Multiple sequence alignment - TraesCS5D01G244000

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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 TraesCS5D01G244000 chr5D 100.000 2708 0 0 1 2708 352455771 352453064 0.000000e+00 5001
1 TraesCS5D01G244000 chr5A 91.998 2337 83 44 418 2708 453518563 453520841 0.000000e+00 3184
2 TraesCS5D01G244000 chr5B 94.482 1903 64 18 820 2708 415128257 415126382 0.000000e+00 2894
3 TraesCS5D01G244000 chr5B 90.185 540 31 9 239 765 415128785 415128255 0.000000e+00 684
4 TraesCS5D01G244000 chr6A 94.426 1471 54 12 558 2020 116814021 116812571 0.000000e+00 2237
5 TraesCS5D01G244000 chr3A 96.821 755 13 3 1266 2020 398879899 398879156 0.000000e+00 1251
6 TraesCS5D01G244000 chr2B 92.321 599 27 10 558 1147 712610589 712611177 0.000000e+00 833
7 TraesCS5D01G244000 chr2B 96.421 447 5 3 1571 2017 712611174 712611609 0.000000e+00 726
8 TraesCS5D01G244000 chr7A 90.625 288 27 0 1361 1648 258824369 258824656 1.520000e-102 383
9 TraesCS5D01G244000 chr7A 92.958 213 13 2 15 227 604403904 604403694 2.620000e-80 309
10 TraesCS5D01G244000 chr7D 90.278 288 28 0 1361 1648 243808054 243808341 7.080000e-101 377
11 TraesCS5D01G244000 chr7D 82.353 204 36 0 1432 1635 123219587 123219790 7.700000e-41 178
12 TraesCS5D01G244000 chr7B 88.889 288 32 0 1361 1648 218976152 218975865 3.320000e-94 355
13 TraesCS5D01G244000 chr7B 92.609 230 13 4 15 243 388177173 388176947 7.230000e-86 327
14 TraesCS5D01G244000 chr7B 92.958 213 13 2 15 227 152487092 152486882 2.620000e-80 309
15 TraesCS5D01G244000 chr7B 81.604 212 35 3 1432 1641 84389122 84389331 3.580000e-39 172
16 TraesCS5D01G244000 chr2A 93.897 213 11 2 15 227 763213607 763213817 1.210000e-83 320
17 TraesCS5D01G244000 chr1B 92.694 219 14 2 15 233 37692690 37692474 5.630000e-82 315
18 TraesCS5D01G244000 chr4B 92.958 213 13 2 15 227 530233921 530234131 2.620000e-80 309
19 TraesCS5D01G244000 chr2D 92.958 213 13 2 15 227 460298821 460299031 2.620000e-80 309
20 TraesCS5D01G244000 chr6D 90.749 227 18 3 15 240 217731947 217732171 1.580000e-77 300
21 TraesCS5D01G244000 chr4A 90.991 222 17 3 15 236 91314458 91314240 2.040000e-76 296


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 TraesCS5D01G244000 chr5D 352453064 352455771 2707 True 5001.0 5001 100.0000 1 2708 1 chr5D.!!$R1 2707
1 TraesCS5D01G244000 chr5A 453518563 453520841 2278 False 3184.0 3184 91.9980 418 2708 1 chr5A.!!$F1 2290
2 TraesCS5D01G244000 chr5B 415126382 415128785 2403 True 1789.0 2894 92.3335 239 2708 2 chr5B.!!$R1 2469
3 TraesCS5D01G244000 chr6A 116812571 116814021 1450 True 2237.0 2237 94.4260 558 2020 1 chr6A.!!$R1 1462
