Multiple sequence alignment - TraesCS2D01G103200

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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 TraesCS2D01G103200 chr2D 100.000 2972 0 0 1 2972 55714384 55711413 0.000000e+00 5489.0
1 TraesCS2D01G103200 chr2D 92.446 1390 62 19 833 2206 39410113 39411475 0.000000e+00 1945.0
2 TraesCS2D01G103200 chr2D 88.971 408 23 7 2399 2806 39412585 39412970 4.450000e-133 484.0
3 TraesCS2D01G103200 chr2B 92.234 1764 74 32 818 2544 88418931 88417194 0.000000e+00 2440.0
4 TraesCS2D01G103200 chr2B 87.710 1310 86 33 1409 2662 88251457 88250167 0.000000e+00 1458.0
5 TraesCS2D01G103200 chr2B 87.200 625 67 9 1 614 88420033 88419411 0.000000e+00 699.0
6 TraesCS2D01G103200 chr2B 90.717 237 9 3 2578 2806 88417193 88416962 1.340000e-78 303.0
7 TraesCS2D01G103200 chr2B 92.053 151 8 3 2660 2806 88249742 88249592 3.000000e-50 209.0
8 TraesCS2D01G103200 chr2A 91.615 1622 71 28 528 2133 57150763 57149191 0.000000e+00 2182.0
9 TraesCS2D01G103200 chr2A 84.984 626 80 11 1 614 676343663 676344286 9.050000e-175 623.0
10 TraesCS2D01G103200 chr2A 84.984 626 79 12 1 614 695418659 695419281 3.250000e-174 621.0
11 TraesCS2D01G103200 chr2A 94.986 359 17 1 2449 2806 57148684 57148326 2.000000e-156 562.0
12 TraesCS2D01G103200 chr2A 83.438 320 31 11 2156 2454 57149197 57148879 8.110000e-71 278.0
13 TraesCS2D01G103200 chr7D 86.240 625 73 10 1 614 518562636 518562014 0.000000e+00 665.0
14 TraesCS2D01G103200 chr3D 85.623 626 76 11 1 614 485191562 485190939 0.000000e+00 645.0
15 TraesCS2D01G103200 chr6D 85.440 625 78 9 1 614 4396788 4397410 3.230000e-179 638.0
16 TraesCS2D01G103200 chr3A 85.440 625 77 11 1 614 699311343 699310722 3.230000e-179 638.0
17 TraesCS2D01G103200 chr3A 85.304 626 77 12 1 614 723358911 723358289 1.500000e-177 632.0
18 TraesCS2D01G103200 chr3A 85.144 626 79 11 1 614 728391668 728392291 1.940000e-176 628.0
19 TraesCS2D01G103200 chr7A 85.496 131 19 0 1043 1173 299527340 299527470 1.440000e-28 137.0
20 TraesCS2D01G103200 chrUn 86.777 121 16 0 1053 1173 13816686 13816566 5.170000e-28 135.0
21 TraesCS2D01G103200 chr5B 92.105 38 3 0 2934 2971 401132589 401132626 1.000000e-03 54.7


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 TraesCS2D01G103200 chr2D 55711413 55714384 2971 True 5489.000000 5489 100.000000 1 2972 1 chr2D.!!$R1 2971
1 TraesCS2D01G103200 chr2D 39410113 39412970 2857 False 1214.500000 1945 90.708500 833 2806 2 chr2D.!!$F1 1973
2 TraesCS2D01G103200 chr2B 88416962 88420033 3071 True 1147.333333 2440 90.050333 1 2806 3 chr2B.!!$R2 2805
3 TraesCS2D01G103200 chr2B 88249592 88251457 1865 True 833.500000 1458 89.881500 1409 2806 2 chr2B.!!$R1 1397
4 TraesCS2D01G103200 chr2A 57148326 57150763 2437 True 1007.333333 2182 90.013000 528 2806 3 chr2A.!!$R1 2278
5 TraesCS2D01G103200 chr2A 676343663 676344286 623 False 623.000000 623 84.984000 1 614 1 chr2A.!!$F1 613
6 TraesCS2D01G103200 chr2A 695418659 695419281 622 False 621.000000 621 84.984000 1 614 1 chr2A.!!$F2 613
