Multiple sequence alignment - TraesCS5D01G198200

Loading Multiple Alignment...

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 TraesCS5D01G198200 chr5D 100.000 5820 0 0 1 5820 301118148 301112329 0.000000e+00 10748
1 TraesCS5D01G198200 chr5D 86.239 436 35 9 2154 2570 461346114 461345685 3.200000e-122 449
2 TraesCS5D01G198200 chr5D 94.248 226 12 1 969 1194 461346915 461346691 1.550000e-90 344
3 TraesCS5D01G198200 chr5D 89.744 234 15 6 1250 1483 461346620 461346396 2.050000e-74 291
4 TraesCS5D01G198200 chr5D 87.500 232 20 6 1252 1483 461345656 461345434 5.790000e-65 259
5 TraesCS5D01G198200 chr5D 87.336 229 16 2 1532 1748 461345414 461345187 3.480000e-62 250
6 TraesCS5D01G198200 chr5D 85.652 230 20 2 1532 1748 461346376 461346147 4.540000e-56 230
7 TraesCS5D01G198200 chr5D 86.301 146 4 5 722 851 301124411 301124556 1.690000e-30 145
8 TraesCS5D01G198200 chr5D 96.667 60 2 0 665 724 301123807 301123866 3.710000e-17 100
9 TraesCS5D01G198200 chr5A 92.345 3122 138 26 852 3918 398285372 398282297 0.000000e+00 4348
10 TraesCS5D01G198200 chr5A 92.838 1480 70 18 4356 5820 398281515 398280057 0.000000e+00 2113
11 TraesCS5D01G198200 chr5A 92.449 437 25 7 3902 4332 398282285 398281851 8.290000e-173 617
12 TraesCS5D01G198200 chr5A 86.338 527 35 13 972 1483 220913182 220912678 1.850000e-149 540
13 TraesCS5D01G198200 chr5A 86.871 457 36 9 2133 2570 220912437 220911986 1.880000e-134 490
14 TraesCS5D01G198200 chr5A 85.532 235 19 4 1527 1748 220912666 220912434 1.260000e-56 231
15 TraesCS5D01G198200 chr5B 94.805 2618 116 12 1730 4332 344315017 344312405 0.000000e+00 4063
16 TraesCS5D01G198200 chr5B 92.247 1019 52 17 4354 5362 344311326 344310325 0.000000e+00 1419
17 TraesCS5D01G198200 chr5B 92.626 895 31 11 852 1721 344317767 344316883 0.000000e+00 1254
18 TraesCS5D01G198200 chr5B 95.270 444 10 5 5388 5820 344310339 344309896 0.000000e+00 693
19 TraesCS5D01G198200 chr5B 86.842 228 13 6 646 856 137118696 137118469 7.540000e-59 239
20 TraesCS5D01G198200 chr5B 78.333 360 44 21 516 851 408954599 408954948 9.890000e-48 202
21 TraesCS5D01G198200 chr6A 90.939 905 43 13 1 867 595566035 595565132 0.000000e+00 1181
22 TraesCS5D01G198200 chr6A 88.288 222 10 5 646 851 595574755 595574976 9.680000e-63 252
23 TraesCS5D01G198200 chr7B 93.817 744 24 9 138 863 75271 74532 0.000000e+00 1099
24 TraesCS5D01G198200 chr7B 98.592 142 1 1 1 142 83929 83789 3.480000e-62 250
25 TraesCS5D01G198200 chr7B 87.783 221 11 3 657 862 110175 110394 1.620000e-60 244
26 TraesCS5D01G198200 chr7B 98.387 62 1 0 790 851 710691635 710691574 6.170000e-20 110
27 TraesCS5D01G198200 chr4B 89.181 684 40 14 202 851 540466559 540467242 0.000000e+00 822
28 TraesCS5D01G198200 chr4B 96.104 154 5 1 65 218 540466361 540466513 3.480000e-62 250
29 TraesCS5D01G198200 chr3A 89.515 515 33 9 969 1483 737829596 737830089 2.960000e-177 632
