Multiple sequence alignment - TraesCS7D01G353700

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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 TraesCS7D01G353700 chr7D 100.000 3060 0 0 974 4033 457184625 457187684 0.000000e+00 5651.0
1 TraesCS7D01G353700 chr7D 94.681 2162 100 11 1116 3275 201196087 201193939 0.000000e+00 3341.0
2 TraesCS7D01G353700 chr7D 94.626 763 35 1 3271 4033 503843761 503843005 0.000000e+00 1177.0
3 TraesCS7D01G353700 chr7D 94.226 762 36 1 3271 4032 32565775 32565022 0.000000e+00 1157.0
4 TraesCS7D01G353700 chr7D 100.000 600 0 0 1 600 457183652 457184251 0.000000e+00 1109.0
5 TraesCS7D01G353700 chr7D 84.483 174 15 5 435 596 201196744 201196571 1.160000e-35 161.0
6 TraesCS7D01G353700 chr7B 94.637 2256 86 16 974 3221 479491692 479493920 0.000000e+00 3463.0
7 TraesCS7D01G353700 chr7B 92.419 277 6 6 335 596 479491394 479491670 8.180000e-102 381.0
8 TraesCS7D01G353700 chr7B 91.364 220 17 2 30 249 479490952 479491169 2.360000e-77 300.0
9 TraesCS7D01G353700 chr7A 93.801 2307 101 22 974 3270 543067219 543064945 0.000000e+00 3430.0
10 TraesCS7D01G353700 chr7A 90.741 54 5 0 440 493 543068151 543068098 5.590000e-09 73.1
11 TraesCS7D01G353700 chrUn 94.488 762 36 1 3271 4032 103459989 103459234 0.000000e+00 1170.0
12 TraesCS7D01G353700 chr1D 93.487 783 33 5 3263 4033 24077274 24078050 0.000000e+00 1147.0
13 TraesCS7D01G353700 chr1D 96.970 33 1 0 1 33 48115526 48115494 5.630000e-04 56.5
14 TraesCS7D01G353700 chr5D 93.455 764 38 7 3271 4033 298026900 298027652 0.000000e+00 1123.0
15 TraesCS7D01G353700 chr5D 92.636 774 39 5 3270 4032 438397507 438396741 0.000000e+00 1098.0
16 TraesCS7D01G353700 chr5D 92.699 767 38 6 3268 4032 43405451 43404701 0.000000e+00 1090.0
17 TraesCS7D01G353700 chr5D 74.703 589 133 14 2443 3024 305731755 305732334 8.660000e-62 248.0
18 TraesCS7D01G353700 chr5D 100.000 29 0 0 1 29 328065203 328065175 2.000000e-03 54.7
19 TraesCS7D01G353700 chr3D 92.147 764 43 13 3270 4031 12308049 12307301 0.000000e+00 1062.0
20 TraesCS7D01G353700 chr6B 91.536 768 56 4 3271 4031 32601879 32602644 0.000000e+00 1050.0
21 TraesCS7D01G353700 chr4D 84.865 370 40 8 2630 2998 456086997 456087351 3.830000e-95 359.0
22 TraesCS7D01G353700 chr4D 100.000 29 0 0 1 29 421593252 421593224 2.000000e-03 54.7
23 TraesCS7D01G353700 chr5B 74.106 587 137 12 2443 3024 350413314 350413890 1.130000e-55 228.0
24 TraesCS7D01G353700 chr2D 100.000 30 0 0 319 348 80142645 80142674 5.630000e-04 56.5
25 TraesCS7D01G353700 chr6D 100.000 29 0 0 1 29 404089458 404089486 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 TraesCS7D01G353700 chr7D 457183652 457187684 4032 False 3380.000000 5651 100.000000 1 4033 2 chr7D.!!$F1 4032
