Multiple sequence alignment - TraesCS3A01G235600

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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 TraesCS3A01G235600 chr3A 100.000 2644 0 0 1 2644 439289001 439291644 0.000000e+00 4883.0
1 TraesCS3A01G235600 chr3A 100.000 87 0 0 2973 3059 439291973 439292059 8.780000e-36 161.0
2 TraesCS3A01G235600 chr3D 94.649 1682 58 8 451 2111 325978297 325976627 0.000000e+00 2579.0
3 TraesCS3A01G235600 chr3D 92.328 378 27 1 2194 2571 325974362 325973987 1.250000e-148 536.0
4 TraesCS3A01G235600 chr3D 86.031 451 43 8 23 464 325980540 325980101 1.660000e-127 466.0
5 TraesCS3A01G235600 chr3D 95.402 87 4 0 2973 3059 325973911 325973825 4.110000e-29 139.0
6 TraesCS3A01G235600 chr3B 95.920 1201 44 2 930 2130 423365265 423364070 0.000000e+00 1941.0
7 TraesCS3A01G235600 chr3B 93.172 454 28 2 2194 2644 423363937 423363484 0.000000e+00 664.0
8 TraesCS3A01G235600 chr3B 86.919 344 27 5 593 921 423365642 423365302 1.340000e-98 370.0
9 TraesCS3A01G235600 chr3B 94.253 87 5 0 2973 3059 423363448 423363362 1.910000e-27 134.0
10 TraesCS3A01G235600 chr3B 97.143 70 2 0 2130 2199 423364039 423363970 5.360000e-23 119.0
11 TraesCS3A01G235600 chr1D 93.333 45 3 0 660 704 350651518 350651562 1.970000e-07 67.6


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 TraesCS3A01G235600 chr3A 439289001 439292059 3058 False 2522.0 4883 100.0000 1 3059 2 chr3A.!!$F1 3058
1 TraesCS3A01G235600 chr3D 325973825 325980540 6715 True 930.0 2579 92.1025 23 3059 4 chr3D.!!$R1 3036
2 TraesCS3A01G235600 chr3B 423363362 423365642 2280 True 645.6 1941 93.4814 593 3059 5 chr3B.!!$R1 2466

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
509 2332 0.313672 GCTACCTCGAGGAGCTCATG 59.686 60.000 37.69 17.77 38.94 3.07 F
1076 2963 0.034896 ACGCTCCTTGTTCCGATGTT 59.965 50.000 0.00 0.00 0.00 2.71 F
1500 3387 1.067846 CACTACCTCTACTGCGCACAA 60.068 52.381 5.66 0.00 0.00 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2013 3900 0.595310 GGACGATGAGACGCTTAGCC 60.595 60.000 0.0 0.0 36.7 3.93 R
2036 3923 0.609131 ACTCGAACCAGCCCCAAATG 60.609 55.000 0.0 0.0 0.0 2.32 R
2565 6637 2.631062 TGTCTATCACACAAAGGACGGT 59.369 45.455 0.0 0.0 0.0 4.83 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 2.190981 CGTCAGTTCATAACGTAGGCC 58.809 52.381 0.00 0.00 36.23 5.19
