Multiple sequence alignment - TraesCS7B01G060000

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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 TraesCS7B01G060000 chr7B 100.000 3379 0 0 1 3379 62688897 62685519 0.000000e+00 6240.0
1 TraesCS7B01G060000 chr7B 91.085 258 15 5 1000 1255 134439467 134439216 3.230000e-90 342.0
2 TraesCS7B01G060000 chr7A 88.266 1943 143 32 13 1932 108810303 108808423 0.000000e+00 2246.0
3 TraesCS7B01G060000 chr7A 87.366 839 82 18 1000 1824 418348140 418348968 0.000000e+00 941.0
4 TraesCS7B01G060000 chr7A 88.738 737 53 13 1931 2641 108808354 108807622 0.000000e+00 874.0
5 TraesCS7B01G060000 chr7A 87.282 401 24 7 3000 3379 108807061 108806667 1.860000e-117 433.0
6 TraesCS7B01G060000 chr7A 85.714 70 10 0 2668 2737 108807457 108807388 1.300000e-09 75.0
7 TraesCS7B01G060000 chr7D 88.149 1848 148 38 2 1814 104568151 104566340 0.000000e+00 2134.0
8 TraesCS7B01G060000 chr7D 88.941 642 24 13 2782 3379 104565101 104564463 0.000000e+00 749.0
9 TraesCS7B01G060000 chr7D 93.137 408 15 3 2245 2640 104565912 104565506 1.350000e-163 586.0
10 TraesCS7B01G060000 chr7D 93.548 93 6 0 2669 2761 104565298 104565206 4.550000e-29 139.0
11 TraesCS7B01G060000 chr3B 87.976 840 79 17 1001 1827 632817314 632818144 0.000000e+00 972.0
12 TraesCS7B01G060000 chr5B 89.557 699 60 11 1000 1692 453116850 453116159 0.000000e+00 874.0
13 TraesCS7B01G060000 chr3A 86.473 791 83 19 1051 1827 56494202 56494982 0.000000e+00 846.0
14 TraesCS7B01G060000 chr3A 92.607 257 12 4 1000 1255 71904675 71904925 2.480000e-96 363.0
15 TraesCS7B01G060000 chr1D 92.410 527 33 6 1123 1644 10037457 10037981 0.000000e+00 745.0
16 TraesCS7B01G060000 chr1D 91.985 524 35 6 1126 1644 9923766 9923245 0.000000e+00 728.0
17 TraesCS7B01G060000 chr5A 92.218 257 13 6 1000 1255 43768950 43768700 1.150000e-94 357.0
18 TraesCS7B01G060000 chr5A 81.749 263 30 10 3132 3379 257227613 257227354 1.590000e-48 204.0
19 TraesCS7B01G060000 chr1B 91.235 251 22 0 1439 1689 40285020 40284770 3.230000e-90 342.0
20 TraesCS7B01G060000 chrUn 90.041 241 22 2 1171 1410 74596248 74596487 9.100000e-81 311.0
21 TraesCS7B01G060000 chr1A 83.168 101 6 4 3075 3175 263966329 263966418 7.770000e-12 82.4


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 TraesCS7B01G060000 chr7B 62685519 62688897 3378 True 6240 6240 100.00000 1 3379 1 chr7B.!!$R1 3378
1 TraesCS7B01G060000 chr7A 418348140 418348968 828 False 941 941 87.36600 1000 1824 1 chr7A.!!$F1 824
2 TraesCS7B01G060000 chr7A 108806667 108810303 3636 True 907 2246 87.50000 13 3379 4 chr7A.!!$R1 3366
3 TraesCS7B01G060000 chr7D 104564463 104568151 3688 True 902 2134 90.94375 2 3379 4 chr7D.!!$R1 3377
4 TraesCS7B01G060000 chr3B 632817314 632818144 830 False 972 972 87.97600 1001 1827 1 chr3B.!!$F1 826
5 TraesCS7B01G060000 chr5B 453116159 453116850 691 True 874 874 89.55700 1000 1692 1 chr5B.!!$R1 692
6 TraesCS7B01G060000 chr3A 56494202 56494982 780 False 846 846 86.47300 1051 1827 1 chr3A.!!$F1 776
7 TraesCS7B01G060000 chr1D 10037457 10037981 524 False 745 745 92.41000 1123 1644 1 chr1D.!!$F1 521
