Multiple sequence alignment - TraesCS5D01G156400

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 TraesCS5D01G156400 chr5D 100.000 4085 0 0 1 4085 244621558 244625642 0.000000e+00 7544.0
1 TraesCS5D01G156400 chr5D 91.262 103 6 1 2614 2716 250069618 250069717 1.980000e-28 137.0
2 TraesCS5D01G156400 chr5B 90.742 3910 207 61 233 4085 278009505 278013316 0.000000e+00 5072.0
3 TraesCS5D01G156400 chr5B 92.273 220 11 2 1 220 278009306 278009519 1.430000e-79 307.0
4 TraesCS5D01G156400 chr5B 93.750 96 4 2 2622 2715 461134383 461134478 4.260000e-30 143.0
5 TraesCS5D01G156400 chr5A 93.266 2985 139 33 233 3198 328802348 328805289 0.000000e+00 4342.0
6 TraesCS5D01G156400 chr5A 97.680 819 15 3 3267 4085 328807079 328807893 0.000000e+00 1404.0
7 TraesCS5D01G156400 chr5A 92.825 223 9 5 1 223 328802149 328802364 2.370000e-82 316.0
8 TraesCS5D01G156400 chr5A 87.705 244 25 4 465 708 503771660 503771422 3.110000e-71 279.0
9 TraesCS5D01G156400 chr5A 91.346 104 8 1 2609 2711 698639622 698639725 1.530000e-29 141.0
10 TraesCS5D01G156400 chr5A 94.805 77 4 0 3194 3270 328805504 328805580 1.990000e-23 121.0
11 TraesCS5D01G156400 chr3B 80.187 641 99 18 3456 4085 597547158 597546535 4.810000e-124 455.0
12 TraesCS5D01G156400 chr3A 80.187 641 99 19 3456 4085 596796029 596795406 4.810000e-124 455.0
13 TraesCS5D01G156400 chr3D 80.031 641 100 18 3456 4085 454747753 454747130 2.240000e-122 449.0
14 TraesCS5D01G156400 chr3D 77.093 227 37 13 2049 2262 443422349 443422573 2.580000e-22 117.0
15 TraesCS5D01G156400 chr3D 96.875 32 1 0 2049 2080 443365064 443365095 2.000000e-03 54.7
16 TraesCS5D01G156400 chr4B 79.412 272 27 16 2053 2309 565735134 565735391 9.080000e-37 165.0
17 TraesCS5D01G156400 chr2A 78.491 265 27 16 2059 2310 324633797 324633550 3.290000e-31 147.0
18 TraesCS5D01G156400 chr2D 92.929 99 6 1 2624 2721 15192879 15192977 4.260000e-30 143.0
19 TraesCS5D01G156400 chr2B 80.000 210 28 4 504 713 202269867 202270062 4.260000e-30 143.0
20 TraesCS5D01G156400 chr2B 90.476 105 6 4 2617 2720 559179501 559179602 7.120000e-28 135.0
21 TraesCS5D01G156400 chr2B 78.539 219 34 9 2049 2256 66667769 66667985 9.210000e-27 132.0
22 TraesCS5D01G156400 chr6D 92.079 101 6 2 2627 2727 59623259 59623161 1.530000e-29 141.0
23 TraesCS5D01G156400 chr6D 75.385 195 44 3 3563 3755 452497322 452497514 1.560000e-14 91.6
