Multiple sequence alignment - TraesCS3D01G401200

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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 TraesCS3D01G401200 chr3D 100.000 3525 0 0 1 3525 515775427 515778951 0.000000e+00 6510.0
1 TraesCS3D01G401200 chr3B 89.197 2814 140 67 173 2917 678547486 678550204 0.000000e+00 3362.0
2 TraesCS3D01G401200 chr3B 89.982 569 42 8 2960 3522 678550327 678550886 0.000000e+00 721.0
3 TraesCS3D01G401200 chr3B 87.402 127 7 5 1 127 678547375 678547492 1.710000e-28 137.0
4 TraesCS3D01G401200 chr3A 90.977 2405 101 37 983 3324 650056157 650058508 0.000000e+00 3133.0
5 TraesCS3D01G401200 chr3A 88.907 613 16 20 319 904 650055547 650056134 0.000000e+00 708.0
6 TraesCS3D01G401200 chr3A 90.643 171 10 3 3305 3470 650059019 650059188 4.580000e-54 222.0
7 TraesCS3D01G401200 chr3A 100.000 29 0 0 166 194 650055411 650055439 2.000000e-03 54.7
8 TraesCS3D01G401200 chr1D 85.393 534 63 11 1012 1536 359666076 359665549 1.110000e-149 540.0
9 TraesCS3D01G401200 chr1D 83.624 287 26 12 2249 2523 359664916 359664639 2.100000e-62 250.0
10 TraesCS3D01G401200 chr1B 84.843 541 56 17 1012 1536 481542356 481541826 4.030000e-144 521.0
11 TraesCS3D01G401200 chr1B 81.882 287 31 12 2249 2523 481541192 481540915 4.580000e-54 222.0
12 TraesCS3D01G401200 chr1A 93.728 287 18 0 1250 1536 459188154 459187868 6.990000e-117 431.0
13 TraesCS3D01G401200 chr1A 91.071 168 15 0 1012 1179 459188408 459188241 9.840000e-56 228.0
14 TraesCS3D01G401200 chr1A 79.861 288 23 14 2249 2527 459187294 459187033 1.010000e-40 178.0
15 TraesCS3D01G401200 chr4A 91.064 235 19 2 1279 1512 521919706 521919473 2.040000e-82 316.0
16 TraesCS3D01G401200 chr4B 90.638 235 20 2 1279 1512 103056204 103055971 9.500000e-81 311.0
17 TraesCS3D01G401200 chr4D 90.213 235 21 2 1279 1512 69679958 69679725 4.420000e-79 305.0
18 TraesCS3D01G401200 chr2B 76.364 495 82 29 1025 1498 85177909 85177429 2.120000e-57 233.0
19 TraesCS3D01G401200 chr2D 76.258 497 81 29 1025 1498 54487978 54487496 2.740000e-56 230.0
20 TraesCS3D01G401200 chr2D 75.820 488 87 26 1025 1495 54317525 54317998 5.920000e-53 219.0
21 TraesCS3D01G401200 chr2D 78.309 272 41 12 1256 1512 175331615 175331883 3.640000e-35 159.0
22 TraesCS3D01G401200 chr6D 86.164 159 13 8 1011 1165 27820285 27820132 2.820000e-36 163.0
23 TraesCS3D01G401200 chr6B 86.164 159 13 8 1011 1165 51580396 51580243 2.820000e-36 163.0
24 TraesCS3D01G401200 chr6B 100.000 28 0 0 2817 2844 321823924 321823897 6.000000e-03 52.8
25 TraesCS3D01G401200 chr6A 86.164 159 13 8 1011 1165 30191214 30191061 2.820000e-36 163.0


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 TraesCS3D01G401200 chr3D 515775427 515778951 3524 False 6510.000000 6510 100.000000 1 3525 1 chr3D.!!$F1 3524
1 TraesCS3D01G401200 chr3B 678547375 678550886 3511 False 1406.666667 3362 88.860333 1 3522 3 chr3B.!!$F1 3521
2 TraesCS3D01G401200 chr3A 650055411 650059188 3777 False 1029.425000 3133 92.631750 166 3470 4 chr3A.!!$F1 3304
3 TraesCS3D01G401200 chr1D 359664639 359666076 1437 True 395.000000 540 84.508500 1012 2523 2 chr1D.!!$R1 1511
4 TraesCS3D01G401200 chr1B 481540915 481542356 1441 True 371.500000 521 83.362500 1012 2523 2 chr1B.!!$R1 1511
5 TraesCS3D01G401200 chr1A 459187033 459188408 1375 True 279.000000 431 88.220000 1012 2527 3 chr1A.!!$R1 1515