8 TraesCS7B01G060000 chr1D 9923245 9923766 521 True 728 728 91.98500 1126 1644 1 chr1D.!!$R1 518

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
313 315 0.035820 AGCGCCCGGATTTACAGAAA 60.036 50.0 0.73 0.0 0.00 2.52 F
1140 1179 0.036732 TTCTTGGTGCGGATTGAGCT 59.963 50.0 0.00 0.0 35.28 4.09 F
1445 1484 0.098376 CTTTCGATGAGCTGCTTGCC 59.902 55.0 2.53 0.0 44.23 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1465 0.098376 GGCAAGCAGCTCATCGAAAG 59.902 55.000 0.00 0.0 44.79 2.62 R
2317 2518 1.466950 GCAACGTTAGCATAGCCAACA 59.533 47.619 14.97 0.0 0.00 3.33 R
2770 3184 1.532868 GCAAGAGATGTTTGCGAGTGT 59.467 47.619 0.00 0.0 41.16 3.55 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
26 27 2.697431 TACCAACAAAAGCATGCGAC 57.303 45.000 13.01 0.00 0.00 5.19
31 32 3.127548 CCAACAAAAGCATGCGACTATCT 59.872 43.478 13.01 0.00 0.00 1.98
50 51 9.781834 GACTATCTAGGATTAAGATGATGAACG 57.218 37.037 0.00 0.00 35.36 3.95
63 64 6.892691 AGATGATGAACGAAACTTTCTTCAC 58.107 36.000 13.84 10.52 38.95 3.18
129 131 1.838112 TGGAGAATCAAGCCGCAATT 58.162 45.000 0.00 0.00 36.25 2.32
134 136 3.018856 AGAATCAAGCCGCAATTGATGA 58.981 40.909 10.34 5.32 44.57 2.92
164 166 6.349300 AGAATGTATACAGCCACAAAGTAGG 58.651 40.000 11.91 0.00 0.00 3.18
194 196 7.522562 GCCTAGAGTGTAATACTTAGGAAGAGC 60.523 44.444 14.13 0.00 40.53 4.09
197 199 6.097129 AGAGTGTAATACTTAGGAAGAGCCAC 59.903 42.308 0.00 0.00 40.53 5.01
208 210 7.567622 ACTTAGGAAGAGCCACATATAACCTAA 59.432 37.037 0.00 0.00 40.02 2.69
220 222 7.061326 CCACATATAACCTAAAAACAACGCAAC 59.939 37.037 0.00 0.00 0.00 4.17
222 224 5.777850 ATAACCTAAAAACAACGCAACCT 57.222 34.783 0.00 0.00 0.00 3.50
227 229 1.326951 AAAACAACGCAACCTGGCCT 61.327 50.000 3.32 0.00 0.00 5.19
231 233 0.887933 CAACGCAACCTGGCCTTAAT 59.112 50.000 3.32 0.00 0.00 1.40
234 236 2.089201 ACGCAACCTGGCCTTAATAAC 58.911 47.619 3.32 0.00 0.00 1.89
253 255 1.063469 ACGGTGAAGCACGAACAAAAG 59.937 47.619 0.00 0.00 34.83 2.27
254 256 1.477105 GGTGAAGCACGAACAAAAGC 58.523 50.000 0.00 0.00 34.83 3.51
293 295 6.310711 GCATATTCGAACCCTAGTAGCATAAC 59.689 42.308 0.00 0.00 0.00 1.89
313 315 0.035820 AGCGCCCGGATTTACAGAAA 60.036 50.000 0.73 0.00 0.00 2.52
316 318 2.540973 GCGCCCGGATTTACAGAAATTC 60.541 50.000 0.73 0.00 35.33 2.17
317 319 2.032924 CGCCCGGATTTACAGAAATTCC 59.967 50.000 0.73 0.00 35.33 3.01
373 376 2.556622 GGGAGAAACTTCCAAATTCGCA 59.443 45.455 0.00 0.00 39.09 5.10
375 378 4.321974 GGGAGAAACTTCCAAATTCGCAAT 60.322 41.667 0.00 0.00 39.09 3.56
380 383 2.161609 ACTTCCAAATTCGCAATCGACC 59.838 45.455 0.00 0.00 45.43 4.79
386 389 2.020836 ATTCGCAATCGACCGAACGC 62.021 55.000 16.34 1.53 44.89 4.84
402 415 2.202298 GCGCCGTCGACAAATTGG 60.202 61.111 17.16 9.22 38.10 3.16
407 420 1.399727 GCCGTCGACAAATTGGTGAAG 60.400 52.381 17.16 0.00 0.00 3.02
420 433 0.462759 GGTGAAGAAGATCGGGGCAG 60.463 60.000 0.00 0.00 0.00 4.85
514 527 2.983592 GTTGAACTGGGCACGGGG 60.984 66.667 0.00 0.00 0.00 5.73
533 546 3.607661 GAGCGGACCTCGGATCCC 61.608 72.222 6.06 0.00 39.69 3.85
720 735 2.504175 GTTAAGTGGACTCATGGGCCTA 59.496 50.000 4.53 0.00 45.52 3.93
