Multiple sequence alignment - TraesCS5B01G350800

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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 TraesCS5B01G350800 chr5B 100.000 3397 0 0 1 3397 531531007 531534403 0.000000e+00 6274.0
1 TraesCS5B01G350800 chr5B 78.571 252 35 12 1428 1677 531532371 531532605 7.590000e-32 148.0
2 TraesCS5B01G350800 chr5B 91.071 112 7 2 1365 1473 531532434 531532545 7.590000e-32 148.0
3 TraesCS5B01G350800 chr5D 91.780 3236 172 31 209 3397 437334863 437338051 0.000000e+00 4416.0
4 TraesCS5B01G350800 chr5D 79.615 260 43 8 1420 1677 437336000 437336251 9.690000e-41 178.0
5 TraesCS5B01G350800 chr5D 91.736 121 9 1 1 121 437334713 437334832 2.100000e-37 167.0
6 TraesCS5B01G350800 chr5D 91.525 118 7 1 1365 1479 437336071 437336188 3.510000e-35 159.0
7 TraesCS5B01G350800 chr5D 100.000 40 0 0 471 510 87100051 87100012 1.310000e-09 75.0
8 TraesCS5B01G350800 chr5D 100.000 40 0 0 471 510 399569949 399569910 1.310000e-09 75.0
9 TraesCS5B01G350800 chr5D 100.000 40 0 0 471 510 551597923 551597884 1.310000e-09 75.0
10 TraesCS5B01G350800 chr5A 89.933 3437 188 56 6 3397 552512965 552516288 0.000000e+00 4285.0
11 TraesCS5B01G350800 chr5A 79.767 257 32 13 1428 1677 552514282 552514525 5.830000e-38 169.0
12 TraesCS5B01G350800 chr5A 78.764 259 31 12 1365 1599 552514345 552514603 5.870000e-33 152.0
13 TraesCS5B01G350800 chr3D 100.000 41 0 0 470 510 17874168 17874128 3.630000e-10 76.8
14 TraesCS5B01G350800 chr4D 100.000 40 0 0 471 510 255797111 255797072 1.310000e-09 75.0
15 TraesCS5B01G350800 chr4A 100.000 40 0 0 471 510 560894848 560894887 1.310000e-09 75.0
16 TraesCS5B01G350800 chr2A 95.349 43 2 0 470 512 775069559 775069601 6.080000e-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 TraesCS5B01G350800 chr5B 531531007 531534403 3396 False 2190.000000 6274 89.880667 1 3397 3 chr5B.!!$F1 3396
1 TraesCS5B01G350800 chr5D 437334713 437338051 3338 False 1230.000000 4416 88.664000 1 3397 4 chr5D.!!$F1 3396
2 TraesCS5B01G350800 chr5A 552512965 552516288 3323 False 1535.333333 4285 82.821333 6 3397 3 chr5A.!!$F1 3391

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
446 460 1.278985 TGACTTGATTGCGGAGTGGAT 59.721 47.619 0.0 0.0 0.0 3.41 F
514 528 1.358787 TGGGACGGAGGGAGTAGTTAA 59.641 52.381 0.0 0.0 0.0 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 1483 1.005394 GGAGACGCGGAAACAGGAA 60.005 57.895 12.47 0.00 0.0 3.36 R
