Multiple sequence alignment - TraesCS1D01G354300

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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 TraesCS1D01G354300 chr1D 100.000 2656 0 0 1 2656 439505705 439508360 0.000000e+00 4905.0
1 TraesCS1D01G354300 chr1D 94.609 575 19 1 2082 2656 439553980 439554542 0.000000e+00 880.0
2 TraesCS1D01G354300 chr1A 93.046 1625 74 24 724 2325 539316993 539315385 0.000000e+00 2338.0
3 TraesCS1D01G354300 chr1A 94.097 288 12 3 17 301 539317713 539317428 1.460000e-117 433.0
4 TraesCS1D01G354300 chr1A 82.985 335 28 15 336 658 539317427 539317110 2.600000e-70 276.0
5 TraesCS1D01G354300 chr1A 92.982 171 9 1 2362 2532 539314829 539314662 2.040000e-61 246.0
6 TraesCS1D01G354300 chr1A 89.381 113 12 0 2544 2656 539288673 539288561 2.760000e-30 143.0
7 TraesCS1D01G354300 chr1B 90.937 1291 55 15 560 1801 596307529 596308806 0.000000e+00 1679.0
8 TraesCS1D01G354300 chr1B 85.521 518 31 16 1 515 596307036 596307512 3.950000e-138 501.0
9 TraesCS1D01G354300 chr1B 93.548 62 4 0 1980 2041 596313525 596313586 2.820000e-15 93.5
10 TraesCS1D01G354300 chr1B 93.617 47 2 1 518 564 428647066 428647021 4.740000e-08 69.4
11 TraesCS1D01G354300 chr4B 97.674 43 1 0 516 558 39292632 39292590 1.020000e-09 75.0
12 TraesCS1D01G354300 chr4B 97.561 41 1 0 518 558 15599907 15599867 1.320000e-08 71.3
13 TraesCS1D01G354300 chr2D 97.674 43 1 0 518 560 646424969 646425011 1.020000e-09 75.0
14 TraesCS1D01G354300 chr2D 95.349 43 2 0 518 560 421789905 421789947 4.740000e-08 69.4
15 TraesCS1D01G354300 chr7B 95.349 43 2 0 518 560 513813931 513813889 4.740000e-08 69.4
16 TraesCS1D01G354300 chr5D 95.349 43 2 0 518 560 352456282 352456324 4.740000e-08 69.4
17 TraesCS1D01G354300 chr5B 95.349 43 2 0 518 560 653710095 653710053 4.740000e-08 69.4
18 TraesCS1D01G354300 chr6A 93.478 46 2 1 519 564 79953767 79953811 1.710000e-07 67.6


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 TraesCS1D01G354300 chr1D 439505705 439508360 2655 False 4905.00 4905 100.0000 1 2656 1 chr1D.!!$F1 2655
1 TraesCS1D01G354300 chr1D 439553980 439554542 562 False 880.00 880 94.6090 2082 2656 1 chr1D.!!$F2 574
2 TraesCS1D01G354300 chr1A 539314662 539317713 3051 True 823.25 2338 90.7775 17 2532 4 chr1A.!!$R2 2515
3 TraesCS1D01G354300 chr1B 596307036 596308806 1770 False 1090.00 1679 88.2290 1 1801 2 chr1B.!!$F2 1800

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