7 TraesCS2D01G103200 chr7D 518562014 518562636 622 True 665.000000 665 86.240000 1 614 1 chr7D.!!$R1 613
8 TraesCS2D01G103200 chr3D 485190939 485191562 623 True 645.000000 645 85.623000 1 614 1 chr3D.!!$R1 613
9 TraesCS2D01G103200 chr6D 4396788 4397410 622 False 638.000000 638 85.440000 1 614 1 chr6D.!!$F1 613
10 TraesCS2D01G103200 chr3A 699310722 699311343 621 True 638.000000 638 85.440000 1 614 1 chr3A.!!$R1 613
11 TraesCS2D01G103200 chr3A 723358289 723358911 622 True 632.000000 632 85.304000 1 614 1 chr3A.!!$R2 613
12 TraesCS2D01G103200 chr3A 728391668 728392291 623 False 628.000000 628 85.144000 1 614 1 chr3A.!!$F1 613

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
755 1133 0.387565 GCCGTCCACACCACAAAAAT 59.612 50.000 0.0 0.0 0.0 1.82 F
758 1136 1.066908 CGTCCACACCACAAAAATGCT 59.933 47.619 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 1980 0.035881 AGACGACGGTGAGGTAGACA 59.964 55.0 0.0 0.0 0.0 3.41 R
2046 2441 0.401738 CAATGGTGGACAGGTGGAGT 59.598 55.0 0.0 0.0 0.0 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
25 26 6.627087 TGAGATTTCCTCCAACTCTAATGT 57.373 37.500 0.00 0.00 41.25 2.71
80 83 0.531974 TCTTGTTCGTGCGGCTCTTT 60.532 50.000 0.00 0.00 0.00 2.52
135 138 4.282068 CTCAATGTTCACCTTCGTGTTTG 58.718 43.478 0.00 0.00 41.09 2.93
151 154 1.963515 GTTTGTGATGGTGAGCCCTTT 59.036 47.619 0.00 0.00 0.00 3.11
188 191 6.034591 CGTTATCGTCATCTTGTTAGGAGTT 58.965 40.000 0.00 0.00 0.00 3.01
191 194 8.718734 GTTATCGTCATCTTGTTAGGAGTTTTT 58.281 33.333 0.00 0.00 0.00 1.94
212 215 7.823745 TTTTTCTATCTTGCTTTCACTCCTT 57.176 32.000 0.00 0.00 0.00 3.36
227 230 8.789767 TTTCACTCCTTCAGATATCTCCTATT 57.210 34.615 1.03 0.00 0.00 1.73
230 233 7.888021 TCACTCCTTCAGATATCTCCTATTCTC 59.112 40.741 1.03 0.00 0.00 2.87
258 262 1.138069 TCCGAGTCAGTTGTTTCTGCA 59.862 47.619 0.00 0.00 35.63 4.41
317 321 2.998668 CGACATCTTCGTGGCATAAC 57.001 50.000 0.00 0.00 43.24 1.89
340 351 2.578786 GTCTCTTTTTCCCCGTTCCAA 58.421 47.619 0.00 0.00 0.00 3.53
381 392 4.022589 CCTATTCAAATGCTATGTGGGCTG 60.023 45.833 0.00 0.00 0.00 4.85
430 441 6.751514 TTCTGCTTACTGTGTTTTTCTTGA 57.248 33.333 0.00 0.00 0.00 3.02
431 442 6.119144 TCTGCTTACTGTGTTTTTCTTGAC 57.881 37.500 0.00 0.00 0.00 3.18
482 493 2.290641 ACATACTGCAATTCCCCGTTCA 60.291 45.455 0.00 0.00 0.00 3.18
508 519 4.443266 AGGCCGAGTTGCGAGCTC 62.443 66.667 2.73 2.73 44.57 4.09
526 537 3.376935 CTGGCTCTTCCGACGGCAT 62.377 63.158 9.66 0.00 37.80 4.40
542 553 3.244284 ACGGCATAAGTGACTTGGTTACA 60.244 43.478 8.33 0.00 0.00 2.41
549 560 5.514274 AAGTGACTTGGTTACAATGGTTG 57.486 39.130 0.00 0.00 35.73 3.77
554 565 3.572255 ACTTGGTTACAATGGTTGCGAAT 59.428 39.130 0.00 0.00 35.73 3.34
555 566 4.038642 ACTTGGTTACAATGGTTGCGAATT 59.961 37.500 0.00 0.00 35.73 2.17
556 567 4.592485 TGGTTACAATGGTTGCGAATTT 57.408 36.364 0.00 0.00 0.00 1.82
557 568 4.950050 TGGTTACAATGGTTGCGAATTTT 58.050 34.783 0.00 0.00 0.00 1.82
596 607 6.938698 TTTTACACCTACCATCCTCTTGTA 57.061 37.500 0.00 0.00 0.00 2.41