2459 2528 0.889994 TGACCATGTTGCAGCATTCC 59.110 50.000 13.95 6.48 0.0 3.01 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
89 95 3.683847 GCCTAGAATTGACCTGACTGCAT 60.684 47.826 0.00 0.00 0.00 3.96
90 96 4.521146 CCTAGAATTGACCTGACTGCATT 58.479 43.478 0.00 0.00 0.00 3.56
99 105 4.009675 GACCTGACTGCATTGTGGATAAA 58.990 43.478 0.00 0.00 0.00 1.40
100 106 3.758554 ACCTGACTGCATTGTGGATAAAC 59.241 43.478 0.00 0.00 0.00 2.01
101 107 3.758023 CCTGACTGCATTGTGGATAAACA 59.242 43.478 0.00 0.00 0.00 2.83
102 108 4.379813 CCTGACTGCATTGTGGATAAACAC 60.380 45.833 0.00 0.00 41.68 3.32
103 109 3.188254 TGACTGCATTGTGGATAAACACG 59.812 43.478 0.00 0.00 44.21 4.49
104 110 3.146066 ACTGCATTGTGGATAAACACGT 58.854 40.909 0.00 0.00 44.21 4.49
106 112 2.486203 TGCATTGTGGATAAACACGTCC 59.514 45.455 0.00 0.00 44.21 4.79
107 113 2.747446 GCATTGTGGATAAACACGTCCT 59.253 45.455 0.00 0.00 44.21 3.85
108 114 3.426159 GCATTGTGGATAAACACGTCCTG 60.426 47.826 0.00 0.00 44.21 3.86
109 115 3.478857 TTGTGGATAAACACGTCCTGT 57.521 42.857 0.00 0.00 44.21 4.00
141 154 3.450457 AGTCATGCCCTGTTTGTTTTCAA 59.550 39.130 0.00 0.00 38.10 2.69
142 155 3.555547 GTCATGCCCTGTTTGTTTTCAAC 59.444 43.478 0.00 0.00 39.73 3.18
143 156 3.450457 TCATGCCCTGTTTGTTTTCAACT 59.550 39.130 0.00 0.00 39.73 3.16
144 157 3.971245 TGCCCTGTTTGTTTTCAACTT 57.029 38.095 0.00 0.00 39.73 2.66
145 158 4.278975 TGCCCTGTTTGTTTTCAACTTT 57.721 36.364 0.00 0.00 39.73 2.66
146 159 4.646572 TGCCCTGTTTGTTTTCAACTTTT 58.353 34.783 0.00 0.00 39.73 2.27
147 160 4.693095 TGCCCTGTTTGTTTTCAACTTTTC 59.307 37.500 0.00 0.00 39.73 2.29
148 161 4.693095 GCCCTGTTTGTTTTCAACTTTTCA 59.307 37.500 0.00 0.00 39.73 2.69
149 162 5.353956 GCCCTGTTTGTTTTCAACTTTTCAT 59.646 36.000 0.00 0.00 39.73 2.57
150 163 6.536941 GCCCTGTTTGTTTTCAACTTTTCATA 59.463 34.615 0.00 0.00 39.73 2.15
151 164 7.254421 GCCCTGTTTGTTTTCAACTTTTCATAG 60.254 37.037 0.00 0.00 39.73 2.23
152 165 7.978975 CCCTGTTTGTTTTCAACTTTTCATAGA 59.021 33.333 0.00 0.00 39.73 1.98
203 216 5.635549 TTTCAATATACATGTGCTCGTCG 57.364 39.130 9.11 0.00 0.00 5.12
236 249 1.686052 GTTGTTCTTGGTGGAATGCCA 59.314 47.619 0.00 0.00 43.47 4.92
252 266 1.520666 CCATCGACGGGTTAGCCTT 59.479 57.895 0.00 0.00 34.45 4.35
386 400 9.304731 TGATTGCATTTGCTTAATTACATTCTC 57.695 29.630 3.94 0.00 42.66 2.87
387 401 9.525409 GATTGCATTTGCTTAATTACATTCTCT 57.475 29.630 3.94 0.00 42.66 3.10
391 405 8.405531 GCATTTGCTTAATTACATTCTCTGGTA 58.594 33.333 0.00 0.00 38.21 3.25
