Multiple sequence alignment - TraesCS1B01G449200

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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 TraesCS1B01G449200 chr1B 100.000 2385 0 0 1 2385 667964704 667967088 0.000000e+00 4405.0
1 TraesCS1B01G449200 chr1B 78.049 205 20 9 1558 1743 667975143 667974945 3.240000e-19 106.0
2 TraesCS1B01G449200 chr1D 88.320 1935 114 49 1 1858 479738892 479736993 0.000000e+00 2218.0
3 TraesCS1B01G449200 chr1D 86.629 531 56 7 1857 2385 479668728 479669245 7.390000e-160 573.0
4 TraesCS1B01G449200 chr1D 76.598 876 131 46 609 1453 479751217 479750385 4.740000e-112 414.0
5 TraesCS1B01G449200 chr1D 83.333 120 13 7 1506 1618 479750289 479750170 1.170000e-18 104.0
6 TraesCS1B01G449200 chr1D 80.000 165 10 7 1558 1704 479758791 479758632 1.510000e-17 100.0
7 TraesCS1B01G449200 chr1A 92.692 1081 35 18 815 1882 576078447 576077398 0.000000e+00 1519.0
8 TraesCS1B01G449200 chr1A 77.361 932 128 47 598 1480 576203963 576203066 2.150000e-130 475.0
9 TraesCS1B01G449200 chr1A 85.859 396 42 9 1 392 576079138 576078753 2.210000e-110 409.0
10 TraesCS1B01G449200 chr1A 85.382 301 23 9 475 774 576078728 576078448 2.320000e-75 292.0
11 TraesCS1B01G449200 chr1A 90.323 93 7 2 1899 1991 576077410 576077320 1.160000e-23 121.0
12 TraesCS1B01G449200 chr1A 92.063 63 4 1 1558 1619 576138552 576138490 1.170000e-13 87.9


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 TraesCS1B01G449200 chr1B 667964704 667967088 2384 False 4405.00 4405 100.0000 1 2385 1 chr1B.!!$F1 2384
1 TraesCS1B01G449200 chr1D 479736993 479738892 1899 True 2218.00 2218 88.3200 1 1858 1 chr1D.!!$R1 1857
2 TraesCS1B01G449200 chr1D 479668728 479669245 517 False 573.00 573 86.6290 1857 2385 1 chr1D.!!$F1 528
3 TraesCS1B01G449200 chr1D 479750170 479751217 1047 True 259.00 414 79.9655 609 1618 2 chr1D.!!$R3 1009
4 TraesCS1B01G449200 chr1A 576077320 576079138 1818 True 585.25 1519 88.5640 1 1991 4 chr1A.!!$R3 1990
5 TraesCS1B01G449200 chr1A 576203066 576203963 897 True 475.00 475 77.3610 598 1480 1 chr1A.!!$R2 882

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
653 681 0.537188 GGAGGTCGAGAAAGGATGCA 59.463 55.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 2538 0.179084 AATGTCCATAGGCGTGTCCG 60.179 55.0 0.0 0.0 40.77 4.79 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
35 36 1.570347 TTCGTATGGCCAACACGCAC 61.570 55.000 28.99 12.64 35.70 5.34
60 61 6.430962 TGAATTTTGGTGATGGAATCCAAA 57.569 33.333 5.89 4.76 44.73 3.28
61 62 7.018487 TGAATTTTGGTGATGGAATCCAAAT 57.982 32.000 5.89 0.00 46.15 2.32