630 655 0.036105 TAGCTCCACATGCAGGTGTG 60.036 55.0 27.83 20.17 46.98 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2029 2188 0.749649 ATGCTAACAGAGAGAGCCCG 59.25 55.0 0.0 0.0 35.24 6.13 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
177 179 6.644592 TGCCCTTAATCTTTCGTTTTTCATTG 59.355 34.615 0.00 0.00 0.00 2.82
190 192 2.715749 TTCATTGCATGGACCGAGAT 57.284 45.000 0.00 0.00 0.00 2.75
301 306 8.088981 ACTCATCTATTTTAATAGGGTAGTGCG 58.911 37.037 9.08 0.00 39.06 5.34
302 307 7.959175 TCATCTATTTTAATAGGGTAGTGCGT 58.041 34.615 9.08 0.00 39.06 5.24
303 308 7.870954 TCATCTATTTTAATAGGGTAGTGCGTG 59.129 37.037 9.08 0.00 39.06 5.34
304 309 5.987347 TCTATTTTAATAGGGTAGTGCGTGC 59.013 40.000 9.08 0.00 39.06 5.34
305 310 2.607631 TTAATAGGGTAGTGCGTGCC 57.392 50.000 0.00 0.00 0.00 5.01
306 311 0.386476 TAATAGGGTAGTGCGTGCCG 59.614 55.000 0.00 0.00 0.00 5.69
307 312 1.324740 AATAGGGTAGTGCGTGCCGA 61.325 55.000 0.00 0.00 0.00 5.54
308 313 1.113517 ATAGGGTAGTGCGTGCCGAT 61.114 55.000 0.00 0.00 0.00 4.18
309 314 1.731433 TAGGGTAGTGCGTGCCGATC 61.731 60.000 0.00 0.00 0.00 3.69
310 315 2.585247 GGTAGTGCGTGCCGATCC 60.585 66.667 0.00 0.00 0.00 3.36
311 316 2.183300 GTAGTGCGTGCCGATCCA 59.817 61.111 0.00 0.00 0.00 3.41
312 317 1.447140 GTAGTGCGTGCCGATCCAA 60.447 57.895 0.00 0.00 0.00 3.53
313 318 0.810031 GTAGTGCGTGCCGATCCAAT 60.810 55.000 0.00 0.00 0.00 3.16
314 319 0.809636 TAGTGCGTGCCGATCCAATG 60.810 55.000 0.00 0.00 0.00 2.82
315 320 2.046411 TGCGTGCCGATCCAATGT 60.046 55.556 0.00 0.00 0.00 2.71
316 321 1.087202 GTGCGTGCCGATCCAATGTA 61.087 55.000 0.00 0.00 0.00 2.29
317 322 0.809636 TGCGTGCCGATCCAATGTAG 60.810 55.000 0.00 0.00 0.00 2.74
318 323 0.810031 GCGTGCCGATCCAATGTAGT 60.810 55.000 0.00 0.00 0.00 2.73
319 324 0.930310 CGTGCCGATCCAATGTAGTG 59.070 55.000 0.00 0.00 0.00 2.74
320 325 0.657840 GTGCCGATCCAATGTAGTGC 59.342 55.000 0.00 0.00 0.00 4.40
321 326 0.251634 TGCCGATCCAATGTAGTGCA 59.748 50.000 0.00 0.00 0.00 4.57
322 327 0.940126 GCCGATCCAATGTAGTGCAG 59.060 55.000 0.00 0.00 0.00 4.41
323 328 1.743772 GCCGATCCAATGTAGTGCAGT 60.744 52.381 0.00 0.00 0.00 4.40
324 329 2.483013 GCCGATCCAATGTAGTGCAGTA 60.483 50.000 0.00 0.00 0.00 2.74
325 330 3.384668 CCGATCCAATGTAGTGCAGTAG 58.615 50.000 0.18 0.00 0.00 2.57
326 331 3.181475 CCGATCCAATGTAGTGCAGTAGT 60.181 47.826 0.18 0.00 0.00 2.73
327 332 4.037565 CCGATCCAATGTAGTGCAGTAGTA 59.962 45.833 0.18 0.00 0.00 1.82