4 TraesCS5D01G244000 chr3A 398879156 398879899 743 True 1251.0 1251 96.8210 1266 2020 1 chr3A.!!$R1 754
5 TraesCS5D01G244000 chr2B 712610589 712611609 1020 False 779.5 833 94.3710 558 2017 2 chr2B.!!$F1 1459

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
933 953 0.099082 CGCTCGTAGTCCAGTCCTTC 59.901 60.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2550 2612 0.039527 CAAAGTTAACCTGCGTGCCC 60.04 55.0 0.88 0.0 0.0 5.36 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 3.743521 GGTGGTAACTAAAAACCTCCGT 58.256 45.455 0.00 0.00 39.06 4.69
22 23 3.748048 GGTGGTAACTAAAAACCTCCGTC 59.252 47.826 0.00 0.00 39.06 4.79
23 24 4.503817 GGTGGTAACTAAAAACCTCCGTCT 60.504 45.833 0.00 0.00 39.06 4.18
24 25 4.687948 GTGGTAACTAAAAACCTCCGTCTC 59.312 45.833 0.00 0.00 36.67 3.36
25 26 3.922850 GGTAACTAAAAACCTCCGTCTCG 59.077 47.826 0.00 0.00 32.72 4.04
26 27 7.518600 TGGTAACTAAAAACCTCCGTCTCGG 62.519 48.000 1.45 1.45 39.93 4.63
37 38 2.933495 CCGTCTCGGTGAATAAGTCA 57.067 50.000 0.00 0.00 42.73 3.41
38 39 3.438297 CCGTCTCGGTGAATAAGTCAT 57.562 47.619 0.00 0.00 42.73 3.06
39 40 3.782046 CCGTCTCGGTGAATAAGTCATT 58.218 45.455 0.00 0.00 42.73 2.57
40 41 4.181578 CCGTCTCGGTGAATAAGTCATTT 58.818 43.478 0.00 0.00 42.73 2.32
41 42 5.345702 CCGTCTCGGTGAATAAGTCATTTA 58.654 41.667 0.00 0.00 42.73 1.40
42 43 5.231568 CCGTCTCGGTGAATAAGTCATTTAC 59.768 44.000 0.00 0.00 42.73 2.01
43 44 5.052567 CGTCTCGGTGAATAAGTCATTTACG 60.053 44.000 0.00 0.00 38.90 3.18
44 45 5.803967 GTCTCGGTGAATAAGTCATTTACGT 59.196 40.000 0.00 0.00 38.90 3.57
45 46 6.968904 GTCTCGGTGAATAAGTCATTTACGTA 59.031 38.462 0.00 0.00 38.90 3.57
46 47 7.165483 GTCTCGGTGAATAAGTCATTTACGTAG 59.835 40.741 0.00 0.00 38.90 3.51
47 48 6.855836 TCGGTGAATAAGTCATTTACGTAGT 58.144 36.000 0.00 0.00 41.55 2.73
48 49 7.315142 TCGGTGAATAAGTCATTTACGTAGTT 58.685 34.615 0.00 0.00 39.68 2.24
49 50 7.485913 TCGGTGAATAAGTCATTTACGTAGTTC 59.514 37.037 0.00 0.00 39.68 3.01
50 51 7.487189 CGGTGAATAAGTCATTTACGTAGTTCT 59.513 37.037 0.00 0.00 39.68 3.01
51 52 8.805688 GGTGAATAAGTCATTTACGTAGTTCTC 58.194 37.037 0.00 0.00 39.68 2.87
52 53 8.521860 GTGAATAAGTCATTTACGTAGTTCTCG 58.478 37.037 0.00 0.00 39.68 4.04
53 54 8.453320 TGAATAAGTCATTTACGTAGTTCTCGA 58.547 33.333 0.00 0.00 37.78 4.04
54 55 9.448294 GAATAAGTCATTTACGTAGTTCTCGAT 57.552 33.333 0.00 0.00 37.78 3.59
55 56 9.798994 AATAAGTCATTTACGTAGTTCTCGATT 57.201 29.630 0.00 0.00 37.78 3.34
56 57 7.507672 AAGTCATTTACGTAGTTCTCGATTG 57.492 36.000 0.00 0.00 37.78 2.67
57 58 6.849502 AGTCATTTACGTAGTTCTCGATTGA 58.150 36.000 0.00 0.00 37.78 2.57
58 59 6.746364 AGTCATTTACGTAGTTCTCGATTGAC 59.254 38.462 0.00 2.30 37.78 3.18
59 60 5.735892 TCATTTACGTAGTTCTCGATTGACG 59.264 40.000 0.00 0.00 37.78 4.35