393 407 7.534085 TTGCTTAATTACATTCTCTGGTACG 57.466 36.000 0.00 0.00 0.00 3.67
402 416 3.814005 TTCTCTGGTACGCTTAATCCC 57.186 47.619 0.00 0.00 0.00 3.85
405 419 1.679680 TCTGGTACGCTTAATCCCGAG 59.320 52.381 0.00 0.00 0.00 4.63
406 420 1.407979 CTGGTACGCTTAATCCCGAGT 59.592 52.381 0.00 0.00 0.00 4.18
418 432 4.900635 AATCCCGAGTGATAACAAATGC 57.099 40.909 0.00 0.00 0.00 3.56
446 460 1.278985 TGACTTGATTGCGGAGTGGAT 59.721 47.619 0.00 0.00 0.00 3.41
514 528 1.358787 TGGGACGGAGGGAGTAGTTAA 59.641 52.381 0.00 0.00 0.00 2.01
524 538 4.092279 AGGGAGTAGTTAACTTAGCCGTT 58.908 43.478 14.49 2.55 39.07 4.44
540 554 1.923864 CCGTTGCCTGTTTGTTTTCAC 59.076 47.619 0.00 0.00 0.00 3.18
544 558 4.241681 GTTGCCTGTTTGTTTTCACAGAA 58.758 39.130 0.79 0.00 33.22 3.02
634 651 7.734924 TGAGCTAAATCTGCATAAACCATAG 57.265 36.000 0.00 0.00 0.00 2.23
636 653 6.064060 AGCTAAATCTGCATAAACCATAGCA 58.936 36.000 12.40 0.00 36.56 3.49
699 716 5.061179 CAGGTAGGTAGTAGAGAGAAGCTC 58.939 50.000 0.00 0.00 44.29 4.09
769 786 4.877823 TGCACTCTAGCATTTTGTGGATAG 59.122 41.667 0.00 0.00 40.11 2.08
788 805 3.611766 AGCAGCATTAGTAAAGGTCGT 57.388 42.857 0.00 0.00 0.00 4.34
789 806 3.262420 AGCAGCATTAGTAAAGGTCGTG 58.738 45.455 0.00 0.00 0.00 4.35
837 871 8.469200 AGATTGTGACTTGAAACTGAATTTTCA 58.531 29.630 0.00 0.00 42.47 2.69
886 920 4.236935 CCAAGTTGGTACATGTTGATTGC 58.763 43.478 14.21 0.00 39.30 3.56
899 933 5.493133 TGTTGATTGCGTAACTTGTTCTT 57.507 34.783 0.00 0.00 0.00 2.52
934 968 6.089820 TCGTAGTACCTACTTTGCAAATTTCG 59.910 38.462 13.23 3.33 37.73 3.46
1080 1118 4.943705 TCACCTAAGCAATCCAAGAATGAC 59.056 41.667 0.00 0.00 0.00 3.06
1082 1120 2.927553 AAGCAATCCAAGAATGACGC 57.072 45.000 0.00 0.00 0.00 5.19
1321 1362 4.283467 TGAGCTCAAAGAAACCTGCTACTA 59.717 41.667 15.67 0.00 0.00 1.82
1384 1425 1.419012 CTCATGCCCAATCAGCTCCTA 59.581 52.381 0.00 0.00 0.00 2.94
1442 1483 2.379005 TGCGTCTCATACTCCATCAGT 58.621 47.619 0.00 0.00 39.41 3.41
1520 1561 2.740055 AGCTCCTGTTTCTGCGCG 60.740 61.111 0.00 0.00 0.00 6.86
1768 1818 1.337823 TGCCTCAGAACTTTACGGCTC 60.338 52.381 0.00 0.00 38.33 4.70
1857 1907 3.729762 CGACACGTAATCCGACTGATTCA 60.730 47.826 0.00 0.00 42.75 2.57
1938 1988 5.245531 AGAAATAACGAGCAATCAGGACAA 58.754 37.500 0.00 0.00 0.00 3.18
2015 2065 7.017645 CACAACTGCTATCTAAAACATGTGTC 58.982 38.462 0.00 0.00 32.11 3.67
2054 2104 1.736681 GCTCCAGTCTTTGTCATCTGC 59.263 52.381 0.00 0.00 0.00 4.26
