Multiple sequence alignment - TraesCS1B01G342500

Loading Multiple Alignment...

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 TraesCS1B01G342500 chr1B 100.000 2810 0 0 1 2810 570524909 570527718 0.000000e+00 5190
1 TraesCS1B01G342500 chr1B 81.843 1118 86 39 1460 2565 570831730 570832742 0.000000e+00 832
2 TraesCS1B01G342500 chr1B 78.529 680 69 39 1637 2281 570720157 570720794 2.640000e-100 375
3 TraesCS1B01G342500 chr1B 95.139 144 6 1 766 908 570820643 570820786 2.820000e-55 226
4 TraesCS1B01G342500 chr1B 94.406 143 7 1 385 527 570704726 570704867 4.710000e-53 219
5 TraesCS1B01G342500 chr1B 94.030 134 7 1 385 518 570726669 570726801 4.750000e-48 202
6 TraesCS1B01G342500 chr1B 93.600 125 6 1 900 1024 570824786 570824908 4.780000e-43 185
7 TraesCS1B01G342500 chr1A 83.771 2514 215 88 372 2775 517519085 517521515 0.000000e+00 2204
8 TraesCS1B01G342500 chr1D 89.172 1413 104 26 924 2307 421464761 421466153 0.000000e+00 1716
9 TraesCS1B01G342500 chr1D 87.859 1359 100 29 638 1944 421225883 421227228 0.000000e+00 1535
10 TraesCS1B01G342500 chr1D 85.145 828 53 29 134 900 421463946 421464764 0.000000e+00 784
11 TraesCS1B01G342500 chr1D 83.789 549 27 20 1 527 421225263 421225771 5.480000e-127 464
12 TraesCS1B01G342500 chr1D 89.615 260 17 8 1997 2253 421227236 421227488 3.490000e-84 322
13 TraesCS1B01G342500 chr1D 83.908 174 23 4 2312 2483 365844578 365844408 8.060000e-36 161
14 TraesCS1B01G342500 chr4A 76.907 957 161 43 857 1760 613544516 613543567 3.250000e-134 488
15 TraesCS1B01G342500 chr4A 78.684 760 116 30 1039 1760 604940680 604941431 5.480000e-127 464
16 TraesCS1B01G342500 chr4A 82.877 438 62 11 1333 1760 604857067 604857501 5.680000e-102 381
17 TraesCS1B01G342500 chr5B 78.429 751 104 30 1054 1760 710314394 710313658 1.200000e-118 436
18 TraesCS1B01G342500 chr5B 83.498 406 55 9 1364 1760 694203388 694202986 4.420000e-98 368
19 TraesCS1B01G342500 chr5D 77.749 782 118 34 1029 1760 559979058 559978283 2.000000e-116 429
20 TraesCS1B01G342500 chr2A 79.898 393 58 13 2399 2772 772237070 772236680 4.610000e-68 268
21 TraesCS1B01G342500 chr2A 80.156 257 35 13 1032 1283 643231162 643230917 8.000000e-41 178
22 TraesCS1B01G342500 chr2D 84.211 209 24 7 2308 2513 159308719 159308921 7.940000e-46 195
23 TraesCS1B01G342500 chr2D 86.928 153 16 3 2332 2483 142000074 142000223 4.810000e-38 169
24 TraesCS1B01G342500 chr2B 80.078 256 37 11 1032 1283 585757421 585757176 8.000000e-41 178
25 TraesCS1B01G342500 chr4B 84.239 184 23 4 2302 2483 174086872 174087051 1.030000e-39 174
26 TraesCS1B01G342500 chr3A 83.889 180 24 4 2306 2483 684326886 684327062 1.730000e-37 167
27 TraesCS1B01G342500 chr7D 81.667 180 27 4 2304 2482 110794788 110794614 8.110000e-31 145
28 TraesCS1B01G342500 chr6A 79.695 197 31 9 2307 2499 355383802 355383611 1.760000e-27 134
29 TraesCS1B01G342500 chr6D 79.688 192 31 5 2312 2497 263436716 263436905 6.320000e-27 132


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 TraesCS1B01G342500 chr1B 570524909 570527718 2809 False 5190.000000 5190 100.000000 1 2810 1 chr1B.!!$F1 2809