60 61 4.926860 TTACGTAGTTCTCGATTGACGA 57.073 40.909 10.98 0.00 44.88 4.20
61 62 5.475273 TTACGTAGTTCTCGATTGACGAT 57.525 39.130 10.98 0.00 45.72 3.73
62 63 4.352600 ACGTAGTTCTCGATTGACGATT 57.647 40.909 10.98 0.00 45.72 3.34
63 64 4.730657 ACGTAGTTCTCGATTGACGATTT 58.269 39.130 10.98 0.00 45.72 2.17
64 65 5.872635 ACGTAGTTCTCGATTGACGATTTA 58.127 37.500 10.98 0.00 45.72 1.40
65 66 6.317088 ACGTAGTTCTCGATTGACGATTTAA 58.683 36.000 10.98 0.00 45.72 1.52
66 67 6.250104 ACGTAGTTCTCGATTGACGATTTAAC 59.750 38.462 10.98 0.00 45.72 2.01
67 68 7.836486 ACGTAGTTCTCGATTGACGATTTAACT 60.836 37.037 10.98 0.95 45.72 2.24
195 196 8.970859 ATTCCTCAAATCGATGATCTAAAACT 57.029 30.769 0.00 0.00 0.00 2.66
197 198 8.873215 TCCTCAAATCGATGATCTAAAACTAC 57.127 34.615 0.00 0.00 0.00 2.73
198 199 7.648112 TCCTCAAATCGATGATCTAAAACTACG 59.352 37.037 0.00 0.00 0.00 3.51
199 200 7.161829 TCAAATCGATGATCTAAAACTACGC 57.838 36.000 0.00 0.00 0.00 4.42
200 201 6.754675 TCAAATCGATGATCTAAAACTACGCA 59.245 34.615 0.00 0.00 0.00 5.24
201 202 7.276878 TCAAATCGATGATCTAAAACTACGCAA 59.723 33.333 0.00 0.00 0.00 4.85
202 203 7.534085 AATCGATGATCTAAAACTACGCAAA 57.466 32.000 0.00 0.00 0.00 3.68
203 204 7.715265 ATCGATGATCTAAAACTACGCAAAT 57.285 32.000 0.00 0.00 0.00 2.32
204 205 8.812147 ATCGATGATCTAAAACTACGCAAATA 57.188 30.769 0.00 0.00 0.00 1.40
205 206 8.637281 TCGATGATCTAAAACTACGCAAATAA 57.363 30.769 0.00 0.00 0.00 1.40
206 207 8.537223 TCGATGATCTAAAACTACGCAAATAAC 58.463 33.333 0.00 0.00 0.00 1.89
207 208 8.540492 CGATGATCTAAAACTACGCAAATAACT 58.460 33.333 0.00 0.00 0.00 2.24
215 216 8.959734 AAAACTACGCAAATAACTTATTCACC 57.040 30.769 0.00 0.00 0.00 4.02
216 217 7.916914 AACTACGCAAATAACTTATTCACCT 57.083 32.000 0.00 0.00 0.00 4.00
217 218 9.439500 AAACTACGCAAATAACTTATTCACCTA 57.561 29.630 0.00 0.00 0.00 3.08
218 219 8.644318 ACTACGCAAATAACTTATTCACCTAG 57.356 34.615 0.00 0.00 0.00 3.02
219 220 8.472413 ACTACGCAAATAACTTATTCACCTAGA 58.528 33.333 0.00 0.00 0.00 2.43
220 221 7.535489 ACGCAAATAACTTATTCACCTAGAC 57.465 36.000 0.00 0.00 0.00 2.59
221 222 6.255020 ACGCAAATAACTTATTCACCTAGACG 59.745 38.462 0.00 0.00 0.00 4.18
222 223 6.292168 CGCAAATAACTTATTCACCTAGACGG 60.292 42.308 0.00 0.00 39.35 4.79
223 224 6.759827 GCAAATAACTTATTCACCTAGACGGA 59.240 38.462 0.00 0.00 36.31 4.69
224 225 7.042658 GCAAATAACTTATTCACCTAGACGGAG 60.043 40.741 0.00 0.00 36.31 4.63
225 226 6.651975 ATAACTTATTCACCTAGACGGAGG 57.348 41.667 0.00 0.00 42.89 4.30
236 237 5.883503 CCTAGACGGAGGTGATAGTATTC 57.116 47.826 0.00 0.00 33.16 1.75
237 238 5.562635 CCTAGACGGAGGTGATAGTATTCT 58.437 45.833 0.00 0.00 33.16 2.40