328 333 5.451381 CCGATCCAATGTAGTGCAGTAGTAA 60.451 44.000 0.18 0.00 0.00 2.24
329 334 6.216569 CGATCCAATGTAGTGCAGTAGTAAT 58.783 40.000 0.18 0.00 0.00 1.89
330 335 7.368059 CGATCCAATGTAGTGCAGTAGTAATA 58.632 38.462 0.18 0.00 0.00 0.98
331 336 7.326305 CGATCCAATGTAGTGCAGTAGTAATAC 59.674 40.741 0.18 0.00 32.61 1.89
332 337 7.655521 TCCAATGTAGTGCAGTAGTAATACT 57.344 36.000 0.18 0.00 33.08 2.12
333 338 8.074613 TCCAATGTAGTGCAGTAGTAATACTT 57.925 34.615 0.18 0.00 33.08 2.24
334 339 9.192642 TCCAATGTAGTGCAGTAGTAATACTTA 57.807 33.333 0.18 0.00 33.08 2.24
383 388 2.105477 GGCATCATGTGGGAGTAGTCAT 59.895 50.000 0.00 0.00 0.00 3.06
434 439 3.477530 ACCCTGTCAAAGTAAACTCAGC 58.522 45.455 0.00 0.00 0.00 4.26
443 448 3.214696 AGTAAACTCAGCCAGCAAGTT 57.785 42.857 5.02 5.02 34.81 2.66
449 454 0.761187 TCAGCCAGCAAGTTCAGTCT 59.239 50.000 0.00 0.00 0.00 3.24
476 484 4.436332 ACCCGTTACCGATTTAAGCTTAG 58.564 43.478 6.24 0.00 35.63 2.18
488 496 2.737830 GCTTAGCTAGCCGAGGGG 59.262 66.667 12.13 0.00 44.48 4.79
508 518 2.483714 GGCAGAGCGGATGATGAACTAA 60.484 50.000 0.00 0.00 0.00 2.24
518 539 6.620678 CGGATGATGAACTAAATTTGTTGGT 58.379 36.000 0.00 0.00 0.00 3.67
521 542 8.739972 GGATGATGAACTAAATTTGTTGGTACT 58.260 33.333 0.00 0.00 0.00 2.73
524 545 8.573035 TGATGAACTAAATTTGTTGGTACTTCC 58.427 33.333 0.00 0.00 0.00 3.46
525 546 8.706322 ATGAACTAAATTTGTTGGTACTTCCT 57.294 30.769 0.00 0.00 37.07 3.36
526 547 8.161699 TGAACTAAATTTGTTGGTACTTCCTC 57.838 34.615 0.00 0.00 37.07 3.71
527 548 7.229907 TGAACTAAATTTGTTGGTACTTCCTCC 59.770 37.037 0.00 0.00 37.07 4.30
528 549 5.704053 ACTAAATTTGTTGGTACTTCCTCCG 59.296 40.000 0.00 0.00 37.07 4.63
530 551 3.564053 TTTGTTGGTACTTCCTCCGTT 57.436 42.857 0.00 0.00 37.07 4.44
531 552 2.825861 TGTTGGTACTTCCTCCGTTC 57.174 50.000 0.00 0.00 37.07 3.95
532 553 1.000060 TGTTGGTACTTCCTCCGTTCG 60.000 52.381 0.00 0.00 37.07 3.95
533 554 0.604578 TTGGTACTTCCTCCGTTCGG 59.395 55.000 4.74 4.74 37.07 4.30
534 555 0.251297 TGGTACTTCCTCCGTTCGGA 60.251 55.000 13.34 13.34 37.07 4.55
535 556 0.890683 GGTACTTCCTCCGTTCGGAA 59.109 55.000 14.79 0.00 38.18 4.30
536 557 1.273327 GGTACTTCCTCCGTTCGGAAA 59.727 52.381 14.79 6.77 39.86 3.13
537 558 2.093816 GGTACTTCCTCCGTTCGGAAAT 60.094 50.000 14.79 2.39 39.86 2.17
538 559 3.131046 GGTACTTCCTCCGTTCGGAAATA 59.869 47.826 14.79 1.22 39.86 1.40
539 560 3.242549 ACTTCCTCCGTTCGGAAATAC 57.757 47.619 14.79 0.00 39.86 1.89