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
972 1055 0.030101 GAGGAGATTCGCGTGAGGAG 59.97 60.0 5.77 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2747 3292 0.039256 TTGAAGCATCTTTGGCGCAC 60.039 50.0 10.83 0.0 36.08 5.34 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
55 56 1.370609 TTTCGTGTCGGTTTTCTGCA 58.629 45.000 0.00 0.00 0.00 4.41
56 57 0.653636 TTCGTGTCGGTTTTCTGCAC 59.346 50.000 0.00 0.00 33.32 4.57
62 63 2.597510 GGTTTTCTGCACCGGGCT 60.598 61.111 6.32 0.00 45.15 5.19
63 64 2.644992 GTTTTCTGCACCGGGCTG 59.355 61.111 6.32 10.85 45.15 4.85
104 105 1.004918 CGAACCAAGAGAGGCGGTT 60.005 57.895 0.00 0.00 45.64 4.44
115 116 1.492176 AGAGGCGGTTGATTGATGGAT 59.508 47.619 0.00 0.00 0.00 3.41
120 121 3.304928 GGCGGTTGATTGATGGATTGATC 60.305 47.826 0.00 0.00 0.00 2.92
121 122 3.607775 GCGGTTGATTGATGGATTGATCG 60.608 47.826 0.00 0.00 0.00 3.69
122 123 3.809279 CGGTTGATTGATGGATTGATCGA 59.191 43.478 0.00 0.00 0.00 3.59
123 124 4.453478 CGGTTGATTGATGGATTGATCGAT 59.547 41.667 0.00 0.00 0.00 3.59
124 125 5.390251 CGGTTGATTGATGGATTGATCGATC 60.390 44.000 18.72 18.72 41.18 3.69
125 126 5.390251 GGTTGATTGATGGATTGATCGATCG 60.390 44.000 20.03 9.36 42.72 3.69
126 127 5.138125 TGATTGATGGATTGATCGATCGA 57.862 39.130 21.86 21.86 42.72 3.59
127 128 4.925646 TGATTGATGGATTGATCGATCGAC 59.074 41.667 22.06 14.65 42.72 4.20
128 129 3.303881 TGATGGATTGATCGATCGACC 57.696 47.619 22.06 16.93 42.66 4.79
129 130 2.254459 GATGGATTGATCGATCGACCG 58.746 52.381 22.06 0.00 33.46 4.79
130 131 1.314730 TGGATTGATCGATCGACCGA 58.685 50.000 22.06 11.76 43.16 4.69
131 132 1.266989 TGGATTGATCGATCGACCGAG 59.733 52.381 22.06 0.00 42.21 4.63
132 133 1.332178 GATTGATCGATCGACCGAGC 58.668 55.000 22.06 11.28 44.24 5.03
138 139 3.999051 GATCGACCGAGCGGAAAG 58.001 61.111 16.83 6.34 38.96 2.62
149 150 3.916439 CGGAAAGCAACAAACCGC 58.084 55.556 0.00 0.00 37.32 5.68
150 151 1.660264 CGGAAAGCAACAAACCGCC 60.660 57.895 0.00 0.00 37.32 6.13
151 152 1.300620 GGAAAGCAACAAACCGCCC 60.301 57.895 0.00 0.00 0.00 6.13
152 153 1.660264 GAAAGCAACAAACCGCCCG 60.660 57.895 0.00 0.00 0.00 6.13
153 154 3.783478 AAAGCAACAAACCGCCCGC 62.783 57.895 0.00 0.00 0.00 6.13
156 157 4.383602 CAACAAACCGCCCGCGAG 62.384 66.667 8.23 0.00 42.83 5.03
194 195 0.663688 TCGAGCTCGCTGGAATCTAC 59.336 55.000 30.97 0.00 39.60 2.59
196 197 0.747255 GAGCTCGCTGGAATCTACCA 59.253 55.000 0.00 0.00 38.33 3.25
217 218 1.202582 GTCCTATCCATCCGTCCATCG 59.797 57.143 0.00 0.00 39.52 3.84
233 234 0.877649 ATCGATCTGCGCGCATTTCT 60.878 50.000 36.48 19.03 40.61 2.52
267 291 2.589720 CATGCCATGGATCCAAAGCTA 58.410 47.619 29.33 20.10 0.00 3.32
288 312 0.767375 AGGCAGCTCCTCAACAGAAA 59.233 50.000 0.00 0.00 43.20 2.52
305 329 3.008049 CAGAAAACCCTAGCACTGTACCT 59.992 47.826 0.00 0.00 0.00 3.08
307 331 4.104261 AGAAAACCCTAGCACTGTACCTTT 59.896 41.667 0.00 0.00 0.00 3.11
308 332 3.418684 AACCCTAGCACTGTACCTTTG 57.581 47.619 0.00 0.00 0.00 2.77
309 333 2.335933 ACCCTAGCACTGTACCTTTGT 58.664 47.619 0.00 0.00 0.00 2.83
311 335 3.244457 ACCCTAGCACTGTACCTTTGTTC 60.244 47.826 0.00 0.00 0.00 3.18
312 336 2.993899 CCTAGCACTGTACCTTTGTTCG 59.006 50.000 0.00 0.00 0.00 3.95
313 337 2.902705 AGCACTGTACCTTTGTTCGA 57.097 45.000 0.00 0.00 0.00 3.71
