Multiple sequence alignment - TraesCS6B01G282300

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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 TraesCS6B01G282300 chr6B 100.000 5271 0 0 1 5271 508607914 508613184 0.000000e+00 9734.0
1 TraesCS6B01G282300 chr6D 94.036 5315 207 52 1 5271 316100886 316095638 0.000000e+00 7958.0
2 TraesCS6B01G282300 chr6A 92.991 4808 212 61 1 4727 453908170 453903407 0.000000e+00 6896.0
3 TraesCS6B01G282300 chr6A 90.426 470 41 4 4717 5185 453902756 453902290 2.700000e-172 616.0
4 TraesCS6B01G282300 chr6A 80.139 287 38 11 1887 2159 410325005 410324724 4.160000e-46 196.0
5 TraesCS6B01G282300 chr2B 91.555 1338 78 11 1440 2751 199221956 199220628 0.000000e+00 1812.0
6 TraesCS6B01G282300 chr1B 90.800 1337 80 16 1440 2751 342128108 342126790 0.000000e+00 1748.0
7 TraesCS6B01G282300 chr5B 89.776 1340 95 16 1440 2751 356196768 356198093 0.000000e+00 1677.0
8 TraesCS6B01G282300 chr7A 81.053 285 37 10 1887 2159 220118943 220118664 1.490000e-50 211.0
9 TraesCS6B01G282300 chr7A 80.070 286 42 8 1884 2159 121908317 121908597 1.160000e-46 198.0
10 TraesCS6B01G282300 chr3A 80.702 285 42 6 1884 2159 23263288 23263568 5.350000e-50 209.0
11 TraesCS6B01G282300 chr3A 92.727 55 1 3 5093 5145 434000936 434000883 5.660000e-10 76.8
12 TraesCS6B01G282300 chr3A 94.000 50 1 2 5088 5135 35061073 35061122 2.040000e-09 75.0
13 TraesCS6B01G282300 chr3A 94.000 50 1 2 5088 5135 35109276 35109325 2.040000e-09 75.0
14 TraesCS6B01G282300 chr3B 97.826 46 0 1 5092 5136 739570434 739570389 1.570000e-10 78.7
15 TraesCS6B01G282300 chr3B 92.157 51 2 2 5097 5145 419767070 419767020 2.630000e-08 71.3
16 TraesCS6B01G282300 chrUn 92.593 54 3 1 5088 5140 300835219 300835272 5.660000e-10 76.8
17 TraesCS6B01G282300 chr1D 100.000 41 0 0 5097 5137 466370176 466370216 5.660000e-10 76.8
18 TraesCS6B01G282300 chr3D 100.000 40 0 0 5097 5136 557459139 557459100 2.040000e-09 75.0


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 TraesCS6B01G282300 chr6B 508607914 508613184 5270 False 9734 9734 100.0000 1 5271 1 chr6B.!!$F1 5270
1 TraesCS6B01G282300 chr6D 316095638 316100886 5248 True 7958 7958 94.0360 1 5271 1 chr6D.!!$R1 5270
2 TraesCS6B01G282300 chr6A 453902290 453908170 5880 True 3756 6896 91.7085 1 5185 2 chr6A.!!$R2 5184
3 TraesCS6B01G282300 chr2B 199220628 199221956 1328 True 1812 1812 91.5550 1440 2751 1 chr2B.!!$R1 1311
