Multiple sequence alignment - TraesCS7D01G327600

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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 TraesCS7D01G327600 chr7D 100.000 2972 0 0 1 2972 418949983 418947012 0.000000e+00 5489
1 TraesCS7D01G327600 chr7D 99.379 161 1 0 1 161 562129265 562129425 2.900000e-75 292
2 TraesCS7D01G327600 chr7D 98.137 161 3 0 1 161 491878330 491878170 6.270000e-72 281
3 TraesCS7D01G327600 chr7D 98.020 101 2 0 550 650 418948904 418948804 3.040000e-40 176
4 TraesCS7D01G327600 chr7D 98.020 101 2 0 1080 1180 418949434 418949334 3.040000e-40 176
5 TraesCS7D01G327600 chr7B 95.395 1303 45 6 824 2113 434831733 434830433 0.000000e+00 2060
6 TraesCS7D01G327600 chr7B 95.104 674 29 4 162 832 434833581 434832909 0.000000e+00 1059
7 TraesCS7D01G327600 chr7B 97.516 161 4 0 1 161 508200955 508200795 2.920000e-70 276
8 TraesCS7D01G327600 chr7B 96.040 101 3 1 1081 1180 434833191 434833091 2.370000e-36 163
9 TraesCS7D01G327600 chr7B 95.050 101 5 0 550 650 434831471 434831371 3.070000e-35 159
10 TraesCS7D01G327600 chr7A 91.885 1220 81 9 804 2010 514701913 514703127 0.000000e+00 1688
11 TraesCS7D01G327600 chr7A 90.375 800 59 7 2179 2972 205103036 205103823 0.000000e+00 1035
12 TraesCS7D01G327600 chr7A 90.000 140 4 1 675 814 514687782 514687911 3.940000e-39 172
13 TraesCS7D01G327600 chr3A 91.914 841 65 3 2115 2953 75636711 75637550 0.000000e+00 1173
14 TraesCS7D01G327600 chr3A 90.151 863 58 13 2115 2972 1319166 1320006 0.000000e+00 1098
15 TraesCS7D01G327600 chr3A 80.065 923 143 29 1075 1973 51408926 51408021 0.000000e+00 647
16 TraesCS7D01G327600 chr1D 89.044 858 63 9 2115 2972 111398651 111399477 0.000000e+00 1035
17 TraesCS7D01G327600 chr1D 98.758 161 2 0 1 161 269817937 269818097 1.350000e-73 287
18 TraesCS7D01G327600 chr1D 88.816 152 16 1 2109 2260 12251107 12251257 5.060000e-43 185
19 TraesCS7D01G327600 chr1D 88.312 154 16 2 2114 2265 440869104 440868951 1.820000e-42 183
20 TraesCS7D01G327600 chr2B 90.521 749 61 6 2232 2972 743663063 743663809 0.000000e+00 981
21 TraesCS7D01G327600 chr3B 80.092 869 131 27 1132 1976 63399407 63398557 2.530000e-170 608
22 TraesCS7D01G327600 chr3B 82.301 339 42 10 2117 2451 602440585 602440261 8.110000e-71 278
23 TraesCS7D01G327600 chr3D 79.508 854 145 20 1141 1976 39621206 39620365 5.520000e-162 580
24 TraesCS7D01G327600 chr3D 100.000 161 0 0 1 161 607834822 607834982 6.230000e-77 298
25 TraesCS7D01G327600 chr5D 98.758 161 2 0 1 161 303829789 303829629 1.350000e-73 287
26 TraesCS7D01G327600 chr5D 87.500 168 18 3 2098 2263 268692158 268692324 1.090000e-44 191
27 TraesCS7D01G327600 chr5B 98.137 161 3 0 1 161 396437514 396437674 6.270000e-72 281
28 TraesCS7D01G327600 chr1B 97.516 161 4 0 1 161 667721401 667721241 2.920000e-70 276
29 TraesCS7D01G327600 chr1B 79.822 337 47 14 2115 2446 679125153 679125473 2.980000e-55 226
