Multiple sequence alignment - TraesCS6A01G012600

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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 TraesCS6A01G012600 chr6A 100.000 3845 0 0 1 3845 5860573 5864417 0.000000e+00 7101.0
1 TraesCS6A01G012600 chr6D 94.964 1509 70 4 953 2460 6319372 6320875 0.000000e+00 2361.0
2 TraesCS6A01G012600 chr6D 95.748 1176 46 3 2481 3655 6320862 6322034 0.000000e+00 1892.0
3 TraesCS6A01G012600 chr6D 94.472 796 43 1 1 796 469591059 469591853 0.000000e+00 1225.0
4 TraesCS6A01G012600 chr6D 93.300 791 51 1 1 791 390167264 390166476 0.000000e+00 1166.0
5 TraesCS6A01G012600 chr6D 93.681 364 23 0 2481 2844 6328556 6328919 2.610000e-151 545.0
6 TraesCS6A01G012600 chr6D 98.020 202 4 0 3644 3845 6322291 6322492 6.110000e-93 351.0
7 TraesCS6A01G012600 chr6D 80.000 120 7 4 838 954 6319105 6319210 5.330000e-09 73.1
8 TraesCS6A01G012600 chr6B 93.359 1024 59 7 943 1960 11574644 11575664 0.000000e+00 1506.0
9 TraesCS6A01G012600 chr6B 88.640 1118 90 19 2481 3590 11577733 11578821 0.000000e+00 1327.0
10 TraesCS6A01G012600 chr6B 90.441 272 26 0 3574 3845 11578840 11579111 3.650000e-95 359.0
11 TraesCS6A01G012600 chr3D 94.095 796 46 1 1 795 563634463 563635258 0.000000e+00 1208.0
12 TraesCS6A01G012600 chr3D 86.022 93 7 2 1978 2069 612635531 612635444 1.140000e-15 95.3
13 TraesCS6A01G012600 chr5D 94.081 794 45 2 1 792 13738497 13737704 0.000000e+00 1205.0
14 TraesCS6A01G012600 chr5D 92.701 822 51 5 1 817 525598769 525599586 0.000000e+00 1177.0
15 TraesCS6A01G012600 chr7D 93.939 792 44 2 1 791 466847352 466846564 0.000000e+00 1194.0
16 TraesCS6A01G012600 chr7D 88.017 943 90 14 1000 1936 522504194 522503269 0.000000e+00 1094.0
17 TraesCS6A01G012600 chr7D 83.495 103 10 2 1967 2069 544625527 544625432 5.290000e-14 89.8
18 TraesCS6A01G012600 chr4B 93.593 796 48 3 1 795 180942629 180943422 0.000000e+00 1184.0
19 TraesCS6A01G012600 chr1A 93.569 793 46 5 1 792 34976434 34977222 0.000000e+00 1177.0
20 TraesCS6A01G012600 chr1D 93.208 795 53 1 1 795 470741800 470742593 0.000000e+00 1168.0
21 TraesCS6A01G012600 chr1D 89.041 73 7 1 1998 2069 231024324 231024396 5.290000e-14 89.8
22 TraesCS6A01G012600 chr7B 87.063 943 105 12 1000 1936 556458519 556457588 0.000000e+00 1050.0
23 TraesCS6A01G012600 chr7B 87.399 373 38 3 2481 2844 556456780 556456408 1.650000e-113 420.0
