Multiple sequence alignment - TraesCS2D01G219300

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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 TraesCS2D01G219300 chr2D 100.000 2990 0 0 1 2990 185365422 185368411 0.000000e+00 5522.0
1 TraesCS2D01G219300 chr2D 99.078 434 4 0 2557 2990 440767076 440767509 0.000000e+00 780.0
2 TraesCS2D01G219300 chr2D 87.912 273 19 7 167 437 185369274 185369014 2.890000e-80 309.0
3 TraesCS2D01G219300 chr2D 90.909 99 6 1 2237 2332 185365945 185365847 2.420000e-26 130.0
4 TraesCS2D01G219300 chr5D 93.906 2248 101 9 109 2329 42725113 42727351 0.000000e+00 3360.0
5 TraesCS2D01G219300 chr5D 93.949 2132 79 15 230 2333 249911940 249914049 0.000000e+00 3177.0
6 TraesCS2D01G219300 chr5D 90.345 435 32 7 109 534 249914367 249913934 2.010000e-156 562.0
7 TraesCS2D01G219300 chr5D 86.866 434 30 9 109 534 42727654 42727240 7.550000e-126 460.0
8 TraesCS2D01G219300 chr5D 97.235 217 5 1 2329 2545 3524120 3523905 1.690000e-97 366.0
9 TraesCS2D01G219300 chr5D 94.372 231 12 1 2315 2545 525305650 525305421 1.320000e-93 353.0
10 TraesCS2D01G219300 chr5D 93.548 186 11 1 109 293 435613595 435613410 2.940000e-70 276.0
11 TraesCS2D01G219300 chr2A 92.311 2250 108 23 108 2329 768058554 768060766 0.000000e+00 3136.0
12 TraesCS2D01G219300 chr2A 98.013 453 9 0 2538 2990 584510794 584511246 0.000000e+00 787.0
13 TraesCS2D01G219300 chr2A 89.631 434 36 4 109 534 768061087 768060655 7.290000e-151 544.0
14 TraesCS2D01G219300 chr2A 93.989 183 11 0 111 293 277334619 277334437 8.160000e-71 278.0
15 TraesCS2D01G219300 chr2A 96.629 89 3 0 1 89 93898206 93898118 6.680000e-32 148.0
16 TraesCS2D01G219300 chr1D 93.489 1889 88 12 374 2234 375990046 375991927 0.000000e+00 2774.0
17 TraesCS2D01G219300 chr1D 90.741 54 5 0 294 347 375992520 375992467 4.130000e-09 73.1
18 TraesCS2D01G219300 chr1A 91.711 1894 106 22 374 2229 474791960 474793840 0.000000e+00 2580.0
19 TraesCS2D01G219300 chr1A 93.301 1657 81 9 108 1745 59211956 59210311 0.000000e+00 2418.0
20 TraesCS2D01G219300 chr1A 93.976 83 5 0 294 376 474794395 474794313 3.130000e-25 126.0
21 TraesCS2D01G219300 chr1A 91.781 73 6 0 2257 2329 474792087 474792015 5.270000e-18 102.0
22 TraesCS2D01G219300 chr1B 91.200 1909 99 21 374 2234 502218345 502220232 0.000000e+00 2531.0
23 TraesCS2D01G219300 chr1B 91.781 73 6 0 2257 2329 502218472 502218400 5.270000e-18 102.0
