Multiple sequence alignment - TraesCS2A01G061900

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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 TraesCS2A01G061900 chr2A 100.000 2363 0 0 1 2363 27627467 27629829 0.000000e+00 4364
1 TraesCS2A01G061900 chr2A 90.905 2199 148 17 115 2290 27637913 27640082 0.000000e+00 2905
2 TraesCS2A01G061900 chr2A 89.067 375 41 0 115 489 27636977 27637351 1.510000e-127 466
3 TraesCS2A01G061900 chr2A 87.724 391 29 7 783 1154 27912818 27912428 3.290000e-119 438
4 TraesCS2A01G061900 chr2A 86.082 388 30 10 784 1153 27940911 27940530 2.010000e-106 396
5 TraesCS2A01G061900 chr2A 80.916 524 51 26 666 1154 27743657 27743148 4.380000e-98 368
6 TraesCS2A01G061900 chr2A 79.467 375 50 17 283 638 27642251 27642617 9.960000e-60 241
7 TraesCS2A01G061900 chr2A 100.000 85 0 0 2699 2783 27630165 27630249 1.030000e-34 158
8 TraesCS2A01G061900 chr2A 92.941 85 6 0 2699 2783 27640328 27640412 1.050000e-24 124
9 TraesCS2A01G061900 chrUn 90.191 1784 114 29 376 2134 24837712 24835965 0.000000e+00 2268
10 TraesCS2A01G061900 chrUn 90.078 1784 116 29 376 2134 212870480 212868733 0.000000e+00 2257
11 TraesCS2A01G061900 chrUn 89.736 721 53 10 1421 2134 212865730 212865024 0.000000e+00 902
12 TraesCS2A01G061900 chrUn 87.304 701 68 15 1291 1975 162951480 162952175 0.000000e+00 782
13 TraesCS2A01G061900 chrUn 87.304 701 68 15 1291 1975 430856542 430855847 0.000000e+00 782
14 TraesCS2A01G061900 chrUn 87.092 705 70 15 1287 1975 162979093 162979792 0.000000e+00 778
15 TraesCS2A01G061900 chrUn 87.092 705 70 15 1287 1975 310275985 310275286 0.000000e+00 778
16 TraesCS2A01G061900 chrUn 90.055 362 28 2 789 1150 24809010 24808657 1.950000e-126 462
17 TraesCS2A01G061900 chrUn 89.189 370 40 0 115 484 478028464 478028095 1.950000e-126 462
18 TraesCS2A01G061900 chrUn 83.243 370 37 17 1893 2250 163007209 163007565 1.610000e-82 316
19 TraesCS2A01G061900 chrUn 83.243 370 37 17 1893 2250 363576252 363575896 1.610000e-82 316
20 TraesCS2A01G061900 chrUn 83.243 370 37 17 1893 2250 363601059 363601415 1.610000e-82 316
21 TraesCS2A01G061900 chrUn 75.486 669 91 51 302 918 162950562 162951209 2.750000e-65 259
22 TraesCS2A01G061900 chrUn 84.810 158 13 7 654 809 162966046 162966194 6.210000e-32 148
23 TraesCS2A01G061900 chrUn 84.810 158 13 7 654 809 163005423 163005571 6.210000e-32 148
24 TraesCS2A01G061900 chrUn 84.810 158 13 7 654 809 163025387 163025535 6.210000e-32 148
25 TraesCS2A01G061900 chrUn 84.810 158 13 7 654 809 363577357 363577209 6.210000e-32 148
26 TraesCS2A01G061900 chrUn 84.810 158 13 7 654 809 363599954 363600102 6.210000e-32 148
27 TraesCS2A01G061900 chrUn 84.810 158 13 7 654 809 364951397 364951249 6.210000e-32 148
28 TraesCS2A01G061900 chr2B 87.704 1041 87 22 1287 2309 41070792 41071809 0.000000e+00 1175
29 TraesCS2A01G061900 chr2B 88.144 970 89 16 1287 2248 40954084 40955035 0.000000e+00 1131
30 TraesCS2A01G061900 chr2B 84.143 391 30 10 784 1154 41115024 41114646 1.590000e-92 350
