Multiple sequence alignment - TraesCS2D01G220900

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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 TraesCS2D01G220900 chr2D 100.000 4679 0 0 1 4679 188506329 188501651 0.000000e+00 8641.0
1 TraesCS2D01G220900 chr2B 96.220 2725 66 9 1982 4679 244571369 244568655 0.000000e+00 4427.0
2 TraesCS2D01G220900 chr2B 93.120 1875 105 15 80 1943 244573420 244571559 0.000000e+00 2726.0
3 TraesCS2D01G220900 chr2A 94.897 2724 96 16 1983 4679 202049218 202046511 0.000000e+00 4220.0
4 TraesCS2D01G220900 chr2A 91.794 1304 57 9 693 1982 202050609 202049342 0.000000e+00 1770.0
5 TraesCS2D01G220900 chr4B 80.619 1357 174 47 2252 3560 667877710 667876395 0.000000e+00 966.0
6 TraesCS2D01G220900 chr4B 84.000 475 70 3 1186 1655 667879821 667879348 7.140000e-123 451.0
7 TraesCS2D01G220900 chr4B 83.768 345 39 15 1698 2035 667879181 667878847 1.260000e-80 311.0
8 TraesCS2D01G220900 chr4B 80.147 136 13 8 986 1110 667880058 667879926 6.450000e-14 89.8
9 TraesCS2D01G220900 chrUn 81.302 845 112 27 2744 3560 29785557 29786383 1.100000e-180 643.0
10 TraesCS2D01G220900 chrUn 84.673 398 42 10 2252 2631 29785044 29785440 3.420000e-101 379.0
11 TraesCS2D01G220900 chrUn 88.000 250 27 3 1698 1946 29784161 29784408 4.580000e-75 292.0
12 TraesCS2D01G220900 chrUn 79.562 137 12 10 986 1110 29783155 29783287 3.000000e-12 84.2
13 TraesCS2D01G220900 chr5A 80.992 847 115 25 2742 3560 706242194 706243022 8.540000e-177 630.0
14 TraesCS2D01G220900 chr5A 86.450 369 39 4 2274 2631 706241697 706242065 1.220000e-105 394.0
15 TraesCS2D01G220900 chr5A 84.810 79 9 1 987 1062 706239747 706239825 5.020000e-10 76.8
16 TraesCS2D01G220900 chr4D 84.043 94 12 3 206 297 8152332 8152240 2.320000e-13 87.9
17 TraesCS2D01G220900 chr5D 90.000 60 4 2 351 410 379131378 379131435 5.020000e-10 76.8
18 TraesCS2D01G220900 chr5B 83.333 60 8 2 355 413 371769307 371769249 2.000000e-03 54.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G220900 chr2D 188501651 188506329 4678 True 8641.000000 8641 100.00000 1 4679 1 chr2D.!!$R1 4678
1 TraesCS2D01G220900 chr2B 244568655 244573420 4765 True 3576.500000 4427 94.67000 80 4679 2 chr2B.!!$R1 4599
2 TraesCS2D01G220900 chr2A 202046511 202050609 4098 True 2995.000000 4220 93.34550 693 4679 2 chr2A.!!$R1 3986
3 TraesCS2D01G220900 chr4B 667876395 667880058 3663 True 454.450000 966 82.13350 986 3560 4 chr4B.!!$R1 2574
4 TraesCS2D01G220900 chrUn 29783155 29786383 3228 False 349.550000 643 83.38425 986 3560 4 chrUn.!!$F1 2574
5 TraesCS2D01G220900 chr5A 706239747 706243022 3275 False 366.933333 630 84.08400 987 3560 3 chr5A.!!$F1 2573

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
54 55 0.035820 GACCACTACCATTGCCGGAA 60.036 55.000 5.05 0.00 0.00 4.30 F
72 73 0.251653 AACGAGCCTCTCCTACACCA 60.252 55.000 0.00 0.00 0.00 4.17 F
135 136 0.373716 CGCGTGCCCTTAAGAATCAC 59.626 55.000 3.36 7.69 0.00 3.06 F
507 514 0.479378 GGGGTGTCTGGTTGGGTTTA 59.521 55.000 0.00 0.00 0.00 2.01 F
1245 1316 0.525882 TCGTGAGCGTCGACAACAAA 60.526 50.000 17.16 1.86 39.49 2.83 F
1581 1652 1.128188 ACCTCACCCTTGGAGTGGAC 61.128 60.000 5.80 0.00 35.87 4.02 F