1 TraesCS7D01G353700 chr7D 201193939 201196744 2805 True 1751.000000 3341 89.582000 435 3275 2 chr7D.!!$R3 2840
2 TraesCS7D01G353700 chr7D 503843005 503843761 756 True 1177.000000 1177 94.626000 3271 4033 1 chr7D.!!$R2 762
3 TraesCS7D01G353700 chr7D 32565022 32565775 753 True 1157.000000 1157 94.226000 3271 4032 1 chr7D.!!$R1 761
4 TraesCS7D01G353700 chr7B 479490952 479493920 2968 False 1381.333333 3463 92.806667 30 3221 3 chr7B.!!$F1 3191
5 TraesCS7D01G353700 chr7A 543064945 543068151 3206 True 1751.550000 3430 92.271000 440 3270 2 chr7A.!!$R1 2830
6 TraesCS7D01G353700 chrUn 103459234 103459989 755 True 1170.000000 1170 94.488000 3271 4032 1 chrUn.!!$R1 761
7 TraesCS7D01G353700 chr1D 24077274 24078050 776 False 1147.000000 1147 93.487000 3263 4033 1 chr1D.!!$F1 770
8 TraesCS7D01G353700 chr5D 298026900 298027652 752 False 1123.000000 1123 93.455000 3271 4033 1 chr5D.!!$F1 762
9 TraesCS7D01G353700 chr5D 438396741 438397507 766 True 1098.000000 1098 92.636000 3270 4032 1 chr5D.!!$R3 762
10 TraesCS7D01G353700 chr5D 43404701 43405451 750 True 1090.000000 1090 92.699000 3268 4032 1 chr5D.!!$R1 764
11 TraesCS7D01G353700 chr5D 305731755 305732334 579 False 248.000000 248 74.703000 2443 3024 1 chr5D.!!$F2 581
12 TraesCS7D01G353700 chr3D 12307301 12308049 748 True 1062.000000 1062 92.147000 3270 4031 1 chr3D.!!$R1 761
13 TraesCS7D01G353700 chr6B 32601879 32602644 765 False 1050.000000 1050 91.536000 3271 4031 1 chr6B.!!$F1 760
14 TraesCS7D01G353700 chr5B 350413314 350413890 576 False 228.000000 228 74.106000 2443 3024 1 chr5B.!!$F1 581

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
125 126 0.251354 ATGCAAGAGAGATGCGGTGT 59.749 50.000 0.00 0.0 46.76 4.16 F
244 245 0.457853 CGCTCGGGAAGACGATCAAA 60.458 55.000 0.00 0.0 42.62 2.69 F
1822 3039 0.947244 CCAAATCGGATGCTACAGGC 59.053 55.000 0.00 0.0 38.17 4.85 F
1947 3164 1.690893 GTCCCTGCAGAGATGATGCTA 59.309 52.381 17.39 0.0 44.17 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1822 3039 0.512518 TGACAAACGCAGCGAGAATG 59.487 50.000 24.65 15.92 0.00 2.67 R
2111 3328 4.386711 CCCGAAAAACAGAGGTCTTAAGT 58.613 43.478 1.63 0.00 0.00 2.24 R
2894 4118 1.003118 CACCGAAAGAGTGATTCCCCA 59.997 52.381 0.00 0.00 37.42 4.96 R
3776 5027 1.045407 AGTACGTGAAGTTGGAGGCA 58.955 50.000 0.00 0.00 0.00 4.75 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
24 25 2.029838 ACCATTTGAGGTCTGATCGC 57.970 50.000 0.00 0.00 37.28 4.58
25 26 1.556911 ACCATTTGAGGTCTGATCGCT 59.443 47.619 0.00 0.00 37.28 4.93
26 27 2.766263 ACCATTTGAGGTCTGATCGCTA 59.234 45.455 0.00 0.00 37.28 4.26
27 28 3.126831 CCATTTGAGGTCTGATCGCTAC 58.873 50.000 0.00 0.00 0.00 3.58
28 29 3.430790 CCATTTGAGGTCTGATCGCTACA 60.431 47.826 0.00 0.00 0.00 2.74
