Multiple sequence alignment - TraesCS6B01G032700

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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 TraesCS6B01G032700 chr6B 100.000 4248 0 0 1001 5248 19125142 19129389 0.000000e+00 7845.0
1 TraesCS6B01G032700 chr6B 100.000 714 0 0 1 714 19124142 19124855 0.000000e+00 1319.0
2 TraesCS6B01G032700 chr6B 96.990 731 22 0 4518 5248 641301636 641300906 0.000000e+00 1229.0
3 TraesCS6B01G032700 chr6D 95.377 3461 132 15 1001 4447 10414253 10417699 0.000000e+00 5480.0
4 TraesCS6B01G032700 chr6D 82.416 654 58 26 1 621 10413398 10414027 7.790000e-143 518.0
5 TraesCS6B01G032700 chr6D 91.228 57 5 0 2881 2937 10420706 10420762 1.570000e-10 78.7
6 TraesCS6B01G032700 chr6A 94.757 3452 150 18 1001 4447 11963654 11967079 0.000000e+00 5343.0
7 TraesCS6B01G032700 chr6A 80.666 631 69 26 1 600 11962826 11963434 1.730000e-119 440.0
8 TraesCS6B01G032700 chr6A 91.228 57 5 0 2881 2937 11970060 11970116 1.570000e-10 78.7
9 TraesCS6B01G032700 chr7B 96.671 751 25 0 4498 5248 632802182 632802932 0.000000e+00 1249.0
10 TraesCS6B01G032700 chr7B 93.552 822 34 3 4445 5248 28973087 28972267 0.000000e+00 1206.0
11 TraesCS6B01G032700 chr3B 96.649 746 25 0 4503 5248 2343050 2342305 0.000000e+00 1240.0
12 TraesCS6B01G032700 chr3B 94.370 817 29 1 4449 5248 256360419 256361235 0.000000e+00 1238.0
13 TraesCS6B01G032700 chr4B 94.212 812 30 2 4453 5248 37870591 37869781 0.000000e+00 1223.0
14 TraesCS6B01G032700 chr1B 94.010 818 31 2 4449 5248 629922535 629923352 0.000000e+00 1223.0
15 TraesCS6B01G032700 chr1B 92.805 820 39 4 4447 5248 56262038 56261221 0.000000e+00 1170.0
16 TraesCS6B01G032700 chr5B 95.872 751 31 0 4498 5248 65534090 65534840 0.000000e+00 1216.0
17 TraesCS6B01G032700 chr5B 95.745 752 31 1 4498 5248 692128209 692127458 0.000000e+00 1210.0
18 TraesCS6B01G032700 chr2B 94.074 810 30 2 4457 5248 423911347 423910538 0.000000e+00 1214.0
19 TraesCS6B01G032700 chr2B 93.758 817 34 1 4449 5248 232451686 232452502 0.000000e+00 1210.0
20 TraesCS6B01G032700 chr2B 93.276 818 36 4 4449 5248 757563515 757562699 0.000000e+00 1188.0
21 TraesCS6B01G032700 chr2B 100.000 56 0 0 4447 4502 615358916 615358861 2.590000e-18 104.0
22 TraesCS6B01G032700 chr2B 92.500 40 2 1 454 493 779043653 779043615 7.340000e-04 56.5
23 TraesCS6B01G032700 chr3A 92.770 816 41 3 4449 5248 163874785 163873972 0.000000e+00 1164.0
24 TraesCS6B01G032700 chr7D 92.525 816 43 2 4449 5248 34675443 34674630 0.000000e+00 1153.0
25 TraesCS6B01G032700 chrUn 90.083 363 18 2 4449 4795 10529636 10529996 6.200000e-124 455.0


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 TraesCS6B01G032700 chr6B 19124142 19129389 5247 False 4582.000000 7845 100.000000 1 5248 2 chr6B.!!$F1 5247
1 TraesCS6B01G032700 chr6B 641300906 641301636 730 True 1229.000000 1229 96.990000 4518 5248 1 chr6B.!!$R1 730
