Multiple sequence alignment - TraesCS2D01G075700

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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 TraesCS2D01G075700 chr2D 100.000 4020 0 0 1 4020 32469054 32473073 0.000000e+00 7424.0
1 TraesCS2D01G075700 chr2A 90.722 2037 144 15 963 2966 35489086 35491110 0.000000e+00 2673.0
2 TraesCS2D01G075700 chr2A 93.482 1074 38 3 2976 4020 35491724 35492794 0.000000e+00 1567.0
3 TraesCS2D01G075700 chr2B 87.216 2245 187 40 754 2958 53147407 53149591 0.000000e+00 2464.0
4 TraesCS2D01G075700 chr2B 84.392 2236 287 33 754 2956 53297779 53299985 0.000000e+00 2139.0
5 TraesCS2D01G075700 chr2B 81.628 1965 299 45 754 2692 53429399 53431327 0.000000e+00 1572.0
6 TraesCS2D01G075700 chr2B 83.487 975 134 14 1012 1969 53407008 53407972 0.000000e+00 883.0
7 TraesCS2D01G075700 chr2B 84.379 813 100 14 2142 2936 53458981 53459784 0.000000e+00 773.0
8 TraesCS2D01G075700 chr2B 82.031 640 72 27 3376 3977 53414517 53415151 4.640000e-139 505.0
9 TraesCS2D01G075700 chr2B 86.981 361 35 5 3533 3884 53452743 53453100 2.910000e-106 396.0
10 TraesCS2D01G075700 chr2B 85.000 400 30 17 3602 3977 53464633 53465026 2.930000e-101 379.0
11 TraesCS2D01G075700 chr2B 88.599 307 32 1 1041 1344 53458468 53458774 1.760000e-98 370.0
12 TraesCS2D01G075700 chr2B 84.874 357 37 10 3188 3536 53445597 53445944 1.070000e-90 344.0
13 TraesCS2D01G075700 chr2B 85.075 201 20 4 3188 3381 53402837 53403034 3.170000e-46 196.0
14 TraesCS2D01G075700 chr2B 93.333 60 4 0 3140 3199 53414105 53414164 5.530000e-14 89.8
15 TraesCS2D01G075700 chr2B 86.301 73 8 2 2963 3035 53441904 53441974 1.200000e-10 78.7
16 TraesCS2D01G075700 chr2B 100.000 32 0 0 3989 4020 53465023 53465054 4.340000e-05 60.2
17 TraesCS2D01G075700 chr5D 97.465 710 18 0 1 710 441123898 441123189 0.000000e+00 1212.0
18 TraesCS2D01G075700 chr4D 97.316 708 19 0 1 708 127556350 127555643 0.000000e+00 1203.0
19 TraesCS2D01G075700 chr1D 97.042 710 18 1 1 710 480621136 480620430 0.000000e+00 1192.0
20 TraesCS2D01G075700 chr1D 96.761 710 23 0 1 710 61949410 61950119 0.000000e+00 1184.0
21 TraesCS2D01G075700 chr1D 96.761 710 23 0 1 710 467782496 467783205 0.000000e+00 1184.0
22 TraesCS2D01G075700 chr7D 96.901 710 22 0 1 710 162016427 162015718 0.000000e+00 1190.0
23 TraesCS2D01G075700 chr7D 96.901 710 22 0 1 710 614652240 614652949 0.000000e+00 1190.0
24 TraesCS2D01G075700 chr7D 78.936 451 85 9 1049 1497 622271375 622271817 8.450000e-77 298.0
25 TraesCS2D01G075700 chrUn 96.761 710 22 1 1 710 221301799 221302507 0.000000e+00 1182.0
26 TraesCS2D01G075700 chrUn 96.761 710 22 1 1 710 245442212 245442920 0.000000e+00 1182.0