76 77 4.695396 TGTAAAGTCCAAAGTAAGCACGA 58.305 39.130 0.00 0.00 0.00 4.35
91 92 1.389106 GCACGACGCTAAAACTCGAAT 59.611 47.619 0.00 0.00 37.77 3.34
92 93 2.532388 GCACGACGCTAAAACTCGAATC 60.532 50.000 0.00 0.00 37.77 2.52
124 125 1.376543 AATGCAAGAGAGATGCGGTG 58.623 50.000 0.00 0.00 46.76 4.94
125 126 0.251354 ATGCAAGAGAGATGCGGTGT 59.749 50.000 0.00 0.00 46.76 4.16
130 131 2.125912 AGAGATGCGGTGTCGTGC 60.126 61.111 0.00 0.00 38.89 5.34
139 140 3.645975 GTGTCGTGCGGTTGTGGG 61.646 66.667 0.00 0.00 0.00 4.61
208 209 2.871096 TTTTTAGCCTGGTGGATCGT 57.129 45.000 0.00 0.00 32.27 3.73
213 214 2.718073 GCCTGGTGGATCGTACGGT 61.718 63.158 16.52 8.53 34.57 4.83
244 245 0.457853 CGCTCGGGAAGACGATCAAA 60.458 55.000 0.00 0.00 42.62 2.69
245 246 1.000145 GCTCGGGAAGACGATCAAAC 59.000 55.000 0.00 0.00 42.62 2.93
246 247 1.404315 GCTCGGGAAGACGATCAAACT 60.404 52.381 0.00 0.00 42.62 2.66
247 248 2.263077 CTCGGGAAGACGATCAAACTG 58.737 52.381 0.00 0.00 42.62 3.16
248 249 1.890489 TCGGGAAGACGATCAAACTGA 59.110 47.619 0.00 0.00 38.06 3.41
249 250 2.094700 TCGGGAAGACGATCAAACTGAG 60.095 50.000 0.00 0.00 38.06 3.35
250 251 2.352814 CGGGAAGACGATCAAACTGAGT 60.353 50.000 0.00 0.00 35.47 3.41
251 252 2.996621 GGGAAGACGATCAAACTGAGTG 59.003 50.000 0.00 0.00 0.00 3.51
252 253 3.306088 GGGAAGACGATCAAACTGAGTGA 60.306 47.826 0.00 0.00 0.00 3.41
253 254 4.307432 GGAAGACGATCAAACTGAGTGAA 58.693 43.478 0.00 0.00 0.00 3.18
254 255 4.150804 GGAAGACGATCAAACTGAGTGAAC 59.849 45.833 0.00 0.00 0.00 3.18
255 256 4.592485 AGACGATCAAACTGAGTGAACT 57.408 40.909 0.00 0.00 0.00 3.01
256 257 4.302455 AGACGATCAAACTGAGTGAACTG 58.698 43.478 0.00 0.00 0.00 3.16
257 258 4.038042 AGACGATCAAACTGAGTGAACTGA 59.962 41.667 0.00 0.00 0.00 3.41
258 259 4.051922 ACGATCAAACTGAGTGAACTGAC 58.948 43.478 0.00 0.00 0.00 3.51
259 260 4.051237 CGATCAAACTGAGTGAACTGACA 58.949 43.478 0.00 0.00 0.00 3.58
260 261 4.687948 CGATCAAACTGAGTGAACTGACAT 59.312 41.667 0.00 0.00 0.00 3.06
261 262 5.178252 CGATCAAACTGAGTGAACTGACATT 59.822 40.000 0.00 0.00 0.00 2.71
262 263 5.991328 TCAAACTGAGTGAACTGACATTC 57.009 39.130 0.00 0.00 0.00 2.67
263 264 4.507756 TCAAACTGAGTGAACTGACATTCG 59.492 41.667 0.00 0.00 30.84 3.34
264 265 2.408050 ACTGAGTGAACTGACATTCGC 58.592 47.619 0.00 0.00 39.02 4.70
265 266 2.224042 ACTGAGTGAACTGACATTCGCA 60.224 45.455 11.28 0.00 40.80 5.10
266 267 2.998670 CTGAGTGAACTGACATTCGCAT 59.001 45.455 11.28 1.41 40.80 4.73
267 268 4.176271 CTGAGTGAACTGACATTCGCATA 58.824 43.478 11.28 2.90 40.80 3.14
268 269 4.565022 TGAGTGAACTGACATTCGCATAA 58.435 39.130 11.28 0.00 40.80 1.90
269 270 4.627035 TGAGTGAACTGACATTCGCATAAG 59.373 41.667 11.28 0.00 40.80 1.73