24 TraesCS5D01G156400 chr1A 87.826 115 11 2 2613 2727 427520594 427520483 9.210000e-27 132.0
25 TraesCS5D01G156400 chr7D 96.774 31 1 0 824 854 598023132 598023162 7.000000e-03 52.8


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 TraesCS5D01G156400 chr5D 244621558 244625642 4084 False 7544.00 7544 100.0000 1 4085 1 chr5D.!!$F1 4084
1 TraesCS5D01G156400 chr5B 278009306 278013316 4010 False 2689.50 5072 91.5075 1 4085 2 chr5B.!!$F2 4084
2 TraesCS5D01G156400 chr5A 328802149 328807893 5744 False 1545.75 4342 94.6440 1 4085 4 chr5A.!!$F2 4084
3 TraesCS5D01G156400 chr3B 597546535 597547158 623 True 455.00 455 80.1870 3456 4085 1 chr3B.!!$R1 629
4 TraesCS5D01G156400 chr3A 596795406 596796029 623 True 455.00 455 80.1870 3456 4085 1 chr3A.!!$R1 629
5 TraesCS5D01G156400 chr3D 454747130 454747753 623 True 449.00 449 80.0310 3456 4085 1 chr3D.!!$R1 629

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
427 455 0.038159 ACTGCAGTACTCCGCTTGAC 60.038 55.0 20.16 0.00 0.00 3.18 F
1279 1338 0.521735 CAAACGGCTTCAACCCTAGC 59.478 55.0 0.00 0.00 36.66 3.42 F
1964 2037 0.395586 TAACCCCTGTCATGCATGCC 60.396 55.0 22.25 11.84 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1385 1444 0.657840 AAACTGACAAGACGCACAGC 59.342 50.0 0.0 0.0 34.25 4.40 R
2575 2659 0.180406 CCTAGTTCCCATCCAACCCG 59.820 60.0 0.0 0.0 0.00 5.28 R
3171 3260 1.155889 TCATTTACCACTGCACTGCG 58.844 50.0 0.0 0.0 0.00 5.18 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
54 55 3.455469 GCACCATTGGAGGCTGGC 61.455 66.667 10.37 0.00 35.88 4.85
81 82 0.828022 ATGGCATGCTTGATGTTGGG 59.172 50.000 18.92 0.00 34.14 4.12
96 97 2.813908 GGGTCGTGTAAGCTGCGG 60.814 66.667 0.00 0.00 0.00 5.69
183 184 1.205893 GAGGCTGTTGCTAGCTAGTGT 59.794 52.381 21.62 3.69 43.22 3.55
193 194 3.118992 TGCTAGCTAGTGTGGAGTTCATG 60.119 47.826 21.62 0.00 0.00 3.07
194 195 3.118956 GCTAGCTAGTGTGGAGTTCATGT 60.119 47.826 21.62 0.00 0.00 3.21
195 196 4.621747 GCTAGCTAGTGTGGAGTTCATGTT 60.622 45.833 21.62 0.00 0.00 2.71
196 197 3.931578 AGCTAGTGTGGAGTTCATGTTC 58.068 45.455 0.00 0.00 0.00 3.18
197 198 3.324846 AGCTAGTGTGGAGTTCATGTTCA 59.675 43.478 0.00 0.00 0.00 3.18
198 199 4.019860 AGCTAGTGTGGAGTTCATGTTCAT 60.020 41.667 0.00 0.00 0.00 2.57
210 211 4.801521 TCATGTTCATCCCATGGATCTT 57.198 40.909 15.22 0.00 40.98 2.40
211 212 5.910355 TCATGTTCATCCCATGGATCTTA 57.090 39.130 15.22 0.00 40.98 2.10
212 213 6.264771 TCATGTTCATCCCATGGATCTTAA 57.735 37.500 15.22 0.00 40.98 1.85
