Multiple sequence alignment - TraesCS2A01G300000

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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 TraesCS2A01G300000 chr2A 100.000 5927 0 0 1 5927 515497262 515491336 0.000000e+00 10946
1 TraesCS2A01G300000 chr2A 93.108 5630 338 27 1 5609 127164749 127170349 0.000000e+00 8202
2 TraesCS2A01G300000 chr2A 92.606 5626 335 41 1 5600 749461756 749467326 0.000000e+00 8010
3 TraesCS2A01G300000 chr2A 94.125 3098 149 16 2836 5927 458999747 458996677 0.000000e+00 4682
4 TraesCS2A01G300000 chr5A 94.190 5938 276 21 1 5927 482758552 482752673 0.000000e+00 8990
5 TraesCS2A01G300000 chr2B 92.105 5953 408 44 1 5927 769024615 769018699 0.000000e+00 8333
6 TraesCS2A01G300000 chr2B 87.934 6017 579 93 1 5927 665892119 665886160 0.000000e+00 6953
7 TraesCS2A01G300000 chr2B 90.054 553 52 3 5375 5925 260632639 260633190 0.000000e+00 713
8 TraesCS2A01G300000 chr2B 83.441 465 63 12 5472 5927 503648921 503649380 2.550000e-113 420
9 TraesCS2A01G300000 chr2B 85.897 390 52 3 5541 5927 621616654 621616265 4.270000e-111 412
10 TraesCS2A01G300000 chr5B 92.097 5947 393 45 1 5927 658940712 658934823 0.000000e+00 8307
11 TraesCS2A01G300000 chr5B 90.920 5738 437 58 1 5682 194203144 194197435 0.000000e+00 7633
12 TraesCS2A01G300000 chr1B 91.219 5979 461 48 1 5927 306216181 306222147 0.000000e+00 8074
13 TraesCS2A01G300000 chr1B 89.882 5752 501 61 1 5686 275813505 275807769 0.000000e+00 7323
14 TraesCS2A01G300000 chr6B 91.165 5976 433 61 1 5925 698947970 698942039 0.000000e+00 8022
15 TraesCS2A01G300000 chr7A 92.595 5631 336 41 1 5609 699086974 699081403 0.000000e+00 8013
16 TraesCS2A01G300000 chr7A 94.131 4430 218 15 1 4421 67379434 67375038 0.000000e+00 6702
17 TraesCS2A01G300000 chr7A 95.071 2759 127 8 3175 5926 595119845 595122601 0.000000e+00 4333
18 TraesCS2A01G300000 chr4B 90.557 5994 474 63 1 5924 451485259 451479288 0.000000e+00 7849
19 TraesCS2A01G300000 chr3B 90.199 5989 492 62 1 5927 178563211 178569166 0.000000e+00 7720
20 TraesCS2A01G300000 chr3B 89.935 6011 505 62 1 5926 361609645 361603650 0.000000e+00 7657
21 TraesCS2A01G300000 chr3B 87.858 5897 576 92 1 5794 698404415 698398556 0.000000e+00 6794
22 TraesCS2A01G300000 chr6A 94.072 4099 205 21 1840 5927 54963062 54958991 0.000000e+00 6189
23 TraesCS2A01G300000 chr1A 94.122 2501 134 11 3438 5927 399798851 399796353 0.000000e+00 3792


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 TraesCS2A01G300000 chr2A 515491336 515497262 5926 True 10946 10946 100.000 1 5927 1 chr2A.!!$R2 5926