663 1041 4.774726 TGATCTGCCCCTGAATATCTAGAC 59.225 45.833 0.00 0.00 0.00 2.59
704 1082 7.159322 TCAGAGTAGGAGTTTATCAACACTC 57.841 40.000 1.59 1.59 39.04 3.51
717 1095 0.902531 AACACTCGGTCCCATCGATT 59.097 50.000 0.00 0.00 36.01 3.34
725 1103 1.344763 GGTCCCATCGATTCCCTACTG 59.655 57.143 0.00 0.00 0.00 2.74
735 1113 3.809832 CGATTCCCTACTGAAATTCGCAT 59.190 43.478 0.00 0.00 0.00 4.73
751 1129 1.896183 CATGCCGTCCACACCACAA 60.896 57.895 0.00 0.00 0.00 3.33
752 1130 1.152860 ATGCCGTCCACACCACAAA 60.153 52.632 0.00 0.00 0.00 2.83
753 1131 0.753479 ATGCCGTCCACACCACAAAA 60.753 50.000 0.00 0.00 0.00 2.44
754 1132 0.965866 TGCCGTCCACACCACAAAAA 60.966 50.000 0.00 0.00 0.00 1.94
755 1133 0.387565 GCCGTCCACACCACAAAAAT 59.612 50.000 0.00 0.00 0.00 1.82
756 1134 1.867698 GCCGTCCACACCACAAAAATG 60.868 52.381 0.00 0.00 0.00 2.32
757 1135 1.486439 CGTCCACACCACAAAAATGC 58.514 50.000 0.00 0.00 0.00 3.56
758 1136 1.066908 CGTCCACACCACAAAAATGCT 59.933 47.619 0.00 0.00 0.00 3.79
759 1137 2.292016 CGTCCACACCACAAAAATGCTA 59.708 45.455 0.00 0.00 0.00 3.49
760 1138 3.243234 CGTCCACACCACAAAAATGCTAA 60.243 43.478 0.00 0.00 0.00 3.09
761 1139 4.688021 GTCCACACCACAAAAATGCTAAA 58.312 39.130 0.00 0.00 0.00 1.85
762 1140 4.506288 GTCCACACCACAAAAATGCTAAAC 59.494 41.667 0.00 0.00 0.00 2.01
763 1141 3.489047 CCACACCACAAAAATGCTAAACG 59.511 43.478 0.00 0.00 0.00 3.60
764 1142 3.060607 CACACCACAAAAATGCTAAACGC 60.061 43.478 0.00 0.00 39.77 4.84
776 1154 1.651987 CTAAACGCACCACATCCGAT 58.348 50.000 0.00 0.00 0.00 4.18
811 1189 7.342284 TCCAAGTCCAACTAATAAACCAAACAA 59.658 33.333 0.00 0.00 0.00 2.83
812 1190 7.982354 CCAAGTCCAACTAATAAACCAAACAAA 59.018 33.333 0.00 0.00 0.00 2.83
813 1191 9.030301 CAAGTCCAACTAATAAACCAAACAAAG 57.970 33.333 0.00 0.00 0.00 2.77
828 1206 6.040247 CCAAACAAAGAAGTTTCCAAGGTAC 58.960 40.000 0.00 0.00 39.55 3.34
1566 1956 2.049156 TTCCTCGACGTGCTGCTG 60.049 61.111 0.00 0.00 0.00 4.41
1590 1980 2.179517 CTCGCGTCGCTCTTCCTT 59.820 61.111 16.36 0.00 0.00 3.36
1972 2362 0.959553 GCCCAATGGAGATGCATGAG 59.040 55.000 2.46 0.00 0.00 2.90
1973 2363 1.617322 CCCAATGGAGATGCATGAGG 58.383 55.000 2.46 0.00 0.00 3.86
2053 2448 8.269317 ACTGCTAGTAGAGATATATACTCCACC 58.731 40.741 15.37 0.00 34.21 4.61
2054 2449 8.395288 TGCTAGTAGAGATATATACTCCACCT 57.605 38.462 0.00 5.53 34.21 4.00
2055 2450 8.268605 TGCTAGTAGAGATATATACTCCACCTG 58.731 40.741 0.00 4.07 34.21 4.00
2084 2479 6.890558 CCATTGTTATGGTTTCAGCAAAAAG 58.109 36.000 0.00 0.00 45.34 2.27
2088 2483 8.553459 TTGTTATGGTTTCAGCAAAAAGAAAA 57.447 26.923 0.00 0.00 35.71 2.29
2089 2484 8.553459 TGTTATGGTTTCAGCAAAAAGAAAAA 57.447 26.923 0.00 0.00 35.71 1.94
2137 2534 8.755018 CAAAGAAAATACAGAAAGAAATTGCGT 58.245 29.630 0.00 0.00 0.00 5.24
2138 2535 7.858052 AGAAAATACAGAAAGAAATTGCGTG 57.142 32.000 0.00 0.00 0.00 5.34
2291 3776 7.960262 TCCTTATCTGAGCATGCATATATAGG 58.040 38.462 21.98 16.62 0.00 2.57
2397 3918 3.304592 CGTTGTCACATTCAAATCCAGCA 60.305 43.478 0.00 0.00 0.00 4.41