31 TraesCS2A01G061900 chr2B 82.836 402 33 15 784 1154 41125237 41124841 7.430000e-86 327
32 TraesCS2A01G061900 chr2B 89.778 225 17 4 376 596 40922548 40922770 1.630000e-72 283
33 TraesCS2A01G061900 chr2D 90.055 362 28 2 789 1150 25319739 25319386 1.950000e-126 462
34 TraesCS2A01G061900 chr2D 86.423 383 27 11 784 1154 25332766 25332397 2.010000e-106 396
35 TraesCS2A01G061900 chr2D 90.222 225 16 2 376 597 25209016 25209237 3.510000e-74 289


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 TraesCS2A01G061900 chr2A 27627467 27630249 2782 False 2261.0 4364 100.0000 1 2783 2 chr2A.!!$F1 2782
1 TraesCS2A01G061900 chr2A 27636977 27642617 5640 False 934.0 2905 88.0950 115 2783 4 chr2A.!!$F2 2668
2 TraesCS2A01G061900 chr2A 27743148 27743657 509 True 368.0 368 80.9160 666 1154 1 chr2A.!!$R1 488
3 TraesCS2A01G061900 chrUn 24835965 24837712 1747 True 2268.0 2268 90.1910 376 2134 1 chrUn.!!$R2 1758
4 TraesCS2A01G061900 chrUn 212865024 212870480 5456 True 1579.5 2257 89.9070 376 2134 2 chrUn.!!$R7 1758
5 TraesCS2A01G061900 chrUn 430855847 430856542 695 True 782.0 782 87.3040 1291 1975 1 chrUn.!!$R5 684
6 TraesCS2A01G061900 chrUn 162979093 162979792 699 False 778.0 778 87.0920 1287 1975 1 chrUn.!!$F2 688
7 TraesCS2A01G061900 chrUn 310275286 310275985 699 True 778.0 778 87.0920 1287 1975 1 chrUn.!!$R3 688
8 TraesCS2A01G061900 chrUn 162950562 162952175 1613 False 520.5 782 81.3950 302 1975 2 chrUn.!!$F4 1673
9 TraesCS2A01G061900 chrUn 163005423 163007565 2142 False 232.0 316 84.0265 654 2250 2 chrUn.!!$F5 1596
10 TraesCS2A01G061900 chrUn 363575896 363577357 1461 True 232.0 316 84.0265 654 2250 2 chrUn.!!$R8 1596
11 TraesCS2A01G061900 chrUn 363599954 363601415 1461 False 232.0 316 84.0265 654 2250 2 chrUn.!!$F6 1596
12 TraesCS2A01G061900 chr2B 41070792 41071809 1017 False 1175.0 1175 87.7040 1287 2309 1 chr2B.!!$F3 1022
13 TraesCS2A01G061900 chr2B 40954084 40955035 951 False 1131.0 1131 88.1440 1287 2248 1 chr2B.!!$F2 961

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
989 2068 0.602638 CACAGGCAAGCGAGTGGTAA 60.603 55.0 7.38 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2314 7773 0.327964 AAATGAGAGGGAGGGGAGGG 60.328 60.0 0.0 0.0 0.0 4.3 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 3.665745 AATGCAGACCATTTGTCCAAC 57.334 42.857 0.00 0.00 45.68 3.77
22 23 2.064434 TGCAGACCATTTGTCCAACA 57.936 45.000 0.00 0.00 45.68 3.33
23 24 2.382882 TGCAGACCATTTGTCCAACAA 58.617 42.857 0.00 0.00 45.68 2.83
24 25 2.100584 TGCAGACCATTTGTCCAACAAC 59.899 45.455 0.00 0.00 45.68 3.32
25 26 2.100584 GCAGACCATTTGTCCAACAACA 59.899 45.455 0.00 0.00 45.68 3.33
26 27 3.243839 GCAGACCATTTGTCCAACAACAT 60.244 43.478 0.00 0.00 45.68 2.71
27 28 4.300803 CAGACCATTTGTCCAACAACATG 58.699 43.478 0.00 0.00 45.68 3.21
28 29 3.059166 GACCATTTGTCCAACAACATGC 58.941 45.455 0.00 0.00 37.90 4.06
29 30 2.433604 ACCATTTGTCCAACAACATGCA 59.566 40.909 0.00 0.00 37.90 3.96
30 31 3.071312 ACCATTTGTCCAACAACATGCAT 59.929 39.130 0.00 0.00 37.90 3.96
31 32 4.282957 ACCATTTGTCCAACAACATGCATA 59.717 37.500 0.00 0.00 37.90 3.14
