Multiple sequence alignment - TraesCS3B01G068100

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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 TraesCS3B01G068100 chr3B 100.000 2660 0 0 1 2660 40247814 40245155 0.000000e+00 4913.0
1 TraesCS3B01G068100 chr3B 82.692 104 16 2 206 308 40398035 40397933 1.010000e-14 91.6
2 TraesCS3B01G068100 chr3A 91.030 2642 156 43 44 2660 32153949 32151364 0.000000e+00 3491.0
3 TraesCS3B01G068100 chr3D 89.718 1770 117 34 178 1925 23065540 23063814 0.000000e+00 2200.0
4 TraesCS3B01G068100 chr3D 95.389 694 30 1 1969 2660 23063817 23063124 0.000000e+00 1103.0
5 TraesCS3B01G068100 chr3D 87.719 285 33 2 201 484 23088422 23088139 5.490000e-87 331.0
6 TraesCS3B01G068100 chr1D 89.373 1722 114 37 178 1877 225395865 225397539 0.000000e+00 2102.0
7 TraesCS3B01G068100 chr2A 88.361 421 47 2 2223 2642 570785192 570784773 3.060000e-139 505.0
8 TraesCS3B01G068100 chr2D 88.124 421 48 2 2223 2642 419040491 419040910 1.420000e-137 499.0
9 TraesCS3B01G068100 chr2B 87.886 421 49 2 2223 2642 491181323 491181742 6.610000e-136 494.0
10 TraesCS3B01G068100 chr5D 93.939 198 12 0 279 476 546817803 546818000 1.550000e-77 300.0
11 TraesCS3B01G068100 chr5B 92.965 199 10 3 279 475 689915681 689915485 1.200000e-73 287.0
12 TraesCS3B01G068100 chr4A 92.462 199 12 3 279 476 622182322 622182126 5.610000e-72 281.0
13 TraesCS3B01G068100 chr1A 92.424 198 13 2 279 475 456937673 456937869 5.610000e-72 281.0
14 TraesCS3B01G068100 chr4B 91.176 204 13 5 276 476 37855665 37855464 3.370000e-69 272.0


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 TraesCS3B01G068100 chr3B 40245155 40247814 2659 True 4913.0 4913 100.0000 1 2660 1 chr3B.!!$R1 2659
1 TraesCS3B01G068100 chr3A 32151364 32153949 2585 True 3491.0 3491 91.0300 44 2660 1 chr3A.!!$R1 2616
2 TraesCS3B01G068100 chr3D 23063124 23065540 2416 True 1651.5 2200 92.5535 178 2660 2 chr3D.!!$R2 2482
3 TraesCS3B01G068100 chr1D 225395865 225397539 1674 False 2102.0 2102 89.3730 178 1877 1 chr1D.!!$F1 1699

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
826 846 0.198696 TTCCCTTCCCTTCCCTTCCT 59.801 55.0 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 1965 0.252239 GGGCCATTTCTCCCCAAAGT 60.252 55.0 4.39 0.0 38.7 2.66 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
