Multiple sequence alignment - TraesCS6D01G147400

Loading Multiple Alignment...

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 TraesCS6D01G147400 chr6D 100.000 4171 0 0 1 4171 119994568 119998738 0.000000e+00 7703.0
1 TraesCS6D01G147400 chr6D 84.584 493 72 4 3682 4171 149895944 149896435 1.740000e-133 486.0
2 TraesCS6D01G147400 chr6A 92.261 2636 85 42 1 2560 148247574 148250166 0.000000e+00 3627.0
3 TraesCS6D01G147400 chr6A 94.667 1575 57 9 2606 4171 148250551 148252107 0.000000e+00 2418.0
4 TraesCS6D01G147400 chr6A 85.496 131 17 2 1018 1147 5358370 5358499 7.270000e-28 135.0
5 TraesCS6D01G147400 chr6B 91.569 2123 92 17 1639 3736 212969628 212967568 0.000000e+00 2848.0
6 TraesCS6D01G147400 chr6B 89.223 798 34 23 1 780 212971210 212970447 0.000000e+00 950.0
7 TraesCS6D01G147400 chr6B 87.265 691 44 22 806 1465 212970382 212969705 0.000000e+00 749.0
8 TraesCS6D01G147400 chr6B 93.750 448 27 1 3724 4171 212967267 212966821 0.000000e+00 671.0
9 TraesCS6D01G147400 chr3B 77.086 755 87 43 1299 1996 45154426 45155151 1.430000e-94 357.0
10 TraesCS6D01G147400 chr5A 77.812 320 34 11 1298 1593 680359689 680359995 3.340000e-36 163.0
11 TraesCS6D01G147400 chr5A 80.769 182 33 2 995 1175 587423246 587423066 1.560000e-29 141.0
12 TraesCS6D01G147400 chr5D 77.370 327 36 14 1298 1600 152770591 152770903 4.320000e-35 159.0
13 TraesCS6D01G147400 chr5D 81.868 182 31 2 995 1175 467184284 467184104 7.220000e-33 152.0
14 TraesCS6D01G147400 chr5B 81.868 182 31 2 995 1175 573815909 573815729 7.220000e-33 152.0
15 TraesCS6D01G147400 chr2B 81.183 186 31 4 995 1178 180059842 180059659 3.360000e-31 147.0
16 TraesCS6D01G147400 chr2D 80.645 186 32 4 995 1178 126149546 126149363 1.560000e-29 141.0
17 TraesCS6D01G147400 chr2D 79.874 159 27 4 3955 4111 403208378 403208223 1.230000e-20 111.0
18 TraesCS6D01G147400 chr2A 80.000 185 33 4 996 1178 132876429 132876247 2.620000e-27 134.0
19 TraesCS6D01G147400 chr7D 81.529 157 26 2 3942 4098 540430465 540430618 4.380000e-25 126.0
20 TraesCS6D01G147400 chr7D 87.156 109 14 0 3954 4062 536143453 536143345 1.570000e-24 124.0
21 TraesCS6D01G147400 chr7D 100.000 38 0 0 3639 3676 462295422 462295385 2.080000e-08 71.3
22 TraesCS6D01G147400 chr3D 84.800 125 19 0 3955 4079 100513443 100513319 4.380000e-25 126.0
23 TraesCS6D01G147400 chr3A 84.298 121 19 0 3954 4074 338690869 338690989 7.330000e-23 119.0