1 TraesCS2A01G300000 chr2A 127164749 127170349 5600 False 8202 8202 93.108 1 5609 1 chr2A.!!$F1 5608
2 TraesCS2A01G300000 chr2A 749461756 749467326 5570 False 8010 8010 92.606 1 5600 1 chr2A.!!$F2 5599
3 TraesCS2A01G300000 chr2A 458996677 458999747 3070 True 4682 4682 94.125 2836 5927 1 chr2A.!!$R1 3091
4 TraesCS2A01G300000 chr5A 482752673 482758552 5879 True 8990 8990 94.190 1 5927 1 chr5A.!!$R1 5926
5 TraesCS2A01G300000 chr2B 769018699 769024615 5916 True 8333 8333 92.105 1 5927 1 chr2B.!!$R3 5926
6 TraesCS2A01G300000 chr2B 665886160 665892119 5959 True 6953 6953 87.934 1 5927 1 chr2B.!!$R2 5926
7 TraesCS2A01G300000 chr2B 260632639 260633190 551 False 713 713 90.054 5375 5925 1 chr2B.!!$F1 550
8 TraesCS2A01G300000 chr5B 658934823 658940712 5889 True 8307 8307 92.097 1 5927 1 chr5B.!!$R2 5926
9 TraesCS2A01G300000 chr5B 194197435 194203144 5709 True 7633 7633 90.920 1 5682 1 chr5B.!!$R1 5681
10 TraesCS2A01G300000 chr1B 306216181 306222147 5966 False 8074 8074 91.219 1 5927 1 chr1B.!!$F1 5926
11 TraesCS2A01G300000 chr1B 275807769 275813505 5736 True 7323 7323 89.882 1 5686 1 chr1B.!!$R1 5685
12 TraesCS2A01G300000 chr6B 698942039 698947970 5931 True 8022 8022 91.165 1 5925 1 chr6B.!!$R1 5924
13 TraesCS2A01G300000 chr7A 699081403 699086974 5571 True 8013 8013 92.595 1 5609 1 chr7A.!!$R2 5608
14 TraesCS2A01G300000 chr7A 67375038 67379434 4396 True 6702 6702 94.131 1 4421 1 chr7A.!!$R1 4420
15 TraesCS2A01G300000 chr7A 595119845 595122601 2756 False 4333 4333 95.071 3175 5926 1 chr7A.!!$F1 2751
16 TraesCS2A01G300000 chr4B 451479288 451485259 5971 True 7849 7849 90.557 1 5924 1 chr4B.!!$R1 5923
17 TraesCS2A01G300000 chr3B 178563211 178569166 5955 False 7720 7720 90.199 1 5927 1 chr3B.!!$F1 5926
18 TraesCS2A01G300000 chr3B 361603650 361609645 5995 True 7657 7657 89.935 1 5926 1 chr3B.!!$R1 5925
19 TraesCS2A01G300000 chr3B 698398556 698404415 5859 True 6794 6794 87.858 1 5794 1 chr3B.!!$R2 5793
20 TraesCS2A01G300000 chr6A 54958991 54963062 4071 True 6189 6189 94.072 1840 5927 1 chr6A.!!$R1 4087
21 TraesCS2A01G300000 chr1A 399796353 399798851 2498 True 3792 3792 94.122 3438 5927 1 chr1A.!!$R1 2489

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
730 745 0.041833 AGCTGCTAGGAGGAGGTTCA 59.958 55.0 13.67 0.00 41.68 3.18 F
2068 2172 0.103208 CTCCTGTCGGTGCAGATACC 59.897 60.0 0.00 0.00 38.70 2.73 F
2468 2572 0.106868 GCCCCGCCCTACAAATAAGT 60.107 55.0 0.00 0.00 0.00 2.24 F
3527 3690 0.250295 CGAAGTCAGGGCCACAAAGA 60.250 55.0 6.18 0.00 0.00 2.52 F
