.24
920 972 4.043310 AGTTGGGAATCCTCACTGAATTCA 59.957 41.667 8.12 8.12 0.00 2.57
1122 1174 0.468648 GTACTACCTGCCATGACCCC 59.531 60.000 0.00 0.00 0.00 4.95
1152 1204 7.276218 GCAATTTGCGCATTGGATATTATGTAT 59.724 33.333 21.66 0.00 35.07 2.29
1153 1205 9.142515 CAATTTGCGCATTGGATATTATGTATT 57.857 29.630 12.75 0.00 31.43 1.89
1164 1216 9.761504 TTGGATATTATGTATTTTAACGACCGA 57.238 29.630 0.00 0.00 0.00 4.69
1274 1326 5.642919 GCTAGTGGATCATGAGAATTCATCC 59.357 44.000 8.44 11.00 42.12 3.51
1359 1417 1.476891 AGCAGTATGATGACGTTCCGT 59.523 47.619 0.00 0.00 40.77 4.69
1394 1452 1.136305 GCCGTGGAGAACTGTATAGCA 59.864 52.381 0.00 0.00 0.00 3.49
1421 1479 2.032681 GGTGTGTGTGCCTCTCCC 59.967 66.667 0.00 0.00 0.00 4.30
1643 1701 3.502164 GGTGCAGCAACCTATGGAT 57.498 52.632 11.86 0.00 37.24 3.41
1754 1812 1.273048 GTGCCTTTGTGCATCCATGAA 59.727 47.619 0.00 0.00 44.30 2.57
1765 1823 1.133025 CATCCATGAAAAGGACCGCAC 59.867 52.381 0.00 0.00 38.13 5.34
1778 1836 3.006728 CGCACCACCTCCCCCTTA 61.007 66.667 0.00 0.00 0.00 2.69
1986 2044 4.578516 TGTCCAATAAAGGTATGGCAATCG 59.421 41.667 0.00 0.00 0.00 3.34
2007 2065 6.687081 TCGTCATCACAAAGTTAACCTTTT 57.313 33.333 0.88 0.00 41.51 2.27
2023 2081 1.538950 CTTTTGCTTCTCCACAGGCTC 59.461 52.381 0.00 0.00 0.00 4.70
2031 2089 2.551270 TCTCCACAGGCTCCATAGTTT 58.449 47.619 0.00 0.00 0.00 2.66
2035 2093 2.092212 CCACAGGCTCCATAGTTTCCAT 60.092 50.000 0.00 0.00 0.00 3.41
2036 2094 3.136443 CCACAGGCTCCATAGTTTCCATA 59.864 47.826 0.00 0.00 0.00 2.74
2037 2095 4.385199 CCACAGGCTCCATAGTTTCCATAA 60.385 45.833 0.00 0.00 0.00 1.90
2038 2096 5.192927 CACAGGCTCCATAGTTTCCATAAA 58.807 41.667 0.00 0.00 0.00 1.40
2039 2097 5.066505 CACAGGCTCCATAGTTTCCATAAAC 59.933 44.000 0.00 0.00 44.47 2.01
2054 2112 9.331282 GTTTCCATAAACTAGAGAAGCATATGT 57.669 33.333 4.29 0.00 41.52 2.29
2055 2113 9.547753 TTTCCATAAACTAGAGAAGCATATGTC 57.452 33.333 4.29 0.00 30.49 3.06
2056 2114 8.484214 TCCATAAACTAGAGAAGCATATGTCT 57.516 34.615 4.29 0.00 30.49 3.41
2057 2115 8.928448 TCCATAAACTAGAGAAGCATATGTCTT 58.072 33.333 4.29 8.20 30.49 3.01
2058 2116 9.553064 CCATAAACTAGAGAAGCATATGTCTTT 57.447 33.333 4.29 0.00 30.49 2.52
2323 2384 3.181511 CGTTTACCTCGTACGGTGATACA 60.182 47.826 16.52 0.00 37.93 2.29
2707 2773 4.088634 ACTGGTTGGTGATATTGCATTGT 58.911 39.130 0.00 0.00 0.00 2.71
2743 2809 5.447573 GTGAAATCTGCAACAGTTCTTCTC 58.552 41.667 6.96 0.00 32.61 2.87