750 765 1.299541 CGCAGTGAGGTCAAACAAGT 58.700 50.000 0.00 0.00 0.00 3.16
774 790 3.947173 CCCATGCGGCCCATTTAA 58.053 55.556 0.00 0.00 29.71 1.52
785 801 1.401018 GCCCATTTAACGCTGTGACAC 60.401 52.381 0.00 0.00 0.00 3.67
790 806 2.212869 TTAACGCTGTGACACTCGTT 57.787 45.000 28.20 28.20 45.46 3.85
903 919 0.323629 TGCCTACATATAAGCCGCCC 59.676 55.000 0.00 0.00 0.00 6.13
1020 1046 2.741092 GTGAAGGGACGCACTGGA 59.259 61.111 0.00 0.00 36.05 3.86
1085 1121 2.747855 GTGAGCGGCCCCTTCTTG 60.748 66.667 0.00 0.00 0.00 3.02
1086 1122 4.033776 TGAGCGGCCCCTTCTTGG 62.034 66.667 0.00 0.00 0.00 3.61
1124 1160 3.563223 CTGGATCTGGCCATTCATTTCT 58.437 45.455 5.51 0.00 37.30 2.52
1140 1179 0.036732 TTCTTGGTGCGGATTGAGCT 59.963 50.000 0.00 0.00 35.28 4.09
1435 1474 0.179084 CCGCCCTTAGCTTTCGATGA 60.179 55.000 0.00 0.00 40.39 2.92
1445 1484 0.098376 CTTTCGATGAGCTGCTTGCC 59.902 55.000 2.53 0.00 44.23 4.52
1452 1495 2.114625 AGCTGCTTGCCTGCTTGA 59.885 55.556 0.00 0.00 45.16 3.02
1485 1528 2.739609 GCTGAGGCTGTTTGTTGCTTTT 60.740 45.455 0.00 0.00 35.22 2.27
1486 1529 2.861935 CTGAGGCTGTTTGTTGCTTTTG 59.138 45.455 0.00 0.00 0.00 2.44
1487 1530 2.233431 TGAGGCTGTTTGTTGCTTTTGT 59.767 40.909 0.00 0.00 0.00 2.83
1516 1562 3.712907 GGGCGCAAGGTCAGGGTA 61.713 66.667 10.83 0.00 38.28 3.69
1585 1634 4.440758 CGTTGATGTTTGTTTAAGGCTGTG 59.559 41.667 0.00 0.00 0.00 3.66
1591 1640 3.726291 TTGTTTAAGGCTGTGGCTTTC 57.274 42.857 11.42 4.64 46.16 2.62
1619 1669 5.525012 TGCATGATTTACTCTAGCATGTGTC 59.475 40.000 0.00 0.00 38.76 3.67
1678 1728 9.354673 GGATGGATTTTATAGAATTCCAAGTGA 57.645 33.333 0.65 0.00 0.00 3.41
1731 1781 3.384146 TGAACTTGTGCAATGTGTCCATT 59.616 39.130 0.00 0.00 42.03 3.16
1761 1818 2.685106 TGGTTTGGCTTGGGTCAATA 57.315 45.000 0.00 0.00 36.89 1.90
1783 1844 4.908601 TGGTTGATGTAGGATTCTGTGT 57.091 40.909 0.00 0.00 0.00 3.72
1789 1850 7.301054 GTTGATGTAGGATTCTGTGTTCTTTG 58.699 38.462 0.00 0.00 0.00 2.77
1790 1851 6.768483 TGATGTAGGATTCTGTGTTCTTTGA 58.232 36.000 0.00 0.00 0.00 2.69
1791 1852 7.397221 TGATGTAGGATTCTGTGTTCTTTGAT 58.603 34.615 0.00 0.00 0.00 2.57
1793 1854 8.641498 ATGTAGGATTCTGTGTTCTTTGATTT 57.359 30.769 0.00 0.00 0.00 2.17
1794 1855 7.874940 TGTAGGATTCTGTGTTCTTTGATTTG 58.125 34.615 0.00 0.00 0.00 2.32
1816 1877 4.889409 TGTTTTATCCCTGAATGATGCCTC 59.111 41.667 0.00 0.00 0.00 4.70
1866 1940 3.198068 CTGTGTATCCAGTTTGATCCGG 58.802 50.000 0.00 0.00 0.00 5.14
1867 1941 2.093181 TGTGTATCCAGTTTGATCCGGG 60.093 50.000 0.00 0.00 0.00 5.73
1901 1975 9.950680 TCAATTATTATTAGCTTTGTTGCTAGC 57.049 29.630 8.10 8.10 44.94 3.42
1911 1985 4.676924 GCTTTGTTGCTAGCTTTAGTGTTG 59.323 41.667 17.23 0.00 34.57 3.33
1915 1989 4.272504 TGTTGCTAGCTTTAGTGTTGTGTC 59.727 41.667 17.23 0.00 0.00 3.67
1917 1991 4.058124 TGCTAGCTTTAGTGTTGTGTCTG 58.942 43.478 17.23 0.00 0.00 3.51
1927 2001 3.378112 AGTGTTGTGTCTGTGGAATGTTG 59.622 43.478 0.00 0.00 0.00 3.33
1935 2079 6.017192 TGTGTCTGTGGAATGTTGTTTAGATG 60.017 38.462 0.00 0.00 0.00 2.90
1963 2107 3.304391 GCTTGTGCCGTTTGTCAATCTAA 60.304 43.478 0.00 0.00 0.00 2.10