30 TraesCS5D01G198200 chr3A 89.147 516 34 10 969 1483 737838254 737838748 1.780000e-174 623
31 TraesCS5D01G198200 chr3A 89.147 516 34 10 969 1483 737855092 737855586 1.780000e-174 623
32 TraesCS5D01G198200 chr3A 87.004 454 35 9 2133 2567 737830333 737830781 1.880000e-134 490
33 TraesCS5D01G198200 chr3A 87.004 454 35 9 2133 2567 737838991 737839439 1.880000e-134 490
34 TraesCS5D01G198200 chr3A 86.784 454 36 9 2133 2567 737855829 737856277 8.770000e-133 484
35 TraesCS5D01G198200 chr3A 94.810 289 7 5 1 287 734269452 734269170 1.490000e-120 444
36 TraesCS5D01G198200 chr3A 84.127 252 22 6 1514 1748 737830085 737830335 1.630000e-55 228
37 TraesCS5D01G198200 chr3A 83.730 252 23 6 1514 1748 737838744 737838994 7.590000e-54 222
38 TraesCS5D01G198200 chr3A 83.730 252 23 6 1514 1748 737855582 737855832 7.590000e-54 222
39 TraesCS5D01G198200 chr3B 92.027 439 33 2 2130 2567 582286415 582286852 2.980000e-172 616
40 TraesCS5D01G198200 chr3B 87.451 255 14 7 1514 1750 582286171 582286425 1.600000e-70 278
41 TraesCS5D01G198200 chr3B 75.200 500 67 27 396 860 16624021 16623544 3.580000e-42 183
42 TraesCS5D01G198200 chr3B 79.821 223 20 13 644 851 156826332 156826544 7.860000e-29 139
43 TraesCS5D01G198200 chr3B 78.205 234 24 15 644 861 133429801 133429579 2.200000e-24 124
44 TraesCS5D01G198200 chr3B 77.966 177 30 7 313 485 156824603 156824432 1.030000e-17 102
45 TraesCS5D01G198200 chr3D 89.316 468 29 8 969 1436 141475360 141475806 8.460000e-158 568
46 TraesCS5D01G198200 chr3D 91.642 335 25 2 2233 2567 141476592 141476923 1.480000e-125 460
47 TraesCS5D01G198200 chr3D 89.855 345 18 5 969 1313 141533435 141533762 1.500000e-115 427
48 TraesCS5D01G198200 chr3D 76.010 421 55 28 458 851 467466717 467466316 5.990000e-40 176
49 TraesCS5D01G198200 chr1B 85.798 514 46 11 972 1483 638058793 638058305 2.400000e-143 520
50 TraesCS5D01G198200 chr1B 87.660 235 16 3 1527 1748 638058292 638058058 1.610000e-65 261
51 TraesCS5D01G198200 chr1A 74.798 619 97 31 270 853 540416255 540415661 2.110000e-54 224
52 TraesCS5D01G198200 chr4D 76.824 466 54 24 392 851 123148155 123147738 4.570000e-51 213
53 TraesCS5D01G198200 chr7A 76.072 443 61 25 437 851 143097266 143096841 7.700000e-44 189
54 TraesCS5D01G198200 chr2A 74.317 549 86 25 336 851 765672841 765672315 1.290000e-41 182


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 TraesCS5D01G198200 chr5D 301112329 301118148 5819 True 10748.000000 10748 100.000000 1 5820 1 chr5D.!!$R1 5819
1 TraesCS5D01G198200 chr5D 461345187 461346915 1728 True 303.833333 449 88.453167 969 2570 6 chr5D.!!$R2 1601
2 TraesCS5D01G198200 chr5A 398280057 398285372 5315 True 2359.333333 4348 92.544000 852 5820 3 chr5A.!!$R2 4968
3 TraesCS5D01G198200 chr5A 220911986 220913182 1196 True 420.333333 540 86.247000 972 2570 3 chr5A.!!$R1 1598
4 TraesCS5D01G198200 chr5B 344309896 344317767 7871 True 1857.250000 4063 93.737000 852 5820 4 chr5B.!!$R2 4968