1900 2237 1.688735 CCATCGTATCCTCAGAGCCAA 59.311 52.381 0.00 0.00 0.00 4.52 F
2487 4094 2.289195 GGACAACGGAACATACCTCACA 60.289 50.000 0.00 0.00 0.00 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1716 2053 0.107508 CTACCATGAGCACACTGGGG 60.108 60.000 13.88 5.03 32.79 4.96 R
1810 2147 2.007608 GTACCGGCATCCAAGAACTTC 58.992 52.381 0.00 0.00 0.00 3.01 R
2085 2714 4.629200 TGAAATTGCCATTTTATCCAACGC 59.371 37.500 0.00 0.00 32.35 4.84 R
2487 4094 3.463704 ACAGGAAAAACTTCCCCTTCTCT 59.536 43.478 0.21 0.00 42.06 3.10 R
2952 4624 2.781300 GCCTCTTCGCTTTGCTCG 59.219 61.111 0.00 0.00 0.00 5.03 R
3540 5243 2.250031 TCTTTAACTGGCAGGTCGGTA 58.750 47.619 20.34 0.00 0.00 4.02 R
3654 5357 0.759346 AAGCACGTCTTGACCCTCTT 59.241 50.000 0.00 0.00 32.79 2.85 R
4294 5998 0.108585 TGTTTGGTGGACTCTGGCTC 59.891 55.000 0.00 0.00 0.00 4.70 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
34 35 4.990288 GTCCTCAGACCACCGAAC 57.010 61.111 0.00 0.00 37.00 3.95
35 36 1.080705 GTCCTCAGACCACCGAACG 60.081 63.158 0.00 0.00 37.00 3.95
36 37 1.228337 TCCTCAGACCACCGAACGA 60.228 57.895 0.00 0.00 0.00 3.85
37 38 1.080705 CCTCAGACCACCGAACGAC 60.081 63.158 0.00 0.00 0.00 4.34
38 39 1.080705 CTCAGACCACCGAACGACC 60.081 63.158 0.00 0.00 0.00 4.79
39 40 1.802337 CTCAGACCACCGAACGACCA 61.802 60.000 0.00 0.00 0.00 4.02
40 41 1.663702 CAGACCACCGAACGACCAC 60.664 63.158 0.00 0.00 0.00 4.16
41 42 1.831286 AGACCACCGAACGACCACT 60.831 57.895 0.00 0.00 0.00 4.00
42 43 0.538057 AGACCACCGAACGACCACTA 60.538 55.000 0.00 0.00 0.00 2.74
43 44 0.387750 GACCACCGAACGACCACTAC 60.388 60.000 0.00 0.00 0.00 2.73
44 45 1.080298 CCACCGAACGACCACTACC 60.080 63.158 0.00 0.00 0.00 3.18
45 46 1.661480 CACCGAACGACCACTACCA 59.339 57.895 0.00 0.00 0.00 3.25
46 47 0.245539 CACCGAACGACCACTACCAT 59.754 55.000 0.00 0.00 0.00 3.55
47 48 0.971386 ACCGAACGACCACTACCATT 59.029 50.000 0.00 0.00 0.00 3.16
48 49 1.337447 ACCGAACGACCACTACCATTG 60.337 52.381 0.00 0.00 0.00 2.82
49 50 0.719465 CGAACGACCACTACCATTGC 59.281 55.000 0.00 0.00 0.00 3.56
50 51 1.084289 GAACGACCACTACCATTGCC 58.916 55.000 0.00 0.00 0.00 4.52
51 52 0.672401 AACGACCACTACCATTGCCG 60.672 55.000 0.00 0.00 0.00 5.69
52 53 1.813753 CGACCACTACCATTGCCGG 60.814 63.158 0.00 0.00 0.00 6.13
53 54 1.600107 GACCACTACCATTGCCGGA 59.400 57.895 5.05 0.00 0.00 5.14
54 55 0.035820 GACCACTACCATTGCCGGAA 60.036 55.000 5.05 0.00 0.00 4.30
55 56 0.322187 ACCACTACCATTGCCGGAAC 60.322 55.000 5.05 0.00 0.00 3.62
69 70 2.883572 GGAACGAGCCTCTCCTACA 58.116 57.895 0.00 0.00 0.00 2.74
70 71 0.456628 GGAACGAGCCTCTCCTACAC 59.543 60.000 0.00 0.00 0.00 2.90
71 72 0.456628 GAACGAGCCTCTCCTACACC 59.543 60.000 0.00 0.00 0.00 4.16
72 73 0.251653 AACGAGCCTCTCCTACACCA 60.252 55.000 0.00 0.00 0.00 4.17
73 74 0.681564 ACGAGCCTCTCCTACACCAG 60.682 60.000 0.00 0.00 0.00 4.00
74 75 0.394488 CGAGCCTCTCCTACACCAGA 60.394 60.000 0.00 0.00 0.00 3.86
75 76 1.398692 GAGCCTCTCCTACACCAGAG 58.601 60.000 0.00 0.00 36.63 3.35
76 77 0.707616 AGCCTCTCCTACACCAGAGT 59.292 55.000 0.00 0.00 35.29 3.24
77 78 1.107945 GCCTCTCCTACACCAGAGTC 58.892 60.000 0.00 0.00 35.29 3.36
78 79 1.617263 GCCTCTCCTACACCAGAGTCA 60.617 57.143 0.00 0.00 35.29 3.41
