Multiple sequence alignment - TraesCS5B01G401400

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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 TraesCS5B01G401400 chr5B 100.000 6169 0 0 1 6169 578363766 578369934 0.000000e+00 11393.0
1 TraesCS5B01G401400 chr5D 96.395 6185 134 32 1 6169 471043339 471049450 0.000000e+00 10104.0
2 TraesCS5B01G401400 chr5D 74.969 795 156 32 3165 3938 470770299 470771071 5.960000e-85 326.0
3 TraesCS5B01G401400 chr5A 96.185 6029 147 25 1 6008 591314623 591320589 0.000000e+00 9782.0
4 TraesCS5B01G401400 chr5A 73.899 1272 253 54 3165 4412 591154628 591155844 2.640000e-118 436.0
5 TraesCS5B01G401400 chr5A 98.077 52 1 0 6006 6057 591321256 591321307 2.370000e-14 91.6
6 TraesCS5B01G401400 chrUn 96.243 346 7 2 5312 5656 480431261 480431601 4.180000e-156 562.0


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 TraesCS5B01G401400 chr5B 578363766 578369934 6168 False 11393.0 11393 100.000 1 6169 1 chr5B.!!$F1 6168
1 TraesCS5B01G401400 chr5D 471043339 471049450 6111 False 10104.0 10104 96.395 1 6169 1 chr5D.!!$F2 6168
2 TraesCS5B01G401400 chr5D 470770299 470771071 772 False 326.0 326 74.969 3165 3938 1 chr5D.!!$F1 773
3 TraesCS5B01G401400 chr5A 591314623 591321307 6684 False 4936.8 9782 97.131 1 6057 2 chr5A.!!$F2 6056
4 TraesCS5B01G401400 chr5A 591154628 591155844 1216 False 436.0 436 73.899 3165 4412 1 chr5A.!!$F1 1247

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
60 61 1.654105 GCTACCATTGTCAGTTCGTCG 59.346 52.381 0.00 0.00 0.00 5.12 F
1214 1217 0.534412 TGTTTGGGTGTTGCACTTGG 59.466 50.000 0.00 0.00 34.40 3.61 F
2330 2333 0.107017 AACCTCCGAATGATGCCAGG 60.107 55.000 0.00 0.00 0.00 4.45 F
2336 2339 0.392863 CGAATGATGCCAGGGTCACA 60.393 55.000 0.00 0.00 0.00 3.58 F
2355 2358 0.610232 ATTCAGTGGTGCAGAAGGCC 60.610 55.000 0.00 0.00 43.89 5.19 F
2497 2500 0.847373 TCCGTATCCAGAGCTCTCCT 59.153 55.000 14.96 3.77 0.00 3.69 F
2521 2524 1.140312 ACCTTGGAGAACTCTTGGCA 58.860 50.000 1.86 0.00 0.00 4.92 F
4229 4241 1.268743 GCTGCTGAAGGTGTTGTCAAC 60.269 52.381 8.86 8.86 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1441 1444 1.478631 AGCTTTTGGAATAGCAGCCC 58.521 50.000 4.89 0.00 39.85 5.19 R
2335 2338 0.524862 GCCTTCTGCACCACTGAATG 59.475 55.000 0.00 0.00 40.77 2.67 R
4241 4253 0.872388 ACAAATTTCTGACGACGGCC 59.128 50.000 0.00 0.00 0.00 6.13 R
4292 4304 5.048434 TGACACTACTGATGACTCTGAGTTG 60.048 44.000 12.27 5.37 0.00 3.16 R
4473 4485 2.811431 CTGTAGCGGATGGAAAACACAA 59.189 45.455 0.00 0.00 0.00 3.33 R
4577 4589 3.304257 CCATGTTTGATATTGCGAGCTCC 60.304 47.826 8.47 1.40 0.00 4.70 R
4814 4826 2.433318 AAGTCTCGCTTCTGCCGC 60.433 61.111 0.00 0.00 35.36 6.53 R
5206 5224 0.178767 CCACCGCAATCTCTGATGGA 59.821 55.000 0.00 0.00 0.00 3.41 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
60 61 1.654105 GCTACCATTGTCAGTTCGTCG 59.346 52.381 0.00 0.00 0.00 5.12
312 313 6.597562 TGGGACTCTTTGTGTTATAACTTGT 58.402 36.000 16.33 5.16 0.00 3.16