30 TraesCS7D01G327600 chr6B 96.894 161 5 0 1 161 210271641 210271481 1.360000e-68 270


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 TraesCS7D01G327600 chr7D 418947012 418949983 2971 True 1947.00 5489 98.68000 1 2972 3 chr7D.!!$R2 2971
1 TraesCS7D01G327600 chr7B 434830433 434833581 3148 True 860.25 2060 95.39725 162 2113 4 chr7B.!!$R2 1951
2 TraesCS7D01G327600 chr7A 514701913 514703127 1214 False 1688.00 1688 91.88500 804 2010 1 chr7A.!!$F3 1206
3 TraesCS7D01G327600 chr7A 205103036 205103823 787 False 1035.00 1035 90.37500 2179 2972 1 chr7A.!!$F1 793
4 TraesCS7D01G327600 chr3A 75636711 75637550 839 False 1173.00 1173 91.91400 2115 2953 1 chr3A.!!$F2 838
5 TraesCS7D01G327600 chr3A 1319166 1320006 840 False 1098.00 1098 90.15100 2115 2972 1 chr3A.!!$F1 857
6 TraesCS7D01G327600 chr3A 51408021 51408926 905 True 647.00 647 80.06500 1075 1973 1 chr3A.!!$R1 898
7 TraesCS7D01G327600 chr1D 111398651 111399477 826 False 1035.00 1035 89.04400 2115 2972 1 chr1D.!!$F2 857
8 TraesCS7D01G327600 chr2B 743663063 743663809 746 False 981.00 981 90.52100 2232 2972 1 chr2B.!!$F1 740
9 TraesCS7D01G327600 chr3B 63398557 63399407 850 True 608.00 608 80.09200 1132 1976 1 chr3B.!!$R1 844
10 TraesCS7D01G327600 chr3D 39620365 39621206 841 True 580.00 580 79.50800 1141 1976 1 chr3D.!!$R1 835

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
121 122 0.108615 ATCTTTGAGCGAGTGGTCGG 60.109 55.000 0.00 0.00 46.91 4.79 F
151 152 0.796927 GACGGTGGTTAGCTTGAAGC 59.203 55.000 9.59 9.59 42.84 3.86 F
1830 3061 1.296715 GGACAGGCTCGACACCAAT 59.703 57.895 2.71 0.00 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 3061 0.889186 GCGTTCCCTTCTTCTTGCCA 60.889 55.000 0.0 0.0 0.0 4.92 R
1911 3142 1.529244 AAAGGAGCACACCACCAGC 60.529 57.895 0.0 0.0 0.0 4.85 R
2645 3904 1.901238 GCAAAATCCATTCCCCACCCT 60.901 52.381 0.0 0.0 0.0 4.34 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
20 21 2.611518 CTTGTTCTTGTCCCTAGCTCG 58.388 52.381 0.00 0.00 0.00 5.03
21 22 0.895530 TGTTCTTGTCCCTAGCTCGG 59.104 55.000 0.00 0.00 0.00 4.63
22 23 0.896226 GTTCTTGTCCCTAGCTCGGT 59.104 55.000 3.23 0.00 0.00 4.69
23 24 2.097825 GTTCTTGTCCCTAGCTCGGTA 58.902 52.381 3.23 0.00 0.00 4.02
24 25 2.494870 GTTCTTGTCCCTAGCTCGGTAA 59.505 50.000 3.23 0.00 0.00 2.85
25 26 2.811410 TCTTGTCCCTAGCTCGGTAAA 58.189 47.619 3.23 0.00 0.00 2.01
26 27 3.371965 TCTTGTCCCTAGCTCGGTAAAT 58.628 45.455 3.23 0.00 0.00 1.40
27 28 3.383825 TCTTGTCCCTAGCTCGGTAAATC 59.616 47.826 3.23 0.00 0.00 2.17
28 29 3.028094 TGTCCCTAGCTCGGTAAATCT 57.972 47.619 3.23 0.00 0.00 2.40
29 30 2.693591 TGTCCCTAGCTCGGTAAATCTG 59.306 50.000 3.23 0.00 0.00 2.90
30 31 2.036089 GTCCCTAGCTCGGTAAATCTGG 59.964 54.545 3.23 0.00 0.00 3.86
31 32 2.040178 CCCTAGCTCGGTAAATCTGGT 58.960 52.381 3.23 0.00 0.00 4.00
32 33 2.434702 CCCTAGCTCGGTAAATCTGGTT 59.565 50.000 3.23 0.00 0.00 3.67
33 34 3.458189 CCTAGCTCGGTAAATCTGGTTG 58.542 50.000 0.00 0.00 0.00 3.77