2426 3947 0.100682 CAGCCAATGCATCACAGAGC 59.899 55.000 0.00 0.00 41.13 4.09
2434 3959 5.271625 CAATGCATCACAGAGCTTGTAATC 58.728 41.667 0.00 0.00 38.16 1.75
2460 4185 8.794406 CAAGAAAACCGATAAATAATCAAACCG 58.206 33.333 0.00 0.00 33.87 4.44
2525 4251 1.933853 CCGGTACATGCTTAGCAACTC 59.066 52.381 12.08 2.39 43.62 3.01
2555 4281 5.163571 GGAGCAAGGAAAGAATGGAAAGATC 60.164 44.000 0.00 0.00 0.00 2.75
2714 4880 2.031616 CGATCCGGCCATGCAGAT 59.968 61.111 2.24 0.00 0.00 2.90
2715 4881 1.598962 CGATCCGGCCATGCAGATT 60.599 57.895 2.24 0.00 0.00 2.40
2718 4885 3.908081 CCGGCCATGCAGATTGCC 61.908 66.667 2.24 8.15 44.23 4.52
2806 4974 9.243637 TGTGCAAAGTTGATTGTTAGTTTAATC 57.756 29.630 0.00 0.00 34.64 1.75
2808 4976 9.462174 TGCAAAGTTGATTGTTAGTTTAATCAG 57.538 29.630 0.00 0.00 42.35 2.90
2809 4977 9.463443 GCAAAGTTGATTGTTAGTTTAATCAGT 57.537 29.630 0.00 0.00 42.35 3.41
2823 4991 8.974060 AGTTTAATCAGTTTTGGTAAGTCTCA 57.026 30.769 0.00 0.00 0.00 3.27
2824 4992 9.057089 AGTTTAATCAGTTTTGGTAAGTCTCAG 57.943 33.333 0.00 0.00 0.00 3.35
2825 4993 8.837389 GTTTAATCAGTTTTGGTAAGTCTCAGT 58.163 33.333 0.00 0.00 0.00 3.41
2826 4994 8.603242 TTAATCAGTTTTGGTAAGTCTCAGTC 57.397 34.615 0.00 0.00 0.00 3.51
2827 4995 4.617959 TCAGTTTTGGTAAGTCTCAGTCG 58.382 43.478 0.00 0.00 0.00 4.18
2828 4996 4.340097 TCAGTTTTGGTAAGTCTCAGTCGA 59.660 41.667 0.00 0.00 0.00 4.20
2829 4997 4.444720 CAGTTTTGGTAAGTCTCAGTCGAC 59.555 45.833 7.70 7.70 0.00 4.20
2830 4998 4.341520 AGTTTTGGTAAGTCTCAGTCGACT 59.658 41.667 13.58 13.58 45.73 4.18
2840 5008 6.334102 AGTCTCAGTCGACTTAGATTTTGT 57.666 37.500 27.34 11.15 41.27 2.83
2841 5009 6.750148 AGTCTCAGTCGACTTAGATTTTGTT 58.250 36.000 27.34 10.42 41.27 2.83
2842 5010 7.883217 AGTCTCAGTCGACTTAGATTTTGTTA 58.117 34.615 27.34 4.85 41.27 2.41
2843 5011 8.524487 AGTCTCAGTCGACTTAGATTTTGTTAT 58.476 33.333 27.34 8.20 41.27 1.89
2844 5012 8.587950 GTCTCAGTCGACTTAGATTTTGTTATG 58.412 37.037 27.34 8.71 29.97 1.90
2845 5013 8.304596 TCTCAGTCGACTTAGATTTTGTTATGT 58.695 33.333 22.49 0.00 0.00 2.29
2846 5014 8.462143 TCAGTCGACTTAGATTTTGTTATGTC 57.538 34.615 17.26 0.00 0.00 3.06
2847 5015 8.304596 TCAGTCGACTTAGATTTTGTTATGTCT 58.695 33.333 17.26 0.00 0.00 3.41
2848 5016 8.926710 CAGTCGACTTAGATTTTGTTATGTCTT 58.073 33.333 17.26 0.00 0.00 3.01
2849 5017 9.141400 AGTCGACTTAGATTTTGTTATGTCTTC 57.859 33.333 13.58 0.00 0.00 2.87
2850 5018 8.922676 GTCGACTTAGATTTTGTTATGTCTTCA 58.077 33.333 8.70 0.00 0.00 3.02
2851 5019 9.653287 TCGACTTAGATTTTGTTATGTCTTCAT 57.347 29.630 0.00 0.00 38.00 2.57
2852 5020 9.907576 CGACTTAGATTTTGTTATGTCTTCATC 57.092 33.333 0.00 0.00 35.70 2.92
2853 5021 9.907576 GACTTAGATTTTGTTATGTCTTCATCG 57.092 33.333 0.00 0.00 35.70 3.84
2854 5022 9.653287 ACTTAGATTTTGTTATGTCTTCATCGA 57.347 29.630 0.00 0.00 35.70 3.59
2857 5025 7.412853 AGATTTTGTTATGTCTTCATCGATGC 58.587 34.615 20.81 7.15 35.70 3.91
2858 5026 6.741992 TTTTGTTATGTCTTCATCGATGCT 57.258 33.333 20.81 3.55 35.70 3.79
2859 5027 7.841915 TTTTGTTATGTCTTCATCGATGCTA 57.158 32.000 20.81 9.89 35.70 3.49