116 117 3.063452 TGACAACTGAAAAGTCTTCGTGC 59.937 43.478 0.00 0.00 33.56 5.34
135 136 0.373716 CGCGTGCCCTTAAGAATCAC 59.626 55.000 3.36 7.69 0.00 3.06
138 139 0.733150 GTGCCCTTAAGAATCACCGC 59.267 55.000 3.36 0.00 0.00 5.68
145 146 3.877508 CCTTAAGAATCACCGCCCTAAAG 59.122 47.826 3.36 0.00 0.00 1.85
148 149 1.076995 AATCACCGCCCTAAAGCCC 60.077 57.895 0.00 0.00 0.00 5.19
154 155 2.966732 CGCCCTAAAGCCCCAGTCA 61.967 63.158 0.00 0.00 0.00 3.41
170 172 3.618594 CCAGTCATGACGTTGAATCGATT 59.381 43.478 19.85 11.20 36.20 3.34
172 174 5.017612 CAGTCATGACGTTGAATCGATTTG 58.982 41.667 19.85 4.02 36.20 2.32
200 202 2.099405 TGACATCAGATACTGTGCCGA 58.901 47.619 0.00 0.00 32.61 5.54
208 210 3.068165 CAGATACTGTGCCGAACCTATGA 59.932 47.826 0.00 0.00 0.00 2.15
209 211 3.898123 AGATACTGTGCCGAACCTATGAT 59.102 43.478 0.00 0.00 0.00 2.45
210 212 5.048013 CAGATACTGTGCCGAACCTATGATA 60.048 44.000 0.00 0.00 0.00 2.15
222 224 6.704937 CCGAACCTATGATAAGAAACCCTAAC 59.295 42.308 0.00 0.00 0.00 2.34
228 230 8.097662 CCTATGATAAGAAACCCTAACCTCATC 58.902 40.741 0.00 0.00 0.00 2.92
230 232 5.424252 TGATAAGAAACCCTAACCTCATCGT 59.576 40.000 0.00 0.00 0.00 3.73
232 234 2.500504 AGAAACCCTAACCTCATCGTCC 59.499 50.000 0.00 0.00 0.00 4.79
248 250 1.553706 GTCCCAAGAGACGGTAGGAA 58.446 55.000 0.00 0.00 0.00 3.36
249 251 2.108970 GTCCCAAGAGACGGTAGGAAT 58.891 52.381 0.00 0.00 0.00 3.01
250 252 3.294214 GTCCCAAGAGACGGTAGGAATA 58.706 50.000 0.00 0.00 0.00 1.75
251 253 3.896272 GTCCCAAGAGACGGTAGGAATAT 59.104 47.826 0.00 0.00 0.00 1.28
255 261 6.041296 TCCCAAGAGACGGTAGGAATATAAAC 59.959 42.308 0.00 0.00 0.00 2.01
265 271 6.183360 CGGTAGGAATATAAACCAGAGTTCCA 60.183 42.308 4.94 0.00 38.02 3.53
269 275 6.326583 AGGAATATAAACCAGAGTTCCATCGA 59.673 38.462 4.94 0.00 38.02 3.59
273 279 0.811915 ACCAGAGTTCCATCGACTCG 59.188 55.000 0.00 0.00 46.29 4.18
280 286 1.134367 GTTCCATCGACTCGGTCATGA 59.866 52.381 0.00 0.00 32.09 3.07
283 289 1.135112 CCATCGACTCGGTCATGACAA 60.135 52.381 26.47 13.31 32.09 3.18
291 297 3.432252 ACTCGGTCATGACAAACGAAATC 59.568 43.478 26.47 5.61 32.80 2.17
295 301 3.181520 GGTCATGACAAACGAAATCGAGG 60.182 47.826 26.47 1.16 43.02 4.63
307 313 3.438781 CGAAATCGAGGATCAAAACCCAA 59.561 43.478 0.00 0.00 43.02 4.12
321 327 6.133356 TCAAAACCCAAAAGACCTACTCAAT 58.867 36.000 0.00 0.00 0.00 2.57
322 328 6.040391 TCAAAACCCAAAAGACCTACTCAATG 59.960 38.462 0.00 0.00 0.00 2.82
328 334 6.094603 CCCAAAAGACCTACTCAATGATGAAG 59.905 42.308 0.00 0.00 34.49 3.02
331 337 6.865834 AAGACCTACTCAATGATGAAGAGT 57.134 37.500 0.00 0.00 44.25 3.24
441 448 1.899437 GACAGGCCCGTTGATGGAGA 61.899 60.000 0.00 0.00 0.00 3.71
443 450 2.190578 GGCCCGTTGATGGAGAGG 59.809 66.667 0.00 0.00 0.00 3.69
453 460 1.307343 ATGGAGAGGGTGAGGTGGG 60.307 63.158 0.00 0.00 0.00 4.61
454 461 3.403558 GGAGAGGGTGAGGTGGGC 61.404 72.222 0.00 0.00 0.00 5.36
488 495 4.151883 CCCCCAAATCACCACATATTAGG 58.848 47.826 0.00 0.00 0.00 2.69
507 514 0.479378 GGGGTGTCTGGTTGGGTTTA 59.521 55.000 0.00 0.00 0.00 2.01
508 515 1.076513 GGGGTGTCTGGTTGGGTTTAT 59.923 52.381 0.00 0.00 0.00 1.40
569 577 2.228545 TTATGGGCATGTGGCTTCAA 57.771 45.000 6.52 0.00 44.01 2.69