2 TraesCS6B01G032700 chr6D 10413398 10420762 7364 False 2025.566667 5480 89.673667 1 4447 3 chr6D.!!$F1 4446
3 TraesCS6B01G032700 chr6A 11962826 11970116 7290 False 1953.900000 5343 88.883667 1 4447 3 chr6A.!!$F1 4446
4 TraesCS6B01G032700 chr7B 632802182 632802932 750 False 1249.000000 1249 96.671000 4498 5248 1 chr7B.!!$F1 750
5 TraesCS6B01G032700 chr7B 28972267 28973087 820 True 1206.000000 1206 93.552000 4445 5248 1 chr7B.!!$R1 803
6 TraesCS6B01G032700 chr3B 2342305 2343050 745 True 1240.000000 1240 96.649000 4503 5248 1 chr3B.!!$R1 745
7 TraesCS6B01G032700 chr3B 256360419 256361235 816 False 1238.000000 1238 94.370000 4449 5248 1 chr3B.!!$F1 799
8 TraesCS6B01G032700 chr4B 37869781 37870591 810 True 1223.000000 1223 94.212000 4453 5248 1 chr4B.!!$R1 795
9 TraesCS6B01G032700 chr1B 629922535 629923352 817 False 1223.000000 1223 94.010000 4449 5248 1 chr1B.!!$F1 799
10 TraesCS6B01G032700 chr1B 56261221 56262038 817 True 1170.000000 1170 92.805000 4447 5248 1 chr1B.!!$R1 801
11 TraesCS6B01G032700 chr5B 65534090 65534840 750 False 1216.000000 1216 95.872000 4498 5248 1 chr5B.!!$F1 750
12 TraesCS6B01G032700 chr5B 692127458 692128209 751 True 1210.000000 1210 95.745000 4498 5248 1 chr5B.!!$R1 750
13 TraesCS6B01G032700 chr2B 423910538 423911347 809 True 1214.000000 1214 94.074000 4457 5248 1 chr2B.!!$R1 791
14 TraesCS6B01G032700 chr2B 232451686 232452502 816 False 1210.000000 1210 93.758000 4449 5248 1 chr2B.!!$F1 799
15 TraesCS6B01G032700 chr2B 757562699 757563515 816 True 1188.000000 1188 93.276000 4449 5248 1 chr2B.!!$R3 799
16 TraesCS6B01G032700 chr3A 163873972 163874785 813 True 1164.000000 1164 92.770000 4449 5248 1 chr3A.!!$R1 799
17 TraesCS6B01G032700 chr7D 34674630 34675443 813 True 1153.000000 1153 92.525000 4449 5248 1 chr7D.!!$R1 799

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
125 139 0.032017 TTCTCCCCTCTGCCTCTACC 60.032 60.0 0.0 0.0 0.00 3.18 F
689 777 0.400670 AGCCCATACTCCCTTCCTCC 60.401 60.0 0.0 0.0 0.00 4.30 F
1246 1344 0.179020 GGTGCATCGGATTCCCATCA 60.179 55.0 0.0 0.0 0.00 3.07 F
1491 1601 0.037975 CCTTGGCTGATGTTGTTGCC 60.038 55.0 0.0 0.0 45.10 4.52 F
2103 2215 0.736325 AATCTGAAGGCGGTTCGTCG 60.736 55.0 0.0 0.0 38.09 5.12 F
2256 2368 0.754957 TTCTGTTTGGTGGCTGTGGG 60.755 55.0 0.0 0.0 0.00 4.61 F
4000 4115 0.601558 CTGCTTCAATGTGGCTTGCT 59.398 50.0 0.0 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1227 1325 0.179020 TGATGGGAATCCGATGCACC 60.179 55.000 0.27 0.0 35.24 5.01 R
1491 1601 0.732880 CGTGCCTAGAACAGTGACCG 60.733 60.000 0.00 0.0 0.00 4.79 R
2568 2680 0.747283 CCTGCTGGCCTCTCATGTTC 60.747 60.000 3.32 0.0 0.00 3.18 R
2996 3108 3.244491 TGCCAAAACTTCCAATTGGATGG 60.244 43.478 32.47 30.6 45.14 3.51 R
3496 3611 0.028902 ACTGAAAACACGAAAGGCGC 59.971 50.000 0.00 0.0 46.04 6.53 R