314 338 3.402628 AGCACTGTACCTTTGTTCGAT 57.597 42.857 0.00 0.00 0.00 3.59
315 339 4.530710 AGCACTGTACCTTTGTTCGATA 57.469 40.909 0.00 0.00 0.00 2.92
316 340 4.890088 AGCACTGTACCTTTGTTCGATAA 58.110 39.130 0.00 0.00 0.00 1.75
317 341 5.302360 AGCACTGTACCTTTGTTCGATAAA 58.698 37.500 0.00 0.00 0.00 1.40
328 352 4.530710 TGTTCGATAAACCTAGCACTGT 57.469 40.909 0.00 0.00 37.03 3.55
332 356 5.496133 TCGATAAACCTAGCACTGTACTC 57.504 43.478 0.00 0.00 0.00 2.59
333 357 4.337555 TCGATAAACCTAGCACTGTACTCC 59.662 45.833 0.00 0.00 0.00 3.85
335 359 2.625282 AACCTAGCACTGTACTCCCT 57.375 50.000 0.00 0.00 0.00 4.20
336 360 1.853963 ACCTAGCACTGTACTCCCTG 58.146 55.000 0.00 0.00 0.00 4.45
337 361 0.461961 CCTAGCACTGTACTCCCTGC 59.538 60.000 0.00 0.00 0.00 4.85
338 362 0.461961 CTAGCACTGTACTCCCTGCC 59.538 60.000 0.00 0.00 0.00 4.85
384 409 0.186386 CCTACCAACCCCCAACAACA 59.814 55.000 0.00 0.00 0.00 3.33
385 410 1.324383 CTACCAACCCCCAACAACAC 58.676 55.000 0.00 0.00 0.00 3.32
386 411 0.465824 TACCAACCCCCAACAACACG 60.466 55.000 0.00 0.00 0.00 4.49
387 412 1.755008 CCAACCCCCAACAACACGT 60.755 57.895 0.00 0.00 0.00 4.49
427 459 2.362047 ACACAACGCATCGTCGTCG 61.362 57.895 0.00 0.00 42.46 5.12
428 460 2.050714 ACAACGCATCGTCGTCGT 60.051 55.556 1.33 0.00 42.46 4.34
429 461 2.078914 ACAACGCATCGTCGTCGTC 61.079 57.895 1.33 0.00 42.46 4.20
869 931 1.519719 CTCCCACCTAGAGCAGCAC 59.480 63.158 0.00 0.00 0.00 4.40
870 932 1.229177 TCCCACCTAGAGCAGCACA 60.229 57.895 0.00 0.00 0.00 4.57
874 938 1.405256 CCACCTAGAGCAGCACAAGAG 60.405 57.143 0.00 0.00 0.00 2.85
875 939 1.547820 CACCTAGAGCAGCACAAGAGA 59.452 52.381 0.00 0.00 0.00 3.10
880 944 3.482156 AGAGCAGCACAAGAGAAGAAA 57.518 42.857 0.00 0.00 0.00 2.52
884 948 4.396522 AGCAGCACAAGAGAAGAAAGAAT 58.603 39.130 0.00 0.00 0.00 2.40
907 977 2.235650 AGCAGTAGAATTCAGAGCAGCA 59.764 45.455 8.44 0.00 0.00 4.41
909 979 3.859443 CAGTAGAATTCAGAGCAGCAGT 58.141 45.455 8.44 0.00 0.00 4.40
919 989 2.125753 GCAGCAGTAGCAGCGAGT 60.126 61.111 0.00 0.00 43.44 4.18
920 990 2.451167 GCAGCAGTAGCAGCGAGTG 61.451 63.158 5.99 5.99 43.44 3.51
931 1014 1.601663 GCAGCGAGTGAGCGATAGAAT 60.602 52.381 0.00 0.00 43.00 2.40
932 1015 2.315011 CAGCGAGTGAGCGATAGAATC 58.685 52.381 0.00 0.00 43.00 2.52
942 1025 2.131183 GCGATAGAATCACAGTGAGGC 58.869 52.381 9.64 3.45 39.76 4.70
944 1027 3.637432 CGATAGAATCACAGTGAGGCTC 58.363 50.000 9.64 7.79 39.76 4.70
954 1037 0.965866 AGTGAGGCTCGTTGGATCGA 60.966 55.000 10.42 0.00 38.19 3.59
963 1046 1.333931 TCGTTGGATCGAGGAGATTCG 59.666 52.381 0.00 0.00 40.26 3.34
964 1047 1.492720 GTTGGATCGAGGAGATTCGC 58.507 55.000 0.00 0.00 40.26 4.70
965 1048 0.030773 TTGGATCGAGGAGATTCGCG 59.969 55.000 0.00 0.00 40.26 5.87
966 1049 1.101635 TGGATCGAGGAGATTCGCGT 61.102 55.000 5.77 0.00 40.26 6.01
967 1050 0.661780 GGATCGAGGAGATTCGCGTG 60.662 60.000 5.77 0.00 40.26 5.34
968 1051 0.308068 GATCGAGGAGATTCGCGTGA 59.692 55.000 5.77 0.00 40.26 4.35
969 1052 0.309302 ATCGAGGAGATTCGCGTGAG 59.691 55.000 5.77 0.00 40.29 3.51
970 1053 1.298713 CGAGGAGATTCGCGTGAGG 60.299 63.158 5.77 0.00 33.39 3.86
971 1054 1.715862 CGAGGAGATTCGCGTGAGGA 61.716 60.000 5.77 0.00 33.39 3.71
972 1055 0.030101 GAGGAGATTCGCGTGAGGAG 59.970 60.000 5.77 0.00 0.00 3.69
973 1056 1.066587 GGAGATTCGCGTGAGGAGG 59.933 63.158 5.77 0.00 0.00 4.30