347 350 9.899661 ATTTATTTTGGGCCTTTTATTAGGTTC 57.100 29.630 4.53 0.00 37.63 3.62
405 408 3.311322 GTGTGACGTTTCAGTTGGATTGA 59.689 43.478 0.00 0.00 30.10 2.57
409 412 2.940410 ACGTTTCAGTTGGATTGAACGT 59.060 40.909 6.29 6.29 37.41 3.99
430 433 4.585364 GTGAGAAGTCAATGATTGCATCG 58.415 43.478 0.00 0.00 33.27 3.84
432 435 3.873361 GAGAAGTCAATGATTGCATCGGA 59.127 43.478 0.00 0.00 32.35 4.55
566 569 6.757478 CGTCTTCTCTCCTTTAGTTATTTCCC 59.243 42.308 0.00 0.00 0.00 3.97
596 599 7.860373 CGATGAATTTAGAAACAAACAGGTGAA 59.140 33.333 0.00 0.00 0.00 3.18
619 622 7.666804 TGAAGTGCATATTCTATGCCATTATGT 59.333 33.333 14.67 0.00 43.94 2.29
693 696 7.377766 TGCTGTCTAGGTTTGTTTGATTATC 57.622 36.000 0.00 0.00 0.00 1.75
764 767 5.832060 AGCATCTTATTTCCCAGATCCTTTG 59.168 40.000 0.00 0.00 0.00 2.77
806 809 9.736023 GTATTTATTGGCAGGTTATTTCTCTTG 57.264 33.333 0.00 0.00 0.00 3.02
812 815 5.003804 GGCAGGTTATTTCTCTTGAAGTGA 58.996 41.667 0.00 0.00 33.28 3.41
813 816 5.649831 GGCAGGTTATTTCTCTTGAAGTGAT 59.350 40.000 0.00 0.00 33.28 3.06
825 828 8.082672 TCTCTTGAAGTGATATTCAGATTGGA 57.917 34.615 0.00 0.00 40.16 3.53
900 903 6.454186 GCATTAAAGATTGGAATTTCACACGC 60.454 38.462 0.00 0.00 0.00 5.34
1042 1045 7.855784 ATTTATCAATGGAACCCCTAAATCC 57.144 36.000 0.00 0.00 0.00 3.01
1167 1170 2.027192 TGCCGAGGATCTTAAAAGCACT 60.027 45.455 0.00 0.00 0.00 4.40
1168 1171 3.196901 TGCCGAGGATCTTAAAAGCACTA 59.803 43.478 0.00 0.00 0.00 2.74
1169 1172 4.141711 TGCCGAGGATCTTAAAAGCACTAT 60.142 41.667 0.00 0.00 0.00 2.12
1170 1173 4.449405 GCCGAGGATCTTAAAAGCACTATC 59.551 45.833 0.00 0.00 0.00 2.08
1171 1174 5.601662 CCGAGGATCTTAAAAGCACTATCA 58.398 41.667 0.00 0.00 0.00 2.15
1172 1175 6.049149 CCGAGGATCTTAAAAGCACTATCAA 58.951 40.000 0.00 0.00 0.00 2.57
1214 1217 0.534412 TGTTTGGGTGTTGCACTTGG 59.466 50.000 0.00 0.00 34.40 3.61
1217 1220 1.561643 TTGGGTGTTGCACTTGGAAA 58.438 45.000 0.00 0.00 34.40 3.13
1254 1257 2.427453 AGTATGCTGTACGCTACTTGCT 59.573 45.455 10.27 1.51 40.11 3.91
1312 1315 6.512342 TCACATTATGATTGTCAACATGCA 57.488 33.333 0.00 0.00 29.99 3.96
1313 1316 6.921914 TCACATTATGATTGTCAACATGCAA 58.078 32.000 0.00 0.00 29.99 4.08
1314 1317 7.376615 TCACATTATGATTGTCAACATGCAAA 58.623 30.769 0.00 0.00 29.99 3.68
1315 1318 8.035984 TCACATTATGATTGTCAACATGCAAAT 58.964 29.630 0.00 0.00 29.99 2.32
1316 1319 8.113675 CACATTATGATTGTCAACATGCAAATG 58.886 33.333 0.00 13.54 0.00 2.32
1362 1365 7.987458 TCTAGTTGACTTTGATGTTTCTCTTGT 59.013 33.333 0.00 0.00 0.00 3.16
1637 1640 4.399618 GCGCTCTCCATACTATGAGGATAA 59.600 45.833 0.00 0.00 0.00 1.75
1638 1641 5.449862 GCGCTCTCCATACTATGAGGATAAG 60.450 48.000 0.00 0.00 0.00 1.73
1650 1653 7.456725 ACTATGAGGATAAGACATCAAATGGG 58.543 38.462 0.00 0.00 34.41 4.00
1674 1677 3.436704 AGTTGTACAATGGCTTCATGACG 59.563 43.478 12.26 0.00 0.00 4.35
1686 1689 0.390340 TCATGACGAAGCAGGCAGAC 60.390 55.000 0.00 0.00 29.56 3.51
1804 1807 6.542852 ACGTAAACATCTTAATGCATGACAC 58.457 36.000 0.00 0.00 36.26 3.67