2788 2866 7.477144 TCTGTACATAATTAAGGAATGCACG 57.523 36.000 0.00 0.00 0.00 5.34
2821 2899 2.663826 AATTGCTGAGTCGAGAGGTC 57.336 50.000 0.00 0.00 0.00 3.85
2828 2906 3.017442 CTGAGTCGAGAGGTCATGGTTA 58.983 50.000 0.00 0.00 0.00 2.85
2829 2907 3.017442 TGAGTCGAGAGGTCATGGTTAG 58.983 50.000 0.00 0.00 0.00 2.34
2874 2954 9.299963 CAGAACAAATTCATTACACAGTGAAAA 57.700 29.630 7.81 1.40 37.82 2.29
2891 2971 4.766891 GTGAAAATTCTCCCCTCATGACAA 59.233 41.667 0.00 0.00 0.00 3.18
3055 3204 1.812571 CAAGCTAGAATTTGCCACGGT 59.187 47.619 0.00 0.00 0.00 4.83
3215 3364 8.617809 TGAAGTTGTTTCTTGTGTCTTTATACC 58.382 33.333 0.00 0.00 36.71 2.73
3243 3392 7.264947 AGTTTTGGTTTAGGAAGACAATTGTG 58.735 34.615 17.58 0.00 0.00 3.33
3424 3575 1.760613 TCTCCAAACCGTGTTCAGAGT 59.239 47.619 11.88 0.00 0.00 3.24
3561 3712 2.978010 CAAGTCAAAGCGGCCCGT 60.978 61.111 4.45 0.00 0.00 5.28
3657 3808 0.534203 GGAACAGGAAGGTTCGTGCA 60.534 55.000 11.40 0.00 46.34 4.57
3658 3809 1.523758 GAACAGGAAGGTTCGTGCAT 58.476 50.000 11.40 2.54 44.49 3.96
3659 3810 1.197721 GAACAGGAAGGTTCGTGCATG 59.802 52.381 11.40 0.00 44.49 4.06
3679 3830 8.068977 GTGCATGAATGATTTCTCTCTATTGAC 58.931 37.037 0.00 0.00 32.78 3.18
3680 3831 7.771826 TGCATGAATGATTTCTCTCTATTGACA 59.228 33.333 0.00 0.00 32.78 3.58
3681 3832 8.068977 GCATGAATGATTTCTCTCTATTGACAC 58.931 37.037 0.00 0.00 32.78 3.67
3788 3945 6.513556 CGTTCGACAATACTGATCATAGGACT 60.514 42.308 0.00 0.00 0.00 3.85
4220 4407 6.590234 ACTCACAGGTCATTTTATTTTCCC 57.410 37.500 0.00 0.00 0.00 3.97
4272 4462 1.542030 GTGCTCTCTTTCCTCTGTCGA 59.458 52.381 0.00 0.00 0.00 4.20
4299 4489 3.487120 AGAGAAACTAAACGCCTGGTT 57.513 42.857 0.00 0.00 41.76 3.67
4418 4608 8.969121 TTGCACATTTTCTCATTACTACATTG 57.031 30.769 0.00 0.00 0.00 2.82
4444 4635 5.824904 ATTATCACACTGTCTTCCATTGC 57.175 39.130 0.00 0.00 0.00 3.56
4449 4640 3.067180 CACACTGTCTTCCATTGCAGTTT 59.933 43.478 0.00 0.00 39.82 2.66
4480 4671 8.425577 TCTTGAGAGAAATCGGATTATTGTTC 57.574 34.615 3.22 0.00 0.00 3.18
4485 4677 9.709600 GAGAGAAATCGGATTATTGTTCTTTTC 57.290 33.333 3.22 2.50 0.00 2.29
4488 4680 7.396055 AGAAATCGGATTATTGTTCTTTTCCCA 59.604 33.333 3.22 0.00 0.00 4.37
4496 4688 9.927668 GATTATTGTTCTTTTCCCATCAGAAAA 57.072 29.630 0.00 0.00 42.07 2.29
4639 4845 4.736473 TGTGCTATACTGTCCCAGCTATA 58.264 43.478 8.90 0.00 34.37 1.31
4670 4876 3.447918 GCGAGGGCTACATTGTAGTTA 57.552 47.619 21.70 0.00 35.83 2.24