241 242 2.488545 CGGAGGTGATAGTATTCTCCCG 59.511 54.545 16.11 8.85 40.50 5.14
266 267 1.800586 CGATTCATCGCCCATAACCTG 59.199 52.381 0.00 0.00 43.84 4.00
279 280 0.535335 TAACCTGCATCAGTCCGACC 59.465 55.000 0.00 0.00 0.00 4.79
317 318 1.974543 CCCCACTGCATGTTTTCCC 59.025 57.895 0.00 0.00 0.00 3.97
337 338 1.728971 CTTTCGAAGCCAGCTACACTG 59.271 52.381 0.00 0.00 46.77 3.66
355 356 1.375268 GCAGAGTGCTCCACTGACC 60.375 63.158 2.12 0.00 45.44 4.02
357 358 1.228583 AGAGTGCTCCACTGACCGA 60.229 57.895 2.12 0.00 45.44 4.69
358 359 1.080434 GAGTGCTCCACTGACCGAC 60.080 63.158 2.12 0.00 45.44 4.79
359 360 1.806461 GAGTGCTCCACTGACCGACA 61.806 60.000 2.12 0.00 45.44 4.35
360 361 1.664965 GTGCTCCACTGACCGACAC 60.665 63.158 0.00 0.00 0.00 3.67
361 362 2.430921 GCTCCACTGACCGACACG 60.431 66.667 0.00 0.00 0.00 4.49
406 410 2.845752 TAATCCACGTGTCAGGCCGC 62.846 60.000 15.65 0.00 0.00 6.53
436 440 3.766691 GACCCTCGCCGCTAACCA 61.767 66.667 0.00 0.00 0.00 3.67
446 450 0.451783 CCGCTAACCAAATCAGGTGC 59.548 55.000 0.00 0.00 42.25 5.01
497 502 3.118920 TCGTCGGCATTCTTAATTCTGGA 60.119 43.478 0.00 0.00 0.00 3.86
577 582 9.095065 ACGAAAGCGAAAGTTTATCTATACATT 57.905 29.630 0.00 0.00 41.64 2.71
658 663 9.901172 AGGAAAGGACGTATACAGAAATAAAAT 57.099 29.630 3.32 0.00 0.00 1.82
705 713 8.893727 GGGAAATAATTGAAAAGAAGAGATCGA 58.106 33.333 0.00 0.00 0.00 3.59
849 868 2.281484 TGCCTCCACTTGCGGTTC 60.281 61.111 0.00 0.00 0.00 3.62
933 953 0.099082 CGCTCGTAGTCCAGTCCTTC 59.901 60.000 0.00 0.00 0.00 3.46
940 960 1.301716 GTCCAGTCCTTCGCAGCAA 60.302 57.895 0.00 0.00 0.00 3.91
941 961 1.004560 TCCAGTCCTTCGCAGCAAG 60.005 57.895 0.00 0.00 0.00 4.01
946 966 1.669115 TCCTTCGCAGCAAGAGCAC 60.669 57.895 6.25 0.00 45.49 4.40
947 967 2.473378 CTTCGCAGCAAGAGCACG 59.527 61.111 0.00 0.00 45.49 5.34
948 968 3.642008 CTTCGCAGCAAGAGCACGC 62.642 63.158 0.00 0.00 45.49 5.34
949 969 4.669842 TCGCAGCAAGAGCACGCT 62.670 61.111 0.00 0.00 45.49 5.07
955 975 3.024782 GCAAGAGCACGCTGAGCAG 62.025 63.158 4.88 0.00 41.58 4.24
1012 1032 4.226846 AGTGATCATCCATGGACTTTGACT 59.773 41.667 18.99 13.62 0.00 3.41
1110 1130 1.627329 CAGTCGATGATGATGGGGGAT 59.373 52.381 0.00 0.00 0.00 3.85
1233 1253 3.736224 CAGGACCTGCAGGCCCAT 61.736 66.667 36.25 21.98 40.62 4.00
1389 1409 2.411904 GAGATGATCTTCCACATCGCC 58.588 52.381 0.00 0.00 44.92 5.54
1753 1773 1.863454 GACGCTTCAGCTACCATGATG 59.137 52.381 0.00 0.00 39.32 3.07
1754 1774 1.482182 ACGCTTCAGCTACCATGATGA 59.518 47.619 0.00 0.00 39.32 2.92
1755 1775 2.103771 ACGCTTCAGCTACCATGATGAT 59.896 45.455 0.00 0.00 39.32 2.45
1942 1962 9.668497 AGGAACCTTCTAGTTACATTTATTGTC 57.332 33.333 0.00 0.00 39.87 3.18
2076 2119 9.638239 TTTTCACCTTATCAATGCAGTATTTTC 57.362 29.630 0.00 0.00 0.00 2.29
