Multiple sequence alignment - TraesCS4B01G093700

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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 TraesCS4B01G093700 chr4B 100.000 3369 0 0 1 3369 96273462 96270094 0.000000e+00 6222.0
1 TraesCS4B01G093700 chr4D 95.572 2507 78 10 361 2838 65578853 65576351 0.000000e+00 3984.0
2 TraesCS4B01G093700 chr4D 83.951 243 20 8 84 315 65579191 65578957 7.320000e-52 215.0
3 TraesCS4B01G093700 chr4D 97.561 41 1 0 2836 2876 25361786 25361746 1.680000e-08 71.3
4 TraesCS4B01G093700 chr4A 93.639 2531 99 22 361 2838 530121141 530123662 0.000000e+00 3725.0
5 TraesCS4B01G093700 chr4A 97.561 41 1 0 2836 2876 673404269 673404309 1.680000e-08 71.3
6 TraesCS4B01G093700 chr4A 97.561 41 1 0 2836 2876 689577013 689577053 1.680000e-08 71.3
7 TraesCS4B01G093700 chr7D 90.993 544 19 11 2839 3369 84997603 84997077 0.000000e+00 706.0
8 TraesCS4B01G093700 chr7D 95.522 402 16 1 2864 3263 506655026 506655427 2.830000e-180 641.0
9 TraesCS4B01G093700 chr2D 95.227 419 17 2 2864 3280 69921790 69921373 0.000000e+00 660.0
10 TraesCS4B01G093700 chr2D 95.782 403 14 1 2864 3263 550275822 550275420 0.000000e+00 647.0
11 TraesCS4B01G093700 chr2D 81.553 206 33 5 1379 1581 520537008 520536805 7.480000e-37 165.0
12 TraesCS4B01G093700 chr2D 84.848 66 7 3 2775 2838 618397508 618397572 2.810000e-06 63.9
13 TraesCS4B01G093700 chrUn 96.939 392 10 1 2874 3263 108772578 108772969 0.000000e+00 656.0
14 TraesCS4B01G093700 chrUn 96.190 105 4 0 3265 3369 323141679 323141575 4.470000e-39 172.0
15 TraesCS4B01G093700 chr1D 96.939 392 10 1 2874 3263 475252016 475252407 0.000000e+00 656.0
16 TraesCS4B01G093700 chr1D 97.143 105 3 0 3265 3369 450504253 450504357 9.610000e-41 178.0
17 TraesCS4B01G093700 chr1D 97.143 105 3 0 3265 3369 475252484 475252588 9.610000e-41 178.0
18 TraesCS4B01G093700 chr3D 94.091 440 11 5 2839 3263 562435210 562434771 0.000000e+00 654.0
19 TraesCS4B01G093700 chr3D 94.866 409 19 2 2857 3263 572025177 572025585 3.670000e-179 638.0
20 TraesCS4B01G093700 chr3D 95.413 109 4 1 3262 3369 3296177 3296069 4.470000e-39 172.0
21 TraesCS4B01G093700 chr1B 94.118 425 22 2 2839 3262 632682559 632682137 0.000000e+00 643.0
22 TraesCS4B01G093700 chr1B 96.190 105 4 0 3265 3369 24639592 24639696 4.470000e-39 172.0
23 TraesCS4B01G093700 chr5D 91.284 218 19 0 1360 1577 205995758 205995975 7.070000e-77 298.0
24 TraesCS4B01G093700 chr5D 83.957 187 26 4 1379 1563 539014529 539014713 3.450000e-40 176.0
25 TraesCS4B01G093700 chr5D 96.190 105 4 0 3265 3369 497846553 497846657 4.470000e-39 172.0
26 TraesCS4B01G093700 chr5D 86.207 58 3 4 1902 1958 205996261 205996314 1.310000e-04 58.4
27 TraesCS4B01G093700 chr5A 90.826 218 20 0 1360 1577 264421478 264421695 3.290000e-75 292.0
28 TraesCS4B01G093700 chr5A 84.211 57 6 2 1902 1958 264421981 264422034 6.000000e-03 52.8
29 TraesCS4B01G093700 chr5B 90.367 218 21 0 1360 1577 206102422 206102205 1.530000e-73 287.0