1991 2141 5.255397 TCACAGTATGAAAAGTGGGGAAT 57.745 39.130 0.00 0.00 39.69 3.01
1992 2142 5.009631 TCACAGTATGAAAAGTGGGGAATG 58.990 41.667 0.00 0.00 39.69 2.67
1999 2149 3.572255 TGAAAAGTGGGGAATGCACTTAC 59.428 43.478 0.00 0.00 38.10 2.34
2002 2152 3.004752 AGTGGGGAATGCACTTACATC 57.995 47.619 0.00 0.00 0.00 3.06
2016 2167 8.055609 TGCACTTACATCAAACGTTTTTATTG 57.944 30.769 11.66 8.95 0.00 1.90
2017 2168 7.702772 TGCACTTACATCAAACGTTTTTATTGT 59.297 29.630 11.66 13.93 0.00 2.71
2018 2172 8.536407 GCACTTACATCAAACGTTTTTATTGTT 58.464 29.630 11.66 0.00 0.00 2.83
2070 2224 5.437289 TTTGTACCTCAAACTGCTGATTG 57.563 39.130 7.19 7.19 40.56 2.67
2075 2229 4.936891 ACCTCAAACTGCTGATTGTTTTC 58.063 39.130 12.22 0.00 34.60 2.29
2124 2306 9.726438 AGGTATTAGATTTGATGTTATGGTAGC 57.274 33.333 0.00 0.00 0.00 3.58
2186 2377 5.184892 ACATCAGAAGTTTGAGGGCTATT 57.815 39.130 5.25 0.00 33.41 1.73
2204 2395 5.928264 GGCTATTATTTCATTGGAATGCCAC 59.072 40.000 10.47 0.00 45.94 5.01
2215 2406 5.659440 TTGGAATGCCACTCCTTATTTTC 57.341 39.130 0.00 0.00 45.94 2.29
2229 2420 7.088589 TCCTTATTTTCAGCAGCATAAAGTC 57.911 36.000 0.00 0.00 0.00 3.01
2230 2421 6.886459 TCCTTATTTTCAGCAGCATAAAGTCT 59.114 34.615 0.00 0.00 0.00 3.24
2251 2452 4.697352 TCTGCCTTATTTTCTGCTGTCTTC 59.303 41.667 0.00 0.00 0.00 2.87
2282 2483 7.279313 GCCTCAAATTATGAACATGATTTGCTT 59.721 33.333 25.89 4.99 46.05 3.91
2317 2518 3.306225 GCCATGTTTGACACATCCATTGT 60.306 43.478 0.00 0.00 43.17 2.71
2466 2678 5.065218 GCAACCGAAACTGATCATGTATTCT 59.935 40.000 0.00 0.00 0.00 2.40
2577 2789 5.879237 TGTCATGAGTTTGTGACTGTTTTC 58.121 37.500 0.00 0.00 43.87 2.29
2586 2798 6.934083 AGTTTGTGACTGTTTTCCAATGTTTT 59.066 30.769 0.00 0.00 37.17 2.43
2632 2846 8.260114 TCTGCTGTTTGATCTTATGATAACTCA 58.740 33.333 0.00 0.00 35.41 3.41
2634 2848 8.886719 TGCTGTTTGATCTTATGATAACTCAAG 58.113 33.333 0.00 0.00 34.37 3.02
2661 2918 1.213430 TCCTGATGCCAGCATGAATGA 59.787 47.619 10.41 0.00 39.69 2.57
2663 2920 2.029918 CCTGATGCCAGCATGAATGATG 60.030 50.000 10.41 1.53 43.38 3.07
2689 3103 8.135529 GGTCTATTTATTTATGTTCTTGTGGCC 58.864 37.037 0.00 0.00 0.00 5.36
2690 3104 8.903820 GTCTATTTATTTATGTTCTTGTGGCCT 58.096 33.333 3.32 0.00 0.00 5.19
2696 3110 0.764890 TGTTCTTGTGGCCTGCTAGT 59.235 50.000 3.32 0.00 0.00 2.57
2702 3116 2.359850 TGGCCTGCTAGTTTGGCG 60.360 61.111 3.32 0.00 46.97 5.69
2703 3117 2.046314 GGCCTGCTAGTTTGGCGA 60.046 61.111 13.70 0.00 46.97 5.54
2812 3310 4.792704 GCATCTGGCATAATAAACCAACGG 60.793 45.833 0.00 0.00 43.97 4.44
2919 3490 3.055094 ACAACTGGCCACTAGACCATAAG 60.055 47.826 0.00 0.00 34.82 1.73
2921 3492 0.837272 TGGCCACTAGACCATAAGGC 59.163 55.000 0.00 0.00 41.29 4.35
2922 3493 0.837272 GGCCACTAGACCATAAGGCA 59.163 55.000 0.00 0.00 43.72 4.75
2923 3494 1.202698 GGCCACTAGACCATAAGGCAG 60.203 57.143 0.00 0.00 43.72 4.85
2932 3504 5.184892 AGACCATAAGGCAGACAAAGATT 57.815 39.130 0.00 0.00 39.06 2.40
2945 3517 6.527023 GCAGACAAAGATTCATCAAAGTCATG 59.473 38.462 0.00 0.00 0.00 3.07
2970 3542 2.031157 CCTTTAGGTTTGAGTGGCAACG 60.031 50.000 0.00 0.00 35.91 4.10
2971 3543 2.335316 TTAGGTTTGAGTGGCAACGT 57.665 45.000 0.00 0.00 35.91 3.99
