Multiple sequence alignment - TraesCS2B01G197500

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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 TraesCS2B01G197500 chr2B 100.000 1785 0 0 827 2611 175413224 175415008 0.000000e+00 3297.0
1 TraesCS2B01G197500 chr2B 92.123 876 54 11 1659 2526 42189775 42188907 0.000000e+00 1221.0
2 TraesCS2B01G197500 chr2B 89.013 892 71 14 1634 2507 595128565 595129447 0.000000e+00 1079.0
3 TraesCS2B01G197500 chr2B 100.000 541 0 0 1 541 175412398 175412938 0.000000e+00 1000.0
4 TraesCS2B01G197500 chr2B 78.829 222 39 6 1182 1397 565036948 565036729 2.710000e-30 143.0
5 TraesCS2B01G197500 chr2B 89.333 75 7 1 1535 1608 146988690 146988764 2.770000e-15 93.5
6 TraesCS2B01G197500 chr4B 98.878 891 8 2 1633 2523 468249108 468248220 0.000000e+00 1589.0
7 TraesCS2B01G197500 chr4B 90.319 909 65 14 1630 2526 519821410 519820513 0.000000e+00 1170.0
8 TraesCS2B01G197500 chr6B 95.727 866 31 4 1658 2520 685082103 685081241 0.000000e+00 1389.0
9 TraesCS2B01G197500 chr6B 91.971 137 8 3 7 141 32323007 32322872 3.430000e-44 189.0
10 TraesCS2B01G197500 chr6B 75.000 356 85 3 1015 1368 19036886 19037239 7.480000e-36 161.0
11 TraesCS2B01G197500 chr7B 94.855 894 35 10 1632 2520 223665604 223664717 0.000000e+00 1386.0
12 TraesCS2B01G197500 chr7B 94.573 866 35 10 1661 2520 358414566 358413707 0.000000e+00 1328.0
13 TraesCS2B01G197500 chr7B 90.387 905 60 16 1634 2520 700887321 700888216 0.000000e+00 1164.0
14 TraesCS2B01G197500 chr7B 95.000 120 6 0 6 125 517095191 517095072 3.430000e-44 189.0
15 TraesCS2B01G197500 chr5B 90.769 910 61 15 1631 2526 8938879 8937979 0.000000e+00 1194.0
16 TraesCS2B01G197500 chr5B 97.479 119 3 0 7 125 562793821 562793703 1.230000e-48 204.0
17 TraesCS2B01G197500 chr5B 96.552 116 4 0 9 124 544393253 544393368 2.650000e-45 193.0
18 TraesCS2B01G197500 chr5B 94.215 121 7 0 7 127 245963882 245963762 4.440000e-43 185.0
19 TraesCS2B01G197500 chr2D 92.611 812 49 4 827 1633 122396480 122397285 0.000000e+00 1157.0
20 TraesCS2B01G197500 chr2D 83.333 366 24 13 179 537 122396112 122396447 1.170000e-78 303.0
21 TraesCS2B01G197500 chr2D 95.294 85 4 0 2524 2608 122397283 122397367 4.530000e-28 135.0
22 TraesCS2B01G197500 chr2A 93.216 737 42 4 827 1559 126645239 126645971 0.000000e+00 1077.0
23 TraesCS2B01G197500 chr2A 82.061 262 47 0 1061 1322 731378175 731377914 9.400000e-55 224.0
24 TraesCS2B01G197500 chr2A 87.634 186 8 11 122 299 126644466 126644644 4.410000e-48 202.0
25 TraesCS2B01G197500 chr2A 95.890 73 3 0 1561 1633 126646135 126646207 4.560000e-23 119.0
26 TraesCS2B01G197500 chr2A 90.698 86 7 1 2524 2608 126646205 126646290 2.120000e-21 113.0
27 TraesCS2B01G197500 chr3B 76.508 796 168 14 827 1615 139831384 139830601 1.450000e-112 416.0
28 TraesCS2B01G197500 chr3B 95.935 123 4 1 7 129 172008617 172008738 5.700000e-47 198.0