4 TraesCS6B01G282300 chr1B 342126790 342128108 1318 True 1748 1748 90.8000 1440 2751 1 chr1B.!!$R1 1311
5 TraesCS6B01G282300 chr5B 356196768 356198093 1325 False 1677 1677 89.7760 1440 2751 1 chr5B.!!$F1 1311

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
138 152 0.830648 TCAGGCCATGCTAGGTGTAC 59.169 55.000 5.01 0.0 0.00 2.90 F
1038 1103 0.518559 GCTCGTCGTTGATTTTCGCC 60.519 55.000 0.00 0.0 0.00 5.54 F
1880 1967 1.003545 CGGCGCATTGTCCTTAGAATG 60.004 52.381 10.83 0.0 38.94 2.67 F
2054 2141 1.589414 ATAGGAGCTTCAAGCAGGGT 58.411 50.000 13.10 0.0 45.56 4.34 F
3465 3575 1.208293 GACTAAGAGCTGGACCTTGGG 59.792 57.143 0.00 0.0 0.00 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1520 1596 0.716108 CGTCGTCTTGACCTGAATGC 59.284 55.000 0.00 0.0 45.23 3.56 R
3010 3117 1.130955 CCAGTTCACGTTGCATTTGC 58.869 50.000 0.00 0.0 42.50 3.68 R
3044 3151 1.808411 ACGACATGGAGCGTGAAAAT 58.192 45.000 9.26 0.0 39.56 1.82 R
3584 3694 2.020720 TGCTGGCAGAAAAAGAACGAA 58.979 42.857 20.86 0.0 0.00 3.85 R
5061 5847 2.028930 TGCATGCTTCATGATGTGCAAA 60.029 40.909 20.33 8.7 43.81 3.68 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
80 88 5.592282 TGCTCACTCCAGAAACACAATAAAA 59.408 36.000 0.00 0.00 0.00 1.52
94 102 9.705290 AAACACAATAAAAGTTTCACTCAGTTT 57.295 25.926 0.00 0.00 30.19 2.66
138 152 0.830648 TCAGGCCATGCTAGGTGTAC 59.169 55.000 5.01 0.00 0.00 2.90
149 163 7.913821 GCCATGCTAGGTGTACTTTTTATTTAC 59.086 37.037 0.00 0.00 0.00 2.01
222 270 4.154918 CACATCCAAGTTTGAGCCTAAGTC 59.845 45.833 0.00 0.00 0.00 3.01
227 275 3.897141 AGTTTGAGCCTAAGTCTAGCC 57.103 47.619 0.00 0.00 0.00 3.93
319 367 5.571784 TGTTCTCGTGTCTTATCCGTAAT 57.428 39.130 0.00 0.00 0.00 1.89
533 587 8.141909 TGTGCAATGTAGGAGTATAATCACTAC 58.858 37.037 15.83 15.83 35.71 2.73
552 606 1.528161 ACGGCCTTTTACGTTTTCTCG 59.472 47.619 0.00 0.00 40.99 4.04
568 622 2.912025 CGGTGGGCAAAGGCAAGT 60.912 61.111 0.00 0.00 43.71 3.16
569 623 1.602323 CGGTGGGCAAAGGCAAGTA 60.602 57.895 0.00 0.00 43.71 2.24
622 676 5.508224 CGCTCGAATTTTTCTGGTGATTTAC 59.492 40.000 0.00 0.00 0.00 2.01
691 753 2.934553 TGAGAGAGCAAGCAATTCATCG 59.065 45.455 0.00 0.00 0.00 3.84
790 852 7.723324 ACACACGGAATAAAGTAGTAGCATAT 58.277 34.615 0.00 0.00 0.00 1.78
808 870 5.719085 AGCATATAAATCACCAACCACCAAA 59.281 36.000 0.00 0.00 0.00 3.28
930 995 2.433491 CGTCAATGTCGCCGGGAA 60.433 61.111 2.18 0.00 0.00 3.97
963 1028 3.614870 GCAAAGCGAACCCATTCATTTCT 60.615 43.478 0.00 0.00 34.14 2.52
