Multiple sequence alignment - TraesCS3D01G334200

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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 TraesCS3D01G334200 chr3D 100.000 3006 0 0 1 3006 446076642 446073637 0.000000e+00 5552.0
1 TraesCS3D01G334200 chr3D 85.597 1097 93 32 834 1891 446191979 446190909 0.000000e+00 1090.0
2 TraesCS3D01G334200 chr3D 86.804 970 83 23 946 1891 446110205 446109257 0.000000e+00 1040.0
3 TraesCS3D01G334200 chr3D 97.101 69 1 1 848 916 446110273 446110206 6.810000e-22 115.0
4 TraesCS3D01G334200 chr3B 93.268 2154 96 21 809 2930 584985467 584983331 0.000000e+00 3129.0
5 TraesCS3D01G334200 chr3B 85.819 1093 93 30 834 1891 585139274 585138209 0.000000e+00 1103.0
6 TraesCS3D01G334200 chr3B 86.512 860 78 23 1047 1891 585023477 585022641 0.000000e+00 911.0
7 TraesCS3D01G334200 chr3B 81.399 715 57 35 7 695 584986134 584985470 5.750000e-142 514.0
8 TraesCS3D01G334200 chr3B 91.667 120 9 1 690 808 755450202 755450321 6.670000e-37 165.0
9 TraesCS3D01G334200 chr3B 92.308 39 3 0 536 574 756687807 756687845 4.190000e-04 56.5
10 TraesCS3D01G334200 chr3A 88.877 1906 113 39 804 2646 587884997 587883128 0.000000e+00 2254.0
11 TraesCS3D01G334200 chr3A 87.500 1112 99 23 804 1891 587906558 587905463 0.000000e+00 1247.0
12 TraesCS3D01G334200 chr3A 85.128 1096 97 34 834 1892 587966701 587965635 0.000000e+00 1061.0
13 TraesCS3D01G334200 chr3A 91.940 335 22 3 2670 3002 587883140 587882809 5.870000e-127 464.0
14 TraesCS3D01G334200 chr3A 81.585 429 55 16 1 415 587887975 587887557 1.730000e-87 333.0
15 TraesCS3D01G334200 chr3A 92.063 63 5 0 12 74 747604383 747604445 4.130000e-14 89.8
16 TraesCS3D01G334200 chr3A 91.228 57 1 1 612 668 587907170 587907118 1.160000e-09 75.0
17 TraesCS3D01G334200 chr1A 79.603 554 82 19 1184 1711 497192698 497192150 4.730000e-98 368.0
18 TraesCS3D01G334200 chr5A 90.000 130 11 2 684 812 706438903 706439031 1.850000e-37 167.0
19 TraesCS3D01G334200 chr5A 91.057 123 9 2 688 809 27593 27472 6.670000e-37 165.0
20 TraesCS3D01G334200 chr5A 91.057 123 10 1 686 807 421862235 421862357 6.670000e-37 165.0
21 TraesCS3D01G334200 chr2B 91.597 119 9 1 690 807 549196926 549197044 2.400000e-36 163.0
22 TraesCS3D01G334200 chr2B 94.872 39 2 0 536 574 66471993 66471955 9.000000e-06 62.1
23 TraesCS3D01G334200 chr1B 90.984 122 10 1 690 810 137651680 137651559 2.400000e-36 163.0
24 TraesCS3D01G334200 chr1B 92.308 39 3 0 536 574 22740821 22740859 4.190000e-04 56.5