2860 5028 8.437360 TTTTGTTATGTCTTCATCGATGCTAT 57.563 30.769 20.81 11.51 35.70 2.97
2861 5029 9.541143 TTTTGTTATGTCTTCATCGATGCTATA 57.459 29.630 20.81 10.64 35.70 1.31
2862 5030 9.710900 TTTGTTATGTCTTCATCGATGCTATAT 57.289 29.630 20.81 13.07 35.70 0.86
2863 5031 9.710900 TTGTTATGTCTTCATCGATGCTATATT 57.289 29.630 20.81 6.71 35.70 1.28
2864 5032 9.358872 TGTTATGTCTTCATCGATGCTATATTC 57.641 33.333 20.81 7.47 35.70 1.75
2865 5033 8.812329 GTTATGTCTTCATCGATGCTATATTCC 58.188 37.037 20.81 3.64 35.70 3.01
2866 5034 6.596309 TGTCTTCATCGATGCTATATTCCT 57.404 37.500 20.81 0.00 0.00 3.36
2867 5035 6.997655 TGTCTTCATCGATGCTATATTCCTT 58.002 36.000 20.81 0.00 0.00 3.36
2868 5036 7.445121 TGTCTTCATCGATGCTATATTCCTTT 58.555 34.615 20.81 0.00 0.00 3.11
2869 5037 7.386025 TGTCTTCATCGATGCTATATTCCTTTG 59.614 37.037 20.81 0.00 0.00 2.77
2870 5038 7.600375 GTCTTCATCGATGCTATATTCCTTTGA 59.400 37.037 20.81 0.00 0.00 2.69
2871 5039 8.316946 TCTTCATCGATGCTATATTCCTTTGAT 58.683 33.333 20.81 0.00 0.00 2.57
2872 5040 8.484641 TTCATCGATGCTATATTCCTTTGATC 57.515 34.615 20.81 0.00 0.00 2.92
2873 5041 7.845037 TCATCGATGCTATATTCCTTTGATCT 58.155 34.615 20.81 0.00 0.00 2.75
2874 5042 8.316946 TCATCGATGCTATATTCCTTTGATCTT 58.683 33.333 20.81 0.00 0.00 2.40
2875 5043 8.944029 CATCGATGCTATATTCCTTTGATCTTT 58.056 33.333 13.37 0.00 0.00 2.52
2876 5044 8.908786 TCGATGCTATATTCCTTTGATCTTTT 57.091 30.769 0.00 0.00 0.00 2.27
2877 5045 9.996554 TCGATGCTATATTCCTTTGATCTTTTA 57.003 29.630 0.00 0.00 0.00 1.52
2946 5114 9.778741 TCTTACATAAAACACTTGATTGAGTCT 57.221 29.630 0.00 0.00 0.00 3.24
2948 5116 9.554395 TTACATAAAACACTTGATTGAGTCTCA 57.446 29.630 0.00 0.00 0.00 3.27
2949 5117 8.450578 ACATAAAACACTTGATTGAGTCTCAA 57.549 30.769 17.46 17.46 41.09 3.02
2965 5133 4.624336 TCTCAATCGACTGAGACTTAGC 57.376 45.455 21.83 0.00 45.45 3.09
2966 5134 3.378742 TCTCAATCGACTGAGACTTAGCC 59.621 47.826 21.83 0.00 45.45 3.93
2967 5135 3.089284 TCAATCGACTGAGACTTAGCCA 58.911 45.455 0.00 0.00 0.00 4.75
2968 5136 3.119459 TCAATCGACTGAGACTTAGCCAC 60.119 47.826 0.00 0.00 0.00 5.01
2969 5137 1.905637 TCGACTGAGACTTAGCCACA 58.094 50.000 0.00 0.00 0.00 4.17
2970 5138 1.540267 TCGACTGAGACTTAGCCACAC 59.460 52.381 0.00 0.00 0.00 3.82
2971 5139 1.402984 CGACTGAGACTTAGCCACACC 60.403 57.143 0.00 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 69 0.602638 ATCACAAAGAGCCGCACGAA 60.603 50.000 0.00 0.00 0.00 3.85
80 83 2.166254 TCTCAATAGTGCGCTCATCACA 59.834 45.455 9.73 0.00 36.93 3.58
135 138 1.815003 CAGAAAAGGGCTCACCATCAC 59.185 52.381 0.00 0.00 43.89 3.06
151 154 3.060978 CGATAACGTGTCGGATCAGAA 57.939 47.619 13.92 0.00 35.55 3.02
188 191 7.502226 TGAAGGAGTGAAAGCAAGATAGAAAAA 59.498 33.333 0.00 0.00 0.00 1.94
191 194 6.014242 TCTGAAGGAGTGAAAGCAAGATAGAA 60.014 38.462 0.00 0.00 0.00 2.10
203 206 8.231007 AGAATAGGAGATATCTGAAGGAGTGAA 58.769 37.037 10.74 0.00 0.00 3.18
210 213 8.827832 ATGGAGAGAATAGGAGATATCTGAAG 57.172 38.462 10.74 0.00 0.00 3.02