75 76 5.578336 GGAATCCAAATTTTGCAACTAGCTC 59.422 40.000 0.00 0.00 45.94 4.09
87 88 7.979444 TTGCAACTAGCTCTTTGTAAATAGT 57.021 32.000 0.00 0.00 45.94 2.12
135 136 6.372937 AGCTAGCTCCTTGACAAAGAAATAAC 59.627 38.462 12.68 0.00 35.19 1.89
206 208 9.987272 CAAAGGATGGAACTTAGATTTTCTTTT 57.013 29.630 0.00 0.00 0.00 2.27
262 264 0.739561 GTAACAACCCAACGCAACCA 59.260 50.000 0.00 0.00 0.00 3.67
304 306 5.741388 AGAACCAAGATCATCATTTACGC 57.259 39.130 0.00 0.00 0.00 4.42
387 389 2.533266 AGAAGTCAAGACATGCACGT 57.467 45.000 2.72 0.00 0.00 4.49
393 395 1.798223 TCAAGACATGCACGTTGTAGC 59.202 47.619 0.00 0.00 0.00 3.58
412 414 3.916761 AGCACTTGCATAATTTGGTGTG 58.083 40.909 3.62 0.00 45.16 3.82
429 431 8.417780 TTTGGTGTGACAAATAGTTTTGATTG 57.582 30.769 5.52 0.00 44.11 2.67
431 433 7.551585 TGGTGTGACAAATAGTTTTGATTGTT 58.448 30.769 5.52 0.00 44.11 2.83
432 434 7.490725 TGGTGTGACAAATAGTTTTGATTGTTG 59.509 33.333 5.52 0.00 44.11 3.33
434 436 8.531530 GTGTGACAAATAGTTTTGATTGTTGTC 58.468 33.333 5.52 6.67 44.11 3.18
436 438 9.301153 GTGACAAATAGTTTTGATTGTTGTCTT 57.699 29.630 13.06 0.00 44.11 3.01
437 439 9.868277 TGACAAATAGTTTTGATTGTTGTCTTT 57.132 25.926 13.06 0.00 44.11 2.52
455 457 6.205784 TGTCTTTAAACAAAGCACACATAGC 58.794 36.000 0.00 0.00 0.00 2.97
461 463 4.220693 ACAAAGCACACATAGCCATAGA 57.779 40.909 0.00 0.00 0.00 1.98
470 495 6.596703 CACACATAGCCATAGATTTGATTCG 58.403 40.000 0.00 0.00 0.00 3.34
471 496 6.203530 CACACATAGCCATAGATTTGATTCGT 59.796 38.462 0.00 0.00 0.00 3.85
473 498 8.097038 ACACATAGCCATAGATTTGATTCGTAT 58.903 33.333 0.00 0.00 0.00 3.06
484 509 8.641499 AGATTTGATTCGTATTGAGAGAAGAC 57.359 34.615 0.00 0.00 0.00 3.01
496 521 3.967326 TGAGAGAAGACAACCCTCTTTCA 59.033 43.478 0.00 0.00 37.40 2.69
538 563 6.613755 TGAATATGCATCTGTCTTCACATG 57.386 37.500 0.19 0.00 0.00 3.21
644 672 1.077357 GAGCAGGAGGAGGTCGAGA 60.077 63.158 0.00 0.00 0.00 4.04
653 681 0.537188 GGAGGTCGAGAAAGGATGCA 59.463 55.000 0.00 0.00 0.00 3.96
665 693 1.227380 GGATGCAGAGCCGATTCGT 60.227 57.895 5.20 0.00 0.00 3.85
766 798 3.775654 CCTCCTCACTCCGGTGGC 61.776 72.222 8.63 0.00 43.17 5.01
782 814 3.673484 GCGGCTGGCTGCTTCAAA 61.673 61.111 17.87 0.00 44.39 2.69
835 929 4.993584 CACATTATTCTCCATCTTCTCCGG 59.006 45.833 0.00 0.00 0.00 5.14
862 956 2.102925 CAGAGCTGAATCCTTCCTCTCC 59.897 54.545 0.00 0.00 29.46 3.71
874 968 3.386402 CCTTCCTCTCCATTGTCTAGTCC 59.614 52.174 0.00 0.00 0.00 3.85
1170 1290 4.299155 CCGATGATGTCAAACGCTACTAT 58.701 43.478 7.21 0.00 0.00 2.12
1386 1542 5.482908 GTTGAAGCACTTGAAGATCTAGGA 58.517 41.667 0.00 0.00 0.00 2.94
