Multiple sequence alignment - TraesCS3B01G257300

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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 TraesCS3B01G257300 chr3B 100.000 2762 0 0 1 2762 414985839 414988600 0.000000e+00 5101.0
1 TraesCS3B01G257300 chr3B 94.323 1004 56 1 1759 2762 37294414 37293412 0.000000e+00 1537.0
2 TraesCS3B01G257300 chr3B 94.024 1004 55 3 1760 2762 749292242 749293241 0.000000e+00 1517.0
3 TraesCS3B01G257300 chr2B 94.018 1003 58 2 1760 2761 750352634 750351633 0.000000e+00 1519.0
4 TraesCS3B01G257300 chr2B 93.924 1004 58 3 1760 2762 52807949 52806948 0.000000e+00 1513.0
5 TraesCS3B01G257300 chr2B 93.625 1004 61 3 1760 2762 560834472 560835473 0.000000e+00 1496.0
6 TraesCS3B01G257300 chr1B 93.738 1006 59 4 1758 2762 587654843 587653841 0.000000e+00 1506.0
7 TraesCS3B01G257300 chr5B 93.638 1006 62 2 1758 2762 586007987 586008991 0.000000e+00 1502.0
8 TraesCS3B01G257300 chr5B 86.256 211 27 2 1395 1605 532082144 532082352 7.700000e-56 228.0
9 TraesCS3B01G257300 chr4B 93.638 1006 60 3 1760 2762 407799532 407798528 0.000000e+00 1500.0
10 TraesCS3B01G257300 chr4B 79.448 1450 245 26 336 1746 51192296 51190861 0.000000e+00 977.0
11 TraesCS3B01G257300 chr7B 93.452 1008 62 4 1757 2762 6256934 6255929 0.000000e+00 1493.0
12 TraesCS3B01G257300 chr7B 81.102 1651 256 34 141 1759 88270163 88268537 0.000000e+00 1269.0
13 TraesCS3B01G257300 chr5A 75.762 1510 312 32 167 1648 267953463 267951980 0.000000e+00 712.0
14 TraesCS3B01G257300 chr6D 89.041 511 52 1 1245 1751 275165102 275165612 5.020000e-177 630.0
15 TraesCS3B01G257300 chr7A 91.667 48 0 2 70 117 60488910 60488953 2.300000e-06 63.9
16 TraesCS3B01G257300 chr3A 89.583 48 2 2 70 116 218616206 218616161 1.070000e-04 58.4


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 TraesCS3B01G257300 chr3B 414985839 414988600 2761 False 5101 5101 100.000 1 2762 1 chr3B.!!$F1 2761
1 TraesCS3B01G257300 chr3B 37293412 37294414 1002 True 1537 1537 94.323 1759 2762 1 chr3B.!!$R1 1003
2 TraesCS3B01G257300 chr3B 749292242 749293241 999 False 1517 1517 94.024 1760 2762 1 chr3B.!!$F2 1002
3 TraesCS3B01G257300 chr2B 750351633 750352634 1001 True 1519 1519 94.018 1760 2761 1 chr2B.!!$R2 1001
4 TraesCS3B01G257300 chr2B 52806948 52807949 1001 True 1513 1513 93.924 1760 2762 1 chr2B.!!$R1 1002
5 TraesCS3B01G257300 chr2B 560834472 560835473 1001 False 1496 1496 93.625 1760 2762 1 chr2B.!!$F1 1002
6 TraesCS3B01G257300 chr1B 587653841 587654843 1002 True 1506 1506 93.738 1758 2762 1 chr1B.!!$R1 1004
