Multiple sequence alignment - TraesCS4D01G082200

Loading Multiple Alignment...

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 TraesCS4D01G082200 chr4D 100.000 2723 0 0 1 2723 55566003 55568725 0.000000e+00 5029.0
1 TraesCS4D01G082200 chr4D 89.720 107 11 0 1474 1580 508474955 508475061 1.310000e-28 137.0
2 TraesCS4D01G082200 chr4A 94.866 1266 37 17 496 1736 541359049 541357787 0.000000e+00 1953.0
3 TraesCS4D01G082200 chr4A 89.629 916 84 5 1818 2723 717732840 717733754 0.000000e+00 1155.0
4 TraesCS4D01G082200 chr4A 86.016 379 30 13 134 504 541359470 541359107 4.250000e-103 385.0
5 TraesCS4D01G082200 chr4A 96.078 51 2 0 27 77 541359543 541359493 1.740000e-12 84.2
6 TraesCS4D01G082200 chr4B 92.368 1153 38 16 618 1736 82606984 82608120 0.000000e+00 1596.0
7 TraesCS4D01G082200 chr4B 88.974 916 90 7 1818 2723 107854814 107853900 0.000000e+00 1122.0
8 TraesCS4D01G082200 chr4B 89.916 238 19 3 1158 1392 404457864 404458099 4.410000e-78 302.0
9 TraesCS4D01G082200 chr4B 84.688 320 14 16 134 439 82606124 82606422 1.230000e-73 287.0
10 TraesCS4D01G082200 chr3A 91.366 915 70 3 1818 2723 649570599 649569685 0.000000e+00 1243.0
11 TraesCS4D01G082200 chr3A 89.496 238 20 3 1158 1392 265372324 265372089 2.050000e-76 296.0
12 TraesCS4D01G082200 chr3B 88.634 915 94 6 1818 2723 784078804 784079717 0.000000e+00 1105.0
13 TraesCS4D01G082200 chr3B 84.498 916 126 8 1818 2723 45376067 45375158 0.000000e+00 891.0
14 TraesCS4D01G082200 chr5B 91.691 686 57 0 2038 2723 677680974 677680289 0.000000e+00 952.0
15 TraesCS4D01G082200 chr5B 85.357 560 61 14 1109 1656 422567914 422568464 6.580000e-156 560.0
16 TraesCS4D01G082200 chr5B 84.938 405 48 7 1818 2211 529624384 529624786 5.460000e-107 398.0
17 TraesCS4D01G082200 chr2B 82.637 910 148 4 1821 2721 708052924 708052016 0.000000e+00 797.0
18 TraesCS4D01G082200 chr2B 81.271 913 156 8 1821 2722 708024747 708023839 0.000000e+00 725.0
19 TraesCS4D01G082200 chr7B 81.769 916 156 7 1817 2722 567991388 567992302 0.000000e+00 756.0
20 TraesCS4D01G082200 chr7B 90.336 238 17 5 1158 1392 5327154 5326920 9.470000e-80 307.0
21 TraesCS4D01G082200 chr5A 83.129 652 73 23 1109 1732 458791315 458790673 6.580000e-156 560.0
22 TraesCS4D01G082200 chr5D 84.806 566 65 14 1109 1662 357870053 357869497 1.430000e-152 549.0
23 TraesCS4D01G082200 chr1D 90.336 238 18 4 1158 1392 96913019 96913254 9.470000e-80 307.0


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 TraesCS4D01G082200 chr4D 55566003 55568725 2722 False 5029.0 5029 100.000 1 2723 1 chr4D.!!$F1 2722
1 TraesCS4D01G082200 chr4A 717732840 717733754 914 False 1155.0 1155 89.629 1818 2723 1 chr4A.!!$F1 905
2 TraesCS4D01G082200 chr4A 541357787 541359543 1756 True 807.4 1953 92.320 27 1736 3 chr4A.!!$R1 1709
3 TraesCS4D01G082200 chr4B 107853900 107854814 914 True 1122.0 1122 88.974 1818 2723 1 chr4B.!!$R1 905
