Multiple sequence alignment - TraesCS2D01G368400

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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 TraesCS2D01G368400 chr2D 100.000 3026 0 0 1 3026 473089015 473085990 0.000000e+00 5589.0
1 TraesCS2D01G368400 chr2A 94.361 2341 83 17 700 3026 614523651 614521346 0.000000e+00 3546.0
2 TraesCS2D01G368400 chr2A 86.403 581 53 12 70 629 614568928 614568353 1.990000e-171 612.0
3 TraesCS2D01G368400 chr2A 84.407 295 32 7 161 441 63358452 63358746 8.260000e-71 278.0
4 TraesCS2D01G368400 chr2A 100.000 43 0 0 769 811 63359127 63359169 2.500000e-11 80.5
5 TraesCS2D01G368400 chr2B 93.182 2244 80 24 565 2776 552341487 552339285 0.000000e+00 3229.0
6 TraesCS2D01G368400 chr2B 88.686 274 12 6 2768 3026 552339133 552338864 1.750000e-82 316.0
7 TraesCS2D01G368400 chr2B 85.167 209 19 5 223 419 97951037 97951245 1.420000e-48 204.0
8 TraesCS2D01G368400 chr7B 78.323 632 119 18 1355 1977 119700871 119701493 2.830000e-105 392.0
9 TraesCS2D01G368400 chr4D 75.826 666 127 28 1327 1978 328185284 328184639 1.050000e-79 307.0


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 TraesCS2D01G368400 chr2D 473085990 473089015 3025 True 5589.0 5589 100.000 1 3026 1 chr2D.!!$R1 3025
1 TraesCS2D01G368400 chr2A 614521346 614523651 2305 True 3546.0 3546 94.361 700 3026 1 chr2A.!!$R1 2326
2 TraesCS2D01G368400 chr2A 614568353 614568928 575 True 612.0 612 86.403 70 629 1 chr2A.!!$R2 559
3 TraesCS2D01G368400 chr2B 552338864 552341487 2623 True 1772.5 3229 90.934 565 3026 2 chr2B.!!$R1 2461
4 TraesCS2D01G368400 chr7B 119700871 119701493 622 False 392.0 392 78.323 1355 1977 1 chr7B.!!$F1 622
5 TraesCS2D01G368400 chr4D 328184639 328185284 645 True 307.0 307 75.826 1327 1978 1 chr4D.!!$R1 651

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
66 67 0.034059 AGTCGTAGCTGCAGTTTGCT 59.966 50.0 16.64 9.62 45.31 3.91 F
338 346 0.040958 GGAGCTTGCACTTTGTGTCG 60.041 55.0 0.00 0.00 35.75 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1593 1631 0.748729 CGAAGACGGAGGAGTAGGCT 60.749 60.0 0.0 0.0 35.72 4.58 R
2040 2087 1.004277 GACTTGTCACTCCAGCGACG 61.004 60.0 0.0 0.0 34.78 5.12 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
17 18 2.040359 GAGGGGAGGGGAGGAAGG 60.040 72.222 0.00 0.00 0.00 3.46
18 19 2.543637 AGGGGAGGGGAGGAAGGA 60.544 66.667 0.00 0.00 0.00 3.36
19 20 2.040359 GGGGAGGGGAGGAAGGAG 60.040 72.222 0.00 0.00 0.00 3.69
20 21 2.770475 GGGAGGGGAGGAAGGAGC 60.770 72.222 0.00 0.00 0.00 4.70
21 22 3.157949 GGAGGGGAGGAAGGAGCG 61.158 72.222 0.00 0.00 0.00 5.03
22 23 2.042843 GAGGGGAGGAAGGAGCGA 60.043 66.667 0.00 0.00 0.00 4.93
23 24 2.042435 AGGGGAGGAAGGAGCGAG 60.042 66.667 0.00 0.00 0.00 5.03
24 25 3.157949 GGGGAGGAAGGAGCGAGG 61.158 72.222 0.00 0.00 0.00 4.63
