Multiple sequence alignment - TraesCS2D01G398200

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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 TraesCS2D01G398200 chr2D 100.000 5579 0 0 1 5579 510614129 510619707 0.000000e+00 10303.0
1 TraesCS2D01G398200 chr2B 94.557 2719 72 35 254 2961 599999036 600001689 0.000000e+00 4132.0
2 TraesCS2D01G398200 chr2B 93.233 1788 84 18 3825 5579 600002714 600004497 0.000000e+00 2597.0
3 TraesCS2D01G398200 chr2B 93.435 853 38 5 2968 3807 600001777 600002624 0.000000e+00 1249.0
4 TraesCS2D01G398200 chr2B 94.239 243 13 1 1 242 599998595 599998837 2.460000e-98 370.0
5 TraesCS2D01G398200 chr2B 100.000 31 0 0 1929 1959 469524954 469524924 2.170000e-04 58.4
6 TraesCS2D01G398200 chr2A 92.008 2978 117 50 2688 5579 654366355 654369297 0.000000e+00 4069.0
7 TraesCS2D01G398200 chr2A 95.447 2438 101 8 254 2689 654363896 654366325 0.000000e+00 3879.0
8 TraesCS2D01G398200 chr2A 95.868 242 10 0 1 242 654363457 654363698 5.240000e-105 392.0
9 TraesCS2D01G398200 chr6A 87.500 336 40 2 1301 1635 474987120 474986786 2.440000e-103 387.0
10 TraesCS2D01G398200 chr6A 79.924 264 53 0 2200 2463 474986350 474986087 1.590000e-45 195.0
11 TraesCS2D01G398200 chr6B 86.866 335 42 2 1301 1634 485301965 485302298 1.900000e-99 374.0
12 TraesCS2D01G398200 chr6D 86.567 335 45 0 1301 1635 335339360 335339026 2.460000e-98 370.0


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 TraesCS2D01G398200 chr2D 510614129 510619707 5578 False 10303 10303 100.000 1 5579 1 chr2D.!!$F1 5578
1 TraesCS2D01G398200 chr2B 599998595 600004497 5902 False 2087 4132 93.866 1 5579 4 chr2B.!!$F1 5578
2 TraesCS2D01G398200 chr2A 654363457 654369297 5840 False 2780 4069 94.441 1 5579 3 chr2A.!!$F1 5578
3 TraesCS2D01G398200 chr6A 474986087 474987120 1033 True 291 387 83.712 1301 2463 2 chr6A.!!$R1 1162

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
763 953 0.368907 CAAGACGCCGTAATTGGACG 59.631 55.000 6.74 0.0 42.55 4.79 F
1778 1979 1.139095 CTACGAGCCGACCAAGTCC 59.861 63.158 1.50 0.0 0.00 3.85 F
2555 2792 0.170116 GCAGACACTGACGGAGAGAG 59.830 60.000 2.81 0.0 32.44 3.20 F
3700 4066 0.040425 ACGATTTCGGTTGTTGCTGC 60.040 50.000 4.84 0.0 44.95 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1909 2110 0.251386 TGCGGAAGAGAGACAGAGGT 60.251 55.0 0.0 0.0 0.0 3.85 R