21 22 2.416296 CGTCAGTTCATAACGTAGGCCA 60.416 50.000 5.01 0.00 36.23 5.36
22 23 3.187700 GTCAGTTCATAACGTAGGCCAG 58.812 50.000 5.01 0.00 36.23 4.85
23 24 1.933853 CAGTTCATAACGTAGGCCAGC 59.066 52.381 5.01 0.00 36.23 4.85
24 25 1.831736 AGTTCATAACGTAGGCCAGCT 59.168 47.619 5.01 0.00 36.23 4.24
25 26 2.236395 AGTTCATAACGTAGGCCAGCTT 59.764 45.455 5.01 0.00 36.23 3.74
26 27 3.449737 AGTTCATAACGTAGGCCAGCTTA 59.550 43.478 5.01 0.00 36.23 3.09
64 65 1.984990 GTGTACAAATGCAATGCCGTG 59.015 47.619 1.53 0.25 0.00 4.94
79 80 0.547075 CCGTGTCTCCCTCTCCTCTA 59.453 60.000 0.00 0.00 0.00 2.43
80 81 1.144093 CCGTGTCTCCCTCTCCTCTAT 59.856 57.143 0.00 0.00 0.00 1.98
102 103 5.528043 TTGGATGTACAAGTTTGCACAAT 57.472 34.783 0.00 0.00 37.91 2.71
103 104 5.528043 TGGATGTACAAGTTTGCACAATT 57.472 34.783 0.00 0.00 37.91 2.32
113 114 6.257630 ACAAGTTTGCACAATTATTGGTGAAC 59.742 34.615 9.88 8.29 37.18 3.18
130 131 0.387622 AACGTGCGTGTGTAGCGTAT 60.388 50.000 0.00 0.00 37.44 3.06
133 134 1.912756 CGTGCGTGTGTAGCGTATTTA 59.087 47.619 0.00 0.00 37.44 1.40
158 160 2.298163 GGGAGTTCTCACCGTCACTTAA 59.702 50.000 2.24 0.00 0.00 1.85
160 162 3.576648 GAGTTCTCACCGTCACTTAAGG 58.423 50.000 7.53 0.00 0.00 2.69
180 182 2.238521 GCAACTCCAATTGGAAGACCA 58.761 47.619 26.87 4.89 44.91 4.02
214 216 3.483665 TCCGTTTGGATTCGCGCG 61.484 61.111 26.76 26.76 40.17 6.86
215 217 4.514569 CCGTTTGGATTCGCGCGG 62.515 66.667 31.69 11.75 37.49 6.46
222 224 1.226018 GGATTCGCGCGGACAAAAG 60.226 57.895 31.69 0.00 0.00 2.27
231 233 4.056125 GGACAAAAGCCGCAGCCC 62.056 66.667 0.00 0.00 41.25 5.19
232 234 4.056125 GACAAAAGCCGCAGCCCC 62.056 66.667 0.00 0.00 41.25 5.80
234 236 3.384532 CAAAAGCCGCAGCCCCAT 61.385 61.111 0.00 0.00 41.25 4.00
263 272 5.640732 AGCACATTCATGTCCGTTTTAATC 58.359 37.500 0.00 0.00 39.39 1.75
269 278 7.122650 ACATTCATGTCCGTTTTAATCCATTCT 59.877 33.333 0.00 0.00 35.87 2.40
271 280 6.176896 TCATGTCCGTTTTAATCCATTCTCA 58.823 36.000 0.00 0.00 0.00 3.27
314 323 2.104111 AGGTTGAATCAGACGTTGTCCA 59.896 45.455 0.00 0.00 32.18 4.02
315 324 3.074412 GGTTGAATCAGACGTTGTCCAT 58.926 45.455 0.00 0.00 32.18 3.41
318 327 3.738982 TGAATCAGACGTTGTCCATTGT 58.261 40.909 0.00 0.00 32.18 2.71
