Multiple sequence alignment - TraesCS2D01G331700

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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 TraesCS2D01G331700 chr2D 100.000 3241 0 0 1 3241 424016517 424013277 0.000000e+00 5986.0
1 TraesCS2D01G331700 chr2D 79.684 950 101 51 625 1540 624297951 624297060 4.630000e-168 601.0
2 TraesCS2D01G331700 chr2D 81.752 137 21 4 1227 1361 556365634 556365768 9.510000e-21 111.0
3 TraesCS2D01G331700 chr2B 92.777 2312 99 30 100 2366 498311913 498309625 0.000000e+00 3282.0
4 TraesCS2D01G331700 chr2B 85.859 495 44 11 2639 3122 498308122 498307643 1.340000e-138 503.0
5 TraesCS2D01G331700 chr2B 92.509 267 15 4 2358 2622 498308494 498308231 8.490000e-101 377.0
6 TraesCS2D01G331700 chr2A 93.895 2195 70 21 467 2610 564217830 564220011 0.000000e+00 3253.0
7 TraesCS2D01G331700 chr2A 86.977 645 54 20 2608 3240 564220151 564220777 0.000000e+00 699.0
8 TraesCS2D01G331700 chr2A 95.513 156 5 2 270 423 564217666 564217821 6.940000e-62 248.0
9 TraesCS2D01G331700 chr2A 89.011 182 14 2 966 1141 755700321 755700140 1.510000e-53 220.0
10 TraesCS2D01G331700 chrUn 84.483 348 28 15 1220 1541 232286338 232285991 1.450000e-83 320.0
11 TraesCS2D01G331700 chrUn 91.061 179 13 1 966 1141 232287818 232287640 4.180000e-59 239.0
12 TraesCS2D01G331700 chr6B 74.157 356 72 16 1225 1569 574021258 574020912 2.620000e-26 130.0
13 TraesCS2D01G331700 chr4B 86.066 122 13 3 1441 1560 413500304 413500423 9.440000e-26 128.0
14 TraesCS2D01G331700 chr3A 93.976 83 5 0 1443 1525 514611935 514611853 3.390000e-25 126.0
15 TraesCS2D01G331700 chr6D 91.954 87 7 0 1443 1529 432709198 432709112 4.390000e-24 122.0
16 TraesCS2D01G331700 chr4D 91.111 90 8 0 1441 1530 335349330 335349419 4.390000e-24 122.0
17 TraesCS2D01G331700 chr4A 85.124 121 14 3 1441 1559 137523974 137523856 1.580000e-23 121.0
18 TraesCS2D01G331700 chr7B 76.437 174 33 7 2865 3034 156218707 156218876 1.600000e-13 87.9
19 TraesCS2D01G331700 chr5D 82.796 93 15 1 2 93 135083376 135083284 7.450000e-12 82.4
20 TraesCS2D01G331700 chr3D 94.595 37 2 0 48 84 352120180 352120144 1.260000e-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 TraesCS2D01G331700 chr2D 424013277 424016517 3240 True 5986.000000 5986 100.000000 1 3241 1 chr2D.!!$R1 3240
1 TraesCS2D01G331700 chr2D 624297060 624297951 891 True 601.000000 601 79.684000 625 1540 1 chr2D.!!$R2 915
2 TraesCS2D01G331700 chr2B 498307643 498311913 4270 True 1387.333333 3282 90.381667 100 3122 3 chr2B.!!$R1 3022
3 TraesCS2D01G331700 chr2A 564217666 564220777 3111 False 1400.000000 3253 92.128333 270 3240 3 chr2A.!!$F1 2970
4 TraesCS2D01G331700 chrUn 232285991 232287818 1827 True 279.500000 320 87.772000 966 1541 2 chrUn.!!$R1 575

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
200 201 0.028902 GTTGGGTGACAAACTGCGTC 59.971 55.0 0.00 0.0 41.58 5.19 F
503 506 0.593128 CTTTGACTCAAAGGGGTGCG 59.407 55.0 19.95 0.0 44.75 5.34 F
1409 2751 0.316522 GATAGCTGCATCGCTCTGGA 59.683 55.0 3.37 0.0 41.30 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1363 2678 1.333347 CGAGACGACGTGGATCATCTC 60.333 57.143 4.58 5.26 0.00 2.75 R
1640 2988 1.738099 CTCGTCCTTGAAGCACCCG 60.738 63.158 0.00 0.00 0.00 5.28 R