2656 2893 0.543277 CAATCCAGGCTAGGCTCACA 59.457 55.0 17.3 3.2 0.0 3.58 R
3860 4299 0.535797 GTCTAGAACCCTGAACCCCG 59.464 60.0 0.0 0.0 0.0 5.73 R
5556 6046 0.034670 CTTCTGGAAGCAAGAGGGGG 60.035 60.0 0.0 0.0 0.0 5.40 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
31 32 3.442273 GTGTTCCACTGGTGAAAGTTGAA 59.558 43.478 1.93 0.00 31.42 2.69
156 157 9.143631 CCAAGTGAATGTCAATAAAGGATTTTC 57.856 33.333 0.00 0.00 40.09 2.29
178 179 3.328931 CCATCCTAGAGGGTACAATGCAT 59.671 47.826 0.00 0.00 36.25 3.96
242 244 7.841956 GCTATCATAGCCTGAAGGTTAGATTA 58.158 38.462 5.21 0.00 45.95 1.75
244 246 9.814899 CTATCATAGCCTGAAGGTTAGATTATG 57.185 37.037 0.00 0.00 37.44 1.90
245 247 7.618019 TCATAGCCTGAAGGTTAGATTATGT 57.382 36.000 0.00 0.00 34.34 2.29
246 248 7.671302 TCATAGCCTGAAGGTTAGATTATGTC 58.329 38.462 0.00 0.00 34.34 3.06
247 249 4.950050 AGCCTGAAGGTTAGATTATGTCG 58.050 43.478 0.00 0.00 37.57 4.35
249 251 4.693283 CCTGAAGGTTAGATTATGTCGCA 58.307 43.478 0.00 0.00 0.00 5.10
252 254 5.483811 TGAAGGTTAGATTATGTCGCACAA 58.516 37.500 0.00 0.00 0.00 3.33
288 477 2.747855 CCTCGACCAAGGCAAGGC 60.748 66.667 0.00 0.00 0.00 4.35
312 501 1.753368 GAAGCCCGGAGATGAGAGGG 61.753 65.000 0.73 0.00 46.44 4.30
375 564 3.500343 CATGGGGAGAAAACTTGAGGTT 58.500 45.455 0.00 0.00 40.28 3.50
429 618 0.453950 CATGCTTCAAGCGAGTGTGC 60.454 55.000 4.57 0.00 46.26 4.57
521 710 7.751047 AAAGATCATGCGATGAATTTTCAAG 57.249 32.000 0.00 0.00 43.50 3.02
525 714 6.499234 TCATGCGATGAATTTTCAAGAAGA 57.501 33.333 0.00 0.00 41.13 2.87
592 781 7.682628 TCTCATATCATCCTTGCATGTGATAA 58.317 34.615 13.49 2.71 37.18 1.75
595 784 8.596293 TCATATCATCCTTGCATGTGATAAGTA 58.404 33.333 13.49 4.16 37.18 2.24
600 789 5.056480 TCCTTGCATGTGATAAGTATTCCG 58.944 41.667 0.00 0.00 0.00 4.30
602 791 5.178252 CCTTGCATGTGATAAGTATTCCGAG 59.822 44.000 0.00 0.00 0.00 4.63
608 797 5.842907 TGTGATAAGTATTCCGAGTCCATG 58.157 41.667 0.00 0.00 0.00 3.66
701 891 1.531423 ACAATCAAGCTCAGGCAGTG 58.469 50.000 0.00 0.00 41.70 3.66
732 922 9.590451 AATAATGAGCCTAAAACATTGTTGATG 57.410 29.630 2.13 0.00 41.71 3.07
735 925 4.813027 AGCCTAAAACATTGTTGATGCTG 58.187 39.130 2.13 0.00 39.47 4.41
763 953 0.368907 CAAGACGCCGTAATTGGACG 59.631 55.000 6.74 0.00 42.55 4.79
807 997 6.457799 GGGGCTCATACGTAAATTACAAACAG 60.458 42.308 0.00 0.00 0.00 3.16
