Multiple sequence alignment - TraesCS3D01G270100

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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 TraesCS3D01G270100 chr3D 100.000 3889 0 0 1 3889 374925555 374929443 0.000000e+00 7182.0
1 TraesCS3D01G270100 chr3D 83.598 189 27 4 1859 2047 570324462 570324278 1.440000e-39 174.0
2 TraesCS3D01G270100 chr3D 95.556 45 2 0 1 45 537974978 537974934 5.390000e-09 73.1
3 TraesCS3D01G270100 chr3A 95.125 1477 44 15 2428 3889 497648592 497650055 0.000000e+00 2303.0
4 TraesCS3D01G270100 chr3A 94.340 1060 35 11 718 1766 497646611 497647656 0.000000e+00 1602.0
5 TraesCS3D01G270100 chr3A 93.035 603 28 11 1806 2399 497647649 497648246 0.000000e+00 869.0
6 TraesCS3D01G270100 chr3A 87.983 724 71 11 1 714 497645509 497646226 0.000000e+00 841.0
7 TraesCS3D01G270100 chr3A 97.778 45 1 0 3319 3363 497649519 497649563 1.160000e-10 78.7
8 TraesCS3D01G270100 chr3A 93.878 49 2 1 1 49 731228629 731228582 5.390000e-09 73.1
9 TraesCS3D01G270100 chr3B 93.795 1112 50 10 757 1859 488530074 488531175 0.000000e+00 1653.0
10 TraesCS3D01G270100 chr3B 93.956 1092 38 12 2033 3102 488531376 488532461 0.000000e+00 1626.0
11 TraesCS3D01G270100 chr3B 95.135 555 23 2 3338 3889 488535391 488535944 0.000000e+00 872.0
12 TraesCS3D01G270100 chr3B 89.250 400 38 5 196 592 488528862 488529259 2.700000e-136 496.0
13 TraesCS3D01G270100 chr3B 96.053 304 12 0 3100 3403 488535085 488535388 2.700000e-136 496.0
14 TraesCS3D01G270100 chr3B 90.278 144 12 2 1858 2001 488531247 488531388 1.840000e-43 187.0
15 TraesCS3D01G270100 chr3B 81.279 219 37 4 1859 2076 806154211 806154426 1.440000e-39 174.0
16 TraesCS3D01G270100 chr3B 94.444 54 1 2 3312 3365 488535411 488535462 8.960000e-12 82.4
17 TraesCS3D01G270100 chr3B 95.652 46 0 2 3312 3357 488535343 488535386 5.390000e-09 73.1
18 TraesCS3D01G270100 chr4D 85.253 217 30 1 1859 2075 93611348 93611134 5.060000e-54 222.0
19 TraesCS3D01G270100 chr6D 83.243 185 22 7 1858 2041 16175627 16175451 1.120000e-35 161.0
20 TraesCS3D01G270100 chr6D 95.652 46 0 2 1 45 285747877 285747833 5.390000e-09 73.1
21 TraesCS3D01G270100 chr6D 92.308 52 1 3 1 51 87261002 87261051 1.940000e-08 71.3
22 TraesCS3D01G270100 chr1B 89.381 113 11 1 1964 2076 156680953 156680842 1.460000e-29 141.0
23 TraesCS3D01G270100 chr1B 81.437 167 22 7 1850 2012 20050428 20050589 1.130000e-25 128.0
