Multiple sequence alignment - TraesCS5A01G031000

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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 TraesCS5A01G031000 chr5A 100.000 3287 0 0 1 3287 28663497 28666783 0.000000e+00 6071
1 TraesCS5A01G031000 chr5D 90.563 3359 135 76 1 3287 40699202 40702450 0.000000e+00 4279
2 TraesCS5A01G031000 chr5B 91.975 3053 117 55 1 2990 33998364 34001351 0.000000e+00 4163
3 TraesCS5A01G031000 chr5B 94.314 299 14 3 2991 3287 34001380 34001677 3.870000e-124 455


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 TraesCS5A01G031000 chr5A 28663497 28666783 3286 False 6071 6071 100.0000 1 3287 1 chr5A.!!$F1 3286
1 TraesCS5A01G031000 chr5D 40699202 40702450 3248 False 4279 4279 90.5630 1 3287 1 chr5D.!!$F1 3286
2 TraesCS5A01G031000 chr5B 33998364 34001677 3313 False 2309 4163 93.1445 1 3287 2 chr5B.!!$F1 3286

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
633 654 0.167470 CAGACTCAAATGCAGCACCG 59.833 55.0 0.0 0.0 0.0 4.94 F
1107 1167 0.111061 TGGTGAACATGCAGGCTTCT 59.889 50.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1628 0.835276 GGGGTAAGCATAGGACGGTT 59.165 55.0 0.00 0.00 0.0 4.44 R
3013 3139 0.106819 AGAGCCTGATGCCCATCAAC 60.107 55.0 11.67 7.42 46.1 3.18 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
54 55 7.148623 CCTTCAACTAAGAGTCATCGGTTTAAC 60.149 40.741 0.00 0.00 37.38 2.01
55 56 6.751157 TCAACTAAGAGTCATCGGTTTAACA 58.249 36.000 0.00 0.00 0.00 2.41
56 57 6.643770 TCAACTAAGAGTCATCGGTTTAACAC 59.356 38.462 0.00 0.00 0.00 3.32
57 58 6.092955 ACTAAGAGTCATCGGTTTAACACA 57.907 37.500 0.00 0.00 0.00 3.72
58 59 6.698380 ACTAAGAGTCATCGGTTTAACACAT 58.302 36.000 0.00 0.00 0.00 3.21
60 61 4.894784 AGAGTCATCGGTTTAACACATGT 58.105 39.130 0.00 0.00 0.00 3.21
61 62 5.305585 AGAGTCATCGGTTTAACACATGTT 58.694 37.500 0.00 2.32 41.73 2.71
62 63 5.408604 AGAGTCATCGGTTTAACACATGTTC 59.591 40.000 0.00 2.33 39.31 3.18
63 64 4.454504 AGTCATCGGTTTAACACATGTTCC 59.545 41.667 0.00 0.00 39.31 3.62
64 65 4.214545 GTCATCGGTTTAACACATGTTCCA 59.785 41.667 0.00 0.00 39.31 3.53
94 99 5.068987 CCCTAACCCCATGTGATAAATTGTG 59.931 44.000 0.00 0.00 0.00 3.33
108 113 8.550376 GTGATAAATTGTGCAAGTTTTGTTGAT 58.450 29.630 3.00 0.00 30.75 2.57
113 118 3.628032 TGTGCAAGTTTTGTTGATCCGTA 59.372 39.130 0.00 0.00 0.00 4.02
114 119 3.972502 GTGCAAGTTTTGTTGATCCGTAC 59.027 43.478 0.00 0.00 0.00 3.67
115 120 3.628032 TGCAAGTTTTGTTGATCCGTACA 59.372 39.130 0.00 0.00 0.00 2.90
116 121 3.972502 GCAAGTTTTGTTGATCCGTACAC 59.027 43.478 0.00 0.00 0.00 2.90
117 122 4.496673 GCAAGTTTTGTTGATCCGTACACA 60.497 41.667 0.00 0.00 0.00 3.72