570 578 1.766494 TATGGGCATGTGGCTTCAAG 58.234 50.000 6.52 0.00 44.01 3.02
593 601 2.787473 TGGCTTAATCCACAGACTGG 57.213 50.000 7.51 0.00 42.29 4.00
615 623 1.761174 GTGAAGCTTGGAGGGGTGA 59.239 57.895 2.10 0.00 0.00 4.02
633 641 4.202326 GGGTGAAGAACTTTGTCCTAGTCA 60.202 45.833 0.00 0.00 0.00 3.41
637 645 7.309867 GGTGAAGAACTTTGTCCTAGTCATCTA 60.310 40.741 0.00 0.00 0.00 1.98
657 665 3.643159 AAGCGTGATGGAAAGGAAAAC 57.357 42.857 0.00 0.00 0.00 2.43
662 670 3.305335 CGTGATGGAAAGGAAAACAAGGG 60.305 47.826 0.00 0.00 0.00 3.95
687 695 7.228706 GGATGACCCTGTCAATATATTTTCGTT 59.771 37.037 0.46 0.00 45.96 3.85
759 769 3.184379 CACACGTGAACGAATCAGAACAT 59.816 43.478 25.01 0.00 43.02 2.71
778 788 7.555554 CAGAACATTCAGATACCCAATCTTCTT 59.444 37.037 0.00 0.00 42.62 2.52
876 889 3.787001 GCTGGAGAAGGACCCCGG 61.787 72.222 0.00 0.00 0.00 5.73
877 890 3.083997 CTGGAGAAGGACCCCGGG 61.084 72.222 15.80 15.80 0.00 5.73
1064 1095 0.830648 CTCCCGGTAAGCTCCATTCA 59.169 55.000 0.00 0.00 0.00 2.57
1065 1096 0.830648 TCCCGGTAAGCTCCATTCAG 59.169 55.000 0.00 0.00 0.00 3.02
1124 1158 9.177608 CCAAGGATCTAAAAACTCACATTATCA 57.822 33.333 0.00 0.00 0.00 2.15
1152 1214 7.361542 GCATATGATACCCAGCTTATCAACAAG 60.362 40.741 6.97 3.81 38.99 3.16
1153 1215 5.692115 TGATACCCAGCTTATCAACAAGA 57.308 39.130 4.45 0.00 33.83 3.02
1154 1216 6.252599 TGATACCCAGCTTATCAACAAGAT 57.747 37.500 4.45 0.00 40.86 2.40
1155 1217 6.291377 TGATACCCAGCTTATCAACAAGATC 58.709 40.000 4.45 0.00 38.19 2.75
1156 1218 4.851639 ACCCAGCTTATCAACAAGATCT 57.148 40.909 0.00 0.00 38.19 2.75
1195 1262 2.742589 GCAGTAGTTCCACTAACCTTGC 59.257 50.000 0.00 0.00 39.03 4.01
1245 1316 0.525882 TCGTGAGCGTCGACAACAAA 60.526 50.000 17.16 1.86 39.49 2.83
1581 1652 1.128188 ACCTCACCCTTGGAGTGGAC 61.128 60.000 5.80 0.00 35.87 4.02
1631 1702 2.034812 CCGTCCAGGTTAGCTAAGCTAG 59.965 54.545 31.78 26.16 42.34 3.42
1716 2053 5.106157 ACAGCATAGTTGTGATTTTGGTAGC 60.106 40.000 0.00 0.00 0.00 3.58
1900 2237 1.688735 CCATCGTATCCTCAGAGCCAA 59.311 52.381 0.00 0.00 0.00 4.52
1977 2328 6.647067 ACTCTTCTGTTCTTACAAAATCCTCG 59.353 38.462 0.00 0.00 32.92 4.63
2085 2714 5.998454 AAAGTGATTCTGATCATAAGCGG 57.002 39.130 0.00 0.00 43.76 5.52
2187 3780 4.460382 CAGAAGCAAACATAAGACCATGGT 59.540 41.667 19.89 19.89 0.00 3.55
2487 4094 2.289195 GGACAACGGAACATACCTCACA 60.289 50.000 0.00 0.00 0.00 3.58
2620 4230 6.998673 GGCAATCAAAGTAAGTACCATCCTAT 59.001 38.462 0.00 0.00 0.00 2.57
2647 4302 9.409918 AGATCTCAGTGAAAAATCATGATTCAT 57.590 29.630 20.95 12.76 35.70 2.57
3058 4730 9.639563 TTATGGCTCAGGAATTTACAATTATCA 57.360 29.630 0.00 0.00 0.00 2.15
3361 5048 2.751036 TGCCACCCATGCATGTCG 60.751 61.111 24.58 16.30 32.85 4.35
3540 5243 5.143369 GAGCCATTCCCCTTTGATAAGAAT 58.857 41.667 0.00 0.00 32.92 2.40
3675 5378 1.149148 GAGGGTCAAGACGTGCTTTC 58.851 55.000 0.00 0.00 33.60 2.62
3894 5598 9.722056 GTGCTTATAACTTAATGATTGTGAAGG 57.278 33.333 0.00 0.00 0.00 3.46
4000 5704 2.015736 ATAGAAAGTGCGAGCTGTGG 57.984 50.000 0.00 0.00 0.00 4.17
4141 5845 5.720371 TGATTTGGACAATGATCGGTTTT 57.280 34.783 0.00 0.00 0.00 2.43
4174 5878 2.009051 TGATGCAGAGTAACAATGGCG 58.991 47.619 0.00 0.00 0.00 5.69
4195 5899 2.599082 GCATAGCTACAGTTCACGTGAC 59.401 50.000 19.90 13.51 0.00 3.67
