Multiple sequence alignment - TraesCS5A01G156500

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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 TraesCS5A01G156500 chr5A 100.000 8206 0 0 1 8206 335304511 335296306 0.000000e+00 15154
1 TraesCS5A01G156500 chr5D 94.748 5807 181 31 2467 8206 252626383 252620634 0.000000e+00 8920
2 TraesCS5A01G156500 chr5D 94.466 2620 100 17 1 2602 252628976 252626384 0.000000e+00 3993
3 TraesCS5A01G156500 chr5B 96.881 4232 110 13 3822 8040 285047082 285042860 0.000000e+00 7064
4 TraesCS5A01G156500 chr5B 94.439 3830 125 31 1 3797 285050850 285047076 0.000000e+00 5812
5 TraesCS5A01G156500 chr5B 89.320 103 7 2 8104 8206 285042857 285042759 8.650000e-25 126


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 TraesCS5A01G156500 chr5A 335296306 335304511 8205 True 15154.0 15154 100.000000 1 8206 1 chr5A.!!$R1 8205
1 TraesCS5A01G156500 chr5D 252620634 252628976 8342 True 6456.5 8920 94.607000 1 8206 2 chr5D.!!$R1 8205
2 TraesCS5A01G156500 chr5B 285042759 285050850 8091 True 4334.0 7064 93.546667 1 8206 3 chr5B.!!$R1 8205

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
361 369 0.103208 AAAAACACCATTTGGCGCGA 59.897 45.000 12.10 0.0 39.32 5.87 F
904 934 1.103987 TTCGATCAGAGAGAGCCCCG 61.104 60.000 0.00 0.0 0.00 5.73 F
1686 1722 1.002773 ACGTGTGACAGGTAATTCCCC 59.997 52.381 9.41 0.0 36.75 4.81 F
2562 2738 0.466124 GACCGAGGGCTGCTAGAATT 59.534 55.000 0.00 0.0 0.00 2.17 F
3661 3851 1.229428 TCTTTGTTCTGCTTGCTCCG 58.771 50.000 0.00 0.0 0.00 4.63 F
3694 3884 1.272807 AAGCATGCAAATCCTGGCTT 58.727 45.000 21.98 0.0 36.82 4.35 F
5444 5652 1.270625 ACCATGTTGAATGGACGTCGT 60.271 47.619 9.92 0.0 41.64 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1231 0.719465 CGCGTGTGTAAGGTCAATCC 59.281 55.000 0.00 0.00 0.00 3.01 R
2226 2266 1.425412 ACACGCTGATACCGTTGTTC 58.575 50.000 0.00 0.00 36.69 3.18 R
3644 3834 0.944386 GACGGAGCAAGCAGAACAAA 59.056 50.000 0.00 0.00 0.00 2.83 R
3838 4041 0.381801 CCAAATCCATCGAAAGGCGG 59.618 55.000 2.54 0.00 41.33 6.13 R
5444 5652 0.941963 ACATAGGTCCTAGCCCCTCA 59.058 55.000 4.57 0.00 32.08 3.86 R
5812 6020 7.308469 GGGATAGCAAGCTAAAATTCTGATCAG 60.308 40.741 17.07 17.07 31.73 2.90 R
7354 7610 0.904649 AACTCAGGATCATGTCGGCA 59.095 50.000 7.33 0.00 0.00 5.69 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
32 33 3.093057 GTTGTAGAGAAGAGGCCAGAGA 58.907 50.000 5.01 0.00 0.00 3.10
75 76 7.497909 AGTCCACGAGAAAGAAAATGTTAAAGA 59.502 33.333 0.00 0.00 0.00 2.52
93 94 8.559536 TGTTAAAGAATTCCATATCTCGAATGC 58.440 33.333 0.65 0.00 0.00 3.56
118 119 1.139654 CAATCCCATTCTCTCTGGCGA 59.860 52.381 0.00 0.00 32.08 5.54
138 139 3.469863 AAGCAACCACGAAGGCGGA 62.470 57.895 0.00 0.00 43.14 5.54