1387 1543 5.745312 TGAAGCACTTGAAGATCTAGGAA 57.255 39.130 0.00 0.00 0.00 3.36
1414 1578 3.938334 TGGACAATGAATGATACACACCG 59.062 43.478 0.00 0.00 0.00 4.94
1496 1675 1.136113 CATGTCAACGTACGCATGCAA 60.136 47.619 19.57 1.39 33.45 4.08
1497 1676 1.152510 TGTCAACGTACGCATGCAAT 58.847 45.000 19.57 7.65 0.00 3.56
1509 1715 2.882927 CATGCAATGCAAGGCTATGT 57.117 45.000 13.45 0.00 43.62 2.29
1534 1740 6.909909 AGATGCATGCATGTTCATAATACTG 58.090 36.000 36.73 0.00 36.70 2.74
1704 1920 9.355215 GCAGATATGTTATACACACATACTACC 57.645 37.037 0.00 0.00 39.40 3.18
1717 1933 9.344772 ACACACATACTACCAAAAACAAATCTA 57.655 29.630 0.00 0.00 0.00 1.98
1803 2019 1.154205 GGTGGCGGAGATCACGAATG 61.154 60.000 13.12 0.00 34.89 2.67
1804 2020 1.143838 TGGCGGAGATCACGAATGG 59.856 57.895 13.12 0.00 0.00 3.16
1877 2093 6.713450 TGTTCTTTCTTCCTATTAACCACCAC 59.287 38.462 0.00 0.00 0.00 4.16
1934 2150 0.481128 ATATTGGCCCGGGGTTAAGG 59.519 55.000 25.28 0.00 0.00 2.69
1949 2165 0.182537 TAAGGCCACACAACACAGCT 59.817 50.000 5.01 0.00 0.00 4.24
1955 2171 1.093972 CACACAACACAGCTCCAACA 58.906 50.000 0.00 0.00 0.00 3.33
2000 2216 1.838073 ATTCCCGTGACCCAGACCAC 61.838 60.000 0.00 0.00 0.00 4.16
2004 2220 3.456317 GTGACCCAGACCACGACT 58.544 61.111 0.00 0.00 0.00 4.18
2012 2228 2.038033 CCCAGACCACGACTTAAAAGGA 59.962 50.000 0.00 0.00 0.00 3.36
2022 2238 3.303263 CGACTTAAAAGGAAACGCGGAAA 60.303 43.478 12.47 0.00 0.00 3.13
2037 2253 2.098117 GCGGAAACTCATTTCTCCCATG 59.902 50.000 0.23 0.00 43.33 3.66
2078 2294 2.500910 CCAGATAATTTTGGGCCTGCAA 59.499 45.455 4.53 0.00 0.00 4.08
2079 2295 3.055240 CCAGATAATTTTGGGCCTGCAAA 60.055 43.478 4.53 2.35 0.00 3.68
2089 2305 0.821301 GGCCTGCAAAGCTATCCCTC 60.821 60.000 8.19 0.00 0.00 4.30
2096 2312 2.545946 GCAAAGCTATCCCTCGATTGTC 59.454 50.000 0.00 0.00 0.00 3.18
2128 2344 0.331616 CGGACTTCCAAAATCCCCCT 59.668 55.000 0.00 0.00 35.14 4.79
2139 2355 2.435203 AATCCCCCTACTATGTCCCC 57.565 55.000 0.00 0.00 0.00 4.81
2141 2357 1.028638 TCCCCCTACTATGTCCCCAA 58.971 55.000 0.00 0.00 0.00 4.12
2145 2361 2.038557 CCCCTACTATGTCCCCAAATCG 59.961 54.545 0.00 0.00 0.00 3.34
2158 2374 3.004752 CCAAATCGAGGGAAGGAACAT 57.995 47.619 0.00 0.00 0.00 2.71
2160 2376 2.684881 CAAATCGAGGGAAGGAACATGG 59.315 50.000 0.00 0.00 0.00 3.66
2167 2383 1.134491 GGGAAGGAACATGGTAGTCCG 60.134 57.143 0.00 0.00 36.30 4.79
2176 2392 3.858135 ACATGGTAGTCCGGATAATCCT 58.142 45.455 7.81 1.23 33.30 3.24
2179 2395 1.201880 GGTAGTCCGGATAATCCTCGC 59.798 57.143 7.81 0.00 33.30 5.03
2196 2412 3.075005 CGGACCACGTCTCCCCAT 61.075 66.667 3.63 0.00 37.93 4.00
2199 2415 1.338136 GGACCACGTCTCCCCATGAT 61.338 60.000 0.00 0.00 32.47 2.45