24 TraesCS6D01G147400 chr4A 83.200 125 21 0 3955 4079 635453350 635453226 9.480000e-22 115.0


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 TraesCS6D01G147400 chr6D 119994568 119998738 4170 False 7703.0 7703 100.00000 1 4171 1 chr6D.!!$F1 4170
1 TraesCS6D01G147400 chr6A 148247574 148252107 4533 False 3022.5 3627 93.46400 1 4171 2 chr6A.!!$F2 4170
2 TraesCS6D01G147400 chr6B 212966821 212971210 4389 True 1304.5 2848 90.45175 1 4171 4 chr6B.!!$R1 4170
3 TraesCS6D01G147400 chr3B 45154426 45155151 725 False 357.0 357 77.08600 1299 1996 1 chr3B.!!$F1 697

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
180 181 0.039527 GAAGGGTTTGCGCGTCATTT 60.040 50.000 8.43 0.0 36.42 2.32 F
502 527 0.460987 GGTAGCAGCAGCACCAGTAG 60.461 60.000 14.69 0.0 45.49 2.57 F
503 528 0.460987 GTAGCAGCAGCACCAGTAGG 60.461 60.000 3.17 0.0 45.49 3.18 F
606 631 0.695347 TGTGCATATCACCACCACCA 59.305 50.000 0.00 0.0 45.03 4.17 F
793 841 1.136891 GCATCCGGCCTTTTTAGCATT 59.863 47.619 0.00 0.0 36.11 3.56 F
2587 2803 0.322975 GGCATCTGCTATGGATCGGT 59.677 55.000 1.70 0.0 41.70 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1262 1353 0.242555 GAGCTGCTAGTAGATCCGGC 59.757 60.000 14.42 1.84 0.00 6.13 R
2468 2683 0.100325 TGCAACAAGCCAAGAACACG 59.900 50.000 0.00 0.00 44.83 4.49 R
2470 2685 0.102844 GCTGCAACAAGCCAAGAACA 59.897 50.000 0.00 0.00 44.83 3.18 R
2561 2776 1.068127 CCATAGCAGATGCCAAAAGGC 59.932 52.381 0.14 0.00 43.38 4.35 R
2598 2814 1.076332 GCTCACGTAGCGAACCATTT 58.924 50.000 0.00 0.00 42.53 2.32 R
4106 4991 0.254747 TGGCCTTTCTGGGATTACCG 59.745 55.000 3.32 0.00 44.64 4.02 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
26 27 5.848406 TCGACTAACCCAAATTGCAAATTT 58.152 33.333 1.71 2.09 0.00 1.82
29 30 7.040340 TCGACTAACCCAAATTGCAAATTTAGA 60.040 33.333 1.71 0.00 0.00 2.10
35 36 5.925969 CCCAAATTGCAAATTTAGACGACTT 59.074 36.000 1.71 0.00 0.00 3.01
36 37 7.087639 CCCAAATTGCAAATTTAGACGACTTA 58.912 34.615 1.71 0.00 0.00 2.24
37 38 7.061789 CCCAAATTGCAAATTTAGACGACTTAC 59.938 37.037 1.71 0.00 0.00 2.34
38 39 7.593273 CCAAATTGCAAATTTAGACGACTTACA 59.407 33.333 1.71 0.00 0.00 2.41
39 40 9.128107 CAAATTGCAAATTTAGACGACTTACAT 57.872 29.630 1.71 0.00 0.00 2.29
68 69 8.602424 AGTACATATAGCTATTGTGGGCAAATA 58.398 33.333 21.70 6.31 38.21 1.40
71 72 9.396022 ACATATAGCTATTGTGGGCAAATATAC 57.604 33.333 12.39 0.00 38.21 1.47
