Multiple sequence alignment - TraesCS5A01G223400

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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 TraesCS5A01G223400 chr5A 100.000 2246 0 0 953 3198 439189404 439187159 0.000000e+00 4148.0
1 TraesCS5A01G223400 chr5A 100.000 620 0 0 1 620 439190356 439189737 0.000000e+00 1146.0
2 TraesCS5A01G223400 chr5D 94.876 1132 37 9 1952 3079 338245184 338244070 0.000000e+00 1749.0
3 TraesCS5A01G223400 chr5D 92.951 1064 44 10 953 2004 338246217 338245173 0.000000e+00 1520.0
4 TraesCS5A01G223400 chr5D 84.700 634 30 27 31 620 338246843 338246233 3.580000e-159 571.0
5 TraesCS5A01G223400 chr5D 89.024 82 8 1 31 112 220683324 220683244 2.030000e-17 100.0
6 TraesCS5A01G223400 chr5B 92.830 1060 62 6 955 2004 397435657 397434602 0.000000e+00 1524.0
7 TraesCS5A01G223400 chr5B 91.681 577 20 9 1952 2526 397434613 397434063 0.000000e+00 774.0
8 TraesCS5A01G223400 chr5B 85.804 479 16 15 2743 3197 397434056 397433606 8.080000e-126 460.0
9 TraesCS5A01G223400 chr5B 81.343 536 43 26 29 529 397436606 397436093 1.800000e-102 383.0
10 TraesCS5A01G223400 chr5B 87.059 85 9 2 29 112 293535400 293535483 9.440000e-16 95.3
11 TraesCS5A01G223400 chr7B 85.714 105 14 1 31 135 745246574 745246677 3.370000e-20 110.0
12 TraesCS5A01G223400 chr7B 81.905 105 18 1 31 135 745195941 745195838 1.580000e-13 87.9
13 TraesCS5A01G223400 chr7D 89.873 79 7 1 29 107 174148946 174149023 2.030000e-17 100.0
14 TraesCS5A01G223400 chr6D 89.024 82 8 1 31 112 221843127 221843047 2.030000e-17 100.0
15 TraesCS5A01G223400 chr4B 87.500 88 6 5 31 115 631558051 631557966 2.630000e-16 97.1
16 TraesCS5A01G223400 chr3B 87.952 83 8 2 31 112 381481608 381481527 2.630000e-16 97.1
17 TraesCS5A01G223400 chr2A 86.207 87 11 1 31 117 734531153 734531238 3.400000e-15 93.5
18 TraesCS5A01G223400 chr2B 90.625 64 6 0 2712 2775 224586467 224586530 5.680000e-13 86.1
19 TraesCS5A01G223400 chr4A 91.228 57 3 2 2719 2775 614871716 614871662 3.420000e-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 TraesCS5A01G223400 chr5A 439187159 439190356 3197 True 2647.00 4148 100.000000 1 3198 2 chr5A.!!$R1 3197
1 TraesCS5A01G223400 chr5D 338244070 338246843 2773 True 1280.00 1749 90.842333 31 3079 3 chr5D.!!$R2 3048
2 TraesCS5A01G223400 chr5B 397433606 397436606 3000 True 785.25 1524 87.914500 29 3197 4 chr5B.!!$R1 3168

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