140 141 2.030562 CAACCACGAAGGCGGAGT 59.969 61.111 0.00 0.00 43.14 3.85
141 142 2.030562 AACCACGAAGGCGGAGTG 59.969 61.111 0.00 3.02 43.14 3.51
221 229 3.609103 AATTTCAATAGCATCGACGCC 57.391 42.857 0.00 0.00 0.00 5.68
250 258 2.436646 TCGACCCCGACCTCGTAC 60.437 66.667 0.00 0.00 40.30 3.67
259 267 0.247974 CGACCTCGTACCGACATCAC 60.248 60.000 0.00 0.00 34.11 3.06
273 281 4.000325 CGACATCACCAATTAGTCAACCA 59.000 43.478 0.00 0.00 0.00 3.67
302 310 2.038033 ACCCGATATAACCAATCACCCG 59.962 50.000 0.00 0.00 0.00 5.28
332 340 6.096846 AGGGCGACAAATATAAGAAAAAGCAT 59.903 34.615 0.00 0.00 0.00 3.79
361 369 0.103208 AAAAACACCATTTGGCGCGA 59.897 45.000 12.10 0.00 39.32 5.87
517 532 2.772287 TGCACGTTCAACATACCATGA 58.228 42.857 0.00 0.00 0.00 3.07
659 689 4.008933 GGAGCGAGTGGTGGTGCT 62.009 66.667 0.00 0.00 41.11 4.40
660 690 2.031163 GAGCGAGTGGTGGTGCTT 59.969 61.111 0.00 0.00 37.91 3.91
902 932 1.959985 TGATTCGATCAGAGAGAGCCC 59.040 52.381 0.00 0.00 33.59 5.19
903 933 1.272212 GATTCGATCAGAGAGAGCCCC 59.728 57.143 0.00 0.00 0.00 5.80
904 934 1.103987 TTCGATCAGAGAGAGCCCCG 61.104 60.000 0.00 0.00 0.00 5.73
905 935 2.733945 GATCAGAGAGAGCCCCGC 59.266 66.667 0.00 0.00 0.00 6.13
906 936 2.841988 ATCAGAGAGAGCCCCGCC 60.842 66.667 0.00 0.00 0.00 6.13
907 937 3.686098 ATCAGAGAGAGCCCCGCCA 62.686 63.158 0.00 0.00 0.00 5.69
908 938 4.154347 CAGAGAGAGCCCCGCCAC 62.154 72.222 0.00 0.00 0.00 5.01
1028 1058 2.122189 CCTGATCCCTCCTCCCCC 60.122 72.222 0.00 0.00 0.00 5.40
1110 1140 5.356426 GCCCCTGCGTTTATTAATTTGATT 58.644 37.500 0.00 0.00 0.00 2.57
1113 1143 7.038659 CCCCTGCGTTTATTAATTTGATTTGA 58.961 34.615 0.00 0.00 0.00 2.69
1114 1144 7.710475 CCCCTGCGTTTATTAATTTGATTTGAT 59.290 33.333 0.00 0.00 0.00 2.57
1115 1145 8.542132 CCCTGCGTTTATTAATTTGATTTGATG 58.458 33.333 0.00 0.00 0.00 3.07
1116 1146 9.086336 CCTGCGTTTATTAATTTGATTTGATGT 57.914 29.630 0.00 0.00 0.00 3.06
1117 1147 9.890085 CTGCGTTTATTAATTTGATTTGATGTG 57.110 29.630 0.00 0.00 0.00 3.21
1201 1231 1.260561 CCGATTTGTTAGAATCCCGCG 59.739 52.381 0.00 0.00 33.45 6.46
1214 1244 1.219664 CCCGCGGATTGACCTTACA 59.780 57.895 30.73 0.00 36.31 2.41
1274 1304 1.922447 TCCTGTAGCCATGGGATTGTT 59.078 47.619 15.13 0.00 0.00 2.83
1682 1718 1.202710 TGCCACGTGTGACAGGTAATT 60.203 47.619 15.65 0.00 31.07 1.40
1686 1722 1.002773 ACGTGTGACAGGTAATTCCCC 59.997 52.381 9.41 0.00 36.75 4.81
1687 1723 1.734163 GTGTGACAGGTAATTCCCCG 58.266 55.000 0.00 0.00 36.75 5.73
1688 1724 1.002773 GTGTGACAGGTAATTCCCCGT 59.997 52.381 0.00 0.00 36.75 5.28
1692 1728 1.829222 GACAGGTAATTCCCCGTCTCA 59.171 52.381 0.00 0.00 36.66 3.27
1740 1776 3.515286 CGAGGGCTGCCATGCTTG 61.515 66.667 22.05 8.59 0.00 4.01
1807 1843 6.427853 CACAAACTCTTTCCTCATGTATCACA 59.572 38.462 0.00 0.00 0.00 3.58