4338 4550 1.656587 TACATGCAGGTCCTGTTCCT 58.343 50.0 20.24 3.93 33.43 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2468 2572 0.032130 GCCGCTACAGAATGATCGGA 59.968 55.000 2.41 0.0 43.85 4.55 R
3293 3456 0.252881 ATCTTCTCAGGGGTGCCTGA 60.253 55.000 0.00 0.0 43.53 3.86 R
4338 4550 0.401356 TGCAAGCTCCTGGAACATGA 59.599 50.000 6.51 0.0 38.20 3.07 R
4555 4776 1.138036 CGCCACGTACTCAATCGGA 59.862 57.895 0.00 0.0 0.00 4.55 R
5534 5794 3.125146 TGTTTATGCTGAATCTGTCGTGC 59.875 43.478 0.00 0.0 0.00 5.34 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
102 108 3.593442 ACTTTGGAAAGTGGATGGACA 57.407 42.857 3.95 0.00 46.80 4.02
105 111 3.805066 TTGGAAAGTGGATGGACATGA 57.195 42.857 0.00 0.00 0.00 3.07
121 127 2.037772 ACATGAACTCAGCTCCGTCTTT 59.962 45.455 0.00 0.00 0.00 2.52
220 233 2.819608 GGTTGGTCATTGCTGCTTCTTA 59.180 45.455 0.00 0.00 0.00 2.10
388 402 1.183030 TCCCAGAACGGACACATCGT 61.183 55.000 0.00 0.00 43.14 3.73
406 420 2.203280 CCAACTGGTTGCCGTGGA 60.203 61.111 7.84 0.00 39.16 4.02
420 434 2.470196 CGTGGACGGTATGACTACAG 57.530 55.000 0.00 0.00 35.37 2.74
423 437 2.094390 GTGGACGGTATGACTACAGCAA 60.094 50.000 0.00 0.00 0.00 3.91
440 454 2.094675 GCAATTCCCAAGAGCTTGCTA 58.905 47.619 4.72 0.00 38.48 3.49
520 534 2.353803 GGAGAACGTGCAATAGGACACT 60.354 50.000 0.00 0.00 35.57 3.55
533 547 6.430308 GCAATAGGACACTGATGATGATGAAT 59.570 38.462 0.00 0.00 0.00 2.57
554 568 2.605837 TGTTGAAGTTCGTGCAGGTA 57.394 45.000 6.26 0.00 0.00 3.08
658 673 0.553612 ATCAAAGAGGGGGAGGGCTT 60.554 55.000 0.00 0.00 0.00 4.35
695 710 0.402121 GGTTCTCCTGGCAAGAGGTT 59.598 55.000 12.96 0.00 34.36 3.50
730 745 0.041833 AGCTGCTAGGAGGAGGTTCA 59.958 55.000 13.67 0.00 41.68 3.18
776 794 9.959749 GTTTTGTCTATATTTTTGGAACAGACA 57.040 29.630 0.00 0.00 42.39 3.41
783 801 2.879103 TTTGGAACAGACAGATCCCC 57.121 50.000 0.00 0.00 42.39 4.81
974 999 2.899256 CCATTGTTGGTGACATCCCTTT 59.101 45.455 0.00 0.00 42.32 3.11
1010 1035 1.469703 TCGTACGACGATGTCCAACAT 59.530 47.619 15.28 0.00 46.73 2.71
1031 1056 1.296715 GGGATCCTGTCGTGTTGCT 59.703 57.895 12.58 0.00 0.00 3.91
1148 1180 1.003580 ACATGGGCTTCTGTCATCGTT 59.996 47.619 0.00 0.00 0.00 3.85
1164 1197 0.888736 CGTTCCCACATGGCAACTGA 60.889 55.000 3.29 0.00 37.61 3.41
1346 1404 5.364446 TGAAATTGCATTCCTGGCAGATAAT 59.636 36.000 17.94 12.32 43.05 1.28
1347 1405 5.464030 AATTGCATTCCTGGCAGATAATC 57.536 39.130 17.94 9.65 43.05 1.75
1348 1406 3.870538 TGCATTCCTGGCAGATAATCT 57.129 42.857 17.94 0.00 36.11 2.40
1349 1407 3.483421 TGCATTCCTGGCAGATAATCTG 58.517 45.455 17.94 7.33 46.90 2.90
1572 1676 4.353777 TGCAGGGTGAAGAAGACTACTAT 58.646 43.478 0.00 0.00 0.00 2.12