5 TraesCS5D01G198200 chr6A 595565132 595566035 903 True 1181.000000 1181 90.939000 1 867 1 chr6A.!!$R1 866
6 TraesCS5D01G198200 chr7B 74532 75271 739 True 1099.000000 1099 93.817000 138 863 1 chr7B.!!$R1 725
7 TraesCS5D01G198200 chr4B 540466361 540467242 881 False 536.000000 822 92.642500 65 851 2 chr4B.!!$F1 786
8 TraesCS5D01G198200 chr3A 737829596 737830781 1185 False 450.000000 632 86.882000 969 2567 3 chr3A.!!$F1 1598
9 TraesCS5D01G198200 chr3A 737838254 737839439 1185 False 445.000000 623 86.627000 969 2567 3 chr3A.!!$F2 1598
10 TraesCS5D01G198200 chr3A 737855092 737856277 1185 False 443.000000 623 86.553667 969 2567 3 chr3A.!!$F3 1598
11 TraesCS5D01G198200 chr3B 582286171 582286852 681 False 447.000000 616 89.739000 1514 2567 2 chr3B.!!$F2 1053
12 TraesCS5D01G198200 chr3D 141475360 141476923 1563 False 514.000000 568 90.479000 969 2567 2 chr3D.!!$F2 1598
13 TraesCS5D01G198200 chr1B 638058058 638058793 735 True 390.500000 520 86.729000 972 1748 2 chr1B.!!$R1 776
14 TraesCS5D01G198200 chr1A 540415661 540416255 594 True 224.000000 224 74.798000 270 853 1 chr1A.!!$R1 583

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
289 369 1.021202 CGCAGTTGACAAAACAGGGA 58.979 50.000 0.00 0.00 0.0 4.20 F
1356 1512 0.817013 TTGATTTGATTCAGCCGGCC 59.183 50.000 26.15 7.94 0.0 6.13 F
1984 4049 1.002257 TGTGGCCTGCGTTGATGAT 60.002 52.632 3.32 0.00 0.0 2.45 F
3176 5285 1.630369 TCTGGCCACAAGACTTATGCT 59.370 47.619 0.00 0.00 0.0 3.79 F
4417 7632 1.687660 ACAACAAAGTGGCATGCATGA 59.312 42.857 30.64 7.50 0.0 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1643 1.227823 CACGGCACCAACAGGAAGA 60.228 57.895 0.0 0.0 0.00 2.87 R
2973 5082 0.549950 AGGATTGCTCACCCCAGATG 59.450 55.000 0.0 0.0 0.00 2.90 R
3319 5429 2.997897 GACCCACGAGCCCTCAGT 60.998 66.667 0.0 0.0 0.00 3.41 R
4491 7706 1.365699 GCCGACCGCTAAAATCTGAA 58.634 50.000 0.0 0.0 0.00 3.02 R
5304 8529 0.970640 TTAGTCGCTGGTTGGTAGCA 59.029 50.000 0.0 0.0 41.18 3.49 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
38 39 5.801531 TTTACTCTGTAGGAGAAAGTGCA 57.198 39.130 0.00 0.00 44.45 4.57
172 173 2.315176 CCACCCACAACAAATTCTCCA 58.685 47.619 0.00 0.00 0.00 3.86
216 280 6.189859 CAGGGCATAAGATAGAGAGAGAGAT 58.810 44.000 0.00 0.00 0.00 2.75
244 310 2.634940 CCATCGGTTCCAGAGATATGGT 59.365 50.000 0.00 0.00 41.43 3.55
289 369 1.021202 CGCAGTTGACAAAACAGGGA 58.979 50.000 0.00 0.00 0.00 4.20
323 403 3.785887 AGCCACATCTACCCCTAAAATCA 59.214 43.478 0.00 0.00 0.00 2.57
413 495 2.505337 CGATTCCGTCGGCGAACA 60.505 61.111 12.93 0.00 46.47 3.18
429 511 2.360801 CGAACAACACCTGAACCCAAAT 59.639 45.455 0.00 0.00 0.00 2.32
442 524 1.635487 ACCCAAATAGAGGAGCAGCAA 59.365 47.619 0.00 0.00 0.00 3.91
456 538 1.340405 GCAGCAAAGATGGAGGGAGAA 60.340 52.381 0.00 0.00 0.00 2.87
584 673 1.683917 GAGGCGATTCTTCTAGAGGCA 59.316 52.381 0.00 0.00 0.00 4.75