4169 4284 0.474854 TACAGACCCCAAGAGCCCAA 60.475 55.000 0.00 0.0 0.00 4.12 R
4967 6247 1.492176 CCAGATCTAGCAACCCACCAT 59.508 52.381 0.00 0.0 0.00 3.55 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
67 68 5.810080 AGATTAGGTATTACCCTGAGCAC 57.190 43.478 9.31 0.00 39.75 4.40
85 86 4.416738 GAGCAGCACCCCCACCTC 62.417 72.222 0.00 0.00 0.00 3.85
96 110 4.742201 CCACCTCCACGGCGTCAG 62.742 72.222 10.85 9.24 35.61 3.51
108 122 1.515304 GCGTCAGTCGAGCTCCTTC 60.515 63.158 8.47 0.00 42.86 3.46
109 123 1.928706 GCGTCAGTCGAGCTCCTTCT 61.929 60.000 8.47 1.02 42.86 2.85
112 126 0.681564 TCAGTCGAGCTCCTTCTCCC 60.682 60.000 8.47 0.00 0.00 4.30
122 136 1.002792 CCTTCTCCCCTCTGCCTCT 59.997 63.158 0.00 0.00 0.00 3.69
125 139 0.032017 TTCTCCCCTCTGCCTCTACC 60.032 60.000 0.00 0.00 0.00 3.18
126 140 0.926720 TCTCCCCTCTGCCTCTACCT 60.927 60.000 0.00 0.00 0.00 3.08
127 141 0.469144 CTCCCCTCTGCCTCTACCTC 60.469 65.000 0.00 0.00 0.00 3.85
144 158 2.202492 CGGTCGTTGAGCTCCTCG 60.202 66.667 12.15 15.48 32.35 4.63
145 159 2.507324 GGTCGTTGAGCTCCTCGC 60.507 66.667 12.15 11.23 39.57 5.03
164 178 1.826385 CCGAAGGCTCCATTTCACTT 58.174 50.000 0.00 0.00 46.14 3.16
173 187 3.245990 GCTCCATTTCACTTTGTTGTTGC 59.754 43.478 0.00 0.00 0.00 4.17
203 217 0.630673 CCAATGGTGAGGATGGGGAA 59.369 55.000 0.00 0.00 0.00 3.97
208 222 1.010046 TGGTGAGGATGGGGAAGAGAT 59.990 52.381 0.00 0.00 0.00 2.75
212 226 1.696884 GAGGATGGGGAAGAGATGGTC 59.303 57.143 0.00 0.00 0.00 4.02
213 227 1.010046 AGGATGGGGAAGAGATGGTCA 59.990 52.381 0.00 0.00 0.00 4.02
221 235 3.906846 GGGAAGAGATGGTCATGGTAGAT 59.093 47.826 0.00 0.00 0.00 1.98
222 236 4.020662 GGGAAGAGATGGTCATGGTAGATC 60.021 50.000 0.00 0.00 0.00 2.75
223 237 4.837860 GGAAGAGATGGTCATGGTAGATCT 59.162 45.833 0.00 0.00 0.00 2.75
250 264 4.954118 AGTGGACGAGGGGGCACA 62.954 66.667 0.00 0.00 0.00 4.57
251 265 3.717294 GTGGACGAGGGGGCACAT 61.717 66.667 0.00 0.00 0.00 3.21
252 266 2.039787 TGGACGAGGGGGCACATA 59.960 61.111 0.00 0.00 0.00 2.29
253 267 1.383943 TGGACGAGGGGGCACATAT 60.384 57.895 0.00 0.00 0.00 1.78
254 268 1.071471 GGACGAGGGGGCACATATG 59.929 63.158 0.00 0.00 0.00 1.78
255 269 1.696097 GGACGAGGGGGCACATATGT 61.696 60.000 1.41 1.41 0.00 2.29
268 282 1.570501 ACATATGTGATGGGCAGGGTT 59.429 47.619 7.78 0.00 0.00 4.11
340 354 8.851541 AACATGAACATGGCATTTTAAGAAAT 57.148 26.923 17.25 0.00 42.91 2.17
342 356 9.287373 ACATGAACATGGCATTTTAAGAAATTT 57.713 25.926 17.25 0.00 42.91 1.82
435 450 8.954950 TTTTCAAACAATATGTTGGTGACATT 57.045 26.923 7.15 0.00 46.80 2.71
499 517 9.754382 CATAGTTTTATAAAATGCTTCATGCCT 57.246 29.630 13.54 5.10 42.00 4.75
682 770 1.149401 GCCAAGAGCCCATACTCCC 59.851 63.158 0.00 0.00 37.39 4.30
685 773 1.141858 CCAAGAGCCCATACTCCCTTC 59.858 57.143 0.00 0.00 37.39 3.46
687 775 0.644937 AGAGCCCATACTCCCTTCCT 59.355 55.000 0.00 0.00 37.39 3.36