19 20 1.675552 GTAACACCACAAGCACTGGT 58.324 50.000 0.00 0.00 43.22 4.00
32 33 2.370281 CACTGGTGCACGAGATACTT 57.630 50.000 32.20 9.36 0.00 2.24
33 34 2.688507 CACTGGTGCACGAGATACTTT 58.311 47.619 32.20 8.63 0.00 2.66
34 35 2.668457 CACTGGTGCACGAGATACTTTC 59.332 50.000 32.20 5.69 0.00 2.62
35 36 2.271800 CTGGTGCACGAGATACTTTCC 58.728 52.381 23.05 0.00 0.00 3.13
36 37 1.066430 TGGTGCACGAGATACTTTCCC 60.066 52.381 11.45 0.00 0.00 3.97
37 38 1.653151 GTGCACGAGATACTTTCCCC 58.347 55.000 0.00 0.00 0.00 4.81
38 39 0.539986 TGCACGAGATACTTTCCCCC 59.460 55.000 0.00 0.00 0.00 5.40
39 40 0.831307 GCACGAGATACTTTCCCCCT 59.169 55.000 0.00 0.00 0.00 4.79
40 41 2.037144 GCACGAGATACTTTCCCCCTA 58.963 52.381 0.00 0.00 0.00 3.53
41 42 2.633481 GCACGAGATACTTTCCCCCTAT 59.367 50.000 0.00 0.00 0.00 2.57
42 43 3.555168 GCACGAGATACTTTCCCCCTATG 60.555 52.174 0.00 0.00 0.00 2.23
60 61 7.235193 CCCCCTATGATTCTATCTATCTGATGG 59.765 44.444 0.00 0.00 36.65 3.51
66 67 9.941325 ATGATTCTATCTATCTGATGGTGAAAC 57.059 33.333 0.00 4.58 36.65 2.78
95 96 1.003233 GGTCCAGTCCAGAAGTGGC 60.003 63.158 0.00 0.00 46.68 5.01
96 97 1.003233 GTCCAGTCCAGAAGTGGCC 60.003 63.158 0.00 0.00 46.68 5.36
97 98 1.152030 TCCAGTCCAGAAGTGGCCT 60.152 57.895 3.32 0.00 46.68 5.19
98 99 0.768221 TCCAGTCCAGAAGTGGCCTT 60.768 55.000 3.32 0.00 46.68 4.35
99 100 0.607489 CCAGTCCAGAAGTGGCCTTG 60.607 60.000 3.32 0.00 44.60 3.61
101 102 1.347707 CAGTCCAGAAGTGGCCTTGTA 59.652 52.381 3.32 0.00 44.60 2.41
102 103 1.348036 AGTCCAGAAGTGGCCTTGTAC 59.652 52.381 3.32 0.00 44.60 2.90
104 105 1.771854 TCCAGAAGTGGCCTTGTACAA 59.228 47.619 8.28 8.28 44.60 2.41
105 106 2.375174 TCCAGAAGTGGCCTTGTACAAT 59.625 45.455 9.13 0.00 44.60 2.71
118 119 6.038356 GCCTTGTACAATCAATCAAGAATGG 58.962 40.000 9.13 3.16 39.39 3.16
148 149 3.062042 CAGGGACCTACGTGTAACAAAC 58.938 50.000 0.00 0.00 35.74 2.93
252 254 1.657751 GAGGGCACGAATGAAAGGCC 61.658 60.000 0.00 0.00 46.14 5.19
259 261 2.944390 AATGAAAGGCCCCGGGGA 60.944 61.111 44.86 22.56 37.50 4.81
339 341 2.412870 TCTCGATTTGTGCGTGTCATT 58.587 42.857 0.00 0.00 0.00 2.57
441 444 2.679930 GCTCAGGCTTATAAACCGGTGT 60.680 50.000 8.52 4.57 35.22 4.16
447 450 2.934553 GCTTATAAACCGGTGTGTCTCC 59.065 50.000 8.52 0.00 0.00 3.71
451 454 0.472352 AAACCGGTGTGTCTCCCCTA 60.472 55.000 8.52 0.00 0.00 3.53