227 230 4.171878 ACTGACTCGGAATATGGAGAGA 57.828 45.455 8.12 0.00 34.98 3.10
230 233 4.392921 ACAACTGACTCGGAATATGGAG 57.607 45.455 0.00 0.00 36.36 3.86
258 262 5.473504 GTGACTACAATGAATTGAAGTGGGT 59.526 40.000 9.94 0.25 40.14 4.51
317 321 0.250597 AACGGGGAAAAAGAGACGGG 60.251 55.000 0.00 0.00 0.00 5.28
340 351 1.592223 GCCTGGAGCTGTAACGAGT 59.408 57.895 0.00 0.00 38.99 4.18
430 441 0.036010 CCAGGCAATGAGAGAACCGT 60.036 55.000 0.00 0.00 0.00 4.83
431 442 0.250234 TCCAGGCAATGAGAGAACCG 59.750 55.000 0.00 0.00 0.00 4.44
482 493 3.178540 AACTCGGCCTCGGCACTTT 62.179 57.895 10.51 0.00 44.11 2.66
508 519 2.016393 TATGCCGTCGGAAGAGCCAG 62.016 60.000 17.49 0.00 43.49 4.85
526 537 5.009210 GCAACCATTGTAACCAAGTCACTTA 59.991 40.000 0.00 0.00 33.17 2.24
575 586 5.781306 TGTTACAAGAGGATGGTAGGTGTAA 59.219 40.000 0.00 0.00 0.00 2.41
596 607 7.336931 CCTTATAAAGATGGCACTTGTACTGTT 59.663 37.037 0.00 0.00 0.00 3.16
704 1082 0.317479 GTAGGGAATCGATGGGACCG 59.683 60.000 0.00 0.00 0.00 4.79
717 1095 2.288666 GCATGCGAATTTCAGTAGGGA 58.711 47.619 0.00 0.00 0.00 4.20
725 1103 0.523335 GTGGACGGCATGCGAATTTC 60.523 55.000 12.44 2.98 0.00 2.17
735 1113 0.965866 TTTTTGTGGTGTGGACGGCA 60.966 50.000 0.00 0.00 0.00 5.69
757 1135 1.593006 GATCGGATGTGGTGCGTTTAG 59.407 52.381 0.00 0.00 42.81 1.85
758 1136 1.647346 GATCGGATGTGGTGCGTTTA 58.353 50.000 0.00 0.00 42.81 2.01
759 1137 1.358725 CGATCGGATGTGGTGCGTTT 61.359 55.000 7.38 0.00 42.81 3.60
760 1138 1.809619 CGATCGGATGTGGTGCGTT 60.810 57.895 7.38 0.00 42.81 4.84
761 1139 2.202743 CGATCGGATGTGGTGCGT 60.203 61.111 7.38 0.00 42.81 5.24
762 1140 2.961721 CCGATCGGATGTGGTGCG 60.962 66.667 30.62 0.00 43.73 5.34
763 1141 1.883084 GACCGATCGGATGTGGTGC 60.883 63.158 39.55 13.78 38.96 5.01
764 1142 1.029681 TAGACCGATCGGATGTGGTG 58.970 55.000 39.55 11.67 38.96 4.17
765 1143 1.771565 TTAGACCGATCGGATGTGGT 58.228 50.000 39.55 17.21 38.96 4.16
766 1144 2.352814 GGATTAGACCGATCGGATGTGG 60.353 54.545 39.55 13.23 38.96 4.17
767 1145 2.296190 TGGATTAGACCGATCGGATGTG 59.704 50.000 39.55 14.01 38.96 3.21
768 1146 2.594131 TGGATTAGACCGATCGGATGT 58.406 47.619 39.55 23.90 38.96 3.06
769 1147 3.005897 ACTTGGATTAGACCGATCGGATG 59.994 47.826 39.55 18.31 38.96 3.51
770 1148 3.231818 ACTTGGATTAGACCGATCGGAT 58.768 45.455 39.55 27.60 38.96 4.18
776 1154 3.170717 AGTTGGACTTGGATTAGACCGA 58.829 45.455 0.00 0.00 33.43 4.69
811 1189 7.607615 TGTAGTAGTACCTTGGAAACTTCTT 57.392 36.000 5.26 0.68 0.00 2.52
812 1190 7.440198 GTTGTAGTAGTACCTTGGAAACTTCT 58.560 38.462 5.26 3.14 0.00 2.85
813 1191 6.364435 CGTTGTAGTAGTACCTTGGAAACTTC 59.636 42.308 5.26 0.00 0.00 3.01
828 1206 1.336148 TGGGTGAACGCGTTGTAGTAG 60.336 52.381 31.89 0.00 0.00 2.57
863 1245 6.043411 GCTTATAACGAGAGGATTGTTGACT 58.957 40.000 0.00 0.00 36.15 3.41
864 1246 6.043411 AGCTTATAACGAGAGGATTGTTGAC 58.957 40.000 0.00 0.00 36.15 3.18
865 1247 6.222038 AGCTTATAACGAGAGGATTGTTGA 57.778 37.500 0.00 0.00 36.15 3.18
866 1248 5.174035 CGAGCTTATAACGAGAGGATTGTTG 59.826 44.000 0.00 0.00 36.15 3.33