1810 1813 4.833469 TCTTAATGCATGACACGTTACG 57.167 40.909 0.00 2.19 0.00 3.18
1852 1855 3.689649 ACACAGCCGATATTTTCACTTCC 59.310 43.478 0.00 0.00 0.00 3.46
1976 1979 8.746922 TGATGAAGCATTATGAAAACAAAGAC 57.253 30.769 0.00 0.00 0.00 3.01
2035 2038 5.049405 AGACAAATTCGTCATCACAAGTTCC 60.049 40.000 0.00 0.00 38.43 3.62
2183 2186 2.511218 CTCTCCAAATGGATTCCCCTCA 59.489 50.000 1.93 0.00 44.46 3.86
2325 2328 4.616181 GGTACAAAACCTCCGAATGATG 57.384 45.455 0.00 0.00 45.75 3.07
2326 2329 3.181500 GGTACAAAACCTCCGAATGATGC 60.181 47.826 0.00 0.00 45.75 3.91
2327 2330 1.818674 ACAAAACCTCCGAATGATGCC 59.181 47.619 0.00 0.00 0.00 4.40
2328 2331 1.818060 CAAAACCTCCGAATGATGCCA 59.182 47.619 0.00 0.00 0.00 4.92
2329 2332 1.755179 AAACCTCCGAATGATGCCAG 58.245 50.000 0.00 0.00 0.00 4.85
2330 2333 0.107017 AACCTCCGAATGATGCCAGG 60.107 55.000 0.00 0.00 0.00 4.45
2331 2334 1.228063 CCTCCGAATGATGCCAGGG 60.228 63.158 0.00 0.00 0.00 4.45
2332 2335 1.528824 CTCCGAATGATGCCAGGGT 59.471 57.895 0.00 0.00 0.00 4.34
2333 2336 0.533755 CTCCGAATGATGCCAGGGTC 60.534 60.000 0.00 0.00 0.00 4.46
2334 2337 1.224315 CCGAATGATGCCAGGGTCA 59.776 57.895 0.00 0.00 0.00 4.02
2335 2338 1.097547 CCGAATGATGCCAGGGTCAC 61.098 60.000 0.00 0.00 0.00 3.67
2336 2339 0.392863 CGAATGATGCCAGGGTCACA 60.393 55.000 0.00 0.00 0.00 3.58
2337 2340 1.748244 CGAATGATGCCAGGGTCACAT 60.748 52.381 0.00 0.00 0.00 3.21
2338 2341 2.381911 GAATGATGCCAGGGTCACATT 58.618 47.619 0.00 0.00 0.00 2.71
2339 2342 2.062971 ATGATGCCAGGGTCACATTC 57.937 50.000 0.00 0.00 0.00 2.67
2340 2343 0.697658 TGATGCCAGGGTCACATTCA 59.302 50.000 0.00 0.00 0.00 2.57
2341 2344 1.340308 TGATGCCAGGGTCACATTCAG 60.340 52.381 0.00 0.00 0.00 3.02
2355 2358 0.610232 ATTCAGTGGTGCAGAAGGCC 60.610 55.000 0.00 0.00 43.89 5.19
2480 2483 1.900016 GGGTGGAACAAACGGGTCC 60.900 63.158 0.00 0.00 44.16 4.46
2491 2494 2.728817 CGGGTCCGTATCCAGAGC 59.271 66.667 0.55 0.00 34.35 4.09
2497 2500 0.847373 TCCGTATCCAGAGCTCTCCT 59.153 55.000 14.96 3.77 0.00 3.69
2521 2524 1.140312 ACCTTGGAGAACTCTTGGCA 58.860 50.000 1.86 0.00 0.00 4.92
2652 2655 5.804771 GCCAAACTAAGACAGGAGGAGAAAT 60.805 44.000 0.00 0.00 0.00 2.17
2689 2692 7.735326 AAGGTAAGGATAAGCTTCACTTAGA 57.265 36.000 0.00 0.00 44.02 2.10
2710 2713 9.399403 CTTAGAACACCTTTATTTGCTTCTTTC 57.601 33.333 0.00 0.00 0.00 2.62
2782 2785 7.533426 ACATGTATTTACTATATCGGTCGACC 58.467 38.462 25.28 25.28 0.00 4.79
2825 2828 5.289510 AGAGGTAAGGGTTCACTATGGAAT 58.710 41.667 0.00 0.00 0.00 3.01
2874 2880 5.441718 ACCATCTGTTATGTGACTTGGAT 57.558 39.130 0.00 0.00 0.00 3.41
2875 2881 5.819991 ACCATCTGTTATGTGACTTGGATT 58.180 37.500 0.00 0.00 0.00 3.01
2888 2894 2.852449 ACTTGGATTTCATGCCCTCCTA 59.148 45.455 8.22 1.73 0.00 2.94
2988 2994 2.113860 TCCCTTAGCTGTGCATGTTC 57.886 50.000 0.00 0.00 0.00 3.18
2994 3000 5.308014 CCTTAGCTGTGCATGTTCCATATA 58.692 41.667 0.00 0.00 0.00 0.86