270 271 4.820897 AGTGAACTGACATTCGCATAAGA 58.179 39.130 11.28 0.00 40.80 2.10
271 272 5.423015 AGTGAACTGACATTCGCATAAGAT 58.577 37.500 11.28 0.00 40.80 2.40
272 273 5.292834 AGTGAACTGACATTCGCATAAGATG 59.707 40.000 11.28 0.00 40.80 2.90
273 274 5.063944 GTGAACTGACATTCGCATAAGATGT 59.936 40.000 0.00 0.00 38.67 3.06
274 275 5.063817 TGAACTGACATTCGCATAAGATGTG 59.936 40.000 0.00 0.00 41.98 3.21
275 276 4.507710 ACTGACATTCGCATAAGATGTGT 58.492 39.130 0.33 0.00 41.38 3.72
276 277 4.937620 ACTGACATTCGCATAAGATGTGTT 59.062 37.500 0.33 0.00 41.38 3.32
346 517 2.524699 GCGAACCGTAAATCGATTTTGC 59.475 45.455 27.10 18.60 41.43 3.68
596 1499 3.925090 CGCTACCCCCGTGATCCC 61.925 72.222 0.00 0.00 0.00 3.85
597 1500 3.557290 GCTACCCCCGTGATCCCC 61.557 72.222 0.00 0.00 0.00 4.81
991 1894 3.254629 CATCAGGAAGTGGTGGTGG 57.745 57.895 0.00 0.00 33.04 4.61
1070 1991 5.084818 TGTATCGACAAACATGGTGATCT 57.915 39.130 5.73 0.00 30.68 2.75
1094 2015 2.124570 CAAGGCCGATGGTGAGGG 60.125 66.667 0.00 0.00 0.00 4.30
1095 2016 2.610859 AAGGCCGATGGTGAGGGT 60.611 61.111 0.00 0.00 0.00 4.34
1096 2017 2.971598 AAGGCCGATGGTGAGGGTG 61.972 63.158 0.00 0.00 0.00 4.61
1099 2020 4.838152 CCGATGGTGAGGGTGCGG 62.838 72.222 0.00 0.00 0.00 5.69
1100 2021 3.770040 CGATGGTGAGGGTGCGGA 61.770 66.667 0.00 0.00 0.00 5.54
1101 2022 2.125106 GATGGTGAGGGTGCGGAC 60.125 66.667 0.00 0.00 0.00 4.79
1102 2023 2.927856 ATGGTGAGGGTGCGGACA 60.928 61.111 9.96 0.00 0.00 4.02
1405 2619 7.867752 TCTCCAAAGTAACCAAAAACGATTAG 58.132 34.615 0.00 0.00 0.00 1.73
1479 2693 3.382546 CCAGGGATAAAGCCAAACTGATG 59.617 47.826 0.00 0.00 0.00 3.07
1506 2720 2.835764 GGTGTGGGTAAGGAGTGACATA 59.164 50.000 0.00 0.00 0.00 2.29
1534 2748 1.066914 CGAAGAACACAGAGAGCTGC 58.933 55.000 0.00 0.00 46.26 5.25
1541 2755 1.068194 ACACAGAGAGCTGCGTAAGAC 60.068 52.381 0.00 0.00 46.26 3.01
1610 2824 3.686016 TGAAAGTATTCCCTCAGGCAAC 58.314 45.455 0.00 0.00 34.49 4.17
1682 2896 3.520290 TGATACTTCCACCAGTAAGCG 57.480 47.619 0.00 0.00 32.90 4.68
1688 2904 1.174783 TCCACCAGTAAGCGAGTCTC 58.825 55.000 0.00 0.00 0.00 3.36
1689 2905 1.178276 CCACCAGTAAGCGAGTCTCT 58.822 55.000 0.00 0.00 0.00 3.10
1822 3039 0.947244 CCAAATCGGATGCTACAGGC 59.053 55.000 0.00 0.00 38.17 4.85
1947 3164 1.690893 GTCCCTGCAGAGATGATGCTA 59.309 52.381 17.39 0.00 44.17 3.49
1991 3208 7.004086 TCAAGTTAGACATGGTTTCTTTCCAT 58.996 34.615 0.00 0.00 45.29 3.41
2026 3243 7.223260 TCTTGCTCAAGAATGATTGATGTTT 57.777 32.000 9.66 0.00 43.79 2.83
2073 3290 8.167392 TGTTGGTTATCTTCTTTCCTTGGATTA 58.833 33.333 0.00 0.00 0.00 1.75
2086 3303 8.488651 TTTCCTTGGATTAGATCGACTAAAAC 57.511 34.615 10.21 7.72 43.15 2.43
2111 3328 4.898320 AGTCATGTGTGCTCAGATTTGTA 58.102 39.130 0.00 0.00 0.00 2.41
