Multiple sequence alignment - TraesCS5D01G084200

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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 TraesCS5D01G084200 chr5D 100.000 4399 0 0 1 4399 88461997 88457599 0.000000e+00 8124.0
1 TraesCS5D01G084200 chr5D 78.571 938 153 28 1122 2023 88363315 88364240 3.820000e-160 575.0
2 TraesCS5D01G084200 chr5D 88.679 53 5 1 2269 2320 390503917 390503969 3.670000e-06 63.9
3 TraesCS5D01G084200 chr5B 95.602 2160 66 11 1 2136 94045112 94042958 0.000000e+00 3435.0
4 TraesCS5D01G084200 chr5B 95.224 1717 76 3 2686 4399 94040806 94039093 0.000000e+00 2712.0
5 TraesCS5D01G084200 chr5B 94.271 384 12 4 2321 2701 94042915 94042539 2.950000e-161 579.0
6 TraesCS5D01G084200 chr5B 79.725 799 137 17 1106 1893 93827778 93828562 4.970000e-154 555.0
7 TraesCS5D01G084200 chr5B 84.906 106 14 2 3 108 81019144 81019247 6.020000e-19 106.0
8 TraesCS5D01G084200 chr5B 83.019 106 16 2 3 108 80962562 80962665 1.300000e-15 95.3
9 TraesCS5D01G084200 chr7B 86.883 648 72 10 3760 4398 110556908 110556265 0.000000e+00 713.0
10 TraesCS5D01G084200 chr3D 86.801 644 78 7 3760 4399 279208715 279208075 0.000000e+00 712.0
11 TraesCS5D01G084200 chr4B 86.239 654 74 11 3759 4399 451457164 451457814 0.000000e+00 695.0
12 TraesCS5D01G084200 chr4D 86.022 651 76 12 3759 4398 41286411 41287057 0.000000e+00 684.0
13 TraesCS5D01G084200 chr4D 85.846 650 76 10 3762 4399 75308700 75308055 0.000000e+00 676.0
14 TraesCS5D01G084200 chr2D 85.997 657 70 16 3759 4399 64938627 64937977 0.000000e+00 684.0
15 TraesCS5D01G084200 chr2D 85.976 656 72 12 3759 4399 331663057 331663707 0.000000e+00 684.0
16 TraesCS5D01G084200 chr3B 85.824 649 81 7 3760 4399 370924010 370924656 0.000000e+00 678.0
17 TraesCS5D01G084200 chr5A 79.531 811 146 11 1106 1909 81499735 81500532 1.070000e-155 560.0
18 TraesCS5D01G084200 chr5A 85.714 105 13 2 4 108 382297192 382297294 4.650000e-20 110.0
19 TraesCS5D01G084200 chr7D 87.324 71 9 0 2255 2325 138501783 138501713 1.010000e-11 82.4
20 TraesCS5D01G084200 chr6D 86.667 75 9 1 2255 2328 17267485 17267559 1.010000e-11 82.4
21 TraesCS5D01G084200 chr2A 96.875 32 1 0 2294 2325 566099970 566099939 2.000000e-03 54.7
22 TraesCS5D01G084200 chr1D 96.875 32 1 0 2294 2325 30577794 30577763 2.000000e-03 54.7


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 TraesCS5D01G084200 chr5D 88457599 88461997 4398 True 8124 8124 100.000000 1 4399 1 chr5D.!!$R1 4398
1 TraesCS5D01G084200 chr5D 88363315 88364240 925 False 575 575 78.571000 1122 2023 1 chr5D.!!$F1 901
2 TraesCS5D01G084200 chr5B 94039093 94045112 6019 True 2242 3435 95.032333 1 4399 3 chr5B.!!$R1 4398
3 TraesCS5D01G084200 chr5B 93827778 93828562 784 False 555 555 79.725000 1106 1893 1 chr5B.!!$F3 787
4 TraesCS5D01G084200 chr7B 110556265 110556908 643 True 713 713 86.883000 3760 4398 1 chr7B.!!$R1 638