4 TraesCS4D01G082200 chr4B 82606124 82608120 1996 False 941.5 1596 88.528 134 1736 2 chr4B.!!$F2 1602
5 TraesCS4D01G082200 chr3A 649569685 649570599 914 True 1243.0 1243 91.366 1818 2723 1 chr3A.!!$R2 905
6 TraesCS4D01G082200 chr3B 784078804 784079717 913 False 1105.0 1105 88.634 1818 2723 1 chr3B.!!$F1 905
7 TraesCS4D01G082200 chr3B 45375158 45376067 909 True 891.0 891 84.498 1818 2723 1 chr3B.!!$R1 905
8 TraesCS4D01G082200 chr5B 677680289 677680974 685 True 952.0 952 91.691 2038 2723 1 chr5B.!!$R1 685
9 TraesCS4D01G082200 chr5B 422567914 422568464 550 False 560.0 560 85.357 1109 1656 1 chr5B.!!$F1 547
10 TraesCS4D01G082200 chr2B 708052016 708052924 908 True 797.0 797 82.637 1821 2721 1 chr2B.!!$R2 900
11 TraesCS4D01G082200 chr2B 708023839 708024747 908 True 725.0 725 81.271 1821 2722 1 chr2B.!!$R1 901
12 TraesCS4D01G082200 chr7B 567991388 567992302 914 False 756.0 756 81.769 1817 2722 1 chr7B.!!$F1 905
13 TraesCS4D01G082200 chr5A 458790673 458791315 642 True 560.0 560 83.129 1109 1732 1 chr5A.!!$R1 623
14 TraesCS4D01G082200 chr5D 357869497 357870053 556 True 549.0 549 84.806 1109 1662 1 chr5D.!!$R1 553

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
82 83 0.109597 CCGGCAGTTACTACGTTCGT 60.11 55.0 0.0 2.91 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 2300 3.806949 AAGGGCAGAAGTGTTCCATTA 57.193 42.857 0.0 0.0 0.0 1.9 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
18 19 2.793831 AATAACCATGACAGGGCGC 58.206 52.632 5.94 0.00 0.00 6.53
19 20 0.751643 AATAACCATGACAGGGCGCC 60.752 55.000 21.18 21.18 0.00 6.53
20 21 1.920734 ATAACCATGACAGGGCGCCA 61.921 55.000 30.85 7.48 0.00 5.69
21 22 2.535485 TAACCATGACAGGGCGCCAG 62.535 60.000 30.85 22.56 0.00 4.85
22 23 4.415150 CCATGACAGGGCGCCAGT 62.415 66.667 30.85 25.93 0.00 4.00
23 24 3.129502 CATGACAGGGCGCCAGTG 61.130 66.667 30.85 26.26 0.00 3.66
77 78 2.202837 GGCCCGGCAGTTACTACG 60.203 66.667 12.58 2.35 0.00 3.51
78 79 2.575461 GCCCGGCAGTTACTACGT 59.425 61.111 3.91 0.00 0.00 3.57
79 80 1.079612 GCCCGGCAGTTACTACGTT 60.080 57.895 3.91 0.00 0.00 3.99
80 81 1.080435 GCCCGGCAGTTACTACGTTC 61.080 60.000 3.91 0.00 0.00 3.95
81 82 0.799534 CCCGGCAGTTACTACGTTCG 60.800 60.000 0.00 0.00 0.00 3.95
82 83 0.109597 CCGGCAGTTACTACGTTCGT 60.110 55.000 0.00 2.91 0.00 3.85
83 84 0.979811 CGGCAGTTACTACGTTCGTG 59.020 55.000 8.14 1.39 0.00 4.35
86 87 2.095263 GGCAGTTACTACGTTCGTGGTA 60.095 50.000 15.29 15.29 32.31 3.25
88 89 3.609175 GCAGTTACTACGTTCGTGGTACA 60.609 47.826 18.03 9.27 33.08 2.90
89 90 4.153986 CAGTTACTACGTTCGTGGTACAG 58.846 47.826 18.03 9.41 41.80 2.74
90 91 4.065088 AGTTACTACGTTCGTGGTACAGA 58.935 43.478 18.03 4.80 41.80 3.41
93 94 2.880890 ACTACGTTCGTGGTACAGAGTT 59.119 45.455 12.17 0.00 41.80 3.01
94 95 2.129823 ACGTTCGTGGTACAGAGTTG 57.870 50.000 0.00 0.00 41.80 3.16