118 123 5.757886 CAAGTTTTGTTGATCCGTACACAT 58.242 37.500 0.00 0.00 0.00 3.21
119 124 5.356882 AGTTTTGTTGATCCGTACACATG 57.643 39.130 0.00 0.00 0.00 3.21
120 125 4.819630 AGTTTTGTTGATCCGTACACATGT 59.180 37.500 0.00 0.00 0.00 3.21
121 126 5.298276 AGTTTTGTTGATCCGTACACATGTT 59.702 36.000 0.00 0.00 0.00 2.71
122 127 5.351233 TTTGTTGATCCGTACACATGTTC 57.649 39.130 0.00 0.00 0.00 3.18
123 128 3.331150 TGTTGATCCGTACACATGTTCC 58.669 45.455 0.00 0.00 0.00 3.62
124 129 2.287393 TGATCCGTACACATGTTCCG 57.713 50.000 0.00 0.00 0.00 4.30
125 130 1.819903 TGATCCGTACACATGTTCCGA 59.180 47.619 0.00 0.00 0.00 4.55
126 131 2.429250 TGATCCGTACACATGTTCCGAT 59.571 45.455 0.00 0.00 0.00 4.18
127 132 2.287393 TCCGTACACATGTTCCGATG 57.713 50.000 0.00 0.00 0.00 3.84
128 133 1.134936 TCCGTACACATGTTCCGATGG 60.135 52.381 0.00 0.00 0.00 3.51
129 134 1.134936 CCGTACACATGTTCCGATGGA 60.135 52.381 0.00 0.00 0.00 3.41
130 135 2.612604 CGTACACATGTTCCGATGGAA 58.387 47.619 0.00 0.00 39.66 3.53
134 139 2.236146 ACACATGTTCCGATGGAAGCTA 59.764 45.455 0.00 0.00 42.88 3.32
195 204 2.030007 GGGTTGATCATGTGGTGTGTTG 60.030 50.000 0.00 0.00 0.00 3.33
196 205 2.884012 GGTTGATCATGTGGTGTGTTGA 59.116 45.455 0.00 0.00 0.00 3.18
256 265 7.841915 AAAACAAAAACACGGAAGATTCATT 57.158 28.000 0.00 0.00 0.00 2.57
311 323 5.968848 TGTCATACTGCGAAAAGAAACAAAC 59.031 36.000 0.00 0.00 0.00 2.93
356 368 3.131577 ACAAGCATGCATGGTTCAATAGG 59.868 43.478 34.83 25.53 45.69 2.57
422 440 7.479579 TGATCCTATCTTGGTATAGCTAGGTT 58.520 38.462 12.41 6.06 36.09 3.50
616 634 4.333372 GCAAATTGCACCCCAAAATATCAG 59.667 41.667 13.73 0.00 44.26 2.90
618 636 5.343307 AATTGCACCCCAAAATATCAGAC 57.657 39.130 0.00 0.00 36.92 3.51
633 654 0.167470 CAGACTCAAATGCAGCACCG 59.833 55.000 0.00 0.00 0.00 4.94
804 840 2.200955 TGCACTCCCTCTCTCTCTCTA 58.799 52.381 0.00 0.00 0.00 2.43
805 841 2.172505 TGCACTCCCTCTCTCTCTCTAG 59.827 54.545 0.00 0.00 0.00 2.43
806 842 2.438021 GCACTCCCTCTCTCTCTCTAGA 59.562 54.545 0.00 0.00 0.00 2.43
807 843 3.744530 GCACTCCCTCTCTCTCTCTAGAC 60.745 56.522 0.00 0.00 0.00 2.59
866 906 5.442391 ACCTACACCTACACAACAACAATT 58.558 37.500 0.00 0.00 0.00 2.32
927 987 6.126332 ACTCTCTCTCTCTCTCTCTCTCTCTA 60.126 46.154 0.00 0.00 0.00 2.43
928 988 6.065374 TCTCTCTCTCTCTCTCTCTCTCTAC 58.935 48.000 0.00 0.00 0.00 2.59
929 989 6.019656 TCTCTCTCTCTCTCTCTCTCTACT 57.980 45.833 0.00 0.00 0.00 2.57
930 990 6.436027 TCTCTCTCTCTCTCTCTCTCTACTT 58.564 44.000 0.00 0.00 0.00 2.24
931 991 6.547880 TCTCTCTCTCTCTCTCTCTCTACTTC 59.452 46.154 0.00 0.00 0.00 3.01
932 992 6.436027 TCTCTCTCTCTCTCTCTCTACTTCT 58.564 44.000 0.00 0.00 0.00 2.85
933 993 6.547880 TCTCTCTCTCTCTCTCTCTACTTCTC 59.452 46.154 0.00 0.00 0.00 2.87