72 73 6.985188 ATAGCTATTGTGGGCAAATATACG 57.015 37.500 0.00 0.00 38.21 3.06
73 74 4.714632 AGCTATTGTGGGCAAATATACGT 58.285 39.130 0.00 0.00 38.21 3.57
116 117 3.282021 AGTCAATTAATCATGCAGGCGT 58.718 40.909 0.00 0.00 0.00 5.68
123 124 0.673333 ATCATGCAGGCGTCGACAAA 60.673 50.000 17.16 0.00 0.00 2.83
180 181 0.039527 GAAGGGTTTGCGCGTCATTT 60.040 50.000 8.43 0.00 36.42 2.32
185 186 2.159435 GGGTTTGCGCGTCATTTCTATT 60.159 45.455 8.43 0.00 0.00 1.73
446 465 4.201122 GGGCAGCTGGCTAGGCAT 62.201 66.667 35.64 2.51 44.01 4.40
501 526 1.596934 GGTAGCAGCAGCACCAGTA 59.403 57.895 14.69 0.00 45.49 2.74
502 527 0.460987 GGTAGCAGCAGCACCAGTAG 60.461 60.000 14.69 0.00 45.49 2.57
503 528 0.460987 GTAGCAGCAGCACCAGTAGG 60.461 60.000 3.17 0.00 45.49 3.18
606 631 0.695347 TGTGCATATCACCACCACCA 59.305 50.000 0.00 0.00 45.03 4.17
660 686 1.203523 CCTCCTGTCTCTCCGTTCTTG 59.796 57.143 0.00 0.00 0.00 3.02
694 722 2.702270 AAGAATGCCCCTTGTTCCTT 57.298 45.000 0.00 0.00 0.00 3.36
726 754 6.715347 AGTGAAAAATTCCACTTTAGCTGT 57.285 33.333 0.00 0.00 40.40 4.40
757 785 3.583086 CCTCCTAGTTCTTTGGTTCCTCA 59.417 47.826 0.00 0.00 0.00 3.86
758 786 4.041691 CCTCCTAGTTCTTTGGTTCCTCAA 59.958 45.833 0.00 0.00 0.00 3.02
793 841 1.136891 GCATCCGGCCTTTTTAGCATT 59.863 47.619 0.00 0.00 36.11 3.56
818 887 5.652744 TTTCTTTCTTCTACTTGTGCGAC 57.347 39.130 0.00 0.00 0.00 5.19
928 1000 1.391157 GCAGCAGACGGGAGAGAGAT 61.391 60.000 0.00 0.00 0.00 2.75
1262 1353 6.448006 TCTTTCTTTCGACTACTTTGGAGAG 58.552 40.000 0.00 0.00 0.00 3.20
1400 1509 5.751028 TGTCGAATATGCATGTCATCGTAAA 59.249 36.000 10.16 0.00 36.63 2.01
1519 1655 7.219484 TCATTATTCAGACAGATCGATGCTA 57.781 36.000 0.54 0.00 0.00 3.49
1531 1670 9.722056 GACAGATCGATGCTAAATTTTTGTTAT 57.278 29.630 0.54 0.00 0.00 1.89
1584 1729 7.698130 GCTGCTTATATTAATTAATTCAGCGGG 59.302 37.037 26.66 20.82 34.77 6.13
1768 1938 4.698780 ACCTGTTCAGTCATTCACATGATG 59.301 41.667 0.00 0.00 41.64 3.07
1913 2128 2.095059 GCCATCACCAGCAAACTAGTTG 60.095 50.000 9.34 4.88 40.50 3.16
1964 2179 6.894339 TCAACTATCCGATGATGTAGCTTA 57.106 37.500 0.00 0.00 32.18 3.09
2041 2256 3.811083 ACCACGATCAGGTAAACACAAA 58.189 40.909 5.08 0.00 37.67 2.83
2066 2281 7.430441 ACACACACCAAAAATCACTTATTACC 58.570 34.615 0.00 0.00 0.00 2.85
2127 2342 1.376424 CTGACTGCGCACTGGGAAT 60.376 57.895 5.66 0.00 0.00 3.01
2130 2345 1.271108 TGACTGCGCACTGGGAATTTA 60.271 47.619 5.66 0.00 0.00 1.40