24 TraesCS2D01G219300 chr3D 98.341 663 9 1 2330 2990 241044856 241044194 0.000000e+00 1162.0
25 TraesCS2D01G219300 chr3D 91.991 437 33 2 2554 2989 456355645 456355210 1.970000e-171 612.0
26 TraesCS2D01G219300 chr3D 74.586 1027 205 37 989 1990 473483324 473484319 1.670000e-107 399.0
27 TraesCS2D01G219300 chr3D 98.611 216 3 0 2330 2545 241043582 241043797 1.680000e-102 383.0
28 TraesCS2D01G219300 chr3D 97.235 217 6 0 2329 2545 231894166 231894382 4.710000e-98 368.0
29 TraesCS2D01G219300 chr3D 75.748 635 103 26 388 986 473482667 473483286 3.800000e-69 272.0
30 TraesCS2D01G219300 chr6D 97.583 662 16 0 2329 2990 100570626 100569965 0.000000e+00 1134.0
31 TraesCS2D01G219300 chr6D 97.866 656 14 0 2335 2990 216836284 216836939 0.000000e+00 1134.0
32 TraesCS2D01G219300 chr6D 90.654 428 39 1 2563 2989 67037389 67036962 4.330000e-158 568.0
33 TraesCS2D01G219300 chr6D 98.165 218 3 1 2329 2545 216837553 216837336 2.180000e-101 379.0
34 TraesCS2D01G219300 chr7D 98.157 434 7 1 2330 2762 255421993 255422426 0.000000e+00 756.0
35 TraesCS2D01G219300 chr7D 89.703 437 44 1 2554 2989 425950188 425950624 9.360000e-155 556.0
36 TraesCS2D01G219300 chr7D 93.048 187 11 2 109 293 207790331 207790145 3.800000e-69 272.0
37 TraesCS2D01G219300 chr2B 95.730 445 19 0 2546 2990 518739788 518740232 0.000000e+00 717.0
38 TraesCS2D01G219300 chr3B 73.662 1682 308 75 397 1990 629194794 629193160 7.340000e-146 527.0
39 TraesCS2D01G219300 chr3A 74.018 1528 276 65 388 1840 615938966 615940447 7.390000e-141 510.0
40 TraesCS2D01G219300 chr7B 93.478 184 11 1 108 290 88338323 88338506 3.800000e-69 272.0


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 TraesCS2D01G219300 chr2D 185365422 185368411 2989 False 5522.0 5522 100.0000 1 2990 1 chr2D.!!$F1 2989
1 TraesCS2D01G219300 chr2D 185365847 185369274 3427 True 219.5 309 89.4105 167 2332 2 chr2D.!!$R1 2165
2 TraesCS2D01G219300 chr5D 42725113 42727351 2238 False 3360.0 3360 93.9060 109 2329 1 chr5D.!!$F1 2220
3 TraesCS2D01G219300 chr5D 249911940 249914049 2109 False 3177.0 3177 93.9490 230 2333 1 chr5D.!!$F2 2103
4 TraesCS2D01G219300 chr2A 768058554 768060766 2212 False 3136.0 3136 92.3110 108 2329 1 chr2A.!!$F2 2221
5 TraesCS2D01G219300 chr1D 375990046 375991927 1881 False 2774.0 2774 93.4890 374 2234 1 chr1D.!!$F1 1860