476 479 0.252197 GCCGAGGTGGGACTAAACAT 59.748 55.000 0.00 0.00 38.63 2.71
479 482 2.418746 CCGAGGTGGGACTAAACATCAG 60.419 54.545 0.00 0.00 0.00 2.90
481 484 1.066143 AGGTGGGACTAAACATCAGCG 60.066 52.381 0.00 0.00 0.00 5.18
482 485 1.066430 GGTGGGACTAAACATCAGCGA 60.066 52.381 0.00 0.00 0.00 4.93
483 486 2.271800 GTGGGACTAAACATCAGCGAG 58.728 52.381 0.00 0.00 0.00 5.03
484 487 1.899814 TGGGACTAAACATCAGCGAGT 59.100 47.619 0.00 0.00 0.00 4.18
496 499 1.080705 AGCGAGTTTCGTTCCTCCG 60.081 57.895 0.17 0.00 42.81 4.63
500 503 1.071567 GAGTTTCGTTCCTCCGAGCG 61.072 60.000 0.00 0.00 43.36 5.03
501 504 2.431942 TTTCGTTCCTCCGAGCGC 60.432 61.111 0.00 0.00 41.92 5.92
502 505 3.927163 TTTCGTTCCTCCGAGCGCC 62.927 63.158 2.29 0.00 41.92 6.53
656 674 1.507141 CCGCTTTCCTCCACACACAC 61.507 60.000 0.00 0.00 0.00 3.82
657 675 0.813610 CGCTTTCCTCCACACACACA 60.814 55.000 0.00 0.00 0.00 3.72
658 676 0.663153 GCTTTCCTCCACACACACAC 59.337 55.000 0.00 0.00 0.00 3.82
659 677 2.016604 GCTTTCCTCCACACACACACA 61.017 52.381 0.00 0.00 0.00 3.72
660 678 1.670811 CTTTCCTCCACACACACACAC 59.329 52.381 0.00 0.00 0.00 3.82
661 679 0.615850 TTCCTCCACACACACACACA 59.384 50.000 0.00 0.00 0.00 3.72
676 694 4.038642 ACACACACACACCATTATTTTCCC 59.961 41.667 0.00 0.00 0.00 3.97
693 711 2.443016 CCTCCCTCCTCCTGACCG 60.443 72.222 0.00 0.00 0.00 4.79
715 733 4.096003 CCCACCTACCAGCCACCG 62.096 72.222 0.00 0.00 0.00 4.94
803 823 1.505353 CGAGGTACGGACGAGCTTT 59.495 57.895 0.00 0.00 38.46 3.51
808 828 0.245813 GTACGGACGAGCTTTCCCTT 59.754 55.000 9.22 0.95 0.00 3.95
809 829 0.529378 TACGGACGAGCTTTCCCTTC 59.471 55.000 9.22 0.00 0.00 3.46
810 830 1.448013 CGGACGAGCTTTCCCTTCC 60.448 63.158 9.22 0.00 0.00 3.46
811 831 1.078356 GGACGAGCTTTCCCTTCCC 60.078 63.158 4.28 0.00 0.00 3.97
812 832 1.554583 GGACGAGCTTTCCCTTCCCT 61.555 60.000 4.28 0.00 0.00 4.20
813 833 0.325272 GACGAGCTTTCCCTTCCCTT 59.675 55.000 0.00 0.00 0.00 3.95
826 846 0.198696 TTCCCTTCCCTTCCCTTCCT 59.801 55.000 0.00 0.00 0.00 3.36
907 927 4.344474 CTAGATCCGCCCCGTCGC 62.344 72.222 0.00 0.00 0.00 5.19
995 1028 1.304217 TAGATCGATCCCTCCGCCC 60.304 63.158 21.66 0.00 0.00 6.13
1159 1192 2.360980 CGTCCACCTCCTCCTCCT 59.639 66.667 0.00 0.00 0.00 3.69
1160 1193 1.755008 CGTCCACCTCCTCCTCCTC 60.755 68.421 0.00 0.00 0.00 3.71