2137 2352 4.573201 TGCGCACTGGGAATTTAATACTAC 59.427 41.667 5.66 0.00 0.00 2.73
2141 2356 6.495706 GCACTGGGAATTTAATACTACTTGC 58.504 40.000 0.00 0.00 0.00 4.01
2271 2486 3.064987 CTCCCTCGCCGACGTCAAT 62.065 63.158 17.16 0.00 41.18 2.57
2394 2609 2.005451 GCAGCACATGAACTACTCCTG 58.995 52.381 0.00 0.00 0.00 3.86
2426 2641 9.148104 GAACTAGTTCCATCGTTAATTTACTGT 57.852 33.333 22.74 0.00 33.64 3.55
2431 2646 9.798994 AGTTCCATCGTTAATTTACTGTACTAG 57.201 33.333 0.00 0.00 0.00 2.57
2438 2653 9.243105 TCGTTAATTTACTGTACTAGTTACCCT 57.757 33.333 0.00 0.00 40.89 4.34
2467 2682 3.006003 TCATGTCTTGTGTTACTGCCGTA 59.994 43.478 0.00 0.00 0.00 4.02
2468 2683 2.746269 TGTCTTGTGTTACTGCCGTAC 58.254 47.619 0.00 0.00 0.00 3.67
2469 2684 1.717645 GTCTTGTGTTACTGCCGTACG 59.282 52.381 8.69 8.69 0.00 3.67
2470 2685 1.337703 TCTTGTGTTACTGCCGTACGT 59.662 47.619 15.21 0.00 0.00 3.57
2562 2777 7.225523 ACGAATTATCAATTGCTCATTTTGC 57.774 32.000 0.00 0.00 0.00 3.68
2563 2778 6.256321 ACGAATTATCAATTGCTCATTTTGCC 59.744 34.615 0.00 0.00 0.00 4.52
2564 2779 6.477688 CGAATTATCAATTGCTCATTTTGCCT 59.522 34.615 0.00 0.00 0.00 4.75
2585 2801 2.174363 TTGGCATCTGCTATGGATCG 57.826 50.000 1.70 0.00 41.70 3.69
2587 2803 0.322975 GGCATCTGCTATGGATCGGT 59.677 55.000 1.70 0.00 41.70 4.69
2591 2807 3.554960 GCATCTGCTATGGATCGGTTGTA 60.555 47.826 0.00 0.00 38.21 2.41
2598 2814 3.904800 ATGGATCGGTTGTATGTGTGA 57.095 42.857 0.00 0.00 0.00 3.58
2599 2815 3.686916 TGGATCGGTTGTATGTGTGAA 57.313 42.857 0.00 0.00 0.00 3.18
2601 2817 4.584874 TGGATCGGTTGTATGTGTGAAAT 58.415 39.130 0.00 0.00 0.00 2.17
2602 2818 4.394610 TGGATCGGTTGTATGTGTGAAATG 59.605 41.667 0.00 0.00 0.00 2.32
2605 2821 4.138290 TCGGTTGTATGTGTGAAATGGTT 58.862 39.130 0.00 0.00 0.00 3.67
2611 3174 4.390603 TGTATGTGTGAAATGGTTCGCTAC 59.609 41.667 2.12 0.51 43.43 3.58
2868 3433 1.079543 GGTGCTGTCGATGCTGACT 60.080 57.895 13.16 0.00 39.64 3.41
2871 3436 1.216444 GCTGTCGATGCTGACTCCA 59.784 57.895 6.18 0.00 39.64 3.86
3065 3630 5.429130 CCTCCACCTCTGGTAACTAAAATC 58.571 45.833 0.00 0.00 38.90 2.17
3084 3649 2.433436 TCAAGAATCAGTCGACCGAGA 58.567 47.619 13.01 8.70 0.00 4.04
3110 3675 1.985447 GCATGCACCCACATCTGTCG 61.985 60.000 14.21 0.00 0.00 4.35
3370 3938 2.061773 CGTGTGTCTTAGGCTGTTCTG 58.938 52.381 0.00 0.00 0.00 3.02
3440 4010 6.875926 AATGTTGGTACGTACGTAGAAATC 57.124 37.500 27.48 15.29 0.00 2.17