3051 3057 1.347062 TGATGTGGCAGTGGACTACA 58.653 50.000 0.00 0.00 0.00 2.74
3052 3058 1.908619 TGATGTGGCAGTGGACTACAT 59.091 47.619 0.00 0.43 34.91 2.29
3053 3059 2.305635 TGATGTGGCAGTGGACTACATT 59.694 45.455 0.00 0.00 32.58 2.71
3120 3126 8.157476 ACCAATCTGTAGTTCTGTACAAATCTT 58.843 33.333 0.00 0.00 32.49 2.40
3175 3181 4.757149 GTCCTTGATCCGCTATATTGCTTT 59.243 41.667 7.54 0.00 0.00 3.51
3787 3796 2.027460 CACAAACGGCAAGGGCAC 59.973 61.111 0.00 0.00 43.71 5.01
3887 3899 5.070001 AGTTTGCAGCATAGTAAAGGTGAA 58.930 37.500 0.00 0.00 35.37 3.18
4064 4076 3.192001 GCAATTTGTCAGATTCTGCCTCA 59.808 43.478 8.89 5.56 0.00 3.86
4157 4169 7.826918 ATGTAATAAGACTGAGGAGAGTACC 57.173 40.000 0.00 0.00 0.00 3.34
4229 4241 1.268743 GCTGCTGAAGGTGTTGTCAAC 60.269 52.381 8.86 8.86 0.00 3.18
4241 4253 1.917303 GTTGTCAACAAAAGTGGTGCG 59.083 47.619 10.93 0.00 42.67 5.34
4292 4304 6.539826 TGAATGATGATGTACCACATGAAGAC 59.460 38.462 0.00 0.00 39.27 3.01
4448 4460 1.340889 GAATGCACACCTTCTGGCAAA 59.659 47.619 0.00 0.00 40.02 3.68
4473 4485 2.827921 GGTGCATCCAAGGAAGTTGATT 59.172 45.455 0.00 0.00 38.60 2.57
4748 4760 1.349026 CCAGAACCACCACTGACAGAT 59.651 52.381 10.08 0.00 36.38 2.90
4961 4973 3.869473 TTTAACCAGGCGAGCGCGT 62.869 57.895 12.44 6.51 43.06 6.01
4995 5007 0.111639 AGGTAGAAAGCCCCGCAAAA 59.888 50.000 0.00 0.00 0.00 2.44
4998 5010 0.594110 TAGAAAGCCCCGCAAAAACG 59.406 50.000 0.00 0.00 0.00 3.60
5030 5042 1.542472 GTAGAGATAGAAGCCGAGGCC 59.458 57.143 10.95 0.00 43.17 5.19
5031 5043 1.175983 AGAGATAGAAGCCGAGGCCG 61.176 60.000 10.95 0.00 43.17 6.13
5032 5044 1.152735 AGATAGAAGCCGAGGCCGA 60.153 57.895 10.95 0.00 43.17 5.54
5033 5045 1.175983 AGATAGAAGCCGAGGCCGAG 61.176 60.000 10.95 0.00 43.17 4.63
5034 5046 2.148558 GATAGAAGCCGAGGCCGAGG 62.149 65.000 10.95 14.27 43.17 4.63
5060 5072 1.674651 GCCCTCGAAACCCAACTCC 60.675 63.158 0.00 0.00 0.00 3.85
5061 5073 1.758592 CCCTCGAAACCCAACTCCA 59.241 57.895 0.00 0.00 0.00 3.86
5138 5150 4.183686 CGCAAGCCAAGATGCCCG 62.184 66.667 0.00 0.00 39.39 6.13
5140 5152 2.639327 GCAAGCCAAGATGCCCGTT 61.639 57.895 0.00 0.00 36.56 4.44
5156 5168 2.822255 TTGGGCAATAGCGTCGCC 60.822 61.111 14.86 0.00 45.47 5.54
5199 5217 2.660189 TACTGGTCGGTTTCGGATTC 57.340 50.000 0.00 0.00 36.95 2.52
5200 5218 0.682852 ACTGGTCGGTTTCGGATTCA 59.317 50.000 0.00 0.00 36.95 2.57
5201 5219 1.337823 ACTGGTCGGTTTCGGATTCAG 60.338 52.381 0.00 0.00 36.95 3.02
5202 5220 0.970640 TGGTCGGTTTCGGATTCAGA 59.029 50.000 0.00 0.00 36.95 3.27
5203 5221 1.553248 TGGTCGGTTTCGGATTCAGAT 59.447 47.619 0.00 0.00 36.95 2.90
5206 5224 3.522553 GTCGGTTTCGGATTCAGATTCT 58.477 45.455 0.00 0.00 36.95 2.40
5207 5225 3.552294 GTCGGTTTCGGATTCAGATTCTC 59.448 47.826 0.00 0.00 36.95 2.87
5208 5226 2.866762 CGGTTTCGGATTCAGATTCTCC 59.133 50.000 0.00 0.00 0.00 3.71
5209 5227 3.678806 CGGTTTCGGATTCAGATTCTCCA 60.679 47.826 0.00 0.00 0.00 3.86
5210 5228 4.455606 GGTTTCGGATTCAGATTCTCCAT 58.544 43.478 0.00 0.00 0.00 3.41