1161 1194 1.382009 GTCCACCTCCTCCTCCTCC 60.382 68.421 0.00 0.00 0.00 4.30
1629 1668 1.293062 AAGATGAGGGTGATGGCAGT 58.707 50.000 0.00 0.00 0.00 4.40
1705 1745 3.953612 AGTCTGGACAAGAGAGAGCATAG 59.046 47.826 3.51 0.00 34.84 2.23
1711 1751 4.202111 GGACAAGAGAGAGCATAGGAAGTC 60.202 50.000 0.00 0.00 0.00 3.01
1729 1769 2.366916 AGTCGGGCTGATTGATAAGAGG 59.633 50.000 0.00 0.00 0.00 3.69
1735 1775 3.501445 GGCTGATTGATAAGAGGCATGAC 59.499 47.826 0.00 0.00 0.00 3.06
1736 1776 3.186001 GCTGATTGATAAGAGGCATGACG 59.814 47.826 0.00 0.00 0.00 4.35
1741 1781 2.625314 TGATAAGAGGCATGACGGAGAG 59.375 50.000 0.00 0.00 0.00 3.20
1861 1904 0.695924 TGGGTACTGATGGGTTGGTG 59.304 55.000 0.00 0.00 0.00 4.17
1862 1905 0.034477 GGGTACTGATGGGTTGGTGG 60.034 60.000 0.00 0.00 0.00 4.61
1863 1906 0.034477 GGTACTGATGGGTTGGTGGG 60.034 60.000 0.00 0.00 0.00 4.61
1883 1926 4.080807 TGGGAGTTTAGTTGAAGTGTCACA 60.081 41.667 5.62 0.00 31.90 3.58
1886 1929 4.451900 AGTTTAGTTGAAGTGTCACAGGG 58.548 43.478 5.62 0.00 31.90 4.45
1948 1992 2.091333 GGGAGAAATGGCCCCAAATCTA 60.091 50.000 0.00 0.00 39.89 1.98
1951 1995 4.473444 GAGAAATGGCCCCAAATCTATGA 58.527 43.478 0.00 0.00 0.00 2.15
1962 2006 5.002516 CCCAAATCTATGAGCTCTGGATTC 58.997 45.833 16.19 0.00 0.00 2.52
1981 2025 6.168389 GGATTCTGGTTGCTTGATTTTGATT 58.832 36.000 0.00 0.00 0.00 2.57
1990 2034 7.096065 GGTTGCTTGATTTTGATTTGACAGTAC 60.096 37.037 0.00 0.00 0.00 2.73
2038 2084 8.682128 TTGAATTATTGTGTAAAATTCTCGCC 57.318 30.769 8.10 0.00 0.00 5.54
2045 2091 6.249035 TGTGTAAAATTCTCGCCTTAAAGG 57.751 37.500 0.00 0.00 38.80 3.11
2063 2109 7.116805 CCTTAAAGGTTTGAGCAATGTGAAATC 59.883 37.037 0.00 0.00 0.00 2.17
2064 2110 4.164822 AGGTTTGAGCAATGTGAAATCG 57.835 40.909 0.00 0.00 0.00 3.34
2076 2122 5.947228 ATGTGAAATCGTGTGATTGAAGT 57.053 34.783 0.00 0.00 44.02 3.01
2120 2166 8.125448 CAGTAACAATGGCTAGATTTAAGCTTC 58.875 37.037 0.00 0.00 39.97 3.86
2212 2258 5.105567 TGACCTTTGGTGACTGTTAGAAA 57.894 39.130 0.00 0.00 35.25 2.52
2219 2265 3.139077 GGTGACTGTTAGAAACCACAGG 58.861 50.000 4.44 0.00 44.12 4.00
2221 2267 1.798813 GACTGTTAGAAACCACAGGCG 59.201 52.381 4.44 0.00 44.12 5.52
2222 2268 1.156736 CTGTTAGAAACCACAGGCGG 58.843 55.000 0.00 0.00 37.37 6.13
2254 2300 1.377333 GCCTGCTAAGCTTTCCCGT 60.377 57.895 3.20 0.00 0.00 5.28
2275 2321 2.840038 TGAGGAGAATGTGTACATGGCT 59.160 45.455 0.00 0.00 36.56 4.75
