Multiple sequence alignment - TraesCS2D01G216100

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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 TraesCS2D01G216100 chr2D 100.000 3212 0 0 1 3212 178858323 178855112 0.000000e+00 5932.0
1 TraesCS2D01G216100 chr2D 96.275 1772 54 6 1422 3187 178671187 178669422 0.000000e+00 2896.0
2 TraesCS2D01G216100 chr2D 96.903 1098 19 7 2124 3212 178508683 178507592 0.000000e+00 1825.0
3 TraesCS2D01G216100 chr2D 95.561 811 32 2 905 1715 178518248 178517442 0.000000e+00 1295.0
4 TraesCS2D01G216100 chr2D 96.526 403 13 1 1024 1426 178691495 178691094 0.000000e+00 665.0
5 TraesCS2D01G216100 chr2D 93.784 370 23 0 1752 2121 178517450 178517081 1.010000e-154 556.0
6 TraesCS2D01G216100 chr2D 83.200 375 41 12 369 735 178692438 178692078 1.110000e-84 324.0
7 TraesCS2D01G216100 chr2D 85.915 284 38 2 6 288 178692724 178692442 5.210000e-78 302.0
8 TraesCS2D01G216100 chr2D 79.950 404 48 18 497 878 178518634 178518242 1.900000e-67 267.0
9 TraesCS2D01G216100 chr2A 96.949 1901 50 2 905 2800 193551928 193550031 0.000000e+00 3182.0
10 TraesCS2D01G216100 chr2A 90.909 286 12 5 2799 3083 193549949 193549677 3.910000e-99 372.0
11 TraesCS2D01G216100 chr2A 100.000 33 0 0 3 35 193576777 193576745 9.620000e-06 62.1
12 TraesCS2D01G216100 chr2B 95.857 1907 73 2 905 2805 235601158 235599252 0.000000e+00 3079.0
13 TraesCS2D01G216100 chr2B 95.783 1399 55 2 905 2302 235055743 235054348 0.000000e+00 2254.0
14 TraesCS2D01G216100 chr2B 93.359 783 26 6 2306 3083 235054183 235053422 0.000000e+00 1134.0
15 TraesCS2D01G216100 chr2B 94.035 285 15 2 2800 3083 235597302 235597019 6.370000e-117 431.0
16 TraesCS2D01G216100 chr2B 81.989 372 47 13 370 735 235057469 235057112 6.740000e-77 298.0
17 TraesCS2D01G216100 chr2B 83.036 224 29 5 515 735 235601526 235601309 9.090000e-46 195.0
18 TraesCS2D01G216100 chr2B 90.977 133 7 3 3083 3212 235053155 235053025 1.180000e-39 174.0
19 TraesCS2D01G216100 chr2B 94.737 57 1 2 269 325 235057533 235057479 1.590000e-13 87.9
20 TraesCS2D01G216100 chr2B 92.857 56 4 0 2 57 235900812 235900757 7.390000e-12 82.4
21 TraesCS2D01G216100 chrUn 75.294 850 161 31 1045 1874 421073048 421072228 8.470000e-96 361.0
22 TraesCS2D01G216100 chrUn 72.987 596 116 27 1297 1874 419113180 419113748 1.980000e-37 167.0
23 TraesCS2D01G216100 chr7B 75.235 852 164 29 1042 1874 684930448 684931271 8.470000e-96 361.0
24 TraesCS2D01G216100 chr7B 72.987 596 116 27 1297 1874 684935963 684936531 1.980000e-37 167.0
25 TraesCS2D01G216100 chr7B 77.444 133 20 8 2163 2290 684970734 684970861 1.600000e-08 71.3
26 TraesCS2D01G216100 chr7B 77.444 133 20 8 2163 2290 694195359 694195486 1.600000e-08 71.3
27 TraesCS2D01G216100 chr5B 75.836 269 51 8 84 350 608205466 608205210 1.210000e-24 124.0
28 TraesCS2D01G216100 chr3B 76.170 235 52 4 103 336 813374038 813374269 1.570000e-23 121.0
29 TraesCS2D01G216100 chr6B 71.104 616 128 31 1031 1630 35939184 35939765 4.380000e-19 106.0
30 TraesCS2D01G216100 chr7A 74.486 243 45 12 2090 2322 700073250 700073015 4.410000e-14 89.8