24 TraesCS3D01G270100 chr1D 86.842 114 13 1 1963 2076 96769930 96770041 4.080000e-25 126.0
25 TraesCS3D01G270100 chr1D 100.000 42 0 0 1 42 216355765 216355806 1.160000e-10 78.7
26 TraesCS3D01G270100 chr6B 87.037 108 13 1 1970 2077 620907102 620907208 1.900000e-23 121.0
27 TraesCS3D01G270100 chr6B 90.741 54 4 1 1 54 551305016 551305068 1.940000e-08 71.3
28 TraesCS3D01G270100 chr4B 79.459 185 20 10 1860 2044 33348921 33349087 8.830000e-22 115.0
29 TraesCS3D01G270100 chr6A 88.608 79 7 2 1857 1935 15949497 15949421 1.150000e-15 95.3
30 TraesCS3D01G270100 chr7D 87.342 79 9 1 1859 1937 279743787 279743710 5.350000e-14 89.8
31 TraesCS3D01G270100 chr5A 85.526 76 9 2 1860 1935 565553558 565553485 1.160000e-10 78.7
32 TraesCS3D01G270100 chr5A 89.474 57 3 3 1 56 409343581 409343527 6.970000e-08 69.4
33 TraesCS3D01G270100 chr5B 86.154 65 8 1 1 65 294181902 294181839 6.970000e-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 TraesCS3D01G270100 chr3D 374925555 374929443 3888 False 7182.0000 7182 100.000000 1 3889 1 chr3D.!!$F1 3888
1 TraesCS3D01G270100 chr3A 497645509 497650055 4546 False 1138.7400 2303 93.652200 1 3889 5 chr3A.!!$F1 3888
2 TraesCS3D01G270100 chr3B 488528862 488535944 7082 False 685.6875 1653 93.570375 196 3889 8 chr3B.!!$F2 3693

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
533 538 0.106708 GAATGCCCAGTATCCGAGCA 59.893 55.0 0.0 0.0 37.94 4.26 F
1087 2033 0.316204 CCAAACCCAGAGCAAGCAAG 59.684 55.0 0.0 0.0 0.00 4.01 F
1088 2034 0.319297 CAAACCCAGAGCAAGCAAGC 60.319 55.0 0.0 0.0 0.00 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2286 3321 0.409092 TGGCCATCCATGTTTCAGGT 59.591 50.000 0.0 0.00 37.47 4.00 R
2417 3758 1.112315 AATTGCAACAGGCCCGTTCA 61.112 50.000 0.0 0.77 43.89 3.18 R
2928 4290 1.486310 ACTCTGAAGTCACTTGCACCA 59.514 47.619 0.0 0.00 0.00 4.17 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
44 45 5.163519 CCTTTAGGGCATATTTCCAACACAG 60.164 44.000 0.00 0.00 0.00 3.66
49 50 4.021544 GGGCATATTTCCAACACAGACAAA 60.022 41.667 0.00 0.00 0.00 2.83
63 64 0.108585 GACAAAGGGCTCACTGGACA 59.891 55.000 0.00 0.00 0.00 4.02
64 65 0.109342 ACAAAGGGCTCACTGGACAG 59.891 55.000 0.00 0.00 0.00 3.51
71 72 1.271597 GGCTCACTGGACAGAAACCAT 60.272 52.381 6.29 0.00 36.79 3.55
79 80 2.224523 TGGACAGAAACCATGACTGGAC 60.225 50.000 0.00 0.00 46.37 4.02
84 85 0.670546 AAACCATGACTGGACGAGCG 60.671 55.000 0.00 0.00 46.37 5.03
92 93 4.492160 TGGACGAGCGATGGCGAC 62.492 66.667 0.00 0.00 46.35 5.19