1 TraesCS1B01G342500 chr1B 570831730 570832742 1012 False 832.000000 832 81.843000 1460 2565 1 chr1B.!!$F7 1105
2 TraesCS1B01G342500 chr1B 570720157 570720794 637 False 375.000000 375 78.529000 1637 2281 1 chr1B.!!$F3 644
3 TraesCS1B01G342500 chr1A 517519085 517521515 2430 False 2204.000000 2204 83.771000 372 2775 1 chr1A.!!$F1 2403
4 TraesCS1B01G342500 chr1D 421463946 421466153 2207 False 1250.000000 1716 87.158500 134 2307 2 chr1D.!!$F2 2173
5 TraesCS1B01G342500 chr1D 421225263 421227488 2225 False 773.666667 1535 87.087667 1 2253 3 chr1D.!!$F1 2252
6 TraesCS1B01G342500 chr4A 613543567 613544516 949 True 488.000000 488 76.907000 857 1760 1 chr4A.!!$R1 903
7 TraesCS1B01G342500 chr4A 604940680 604941431 751 False 464.000000 464 78.684000 1039 1760 1 chr4A.!!$F2 721
8 TraesCS1B01G342500 chr5B 710313658 710314394 736 True 436.000000 436 78.429000 1054 1760 1 chr5B.!!$R2 706
9 TraesCS1B01G342500 chr5D 559978283 559979058 775 True 429.000000 429 77.749000 1029 1760 1 chr5D.!!$R1 731

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
210 222 0.17576 ATATTGACTCACGTGCGGCT 59.824 50.0 13.41 0.0 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 2179 0.178975 AATTCTGGAACCGCCCACAA 60.179 50.0 0.0 0.0 34.97 3.33 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
29 30 2.909662 AGAAAGGAGGAGGAAGGAACAG 59.090 50.000 0.00 0.00 0.00 3.16
46 47 1.273886 ACAGGCGAAAGAAGGAGAGAC 59.726 52.381 0.00 0.00 0.00 3.36
56 57 2.685897 AGAAGGAGAGACGGAAGATTCG 59.314 50.000 0.00 0.00 0.00 3.34
57 58 2.131776 AGGAGAGACGGAAGATTCGT 57.868 50.000 0.00 0.00 44.03 3.85
58 59 3.278668 AGGAGAGACGGAAGATTCGTA 57.721 47.619 0.00 0.00 41.22 3.43
59 60 3.822940 AGGAGAGACGGAAGATTCGTAT 58.177 45.455 0.00 0.00 41.22 3.06
60 61 3.566322 AGGAGAGACGGAAGATTCGTATG 59.434 47.826 0.00 0.00 41.22 2.39
61 62 3.304794 GGAGAGACGGAAGATTCGTATGG 60.305 52.174 0.00 0.00 41.22 2.74
62 63 3.552875 AGAGACGGAAGATTCGTATGGA 58.447 45.455 0.00 0.00 41.22 3.41
63 64 3.952323 AGAGACGGAAGATTCGTATGGAA 59.048 43.478 0.00 0.00 41.22 3.53
64 65 4.043037 AGACGGAAGATTCGTATGGAAC 57.957 45.455 0.00 0.00 41.22 3.62
65 66 3.121544 GACGGAAGATTCGTATGGAACC 58.878 50.000 0.00 0.00 41.22 3.62
66 67 2.124903 CGGAAGATTCGTATGGAACCG 58.875 52.381 0.00 0.00 37.50 4.44
67 68 2.480845 GGAAGATTCGTATGGAACCGG 58.519 52.381 0.00 0.00 37.50 5.28
68 69 2.159000 GGAAGATTCGTATGGAACCGGT 60.159 50.000 0.00 0.00 37.50 5.28
69 70 2.596904 AGATTCGTATGGAACCGGTG 57.403 50.000 8.52 0.00 37.50 4.94
141 142 1.485032 GCACGTCCCGCCTAATTACG 61.485 60.000 0.00 0.00 39.37 3.18
149 150 2.691927 CCGCCTAATTACGGGGTTATC 58.308 52.381 6.62 0.00 45.74 1.75
210 222 0.175760 ATATTGACTCACGTGCGGCT 59.824 50.000 13.41 0.00 0.00 5.52
249 264 6.897259 TGCAGTAACATAATTAACCGTCTC 57.103 37.500 0.00 0.00 0.00 3.36
250 265 5.517411 TGCAGTAACATAATTAACCGTCTCG 59.483 40.000 0.00 0.00 0.00 4.04
251 266 5.555818 GCAGTAACATAATTAACCGTCTCGC 60.556 44.000 0.00 0.00 0.00 5.03