2088 2138 1.676529 CATGCCATTGAGCTGGAGAAG 59.323 52.381 0.00 0.00 38.69 2.85
2097 2147 2.099431 GCTGGAGAAGCGAGCAGTG 61.099 63.158 0.00 0.00 46.36 3.66
2106 2156 2.007360 AGCGAGCAGTGAATCTCTTG 57.993 50.000 0.00 0.00 0.00 3.02
2120 2170 7.069331 AGTGAATCTCTTGATCGAAGAAGGTAT 59.931 37.037 6.88 0.24 43.58 2.73
2123 2173 8.017418 AATCTCTTGATCGAAGAAGGTATTCT 57.983 34.615 6.88 0.00 43.58 2.40
2163 2213 0.315886 TGCAGCTTTGGACTTGCATG 59.684 50.000 0.00 0.00 41.23 4.06
2175 2226 4.168760 GGACTTGCATGTTAACATTGCTC 58.831 43.478 27.70 21.19 33.61 4.26
2176 2227 4.168760 GACTTGCATGTTAACATTGCTCC 58.831 43.478 27.70 17.28 33.61 4.70
2177 2228 3.573538 ACTTGCATGTTAACATTGCTCCA 59.426 39.130 27.70 15.85 33.61 3.86
2179 2231 3.156293 TGCATGTTAACATTGCTCCAGT 58.844 40.909 27.70 5.87 33.61 4.00
2181 2233 3.922240 GCATGTTAACATTGCTCCAGTTG 59.078 43.478 18.50 6.28 33.61 3.16
2193 2245 5.843673 TGCTCCAGTTGTTTGTATTTTCA 57.156 34.783 0.00 0.00 0.00 2.69
2194 2246 6.214191 TGCTCCAGTTGTTTGTATTTTCAA 57.786 33.333 0.00 0.00 0.00 2.69
2196 2248 7.271511 TGCTCCAGTTGTTTGTATTTTCAAAT 58.728 30.769 0.00 0.00 39.09 2.32
2197 2249 7.224362 TGCTCCAGTTGTTTGTATTTTCAAATG 59.776 33.333 0.00 0.00 39.09 2.32
2221 2274 7.687445 TGTTGATCATCATGAATCTGTTTACG 58.313 34.615 0.00 0.00 0.00 3.18
2232 2285 5.520288 TGAATCTGTTTACGATAGCTTGAGC 59.480 40.000 0.00 0.00 42.67 4.26
2245 2298 3.073144 GCTTGAGCGTTTGGTTTTACA 57.927 42.857 0.00 0.00 0.00 2.41
2247 2300 3.425193 GCTTGAGCGTTTGGTTTTACATG 59.575 43.478 0.00 0.00 0.00 3.21
2248 2301 4.606961 CTTGAGCGTTTGGTTTTACATGT 58.393 39.130 2.69 2.69 0.00 3.21
2249 2302 4.640789 TGAGCGTTTGGTTTTACATGTT 57.359 36.364 2.30 0.00 0.00 2.71
2250 2303 5.000012 TGAGCGTTTGGTTTTACATGTTT 58.000 34.783 2.30 0.00 0.00 2.83
2255 2308 5.276631 GCGTTTGGTTTTACATGTTTCCTTG 60.277 40.000 2.30 0.00 0.00 3.61
2257 2310 6.020201 CGTTTGGTTTTACATGTTTCCTTGTC 60.020 38.462 2.30 0.00 31.92 3.18
2258 2311 5.523438 TGGTTTTACATGTTTCCTTGTCC 57.477 39.130 2.30 0.00 31.92 4.02
2259 2312 4.342665 TGGTTTTACATGTTTCCTTGTCCC 59.657 41.667 2.30 0.00 31.92 4.46
2267 2320 1.423921 GTTTCCTTGTCCCCTTCAGGA 59.576 52.381 0.00 0.00 38.24 3.86
2279 2332 1.901591 CTTCAGGAAAGGAGCTGCAA 58.098 50.000 8.35 0.00 0.00 4.08
2300 2353 6.207221 TGCAAAAGATGAAAGCTCTGAATGTA 59.793 34.615 0.00 0.00 0.00 2.29
2303 2356 7.992754 AAAGATGAAAGCTCTGAATGTACTT 57.007 32.000 0.00 0.00 0.00 2.24
2306 2359 4.326826 TGAAAGCTCTGAATGTACTTGGG 58.673 43.478 0.00 0.00 0.00 4.12