689 777 0.400670 AGCCCATACTCCCTTCCTCC 60.401 60.000 0.00 0.00 0.00 4.30
690 778 0.400670 GCCCATACTCCCTTCCTCCT 60.401 60.000 0.00 0.00 0.00 3.69
691 779 1.428869 CCCATACTCCCTTCCTCCTG 58.571 60.000 0.00 0.00 0.00 3.86
693 781 2.482494 CCATACTCCCTTCCTCCTGTT 58.518 52.381 0.00 0.00 0.00 3.16
694 782 2.436173 CCATACTCCCTTCCTCCTGTTC 59.564 54.545 0.00 0.00 0.00 3.18
695 783 2.249309 TACTCCCTTCCTCCTGTTCC 57.751 55.000 0.00 0.00 0.00 3.62
696 784 0.494095 ACTCCCTTCCTCCTGTTCCT 59.506 55.000 0.00 0.00 0.00 3.36
697 785 1.132365 ACTCCCTTCCTCCTGTTCCTT 60.132 52.381 0.00 0.00 0.00 3.36
698 786 2.113777 ACTCCCTTCCTCCTGTTCCTTA 59.886 50.000 0.00 0.00 0.00 2.69
1042 1140 4.148825 CGCCTCCTGTCCCCTTCG 62.149 72.222 0.00 0.00 0.00 3.79
1046 1144 4.332543 TCCTGTCCCCTTCGCCCT 62.333 66.667 0.00 0.00 0.00 5.19
1147 1245 3.718210 CTTCTCCGGCTGGTACGCC 62.718 68.421 12.43 1.89 42.73 5.68
1148 1246 4.753662 TCTCCGGCTGGTACGCCT 62.754 66.667 12.43 0.00 43.66 5.52
1164 1262 0.747255 GCCTCCAGCACGATCTTCTA 59.253 55.000 0.00 0.00 42.97 2.10
1183 1281 0.537188 ACCTCGCAATCCGATGTCTT 59.463 50.000 0.00 0.00 46.31 3.01
1192 1290 4.194640 CAATCCGATGTCTTGATTCCAGT 58.805 43.478 0.00 0.00 0.00 4.00
1195 1293 2.932614 CCGATGTCTTGATTCCAGTCAC 59.067 50.000 0.00 0.00 0.00 3.67
1196 1294 3.588955 CGATGTCTTGATTCCAGTCACA 58.411 45.455 0.00 0.00 0.00 3.58
1197 1295 3.369147 CGATGTCTTGATTCCAGTCACAC 59.631 47.826 0.00 0.00 0.00 3.82
1246 1344 0.179020 GGTGCATCGGATTCCCATCA 60.179 55.000 0.00 0.00 0.00 3.07
1438 1548 2.306219 AGCTCCCCCTTTTCTTCAGTAC 59.694 50.000 0.00 0.00 0.00 2.73
1458 1568 6.422100 CAGTACACTATACATGATGCTGAACC 59.578 42.308 0.00 0.00 0.00 3.62
1491 1601 0.037975 CCTTGGCTGATGTTGTTGCC 60.038 55.000 0.00 0.00 45.10 4.52
1564 1674 1.672356 GACATGGAGTTGGCGCAGT 60.672 57.895 10.83 0.00 0.00 4.40
1595 1705 3.935203 GCTGCAGAATTGAGCACTAGTAA 59.065 43.478 20.43 0.00 36.62 2.24
1620 1730 1.929836 GTGGTAAGATCTTGCTCGCAG 59.070 52.381 20.91 0.00 0.00 5.18
1727 1838 5.760253 GGCACATGTACTTGCTGTTATATCT 59.240 40.000 8.58 0.00 38.85 1.98
1908 2020 2.028476 TGTACCTCAACATAGCAAGCGT 60.028 45.455 0.00 0.00 0.00 5.07
2097 2209 3.558674 CCTTGAATCTGAAGGCGGT 57.441 52.632 0.00 0.00 33.84 5.68
2100 2212 1.394917 CTTGAATCTGAAGGCGGTTCG 59.605 52.381 0.00 0.00 38.09 3.95
2103 2215 0.736325 AATCTGAAGGCGGTTCGTCG 60.736 55.000 0.00 0.00 38.09 5.12
2122 2234 5.472478 TCGTCGACAAGTATAATATCAGGCT 59.528 40.000 17.16 0.00 0.00 4.58
2149 2261 5.082251 TGACCATCATCAGAGTCTTTCAG 57.918 43.478 0.00 0.00 0.00 3.02
2151 2263 3.204526 CCATCATCAGAGTCTTTCAGCC 58.795 50.000 0.00 0.00 0.00 4.85
2221 2333 4.916249 GCTCTCATTTGTTGAAGCAAAGAG 59.084 41.667 0.00 5.90 41.00 2.85
2247 2359 2.040178 ACGAGAGAGGTTCTGTTTGGT 58.960 47.619 0.00 0.00 35.87 3.67
2256 2368 0.754957 TTCTGTTTGGTGGCTGTGGG 60.755 55.000 0.00 0.00 0.00 4.61