2201 2417 1.524621 CCACGTCTCCCCATGATGC 60.525 63.158 0.00 0.00 0.00 3.91
2213 2429 1.284657 CATGATGCACGTCTCTCCAC 58.715 55.000 0.00 0.00 0.00 4.02
2215 2431 1.834188 TGATGCACGTCTCTCCACTA 58.166 50.000 0.00 0.00 0.00 2.74
2235 2453 7.896496 TCCACTAATCTCTTTCTCCTCTTAGTT 59.104 37.037 0.00 0.00 0.00 2.24
2244 2462 5.667539 TTCTCCTCTTAGTTGATGTCCAG 57.332 43.478 0.00 0.00 0.00 3.86
2263 2481 2.834113 AGCCCACTGATAGTTACACCT 58.166 47.619 0.00 0.00 0.00 4.00
2266 2484 3.679083 GCCCACTGATAGTTACACCTCAC 60.679 52.174 0.00 0.00 0.00 3.51
2301 2519 3.164269 ATACCGCTGGAGGGCCTG 61.164 66.667 12.95 0.00 36.29 4.85
2317 2535 0.683973 CCTGAGCCCGATCAGCTATT 59.316 55.000 7.20 0.00 44.47 1.73
2318 2536 1.337635 CCTGAGCCCGATCAGCTATTC 60.338 57.143 7.20 0.00 44.47 1.75
2320 2538 1.005630 AGCCCGATCAGCTATTCGC 60.006 57.895 11.02 0.76 39.29 4.70
2327 2545 0.595053 ATCAGCTATTCGCGGACACG 60.595 55.000 6.13 0.00 45.44 4.49
2355 2573 0.953471 CATTTGAGGGCGTCCGTTCA 60.953 55.000 0.00 0.00 38.33 3.18
2358 2576 2.434359 GAGGGCGTCCGTTCAAGG 60.434 66.667 0.00 0.00 38.33 3.61
2369 2587 0.174845 CGTTCAAGGGATAGCGGTGA 59.825 55.000 0.00 0.00 0.00 4.02
2375 2593 1.794714 AGGGATAGCGGTGAAGATGT 58.205 50.000 0.00 0.00 0.00 3.06
2378 2596 1.270358 GGATAGCGGTGAAGATGTCCC 60.270 57.143 0.00 0.00 32.65 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 4.467082 TGGATTCCATCACCAAAATTCAGG 59.533 41.667 0.00 0.00 0.00 3.86
60 61 9.846248 CTATTTACAAAGAGCTAGTTGCAAAAT 57.154 29.630 0.00 17.68 45.94 1.82
61 62 8.846211 ACTATTTACAAAGAGCTAGTTGCAAAA 58.154 29.630 0.00 10.05 45.94 2.44
262 264 8.818860 TGGTTCTACCACTAACATATTTACTGT 58.181 33.333 0.00 0.00 44.79 3.55
299 301 4.060205 GGTTCAACTAACTCCTTGCGTAA 58.940 43.478 0.00 0.00 38.23 3.18
300 302 3.069872 TGGTTCAACTAACTCCTTGCGTA 59.930 43.478 0.00 0.00 38.23 4.42
304 306 8.166422 AGTATTTTGGTTCAACTAACTCCTTG 57.834 34.615 0.00 0.00 38.23 3.61
352 354 9.793259 TCTTGACTTCTTATTTAGACCACAAAT 57.207 29.630 0.00 0.00 30.90 2.32
361 363 7.148573 ACGTGCATGTCTTGACTTCTTATTTAG 60.149 37.037 5.51 0.00 0.00 1.85
387 389 5.010516 ACACCAAATTATGCAAGTGCTACAA 59.989 36.000 4.69 0.00 42.66 2.41
393 395 4.869215 TGTCACACCAAATTATGCAAGTG 58.131 39.130 0.00 0.00 0.00 3.16
421 423 8.993121 TGCTTTGTTTAAAGACAACAATCAAAA 58.007 25.926 4.10 0.00 44.87 2.44
424 426 7.062839 GTGTGCTTTGTTTAAAGACAACAATCA 59.937 33.333 4.10 0.00 44.87 2.57
425 427 7.062839 TGTGTGCTTTGTTTAAAGACAACAATC 59.937 33.333 4.10 0.00 44.87 2.67
428 430 5.773575 TGTGTGCTTTGTTTAAAGACAACA 58.226 33.333 4.10 2.71 44.87 3.33
