Multiple sequence alignment - TraesCS1B01G103800

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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 TraesCS1B01G103800 chr1B 100.000 3041 0 0 1 3041 113568999 113565959 0.000000e+00 5616.0
1 TraesCS1B01G103800 chr1B 86.383 705 74 11 2346 3038 113816721 113816027 0.000000e+00 750.0
2 TraesCS1B01G103800 chr1B 90.231 389 26 8 1006 1394 113818231 113817855 5.860000e-137 497.0
3 TraesCS1B01G103800 chr1B 85.897 312 31 7 763 1070 113818565 113818263 1.360000e-83 320.0
4 TraesCS1B01G103800 chr1B 90.667 150 13 1 1236 1384 50992402 50992551 6.650000e-47 198.0
5 TraesCS1B01G103800 chr1B 75.969 129 24 6 2528 2651 542761399 542761273 3.270000e-05 60.2
6 TraesCS1B01G103800 chr1D 93.584 2151 95 23 763 2895 72502335 72500210 0.000000e+00 3168.0
7 TraesCS1B01G103800 chr1D 95.364 151 7 0 2891 3041 72499858 72499708 1.090000e-59 241.0
8 TraesCS1B01G103800 chr3A 92.364 681 40 8 7 678 823076 823753 0.000000e+00 959.0
9 TraesCS1B01G103800 chr3A 82.258 186 28 5 99 281 711085225 711085042 4.060000e-34 156.0
10 TraesCS1B01G103800 chr3A 90.526 95 9 0 583 677 821785 821879 3.180000e-25 126.0
11 TraesCS1B01G103800 chr3A 94.643 56 2 1 8 62 814126 814181 5.400000e-13 86.1
12 TraesCS1B01G103800 chr1A 87.734 693 60 12 2359 3041 71787142 71786465 0.000000e+00 785.0
13 TraesCS1B01G103800 chr1A 85.455 660 54 16 763 1399 71790514 71789874 0.000000e+00 649.0
14 TraesCS1B01G103800 chr1A 85.463 227 30 1 1158 1384 32190985 32191208 1.820000e-57 233.0
15 TraesCS1B01G103800 chr1A 81.818 231 36 4 1160 1384 71725061 71724831 4.000000e-44 189.0
16 TraesCS1B01G103800 chr5B 90.141 142 14 0 1239 1380 631391833 631391692 5.180000e-43 185.0
17 TraesCS1B01G103800 chr6B 80.567 247 32 11 110 353 585253803 585254036 3.120000e-40 176.0
18 TraesCS1B01G103800 chr6B 80.567 247 31 11 110 353 585265835 585266067 1.120000e-39 174.0
19 TraesCS1B01G103800 chr6B 80.631 222 39 4 1161 1380 145576210 145575991 5.210000e-38 169.0
20 TraesCS1B01G103800 chr6D 81.081 222 38 3 1161 1380 71053284 71053065 1.120000e-39 174.0
21 TraesCS1B01G103800 chr6D 82.258 186 23 6 110 293 463163957 463163780 5.250000e-33 152.0
22 TraesCS1B01G103800 chr6D 86.111 72 7 3 574 643 192109416 192109486 1.170000e-09 75.0
23 TraesCS1B01G103800 chr3B 83.333 186 26 5 99 281 766360670 766360853 1.880000e-37 167.0
24 TraesCS1B01G103800 chr5D 78.049 246 34 11 110 353 409503040 409503267 1.470000e-28 137.0
25 TraesCS1B01G103800 chr5D 85.897 78 2 4 574 643 426293900 426293824 1.170000e-09 75.0
26 TraesCS1B01G103800 chrUn 80.147 136 25 2 2236 2370 102565557 102565423 1.930000e-17 100.0
27 TraesCS1B01G103800 chr5A 89.744 78 5 3 574 651 626512587 626512513 2.500000e-16 97.1
28 TraesCS1B01G103800 chr5A 89.744 78 5 3 574 651 626608707 626608633 2.500000e-16 97.1
29 TraesCS1B01G103800 chr5A 89.744 78 5 3 574 651 627667143 627667069 2.500000e-16 97.1