964 1029 3.855689 AAGCGAACCCATTCATTTCTG 57.144 42.857 0.00 0.00 34.14 3.02
994 1059 3.700350 CCCTCCACCCTCCCTCCT 61.700 72.222 0.00 0.00 0.00 3.69
998 1063 2.184631 TCCACCCTCCCTCCTTCCT 61.185 63.158 0.00 0.00 0.00 3.36
1038 1103 0.518559 GCTCGTCGTTGATTTTCGCC 60.519 55.000 0.00 0.00 0.00 5.54
1045 1110 2.395360 TTGATTTTCGCCTCGGCCG 61.395 57.895 22.12 22.12 37.98 6.13
1132 1198 4.378774 CTCCTATGTCTCTTCCAATGCAG 58.621 47.826 0.00 0.00 0.00 4.41
1147 1213 1.008875 TGCAGACGATTCACGAGTGC 61.009 55.000 0.00 0.00 46.10 4.40
1186 1252 2.894731 TCTCTCATCAGGTTCAGGTGT 58.105 47.619 0.00 0.00 0.00 4.16
1282 1349 5.384063 TTTTCTCCGCATTCTGCAAAATA 57.616 34.783 0.00 0.00 45.36 1.40
1306 1373 2.019807 ACCCTCCGTGGTTTTCTCTA 57.980 50.000 0.00 0.00 33.91 2.43
1332 1399 3.243035 TGGTTGAACTGAATTCTTGTGCG 60.243 43.478 7.05 0.00 38.25 5.34
1510 1577 5.186992 TCGAGGTTCAGGTTTGATCAGAATA 59.813 40.000 0.00 0.00 32.27 1.75
1516 1583 7.121168 GGTTCAGGTTTGATCAGAATATGTTCA 59.879 37.037 4.92 0.00 36.14 3.18
1520 1596 9.297586 CAGGTTTGATCAGAATATGTTCATTTG 57.702 33.333 4.92 0.00 37.45 2.32
1521 1597 7.977853 AGGTTTGATCAGAATATGTTCATTTGC 59.022 33.333 4.92 0.00 37.45 3.68
1522 1598 7.760794 GGTTTGATCAGAATATGTTCATTTGCA 59.239 33.333 4.92 0.00 37.45 4.08
1622 1698 4.965762 CACGATAACAAGTAAGCATGCATG 59.034 41.667 22.70 22.70 0.00 4.06
1652 1728 5.121380 ACATACATGCTCCAGGATTCTTT 57.879 39.130 0.00 0.00 0.00 2.52
1669 1745 7.671398 AGGATTCTTTATTTGGTTCTGATGTGT 59.329 33.333 0.00 0.00 0.00 3.72
1797 1873 3.127533 GCCAGCACCGACATGGAC 61.128 66.667 0.00 0.00 42.00 4.02
1823 1901 1.302033 CCCCTGACACAGTGAGCAC 60.302 63.158 7.81 0.00 0.00 4.40
1824 1902 1.750930 CCCTGACACAGTGAGCACT 59.249 57.895 7.81 0.00 43.61 4.40
1861 1948 5.188327 TCACTGGTTTCTATGATCTAGCG 57.812 43.478 0.00 0.00 0.00 4.26
1862 1949 4.038042 TCACTGGTTTCTATGATCTAGCGG 59.962 45.833 0.00 0.00 0.00 5.52
1872 1959 1.560860 GATCTAGCGGCGCATTGTCC 61.561 60.000 35.02 14.13 0.00 4.02
1874 1961 1.815421 CTAGCGGCGCATTGTCCTT 60.815 57.895 35.02 13.23 0.00 3.36
1880 1967 1.003545 CGGCGCATTGTCCTTAGAATG 60.004 52.381 10.83 0.00 38.94 2.67
1885 1972 5.343249 GCGCATTGTCCTTAGAATGAAATT 58.657 37.500 0.30 0.00 38.36 1.82
1909 1996 5.387113 TTGGCATTCCACCAACTATATCT 57.613 39.130 0.00 0.00 42.23 1.98
2054 2141 1.589414 ATAGGAGCTTCAAGCAGGGT 58.411 50.000 13.10 0.00 45.56 4.34
2096 2183 6.950619 TGAGATTGGCTAGCTCTATCATCTAA 59.049 38.462 15.72 3.50 0.00 2.10