934 994 6.436027 TCTCTCTCTCTCTCTCTACTTCTCT 58.564 44.000 0.00 0.00 0.00 3.10
935 995 6.547880 TCTCTCTCTCTCTCTCTACTTCTCTC 59.452 46.154 0.00 0.00 0.00 3.20
936 996 5.598830 TCTCTCTCTCTCTCTACTTCTCTCC 59.401 48.000 0.00 0.00 0.00 3.71
937 997 4.654262 TCTCTCTCTCTCTACTTCTCTCCC 59.346 50.000 0.00 0.00 0.00 4.30
938 998 4.631234 TCTCTCTCTCTACTTCTCTCCCT 58.369 47.826 0.00 0.00 0.00 4.20
939 999 4.654262 TCTCTCTCTCTACTTCTCTCCCTC 59.346 50.000 0.00 0.00 0.00 4.30
940 1000 4.631234 TCTCTCTCTACTTCTCTCCCTCT 58.369 47.826 0.00 0.00 0.00 3.69
941 1001 4.654262 TCTCTCTCTACTTCTCTCCCTCTC 59.346 50.000 0.00 0.00 0.00 3.20
942 1002 4.631234 TCTCTCTACTTCTCTCCCTCTCT 58.369 47.826 0.00 0.00 0.00 3.10
943 1003 4.654262 TCTCTCTACTTCTCTCCCTCTCTC 59.346 50.000 0.00 0.00 0.00 3.20
944 1004 4.631234 TCTCTACTTCTCTCCCTCTCTCT 58.369 47.826 0.00 0.00 0.00 3.10
945 1005 4.654262 TCTCTACTTCTCTCCCTCTCTCTC 59.346 50.000 0.00 0.00 0.00 3.20
946 1006 4.631234 TCTACTTCTCTCCCTCTCTCTCT 58.369 47.826 0.00 0.00 0.00 3.10
947 1007 3.933861 ACTTCTCTCCCTCTCTCTCTC 57.066 52.381 0.00 0.00 0.00 3.20
948 1008 2.509964 ACTTCTCTCCCTCTCTCTCTCC 59.490 54.545 0.00 0.00 0.00 3.71
949 1009 1.518367 TCTCTCCCTCTCTCTCTCCC 58.482 60.000 0.00 0.00 0.00 4.30
950 1010 1.010793 TCTCTCCCTCTCTCTCTCCCT 59.989 57.143 0.00 0.00 0.00 4.20
951 1011 1.421646 CTCTCCCTCTCTCTCTCCCTC 59.578 61.905 0.00 0.00 0.00 4.30
952 1012 1.010793 TCTCCCTCTCTCTCTCCCTCT 59.989 57.143 0.00 0.00 0.00 3.69
953 1013 1.421646 CTCCCTCTCTCTCTCCCTCTC 59.578 61.905 0.00 0.00 0.00 3.20
954 1014 1.010793 TCCCTCTCTCTCTCCCTCTCT 59.989 57.143 0.00 0.00 0.00 3.10
955 1015 2.251605 TCCCTCTCTCTCTCCCTCTCTA 59.748 54.545 0.00 0.00 0.00 2.43
956 1016 2.372172 CCCTCTCTCTCTCCCTCTCTAC 59.628 59.091 0.00 0.00 0.00 2.59
957 1017 2.372172 CCTCTCTCTCTCCCTCTCTACC 59.628 59.091 0.00 0.00 0.00 3.18
958 1018 3.318313 CTCTCTCTCTCCCTCTCTACCT 58.682 54.545 0.00 0.00 0.00 3.08
959 1019 3.314693 TCTCTCTCTCCCTCTCTACCTC 58.685 54.545 0.00 0.00 0.00 3.85
960 1020 3.051341 TCTCTCTCTCCCTCTCTACCTCT 60.051 52.174 0.00 0.00 0.00 3.69
1105 1165 1.530013 GCTGGTGAACATGCAGGCTT 61.530 55.000 0.00 0.00 0.00 4.35
1107 1167 0.111061 TGGTGAACATGCAGGCTTCT 59.889 50.000 0.00 0.00 0.00 2.85
1115 1175 1.267574 ATGCAGGCTTCTCCGGAGAA 61.268 55.000 37.80 37.80 44.47 2.87
1120 1180 0.176910 GGCTTCTCCGGAGAAAGAGG 59.823 60.000 38.83 29.70 45.75 3.69
1121 1181 0.461163 GCTTCTCCGGAGAAAGAGGC 60.461 60.000 38.83 33.81 45.75 4.70
1538 1601 1.201343 GTACGAGGCGAAGAAGATGC 58.799 55.000 0.00 0.00 0.00 3.91
1635 1698 4.314440 AAAGCGAGGCTGACGGCA 62.314 61.111 8.86 0.00 44.01 5.69
1752 1815 1.300697 GGACAAGAGCGTGGTCGTT 60.301 57.895 0.00 0.00 39.49 3.85