974 1057 1.590259 GAGATTCGCGTGAGGAGGC 60.590 63.158 5.77 0.00 0.00 4.70
975 1058 2.586357 GATTCGCGTGAGGAGGCC 60.586 66.667 5.77 0.00 0.00 5.19
976 1059 4.514577 ATTCGCGTGAGGAGGCCG 62.515 66.667 5.77 0.00 0.00 6.13
979 1062 4.514577 CGCGTGAGGAGGCCGATT 62.515 66.667 0.00 0.00 0.00 3.34
980 1063 2.812499 GCGTGAGGAGGCCGATTA 59.188 61.111 0.00 0.00 0.00 1.75
981 1064 1.300233 GCGTGAGGAGGCCGATTAG 60.300 63.158 0.00 0.00 0.00 1.73
982 1065 1.300233 CGTGAGGAGGCCGATTAGC 60.300 63.158 0.00 0.00 0.00 3.09
1071 1154 2.276116 GGACGAGGAGCTGGTGACA 61.276 63.158 0.00 0.00 39.59 3.58
1196 1279 0.811616 ATCAATCCTCCACGCGCTTC 60.812 55.000 5.73 0.00 0.00 3.86
1207 1290 2.125512 GCGCTTCATCCGTCCAGT 60.126 61.111 0.00 0.00 0.00 4.00
1252 1360 0.179089 GCATGTCCTCGTGATCTGCT 60.179 55.000 0.00 0.00 33.09 4.24
1645 2060 4.260294 CGCCGTAGATAGATTAGATCGACC 60.260 50.000 0.00 0.00 0.00 4.79
1647 2062 5.107824 CCGTAGATAGATTAGATCGACCGA 58.892 45.833 0.00 0.00 0.00 4.69
1869 2316 4.399303 CCTTTCAGTTTATGGACCCATGAC 59.601 45.833 11.61 9.76 37.82 3.06
1874 2321 2.936498 GTTTATGGACCCATGACTCGTG 59.064 50.000 11.61 0.00 37.82 4.35
1876 2323 1.552799 ATGGACCCATGACTCGTGCA 61.553 55.000 0.00 0.00 35.03 4.57
1883 2330 1.450848 ATGACTCGTGCAGCCATGG 60.451 57.895 7.63 7.63 0.00 3.66
1935 2388 3.126528 GGCGCTGTACCGGTAGAT 58.873 61.111 16.41 0.00 0.00 1.98
1942 2395 2.414293 GCTGTACCGGTAGATAGCATCG 60.414 54.545 27.65 12.15 0.00 3.84
2003 2458 5.352569 AGCTTTCTAAATGATTCGACTGGTG 59.647 40.000 0.00 0.00 0.00 4.17
2006 2461 7.591006 TTTCTAAATGATTCGACTGGTGTAC 57.409 36.000 0.00 0.00 0.00 2.90
2025 2480 2.341257 ACTTCGTCATGTGTGATCTGC 58.659 47.619 0.00 0.00 36.60 4.26
2050 2505 3.935828 TCGTTTGTCTGACATGTTTGTGA 59.064 39.130 11.86 0.98 35.79 3.58
2059 2514 5.970612 TCTGACATGTTTGTGATTTTGTTCG 59.029 36.000 0.00 0.00 35.79 3.95
2709 3252 3.195698 GAAGGTGGCGGCGATGAC 61.196 66.667 12.98 2.50 0.00 3.06
2747 3292 1.004595 CTCACCAGCATGACATGACG 58.995 55.000 19.76 8.42 39.69 4.35
2748 3293 0.321346 TCACCAGCATGACATGACGT 59.679 50.000 19.76 7.98 39.69 4.34
2749 3294 0.445043 CACCAGCATGACATGACGTG 59.555 55.000 19.76 15.47 39.69 4.49
2754 3302 2.047370 ATGACATGACGTGCGCCA 60.047 55.556 4.18 0.00 0.00 5.69
2789 3337 0.307453 GTTCGCCGCATTGCATCATA 59.693 50.000 9.69 0.00 0.00 2.15
2790 3338 1.069022 GTTCGCCGCATTGCATCATAT 60.069 47.619 9.69 0.00 0.00 1.78
3025 3657 0.179936 CCCCTCCACTTGCTGAGATC 59.820 60.000 0.00 0.00 0.00 2.75
3027 3659 1.134461 CCCTCCACTTGCTGAGATCTG 60.134 57.143 0.00 0.00 0.00 2.90
3064 3696 3.588277 GGCTGAATTAGGCGATCGA 57.412 52.632 21.57 0.00 42.55 3.59
3065 3697 1.423395 GGCTGAATTAGGCGATCGAG 58.577 55.000 21.57 5.50 42.55 4.04
3066 3698 0.787183 GCTGAATTAGGCGATCGAGC 59.213 55.000 21.57 12.37 0.00 5.03
3067 3699 1.604185 GCTGAATTAGGCGATCGAGCT 60.604 52.381 21.57 0.00 37.29 4.09
3068 3700 2.057316 CTGAATTAGGCGATCGAGCTG 58.943 52.381 21.57 0.00 37.29 4.24
3069 3701 0.787183 GAATTAGGCGATCGAGCTGC 59.213 55.000 21.57 8.61 37.29 5.25
3070 3702 0.941463 AATTAGGCGATCGAGCTGCG 60.941 55.000 21.57 0.00 42.69 5.18
3071 3703 2.755542 ATTAGGCGATCGAGCTGCGG 62.756 60.000 21.57 0.00 41.33 5.69
3074 3706 3.918220 GCGATCGAGCTGCGGTTG 61.918 66.667 21.57 0.00 41.33 3.77
3078 3711 2.835701 GATCGAGCTGCGGTTGGTGA 62.836 60.000 0.00 0.00 41.33 4.02