2161 2213 3.245052 ACCCATTGTCCTTTCTCTCCTTG 60.245 47.826 0.00 0.00 0.00 3.61
2260 2312 1.859080 GCAATGGCAGTACTACGTAGC 59.141 52.381 22.40 8.83 40.72 3.58
2270 2322 0.747283 ACTACGTAGCACTCCCTCCG 60.747 60.000 22.40 0.00 0.00 4.63
2271 2323 0.747283 CTACGTAGCACTCCCTCCGT 60.747 60.000 10.14 0.00 0.00 4.69
2276 2328 1.134560 GTAGCACTCCCTCCGTGTAAG 59.865 57.143 0.00 0.00 34.91 2.34
2279 2331 1.486211 CACTCCCTCCGTGTAAGGAT 58.514 55.000 0.00 0.00 39.96 3.24
2377 2429 2.277756 GGCTACCTCGCACGTACG 60.278 66.667 15.01 15.01 0.00 3.67
2378 2430 2.482374 GCTACCTCGCACGTACGT 59.518 61.111 16.72 16.72 0.00 3.57
2379 2431 1.705337 GGCTACCTCGCACGTACGTA 61.705 60.000 22.34 4.71 0.00 3.57
2380 2432 0.587489 GCTACCTCGCACGTACGTAC 60.587 60.000 22.34 15.19 0.00 3.67
2429 2481 1.228552 GCACAAGCAGGAAAGGGGA 60.229 57.895 0.00 0.00 41.58 4.81
2431 2483 1.075659 ACAAGCAGGAAAGGGGAGC 59.924 57.895 0.00 0.00 0.00 4.70
2479 2534 4.814294 CGTAGCACTGCCGGGGTC 62.814 72.222 2.18 0.00 0.00 4.46
2641 2707 4.704833 CGGCAGGGGTCAGGTGTG 62.705 72.222 0.00 0.00 0.00 3.82
2643 2709 4.269523 GCAGGGGTCAGGTGTGCA 62.270 66.667 0.00 0.00 34.18 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.743521 ACGGAGGTTTTTAGTTACCACC 58.256 45.455 0.00 0.00 40.52 4.61
1 2 4.635223 AGACGGAGGTTTTTAGTTACCAC 58.365 43.478 0.00 0.00 36.87 4.16
2 3 4.559300 CGAGACGGAGGTTTTTAGTTACCA 60.559 45.833 0.00 0.00 36.87 3.25
3 4 3.922850 CGAGACGGAGGTTTTTAGTTACC 59.077 47.826 0.00 0.00 34.54 2.85
19 20 5.052567 CGTAAATGACTTATTCACCGAGACG 60.053 44.000 0.00 0.00 36.92 4.18
20 21 5.803967 ACGTAAATGACTTATTCACCGAGAC 59.196 40.000 0.00 0.00 36.92 3.36
21 22 5.957798 ACGTAAATGACTTATTCACCGAGA 58.042 37.500 0.00 0.00 36.92 4.04
22 23 6.971184 ACTACGTAAATGACTTATTCACCGAG 59.029 38.462 0.00 0.00 36.92 4.63
23 24 6.855836 ACTACGTAAATGACTTATTCACCGA 58.144 36.000 0.00 0.00 36.92 4.69
24 25 7.487189 AGAACTACGTAAATGACTTATTCACCG 59.513 37.037 0.00 0.00 36.92 4.94
25 26 8.699283 AGAACTACGTAAATGACTTATTCACC 57.301 34.615 0.00 0.00 36.92 4.02
26 27 8.521860 CGAGAACTACGTAAATGACTTATTCAC 58.478 37.037 0.00 0.00 36.92 3.18
27 28 8.453320 TCGAGAACTACGTAAATGACTTATTCA 58.547 33.333 0.00 0.00 39.11 2.57
28 29 8.832487 TCGAGAACTACGTAAATGACTTATTC 57.168 34.615 0.00 0.00 0.00 1.75
29 30 9.798994 AATCGAGAACTACGTAAATGACTTATT 57.201 29.630 0.00 0.00 0.00 1.40
30 31 9.234384 CAATCGAGAACTACGTAAATGACTTAT 57.766 33.333 0.00 0.00 0.00 1.73
31 32 8.453320 TCAATCGAGAACTACGTAAATGACTTA 58.547 33.333 0.00 0.00 0.00 2.24
32 33 7.272948 GTCAATCGAGAACTACGTAAATGACTT 59.727 37.037 0.00 0.00 33.06 3.01
33 34 6.746364 GTCAATCGAGAACTACGTAAATGACT 59.254 38.462 0.00 0.00 33.06 3.41