30 TraesCS1B01G103800 chr4A 89.024 82 1 5 574 647 588933601 588933520 8.980000e-16 95.3
31 TraesCS1B01G103800 chr4D 89.394 66 0 5 584 643 506872335 506872399 3.250000e-10 76.8


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 TraesCS1B01G103800 chr1B 113565959 113568999 3040 True 5616.000000 5616 100.000000 1 3041 1 chr1B.!!$R1 3040
1 TraesCS1B01G103800 chr1B 113816027 113818565 2538 True 522.333333 750 87.503667 763 3038 3 chr1B.!!$R3 2275
2 TraesCS1B01G103800 chr1D 72499708 72502335 2627 True 1704.500000 3168 94.474000 763 3041 2 chr1D.!!$R1 2278
3 TraesCS1B01G103800 chr3A 821785 823753 1968 False 542.500000 959 91.445000 7 678 2 chr3A.!!$F2 671
4 TraesCS1B01G103800 chr1A 71786465 71790514 4049 True 717.000000 785 86.594500 763 3041 2 chr1A.!!$R2 2278

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
866 2175 0.107945 CCAGCAACCTGACTAGCCTC 60.108 60.0 0.0 0.0 41.77 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2707 5950 0.03601 CCACTCCTAGCAACCTGTGG 60.036 60.0 0.0 0.0 38.87 4.17 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
25 1311 5.643777 ACAGATTTCTTATTGTCGAGGTTGG 59.356 40.000 0.00 0.00 0.00 3.77
51 1337 3.262151 TGGACCAATTCATTACTCCGTGA 59.738 43.478 0.00 0.00 0.00 4.35
78 1364 8.065407 GCAATTCATTACACCATTTATTGCATG 58.935 33.333 0.00 0.00 43.54 4.06
128 1414 9.871238 AATAAGTCGTGTATCAAATACTTCTGT 57.129 29.630 0.00 0.00 36.70 3.41
182 1468 4.025145 CAGTCTGTTTTAACAAGTCCGTCC 60.025 45.833 0.00 0.00 38.66 4.79
184 1470 4.025145 GTCTGTTTTAACAAGTCCGTCCAG 60.025 45.833 0.00 0.00 38.66 3.86
240 1528 5.615925 TTCTAAGACTTCTAAGGGATGGC 57.384 43.478 0.00 0.00 0.00 4.40
253 1541 5.603170 AAGGGATGGCATTTTAGTTCATG 57.397 39.130 0.00 0.00 0.00 3.07
309 1598 7.564128 CGTGCATTATGTATTAAGTGGTACTG 58.436 38.462 0.00 0.00 0.00 2.74
322 1611 4.324267 AGTGGTACTGCATAAACTGGTTC 58.676 43.478 0.00 0.00 0.00 3.62
338 1627 6.808008 ACTGGTTCATGTTGTATCTGAAAG 57.192 37.500 0.00 0.00 31.21 2.62
354 1643 6.859112 TCTGAAAGAGTTCTGTATAAGCCT 57.141 37.500 0.00 0.00 38.67 4.58
355 1644 7.956328 TCTGAAAGAGTTCTGTATAAGCCTA 57.044 36.000 0.00 0.00 38.67 3.93
366 1655 9.717892 GTTCTGTATAAGCCTAATAACTTTTGC 57.282 33.333 0.00 0.00 0.00 3.68
389 1678 5.257082 TGTTTGGTTTTCTAGGTGCTTTC 57.743 39.130 0.00 0.00 0.00 2.62
390 1679 4.201970 TGTTTGGTTTTCTAGGTGCTTTCG 60.202 41.667 0.00 0.00 0.00 3.46
391 1680 3.202829 TGGTTTTCTAGGTGCTTTCGT 57.797 42.857 0.00 0.00 0.00 3.85
392 1681 3.547746 TGGTTTTCTAGGTGCTTTCGTT 58.452 40.909 0.00 0.00 0.00 3.85
408 1697 5.163754 GCTTTCGTTATATGCACACTTCCTT 60.164 40.000 0.00 0.00 0.00 3.36
454 1743 9.809096 ATTACTTGAGTATCTTAGTGTCATGTG 57.191 33.333 0.00 0.00 33.80 3.21
474 1763 4.301072 TGGAAGAATGTCCAACTTAGGG 57.699 45.455 0.00 0.00 44.91 3.53
496 1785 0.257039 AGCCATGTGGAAGGATGTCC 59.743 55.000 2.55 0.00 37.39 4.02