2324 2377 4.699522 AAGCTTCCGCCCACCGAC 62.700 66.667 0.00 0.00 40.02 4.79
2333 2386 2.108976 CCCACCGACCATCCATCG 59.891 66.667 0.00 0.00 39.33 3.84
2459 2528 0.670546 ATGACGAACTCTTGCCACCG 60.671 55.000 0.00 0.00 0.00 4.94
2463 2532 0.673644 CGAACTCTTGCCACCGGAAT 60.674 55.000 9.46 0.00 0.00 3.01
2526 2595 3.505680 AGCTTTTCATGCGTATGTCCAAA 59.494 39.130 13.39 9.85 35.73 3.28
2529 2598 3.840890 TTCATGCGTATGTCCAAAACC 57.159 42.857 13.39 0.00 35.73 3.27
2550 2619 4.081420 ACCTAATGGTAGCTGAACAGACAG 60.081 45.833 5.97 0.00 46.43 3.51
2591 2660 2.163818 GCATAATAGCGGTGCACCTA 57.836 50.000 32.28 19.83 38.68 3.08
2613 2682 1.672881 GCCCGAACTTTGATGGATCTG 59.327 52.381 0.00 0.00 0.00 2.90
3030 3100 8.853077 TGATCTTCTCTGATTCTCTCTATCTC 57.147 38.462 0.00 0.00 0.00 2.75
3031 3101 8.439172 TGATCTTCTCTGATTCTCTCTATCTCA 58.561 37.037 0.00 0.00 0.00 3.27
3161 3234 5.293324 GGTTTTTACCTCTTTGCTTTGTTGG 59.707 40.000 0.00 0.00 0.00 3.77
3165 3238 2.036346 ACCTCTTTGCTTTGTTGGCATC 59.964 45.455 0.00 0.00 39.54 3.91
3174 3247 3.503748 GCTTTGTTGGCATCTCTGTAACT 59.496 43.478 0.00 0.00 0.00 2.24
3176 3249 5.181245 GCTTTGTTGGCATCTCTGTAACTTA 59.819 40.000 0.00 0.00 0.00 2.24
3178 3251 5.483685 TGTTGGCATCTCTGTAACTTAGT 57.516 39.130 0.00 0.00 0.00 2.24
3195 3268 6.852420 ACTTAGTTAGCATACTGAACCTCA 57.148 37.500 1.38 0.00 0.00 3.86
3217 3290 1.381928 CGCCTGAATTGAGCATGGCT 61.382 55.000 0.00 0.00 43.88 4.75
3277 3350 3.749609 TCTAAGACTTCACGACATCGACA 59.250 43.478 8.54 0.00 43.02 4.35
3304 3377 5.062809 GTCAAGGAGATCAAACTAAGCTTCG 59.937 44.000 0.00 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.490328 AAATGCAACCAACTCGTGTG 57.510 45.000 0.00 0.00 0.00 3.82
89 95 3.135225 CACAGGACGTGTTTATCCACAA 58.865 45.455 0.00 0.00 41.03 3.33
90 96 2.365941 TCACAGGACGTGTTTATCCACA 59.634 45.455 0.00 0.00 46.44 4.17
99 105 3.830755 ACTAGGTTAATCACAGGACGTGT 59.169 43.478 0.00 0.00 46.44 4.49
101 107 4.084287 TGACTAGGTTAATCACAGGACGT 58.916 43.478 0.00 0.00 0.00 4.34
102 108 4.713824 TGACTAGGTTAATCACAGGACG 57.286 45.455 0.00 0.00 0.00 4.79
103 109 4.811557 GCATGACTAGGTTAATCACAGGAC 59.188 45.833 0.00 0.00 0.00 3.85
104 110 4.141711 GGCATGACTAGGTTAATCACAGGA 60.142 45.833 0.00 0.00 0.00 3.86
106 112 4.130118 GGGCATGACTAGGTTAATCACAG 58.870 47.826 0.00 0.00 0.00 3.66
107 113 3.780294 AGGGCATGACTAGGTTAATCACA 59.220 43.478 0.00 0.00 0.00 3.58
108 114 4.130118 CAGGGCATGACTAGGTTAATCAC 58.870 47.826 0.00 0.00 0.00 3.06