5211 5229 4.513318 GGTTTCGGATTCAGATTCTCCATC 59.487 45.833 0.00 0.00 0.00 3.51
5212 5230 5.118990 GTTTCGGATTCAGATTCTCCATCA 58.881 41.667 4.68 0.00 33.75 3.07
5328 5360 4.093998 CAGAGATTTCAGGTCGAAACATGG 59.906 45.833 0.00 0.00 46.22 3.66
5415 5448 1.937924 ATTAAGCTGGGTCCAGGGCC 61.938 60.000 17.67 0.00 43.77 5.80
5416 5449 3.579451 TAAGCTGGGTCCAGGGCCT 62.579 63.158 10.88 0.00 43.77 5.19
5419 5452 3.406200 CTGGGTCCAGGGCCTGAG 61.406 72.222 34.84 23.27 40.17 3.35
5478 5511 1.218316 CCTTGACTGGCCGGTACTC 59.782 63.158 19.73 6.01 0.00 2.59
5555 5588 9.562583 TGTTTTGTGTTTCTGTATGTAAGTTTC 57.437 29.630 0.00 0.00 0.00 2.78
5573 5606 9.859692 GTAAGTTTCTGTGTTTCTGTATGTAAC 57.140 33.333 0.00 0.00 0.00 2.50
5616 5649 1.167155 TTTTGCTTCGCGGCCTGTAA 61.167 50.000 6.13 0.00 0.00 2.41
5656 5689 1.074850 TGGAGACTGGACACCACCA 60.075 57.895 0.00 0.00 38.33 4.17
5657 5690 1.371558 GGAGACTGGACACCACCAC 59.628 63.158 0.00 0.00 35.91 4.16
5658 5691 1.371558 GAGACTGGACACCACCACC 59.628 63.158 0.00 0.00 35.91 4.61
5659 5692 1.383943 AGACTGGACACCACCACCA 60.384 57.895 0.00 0.00 35.91 4.17
5660 5693 1.227853 GACTGGACACCACCACCAC 60.228 63.158 0.00 0.00 35.91 4.16
5661 5694 2.113139 CTGGACACCACCACCACC 59.887 66.667 0.00 0.00 35.91 4.61
5667 5700 0.475044 ACACCACCACCACCGTTAAT 59.525 50.000 0.00 0.00 0.00 1.40
5777 5810 4.078639 CTTTGAGAAAGGAGAGTGTGGT 57.921 45.455 0.00 0.00 34.85 4.16
5951 5984 0.102300 GCTTCCTCGCCTTCTCTCTC 59.898 60.000 0.00 0.00 0.00 3.20
5952 5985 1.762708 CTTCCTCGCCTTCTCTCTCT 58.237 55.000 0.00 0.00 0.00 3.10
5953 5986 1.676006 CTTCCTCGCCTTCTCTCTCTC 59.324 57.143 0.00 0.00 0.00 3.20
6086 6788 2.487986 GCAGATTAGGCTTAGGGCATGT 60.488 50.000 0.10 0.00 44.01 3.21
6087 6789 3.825328 CAGATTAGGCTTAGGGCATGTT 58.175 45.455 0.10 0.00 44.01 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.610859 AGGCACGGAGGTGGGAAT 60.611 61.111 0.00 0.00 44.54 3.01
60 61 0.169009 GGAAACTGAGGCAATCGCAC 59.831 55.000 0.00 0.00 41.24 5.34
312 313 8.753497 AAAGGCCCAAAATAAATTACAACAAA 57.247 26.923 0.00 0.00 0.00 2.83
325 328 5.105106 CGGAACCTAATAAAAGGCCCAAAAT 60.105 40.000 0.00 0.00 40.62 1.82
329 332 2.357361 CCGGAACCTAATAAAAGGCCCA 60.357 50.000 0.00 0.00 40.62 5.36
347 350 5.227152 CAAAACAGAAAATAAGAACCCCGG 58.773 41.667 0.00 0.00 0.00 5.73
405 408 3.814842 TGCAATCATTGACTTCTCACGTT 59.185 39.130 0.00 0.00 0.00 3.99
409 412 3.624410 CCGATGCAATCATTGACTTCTCA 59.376 43.478 0.00 0.00 45.97 3.27
430 433 5.243954 GGAAAATAGAAACCTATGGCCATCC 59.756 44.000 24.80 9.19 0.00 3.51
432 435 5.598417 GTGGAAAATAGAAACCTATGGCCAT 59.402 40.000 24.45 24.45 31.09 4.40
517 520 0.322322 AACCGGCGATAGTTCAACCA 59.678 50.000 9.30 0.00 39.35 3.67
566 569 4.349663 TTGTTTCTAAATTCATCGGGCG 57.650 40.909 0.00 0.00 0.00 6.13
596 599 7.170277 TCACATAATGGCATAGAATATGCACT 58.830 34.615 20.09 8.68 46.21 4.40
641 644 5.144832 AGTAAACAACACCAAAGGCCTAAT 58.855 37.500 5.16 0.00 0.00 1.73
644 647 2.956333 GAGTAAACAACACCAAAGGCCT 59.044 45.455 0.00 0.00 0.00 5.19