31 TraesCS2D01G216100 chr7A 72.862 269 45 20 104 356 286118696 286118952 2.070000e-07 67.6
32 TraesCS2D01G216100 chr3A 82.979 94 14 2 88 180 695085300 695085392 2.050000e-12 84.2
33 TraesCS2D01G216100 chr1B 71.354 384 84 19 1951 2321 676215553 676215183 3.440000e-10 76.8


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 TraesCS2D01G216100 chr2D 178855112 178858323 3211 True 5932.000000 5932 100.000 1 3212 1 chr2D.!!$R3 3211
1 TraesCS2D01G216100 chr2D 178669422 178671187 1765 True 2896.000000 2896 96.275 1422 3187 1 chr2D.!!$R2 1765
2 TraesCS2D01G216100 chr2D 178507592 178508683 1091 True 1825.000000 1825 96.903 2124 3212 1 chr2D.!!$R1 1088
3 TraesCS2D01G216100 chr2D 178517081 178518634 1553 True 706.000000 1295 89.765 497 2121 3 chr2D.!!$R4 1624
4 TraesCS2D01G216100 chr2D 178691094 178692724 1630 True 430.333333 665 88.547 6 1426 3 chr2D.!!$R5 1420
5 TraesCS2D01G216100 chr2A 193549677 193551928 2251 True 1777.000000 3182 93.929 905 3083 2 chr2A.!!$R2 2178
6 TraesCS2D01G216100 chr2B 235597019 235601526 4507 True 1235.000000 3079 90.976 515 3083 3 chr2B.!!$R3 2568
7 TraesCS2D01G216100 chr2B 235053025 235057533 4508 True 789.580000 2254 91.369 269 3212 5 chr2B.!!$R2 2943
8 TraesCS2D01G216100 chrUn 421072228 421073048 820 True 361.000000 361 75.294 1045 1874 1 chrUn.!!$R1 829
9 TraesCS2D01G216100 chr7B 684930448 684931271 823 False 361.000000 361 75.235 1042 1874 1 chr7B.!!$F1 832

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
436 438 0.122435 TTAGAATCAGGGGGTGGGGT 59.878 55.0 0.00 0.0 0.00 4.95 F
824 1059 0.453950 GCAGAGTGCGCTTTCACATG 60.454 55.0 9.73 2.8 39.35 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1602 2846 1.227089 CCATTCTCCGGTGCTCGAG 60.227 63.158 8.45 8.45 42.43 4.04 R
2687 4160 3.323691 TGTCTGTTTGCTAGGTTCAGCTA 59.676 43.478 0.00 0.00 42.30 3.32 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
53 54 1.730593 CGATGCGGTCTTCGTTCGTC 61.731 60.000 0.00 0.00 39.72 4.20
71 73 6.530534 CGTTCGTCTGTCTAATGTTAAATCCT 59.469 38.462 0.00 0.00 0.00 3.24
72 74 7.699391 CGTTCGTCTGTCTAATGTTAAATCCTA 59.301 37.037 0.00 0.00 0.00 2.94
75 77 9.132923 TCGTCTGTCTAATGTTAAATCCTATCT 57.867 33.333 0.00 0.00 0.00 1.98
76 78 9.186323 CGTCTGTCTAATGTTAAATCCTATCTG 57.814 37.037 0.00 0.00 0.00 2.90
81 83 8.983724 GTCTAATGTTAAATCCTATCTGTCTGC 58.016 37.037 0.00 0.00 0.00 4.26
88 90 4.782019 ATCCTATCTGTCTGCGATTCTC 57.218 45.455 0.00 0.00 0.00 2.87
91 93 4.277174 TCCTATCTGTCTGCGATTCTCTTC 59.723 45.833 0.00 0.00 0.00 2.87
95 97 2.788233 CTGTCTGCGATTCTCTTCATCG 59.212 50.000 0.00 0.00 45.26 3.84
96 98 2.423538 TGTCTGCGATTCTCTTCATCGA 59.576 45.455 6.50 0.00 45.30 3.59
106 108 3.515630 TCTCTTCATCGATGACAGTTGC 58.484 45.455 27.28 0.00 36.36 4.17
119 121 0.454957 CAGTTGCTGTTATGGTGCGC 60.455 55.000 0.00 0.00 0.00 6.09
120 122 1.154035 GTTGCTGTTATGGTGCGCC 60.154 57.895 10.11 10.11 0.00 6.53
125 127 3.199891 GTTATGGTGCGCCGGTCC 61.200 66.667 12.58 2.77 37.67 4.46
139 141 0.903454 CGGTCCTGTGGGGTCTTAGT 60.903 60.000 0.00 0.00 36.25 2.24