325 334 0.790207 CGTTGTCCATTGTCCGTCTG 59.210 55.000 0.00 0.00 0.00 3.51
326 335 1.872237 CGTTGTCCATTGTCCGTCTGT 60.872 52.381 0.00 0.00 0.00 3.41
328 337 0.756294 TGTCCATTGTCCGTCTGTGT 59.244 50.000 0.00 0.00 0.00 3.72
331 340 1.014044 CCATTGTCCGTCTGTGTCCG 61.014 60.000 0.00 0.00 0.00 4.79
333 342 2.781595 ATTGTCCGTCTGTGTCCGGC 62.782 60.000 0.00 0.00 43.87 6.13
334 343 3.681835 GTCCGTCTGTGTCCGGCT 61.682 66.667 0.00 0.00 43.87 5.52
335 344 2.915659 TCCGTCTGTGTCCGGCTT 60.916 61.111 0.00 0.00 43.87 4.35
336 345 2.738521 CCGTCTGTGTCCGGCTTG 60.739 66.667 0.00 0.00 37.43 4.01
337 346 2.338620 CGTCTGTGTCCGGCTTGA 59.661 61.111 0.00 0.00 0.00 3.02
338 347 2.022129 CGTCTGTGTCCGGCTTGAC 61.022 63.158 0.00 0.00 35.77 3.18
339 348 1.069090 GTCTGTGTCCGGCTTGACA 59.931 57.895 0.00 4.99 42.75 3.58
357 366 0.620410 CACACCACCCATCCCTCCTA 60.620 60.000 0.00 0.00 0.00 2.94
358 367 0.346932 ACACCACCCATCCCTCCTAT 59.653 55.000 0.00 0.00 0.00 2.57
375 384 1.150986 CTATCTCTCTCCCCCACCCAT 59.849 57.143 0.00 0.00 0.00 4.00
388 397 1.449271 CACCCATCCACCTATCCCAT 58.551 55.000 0.00 0.00 0.00 4.00
393 402 2.713167 CCATCCACCTATCCCATGACTT 59.287 50.000 0.00 0.00 0.00 3.01
400 409 2.158755 CCTATCCCATGACTTCACCCAC 60.159 54.545 0.00 0.00 0.00 4.61
401 410 0.625849 ATCCCATGACTTCACCCACC 59.374 55.000 0.00 0.00 0.00 4.61
407 416 1.065410 TGACTTCACCCACCACCCAT 61.065 55.000 0.00 0.00 0.00 4.00
432 441 2.261671 GCGACGGAGGCAAGAGAA 59.738 61.111 0.00 0.00 0.00 2.87
509 2332 0.313672 GCTACCTCGAGGAGCTCATG 59.686 60.000 37.69 17.77 38.94 3.07
555 2378 1.896220 TGCCTCTGTTGTGGAATGAC 58.104 50.000 0.00 0.00 0.00 3.06
563 2386 2.301583 TGTTGTGGAATGACGATCTCCA 59.698 45.455 0.00 0.00 36.89 3.86
566 2389 2.501316 TGTGGAATGACGATCTCCATGT 59.499 45.455 4.12 0.00 41.21 3.21
571 2394 1.300233 GACGATCTCCATGTCCGCC 60.300 63.158 0.00 0.00 0.00 6.13
573 2396 2.796193 CGATCTCCATGTCCGCCCA 61.796 63.158 0.00 0.00 0.00 5.36
575 2398 0.604780 GATCTCCATGTCCGCCCATG 60.605 60.000 5.76 5.76 41.52 3.66
651 2484 4.853924 AGCGACCAAATCAGACAAAAAT 57.146 36.364 0.00 0.00 0.00 1.82
719 2557 0.949105 CGTTTGGGTCGTTCCTCCTG 60.949 60.000 0.30 0.00 36.25 3.86
887 2739 2.149803 TTGGCCGCGCGTATATAGCT 62.150 55.000 29.95 0.00 0.00 3.32
923 2776 1.448540 GCCTGATCACCACACGAGG 60.449 63.158 0.00 0.00 0.00 4.63