213 214 6.855667 TCATGTTCATCCCATGGATCTTAAT 58.144 36.000 15.22 0.00 40.98 1.40
214 215 7.987820 TCATGTTCATCCCATGGATCTTAATA 58.012 34.615 15.22 0.00 40.98 0.98
215 216 8.105197 TCATGTTCATCCCATGGATCTTAATAG 58.895 37.037 15.22 0.00 40.98 1.73
216 217 7.392766 TGTTCATCCCATGGATCTTAATAGT 57.607 36.000 15.22 0.00 40.98 2.12
217 218 7.226441 TGTTCATCCCATGGATCTTAATAGTG 58.774 38.462 15.22 0.00 40.98 2.74
218 219 5.809001 TCATCCCATGGATCTTAATAGTGC 58.191 41.667 15.22 0.00 40.98 4.40
219 220 5.549228 TCATCCCATGGATCTTAATAGTGCT 59.451 40.000 15.22 0.00 40.98 4.40
220 221 5.912149 TCCCATGGATCTTAATAGTGCTT 57.088 39.130 15.22 0.00 0.00 3.91
221 222 7.237471 TCATCCCATGGATCTTAATAGTGCTTA 59.763 37.037 15.22 0.00 40.98 3.09
222 223 7.574021 TCCCATGGATCTTAATAGTGCTTAT 57.426 36.000 15.22 0.00 0.00 1.73
223 224 7.988937 TCCCATGGATCTTAATAGTGCTTATT 58.011 34.615 15.22 0.00 36.05 1.40
224 225 8.448008 TCCCATGGATCTTAATAGTGCTTATTT 58.552 33.333 15.22 0.00 33.96 1.40
225 226 9.082313 CCCATGGATCTTAATAGTGCTTATTTT 57.918 33.333 15.22 0.00 33.96 1.82
324 325 3.461946 GCAGATGCTGTATATTTCCGC 57.538 47.619 0.00 0.00 38.21 5.54
337 338 4.896829 TCCGCCCCGCAAAACCAA 62.897 61.111 0.00 0.00 0.00 3.67
358 359 2.949177 TTGCAGCTCTCCCTAAAACA 57.051 45.000 0.00 0.00 0.00 2.83
365 366 5.006386 CAGCTCTCCCTAAAACAGATTTGT 58.994 41.667 0.00 0.00 39.87 2.83
373 374 7.410174 TCCCTAAAACAGATTTGTGGTATCAT 58.590 34.615 0.00 0.00 37.67 2.45
383 384 7.335171 CAGATTTGTGGTATCATGAGACTTCAA 59.665 37.037 19.26 19.01 36.78 2.69
385 386 5.745312 TGTGGTATCATGAGACTTCAAGT 57.255 39.130 19.26 0.00 36.78 3.16
405 406 1.212751 GAACAGATGCCGCAAACCC 59.787 57.895 0.00 0.00 0.00 4.11
414 415 2.677003 CCGCAAACCCGTACTGCAG 61.677 63.158 13.48 13.48 35.78 4.41
415 416 1.959226 CGCAAACCCGTACTGCAGT 60.959 57.895 25.12 25.12 35.78 4.40
416 417 0.668096 CGCAAACCCGTACTGCAGTA 60.668 55.000 22.67 22.67 35.78 2.74
417 418 0.794473 GCAAACCCGTACTGCAGTAC 59.206 55.000 36.64 36.64 45.47 2.73
419 420 2.334838 CAAACCCGTACTGCAGTACTC 58.665 52.381 39.83 24.25 46.43 2.59
420 421 0.893447 AACCCGTACTGCAGTACTCC 59.107 55.000 39.83 23.64 46.43 3.85
423 424 1.654954 CCGTACTGCAGTACTCCGCT 61.655 60.000 39.83 13.86 46.43 5.52
424 425 0.170561 CGTACTGCAGTACTCCGCTT 59.829 55.000 39.83 13.18 46.43 4.68
427 455 0.038159 ACTGCAGTACTCCGCTTGAC 60.038 55.000 20.16 0.00 0.00 3.18