24 TraesCS6A01G012600 chr7A 87.063 943 105 12 1000 1936 602806353 602805422 0.000000e+00 1050.0


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 TraesCS6A01G012600 chr6A 5860573 5864417 3844 False 7101.000 7101 100.000000 1 3845 1 chr6A.!!$F1 3844
1 TraesCS6A01G012600 chr6D 469591059 469591853 794 False 1225.000 1225 94.472000 1 796 1 chr6D.!!$F2 795
2 TraesCS6A01G012600 chr6D 6319105 6322492 3387 False 1169.275 2361 92.183000 838 3845 4 chr6D.!!$F3 3007
3 TraesCS6A01G012600 chr6D 390166476 390167264 788 True 1166.000 1166 93.300000 1 791 1 chr6D.!!$R1 790
4 TraesCS6A01G012600 chr6B 11574644 11579111 4467 False 1064.000 1506 90.813333 943 3845 3 chr6B.!!$F1 2902
5 TraesCS6A01G012600 chr3D 563634463 563635258 795 False 1208.000 1208 94.095000 1 795 1 chr3D.!!$F1 794
6 TraesCS6A01G012600 chr5D 13737704 13738497 793 True 1205.000 1205 94.081000 1 792 1 chr5D.!!$R1 791
7 TraesCS6A01G012600 chr5D 525598769 525599586 817 False 1177.000 1177 92.701000 1 817 1 chr5D.!!$F1 816
8 TraesCS6A01G012600 chr7D 466846564 466847352 788 True 1194.000 1194 93.939000 1 791 1 chr7D.!!$R1 790
9 TraesCS6A01G012600 chr7D 522503269 522504194 925 True 1094.000 1094 88.017000 1000 1936 1 chr7D.!!$R2 936
10 TraesCS6A01G012600 chr4B 180942629 180943422 793 False 1184.000 1184 93.593000 1 795 1 chr4B.!!$F1 794
11 TraesCS6A01G012600 chr1A 34976434 34977222 788 False 1177.000 1177 93.569000 1 792 1 chr1A.!!$F1 791
12 TraesCS6A01G012600 chr1D 470741800 470742593 793 False 1168.000 1168 93.208000 1 795 1 chr1D.!!$F2 794
13 TraesCS6A01G012600 chr7B 556456408 556458519 2111 True 735.000 1050 87.231000 1000 2844 2 chr7B.!!$R1 1844
14 TraesCS6A01G012600 chr7A 602805422 602806353 931 True 1050.000 1050 87.063000 1000 1936 1 chr7A.!!$R1 936

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
282 289 0.250513 GATGGCTTCTTCGGTGGAGT 59.749 55.0 0.0 0.0 0.00 3.85 F
1029 1203 0.179150 CTCTCCCGTTGCTTCTCTCG 60.179 60.0 0.0 0.0 0.00 4.04 F
2462 4689 0.539669 CCAAGGGGACGGAGCTTTTT 60.540 55.0 0.0 0.0 35.59 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1721 1.522806 GGAGTTGGTCGTGCACACA 60.523 57.895 18.64 9.71 0.0 3.72 R
2479 4706 0.396001 ACTAGAAGCTCCGTCCCCTC 60.396 60.000 0.00 0.00 0.0 4.30 R
3266 5510 2.612972 CGGTTTGTACATGAGACTGGCT 60.613 50.000 0.00 0.00 0.0 4.75 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