34 35 3.132289 CCTAGCTCGGTAAATCTGGTTGA 59.868 47.826 0.00 0.00 0.00 3.18
35 36 3.695830 AGCTCGGTAAATCTGGTTGAA 57.304 42.857 0.00 0.00 0.00 2.69
36 37 4.015872 AGCTCGGTAAATCTGGTTGAAA 57.984 40.909 0.00 0.00 0.00 2.69
37 38 4.589908 AGCTCGGTAAATCTGGTTGAAAT 58.410 39.130 0.00 0.00 0.00 2.17
38 39 4.636206 AGCTCGGTAAATCTGGTTGAAATC 59.364 41.667 0.00 0.00 0.00 2.17
39 40 4.201920 GCTCGGTAAATCTGGTTGAAATCC 60.202 45.833 0.00 0.00 0.00 3.01
40 41 4.266714 TCGGTAAATCTGGTTGAAATCCC 58.733 43.478 0.00 0.00 0.00 3.85
41 42 3.380320 CGGTAAATCTGGTTGAAATCCCC 59.620 47.826 0.00 0.00 0.00 4.81
42 43 3.380320 GGTAAATCTGGTTGAAATCCCCG 59.620 47.826 0.00 0.00 0.00 5.73
43 44 2.143876 AATCTGGTTGAAATCCCCGG 57.856 50.000 0.00 0.00 0.00 5.73
44 45 1.295020 ATCTGGTTGAAATCCCCGGA 58.705 50.000 0.73 0.00 38.00 5.14
45 46 0.618458 TCTGGTTGAAATCCCCGGAG 59.382 55.000 0.73 0.00 0.00 4.63
63 64 2.437895 GCTAACCAAGCGACCCCC 60.438 66.667 0.00 0.00 42.53 5.40
64 65 2.125269 CTAACCAAGCGACCCCCG 60.125 66.667 0.00 0.00 42.21 5.73
80 81 3.730761 CGCAGGTGGCTTCTGTGC 61.731 66.667 7.91 0.00 41.67 4.57
81 82 2.595463 GCAGGTGGCTTCTGTGCA 60.595 61.111 8.84 0.00 40.25 4.57
82 83 2.195567 GCAGGTGGCTTCTGTGCAA 61.196 57.895 0.00 0.00 40.25 4.08
83 84 1.656441 CAGGTGGCTTCTGTGCAAC 59.344 57.895 0.00 0.00 36.21 4.17
95 96 3.646650 GTGCAACAAGCTCAGCAAA 57.353 47.368 0.00 0.00 45.94 3.68
96 97 1.484356 GTGCAACAAGCTCAGCAAAG 58.516 50.000 0.00 0.00 45.94 2.77
97 98 1.066002 GTGCAACAAGCTCAGCAAAGA 59.934 47.619 0.00 0.00 45.94 2.52
98 99 1.750206 TGCAACAAGCTCAGCAAAGAA 59.250 42.857 0.00 0.00 45.94 2.52
99 100 2.122564 GCAACAAGCTCAGCAAAGAAC 58.877 47.619 0.00 0.00 41.15 3.01
100 101 2.480073 GCAACAAGCTCAGCAAAGAACA 60.480 45.455 0.00 0.00 41.15 3.18
101 102 3.111098 CAACAAGCTCAGCAAAGAACAC 58.889 45.455 0.00 0.00 0.00 3.32
102 103 2.368439 ACAAGCTCAGCAAAGAACACA 58.632 42.857 0.00 0.00 0.00 3.72
103 104 2.954318 ACAAGCTCAGCAAAGAACACAT 59.046 40.909 0.00 0.00 0.00 3.21
104 105 3.004106 ACAAGCTCAGCAAAGAACACATC 59.996 43.478 0.00 0.00 0.00 3.06
105 106 3.137446 AGCTCAGCAAAGAACACATCT 57.863 42.857 0.00 0.00 41.32 2.90
115 116 3.393089 AGAACACATCTTTGAGCGAGT 57.607 42.857 0.00 0.00 33.39 4.18
116 117 3.062763 AGAACACATCTTTGAGCGAGTG 58.937 45.455 0.00 0.00 33.39 3.51
117 118 1.800805 ACACATCTTTGAGCGAGTGG 58.199 50.000 0.00 0.00 0.00 4.00
118 119 1.070758 ACACATCTTTGAGCGAGTGGT 59.929 47.619 0.00 0.00 0.00 4.16
119 120 1.728971 CACATCTTTGAGCGAGTGGTC 59.271 52.381 0.00 0.00 42.98 4.02
121 122 0.108615 ATCTTTGAGCGAGTGGTCGG 60.109 55.000 0.00 0.00 46.91 4.79
127 128 4.509737 GCGAGTGGTCGGTAGGGC 62.510 72.222 0.00 0.00 46.91 5.19
128 129 3.834799 CGAGTGGTCGGTAGGGCC 61.835 72.222 0.00 0.00 42.87 5.80
147 148 1.625616 CGTAGACGGTGGTTAGCTTG 58.374 55.000 0.00 0.00 35.37 4.01
148 149 1.200716 CGTAGACGGTGGTTAGCTTGA 59.799 52.381 0.00 0.00 35.37 3.02