25 TraesCS3D01G334200 chr2D 87.143 140 16 2 678 815 648554220 648554081 1.120000e-34 158.0
26 TraesCS3D01G334200 chr2D 94.872 39 2 0 536 574 578878870 578878832 9.000000e-06 62.1
27 TraesCS3D01G334200 chr2D 94.872 39 2 0 536 574 618903427 618903389 9.000000e-06 62.1
28 TraesCS3D01G334200 chr2A 86.111 144 17 3 677 818 546942105 546942247 5.190000e-33 152.0
29 TraesCS3D01G334200 chr2A 86.111 144 17 3 677 818 547133206 547133348 5.190000e-33 152.0
30 TraesCS3D01G334200 chr5D 94.872 39 2 0 536 574 443263856 443263894 9.000000e-06 62.1
31 TraesCS3D01G334200 chr4D 97.143 35 1 0 536 570 84422718 84422684 3.240000e-05 60.2
32 TraesCS3D01G334200 chr4D 94.444 36 2 0 539 574 133626293 133626258 4.190000e-04 56.5
33 TraesCS3D01G334200 chr7A 96.774 31 1 0 540 570 27890351 27890381 5.000000e-03 52.8


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 TraesCS3D01G334200 chr3D 446073637 446076642 3005 True 5552.0 5552 100.000000 1 3006 1 chr3D.!!$R1 3005
1 TraesCS3D01G334200 chr3D 446190909 446191979 1070 True 1090.0 1090 85.597000 834 1891 1 chr3D.!!$R2 1057
2 TraesCS3D01G334200 chr3D 446109257 446110273 1016 True 577.5 1040 91.952500 848 1891 2 chr3D.!!$R3 1043
3 TraesCS3D01G334200 chr3B 584983331 584986134 2803 True 1821.5 3129 87.333500 7 2930 2 chr3B.!!$R3 2923
4 TraesCS3D01G334200 chr3B 585138209 585139274 1065 True 1103.0 1103 85.819000 834 1891 1 chr3B.!!$R2 1057
5 TraesCS3D01G334200 chr3B 585022641 585023477 836 True 911.0 911 86.512000 1047 1891 1 chr3B.!!$R1 844
6 TraesCS3D01G334200 chr3A 587965635 587966701 1066 True 1061.0 1061 85.128000 834 1892 1 chr3A.!!$R1 1058
7 TraesCS3D01G334200 chr3A 587882809 587887975 5166 True 1017.0 2254 87.467333 1 3002 3 chr3A.!!$R2 3001
8 TraesCS3D01G334200 chr3A 587905463 587907170 1707 True 661.0 1247 89.364000 612 1891 2 chr3A.!!$R3 1279
9 TraesCS3D01G334200 chr1A 497192150 497192698 548 True 368.0 368 79.603000 1184 1711 1 chr1A.!!$R1 527

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
474 2867 1.002201 TCGCCCTCCGTTGATTTGTTA 59.998 47.619 0.0 0.0 38.35 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 5090 0.584876 AAACTCGCAAGCCACGTAAC 59.415 50.0 0.0 0.0 37.18 2.5 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
111 113 6.263842 TGACATTCTGAGCAACTTTGAAAGAT 59.736 34.615 12.53 0.00 0.00 2.40
175 188 6.347696 TGTGGATCTTTGTGAGCAAAATTTT 58.652 32.000 0.00 0.00 43.17 1.82
185 200 9.683069 TTTGTGAGCAAAATTTTAAAAAGCAAA 57.317 22.222 4.44 8.38 41.15 3.68
186 201 8.666580 TGTGAGCAAAATTTTAAAAAGCAAAC 57.333 26.923 4.44 9.37 0.00 2.93