27 TraesCS2D01G075700 chr6A 80.306 523 89 11 1038 1553 35150778 35150263 2.270000e-102 383.0
28 TraesCS2D01G075700 chr7B 77.711 166 34 3 1241 1404 709851021 709850857 9.190000e-17 99.0


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 TraesCS2D01G075700 chr2D 32469054 32473073 4019 False 7424.00 7424 100.0000 1 4020 1 chr2D.!!$F1 4019
1 TraesCS2D01G075700 chr2A 35489086 35492794 3708 False 2120.00 2673 92.1020 963 4020 2 chr2A.!!$F1 3057
2 TraesCS2D01G075700 chr2B 53147407 53149591 2184 False 2464.00 2464 87.2160 754 2958 1 chr2B.!!$F1 2204
3 TraesCS2D01G075700 chr2B 53297779 53299985 2206 False 2139.00 2139 84.3920 754 2956 1 chr2B.!!$F2 2202
4 TraesCS2D01G075700 chr2B 53429399 53431327 1928 False 1572.00 1572 81.6280 754 2692 1 chr2B.!!$F3 1938
5 TraesCS2D01G075700 chr2B 53458468 53459784 1316 False 571.50 773 86.4890 1041 2936 2 chr2B.!!$F8 1895
6 TraesCS2D01G075700 chr2B 53402837 53407972 5135 False 539.50 883 84.2810 1012 3381 2 chr2B.!!$F5 2369
7 TraesCS2D01G075700 chr2B 53414105 53415151 1046 False 297.40 505 87.6820 3140 3977 2 chr2B.!!$F6 837
8 TraesCS2D01G075700 chr2B 53441904 53445944 4040 False 211.35 344 85.5875 2963 3536 2 chr2B.!!$F7 573
9 TraesCS2D01G075700 chr5D 441123189 441123898 709 True 1212.00 1212 97.4650 1 710 1 chr5D.!!$R1 709
10 TraesCS2D01G075700 chr4D 127555643 127556350 707 True 1203.00 1203 97.3160 1 708 1 chr4D.!!$R1 707
11 TraesCS2D01G075700 chr1D 480620430 480621136 706 True 1192.00 1192 97.0420 1 710 1 chr1D.!!$R1 709
12 TraesCS2D01G075700 chr1D 61949410 61950119 709 False 1184.00 1184 96.7610 1 710 1 chr1D.!!$F1 709
13 TraesCS2D01G075700 chr1D 467782496 467783205 709 False 1184.00 1184 96.7610 1 710 1 chr1D.!!$F2 709
14 TraesCS2D01G075700 chr7D 162015718 162016427 709 True 1190.00 1190 96.9010 1 710 1 chr7D.!!$R1 709
15 TraesCS2D01G075700 chr7D 614652240 614652949 709 False 1190.00 1190 96.9010 1 710 1 chr7D.!!$F1 709
16 TraesCS2D01G075700 chrUn 221301799 221302507 708 False 1182.00 1182 96.7610 1 710 1 chrUn.!!$F1 709
17 TraesCS2D01G075700 chrUn 245442212 245442920 708 False 1182.00 1182 96.7610 1 710 1 chrUn.!!$F2 709
18 TraesCS2D01G075700 chr6A 35150263 35150778 515 True 383.00 383 80.3060 1038 1553 1 chr6A.!!$R1 515

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
719 720 0.173708 GACGCGAGGGTCTGATTCTT 59.826 55.0 15.93 0.0 34.09 2.52 F
791 797 0.250727 TCCACCTTTTCCCTTGCTCG 60.251 55.0 0.00 0.0 0.00 5.03 F
2477 5684 0.170339 GAACATAAACGCCTGCCACC 59.830 55.0 0.00 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 5372 0.250209 CCTTCCCATCCATCTCGCAG 60.250 60.0 0.00 0.0 0.00 5.18 R
2615 5828 1.115930 ATCCTCGGCCGAGCTGTATT 61.116 55.0 43.11 22.7 40.69 1.89 R
