Multiple sequence alignment - TraesCS4D01G199200

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 TraesCS4D01G199200 chr4D 100.000 3326 0 0 1 3326 346134617 346131292 0.000000e+00 6143.0
1 TraesCS4D01G199200 chr4B 95.381 2295 86 13 740 3029 427274281 427272002 0.000000e+00 3633.0
2 TraesCS4D01G199200 chr4B 81.170 547 66 20 3 515 427275906 427275363 4.000000e-109 405.0
3 TraesCS4D01G199200 chr4B 94.574 258 13 1 3069 3326 427270252 427269996 6.690000e-107 398.0
4 TraesCS4D01G199200 chr4B 93.478 46 3 0 3029 3074 427270337 427270292 5.950000e-08 69.4
5 TraesCS4D01G199200 chr4A 96.578 1841 44 6 676 2506 119781393 119783224 0.000000e+00 3033.0
6 TraesCS4D01G199200 chr4A 96.820 566 15 2 2507 3071 119783326 119783889 0.000000e+00 942.0
7 TraesCS4D01G199200 chr4A 95.951 247 9 1 3081 3326 119787226 119787472 1.860000e-107 399.0
8 TraesCS4D01G199200 chr4A 87.783 221 23 4 333 550 119703962 119704181 4.260000e-64 255.0
9 TraesCS4D01G199200 chr2D 91.304 46 4 0 571 616 586166251 586166206 2.770000e-06 63.9


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 TraesCS4D01G199200 chr4D 346131292 346134617 3325 True 6143.00 6143 100.000000 1 3326 1 chr4D.!!$R1 3325
1 TraesCS4D01G199200 chr4B 427269996 427275906 5910 True 1126.35 3633 91.150750 3 3326 4 chr4B.!!$R1 3323
2 TraesCS4D01G199200 chr4A 119781393 119787472 6079 False 1458.00 3033 96.449667 676 3326 3 chr4A.!!$F2 2650

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
331 357 0.112412 GGGAAAGGGAGGCTGTTGAA 59.888 55.000 0.0 0.0 0.00 2.69 F
338 364 1.093159 GGAGGCTGTTGAAGATGCTG 58.907 55.000 0.0 0.0 0.00 4.41 F
708 777 1.144057 CCGGGTGTAGATGGACAGC 59.856 63.158 0.0 0.0 45.15 4.40 F
932 1851 1.276421 CCACACTCCAGTTCGAATCCT 59.724 52.381 0.0 0.0 0.00 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 2869 0.247460 CAGAGTCCACCAATGCGAGA 59.753 55.0 0.0 0.0 0.00 4.04 R
2007 2926 0.396435 ACGACATGTTCTTGGAGCCA 59.604 50.0 0.0 0.0 0.00 4.75 R
2052 2971 0.946221 CGCCGAGCCACTTGATATCC 60.946 60.0 0.0 0.0 0.00 2.59 R
2734 3756 0.958382 GGGACTGCCGCACAAATGTA 60.958 55.0 0.0 0.0 33.83 2.29 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
57 58 8.893219 ATCTAGTTTCAAGATATCAATGCGAA 57.107 30.769 5.32 0.00 31.88 4.70
60 61 9.214953 CTAGTTTCAAGATATCAATGCGAAAAC 57.785 33.333 5.32 9.79 0.00 2.43
62 63 6.757897 TTCAAGATATCAATGCGAAAACCT 57.242 33.333 5.32 0.00 0.00 3.50
66 67 6.124088 AGATATCAATGCGAAAACCTCAAC 57.876 37.500 5.32 0.00 0.00 3.18
68 69 1.265635 TCAATGCGAAAACCTCAACGG 59.734 47.619 0.00 0.00 39.35 4.44