1993 2056 3.490348 CAAGAATTCCACAGGAACCAGT 58.510 45.455 0.65 0.00 45.07 4.00
2131 2194 2.984989 AGGAGGTTGGGGGTATTAGT 57.015 50.000 0.00 0.00 0.00 2.24
2134 2197 2.579400 GGAGGTTGGGGGTATTAGTTGT 59.421 50.000 0.00 0.00 0.00 3.32
2142 2205 7.270779 GTTGGGGGTATTAGTTGTCTAGTAAG 58.729 42.308 0.00 0.00 0.00 2.34
2225 2292 0.457851 AGAGGTACATCAGCGACAGC 59.542 55.000 10.58 0.00 45.58 4.40
2254 2321 1.160137 GCACTTCGATGAGGCTTTGT 58.840 50.000 5.16 0.00 0.00 2.83
2255 2322 2.028112 AGCACTTCGATGAGGCTTTGTA 60.028 45.455 13.46 0.00 0.00 2.41
2256 2323 2.742053 GCACTTCGATGAGGCTTTGTAA 59.258 45.455 5.16 0.00 0.00 2.41
2298 2365 9.303116 AGAACAGTGAATAAACTAAGAGAGAGA 57.697 33.333 0.00 0.00 0.00 3.10
2299 2366 9.567848 GAACAGTGAATAAACTAAGAGAGAGAG 57.432 37.037 0.00 0.00 0.00 3.20
2300 2367 8.871629 ACAGTGAATAAACTAAGAGAGAGAGA 57.128 34.615 0.00 0.00 0.00 3.10
2301 2368 8.956426 ACAGTGAATAAACTAAGAGAGAGAGAG 58.044 37.037 0.00 0.00 0.00 3.20
2302 2369 9.173021 CAGTGAATAAACTAAGAGAGAGAGAGA 57.827 37.037 0.00 0.00 0.00 3.10
2303 2370 9.396022 AGTGAATAAACTAAGAGAGAGAGAGAG 57.604 37.037 0.00 0.00 0.00 3.20
2304 2371 9.391006 GTGAATAAACTAAGAGAGAGAGAGAGA 57.609 37.037 0.00 0.00 0.00 3.10
2305 2372 9.613428 TGAATAAACTAAGAGAGAGAGAGAGAG 57.387 37.037 0.00 0.00 0.00 3.20
2306 2373 9.832445 GAATAAACTAAGAGAGAGAGAGAGAGA 57.168 37.037 0.00 0.00 0.00 3.10
2307 2374 9.838339 AATAAACTAAGAGAGAGAGAGAGAGAG 57.162 37.037 0.00 0.00 0.00 3.20
2308 2375 7.496346 AAACTAAGAGAGAGAGAGAGAGAGA 57.504 40.000 0.00 0.00 0.00 3.10
2309 2376 6.723298 ACTAAGAGAGAGAGAGAGAGAGAG 57.277 45.833 0.00 0.00 0.00 3.20
2310 2377 6.436027 ACTAAGAGAGAGAGAGAGAGAGAGA 58.564 44.000 0.00 0.00 0.00 3.10
2311 2378 5.867903 AAGAGAGAGAGAGAGAGAGAGAG 57.132 47.826 0.00 0.00 0.00 3.20
2312 2379 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
2313 2380 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2314 2381 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
2478 2548 1.303643 GGTCAGAAAGTGGGCCCAG 60.304 63.158 29.55 13.23 0.00 4.45
2486 2556 1.719063 AAGTGGGCCCAGCTCAAGAA 61.719 55.000 29.55 0.00 42.30 2.52
2570 2640 7.931578 TGGAAACTTTAAGTCAGTTTGAGAA 57.068 32.000 8.19 0.00 43.16 2.87
2604 2674 9.841295 ACTGTCTAGTTGTAAGTTGGATAAAAA 57.159 29.630 0.00 0.00 31.66 1.94
2606 2676 9.841295 TGTCTAGTTGTAAGTTGGATAAAAACT 57.159 29.630 0.00 0.00 39.55 2.66
2635 2716 1.742268 GCTCACTTGATCTCCTTTGGC 59.258 52.381 0.00 0.00 0.00 4.52
2680 2774 4.647564 ACAATCAACTGAGGGATCTTGT 57.352 40.909 0.00 0.00 0.00 3.16
2946 3044 9.900710 CCTAATTGCACTATGAGTAGTAAGTAG 57.099 37.037 0.00 0.00 39.12 2.57