542 1831 5.717078 AGTGAACATGCTGATTGTCAATT 57.283 34.783 0.00 0.00 0.00 2.32
577 1867 5.073965 ACCCAAACTCCAATAAACTACTCCA 59.926 40.000 0.00 0.00 0.00 3.86
583 1873 5.491078 ACTCCAATAAACTACTCCATCCCAA 59.509 40.000 0.00 0.00 0.00 4.12
584 1874 6.011981 ACTCCAATAAACTACTCCATCCCAAA 60.012 38.462 0.00 0.00 0.00 3.28
585 1875 6.980577 TCCAATAAACTACTCCATCCCAAAT 58.019 36.000 0.00 0.00 0.00 2.32
586 1876 7.418378 TCCAATAAACTACTCCATCCCAAATT 58.582 34.615 0.00 0.00 0.00 1.82
588 1878 8.630037 CCAATAAACTACTCCATCCCAAATTAC 58.370 37.037 0.00 0.00 0.00 1.89
627 1922 9.333724 TGTCTAGATACAAATCTACGACATGTA 57.666 33.333 0.00 0.00 41.55 2.29
634 1929 7.083875 ACAAATCTACGACATGTAATTTGGG 57.916 36.000 21.42 8.78 40.73 4.12
635 1930 6.882140 ACAAATCTACGACATGTAATTTGGGA 59.118 34.615 21.42 8.71 40.73 4.37
636 1931 6.920569 AATCTACGACATGTAATTTGGGAC 57.079 37.500 0.00 0.00 31.20 4.46
650 1945 4.637387 TTTGGGACGGAGGTTGTATTTA 57.363 40.909 0.00 0.00 0.00 1.40
687 1982 6.816134 ATTTGCCACAATTTATTTTGGGAC 57.184 33.333 9.12 0.00 31.38 4.46
688 1983 5.559148 TTGCCACAATTTATTTTGGGACT 57.441 34.783 9.12 0.00 31.38 3.85
689 1984 6.672266 TTGCCACAATTTATTTTGGGACTA 57.328 33.333 9.12 0.00 31.38 2.59
690 1985 6.865834 TGCCACAATTTATTTTGGGACTAT 57.134 33.333 9.12 0.00 31.38 2.12
691 1986 7.962995 TGCCACAATTTATTTTGGGACTATA 57.037 32.000 9.12 0.00 31.38 1.31
692 1987 8.006298 TGCCACAATTTATTTTGGGACTATAG 57.994 34.615 9.12 0.00 31.38 1.31
693 1988 7.617723 TGCCACAATTTATTTTGGGACTATAGT 59.382 33.333 4.68 4.68 31.38 2.12
694 1989 8.474831 GCCACAATTTATTTTGGGACTATAGTT 58.525 33.333 6.88 0.00 31.38 2.24
703 1998 8.721133 ATTTTGGGACTATAGTTTTGGAACTT 57.279 30.769 6.88 0.00 43.48 2.66
704 1999 7.754851 TTTGGGACTATAGTTTTGGAACTTC 57.245 36.000 6.88 0.00 43.48 3.01
705 2000 5.812286 TGGGACTATAGTTTTGGAACTTCC 58.188 41.667 6.88 0.20 43.48 3.46
706 2001 4.874396 GGGACTATAGTTTTGGAACTTCCG 59.126 45.833 6.88 0.00 43.48 4.30
707 2002 5.337813 GGGACTATAGTTTTGGAACTTCCGA 60.338 44.000 6.88 0.00 43.48 4.55
708 2003 5.579904 GGACTATAGTTTTGGAACTTCCGAC 59.420 44.000 6.88 2.65 43.48 4.79
709 2004 5.485620 ACTATAGTTTTGGAACTTCCGACC 58.514 41.667 0.00 0.00 43.48 4.79
710 2005 2.721425 AGTTTTGGAACTTCCGACCA 57.279 45.000 3.28 0.00 43.48 4.02
711 2006 3.223674 AGTTTTGGAACTTCCGACCAT 57.776 42.857 3.28 0.00 43.48 3.55
712 2007 3.562182 AGTTTTGGAACTTCCGACCATT 58.438 40.909 3.28 0.00 43.48 3.16
713 2008 3.568430 AGTTTTGGAACTTCCGACCATTC 59.432 43.478 3.28 0.00 43.48 2.67
714 2009 3.502123 TTTGGAACTTCCGACCATTCT 57.498 42.857 3.28 0.00 40.17 2.40
715 2010 4.627284 TTTGGAACTTCCGACCATTCTA 57.373 40.909 3.28 0.00 40.17 2.10
716 2011 4.837093 TTGGAACTTCCGACCATTCTAT 57.163 40.909 3.28 0.00 40.17 1.98
717 2012 4.402056 TGGAACTTCCGACCATTCTATC 57.598 45.455 3.28 0.00 40.17 2.08
718 2013 3.772572 TGGAACTTCCGACCATTCTATCA 59.227 43.478 3.28 0.00 40.17 2.15
719 2014 4.408921 TGGAACTTCCGACCATTCTATCAT 59.591 41.667 3.28 0.00 40.17 2.45