429 431 6.885735 ATGTGTGCTTTGTTTAAAGACAAC 57.114 33.333 4.10 0.50 44.87 3.32
431 433 6.205784 GCTATGTGTGCTTTGTTTAAAGACA 58.794 36.000 4.10 0.76 44.87 3.41
432 434 5.629435 GGCTATGTGTGCTTTGTTTAAAGAC 59.371 40.000 4.10 1.24 44.87 3.01
434 436 5.527951 TGGCTATGTGTGCTTTGTTTAAAG 58.472 37.500 0.00 0.00 44.86 1.85
436 438 5.720371 ATGGCTATGTGTGCTTTGTTTAA 57.280 34.783 0.00 0.00 0.00 1.52
437 439 6.176896 TCTATGGCTATGTGTGCTTTGTTTA 58.823 36.000 0.00 0.00 0.00 2.01
440 442 4.220693 TCTATGGCTATGTGTGCTTTGT 57.779 40.909 0.00 0.00 0.00 2.83
441 443 5.762825 AATCTATGGCTATGTGTGCTTTG 57.237 39.130 0.00 0.00 0.00 2.77
443 445 5.439721 TCAAATCTATGGCTATGTGTGCTT 58.560 37.500 0.00 0.00 0.00 3.91
444 446 5.039920 TCAAATCTATGGCTATGTGTGCT 57.960 39.130 0.00 0.00 0.00 4.40
445 447 5.954296 ATCAAATCTATGGCTATGTGTGC 57.046 39.130 0.00 0.00 0.00 4.57
447 449 6.291377 ACGAATCAAATCTATGGCTATGTGT 58.709 36.000 0.00 0.00 0.00 3.72
448 450 6.791887 ACGAATCAAATCTATGGCTATGTG 57.208 37.500 0.00 0.00 0.00 3.21
449 451 8.939929 CAATACGAATCAAATCTATGGCTATGT 58.060 33.333 0.00 0.00 0.00 2.29
455 457 9.481340 TTCTCTCAATACGAATCAAATCTATGG 57.519 33.333 0.00 0.00 0.00 2.74
461 463 8.660373 GTTGTCTTCTCTCAATACGAATCAAAT 58.340 33.333 0.00 0.00 0.00 2.32
470 495 5.669164 AGAGGGTTGTCTTCTCTCAATAC 57.331 43.478 0.00 0.00 33.01 1.89
471 496 6.270000 TGAAAGAGGGTTGTCTTCTCTCAATA 59.730 38.462 0.00 0.00 35.65 1.90
473 498 4.408921 TGAAAGAGGGTTGTCTTCTCTCAA 59.591 41.667 0.00 0.00 35.65 3.02
484 509 1.818642 CAGAGGCTGAAAGAGGGTTG 58.181 55.000 0.00 0.00 34.07 3.77
525 550 6.840780 TCTCATAGTTCATGTGAAGACAGA 57.159 37.500 0.00 0.00 34.91 3.41
526 551 6.034363 CGTTCTCATAGTTCATGTGAAGACAG 59.966 42.308 0.00 0.00 43.96 3.51
533 558 7.382218 TGCATATACGTTCTCATAGTTCATGTG 59.618 37.037 0.00 0.00 35.96 3.21
538 563 7.875316 ACATGCATATACGTTCTCATAGTTC 57.125 36.000 0.00 0.00 0.00 3.01
584 610 6.516739 TGGAAATATATGTCCACGCAAAAA 57.483 33.333 19.25 0.00 39.04 1.94
585 611 6.707440 ATGGAAATATATGTCCACGCAAAA 57.293 33.333 24.40 2.84 46.53 2.44
586 612 6.707440 AATGGAAATATATGTCCACGCAAA 57.293 33.333 24.40 3.53 46.53 3.68
587 613 6.707440 AAATGGAAATATATGTCCACGCAA 57.293 33.333 24.40 4.24 46.53 4.85
588 614 6.707440 AAAATGGAAATATATGTCCACGCA 57.293 33.333 24.40 4.60 46.53 5.24
589 615 8.349983 AGTAAAAATGGAAATATATGTCCACGC 58.650 33.333 24.40 12.01 46.53 5.34
605 631 8.592105 TGCTCAAAGATTCAAAGTAAAAATGG 57.408 30.769 0.00 0.00 0.00 3.16
644 672 1.673168 GAATCGGCTCTGCATCCTTT 58.327 50.000 0.00 0.00 0.00 3.11
653 681 2.490217 CCGTCACGAATCGGCTCT 59.510 61.111 7.80 0.00 40.28 4.09