716 811 2.811504 CGCCTAATCAGAATCATGGGCA 60.812 50.000 0.00 0.00 38.37 5.36
788 883 2.752903 CCGGTTTGAGTAATTTCAGGGG 59.247 50.000 0.00 0.00 0.00 4.79
892 1003 3.731728 GCCCAGCCCAGACCATCA 61.732 66.667 0.00 0.00 0.00 3.07
895 1006 1.611419 CCAGCCCAGACCATCACAT 59.389 57.895 0.00 0.00 0.00 3.21
903 1015 3.198068 CCAGACCATCACATTCTTACCG 58.802 50.000 0.00 0.00 0.00 4.02
956 1068 1.541310 CCTGTACCTCACTGCCGGAA 61.541 60.000 5.05 0.00 0.00 4.30
1356 1512 0.817013 TTGATTTGATTCAGCCGGCC 59.183 50.000 26.15 7.94 0.00 6.13
1485 1643 6.661304 ATGCTTCTTCTTTCTGACCAATTT 57.339 33.333 0.00 0.00 0.00 1.82
1488 1646 6.322201 TGCTTCTTCTTTCTGACCAATTTCTT 59.678 34.615 0.00 0.00 0.00 2.52
1489 1647 6.860539 GCTTCTTCTTTCTGACCAATTTCTTC 59.139 38.462 0.00 0.00 0.00 2.87
1554 1718 5.291293 AGGAAAATTTACAACGTGATCCG 57.709 39.130 0.00 2.55 44.03 4.18
1684 1860 6.569179 TTGGTTTGCTAGATTAGTTGGAAC 57.431 37.500 0.00 0.00 0.00 3.62
1693 1869 6.763610 GCTAGATTAGTTGGAACTGTGCTTAT 59.236 38.462 2.14 0.00 40.07 1.73
1711 1887 6.258068 GTGCTTATCCACCTGTTCTTACATAC 59.742 42.308 0.00 0.00 32.86 2.39
1813 3850 8.738106 TGCATAGTCTCAGTCTCATCTTATATG 58.262 37.037 0.00 0.00 0.00 1.78
1899 3964 8.500837 TCTAAATCAACAATTGTAAAAGTGCG 57.499 30.769 12.39 0.00 0.00 5.34
1905 3970 7.589395 TCAACAATTGTAAAAGTGCGTGATAT 58.411 30.769 12.39 0.00 0.00 1.63
1984 4049 1.002257 TGTGGCCTGCGTTGATGAT 60.002 52.632 3.32 0.00 0.00 2.45
2387 4491 6.923508 GCAATTAGCAAACAGGTTAGTTCTTT 59.076 34.615 0.00 0.00 44.79 2.52
2389 4493 9.612620 CAATTAGCAAACAGGTTAGTTCTTTAG 57.387 33.333 0.00 0.00 0.00 1.85
2399 4503 9.686683 ACAGGTTAGTTCTTTAGATTTGCATAT 57.313 29.630 0.00 0.00 0.00 1.78
2483 4587 7.856145 ATTCTTCTCGTAGAATGCTTGATTT 57.144 32.000 8.61 0.00 41.94 2.17
2601 4705 5.638530 TGCTGGGATGTGGTATGTATTTA 57.361 39.130 0.00 0.00 0.00 1.40
2670 4774 8.707938 AATGAAATATGCTTTTGCCTAAGAAC 57.292 30.769 0.00 0.00 46.87 3.01
2676 4780 4.630111 TGCTTTTGCCTAAGAACCATTTG 58.370 39.130 0.00 0.00 46.87 2.32
2706 4810 9.376075 CACAAGCTTCCATATCCATAGTATTAG 57.624 37.037 0.00 0.00 0.00 1.73
2741 4848 4.202357 ACTGCTTGAGGTGTCTGACAATAA 60.202 41.667 12.81 4.85 0.00 1.40
2958 5067 6.442541 TTTTAGGTGGTAACTGGATCAGAA 57.557 37.500 1.59 0.00 35.18 3.02
3001 5110 3.614092 GGTGAGCAATCCTCTCAATTCA 58.386 45.455 0.00 0.00 41.66 2.57
3011 5120 7.328005 GCAATCCTCTCAATTCAAGAAAGTTTC 59.672 37.037 7.57 7.57 0.00 2.78
3020 5129 9.663904 TCAATTCAAGAAAGTTTCTGTATTTCG 57.336 29.630 18.70 5.95 40.59 3.46
3164 5273 6.539103 CCTATTAGTTTTACTTCTCTGGCCAC 59.461 42.308 0.00 0.00 0.00 5.01
3171 5280 1.771255 ACTTCTCTGGCCACAAGACTT 59.229 47.619 17.55 4.79 0.00 3.01
3176 5285 1.630369 TCTGGCCACAAGACTTATGCT 59.370 47.619 0.00 0.00 0.00 3.79
3263 5373 2.369860 TCATGCTCTTTGTGGACACTCT 59.630 45.455 3.91 0.00 0.00 3.24
3319 5429 4.761975 ACGTCCAGTACAGAACAAGAAAA 58.238 39.130 0.00 0.00 0.00 2.29