6 TraesCS2D01G219300 chr1A 474791960 474793840 1880 False 2580.0 2580 91.7110 374 2229 1 chr1A.!!$F1 1855
7 TraesCS2D01G219300 chr1A 59210311 59211956 1645 True 2418.0 2418 93.3010 108 1745 1 chr1A.!!$R1 1637
8 TraesCS2D01G219300 chr1B 502218345 502220232 1887 False 2531.0 2531 91.2000 374 2234 1 chr1B.!!$F1 1860
9 TraesCS2D01G219300 chr3D 241044194 241044856 662 True 1162.0 1162 98.3410 2330 2990 1 chr3D.!!$R1 660
10 TraesCS2D01G219300 chr3D 473482667 473484319 1652 False 335.5 399 75.1670 388 1990 2 chr3D.!!$F3 1602
11 TraesCS2D01G219300 chr6D 100569965 100570626 661 True 1134.0 1134 97.5830 2329 2990 1 chr6D.!!$R2 661
12 TraesCS2D01G219300 chr6D 216836284 216836939 655 False 1134.0 1134 97.8660 2335 2990 1 chr6D.!!$F1 655
13 TraesCS2D01G219300 chr3B 629193160 629194794 1634 True 527.0 527 73.6620 397 1990 1 chr3B.!!$R1 1593
14 TraesCS2D01G219300 chr3A 615938966 615940447 1481 False 510.0 510 74.0180 388 1840 1 chr3A.!!$F1 1452

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
58 59 0.510359 GATGCAGCGGAATCGATCAC 59.490 55.0 0.00 0.0 39.00 3.06 F
273 277 0.826256 AGAAACCCCCTGCCGTTTTC 60.826 55.0 0.00 0.0 32.46 2.29 F
1342 3396 0.400213 AAGGTCATTCGAAGTGCCCA 59.600 50.0 3.35 0.0 0.00 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1329 3383 0.178975 TTGGGTTGGGCACTTCGAAT 60.179 50.000 0.0 0.0 0.00 3.34 R
1788 3872 1.367471 CACGCACTGGTCTTCCTGA 59.633 57.895 0.0 0.0 36.65 3.86 R
2234 4523 1.378762 CCCACCGAATTCCACCAGT 59.621 57.895 0.0 0.0 0.00 4.00 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
24 25 4.950479 GCCACTAGCTGCACATCT 57.050 55.556 1.02 0.00 38.99 2.90
25 26 3.165606 GCCACTAGCTGCACATCTT 57.834 52.632 1.02 0.00 38.99 2.40
26 27 1.457346 GCCACTAGCTGCACATCTTT 58.543 50.000 1.02 0.00 38.99 2.52
27 28 1.815003 GCCACTAGCTGCACATCTTTT 59.185 47.619 1.02 0.00 38.99 2.27
28 29 2.229784 GCCACTAGCTGCACATCTTTTT 59.770 45.455 1.02 0.00 38.99 1.94
29 30 3.440173 GCCACTAGCTGCACATCTTTTTA 59.560 43.478 1.02 0.00 38.99 1.52
30 31 4.082787 GCCACTAGCTGCACATCTTTTTAA 60.083 41.667 1.02 0.00 38.99 1.52
31 32 5.564651 GCCACTAGCTGCACATCTTTTTAAA 60.565 40.000 1.02 0.00 38.99 1.52
32 33 6.624423 CCACTAGCTGCACATCTTTTTAAAT 58.376 36.000 1.02 0.00 0.00 1.40
33 34 6.749118 CCACTAGCTGCACATCTTTTTAAATC 59.251 38.462 1.02 0.00 0.00 2.17