720 2015 4.991687 GGAACTTCCGACCATTCTATCATC 59.008 45.833 0.00 0.00 0.00 2.92
721 2016 5.453339 GGAACTTCCGACCATTCTATCATCA 60.453 44.000 0.00 0.00 0.00 3.07
722 2017 5.614324 ACTTCCGACCATTCTATCATCAA 57.386 39.130 0.00 0.00 0.00 2.57
723 2018 5.989477 ACTTCCGACCATTCTATCATCAAA 58.011 37.500 0.00 0.00 0.00 2.69
724 2019 6.414732 ACTTCCGACCATTCTATCATCAAAA 58.585 36.000 0.00 0.00 0.00 2.44
725 2020 7.056635 ACTTCCGACCATTCTATCATCAAAAT 58.943 34.615 0.00 0.00 0.00 1.82
726 2021 7.557719 ACTTCCGACCATTCTATCATCAAAATT 59.442 33.333 0.00 0.00 0.00 1.82
727 2022 7.263100 TCCGACCATTCTATCATCAAAATTG 57.737 36.000 0.00 0.00 0.00 2.32
728 2023 7.053498 TCCGACCATTCTATCATCAAAATTGA 58.947 34.615 0.00 0.00 42.14 2.57
729 2024 7.012327 TCCGACCATTCTATCATCAAAATTGAC 59.988 37.037 0.00 0.00 40.49 3.18
730 2025 6.847792 CGACCATTCTATCATCAAAATTGACG 59.152 38.462 0.00 0.00 40.49 4.35
731 2026 7.254421 CGACCATTCTATCATCAAAATTGACGA 60.254 37.037 0.00 0.00 40.49 4.20
732 2027 8.279970 ACCATTCTATCATCAAAATTGACGAA 57.720 30.769 0.00 0.00 40.49 3.85
733 2028 8.184192 ACCATTCTATCATCAAAATTGACGAAC 58.816 33.333 0.00 0.00 40.49 3.95
734 2029 7.374228 CCATTCTATCATCAAAATTGACGAACG 59.626 37.037 0.00 0.00 40.49 3.95
735 2030 6.344572 TCTATCATCAAAATTGACGAACGG 57.655 37.500 0.00 0.00 40.49 4.44
736 2031 6.103330 TCTATCATCAAAATTGACGAACGGA 58.897 36.000 0.00 0.00 40.49 4.69
737 2032 4.661993 TCATCAAAATTGACGAACGGAG 57.338 40.909 0.00 0.00 40.49 4.63
738 2033 2.961522 TCAAAATTGACGAACGGAGC 57.038 45.000 0.00 0.00 31.01 4.70
739 2034 2.214347 TCAAAATTGACGAACGGAGCA 58.786 42.857 0.00 0.00 31.01 4.26
740 2035 2.614520 TCAAAATTGACGAACGGAGCAA 59.385 40.909 0.00 1.22 31.01 3.91
741 2036 2.681152 AAATTGACGAACGGAGCAAC 57.319 45.000 0.00 0.00 0.00 4.17
742 2037 0.511221 AATTGACGAACGGAGCAACG 59.489 50.000 0.00 0.00 40.31 4.10
743 2038 1.897398 ATTGACGAACGGAGCAACGC 61.897 55.000 0.00 0.00 37.37 4.84
744 2039 4.117372 GACGAACGGAGCAACGCG 62.117 66.667 3.53 3.53 37.37 6.01
754 2049 2.865151 GCAACGCGCGTCATCAAC 60.865 61.111 37.77 17.56 0.00 3.18
866 2175 0.107945 CCAGCAACCTGACTAGCCTC 60.108 60.000 0.00 0.00 41.77 4.70
901 2220 3.003763 GCTCCCCACTCTCCGGTT 61.004 66.667 0.00 0.00 0.00 4.44
948 2267 2.726822 GAAACGACGGCAGAACCCCT 62.727 60.000 0.00 0.00 33.26 4.79
985 2304 4.463879 CCCAGCACTCTCCGCCTG 62.464 72.222 0.00 0.00 0.00 4.85
986 2305 3.699894 CCAGCACTCTCCGCCTGT 61.700 66.667 0.00 0.00 0.00 4.00
1061 2386 3.288308 CTGCCAAGACGAGAGCGGT 62.288 63.158 0.00 0.00 43.17 5.68
1131 2543 1.801178 GCCAAGAAGAAGAAGACGGTG 59.199 52.381 0.00 0.00 0.00 4.94
1150 2562 1.003355 CCCGCAGCCAAGAAGAAGA 60.003 57.895 0.00 0.00 0.00 2.87
1151 2563 0.606401 CCCGCAGCCAAGAAGAAGAA 60.606 55.000 0.00 0.00 0.00 2.52
1156 2568 3.233355 GCCAAGAAGAAGAAGGCGA 57.767 52.632 0.00 0.00 35.42 5.54
1269 2681 0.250234 TCATCAGCAACCTTCCGGAG 59.750 55.000 3.34 0.00 0.00 4.63