3083 3716 2.109126 GCTGCGGTTGGTGATCTCC 61.109 63.158 6.88 6.88 0.00 3.71
3131 3764 4.992319 TGATATTCTTGGCGTATTTACCCG 59.008 41.667 0.00 0.00 0.00 5.28
3137 3770 1.952635 GCGTATTTACCCGCTCCCG 60.953 63.158 0.00 0.00 46.08 5.14
3158 3792 2.049063 AGCACTCTTCACCGACGC 60.049 61.111 0.00 0.00 0.00 5.19
3171 3809 1.941734 CGACGCTAGCTAGCTGCAC 60.942 63.158 36.02 24.61 46.85 4.57
3175 3813 2.656651 CTAGCTAGCTGCACGCGG 60.657 66.667 27.68 0.00 45.94 6.46
3194 3832 1.229951 TCCAGCTGTGGGGGAGATT 60.230 57.895 13.81 0.00 45.11 2.40
3280 3918 3.386867 GAAATCAGCGGTGCAGGCG 62.387 63.158 10.38 0.77 35.00 5.52
3328 4495 1.334689 CGTACGGCTGATGCTTATCGA 60.335 52.381 7.57 0.00 39.59 3.59
3337 4504 2.034685 TGATGCTTATCGAGGAAGACCG 59.965 50.000 12.76 0.00 41.83 4.79
3441 4613 1.369625 GTGGATGGATCACGTTGGAC 58.630 55.000 0.00 0.00 0.00 4.02
3505 4677 1.811266 CATCGTCAAGGCTCACCCG 60.811 63.158 0.00 0.00 39.21 5.28
3522 4694 1.067582 CGTCCGCCAGACTATTCCC 59.932 63.158 0.55 0.00 43.91 3.97
3523 4695 1.067582 GTCCGCCAGACTATTCCCG 59.932 63.158 0.00 0.00 42.69 5.14
3524 4696 1.076559 TCCGCCAGACTATTCCCGA 60.077 57.895 0.00 0.00 0.00 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 0.653636 GTGCAGAAAACCGACACGAA 59.346 50.000 0.00 0.00 0.00 3.85
78 79 3.952628 CTCTTGGTTCGTCCCCGGC 62.953 68.421 0.00 0.00 34.77 6.13
104 105 4.925646 GTCGATCGATCAATCCATCAATCA 59.074 41.667 22.50 0.00 0.00 2.57
115 116 1.010013 CGCTCGGTCGATCGATCAA 60.010 57.895 26.79 9.21 38.55 2.57
120 121 1.939785 CTTTCCGCTCGGTCGATCG 60.940 63.158 12.98 12.98 36.47 3.69
121 122 2.231618 GCTTTCCGCTCGGTCGATC 61.232 63.158 8.28 0.00 36.47 3.69
122 123 2.202756 GCTTTCCGCTCGGTCGAT 60.203 61.111 8.28 0.00 36.47 3.59
123 124 3.215597 TTGCTTTCCGCTCGGTCGA 62.216 57.895 8.28 0.00 40.11 4.20
124 125 2.736995 TTGCTTTCCGCTCGGTCG 60.737 61.111 8.28 0.00 40.11 4.79
125 126 1.503818 TTGTTGCTTTCCGCTCGGTC 61.504 55.000 8.28 0.00 40.11 4.79
126 127 1.098712 TTTGTTGCTTTCCGCTCGGT 61.099 50.000 8.28 0.00 40.11 4.69
127 128 0.660300 GTTTGTTGCTTTCCGCTCGG 60.660 55.000 1.14 1.14 40.11 4.63
128 129 0.660300 GGTTTGTTGCTTTCCGCTCG 60.660 55.000 0.00 0.00 40.11 5.03
129 130 0.660300 CGGTTTGTTGCTTTCCGCTC 60.660 55.000 0.00 0.00 40.11 5.03
130 131 1.358759 CGGTTTGTTGCTTTCCGCT 59.641 52.632 0.00 0.00 40.11 5.52
131 132 3.916439 CGGTTTGTTGCTTTCCGC 58.084 55.556 0.00 0.00 35.01 5.54
132 133 1.660264 GGCGGTTTGTTGCTTTCCG 60.660 57.895 0.00 0.00 43.37 4.30
133 134 1.300620 GGGCGGTTTGTTGCTTTCC 60.301 57.895 0.00 0.00 0.00 3.13
134 135 1.660264 CGGGCGGTTTGTTGCTTTC 60.660 57.895 0.00 0.00 0.00 2.62
135 136 2.415426 CGGGCGGTTTGTTGCTTT 59.585 55.556 0.00 0.00 0.00 3.51
136 137 4.279043 GCGGGCGGTTTGTTGCTT 62.279 61.111 0.00 0.00 0.00 3.91
139 140 4.383602 CTCGCGGGCGGTTTGTTG 62.384 66.667 13.60 0.00 40.25 3.33
153 154 4.680237 TGTTGGACGCCCAGCTCG 62.680 66.667 6.13 0.00 44.60 5.03
154 155 3.050275 GTGTTGGACGCCCAGCTC 61.050 66.667 6.13 0.00 44.60 4.09
155 156 4.643387 GGTGTTGGACGCCCAGCT 62.643 66.667 6.13 0.00 42.80 4.24
157 158 3.605749 ATCGGTGTTGGACGCCCAG 62.606 63.158 5.18 0.00 45.71 4.45
158 159 3.599285 GATCGGTGTTGGACGCCCA 62.599 63.158 5.18 0.00 45.71 5.36
159 160 2.818274 GATCGGTGTTGGACGCCC 60.818 66.667 5.18 0.00 45.71 6.13
160 161 3.186047 CGATCGGTGTTGGACGCC 61.186 66.667 7.38 0.61 45.04 5.68