5 TraesCS5D01G084200 chr3D 279208075 279208715 640 True 712 712 86.801000 3760 4399 1 chr3D.!!$R1 639
6 TraesCS5D01G084200 chr4B 451457164 451457814 650 False 695 695 86.239000 3759 4399 1 chr4B.!!$F1 640
7 TraesCS5D01G084200 chr4D 41286411 41287057 646 False 684 684 86.022000 3759 4398 1 chr4D.!!$F1 639
8 TraesCS5D01G084200 chr4D 75308055 75308700 645 True 676 676 85.846000 3762 4399 1 chr4D.!!$R1 637
9 TraesCS5D01G084200 chr2D 64937977 64938627 650 True 684 684 85.997000 3759 4399 1 chr2D.!!$R1 640
10 TraesCS5D01G084200 chr2D 331663057 331663707 650 False 684 684 85.976000 3759 4399 1 chr2D.!!$F1 640
11 TraesCS5D01G084200 chr3B 370924010 370924656 646 False 678 678 85.824000 3760 4399 1 chr3B.!!$F1 639
12 TraesCS5D01G084200 chr5A 81499735 81500532 797 False 560 560 79.531000 1106 1909 1 chr5A.!!$F1 803

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
297 298 1.064611 TCTGGACCGGGTTTTGTTCAA 60.065 47.619 6.32 0.00 0.00 2.69 F
1695 1722 0.475475 TGATCATGGCCATGGTCTCC 59.525 55.000 43.60 28.13 46.44 3.71 F
2172 2227 0.105408 ACGGTGCGAAGTGTTTACCT 59.895 50.000 0.00 0.00 0.00 3.08 F
2948 4755 0.107456 ACCTCCGATGCATCATCACC 59.893 55.000 25.70 0.00 40.54 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 1831 0.035439 GTCCTCCCGAAATCCAGCAA 60.035 55.0 0.0 0.00 0.00 3.91 R
3092 4899 0.824109 TGTCTGGATCATCCCACGAC 59.176 55.0 0.0 6.11 35.03 4.34 R
3242 5049 0.977108 ATTGCAACATCCCCGCCAAT 60.977 50.0 0.0 0.00 0.00 3.16 R
4255 6074 6.479884 AGTAGAGGTAGGTTTCGAACTAGAA 58.520 40.0 0.0 0.00 0.00 2.10 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
132 133 7.476540 TGACTCTTATAGCACCACTTCTAAA 57.523 36.000 0.00 0.00 0.00 1.85
180 181 1.257936 CGATCGTATTTGGCGAACCTG 59.742 52.381 7.03 0.00 41.84 4.00
225 226 6.302269 AGCACTCCTAATTATGGGAATCTTG 58.698 40.000 0.00 0.00 35.52 3.02
297 298 1.064611 TCTGGACCGGGTTTTGTTCAA 60.065 47.619 6.32 0.00 0.00 2.69
543 546 2.474735 CCGGCAAACTTTTTCAAATCCG 59.525 45.455 0.00 0.00 0.00 4.18
565 568 6.016693 TCCGTGAGCTTTTTGAATACATGAAA 60.017 34.615 0.00 0.00 0.00 2.69
738 750 2.294233 TGGCTCAAATGCTCACTTTCAC 59.706 45.455 0.00 0.00 0.00 3.18
743 755 5.734220 GCTCAAATGCTCACTTTCACTTTCA 60.734 40.000 0.00 0.00 0.00 2.69
753 765 7.332926 GCTCACTTTCACTTTCATGAAGAGATA 59.667 37.037 18.50 9.35 39.68 1.98
758 770 5.111989 TCACTTTCATGAAGAGATAAGGCG 58.888 41.667 18.50 6.38 38.77 5.52
902 914 2.702261 GTGTAACTATCCACCCGCAAA 58.298 47.619 0.00 0.00 0.00 3.68
909 921 4.086457 ACTATCCACCCGCAAAGAAAAAT 58.914 39.130 0.00 0.00 0.00 1.82
962 974 1.517242 GCTGAAGTTGTGGAGTGGAG 58.483 55.000 0.00 0.00 0.00 3.86
1103 1115 4.758165 TGCTAAGCACAAAGGTACTTTACC 59.242 41.667 0.00 0.00 45.82 2.85
1167 1179 6.026186 TCTTCTCCTCCTCTTGTATTTCCTT 58.974 40.000 0.00 0.00 0.00 3.36
1224 1236 0.830648 TCAAGAGTATCCCAAGCCCG 59.169 55.000 0.00 0.00 33.66 6.13
1335 1347 4.477975 GACGGCGTCGGTCTCCTG 62.478 72.222 25.42 0.00 41.39 3.86