540 561 2.830321 ACTTCCTCCGTTCGGAAATACT 59.170 45.455 14.79 0.00 39.86 2.12
541 562 3.260128 ACTTCCTCCGTTCGGAAATACTT 59.740 43.478 14.79 0.00 39.86 2.24
542 563 3.241067 TCCTCCGTTCGGAAATACTTG 57.759 47.619 14.79 1.97 33.41 3.16
543 564 2.564062 TCCTCCGTTCGGAAATACTTGT 59.436 45.455 14.79 0.00 33.41 3.16
544 565 2.928116 CCTCCGTTCGGAAATACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
545 566 2.597305 CTCCGTTCGGAAATACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
546 567 2.228582 TCCGTTCGGAAATACTTGTCGA 59.771 45.455 11.66 0.00 0.00 4.20
547 568 2.988493 CCGTTCGGAAATACTTGTCGAA 59.012 45.455 5.19 0.00 37.48 3.71
548 569 3.060363 CCGTTCGGAAATACTTGTCGAAG 59.940 47.826 5.19 0.00 39.89 3.79
549 570 3.916172 CGTTCGGAAATACTTGTCGAAGA 59.084 43.478 0.00 0.00 39.89 2.87
550 571 4.383649 CGTTCGGAAATACTTGTCGAAGAA 59.616 41.667 0.00 0.00 39.69 2.52
551 572 5.107760 CGTTCGGAAATACTTGTCGAAGAAA 60.108 40.000 0.00 0.00 39.69 2.52
552 573 6.400727 CGTTCGGAAATACTTGTCGAAGAAAT 60.401 38.462 0.00 0.00 39.69 2.17
553 574 6.403333 TCGGAAATACTTGTCGAAGAAATG 57.597 37.500 0.00 0.00 39.69 2.32
554 575 5.350365 TCGGAAATACTTGTCGAAGAAATGG 59.650 40.000 0.00 0.00 39.69 3.16
555 576 5.350365 CGGAAATACTTGTCGAAGAAATGGA 59.650 40.000 0.00 0.00 39.69 3.41
556 577 6.037172 CGGAAATACTTGTCGAAGAAATGGAT 59.963 38.462 0.00 0.00 39.69 3.41
557 578 7.189512 GGAAATACTTGTCGAAGAAATGGATG 58.810 38.462 0.00 0.00 39.69 3.51
558 579 7.148239 GGAAATACTTGTCGAAGAAATGGATGT 60.148 37.037 0.00 0.00 39.69 3.06
586 607 1.968017 CAGCAAGCGCCAAGAAGGA 60.968 57.895 2.29 0.00 41.22 3.36
630 655 0.036105 TAGCTCCACATGCAGGTGTG 60.036 55.000 27.83 20.17 46.98 3.82
631 656 1.601759 GCTCCACATGCAGGTGTGT 60.602 57.895 27.83 7.84 46.21 3.72
633 661 1.881925 GCTCCACATGCAGGTGTGTAA 60.882 52.381 27.83 11.02 46.21 2.41
695 792 1.676635 GTGCTTCCATGCCTGCAGA 60.677 57.895 17.39 0.00 36.03 4.26
737 842 3.488778 TTTGTTTAGAACCCTACGGCA 57.511 42.857 0.00 0.00 0.00 5.69
746 851 1.041447 ACCCTACGGCATCGCTAGTT 61.041 55.000 0.00 0.00 40.63 2.24
790 895 2.335092 CTGCAGCCGGAATCCCATCT 62.335 60.000 5.05 0.00 0.00 2.90
935 1058 1.031235 TTAACGTCTCACCACCGTCA 58.969 50.000 0.00 0.00 32.95 4.35
967 1091 1.246737 AAAACAGCAGCTAGGCAGGC 61.247 55.000 0.00 0.00 35.83 4.85
975 1102 0.689080 AGCTAGGCAGGCAGCTAAGA 60.689 55.000 16.07 0.00 46.14 2.10
976 1103 0.179000 GCTAGGCAGGCAGCTAAGAA 59.821 55.000 0.81 0.00 44.79 2.52