95 96 1.677576 ACGTTCGTGGTACAGAGTTGA 59.322 47.619 0.00 0.00 41.80 3.18
96 97 2.099592 ACGTTCGTGGTACAGAGTTGAA 59.900 45.455 0.00 0.00 41.80 2.69
97 98 2.724690 CGTTCGTGGTACAGAGTTGAAG 59.275 50.000 0.00 0.00 41.80 3.02
98 99 3.057734 GTTCGTGGTACAGAGTTGAAGG 58.942 50.000 0.00 0.00 41.80 3.46
99 100 1.000506 TCGTGGTACAGAGTTGAAGGC 59.999 52.381 0.00 0.00 41.80 4.35
100 101 1.809684 GTGGTACAGAGTTGAAGGCC 58.190 55.000 0.00 0.00 41.80 5.19
101 102 1.348036 GTGGTACAGAGTTGAAGGCCT 59.652 52.381 0.00 0.00 41.80 5.19
102 103 1.623811 TGGTACAGAGTTGAAGGCCTC 59.376 52.381 5.23 0.00 0.00 4.70
103 104 1.066071 GGTACAGAGTTGAAGGCCTCC 60.066 57.143 5.23 0.00 0.00 4.30
104 105 0.895530 TACAGAGTTGAAGGCCTCCG 59.104 55.000 5.23 0.00 0.00 4.63
105 106 0.832135 ACAGAGTTGAAGGCCTCCGA 60.832 55.000 5.23 0.00 0.00 4.55
106 107 0.390472 CAGAGTTGAAGGCCTCCGAC 60.390 60.000 5.23 2.24 0.00 4.79
107 108 1.446272 GAGTTGAAGGCCTCCGACG 60.446 63.158 5.23 0.00 0.00 5.12
108 109 2.434359 GTTGAAGGCCTCCGACGG 60.434 66.667 5.23 7.84 0.00 4.79
109 110 2.602267 TTGAAGGCCTCCGACGGA 60.602 61.111 17.28 17.28 0.00 4.69
110 111 1.987855 TTGAAGGCCTCCGACGGAT 60.988 57.895 18.71 0.88 0.00 4.18
111 112 1.956629 TTGAAGGCCTCCGACGGATC 61.957 60.000 18.71 12.21 0.00 3.36
112 113 2.363795 AAGGCCTCCGACGGATCA 60.364 61.111 18.71 0.00 0.00 2.92
113 114 1.956629 GAAGGCCTCCGACGGATCAA 61.957 60.000 18.71 0.00 0.00 2.57
114 115 2.202892 GGCCTCCGACGGATCAAC 60.203 66.667 18.71 7.03 0.00 3.18
115 116 2.722201 GGCCTCCGACGGATCAACT 61.722 63.158 18.71 0.00 0.00 3.16
116 117 1.227002 GCCTCCGACGGATCAACTC 60.227 63.158 18.71 0.00 0.00 3.01
117 118 1.064296 CCTCCGACGGATCAACTCG 59.936 63.158 18.71 3.37 0.00 4.18
118 119 1.064296 CTCCGACGGATCAACTCGG 59.936 63.158 18.71 15.40 46.95 4.63
119 120 2.582498 CCGACGGATCAACTCGGC 60.582 66.667 8.64 0.00 40.52 5.54
121 122 3.255379 GACGGATCAACTCGGCGC 61.255 66.667 0.00 0.00 0.00 6.53
122 123 3.982372 GACGGATCAACTCGGCGCA 62.982 63.158 10.83 0.00 0.00 6.09
123 124 3.554692 CGGATCAACTCGGCGCAC 61.555 66.667 10.83 0.00 0.00 5.34
124 125 3.195698 GGATCAACTCGGCGCACC 61.196 66.667 10.83 0.00 0.00 5.01
125 126 2.434185 GATCAACTCGGCGCACCA 60.434 61.111 10.83 0.00 34.57 4.17
126 127 1.815421 GATCAACTCGGCGCACCAT 60.815 57.895 10.83 0.00 34.57 3.55
127 128 1.766143 GATCAACTCGGCGCACCATC 61.766 60.000 10.83 0.00 34.57 3.51
128 129 2.244117 ATCAACTCGGCGCACCATCT 62.244 55.000 10.83 0.00 34.57 2.90
129 130 2.434884 AACTCGGCGCACCATCTG 60.435 61.111 10.83 0.00 34.57 2.90
147 148 3.294079 GCAACTGCAATGCAAACCT 57.706 47.368 9.92 0.00 43.29 3.50
151 152 2.243602 ACTGCAATGCAAACCTTTGG 57.756 45.000 9.92 0.00 38.41 3.28
157 158 3.876320 GCAATGCAAACCTTTGGAGAAAA 59.124 39.130 0.00 0.00 41.77 2.29
158 159 4.516321 GCAATGCAAACCTTTGGAGAAAAT 59.484 37.500 0.00 0.00 41.77 1.82
159 160 5.008911 GCAATGCAAACCTTTGGAGAAAATT 59.991 36.000 0.00 0.00 41.77 1.82
