Multiple sequence alignment - TraesCS5A01G095800

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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 TraesCS5A01G095800 chr5A 100.000 6609 0 0 1 6609 134090233 134083625 0.000000e+00 12205
1 TraesCS5A01G095800 chr5D 96.426 6631 188 21 1 6599 122202710 122196097 0.000000e+00 10887
2 TraesCS5A01G095800 chr5D 93.182 88 5 1 4175 4261 498655370 498655283 1.930000e-25 128
3 TraesCS5A01G095800 chr5B 93.310 2302 111 13 4128 6408 134917900 134915621 0.000000e+00 3358
4 TraesCS5A01G095800 chr5B 93.032 2210 109 18 717 2887 134921430 134919227 0.000000e+00 3186
5 TraesCS5A01G095800 chr5B 94.338 1201 60 6 2886 4083 134919103 134917908 0.000000e+00 1834
6 TraesCS5A01G095800 chr5B 93.981 731 34 3 1 721 134922207 134921477 0.000000e+00 1098
7 TraesCS5A01G095800 chr4B 95.556 90 3 1 4172 4260 656162614 656162703 6.910000e-30 143
8 TraesCS5A01G095800 chr7A 94.318 88 5 0 4174 4261 40538157 40538244 1.160000e-27 135
9 TraesCS5A01G095800 chr4D 94.318 88 4 1 4176 4263 504090711 504090797 4.160000e-27 134
10 TraesCS5A01G095800 chr4D 92.135 89 7 0 4172 4260 497058800 497058712 6.960000e-25 126
11 TraesCS5A01G095800 chr4A 92.308 91 7 0 4174 4264 647209391 647209301 5.380000e-26 130
12 TraesCS5A01G095800 chr2B 93.182 88 6 0 4176 4263 14834409 14834322 5.380000e-26 130


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 TraesCS5A01G095800 chr5A 134083625 134090233 6608 True 12205 12205 100.00000 1 6609 1 chr5A.!!$R1 6608
1 TraesCS5A01G095800 chr5D 122196097 122202710 6613 True 10887 10887 96.42600 1 6599 1 chr5D.!!$R1 6598
2 TraesCS5A01G095800 chr5B 134915621 134922207 6586 True 2369 3358 93.66525 1 6408 4 chr5B.!!$R1 6407

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
183 184 1.428448 TGTACATGACACTGCTTCGC 58.572 50.000 0.00 0.00 31.20 4.70 F
203 204 1.770957 GTGCTTTGCCTGTTAGTTGC 58.229 50.000 0.00 0.00 0.00 4.17 F
474 485 2.309528 TACTGGCTGATAAGTTGGCG 57.690 50.000 0.00 0.00 0.00 5.69 F
1167 1235 3.007614 TCCACCAGAGTAAAACCAGTAGC 59.992 47.826 0.00 0.00 0.00 3.58 F
1224 1292 4.121317 CCAGCTGTTTTCTTGATTGCAAA 58.879 39.130 13.81 0.00 32.73 3.68 F
2619 2712 0.593128 ACATTTGCTTGGCGTGACTC 59.407 50.000 0.00 0.00 0.00 3.36 F
4357 4589 0.454600 TCTGTGTTACGCGAGGATCC 59.545 55.000 15.93 2.48 0.00 3.36 F