149 150 2.352030 CGTAGACGGTGGTTAGCTTGAA 60.352 50.000 0.00 0.00 35.37 2.69
150 151 2.457366 AGACGGTGGTTAGCTTGAAG 57.543 50.000 0.00 0.00 0.00 3.02
151 152 0.796927 GACGGTGGTTAGCTTGAAGC 59.203 55.000 9.59 9.59 42.84 3.86
160 161 3.793144 GCTTGAAGCTCACGCCCG 61.793 66.667 10.44 0.00 35.85 6.13
224 226 6.631971 TTTTGACTTTGTCAGCATGTATGA 57.368 33.333 0.00 0.00 43.69 2.15
238 240 5.104360 AGCATGTATGAGTTTAGGATGTGGT 60.104 40.000 0.00 0.00 0.00 4.16
249 251 5.537300 TTAGGATGTGGTTAGATCTCAGC 57.463 43.478 0.00 0.00 0.00 4.26
251 253 2.546795 GGATGTGGTTAGATCTCAGCCG 60.547 54.545 0.00 0.00 0.00 5.52
281 283 7.588143 AACTTAATCAAGTCTCGATCAACTG 57.412 36.000 0.00 0.00 44.41 3.16
283 285 6.809196 ACTTAATCAAGTCTCGATCAACTGAC 59.191 38.462 0.00 0.00 41.25 3.51
304 306 8.774586 ACTGACACAACATATAGAAAACAAGAC 58.225 33.333 0.00 0.00 0.00 3.01
404 407 3.450817 TCTCAGTCGATTTAGCAATCCCA 59.549 43.478 0.00 0.00 36.18 4.37
409 412 5.180117 CAGTCGATTTAGCAATCCCATTAGG 59.820 44.000 0.00 0.00 36.18 2.69
429 432 9.232473 CATTAGGTTTATCCTCTATAAAAGCCC 57.768 37.037 0.00 0.00 44.42 5.19
458 461 5.984233 TGTGCATGTTTCTATCCGAATAC 57.016 39.130 0.00 0.00 0.00 1.89
469 472 3.924114 ATCCGAATACCCAATCACACA 57.076 42.857 0.00 0.00 0.00 3.72
491 494 4.500837 CACAGATACACAAGAGACATACGC 59.499 45.833 0.00 0.00 0.00 4.42
494 497 6.039382 ACAGATACACAAGAGACATACGCATA 59.961 38.462 0.00 0.00 0.00 3.14
549 552 7.285401 CCAAGAAAACATAGGCTGTAATATGGT 59.715 37.037 0.00 0.00 36.98 3.55
748 752 1.387084 GTGCAACTCGAAAGACTAGCG 59.613 52.381 0.00 0.00 35.39 4.26
796 800 2.167693 ACGTGTCAAGTCTTCAACCTCA 59.832 45.455 0.00 0.00 0.00 3.86
952 2144 3.142174 CTCCTGTTGTCCTTTCTTGACC 58.858 50.000 0.00 0.00 31.60 4.02
975 2167 2.298610 GTCAGCATTTAGGCCTAACCC 58.701 52.381 25.13 15.10 40.58 4.11
977 2169 2.024414 CAGCATTTAGGCCTAACCCAC 58.976 52.381 25.13 14.18 40.58 4.61
1009 2210 3.436704 CCTCACAACGTGCATGTTTCTAT 59.563 43.478 21.60 5.29 32.98 1.98
1021 2222 4.452455 GCATGTTTCTATCCGAATACCCAG 59.548 45.833 0.00 0.00 0.00 4.45
1028 2229 1.624336 TCCGAATACCCAGATACCCG 58.376 55.000 0.00 0.00 0.00 5.28
1111 2321 3.826754 TACTGCTCTGCTCGGCCG 61.827 66.667 22.12 22.12 0.00 6.13
1551 2779 3.138798 TACGCGCCAGAGTCTCCC 61.139 66.667 5.73 0.00 0.00 4.30
1576 2804 2.100631 GGCCTCAACGTCACCATCG 61.101 63.158 0.00 0.00 0.00 3.84
1642 2870 3.196913 TACAACGCCGTCGAGCACA 62.197 57.895 0.00 0.00 39.41 4.57
1647 2875 2.805546 GCCGTCGAGCACATCCTA 59.194 61.111 0.00 0.00 0.00 2.94
1830 3061 1.296715 GGACAGGCTCGACACCAAT 59.703 57.895 2.71 0.00 0.00 3.16
1911 3142 4.498520 ACTGCCGCCATCGTCTCG 62.499 66.667 0.00 0.00 0.00 4.04
2087 3325 0.803740 ACGAGTGAAGAGAGCGTACC 59.196 55.000 0.00 0.00 32.94 3.34
2238 3479 3.990806 TCACGCGCGTCCGTTTTG 61.991 61.111 35.61 20.40 39.83 2.44
2303 3544 2.437359 GTCATTCCCGCAGCAGCT 60.437 61.111 0.00 0.00 39.10 4.24
2335 3576 4.227134 CTGGGAGGGCGACGATGG 62.227 72.222 0.00 0.00 0.00 3.51