3926 11509 1.301677 GCAGTACCAGCAGCAACCTC 61.302 60.0 0.00 0.0 0.00 3.85 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
76 77 1.154454 GGGTTTCCCCCGGAACTTT 59.846 57.895 0.73 0.00 45.80 2.66
77 78 0.470456 GGGTTTCCCCCGGAACTTTT 60.470 55.000 0.73 0.00 45.80 2.27
87 88 2.000447 CCGGAACTTTTCGATCAGGTC 59.000 52.381 0.00 1.51 0.00 3.85
715 716 4.194720 GCGACGCGAGGGTCTGAT 62.195 66.667 15.93 0.00 34.75 2.90
716 717 2.490217 CGACGCGAGGGTCTGATT 59.510 61.111 15.93 0.00 34.75 2.57
717 718 1.586564 CGACGCGAGGGTCTGATTC 60.587 63.158 15.93 0.00 34.75 2.52
718 719 1.810532 GACGCGAGGGTCTGATTCT 59.189 57.895 15.93 0.00 34.09 2.40
719 720 0.173708 GACGCGAGGGTCTGATTCTT 59.826 55.000 15.93 0.00 34.09 2.52
721 722 1.002087 ACGCGAGGGTCTGATTCTTTT 59.998 47.619 15.93 0.00 0.00 2.27
722 723 1.661112 CGCGAGGGTCTGATTCTTTTC 59.339 52.381 0.00 0.00 0.00 2.29
723 724 2.675317 CGCGAGGGTCTGATTCTTTTCT 60.675 50.000 0.00 0.00 0.00 2.52
724 725 3.339141 GCGAGGGTCTGATTCTTTTCTT 58.661 45.455 0.00 0.00 0.00 2.52
726 727 4.216472 GCGAGGGTCTGATTCTTTTCTTTT 59.784 41.667 0.00 0.00 0.00 2.27
727 728 5.278512 GCGAGGGTCTGATTCTTTTCTTTTT 60.279 40.000 0.00 0.00 0.00 1.94
728 729 6.374578 CGAGGGTCTGATTCTTTTCTTTTTC 58.625 40.000 0.00 0.00 0.00 2.29
729 730 6.205658 CGAGGGTCTGATTCTTTTCTTTTTCT 59.794 38.462 0.00 0.00 0.00 2.52
730 731 7.255277 CGAGGGTCTGATTCTTTTCTTTTTCTT 60.255 37.037 0.00 0.00 0.00 2.52
731 732 8.996651 AGGGTCTGATTCTTTTCTTTTTCTTA 57.003 30.769 0.00 0.00 0.00 2.10
741 742 9.840427 TTCTTTTCTTTTTCTTATATGGAAGCG 57.160 29.630 0.00 0.00 0.00 4.68
743 744 9.495754 CTTTTCTTTTTCTTATATGGAAGCGAG 57.504 33.333 0.00 0.00 0.00 5.03
744 745 6.604735 TCTTTTTCTTATATGGAAGCGAGC 57.395 37.500 0.00 0.00 0.00 5.03
745 746 6.112734 TCTTTTTCTTATATGGAAGCGAGCA 58.887 36.000 0.00 0.00 0.00 4.26
746 747 5.734855 TTTTCTTATATGGAAGCGAGCAC 57.265 39.130 0.00 0.00 0.00 4.40
747 748 4.400529 TTCTTATATGGAAGCGAGCACA 57.599 40.909 0.00 0.00 0.00 4.57
748 749 3.717707 TCTTATATGGAAGCGAGCACAC 58.282 45.455 0.00 0.00 0.00 3.82
749 750 3.132111 TCTTATATGGAAGCGAGCACACA 59.868 43.478 0.00 0.00 0.00 3.72
750 751 2.627515 ATATGGAAGCGAGCACACAT 57.372 45.000 0.00 1.21 0.00 3.21
751 752 1.655484 TATGGAAGCGAGCACACATG 58.345 50.000 0.00 0.00 0.00 3.21
788 794 1.821136 CTGATCCACCTTTTCCCTTGC 59.179 52.381 0.00 0.00 0.00 4.01
791 797 0.250727 TCCACCTTTTCCCTTGCTCG 60.251 55.000 0.00 0.00 0.00 5.03
971 995 6.421801 GTCAAGTTTAGCAACCGTACTTAGAA 59.578 38.462 0.00 0.00 32.70 2.10
1012 1036 1.167851 CCATTTCAGCGGAGAAGCAA 58.832 50.000 0.00 0.00 40.15 3.91
1013 1037 1.747355 CCATTTCAGCGGAGAAGCAAT 59.253 47.619 0.00 0.00 40.15 3.56