34 35 6.749118 CACTAGCTGCACATCTTTTTAAATCC 59.251 38.462 1.02 0.00 0.00 3.01
35 36 5.726980 AGCTGCACATCTTTTTAAATCCA 57.273 34.783 1.02 0.00 0.00 3.41
36 37 5.473039 AGCTGCACATCTTTTTAAATCCAC 58.527 37.500 1.02 0.00 0.00 4.02
37 38 5.244626 AGCTGCACATCTTTTTAAATCCACT 59.755 36.000 1.02 0.00 0.00 4.00
38 39 5.574443 GCTGCACATCTTTTTAAATCCACTC 59.426 40.000 0.00 0.00 0.00 3.51
39 40 5.698832 TGCACATCTTTTTAAATCCACTCG 58.301 37.500 0.00 0.00 0.00 4.18
40 41 5.471797 TGCACATCTTTTTAAATCCACTCGA 59.528 36.000 0.00 0.00 0.00 4.04
41 42 6.150976 TGCACATCTTTTTAAATCCACTCGAT 59.849 34.615 0.00 0.00 0.00 3.59
42 43 6.470235 GCACATCTTTTTAAATCCACTCGATG 59.530 38.462 0.00 0.00 33.78 3.84
43 44 6.470235 CACATCTTTTTAAATCCACTCGATGC 59.530 38.462 0.00 0.00 31.47 3.91
44 45 6.150976 ACATCTTTTTAAATCCACTCGATGCA 59.849 34.615 0.00 0.00 31.47 3.96
45 46 6.182039 TCTTTTTAAATCCACTCGATGCAG 57.818 37.500 0.00 0.00 0.00 4.41
46 47 4.355543 TTTTAAATCCACTCGATGCAGC 57.644 40.909 0.00 0.00 0.00 5.25
47 48 1.570813 TAAATCCACTCGATGCAGCG 58.429 50.000 20.14 20.14 0.00 5.18
48 49 1.091771 AAATCCACTCGATGCAGCGG 61.092 55.000 25.69 17.28 0.00 5.52
49 50 1.960040 AATCCACTCGATGCAGCGGA 61.960 55.000 25.69 14.07 0.00 5.54
50 51 1.960040 ATCCACTCGATGCAGCGGAA 61.960 55.000 25.69 4.84 0.00 4.30
51 52 1.522355 CCACTCGATGCAGCGGAAT 60.522 57.895 25.69 7.34 0.00 3.01
52 53 1.493950 CCACTCGATGCAGCGGAATC 61.494 60.000 25.69 0.00 0.00 2.52
57 58 2.904664 GATGCAGCGGAATCGATCA 58.095 52.632 0.00 0.00 39.00 2.92
58 59 0.510359 GATGCAGCGGAATCGATCAC 59.490 55.000 0.00 0.00 39.00 3.06
59 60 1.217585 ATGCAGCGGAATCGATCACG 61.218 55.000 14.97 14.97 39.00 4.35
72 73 4.921470 TCGATCACGACAAAATTTCTCC 57.079 40.909 0.00 0.00 43.81 3.71
73 74 4.566004 TCGATCACGACAAAATTTCTCCT 58.434 39.130 0.00 0.00 43.81 3.69
74 75 4.625742 TCGATCACGACAAAATTTCTCCTC 59.374 41.667 0.00 0.00 43.81 3.71
75 76 4.627467 CGATCACGACAAAATTTCTCCTCT 59.373 41.667 0.00 0.00 42.66 3.69
76 77 5.220303 CGATCACGACAAAATTTCTCCTCTC 60.220 44.000 0.00 0.00 42.66 3.20
77 78 4.956085 TCACGACAAAATTTCTCCTCTCA 58.044 39.130 0.00 0.00 0.00 3.27
78 79 5.551233 TCACGACAAAATTTCTCCTCTCAT 58.449 37.500 0.00 0.00 0.00 2.90
79 80 6.697395 TCACGACAAAATTTCTCCTCTCATA 58.303 36.000 0.00 0.00 0.00 2.15
80 81 7.331026 TCACGACAAAATTTCTCCTCTCATAT 58.669 34.615 0.00 0.00 0.00 1.78