1836 1872 3.304391 GCCTTGCAACTTACGTTCATTCA 60.304 43.478 0.00 0.00 0.00 2.57
2102 2139 6.591834 GTGACACTGTAAATTGTAGCTCTGAT 59.408 38.462 0.00 0.00 0.00 2.90
2226 2266 1.081892 CTTCCCAGCAGACATCAACG 58.918 55.000 0.00 0.00 0.00 4.10
2317 2357 6.202762 GTCCGATGCTACAATCACATTGATAA 59.797 38.462 3.24 0.00 42.83 1.75
2337 2377 8.734218 TGATAATATCGAGTGACTACTATCCC 57.266 38.462 0.00 0.00 37.25 3.85
2382 2422 4.381411 CTGTAGCCTTTAATACCTGCCTC 58.619 47.826 0.00 0.00 0.00 4.70
2436 2476 4.523083 AGTAAAGTGAGAGTTTGGTTGCA 58.477 39.130 0.00 0.00 0.00 4.08
2511 2551 3.587061 TGACATGTCCTTGATACAACCCT 59.413 43.478 22.85 0.00 0.00 4.34
2562 2738 0.466124 GACCGAGGGCTGCTAGAATT 59.534 55.000 0.00 0.00 0.00 2.17
2567 2743 3.499918 CCGAGGGCTGCTAGAATTTTATG 59.500 47.826 0.00 0.00 0.00 1.90
2638 2814 5.646577 AGCTGTCTAGTGTCGTAAAATCT 57.353 39.130 0.00 0.00 0.00 2.40
2789 2965 6.295719 TCAGTTTCCTTAGGGTAGATTGTC 57.704 41.667 0.00 0.00 0.00 3.18
2815 2991 4.807304 TCTTCGGTGAGTACAAAGTTTCAC 59.193 41.667 0.00 0.00 39.29 3.18
2816 2992 4.126208 TCGGTGAGTACAAAGTTTCACA 57.874 40.909 11.43 0.00 41.22 3.58
2889 3065 5.959618 TGATGTACCTAGTCATATGGTCG 57.040 43.478 2.13 0.00 35.48 4.79
2898 3074 7.378966 ACCTAGTCATATGGTCGTAATGATTG 58.621 38.462 2.13 0.00 32.60 2.67
2944 3120 5.452078 TTGAAATAACTTGAGGCTGTTGG 57.548 39.130 0.00 0.00 0.00 3.77
2954 3130 2.271800 GAGGCTGTTGGATGAAGTACG 58.728 52.381 0.00 0.00 0.00 3.67
3065 3243 3.394719 GAGTGAAAACTCTGGTGGACTC 58.605 50.000 0.00 0.00 34.12 3.36
3442 3631 5.581126 TGGTACAATTGATGCTTCATTCC 57.419 39.130 13.59 0.00 31.92 3.01
3661 3851 1.229428 TCTTTGTTCTGCTTGCTCCG 58.771 50.000 0.00 0.00 0.00 4.63
3691 3881 2.034305 GCTCTAAGCATGCAAATCCTGG 59.966 50.000 21.98 3.20 41.89 4.45
3692 3882 2.026641 TCTAAGCATGCAAATCCTGGC 58.973 47.619 21.98 0.00 0.00 4.85
3693 3883 2.029623 CTAAGCATGCAAATCCTGGCT 58.970 47.619 21.98 0.00 0.00 4.75
3694 3884 1.272807 AAGCATGCAAATCCTGGCTT 58.727 45.000 21.98 0.00 36.82 4.35
3695 3885 2.148446 AGCATGCAAATCCTGGCTTA 57.852 45.000 21.98 0.00 0.00 3.09
3696 3886 2.674420 AGCATGCAAATCCTGGCTTAT 58.326 42.857 21.98 0.00 0.00 1.73
3697 3887 3.836146 AGCATGCAAATCCTGGCTTATA 58.164 40.909 21.98 0.00 0.00 0.98
3698 3888 4.413760 AGCATGCAAATCCTGGCTTATAT 58.586 39.130 21.98 0.00 0.00 0.86
3699 3889 4.219944 AGCATGCAAATCCTGGCTTATATG 59.780 41.667 21.98 0.00 0.00 1.78
3700 3890 4.219070 GCATGCAAATCCTGGCTTATATGA 59.781 41.667 14.21 0.00 0.00 2.15
3701 3891 5.105473 GCATGCAAATCCTGGCTTATATGAT 60.105 40.000 14.21 0.00 0.00 2.45
3802 4005 4.917906 AGAAGCTCCTGGTCTAATGTTT 57.082 40.909 0.00 0.00 0.00 2.83
3806 4009 2.619074 GCTCCTGGTCTAATGTTTGGCT 60.619 50.000 0.00 0.00 0.00 4.75
3838 4041 5.128991 ACACTAATGGCCTAGTAGGAAGTTC 59.871 44.000 21.02 1.17 37.67 3.01