1039 1229 1.880340 GCTTCTCTCCGCATCACCG 60.880 63.158 0.00 0.00 0.00 4.94
1074 1264 5.491982 CTGTCCCCAAGAATATATAGCACC 58.508 45.833 0.00 0.00 0.00 5.01
1718 1908 6.089476 GCTAATGCAGGTTCTTTCTTTTCTC 58.911 40.000 0.00 0.00 39.41 2.87
1778 1979 1.139095 CTACGAGCCGACCAAGTCC 59.861 63.158 1.50 0.00 0.00 3.85
1901 2102 2.327568 CCACGCCACACATTTCATTTC 58.672 47.619 0.00 0.00 0.00 2.17
1902 2103 2.327568 CACGCCACACATTTCATTTCC 58.672 47.619 0.00 0.00 0.00 3.13
1909 2110 0.252012 ACATTTCATTTCCCCCGGCA 60.252 50.000 0.00 0.00 0.00 5.69
1916 2117 4.974438 TTCCCCCGGCACCTCTGT 62.974 66.667 0.00 0.00 0.00 3.41
1955 2161 4.842029 GCAGCAGCTGTGAATTAATCTAC 58.158 43.478 23.60 0.00 37.91 2.59
1956 2162 4.333649 GCAGCAGCTGTGAATTAATCTACA 59.666 41.667 23.60 5.08 37.91 2.74
1957 2163 5.503683 GCAGCAGCTGTGAATTAATCTACAG 60.504 44.000 23.60 19.86 38.81 2.74
1958 2164 5.583854 CAGCAGCTGTGAATTAATCTACAGT 59.416 40.000 22.66 13.04 38.43 3.55
1959 2165 6.758416 CAGCAGCTGTGAATTAATCTACAGTA 59.242 38.462 22.66 4.92 38.43 2.74
2159 2396 3.556633 CCTGCTTGATTGACAGAGAGTGT 60.557 47.826 0.00 0.00 44.49 3.55
2216 2453 1.065410 TGGTGCAGGGGAGGAAGAAA 61.065 55.000 0.00 0.00 0.00 2.52
2396 2633 4.415332 TTCGAGACCACGGCGCTC 62.415 66.667 6.90 4.28 0.00 5.03
2485 2722 3.054503 CTGCCACTGCCACAGAGC 61.055 66.667 0.78 4.71 35.84 4.09
2494 2731 2.770802 ACTGCCACAGAGCTAATGAGAT 59.229 45.455 5.45 0.00 35.18 2.75
2495 2732 3.963374 ACTGCCACAGAGCTAATGAGATA 59.037 43.478 5.45 0.00 35.18 1.98
2517 2754 8.200120 AGATAATTAGCCAGGCAAATTTCTTTC 58.800 33.333 15.80 0.00 0.00 2.62
2555 2792 0.170116 GCAGACACTGACGGAGAGAG 59.830 60.000 2.81 0.00 32.44 3.20
2656 2893 1.827344 TCGATGACCTTCACAGCTCAT 59.173 47.619 0.00 0.00 0.00 2.90
2826 3095 3.318384 TCCCAACGCTGCAGGCTA 61.318 61.111 17.12 0.00 39.13 3.93
2829 3098 2.680913 CCAACGCTGCAGGCTACAC 61.681 63.158 17.12 0.00 39.13 2.90
2889 3158 1.134280 CAAGTCCCAATCTCCGATGCT 60.134 52.381 0.00 0.00 0.00 3.79
2949 3218 5.437060 AGAACTTTCTTGAACAAGCCTGTA 58.563 37.500 9.38 0.00 38.28 2.74
2954 3225 8.045176 ACTTTCTTGAACAAGCCTGTATAATC 57.955 34.615 9.38 0.00 38.28 1.75
2961 3232 5.636903 ACAAGCCTGTATAATCTCACCAT 57.363 39.130 0.00 0.00 32.54 3.55
2963 3234 7.321717 ACAAGCCTGTATAATCTCACCATAT 57.678 36.000 0.00 0.00 32.54 1.78