2995 3121 4.961585 AGGGTAGGTTTAGATCTTGAGGT 58.038 43.478 0.00 0.00 0.00 3.85
3064 3190 5.459505 TCTTGGGATGAACAGGGTTAAAAA 58.540 37.500 0.00 0.00 0.00 1.94
3154 3282 4.459337 CCCATCTTAACACAAGGAAAGTCC 59.541 45.833 0.00 0.00 36.58 3.85
3181 3309 6.167685 TCTGCAAGCAAATTAAGCAAATGAT 58.832 32.000 5.70 0.00 34.45 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 1.259609 AGGGCACATTGGAACATGTG 58.740 50.000 0.00 9.08 44.51 3.21
55 56 2.825532 GTTAGGGCACATTGGAACATGT 59.174 45.455 0.00 0.00 39.30 3.21
56 57 2.166254 GGTTAGGGCACATTGGAACATG 59.834 50.000 0.00 0.00 39.30 3.21
57 58 2.456577 GGTTAGGGCACATTGGAACAT 58.543 47.619 0.00 0.00 39.30 2.71
58 59 1.549037 GGGTTAGGGCACATTGGAACA 60.549 52.381 0.00 0.00 0.00 3.18
60 61 0.040499 GGGGTTAGGGCACATTGGAA 59.960 55.000 0.00 0.00 0.00 3.53
61 62 1.143329 TGGGGTTAGGGCACATTGGA 61.143 55.000 0.00 0.00 0.00 3.53
62 63 0.032217 ATGGGGTTAGGGCACATTGG 60.032 55.000 0.00 0.00 0.00 3.16
63 64 1.113788 CATGGGGTTAGGGCACATTG 58.886 55.000 0.00 0.00 0.00 2.82
64 65 0.709992 ACATGGGGTTAGGGCACATT 59.290 50.000 0.00 0.00 0.00 2.71
94 99 3.972502 GTGTACGGATCAACAAAACTTGC 59.027 43.478 0.00 0.00 0.00 4.01
108 113 1.134936 CCATCGGAACATGTGTACGGA 60.135 52.381 14.47 11.79 32.05 4.69
113 118 1.003580 AGCTTCCATCGGAACATGTGT 59.996 47.619 0.00 0.00 36.71 3.72
114 119 1.742761 AGCTTCCATCGGAACATGTG 58.257 50.000 0.00 0.00 36.71 3.21
115 120 2.743183 GCTAGCTTCCATCGGAACATGT 60.743 50.000 7.70 0.00 36.71 3.21
116 121 1.869767 GCTAGCTTCCATCGGAACATG 59.130 52.381 7.70 0.00 36.71 3.21
117 122 1.486310 TGCTAGCTTCCATCGGAACAT 59.514 47.619 17.23 0.00 36.71 2.71
118 123 0.901827 TGCTAGCTTCCATCGGAACA 59.098 50.000 17.23 0.00 36.71 3.18
119 124 2.246719 ATGCTAGCTTCCATCGGAAC 57.753 50.000 17.23 0.00 36.71 3.62
120 125 3.306989 CCATATGCTAGCTTCCATCGGAA 60.307 47.826 17.23 0.00 39.66 4.30
121 126 2.234661 CCATATGCTAGCTTCCATCGGA 59.765 50.000 17.23 0.00 0.00 4.55
122 127 2.625737 CCATATGCTAGCTTCCATCGG 58.374 52.381 17.23 3.64 0.00 4.18
123 128 2.625737 CCCATATGCTAGCTTCCATCG 58.374 52.381 17.23 0.00 0.00 3.84
124 129 2.363683 GCCCATATGCTAGCTTCCATC 58.636 52.381 17.23 0.00 0.00 3.51
125 130 1.339438 CGCCCATATGCTAGCTTCCAT 60.339 52.381 17.23 3.23 0.00 3.41
126 131 0.035317 CGCCCATATGCTAGCTTCCA 59.965 55.000 17.23 0.00 0.00 3.53
127 132 0.035458 ACGCCCATATGCTAGCTTCC 59.965 55.000 17.23 0.00 0.00 3.46
128 133 2.028930 AGTACGCCCATATGCTAGCTTC 60.029 50.000 17.23 0.00 0.00 3.86
129 134 1.971357 AGTACGCCCATATGCTAGCTT 59.029 47.619 17.23 12.56 0.00 3.74
130 135 1.633774 AGTACGCCCATATGCTAGCT 58.366 50.000 17.23 4.07 0.00 3.32
134 139 8.879427 TCATATATATAGTACGCCCATATGCT 57.121 34.615 0.00 0.00 0.00 3.79