94 95 2.713770 GACGAGCGATGGCGACTA 59.286 61.111 0.00 0.00 46.35 2.59
96 97 2.049475 GACGAGCGATGGCGACTACT 62.049 60.000 0.00 0.00 46.35 2.57
106 109 2.959516 TGGCGACTACTTCTGTGAATG 58.040 47.619 0.00 0.00 0.00 2.67
114 117 6.026947 ACTACTTCTGTGAATGTGTAGTCC 57.973 41.667 0.00 0.00 36.80 3.85
115 118 4.273148 ACTTCTGTGAATGTGTAGTCCC 57.727 45.455 0.00 0.00 0.00 4.46
117 120 5.084519 ACTTCTGTGAATGTGTAGTCCCTA 58.915 41.667 0.00 0.00 0.00 3.53
137 140 5.103000 CCTATTGAGGTCGACACTTTACAG 58.897 45.833 18.91 5.64 38.16 2.74
149 152 1.421646 ACTTTACAGTGGAAGGCTGCT 59.578 47.619 11.67 0.00 37.47 4.24
154 157 0.177604 CAGTGGAAGGCTGCTAGAGG 59.822 60.000 0.00 0.00 0.00 3.69
162 165 0.108138 GGCTGCTAGAGGCGAAGAAA 60.108 55.000 0.00 0.00 45.43 2.52
165 168 0.608130 TGCTAGAGGCGAAGAAAGCA 59.392 50.000 0.00 0.00 45.43 3.91
168 171 0.458543 TAGAGGCGAAGAAAGCAGCG 60.459 55.000 0.00 0.00 36.08 5.18
169 172 1.738099 GAGGCGAAGAAAGCAGCGA 60.738 57.895 0.00 0.00 36.08 4.93
285 289 1.421646 CCTGTTGTGGAGGAGGAGTTT 59.578 52.381 0.00 0.00 31.48 2.66
300 304 4.735132 TTTCGTCCTGAGCGGCCG 62.735 66.667 24.05 24.05 0.00 6.13
354 358 1.290955 CGCCACCCTTGTCGTTCTA 59.709 57.895 0.00 0.00 0.00 2.10
359 363 1.203994 CACCCTTGTCGTTCTACCGAT 59.796 52.381 0.00 0.00 39.34 4.18
366 370 1.002684 GTCGTTCTACCGATCGAGCAT 60.003 52.381 18.66 1.35 40.76 3.79
372 376 2.138320 CTACCGATCGAGCATTTGCAT 58.862 47.619 18.66 0.00 45.16 3.96
416 421 2.397751 GATGCACATCGTGAAGGGG 58.602 57.895 0.00 0.00 35.23 4.79
421 426 0.608130 CACATCGTGAAGGGGTCTCA 59.392 55.000 0.00 0.00 35.23 3.27
435 440 1.822186 TCTCACGGATCCATCGCGA 60.822 57.895 13.09 13.09 0.00 5.87
438 443 3.206957 ACGGATCCATCGCGACGA 61.207 61.111 12.93 11.07 41.13 4.20
451 456 2.577059 GACGATGGCGGAACAGGA 59.423 61.111 0.00 0.00 43.17 3.86
461 466 0.109723 CGGAACAGGAGGGGACAAAA 59.890 55.000 0.00 0.00 0.00 2.44
462 467 1.477923 CGGAACAGGAGGGGACAAAAA 60.478 52.381 0.00 0.00 0.00 1.94
466 471 1.235724 CAGGAGGGGACAAAAACGAC 58.764 55.000 0.00 0.00 0.00 4.34
473 478 1.281656 GACAAAAACGACCAGGGCG 59.718 57.895 15.24 15.24 0.00 6.13
509 514 1.153628 CGCGGAAAGAGTGGTAGGG 60.154 63.158 0.00 0.00 0.00 3.53
523 528 1.463674 GTAGGGTTGTGAATGCCCAG 58.536 55.000 0.00 0.00 44.69 4.45
524 529 1.072266 TAGGGTTGTGAATGCCCAGT 58.928 50.000 0.00 0.00 44.69 4.00
533 538 0.106708 GAATGCCCAGTATCCGAGCA 59.893 55.000 0.00 0.00 37.94 4.26