1682 1786 2.869801 CCAGTCGACAAAACTGCTGTTA 59.130 45.455 19.50 0.00 42.26 2.41
1689 1793 4.551990 CGACAAAACTGCTGTTACATCGTT 60.552 41.667 19.21 5.81 34.96 3.85
1833 1937 5.324409 TGAAATATTGCCAACTCTTCTGGT 58.676 37.500 0.00 0.00 36.24 4.00
1863 1967 1.304630 TTGCTGTGAGCCATGCCAT 60.305 52.632 0.00 0.00 41.51 4.40
1937 2041 1.847328 TTCCCGCTCATCTGACACTA 58.153 50.000 0.00 0.00 0.00 2.74
1964 2068 3.209097 GCGTGTGTGGTGGCACTT 61.209 61.111 18.45 0.00 39.89 3.16
1967 2071 0.249699 CGTGTGTGGTGGCACTTCTA 60.250 55.000 18.45 0.00 39.89 2.10
1972 2076 1.977854 TGTGGTGGCACTTCTATGTCT 59.022 47.619 18.45 0.00 0.00 3.41
2024 2128 8.608185 TCATAATGATATGCCATCTACAGGTA 57.392 34.615 0.00 0.00 39.04 3.08
2068 2172 0.103208 CTCCTGTCGGTGCAGATACC 59.897 60.000 0.00 0.00 38.70 2.73
2069 2173 1.144057 CCTGTCGGTGCAGATACCC 59.856 63.158 0.00 0.00 38.70 3.69
2118 2222 2.282674 ACCGAGGTGTCGTAGCCA 60.283 61.111 0.00 0.00 45.30 4.75
2134 2238 1.959085 CCACCGCAAGCAATCAACT 59.041 52.632 0.00 0.00 0.00 3.16
2347 2451 1.002134 CGCAGTGGAAATCCCCAGT 60.002 57.895 0.00 0.00 40.37 4.00
2392 2496 1.202927 CCAGTCAATGTTGGTGTCCCT 60.203 52.381 0.00 0.00 0.00 4.20
2414 2518 5.710099 CCTTACAGCCCAAACAAGAAGATTA 59.290 40.000 0.00 0.00 0.00 1.75
2446 2550 1.945387 CGGCTGATACTGCTGACAAT 58.055 50.000 0.00 0.00 36.94 2.71
2468 2572 0.106868 GCCCCGCCCTACAAATAAGT 60.107 55.000 0.00 0.00 0.00 2.24
2519 2626 6.947733 AGATATGTTTGTTGATCTTTCACCCA 59.052 34.615 0.00 0.00 0.00 4.51
2527 2634 3.902218 TGATCTTTCACCCATGGATTCC 58.098 45.455 15.22 0.00 0.00 3.01
2663 2770 0.390492 GCCAGTTGCCTTTGCTTTCT 59.610 50.000 0.00 0.00 38.71 2.52
3139 3271 2.811431 TGGCAACTACAATGCACTACAC 59.189 45.455 0.00 0.00 45.60 2.90
3140 3272 2.811431 GGCAACTACAATGCACTACACA 59.189 45.455 0.00 0.00 45.60 3.72
3141 3273 3.440173 GGCAACTACAATGCACTACACAT 59.560 43.478 0.00 0.00 45.60 3.21
3142 3274 4.406069 GCAACTACAATGCACTACACATG 58.594 43.478 0.00 0.00 43.29 3.21
3143 3275 4.672542 GCAACTACAATGCACTACACATGG 60.673 45.833 0.00 0.00 43.29 3.66
3144 3276 3.009723 ACTACAATGCACTACACATGGC 58.990 45.455 0.00 0.00 0.00 4.40
3145 3277 1.908344 ACAATGCACTACACATGGCA 58.092 45.000 0.00 0.00 41.00 4.92
3146 3278 2.237643 ACAATGCACTACACATGGCAA 58.762 42.857 0.00 0.00 40.02 4.52
3147 3279 2.030007 ACAATGCACTACACATGGCAAC 60.030 45.455 0.00 0.00 40.02 4.17
3148 3280 2.205022 ATGCACTACACATGGCAACT 57.795 45.000 0.00 0.00 40.02 3.16
3149 3281 2.849294 TGCACTACACATGGCAACTA 57.151 45.000 0.00 0.00 32.54 2.24
3150 3282 2.422597 TGCACTACACATGGCAACTAC 58.577 47.619 0.00 0.00 32.54 2.73
3151 3283 2.224402 TGCACTACACATGGCAACTACA 60.224 45.455 0.00 0.00 32.54 2.74