29 TraesCS2B01G197500 chr5D 77.937 630 127 8 994 1614 390261653 390261027 1.470000e-102 383.0
30 TraesCS2B01G197500 chr5D 86.159 289 34 4 1212 1497 547251177 547251462 9.080000e-80 307.0
31 TraesCS2B01G197500 chr6D 77.653 622 110 15 1021 1618 269235483 269234867 4.130000e-93 351.0
32 TraesCS2B01G197500 chr1D 95.726 117 5 0 8 124 392560974 392561090 3.430000e-44 189.0
33 TraesCS2B01G197500 chr1B 95.000 120 6 0 5 124 72876074 72876193 3.430000e-44 189.0
34 TraesCS2B01G197500 chr1B 92.308 130 9 1 3 131 564919114 564918985 1.600000e-42 183.0


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 TraesCS2B01G197500 chr2B 175412398 175415008 2610 False 2148.500000 3297 100.000000 1 2611 2 chr2B.!!$F3 2610
1 TraesCS2B01G197500 chr2B 42188907 42189775 868 True 1221.000000 1221 92.123000 1659 2526 1 chr2B.!!$R1 867
2 TraesCS2B01G197500 chr2B 595128565 595129447 882 False 1079.000000 1079 89.013000 1634 2507 1 chr2B.!!$F2 873
3 TraesCS2B01G197500 chr4B 468248220 468249108 888 True 1589.000000 1589 98.878000 1633 2523 1 chr4B.!!$R1 890
4 TraesCS2B01G197500 chr4B 519820513 519821410 897 True 1170.000000 1170 90.319000 1630 2526 1 chr4B.!!$R2 896
5 TraesCS2B01G197500 chr6B 685081241 685082103 862 True 1389.000000 1389 95.727000 1658 2520 1 chr6B.!!$R2 862
6 TraesCS2B01G197500 chr7B 223664717 223665604 887 True 1386.000000 1386 94.855000 1632 2520 1 chr7B.!!$R1 888
7 TraesCS2B01G197500 chr7B 358413707 358414566 859 True 1328.000000 1328 94.573000 1661 2520 1 chr7B.!!$R2 859
8 TraesCS2B01G197500 chr7B 700887321 700888216 895 False 1164.000000 1164 90.387000 1634 2520 1 chr7B.!!$F1 886
9 TraesCS2B01G197500 chr5B 8937979 8938879 900 True 1194.000000 1194 90.769000 1631 2526 1 chr5B.!!$R1 895
10 TraesCS2B01G197500 chr2D 122396112 122397367 1255 False 531.666667 1157 90.412667 179 2608 3 chr2D.!!$F1 2429
11 TraesCS2B01G197500 chr2A 126644466 126646290 1824 False 377.750000 1077 91.859500 122 2608 4 chr2A.!!$F1 2486
12 TraesCS2B01G197500 chr3B 139830601 139831384 783 True 416.000000 416 76.508000 827 1615 1 chr3B.!!$R1 788
13 TraesCS2B01G197500 chr5D 390261027 390261653 626 True 383.000000 383 77.937000 994 1614 1 chr5D.!!$R1 620
14 TraesCS2B01G197500 chr6D 269234867 269235483 616 True 351.000000 351 77.653000 1021 1618 1 chr6D.!!$R1 597

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
890 1247 0.669077 GGCAGATCTACGGTCGTCAT 59.331 55.0 0.0 0.0 0.0 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1762 2312 1.805345 GTGCATGAGATGAGCATAGCC 59.195 52.381 0.0 0.0 40.78 3.93 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
21 22 3.543680 ATGTTGTACTCCCTCCATTCG 57.456 47.619 0.00 0.00 0.00 3.34
22 23 2.531771 TGTTGTACTCCCTCCATTCGA 58.468 47.619 0.00 0.00 0.00 3.71
23 24 2.901192 TGTTGTACTCCCTCCATTCGAA 59.099 45.455 0.00 0.00 0.00 3.71
