Multiple sequence alignment - TraesCS4A01G103200

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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 TraesCS4A01G103200 chr4A 100.000 5861 0 0 1 5861 116470828 116476688 0 10824
1 TraesCS4A01G103200 chr4B 92.200 5949 261 72 1 5861 428971752 428965919 0 8227
2 TraesCS4A01G103200 chr4D 96.534 4963 128 20 1 4950 348803100 348798169 0 8172
3 TraesCS4A01G103200 chr4D 88.851 888 55 27 4994 5861 348797747 348796884 0 1051


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 TraesCS4A01G103200 chr4A 116470828 116476688 5860 False 10824.0 10824 100.0000 1 5861 1 chr4A.!!$F1 5860
1 TraesCS4A01G103200 chr4B 428965919 428971752 5833 True 8227.0 8227 92.2000 1 5861 1 chr4B.!!$R1 5860
2 TraesCS4A01G103200 chr4D 348796884 348803100 6216 True 4611.5 8172 92.6925 1 5861 2 chr4D.!!$R1 5860

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
69 70 0.614979 TTCTTCTCCAGCCCGCTAGT 60.615 55.000 0.00 0.0 0.00 2.57 F
255 285 0.796113 GACTCGGCGGTTACTTCGAC 60.796 60.000 7.21 0.0 0.00 4.20 F
1088 1129 0.179111 TACGCGGCTTTCCATCTCTG 60.179 55.000 12.47 0.0 0.00 3.35 F
2087 2128 1.003233 GGTTCCTGCACCAGTCTCC 60.003 63.158 0.00 0.0 36.73 3.71 F
2772 2813 1.339151 CCTCCAACCCTACAGCTGAAC 60.339 57.143 23.35 0.0 0.00 3.18 F
4610 4651 0.252927 AGGTTTGGGGAGAGGAGAGG 60.253 60.000 0.00 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1068 1109 0.535335 AGAGATGGAAAGCCGCGTAA 59.465 50.000 4.92 0.00 36.79 3.18 R
1354 1395 1.779569 GCCTTTCTTCTCGTTCGTCA 58.220 50.000 0.00 0.00 0.00 4.35 R
3068 3109 0.179936 GCTCCTCCTCACCTGAATGG 59.820 60.000 0.00 0.00 42.93 3.16 R
3734 3775 0.893270 AATACGCACAGGGCAAAGCA 60.893 50.000 0.00 0.00 45.17 3.91 R
4734 4775 1.704628 TCCATTCTGTTCCTGAAGCCA 59.295 47.619 0.00 0.00 0.00 4.75 R
5445 5903 0.102844 ATTCGATGCAAATTGCCCGG 59.897 50.000 22.43 10.32 44.23 5.73 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
35 36 1.219393 CGCACCCTCCTCTTCTTCC 59.781 63.158 0.00 0.00 0.00 3.46
39 40 2.821437 CACCCTCCTCTTCTTCCACTA 58.179 52.381 0.00 0.00 0.00 2.74
42 43 3.596956 ACCCTCCTCTTCTTCCACTACTA 59.403 47.826 0.00 0.00 0.00 1.82
44 45 4.325501 CCCTCCTCTTCTTCCACTACTACT 60.326 50.000 0.00 0.00 0.00 2.57
45 46 4.642885 CCTCCTCTTCTTCCACTACTACTG 59.357 50.000 0.00 0.00 0.00 2.74
69 70 0.614979 TTCTTCTCCAGCCCGCTAGT 60.615 55.000 0.00 0.00 0.00 2.57
73 74 4.096003 TCCAGCCCGCTAGTTGCC 62.096 66.667 0.00 0.00 38.78 4.52
138 147 7.725818 GGTAACTTTGAAGTAAGCTTGTACT 57.274 36.000 9.86 2.08 38.57 2.73