164 170 0.436531 GAAGAGCAGTTGAACTCGCG 59.563 55.0 0.00 0.0 37.99 5.87 F
1282 1680 0.097325 TTGTTTGTCGGCGTCACAAC 59.903 50.0 12.91 15.7 33.42 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1815 2220 0.107214 TGGACGGCCCTTCATTGATC 60.107 55.0 3.83 0.00 35.38 2.92 R
3103 3576 0.025898 CGATCTGCAGTGCAACATCG 59.974 55.0 30.08 30.08 41.53 3.84 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
41 42 8.894409 TTTTTGCGAGTGATTATAAGATGTTG 57.106 30.769 0.00 0.00 0.00 3.33
106 107 4.214545 TGTGTTTGTTCACTCGTTTCAGTT 59.785 37.500 0.00 0.00 38.90 3.16
107 108 4.786575 GTGTTTGTTCACTCGTTTCAGTTC 59.213 41.667 0.00 0.00 35.68 3.01
108 109 3.918258 TTGTTCACTCGTTTCAGTTCG 57.082 42.857 0.00 0.00 0.00 3.95
109 110 2.883574 TGTTCACTCGTTTCAGTTCGT 58.116 42.857 0.00 0.00 0.00 3.85
110 111 4.031418 TGTTCACTCGTTTCAGTTCGTA 57.969 40.909 0.00 0.00 0.00 3.43
112 113 5.045215 TGTTCACTCGTTTCAGTTCGTATT 58.955 37.500 0.00 0.00 0.00 1.89
116 117 7.697352 TCACTCGTTTCAGTTCGTATTAAAA 57.303 32.000 0.00 0.00 0.00 1.52
117 118 8.129161 TCACTCGTTTCAGTTCGTATTAAAAA 57.871 30.769 0.00 0.00 0.00 1.94
161 167 5.988561 CCATATAGGAAGAGCAGTTGAACTC 59.011 44.000 0.00 0.00 41.22 3.01
164 170 0.436531 GAAGAGCAGTTGAACTCGCG 59.563 55.000 0.00 0.00 37.99 5.87
201 207 0.974383 AAGAACAGTACCGTGGAGGG 59.026 55.000 0.00 0.00 46.96 4.30
203 209 0.901580 GAACAGTACCGTGGAGGGGA 60.902 60.000 0.00 0.00 46.96 4.81
204 210 1.190178 AACAGTACCGTGGAGGGGAC 61.190 60.000 0.00 0.00 46.96 4.46
242 255 2.829592 CCCAGGATACCGGGAAGC 59.170 66.667 6.32 0.00 41.43 3.86
248 261 1.749033 GATACCGGGAAGCCAGAGG 59.251 63.158 6.32 0.00 0.00 3.69
281 308 1.001764 CATGGAGGGAAGCTGCACA 60.002 57.895 0.00 0.00 0.00 4.57
289 316 2.437359 AAGCTGCACATCTCGCCC 60.437 61.111 1.02 0.00 0.00 6.13
374 409 3.305516 CCAAACCCAGCACCAGCC 61.306 66.667 0.00 0.00 43.56 4.85
376 411 4.204028 AAACCCAGCACCAGCCGT 62.204 61.111 0.00 0.00 43.56 5.68
377 412 4.643387 AACCCAGCACCAGCCGTC 62.643 66.667 0.00 0.00 43.56 4.79
398 435 1.457831 CCCTCCCTCCCTACCTTCG 60.458 68.421 0.00 0.00 0.00 3.79
502 553 4.371231 CTCCCCCTCCCCAACCCT 62.371 72.222 0.00 0.00 0.00 4.34
573 953 2.364961 CTCTCGGTTCCCCTCCCT 59.635 66.667 0.00 0.00 0.00 4.20
576 956 2.285144 TCGGTTCCCCTCCCTTCC 60.285 66.667 0.00 0.00 0.00 3.46
1124 1505 1.379309 ACAGGCTCGACTCCCTCTC 60.379 63.158 0.00 0.00 0.00 3.20
1158 1539 0.962356 ATTTGCTCAAGGTGCTCCCG 60.962 55.000 0.00 0.00 38.74 5.14