2298 2410 4.121317 CACTTCAGAGATGGCTTGAGATC 58.879 47.826 0.00 0.00 0.00 2.75
2344 2456 3.236816 GTTGGTGCAAGTCATTTCGATG 58.763 45.455 0.00 0.00 0.00 3.84
2377 2489 2.092914 GGTGTCAAGAAGTGGATAGGGG 60.093 54.545 0.00 0.00 0.00 4.79
2568 2680 4.734398 ACTTAGTCAAGAGGATGCTGAG 57.266 45.455 0.00 0.00 35.60 3.35
2692 2804 9.823098 GCGATAAAACGTAAGAGAATCTCTATA 57.177 33.333 13.82 5.76 39.21 1.31
2734 2846 0.839277 CCCACCATCTGTATGCCTGA 59.161 55.000 0.00 0.00 0.00 3.86
2742 2854 4.418392 CATCTGTATGCCTGAAGTTTTGC 58.582 43.478 0.00 0.00 0.00 3.68
2778 2890 9.305110 CAAATTTGTTAATTGCGAAGATTGTTC 57.695 29.630 10.15 0.00 34.27 3.18
3003 3115 7.237982 TCTCTTATTTTGAACTTCCCATCCAA 58.762 34.615 0.00 0.00 0.00 3.53
3066 3178 8.996024 TTTTCCAAATAATGTAGCTTAAAGGC 57.004 30.769 0.00 0.00 0.00 4.35
3070 3182 6.321181 CCAAATAATGTAGCTTAAAGGCTCCA 59.679 38.462 0.00 0.00 42.97 3.86
3079 3191 6.001449 AGCTTAAAGGCTCCATTATGTGTA 57.999 37.500 0.00 0.00 38.24 2.90
3114 3226 2.173782 TGGTGCCCAGTTTTCTGTTCTA 59.826 45.455 0.00 0.00 45.68 2.10
3201 3314 4.494091 TGAGATTGATCCTGAACCCTTC 57.506 45.455 0.00 0.00 0.00 3.46
3205 3318 3.874383 TTGATCCTGAACCCTTCAACA 57.126 42.857 0.00 0.00 39.58 3.33
3206 3319 4.387026 TTGATCCTGAACCCTTCAACAT 57.613 40.909 0.00 0.00 39.58 2.71
3378 3492 0.967380 AAAAAGGATGGCCGAGGCTG 60.967 55.000 14.33 0.00 41.60 4.85
3466 3580 9.906660 AAATATGAATTTTAGACGCTTGACAAA 57.093 25.926 0.00 0.00 30.98 2.83
3825 3940 0.951040 GGTGTTCTGTCTCAAGGCGG 60.951 60.000 0.00 0.00 0.00 6.13
3978 4093 1.734465 CTTGGCGCCTCTACAAAGAAG 59.266 52.381 29.70 15.29 0.00 2.85
4000 4115 0.601558 CTGCTTCAATGTGGCTTGCT 59.398 50.000 0.00 0.00 0.00 3.91
4122 4237 4.330620 GTGACAGTCTCGTGTTGGTTTTAA 59.669 41.667 1.31 0.00 0.00 1.52
4169 4284 0.958382 TTTGTTGCGCCGCTATCCTT 60.958 50.000 11.67 0.00 0.00 3.36
4234 4349 0.100682 TCTCACGGAGCGCACTATTC 59.899 55.000 11.47 0.00 0.00 1.75
4238 4353 0.818296 ACGGAGCGCACTATTCTCTT 59.182 50.000 11.47 0.00 0.00 2.85
4412 4528 1.949525 ACACATAGGATGGCAAATCGC 59.050 47.619 0.00 0.00 41.28 4.58
4433 4549 1.428448 GTACGCACAGCACATTCAGA 58.572 50.000 0.00 0.00 0.00 3.27
4447 4563 6.600822 AGCACATTCAGATTATTAGTTGCTGT 59.399 34.615 0.00 0.00 0.00 4.40
4678 5456 6.408858 TGACAACGCTGAATAAAGATTCTC 57.591 37.500 0.00 0.00 41.87 2.87
4967 6247 1.614903 TCTCCTTCGGCGTTTTAGTCA 59.385 47.619 6.85 0.00 0.00 3.41
5087 6367 2.202566 GAGGTCCGTAAAGCTGCATAC 58.797 52.381 1.02 4.01 0.00 2.39
5122 6402 0.678366 GTCGAGCTCAGGTCAGGAGA 60.678 60.000 15.40 0.00 34.24 3.71
5242 7759 5.007234 CAGTTTTGTCATGTCGGTCTTTACA 59.993 40.000 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 5.475909 CGTGCTCAGGGTAATACCTAATCTA 59.524 44.000 9.58 0.00 39.34 1.98
52 53 1.136305 TGCTCGTGCTCAGGGTAATAC 59.864 52.381 11.19 0.00 40.48 1.89
55 56 1.591703 CTGCTCGTGCTCAGGGTAA 59.408 57.895 11.19 0.00 40.48 2.85