144 146 0.537188 CTGTGGGGTCTTAGTGCGAT 59.463 55.000 0.00 0.00 0.00 4.58
151 153 2.166664 GGGTCTTAGTGCGATGACTTCT 59.833 50.000 0.00 0.00 0.00 2.85
153 155 3.119459 GGTCTTAGTGCGATGACTTCTCA 60.119 47.826 0.00 0.00 0.00 3.27
155 157 4.324936 GTCTTAGTGCGATGACTTCTCAAC 59.675 45.833 0.00 0.00 0.00 3.18
161 163 3.506067 TGCGATGACTTCTCAACTGTCTA 59.494 43.478 0.00 0.00 0.00 2.59
165 167 6.252281 CGATGACTTCTCAACTGTCTACTAC 58.748 44.000 0.00 0.00 0.00 2.73
178 180 4.131596 TGTCTACTACAACCAAGTTTGCC 58.868 43.478 0.00 0.00 34.29 4.52
180 182 2.445682 ACTACAACCAAGTTTGCCCA 57.554 45.000 0.00 0.00 0.00 5.36
181 183 2.741145 ACTACAACCAAGTTTGCCCAA 58.259 42.857 0.00 0.00 0.00 4.12
192 194 3.950397 AGTTTGCCCAATGTCGATAAGA 58.050 40.909 0.00 0.00 0.00 2.10
206 208 2.412195 CGATAAGAGAGAGGCGATGACG 60.412 54.545 0.00 0.00 42.93 4.35
237 239 2.192664 TTGGCTCGTTCCAATGCTTA 57.807 45.000 6.97 0.00 40.92 3.09
245 247 5.163754 GCTCGTTCCAATGCTTATAGTTGTT 60.164 40.000 0.00 0.00 0.00 2.83
260 262 6.932356 ATAGTTGTTGCTTGGTGATCTATG 57.068 37.500 0.00 0.00 0.00 2.23
264 266 6.435277 AGTTGTTGCTTGGTGATCTATGAATT 59.565 34.615 0.00 0.00 0.00 2.17
265 267 6.441093 TGTTGCTTGGTGATCTATGAATTC 57.559 37.500 0.00 0.00 0.00 2.17
266 268 5.945191 TGTTGCTTGGTGATCTATGAATTCA 59.055 36.000 11.26 11.26 0.00 2.57
320 322 8.856153 TTTGTACTGCCTTAATAGTTGATGAA 57.144 30.769 0.00 0.00 0.00 2.57
321 323 9.461312 TTTGTACTGCCTTAATAGTTGATGAAT 57.539 29.630 0.00 0.00 0.00 2.57
323 325 9.764363 TGTACTGCCTTAATAGTTGATGAATAG 57.236 33.333 0.00 0.00 0.00 1.73
324 326 9.982651 GTACTGCCTTAATAGTTGATGAATAGA 57.017 33.333 0.00 0.00 0.00 1.98
326 328 9.717942 ACTGCCTTAATAGTTGATGAATAGATC 57.282 33.333 0.00 0.00 0.00 2.75
367 369 5.746307 AAAAGAACAAACGGACTTCCTAC 57.254 39.130 0.00 0.00 0.00 3.18
368 370 3.397849 AGAACAAACGGACTTCCTACC 57.602 47.619 0.00 0.00 0.00 3.18
369 371 2.970640 AGAACAAACGGACTTCCTACCT 59.029 45.455 0.00 0.00 0.00 3.08
370 372 2.833631 ACAAACGGACTTCCTACCTG 57.166 50.000 0.00 0.00 0.00 4.00
371 373 2.322658 ACAAACGGACTTCCTACCTGA 58.677 47.619 0.00 0.00 0.00 3.86
372 374 2.904434 ACAAACGGACTTCCTACCTGAT 59.096 45.455 0.00 0.00 0.00 2.90
373 375 3.262420 CAAACGGACTTCCTACCTGATG 58.738 50.000 0.00 0.00 0.00 3.07
374 376 2.526888 ACGGACTTCCTACCTGATGA 57.473 50.000 0.00 0.00 0.00 2.92
408 410 6.628919 ATTAAGTTACAAGTTGTGGTGTCC 57.371 37.500 18.90 0.30 0.00 4.02
419 421 3.866703 TGTGGTGTCCAGAATTGGTTA 57.133 42.857 0.00 0.00 45.26 2.85
425 427 5.222027 TGGTGTCCAGAATTGGTTAGAATCA 60.222 40.000 0.00 0.00 45.26 2.57
426 428 5.355350 GGTGTCCAGAATTGGTTAGAATCAG 59.645 44.000 0.00 0.00 45.26 2.90
427 429 5.355350 GTGTCCAGAATTGGTTAGAATCAGG 59.645 44.000 0.00 0.00 45.26 3.86
429 431 4.079787 TCCAGAATTGGTTAGAATCAGGGG 60.080 45.833 0.00 0.00 45.26 4.79
430 432 4.210331 CAGAATTGGTTAGAATCAGGGGG 58.790 47.826 0.00 0.00 0.00 5.40
431 433 3.858638 AGAATTGGTTAGAATCAGGGGGT 59.141 43.478 0.00 0.00 0.00 4.95
432 434 3.669939 ATTGGTTAGAATCAGGGGGTG 57.330 47.619 0.00 0.00 0.00 4.61