3563 4134 2.335681 ACCCCATTTAAAACCCCCAG 57.664 50.000 0.00 0.00 0.00 4.45
3621 4192 5.221661 ACAATTTCCCTCGACTTTGACTAGT 60.222 40.000 0.00 0.00 0.00 2.57
3628 4199 3.159472 TCGACTTTGACTAGTTAGGCCA 58.841 45.455 5.01 0.00 0.00 5.36
3629 4200 3.057033 TCGACTTTGACTAGTTAGGCCAC 60.057 47.826 5.01 0.00 0.00 5.01
3631 4202 4.496360 GACTTTGACTAGTTAGGCCACTC 58.504 47.826 5.01 0.00 0.00 3.51
3676 4249 9.284968 AGGCATACGCTTGACTTTATAAATAAT 57.715 29.630 0.00 0.00 38.60 1.28
3677 4250 9.893305 GGCATACGCTTGACTTTATAAATAATT 57.107 29.630 0.00 0.00 38.60 1.40
3790 4675 2.957680 ACAACATCACAGCCAAACATCA 59.042 40.909 0.00 0.00 0.00 3.07
3793 4678 2.957680 ACATCACAGCCAAACATCAACA 59.042 40.909 0.00 0.00 0.00 3.33
3812 4697 2.180159 AACACGCAGGCCGGATAAGT 62.180 55.000 5.05 0.00 42.52 2.24
3974 4859 5.277857 ACCTTAGTCAATAATCTCCACCG 57.722 43.478 0.00 0.00 0.00 4.94
3986 4871 0.957395 CTCCACCGCTGCAGAAACAT 60.957 55.000 20.43 0.00 0.00 2.71
4057 4942 6.833041 TCAATGGTAAACTTGTTCCTAGTCA 58.167 36.000 0.00 0.00 0.00 3.41
4079 4964 3.884895 TCCATAATGACCAGCAAATCGT 58.115 40.909 0.00 0.00 0.00 3.73
4102 4987 3.187022 GGCAAAACCAATTCAGAACATGC 59.813 43.478 0.00 0.00 38.86 4.06
4147 5032 0.250901 TGCCAAGGTTCTGAGCTTCC 60.251 55.000 0.00 0.00 41.44 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 5.694458 GTCGTCTAAATTTGCAATTTGGGTT 59.306 36.000 0.00 0.00 0.00 4.11
18 19 9.811995 ACTATATGTAAGTCGTCTAAATTTGCA 57.188 29.630 0.00 0.00 0.00 4.08
37 38 9.698309 GCCCACAATAGCTATATGTACTATATG 57.302 37.037 6.68 0.00 0.00 1.78
38 39 9.434275 TGCCCACAATAGCTATATGTACTATAT 57.566 33.333 6.68 0.00 0.00 0.86
39 40 8.832458 TGCCCACAATAGCTATATGTACTATA 57.168 34.615 6.68 0.00 0.00 1.31
40 41 7.733773 TGCCCACAATAGCTATATGTACTAT 57.266 36.000 6.68 0.00 0.00 2.12
41 42 7.547697 TTGCCCACAATAGCTATATGTACTA 57.452 36.000 6.68 2.65 0.00 1.82
42 43 6.433847 TTGCCCACAATAGCTATATGTACT 57.566 37.500 6.68 0.00 0.00 2.73
43 44 7.687941 ATTTGCCCACAATAGCTATATGTAC 57.312 36.000 6.68 7.49 35.21 2.90
68 69 6.701841 CCATGCATAAAGTTAGACTGACGTAT 59.298 38.462 0.00 0.00 0.00 3.06
71 72 4.870426 ACCATGCATAAAGTTAGACTGACG 59.130 41.667 0.00 0.00 0.00 4.35
72 73 7.042335 ACTACCATGCATAAAGTTAGACTGAC 58.958 38.462 0.00 0.00 0.00 3.51
73 74 7.093509 TGACTACCATGCATAAAGTTAGACTGA 60.094 37.037 0.00 0.00 0.00 3.41
138 139 5.905331 TCTCTCCCCTTCATAATTGCTTCTA 59.095 40.000 0.00 0.00 0.00 2.10