161 162 2.126228 TCGATCGGTGTTGGACGC 60.126 61.111 16.41 0.00 0.00 5.19
162 163 2.158959 GCTCGATCGGTGTTGGACG 61.159 63.158 16.41 0.00 0.00 4.79
163 164 0.802607 GAGCTCGATCGGTGTTGGAC 60.803 60.000 16.41 0.00 0.00 4.02
164 165 1.511305 GAGCTCGATCGGTGTTGGA 59.489 57.895 16.41 0.00 0.00 3.53
194 195 0.969894 GGACGGATGGATAGGACTGG 59.030 60.000 0.00 0.00 0.00 4.00
196 197 2.530701 GATGGACGGATGGATAGGACT 58.469 52.381 0.00 0.00 0.00 3.85
197 198 1.202582 CGATGGACGGATGGATAGGAC 59.797 57.143 0.00 0.00 38.46 3.85
202 203 1.547820 CAGATCGATGGACGGATGGAT 59.452 52.381 0.54 0.00 42.82 3.41
203 204 0.961753 CAGATCGATGGACGGATGGA 59.038 55.000 0.54 0.00 42.82 3.41
204 205 0.668706 GCAGATCGATGGACGGATGG 60.669 60.000 0.54 0.00 42.82 3.51
205 206 1.005804 CGCAGATCGATGGACGGATG 61.006 60.000 0.54 0.00 42.82 3.51
217 218 0.930310 TGTAGAAATGCGCGCAGATC 59.070 50.000 38.44 33.88 0.00 2.75
233 234 1.451207 GCATGGCACGGGTGATGTA 60.451 57.895 2.38 0.00 0.00 2.29
288 312 2.709397 ACAAAGGTACAGTGCTAGGGTT 59.291 45.455 0.00 0.00 0.00 4.11
305 329 5.302360 ACAGTGCTAGGTTTATCGAACAAA 58.698 37.500 0.00 0.00 40.13 2.83
307 331 4.530710 ACAGTGCTAGGTTTATCGAACA 57.469 40.909 0.00 0.00 40.13 3.18
308 332 5.648572 AGTACAGTGCTAGGTTTATCGAAC 58.351 41.667 0.00 0.00 37.53 3.95
309 333 5.163581 GGAGTACAGTGCTAGGTTTATCGAA 60.164 44.000 0.00 0.00 0.00 3.71
311 335 4.499357 GGGAGTACAGTGCTAGGTTTATCG 60.499 50.000 0.00 0.00 0.00 2.92
312 336 4.650131 AGGGAGTACAGTGCTAGGTTTATC 59.350 45.833 0.00 0.00 0.00 1.75
313 337 4.406003 CAGGGAGTACAGTGCTAGGTTTAT 59.594 45.833 0.00 0.00 0.00 1.40
314 338 3.767673 CAGGGAGTACAGTGCTAGGTTTA 59.232 47.826 0.00 0.00 0.00 2.01
315 339 2.567615 CAGGGAGTACAGTGCTAGGTTT 59.432 50.000 0.00 0.00 0.00 3.27
316 340 2.180276 CAGGGAGTACAGTGCTAGGTT 58.820 52.381 0.00 0.00 0.00 3.50
317 341 1.853963 CAGGGAGTACAGTGCTAGGT 58.146 55.000 0.00 0.00 0.00 3.08
336 360 4.123506 GTGGAGAAGACTAAGCAATAGGC 58.876 47.826 2.18 0.00 40.28 3.93
337 361 4.443598 GGGTGGAGAAGACTAAGCAATAGG 60.444 50.000 2.18 0.00 35.81 2.57
338 362 4.162320 TGGGTGGAGAAGACTAAGCAATAG 59.838 45.833 0.00 0.00 37.66 1.73
386 411 0.597118 TGTGTGTTGGGCGTACGTAC 60.597 55.000 17.90 15.90 0.00 3.67
387 412 0.597118 GTGTGTGTTGGGCGTACGTA 60.597 55.000 17.90 0.79 0.00 3.57
427 459 2.292016 ACGATGAGGACGATGATGAGAC 59.708 50.000 0.00 0.00 34.70 3.36
428 460 2.550180 GACGATGAGGACGATGATGAGA 59.450 50.000 0.00 0.00 34.70 3.27
429 461 2.664151 CGACGATGAGGACGATGATGAG 60.664 54.545 0.00 0.00 34.70 2.90
523 561 4.418401 TACGTACGGGTGCGGTGC 62.418 66.667 21.06 0.00 42.92 5.01
533 582 2.504681 GGCGTGGTGGTACGTACG 60.505 66.667 18.98 15.01 45.36 3.67
534 583 2.504681 CGGCGTGGTGGTACGTAC 60.505 66.667 17.56 17.56 45.36 3.67
535 584 4.418401 GCGGCGTGGTGGTACGTA 62.418 66.667 9.37 0.00 45.36 3.57
661 719 1.002366 CTGTCATGGCTTACGTCAGC 58.998 55.000 13.37 13.37 39.28 4.26
869 931 8.994429 TCTACTGCTAATTCTTTCTTCTCTTG 57.006 34.615 0.00 0.00 0.00 3.02
875 939 9.950496 TCTGAATTCTACTGCTAATTCTTTCTT 57.050 29.630 7.05 0.00 40.92 2.52
880 944 6.882656 TGCTCTGAATTCTACTGCTAATTCT 58.117 36.000 7.05 0.00 40.92 2.40
884 948 4.081476 TGCTGCTCTGAATTCTACTGCTAA 60.081 41.667 7.05 0.00 0.00 3.09
907 977 1.380403 ATCGCTCACTCGCTGCTACT 61.380 55.000 0.00 0.00 0.00 2.57
909 979 0.588737 CTATCGCTCACTCGCTGCTA 59.411 55.000 0.00 0.00 0.00 3.49