977 1104 1.809651 GCTAGGCAGGCAGCTAAGAAG 60.810 57.143 0.81 0.00 44.79 2.85
1038 1165 2.124151 ATCCATGGAGCCGTTGCC 60.124 61.111 21.33 0.00 38.69 4.52
1050 1177 2.185608 GTTGCCGCTCTCCTCCTC 59.814 66.667 0.00 0.00 0.00 3.71
1060 1187 3.347590 TCCTCCTCGGCTCCCTCA 61.348 66.667 0.00 0.00 0.00 3.86
1062 1189 1.764054 CCTCCTCGGCTCCCTCATT 60.764 63.158 0.00 0.00 0.00 2.57
1257 1408 1.728672 GTCCTCCTCCGACGACATC 59.271 63.158 0.00 0.00 0.00 3.06
1258 1409 1.453379 TCCTCCTCCGACGACATCC 60.453 63.158 0.00 0.00 0.00 3.51
1293 1449 1.672737 CCCTAACCCCGTCGTGTTAAC 60.673 57.143 0.00 0.00 0.00 2.01
1295 1451 0.320050 TAACCCCGTCGTGTTAACCC 59.680 55.000 2.48 0.00 0.00 4.11
1558 1714 3.692406 GGAGGTGAGGCCGTCGTT 61.692 66.667 0.00 0.00 43.70 3.85
1640 1796 4.506255 GCCAAGTGCCCGGCCTAT 62.506 66.667 7.03 0.00 42.82 2.57
1657 1816 3.504520 GCCTATACTACTGAGGAGTGAGC 59.495 52.174 7.80 1.04 33.21 4.26
1668 1827 1.373497 GAGTGAGCAGTGTGGACGG 60.373 63.158 0.00 0.00 0.00 4.79
1744 1903 1.136147 CCACGAACGTAGTCGGAGG 59.864 63.158 13.69 10.80 45.00 4.30
1795 1954 1.620413 CGCGTAGGTTTGGGTCGTTC 61.620 60.000 0.00 0.00 0.00 3.95
1844 2003 3.432252 CCATCGAGTACTTGTTGTGGTTC 59.568 47.826 16.60 0.00 0.00 3.62
1848 2007 3.060740 CGAGTACTTGTTGTGGTTCGAAC 60.061 47.826 20.14 20.14 32.69 3.95
1943 2102 5.752892 AGTCGTTCGTCATATATGAGTGT 57.247 39.130 15.83 0.00 37.51 3.55
1989 2148 1.066430 TGACCTCCATTTACACTCCGC 60.066 52.381 0.00 0.00 0.00 5.54
2010 2169 2.557056 CCATGGATAATGAGCAGCCTTG 59.443 50.000 5.56 0.00 38.72 3.61
2029 2188 7.440856 CAGCCTTGGTAGAGATATTTTCTTCTC 59.559 40.741 0.00 0.00 38.93 2.87
2044 2203 2.026169 TCTTCTCGGGCTCTCTCTGTTA 60.026 50.000 0.00 0.00 0.00 2.41
2052 2211 2.167281 GGCTCTCTCTGTTAGCATGTCA 59.833 50.000 0.00 0.00 38.01 3.58
2234 2417 2.029828 TGCTTTCGGTGTTGTTGTTGTT 60.030 40.909 0.00 0.00 0.00 2.83
2235 2418 2.344142 GCTTTCGGTGTTGTTGTTGTTG 59.656 45.455 0.00 0.00 0.00 3.33
2236 2419 3.570559 CTTTCGGTGTTGTTGTTGTTGT 58.429 40.909 0.00 0.00 0.00 3.32
2237 2420 3.644884 TTCGGTGTTGTTGTTGTTGTT 57.355 38.095 0.00 0.00 0.00 2.83
2238 2421 2.935042 TCGGTGTTGTTGTTGTTGTTG 58.065 42.857 0.00 0.00 0.00 3.33
2239 2422 2.293677 TCGGTGTTGTTGTTGTTGTTGT 59.706 40.909 0.00 0.00 0.00 3.32
2240 2423 3.053455 CGGTGTTGTTGTTGTTGTTGTT 58.947 40.909 0.00 0.00 0.00 2.83
2241 2424 3.121194 CGGTGTTGTTGTTGTTGTTGTTG 60.121 43.478 0.00 0.00 0.00 3.33