3839 4042 4.654724 ACTAATGGCCTAGTAGGAAGTTCC 59.345 45.833 21.02 14.54 37.67 3.62
3866 4069 6.265196 CCTTTCGATGGATTTGGATTTGGATA 59.735 38.462 0.00 0.00 0.00 2.59
3910 4113 9.636789 ACCTACTTTTGGTAGTTTGATTTTAGT 57.363 29.630 0.00 0.00 44.66 2.24
4253 4461 6.071896 GCTACACTAATGGCCTTCTTTTTCTT 60.072 38.462 3.32 0.00 0.00 2.52
4322 4530 2.670148 GGGAGGTCCACGCTTCCAT 61.670 63.158 0.00 0.00 37.91 3.41
4341 4549 4.655649 TCCATCAGCTACTTCATGGTATGT 59.344 41.667 0.00 0.00 37.62 2.29
4378 4586 5.549347 TGTTCTGCCACATTTAAAATGCAT 58.451 33.333 0.00 0.00 0.00 3.96
4674 4882 2.592102 AACCCAAGCTGTGACATCAT 57.408 45.000 0.00 0.00 0.00 2.45
4797 5005 8.560355 AAAGCAAGTTGTAAATGGAAAGTTTT 57.440 26.923 4.48 0.00 0.00 2.43
4955 5163 6.003950 TGGTTCTGTTTTAAAGAGGGATGAG 58.996 40.000 2.04 0.00 0.00 2.90
4963 5171 2.649742 AAGAGGGATGAGGGTGAGAA 57.350 50.000 0.00 0.00 0.00 2.87
5050 5258 8.023021 AGCAAAGATACAGTTCATAGTATGGA 57.977 34.615 10.26 0.00 31.45 3.41
5089 5297 1.949257 CAGTTCCCAACACTTCCGC 59.051 57.895 0.00 0.00 0.00 5.54
5102 5310 3.179888 TTCCGCCGTGGTGCCTTTA 62.180 57.895 0.00 0.00 39.52 1.85
5414 5622 5.009610 GCAAACCAGGTTATCTTCAACTGAA 59.990 40.000 4.87 0.00 0.00 3.02
5444 5652 1.270625 ACCATGTTGAATGGACGTCGT 60.271 47.619 9.92 0.00 41.64 4.34
5812 6020 5.125100 TCATCTTTCAGAAATTGTGGCAC 57.875 39.130 11.55 11.55 0.00 5.01
5887 6095 0.458370 GGTGTTGCATTCCAATCGCC 60.458 55.000 0.00 0.00 35.55 5.54
5963 6172 4.499188 GCTGGTGAGTATGATACTTGCGTA 60.499 45.833 6.56 0.00 39.59 4.42
6000 6209 6.096846 ACTGAACAGGAAAGTATTTTTGTGCT 59.903 34.615 6.76 0.00 39.27 4.40
6131 6340 4.148079 TGGGTAAACATTGCAACTCATGA 58.852 39.130 0.00 0.00 0.00 3.07
6209 6429 2.009051 CAATGGCTCGTTGCTGATGTA 58.991 47.619 3.58 0.00 42.39 2.29
6593 6849 5.763204 TCCACATTCTCAGGTTTGTTTACTC 59.237 40.000 0.00 0.00 0.00 2.59
6601 6857 5.352264 TCAGGTTTGTTTACTCCCCCTATA 58.648 41.667 0.00 0.00 0.00 1.31
6606 6862 7.837689 AGGTTTGTTTACTCCCCCTATATTTTC 59.162 37.037 0.00 0.00 0.00 2.29
6734 6990 6.187682 TCAACCTCAGATATCTAGACACACA 58.812 40.000 4.54 0.00 0.00 3.72
6825 7081 5.683876 TTCAGGGTTGGATTTGAAAAACA 57.316 34.783 0.00 0.00 0.00 2.83
7533 7789 1.603802 CCGGCACATTAATGATCGCTT 59.396 47.619 22.16 0.00 0.00 4.68
7534 7790 2.602933 CCGGCACATTAATGATCGCTTG 60.603 50.000 22.16 9.47 0.00 4.01
7655 7917 2.469952 AGCTGGCTTGAGAAGAGAGAT 58.530 47.619 0.00 0.00 0.00 2.75
7687 7949 4.608445 GCGTGTATGTTCTATTTCGCCATC 60.608 45.833 0.00 0.00 37.14 3.51
7771 8033 0.321653 CTTGCCGCTGGTAGGTCTTT 60.322 55.000 0.00 0.00 0.00 2.52
7772 8034 0.109723 TTGCCGCTGGTAGGTCTTTT 59.890 50.000 0.00 0.00 0.00 2.27
7888 8151 4.589216 TTTGGCATCAAACTGAAGGAAG 57.411 40.909 0.00 0.00 37.89 3.46
7920 8183 9.990360 TGACTACATTTGATGTTTGTTACTAGA 57.010 29.630 0.00 0.00 41.63 2.43