2633 5275 0.112995 TTGGTGCCCAGCAGATCTTT 59.887 50.000 0.00 0.00 40.08 2.52 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 3.388841 ACGGGTGCAGAGTAAGGG 58.611 61.111 0.00 0.00 0.00 3.95
18 19 2.291043 ACGGGTGCAGAGTAAGGGG 61.291 63.158 0.00 0.00 0.00 4.79
19 20 2.998949 GGGTGCAGAGTAAGGGGG 59.001 66.667 0.00 0.00 0.00 5.40
20 21 1.615424 GGGTGCAGAGTAAGGGGGA 60.615 63.158 0.00 0.00 0.00 4.81
21 22 1.205460 GGGTGCAGAGTAAGGGGGAA 61.205 60.000 0.00 0.00 0.00 3.97
22 23 0.253327 GGTGCAGAGTAAGGGGGAAG 59.747 60.000 0.00 0.00 0.00 3.46
23 24 0.253327 GTGCAGAGTAAGGGGGAAGG 59.747 60.000 0.00 0.00 0.00 3.46
24 25 0.914417 TGCAGAGTAAGGGGGAAGGG 60.914 60.000 0.00 0.00 0.00 3.95
25 26 0.620700 GCAGAGTAAGGGGGAAGGGA 60.621 60.000 0.00 0.00 0.00 4.20
26 27 1.205055 CAGAGTAAGGGGGAAGGGAC 58.795 60.000 0.00 0.00 0.00 4.46
27 28 0.797579 AGAGTAAGGGGGAAGGGACA 59.202 55.000 0.00 0.00 0.00 4.02
28 29 1.153565 AGAGTAAGGGGGAAGGGACAA 59.846 52.381 0.00 0.00 0.00 3.18
29 30 1.990327 GAGTAAGGGGGAAGGGACAAA 59.010 52.381 0.00 0.00 0.00 2.83
30 31 2.377531 GAGTAAGGGGGAAGGGACAAAA 59.622 50.000 0.00 0.00 0.00 2.44
31 32 2.792967 AGTAAGGGGGAAGGGACAAAAA 59.207 45.455 0.00 0.00 0.00 1.94
32 33 2.097110 AAGGGGGAAGGGACAAAAAC 57.903 50.000 0.00 0.00 0.00 2.43
33 34 0.938192 AGGGGGAAGGGACAAAAACA 59.062 50.000 0.00 0.00 0.00 2.83
34 35 1.045407 GGGGGAAGGGACAAAAACAC 58.955 55.000 0.00 0.00 0.00 3.32
35 36 0.671796 GGGGAAGGGACAAAAACACG 59.328 55.000 0.00 0.00 0.00 4.49
36 37 0.671796 GGGAAGGGACAAAAACACGG 59.328 55.000 0.00 0.00 0.00 4.94
37 38 0.671796 GGAAGGGACAAAAACACGGG 59.328 55.000 0.00 0.00 0.00 5.28
38 39 1.395635 GAAGGGACAAAAACACGGGT 58.604 50.000 0.00 0.00 0.00 5.28
39 40 1.752498 GAAGGGACAAAAACACGGGTT 59.248 47.619 0.00 0.00 39.43 4.11
41 42 1.478916 AGGGACAAAAACACGGGTTTG 59.521 47.619 18.07 8.77 46.20 2.93
42 43 1.471851 GGGACAAAAACACGGGTTTGG 60.472 52.381 18.07 14.62 46.20 3.28
43 44 1.471851 GGACAAAAACACGGGTTTGGG 60.472 52.381 18.07 14.25 46.20 4.12
44 45 1.205179 GACAAAAACACGGGTTTGGGT 59.795 47.619 18.07 17.47 46.20 4.51
45 46 1.066787 ACAAAAACACGGGTTTGGGTG 60.067 47.619 18.07 16.93 46.20 4.61
46 47 1.204941 CAAAAACACGGGTTTGGGTGA 59.795 47.619 18.07 0.00 46.20 4.02
47 48 1.107945 AAAACACGGGTTTGGGTGAG 58.892 50.000 18.07 0.00 46.20 3.51
48 49 0.753848 AAACACGGGTTTGGGTGAGG 60.754 55.000 16.48 0.00 45.22 3.86
49 50 1.928714 AACACGGGTTTGGGTGAGGT 61.929 55.000 0.00 0.00 37.58 3.85
50 51 1.152839 CACGGGTTTGGGTGAGGTT 60.153 57.895 0.00 0.00 36.25 3.50
51 52 0.753848 CACGGGTTTGGGTGAGGTTT 60.754 55.000 0.00 0.00 36.25 3.27
52 53 0.032912 ACGGGTTTGGGTGAGGTTTT 60.033 50.000 0.00 0.00 0.00 2.43
53 54 1.116308 CGGGTTTGGGTGAGGTTTTT 58.884 50.000 0.00 0.00 0.00 1.94
67 68 3.017139 TTTTTGTGGGTCGGGGGT 58.983 55.556 0.00 0.00 0.00 4.95
68 69 1.455959 TTTTTGTGGGTCGGGGGTG 60.456 57.895 0.00 0.00 0.00 4.61
69 70 2.226149 TTTTTGTGGGTCGGGGGTGT 62.226 55.000 0.00 0.00 0.00 4.16
70 71 2.627839 TTTTGTGGGTCGGGGGTGTC 62.628 60.000 0.00 0.00 0.00 3.67
73 74 4.938074 TGGGTCGGGGGTGTCGAA 62.938 66.667 0.00 0.00 38.42 3.71
74 75 4.078516 GGGTCGGGGGTGTCGAAG 62.079 72.222 0.00 0.00 38.42 3.79