32 33 5.046448 ACCATTTGTCCAACAACATGCATAT 60.046 36.000 0.00 0.00 37.90 1.78
33 34 6.154192 ACCATTTGTCCAACAACATGCATATA 59.846 34.615 0.00 0.00 37.90 0.86
34 35 7.147689 ACCATTTGTCCAACAACATGCATATAT 60.148 33.333 0.00 0.00 37.90 0.86
35 36 7.383029 CCATTTGTCCAACAACATGCATATATC 59.617 37.037 0.00 0.00 37.90 1.63
36 37 7.401955 TTTGTCCAACAACATGCATATATCA 57.598 32.000 0.00 0.00 37.90 2.15
37 38 7.585579 TTGTCCAACAACATGCATATATCAT 57.414 32.000 0.00 0.00 32.34 2.45
38 39 7.205737 TGTCCAACAACATGCATATATCATC 57.794 36.000 0.00 0.00 0.00 2.92
39 40 6.999871 TGTCCAACAACATGCATATATCATCT 59.000 34.615 0.00 0.00 0.00 2.90
40 41 8.156165 TGTCCAACAACATGCATATATCATCTA 58.844 33.333 0.00 0.00 0.00 1.98
41 42 8.446273 GTCCAACAACATGCATATATCATCTAC 58.554 37.037 0.00 0.00 0.00 2.59
42 43 8.377799 TCCAACAACATGCATATATCATCTACT 58.622 33.333 0.00 0.00 0.00 2.57
43 44 8.448615 CCAACAACATGCATATATCATCTACTG 58.551 37.037 0.00 0.00 0.00 2.74
44 45 8.448615 CAACAACATGCATATATCATCTACTGG 58.551 37.037 0.00 0.00 0.00 4.00
45 46 7.683578 ACAACATGCATATATCATCTACTGGT 58.316 34.615 0.00 0.00 0.00 4.00
46 47 8.159447 ACAACATGCATATATCATCTACTGGTT 58.841 33.333 0.00 0.00 0.00 3.67
47 48 9.657419 CAACATGCATATATCATCTACTGGTTA 57.343 33.333 0.00 0.00 0.00 2.85
66 67 9.959721 ACTGGTTATAACAAACATCTAATCACT 57.040 29.630 17.16 0.00 0.00 3.41
71 72 9.747898 TTATAACAAACATCTAATCACTTGGGT 57.252 29.630 0.00 0.00 0.00 4.51
72 73 6.575162 AACAAACATCTAATCACTTGGGTC 57.425 37.500 0.00 0.00 0.00 4.46
73 74 5.880901 ACAAACATCTAATCACTTGGGTCT 58.119 37.500 0.00 0.00 0.00 3.85
74 75 7.016153 ACAAACATCTAATCACTTGGGTCTA 57.984 36.000 0.00 0.00 0.00 2.59
75 76 7.458397 ACAAACATCTAATCACTTGGGTCTAA 58.542 34.615 0.00 0.00 0.00 2.10
76 77 8.109634 ACAAACATCTAATCACTTGGGTCTAAT 58.890 33.333 0.00 0.00 0.00 1.73
77 78 8.400947 CAAACATCTAATCACTTGGGTCTAATG 58.599 37.037 0.00 0.00 0.00 1.90
78 79 7.200434 ACATCTAATCACTTGGGTCTAATGT 57.800 36.000 0.00 0.00 0.00 2.71
79 80 7.633789 ACATCTAATCACTTGGGTCTAATGTT 58.366 34.615 0.00 0.00 0.00 2.71
80 81 8.768397 ACATCTAATCACTTGGGTCTAATGTTA 58.232 33.333 0.00 0.00 0.00 2.41
81 82 9.784531 CATCTAATCACTTGGGTCTAATGTTAT 57.215 33.333 0.00 0.00 0.00 1.89
107 108 5.999205 AAACATTCCTCCAATAACATGCA 57.001 34.783 0.00 0.00 0.00 3.96
108 109 5.999205 AACATTCCTCCAATAACATGCAA 57.001 34.783 0.00 0.00 0.00 4.08
109 110 5.999205 ACATTCCTCCAATAACATGCAAA 57.001 34.783 0.00 0.00 0.00 3.68
110 111 5.723295 ACATTCCTCCAATAACATGCAAAC 58.277 37.500 0.00 0.00 0.00 2.93
111 112 5.245751 ACATTCCTCCAATAACATGCAAACA 59.754 36.000 0.00 0.00 0.00 2.83
112 113 5.798125 TTCCTCCAATAACATGCAAACAA 57.202 34.783 0.00 0.00 0.00 2.83
113 114 5.132897 TCCTCCAATAACATGCAAACAAC 57.867 39.130 0.00 0.00 0.00 3.32
119 120 5.233050 CCAATAACATGCAAACAACGTTTCA 59.767 36.000 0.00 0.00 30.60 2.69
136 137 6.738114 ACGTTTCAGATGTTTGTCATTCATT 58.262 32.000 0.00 0.00 36.83 2.57
189 190 2.100989 AGCTCCGACCTCGATTTAGTT 58.899 47.619 0.00 0.00 43.02 2.24
192 193 5.068636 AGCTCCGACCTCGATTTAGTTATA 58.931 41.667 0.00 0.00 43.02 0.98