1014 1038 2.479049 CCATTTCAGCGGAGAAGCAATG 60.479 50.000 2.37 2.37 40.15 2.82
1015 1039 0.523072 TTTCAGCGGAGAAGCAATGC 59.477 50.000 0.00 0.00 40.15 3.56
1209 4374 1.945394 ACGACGGCGATATACACTCTT 59.055 47.619 22.49 0.00 41.64 2.85
1362 4539 1.739562 CCACCTGCAGAGCTTCGTC 60.740 63.158 17.39 0.00 0.00 4.20
1374 4551 1.006102 CTTCGTCGTGCAGGTCCTT 60.006 57.895 6.26 0.00 0.00 3.36
1641 4821 2.093306 TGAACGTACCCAAGCATCTG 57.907 50.000 0.00 0.00 0.00 2.90
1809 4989 0.527565 ATTGCATCCGTGTTGCCTTC 59.472 50.000 0.00 0.00 39.39 3.46
1865 5048 3.119955 CGTCGAGTAGGTGACAAAGATGA 60.120 47.826 0.00 0.00 34.78 2.92
1965 5148 0.921896 CCATGTCCTCCACCTGGATT 59.078 55.000 0.00 0.00 42.13 3.01
1967 5150 2.372264 CATGTCCTCCACCTGGATTTG 58.628 52.381 0.00 0.00 44.46 2.32
1976 5159 0.678950 ACCTGGATTTGCCCGTTTTG 59.321 50.000 0.00 0.00 34.97 2.44
1980 5163 0.732538 GGATTTGCCCGTTTTGCGAG 60.733 55.000 0.00 0.00 44.77 5.03
1994 5177 1.884464 GCGAGCGCATCCTCAATCA 60.884 57.895 11.47 0.00 41.49 2.57
1995 5178 1.431488 GCGAGCGCATCCTCAATCAA 61.431 55.000 11.47 0.00 41.49 2.57
1996 5179 1.009078 CGAGCGCATCCTCAATCAAA 58.991 50.000 11.47 0.00 0.00 2.69
1997 5180 1.004185 CGAGCGCATCCTCAATCAAAG 60.004 52.381 11.47 0.00 0.00 2.77
2000 5183 2.421424 AGCGCATCCTCAATCAAAGTTC 59.579 45.455 11.47 0.00 0.00 3.01
2001 5184 2.478539 GCGCATCCTCAATCAAAGTTCC 60.479 50.000 0.30 0.00 0.00 3.62
2002 5185 2.749076 CGCATCCTCAATCAAAGTTCCA 59.251 45.455 0.00 0.00 0.00 3.53
2003 5186 3.379372 CGCATCCTCAATCAAAGTTCCAT 59.621 43.478 0.00 0.00 0.00 3.41
2004 5187 4.679662 GCATCCTCAATCAAAGTTCCATG 58.320 43.478 0.00 0.00 0.00 3.66
2007 5190 4.410099 TCCTCAATCAAAGTTCCATGCTT 58.590 39.130 0.00 0.00 0.00 3.91
2022 5214 6.211587 TCCATGCTTTCTATTCCATTGTTG 57.788 37.500 0.00 0.00 0.00 3.33
2025 5217 5.389859 TGCTTTCTATTCCATTGTTGTGG 57.610 39.130 0.00 0.00 40.76 4.17
2032 5224 4.525912 ATTCCATTGTTGTGGCTTCTTC 57.474 40.909 0.00 0.00 39.19 2.87
2033 5225 3.228188 TCCATTGTTGTGGCTTCTTCT 57.772 42.857 0.00 0.00 39.19 2.85
2045 5237 3.758554 TGGCTTCTTCTCCTTGTATTTGC 59.241 43.478 0.00 0.00 0.00 3.68
2062 5257 2.464459 GCATTTGGGGAGCTCGTCG 61.464 63.158 7.83 0.00 0.00 5.12
2157 5355 0.692476 TGTGCAGCCACTGTAAGGAT 59.308 50.000 0.00 0.00 42.54 3.24
2174 5372 1.202188 GGATAGCCGAAGCAGCAAAAC 60.202 52.381 0.00 0.00 43.56 2.43
2260 5458 5.163509 CCCGTCTCAGAAGATTTCAGTATGA 60.164 44.000 0.00 0.00 37.29 2.15
2263 5461 6.977502 CGTCTCAGAAGATTTCAGTATGATGT 59.022 38.462 0.00 0.00 38.41 3.06
2297 5495 1.079336 GGGGAAGTGTAGGCGTCAC 60.079 63.158 6.93 6.93 36.22 3.67
2336 5534 0.786435 ATCCAAAACTCAAGGGGCCT 59.214 50.000 0.84 0.00 0.00 5.19
2477 5684 0.170339 GAACATAAACGCCTGCCACC 59.830 55.000 0.00 0.00 0.00 4.61