30 TraesCS4B01G093700 chr6D 84.519 239 32 4 1358 1592 393936217 393935980 7.270000e-57 231.0
31 TraesCS4B01G093700 chr6A 84.519 239 32 4 1358 1592 540145669 540145432 7.270000e-57 231.0
32 TraesCS4B01G093700 chr6A 97.561 41 1 0 2836 2876 191028913 191028953 1.680000e-08 71.3
33 TraesCS4B01G093700 chr3B 97.143 105 3 0 3265 3369 753704758 753704862 9.610000e-41 178.0
34 TraesCS4B01G093700 chr3B 100.000 40 0 0 2837 2876 761147626 761147587 1.300000e-09 75.0
35 TraesCS4B01G093700 chr3B 100.000 39 0 0 2839 2877 10926874 10926836 4.660000e-09 73.1
36 TraesCS4B01G093700 chr2B 97.143 105 3 0 3265 3369 51151962 51152066 9.610000e-41 178.0
37 TraesCS4B01G093700 chr1A 96.190 105 4 0 3265 3369 32859981 32860085 4.470000e-39 172.0
38 TraesCS4B01G093700 chr7B 100.000 40 0 0 2837 2876 673437447 673437486 1.300000e-09 75.0
39 TraesCS4B01G093700 chr7A 87.931 58 5 2 2819 2876 100061183 100061238 2.170000e-07 67.6
40 TraesCS4B01G093700 chr6B 100.000 32 0 0 1711 1742 12118379 12118348 3.630000e-05 60.2


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 TraesCS4B01G093700 chr4B 96270094 96273462 3368 True 6222.0 6222 100.0000 1 3369 1 chr4B.!!$R1 3368
1 TraesCS4B01G093700 chr4D 65576351 65579191 2840 True 2099.5 3984 89.7615 84 2838 2 chr4D.!!$R2 2754
2 TraesCS4B01G093700 chr4A 530121141 530123662 2521 False 3725.0 3725 93.6390 361 2838 1 chr4A.!!$F1 2477
3 TraesCS4B01G093700 chr7D 84997077 84997603 526 True 706.0 706 90.9930 2839 3369 1 chr7D.!!$R1 530
4 TraesCS4B01G093700 chr1D 475252016 475252588 572 False 417.0 656 97.0410 2874 3369 2 chr1D.!!$F2 495

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
225 235 0.039618 ACCGGCCATCCAATCAACTT 59.960 50.0 0.0 0.0 0.0 2.66 F
475 551 0.179200 GCAGACAAATTACCACGCCG 60.179 55.0 0.0 0.0 0.0 6.46 F
1363 1441 0.318441 CGTCAGAGAAGAAGGTGGCA 59.682 55.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 1136 2.346803 CTAGGCACAGTTACATGCGTT 58.653 47.619 10.99 3.37 43.02 4.84 R
2278 2368 0.328926 TCACCATGCCAGATGCTTGA 59.671 50.000 2.06 0.00 45.47 3.02 R
3264 3409 0.325602 TGGCCTTTAGTACCGGTTGG 59.674 55.000 15.04 7.23 42.84 3.77 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
26 27 9.709495 ACGTATTACATAAAAGTTAACAGGACA 57.291 29.630 8.61 0.00 0.00 4.02
36 37 8.458573 AAAAGTTAACAGGACAACATATGTGA 57.541 30.769 9.63 0.00 44.12 3.58
37 38 8.635765 AAAGTTAACAGGACAACATATGTGAT 57.364 30.769 9.63 0.00 44.12 3.06
38 39 8.635765 AAGTTAACAGGACAACATATGTGATT 57.364 30.769 9.63 0.00 44.12 2.57
39 40 9.733556 AAGTTAACAGGACAACATATGTGATTA 57.266 29.630 9.63 0.00 44.12 1.75
40 41 9.162764 AGTTAACAGGACAACATATGTGATTAC 57.837 33.333 9.63 0.00 44.12 1.89
41 42 9.162764 GTTAACAGGACAACATATGTGATTACT 57.837 33.333 9.63 0.00 44.12 2.24
42 43 9.733556 TTAACAGGACAACATATGTGATTACTT 57.266 29.630 9.63 0.00 44.12 2.24
43 44 7.849804 ACAGGACAACATATGTGATTACTTC 57.150 36.000 9.63 0.00 44.12 3.01