8012 8286 6.537355 AGTTTTGAGATGAACATTCCTCTGA 58.463 36.000 4.39 0.00 33.23 3.27
8064 8338 5.698832 TCTTATTTGGCGTGTGATTTTGAG 58.301 37.500 0.00 0.00 0.00 3.02
8074 8348 2.223688 TGTGATTTTGAGTGCAAACCCG 60.224 45.455 0.00 0.00 43.27 5.28
8078 8352 0.313672 TTTGAGTGCAAACCCGCATC 59.686 50.000 0.00 0.00 45.26 3.91
8084 8358 1.675641 GCAAACCCGCATCCTGTCT 60.676 57.895 0.00 0.00 0.00 3.41
8085 8359 0.392461 GCAAACCCGCATCCTGTCTA 60.392 55.000 0.00 0.00 0.00 2.59
8111 8385 2.852449 TCTATTTGCCCCATCTCCTTGT 59.148 45.455 0.00 0.00 0.00 3.16
8113 8387 0.039618 TTTGCCCCATCTCCTTGTCC 59.960 55.000 0.00 0.00 0.00 4.02
8169 8443 6.925165 AGTTTGAAACCAATATGAAGCACAAG 59.075 34.615 4.14 0.00 0.00 3.16
8180 8454 4.637483 TGAAGCACAAGAACAAGGAAAG 57.363 40.909 0.00 0.00 0.00 2.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 4.777896 TGGCCTCTTCTCTACAACTTATGT 59.222 41.667 3.32 0.00 46.36 2.29
32 33 5.705905 CGTGGACTTTTCTTTCCCTCTTTAT 59.294 40.000 0.00 0.00 0.00 1.40
75 76 4.371624 TGGGCATTCGAGATATGGAATT 57.628 40.909 0.00 0.00 30.76 2.17
93 94 3.498121 CCAGAGAGAATGGGATTGATGGG 60.498 52.174 0.00 0.00 33.94 4.00
118 119 2.542907 CGCCTTCGTGGTTGCTTGT 61.543 57.895 0.00 0.00 38.35 3.16
138 139 2.779755 TGAACCTTGTGTGTGTCACT 57.220 45.000 4.27 0.00 46.27 3.41
140 141 3.680490 TCTTTGAACCTTGTGTGTGTCA 58.320 40.909 0.00 0.00 0.00 3.58
141 142 4.695217 TTCTTTGAACCTTGTGTGTGTC 57.305 40.909 0.00 0.00 0.00 3.67
149 150 4.829064 TCATCGGTTTCTTTGAACCTTG 57.171 40.909 5.38 3.59 45.53 3.61
151 152 3.253432 GCTTCATCGGTTTCTTTGAACCT 59.747 43.478 5.38 0.00 45.53 3.50
152 153 3.565516 GCTTCATCGGTTTCTTTGAACC 58.434 45.455 0.00 0.00 44.51 3.62
153 154 3.059188 TCGCTTCATCGGTTTCTTTGAAC 60.059 43.478 0.00 0.00 0.00 3.18
154 155 3.135225 TCGCTTCATCGGTTTCTTTGAA 58.865 40.909 0.00 0.00 0.00 2.69
155 156 2.761559 TCGCTTCATCGGTTTCTTTGA 58.238 42.857 0.00 0.00 0.00 2.69
156 157 3.536158 TTCGCTTCATCGGTTTCTTTG 57.464 42.857 0.00 0.00 0.00 2.77
157 158 3.058224 CCTTTCGCTTCATCGGTTTCTTT 60.058 43.478 0.00 0.00 0.00 2.52
165 173 5.718649 TTTATCTTCCTTTCGCTTCATCG 57.281 39.130 0.00 0.00 0.00 3.84
221 229 1.578583 GGGGTCGACGAATATTGGTG 58.421 55.000 9.92 1.47 0.00 4.17
250 258 3.374058 GGTTGACTAATTGGTGATGTCGG 59.626 47.826 0.00 0.00 0.00 4.79
259 267 6.447162 GGTTTTCTCTTGGTTGACTAATTGG 58.553 40.000 0.00 0.00 0.00 3.16
273 281 7.282450 GTGATTGGTTATATCGGGTTTTCTCTT 59.718 37.037 0.00 0.00 0.00 2.85
302 310 4.448210 TCTTATATTTGTCGCCCTCCAAC 58.552 43.478 0.00 0.00 0.00 3.77
346 354 0.103208 TTTTTCGCGCCAAATGGTGT 59.897 45.000 14.07 0.00 46.99 4.16
361 369 4.373348 TTGTTGTTTCCGACCGATTTTT 57.627 36.364 0.00 0.00 0.00 1.94
465 473 1.383523 TTGGTGCAAACGTCACATGA 58.616 45.000 0.00 0.00 36.22 3.07