2561 5768 1.065102 CATGCTGCCTGACAATGCTAC 59.935 52.381 0.00 0.00 0.00 3.58
2614 5827 5.609423 AGGTGATCTATCATCTGAAACTGC 58.391 41.667 4.93 0.00 46.01 4.40
2615 5828 5.129980 AGGTGATCTATCATCTGAAACTGCA 59.870 40.000 4.93 0.00 46.01 4.41
2616 5829 5.819379 GGTGATCTATCATCTGAAACTGCAA 59.181 40.000 0.00 0.00 39.30 4.08
2751 6000 4.923871 AGTAGTGTAACATTTGACAGAGCG 59.076 41.667 0.00 0.00 41.43 5.03
2937 6192 4.091800 GTCGTTGCCATTTTGATGGAATTG 59.908 41.667 9.52 0.00 44.39 2.32
2944 6199 6.544931 TGCCATTTTGATGGAATTGTTGAAAA 59.455 30.769 9.52 0.00 44.39 2.29
2946 6201 7.361894 CCATTTTGATGGAATTGTTGAAAACC 58.638 34.615 0.00 0.00 44.93 3.27
2964 6219 7.149918 GAAAACCGATTTTCTGAACTTCAAC 57.850 36.000 7.79 0.00 46.90 3.18
2965 6220 5.828299 AACCGATTTTCTGAACTTCAACA 57.172 34.783 0.00 0.00 0.00 3.33
2966 6221 5.424121 ACCGATTTTCTGAACTTCAACAG 57.576 39.130 0.00 0.00 35.72 3.16
2967 6222 4.881850 ACCGATTTTCTGAACTTCAACAGT 59.118 37.500 0.00 0.00 37.30 3.55
2968 6223 5.207768 CCGATTTTCTGAACTTCAACAGTG 58.792 41.667 0.00 0.00 35.12 3.66
2970 6225 4.981806 TTTTCTGAACTTCAACAGTGGG 57.018 40.909 0.00 0.00 35.12 4.61
2971 6226 3.644966 TTCTGAACTTCAACAGTGGGT 57.355 42.857 0.00 0.00 35.12 4.51
2972 6227 3.644966 TCTGAACTTCAACAGTGGGTT 57.355 42.857 0.00 0.00 41.47 4.11
2984 6844 2.446994 TGGGTTGAGGACGGTGGT 60.447 61.111 0.00 0.00 0.00 4.16
2985 6845 2.032071 GGGTTGAGGACGGTGGTG 59.968 66.667 0.00 0.00 0.00 4.17
3069 7878 7.267857 GGGTATCGTGGTAAGTTTATAACACT 58.732 38.462 1.55 0.00 40.57 3.55
3070 7879 8.413229 GGGTATCGTGGTAAGTTTATAACACTA 58.587 37.037 1.55 0.00 40.57 2.74
3195 10525 1.194218 TGAATGGAGGAGCGACATGA 58.806 50.000 0.00 0.00 0.00 3.07
3199 10529 1.847328 TGGAGGAGCGACATGACTAA 58.153 50.000 0.00 0.00 0.00 2.24
3200 10530 1.476891 TGGAGGAGCGACATGACTAAC 59.523 52.381 0.00 0.00 0.00 2.34
3209 10539 2.000447 GACATGACTAACCTCCAACGC 59.000 52.381 0.00 0.00 0.00 4.84
3228 10558 2.283086 CGCGAAGTTGACAGTTACAACA 59.717 45.455 0.00 0.00 46.58 3.33
3233 10563 2.032030 AGTTGACAGTTACAACATGCGC 60.032 45.455 0.00 0.00 46.58 6.09
3252 10582 3.357823 GCGCGAAGTTTGTATTGTTTGAG 59.642 43.478 12.10 0.00 0.00 3.02
3400 10944 1.454653 GTGAAACTACGACACCGAAGC 59.545 52.381 0.00 0.00 39.50 3.86
3432 10976 4.382577 CCACAACAGGCTTGTTTAAAAGGT 60.383 41.667 12.08 2.88 45.01 3.50
3579 11153 6.266103 TGTTCTGAAAATTCTGCTTTCATCCT 59.734 34.615 0.00 0.00 40.89 3.24
3645 11219 7.391275 TGATATCAGCATTTCACAAGTTTCTCA 59.609 33.333 0.00 0.00 0.00 3.27
3646 11220 5.833406 TCAGCATTTCACAAGTTTCTCAA 57.167 34.783 0.00 0.00 0.00 3.02
3843 11426 7.745620 AACTACTCCAAACAAAAGTATCAGG 57.254 36.000 0.00 0.00 0.00 3.86