197 198 7.646314 TCCGACCTCGATTTAGTTATAGAAAG 58.354 38.462 0.00 0.00 43.02 2.62
220 221 7.792374 AGTACTTATCAACATATTGTGGCAG 57.208 36.000 0.00 0.00 37.11 4.85
235 236 9.918630 ATATTGTGGCAGCAATTAATAGAAATC 57.081 29.630 16.54 0.00 39.50 2.17
236 237 6.147864 TGTGGCAGCAATTAATAGAAATCC 57.852 37.500 0.00 0.00 0.00 3.01
240 241 5.215160 GCAGCAATTAATAGAAATCCCACG 58.785 41.667 0.00 0.00 0.00 4.94
243 244 7.257722 CAGCAATTAATAGAAATCCCACGTTT 58.742 34.615 0.00 0.00 0.00 3.60
244 245 7.220683 CAGCAATTAATAGAAATCCCACGTTTG 59.779 37.037 0.00 0.00 0.00 2.93
250 251 4.286297 AGAAATCCCACGTTTGATGAGA 57.714 40.909 0.00 0.00 0.00 3.27
251 252 4.848357 AGAAATCCCACGTTTGATGAGAT 58.152 39.130 0.00 0.00 0.00 2.75
252 253 4.637534 AGAAATCCCACGTTTGATGAGATG 59.362 41.667 0.00 0.00 0.00 2.90
255 256 2.835156 TCCCACGTTTGATGAGATGGTA 59.165 45.455 0.00 0.00 0.00 3.25
259 260 3.547868 CACGTTTGATGAGATGGTAGTCG 59.452 47.826 0.00 0.00 0.00 4.18
263 264 5.448768 CGTTTGATGAGATGGTAGTCGTAGT 60.449 44.000 0.00 0.00 0.00 2.73
324 325 7.081349 TGAACTGCAGAACAAAATATTTACGG 58.919 34.615 23.35 0.00 0.00 4.02
330 331 6.399564 GCAGAACAAAATATTTACGGTTGCAC 60.400 38.462 14.06 4.55 0.00 4.57
386 387 6.183360 TGTTTATGTTATTGTGCCACTTGTGT 60.183 34.615 0.00 0.00 0.00 3.72
392 393 1.009675 GTGCCACTTGTGTTGCTCG 60.010 57.895 0.00 0.00 36.03 5.03
722 1745 2.727798 CCGAGTAATGACAAACGACGTT 59.272 45.455 7.57 7.57 0.00 3.99
877 1921 2.294979 GAACATGCAGCCAGATCATCA 58.705 47.619 0.00 0.00 0.00 3.07
905 1962 1.143481 TGGATGGATCAATGCGGATGT 59.857 47.619 0.00 0.00 0.00 3.06
989 2068 0.602638 CACAGGCAAGCGAGTGGTAA 60.603 55.000 7.38 0.00 0.00 2.85
1156 2247 4.563580 CCTTCAAAGGTGAGCTAGCTACAA 60.564 45.833 19.38 3.42 41.41 2.41
1220 2311 1.094650 ATGTGCACACTTCACACGCA 61.095 50.000 24.37 0.00 45.83 5.24
1299 2390 4.993705 AATTTTGTCAGGTCTCCAGGTA 57.006 40.909 0.00 0.00 0.00 3.08
1323 2414 1.873591 GTCAAGTGCAAGAACGTCCAT 59.126 47.619 0.00 0.00 0.00 3.41
1345 2436 0.798771 CGACTACGAGAGCAAGGCAC 60.799 60.000 0.00 0.00 42.66 5.01
1431 2522 2.029666 GTCGCACAGCTCCACAGT 59.970 61.111 0.00 0.00 0.00 3.55
2012 7442 9.928236 TGTGTATTTTGCTTTTTAAAGATTTGC 57.072 25.926 6.41 0.00 38.28 3.68
2036 7466 6.129300 GCAATTTCGGTGTGTGTTTTGTATAC 60.129 38.462 0.00 0.00 0.00 1.47
2188 7626 6.753107 TGTTATAGGCTTGCTTTTACCTTC 57.247 37.500 0.00 0.00 33.60 3.46
2278 7734 0.607217 CGGGCTCTTTACGGGGTTTT 60.607 55.000 0.00 0.00 0.00 2.43
2309 7768 0.973632 CCCAAACTAAACTTGCCCCC 59.026 55.000 0.00 0.00 0.00 5.40
2329 7788 4.179599 CCCCCTCCCCTCCCTCTC 62.180 77.778 0.00 0.00 0.00 3.20
2330 7789 3.368501 CCCCTCCCCTCCCTCTCA 61.369 72.222 0.00 0.00 0.00 3.27
2331 7790 2.731461 CCCCTCCCCTCCCTCTCAT 61.731 68.421 0.00 0.00 0.00 2.90
2332 7791 1.319799 CCCTCCCCTCCCTCTCATT 59.680 63.158 0.00 0.00 0.00 2.57
2333 7792 0.327964 CCCTCCCCTCCCTCTCATTT 60.328 60.000 0.00 0.00 0.00 2.32
2334 7793 1.601248 CCTCCCCTCCCTCTCATTTT 58.399 55.000 0.00 0.00 0.00 1.82
2335 7794 1.492599 CCTCCCCTCCCTCTCATTTTC 59.507 57.143 0.00 0.00 0.00 2.29