433 435 1.295020 TGGTTAGAATCAGGGGGTGG 58.705 55.000 0.00 0.00 0.00 4.61
434 436 0.551396 GGTTAGAATCAGGGGGTGGG 59.449 60.000 0.00 0.00 0.00 4.61
435 437 0.551396 GTTAGAATCAGGGGGTGGGG 59.449 60.000 0.00 0.00 0.00 4.96
436 438 0.122435 TTAGAATCAGGGGGTGGGGT 59.878 55.000 0.00 0.00 0.00 4.95
471 475 2.747446 CACCGGTCAAACAAAGGGATAG 59.253 50.000 2.59 0.00 0.00 2.08
477 481 6.017109 CCGGTCAAACAAAGGGATAGATTATG 60.017 42.308 0.00 0.00 0.00 1.90
489 493 7.021873 AGGGATAGATTATGGAGAGATGTGTT 58.978 38.462 0.00 0.00 0.00 3.32
525 529 0.821301 TTGATTGCGAACAGGGTGCA 60.821 50.000 0.00 0.00 36.72 4.57
552 556 6.612247 TTCTCTGACGCAAACAAAGAAATA 57.388 33.333 0.00 0.00 0.00 1.40
571 575 0.914417 AGGCCCGGAGAAAGGAATCA 60.914 55.000 0.73 0.00 0.00 2.57
579 583 4.323104 CCGGAGAAAGGAATCAGTCTCTTT 60.323 45.833 0.00 0.00 37.31 2.52
585 589 4.817318 AGGAATCAGTCTCTTTGGTCTC 57.183 45.455 0.00 0.00 0.00 3.36
586 590 4.163427 AGGAATCAGTCTCTTTGGTCTCA 58.837 43.478 0.00 0.00 0.00 3.27
603 607 3.755378 GTCTCACACATGCCTCAAATTCT 59.245 43.478 0.00 0.00 0.00 2.40
604 608 4.005650 TCTCACACATGCCTCAAATTCTC 58.994 43.478 0.00 0.00 0.00 2.87
605 609 4.008330 CTCACACATGCCTCAAATTCTCT 58.992 43.478 0.00 0.00 0.00 3.10
608 614 4.094590 CACACATGCCTCAAATTCTCTCTC 59.905 45.833 0.00 0.00 0.00 3.20
649 655 5.389859 TCCTTAATTTTGCACCACAGATG 57.610 39.130 0.00 0.00 0.00 2.90
665 674 7.857885 CACCACAGATGTTTTTCTAGAAGTTTC 59.142 37.037 5.12 0.93 0.00 2.78
707 716 4.235939 TGATCGGTTTTGGTTTGACATG 57.764 40.909 0.00 0.00 0.00 3.21
713 722 6.987386 TCGGTTTTGGTTTGACATGATTTAT 58.013 32.000 0.00 0.00 0.00 1.40
728 737 4.580868 TGATTTATGCGTTACTGGTTCCA 58.419 39.130 0.00 0.00 0.00 3.53
735 744 2.420129 GCGTTACTGGTTCCAGGATGAT 60.420 50.000 20.88 4.34 39.69 2.45
736 745 3.198068 CGTTACTGGTTCCAGGATGATG 58.802 50.000 20.88 2.74 39.69 3.07
738 747 4.192317 GTTACTGGTTCCAGGATGATGAC 58.808 47.826 20.88 5.60 39.69 3.06
739 748 2.269023 ACTGGTTCCAGGATGATGACA 58.731 47.619 20.88 0.00 39.69 3.58
741 750 4.040047 ACTGGTTCCAGGATGATGACATA 58.960 43.478 20.88 0.00 39.69 2.29
742 751 4.474651 ACTGGTTCCAGGATGATGACATAA 59.525 41.667 20.88 0.00 39.69 1.90
822 1057 2.253758 GGCAGAGTGCGCTTTCACA 61.254 57.895 9.73 0.00 46.21 3.58
824 1059 0.453950 GCAGAGTGCGCTTTCACATG 60.454 55.000 9.73 2.80 39.35 3.21
832 1067 1.130561 GCGCTTTCACATGGGAGTAAC 59.869 52.381 0.00 0.00 0.00 2.50
836 1071 3.810743 GCTTTCACATGGGAGTAACCACT 60.811 47.826 0.00 0.00 44.72 4.00
846 1081 4.065789 GGGAGTAACCACTTCTGACTTTG 58.934 47.826 0.00 0.00 41.20 2.77
847 1082 4.444449 GGGAGTAACCACTTCTGACTTTGT 60.444 45.833 0.00 0.00 41.20 2.83
868 1108 4.530161 TGTAGGCCAAACCATTTTATTGCT 59.470 37.500 5.01 0.00 43.14 3.91
869 1109 3.941573 AGGCCAAACCATTTTATTGCTG 58.058 40.909 5.01 0.00 43.14 4.41
871 1111 3.009026 GCCAAACCATTTTATTGCTGGG 58.991 45.455 0.00 0.00 34.21 4.45
873 1113 4.252878 CCAAACCATTTTATTGCTGGGAC 58.747 43.478 0.00 0.00 34.21 4.46
874 1114 4.020307 CCAAACCATTTTATTGCTGGGACT 60.020 41.667 0.00 0.00 34.21 3.85
875 1115 5.512921 CCAAACCATTTTATTGCTGGGACTT 60.513 40.000 0.00 0.00 34.21 3.01
