Multiple sequence alignment - TraesCS1A01G270100

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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 TraesCS1A01G270100 chr1A 100.000 2498 0 0 1 2498 464114695 464117192 0.000000e+00 4614.0
1 TraesCS1A01G270100 chr1A 82.819 908 77 35 874 1747 464121636 464122498 0.000000e+00 739.0
2 TraesCS1A01G270100 chr1A 89.189 74 7 1 1767 1840 299643705 299643633 9.510000e-15 91.6
3 TraesCS1A01G270100 chr1D 86.638 2537 224 51 49 2498 365244097 365246605 0.000000e+00 2700.0
4 TraesCS1A01G270100 chr1D 82.784 970 81 40 843 1765 365297908 365298838 0.000000e+00 787.0
5 TraesCS1A01G270100 chr1B 84.244 1555 153 51 582 2078 488658497 488660017 0.000000e+00 1430.0
6 TraesCS1A01G270100 chr1B 84.562 719 68 28 843 1533 488749809 488750512 0.000000e+00 673.0
7 TraesCS1A01G270100 chr1B 87.081 418 50 4 2084 2498 488660066 488660482 1.050000e-128 470.0
8 TraesCS1A01G270100 chr2A 83.453 278 31 9 326 592 194713401 194713128 6.900000e-61 244.0
9 TraesCS1A01G270100 chr7B 84.677 248 25 10 337 577 13129792 13130033 4.150000e-58 235.0
10 TraesCS1A01G270100 chr7B 83.794 253 32 7 338 584 540063448 540063199 5.370000e-57 231.0
11 TraesCS1A01G270100 chr6D 84.400 250 28 7 341 584 411402484 411402240 4.150000e-58 235.0
12 TraesCS1A01G270100 chr6D 78.545 275 53 4 1766 2037 13034108 13034379 2.550000e-40 176.0
13 TraesCS1A01G270100 chr2D 84.252 254 26 11 339 584 62062955 62063202 4.150000e-58 235.0
14 TraesCS1A01G270100 chr5B 83.271 269 30 12 325 584 527760359 527760621 1.490000e-57 233.0
15 TraesCS1A01G270100 chr5B 93.103 58 4 0 1767 1824 603144259 603144316 4.430000e-13 86.1
16 TraesCS1A01G270100 chr5B 100.000 29 0 0 286 314 278466860 278466888 1.000000e-03 54.7
17 TraesCS1A01G270100 chr7D 83.019 265 36 7 326 584 485106721 485106460 5.370000e-57 231.0
18 TraesCS1A01G270100 chr7D 84.211 76 10 2 1964 2038 74429945 74430019 3.450000e-09 73.1
19 TraesCS1A01G270100 chr2B 82.528 269 37 8 323 584 45729805 45729540 6.950000e-56 228.0
20 TraesCS1A01G270100 chr3B 83.092 207 30 5 1767 1970 671846497 671846701 1.530000e-42 183.0
21 TraesCS1A01G270100 chr6B 84.416 77 12 0 1962 2038 255277193 255277269 2.660000e-10 76.8
22 TraesCS1A01G270100 chr3A 86.567 67 9 0 1767 1833 728692990 728692924 9.580000e-10 75.0
23 TraesCS1A01G270100 chr7A 84.722 72 11 0 1769 1840 688375614 688375543 3.450000e-09 73.1
24 TraesCS1A01G270100 chr5D 100.000 29 0 0 286 314 245197740 245197768 1.000000e-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 TraesCS1A01G270100 chr1A 464114695 464117192 2497 False 4614 4614 100.0000 1 2498 1 chr1A.!!$F1 2497
1 TraesCS1A01G270100 chr1A 464121636 464122498 862 False 739 739 82.8190 874 1747 1 chr1A.!!$F2 873
2 TraesCS1A01G270100 chr1D 365244097 365246605 2508 False 2700 2700 86.6380 49 2498 1 chr1D.!!$F1 2449
3 TraesCS1A01G270100 chr1D 365297908 365298838 930 False 787 787 82.7840 843 1765 1 chr1D.!!$F2 922
4 TraesCS1A01G270100 chr1B 488658497 488660482 1985 False 950 1430 85.6625 582 2498 2 chr1B.!!$F2 1916
5 TraesCS1A01G270100 chr1B 488749809 488750512 703 False 673 673 84.5620 843 1533 1 chr1B.!!$F1 690

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