75 76 3.308705 GGTCGGGGGTGTCGAAGT 61.309 66.667 0.00 0.00 38.42 3.01
76 77 2.260743 GTCGGGGGTGTCGAAGTC 59.739 66.667 0.00 0.00 38.42 3.01
77 78 2.993264 TCGGGGGTGTCGAAGTCC 60.993 66.667 0.00 0.00 33.42 3.85
78 79 2.995574 CGGGGGTGTCGAAGTCCT 60.996 66.667 0.00 0.00 0.00 3.85
79 80 1.679977 CGGGGGTGTCGAAGTCCTA 60.680 63.158 0.00 0.00 0.00 2.94
80 81 1.895966 GGGGGTGTCGAAGTCCTAC 59.104 63.158 0.00 0.00 0.00 3.18
81 82 1.509923 GGGGTGTCGAAGTCCTACG 59.490 63.158 0.00 0.00 0.00 3.51
82 83 1.246737 GGGGTGTCGAAGTCCTACGT 61.247 60.000 0.00 0.00 0.00 3.57
83 84 0.109412 GGGTGTCGAAGTCCTACGTG 60.109 60.000 0.00 0.00 0.00 4.49
84 85 0.109412 GGTGTCGAAGTCCTACGTGG 60.109 60.000 0.00 0.00 37.10 4.94
85 86 0.731855 GTGTCGAAGTCCTACGTGGC 60.732 60.000 0.00 0.00 35.26 5.01
86 87 1.174078 TGTCGAAGTCCTACGTGGCA 61.174 55.000 0.00 0.00 35.26 4.92
87 88 0.456312 GTCGAAGTCCTACGTGGCAG 60.456 60.000 0.00 0.00 35.26 4.85
88 89 0.607217 TCGAAGTCCTACGTGGCAGA 60.607 55.000 0.00 0.00 35.26 4.26
89 90 0.179161 CGAAGTCCTACGTGGCAGAG 60.179 60.000 0.00 0.00 35.26 3.35
90 91 0.173708 GAAGTCCTACGTGGCAGAGG 59.826 60.000 0.00 0.00 35.26 3.69
91 92 0.542232 AAGTCCTACGTGGCAGAGGT 60.542 55.000 0.00 1.24 35.26 3.85
92 93 0.966370 AGTCCTACGTGGCAGAGGTC 60.966 60.000 0.00 4.97 35.26 3.85
93 94 0.966370 GTCCTACGTGGCAGAGGTCT 60.966 60.000 0.00 0.00 35.26 3.85
94 95 0.965866 TCCTACGTGGCAGAGGTCTG 60.966 60.000 0.00 2.37 46.40 3.51
95 96 1.513158 CTACGTGGCAGAGGTCTGG 59.487 63.158 9.03 0.00 43.94 3.86
96 97 0.965866 CTACGTGGCAGAGGTCTGGA 60.966 60.000 9.03 0.00 43.94 3.86
97 98 1.248785 TACGTGGCAGAGGTCTGGAC 61.249 60.000 9.03 0.00 43.94 4.02
98 99 2.574018 CGTGGCAGAGGTCTGGACA 61.574 63.158 9.03 0.00 43.94 4.02
142 143 3.509442 TGCATCCTGTTTCTGGGATTTT 58.491 40.909 0.00 0.00 40.01 1.82
158 159 2.035237 TTTTGGACAGCCGGACGAGT 62.035 55.000 5.05 0.86 36.79 4.18
175 176 1.267806 GAGTCCAAGAACGTGTACGGA 59.732 52.381 9.40 0.00 44.95 4.69
176 177 1.682854 AGTCCAAGAACGTGTACGGAA 59.317 47.619 9.40 0.00 44.95 4.30
200 201 0.028902 GTTGGGTGACAAACTGCGTC 59.971 55.000 0.00 0.00 41.58 5.19
204 205 1.279840 GTGACAAACTGCGTCCAGC 59.720 57.895 0.00 0.00 43.02 4.85
423 426 5.832539 TGGAGAGAAAAATCTGGAGTCTT 57.167 39.130 0.00 0.00 0.00 3.01
442 445 6.767456 AGTCTTTGTCTCTCTGAATGAATGT 58.233 36.000 0.00 0.00 0.00 2.71
444 447 6.648310 GTCTTTGTCTCTCTGAATGAATGTCA 59.352 38.462 0.00 0.00 0.00 3.58
445 448 7.333921 GTCTTTGTCTCTCTGAATGAATGTCAT 59.666 37.037 0.00 0.00 39.09 3.06
447 450 6.980051 TGTCTCTCTGAATGAATGTCATTG 57.020 37.500 8.16 0.00 46.20 2.82
448 451 5.353400 TGTCTCTCTGAATGAATGTCATTGC 59.647 40.000 8.16 1.97 46.20 3.56
449 452 5.353400 GTCTCTCTGAATGAATGTCATTGCA 59.647 40.000 8.16 1.80 46.20 4.08
450 453 5.941647 TCTCTCTGAATGAATGTCATTGCAA 59.058 36.000 0.00 0.00 46.20 4.08
451 454 6.602009 TCTCTCTGAATGAATGTCATTGCAAT 59.398 34.615 5.99 5.99 46.20 3.56
454 457 6.103330 TCTGAATGAATGTCATTGCAATTGG 58.897 36.000 9.83 0.00 46.20 3.16
455 458 6.038997 TGAATGAATGTCATTGCAATTGGA 57.961 33.333 9.83 0.23 46.20 3.53
456 459 6.465084 TGAATGAATGTCATTGCAATTGGAA 58.535 32.000 15.13 15.13 46.20 3.53
503 506 0.593128 CTTTGACTCAAAGGGGTGCG 59.407 55.000 19.95 0.00 44.75 5.34