179 188 2.218953 TTCGGCGGTATGAGATGTTC 57.781 50.000 7.21 0.00 0.00 3.18
182 191 2.128035 CGGCGGTATGAGATGTTCTTC 58.872 52.381 0.00 0.00 0.00 2.87
233 263 3.253677 TCTTTCTAGATCGATCTTCCGCC 59.746 47.826 31.55 1.22 38.32 6.13
237 267 2.520982 ATCGATCTTCCGCCGGGA 60.521 61.111 1.90 0.00 41.83 5.14
238 268 2.750715 GATCGATCTTCCGCCGGGAC 62.751 65.000 18.29 0.00 43.74 4.46
255 285 0.796113 GACTCGGCGGTTACTTCGAC 60.796 60.000 7.21 0.00 0.00 4.20
276 306 5.270893 ACTGTTTTCTTTTGCGGGTTAAT 57.729 34.783 0.00 0.00 0.00 1.40
316 349 2.996621 CTCCTTGGTGAGATTCGTGAAC 59.003 50.000 0.00 0.00 34.11 3.18
458 495 2.223135 GGATTCTGCTGCGCTTTTACTC 60.223 50.000 9.73 0.00 0.00 2.59
500 539 7.230510 AGTTTGTATCCAGTGTGAAATTGCTTA 59.769 33.333 0.00 0.00 0.00 3.09
501 540 7.701539 TTGTATCCAGTGTGAAATTGCTTAT 57.298 32.000 0.00 0.00 0.00 1.73
503 542 8.121305 TGTATCCAGTGTGAAATTGCTTATTT 57.879 30.769 0.00 0.00 39.15 1.40
579 618 9.939802 ATCGGTAGTATTCATAAAGGAATTACC 57.060 33.333 7.64 7.64 37.32 2.85
593 632 6.394345 AGGAATTACCACTTCTTCTTGGAT 57.606 37.500 0.00 0.00 42.04 3.41
630 669 3.053455 GCAGTAAGTATGCCATCGAGTC 58.947 50.000 0.00 0.00 37.73 3.36
736 776 5.651387 ATTCTCTGACTCGTTCTCATGAA 57.349 39.130 0.00 0.00 0.00 2.57
766 806 5.064325 ACTTGTCGTGTCTTGGAAGTTAAAC 59.936 40.000 0.00 0.00 0.00 2.01
871 912 1.337260 CGTACCATCTGCCTGGCTATC 60.337 57.143 21.03 1.28 40.15 2.08
984 1025 6.485171 AGAAAACAGGTTATTGTCTGCCTAT 58.515 36.000 0.00 0.00 34.57 2.57
989 1030 5.070580 ACAGGTTATTGTCTGCCTATCTACC 59.929 44.000 0.00 0.00 34.57 3.18
1033 1074 1.546476 AGAAGGACGAGGTACTTGCAG 59.454 52.381 0.00 0.00 45.68 4.41
1068 1109 6.719370 TGAATGTTAATTCTAGGTTGCTTGGT 59.281 34.615 0.00 0.00 42.40 3.67
1072 1113 6.148150 TGTTAATTCTAGGTTGCTTGGTTACG 59.852 38.462 0.00 0.00 0.00 3.18
1075 1116 0.671163 TAGGTTGCTTGGTTACGCGG 60.671 55.000 12.47 0.00 0.00 6.46
1084 1125 1.022451 TGGTTACGCGGCTTTCCATC 61.022 55.000 12.47 0.00 0.00 3.51
1088 1129 0.179111 TACGCGGCTTTCCATCTCTG 60.179 55.000 12.47 0.00 0.00 3.35
1105 1146 8.297426 TCCATCTCTGTATGTACATAAATCGTC 58.703 37.037 17.07 4.74 35.36 4.20
1106 1147 7.271438 CCATCTCTGTATGTACATAAATCGTCG 59.729 40.741 17.07 0.42 35.36 5.12
1112 1153 8.637281 TGTATGTACATAAATCGTCGATGTTT 57.363 30.769 17.07 3.78 35.48 2.83
1145 1186 2.825836 GGTCATCCGCTTGGGCTG 60.826 66.667 0.00 0.00 36.09 4.85
1190 1231 2.823154 TGTTCCCATTAAGAAAAGGCCG 59.177 45.455 0.00 0.00 0.00 6.13
1354 1395 5.021458 TCCCAGTAGATCTTTTACTCCGTT 58.979 41.667 0.00 0.00 0.00 4.44
1629 1670 5.045286 AGTGGCATGGAATCTTCTTCTAACT 60.045 40.000 0.00 0.00 0.00 2.24