464 492 9.813446 ACCGTAAATCTGTTTTAGTTAGATAGG 57.187 33.333 0.00 0.00 30.46 2.57
465 493 8.762426 CCGTAAATCTGTTTTAGTTAGATAGGC 58.238 37.037 0.00 0.00 30.46 3.93
466 494 9.309516 CGTAAATCTGTTTTAGTTAGATAGGCA 57.690 33.333 0.00 0.00 30.46 4.75
472 500 9.733556 TCTGTTTTAGTTAGATAGGCAAAATCA 57.266 29.630 0.00 0.00 0.00 2.57
477 505 8.827177 TTAGTTAGATAGGCAAAATCATACCG 57.173 34.615 0.00 0.00 0.00 4.02
478 506 6.827727 AGTTAGATAGGCAAAATCATACCGT 58.172 36.000 0.00 0.00 0.00 4.83
479 507 7.959175 AGTTAGATAGGCAAAATCATACCGTA 58.041 34.615 0.00 0.00 0.00 4.02
480 508 8.426489 AGTTAGATAGGCAAAATCATACCGTAA 58.574 33.333 0.00 0.00 0.00 3.18
481 509 9.048446 GTTAGATAGGCAAAATCATACCGTAAA 57.952 33.333 0.00 0.00 0.00 2.01
482 510 9.787435 TTAGATAGGCAAAATCATACCGTAAAT 57.213 29.630 0.00 0.00 0.00 1.40
483 511 8.324163 AGATAGGCAAAATCATACCGTAAATC 57.676 34.615 0.00 0.00 0.00 2.17
484 512 5.767816 AGGCAAAATCATACCGTAAATCC 57.232 39.130 0.00 0.00 0.00 3.01
485 513 4.274950 AGGCAAAATCATACCGTAAATCCG 59.725 41.667 0.00 0.00 0.00 4.18
486 514 4.035909 GGCAAAATCATACCGTAAATCCGT 59.964 41.667 0.00 0.00 0.00 4.69
487 515 5.449451 GGCAAAATCATACCGTAAATCCGTT 60.449 40.000 0.00 0.00 0.00 4.44
488 516 6.031471 GCAAAATCATACCGTAAATCCGTTT 58.969 36.000 0.00 0.00 0.00 3.60
489 517 6.528774 GCAAAATCATACCGTAAATCCGTTTT 59.471 34.615 0.00 0.00 0.00 2.43
490 518 7.697291 GCAAAATCATACCGTAAATCCGTTTTA 59.303 33.333 0.00 0.00 0.00 1.52
491 519 9.217223 CAAAATCATACCGTAAATCCGTTTTAG 57.783 33.333 0.00 0.00 30.46 1.85
492 520 8.496707 AAATCATACCGTAAATCCGTTTTAGT 57.503 30.769 0.00 0.00 30.46 2.24
493 521 8.496707 AATCATACCGTAAATCCGTTTTAGTT 57.503 30.769 0.00 0.00 30.46 2.24
494 522 9.598517 AATCATACCGTAAATCCGTTTTAGTTA 57.401 29.630 0.00 0.00 30.46 2.24
495 523 8.633075 TCATACCGTAAATCCGTTTTAGTTAG 57.367 34.615 0.00 0.00 30.46 2.34
496 524 8.465999 TCATACCGTAAATCCGTTTTAGTTAGA 58.534 33.333 0.00 0.00 30.46 2.10
497 525 9.252962 CATACCGTAAATCCGTTTTAGTTAGAT 57.747 33.333 0.00 0.00 30.46 1.98
499 527 8.862550 ACCGTAAATCCGTTTTAGTTAGATAG 57.137 34.615 0.00 0.00 30.46 2.08
745 778 2.556559 GGCAGGAACAAGGTTCCCATTA 60.557 50.000 21.22 0.00 39.39 1.90
858 914 1.414919 ACGAGCGGCAAATAGGGAATA 59.585 47.619 1.45 0.00 0.00 1.75
1021 1080 1.000612 GACGGGGAGGAGGAGAACT 59.999 63.158 0.00 0.00 0.00 3.01
1142 1201 3.267031 CCTACCTCCTTGGATTCCACTTT 59.733 47.826 4.45 0.00 39.71 2.66