25 26 2.364448 GGGAGGAAGGAGCGAGGT 60.364 66.667 0.00 0.00 0.00 3.85
26 27 2.726351 GGGAGGAAGGAGCGAGGTG 61.726 68.421 0.00 0.00 0.00 4.00
27 28 2.726351 GGAGGAAGGAGCGAGGTGG 61.726 68.421 0.00 0.00 0.00 4.61
28 29 1.985116 GAGGAAGGAGCGAGGTGGT 60.985 63.158 0.00 0.00 0.00 4.16
29 30 2.232298 GAGGAAGGAGCGAGGTGGTG 62.232 65.000 0.00 0.00 0.00 4.17
30 31 2.283529 GGAAGGAGCGAGGTGGTGA 61.284 63.158 0.00 0.00 0.00 4.02
31 32 1.079750 GAAGGAGCGAGGTGGTGAC 60.080 63.158 0.00 0.00 0.00 3.67
32 33 1.816863 GAAGGAGCGAGGTGGTGACA 61.817 60.000 0.00 0.00 38.70 3.58
33 34 1.407656 AAGGAGCGAGGTGGTGACAA 61.408 55.000 0.00 0.00 46.06 3.18
50 51 4.003519 GACAACATATTGGCGTGAAGTC 57.996 45.455 0.00 0.00 40.42 3.01
51 52 2.415168 ACAACATATTGGCGTGAAGTCG 59.585 45.455 0.00 0.00 40.42 4.18
52 53 2.380084 ACATATTGGCGTGAAGTCGT 57.620 45.000 0.00 0.00 0.00 4.34
53 54 3.513680 ACATATTGGCGTGAAGTCGTA 57.486 42.857 0.00 0.00 0.00 3.43
54 55 3.444916 ACATATTGGCGTGAAGTCGTAG 58.555 45.455 0.00 0.00 0.00 3.51
55 56 1.917273 TATTGGCGTGAAGTCGTAGC 58.083 50.000 0.00 0.00 0.00 3.58
56 57 0.246635 ATTGGCGTGAAGTCGTAGCT 59.753 50.000 0.00 0.00 0.00 3.32
57 58 0.666274 TTGGCGTGAAGTCGTAGCTG 60.666 55.000 0.00 0.00 0.00 4.24
58 59 2.445438 GGCGTGAAGTCGTAGCTGC 61.445 63.158 0.00 0.00 0.00 5.25
59 60 1.733041 GCGTGAAGTCGTAGCTGCA 60.733 57.895 1.02 0.00 0.00 4.41
60 61 1.678269 GCGTGAAGTCGTAGCTGCAG 61.678 60.000 10.11 10.11 0.00 4.41
61 62 0.387367 CGTGAAGTCGTAGCTGCAGT 60.387 55.000 16.64 4.79 0.00 4.40
62 63 1.784525 GTGAAGTCGTAGCTGCAGTT 58.215 50.000 16.64 12.62 0.00 3.16
63 64 2.135933 GTGAAGTCGTAGCTGCAGTTT 58.864 47.619 16.64 6.84 0.00 2.66
64 65 2.096713 GTGAAGTCGTAGCTGCAGTTTG 60.097 50.000 16.64 5.87 0.00 2.93
65 66 0.868406 AAGTCGTAGCTGCAGTTTGC 59.132 50.000 16.64 6.96 45.29 3.68
66 67 0.034059 AGTCGTAGCTGCAGTTTGCT 59.966 50.000 16.64 9.62 45.31 3.91
67 68 0.164647 GTCGTAGCTGCAGTTTGCTG 59.835 55.000 16.64 3.23 45.31 4.41
68 69 0.950555 TCGTAGCTGCAGTTTGCTGG 60.951 55.000 16.64 4.11 45.31 4.85
69 70 1.878775 GTAGCTGCAGTTTGCTGGG 59.121 57.895 16.64 0.00 45.31 4.45
70 71 1.973281 TAGCTGCAGTTTGCTGGGC 60.973 57.895 16.64 0.00 45.31 5.36
71 72 2.695520 TAGCTGCAGTTTGCTGGGCA 62.696 55.000 16.64 0.00 45.31 5.36
72 73 2.939261 GCTGCAGTTTGCTGGGCAT 61.939 57.895 16.64 0.00 45.31 4.40
102 103 4.842531 TCAACTATGACACATGATGGGT 57.157 40.909 0.00 0.00 36.19 4.51
115 116 1.065998 TGATGGGTGGCGTAAAGGTAC 60.066 52.381 0.00 0.00 0.00 3.34
127 128 5.390567 GGCGTAAAGGTACAATGTTTCTCTG 60.391 44.000 0.00 0.00 0.00 3.35
129 130 6.092259 GCGTAAAGGTACAATGTTTCTCTGAT 59.908 38.462 0.00 0.00 0.00 2.90
157 158 2.705658 TGGTGGATGAAGTCAGAGTTGT 59.294 45.455 0.00 0.00 0.00 3.32
