Multiple sequence alignment - TraesCS1A01G041300

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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 TraesCS1A01G041300 chr1A 100.000 2700 0 0 1 2700 22635133 22632434 0.000000e+00 4987.0
1 TraesCS1A01G041300 chr1A 94.618 1059 56 1 914 1971 12698839 12697781 0.000000e+00 1639.0
2 TraesCS1A01G041300 chr1A 92.121 330 24 2 2055 2383 12688957 12688629 5.270000e-127 464.0
3 TraesCS1A01G041300 chr1A 93.103 145 2 3 2373 2517 12686710 12686574 3.520000e-49 206.0
4 TraesCS1A01G041300 chr1D 97.227 2308 40 10 401 2700 11123124 11125415 0.000000e+00 3886.0
5 TraesCS1A01G041300 chr1D 96.175 732 21 3 401 1125 11040434 11041165 0.000000e+00 1190.0
6 TraesCS1A01G041300 chr1D 94.476 706 17 9 427 1125 11089186 11089876 0.000000e+00 1068.0
7 TraesCS1A01G041300 chr1D 90.881 658 24 7 2046 2700 11041514 11042138 0.000000e+00 850.0
8 TraesCS1A01G041300 chr1D 90.592 659 25 8 2046 2700 11090228 11090853 0.000000e+00 839.0
9 TraesCS1A01G041300 chr1D 94.393 107 6 0 401 507 11009241 11009347 5.980000e-37 165.0
10 TraesCS1A01G041300 chr1B 91.316 2326 170 23 389 2697 16477744 16480054 0.000000e+00 3147.0
11 TraesCS1A01G041300 chr1B 92.219 1568 107 12 433 1992 16692501 16694061 0.000000e+00 2206.0
12 TraesCS1A01G041300 chr1B 92.862 1429 85 7 1217 2641 16645423 16646838 0.000000e+00 2058.0
13 TraesCS1A01G041300 chr1B 82.731 249 36 6 130 374 441523492 441523247 5.850000e-52 215.0
14 TraesCS1A01G041300 chr1B 96.429 56 2 0 2628 2683 16646852 16646907 2.860000e-15 93.5
15 TraesCS1A01G041300 chr7D 83.264 239 36 3 160 395 104485168 104485405 1.630000e-52 217.0
16 TraesCS1A01G041300 chr7D 82.192 219 31 3 139 350 52486342 52486125 5.940000e-42 182.0
17 TraesCS1A01G041300 chr5B 83.761 234 32 6 172 402 257014968 257014738 1.630000e-52 217.0
18 TraesCS1A01G041300 chr5A 84.141 227 31 5 172 395 44990306 44990530 5.850000e-52 215.0
19 TraesCS1A01G041300 chr7A 81.387 274 39 11 128 395 77913544 77913811 2.110000e-51 213.0
20 TraesCS1A01G041300 chr7A 81.250 272 42 9 129 395 119504926 119505193 7.570000e-51 211.0
21 TraesCS1A01G041300 chr7A 81.022 274 40 11 128 395 77914357 77914624 9.800000e-50 207.0
22 TraesCS1A01G041300 chr7B 93.103 145 2 3 2373 2517 192786231 192786095 3.520000e-49 206.0
23 TraesCS1A01G041300 chr2B 93.103 145 2 3 2373 2517 47184053 47184189 3.520000e-49 206.0
24 TraesCS1A01G041300 chr6B 80.515 272 46 6 128 395 148149328 148149596 4.560000e-48 202.0


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 TraesCS1A01G041300 chr1A 22632434 22635133 2699 True 4987.00 4987 100.0000 1 2700 1 chr1A.!!$R2 2699
1 TraesCS1A01G041300 chr1A 12697781 12698839 1058 True 1639.00 1639 94.6180 914 1971 1 chr1A.!!$R1 1057
2 TraesCS1A01G041300 chr1A 12686574 12688957 2383 True 335.00 464 92.6120 2055 2517 2 chr1A.!!$R3 462
