Multiple sequence alignment - TraesCS1D01G208400

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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 TraesCS1D01G208400 chr1D 100.000 3748 0 0 1 3748 294404377 294408124 0.000000e+00 6922
1 TraesCS1D01G208400 chr1B 91.959 2537 100 34 594 3088 396116620 396119094 0.000000e+00 3459
2 TraesCS1D01G208400 chr1B 88.455 589 57 7 10 591 396115713 396116297 0.000000e+00 701
3 TraesCS1D01G208400 chr1B 84.685 666 82 17 3088 3748 396120485 396121135 0.000000e+00 647
4 TraesCS1D01G208400 chr1A 91.614 1574 67 17 1594 3142 367381964 367383497 0.000000e+00 2115
5 TraesCS1D01G208400 chr1A 92.178 1483 82 14 13 1479 367380465 367381929 0.000000e+00 2065
6 TraesCS1D01G208400 chr1A 86.143 433 55 4 156 584 367375429 367375860 2.640000e-126 462
7 TraesCS1D01G208400 chr1A 88.000 300 26 8 3454 3748 367395826 367396120 2.770000e-91 346
8 TraesCS1D01G208400 chr2A 78.614 664 105 24 3095 3747 699167879 699168516 4.510000e-109 405
9 TraesCS1D01G208400 chr2D 75.296 591 109 32 11 574 136609782 136610362 8.040000e-62 248


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 TraesCS1D01G208400 chr1D 294404377 294408124 3747 False 6922.000000 6922 100.000000 1 3748 1 chr1D.!!$F1 3747
1 TraesCS1D01G208400 chr1B 396115713 396121135 5422 False 1602.333333 3459 88.366333 10 3748 3 chr1B.!!$F1 3738
2 TraesCS1D01G208400 chr1A 367380465 367383497 3032 False 2090.000000 2115 91.896000 13 3142 2 chr1A.!!$F3 3129
3 TraesCS1D01G208400 chr2A 699167879 699168516 637 False 405.000000 405 78.614000 3095 3747 1 chr2A.!!$F1 652
4 TraesCS1D01G208400 chr2D 136609782 136610362 580 False 248.000000 248 75.296000 11 574 1 chr2D.!!$F1 563

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
506 531 0.107703 GGTGAGCCATCGGATGACAA 60.108 55.0 19.3 0.0 34.09 3.18 F
1627 2003 0.387202 CGTGGTTTGGTTTGCATGGA 59.613 50.0 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2523 0.543749 AGGATAGCACCTCTGCAACC 59.456 55.0 0.0 0.0 46.97 3.77 R
2771 3179 0.759346 ATTACAGGCAGGGGATCGAC 59.241 55.0 0.0 0.0 0.00 4.20 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
27 28 3.041940 CACCCGACAACGCCACTC 61.042 66.667 0.00 0.00 38.29 3.51
31 32 4.657824 CGACAACGCCACTCCGGT 62.658 66.667 0.00 0.00 36.97 5.28
49 50 4.827087 CGCCTCCGTGCTGCTCAT 62.827 66.667 0.00 0.00 0.00 2.90
50 51 2.437359 GCCTCCGTGCTGCTCATT 60.437 61.111 0.00 0.00 0.00 2.57
72 75 0.298707 CGCCACGAAATGAGATCACG 59.701 55.000 0.00 0.00 0.00 4.35
84 87 5.832539 ATGAGATCACGGAGGGATTTTAT 57.167 39.130 0.00 0.00 0.00 1.40
99 102 4.325030 GGATTTTATGGTCTCCCAACCTCA 60.325 45.833 0.00 0.00 46.04 3.86