94 97 9.034544 GTGAAAATAGTTCATAATTTGGATGCC 57.965 33.333 0.00 0.00 0.00 4.40
111 114 5.215160 GGATGCCTAGCAAAACATATTTCG 58.785 41.667 0.00 0.00 43.62 3.46
115 118 6.862209 TGCCTAGCAAAACATATTTCGATTT 58.138 32.000 0.00 0.00 34.76 2.17
116 119 7.990917 TGCCTAGCAAAACATATTTCGATTTA 58.009 30.769 0.00 0.00 34.76 1.40
146 149 9.982291 TTTAGATCGCACAAAAATAAGATGTAC 57.018 29.630 0.00 0.00 0.00 2.90
147 150 7.609760 AGATCGCACAAAAATAAGATGTACA 57.390 32.000 0.00 0.00 0.00 2.90
148 151 7.688372 AGATCGCACAAAAATAAGATGTACAG 58.312 34.615 0.33 0.00 0.00 2.74
149 152 6.795098 TCGCACAAAAATAAGATGTACAGT 57.205 33.333 0.33 0.00 0.00 3.55
150 153 6.598525 TCGCACAAAAATAAGATGTACAGTG 58.401 36.000 0.33 1.01 0.00 3.66
151 154 6.425417 TCGCACAAAAATAAGATGTACAGTGA 59.575 34.615 0.33 0.00 0.00 3.41
189 215 0.537143 TTGACAGATGGGGCACACAC 60.537 55.000 0.00 0.00 0.00 3.82
207 233 3.919804 CACACGGTATTTGATGCAAAAGG 59.080 43.478 0.00 0.00 36.90 3.11
209 235 4.762765 ACACGGTATTTGATGCAAAAGGTA 59.237 37.500 0.00 0.00 36.90 3.08
245 271 0.470341 AAGAGCGCCCCTAAATCCTC 59.530 55.000 2.29 0.00 0.00 3.71
247 273 2.113351 GCGCCCCTAAATCCTCCC 59.887 66.667 0.00 0.00 0.00 4.30
249 275 1.125711 GCGCCCCTAAATCCTCCCTA 61.126 60.000 0.00 0.00 0.00 3.53
256 282 4.202577 CCCCTAAATCCTCCCTATTTGTCC 60.203 50.000 0.00 0.00 0.00 4.02
263 289 2.026636 CCTCCCTATTTGTCCAAACGGA 60.027 50.000 10.06 7.70 32.51 4.69
273 299 1.946984 TCCAAACGGATAGGACAGGT 58.053 50.000 0.00 0.00 0.00 4.00
303 329 7.715267 TTTCCTAACTCCCCCAATATATGAA 57.285 36.000 0.00 0.00 0.00 2.57
330 356 0.772124 AGGGAAAGGGAGGCTGTTGA 60.772 55.000 0.00 0.00 0.00 3.18
331 357 0.112412 GGGAAAGGGAGGCTGTTGAA 59.888 55.000 0.00 0.00 0.00 2.69
335 361 2.503895 AAGGGAGGCTGTTGAAGATG 57.496 50.000 0.00 0.00 0.00 2.90
338 364 1.093159 GGAGGCTGTTGAAGATGCTG 58.907 55.000 0.00 0.00 0.00 4.41
343 369 2.813754 GGCTGTTGAAGATGCTGTAACA 59.186 45.455 0.00 0.00 0.00 2.41
346 372 4.214119 GCTGTTGAAGATGCTGTAACAAGA 59.786 41.667 0.00 0.00 31.67 3.02
362 389 8.801882 TGTAACAAGAATAAAATAGGGGTCTG 57.198 34.615 0.00 0.00 0.00 3.51
365 392 7.027874 ACAAGAATAAAATAGGGGTCTGTCA 57.972 36.000 0.00 0.00 0.00 3.58
367 394 7.775561 ACAAGAATAAAATAGGGGTCTGTCATC 59.224 37.037 0.00 0.00 0.00 2.92
370 400 9.225682 AGAATAAAATAGGGGTCTGTCATCTAA 57.774 33.333 0.00 0.00 0.00 2.10
382 412 8.122952 GGGTCTGTCATCTAATAATTCAAAACG 58.877 37.037 0.00 0.00 0.00 3.60
388 418 9.722056 GTCATCTAATAATTCAAAACGATGCTT 57.278 29.630 0.00 0.00 0.00 3.91