160 161 6.204495 GCAATGCAAACCTTTGGAGAAAATTA 59.796 34.615 0.00 0.00 41.77 1.40
161 162 7.255070 GCAATGCAAACCTTTGGAGAAAATTAA 60.255 33.333 0.00 0.00 41.77 1.40
162 163 8.619546 CAATGCAAACCTTTGGAGAAAATTAAA 58.380 29.630 0.00 0.00 41.77 1.52
163 164 8.744568 ATGCAAACCTTTGGAGAAAATTAAAA 57.255 26.923 0.00 0.00 41.77 1.52
205 210 4.146564 TGGGCATTCATTCATTCATCGAT 58.853 39.130 0.00 0.00 0.00 3.59
206 211 4.585581 TGGGCATTCATTCATTCATCGATT 59.414 37.500 0.00 0.00 0.00 3.34
208 213 4.921515 GGCATTCATTCATTCATCGATTGG 59.078 41.667 0.00 0.00 0.00 3.16
250 255 1.160137 GGTCTCCACTCAACATGCAC 58.840 55.000 0.00 0.00 0.00 4.57
251 256 0.792640 GTCTCCACTCAACATGCACG 59.207 55.000 0.00 0.00 0.00 5.34
254 259 0.606130 TCCACTCAACATGCACGCAT 60.606 50.000 0.00 0.00 37.08 4.73
259 264 2.352651 ACTCAACATGCACGCATATGAC 59.647 45.455 6.97 0.00 34.91 3.06
338 343 2.569404 CTCCAAGTACAAAGGAGGAGCT 59.431 50.000 16.32 0.00 44.10 4.09
339 344 3.769844 CTCCAAGTACAAAGGAGGAGCTA 59.230 47.826 16.32 0.00 44.10 3.32
340 345 3.769844 TCCAAGTACAAAGGAGGAGCTAG 59.230 47.826 0.00 0.00 0.00 3.42
341 346 3.526534 CAAGTACAAAGGAGGAGCTAGC 58.473 50.000 6.62 6.62 0.00 3.42
344 349 1.880340 CAAAGGAGGAGCTAGCGCG 60.880 63.158 12.54 0.00 42.32 6.86
477 496 3.247648 GTCAGCTTCAAAACGTAAGAGCA 59.752 43.478 0.00 0.00 43.62 4.26
595 743 8.908786 TGAATACTGACAGAAAATTCTCAAGT 57.091 30.769 10.08 0.94 34.74 3.16
694 1123 6.833342 TCGATCATATATACACATGCATGC 57.167 37.500 26.53 11.82 0.00 4.06
713 1142 4.155063 TGCATGTATACAATGCTCAGGT 57.845 40.909 26.31 3.75 41.52 4.00
734 1166 5.433051 AGGTATCCCTTGGATCAAGATGAAA 59.567 40.000 9.01 0.00 43.42 2.69
737 1169 5.722172 TCCCTTGGATCAAGATGAAAGAT 57.278 39.130 9.01 0.00 43.42 2.40
751 1187 5.942826 AGATGAAAGATTGGTCCAAAGAGAC 59.057 40.000 8.75 1.84 35.95 3.36
785 1221 7.149973 TGCATCTTCAAATTTCTCTTGAAAGG 58.850 34.615 0.00 0.00 44.25 3.11
831 1277 5.728637 TGTATTGAGCATCTGGATACGAT 57.271 39.130 0.00 0.00 42.51 3.73
833 1279 4.879197 ATTGAGCATCTGGATACGATCA 57.121 40.909 0.00 0.00 42.51 2.92
836 1282 4.371786 TGAGCATCTGGATACGATCAAAC 58.628 43.478 0.00 0.00 42.51 2.93
887 1338 0.618981 CCCAACCTCTACTTCCACCC 59.381 60.000 0.00 0.00 0.00 4.61
961 1412 1.482621 CGATCCAATGCACCGACTCG 61.483 60.000 0.00 0.00 0.00 4.18
963 1414 3.499737 CCAATGCACCGACTCGCC 61.500 66.667 0.00 0.00 0.00 5.54
1736 2220 8.139521 AGGAAGAAGTAAAGAAAACAACTACG 57.860 34.615 0.00 0.00 0.00 3.51
1737 2221 7.226128 AGGAAGAAGTAAAGAAAACAACTACGG 59.774 37.037 0.00 0.00 0.00 4.02
1738 2222 7.225341 GGAAGAAGTAAAGAAAACAACTACGGA 59.775 37.037 0.00 0.00 0.00 4.69
1739 2223 7.710766 AGAAGTAAAGAAAACAACTACGGAG 57.289 36.000 0.00 0.00 0.00 4.63
1741 2225 8.416329 AGAAGTAAAGAAAACAACTACGGAGTA 58.584 33.333 0.00 0.00 45.11 2.59
1758 2242 7.161773 ACGGAGTAGTTACATTTAAGTAGCA 57.838 36.000 0.00 0.00 41.94 3.49