4821 5059 2.666190 TGCTCGGAACAGCAGCAC 60.666 61.111 0.00 0.00 44.73 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1728 1799 2.483877 TGATAAAGGCACGCAGAAGTTG 59.516 45.455 0.00 0.0 0.00 3.16 R
2060 2136 5.760253 CAGCGGACCTTCAATATAAGATGTT 59.240 40.000 0.00 0.0 0.00 2.71 R
2331 2423 1.184970 AACGACATGGGGCCTTTTGG 61.185 55.000 0.84 0.0 44.18 3.28 R
2474 2566 2.785477 AGTAATCGAACGAATAACGCCG 59.215 45.455 0.12 0.0 46.94 6.46 R
2646 2747 4.564199 CCAGATCAGTTCAATGGACTCACA 60.564 45.833 0.00 0.0 32.55 3.58 R
4411 4643 0.310854 ACAGGCGCAAGTTTTACAGC 59.689 50.000 10.83 0.0 41.68 4.40 R
5281 5520 0.841289 TGCCATGCAGATCTGGATCA 59.159 50.000 25.22 18.4 39.70 2.92 R
6584 6839 0.181114 TTTGATGATGGAGGAGGGCG 59.819 55.000 0.00 0.0 0.00 6.13 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 6.086502 CGTAATTCGATCTAACTCCGTGATTC 59.913 42.308 0.00 0.00 42.86 2.52
143 144 6.206829 CGACTAGTGGAATGATCATAGGTGTA 59.793 42.308 9.04 0.00 0.00 2.90
144 145 7.094162 CGACTAGTGGAATGATCATAGGTGTAT 60.094 40.741 9.04 0.00 0.00 2.29
183 184 1.428448 TGTACATGACACTGCTTCGC 58.572 50.000 0.00 0.00 31.20 4.70
203 204 1.770957 GTGCTTTGCCTGTTAGTTGC 58.229 50.000 0.00 0.00 0.00 4.17
248 249 6.982141 ACGTTTAAGTGTAGTGTGATCTGAAA 59.018 34.615 0.00 0.00 0.00 2.69
377 378 9.166173 TCAATGTAACATCAGTTCAATTCTAGG 57.834 33.333 0.00 0.00 39.15 3.02
455 466 3.932545 TGCAAATGGAACTTACGCAAT 57.067 38.095 0.00 0.00 0.00 3.56
474 485 2.309528 TACTGGCTGATAAGTTGGCG 57.690 50.000 0.00 0.00 0.00 5.69
527 538 8.077991 ACTATATTCACAATTTTCATGGCGATG 58.922 33.333 1.66 1.66 0.00 3.84
677 688 3.681897 GTGGACATCAGCAACTTCTAGTG 59.318 47.826 0.00 0.00 0.00 2.74
802 869 3.059884 CACATACCGGTGACATATCTGC 58.940 50.000 19.93 0.00 41.32 4.26
870 937 7.136822 TGACCAGGCATATAATCAAACTACT 57.863 36.000 0.00 0.00 0.00 2.57
925 992 3.362870 TGCAACATGATATCACCCACA 57.637 42.857 7.78 0.47 0.00 4.17
1167 1235 3.007614 TCCACCAGAGTAAAACCAGTAGC 59.992 47.826 0.00 0.00 0.00 3.58
1202 1270 8.937634 ATAAAATTCAAGTCATGATGCCTTTC 57.062 30.769 0.00 0.00 38.03 2.62
1224 1292 4.121317 CCAGCTGTTTTCTTGATTGCAAA 58.879 39.130 13.81 0.00 32.73 3.68
1230 1298 7.712205 AGCTGTTTTCTTGATTGCAAAACTATT 59.288 29.630 1.71 0.00 39.64 1.73
1308 1376 4.142687 CCATTTTCACGAATACCTGTGACC 60.143 45.833 0.00 0.00 44.25 4.02
1360 1428 5.923733 ATCTCTGTTTGGAGGTAGTGTAG 57.076 43.478 0.00 0.00 34.39 2.74