161 162 3.511540 TGGATGAAGTCAGAGTTGTCGAT 59.488 43.478 0.00 0.00 0.00 3.59
164 165 2.029020 TGAAGTCAGAGTTGTCGATGGG 60.029 50.000 0.00 0.00 0.00 4.00
165 166 0.247736 AGTCAGAGTTGTCGATGGGC 59.752 55.000 0.00 0.00 0.00 5.36
186 187 3.500982 CGGCAATGTTTAGGATGTGTTG 58.499 45.455 0.00 0.00 0.00 3.33
194 195 1.917872 TAGGATGTGTTGGTTTGGGC 58.082 50.000 0.00 0.00 0.00 5.36
196 197 1.427368 AGGATGTGTTGGTTTGGGCTA 59.573 47.619 0.00 0.00 0.00 3.93
200 201 2.513753 TGTGTTGGTTTGGGCTATCTG 58.486 47.619 0.00 0.00 0.00 2.90
202 203 1.272425 TGTTGGTTTGGGCTATCTGGG 60.272 52.381 0.00 0.00 0.00 4.45
205 206 1.431243 TGGTTTGGGCTATCTGGGTTT 59.569 47.619 0.00 0.00 0.00 3.27
207 208 2.556559 GGTTTGGGCTATCTGGGTTTGA 60.557 50.000 0.00 0.00 0.00 2.69
213 221 4.202461 TGGGCTATCTGGGTTTGATATGAC 60.202 45.833 0.00 0.00 0.00 3.06
214 222 4.202461 GGGCTATCTGGGTTTGATATGACA 60.202 45.833 0.00 0.00 0.00 3.58
217 225 6.072286 GGCTATCTGGGTTTGATATGACATTG 60.072 42.308 0.00 0.00 0.00 2.82
220 228 7.722949 ATCTGGGTTTGATATGACATTGTTT 57.277 32.000 0.00 0.00 0.00 2.83
245 253 0.464373 CATGCCGGTGGTGCTAAGAT 60.464 55.000 1.90 0.00 0.00 2.40
257 265 3.701205 TGCTAAGATGTGGAGCAAGAA 57.299 42.857 0.00 0.00 43.03 2.52
262 270 1.556911 AGATGTGGAGCAAGAATCGGT 59.443 47.619 0.00 0.00 0.00 4.69
273 281 0.323542 AGAATCGGTGAGTCGAGGGT 60.324 55.000 0.00 0.00 42.69 4.34
274 282 0.179134 GAATCGGTGAGTCGAGGGTG 60.179 60.000 0.00 0.00 42.69 4.61
290 298 0.309922 GGTGCTTGATGATGATGGCG 59.690 55.000 0.00 0.00 0.00 5.69
308 316 1.001624 CGATGACGCTGATGAGCAAA 58.998 50.000 4.68 0.00 46.62 3.68
317 325 2.737679 GCTGATGAGCAAAATTGAGGGC 60.738 50.000 0.00 0.00 45.46 5.19
335 343 0.318445 GCTGGAGCTTGCACTTTGTG 60.318 55.000 0.00 0.00 38.21 3.33
338 346 0.040958 GGAGCTTGCACTTTGTGTCG 60.041 55.000 0.00 0.00 35.75 4.35
359 367 0.310854 GTTTGGCTTGTTCGGGTCTG 59.689 55.000 0.00 0.00 0.00 3.51
363 371 1.891919 GCTTGTTCGGGTCTGTGCA 60.892 57.895 0.00 0.00 0.00 4.57
365 373 0.249868 CTTGTTCGGGTCTGTGCAGA 60.250 55.000 0.00 0.00 34.56 4.26
367 375 1.367840 GTTCGGGTCTGTGCAGAGT 59.632 57.895 11.09 0.00 38.27 3.24
379 387 0.181114 TGCAGAGTCTGGCTTGTTGT 59.819 50.000 21.54 0.00 31.21 3.32
431 439 8.708742 GGTTTTTGCTAATTAATTGGACAACTC 58.291 33.333 15.09 10.11 0.00 3.01
445 453 4.574828 TGGACAACTCTCTTGTGCTTTAAC 59.425 41.667 6.32 0.00 40.69 2.01
447 455 3.560068 ACAACTCTCTTGTGCTTTAACGG 59.440 43.478 0.00 0.00 0.00 4.44
453 461 3.811083 TCTTGTGCTTTAACGGAAAGGA 58.189 40.909 12.37 7.89 44.21 3.36
501 509 6.711277 ACTCTCATGTGCTCAATTAACCTAA 58.289 36.000 0.00 0.00 0.00 2.69
550 558 1.661112 CTTGTGCGAGCCTTACTAAGC 59.339 52.381 0.00 0.00 33.92 3.09
551 559 0.895530 TGTGCGAGCCTTACTAAGCT 59.104 50.000 0.00 0.00 43.55 3.74
552 560 1.275291 TGTGCGAGCCTTACTAAGCTT 59.725 47.619 3.48 3.48 40.11 3.74