1165 1546 1.077625 AAGGTGCTCCCGTCTCTCT 59.922 57.895 0.00 0.00 38.74 3.10
1216 1600 1.401199 CTCGTCGAACCTCTTCCTACC 59.599 57.143 0.00 0.00 0.00 3.18
1220 1604 1.076677 TCGAACCTCTTCCTACCCTGT 59.923 52.381 0.00 0.00 0.00 4.00
1229 1613 5.302313 CCTCTTCCTACCCTGTATACAAGTC 59.698 48.000 7.06 0.00 0.00 3.01
1282 1680 0.097325 TTGTTTGTCGGCGTCACAAC 59.903 50.000 12.91 15.70 33.42 3.32
1284 1682 2.181521 TTTGTCGGCGTCACAACCC 61.182 57.895 12.91 0.00 33.42 4.11
1285 1683 4.953868 TGTCGGCGTCACAACCCG 62.954 66.667 6.85 0.00 39.29 5.28
1318 1716 2.345641 CGCCGTTTGATCTTCTGTACTG 59.654 50.000 0.00 0.00 0.00 2.74
1346 1747 2.555325 TGCTTTTCTGTCTGATTGCTGG 59.445 45.455 0.00 0.00 0.00 4.85
1389 1791 5.221244 GGATTGTTAAATTCGGGATTGAGGG 60.221 44.000 0.00 0.00 0.00 4.30
1448 1852 5.856126 TTCACCGTGTCAATGAATTAGTC 57.144 39.130 0.00 0.00 0.00 2.59
1673 2078 8.519799 TGTTATCATCTGGTTTTATTCCCTTC 57.480 34.615 0.00 0.00 0.00 3.46
1676 2081 5.898120 TCATCTGGTTTTATTCCCTTCCAA 58.102 37.500 0.00 0.00 0.00 3.53
1685 2090 7.386059 GTTTTATTCCCTTCCAATGACATTGT 58.614 34.615 23.27 7.87 38.59 2.71
1724 2129 0.107993 TCTGCCAGATTCTTGCGGAG 60.108 55.000 15.36 4.41 33.50 4.63
1746 2151 3.252458 GGAAGTACAGTTCGTTTGCCAAT 59.748 43.478 0.00 0.00 0.00 3.16
1807 2212 2.371658 AGCTAAGCAAATCCCATCCC 57.628 50.000 0.00 0.00 0.00 3.85
1808 2213 1.133356 AGCTAAGCAAATCCCATCCCC 60.133 52.381 0.00 0.00 0.00 4.81
1836 2241 1.002134 CAATGAAGGGCCGTCCACT 60.002 57.895 17.02 0.00 38.24 4.00
1898 2303 6.538021 GCAATGGTATGTTTTGAAATGCCATA 59.462 34.615 5.82 0.00 45.23 2.74
1926 2331 7.122799 AGTCAGACTGTAGCTGTAATGTGAATA 59.877 37.037 0.91 0.00 34.98 1.75
2031 2486 4.426313 GGGAGCCGGTTTCCAGGG 62.426 72.222 23.16 0.00 36.40 4.45
2032 2487 4.426313 GGAGCCGGTTTCCAGGGG 62.426 72.222 18.76 0.00 34.74 4.79
2033 2488 3.647771 GAGCCGGTTTCCAGGGGT 61.648 66.667 1.90 0.00 0.00 4.95
2034 2489 2.204029 AGCCGGTTTCCAGGGGTA 60.204 61.111 1.90 0.00 0.00 3.69
2035 2490 2.045634 GCCGGTTTCCAGGGGTAC 60.046 66.667 1.90 0.00 0.00 3.34
2107 2562 9.381033 GAAGATATGATGACCTCCAATATCAAG 57.619 37.037 0.00 0.00 33.71 3.02
2280 2736 2.162608 TGGTTTCGTCAAATATTGCCCG 59.837 45.455 0.00 0.00 0.00 6.13
2341 2797 4.520111 TGCTTCATGTTTACAGTTCATGCT 59.480 37.500 0.00 0.00 38.82 3.79
2406 2862 9.095065 ACAAGTTCGATCCTATTACAATGTTAC 57.905 33.333 0.00 0.00 0.00 2.50
2432 2889 0.984230 TCCAGCCTGGATTTCGAGTT 59.016 50.000 10.05 0.00 42.67 3.01