34 35 6.290437 CGTCAATCGAGAACTACGTAAATGAC 60.290 42.308 0.00 0.00 42.86 3.06
35 36 5.735892 CGTCAATCGAGAACTACGTAAATGA 59.264 40.000 0.00 0.00 42.86 2.57
36 37 5.735892 TCGTCAATCGAGAACTACGTAAATG 59.264 40.000 0.00 0.00 44.01 2.32
37 38 5.872635 TCGTCAATCGAGAACTACGTAAAT 58.127 37.500 0.00 0.00 44.01 1.40
38 39 5.281693 TCGTCAATCGAGAACTACGTAAA 57.718 39.130 0.00 0.00 44.01 2.01
39 40 4.926860 TCGTCAATCGAGAACTACGTAA 57.073 40.909 0.00 0.00 44.01 3.18
169 170 9.401058 AGTTTTAGATCATCGATTTGAGGAATT 57.599 29.630 0.00 0.00 41.37 2.17
170 171 8.970859 AGTTTTAGATCATCGATTTGAGGAAT 57.029 30.769 0.00 0.00 41.37 3.01
171 172 9.314321 GTAGTTTTAGATCATCGATTTGAGGAA 57.686 33.333 0.00 0.00 41.37 3.36
172 173 7.648112 CGTAGTTTTAGATCATCGATTTGAGGA 59.352 37.037 0.00 0.00 42.40 3.71
173 174 7.567771 GCGTAGTTTTAGATCATCGATTTGAGG 60.568 40.741 0.00 0.00 0.00 3.86
174 175 7.043391 TGCGTAGTTTTAGATCATCGATTTGAG 60.043 37.037 0.00 0.00 0.00 3.02
175 176 6.754675 TGCGTAGTTTTAGATCATCGATTTGA 59.245 34.615 0.00 0.00 0.00 2.69
176 177 6.933130 TGCGTAGTTTTAGATCATCGATTTG 58.067 36.000 0.00 0.00 0.00 2.32
177 178 7.534085 TTGCGTAGTTTTAGATCATCGATTT 57.466 32.000 0.00 0.00 0.00 2.17
178 179 7.534085 TTTGCGTAGTTTTAGATCATCGATT 57.466 32.000 0.00 0.00 0.00 3.34
179 180 7.715265 ATTTGCGTAGTTTTAGATCATCGAT 57.285 32.000 0.00 0.00 0.00 3.59
180 181 8.537223 GTTATTTGCGTAGTTTTAGATCATCGA 58.463 33.333 0.00 0.00 0.00 3.59
181 182 8.540492 AGTTATTTGCGTAGTTTTAGATCATCG 58.460 33.333 0.00 0.00 0.00 3.84
190 191 8.789762 AGGTGAATAAGTTATTTGCGTAGTTTT 58.210 29.630 9.47 0.00 0.00 2.43
191 192 8.331730 AGGTGAATAAGTTATTTGCGTAGTTT 57.668 30.769 9.47 0.00 0.00 2.66
192 193 7.916914 AGGTGAATAAGTTATTTGCGTAGTT 57.083 32.000 9.47 0.00 0.00 2.24
193 194 8.472413 TCTAGGTGAATAAGTTATTTGCGTAGT 58.528 33.333 22.32 7.96 31.06 2.73
194 195 8.753175 GTCTAGGTGAATAAGTTATTTGCGTAG 58.247 37.037 20.09 20.09 0.00 3.51
195 196 7.433131 CGTCTAGGTGAATAAGTTATTTGCGTA 59.567 37.037 9.47 9.78 0.00 4.42
196 197 6.255020 CGTCTAGGTGAATAAGTTATTTGCGT 59.745 38.462 9.47 9.26 0.00 5.24
197 198 6.292168 CCGTCTAGGTGAATAAGTTATTTGCG 60.292 42.308 9.47 6.06 34.51 4.85
198 199 6.759827 TCCGTCTAGGTGAATAAGTTATTTGC 59.240 38.462 9.47 5.87 41.99 3.68
199 200 7.438459 CCTCCGTCTAGGTGAATAAGTTATTTG 59.562 40.741 9.47 0.00 41.99 2.32
200 201 7.498443 CCTCCGTCTAGGTGAATAAGTTATTT 58.502 38.462 9.47 0.00 41.99 1.40
201 202 7.052142 CCTCCGTCTAGGTGAATAAGTTATT 57.948 40.000 7.87 7.87 41.99 1.40
202 203 6.651975 CCTCCGTCTAGGTGAATAAGTTAT 57.348 41.667 0.00 0.00 41.99 1.89
214 215 5.562635 AGAATACTATCACCTCCGTCTAGG 58.437 45.833 0.00 0.00 42.82 3.02
215 216 5.644636 GGAGAATACTATCACCTCCGTCTAG 59.355 48.000 0.00 0.00 34.75 2.43