7 TraesCS3B01G257300 chr5B 586007987 586008991 1004 False 1502 1502 93.638 1758 2762 1 chr5B.!!$F2 1004
8 TraesCS3B01G257300 chr4B 407798528 407799532 1004 True 1500 1500 93.638 1760 2762 1 chr4B.!!$R2 1002
9 TraesCS3B01G257300 chr4B 51190861 51192296 1435 True 977 977 79.448 336 1746 1 chr4B.!!$R1 1410
10 TraesCS3B01G257300 chr7B 6255929 6256934 1005 True 1493 1493 93.452 1757 2762 1 chr7B.!!$R1 1005
11 TraesCS3B01G257300 chr7B 88268537 88270163 1626 True 1269 1269 81.102 141 1759 1 chr7B.!!$R2 1618
12 TraesCS3B01G257300 chr5A 267951980 267953463 1483 True 712 712 75.762 167 1648 1 chr5A.!!$R1 1481
13 TraesCS3B01G257300 chr6D 275165102 275165612 510 False 630 630 89.041 1245 1751 1 chr6D.!!$F1 506

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
98 99 0.248866 CAAAAGGGCTCGTGCGTTTT 60.249 50.0 12.67 12.67 40.82 2.43 F
99 100 0.248866 AAAAGGGCTCGTGCGTTTTG 60.249 50.0 15.96 0.00 40.82 2.44 F
1107 1136 0.680921 ATGTGGATTTCGGCTGTGGG 60.681 55.0 0.00 0.00 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1178 1207 0.106369 TCGATCCACCATACGGTCCT 60.106 55.0 0.0 0.0 44.71 3.85 R
1246 1275 0.323633 CCAACATCCCATGACTGGCA 60.324 55.0 0.0 0.0 41.64 4.92 R
2738 2787 0.389037 GATCACTGCTGTCGCACTCA 60.389 55.0 0.0 0.0 42.25 3.41 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
17 18 2.591429 CTGTGAGCGGGCAACACA 60.591 61.111 17.54 17.54 41.27 3.72
18 19 2.591429 TGTGAGCGGGCAACACAG 60.591 61.111 15.65 0.00 39.17 3.66
19 20 4.030452 GTGAGCGGGCAACACAGC 62.030 66.667 13.23 0.00 39.74 4.40
36 37 3.933155 CAGCCGTACTGTCATGATTTC 57.067 47.619 0.00 0.00 41.86 2.17
37 38 3.261580 CAGCCGTACTGTCATGATTTCA 58.738 45.455 0.00 0.00 41.86 2.69
38 39 3.684305 CAGCCGTACTGTCATGATTTCAA 59.316 43.478 0.00 0.00 41.86 2.69
39 40 3.684788 AGCCGTACTGTCATGATTTCAAC 59.315 43.478 0.00 0.00 0.00 3.18
40 41 3.181510 GCCGTACTGTCATGATTTCAACC 60.182 47.826 0.00 0.00 0.00 3.77
41 42 3.062099 CCGTACTGTCATGATTTCAACCG 59.938 47.826 0.00 0.00 0.00 4.44
42 43 3.483574 CGTACTGTCATGATTTCAACCGC 60.484 47.826 0.00 0.00 0.00 5.68
43 44 2.783135 ACTGTCATGATTTCAACCGCT 58.217 42.857 0.00 0.00 0.00 5.52
44 45 2.744202 ACTGTCATGATTTCAACCGCTC 59.256 45.455 0.00 0.00 0.00 5.03
45 46 1.731709 TGTCATGATTTCAACCGCTCG 59.268 47.619 0.00 0.00 0.00 5.03
46 47 0.726827 TCATGATTTCAACCGCTCGC 59.273 50.000 0.00 0.00 0.00 5.03
47 48 0.729116 CATGATTTCAACCGCTCGCT 59.271 50.000 0.00 0.00 0.00 4.93
48 49 1.009829 ATGATTTCAACCGCTCGCTC 58.990 50.000 0.00 0.00 0.00 5.03