1371 1439 5.222192 TGGAGGTAGTGTAGTGACCTTAGAA 60.222 44.000 0.00 0.00 43.78 2.10
1385 1453 6.431234 GTGACCTTAGAAATTTCACCATCTGT 59.569 38.462 19.99 7.50 32.12 3.41
1523 1592 7.945033 AATGCTCATTGTTTGAAAAACGTAT 57.055 28.000 0.00 0.00 32.78 3.06
1606 1677 5.469421 GCAGATGAGGTGATTAATGAGAAGG 59.531 44.000 0.00 0.00 0.00 3.46
1681 1752 4.943705 TGCTTGATGAAGATGGTAAGTTCC 59.056 41.667 0.00 0.00 0.00 3.62
1707 1778 4.639310 CCATTTCTTGAACCAGGAGATCAG 59.361 45.833 0.00 0.00 0.00 2.90
1728 1799 6.678878 TCAGAGACTCACACACTAACATTAC 58.321 40.000 5.02 0.00 0.00 1.89
2060 2136 6.209192 TCATTTTCTGCTTCCAATTTGAGCTA 59.791 34.615 10.39 0.00 37.32 3.32
2238 2314 7.261325 CAGACTAGTCAGTGCATAAACTACAT 58.739 38.462 24.44 0.00 34.21 2.29
2612 2705 3.059166 CCTTGTTACACATTTGCTTGGC 58.941 45.455 0.00 0.00 0.00 4.52
2619 2712 0.593128 ACATTTGCTTGGCGTGACTC 59.407 50.000 0.00 0.00 0.00 3.36
2875 2976 7.424227 TGTTTATTTACTTTGGGTGTCTACG 57.576 36.000 0.00 0.00 0.00 3.51
2880 2981 5.789643 TTACTTTGGGTGTCTACGTTACT 57.210 39.130 0.00 0.00 0.00 2.24
3064 3291 5.163561 TGACTTTGAGTTGACCAATGGAAAC 60.164 40.000 6.16 10.27 0.00 2.78
3196 3423 9.180678 CTTGAAACATTTCACCTTTGTATGTAC 57.819 33.333 6.55 0.00 45.99 2.90
3216 3443 6.884832 TGTACTGCTGTTATTAGTATTGCCT 58.115 36.000 0.09 0.00 30.47 4.75
3295 3522 8.034804 GCCCACTTTTGTTTAGATGTGAAATAT 58.965 33.333 0.00 0.00 0.00 1.28
3359 3586 5.078411 CTACAGAGGTAGCAGATGTGTTT 57.922 43.478 6.87 0.00 40.50 2.83
3464 3691 3.192633 GGTCAGGTTTTAATCGTGCCATT 59.807 43.478 0.00 0.00 0.00 3.16
3682 3913 5.012975 TGGCCTTTGCAGAAATAATTTCCTT 59.987 36.000 3.32 0.00 40.54 3.36
3705 3936 3.746045 TCGACAGCATCCCCTTTATAC 57.254 47.619 0.00 0.00 0.00 1.47
3732 3963 8.074370 GTCCTATAAATTTAAAATCAGTCCGCC 58.926 37.037 1.21 0.00 0.00 6.13
3822 4054 3.375299 GCCAACATGATGTCTGGAGTTAC 59.625 47.826 22.34 7.71 33.40 2.50
3827 4059 1.476891 TGATGTCTGGAGTTACTCGCC 59.523 52.381 6.27 0.00 36.53 5.54
3865 4097 9.606631 GAATGATGTCTAGGAGTGAATTTTACT 57.393 33.333 0.00 0.00 0.00 2.24
4035 4267 2.103941 TGGGGTTTCCAGTTTCAAATGC 59.896 45.455 0.00 0.00 41.46 3.56
4202 4434 6.269194 TCCCTCCGTCCCATAATATAAGATT 58.731 40.000 0.00 0.00 0.00 2.40
4205 4437 7.042335 CCTCCGTCCCATAATATAAGATTGTC 58.958 42.308 0.00 0.00 0.00 3.18
4248 4480 7.447374 TGCAAAACGATCTTATATTATGGGG 57.553 36.000 0.00 0.00 0.00 4.96
4265 4497 1.272872 GGGGCGGAGGGAGTATATGTA 60.273 57.143 0.00 0.00 0.00 2.29