1759 2243 7.031975 ACGGAGTAGTTACATTTAAGTAGCAC 58.968 38.462 0.00 0.00 41.94 4.40
1760 2244 7.031372 CGGAGTAGTTACATTTAAGTAGCACA 58.969 38.462 0.00 0.00 0.00 4.57
1761 2245 7.008992 CGGAGTAGTTACATTTAAGTAGCACAC 59.991 40.741 0.00 0.00 0.00 3.82
1762 2246 7.816031 GGAGTAGTTACATTTAAGTAGCACACA 59.184 37.037 0.00 0.00 0.00 3.72
1763 2247 9.367444 GAGTAGTTACATTTAAGTAGCACACAT 57.633 33.333 0.00 0.00 0.00 3.21
1771 2255 9.798994 ACATTTAAGTAGCACACATACTACTAC 57.201 33.333 3.31 0.00 46.46 2.73
1772 2256 8.955002 CATTTAAGTAGCACACATACTACTACG 58.045 37.037 3.31 0.00 46.46 3.51
1773 2257 7.848223 TTAAGTAGCACACATACTACTACGA 57.152 36.000 3.31 0.00 46.46 3.43
1774 2258 6.748333 AAGTAGCACACATACTACTACGAA 57.252 37.500 3.31 0.00 46.46 3.85
1775 2259 6.939132 AGTAGCACACATACTACTACGAAT 57.061 37.500 0.98 0.00 45.58 3.34
1776 2260 8.442632 AAGTAGCACACATACTACTACGAATA 57.557 34.615 3.31 0.00 46.46 1.75
1777 2261 7.859598 AGTAGCACACATACTACTACGAATAC 58.140 38.462 0.98 0.00 45.58 1.89
1778 2262 6.939132 AGCACACATACTACTACGAATACT 57.061 37.500 0.00 0.00 0.00 2.12
1779 2263 6.726230 AGCACACATACTACTACGAATACTG 58.274 40.000 0.00 0.00 0.00 2.74
1780 2264 6.318144 AGCACACATACTACTACGAATACTGT 59.682 38.462 0.00 0.00 0.00 3.55
1781 2265 6.971184 GCACACATACTACTACGAATACTGTT 59.029 38.462 0.00 0.00 0.00 3.16
1782 2266 7.487189 GCACACATACTACTACGAATACTGTTT 59.513 37.037 0.00 0.00 0.00 2.83
1783 2267 9.992910 CACACATACTACTACGAATACTGTTTA 57.007 33.333 0.00 0.00 0.00 2.01
1906 2390 5.734855 TTCTATTCCTTATTTGCGCAGAC 57.265 39.130 11.31 0.00 0.00 3.51
1907 2391 4.765273 TCTATTCCTTATTTGCGCAGACA 58.235 39.130 11.31 0.00 0.00 3.41
1972 2465 0.030369 GTGGGAGTATACGCTCACCG 59.970 60.000 24.50 0.00 40.60 4.94
2015 2508 2.927014 GCGGACGACAGTCTCATCTTTT 60.927 50.000 0.00 0.00 46.29 2.27
2134 2627 1.255882 ATTTCAGCCCGAATGCACAA 58.744 45.000 0.00 0.00 32.32 3.33
2137 2630 1.081242 CAGCCCGAATGCACAACAC 60.081 57.895 0.00 0.00 0.00 3.32
2205 2699 5.622233 AAGCTTTCACGGAAAGATATTTGGC 60.622 40.000 22.63 10.67 45.62 4.52
2227 2721 0.895100 TACCAACTGCGGTAGGACGT 60.895 55.000 0.00 0.00 40.67 4.34
2291 2785 1.614051 CCAGTATGCAAGGCTGGTCAA 60.614 52.381 20.04 0.00 43.42 3.18
2342 2836 7.398024 AGAGGTATTGCTGAAGTCAGTTATTT 58.602 34.615 9.94 0.00 45.45 1.40
2417 2911 4.022935 GCAAACAACTCACATCCTCAATGA 60.023 41.667 0.00 0.00 38.83 2.57
2441 2935 2.634815 ATATTGGTGGAGCAGCTCTG 57.365 50.000 21.99 0.00 32.61 3.35
2464 2958 1.553690 ATAGGCGGTCCTTGCACTGT 61.554 55.000 0.00 0.00 40.66 3.55
2647 3141 3.577848 ACTGTGATTTTATGCAGGCCAAA 59.422 39.130 5.01 0.00 33.62 3.28
2699 3193 2.094675 CAATCATTGCGGGGAGAAAGT 58.905 47.619 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.751643 GGCGCCCTGTCATGGTTATT 60.752 55.000 18.11 0.00 0.00 1.40
1 2 1.152963 GGCGCCCTGTCATGGTTAT 60.153 57.895 18.11 0.00 0.00 1.89