93 95 2.910360 CCGGTGATGAGGATGCCA 59.090 61.111 0.00 0.00 0.00 4.92
147 153 2.178106 AGGTACAAATCCCAAACCCACA 59.822 45.455 0.00 0.00 0.00 4.17
240 247 0.749454 GGCGGCATTCTTGGAGATGT 60.749 55.000 3.07 0.00 0.00 3.06
282 289 0.250513 GATGGCTTCTTCGGTGGAGT 59.749 55.000 0.00 0.00 0.00 3.85
377 384 1.751563 TGATGGACACACGCAGGAA 59.248 52.632 0.00 0.00 0.00 3.36
593 604 6.270231 AGGTCTTAAATGTTAGGTCTGACTGT 59.730 38.462 7.85 0.00 0.00 3.55
655 666 6.183361 CCCTTCATCAATTGGATAGGTGTAGA 60.183 42.308 5.42 0.00 32.05 2.59
677 688 5.301298 AGAGACAGTTGTTACTTAGACGGTT 59.699 40.000 0.00 0.00 30.26 4.44
682 693 4.748600 AGTTGTTACTTAGACGGTTGCTTC 59.251 41.667 0.00 0.00 0.00 3.86
684 695 4.695396 TGTTACTTAGACGGTTGCTTCAA 58.305 39.130 0.00 0.00 0.00 2.69
719 730 7.276658 TGTATGACTTTGTAAGGTCTTGTGAA 58.723 34.615 8.11 0.00 34.01 3.18
784 795 3.672066 GGGGTCCTCCTCCTTTTTG 57.328 57.895 0.00 0.00 35.33 2.44
818 829 8.421673 AATATAAGCGAAAGTTACAAGAGACC 57.578 34.615 0.00 0.00 0.00 3.85
819 830 3.746045 AGCGAAAGTTACAAGAGACCA 57.254 42.857 0.00 0.00 0.00 4.02
820 831 4.273148 AGCGAAAGTTACAAGAGACCAT 57.727 40.909 0.00 0.00 0.00 3.55
821 832 5.401531 AGCGAAAGTTACAAGAGACCATA 57.598 39.130 0.00 0.00 0.00 2.74
822 833 5.978814 AGCGAAAGTTACAAGAGACCATAT 58.021 37.500 0.00 0.00 0.00 1.78
823 834 6.407202 AGCGAAAGTTACAAGAGACCATATT 58.593 36.000 0.00 0.00 0.00 1.28
824 835 7.553334 AGCGAAAGTTACAAGAGACCATATTA 58.447 34.615 0.00 0.00 0.00 0.98
825 836 7.707035 AGCGAAAGTTACAAGAGACCATATTAG 59.293 37.037 0.00 0.00 0.00 1.73
826 837 7.491696 GCGAAAGTTACAAGAGACCATATTAGT 59.508 37.037 0.00 0.00 0.00 2.24
827 838 8.808529 CGAAAGTTACAAGAGACCATATTAGTG 58.191 37.037 0.00 0.00 0.00 2.74
828 839 9.654663 GAAAGTTACAAGAGACCATATTAGTGT 57.345 33.333 0.00 0.00 0.00 3.55
831 842 9.476928 AGTTACAAGAGACCATATTAGTGTAGT 57.523 33.333 0.00 0.00 0.00 2.73
865 876 5.038033 AGATAAGCGAAAGTTAGAAGCGAG 58.962 41.667 0.00 0.00 0.00 5.03
869 880 2.271800 CGAAAGTTAGAAGCGAGCCAT 58.728 47.619 0.00 0.00 0.00 4.40
883 894 4.081972 AGCGAGCCATATTATAGTCAGTGG 60.082 45.833 0.00 0.00 0.00 4.00
886 897 6.405953 GCGAGCCATATTATAGTCAGTGGTAT 60.406 42.308 0.00 0.00 0.00 2.73
887 898 7.201794 GCGAGCCATATTATAGTCAGTGGTATA 60.202 40.741 0.00 0.00 0.00 1.47
888 899 8.346300 CGAGCCATATTATAGTCAGTGGTATAG 58.654 40.741 0.00 0.00 0.00 1.31