2103 2190 6.542370 GGCTAGCTCTATCATCTAAGTAGGAG 59.458 46.154 15.72 0.00 0.00 3.69
2260 2347 7.721842 TCACATGTTTATTTAGAAACCTGACCA 59.278 33.333 10.71 0.00 37.20 4.02
2336 2429 4.689612 TTAGACTTGACAGGCTTGAAGT 57.310 40.909 1.40 2.36 32.45 3.01
2540 2643 8.767478 AATTGTGAAAAGAGCAAATATGGAAG 57.233 30.769 0.00 0.00 0.00 3.46
2541 2644 5.713025 TGTGAAAAGAGCAAATATGGAAGC 58.287 37.500 0.00 0.00 0.00 3.86
2559 2663 2.522185 AGCAGGACAATGTTCAAGCAT 58.478 42.857 10.87 0.00 0.00 3.79
2563 2667 4.619863 GCAGGACAATGTTCAAGCATCATT 60.620 41.667 4.57 0.00 32.93 2.57
2637 2741 1.746615 CTTCCAGGCCGGTGTCATG 60.747 63.158 1.90 0.00 35.57 3.07
2827 2934 7.814107 TCCAAAAATCATGATTCTAAAGTGTGC 59.186 33.333 20.95 0.00 0.00 4.57
3010 3117 6.976925 GGGATAACAATCTTCAGCAAAATCAG 59.023 38.462 0.00 0.00 0.00 2.90
3044 3151 4.935205 GTGAACTGGTGCTGTATATTGACA 59.065 41.667 0.00 0.00 0.00 3.58
3092 3199 6.640518 ACTCACTGTTTTAGTTCAGTTCAGA 58.359 36.000 0.00 0.00 42.05 3.27
3103 3210 6.672266 AGTTCAGTTCAGATCCTAGTTTGA 57.328 37.500 0.00 0.00 0.00 2.69
3104 3211 6.459923 AGTTCAGTTCAGATCCTAGTTTGAC 58.540 40.000 0.00 0.00 0.00 3.18
3108 3215 8.367660 TCAGTTCAGATCCTAGTTTGACTAAT 57.632 34.615 0.00 0.00 29.00 1.73
3143 3250 9.670279 CATCAGGATTTTGATGCTTTTGCTTGC 62.670 40.741 3.37 0.00 45.49 4.01
3166 3273 6.660521 TGCTTCTCACTGTTTGAATCCATAAT 59.339 34.615 0.00 0.00 32.21 1.28
3202 3309 9.976511 AAAAGGCAGATAATGATGAATGTTATG 57.023 29.630 0.00 0.00 0.00 1.90
3350 3457 3.194542 TGATTACCATTTTTCCCTTGCCG 59.805 43.478 0.00 0.00 0.00 5.69
3465 3575 1.208293 GACTAAGAGCTGGACCTTGGG 59.792 57.143 0.00 0.00 0.00 4.12
3479 3589 3.388913 ACCTTGGGAATGGAAAACCAAA 58.611 40.909 0.00 0.00 41.96 3.28
3584 3694 4.444876 GGATATGCCATGGTGTCTACTGTT 60.445 45.833 14.67 0.00 36.34 3.16
3617 3728 2.545526 CTGCCAGCAGTTAATATGGTCG 59.454 50.000 11.55 0.00 39.10 4.79
4039 4153 2.877300 GCTCAGTTTCCAGATGCTTGGA 60.877 50.000 1.71 1.71 45.34 3.53
4163 4277 1.531149 CGTGTTTGCTTCGTCTTCCAT 59.469 47.619 0.00 0.00 0.00 3.41
4275 4391 6.551227 AGAAATGTAAAGGCTGAAAAGGAAGT 59.449 34.615 0.00 0.00 0.00 3.01
4286 4402 6.374333 GGCTGAAAAGGAAGTATGTGTTATCA 59.626 38.462 0.00 0.00 0.00 2.15
4301 4417 5.104941 TGTGTTATCAATCCTAGTGACCCTG 60.105 44.000 0.00 0.00 0.00 4.45
4318 4434 3.818773 ACCCTGTTTCAAAATGTAGGACG 59.181 43.478 0.00 0.00 0.00 4.79
4329 4445 7.292292 TCAAAATGTAGGACGTATTTTGTTCG 58.708 34.615 23.01 7.39 45.26 3.95