2164 3381 9.487790 AACCCATTTTGAAATACATGTTAACTG 57.512 29.630 2.30 5.45 0.00 3.16
2284 3502 7.148255 GCGGTTGGCAAGATATATAAATGATGA 60.148 37.037 0.00 0.00 42.87 2.92
2336 3554 7.640616 TGCATTTCAACACAAGTGAAATATG 57.359 32.000 7.28 4.67 39.40 1.78
2398 3620 8.836268 AAACATGATGTGCAATGTCTTATTTT 57.164 26.923 0.00 0.00 0.00 1.82
2468 3692 7.494625 TGTTTAGTTCTAACCAGAGTTGTCAAG 59.505 37.037 0.00 0.00 36.68 3.02
2469 3693 5.871396 AGTTCTAACCAGAGTTGTCAAGA 57.129 39.130 0.00 0.00 36.68 3.02
2470 3694 5.848406 AGTTCTAACCAGAGTTGTCAAGAG 58.152 41.667 0.00 0.00 36.68 2.85
2603 3827 5.280945 GCTGACAAACAAATACTTTCTGCA 58.719 37.500 0.00 0.00 0.00 4.41
3249 4477 9.952030 ATTGTTTTTCTTTTCCCTTTAGTTTGA 57.048 25.926 0.00 0.00 0.00 2.69
3259 4487 6.515272 TCCCTTTAGTTTGATTGCATCTTC 57.485 37.500 0.00 0.00 0.00 2.87
3353 4581 6.376299 TGTCTTCCTCTGTATGTACGTGTATT 59.624 38.462 0.00 0.00 0.00 1.89
3401 4629 8.705594 GCATCCCTTGTACCTATATATATGTGT 58.294 37.037 5.44 5.10 0.00 3.72
3465 4693 7.612668 TCTCTACATGGTATCTATCGTAAGC 57.387 40.000 0.00 0.00 37.18 3.09
3483 4711 0.741221 GCCGATCTTTCAGCTTCCGT 60.741 55.000 0.00 0.00 0.00 4.69
3674 4925 1.383248 CCCTCCCCACGATCTCCTT 60.383 63.158 0.00 0.00 0.00 3.36
3776 5027 2.194212 CGTCCCCGTGATCCTCGAT 61.194 63.158 8.60 0.00 0.00 3.59
3787 5038 1.139853 GATCCTCGATGCCTCCAACTT 59.860 52.381 0.00 0.00 0.00 2.66
3873 5124 2.607750 ATGGCACCGTGGACTCCT 60.608 61.111 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.556911 AGCGATCAGACCTCAAATGGT 59.443 47.619 0.00 0.00 44.10 3.55
6 7 2.322355 AGCGATCAGACCTCAAATGG 57.678 50.000 0.00 0.00 0.00 3.16
7 8 3.553511 GTGTAGCGATCAGACCTCAAATG 59.446 47.826 0.00 0.00 0.00 2.32
8 9 3.195610 TGTGTAGCGATCAGACCTCAAAT 59.804 43.478 0.00 0.00 0.00 2.32
9 10 2.560981 TGTGTAGCGATCAGACCTCAAA 59.439 45.455 0.00 0.00 0.00 2.69
10 11 2.167662 TGTGTAGCGATCAGACCTCAA 58.832 47.619 0.00 0.00 0.00 3.02
11 12 1.834188 TGTGTAGCGATCAGACCTCA 58.166 50.000 0.00 0.00 0.00 3.86
12 13 2.094700 TGTTGTGTAGCGATCAGACCTC 60.095 50.000 0.00 0.00 0.00 3.85
13 14 1.893137 TGTTGTGTAGCGATCAGACCT 59.107 47.619 0.00 0.00 0.00 3.85
14 15 2.363788 TGTTGTGTAGCGATCAGACC 57.636 50.000 0.00 0.00 0.00 3.85
15 16 4.862574 TGTAATGTTGTGTAGCGATCAGAC 59.137 41.667 0.00 0.00 0.00 3.51
16 17 5.066968 TGTAATGTTGTGTAGCGATCAGA 57.933 39.130 0.00 0.00 0.00 3.27
17 18 5.778161 TTGTAATGTTGTGTAGCGATCAG 57.222 39.130 0.00 0.00 0.00 2.90
18 19 6.735678 ATTTGTAATGTTGTGTAGCGATCA 57.264 33.333 0.00 0.00 0.00 2.92
19 20 9.158364 CATAATTTGTAATGTTGTGTAGCGATC 57.842 33.333 0.00 0.00 0.00 3.69
20 21 8.128582 CCATAATTTGTAATGTTGTGTAGCGAT 58.871 33.333 0.00 0.00 0.00 4.58
21 22 7.119992 ACCATAATTTGTAATGTTGTGTAGCGA 59.880 33.333 0.00 0.00 0.00 4.93