1649 1676 3.766691 GCCGGTTAGCGTGAGGGA 61.767 66.667 1.90 0.00 0.00 4.20
1656 1683 3.640257 TAGCGTGAGGGAGACGGCT 62.640 63.158 0.00 0.00 37.30 5.52
1695 1722 0.475475 TGATCATGGCCATGGTCTCC 59.525 55.000 43.60 28.13 46.44 3.71
1836 1863 1.617533 GGGAGGACGAGGAGAAGTCTT 60.618 57.143 0.00 0.00 37.52 3.01
2025 2079 1.310933 CCCTCTGCATGGTGAGTTGC 61.311 60.000 0.00 0.00 39.33 4.17
2056 2110 1.014044 CGCATGCGTCAGGTAGTTGT 61.014 55.000 31.33 0.00 34.35 3.32
2068 2122 6.380190 GTCAGGTAGTTGTTACACTGACTAG 58.620 44.000 19.23 0.00 45.32 2.57
2078 2132 9.599322 GTTGTTACACTGACTAGATGATTTTTG 57.401 33.333 0.00 0.00 0.00 2.44
2136 2191 2.202892 GCGTACCTGCTACCAGCC 60.203 66.667 0.00 0.00 41.51 4.85
2137 2192 2.104331 CGTACCTGCTACCAGCCG 59.896 66.667 0.00 0.00 41.51 5.52
2138 2193 2.202892 GTACCTGCTACCAGCCGC 60.203 66.667 0.00 0.00 41.51 6.53
2139 2194 2.363795 TACCTGCTACCAGCCGCT 60.364 61.111 0.00 0.00 41.51 5.52
2140 2195 2.721167 TACCTGCTACCAGCCGCTG 61.721 63.158 13.82 13.82 41.51 5.18
2141 2196 3.774528 CCTGCTACCAGCCGCTGA 61.775 66.667 22.35 1.49 41.51 4.26
2142 2197 2.510238 CTGCTACCAGCCGCTGAC 60.510 66.667 22.35 8.59 41.51 3.51
2143 2198 2.997315 TGCTACCAGCCGCTGACT 60.997 61.111 22.35 8.71 41.51 3.41
2144 2199 2.202810 GCTACCAGCCGCTGACTC 60.203 66.667 22.35 4.26 34.48 3.36
2145 2200 2.103143 CTACCAGCCGCTGACTCG 59.897 66.667 22.35 7.37 32.44 4.18
2152 2207 4.796231 CCGCTGACTCGGGTTCGG 62.796 72.222 9.70 9.70 45.38 4.30
2153 2208 3.744719 CGCTGACTCGGGTTCGGA 61.745 66.667 0.00 0.00 36.95 4.55
2154 2209 2.126031 GCTGACTCGGGTTCGGAC 60.126 66.667 0.00 0.00 36.95 4.79
2155 2210 2.178521 CTGACTCGGGTTCGGACG 59.821 66.667 0.00 0.00 36.95 4.79
2156 2211 3.338126 CTGACTCGGGTTCGGACGG 62.338 68.421 0.00 0.00 36.95 4.79
2157 2212 3.368571 GACTCGGGTTCGGACGGT 61.369 66.667 0.00 0.00 36.95 4.83
2158 2213 3.621892 GACTCGGGTTCGGACGGTG 62.622 68.421 0.00 0.00 36.95 4.94
2165 2220 2.355363 TTCGGACGGTGCGAAGTG 60.355 61.111 29.31 0.00 44.92 3.16
2166 2221 3.141522 TTCGGACGGTGCGAAGTGT 62.142 57.895 29.31 0.00 44.92 3.55
2167 2222 2.632136 TTCGGACGGTGCGAAGTGTT 62.632 55.000 29.31 0.00 44.92 3.32
2168 2223 2.241880 CGGACGGTGCGAAGTGTTT 61.242 57.895 17.47 0.00 30.86 2.83
2169 2224 0.940519 CGGACGGTGCGAAGTGTTTA 60.941 55.000 17.47 0.00 30.86 2.01
2170 2225 0.509929 GGACGGTGCGAAGTGTTTAC 59.490 55.000 0.00 0.00 0.00 2.01
2171 2226 0.509929 GACGGTGCGAAGTGTTTACC 59.490 55.000 0.00 0.00 0.00 2.85
2172 2227 0.105408 ACGGTGCGAAGTGTTTACCT 59.895 50.000 0.00 0.00 0.00 3.08
2173 2228 0.511221 CGGTGCGAAGTGTTTACCTG 59.489 55.000 0.00 0.00 0.00 4.00
2174 2229 1.870580 CGGTGCGAAGTGTTTACCTGA 60.871 52.381 0.00 0.00 0.00 3.86
2175 2230 2.423577 GGTGCGAAGTGTTTACCTGAT 58.576 47.619 0.00 0.00 0.00 2.90
2176 2231 2.159627 GGTGCGAAGTGTTTACCTGATG 59.840 50.000 0.00 0.00 0.00 3.07
2177 2232 1.804151 TGCGAAGTGTTTACCTGATGC 59.196 47.619 0.00 0.00 0.00 3.91