915 985 3.242903 ACTGTGATTCTATCGCTCACTCG 60.243 47.826 3.86 0.00 39.94 4.18
916 986 4.041049 CACTGTGATTCTATCGCTCACTC 58.959 47.826 0.32 0.00 39.94 3.51
917 987 3.696548 TCACTGTGATTCTATCGCTCACT 59.303 43.478 6.36 0.00 39.94 3.41
918 988 4.033990 TCACTGTGATTCTATCGCTCAC 57.966 45.455 6.36 0.00 40.37 3.51
919 989 3.067320 CCTCACTGTGATTCTATCGCTCA 59.933 47.826 11.45 0.00 40.37 4.26
920 990 3.637432 CCTCACTGTGATTCTATCGCTC 58.363 50.000 11.45 0.00 40.37 5.03
931 1014 1.112916 TCCAACGAGCCTCACTGTGA 61.113 55.000 10.50 10.50 0.00 3.58
932 1015 0.036952 ATCCAACGAGCCTCACTGTG 60.037 55.000 0.17 0.17 0.00 3.66
937 1020 4.012138 TCGATCCAACGAGCCTCA 57.988 55.556 0.00 0.00 37.37 3.86
944 1027 1.759994 CGAATCTCCTCGATCCAACG 58.240 55.000 0.00 0.00 41.44 4.10
954 1037 1.388065 CCTCCTCACGCGAATCTCCT 61.388 60.000 15.93 0.00 0.00 3.69
955 1038 1.066587 CCTCCTCACGCGAATCTCC 59.933 63.158 15.93 0.00 0.00 3.71
958 1041 2.586357 GGCCTCCTCACGCGAATC 60.586 66.667 15.93 0.00 0.00 2.52
959 1042 4.514577 CGGCCTCCTCACGCGAAT 62.515 66.667 15.93 0.00 0.00 3.34
962 1045 3.133767 TAATCGGCCTCCTCACGCG 62.134 63.158 3.53 3.53 0.00 6.01
963 1046 1.300233 CTAATCGGCCTCCTCACGC 60.300 63.158 0.00 0.00 0.00 5.34
964 1047 1.300233 GCTAATCGGCCTCCTCACG 60.300 63.158 0.00 0.00 0.00 4.35
965 1048 4.760757 GCTAATCGGCCTCCTCAC 57.239 61.111 0.00 0.00 0.00 3.51
973 1056 1.733399 GATCGGTCGGCTAATCGGC 60.733 63.158 0.00 0.00 0.00 5.54
974 1057 1.442184 CGATCGGTCGGCTAATCGG 60.442 63.158 11.03 0.34 44.00 4.18
975 1058 4.132426 CGATCGGTCGGCTAATCG 57.868 61.111 11.03 9.47 44.00 3.34
987 1070 1.081774 GCTCATCTCCGGTCGATCG 60.082 63.158 12.09 12.09 0.00 3.69
1071 1154 3.760035 CGGCGGCAGAGGTAGTGT 61.760 66.667 10.53 0.00 0.00 3.55
1196 1279 9.273016 AGATTAAAACATATAACTGGACGGATG 57.727 33.333 0.00 0.00 0.00 3.51
1239 1346 0.108472 TCTGCAAGCAGATCACGAGG 60.108 55.000 20.00 0.00 46.80 4.63
1252 1360 0.740868 GTACAGCGCCATCTCTGCAA 60.741 55.000 2.29 0.00 33.80 4.08
1645 2060 8.708742 TGGAAATATCGCACTAAAATATCTTCG 58.291 33.333 0.00 0.00 0.00 3.79
1647 2062 8.495949 CGTGGAAATATCGCACTAAAATATCTT 58.504 33.333 0.00 0.00 0.00 2.40
1796 2235 1.796617 GCGAATCATTGAGCAAGTGGC 60.797 52.381 0.00 0.00 45.30 5.01
1797 2236 1.530441 CGCGAATCATTGAGCAAGTGG 60.530 52.381 0.00 0.00 0.00 4.00
1798 2237 1.806511 CGCGAATCATTGAGCAAGTG 58.193 50.000 0.00 0.00 0.00 3.16
1843 2290 3.245122 TGGGTCCATAAACTGAAAGGGAC 60.245 47.826 0.00 0.00 38.90 4.46
1869 2316 2.513204 CTCCCATGGCTGCACGAG 60.513 66.667 6.09 2.35 0.00 4.18
1919 2372 0.386985 GCTATCTACCGGTACAGCGC 60.387 60.000 11.16 7.78 0.00 5.92
1935 2388 2.108514 GCCAGTTGCTGCGATGCTA 61.109 57.895 0.00 0.00 36.87 3.49
1942 2395 3.426568 GAGTCGGCCAGTTGCTGC 61.427 66.667 2.24 0.00 46.56 5.25
1986 2439 5.803461 CGAAGTACACCAGTCGAATCATTTA 59.197 40.000 0.00 0.00 35.54 1.40
2006 2461 1.322637 CGCAGATCACACATGACGAAG 59.677 52.381 0.00 0.00 37.79 3.79
2025 2480 4.143835 CAAACATGTCAGACAAACGATCG 58.856 43.478 14.88 14.88 0.00 3.69
2050 2505 2.028130 TCCAACTGCACCGAACAAAAT 58.972 42.857 0.00 0.00 0.00 1.82
2059 2514 0.819582 CCCAATCATCCAACTGCACC 59.180 55.000 0.00 0.00 0.00 5.01
2737 3282 1.233950 TTTGGCGCACGTCATGTCAT 61.234 50.000 10.83 0.00 0.00 3.06
2747 3292 0.039256 TTGAAGCATCTTTGGCGCAC 60.039 50.000 10.83 0.00 36.08 5.34