1838 1879 4.594123 TGACAATACTCTGAAACCGTCA 57.406 40.909 0.00 0.00 34.17 4.35
1840 1881 4.988540 TGACAATACTCTGAAACCGTCAAG 59.011 41.667 0.00 0.00 35.22 3.02
1868 1909 8.768955 GCATATCAACTTCCTAATAAGAGTGTG 58.231 37.037 0.00 0.00 0.00 3.82
1916 1957 2.242708 ACTTAAACCACCAACCAGACCA 59.757 45.455 0.00 0.00 0.00 4.02
2030 2071 8.310406 TGAATGTTCCTGATGCTATATTTACG 57.690 34.615 0.00 0.00 0.00 3.18
2087 2128 1.003233 GGTTCCTGCACCAGTCTCC 60.003 63.158 0.00 0.00 36.73 3.71
2088 2129 1.754745 GTTCCTGCACCAGTCTCCA 59.245 57.895 0.00 0.00 0.00 3.86
2121 2162 5.171476 CAGCTGAGAAGATTTCGAAACCTA 58.829 41.667 13.81 0.00 34.02 3.08
2159 2200 1.518056 CTCACACCACCATGCCACAC 61.518 60.000 0.00 0.00 0.00 3.82
2160 2201 1.529010 CACACCACCATGCCACACT 60.529 57.895 0.00 0.00 0.00 3.55
2372 2413 5.241506 TGGCTTTGATTTGTACTCTGGAAAG 59.758 40.000 0.00 0.00 0.00 2.62
2431 2472 3.601443 AGTGACTGATAGTGTTCCTGC 57.399 47.619 0.00 0.00 0.00 4.85
2674 2715 8.024145 AGCTGTAATCCTGTTAAAGCTACTAT 57.976 34.615 10.03 0.00 42.19 2.12
2710 2751 5.296035 CAGCAGTTAATCAGATTCATGCTCA 59.704 40.000 19.52 0.00 40.58 4.26
2744 2785 2.158900 CCGGAAGCCTTGTGATGTATCT 60.159 50.000 0.00 0.00 0.00 1.98
2772 2813 1.339151 CCTCCAACCCTACAGCTGAAC 60.339 57.143 23.35 0.00 0.00 3.18
2775 2816 1.339151 CCAACCCTACAGCTGAACCTC 60.339 57.143 23.35 0.00 0.00 3.85
2891 2932 3.871594 CACAGCTGCCTACTACCAATAAC 59.128 47.826 15.27 0.00 0.00 1.89
2896 2937 2.696707 TGCCTACTACCAATAACCCTCG 59.303 50.000 0.00 0.00 0.00 4.63
3068 3109 1.811860 GCCAGATGTCATTGCCACC 59.188 57.895 0.00 0.00 0.00 4.61
3720 3761 2.118228 TGTTTTCGCAGTCATGTTGC 57.882 45.000 12.83 12.83 38.18 4.17
3761 3802 5.431420 TGCCCTGTGCGTATTTATATTTG 57.569 39.130 0.00 0.00 45.60 2.32
3909 3950 5.097742 ACATGAACAATCAACGGAGGATA 57.902 39.130 0.00 0.00 39.49 2.59
3949 3990 1.143684 GTGGTGGTGGATATCATGGCT 59.856 52.381 4.83 0.00 0.00 4.75
4610 4651 0.252927 AGGTTTGGGGAGAGGAGAGG 60.253 60.000 0.00 0.00 0.00 3.69
4665 4706 1.719725 GCGACGAGGAGATGCTCTCA 61.720 60.000 0.00 0.00 45.12 3.27
4667 4708 2.147150 CGACGAGGAGATGCTCTCATA 58.853 52.381 13.06 0.00 45.12 2.15
4668 4709 2.095969 CGACGAGGAGATGCTCTCATAC 60.096 54.545 13.06 5.19 45.12 2.39
4669 4710 2.227865 GACGAGGAGATGCTCTCATACC 59.772 54.545 13.06 0.00 45.12 2.73
4728 4769 3.083997 GGTCCACGGGAGCCTGAT 61.084 66.667 10.07 0.00 43.62 2.90
4883 4930 1.700955 AGCAAGGGATGGATGAATGC 58.299 50.000 0.00 0.00 0.00 3.56
4957 5004 3.436704 TCGCTTCTGTTAGCCAAATCAAG 59.563 43.478 0.00 0.00 37.90 3.02
4965 5012 6.017109 TCTGTTAGCCAAATCAAGAAGTGTTC 60.017 38.462 0.00 0.00 0.00 3.18