2192 2247 1.153025 ATGCATGCATCTCACGGCT 60.153 52.632 27.46 2.73 29.42 5.52
2225 2281 3.969466 GGGACCTACTAACTACTCCCT 57.031 52.381 0.00 0.00 35.37 4.20
2226 2282 3.831323 GGGACCTACTAACTACTCCCTC 58.169 54.545 0.00 0.00 35.37 4.30
2227 2283 3.475575 GGACCTACTAACTACTCCCTCG 58.524 54.545 0.00 0.00 0.00 4.63
2228 2284 3.118075 GGACCTACTAACTACTCCCTCGT 60.118 52.174 0.00 0.00 0.00 4.18
2229 2285 4.101741 GGACCTACTAACTACTCCCTCGTA 59.898 50.000 0.00 0.00 0.00 3.43
2230 2286 5.396884 GGACCTACTAACTACTCCCTCGTAA 60.397 48.000 0.00 0.00 0.00 3.18
2231 2287 6.067217 ACCTACTAACTACTCCCTCGTAAA 57.933 41.667 0.00 0.00 0.00 2.01
2232 2288 5.883115 ACCTACTAACTACTCCCTCGTAAAC 59.117 44.000 0.00 0.00 0.00 2.01
2233 2289 6.118852 CCTACTAACTACTCCCTCGTAAACT 58.881 44.000 0.00 0.00 0.00 2.66
2234 2290 7.092846 ACCTACTAACTACTCCCTCGTAAACTA 60.093 40.741 0.00 0.00 0.00 2.24
2235 2291 7.770897 CCTACTAACTACTCCCTCGTAAACTAA 59.229 40.741 0.00 0.00 0.00 2.24
2236 2292 9.336171 CTACTAACTACTCCCTCGTAAACTAAT 57.664 37.037 0.00 0.00 0.00 1.73
2238 2294 9.859152 ACTAACTACTCCCTCGTAAACTAATAT 57.141 33.333 0.00 0.00 0.00 1.28
2422 2478 7.177041 TCACTACAAGTTTTAAAAAGTGGGTGT 59.823 33.333 21.20 13.28 34.91 4.16
2423 2479 7.274686 CACTACAAGTTTTAAAAAGTGGGTGTG 59.725 37.037 16.73 14.81 31.46 3.82
2425 2481 4.746535 AGTTTTAAAAAGTGGGTGTGGG 57.253 40.909 1.31 0.00 0.00 4.61
2427 2483 4.081365 AGTTTTAAAAAGTGGGTGTGGGTG 60.081 41.667 1.31 0.00 0.00 4.61
2428 2484 1.404843 TAAAAAGTGGGTGTGGGTGC 58.595 50.000 0.00 0.00 0.00 5.01
2429 2485 0.616111 AAAAAGTGGGTGTGGGTGCA 60.616 50.000 0.00 0.00 0.00 4.57
2430 2486 1.042559 AAAAGTGGGTGTGGGTGCAG 61.043 55.000 0.00 0.00 0.00 4.41
2431 2487 2.223464 AAAGTGGGTGTGGGTGCAGT 62.223 55.000 0.00 0.00 0.00 4.40
2432 2488 2.906897 GTGGGTGTGGGTGCAGTG 60.907 66.667 0.00 0.00 0.00 3.66
2439 2495 0.534877 TGTGGGTGCAGTGCTAGTTG 60.535 55.000 17.60 0.00 0.00 3.16
2546 2604 3.605486 GCTAACGTCGAACGACAATAAGT 59.395 43.478 23.37 12.05 46.05 2.24
2584 2642 4.503007 GCGAGCAAGAAACTAATGTCGATA 59.497 41.667 0.00 0.00 0.00 2.92
2602 2660 5.356751 GTCGATAGCTATGATCCACTCATCT 59.643 44.000 11.94 0.00 43.70 2.90
2603 2661 6.540551 GTCGATAGCTATGATCCACTCATCTA 59.459 42.308 11.94 0.00 43.70 1.98
2636 2694 9.075678 TCTCTAATTACCTAGTATAGCACAACC 57.924 37.037 0.00 0.00 37.37 3.77
2679 2737 7.386059 TGCTAATTGATCTAGTTGAGTTGACA 58.614 34.615 0.00 0.00 0.00 3.58
2680 2738 8.043113 TGCTAATTGATCTAGTTGAGTTGACAT 58.957 33.333 0.00 0.00 0.00 3.06
2681 2739 9.534565 GCTAATTGATCTAGTTGAGTTGACATA 57.465 33.333 0.00 0.00 0.00 2.29
2684 2742 7.776933 TTGATCTAGTTGAGTTGACATATGC 57.223 36.000 1.58 0.00 0.00 3.14
2763 4570 8.082242 ACTAATCTTATTTCAACTTTGGTGCAC 58.918 33.333 8.80 8.80 0.00 4.57
2807 4614 1.982223 GACACATCATCTAGCGCGATC 59.018 52.381 12.10 0.00 0.00 3.69
2847 4654 1.346395 TGCTCAATAACCCAGACGTGT 59.654 47.619 0.00 0.00 0.00 4.49