665 693 2.672651 TTCGGCGTAGTCCCGTCA 60.673 61.111 6.85 0.00 45.71 4.35
835 929 1.452833 GGATTCAGCTCTGTGGGGC 60.453 63.158 0.00 0.00 0.00 5.80
862 956 1.227263 CCGGCCGGACTAGACAATG 60.227 63.158 41.82 6.81 37.50 2.82
1101 1221 4.539083 ACGTTGTGCCAGCGGTCA 62.539 61.111 13.89 0.00 42.05 4.02
1170 1290 2.983592 TCGTGGACGAGCAGCTCA 60.984 61.111 22.49 0.00 44.22 4.26
1327 1478 5.975693 TTACAAGATTAACCCCAGCTTTG 57.024 39.130 0.00 0.00 0.00 2.77
1386 1542 6.153170 TGTGTATCATTCATTGTCCATTGCTT 59.847 34.615 0.00 0.00 0.00 3.91
1387 1543 5.653330 TGTGTATCATTCATTGTCCATTGCT 59.347 36.000 0.00 0.00 0.00 3.91
1414 1578 3.667497 TCCAGTTCCATCGATCTATGC 57.333 47.619 0.00 0.00 0.00 3.14
1496 1675 3.497103 TGCATCTACATAGCCTTGCAT 57.503 42.857 0.00 0.00 0.00 3.96
1497 1676 3.143728 CATGCATCTACATAGCCTTGCA 58.856 45.455 0.00 11.08 35.47 4.08
1498 1677 2.095364 GCATGCATCTACATAGCCTTGC 60.095 50.000 14.21 0.00 32.13 4.01
1499 1678 3.143728 TGCATGCATCTACATAGCCTTG 58.856 45.455 18.46 0.00 0.00 3.61
1509 1715 7.361457 GCAGTATTATGAACATGCATGCATCTA 60.361 37.037 30.07 16.20 33.90 1.98
1534 1740 2.555199 CCATAGACCACTTGCTACTGC 58.445 52.381 0.00 0.00 40.20 4.40
1613 1829 4.368315 TGGTTACATGTGCAGACGATATC 58.632 43.478 9.11 0.00 0.00 1.63
1641 1857 8.816640 TTTCTTTTCTCTTTTGATTGGTATGC 57.183 30.769 0.00 0.00 0.00 3.14
1717 1933 4.502645 GCTTGAAACGCACTGTATTTGTTT 59.497 37.500 0.00 0.00 35.61 2.83
1853 2069 6.150641 GGTGGTGGTTAATAGGAAGAAAGAAC 59.849 42.308 0.00 0.00 0.00 3.01
1897 2113 8.474831 GGCCAATATAGAAATGTTTGGTAGTTT 58.525 33.333 0.00 0.00 0.00 2.66
1899 2115 6.549736 GGGCCAATATAGAAATGTTTGGTAGT 59.450 38.462 4.39 0.00 0.00 2.73
1901 2117 5.533154 CGGGCCAATATAGAAATGTTTGGTA 59.467 40.000 4.39 0.00 0.00 3.25
1902 2118 4.340950 CGGGCCAATATAGAAATGTTTGGT 59.659 41.667 4.39 0.00 0.00 3.67
1903 2119 4.261994 CCGGGCCAATATAGAAATGTTTGG 60.262 45.833 4.39 0.00 0.00 3.28
1904 2120 4.261994 CCCGGGCCAATATAGAAATGTTTG 60.262 45.833 8.08 0.00 0.00 2.93
1905 2121 3.895041 CCCGGGCCAATATAGAAATGTTT 59.105 43.478 8.08 0.00 0.00 2.83
1934 2150 1.383456 TTGGAGCTGTGTTGTGTGGC 61.383 55.000 0.00 0.00 0.00 5.01
1949 2165 1.140312 AGAAGGGAGCTTGTGTTGGA 58.860 50.000 0.00 0.00 0.00 3.53
1955 2171 1.071699 TGCGTTAAGAAGGGAGCTTGT 59.928 47.619 0.00 0.00 0.00 3.16
2000 2216 1.794116 TCCGCGTTTCCTTTTAAGTCG 59.206 47.619 4.92 0.00 0.00 4.18
2001 2217 3.883631 TTCCGCGTTTCCTTTTAAGTC 57.116 42.857 4.92 0.00 0.00 3.01
2004 2220 3.626670 TGAGTTTCCGCGTTTCCTTTTAA 59.373 39.130 4.92 0.00 0.00 1.52
2012 2228 2.225727 GGAGAAATGAGTTTCCGCGTTT 59.774 45.455 4.92 0.00 43.82 3.60