4974 5021 1.261619 CAAGAAGTGTTCGCTGACCAC 59.738 52.381 0.00 0.00 34.02 4.16
5024 5449 2.102420 TGTTGCGTTCTTTCTCAGGAGA 59.898 45.455 0.00 0.00 35.27 3.71
5036 5461 3.282036 TCTCAGGAGATATGCTGCAGCA 61.282 50.000 41.05 41.05 43.41 4.41
5037 5462 4.576933 TCTCAGGAGATATGCTGCAGCAT 61.577 47.826 45.30 45.30 46.87 3.79
5081 5506 6.647229 ACACATGTTACACTGATGAGATGAT 58.353 36.000 0.00 0.00 0.00 2.45
5082 5507 7.108194 ACACATGTTACACTGATGAGATGATT 58.892 34.615 0.00 0.00 0.00 2.57
5105 5530 1.099879 ATCGGCTGGCTGCATCTTTC 61.100 55.000 18.32 0.00 45.15 2.62
5113 5538 0.942962 GCTGCATCTTTCGATCCTGG 59.057 55.000 0.00 0.00 0.00 4.45
5118 5543 1.672881 CATCTTTCGATCCTGGTTGGC 59.327 52.381 0.00 0.00 35.26 4.52
5213 5654 3.760580 AGCTACTTGCAGAAGTGTCTT 57.239 42.857 1.14 0.00 42.66 3.01
5215 5656 5.215252 AGCTACTTGCAGAAGTGTCTTTA 57.785 39.130 1.14 0.00 42.66 1.85
5219 5660 7.036220 GCTACTTGCAGAAGTGTCTTTATCTA 58.964 38.462 1.14 0.00 42.66 1.98
5223 5664 8.972127 ACTTGCAGAAGTGTCTTTATCTATCTA 58.028 33.333 0.00 0.00 41.12 1.98
5224 5665 9.979578 CTTGCAGAAGTGTCTTTATCTATCTAT 57.020 33.333 0.00 0.00 28.78 1.98
5225 5666 9.973450 TTGCAGAAGTGTCTTTATCTATCTATC 57.027 33.333 0.00 0.00 28.78 2.08
5226 5667 8.580720 TGCAGAAGTGTCTTTATCTATCTATCC 58.419 37.037 0.00 0.00 28.78 2.59
5227 5668 7.753132 GCAGAAGTGTCTTTATCTATCTATCCG 59.247 40.741 0.00 0.00 28.78 4.18
5228 5669 8.240682 CAGAAGTGTCTTTATCTATCTATCCGG 58.759 40.741 0.00 0.00 28.78 5.14
5229 5670 7.394923 AGAAGTGTCTTTATCTATCTATCCGGG 59.605 40.741 0.00 0.00 0.00 5.73
5230 5671 5.419471 AGTGTCTTTATCTATCTATCCGGGC 59.581 44.000 0.00 0.00 0.00 6.13
5231 5672 5.419471 GTGTCTTTATCTATCTATCCGGGCT 59.581 44.000 0.00 0.00 0.00 5.19
5232 5673 6.017192 TGTCTTTATCTATCTATCCGGGCTT 58.983 40.000 0.00 0.00 0.00 4.35
5295 5744 8.635877 ATTAAAGCGACTTGTCTTCACTATAG 57.364 34.615 0.00 0.00 0.00 1.31
5314 5763 2.583143 AGTTTGCCTAGTTGTTGGTCC 58.417 47.619 0.00 0.00 0.00 4.46
5475 5933 1.326245 TGCATCGAATAAAAGTCCGCG 59.674 47.619 0.00 0.00 0.00 6.46
5483 5941 1.219646 TAAAAGTCCGCGGTGTGTTC 58.780 50.000 27.15 9.74 0.00 3.18
5544 6018 0.537600 AGCAGCTCATGATGGATGCC 60.538 55.000 18.34 4.64 34.24 4.40
5557 6031 2.281484 ATGCCCGTCTTGTGCGTT 60.281 55.556 0.00 0.00 0.00 4.84
5558 6032 1.004320 ATGCCCGTCTTGTGCGTTA 60.004 52.632 0.00 0.00 0.00 3.18
5623 6097 1.487482 CGACGATGCGTATCATTGGT 58.513 50.000 14.06 3.01 41.37 3.67
5705 6179 3.448660 GTGGAAATTATGCCCAGCTCTTT 59.551 43.478 0.00 0.00 0.00 2.52
5706 6180 3.448301 TGGAAATTATGCCCAGCTCTTTG 59.552 43.478 0.00 0.00 0.00 2.77