4294 5998 2.670401 GTTGTTTCCAACGAGCAGAG 57.330 50.000 0.00 0.00 41.41 3.35
4295 5999 2.210116 GTTGTTTCCAACGAGCAGAGA 58.790 47.619 0.00 0.00 41.41 3.10
4296 6000 2.154854 TGTTTCCAACGAGCAGAGAG 57.845 50.000 0.00 0.00 0.00 3.20
4511 6216 5.672819 GCGGAAACCTATGAATACACACAAC 60.673 44.000 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.080705 CGTTCGGTGGTCTGAGGAC 60.081 63.158 0.00 0.00 41.43 3.85
18 19 1.228337 TCGTTCGGTGGTCTGAGGA 60.228 57.895 0.00 0.00 0.00 3.71
19 20 1.080705 GTCGTTCGGTGGTCTGAGG 60.081 63.158 0.00 0.00 0.00 3.86
20 21 1.080705 GGTCGTTCGGTGGTCTGAG 60.081 63.158 0.00 0.00 0.00 3.35
21 22 1.829096 TGGTCGTTCGGTGGTCTGA 60.829 57.895 0.00 0.00 0.00 3.27
22 23 1.663702 GTGGTCGTTCGGTGGTCTG 60.664 63.158 0.00 0.00 0.00 3.51
23 24 0.538057 TAGTGGTCGTTCGGTGGTCT 60.538 55.000 0.00 0.00 0.00 3.85
24 25 0.387750 GTAGTGGTCGTTCGGTGGTC 60.388 60.000 0.00 0.00 0.00 4.02
25 26 1.662044 GTAGTGGTCGTTCGGTGGT 59.338 57.895 0.00 0.00 0.00 4.16
26 27 1.080298 GGTAGTGGTCGTTCGGTGG 60.080 63.158 0.00 0.00 0.00 4.61
27 28 0.245539 ATGGTAGTGGTCGTTCGGTG 59.754 55.000 0.00 0.00 0.00 4.94
28 29 0.971386 AATGGTAGTGGTCGTTCGGT 59.029 50.000 0.00 0.00 0.00 4.69
29 30 1.355971 CAATGGTAGTGGTCGTTCGG 58.644 55.000 0.00 0.00 0.00 4.30
30 31 0.719465 GCAATGGTAGTGGTCGTTCG 59.281 55.000 0.00 0.00 0.00 3.95
31 32 1.084289 GGCAATGGTAGTGGTCGTTC 58.916 55.000 0.00 0.00 0.00 3.95
32 33 0.672401 CGGCAATGGTAGTGGTCGTT 60.672 55.000 0.00 0.00 0.00 3.85
33 34 1.079405 CGGCAATGGTAGTGGTCGT 60.079 57.895 0.00 0.00 0.00 4.34
34 35 1.813753 CCGGCAATGGTAGTGGTCG 60.814 63.158 0.00 0.00 0.00 4.79
35 36 0.035820 TTCCGGCAATGGTAGTGGTC 60.036 55.000 0.00 0.00 0.00 4.02
36 37 0.322187 GTTCCGGCAATGGTAGTGGT 60.322 55.000 0.00 0.00 0.00 4.16
37 38 1.366111 CGTTCCGGCAATGGTAGTGG 61.366 60.000 0.00 0.00 0.00 4.00
38 39 0.390603 TCGTTCCGGCAATGGTAGTG 60.391 55.000 0.00 0.00 0.00 2.74
39 40 0.108329 CTCGTTCCGGCAATGGTAGT 60.108 55.000 0.00 0.00 0.00 2.73
40 41 1.429148 GCTCGTTCCGGCAATGGTAG 61.429 60.000 0.00 0.00 0.00 3.18
41 42 1.448893 GCTCGTTCCGGCAATGGTA 60.449 57.895 0.00 0.00 0.00 3.25
42 43 2.746277 GCTCGTTCCGGCAATGGT 60.746 61.111 0.00 0.00 0.00 3.55
43 44 3.508840 GGCTCGTTCCGGCAATGG 61.509 66.667 0.00 0.00 0.00 3.16
44 45 2.436646 AGGCTCGTTCCGGCAATG 60.437 61.111 0.00 0.00 0.00 2.82
45 46 2.125106 GAGGCTCGTTCCGGCAAT 60.125 61.111 0.00 0.00 0.00 3.56
46 47 3.296709 GAGAGGCTCGTTCCGGCAA 62.297 63.158 9.22 0.00 0.00 4.52
47 48 3.760035 GAGAGGCTCGTTCCGGCA 61.760 66.667 9.22 0.00 0.00 5.69
48 49 4.516195 GGAGAGGCTCGTTCCGGC 62.516 72.222 9.22 0.00 0.00 6.13
49 50 1.453379 TAGGAGAGGCTCGTTCCGG 60.453 63.158 14.98 0.00 36.11 5.14
50 51 1.030488 TGTAGGAGAGGCTCGTTCCG 61.030 60.000 14.98 0.00 36.11 4.30
51 52 0.456628 GTGTAGGAGAGGCTCGTTCC 59.543 60.000 13.51 13.51 30.95 3.62
52 53 0.456628 GGTGTAGGAGAGGCTCGTTC 59.543 60.000 9.22 1.72 30.95 3.95
53 54 0.251653 TGGTGTAGGAGAGGCTCGTT 60.252 55.000 9.22 1.26 30.95 3.85
54 55 0.681564 CTGGTGTAGGAGAGGCTCGT 60.682 60.000 9.22 0.38 33.11 4.18
55 56 0.394488 TCTGGTGTAGGAGAGGCTCG 60.394 60.000 9.22 0.00 0.00 5.03