504 507 0.821711 TTTGACTCAAAGGGGTGCGG 60.822 55.000 0.00 0.00 0.00 5.69
505 508 3.056328 GACTCAAAGGGGTGCGGC 61.056 66.667 0.00 0.00 0.00 6.53
506 509 4.660938 ACTCAAAGGGGTGCGGCC 62.661 66.667 0.00 0.00 0.00 6.13
769 798 4.496336 ATGCCTCCTTCGCCCAGC 62.496 66.667 0.00 0.00 0.00 4.85
1192 2494 1.061887 GAACGTGCGTTGCTGTTGT 59.938 52.632 14.89 0.00 38.60 3.32
1363 2678 1.736645 CGTCGGCAACAGGTACCAG 60.737 63.158 15.94 9.05 0.00 4.00
1376 2698 2.032620 GGTACCAGAGATGATCCACGT 58.967 52.381 7.15 0.00 0.00 4.49
1409 2751 0.316522 GATAGCTGCATCGCTCTGGA 59.683 55.000 3.37 0.00 41.30 3.86
1547 2895 2.526624 TCCGGGATGGGCATCGAT 60.527 61.111 0.00 0.00 38.69 3.59
2099 3447 0.182775 AGGAAAAGGGCAACGACAGT 59.817 50.000 0.00 0.00 37.60 3.55
2319 3674 2.789409 AGCCTAGAGCCAAACGATTT 57.211 45.000 0.00 0.00 45.47 2.17
2389 4883 1.067846 GGGAAACTGGAAAATGGCGTC 60.068 52.381 0.00 0.00 0.00 5.19
2394 4888 0.811281 CTGGAAAATGGCGTCCCTTC 59.189 55.000 0.00 0.00 32.48 3.46
2563 5065 6.639279 ACATGTCAATGTTTTAGTAAAACCGC 59.361 34.615 27.59 16.52 44.94 5.68
2591 5094 2.314561 TTTGAAATGAAGCTGACGCG 57.685 45.000 3.53 3.53 42.32 6.01
2600 5103 1.128692 GAAGCTGACGCGCTGTAATTT 59.871 47.619 5.73 0.00 40.79 1.82
2675 5317 2.000447 CGTGCTACACTTTTAGGGCTC 59.000 52.381 0.00 0.00 31.34 4.70
2760 5402 2.543012 TGCGCAAAACAAATGATTGGTG 59.457 40.909 8.16 0.00 41.01 4.17
2778 5420 4.452825 TGGTGAACACGGAGATTGTTAAA 58.547 39.130 0.00 0.00 37.31 1.52
2802 5451 7.039722 AGGTTTCTATTAACTGAATTGGGGA 57.960 36.000 0.00 0.00 0.00 4.81
2804 5453 6.183360 GGTTTCTATTAACTGAATTGGGGAGC 60.183 42.308 0.00 0.00 0.00 4.70
2807 5456 1.681229 TAACTGAATTGGGGAGCCCT 58.319 50.000 5.38 0.00 45.70 5.19
2845 5495 2.979813 CACGGAAATTCTGCCTTTTTCG 59.020 45.455 1.01 0.00 39.24 3.46
2853 5504 1.203001 TCTGCCTTTTTCGTGGGGAAT 60.203 47.619 0.00 0.00 33.85 3.01
2886 5537 4.000325 TGGGTGTACGATTCACAAGAATG 59.000 43.478 0.00 0.00 44.30 2.67
2888 5539 3.374058 GGTGTACGATTCACAAGAATGGG 59.626 47.826 0.00 0.00 44.30 4.00
2898 5549 5.667539 TCACAAGAATGGGAAAACACAAA 57.332 34.783 0.00 0.00 35.57 2.83
2904 5555 6.245890 AGAATGGGAAAACACAAAAATCCA 57.754 33.333 0.00 0.00 31.63 3.41
2917 5568 8.744568 ACACAAAAATCCAAATAAACATGGTT 57.255 26.923 0.00 0.00 0.00 3.67
2945 5597 5.544136 AAAGTCAAACCACACAAAAATGC 57.456 34.783 0.00 0.00 0.00 3.56
2987 5639 4.081642 TGCCACTAAGGATGTTAGTCTCAC 60.082 45.833 0.00 0.00 41.22 3.51
2990 5642 5.449314 CCACTAAGGATGTTAGTCTCACTCG 60.449 48.000 0.00 0.00 41.22 4.18
3009 5661 6.371548 TCACTCGTGGATAGGAATTTGAAAAG 59.628 38.462 0.00 0.00 0.00 2.27
3042 5694 8.906867 CAGGTGGATATTAGAATTGATGTGTTT 58.093 33.333 0.00 0.00 0.00 2.83
3044 5696 9.736023 GGTGGATATTAGAATTGATGTGTTTTC 57.264 33.333 0.00 0.00 0.00 2.29
3124 5776 4.389992 CCAAATGCATGGATAGTACTAGCG 59.610 45.833 11.81 0.04 43.54 4.26
3126 5778 5.977489 AATGCATGGATAGTACTAGCGTA 57.023 39.130 11.81 4.35 0.00 4.42
3165 5817 3.750922 CGTTTTTCCTCCCCTTCTCCTTT 60.751 47.826 0.00 0.00 0.00 3.11
3169 5821 1.985895 TCCTCCCCTTCTCCTTTGAAC 59.014 52.381 0.00 0.00 0.00 3.18
3179 5831 1.273606 CTCCTTTGAACGAGAGAGGCA 59.726 52.381 0.00 0.00 0.00 4.75
3198 5851 7.398024 AGAGGCACTTTTAAGATGAACACTAT 58.602 34.615 0.00 0.00 41.55 2.12