5707 6181 3.181472 GGAAATTATGCCCAGCTCTTTGG 60.181 47.826 0.00 0.00 38.00 3.28
5708 6182 3.386932 AATTATGCCCAGCTCTTTGGA 57.613 42.857 0.00 0.00 40.87 3.53
5709 6183 3.607490 ATTATGCCCAGCTCTTTGGAT 57.393 42.857 0.00 0.00 40.87 3.41
5710 6184 2.353357 TATGCCCAGCTCTTTGGATG 57.647 50.000 0.00 0.00 40.87 3.51
5711 6185 0.396695 ATGCCCAGCTCTTTGGATGG 60.397 55.000 0.00 0.00 40.87 3.51
5712 6186 2.421399 GCCCAGCTCTTTGGATGGC 61.421 63.158 0.00 0.00 40.99 4.40
5718 6192 1.244019 GCTCTTTGGATGGCGTGGTT 61.244 55.000 0.00 0.00 0.00 3.67
5730 6204 1.915614 GCGTGGTTGAGCTGTGGATG 61.916 60.000 0.00 0.00 0.00 3.51
5754 6232 2.225963 AGTAGACTACGCAGACACACAC 59.774 50.000 6.98 0.00 0.00 3.82
5762 6240 1.129251 CGCAGACACACACCATCATTC 59.871 52.381 0.00 0.00 0.00 2.67
5793 6271 1.308998 GTTGGGCAGAATATGGTCCG 58.691 55.000 0.00 0.00 0.00 4.79
5833 6311 4.681978 GAGGACCAACGGCAGCGT 62.682 66.667 0.00 0.00 0.00 5.07
5846 6328 2.032981 CAGCGTTTGTTTGGCTCCT 58.967 52.632 0.00 0.00 34.13 3.69
5847 6329 0.385390 CAGCGTTTGTTTGGCTCCTT 59.615 50.000 0.00 0.00 34.13 3.36
5848 6330 0.385390 AGCGTTTGTTTGGCTCCTTG 59.615 50.000 0.00 0.00 29.31 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 5.648526 TGGAGAAGAAGTAGCAGTAGTAGTG 59.351 44.000 0.17 0.17 0.00 2.74
39 40 3.445805 GCTGGAGAAGAAGTAGCAGTAGT 59.554 47.826 0.00 0.00 34.64 2.73
42 43 1.552792 GGCTGGAGAAGAAGTAGCAGT 59.447 52.381 0.00 0.00 36.15 4.40
44 45 0.905357 GGGCTGGAGAAGAAGTAGCA 59.095 55.000 0.00 0.00 36.15 3.49
45 46 0.179097 CGGGCTGGAGAAGAAGTAGC 60.179 60.000 0.00 0.00 0.00 3.58
138 147 9.903682 CCGAAATAAGACGAGGAAAATATACTA 57.096 33.333 0.00 0.00 0.00 1.82
179 188 5.801350 TCTCACTCACAAACAACAAGAAG 57.199 39.130 0.00 0.00 0.00 2.85
182 191 5.066375 TCCAATCTCACTCACAAACAACAAG 59.934 40.000 0.00 0.00 0.00 3.16
233 263 2.879039 GAAGTAACCGCCGAGTCCCG 62.879 65.000 0.00 0.00 38.18 5.14
237 267 1.211190 GTCGAAGTAACCGCCGAGT 59.789 57.895 0.00 0.00 0.00 4.18
238 268 0.797249 CAGTCGAAGTAACCGCCGAG 60.797 60.000 0.00 0.00 0.00 4.63
255 285 5.558083 GCAATTAACCCGCAAAAGAAAACAG 60.558 40.000 0.00 0.00 0.00 3.16
276 306 3.006967 GGAGAAGAGAACTACCACAGCAA 59.993 47.826 0.00 0.00 0.00 3.91
316 349 2.572104 GCCCCCATTATACCACTAGGAG 59.428 54.545 0.00 0.00 38.69 3.69
458 495 1.226746 AACTGTCGGCGGAAAAAGAG 58.773 50.000 7.21 0.00 0.00 2.85
572 611 7.872113 ATCATCCAAGAAGAAGTGGTAATTC 57.128 36.000 0.00 0.00 36.23 2.17
579 618 5.738909 ACCAGTATCATCCAAGAAGAAGTG 58.261 41.667 0.00 0.00 0.00 3.16
586 625 6.126796 TGCAAATCTACCAGTATCATCCAAGA 60.127 38.462 0.00 0.00 0.00 3.02