49 50 0.320334 TGATTTCAACCGCTCGCTCA 60.320 50.000 0.00 0.00 0.00 4.26
50 51 0.371645 GATTTCAACCGCTCGCTCAG 59.628 55.000 0.00 0.00 0.00 3.35
51 52 0.320771 ATTTCAACCGCTCGCTCAGT 60.321 50.000 0.00 0.00 0.00 3.41
52 53 0.531974 TTTCAACCGCTCGCTCAGTT 60.532 50.000 0.00 0.00 0.00 3.16
53 54 0.531974 TTCAACCGCTCGCTCAGTTT 60.532 50.000 0.00 0.00 0.00 2.66
54 55 0.944311 TCAACCGCTCGCTCAGTTTC 60.944 55.000 0.00 0.00 0.00 2.78
55 56 0.946221 CAACCGCTCGCTCAGTTTCT 60.946 55.000 0.00 0.00 0.00 2.52
56 57 0.667792 AACCGCTCGCTCAGTTTCTC 60.668 55.000 0.00 0.00 0.00 2.87
57 58 1.080501 CCGCTCGCTCAGTTTCTCA 60.081 57.895 0.00 0.00 0.00 3.27
58 59 0.459237 CCGCTCGCTCAGTTTCTCAT 60.459 55.000 0.00 0.00 0.00 2.90
59 60 1.354040 CGCTCGCTCAGTTTCTCATT 58.646 50.000 0.00 0.00 0.00 2.57
60 61 1.322936 CGCTCGCTCAGTTTCTCATTC 59.677 52.381 0.00 0.00 0.00 2.67
61 62 2.341257 GCTCGCTCAGTTTCTCATTCA 58.659 47.619 0.00 0.00 0.00 2.57
62 63 2.738846 GCTCGCTCAGTTTCTCATTCAA 59.261 45.455 0.00 0.00 0.00 2.69
63 64 3.373439 GCTCGCTCAGTTTCTCATTCAAT 59.627 43.478 0.00 0.00 0.00 2.57
64 65 4.568359 GCTCGCTCAGTTTCTCATTCAATA 59.432 41.667 0.00 0.00 0.00 1.90
65 66 5.236047 GCTCGCTCAGTTTCTCATTCAATAT 59.764 40.000 0.00 0.00 0.00 1.28
66 67 6.422100 GCTCGCTCAGTTTCTCATTCAATATA 59.578 38.462 0.00 0.00 0.00 0.86
67 68 7.568497 GCTCGCTCAGTTTCTCATTCAATATAC 60.568 40.741 0.00 0.00 0.00 1.47
68 69 6.417930 TCGCTCAGTTTCTCATTCAATATACG 59.582 38.462 0.00 0.00 0.00 3.06
69 70 6.199154 CGCTCAGTTTCTCATTCAATATACGT 59.801 38.462 0.00 0.00 0.00 3.57
70 71 7.378728 CGCTCAGTTTCTCATTCAATATACGTA 59.621 37.037 0.00 0.00 0.00 3.57
71 72 9.197694 GCTCAGTTTCTCATTCAATATACGTAT 57.802 33.333 13.54 13.54 0.00 3.06
87 88 9.813446 AATATACGTATATACTAGCAAAAGGGC 57.187 33.333 24.63 0.00 0.00 5.19
89 90 5.780984 ACGTATATACTAGCAAAAGGGCTC 58.219 41.667 11.05 0.00 44.54 4.70
90 91 4.857588 CGTATATACTAGCAAAAGGGCTCG 59.142 45.833 11.05 0.00 44.54 5.03
91 92 4.957684 ATATACTAGCAAAAGGGCTCGT 57.042 40.909 0.00 0.00 44.54 4.18
92 93 2.380084 TACTAGCAAAAGGGCTCGTG 57.620 50.000 3.01 0.00 44.54 4.35
93 94 0.955919 ACTAGCAAAAGGGCTCGTGC 60.956 55.000 0.00 0.00 44.54 5.34
94 95 1.970917 CTAGCAAAAGGGCTCGTGCG 61.971 60.000 3.02 0.00 44.54 5.34
95 96 2.725203 TAGCAAAAGGGCTCGTGCGT 62.725 55.000 3.02 0.00 44.54 5.24
96 97 3.030652 CAAAAGGGCTCGTGCGTT 58.969 55.556 3.02 0.00 40.82 4.84
97 98 1.358759 CAAAAGGGCTCGTGCGTTT 59.641 52.632 3.02 3.24 40.82 3.60
98 99 0.248866 CAAAAGGGCTCGTGCGTTTT 60.249 50.000 12.67 12.67 40.82 2.43