252 267 5.747197 CAGTAACATAATTAACCGTCTCGCT 59.253 40.000 0.00 0.00 0.00 4.93
253 268 5.975939 AGTAACATAATTAACCGTCTCGCTC 59.024 40.000 0.00 0.00 0.00 5.03
254 269 3.369385 ACATAATTAACCGTCTCGCTCG 58.631 45.455 0.00 0.00 0.00 5.03
260 275 4.838486 CCGTCTCGCTCGGCTCAC 62.838 72.222 0.00 0.00 41.48 3.51
261 276 4.103103 CGTCTCGCTCGGCTCACA 62.103 66.667 0.00 0.00 0.00 3.58
262 277 2.505118 GTCTCGCTCGGCTCACAC 60.505 66.667 0.00 0.00 0.00 3.82
292 321 0.896940 AATTGCAGCCAGTGGAGTGG 60.897 55.000 15.20 0.00 41.01 4.00
293 322 1.782201 ATTGCAGCCAGTGGAGTGGA 61.782 55.000 15.20 7.78 40.44 4.02
294 323 2.046507 GCAGCCAGTGGAGTGGAG 60.047 66.667 15.20 0.00 40.44 3.86
295 324 2.888447 GCAGCCAGTGGAGTGGAGT 61.888 63.158 15.20 0.00 40.44 3.85
296 325 1.004080 CAGCCAGTGGAGTGGAGTG 60.004 63.158 15.20 0.00 40.44 3.51
297 326 1.460305 AGCCAGTGGAGTGGAGTGT 60.460 57.895 15.20 0.00 40.44 3.55
298 327 0.178932 AGCCAGTGGAGTGGAGTGTA 60.179 55.000 15.20 0.00 40.44 2.90
319 348 7.831193 AGTGTATTATGCTTGGAAACTTCAGAT 59.169 33.333 0.00 0.00 0.00 2.90
320 349 9.109393 GTGTATTATGCTTGGAAACTTCAGATA 57.891 33.333 0.00 0.00 0.00 1.98
329 358 4.133078 GGAAACTTCAGATAGATGCCAGG 58.867 47.826 0.00 0.00 0.00 4.45
355 392 4.693566 ACGAATGGTGGTAATAATATGCCG 59.306 41.667 0.00 0.00 0.00 5.69
520 576 7.973048 ACTCCCACTTGATCATACTTAAGTA 57.027 36.000 17.41 17.41 32.53 2.24
527 583 8.085296 CACTTGATCATACTTAAGTAGGCTAGG 58.915 40.741 19.91 11.98 32.85 3.02
528 584 6.591750 TGATCATACTTAAGTAGGCTAGGC 57.408 41.667 19.91 8.55 32.85 3.93
529 585 6.315714 TGATCATACTTAAGTAGGCTAGGCT 58.684 40.000 23.67 23.67 32.85 4.58
545 629 5.312079 GCTAGGCTATTTTCCATGATCACT 58.688 41.667 0.00 0.00 0.00 3.41
553 637 1.856802 TCCATGATCACTGATTCGCG 58.143 50.000 0.00 0.00 0.00 5.87
582 666 4.514401 GGTGGGGTCTGAAATACTTGTAG 58.486 47.826 0.00 0.00 0.00 2.74
602 686 1.826385 CCCTGAAATTTCGAGCCAGT 58.174 50.000 13.34 0.00 0.00 4.00
604 688 2.162408 CCCTGAAATTTCGAGCCAGTTC 59.838 50.000 13.34 0.00 0.00 3.01
622 706 7.607607 AGCCAGTTCCAATCCAAAATTTAAATC 59.392 33.333 0.10 0.00 0.00 2.17
623 707 7.390162 GCCAGTTCCAATCCAAAATTTAAATCA 59.610 33.333 0.10 0.00 0.00 2.57
745 846 3.008594 TCCGAAATGAAGAACCTTGGCTA 59.991 43.478 0.00 0.00 0.00 3.93
749 850 4.640771 AATGAAGAACCTTGGCTACTGA 57.359 40.909 0.00 0.00 0.00 3.41
806 910 3.521765 ATTTTGTGGAGCCCCGGCA 62.522 57.895 8.74 0.00 44.88 5.69
844 958 1.756538 CAAAGGCACCCAGAAACAGTT 59.243 47.619 0.00 0.00 0.00 3.16
845 959 1.692411 AAGGCACCCAGAAACAGTTC 58.308 50.000 0.00 0.00 0.00 3.01
867 981 1.742268 GAAACCAGGAAGCAGAGCATC 59.258 52.381 0.00 0.00 0.00 3.91
913 1032 0.321671 CCCCTGCTTCGTTCTCTTCA 59.678 55.000 0.00 0.00 0.00 3.02
1419 1673 4.189188 CGGGACTCGACGCGGAAT 62.189 66.667 12.47 0.00 42.43 3.01
1431 1685 2.046314 CGGAATGGCGTCAGGGTT 60.046 61.111 0.00 0.00 0.00 4.11
1792 2063 0.248661 CTACGACTCATGGTGCTCGG 60.249 60.000 0.00 0.00 0.00 4.63
1823 2095 2.873472 CCATCTGATGCAAGAAGAGAGC 59.127 50.000 12.17 0.00 0.00 4.09
1827 2099 1.627329 TGATGCAAGAAGAGAGCTGGT 59.373 47.619 0.00 0.00 0.00 4.00