4348 4464 7.812309 TGTTCGTAGACTTTGATCAATAGTG 57.188 36.000 20.69 10.64 34.32 2.74
4395 4511 9.743057 AATTGATAGAAATTCGTGTTCAAAACA 57.257 25.926 6.89 0.00 39.52 2.83
4396 4512 9.912634 ATTGATAGAAATTCGTGTTCAAAACAT 57.087 25.926 0.00 0.00 44.35 2.71
4512 4634 5.545723 ACATATCTCTGAATTGGGGGAGTAG 59.454 44.000 0.00 0.00 0.00 2.57
4727 5512 9.893305 AAATTACTTTGAAGAATTAGGTGTTCG 57.107 29.630 0.00 0.00 0.00 3.95
4766 5551 7.114754 AGAAACATAGAAATGCTTCCATGAGA 58.885 34.615 0.00 0.00 38.45 3.27
4775 5560 3.785486 TGCTTCCATGAGATTGTACTCG 58.215 45.455 0.00 0.00 39.49 4.18
4776 5561 3.195610 TGCTTCCATGAGATTGTACTCGT 59.804 43.478 0.00 0.00 39.49 4.18
4825 5611 8.911918 TGCAAACTAGTTTATAGGAAAACTGA 57.088 30.769 20.15 0.00 46.49 3.41
4850 5636 9.901172 GAAAGACCCTAAAAATACATTCCTCTA 57.099 33.333 0.00 0.00 0.00 2.43
4915 5701 5.670485 TCATGACGGTATTAGATTGCAGTT 58.330 37.500 0.00 0.00 0.00 3.16
5076 5862 3.855379 CGACCAATTTGCACATCATGAAG 59.145 43.478 0.00 0.00 0.00 3.02
5141 5927 5.662674 ACTTTACAGAGGGAGTACATGAC 57.337 43.478 0.00 0.00 0.00 3.06
5161 5947 7.545965 ACATGACTGTCGTCCTAGAAATAAAAG 59.454 37.037 0.00 0.00 39.47 2.27
5162 5948 6.989659 TGACTGTCGTCCTAGAAATAAAAGT 58.010 36.000 2.98 0.00 39.47 2.66
5163 5949 6.866770 TGACTGTCGTCCTAGAAATAAAAGTG 59.133 38.462 2.98 0.00 39.47 3.16
5164 5950 6.756221 ACTGTCGTCCTAGAAATAAAAGTGT 58.244 36.000 0.00 0.00 0.00 3.55
5169 5957 7.333672 GTCGTCCTAGAAATAAAAGTGTGGATT 59.666 37.037 0.00 0.00 0.00 3.01
5171 5959 8.818057 CGTCCTAGAAATAAAAGTGTGGATTAG 58.182 37.037 0.00 0.00 0.00 1.73
5186 5974 9.620259 AGTGTGGATTAGAGATAATCTTTTTCC 57.380 33.333 7.67 0.00 39.64 3.13
5187 5975 9.620259 GTGTGGATTAGAGATAATCTTTTTCCT 57.380 33.333 7.67 0.00 39.64 3.36
5236 6024 1.496060 TGCCCCCATACTGAGTACTG 58.504 55.000 0.00 0.00 0.00 2.74
5255 6043 1.898154 CCTGGTACTCCCAAGTCCG 59.102 63.158 0.00 0.00 44.65 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.244721 GCAATGTGAGTTTCCAGGGC 59.755 55.000 0.00 0.00 0.00 5.19
94 102 4.096833 GCTTCCATGTCATACAGATTTGCA 59.903 41.667 0.00 0.00 0.00 4.08
222 270 6.879400 TCTTTCTTCTTAGCTTAAGGGCTAG 58.121 40.000 4.29 0.00 44.23 3.42
260 308 6.096282 GGACCCAGTTATTGCTTGCTTTAATA 59.904 38.462 0.00 0.00 0.00 0.98
319 367 4.555262 GAGGTTTTCAATCATTTTCGCCA 58.445 39.130 0.00 0.00 0.00 5.69
420 468 1.462283 CGTTCGGTACTCTTCTCGACA 59.538 52.381 0.00 0.00 0.00 4.35
423 471 2.888513 TTCGTTCGGTACTCTTCTCG 57.111 50.000 0.00 0.00 0.00 4.04