2242 2425 3.804873 GGTGTTGTTGTTGTTGTTGTTGT 59.195 39.130 0.00 0.00 0.00 3.32
2243 2426 4.271291 GGTGTTGTTGTTGTTGTTGTTGTT 59.729 37.500 0.00 0.00 0.00 2.83
2244 2427 5.193936 GTGTTGTTGTTGTTGTTGTTGTTG 58.806 37.500 0.00 0.00 0.00 3.33
2245 2428 4.870426 TGTTGTTGTTGTTGTTGTTGTTGT 59.130 33.333 0.00 0.00 0.00 3.32
2292 2475 0.542938 CCTCTGGTGGTCTGTCCTGA 60.543 60.000 0.00 0.00 37.07 3.86
2339 2616 0.390124 TTGCCGTGTACTTTCTCCGT 59.610 50.000 0.00 0.00 0.00 4.69
2465 3167 6.653320 TCGTGCTGGTTCAAATCTTAACTAAT 59.347 34.615 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 3.555547 AGCAAACTTCAAATTCGGCAAAC 59.444 39.130 0.00 0.00 0.00 2.93
155 157 7.636259 TGCAATGAAAAACGAAAGATTAAGG 57.364 32.000 0.00 0.00 0.00 2.69
177 179 1.957177 TCTACTCATCTCGGTCCATGC 59.043 52.381 0.00 0.00 0.00 4.06
190 192 3.244345 CGACGTTTGTTTGCTTCTACTCA 59.756 43.478 0.00 0.00 0.00 3.41
248 253 7.821359 AGATGGGTAGATTAATTGATCATGTCG 59.179 37.037 12.29 0.00 0.00 4.35
301 306 0.657840 GCACTACATTGGATCGGCAC 59.342 55.000 0.00 0.00 0.00 5.01
302 307 0.251634 TGCACTACATTGGATCGGCA 59.748 50.000 0.00 0.00 0.00 5.69
303 308 0.940126 CTGCACTACATTGGATCGGC 59.060 55.000 0.00 0.00 0.00 5.54
304 309 2.315925 ACTGCACTACATTGGATCGG 57.684 50.000 0.00 0.00 0.00 4.18
305 310 4.046938 ACTACTGCACTACATTGGATCG 57.953 45.455 0.00 0.00 0.00 3.69
306 311 8.361139 AGTATTACTACTGCACTACATTGGATC 58.639 37.037 0.00 0.00 36.81 3.36
307 312 8.251383 AGTATTACTACTGCACTACATTGGAT 57.749 34.615 0.00 0.00 36.81 3.41
308 313 7.655521 AGTATTACTACTGCACTACATTGGA 57.344 36.000 0.00 0.00 36.81 3.53
309 314 9.982651 ATAAGTATTACTACTGCACTACATTGG 57.017 33.333 0.00 0.00 38.23 3.16
383 388 5.514834 CCCTCCCTTTTACTGAACTGAATCA 60.515 44.000 0.00 0.00 0.00 2.57
434 439 4.246458 GGTAGTAAGACTGAACTTGCTGG 58.754 47.826 15.00 0.00 41.40 4.85
488 496 2.515926 TAGTTCATCATCCGCTCTGC 57.484 50.000 0.00 0.00 0.00 4.26
508 518 4.094830 ACGGAGGAAGTACCAACAAATT 57.905 40.909 0.00 0.00 42.04 1.82
521 542 3.007182 ACAAGTATTTCCGAACGGAGGAA 59.993 43.478 15.34 9.10 46.06 3.36
522 543 2.564062 ACAAGTATTTCCGAACGGAGGA 59.436 45.455 15.34 9.43 46.06 3.71
523 544 2.928116 GACAAGTATTTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
524 545 2.597305 CGACAAGTATTTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
525 546 2.228582 TCGACAAGTATTTCCGAACGGA 59.771 45.455 12.04 12.04 43.52 4.69
526 547 2.598589 TCGACAAGTATTTCCGAACGG 58.401 47.619 6.94 6.94 0.00 4.44