195 204 9.495754 CTTGCTTTATGTACTCTGCTTAAATTC 57.504 33.333 0.00 0.00 0.00 2.17
196 205 7.970614 GCTTGCTTTATGTACTCTGCTTAAATT 59.029 33.333 0.00 0.00 0.00 1.82
237 246 8.141268 ACATGTTAATGAATCTTCCGTGTTTTT 58.859 29.630 0.00 0.00 37.24 1.94
277 289 8.710835 TTTTCGCAGTATGACATTATTGAGTA 57.289 30.769 0.00 0.00 39.69 2.59
356 368 0.175531 AAACCACTGCCTTGTTGTGC 59.824 50.000 0.00 0.00 0.00 4.57
422 440 5.274015 TCTTATATCTACACCACACACCCA 58.726 41.667 0.00 0.00 0.00 4.51
459 477 2.926838 GTGCGTTTTGGAAAAGCAAAGA 59.073 40.909 13.87 0.00 35.46 2.52
616 634 0.166814 GACGGTGCTGCATTTGAGTC 59.833 55.000 5.27 7.76 0.00 3.36
618 636 0.806868 ATGACGGTGCTGCATTTGAG 59.193 50.000 5.27 0.00 0.00 3.02
804 840 4.067896 GTGAGAATGATTGGTGTGTGTCT 58.932 43.478 0.00 0.00 0.00 3.41
805 841 4.067896 AGTGAGAATGATTGGTGTGTGTC 58.932 43.478 0.00 0.00 0.00 3.67
806 842 4.067896 GAGTGAGAATGATTGGTGTGTGT 58.932 43.478 0.00 0.00 0.00 3.72
807 843 4.067192 TGAGTGAGAATGATTGGTGTGTG 58.933 43.478 0.00 0.00 0.00 3.82
927 987 2.509964 GGAGAGAGAGAGGGAGAGAAGT 59.490 54.545 0.00 0.00 0.00 3.01
928 988 2.158608 GGGAGAGAGAGAGGGAGAGAAG 60.159 59.091 0.00 0.00 0.00 2.85
929 989 1.850345 GGGAGAGAGAGAGGGAGAGAA 59.150 57.143 0.00 0.00 0.00 2.87
930 990 1.010793 AGGGAGAGAGAGAGGGAGAGA 59.989 57.143 0.00 0.00 0.00 3.10
931 991 1.421646 GAGGGAGAGAGAGAGGGAGAG 59.578 61.905 0.00 0.00 0.00 3.20
932 992 1.010793 AGAGGGAGAGAGAGAGGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
933 993 1.421646 GAGAGGGAGAGAGAGAGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
934 994 1.010793 AGAGAGGGAGAGAGAGAGGGA 59.989 57.143 0.00 0.00 0.00 4.20
935 995 1.522900 AGAGAGGGAGAGAGAGAGGG 58.477 60.000 0.00 0.00 0.00 4.30
936 996 2.372172 GGTAGAGAGGGAGAGAGAGAGG 59.628 59.091 0.00 0.00 0.00 3.69
937 997 3.318313 AGGTAGAGAGGGAGAGAGAGAG 58.682 54.545 0.00 0.00 0.00 3.20
938 998 3.051341 AGAGGTAGAGAGGGAGAGAGAGA 60.051 52.174 0.00 0.00 0.00 3.10
939 999 3.318313 AGAGGTAGAGAGGGAGAGAGAG 58.682 54.545 0.00 0.00 0.00 3.20
940 1000 3.314693 GAGAGGTAGAGAGGGAGAGAGA 58.685 54.545 0.00 0.00 0.00 3.10
941 1001 2.372172 GGAGAGGTAGAGAGGGAGAGAG 59.628 59.091 0.00 0.00 0.00 3.20
942 1002 2.414612 GGAGAGGTAGAGAGGGAGAGA 58.585 57.143 0.00 0.00 0.00 3.10
943 1003 1.423921 GGGAGAGGTAGAGAGGGAGAG 59.576 61.905 0.00 0.00 0.00 3.20
944 1004 1.525175 GGGAGAGGTAGAGAGGGAGA 58.475 60.000 0.00 0.00 0.00 3.71
945 1005 0.481128 GGGGAGAGGTAGAGAGGGAG 59.519 65.000 0.00 0.00 0.00 4.30
946 1006 0.048117 AGGGGAGAGGTAGAGAGGGA 59.952 60.000 0.00 0.00 0.00 4.20
947 1007 1.835895 TAGGGGAGAGGTAGAGAGGG 58.164 60.000 0.00 0.00 0.00 4.30