924 2777 1.219124 CCTGATCACCACACGAGGG 59.781 63.158 0.00 0.00 0.00 4.30
925 2778 1.257750 CCTGATCACCACACGAGGGA 61.258 60.000 0.00 0.00 0.00 4.20
927 2780 0.608130 TGATCACCACACGAGGGAAG 59.392 55.000 0.00 0.00 0.00 3.46
928 2781 0.741221 GATCACCACACGAGGGAAGC 60.741 60.000 0.00 0.00 0.00 3.86
941 2822 1.482593 AGGGAAGCATAGACGGACTTG 59.517 52.381 0.00 0.00 0.00 3.16
970 2851 2.214181 GACTCCGTGTCATCCGCAGT 62.214 60.000 1.60 0.00 44.73 4.40
974 2855 1.212751 CGTGTCATCCGCAGTCTCA 59.787 57.895 0.00 0.00 0.00 3.27
1076 2963 0.034896 ACGCTCCTTGTTCCGATGTT 59.965 50.000 0.00 0.00 0.00 2.71
1396 3283 2.171725 CCCGTCGCCGATTTCCTTC 61.172 63.158 0.00 0.00 35.63 3.46
1446 3333 4.847444 GGCCTCGCCCTGCTCTTC 62.847 72.222 0.00 0.00 44.06 2.87
1500 3387 1.067846 CACTACCTCTACTGCGCACAA 60.068 52.381 5.66 0.00 0.00 3.33
1533 3420 2.612212 GCTCGATCTCGTCTTCTCTTCT 59.388 50.000 0.00 0.00 40.80 2.85
1688 3575 3.488090 GTACAAGCCGGTGCGAGC 61.488 66.667 1.90 0.00 44.33 5.03
1903 3790 1.375551 GTACCTTATTGGCACCACCG 58.624 55.000 0.00 0.00 43.94 4.94
1989 3876 3.164269 ATTCAGGAGGCCGCCGAT 61.164 61.111 20.86 12.63 0.00 4.18
2013 3900 2.332654 GCAGTTGGTTAGGGCCGTG 61.333 63.158 8.57 0.00 0.00 4.94
2036 3923 2.267681 AAGCGTCTCATCGTCCGTCC 62.268 60.000 0.00 0.00 0.00 4.79
2064 3951 2.416162 GGCTGGTTCGAGTTAGAGACAG 60.416 54.545 0.00 0.00 0.00 3.51
2065 3952 2.869897 CTGGTTCGAGTTAGAGACAGC 58.130 52.381 0.00 0.00 0.00 4.40
2066 3953 2.490115 CTGGTTCGAGTTAGAGACAGCT 59.510 50.000 0.00 0.00 0.00 4.24
2111 3998 5.008712 CAGGATATTTCGGGCTTTTCTTACC 59.991 44.000 0.00 0.00 0.00 2.85
2143 4101 1.134670 GTGGCCGATTCTACTTCTGCT 60.135 52.381 0.00 0.00 0.00 4.24
2210 6279 3.939592 GACGAACTTTATTTCTCCCTGGG 59.060 47.826 6.33 6.33 0.00 4.45
2257 6326 5.971202 CCAAATAAGTATGTCATGCGTTTCC 59.029 40.000 0.00 0.00 0.00 3.13
2327 6399 7.789273 TCGTTTGTGAGAAAGGTTACAATTA 57.211 32.000 0.00 0.00 33.56 1.40
2348 6420 4.917906 ACATCTAAAGGCTCCTCAAACT 57.082 40.909 0.00 0.00 0.00 2.66
2360 6432 4.836825 CTCCTCAAACTAATCAAGAGGCA 58.163 43.478 0.00 0.00 44.29 4.75
2361 6433 5.241403 TCCTCAAACTAATCAAGAGGCAA 57.759 39.130 0.00 0.00 44.29 4.52
2429 6501 7.280876 TCGCTTCTCTATTACAAATGCTCAAAT 59.719 33.333 0.00 0.00 0.00 2.32