479 527 7.956328 ATTAAGAAGTACAAAAAGGGGATCC 57.044 36.000 1.92 1.92 0.00 3.36
533 587 1.136169 CCGAGAAAACGTAAAAGGCCG 60.136 52.381 0.00 0.00 0.00 6.13
552 606 0.532115 CATACTTGCCTTTGCCCACC 59.468 55.000 0.00 0.00 36.33 4.61
568 622 6.496218 AGAGATAGTGAGATCATGTTGCCATA 59.504 38.462 0.00 0.00 0.00 2.74
569 623 5.307456 AGAGATAGTGAGATCATGTTGCCAT 59.693 40.000 0.00 0.00 0.00 4.40
691 753 2.829741 TTTTACCCAAATGCACTGGC 57.170 45.000 10.63 0.00 41.68 4.85
712 774 2.380064 TCATGTTTTGGGAGCACCTT 57.620 45.000 0.00 0.00 41.11 3.50
765 827 5.395682 TGCTACTACTTTATTCCGTGTGT 57.604 39.130 0.00 0.00 0.00 3.72
815 878 9.771534 GAACAGCACTATTCCTTTATCTAATCT 57.228 33.333 0.00 0.00 0.00 2.40
865 930 0.385390 CTGGCAGTTTGCGTTTTCCT 59.615 50.000 6.28 0.00 46.21 3.36
866 931 1.215014 GCTGGCAGTTTGCGTTTTCC 61.215 55.000 17.16 0.00 46.21 3.13
963 1028 1.132527 TGGAGGGGAGGAAGAAAGACA 60.133 52.381 0.00 0.00 0.00 3.41
964 1029 1.279558 GTGGAGGGGAGGAAGAAAGAC 59.720 57.143 0.00 0.00 0.00 3.01
994 1059 1.663911 TTCGGGGGAGAAATGAGGAA 58.336 50.000 0.00 0.00 0.00 3.36
998 1063 0.179056 GCGATTCGGGGGAGAAATGA 60.179 55.000 8.34 0.00 33.43 2.57
1056 1121 1.608283 CCCAACCTTTCTGTCGAGGAC 60.608 57.143 0.00 0.00 36.84 3.85
1132 1198 3.374330 CGGCACTCGTGAATCGTC 58.626 61.111 0.39 0.00 40.80 4.20
1155 1221 1.555075 TGATGAGAGAAACGGGGAAGG 59.445 52.381 0.00 0.00 0.00 3.46
1186 1252 2.989639 CTCCTCCCACCATTGCGA 59.010 61.111 0.00 0.00 0.00 5.10
1288 1355 1.403780 CGTAGAGAAAACCACGGAGGG 60.404 57.143 1.11 0.00 43.89 4.30
1306 1373 4.398044 ACAAGAATTCAGTTCAACCAACGT 59.602 37.500 8.44 0.00 40.32 3.99
1332 1399 3.037485 GCTTGTCCAGCTCGACTAC 57.963 57.895 12.86 0.00 46.27 2.73
1463 1530 2.732412 TCTTCAAGAGCTTCACCGAG 57.268 50.000 0.00 0.00 0.00 4.63
1510 1577 5.244402 TCTTGACCTGAATGCAAATGAACAT 59.756 36.000 0.00 0.00 0.00 2.71
1516 1583 3.189287 GTCGTCTTGACCTGAATGCAAAT 59.811 43.478 0.00 0.00 42.04 2.32
1520 1596 0.716108 CGTCGTCTTGACCTGAATGC 59.284 55.000 0.00 0.00 45.23 3.56
1521 1597 1.986378 GACGTCGTCTTGACCTGAATG 59.014 52.381 18.09 0.00 45.23 2.67
1522 1598 1.887198 AGACGTCGTCTTGACCTGAAT 59.113 47.619 22.05 0.00 45.23 2.57
1622 1698 5.105187 TCCTGGAGCATGTATGTATCTATGC 60.105 44.000 0.00 0.00 44.63 3.14
1626 1702 5.784390 AGAATCCTGGAGCATGTATGTATCT 59.216 40.000 1.52 0.00 0.00 1.98
1627 1703 6.047511 AGAATCCTGGAGCATGTATGTATC 57.952 41.667 1.52 0.00 0.00 2.24
1638 1714 5.654209 AGAACCAAATAAAGAATCCTGGAGC 59.346 40.000 1.52 0.00 0.00 4.70