4349 4581 1.732259 CATGAAGGGTCTGTGTTACGC 59.268 52.381 0.00 0.00 0.00 4.42
4357 4589 0.454600 TCTGTGTTACGCGAGGATCC 59.545 55.000 15.93 2.48 0.00 3.36
4411 4643 8.299570 GTCCTATATTATTTCACATTGGCTTGG 58.700 37.037 0.00 0.00 0.00 3.61
4700 4938 6.092670 ACACAGCTATGCAAGTAATACAACTG 59.907 38.462 0.00 0.00 0.00 3.16
4821 5059 2.666190 TGCTCGGAACAGCAGCAC 60.666 61.111 0.00 0.00 44.73 4.40
5105 5344 5.511363 TCCTTCTTCAAAAACCACAGGTTA 58.489 37.500 1.26 0.00 46.20 2.85
5119 5358 8.128816 AAACCACAGGTTAGAGCTGGATTTTAA 61.129 37.037 11.32 0.00 46.20 1.52
5328 5567 9.737844 ATAATTTCAGGCATTTAATTTTGGTGT 57.262 25.926 0.00 0.00 0.00 4.16
5534 5774 2.989422 AACAAATGAGGCGTGCTTAC 57.011 45.000 0.00 0.00 0.00 2.34
5540 5780 3.751479 ATGAGGCGTGCTTACATCATA 57.249 42.857 0.00 0.00 0.00 2.15
5648 5892 7.037658 AGCCCATTGATTGGTATTTACCTTTTT 60.038 33.333 8.19 0.00 46.58 1.94
5697 5941 3.640498 TGGAATTTGGTGCTGAACAATGA 59.360 39.130 0.00 0.00 0.00 2.57
5947 6191 3.388024 TCTGTAGGCTTGTTGACTCTTGT 59.612 43.478 0.00 0.00 34.56 3.16
6077 6321 0.610232 ATGTCCTCCAAACCAGCAGC 60.610 55.000 0.00 0.00 0.00 5.25
6164 6409 6.870769 CCTCATGGCACTTTTATTCAATCTT 58.129 36.000 0.00 0.00 0.00 2.40
6177 6422 5.603170 ATTCAATCTTTGGCAGGGTTATG 57.397 39.130 0.00 0.00 0.00 1.90
6262 6507 5.041191 AGAATCATAACAACCCCTAGCAG 57.959 43.478 0.00 0.00 0.00 4.24
6282 6527 6.633500 GCAGGATAATGTGCTAAACCATAA 57.367 37.500 0.00 0.00 36.71 1.90
6323 6578 6.606796 TGCCTAAATGAAATCCATGAGCTAAA 59.393 34.615 0.00 0.00 35.24 1.85
6324 6579 7.288389 TGCCTAAATGAAATCCATGAGCTAAAT 59.712 33.333 0.00 0.00 35.24 1.40
6384 6639 6.138263 TCCATATTTCAATCTTCCCATTGCT 58.862 36.000 0.00 0.00 34.26 3.91
6385 6640 7.296856 TCCATATTTCAATCTTCCCATTGCTA 58.703 34.615 0.00 0.00 34.26 3.49
6446 6701 4.525487 CCTTGGTACAGCCGACCTTATATA 59.475 45.833 0.00 0.00 42.39 0.86
6447 6702 5.336531 CCTTGGTACAGCCGACCTTATATAG 60.337 48.000 0.00 0.00 42.39 1.31
6459 6714 8.521176 GCCGACCTTATATAGAGTAATTTCAGA 58.479 37.037 0.00 0.00 0.00 3.27
6473 6728 0.391130 TTCAGACCGCGAATTCCAGG 60.391 55.000 8.23 11.16 0.00 4.45
6476 6731 1.079405 GACCGCGAATTCCAGGTGA 60.079 57.895 20.29 0.00 37.07 4.02
6480 6735 1.086696 CGCGAATTCCAGGTGATGTT 58.913 50.000 0.00 0.00 0.00 2.71
6508 6763 0.678048 AAGGATTCTGCAGTTCGGGC 60.678 55.000 14.67 0.55 0.00 6.13
6537 6792 6.150809 TGAGAGTATGATCGAGATTCTGATGG 59.849 42.308 0.00 0.00 0.00 3.51