154 155 1.377333 CGCAAACCCTTCTCTCCCC 60.377 63.158 0.00 0.00 0.00 4.81
185 186 9.913310 CACATATGGAAGAGGTCTCTATATAGA 57.087 37.037 11.94 11.94 39.39 1.98
296 298 1.008995 GTTTCTTTCTTGCGCGGCA 60.009 52.632 8.83 3.20 36.47 5.69
393 404 4.320608 AAATAATGGTAAATGCCTGGCG 57.679 40.909 14.98 0.00 0.00 5.69
443 462 0.179702 TCTCCTCACATCCTGCATGC 59.820 55.000 11.82 11.82 35.65 4.06
444 463 2.768698 GATCTCCTCACATCCTGCATG 58.231 52.381 0.00 0.00 38.64 4.06
445 464 1.343789 CGATCTCCTCACATCCTGCAT 59.656 52.381 0.00 0.00 0.00 3.96
446 465 0.749049 CGATCTCCTCACATCCTGCA 59.251 55.000 0.00 0.00 0.00 4.41
495 520 2.379226 AGTGAGGTAGTGTCCTACTGGT 59.621 50.000 0.00 0.00 42.71 4.00
501 526 1.997040 AGGAGAGTGAGGTAGTGTCCT 59.003 52.381 0.00 0.00 45.24 3.85
502 527 2.517998 AGGAGAGTGAGGTAGTGTCC 57.482 55.000 0.00 0.00 41.42 4.02
503 528 3.692690 AGAAGGAGAGTGAGGTAGTGTC 58.307 50.000 0.00 0.00 0.00 3.67
694 722 8.729805 AAGTGGAATTTTTCACTAAATTTGCA 57.270 26.923 4.69 0.00 42.67 4.08
726 754 1.133450 AGAACTAGGAGGCGGATGCTA 60.133 52.381 0.00 0.00 42.25 3.49
757 785 4.440525 CCGGATGCAGCACTCATAATTTTT 60.441 41.667 3.51 0.00 0.00 1.94
758 786 3.067180 CCGGATGCAGCACTCATAATTTT 59.933 43.478 3.51 0.00 0.00 1.82
793 841 7.656137 AGTCGCACAAGTAGAAGAAAGAAAATA 59.344 33.333 0.00 0.00 0.00 1.40
808 877 1.396996 GAACAACACAGTCGCACAAGT 59.603 47.619 0.00 0.00 0.00 3.16
818 887 3.588955 TGGATCTGATCGAACAACACAG 58.411 45.455 11.28 0.00 0.00 3.66
881 950 2.344025 AGAACAACGAGGGTTAATCGC 58.656 47.619 0.00 0.00 43.91 4.58
965 1037 1.267038 CGATCGATGCAAACAGGAACG 60.267 52.381 10.26 0.00 0.00 3.95
1262 1353 0.242555 GAGCTGCTAGTAGATCCGGC 59.757 60.000 14.42 1.84 0.00 6.13
1400 1509 0.773644 ACAGACCAGCAAATCCAGGT 59.226 50.000 0.00 0.00 37.00 4.00
1519 1655 7.380065 ACGCGTACATGTTGATAACAAAAATTT 59.620 29.630 11.67 0.00 45.86 1.82
1584 1729 8.241367 TGATCATATAAATGTCTTCATGCATGC 58.759 33.333 22.25 11.82 34.19 4.06
1614 1775 6.882140 TCATGGATTCACTACAAAACCGTAAT 59.118 34.615 0.00 0.00 0.00 1.89
1964 2179 3.135530 GGTACTGCTCAATGAGATCCCTT 59.864 47.826 15.38 0.00 0.00 3.95
2041 2256 7.068839 TGGTAATAAGTGATTTTTGGTGTGTGT 59.931 33.333 0.00 0.00 0.00 3.72
2066 2281 7.312154 TGCAGGCAAATTAATTACTAACAGTG 58.688 34.615 0.01 0.00 0.00 3.66
2102 2317 1.070577 CAGTGCGCAGTCAGTTTGTAC 60.071 52.381 16.49 0.00 0.00 2.90
2127 2342 9.002600 CATCCATGCATAGCAAGTAGTATTAAA 57.997 33.333 0.00 0.00 43.62 1.52