2352 3596 3.092511 GCTGGATCTGGGAGGGCA 61.093 66.667 0.00 0.00 0.00 5.36
2449 3706 1.775459 AGCAGGTACGGATCTCCTCTA 59.225 52.381 0.00 0.00 0.00 2.43
2516 3773 0.179067 TTGTTGCTCCGGTCGAGTTT 60.179 50.000 0.00 0.00 41.10 2.66
2574 3831 4.111016 CGAGTGGCTACGCGGTGA 62.111 66.667 18.18 0.00 44.74 4.02
2645 3904 3.263425 GTGGGGAATTGACTAGGAACTCA 59.737 47.826 0.00 0.00 41.75 3.41
2694 3953 0.038599 TTGTGAGCATGAGTGGCCAT 59.961 50.000 9.72 0.00 0.00 4.40
2769 4028 4.449638 CACCTGGAGAGGAGCAGA 57.550 61.111 0.00 0.00 42.93 4.26
2772 4031 0.178921 ACCTGGAGAGGAGCAGACAA 60.179 55.000 0.00 0.00 42.93 3.18
2908 4167 1.597742 AGTTGTAGCACAGGCACAAG 58.402 50.000 0.00 0.00 44.61 3.16
2921 4180 3.103742 AGGCACAAGAAGTTTTTCCCAA 58.896 40.909 0.00 0.00 33.64 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.611518 CGAGCTAGGGACAAGAACAAG 58.388 52.381 0.00 0.00 0.00 3.16
1 2 1.275291 CCGAGCTAGGGACAAGAACAA 59.725 52.381 4.68 0.00 0.00 2.83
2 3 0.895530 CCGAGCTAGGGACAAGAACA 59.104 55.000 4.68 0.00 0.00 3.18
3 4 0.896226 ACCGAGCTAGGGACAAGAAC 59.104 55.000 17.90 0.00 35.02 3.01
4 5 2.519771 TACCGAGCTAGGGACAAGAA 57.480 50.000 17.90 0.00 35.02 2.52
5 6 2.519771 TTACCGAGCTAGGGACAAGA 57.480 50.000 17.90 0.00 35.02 3.02
6 7 3.385111 AGATTTACCGAGCTAGGGACAAG 59.615 47.826 17.90 0.00 35.02 3.16
8 9 2.693591 CAGATTTACCGAGCTAGGGACA 59.306 50.000 17.90 1.38 35.02 4.02
10 11 2.317040 CCAGATTTACCGAGCTAGGGA 58.683 52.381 17.90 5.58 35.02 4.20
11 12 2.040178 ACCAGATTTACCGAGCTAGGG 58.960 52.381 17.90 9.78 35.02 3.53
12 13 3.132289 TCAACCAGATTTACCGAGCTAGG 59.868 47.826 11.86 11.86 37.30 3.02
13 14 4.386867 TCAACCAGATTTACCGAGCTAG 57.613 45.455 0.00 0.00 0.00 3.42
14 15 4.811969 TTCAACCAGATTTACCGAGCTA 57.188 40.909 0.00 0.00 0.00 3.32
15 16 3.695830 TTCAACCAGATTTACCGAGCT 57.304 42.857 0.00 0.00 0.00 4.09
16 17 4.201920 GGATTTCAACCAGATTTACCGAGC 60.202 45.833 0.00 0.00 0.00 5.03
17 18 4.335594 GGGATTTCAACCAGATTTACCGAG 59.664 45.833 0.00 0.00 0.00 4.63
18 19 4.266714 GGGATTTCAACCAGATTTACCGA 58.733 43.478 0.00 0.00 0.00 4.69
19 20 3.380320 GGGGATTTCAACCAGATTTACCG 59.620 47.826 0.00 0.00 0.00 4.02
20 21 3.380320 CGGGGATTTCAACCAGATTTACC 59.620 47.826 0.00 0.00 0.00 2.85
21 22 3.380320 CCGGGGATTTCAACCAGATTTAC 59.620 47.826 0.00 0.00 0.00 2.01
22 23 3.267291 TCCGGGGATTTCAACCAGATTTA 59.733 43.478 0.00 0.00 0.00 1.40
23 24 2.042433 TCCGGGGATTTCAACCAGATTT 59.958 45.455 0.00 0.00 0.00 2.17
24 25 1.638589 TCCGGGGATTTCAACCAGATT 59.361 47.619 0.00 0.00 0.00 2.40
25 26 1.212935 CTCCGGGGATTTCAACCAGAT 59.787 52.381 0.00 0.00 0.00 2.90
26 27 0.618458 CTCCGGGGATTTCAACCAGA 59.382 55.000 0.00 0.00 0.00 3.86
27 28 0.394352 CCTCCGGGGATTTCAACCAG 60.394 60.000 0.37 0.00 37.23 4.00
28 29 1.688811 CCTCCGGGGATTTCAACCA 59.311 57.895 0.37 0.00 37.23 3.67
29 30 1.753078 GCCTCCGGGGATTTCAACC 60.753 63.158 0.37 0.00 37.23 3.77