24 25 3.325425 TGTTGTACTCCCTCCATTCGAAA 59.675 43.478 0.00 0.00 0.00 3.46
25 26 4.019681 TGTTGTACTCCCTCCATTCGAAAT 60.020 41.667 0.00 0.00 0.00 2.17
26 27 4.837093 TGTACTCCCTCCATTCGAAATT 57.163 40.909 0.00 0.00 0.00 1.82
27 28 5.943349 TGTACTCCCTCCATTCGAAATTA 57.057 39.130 0.00 0.00 0.00 1.40
28 29 5.667466 TGTACTCCCTCCATTCGAAATTAC 58.333 41.667 0.00 0.00 0.00 1.89
29 30 5.424252 TGTACTCCCTCCATTCGAAATTACT 59.576 40.000 0.00 0.00 0.00 2.24
30 31 5.024785 ACTCCCTCCATTCGAAATTACTC 57.975 43.478 0.00 0.00 0.00 2.59
31 32 4.051922 CTCCCTCCATTCGAAATTACTCG 58.948 47.826 0.00 0.00 40.25 4.18
32 33 3.449737 TCCCTCCATTCGAAATTACTCGT 59.550 43.478 0.00 0.00 39.84 4.18
33 34 3.802685 CCCTCCATTCGAAATTACTCGTC 59.197 47.826 0.00 0.00 39.84 4.20
34 35 3.802685 CCTCCATTCGAAATTACTCGTCC 59.197 47.826 0.00 0.00 39.84 4.79
35 36 4.430007 CTCCATTCGAAATTACTCGTCCA 58.570 43.478 0.00 0.00 39.84 4.02
36 37 4.823157 TCCATTCGAAATTACTCGTCCAA 58.177 39.130 0.00 0.00 39.84 3.53
37 38 4.868171 TCCATTCGAAATTACTCGTCCAAG 59.132 41.667 0.00 0.00 39.84 3.61
38 39 4.868171 CCATTCGAAATTACTCGTCCAAGA 59.132 41.667 0.00 0.00 39.84 3.02
39 40 5.350365 CCATTCGAAATTACTCGTCCAAGAA 59.650 40.000 0.00 0.00 39.84 2.52
40 41 6.128391 CCATTCGAAATTACTCGTCCAAGAAA 60.128 38.462 0.00 0.00 39.84 2.52
41 42 7.414098 CCATTCGAAATTACTCGTCCAAGAAAT 60.414 37.037 0.00 0.00 39.84 2.17
42 43 6.403333 TCGAAATTACTCGTCCAAGAAATG 57.597 37.500 0.00 0.00 39.84 2.32
43 44 6.160684 TCGAAATTACTCGTCCAAGAAATGA 58.839 36.000 0.00 0.00 39.84 2.57
44 45 6.647481 TCGAAATTACTCGTCCAAGAAATGAA 59.353 34.615 0.00 0.00 39.84 2.57
45 46 7.333423 TCGAAATTACTCGTCCAAGAAATGAAT 59.667 33.333 0.00 0.00 39.84 2.57
46 47 7.426456 CGAAATTACTCGTCCAAGAAATGAATG 59.574 37.037 0.00 0.00 34.08 2.67
47 48 7.687941 AATTACTCGTCCAAGAAATGAATGT 57.312 32.000 0.00 0.00 0.00 2.71
48 49 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
49 50 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
50 51 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
51 52 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
52 53 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
53 54 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
54 55 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
55 56 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
56 57 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
57 58 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
113 114 9.453325 TCATTTTTGTAACAAGTAATTCCGAAC 57.547 29.630 0.00 0.00 0.00 3.95
114 115 7.895582 TTTTTGTAACAAGTAATTCCGAACG 57.104 32.000 0.00 0.00 0.00 3.95
115 116 5.594724 TTGTAACAAGTAATTCCGAACGG 57.405 39.130 6.94 6.94 0.00 4.44
116 117 4.880759 TGTAACAAGTAATTCCGAACGGA 58.119 39.130 12.04 12.04 43.52 4.69