889 900 9.191479 GAGCCATATTATAGTCAGTGGTATAGT 57.809 37.037 0.00 0.00 0.00 2.12
890 901 8.972127 AGCCATATTATAGTCAGTGGTATAGTG 58.028 37.037 0.00 0.00 0.00 2.74
891 902 8.750298 GCCATATTATAGTCAGTGGTATAGTGT 58.250 37.037 0.00 0.00 0.00 3.55
905 916 1.520494 TAGTGTATCCGCCGAGCTAG 58.480 55.000 0.00 0.00 0.00 3.42
911 922 1.519751 ATCCGCCGAGCTAGCTAGTG 61.520 60.000 19.38 17.95 0.00 2.74
913 924 2.808315 GCCGAGCTAGCTAGTGCA 59.192 61.111 19.38 0.00 42.74 4.57
914 925 1.141881 GCCGAGCTAGCTAGTGCAA 59.858 57.895 19.38 0.00 42.74 4.08
915 926 0.460284 GCCGAGCTAGCTAGTGCAAA 60.460 55.000 19.38 0.00 42.74 3.68
917 928 1.134965 CCGAGCTAGCTAGTGCAAACT 60.135 52.381 19.38 9.14 42.74 2.66
919 930 2.996621 CGAGCTAGCTAGTGCAAACTTT 59.003 45.455 19.38 0.00 42.74 2.66
920 931 3.061429 CGAGCTAGCTAGTGCAAACTTTC 59.939 47.826 19.38 0.00 42.74 2.62
921 932 3.339141 AGCTAGCTAGTGCAAACTTTCC 58.661 45.455 17.69 0.88 42.74 3.13
922 933 3.008485 AGCTAGCTAGTGCAAACTTTCCT 59.992 43.478 17.69 3.22 42.74 3.36
923 934 3.372514 GCTAGCTAGTGCAAACTTTCCTC 59.627 47.826 21.62 0.00 42.74 3.71
980 1154 4.433283 GCATCAACATTCGAACATTTGCAC 60.433 41.667 0.00 0.00 0.00 4.57
1029 1203 0.179150 CTCTCCCGTTGCTTCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
1066 1240 4.559153 CGTGACCATATGCTATGTCATCA 58.441 43.478 13.43 0.00 0.00 3.07
1067 1241 5.173664 CGTGACCATATGCTATGTCATCAT 58.826 41.667 13.43 0.00 38.00 2.45
1068 1242 5.290400 CGTGACCATATGCTATGTCATCATC 59.710 44.000 13.43 3.30 35.70 2.92
1069 1243 6.404708 GTGACCATATGCTATGTCATCATCT 58.595 40.000 13.43 0.00 35.70 2.90
1182 1365 1.291184 CGCATCAGACCTTGCACGAA 61.291 55.000 0.00 0.00 38.80 3.85
1192 1375 1.666888 CCTTGCACGAAATGACAAGGC 60.667 52.381 7.62 0.00 46.34 4.35
1457 1640 4.129737 CTCCGAGCCTTCCGCGAA 62.130 66.667 8.23 0.00 44.76 4.70
1530 1713 2.434185 CGGTAGCGCTGGCAAAGA 60.434 61.111 22.90 0.00 43.41 2.52
1538 1721 2.690778 GCTGGCAAAGACGGCGAAT 61.691 57.895 16.62 0.00 31.32 3.34
1554 1737 0.944386 GAATGTGTGCACGACCAACT 59.056 50.000 13.13 0.99 0.00 3.16
1591 1774 3.961414 GGGGCTCCGGGTGTTTGA 61.961 66.667 0.00 0.00 0.00 2.69
2139 3915 3.857052 AGCTCAACATGGCAAATTCATG 58.143 40.909 0.00 4.51 45.31 3.07
2141 3917 3.863424 GCTCAACATGGCAAATTCATGAG 59.137 43.478 11.43 1.57 43.25 2.90
2183 4410 2.029739 TGCATGCATCCAGAACTTGTTG 60.030 45.455 18.46 0.00 0.00 3.33
2240 4467 1.525535 GGCGATGGCTGAGCTGATT 60.526 57.895 3.72 0.00 39.81 2.57