403 433 5.109903 ACGATGCTTAGGTTCATCTACAAC 58.890 41.667 0.00 0.00 37.52 3.32
425 455 8.641541 ACAACAGATGAACAGTAAATTTGGAAT 58.358 29.630 0.00 0.00 0.00 3.01
469 502 1.607628 GCATCCAAGATGCTCATGTCC 59.392 52.381 19.69 0.00 41.52 4.02
470 503 2.927028 CATCCAAGATGCTCATGTCCA 58.073 47.619 0.00 0.00 0.00 4.02
481 514 7.262772 AGATGCTCATGTCCATGTAAATTTTG 58.737 34.615 7.13 0.00 39.72 2.44
482 515 6.587206 TGCTCATGTCCATGTAAATTTTGA 57.413 33.333 7.13 0.00 39.72 2.69
506 541 1.543944 TTGCACATCCGAGGAGCTCA 61.544 55.000 17.19 0.00 0.00 4.26
546 581 2.427453 TCTCGGCTCTGAATAGTGTTCC 59.573 50.000 0.00 0.00 0.00 3.62
550 585 3.619038 CGGCTCTGAATAGTGTTCCTTTC 59.381 47.826 0.00 0.00 0.00 2.62
551 586 4.579869 GGCTCTGAATAGTGTTCCTTTCA 58.420 43.478 0.00 0.00 0.00 2.69
552 587 4.633565 GGCTCTGAATAGTGTTCCTTTCAG 59.366 45.833 5.39 5.39 44.03 3.02
557 592 7.099764 TCTGAATAGTGTTCCTTTCAGATGTC 58.900 38.462 9.48 0.00 45.45 3.06
558 593 6.173339 TGAATAGTGTTCCTTTCAGATGTCC 58.827 40.000 0.00 0.00 0.00 4.02
559 594 5.762179 ATAGTGTTCCTTTCAGATGTCCA 57.238 39.130 0.00 0.00 0.00 4.02
560 595 4.437682 AGTGTTCCTTTCAGATGTCCAA 57.562 40.909 0.00 0.00 0.00 3.53
561 596 4.792068 AGTGTTCCTTTCAGATGTCCAAA 58.208 39.130 0.00 0.00 0.00 3.28
562 597 5.388654 AGTGTTCCTTTCAGATGTCCAAAT 58.611 37.500 0.00 0.00 0.00 2.32
563 598 6.542821 AGTGTTCCTTTCAGATGTCCAAATA 58.457 36.000 0.00 0.00 0.00 1.40
564 599 7.177878 AGTGTTCCTTTCAGATGTCCAAATAT 58.822 34.615 0.00 0.00 0.00 1.28
568 603 6.720309 TCCTTTCAGATGTCCAAATATCACA 58.280 36.000 0.00 0.00 0.00 3.58
569 604 7.174413 TCCTTTCAGATGTCCAAATATCACAA 58.826 34.615 0.00 0.00 0.00 3.33
571 606 6.441093 TTCAGATGTCCAAATATCACAAGC 57.559 37.500 0.00 0.00 0.00 4.01
572 607 5.748402 TCAGATGTCCAAATATCACAAGCT 58.252 37.500 0.00 0.00 0.00 3.74
573 608 5.819379 TCAGATGTCCAAATATCACAAGCTC 59.181 40.000 0.00 0.00 0.00 4.09
574 609 5.008415 CAGATGTCCAAATATCACAAGCTCC 59.992 44.000 0.00 0.00 0.00 4.70
577 638 3.557595 GTCCAAATATCACAAGCTCCTCG 59.442 47.826 0.00 0.00 0.00 4.63
623 689 4.116238 TGCACGAATCTTGCGTATATGAA 58.884 39.130 7.22 0.00 43.34 2.57
628 694 7.125755 CACGAATCTTGCGTATATGAACATTT 58.874 34.615 0.00 0.00 40.44 2.32
708 777 1.144057 CCGGGTGTAGATGGACAGC 59.856 63.158 0.00 0.00 45.15 4.40
738 1651 6.451064 AAAAACTTCACGGAGACATCTTTT 57.549 33.333 0.00 0.00 0.00 2.27
739 1652 6.451064 AAAACTTCACGGAGACATCTTTTT 57.549 33.333 0.00 0.00 0.00 1.94
817 1736 4.269523 TGTTGCTGGGCCGAGCTT 62.270 61.111 35.46 0.00 39.90 3.74
932 1851 1.276421 CCACACTCCAGTTCGAATCCT 59.724 52.381 0.00 0.00 0.00 3.24