267 268 0.030908 CCTATCTTCTGTCCGCGGAC 59.969 60.0 43.88 43.88 44.77 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 2206 0.917648 GACACACGTGCACGAAAACG 60.918 55.0 42.94 26.42 45.15 3.6 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
21 22 1.891150 GTTTAGACTGGACTGTCCGGA 59.109 52.381 35.97 15.89 45.95 5.14
22 23 1.542492 TTAGACTGGACTGTCCGGAC 58.458 55.000 35.97 30.07 45.95 4.79
23 24 0.402887 TAGACTGGACTGTCCGGACA 59.597 55.000 35.97 34.13 45.95 4.02
24 25 1.179814 AGACTGGACTGTCCGGACAC 61.180 60.000 35.97 23.46 45.95 3.67
25 26 1.152525 ACTGGACTGTCCGGACACT 60.153 57.895 35.97 24.03 45.95 3.55
26 27 0.759436 ACTGGACTGTCCGGACACTT 60.759 55.000 35.97 22.40 45.95 3.16
27 28 0.393077 CTGGACTGTCCGGACACTTT 59.607 55.000 33.23 19.77 45.95 2.66
28 29 0.834612 TGGACTGTCCGGACACTTTT 59.165 50.000 33.23 17.19 40.17 2.27
29 30 2.036733 CTGGACTGTCCGGACACTTTTA 59.963 50.000 33.23 16.66 45.95 1.52
30 31 2.435069 TGGACTGTCCGGACACTTTTAA 59.565 45.455 33.23 13.78 40.17 1.52
31 32 2.804527 GGACTGTCCGGACACTTTTAAC 59.195 50.000 33.23 17.03 36.21 2.01
32 33 3.460103 GACTGTCCGGACACTTTTAACA 58.540 45.455 33.23 9.97 36.21 2.41
33 34 3.872771 GACTGTCCGGACACTTTTAACAA 59.127 43.478 33.23 8.50 36.21 2.83
34 35 4.457466 ACTGTCCGGACACTTTTAACAAT 58.543 39.130 33.23 0.00 36.21 2.71
35 36 4.885325 ACTGTCCGGACACTTTTAACAATT 59.115 37.500 33.23 0.49 36.21 2.32
36 37 5.008316 ACTGTCCGGACACTTTTAACAATTC 59.992 40.000 33.23 1.54 36.21 2.17
37 38 4.882427 TGTCCGGACACTTTTAACAATTCA 59.118 37.500 33.23 4.55 36.21 2.57
38 39 5.357314 TGTCCGGACACTTTTAACAATTCAA 59.643 36.000 33.23 4.05 36.21 2.69
39 40 6.039941 TGTCCGGACACTTTTAACAATTCAAT 59.960 34.615 33.23 0.00 36.21 2.57
40 41 7.228906 TGTCCGGACACTTTTAACAATTCAATA 59.771 33.333 33.23 3.30 36.21 1.90
41 42 7.749126 GTCCGGACACTTTTAACAATTCAATAG 59.251 37.037 29.75 0.00 0.00 1.73
42 43 7.662258 TCCGGACACTTTTAACAATTCAATAGA 59.338 33.333 0.00 0.00 0.00 1.98
43 44 8.458843 CCGGACACTTTTAACAATTCAATAGAT 58.541 33.333 0.00 0.00 0.00 1.98
56 57 9.911788 ACAATTCAATAGATACATCAAAGGTCT 57.088 29.630 0.00 0.00 0.00 3.85
72 73 1.771255 GGTCTATGGAGCAATCTGGGT 59.229 52.381 3.07 0.00 39.51 4.51
85 86 3.922171 ATCTGGGTGTCTGAATTCCTC 57.078 47.619 2.27 0.00 0.00 3.71
121 122 9.533253 AACAAATGTAGAAATGGTTTGAAAGAG 57.467 29.630 0.00 0.00 34.71 2.85
125 126 6.954944 TGTAGAAATGGTTTGAAAGAGTTCG 58.045 36.000 0.00 0.00 36.46 3.95
135 136 3.973657 TGAAAGAGTTCGGACACACTAC 58.026 45.455 0.00 0.00 36.46 2.73
136 137 3.382227 TGAAAGAGTTCGGACACACTACA 59.618 43.478 0.00 0.00 36.46 2.74
137 138 3.644884 AAGAGTTCGGACACACTACAG 57.355 47.619 0.00 0.00 0.00 2.74
138 139 2.860009 AGAGTTCGGACACACTACAGA 58.140 47.619 0.00 0.00 0.00 3.41
139 140 3.422796 AGAGTTCGGACACACTACAGAT 58.577 45.455 0.00 0.00 0.00 2.90
140 141 4.586884 AGAGTTCGGACACACTACAGATA 58.413 43.478 0.00 0.00 0.00 1.98
150 151 4.184629 CACACTACAGATAAGCCTTGGAC 58.815 47.826 0.00 0.00 0.00 4.02
155 156 0.919710 AGATAAGCCTTGGACCCACC 59.080 55.000 0.00 0.00 39.54 4.61
179 180 4.682021 AAATCCACATTTTCCTCCTCCT 57.318 40.909 0.00 0.00 0.00 3.69
180 181 3.941704 ATCCACATTTTCCTCCTCCTC 57.058 47.619 0.00 0.00 0.00 3.71
181 182 1.916181 TCCACATTTTCCTCCTCCTCC 59.084 52.381 0.00 0.00 0.00 4.30
182 183 1.064389 CCACATTTTCCTCCTCCTCCC 60.064 57.143 0.00 0.00 0.00 4.30
187 188 2.743131 TTTCCTCCTCCTCCCTTCTT 57.257 50.000 0.00 0.00 0.00 2.52
207 208 5.414360 TCTTTCTCATCTCTTCATTGGACG 58.586 41.667 0.00 0.00 0.00 4.79