2964 3235 7.164122 ACAAGCCTGTATAATCTCACCATATG 58.836 38.462 0.00 0.00 32.54 1.78
3060 3414 2.659428 CCCTGTCCCTCAATTTCCATC 58.341 52.381 0.00 0.00 0.00 3.51
3061 3415 2.659428 CCTGTCCCTCAATTTCCATCC 58.341 52.381 0.00 0.00 0.00 3.51
3069 3423 3.950395 CCTCAATTTCCATCCTGAAGGTC 59.050 47.826 0.00 0.00 36.34 3.85
3072 3426 5.195940 TCAATTTCCATCCTGAAGGTCATC 58.804 41.667 0.00 0.00 36.34 2.92
3251 3605 0.248866 GTTGTGTTTGCCACCTTCGG 60.249 55.000 0.00 0.00 43.85 4.30
3433 3787 0.378257 CTTTCCGGTTGATGATGGCG 59.622 55.000 0.00 0.00 0.00 5.69
3439 3793 1.173043 GGTTGATGATGGCGGTTCAA 58.827 50.000 0.00 0.00 0.00 2.69
3449 3803 1.210155 GCGGTTCAAGTCATGGTGC 59.790 57.895 0.00 0.00 0.00 5.01
3451 3805 0.606401 CGGTTCAAGTCATGGTGCCT 60.606 55.000 0.00 0.00 0.00 4.75
3476 3830 2.287915 CGTTCAGTTTGTTCCTGTCCTG 59.712 50.000 0.00 0.00 0.00 3.86
3522 3876 1.203063 AGTAGGAGGCGCCATGATCTA 60.203 52.381 31.54 18.06 40.02 1.98
3529 3883 1.835483 GCGCCATGATCTAACCTGCG 61.835 60.000 0.00 0.00 43.05 5.18
3576 3942 4.142403 CCATTAAAGCAGAAATCGCAGGAA 60.142 41.667 0.00 0.00 0.00 3.36
3617 3983 7.759489 ACTGCAGAGTTCCAATTATTAACAA 57.241 32.000 23.35 0.00 0.00 2.83
3698 4064 1.265905 GGAACGATTTCGGTTGTTGCT 59.734 47.619 4.84 0.00 40.66 3.91
3699 4065 2.307049 GAACGATTTCGGTTGTTGCTG 58.693 47.619 4.84 0.00 40.66 4.41
3700 4066 0.040425 ACGATTTCGGTTGTTGCTGC 60.040 50.000 4.84 0.00 44.95 5.25
3716 4082 1.383409 TGCCCATGCAGGATGTGAA 59.617 52.632 0.00 0.00 44.23 3.18
3717 4083 0.681887 TGCCCATGCAGGATGTGAAG 60.682 55.000 0.00 0.00 44.23 3.02
3718 4084 2.012902 GCCCATGCAGGATGTGAAGC 62.013 60.000 0.00 0.00 41.22 3.86
3743 4109 0.391130 CATCGCCGAAACTTCCCTGA 60.391 55.000 0.00 0.00 0.00 3.86
3811 4178 6.986817 AGTACATGCCTATGTCTATGAACAAC 59.013 38.462 0.00 0.00 44.00 3.32
3860 4299 6.873076 TCTGGCCATTGTTTATTTTCATGTTC 59.127 34.615 5.51 0.00 0.00 3.18
3901 4340 6.015856 AGACTGACAATATCTCAATCCGGTAG 60.016 42.308 0.00 0.00 0.00 3.18
4036 4476 3.057736 ACATGTATCTACGGATGCGGTAC 60.058 47.826 12.44 8.87 37.37 3.34
4064 4515 5.061721 TCACTGTATCCTGCTAGGTGATA 57.938 43.478 0.00 0.00 36.53 2.15
4101 4552 7.224753 TGGCATTGTCGAGTAAATAAGATTCTC 59.775 37.037 0.00 0.00 0.00 2.87
4107 4558 6.199342 GTCGAGTAAATAAGATTCTCTGGCAC 59.801 42.308 0.00 0.00 0.00 5.01
4133 4584 4.331992 CCAAGATTGTGTGAGATGTGCTAG 59.668 45.833 0.00 0.00 0.00 3.42