3152 3284 2.811431 GCACTACACATGGCAACTACAA 59.189 45.455 0.00 0.00 37.61 2.41
3153 3285 3.440173 GCACTACACATGGCAACTACAAT 59.560 43.478 0.00 0.00 37.61 2.71
3154 3286 4.672542 GCACTACACATGGCAACTACAATG 60.673 45.833 0.00 0.00 37.61 2.82
3155 3287 3.440173 ACTACACATGGCAACTACAATGC 59.560 43.478 0.00 0.00 43.08 3.56
3156 3288 2.237643 ACACATGGCAACTACAATGCA 58.762 42.857 0.00 0.00 45.60 3.96
3157 3289 2.030007 ACACATGGCAACTACAATGCAC 60.030 45.455 0.00 0.00 45.60 4.57
3158 3290 2.229543 CACATGGCAACTACAATGCACT 59.770 45.455 0.00 0.00 45.60 4.40
3159 3291 3.439825 CACATGGCAACTACAATGCACTA 59.560 43.478 0.00 0.00 45.60 2.74
3160 3292 3.440173 ACATGGCAACTACAATGCACTAC 59.560 43.478 0.00 0.00 45.60 2.73
3161 3293 3.133141 TGGCAACTACAATGCACTACA 57.867 42.857 0.00 0.00 45.60 2.74
3197 3353 1.687612 CCTCCACATGGCAACTCCT 59.312 57.895 0.00 0.00 35.26 3.69
3459 3622 4.284550 TGCCACCCCTGGTTCTGC 62.285 66.667 0.00 0.00 40.17 4.26
3527 3690 0.250295 CGAAGTCAGGGCCACAAAGA 60.250 55.000 6.18 0.00 0.00 2.52
3575 3738 2.083774 AGCGATTTGAAAATGCGAGGA 58.916 42.857 9.99 0.00 31.94 3.71
3623 3804 6.561737 TGAAAGCGTAATGACCACATTTTA 57.438 33.333 0.00 0.00 43.17 1.52
3950 4145 4.776837 TGCAAAATATGGGATGGTGACTTT 59.223 37.500 0.00 0.00 0.00 2.66
3968 4163 4.792068 ACTTTCACCACAAAATCCTGAGA 58.208 39.130 0.00 0.00 0.00 3.27
4043 4240 5.685728 AGTATTCCTTCCCTATTTGCACTC 58.314 41.667 0.00 0.00 0.00 3.51
4302 4513 4.883585 TGTTCTTCATGTGAACTCTGCTTT 59.116 37.500 23.68 0.00 42.86 3.51
4338 4550 1.656587 TACATGCAGGTCCTGTTCCT 58.343 50.000 20.24 3.93 33.43 3.36
4555 4776 5.634118 TCAAAGGTCCAGATCAGACATTTT 58.366 37.500 19.62 14.35 43.48 1.82
4588 4809 1.135199 GTGGCGACTACGAATCAAGGA 60.135 52.381 0.00 0.00 42.66 3.36
4894 5129 1.372499 CGCGAGTTCGTGGAGGAAA 60.372 57.895 0.00 0.00 45.14 3.13
4898 5133 1.000607 CGAGTTCGTGGAGGAAACTGA 60.001 52.381 0.00 0.00 35.95 3.41
4991 5226 3.382546 GCCGAGGAATGTAAGGTACTACA 59.617 47.826 0.00 0.00 38.49 2.74
5008 5249 7.873505 AGGTACTACATTCTGTTCTTCTCAAAC 59.126 37.037 0.00 0.00 36.02 2.93
5227 5472 7.257003 TGAATGCGTGCATTATGTTCTAAAAT 58.743 30.769 19.18 0.00 45.50 1.82
5534 5794 3.937706 CAGGGCAGATTCAGTACAAAGAG 59.062 47.826 0.00 0.00 0.00 2.85
5616 5876 7.214381 TGAGTATAATTAACATGGAAGACCCG 58.786 38.462 0.00 0.00 37.93 5.28
5705 6087 7.920151 GCAGATTAAACACATATAACATGGCAA 59.080 33.333 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 80 3.704061 TCCACTTTCCAAAGTTTTGAGGG 59.296 43.478 6.18 0.63 46.52 4.30
102 108 2.354203 GGAAAGACGGAGCTGAGTTCAT 60.354 50.000 0.00 0.00 0.00 2.57