187 202 8.292448 TGTGAGCAAAATTTTAAAAAGCAAACA 58.708 25.926 4.44 11.32 0.00 2.83
188 203 8.574627 GTGAGCAAAATTTTAAAAAGCAAACAC 58.425 29.630 4.44 12.82 0.00 3.32
189 204 8.510505 TGAGCAAAATTTTAAAAAGCAAACACT 58.489 25.926 4.44 0.00 0.00 3.55
190 205 9.340695 GAGCAAAATTTTAAAAAGCAAACACTT 57.659 25.926 4.44 0.00 0.00 3.16
191 206 9.689976 AGCAAAATTTTAAAAAGCAAACACTTT 57.310 22.222 4.44 0.00 41.60 2.66
356 374 4.378874 GGCTTCCGTGAATTGAAGAAGAAG 60.379 45.833 9.28 2.58 40.30 2.85
384 404 6.749139 AGAAAGAAAGGAACTAAATTGGCAC 58.251 36.000 0.00 0.00 38.49 5.01
385 405 6.551227 AGAAAGAAAGGAACTAAATTGGCACT 59.449 34.615 0.00 0.00 38.49 4.40
386 406 7.724061 AGAAAGAAAGGAACTAAATTGGCACTA 59.276 33.333 0.00 0.00 38.49 2.74
403 423 5.661312 TGGCACTAGTGTTAAGATGTCCTAT 59.339 40.000 23.44 0.00 0.00 2.57
445 2838 9.145865 CTCTCTAAACAAAGAGGTCATAAGTTC 57.854 37.037 1.32 0.00 42.78 3.01
446 2839 8.647796 TCTCTAAACAAAGAGGTCATAAGTTCA 58.352 33.333 1.32 0.00 42.78 3.18
455 2848 5.869888 AGAGGTCATAAGTTCAATTCACGTC 59.130 40.000 0.00 0.00 0.00 4.34
457 2850 4.323751 GTCATAAGTTCAATTCACGTCGC 58.676 43.478 0.00 0.00 0.00 5.19
469 2862 2.125673 CGTCGCCCTCCGTTGATT 60.126 61.111 0.00 0.00 38.35 2.57
474 2867 1.002201 TCGCCCTCCGTTGATTTGTTA 59.998 47.619 0.00 0.00 38.35 2.41
476 2869 2.159572 CGCCCTCCGTTGATTTGTTAAG 60.160 50.000 0.00 0.00 0.00 1.85
491 2886 5.750352 TTGTTAAGGAGGATTACCGAAGT 57.250 39.130 0.00 0.00 41.83 3.01
493 2888 6.855763 TGTTAAGGAGGATTACCGAAGTAA 57.144 37.500 0.00 0.00 42.54 2.24
500 2895 8.087303 AGGAGGATTACCGAAGTAAAAGTTAT 57.913 34.615 0.00 0.00 41.68 1.89
509 2904 8.095937 ACCGAAGTAAAAGTTATCTTTCTTGG 57.904 34.615 0.00 6.83 42.26 3.61
510 2905 7.174426 ACCGAAGTAAAAGTTATCTTTCTTGGG 59.826 37.037 17.83 17.83 42.26 4.12
511 2906 7.389607 CCGAAGTAAAAGTTATCTTTCTTGGGA 59.610 37.037 16.06 0.00 40.92 4.37
512 2907 8.780249 CGAAGTAAAAGTTATCTTTCTTGGGAA 58.220 33.333 0.00 0.00 42.26 3.97
517 2912 6.455690 AAGTTATCTTTCTTGGGAAGAGGT 57.544 37.500 0.00 0.00 39.03 3.85
518 2913 6.455690 AGTTATCTTTCTTGGGAAGAGGTT 57.544 37.500 0.00 0.00 39.03 3.50
519 2914 6.241645 AGTTATCTTTCTTGGGAAGAGGTTG 58.758 40.000 0.00 0.00 39.03 3.77
520 2915 6.044404 AGTTATCTTTCTTGGGAAGAGGTTGA 59.956 38.462 0.00 0.00 39.03 3.18
521 2916 5.527026 ATCTTTCTTGGGAAGAGGTTGAT 57.473 39.130 0.00 0.00 39.03 2.57
522 2917 5.324832 TCTTTCTTGGGAAGAGGTTGATT 57.675 39.130 0.00 0.00 39.03 2.57
523 2918 5.705400 TCTTTCTTGGGAAGAGGTTGATTT 58.295 37.500 0.00 0.00 39.03 2.17