117 118 4.925054 TGTAACAAGTAATTCCGAACGGAG 59.075 41.667 15.34 5.60 46.06 4.63
118 119 2.968675 ACAAGTAATTCCGAACGGAGG 58.031 47.619 15.34 4.52 46.06 4.30
119 120 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
120 121 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
138 139 4.607239 AGGGAGTACGTAGGATTCAAGAA 58.393 43.478 0.00 0.00 0.00 2.52
143 144 5.014858 AGTACGTAGGATTCAAGAAGGACA 58.985 41.667 0.00 0.00 0.00 4.02
144 145 5.657302 AGTACGTAGGATTCAAGAAGGACAT 59.343 40.000 0.00 0.00 0.00 3.06
146 147 3.557595 CGTAGGATTCAAGAAGGACATGC 59.442 47.826 0.00 0.00 0.00 4.06
165 166 7.363793 GGACATGCCACTTAATCCTATGTTTTT 60.364 37.037 0.00 0.00 36.34 1.94
174 175 9.588096 ACTTAATCCTATGTTTTTCTTCTTGGT 57.412 29.630 0.00 0.00 0.00 3.67
223 225 0.892755 TAGGGTCACGTACTGCTTGG 59.107 55.000 0.00 0.00 0.00 3.61
267 276 2.572104 AGCAACTCTAACCGATTTCCCT 59.428 45.455 0.00 0.00 0.00 4.20
279 288 6.812879 ACCGATTTCCCTAAAACACTTTAG 57.187 37.500 0.00 0.00 42.52 1.85
281 290 7.173032 ACCGATTTCCCTAAAACACTTTAGAT 58.827 34.615 6.27 0.00 44.70 1.98
282 291 7.120726 ACCGATTTCCCTAAAACACTTTAGATG 59.879 37.037 6.27 0.00 44.70 2.90
283 292 7.335924 CCGATTTCCCTAAAACACTTTAGATGA 59.664 37.037 6.27 1.19 44.70 2.92
284 293 8.391106 CGATTTCCCTAAAACACTTTAGATGAG 58.609 37.037 6.27 0.00 44.70 2.90
285 294 9.232473 GATTTCCCTAAAACACTTTAGATGAGT 57.768 33.333 6.27 0.00 44.70 3.41
289 298 9.498176 TCCCTAAAACACTTTAGATGAGTAAAC 57.502 33.333 6.27 0.00 44.70 2.01
290 299 9.503399 CCCTAAAACACTTTAGATGAGTAAACT 57.497 33.333 6.27 0.00 44.70 2.66
296 305 9.614792 AACACTTTAGATGAGTAAACTTTCACT 57.385 29.630 0.00 0.00 0.00 3.41
297 306 9.614792 ACACTTTAGATGAGTAAACTTTCACTT 57.385 29.630 0.00 0.00 0.00 3.16
300 309 9.798885 CTTTAGATGAGTAAACTTTCACTTTCG 57.201 33.333 0.00 0.00 0.00 3.46
301 310 6.229561 AGATGAGTAAACTTTCACTTTCGC 57.770 37.500 0.00 0.00 0.00 4.70
302 311 5.992217 AGATGAGTAAACTTTCACTTTCGCT 59.008 36.000 0.00 0.00 0.00 4.93
303 312 6.483640 AGATGAGTAAACTTTCACTTTCGCTT 59.516 34.615 0.00 0.00 0.00 4.68
304 313 6.431198 TGAGTAAACTTTCACTTTCGCTTT 57.569 33.333 0.00 0.00 0.00 3.51
305 314 7.542534 TGAGTAAACTTTCACTTTCGCTTTA 57.457 32.000 0.00 0.00 0.00 1.85
306 315 7.627340 TGAGTAAACTTTCACTTTCGCTTTAG 58.373 34.615 0.00 0.00 0.00 1.85
307 316 7.493320 TGAGTAAACTTTCACTTTCGCTTTAGA 59.507 33.333 0.00 0.00 0.00 2.10
308 317 7.628235 AGTAAACTTTCACTTTCGCTTTAGAC 58.372 34.615 0.00 0.00 0.00 2.59
331 340 6.814043 ACGAGTAACCTTTCACTTTTACTCT 58.186 36.000 14.97 3.89 44.28 3.24
350 359 3.437213 TCTACTAAACTGCACCTAGCCA 58.563 45.455 0.00 0.00 44.83 4.75
353 362 2.372172 ACTAAACTGCACCTAGCCAACT 59.628 45.455 0.00 0.00 44.83 3.16
416 425 4.758165 CCGCCCCAACTCGTATATTTAATT 59.242 41.667 0.00 0.00 0.00 1.40
451 460 3.072211 CCGAGTAAAAAGTGTTCCCCTC 58.928 50.000 0.00 0.00 0.00 4.30
478 487 4.596585 CCGCACCCACCCAACCTT 62.597 66.667 0.00 0.00 0.00 3.50