2 3 2.270850 GGCGCCCTGTCATGGTTA 59.729 61.111 18.11 0.00 0.00 2.85
3 4 3.925630 CTGGCGCCCTGTCATGGTT 62.926 63.158 26.77 0.00 0.00 3.67
4 5 4.415150 CTGGCGCCCTGTCATGGT 62.415 66.667 26.77 0.00 0.00 3.55
5 6 4.415150 ACTGGCGCCCTGTCATGG 62.415 66.667 26.77 6.12 29.71 3.66
6 7 3.129502 CACTGGCGCCCTGTCATG 61.130 66.667 26.77 9.12 33.44 3.07
39 40 3.046087 GCAAGCAGCTCACGCTCA 61.046 61.111 0.00 0.00 45.15 4.26
69 70 4.083802 ACTCTGTACCACGAACGTAGTAAC 60.084 45.833 7.13 3.91 45.00 2.50
77 78 3.057734 CCTTCAACTCTGTACCACGAAC 58.942 50.000 0.00 0.00 0.00 3.95
78 79 2.547218 GCCTTCAACTCTGTACCACGAA 60.547 50.000 0.00 0.00 0.00 3.85
79 80 1.000506 GCCTTCAACTCTGTACCACGA 59.999 52.381 0.00 0.00 0.00 4.35
80 81 1.429463 GCCTTCAACTCTGTACCACG 58.571 55.000 0.00 0.00 0.00 4.94
81 82 1.348036 AGGCCTTCAACTCTGTACCAC 59.652 52.381 0.00 0.00 0.00 4.16
82 83 1.623811 GAGGCCTTCAACTCTGTACCA 59.376 52.381 6.77 0.00 0.00 3.25
83 84 1.066071 GGAGGCCTTCAACTCTGTACC 60.066 57.143 6.77 0.00 34.22 3.34
86 87 0.832135 TCGGAGGCCTTCAACTCTGT 60.832 55.000 12.82 0.00 40.26 3.41
88 89 1.878656 CGTCGGAGGCCTTCAACTCT 61.879 60.000 12.82 0.00 34.22 3.24
89 90 1.446272 CGTCGGAGGCCTTCAACTC 60.446 63.158 12.82 0.00 0.00 3.01
90 91 2.657237 CGTCGGAGGCCTTCAACT 59.343 61.111 12.82 0.00 0.00 3.16
93 94 2.363795 ATCCGTCGGAGGCCTTCA 60.364 61.111 20.50 0.00 34.05 3.02
94 95 1.956629 TTGATCCGTCGGAGGCCTTC 61.957 60.000 20.50 2.57 34.05 3.46
95 96 1.987855 TTGATCCGTCGGAGGCCTT 60.988 57.895 20.50 1.47 34.05 4.35
96 97 2.363795 TTGATCCGTCGGAGGCCT 60.364 61.111 20.50 3.86 34.05 5.19
97 98 2.202892 GTTGATCCGTCGGAGGCC 60.203 66.667 20.50 11.56 34.05 5.19
98 99 1.227002 GAGTTGATCCGTCGGAGGC 60.227 63.158 20.50 14.32 34.05 4.70
99 100 1.064296 CGAGTTGATCCGTCGGAGG 59.936 63.158 20.50 0.00 34.05 4.30
100 101 4.692129 CGAGTTGATCCGTCGGAG 57.308 61.111 20.50 0.00 34.05 4.63
103 104 2.949678 CGCCGAGTTGATCCGTCG 60.950 66.667 0.00 0.00 0.00 5.12
104 105 3.255379 GCGCCGAGTTGATCCGTC 61.255 66.667 0.00 0.00 0.00 4.79
105 106 4.063967 TGCGCCGAGTTGATCCGT 62.064 61.111 4.18 0.00 0.00 4.69
106 107 3.554692 GTGCGCCGAGTTGATCCG 61.555 66.667 4.18 0.00 0.00 4.18
107 108 3.195698 GGTGCGCCGAGTTGATCC 61.196 66.667 4.18 0.00 0.00 3.36
108 109 1.766143 GATGGTGCGCCGAGTTGATC 61.766 60.000 12.58 3.99 37.67 2.92
109 110 1.815421 GATGGTGCGCCGAGTTGAT 60.815 57.895 12.58 0.00 37.67 2.57
110 111 2.434185 GATGGTGCGCCGAGTTGA 60.434 61.111 12.58 0.00 37.67 3.18
111 112 2.434884 AGATGGTGCGCCGAGTTG 60.435 61.111 12.58 0.00 37.67 3.16
112 113 2.434884 CAGATGGTGCGCCGAGTT 60.435 61.111 12.58 0.00 37.67 3.01
129 130 1.585297 AAGGTTTGCATTGCAGTTGC 58.415 45.000 11.76 14.80 40.61 4.17
130 131 2.288458 CCAAAGGTTTGCATTGCAGTTG 59.712 45.455 11.76 11.38 40.61 3.16
131 132 2.170187 TCCAAAGGTTTGCATTGCAGTT 59.830 40.909 11.76 2.03 40.61 3.16