877 1117 5.151297 ACCATTTTATTGCTGGGACTTTG 57.849 39.130 0.00 0.00 34.21 2.77
878 1118 3.934579 CCATTTTATTGCTGGGACTTTGC 59.065 43.478 0.00 0.00 0.00 3.68
879 1119 3.676291 TTTTATTGCTGGGACTTTGCC 57.324 42.857 0.00 0.00 0.00 4.52
887 1127 2.582436 GGACTTTGCCCCGATCGA 59.418 61.111 18.66 0.00 0.00 3.59
888 1128 1.521681 GGACTTTGCCCCGATCGAG 60.522 63.158 18.66 2.11 0.00 4.04
890 1130 2.125147 CTTTGCCCCGATCGAGCA 60.125 61.111 23.37 23.37 33.97 4.26
891 1131 2.125147 TTTGCCCCGATCGAGCAG 60.125 61.111 24.95 10.11 37.89 4.24
895 1135 2.587194 CCCCGATCGAGCAGCAAG 60.587 66.667 18.66 0.00 0.00 4.01
896 1136 3.267860 CCCGATCGAGCAGCAAGC 61.268 66.667 18.66 0.00 46.19 4.01
975 2216 2.620108 GCCAAAGCTCCTTCCTTCATCT 60.620 50.000 0.00 0.00 35.50 2.90
1602 2846 1.153804 GGTCGCCTTCGTCTTCTCC 60.154 63.158 0.00 0.00 36.96 3.71
1605 2849 1.226435 CGCCTTCGTCTTCTCCTCG 60.226 63.158 0.00 0.00 0.00 4.63
1665 2909 1.165270 GCGATTTGTTAGTGGGCACT 58.835 50.000 0.00 0.00 45.02 4.40
2247 3548 6.995091 ACTCTGTTGCATTCTAATTATCTCCC 59.005 38.462 0.00 0.00 0.00 4.30
2268 3569 5.606749 TCCCTACCTGCATAGTTATCACATT 59.393 40.000 0.00 0.00 0.00 2.71
2269 3570 5.934625 CCCTACCTGCATAGTTATCACATTC 59.065 44.000 0.00 0.00 0.00 2.67
2302 3606 7.936496 TTGGTGCTTGATAGTTCATTATTGA 57.064 32.000 0.00 0.00 0.00 2.57
2304 3769 8.523915 TGGTGCTTGATAGTTCATTATTGAAT 57.476 30.769 3.53 0.00 43.49 2.57
2356 3821 1.566211 TTCTCCTGAGCTTCTGGGAG 58.434 55.000 14.82 14.82 44.69 4.30
2613 4079 6.751514 ATCCTTTTACGTATGCAATTGTGA 57.248 33.333 7.40 0.00 0.00 3.58
2687 4160 1.337384 TCCTGCGGATGTAGGCACAT 61.337 55.000 0.00 2.83 46.67 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.068741 GAAGACAACCACTGACCGAGT 59.931 52.381 0.00 0.00 34.02 4.18
1 2 1.784525 GAAGACAACCACTGACCGAG 58.215 55.000 0.00 0.00 0.00 4.63
2 3 0.031585 CGAAGACAACCACTGACCGA 59.968 55.000 0.00 0.00 0.00 4.69
3 4 0.031585 TCGAAGACAACCACTGACCG 59.968 55.000 0.00 0.00 0.00 4.79
4 5 2.069273 CATCGAAGACAACCACTGACC 58.931 52.381 0.00 0.00 42.51 4.02
71 73 5.561725 CGATGAAGAGAATCGCAGACAGATA 60.562 44.000 0.00 0.00 42.51 1.98
72 74 4.619973 GATGAAGAGAATCGCAGACAGAT 58.380 43.478 0.00 0.00 42.51 2.90
75 77 2.423538 TCGATGAAGAGAATCGCAGACA 59.576 45.455 1.08 0.00 45.09 3.41
76 78 3.071786 TCGATGAAGAGAATCGCAGAC 57.928 47.619 1.08 0.00 45.09 3.51
80 82 3.375642 TGTCATCGATGAAGAGAATCGC 58.624 45.455 28.83 13.81 45.09 4.58
81 83 4.605968 ACTGTCATCGATGAAGAGAATCG 58.394 43.478 28.83 13.03 46.47 3.34
88 90 2.998670 ACAGCAACTGTCATCGATGAAG 59.001 45.455 28.83 25.85 41.21 3.02
91 93 4.260497 CCATAACAGCAACTGTCATCGATG 60.260 45.833 19.61 19.61 44.62 3.84
95 97 3.426695 GCACCATAACAGCAACTGTCATC 60.427 47.826 0.00 0.00 44.62 2.92
96 98 2.489329 GCACCATAACAGCAACTGTCAT 59.511 45.455 0.00 0.00 44.62 3.06
106 108 2.435938 ACCGGCGCACCATAACAG 60.436 61.111 10.83 0.00 34.57 3.16
119 121 1.611261 TAAGACCCCACAGGACCGG 60.611 63.158 0.00 0.00 39.89 5.28
120 122 0.903454 ACTAAGACCCCACAGGACCG 60.903 60.000 0.00 0.00 39.89 4.79