554 562 1.201343 GCGAGCCTTACTAAGCTTCG 58.799 55.000 0.00 0.00 40.11 3.79
556 564 1.536284 CGAGCCTTACTAAGCTTCGGG 60.536 57.143 0.00 0.38 40.11 5.14
557 565 0.178301 AGCCTTACTAAGCTTCGGGC 59.822 55.000 0.00 10.79 35.22 6.13
569 590 1.533625 CTTCGGGCTGAACCAAATCA 58.466 50.000 4.22 0.00 42.05 2.57
636 657 1.082169 GCACGCAAAGATCACGCAA 60.082 52.632 0.00 0.00 0.00 4.85
640 661 1.866237 GCAAAGATCACGCAACCGA 59.134 52.632 0.00 0.00 38.29 4.69
692 713 3.462678 GTCTCGTCTGCCTCCCCC 61.463 72.222 0.00 0.00 0.00 5.40
693 714 3.673597 TCTCGTCTGCCTCCCCCT 61.674 66.667 0.00 0.00 0.00 4.79
694 715 3.151022 CTCGTCTGCCTCCCCCTC 61.151 72.222 0.00 0.00 0.00 4.30
695 716 4.779733 TCGTCTGCCTCCCCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
696 717 4.787280 CGTCTGCCTCCCCCTCCT 62.787 72.222 0.00 0.00 0.00 3.69
697 718 2.285743 GTCTGCCTCCCCCTCCTT 60.286 66.667 0.00 0.00 0.00 3.36
698 719 2.041265 TCTGCCTCCCCCTCCTTC 59.959 66.667 0.00 0.00 0.00 3.46
707 728 3.148279 CCCTCCTTCCCCGTCGAG 61.148 72.222 0.00 0.00 0.00 4.04
721 742 1.531264 CGTCGAGATCGTAACCACCAG 60.531 57.143 1.70 0.00 40.80 4.00
726 748 0.824759 GATCGTAACCACCAGAGCCT 59.175 55.000 0.00 0.00 0.00 4.58
853 876 1.134699 CCGCCTCTTAACTCTGCATCA 60.135 52.381 0.00 0.00 0.00 3.07
929 952 1.446016 CCCCCTCCCCGATTCTTTAT 58.554 55.000 0.00 0.00 0.00 1.40
931 954 1.351350 CCCCTCCCCGATTCTTTATCC 59.649 57.143 0.00 0.00 0.00 2.59
2061 2111 0.750249 TCGCTGGAGTGACAAGTCAA 59.250 50.000 4.20 0.00 41.85 3.18
2160 2210 3.000819 TCGGTGTAGGGGCAGTGG 61.001 66.667 0.00 0.00 0.00 4.00
2195 2245 4.039092 CCTGGTGGCCTCACAGGG 62.039 72.222 24.58 10.03 45.32 4.45
2476 2539 1.202325 CGTGCTACTATAACACCGCCA 60.202 52.381 0.00 0.00 0.00 5.69
2503 2566 6.709018 AATAATCGAGGGGGTATTTTTGTG 57.291 37.500 0.00 0.00 0.00 3.33
2525 2588 2.227626 TGCATGTTTTCGGTGGTGTATG 59.772 45.455 0.00 0.00 0.00 2.39
2529 2592 2.873472 TGTTTTCGGTGGTGTATGTCAC 59.127 45.455 0.00 0.00 45.47 3.67
2579 2646 5.059710 GTGTCAAGTGCATTTCTTAATTCGC 59.940 40.000 0.00 0.00 0.00 4.70
2594 2661 2.586258 TTCGCTGAGAGCAGATAACC 57.414 50.000 0.00 0.00 45.17 2.85
2659 2726 1.043116 TCAGGAATCTGATCCGGCGT 61.043 55.000 6.01 0.00 44.39 5.68
2660 2727 0.179073 CAGGAATCTGATCCGGCGTT 60.179 55.000 6.01 0.00 44.60 4.84
2661 2728 0.541863 AGGAATCTGATCCGGCGTTT 59.458 50.000 6.01 0.00 44.60 3.60
2662 2729 0.938008 GGAATCTGATCCGGCGTTTC 59.062 55.000 6.01 2.46 0.00 2.78
2663 2730 0.938008 GAATCTGATCCGGCGTTTCC 59.062 55.000 6.01 0.00 0.00 3.13
2664 2731 0.463833 AATCTGATCCGGCGTTTCCC 60.464 55.000 6.01 0.00 0.00 3.97
2703 2770 2.046285 GTTGATGGGCCCTGAACGG 61.046 63.158 25.70 0.00 0.00 4.44
2765 2832 3.626924 AAGTGCTCGGGCGGAACT 61.627 61.111 1.14 0.00 42.25 3.01