492 501 2.360350 CCTTGTGCCGCATCCACT 60.360 61.111 0.00 0.00 34.38 4.00
519 875 2.656069 GCCCTAGTTGCCTCCGTCA 61.656 63.158 0.00 0.00 0.00 4.35
524 880 1.476845 TAGTTGCCTCCGTCAGCCAA 61.477 55.000 0.00 0.00 0.00 4.52
527 883 2.281484 GCCTCCGTCAGCCAACAA 60.281 61.111 0.00 0.00 0.00 2.83
889 1246 1.712018 CGGCAGATCTACGGTCGTCA 61.712 60.000 10.28 0.00 37.07 4.35
890 1247 0.669077 GGCAGATCTACGGTCGTCAT 59.331 55.000 0.00 0.00 0.00 3.06
924 1281 2.181021 GACGCACCTAGTCACCGG 59.819 66.667 0.00 0.00 38.42 5.28
928 1285 4.814294 CACCTAGTCACCGGCGCC 62.814 72.222 19.07 19.07 0.00 6.53
930 1287 4.077184 CCTAGTCACCGGCGCCAA 62.077 66.667 28.98 5.35 0.00 4.52
948 1305 2.839474 CAACGCGTTTTGGAGAGATTC 58.161 47.619 24.21 0.00 0.00 2.52
949 1306 2.163818 ACGCGTTTTGGAGAGATTCA 57.836 45.000 5.58 0.00 0.00 2.57
958 1316 2.466846 TGGAGAGATTCAACGGGATCA 58.533 47.619 0.00 0.00 0.00 2.92
1011 1373 1.611519 CTCTCGGTATGTCCTCCTCC 58.388 60.000 0.00 0.00 0.00 4.30
1176 1538 1.164411 TTTCGAGCATGCCGAAACAT 58.836 45.000 33.38 11.81 46.77 2.71
1180 1543 1.001020 AGCATGCCGAAACATCCCA 60.001 52.632 15.66 0.00 0.00 4.37
1251 1615 5.766150 ACGGTTGTTCTTCAAATTCATCA 57.234 34.783 0.00 0.00 37.81 3.07
1502 1889 6.185511 TCAAGAGATGGAGAAAGCATTGATT 58.814 36.000 0.00 0.00 0.00 2.57
1611 2160 7.458397 AGTGAAGAATTGGTGGAGTATGTAAA 58.542 34.615 0.00 0.00 0.00 2.01
1668 2217 3.360296 TGCATGAAGGGTGCATGAA 57.640 47.368 7.68 0.00 46.76 2.57
1762 2312 0.954452 GATGCATAAAAGGGCCCTCG 59.046 55.000 28.84 12.70 0.00 4.63
2522 3118 2.794103 TGCATGCTACCAAACACATCT 58.206 42.857 20.33 0.00 0.00 2.90
2599 3196 7.496346 AAGTATCAGGGATCAGTTAGAAACA 57.504 36.000 0.00 0.00 0.00 2.83
2608 3205 6.325596 GGATCAGTTAGAAACAGCCATTTTC 58.674 40.000 0.00 0.00 33.81 2.29
2609 3206 6.151817 GGATCAGTTAGAAACAGCCATTTTCT 59.848 38.462 9.15 9.15 43.97 2.52
2610 3207 7.336931 GGATCAGTTAGAAACAGCCATTTTCTA 59.663 37.037 7.57 7.57 42.19 2.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.517901 TCGAATGGAGGGAGTACAACATT 59.482 43.478 0.00 0.00 0.00 2.71
1 2 3.104512 TCGAATGGAGGGAGTACAACAT 58.895 45.455 0.00 0.00 0.00 2.71
2 3 2.531771 TCGAATGGAGGGAGTACAACA 58.468 47.619 0.00 0.00 0.00 3.33
3 4 3.604875 TTCGAATGGAGGGAGTACAAC 57.395 47.619 0.00 0.00 0.00 3.32
4 5 4.837093 ATTTCGAATGGAGGGAGTACAA 57.163 40.909 0.00 0.00 0.00 2.41
5 6 4.837093 AATTTCGAATGGAGGGAGTACA 57.163 40.909 0.00 0.00 0.00 2.90
6 7 5.915175 AGTAATTTCGAATGGAGGGAGTAC 58.085 41.667 0.00 0.00 0.00 2.73
7 8 5.221185 CGAGTAATTTCGAATGGAGGGAGTA 60.221 44.000 0.00 0.00 43.03 2.59
8 9 4.441634 CGAGTAATTTCGAATGGAGGGAGT 60.442 45.833 0.00 0.00 43.03 3.85
9 10 4.051922 CGAGTAATTTCGAATGGAGGGAG 58.948 47.826 0.00 0.00 43.03 4.30
10 11 3.449737 ACGAGTAATTTCGAATGGAGGGA 59.550 43.478 6.54 0.00 43.03 4.20
11 12 3.793559 ACGAGTAATTTCGAATGGAGGG 58.206 45.455 6.54 0.00 43.03 4.30