948 1008 5.602291 TTTATAGGGGAGAGGTAGAGAGG 57.398 47.826 0.00 0.00 0.00 3.69
949 1009 6.014012 CCTTTTATAGGGGAGAGGTAGAGAG 58.986 48.000 0.00 0.00 40.67 3.20
950 1010 5.680074 TCCTTTTATAGGGGAGAGGTAGAGA 59.320 44.000 0.00 0.00 44.86 3.10
951 1011 5.776208 GTCCTTTTATAGGGGAGAGGTAGAG 59.224 48.000 0.00 0.00 44.86 2.43
952 1012 5.197189 TGTCCTTTTATAGGGGAGAGGTAGA 59.803 44.000 0.00 0.00 44.86 2.59
953 1013 5.464984 TGTCCTTTTATAGGGGAGAGGTAG 58.535 45.833 0.00 0.00 44.86 3.18
954 1014 5.492565 TGTCCTTTTATAGGGGAGAGGTA 57.507 43.478 0.00 0.00 44.86 3.08
955 1015 4.363546 TGTCCTTTTATAGGGGAGAGGT 57.636 45.455 0.00 0.00 44.86 3.85
956 1016 5.158889 AGATGTCCTTTTATAGGGGAGAGG 58.841 45.833 0.00 0.00 44.86 3.69
957 1017 5.841237 TGAGATGTCCTTTTATAGGGGAGAG 59.159 44.000 0.00 0.00 44.86 3.20
958 1018 5.788430 TGAGATGTCCTTTTATAGGGGAGA 58.212 41.667 0.00 0.00 44.86 3.71
959 1019 6.694445 ATGAGATGTCCTTTTATAGGGGAG 57.306 41.667 0.00 0.00 44.86 4.30
960 1020 6.619437 TGAATGAGATGTCCTTTTATAGGGGA 59.381 38.462 0.00 0.00 44.86 4.81
1052 1112 0.938008 GCAGTATACGCTTTGGGCTC 59.062 55.000 10.99 0.00 39.13 4.70
1066 1126 0.597568 GGCAGCATGTGTTTGCAGTA 59.402 50.000 13.03 0.00 45.23 2.74
1105 1165 0.972983 CTGGCCTCTTTCTCCGGAGA 60.973 60.000 30.49 30.49 35.27 3.71
1107 1167 2.660064 GCTGGCCTCTTTCTCCGGA 61.660 63.158 2.93 2.93 0.00 5.14
1121 1181 3.997400 ATCTGCTGCTGCCTGCTGG 62.997 63.158 13.47 5.03 43.37 4.85
1430 1493 2.126580 GTTGGTCCTCGACGACGG 60.127 66.667 7.55 0.00 40.21 4.79
1565 1628 0.835276 GGGGTAAGCATAGGACGGTT 59.165 55.000 0.00 0.00 0.00 4.44
1612 1675 1.301716 TCAGCCTCGCTTTCACCAC 60.302 57.895 0.00 0.00 36.40 4.16
1635 1698 4.093291 CTCGCCAGGCTCCTGCTT 62.093 66.667 10.54 0.00 42.35 3.91
1716 1779 3.748660 CTGCACCACCACCGTGTCA 62.749 63.158 0.00 0.00 38.41 3.58
1717 1780 2.972505 CTGCACCACCACCGTGTC 60.973 66.667 0.00 0.00 38.41 3.67
1718 1781 4.562425 CCTGCACCACCACCGTGT 62.562 66.667 0.00 0.00 38.41 4.49
1720 1783 4.250305 GTCCTGCACCACCACCGT 62.250 66.667 0.00 0.00 0.00 4.83
1721 1784 3.765894 TTGTCCTGCACCACCACCG 62.766 63.158 0.00 0.00 0.00 4.94
1752 1815 1.251527 GGAGCTTCTCGTCCCTCACA 61.252 60.000 0.00 0.00 0.00 3.58
2131 2194 8.647256 AAGCTCCTTACTAACTTACTAGACAA 57.353 34.615 0.00 0.00 0.00 3.18
2134 2197 7.641249 AGGAAGCTCCTTACTAACTTACTAGA 58.359 38.462 0.00 0.00 46.91 2.43
2225 2292 3.695816 TCATCGAAGTGCTACAATCTCG 58.304 45.455 0.00 0.00 0.00 4.04
2254 2321 7.703197 CACTGTTCTCATGCATGCAAAATATTA 59.297 33.333 26.68 8.75 0.00 0.98
2255 2322 6.533723 CACTGTTCTCATGCATGCAAAATATT 59.466 34.615 26.68 3.45 0.00 1.28
2256 2323 6.040247 CACTGTTCTCATGCATGCAAAATAT 58.960 36.000 26.68 4.34 0.00 1.28
2298 2365 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