2862 4669 2.597217 TGTTGGCCAAGGCGAAGG 60.597 61.111 21.21 0.00 39.36 3.46
2874 4681 1.941734 GCGAAGGCTGAGATCGACG 60.942 63.158 10.30 0.00 38.82 5.12
2924 4731 0.839946 AGTGTGACCTGGAAGTGCTT 59.160 50.000 0.00 0.00 0.00 3.91
2948 4755 0.107456 ACCTCCGATGCATCATCACC 59.893 55.000 25.70 0.00 40.54 4.02
2990 4797 2.745037 GCACCCAACCTCGTACCA 59.255 61.111 0.00 0.00 0.00 3.25
3056 4863 1.169661 TTGCACGTGGAACCATGGTC 61.170 55.000 20.07 11.65 37.27 4.02
3092 4899 1.813753 CATACAACGGGACCCTGCG 60.814 63.158 9.41 0.00 0.00 5.18
3128 4935 2.836372 AGACATGTTCATGCCAGAGAGA 59.164 45.455 12.00 0.00 0.00 3.10
3151 4958 0.249826 GTGGGTGGCAATGTTTGTGG 60.250 55.000 0.00 0.00 0.00 4.17
3191 4998 2.759560 ATGCCGTTTGGGATGGGC 60.760 61.111 0.00 0.00 45.83 5.36
3242 5049 1.681327 GAGGACGGTGGGAGTAGCA 60.681 63.158 0.00 0.00 0.00 3.49
3314 5121 0.904865 TGGACATGAGCGAGGGTTCT 60.905 55.000 0.00 0.00 0.00 3.01
3334 5141 0.394216 GGGCTCACCATGCACATGTA 60.394 55.000 9.63 0.00 39.85 2.29
3356 5163 1.961277 GCCGCTAGTTGCAGTGTGT 60.961 57.895 0.00 0.00 43.06 3.72
3362 5169 1.000163 CTAGTTGCAGTGTGTCGACCT 60.000 52.381 14.12 0.00 0.00 3.85
3415 5222 5.552178 CCTTTAGAAGTGTGCTCCTTAAGT 58.448 41.667 0.97 0.00 0.00 2.24
3431 5238 5.924254 TCCTTAAGTGTTGTGAGTTGATACG 59.076 40.000 0.97 0.00 0.00 3.06
3514 5321 5.248870 AGTGACCTTTTGAACATTGACAC 57.751 39.130 0.00 0.00 0.00 3.67
3636 5443 7.241376 CCATAAAGTTTTGTGATCCGAGTTAC 58.759 38.462 0.00 0.00 31.84 2.50
3637 5444 7.094975 CCATAAAGTTTTGTGATCCGAGTTACA 60.095 37.037 0.00 0.00 31.84 2.41
3646 5453 8.697846 TTGTGATCCGAGTTACAGTTAATTAG 57.302 34.615 0.00 0.00 0.00 1.73
3738 5545 0.321830 TAGCCCAACTAAACGCACCC 60.322 55.000 0.00 0.00 0.00 4.61
3860 5668 5.455392 CAAAACCAAGTTAGATGTGCTCTG 58.545 41.667 0.00 0.00 35.28 3.35
3975 5786 4.457466 AGATTAACTTTCGGGTGTGTGTT 58.543 39.130 0.00 0.00 0.00 3.32
3982 5793 4.885325 ACTTTCGGGTGTGTGTTAAAGAAT 59.115 37.500 0.00 0.00 0.00 2.40
4140 5956 2.161486 GCAGATCGTCGACAGCCAC 61.161 63.158 17.16 1.94 0.00 5.01
4142 5958 0.388520 CAGATCGTCGACAGCCACAA 60.389 55.000 17.16 0.00 0.00 3.33
4247 6066 4.647564 AGAACATCAAACCCTCACATCT 57.352 40.909 0.00 0.00 0.00 2.90
4255 6074 5.630121 TCAAACCCTCACATCTACATGTTT 58.370 37.500 2.30 0.00 40.66 2.83
4261 6080 6.213600 ACCCTCACATCTACATGTTTTCTAGT 59.786 38.462 2.30 0.00 40.66 2.57
4273 6092 6.426025 ACATGTTTTCTAGTTCGAAACCTACC 59.574 38.462 0.00 0.00 32.99 3.18
4322 6147 2.301009 ACTGTTGGGAAACGTAGTAGGG 59.699 50.000 0.00 0.00 45.00 3.53
4351 6176 1.606224 GCCCTACGTTCAACGAGGAAA 60.606 52.381 18.84 0.00 46.05 3.13
4393 6218 3.241868 GGTTTGGATCAACGATCGTTACG 60.242 47.826 31.27 20.61 39.72 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 7.925703 TTTTAAAAATGTATTCCAAACGCGA 57.074 28.000 15.93 0.00 0.00 5.87
53 54 8.012809 CCCGCTTTTTAAAAATGTATTCCAAAC 58.987 33.333 13.55 0.00 0.00 2.93