2336 7795 2.200081 CTCCCCTCCCTCTCATTTTCA 58.800 52.381 0.00 0.00 0.00 2.69
2337 7796 2.172293 CTCCCCTCCCTCTCATTTTCAG 59.828 54.545 0.00 0.00 0.00 3.02
2338 7797 1.213926 CCCCTCCCTCTCATTTTCAGG 59.786 57.143 0.00 0.00 0.00 3.86
2339 7798 2.200081 CCCTCCCTCTCATTTTCAGGA 58.800 52.381 0.00 0.00 0.00 3.86
2340 7799 2.578021 CCCTCCCTCTCATTTTCAGGAA 59.422 50.000 0.00 0.00 0.00 3.36
2341 7800 3.371380 CCCTCCCTCTCATTTTCAGGAAG 60.371 52.174 0.00 0.00 0.00 3.46
2342 7801 3.371380 CCTCCCTCTCATTTTCAGGAAGG 60.371 52.174 0.00 0.00 0.00 3.46
2343 7802 2.025887 TCCCTCTCATTTTCAGGAAGGC 60.026 50.000 0.00 0.00 0.00 4.35
2344 7803 2.291153 CCCTCTCATTTTCAGGAAGGCA 60.291 50.000 0.00 0.00 0.00 4.75
2345 7804 3.015327 CCTCTCATTTTCAGGAAGGCAG 58.985 50.000 0.00 0.00 0.00 4.85
2346 7805 3.015327 CTCTCATTTTCAGGAAGGCAGG 58.985 50.000 0.00 0.00 0.00 4.85
2347 7806 2.097825 CTCATTTTCAGGAAGGCAGGG 58.902 52.381 0.00 0.00 0.00 4.45
2348 7807 0.533951 CATTTTCAGGAAGGCAGGGC 59.466 55.000 0.00 0.00 0.00 5.19
2761 8365 5.537188 AGCATTGCTCGAAAAATGGTTTTA 58.463 33.333 15.13 0.00 40.58 1.52
2763 8367 5.389411 GCATTGCTCGAAAAATGGTTTTACC 60.389 40.000 17.05 0.00 37.07 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.148079 TGTTGGACAAATGGTCTGCATTA 58.852 39.130 0.00 0.00 46.16 1.90
1 2 2.964464 TGTTGGACAAATGGTCTGCATT 59.036 40.909 0.00 0.00 46.16 3.56
2 3 2.596346 TGTTGGACAAATGGTCTGCAT 58.404 42.857 0.00 0.00 46.16 3.96
3 4 2.064434 TGTTGGACAAATGGTCTGCA 57.936 45.000 0.00 0.00 46.16 4.41
4 5 2.100584 TGTTGTTGGACAAATGGTCTGC 59.899 45.455 0.00 0.00 46.16 4.26
5 6 4.300803 CATGTTGTTGGACAAATGGTCTG 58.699 43.478 0.00 0.00 46.16 3.51
6 7 3.243839 GCATGTTGTTGGACAAATGGTCT 60.244 43.478 0.00 0.00 46.16 3.85
7 8 3.059166 GCATGTTGTTGGACAAATGGTC 58.941 45.455 0.00 0.00 40.15 4.02
8 9 2.433604 TGCATGTTGTTGGACAAATGGT 59.566 40.909 0.00 0.00 40.15 3.55
9 10 3.109044 TGCATGTTGTTGGACAAATGG 57.891 42.857 0.00 2.51 40.15 3.16
10 11 7.921745 TGATATATGCATGTTGTTGGACAAATG 59.078 33.333 10.16 4.09 40.15 2.32
11 12 8.009622 TGATATATGCATGTTGTTGGACAAAT 57.990 30.769 10.16 0.00 40.15 2.32
12 13 7.401955 TGATATATGCATGTTGTTGGACAAA 57.598 32.000 10.16 0.00 40.15 2.83
13 14 7.503230 AGATGATATATGCATGTTGTTGGACAA 59.497 33.333 10.16 0.00 35.42 3.18
14 15 6.999871 AGATGATATATGCATGTTGTTGGACA 59.000 34.615 10.16 0.00 0.00 4.02
15 16 7.444629 AGATGATATATGCATGTTGTTGGAC 57.555 36.000 10.16 0.00 0.00 4.02
16 17 8.377799 AGTAGATGATATATGCATGTTGTTGGA 58.622 33.333 10.16 0.00 0.00 3.53
17 18 8.448615 CAGTAGATGATATATGCATGTTGTTGG 58.551 37.037 10.16 0.00 0.00 3.77
18 19 8.448615 CCAGTAGATGATATATGCATGTTGTTG 58.551 37.037 10.16 0.00 0.00 3.33
19 20 8.159447 ACCAGTAGATGATATATGCATGTTGTT 58.841 33.333 10.16 0.00 0.00 2.83
20 21 7.683578 ACCAGTAGATGATATATGCATGTTGT 58.316 34.615 10.16 0.00 0.00 3.32
21 22 8.557592 AACCAGTAGATGATATATGCATGTTG 57.442 34.615 10.16 0.00 0.00 3.33
40 41 9.959721 AGTGATTAGATGTTTGTTATAACCAGT 57.040 29.630 13.01 0.00 0.00 4.00
45 46 9.747898 ACCCAAGTGATTAGATGTTTGTTATAA 57.252 29.630 0.00 0.00 0.00 0.98