213 214 2.808919 TCTCTTCATTGGACGAGAGGT 58.191 47.619 0.00 0.00 41.81 3.85
249 250 2.042639 ATTGGATGGCAGCCCACC 60.043 61.111 20.74 12.89 45.77 4.61
254 255 1.422161 GGATGGCAGCCCACCTATCT 61.422 60.000 11.60 0.00 45.77 1.98
255 256 0.475906 GATGGCAGCCCACCTATCTT 59.524 55.000 9.64 0.00 45.77 2.40
259 260 0.543749 GCAGCCCACCTATCTTCTGT 59.456 55.000 0.00 0.00 0.00 3.41
261 262 1.139853 CAGCCCACCTATCTTCTGTCC 59.860 57.143 0.00 0.00 0.00 4.02
267 268 0.030908 CCTATCTTCTGTCCGCGGAC 59.969 60.000 43.88 43.88 44.77 4.79
290 291 2.354403 CGTCCGGACTACCCTTTTTGAT 60.354 50.000 30.92 0.00 0.00 2.57
299 300 3.217681 ACCCTTTTTGATGTACACCGT 57.782 42.857 0.00 0.00 0.00 4.83
331 332 3.195610 CCTAAGTCATGCAGGTGTACTCA 59.804 47.826 0.00 0.00 0.00 3.41
368 369 5.975410 ACTTCGCATATTAGCTTTGTCTC 57.025 39.130 0.00 0.00 0.00 3.36
369 370 4.504461 ACTTCGCATATTAGCTTTGTCTCG 59.496 41.667 0.00 0.00 0.00 4.04
370 371 2.794910 TCGCATATTAGCTTTGTCTCGC 59.205 45.455 0.00 0.00 0.00 5.03
373 374 3.001330 GCATATTAGCTTTGTCTCGCGTT 59.999 43.478 5.77 0.00 0.00 4.84
464 466 9.125026 ACCATTAGAATCAATTCAACATACTCC 57.875 33.333 5.59 0.00 39.23 3.85
468 470 7.545362 AGAATCAATTCAACATACTCCTTCG 57.455 36.000 5.59 0.00 39.23 3.79
476 478 6.140303 TCAACATACTCCTTCGTACCATAC 57.860 41.667 0.00 0.00 0.00 2.39
598 600 3.131396 AGGAGTATTTTCATTAGCGCCG 58.869 45.455 2.29 0.00 0.00 6.46
637 641 3.021269 TGTGACAGGATTACACACGTC 57.979 47.619 0.00 0.00 39.17 4.34
667 671 1.338020 CCCTCACTGAAACAGCCAAAC 59.662 52.381 0.00 0.00 34.37 2.93
716 728 2.564947 AGTGAGGACAGACTTAGCCAAG 59.435 50.000 0.00 0.00 37.81 3.61
717 729 1.276421 TGAGGACAGACTTAGCCAAGC 59.724 52.381 0.00 0.00 34.94 4.01
861 877 4.935495 CCACCACTGTGCGCCACT 62.935 66.667 4.18 0.00 41.35 4.00
862 878 3.653009 CACCACTGTGCGCCACTG 61.653 66.667 4.18 9.94 38.85 3.66
974 1014 3.504906 CCTGAGCAAAGAGAAGCAAATCA 59.495 43.478 0.00 0.00 0.00 2.57
975 1015 4.474113 CTGAGCAAAGAGAAGCAAATCAC 58.526 43.478 0.00 0.00 0.00 3.06
976 1016 3.884693 TGAGCAAAGAGAAGCAAATCACA 59.115 39.130 0.00 0.00 0.00 3.58
980 1020 5.068198 AGCAAAGAGAAGCAAATCACAAGAA 59.932 36.000 0.00 0.00 0.00 2.52
1056 1119 2.766400 CGTCGTCCTCCTGCTCCTC 61.766 68.421 0.00 0.00 0.00 3.71
1083 1146 3.336122 GATCACCTGATCCATGCCC 57.664 57.895 4.17 0.00 43.85 5.36
1089 1154 2.173356 CACCTGATCCATGCCCTTAGAA 59.827 50.000 0.00 0.00 0.00 2.10
1117 1182 3.806257 GCACATGCATGCTACGTAC 57.194 52.632 26.53 4.31 42.62 3.67
1118 1183 0.043053 GCACATGCATGCTACGTACG 60.043 55.000 26.53 15.01 42.62 3.67
1119 1184 1.277326 CACATGCATGCTACGTACGT 58.723 50.000 26.53 25.98 0.00 3.57
1240 1309 0.542805 ATGCATGGGGTTCATTTGCC 59.457 50.000 0.00 0.00 32.06 4.52
1246 1315 1.274712 GGGGTTCATTTGCCAATCCA 58.725 50.000 0.00 0.00 0.00 3.41
1259 1328 1.407299 CCAATCCAGCCGACTTGATCA 60.407 52.381 0.00 0.00 28.40 2.92
1282 1356 2.876550 TCGGTACCAGACGACTGATATG 59.123 50.000 16.58 2.07 46.03 1.78
1284 1358 3.548214 CGGTACCAGACGACTGATATGTG 60.548 52.174 16.58 0.98 46.03 3.21
1285 1359 3.630769 GGTACCAGACGACTGATATGTGA 59.369 47.826 16.58 0.00 46.03 3.58
1366 1441 3.310860 AAGTCGAGCCGGCCGAATT 62.311 57.895 32.37 32.37 39.11 2.17
1499 1574 1.597797 CGCCACAAGTGCCCATGATT 61.598 55.000 0.00 0.00 0.00 2.57
1540 1623 2.228103 CGGTCGAGGCTAATGCATACTA 59.772 50.000 0.00 0.00 41.91 1.82