527 548 3.916172 TCTTCGACAAGTATTTCCGAACG 59.084 43.478 0.00 0.00 35.71 3.95
528 549 5.834239 TTCTTCGACAAGTATTTCCGAAC 57.166 39.130 0.00 0.00 35.71 3.95
530 551 5.350365 CCATTTCTTCGACAAGTATTTCCGA 59.650 40.000 0.00 0.00 0.00 4.55
531 552 5.350365 TCCATTTCTTCGACAAGTATTTCCG 59.650 40.000 0.00 0.00 0.00 4.30
532 553 6.737254 TCCATTTCTTCGACAAGTATTTCC 57.263 37.500 0.00 0.00 0.00 3.13
533 554 7.752695 ACATCCATTTCTTCGACAAGTATTTC 58.247 34.615 0.00 0.00 0.00 2.17
534 555 7.687941 ACATCCATTTCTTCGACAAGTATTT 57.312 32.000 0.00 0.00 0.00 1.40
535 556 8.041323 AGTACATCCATTTCTTCGACAAGTATT 58.959 33.333 0.00 0.00 0.00 1.89
536 557 7.492669 CAGTACATCCATTTCTTCGACAAGTAT 59.507 37.037 0.00 0.00 0.00 2.12
537 558 6.811665 CAGTACATCCATTTCTTCGACAAGTA 59.188 38.462 0.00 0.00 0.00 2.24
538 559 5.639506 CAGTACATCCATTTCTTCGACAAGT 59.360 40.000 0.00 0.00 0.00 3.16
539 560 5.639506 ACAGTACATCCATTTCTTCGACAAG 59.360 40.000 0.00 0.00 0.00 3.16
540 561 5.547465 ACAGTACATCCATTTCTTCGACAA 58.453 37.500 0.00 0.00 0.00 3.18
541 562 5.147330 ACAGTACATCCATTTCTTCGACA 57.853 39.130 0.00 0.00 0.00 4.35
542 563 7.042658 GGATAACAGTACATCCATTTCTTCGAC 60.043 40.741 8.62 0.00 40.48 4.20
543 564 6.984474 GGATAACAGTACATCCATTTCTTCGA 59.016 38.462 8.62 0.00 40.48 3.71
544 565 6.761242 TGGATAACAGTACATCCATTTCTTCG 59.239 38.462 11.29 0.00 44.55 3.79
570 591 1.431036 GATCCTTCTTGGCGCTTGC 59.569 57.895 7.64 0.00 35.26 4.01
586 607 0.033796 CAGGCATGAACCACCAGGAT 60.034 55.000 0.00 0.00 38.69 3.24
633 661 3.071312 TGCCAGAATGTTGCCATCTTTTT 59.929 39.130 0.00 0.00 0.00 1.94
638 666 0.889994 TGTGCCAGAATGTTGCCATC 59.110 50.000 0.00 0.00 0.00 3.51
655 683 3.317149 CCGATTCATTTCATGCATCCTGT 59.683 43.478 0.00 0.00 30.57 4.00
674 771 2.046023 CAGGCATGGAAGCACCGA 60.046 61.111 0.00 0.00 42.61 4.69
737 842 2.778299 TGTCTTGCCAAAACTAGCGAT 58.222 42.857 0.00 0.00 0.00 4.58
746 851 3.325293 TGCTTTTGTTGTCTTGCCAAA 57.675 38.095 0.00 0.00 0.00 3.28
777 882 1.293498 CGGCTAGATGGGATTCCGG 59.707 63.158 0.00 0.00 35.24 5.14
988 1115 2.229792 GGACACCATTTTCACTGAGCA 58.770 47.619 0.00 0.00 0.00 4.26
1038 1165 3.591835 GAGCCGAGGAGGAGAGCG 61.592 72.222 0.00 0.00 45.00 5.03
1050 1177 0.539051 AACAGAGAATGAGGGAGCCG 59.461 55.000 0.00 0.00 0.00 5.52
1060 1187 0.389948 GACGCACCGGAACAGAGAAT 60.390 55.000 9.46 0.00 0.00 2.40
1062 1189 2.649034 GACGCACCGGAACAGAGA 59.351 61.111 9.46 0.00 0.00 3.10