3 TraesCS1A01G041300 chr1D 11123124 11125415 2291 False 3886.00 3886 97.2270 401 2700 1 chr1D.!!$F2 2299
4 TraesCS1A01G041300 chr1D 11040434 11042138 1704 False 1020.00 1190 93.5280 401 2700 2 chr1D.!!$F3 2299
5 TraesCS1A01G041300 chr1D 11089186 11090853 1667 False 953.50 1068 92.5340 427 2700 2 chr1D.!!$F4 2273
6 TraesCS1A01G041300 chr1B 16477744 16480054 2310 False 3147.00 3147 91.3160 389 2697 1 chr1B.!!$F1 2308
7 TraesCS1A01G041300 chr1B 16692501 16694061 1560 False 2206.00 2206 92.2190 433 1992 1 chr1B.!!$F2 1559
8 TraesCS1A01G041300 chr1B 16645423 16646907 1484 False 1075.75 2058 94.6455 1217 2683 2 chr1B.!!$F3 1466
9 TraesCS1A01G041300 chr7A 77913544 77914624 1080 False 210.00 213 81.2045 128 395 2 chr7A.!!$F2 267

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
217 220 0.040514 CGCAAAAGAACATGCCACGA 60.041 50.0 0.0 0.0 39.39 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2119 0.471591 AATGGGAAGTTTGGGCTGCA 60.472 50.0 0.5 0.0 0.0 4.41 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
26 27 9.031360 CATAGTATAAATAAGTGAACGTGTGCT 57.969 33.333 0.00 0.00 0.00 4.40
29 30 9.245962 AGTATAAATAAGTGAACGTGTGCTATC 57.754 33.333 0.00 0.00 0.00 2.08
30 31 9.027129 GTATAAATAAGTGAACGTGTGCTATCA 57.973 33.333 0.00 0.00 0.00 2.15
31 32 6.408858 AAATAAGTGAACGTGTGCTATCAG 57.591 37.500 0.00 0.00 0.00 2.90
32 33 3.660501 AAGTGAACGTGTGCTATCAGA 57.339 42.857 0.00 0.00 0.00 3.27
33 34 3.660501 AGTGAACGTGTGCTATCAGAA 57.339 42.857 0.00 0.00 0.00 3.02
34 35 3.990092 AGTGAACGTGTGCTATCAGAAA 58.010 40.909 0.00 0.00 0.00 2.52
35 36 3.741344 AGTGAACGTGTGCTATCAGAAAC 59.259 43.478 0.00 0.00 0.00 2.78
36 37 3.493129 GTGAACGTGTGCTATCAGAAACA 59.507 43.478 0.00 0.00 0.00 2.83
37 38 4.152402 GTGAACGTGTGCTATCAGAAACAT 59.848 41.667 0.00 0.00 0.00 2.71
38 39 4.152223 TGAACGTGTGCTATCAGAAACATG 59.848 41.667 0.00 0.00 35.99 3.21
39 40 3.002791 ACGTGTGCTATCAGAAACATGG 58.997 45.455 0.00 0.00 34.54 3.66
40 41 3.002791 CGTGTGCTATCAGAAACATGGT 58.997 45.455 0.00 0.00 0.00 3.55
41 42 4.180817 CGTGTGCTATCAGAAACATGGTA 58.819 43.478 0.00 0.00 0.00 3.25
42 43 4.032900 CGTGTGCTATCAGAAACATGGTAC 59.967 45.833 0.00 0.00 0.00 3.34
54 55 3.918977 TGGTACACAGTGGCGCGT 61.919 61.111 8.43 0.00 0.00 6.01
55 56 2.663852 GGTACACAGTGGCGCGTT 60.664 61.111 8.43 0.00 0.00 4.84
56 57 2.549282 GTACACAGTGGCGCGTTG 59.451 61.111 8.43 1.64 0.00 4.10
57 58 2.663520 TACACAGTGGCGCGTTGG 60.664 61.111 8.43 0.00 0.00 3.77
58 59 3.448533 TACACAGTGGCGCGTTGGT 62.449 57.895 8.43 3.02 0.00 3.67
59 60 4.012895 CACAGTGGCGCGTTGGTC 62.013 66.667 8.43 0.00 0.00 4.02
60 61 4.539083 ACAGTGGCGCGTTGGTCA 62.539 61.111 8.43 0.00 0.00 4.02
61 62 3.716006 CAGTGGCGCGTTGGTCAG 61.716 66.667 8.43 0.00 0.00 3.51
62 63 3.923864 AGTGGCGCGTTGGTCAGA 61.924 61.111 8.43 0.00 0.00 3.27