12 13 3.802685 GGACGAGTAATTTCGAATGGAGG 59.197 47.826 6.54 0.00 43.03 4.30
13 14 4.430007 TGGACGAGTAATTTCGAATGGAG 58.570 43.478 6.54 0.00 43.03 3.86
14 15 4.459390 TGGACGAGTAATTTCGAATGGA 57.541 40.909 6.54 0.00 43.03 3.41
15 16 4.868171 TCTTGGACGAGTAATTTCGAATGG 59.132 41.667 6.54 0.00 43.03 3.16
16 17 6.403333 TTCTTGGACGAGTAATTTCGAATG 57.597 37.500 6.54 0.00 43.03 2.67
17 18 7.333423 TCATTTCTTGGACGAGTAATTTCGAAT 59.667 33.333 6.54 0.00 43.03 3.34
18 19 6.647481 TCATTTCTTGGACGAGTAATTTCGAA 59.353 34.615 6.54 0.00 43.03 3.71
19 20 6.160684 TCATTTCTTGGACGAGTAATTTCGA 58.839 36.000 6.54 0.00 43.03 3.71
20 21 6.403333 TCATTTCTTGGACGAGTAATTTCG 57.597 37.500 0.00 0.00 45.70 3.46
21 22 8.237267 ACATTCATTTCTTGGACGAGTAATTTC 58.763 33.333 0.00 0.00 0.00 2.17
22 23 8.110860 ACATTCATTTCTTGGACGAGTAATTT 57.889 30.769 0.00 0.00 0.00 1.82
23 24 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
24 25 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
25 26 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
26 27 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
27 28 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
28 29 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
29 30 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
30 31 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
31 32 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
87 88 9.453325 GTTCGGAATTACTTGTTACAAAAATGA 57.547 29.630 0.00 0.00 0.00 2.57
88 89 8.414173 CGTTCGGAATTACTTGTTACAAAAATG 58.586 33.333 0.00 0.00 0.00 2.32
89 90 7.592164 CCGTTCGGAATTACTTGTTACAAAAAT 59.408 33.333 5.19 0.00 0.00 1.82
90 91 6.911511 CCGTTCGGAATTACTTGTTACAAAAA 59.088 34.615 5.19 0.00 0.00 1.94
91 92 6.259608 TCCGTTCGGAATTACTTGTTACAAAA 59.740 34.615 11.66 0.00 0.00 2.44
92 93 5.757320 TCCGTTCGGAATTACTTGTTACAAA 59.243 36.000 11.66 0.00 0.00 2.83
93 94 5.295950 TCCGTTCGGAATTACTTGTTACAA 58.704 37.500 11.66 0.00 0.00 2.41
94 95 4.880759 TCCGTTCGGAATTACTTGTTACA 58.119 39.130 11.66 0.00 0.00 2.41
95 96 4.328169 CCTCCGTTCGGAATTACTTGTTAC 59.672 45.833 14.79 0.00 33.41 2.50
96 97 4.497300 CCTCCGTTCGGAATTACTTGTTA 58.503 43.478 14.79 0.00 33.41 2.41
97 98 3.332034 CCTCCGTTCGGAATTACTTGTT 58.668 45.455 14.79 0.00 33.41 2.83
98 99 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
99 100 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
100 101 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
101 102 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
102 103 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
103 104 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
104 105 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
105 106 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
106 107 1.308069 CGTACTCCCTCCGTTCGGAA 61.308 60.000 14.79 0.04 33.41 4.30