3320 5430 4.569564 ACGTCCAGTACAGAACAAGAAAAC 59.430 41.667 0.00 0.00 0.00 2.43
3609 5720 7.840342 AAATCAAGTAAGTGCTGATCTGTAG 57.160 36.000 1.27 0.00 0.00 2.74
3658 5769 6.465084 CAAGTAAGACCTTTAGTTAGCTGGT 58.535 40.000 0.00 0.00 0.00 4.00
3813 5933 6.849588 AACCGAGAACACGTTTAGTAAAAT 57.150 33.333 0.00 0.00 0.00 1.82
3893 6013 4.264253 TGATTCAGATGGCCACTAAACTG 58.736 43.478 8.16 13.03 0.00 3.16
3919 6069 4.385825 CAGTAAACTGGTAAGGTTGCTCA 58.614 43.478 2.01 0.00 41.70 4.26
3939 6089 7.700505 TGCTCAATGCTCATTGTTAGAAATAG 58.299 34.615 18.68 9.69 46.15 1.73
4069 6224 6.782494 TGTAGATAGGCAGGAAATGATCAGTA 59.218 38.462 0.09 0.00 0.00 2.74
4086 6241 7.805163 TGATCAGTATATGGTGAACTTCCAAT 58.195 34.615 0.00 0.00 38.52 3.16
4263 6418 5.073554 TCCATGCATCTGATATGGTTAAGGT 59.926 40.000 15.65 0.00 41.61 3.50
4417 7632 1.687660 ACAACAAAGTGGCATGCATGA 59.312 42.857 30.64 7.50 0.00 3.07
4461 7676 3.243068 CCAATAGCATGCTAACCGTTTCC 60.243 47.826 30.06 0.00 31.73 3.13
4491 7706 4.860802 TTCCTGTTCATACCACATCCAT 57.139 40.909 0.00 0.00 0.00 3.41
4507 7722 4.576463 ACATCCATTCAGATTTTAGCGGTC 59.424 41.667 0.00 0.00 0.00 4.79
4591 7806 1.748591 GCTCCTCCATCGGCATTTTCT 60.749 52.381 0.00 0.00 0.00 2.52
4666 7888 3.055530 ACTTCTTGGATCTGCGTCATCTT 60.056 43.478 0.00 0.00 0.00 2.40
4774 7996 3.524789 TGGTGGATGTCATCTCTGGATTT 59.475 43.478 12.54 0.00 0.00 2.17
4909 8132 5.298276 TGGAGTGCGAAACTGTATTTCTTTT 59.702 36.000 0.00 0.00 40.07 2.27
4910 8133 6.183360 TGGAGTGCGAAACTGTATTTCTTTTT 60.183 34.615 0.00 0.00 40.07 1.94
4930 8153 3.880047 TCCCCTCACTGTTGTAATACG 57.120 47.619 0.00 0.00 0.00 3.06
4934 8157 4.400251 CCCCTCACTGTTGTAATACGAGTA 59.600 45.833 0.00 0.00 0.00 2.59
4935 8158 5.068723 CCCCTCACTGTTGTAATACGAGTAT 59.931 44.000 0.00 0.00 0.00 2.12
4936 8159 6.207213 CCCTCACTGTTGTAATACGAGTATC 58.793 44.000 0.00 0.00 0.00 2.24
4937 8160 6.183360 CCCTCACTGTTGTAATACGAGTATCA 60.183 42.308 0.00 0.00 33.17 2.15
4938 8161 6.913132 CCTCACTGTTGTAATACGAGTATCAG 59.087 42.308 0.00 2.59 33.17 2.90
4943 8166 7.754027 ACTGTTGTAATACGAGTATCAGTTCAC 59.246 37.037 8.03 0.00 31.02 3.18
4953 8176 5.335269 CGAGTATCAGTTCACTTCAGTCTGT 60.335 44.000 0.00 0.00 33.17 3.41
4963 8186 5.240891 TCACTTCAGTCTGTGGAATGATTC 58.759 41.667 0.00 0.00 44.33 2.52
5001 8224 8.463930 AGATTCTTTGTAAATGTCCTTGTTCA 57.536 30.769 0.00 0.00 0.00 3.18
5002 8225 8.912988 AGATTCTTTGTAAATGTCCTTGTTCAA 58.087 29.630 0.00 0.00 0.00 2.69
5069 8292 9.703892 TGTTTCACATATGTTAATTTTTGGAGG 57.296 29.630 5.37 0.00 0.00 4.30
5202 8427 6.563222 AAAGATGAAATTGCCACCAAATTG 57.437 33.333 0.00 0.00 34.05 2.32
5203 8428 5.231702 AGATGAAATTGCCACCAAATTGT 57.768 34.783 0.00 0.00 34.05 2.71
5244 8469 5.934625 CACCAAGCTGAGTAATACAACTTCT 59.065 40.000 0.00 0.00 0.00 2.85
5304 8529 3.073946 ACAGCCCAGGTTTACATGTAGTT 59.926 43.478 5.56 0.00 0.00 2.24
5521 8746 2.024414 GGTGTGCCAGAAATACCCATC 58.976 52.381 0.00 0.00 34.09 3.51