2505 6577 2.677228 CCCCCGCAGATTGTCCTT 59.323 61.111 0.00 0.00 0.00 3.36
2519 6591 6.825213 CAGATTGTCCTTCATTCTTCATGGTA 59.175 38.462 0.00 0.00 35.43 3.25
2520 6592 6.825721 AGATTGTCCTTCATTCTTCATGGTAC 59.174 38.462 0.00 0.00 34.39 3.34
2527 6599 8.281531 TCCTTCATTCTTCATGGTACCAATAAT 58.718 33.333 20.76 11.08 33.07 1.28
2565 6637 5.588240 AGTTAATGACGAGACGATTGCATA 58.412 37.500 0.00 0.00 0.00 3.14
2566 6638 5.459107 AGTTAATGACGAGACGATTGCATAC 59.541 40.000 0.00 0.00 0.00 2.39
2587 6659 3.070446 ACCGTCCTTTGTGTGATAGACAA 59.930 43.478 0.00 0.00 35.91 3.18
2604 6676 3.157087 GACAAAATCTGAGGGCCAAAGA 58.843 45.455 6.18 8.65 0.00 2.52
2635 6707 6.604396 TCATTAATCCATCAGCACACAAATCT 59.396 34.615 0.00 0.00 0.00 2.40
2640 6712 4.080413 TCCATCAGCACACAAATCTATCCA 60.080 41.667 0.00 0.00 0.00 3.41
3012 7084 0.542333 GCCCCTAAGGAGGTCTTGAC 59.458 60.000 0.00 0.00 41.95 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.190981 GGCCTACGTTATGAACTGACG 58.809 52.381 0.00 0.00 42.17 4.35
1 2 3.187700 CTGGCCTACGTTATGAACTGAC 58.812 50.000 3.32 0.00 0.00 3.51
4 5 1.831736 AGCTGGCCTACGTTATGAACT 59.168 47.619 3.32 0.00 0.00 3.01
5 6 2.311124 AGCTGGCCTACGTTATGAAC 57.689 50.000 3.32 0.00 0.00 3.18
6 7 4.475051 TTAAGCTGGCCTACGTTATGAA 57.525 40.909 3.32 0.00 0.00 2.57
7 8 4.141801 ACATTAAGCTGGCCTACGTTATGA 60.142 41.667 3.32 0.00 0.00 2.15
8 9 4.127171 ACATTAAGCTGGCCTACGTTATG 58.873 43.478 3.32 6.63 0.00 1.90
9 10 4.377897 GACATTAAGCTGGCCTACGTTAT 58.622 43.478 3.32 0.00 0.00 1.89
10 11 3.431207 GGACATTAAGCTGGCCTACGTTA 60.431 47.826 3.32 0.00 41.52 3.18
11 12 2.629051 GACATTAAGCTGGCCTACGTT 58.371 47.619 3.32 0.00 0.00 3.99
12 13 1.134491 GGACATTAAGCTGGCCTACGT 60.134 52.381 3.32 0.00 41.52 3.57
13 14 1.134521 TGGACATTAAGCTGGCCTACG 60.135 52.381 3.32 0.00 45.37 3.51
14 15 2.710096 TGGACATTAAGCTGGCCTAC 57.290 50.000 3.32 0.00 45.37 3.18
15 16 3.714280 TGTATGGACATTAAGCTGGCCTA 59.286 43.478 3.32 0.00 45.37 3.93
16 17 2.509548 TGTATGGACATTAAGCTGGCCT 59.490 45.455 3.32 0.00 45.37 5.19
17 18 2.930950 TGTATGGACATTAAGCTGGCC 58.069 47.619 0.00 0.00 45.37 5.36
18 19 3.947834 ACTTGTATGGACATTAAGCTGGC 59.052 43.478 0.00 0.00 34.86 4.85
19 20 6.515272 AAACTTGTATGGACATTAAGCTGG 57.485 37.500 0.00 0.00 34.86 4.85
20 21 6.128282 ACGAAACTTGTATGGACATTAAGCTG 60.128 38.462 0.00 0.00 34.86 4.24