1582 1668 5.674052 ATATCCCATCAAGCTAGCTACAG 57.326 43.478 19.70 11.42 0.00 2.74
1605 1694 4.499357 GCCAACGATAACTAGACTACCAGG 60.499 50.000 0.00 0.00 0.00 4.45
1673 1774 3.266510 TGTACCTTGTGCTCATCCATC 57.733 47.619 0.00 0.00 0.00 3.51
1771 1887 7.618502 AAACAATTAGTGCGTATGGTATTGA 57.381 32.000 0.00 0.00 0.00 2.57
1775 1891 8.682710 ACAATTAGTGCGTATGGTATTGAATTT 58.317 29.630 0.00 0.00 0.00 1.82
1781 1897 9.204570 AGTGCGTATGGTATTGAATTTATACTC 57.795 33.333 9.95 0.00 0.00 2.59
1794 1910 6.543465 TGAATTTATACTCCAGCCAACTCATG 59.457 38.462 0.00 0.00 0.00 3.07
1813 1929 7.445121 ACTCATGTAAAAGTCTGAACTGATGA 58.555 34.615 0.00 0.00 35.36 2.92
1835 1951 7.101652 TGAAGAGAGGCGGACAATATATATC 57.898 40.000 0.00 0.00 0.00 1.63
1900 2038 0.839946 AGGATTTGTCTAGGCCGCAT 59.160 50.000 0.00 0.00 0.00 4.73
1936 2075 0.537188 CTGCGTTGGTAGGGTCTGAT 59.463 55.000 0.00 0.00 0.00 2.90
1973 2112 5.352569 CGGCTCTGATACCATATTGAATTCC 59.647 44.000 2.27 0.00 0.00 3.01
1985 2124 6.238676 CCATATTGAATTCCTGCTTCAGTCAG 60.239 42.308 2.27 0.00 34.33 3.51
1986 2125 3.777106 TGAATTCCTGCTTCAGTCAGT 57.223 42.857 2.27 0.00 0.00 3.41
1991 2130 6.716628 TGAATTCCTGCTTCAGTCAGTTTATT 59.283 34.615 2.27 0.00 0.00 1.40
2000 2139 6.858478 GCTTCAGTCAGTTTATTCAAAAGTCC 59.142 38.462 0.00 0.00 0.00 3.85
2017 2156 4.873746 AGTCCGAACTGATGAAGAAAGA 57.126 40.909 0.00 0.00 33.32 2.52
2023 2162 4.032217 CGAACTGATGAAGAAAGACGGATG 59.968 45.833 0.00 0.00 0.00 3.51
2062 2201 7.812690 ATGTTCATATGAGCATGTGTGTATT 57.187 32.000 28.02 7.34 42.97 1.89
2063 2202 7.628769 TGTTCATATGAGCATGTGTGTATTT 57.371 32.000 17.28 0.00 32.61 1.40
2067 2206 3.557577 TGAGCATGTGTGTATTTGTGC 57.442 42.857 0.00 0.00 0.00 4.57
2068 2207 2.095819 TGAGCATGTGTGTATTTGTGCG 60.096 45.455 0.00 0.00 37.63 5.34
2069 2208 1.879380 AGCATGTGTGTATTTGTGCGT 59.121 42.857 0.00 0.00 37.63 5.24
2086 2269 0.917648 CGTTTTCGTGCACGTGTGTC 60.918 55.000 35.74 21.79 40.80 3.67
2115 2298 2.685897 GCTCATAGTCCTCGTCAAGTCT 59.314 50.000 0.00 0.00 0.00 3.24
2151 2334 3.102515 CGAGTTGTTCGTCGGTGAT 57.897 52.632 0.00 0.00 44.27 3.06
2161 2345 3.822192 TCGGTGATGGGAGCGTCG 61.822 66.667 0.00 0.00 38.04 5.12
2206 2404 1.637338 AGTCAGTGATGGAGCAGTCA 58.363 50.000 0.00 0.00 0.00 3.41
2290 2488 1.227380 GAGGGCGATGATGCTCGTT 60.227 57.895 0.00 0.00 41.40 3.85
2293 2491 1.089481 GGGCGATGATGCTCGTTCAA 61.089 55.000 0.00 0.00 40.73 2.69
2297 2495 1.731709 CGATGATGCTCGTTCAAACCA 59.268 47.619 0.00 0.00 34.00 3.67
2298 2496 2.159430 CGATGATGCTCGTTCAAACCAA 59.841 45.455 0.00 0.00 34.00 3.67
2300 2498 3.557577 TGATGCTCGTTCAAACCAATG 57.442 42.857 0.00 0.00 0.00 2.82
2321 2519 0.119155 AGTCTCCCCTTCCATCACCA 59.881 55.000 0.00 0.00 0.00 4.17
2323 2521 1.225704 CTCCCCTTCCATCACCAGC 59.774 63.158 0.00 0.00 0.00 4.85
2334 2560 1.683385 CATCACCAGCTCGAGGATGTA 59.317 52.381 15.58 0.00 32.68 2.29
2355 2581 3.454858 AGAAGGAGATGGAGCCTTACAA 58.545 45.455 0.00 0.00 44.23 2.41
2360 2586 1.020437 GATGGAGCCTTACAAGCAGC 58.980 55.000 0.00 0.00 0.00 5.25
2367 2593 2.014068 GCCTTACAAGCAGCGAAGGAT 61.014 52.381 17.71 0.00 40.88 3.24
2407 2633 2.997986 CCATTCTTTGTCATTGGCTTGC 59.002 45.455 0.00 0.00 0.00 4.01
2411 2637 1.814772 TTTGTCATTGGCTTGCGGGG 61.815 55.000 0.00 0.00 0.00 5.73
2432 2658 0.040870 CTCCGTGTCGAGATGATCCG 60.041 60.000 2.82 0.00 30.97 4.18