547 552 0.322456 CGAGCAGGGTTTTGGATGGA 60.322 55.000 0.00 0.00 0.00 3.41
570 576 0.770166 TGGGTGTGGGAGTCCATCAA 60.770 55.000 12.30 0.00 46.09 2.57
572 578 0.984230 GGTGTGGGAGTCCATCAAGA 59.016 55.000 12.30 0.00 46.09 3.02
633 642 1.616159 ACCGGTCCAACTCAATTTGG 58.384 50.000 0.00 0.00 46.64 3.28
639 648 2.031157 GTCCAACTCAATTTGGTGACCG 60.031 50.000 0.00 0.00 45.60 4.79
640 649 1.953686 CCAACTCAATTTGGTGACCGT 59.046 47.619 0.00 0.00 41.18 4.83
641 650 2.360801 CCAACTCAATTTGGTGACCGTT 59.639 45.455 0.00 0.00 41.18 4.44
645 657 3.888930 ACTCAATTTGGTGACCGTTGAAT 59.111 39.130 14.76 5.65 0.00 2.57
682 694 3.547746 GACCGTTTGGCCCAGATATTTA 58.452 45.455 0.00 0.00 39.70 1.40
686 698 2.621526 GTTTGGCCCAGATATTTACGGG 59.378 50.000 0.00 0.00 42.03 5.28
714 726 7.800155 TTTGATGAAATGCGTTGGAGATATA 57.200 32.000 0.00 0.00 0.00 0.86
716 728 9.500785 TTTGATGAAATGCGTTGGAGATATATA 57.499 29.630 0.00 0.00 0.00 0.86
717 729 9.671279 TTGATGAAATGCGTTGGAGATATATAT 57.329 29.630 0.00 0.00 0.00 0.86
718 730 9.671279 TGATGAAATGCGTTGGAGATATATATT 57.329 29.630 0.00 0.00 0.00 1.28
838 1773 6.015940 CCAAGATTATTTACCCAGGATTCTGC 60.016 42.308 0.00 0.00 39.61 4.26
865 1800 1.133809 TTGCTGAGCAGGGTAGGGTT 61.134 55.000 7.39 0.00 40.61 4.11
1086 2032 1.114722 CCCAAACCCAGAGCAAGCAA 61.115 55.000 0.00 0.00 0.00 3.91
1087 2033 0.316204 CCAAACCCAGAGCAAGCAAG 59.684 55.000 0.00 0.00 0.00 4.01
1088 2034 0.319297 CAAACCCAGAGCAAGCAAGC 60.319 55.000 0.00 0.00 0.00 4.01
1089 2035 1.799258 AAACCCAGAGCAAGCAAGCG 61.799 55.000 0.00 0.00 40.15 4.68
1090 2036 4.112341 CCCAGAGCAAGCAAGCGC 62.112 66.667 0.00 0.00 40.15 5.92
1091 2037 3.359523 CCAGAGCAAGCAAGCGCA 61.360 61.111 11.47 0.00 42.27 6.09
1092 2038 2.640989 CAGAGCAAGCAAGCGCAA 59.359 55.556 11.47 0.00 42.27 4.85
1160 2106 1.081641 GTGGTTCGACGAGAGCGAA 60.082 57.895 0.00 0.00 43.44 4.70
1301 2248 4.369182 ACAGATCGAGAAAAACGAAGTGT 58.631 39.130 0.00 0.00 45.00 3.55
1321 2272 2.610374 GTGCGTTTGACCTCTTGTAACA 59.390 45.455 0.00 0.00 0.00 2.41
1354 2305 2.017049 GGCTGAATTGTTAGCGGATGT 58.983 47.619 0.00 0.00 40.78 3.06
1428 2380 6.652900 CCCTCTAAATCTAGATTTGCTTAGGC 59.347 42.308 31.96 0.00 40.83 3.93
1468 2420 5.414454 TCCTCCGGAATTGATTTACTTTGTG 59.586 40.000 5.23 0.00 0.00 3.33
1473 2425 5.391097 CGGAATTGATTTACTTTGTGCCGTA 60.391 40.000 0.00 0.00 0.00 4.02
1474 2426 6.383415 GGAATTGATTTACTTTGTGCCGTAA 58.617 36.000 0.00 0.00 0.00 3.18