21 22 5.938125 ACGAAACTTGTATGGACATTAAGCT 59.062 36.000 0.00 0.00 34.86 3.74
22 23 6.021596 CACGAAACTTGTATGGACATTAAGC 58.978 40.000 0.00 0.00 34.86 3.09
23 24 7.129109 ACACGAAACTTGTATGGACATTAAG 57.871 36.000 0.00 0.00 34.86 1.85
24 25 7.656542 TGTACACGAAACTTGTATGGACATTAA 59.343 33.333 0.00 0.00 34.86 1.40
25 26 7.153315 TGTACACGAAACTTGTATGGACATTA 58.847 34.615 0.00 0.00 34.86 1.90
26 27 5.992829 TGTACACGAAACTTGTATGGACATT 59.007 36.000 0.00 0.00 34.86 2.71
64 65 3.603965 TCCAATAGAGGAGAGGGAGAC 57.396 52.381 0.00 0.00 32.77 3.36
102 103 1.261885 CACACGCACGTTCACCAATAA 59.738 47.619 0.00 0.00 0.00 1.40
103 104 0.862490 CACACGCACGTTCACCAATA 59.138 50.000 0.00 0.00 0.00 1.90
113 114 0.711670 AAATACGCTACACACGCACG 59.288 50.000 0.00 0.00 0.00 5.34
130 131 2.640826 ACGGTGAGAACTCCCCAATAAA 59.359 45.455 4.45 0.00 0.00 1.40
133 134 0.613777 GACGGTGAGAACTCCCCAAT 59.386 55.000 4.45 0.00 0.00 3.16
158 160 2.519013 GTCTTCCAATTGGAGTTGCCT 58.481 47.619 25.69 0.00 46.36 4.75
160 162 2.238521 TGGTCTTCCAATTGGAGTTGC 58.761 47.619 25.69 16.77 46.36 4.17
180 182 7.041107 CCAAACGGACATATCCAAATGAAATT 58.959 34.615 0.00 0.00 46.67 1.82
188 190 3.874543 CGAATCCAAACGGACATATCCAA 59.125 43.478 0.00 0.00 46.67 3.53
194 196 1.977594 GCGCGAATCCAAACGGACAT 61.978 55.000 12.10 0.00 34.62 3.06
214 216 4.056125 GGGCTGCGGCTTTTGTCC 62.056 66.667 18.85 4.83 38.73 4.02
215 217 4.056125 GGGGCTGCGGCTTTTGTC 62.056 66.667 18.85 0.00 38.73 3.18
225 227 3.834799 GCTTCTGCATGGGGCTGC 61.835 66.667 0.00 0.00 45.15 5.25
234 236 3.763380 CGGACATGAATGTGCTTCTGCA 61.763 50.000 12.31 0.00 45.49 4.41
240 242 5.393027 GGATTAAAACGGACATGAATGTGCT 60.393 40.000 12.31 0.00 45.49 4.40
245 247 7.339212 TGAGAATGGATTAAAACGGACATGAAT 59.661 33.333 0.00 0.00 0.00 2.57
263 272 9.128404 TCTGATCCAAATTTAAGATGAGAATGG 57.872 33.333 13.59 0.00 29.04 3.16
286 295 6.147821 ACAACGTCTGATTCAACCTAAATCTG 59.852 38.462 0.00 0.00 34.80 2.90
293 302 2.104111 TGGACAACGTCTGATTCAACCT 59.896 45.455 0.00 0.00 32.47 3.50
295 304 4.024048 ACAATGGACAACGTCTGATTCAAC 60.024 41.667 0.00 0.00 32.47 3.18
297 306 3.738982 ACAATGGACAACGTCTGATTCA 58.261 40.909 0.00 0.00 32.47 2.57
314 323 4.988065 CGGACACAGACGGACAAT 57.012 55.556 0.00 0.00 0.00 2.71