63 64 3.414700 GTGGCGCGTTGGTCAGAG 61.415 66.667 8.43 0.00 0.00 3.35
64 65 3.611674 TGGCGCGTTGGTCAGAGA 61.612 61.111 8.43 0.00 0.00 3.10
65 66 2.125512 GGCGCGTTGGTCAGAGAT 60.126 61.111 8.43 0.00 0.00 2.75
66 67 1.741770 GGCGCGTTGGTCAGAGATT 60.742 57.895 8.43 0.00 0.00 2.40
67 68 1.421485 GCGCGTTGGTCAGAGATTG 59.579 57.895 8.43 0.00 0.00 2.67
68 69 1.421485 CGCGTTGGTCAGAGATTGC 59.579 57.895 0.00 0.00 0.00 3.56
69 70 1.421485 GCGTTGGTCAGAGATTGCG 59.579 57.895 0.00 0.00 0.00 4.85
70 71 1.421485 CGTTGGTCAGAGATTGCGC 59.579 57.895 0.00 0.00 0.00 6.09
71 72 1.291184 CGTTGGTCAGAGATTGCGCA 61.291 55.000 5.66 5.66 0.00 6.09
72 73 1.089920 GTTGGTCAGAGATTGCGCAT 58.910 50.000 12.75 0.40 0.00 4.73
73 74 1.089112 TTGGTCAGAGATTGCGCATG 58.911 50.000 12.75 6.20 0.00 4.06
74 75 1.354506 GGTCAGAGATTGCGCATGC 59.645 57.895 12.75 7.91 43.20 4.06
75 76 1.354506 GTCAGAGATTGCGCATGCC 59.645 57.895 12.75 5.63 41.78 4.40
76 77 1.078285 TCAGAGATTGCGCATGCCA 60.078 52.632 12.75 8.49 41.78 4.92
77 78 1.093496 TCAGAGATTGCGCATGCCAG 61.093 55.000 12.75 0.00 41.78 4.85
78 79 1.822613 AGAGATTGCGCATGCCAGG 60.823 57.895 12.75 0.00 41.78 4.45
79 80 2.044650 AGATTGCGCATGCCAGGT 60.045 55.556 12.75 4.23 41.78 4.00
80 81 1.660560 GAGATTGCGCATGCCAGGTT 61.661 55.000 12.75 0.68 41.78 3.50
81 82 1.226773 GATTGCGCATGCCAGGTTC 60.227 57.895 12.75 6.19 41.78 3.62
82 83 2.924922 GATTGCGCATGCCAGGTTCG 62.925 60.000 12.75 0.00 41.78 3.95
83 84 4.695993 TGCGCATGCCAGGTTCGA 62.696 61.111 13.15 0.00 41.78 3.71
84 85 3.430862 GCGCATGCCAGGTTCGAA 61.431 61.111 13.15 0.00 33.98 3.71
85 86 2.764314 GCGCATGCCAGGTTCGAAT 61.764 57.895 13.15 0.00 33.98 3.34
86 87 1.353103 CGCATGCCAGGTTCGAATC 59.647 57.895 13.15 0.00 0.00 2.52
87 88 1.729881 GCATGCCAGGTTCGAATCC 59.270 57.895 6.36 6.73 0.00 3.01
88 89 1.728490 GCATGCCAGGTTCGAATCCC 61.728 60.000 6.36 0.05 0.00 3.85
89 90 1.153168 ATGCCAGGTTCGAATCCCG 60.153 57.895 4.40 0.00 40.25 5.14
90 91 1.910580 ATGCCAGGTTCGAATCCCGT 61.911 55.000 4.40 0.00 39.75 5.28
91 92 1.814169 GCCAGGTTCGAATCCCGTC 60.814 63.158 4.40 0.00 39.75 4.79
92 93 1.518572 CCAGGTTCGAATCCCGTCG 60.519 63.158 4.40 0.00 42.48 5.12
93 94 2.165301 CAGGTTCGAATCCCGTCGC 61.165 63.158 4.40 0.00 40.88 5.19
94 95 2.889018 GGTTCGAATCCCGTCGCC 60.889 66.667 0.00 0.00 40.88 5.54
95 96 2.889018 GTTCGAATCCCGTCGCCC 60.889 66.667 0.00 0.00 40.88 6.13
96 97 4.501714 TTCGAATCCCGTCGCCCG 62.502 66.667 0.00 0.00 40.88 6.13
118 119 2.701073 CTCCCGCGAGTATATTTCGT 57.299 50.000 8.23 0.00 40.08 3.85
119 120 3.818961 CTCCCGCGAGTATATTTCGTA 57.181 47.619 8.23 0.00 40.08 3.43
120 121 3.486584 CTCCCGCGAGTATATTTCGTAC 58.513 50.000 8.23 0.00 40.08 3.67
121 122 2.877786 TCCCGCGAGTATATTTCGTACA 59.122 45.455 8.23 0.00 40.08 2.90