22 23 7.247728 ACCATAATTTGTAATGTTGTGTAGCG 58.752 34.615 0.00 0.00 0.00 4.26
23 24 8.240682 TGACCATAATTTGTAATGTTGTGTAGC 58.759 33.333 0.00 0.00 0.00 3.58
26 27 9.995003 ATTTGACCATAATTTGTAATGTTGTGT 57.005 25.926 0.00 0.00 0.00 3.72
51 52 6.261381 TCGTGCTTACTTTGGACTTTACAAAT 59.739 34.615 0.00 0.00 37.22 2.32
53 54 5.006941 GTCGTGCTTACTTTGGACTTTACAA 59.993 40.000 0.00 0.00 0.00 2.41
76 77 1.406477 GGGGGATTCGAGTTTTAGCGT 60.406 52.381 0.00 0.00 0.00 5.07
103 104 2.543012 CACCGCATCTCTCTTGCATTAG 59.457 50.000 0.00 0.00 40.14 1.73
107 108 0.390340 GACACCGCATCTCTCTTGCA 60.390 55.000 0.00 0.00 40.14 4.08
110 111 0.109086 CACGACACCGCATCTCTCTT 60.109 55.000 0.00 0.00 39.95 2.85
124 125 3.041940 CTCCCACAACCGCACGAC 61.042 66.667 0.00 0.00 0.00 4.34
125 126 4.308458 CCTCCCACAACCGCACGA 62.308 66.667 0.00 0.00 0.00 4.35
130 131 0.903454 ACCTCTACCTCCCACAACCG 60.903 60.000 0.00 0.00 0.00 4.44
135 136 0.335361 TCCTGACCTCTACCTCCCAC 59.665 60.000 0.00 0.00 0.00 4.61
139 140 1.064314 TGCTCTCCTGACCTCTACCTC 60.064 57.143 0.00 0.00 0.00 3.85
165 166 0.692476 CCCCTCAGATCAACACACCA 59.308 55.000 0.00 0.00 0.00 4.17
166 167 0.678048 GCCCCTCAGATCAACACACC 60.678 60.000 0.00 0.00 0.00 4.16
200 201 2.642139 TTTCTGACCGTACGATCCAC 57.358 50.000 18.76 3.69 0.00 4.02
213 214 4.238385 CGAGCGACGGTTTTCTGA 57.762 55.556 0.00 0.00 38.46 3.27
244 245 2.224042 TGCGAATGTCAGTTCACTCAGT 60.224 45.455 0.00 0.00 0.00 3.41
245 246 2.407090 TGCGAATGTCAGTTCACTCAG 58.593 47.619 0.00 0.00 0.00 3.35
246 247 2.524569 TGCGAATGTCAGTTCACTCA 57.475 45.000 0.00 0.00 0.00 3.41
247 248 4.864806 TCTTATGCGAATGTCAGTTCACTC 59.135 41.667 0.00 0.00 0.00 3.51
248 249 4.820897 TCTTATGCGAATGTCAGTTCACT 58.179 39.130 0.00 0.00 0.00 3.41
249 250 5.063944 ACATCTTATGCGAATGTCAGTTCAC 59.936 40.000 0.00 0.00 0.00 3.18
250 251 5.063817 CACATCTTATGCGAATGTCAGTTCA 59.936 40.000 0.00 0.00 0.00 3.18
251 252 5.063944 ACACATCTTATGCGAATGTCAGTTC 59.936 40.000 0.00 0.00 0.00 3.01
252 253 4.937620 ACACATCTTATGCGAATGTCAGTT 59.062 37.500 0.00 0.00 0.00 3.16
253 254 4.507710 ACACATCTTATGCGAATGTCAGT 58.492 39.130 0.00 0.00 0.00 3.41
254 255 5.475273 AACACATCTTATGCGAATGTCAG 57.525 39.130 0.00 0.00 0.00 3.51
255 256 6.037062 CCTTAACACATCTTATGCGAATGTCA 59.963 38.462 0.00 0.00 0.00 3.58
256 257 6.257849 TCCTTAACACATCTTATGCGAATGTC 59.742 38.462 0.00 0.00 0.00 3.06
257 258 6.112734 TCCTTAACACATCTTATGCGAATGT 58.887 36.000 0.00 0.00 0.00 2.71
258 259 6.603237 TCCTTAACACATCTTATGCGAATG 57.397 37.500 0.00 0.00 0.00 2.67
259 260 7.624360 TTTCCTTAACACATCTTATGCGAAT 57.376 32.000 0.00 0.00 0.00 3.34
260 261 7.441890 TTTTCCTTAACACATCTTATGCGAA 57.558 32.000 0.00 0.00 0.00 4.70
261 262 7.441890 TTTTTCCTTAACACATCTTATGCGA 57.558 32.000 0.00 0.00 0.00 5.10