4260 4716 0.958822 ACAAACCTGAAATCACCGGC 59.041 50.000 0.00 0.00 0.00 6.13
4497 4956 5.488262 TTCTCATGTTCAGATGGAAGACA 57.512 39.130 0.00 0.00 35.82 3.41
4500 4959 5.716703 TCTCATGTTCAGATGGAAGACAGTA 59.283 40.000 0.00 0.00 35.82 2.74
4610 5070 8.634475 TTTGATGATATCTCGACAGTTTAGTG 57.366 34.615 3.98 0.00 0.00 2.74
4634 5094 5.810074 GGTTGCAGTTAAACACAAGATTGTT 59.190 36.000 0.00 0.00 41.62 2.83
4649 5111 5.382618 AGATTGTTCCTGCAAAAGATCAC 57.617 39.130 0.00 0.00 31.63 3.06
4665 5127 9.709495 CAAAAGATCACATTTTAGGATGGAAAA 57.291 29.630 0.00 0.00 0.00 2.29
4685 5147 8.701895 TGGAAAACCATATACTTAGTCTAGTGG 58.298 37.037 0.00 0.00 0.00 4.00
4698 5160 8.060075 ACTTAGTCTAGTGGTAGGATACACATT 58.940 37.037 0.00 0.00 45.43 2.71
4727 5189 7.152645 AGTTATAACTACAGTCATATTGCCGG 58.847 38.462 16.60 0.00 37.52 6.13
4824 5287 6.647334 ATCCATGTGTTGTGTGTAAATCAA 57.353 33.333 0.00 0.00 0.00 2.57
4882 5345 3.313526 ACTGTGTGCATGAAACTGTTCTC 59.686 43.478 0.00 0.00 34.60 2.87
5005 5470 4.114073 CGGTAACTGTTACAATGCCGATA 58.886 43.478 26.67 0.00 40.27 2.92
5099 5564 4.699735 TGAAATTAGCGTGTCATGGACAAT 59.300 37.500 0.00 0.00 44.49 2.71
5270 5753 2.315011 CGCTTAAATTTTGCTCGCACA 58.685 42.857 0.00 0.00 0.00 4.57
5289 5772 2.561885 CGGGAGGCGTAGATAGCG 59.438 66.667 0.00 0.00 35.00 4.26
5314 5799 4.610333 AGGGGGATTTAAAACTGATGGTC 58.390 43.478 0.00 0.00 0.00 4.02
5365 5850 1.288188 TGGGGCAGATGTGATCAAGA 58.712 50.000 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 3.435105 TGCTTTTGAGCATGTTTTCGT 57.565 38.095 0.00 0.00 40.23 3.85
59 60 6.479990 TCGACGATGCTTTCAAATATGAAGAT 59.520 34.615 0.00 0.00 45.82 2.40
156 157 2.705658 TGCATTGTACCCTCTAGGATGG 59.294 50.000 0.00 0.00 39.89 3.51
178 179 3.700539 CCAGATATGGCATTGTTGGTTCA 59.299 43.478 4.78 0.00 0.00 3.18
242 244 2.611473 CCTCTTGTCTCTTGTGCGACAT 60.611 50.000 0.00 0.00 37.69 3.06
244 246 1.000163 TCCTCTTGTCTCTTGTGCGAC 60.000 52.381 0.00 0.00 0.00 5.19
245 247 1.000163 GTCCTCTTGTCTCTTGTGCGA 60.000 52.381 0.00 0.00 0.00 5.10
246 248 1.269778 TGTCCTCTTGTCTCTTGTGCG 60.270 52.381 0.00 0.00 0.00 5.34
247 249 2.533266 TGTCCTCTTGTCTCTTGTGC 57.467 50.000 0.00 0.00 0.00 4.57
249 251 4.503991 GGTCATTGTCCTCTTGTCTCTTGT 60.504 45.833 0.00 0.00 0.00 3.16
252 254 3.513515 GAGGTCATTGTCCTCTTGTCTCT 59.486 47.826 19.02 0.00 45.56 3.10