122 123 3.314913 TCCCGCGAGTATATTTCGTACAA 59.685 43.478 8.23 0.00 40.08 2.41
123 124 4.022935 TCCCGCGAGTATATTTCGTACAAT 60.023 41.667 8.23 0.00 40.08 2.71
124 125 5.181056 TCCCGCGAGTATATTTCGTACAATA 59.819 40.000 8.23 0.00 40.08 1.90
125 126 6.032094 CCCGCGAGTATATTTCGTACAATAT 58.968 40.000 8.23 0.00 40.08 1.28
126 127 7.065683 TCCCGCGAGTATATTTCGTACAATATA 59.934 37.037 8.23 0.00 40.08 0.86
150 151 3.312736 TTTCTGGCAAGACCCTCTTTT 57.687 42.857 0.00 0.00 33.78 2.27
151 152 2.568623 TCTGGCAAGACCCTCTTTTC 57.431 50.000 0.00 0.00 33.78 2.29
154 155 0.889186 GGCAAGACCCTCTTTTCGCA 60.889 55.000 0.00 0.00 33.78 5.10
157 158 2.858646 GCAAGACCCTCTTTTCGCAAAC 60.859 50.000 0.00 0.00 33.78 2.93
158 159 1.226746 AGACCCTCTTTTCGCAAACG 58.773 50.000 0.00 0.00 42.01 3.60
159 160 4.838040 CAAGACCCTCTTTTCGCAAACGA 61.838 47.826 0.00 0.00 39.83 3.85
210 213 3.462982 GGGTTTTTCCGCAAAAGAACAT 58.537 40.909 4.54 0.00 34.90 2.71
217 220 0.040514 CGCAAAAGAACATGCCACGA 60.041 50.000 0.00 0.00 39.39 4.35
222 225 1.237285 AAGAACATGCCACGACAGCC 61.237 55.000 0.00 0.00 0.00 4.85
230 233 2.425592 CACGACAGCCCCTGACAA 59.574 61.111 0.00 0.00 35.18 3.18
233 236 2.753029 GACAGCCCCTGACAAGCT 59.247 61.111 0.00 0.00 37.32 3.74
238 241 4.748144 CCCCTGACAAGCTGGCCC 62.748 72.222 0.00 0.00 34.47 5.80
251 254 1.613928 TGGCCCCAACCGTCAGATA 60.614 57.895 0.00 0.00 0.00 1.98
255 258 0.902531 CCCCAACCGTCAGATACACT 59.097 55.000 0.00 0.00 0.00 3.55
256 259 1.405526 CCCCAACCGTCAGATACACTG 60.406 57.143 0.00 0.00 46.97 3.66
267 270 5.513141 CGTCAGATACACTGTCAATACACTG 59.487 44.000 0.00 0.00 45.86 3.66
284 287 8.988934 CAATACACTGTTATATGCGGTTTAGAT 58.011 33.333 0.00 0.00 0.00 1.98
296 299 9.872757 ATATGCGGTTTAGATTATTTTGTAACG 57.127 29.630 0.00 0.00 0.00 3.18
297 300 7.361889 TGCGGTTTAGATTATTTTGTAACGA 57.638 32.000 0.00 0.00 0.00 3.85
299 302 7.745594 TGCGGTTTAGATTATTTTGTAACGAAC 59.254 33.333 0.00 0.00 0.00 3.95
301 304 9.257865 CGGTTTAGATTATTTTGTAACGAACTG 57.742 33.333 0.00 0.00 0.00 3.16
305 308 7.448748 AGATTATTTTGTAACGAACTGCCTT 57.551 32.000 0.00 0.00 0.00 4.35
343 346 8.407064 TGACATGTAAAAATTACGAAAAGTGGT 58.593 29.630 0.00 0.00 0.00 4.16
347 350 7.351223 TGTAAAAATTACGAAAAGTGGTACCG 58.649 34.615 7.57 0.00 0.00 4.02
350 353 6.806388 AAATTACGAAAAGTGGTACCGATT 57.194 33.333 7.57 1.09 0.00 3.34
355 358 2.396590 AAAGTGGTACCGATTCGCAT 57.603 45.000 7.57 0.00 0.00 4.73
356 359 2.396590 AAGTGGTACCGATTCGCATT 57.603 45.000 7.57 0.00 0.00 3.56
359 362 1.593006 GTGGTACCGATTCGCATTCAG 59.407 52.381 7.57 0.00 0.00 3.02
360 363 1.217882 GGTACCGATTCGCATTCAGG 58.782 55.000 0.00 0.00 0.00 3.86
363 366 2.546494 CCGATTCGCATTCAGGGCC 61.546 63.158 0.00 0.00 0.00 5.80
364 367 2.885676 CGATTCGCATTCAGGGCCG 61.886 63.158 0.00 0.00 0.00 6.13
381 384 2.568090 GCAATTGTGGCCACCTCG 59.432 61.111 32.62 18.80 0.00 4.63