44 45 6.535150 ACAGGACAACATATGTGATTACTTCG 59.465 38.462 9.63 0.00 44.12 3.79
45 46 6.535150 CAGGACAACATATGTGATTACTTCGT 59.465 38.462 9.63 0.00 44.12 3.85
46 47 7.704899 CAGGACAACATATGTGATTACTTCGTA 59.295 37.037 9.63 0.00 44.12 3.43
47 48 7.705325 AGGACAACATATGTGATTACTTCGTAC 59.295 37.037 9.63 0.00 44.12 3.67
48 49 7.305820 GGACAACATATGTGATTACTTCGTACG 60.306 40.741 9.63 9.53 44.12 3.67
49 50 7.031372 ACAACATATGTGATTACTTCGTACGT 58.969 34.615 16.05 0.00 41.93 3.57
50 51 7.008901 ACAACATATGTGATTACTTCGTACGTG 59.991 37.037 16.05 11.86 41.93 4.49
51 52 6.558009 ACATATGTGATTACTTCGTACGTGT 58.442 36.000 16.05 16.81 0.00 4.49
52 53 7.031372 ACATATGTGATTACTTCGTACGTGTT 58.969 34.615 16.05 2.90 0.00 3.32
53 54 8.183536 ACATATGTGATTACTTCGTACGTGTTA 58.816 33.333 16.05 9.82 0.00 2.41
54 55 9.177304 CATATGTGATTACTTCGTACGTGTTAT 57.823 33.333 16.05 13.85 0.00 1.89
84 85 8.784043 AGTAATAAGTCACACATTCAAGAAACC 58.216 33.333 0.00 0.00 0.00 3.27
85 86 4.552166 AAGTCACACATTCAAGAAACCG 57.448 40.909 0.00 0.00 0.00 4.44
86 87 3.541632 AGTCACACATTCAAGAAACCGT 58.458 40.909 0.00 0.00 0.00 4.83
87 88 4.699637 AGTCACACATTCAAGAAACCGTA 58.300 39.130 0.00 0.00 0.00 4.02
88 89 5.305585 AGTCACACATTCAAGAAACCGTAT 58.694 37.500 0.00 0.00 0.00 3.06
89 90 6.460781 AGTCACACATTCAAGAAACCGTATA 58.539 36.000 0.00 0.00 0.00 1.47
90 91 6.367969 AGTCACACATTCAAGAAACCGTATAC 59.632 38.462 0.00 0.00 0.00 1.47
128 129 3.132925 GGTTGTAGGACGTACTTGCAAA 58.867 45.455 5.12 0.00 32.98 3.68
130 131 4.319261 GGTTGTAGGACGTACTTGCAAAAG 60.319 45.833 5.12 0.00 32.98 2.27
137 147 4.451096 GGACGTACTTGCAAAAGAGAATGA 59.549 41.667 0.00 0.00 0.00 2.57
151 161 7.929941 AAAGAGAATGATAACAACTTCTCCC 57.070 36.000 10.91 0.00 40.30 4.30
152 162 5.665459 AGAGAATGATAACAACTTCTCCCG 58.335 41.667 10.91 0.00 40.30 5.14
161 171 2.567169 ACAACTTCTCCCGATGTCATGA 59.433 45.455 0.00 0.00 0.00 3.07
162 172 2.932614 CAACTTCTCCCGATGTCATGAC 59.067 50.000 19.27 19.27 0.00 3.06
163 173 2.461695 ACTTCTCCCGATGTCATGACT 58.538 47.619 25.55 11.93 0.00 3.41
164 174 2.834549 ACTTCTCCCGATGTCATGACTT 59.165 45.455 25.55 19.77 0.00 3.01
165 175 2.967599 TCTCCCGATGTCATGACTTG 57.032 50.000 25.55 14.84 0.00 3.16
166 176 2.456577 TCTCCCGATGTCATGACTTGA 58.543 47.619 25.55 12.41 0.00 3.02
179 189 3.593442 TGACTTGACTGGGGTTTGATT 57.407 42.857 0.00 0.00 0.00 2.57
192 202 3.385755 GGGTTTGATTCATGAAGGGATGG 59.614 47.826 14.54 0.00 0.00 3.51
200 210 1.684983 CATGAAGGGATGGGATTGCAC 59.315 52.381 0.00 0.00 0.00 4.57
224 234 0.680921 CACCGGCCATCCAATCAACT 60.681 55.000 0.00 0.00 0.00 3.16
225 235 0.039618 ACCGGCCATCCAATCAACTT 59.960 50.000 0.00 0.00 0.00 2.66
233 243 5.047377 GGCCATCCAATCAACTTTTAGTTCA 60.047 40.000 0.00 0.00 36.03 3.18
291 302 2.897271 AATGGGTAGCACATGGTGAA 57.103 45.000 0.00 0.00 35.23 3.18
296 307 2.625790 GGGTAGCACATGGTGAAACAAA 59.374 45.455 0.00 0.00 39.98 2.83