46 47 9.391006 GACCCAAGTGATTAGATGTTTGTTATA 57.609 33.333 0.00 0.00 0.00 0.98
47 48 8.109634 AGACCCAAGTGATTAGATGTTTGTTAT 58.890 33.333 0.00 0.00 0.00 1.89
48 49 7.458397 AGACCCAAGTGATTAGATGTTTGTTA 58.542 34.615 0.00 0.00 0.00 2.41
49 50 6.306987 AGACCCAAGTGATTAGATGTTTGTT 58.693 36.000 0.00 0.00 0.00 2.83
50 51 5.880901 AGACCCAAGTGATTAGATGTTTGT 58.119 37.500 0.00 0.00 0.00 2.83
51 52 7.921786 TTAGACCCAAGTGATTAGATGTTTG 57.078 36.000 0.00 0.00 0.00 2.93
52 53 8.109634 ACATTAGACCCAAGTGATTAGATGTTT 58.890 33.333 0.00 0.00 0.00 2.83
53 54 7.633789 ACATTAGACCCAAGTGATTAGATGTT 58.366 34.615 0.00 0.00 0.00 2.71
54 55 7.200434 ACATTAGACCCAAGTGATTAGATGT 57.800 36.000 0.00 0.00 0.00 3.06
55 56 9.784531 ATAACATTAGACCCAAGTGATTAGATG 57.215 33.333 0.00 0.00 0.00 2.90
81 82 9.194972 TGCATGTTATTGGAGGAATGTTTATTA 57.805 29.630 0.00 0.00 0.00 0.98
82 83 8.076910 TGCATGTTATTGGAGGAATGTTTATT 57.923 30.769 0.00 0.00 0.00 1.40
83 84 7.658525 TGCATGTTATTGGAGGAATGTTTAT 57.341 32.000 0.00 0.00 0.00 1.40
84 85 7.473735 TTGCATGTTATTGGAGGAATGTTTA 57.526 32.000 0.00 0.00 0.00 2.01
85 86 5.999205 TGCATGTTATTGGAGGAATGTTT 57.001 34.783 0.00 0.00 0.00 2.83
86 87 5.999205 TTGCATGTTATTGGAGGAATGTT 57.001 34.783 0.00 0.00 0.00 2.71
87 88 5.245751 TGTTTGCATGTTATTGGAGGAATGT 59.754 36.000 0.00 0.00 0.00 2.71
88 89 5.722263 TGTTTGCATGTTATTGGAGGAATG 58.278 37.500 0.00 0.00 0.00 2.67
89 90 5.999205 TGTTTGCATGTTATTGGAGGAAT 57.001 34.783 0.00 0.00 0.00 3.01
90 91 5.537188 GTTGTTTGCATGTTATTGGAGGAA 58.463 37.500 0.00 0.00 0.00 3.36
91 92 4.320861 CGTTGTTTGCATGTTATTGGAGGA 60.321 41.667 0.00 0.00 0.00 3.71
92 93 3.919804 CGTTGTTTGCATGTTATTGGAGG 59.080 43.478 0.00 0.00 0.00 4.30
93 94 4.545610 ACGTTGTTTGCATGTTATTGGAG 58.454 39.130 0.00 0.00 0.00 3.86
94 95 4.576216 ACGTTGTTTGCATGTTATTGGA 57.424 36.364 0.00 0.00 0.00 3.53
95 96 5.233050 TGAAACGTTGTTTGCATGTTATTGG 59.767 36.000 0.00 0.00 0.00 3.16
96 97 6.198029 TCTGAAACGTTGTTTGCATGTTATTG 59.802 34.615 0.00 0.00 0.00 1.90
97 98 6.269315 TCTGAAACGTTGTTTGCATGTTATT 58.731 32.000 0.00 0.00 0.00 1.40
98 99 5.826586 TCTGAAACGTTGTTTGCATGTTAT 58.173 33.333 0.00 0.00 0.00 1.89
99 100 5.236655 TCTGAAACGTTGTTTGCATGTTA 57.763 34.783 0.00 0.00 0.00 2.41
100 101 4.103365 TCTGAAACGTTGTTTGCATGTT 57.897 36.364 0.00 0.00 0.00 2.71
101 102 3.773860 TCTGAAACGTTGTTTGCATGT 57.226 38.095 0.00 0.00 0.00 3.21
102 103 4.043750 ACATCTGAAACGTTGTTTGCATG 58.956 39.130 0.00 2.80 0.00 4.06
103 104 4.305989 ACATCTGAAACGTTGTTTGCAT 57.694 36.364 0.00 0.00 0.00 3.96
104 105 3.773860 ACATCTGAAACGTTGTTTGCA 57.226 38.095 0.00 0.00 0.00 4.08
105 106 4.810125 CAAACATCTGAAACGTTGTTTGC 58.190 39.130 21.54 4.08 46.66 3.68
107 108 5.704888 TGACAAACATCTGAAACGTTGTTT 58.295 33.333 0.00 4.64 41.58 2.83
108 109 5.303747 TGACAAACATCTGAAACGTTGTT 57.696 34.783 0.00 0.00 33.93 2.83
109 110 4.955925 TGACAAACATCTGAAACGTTGT 57.044 36.364 0.00 0.00 0.00 3.32
110 111 5.970612 TGAATGACAAACATCTGAAACGTTG 59.029 36.000 0.00 0.00 38.38 4.10
111 112 6.130298 TGAATGACAAACATCTGAAACGTT 57.870 33.333 0.00 0.00 38.38 3.99