869 1251 3.670991 GCGAGCTTATAACGAGAGGATTG 59.329 47.826 0.00 0.00 0.00 2.67
1121 1503 1.194781 GGAGTTGGTGAGGAGGAGCA 61.195 60.000 0.00 0.00 0.00 4.26
1515 1905 3.111939 CGCTCCAGGAGGTAGACG 58.888 66.667 18.83 8.73 35.89 4.18
1590 1980 0.035881 AGACGACGGTGAGGTAGACA 59.964 55.000 0.00 0.00 0.00 3.41
1933 2323 2.408050 CAGCTTGGCGTATCTGTATCC 58.592 52.381 0.00 0.00 0.00 2.59
1972 2362 6.587608 GGGAATGAATTGATCAAATATTCGCC 59.412 38.462 27.25 23.27 42.54 5.54
1973 2363 7.373493 AGGGAATGAATTGATCAAATATTCGC 58.627 34.615 28.57 28.57 42.54 4.70
2045 2440 1.628340 CAATGGTGGACAGGTGGAGTA 59.372 52.381 0.00 0.00 0.00 2.59
2046 2441 0.401738 CAATGGTGGACAGGTGGAGT 59.598 55.000 0.00 0.00 0.00 3.85
2047 2442 0.401738 ACAATGGTGGACAGGTGGAG 59.598 55.000 0.00 0.00 0.00 3.86
2048 2443 0.850100 AACAATGGTGGACAGGTGGA 59.150 50.000 0.00 0.00 0.00 4.02
2049 2444 2.577606 TAACAATGGTGGACAGGTGG 57.422 50.000 0.00 0.00 0.00 4.61
2050 2445 2.754552 CCATAACAATGGTGGACAGGTG 59.245 50.000 0.00 0.00 36.95 4.00
2051 2446 3.085952 CCATAACAATGGTGGACAGGT 57.914 47.619 0.00 0.00 36.95 4.00
2137 2534 0.627451 TTACGGGAGGACTAGCTCCA 59.373 55.000 15.78 0.00 42.46 3.86
2138 2535 1.133853 TCTTACGGGAGGACTAGCTCC 60.134 57.143 7.67 7.67 39.81 4.70
2257 3742 7.442364 TGCATGCTCAGATAAGGATAACTTTAC 59.558 37.037 20.33 0.00 40.64 2.01
2275 3760 6.669125 ATCTCTCCCTATATATGCATGCTC 57.331 41.667 20.33 0.00 0.00 4.26
2280 3765 9.492730 TGATTTGTATCTCTCCCTATATATGCA 57.507 33.333 0.00 0.00 0.00 3.96
2290 3775 7.929941 AGTTCTTTTGATTTGTATCTCTCCC 57.070 36.000 0.00 0.00 0.00 4.30
2291 3776 8.884726 GGTAGTTCTTTTGATTTGTATCTCTCC 58.115 37.037 0.00 0.00 0.00 3.71
2397 3918 0.610232 GCATTGGCTGTCCTTGTCCT 60.610 55.000 0.00 0.00 36.96 3.85
2404 3925 0.454600 CTGTGATGCATTGGCTGTCC 59.545 55.000 0.00 0.00 41.91 4.02
2434 3959 8.794406 CGGTTTGATTATTTATCGGTTTTCTTG 58.206 33.333 0.00 0.00 35.94 3.02
2460 4185 2.396590 TTATGGTCTTTGTCTCCGCC 57.603 50.000 0.00 0.00 0.00 6.13
2525 4251 3.692257 TTCTTTCCTTGCTCCTCTCAG 57.308 47.619 0.00 0.00 0.00 3.35
2555 4281 2.076622 CTACGGGCTCCACGAGGATG 62.077 65.000 0.78 0.00 44.70 3.51
2718 4885 4.758251 TGCCGTGTCATGCCCTCG 62.758 66.667 0.00 0.00 0.00 4.63
2806 4974 4.444720 GTCGACTGAGACTTACCAAAACTG 59.555 45.833 8.70 0.00 38.09 3.16
2808 4976 4.968660 GTCGACTGAGACTTACCAAAAC 57.031 45.455 8.70 0.00 38.09 2.43
2818 4986 8.587950 CATAACAAAATCTAAGTCGACTGAGAC 58.412 37.037 30.97 0.00 36.33 3.36
2819 4987 8.304596 ACATAACAAAATCTAAGTCGACTGAGA 58.695 33.333 30.58 30.58 37.84 3.27
2820 4988 8.467402 ACATAACAAAATCTAAGTCGACTGAG 57.533 34.615 22.32 22.32 0.00 3.35
2821 4989 8.304596 AGACATAACAAAATCTAAGTCGACTGA 58.695 33.333 20.85 13.61 0.00 3.41
2822 4990 8.467402 AGACATAACAAAATCTAAGTCGACTG 57.533 34.615 20.85 7.79 0.00 3.51
2823 4991 9.141400 GAAGACATAACAAAATCTAAGTCGACT 57.859 33.333 13.58 13.58 0.00 4.18
2824 4992 8.922676 TGAAGACATAACAAAATCTAAGTCGAC 58.077 33.333 7.70 7.70 0.00 4.20
2825 4993 9.653287 ATGAAGACATAACAAAATCTAAGTCGA 57.347 29.630 0.00 0.00 34.71 4.20