125 127 0.537188 ATCGCACTAAGACCCCACAG 59.463 55.000 0.00 0.00 0.00 3.66
133 135 4.218635 AGTTGAGAAGTCATCGCACTAAGA 59.781 41.667 0.00 0.00 37.60 2.10
135 137 4.237724 CAGTTGAGAAGTCATCGCACTAA 58.762 43.478 0.00 0.00 37.60 2.24
139 141 2.297315 AGACAGTTGAGAAGTCATCGCA 59.703 45.455 0.00 0.00 35.94 5.10
144 146 6.238953 GGTTGTAGTAGACAGTTGAGAAGTCA 60.239 42.308 0.00 0.00 39.88 3.41
151 153 5.864418 ACTTGGTTGTAGTAGACAGTTGA 57.136 39.130 0.00 0.00 39.88 3.18
153 155 5.296035 GCAAACTTGGTTGTAGTAGACAGTT 59.704 40.000 0.21 0.00 39.88 3.16
155 157 4.213482 GGCAAACTTGGTTGTAGTAGACAG 59.787 45.833 0.21 0.00 39.88 3.51
161 163 2.445682 TGGGCAAACTTGGTTGTAGT 57.554 45.000 0.21 0.00 0.00 2.73
165 167 2.482864 GACATTGGGCAAACTTGGTTG 58.517 47.619 0.00 0.00 0.00 3.77
178 180 3.648009 GCCTCTCTCTTATCGACATTGG 58.352 50.000 0.00 0.00 0.00 3.16
180 182 3.215151 TCGCCTCTCTCTTATCGACATT 58.785 45.455 0.00 0.00 0.00 2.71
181 183 2.852449 TCGCCTCTCTCTTATCGACAT 58.148 47.619 0.00 0.00 0.00 3.06
192 194 3.893763 CGCCGTCATCGCCTCTCT 61.894 66.667 0.00 0.00 35.54 3.10
219 221 2.418368 ATAAGCATTGGAACGAGCCA 57.582 45.000 0.00 0.00 35.78 4.75
229 231 5.574055 CACCAAGCAACAACTATAAGCATTG 59.426 40.000 0.00 0.00 0.00 2.82
237 239 6.653020 TCATAGATCACCAAGCAACAACTAT 58.347 36.000 0.00 0.00 0.00 2.12
245 247 5.993055 TCTGAATTCATAGATCACCAAGCA 58.007 37.500 8.96 0.00 0.00 3.91
300 302 9.717942 GATCTATTCATCAACTATTAAGGCAGT 57.282 33.333 0.00 0.00 0.00 4.40
344 346 5.066893 GGTAGGAAGTCCGTTTGTTCTTTTT 59.933 40.000 0.00 0.00 42.08 1.94
345 347 4.577693 GGTAGGAAGTCCGTTTGTTCTTTT 59.422 41.667 0.00 0.00 42.08 2.27
346 348 4.132336 GGTAGGAAGTCCGTTTGTTCTTT 58.868 43.478 0.00 0.00 42.08 2.52
347 349 3.390311 AGGTAGGAAGTCCGTTTGTTCTT 59.610 43.478 0.00 0.00 42.08 2.52
348 350 2.970640 AGGTAGGAAGTCCGTTTGTTCT 59.029 45.455 0.00 0.00 42.08 3.01
349 351 3.064931 CAGGTAGGAAGTCCGTTTGTTC 58.935 50.000 0.00 0.00 42.08 3.18
350 352 2.701951 TCAGGTAGGAAGTCCGTTTGTT 59.298 45.455 0.00 0.00 42.08 2.83
351 353 2.322658 TCAGGTAGGAAGTCCGTTTGT 58.677 47.619 0.00 0.00 42.08 2.83
352 354 3.056107 TCATCAGGTAGGAAGTCCGTTTG 60.056 47.826 0.00 0.00 42.08 2.93
353 355 3.170717 TCATCAGGTAGGAAGTCCGTTT 58.829 45.455 0.00 0.00 42.08 3.60
354 356 2.816411 TCATCAGGTAGGAAGTCCGTT 58.184 47.619 0.00 0.00 42.08 4.44
355 357 2.526888 TCATCAGGTAGGAAGTCCGT 57.473 50.000 0.00 0.00 42.08 4.69
356 358 4.408182 AAATCATCAGGTAGGAAGTCCG 57.592 45.455 0.00 0.00 42.08 4.79
357 359 5.753921 CGTAAAATCATCAGGTAGGAAGTCC 59.246 44.000 0.00 0.00 0.00 3.85
358 360 5.753921 CCGTAAAATCATCAGGTAGGAAGTC 59.246 44.000 0.00 0.00 0.00 3.01
359 361 5.396436 CCCGTAAAATCATCAGGTAGGAAGT 60.396 44.000 0.00 0.00 0.00 3.01
360 362 5.057149 CCCGTAAAATCATCAGGTAGGAAG 58.943 45.833 0.00 0.00 0.00 3.46
361 363 4.717778 TCCCGTAAAATCATCAGGTAGGAA 59.282 41.667 0.00 0.00 0.00 3.36
362 364 4.291792 TCCCGTAAAATCATCAGGTAGGA 58.708 43.478 0.00 0.00 0.00 2.94
363 365 4.682778 TCCCGTAAAATCATCAGGTAGG 57.317 45.455 0.00 0.00 0.00 3.18
364 366 8.671384 TTAATTCCCGTAAAATCATCAGGTAG 57.329 34.615 0.00 0.00 0.00 3.18