1843 2122 3.134623 AGCTGGTAACGATGGATTGATCA 59.865 43.478 0.00 0.00 42.51 2.92
1844 2123 3.248602 GCTGGTAACGATGGATTGATCAC 59.751 47.826 0.00 0.00 42.51 3.06
1845 2124 3.804036 TGGTAACGATGGATTGATCACC 58.196 45.455 0.00 0.00 42.51 4.02
1846 2125 3.198853 TGGTAACGATGGATTGATCACCA 59.801 43.478 7.46 7.46 39.26 4.17
1848 2127 4.214119 GGTAACGATGGATTGATCACCATG 59.786 45.833 19.69 14.38 45.41 3.66
1849 2128 3.843893 ACGATGGATTGATCACCATGA 57.156 42.857 19.69 0.00 45.41 3.07
1850 2129 3.470709 ACGATGGATTGATCACCATGAC 58.529 45.455 19.69 7.90 45.41 3.06
1887 2176 1.032014 TTCTTCCCTGTTGCTGTTGC 58.968 50.000 0.00 0.00 40.20 4.17
1890 2179 0.395586 TTCCCTGTTGCTGTTGCTGT 60.396 50.000 0.00 0.00 40.48 4.40
1894 2183 1.552226 CTGTTGCTGTTGCTGTTGTG 58.448 50.000 0.00 0.00 40.48 3.33
1896 2185 0.528249 GTTGCTGTTGCTGTTGTGGG 60.528 55.000 0.00 0.00 40.48 4.61
1897 2186 2.028043 GCTGTTGCTGTTGTGGGC 59.972 61.111 0.00 0.00 36.03 5.36
1929 2234 9.421806 CAGAATTTAGATAGCTTCTGTAGGATG 57.578 37.037 0.00 0.00 39.67 3.51
1943 2249 0.322546 AGGATGGAGAAACGGGTTGC 60.323 55.000 0.00 0.00 0.00 4.17
1974 2280 3.328505 GGCATGTTTGGGTCTGAATTTG 58.671 45.455 0.00 0.00 0.00 2.32
2012 2322 3.123050 GTGAAGTGACAAATGTTTGGGC 58.877 45.455 9.98 2.87 42.34 5.36
2049 2373 7.392953 TCAAAATGACTGCATGGTTGTAGATAA 59.607 33.333 0.00 0.00 37.75 1.75
2088 2412 2.482839 CGAATTTTGTGTGGCTTGGGTT 60.483 45.455 0.00 0.00 0.00 4.11
2171 2514 1.002315 GTTGGCGGGTAAAGTGGACTA 59.998 52.381 0.00 0.00 0.00 2.59
2174 2517 1.761198 GGCGGGTAAAGTGGACTAGAT 59.239 52.381 0.00 0.00 0.00 1.98
2228 2571 4.097892 GTCAAGTCCAAAGTCCAAACATGT 59.902 41.667 0.00 0.00 0.00 3.21
2229 2572 4.338118 TCAAGTCCAAAGTCCAAACATGTC 59.662 41.667 0.00 0.00 0.00 3.06
2263 2608 1.065998 ACGTTGGTGTGTGTTGGTAGT 60.066 47.619 0.00 0.00 0.00 2.73
2273 2618 2.950975 TGTGTTGGTAGTCAGTCACGTA 59.049 45.455 0.00 0.00 36.00 3.57
2292 2637 5.394613 CACGTACGAGTATATGTGTACAAGC 59.605 44.000 24.41 0.00 37.32 4.01
2310 2655 9.938280 TGTACAAGCTAAACACAATACTAAGAT 57.062 29.630 0.00 0.00 0.00 2.40
2338 2683 9.967346 ATCTTCAATAGATGATGCAAATTTGAG 57.033 29.630 22.31 5.05 42.11 3.02
2343 2688 4.945246 AGATGATGCAAATTTGAGGATGC 58.055 39.130 22.31 6.48 39.22 3.91
2349 2694 5.676532 TGCAAATTTGAGGATGCAAAAAG 57.323 34.783 22.31 0.00 45.04 2.27
2352 2697 5.106830 GCAAATTTGAGGATGCAAAAAGGAG 60.107 40.000 22.31 0.00 40.72 3.69
2353 2698 6.225318 CAAATTTGAGGATGCAAAAAGGAGA 58.775 36.000 13.08 0.00 40.72 3.71
2354 2699 6.616237 AATTTGAGGATGCAAAAAGGAGAT 57.384 33.333 0.00 0.00 40.72 2.75
2355 2700 5.395682 TTTGAGGATGCAAAAAGGAGATG 57.604 39.130 0.00 0.00 35.03 2.90
2356 2701 4.038271 TGAGGATGCAAAAAGGAGATGT 57.962 40.909 0.00 0.00 0.00 3.06
2360 2707 6.071952 TGAGGATGCAAAAAGGAGATGTAAAC 60.072 38.462 0.00 0.00 0.00 2.01
2426 2773 1.398390 GTCAACTCCAACCGATGATGC 59.602 52.381 0.00 0.00 0.00 3.91
2479 2869 1.608055 TGGTGCAAAGTGGAGATGTG 58.392 50.000 0.00 0.00 0.00 3.21
2485 2875 2.622942 GCAAAGTGGAGATGTGAAACCA 59.377 45.455 0.00 0.00 34.36 3.67