303 314 6.392354 AGCACATGGTGAAACAAATAGATTG 58.608 36.000 0.00 0.00 39.98 2.67
359 398 9.981114 ATAATAAAATAAGGGAAAATGAAGGCG 57.019 29.630 0.00 0.00 0.00 5.52
363 432 0.323451 AGGGAAAATGAAGGCGGTCC 60.323 55.000 0.00 0.00 0.00 4.46
366 435 1.616374 GGAAAATGAAGGCGGTCCAAA 59.384 47.619 0.00 0.00 33.74 3.28
381 450 2.805099 GTCCAAATTGCCATGCGAAAAA 59.195 40.909 0.00 0.00 0.00 1.94
382 451 2.805099 TCCAAATTGCCATGCGAAAAAC 59.195 40.909 0.00 0.00 0.00 2.43
415 490 4.142491 TGACATGTTTGTAATGGATTCGCC 60.142 41.667 0.00 0.00 35.79 5.54
445 520 6.489700 TCTGAAGTGAAATTTGCCATCTTGTA 59.510 34.615 0.00 0.00 0.00 2.41
475 551 0.179200 GCAGACAAATTACCACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
476 552 1.434555 CAGACAAATTACCACGCCGA 58.565 50.000 0.00 0.00 0.00 5.54
477 553 1.801771 CAGACAAATTACCACGCCGAA 59.198 47.619 0.00 0.00 0.00 4.30
498 574 2.821969 AGAGAGAAATTGCCATGCGTTT 59.178 40.909 0.00 0.00 0.00 3.60
502 578 3.514645 AGAAATTGCCATGCGTTTGATC 58.485 40.909 0.00 0.00 0.00 2.92
509 586 1.935873 CCATGCGTTTGATCGTGATCT 59.064 47.619 10.91 0.00 38.60 2.75
574 651 5.753744 GTGTTCACACGTTATTGAAATCCA 58.246 37.500 5.75 0.00 37.10 3.41
617 695 5.783111 ACAAACAGCTGTATTTCCATTTCC 58.217 37.500 22.01 0.00 0.00 3.13
650 728 3.411415 GATTCACAAATCCCAAGCTCG 57.589 47.619 0.00 0.00 36.12 5.03
729 807 0.531532 GCCAGGTCATGATCCTCACG 60.532 60.000 12.31 6.22 32.37 4.35
781 859 3.124921 CTTGCCCTACCCAACGCG 61.125 66.667 3.53 3.53 0.00 6.01
793 871 1.652012 CAACGCGAACCATGGTTGT 59.348 52.632 34.47 22.39 38.60 3.32
794 872 0.660005 CAACGCGAACCATGGTTGTG 60.660 55.000 34.47 29.07 38.60 3.33
825 903 7.038941 TGGTTATATAAGAGAGGAAAGCTAGGC 60.039 40.741 0.00 0.00 0.00 3.93
956 1034 1.283613 GTCTGACCTCTCTCTCCTCCA 59.716 57.143 0.00 0.00 0.00 3.86
1267 1345 2.892425 CCGTTCATGGGCTCGCTC 60.892 66.667 0.00 0.00 0.00 5.03
1363 1441 0.318441 CGTCAGAGAAGAAGGTGGCA 59.682 55.000 0.00 0.00 0.00 4.92
1633 1711 2.846532 CCCTTCCAGCACCACCTT 59.153 61.111 0.00 0.00 0.00 3.50
2029 2110 5.287226 CAGTTCATTTCAAGAAGCAGCTTT 58.713 37.500 9.62 0.00 0.00 3.51
2065 2146 0.807667 ACACGAATCTCGGCATGCTC 60.808 55.000 18.92 6.88 45.59 4.26
2265 2355 1.592400 AACGAGAGCCATCCGTTCGA 61.592 55.000 0.00 0.00 37.61 3.71
2278 2368 1.468520 CCGTTCGAGCAACCAATCATT 59.531 47.619 0.00 0.00 0.00 2.57
2672 2773 1.591059 TTGCCATGCGTTGCAACAC 60.591 52.632 28.01 19.82 43.62 3.32
2681 2782 1.211709 GTTGCAACACGGGCATACC 59.788 57.895 24.52 0.00 41.58 2.73
2734 2865 7.523380 GCCCGACATATATACACCTACCATATC 60.523 44.444 0.00 0.00 0.00 1.63
2790 2921 7.576649 AGGTATAGGTAGGGAAATTCAAGGAAT 59.423 37.037 0.00 0.00 33.25 3.01
2871 3002 4.320608 AACGACTTTTAGTACCGGTTCA 57.679 40.909 15.04 0.00 0.00 3.18
2872 3003 4.525912 ACGACTTTTAGTACCGGTTCAT 57.474 40.909 15.04 0.95 0.00 2.57
2890 3033 5.189145 GGTTCATAAGAGTGGGGACTAAAGA 59.811 44.000 0.00 0.00 0.00 2.52
3033 3178 7.622893 TTTTGAAATAAAGCAAAAACAGCCT 57.377 28.000 0.00 0.00 40.02 4.58