3926 11509 2.764251 CTTCCACGAGCCGTTTTGCG 62.764 60.000 0.00 0.00 38.32 4.85
3993 11576 2.172293 GGATCAGCCACCTTGAGATCTT 59.828 50.000 0.00 0.00 36.30 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 1.781555 GTCGTTGCAGGTCACATCG 59.218 57.895 0.00 0.00 0.00 3.84
655 656 4.446413 CCGAAACCCTAGCGCCGT 62.446 66.667 2.29 0.00 0.00 5.68
715 716 9.840427 CGCTTCCATATAAGAAAAAGAAAAGAA 57.160 29.630 0.00 0.00 0.00 2.52
716 717 9.226606 TCGCTTCCATATAAGAAAAAGAAAAGA 57.773 29.630 0.00 0.00 0.00 2.52
717 718 9.495754 CTCGCTTCCATATAAGAAAAAGAAAAG 57.504 33.333 0.00 0.00 0.00 2.27
718 719 7.968405 GCTCGCTTCCATATAAGAAAAAGAAAA 59.032 33.333 0.00 0.00 0.00 2.29
719 720 7.120579 TGCTCGCTTCCATATAAGAAAAAGAAA 59.879 33.333 0.00 0.00 0.00 2.52
721 722 6.037172 GTGCTCGCTTCCATATAAGAAAAAGA 59.963 38.462 0.00 0.00 0.00 2.52
722 723 6.183360 TGTGCTCGCTTCCATATAAGAAAAAG 60.183 38.462 0.00 0.00 0.00 2.27
723 724 5.645929 TGTGCTCGCTTCCATATAAGAAAAA 59.354 36.000 0.00 0.00 0.00 1.94
724 725 5.064707 GTGTGCTCGCTTCCATATAAGAAAA 59.935 40.000 0.00 0.00 0.00 2.29
726 727 4.119862 GTGTGCTCGCTTCCATATAAGAA 58.880 43.478 0.00 0.00 0.00 2.52
727 728 3.132111 TGTGTGCTCGCTTCCATATAAGA 59.868 43.478 0.56 0.00 0.00 2.10
728 729 3.457234 TGTGTGCTCGCTTCCATATAAG 58.543 45.455 0.56 0.00 0.00 1.73
729 730 3.535280 TGTGTGCTCGCTTCCATATAA 57.465 42.857 0.56 0.00 0.00 0.98
730 731 3.392882 CATGTGTGCTCGCTTCCATATA 58.607 45.455 0.56 0.00 0.00 0.86
731 732 2.216046 CATGTGTGCTCGCTTCCATAT 58.784 47.619 0.56 0.00 0.00 1.78
734 735 3.970721 CATGTGTGCTCGCTTCCA 58.029 55.556 0.56 0.00 0.00 3.53
743 744 5.236773 AATGAGAACCATGGCATGTGTGC 62.237 47.826 24.80 19.55 41.85 4.57
744 745 1.536940 TGAGAACCATGGCATGTGTG 58.463 50.000 24.80 12.97 0.00 3.82
745 746 2.519771 ATGAGAACCATGGCATGTGT 57.480 45.000 24.80 18.74 33.39 3.72
746 747 3.429822 GGAAATGAGAACCATGGCATGTG 60.430 47.826 24.80 18.13 35.24 3.21
747 748 2.762327 GGAAATGAGAACCATGGCATGT 59.238 45.455 24.80 8.54 35.24 3.21
748 749 3.028850 AGGAAATGAGAACCATGGCATG 58.971 45.455 20.56 20.56 35.24 4.06
749 750 3.028850 CAGGAAATGAGAACCATGGCAT 58.971 45.455 13.04 3.99 35.24 4.40
750 751 2.041485 TCAGGAAATGAGAACCATGGCA 59.959 45.455 13.04 1.19 35.24 4.92
751 752 2.726821 TCAGGAAATGAGAACCATGGC 58.273 47.619 13.04 0.00 35.24 4.40
752 753 3.887716 GGATCAGGAAATGAGAACCATGG 59.112 47.826 11.19 11.19 42.53 3.66
758 759 4.934797 AAGGTGGATCAGGAAATGAGAA 57.065 40.909 0.00 0.00 42.53 2.87
788 794 0.102120 CTGAAGCTAGCAGGGACGAG 59.898 60.000 18.83 0.00 0.00 4.18
791 797 1.153269 GGCTGAAGCTAGCAGGGAC 60.153 63.158 18.83 2.14 45.46 4.46
829 835 5.740099 CGATCTTGATCGATGAGATGAGATG 59.260 44.000 23.64 3.72 46.12 2.90