2435 2892 1.927174 CAGCCTGGATTTCGAGTTACG 59.073 52.381 0.00 0.00 44.09 3.18
2452 2909 2.200373 ACGGTTCTTTGCCTATGCTT 57.800 45.000 0.00 0.00 38.71 3.91
2463 2920 7.444299 TCTTTGCCTATGCTTTTTCTTTTGAT 58.556 30.769 0.00 0.00 38.71 2.57
2466 2923 4.032104 GCCTATGCTTTTTCTTTTGATGCG 59.968 41.667 0.00 0.00 33.53 4.73
2528 2985 6.672147 AGTTCAGATCAATTGTGTAGTTTGC 58.328 36.000 5.13 0.00 0.00 3.68
2622 3082 8.613060 TCATATTTCTGTGAATATTCAGGAGC 57.387 34.615 18.47 7.53 37.98 4.70
2642 3102 0.609131 GTGCCAACTGCCAGGTGTAT 60.609 55.000 9.27 0.00 40.16 2.29
2643 3103 0.322456 TGCCAACTGCCAGGTGTATC 60.322 55.000 9.27 0.00 40.16 2.24
2644 3104 1.032114 GCCAACTGCCAGGTGTATCC 61.032 60.000 9.27 0.00 28.73 2.59
2679 3139 4.277672 GCATGTTAATGAGCAGATCCACAT 59.722 41.667 0.00 0.00 35.67 3.21
2688 3148 2.230508 AGCAGATCCACATTTGCTTGTG 59.769 45.455 0.00 7.70 45.95 3.33
2717 3177 5.061920 ACAATCTTCTGTTCCTAGACGTC 57.938 43.478 7.70 7.70 0.00 4.34
2818 3280 6.350194 GCAAATAAACCTTTCTTCCTACTGGG 60.350 42.308 0.00 0.00 0.00 4.45
2917 3380 7.106890 TCACATGGCATGAATCATTGAAAATT 58.893 30.769 32.74 3.01 0.00 1.82
2918 3381 8.258708 TCACATGGCATGAATCATTGAAAATTA 58.741 29.630 32.74 0.87 0.00 1.40
2919 3382 8.332464 CACATGGCATGAATCATTGAAAATTAC 58.668 33.333 32.74 0.00 0.00 1.89
2920 3383 8.262227 ACATGGCATGAATCATTGAAAATTACT 58.738 29.630 32.74 1.55 0.00 2.24
2921 3384 8.761497 CATGGCATGAATCATTGAAAATTACTC 58.239 33.333 22.91 0.00 0.00 2.59
2922 3385 7.267128 TGGCATGAATCATTGAAAATTACTCC 58.733 34.615 0.00 0.00 0.00 3.85
3005 3468 7.742556 TGCCATCACATAATTCGAATGAATA 57.257 32.000 12.25 0.59 44.02 1.75
3095 3568 1.374252 GACACGGCGATGTTCCAGT 60.374 57.895 16.62 0.00 31.24 4.00
3100 3573 1.635663 CGGCGATGTTCCAGTGTTCC 61.636 60.000 0.00 0.00 0.00 3.62
3103 3576 1.156736 CGATGTTCCAGTGTTCCACC 58.843 55.000 0.00 0.00 34.49 4.61
3121 3594 0.376152 CCGATGTTGCACTGCAGATC 59.624 55.000 23.35 10.69 40.61 2.75
3163 3647 0.401738 TCCACTTTCTCCCAAGGCAG 59.598 55.000 0.00 0.00 0.00 4.85
3178 3662 3.710209 AGGCAGTTCATTCTTGCTACT 57.290 42.857 0.00 0.00 0.00 2.57
3197 3681 2.108952 ACTTGAGCCATCCAAAGGAAGT 59.891 45.455 0.00 0.00 34.34 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.511321 ACAACATCTTATAATCACTCGCAAAAA 58.489 29.630 0.00 0.00 0.00 1.94
17 18 8.039603 ACAACATCTTATAATCACTCGCAAAA 57.960 30.769 0.00 0.00 0.00 2.44
18 19 7.609760 ACAACATCTTATAATCACTCGCAAA 57.390 32.000 0.00 0.00 0.00 3.68