56 57 1.341581 ACTCTGGTGTAGGAGAGGCTC 60.342 57.143 6.34 6.34 40.16 4.70
57 58 0.707616 ACTCTGGTGTAGGAGAGGCT 59.292 55.000 0.00 0.00 40.16 4.58
58 59 1.107945 GACTCTGGTGTAGGAGAGGC 58.892 60.000 0.00 0.00 40.16 4.70
59 60 2.516227 TGACTCTGGTGTAGGAGAGG 57.484 55.000 0.00 0.00 40.16 3.69
60 61 2.955660 GGATGACTCTGGTGTAGGAGAG 59.044 54.545 0.00 0.00 41.39 3.20
61 62 2.583101 AGGATGACTCTGGTGTAGGAGA 59.417 50.000 0.00 0.00 34.11 3.71
62 63 3.025322 AGGATGACTCTGGTGTAGGAG 57.975 52.381 0.00 0.00 35.86 3.69
63 64 4.279145 GTTAGGATGACTCTGGTGTAGGA 58.721 47.826 0.00 0.00 0.00 2.94
64 65 3.385111 GGTTAGGATGACTCTGGTGTAGG 59.615 52.174 0.00 0.00 0.00 3.18
65 66 4.282496 AGGTTAGGATGACTCTGGTGTAG 58.718 47.826 0.00 0.00 0.00 2.74
66 67 4.332683 AGGTTAGGATGACTCTGGTGTA 57.667 45.455 0.00 0.00 0.00 2.90
67 68 3.191888 AGGTTAGGATGACTCTGGTGT 57.808 47.619 0.00 0.00 0.00 4.16
68 69 3.261897 ACAAGGTTAGGATGACTCTGGTG 59.738 47.826 0.00 0.00 0.00 4.17
69 70 3.521727 ACAAGGTTAGGATGACTCTGGT 58.478 45.455 0.00 0.00 0.00 4.00
70 71 4.020218 TCAACAAGGTTAGGATGACTCTGG 60.020 45.833 0.00 0.00 0.00 3.86
71 72 5.152623 TCAACAAGGTTAGGATGACTCTG 57.847 43.478 0.00 0.00 0.00 3.35
72 73 5.485353 TCATCAACAAGGTTAGGATGACTCT 59.515 40.000 7.59 0.00 39.37 3.24
73 74 5.734720 TCATCAACAAGGTTAGGATGACTC 58.265 41.667 7.59 0.00 39.37 3.36
74 75 5.762179 TCATCAACAAGGTTAGGATGACT 57.238 39.130 7.59 0.00 39.37 3.41
76 77 5.497464 TGTCATCAACAAGGTTAGGATGA 57.503 39.130 7.59 7.59 41.31 2.92
116 117 0.373716 GTGATTCTTAAGGGCACGCG 59.626 55.000 3.53 3.53 0.00 6.01
124 125 3.312697 GCTTTAGGGCGGTGATTCTTAAG 59.687 47.826 0.00 0.00 0.00 1.85
135 136 3.699134 GACTGGGGCTTTAGGGCGG 62.699 68.421 0.00 0.00 41.87 6.13
138 139 0.918983 TCATGACTGGGGCTTTAGGG 59.081 55.000 0.00 0.00 0.00 3.53
145 146 0.605319 TTCAACGTCATGACTGGGGC 60.605 55.000 22.95 0.00 0.00 5.80
148 149 2.606108 TCGATTCAACGTCATGACTGG 58.394 47.619 22.95 11.35 34.70 4.00
154 155 5.179368 ACACTTCAAATCGATTCAACGTCAT 59.821 36.000 11.83 0.00 34.70 3.06
192 194 4.322080 TCTTATCATAGGTTCGGCACAG 57.678 45.455 0.00 0.00 0.00 3.66
196 198 3.813724 GGGTTTCTTATCATAGGTTCGGC 59.186 47.826 0.00 0.00 0.00 5.54
200 202 7.404980 TGAGGTTAGGGTTTCTTATCATAGGTT 59.595 37.037 0.00 0.00 0.00 3.50
208 210 5.163332 GGACGATGAGGTTAGGGTTTCTTAT 60.163 44.000 0.00 0.00 0.00 1.73
209 211 4.161001 GGACGATGAGGTTAGGGTTTCTTA 59.839 45.833 0.00 0.00 0.00 2.10
210 212 3.055312 GGACGATGAGGTTAGGGTTTCTT 60.055 47.826 0.00 0.00 0.00 2.52
230 232 2.544844 ATTCCTACCGTCTCTTGGGA 57.455 50.000 0.00 0.00 0.00 4.37
232 234 6.183360 TGGTTTATATTCCTACCGTCTCTTGG 60.183 42.308 0.00 0.00 33.29 3.61
241 243 7.133133 TGGAACTCTGGTTTATATTCCTACC 57.867 40.000 0.00 0.00 37.18 3.18
242 244 7.599245 CGATGGAACTCTGGTTTATATTCCTAC 59.401 40.741 0.00 0.00 37.18 3.18
246 248 7.210873 AGTCGATGGAACTCTGGTTTATATTC 58.789 38.462 0.00 0.00 35.58 1.75
248 250 6.515200 CGAGTCGATGGAACTCTGGTTTATAT 60.515 42.308 6.73 0.00 35.58 0.86
249 251 5.220989 CGAGTCGATGGAACTCTGGTTTATA 60.221 44.000 6.73 0.00 35.58 0.98
250 252 4.440250 CGAGTCGATGGAACTCTGGTTTAT 60.440 45.833 6.73 0.00 35.58 1.40
251 253 3.119602 CGAGTCGATGGAACTCTGGTTTA 60.120 47.826 6.73 0.00 35.58 2.01