2878 3120 2.067013 CTCGGTCGGTTTCTTCCTTTC 58.933 52.381 0.00 0.00 0.00 2.62
2906 3150 1.069668 GTTACTGTCTCCGGTTGGTGT 59.930 52.381 0.00 0.00 36.30 4.16
2960 3205 3.059935 TGTTGTGAATGATGTTGTCGTCG 60.060 43.478 0.00 0.00 32.69 5.12
2962 3207 2.066262 GTGAATGATGTTGTCGTCGGT 58.934 47.619 0.00 0.00 32.69 4.69
2979 3224 1.658409 GTCGTTGGCTTTGTGCAGC 60.658 57.895 0.00 0.00 45.15 5.25
3015 3260 1.215647 CGAGGAGTACAGCCACACC 59.784 63.158 7.43 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.543637 TCCTTCCTCCCCTCCCCT 60.544 66.667 0.00 0.00 0.00 4.79
2 3 2.040359 CTCCTTCCTCCCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
3 4 2.770475 GCTCCTTCCTCCCCTCCC 60.770 72.222 0.00 0.00 0.00 4.30
4 5 3.157949 CGCTCCTTCCTCCCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
5 6 2.042843 TCGCTCCTTCCTCCCCTC 60.043 66.667 0.00 0.00 0.00 4.30
6 7 2.042435 CTCGCTCCTTCCTCCCCT 60.042 66.667 0.00 0.00 0.00 4.79
7 8 3.157949 CCTCGCTCCTTCCTCCCC 61.158 72.222 0.00 0.00 0.00 4.81
8 9 2.364448 ACCTCGCTCCTTCCTCCC 60.364 66.667 0.00 0.00 0.00 4.30
9 10 2.726351 CCACCTCGCTCCTTCCTCC 61.726 68.421 0.00 0.00 0.00 4.30
10 11 1.985116 ACCACCTCGCTCCTTCCTC 60.985 63.158 0.00 0.00 0.00 3.71
11 12 2.120718 ACCACCTCGCTCCTTCCT 59.879 61.111 0.00 0.00 0.00 3.36
12 13 2.266055 CACCACCTCGCTCCTTCC 59.734 66.667 0.00 0.00 0.00 3.46
13 14 1.079750 GTCACCACCTCGCTCCTTC 60.080 63.158 0.00 0.00 0.00 3.46
14 15 1.407656 TTGTCACCACCTCGCTCCTT 61.408 55.000 0.00 0.00 0.00 3.36
15 16 1.837051 TTGTCACCACCTCGCTCCT 60.837 57.895 0.00 0.00 0.00 3.69
16 17 1.668151 GTTGTCACCACCTCGCTCC 60.668 63.158 0.00 0.00 0.00 4.70
17 18 0.320771 ATGTTGTCACCACCTCGCTC 60.321 55.000 0.00 0.00 0.00 5.03
18 19 0.973632 TATGTTGTCACCACCTCGCT 59.026 50.000 0.00 0.00 0.00 4.93
19 20 2.024176 ATATGTTGTCACCACCTCGC 57.976 50.000 0.00 0.00 0.00 5.03
20 21 2.677836 CCAATATGTTGTCACCACCTCG 59.322 50.000 1.26 0.00 33.36 4.63
21 22 2.423538 GCCAATATGTTGTCACCACCTC 59.576 50.000 1.26 0.00 33.36 3.85
22 23 2.446435 GCCAATATGTTGTCACCACCT 58.554 47.619 1.26 0.00 33.36 4.00
23 24 1.132262 CGCCAATATGTTGTCACCACC 59.868 52.381 1.26 0.00 33.36 4.61
24 25 1.810151 ACGCCAATATGTTGTCACCAC 59.190 47.619 1.26 0.00 33.36 4.16
25 26 1.809547 CACGCCAATATGTTGTCACCA 59.190 47.619 1.26 0.00 33.36 4.17
26 27 2.080693 TCACGCCAATATGTTGTCACC 58.919 47.619 1.26 0.00 33.36 4.02
27 28 3.188460 ACTTCACGCCAATATGTTGTCAC 59.812 43.478 1.26 0.00 33.36 3.67
28 29 3.407698 ACTTCACGCCAATATGTTGTCA 58.592 40.909 1.26 0.00 33.36 3.58
29 30 3.483574 CGACTTCACGCCAATATGTTGTC 60.484 47.826 1.26 0.00 33.36 3.18
30 31 2.415168 CGACTTCACGCCAATATGTTGT 59.585 45.455 1.26 0.00 33.36 3.32
31 32 2.415168 ACGACTTCACGCCAATATGTTG 59.585 45.455 0.00 0.00 36.70 3.33