112 113 5.749596 TGAATGACAAACATCTGAAACGT 57.250 34.783 0.00 0.00 38.38 3.99
113 114 8.900511 ATAATGAATGACAAACATCTGAAACG 57.099 30.769 0.00 0.00 38.38 3.60
157 158 6.377429 TCGAGGTCGGAGCTAATATATGAATT 59.623 38.462 10.08 0.00 40.29 2.17
158 159 5.886474 TCGAGGTCGGAGCTAATATATGAAT 59.114 40.000 10.08 0.00 40.29 2.57
171 172 6.798315 TCTATAACTAAATCGAGGTCGGAG 57.202 41.667 0.00 0.00 40.29 4.63
192 193 8.893727 GCCACAATATGTTGATAAGTACTTTCT 58.106 33.333 14.49 1.49 38.71 2.52
197 198 6.038161 TGCTGCCACAATATGTTGATAAGTAC 59.962 38.462 9.40 0.00 38.71 2.73
203 204 5.347620 AATTGCTGCCACAATATGTTGAT 57.652 34.783 9.40 0.00 39.32 2.57
220 221 7.254852 TCAAACGTGGGATTTCTATTAATTGC 58.745 34.615 0.00 0.00 0.00 3.56
235 236 2.113860 ACCATCTCATCAAACGTGGG 57.886 50.000 0.00 0.00 0.00 4.61
236 237 3.861840 ACTACCATCTCATCAAACGTGG 58.138 45.455 0.00 0.00 0.00 4.94
240 241 5.744345 CACTACGACTACCATCTCATCAAAC 59.256 44.000 0.00 0.00 0.00 2.93
243 244 3.315470 GCACTACGACTACCATCTCATCA 59.685 47.826 0.00 0.00 0.00 3.07
244 245 3.315470 TGCACTACGACTACCATCTCATC 59.685 47.826 0.00 0.00 0.00 2.92
250 251 3.955650 AAGTTGCACTACGACTACCAT 57.044 42.857 0.00 0.00 42.62 3.55
251 252 3.738830 AAAGTTGCACTACGACTACCA 57.261 42.857 0.00 0.00 42.62 3.25
252 253 5.693555 ACTTTAAAGTTGCACTACGACTACC 59.306 40.000 15.22 0.00 42.62 3.18
255 256 7.775397 TTTACTTTAAAGTTGCACTACGACT 57.225 32.000 25.07 0.00 45.61 4.18
259 260 9.738832 TTCCATTTTACTTTAAAGTTGCACTAC 57.261 29.630 25.07 0.00 40.37 2.73
287 288 4.889832 CTGCAGTTCAGAAGAAAGTTGT 57.110 40.909 5.25 0.00 45.72 3.32
324 325 1.018910 ATAATAACGCCGGGTGCAAC 58.981 50.000 7.67 0.00 41.33 4.17
330 331 3.375922 ACTTTGAACATAATAACGCCGGG 59.624 43.478 2.18 0.00 0.00 5.73
344 345 8.911247 ACATAAACACTTCTCAAACTTTGAAC 57.089 30.769 5.72 0.00 39.58 3.18
362 363 6.212955 ACACAAGTGGCACAATAACATAAAC 58.787 36.000 21.41 0.00 44.16 2.01
386 387 0.960364 GGATTTGAGCACCCGAGCAA 60.960 55.000 0.00 0.00 36.85 3.91
392 393 1.840635 AGAGGTAGGATTTGAGCACCC 59.159 52.381 0.00 0.00 0.00 4.61
641 1608 1.645034 CTTCTCGTTCGTGCATGGAT 58.355 50.000 5.98 0.00 0.00 3.41
648 1615 0.040692 TCGTGTCCTTCTCGTTCGTG 60.041 55.000 0.00 0.00 35.06 4.35
820 1854 1.071605 GTGATGCCTGACAACGAGAC 58.928 55.000 0.00 0.00 0.00 3.36
877 1921 0.911769 TTGATCCATCCAGCTCGGTT 59.088 50.000 0.00 0.00 35.57 4.44
905 1962 2.416836 GGCGACGCATGGCTTATATAGA 60.417 50.000 23.09 0.00 0.00 1.98
989 2068 2.357836 CTGCCATGCCTGAACCCT 59.642 61.111 0.00 0.00 0.00 4.34
1107 2192 1.351017 TCGGCCTTCATGTTCTTCCTT 59.649 47.619 0.00 0.00 0.00 3.36
1202 2293 1.094650 ATGCGTGTGAAGTGTGCACA 61.095 50.000 17.42 17.42 43.41 4.57
1220 2311 8.819845 TGTGAGCTGATCTCCATACATTTATAT 58.180 33.333 0.00 0.00 41.18 0.86
1299 2390 0.940126 CGTTCTTGCACTTGACTGCT 59.060 50.000 0.00 0.00 38.07 4.24
1323 2414 1.506718 CTTGCTCTCGTAGTCGCCA 59.493 57.895 0.00 0.00 36.96 5.69
1560 2651 2.591753 CCGCACAGGGTCATGGAT 59.408 61.111 0.00 0.00 35.97 3.41
1761 7168 1.153706 GTGGTGTCCGTGGTATCCG 60.154 63.158 0.00 0.00 0.00 4.18
1800 7207 3.664025 TTCATCGCTGGGCAGGACG 62.664 63.158 0.00 0.00 0.00 4.79