3109 3254 4.157120 GATGCAGGCCCGTACGGT 62.157 66.667 31.24 12.37 0.00 4.83
3254 3399 4.069304 GTGGGACTAAACATTGTGCACTA 58.931 43.478 19.41 11.52 0.00 2.74
3263 3408 2.124507 ATTGTGCACTACGGGTGGCT 62.125 55.000 19.41 0.00 45.44 4.75
3264 3409 2.434359 GTGCACTACGGGTGGCTC 60.434 66.667 10.32 3.52 45.44 4.70
3266 3411 3.702048 GCACTACGGGTGGCTCCA 61.702 66.667 8.03 0.00 45.44 3.86
3267 3412 3.065306 CACTACGGGTGGCTCCAA 58.935 61.111 8.03 0.00 41.90 3.53
3268 3413 1.375523 CACTACGGGTGGCTCCAAC 60.376 63.158 8.03 0.00 41.90 3.77
3273 3418 3.324108 GGGTGGCTCCAACCGGTA 61.324 66.667 8.00 0.00 44.58 4.02
3274 3419 2.046604 GGTGGCTCCAACCGGTAC 60.047 66.667 8.00 0.00 35.97 3.34
3275 3420 2.590114 GGTGGCTCCAACCGGTACT 61.590 63.158 8.00 0.00 35.97 2.73
3276 3421 1.259840 GGTGGCTCCAACCGGTACTA 61.260 60.000 8.00 0.00 35.97 1.82
3277 3422 0.609662 GTGGCTCCAACCGGTACTAA 59.390 55.000 8.00 0.00 0.00 2.24
3278 3423 1.002315 GTGGCTCCAACCGGTACTAAA 59.998 52.381 8.00 0.00 0.00 1.85
3279 3424 1.276989 TGGCTCCAACCGGTACTAAAG 59.723 52.381 8.00 2.56 0.00 1.85
3280 3425 1.406477 GGCTCCAACCGGTACTAAAGG 60.406 57.143 8.00 3.51 0.00 3.11
3281 3426 2.010544 GCTCCAACCGGTACTAAAGGC 61.011 57.143 8.00 2.61 0.00 4.35
3282 3427 0.614812 TCCAACCGGTACTAAAGGCC 59.385 55.000 8.00 0.00 0.00 5.19
3283 3428 0.325602 CCAACCGGTACTAAAGGCCA 59.674 55.000 8.00 0.00 0.00 5.36
3284 3429 1.445871 CAACCGGTACTAAAGGCCAC 58.554 55.000 8.00 0.00 0.00 5.01
3285 3430 0.325933 AACCGGTACTAAAGGCCACC 59.674 55.000 8.00 0.51 0.00 4.61
3286 3431 0.837260 ACCGGTACTAAAGGCCACCA 60.837 55.000 4.49 0.00 0.00 4.17
3287 3432 0.392060 CCGGTACTAAAGGCCACCAC 60.392 60.000 5.01 0.00 0.00 4.16
3288 3433 0.392060 CGGTACTAAAGGCCACCACC 60.392 60.000 5.01 2.01 0.00 4.61
3289 3434 0.989602 GGTACTAAAGGCCACCACCT 59.010 55.000 5.01 0.00 43.91 4.00
3295 3440 3.396611 ACTAAAGGCCACCACCTCTTTAA 59.603 43.478 5.01 0.00 39.93 1.52
3304 3449 3.937079 CACCACCTCTTTAATACCGGTTC 59.063 47.826 15.04 0.00 0.00 3.62
3310 3455 2.028294 TCTTTAATACCGGTTCGTGGCA 60.028 45.455 15.04 0.00 0.00 4.92
3312 3457 0.458197 TAATACCGGTTCGTGGCACG 60.458 55.000 32.75 32.75 44.19 5.34
3350 3587 3.351740 TCACCACGAACCGGTACTAATA 58.648 45.455 8.00 0.00 34.02 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.709495 TGTCCTGTTAACTTTTATGTAATACGT 57.291 29.630 7.22 0.00 0.00 3.57
10 11 9.562408 TCACATATGTTGTCCTGTTAACTTTTA 57.438 29.630 5.37 0.00 36.00 1.52
11 12 8.458573 TCACATATGTTGTCCTGTTAACTTTT 57.541 30.769 5.37 0.00 36.00 2.27
12 13 8.635765 ATCACATATGTTGTCCTGTTAACTTT 57.364 30.769 5.37 0.00 36.00 2.66
13 14 8.635765 AATCACATATGTTGTCCTGTTAACTT 57.364 30.769 5.37 0.00 36.00 2.66
14 15 9.162764 GTAATCACATATGTTGTCCTGTTAACT 57.837 33.333 5.37 0.00 36.00 2.24
15 16 9.162764 AGTAATCACATATGTTGTCCTGTTAAC 57.837 33.333 5.37 0.00 36.00 2.01
16 17 9.733556 AAGTAATCACATATGTTGTCCTGTTAA 57.266 29.630 5.37 0.00 36.00 2.01