132 133 1.761784 TCCAAAGGTTTGCATTGCAGT 59.238 42.857 11.76 0.00 40.61 4.40
147 148 7.697691 TGCGCAAAATTTTAATTTTCTCCAAA 58.302 26.923 8.16 0.00 44.38 3.28
151 152 7.184307 GCATGCGCAAAATTTTAATTTTCTC 57.816 32.000 17.11 5.31 44.38 2.87
226 231 3.691342 TTGAGTGGAGACCGGCCG 61.691 66.667 21.04 21.04 0.00 6.13
227 232 2.047179 GTTGAGTGGAGACCGGCC 60.047 66.667 0.00 0.00 0.00 6.13
228 233 1.021390 CATGTTGAGTGGAGACCGGC 61.021 60.000 0.00 0.00 0.00 6.13
250 255 2.238942 TTACAGCTGGGTCATATGCG 57.761 50.000 19.93 0.00 0.00 4.73
251 256 2.291741 GCTTTACAGCTGGGTCATATGC 59.708 50.000 19.93 7.29 43.51 3.14
254 259 1.742411 GCGCTTTACAGCTGGGTCATA 60.742 52.381 19.93 0.00 44.85 2.15
259 264 4.166011 GCGCGCTTTACAGCTGGG 62.166 66.667 26.67 6.29 44.85 4.45
338 343 5.862323 TGTTTAATTAAATTTTGCCGCGCTA 59.138 32.000 13.54 0.00 0.00 4.26
339 344 4.686554 TGTTTAATTAAATTTTGCCGCGCT 59.313 33.333 13.54 0.00 0.00 5.92
340 345 4.947420 TGTTTAATTAAATTTTGCCGCGC 58.053 34.783 13.54 0.00 0.00 6.86
341 346 6.676578 GTGATGTTTAATTAAATTTTGCCGCG 59.323 34.615 13.54 0.00 0.00 6.46
344 349 6.958752 GCCGTGATGTTTAATTAAATTTTGCC 59.041 34.615 13.54 1.15 0.00 4.52
346 351 7.943952 TCGCCGTGATGTTTAATTAAATTTTG 58.056 30.769 13.54 3.25 0.00 2.44
347 352 8.696410 ATCGCCGTGATGTTTAATTAAATTTT 57.304 26.923 13.54 2.55 35.45 1.82
595 743 5.885912 AGCTTGGAACTGTTTCTAAGTTGAA 59.114 36.000 10.89 0.00 46.80 2.69
666 1091 7.428826 TGCATGTGTATATATGATCGATCTCC 58.571 38.462 25.02 1.09 0.00 3.71
694 1123 6.974932 GGATACCTGAGCATTGTATACATG 57.025 41.667 6.36 8.40 0.00 3.21
713 1142 6.829985 TCTTTCATCTTGATCCAAGGGATA 57.170 37.500 6.83 1.44 43.27 2.59
751 1187 0.394216 TTGAAGATGCATGGTCCCGG 60.394 55.000 2.46 0.00 0.00 5.73
752 1188 1.462616 TTTGAAGATGCATGGTCCCG 58.537 50.000 2.46 0.00 0.00 5.14
785 1221 5.621193 TGGCAAAATTATCCTAGCTAGTCC 58.379 41.667 19.31 5.32 0.00 3.85
831 1277 9.829507 ATTTTGATTATGTGTTTTGGAGTTTGA 57.170 25.926 0.00 0.00 0.00 2.69
833 1279 9.829507 TGATTTTGATTATGTGTTTTGGAGTTT 57.170 25.926 0.00 0.00 0.00 2.66
887 1338 3.553105 GGTGCTACGTCGTTATTTAAGGG 59.447 47.826 1.78 0.00 0.00 3.95
961 1412 1.153086 ATGATTCGGCTGGAGTGGC 60.153 57.895 0.00 0.00 0.00 5.01
963 1414 0.877649 CGGATGATTCGGCTGGAGTG 60.878 60.000 0.00 0.00 0.00 3.51
1736 2220 7.816031 TGTGTGCTACTTAAATGTAACTACTCC 59.184 37.037 0.00 0.00 0.00 3.85
1737 2221 8.752766 TGTGTGCTACTTAAATGTAACTACTC 57.247 34.615 0.00 0.00 0.00 2.59
1753 2237 7.797587 CAGTATTCGTAGTAGTATGTGTGCTAC 59.202 40.741 0.00 0.00 42.00 3.58
1754 2238 7.496920 ACAGTATTCGTAGTAGTATGTGTGCTA 59.503 37.037 0.00 0.00 0.00 3.49
1755 2239 6.318144 ACAGTATTCGTAGTAGTATGTGTGCT 59.682 38.462 0.00 0.00 0.00 4.40
1756 2240 6.493116 ACAGTATTCGTAGTAGTATGTGTGC 58.507 40.000 0.00 0.00 0.00 4.57
1757 2241 8.906636 AAACAGTATTCGTAGTAGTATGTGTG 57.093 34.615 0.00 0.00 0.00 3.82
1795 2279 8.733458 CCATTATTCATCTTTCTCTTCACACAA 58.267 33.333 0.00 0.00 0.00 3.33