216 217 5.514484 GGGAGAATACTATCACCTCCGTCTA 60.514 48.000 0.00 0.00 43.19 2.59
217 218 4.400120 GGAGAATACTATCACCTCCGTCT 58.600 47.826 0.00 0.00 34.75 4.18
218 219 3.506844 GGGAGAATACTATCACCTCCGTC 59.493 52.174 0.00 0.00 43.19 4.79
219 220 3.498334 GGGAGAATACTATCACCTCCGT 58.502 50.000 0.00 0.00 43.19 4.69
220 221 2.488545 CGGGAGAATACTATCACCTCCG 59.511 54.545 0.00 0.00 43.19 4.63
221 222 2.231721 GCGGGAGAATACTATCACCTCC 59.768 54.545 0.00 0.00 41.92 4.30
222 223 2.095161 CGCGGGAGAATACTATCACCTC 60.095 54.545 0.00 0.00 31.51 3.85
223 224 1.887198 CGCGGGAGAATACTATCACCT 59.113 52.381 0.00 0.00 31.51 4.00
224 225 1.669211 GCGCGGGAGAATACTATCACC 60.669 57.143 8.83 0.00 0.00 4.02
225 226 1.699343 GCGCGGGAGAATACTATCAC 58.301 55.000 8.83 0.00 0.00 3.06
226 227 0.240145 CGCGCGGGAGAATACTATCA 59.760 55.000 24.84 0.00 0.00 2.15
227 228 1.071567 GCGCGCGGGAGAATACTATC 61.072 60.000 33.06 5.61 0.00 2.08
228 229 1.080705 GCGCGCGGGAGAATACTAT 60.081 57.895 33.06 0.00 0.00 2.12
229 230 2.333938 GCGCGCGGGAGAATACTA 59.666 61.111 33.06 0.00 0.00 1.82
230 231 4.925576 CGCGCGCGGGAGAATACT 62.926 66.667 43.28 0.00 35.56 2.12
248 249 1.133823 TGCAGGTTATGGGCGATGAAT 60.134 47.619 0.00 0.00 0.00 2.57
257 258 1.138859 TCGGACTGATGCAGGTTATGG 59.861 52.381 0.00 0.00 35.51 2.74
261 262 1.194781 AGGTCGGACTGATGCAGGTT 61.195 55.000 8.23 0.00 35.51 3.50
266 267 1.142748 CTCCAGGTCGGACTGATGC 59.857 63.158 8.23 0.00 39.64 3.91
300 301 1.341080 AAGGGAAAACATGCAGTGGG 58.659 50.000 0.00 0.00 0.00 4.61
317 318 1.728971 CAGTGTAGCTGGCTTCGAAAG 59.271 52.381 0.00 0.00 41.42 2.62
337 338 1.375268 GGTCAGTGGAGCACTCTGC 60.375 63.158 0.00 0.00 43.43 4.26
355 356 0.042188 CTTTTGCTGTCCACGTGTCG 60.042 55.000 15.65 0.00 0.00 4.35
357 358 1.727467 GCTTTTGCTGTCCACGTGT 59.273 52.632 15.65 0.00 43.35 4.49
358 359 1.369209 CGCTTTTGCTGTCCACGTG 60.369 57.895 9.08 9.08 44.80 4.49
359 360 1.522806 TCGCTTTTGCTGTCCACGT 60.523 52.632 0.00 0.00 44.80 4.49
360 361 1.082756 GTCGCTTTTGCTGTCCACG 60.083 57.895 0.00 0.00 44.80 4.94
361 362 1.282875 GGTCGCTTTTGCTGTCCAC 59.717 57.895 0.00 0.00 44.80 4.02
406 410 1.935327 GAGGGTCGGTCAGTTCTCGG 61.935 65.000 0.00 0.00 0.00 4.63
407 411 1.507174 GAGGGTCGGTCAGTTCTCG 59.493 63.158 0.00 0.00 0.00 4.04
409 413 2.637383 GCGAGGGTCGGTCAGTTCT 61.637 63.158 0.00 0.00 40.84 3.01
433 437 1.247567 CTTTCCGCACCTGATTTGGT 58.752 50.000 0.00 0.00 41.77 3.67
436 440 1.620822 AAGCTTTCCGCACCTGATTT 58.379 45.000 0.00 0.00 42.61 2.17
446 450 1.267383 GCCGTCGAATTAAGCTTTCCG 60.267 52.381 3.20 3.72 0.00 4.30
519 524 4.982916 ACGTCTCTACAAAATGTCTCACAC 59.017 41.667 0.00 0.00 0.00 3.82
678 686 7.852945 CGATCTCTTCTTTTCAATTATTTCCCG 59.147 37.037 0.00 0.00 0.00 5.14