1014 1038 0.249826 GATCTAGTCCTGCTGCCAGC 60.250 60.000 10.45 10.45 42.82 4.85
1015 1039 0.392336 GGATCTAGTCCTGCTGCCAG 59.608 60.000 0.00 0.00 44.16 4.85
1447 4624 1.270839 ACCAACCACGAACATGAGGAG 60.271 52.381 0.00 0.00 0.00 3.69
1568 4746 5.910614 ACGAAGTAATGGTAGTATTGGGTC 58.089 41.667 0.00 0.00 41.94 4.46
1569 4747 5.945144 ACGAAGTAATGGTAGTATTGGGT 57.055 39.130 0.00 0.00 41.94 4.51
1641 4821 0.463295 GAGGTAACGGCCCCTTAAGC 60.463 60.000 0.00 0.00 46.39 3.09
1865 5048 5.163814 GCAACGAGATCTACTTTGCTGAAAT 60.164 40.000 20.49 0.00 38.53 2.17
1976 5159 1.431488 TTGATTGAGGATGCGCTCGC 61.431 55.000 9.73 7.38 42.35 5.03
1980 5163 2.478539 GGAACTTTGATTGAGGATGCGC 60.479 50.000 0.00 0.00 0.00 6.09
1988 5171 7.707624 ATAGAAAGCATGGAACTTTGATTGA 57.292 32.000 2.04 0.00 37.47 2.57
1991 5174 6.664816 TGGAATAGAAAGCATGGAACTTTGAT 59.335 34.615 2.04 0.00 37.47 2.57
1994 5177 7.038799 ACAATGGAATAGAAAGCATGGAACTTT 60.039 33.333 0.00 0.00 39.99 2.66
1995 5178 6.438425 ACAATGGAATAGAAAGCATGGAACTT 59.562 34.615 0.00 0.00 0.00 2.66
1996 5179 5.954150 ACAATGGAATAGAAAGCATGGAACT 59.046 36.000 0.00 0.00 0.00 3.01
1997 5180 6.212888 ACAATGGAATAGAAAGCATGGAAC 57.787 37.500 0.00 0.00 0.00 3.62
2000 5183 5.808540 CACAACAATGGAATAGAAAGCATGG 59.191 40.000 0.00 0.00 0.00 3.66
2001 5184 5.808540 CCACAACAATGGAATAGAAAGCATG 59.191 40.000 0.00 0.00 43.02 4.06
2002 5185 5.625197 GCCACAACAATGGAATAGAAAGCAT 60.625 40.000 0.00 0.00 43.02 3.79
2003 5186 4.321899 GCCACAACAATGGAATAGAAAGCA 60.322 41.667 0.00 0.00 43.02 3.91
2004 5187 4.082026 AGCCACAACAATGGAATAGAAAGC 60.082 41.667 0.00 0.00 43.02 3.51
2007 5190 5.324409 AGAAGCCACAACAATGGAATAGAA 58.676 37.500 0.00 0.00 43.02 2.10
2022 5214 4.379918 GCAAATACAAGGAGAAGAAGCCAC 60.380 45.833 0.00 0.00 0.00 5.01
2025 5217 5.573337 ATGCAAATACAAGGAGAAGAAGC 57.427 39.130 0.00 0.00 0.00 3.86
2032 5224 3.768757 TCCCCAAATGCAAATACAAGGAG 59.231 43.478 0.00 0.00 0.00 3.69
2033 5225 3.768757 CTCCCCAAATGCAAATACAAGGA 59.231 43.478 0.00 0.00 0.00 3.36
2045 5237 1.815421 CCGACGAGCTCCCCAAATG 60.815 63.158 8.47 0.00 0.00 2.32
2062 5257 2.109425 ACTTTCTGTATTGCCCGTCC 57.891 50.000 0.00 0.00 0.00 4.79
2157 5355 0.874390 CAGTTTTGCTGCTTCGGCTA 59.126 50.000 0.00 0.00 42.37 3.93
2174 5372 0.250209 CCTTCCCATCCATCTCGCAG 60.250 60.000 0.00 0.00 0.00 5.18
2260 5458 4.105697 TCCCCTTAGTTGTTCCTTCAACAT 59.894 41.667 11.22 1.31 44.77 2.71
2263 5461 4.167307 ACTTCCCCTTAGTTGTTCCTTCAA 59.833 41.667 0.00 0.00 0.00 2.69
2297 5495 3.319137 TGTGGTCTCGATTCTCTTTGG 57.681 47.619 0.00 0.00 0.00 3.28
2336 5534 3.939837 CTCTTCTTCAGCGCCGCCA 62.940 63.158 4.98 0.00 0.00 5.69
2477 5684 1.614317 CCTGGGTTACCTTTGCAGGAG 60.614 57.143 16.23 0.00 44.19 3.69