1796 2280 8.102676 TCCATTATTCATCTTTCTCTTCACACA 58.897 33.333 0.00 0.00 0.00 3.72
1797 2281 8.498054 TCCATTATTCATCTTTCTCTTCACAC 57.502 34.615 0.00 0.00 0.00 3.82
1798 2282 8.950210 GTTCCATTATTCATCTTTCTCTTCACA 58.050 33.333 0.00 0.00 0.00 3.58
1799 2283 8.950210 TGTTCCATTATTCATCTTTCTCTTCAC 58.050 33.333 0.00 0.00 0.00 3.18
1800 2284 8.950210 GTGTTCCATTATTCATCTTTCTCTTCA 58.050 33.333 0.00 0.00 0.00 3.02
1801 2285 9.171877 AGTGTTCCATTATTCATCTTTCTCTTC 57.828 33.333 0.00 0.00 0.00 2.87
1802 2286 9.525826 AAGTGTTCCATTATTCATCTTTCTCTT 57.474 29.630 0.00 0.00 0.00 2.85
1803 2287 9.171877 GAAGTGTTCCATTATTCATCTTTCTCT 57.828 33.333 0.00 0.00 0.00 3.10
1804 2288 9.171877 AGAAGTGTTCCATTATTCATCTTTCTC 57.828 33.333 0.00 0.00 0.00 2.87
1805 2289 8.954350 CAGAAGTGTTCCATTATTCATCTTTCT 58.046 33.333 0.00 0.00 0.00 2.52
1806 2290 7.699812 GCAGAAGTGTTCCATTATTCATCTTTC 59.300 37.037 0.00 0.00 0.00 2.62
1807 2291 7.363268 GGCAGAAGTGTTCCATTATTCATCTTT 60.363 37.037 0.00 0.00 0.00 2.52
1808 2292 6.096001 GGCAGAAGTGTTCCATTATTCATCTT 59.904 38.462 0.00 0.00 0.00 2.40
1809 2293 5.591877 GGCAGAAGTGTTCCATTATTCATCT 59.408 40.000 0.00 0.00 0.00 2.90
1810 2294 5.221126 GGGCAGAAGTGTTCCATTATTCATC 60.221 44.000 0.00 0.00 0.00 2.92
1811 2295 4.646492 GGGCAGAAGTGTTCCATTATTCAT 59.354 41.667 0.00 0.00 0.00 2.57
1812 2296 4.016444 GGGCAGAAGTGTTCCATTATTCA 58.984 43.478 0.00 0.00 0.00 2.57
1813 2297 4.273318 AGGGCAGAAGTGTTCCATTATTC 58.727 43.478 0.00 0.00 0.00 1.75
1814 2298 4.322057 AGGGCAGAAGTGTTCCATTATT 57.678 40.909 0.00 0.00 0.00 1.40
1815 2299 4.322057 AAGGGCAGAAGTGTTCCATTAT 57.678 40.909 0.00 0.00 0.00 1.28
1816 2300 3.806949 AAGGGCAGAAGTGTTCCATTA 57.193 42.857 0.00 0.00 0.00 1.90
1906 2390 8.560576 AATTGTTCATTAACGAAGTGAAACTG 57.439 30.769 0.00 0.00 45.00 3.16
1907 2391 9.581099 AAAATTGTTCATTAACGAAGTGAAACT 57.419 25.926 0.00 0.00 45.00 2.66
2134 2627 3.764237 ACTATTTCACGAACAGGGTGT 57.236 42.857 0.00 0.00 36.76 4.16
2137 2630 4.693566 TGCTTTACTATTTCACGAACAGGG 59.306 41.667 0.00 0.00 0.00 4.45
2205 2699 1.134560 GTCCTACCGCAGTTGGTAGAG 59.865 57.143 18.97 10.54 43.56 2.43
2227 2721 0.387929 CGAAGGAGCCGCTGGTTATA 59.612 55.000 0.00 0.00 0.00 0.98
2291 2785 1.582968 CACATGCAAGGAAGCGCTT 59.417 52.632 25.35 25.35 37.31 4.68
2342 2836 3.130734 ACTGAAGGTAGGGATGGCTTA 57.869 47.619 0.00 0.00 0.00 3.09
2417 2911 3.434309 AGCTGCTCCACCAATATTTTGT 58.566 40.909 0.00 0.00 0.00 2.83
2441 2935 0.392461 TGCAAGGACCGCCTATCAAC 60.392 55.000 0.00 0.00 46.28 3.18
2464 2958 4.639078 TGACAAATTCTCCCATGACAGA 57.361 40.909 0.00 0.00 0.00 3.41
2647 3141 1.305297 TGACGAGGTGGATGGAGCT 60.305 57.895 0.00 0.00 0.00 4.09
2699 3193 3.153130 TGATCAATCCCGTTTGCAAAGA 58.847 40.909 13.26 7.11 0.00 2.52


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

AutoCloner maintained by Alex Coulton.