693 696 3.992427 GACAAAAACTCACTACCCCTACG 59.008 47.826 0.00 0.00 0.00 3.51
748 751 8.336235 TGAGTAATAACAAAGGATCTGGGAAAT 58.664 33.333 0.00 0.00 0.00 2.17
806 809 8.207545 ACTACCTTCCAATCTGAATATCACTTC 58.792 37.037 0.00 0.00 0.00 3.01
825 828 5.189736 TGCTCAGGTGAATCAATACTACCTT 59.810 40.000 0.00 0.00 39.63 3.50
900 903 1.069091 TCACAGTGTGAATGCAATGCG 60.069 47.619 23.55 0.00 39.78 4.73
1167 1170 6.389830 ACACAGTGCAGACAAATTTTGATA 57.610 33.333 15.81 0.00 0.00 2.15
1168 1171 5.266733 ACACAGTGCAGACAAATTTTGAT 57.733 34.783 15.81 1.42 0.00 2.57
1169 1172 4.717233 ACACAGTGCAGACAAATTTTGA 57.283 36.364 15.81 0.00 0.00 2.69
1170 1173 7.467557 AATAACACAGTGCAGACAAATTTTG 57.532 32.000 7.59 7.59 0.00 2.44
1171 1174 7.548780 ACAAATAACACAGTGCAGACAAATTTT 59.451 29.630 0.00 0.00 0.00 1.82
1172 1175 7.041107 ACAAATAACACAGTGCAGACAAATTT 58.959 30.769 0.00 0.00 0.00 1.82
1214 1217 6.346838 GCATACTGCTTGTTGAATGGTTTTTC 60.347 38.462 0.00 0.00 40.96 2.29
1217 1220 4.559153 GCATACTGCTTGTTGAATGGTTT 58.441 39.130 0.00 0.00 40.96 3.27
1312 1315 8.370182 AGATGTTGCAACTTTATTTCCTCATTT 58.630 29.630 28.61 3.63 0.00 2.32
1313 1316 7.899973 AGATGTTGCAACTTTATTTCCTCATT 58.100 30.769 28.61 0.58 0.00 2.57
1314 1317 7.472334 AGATGTTGCAACTTTATTTCCTCAT 57.528 32.000 28.61 10.44 0.00 2.90
1315 1318 6.899393 AGATGTTGCAACTTTATTTCCTCA 57.101 33.333 28.61 5.81 0.00 3.86
1316 1319 8.045176 ACTAGATGTTGCAACTTTATTTCCTC 57.955 34.615 28.61 9.30 0.00 3.71
1441 1444 1.478631 AGCTTTTGGAATAGCAGCCC 58.521 50.000 4.89 0.00 39.85 5.19
1637 1640 2.880443 ACAACTGCCCATTTGATGTCT 58.120 42.857 5.52 0.00 0.00 3.41
1638 1641 3.505680 TGTACAACTGCCCATTTGATGTC 59.494 43.478 0.00 0.00 0.00 3.06
1650 1653 3.191162 TCATGAAGCCATTGTACAACTGC 59.809 43.478 18.73 18.73 0.00 4.40
1674 1677 1.666189 GAATAACCGTCTGCCTGCTTC 59.334 52.381 0.00 0.00 0.00 3.86
1686 1689 4.794762 TCGTTGTCGTATTCTGAATAACCG 59.205 41.667 11.46 11.70 38.33 4.44
1804 1807 6.238508 CCTGCAGTTTATACTTTTCGTAACG 58.761 40.000 13.81 0.00 30.26 3.18
1810 1813 5.154222 GTGTGCCTGCAGTTTATACTTTTC 58.846 41.667 13.81 0.00 30.26 2.29
1891 1894 9.740239 CATAAACCTGGATAATGATTTCAGTTG 57.260 33.333 0.00 0.00 0.00 3.16
1976 1979 2.481568 CAGTTCTGGGTATGCATATGCG 59.518 50.000 22.21 6.68 45.83 4.73
2035 2038 4.730949 ATCATCTTTGAGCCATTTGGTG 57.269 40.909 0.00 0.00 34.73 4.17
2183 2186 6.426633 GCTTGGTATTTAAAGCAACACCATTT 59.573 34.615 2.66 0.00 46.45 2.32
2321 2324 0.697658 TGAATGTGACCCTGGCATCA 59.302 50.000 0.00 0.00 0.00 3.07
2322 2325 1.340405 ACTGAATGTGACCCTGGCATC 60.340 52.381 0.00 0.00 0.00 3.91
2323 2326 0.700564 ACTGAATGTGACCCTGGCAT 59.299 50.000 0.00 0.00 0.00 4.40
2324 2327 2.154139 ACTGAATGTGACCCTGGCA 58.846 52.632 0.00 0.00 0.00 4.92
2333 2336 1.538512 CCTTCTGCACCACTGAATGTG 59.461 52.381 0.00 0.00 45.80 3.21
2334 2337 1.901591 CCTTCTGCACCACTGAATGT 58.098 50.000 0.00 0.00 35.88 2.71
2335 2338 0.524862 GCCTTCTGCACCACTGAATG 59.475 55.000 0.00 0.00 40.77 2.67