99 100 0.248866 AAAAGGGCTCGTGCGTTTTG 60.249 50.000 15.96 0.00 40.82 2.44
100 101 2.677573 AAAGGGCTCGTGCGTTTTGC 62.678 55.000 3.02 0.00 46.70 3.68
136 137 9.855021 AAAAATAACATATCTTTCTGAAACCGG 57.145 29.630 0.00 0.00 0.00 5.28
137 138 8.575649 AAATAACATATCTTTCTGAAACCGGT 57.424 30.769 0.00 0.00 0.00 5.28
138 139 7.787725 ATAACATATCTTTCTGAAACCGGTC 57.212 36.000 8.04 0.00 0.00 4.79
139 140 4.181578 ACATATCTTTCTGAAACCGGTCG 58.818 43.478 8.04 0.00 0.00 4.79
426 434 3.644606 CCAGGTGCAGGCCTCAGT 61.645 66.667 0.00 0.00 36.58 3.41
481 489 2.361357 CGTCGGTCCCCTGTCTCT 60.361 66.667 0.00 0.00 0.00 3.10
487 495 3.673597 TCCCCTGTCTCTCGCCCT 61.674 66.667 0.00 0.00 0.00 5.19
520 528 4.465446 CTCTCCTCCCGCCCTCCA 62.465 72.222 0.00 0.00 0.00 3.86
893 922 3.858868 GAAGCGTGGACAGCGTGGA 62.859 63.158 0.00 0.00 40.04 4.02
894 923 3.240134 AAGCGTGGACAGCGTGGAT 62.240 57.895 0.00 0.00 40.04 3.41
899 928 4.101448 GGACAGCGTGGATGGGCT 62.101 66.667 0.00 0.00 40.90 5.19
912 941 1.972660 ATGGGCTACAGTTCTCCGCC 61.973 60.000 0.00 0.00 39.98 6.13
945 974 3.371063 GAGGAGGTGTCGCCACGA 61.371 66.667 4.97 0.00 42.80 4.35
984 1013 0.822121 GTTGTTTCTTGGAGGCGGGT 60.822 55.000 0.00 0.00 0.00 5.28
987 1016 3.126703 TTTCTTGGAGGCGGGTGCA 62.127 57.895 0.00 0.00 45.35 4.57
997 1026 1.218047 GCGGGTGCAGACATCTGTA 59.782 57.895 10.50 3.11 45.45 2.74
1008 1037 3.448660 CAGACATCTGTACCATGGAGTCA 59.551 47.826 21.47 12.81 39.09 3.41
1012 1041 3.458044 TCTGTACCATGGAGTCAGAGT 57.542 47.619 21.47 0.00 32.49 3.24
1015 1044 2.567169 TGTACCATGGAGTCAGAGTTGG 59.433 50.000 21.47 0.00 0.00 3.77
1082 1111 0.742281 CTTGCTGATGCTACTGCGGT 60.742 55.000 2.42 2.42 43.34 5.68
1086 1115 1.150567 CTGATGCTACTGCGGTGCTC 61.151 60.000 8.92 9.66 43.34 4.26
1107 1136 0.680921 ATGTGGATTTCGGCTGTGGG 60.681 55.000 0.00 0.00 0.00 4.61
1143 1172 1.301401 CCACGCGTTCTTCCTGGAA 60.301 57.895 10.22 9.14 0.00 3.53
1178 1207 3.059982 CAGGACGGTGGAGCTCAA 58.940 61.111 17.19 0.00 0.00 3.02
1292 1321 0.184211 ATGCCATATCTGGTGCAGCA 59.816 50.000 19.03 19.03 45.10 4.41
1341 1370 4.015406 TCTCGGCGGGCAACACAT 62.015 61.111 7.21 0.00 39.74 3.21
1344 1373 3.361158 CGGCGGGCAACACATGAA 61.361 61.111 0.00 0.00 39.74 2.57
1347 1376 1.659794 GCGGGCAACACATGAAGTT 59.340 52.632 0.00 0.55 39.74 2.66
1390 1419 3.583276 AAGGTCGCGGATTGCACGA 62.583 57.895 6.13 0.00 46.97 4.35
1393 1422 4.365505 TCGCGGATTGCACGACCA 62.366 61.111 6.13 0.00 46.97 4.02
1396 1425 2.047274 CGGATTGCACGACCAGGT 60.047 61.111 0.00 0.00 0.00 4.00