326 335 2.110213 GGTGTGTCAAGCCGGACA 59.890 61.111 5.05 0.00 45.06 4.02
328 337 2.110213 GTGGTGTGTCAAGCCGGA 59.890 61.111 5.05 0.00 0.00 5.14
331 340 1.228552 ATGGGTGGTGTGTCAAGCC 60.229 57.895 0.00 0.00 0.00 4.35
333 342 0.609131 GGGATGGGTGGTGTGTCAAG 60.609 60.000 0.00 0.00 0.00 3.02
334 343 1.065410 AGGGATGGGTGGTGTGTCAA 61.065 55.000 0.00 0.00 0.00 3.18
335 344 1.463214 AGGGATGGGTGGTGTGTCA 60.463 57.895 0.00 0.00 0.00 3.58
336 345 1.299976 GAGGGATGGGTGGTGTGTC 59.700 63.158 0.00 0.00 0.00 3.67
337 346 2.231380 GGAGGGATGGGTGGTGTGT 61.231 63.158 0.00 0.00 0.00 3.72
338 347 0.620410 TAGGAGGGATGGGTGGTGTG 60.620 60.000 0.00 0.00 0.00 3.82
339 348 0.346932 ATAGGAGGGATGGGTGGTGT 59.653 55.000 0.00 0.00 0.00 4.16
340 349 1.059913 GATAGGAGGGATGGGTGGTG 58.940 60.000 0.00 0.00 0.00 4.17
341 350 0.952659 AGATAGGAGGGATGGGTGGT 59.047 55.000 0.00 0.00 0.00 4.16
357 366 0.104725 GATGGGTGGGGGAGAGAGAT 60.105 60.000 0.00 0.00 0.00 2.75
358 367 1.314867 GATGGGTGGGGGAGAGAGA 59.685 63.158 0.00 0.00 0.00 3.10
375 384 2.771943 GTGAAGTCATGGGATAGGTGGA 59.228 50.000 0.00 0.00 0.00 4.02
388 397 1.065410 ATGGGTGGTGGGTGAAGTCA 61.065 55.000 0.00 0.00 0.00 3.41
393 402 2.938798 GGGATGGGTGGTGGGTGA 60.939 66.667 0.00 0.00 0.00 4.02
469 478 3.709633 TCCATGACGGCTGCTGCT 61.710 61.111 15.64 0.00 39.59 4.24
478 2301 1.858091 GAGGTAGCATGTCCATGACG 58.142 55.000 11.35 0.00 41.20 4.35
480 2303 1.683385 CTCGAGGTAGCATGTCCATGA 59.317 52.381 11.35 0.00 41.20 3.07
532 2355 2.655090 TTCCACAACAGAGGCATCAA 57.345 45.000 0.00 0.00 0.00 2.57
555 2378 2.029666 GGGCGGACATGGAGATCG 59.970 66.667 0.00 0.00 0.00 3.69
563 2386 3.399181 ACGGACATGGGCGGACAT 61.399 61.111 0.00 0.00 0.00 3.06
566 2389 4.077184 GACACGGACATGGGCGGA 62.077 66.667 0.00 0.00 0.00 5.54
571 2394 0.810648 CCCATTTGACACGGACATGG 59.189 55.000 0.00 0.00 0.00 3.66
573 2396 2.304761 ACTACCCATTTGACACGGACAT 59.695 45.455 0.00 0.00 0.00 3.06
575 2398 2.073816 CACTACCCATTTGACACGGAC 58.926 52.381 0.00 0.00 0.00 4.79
669 2502 1.566703 TCCAACCAAGAGACCCAAACA 59.433 47.619 0.00 0.00 0.00 2.83
719 2557 2.203195 TGCACTGCACAGACCACC 60.203 61.111 4.31 0.00 31.71 4.61
923 2776 2.094182 TGACAAGTCCGTCTATGCTTCC 60.094 50.000 0.00 0.00 36.82 3.46
924 2777 3.232213 TGACAAGTCCGTCTATGCTTC 57.768 47.619 0.00 0.00 36.82 3.86