288 477 1.045350 TCATCTCCGGGCTTCTCCTG 61.045 60.000 0.00 0.00 41.11 3.86
412 601 2.597713 CGCACACTCGCTTGAAGCA 61.598 57.895 18.22 3.68 42.58 3.91
521 710 6.149142 ACATGTCATGCTCTCTTCTTTTCTTC 59.851 38.462 12.91 0.00 0.00 2.87
525 714 5.558818 AGACATGTCATGCTCTCTTCTTTT 58.441 37.500 27.02 0.00 0.00 2.27
592 781 3.004839 CGTGATCATGGACTCGGAATACT 59.995 47.826 7.06 0.00 0.00 2.12
595 784 2.031870 TCGTGATCATGGACTCGGAAT 58.968 47.619 14.91 0.00 0.00 3.01
600 789 4.377943 CGACTATCTCGTGATCATGGACTC 60.378 50.000 14.91 6.38 37.64 3.36
602 791 3.498777 TCGACTATCTCGTGATCATGGAC 59.501 47.826 14.91 0.00 43.45 4.02
608 797 4.386350 TCTCGATTCGACTATCTCGTGATC 59.614 45.833 4.29 0.00 43.45 2.92
732 922 0.179205 GCGTCTTGATGCAGTTCAGC 60.179 55.000 9.66 0.00 0.00 4.26
735 925 1.291877 ACGGCGTCTTGATGCAGTTC 61.292 55.000 6.77 0.00 36.05 3.01
749 939 2.661675 CTGATATCGTCCAATTACGGCG 59.338 50.000 4.80 4.80 43.05 6.46
763 953 4.759183 GCCCCTTTTCATCTCACTGATATC 59.241 45.833 0.00 0.00 33.36 1.63
807 997 3.348647 AATTGCATTTGCCCCCTTTAC 57.651 42.857 0.00 0.00 41.18 2.01
1074 1264 0.250209 CCATGGCCTCGAGGAAGATG 60.250 60.000 35.69 27.34 37.39 2.90
1599 1789 0.669318 GCCCGTCTTTGATGTCGACA 60.669 55.000 22.48 22.48 0.00 4.35
1730 1931 5.125097 CAGCTTCTTGGCAGTAAGATCAAAT 59.875 40.000 13.28 0.00 36.63 2.32
1742 1943 1.746615 GCCGATCAGCTTCTTGGCA 60.747 57.895 15.81 0.00 42.03 4.92
1902 2103 3.775654 GAGACAGAGGTGCCGGGG 61.776 72.222 2.18 0.00 0.00 5.73
1909 2110 0.251386 TGCGGAAGAGAGACAGAGGT 60.251 55.000 0.00 0.00 0.00 3.85
1916 2117 0.681243 TGCTAGCTGCGGAAGAGAGA 60.681 55.000 17.23 0.00 46.63 3.10
1917 2118 1.812525 TGCTAGCTGCGGAAGAGAG 59.187 57.895 17.23 0.00 46.63 3.20
1958 2164 7.552687 AAGCTATACTTTTGTGCAACTATGCTA 59.447 33.333 2.22 0.00 44.42 3.49
1959 2165 6.375455 AAGCTATACTTTTGTGCAACTATGCT 59.625 34.615 2.22 0.00 44.42 3.79
2116 2352 6.290294 AGGGAACTGAATTTGATGGAAATG 57.710 37.500 0.00 0.00 41.13 2.32
2182 2419 4.489810 CTGCACCACCGCAAATTTATTAA 58.510 39.130 0.00 0.00 42.45 1.40
2183 2420 3.119316 CCTGCACCACCGCAAATTTATTA 60.119 43.478 0.00 0.00 42.45 0.98
2187 2424 1.367102 CCTGCACCACCGCAAATTT 59.633 52.632 0.00 0.00 42.45 1.82
2216 2453 0.392193 CCTTGAGCACCTTCATCGCT 60.392 55.000 0.00 0.00 39.12 4.93
2485 2722 7.750229 TTTGCCTGGCTAATTATCTCATTAG 57.250 36.000 21.03 0.00 39.06 1.73