30 31 0.544697 TAGCCTCCGGGGATTTCAAC 59.455 55.000 0.37 0.00 37.23 3.18
31 32 1.064979 GTTAGCCTCCGGGGATTTCAA 60.065 52.381 0.37 0.00 37.23 2.69
32 33 0.544697 GTTAGCCTCCGGGGATTTCA 59.455 55.000 0.37 0.00 37.23 2.69
33 34 0.179026 GGTTAGCCTCCGGGGATTTC 60.179 60.000 0.37 0.00 37.23 2.17
34 35 0.917333 TGGTTAGCCTCCGGGGATTT 60.917 55.000 0.37 0.00 37.23 2.17
35 36 0.917333 TTGGTTAGCCTCCGGGGATT 60.917 55.000 0.37 0.00 37.23 3.01
36 37 1.307517 TTGGTTAGCCTCCGGGGAT 60.308 57.895 0.37 3.40 37.23 3.85
37 38 1.993391 CTTGGTTAGCCTCCGGGGA 60.993 63.158 0.37 0.00 37.23 4.81
38 39 2.590092 CTTGGTTAGCCTCCGGGG 59.410 66.667 0.00 0.00 35.27 5.73
39 40 2.124695 GCTTGGTTAGCCTCCGGG 60.125 66.667 0.00 0.00 44.48 5.73
46 47 2.437895 GGGGGTCGCTTGGTTAGC 60.438 66.667 0.00 0.00 46.83 3.09
47 48 2.125269 CGGGGGTCGCTTGGTTAG 60.125 66.667 0.00 0.00 0.00 2.34
64 65 2.195567 TTGCACAGAAGCCACCTGC 61.196 57.895 0.00 0.00 41.71 4.85
65 66 1.102809 TGTTGCACAGAAGCCACCTG 61.103 55.000 0.00 0.00 37.64 4.00
66 67 0.395586 TTGTTGCACAGAAGCCACCT 60.396 50.000 0.00 0.00 29.75 4.00
67 68 0.031178 CTTGTTGCACAGAAGCCACC 59.969 55.000 0.00 0.00 29.75 4.61
68 69 0.595825 GCTTGTTGCACAGAAGCCAC 60.596 55.000 15.24 0.00 42.31 5.01
69 70 0.752743 AGCTTGTTGCACAGAAGCCA 60.753 50.000 19.63 0.00 45.94 4.75
70 71 0.039708 GAGCTTGTTGCACAGAAGCC 60.040 55.000 19.63 11.90 45.94 4.35
71 72 0.664761 TGAGCTTGTTGCACAGAAGC 59.335 50.000 17.20 17.20 45.94 3.86
76 77 0.816373 TTTGCTGAGCTTGTTGCACA 59.184 45.000 5.83 0.00 45.94 4.57
77 78 1.066002 TCTTTGCTGAGCTTGTTGCAC 59.934 47.619 5.83 0.00 45.94 4.57
78 79 1.391577 TCTTTGCTGAGCTTGTTGCA 58.608 45.000 5.83 0.00 45.94 4.08
79 80 2.122564 GTTCTTTGCTGAGCTTGTTGC 58.877 47.619 5.83 0.00 43.29 4.17
80 81 3.111098 GTGTTCTTTGCTGAGCTTGTTG 58.889 45.455 5.83 0.00 0.00 3.33
81 82 2.754552 TGTGTTCTTTGCTGAGCTTGTT 59.245 40.909 5.83 0.00 0.00 2.83
82 83 2.368439 TGTGTTCTTTGCTGAGCTTGT 58.632 42.857 5.83 0.00 0.00 3.16
83 84 3.252701 AGATGTGTTCTTTGCTGAGCTTG 59.747 43.478 5.83 0.00 0.00 4.01
84 85 3.484407 AGATGTGTTCTTTGCTGAGCTT 58.516 40.909 5.83 0.00 0.00 3.74
85 86 3.137446 AGATGTGTTCTTTGCTGAGCT 57.863 42.857 5.83 0.00 0.00 4.09
86 87 3.911661 AAGATGTGTTCTTTGCTGAGC 57.088 42.857 0.00 0.00 42.15 4.26
94 95 3.496130 CACTCGCTCAAAGATGTGTTCTT 59.504 43.478 0.00 0.00 46.92 2.52
95 96 3.062763 CACTCGCTCAAAGATGTGTTCT 58.937 45.455 0.00 0.00 35.70 3.01
96 97 2.158449 CCACTCGCTCAAAGATGTGTTC 59.842 50.000 0.00 0.00 0.00 3.18
97 98 2.146342 CCACTCGCTCAAAGATGTGTT 58.854 47.619 0.00 0.00 0.00 3.32
98 99 1.070758 ACCACTCGCTCAAAGATGTGT 59.929 47.619 0.00 0.00 0.00 3.72
99 100 1.728971 GACCACTCGCTCAAAGATGTG 59.271 52.381 0.00 0.00 0.00 3.21
100 101 1.670087 CGACCACTCGCTCAAAGATGT 60.670 52.381 0.00 0.00 31.91 3.06
101 102 0.994995 CGACCACTCGCTCAAAGATG 59.005 55.000 0.00 0.00 31.91 2.90
102 103 0.108615 CCGACCACTCGCTCAAAGAT 60.109 55.000 0.00 0.00 38.70 2.40