2451 2677 1.136984 CGAGCTCGTACTGGGTGAC 59.863 63.158 27.79 0.00 34.11 3.67
2452 2678 1.583495 CGAGCTCGTACTGGGTGACA 61.583 60.000 27.79 0.00 34.11 3.58
2453 2679 0.109226 GAGCTCGTACTGGGTGACAC 60.109 60.000 0.00 0.00 0.00 3.67
2454 2680 0.826256 AGCTCGTACTGGGTGACACA 60.826 55.000 8.08 0.00 0.00 3.72
2456 2682 1.779569 CTCGTACTGGGTGACACAAC 58.220 55.000 8.08 0.05 0.00 3.32
2457 2683 1.067974 CTCGTACTGGGTGACACAACA 59.932 52.381 8.08 5.04 0.00 3.33
2474 2701 1.569493 CACGGAAGAAAGTGTGCCG 59.431 57.895 0.00 0.00 46.83 5.69
2479 2706 0.661483 GAAGAAAGTGTGCCGCTTGC 60.661 55.000 2.37 1.00 34.24 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.616865 CCGGACAGTCCAGTCTAAACA 59.383 52.381 20.13 0.00 35.91 2.83
1 2 1.891150 TCCGGACAGTCCAGTCTAAAC 59.109 52.381 20.13 0.00 35.91 2.01
2 3 1.891150 GTCCGGACAGTCCAGTCTAAA 59.109 52.381 29.75 0.00 35.91 1.85
3 4 1.202964 TGTCCGGACAGTCCAGTCTAA 60.203 52.381 33.23 5.92 35.91 2.10
5 6 1.153061 TGTCCGGACAGTCCAGTCT 59.847 57.895 33.23 0.00 35.91 3.24
6 7 1.179814 AGTGTCCGGACAGTCCAGTC 61.180 60.000 37.04 22.62 40.76 3.51
7 8 0.759436 AAGTGTCCGGACAGTCCAGT 60.759 55.000 38.29 23.81 43.66 4.00
8 9 0.393077 AAAGTGTCCGGACAGTCCAG 59.607 55.000 38.29 8.57 43.66 3.86
9 10 0.834612 AAAAGTGTCCGGACAGTCCA 59.165 50.000 38.29 16.19 43.66 4.02
10 11 2.804527 GTTAAAAGTGTCCGGACAGTCC 59.195 50.000 38.29 26.52 43.66 3.85
13 14 5.008217 TGAATTGTTAAAAGTGTCCGGACAG 59.992 40.000 37.04 0.00 42.74 3.51
14 15 4.882427 TGAATTGTTAAAAGTGTCCGGACA 59.118 37.500 33.23 33.23 39.32 4.02
15 16 5.427036 TGAATTGTTAAAAGTGTCCGGAC 57.573 39.130 28.17 28.17 0.00 4.79
16 17 6.642707 ATTGAATTGTTAAAAGTGTCCGGA 57.357 33.333 0.00 0.00 0.00 5.14
17 18 7.812648 TCTATTGAATTGTTAAAAGTGTCCGG 58.187 34.615 0.00 0.00 0.00 5.14
30 31 9.911788 AGACCTTTGATGTATCTATTGAATTGT 57.088 29.630 0.00 0.00 0.00 2.71
35 36 9.379770 TCCATAGACCTTTGATGTATCTATTGA 57.620 33.333 0.00 0.00 31.66 2.57
36 37 9.650539 CTCCATAGACCTTTGATGTATCTATTG 57.349 37.037 0.00 0.00 31.66 1.90
37 38 8.317679 GCTCCATAGACCTTTGATGTATCTATT 58.682 37.037 0.00 0.00 31.66 1.73
38 39 7.455953 TGCTCCATAGACCTTTGATGTATCTAT 59.544 37.037 0.00 0.00 33.78 1.98
39 40 6.782494 TGCTCCATAGACCTTTGATGTATCTA 59.218 38.462 0.00 0.00 0.00 1.98
40 41 5.604231 TGCTCCATAGACCTTTGATGTATCT 59.396 40.000 0.00 0.00 0.00 1.98
41 42 5.858381 TGCTCCATAGACCTTTGATGTATC 58.142 41.667 0.00 0.00 0.00 2.24
42 43 5.894298 TGCTCCATAGACCTTTGATGTAT 57.106 39.130 0.00 0.00 0.00 2.29
43 44 5.692115 TTGCTCCATAGACCTTTGATGTA 57.308 39.130 0.00 0.00 0.00 2.29
44 45 4.574674 TTGCTCCATAGACCTTTGATGT 57.425 40.909 0.00 0.00 0.00 3.06
45 46 5.238868 CAGATTGCTCCATAGACCTTTGATG 59.761 44.000 0.00 0.00 0.00 3.07
46 47 5.374921 CAGATTGCTCCATAGACCTTTGAT 58.625 41.667 0.00 0.00 0.00 2.57
47 48 4.384537 CCAGATTGCTCCATAGACCTTTGA 60.385 45.833 0.00 0.00 0.00 2.69
48 49 3.881688 CCAGATTGCTCCATAGACCTTTG 59.118 47.826 0.00 0.00 0.00 2.77
49 50 3.117738 CCCAGATTGCTCCATAGACCTTT 60.118 47.826 0.00 0.00 0.00 3.11
50 51 2.441001 CCCAGATTGCTCCATAGACCTT 59.559 50.000 0.00 0.00 0.00 3.50
51 52 2.053244 CCCAGATTGCTCCATAGACCT 58.947 52.381 0.00 0.00 0.00 3.85
52 53 1.771255 ACCCAGATTGCTCCATAGACC 59.229 52.381 0.00 0.00 0.00 3.85
53 54 2.171448 ACACCCAGATTGCTCCATAGAC 59.829 50.000 0.00 0.00 0.00 2.59