2314 2360 3.280295 TGAGAGGTACGAAGAGATGGTC 58.720 50.000 0.00 0.00 0.00 4.02
2383 2429 2.097038 CGAGGAGCGCAACCTTCTG 61.097 63.158 23.11 14.29 37.93 3.02
2473 2519 2.035442 GGAAGAGAGCCGTGGCAAC 61.035 63.158 14.29 6.81 44.88 4.17
2587 2633 1.208165 ACCTTGTCCCCTCATCCACC 61.208 60.000 0.00 0.00 0.00 4.61
2635 2681 6.617371 ACCTGAAGATGAAGGGTGATTACTAT 59.383 38.462 0.00 0.00 37.94 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.370281 AAGTATCTCGTGCACCAGTG 57.630 50.000 12.15 0.00 0.00 3.66
14 15 2.353803 GGAAAGTATCTCGTGCACCAGT 60.354 50.000 12.15 1.64 0.00 4.00
15 16 2.271800 GGAAAGTATCTCGTGCACCAG 58.728 52.381 12.15 8.45 0.00 4.00
16 17 1.066430 GGGAAAGTATCTCGTGCACCA 60.066 52.381 12.15 0.00 0.00 4.17
17 18 1.653151 GGGAAAGTATCTCGTGCACC 58.347 55.000 12.15 0.00 0.00 5.01
18 19 1.653151 GGGGAAAGTATCTCGTGCAC 58.347 55.000 6.82 6.82 0.00 4.57
19 20 0.539986 GGGGGAAAGTATCTCGTGCA 59.460 55.000 0.00 0.00 0.00 4.57
20 21 0.831307 AGGGGGAAAGTATCTCGTGC 59.169 55.000 0.00 0.00 0.00 5.34
21 22 3.895656 TCATAGGGGGAAAGTATCTCGTG 59.104 47.826 0.00 0.00 0.00 4.35
22 23 4.194678 TCATAGGGGGAAAGTATCTCGT 57.805 45.455 0.00 0.00 0.00 4.18
23 24 5.482175 AGAATCATAGGGGGAAAGTATCTCG 59.518 44.000 0.00 0.00 0.00 4.04
24 25 6.943899 AGAATCATAGGGGGAAAGTATCTC 57.056 41.667 0.00 0.00 0.00 2.75
25 26 8.413821 AGATAGAATCATAGGGGGAAAGTATCT 58.586 37.037 0.00 0.00 0.00 1.98
26 27 8.616799 AGATAGAATCATAGGGGGAAAGTATC 57.383 38.462 0.00 0.00 0.00 2.24
28 29 9.716556 GATAGATAGAATCATAGGGGGAAAGTA 57.283 37.037 0.00 0.00 0.00 2.24
29 30 8.413821 AGATAGATAGAATCATAGGGGGAAAGT 58.586 37.037 0.00 0.00 0.00 2.66
30 31 8.703743 CAGATAGATAGAATCATAGGGGGAAAG 58.296 40.741 0.00 0.00 0.00 2.62
31 32 8.409825 TCAGATAGATAGAATCATAGGGGGAAA 58.590 37.037 0.00 0.00 0.00 3.13
32 33 7.955244 TCAGATAGATAGAATCATAGGGGGAA 58.045 38.462 0.00 0.00 0.00 3.97
33 34 7.545698 TCAGATAGATAGAATCATAGGGGGA 57.454 40.000 0.00 0.00 0.00 4.81
34 35 7.235193 CCATCAGATAGATAGAATCATAGGGGG 59.765 44.444 0.00 0.00 34.43 5.40
35 36 7.788867 ACCATCAGATAGATAGAATCATAGGGG 59.211 40.741 0.00 0.00 34.43 4.79
36 37 8.640651 CACCATCAGATAGATAGAATCATAGGG 58.359 40.741 0.00 0.00 34.43 3.53
37 38 9.418839 TCACCATCAGATAGATAGAATCATAGG 57.581 37.037 0.00 0.00 34.43 2.57
40 41 9.941325 GTTTCACCATCAGATAGATAGAATCAT 57.059 33.333 0.00 0.00 34.43 2.45