83 84 3.669036 CTCGACTGACGCCGTGGAG 62.669 68.421 0.00 0.00 42.26 3.86
84 85 3.733960 CTCGACTGACGCCGTGGA 61.734 66.667 0.00 0.00 42.26 4.02
86 87 4.406173 AGCTCGACTGACGCCGTG 62.406 66.667 0.00 0.00 42.26 4.94
96 110 1.380650 AGGGGAGAAGGAGCTCGAC 60.381 63.158 7.83 1.43 35.74 4.20
108 122 0.469144 GAGGTAGAGGCAGAGGGGAG 60.469 65.000 0.00 0.00 0.00 4.30
109 123 1.621377 GAGGTAGAGGCAGAGGGGA 59.379 63.158 0.00 0.00 0.00 4.81
112 126 1.076632 ACCGAGGTAGAGGCAGAGG 60.077 63.158 0.00 0.00 0.00 3.69
122 136 1.310933 GGAGCTCAACGACCGAGGTA 61.311 60.000 17.19 0.00 41.13 3.08
125 139 1.137825 GAGGAGCTCAACGACCGAG 59.862 63.158 17.19 0.00 0.00 4.63
126 140 2.687805 CGAGGAGCTCAACGACCGA 61.688 63.158 21.41 0.00 0.00 4.69
127 141 2.202492 CGAGGAGCTCAACGACCG 60.202 66.667 21.41 9.32 0.00 4.79
145 159 1.826385 AAGTGAAATGGAGCCTTCGG 58.174 50.000 0.00 0.00 0.00 4.30
156 170 3.186119 CACGGCAACAACAAAGTGAAAT 58.814 40.909 0.00 0.00 0.00 2.17
158 172 1.542030 ACACGGCAACAACAAAGTGAA 59.458 42.857 0.19 0.00 34.16 3.18
164 178 0.960861 TCACCACACGGCAACAACAA 60.961 50.000 0.00 0.00 34.57 2.83
173 187 1.228124 ACCATTGGTCACCACACGG 60.228 57.895 0.00 0.00 30.78 4.94
203 217 4.078537 CGAGATCTACCATGACCATCTCT 58.921 47.826 15.81 3.95 38.13 3.10
208 222 2.748209 TCCGAGATCTACCATGACCA 57.252 50.000 0.00 0.00 0.00 4.02
212 226 4.100189 ACTTTCCTTCCGAGATCTACCATG 59.900 45.833 0.00 0.00 0.00 3.66
213 227 4.100189 CACTTTCCTTCCGAGATCTACCAT 59.900 45.833 0.00 0.00 0.00 3.55
221 235 0.601558 CGTCCACTTTCCTTCCGAGA 59.398 55.000 0.00 0.00 0.00 4.04
222 236 0.601558 TCGTCCACTTTCCTTCCGAG 59.398 55.000 0.00 0.00 0.00 4.63
223 237 0.601558 CTCGTCCACTTTCCTTCCGA 59.398 55.000 0.00 0.00 0.00 4.55
250 264 1.570501 ACAACCCTGCCCATCACATAT 59.429 47.619 0.00 0.00 0.00 1.78
251 265 0.998928 ACAACCCTGCCCATCACATA 59.001 50.000 0.00 0.00 0.00 2.29
252 266 0.323725 GACAACCCTGCCCATCACAT 60.324 55.000 0.00 0.00 0.00 3.21
253 267 1.074775 GACAACCCTGCCCATCACA 59.925 57.895 0.00 0.00 0.00 3.58
254 268 0.962356 CTGACAACCCTGCCCATCAC 60.962 60.000 0.00 0.00 0.00 3.06
255 269 1.379916 CTGACAACCCTGCCCATCA 59.620 57.895 0.00 0.00 0.00 3.07
256 270 0.962356 CACTGACAACCCTGCCCATC 60.962 60.000 0.00 0.00 0.00 3.51
257 271 1.075482 CACTGACAACCCTGCCCAT 59.925 57.895 0.00 0.00 0.00 4.00
258 272 2.515398 CACTGACAACCCTGCCCA 59.485 61.111 0.00 0.00 0.00 5.36
259 273 2.282462 CCACTGACAACCCTGCCC 60.282 66.667 0.00 0.00 0.00 5.36
260 274 2.282462 CCCACTGACAACCCTGCC 60.282 66.667 0.00 0.00 0.00 4.85
261 275 2.985847 GCCCACTGACAACCCTGC 60.986 66.667 0.00 0.00 0.00 4.85
262 276 2.669569 CGCCCACTGACAACCCTG 60.670 66.667 0.00 0.00 0.00 4.45
263 277 4.643387 GCGCCCACTGACAACCCT 62.643 66.667 0.00 0.00 0.00 4.34
268 282 4.961511 GTCACGCGCCCACTGACA 62.962 66.667 18.54 0.00 35.39 3.58