54 55 2.435805 GACACCCAGATTGCTCCATAGA 59.564 50.000 0.00 0.00 0.00 1.98
55 56 2.437281 AGACACCCAGATTGCTCCATAG 59.563 50.000 0.00 0.00 0.00 2.23
56 57 2.171237 CAGACACCCAGATTGCTCCATA 59.829 50.000 0.00 0.00 0.00 2.74
57 58 1.064906 CAGACACCCAGATTGCTCCAT 60.065 52.381 0.00 0.00 0.00 3.41
58 59 0.325933 CAGACACCCAGATTGCTCCA 59.674 55.000 0.00 0.00 0.00 3.86
59 60 0.615331 TCAGACACCCAGATTGCTCC 59.385 55.000 0.00 0.00 0.00 4.70
60 61 2.479566 TTCAGACACCCAGATTGCTC 57.520 50.000 0.00 0.00 0.00 4.26
72 73 8.474831 TGTTATCGATTTAGAGGAATTCAGACA 58.525 33.333 1.71 0.00 0.00 3.41
101 102 6.017440 CCGAACTCTTTCAAACCATTTCTACA 60.017 38.462 0.00 0.00 0.00 2.74
104 105 5.008712 GTCCGAACTCTTTCAAACCATTTCT 59.991 40.000 0.00 0.00 0.00 2.52
108 109 3.564225 GTGTCCGAACTCTTTCAAACCAT 59.436 43.478 0.00 0.00 0.00 3.55
118 119 2.860009 TCTGTAGTGTGTCCGAACTCT 58.140 47.619 0.00 0.00 0.00 3.24
121 122 3.858238 GCTTATCTGTAGTGTGTCCGAAC 59.142 47.826 0.00 0.00 0.00 3.95
125 126 4.184629 CAAGGCTTATCTGTAGTGTGTCC 58.815 47.826 0.00 0.00 0.00 4.02
135 136 1.408822 GGTGGGTCCAAGGCTTATCTG 60.409 57.143 0.00 0.00 35.97 2.90
136 137 0.919710 GGTGGGTCCAAGGCTTATCT 59.080 55.000 0.00 0.00 35.97 1.98
137 138 0.623723 TGGTGGGTCCAAGGCTTATC 59.376 55.000 0.00 0.00 44.12 1.75
138 139 2.799576 TGGTGGGTCCAAGGCTTAT 58.200 52.632 0.00 0.00 44.12 1.73
139 140 4.341199 TGGTGGGTCCAAGGCTTA 57.659 55.556 0.00 0.00 44.12 3.09
150 151 4.716287 AGGAAAATGTGGATTTATGGTGGG 59.284 41.667 0.00 0.00 31.18 4.61
155 156 6.131961 AGGAGGAGGAAAATGTGGATTTATG 58.868 40.000 0.00 0.00 31.18 1.90
179 180 6.413052 CAATGAAGAGATGAGAAAGAAGGGA 58.587 40.000 0.00 0.00 0.00 4.20
180 181 5.589452 CCAATGAAGAGATGAGAAAGAAGGG 59.411 44.000 0.00 0.00 0.00 3.95
181 182 6.315891 GTCCAATGAAGAGATGAGAAAGAAGG 59.684 42.308 0.00 0.00 0.00 3.46
182 183 6.035866 CGTCCAATGAAGAGATGAGAAAGAAG 59.964 42.308 0.00 0.00 0.00 2.85
187 188 4.706962 TCTCGTCCAATGAAGAGATGAGAA 59.293 41.667 8.35 0.00 46.69 2.87
207 208 3.316308 AGTGCACAAAATGTTCACCTCTC 59.684 43.478 21.04 0.00 43.80 3.20
213 214 5.534278 TCCAATCTAGTGCACAAAATGTTCA 59.466 36.000 21.04 0.00 0.00 3.18
229 230 0.183492 GTGGGCTGCCATCCAATCTA 59.817 55.000 22.05 0.00 34.47 1.98
230 231 1.076485 GTGGGCTGCCATCCAATCT 60.076 57.895 22.05 0.00 34.47 2.40
249 250 3.553597 GTCCGCGGACAGAAGATAG 57.446 57.895 44.88 8.87 44.02 2.08
267 268 0.319405 AAAAGGGTAGTCCGGACGTG 59.681 55.000 28.26 0.00 41.52 4.49
270 271 2.845363 TCAAAAAGGGTAGTCCGGAC 57.155 50.000 27.67 27.67 41.52 4.79
279 280 3.217681 ACGGTGTACATCAAAAAGGGT 57.782 42.857 6.97 0.00 0.00 4.34
280 281 3.305064 CCAACGGTGTACATCAAAAAGGG 60.305 47.826 6.97 0.00 0.00 3.95
290 291 0.036765 GGCATCTCCAACGGTGTACA 60.037 55.000 0.00 0.00 34.01 2.90
299 300 2.421952 GCATGACTTAGGGCATCTCCAA 60.422 50.000 0.00 0.00 36.21 3.53
350 351 2.408991 CGCGAGACAAAGCTAATATGCG 60.409 50.000 0.00 0.00 38.13 4.73
420 422 9.913310 TCTAATGGTATTGATTTGGTATTGTGA 57.087 29.630 0.00 0.00 0.00 3.58
439 441 9.347240 AGGAGTATGTTGAATTGATTCTAATGG 57.653 33.333 5.42 0.00 37.67 3.16
451 453 5.670792 TGGTACGAAGGAGTATGTTGAAT 57.329 39.130 0.00 0.00 0.00 2.57
491 493 9.981114 CAAGTTTATCAAAACCAATCTAAACCT 57.019 29.630 0.00 0.00 45.11 3.50
492 494 9.974980 TCAAGTTTATCAAAACCAATCTAAACC 57.025 29.630 0.00 0.00 45.11 3.27
598 600 1.956170 CTCCGTGACTGCACACACC 60.956 63.158 8.06 0.00 45.41 4.16