41 42 8.084684 CGTTTCACCATCAGATAGATAGAATCA 58.915 37.037 0.00 0.00 34.43 2.57
42 43 8.300286 TCGTTTCACCATCAGATAGATAGAATC 58.700 37.037 0.00 0.00 34.43 2.52
60 61 2.405172 GACCTCCACTTCTCGTTTCAC 58.595 52.381 0.00 0.00 0.00 3.18
66 67 0.528470 GACTGGACCTCCACTTCTCG 59.472 60.000 0.00 0.00 42.01 4.04
94 95 6.038356 CCATTCTTGATTGATTGTACAAGGC 58.962 40.000 14.65 9.13 39.74 4.35
95 96 6.038356 GCCATTCTTGATTGATTGTACAAGG 58.962 40.000 14.65 5.94 39.74 3.61
96 97 6.623486 TGCCATTCTTGATTGATTGTACAAG 58.377 36.000 14.65 0.00 40.37 3.16
97 98 6.587206 TGCCATTCTTGATTGATTGTACAA 57.413 33.333 11.41 11.41 0.00 2.41
98 99 6.015603 TGTTGCCATTCTTGATTGATTGTACA 60.016 34.615 0.00 0.00 0.00 2.90
99 100 6.389091 TGTTGCCATTCTTGATTGATTGTAC 58.611 36.000 0.00 0.00 0.00 2.90
101 102 5.244402 TCTGTTGCCATTCTTGATTGATTGT 59.756 36.000 0.00 0.00 0.00 2.71
102 103 5.716094 TCTGTTGCCATTCTTGATTGATTG 58.284 37.500 0.00 0.00 0.00 2.67
104 105 4.142227 GCTCTGTTGCCATTCTTGATTGAT 60.142 41.667 0.00 0.00 0.00 2.57
105 106 3.192001 GCTCTGTTGCCATTCTTGATTGA 59.808 43.478 0.00 0.00 0.00 2.57
118 119 0.391793 GTAGGTCCCTGCTCTGTTGC 60.392 60.000 0.00 0.00 0.00 4.17
148 149 2.093106 ACTGTGGCCGACTAGTCTTAG 58.907 52.381 20.34 10.17 0.00 2.18
176 177 1.332997 GGCGATGATCTCTTTGCCTTG 59.667 52.381 14.26 0.00 43.53 3.61
252 254 2.104281 CCTTACAGATAAGTTCCCCGGG 59.896 54.545 15.80 15.80 36.77 5.73
259 261 6.023603 TCCCTGAGTTCCTTACAGATAAGTT 58.976 40.000 0.00 0.00 36.77 2.66
421 424 2.936498 CACACCGGTTTATAAGCCTGAG 59.064 50.000 15.11 10.32 0.00 3.35
422 425 2.303600 ACACACCGGTTTATAAGCCTGA 59.696 45.455 15.11 0.00 0.00 3.86
424 427 2.570302 AGACACACCGGTTTATAAGCCT 59.430 45.455 2.97 0.00 0.00 4.58
441 444 3.075005 GCCAGCGTAGGGGAGACA 61.075 66.667 0.00 0.00 0.00 3.41
462 465 1.066430 TCGCTGATGTTTAGTCCCACC 60.066 52.381 0.00 0.00 0.00 4.61
476 479 0.038526 GGAGGAACGAAACTCGCTGA 60.039 55.000 0.00 0.00 45.12 4.26
479 482 1.071567 CTCGGAGGAACGAAACTCGC 61.072 60.000 0.00 0.00 45.12 5.03
481 484 1.071567 CGCTCGGAGGAACGAAACTC 61.072 60.000 7.20 0.00 42.98 3.01
482 485 1.080705 CGCTCGGAGGAACGAAACT 60.081 57.895 7.20 0.00 42.98 2.66
483 486 2.727684 GCGCTCGGAGGAACGAAAC 61.728 63.158 7.20 0.00 42.98 2.78
484 487 2.431942 GCGCTCGGAGGAACGAAA 60.432 61.111 7.20 0.00 42.98 3.46