1503 2915 1.975407 ACCGACGGACTCCATCGTT 60.975 57.895 23.38 0.00 39.88 3.85
1526 2938 1.075896 GGATCCTCTCCGACCACCT 60.076 63.158 3.84 0.00 33.29 4.00
1634 3046 1.079057 GGTTCCACTCTCGAAGCCC 60.079 63.158 0.00 0.00 32.77 5.19
1653 3065 0.037326 CGCACAACCTTCAGGAGCTA 60.037 55.000 0.00 0.00 38.94 3.32
1847 3259 2.158842 CCATGTCAGAGGATGTCTTCCC 60.159 54.545 1.13 0.00 46.81 3.97
1849 3261 2.461695 TGTCAGAGGATGTCTTCCCTC 58.538 52.381 0.00 0.00 46.81 4.30
1907 3319 7.714377 CCTATATCTGCAGGGAAATGCTTATAG 59.286 40.741 15.13 9.97 46.63 1.31
1930 3343 1.227674 CCCTCCACATTAGCTCGCC 60.228 63.158 0.00 0.00 0.00 5.54
1974 3387 5.527951 TCAGTCATTGTTATGTTGGCAAAC 58.472 37.500 0.00 0.00 36.78 2.93
2007 3420 3.003763 AGGACACCCCTCGCCTTC 61.004 66.667 0.00 0.00 43.31 3.46
2034 3447 3.538591 CTGCTTTGTCCATGCTCAGATA 58.461 45.455 0.00 0.00 0.00 1.98
2058 3471 9.734984 ATAGTTTGAATATCCGGGTAAATAAGG 57.265 33.333 0.00 0.00 0.00 2.69
2059 3472 6.489022 AGTTTGAATATCCGGGTAAATAAGGC 59.511 38.462 0.00 0.00 0.00 4.35
2060 3473 5.570205 TGAATATCCGGGTAAATAAGGCA 57.430 39.130 0.00 0.00 0.00 4.75
2081 3494 4.884164 GCAGCACCTAAACTGGAGATATTT 59.116 41.667 0.00 0.00 34.38 1.40
2233 3649 2.781945 GTTCCAACCAGCTTGAACAG 57.218 50.000 0.00 0.00 30.42 3.16
2366 3786 4.034975 GTGAGTATTCATCTTGGCTTGCTC 59.965 45.833 0.00 0.00 35.39 4.26
2413 5647 8.968242 GTTACTCCAAAAAGAATTGATTGACAC 58.032 33.333 0.00 0.00 30.00 3.67
2414 5648 7.111247 ACTCCAAAAAGAATTGATTGACACA 57.889 32.000 0.00 0.00 30.00 3.72
2415 5649 7.729116 ACTCCAAAAAGAATTGATTGACACAT 58.271 30.769 0.00 0.00 30.00 3.21
2416 5650 8.859090 ACTCCAAAAAGAATTGATTGACACATA 58.141 29.630 0.00 0.00 30.00 2.29
2500 5742 7.411486 TTTCCAGTGGAACAAATACTTGAAA 57.589 32.000 24.52 1.93 44.16 2.69
2651 5894 3.186409 TGTTCTGAATGCGAAAGTGCTAC 59.814 43.478 0.00 0.00 35.36 3.58
2687 5930 2.606308 GGCGTTAGTGAGAAGTTCGACA 60.606 50.000 9.81 6.35 0.00 4.35
2707 5950 2.134789 AGAAATGGGTGGCTGATCAC 57.865 50.000 0.00 0.00 36.95 3.06
2772 6015 6.869473 TCGAGTTTAAACATTGTTCGTACTG 58.131 36.000 20.06 3.08 0.00 2.74
2777 6020 7.698970 AGTTTAAACATTGTTCGTACTGTTTGG 59.301 33.333 20.06 0.00 40.81 3.28
2781 6024 5.305585 ACATTGTTCGTACTGTTTGGATCT 58.694 37.500 0.00 0.00 0.00 2.75
2940 6539 5.523552 GTCTTTTGCTTGTTTTTATGGTGCT 59.476 36.000 0.00 0.00 0.00 4.40
3000 6599 9.516314 GCTTGTTTCTCTGTTTGTAGTTTAATT 57.484 29.630 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.816640 CCAACCTCGACAATAAGAAATCTGTA 59.183 38.462 0.00 0.00 0.00 2.74
2 3 5.643777 ACCAACCTCGACAATAAGAAATCTG 59.356 40.000 0.00 0.00 0.00 2.90
3 4 5.805728 ACCAACCTCGACAATAAGAAATCT 58.194 37.500 0.00 0.00 0.00 2.40
4 5 5.064834 GGACCAACCTCGACAATAAGAAATC 59.935 44.000 0.00 0.00 35.41 2.17
25 1311 4.200092 GGAGTAATGAATTGGTCCAGGAC 58.800 47.826 11.70 11.70 0.00 3.85
33 1319 3.270027 TGCTCACGGAGTAATGAATTGG 58.730 45.455 3.38 0.00 41.61 3.16