17 18 9.378551 GAAGTAATCACATATGTTGTCCTGTTA 57.621 33.333 5.37 0.00 36.00 2.41
18 19 7.064609 CGAAGTAATCACATATGTTGTCCTGTT 59.935 37.037 5.37 0.00 36.00 3.16
19 20 6.535150 CGAAGTAATCACATATGTTGTCCTGT 59.465 38.462 5.37 0.00 36.00 4.00
20 21 6.535150 ACGAAGTAATCACATATGTTGTCCTG 59.465 38.462 5.37 0.00 41.94 3.86
21 22 6.640518 ACGAAGTAATCACATATGTTGTCCT 58.359 36.000 5.37 0.00 41.94 3.85
22 23 6.903883 ACGAAGTAATCACATATGTTGTCC 57.096 37.500 5.37 0.00 41.94 4.02
58 59 8.784043 GGTTTCTTGAATGTGTGACTTATTACT 58.216 33.333 0.00 0.00 0.00 2.24
59 60 7.744715 CGGTTTCTTGAATGTGTGACTTATTAC 59.255 37.037 0.00 0.00 0.00 1.89
60 61 7.442969 ACGGTTTCTTGAATGTGTGACTTATTA 59.557 33.333 0.00 0.00 0.00 0.98
61 62 6.262273 ACGGTTTCTTGAATGTGTGACTTATT 59.738 34.615 0.00 0.00 0.00 1.40
62 63 5.763204 ACGGTTTCTTGAATGTGTGACTTAT 59.237 36.000 0.00 0.00 0.00 1.73
63 64 5.120399 ACGGTTTCTTGAATGTGTGACTTA 58.880 37.500 0.00 0.00 0.00 2.24
64 65 3.945285 ACGGTTTCTTGAATGTGTGACTT 59.055 39.130 0.00 0.00 0.00 3.01
65 66 3.541632 ACGGTTTCTTGAATGTGTGACT 58.458 40.909 0.00 0.00 0.00 3.41
66 67 3.963383 ACGGTTTCTTGAATGTGTGAC 57.037 42.857 0.00 0.00 0.00 3.67
67 68 6.460781 AGTATACGGTTTCTTGAATGTGTGA 58.539 36.000 0.00 0.00 0.00 3.58
68 69 6.721571 AGTATACGGTTTCTTGAATGTGTG 57.278 37.500 0.00 0.00 0.00 3.82
69 70 6.148811 CCAAGTATACGGTTTCTTGAATGTGT 59.851 38.462 15.75 0.00 39.39 3.72
70 71 6.148811 ACCAAGTATACGGTTTCTTGAATGTG 59.851 38.462 15.75 6.39 39.39 3.21
71 72 6.148811 CACCAAGTATACGGTTTCTTGAATGT 59.851 38.462 15.75 7.28 39.39 2.71
72 73 6.148811 ACACCAAGTATACGGTTTCTTGAATG 59.851 38.462 15.75 14.91 39.39 2.67
73 74 6.235664 ACACCAAGTATACGGTTTCTTGAAT 58.764 36.000 15.75 6.16 39.39 2.57
74 75 5.613329 ACACCAAGTATACGGTTTCTTGAA 58.387 37.500 15.75 0.00 39.39 2.69
75 76 5.217978 ACACCAAGTATACGGTTTCTTGA 57.782 39.130 15.75 0.00 39.39 3.02
76 77 5.934935 AACACCAAGTATACGGTTTCTTG 57.065 39.130 0.07 10.48 37.57 3.02
77 78 6.056884 TGAAACACCAAGTATACGGTTTCTT 58.943 36.000 23.81 11.27 42.60 2.52
78 79 5.613329 TGAAACACCAAGTATACGGTTTCT 58.387 37.500 23.81 3.19 42.60 2.52
79 80 5.927954 TGAAACACCAAGTATACGGTTTC 57.072 39.130 20.51 20.51 42.52 2.78
80 81 5.278120 GCTTGAAACACCAAGTATACGGTTT 60.278 40.000 0.07 6.17 43.96 3.27
81 82 4.214758 GCTTGAAACACCAAGTATACGGTT 59.785 41.667 0.07 0.00 43.96 4.44
82 83 3.749609 GCTTGAAACACCAAGTATACGGT 59.250 43.478 0.00 0.00 43.96 4.83
83 84 3.749088 TGCTTGAAACACCAAGTATACGG 59.251 43.478 0.00 0.00 43.96 4.02
84 85 5.351233 TTGCTTGAAACACCAAGTATACG 57.649 39.130 0.00 0.00 43.96 3.06
85 86 5.240844 ACCTTGCTTGAAACACCAAGTATAC 59.759 40.000 0.00 0.00 43.96 1.47
86 87 5.381757 ACCTTGCTTGAAACACCAAGTATA 58.618 37.500 0.00 0.00 43.96 1.47
87 88 4.215109 ACCTTGCTTGAAACACCAAGTAT 58.785 39.130 0.00 0.00 43.96 2.12
88 89 3.626930 ACCTTGCTTGAAACACCAAGTA 58.373 40.909 0.00 0.00 43.96 2.24
89 90 2.456577 ACCTTGCTTGAAACACCAAGT 58.543 42.857 0.00 0.00 43.96 3.16