103 104 1.289066 CCGACCACTCGCTCAAAGA 59.711 57.895 0.00 0.00 38.70 2.52
104 105 0.242825 TACCGACCACTCGCTCAAAG 59.757 55.000 0.00 0.00 38.70 2.77
105 106 0.242825 CTACCGACCACTCGCTCAAA 59.757 55.000 0.00 0.00 38.70 2.69
106 107 1.592400 CCTACCGACCACTCGCTCAA 61.592 60.000 0.00 0.00 38.70 3.02
107 108 2.044555 CCTACCGACCACTCGCTCA 61.045 63.158 0.00 0.00 38.70 4.26
108 109 2.772691 CCCTACCGACCACTCGCTC 61.773 68.421 0.00 0.00 38.70 5.03
109 110 2.754658 CCCTACCGACCACTCGCT 60.755 66.667 0.00 0.00 38.70 4.93
110 111 4.509737 GCCCTACCGACCACTCGC 62.510 72.222 0.00 0.00 38.70 5.03
111 112 3.834799 GGCCCTACCGACCACTCG 61.835 72.222 0.00 0.00 39.83 4.18
128 129 1.200716 TCAAGCTAACCACCGTCTACG 59.799 52.381 0.00 0.00 39.44 3.51
129 130 3.251571 CTTCAAGCTAACCACCGTCTAC 58.748 50.000 0.00 0.00 0.00 2.59
130 131 2.353406 GCTTCAAGCTAACCACCGTCTA 60.353 50.000 0.71 0.00 38.45 2.59
131 132 1.608283 GCTTCAAGCTAACCACCGTCT 60.608 52.381 0.71 0.00 38.45 4.18
132 133 0.796927 GCTTCAAGCTAACCACCGTC 59.203 55.000 0.71 0.00 38.45 4.79
133 134 2.928416 GCTTCAAGCTAACCACCGT 58.072 52.632 0.71 0.00 38.45 4.83
151 152 1.025812 ATAGAGAAGACGGGCGTGAG 58.974 55.000 0.00 0.00 0.00 3.51
152 153 0.738975 CATAGAGAAGACGGGCGTGA 59.261 55.000 0.00 0.00 0.00 4.35
153 154 0.456221 ACATAGAGAAGACGGGCGTG 59.544 55.000 0.00 0.00 0.00 5.34
154 155 1.183549 AACATAGAGAAGACGGGCGT 58.816 50.000 0.00 0.00 0.00 5.68
155 156 1.927174 CAAACATAGAGAAGACGGGCG 59.073 52.381 0.00 0.00 0.00 6.13
156 157 2.930682 GTCAAACATAGAGAAGACGGGC 59.069 50.000 0.00 0.00 0.00 6.13
157 158 4.457834 AGTCAAACATAGAGAAGACGGG 57.542 45.455 0.00 0.00 0.00 5.28
158 159 6.197364 ACTAGTCAAACATAGAGAAGACGG 57.803 41.667 0.00 0.00 0.00 4.79
159 160 9.866936 GTATACTAGTCAAACATAGAGAAGACG 57.133 37.037 0.00 0.00 0.00 4.18
207 209 6.595326 TCCTAAACTCATACATGCTGACAAAG 59.405 38.462 0.00 0.00 0.00 2.77
219 221 8.643324 AGATCTAACCACATCCTAAACTCATAC 58.357 37.037 0.00 0.00 0.00 2.39
223 225 7.113658 TGAGATCTAACCACATCCTAAACTC 57.886 40.000 0.00 0.00 0.00 3.01
224 226 6.407525 GCTGAGATCTAACCACATCCTAAACT 60.408 42.308 0.00 0.00 0.00 2.66
238 240 3.764434 AGTTTCACTCGGCTGAGATCTAA 59.236 43.478 29.29 13.31 45.57 2.10
249 251 5.061064 CGAGACTTGATTAAGTTTCACTCGG 59.939 44.000 21.60 10.34 46.79 4.63
251 253 7.542477 TGATCGAGACTTGATTAAGTTTCACTC 59.458 37.037 17.54 13.60 46.79 3.51
281 283 9.944663 TTTGTCTTGTTTTCTATATGTTGTGTC 57.055 29.630 0.00 0.00 0.00 3.67
311 314 8.713271 GGACATCCGTGCAAAATTTTATTTTAA 58.287 29.630 2.44 0.00 32.83 1.52
376 379 7.439655 GGATTGCTAAATCGACTGAGACTTAAT 59.560 37.037 0.00 0.00 42.77 1.40
386 389 5.163195 ACCTAATGGGATTGCTAAATCGACT 60.163 40.000 0.00 0.00 42.77 4.18
409 412 7.736893 TGAGAGGGCTTTTATAGAGGATAAAC 58.263 38.462 0.00 0.00 39.28 2.01
429 432 5.277202 CGGATAGAAACATGCACATTGAGAG 60.277 44.000 0.00 0.00 0.00 3.20
458 461 3.673902 TGTGTATCTGTGTGTGATTGGG 58.326 45.455 0.00 0.00 0.00 4.12