81 82 7.824289 TCACGACAAAATTTCTCCTCTCATATT 59.176 33.333 0.00 0.00 0.00 1.28
82 83 8.454106 CACGACAAAATTTCTCCTCTCATATTT 58.546 33.333 0.00 0.00 0.00 1.40
83 84 9.014297 ACGACAAAATTTCTCCTCTCATATTTT 57.986 29.630 0.00 0.00 0.00 1.82
84 85 9.846248 CGACAAAATTTCTCCTCTCATATTTTT 57.154 29.630 0.00 0.00 0.00 1.94
104 105 8.602472 ATTTTTAAATGAGGTAATAGCACCCA 57.398 30.769 0.00 0.00 39.62 4.51
105 106 7.639113 TTTTAAATGAGGTAATAGCACCCAG 57.361 36.000 0.00 0.00 39.62 4.45
106 107 3.864789 AATGAGGTAATAGCACCCAGG 57.135 47.619 0.00 0.00 39.62 4.45
135 136 9.383519 GAATGTGATGATTCAGTCCTAAACTTA 57.616 33.333 0.00 0.00 35.45 2.24
239 240 4.394712 GTGGCTGGACCGGTCAGG 62.395 72.222 34.40 25.42 43.94 3.86
272 276 1.112916 CAGAAACCCCCTGCCGTTTT 61.113 55.000 0.00 0.00 32.46 2.43
273 277 0.826256 AGAAACCCCCTGCCGTTTTC 60.826 55.000 0.00 0.00 32.46 2.29
290 294 4.612943 GTTTTCTTTAATCAACCCGCACA 58.387 39.130 0.00 0.00 0.00 4.57
337 341 4.764336 CACGAACGGCGGCTCGTA 62.764 66.667 29.75 0.00 46.04 3.43
524 1821 1.075836 CCCCACCGAATTCCACCAA 59.924 57.895 0.00 0.00 0.00 3.67
843 2848 1.608717 GCTCAAGAAGGAGGAGGCGA 61.609 60.000 0.00 0.00 35.41 5.54
961 2979 2.701780 GCTCGGAGTTCGCCAGAGA 61.702 63.158 6.90 0.00 39.05 3.10
1098 3152 4.052518 ATTGGCCTTGGCCGAGCT 62.053 61.111 23.40 7.41 0.00 4.09
1329 3383 1.367471 CTCCGTGCTGACAAGGTCA 59.633 57.895 0.00 0.00 44.88 4.02
1342 3396 0.400213 AAGGTCATTCGAAGTGCCCA 59.600 50.000 3.35 0.00 0.00 5.36
1364 3418 3.907130 AAAGCCAGCCCCTGCAGT 61.907 61.111 13.81 0.00 41.13 4.40
1683 3755 1.215382 CAACGTCGGGATGCAGAGA 59.785 57.895 0.00 0.00 0.00 3.10
1700 3772 1.007502 GATGCAACAGCAACGCCAA 60.008 52.632 0.00 0.00 42.37 4.52
2055 4207 2.421775 TCGAGTTGTTTCTTTGCAGCAA 59.578 40.909 2.83 2.83 0.00 3.91
2066 4218 3.499537 TCTTTGCAGCAACAGTAGTGATG 59.500 43.478 7.54 3.78 0.00 3.07
2102 4260 8.568617 AGTATGATTAAGGTCTGATTAAGGGT 57.431 34.615 0.00 0.00 0.00 4.34
2234 4523 1.664016 GCTTCTGTTCGTCGTCGGTAA 60.664 52.381 1.55 0.00 37.69 2.85
2352 4650 5.648092 GGAGTAAATTGCACAGAAGTACCAT 59.352 40.000 0.00 0.00 0.00 3.55
2448 4746 6.703165 AGACGTTACAAAAAGGTCTAAATCGT 59.297 34.615 10.43 0.00 41.76 3.73
2478 4776 4.202020 ACGCGTATTGACAGTGTATCTGAT 60.202 41.667 11.67 0.00 46.27 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.457346 AAAGATGTGCAGCTAGTGGC 58.543 50.000 0.00 0.00 42.19 5.01