2529 2919 1.949847 AACTAGTCGGCATGAGCGCT 61.950 55.000 11.27 11.27 43.41 5.92
2531 2921 2.341807 CTAGTCGGCATGAGCGCTGA 62.342 60.000 18.48 6.95 45.00 4.26
2558 2948 1.826054 CGCCGAGAGACAGGAGGAT 60.826 63.158 0.00 0.00 0.00 3.24
2561 2951 0.464735 CCGAGAGACAGGAGGATCGT 60.465 60.000 0.00 0.00 34.37 3.73
2632 3022 2.279784 GAGGAGCTCGAATGGCCG 60.280 66.667 7.83 0.00 0.00 6.13
2657 3047 1.007271 CGGCTATGAATCGAGCGGT 60.007 57.895 0.00 0.00 39.72 5.68
2659 3049 0.946221 GGCTATGAATCGAGCGGTGG 60.946 60.000 0.00 0.00 39.72 4.61
2718 3113 2.463589 ATCAAGTCTGGCGGCGGAAA 62.464 55.000 23.53 8.88 0.00 3.13
2756 3151 1.796151 CATGTGTGCCGCTCGAATT 59.204 52.632 0.00 0.00 0.00 2.17
2757 3152 0.247814 CATGTGTGCCGCTCGAATTC 60.248 55.000 0.00 0.00 0.00 2.17
2793 3188 4.938756 AGGGGGTGTGGGGCTCAA 62.939 66.667 0.00 0.00 0.00 3.02
2794 3189 3.909651 GGGGGTGTGGGGCTCAAA 61.910 66.667 0.00 0.00 0.00 2.69
2795 3190 2.445155 GGGGTGTGGGGCTCAAAT 59.555 61.111 0.00 0.00 0.00 2.32
2796 3191 1.682344 GGGGTGTGGGGCTCAAATC 60.682 63.158 0.00 0.00 0.00 2.17
2797 3192 1.076549 GGGTGTGGGGCTCAAATCA 59.923 57.895 0.00 0.00 0.00 2.57
2798 3193 1.250840 GGGTGTGGGGCTCAAATCAC 61.251 60.000 0.00 0.00 0.00 3.06
2799 3194 1.586154 GGTGTGGGGCTCAAATCACG 61.586 60.000 0.00 0.00 33.25 4.35
2800 3195 1.971167 TGTGGGGCTCAAATCACGC 60.971 57.895 0.00 0.00 33.25 5.34
2801 3196 2.745884 TGGGGCTCAAATCACGCG 60.746 61.111 3.53 3.53 0.00 6.01
2802 3197 3.508840 GGGGCTCAAATCACGCGG 61.509 66.667 12.47 0.00 0.00 6.46
2803 3198 2.746277 GGGCTCAAATCACGCGGT 60.746 61.111 12.47 0.00 0.00 5.68
2804 3199 2.480555 GGCTCAAATCACGCGGTG 59.519 61.111 12.47 6.71 34.45 4.94
2805 3200 2.202349 GCTCAAATCACGCGGTGC 60.202 61.111 12.47 0.00 32.98 5.01
2806 3201 2.965147 GCTCAAATCACGCGGTGCA 61.965 57.895 12.47 0.00 32.98 4.57
2807 3202 1.154413 CTCAAATCACGCGGTGCAC 60.154 57.895 12.47 8.80 32.98 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.219393 CGCCTGTTCCTTCCTCCTC 59.781 63.158 0.00 0.00 0.00 3.71
17 18 1.002087 TCTTTCGCCTGTTCCTTCCTC 59.998 52.381 0.00 0.00 0.00 3.71
29 30 0.458716 CCGTCTCTCCTTCTTTCGCC 60.459 60.000 0.00 0.00 0.00 5.54
46 47 2.124903 CGGTTCCATACGAATCTTCCG 58.875 52.381 0.00 0.00 32.20 4.30
56 57 1.742750 GCTCCTTCACCGGTTCCATAC 60.743 57.143 2.97 0.00 0.00 2.39
57 58 0.539986 GCTCCTTCACCGGTTCCATA 59.460 55.000 2.97 0.00 0.00 2.74
58 59 1.299976 GCTCCTTCACCGGTTCCAT 59.700 57.895 2.97 0.00 0.00 3.41
59 60 2.111999 CTGCTCCTTCACCGGTTCCA 62.112 60.000 2.97 0.00 0.00 3.53
60 61 1.376037 CTGCTCCTTCACCGGTTCC 60.376 63.158 2.97 0.00 0.00 3.62
61 62 2.035442 GCTGCTCCTTCACCGGTTC 61.035 63.158 2.97 0.00 0.00 3.62
62 63 2.032681 GCTGCTCCTTCACCGGTT 59.967 61.111 2.97 0.00 0.00 4.44
63 64 4.379243 CGCTGCTCCTTCACCGGT 62.379 66.667 0.00 0.00 0.00 5.28
65 66 4.749310 AGCGCTGCTCCTTCACCG 62.749 66.667 10.39 0.00 30.62 4.94
66 67 3.123620 CAGCGCTGCTCCTTCACC 61.124 66.667 26.68 0.00 36.40 4.02
88 89 2.434884 ATTGCACCTCGCCAGACG 60.435 61.111 0.00 0.00 45.62 4.18