120 132 4.814294 AATCACTCCGCCGCCGAC 62.814 66.667 0.00 0.00 36.29 4.79
130 142 3.554692 CCGCCGACAATCGTCTGC 61.555 66.667 0.00 0.00 45.80 4.26
141 153 2.264005 ATCGTCTGCCTCTCGATACT 57.736 50.000 0.00 0.00 41.46 2.12
150 162 4.933330 TGCCTCTCGATACTAATTGTCAC 58.067 43.478 0.00 0.00 0.00 3.67
152 164 4.497674 GCCTCTCGATACTAATTGTCACGT 60.498 45.833 0.00 0.00 0.00 4.49
161 173 8.857216 CGATACTAATTGTCACGTTCTAAGTTT 58.143 33.333 0.00 0.00 0.00 2.66
182 194 7.441836 AGTTTTGAATGGAGGAATTTAACACC 58.558 34.615 0.00 0.00 0.00 4.16
207 219 7.254387 CCGAATCACTCAATTTCAGAGAAGATC 60.254 40.741 0.00 0.00 36.91 2.75
248 260 3.009723 TCGATTGCTTAGAAAAGGGCAG 58.990 45.455 0.00 0.00 36.06 4.85
287 300 2.107552 ACTGGCAAGCTAGGGTTTACAA 59.892 45.455 10.22 0.00 0.00 2.41
322 340 2.649312 ACATGGTCCAAAATGAGGAGGA 59.351 45.455 0.00 0.00 35.42 3.71
323 341 3.285484 CATGGTCCAAAATGAGGAGGAG 58.715 50.000 0.00 0.00 35.42 3.69
324 342 1.635487 TGGTCCAAAATGAGGAGGAGG 59.365 52.381 0.00 0.00 35.42 4.30
447 472 2.223595 GCCGTCAGATCGAAGATCAAGA 60.224 50.000 11.94 6.88 45.12 3.02
506 531 0.107703 GGTGAGCCATCGGATGACAA 60.108 55.000 19.30 0.00 34.09 3.18
517 542 1.202065 CGGATGACAAATCAACGCCTG 60.202 52.381 0.00 0.00 38.69 4.85
518 543 2.083774 GGATGACAAATCAACGCCTGA 58.916 47.619 0.00 0.00 38.69 3.86
519 544 2.159517 GGATGACAAATCAACGCCTGAC 60.160 50.000 0.00 0.00 38.69 3.51
520 545 2.254546 TGACAAATCAACGCCTGACT 57.745 45.000 0.00 0.00 36.69 3.41
522 547 2.948979 TGACAAATCAACGCCTGACTTT 59.051 40.909 0.00 0.00 36.69 2.66
523 548 3.003275 TGACAAATCAACGCCTGACTTTC 59.997 43.478 0.00 0.00 36.69 2.62
584 614 0.549950 ATGATGGACTTGGGCCTGAG 59.450 55.000 4.53 5.45 0.00 3.35
598 948 3.389329 GGGCCTGAGATCTTAACTCATCA 59.611 47.826 0.84 0.00 42.32 3.07
655 1005 1.737793 GGTCGGGTGTTAAGCTGAATG 59.262 52.381 0.00 0.00 40.78 2.67
658 1008 3.689649 GTCGGGTGTTAAGCTGAATGAAT 59.310 43.478 0.00 0.00 40.78 2.57
659 1009 4.873827 GTCGGGTGTTAAGCTGAATGAATA 59.126 41.667 0.00 0.00 40.78 1.75
660 1010 5.353123 GTCGGGTGTTAAGCTGAATGAATAA 59.647 40.000 0.00 0.00 40.78 1.40
661 1011 5.941058 TCGGGTGTTAAGCTGAATGAATAAA 59.059 36.000 0.00 0.00 36.26 1.40
668 1018 4.978083 AGCTGAATGAATAAACAGGCTG 57.022 40.909 14.16 14.16 0.00 4.85
669 1019 4.592942 AGCTGAATGAATAAACAGGCTGA 58.407 39.130 23.66 0.00 0.00 4.26
707 1057 4.329545 GCTGCACCCACCGGAAGA 62.330 66.667 9.46 0.00 0.00 2.87
826 1176 1.279271 CCCGACCACAGATTTCCTCTT 59.721 52.381 0.00 0.00 29.16 2.85
853 1203 1.133407 CGCGCCGCTATTTATACACA 58.867 50.000 7.78 0.00 0.00 3.72
886 1236 1.410365 CCTCGTCTCCACTACCATCCT 60.410 57.143 0.00 0.00 0.00 3.24