2826 4994 9.907576 GATGAAGACATAACAAAATCTAAGTCG 57.092 33.333 0.00 0.00 36.82 4.18
2827 4995 9.907576 CGATGAAGACATAACAAAATCTAAGTC 57.092 33.333 0.00 0.00 36.82 3.01
2828 4996 9.653287 TCGATGAAGACATAACAAAATCTAAGT 57.347 29.630 0.00 0.00 36.82 2.24
2831 4999 8.551205 GCATCGATGAAGACATAACAAAATCTA 58.449 33.333 29.20 0.00 36.82 1.98
2832 5000 7.281774 AGCATCGATGAAGACATAACAAAATCT 59.718 33.333 29.20 6.97 36.82 2.40
2833 5001 7.412853 AGCATCGATGAAGACATAACAAAATC 58.587 34.615 29.20 4.70 36.82 2.17
2834 5002 7.325660 AGCATCGATGAAGACATAACAAAAT 57.674 32.000 29.20 0.00 36.82 1.82
2835 5003 6.741992 AGCATCGATGAAGACATAACAAAA 57.258 33.333 29.20 0.00 36.82 2.44
2836 5004 9.710900 ATATAGCATCGATGAAGACATAACAAA 57.289 29.630 29.20 1.18 36.82 2.83
2837 5005 9.710900 AATATAGCATCGATGAAGACATAACAA 57.289 29.630 29.20 1.43 36.82 2.83
2838 5006 9.358872 GAATATAGCATCGATGAAGACATAACA 57.641 33.333 29.20 2.44 36.82 2.41
2839 5007 8.812329 GGAATATAGCATCGATGAAGACATAAC 58.188 37.037 29.20 7.63 36.82 1.89
2840 5008 8.753133 AGGAATATAGCATCGATGAAGACATAA 58.247 33.333 29.20 5.50 36.82 1.90
2841 5009 8.298729 AGGAATATAGCATCGATGAAGACATA 57.701 34.615 29.20 15.88 36.82 2.29
2842 5010 7.180322 AGGAATATAGCATCGATGAAGACAT 57.820 36.000 29.20 14.39 39.67 3.06
2843 5011 6.596309 AGGAATATAGCATCGATGAAGACA 57.404 37.500 29.20 9.35 0.00 3.41
2844 5012 7.600375 TCAAAGGAATATAGCATCGATGAAGAC 59.400 37.037 29.20 10.98 0.00 3.01
2845 5013 7.670364 TCAAAGGAATATAGCATCGATGAAGA 58.330 34.615 29.20 13.26 0.00 2.87
2846 5014 7.895975 TCAAAGGAATATAGCATCGATGAAG 57.104 36.000 29.20 2.92 0.00 3.02
2847 5015 8.316946 AGATCAAAGGAATATAGCATCGATGAA 58.683 33.333 29.20 15.83 0.00 2.57
2848 5016 7.845037 AGATCAAAGGAATATAGCATCGATGA 58.155 34.615 29.20 9.55 0.00 2.92
2849 5017 8.489990 AAGATCAAAGGAATATAGCATCGATG 57.510 34.615 21.27 21.27 0.00 3.84
2850 5018 9.512588 AAAAGATCAAAGGAATATAGCATCGAT 57.487 29.630 0.00 0.00 0.00 3.59
2851 5019 8.908786 AAAAGATCAAAGGAATATAGCATCGA 57.091 30.769 0.00 0.00 0.00 3.59
2920 5088 9.778741 AGACTCAATCAAGTGTTTTATGTAAGA 57.221 29.630 0.00 0.00 0.00 2.10
2922 5090 9.554395 TGAGACTCAATCAAGTGTTTTATGTAA 57.446 29.630 1.64 0.00 0.00 2.41
2923 5091 9.554395 TTGAGACTCAATCAAGTGTTTTATGTA 57.446 29.630 13.99 0.00 30.26 2.29
2924 5092 8.450578 TTGAGACTCAATCAAGTGTTTTATGT 57.549 30.769 13.99 0.00 30.26 2.29
2945 5113 3.129462 TGGCTAAGTCTCAGTCGATTGAG 59.871 47.826 27.00 27.00 44.74 3.02
2946 5114 3.089284 TGGCTAAGTCTCAGTCGATTGA 58.911 45.455 10.44 10.44 0.00 2.57
2947 5115 3.182967 GTGGCTAAGTCTCAGTCGATTG 58.817 50.000 0.68 0.68 0.00 2.67
2948 5116 2.826128 TGTGGCTAAGTCTCAGTCGATT 59.174 45.455 0.00 0.00 0.00 3.34
2949 5117 2.164624 GTGTGGCTAAGTCTCAGTCGAT 59.835 50.000 0.00 0.00 0.00 3.59
2950 5118 1.540267 GTGTGGCTAAGTCTCAGTCGA 59.460 52.381 0.00 0.00 0.00 4.20
2951 5119 1.402984 GGTGTGGCTAAGTCTCAGTCG 60.403 57.143 0.00 0.00 0.00 4.18
2952 5120 2.371910 GGTGTGGCTAAGTCTCAGTC 57.628 55.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.