2561 5768 4.876107 ACAGTTCAATATACCTTTGGCGAG 59.124 41.667 0.00 0.00 0.00 5.03
2612 5825 2.511373 CGGCCGAGCTGTATTGCA 60.511 61.111 24.07 0.00 34.99 4.08
2613 5826 2.202878 TCGGCCGAGCTGTATTGC 60.203 61.111 27.28 0.00 36.18 3.56
2614 5827 1.592669 CCTCGGCCGAGCTGTATTG 60.593 63.158 43.11 26.70 40.69 1.90
2615 5828 1.115930 ATCCTCGGCCGAGCTGTATT 61.116 55.000 43.11 22.70 40.69 1.89
2616 5829 1.115930 AATCCTCGGCCGAGCTGTAT 61.116 55.000 43.11 29.65 40.69 2.29
2751 6000 1.905922 GCTTCGAGCCAAGCTGACAC 61.906 60.000 0.00 0.00 44.71 3.67
2859 6114 1.982660 CATGAGAATCTGGCCTGCAT 58.017 50.000 3.32 0.00 34.92 3.96
2944 6199 4.881850 ACTGTTGAAGTTCAGAAAATCGGT 59.118 37.500 5.56 3.13 34.57 4.69
2946 6201 5.207768 CCACTGTTGAAGTTCAGAAAATCG 58.792 41.667 5.56 0.00 36.83 3.34
2962 6217 1.342672 ACCGTCCTCAACCCACTGTT 61.343 55.000 0.00 0.00 37.80 3.16
2964 6219 1.301716 CACCGTCCTCAACCCACTG 60.302 63.158 0.00 0.00 0.00 3.66
2965 6220 2.516888 CCACCGTCCTCAACCCACT 61.517 63.158 0.00 0.00 0.00 4.00
2966 6221 2.032071 CCACCGTCCTCAACCCAC 59.968 66.667 0.00 0.00 0.00 4.61
2967 6222 2.446994 ACCACCGTCCTCAACCCA 60.447 61.111 0.00 0.00 0.00 4.51
2968 6223 2.032071 CACCACCGTCCTCAACCC 59.968 66.667 0.00 0.00 0.00 4.11
2970 6225 1.301479 GGTCACCACCGTCCTCAAC 60.301 63.158 0.00 0.00 31.06 3.18
2971 6226 3.144285 GGTCACCACCGTCCTCAA 58.856 61.111 0.00 0.00 31.06 3.02
2984 6844 7.280876 GCAGATAATTGTATCAACTTCTGGTCA 59.719 37.037 14.16 0.00 38.95 4.02
2985 6845 7.254932 GGCAGATAATTGTATCAACTTCTGGTC 60.255 40.741 14.16 5.02 38.95 4.02
3064 7873 5.398012 GCAAATTCTCCTCCCCTATAGTGTT 60.398 44.000 0.00 0.00 0.00 3.32
3069 7878 4.726825 ACTTGCAAATTCTCCTCCCCTATA 59.273 41.667 0.00 0.00 0.00 1.31
3070 7879 3.529319 ACTTGCAAATTCTCCTCCCCTAT 59.471 43.478 0.00 0.00 0.00 2.57
3195 10525 0.677842 ACTTCGCGTTGGAGGTTAGT 59.322 50.000 5.77 0.00 0.00 2.24
3209 10539 4.211389 GCATGTTGTAACTGTCAACTTCG 58.789 43.478 11.96 4.07 43.54 3.79
3228 10558 3.552604 AACAATACAAACTTCGCGCAT 57.447 38.095 8.75 0.00 0.00 4.73
3233 10563 4.840772 CGAGCTCAAACAATACAAACTTCG 59.159 41.667 15.40 0.00 0.00 3.79
3252 10582 1.207377 GCGTCGTTCTAATCCCGAGC 61.207 60.000 0.00 0.00 0.00 5.03
3400 10944 2.301346 AGCCTGTTGTGGTTTCTTGAG 58.699 47.619 0.00 0.00 0.00 3.02
3579 11153 3.517901 CTGGAGGTCAGGTTAATGGTACA 59.482 47.826 0.00 0.00 40.95 2.90
3843 11426 2.171489 GACCGGCTGCGTCAAGTTTC 62.171 60.000 0.00 0.00 0.00 2.78
3926 11509 1.301677 GCAGTACCAGCAGCAACCTC 61.302 60.000 0.00 0.00 0.00 3.85
3993 11576 2.686405 ACATTATCAGGTACGACGCTGA 59.314 45.455 6.19 6.19 32.67 4.26


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

AutoCloner maintained by Alex Coulton.