4690 4896 1.065126 AGTGAGGCCAGGCTGAATTAC 60.065 52.381 17.94 8.10 0.00 1.89
4701 4907 2.565841 GCTGAATTACCTAGCCCAGTG 58.434 52.381 0.00 0.00 0.00 3.66
4705 4911 4.562767 TGAATTACCTAGCCCAGTGGATA 58.437 43.478 11.95 2.12 0.00 2.59
4734 4940 0.896940 AGCCCAACAACATCCAGCAG 60.897 55.000 0.00 0.00 0.00 4.24
4754 4966 1.550130 TTTACCACTCCTCTGCCCCG 61.550 60.000 0.00 0.00 0.00 5.73
4971 5183 2.511600 CTGTTCGACCGGATGCCC 60.512 66.667 9.46 0.00 0.00 5.36
5091 5303 2.480555 GCCAACAATGACGGCGAG 59.519 61.111 16.62 0.00 35.79 5.03
5092 5304 2.480555 CCAACAATGACGGCGAGC 59.519 61.111 16.62 5.63 0.00 5.03
5093 5305 2.480555 CAACAATGACGGCGAGCC 59.519 61.111 16.62 3.59 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.436998 CGACCTGACCACCTCGCC 62.437 72.222 0.00 0.00 0.00 5.54
2 3 0.246635 AATTCGACCTGACCACCTCG 59.753 55.000 0.00 0.00 0.00 4.63
4 5 2.420129 GCATAATTCGACCTGACCACCT 60.420 50.000 0.00 0.00 0.00 4.00
5 6 1.940613 GCATAATTCGACCTGACCACC 59.059 52.381 0.00 0.00 0.00 4.61
6 7 2.866762 GAGCATAATTCGACCTGACCAC 59.133 50.000 0.00 0.00 0.00 4.16
7 8 2.158957 GGAGCATAATTCGACCTGACCA 60.159 50.000 0.00 0.00 0.00 4.02
8 9 2.484889 GGAGCATAATTCGACCTGACC 58.515 52.381 0.00 0.00 0.00 4.02
9 10 2.128035 CGGAGCATAATTCGACCTGAC 58.872 52.381 0.00 0.00 0.00 3.51
10 11 2.509052 CGGAGCATAATTCGACCTGA 57.491 50.000 0.00 0.00 0.00 3.86
54 55 2.647949 GGAGGGAGGGAGGAAGGGA 61.648 68.421 0.00 0.00 0.00 4.20
55 56 2.040359 GGAGGGAGGGAGGAAGGG 60.040 72.222 0.00 0.00 0.00 3.95
56 57 2.040359 GGGAGGGAGGGAGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
57 58 2.444895 CGGGAGGGAGGGAGGAAG 60.445 72.222 0.00 0.00 0.00 3.46
187 188 3.191371 AGAACATGGCGAAATTCAACTCC 59.809 43.478 0.00 0.00 0.00 3.85
202 204 3.828451 ACCAAGGAACATCCAAGAACATG 59.172 43.478 0.00 0.00 39.61 3.21
203 205 4.082125 GACCAAGGAACATCCAAGAACAT 58.918 43.478 0.00 0.00 39.61 2.71
220 222 0.970937 AGATTCGGAGAGGCGACCAA 60.971 55.000 0.00 0.00 38.43 3.67
236 238 0.320374 TTTGCGACGACTGGGAAGAT 59.680 50.000 0.00 0.00 0.00 2.40
278 288 2.253452 CACCTGCAGCTTGAACGC 59.747 61.111 8.66 0.00 0.00 4.84
279 289 1.280746 CACACCTGCAGCTTGAACG 59.719 57.895 17.80 1.84 0.00 3.95
413 430 0.908198 ACCAAACAAGGCAGCCAAAA 59.092 45.000 15.80 0.00 0.00 2.44
421 438 3.910490 TGGCGCACCAAACAAGGC 61.910 61.111 10.83 0.00 45.37 4.35