708 716 1.153745 GCGCACACTAGCAGCTAGT 60.154 57.895 26.87 26.87 46.75 2.57
913 933 0.322277 AAGGACTGGACTACGAGCGA 60.322 55.000 0.00 0.00 0.00 4.93
914 934 0.099082 GAAGGACTGGACTACGAGCG 59.901 60.000 0.00 0.00 0.00 5.03
940 960 2.261052 GTCTGCTCAGCGTGCTCT 59.739 61.111 0.00 0.00 0.00 4.09
941 961 3.177920 CGTCTGCTCAGCGTGCTC 61.178 66.667 0.00 0.00 0.00 4.26
946 966 1.799519 GTGAGACGTCTGCTCAGCG 60.800 63.158 25.58 10.50 42.57 5.18
947 967 0.732196 CAGTGAGACGTCTGCTCAGC 60.732 60.000 25.58 7.85 42.57 4.26
948 968 0.877743 TCAGTGAGACGTCTGCTCAG 59.122 55.000 25.58 11.90 42.57 3.35
949 969 0.877743 CTCAGTGAGACGTCTGCTCA 59.122 55.000 25.58 12.64 39.90 4.26
950 970 1.130373 CTCTCAGTGAGACGTCTGCTC 59.870 57.143 25.58 14.61 45.39 4.26
951 971 1.164411 CTCTCAGTGAGACGTCTGCT 58.836 55.000 25.58 17.53 45.39 4.24
952 972 0.455972 GCTCTCAGTGAGACGTCTGC 60.456 60.000 25.58 15.98 45.39 4.26
955 975 1.975837 CTTGCTCTCAGTGAGACGTC 58.024 55.000 19.10 7.70 45.39 4.34
1044 1064 1.430632 CATGGTGTTCATCAGCGCC 59.569 57.895 2.29 0.00 46.24 6.53
1263 1283 3.702048 TACTCCTGGTGCACGCCC 61.702 66.667 11.45 0.00 0.00 6.13
1539 1559 3.329889 TCCATCTTGGTGCCGCCT 61.330 61.111 0.00 0.00 39.03 5.52
1754 1774 9.579932 GGAAGGAAAGGATTATTGAATCACTAT 57.420 33.333 0.51 0.00 42.95 2.12
1755 1775 7.715249 CGGAAGGAAAGGATTATTGAATCACTA 59.285 37.037 0.51 0.00 42.95 2.74
1773 1793 0.601841 GGCGACAGAAACGGAAGGAA 60.602 55.000 0.00 0.00 0.00 3.36
1898 1918 5.803967 GGTTCCTACTACACATCTTTACACG 59.196 44.000 0.00 0.00 0.00 4.49
1940 1960 0.092351 CATGCGGTAACAACGACGAC 59.908 55.000 0.00 0.00 0.00 4.34
1941 1961 1.619526 GCATGCGGTAACAACGACGA 61.620 55.000 0.00 0.00 0.00 4.20
1942 1962 1.225637 GCATGCGGTAACAACGACG 60.226 57.895 0.00 0.00 0.00 5.12
2260 2312 1.486211 ATCCTTACACGGAGGGAGTG 58.514 55.000 0.00 0.00 44.57 3.51
2270 2322 9.883142 ACCTCTACGTAGTATATATCCTTACAC 57.117 37.037 21.53 0.00 44.56 2.90
2276 2328 6.018343 GGCGAACCTCTACGTAGTATATATCC 60.018 46.154 21.53 12.74 44.56 2.59
2279 2331 6.042638 AGGCGAACCTCTACGTAGTATATA 57.957 41.667 21.53 1.65 46.34 0.86
2377 2429 4.874977 GCCGGCGAGCAGAGGTAC 62.875 72.222 12.58 0.00 0.00 3.34
2422 2474 3.994931 ACTTATTACGTGCTCCCCTTT 57.005 42.857 0.00 0.00 0.00 3.11
2429 2481 6.264088 GTCAAGTAGCTACTTATTACGTGCT 58.736 40.000 33.06 9.87 44.19 4.40
2431 2483 5.680229 CGGTCAAGTAGCTACTTATTACGTG 59.320 44.000 33.06 21.92 44.19 4.49
2550 2612 0.039527 CAAAGTTAACCTGCGTGCCC 60.040 55.000 0.88 0.00 0.00 5.36
2583 2649 2.102070 TCGCATGGTTCACCGTTTAT 57.898 45.000 0.00 0.00 39.43 1.40


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

AutoCloner maintained by Alex Coulton.