90 91 2.747460 GCATTGCACCTCGCCAGA 60.747 61.111 3.15 0.00 41.33 3.86
92 93 2.361483 ATGCATTGCACCTCGCCA 60.361 55.556 14.66 0.00 43.04 5.69
93 94 2.410469 GATGCATTGCACCTCGCC 59.590 61.111 14.66 0.00 43.04 5.54
94 95 1.731433 ATGGATGCATTGCACCTCGC 61.731 55.000 14.66 4.01 43.04 5.03
141 142 2.525105 TTCCAAGCAAGGATAACCCC 57.475 50.000 0.00 0.00 37.56 4.95
142 143 5.419542 GAAATTTCCAAGCAAGGATAACCC 58.580 41.667 6.95 0.00 37.56 4.11
180 181 6.161381 ACGTGAGTCAATATTTTAACGTCCT 58.839 36.000 0.00 0.00 44.19 3.85
210 222 3.407698 ACTGCAAATGGTACGTGATGAA 58.592 40.909 0.00 0.00 0.00 2.57
251 266 3.596066 CTGGGTGGTGTGAGCCGAG 62.596 68.421 0.00 0.00 36.18 4.63
252 267 3.625897 CTGGGTGGTGTGAGCCGA 61.626 66.667 0.00 0.00 36.18 5.54
254 269 2.124507 TTAGCTGGGTGGTGTGAGCC 62.125 60.000 0.00 0.00 31.43 4.70
255 270 0.250727 TTTAGCTGGGTGGTGTGAGC 60.251 55.000 0.00 0.00 0.00 4.26
256 271 2.489329 CAATTTAGCTGGGTGGTGTGAG 59.511 50.000 0.00 0.00 0.00 3.51
257 272 2.513753 CAATTTAGCTGGGTGGTGTGA 58.486 47.619 0.00 0.00 0.00 3.58
258 273 1.067635 GCAATTTAGCTGGGTGGTGTG 60.068 52.381 0.00 0.00 0.00 3.82
259 274 1.256812 GCAATTTAGCTGGGTGGTGT 58.743 50.000 0.00 0.00 0.00 4.16
260 275 1.203052 CTGCAATTTAGCTGGGTGGTG 59.797 52.381 0.00 0.00 34.99 4.17
261 276 1.549203 CTGCAATTTAGCTGGGTGGT 58.451 50.000 0.00 0.00 34.99 4.16
262 277 0.174162 GCTGCAATTTAGCTGGGTGG 59.826 55.000 0.00 0.00 38.14 4.61
292 321 7.334421 TCTGAAGTTTCCAAGCATAATACACTC 59.666 37.037 0.00 0.00 0.00 3.51
293 322 7.168219 TCTGAAGTTTCCAAGCATAATACACT 58.832 34.615 0.00 0.00 0.00 3.55
294 323 7.377766 TCTGAAGTTTCCAAGCATAATACAC 57.622 36.000 0.00 0.00 0.00 2.90
295 324 9.330063 CTATCTGAAGTTTCCAAGCATAATACA 57.670 33.333 0.00 0.00 0.00 2.29
296 325 9.547753 TCTATCTGAAGTTTCCAAGCATAATAC 57.452 33.333 0.00 0.00 0.00 1.89
298 327 9.064706 CATCTATCTGAAGTTTCCAAGCATAAT 57.935 33.333 0.00 0.00 0.00 1.28
319 348 0.249447 CATTCGTCGCCTGGCATCTA 60.249 55.000 20.29 0.00 0.00 1.98
320 349 1.522355 CATTCGTCGCCTGGCATCT 60.522 57.895 20.29 0.00 0.00 2.90
329 358 5.670341 GCATATTATTACCACCATTCGTCGC 60.670 44.000 0.00 0.00 0.00 5.19
355 392 0.837272 TTAGGCAGTGGCTACCATCC 59.163 55.000 24.86 0.00 40.35 3.51
520 576 4.352001 TGATCATGGAAAATAGCCTAGCCT 59.648 41.667 0.00 0.00 0.00 4.58
527 583 6.369005 CGAATCAGTGATCATGGAAAATAGC 58.631 40.000 5.98 0.00 0.00 2.97
528 584 6.369005 GCGAATCAGTGATCATGGAAAATAG 58.631 40.000 5.98 0.00 0.00 1.73
529 585 5.050159 CGCGAATCAGTGATCATGGAAAATA 60.050 40.000 5.98 0.00 0.00 1.40
545 629 1.282817 CCACCGAAATACGCGAATCA 58.717 50.000 15.93 0.00 41.07 2.57
553 637 2.773993 TTCAGACCCCACCGAAATAC 57.226 50.000 0.00 0.00 0.00 1.89
582 666 0.453390 CTGGCTCGAAATTTCAGGGC 59.547 55.000 19.91 19.91 0.00 5.19
655 756 8.655970 AGAAATTCTTTCGGTTTTTGAGTTTTG 58.344 29.630 0.00 0.00 44.29 2.44
683 784 3.339695 GTCGCCGAAATACGTGAAATTC 58.660 45.455 0.00 0.00 40.78 2.17
745 846 7.392673 ACAGCAATTGTGAAAGAAGATATCAGT 59.607 33.333 7.40 0.00 38.99 3.41
749 850 8.671921 CACTACAGCAATTGTGAAAGAAGATAT 58.328 33.333 7.40 0.00 41.10 1.63