1652 1728 2.161410 GCGCACACATCAGAACCAAATA 59.839 45.455 0.30 0.00 0.00 1.40
1669 1745 0.890542 AACAAGAAGGCAGATGCGCA 60.891 50.000 14.96 14.96 43.26 6.09
1713 1789 2.180276 TCTGGAGGGTACTCTTTCTGC 58.820 52.381 0.00 0.00 43.46 4.26
1815 1893 9.890629 TGATTATGAGTTTTATTAGTGCTCACT 57.109 29.630 7.73 7.73 45.02 3.41
1861 1948 2.288666 TCATTCTAAGGACAATGCGCC 58.711 47.619 4.18 0.00 31.15 6.53
1862 1949 4.355543 TTTCATTCTAAGGACAATGCGC 57.644 40.909 0.00 0.00 31.15 6.09
1908 1995 7.546250 ACTGAGGGATACATATAAAGGTGAG 57.454 40.000 0.00 0.00 39.74 3.51
1909 1996 7.567250 TGAACTGAGGGATACATATAAAGGTGA 59.433 37.037 0.00 0.00 39.74 4.02
1925 2012 1.884067 GCCTCCTTGTTGAACTGAGGG 60.884 57.143 21.68 12.10 42.32 4.30
2054 2141 2.437895 ACCGAGAGATCGTCGCCA 60.438 61.111 13.33 0.00 36.06 5.69
2096 2183 5.011533 GCAGATCCAACATATGTCTCCTACT 59.988 44.000 9.23 2.63 0.00 2.57
2336 2429 6.978659 CGCAATATTACAGAGTTTGGTAGAGA 59.021 38.462 0.00 0.00 0.00 3.10
2389 2482 6.151817 ACTGCAAAAAGATCCTAAGATGAACC 59.848 38.462 0.00 0.00 30.90 3.62
2538 2641 2.309613 TGCTTGAACATTGTCCTGCTT 58.690 42.857 0.00 0.00 0.00 3.91
2540 2643 2.229543 TGATGCTTGAACATTGTCCTGC 59.770 45.455 0.00 0.00 0.00 4.85
2541 2644 4.713824 ATGATGCTTGAACATTGTCCTG 57.286 40.909 0.00 0.00 0.00 3.86
2584 2688 4.371855 TCTCACGCTCGATCAACTTTAT 57.628 40.909 0.00 0.00 0.00 1.40
2637 2741 2.224646 GGCATCCCTTCCTACCTCAATC 60.225 54.545 0.00 0.00 0.00 2.67
2849 2956 9.309516 CTTGATCATAAAAGTTAATTGCTGCAT 57.690 29.630 1.84 0.00 0.00 3.96
3010 3117 1.130955 CCAGTTCACGTTGCATTTGC 58.869 50.000 0.00 0.00 42.50 3.68
3044 3151 1.808411 ACGACATGGAGCGTGAAAAT 58.192 45.000 9.26 0.00 39.56 1.82
3120 3227 4.378046 GCAAGCAAAAGCATCAAAATCCTG 60.378 41.667 0.00 0.00 0.00 3.86
3121 3228 3.749609 GCAAGCAAAAGCATCAAAATCCT 59.250 39.130 0.00 0.00 0.00 3.24
3321 3428 4.019771 GGGAAAAATGGTAATCAGGCCAAA 60.020 41.667 5.01 0.00 38.38 3.28
3327 3434 4.677779 CGGCAAGGGAAAAATGGTAATCAG 60.678 45.833 0.00 0.00 0.00 2.90
3350 3457 8.810652 TTGCTAAAACATCCACAAAGATTTAC 57.189 30.769 0.00 0.00 0.00 2.01
3479 3589 3.819564 TTGAGCTAACGCCATAGTGAT 57.180 42.857 0.00 0.00 36.60 3.06
3584 3694 2.020720 TGCTGGCAGAAAAAGAACGAA 58.979 42.857 20.86 0.00 0.00 3.85
3617 3728 7.464830 TTTCTGTTATATCAGCGTCTAAAGC 57.535 36.000 6.00 0.00 35.63 3.51
3833 3944 5.359009 CCTCAGCATGTCCTGAAATGTTAAT 59.641 40.000 4.82 0.00 41.02 1.40