32 33 2.695359 ACGACTTCACGCCAATATGTT 58.305 42.857 0.00 0.00 36.70 2.71
33 34 2.380084 ACGACTTCACGCCAATATGT 57.620 45.000 0.00 0.00 36.70 2.29
34 35 2.218759 GCTACGACTTCACGCCAATATG 59.781 50.000 0.00 0.00 36.70 1.78
35 36 2.100916 AGCTACGACTTCACGCCAATAT 59.899 45.455 0.00 0.00 36.70 1.28
36 37 1.475280 AGCTACGACTTCACGCCAATA 59.525 47.619 0.00 0.00 36.70 1.90
37 38 0.246635 AGCTACGACTTCACGCCAAT 59.753 50.000 0.00 0.00 36.70 3.16
38 39 0.666274 CAGCTACGACTTCACGCCAA 60.666 55.000 0.00 0.00 36.70 4.52
39 40 1.080772 CAGCTACGACTTCACGCCA 60.081 57.895 0.00 0.00 36.70 5.69
40 41 2.445438 GCAGCTACGACTTCACGCC 61.445 63.158 0.00 0.00 36.70 5.68
41 42 1.678269 CTGCAGCTACGACTTCACGC 61.678 60.000 0.00 0.00 36.70 5.34
42 43 0.387367 ACTGCAGCTACGACTTCACG 60.387 55.000 15.27 0.00 39.31 4.35
43 44 1.784525 AACTGCAGCTACGACTTCAC 58.215 50.000 15.27 0.00 0.00 3.18
44 45 2.135139 CAAACTGCAGCTACGACTTCA 58.865 47.619 15.27 0.00 0.00 3.02
45 46 1.136224 GCAAACTGCAGCTACGACTTC 60.136 52.381 15.27 0.00 44.26 3.01
46 47 0.868406 GCAAACTGCAGCTACGACTT 59.132 50.000 15.27 0.00 44.26 3.01
47 48 2.533318 GCAAACTGCAGCTACGACT 58.467 52.632 15.27 0.00 44.26 4.18
57 58 1.080298 GTCATGCCCAGCAAACTGC 60.080 57.895 0.00 0.00 43.62 4.40
58 59 0.675083 TTGTCATGCCCAGCAAACTG 59.325 50.000 0.00 0.00 43.62 3.16
59 60 0.963962 CTTGTCATGCCCAGCAAACT 59.036 50.000 0.00 0.00 43.62 2.66
60 61 0.675633 ACTTGTCATGCCCAGCAAAC 59.324 50.000 0.00 0.00 43.62 2.93
61 62 0.675083 CACTTGTCATGCCCAGCAAA 59.325 50.000 0.00 0.00 43.62 3.68
62 63 0.467844 ACACTTGTCATGCCCAGCAA 60.468 50.000 0.00 0.00 43.62 3.91
63 64 0.890542 GACACTTGTCATGCCCAGCA 60.891 55.000 4.43 0.00 44.18 4.41
64 65 1.878775 GACACTTGTCATGCCCAGC 59.121 57.895 4.43 0.00 44.18 4.85
84 85 2.421952 GCCACCCATCATGTGTCATAGT 60.422 50.000 0.00 0.00 31.71 2.12
86 87 1.474855 CGCCACCCATCATGTGTCATA 60.475 52.381 0.00 0.00 31.71 2.15
97 98 0.985760 TGTACCTTTACGCCACCCAT 59.014 50.000 0.00 0.00 0.00 4.00
101 102 4.214758 AGAAACATTGTACCTTTACGCCAC 59.785 41.667 0.00 0.00 0.00 5.01
102 103 4.391155 AGAAACATTGTACCTTTACGCCA 58.609 39.130 0.00 0.00 0.00 5.69
115 116 7.080099 CACCACAAAGTATCAGAGAAACATTG 58.920 38.462 0.00 0.00 0.00 2.82
127 128 5.245531 TGACTTCATCCACCACAAAGTATC 58.754 41.667 0.00 0.00 30.68 2.24
129 130 4.346709 TCTGACTTCATCCACCACAAAGTA 59.653 41.667 0.00 0.00 30.68 2.24
133 134 2.705658 ACTCTGACTTCATCCACCACAA 59.294 45.455 0.00 0.00 0.00 3.33
157 158 0.393132 TAAACATTGCCGCCCATCGA 60.393 50.000 0.00 0.00 41.67 3.59
161 162 0.033601 ATCCTAAACATTGCCGCCCA 60.034 50.000 0.00 0.00 0.00 5.36
164 165 1.472480 ACACATCCTAAACATTGCCGC 59.528 47.619 0.00 0.00 0.00 6.53
165 166 3.500982 CAACACATCCTAAACATTGCCG 58.499 45.455 0.00 0.00 0.00 5.69
186 187 1.824852 CAAACCCAGATAGCCCAAACC 59.175 52.381 0.00 0.00 0.00 3.27