8 9 5.627499 TTAAAAAGATGTGCAGCTAGTGG 57.373 39.130 0.00 0.00 0.00 4.00
9 10 6.749118 GGATTTAAAAAGATGTGCAGCTAGTG 59.251 38.462 0.00 0.00 0.00 2.74
10 11 6.434028 TGGATTTAAAAAGATGTGCAGCTAGT 59.566 34.615 0.00 0.00 0.00 2.57
11 12 6.749118 GTGGATTTAAAAAGATGTGCAGCTAG 59.251 38.462 0.00 0.00 0.00 3.42
12 13 6.434028 AGTGGATTTAAAAAGATGTGCAGCTA 59.566 34.615 0.00 0.00 0.00 3.32
13 14 5.244626 AGTGGATTTAAAAAGATGTGCAGCT 59.755 36.000 0.00 0.00 0.00 4.24
14 15 5.473039 AGTGGATTTAAAAAGATGTGCAGC 58.527 37.500 0.00 0.00 0.00 5.25
15 16 5.796935 CGAGTGGATTTAAAAAGATGTGCAG 59.203 40.000 0.00 0.00 0.00 4.41
16 17 5.471797 TCGAGTGGATTTAAAAAGATGTGCA 59.528 36.000 0.00 0.00 0.00 4.57
17 18 5.938322 TCGAGTGGATTTAAAAAGATGTGC 58.062 37.500 0.00 0.00 0.00 4.57
18 19 6.470235 GCATCGAGTGGATTTAAAAAGATGTG 59.530 38.462 0.00 0.00 36.36 3.21
19 20 6.150976 TGCATCGAGTGGATTTAAAAAGATGT 59.849 34.615 0.00 0.00 36.36 3.06
20 21 6.554419 TGCATCGAGTGGATTTAAAAAGATG 58.446 36.000 0.00 2.14 36.86 2.90
21 22 6.678900 GCTGCATCGAGTGGATTTAAAAAGAT 60.679 38.462 0.00 0.00 31.28 2.40
22 23 5.391950 GCTGCATCGAGTGGATTTAAAAAGA 60.392 40.000 0.00 0.00 31.28 2.52
23 24 4.795278 GCTGCATCGAGTGGATTTAAAAAG 59.205 41.667 0.00 0.00 31.28 2.27
24 25 4.671508 CGCTGCATCGAGTGGATTTAAAAA 60.672 41.667 3.33 0.00 31.28 1.94
25 26 3.181511 CGCTGCATCGAGTGGATTTAAAA 60.182 43.478 3.33 0.00 31.28 1.52
26 27 2.351418 CGCTGCATCGAGTGGATTTAAA 59.649 45.455 3.33 0.00 31.28 1.52
27 28 1.933181 CGCTGCATCGAGTGGATTTAA 59.067 47.619 3.33 0.00 31.28 1.52
28 29 1.570813 CGCTGCATCGAGTGGATTTA 58.429 50.000 3.33 0.00 31.28 1.40
29 30 1.091771 CCGCTGCATCGAGTGGATTT 61.092 55.000 12.26 0.00 45.19 2.17
30 31 1.522355 CCGCTGCATCGAGTGGATT 60.522 57.895 12.26 0.00 45.19 3.01
31 32 2.107750 CCGCTGCATCGAGTGGAT 59.892 61.111 12.26 0.00 45.19 3.41
33 34 1.493950 GATTCCGCTGCATCGAGTGG 61.494 60.000 12.26 4.05 43.93 4.00
34 35 1.815212 CGATTCCGCTGCATCGAGTG 61.815 60.000 12.26 0.00 44.18 3.51
35 36 1.589993 CGATTCCGCTGCATCGAGT 60.590 57.895 12.26 0.00 44.18 4.18
36 37 1.299392 TCGATTCCGCTGCATCGAG 60.299 57.895 16.47 1.75 44.87 4.04
37 38 2.804856 TCGATTCCGCTGCATCGA 59.195 55.556 16.47 16.47 46.95 3.59
38 39 0.940991 TGATCGATTCCGCTGCATCG 60.941 55.000 12.89 12.89 43.05 3.84
39 40 0.510359 GTGATCGATTCCGCTGCATC 59.490 55.000 0.00 0.00 35.37 3.91
40 41 1.217585 CGTGATCGATTCCGCTGCAT 61.218 55.000 0.00 0.00 39.71 3.96