2279 4506 1.544825 AACAGGCGCAGGAAGAGCTA 61.545 55.000 10.83 0.00 43.21 3.32
2378 4605 4.660938 ACTTTCCGGCTGCACCCC 62.661 66.667 0.50 0.00 33.26 4.95
2429 4656 2.811317 GAGGACTGCAAGGTCGCG 60.811 66.667 0.00 0.00 39.30 5.87
2460 4687 2.757077 CCAAGGGGACGGAGCTTT 59.243 61.111 0.00 0.00 35.59 3.51
2461 4688 1.074951 CCAAGGGGACGGAGCTTTT 59.925 57.895 0.00 0.00 35.59 2.27
2462 4689 0.539669 CCAAGGGGACGGAGCTTTTT 60.540 55.000 0.00 0.00 35.59 1.94
2488 4715 1.765074 TTTTTGAGGGAGGGGACGG 59.235 57.895 0.00 0.00 0.00 4.79
2489 4716 0.768997 TTTTTGAGGGAGGGGACGGA 60.769 55.000 0.00 0.00 0.00 4.69
2490 4717 1.198759 TTTTGAGGGAGGGGACGGAG 61.199 60.000 0.00 0.00 0.00 4.63
2491 4718 4.779733 TGAGGGAGGGGACGGAGC 62.780 72.222 0.00 0.00 0.00 4.70
2559 4786 2.670148 CCCGCTGGAGTTTAGGCCT 61.670 63.158 11.78 11.78 0.00 5.19
2616 4843 1.070289 GACGTCAAGGGAGGTGACTTT 59.930 52.381 11.55 0.00 44.43 2.66
2715 4942 2.203015 ACGCTGGTGCACTCGTTT 60.203 55.556 17.98 0.88 39.64 3.60
2861 5097 1.872388 TAGCGTTGCTTGTGTGCTAA 58.128 45.000 0.00 0.00 40.44 3.09
2862 5098 1.238439 AGCGTTGCTTGTGTGCTAAT 58.762 45.000 0.00 0.00 33.89 1.73
2903 5146 2.733956 AGCCAGTGTCACAAGGAAAAA 58.266 42.857 16.23 0.00 0.00 1.94
2989 5232 8.776680 AACATCGTTTTGTTGTCACTAATAAC 57.223 30.769 1.43 0.00 38.37 1.89
3054 5298 4.497966 CAGATGCAAATGCTCATACAAACG 59.502 41.667 6.97 0.00 42.66 3.60
3063 5307 3.938334 TGCTCATACAAACGCACATACAT 59.062 39.130 0.00 0.00 0.00 2.29
3075 5319 3.686241 CGCACATACATTCATCCCTATGG 59.314 47.826 0.00 0.00 33.61 2.74
3076 5320 4.012374 GCACATACATTCATCCCTATGGG 58.988 47.826 0.00 0.00 46.11 4.00
3082 5326 4.307259 ACATTCATCCCTATGGGTACACT 58.693 43.478 0.00 0.00 44.74 3.55
3099 5343 1.668294 CTCAAGACTGAGCACCGGT 59.332 57.895 0.00 0.00 42.66 5.28
3106 5350 0.246635 ACTGAGCACCGGTACATCAC 59.753 55.000 6.87 0.00 31.20 3.06
3151 5395 1.321474 ACGTCTTTGTAGTCCACGGA 58.679 50.000 0.00 0.00 34.75 4.69
3169 5413 1.202604 GGAAACGTCTCCCACTGAACA 60.203 52.381 0.00 0.00 0.00 3.18
3214 5458 1.901464 AACGGGCCAATTTGCGACT 60.901 52.632 4.39 0.00 0.00 4.18
3314 5558 2.549754 ACGAGCTTCACCACAAGATTTG 59.450 45.455 0.00 0.00 0.00 2.32
3355 5599 8.456471 CAATCGGCACATATCTTCATATGAAAT 58.544 33.333 18.47 15.70 43.37 2.17
3597 5878 6.076981 ACAAACACAATGGAAGAACTCATC 57.923 37.500 0.00 0.00 0.00 2.92