194 195 8.455903 AACAATGTCATATCAAACCCAGATAG 57.544 34.615 0.00 0.00 32.00 2.08
196 197 7.722949 AAACAATGTCATATCAAACCCAGAT 57.277 32.000 0.00 0.00 0.00 2.90
220 228 0.315568 GCACCACCGGCATGTAAAAA 59.684 50.000 0.00 0.00 0.00 1.94
230 238 0.744414 CCACATCTTAGCACCACCGG 60.744 60.000 0.00 0.00 0.00 5.28
237 245 3.701205 TTCTTGCTCCACATCTTAGCA 57.299 42.857 0.00 0.00 44.15 3.49
245 253 0.684535 TCACCGATTCTTGCTCCACA 59.315 50.000 0.00 0.00 0.00 4.17
257 265 2.711922 GCACCCTCGACTCACCGAT 61.712 63.158 0.00 0.00 37.96 4.18
262 270 0.247460 CATCAAGCACCCTCGACTCA 59.753 55.000 0.00 0.00 0.00 3.41
273 281 1.877443 CATCGCCATCATCATCAAGCA 59.123 47.619 0.00 0.00 0.00 3.91
274 282 2.095869 GTCATCGCCATCATCATCAAGC 60.096 50.000 0.00 0.00 0.00 4.01
308 316 0.969409 GCAAGCTCCAGCCCTCAATT 60.969 55.000 0.00 0.00 43.38 2.32
317 325 1.002033 GACACAAAGTGCAAGCTCCAG 60.002 52.381 0.00 0.00 36.98 3.86
335 343 0.234884 CCGAACAAGCCAAACTCGAC 59.765 55.000 0.00 0.00 0.00 4.20
338 346 0.591659 GACCCGAACAAGCCAAACTC 59.408 55.000 0.00 0.00 0.00 3.01
359 367 0.590195 CAACAAGCCAGACTCTGCAC 59.410 55.000 0.00 0.00 0.00 4.57
363 371 0.536006 GCCACAACAAGCCAGACTCT 60.536 55.000 0.00 0.00 0.00 3.24
365 373 4.164258 GCCACAACAAGCCAGACT 57.836 55.556 0.00 0.00 0.00 3.24
379 387 2.035632 CAAACCTTACAACCTTGGCCA 58.964 47.619 0.00 0.00 0.00 5.36
406 414 9.476202 AGAGTTGTCCAATTAATTAGCAAAAAC 57.524 29.630 0.00 2.30 0.00 2.43
431 439 3.813166 TCCTTTCCGTTAAAGCACAAGAG 59.187 43.478 2.73 0.00 42.85 2.85
445 453 0.734253 CGTGCTCTCACTCCTTTCCG 60.734 60.000 0.00 0.00 40.99 4.30
447 455 0.318762 ACCGTGCTCTCACTCCTTTC 59.681 55.000 0.00 0.00 40.99 2.62
453 461 2.325583 TTTTCAACCGTGCTCTCACT 57.674 45.000 0.00 0.00 40.99 3.41
520 528 0.320374 CTCGCACAAGACCCCTACAA 59.680 55.000 0.00 0.00 0.00 2.41
523 531 2.656069 GGCTCGCACAAGACCCCTA 61.656 63.158 0.00 0.00 0.00 3.53
525 533 2.180159 TAAGGCTCGCACAAGACCCC 62.180 60.000 0.00 0.00 0.00 4.95
550 558 1.470098 CTGATTTGGTTCAGCCCGAAG 59.530 52.381 0.00 0.00 36.96 3.79
551 559 1.533625 CTGATTTGGTTCAGCCCGAA 58.466 50.000 0.00 0.00 36.96 4.30
552 560 3.248043 CTGATTTGGTTCAGCCCGA 57.752 52.632 0.00 0.00 36.96 5.14
557 565 1.180029 CCCCAGCTGATTTGGTTCAG 58.820 55.000 17.39 0.00 44.87 3.02
559 567 1.893062 GCCCCAGCTGATTTGGTTC 59.107 57.895 17.39 0.00 33.73 3.62
560 568 4.118584 GCCCCAGCTGATTTGGTT 57.881 55.556 17.39 0.00 33.73 3.67
692 713 1.787057 CGATCTCGACGGGGAAGGAG 61.787 65.000 0.00 0.00 43.02 3.69
693 714 1.822613 CGATCTCGACGGGGAAGGA 60.823 63.158 0.00 0.00 43.02 3.36
694 715 0.816825 TACGATCTCGACGGGGAAGG 60.817 60.000 6.60 0.00 43.02 3.46
695 716 1.019673 TTACGATCTCGACGGGGAAG 58.980 55.000 6.60 0.00 43.02 3.46