524 2919 5.770162 TCTTTCTTGGGAAGAGGTTGATTTC 59.230 40.000 0.00 0.00 39.03 2.17
525 2920 4.722526 TCTTGGGAAGAGGTTGATTTCA 57.277 40.909 0.00 0.00 32.71 2.69
526 2921 5.261040 TCTTGGGAAGAGGTTGATTTCAT 57.739 39.130 0.00 0.00 32.71 2.57
529 2924 5.726980 TGGGAAGAGGTTGATTTCATTTG 57.273 39.130 0.00 0.00 0.00 2.32
530 2925 5.392995 TGGGAAGAGGTTGATTTCATTTGA 58.607 37.500 0.00 0.00 0.00 2.69
531 2926 5.837979 TGGGAAGAGGTTGATTTCATTTGAA 59.162 36.000 0.00 0.00 0.00 2.69
532 2927 6.497954 TGGGAAGAGGTTGATTTCATTTGAAT 59.502 34.615 0.00 0.00 33.54 2.57
533 2928 7.673504 TGGGAAGAGGTTGATTTCATTTGAATA 59.326 33.333 0.00 0.00 33.54 1.75
575 2970 7.295196 TGTGAGATCCTATACTAGTCTACCCTT 59.705 40.741 0.00 0.00 0.00 3.95
576 2971 7.608761 GTGAGATCCTATACTAGTCTACCCTTG 59.391 44.444 0.00 0.00 0.00 3.61
578 2973 8.290463 AGATCCTATACTAGTCTACCCTTGAA 57.710 38.462 0.00 0.00 0.00 2.69
579 2974 8.165397 AGATCCTATACTAGTCTACCCTTGAAC 58.835 40.741 0.00 0.00 0.00 3.18
580 2975 7.463054 TCCTATACTAGTCTACCCTTGAACT 57.537 40.000 0.00 0.00 0.00 3.01
581 2976 7.516452 TCCTATACTAGTCTACCCTTGAACTC 58.484 42.308 0.00 0.00 0.00 3.01
582 2977 7.350389 TCCTATACTAGTCTACCCTTGAACTCT 59.650 40.741 0.00 0.00 0.00 3.24
586 2981 4.120946 AGTCTACCCTTGAACTCTGTCT 57.879 45.455 0.00 0.00 0.00 3.41
587 2982 3.829601 AGTCTACCCTTGAACTCTGTCTG 59.170 47.826 0.00 0.00 0.00 3.51
639 3034 3.822996 CAGCAGCATTCTCAAGTTCTTG 58.177 45.455 6.24 6.24 0.00 3.02
684 3194 3.146066 TCAGCAGCCGAGTTTGTTATTT 58.854 40.909 0.00 0.00 0.00 1.40
685 3195 3.568007 TCAGCAGCCGAGTTTGTTATTTT 59.432 39.130 0.00 0.00 0.00 1.82
716 3559 6.289064 ACTCTCTCCGTTCAAAAATACTTGT 58.711 36.000 0.00 0.00 0.00 3.16
717 3560 6.766467 ACTCTCTCCGTTCAAAAATACTTGTT 59.234 34.615 0.00 0.00 0.00 2.83
719 3562 8.842358 TCTCTCCGTTCAAAAATACTTGTTAT 57.158 30.769 0.00 0.00 0.00 1.89
720 3563 9.280174 TCTCTCCGTTCAAAAATACTTGTTATT 57.720 29.630 0.00 0.00 31.07 1.40
721 3564 9.329913 CTCTCCGTTCAAAAATACTTGTTATTG 57.670 33.333 0.00 0.00 30.21 1.90
814 3660 2.630580 GGATGGAGGGAGTAGTAGCAAG 59.369 54.545 0.00 0.00 0.00 4.01
820 3666 3.379452 AGGGAGTAGTAGCAAGCAATCT 58.621 45.455 0.00 0.00 0.00 2.40
1097 3986 2.950781 TGAGCCCTCATCGATACTCTT 58.049 47.619 0.00 0.00 34.14 2.85
1218 4110 3.050275 GTGTGGCGCAAGTCCCTC 61.050 66.667 10.83 0.00 45.49 4.30
1293 4185 2.277373 GTCGACAGCTACGCCTCG 60.277 66.667 11.55 0.25 32.67 4.63
1675 4609 1.518133 GCGCTCGAGCAGATGTTCT 60.518 57.895 34.69 0.00 42.21 3.01
1680 4614 1.747924 CTCGAGCAGATGTTCTCCAGA 59.252 52.381 0.00 0.00 0.00 3.86