109 115 3.780294 ACAGGGCATGACTAGGTTAATCA 59.220 43.478 5.99 0.00 0.00 2.57
110 116 4.423625 ACAGGGCATGACTAGGTTAATC 57.576 45.455 5.99 0.00 0.00 1.75
141 154 9.685828 GACTCGCTTATTCTATCTATGAAAAGT 57.314 33.333 0.00 0.00 0.00 2.66
142 155 9.906660 AGACTCGCTTATTCTATCTATGAAAAG 57.093 33.333 0.00 0.00 0.00 2.27
145 158 9.900710 GAAAGACTCGCTTATTCTATCTATGAA 57.099 33.333 0.00 0.00 35.24 2.57
146 159 9.290988 AGAAAGACTCGCTTATTCTATCTATGA 57.709 33.333 0.00 0.00 35.24 2.15
147 160 9.554724 GAGAAAGACTCGCTTATTCTATCTATG 57.445 37.037 0.00 0.00 35.24 2.23
177 190 8.435430 CGACGAGCACATGTATATTGAAAATAT 58.565 33.333 0.00 0.00 0.00 1.28
178 191 7.783209 CGACGAGCACATGTATATTGAAAATA 58.217 34.615 0.00 0.00 0.00 1.40
179 192 6.649436 CGACGAGCACATGTATATTGAAAAT 58.351 36.000 0.00 0.00 0.00 1.82
180 193 6.031549 CGACGAGCACATGTATATTGAAAA 57.968 37.500 0.00 0.00 0.00 2.29
181 194 5.635549 CGACGAGCACATGTATATTGAAA 57.364 39.130 0.00 0.00 0.00 2.69
218 231 2.170166 GATGGCATTCCACCAAGAACA 58.830 47.619 0.00 0.00 46.92 3.18
236 249 1.683418 GGGAAGGCTAACCCGTCGAT 61.683 60.000 12.76 0.00 42.34 3.59
252 266 1.600058 AGATGAAGAGCATTGGGGGA 58.400 50.000 0.00 0.00 37.34 4.81
314 328 5.142639 CAATCCAATCCAATCCACCACTAT 58.857 41.667 0.00 0.00 0.00 2.12
324 338 4.041198 GCATCCAATCCAATCCAATCCAAT 59.959 41.667 0.00 0.00 0.00 3.16
386 400 1.407979 ACTCGGGATTAAGCGTACCAG 59.592 52.381 0.00 0.00 0.00 4.00
387 401 1.135527 CACTCGGGATTAAGCGTACCA 59.864 52.381 0.00 0.00 0.00 3.25
391 405 3.131577 TGTTATCACTCGGGATTAAGCGT 59.868 43.478 0.00 0.00 0.00 5.07
393 407 6.430451 CATTTGTTATCACTCGGGATTAAGC 58.570 40.000 0.00 0.00 0.00 3.09
402 416 8.337532 TCAATTCTATGCATTTGTTATCACTCG 58.662 33.333 3.54 0.00 0.00 4.18
405 419 9.793252 AAGTCAATTCTATGCATTTGTTATCAC 57.207 29.630 3.54 0.00 0.00 3.06
406 420 9.791820 CAAGTCAATTCTATGCATTTGTTATCA 57.208 29.630 3.54 0.00 0.00 2.15
418 432 5.295292 ACTCCGCAATCAAGTCAATTCTATG 59.705 40.000 0.00 0.00 0.00 2.23
446 460 3.446161 CGGAGGGAGTACAAGATGTGTTA 59.554 47.826 0.00 0.00 41.98 2.41
514 528 0.951558 CAAACAGGCAACGGCTAAGT 59.048 50.000 0.00 0.00 46.39 2.24
524 538 4.527509 TTTCTGTGAAAACAAACAGGCA 57.472 36.364 3.21 0.00 43.28 4.75
589 605 9.558396 AGCTCAATTCATATTCTCTCTAAAAGG 57.442 33.333 0.00 0.00 0.00 3.11
769 786 3.000727 ACACGACCTTTACTAATGCTGC 58.999 45.455 0.00 0.00 0.00 5.25
837 871 5.010012 GGTCCATCAACACAACTGAAATTCT 59.990 40.000 0.00 0.00 0.00 2.40