620 624 2.029290 ACTGGACGTGTGTAATCCTGTC 60.029 50.000 0.00 0.00 39.67 3.51
624 628 3.192001 TCTGTACTGGACGTGTGTAATCC 59.808 47.826 0.00 0.00 0.00 3.01
626 630 3.057033 GGTCTGTACTGGACGTGTGTAAT 60.057 47.826 0.00 0.00 34.82 1.89
637 641 1.924731 TCAGTGAGGGTCTGTACTGG 58.075 55.000 0.00 0.00 40.59 4.00
667 671 3.615110 GCCCTGATCACTGGACATATACG 60.615 52.174 10.15 0.00 37.31 3.06
716 728 1.738099 ACTCGTTGCGTCCATCAGC 60.738 57.895 0.00 0.00 0.00 4.26
717 729 1.354337 CCACTCGTTGCGTCCATCAG 61.354 60.000 0.00 0.00 0.00 2.90
837 849 2.256591 GCACAGTGGTGGCACAGAG 61.257 63.158 20.82 8.42 45.38 3.35
838 850 2.203195 GCACAGTGGTGGCACAGA 60.203 61.111 20.82 1.72 45.38 3.41
839 851 3.653009 CGCACAGTGGTGGCACAG 61.653 66.667 20.82 8.42 45.38 3.66
974 1014 2.350772 CCGATTTGCTTCGCTTTCTTGT 60.351 45.455 0.00 0.00 37.80 3.16
975 1015 2.245096 CCGATTTGCTTCGCTTTCTTG 58.755 47.619 0.00 0.00 37.80 3.02
976 1016 1.401539 GCCGATTTGCTTCGCTTTCTT 60.402 47.619 0.00 0.00 37.80 2.52
980 1020 2.480555 CGCCGATTTGCTTCGCTT 59.519 55.556 0.00 0.00 37.80 4.68
1009 1072 0.729116 CACATGAACGCCCTAGCTTG 59.271 55.000 0.00 0.00 36.60 4.01
1081 1144 3.198635 TGTGCTCTGGAAGATTCTAAGGG 59.801 47.826 0.00 0.00 45.62 3.95
1083 1146 4.272991 GCATGTGCTCTGGAAGATTCTAAG 59.727 45.833 0.00 0.00 45.62 2.18
1089 1154 2.298610 CATGCATGTGCTCTGGAAGAT 58.701 47.619 18.91 0.00 45.62 2.40
1113 1178 1.136169 GCTAGGCAACCAAAACGTACG 60.136 52.381 15.01 15.01 37.17 3.67
1115 1180 2.554370 AGCTAGGCAACCAAAACGTA 57.446 45.000 0.00 0.00 37.17 3.57
1116 1181 2.554370 TAGCTAGGCAACCAAAACGT 57.446 45.000 0.00 0.00 37.17 3.99
1117 1182 3.252458 AGTTTAGCTAGGCAACCAAAACG 59.748 43.478 3.65 0.00 32.18 3.60
1118 1183 4.612939 CGAGTTTAGCTAGGCAACCAAAAC 60.613 45.833 3.65 0.00 37.17 2.43
1119 1184 3.500680 CGAGTTTAGCTAGGCAACCAAAA 59.499 43.478 3.65 0.00 37.17 2.44
1224 1293 2.420408 GGATTGGCAAATGAACCCCATG 60.420 50.000 3.01 0.00 35.24 3.66
1225 1294 1.839354 GGATTGGCAAATGAACCCCAT 59.161 47.619 3.01 0.00 36.99 4.00
1226 1295 1.274712 GGATTGGCAAATGAACCCCA 58.725 50.000 3.01 0.00 0.00 4.96
1227 1296 1.207811 CTGGATTGGCAAATGAACCCC 59.792 52.381 3.01 0.00 0.00 4.95
1240 1309 2.028420 TGATCAAGTCGGCTGGATTG 57.972 50.000 8.65 0.00 35.59 2.67
1246 1315 3.369381 CCGATTGATCAAGTCGGCT 57.631 52.632 29.40 10.49 46.90 5.52
1259 1328 1.830279 TCAGTCGTCTGGTACCGATT 58.170 50.000 7.57 0.00 41.59 3.34
1265 1334 6.374613 GGATATCACATATCAGTCGTCTGGTA 59.625 42.308 9.79 7.46 42.68 3.25
1366 1441 3.898509 GCACGCCCTGTTGCACAA 61.899 61.111 0.00 0.00 0.00 3.33
1499 1574 2.257371 CGTCGAGAAGGCGGTTGA 59.743 61.111 0.00 0.00 45.57 3.18
1521 1604 4.768130 TCTAGTATGCATTAGCCTCGAC 57.232 45.455 3.54 0.00 41.13 4.20
1540 1623 4.679373 ATTTACTGAGACGCCATGATCT 57.321 40.909 0.00 0.00 0.00 2.75
1582 1668 4.499357 CCTGGTAGTCTAGTTATCGTTGGC 60.499 50.000 0.00 0.00 0.00 4.52
1605 1694 4.307443 TGATATCATATCGATCGTGCCC 57.693 45.455 15.94 0.00 35.39 5.36
1648 1739 2.691409 TGAGCACAAGGTACATAGGC 57.309 50.000 0.00 0.00 0.00 3.93
1711 1820 2.412847 GCAATTACCACTGCGTGAGAAC 60.413 50.000 9.75 0.00 35.23 3.01
1771 1887 6.426587 ACATGAGTTGGCTGGAGTATAAATT 58.573 36.000 0.00 0.00 0.00 1.82
1775 1891 6.553953 TTTACATGAGTTGGCTGGAGTATA 57.446 37.500 0.00 0.00 0.00 1.47
1781 1897 4.074970 AGACTTTTACATGAGTTGGCTGG 58.925 43.478 0.00 0.00 0.00 4.85