90 91 3.189285 CAACCTTGCTTGAAACACCAAG 58.811 45.455 0.00 0.00 44.67 3.61
128 129 6.070767 TCGGGAGAAGTTGTTATCATTCTCTT 60.071 38.462 12.12 0.00 44.52 2.85
130 131 5.661458 TCGGGAGAAGTTGTTATCATTCTC 58.339 41.667 5.44 5.44 44.44 2.87
137 147 4.819105 TGACATCGGGAGAAGTTGTTAT 57.181 40.909 0.00 0.00 41.40 1.89
161 171 3.593442 TGAATCAAACCCCAGTCAAGT 57.407 42.857 0.00 0.00 0.00 3.16
162 172 4.081406 TCATGAATCAAACCCCAGTCAAG 58.919 43.478 0.00 0.00 0.00 3.02
163 173 4.111255 TCATGAATCAAACCCCAGTCAA 57.889 40.909 0.00 0.00 0.00 3.18
164 174 3.805066 TCATGAATCAAACCCCAGTCA 57.195 42.857 0.00 0.00 0.00 3.41
165 175 3.445096 CCTTCATGAATCAAACCCCAGTC 59.555 47.826 8.96 0.00 0.00 3.51
166 176 3.434309 CCTTCATGAATCAAACCCCAGT 58.566 45.455 8.96 0.00 0.00 4.00
167 177 2.762327 CCCTTCATGAATCAAACCCCAG 59.238 50.000 8.96 0.00 0.00 4.45
168 178 2.381618 TCCCTTCATGAATCAAACCCCA 59.618 45.455 8.96 0.00 0.00 4.96
169 179 3.100207 TCCCTTCATGAATCAAACCCC 57.900 47.619 8.96 0.00 0.00 4.95
170 180 3.385755 CCATCCCTTCATGAATCAAACCC 59.614 47.826 8.96 0.00 0.00 4.11
171 181 3.385755 CCCATCCCTTCATGAATCAAACC 59.614 47.826 8.96 0.00 0.00 3.27
179 189 1.570024 TGCAATCCCATCCCTTCATGA 59.430 47.619 0.00 0.00 0.00 3.07
192 202 3.061848 CGGTGGTGGGTGCAATCC 61.062 66.667 0.00 0.00 0.00 3.01
261 272 4.892934 TGTGCTACCCATTTTCTCAGTTTT 59.107 37.500 0.00 0.00 0.00 2.43
265 276 3.379372 CCATGTGCTACCCATTTTCTCAG 59.621 47.826 0.00 0.00 0.00 3.35
274 285 1.143889 TGTTTCACCATGTGCTACCCA 59.856 47.619 0.00 0.00 32.98 4.51
280 291 6.158598 ACAATCTATTTGTTTCACCATGTGC 58.841 36.000 0.00 0.00 46.51 4.57
351 390 0.532115 GCAATTTGGACCGCCTTCAT 59.468 50.000 0.00 0.00 34.31 2.57
355 394 1.305213 ATGGCAATTTGGACCGCCT 60.305 52.632 8.58 0.00 45.13 5.52
358 397 1.516821 CGCATGGCAATTTGGACCG 60.517 57.895 0.00 0.00 0.00 4.79
359 398 0.246086 TTCGCATGGCAATTTGGACC 59.754 50.000 0.00 0.00 0.00 4.46
363 432 3.874400 TGTTTTTCGCATGGCAATTTG 57.126 38.095 0.00 0.00 0.00 2.32
366 435 7.840342 TTTTATATGTTTTTCGCATGGCAAT 57.160 28.000 0.00 0.00 0.00 3.56
412 487 1.159285 TTTCACTTCAGAGCATGGCG 58.841 50.000 0.00 0.00 0.00 5.69
415 490 3.924686 GGCAAATTTCACTTCAGAGCATG 59.075 43.478 0.00 0.00 0.00 4.06
451 527 3.758300 CGTGGTAATTTGTCTGCCATTC 58.242 45.455 0.00 0.00 0.00 2.67
475 551 2.421424 ACGCATGGCAATTTCTCTCTTC 59.579 45.455 0.00 0.00 0.00 2.87
476 552 2.440409 ACGCATGGCAATTTCTCTCTT 58.560 42.857 0.00 0.00 0.00 2.85
477 553 2.119801 ACGCATGGCAATTTCTCTCT 57.880 45.000 0.00 0.00 0.00 3.10
498 574 1.342496 GGAGCCATCAGATCACGATCA 59.658 52.381 9.60 0.00 40.22 2.92
502 578 0.318529 CTCGGAGCCATCAGATCACG 60.319 60.000 0.00 0.00 0.00 4.35
509 586 1.473257 CGAATTTCCTCGGAGCCATCA 60.473 52.381 0.00 0.00 35.14 3.07
552 629 6.378710 TTGGATTTCAATAACGTGTGAACA 57.621 33.333 8.60 3.06 33.58 3.18
794 872 9.438228 GCTTTCCTCTCTTATATAACCATAACC 57.562 37.037 0.00 0.00 0.00 2.85
825 903 0.106619 ACCTACTCCTCCGTAGCCTG 60.107 60.000 0.00 0.00 36.41 4.85