1835 4788 0.658368 ACCGTGAGAGTCGATCGATG 59.342 55.000 22.50 2.65 0.00 3.84
1841 4794 3.252215 GTGAGAGTCGATCGATGGATCTT 59.748 47.826 22.50 3.15 45.66 2.40
1897 4850 3.385314 TGATGCCCTCCAAATCAATCA 57.615 42.857 0.00 0.00 0.00 2.57
1908 4866 7.331934 CCCTCCAAATCAATCACATATACTACG 59.668 40.741 0.00 0.00 0.00 3.51
1957 4916 4.510340 GTCTTTTGGTCTGTCGTTGTGTAT 59.490 41.667 0.00 0.00 0.00 2.29
1965 4924 7.423199 TGGTCTGTCGTTGTGTATATATTCTC 58.577 38.462 0.00 0.00 0.00 2.87
1998 4964 8.816894 AGAGAGTGAAGGAATATAAACAGTTCA 58.183 33.333 0.00 0.00 0.00 3.18
2278 5266 3.814268 CCGGCTGCGTTTCCATGG 61.814 66.667 4.97 4.97 0.00 3.66
2500 5504 2.024319 GCTATCCATCTGCGCCGTC 61.024 63.158 4.18 0.00 0.00 4.79
2542 5546 2.223479 CCGTCTTGGTTTCTTGTGTTGG 60.223 50.000 0.00 0.00 0.00 3.77
2619 5629 2.351738 CGTGAGTCATGTGCTGTGAGTA 60.352 50.000 4.02 0.00 29.71 2.59
2620 5630 3.249091 GTGAGTCATGTGCTGTGAGTAG 58.751 50.000 0.00 0.00 29.71 2.57
2621 5631 2.893489 TGAGTCATGTGCTGTGAGTAGT 59.107 45.455 0.00 0.00 29.71 2.73
2645 5655 4.205587 GTCTGTCCTTCTCCTATAACCGA 58.794 47.826 0.00 0.00 0.00 4.69
2716 5726 0.665835 TCGGCAACAATCGCTGTTTT 59.334 45.000 0.49 0.00 46.49 2.43
2937 5949 3.302480 CGTCAAAGTTCAGTTTCCGTGAG 60.302 47.826 0.00 0.00 0.00 3.51
2951 5963 1.727467 GTGAGGTGCAGCGTGTTTT 59.273 52.632 10.78 0.00 0.00 2.43
2981 5993 4.142966 GGTAATGTTAACCAGCTGACGTTC 60.143 45.833 17.39 7.09 36.96 3.95
2982 5994 2.902705 TGTTAACCAGCTGACGTTCT 57.097 45.000 17.39 0.00 0.00 3.01
2983 5995 2.750948 TGTTAACCAGCTGACGTTCTC 58.249 47.619 17.39 8.83 0.00 2.87
2994 6006 1.099689 GACGTTCTCTGAGAGAGGGG 58.900 60.000 12.50 8.36 42.54 4.79
2997 6009 1.190643 GTTCTCTGAGAGAGGGGTGG 58.809 60.000 12.50 0.00 42.54 4.61
3002 6014 2.270527 GAGAGAGGGGTGGCAAGC 59.729 66.667 0.00 0.00 0.00 4.01
3003 6015 2.530151 AGAGAGGGGTGGCAAGCA 60.530 61.111 0.00 0.00 0.00 3.91
3004 6016 2.129555 GAGAGAGGGGTGGCAAGCAA 62.130 60.000 0.00 0.00 0.00 3.91
3005 6017 1.228552 GAGAGGGGTGGCAAGCAAA 60.229 57.895 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 152 6.647334 TTGCTCACAAAGATCCACATTTAA 57.353 33.333 0.00 0.00 31.21 1.52
147 153 6.647334 TTTGCTCACAAAGATCCACATTTA 57.353 33.333 0.00 0.00 40.84 1.40
158 164 8.892887 TGCTTTTTAAAATTTTGCTCACAAAG 57.107 26.923 13.76 9.07 46.08 2.77
162 175 8.574627 GTGTTTGCTTTTTAAAATTTTGCTCAC 58.425 29.630 13.76 12.92 0.00 3.51
287 303 3.020984 TGTCAAACTGGTCTTTTCCACC 58.979 45.455 0.00 0.00 33.55 4.61
313 331 1.531365 CTGGTTTTGCTGGGCTGGA 60.531 57.895 0.00 0.00 0.00 3.86