365 367 8.269317 ACTTAATTCCCGTAAAATCATCAGGTA 58.731 33.333 0.00 0.00 0.00 3.08
366 368 7.116736 ACTTAATTCCCGTAAAATCATCAGGT 58.883 34.615 0.00 0.00 0.00 4.00
367 369 7.568199 ACTTAATTCCCGTAAAATCATCAGG 57.432 36.000 0.00 0.00 0.00 3.86
368 370 9.931210 GTAACTTAATTCCCGTAAAATCATCAG 57.069 33.333 0.00 0.00 0.00 2.90
369 371 9.451002 TGTAACTTAATTCCCGTAAAATCATCA 57.549 29.630 0.00 0.00 0.00 3.07
372 374 9.287373 ACTTGTAACTTAATTCCCGTAAAATCA 57.713 29.630 0.00 0.00 0.00 2.57
374 376 9.902196 CAACTTGTAACTTAATTCCCGTAAAAT 57.098 29.630 0.00 0.00 0.00 1.82
408 410 4.210331 CCCCCTGATTCTAACCAATTCTG 58.790 47.826 0.00 0.00 0.00 3.02
419 421 1.930656 CACCCCACCCCCTGATTCT 60.931 63.158 0.00 0.00 0.00 2.40
457 459 8.213679 TCTCTCCATAATCTATCCCTTTGTTTG 58.786 37.037 0.00 0.00 0.00 2.93
461 463 7.823310 CACATCTCTCCATAATCTATCCCTTTG 59.177 40.741 0.00 0.00 0.00 2.77
462 464 7.515514 ACACATCTCTCCATAATCTATCCCTTT 59.484 37.037 0.00 0.00 0.00 3.11
463 465 7.021873 ACACATCTCTCCATAATCTATCCCTT 58.978 38.462 0.00 0.00 0.00 3.95
471 475 7.203910 ACTTACGAACACATCTCTCCATAATC 58.796 38.462 0.00 0.00 0.00 1.75
477 481 5.952033 ACTAACTTACGAACACATCTCTCC 58.048 41.667 0.00 0.00 0.00 3.71
519 523 0.460987 CGTCAGAGAATCCTGCACCC 60.461 60.000 0.00 0.00 33.66 4.61
525 529 2.839486 TGTTTGCGTCAGAGAATCCT 57.161 45.000 0.00 0.00 33.66 3.24
552 556 0.914417 TGATTCCTTTCTCCGGGCCT 60.914 55.000 0.84 0.00 0.00 5.19
571 575 3.805108 GCATGTGTGAGACCAAAGAGACT 60.805 47.826 0.00 0.00 0.00 3.24
579 583 0.764271 TTGAGGCATGTGTGAGACCA 59.236 50.000 0.00 0.00 0.00 4.02
585 589 4.008330 AGAGAGAATTTGAGGCATGTGTG 58.992 43.478 0.00 0.00 0.00 3.82
586 590 4.019501 AGAGAGAGAATTTGAGGCATGTGT 60.020 41.667 0.00 0.00 0.00 3.72
629 635 7.481275 AAAACATCTGTGGTGCAAAATTAAG 57.519 32.000 0.00 0.00 0.00 1.85
649 655 8.851960 AAACGGATTGAAACTTCTAGAAAAAC 57.148 30.769 6.63 0.00 0.00 2.43
707 716 4.035208 CCTGGAACCAGTAACGCATAAATC 59.965 45.833 17.92 0.00 42.15 2.17
713 722 0.981183 ATCCTGGAACCAGTAACGCA 59.019 50.000 17.92 0.00 42.15 5.24
773 817 6.098982 TGACCAAGTCTCTCTCTCTTCTTTTT 59.901 38.462 0.00 0.00 33.15 1.94
774 818 5.600484 TGACCAAGTCTCTCTCTCTTCTTTT 59.400 40.000 0.00 0.00 33.15 2.27
775 819 5.010617 GTGACCAAGTCTCTCTCTCTTCTTT 59.989 44.000 0.00 0.00 33.15 2.52
776 820 4.522789 GTGACCAAGTCTCTCTCTCTTCTT 59.477 45.833 0.00 0.00 33.15 2.52
777 821 4.079253 GTGACCAAGTCTCTCTCTCTTCT 58.921 47.826 0.00 0.00 33.15 2.85
778 822 3.823873 TGTGACCAAGTCTCTCTCTCTTC 59.176 47.826 0.00 0.00 33.15 2.87
779 823 3.838565 TGTGACCAAGTCTCTCTCTCTT 58.161 45.455 0.00 0.00 33.15 2.85
780 824 3.517296 TGTGACCAAGTCTCTCTCTCT 57.483 47.619 0.00 0.00 33.15 3.10
781 825 3.823873 TCTTGTGACCAAGTCTCTCTCTC 59.176 47.826 2.69 0.00 46.70 3.20
782 826 3.826157 CTCTTGTGACCAAGTCTCTCTCT 59.174 47.826 2.69 0.00 46.70 3.10
783 827 3.056891 CCTCTTGTGACCAAGTCTCTCTC 60.057 52.174 2.69 0.00 46.70 3.20
784 828 2.896685 CCTCTTGTGACCAAGTCTCTCT 59.103 50.000 2.69 0.00 46.70 3.10
785 829 2.611722 GCCTCTTGTGACCAAGTCTCTC 60.612 54.545 2.69 0.00 46.70 3.20