954 1873 3.437795 CCGTCTCCGCCGTAGTGT 61.438 66.667 0.00 0.00 0.00 3.55
967 1886 3.612115 TAGTGTCCCCCACCCCTCG 62.612 68.421 0.00 0.00 45.74 4.63
1231 2150 3.677284 CTCTCCGAGGACGACCCGA 62.677 68.421 14.12 2.00 42.66 5.14
1590 2509 4.035843 GACCAGTCCCAGTCGGAT 57.964 61.111 0.00 0.00 44.66 4.18
1623 2542 2.110967 CGTCTCCTGCATGCTTGGG 61.111 63.158 20.33 17.37 0.00 4.12
1776 2695 4.625800 GACAGGGTGTCAGGCATC 57.374 61.111 2.12 0.00 46.22 3.91
1818 2737 1.538047 TGCTTGTGGAGAAAGATGCC 58.462 50.000 0.00 0.00 0.00 4.40
1887 2806 3.243636 GCATCATATTGACAGCAAAGGGG 60.244 47.826 0.00 0.00 37.59 4.79
1995 2914 4.445305 CCATATGGGCTGAAGATCTTGTCA 60.445 45.833 14.00 4.70 0.00 3.58
2001 2920 3.929610 GGCTGAAGATCTTGTCAGTGTAC 59.070 47.826 20.50 8.15 42.72 2.90
2007 2926 5.474578 AGATCTTGTCAGTGTACATGTGT 57.525 39.130 9.11 0.00 0.00 3.72
2052 2971 0.179200 GTGCCAATCTTACAACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
2355 3274 3.072038 TCTGATGGCAGGTGAATAGATGG 59.928 47.826 0.00 0.00 42.53 3.51
2359 3278 1.221414 GCAGGTGAATAGATGGTCGC 58.779 55.000 0.00 0.00 0.00 5.19
2694 3716 2.450476 AGGAGCATCAATTTGACACCC 58.550 47.619 0.15 1.63 36.25 4.61
2734 3756 3.572632 ATACCTCATCTGTGCTGCATT 57.427 42.857 5.27 0.00 0.00 3.56
2957 3979 3.431922 AGCATTCGCATCTGGAAAATG 57.568 42.857 0.00 0.00 42.27 2.32
2976 3998 5.441718 AATGGGTTGCAAGAGATTAGAGA 57.558 39.130 0.00 0.00 0.00 3.10
2977 3999 4.478206 TGGGTTGCAAGAGATTAGAGAG 57.522 45.455 0.00 0.00 0.00 3.20
2995 4017 5.205056 AGAGAGCTACTGCCATACTTTAGT 58.795 41.667 0.00 0.00 40.80 2.24
3181 9198 5.937975 ATTTGTGGATTGGTTAGGATTGG 57.062 39.130 0.00 0.00 0.00 3.16
3183 9200 4.666412 TGTGGATTGGTTAGGATTGGAA 57.334 40.909 0.00 0.00 0.00 3.53
3229 9246 7.952930 AGGATTCCACTGTACTACATCTCATAT 59.047 37.037 5.29 0.00 0.00 1.78
3230 9247 8.247562 GGATTCCACTGTACTACATCTCATATC 58.752 40.741 0.00 0.00 0.00 1.63
3258 9276 2.373169 AGCATCCACTCAAACCTCTTGA 59.627 45.455 0.00 0.00 0.00 3.02
3261 9279 4.557496 GCATCCACTCAAACCTCTTGAAAC 60.557 45.833 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 8.893219 TCGCATTGATATCTTGAAACTAGATT 57.107 30.769 3.98 0.00 34.35 2.40
62 63 9.619316 CAAATTATGAACTATTTTCACCGTTGA 57.381 29.630 0.00 0.00 0.00 3.18
66 67 9.236691 CATCCAAATTATGAACTATTTTCACCG 57.763 33.333 0.00 0.00 0.00 4.94
68 69 9.034544 GGCATCCAAATTATGAACTATTTTCAC 57.965 33.333 0.00 0.00 0.00 3.18
77 80 5.772825 TGCTAGGCATCCAAATTATGAAC 57.227 39.130 0.00 0.00 31.71 3.18