593 632 7.182817 ACTTACTGCAAATCTACCAGTATCA 57.817 36.000 0.00 0.00 40.54 2.15
630 669 6.460123 GCAAATCTACCAGGTGTTAATGATGG 60.460 42.308 0.76 0.00 37.07 3.51
766 806 6.226787 TGCAACACCAAGGGTAAATTAATTG 58.773 36.000 0.39 0.00 32.11 2.32
778 818 4.582701 TTGTCTATTTGCAACACCAAGG 57.417 40.909 0.00 0.00 0.00 3.61
830 871 6.636562 ACGGTGGATCATACTACTAAGAAG 57.363 41.667 0.00 0.00 0.00 2.85
835 876 5.308976 TGGTACGGTGGATCATACTACTA 57.691 43.478 0.00 0.00 0.00 1.82
836 877 4.174704 TGGTACGGTGGATCATACTACT 57.825 45.455 0.00 0.00 0.00 2.57
837 878 4.765856 AGATGGTACGGTGGATCATACTAC 59.234 45.833 0.00 0.00 0.00 2.73
871 912 1.133915 AGTAATGCATACCAACCGGGG 60.134 52.381 6.32 0.00 42.91 5.73
984 1025 2.352715 CGACATCTTGCTGTGTGGTAGA 60.353 50.000 0.00 0.00 0.00 2.59
989 1030 1.995484 CTACCGACATCTTGCTGTGTG 59.005 52.381 0.00 0.00 0.00 3.82
1068 1109 0.535335 AGAGATGGAAAGCCGCGTAA 59.465 50.000 4.92 0.00 36.79 3.18
1072 1113 1.869767 CATACAGAGATGGAAAGCCGC 59.130 52.381 0.00 0.00 36.79 6.53
1075 1116 8.662781 TTTATGTACATACAGAGATGGAAAGC 57.337 34.615 15.20 0.00 39.92 3.51
1084 1125 7.803659 ACATCGACGATTTATGTACATACAGAG 59.196 37.037 15.20 9.41 39.92 3.35
1088 1129 9.353353 CAAAACATCGACGATTTATGTACATAC 57.647 33.333 15.20 3.70 33.59 2.39
1105 1146 3.044986 CAAACCTGCTCACAAAACATCG 58.955 45.455 0.00 0.00 0.00 3.84
1106 1147 2.796593 GCAAACCTGCTCACAAAACATC 59.203 45.455 0.00 0.00 45.74 3.06
1190 1231 6.496338 ACTGATTTGTCGGATAAGAAAACC 57.504 37.500 0.00 0.00 0.00 3.27
1354 1395 1.779569 GCCTTTCTTCTCGTTCGTCA 58.220 50.000 0.00 0.00 0.00 4.35
1838 1879 9.553064 CTCTTATTAGGAAGTTGATATGCACTT 57.447 33.333 0.00 0.00 0.00 3.16
1840 1881 8.768955 CACTCTTATTAGGAAGTTGATATGCAC 58.231 37.037 0.00 0.00 0.00 4.57
1868 1909 3.543680 TCTAAGGTAACATCAGCTGCC 57.456 47.619 9.47 2.90 41.41 4.85
2030 2071 2.550180 GGCTCTTTCAACAGGTTCAGAC 59.450 50.000 0.00 0.00 0.00 3.51
2087 2128 6.939132 ATCTTCTCAGCTGGTGATTTATTG 57.061 37.500 15.13 0.00 33.51 1.90
2088 2129 7.201679 CGAAATCTTCTCAGCTGGTGATTTATT 60.202 37.037 23.32 15.12 35.24 1.40
2121 2162 4.574828 GTGAGGATTTACATTACACGCCAT 59.425 41.667 0.00 0.00 0.00 4.40
2159 2200 4.645535 TCTCCACATTTCCAGAAACTGAG 58.354 43.478 0.00 0.57 32.44 3.35
2160 2201 4.705110 TCTCCACATTTCCAGAAACTGA 57.295 40.909 0.00 0.00 32.44 3.41
2372 2413 3.254903 GGACACCACTACCATTTGGAAAC 59.745 47.826 3.01 0.00 38.94 2.78
2431 2472 3.057596 ACCACACAACTTGTCAGTTTGTG 60.058 43.478 19.64 19.64 40.66 3.33
2674 2715 7.446931 TCTGATTAACTGCTGGTTTACAATCAA 59.553 33.333 14.43 8.12 38.66 2.57