315 329 8.851541 ATTTCTTAAAATGCCATGTTCATGTT 57.148 26.923 11.13 6.06 33.78 2.71
408 423 8.954950 TGTCACCAACATATTGTTTGAAAAAT 57.045 26.923 0.00 0.00 38.77 1.82
534 552 7.871973 ACATGCTGTGAATTGTTTTGCTAATAA 59.128 29.630 0.00 0.00 0.00 1.40
622 710 8.784043 GGACACTGCGGATTTATTATTTTCTAT 58.216 33.333 0.00 0.00 0.00 1.98
625 713 6.791303 TGGACACTGCGGATTTATTATTTTC 58.209 36.000 0.00 0.00 0.00 2.29
631 719 5.290493 TCTATGGACACTGCGGATTTATT 57.710 39.130 0.00 0.00 0.00 1.40
678 766 1.662686 AAGGAACAGGAGGAAGGGAG 58.337 55.000 0.00 0.00 0.00 4.30
682 770 8.687242 GGATTAAAAATAAGGAACAGGAGGAAG 58.313 37.037 0.00 0.00 0.00 3.46
685 773 6.459710 GCGGATTAAAAATAAGGAACAGGAGG 60.460 42.308 0.00 0.00 0.00 4.30
687 775 5.946972 TGCGGATTAAAAATAAGGAACAGGA 59.053 36.000 0.00 0.00 0.00 3.86
689 777 6.852664 ACTGCGGATTAAAAATAAGGAACAG 58.147 36.000 0.00 0.00 0.00 3.16
690 778 6.827586 ACTGCGGATTAAAAATAAGGAACA 57.172 33.333 0.00 0.00 0.00 3.18
1025 1123 4.148825 CGAAGGGGACAGGAGGCG 62.149 72.222 0.00 0.00 0.00 5.52
1029 1127 4.332543 AGGGCGAAGGGGACAGGA 62.333 66.667 0.00 0.00 0.00 3.86
1065 1163 3.827898 GACTGGAGGCGGGTCGAG 61.828 72.222 0.00 0.00 0.00 4.04
1147 1245 2.028130 AGGTAGAAGATCGTGCTGGAG 58.972 52.381 0.00 0.00 0.00 3.86
1148 1246 2.025155 GAGGTAGAAGATCGTGCTGGA 58.975 52.381 0.00 0.00 0.00 3.86
1154 1252 2.034812 GGATTGCGAGGTAGAAGATCGT 59.965 50.000 0.00 0.00 38.66 3.73
1164 1262 0.537188 AAGACATCGGATTGCGAGGT 59.463 50.000 17.52 17.52 32.98 3.85
1183 1281 1.135960 TGGTGGTGTGACTGGAATCA 58.864 50.000 0.00 0.00 0.00 2.57
1192 1290 0.598942 CGTCAATCGTGGTGGTGTGA 60.599 55.000 0.00 0.00 34.52 3.58
1195 1293 2.032634 CCCGTCAATCGTGGTGGTG 61.033 63.158 0.00 0.00 37.94 4.17
1196 1294 2.345991 CCCGTCAATCGTGGTGGT 59.654 61.111 0.00 0.00 37.94 4.16
1197 1295 3.124921 GCCCGTCAATCGTGGTGG 61.125 66.667 0.00 0.00 37.94 4.61
1227 1325 0.179020 TGATGGGAATCCGATGCACC 60.179 55.000 0.27 0.00 35.24 5.01
1231 1329 4.934001 CAGAACTATGATGGGAATCCGATG 59.066 45.833 0.27 0.00 35.24 3.84
1246 1344 9.751542 CGAAATCTTGTATAAGGACAGAACTAT 57.248 33.333 0.00 0.00 34.59 2.12
1289 1387 5.998454 ATCAAGAATTATCGCTGTTCCTG 57.002 39.130 0.00 0.00 0.00 3.86
1438 1548 9.881649 ATTATAGGTTCAGCATCATGTATAGTG 57.118 33.333 0.00 0.00 0.00 2.74
1458 1568 6.942532 TCAGCCAAGGCAGTAAAATTATAG 57.057 37.500 14.40 0.00 44.88 1.31
1491 1601 0.732880 CGTGCCTAGAACAGTGACCG 60.733 60.000 0.00 0.00 0.00 4.79
1575 1685 5.491070 ACATTACTAGTGCTCAATTCTGCA 58.509 37.500 5.39 0.00 36.79 4.41
1595 1705 3.735208 CGAGCAAGATCTTACCACGACAT 60.735 47.826 7.86 0.00 0.00 3.06
1908 2020 3.028850 AGAATCGTCATTAGGGAACGGA 58.971 45.455 0.00 0.00 0.00 4.69
2097 2209 6.016527 AGCCTGATATTATACTTGTCGACGAA 60.017 38.462 11.62 5.72 0.00 3.85
2100 2212 8.244802 ACATAGCCTGATATTATACTTGTCGAC 58.755 37.037 9.11 9.11 0.00 4.20