395 398 1.393539 CACCTCGGTGCAATTAACTCG 59.606 52.381 2.72 0.00 39.39 4.18
396 399 1.001633 ACCTCGGTGCAATTAACTCGT 59.998 47.619 0.00 0.00 0.00 4.18
397 400 2.231964 ACCTCGGTGCAATTAACTCGTA 59.768 45.455 0.00 0.00 0.00 3.43
398 401 3.118884 ACCTCGGTGCAATTAACTCGTAT 60.119 43.478 0.00 0.00 0.00 3.06
399 402 3.245284 CCTCGGTGCAATTAACTCGTATG 59.755 47.826 0.00 0.00 0.00 2.39
418 422 5.336531 CGTATGTTGAGTTACTCCCTTGTCT 60.337 44.000 10.10 0.00 0.00 3.41
636 645 7.932683 ACTAGTAGGGCTAATAAACCTTGAT 57.067 36.000 1.45 0.00 35.84 2.57
669 678 3.300857 CAAGTAGCCGACATGATCTACG 58.699 50.000 0.00 0.00 37.18 3.51
916 926 6.347696 CATCTTATCTTCTCTCCTGCTTGTT 58.652 40.000 0.00 0.00 0.00 2.83
929 939 2.984471 CTGCTTGTTTCATGCATGTGAC 59.016 45.455 25.43 22.62 42.13 3.67
1047 1060 5.354842 AGGTCCATTTAGCTGGTTAGTAC 57.645 43.478 0.00 0.00 37.57 2.73
1512 1533 0.109272 ATCGTTGACACTGTCGCGAT 60.109 50.000 24.00 24.00 42.97 4.58
1838 1860 8.315482 ACCTTAATCAACTTAGAGAAGAACTCC 58.685 37.037 0.00 0.00 45.96 3.85
1995 2022 8.255394 TGCCGACATATAAGAAACATGATATG 57.745 34.615 0.00 4.04 37.97 1.78
2141 2170 4.452114 TCGCAACACTAAGTAACTACTCGA 59.548 41.667 0.00 0.00 34.99 4.04
2354 2392 2.989824 ACCAGGTGAGGACGTCGG 60.990 66.667 9.92 5.65 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.031360 AGCACACGTTCACTTATTTATACTATG 57.969 33.333 0.00 0.00 0.00 2.23
3 4 9.245962 GATAGCACACGTTCACTTATTTATACT 57.754 33.333 0.00 0.00 0.00 2.12
4 5 9.027129 TGATAGCACACGTTCACTTATTTATAC 57.973 33.333 0.00 0.00 0.00 1.47
6 7 7.979537 TCTGATAGCACACGTTCACTTATTTAT 59.020 33.333 0.00 0.00 0.00 1.40
9 10 5.720202 TCTGATAGCACACGTTCACTTATT 58.280 37.500 0.00 0.00 0.00 1.40
10 11 5.324784 TCTGATAGCACACGTTCACTTAT 57.675 39.130 0.00 0.00 0.00 1.73
12 13 3.660501 TCTGATAGCACACGTTCACTT 57.339 42.857 0.00 0.00 0.00 3.16
13 14 3.660501 TTCTGATAGCACACGTTCACT 57.339 42.857 0.00 0.00 0.00 3.41
14 15 3.493129 TGTTTCTGATAGCACACGTTCAC 59.507 43.478 0.00 0.00 0.00 3.18
15 16 3.723260 TGTTTCTGATAGCACACGTTCA 58.277 40.909 0.00 0.00 0.00 3.18
16 17 4.436050 CCATGTTTCTGATAGCACACGTTC 60.436 45.833 0.00 0.00 0.00 3.95
17 18 3.436704 CCATGTTTCTGATAGCACACGTT 59.563 43.478 0.00 0.00 0.00 3.99
18 19 3.002791 CCATGTTTCTGATAGCACACGT 58.997 45.455 0.00 0.00 0.00 4.49
19 20 3.002791 ACCATGTTTCTGATAGCACACG 58.997 45.455 0.00 0.00 0.00 4.49
20 21 4.935205 TGTACCATGTTTCTGATAGCACAC 59.065 41.667 0.00 0.00 0.00 3.82
21 22 4.935205 GTGTACCATGTTTCTGATAGCACA 59.065 41.667 0.00 0.00 0.00 4.57
22 23 4.935205 TGTGTACCATGTTTCTGATAGCAC 59.065 41.667 0.00 0.00 0.00 4.40
23 24 5.159273 TGTGTACCATGTTTCTGATAGCA 57.841 39.130 0.00 0.00 0.00 3.49
24 25 5.063944 CACTGTGTACCATGTTTCTGATAGC 59.936 44.000 0.00 0.00 0.00 2.97
25 26 5.582269 CCACTGTGTACCATGTTTCTGATAG 59.418 44.000 7.08 0.00 0.00 2.08