3664 6212 9.448438 TTCAACTAGTATCACATGCAAAATACT 57.552 29.630 14.27 14.27 38.26 2.12
3783 6331 8.436046 TTTTGATTGAAAAGAAAGGTGAATGG 57.564 30.769 0.00 0.00 0.00 3.16
3830 6378 2.489938 TGGTGGCACTAGAAATCCAC 57.510 50.000 18.45 14.49 46.10 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
86 88 4.074970 AGGAAACGATGATAATGGCATCC 58.925 43.478 0.00 0.00 39.10 3.51
171 177 4.122046 CGCTGTCATCCAATCAACTGATA 58.878 43.478 0.00 0.00 33.73 2.15
182 188 0.107066 ATGAATGCCGCTGTCATCCA 60.107 50.000 4.15 0.00 0.00 3.41
262 269 0.539051 CTCCACCGAAGAAGCCATCT 59.461 55.000 0.00 0.00 41.32 2.90
282 289 7.148086 GCCATGAATATGTAGAAAGAAACACCA 60.148 37.037 0.00 0.00 32.21 4.17
340 347 0.179032 ACCACACATCTGACGCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
593 604 4.523083 GGCCTAATACCAAACAGACATCA 58.477 43.478 0.00 0.00 0.00 3.07
655 666 5.287226 CAACCGTCTAAGTAACAACTGTCT 58.713 41.667 0.00 0.00 0.00 3.41
677 688 7.161404 AGTCATACAACAGTAAGATTGAAGCA 58.839 34.615 0.00 0.00 0.00 3.91
684 695 9.436957 CCTTACAAAGTCATACAACAGTAAGAT 57.563 33.333 0.00 0.00 39.45 2.40
719 730 6.423604 GCATGCGGCCACTTTATTAATTATTT 59.576 34.615 0.00 0.00 36.11 1.40
796 807 5.790593 TGGTCTCTTGTAACTTTCGCTTAT 58.209 37.500 0.00 0.00 0.00 1.73
797 808 5.204409 TGGTCTCTTGTAACTTTCGCTTA 57.796 39.130 0.00 0.00 0.00 3.09
798 809 4.067972 TGGTCTCTTGTAACTTTCGCTT 57.932 40.909 0.00 0.00 0.00 4.68
800 811 6.663944 AATATGGTCTCTTGTAACTTTCGC 57.336 37.500 0.00 0.00 0.00 4.70
824 835 9.894783 CGCTTATCTACAACAATATACTACACT 57.105 33.333 0.00 0.00 0.00 3.55
825 836 9.888878 TCGCTTATCTACAACAATATACTACAC 57.111 33.333 0.00 0.00 0.00 2.90
834 845 8.997621 TCTAACTTTCGCTTATCTACAACAAT 57.002 30.769 0.00 0.00 0.00 2.71
835 846 8.821147 TTCTAACTTTCGCTTATCTACAACAA 57.179 30.769 0.00 0.00 0.00 2.83
836 847 7.063074 GCTTCTAACTTTCGCTTATCTACAACA 59.937 37.037 0.00 0.00 0.00 3.33
837 848 7.392556 GCTTCTAACTTTCGCTTATCTACAAC 58.607 38.462 0.00 0.00 0.00 3.32
838 849 6.252869 CGCTTCTAACTTTCGCTTATCTACAA 59.747 38.462 0.00 0.00 0.00 2.41
839 850 5.742453 CGCTTCTAACTTTCGCTTATCTACA 59.258 40.000 0.00 0.00 0.00 2.74
858 869 5.574830 CACTGACTATAATATGGCTCGCTTC 59.425 44.000 0.00 0.00 0.00 3.86
865 876 8.750298 ACACTATACCACTGACTATAATATGGC 58.250 37.037 0.00 0.00 0.00 4.40
883 894 1.811359 AGCTCGGCGGATACACTATAC 59.189 52.381 7.21 0.00 0.00 1.47
886 897 1.520494 CTAGCTCGGCGGATACACTA 58.480 55.000 7.21 0.00 0.00 2.74