105 111 0.321996 GGGAAAGACGGAGCTGAGTT 59.678 55.000 0.00 0.00 0.00 3.01
220 233 2.034879 CCTCGCCTGTGCACGAAAT 61.035 57.895 13.13 0.00 37.94 2.17
348 361 6.670464 TGGGATAAATGTAGTGAACTACCTCA 59.330 38.462 16.09 4.88 46.22 3.86
353 366 7.262772 CGTTCTGGGATAAATGTAGTGAACTA 58.737 38.462 0.00 0.00 31.98 2.24
368 382 0.175760 CGATGTGTCCGTTCTGGGAT 59.824 55.000 0.00 0.00 38.61 3.85
388 402 2.203280 CCACGGCAACCAGTTGGA 60.203 61.111 12.20 0.00 40.74 3.53
406 420 3.431766 GGGAATTGCTGTAGTCATACCGT 60.432 47.826 0.00 0.00 0.00 4.83
420 434 0.893447 AGCAAGCTCTTGGGAATTGC 59.107 50.000 11.15 0.11 41.04 3.56
423 437 3.084786 GTGTTAGCAAGCTCTTGGGAAT 58.915 45.455 11.15 0.00 40.74 3.01
440 454 6.014242 TCTCCATCTAGTTCATCTTGTGTGTT 60.014 38.462 0.00 0.00 0.00 3.32
478 492 2.223180 CGTGTCATCGTCGTCATCCTTA 60.223 50.000 0.00 0.00 0.00 2.69
520 534 8.553696 CGAACTTCAACATATTCATCATCATCA 58.446 33.333 0.00 0.00 0.00 3.07
533 547 3.120321 ACCTGCACGAACTTCAACATA 57.880 42.857 0.00 0.00 0.00 2.29
554 568 2.426842 GCATCCTTGCCCTTCTTACT 57.573 50.000 0.00 0.00 43.38 2.24
658 673 1.565390 CCCTGCCCAACATCCTCTGA 61.565 60.000 0.00 0.00 0.00 3.27
695 710 2.872732 CAGCTACGGGATAGGTCCTAA 58.127 52.381 1.78 0.00 44.44 2.69
703 718 1.271982 CCTCCTAGCAGCTACGGGATA 60.272 57.143 10.20 0.00 0.00 2.59
776 794 4.980339 AAACAAATGCAAAAGGGGATCT 57.020 36.364 0.00 0.00 0.00 2.75
783 801 5.393163 CGCTTAGCAAAAACAAATGCAAAAG 59.607 36.000 4.70 4.88 44.95 2.27
974 999 0.039764 ACGAGGAGATGACCTGGTGA 59.960 55.000 2.82 0.00 44.84 4.02
1010 1035 1.608336 AACACGACAGGATCCCCGA 60.608 57.895 20.97 0.00 37.58 5.14
1031 1056 2.889512 TGACTGGCTTTCTCAGGTCTA 58.110 47.619 0.00 0.00 36.62 2.59
1148 1180 0.405198 ACATCAGTTGCCATGTGGGA 59.595 50.000 0.54 0.00 40.01 4.37
1164 1197 9.631257 AAAGGAAGGAAATCATTTGAAAAACAT 57.369 25.926 0.00 0.00 32.59 2.71
1221 1273 3.882888 GCCTAAATAGCAGTTGCCATGTA 59.117 43.478 0.00 0.00 43.38 2.29
1346 1404 7.867403 GCCAACTTGAAGAATGATAAAAACAGA 59.133 33.333 0.00 0.00 0.00 3.41
1347 1405 7.869429 AGCCAACTTGAAGAATGATAAAAACAG 59.131 33.333 0.00 0.00 0.00 3.16
1348 1406 7.725251 AGCCAACTTGAAGAATGATAAAAACA 58.275 30.769 0.00 0.00 0.00 2.83
1349 1407 9.346725 CTAGCCAACTTGAAGAATGATAAAAAC 57.653 33.333 0.00 0.00 0.00 2.43
1572 1676 2.725203 GATATGCTTGGCCCCGCGTA 62.725 60.000 15.19 15.19 32.74 4.42
1682 1786 3.764237 AGTGGGAACAGTTAACGATGT 57.236 42.857 0.00 0.00 42.89 3.06
1689 1793 4.022589 CGTCAGAGTTAGTGGGAACAGTTA 60.023 45.833 0.00 0.00 42.89 2.24
1833 1937 3.691118 GCTCACAGCAACATCCTTCATTA 59.309 43.478 0.00 0.00 41.89 1.90