26 27 5.487433 CCACTGTGTACCATGTTTCTGATA 58.513 41.667 7.08 0.00 0.00 2.15
27 28 4.326826 CCACTGTGTACCATGTTTCTGAT 58.673 43.478 7.08 0.00 0.00 2.90
28 29 3.738982 CCACTGTGTACCATGTTTCTGA 58.261 45.455 7.08 0.00 0.00 3.27
29 30 2.226437 GCCACTGTGTACCATGTTTCTG 59.774 50.000 7.08 0.00 0.00 3.02
30 31 2.504367 GCCACTGTGTACCATGTTTCT 58.496 47.619 7.08 0.00 0.00 2.52
31 32 1.196808 CGCCACTGTGTACCATGTTTC 59.803 52.381 7.08 0.00 0.00 2.78
32 33 1.234821 CGCCACTGTGTACCATGTTT 58.765 50.000 7.08 0.00 0.00 2.83
33 34 1.234615 GCGCCACTGTGTACCATGTT 61.235 55.000 7.08 0.00 0.00 2.71
34 35 1.671054 GCGCCACTGTGTACCATGT 60.671 57.895 7.08 0.00 0.00 3.21
35 36 2.739704 CGCGCCACTGTGTACCATG 61.740 63.158 0.00 0.00 0.00 3.66
36 37 2.434185 CGCGCCACTGTGTACCAT 60.434 61.111 0.00 0.00 0.00 3.55
37 38 3.448533 AACGCGCCACTGTGTACCA 62.449 57.895 5.73 0.00 31.10 3.25
38 39 2.663852 AACGCGCCACTGTGTACC 60.664 61.111 5.73 0.00 31.10 3.34
39 40 2.549282 CAACGCGCCACTGTGTAC 59.451 61.111 5.73 0.00 31.10 2.90
40 41 2.663520 CCAACGCGCCACTGTGTA 60.664 61.111 5.73 0.00 31.10 2.90
41 42 4.849310 ACCAACGCGCCACTGTGT 62.849 61.111 5.73 0.00 0.00 3.72
42 43 4.012895 GACCAACGCGCCACTGTG 62.013 66.667 5.73 0.00 0.00 3.66
43 44 4.539083 TGACCAACGCGCCACTGT 62.539 61.111 5.73 0.00 0.00 3.55
44 45 3.716006 CTGACCAACGCGCCACTG 61.716 66.667 5.73 0.00 0.00 3.66
45 46 3.865929 CTCTGACCAACGCGCCACT 62.866 63.158 5.73 0.00 0.00 4.00
46 47 3.414700 CTCTGACCAACGCGCCAC 61.415 66.667 5.73 0.00 0.00 5.01
47 48 2.449031 AATCTCTGACCAACGCGCCA 62.449 55.000 5.73 0.00 0.00 5.69
48 49 1.741770 AATCTCTGACCAACGCGCC 60.742 57.895 5.73 0.00 0.00 6.53
49 50 1.421485 CAATCTCTGACCAACGCGC 59.579 57.895 5.73 0.00 0.00 6.86
50 51 1.421485 GCAATCTCTGACCAACGCG 59.579 57.895 3.53 3.53 0.00 6.01
51 52 1.421485 CGCAATCTCTGACCAACGC 59.579 57.895 0.00 0.00 0.00 4.84
52 53 1.291184 TGCGCAATCTCTGACCAACG 61.291 55.000 8.16 0.00 0.00 4.10
53 54 1.089920 ATGCGCAATCTCTGACCAAC 58.910 50.000 17.11 0.00 0.00 3.77
54 55 1.089112 CATGCGCAATCTCTGACCAA 58.911 50.000 17.11 0.00 0.00 3.67
55 56 1.371337 GCATGCGCAATCTCTGACCA 61.371 55.000 17.11 0.00 38.36 4.02
56 57 1.354506 GCATGCGCAATCTCTGACC 59.645 57.895 17.11 0.00 38.36 4.02
57 58 1.354506 GGCATGCGCAATCTCTGAC 59.645 57.895 17.11 5.98 41.24 3.51
58 59 1.078285 TGGCATGCGCAATCTCTGA 60.078 52.632 17.11 0.00 41.24 3.27
59 60 1.355563 CTGGCATGCGCAATCTCTG 59.644 57.895 17.11 9.24 41.24 3.35
60 61 1.822613 CCTGGCATGCGCAATCTCT 60.823 57.895 17.11 0.00 41.24 3.10
61 62 1.660560 AACCTGGCATGCGCAATCTC 61.661 55.000 17.11 5.24 41.24 2.75
62 63 1.660560 GAACCTGGCATGCGCAATCT 61.661 55.000 17.11 0.00 41.24 2.40
63 64 1.226773 GAACCTGGCATGCGCAATC 60.227 57.895 17.11 9.20 41.24 2.67
64 65 2.887360 GAACCTGGCATGCGCAAT 59.113 55.556 17.11 0.00 41.24 3.56
65 66 3.736100 CGAACCTGGCATGCGCAA 61.736 61.111 17.11 0.00 41.24 4.85