1411 1440 1.913262 AGGTGGAGCGACATGTCCA 60.913 57.895 20.03 10.04 40.72 4.02
1479 1508 2.124983 CGCATCCTGGTGGTGGAG 60.125 66.667 0.00 0.00 36.99 3.86
1553 1582 2.632996 GGTATCCGGTGGAGATCATCAA 59.367 50.000 0.00 0.00 34.05 2.57
1558 1587 1.759445 CGGTGGAGATCATCAAGGAGT 59.241 52.381 0.00 0.00 0.00 3.85
1564 1593 1.123928 GATCATCAAGGAGTCCCCGT 58.876 55.000 5.25 0.00 40.87 5.28
1568 1597 0.840722 ATCAAGGAGTCCCCGTTGGT 60.841 55.000 5.25 0.00 40.87 3.67
1634 1669 4.803426 CCGCCGCCAGACTCTGAC 62.803 72.222 7.69 0.00 32.44 3.51
1649 1684 0.826715 CTGACGAGGATGTGGATGGT 59.173 55.000 0.00 0.00 0.00 3.55
1668 1703 4.041762 GCGGTGGTGGGGATGGAA 62.042 66.667 0.00 0.00 0.00 3.53
1673 1708 2.045340 GGTGGGGATGGAACGTGG 60.045 66.667 0.00 0.00 0.00 4.94
1778 1822 4.500887 GCGGTGATGAAGCTATGTACCTAA 60.501 45.833 0.00 0.00 0.00 2.69
1831 1875 1.137872 CCCAAGGACATCTCGAGAAGG 59.862 57.143 20.91 16.84 0.00 3.46
1834 1878 3.055819 CCAAGGACATCTCGAGAAGGAAA 60.056 47.826 20.91 0.00 0.00 3.13
2022 2066 5.010314 TCAGTAACGCCGGATCTTAATGTAT 59.990 40.000 5.05 0.00 0.00 2.29
2278 2325 5.202004 CCCCTACACTACTGTCAGACTTAT 58.798 45.833 6.91 0.00 0.00 1.73
2348 2396 2.229792 TGGAGAAGTTGCGATTTTGCT 58.770 42.857 0.00 0.00 35.36 3.91
2448 2496 1.448540 CGACTCCGCTTGGCTTCAT 60.449 57.895 0.00 0.00 0.00 2.57
2738 2787 1.028905 GCTCCGCAGAGACTACATCT 58.971 55.000 0.00 0.00 43.39 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.591429 CTGTGTTGCCCGCTCACA 60.591 61.111 14.02 14.02 39.31 3.58
17 18 3.610040 TGAAATCATGACAGTACGGCT 57.390 42.857 0.00 0.00 0.00 5.52
18 19 3.181510 GGTTGAAATCATGACAGTACGGC 60.182 47.826 0.00 0.00 0.00 5.68
19 20 3.062099 CGGTTGAAATCATGACAGTACGG 59.938 47.826 0.00 0.00 0.00 4.02
20 21 3.483574 GCGGTTGAAATCATGACAGTACG 60.484 47.826 0.00 0.00 0.00 3.67
21 22 3.684788 AGCGGTTGAAATCATGACAGTAC 59.315 43.478 0.00 0.00 0.00 2.73
22 23 3.932710 GAGCGGTTGAAATCATGACAGTA 59.067 43.478 0.00 0.00 0.00 2.74
23 24 2.744202 GAGCGGTTGAAATCATGACAGT 59.256 45.455 0.00 0.00 0.00 3.55
24 25 2.222886 CGAGCGGTTGAAATCATGACAG 60.223 50.000 0.00 0.00 0.00 3.51
25 26 1.731709 CGAGCGGTTGAAATCATGACA 59.268 47.619 0.00 0.00 0.00 3.58
26 27 1.529826 GCGAGCGGTTGAAATCATGAC 60.530 52.381 5.91 0.00 0.00 3.06
27 28 0.726827 GCGAGCGGTTGAAATCATGA 59.273 50.000 5.91 0.00 0.00 3.07
28 29 0.729116 AGCGAGCGGTTGAAATCATG 59.271 50.000 5.91 0.00 0.00 3.07
29 30 1.009829 GAGCGAGCGGTTGAAATCAT 58.990 50.000 5.91 0.00 0.00 2.45
30 31 0.320334 TGAGCGAGCGGTTGAAATCA 60.320 50.000 5.91 3.52 0.00 2.57