876 910 5.689383 AGAACAAGTTACGCAATCAACAT 57.311 34.783 0.00 0.00 0.00 2.71
886 920 6.678663 CGAATATCAGCAAAGAACAAGTTACG 59.321 38.462 0.00 0.00 0.00 3.18
1080 1118 2.990042 GCTCTGGCTTGCTGATTAGCG 61.990 57.143 4.88 0.00 43.27 4.26
1321 1362 2.738213 CTTTGCTCCTGCGGTCCACT 62.738 60.000 0.00 0.00 43.34 4.00
1384 1425 1.448540 CAGCAGGAGACGCGGAAAT 60.449 57.895 12.47 0.00 35.50 2.17
1442 1483 1.005394 GGAGACGCGGAAACAGGAA 60.005 57.895 12.47 0.00 0.00 3.36
1533 1583 4.608774 TGCAAAGCAGGGGCAGCT 62.609 61.111 0.00 0.00 45.97 4.24
1534 1584 4.368543 GTGCAAAGCAGGGGCAGC 62.369 66.667 0.00 0.00 44.61 5.25
1746 1796 2.500098 AGCCGTAAAGTTCTGAGGCATA 59.500 45.455 7.05 0.00 46.34 3.14
1768 1818 3.882888 ACATTACAAGGCGATGTATTGGG 59.117 43.478 21.30 10.33 39.61 4.12
1857 1907 5.198965 CAATCTTGATCCCCTGATCTTTGT 58.801 41.667 4.39 0.00 46.34 2.83
1923 1973 2.964740 TCTTCTTGTCCTGATTGCTCG 58.035 47.619 0.00 0.00 0.00 5.03
1938 1988 5.599999 ACTTACTGCGGATGTATTCTTCT 57.400 39.130 0.00 0.00 0.00 2.85
1987 2037 5.940192 TGTTTTAGATAGCAGTTGTGGTG 57.060 39.130 0.00 0.00 35.51 4.17
2015 2065 3.733337 AGCACTACAGTTCAGACAAAGG 58.267 45.455 0.00 0.00 0.00 3.11
2054 2104 3.515286 CATGCTTGCTCCGGCCAG 61.515 66.667 2.24 0.00 37.74 4.85
2088 2138 2.001812 TCAAGAGATTCACTGCTCGC 57.998 50.000 0.00 0.00 36.29 5.03
2097 2147 8.141268 AGAATACCTTCTTCGATCAAGAGATTC 58.859 37.037 14.81 14.81 42.37 2.52
2154 2204 4.168760 GGAGCAATGTTAACATGCAAGTC 58.831 43.478 28.61 21.60 36.56 3.01
2155 2205 3.573538 TGGAGCAATGTTAACATGCAAGT 59.426 39.130 28.61 17.30 36.56 3.16
2163 2213 5.348164 ACAAACAACTGGAGCAATGTTAAC 58.652 37.500 0.00 0.00 35.09 2.01
2175 2226 8.877779 TCAACATTTGAAAATACAAACAACTGG 58.122 29.630 0.00 0.00 41.49 4.00
2196 2248 7.548780 TCGTAAACAGATTCATGATGATCAACA 59.451 33.333 8.23 8.23 0.00 3.33
2197 2249 7.909267 TCGTAAACAGATTCATGATGATCAAC 58.091 34.615 0.00 0.00 0.00 3.18
2209 2262 5.331905 CGCTCAAGCTATCGTAAACAGATTC 60.332 44.000 0.00 0.00 39.32 2.52
2221 2274 3.831715 AAACCAAACGCTCAAGCTATC 57.168 42.857 0.00 0.00 39.32 2.08
2232 2285 5.808030 ACAAGGAAACATGTAAAACCAAACG 59.192 36.000 0.00 0.00 41.16 3.60
2238 2291 4.587262 AGGGGACAAGGAAACATGTAAAAC 59.413 41.667 0.00 0.00 43.38 2.43
2239 2292 4.810345 AGGGGACAAGGAAACATGTAAAA 58.190 39.130 0.00 0.00 43.38 1.52
2241 2294 4.141135 TGAAGGGGACAAGGAAACATGTAA 60.141 41.667 0.00 0.00 43.38 2.41
2242 2295 3.396276 TGAAGGGGACAAGGAAACATGTA 59.604 43.478 0.00 0.00 43.38 2.29