2130 2345 5.942236 CCATCCATGCATAGCAAGTAGTATT 59.058 40.000 0.00 0.00 43.62 1.89
2137 2352 3.850122 CATCCATCCATGCATAGCAAG 57.150 47.619 0.00 0.00 43.62 4.01
2349 2564 8.068380 GCAAGTAAGTAAAAGTAACCAGTTCAG 58.932 37.037 0.00 0.00 0.00 3.02
2416 2631 8.599624 AGCAGGGTAACTAGTACAGTAAATTA 57.400 34.615 0.00 0.00 36.04 1.40
2417 2632 7.492077 AGCAGGGTAACTAGTACAGTAAATT 57.508 36.000 0.00 0.00 36.04 1.82
2426 2641 7.563924 AGACATGAATTAGCAGGGTAACTAGTA 59.436 37.037 0.00 0.00 0.00 1.82
2431 2646 5.648092 ACAAGACATGAATTAGCAGGGTAAC 59.352 40.000 0.00 0.00 0.00 2.50
2438 2653 6.348458 GCAGTAACACAAGACATGAATTAGCA 60.348 38.462 0.00 0.00 0.00 3.49
2467 2682 0.100503 GCAACAAGCCAAGAACACGT 59.899 50.000 0.00 0.00 37.23 4.49
2468 2683 0.100325 TGCAACAAGCCAAGAACACG 59.900 50.000 0.00 0.00 44.83 4.49
2469 2684 1.843992 CTGCAACAAGCCAAGAACAC 58.156 50.000 0.00 0.00 44.83 3.32
2470 2685 0.102844 GCTGCAACAAGCCAAGAACA 59.897 50.000 0.00 0.00 44.83 3.18
2561 2776 1.068127 CCATAGCAGATGCCAAAAGGC 59.932 52.381 0.14 0.00 43.38 4.35
2562 2777 2.658285 TCCATAGCAGATGCCAAAAGG 58.342 47.619 0.14 0.00 43.38 3.11
2563 2778 3.058432 CGATCCATAGCAGATGCCAAAAG 60.058 47.826 0.14 0.00 43.38 2.27
2564 2779 2.880268 CGATCCATAGCAGATGCCAAAA 59.120 45.455 0.14 0.00 43.38 2.44
2580 2796 4.201910 CCATTTCACACATACAACCGATCC 60.202 45.833 0.00 0.00 0.00 3.36
2585 2801 4.472286 CGAACCATTTCACACATACAACC 58.528 43.478 0.00 0.00 0.00 3.77
2587 2803 3.818210 AGCGAACCATTTCACACATACAA 59.182 39.130 0.00 0.00 0.00 2.41
2591 2807 2.415168 CGTAGCGAACCATTTCACACAT 59.585 45.455 0.00 0.00 0.00 3.21
2598 2814 1.076332 GCTCACGTAGCGAACCATTT 58.924 50.000 0.00 0.00 42.53 2.32
2599 2815 2.750815 GCTCACGTAGCGAACCATT 58.249 52.632 0.00 0.00 42.53 3.16
2611 3174 8.567796 TGATCAATCAATTAGCAACGCTCACG 62.568 42.308 0.00 0.00 38.53 4.35
2823 3388 4.143333 ACCGCCATCTTCCCGTCG 62.143 66.667 0.00 0.00 0.00 5.12
2895 3460 1.742880 CGACGACTCCTCACCCGTA 60.743 63.158 0.00 0.00 35.22 4.02
2901 3466 2.333417 GGTGCTCGACGACTCCTCA 61.333 63.158 0.00 0.00 0.00 3.86
3065 3630 2.917971 GTTCTCGGTCGACTGATTCTTG 59.082 50.000 26.62 14.95 0.00 3.02
3084 3649 1.114119 TGTGGGTGCATGCATGTGTT 61.114 50.000 25.64 0.00 0.00 3.32
3110 3675 2.890808 TATCTGGCCGTGACTGAATC 57.109 50.000 0.00 0.00 0.00 2.52
3370 3938 4.330074 AGCTTAAGTACGCAACATGATGAC 59.670 41.667 7.22 0.00 0.00 3.06