6584 6839 4.621068 TCCGAAGAATTGCAATGATCAC 57.379 40.909 13.82 5.65 0.00 3.06
6599 6854 0.765903 ATCACGCCCTCCTCCATCAT 60.766 55.000 0.00 0.00 0.00 2.45
6600 6855 1.070445 CACGCCCTCCTCCATCATC 59.930 63.158 0.00 0.00 0.00 2.92
6601 6856 1.383109 ACGCCCTCCTCCATCATCA 60.383 57.895 0.00 0.00 0.00 3.07
6602 6857 0.982852 ACGCCCTCCTCCATCATCAA 60.983 55.000 0.00 0.00 0.00 2.57
6603 6858 0.181114 CGCCCTCCTCCATCATCAAA 59.819 55.000 0.00 0.00 0.00 2.69
6604 6859 1.813092 CGCCCTCCTCCATCATCAAAG 60.813 57.143 0.00 0.00 0.00 2.77
6605 6860 1.492176 GCCCTCCTCCATCATCAAAGA 59.508 52.381 0.00 0.00 0.00 2.52
6606 6861 2.092212 GCCCTCCTCCATCATCAAAGAA 60.092 50.000 0.00 0.00 0.00 2.52
6607 6862 3.625716 GCCCTCCTCCATCATCAAAGAAA 60.626 47.826 0.00 0.00 0.00 2.52
6608 6863 4.205587 CCCTCCTCCATCATCAAAGAAAG 58.794 47.826 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.767505 AGTCAGGGCTTCACTAAAACG 58.232 47.619 0.00 0.00 0.00 3.60
143 144 7.714813 TGTACAATGTGACAATCCGAATATCAT 59.285 33.333 0.00 0.00 0.00 2.45
144 145 7.044798 TGTACAATGTGACAATCCGAATATCA 58.955 34.615 0.00 0.00 0.00 2.15
152 153 5.878332 TGTCATGTACAATGTGACAATCC 57.122 39.130 22.41 2.95 46.45 3.01
183 184 1.925946 GCAACTAACAGGCAAAGCACG 60.926 52.381 0.00 0.00 0.00 5.34
203 204 4.844511 GTTTCAAACAACGATAAGTGCG 57.155 40.909 0.00 0.00 0.00 5.34
248 249 3.288964 CACCATTACGTCCTCTCCTACT 58.711 50.000 0.00 0.00 0.00 2.57
455 466 1.828595 TCGCCAACTTATCAGCCAGTA 59.171 47.619 0.00 0.00 0.00 2.74
474 485 3.983044 AACTCAATACCCTGTCACCTC 57.017 47.619 0.00 0.00 0.00 3.85
515 526 3.461061 CTCTCTAAGCATCGCCATGAAA 58.539 45.455 0.00 0.00 30.57 2.69
640 651 5.477637 TGATGTCCACAATTCAACATGTCAT 59.522 36.000 0.00 0.00 32.70 3.06
677 688 9.914923 CTAGAAACAAACTTAAAAACATTTGGC 57.085 29.630 0.00 0.00 36.55 4.52
802 869 0.378257 CCATGGAGAAAACGGATGCG 59.622 55.000 5.56 4.58 0.00 4.73
870 937 6.402118 GCAATGCGTTCACTAATTCAGAACTA 60.402 38.462 12.72 5.54 39.48 2.24
1202 1270 3.374220 TGCAATCAAGAAAACAGCTGG 57.626 42.857 19.93 0.00 0.00 4.85
1360 1428 6.431234 ACAGATGGTGAAATTTCTAAGGTCAC 59.569 38.462 18.64 7.58 38.28 3.67
1371 1439 5.018809 ACCTTGCATACAGATGGTGAAATT 58.981 37.500 0.00 0.00 33.26 1.82
1606 1677 4.137116 TGTGTAGGATATGTGAAGCACC 57.863 45.455 0.00 0.00 32.73 5.01
1681 1752 4.655963 TCTCCTGGTTCAAGAAATGGAAG 58.344 43.478 0.00 0.00 0.00 3.46