1863 1967 0.250684 TTCAACGCTTGCTGATGGGA 60.251 50.000 0.00 0.00 0.00 4.37
1937 2041 1.282570 CACACACGCGCTTGGAATT 59.717 52.632 18.82 0.00 0.00 2.17
1972 2076 0.888619 CCTCAGCCACTTCTGTCGTA 59.111 55.000 0.00 0.00 35.63 3.43
2024 2128 0.536006 GCTGTTGTGCCAAGACTCCT 60.536 55.000 0.00 0.00 0.00 3.69
2068 2172 1.439679 GTGAAACAGTCGCCTTAGGG 58.560 55.000 0.00 0.00 36.32 3.53
2069 2173 1.068474 CGTGAAACAGTCGCCTTAGG 58.932 55.000 0.00 0.00 35.74 2.69
2108 2212 2.048597 CTTGCGGTGGCTACGACA 60.049 61.111 5.63 0.00 40.82 4.35
2118 2222 0.593128 GTCAGTTGATTGCTTGCGGT 59.407 50.000 0.00 0.00 0.00 5.68
2134 2238 0.321210 CTGGTGCGTTGGGTATGTCA 60.321 55.000 0.00 0.00 0.00 3.58
2167 2271 5.204292 ACATAACCAGACTCATCTCTGCTA 58.796 41.667 0.00 0.00 37.01 3.49
2347 2451 2.487762 CCTGGAAGTGCGCAGATTTAAA 59.512 45.455 12.22 0.00 0.00 1.52
2392 2496 6.945435 TGATAATCTTCTTGTTTGGGCTGTAA 59.055 34.615 0.00 0.00 0.00 2.41
2446 2550 1.047596 TATTTGTAGGGCGGGGCGTA 61.048 55.000 0.00 0.00 0.00 4.42
2468 2572 0.032130 GCCGCTACAGAATGATCGGA 59.968 55.000 2.41 0.00 43.85 4.55
2519 2626 4.122149 TTGCGGGGCGGAATCCAT 62.122 61.111 0.00 0.00 31.36 3.41
2527 2634 3.283684 TGAACAACTTGCGGGGCG 61.284 61.111 0.00 0.00 0.00 6.13
2900 3026 3.734597 GCCGAATGTAAAATGCAGCATGA 60.735 43.478 9.18 0.00 39.69 3.07
3139 3271 3.439825 TGTAGTGCATTGTAGTTGCCATG 59.560 43.478 0.00 0.00 39.39 3.66
3140 3272 3.440173 GTGTAGTGCATTGTAGTTGCCAT 59.560 43.478 0.00 0.00 39.39 4.40
3141 3273 2.811431 GTGTAGTGCATTGTAGTTGCCA 59.189 45.455 0.00 0.00 39.39 4.92
3142 3274 2.811431 TGTGTAGTGCATTGTAGTTGCC 59.189 45.455 0.00 0.00 39.39 4.52
3143 3275 4.406069 CATGTGTAGTGCATTGTAGTTGC 58.594 43.478 0.00 0.00 40.55 4.17
3144 3276 4.672542 GCCATGTGTAGTGCATTGTAGTTG 60.673 45.833 0.00 0.00 0.00 3.16
3145 3277 3.440173 GCCATGTGTAGTGCATTGTAGTT 59.560 43.478 0.00 0.00 0.00 2.24
3146 3278 3.009723 GCCATGTGTAGTGCATTGTAGT 58.990 45.455 0.00 0.00 0.00 2.73
3147 3279 3.009026 TGCCATGTGTAGTGCATTGTAG 58.991 45.455 0.00 0.00 0.00 2.74
3148 3280 3.064900 TGCCATGTGTAGTGCATTGTA 57.935 42.857 0.00 0.00 0.00 2.41
3149 3281 1.908344 TGCCATGTGTAGTGCATTGT 58.092 45.000 0.00 0.00 0.00 2.71
3150 3282 2.229543 AGTTGCCATGTGTAGTGCATTG 59.770 45.455 0.00 0.00 33.08 2.82
3151 3283 2.229543 CAGTTGCCATGTGTAGTGCATT 59.770 45.455 0.00 0.00 33.08 3.56
3152 3284 1.814394 CAGTTGCCATGTGTAGTGCAT 59.186 47.619 0.00 0.00 33.08 3.96
3153 3285 1.237533 CAGTTGCCATGTGTAGTGCA 58.762 50.000 0.00 0.00 0.00 4.57
3154 3286 0.523072 CCAGTTGCCATGTGTAGTGC 59.477 55.000 0.00 0.00 0.00 4.40
3155 3287 2.183478 TCCAGTTGCCATGTGTAGTG 57.817 50.000 0.00 0.00 0.00 2.74