1058 1136 2.346803 CTAGGCACAGTTACATGCGTT 58.653 47.619 10.99 3.37 43.02 4.84
1363 1441 3.948719 TCCTTGGTCGGCCGCTTT 61.949 61.111 23.51 0.00 37.67 3.51
2265 2355 3.767673 AGATGCTTGAATGATTGGTTGCT 59.232 39.130 0.00 0.00 0.00 3.91
2278 2368 0.328926 TCACCATGCCAGATGCTTGA 59.671 50.000 2.06 0.00 45.47 3.02
2672 2773 5.047306 TGAATCACTAGAATAGGTATGCCCG 60.047 44.000 0.00 0.00 44.97 6.13
2765 2896 6.758806 TCCTTGAATTTCCCTACCTATACC 57.241 41.667 0.00 0.00 0.00 2.73
2890 3033 3.124861 TGAACCGGTATTAAAGGGGGAT 58.875 45.455 8.00 0.00 0.00 3.85
3109 3254 2.285368 CCTGTGGGGCCTACTGGA 60.285 66.667 33.36 9.11 38.88 3.86
3263 3408 0.614812 GGCCTTTAGTACCGGTTGGA 59.385 55.000 15.04 0.00 39.21 3.53
3264 3409 0.325602 TGGCCTTTAGTACCGGTTGG 59.674 55.000 15.04 7.23 42.84 3.77
3266 3411 0.325933 GGTGGCCTTTAGTACCGGTT 59.674 55.000 15.04 0.00 0.00 4.44
3267 3412 0.837260 TGGTGGCCTTTAGTACCGGT 60.837 55.000 13.98 13.98 35.98 5.28
3268 3413 0.392060 GTGGTGGCCTTTAGTACCGG 60.392 60.000 3.32 0.00 35.98 5.28
3270 3415 0.989602 AGGTGGTGGCCTTTAGTACC 59.010 55.000 3.32 1.76 34.71 3.34
3271 3416 1.907255 AGAGGTGGTGGCCTTTAGTAC 59.093 52.381 3.32 0.00 39.34 2.73
3272 3417 2.337359 AGAGGTGGTGGCCTTTAGTA 57.663 50.000 3.32 0.00 39.34 1.82
3273 3418 1.446016 AAGAGGTGGTGGCCTTTAGT 58.554 50.000 3.32 0.00 39.34 2.24
3274 3419 2.586648 AAAGAGGTGGTGGCCTTTAG 57.413 50.000 3.32 0.00 39.34 1.85
3275 3420 4.668138 ATTAAAGAGGTGGTGGCCTTTA 57.332 40.909 3.32 0.00 39.34 1.85
3276 3421 3.542969 ATTAAAGAGGTGGTGGCCTTT 57.457 42.857 3.32 0.00 39.34 3.11
3277 3422 3.308904 GGTATTAAAGAGGTGGTGGCCTT 60.309 47.826 3.32 0.00 39.34 4.35
3278 3423 2.241430 GGTATTAAAGAGGTGGTGGCCT 59.759 50.000 3.32 0.00 42.53 5.19
3279 3424 2.651455 GGTATTAAAGAGGTGGTGGCC 58.349 52.381 0.00 0.00 0.00 5.36
3280 3425 2.285977 CGGTATTAAAGAGGTGGTGGC 58.714 52.381 0.00 0.00 0.00 5.01
3281 3426 2.237893 ACCGGTATTAAAGAGGTGGTGG 59.762 50.000 4.49 0.00 33.37 4.61
3282 3427 3.622166 ACCGGTATTAAAGAGGTGGTG 57.378 47.619 4.49 0.00 33.37 4.17
3283 3428 3.368739 CGAACCGGTATTAAAGAGGTGGT 60.369 47.826 8.00 0.00 35.08 4.16
3284 3429 3.192466 CGAACCGGTATTAAAGAGGTGG 58.808 50.000 8.00 0.00 35.08 4.61
3285 3430 3.615496 CACGAACCGGTATTAAAGAGGTG 59.385 47.826 8.00 2.11 35.08 4.00
3286 3431 3.368739 CCACGAACCGGTATTAAAGAGGT 60.369 47.826 8.00 0.00 36.66 3.85
3287 3432 3.192466 CCACGAACCGGTATTAAAGAGG 58.808 50.000 8.00 0.17 0.00 3.69
3288 3433 2.606272 GCCACGAACCGGTATTAAAGAG 59.394 50.000 8.00 0.00 0.00 2.85
3289 3434 2.028294 TGCCACGAACCGGTATTAAAGA 60.028 45.455 8.00 0.00 0.00 2.52
3295 3440 2.125832 CGTGCCACGAACCGGTAT 60.126 61.111 12.85 0.00 46.05 2.73
3304 3449 2.198906 TAGTACCGGTTCGTGCCACG 62.199 60.000 15.04 11.80 44.19 4.94
3310 3455 3.303881 GAACCTTTAGTACCGGTTCGT 57.696 47.619 15.04 0.00 44.86 3.85


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

AutoCloner maintained by Alex Coulton.