1707 1778 6.924060 AGTTGTAATGTTAGTGTGTGAGTCTC 59.076 38.462 0.00 0.00 0.00 3.36
1728 1799 2.483877 TGATAAAGGCACGCAGAAGTTG 59.516 45.455 0.00 0.00 0.00 3.16
2018 2094 7.397192 CAGAAAATGAAAAAGGGGGAATCTAGA 59.603 37.037 0.00 0.00 0.00 2.43
2060 2136 5.760253 CAGCGGACCTTCAATATAAGATGTT 59.240 40.000 0.00 0.00 0.00 2.71
2238 2314 5.105146 AGCATTGTTTCCAACCAAAACAGTA 60.105 36.000 2.19 0.00 44.75 2.74
2331 2423 1.184970 AACGACATGGGGCCTTTTGG 61.185 55.000 0.84 0.00 44.18 3.28
2474 2566 2.785477 AGTAATCGAACGAATAACGCCG 59.215 45.455 0.12 0.00 46.94 6.46
2646 2747 4.564199 CCAGATCAGTTCAATGGACTCACA 60.564 45.833 0.00 0.00 32.55 3.58
2818 2919 8.614994 AATTGTTTCGCATAAGCTATTAACAC 57.385 30.769 0.00 0.00 39.10 3.32
2868 2969 5.998553 GCATATAGCAGAGTAACGTAGACA 58.001 41.667 0.00 0.00 44.79 3.41
2924 3151 8.533569 AACGGAAATCCATATAACAAGGAATT 57.466 30.769 0.00 0.00 34.62 2.17
3064 3291 8.526681 GCAATAGAATTTAAATGTTTGCTCTCG 58.473 33.333 19.72 7.24 36.27 4.04
3196 3423 5.237344 GTGGAGGCAATACTAATAACAGCAG 59.763 44.000 0.00 0.00 0.00 4.24
3216 3443 6.797852 GCTAATGCAAACCACAAACGTGGA 62.798 45.833 18.15 0.00 46.75 4.02
3295 3522 7.565029 TCTCTAGATAATGGACTTGGATTGACA 59.435 37.037 0.00 0.00 0.00 3.58
3298 3525 9.790344 ATTTCTCTAGATAATGGACTTGGATTG 57.210 33.333 0.00 0.00 0.00 2.67
3350 3577 3.864789 ACCCAAGAGTCAAACACATCT 57.135 42.857 0.00 0.00 0.00 2.90
3359 3586 0.183492 AAGCTGCAACCCAAGAGTCA 59.817 50.000 1.02 0.00 0.00 3.41
3638 3869 4.542735 CCAACCAATTCCGTGTTTAAGAC 58.457 43.478 0.00 0.00 0.00 3.01
3682 3913 4.974645 ATAAAGGGGATGCTGTCGAATA 57.025 40.909 0.00 0.00 0.00 1.75
3705 3936 7.797123 GCGGACTGATTTTAAATTTATAGGACG 59.203 37.037 0.00 4.37 0.00 4.79
3835 4067 5.136068 TCACTCCTAGACATCATTCTCCT 57.864 43.478 0.00 0.00 0.00 3.69
3865 4097 6.377146 GCTTCAACCCCAGAAGAATAACATAA 59.623 38.462 7.08 0.00 44.00 1.90
4035 4267 2.074547 ACAAACCGACATCCGTGTAG 57.925 50.000 0.00 0.00 39.09 2.74
4215 4447 7.796958 ATAAGATCGTTTTGCAAGCTAAAAC 57.203 32.000 11.65 11.65 41.97 2.43
4248 4480 8.693625 AGTATATTTTACATATACTCCCTCCGC 58.306 37.037 5.49 0.00 41.45 5.54
4337 4569 1.546834 GATCCTCGCGTAACACAGAC 58.453 55.000 5.77 0.00 0.00 3.51
4349 4581 1.437986 GTTCCCACTCGGATCCTCG 59.562 63.158 10.75 2.75 41.63 4.63
4411 4643 0.310854 ACAGGCGCAAGTTTTACAGC 59.689 50.000 10.83 0.00 41.68 4.40