327 328 3.993547 TCGCAAAATCGATTTACGGTTC 58.006 40.909 30.10 11.30 45.00 3.62
330 331 5.563751 CCATATTCGCAAAATCGATTTACGG 59.436 40.000 30.10 21.32 42.82 4.02
346 517 8.607441 TTCAGATGTCCTAAATTCCATATTCG 57.393 34.615 0.00 0.00 0.00 3.34
348 519 9.790344 CTCTTCAGATGTCCTAAATTCCATATT 57.210 33.333 0.00 0.00 0.00 1.28
349 520 8.943085 ACTCTTCAGATGTCCTAAATTCCATAT 58.057 33.333 0.00 0.00 0.00 1.78
443 627 0.635731 GAGCGAGATGAACGAACACG 59.364 55.000 0.00 0.00 0.00 4.49
444 628 0.635731 CGAGCGAGATGAACGAACAC 59.364 55.000 0.00 0.00 0.00 3.32
973 1876 0.692476 TCCACCACCACTTCCTGATG 59.308 55.000 0.00 0.00 0.00 3.07
974 1877 0.987294 CTCCACCACCACTTCCTGAT 59.013 55.000 0.00 0.00 0.00 2.90
975 1878 1.127567 CCTCCACCACCACTTCCTGA 61.128 60.000 0.00 0.00 0.00 3.86
976 1879 1.376466 CCTCCACCACCACTTCCTG 59.624 63.158 0.00 0.00 0.00 3.86
977 1880 1.847968 CCCTCCACCACCACTTCCT 60.848 63.158 0.00 0.00 0.00 3.36
978 1881 2.757077 CCCTCCACCACCACTTCC 59.243 66.667 0.00 0.00 0.00 3.46
979 1882 2.757077 CCCCTCCACCACCACTTC 59.243 66.667 0.00 0.00 0.00 3.01
980 1883 2.858974 CCCCCTCCACCACCACTT 60.859 66.667 0.00 0.00 0.00 3.16
981 1884 3.869934 TCCCCCTCCACCACCACT 61.870 66.667 0.00 0.00 0.00 4.00
982 1885 3.330720 CTCCCCCTCCACCACCAC 61.331 72.222 0.00 0.00 0.00 4.16
983 1886 2.892702 ATCTCCCCCTCCACCACCA 61.893 63.158 0.00 0.00 0.00 4.17
984 1887 2.042930 ATCTCCCCCTCCACCACC 59.957 66.667 0.00 0.00 0.00 4.61
985 1888 2.378634 CCATCTCCCCCTCCACCAC 61.379 68.421 0.00 0.00 0.00 4.16
986 1889 2.042762 CCATCTCCCCCTCCACCA 59.957 66.667 0.00 0.00 0.00 4.17
987 1890 2.042930 ACCATCTCCCCCTCCACC 59.957 66.667 0.00 0.00 0.00 4.61
988 1891 2.378634 CCACCATCTCCCCCTCCAC 61.379 68.421 0.00 0.00 0.00 4.02
989 1892 2.042762 CCACCATCTCCCCCTCCA 59.957 66.667 0.00 0.00 0.00 3.86
990 1893 3.493303 GCCACCATCTCCCCCTCC 61.493 72.222 0.00 0.00 0.00 4.30
991 1894 3.866582 CGCCACCATCTCCCCCTC 61.867 72.222 0.00 0.00 0.00 4.30
1086 2007 3.936203 GTGTCCGCACCCTCACCA 61.936 66.667 0.00 0.00 39.61 4.17
1094 2015 5.796350 AACTGAAAATATAGTGTCCGCAC 57.204 39.130 0.00 0.00 45.57 5.34
1095 2016 7.985184 AGATTAACTGAAAATATAGTGTCCGCA 59.015 33.333 0.00 0.00 0.00 5.69
1096 2017 8.366671 AGATTAACTGAAAATATAGTGTCCGC 57.633 34.615 0.00 0.00 0.00 5.54
1405 2619 3.932710 TGTAGCATCAATCAGTCGGAAAC 59.067 43.478 0.00 0.00 0.00 2.78
1408 2622 4.122046 CAATGTAGCATCAATCAGTCGGA 58.878 43.478 0.00 0.00 0.00 4.55
1453 2667 3.012844 AGTTTGGCTTTATCCCTGGGAAT 59.987 43.478 21.42 10.94 34.34 3.01
1464 2678 3.084039 CCTCTGCATCAGTTTGGCTTTA 58.916 45.455 0.00 0.00 32.61 1.85
1479 2693 1.198759 TCCTTACCCACACCCTCTGC 61.199 60.000 0.00 0.00 0.00 4.26
1506 2720 5.175859 TCTCTGTGTTCTTCGTTCTGTTTT 58.824 37.500 0.00 0.00 0.00 2.43