2494 2731 6.212388 TGGAAAGAAATTTGCCTGGCTAATTA 59.788 34.615 31.30 17.16 41.39 1.40
2495 2732 5.012975 TGGAAAGAAATTTGCCTGGCTAATT 59.987 36.000 27.68 27.68 43.28 1.40
2503 2740 5.993441 CAGTCAAATGGAAAGAAATTTGCCT 59.007 36.000 0.00 0.00 41.47 4.75
2517 2754 4.219070 TCTGCTTCATTTCCAGTCAAATGG 59.781 41.667 6.17 0.00 42.02 3.16
2555 2792 0.531974 TGTTCCTCCTGTTCACGTGC 60.532 55.000 11.67 0.00 0.00 5.34
2615 2852 1.537814 TTGTACTCGGCCCACGTGAT 61.538 55.000 19.30 0.00 44.69 3.06
2656 2893 0.543277 CAATCCAGGCTAGGCTCACA 59.457 55.000 17.30 3.20 0.00 3.58
2826 3095 2.445396 TCTGAAGCTGCAGAGGTGT 58.555 52.632 21.25 0.00 39.84 4.16
2954 3225 8.367911 TCTACCTTATTACTTGCATATGGTGAG 58.632 37.037 4.56 0.00 36.07 3.51
3005 3359 8.859236 TCAGAAATTCAGAGTTCAGAAATGAT 57.141 30.769 0.00 0.00 32.49 2.45
3007 3361 9.178427 GTTTCAGAAATTCAGAGTTCAGAAATG 57.822 33.333 14.40 0.00 42.80 2.32
3060 3414 3.554544 CGATCTCCATGATGACCTTCAGG 60.555 52.174 0.00 0.00 37.02 3.86
3061 3415 3.069300 ACGATCTCCATGATGACCTTCAG 59.931 47.826 0.00 0.00 35.14 3.02
3069 3423 3.608941 CGAGTCTGACGATCTCCATGATG 60.609 52.174 1.52 0.00 35.14 3.07
3072 3426 1.599171 GCGAGTCTGACGATCTCCATG 60.599 57.143 1.52 0.00 0.00 3.66
3251 3605 3.488090 GAACCGTGTAGCCTGCGC 61.488 66.667 0.00 0.00 0.00 6.09
3420 3774 1.133025 CTTGAACCGCCATCATCAACC 59.867 52.381 0.00 0.00 0.00 3.77
3433 3787 0.883833 CAGGCACCATGACTTGAACC 59.116 55.000 0.00 0.00 29.42 3.62
3439 3793 1.768684 AACGACCAGGCACCATGACT 61.769 55.000 0.00 0.00 34.86 3.41
3449 3803 1.602377 GGAACAAACTGAACGACCAGG 59.398 52.381 12.00 0.00 38.44 4.45
3451 3805 2.285083 CAGGAACAAACTGAACGACCA 58.715 47.619 0.00 0.00 38.20 4.02
3476 3830 4.004196 AGGTACTGTAGCTCCAAACAAC 57.996 45.455 13.43 0.00 37.18 3.32
3522 3876 2.594962 CGAGTTCGTTGCGCAGGTT 61.595 57.895 11.31 0.00 34.11 3.50
3529 3883 4.431728 CGAGAATATATGCGAGTTCGTTGC 60.432 45.833 3.27 0.00 42.22 4.17
3576 3942 6.759272 TCTGCAGTTGATTAGAGTACTGTTT 58.241 36.000 14.67 0.00 40.02 2.83
3699 4065 2.012902 GCTTCACATCCTGCATGGGC 62.013 60.000 0.00 0.00 35.59 5.36
3700 4066 1.389609 GGCTTCACATCCTGCATGGG 61.390 60.000 0.00 0.00 37.23 4.00
3718 4084 1.296056 AAGTTTCGGCGATGGTTCGG 61.296 55.000 11.76 0.00 45.59 4.30
3743 4109 7.607615 TTGACCTCCTTGTTAAACTACTAGT 57.392 36.000 0.00 0.00 0.00 2.57