1828 7238 1.485066 ACTCACTGACTTTGAACCCGT 59.515 47.619 0.00 0.00 0.00 5.28
2012 7442 6.085718 CGTATACAAAACACACACCGAAATTG 59.914 38.462 3.32 0.00 0.00 2.32
2036 7466 9.490663 GATTAAATTACTTGATCCACAACTTCG 57.509 33.333 0.00 0.00 34.56 3.79
2072 7509 4.467082 TGCAGTAATTCCATTGGCTCAAAT 59.533 37.500 0.00 0.00 0.00 2.32
2073 7510 3.831333 TGCAGTAATTCCATTGGCTCAAA 59.169 39.130 0.00 0.00 0.00 2.69
2074 7511 3.429492 TGCAGTAATTCCATTGGCTCAA 58.571 40.909 0.00 0.00 0.00 3.02
2278 7734 1.420430 AGTTTGGGAGAGTCCGTTGA 58.580 50.000 0.00 0.00 37.43 3.18
2312 7771 4.179599 GAGAGGGAGGGGAGGGGG 62.180 77.778 0.00 0.00 0.00 5.40
2313 7772 2.277126 AATGAGAGGGAGGGGAGGGG 62.277 65.000 0.00 0.00 0.00 4.79
2314 7773 0.327964 AAATGAGAGGGAGGGGAGGG 60.328 60.000 0.00 0.00 0.00 4.30
2315 7774 1.492599 GAAAATGAGAGGGAGGGGAGG 59.507 57.143 0.00 0.00 0.00 4.30
2316 7775 2.172293 CTGAAAATGAGAGGGAGGGGAG 59.828 54.545 0.00 0.00 0.00 4.30
2317 7776 2.200081 CTGAAAATGAGAGGGAGGGGA 58.800 52.381 0.00 0.00 0.00 4.81
2318 7777 1.213926 CCTGAAAATGAGAGGGAGGGG 59.786 57.143 0.00 0.00 0.00 4.79
2319 7778 2.200081 TCCTGAAAATGAGAGGGAGGG 58.800 52.381 0.00 0.00 0.00 4.30
2320 7779 3.371380 CCTTCCTGAAAATGAGAGGGAGG 60.371 52.174 0.00 0.00 44.78 4.30
2321 7780 3.883669 CCTTCCTGAAAATGAGAGGGAG 58.116 50.000 0.00 0.00 32.73 4.30
2322 7781 2.025887 GCCTTCCTGAAAATGAGAGGGA 60.026 50.000 0.00 0.00 0.00 4.20
2323 7782 2.291153 TGCCTTCCTGAAAATGAGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
2324 7783 3.015327 CTGCCTTCCTGAAAATGAGAGG 58.985 50.000 0.00 0.00 0.00 3.69
2325 7784 3.015327 CCTGCCTTCCTGAAAATGAGAG 58.985 50.000 0.00 0.00 0.00 3.20
2326 7785 2.291153 CCCTGCCTTCCTGAAAATGAGA 60.291 50.000 0.00 0.00 0.00 3.27
2327 7786 2.097825 CCCTGCCTTCCTGAAAATGAG 58.902 52.381 0.00 0.00 0.00 2.90
2328 7787 1.892329 GCCCTGCCTTCCTGAAAATGA 60.892 52.381 0.00 0.00 0.00 2.57
2329 7788 0.533951 GCCCTGCCTTCCTGAAAATG 59.466 55.000 0.00 0.00 0.00 2.32
2330 7789 0.615827 GGCCCTGCCTTCCTGAAAAT 60.616 55.000 0.00 0.00 46.69 1.82
2331 7790 1.228862 GGCCCTGCCTTCCTGAAAA 60.229 57.895 0.00 0.00 46.69 2.29
2332 7791 2.440599 GGCCCTGCCTTCCTGAAA 59.559 61.111 0.00 0.00 46.69 2.69
2345 7804 4.118312 TAAGGGGGAGAGGGGCCC 62.118 72.222 17.12 17.12 45.25 5.80
2698 8302 5.845103 ACGAATGTTTTACGGGGAATTTTT 58.155 33.333 0.00 0.00 0.00 1.94
2699 8303 5.456548 ACGAATGTTTTACGGGGAATTTT 57.543 34.783 0.00 0.00 0.00 1.82
2700 8304 6.572167 TTACGAATGTTTTACGGGGAATTT 57.428 33.333 0.00 0.00 0.00 1.82
2701 8305 6.404954 CCATTACGAATGTTTTACGGGGAATT 60.405 38.462 0.00 0.00 37.18 2.17
2702 8306 5.066764 CCATTACGAATGTTTTACGGGGAAT 59.933 40.000 0.00 0.00 37.18 3.01
2703 8307 4.395542 CCATTACGAATGTTTTACGGGGAA 59.604 41.667 0.00 0.00 37.18 3.97
2704 8308 3.940221 CCATTACGAATGTTTTACGGGGA 59.060 43.478 0.00 0.00 37.18 4.81
2728 8332 1.926510 CGAGCAATGCTACATCAACGA 59.073 47.619 8.12 0.00 39.88 3.85
2761 8365 2.626266 TCTCACACGACTACACAATGGT 59.374 45.455 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.