5615 8845 2.170166 CCAGCAAGGCTTCCAAATACA 58.830 47.619 0.00 0.00 36.40 2.29
5669 8899 4.962362 TCCTACTCCACAAAGCAGATATCA 59.038 41.667 5.32 0.00 0.00 2.15
5768 9005 1.210204 TCCAGCCAAGGAGCAATCCT 61.210 55.000 0.00 0.00 43.04 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 9.362151 TCAAGATAATTTGGTGTAGGAAAACTT 57.638 29.630 0.00 0.00 0.00 2.66
79 80 2.806945 TGCAAGGAGAATTGGTAGGG 57.193 50.000 0.00 0.00 0.00 3.53
172 173 6.712276 CCCTGTTTCTCCTACAGAGTAAATT 58.288 40.000 4.66 0.00 44.52 1.82
216 280 2.567169 CTCTGGAACCGATGGCCATATA 59.433 50.000 20.84 0.00 0.00 0.86
268 348 1.268539 CCCTGTTTTGTCAACTGCGTC 60.269 52.381 0.00 0.00 0.00 5.19
289 369 6.351286 GGGTAGATGTGGCTTTTTGATTGATT 60.351 38.462 0.00 0.00 0.00 2.57
413 495 3.655777 TCCTCTATTTGGGTTCAGGTGTT 59.344 43.478 0.00 0.00 0.00 3.32
429 511 2.433604 CTCCATCTTTGCTGCTCCTCTA 59.566 50.000 0.00 0.00 0.00 2.43
442 524 0.915364 GGTGCTTCTCCCTCCATCTT 59.085 55.000 0.00 0.00 0.00 2.40
456 538 0.185901 AAACCATGTGTCCAGGTGCT 59.814 50.000 0.00 0.00 35.42 4.40
584 673 3.556004 CCCTTTTTCTTCGTCAGAGCTCT 60.556 47.826 11.45 11.45 31.12 4.09
716 811 3.350219 AATCTGGAGCGGTTTATGTGT 57.650 42.857 0.00 0.00 0.00 3.72
788 883 3.434940 ACATACCCCCTGAACTCAAAC 57.565 47.619 0.00 0.00 0.00 2.93
886 997 2.420129 GCCTCGGTAAGAATGTGATGGT 60.420 50.000 0.00 0.00 0.00 3.55
890 1001 0.539986 GGGCCTCGGTAAGAATGTGA 59.460 55.000 0.84 0.00 0.00 3.58
892 1003 0.541863 CTGGGCCTCGGTAAGAATGT 59.458 55.000 4.53 0.00 0.00 2.71
895 1006 2.666098 GGCTGGGCCTCGGTAAGAA 61.666 63.158 4.53 0.00 46.69 2.52
983 1101 2.555199 CCATCTCCTCGCGATTCTTTT 58.445 47.619 10.36 0.00 0.00 2.27
1485 1643 1.227823 CACGGCACCAACAGGAAGA 60.228 57.895 0.00 0.00 0.00 2.87
1488 1646 4.263572 CCCACGGCACCAACAGGA 62.264 66.667 0.00 0.00 0.00 3.86
1489 1647 3.567579 ATCCCACGGCACCAACAGG 62.568 63.158 0.00 0.00 0.00 4.00
1554 1718 1.369689 CGCAGCTGTCACAAGCAAC 60.370 57.895 16.64 0.00 46.08 4.17
1684 1860 3.340814 AGAACAGGTGGATAAGCACAG 57.659 47.619 0.00 0.00 0.00 3.66
1693 1869 5.755409 ACATGTATGTAAGAACAGGTGGA 57.245 39.130 0.00 0.00 39.00 4.02
1748 3784 5.330295 GCAAGATTGACATCTTTGCTAGTG 58.670 41.667 9.68 0.00 46.07 2.74
1772 3809 2.649331 ATGCACAAGAAGCTGAATGC 57.351 45.000 0.00 0.00 43.29 3.56
1813 3850 8.296713 TCTTTATTCAACTGCTGTAAATCAACC 58.703 33.333 0.00 0.00 0.00 3.77
1899 3964 7.776933 TCATAGAAGTGAGCACAAATATCAC 57.223 36.000 3.19 0.00 42.91 3.06
1905 3970 6.054941 TCAGTTTCATAGAAGTGAGCACAAA 58.945 36.000 3.19 0.00 34.83 2.83
2027 4094 3.248363 TGATTTGTTTCACTCTGCACTCG 59.752 43.478 0.00 0.00 0.00 4.18
2090 4157 9.740239 CAAAATAAGTGCTCTACCTATTACGTA 57.260 33.333 0.00 0.00 28.26 3.57
2091 4158 8.472413 TCAAAATAAGTGCTCTACCTATTACGT 58.528 33.333 0.00 0.00 28.26 3.57
2092 4159 8.867112 TCAAAATAAGTGCTCTACCTATTACG 57.133 34.615 0.00 0.00 28.26 3.18
2208 4293 6.095300 TGCATGTCCAATTGTTTAGTATGGAG 59.905 38.462 4.43 0.00 40.65 3.86