1794 1910 7.330700 CCTCTCTTCATCAGTTCAGACTTTTAC 59.669 40.741 0.00 0.00 32.54 2.01
1813 1929 7.834681 TGTAGATATATATTGTCCGCCTCTCTT 59.165 37.037 0.00 0.00 0.00 2.85
1835 1951 1.825474 ACGTGAGGGAGAATGGTGTAG 59.175 52.381 0.00 0.00 0.00 2.74
1888 2026 2.150397 AACGATTATGCGGCCTAGAC 57.850 50.000 0.00 0.00 35.12 2.59
1948 2087 5.745312 ATTCAATATGGTATCAGAGCCGA 57.255 39.130 0.00 0.00 0.00 5.54
1973 2112 7.420800 ACTTTTGAATAAACTGACTGAAGCAG 58.579 34.615 0.00 0.00 39.26 4.24
1985 2124 7.581476 TCATCAGTTCGGACTTTTGAATAAAC 58.419 34.615 0.00 0.00 32.54 2.01
1986 2125 7.737972 TCATCAGTTCGGACTTTTGAATAAA 57.262 32.000 0.00 0.00 32.54 1.40
1991 2130 4.956085 TCTTCATCAGTTCGGACTTTTGA 58.044 39.130 0.00 0.00 32.54 2.69
2000 2139 3.575630 TCCGTCTTTCTTCATCAGTTCG 58.424 45.455 0.00 0.00 0.00 3.95
2049 2188 1.879380 ACGCACAAATACACACATGCT 59.121 42.857 0.00 0.00 0.00 3.79
2053 2192 3.181509 ACGAAAACGCACAAATACACACA 60.182 39.130 0.00 0.00 0.00 3.72
2067 2206 0.917648 GACACACGTGCACGAAAACG 60.918 55.000 42.94 26.42 45.15 3.60
2068 2207 0.917648 CGACACACGTGCACGAAAAC 60.918 55.000 42.94 26.03 43.02 2.43
2069 2208 1.345516 CGACACACGTGCACGAAAA 59.654 52.632 42.94 0.00 43.02 2.29
2115 2298 1.065345 TCGTCCACAACACCCTCAAAA 60.065 47.619 0.00 0.00 0.00 2.44
2161 2345 1.808945 CACAAGCAGAAGATGGTGGTC 59.191 52.381 0.00 0.00 41.78 4.02
2191 2375 1.065636 CATGGTGACTGCTCCATCACT 60.066 52.381 4.53 0.00 44.36 3.41
2257 2455 1.433879 CCTCTTCCGCGACTACCAG 59.566 63.158 8.23 0.00 0.00 4.00
2290 2488 3.256704 AGGGGAGACTACATTGGTTTGA 58.743 45.455 0.00 0.00 0.00 2.69
2293 2491 2.576648 GGAAGGGGAGACTACATTGGTT 59.423 50.000 0.00 0.00 0.00 3.67
2297 2495 3.456277 GTGATGGAAGGGGAGACTACATT 59.544 47.826 0.00 0.00 0.00 2.71
2298 2496 3.041946 GTGATGGAAGGGGAGACTACAT 58.958 50.000 0.00 0.00 0.00 2.29
2300 2498 1.763545 GGTGATGGAAGGGGAGACTAC 59.236 57.143 0.00 0.00 0.00 2.73
2321 2519 2.173782 TCTCCTTCTACATCCTCGAGCT 59.826 50.000 6.99 0.00 0.00 4.09
2323 2521 3.505680 CCATCTCCTTCTACATCCTCGAG 59.494 52.174 5.13 5.13 0.00 4.04
2334 2560 3.121929 TGTAAGGCTCCATCTCCTTCT 57.878 47.619 0.00 0.00 41.47 2.85
2355 2581 1.525535 GCCATCATCCTTCGCTGCT 60.526 57.895 0.00 0.00 0.00 4.24
2360 2586 0.936764 CTCGACGCCATCATCCTTCG 60.937 60.000 0.00 0.00 0.00 3.79
2388 2614 2.353011 CCGCAAGCCAATGACAAAGAAT 60.353 45.455 0.00 0.00 0.00 2.40
2394 2620 2.676121 CCCCGCAAGCCAATGACA 60.676 61.111 0.00 0.00 0.00 3.58
2411 2637 0.318275 GATCATCTCGACACGGAGGC 60.318 60.000 0.00 0.00 34.74 4.70
2417 2643 0.658829 CTCGCGGATCATCTCGACAC 60.659 60.000 6.13 0.00 0.00 3.67
2432 2658 2.202623 CACCCAGTACGAGCTCGC 60.203 66.667 34.83 20.10 44.43 5.03
2451 2677 2.791158 GCACACTTTCTTCCGTGTTGTG 60.791 50.000 0.00 0.00 42.05 3.33
2452 2678 1.400494 GCACACTTTCTTCCGTGTTGT 59.600 47.619 0.00 0.00 42.05 3.32
2453 2679 1.268539 GGCACACTTTCTTCCGTGTTG 60.269 52.381 0.00 0.00 42.05 3.33
2454 2680 1.021968 GGCACACTTTCTTCCGTGTT 58.978 50.000 0.00 0.00 42.05 3.32
2456 2682 1.569493 CGGCACACTTTCTTCCGTG 59.431 57.895 0.00 0.00 35.75 4.94
2457 2683 2.251642 GCGGCACACTTTCTTCCGT 61.252 57.895 0.00 0.00 41.89 4.69
2474 2701 1.536709 CCACACCAAACTTCAGCAAGC 60.537 52.381 0.00 0.00 32.09 4.01


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

AutoCloner maintained by Alex Coulton.