696 717 0.734889 GTTACGATCTCGACGGGGAA 59.265 55.000 6.60 0.00 43.02 3.97
697 718 1.097547 GGTTACGATCTCGACGGGGA 61.098 60.000 6.60 0.00 43.02 4.81
698 719 1.358046 GGTTACGATCTCGACGGGG 59.642 63.158 6.60 0.00 43.02 5.73
707 728 0.824759 AGGCTCTGGTGGTTACGATC 59.175 55.000 0.00 0.00 0.00 3.69
721 742 1.462283 GTTTTTCCGGACGTTAGGCTC 59.538 52.381 1.83 0.00 0.00 4.70
726 748 5.557891 TTTTTGAGTTTTTCCGGACGTTA 57.442 34.783 1.83 0.00 0.00 3.18
1059 1097 2.125350 CTGAACTCGGGCAGCTCC 60.125 66.667 0.00 0.00 0.00 4.70
1116 1154 3.774599 GATGTGGATCGTGGGGGCC 62.775 68.421 0.00 0.00 0.00 5.80
1593 1631 0.748729 CGAAGACGGAGGAGTAGGCT 60.749 60.000 0.00 0.00 35.72 4.58
1758 1805 4.698625 AGGAGGAACGGCGGGAGT 62.699 66.667 13.24 0.00 0.00 3.85
2040 2087 1.004277 GACTTGTCACTCCAGCGACG 61.004 60.000 0.00 0.00 34.78 5.12
2459 2521 4.950434 TTTTTGGCGGTGTTATAGTAGC 57.050 40.909 0.00 0.00 0.00 3.58
2503 2566 0.383949 ACACCACCGAAAACATGCAC 59.616 50.000 0.00 0.00 0.00 4.57
2525 2588 1.375523 CCACCCCTTAGCACGTGAC 60.376 63.158 22.23 10.94 0.00 3.67
2529 2592 1.376812 GTTCCCACCCCTTAGCACG 60.377 63.158 0.00 0.00 0.00 5.34
2530 2593 1.001269 GGTTCCCACCCCTTAGCAC 60.001 63.158 0.00 0.00 37.03 4.40
2533 2596 2.563039 TCTAGGTTCCCACCCCTTAG 57.437 55.000 0.00 0.00 45.63 2.18
2548 2611 6.492007 AGAAATGCACTTGACACAATCTAG 57.508 37.500 0.00 0.00 36.37 2.43
2579 2646 0.249657 GCCCGGTTATCTGCTCTCAG 60.250 60.000 0.00 0.00 41.67 3.35
2594 2661 4.676586 GCCACAAAACGACGCCCG 62.677 66.667 0.00 0.00 45.44 6.13
2659 2726 6.622427 TTTAAACCAAAGTGGAAAGGGAAA 57.378 33.333 0.18 0.00 40.96 3.13
2660 2727 5.395879 GCTTTAAACCAAAGTGGAAAGGGAA 60.396 40.000 0.18 0.00 44.73 3.97
2661 2728 4.100344 GCTTTAAACCAAAGTGGAAAGGGA 59.900 41.667 0.18 0.00 44.73 4.20
2662 2729 4.377021 GCTTTAAACCAAAGTGGAAAGGG 58.623 43.478 0.18 0.00 44.73 3.95
2663 2730 4.048504 CGCTTTAAACCAAAGTGGAAAGG 58.951 43.478 0.18 0.00 46.54 3.11
2703 2770 5.575019 CAACAAACCACACACTAACCTAAC 58.425 41.667 0.00 0.00 0.00 2.34
2840 3082 2.740256 CGAGCCCTTTCTTAAGCCTCTC 60.740 54.545 0.00 0.00 31.45 3.20
2878 3120 0.531200 GGAGACAGTAACACGGGAGG 59.469 60.000 0.00 0.00 0.00 4.30
2906 3150 2.432146 AGCAAGCGAGTGATCATCCTTA 59.568 45.455 0.00 0.00 0.00 2.69
2960 3205 1.008538 CTGCACAAAGCCAACGACC 60.009 57.895 0.00 0.00 44.83 4.79
2962 3207 2.721231 GCTGCACAAAGCCAACGA 59.279 55.556 0.00 0.00 44.83 3.85
2979 3224 0.531532 CGGATCTGCAGTAAGCCTGG 60.532 60.000 14.67 0.00 44.83 4.45
2980 3225 0.461548 TCGGATCTGCAGTAAGCCTG 59.538 55.000 14.67 4.61 44.83 4.85
2981 3226 0.749649 CTCGGATCTGCAGTAAGCCT 59.250 55.000 14.67 0.00 44.83 4.58
2982 3227 0.249657 CCTCGGATCTGCAGTAAGCC 60.250 60.000 14.67 6.62 44.83 4.35


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

AutoCloner maintained by Alex Coulton.