2387 4491 9.409312 CAAACAGTGTGAAAATATGCAAATCTA 57.591 29.630 0.00 0.00 0.00 1.98
2389 4493 8.296799 TCAAACAGTGTGAAAATATGCAAATC 57.703 30.769 0.00 0.00 0.00 2.17
2399 4503 5.777802 TGCTTTCTTCAAACAGTGTGAAAA 58.222 33.333 7.60 0.00 34.68 2.29
2432 4536 1.905215 AGACTGCACATAAGAGGCTGT 59.095 47.619 0.00 0.00 41.47 4.40
2498 4602 8.168725 AGCATAGTGGAGAAAATCAATATCCAT 58.831 33.333 0.00 0.00 41.81 3.41
2643 4747 8.931385 TCTTAGGCAAAAGCATATTTCATTTC 57.069 30.769 0.00 0.00 0.00 2.17
2659 4763 4.518970 GTGACTCAAATGGTTCTTAGGCAA 59.481 41.667 0.00 0.00 0.00 4.52
2670 4774 2.886523 TGGAAGCTTGTGACTCAAATGG 59.113 45.455 2.10 0.00 35.48 3.16
2676 4780 4.142609 TGGATATGGAAGCTTGTGACTC 57.857 45.455 2.10 0.00 0.00 3.36
2706 4810 3.681897 CCTCAAGCAGTCACATAGAACAC 59.318 47.826 0.00 0.00 0.00 3.32
2741 4848 4.511527 AGACAAGCAGACATGATCGAAAT 58.488 39.130 0.00 0.00 0.00 2.17
2878 4986 8.028938 GCAAAATCTAGCAGGTTTTCATAAGAA 58.971 33.333 4.72 0.00 0.00 2.52
2973 5082 0.549950 AGGATTGCTCACCCCAGATG 59.450 55.000 0.00 0.00 0.00 2.90
3001 5110 9.634163 ACAAAAACGAAATACAGAAACTTTCTT 57.366 25.926 0.92 0.00 38.11 2.52
3038 5147 4.287067 AGGAACTGGAAGAGCACAGATAAA 59.713 41.667 0.00 0.00 37.18 1.40
3263 5373 3.327757 ACACTTCCCACTTCTGCAATCTA 59.672 43.478 0.00 0.00 0.00 1.98
3319 5429 2.997897 GACCCACGAGCCCTCAGT 60.998 66.667 0.00 0.00 0.00 3.41
3320 5430 4.135153 CGACCCACGAGCCCTCAG 62.135 72.222 0.00 0.00 45.77 3.35
3609 5720 4.619160 GCAGGGAGGAAACAAATGAACATC 60.619 45.833 0.00 0.00 0.00 3.06
3784 5904 6.503524 ACTAAACGTGTTCTCGGTTAAGTTA 58.496 36.000 0.00 0.00 41.36 2.24
3857 5977 6.820152 CCATCTGAATCATGAGTTACACTGAA 59.180 38.462 0.09 0.00 0.00 3.02
3919 6069 8.970859 AGTAGCTATTTCTAACAATGAGCATT 57.029 30.769 0.00 0.00 0.00 3.56
4041 6196 7.520798 TGATCATTTCCTGCCTATCTACAAAT 58.479 34.615 0.00 0.00 0.00 2.32
4069 6224 7.402054 TGAGTAACATTGGAAGTTCACCATAT 58.598 34.615 5.01 0.00 37.26 1.78
4086 6241 6.000246 TCTAATGATGGGCATTGAGTAACA 58.000 37.500 0.00 0.00 46.38 2.41
4263 6418 2.692557 CACCAGTGGGAATTGTTGTTCA 59.307 45.455 15.21 0.00 38.05 3.18
4309 6464 6.370442 TGGTGGTGTCTTTAGTGATAAATTCG 59.630 38.462 0.00 0.00 0.00 3.34
4417 7632 7.765695 TGGAAGCAAAAGAGTTGAGATAAAT 57.234 32.000 0.00 0.00 0.00 1.40
4470 7685 4.860802 ATGGATGTGGTATGAACAGGAA 57.139 40.909 0.00 0.00 0.00 3.36
4471 7686 4.227073 TGAATGGATGTGGTATGAACAGGA 59.773 41.667 0.00 0.00 0.00 3.86
4472 7687 4.525996 TGAATGGATGTGGTATGAACAGG 58.474 43.478 0.00 0.00 0.00 4.00
4473 7688 5.430886 TCTGAATGGATGTGGTATGAACAG 58.569 41.667 0.00 0.00 0.00 3.16
4475 7690 6.949352 AATCTGAATGGATGTGGTATGAAC 57.051 37.500 0.00 0.00 0.00 3.18
4476 7691 7.959658 AAAATCTGAATGGATGTGGTATGAA 57.040 32.000 0.00 0.00 0.00 2.57
4477 7692 7.229306 GCTAAAATCTGAATGGATGTGGTATGA 59.771 37.037 0.00 0.00 0.00 2.15
4478 7693 7.365741 GCTAAAATCTGAATGGATGTGGTATG 58.634 38.462 0.00 0.00 0.00 2.39