51 1337 7.329499 TGCAATAAATGGTGTAATGAATTGCT 58.671 30.769 15.25 0.00 45.03 3.91
78 1364 8.986477 TTTAGCCTCTCATTGAAATTTTAAGC 57.014 30.769 1.69 0.00 0.00 3.09
141 1427 8.405418 ACAGACTGTACATAAGAAGTGTTCTA 57.595 34.615 6.24 0.00 39.61 2.10
174 1460 1.755008 GGCTAGAGCTGGACGGACT 60.755 63.158 0.00 0.00 41.70 3.85
182 1468 5.112686 CCTACTTTTACAAGGCTAGAGCTG 58.887 45.833 0.00 0.00 41.70 4.24
268 1556 4.764679 TGCACGCAGTTGAAAATTATCT 57.235 36.364 0.00 0.00 41.61 1.98
271 1559 6.385843 ACATAATGCACGCAGTTGAAAATTA 58.614 32.000 0.00 0.00 41.61 1.40
309 1598 6.968904 CAGATACAACATGAACCAGTTTATGC 59.031 38.462 13.45 0.00 39.34 3.14
322 1611 7.664082 ACAGAACTCTTTCAGATACAACATG 57.336 36.000 0.00 0.00 33.72 3.21
340 1629 9.717892 GCAAAAGTTATTAGGCTTATACAGAAC 57.282 33.333 0.00 0.00 0.00 3.01
343 1632 8.893727 ACAGCAAAAGTTATTAGGCTTATACAG 58.106 33.333 0.00 0.00 0.00 2.74
349 1638 6.183360 ACCAAACAGCAAAAGTTATTAGGCTT 60.183 34.615 0.00 0.00 0.00 4.35
355 1644 9.313118 CTAGAAAACCAAACAGCAAAAGTTATT 57.687 29.630 0.00 0.00 0.00 1.40
366 1655 4.918810 AAGCACCTAGAAAACCAAACAG 57.081 40.909 0.00 0.00 0.00 3.16
389 1678 5.794687 TGAAAGGAAGTGTGCATATAACG 57.205 39.130 0.00 0.00 0.00 3.18
390 1679 6.095440 ACCATGAAAGGAAGTGTGCATATAAC 59.905 38.462 0.00 0.00 0.00 1.89
391 1680 6.186957 ACCATGAAAGGAAGTGTGCATATAA 58.813 36.000 0.00 0.00 0.00 0.98
392 1681 5.754782 ACCATGAAAGGAAGTGTGCATATA 58.245 37.500 0.00 0.00 0.00 0.86
401 1690 4.664688 AGATTGGACCATGAAAGGAAGT 57.335 40.909 0.00 0.00 0.00 3.01
431 1720 6.437477 TCCACATGACACTAAGATACTCAAGT 59.563 38.462 0.00 0.00 0.00 3.16
452 1741 4.010349 CCCTAAGTTGGACATTCTTCCAC 58.990 47.826 0.00 0.00 45.80 4.02
454 1743 3.621558 CCCCTAAGTTGGACATTCTTCC 58.378 50.000 0.00 0.00 36.03 3.46
468 1757 1.454479 CCACATGGCTGCCCCTAAG 60.454 63.158 17.53 3.86 0.00 2.18
474 1763 1.076485 ATCCTTCCACATGGCTGCC 60.076 57.895 12.87 12.87 34.44 4.85
496 1785 0.320771 ACCTGACTGCGCCTAAGTTG 60.321 55.000 4.18 0.00 0.00 3.16
503 1792 0.108138 ACTATTCACCTGACTGCGCC 60.108 55.000 4.18 0.00 0.00 6.53
542 1831 9.535170 TTATTGGAGTTTGGGTTGATTTGTATA 57.465 29.630 0.00 0.00 0.00 1.47
559 1849 5.036916 TGGGATGGAGTAGTTTATTGGAGT 58.963 41.667 0.00 0.00 0.00 3.85
577 1867 9.533831 ACAAATCTAAGACAAGTAATTTGGGAT 57.466 29.630 9.60 0.00 41.25 3.85
627 1922 3.732048 ATACAACCTCCGTCCCAAATT 57.268 42.857 0.00 0.00 0.00 1.82
634 1929 8.658499 ATCACTAATTAAATACAACCTCCGTC 57.342 34.615 0.00 0.00 0.00 4.79
665 1960 5.934781 AGTCCCAAAATAAATTGTGGCAAA 58.065 33.333 6.40 0.00 42.66 3.68
668 1963 8.007405 ACTATAGTCCCAAAATAAATTGTGGC 57.993 34.615 6.40 0.00 42.66 5.01
678 1973 8.721133 AAGTTCCAAAACTATAGTCCCAAAAT 57.279 30.769 5.70 0.00 45.07 1.82
679 1974 7.231925 GGAAGTTCCAAAACTATAGTCCCAAAA 59.768 37.037 17.44 0.00 45.07 2.44
680 1975 6.717997 GGAAGTTCCAAAACTATAGTCCCAAA 59.282 38.462 17.44 0.00 45.07 3.28