255 261 0.101399 CCGAGTCGATGGAACTCTGG 59.899 60.000 15.64 0.00 0.00 3.86
265 271 2.607187 GTTTGTCATGACCGAGTCGAT 58.393 47.619 22.85 0.00 34.95 3.59
269 275 2.519377 TTCGTTTGTCATGACCGAGT 57.481 45.000 22.85 0.00 0.00 4.18
273 279 3.181520 CCTCGATTTCGTTTGTCATGACC 60.182 47.826 22.85 6.94 40.80 4.02
280 286 5.449304 GTTTTGATCCTCGATTTCGTTTGT 58.551 37.500 0.00 0.00 40.80 2.83
283 289 3.439129 GGGTTTTGATCCTCGATTTCGTT 59.561 43.478 0.00 0.00 40.80 3.85
291 297 3.057526 GGTCTTTTGGGTTTTGATCCTCG 60.058 47.826 0.00 0.00 0.00 4.63
295 301 5.768164 TGAGTAGGTCTTTTGGGTTTTGATC 59.232 40.000 0.00 0.00 0.00 2.92
307 313 7.251321 ACTCTTCATCATTGAGTAGGTCTTT 57.749 36.000 0.00 0.00 39.02 2.52
321 327 5.522456 GTTGCAAATGACAACTCTTCATCA 58.478 37.500 0.00 0.00 43.23 3.07
322 328 4.614284 CGTTGCAAATGACAACTCTTCATC 59.386 41.667 0.00 0.00 44.15 2.92
374 380 2.829003 CTAGTGCCTCGGCTCCGA 60.829 66.667 10.84 10.84 46.87 4.55
375 381 1.739338 ATTCTAGTGCCTCGGCTCCG 61.739 60.000 9.65 1.14 42.51 4.63
410 416 2.603473 CCTGTCCTCCGGTGACCA 60.603 66.667 19.45 8.96 31.60 4.02
411 417 4.083862 GCCTGTCCTCCGGTGACC 62.084 72.222 19.45 0.00 31.60 4.02
418 425 2.670148 ATCAACGGGCCTGTCCTCC 61.670 63.158 20.00 0.00 34.39 4.30
422 429 1.450312 CTCCATCAACGGGCCTGTC 60.450 63.158 20.00 0.00 0.00 3.51
433 440 0.618680 CCACCTCACCCTCTCCATCA 60.619 60.000 0.00 0.00 0.00 3.07
460 467 1.984026 GGTGATTTGGGGGCCTGTG 60.984 63.158 0.84 0.00 0.00 3.66
488 495 0.479378 TAAACCCAACCAGACACCCC 59.521 55.000 0.00 0.00 0.00 4.95
558 566 2.041701 AGCCAAAACTTGAAGCCACAT 58.958 42.857 0.00 0.00 0.00 3.21
569 577 4.520492 CAGTCTGTGGATTAAGCCAAAACT 59.480 41.667 15.34 14.54 40.20 2.66
570 578 4.798574 CAGTCTGTGGATTAAGCCAAAAC 58.201 43.478 15.34 12.52 40.20 2.43
593 601 1.376037 CCCTCCAAGCTTCACCGTC 60.376 63.158 0.00 0.00 0.00 4.79
594 602 2.750350 CCCTCCAAGCTTCACCGT 59.250 61.111 0.00 0.00 0.00 4.83
597 605 0.110486 TTCACCCCTCCAAGCTTCAC 59.890 55.000 0.00 0.00 0.00 3.18
615 623 7.100409 GCTTAGATGACTAGGACAAAGTTCTT 58.900 38.462 0.00 0.00 0.00 2.52
633 641 4.487714 TTCCTTTCCATCACGCTTAGAT 57.512 40.909 0.00 0.00 0.00 1.98
637 645 2.955660 TGTTTTCCTTTCCATCACGCTT 59.044 40.909 0.00 0.00 0.00 4.68
662 670 7.730364 ACGAAAATATATTGACAGGGTCATC 57.270 36.000 0.00 0.00 42.40 2.92
687 695 7.601886 TCAGGTTTAAATACGTTATCCGACAAA 59.398 33.333 0.00 0.00 40.70 2.83
759 769 5.488919 ACTGGAAGAAGATTGGGTATCTGAA 59.511 40.000 0.00 0.00 39.17 3.02
778 788 8.493607 TGATATCATATTTTCCTTGTCACTGGA 58.506 33.333 0.00 0.00 0.00 3.86
877 890 4.565850 AGGGATCGGAGGAGGGGC 62.566 72.222 0.00 0.00 0.00 5.80
888 901 7.542824 GTCTATTTATACTGCGAAAGAGGGATC 59.457 40.741 0.00 0.00 0.00 3.36
889 902 7.379750 GTCTATTTATACTGCGAAAGAGGGAT 58.620 38.462 0.00 0.00 0.00 3.85
890 903 6.239232 GGTCTATTTATACTGCGAAAGAGGGA 60.239 42.308 0.00 0.00 0.00 4.20
891 904 5.927115 GGTCTATTTATACTGCGAAAGAGGG 59.073 44.000 0.00 0.00 0.00 4.30
892 905 5.927115 GGGTCTATTTATACTGCGAAAGAGG 59.073 44.000 0.00 0.00 0.00 3.69
1064 1095 2.124570 CATGGTGCTTAGCGGGCT 60.125 61.111 0.00 0.00 0.00 5.19
1065 1096 3.211963 CCATGGTGCTTAGCGGGC 61.212 66.667 2.57 0.00 0.00 6.13