470 478 2.425312 AGTCATTTTGGTGCAAACGTCA 59.575 40.909 0.00 0.00 32.79 4.35
517 532 7.290948 TGGAACTAGATCATGTAGATTGGATGT 59.709 37.037 0.00 0.00 37.00 3.06
659 689 1.976474 GAAGGGATTGCCGCACCAA 60.976 57.895 0.00 0.00 33.83 3.67
660 690 2.361104 GAAGGGATTGCCGCACCA 60.361 61.111 0.00 0.00 33.83 4.17
765 795 6.149633 TGAGTCGATGTGTATGTATGTATGC 58.850 40.000 0.00 0.00 0.00 3.14
1040 1070 2.286418 CCAAATCTGCGCGGAAGATTAC 60.286 50.000 25.06 0.00 42.26 1.89
1110 1140 4.275689 GGATTGCATCGGATTACACATCAA 59.724 41.667 0.00 0.00 0.00 2.57
1113 1143 3.817084 CTGGATTGCATCGGATTACACAT 59.183 43.478 0.00 0.00 0.00 3.21
1114 1144 3.205338 CTGGATTGCATCGGATTACACA 58.795 45.455 0.00 0.00 0.00 3.72
1115 1145 2.031682 GCTGGATTGCATCGGATTACAC 60.032 50.000 0.00 0.00 0.00 2.90
1116 1146 2.158769 AGCTGGATTGCATCGGATTACA 60.159 45.455 0.00 0.00 34.99 2.41
1117 1147 2.481952 GAGCTGGATTGCATCGGATTAC 59.518 50.000 0.00 0.00 34.99 1.89
1201 1231 0.719465 CGCGTGTGTAAGGTCAATCC 59.281 55.000 0.00 0.00 0.00 3.01
1263 1293 6.845758 AATCCATATAGCAACAATCCCATG 57.154 37.500 0.00 0.00 0.00 3.66
1274 1304 7.180051 AGGACCAAAAACAAAATCCATATAGCA 59.820 33.333 0.00 0.00 0.00 3.49
1682 1718 1.766496 AGTGAAAGTTTGAGACGGGGA 59.234 47.619 0.00 0.00 0.00 4.81
1686 1722 7.518161 TGCATATAAAGTGAAAGTTTGAGACG 58.482 34.615 0.00 0.00 40.30 4.18
1687 1723 9.846248 AATGCATATAAAGTGAAAGTTTGAGAC 57.154 29.630 0.00 0.00 40.30 3.36
1740 1776 1.776034 GAATCTCCGGTTGATGGCGC 61.776 60.000 0.00 0.00 0.00 6.53
1807 1843 4.882671 CGTAAGTTGCAAGGCTATCATT 57.117 40.909 0.00 0.00 0.00 2.57
1836 1872 3.704566 TCTGCTACCGTTCTGTATCCATT 59.295 43.478 0.00 0.00 0.00 3.16
2049 2085 7.549488 CGTCCTAACAGAATCCAAATCTTAACT 59.451 37.037 0.00 0.00 0.00 2.24
2050 2086 7.548075 TCGTCCTAACAGAATCCAAATCTTAAC 59.452 37.037 0.00 0.00 0.00 2.01
2051 2087 7.617225 TCGTCCTAACAGAATCCAAATCTTAA 58.383 34.615 0.00 0.00 0.00 1.85
2052 2088 7.093465 ACTCGTCCTAACAGAATCCAAATCTTA 60.093 37.037 0.00 0.00 0.00 2.10
2073 2110 4.684703 GCTACAATTTACAGTGTCACTCGT 59.315 41.667 1.37 7.78 32.24 4.18
2102 2139 8.588290 AAACAAGGATAATAGTAATGTTGGCA 57.412 30.769 0.00 0.00 30.64 4.92
2226 2266 1.425412 ACACGCTGATACCGTTGTTC 58.575 50.000 0.00 0.00 36.69 3.18
2317 2357 5.014333 AGGTGGGATAGTAGTCACTCGATAT 59.986 44.000 0.00 0.00 36.14 1.63
2436 2476 8.664669 ACTTTTGATGGAAAACCACCTAATAT 57.335 30.769 0.00 0.00 30.13 1.28
2562 2738 8.363390 TCAAATGTTCTTTACACATGCCATAAA 58.637 29.630 0.00 0.00 40.19 1.40
2567 2743 6.473455 GCTATCAAATGTTCTTTACACATGCC 59.527 38.462 0.00 0.00 40.19 4.40
2652 2828 9.331282 ACTGAAACAGGCACTTCTATATTTATC 57.669 33.333 0.00 0.00 34.60 1.75
2713 2889 4.935205 TCAGTAAACATGGGAAATGTCTCG 59.065 41.667 0.00 0.00 0.00 4.04
2789 2965 3.378339 ACTTTGTACTCACCGAAGAACG 58.622 45.455 0.00 0.00 42.18 3.95