2972 3544 3.472283 TTAGGTTTGAGTGGCAACGTA 57.528 42.857 0.00 0.00 35.91 3.57
2973 3545 1.878953 AGGTTTGAGTGGCAACGTAG 58.121 50.000 0.00 0.00 35.91 3.51
2975 3547 1.529865 GGTTTGAGTGGCAACGTAGTC 59.470 52.381 0.00 0.00 45.00 2.59
2976 3548 2.480845 GTTTGAGTGGCAACGTAGTCT 58.519 47.619 0.00 0.00 45.00 3.24
2977 3549 2.433868 TTGAGTGGCAACGTAGTCTC 57.566 50.000 0.00 0.00 45.00 3.36
2978 3550 1.617322 TGAGTGGCAACGTAGTCTCT 58.383 50.000 0.00 0.00 45.00 3.10
2989 3566 2.308275 ACGTAGTCTCTCCCTTGGTACT 59.692 50.000 0.00 0.00 29.74 2.73
3032 3609 1.012486 CGCGGTTACAGGAGTTGGTC 61.012 60.000 0.00 0.00 0.00 4.02
3054 3632 3.242712 CGCGATTTTATTTGACCAATGCC 59.757 43.478 0.00 0.00 0.00 4.40
3062 3640 4.996788 ATTTGACCAATGCCTCTCATTC 57.003 40.909 0.00 0.00 43.21 2.67
3065 3643 3.765381 TGACCAATGCCTCTCATTCAAA 58.235 40.909 0.00 0.00 43.21 2.69
3066 3644 4.346730 TGACCAATGCCTCTCATTCAAAT 58.653 39.130 0.00 0.00 43.21 2.32
3125 3716 5.979993 TGCAAGATATTTTTCATGTGCCAT 58.020 33.333 0.00 0.00 0.00 4.40
3199 3790 6.720288 AGTACTATAGCGGGAGATGTTATGTT 59.280 38.462 0.00 0.00 0.00 2.71
3277 3868 2.867287 TTGCCATTGTTGTGTGTCTG 57.133 45.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.576384 CGCATGCTTTTGTTGGTATTTATGT 59.424 36.000 17.13 0.00 0.00 2.29
7 8 2.226330 AGTCGCATGCTTTTGTTGGTA 58.774 42.857 17.13 0.00 0.00 3.25
11 12 4.572389 CCTAGATAGTCGCATGCTTTTGTT 59.428 41.667 17.13 0.00 0.00 2.83
31 32 9.667107 AAAGTTTCGTTCATCATCTTAATCCTA 57.333 29.630 0.00 0.00 0.00 2.94
50 51 5.273944 AGTGAAATGCGTGAAGAAAGTTTC 58.726 37.500 7.57 7.57 0.00 2.78
63 64 2.050477 AAAAAGCCGAGTGAAATGCG 57.950 45.000 0.00 0.00 0.00 4.73
122 124 5.237996 ACATTCTAGTCATCATCAATTGCGG 59.762 40.000 0.00 0.00 0.00 5.69
129 131 7.233348 TGGCTGTATACATTCTAGTCATCATCA 59.767 37.037 5.91 0.00 0.00 3.07
134 136 6.731292 TGTGGCTGTATACATTCTAGTCAT 57.269 37.500 5.91 0.00 0.00 3.06
164 166 6.015350 TCCTAAGTATTACACTCTAGGCATGC 60.015 42.308 9.90 9.90 37.63 4.06
194 196 6.613233 TGCGTTGTTTTTAGGTTATATGTGG 58.387 36.000 0.00 0.00 0.00 4.17
197 199 7.272515 CAGGTTGCGTTGTTTTTAGGTTATATG 59.727 37.037 0.00 0.00 0.00 1.78
203 205 2.100087 CCAGGTTGCGTTGTTTTTAGGT 59.900 45.455 0.00 0.00 0.00 3.08
208 210 1.142965 GGCCAGGTTGCGTTGTTTT 59.857 52.632 0.00 0.00 0.00 2.43
220 222 2.702592 TCACCGTTATTAAGGCCAGG 57.297 50.000 5.01 0.00 0.00 4.45
222 224 2.290387 TGCTTCACCGTTATTAAGGCCA 60.290 45.455 5.01 0.00 0.00 5.36
227 229 4.056740 TGTTCGTGCTTCACCGTTATTAA 58.943 39.130 0.00 0.00 0.00 1.40
231 233 1.937278 TTGTTCGTGCTTCACCGTTA 58.063 45.000 0.00 0.00 0.00 3.18
234 236 1.741993 CTTTTGTTCGTGCTTCACCG 58.258 50.000 0.00 0.00 0.00 4.94
253 255 4.148348 CGAATATGCTTGGTAACTAGTCGC 59.852 45.833 0.00 0.00 41.86 5.19
254 256 5.516996 TCGAATATGCTTGGTAACTAGTCG 58.483 41.667 0.00 0.00 41.86 4.18
293 295 0.742990 TTCTGTAAATCCGGGCGCTG 60.743 55.000 7.64 0.00 0.00 5.18
313 315 1.455822 TGGTTCCCCTTCACAGGAAT 58.544 50.000 0.00 0.00 44.19 3.01
316 318 2.080654 TTTTGGTTCCCCTTCACAGG 57.919 50.000 0.00 0.00 40.45 4.00