3228 5881 7.881775 AAGGTTTATATGTGGACTCAAATCC 57.118 36.000 0.00 0.00 39.45 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.584608 CCCCTTACTCTGCACCCG 59.415 66.667 0.00 0.00 0.00 5.28
2 3 1.205460 TTCCCCCTTACTCTGCACCC 61.205 60.000 0.00 0.00 0.00 4.61
3 4 0.253327 CTTCCCCCTTACTCTGCACC 59.747 60.000 0.00 0.00 0.00 5.01
4 5 0.253327 CCTTCCCCCTTACTCTGCAC 59.747 60.000 0.00 0.00 0.00 4.57
5 6 0.914417 CCCTTCCCCCTTACTCTGCA 60.914 60.000 0.00 0.00 0.00 4.41
6 7 0.620700 TCCCTTCCCCCTTACTCTGC 60.621 60.000 0.00 0.00 0.00 4.26
7 8 1.205055 GTCCCTTCCCCCTTACTCTG 58.795 60.000 0.00 0.00 0.00 3.35
8 9 0.797579 TGTCCCTTCCCCCTTACTCT 59.202 55.000 0.00 0.00 0.00 3.24
9 10 1.665137 TTGTCCCTTCCCCCTTACTC 58.335 55.000 0.00 0.00 0.00 2.59
10 11 2.143231 TTTGTCCCTTCCCCCTTACT 57.857 50.000 0.00 0.00 0.00 2.24
11 12 2.895404 GTTTTTGTCCCTTCCCCCTTAC 59.105 50.000 0.00 0.00 0.00 2.34
12 13 2.518834 TGTTTTTGTCCCTTCCCCCTTA 59.481 45.455 0.00 0.00 0.00 2.69
13 14 1.292546 TGTTTTTGTCCCTTCCCCCTT 59.707 47.619 0.00 0.00 0.00 3.95
14 15 0.938192 TGTTTTTGTCCCTTCCCCCT 59.062 50.000 0.00 0.00 0.00 4.79
15 16 1.045407 GTGTTTTTGTCCCTTCCCCC 58.955 55.000 0.00 0.00 0.00 5.40
16 17 0.671796 CGTGTTTTTGTCCCTTCCCC 59.328 55.000 0.00 0.00 0.00 4.81
17 18 0.671796 CCGTGTTTTTGTCCCTTCCC 59.328 55.000 0.00 0.00 0.00 3.97
18 19 0.671796 CCCGTGTTTTTGTCCCTTCC 59.328 55.000 0.00 0.00 0.00 3.46
19 20 1.395635 ACCCGTGTTTTTGTCCCTTC 58.604 50.000 0.00 0.00 0.00 3.46
20 21 1.855295 AACCCGTGTTTTTGTCCCTT 58.145 45.000 0.00 0.00 0.00 3.95
21 22 1.478916 CAAACCCGTGTTTTTGTCCCT 59.521 47.619 0.00 0.00 41.92 4.20
22 23 1.471851 CCAAACCCGTGTTTTTGTCCC 60.472 52.381 0.00 0.00 41.92 4.46
23 24 1.471851 CCCAAACCCGTGTTTTTGTCC 60.472 52.381 0.00 0.00 41.92 4.02
24 25 1.205179 ACCCAAACCCGTGTTTTTGTC 59.795 47.619 0.00 0.00 41.92 3.18
25 26 1.066787 CACCCAAACCCGTGTTTTTGT 60.067 47.619 0.00 0.00 41.92 2.83
26 27 1.204941 TCACCCAAACCCGTGTTTTTG 59.795 47.619 0.00 0.00 41.92 2.44
27 28 1.478916 CTCACCCAAACCCGTGTTTTT 59.521 47.619 0.00 0.00 41.92 1.94
28 29 1.107945 CTCACCCAAACCCGTGTTTT 58.892 50.000 0.00 0.00 41.92 2.43
29 30 0.753848 CCTCACCCAAACCCGTGTTT 60.754 55.000 0.00 0.00 45.46 2.83
30 31 1.152839 CCTCACCCAAACCCGTGTT 60.153 57.895 0.00 0.00 35.82 3.32
31 32 1.928714 AACCTCACCCAAACCCGTGT 61.929 55.000 0.00 0.00 0.00 4.49
32 33 0.753848 AAACCTCACCCAAACCCGTG 60.754 55.000 0.00 0.00 0.00 4.94
33 34 0.032912 AAAACCTCACCCAAACCCGT 60.033 50.000 0.00 0.00 0.00 5.28
34 35 1.116308 AAAAACCTCACCCAAACCCG 58.884 50.000 0.00 0.00 0.00 5.28
50 51 1.455959 CACCCCCGACCCACAAAAA 60.456 57.895 0.00 0.00 0.00 1.94
51 52 2.196229 CACCCCCGACCCACAAAA 59.804 61.111 0.00 0.00 0.00 2.44
52 53 3.097830 ACACCCCCGACCCACAAA 61.098 61.111 0.00 0.00 0.00 2.83
53 54 3.562232 GACACCCCCGACCCACAA 61.562 66.667 0.00 0.00 0.00 3.33
56 57 4.938074 TTCGACACCCCCGACCCA 62.938 66.667 0.00 0.00 35.61 4.51
57 58 4.078516 CTTCGACACCCCCGACCC 62.079 72.222 0.00 0.00 35.61 4.46
58 59 3.292500 GACTTCGACACCCCCGACC 62.293 68.421 0.00 0.00 35.61 4.79
59 60 2.260743 GACTTCGACACCCCCGAC 59.739 66.667 0.00 0.00 35.61 4.79
60 61 2.141011 TAGGACTTCGACACCCCCGA 62.141 60.000 0.00 0.00 0.00 5.14