2710 2751 0.678950 CTTCCGGGCCACATTTTTGT 59.321 50.000 4.39 0.00 0.00 2.83
2744 2785 1.897802 GTAGGGTTGGAGGAACTTCGA 59.102 52.381 0.00 0.00 41.55 3.71
2772 2813 3.822735 TGCAGAGAATTGAAAACCAGAGG 59.177 43.478 0.00 0.00 0.00 3.69
2775 2816 3.610114 CGGTGCAGAGAATTGAAAACCAG 60.610 47.826 0.00 0.00 0.00 4.00
2891 2932 1.442769 CCAATGACTCAACACGAGGG 58.557 55.000 0.00 0.00 46.98 4.30
2896 2937 6.170506 TGACTATTACCCAATGACTCAACAC 58.829 40.000 0.00 0.00 0.00 3.32
3068 3109 0.179936 GCTCCTCCTCACCTGAATGG 59.820 60.000 0.00 0.00 42.93 3.16
3504 3545 1.333177 AGTTGACTGGTCGAAGCTCT 58.667 50.000 0.00 0.00 0.00 4.09
3687 3728 4.803088 TGCGAAAACAAAAGAATGACAAGG 59.197 37.500 0.00 0.00 0.00 3.61
3693 3734 5.459762 ACATGACTGCGAAAACAAAAGAATG 59.540 36.000 0.00 0.00 0.00 2.67
3734 3775 0.893270 AATACGCACAGGGCAAAGCA 60.893 50.000 0.00 0.00 45.17 3.91
3761 3802 6.635030 ACAAGAGTCAAGGATAAAACCAAC 57.365 37.500 0.00 0.00 0.00 3.77
3949 3990 2.844348 GACCCCTGAAGTTCCTTGGATA 59.156 50.000 0.00 0.00 0.00 2.59
4610 4651 2.740452 GTTCCAAGGATCGACGATACC 58.260 52.381 16.53 15.45 0.00 2.73
4665 4706 2.504032 CCATCGCCGTGGTGGTAT 59.496 61.111 2.77 0.00 41.21 2.73
4728 4769 3.565214 TTCCTGAAGCCACGGCCA 61.565 61.111 2.24 0.00 43.17 5.36
4733 4774 1.815003 CCATTCTGTTCCTGAAGCCAC 59.185 52.381 0.00 0.00 0.00 5.01
4734 4775 1.704628 TCCATTCTGTTCCTGAAGCCA 59.295 47.619 0.00 0.00 0.00 4.75
4735 4776 2.363683 CTCCATTCTGTTCCTGAAGCC 58.636 52.381 0.00 0.00 0.00 4.35
4883 4930 8.568794 TGTATTAGTCGGTAGAAGATTCAGATG 58.431 37.037 0.00 0.00 0.00 2.90
5044 5469 7.976175 AGTGTAACATGTGTATCACTGTAGATG 59.024 37.037 18.05 0.00 41.43 2.90
5081 5506 2.747460 GCAGCCAGCCGATGACAA 60.747 61.111 0.00 0.00 37.23 3.18
5082 5507 3.333899 ATGCAGCCAGCCGATGACA 62.334 57.895 0.00 0.00 44.83 3.58
5105 5530 0.947244 GCTTATGCCAACCAGGATCG 59.053 55.000 0.00 0.00 41.22 3.69
5118 5543 9.064833 ATGTTGACATGCTAGCTTCAGCTTATG 62.065 40.741 17.23 10.76 41.16 1.90
5136 5561 3.576078 AAACTGTCCTCCATGTTGACA 57.424 42.857 8.38 8.38 37.45 3.58
5147 5575 4.405358 TGAAGATTTGGCAAAAACTGTCCT 59.595 37.500 17.70 0.00 29.64 3.85
5153 5581 7.634432 CGTTTAGTTTGAAGATTTGGCAAAAAC 59.366 33.333 17.70 14.70 33.80 2.43
5213 5654 6.500336 AGGTAAAGCCCGGATAGATAGATAA 58.500 40.000 0.73 0.00 38.26 1.75
5215 5656 4.949121 AGGTAAAGCCCGGATAGATAGAT 58.051 43.478 0.73 0.00 38.26 1.98
5219 5660 4.129317 AGTAGGTAAAGCCCGGATAGAT 57.871 45.455 0.73 0.00 38.26 1.98
5223 5664 1.134189 GCAAGTAGGTAAAGCCCGGAT 60.134 52.381 0.73 0.00 38.26 4.18
5224 5665 0.251073 GCAAGTAGGTAAAGCCCGGA 59.749 55.000 0.73 0.00 38.26 5.14