317 319 3.803368 GCAATTTTGGTTCCCCTTCACAG 60.803 47.826 0.00 0.00 0.00 3.66
353 356 3.915437 TGCGAATTTGGAAGTTTCTCC 57.085 42.857 0.00 0.00 35.88 3.71
386 389 1.154488 CACCAATTTGTCGACGGCG 60.154 57.895 2.87 2.87 39.35 6.46
390 393 5.613358 ATCTTCTTCACCAATTTGTCGAC 57.387 39.130 9.11 9.11 0.00 4.20
402 415 0.462759 CCTGCCCCGATCTTCTTCAC 60.463 60.000 0.00 0.00 0.00 3.18
407 420 2.812619 CCTCCCTGCCCCGATCTTC 61.813 68.421 0.00 0.00 0.00 2.87
420 433 2.828661 AAGCCCTAATTTCACCTCCC 57.171 50.000 0.00 0.00 0.00 4.30
514 527 3.607661 GATCCGAGGTCCGCTCCC 61.608 72.222 0.00 0.00 36.84 4.30
533 546 3.213402 GACGAGCTCTCCCTCCCG 61.213 72.222 12.85 0.00 0.00 5.14
652 666 2.693285 CGATCGTTTCGTTCCGCC 59.307 61.111 7.03 0.00 43.01 6.13
663 678 1.520787 GCCACCCGATTTCGATCGT 60.521 57.895 15.94 0.00 42.07 3.73
688 703 1.080974 CACTTAACGGGTCGCGAGT 60.081 57.895 10.24 0.00 0.00 4.18
734 749 2.421529 GGTGGACTTGTTTGACCTCACT 60.422 50.000 0.00 0.00 0.00 3.41
736 751 1.474320 CGGTGGACTTGTTTGACCTCA 60.474 52.381 0.00 0.00 0.00 3.86
742 757 1.178534 ATGGGCGGTGGACTTGTTTG 61.179 55.000 0.00 0.00 0.00 2.93
764 779 0.170339 GTCACAGCGTTAAATGGGCC 59.830 55.000 0.00 0.00 0.00 5.80
771 786 2.212869 AACGAGTGTCACAGCGTTAA 57.787 45.000 25.38 0.00 44.07 2.01
774 790 1.856597 GTTTAACGAGTGTCACAGCGT 59.143 47.619 15.41 15.41 38.81 5.07
778 794 3.553508 GCTAGGGTTTAACGAGTGTCACA 60.554 47.826 5.62 0.00 0.00 3.58
785 801 0.808847 GCGGGCTAGGGTTTAACGAG 60.809 60.000 0.00 0.00 0.00 4.18
790 806 2.428925 CGGAGCGGGCTAGGGTTTA 61.429 63.158 0.00 0.00 0.00 2.01
998 1024 1.003839 GTGCGTCCCTTCACCATGA 60.004 57.895 0.00 0.00 0.00 3.07
1093 1129 3.222855 AGATCCAGCGCCCGAGAG 61.223 66.667 2.29 0.00 0.00 3.20
1094 1130 3.531207 CAGATCCAGCGCCCGAGA 61.531 66.667 2.29 0.00 0.00 4.04
1095 1131 4.598894 CCAGATCCAGCGCCCGAG 62.599 72.222 2.29 0.00 0.00 4.63
1099 1135 4.575973 ATGGCCAGATCCAGCGCC 62.576 66.667 13.05 3.61 39.89 6.53
1100 1136 2.517875 AATGGCCAGATCCAGCGC 60.518 61.111 13.05 0.00 39.89 5.92
1104 1140 3.675348 AGAAATGAATGGCCAGATCCA 57.325 42.857 13.05 6.60 40.97 3.41
1124 1160 2.334946 GCAGCTCAATCCGCACCAA 61.335 57.895 0.00 0.00 0.00 3.67
1154 1193 1.212688 CTGCAGATCAACCCCCACATA 59.787 52.381 8.42 0.00 0.00 2.29
1426 1465 0.098376 GGCAAGCAGCTCATCGAAAG 59.902 55.000 0.00 0.00 44.79 2.62
1435 1474 1.304217 ATCAAGCAGGCAAGCAGCT 60.304 52.632 5.57 5.57 44.79 4.24
1445 1484 1.938016 GCAAAAGGCACCATCAAGCAG 60.938 52.381 0.00 0.00 43.97 4.24
1485 1528 2.780094 CGCCCCTGCACACAAAACA 61.780 57.895 0.00 0.00 37.32 2.83
1486 1529 2.027460 CGCCCCTGCACACAAAAC 59.973 61.111 0.00 0.00 37.32 2.43
1487 1530 3.910490 GCGCCCCTGCACACAAAA 61.910 61.111 0.00 0.00 37.32 2.44
1516 1562 0.541392 TGCTGCTCGGGTACATGAAT 59.459 50.000 0.00 0.00 0.00 2.57
1564 1610 4.739137 GCCACAGCCTTAAACAAACATCAA 60.739 41.667 0.00 0.00 0.00 2.57
1585 1634 3.950395 AGTAAATCATGCAGAGGAAAGCC 59.050 43.478 0.00 0.00 0.00 4.35
1591 1640 4.953667 TGCTAGAGTAAATCATGCAGAGG 58.046 43.478 0.00 0.00 34.79 3.69
1619 1669 5.010282 ACAAGGCCTAGGACAAAATGTAAG 58.990 41.667 19.45 0.00 0.00 2.34