513 516 2.997897 GAGGACACGAGGCTGGGT 60.998 66.667 0.51 0.00 0.00 4.51
514 517 4.135153 CGAGGACACGAGGCTGGG 62.135 72.222 0.51 0.00 35.09 4.45
656 674 3.831911 AGGGGAAAATAATGGTGTGTGTG 59.168 43.478 0.00 0.00 0.00 3.82
657 675 4.086457 GAGGGGAAAATAATGGTGTGTGT 58.914 43.478 0.00 0.00 0.00 3.72
658 676 3.447229 GGAGGGGAAAATAATGGTGTGTG 59.553 47.826 0.00 0.00 0.00 3.82
659 677 3.565670 GGGAGGGGAAAATAATGGTGTGT 60.566 47.826 0.00 0.00 0.00 3.72
660 678 3.031013 GGGAGGGGAAAATAATGGTGTG 58.969 50.000 0.00 0.00 0.00 3.82
661 679 2.933139 AGGGAGGGGAAAATAATGGTGT 59.067 45.455 0.00 0.00 0.00 4.16
676 694 2.443016 CGGTCAGGAGGAGGGAGG 60.443 72.222 0.00 0.00 0.00 4.30
693 711 4.426313 GCTGGTAGGTGGGTGGGC 62.426 72.222 0.00 0.00 0.00 5.36
803 823 1.230182 GGGAAGGGAAGGGAAGGGA 60.230 63.158 0.00 0.00 0.00 4.20
808 828 0.198696 AAGGAAGGGAAGGGAAGGGA 59.801 55.000 0.00 0.00 0.00 4.20
809 829 1.006043 GAAAGGAAGGGAAGGGAAGGG 59.994 57.143 0.00 0.00 0.00 3.95
810 830 1.006043 GGAAAGGAAGGGAAGGGAAGG 59.994 57.143 0.00 0.00 0.00 3.46
811 831 1.006043 GGGAAAGGAAGGGAAGGGAAG 59.994 57.143 0.00 0.00 0.00 3.46
812 832 1.081481 GGGAAAGGAAGGGAAGGGAA 58.919 55.000 0.00 0.00 0.00 3.97
813 833 0.849540 GGGGAAAGGAAGGGAAGGGA 60.850 60.000 0.00 0.00 0.00 4.20
826 846 2.375345 GGAGGATCGCTGGGGGAAA 61.375 63.158 0.00 0.00 34.37 3.13
907 927 2.126071 ATCGAACACCTGCGGACG 60.126 61.111 0.00 0.00 0.00 4.79
909 929 2.577059 GGATCGAACACCTGCGGA 59.423 61.111 0.00 0.00 0.00 5.54
1159 1192 2.363018 CGGAGGCTGTGAGGAGGA 60.363 66.667 0.00 0.00 0.00 3.71
1160 1193 4.154347 GCGGAGGCTGTGAGGAGG 62.154 72.222 0.00 0.00 35.83 4.30
1426 1459 2.434185 GATGGAGACGGCGTGCAA 60.434 61.111 21.19 2.45 0.00 4.08
1488 1521 2.121506 TGCCTTCCCCTTCCCTGT 60.122 61.111 0.00 0.00 0.00 4.00
1629 1668 1.279025 GCCCACCTCCACCCTTATCA 61.279 60.000 0.00 0.00 0.00 2.15
1664 1703 1.740025 CTAGCTGTTAGGCAAACCAGC 59.260 52.381 0.00 8.98 40.01 4.85
1705 1745 2.910688 TATCAATCAGCCCGACTTCC 57.089 50.000 0.00 0.00 0.00 3.46
1711 1751 1.202687 TGCCTCTTATCAATCAGCCCG 60.203 52.381 0.00 0.00 0.00 6.13
1729 1769 1.142748 CACTCCCTCTCCGTCATGC 59.857 63.158 0.00 0.00 0.00 4.06
1735 1775 2.055042 CAGTCCCACTCCCTCTCCG 61.055 68.421 0.00 0.00 0.00 4.63
1736 1776 2.363172 GCAGTCCCACTCCCTCTCC 61.363 68.421 0.00 0.00 0.00 3.71