1491 2443 5.102313 GCCGTAAAATAGCTGCAAGATTTT 58.898 37.500 17.86 17.86 35.40 1.82
1684 2636 9.443283 TTGTTTTTGTTTCACTGTTTCAATTTG 57.557 25.926 0.00 0.00 0.00 2.32
1793 2748 2.866085 ATCTGCTCCTGCCGCAAGAC 62.866 60.000 0.00 0.00 36.88 3.01
1803 2758 1.468520 TGCCGCAAGACTATTTTGCTC 59.531 47.619 8.15 1.56 46.62 4.26
1870 2899 4.586421 TGTTTTGTAGACCATGGCAAATCA 59.414 37.500 13.04 15.18 31.99 2.57
1873 2902 4.782019 TGTAGACCATGGCAAATCAAAC 57.218 40.909 13.04 5.29 0.00 2.93
1874 2903 4.148079 TGTAGACCATGGCAAATCAAACA 58.852 39.130 13.04 7.79 0.00 2.83
1876 2905 4.460948 AGACCATGGCAAATCAAACATC 57.539 40.909 13.04 0.00 0.00 3.06
1889 2918 8.238631 GCAAATCAAACATCTTTTATGGCAATT 58.761 29.630 0.00 0.00 0.00 2.32
2053 3083 3.104519 TGCCATGGTCAAATCCTGAAT 57.895 42.857 14.67 0.00 35.22 2.57
2062 3092 4.467438 GGTCAAATCCTGAATGTTTGGGAT 59.533 41.667 0.00 0.00 39.91 3.85
2094 3124 6.381801 CGTCCAAGAAAAAGCACTCATATTT 58.618 36.000 0.00 0.00 0.00 1.40
2355 3390 7.759465 TGAGTTCTTAGTGTTCTCCGTATAAG 58.241 38.462 0.00 0.00 0.00 1.73
2417 3758 6.593770 TCATATTTAGTGAATGTGTGAACGCT 59.406 34.615 4.64 0.00 37.88 5.07
2668 4028 5.350914 CACTTGGTCTTGAGCTTGATCTTAG 59.649 44.000 0.00 0.00 0.00 2.18
2669 4029 5.012561 ACTTGGTCTTGAGCTTGATCTTAGT 59.987 40.000 0.00 0.00 0.00 2.24
2687 4047 3.990959 AGTGAGAAAGGATTGGGTCTC 57.009 47.619 0.00 0.00 37.59 3.36
2837 4197 1.493950 GAATCGCAGCGATCACCCAG 61.494 60.000 29.89 0.00 46.30 4.45
2928 4290 8.023128 GTGCATTTCTTCATGTACTTTATGTGT 58.977 33.333 0.00 0.00 36.96 3.72
3030 4392 3.823873 GTGGGTGGTATTTGTGTGAATCA 59.176 43.478 0.00 0.00 0.00 2.57
3175 7163 3.571401 GCATGCTATTGATGCTTTAGGGT 59.429 43.478 11.37 0.00 42.52 4.34
3242 7230 6.371825 ACGAGAAGGAAATTTACATCACTTCC 59.628 38.462 8.29 0.00 34.86 3.46
3261 7249 3.375699 TCCTCCCCAATCTCACTTACTC 58.624 50.000 0.00 0.00 0.00 2.59
3382 7441 1.330655 ACTGCCCGTCTCACCTATGG 61.331 60.000 0.00 0.00 0.00 2.74
3423 7488 1.297304 CAACACCGCACACGTTCAC 60.297 57.895 0.00 0.00 37.70 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 4.947388 GTCTGTGTTGGAAATATGCCCTAA 59.053 41.667 0.00 0.00 0.00 2.69
44 45 0.108585 TGTCCAGTGAGCCCTTTGTC 59.891 55.000 0.00 0.00 0.00 3.18
49 50 0.398318 GTTTCTGTCCAGTGAGCCCT 59.602 55.000 0.00 0.00 0.00 5.19
71 72 2.885113 CCATCGCTCGTCCAGTCA 59.115 61.111 0.00 0.00 0.00 3.41
79 80 0.930742 GAAGTAGTCGCCATCGCTCG 60.931 60.000 0.00 0.00 35.26 5.03
84 85 2.941453 TCACAGAAGTAGTCGCCATC 57.059 50.000 0.00 0.00 0.00 3.51