1635 1685 3.209410 CATCCTAGTCATTCACAAGGCC 58.791 50.000 0.00 0.00 0.00 5.19
1660 1710 7.177832 TCGACCTCACTTGGAATTCTATAAA 57.822 36.000 5.23 0.00 0.00 1.40
1698 1748 7.607607 ACATTGCACAAGTTCATATACTTCAGA 59.392 33.333 0.00 0.00 36.24 3.27
1731 1781 5.192927 CCAAGCCAAACCATTAGTATCTCA 58.807 41.667 0.00 0.00 0.00 3.27
1738 1788 2.524306 TGACCCAAGCCAAACCATTAG 58.476 47.619 0.00 0.00 0.00 1.73
1761 1818 5.441718 ACACAGAATCCTACATCAACCAT 57.558 39.130 0.00 0.00 0.00 3.55
1783 1844 9.709495 CATTCAGGGATAAAACAAATCAAAGAA 57.291 29.630 0.00 0.00 0.00 2.52
1789 1850 6.703165 GGCATCATTCAGGGATAAAACAAATC 59.297 38.462 0.00 0.00 0.00 2.17
1790 1851 6.384886 AGGCATCATTCAGGGATAAAACAAAT 59.615 34.615 0.00 0.00 0.00 2.32
1791 1852 5.721000 AGGCATCATTCAGGGATAAAACAAA 59.279 36.000 0.00 0.00 0.00 2.83
1793 1854 4.870636 AGGCATCATTCAGGGATAAAACA 58.129 39.130 0.00 0.00 0.00 2.83
1794 1855 4.279420 GGAGGCATCATTCAGGGATAAAAC 59.721 45.833 0.00 0.00 0.00 2.43
1866 1940 9.783256 AAAGCTAATAATAATTGACAACGTTCC 57.217 29.630 0.00 0.00 0.00 3.62
1901 1975 5.296780 ACATTCCACAGACACAACACTAAAG 59.703 40.000 0.00 0.00 0.00 1.85
1911 1985 6.373779 CATCTAAACAACATTCCACAGACAC 58.626 40.000 0.00 0.00 0.00 3.67
1915 1989 4.218200 TGGCATCTAAACAACATTCCACAG 59.782 41.667 0.00 0.00 0.00 3.66
1917 1991 4.782019 TGGCATCTAAACAACATTCCAC 57.218 40.909 0.00 0.00 0.00 4.02
1927 2001 2.672195 GCACAAGCCTTGGCATCTAAAC 60.672 50.000 14.54 0.00 34.12 2.01
1963 2107 4.520492 CCACTTTTCATACTGTGAGCCTTT 59.480 41.667 0.00 0.00 38.29 3.11
1991 2141 7.702772 ACAATAAAAACGTTTGATGTAAGTGCA 59.297 29.630 15.46 0.00 29.93 4.57
1992 2142 8.056710 ACAATAAAAACGTTTGATGTAAGTGC 57.943 30.769 15.46 0.00 29.93 4.40
2075 2229 6.925165 CCTGCTTACCAATAATTTGCAATAGG 59.075 38.462 0.00 0.00 0.00 2.57
2186 2377 4.870636 AGGAGTGGCATTCCAATGAAATA 58.129 39.130 28.09 0.00 45.53 1.40
2204 2395 7.066766 AGACTTTATGCTGCTGAAAATAAGGAG 59.933 37.037 0.00 0.00 36.29 3.69
2229 2420 4.699257 AGAAGACAGCAGAAAATAAGGCAG 59.301 41.667 0.00 0.00 0.00 4.85
2230 2421 4.456911 CAGAAGACAGCAGAAAATAAGGCA 59.543 41.667 0.00 0.00 0.00 4.75
2251 2452 6.623486 TCATGTTCATAATTTGAGGCAACAG 58.377 36.000 0.00 0.00 35.27 3.16
2282 2483 7.064016 GTGTCAAACATGGCTAGAAAAACAAAA 59.936 33.333 0.00 0.00 0.00 2.44
2317 2518 1.466950 GCAACGTTAGCATAGCCAACA 59.533 47.619 14.97 0.00 0.00 3.33
2466 2678 3.287222 CCAAAACTTCCACAGGTTCTCA 58.713 45.455 0.00 0.00 27.25 3.27
2632 2846 5.509832 TGCTGGCATCAGGAATATATCTT 57.490 39.130 0.00 0.00 38.42 2.40
2634 2848 5.434408 TCATGCTGGCATCAGGAATATATC 58.566 41.667 2.89 0.00 44.38 1.63
2663 2920 8.135529 GGCCACAAGAACATAAATAAATAGACC 58.864 37.037 0.00 0.00 0.00 3.85
2664 2921 8.903820 AGGCCACAAGAACATAAATAAATAGAC 58.096 33.333 5.01 0.00 0.00 2.59
2665 2922 8.902806 CAGGCCACAAGAACATAAATAAATAGA 58.097 33.333 5.01 0.00 0.00 1.98
2666 2923 7.649306 GCAGGCCACAAGAACATAAATAAATAG 59.351 37.037 5.01 0.00 0.00 1.73
2672 3086 3.434309 AGCAGGCCACAAGAACATAAAT 58.566 40.909 5.01 0.00 0.00 1.40
2689 3103 2.927004 TGGTTCGCCAAACTAGCAG 58.073 52.632 0.00 0.00 45.88 4.24