356 374 8.765219 GCCAATTTAGTTCCTTTCTTTCTTTTC 58.235 33.333 0.00 0.00 0.00 2.29
369 387 5.959618 AACACTAGTGCCAATTTAGTTCC 57.040 39.130 22.90 0.00 0.00 3.62
370 388 8.319143 TCTTAACACTAGTGCCAATTTAGTTC 57.681 34.615 22.90 0.00 0.00 3.01
386 406 8.603304 ACTAACCAAATAGGACATCTTAACACT 58.397 33.333 0.00 0.00 41.22 3.55
403 423 6.488769 TTAGAGAGAACCACACTAACCAAA 57.511 37.500 0.00 0.00 0.00 3.28
445 2838 2.452813 CGGAGGGCGACGTGAATTG 61.453 63.158 0.00 0.00 0.00 2.32
446 2839 2.125673 CGGAGGGCGACGTGAATT 60.126 61.111 0.00 0.00 0.00 2.17
455 2848 1.444836 TAACAAATCAACGGAGGGCG 58.555 50.000 0.00 0.00 0.00 6.13
457 2850 3.681593 TCCTTAACAAATCAACGGAGGG 58.318 45.455 0.00 0.00 0.00 4.30
469 2862 5.750352 ACTTCGGTAATCCTCCTTAACAA 57.250 39.130 0.00 0.00 0.00 2.83
474 2867 6.370186 ACTTTTACTTCGGTAATCCTCCTT 57.630 37.500 0.00 0.00 39.74 3.36
476 2869 8.202811 AGATAACTTTTACTTCGGTAATCCTCC 58.797 37.037 0.00 0.00 39.74 4.30
491 2886 8.445588 ACCTCTTCCCAAGAAAGATAACTTTTA 58.554 33.333 0.00 0.00 44.97 1.52
500 2895 5.324832 AATCAACCTCTTCCCAAGAAAGA 57.675 39.130 0.00 0.00 37.02 2.52
506 2901 5.837979 TCAAATGAAATCAACCTCTTCCCAA 59.162 36.000 0.00 0.00 0.00 4.12
507 2902 5.392995 TCAAATGAAATCAACCTCTTCCCA 58.607 37.500 0.00 0.00 0.00 4.37
508 2903 5.982890 TCAAATGAAATCAACCTCTTCCC 57.017 39.130 0.00 0.00 0.00 3.97
541 2936 8.449625 ACTAGTATAGGATCTCACATTAGGTGT 58.550 37.037 0.00 0.00 45.20 4.16
547 2942 8.110908 GGGTAGACTAGTATAGGATCTCACATT 58.889 40.741 0.00 0.00 44.97 2.71
548 2943 7.462972 AGGGTAGACTAGTATAGGATCTCACAT 59.537 40.741 0.00 0.00 44.97 3.21
549 2944 6.793482 AGGGTAGACTAGTATAGGATCTCACA 59.207 42.308 0.00 0.00 44.97 3.58
570 2965 1.071385 CAGCAGACAGAGTTCAAGGGT 59.929 52.381 0.00 0.00 0.00 4.34
575 2970 0.034476 CTGCCAGCAGACAGAGTTCA 59.966 55.000 14.54 0.00 46.30 3.18
576 2971 0.319728 TCTGCCAGCAGACAGAGTTC 59.680 55.000 18.14 0.00 46.80 3.01
578 2973 4.204970 TCTGCCAGCAGACAGAGT 57.795 55.556 18.14 0.00 46.80 3.24
586 2981 1.076024 AGGAGGAATTTTCTGCCAGCA 59.924 47.619 0.00 0.00 0.00 4.41
587 2982 1.844687 AGGAGGAATTTTCTGCCAGC 58.155 50.000 0.00 0.00 0.00 4.85
639 3034 3.064931 CAAAGACCGAAGTTACCCTCAC 58.935 50.000 0.00 0.00 0.00 3.51
684 3194 8.721019 TTTTTGAACGGAGAGAGTACTAAAAA 57.279 30.769 0.00 0.00 0.00 1.94
685 3195 8.897872 ATTTTTGAACGGAGAGAGTACTAAAA 57.102 30.769 0.00 0.00 0.00 1.52
690 3200 7.384387 ACAAGTATTTTTGAACGGAGAGAGTAC 59.616 37.037 0.00 0.00 0.00 2.73
691 3201 7.439381 ACAAGTATTTTTGAACGGAGAGAGTA 58.561 34.615 0.00 0.00 0.00 2.59