41 42 1.878069 CGTGATCGATTCCGCTGCA 60.878 57.895 0.00 0.00 39.71 4.41
42 43 1.588932 TCGTGATCGATTCCGCTGC 60.589 57.895 0.00 0.00 41.35 5.25
43 44 4.709982 TCGTGATCGATTCCGCTG 57.290 55.556 0.00 0.00 41.35 5.18
51 52 4.566004 AGGAGAAATTTTGTCGTGATCGA 58.434 39.130 1.21 0.00 44.12 3.59
52 53 4.627467 AGAGGAGAAATTTTGTCGTGATCG 59.373 41.667 6.26 0.00 38.55 3.69
53 54 5.639506 TGAGAGGAGAAATTTTGTCGTGATC 59.360 40.000 6.26 5.45 0.00 2.92
54 55 5.551233 TGAGAGGAGAAATTTTGTCGTGAT 58.449 37.500 6.26 0.00 0.00 3.06
55 56 4.956085 TGAGAGGAGAAATTTTGTCGTGA 58.044 39.130 6.26 0.00 0.00 4.35
56 57 5.869753 ATGAGAGGAGAAATTTTGTCGTG 57.130 39.130 6.26 0.00 0.00 4.35
57 58 8.567285 AAATATGAGAGGAGAAATTTTGTCGT 57.433 30.769 1.59 1.59 0.00 4.34
58 59 9.846248 AAAAATATGAGAGGAGAAATTTTGTCG 57.154 29.630 0.00 0.00 29.60 4.35
78 79 9.702253 TGGGTGCTATTACCTCATTTAAAAATA 57.298 29.630 0.00 0.00 40.66 1.40
79 80 8.602472 TGGGTGCTATTACCTCATTTAAAAAT 57.398 30.769 0.00 0.00 40.66 1.82
80 81 7.123547 CCTGGGTGCTATTACCTCATTTAAAAA 59.876 37.037 0.00 0.00 40.66 1.94
81 82 6.605594 CCTGGGTGCTATTACCTCATTTAAAA 59.394 38.462 0.00 0.00 40.66 1.52
82 83 6.126409 CCTGGGTGCTATTACCTCATTTAAA 58.874 40.000 0.00 0.00 40.66 1.52
83 84 5.192923 ACCTGGGTGCTATTACCTCATTTAA 59.807 40.000 0.00 0.00 40.66 1.52
84 85 4.724798 ACCTGGGTGCTATTACCTCATTTA 59.275 41.667 0.00 0.00 40.66 1.40
85 86 3.527665 ACCTGGGTGCTATTACCTCATTT 59.472 43.478 0.00 0.00 40.66 2.32
86 87 3.123273 ACCTGGGTGCTATTACCTCATT 58.877 45.455 0.00 0.00 40.66 2.57
87 88 2.776665 ACCTGGGTGCTATTACCTCAT 58.223 47.619 0.00 0.00 40.66 2.90
88 89 2.263895 ACCTGGGTGCTATTACCTCA 57.736 50.000 0.00 0.00 40.66 3.86
89 90 3.573695 TCTACCTGGGTGCTATTACCTC 58.426 50.000 2.07 0.00 40.66 3.85
90 91 3.700863 TCTACCTGGGTGCTATTACCT 57.299 47.619 2.07 0.00 40.66 3.08
91 92 4.102681 ACATTCTACCTGGGTGCTATTACC 59.897 45.833 2.07 0.00 40.10 2.85
92 93 5.057149 CACATTCTACCTGGGTGCTATTAC 58.943 45.833 2.07 0.00 0.00 1.89
93 94 4.966168 TCACATTCTACCTGGGTGCTATTA 59.034 41.667 2.07 0.00 0.00 0.98
94 95 3.780294 TCACATTCTACCTGGGTGCTATT 59.220 43.478 2.07 0.00 0.00 1.73
95 96 3.384168 TCACATTCTACCTGGGTGCTAT 58.616 45.455 2.07 0.00 0.00 2.97
96 97 2.827755 TCACATTCTACCTGGGTGCTA 58.172 47.619 2.07 0.00 0.00 3.49
97 98 1.656587 TCACATTCTACCTGGGTGCT 58.343 50.000 2.07 0.00 0.00 4.40