66 67 4.695993 TCGAACCTGGCATGCGCA 62.696 61.111 14.96 14.96 41.24 6.09
67 68 2.652893 GATTCGAACCTGGCATGCGC 62.653 60.000 12.44 0.00 37.44 6.09
68 69 1.353103 GATTCGAACCTGGCATGCG 59.647 57.895 12.44 0.00 0.00 4.73
69 70 1.728490 GGGATTCGAACCTGGCATGC 61.728 60.000 9.90 9.90 0.00 4.06
70 71 1.439353 CGGGATTCGAACCTGGCATG 61.439 60.000 0.00 0.00 42.43 4.06
71 72 1.153168 CGGGATTCGAACCTGGCAT 60.153 57.895 0.00 0.00 42.43 4.40
72 73 2.267642 CGGGATTCGAACCTGGCA 59.732 61.111 0.00 0.00 42.43 4.92
73 74 1.814169 GACGGGATTCGAACCTGGC 60.814 63.158 21.82 18.02 42.43 4.85
74 75 1.518572 CGACGGGATTCGAACCTGG 60.519 63.158 21.82 14.11 41.78 4.45
75 76 2.165301 GCGACGGGATTCGAACCTG 61.165 63.158 18.40 18.40 41.78 4.00
76 77 2.183555 GCGACGGGATTCGAACCT 59.816 61.111 0.00 0.00 41.78 3.50
77 78 2.889018 GGCGACGGGATTCGAACC 60.889 66.667 0.00 4.00 41.78 3.62
78 79 2.889018 GGGCGACGGGATTCGAAC 60.889 66.667 0.00 0.00 41.78 3.95
79 80 4.501714 CGGGCGACGGGATTCGAA 62.502 66.667 0.00 0.00 41.78 3.71
99 100 2.701073 ACGAAATATACTCGCGGGAG 57.299 50.000 26.24 26.24 46.13 4.30
100 101 2.877786 TGTACGAAATATACTCGCGGGA 59.122 45.455 15.95 0.92 39.97 5.14
101 102 3.272439 TGTACGAAATATACTCGCGGG 57.728 47.619 3.27 3.27 39.97 6.13
102 103 8.778141 ATATATTGTACGAAATATACTCGCGG 57.222 34.615 6.13 0.00 37.65 6.46
139 140 1.202604 TCGTTTGCGAAAAGAGGGTCT 60.203 47.619 0.00 0.00 44.92 3.85
141 142 3.390003 TCGTTTGCGAAAAGAGGGT 57.610 47.368 0.00 0.00 44.92 4.34
150 151 3.069016 ACATGTATATCCCTCGTTTGCGA 59.931 43.478 0.00 0.00 45.79 5.10
151 152 3.184379 CACATGTATATCCCTCGTTTGCG 59.816 47.826 0.00 0.00 39.92 4.85
154 155 9.621629 TTTTAATCACATGTATATCCCTCGTTT 57.378 29.630 0.00 0.00 0.00 3.60
186 189 2.112190 TCTTTTGCGGAAAAACCCCTT 58.888 42.857 15.86 0.00 34.08 3.95
188 191 2.206750 GTTCTTTTGCGGAAAAACCCC 58.793 47.619 15.86 1.36 34.08 4.95
191 194 3.303066 GGCATGTTCTTTTGCGGAAAAAC 60.303 43.478 15.86 12.27 39.78 2.43
192 195 2.869192 GGCATGTTCTTTTGCGGAAAAA 59.131 40.909 15.86 1.53 39.78 1.94
197 200 1.003262 CGTGGCATGTTCTTTTGCGG 61.003 55.000 0.00 0.00 39.78 5.69
198 201 0.040514 TCGTGGCATGTTCTTTTGCG 60.041 50.000 6.60 0.00 39.78 4.85
217 220 2.433446 CAGCTTGTCAGGGGCTGT 59.567 61.111 13.08 0.00 45.59 4.40
222 225 4.748144 GGGGCCAGCTTGTCAGGG 62.748 72.222 4.39 0.00 0.00 4.45
233 236 1.613928 TATCTGACGGTTGGGGCCA 60.614 57.895 4.39 0.00 0.00 5.36
238 241 2.029380 TGACAGTGTATCTGACGGTTGG 60.029 50.000 0.00 0.00 46.27 3.77
255 258 5.666462 ACCGCATATAACAGTGTATTGACA 58.334 37.500 0.00 0.00 0.00 3.58
256 259 6.598753 AACCGCATATAACAGTGTATTGAC 57.401 37.500 0.00 0.00 0.00 3.18
273 276 7.361889 TCGTTACAAAATAATCTAAACCGCA 57.638 32.000 0.00 0.00 0.00 5.69
284 287 8.404000 TGTTTAAGGCAGTTCGTTACAAAATAA 58.596 29.630 0.00 0.00 0.00 1.40