31 32 0.371645 CTGAGCGAGCGGTTGAAATC 59.628 55.000 5.91 0.79 0.00 2.17
32 33 0.320771 ACTGAGCGAGCGGTTGAAAT 60.321 50.000 5.91 0.00 0.00 2.17
33 34 0.531974 AACTGAGCGAGCGGTTGAAA 60.532 50.000 5.91 0.00 36.09 2.69
34 35 0.531974 AAACTGAGCGAGCGGTTGAA 60.532 50.000 5.91 0.00 37.43 2.69
35 36 0.944311 GAAACTGAGCGAGCGGTTGA 60.944 55.000 5.91 0.00 37.43 3.18
36 37 0.946221 AGAAACTGAGCGAGCGGTTG 60.946 55.000 0.00 0.00 37.43 3.77
37 38 0.667792 GAGAAACTGAGCGAGCGGTT 60.668 55.000 0.00 0.00 38.96 4.44
38 39 1.080434 GAGAAACTGAGCGAGCGGT 60.080 57.895 0.00 0.00 0.00 5.68
39 40 0.459237 ATGAGAAACTGAGCGAGCGG 60.459 55.000 0.00 0.00 0.00 5.52
40 41 1.322936 GAATGAGAAACTGAGCGAGCG 59.677 52.381 0.00 0.00 0.00 5.03
41 42 2.341257 TGAATGAGAAACTGAGCGAGC 58.659 47.619 0.00 0.00 0.00 5.03
42 43 6.841443 ATATTGAATGAGAAACTGAGCGAG 57.159 37.500 0.00 0.00 0.00 5.03
43 44 6.417930 CGTATATTGAATGAGAAACTGAGCGA 59.582 38.462 0.00 0.00 0.00 4.93
44 45 6.199154 ACGTATATTGAATGAGAAACTGAGCG 59.801 38.462 0.00 0.00 0.00 5.03
45 46 7.470289 ACGTATATTGAATGAGAAACTGAGC 57.530 36.000 0.00 0.00 0.00 4.26
61 62 9.813446 GCCCTTTTGCTAGTATATACGTATATT 57.187 33.333 28.16 16.52 31.69 1.28
62 63 9.198475 AGCCCTTTTGCTAGTATATACGTATAT 57.802 33.333 26.67 26.67 40.56 0.86
63 64 8.585471 AGCCCTTTTGCTAGTATATACGTATA 57.415 34.615 17.24 17.24 40.56 1.47
64 65 7.477945 AGCCCTTTTGCTAGTATATACGTAT 57.522 36.000 13.54 13.54 40.56 3.06
65 66 6.348786 CGAGCCCTTTTGCTAGTATATACGTA 60.349 42.308 7.23 0.00 42.95 3.57
66 67 5.564259 CGAGCCCTTTTGCTAGTATATACGT 60.564 44.000 7.23 0.00 42.95 3.57
67 68 4.857588 CGAGCCCTTTTGCTAGTATATACG 59.142 45.833 7.23 0.00 42.95 3.06
68 69 5.634020 CACGAGCCCTTTTGCTAGTATATAC 59.366 44.000 4.60 4.60 43.98 1.47
69 70 5.779922 CACGAGCCCTTTTGCTAGTATATA 58.220 41.667 0.00 0.00 43.98 0.86
70 71 4.632153 CACGAGCCCTTTTGCTAGTATAT 58.368 43.478 0.00 0.00 43.98 0.86
71 72 3.740141 GCACGAGCCCTTTTGCTAGTATA 60.740 47.826 0.00 0.00 43.98 1.47
72 73 2.906354 CACGAGCCCTTTTGCTAGTAT 58.094 47.619 0.00 0.00 43.98 2.12
73 74 1.674817 GCACGAGCCCTTTTGCTAGTA 60.675 52.381 0.00 0.00 43.98 1.82
74 75 0.955919 GCACGAGCCCTTTTGCTAGT 60.956 55.000 0.00 0.00 46.25 2.57
75 76 1.796796 GCACGAGCCCTTTTGCTAG 59.203 57.895 0.00 0.00 42.95 3.42
76 77 2.032634 CGCACGAGCCCTTTTGCTA 61.033 57.895 0.00 0.00 42.95 3.49
77 78 3.357079 CGCACGAGCCCTTTTGCT 61.357 61.111 0.00 0.00 46.37 3.91
78 79 2.677573 AAACGCACGAGCCCTTTTGC 62.678 55.000 0.00 0.00 37.52 3.68
79 80 0.248866 AAAACGCACGAGCCCTTTTG 60.249 50.000 0.00 0.00 37.52 2.44