61 62 1.679977 TAGGACTTCGACACCCCCG 60.680 63.158 0.00 0.00 0.00 5.73
62 63 1.895966 GTAGGACTTCGACACCCCC 59.104 63.158 0.00 0.00 0.00 5.40
63 64 1.246737 ACGTAGGACTTCGACACCCC 61.247 60.000 5.37 0.00 0.00 4.95
64 65 0.109412 CACGTAGGACTTCGACACCC 60.109 60.000 5.37 0.00 0.00 4.61
65 66 0.109412 CCACGTAGGACTTCGACACC 60.109 60.000 5.37 0.00 41.22 4.16
66 67 0.731855 GCCACGTAGGACTTCGACAC 60.732 60.000 5.37 0.00 41.22 3.67
67 68 1.174078 TGCCACGTAGGACTTCGACA 61.174 55.000 5.37 0.00 41.22 4.35
68 69 0.456312 CTGCCACGTAGGACTTCGAC 60.456 60.000 5.37 0.00 41.22 4.20
69 70 0.607217 TCTGCCACGTAGGACTTCGA 60.607 55.000 5.37 0.00 41.22 3.71
70 71 0.179161 CTCTGCCACGTAGGACTTCG 60.179 60.000 8.04 0.00 41.22 3.79
71 72 0.173708 CCTCTGCCACGTAGGACTTC 59.826 60.000 8.04 0.00 41.22 3.01
72 73 0.542232 ACCTCTGCCACGTAGGACTT 60.542 55.000 8.31 0.00 41.22 3.01
73 74 0.966370 GACCTCTGCCACGTAGGACT 60.966 60.000 8.31 0.00 41.22 3.85
74 75 0.966370 AGACCTCTGCCACGTAGGAC 60.966 60.000 8.31 2.20 41.22 3.85
75 76 0.965866 CAGACCTCTGCCACGTAGGA 60.966 60.000 8.31 0.00 40.02 2.94
76 77 1.513158 CAGACCTCTGCCACGTAGG 59.487 63.158 0.00 0.00 37.15 3.18
77 78 0.965866 TCCAGACCTCTGCCACGTAG 60.966 60.000 0.00 0.00 42.47 3.51
78 79 1.076014 TCCAGACCTCTGCCACGTA 59.924 57.895 0.00 0.00 42.47 3.57
79 80 2.203640 TCCAGACCTCTGCCACGT 60.204 61.111 0.00 0.00 42.47 4.49
80 81 2.262915 GTCCAGACCTCTGCCACG 59.737 66.667 0.00 0.00 42.47 4.94
81 82 1.004440 GTGTCCAGACCTCTGCCAC 60.004 63.158 0.00 2.89 42.47 5.01
82 83 2.217038 GGTGTCCAGACCTCTGCCA 61.217 63.158 0.00 0.00 42.47 4.92
83 84 2.665603 GGTGTCCAGACCTCTGCC 59.334 66.667 0.00 0.00 42.47 4.85
84 85 1.915769 AGGGTGTCCAGACCTCTGC 60.916 63.158 0.00 0.00 42.47 4.26
85 86 1.978473 CAGGGTGTCCAGACCTCTG 59.022 63.158 0.00 0.00 43.40 3.35
86 87 1.915769 GCAGGGTGTCCAGACCTCT 60.916 63.158 0.00 0.00 36.14 3.69
87 88 1.768684 TTGCAGGGTGTCCAGACCTC 61.769 60.000 0.00 0.00 36.14 3.85
88 89 1.352622 TTTGCAGGGTGTCCAGACCT 61.353 55.000 0.00 0.00 36.14 3.85
89 90 0.467290 TTTTGCAGGGTGTCCAGACC 60.467 55.000 0.00 0.00 34.83 3.85
90 91 0.668535 GTTTTGCAGGGTGTCCAGAC 59.331 55.000 0.00 0.00 34.83 3.51
91 92 0.550914 AGTTTTGCAGGGTGTCCAGA 59.449 50.000 0.00 0.00 34.83 3.86
92 93 0.954452 GAGTTTTGCAGGGTGTCCAG 59.046 55.000 0.00 0.00 34.83 3.86
93 94 0.467290 GGAGTTTTGCAGGGTGTCCA 60.467 55.000 0.00 0.00 34.83 4.02
94 95 1.179174 GGGAGTTTTGCAGGGTGTCC 61.179 60.000 0.00 0.00 0.00 4.02
95 96 1.515521 CGGGAGTTTTGCAGGGTGTC 61.516 60.000 0.00 0.00 0.00 3.67
96 97 1.528309 CGGGAGTTTTGCAGGGTGT 60.528 57.895 0.00 0.00 0.00 4.16
97 98 2.919494 GCGGGAGTTTTGCAGGGTG 61.919 63.158 0.00 0.00 0.00 4.61
98 99 2.597510 GCGGGAGTTTTGCAGGGT 60.598 61.111 0.00 0.00 0.00 4.34
128 129 2.627699 GCTGTCCAAAATCCCAGAAACA 59.372 45.455 0.00 0.00 0.00 2.83
133 134 1.315257 CCGGCTGTCCAAAATCCCAG 61.315 60.000 0.00 0.00 0.00 4.45
134 135 1.304052 CCGGCTGTCCAAAATCCCA 60.304 57.895 0.00 0.00 0.00 4.37
135 136 1.001393 TCCGGCTGTCCAAAATCCC 60.001 57.895 0.00 0.00 0.00 3.85
142 143 3.371063 GACTCGTCCGGCTGTCCA 61.371 66.667 0.00 0.00 0.00 4.02
158 159 1.600164 CGTTCCGTACACGTTCTTGGA 60.600 52.381 0.58 0.00 37.74 3.53
161 162 2.287788 ACATCGTTCCGTACACGTTCTT 60.288 45.455 4.41 0.00 38.81 2.52