925 2778 3.895232 ATGACAAGTCCGTCTATGCTT 57.105 42.857 0.00 0.00 36.82 3.91
927 2780 3.521560 TCAATGACAAGTCCGTCTATGC 58.478 45.455 0.00 0.00 36.82 3.14
928 2781 4.442403 CGATCAATGACAAGTCCGTCTATG 59.558 45.833 0.00 0.00 36.82 2.23
941 2822 2.186076 GACACGGAGTCGATCAATGAC 58.814 52.381 0.00 0.00 41.61 3.06
1162 3049 0.602905 AACAAGCACGGCAGGTAGAC 60.603 55.000 0.00 0.00 0.00 2.59
1500 3387 3.701241 GAGATCGAGCGTGAGAAAGATT 58.299 45.455 0.00 0.00 0.00 2.40
1599 3486 2.126888 TCGTTAACCGACGCGACC 60.127 61.111 15.93 2.61 41.60 4.79
1989 3876 1.599518 CCTAACCAACTGCACCGCA 60.600 57.895 0.00 0.00 36.92 5.69
1996 3883 1.674322 CCACGGCCCTAACCAACTG 60.674 63.158 0.00 0.00 0.00 3.16
2013 3900 0.595310 GGACGATGAGACGCTTAGCC 60.595 60.000 0.00 0.00 36.70 3.93
2036 3923 0.609131 ACTCGAACCAGCCCCAAATG 60.609 55.000 0.00 0.00 0.00 2.32
2066 3953 5.213891 TGACAGCTGAATGTTACTCTTCA 57.786 39.130 23.35 5.90 32.25 3.02
2111 3998 3.685139 ATCGGCCACAGATTATACCTG 57.315 47.619 2.24 0.00 37.64 4.00
2210 6279 5.454897 GGACCAATAGGAAGAGGTTACATCC 60.455 48.000 0.00 0.00 38.69 3.51
2292 6364 7.042321 CCTTTCTCACAAACGATGTACTTGTTA 60.042 37.037 0.00 0.00 41.46 2.41
2305 6377 9.394477 GATGTAATTGTAACCTTTCTCACAAAC 57.606 33.333 0.00 0.00 34.79 2.93
2327 6399 4.917906 AGTTTGAGGAGCCTTTAGATGT 57.082 40.909 0.00 0.00 0.00 3.06
2348 6420 7.013655 GGCTAGATTTCATTTGCCTCTTGATTA 59.986 37.037 0.00 0.00 37.58 1.75
2429 6501 4.949856 GGCTGTGATTTCCCTATTTCTTCA 59.050 41.667 0.00 0.00 0.00 3.02
2505 6577 9.342308 GAAGATTATTGGTACCATGAAGAATGA 57.658 33.333 17.17 1.96 38.72 2.57
2519 6591 6.659242 ACTCGGACAATTTGAAGATTATTGGT 59.341 34.615 2.79 0.00 34.40 3.67
2520 6592 7.088589 ACTCGGACAATTTGAAGATTATTGG 57.911 36.000 2.79 0.00 34.40 3.16
2527 6599 6.128661 CGTCATTAACTCGGACAATTTGAAGA 60.129 38.462 2.79 0.00 0.00 2.87
2565 6637 2.631062 TGTCTATCACACAAAGGACGGT 59.369 45.455 0.00 0.00 0.00 4.83
2566 6638 3.313012 TGTCTATCACACAAAGGACGG 57.687 47.619 0.00 0.00 0.00 4.79
2587 6659 4.021916 CTGAATCTTTGGCCCTCAGATTT 58.978 43.478 17.78 6.51 36.44 2.17
2604 6676 6.039047 GTGTGCTGATGGATTAATGACTGAAT 59.961 38.462 0.00 0.00 0.00 2.57
3012 7084 5.460646 ACTTAATGTTGACGCATCTTTTGG 58.539 37.500 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.