4479 7694 6.205464 CGCTAAAATCTGAATGGATGTGGTAT 59.795 38.462 0.00 0.00 0.00 2.73
4480 7695 5.527214 CGCTAAAATCTGAATGGATGTGGTA 59.473 40.000 0.00 0.00 0.00 3.25
4482 7697 4.261322 CCGCTAAAATCTGAATGGATGTGG 60.261 45.833 0.00 0.00 0.00 4.17
4483 7698 4.336433 ACCGCTAAAATCTGAATGGATGTG 59.664 41.667 0.00 0.00 0.00 3.21
4484 7699 4.526970 ACCGCTAAAATCTGAATGGATGT 58.473 39.130 0.00 0.00 0.00 3.06
4485 7700 4.319046 CGACCGCTAAAATCTGAATGGATG 60.319 45.833 0.00 0.00 0.00 3.51
4486 7701 3.809832 CGACCGCTAAAATCTGAATGGAT 59.190 43.478 0.00 0.00 0.00 3.41
4491 7706 1.365699 GCCGACCGCTAAAATCTGAA 58.634 50.000 0.00 0.00 0.00 3.02
4507 7722 4.749310 AGAGCAGGTTCAGCGCCG 62.749 66.667 2.29 0.00 37.01 6.46
4774 7996 4.166888 GCGCAGAGATGGCTCCCA 62.167 66.667 0.30 0.00 42.30 4.37
4798 8020 2.109799 CTATCCAGGCCACGGCAG 59.890 66.667 10.83 1.91 44.11 4.85
4909 8132 3.833650 TCGTATTACAACAGTGAGGGGAA 59.166 43.478 0.00 0.00 0.00 3.97
4910 8133 3.433343 TCGTATTACAACAGTGAGGGGA 58.567 45.455 0.00 0.00 0.00 4.81
4930 8153 5.861251 CACAGACTGAAGTGAACTGATACTC 59.139 44.000 10.08 0.00 37.97 2.59
4934 8157 3.643320 TCCACAGACTGAAGTGAACTGAT 59.357 43.478 10.08 0.00 37.97 2.90
4935 8158 3.031013 TCCACAGACTGAAGTGAACTGA 58.969 45.455 10.08 0.00 37.97 3.41
4936 8159 3.459232 TCCACAGACTGAAGTGAACTG 57.541 47.619 10.08 0.00 37.97 3.16
4937 8160 4.101585 TCATTCCACAGACTGAAGTGAACT 59.898 41.667 10.08 0.00 37.97 3.01
4938 8161 4.380531 TCATTCCACAGACTGAAGTGAAC 58.619 43.478 10.08 0.00 37.97 3.18
4963 8186 5.749462 ACAAAGAATCTATCCTTGTCAGGG 58.251 41.667 0.00 0.00 38.08 4.45
5001 8224 6.472887 TCGAAACCTCCAACAGAATATCTTT 58.527 36.000 0.00 0.00 0.00 2.52
5002 8225 6.049955 TCGAAACCTCCAACAGAATATCTT 57.950 37.500 0.00 0.00 0.00 2.40
5159 8382 8.605746 CATCTTTTTGTTGTTGTTGTTGATGAT 58.394 29.630 0.00 0.00 31.18 2.45
5160 8383 7.816513 TCATCTTTTTGTTGTTGTTGTTGATGA 59.183 29.630 0.00 0.00 34.87 2.92
5161 8384 7.961855 TCATCTTTTTGTTGTTGTTGTTGATG 58.038 30.769 0.00 0.00 0.00 3.07
5170 8393 6.687958 GTGGCAATTTCATCTTTTTGTTGTTG 59.312 34.615 0.00 0.00 0.00 3.33
5202 8427 2.544267 GGTGTTGACTAACTGAGCACAC 59.456 50.000 0.00 0.00 37.68 3.82
5203 8428 2.169561 TGGTGTTGACTAACTGAGCACA 59.830 45.455 0.00 0.00 37.68 4.57
5304 8529 0.970640 TTAGTCGCTGGTTGGTAGCA 59.029 50.000 0.00 0.00 41.18 3.49
5347 8572 7.040755 ACTGCAAGCATATGTAACTTTGTTGTA 60.041 33.333 4.29 0.00 37.60 2.41
5521 8746 7.415206 GGGTTTTAGTGTACATATTTGCCAGAG 60.415 40.741 0.00 0.00 0.00 3.35
5582 8808 2.702478 CCTTGCTGGTGATATCTCTCCA 59.298 50.000 3.98 9.01 41.57 3.86
5615 8845 8.655935 AAATGATGGAATTCTTAGAACCACTT 57.344 30.769 6.48 0.00 33.38 3.16
5669 8899 2.644060 AGGTGGTAGGTAAAGCTCCT 57.356 50.000 0.00 0.00 36.34 3.69
5768 9005 1.739929 CGTAGGCATCGTTGGTGCA 60.740 57.895 4.25 0.00 44.25 4.57


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

AutoCloner maintained by Alex Coulton.