681 1976 6.243148 GGAAGTTCCAAAACTATAGTCCCAA 58.757 40.000 17.44 0.00 45.07 4.12
682 1977 5.570034 CGGAAGTTCCAAAACTATAGTCCCA 60.570 44.000 21.76 0.00 45.07 4.37
683 1978 4.874396 CGGAAGTTCCAAAACTATAGTCCC 59.126 45.833 21.76 0.00 45.07 4.46
684 1979 5.579904 GTCGGAAGTTCCAAAACTATAGTCC 59.420 44.000 21.76 0.00 45.07 3.85
685 1980 5.579904 GGTCGGAAGTTCCAAAACTATAGTC 59.420 44.000 21.76 0.30 45.07 2.59
686 1981 5.012354 TGGTCGGAAGTTCCAAAACTATAGT 59.988 40.000 21.76 0.00 45.07 2.12
687 1982 5.484715 TGGTCGGAAGTTCCAAAACTATAG 58.515 41.667 21.76 0.00 45.07 1.31
688 1983 5.486735 TGGTCGGAAGTTCCAAAACTATA 57.513 39.130 21.76 5.32 45.07 1.31
689 1984 4.360951 TGGTCGGAAGTTCCAAAACTAT 57.639 40.909 21.76 0.00 45.07 2.12
690 1985 3.842007 TGGTCGGAAGTTCCAAAACTA 57.158 42.857 21.76 11.11 45.07 2.24
692 1987 3.568430 AGAATGGTCGGAAGTTCCAAAAC 59.432 43.478 21.76 14.94 38.87 2.43
693 1988 3.827722 AGAATGGTCGGAAGTTCCAAAA 58.172 40.909 21.76 3.71 38.87 2.44
694 1989 3.502123 AGAATGGTCGGAAGTTCCAAA 57.498 42.857 21.76 6.31 38.87 3.28
695 1990 4.224147 TGATAGAATGGTCGGAAGTTCCAA 59.776 41.667 21.76 0.00 38.87 3.53
696 1991 3.772572 TGATAGAATGGTCGGAAGTTCCA 59.227 43.478 21.76 6.35 35.91 3.53
697 1992 4.402056 TGATAGAATGGTCGGAAGTTCC 57.598 45.455 12.27 12.27 0.00 3.62
698 1993 5.601662 TGATGATAGAATGGTCGGAAGTTC 58.398 41.667 0.00 0.00 0.00 3.01
699 1994 5.614324 TGATGATAGAATGGTCGGAAGTT 57.386 39.130 0.00 0.00 0.00 2.66
700 1995 5.614324 TTGATGATAGAATGGTCGGAAGT 57.386 39.130 0.00 0.00 0.00 3.01
701 1996 6.925610 TTTTGATGATAGAATGGTCGGAAG 57.074 37.500 0.00 0.00 0.00 3.46
702 1997 7.555914 TCAATTTTGATGATAGAATGGTCGGAA 59.444 33.333 0.00 0.00 31.01 4.30
703 1998 7.012327 GTCAATTTTGATGATAGAATGGTCGGA 59.988 37.037 0.00 0.00 39.73 4.55
704 1999 7.134815 GTCAATTTTGATGATAGAATGGTCGG 58.865 38.462 0.00 0.00 39.73 4.79
705 2000 6.847792 CGTCAATTTTGATGATAGAATGGTCG 59.152 38.462 6.67 0.00 44.92 4.79
706 2001 7.919690 TCGTCAATTTTGATGATAGAATGGTC 58.080 34.615 10.43 0.00 45.50 4.02
707 2002 7.864108 TCGTCAATTTTGATGATAGAATGGT 57.136 32.000 10.43 0.00 45.50 3.55
717 2012 3.163594 GCTCCGTTCGTCAATTTTGATG 58.836 45.455 6.23 6.23 43.79 3.07
718 2013 2.811431 TGCTCCGTTCGTCAATTTTGAT 59.189 40.909 0.00 0.00 39.73 2.57
719 2014 2.214347 TGCTCCGTTCGTCAATTTTGA 58.786 42.857 0.00 0.00 34.20 2.69
720 2015 2.679355 TGCTCCGTTCGTCAATTTTG 57.321 45.000 0.00 0.00 0.00 2.44
721 2016 2.601266 CGTTGCTCCGTTCGTCAATTTT 60.601 45.455 0.00 0.00 0.00 1.82
722 2017 1.070175 CGTTGCTCCGTTCGTCAATTT 60.070 47.619 0.00 0.00 0.00 1.82
723 2018 0.511221 CGTTGCTCCGTTCGTCAATT 59.489 50.000 0.00 0.00 0.00 2.32
724 2019 1.897398 GCGTTGCTCCGTTCGTCAAT 61.897 55.000 0.00 0.00 0.00 2.57
725 2020 2.591311 GCGTTGCTCCGTTCGTCAA 61.591 57.895 0.00 0.00 0.00 3.18
726 2021 3.033764 GCGTTGCTCCGTTCGTCA 61.034 61.111 0.00 0.00 0.00 4.35
727 2022 4.117372 CGCGTTGCTCCGTTCGTC 62.117 66.667 0.00 0.00 0.00 4.20