1279 1338 0.521735 CAAACGGCTTCAACCCTAGC 59.478 55.000 0.00 0.00 36.66 3.42
1321 1380 4.647424 TCTTTGTTGATTCGCCTGTTTT 57.353 36.364 0.00 0.00 0.00 2.43
1322 1381 5.004922 TCTTTGTTGATTCGCCTGTTTTT 57.995 34.783 0.00 0.00 0.00 1.94
1349 1408 2.826128 TCTTAGGCAGTCTGTCGTTGAT 59.174 45.455 0.93 0.00 0.00 2.57
1385 1444 5.182001 AGTTACTGCTAGTTCCTGCAAATTG 59.818 40.000 0.00 0.00 38.81 2.32
1638 1697 4.159506 TGTGGTTTTCTGAAGTTTCAAGGG 59.840 41.667 0.00 0.00 36.64 3.95
1687 1746 6.534634 ACAAACTTTGCAATCTACTCCTAGT 58.465 36.000 0.00 0.00 0.00 2.57
1688 1747 7.676947 ACAAACTTTGCAATCTACTCCTAGTA 58.323 34.615 0.00 0.00 0.00 1.82
1861 1926 4.819105 TCGATCTTTGTAACACCATCCT 57.181 40.909 0.00 0.00 0.00 3.24
1862 1927 4.503910 TCGATCTTTGTAACACCATCCTG 58.496 43.478 0.00 0.00 0.00 3.86
1867 1932 7.362056 CGATCTTTGTAACACCATCCTGATTTT 60.362 37.037 0.00 0.00 0.00 1.82
1946 2019 4.527944 TGCACGGGTGGATTGAATTATTA 58.472 39.130 0.43 0.00 0.00 0.98
1960 2033 5.514169 TGAATTATTAACCCCTGTCATGCA 58.486 37.500 0.00 0.00 0.00 3.96
1961 2034 6.135454 TGAATTATTAACCCCTGTCATGCAT 58.865 36.000 0.00 0.00 0.00 3.96
1962 2035 6.040729 TGAATTATTAACCCCTGTCATGCATG 59.959 38.462 21.07 21.07 0.00 4.06
1963 2036 1.473258 TTAACCCCTGTCATGCATGC 58.527 50.000 22.25 11.82 0.00 4.06
1964 2037 0.395586 TAACCCCTGTCATGCATGCC 60.396 55.000 22.25 11.84 0.00 4.40
2008 2081 6.587206 TGAGCATCATGGTTTGAATGTAAA 57.413 33.333 0.00 0.00 42.56 2.01
2051 2130 7.246674 TGATTTAGCATTTCGGTGTAGAATC 57.753 36.000 0.00 0.00 0.00 2.52
2550 2634 3.058639 GCGGTAAGATCTTTCATGGATGC 60.059 47.826 14.36 3.68 0.00 3.91
2575 2659 7.703197 GCTTTACAAGAGGTGAGTAGAATAGAC 59.297 40.741 0.00 0.00 0.00 2.59
2603 2688 3.954258 GGATGGGAACTAGGAAATTGTGG 59.046 47.826 0.00 0.00 0.00 4.17
2762 2848 6.265422 AGAAGATTTTTACCCCTGAACTGTTG 59.735 38.462 0.00 0.00 0.00 3.33
3015 3101 4.910195 TGGAGTTATGTTCAATGCAGTCT 58.090 39.130 0.00 0.00 0.00 3.24
3101 3190 1.069358 CTAGCCAAGTAGTAGCCAGGC 59.931 57.143 1.84 1.84 42.31 4.85
3171 3260 2.032924 GCTGGTGGTTGTGTACTTCAAC 59.967 50.000 18.94 18.94 42.76 3.18
3234 3545 7.010552 GCACTAAGATTGATTTCAGTGTACGAT 59.989 37.037 0.00 0.00 36.59 3.73
3423 5236 6.096846 ACATTGCCCCAAATAATCAGTAGAAC 59.903 38.462 0.00 0.00 0.00 3.01
3626 5447 0.033796 ATGACAGCCCACCCATTCAG 60.034 55.000 0.00 0.00 0.00 3.02
3987 5808 2.359404 GAGACGGTGGAGGGGAGA 59.641 66.667 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 0.179111 CAAGCATGCCATGGCTTCTG 60.179 55.000 35.53 28.01 46.82 3.02