475 492 7.652909 CAGCTCCATGAATTGAAACAAAAAGTA 59.347 33.333 0.00 0.00 0.00 2.24
476 493 6.480981 CAGCTCCATGAATTGAAACAAAAAGT 59.519 34.615 0.00 0.00 0.00 2.66
532 549 6.419413 TCATCGGTTTCTGCAAACAAATAAAC 59.581 34.615 3.80 0.00 43.41 2.01
536 553 4.582701 TCATCGGTTTCTGCAAACAAAT 57.417 36.364 3.80 0.00 43.41 2.32
538 555 4.377839 TTTCATCGGTTTCTGCAAACAA 57.622 36.364 3.80 0.00 43.41 2.83
584 615 2.996621 CTGAAACGAGTCACCCAAGATC 59.003 50.000 0.00 0.00 0.00 2.75
677 708 2.119495 GAGGAGGAGGAGTTGCCATAA 58.881 52.381 0.00 0.00 40.02 1.90
899 951 4.656100 TGAATTCAGTGAGGATTCCCAA 57.344 40.909 3.38 0.00 33.88 4.12
1152 1204 4.316645 TGAATCACCATCGGTCGTTAAAA 58.683 39.130 0.00 0.00 31.02 1.52
1153 1205 3.927854 TGAATCACCATCGGTCGTTAAA 58.072 40.909 0.00 0.00 31.02 1.52
1164 1216 1.955208 GCGTTTCCCCTGAATCACCAT 60.955 52.381 0.00 0.00 0.00 3.55
1251 1303 6.766429 TGGATGAATTCTCATGATCCACTAG 58.234 40.000 16.58 0.00 42.60 2.57
1364 1422 2.192664 TCTCCACGGCAATGCTTTTA 57.807 45.000 4.82 0.00 0.00 1.52
1394 1452 0.107214 CACACACACCACCAGAACCT 60.107 55.000 0.00 0.00 0.00 3.50
1421 1479 1.747709 AGCAGATGTTAGCTTGCCTG 58.252 50.000 2.23 0.54 38.01 4.85
1754 1812 2.430367 GAGGTGGTGCGGTCCTTT 59.570 61.111 0.00 0.00 0.00 3.11
1765 1823 1.363530 ATGGCATAAGGGGGAGGTGG 61.364 60.000 0.00 0.00 0.00 4.61
1778 1836 1.822613 CCTCGCTTCAGCATGGCAT 60.823 57.895 0.00 0.00 42.21 4.40
2007 2065 1.203441 ATGGAGCCTGTGGAGAAGCA 61.203 55.000 0.00 0.00 0.00 3.91
2031 2089 8.484214 AGACATATGCTTCTCTAGTTTATGGA 57.516 34.615 1.58 0.00 31.01 3.41
2051 2109 8.934023 TGGTGGTAGAAAGATTTAAAAGACAT 57.066 30.769 0.00 0.00 0.00 3.06
2052 2110 8.934023 ATGGTGGTAGAAAGATTTAAAAGACA 57.066 30.769 0.00 0.00 0.00 3.41
2323 2384 4.397420 TGACTCTGTGCAATGTACCAATT 58.603 39.130 0.00 0.00 0.00 2.32
2567 2633 9.131791 ACTTGATTCTTAGCTTAACTGGAAAAA 57.868 29.630 0.00 0.00 0.00 1.94
2707 2773 4.022935 GCAGATTTCACCAATCACAGTTCA 60.023 41.667 0.00 0.00 43.63 3.18
2788 2866 7.410942 CGACTCAGCAATTACAGAAAGTAACTC 60.411 40.741 0.00 0.00 44.95 3.01
2874 2954 8.480501 CAATTAAAATTGTCATGAGGGGAGAAT 58.519 33.333 0.00 0.00 40.61 2.40
3214 3363 5.058490 TGTCTTCCTAAACCAAAACTACGG 58.942 41.667 0.00 0.00 0.00 4.02
3215 3364 6.607735 TTGTCTTCCTAAACCAAAACTACG 57.392 37.500 0.00 0.00 0.00 3.51
3243 3392 8.830201 ATATAGAAACTGTCAGATGCATCTTC 57.170 34.615 26.70 20.97 34.22 2.87
3532 3683 0.100325 TTGACTTGCAAACAGGCACG 59.900 50.000 0.00 0.00 44.86 5.34