19 20 7.609760 AACAACATCTTATAATCACTCGCAA 57.390 32.000 0.00 0.00 0.00 4.85
20 21 8.600625 GTTAACAACATCTTATAATCACTCGCA 58.399 33.333 0.00 0.00 0.00 5.10
21 22 8.818057 AGTTAACAACATCTTATAATCACTCGC 58.182 33.333 8.61 0.00 0.00 5.03
69 70 7.008266 GTGAACAAACACACTAAAACATGTCTG 59.992 37.037 0.00 0.00 40.11 3.51
75 76 5.179742 ACGAGTGAACAAACACACTAAAACA 59.820 36.000 0.00 0.00 45.54 2.83
126 127 9.494055 TGCTCTTCCTATATGGCTATAAATACT 57.506 33.333 0.00 0.00 35.26 2.12
127 128 9.757227 CTGCTCTTCCTATATGGCTATAAATAC 57.243 37.037 0.00 0.00 35.26 1.89
139 140 5.737635 GCGAGTTCAACTGCTCTTCCTATAT 60.738 44.000 0.00 0.00 0.00 0.86
161 167 1.003769 GCTTTTTCTTTGCCTCCGCG 61.004 55.000 0.00 0.00 38.08 6.46
164 170 2.365293 TCTTGGCTTTTTCTTTGCCTCC 59.635 45.455 0.00 0.00 46.23 4.30
201 207 0.392595 GGGATTGTTGTCCTCGGTCC 60.393 60.000 0.00 0.00 38.38 4.46
203 209 1.683441 GGGGATTGTTGTCCTCGGT 59.317 57.895 0.00 0.00 38.38 4.69
204 210 4.637771 GGGGATTGTTGTCCTCGG 57.362 61.111 0.00 0.00 38.38 4.63
211 217 4.374584 TGGGGCCGGGGATTGTTG 62.375 66.667 2.18 0.00 0.00 3.33
212 218 4.060667 CTGGGGCCGGGGATTGTT 62.061 66.667 2.18 0.00 0.00 2.83
235 248 2.602676 TTTCCCCTCTGGCTTCCCG 61.603 63.158 0.00 0.00 0.00 5.14
236 249 1.000771 GTTTCCCCTCTGGCTTCCC 60.001 63.158 0.00 0.00 0.00 3.97
248 261 3.084786 CTCCATGAAGTTCCAGTTTCCC 58.915 50.000 0.00 0.00 0.00 3.97
376 411 4.153330 GTAGGGAGGGAGGGCGGA 62.153 72.222 0.00 0.00 0.00 5.54
378 413 3.698263 AAGGTAGGGAGGGAGGGCG 62.698 68.421 0.00 0.00 0.00 6.13
379 414 1.766864 GAAGGTAGGGAGGGAGGGC 60.767 68.421 0.00 0.00 0.00 5.19
381 416 0.756070 GACGAAGGTAGGGAGGGAGG 60.756 65.000 0.00 0.00 0.00 4.30
382 417 1.102222 CGACGAAGGTAGGGAGGGAG 61.102 65.000 0.00 0.00 0.00 4.30
383 418 1.077212 CGACGAAGGTAGGGAGGGA 60.077 63.158 0.00 0.00 0.00 4.20
398 435 0.168568 GACCGAGAGAGACAACCGAC 59.831 60.000 0.00 0.00 0.00 4.79
452 503 3.487372 ACGTCCATCTTCATCTATCCGA 58.513 45.455 0.00 0.00 0.00 4.55
499 550 3.925914 AACGGGAGGGAGGTGAGGG 62.926 68.421 0.00 0.00 0.00 4.30
502 553 2.284405 GGAACGGGAGGGAGGTGA 60.284 66.667 0.00 0.00 0.00 4.02
573 953 0.481567 AGATAGATCCGGACGGGGAA 59.518 55.000 6.12 0.00 40.09 3.97
576 956 1.004511 AGGTAGATAGATCCGGACGGG 59.995 57.143 6.12 1.55 35.59 5.28
974 1355 4.803426 CGAGACCGAGCACCCAGC 62.803 72.222 0.00 0.00 46.19 4.85
1158 1539 1.596895 AACGGCGGAAGGAGAGAGAC 61.597 60.000 13.24 0.00 0.00 3.36