2022 2238 5.965033 AGACATACATGGGAGAAATGAGT 57.035 39.130 0.00 0.00 0.00 3.41
2062 2278 1.977129 AGCTTTGCAGGCCCAAAATTA 59.023 42.857 0.00 0.00 34.59 1.40
2064 2280 1.643310 TAGCTTTGCAGGCCCAAAAT 58.357 45.000 0.00 0.00 34.59 1.82
2073 2289 2.540265 ATCGAGGGATAGCTTTGCAG 57.460 50.000 0.00 0.00 0.00 4.41
2075 2291 2.545946 GACAATCGAGGGATAGCTTTGC 59.454 50.000 0.00 0.00 31.01 3.68
2078 2294 1.341531 CGGACAATCGAGGGATAGCTT 59.658 52.381 0.00 0.00 31.01 3.74
2079 2295 0.962489 CGGACAATCGAGGGATAGCT 59.038 55.000 0.00 0.00 31.01 3.32
2108 2324 0.330267 GGGGGATTTTGGAAGTCCGA 59.670 55.000 0.00 0.00 39.43 4.55
2116 2332 3.181433 GGGACATAGTAGGGGGATTTTGG 60.181 52.174 0.00 0.00 0.00 3.28
2119 2335 2.020441 TGGGGACATAGTAGGGGGATTT 60.020 50.000 0.00 0.00 33.40 2.17
2123 2339 1.901648 TTTGGGGACATAGTAGGGGG 58.098 55.000 0.00 0.00 42.32 5.40
2128 2344 2.969950 CCCTCGATTTGGGGACATAGTA 59.030 50.000 1.10 0.00 45.18 1.82
2139 2355 2.684881 CCATGTTCCTTCCCTCGATTTG 59.315 50.000 0.00 0.00 0.00 2.32
2141 2357 1.916181 ACCATGTTCCTTCCCTCGATT 59.084 47.619 0.00 0.00 0.00 3.34
2145 2361 2.170817 GGACTACCATGTTCCTTCCCTC 59.829 54.545 0.00 0.00 35.97 4.30
2158 2374 2.511659 CGAGGATTATCCGGACTACCA 58.488 52.381 6.12 0.00 42.75 3.25
2160 2376 1.135746 CGCGAGGATTATCCGGACTAC 60.136 57.143 6.12 0.00 42.75 2.73
2179 2395 3.075005 ATGGGGAGACGTGGTCCG 61.075 66.667 0.00 0.00 44.03 4.79
2196 2412 1.834188 TAGTGGAGAGACGTGCATCA 58.166 50.000 0.00 0.00 0.00 3.07
2199 2415 2.423892 GAGATTAGTGGAGAGACGTGCA 59.576 50.000 0.00 0.00 0.00 4.57
2201 2417 4.974368 AAGAGATTAGTGGAGAGACGTG 57.026 45.455 0.00 0.00 0.00 4.49
2213 2429 9.748708 CATCAACTAAGAGGAGAAAGAGATTAG 57.251 37.037 0.00 0.00 0.00 1.73
2215 2431 8.144862 ACATCAACTAAGAGGAGAAAGAGATT 57.855 34.615 0.00 0.00 0.00 2.40
2235 2453 1.764723 CTATCAGTGGGCTGGACATCA 59.235 52.381 0.00 0.00 42.78 3.07
2244 2462 2.500098 TGAGGTGTAACTATCAGTGGGC 59.500 50.000 0.00 0.00 36.74 5.36
2280 2498 2.122813 CCCTCCAGCGGTATCCCT 60.123 66.667 0.00 0.00 0.00 4.20
2301 2519 1.011451 GCGAATAGCTGATCGGGCTC 61.011 60.000 20.12 4.49 44.04 4.70
2303 2521 2.375766 CGCGAATAGCTGATCGGGC 61.376 63.158 20.98 2.91 43.38 6.13
2308 2526 0.595053 CGTGTCCGCGAATAGCTGAT 60.595 55.000 8.23 0.00 45.59 2.90
2320 2538 0.179084 AATGTCCATAGGCGTGTCCG 60.179 55.000 0.00 0.00 40.77 4.79
2327 2545 1.322442 GCCCTCAAATGTCCATAGGC 58.678 55.000 0.00 0.00 0.00 3.93
2355 2573 2.103263 GACATCTTCACCGCTATCCCTT 59.897 50.000 0.00 0.00 0.00 3.95
2358 2576 1.270358 GGGACATCTTCACCGCTATCC 60.270 57.143 0.00 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.