2336 2339 0.610232 GGCCTTCTGCACCACTGAAT 60.610 55.000 0.00 0.00 43.89 2.57
2337 2340 1.228245 GGCCTTCTGCACCACTGAA 60.228 57.895 0.00 0.00 43.89 3.02
2338 2341 2.149383 AGGCCTTCTGCACCACTGA 61.149 57.895 0.00 0.00 43.89 3.41
2339 2342 1.970114 CAGGCCTTCTGCACCACTG 60.970 63.158 0.00 0.00 43.89 3.66
2340 2343 2.433446 CAGGCCTTCTGCACCACT 59.567 61.111 0.00 0.00 43.89 4.00
2341 2344 2.674380 CCAGGCCTTCTGCACCAC 60.674 66.667 0.00 0.00 43.89 4.16
2355 2358 5.006386 GCTATTATCATTGAACCTCCCCAG 58.994 45.833 0.00 0.00 0.00 4.45
2480 2483 1.686355 ACAGGAGAGCTCTGGATACG 58.314 55.000 23.91 5.82 42.51 3.06
2497 2500 4.081087 GCCAAGAGTTCTCCAAGGTATACA 60.081 45.833 5.01 0.00 0.00 2.29
2521 2524 3.607741 CTTGATCTCACTGCAGATTGGT 58.392 45.455 23.35 5.34 32.94 3.67
2689 2692 6.731292 AGGAAAGAAGCAAATAAAGGTGTT 57.269 33.333 0.00 0.00 0.00 3.32
2710 2713 7.798596 ACATAGAAAGATAAGCATGACAAGG 57.201 36.000 0.00 0.00 0.00 3.61
2858 2864 5.105797 GGCATGAAATCCAAGTCACATAACA 60.106 40.000 0.00 0.00 0.00 2.41
2874 2880 3.130734 AGGTACTAGGAGGGCATGAAA 57.869 47.619 0.00 0.00 36.02 2.69
2875 2881 2.868964 AGGTACTAGGAGGGCATGAA 57.131 50.000 0.00 0.00 36.02 2.57
2911 2917 4.989044 TCACATGCAGTTGAAATGCTATG 58.011 39.130 18.66 19.51 44.17 2.23
2988 2994 7.510549 AAAGAATGGTCGGAAACATATATGG 57.489 36.000 16.96 0.00 0.00 2.74
2994 3000 6.405278 AAGAAAAAGAATGGTCGGAAACAT 57.595 33.333 0.00 0.00 0.00 2.71
3079 3085 9.764363 CTACAGATTGGTTATAAACAGCATAGA 57.236 33.333 2.94 0.00 0.00 1.98
3120 3126 4.588899 ACAGAGCAGTAACCAAATATGCA 58.411 39.130 0.00 0.00 39.34 3.96
3175 3181 7.068103 TGCTGACTTGTTTTCCTGAAAGAATTA 59.932 33.333 0.00 0.00 34.07 1.40
3406 3415 2.686915 GGAATGGAGATTGGAGCAACAG 59.313 50.000 0.00 0.00 0.00 3.16
3787 3796 9.853921 GTGCTTCATTCAAATTAAAGTTCTTTG 57.146 29.630 7.90 0.00 0.00 2.77
3887 3899 5.072872 CCAAGAGATCCCAAATACTGATCCT 59.927 44.000 0.00 0.00 36.41 3.24
4064 4076 1.053424 TTCTGCAACCTAGGGACGTT 58.947 50.000 14.81 0.00 0.00 3.99
4157 4169 5.666969 TTGAAAGTGGTAAATGTCTCGTG 57.333 39.130 0.00 0.00 0.00 4.35
4229 4241 3.536498 GACGGCCGCACCACTTTTG 62.536 63.158 28.58 0.00 39.03 2.44
4241 4253 0.872388 ACAAATTTCTGACGACGGCC 59.128 50.000 0.00 0.00 0.00 6.13
4292 4304 5.048434 TGACACTACTGATGACTCTGAGTTG 60.048 44.000 12.27 5.37 0.00 3.16
4468 4480 3.320541 AGCGGATGGAAAACACAAATCAA 59.679 39.130 0.00 0.00 0.00 2.57
4473 4485 2.811431 CTGTAGCGGATGGAAAACACAA 59.189 45.455 0.00 0.00 0.00 3.33
4577 4589 3.304257 CCATGTTTGATATTGCGAGCTCC 60.304 47.826 8.47 1.40 0.00 4.70
4814 4826 2.433318 AAGTCTCGCTTCTGCCGC 60.433 61.111 0.00 0.00 35.36 6.53
4961 4973 1.122632 TACCTCTTGTTCGCCCACCA 61.123 55.000 0.00 0.00 0.00 4.17
4995 5007 0.679002 TCTACGGTAGCTGGCTCGTT 60.679 55.000 10.34 1.27 37.10 3.85
4998 5010 1.611519 ATCTCTACGGTAGCTGGCTC 58.388 55.000 10.34 0.00 0.00 4.70
5039 5051 4.338710 TTGGGTTTCGAGGGCGGG 62.339 66.667 0.00 0.00 38.28 6.13