2915 3091 6.012745 AGCCTCAAGTTATTTCAAAGTCCAT 58.987 36.000 0.00 0.00 0.00 3.41
2925 3101 5.324409 TCATCCAACAGCCTCAAGTTATTT 58.676 37.500 0.00 0.00 0.00 1.40
2944 3120 6.663944 AACTGAATAAAGGCGTACTTCATC 57.336 37.500 0.00 0.00 38.85 2.92
3022 3200 3.621558 GTGGGTCTCCTTATTTTCAGGG 58.378 50.000 0.00 0.00 31.50 4.45
3065 3243 3.384146 AGCTGAGTAGACATGATGGACAG 59.616 47.826 0.00 3.19 0.00 3.51
3442 3631 4.175787 AGAGTACTGGTAAAAGCTGTCG 57.824 45.455 0.00 0.00 0.00 4.35
3590 3780 6.499350 AGGAAGTCAAGTGTTACCTGGTATAA 59.501 38.462 7.50 0.00 0.00 0.98
3644 3834 0.944386 GACGGAGCAAGCAGAACAAA 59.056 50.000 0.00 0.00 0.00 2.83
3802 4005 2.771943 CCATTAGTGTAGGGAGAAGCCA 59.228 50.000 0.00 0.00 38.95 4.75
3806 4009 3.130734 AGGCCATTAGTGTAGGGAGAA 57.869 47.619 5.01 0.00 0.00 2.87
3838 4041 0.381801 CCAAATCCATCGAAAGGCGG 59.618 55.000 2.54 0.00 41.33 6.13
3839 4042 1.378531 TCCAAATCCATCGAAAGGCG 58.621 50.000 2.54 0.00 42.69 5.52
4253 4461 0.403655 TGGCCTGTGGTATTCTGCAA 59.596 50.000 3.32 0.00 0.00 4.08
4322 4530 5.189736 AGGAAACATACCATGAAGTAGCTGA 59.810 40.000 0.00 0.00 0.00 4.26
4341 4549 2.567615 GCAGAACAGTCTAGGGAGGAAA 59.432 50.000 0.00 0.00 30.85 3.13
4378 4586 6.412362 ACACACCCAAATTTAGCAATACAA 57.588 33.333 0.00 0.00 0.00 2.41
4457 4665 9.507329 TCTGCTTTTGATTTAGTAAGAGATTGT 57.493 29.630 0.00 0.00 0.00 2.71
4479 4687 2.221981 GTGAATTACTATGCGCCTCTGC 59.778 50.000 4.18 0.00 0.00 4.26
4674 4882 3.830178 TCTATGTCCAACGAAGACTCCAA 59.170 43.478 0.00 0.00 35.21 3.53
4797 5005 3.573967 GGTTTTGAGGATGCTGAAGGAAA 59.426 43.478 0.00 0.00 0.00 3.13
4955 5163 1.132500 CCCCAGGTCTATTCTCACCC 58.868 60.000 0.00 0.00 32.45 4.61
4963 5171 2.225650 ACTTCTGTGTCCCCAGGTCTAT 60.226 50.000 0.00 0.00 33.14 1.98
5050 5258 1.756538 CACCCAGCTGTTGGTTTTCTT 59.243 47.619 13.81 0.00 46.25 2.52
5089 5297 1.600023 TTGACTTAAAGGCACCACGG 58.400 50.000 0.00 0.00 29.12 4.94
5102 5310 6.834168 TGTTCCTTCTTCAAACTTTGACTT 57.166 33.333 3.56 0.00 39.87 3.01
5414 5622 5.716228 TCCATTCAACATGGTAGAAGCATTT 59.284 36.000 0.00 0.00 40.06 2.32
5444 5652 0.941963 ACATAGGTCCTAGCCCCTCA 59.058 55.000 4.57 0.00 32.08 3.86
5812 6020 7.308469 GGGATAGCAAGCTAAAATTCTGATCAG 60.308 40.741 17.07 17.07 31.73 2.90
5887 6095 4.216257 TGCTCTTTGAAAAATCTTCCTCCG 59.784 41.667 0.00 0.00 0.00 4.63
5963 6172 7.721399 ACTTTCCTGTTCAGTGAAATACAGAAT 59.279 33.333 20.32 3.34 40.24 2.40
6000 6209 7.450074 TCTATTAGAAAGAACTTCCAACTGCA 58.550 34.615 0.00 0.00 34.21 4.41
6080 6289 4.645762 TGAAAAATACTGCAGTGCACAA 57.354 36.364 29.57 9.38 33.79 3.33
6175 6395 6.208644 ACGAGCCATTGCACATATAAAAATC 58.791 36.000 0.00 0.00 41.13 2.17
6176 6396 6.147864 ACGAGCCATTGCACATATAAAAAT 57.852 33.333 0.00 0.00 41.13 1.82
6177 6397 5.574891 ACGAGCCATTGCACATATAAAAA 57.425 34.783 0.00 0.00 41.13 1.94