2702 3116 4.576053 TGTTATGCAGCTCACATATGGTTC 59.424 41.667 7.80 0.00 30.42 3.62
2703 3117 4.525996 TGTTATGCAGCTCACATATGGTT 58.474 39.130 7.80 0.00 30.42 3.67
2761 3175 2.037902 TGTTTGCGAGTGTATCCAAGGA 59.962 45.455 0.00 0.00 0.00 3.36
2762 3176 2.422597 TGTTTGCGAGTGTATCCAAGG 58.577 47.619 0.00 0.00 0.00 3.61
2763 3177 3.935203 AGATGTTTGCGAGTGTATCCAAG 59.065 43.478 0.00 0.00 0.00 3.61
2764 3178 3.932710 GAGATGTTTGCGAGTGTATCCAA 59.067 43.478 0.00 0.00 0.00 3.53
2765 3179 3.195610 AGAGATGTTTGCGAGTGTATCCA 59.804 43.478 0.00 0.00 0.00 3.41
2766 3180 3.786635 AGAGATGTTTGCGAGTGTATCC 58.213 45.455 0.00 0.00 0.00 2.59
2767 3181 4.493220 GCAAGAGATGTTTGCGAGTGTATC 60.493 45.833 0.00 0.00 41.16 2.24
2768 3182 3.372206 GCAAGAGATGTTTGCGAGTGTAT 59.628 43.478 0.00 0.00 41.16 2.29
2770 3184 1.532868 GCAAGAGATGTTTGCGAGTGT 59.467 47.619 0.00 0.00 41.16 3.55
2771 3185 2.238245 GCAAGAGATGTTTGCGAGTG 57.762 50.000 0.00 0.00 41.16 3.51
2777 3191 3.146618 GCCAGATGCAAGAGATGTTTG 57.853 47.619 0.00 0.00 40.77 2.93
2838 3404 8.837099 ATTTATACAAGGGTCCAAATCAATGA 57.163 30.769 0.00 0.00 0.00 2.57
2847 3413 4.323569 TGCCAATTTATACAAGGGTCCA 57.676 40.909 0.00 0.00 0.00 4.02
2909 3480 5.957771 ATCTTTGTCTGCCTTATGGTCTA 57.042 39.130 0.00 0.00 35.27 2.59
2919 3490 5.048504 TGACTTTGATGAATCTTTGTCTGCC 60.049 40.000 0.00 0.00 0.00 4.85
2921 3492 7.537649 CACATGACTTTGATGAATCTTTGTCTG 59.462 37.037 0.00 0.00 0.00 3.51
2922 3493 7.230108 ACACATGACTTTGATGAATCTTTGTCT 59.770 33.333 0.00 0.00 0.00 3.41
2923 3494 7.365741 ACACATGACTTTGATGAATCTTTGTC 58.634 34.615 0.00 0.00 0.00 3.18
2932 3504 5.939883 CCTAAAGGACACATGACTTTGATGA 59.060 40.000 0.00 0.00 36.07 2.92
2945 3517 2.552743 GCCACTCAAACCTAAAGGACAC 59.447 50.000 2.23 0.00 38.94 3.67
2970 3542 5.692928 TCATAGTACCAAGGGAGAGACTAC 58.307 45.833 0.00 0.00 0.00 2.73
2971 3543 5.163077 CCTCATAGTACCAAGGGAGAGACTA 60.163 48.000 0.00 0.00 0.00 2.59
2972 3544 4.386986 CCTCATAGTACCAAGGGAGAGACT 60.387 50.000 0.00 0.00 0.00 3.24
2973 3545 3.892588 CCTCATAGTACCAAGGGAGAGAC 59.107 52.174 0.00 0.00 0.00 3.36
2974 3546 3.532232 ACCTCATAGTACCAAGGGAGAGA 59.468 47.826 0.00 0.00 32.97 3.10
2975 3547 3.892588 GACCTCATAGTACCAAGGGAGAG 59.107 52.174 5.68 0.00 32.97 3.20
2976 3548 3.532232 AGACCTCATAGTACCAAGGGAGA 59.468 47.826 5.68 0.00 32.97 3.71
2977 3549 3.639094 CAGACCTCATAGTACCAAGGGAG 59.361 52.174 5.68 0.00 32.97 4.30
2978 3550 3.643237 CAGACCTCATAGTACCAAGGGA 58.357 50.000 5.68 0.00 32.97 4.20
2989 3566 4.033009 TCAATCTCCTTGCAGACCTCATA 58.967 43.478 0.00 0.00 34.66 2.15
3032 3609 3.242712 GGCATTGGTCAAATAAAATCGCG 59.757 43.478 0.00 0.00 0.00 5.87
3062 3640 4.154556 CACTGGGCTTGCCAAAAATATTTG 59.845 41.667 14.04 0.00 44.50 2.32
3065 3643 2.905736 ACACTGGGCTTGCCAAAAATAT 59.094 40.909 14.04 0.00 0.00 1.28
3066 3644 2.036992 CACACTGGGCTTGCCAAAAATA 59.963 45.455 14.04 0.00 0.00 1.40
3125 3716 6.867519 TTGTTCAGATATTCCACTAGGTCA 57.132 37.500 0.00 0.00 35.89 4.02
3232 3823 3.374988 TTCACACTGTGAAGCAGAAACAG 59.625 43.478 18.83 7.15 45.88 3.16


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

AutoCloner maintained by Alex Coulton.