63 64 6.363896 ACATACGAACCCGCTTTTTAAAAATG 59.636 34.615 13.55 9.37 39.95 2.32
65 66 5.829829 ACATACGAACCCGCTTTTTAAAAA 58.170 33.333 12.62 12.62 39.95 1.94
160 161 1.257936 CAGGTTCGCCAAATACGATCG 59.742 52.381 14.88 14.88 39.65 3.69
180 181 3.070060 CGCGAAGTCGTGCCTTAC 58.930 61.111 0.00 0.00 43.06 2.34
486 489 9.893305 AAGGTTCACTAATTTGTAGAAATTTCG 57.107 29.630 14.98 9.75 41.22 3.46
527 530 5.262588 AGCTCACGGATTTGAAAAAGTTT 57.737 34.783 0.00 0.00 0.00 2.66
685 697 8.514594 TCATAAATTTCAAAAGAGCTCACGAAT 58.485 29.630 17.77 4.44 0.00 3.34
738 750 4.697514 TCCGCCTTATCTCTTCATGAAAG 58.302 43.478 9.88 9.89 36.22 2.62
743 755 4.080299 ACCTTTTCCGCCTTATCTCTTCAT 60.080 41.667 0.00 0.00 0.00 2.57
753 765 2.160205 GCTTTCTACCTTTTCCGCCTT 58.840 47.619 0.00 0.00 0.00 4.35
758 770 3.751698 ACACATCGCTTTCTACCTTTTCC 59.248 43.478 0.00 0.00 0.00 3.13
962 974 2.922740 TTGGAGTGTGTTGGGACTAC 57.077 50.000 0.00 0.00 0.00 2.73
1103 1115 2.726555 CGTGAGCGAAATCTCCATTG 57.273 50.000 0.00 0.00 41.33 2.82
1510 1525 1.982395 TGACGATGAGGCGGAGGTT 60.982 57.895 0.00 0.00 35.12 3.50
1638 1665 3.138798 GCCGTCTCCCTCACGCTA 61.139 66.667 0.00 0.00 35.87 4.26
1804 1831 0.035439 GTCCTCCCGAAATCCAGCAA 60.035 55.000 0.00 0.00 0.00 3.91
2025 2079 1.060937 GCATGCGACTTTGGCGTAG 59.939 57.895 0.00 0.00 0.00 3.51
2056 2110 9.778741 AAGACAAAAATCATCTAGTCAGTGTAA 57.221 29.630 0.00 0.00 0.00 2.41
2068 2122 6.133392 TCGTGTTCGAAAGACAAAAATCATC 58.867 36.000 0.00 0.00 43.34 2.92
2136 2191 3.744719 TCCGAACCCGAGTCAGCG 61.745 66.667 0.00 0.00 38.22 5.18
2137 2192 2.126031 GTCCGAACCCGAGTCAGC 60.126 66.667 0.00 0.00 38.22 4.26
2138 2193 2.178521 CGTCCGAACCCGAGTCAG 59.821 66.667 0.00 0.00 38.22 3.51
2139 2194 3.367743 CCGTCCGAACCCGAGTCA 61.368 66.667 0.00 0.00 38.22 3.41
2140 2195 3.368571 ACCGTCCGAACCCGAGTC 61.369 66.667 0.00 0.00 38.22 3.36
2141 2196 3.677648 CACCGTCCGAACCCGAGT 61.678 66.667 0.00 0.00 38.22 4.18
2145 2200 4.668118 TTCGCACCGTCCGAACCC 62.668 66.667 0.00 0.00 39.50 4.11
2146 2201 3.110178 CTTCGCACCGTCCGAACC 61.110 66.667 0.00 0.00 39.50 3.62
2147 2202 2.355481 ACTTCGCACCGTCCGAAC 60.355 61.111 0.00 0.00 39.50 3.95
2148 2203 2.355363 CACTTCGCACCGTCCGAA 60.355 61.111 0.00 0.00 41.81 4.30
2149 2204 2.632136 AAACACTTCGCACCGTCCGA 62.632 55.000 0.00 0.00 0.00 4.55
2150 2205 0.940519 TAAACACTTCGCACCGTCCG 60.941 55.000 0.00 0.00 0.00 4.79
2151 2206 0.509929 GTAAACACTTCGCACCGTCC 59.490 55.000 0.00 0.00 0.00 4.79
2152 2207 0.509929 GGTAAACACTTCGCACCGTC 59.490 55.000 0.00 0.00 0.00 4.79
2153 2208 0.105408 AGGTAAACACTTCGCACCGT 59.895 50.000 0.00 0.00 34.36 4.83
2154 2209 0.511221 CAGGTAAACACTTCGCACCG 59.489 55.000 0.00 0.00 34.36 4.94
2155 2210 1.873698 TCAGGTAAACACTTCGCACC 58.126 50.000 0.00 0.00 0.00 5.01
2156 2211 2.412847 GCATCAGGTAAACACTTCGCAC 60.413 50.000 0.00 0.00 0.00 5.34
2157 2212 1.804151 GCATCAGGTAAACACTTCGCA 59.196 47.619 0.00 0.00 0.00 5.10