80 83 6.339730 TGTTTTGCTAGGCATCCAAATTATG 58.660 36.000 0.00 0.00 38.76 1.90
123 126 7.334421 ACTGTACATCTTATTTTTGTGCGATCT 59.666 33.333 0.00 0.00 0.00 2.75
128 131 8.795786 TTTCACTGTACATCTTATTTTTGTGC 57.204 30.769 0.00 0.00 0.00 4.57
156 182 9.442047 CCCCATCTGTCAATATTATAGAGTTTC 57.558 37.037 0.00 0.00 0.00 2.78
159 185 6.501805 TGCCCCATCTGTCAATATTATAGAGT 59.498 38.462 0.00 0.00 0.00 3.24
166 192 3.290710 GTGTGCCCCATCTGTCAATATT 58.709 45.455 0.00 0.00 0.00 1.28
170 196 0.537143 GTGTGTGCCCCATCTGTCAA 60.537 55.000 0.00 0.00 0.00 3.18
177 203 0.039035 AAATACCGTGTGTGCCCCAT 59.961 50.000 0.00 0.00 0.00 4.00
180 206 1.132262 CATCAAATACCGTGTGTGCCC 59.868 52.381 0.00 0.00 0.00 5.36
181 207 1.467374 GCATCAAATACCGTGTGTGCC 60.467 52.381 0.00 0.00 0.00 5.01
189 215 4.339429 CGTACCTTTTGCATCAAATACCG 58.661 43.478 0.00 0.00 33.19 4.02
303 329 5.043356 ACAGCCTCCCTTTCCCTAATAAAAT 60.043 40.000 0.00 0.00 0.00 1.82
322 348 2.813754 TGTTACAGCATCTTCAACAGCC 59.186 45.455 0.00 0.00 0.00 4.85
331 357 9.125026 CCCTATTTTATTCTTGTTACAGCATCT 57.875 33.333 0.00 0.00 0.00 2.90
335 361 7.556635 AGACCCCTATTTTATTCTTGTTACAGC 59.443 37.037 0.00 0.00 0.00 4.40
338 364 8.803397 ACAGACCCCTATTTTATTCTTGTTAC 57.197 34.615 0.00 0.00 0.00 2.50
343 369 8.107196 AGATGACAGACCCCTATTTTATTCTT 57.893 34.615 0.00 0.00 0.00 2.52
362 389 9.722056 AAGCATCGTTTTGAATTATTAGATGAC 57.278 29.630 6.33 0.00 37.12 3.06
370 400 8.050778 TGAACCTAAGCATCGTTTTGAATTAT 57.949 30.769 0.00 0.00 0.00 1.28
382 412 6.341316 TCTGTTGTAGATGAACCTAAGCATC 58.659 40.000 0.00 0.00 40.85 3.91
434 464 9.730705 CATCTTGGATGCCTAAAAGAGATTATA 57.269 33.333 0.00 0.00 32.50 0.98
436 466 6.488006 GCATCTTGGATGCCTAAAAGAGATTA 59.512 38.462 18.37 0.00 39.01 1.75
438 468 4.826183 GCATCTTGGATGCCTAAAAGAGAT 59.174 41.667 18.37 0.00 39.01 2.75
439 469 4.080129 AGCATCTTGGATGCCTAAAAGAGA 60.080 41.667 23.37 0.00 45.59 3.10
440 470 4.205587 AGCATCTTGGATGCCTAAAAGAG 58.794 43.478 23.37 0.00 45.59 2.85
441 471 4.202441 GAGCATCTTGGATGCCTAAAAGA 58.798 43.478 23.37 0.00 45.59 2.52
442 472 3.949754 TGAGCATCTTGGATGCCTAAAAG 59.050 43.478 23.37 0.00 45.59 2.27
443 473 3.966979 TGAGCATCTTGGATGCCTAAAA 58.033 40.909 23.37 7.26 45.59 1.52
444 474 3.650281 TGAGCATCTTGGATGCCTAAA 57.350 42.857 23.37 8.69 45.59 1.85
515 550 0.460987 AGAGCCGAGAGCCGATTTTG 60.461 55.000 0.00 0.00 45.47 2.44
516 551 0.460987 CAGAGCCGAGAGCCGATTTT 60.461 55.000 0.00 0.00 45.47 1.82
517 552 1.142748 CAGAGCCGAGAGCCGATTT 59.857 57.895 0.00 0.00 45.47 2.17
518 553 1.323271 TTCAGAGCCGAGAGCCGATT 61.323 55.000 0.00 0.00 45.47 3.34