949 1299 2.108157 TGCGTGCGTCCTCAGTTT 59.892 55.556 0.00 0.00 0.00 2.66
986 1336 2.032178 AGTTCAACAGTTTGCTTCTCGC 59.968 45.455 0.00 0.00 39.77 5.03
1266 1616 2.752640 TCCATCGAGGTCGCCGAA 60.753 61.111 0.00 0.00 39.62 4.30
1397 1760 5.584913 AGTCCGACTATCCATGGAATAGAT 58.415 41.667 25.56 12.41 31.04 1.98
1510 1873 5.399596 GCCGTTTCAAAACTCTGAAAGAATC 59.600 40.000 4.28 0.00 46.34 2.52
1512 1875 6.972328 CCGTTTCAAAACTCTGAAAGAATCAA 59.028 34.615 4.28 0.00 46.34 2.57
1562 1925 1.279025 GGTGGGAGAGGCCATGGTAA 61.279 60.000 14.67 0.00 38.95 2.85
1627 2003 0.387202 CGTGGTTTGGTTTGCATGGA 59.613 50.000 0.00 0.00 0.00 3.41
1657 2033 8.519492 AGATAAAAACAACAAAATGATGTCGG 57.481 30.769 0.00 0.00 31.97 4.79
1694 2070 6.410914 CGGCATCGAATTTGTACTTTGTTATC 59.589 38.462 0.00 0.00 39.00 1.75
1766 2142 3.543680 TGGAGGCTTATTACTGACTGC 57.456 47.619 0.00 0.00 0.00 4.40
1890 2266 2.491022 GGTAGCGCCTCGACCTCAT 61.491 63.158 2.29 0.00 37.47 2.90
1931 2307 3.968096 CGCACCATGCTTGATTAAATACG 59.032 43.478 0.22 0.00 42.25 3.06
1962 2338 4.539081 GCTCTTTACGACGCGCGC 62.539 66.667 32.58 23.91 46.04 6.86
2074 2450 7.041508 AGCTCATTTGCATTGTCTATAAGCTAC 60.042 37.037 6.88 0.00 33.74 3.58
2120 2496 6.480524 TTCTTGTGAAAGAATCCATACACG 57.519 37.500 0.00 0.00 34.15 4.49
2122 2498 3.669536 TGTGAAAGAATCCATACACGCA 58.330 40.909 0.00 0.00 0.00 5.24
2147 2523 1.818674 AGAGCGGCCTAAAAATGGTTG 59.181 47.619 0.00 0.00 0.00 3.77
2151 2527 2.682836 CGGCCTAAAAATGGTTGGTTG 58.317 47.619 0.00 0.00 0.00 3.77
2193 2569 5.246203 AGCAAATCTTGTAGACCACTCACTA 59.754 40.000 0.00 0.00 0.00 2.74
2215 2591 8.799091 CACTAATTCACACTTGATAAGTCGTAG 58.201 37.037 0.00 0.00 40.46 3.51
2371 2765 9.868277 AAAATATGTCAACACAAGTCAAAAAGA 57.132 25.926 0.00 0.00 35.64 2.52
2803 3211 6.640907 CCCTGCCTGTAATTAAATTAAATCGC 59.359 38.462 0.00 0.00 0.00 4.58
2809 3217 8.487176 CCTGTAATTAAATTAAATCGCCATTGC 58.513 33.333 0.00 0.00 0.00 3.56
2853 3261 1.971695 GGGACCGGTGGCAAAAGAG 60.972 63.158 14.63 0.00 0.00 2.85
2942 3361 0.107643 GGGCTGATCTGGCTTCCTAC 59.892 60.000 22.51 4.46 0.00 3.18
2946 3365 2.695666 GCTGATCTGGCTTCCTACTACA 59.304 50.000 1.46 0.00 0.00 2.74
2980 3399 3.116063 TGCACGTTCTGATTTATTGCG 57.884 42.857 0.00 0.00 0.00 4.85
3027 3458 8.691797 ACACAAGGAAAGCTTAAAATAAACAGA 58.308 29.630 0.00 0.00 0.00 3.41
3030 3461 9.185192 CAAGGAAAGCTTAAAATAAACAGACAG 57.815 33.333 0.00 0.00 0.00 3.51
3142 4964 9.931210 CTGAAACTTGTAGACGAAAACTAAATT 57.069 29.630 0.00 0.00 0.00 1.82
3177 4999 9.466497 AACCTCTAATTCATGTAATCAACACAT 57.534 29.630 0.00 0.00 42.09 3.21
3179 5001 8.278408 CCTCTAATTCATGTAATCAACACATCG 58.722 37.037 0.00 0.00 42.09 3.84