2748 3293 0.672889 TTTGAAGCATCTTTGGCGCA 59.327 45.000 10.83 0.00 36.08 6.09
2749 3294 1.343506 CTTTGAAGCATCTTTGGCGC 58.656 50.000 0.00 0.00 36.08 6.53
2826 3374 4.779696 TCCATATACACACACACATGCAT 58.220 39.130 0.00 0.00 0.00 3.96
2828 3376 4.023792 CCATCCATATACACACACACATGC 60.024 45.833 0.00 0.00 0.00 4.06
2829 3377 4.516321 CCCATCCATATACACACACACATG 59.484 45.833 0.00 0.00 0.00 3.21
2830 3378 4.165950 ACCCATCCATATACACACACACAT 59.834 41.667 0.00 0.00 0.00 3.21
2831 3379 3.521531 ACCCATCCATATACACACACACA 59.478 43.478 0.00 0.00 0.00 3.72
2832 3380 3.876914 CACCCATCCATATACACACACAC 59.123 47.826 0.00 0.00 0.00 3.82
2833 3381 3.521531 ACACCCATCCATATACACACACA 59.478 43.478 0.00 0.00 0.00 3.72
2834 3382 4.150897 ACACCCATCCATATACACACAC 57.849 45.455 0.00 0.00 0.00 3.82
2835 3383 4.717280 TGTACACCCATCCATATACACACA 59.283 41.667 0.00 0.00 0.00 3.72
2836 3384 5.284861 TGTACACCCATCCATATACACAC 57.715 43.478 0.00 0.00 0.00 3.82
2837 3385 6.555360 TGTATGTACACCCATCCATATACACA 59.445 38.462 0.00 0.00 0.00 3.72
2899 3449 4.082571 CCCTTGCAACTAACCAATCAAGAG 60.083 45.833 0.00 0.00 34.49 2.85
2993 3625 3.161866 GTGGAGGGGCAAGAACAATAAA 58.838 45.455 0.00 0.00 0.00 1.40
2997 3629 0.555769 AAGTGGAGGGGCAAGAACAA 59.444 50.000 0.00 0.00 0.00 2.83
2998 3630 0.178992 CAAGTGGAGGGGCAAGAACA 60.179 55.000 0.00 0.00 0.00 3.18
2999 3631 1.527433 GCAAGTGGAGGGGCAAGAAC 61.527 60.000 0.00 0.00 0.00 3.01
3025 3657 4.787598 CCACGGAGAATTTTTCTTGACAG 58.212 43.478 0.00 0.00 40.87 3.51
3027 3659 3.253432 AGCCACGGAGAATTTTTCTTGAC 59.747 43.478 0.00 0.00 40.87 3.18
3061 3693 2.835701 GATCACCAACCGCAGCTCGA 62.836 60.000 7.07 0.00 41.67 4.04
3063 3695 1.078848 AGATCACCAACCGCAGCTC 60.079 57.895 0.00 0.00 0.00 4.09
3064 3696 1.078848 GAGATCACCAACCGCAGCT 60.079 57.895 0.00 0.00 0.00 4.24
3065 3697 2.109126 GGAGATCACCAACCGCAGC 61.109 63.158 4.05 0.00 0.00 5.25
3066 3698 1.811266 CGGAGATCACCAACCGCAG 60.811 63.158 9.99 0.00 38.98 5.18
3067 3699 2.264480 CGGAGATCACCAACCGCA 59.736 61.111 9.99 0.00 38.98 5.69
3068 3700 2.511600 CCGGAGATCACCAACCGC 60.512 66.667 9.99 0.00 43.37 5.68
3069 3701 1.141881 CTCCGGAGATCACCAACCG 59.858 63.158 28.21 8.72 44.16 4.44
3070 3702 0.902531 TTCTCCGGAGATCACCAACC 59.097 55.000 33.97 0.00 37.29 3.77
3071 3703 2.762535 TTTCTCCGGAGATCACCAAC 57.237 50.000 33.97 0.00 37.29 3.77
3072 3704 3.780804 TTTTTCTCCGGAGATCACCAA 57.219 42.857 33.97 21.76 37.29 3.67
3093 3726 7.121168 CCAAGAATATCACTGTTTACACACCAT 59.879 37.037 0.00 0.00 0.00 3.55
3146 3780 1.015109 CTAGCTAGCGTCGGTGAAGA 58.985 55.000 8.05 0.00 0.00 2.87
3158 3792 2.656651 CCGCGTGCAGCTAGCTAG 60.657 66.667 18.86 16.84 45.94 3.42
3175 3813 1.566298 AATCTCCCCCACAGCTGGAC 61.566 60.000 19.93 0.00 40.55 4.02
3194 3832 2.414559 CGTTTCCTCCGTACGAAAGCTA 60.415 50.000 18.76 2.24 37.47 3.32
3280 3918 3.304458 CCAAGGTTAAAAGTCCGCTCAAC 60.304 47.826 0.00 0.00 0.00 3.18
3287 3925 2.031420 GTGCGTCCAAGGTTAAAAGTCC 60.031 50.000 0.00 0.00 0.00 3.85
3488 4660 2.227089 GACGGGTGAGCCTTGACGAT 62.227 60.000 0.00 0.00 34.45 3.73
3489 4661 2.915659 ACGGGTGAGCCTTGACGA 60.916 61.111 0.00 0.00 34.45 4.20
3505 4677 1.067582 CGGGAATAGTCTGGCGGAC 59.932 63.158 18.84 18.84 44.80 4.79


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

AutoCloner maintained by Alex Coulton.