65 66 0.179156 CGACCCAACATCAAGCATGC 60.179 55.000 10.51 10.51 35.65 4.06
81 82 2.048503 ACCCGCAGCTTACACGAC 60.049 61.111 0.00 0.00 0.00 4.34
96 97 4.699522 GACCAGGCCACCGTGACC 62.700 72.222 5.01 0.00 0.00 4.02
183 184 3.623703 CATGGGATGAACATGAACTCCA 58.376 45.455 0.00 0.00 46.60 3.86
193 194 6.150140 GCACTATTAAGATCCATGGGATGAAC 59.850 42.308 13.02 0.00 43.27 3.18
194 195 6.044754 AGCACTATTAAGATCCATGGGATGAA 59.955 38.462 13.02 0.65 43.27 2.57
195 196 5.549228 AGCACTATTAAGATCCATGGGATGA 59.451 40.000 13.02 0.00 43.27 2.92
196 197 5.813383 AGCACTATTAAGATCCATGGGATG 58.187 41.667 13.02 0.00 43.27 3.51
197 198 6.460103 AAGCACTATTAAGATCCATGGGAT 57.540 37.500 13.02 4.02 46.28 3.85
198 199 5.912149 AAGCACTATTAAGATCCATGGGA 57.088 39.130 13.02 0.00 35.55 4.37
224 225 3.146066 AGCACTGTTAGATCGCCAAAAA 58.854 40.909 0.00 0.00 0.00 1.94
225 226 2.778299 AGCACTGTTAGATCGCCAAAA 58.222 42.857 0.00 0.00 0.00 2.44
226 227 2.472695 AGCACTGTTAGATCGCCAAA 57.527 45.000 0.00 0.00 0.00 3.28
227 228 3.118775 ACATAGCACTGTTAGATCGCCAA 60.119 43.478 0.00 0.00 0.00 4.52
228 229 2.430694 ACATAGCACTGTTAGATCGCCA 59.569 45.455 0.00 0.00 0.00 5.69
229 230 3.099267 ACATAGCACTGTTAGATCGCC 57.901 47.619 0.00 0.00 0.00 5.54
230 231 6.583912 TTTAACATAGCACTGTTAGATCGC 57.416 37.500 10.00 0.00 41.32 4.58
261 262 3.758554 GCTGCTATCCTTTGTTCCAGAAA 59.241 43.478 0.00 0.00 0.00 2.52
262 263 3.009473 AGCTGCTATCCTTTGTTCCAGAA 59.991 43.478 0.00 0.00 0.00 3.02
263 264 2.573462 AGCTGCTATCCTTTGTTCCAGA 59.427 45.455 0.00 0.00 0.00 3.86
264 265 2.996631 AGCTGCTATCCTTTGTTCCAG 58.003 47.619 0.00 0.00 0.00 3.86
337 338 3.760684 CTGTTTTAGGGAGAGCTGCAAAT 59.239 43.478 1.02 0.00 0.00 2.32
343 344 5.006386 CACAAATCTGTTTTAGGGAGAGCT 58.994 41.667 0.00 0.00 31.64 4.09
358 359 6.950842 TGAAGTCTCATGATACCACAAATCT 58.049 36.000 7.56 0.00 0.00 2.40
365 366 4.777366 TCCACTTGAAGTCTCATGATACCA 59.223 41.667 7.56 0.00 32.39 3.25
373 374 4.635223 CATCTGTTCCACTTGAAGTCTCA 58.365 43.478 0.00 0.00 32.37 3.27
383 384 0.537143 TTTGCGGCATCTGTTCCACT 60.537 50.000 2.28 0.00 0.00 4.00
385 386 1.523154 GGTTTGCGGCATCTGTTCCA 61.523 55.000 2.28 0.00 0.00 3.53
414 415 2.183555 CGGGGTCAAGCGGAGTAC 59.816 66.667 0.00 0.00 0.00 2.73
415 416 3.766691 GCGGGGTCAAGCGGAGTA 61.767 66.667 0.00 0.00 0.00 2.59
433 461 4.627035 ACTAAAACAGATTTACGGTACCGC 59.373 41.667 33.62 17.07 36.30 5.68