692 3202 6.289064 ACAAGTATTTTTGAACGGAGAGAGT 58.711 36.000 0.00 0.00 0.00 3.24
693 3203 6.787085 ACAAGTATTTTTGAACGGAGAGAG 57.213 37.500 0.00 0.00 0.00 3.20
694 3204 8.842358 ATAACAAGTATTTTTGAACGGAGAGA 57.158 30.769 0.00 0.00 0.00 3.10
695 3205 9.329913 CAATAACAAGTATTTTTGAACGGAGAG 57.670 33.333 0.00 0.00 29.38 3.20
696 3206 9.058174 TCAATAACAAGTATTTTTGAACGGAGA 57.942 29.630 0.00 0.00 29.91 3.71
697 3207 9.672086 TTCAATAACAAGTATTTTTGAACGGAG 57.328 29.630 0.00 0.00 35.75 4.63
775 3618 9.073475 CCTCCATCCGGAAATATTTGTTATTAA 57.927 33.333 9.01 0.00 42.21 1.40
776 3619 7.668052 CCCTCCATCCGGAAATATTTGTTATTA 59.332 37.037 9.01 0.00 42.21 0.98
777 3620 6.493458 CCCTCCATCCGGAAATATTTGTTATT 59.507 38.462 9.01 0.00 42.21 1.40
779 3622 5.132985 TCCCTCCATCCGGAAATATTTGTTA 59.867 40.000 9.01 0.00 42.21 2.41
780 3623 4.079443 TCCCTCCATCCGGAAATATTTGTT 60.079 41.667 9.01 0.00 42.21 2.83
781 3624 3.461831 TCCCTCCATCCGGAAATATTTGT 59.538 43.478 9.01 0.00 42.21 2.83
782 3625 4.074970 CTCCCTCCATCCGGAAATATTTG 58.925 47.826 9.01 0.00 42.21 2.32
783 3626 3.722101 ACTCCCTCCATCCGGAAATATTT 59.278 43.478 9.01 0.00 42.21 1.40
784 3627 3.327439 ACTCCCTCCATCCGGAAATATT 58.673 45.455 9.01 0.00 42.21 1.28
785 3628 2.991580 ACTCCCTCCATCCGGAAATAT 58.008 47.619 9.01 0.00 42.21 1.28
786 3629 2.489528 ACTCCCTCCATCCGGAAATA 57.510 50.000 9.01 0.00 42.21 1.40
787 3630 2.330216 CTACTCCCTCCATCCGGAAAT 58.670 52.381 9.01 0.00 42.21 2.17
788 3631 1.007963 ACTACTCCCTCCATCCGGAAA 59.992 52.381 9.01 0.00 42.21 3.13
789 3632 0.635009 ACTACTCCCTCCATCCGGAA 59.365 55.000 9.01 0.00 42.21 4.30
790 3633 1.424302 CTACTACTCCCTCCATCCGGA 59.576 57.143 6.61 6.61 39.79 5.14
791 3634 1.912417 CTACTACTCCCTCCATCCGG 58.088 60.000 0.00 0.00 0.00 5.14
792 3635 1.249407 GCTACTACTCCCTCCATCCG 58.751 60.000 0.00 0.00 0.00 4.18
793 3636 2.383442 TGCTACTACTCCCTCCATCC 57.617 55.000 0.00 0.00 0.00 3.51
794 3637 2.036604 GCTTGCTACTACTCCCTCCATC 59.963 54.545 0.00 0.00 0.00 3.51
795 3638 2.043227 GCTTGCTACTACTCCCTCCAT 58.957 52.381 0.00 0.00 0.00 3.41
796 3639 1.273041 TGCTTGCTACTACTCCCTCCA 60.273 52.381 0.00 0.00 0.00 3.86
797 3640 1.486211 TGCTTGCTACTACTCCCTCC 58.514 55.000 0.00 0.00 0.00 4.30
798 3641 3.386402 AGATTGCTTGCTACTACTCCCTC 59.614 47.826 0.00 0.00 0.00 4.30
799 3642 3.379452 AGATTGCTTGCTACTACTCCCT 58.621 45.455 0.00 0.00 0.00 4.20
800 3643 3.828875 AGATTGCTTGCTACTACTCCC 57.171 47.619 0.00 0.00 0.00 4.30
801 3644 6.090483 TCATAGATTGCTTGCTACTACTCC 57.910 41.667 0.00 0.00 0.00 3.85