1534 2748 3.304123 CCCAGATCTAGAAGCGTCTTACG 60.304 52.174 7.67 0.00 45.88 3.18
1541 2755 2.625314 TCATGTCCCAGATCTAGAAGCG 59.375 50.000 0.00 0.00 0.00 4.68
1610 2824 3.472298 GCAAAACGCATGCGCCTG 61.472 61.111 38.15 30.19 44.19 4.85
1682 2896 5.096443 AGGGATCAAATCAACAGAGACTC 57.904 43.478 0.00 0.00 0.00 3.36
1688 2904 3.094572 AGGCAAGGGATCAAATCAACAG 58.905 45.455 0.00 0.00 0.00 3.16
1689 2905 3.173953 AGGCAAGGGATCAAATCAACA 57.826 42.857 0.00 0.00 0.00 3.33
1822 3039 0.512518 TGACAAACGCAGCGAGAATG 59.487 50.000 24.65 15.92 0.00 2.67
1947 3164 4.860802 TGATTACCTGGTCAATGGTGAT 57.139 40.909 0.63 0.00 37.74 3.06
2003 3220 8.857216 GTTAAACATCAATCATTCTTGAGCAAG 58.143 33.333 3.87 3.87 38.47 4.01
2026 3243 7.763985 CCAACATACATCTCACACATACTGTTA 59.236 37.037 0.00 0.00 0.00 2.41
2073 3290 7.542477 CACACATGACTAAGTTTTAGTCGATCT 59.458 37.037 18.76 6.14 45.05 2.75
2086 3303 5.410746 ACAAATCTGAGCACACATGACTAAG 59.589 40.000 0.00 0.00 0.00 2.18
2111 3328 4.386711 CCCGAAAAACAGAGGTCTTAAGT 58.613 43.478 1.63 0.00 0.00 2.24
2164 3381 7.514721 TGTAGGAATATTGGGGATCAAAGTAC 58.485 38.462 0.00 0.00 39.05 2.73
2284 3502 7.281098 ACATGCATGTCATTTCTCTCTTCTAT 58.719 34.615 26.61 0.00 35.87 1.98
2336 3554 7.698506 AGTTCCCTTTTAAAGTATAAGGCAC 57.301 36.000 3.91 0.00 36.09 5.01
2387 3609 8.987890 GCCAACATAACAAACAAAATAAGACAT 58.012 29.630 0.00 0.00 0.00 3.06
2398 3620 2.223923 GCCTGTGCCAACATAACAAACA 60.224 45.455 0.00 0.00 35.22 2.83
2495 3719 0.895530 TTCCTCGACAAGGGCTACAG 59.104 55.000 0.00 0.00 46.23 2.74
2603 3827 3.557475 GGCAGCTCTCAATCTCAGCATAT 60.557 47.826 0.00 0.00 35.46 1.78
2894 4118 1.003118 CACCGAAAGAGTGATTCCCCA 59.997 52.381 0.00 0.00 37.42 4.96
2925 4149 2.205022 ACAGGTCCAACATGTCCATG 57.795 50.000 0.00 5.74 39.01 3.66
3205 4433 4.265073 ACAATGGATCAAGTAGCTCCAAC 58.735 43.478 0.00 0.00 45.07 3.77
3223 4451 9.952030 TCAAACTAAAGGGAAAAGAAAAACAAT 57.048 25.926 0.00 0.00 0.00 2.71
3232 4460 7.586714 GATGCAATCAAACTAAAGGGAAAAG 57.413 36.000 0.00 0.00 44.70 2.27
3249 4477 3.508793 CAGAAACCACCAGAAGATGCAAT 59.491 43.478 0.00 0.00 0.00 3.56
3259 4487 3.381272 ACATGTTCAACAGAAACCACCAG 59.619 43.478 0.00 0.00 0.00 4.00
3353 4581 3.379372 CGACCGGTATCTTGTCTCCTAAA 59.621 47.826 7.34 0.00 0.00 1.85
3401 4629 5.009854 TGATTGATTGATCGTGCACTAGA 57.990 39.130 16.19 6.05 0.00 2.43
3465 4693 1.726853 AACGGAAGCTGAAAGATCGG 58.273 50.000 0.00 0.00 34.07 4.18
3473 4701 1.206371 GCTAGGGTTAACGGAAGCTGA 59.794 52.381 14.12 0.00 35.76 4.26
3483 4711 4.165486 GGCGGCGGCTAGGGTTAA 62.165 66.667 27.22 0.00 39.81 2.01
3674 4925 2.045708 GGCGTTGGATGACATGGCA 61.046 57.895 2.18 2.18 32.74 4.92
3776 5027 1.045407 AGTACGTGAAGTTGGAGGCA 58.955 50.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.