806 910 1.703411 TGCCTACTTGCCTTGCTTTT 58.297 45.000 0.00 0.00 0.00 2.27
844 958 0.321671 CTCTGCTTCCTGGTTTCCGA 59.678 55.000 0.00 0.00 0.00 4.55
845 959 1.301677 GCTCTGCTTCCTGGTTTCCG 61.302 60.000 0.00 0.00 0.00 4.30
867 981 9.892130 AGAGTAGAACTGGGATTATGTAAAAAG 57.108 33.333 0.00 0.00 0.00 2.27
874 988 4.284746 GGGGAGAGTAGAACTGGGATTATG 59.715 50.000 0.00 0.00 0.00 1.90
884 998 1.135333 CGAAGCAGGGGAGAGTAGAAC 59.865 57.143 0.00 0.00 0.00 3.01
891 1005 0.251832 AGAGAACGAAGCAGGGGAGA 60.252 55.000 0.00 0.00 0.00 3.71
913 1032 1.227853 GGCGACAGGAGTTGGTTGT 60.228 57.895 0.00 0.00 0.00 3.32
1100 1255 4.969196 CTGCTCGGTGGTGCGTGT 62.969 66.667 0.00 0.00 35.46 4.49
1186 1371 4.962836 GTGGTGGTGGCAGCTGCT 62.963 66.667 35.82 0.00 41.70 4.24
1188 1373 4.584518 TGGTGGTGGTGGCAGCTG 62.585 66.667 18.53 10.11 0.00 4.24
1189 1374 4.586235 GTGGTGGTGGTGGCAGCT 62.586 66.667 18.53 0.00 0.00 4.24
1419 1673 3.884774 AGCCAAACCCTGACGCCA 61.885 61.111 0.00 0.00 0.00 5.69
1431 1685 4.243008 TCGAACGTGCCCAGCCAA 62.243 61.111 0.00 0.00 0.00 4.52
1775 2046 2.573869 CCGAGCACCATGAGTCGT 59.426 61.111 0.00 0.00 0.00 4.34
1779 2050 3.411114 ATGGCCCGAGCACCATGAG 62.411 63.158 0.00 0.00 45.03 2.90
1823 2095 3.809832 GGTGATCAATCCATCGTTACCAG 59.190 47.826 0.00 0.00 0.00 4.00
1827 2099 5.056480 GTCATGGTGATCAATCCATCGTTA 58.944 41.667 13.57 0.29 41.79 3.18
1864 2143 2.856222 ACAGCAACAGGGAAGAAAGAG 58.144 47.619 0.00 0.00 0.00 2.85
1887 2176 2.203280 TGGAACCGCCCACAACAG 60.203 61.111 0.00 0.00 34.97 3.16
1890 2179 0.178975 AATTCTGGAACCGCCCACAA 60.179 50.000 0.00 0.00 34.97 3.33
1894 2183 2.413310 TCTAAATTCTGGAACCGCCC 57.587 50.000 0.00 0.00 34.97 6.13
1896 2185 4.381411 AGCTATCTAAATTCTGGAACCGC 58.619 43.478 0.00 0.00 0.00 5.68
1897 2186 6.201806 CAGAAGCTATCTAAATTCTGGAACCG 59.798 42.308 6.00 0.00 43.09 4.44
1929 2234 1.005394 TCTCGCAACCCGTTTCTCC 60.005 57.895 0.00 0.00 38.35 3.71
1943 2249 1.736645 AAACATGCCGTCGGTCTCG 60.737 57.895 13.94 1.91 37.82 4.04
1974 2280 3.179443 TCACATCTTTCACGGCTATCC 57.821 47.619 0.00 0.00 0.00 2.59
2032 2356 7.361542 GCCTATGAATTATCTACAACCATGCAG 60.362 40.741 0.00 0.00 0.00 4.41
2049 2373 1.134521 TCGAACTTGGCGCCTATGAAT 60.135 47.619 29.70 8.95 0.00 2.57
2123 2462 6.887626 AAAACTAACAACAATCCCGTGTAT 57.112 33.333 0.00 0.00 0.00 2.29
2171 2514 5.067413 CAGGACATGCATGCTTCTTTTATCT 59.933 40.000 26.53 6.20 0.00 1.98
2174 2517 4.334552 TCAGGACATGCATGCTTCTTTTA 58.665 39.130 26.53 6.72 0.00 1.52
2228 2571 0.463654 AACGTCAACTTGCAGGCAGA 60.464 50.000 0.00 0.00 0.00 4.26
2229 2572 0.317269 CAACGTCAACTTGCAGGCAG 60.317 55.000 0.00 0.00 0.00 4.85
2263 2608 4.872124 ACACATATACTCGTACGTGACTGA 59.128 41.667 22.86 6.43 0.00 3.41
2273 2618 7.487189 GTGTTTAGCTTGTACACATATACTCGT 59.513 37.037 16.27 0.00 41.30 4.18
2316 2661 7.885009 TCCTCAAATTTGCATCATCTATTGA 57.115 32.000 13.54 0.00 39.12 2.57
2322 2667 4.689071 TGCATCCTCAAATTTGCATCATC 58.311 39.130 13.54 2.46 39.98 2.92
2338 2683 6.024552 TGTTTACATCTCCTTTTTGCATCC 57.975 37.500 0.00 0.00 0.00 3.51