6178 6398 5.339177 CAACGAGCCATTGCACATATAAAA 58.661 37.500 0.00 0.00 41.13 1.52
6179 6399 4.919206 CAACGAGCCATTGCACATATAAA 58.081 39.130 0.00 0.00 41.13 1.40
6180 6400 4.550577 CAACGAGCCATTGCACATATAA 57.449 40.909 0.00 0.00 41.13 0.98
6209 6429 3.071874 TGAAGACCCTGCGAATGAAAT 57.928 42.857 0.00 0.00 0.00 2.17
6593 6849 4.104738 TGGAGAAGCAGAAAATATAGGGGG 59.895 45.833 0.00 0.00 0.00 5.40
6601 6857 5.612725 TTGGTTTTGGAGAAGCAGAAAAT 57.387 34.783 0.00 0.00 38.16 1.82
6606 6862 9.657419 AAATTATTATTGGTTTTGGAGAAGCAG 57.343 29.630 0.00 0.00 38.16 4.24
6734 6990 8.844244 GCAGGATCAATAAATTCTATGTCACTT 58.156 33.333 0.00 0.00 0.00 3.16
6854 7110 9.606631 AGTAGTTGAAGTCTTGGATCATTATTC 57.393 33.333 0.00 0.00 0.00 1.75
6972 7228 1.296715 GTGGCAGAAGTCGGGATGT 59.703 57.895 0.00 0.00 0.00 3.06
7124 7380 6.904626 AGCTTCAGTTGGATATAACATCCTT 58.095 36.000 4.98 0.00 38.95 3.36
7354 7610 0.904649 AACTCAGGATCATGTCGGCA 59.095 50.000 7.33 0.00 0.00 5.69
7362 7618 7.364232 GGAAGATCTAGTTCAAACTCAGGATCA 60.364 40.741 21.52 0.40 39.40 2.92
7410 7666 9.979578 GTATATCAAATTGGTGGATAAAATGCA 57.020 29.630 0.00 0.00 0.00 3.96
7484 7740 1.202245 GCAACGTTCACAACACCACAT 60.202 47.619 0.00 0.00 0.00 3.21
7533 7789 1.341482 TGACCAAGCAAGGGAACAACA 60.341 47.619 0.00 0.00 0.00 3.33
7534 7790 1.398692 TGACCAAGCAAGGGAACAAC 58.601 50.000 0.00 0.00 0.00 3.32
7687 7949 5.339611 GCAAGAAAACATTTACACAGCTACG 59.660 40.000 0.00 0.00 0.00 3.51
7734 7996 5.794945 CGGCAAGTTACAAAATCATGTACAG 59.205 40.000 0.33 0.00 35.60 2.74
7744 8006 1.394618 ACCAGCGGCAAGTTACAAAA 58.605 45.000 1.45 0.00 0.00 2.44
7771 8033 3.138884 TGAGCTTTCTATGCACCACAA 57.861 42.857 0.00 0.00 0.00 3.33
7772 8034 2.857186 TGAGCTTTCTATGCACCACA 57.143 45.000 0.00 0.00 0.00 4.17
7885 8148 8.871686 AACATCAAATGTAGTCAAAAACCTTC 57.128 30.769 0.00 0.00 44.07 3.46
7888 8151 8.419076 ACAAACATCAAATGTAGTCAAAAACC 57.581 30.769 0.00 0.00 44.07 3.27
7920 8183 6.389830 TTGCTTGAGAACAACACATTACAT 57.610 33.333 0.00 0.00 32.27 2.29
7932 8195 4.045636 TCCAAAAAGCTTGCTTGAGAAC 57.954 40.909 18.60 0.00 0.00 3.01
8012 8286 3.758023 TGCTGGATTCAATTTCATGACGT 59.242 39.130 0.00 0.00 0.00 4.34
8074 8348 6.458888 GGCAAATAGAAAACTAGACAGGATGC 60.459 42.308 0.00 0.00 42.53 3.91
8078 8352 4.640647 GGGGCAAATAGAAAACTAGACAGG 59.359 45.833 0.00 0.00 0.00 4.00
8084 8358 5.193728 AGGAGATGGGGCAAATAGAAAACTA 59.806 40.000 0.00 0.00 0.00 2.24
8085 8359 4.017130 AGGAGATGGGGCAAATAGAAAACT 60.017 41.667 0.00 0.00 0.00 2.66
8169 8443 3.130340 TGGAACTGTTGCTTTCCTTGTTC 59.870 43.478 13.23 0.00 41.76 3.18
8180 8454 1.896220 TGGTGATCTGGAACTGTTGC 58.104 50.000 4.98 4.98 0.00 4.17


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

AutoCloner maintained by Alex Coulton.