292 295 4.391155 ACCATGTTTAAGGCAGTTCGTTA 58.609 39.130 0.00 0.00 0.00 3.18
296 299 5.001232 TCAGTACCATGTTTAAGGCAGTTC 58.999 41.667 0.00 0.00 0.00 3.01
297 300 4.760204 GTCAGTACCATGTTTAAGGCAGTT 59.240 41.667 0.00 0.00 0.00 3.16
299 302 4.323417 TGTCAGTACCATGTTTAAGGCAG 58.677 43.478 0.00 0.00 0.00 4.85
301 304 5.235305 CATGTCAGTACCATGTTTAAGGC 57.765 43.478 3.24 0.00 35.94 4.35
343 346 0.531974 GCCCTGAATGCGAATCGGTA 60.532 55.000 4.35 0.00 0.00 4.02
347 350 3.025619 CGGCCCTGAATGCGAATC 58.974 61.111 0.00 0.00 0.00 2.52
350 353 3.993614 ATTGCGGCCCTGAATGCGA 62.994 57.895 0.00 0.00 0.00 5.10
355 358 2.274645 CCACAATTGCGGCCCTGAA 61.275 57.895 5.05 0.00 0.00 3.02
356 359 2.676121 CCACAATTGCGGCCCTGA 60.676 61.111 5.05 0.00 0.00 3.86
363 366 2.568090 GAGGTGGCCACAATTGCG 59.432 61.111 35.78 0.00 0.00 4.85
364 367 2.568090 CGAGGTGGCCACAATTGC 59.432 61.111 35.78 18.89 0.00 3.56
374 377 1.737793 GAGTTAATTGCACCGAGGTGG 59.262 52.381 22.19 5.97 45.49 4.61
376 379 1.001633 ACGAGTTAATTGCACCGAGGT 59.998 47.619 0.00 0.00 0.00 3.85
377 380 1.722011 ACGAGTTAATTGCACCGAGG 58.278 50.000 0.00 0.00 0.00 4.63
381 384 5.121768 ACTCAACATACGAGTTAATTGCACC 59.878 40.000 0.00 0.00 40.89 5.01
395 398 5.869888 CAGACAAGGGAGTAACTCAACATAC 59.130 44.000 0.00 0.00 31.08 2.39
396 399 5.046591 CCAGACAAGGGAGTAACTCAACATA 60.047 44.000 0.00 0.00 31.08 2.29
397 400 4.263068 CCAGACAAGGGAGTAACTCAACAT 60.263 45.833 0.00 0.00 31.08 2.71
398 401 3.071023 CCAGACAAGGGAGTAACTCAACA 59.929 47.826 0.00 0.00 31.08 3.33
399 402 3.071167 ACCAGACAAGGGAGTAACTCAAC 59.929 47.826 0.00 0.00 31.08 3.18
418 422 3.432378 ACAACGGGGCATAATAAAACCA 58.568 40.909 0.00 0.00 0.00 3.67
510 514 9.932207 TGTATTTGCATTCAAAAGAGAATTCAT 57.068 25.926 8.44 0.00 44.44 2.57
636 645 1.762957 GGCTACTTGCATACTCCCTCA 59.237 52.381 0.00 0.00 45.15 3.86
669 678 2.740714 GATGGACGTGTTGCTCGGC 61.741 63.158 0.00 0.00 35.38 5.54
818 828 2.408050 CCGCATATGCAGAGAAGGTAC 58.592 52.381 26.52 0.00 42.21 3.34
929 939 4.680567 CGACAGAAGATGACATAGATGCTG 59.319 45.833 0.00 0.00 0.00 4.41
939 951 7.043059 GGAAGATTTATCACGACAGAAGATGAC 60.043 40.741 0.00 0.00 0.00 3.06
1169 1189 8.340618 ACTACAGATCAAAACAATGCTAATGT 57.659 30.769 0.00 0.00 0.00 2.71
1512 1533 1.005450 GCTAACCAATGGAAGGGGTGA 59.995 52.381 6.16 0.00 34.51 4.02
1838 1860 5.651139 CCATTTAAGATATCTCATGGGGCTG 59.349 44.000 21.08 7.76 30.28 4.85
2072 2099 7.312899 GCTGCAGTTTATGTGGTAGTTATTTT 58.687 34.615 16.64 0.00 0.00 1.82
2080 2107 1.352687 TGGGCTGCAGTTTATGTGGTA 59.647 47.619 16.64 0.00 0.00 3.25
2092 2119 0.471591 AATGGGAAGTTTGGGCTGCA 60.472 50.000 0.50 0.00 0.00 4.41
2141 2170 6.126449 GGAAGGTGGGGAAAGATAGTCTTAAT 60.126 42.308 0.00 0.00 35.27 1.40
2354 2392 2.506438 GACGTCCAGTGCTACCGC 60.506 66.667 3.51 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.