80 81 0.248866 CAAAACGCACGAGCCCTTTT 60.249 50.000 0.00 0.94 37.52 2.27
81 82 1.358759 CAAAACGCACGAGCCCTTT 59.641 52.632 0.00 0.00 37.52 3.11
82 83 3.030652 CAAAACGCACGAGCCCTT 58.969 55.556 0.00 0.00 37.52 3.95
83 84 3.660111 GCAAAACGCACGAGCCCT 61.660 61.111 0.00 0.00 41.79 5.19
92 93 1.551145 TTTCTTCCGTTGCAAAACGC 58.449 45.000 0.00 0.00 44.18 4.84
110 111 9.855021 CCGGTTTCAGAAAGATATGTTATTTTT 57.145 29.630 0.00 0.00 0.00 1.94
111 112 9.020731 ACCGGTTTCAGAAAGATATGTTATTTT 57.979 29.630 0.00 0.00 0.00 1.82
112 113 8.575649 ACCGGTTTCAGAAAGATATGTTATTT 57.424 30.769 0.00 0.00 0.00 1.40
113 114 7.011109 CGACCGGTTTCAGAAAGATATGTTATT 59.989 37.037 9.42 0.00 0.00 1.40
114 115 6.479001 CGACCGGTTTCAGAAAGATATGTTAT 59.521 38.462 9.42 0.00 0.00 1.89
115 116 5.808540 CGACCGGTTTCAGAAAGATATGTTA 59.191 40.000 9.42 0.00 0.00 2.41
116 117 4.630069 CGACCGGTTTCAGAAAGATATGTT 59.370 41.667 9.42 0.00 0.00 2.71
117 118 4.181578 CGACCGGTTTCAGAAAGATATGT 58.818 43.478 9.42 0.00 0.00 2.29
118 119 3.001330 GCGACCGGTTTCAGAAAGATATG 59.999 47.826 9.42 0.00 0.00 1.78
119 120 3.195661 GCGACCGGTTTCAGAAAGATAT 58.804 45.455 9.42 0.00 0.00 1.63
120 121 2.613691 GCGACCGGTTTCAGAAAGATA 58.386 47.619 9.42 0.00 0.00 1.98
121 122 1.439679 GCGACCGGTTTCAGAAAGAT 58.560 50.000 9.42 0.00 0.00 2.40
122 123 0.942410 CGCGACCGGTTTCAGAAAGA 60.942 55.000 9.42 0.00 0.00 2.52
123 124 1.491563 CGCGACCGGTTTCAGAAAG 59.508 57.895 9.42 0.00 0.00 2.62
124 125 2.600475 GCGCGACCGGTTTCAGAAA 61.600 57.895 12.10 0.00 34.32 2.52
125 126 3.039588 GCGCGACCGGTTTCAGAA 61.040 61.111 12.10 0.00 34.32 3.02
126 127 3.909258 GAGCGCGACCGGTTTCAGA 62.909 63.158 12.10 0.00 46.40 3.27
127 128 3.479269 GAGCGCGACCGGTTTCAG 61.479 66.667 12.10 1.84 46.40 3.02
253 254 4.764771 GGCTCCCCATGCCTGCAA 62.765 66.667 0.00 0.00 46.38 4.08
352 360 3.729489 AGCCGAGGACGAGGAGGA 61.729 66.667 0.00 0.00 42.66 3.71
487 495 2.678934 AGCAAGTCCGACGGCCTA 60.679 61.111 9.66 0.00 0.00 3.93
498 506 3.394836 GGCGGGAGGAGAGCAAGT 61.395 66.667 0.00 0.00 0.00 3.16
520 528 1.836999 TAGCAACACCCATGGAGCGT 61.837 55.000 15.22 3.86 35.55 5.07
573 600 2.110213 GTCGGGTTGGTGCAGTGA 59.890 61.111 0.00 0.00 0.00 3.41
679 706 3.787001 CAGACGAAGGGGAGGGGC 61.787 72.222 0.00 0.00 0.00 5.80
835 864 4.404098 GTCCGACCATGCCCGGTT 62.404 66.667 19.05 0.00 45.48 4.44
893 922 1.522569 GCGGAGAACTGTAGCCCAT 59.477 57.895 0.00 0.00 0.00 4.00
894 923 2.656069 GGCGGAGAACTGTAGCCCA 61.656 63.158 0.00 0.00 41.81 5.36