519 554 1.112315 ATTCAGAGCCGAGAGCCGAT 61.112 55.000 0.00 0.00 45.47 4.18
520 555 0.465642 TATTCAGAGCCGAGAGCCGA 60.466 55.000 0.00 0.00 45.47 5.54
521 556 0.039617 CTATTCAGAGCCGAGAGCCG 60.040 60.000 0.00 0.00 45.47 5.52
522 557 1.036707 ACTATTCAGAGCCGAGAGCC 58.963 55.000 0.00 0.00 45.47 4.70
523 558 1.407258 ACACTATTCAGAGCCGAGAGC 59.593 52.381 0.00 0.00 44.25 4.09
524 559 3.490078 GGAACACTATTCAGAGCCGAGAG 60.490 52.174 0.00 0.00 0.00 3.20
525 560 2.427453 GGAACACTATTCAGAGCCGAGA 59.573 50.000 0.00 0.00 0.00 4.04
526 561 2.428890 AGGAACACTATTCAGAGCCGAG 59.571 50.000 0.00 0.00 0.00 4.63
529 564 4.579869 TGAAAGGAACACTATTCAGAGCC 58.420 43.478 0.00 0.00 0.00 4.70
546 581 6.971184 GCTTGTGATATTTGGACATCTGAAAG 59.029 38.462 0.00 0.00 0.00 2.62
550 585 5.008415 GGAGCTTGTGATATTTGGACATCTG 59.992 44.000 0.00 0.00 0.00 2.90
551 586 5.104193 AGGAGCTTGTGATATTTGGACATCT 60.104 40.000 0.00 0.00 0.00 2.90
552 587 5.128919 AGGAGCTTGTGATATTTGGACATC 58.871 41.667 0.00 0.00 0.00 3.06
554 589 4.517285 GAGGAGCTTGTGATATTTGGACA 58.483 43.478 0.00 0.00 0.00 4.02
557 592 2.874701 CCGAGGAGCTTGTGATATTTGG 59.125 50.000 0.00 0.00 0.00 3.28
558 593 3.797039 TCCGAGGAGCTTGTGATATTTG 58.203 45.455 0.00 0.00 0.00 2.32
559 594 4.141620 ACATCCGAGGAGCTTGTGATATTT 60.142 41.667 0.00 0.00 0.00 1.40
560 595 3.389329 ACATCCGAGGAGCTTGTGATATT 59.611 43.478 0.00 0.00 0.00 1.28
561 596 2.968574 ACATCCGAGGAGCTTGTGATAT 59.031 45.455 0.00 0.00 0.00 1.63
562 597 2.362397 GACATCCGAGGAGCTTGTGATA 59.638 50.000 1.97 0.00 0.00 2.15
563 598 1.137872 GACATCCGAGGAGCTTGTGAT 59.862 52.381 1.97 0.00 0.00 3.06
564 599 0.532573 GACATCCGAGGAGCTTGTGA 59.467 55.000 1.97 0.00 0.00 3.58
568 603 0.984230 TTTGGACATCCGAGGAGCTT 59.016 50.000 0.00 0.00 39.43 3.74
569 604 1.207791 ATTTGGACATCCGAGGAGCT 58.792 50.000 0.00 0.00 39.43 4.09
571 606 2.434336 TGGTATTTGGACATCCGAGGAG 59.566 50.000 0.00 0.00 39.43 3.69
572 607 2.169769 GTGGTATTTGGACATCCGAGGA 59.830 50.000 0.00 0.00 39.43 3.71
573 608 2.093181 TGTGGTATTTGGACATCCGAGG 60.093 50.000 0.00 0.00 39.43 4.63
574 609 3.260475 TGTGGTATTTGGACATCCGAG 57.740 47.619 0.00 0.00 39.43 4.63
599 660 4.749598 TCATATACGCAAGATTCGTGCAAT 59.250 37.500 21.59 16.33 42.33 3.56
606 667 8.128582 TCCAAAATGTTCATATACGCAAGATTC 58.871 33.333 0.00 0.00 43.62 2.52
613 674 4.917415 GGCATCCAAAATGTTCATATACGC 59.083 41.667 0.00 0.00 0.00 4.42
623 689 8.156165 TCTGAAAATTTTAGGCATCCAAAATGT 58.844 29.630 2.75 0.00 35.19 2.71