92 93 5.186021 AGGGACTACACATTCACAGAAGTAG 59.814 44.000 0.00 0.00 36.02 2.57
94 95 3.904339 AGGGACTACACATTCACAGAAGT 59.096 43.478 0.00 0.00 36.02 3.01
114 117 7.333919 CACTGTAAAGTGTCGACCTCAATAGG 61.334 46.154 14.12 0.79 40.57 2.57
115 118 5.573282 CACTGTAAAGTGTCGACCTCAATAG 59.427 44.000 14.12 10.64 35.25 1.73
117 120 4.307432 CACTGTAAAGTGTCGACCTCAAT 58.693 43.478 14.12 0.00 35.25 2.57
137 140 1.153269 GCCTCTAGCAGCCTTCCAC 60.153 63.158 0.00 0.00 42.97 4.02
149 152 0.458543 CGCTGCTTTCTTCGCCTCTA 60.459 55.000 0.00 0.00 0.00 2.43
154 157 0.451792 CACTTCGCTGCTTTCTTCGC 60.452 55.000 0.00 0.00 0.00 4.70
179 182 3.753294 ATTACATCGACCAGCCTAAGG 57.247 47.619 0.00 0.00 0.00 2.69
194 197 6.814644 CCAGTTCATTCCGTTGTACTATTACA 59.185 38.462 0.00 0.00 36.36 2.41
267 271 1.070134 CGAAACTCCTCCTCCACAACA 59.930 52.381 0.00 0.00 0.00 3.33
300 304 3.423154 CAAGAAGGTGGCGGTCGC 61.423 66.667 6.83 6.83 41.06 5.19
354 358 0.659427 CATGCAAATGCTCGATCGGT 59.341 50.000 16.41 0.00 42.66 4.69
359 363 2.763273 CCCGCATGCAAATGCTCGA 61.763 57.895 19.57 0.00 44.90 4.04
366 370 2.030262 GGCAAACCCGCATGCAAA 59.970 55.556 19.57 0.00 44.32 3.68
372 376 4.531426 AACCCAGGCAAACCCGCA 62.531 61.111 0.00 0.00 39.21 5.69
416 421 1.658717 CGCGATGGATCCGTGAGAC 60.659 63.158 12.38 0.00 39.61 3.36
421 426 2.552819 ATCGTCGCGATGGATCCGT 61.553 57.895 26.94 6.04 45.24 4.69
435 440 2.579201 CTCCTGTTCCGCCATCGT 59.421 61.111 0.00 0.00 0.00 3.73
438 443 3.411517 CCCCTCCTGTTCCGCCAT 61.412 66.667 0.00 0.00 0.00 4.40
451 456 0.179001 CCTGGTCGTTTTTGTCCCCT 60.179 55.000 0.00 0.00 0.00 4.79
461 466 2.657237 CTCTTCGCCCTGGTCGTT 59.343 61.111 0.00 0.00 0.00 3.85
462 467 3.382832 CCTCTTCGCCCTGGTCGT 61.383 66.667 0.00 0.00 0.00 4.34
473 478 2.751837 CCAAAGCCCGCCCTCTTC 60.752 66.667 0.00 0.00 0.00 2.87
509 514 1.670811 CGGATACTGGGCATTCACAAC 59.329 52.381 0.00 0.00 0.00 3.32
523 528 1.065709 TCCAAAACCCTGCTCGGATAC 60.066 52.381 0.00 0.00 33.16 2.24
524 529 1.281419 TCCAAAACCCTGCTCGGATA 58.719 50.000 0.00 0.00 33.16 2.59
533 538 2.539302 CCATGTTCCATCCAAAACCCT 58.461 47.619 0.00 0.00 0.00 4.34
547 552 1.065410 TGGACTCCCACACCCATGTT 61.065 55.000 0.00 0.00 36.72 2.71
558 564 0.767998 GGGGATCTTGATGGACTCCC 59.232 60.000 0.00 0.00 44.11 4.30
570 576 0.181350 GCACCAAATCGAGGGGATCT 59.819 55.000 6.78 0.00 33.02 2.75
572 578 1.227383 GGCACCAAATCGAGGGGAT 59.773 57.895 6.78 0.00 36.78 3.85