2299 2366 3.827008 TGCTCTCTCTCTCTCTCTCTC 57.173 52.381 0.00 0.00 0.00 3.20
2300 2367 3.118112 CCTTGCTCTCTCTCTCTCTCTCT 60.118 52.174 0.00 0.00 0.00 3.10
2301 2368 3.209410 CCTTGCTCTCTCTCTCTCTCTC 58.791 54.545 0.00 0.00 0.00 3.20
2302 2369 2.092212 CCCTTGCTCTCTCTCTCTCTCT 60.092 54.545 0.00 0.00 0.00 3.10
2303 2370 2.092429 TCCCTTGCTCTCTCTCTCTCTC 60.092 54.545 0.00 0.00 0.00 3.20
2304 2371 1.922447 TCCCTTGCTCTCTCTCTCTCT 59.078 52.381 0.00 0.00 0.00 3.10
2305 2372 2.092429 TCTCCCTTGCTCTCTCTCTCTC 60.092 54.545 0.00 0.00 0.00 3.20
2306 2373 1.922447 TCTCCCTTGCTCTCTCTCTCT 59.078 52.381 0.00 0.00 0.00 3.10
2307 2374 2.435372 TCTCCCTTGCTCTCTCTCTC 57.565 55.000 0.00 0.00 0.00 3.20
2308 2375 2.669781 CATCTCCCTTGCTCTCTCTCT 58.330 52.381 0.00 0.00 0.00 3.10
2309 2376 1.688197 CCATCTCCCTTGCTCTCTCTC 59.312 57.143 0.00 0.00 0.00 3.20
2310 2377 1.290431 TCCATCTCCCTTGCTCTCTCT 59.710 52.381 0.00 0.00 0.00 3.10
2311 2378 1.786937 TCCATCTCCCTTGCTCTCTC 58.213 55.000 0.00 0.00 0.00 3.20
2312 2379 2.493099 ATCCATCTCCCTTGCTCTCT 57.507 50.000 0.00 0.00 0.00 3.10
2313 2380 3.645687 ACTAATCCATCTCCCTTGCTCTC 59.354 47.826 0.00 0.00 0.00 3.20
2314 2381 3.663198 ACTAATCCATCTCCCTTGCTCT 58.337 45.455 0.00 0.00 0.00 4.09
2348 2418 9.135189 AGCATAATCTTTTAGATAATGGCACAA 57.865 29.630 0.00 0.00 36.17 3.33
2486 2556 8.745590 GGGTGTCTGTGTATAAATATGGTTTTT 58.254 33.333 0.00 0.00 0.00 1.94
2604 2674 6.107901 AGATCAAGTGAGCAGACTTAAAGT 57.892 37.500 0.00 0.00 34.29 2.66
2605 2675 5.580297 GGAGATCAAGTGAGCAGACTTAAAG 59.420 44.000 0.00 0.00 34.29 1.85
2606 2676 5.247110 AGGAGATCAAGTGAGCAGACTTAAA 59.753 40.000 0.00 0.00 34.29 1.52
2607 2677 4.774726 AGGAGATCAAGTGAGCAGACTTAA 59.225 41.667 0.00 0.00 34.29 1.85
2608 2678 4.348486 AGGAGATCAAGTGAGCAGACTTA 58.652 43.478 0.00 0.00 34.29 2.24
2609 2679 3.172339 AGGAGATCAAGTGAGCAGACTT 58.828 45.455 0.00 0.00 36.58 3.01
2610 2680 2.818921 AGGAGATCAAGTGAGCAGACT 58.181 47.619 0.00 0.00 31.88 3.24
2657 2751 5.738909 ACAAGATCCCTCAGTTGATTGTAG 58.261 41.667 0.00 0.00 0.00 2.74
2659 2753 4.647564 ACAAGATCCCTCAGTTGATTGT 57.352 40.909 0.00 0.00 0.00 2.71
2680 2774 3.953612 ACAGAGACAGTCCATTGCAAAAA 59.046 39.130 1.71 0.00 0.00 1.94
2806 2900 4.517285 TCCTCATGTCAAGGCAGATTAAC 58.483 43.478 0.00 0.00 33.65 2.01
2809 2903 3.434739 GGATCCTCATGTCAAGGCAGATT 60.435 47.826 3.84 0.00 33.65 2.40
3013 3139 0.106819 AGAGCCTGATGCCCATCAAC 60.107 55.000 11.67 7.42 46.10 3.18
3154 3282 4.430137 TGCTTAATTTGCTTGCAGAGAG 57.570 40.909 0.00 0.00 0.00 3.20
3261 3389 4.784177 TCTTGCTAGCCATCAATCATCAA 58.216 39.130 13.29 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.