3834 3945 4.701651 CCTCAGCATGTCCTGAAATGTTAA 59.298 41.667 4.82 0.00 41.02 2.01
3835 3946 4.019411 TCCTCAGCATGTCCTGAAATGTTA 60.019 41.667 4.82 0.00 41.02 2.41
4275 4391 6.844388 AGGGTCACTAGGATTGATAACACATA 59.156 38.462 0.00 0.00 0.00 2.29
4286 4402 4.993705 TTGAAACAGGGTCACTAGGATT 57.006 40.909 0.00 0.00 0.00 3.01
4301 4417 8.791355 ACAAAATACGTCCTACATTTTGAAAC 57.209 30.769 27.70 0.00 45.79 2.78
4464 4582 7.870445 TGTGGCATATTTTGGTTTTCTAAGTTC 59.130 33.333 0.00 0.00 0.00 3.01
4674 4798 4.898829 TTGTTCTTGTGGTGTGATCAAG 57.101 40.909 0.00 0.00 39.59 3.02
4683 4807 3.883830 TTTGTGCATTGTTCTTGTGGT 57.116 38.095 0.00 0.00 0.00 4.16
4806 5592 9.163899 GGGTCTTTCAGTTTTCCTATAAACTAG 57.836 37.037 0.00 0.00 44.33 2.57
4822 5608 8.581253 AGGAATGTATTTTTAGGGTCTTTCAG 57.419 34.615 0.00 0.00 0.00 3.02
4823 5609 8.390921 AGAGGAATGTATTTTTAGGGTCTTTCA 58.609 33.333 0.00 0.00 0.00 2.69
4850 5636 7.926018 AGCGTTTCTTTGTTGAATAGGAAATTT 59.074 29.630 0.00 0.00 0.00 1.82
4871 5657 6.935741 TGAGCATAATAATAACCAAGCGTT 57.064 33.333 0.00 0.00 38.57 4.84
4915 5701 3.123273 AGCCCTTATTTTAGAGGAGCCA 58.877 45.455 0.00 0.00 34.91 4.75
5048 5834 4.094739 TGATGTGCAAATTGGTCGACATAG 59.905 41.667 18.91 1.73 0.00 2.23
5052 5838 2.987413 TGATGTGCAAATTGGTCGAC 57.013 45.000 7.13 7.13 0.00 4.20
5061 5847 2.028930 TGCATGCTTCATGATGTGCAAA 60.029 40.909 20.33 8.70 43.81 3.68
5076 5862 6.554419 TCACTCTAAATAAACACATGCATGC 58.446 36.000 26.53 11.82 0.00 4.06
5114 5900 9.656323 TCATGTACTCCCTCTGTAAAGTAATAT 57.344 33.333 0.00 0.00 0.00 1.28
5120 5906 5.186021 ACAGTCATGTACTCCCTCTGTAAAG 59.814 44.000 0.00 0.00 38.09 1.85
5129 5915 2.563471 GACGACAGTCATGTACTCCC 57.437 55.000 0.41 0.00 46.32 4.30
5141 5927 6.090898 CCACACTTTTATTTCTAGGACGACAG 59.909 42.308 0.00 0.00 0.00 3.51
5161 5947 9.620259 AGGAAAAAGATTATCTCTAATCCACAC 57.380 33.333 14.37 0.00 42.85 3.82
5185 5973 7.227512 CCTATGCACTTCCTATTCTACAAAAGG 59.772 40.741 0.00 0.00 0.00 3.11
5186 5974 7.254932 GCCTATGCACTTCCTATTCTACAAAAG 60.255 40.741 0.00 0.00 37.47 2.27
5187 5975 6.542370 GCCTATGCACTTCCTATTCTACAAAA 59.458 38.462 0.00 0.00 37.47 2.44
5188 5976 6.055588 GCCTATGCACTTCCTATTCTACAAA 58.944 40.000 0.00 0.00 37.47 2.83
5189 5977 5.130311 TGCCTATGCACTTCCTATTCTACAA 59.870 40.000 0.00 0.00 44.23 2.41
5215 6003 2.439507 CAGTACTCAGTATGGGGGCATT 59.560 50.000 0.00 0.00 44.94 3.56


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

AutoCloner maintained by Alex Coulton.