1165 1546 2.281208 CCAACAACGGCGGAAGGA 60.281 61.111 13.24 0.00 0.00 3.36
1200 1584 1.076677 ACAGGGTAGGAAGAGGTTCGA 59.923 52.381 0.00 0.00 32.92 3.71
1216 1600 9.784680 GTATTATACGATGGACTTGTATACAGG 57.215 37.037 13.08 13.08 36.72 4.00
1290 1688 3.362851 GATCAAACGGCGGCGTGAC 62.363 63.158 38.07 21.47 0.00 3.67
1291 1689 3.115892 GATCAAACGGCGGCGTGA 61.116 61.111 38.07 29.90 0.00 4.35
1292 1690 2.563086 GAAGATCAAACGGCGGCGTG 62.563 60.000 38.07 25.64 0.00 5.34
1293 1691 2.358247 AAGATCAAACGGCGGCGT 60.358 55.556 32.71 32.71 0.00 5.68
1300 1698 3.325870 TGCCAGTACAGAAGATCAAACG 58.674 45.455 0.00 0.00 0.00 3.60
1318 1716 2.816087 TCAGACAGAAAAGCAATCTGCC 59.184 45.455 11.84 3.20 46.52 4.85
1346 1747 5.678955 ATCCTCCAACTGGACTAGTAAAC 57.321 43.478 0.00 0.00 39.18 2.01
1389 1791 4.852609 AACATTAGCGGTACAATCGAAC 57.147 40.909 0.00 0.00 0.00 3.95
1466 1870 8.435931 ACATATACAGTATCCAAGGCATTAGA 57.564 34.615 0.00 0.00 0.00 2.10
1548 1953 1.336755 CGCTCTAGCCTCCTCTTCTTC 59.663 57.143 0.00 0.00 37.91 2.87
1654 2059 6.380846 TCATTGGAAGGGAATAAAACCAGATG 59.619 38.462 0.00 0.00 0.00 2.90
1673 2078 7.360269 GCAATTCCAAACTTACAATGTCATTGG 60.360 37.037 25.59 12.99 44.42 3.16
1676 2081 5.863397 CGCAATTCCAAACTTACAATGTCAT 59.137 36.000 0.00 0.00 0.00 3.06
1685 2090 5.233263 GCAGAAAAACGCAATTCCAAACTTA 59.767 36.000 0.00 0.00 0.00 2.24
1724 2129 2.215196 TGGCAAACGAACTGTACTTCC 58.785 47.619 0.00 0.00 0.00 3.46
1746 2151 5.005094 TGATGTGTTTGCTCTGAATCATCA 58.995 37.500 0.00 0.00 38.27 3.07
1807 2212 1.144503 CCCTTCATTGATCCCCAGAGG 59.855 57.143 0.00 0.00 0.00 3.69
1808 2213 1.478288 GCCCTTCATTGATCCCCAGAG 60.478 57.143 0.00 0.00 0.00 3.35
1815 2220 0.107214 TGGACGGCCCTTCATTGATC 60.107 55.000 3.83 0.00 35.38 2.92
1836 2241 4.460263 AGTCCACATTTGTGTTCTTGCTA 58.540 39.130 9.66 0.00 44.21 3.49
1926 2331 6.327934 GCAGCAAAAATGTCAGATGTAAGAT 58.672 36.000 0.00 0.00 0.00 2.40
2031 2486 1.209747 GTTCTGGATGGTCCTGGTACC 59.790 57.143 4.43 4.43 37.46 3.34
2032 2487 1.209747 GGTTCTGGATGGTCCTGGTAC 59.790 57.143 0.00 0.00 37.46 3.34
2033 2488 1.080498 AGGTTCTGGATGGTCCTGGTA 59.920 52.381 0.00 0.00 37.46 3.25
2034 2489 0.178861 AGGTTCTGGATGGTCCTGGT 60.179 55.000 0.00 0.00 37.46 4.00
2035 2490 0.254178 CAGGTTCTGGATGGTCCTGG 59.746 60.000 0.00 0.00 41.10 4.45
2036 2491 3.869623 CAGGTTCTGGATGGTCCTG 57.130 57.895 0.00 0.00 37.46 3.86
2140 2595 1.544314 GCCCTCTTATCATCACTGGCC 60.544 57.143 0.00 0.00 0.00 5.36