3440 4010 2.252747 CCATGCGTGCACAACTATTTG 58.747 47.619 18.64 4.02 38.83 2.32
3540 4111 4.574005 TGGGGGTTTTAAATGGGGTAAAA 58.426 39.130 0.00 0.00 0.00 1.52
3563 4134 2.028748 AGCTTGACCCAATGCAACAATC 60.029 45.455 0.00 0.00 0.00 2.67
3621 4192 2.851263 AAACATGACGAGTGGCCTAA 57.149 45.000 3.32 0.00 0.00 2.69
3628 4199 5.701290 CCTTTCCTCTAAAAACATGACGAGT 59.299 40.000 0.00 0.00 0.00 4.18
3629 4200 5.390991 GCCTTTCCTCTAAAAACATGACGAG 60.391 44.000 0.00 0.00 0.00 4.18
3631 4202 4.215399 TGCCTTTCCTCTAAAAACATGACG 59.785 41.667 0.00 0.00 0.00 4.35
3676 4249 8.107095 ACTCTGTCAGGTGGCTTTATTTATAAA 58.893 33.333 0.00 0.00 0.00 1.40
3677 4250 7.630082 ACTCTGTCAGGTGGCTTTATTTATAA 58.370 34.615 0.00 0.00 0.00 0.98
3678 4251 7.195374 ACTCTGTCAGGTGGCTTTATTTATA 57.805 36.000 0.00 0.00 0.00 0.98
3679 4252 6.067217 ACTCTGTCAGGTGGCTTTATTTAT 57.933 37.500 0.00 0.00 0.00 1.40
3680 4253 5.499004 ACTCTGTCAGGTGGCTTTATTTA 57.501 39.130 0.00 0.00 0.00 1.40
3681 4254 4.373156 ACTCTGTCAGGTGGCTTTATTT 57.627 40.909 0.00 0.00 0.00 1.40
3682 4255 4.286032 TGTACTCTGTCAGGTGGCTTTATT 59.714 41.667 0.00 0.00 0.00 1.40
3683 4256 3.838317 TGTACTCTGTCAGGTGGCTTTAT 59.162 43.478 0.00 0.00 0.00 1.40
3684 4257 3.236047 TGTACTCTGTCAGGTGGCTTTA 58.764 45.455 0.00 0.00 0.00 1.85
3685 4258 2.047061 TGTACTCTGTCAGGTGGCTTT 58.953 47.619 0.00 0.00 0.00 3.51
3686 4259 1.717032 TGTACTCTGTCAGGTGGCTT 58.283 50.000 0.00 0.00 0.00 4.35
3694 4267 3.319689 TGTGGTTTCGATGTACTCTGTCA 59.680 43.478 0.00 0.00 0.00 3.58
3696 4269 3.069016 TGTGTGGTTTCGATGTACTCTGT 59.931 43.478 0.00 0.00 0.00 3.41
3790 4675 2.457743 TATCCGGCCTGCGTGTTGTT 62.458 55.000 0.00 0.00 0.00 2.83
3793 4678 1.449601 CTTATCCGGCCTGCGTGTT 60.450 57.895 0.00 0.00 0.00 3.32
3812 4697 1.278985 CCTAGGTGGTGCTTCATGTCA 59.721 52.381 0.00 0.00 0.00 3.58
3974 4859 3.565905 AAGCTTGTATGTTTCTGCAGC 57.434 42.857 9.47 0.00 0.00 5.25
4007 4892 4.844349 ATCTTCCTTGCTAAGCCTGTTA 57.156 40.909 0.00 0.00 0.00 2.41
4021 4906 6.904626 AGTTTACCATTGAGCATATCTTCCT 58.095 36.000 0.00 0.00 0.00 3.36
4057 4942 4.276678 CACGATTTGCTGGTCATTATGGAT 59.723 41.667 0.00 0.00 0.00 3.41
4102 4987 2.277084 CCTTTCTGGGATTACCGAACG 58.723 52.381 0.00 0.00 44.64 3.95
4106 4991 0.254747 TGGCCTTTCTGGGATTACCG 59.745 55.000 3.32 0.00 44.64 4.02
4147 5032 2.352805 GCACCCCACCTCCTTCTG 59.647 66.667 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.