628 694 8.137745 AGAATCTGAAAATTTTAGGCATCCAA 57.862 30.769 2.75 0.00 0.00 3.53
986 1905 2.027385 CCGACATGTGGAGAGATCTGA 58.973 52.381 9.73 0.00 0.00 3.27
1231 2150 2.164332 TAGTTGGAGGAGGCGGAGGT 62.164 60.000 0.00 0.00 0.00 3.85
1590 2509 3.047718 GACGTCGTCGAGGATGGCA 62.048 63.158 24.68 0.00 40.62 4.92
1602 2521 1.446792 AAGCATGCAGGAGACGTCG 60.447 57.895 21.98 0.00 0.00 5.12
1863 2782 4.038763 CCCTTTGCTGTCAATATGATGCAT 59.961 41.667 0.00 0.00 38.06 3.96
1947 2866 0.670546 AGTCCACCAATGCGAGAACG 60.671 55.000 0.00 0.00 42.93 3.95
1950 2869 0.247460 CAGAGTCCACCAATGCGAGA 59.753 55.000 0.00 0.00 0.00 4.04
1995 2914 1.055849 TGGAGCCACACATGTACACT 58.944 50.000 0.00 0.00 0.00 3.55
2001 2920 1.608055 TGTTCTTGGAGCCACACATG 58.392 50.000 0.00 0.00 0.00 3.21
2007 2926 0.396435 ACGACATGTTCTTGGAGCCA 59.604 50.000 0.00 0.00 0.00 4.75
2052 2971 0.946221 CGCCGAGCCACTTGATATCC 60.946 60.000 0.00 0.00 0.00 2.59
2355 3274 3.120649 ACAAAGATAAAGAGCAACGCGAC 60.121 43.478 15.93 0.83 0.00 5.19
2359 3278 5.747565 TGAACACAAAGATAAAGAGCAACG 58.252 37.500 0.00 0.00 0.00 4.10
2407 3326 8.557864 CAAGAAGATGAGAATGTATTGGATCAC 58.442 37.037 0.00 0.00 0.00 3.06
2486 3406 6.787225 ACTACGTAATTCTCAGTCACAGATC 58.213 40.000 0.00 0.00 0.00 2.75
2734 3756 0.958382 GGGACTGCCGCACAAATGTA 60.958 55.000 0.00 0.00 33.83 2.29
2957 3979 3.118445 AGCTCTCTAATCTCTTGCAACCC 60.118 47.826 0.00 0.00 0.00 4.11
3003 4025 6.838382 ACAGATAAACATAAGTATCCCCACC 58.162 40.000 0.00 0.00 0.00 4.61
3071 5761 8.356657 ACAATCTACGAAAATCATTTCAACCAA 58.643 29.630 0.00 0.00 44.24 3.67
3074 5764 9.993881 CAAACAATCTACGAAAATCATTTCAAC 57.006 29.630 0.00 0.00 44.24 3.18
3075 5765 9.190858 CCAAACAATCTACGAAAATCATTTCAA 57.809 29.630 0.00 0.00 44.24 2.69
3076 5766 8.572185 TCCAAACAATCTACGAAAATCATTTCA 58.428 29.630 0.00 0.00 44.24 2.69
3077 5767 8.964420 TCCAAACAATCTACGAAAATCATTTC 57.036 30.769 0.00 0.00 41.27 2.17
3078 5768 8.028938 CCTCCAAACAATCTACGAAAATCATTT 58.971 33.333 0.00 0.00 0.00 2.32
3079 5769 7.393234 TCCTCCAAACAATCTACGAAAATCATT 59.607 33.333 0.00 0.00 0.00 2.57
3163 9180 3.699538 GGTTCCAATCCTAACCAATCCAC 59.300 47.826 0.00 0.00 43.84 4.02
3229 9246 4.518970 GGTTTGAGTGGATGCTAACTTTGA 59.481 41.667 0.00 0.00 0.00 2.69
3230 9247 4.520492 AGGTTTGAGTGGATGCTAACTTTG 59.480 41.667 0.00 0.00 0.00 2.77
3258 9276 2.458620 TGGGAAACAAAGGGTTCGTTT 58.541 42.857 0.00 0.00 39.29 3.60
3261 9279 2.625790 TGATTGGGAAACAAAGGGTTCG 59.374 45.455 0.00 0.00 43.46 3.95


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

AutoCloner maintained by Alex Coulton.