98 99 2.092968 TCATCACATTCTACCTGGGTGC 60.093 50.000 2.07 0.00 0.00 5.01
99 100 3.912496 TCATCACATTCTACCTGGGTG 57.088 47.619 2.07 0.00 0.00 4.61
100 101 4.474651 TGAATCATCACATTCTACCTGGGT 59.525 41.667 0.00 0.00 34.35 4.51
101 102 5.039920 TGAATCATCACATTCTACCTGGG 57.960 43.478 0.00 0.00 34.35 4.45
102 103 5.678583 ACTGAATCATCACATTCTACCTGG 58.321 41.667 0.00 0.00 34.35 4.45
103 104 5.757320 GGACTGAATCATCACATTCTACCTG 59.243 44.000 0.00 0.00 34.35 4.00
104 105 5.664908 AGGACTGAATCATCACATTCTACCT 59.335 40.000 0.00 0.00 34.35 3.08
105 106 5.923204 AGGACTGAATCATCACATTCTACC 58.077 41.667 0.00 0.00 34.35 3.18
106 107 8.821894 GTTTAGGACTGAATCATCACATTCTAC 58.178 37.037 0.00 0.00 34.35 2.59
135 136 5.506708 GGGTATGGTGGAGTCAAGTTTTAT 58.493 41.667 0.00 0.00 0.00 1.40
148 149 0.251564 TGCAAGTTGGGGTATGGTGG 60.252 55.000 4.75 0.00 0.00 4.61
185 186 1.211457 GAGCTGTGATTGGTCTGGGAT 59.789 52.381 0.00 0.00 0.00 3.85
272 276 2.811431 CTGTGTGCGGGTTGATTAAAGA 59.189 45.455 0.00 0.00 0.00 2.52
273 277 2.668279 GCTGTGTGCGGGTTGATTAAAG 60.668 50.000 0.00 0.00 0.00 1.85
290 294 2.280592 GGTTGGTTCGGACGCTGT 60.281 61.111 0.00 0.00 0.00 4.40
413 417 0.907230 GGTGGAAGAGCTCCCAGAGT 60.907 60.000 10.93 0.00 44.69 3.24
421 425 1.228894 TCGTCCTGGTGGAAGAGCT 60.229 57.895 0.00 0.00 43.98 4.09
1098 3152 3.680786 CGTGACAGTGGCGGAGGA 61.681 66.667 0.00 0.00 0.00 3.71
1329 3383 0.178975 TTGGGTTGGGCACTTCGAAT 60.179 50.000 0.00 0.00 0.00 3.34
1342 3396 3.521452 AGGGGCTGGCTTTGGGTT 61.521 61.111 0.00 0.00 0.00 4.11
1364 3418 2.755064 CATTGGTGATGGCGGCCA 60.755 61.111 26.11 26.11 38.19 5.36
1788 3872 1.367471 CACGCACTGGTCTTCCTGA 59.633 57.895 0.00 0.00 36.65 3.86
1957 4071 3.257561 CATGCTCCTCGCGAACGG 61.258 66.667 11.33 9.48 43.27 4.44
2055 4207 5.952947 ACTACTAAGCCTTCATCACTACTGT 59.047 40.000 0.00 0.00 0.00 3.55
2066 4218 8.862085 AGACCTTAATCATACTACTAAGCCTTC 58.138 37.037 0.00 0.00 0.00 3.46
2234 4523 1.378762 CCCACCGAATTCCACCAGT 59.621 57.895 0.00 0.00 0.00 4.00
2316 4614 1.946984 TTTACTCCCACCAGGACGAT 58.053 50.000 0.00 0.00 40.93 3.73
2352 4650 2.109774 CTGCTTCCAATGCCCCAATTA 58.890 47.619 0.00 0.00 0.00 1.40
2448 4746 5.162794 ACACTGTCAATACGCGTTTATACA 58.837 37.500 20.78 16.25 0.00 2.29
2746 5046 4.373116 GCGACTCCTGCGGGTTCA 62.373 66.667 12.43 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.