434 462 6.710692 AACTAAAACAGATTTACGGTACCG 57.289 37.500 32.22 32.22 37.68 4.02
464 492 5.164606 ACGGATTTACGGTATGATTTTGC 57.835 39.130 0.00 0.00 38.39 3.68
465 493 9.217223 CTAAAACGGATTTACGGTATGATTTTG 57.783 33.333 0.00 0.00 38.39 2.44
466 494 8.949177 ACTAAAACGGATTTACGGTATGATTTT 58.051 29.630 0.00 0.00 38.39 1.82
467 495 8.496707 ACTAAAACGGATTTACGGTATGATTT 57.503 30.769 0.00 0.00 38.39 2.17
468 496 8.496707 AACTAAAACGGATTTACGGTATGATT 57.503 30.769 0.00 0.00 38.39 2.57
469 497 9.252962 CTAACTAAAACGGATTTACGGTATGAT 57.747 33.333 0.00 0.00 38.39 2.45
470 498 8.465999 TCTAACTAAAACGGATTTACGGTATGA 58.534 33.333 0.00 0.00 38.39 2.15
471 499 8.633075 TCTAACTAAAACGGATTTACGGTATG 57.367 34.615 0.00 0.00 38.39 2.39
473 501 9.950680 CTATCTAACTAAAACGGATTTACGGTA 57.049 33.333 0.00 0.00 38.39 4.02
474 502 7.922811 CCTATCTAACTAAAACGGATTTACGGT 59.077 37.037 0.00 0.00 38.39 4.83
475 503 7.095899 GCCTATCTAACTAAAACGGATTTACGG 60.096 40.741 0.00 0.00 38.39 4.02
476 504 7.436080 TGCCTATCTAACTAAAACGGATTTACG 59.564 37.037 0.00 0.00 40.31 3.18
477 505 8.652810 TGCCTATCTAACTAAAACGGATTTAC 57.347 34.615 0.00 0.00 32.27 2.01
478 506 9.669887 TTTGCCTATCTAACTAAAACGGATTTA 57.330 29.630 0.00 0.00 32.27 1.40
479 507 8.570068 TTTGCCTATCTAACTAAAACGGATTT 57.430 30.769 0.00 0.00 34.92 2.17
480 508 8.570068 TTTTGCCTATCTAACTAAAACGGATT 57.430 30.769 0.00 0.00 0.00 3.01
481 509 8.747538 ATTTTGCCTATCTAACTAAAACGGAT 57.252 30.769 0.00 0.00 0.00 4.18
482 510 7.825270 TGATTTTGCCTATCTAACTAAAACGGA 59.175 33.333 0.00 0.00 0.00 4.69
483 511 7.981142 TGATTTTGCCTATCTAACTAAAACGG 58.019 34.615 0.00 0.00 0.00 4.44
484 512 9.438291 CATGATTTTGCCTATCTAACTAAAACG 57.562 33.333 0.00 0.00 0.00 3.60
627 659 9.625747 AATTCCAAACCATGTTGTTATTTCTTT 57.374 25.926 0.00 0.00 0.00 2.52
712 744 2.107378 TGTTCCTGCCAGGTTTATGTCA 59.893 45.455 11.27 0.00 36.53 3.58
769 810 5.820404 AGGGTTTATATCGGTTTAGGGAG 57.180 43.478 0.00 0.00 0.00 4.30
839 895 2.069273 CTATTCCCTATTTGCCGCTCG 58.931 52.381 0.00 0.00 0.00 5.03
858 914 3.007920 CCCTCAGTCAGGCAGGCT 61.008 66.667 0.00 0.00 41.80 4.58
1080 1139 4.382541 TCGGAGCTGGAGAGGGCA 62.383 66.667 0.00 0.00 0.00 5.36
1142 1201 2.122769 TGGAGGTTCCACGGGTGA 60.123 61.111 0.00 0.00 42.67 4.02
1321 1380 4.272504 CGACAGACTGCCTAAGAAACAAAA 59.727 41.667 1.25 0.00 0.00 2.44
1322 1381 3.807622 CGACAGACTGCCTAAGAAACAAA 59.192 43.478 1.25 0.00 0.00 2.83