2245 2298 2.225117 CCTGAAGGGGACAAGGAAACAT 60.225 50.000 0.00 0.00 31.34 2.71
2247 2300 1.423921 TCCTGAAGGGGACAAGGAAAC 59.576 52.381 0.00 0.00 34.81 2.78
2248 2301 1.827792 TCCTGAAGGGGACAAGGAAA 58.172 50.000 0.00 0.00 34.81 3.13
2249 2302 1.827792 TTCCTGAAGGGGACAAGGAA 58.172 50.000 0.00 0.00 41.55 3.36
2250 2303 1.705186 CTTTCCTGAAGGGGACAAGGA 59.295 52.381 0.00 0.00 35.62 3.36
2267 2320 4.798593 GCTTTCATCTTTTGCAGCTCCTTT 60.799 41.667 0.00 0.00 31.79 3.11
2279 2332 7.094463 CCAAGTACATTCAGAGCTTTCATCTTT 60.094 37.037 0.00 0.00 0.00 2.52
2315 2368 2.203209 GATGGATGGTCGGTGGGC 60.203 66.667 0.00 0.00 0.00 5.36
2318 2371 2.501128 AGCGATGGATGGTCGGTG 59.499 61.111 0.00 0.00 46.56 4.94
2324 2377 1.138859 TGAGTTGGTAGCGATGGATGG 59.861 52.381 0.00 0.00 0.00 3.51
2333 2386 1.897560 AAGTTGGCTGAGTTGGTAGC 58.102 50.000 0.00 0.00 39.17 3.58
2459 2528 0.889994 TGACCATGTTGCAGCATTCC 59.110 50.000 13.95 6.48 0.00 3.01
2550 2619 2.819984 TTTCGGCACCATGAGAGGGC 62.820 60.000 0.00 0.00 0.00 5.19
2591 2660 2.092212 AGATCCATCAAAGTTCGGGCAT 60.092 45.455 0.00 0.00 0.00 4.40
2633 2703 4.202245 TGTTCACAGCAGTTATCTACCC 57.798 45.455 0.00 0.00 0.00 3.69
2674 2744 1.691434 CTGGTCAGAGATTAGGGGAGC 59.309 57.143 0.00 0.00 0.00 4.70
2741 2811 4.749099 TGCAATTAAACAAGATGCAACACC 59.251 37.500 0.00 0.00 43.39 4.16
3030 3100 9.953697 GTTGGACTATAAGAACTAGTAGTGATG 57.046 37.037 2.90 0.00 29.67 3.07
3031 3101 9.696572 TGTTGGACTATAAGAACTAGTAGTGAT 57.303 33.333 2.90 0.00 29.67 3.06
3051 3121 8.501904 TCTCCATATTATTGAGGATTTGTTGGA 58.498 33.333 5.25 0.00 0.00 3.53
3061 3131 8.930846 ACTTCCATTTCTCCATATTATTGAGG 57.069 34.615 5.25 0.00 0.00 3.86
3152 3225 3.503748 AGTTACAGAGATGCCAACAAAGC 59.496 43.478 0.00 0.00 0.00 3.51
3161 3234 8.138712 AGTATGCTAACTAAGTTACAGAGATGC 58.861 37.037 0.00 0.00 0.00 3.91
3165 3238 9.291664 GTTCAGTATGCTAACTAAGTTACAGAG 57.708 37.037 0.00 0.00 34.76 3.35
3174 3247 5.395324 GGCTGAGGTTCAGTATGCTAACTAA 60.395 44.000 7.80 0.00 45.94 2.24
3176 3249 3.118592 GGCTGAGGTTCAGTATGCTAACT 60.119 47.826 7.80 0.00 45.94 2.24
3178 3251 2.159099 CGGCTGAGGTTCAGTATGCTAA 60.159 50.000 7.80 0.00 45.94 3.09
3195 3268 1.077212 ATGCTCAATTCAGGCGGCT 60.077 52.632 5.25 5.25 0.00 5.52
3277 3350 4.822026 CTTAGTTTGATCTCCTTGACGGT 58.178 43.478 0.00 0.00 0.00 4.83
3304 3377 1.789078 CTGCGCCAATGGTATGCTCC 61.789 60.000 4.18 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.