167 168 1.073177 CCCAACATCGTTCCGTACAC 58.927 55.000 0.00 0.00 0.00 2.90
169 170 1.073177 CACCCAACATCGTTCCGTAC 58.927 55.000 0.00 0.00 0.00 3.67
175 176 2.357637 CAGTTTGTCACCCAACATCGTT 59.642 45.455 0.00 0.00 31.20 3.85
176 177 1.946768 CAGTTTGTCACCCAACATCGT 59.053 47.619 0.00 0.00 31.20 3.73
181 182 2.103410 ACGCAGTTTGTCACCCAAC 58.897 52.632 0.00 0.00 37.78 3.77
182 183 4.647825 ACGCAGTTTGTCACCCAA 57.352 50.000 0.00 0.00 37.78 4.12
200 201 1.935873 CATTCAGACCATACACGCTGG 59.064 52.381 0.00 0.00 39.80 4.85
204 205 3.724716 CGCAAACATTCAGACCATACACG 60.725 47.826 0.00 0.00 0.00 4.49
206 207 2.746904 CCGCAAACATTCAGACCATACA 59.253 45.455 0.00 0.00 0.00 2.29
335 337 6.182627 ACATGAGCAAGTCATATTTCCAAGA 58.817 36.000 0.00 0.00 44.73 3.02
423 426 6.128090 GCAATGACATTCATTCAGAGAGACAA 60.128 38.462 0.00 0.00 43.03 3.18
442 445 5.648526 CCAATTCCAATTCCAATTGCAATGA 59.351 36.000 13.82 3.84 43.38 2.57
444 447 5.817784 TCCAATTCCAATTCCAATTGCAAT 58.182 33.333 5.99 5.99 43.38 3.56
445 448 5.238624 TCCAATTCCAATTCCAATTGCAA 57.761 34.783 0.00 0.00 43.38 4.08
447 450 6.374894 TCAATTCCAATTCCAATTCCAATTGC 59.625 34.615 0.00 0.00 43.38 3.56
448 451 7.148205 GGTCAATTCCAATTCCAATTCCAATTG 60.148 37.037 0.00 0.00 44.12 2.32
449 452 6.885918 GGTCAATTCCAATTCCAATTCCAATT 59.114 34.615 0.00 0.00 0.00 2.32
450 453 6.417258 GGTCAATTCCAATTCCAATTCCAAT 58.583 36.000 0.00 0.00 0.00 3.16
451 454 5.568423 CGGTCAATTCCAATTCCAATTCCAA 60.568 40.000 0.00 0.00 0.00 3.53
454 457 5.072040 ACGGTCAATTCCAATTCCAATTC 57.928 39.130 0.00 0.00 0.00 2.17
455 458 5.714806 ACTACGGTCAATTCCAATTCCAATT 59.285 36.000 0.00 0.00 0.00 2.32
456 459 5.125417 CACTACGGTCAATTCCAATTCCAAT 59.875 40.000 0.00 0.00 0.00 3.16
502 505 4.132441 TACTTACCCGCACGGCCG 62.132 66.667 26.86 26.86 33.26 6.13
503 506 2.510012 GTACTTACCCGCACGGCC 60.510 66.667 2.83 0.00 33.26 6.13
504 507 1.374505 TTGTACTTACCCGCACGGC 60.375 57.895 2.83 0.00 33.26 5.68
505 508 0.037975 AGTTGTACTTACCCGCACGG 60.038 55.000 1.02 1.02 37.81 4.94
506 509 1.068055 AGAGTTGTACTTACCCGCACG 60.068 52.381 0.00 0.00 0.00 5.34
507 510 2.738013 AGAGTTGTACTTACCCGCAC 57.262 50.000 0.00 0.00 0.00 5.34
508 511 2.162208 CGTAGAGTTGTACTTACCCGCA 59.838 50.000 0.00 0.00 0.00 5.69
509 512 2.790387 CGTAGAGTTGTACTTACCCGC 58.210 52.381 0.00 0.00 0.00 6.13
548 559 1.967319 TTCTGACAGTGCAAAGTCCC 58.033 50.000 14.97 0.00 33.89 4.46
598 609 3.797225 GATGCTCCGCTCCGATGCA 62.797 63.158 0.00 0.00 38.54 3.96
1166 2464 2.297912 AACGCACGTTCCTTCGACG 61.298 57.895 1.93 0.00 45.46 5.12
1169 2467 2.127758 GCAACGCACGTTCCTTCG 60.128 61.111 5.28 0.00 36.00 3.79
1363 2678 1.333347 CGAGACGACGTGGATCATCTC 60.333 57.143 4.58 5.26 0.00 2.75
1409 2751 3.311106 CAACGCATTGATCAGCAAAACT 58.689 40.909 7.61 0.00 40.48 2.66
1438 2786 3.254024 ATCACCGACCACCTGCACC 62.254 63.158 0.00 0.00 0.00 5.01
1547 2895 2.028484 GACTTGTGCGTGACGGGA 59.972 61.111 7.25 0.00 0.00 5.14
1640 2988 1.738099 CTCGTCCTTGAAGCACCCG 60.738 63.158 0.00 0.00 0.00 5.28
2319 3674 8.506437 CACTGTCAGAAATTTATGTGCTTCTAA 58.494 33.333 12.28 0.00 0.00 2.10
2342 3697 2.523325 TCTAGCTCTTCTCAGGCACT 57.477 50.000 0.00 0.00 43.88 4.40
2583 5086 2.798834 TTAAATTACAGCGCGTCAGC 57.201 45.000 8.43 0.00 40.74 4.26