2158 2213 1.804151 TGCATCAGGTAAACACTTCGC 59.196 47.619 0.00 0.00 0.00 4.70
2159 2214 3.728864 GCATGCATCAGGTAAACACTTCG 60.729 47.826 14.21 0.00 0.00 3.79
2160 2215 3.191162 TGCATGCATCAGGTAAACACTTC 59.809 43.478 18.46 0.00 0.00 3.01
2161 2216 3.156293 TGCATGCATCAGGTAAACACTT 58.844 40.909 18.46 0.00 0.00 3.16
2162 2217 2.794103 TGCATGCATCAGGTAAACACT 58.206 42.857 18.46 0.00 0.00 3.55
2163 2218 3.788333 ATGCATGCATCAGGTAAACAC 57.212 42.857 27.46 0.00 29.42 3.32
2174 2229 1.153025 AGCCGTGAGATGCATGCAT 60.153 52.632 32.66 32.66 39.69 3.96
2175 2230 2.110352 CAGCCGTGAGATGCATGCA 61.110 57.895 25.04 25.04 31.94 3.96
2176 2231 2.713770 CAGCCGTGAGATGCATGC 59.286 61.111 11.82 11.82 31.94 4.06
2177 2232 1.450848 ACCAGCCGTGAGATGCATG 60.451 57.895 2.46 0.00 0.00 4.06
2204 2259 2.517553 AGGGAGTAGTTAGTAGGTCCCC 59.482 54.545 9.68 0.00 44.25 4.81
2305 2361 9.461312 TGCACATTAATTCCTCTGTAAACTAAT 57.539 29.630 0.00 0.00 0.00 1.73
2306 2362 8.856153 TGCACATTAATTCCTCTGTAAACTAA 57.144 30.769 0.00 0.00 0.00 2.24
2307 2363 9.461312 AATGCACATTAATTCCTCTGTAAACTA 57.539 29.630 0.00 0.00 0.00 2.24
2308 2364 7.944729 ATGCACATTAATTCCTCTGTAAACT 57.055 32.000 0.00 0.00 0.00 2.66
2309 2365 9.722056 CTAATGCACATTAATTCCTCTGTAAAC 57.278 33.333 4.74 0.00 33.34 2.01
2310 2366 8.405531 GCTAATGCACATTAATTCCTCTGTAAA 58.594 33.333 4.74 0.00 39.41 2.01
2311 2367 7.555914 TGCTAATGCACATTAATTCCTCTGTAA 59.444 33.333 4.74 0.00 45.31 2.41
2312 2368 7.053498 TGCTAATGCACATTAATTCCTCTGTA 58.947 34.615 4.74 0.00 45.31 2.74
2313 2369 5.887598 TGCTAATGCACATTAATTCCTCTGT 59.112 36.000 4.74 0.00 45.31 3.41
2314 2370 6.381481 TGCTAATGCACATTAATTCCTCTG 57.619 37.500 4.74 0.00 45.31 3.35
2370 2426 4.167268 GTTTCACCGTGCTTAAACAAACA 58.833 39.130 8.65 0.00 33.16 2.83
2399 2455 6.754675 CCACACCCACTTTTTAAAACTTGTAG 59.245 38.462 0.00 0.00 0.00 2.74
2405 2461 4.185394 CACCCACACCCACTTTTTAAAAC 58.815 43.478 0.00 0.00 0.00 2.43
2422 2478 0.250295 GTCAACTAGCACTGCACCCA 60.250 55.000 3.30 0.00 0.00 4.51
2423 2479 0.250295 TGTCAACTAGCACTGCACCC 60.250 55.000 3.30 0.00 0.00 4.61
2425 2481 2.064762 CTCTGTCAACTAGCACTGCAC 58.935 52.381 3.30 0.00 0.00 4.57
2427 2483 2.064762 CACTCTGTCAACTAGCACTGC 58.935 52.381 0.00 0.00 0.00 4.40
2428 2484 3.055591 CACACTCTGTCAACTAGCACTG 58.944 50.000 0.00 0.00 0.00 3.66
2429 2485 2.546795 GCACACTCTGTCAACTAGCACT 60.547 50.000 0.00 0.00 0.00 4.40
2430 2486 1.795286 GCACACTCTGTCAACTAGCAC 59.205 52.381 0.00 0.00 0.00 4.40
2431 2487 1.270305 GGCACACTCTGTCAACTAGCA 60.270 52.381 0.00 0.00 0.00 3.49
2432 2488 1.270305 TGGCACACTCTGTCAACTAGC 60.270 52.381 0.00 0.00 28.84 3.42
2546 2604 2.425668 TGCTCGCTACAGCATACACTAA 59.574 45.455 1.61 0.00 44.73 2.24
2620 2678 7.551262 TGTTAACAATGGTTGTGCTATACTAGG 59.449 37.037 5.64 0.00 44.59 3.02
2807 4614 3.958147 AAGTGCCATCGCCCACTCG 62.958 63.158 0.00 0.00 41.16 4.18
2862 4669 2.652496 GACGGCGTCGATCTCAGC 60.652 66.667 25.42 0.00 40.11 4.26