5225 5666 0.252197 AGCAAGTAGGTAAAGCCCGG 59.748 55.000 0.00 0.00 38.26 5.73
5226 5667 1.369625 CAGCAAGTAGGTAAAGCCCG 58.630 55.000 0.00 0.00 38.26 6.13
5227 5668 1.095600 GCAGCAAGTAGGTAAAGCCC 58.904 55.000 0.00 0.00 38.26 5.19
5228 5669 1.468914 GTGCAGCAAGTAGGTAAAGCC 59.531 52.381 0.00 0.00 37.58 4.35
5229 5670 1.128692 CGTGCAGCAAGTAGGTAAAGC 59.871 52.381 0.00 0.00 0.00 3.51
5230 5671 1.732259 CCGTGCAGCAAGTAGGTAAAG 59.268 52.381 7.60 0.00 0.00 1.85
5231 5672 1.071071 ACCGTGCAGCAAGTAGGTAAA 59.929 47.619 7.60 0.00 0.00 2.01
5232 5673 0.682852 ACCGTGCAGCAAGTAGGTAA 59.317 50.000 7.60 0.00 0.00 2.85
5295 5744 1.265905 CGGACCAACAACTAGGCAAAC 59.734 52.381 0.00 0.00 0.00 2.93
5314 5763 1.867233 CGTATCCCATCTGCTTTTCCG 59.133 52.381 0.00 0.00 0.00 4.30
5444 5902 1.247419 TTCGATGCAAATTGCCCGGT 61.247 50.000 22.43 6.11 44.23 5.28
5445 5903 0.102844 ATTCGATGCAAATTGCCCGG 59.897 50.000 22.43 10.32 44.23 5.73
5446 5904 2.772568 TATTCGATGCAAATTGCCCG 57.227 45.000 15.98 17.67 44.23 6.13
5475 5933 2.258286 GGCAATGCCGAACACACC 59.742 61.111 9.14 0.00 39.62 4.16
5502 5960 3.005791 GCTTACTTTTCCACTGCACCATT 59.994 43.478 0.00 0.00 0.00 3.16
5507 5965 1.608590 GCTGCTTACTTTTCCACTGCA 59.391 47.619 0.00 0.00 0.00 4.41
5509 5967 2.351157 GCTGCTGCTTACTTTTCCACTG 60.351 50.000 8.53 0.00 36.03 3.66
5544 6018 2.871133 TGACTATAACGCACAAGACGG 58.129 47.619 0.00 0.00 34.00 4.79
5557 6031 5.360999 CAGATCACAGGTGGACTTGACTATA 59.639 44.000 0.00 0.00 0.00 1.31
5558 6032 4.161189 CAGATCACAGGTGGACTTGACTAT 59.839 45.833 0.00 0.00 0.00 2.12
5683 6157 2.659428 AGAGCTGGGCATAATTTCCAC 58.341 47.619 0.00 0.00 0.00 4.02
5705 6179 2.359850 GCTCAACCACGCCATCCA 60.360 61.111 0.00 0.00 0.00 3.41
5706 6180 2.045926 AGCTCAACCACGCCATCC 60.046 61.111 0.00 0.00 0.00 3.51
5707 6181 1.672356 ACAGCTCAACCACGCCATC 60.672 57.895 0.00 0.00 0.00 3.51
5708 6182 1.968017 CACAGCTCAACCACGCCAT 60.968 57.895 0.00 0.00 0.00 4.40
5709 6183 2.591429 CACAGCTCAACCACGCCA 60.591 61.111 0.00 0.00 0.00 5.69
5710 6184 3.357079 CCACAGCTCAACCACGCC 61.357 66.667 0.00 0.00 0.00 5.68
5711 6185 1.672356 ATCCACAGCTCAACCACGC 60.672 57.895 0.00 0.00 0.00 5.34
5712 6186 0.320683 TCATCCACAGCTCAACCACG 60.321 55.000 0.00 0.00 0.00 4.94
5718 6192 3.020274 GTCTACTCTCATCCACAGCTCA 58.980 50.000 0.00 0.00 0.00 4.26
5730 6204 3.001414 TGTGTCTGCGTAGTCTACTCTC 58.999 50.000 8.37 0.00 0.00 3.20
5754 6232 1.325355 GCAGGGGACATGAATGATGG 58.675 55.000 0.00 0.00 36.23 3.51
5833 6311 3.368948 GGACAAACAAGGAGCCAAACAAA 60.369 43.478 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.