887 898 1.797211 GCTAGCTCGGCGGATACACT 61.797 60.000 7.70 0.00 0.00 3.55
888 899 1.371881 GCTAGCTCGGCGGATACAC 60.372 63.158 7.70 0.00 0.00 2.90
889 900 0.250597 TAGCTAGCTCGGCGGATACA 60.251 55.000 23.26 0.00 34.52 2.29
890 901 0.448593 CTAGCTAGCTCGGCGGATAC 59.551 60.000 23.26 0.00 34.52 2.24
891 902 0.036448 ACTAGCTAGCTCGGCGGATA 59.964 55.000 23.26 0.00 34.52 2.59
892 903 1.228306 ACTAGCTAGCTCGGCGGAT 60.228 57.895 23.26 0.00 34.52 4.18
893 904 2.187493 CACTAGCTAGCTCGGCGGA 61.187 63.158 23.26 0.65 34.52 5.54
894 905 2.333225 CACTAGCTAGCTCGGCGG 59.667 66.667 23.26 9.94 34.52 6.13
895 906 2.354072 GCACTAGCTAGCTCGGCG 60.354 66.667 23.26 11.78 37.91 6.46
905 916 6.149474 TCAATAAGAGGAAAGTTTGCACTAGC 59.851 38.462 9.95 0.00 42.57 3.42
911 922 8.866956 CAATGAATCAATAAGAGGAAAGTTTGC 58.133 33.333 0.00 0.00 0.00 3.68
961 1135 2.160117 GCGTGCAAATGTTCGAATGTTG 60.160 45.455 0.00 7.53 0.00 3.33
966 1140 1.684142 CATGCGTGCAAATGTTCGAA 58.316 45.000 0.00 0.00 0.00 3.71
1029 1203 2.607038 GGTCACGGAAATGGCAAAAGTC 60.607 50.000 0.00 0.00 0.00 3.01
1066 1240 1.519455 CGGCGCGGAAGAAGAAGAT 60.519 57.895 9.72 0.00 0.00 2.40
1067 1241 2.126071 CGGCGCGGAAGAAGAAGA 60.126 61.111 9.72 0.00 0.00 2.87
1068 1242 2.126071 TCGGCGCGGAAGAAGAAG 60.126 61.111 15.97 0.00 0.00 2.85
1069 1243 2.431942 GTCGGCGCGGAAGAAGAA 60.432 61.111 19.96 0.00 0.00 2.52
1167 1350 2.143122 GTCATTTCGTGCAAGGTCTGA 58.857 47.619 0.00 0.00 0.00 3.27
1182 1365 2.854522 GCCGTACAGCCTTGTCATT 58.145 52.632 0.00 0.00 38.76 2.57
1192 1375 2.279517 GAGCATCGGGCCGTACAG 60.280 66.667 27.32 14.81 46.50 2.74
1428 1611 4.415332 TCGGAGGTCGTCAAGCGC 62.415 66.667 0.00 0.00 41.07 5.92
1429 1612 2.202492 CTCGGAGGTCGTCAAGCG 60.202 66.667 0.00 0.00 40.32 4.68
1457 1640 1.525995 CATTAACGCGGCCTCCCAT 60.526 57.895 12.47 0.00 0.00 4.00
1530 1713 3.711842 CGTGCACACATTCGCCGT 61.712 61.111 18.64 0.00 0.00 5.68
1538 1721 1.522806 GGAGTTGGTCGTGCACACA 60.523 57.895 18.64 9.71 0.00 3.72
1983 2172 5.874895 TCTAATACGTGATGCTATAGCGT 57.125 39.130 19.42 19.42 45.83 5.07
2071 2306 1.819632 AAAATAGCGCCGGCCTCAG 60.820 57.895 23.46 7.95 41.24 3.35
2104 2375 6.294675 CCATGTTGAGCTACCATCAAAGAAAA 60.295 38.462 0.00 0.00 38.34 2.29
2139 3915 3.452474 AGTGCATTAGACGAATGAGCTC 58.548 45.455 6.82 6.82 46.94 4.09
2141 3917 3.244814 CAGAGTGCATTAGACGAATGAGC 59.755 47.826 11.95 4.04 46.94 4.26