2280 2736 6.012658 TCAATTGTTCATTTACAGAGCACC 57.987 37.500 5.13 0.00 0.00 5.01
2341 2797 2.024941 TCTCAGTCCATGCCTCTACAGA 60.025 50.000 0.00 0.00 0.00 3.41
2432 2889 3.343941 AAGCATAGGCAAAGAACCGTA 57.656 42.857 0.67 0.00 44.61 4.02
2435 2892 5.139435 AGAAAAAGCATAGGCAAAGAACC 57.861 39.130 0.67 0.00 44.61 3.62
2452 2909 6.078202 TCCATAACACGCATCAAAAGAAAA 57.922 33.333 0.00 0.00 0.00 2.29
2463 2920 5.007626 GCTTCTAAATCATCCATAACACGCA 59.992 40.000 0.00 0.00 0.00 5.24
2466 2923 8.408601 ACATTGCTTCTAAATCATCCATAACAC 58.591 33.333 0.00 0.00 0.00 3.32
2595 3055 9.217278 CTCCTGAATATTCACAGAAATATGAGG 57.783 37.037 14.23 9.36 35.59 3.86
2622 3082 3.663176 CACCTGGCAGTTGGCACG 61.663 66.667 14.43 3.89 46.12 5.34
2642 3102 1.913778 ACATGCACTGCAATGAAGGA 58.086 45.000 8.03 0.00 43.62 3.36
2643 3103 2.736144 AACATGCACTGCAATGAAGG 57.264 45.000 8.03 0.00 43.62 3.46
2644 3104 5.404096 TCATTAACATGCACTGCAATGAAG 58.596 37.500 8.03 0.00 43.62 3.02
2688 3148 4.837972 AGGAACAGAAGATTGTAAGGCTC 58.162 43.478 0.00 0.00 0.00 4.70
2696 3156 5.317733 AGACGTCTAGGAACAGAAGATTG 57.682 43.478 18.46 0.00 0.00 2.67
2769 3229 5.716094 TCTGCACGTCTAAAATGCTACTAA 58.284 37.500 0.00 0.00 40.13 2.24
2818 3280 5.841783 AGATTAGAAGATTACCCAGGACCTC 59.158 44.000 0.00 0.00 0.00 3.85
2890 3353 6.963083 TTCAATGATTCATGCCATGTGATA 57.037 33.333 4.31 0.00 0.00 2.15
2917 3380 7.364149 TGACTGGTTTACTGTTTTAGGAGTA 57.636 36.000 0.00 0.00 0.00 2.59
2918 3381 6.243216 TGACTGGTTTACTGTTTTAGGAGT 57.757 37.500 0.00 0.00 0.00 3.85
2919 3382 5.179555 GCTGACTGGTTTACTGTTTTAGGAG 59.820 44.000 0.00 0.00 0.00 3.69
2920 3383 5.061179 GCTGACTGGTTTACTGTTTTAGGA 58.939 41.667 0.00 0.00 0.00 2.94
2921 3384 4.819630 TGCTGACTGGTTTACTGTTTTAGG 59.180 41.667 0.00 0.00 0.00 2.69
2922 3385 5.527582 ACTGCTGACTGGTTTACTGTTTTAG 59.472 40.000 0.00 0.00 0.00 1.85
3095 3568 0.179032 AGTGCAACATCGGTGGAACA 60.179 50.000 0.00 0.00 41.43 3.18
3100 3573 1.208358 CTGCAGTGCAACATCGGTG 59.792 57.895 20.22 0.34 41.43 4.94
3103 3576 0.025898 CGATCTGCAGTGCAACATCG 59.974 55.000 30.08 30.08 41.53 3.84
3141 3614 1.362224 CCTTGGGAGAAAGTGGAGGA 58.638 55.000 0.00 0.00 0.00 3.71
3142 3615 0.322906 GCCTTGGGAGAAAGTGGAGG 60.323 60.000 0.00 0.00 0.00 4.30
3178 3662 2.978156 ACTTCCTTTGGATGGCTCAA 57.022 45.000 4.84 0.00 32.06 3.02


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

AutoCloner maintained by Alex Coulton.