1124 1158 6.317663 TGATAAGCTGGGTATCATATGCAT 57.682 37.500 3.79 3.79 33.92 3.96
1180 1246 2.552743 GTGAAGGCAAGGTTAGTGGAAC 59.447 50.000 0.00 0.00 37.31 3.62
1245 1316 1.030488 TCTCGTCGCCCTTCTCGAAT 61.030 55.000 0.00 0.00 37.73 3.34
1518 1589 2.412325 GCGGTTGGTGTAGAAAATGTCG 60.412 50.000 0.00 0.00 0.00 4.35
1581 1652 0.179089 CATGGAAGAGAGGCTGGTCG 60.179 60.000 0.00 0.00 0.00 4.79
1631 1702 3.539604 CAGGAGAACTGGAATGGTGATC 58.460 50.000 0.00 0.00 43.70 2.92
1712 2049 0.745845 CATGAGCACACTGGGGCTAC 60.746 60.000 0.00 0.00 41.22 3.58
1716 2053 0.107508 CTACCATGAGCACACTGGGG 60.108 60.000 13.88 5.03 32.79 4.96
1810 2147 2.007608 GTACCGGCATCCAAGAACTTC 58.992 52.381 0.00 0.00 0.00 3.01
1973 2324 9.076596 CATCACATGTTACATGTATATACGAGG 57.923 37.037 27.53 17.79 0.00 4.63
1977 2328 9.705290 TGGTCATCACATGTTACATGTATATAC 57.295 33.333 27.53 21.45 0.00 1.47
2085 2714 4.629200 TGAAATTGCCATTTTATCCAACGC 59.371 37.500 0.00 0.00 32.35 4.84
2114 2743 6.798427 TCTCTCAAAAGCCATGAGTAGTAT 57.202 37.500 9.90 0.00 43.77 2.12
2187 3780 4.583489 TGCTTTTACCGTTTAATTGTGGGA 59.417 37.500 0.00 0.00 0.00 4.37
2487 4094 3.463704 ACAGGAAAAACTTCCCCTTCTCT 59.536 43.478 0.21 0.00 42.06 3.10
2620 4230 9.895138 TGAATCATGATTTTTCACTGAGATCTA 57.105 29.630 21.57 0.00 0.00 1.98
2647 4302 5.592282 TGTTTATCAGGCACAACTTCTCAAA 59.408 36.000 0.00 0.00 0.00 2.69
2703 4373 7.054751 ACTTCCTGTTTCTTTAAGCTTGTACT 58.945 34.615 9.86 0.00 0.00 2.73
2715 4385 8.189460 GTGAGTCGTATATACTTCCTGTTTCTT 58.811 37.037 11.05 0.00 0.00 2.52
2716 4386 7.338703 TGTGAGTCGTATATACTTCCTGTTTCT 59.661 37.037 11.05 0.00 0.00 2.52
2720 4390 7.426410 CAATGTGAGTCGTATATACTTCCTGT 58.574 38.462 11.05 0.00 0.00 4.00
2721 4391 6.363626 GCAATGTGAGTCGTATATACTTCCTG 59.636 42.308 11.05 0.00 0.00 3.86
2952 4624 2.781300 GCCTCTTCGCTTTGCTCG 59.219 61.111 0.00 0.00 0.00 5.03
3058 4730 4.134563 AGTGCTTCAGTGTTTCCGTAAAT 58.865 39.130 0.00 0.00 0.00 1.40
3540 5243 2.250031 TCTTTAACTGGCAGGTCGGTA 58.750 47.619 20.34 0.00 0.00 4.02
3654 5357 0.759346 AAGCACGTCTTGACCCTCTT 59.241 50.000 0.00 0.00 32.79 2.85
3675 5378 2.082231 CCTGTGCACCTCAATTCTCAG 58.918 52.381 15.69 0.17 0.00 3.35
4000 5704 9.634163 AATTCCTTTTGTTAATAATGACCGTTC 57.366 29.630 0.00 0.00 0.00 3.95
4174 5878 2.599082 GTCACGTGAACTGTAGCTATGC 59.401 50.000 21.95 0.00 0.00 3.14
4293 5997 0.398318 GTTTGGTGGACTCTGGCTCT 59.602 55.000 0.00 0.00 0.00 4.09
4294 5998 0.108585 TGTTTGGTGGACTCTGGCTC 59.891 55.000 0.00 0.00 0.00 4.70
4295 5999 0.773644 ATGTTTGGTGGACTCTGGCT 59.226 50.000 0.00 0.00 0.00 4.75
4296 6000 0.883833 CATGTTTGGTGGACTCTGGC 59.116 55.000 0.00 0.00 0.00 4.85
4298 6002 3.070018 GAGACATGTTTGGTGGACTCTG 58.930 50.000 0.00 0.00 0.00 3.35
4299 6003 2.039084 GGAGACATGTTTGGTGGACTCT 59.961 50.000 0.00 0.00 0.00 3.24
4303 6007 3.156293 CATTGGAGACATGTTTGGTGGA 58.844 45.455 0.00 0.00 42.32 4.02
4342 6046 2.207590 CATGACGATCCACAGACATGG 58.792 52.381 0.00 0.00 41.57 3.66
4343 6047 2.606272 CACATGACGATCCACAGACATG 59.394 50.000 0.00 0.00 40.24 3.21
4344 6048 2.897436 CACATGACGATCCACAGACAT 58.103 47.619 0.00 0.00 0.00 3.06
4511 6216 2.154462 GGATATGCATGGAAGGAACCG 58.846 52.381 10.16 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.