2338 4565 1.220169 CTTGATGATCGCGCTCAGGG 61.220 60.000 18.32 4.63 0.00 4.45
2417 4644 4.451150 TAGCCCGCGACCTTGCAG 62.451 66.667 8.23 0.00 34.15 4.41
2421 4648 4.452733 GCAGTAGCCCGCGACCTT 62.453 66.667 8.23 0.00 33.58 3.50
2470 4697 0.768997 TCCGTCCCCTCCCTCAAAAA 60.769 55.000 0.00 0.00 0.00 1.94
2471 4698 1.151987 TCCGTCCCCTCCCTCAAAA 60.152 57.895 0.00 0.00 0.00 2.44
2472 4699 1.612442 CTCCGTCCCCTCCCTCAAA 60.612 63.158 0.00 0.00 0.00 2.69
2473 4700 2.038975 CTCCGTCCCCTCCCTCAA 59.961 66.667 0.00 0.00 0.00 3.02
2474 4701 4.779733 GCTCCGTCCCCTCCCTCA 62.780 72.222 0.00 0.00 0.00 3.86
2475 4702 3.986116 AAGCTCCGTCCCCTCCCTC 62.986 68.421 0.00 0.00 0.00 4.30
2476 4703 3.986116 GAAGCTCCGTCCCCTCCCT 62.986 68.421 0.00 0.00 0.00 4.20
2477 4704 2.584873 TAGAAGCTCCGTCCCCTCCC 62.585 65.000 0.00 0.00 0.00 4.30
2478 4705 1.076192 TAGAAGCTCCGTCCCCTCC 60.076 63.158 0.00 0.00 0.00 4.30
2479 4706 0.396001 ACTAGAAGCTCCGTCCCCTC 60.396 60.000 0.00 0.00 0.00 4.30
2480 4707 0.684805 CACTAGAAGCTCCGTCCCCT 60.685 60.000 0.00 0.00 0.00 4.79
2481 4708 0.683504 TCACTAGAAGCTCCGTCCCC 60.684 60.000 0.00 0.00 0.00 4.81
2482 4709 1.135333 CTTCACTAGAAGCTCCGTCCC 59.865 57.143 0.00 0.00 44.25 4.46
2483 4710 2.570442 CTTCACTAGAAGCTCCGTCC 57.430 55.000 0.00 0.00 44.25 4.79
2616 4843 2.727392 CCCGAACGGTATCAGCCCA 61.727 63.158 12.23 0.00 0.00 5.36
2903 5146 7.833285 ACACAAACTTACCATAGGAATGTTT 57.167 32.000 0.00 0.00 0.00 2.83
3039 5283 4.394610 TGTATGTGCGTTTGTATGAGCATT 59.605 37.500 0.00 0.00 41.88 3.56
3041 5285 3.330267 TGTATGTGCGTTTGTATGAGCA 58.670 40.909 0.00 0.00 37.26 4.26
3082 5326 0.601558 GTACCGGTGCTCAGTCTTGA 59.398 55.000 19.93 0.00 0.00 3.02
3151 5395 2.930826 ATGTTCAGTGGGAGACGTTT 57.069 45.000 0.00 0.00 0.00 3.60
3214 5458 2.139917 GTAGGCGTGTGTGATGTTTGA 58.860 47.619 0.00 0.00 0.00 2.69
3266 5510 2.612972 CGGTTTGTACATGAGACTGGCT 60.613 50.000 0.00 0.00 0.00 4.75
3314 5558 6.806249 TGTGCCGATTGAATTTAAGATGAAAC 59.194 34.615 0.00 0.00 0.00 2.78
3437 5683 9.973246 CGTAAGGTCAATCATGTTAATATATGC 57.027 33.333 0.00 0.00 0.00 3.14
3568 5814 3.450457 TCTTCCATTGTGTTTGTTGGCTT 59.550 39.130 0.00 0.00 0.00 4.35
3597 5878 4.811908 TGATGTGATTGTGGCAGAAAATG 58.188 39.130 0.00 0.00 0.00 2.32
3783 6331 9.428097 AGGAAATTTTGCTCTTCATATGTTTTC 57.572 29.630 1.90 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.