5042 5054 1.674651 GGAGTTGGGTTTCGAGGGC 60.675 63.158 0.00 0.00 0.00 5.19
5138 5150 2.403586 GCGACGCTATTGCCCAAC 59.596 61.111 13.73 0.00 35.36 3.77
5181 5193 0.682852 TGAATCCGAAACCGACCAGT 59.317 50.000 0.00 0.00 0.00 4.00
5206 5224 0.178767 CCACCGCAATCTCTGATGGA 59.821 55.000 0.00 0.00 0.00 3.41
5207 5225 0.178767 TCCACCGCAATCTCTGATGG 59.821 55.000 0.00 0.00 0.00 3.51
5208 5226 1.134580 AGTCCACCGCAATCTCTGATG 60.135 52.381 0.00 0.00 0.00 3.07
5209 5227 1.134580 CAGTCCACCGCAATCTCTGAT 60.135 52.381 0.00 0.00 0.00 2.90
5210 5228 0.247460 CAGTCCACCGCAATCTCTGA 59.753 55.000 0.00 0.00 0.00 3.27
5211 5229 0.742281 CCAGTCCACCGCAATCTCTG 60.742 60.000 0.00 0.00 0.00 3.35
5212 5230 1.194781 ACCAGTCCACCGCAATCTCT 61.195 55.000 0.00 0.00 0.00 3.10
5249 5270 1.278699 TGCACACTCATGGCTGTGATA 59.721 47.619 21.26 10.51 40.28 2.15
5310 5332 8.656130 AATGTACACCATGTTTCGACCTGAAAT 61.656 37.037 0.00 0.00 39.79 2.17
5315 5347 3.695830 ATGTACACCATGTTTCGACCT 57.304 42.857 0.00 0.00 30.69 3.85
5371 5404 5.008613 ACAACGCTGTTACAGAAATTGTCAT 59.991 36.000 17.40 0.00 41.29 3.06
5415 5448 2.187424 GCAGGCCTCTCAGCTCAG 59.813 66.667 0.00 0.00 0.00 3.35
5416 5449 2.284478 AGCAGGCCTCTCAGCTCA 60.284 61.111 0.00 0.00 30.05 4.26
5417 5450 1.326213 TACAGCAGGCCTCTCAGCTC 61.326 60.000 12.20 0.00 34.61 4.09
5418 5451 0.906756 TTACAGCAGGCCTCTCAGCT 60.907 55.000 0.00 5.72 37.95 4.24
5419 5452 0.179936 ATTACAGCAGGCCTCTCAGC 59.820 55.000 0.00 2.63 0.00 4.26
5478 5511 3.248602 CCGATTAGCCTCTTTGATTTCCG 59.751 47.826 0.00 0.00 0.00 4.30
5555 5588 6.365839 CAGCAAGTTACATACAGAAACACAG 58.634 40.000 0.00 0.00 0.00 3.66
5573 5606 1.710013 CAGCCAAATGAAGCAGCAAG 58.290 50.000 0.00 0.00 0.00 4.01
5616 5649 1.079543 CAACTAGGCAGCGCTGAGT 60.080 57.895 40.21 29.74 0.00 3.41
5656 5689 3.008594 TGGATCAAGTCATTAACGGTGGT 59.991 43.478 0.00 0.00 0.00 4.16
5657 5690 3.605634 TGGATCAAGTCATTAACGGTGG 58.394 45.455 0.00 0.00 0.00 4.61
5658 5691 4.330074 GTCTGGATCAAGTCATTAACGGTG 59.670 45.833 0.00 0.00 0.00 4.94
5659 5692 4.020573 TGTCTGGATCAAGTCATTAACGGT 60.021 41.667 0.00 0.00 0.00 4.83
5660 5693 4.503910 TGTCTGGATCAAGTCATTAACGG 58.496 43.478 0.00 0.00 0.00 4.44
5661 5694 5.410924 TCTGTCTGGATCAAGTCATTAACG 58.589 41.667 0.00 0.00 0.00 3.18
5667 5700 4.263018 CAGTTCTGTCTGGATCAAGTCA 57.737 45.455 0.00 0.00 0.00 3.41
5775 5808 4.033702 GCCAGTAGCTCGTTTACATTTACC 59.966 45.833 0.00 0.00 38.99 2.85
5776 5809 4.628333 TGCCAGTAGCTCGTTTACATTTAC 59.372 41.667 0.00 0.00 44.23 2.01
5777 5810 4.823157 TGCCAGTAGCTCGTTTACATTTA 58.177 39.130 0.00 0.00 44.23 1.40
5973 6006 2.516225 GAAGGCCCCCGGAAATCG 60.516 66.667 0.73 0.00 38.88 3.34
6086 6788 2.192664 TGTAAGCGCTTCCCATTGAA 57.807 45.000 28.82 2.82 0.00 2.69
6087 6789 2.418368 ATGTAAGCGCTTCCCATTGA 57.582 45.000 28.82 3.72 0.00 2.57
6145 6847 4.338379 ACAGGCTCTTAGAGAAACGTTT 57.662 40.909 14.57 14.57 0.00 3.60


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

AutoCloner maintained by Alex Coulton.