107 108 1.746615 CGTACTCCCTCCGTTCGGA 60.747 63.158 13.34 13.34 0.00 4.55
108 109 0.744414 TACGTACTCCCTCCGTTCGG 60.744 60.000 4.74 4.74 36.12 4.30
109 110 0.654683 CTACGTACTCCCTCCGTTCG 59.345 60.000 0.00 0.00 36.12 3.95
110 111 1.020437 CCTACGTACTCCCTCCGTTC 58.980 60.000 0.00 0.00 36.12 3.95
111 112 0.620556 TCCTACGTACTCCCTCCGTT 59.379 55.000 0.00 0.00 36.12 4.44
112 113 0.842635 ATCCTACGTACTCCCTCCGT 59.157 55.000 0.00 0.00 38.53 4.69
113 114 1.878734 GAATCCTACGTACTCCCTCCG 59.121 57.143 0.00 0.00 0.00 4.63
114 115 2.941480 TGAATCCTACGTACTCCCTCC 58.059 52.381 0.00 0.00 0.00 4.30
115 116 4.205587 TCTTGAATCCTACGTACTCCCTC 58.794 47.826 0.00 0.00 0.00 4.30
116 117 4.246712 TCTTGAATCCTACGTACTCCCT 57.753 45.455 0.00 0.00 0.00 4.20
117 118 4.202131 CCTTCTTGAATCCTACGTACTCCC 60.202 50.000 0.00 0.00 0.00 4.30
118 119 4.643784 TCCTTCTTGAATCCTACGTACTCC 59.356 45.833 0.00 0.00 0.00 3.85
119 120 5.125097 TGTCCTTCTTGAATCCTACGTACTC 59.875 44.000 0.00 0.00 0.00 2.59
120 121 5.014858 TGTCCTTCTTGAATCCTACGTACT 58.985 41.667 0.00 0.00 0.00 2.73
138 139 4.413520 ACATAGGATTAAGTGGCATGTCCT 59.586 41.667 0.00 11.79 39.32 3.85
143 144 7.961326 AGAAAAACATAGGATTAAGTGGCAT 57.039 32.000 0.00 0.00 0.00 4.40
144 145 7.669722 AGAAGAAAAACATAGGATTAAGTGGCA 59.330 33.333 0.00 0.00 0.00 4.92
146 147 9.846248 CAAGAAGAAAAACATAGGATTAAGTGG 57.154 33.333 0.00 0.00 0.00 4.00
174 175 5.358442 TCTTTGATTCACGGGTTTCTCAAAA 59.642 36.000 7.63 0.00 33.62 2.44
223 225 7.278646 TGCTCTAACACAACATGACATCTTATC 59.721 37.037 0.00 0.00 0.00 1.75
263 272 9.498176 GTTTACTCATCTAAAGTGTTTTAGGGA 57.502 33.333 7.08 5.28 43.83 4.20
279 288 6.229561 AGCGAAAGTGAAAGTTTACTCATC 57.770 37.500 0.00 0.00 40.14 2.92
281 290 6.431198 AAAGCGAAAGTGAAAGTTTACTCA 57.569 33.333 0.00 0.00 40.14 3.41
282 291 7.792967 GTCTAAAGCGAAAGTGAAAGTTTACTC 59.207 37.037 0.00 0.00 40.14 2.59
283 292 7.516312 CGTCTAAAGCGAAAGTGAAAGTTTACT 60.516 37.037 0.00 0.00 40.14 2.24
284 293 6.568965 CGTCTAAAGCGAAAGTGAAAGTTTAC 59.431 38.462 0.00 0.00 40.14 2.01
285 294 6.476380 TCGTCTAAAGCGAAAGTGAAAGTTTA 59.524 34.615 0.00 0.00 40.14 2.01
286 295 5.292589 TCGTCTAAAGCGAAAGTGAAAGTTT 59.707 36.000 0.00 0.00 43.41 2.66
287 296 4.807304 TCGTCTAAAGCGAAAGTGAAAGTT 59.193 37.500 0.00 0.00 35.28 2.66
288 297 4.365723 TCGTCTAAAGCGAAAGTGAAAGT 58.634 39.130 0.00 0.00 35.28 2.66
289 298 4.444720 ACTCGTCTAAAGCGAAAGTGAAAG 59.555 41.667 0.00 0.00 37.93 2.62
290 299 4.365723 ACTCGTCTAAAGCGAAAGTGAAA 58.634 39.130 0.00 0.00 37.93 2.69
291 300 3.973657 ACTCGTCTAAAGCGAAAGTGAA 58.026 40.909 0.00 0.00 37.93 3.18
292 301 3.637998 ACTCGTCTAAAGCGAAAGTGA 57.362 42.857 0.00 0.00 37.93 3.41
293 302 4.089636 GGTTACTCGTCTAAAGCGAAAGTG 59.910 45.833 0.00 0.00 37.93 3.16
294 303 4.022503 AGGTTACTCGTCTAAAGCGAAAGT 60.023 41.667 0.00 0.00 37.93 2.66