4523 4755 6.875972 AACACCATCTCATAAGAACTACCT 57.124 37.500 0.00 0.00 34.49 3.08
4524 4756 8.421784 TCATAACACCATCTCATAAGAACTACC 58.578 37.037 0.00 0.00 34.49 3.18
4700 4938 4.437390 CCCATTATTCTGTGACGAGTTTGC 60.437 45.833 0.00 0.00 0.00 3.68
4838 5076 1.987807 ATCACAAGGAGATGGCCCCG 61.988 60.000 0.00 0.00 0.00 5.73
5144 5383 7.867305 TTACTTATTCGACATGGCCAAATTA 57.133 32.000 10.96 0.00 0.00 1.40
5238 5477 4.882427 GTCTTCCCTAACTAAATGCTTCCC 59.118 45.833 0.00 0.00 0.00 3.97
5281 5520 0.841289 TGCCATGCAGATCTGGATCA 59.159 50.000 25.22 18.40 39.70 2.92
5288 5527 5.694910 CCTGAAATTATTTGCCATGCAGATC 59.305 40.000 0.00 0.00 40.61 2.75
5464 5703 2.054799 ACTGGTACAAGAGCCTTCCAA 58.945 47.619 3.64 0.00 38.70 3.53
5540 5780 9.911788 TTTGCCTAGAGAAGAGAAATCAATAAT 57.088 29.630 0.00 0.00 0.00 1.28
5697 5941 4.023980 TGTGAGACCGATCCAAGATTAGT 58.976 43.478 0.00 0.00 0.00 2.24
5935 6179 5.989777 GGTTAGCTTCTAACAAGAGTCAACA 59.010 40.000 15.86 0.00 0.00 3.33
5947 6191 4.595762 ACGAGTTGTGGTTAGCTTCTAA 57.404 40.909 0.00 0.00 0.00 2.10
6062 6306 2.633509 GCTGCTGCTGGTTTGGAGG 61.634 63.158 8.53 0.00 36.03 4.30
6164 6409 0.981183 ACTCGACATAACCCTGCCAA 59.019 50.000 0.00 0.00 0.00 4.52
6177 6422 4.928601 TGTTATGGCATGTACTACTCGAC 58.071 43.478 10.98 0.00 0.00 4.20
6262 6507 6.884280 AGCTTATGGTTTAGCACATTATCC 57.116 37.500 0.00 0.00 39.85 2.59
6282 6527 1.000396 GCATTGTCCCAGGGAAGCT 60.000 57.895 10.89 0.00 31.38 3.74
6323 6578 7.031226 CAGTTTTGGCATACTGCTTACATAT 57.969 36.000 14.73 0.00 44.28 1.78
6324 6579 6.435430 CAGTTTTGGCATACTGCTTACATA 57.565 37.500 14.73 0.00 44.28 2.29
6431 6686 8.304596 TGAAATTACTCTATATAAGGTCGGCTG 58.695 37.037 0.00 0.00 0.00 4.85
6446 6701 3.587797 TTCGCGGTCTGAAATTACTCT 57.412 42.857 6.13 0.00 0.00 3.24
6447 6702 4.260253 GGAATTCGCGGTCTGAAATTACTC 60.260 45.833 6.13 0.00 0.00 2.59
6459 6714 0.744414 CATCACCTGGAATTCGCGGT 60.744 55.000 6.13 10.53 0.00 5.68
6473 6728 3.334583 TCCTTGGCTCTACAACATCAC 57.665 47.619 0.00 0.00 0.00 3.06
6476 6731 4.521146 CAGAATCCTTGGCTCTACAACAT 58.479 43.478 0.00 0.00 0.00 2.71
6480 6735 1.908619 TGCAGAATCCTTGGCTCTACA 59.091 47.619 0.00 0.00 0.00 2.74
6508 6763 6.359352 CAGAATCTCGATCATACTCTCAAACG 59.641 42.308 0.00 0.00 0.00 3.60
6537 6792 1.032114 AACGAAAGCTATGGCAGGGC 61.032 55.000 3.10 6.39 41.70 5.19
6584 6839 0.181114 TTTGATGATGGAGGAGGGCG 59.819 55.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.