2584 5087 7.892445 AAATATTTAAATTACAGCGCGTCAG 57.108 32.000 8.43 0.00 0.00 3.51
2628 5270 3.258123 GGTGCCCAGCAGATCTTTAAAAA 59.742 43.478 0.00 0.00 40.08 1.94
2633 5275 0.112995 TTGGTGCCCAGCAGATCTTT 59.887 50.000 0.00 0.00 40.08 2.52
2675 5317 6.808008 TTCTAGAATCAAGCAACTCAAAGG 57.192 37.500 0.00 0.00 0.00 3.11
2722 5364 3.948851 GCGCATGCATTCATATCCTATG 58.051 45.455 19.57 0.00 42.15 2.23
2760 5402 5.684550 AACCTTTAACAATCTCCGTGTTC 57.315 39.130 0.00 0.00 39.80 3.18
2778 5420 7.039722 TCCCCAATTCAGTTAATAGAAACCT 57.960 36.000 0.00 0.00 0.00 3.50
2814 5463 5.277538 GGCAGAATTTCCGTGCTATTCTAAG 60.278 44.000 9.63 0.00 36.70 2.18
2815 5464 4.574828 GGCAGAATTTCCGTGCTATTCTAA 59.425 41.667 9.63 0.00 36.70 2.10
2817 5466 2.945668 GGCAGAATTTCCGTGCTATTCT 59.054 45.455 9.63 0.00 38.74 2.40
2818 5467 2.945668 AGGCAGAATTTCCGTGCTATTC 59.054 45.455 9.63 0.00 37.37 1.75
2821 5470 2.489938 AAGGCAGAATTTCCGTGCTA 57.510 45.000 9.63 0.00 37.37 3.49
2829 5478 2.037121 CCCCACGAAAAAGGCAGAATTT 59.963 45.455 0.00 0.00 0.00 1.82
2834 5484 1.256812 ATTCCCCACGAAAAAGGCAG 58.743 50.000 0.00 0.00 33.08 4.85
2858 5509 1.887854 TGAATCGTACACCCAACTCGA 59.112 47.619 0.00 0.00 35.14 4.04
2859 5510 1.990563 GTGAATCGTACACCCAACTCG 59.009 52.381 0.00 0.00 32.84 4.18
2860 5511 3.034721 TGTGAATCGTACACCCAACTC 57.965 47.619 0.00 0.00 37.45 3.01
2862 5513 3.395639 TCTTGTGAATCGTACACCCAAC 58.604 45.455 0.00 0.00 37.45 3.77
2863 5514 3.755112 TCTTGTGAATCGTACACCCAA 57.245 42.857 0.00 0.00 37.45 4.12
2872 5523 4.917415 GTGTTTTCCCATTCTTGTGAATCG 59.083 41.667 0.00 0.00 40.61 3.34
2886 5537 8.678199 TGTTTATTTGGATTTTTGTGTTTTCCC 58.322 29.630 0.00 0.00 0.00 3.97
2987 5639 5.880332 TCCTTTTCAAATTCCTATCCACGAG 59.120 40.000 0.00 0.00 0.00 4.18
2990 5642 7.410120 ACATCCTTTTCAAATTCCTATCCAC 57.590 36.000 0.00 0.00 0.00 4.02
3068 5720 3.903090 ACATGCAAAGGGAAAATGAAGGA 59.097 39.130 0.00 0.00 0.00 3.36
3070 5722 5.993441 AGAAACATGCAAAGGGAAAATGAAG 59.007 36.000 0.00 0.00 0.00 3.02
3074 5726 6.827762 TCAAAAGAAACATGCAAAGGGAAAAT 59.172 30.769 0.00 0.00 0.00 1.82
3079 5731 4.273235 GGTTCAAAAGAAACATGCAAAGGG 59.727 41.667 0.00 0.00 0.00 3.95
3137 5789 2.558974 AGGGGAGGAAAAACGTAGGAT 58.441 47.619 0.00 0.00 0.00 3.24
3138 5790 2.034436 AGGGGAGGAAAAACGTAGGA 57.966 50.000 0.00 0.00 0.00 2.94
3140 5792 3.597255 GAGAAGGGGAGGAAAAACGTAG 58.403 50.000 0.00 0.00 0.00 3.51
3141 5793 2.303890 GGAGAAGGGGAGGAAAAACGTA 59.696 50.000 0.00 0.00 0.00 3.57
3143 5795 1.351350 AGGAGAAGGGGAGGAAAAACG 59.649 52.381 0.00 0.00 0.00 3.60
3144 5796 3.527507 AAGGAGAAGGGGAGGAAAAAC 57.472 47.619 0.00 0.00 0.00 2.43
3145 5797 3.465588 TCAAAGGAGAAGGGGAGGAAAAA 59.534 43.478 0.00 0.00 0.00 1.94
3165 5817 2.910688 AAAAGTGCCTCTCTCGTTCA 57.089 45.000 0.00 0.00 0.00 3.18
3169 5821 4.748892 TCATCTTAAAAGTGCCTCTCTCG 58.251 43.478 0.00 0.00 0.00 4.04
3198 5851 8.698973 TGAGTCCACATATAAACCTTTTTCAA 57.301 30.769 0.00 0.00 0.00 2.69
3207 5860 6.238374 CCACGGATTTGAGTCCACATATAAAC 60.238 42.308 0.00 0.00 38.21 2.01
3214 5867 0.605319 GCCACGGATTTGAGTCCACA 60.605 55.000 0.00 0.00 38.21 4.17


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

AutoCloner maintained by Alex Coulton.