3811 4178 8.143835 AGAAACCAATGTGGATCTTTTTACTTG 58.856 33.333 0.18 0.00 40.96 3.16
3860 4299 0.535797 GTCTAGAACCCTGAACCCCG 59.464 60.000 0.00 0.00 0.00 5.73
3901 4340 3.388024 TGGCACATGAGGTTCTATCTACC 59.612 47.826 0.00 0.00 35.85 3.18
3973 4413 4.022503 GCTCTCTGTTTGAAGATTTTGCCT 60.023 41.667 0.00 0.00 0.00 4.75
4036 4476 3.340814 AGCAGGATACAGTGAACTTGG 57.659 47.619 0.00 0.00 41.41 3.61
4064 4515 4.832248 TCGACAATGCCAATTTAGACTCT 58.168 39.130 0.00 0.00 0.00 3.24
4107 4558 3.688185 CACATCTCACACAATCTTGGAGG 59.312 47.826 0.00 0.00 0.00 4.30
4133 4584 2.155665 TGCGCCGCACTTTAAGTAC 58.844 52.632 8.16 0.00 31.71 2.73
4211 4667 4.701651 CAGCAAAGACCAAATCAGTATCCA 59.298 41.667 0.00 0.00 0.00 3.41
4216 4672 3.953612 TGTTCAGCAAAGACCAAATCAGT 59.046 39.130 0.00 0.00 0.00 3.41
4260 4716 1.795162 GCCATGAAATGCTTCGTTCCG 60.795 52.381 0.00 0.00 44.97 4.30
4266 4722 1.538276 CGAACGCCATGAAATGCTTC 58.462 50.000 0.00 0.00 44.97 3.86
4497 4956 4.161754 CGGACTATGTTCCCTCCTTTTACT 59.838 45.833 0.00 0.00 31.03 2.24
4500 4959 2.238898 CCGGACTATGTTCCCTCCTTTT 59.761 50.000 0.00 0.00 31.03 2.27
4598 5058 2.210116 ACTGCAACCACTAAACTGTCG 58.790 47.619 0.00 0.00 0.00 4.35
4607 5067 4.013728 TCTTGTGTTTAACTGCAACCACT 58.986 39.130 0.00 0.00 0.00 4.00
4610 5070 5.348164 ACAATCTTGTGTTTAACTGCAACC 58.652 37.500 0.00 0.00 40.49 3.77
4634 5094 6.009589 TCCTAAAATGTGATCTTTTGCAGGA 58.990 36.000 6.26 6.26 34.38 3.86
4665 5127 8.285350 TCCTACCACTAGACTAAGTATATGGT 57.715 38.462 0.00 0.00 0.00 3.55
4723 5185 2.064581 ATGAGAGGTGGTACCCGGC 61.065 63.158 10.07 0.00 39.75 6.13
4727 5189 1.694696 GGATCCATGAGAGGTGGTACC 59.305 57.143 6.95 4.43 37.96 3.34
4882 5345 2.513204 CTCAGGCATGGCTCCACG 60.513 66.667 20.57 8.48 0.00 4.94
5099 5564 3.451178 GTCAGGTAACAGCTAGATTCCCA 59.549 47.826 0.00 0.00 41.41 4.37
5270 5753 1.902432 GCTATCTACGCCTCCCGGT 60.902 63.158 0.00 0.00 42.52 5.28
5289 5772 4.383010 CCATCAGTTTTAAATCCCCCTTGC 60.383 45.833 0.00 0.00 0.00 4.01
5292 5775 4.294970 AGACCATCAGTTTTAAATCCCCCT 59.705 41.667 0.00 0.00 0.00 4.79
5365 5850 2.157738 GCATGTCCACAGAAAGCTTCT 58.842 47.619 0.00 0.00 41.70 2.85
5556 6046 0.034670 CTTCTGGAAGCAAGAGGGGG 60.035 60.000 0.00 0.00 0.00 5.40


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

AutoCloner maintained by Alex Coulton.