633 642 3.907894 TTTTAGGCATTCAACGGTCAC 57.092 42.857 0.00 0.00 0.00 3.67
639 648 5.405269 GTCCACACATTTTTAGGCATTCAAC 59.595 40.000 0.00 0.00 0.00 3.18
640 649 5.510520 GGTCCACACATTTTTAGGCATTCAA 60.511 40.000 0.00 0.00 0.00 2.69
641 650 4.021544 GGTCCACACATTTTTAGGCATTCA 60.022 41.667 0.00 0.00 0.00 2.57
645 657 1.883275 CGGTCCACACATTTTTAGGCA 59.117 47.619 0.00 0.00 0.00 4.75
714 726 5.740290 ACGTCCGGAGATATTTGGAATAT 57.260 39.130 3.06 0.00 31.04 1.28
716 728 4.417426 AACGTCCGGAGATATTTGGAAT 57.583 40.909 3.06 0.00 31.04 3.01
717 729 3.899052 AACGTCCGGAGATATTTGGAA 57.101 42.857 3.06 0.00 31.04 3.53
718 730 3.899052 AAACGTCCGGAGATATTTGGA 57.101 42.857 3.06 0.00 0.00 3.53
719 731 3.936453 TCAAAACGTCCGGAGATATTTGG 59.064 43.478 21.97 12.21 0.00 3.28
838 1773 1.271656 CCCTGCTCAGCAAGAAAAAGG 59.728 52.381 0.00 0.00 38.41 3.11
1088 2034 2.114670 AATCGGAGCCATGGTTGCG 61.115 57.895 31.68 31.68 40.91 4.85
1089 2035 1.434696 CAATCGGAGCCATGGTTGC 59.565 57.895 14.67 12.34 0.00 4.17
1090 2036 2.008268 GCCAATCGGAGCCATGGTTG 62.008 60.000 14.67 8.53 35.34 3.77
1091 2037 1.754234 GCCAATCGGAGCCATGGTT 60.754 57.895 14.67 7.37 35.34 3.67
1092 2038 2.124151 GCCAATCGGAGCCATGGT 60.124 61.111 14.67 0.00 35.34 3.55
1160 2106 1.196766 TGGAGACCTGCTGCATCTGT 61.197 55.000 10.29 5.04 40.31 3.41
1258 2204 5.004448 TGTTGACTGTTTGTACTGGTGAAA 58.996 37.500 0.00 0.00 0.00 2.69
1301 2248 2.869801 CTGTTACAAGAGGTCAAACGCA 59.130 45.455 0.00 0.00 0.00 5.24
1321 2272 1.709578 TTCAGCCTCGCTATCCATCT 58.290 50.000 0.00 0.00 36.40 2.90
1354 2305 7.148407 GCGAGAAGAAAAAGTCAATCTTGGATA 60.148 37.037 0.00 0.00 36.40 2.59
1407 2359 5.106908 GGCGCCTAAGCAAATCTAGATTTAG 60.107 44.000 26.34 19.98 38.84 1.85
1468 2420 3.971032 ATCTTGCAGCTATTTTACGGC 57.029 42.857 0.00 0.00 0.00 5.68
1491 2443 1.613437 GGAAAAGCTGGCAGTTAAGCA 59.387 47.619 17.16 0.00 42.06 3.91
1715 2667 7.364762 CCACAGGGTAGTGATTAGTGAAGTAAT 60.365 40.741 0.00 0.00 42.05 1.89
1770 2725 2.898738 CGGCAGGAGCAGATCACT 59.101 61.111 0.00 0.00 44.61 3.41
1773 2728 2.124983 TTGCGGCAGGAGCAGATC 60.125 61.111 1.67 0.00 46.01 2.75
1824 2779 4.476479 AGGATAAAGGAGCAACAGAATCCT 59.524 41.667 0.00 0.00 45.50 3.24
1874 2903 9.139174 CGTCAACTAAAAATTGCCATAAAAGAT 57.861 29.630 0.00 0.00 0.00 2.40
1876 2905 7.226772 GCGTCAACTAAAAATTGCCATAAAAG 58.773 34.615 0.00 0.00 0.00 2.27
1889 2918 2.343101 CCATCCTCGCGTCAACTAAAA 58.657 47.619 5.77 0.00 0.00 1.52