469 472 4.157840 TGCGTATGTCTCTTGTGTATCTGT 59.842 41.667 0.00 0.00 0.00 3.41
491 494 4.107622 GCAGGTTGCAGCTTATGTTTATG 58.892 43.478 0.00 0.00 44.26 1.90
494 497 2.730550 GCAGGTTGCAGCTTATGTTT 57.269 45.000 0.00 0.00 44.26 2.83
645 649 3.670055 GCAATGAATCTTTGTCAACGTGG 59.330 43.478 10.01 0.00 0.00 4.94
696 700 3.513406 TCGTGTACGAAACGTGCG 58.487 55.556 4.41 9.23 44.75 5.34
720 724 2.339100 TTCGAGTTGCACCGTCGTGA 62.339 55.000 10.40 0.73 43.14 4.35
748 752 1.633852 CTGCTCTGCTTGCGTTCTCC 61.634 60.000 0.00 0.00 0.00 3.71
774 778 3.382227 TGAGGTTGAAGACTTGACACGTA 59.618 43.478 0.00 0.00 0.00 3.57
952 2144 3.378427 GGTTAGGCCTAAATGCTGACAAG 59.622 47.826 26.78 0.00 0.00 3.16
975 2167 3.316868 ACGTTGTGAGGGGTTTTATTGTG 59.683 43.478 0.00 0.00 0.00 3.33
977 2169 3.855524 GCACGTTGTGAGGGGTTTTATTG 60.856 47.826 0.24 0.00 35.23 1.90
1009 2210 1.145531 TCGGGTATCTGGGTATTCGGA 59.854 52.381 0.00 0.00 0.00 4.55
1021 2222 4.092968 GTCTGTTGTTTGTGATCGGGTATC 59.907 45.833 0.00 0.00 34.93 2.24
1028 2229 2.639751 GTGCGTCTGTTGTTTGTGATC 58.360 47.619 0.00 0.00 0.00 2.92
1642 2870 1.349627 CGACGTACACGCGTAGGAT 59.650 57.895 13.44 0.00 45.79 3.24
1707 2935 3.905153 TTGGCCAGCGAGGGAGAGA 62.905 63.158 5.11 0.00 38.09 3.10
1787 3015 1.001974 TGAGGTCCCAATCACGAACAG 59.998 52.381 0.00 0.00 0.00 3.16
1830 3061 0.889186 GCGTTCCCTTCTTCTTGCCA 60.889 55.000 0.00 0.00 0.00 4.92
1911 3142 1.529244 AAAGGAGCACACCACCAGC 60.529 57.895 0.00 0.00 0.00 4.85
2087 3325 8.623310 TTTTTAAGTAGGAAAAGAAAAGTGCG 57.377 30.769 0.00 0.00 0.00 5.34
2113 3351 2.501261 GGTGAACGTAAGCTTTTCCCT 58.499 47.619 3.20 0.00 45.62 4.20
2175 3413 0.744874 TCCGATCAACAGACGATCCC 59.255 55.000 0.00 0.00 36.69 3.85
2248 3489 3.489416 GGTCATTTTTCTGAAACAACGGC 59.511 43.478 1.58 0.00 0.00 5.68
2261 3502 0.971386 CCAGCTGCAGGGTCATTTTT 59.029 50.000 17.12 0.00 0.00 1.94
2303 3544 4.007644 CAGCCCTCCGAGCACACA 62.008 66.667 0.00 0.00 0.00 3.72
2333 3574 2.367377 CCCTCCCAGATCCAGCCA 60.367 66.667 0.00 0.00 0.00 4.75
2335 3576 3.092511 TGCCCTCCCAGATCCAGC 61.093 66.667 0.00 0.00 0.00 4.85
2449 3706 3.044894 GGAGGAGAAATCACAGGGATCT 58.955 50.000 0.00 0.00 34.28 2.75
2489 3746 2.665185 GGAGCAACAACGTCGGCT 60.665 61.111 0.00 3.33 39.75 5.52
2574 3831 2.437716 CGCCACCGCAACCCTAAT 60.438 61.111 0.00 0.00 34.03 1.73
2602 3861 1.480137 CCAAATTCAGGGGCGCAAATA 59.520 47.619 10.83 0.00 0.00 1.40
2645 3904 1.901238 GCAAAATCCATTCCCCACCCT 60.901 52.381 0.00 0.00 0.00 4.34
2694 3953 5.298276 GTCAGGTGATGAAACAACAAACCTA 59.702 40.000 0.00 0.00 40.43 3.08
2769 4028 8.947055 AACAGAAAAGTTCATGCTAAAATTGT 57.053 26.923 0.00 0.00 0.00 2.71
2772 4031 9.822185 AGAAAACAGAAAAGTTCATGCTAAAAT 57.178 25.926 0.00 0.00 0.00 1.82
2908 4167 8.141909 AGCTACAACTATTTTGGGAAAAACTTC 58.858 33.333 0.00 0.00 33.47 3.01
2921 4180 5.763876 AGTTCCTGGAGCTACAACTATTT 57.236 39.130 11.70 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.