1257 1408 0.269173 AGGGAGAGGTAGAATGGGGG 59.731 60.000 0.00 0.00 0.00 5.40
1258 1409 2.973406 GTTAGGGAGAGGTAGAATGGGG 59.027 54.545 0.00 0.00 0.00 4.96
1359 1515 1.354337 CTCGTCATGTTCAGCACCCG 61.354 60.000 0.00 0.00 0.00 5.28
1639 1795 3.951037 CACTGCTCACTCCTCAGTAGTAT 59.049 47.826 0.00 0.00 38.85 2.12
1640 1796 3.244946 ACACTGCTCACTCCTCAGTAGTA 60.245 47.826 0.00 0.00 38.85 1.82
1657 1816 3.036084 GCGTGTCCGTCCACACTG 61.036 66.667 7.65 3.72 43.97 3.66
1668 1827 4.760047 ATCAGGTGCGGGCGTGTC 62.760 66.667 0.00 0.00 0.00 3.67
1744 1903 2.481952 CTGCTTATTATTGCCTCCGAGC 59.518 50.000 0.00 0.00 0.00 5.03
1795 1954 5.374071 ACAAACTAGACCCAAACCAACTAG 58.626 41.667 0.00 0.00 37.25 2.57
1943 2102 1.959226 GCTCAACTTGGCGACGGAA 60.959 57.895 0.00 0.00 0.00 4.30
1989 2148 2.557056 CAAGGCTGCTCATTATCCATGG 59.443 50.000 4.97 4.97 33.07 3.66
2010 2169 5.011227 AGCCCGAGAAGAAAATATCTCTACC 59.989 44.000 0.00 0.00 39.92 3.18
2029 2188 0.749649 ATGCTAACAGAGAGAGCCCG 59.250 55.000 0.00 0.00 35.24 6.13
2044 2203 2.967599 TAGCGATGAAGTGACATGCT 57.032 45.000 0.00 0.00 37.85 3.79
2052 2211 3.627395 TGGTGGAATTAGCGATGAAGT 57.373 42.857 0.00 0.00 0.00 3.01
2095 2254 2.091852 GAGGAACACTCTGCCTCAAG 57.908 55.000 0.00 0.00 45.89 3.02
2234 2417 4.279671 ACTCAAAAGGTCACAACAACAACA 59.720 37.500 0.00 0.00 0.00 3.33
2235 2418 4.805219 ACTCAAAAGGTCACAACAACAAC 58.195 39.130 0.00 0.00 0.00 3.32
2236 2419 5.461032 AACTCAAAAGGTCACAACAACAA 57.539 34.783 0.00 0.00 0.00 2.83
2237 2420 5.226396 CAAACTCAAAAGGTCACAACAACA 58.774 37.500 0.00 0.00 0.00 3.33
2238 2421 4.091365 GCAAACTCAAAAGGTCACAACAAC 59.909 41.667 0.00 0.00 0.00 3.32
2239 2422 4.241681 GCAAACTCAAAAGGTCACAACAA 58.758 39.130 0.00 0.00 0.00 2.83
2240 2423 3.367910 GGCAAACTCAAAAGGTCACAACA 60.368 43.478 0.00 0.00 0.00 3.33
2241 2424 3.119137 AGGCAAACTCAAAAGGTCACAAC 60.119 43.478 0.00 0.00 0.00 3.32
2242 2425 3.096092 AGGCAAACTCAAAAGGTCACAA 58.904 40.909 0.00 0.00 0.00 3.33
2243 2426 2.687935 GAGGCAAACTCAAAAGGTCACA 59.312 45.455 0.00 0.00 45.85 3.58
2244 2427 3.355626 GAGGCAAACTCAAAAGGTCAC 57.644 47.619 0.00 0.00 45.85 3.67
2292 2475 3.244044 GCAAAGGAGAGAGACTGACAAGT 60.244 47.826 0.00 0.00 40.21 3.16
2339 2616 2.223876 GGCGACGTCTTATATTGTGGGA 60.224 50.000 14.70 0.00 0.00 4.37
2478 3180 1.352156 CCGCTGCAACTCGTCCTTAC 61.352 60.000 0.00 0.00 0.00 2.34


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

AutoCloner maintained by Alex Coulton.