3156 3288 3.439857 AATCCAGTTGCCATGTGTAGT 57.560 42.857 0.00 0.00 0.00 2.73
3157 3289 3.674138 GCAAATCCAGTTGCCATGTGTAG 60.674 47.826 0.16 0.00 46.69 2.74
3158 3290 2.230992 GCAAATCCAGTTGCCATGTGTA 59.769 45.455 0.16 0.00 46.69 2.90
3159 3291 1.001181 GCAAATCCAGTTGCCATGTGT 59.999 47.619 0.16 0.00 46.69 3.72
3160 3292 1.717194 GCAAATCCAGTTGCCATGTG 58.283 50.000 0.16 0.00 46.69 3.21
3293 3456 0.252881 ATCTTCTCAGGGGTGCCTGA 60.253 55.000 0.00 0.00 43.53 3.86
3308 3471 3.753272 CCATCAAGTGACGGTGAAATCTT 59.247 43.478 0.00 0.00 0.00 2.40
3459 3622 1.608717 AACTACCCTCTGCTGCCTCG 61.609 60.000 0.00 0.00 0.00 4.63
3527 3690 3.764237 ATCGTACAACTGGGTCTGTTT 57.236 42.857 0.00 0.00 0.00 2.83
3575 3738 0.824595 TTCATGTGCTTGCTGCTGGT 60.825 50.000 0.00 0.00 43.37 4.00
3623 3804 8.814038 AATATGAATGGTAGAAAGAGCAAAGT 57.186 30.769 0.00 0.00 0.00 2.66
3791 3985 1.685224 GGCAAGATCACCCAGGTCA 59.315 57.895 0.00 0.00 0.00 4.02
3950 4145 5.047566 TCTTTCTCAGGATTTTGTGGTGA 57.952 39.130 0.00 0.00 0.00 4.02
3968 4163 4.142271 TGACCGTGTTGAGCAAAATTCTTT 60.142 37.500 0.00 0.00 0.00 2.52
4024 4219 4.657814 AAGAGTGCAAATAGGGAAGGAA 57.342 40.909 0.00 0.00 0.00 3.36
4194 4398 5.862924 AGTTGTCGTCCATGTATGAAAAG 57.137 39.130 0.00 0.00 0.00 2.27
4302 4513 7.048629 TGCATGTAAAAGTGAAGGAAATGAA 57.951 32.000 0.00 0.00 0.00 2.57
4338 4550 0.401356 TGCAAGCTCCTGGAACATGA 59.599 50.000 6.51 0.00 38.20 3.07
4399 4620 5.009610 GCATTGGTTCTTTAGGTCAAGACAA 59.990 40.000 2.29 0.00 32.28 3.18
4555 4776 1.138036 CGCCACGTACTCAATCGGA 59.862 57.895 0.00 0.00 0.00 4.55
4588 4809 3.689347 GGGGGTAGGAAATTACGTGTTT 58.311 45.455 0.00 0.00 0.00 2.83
4694 4928 5.694995 AGAAAAAGAGTCAGGTGAATCCAA 58.305 37.500 3.88 0.00 39.73 3.53
4695 4929 5.310409 AGAAAAAGAGTCAGGTGAATCCA 57.690 39.130 3.88 0.00 39.73 3.41
4697 4931 6.433766 CACAAGAAAAAGAGTCAGGTGAATC 58.566 40.000 0.00 0.00 39.24 2.52
4698 4932 5.221126 GCACAAGAAAAAGAGTCAGGTGAAT 60.221 40.000 0.00 0.00 0.00 2.57
4750 4985 3.578282 CCTTCCCACTTTGCAAGGTATTT 59.422 43.478 14.45 0.00 32.17 1.40
4898 5133 7.770897 ACTTGTACTTCTTGATGACTTTCTTGT 59.229 33.333 0.00 0.00 0.00 3.16
4991 5226 8.682936 AACATAGTGTTTGAGAAGAACAGAAT 57.317 30.769 0.00 0.00 37.26 2.40
5008 5249 3.190079 AGCATAGCACACGAACATAGTG 58.810 45.455 0.00 0.00 44.57 2.74
5227 5472 5.046663 TGTCTGATGAACTACAGTTGCCATA 60.047 40.000 0.00 0.00 38.56 2.74
5534 5794 3.125146 TGTTTATGCTGAATCTGTCGTGC 59.875 43.478 0.00 0.00 0.00 5.34
5705 6087 3.485394 TGCCATGTGTGTGTACTTGATT 58.515 40.909 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.