802 3645 9.352784 CTTATCATAGATTGCTTGCTACTACTC 57.647 37.037 0.00 0.00 0.00 2.59
832 3678 7.845066 ACGACCTCTTCCTCAATTAATTAAC 57.155 36.000 0.00 0.00 0.00 2.01
1180 4072 4.838486 CAGCGTCGTCGGCTCCTC 62.838 72.222 3.90 0.00 37.56 3.71
1218 4110 1.672356 CCCCTTGCAGTCGAACAGG 60.672 63.158 0.00 0.00 0.00 4.00
1369 4264 2.032528 CCACTGCTCGCCTTGGAA 59.967 61.111 0.76 0.00 0.00 3.53
1675 4609 2.750637 GAGGAGCGACGGTCTGGA 60.751 66.667 24.62 0.00 0.00 3.86
1680 4614 2.752238 CTCCTGAGGAGCGACGGT 60.752 66.667 16.73 0.00 43.29 4.83
1835 4788 1.203052 CATGCCCACACACAAAGATCC 59.797 52.381 0.00 0.00 0.00 3.36
1841 4794 0.890542 GCTCTCATGCCCACACACAA 60.891 55.000 0.00 0.00 0.00 3.33
1908 4866 9.587772 CATGATTTGGCCATACTATAGTAGTAC 57.412 37.037 17.31 8.96 43.46 2.73
1931 4889 3.312421 ACAACGACAGACCAAAAGACATG 59.688 43.478 0.00 0.00 0.00 3.21
1971 4930 9.660180 GAACTGTTTATATTCCTTCACTCTCTT 57.340 33.333 0.00 0.00 0.00 2.85
1998 4964 4.372656 GAAGCTGAGAGCCGTATACAAAT 58.627 43.478 3.32 0.00 43.77 2.32
2025 4991 5.655488 AGACAACAAGATGTTATCTCGAGG 58.345 41.667 13.56 0.00 39.71 4.63
2028 4994 6.712241 ACAAGACAACAAGATGTTATCTCG 57.288 37.500 4.65 0.00 42.67 4.04
2108 5090 0.584876 AAACTCGCAAGCCACGTAAC 59.415 50.000 0.00 0.00 37.18 2.50
2278 5266 2.543067 GATCCTGCCAGTCCACACCC 62.543 65.000 0.00 0.00 0.00 4.61
2500 5504 1.593196 TTGTCCTTCGCAAGTTCTGG 58.407 50.000 0.00 0.00 39.48 3.86
2572 5576 1.251251 AAATTCAGTGAGCCAGCCAC 58.749 50.000 0.00 3.85 34.89 5.01
2619 5629 3.767309 ATAGGAGAAGGACAGACCACT 57.233 47.619 0.00 0.00 42.04 4.00
2620 5630 4.099727 GGTTATAGGAGAAGGACAGACCAC 59.900 50.000 0.00 0.00 42.04 4.16
2621 5631 4.287552 GGTTATAGGAGAAGGACAGACCA 58.712 47.826 0.00 0.00 42.04 4.02
2666 5676 3.251487 GTCAGAGTCGGTTATAGGAGCTC 59.749 52.174 4.71 4.71 0.00 4.09
2668 5678 2.031857 CGTCAGAGTCGGTTATAGGAGC 60.032 54.545 0.00 0.00 0.00 4.70
2716 5726 0.812014 TTCAGCCGTGCTTCGTGAAA 60.812 50.000 0.00 0.00 36.40 2.69
2951 5963 8.354426 GTCAGCTGGTTAACATTACCTTAAAAA 58.646 33.333 15.13 0.00 36.60 1.94
2957 5969 3.007614 ACGTCAGCTGGTTAACATTACCT 59.992 43.478 15.13 0.00 36.60 3.08
2968 5980 0.600557 CTCAGAGAACGTCAGCTGGT 59.399 55.000 15.13 1.12 0.00 4.00
2970 5982 1.809547 TCTCTCAGAGAACGTCAGCTG 59.190 52.381 7.63 7.63 35.59 4.24
2981 5993 0.906756 TTGCCACCCCTCTCTCAGAG 60.907 60.000 0.00 0.00 41.96 3.35
2982 5994 0.906756 CTTGCCACCCCTCTCTCAGA 60.907 60.000 0.00 0.00 0.00 3.27
2983 5995 1.601171 CTTGCCACCCCTCTCTCAG 59.399 63.158 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.