295 304 4.483311 AGGTTACTCGTCTAAAGCGAAAG 58.517 43.478 0.00 0.00 37.93 2.62
296 305 4.510038 AGGTTACTCGTCTAAAGCGAAA 57.490 40.909 0.00 0.00 37.93 3.46
297 306 4.510038 AAGGTTACTCGTCTAAAGCGAA 57.490 40.909 0.00 0.00 37.93 4.70
298 307 4.022935 TGAAAGGTTACTCGTCTAAAGCGA 60.023 41.667 0.00 0.00 36.85 4.93
299 308 4.089636 GTGAAAGGTTACTCGTCTAAAGCG 59.910 45.833 0.00 0.00 0.00 4.68
300 309 5.228665 AGTGAAAGGTTACTCGTCTAAAGC 58.771 41.667 0.00 0.00 0.00 3.51
301 310 7.710766 AAAGTGAAAGGTTACTCGTCTAAAG 57.289 36.000 0.00 0.00 0.00 1.85
302 311 9.034544 GTAAAAGTGAAAGGTTACTCGTCTAAA 57.965 33.333 0.00 0.00 0.00 1.85
303 312 8.416329 AGTAAAAGTGAAAGGTTACTCGTCTAA 58.584 33.333 0.00 0.00 32.62 2.10
304 313 7.945134 AGTAAAAGTGAAAGGTTACTCGTCTA 58.055 34.615 0.00 0.00 32.62 2.59
305 314 6.814043 AGTAAAAGTGAAAGGTTACTCGTCT 58.186 36.000 0.00 0.00 32.62 4.18
306 315 7.103159 GAGTAAAAGTGAAAGGTTACTCGTC 57.897 40.000 6.66 0.00 41.30 4.20
331 340 3.581332 AGTTGGCTAGGTGCAGTTTAGTA 59.419 43.478 0.00 0.00 45.15 1.82
380 389 2.584391 GGGCGGCCGAAGAGGATAT 61.584 63.158 33.48 0.00 45.00 1.63
400 409 4.214758 GGCGGCCAATTAAATATACGAGTT 59.785 41.667 15.62 0.00 0.00 3.01
405 414 3.057104 GGTGGGCGGCCAATTAAATATAC 60.057 47.826 34.51 15.75 0.00 1.47
431 440 3.072211 GGAGGGGAACACTTTTTACTCG 58.928 50.000 0.00 0.00 0.00 4.18
478 487 2.741985 CGAAGTGGATGCGGCACA 60.742 61.111 4.03 0.00 0.00 4.57
519 875 3.591835 CGGTGGCGTTTGTTGGCT 61.592 61.111 0.00 0.00 0.00 4.75
928 1285 2.223144 TGAATCTCTCCAAAACGCGTTG 59.777 45.455 27.34 15.08 0.00 4.10
930 1287 2.163818 TGAATCTCTCCAAAACGCGT 57.836 45.000 5.58 5.58 0.00 6.01
948 1305 2.696759 GCCCGGTTTGATCCCGTTG 61.697 63.158 0.00 1.08 43.98 4.10
949 1306 2.360726 GCCCGGTTTGATCCCGTT 60.361 61.111 0.00 0.00 43.98 4.44
958 1316 2.355115 GAGGTGGATGCCCGGTTT 59.645 61.111 0.00 0.00 34.29 3.27
1011 1373 2.887568 GTGAGATGCGAGCGGTGG 60.888 66.667 0.00 0.00 0.00 4.61
1155 1517 4.370182 TTCGGCATGCTCGAAACA 57.630 50.000 29.37 15.65 42.57 2.83
1180 1543 3.074412 CGCACTTGAAGTAAACCCATCT 58.926 45.455 0.00 0.00 0.00 2.90
1190 1553 1.597663 CGTCCTTTTCGCACTTGAAGT 59.402 47.619 0.00 0.00 0.00 3.01
1279 1644 8.458573 AAATTTGCATCCGTCCTATATACAAA 57.541 30.769 0.00 0.00 0.00 2.83
1502 1889 4.534500 TCCTTAACTGCTCCTGTTAATCCA 59.466 41.667 7.55 0.00 37.23 3.41
1611 2160 6.270231 ACCCTTAGACTTCACTACTCATTTGT 59.730 38.462 0.00 0.00 0.00 2.83
1668 2217 2.814336 GTCGGATTGAGAACTTTTGCCT 59.186 45.455 0.00 0.00 0.00 4.75
1762 2312 1.805345 GTGCATGAGATGAGCATAGCC 59.195 52.381 0.00 0.00 40.78 3.93
2522 3118 9.015367 TCATTTATTTTTGGTCCATCGAGTTAA 57.985 29.630 0.00 0.00 0.00 2.01
2568 3165 5.721225 ACTGATCCCTGATACTTACTGGAT 58.279 41.667 0.00 0.00 0.00 3.41
2572 3169 8.697292 GTTTCTAACTGATCCCTGATACTTACT 58.303 37.037 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.