2103 2215 9.929180 TCAACATAGCCTGATATTATACTTGTC 57.071 33.333 0.00 0.00 0.00 3.18
2122 2234 6.550938 AAGACTCTGATGATGGTCAACATA 57.449 37.500 0.00 0.00 40.72 2.29
2149 2261 1.452108 CCCATCCCTTGTCTTCGGC 60.452 63.158 0.00 0.00 0.00 5.54
2151 2263 0.839946 ATCCCCATCCCTTGTCTTCG 59.160 55.000 0.00 0.00 0.00 3.79
2213 2325 2.036475 TCTCTCGTTTCTGCTCTTTGCT 59.964 45.455 0.00 0.00 43.37 3.91
2221 2333 2.288518 ACAGAACCTCTCTCGTTTCTGC 60.289 50.000 9.54 0.00 29.07 4.26
2232 2344 0.846693 AGCCACCAAACAGAACCTCT 59.153 50.000 0.00 0.00 0.00 3.69
2247 2359 0.754957 CAGGAACAAACCCACAGCCA 60.755 55.000 0.00 0.00 0.00 4.75
2256 2368 3.253432 GTGAAGGGATGTCAGGAACAAAC 59.747 47.826 0.00 0.00 42.37 2.93
2298 2410 4.423732 CATCAAAACCTTTATCCCAAGCG 58.576 43.478 0.00 0.00 0.00 4.68
2344 2456 6.146021 CACTTCTTGACACCATAAATTTTGCC 59.854 38.462 0.00 0.00 0.00 4.52
2377 2489 3.878778 AGAGGGTAACACATTCTGATGC 58.121 45.455 0.00 0.00 36.72 3.91
2568 2680 0.747283 CCTGCTGGCCTCTCATGTTC 60.747 60.000 3.32 0.00 0.00 3.18
2692 2804 7.147141 TGGGATAGGACATTCCATAAACAAGAT 60.147 37.037 0.00 0.00 39.61 2.40
2742 2854 6.031625 GCAATTAACAAATTTGCATGCTTTCG 59.968 34.615 20.33 8.56 41.80 3.46
2753 2865 9.260002 AGAACAATCTTCGCAATTAACAAATTT 57.740 25.926 0.00 0.00 29.15 1.82
2756 2868 9.737427 TTTAGAACAATCTTCGCAATTAACAAA 57.263 25.926 0.00 0.00 37.10 2.83
2981 3093 7.550196 CCAATTGGATGGGAAGTTCAAAATAAG 59.450 37.037 20.50 0.00 36.79 1.73
2996 3108 3.244491 TGCCAAAACTTCCAATTGGATGG 60.244 43.478 32.47 30.60 45.14 3.51
3003 3115 4.486125 AACAACTGCCAAAACTTCCAAT 57.514 36.364 0.00 0.00 0.00 3.16
3044 3156 6.546034 GGAGCCTTTAAGCTACATTATTTGGA 59.454 38.462 0.00 0.00 45.15 3.53
3149 3262 8.585018 TCATCCTCTCGAACAGCATAAATTATA 58.415 33.333 0.00 0.00 0.00 0.98
3170 3283 5.011840 TCAGGATCAATCTCATCAGTCATCC 59.988 44.000 0.00 0.00 0.00 3.51
3491 3606 0.951558 AAACACGAAAGGCGCAAGAT 59.048 45.000 10.83 0.00 46.04 2.40
3496 3611 0.028902 ACTGAAAACACGAAAGGCGC 59.971 50.000 0.00 0.00 46.04 6.53
3825 3940 3.817647 AGCCATCAGAAGTGACAAGAAAC 59.182 43.478 0.00 0.00 34.75 2.78
3978 4093 0.886563 AAGCCACATTGAAGCAGAGC 59.113 50.000 0.00 0.00 0.00 4.09
4122 4237 4.134379 TGGATGTGCAAAAACATGTGTT 57.866 36.364 0.00 0.00 40.50 3.32
4169 4284 0.474854 TACAGACCCCAAGAGCCCAA 60.475 55.000 0.00 0.00 0.00 4.12
4412 4528 1.288419 TGAATGTGCTGTGCGTACGG 61.288 55.000 18.39 8.26 36.22 4.02
4433 4549 7.390718 ACGAGAGGAAAAACAGCAACTAATAAT 59.609 33.333 0.00 0.00 0.00 1.28
4447 4563 3.570912 AAACAGGGACGAGAGGAAAAA 57.429 42.857 0.00 0.00 0.00 1.94
4501 4810 1.807573 GAGAGCGGCGTTGGAAGAG 60.808 63.158 9.37 0.00 0.00 2.85
4967 6247 1.492176 CCAGATCTAGCAACCCACCAT 59.508 52.381 0.00 0.00 0.00 3.55
5112 6392 2.739943 TGACGAATCATCTCCTGACCT 58.260 47.619 0.00 0.00 36.48 3.85


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

AutoCloner maintained by Alex Coulton.