734 2029 4.210304 GATGACGCGCGTTGCTCC 62.210 66.667 38.03 23.77 43.27 4.70
735 2030 3.010585 TTGATGACGCGCGTTGCTC 62.011 57.895 38.03 29.68 43.27 4.26
736 2031 3.041351 TTGATGACGCGCGTTGCT 61.041 55.556 38.03 23.72 43.27 3.91
737 2032 2.865151 GTTGATGACGCGCGTTGC 60.865 61.111 38.03 27.02 41.47 4.17
738 2033 2.568029 CGTTGATGACGCGCGTTG 60.568 61.111 38.03 16.27 45.86 4.10
769 2064 2.544267 CACTCAAGTCCGACCAGTTTTC 59.456 50.000 0.00 0.00 0.00 2.29
901 2220 1.216064 CTGATGGGGATGGAACTGGA 58.784 55.000 0.00 0.00 0.00 3.86
948 2267 2.158325 GGCATCTGGGATGGGGAATTTA 60.158 50.000 9.18 0.00 0.00 1.40
985 2304 2.237143 TCCTCATGTGTGGAGATTGGAC 59.763 50.000 0.00 0.00 33.24 4.02
986 2305 2.550175 TCCTCATGTGTGGAGATTGGA 58.450 47.619 0.00 0.00 33.24 3.53
1075 2454 1.746991 CCTTCTTCTTGGCCTCGGC 60.747 63.158 3.32 0.00 41.06 5.54
1079 2458 1.003233 GTCGCCTTCTTCTTGGCCT 60.003 57.895 3.32 0.00 45.90 5.19
1131 2543 2.672996 TTCTTCTTGGCTGCGGGC 60.673 61.111 13.15 13.15 40.90 6.13
1269 2681 4.101448 ATGGTGCAGAGGACGGCC 62.101 66.667 0.00 0.00 36.45 6.13
1634 3046 0.037326 TAGCTCCTGAAGGTTGTGCG 60.037 55.000 0.00 0.00 36.91 5.34
1653 3065 5.129485 ACACAAGATCGGGAAGAAGATATGT 59.871 40.000 0.00 0.00 31.43 2.29
1847 3259 2.203422 AGGAGGAGATCGCCCGAG 60.203 66.667 12.40 0.00 35.80 4.63
1849 3261 4.292178 GCAGGAGGAGATCGCCCG 62.292 72.222 12.40 0.00 35.80 6.13
1930 3343 1.137872 AGGCGATGCTCCTAAGAGTTG 59.862 52.381 0.00 0.00 42.59 3.16
1974 3387 5.105756 GGGTGTCCTCAATAACCAATTCTTG 60.106 44.000 0.00 0.00 34.18 3.02
2034 3447 6.489022 GCCTTATTTACCCGGATATTCAAACT 59.511 38.462 0.73 0.00 0.00 2.66
2058 3471 2.409948 ATCTCCAGTTTAGGTGCTGC 57.590 50.000 0.00 0.00 0.00 5.25
2059 3472 5.297776 CCAAATATCTCCAGTTTAGGTGCTG 59.702 44.000 0.00 0.00 0.00 4.41
2060 3473 5.440610 CCAAATATCTCCAGTTTAGGTGCT 58.559 41.667 0.00 0.00 0.00 4.40
2081 3494 4.278513 CGGGGTGACAAAGGGCCA 62.279 66.667 6.18 0.00 0.00 5.36
2233 3649 3.262420 ACCTTCACTGTGCATATCGAAC 58.738 45.455 2.12 0.00 0.00 3.95
2463 5705 5.805728 TCCACTGGAAAGGAAATAAGACTC 58.194 41.667 0.00 0.00 0.00 3.36
2500 5742 1.736126 CGCACATTGTTCATCTCTGCT 59.264 47.619 0.00 0.00 0.00 4.24
2651 5894 5.740569 CACTAACGCCAAATTTGATCTCATG 59.259 40.000 19.86 5.90 0.00 3.07
2687 5930 2.450476 GTGATCAGCCACCCATTTCTT 58.550 47.619 0.00 0.00 0.00 2.52
2707 5950 0.036010 CCACTCCTAGCAACCTGTGG 60.036 60.000 0.00 0.00 38.87 4.17
2781 6024 6.615316 TGACAAGTCATGGGGATCTAAATAGA 59.385 38.462 0.00 0.00 34.14 1.98
2792 6035 1.205417 GGCAATTGACAAGTCATGGGG 59.795 52.381 10.34 0.00 39.64 4.96
2940 6539 6.430925 GCAGGCAACATAATATTCAGGTATCA 59.569 38.462 0.00 0.00 41.41 2.15
3000 6599 3.517296 TGCTGGGAATTACAAAGGACA 57.483 42.857 0.00 0.00 0.00 4.02
3001 6600 3.131046 CCATGCTGGGAATTACAAAGGAC 59.869 47.826 0.00 0.00 32.67 3.85


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

AutoCloner maintained by Alex Coulton.