899 928 1.880819 GAACGGGGCGGAGAACTGTA 61.881 60.000 0.00 0.00 0.00 2.74
945 974 2.203788 TCCACCGGCTCTTCCTGT 60.204 61.111 0.00 0.00 31.96 4.00
951 980 1.696097 AACAACAGTCCACCGGCTCT 61.696 55.000 0.00 0.00 0.00 4.09
997 1026 0.326264 GCCAACTCTGACTCCATGGT 59.674 55.000 12.58 0.00 0.00 3.55
1045 1074 4.373116 GTCCAGACTTGGGCGCGA 62.373 66.667 12.10 0.00 45.10 5.87
1086 1115 0.452987 CACAGCCGAAATCCACATGG 59.547 55.000 0.00 0.00 0.00 3.66
1127 1156 2.046938 TCTTCCAGGAAGAACGCGT 58.953 52.632 27.25 5.58 44.37 6.01
1143 1172 2.800250 CTGCAAAGGACCAGGAAATCT 58.200 47.619 0.00 0.00 0.00 2.40
1158 1187 3.240134 GAGCTCCACCGTCCTGCAA 62.240 63.158 0.87 0.00 0.00 4.08
1178 1207 0.106369 TCGATCCACCATACGGTCCT 60.106 55.000 0.00 0.00 44.71 3.85
1246 1275 0.323633 CCAACATCCCATGACTGGCA 60.324 55.000 0.00 0.00 41.64 4.92
1278 1307 1.884464 CGCGTGCTGCACCAGATAT 60.884 57.895 25.61 0.00 46.97 1.63
1336 1365 0.673437 CCCCGCAAAACTTCATGTGT 59.327 50.000 0.00 0.00 0.00 3.72
1338 1367 1.112315 TGCCCCGCAAAACTTCATGT 61.112 50.000 0.00 0.00 34.76 3.21
1341 1370 1.861542 CGATGCCCCGCAAAACTTCA 61.862 55.000 0.00 0.00 43.62 3.02
1344 1373 3.061848 CCGATGCCCCGCAAAACT 61.062 61.111 0.00 0.00 43.62 2.66
1347 1376 2.598985 AAACCGATGCCCCGCAAA 60.599 55.556 0.00 0.00 43.62 3.68
1390 1419 2.172483 GACATGTCGCTCCACCTGGT 62.172 60.000 10.69 0.00 36.34 4.00
1393 1422 1.892819 CTGGACATGTCGCTCCACCT 61.893 60.000 19.33 0.00 32.84 4.00
1396 1425 1.830587 AAGCTGGACATGTCGCTCCA 61.831 55.000 23.16 14.48 35.20 3.86
1411 1440 1.905354 GCAGCCAAACCCTGAAGCT 60.905 57.895 0.00 0.00 32.03 3.74
1511 1540 2.615227 GAAGGCATCCACCGCATCCT 62.615 60.000 0.00 0.00 33.69 3.24
1517 1546 0.469917 ATACCAGAAGGCATCCACCG 59.530 55.000 0.00 0.00 39.06 4.94
1553 1582 2.606826 GGACCAACGGGGACTCCT 60.607 66.667 2.06 0.00 41.15 3.69
1634 1669 1.592669 GCGACCATCCACATCCTCG 60.593 63.158 0.00 0.00 0.00 4.63
1754 1798 2.224066 GGTACATAGCTTCATCACCGCT 60.224 50.000 0.00 0.00 37.77 5.52
1825 1869 2.930826 TGACAGGTGGTTTCCTTCTC 57.069 50.000 0.00 0.00 35.37 2.87
2022 2066 6.555463 CCCTCAGTTATGTAGGGTTTAAGA 57.445 41.667 0.00 0.00 44.34 2.10
2059 2103 3.830755 GGGGTGGCTTATATAGAGTTCGA 59.169 47.826 0.00 0.00 0.00 3.71
2278 2325 1.957186 GCGCCAACTGTCGTGGTTA 60.957 57.895 0.00 0.00 0.00 2.85
2348 2396 5.434408 CTGAAACCATGATGAAGGAGATCA 58.566 41.667 0.00 0.00 34.37 2.92
2738 2787 0.389037 GATCACTGCTGTCGCACTCA 60.389 55.000 0.00 0.00 42.25 3.41


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

AutoCloner maintained by Alex Coulton.