2907 4714 3.706055 GAAGCACTTCCAGGTCACA 57.294 52.632 0.00 0.00 33.64 3.58
2924 4731 1.788229 TGATGCATCGGAGGTAAGGA 58.212 50.000 21.34 0.00 0.00 3.36
2960 4767 1.113517 TGGGTGCGAGAGGGTATAGC 61.114 60.000 0.00 0.00 0.00 2.97
3005 4812 1.633561 CACTAGTGATGGTGCAGTCG 58.366 55.000 18.45 0.00 0.00 4.18
3014 4821 4.707105 TGATGTATTGCCCACTAGTGATG 58.293 43.478 24.68 15.20 0.00 3.07
3015 4822 5.573380 ATGATGTATTGCCCACTAGTGAT 57.427 39.130 24.68 11.82 0.00 3.06
3056 4863 4.330894 TGTATGGAGTACACGTCGACTAAG 59.669 45.833 14.70 5.62 38.37 2.18
3092 4899 0.824109 TGTCTGGATCATCCCACGAC 59.176 55.000 0.00 6.11 35.03 4.34
3128 4935 1.000731 CAAACATTGCCACCCACGAAT 59.999 47.619 0.00 0.00 0.00 3.34
3151 4958 2.151202 TCATTCGCTTTCCACCTTGTC 58.849 47.619 0.00 0.00 0.00 3.18
3219 5026 3.316573 CTCCCACCGTCCTCCAAGC 62.317 68.421 0.00 0.00 0.00 4.01
3229 5036 1.819632 GCCAATGCTACTCCCACCG 60.820 63.158 0.00 0.00 33.53 4.94
3242 5049 0.977108 ATTGCAACATCCCCGCCAAT 60.977 50.000 0.00 0.00 0.00 3.16
3356 5163 2.927028 TCCATATCTTGACGAGGTCGA 58.073 47.619 6.35 0.00 43.02 4.20
3362 5169 4.039609 AGCATGACATCCATATCTTGACGA 59.960 41.667 0.00 0.00 33.31 4.20
3415 5222 2.223144 GCAAGCGTATCAACTCACAACA 59.777 45.455 0.00 0.00 0.00 3.33
3431 5238 1.796796 CTTCGCTACCCTTGCAAGC 59.203 57.895 21.43 9.19 0.00 4.01
3514 5321 9.003658 AGTGGTAAAGTTACATCTTGAAGAATG 57.996 33.333 0.00 1.26 35.37 2.67
3587 5394 5.474578 TTTGGATCGATTCTATGAGGAGG 57.525 43.478 5.06 0.00 0.00 4.30
3636 5443 9.655769 CTTGCACATGCTATAACTAATTAACTG 57.344 33.333 5.31 0.00 42.66 3.16
3637 5444 9.396022 ACTTGCACATGCTATAACTAATTAACT 57.604 29.630 5.31 0.00 42.66 2.24
3703 5510 7.176490 AGTTGGGCTACTATATAGAATCGACT 58.824 38.462 16.79 11.65 0.00 4.18
3705 5512 9.524496 TTTAGTTGGGCTACTATATAGAATCGA 57.476 33.333 16.79 0.00 31.09 3.59
3714 5521 4.441913 GGTGCGTTTAGTTGGGCTACTATA 60.442 45.833 1.86 0.00 31.09 1.31
3715 5522 3.528532 GTGCGTTTAGTTGGGCTACTAT 58.471 45.455 1.86 0.00 31.09 2.12
3738 5545 2.634982 TTTTAGCAATGCTTCGCCTG 57.365 45.000 14.85 0.00 40.44 4.85
3860 5668 8.921670 ACGTAATTAAAATTTGCCAAACTGATC 58.078 29.630 0.00 0.00 0.00 2.92
3982 5793 7.553760 GTGGGGGACGAGATTTTTAAATAACTA 59.446 37.037 0.00 0.00 0.00 2.24
4083 5899 6.989169 GGCTTCATCATAGTCAAGAATAGTGT 59.011 38.462 0.00 0.00 0.00 3.55
4247 6066 7.599998 GGTAGGTTTCGAACTAGAAAACATGTA 59.400 37.037 0.00 0.00 46.99 2.29
4255 6074 6.479884 AGTAGAGGTAGGTTTCGAACTAGAA 58.520 40.000 0.00 0.00 0.00 2.10
4261 6080 6.656902 TCTATGAGTAGAGGTAGGTTTCGAA 58.343 40.000 0.00 0.00 32.04 3.71
4273 6092 6.951062 TCATGAGTGGTTCTATGAGTAGAG 57.049 41.667 0.00 0.00 38.17 2.43
4339 6164 7.094420 TGCATCTTCATATTTTTCCTCGTTGAA 60.094 33.333 0.00 0.00 0.00 2.69
4351 6176 9.028284 CCAAACCCTATATGCATCTTCATATTT 57.972 33.333 0.19 0.00 39.57 1.40


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

AutoCloner maintained by Alex Coulton.