1741 1781 2.352805 CCTTGCAGTCCCACTCCC 59.647 66.667 0.00 0.00 0.00 4.30
1861 1904 4.448210 TGTGACACTTCAACTAAACTCCC 58.552 43.478 7.20 0.00 31.90 4.30
1862 1905 4.511826 CCTGTGACACTTCAACTAAACTCC 59.488 45.833 7.20 0.00 31.90 3.85
1863 1906 4.511826 CCCTGTGACACTTCAACTAAACTC 59.488 45.833 7.20 0.00 31.90 3.01
1905 1948 3.700539 CCAAAGTGATTCCATGTGCCATA 59.299 43.478 0.00 0.00 0.00 2.74
1921 1965 0.252239 GGGCCATTTCTCCCCAAAGT 60.252 55.000 4.39 0.00 38.70 2.66
1948 1992 2.683152 GCAACCAGAATCCAGAGCTCAT 60.683 50.000 17.77 0.00 0.00 2.90
1951 1995 0.990374 AGCAACCAGAATCCAGAGCT 59.010 50.000 0.00 0.00 0.00 4.09
1962 2006 5.754406 TGTCAAATCAAAATCAAGCAACCAG 59.246 36.000 0.00 0.00 0.00 4.00
1981 2025 6.935741 AAGCAACAAACTATGTACTGTCAA 57.064 33.333 0.00 0.00 42.99 3.18
1990 2034 7.704472 TCAAACCAACTTAAGCAACAAACTATG 59.296 33.333 1.29 0.00 0.00 2.23
1996 2040 9.606631 AATAATTCAAACCAACTTAAGCAACAA 57.393 25.926 1.29 0.00 0.00 2.83
2038 2084 7.148918 CGATTTCACATTGCTCAAACCTTTAAG 60.149 37.037 0.00 0.00 0.00 1.85
2045 2091 4.146961 CACACGATTTCACATTGCTCAAAC 59.853 41.667 0.00 0.00 0.00 2.93
2063 2109 2.545526 AGCTTGACACTTCAATCACACG 59.454 45.455 0.00 0.00 41.05 4.49
2064 2110 5.673337 TTAGCTTGACACTTCAATCACAC 57.327 39.130 0.00 0.00 41.05 3.82
2076 2122 8.896320 TGTTACTGAAGTAAATTAGCTTGACA 57.104 30.769 4.52 0.00 41.58 3.58
2086 2132 9.686683 AATCTAGCCATTGTTACTGAAGTAAAT 57.313 29.630 4.52 0.00 41.58 1.40
2120 2166 8.871862 CATTTCATTATTACAACAACCACATGG 58.128 33.333 0.00 0.00 42.17 3.66
2212 2258 1.003355 CATCTTCACCGCCTGTGGT 60.003 57.895 0.00 0.00 45.48 4.16
2219 2265 3.869272 CTGCGCCATCTTCACCGC 61.869 66.667 4.18 0.00 45.99 5.68
2243 2289 1.056660 TTCTCCTCACGGGAAAGCTT 58.943 50.000 0.00 0.00 44.58 3.74
2254 2300 2.840038 AGCCATGTACACATTCTCCTCA 59.160 45.455 0.00 0.00 33.61 3.86
2314 2360 2.009042 GCCACCTTCTCCATGAACTCG 61.009 57.143 0.00 0.00 0.00 4.18
2383 2429 7.538678 CCAATAACATTCTTGTAAGCAACTGAC 59.461 37.037 0.00 0.00 34.06 3.51
2473 2519 1.081376 GAGTGTGACACGGTCCTCG 60.081 63.158 10.41 0.00 45.88 4.63
2587 2633 1.216710 GACCTTGGACTCTGGAGCG 59.783 63.158 0.00 0.00 0.00 5.03
2635 2681 6.422344 TGCCGGTCATTATTGTAATACCTA 57.578 37.500 1.90 0.00 0.00 3.08


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

AutoCloner maintained by Alex Coulton.