1924 2954 1.010419 GCCAGAAAATTGCCGTGCTG 61.010 55.000 0.00 0.00 0.00 4.41
2024 3054 2.198827 TGACCATGGCAAATCGAACT 57.801 45.000 13.04 0.00 0.00 3.01
2025 3055 3.296322 TTTGACCATGGCAAATCGAAC 57.704 42.857 22.50 3.11 30.87 3.95
2026 3056 4.108699 GATTTGACCATGGCAAATCGAA 57.891 40.909 33.86 22.84 46.46 3.71
2053 3083 2.011222 GACGCCGATAAATCCCAAACA 58.989 47.619 0.00 0.00 0.00 2.83
2062 3092 3.365565 GCTTTTTCTTGGACGCCGATAAA 60.366 43.478 0.00 0.00 0.00 1.40
2067 3097 0.660300 GTGCTTTTTCTTGGACGCCG 60.660 55.000 0.00 0.00 0.00 6.46
2094 3124 5.114780 GCATTCATAGAAGAGAGCAGACAA 58.885 41.667 0.00 0.00 0.00 3.18
2218 3248 9.462174 TTTCAGAACATGATAATGAACACAAAC 57.538 29.630 0.00 0.00 37.89 2.93
2285 3320 1.638070 TGGCCATCCATGTTTCAGGTA 59.362 47.619 0.00 0.00 37.47 3.08
2286 3321 0.409092 TGGCCATCCATGTTTCAGGT 59.591 50.000 0.00 0.00 37.47 4.00
2288 3323 1.548081 TGTGGCCATCCATGTTTCAG 58.452 50.000 9.72 0.00 45.62 3.02
2289 3324 1.826096 CATGTGGCCATCCATGTTTCA 59.174 47.619 22.37 8.49 45.62 2.69
2290 3325 2.101783 TCATGTGGCCATCCATGTTTC 58.898 47.619 26.89 6.72 45.62 2.78
2291 3326 2.234896 TCATGTGGCCATCCATGTTT 57.765 45.000 26.89 0.00 45.62 2.83
2355 3390 2.162264 ACCAGGGAGCTACCTTACTC 57.838 55.000 17.49 0.00 39.34 2.59
2417 3758 1.112315 AATTGCAACAGGCCCGTTCA 61.112 50.000 0.00 0.77 43.89 3.18
2532 3892 5.286082 GGTCATTAACTGCAAAACAATAGCG 59.714 40.000 0.00 0.00 0.00 4.26
2668 4028 2.678190 CGGAGACCCAATCCTTTCTCAC 60.678 54.545 0.00 0.00 36.92 3.51
2669 4029 1.555075 CGGAGACCCAATCCTTTCTCA 59.445 52.381 0.00 0.00 36.92 3.27
2928 4290 1.486310 ACTCTGAAGTCACTTGCACCA 59.514 47.619 0.00 0.00 0.00 4.17
3030 4392 6.350445 GCCTGTTGATTTCACAAGGTAATGAT 60.350 38.462 8.69 0.00 33.43 2.45
3157 7145 4.199310 TGTCACCCTAAAGCATCAATAGC 58.801 43.478 0.00 0.00 0.00 2.97
3242 7230 4.026744 TCAGAGTAAGTGAGATTGGGGAG 58.973 47.826 0.00 0.00 0.00 4.30
3261 7249 1.599542 GGCGCCTGTAAAATAGCTCAG 59.400 52.381 22.15 0.00 0.00 3.35
3382 7441 2.821969 TGCTGGATCAAGAAGCTTTTCC 59.178 45.455 0.00 3.59 37.82 3.13
3423 7488 0.456312 GCACGTAGACAAGGTCGAGG 60.456 60.000 0.00 0.00 37.67 4.63
3469 7534 1.620323 GGTGGCAAGCTGAGGAAAATT 59.380 47.619 0.00 0.00 0.00 1.82
3472 7537 1.600636 CGGTGGCAAGCTGAGGAAA 60.601 57.895 0.00 0.00 0.00 3.13
3810 7876 2.031919 TTTCCGGACGTGCTGCAT 59.968 55.556 1.83 0.00 0.00 3.96


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

AutoCloner maintained by Alex Coulton.