2403 2750 2.248248 TCATCGGTTGGAGTTGACTCT 58.752 47.619 10.68 0.00 42.48 3.24
2405 2752 2.936993 GCATCATCGGTTGGAGTTGACT 60.937 50.000 0.00 0.00 0.00 3.41
2406 2753 1.398390 GCATCATCGGTTGGAGTTGAC 59.602 52.381 0.00 0.00 0.00 3.18
2407 2754 1.003003 TGCATCATCGGTTGGAGTTGA 59.997 47.619 0.00 0.00 0.00 3.18
2416 2763 4.259356 CATCTCCAATATGCATCATCGGT 58.741 43.478 0.19 0.00 0.00 4.69
2418 2765 6.973229 TTACATCTCCAATATGCATCATCG 57.027 37.500 0.19 0.00 0.00 3.84
2426 2773 8.218338 AGTTGCTCTTTTACATCTCCAATATG 57.782 34.615 0.00 0.00 0.00 1.78
2462 2852 3.550842 GGTTTCACATCTCCACTTTGCAC 60.551 47.826 0.00 0.00 0.00 4.57
2502 2892 2.717580 TGCCGACTAGTTGTACACAG 57.282 50.000 9.32 0.00 0.00 3.66
2551 2941 1.753463 GTCCACCGACGATCCTCCT 60.753 63.158 0.00 0.00 0.00 3.69
2600 2990 4.812476 CTCCCGCCGCATTCGACA 62.812 66.667 0.00 0.00 38.10 4.35
2616 3006 3.854669 CCGGCCATTCGAGCTCCT 61.855 66.667 8.47 0.00 0.00 3.69
2632 3022 2.591715 ATTCATAGCCGCACCGCC 60.592 61.111 0.00 0.00 0.00 6.13
2637 3027 1.661509 CGCTCGATTCATAGCCGCA 60.662 57.895 0.00 0.00 35.22 5.69
2638 3028 2.375766 CCGCTCGATTCATAGCCGC 61.376 63.158 0.00 0.00 35.22 6.53
2643 3033 2.547855 CCAATCCACCGCTCGATTCATA 60.548 50.000 0.00 0.00 0.00 2.15
2644 3034 1.586422 CAATCCACCGCTCGATTCAT 58.414 50.000 0.00 0.00 0.00 2.57
2645 3035 0.461870 CCAATCCACCGCTCGATTCA 60.462 55.000 0.00 0.00 0.00 2.57
2683 3078 0.108186 TGATCTTCTCGTGCCGCAAT 60.108 50.000 0.00 0.00 0.00 3.56
2684 3079 0.320334 TTGATCTTCTCGTGCCGCAA 60.320 50.000 0.00 0.00 0.00 4.85
2691 3086 1.135257 CGCCAGACTTGATCTTCTCGT 60.135 52.381 0.00 0.00 34.41 4.18
2699 3094 2.463589 TTTCCGCCGCCAGACTTGAT 62.464 55.000 0.00 0.00 0.00 2.57
2702 3097 1.966451 CTTTTCCGCCGCCAGACTT 60.966 57.895 0.00 0.00 0.00 3.01
2703 3098 2.358737 CTTTTCCGCCGCCAGACT 60.359 61.111 0.00 0.00 0.00 3.24
2738 3133 0.247814 GAATTCGAGCGGCACACATG 60.248 55.000 1.45 0.00 0.00 3.21
2740 3135 2.379634 CGAATTCGAGCGGCACACA 61.380 57.895 23.29 0.00 43.02 3.72
2776 3171 4.938756 TTGAGCCCCACACCCCCT 62.939 66.667 0.00 0.00 0.00 4.79
2780 3175 1.586154 CGTGATTTGAGCCCCACACC 61.586 60.000 0.00 0.00 0.00 4.16
2781 3176 1.875963 CGTGATTTGAGCCCCACAC 59.124 57.895 0.00 0.00 0.00 3.82
2782 3177 1.971167 GCGTGATTTGAGCCCCACA 60.971 57.895 0.00 0.00 0.00 4.17
2783 3178 2.877691 GCGTGATTTGAGCCCCAC 59.122 61.111 0.00 0.00 0.00 4.61
2784 3179 2.745884 CGCGTGATTTGAGCCCCA 60.746 61.111 0.00 0.00 0.00 4.96
2785 3180 3.508840 CCGCGTGATTTGAGCCCC 61.509 66.667 4.92 0.00 0.00 5.80
2786 3181 2.746277 ACCGCGTGATTTGAGCCC 60.746 61.111 4.92 0.00 0.00 5.19
2787 3182 2.480555 CACCGCGTGATTTGAGCC 59.519 61.111 4.92 0.00 35.23 4.70
2788 3183 2.202349 GCACCGCGTGATTTGAGC 60.202 61.111 4.92 0.00 35.23 4.26
2789 3184 1.154413 GTGCACCGCGTGATTTGAG 60.154 57.895 5.22 0.00 35.23 3.02
2790 3185 2.942879 GTGCACCGCGTGATTTGA 59.057 55.556 5.22 0.00 35.23 2.69
2791 3186 2.499520 CGTGCACCGCGTGATTTG 60.500 61.111 12.15 0.00 35.23 2.32


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

AutoCloner maintained by Alex Coulton.