1336 1395 6.692486 AGTGATCTTAAATCAACGACAGACT 58.308 36.000 0.00 0.00 0.00 3.24
1337 1396 6.952935 AGTGATCTTAAATCAACGACAGAC 57.047 37.500 0.00 0.00 0.00 3.51
1385 1444 0.657840 AAACTGACAAGACGCACAGC 59.342 50.000 0.00 0.00 34.25 4.40
1638 1697 2.290367 TGTACACACTGCATTGCAACTC 59.710 45.455 13.18 0.00 38.41 3.01
1716 1775 4.475016 AGAAGCAATACCAATACCTGAGGT 59.525 41.667 10.00 10.00 40.16 3.85
1867 1932 3.393472 GCACATGGCAACCCAAAAA 57.607 47.368 0.00 0.00 46.14 1.94
1907 1980 4.377021 CGTGCATAACTTGGGCTCTTATA 58.623 43.478 0.00 0.00 0.00 0.98
1908 1981 3.206150 CGTGCATAACTTGGGCTCTTAT 58.794 45.455 0.00 0.00 0.00 1.73
1909 1982 2.627945 CGTGCATAACTTGGGCTCTTA 58.372 47.619 0.00 0.00 0.00 2.10
1914 1987 1.677633 ACCCGTGCATAACTTGGGC 60.678 57.895 0.00 0.00 44.00 5.36
1946 2019 1.683365 GGCATGCATGACAGGGGTT 60.683 57.895 30.64 0.00 35.34 4.11
1960 2033 3.521126 AGTGAGACAATCTAACAGGGCAT 59.479 43.478 0.00 0.00 29.87 4.40
1961 2034 2.906389 AGTGAGACAATCTAACAGGGCA 59.094 45.455 0.00 0.00 29.87 5.36
1962 2035 3.618690 AGTGAGACAATCTAACAGGGC 57.381 47.619 0.00 0.00 29.87 5.19
1963 2036 6.878317 TCAATAGTGAGACAATCTAACAGGG 58.122 40.000 0.00 0.00 29.87 4.45
2007 2080 6.971726 ATCAGCATGGTGATTGTAATGATT 57.028 33.333 29.98 9.24 33.07 2.57
2008 2081 6.971726 AATCAGCATGGTGATTGTAATGAT 57.028 33.333 38.79 21.06 43.97 2.45
2051 2130 8.752005 TCAATTATTTTAGAATGGAGGGAGTG 57.248 34.615 0.00 0.00 0.00 3.51
2094 2175 6.488006 GTCATAGACATGGCCAGACATAAAAT 59.512 38.462 13.05 0.00 30.02 1.82
2100 2181 2.187100 TGTCATAGACATGGCCAGACA 58.813 47.619 13.05 14.59 37.67 3.41
2575 2659 0.180406 CCTAGTTCCCATCCAACCCG 59.820 60.000 0.00 0.00 0.00 5.28
2603 2688 9.624697 TGTATATGTCAAGAAAGAAATTTGCAC 57.375 29.630 0.00 0.00 0.00 4.57
2691 2776 2.852714 TACTCCCTCCGTCCCATAAA 57.147 50.000 0.00 0.00 0.00 1.40
2762 2848 2.421399 GGCCTCCAGATTTGCCTGC 61.421 63.158 0.00 0.00 40.77 4.85
3035 3121 6.484643 TCTGATAAAAGCACAGATCATTAGGC 59.515 38.462 0.00 0.00 36.04 3.93
3101 3190 2.807967 TGTCGGTCTGCAAAAAGATCTG 59.192 45.455 0.00 0.00 0.00 2.90
3171 3260 1.155889 TCATTTACCACTGCACTGCG 58.844 50.000 0.00 0.00 0.00 5.18
3234 3545 3.937778 TTCCTGCATCATGAGATCCAA 57.062 42.857 0.09 0.00 30.20 3.53
3440 5253 6.347160 GCCAATTTGCTGAAGAAATCAAAGTC 60.347 38.462 0.00 0.00 37.67 3.01


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

AutoCloner maintained by Alex Coulton.