786 830 1.346068 GCCTCTTGTGACCAAGTCTCT 59.654 52.381 2.69 0.00 46.70 3.10
787 831 1.070758 TGCCTCTTGTGACCAAGTCTC 59.929 52.381 2.69 0.00 46.70 3.36
822 1057 3.521727 AGTCAGAAGTGGTTACTCCCAT 58.478 45.455 0.00 0.00 35.69 4.00
824 1059 4.065789 CAAAGTCAGAAGTGGTTACTCCC 58.934 47.826 0.00 0.00 35.69 4.30
832 1067 2.224523 TGGCCTACAAAGTCAGAAGTGG 60.225 50.000 3.32 0.00 0.00 4.00
846 1081 4.869861 CAGCAATAAAATGGTTTGGCCTAC 59.130 41.667 3.32 1.58 38.35 3.18
847 1082 4.081198 CCAGCAATAAAATGGTTTGGCCTA 60.081 41.667 3.32 0.00 38.35 3.93
869 1109 2.513897 CGATCGGGGCAAAGTCCC 60.514 66.667 7.38 0.00 45.53 4.46
871 1111 2.174319 GCTCGATCGGGGCAAAGTC 61.174 63.158 18.35 0.00 0.00 3.01
873 1113 2.125147 TGCTCGATCGGGGCAAAG 60.125 61.111 25.62 12.98 32.79 2.77
874 1114 2.125147 CTGCTCGATCGGGGCAAA 60.125 61.111 26.79 12.98 35.49 3.68
875 1115 4.838152 GCTGCTCGATCGGGGCAA 62.838 66.667 26.79 16.18 35.49 4.52
877 1117 4.838152 TTGCTGCTCGATCGGGGC 62.838 66.667 18.35 19.97 0.00 5.80
878 1118 2.587194 CTTGCTGCTCGATCGGGG 60.587 66.667 18.35 10.67 0.00 5.73
879 1119 3.267860 GCTTGCTGCTCGATCGGG 61.268 66.667 16.41 14.14 38.95 5.14
881 1121 1.357258 AAGTGCTTGCTGCTCGATCG 61.357 55.000 9.36 9.36 43.37 3.69
882 1122 0.801251 AAAGTGCTTGCTGCTCGATC 59.199 50.000 0.00 0.00 43.37 3.69
883 1123 0.520404 CAAAGTGCTTGCTGCTCGAT 59.480 50.000 0.00 0.00 43.37 3.59
887 1127 0.950116 GTCTCAAAGTGCTTGCTGCT 59.050 50.000 0.00 0.00 43.37 4.24
888 1128 0.664761 TGTCTCAAAGTGCTTGCTGC 59.335 50.000 0.00 0.00 43.25 5.25
890 1130 3.633525 TCAAATGTCTCAAAGTGCTTGCT 59.366 39.130 0.00 0.00 34.76 3.91
891 1131 3.732721 GTCAAATGTCTCAAAGTGCTTGC 59.267 43.478 0.00 0.00 34.76 4.01
895 1135 4.540824 GAAGGTCAAATGTCTCAAAGTGC 58.459 43.478 0.00 0.00 0.00 4.40
896 1136 4.580167 TGGAAGGTCAAATGTCTCAAAGTG 59.420 41.667 0.00 0.00 0.00 3.16
897 1137 4.792068 TGGAAGGTCAAATGTCTCAAAGT 58.208 39.130 0.00 0.00 0.00 2.66
898 1138 5.368256 CTGGAAGGTCAAATGTCTCAAAG 57.632 43.478 0.00 0.00 0.00 2.77
1326 2567 3.371063 GTGCGGTCGAGGAGGACA 61.371 66.667 0.00 0.00 38.70 4.02
1602 2846 1.227089 CCATTCTCCGGTGCTCGAG 60.227 63.158 8.45 8.45 42.43 4.04
1605 2849 2.892425 CGCCATTCTCCGGTGCTC 60.892 66.667 0.00 0.00 0.00 4.26
2247 3548 9.197694 GTTAGAATGTGATAACTATGCAGGTAG 57.802 37.037 0.00 0.00 0.00 3.18
2268 3569 6.296026 ACTATCAAGCACCAAACAAGTTAGA 58.704 36.000 0.00 0.00 0.00 2.10
2269 3570 6.560253 ACTATCAAGCACCAAACAAGTTAG 57.440 37.500 0.00 0.00 0.00 2.34
2302 3606 6.553476 ACCCTTTAAACAAGACTTGCCTAATT 59.447 34.615 15.24 5.74 0.00 1.40
2304 3769 5.451354 ACCCTTTAAACAAGACTTGCCTAA 58.549 37.500 15.24 9.75 0.00 2.69
2356 3821 7.921745 ACTATCGCTCCTGATTTAAGTTAGTTC 59.078 37.037 0.00 0.00 0.00 3.01
2613 4079 5.147330 TCATGGTTGTTCGAGTTACATCT 57.853 39.130 0.00 0.00 0.00 2.90
2687 4160 3.323691 TGTCTGTTTGCTAGGTTCAGCTA 59.676 43.478 0.00 0.00 42.30 3.32
3160 6857 1.142748 GGGCAGAGAGATCACGGTG 59.857 63.158 0.56 0.56 0.00 4.94


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

AutoCloner maintained by Alex Coulton.