3561 3712 3.380004 CCTTATGCGTCTTTGCCCAATAA 59.620 43.478 0.00 0.00 0.00 1.40
3679 3830 3.004629 TGTTTGCAGCAATGACCTTAGTG 59.995 43.478 9.12 0.00 0.00 2.74
3680 3831 3.221771 TGTTTGCAGCAATGACCTTAGT 58.778 40.909 9.12 0.00 0.00 2.24
3681 3832 3.921119 TGTTTGCAGCAATGACCTTAG 57.079 42.857 9.12 0.00 0.00 2.18
3788 3945 7.782049 ACTGAATTACCTTGAGATCGACATAA 58.218 34.615 0.00 0.00 0.00 1.90
4013 4198 3.775654 GACCAGTAGGCCTGCGCT 61.776 66.667 17.99 8.09 40.06 5.92
4047 4232 1.002379 AAGCCTTGCCTGAGAGCTG 60.002 57.895 0.00 0.00 33.18 4.24
4048 4233 1.299321 GAAGCCTTGCCTGAGAGCT 59.701 57.895 0.00 0.00 34.64 4.09
4052 4237 0.676151 GTCCTGAAGCCTTGCCTGAG 60.676 60.000 0.00 0.00 0.00 3.35
4220 4407 4.275443 AGCAGCAAACAGAGAAGAAGAAAG 59.725 41.667 0.00 0.00 0.00 2.62
4272 4462 7.827729 ACCAGGCGTTTAGTTTCTCTTATTAAT 59.172 33.333 0.00 0.00 0.00 1.40
4299 4489 0.108207 TTTACAAAGGGGCCGTCGAA 59.892 50.000 0.00 0.00 0.00 3.71
4418 4608 8.072567 GCAATGGAAGACAGTGTGATAATAATC 58.927 37.037 0.00 0.00 46.36 1.75
4427 4618 2.224606 ACTGCAATGGAAGACAGTGTG 58.775 47.619 0.00 0.00 46.36 3.82
4480 4671 9.895138 ATAATCCAATTTTTCTGATGGGAAAAG 57.105 29.630 0.00 0.00 43.22 2.27
4512 4704 2.821969 CCAAATCCAACCACTCAAGGAG 59.178 50.000 0.00 0.00 32.91 3.69
4647 4853 1.409064 CTACAATGTAGCCCTCGCTCA 59.591 52.381 7.55 0.00 43.95 4.26
4660 4866 3.535561 CCTGGCCTCACTAACTACAATG 58.464 50.000 3.32 0.00 0.00 2.82
4664 4870 1.134670 CAGCCTGGCCTCACTAACTAC 60.135 57.143 16.57 0.00 0.00 2.73
4666 4872 0.545309 TCAGCCTGGCCTCACTAACT 60.545 55.000 16.57 0.00 0.00 2.24
4670 4876 1.065126 GTAATTCAGCCTGGCCTCACT 60.065 52.381 16.57 0.00 0.00 3.41
4690 4896 0.398318 GCCTTATCCACTGGGCTAGG 59.602 60.000 2.02 1.07 41.20 3.02
4734 4940 0.035343 GGGGCAGAGGAGTGGTAAAC 60.035 60.000 0.00 0.00 0.00 2.01
4951 5163 2.885644 CATCCGGTCGAACAGGCG 60.886 66.667 0.00 0.00 33.25 5.52
4952 5164 3.195698 GCATCCGGTCGAACAGGC 61.196 66.667 0.00 0.00 33.25 4.85
4965 5177 4.171103 AGGTTACGGCCGGGCATC 62.171 66.667 31.76 13.09 0.00 3.91
4971 5183 2.101770 GAGACGAGGTTACGGCCG 59.898 66.667 26.86 26.86 42.85 6.13
4977 5189 1.684734 GCCCCAGGAGACGAGGTTA 60.685 63.158 0.00 0.00 0.00 2.85
5075 5287 2.480555 GCTCGCCGTCATTGTTGG 59.519 61.111 0.00 0.00 0.00 3.77


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

AutoCloner maintained by Alex Coulton.