3183 5005 5.794687 TCATGTAATCAACACATCGAACC 57.205 39.130 0.00 0.00 42.09 3.62
3193 5015 1.482182 CACATCGAACCCTCTGATCCA 59.518 52.381 0.00 0.00 0.00 3.41
3195 5017 1.759445 CATCGAACCCTCTGATCCAGT 59.241 52.381 0.00 0.00 32.61 4.00
3215 5038 6.263617 TCCAGTTTATTTTAAACCTTGAGCGT 59.736 34.615 6.54 0.00 0.00 5.07
3216 5039 7.444792 TCCAGTTTATTTTAAACCTTGAGCGTA 59.555 33.333 6.54 0.00 0.00 4.42
3228 5051 3.119849 CCTTGAGCGTATTTCCAAACAGG 60.120 47.826 0.00 0.00 39.47 4.00
3245 5068 1.894466 CAGGGATTGTTCATGTGGCAA 59.106 47.619 0.00 0.00 0.00 4.52
3269 5092 3.437213 TGTTGAACCTAGGATCTTCGGA 58.563 45.455 17.98 0.00 0.00 4.55
3275 5098 0.244994 CTAGGATCTTCGGATGCGGG 59.755 60.000 6.82 0.15 45.59 6.13
3302 5125 4.284550 TTGGACCAGCCCACCAGC 62.285 66.667 0.00 0.00 35.62 4.85
3304 5127 4.729918 GGACCAGCCCACCAGCAG 62.730 72.222 0.00 0.00 34.23 4.24
3317 5140 0.313672 CCAGCAGGCGCAAAGTTTTA 59.686 50.000 10.83 0.00 42.27 1.52
3323 5146 4.211164 AGCAGGCGCAAAGTTTTATTTTTC 59.789 37.500 10.83 0.00 42.27 2.29
3325 5148 5.404066 GCAGGCGCAAAGTTTTATTTTTCTA 59.596 36.000 10.83 0.00 38.36 2.10
3326 5149 6.615628 GCAGGCGCAAAGTTTTATTTTTCTAC 60.616 38.462 10.83 0.00 38.36 2.59
3327 5150 6.419413 CAGGCGCAAAGTTTTATTTTTCTACA 59.581 34.615 10.83 0.00 0.00 2.74
3360 5183 7.598118 TCGTAAGATGTGACGTAAAAATACCAA 59.402 33.333 0.00 0.00 45.01 3.67
3361 5184 8.222433 CGTAAGATGTGACGTAAAAATACCAAA 58.778 33.333 0.00 0.00 43.02 3.28
3411 5238 3.181495 CGACCTGTAGCTCTAAAGTCCTG 60.181 52.174 0.00 0.00 0.00 3.86
3417 5244 1.066286 AGCTCTAAAGTCCTGCTGCTG 60.066 52.381 0.00 0.00 32.32 4.41
3434 5261 1.946283 GCTGGCCACTCTAACTGAACC 60.946 57.143 0.00 0.00 0.00 3.62
3630 5458 9.276397 CAAAAATGTGAACAACTTTTTGGAATC 57.724 29.630 18.60 0.00 42.30 2.52
3639 5467 5.105917 ACAACTTTTTGGAATCACGAACAGT 60.106 36.000 0.00 0.00 37.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.860293 CGTTGTCGGGTGCATCAC 59.140 61.111 0.00 0.00 0.00 3.06
5 6 3.047280 GCGTTGTCGGGTGCATCA 61.047 61.111 0.00 0.00 37.56 3.07
6 7 3.799755 GGCGTTGTCGGGTGCATC 61.800 66.667 0.00 0.00 37.56 3.91
7 8 4.634703 TGGCGTTGTCGGGTGCAT 62.635 61.111 0.00 0.00 37.56 3.96
11 12 4.309950 GGAGTGGCGTTGTCGGGT 62.310 66.667 0.00 0.00 37.56 5.28
49 50 0.676466 ATCTCATTTCGTGGCGGCAA 60.676 50.000 15.50 0.00 0.00 4.52
50 51 1.078497 ATCTCATTTCGTGGCGGCA 60.078 52.632 7.97 7.97 0.00 5.69
120 132 2.292016 AGTATCGAGAGGCAGACGATTG 59.708 50.000 15.06 0.00 42.71 2.67
130 142 5.171147 ACGTGACAATTAGTATCGAGAGG 57.829 43.478 0.00 0.00 33.01 3.69
141 153 9.658475 CATTCAAAACTTAGAACGTGACAATTA 57.342 29.630 0.00 0.00 0.00 1.40
150 162 6.554334 TTCCTCCATTCAAAACTTAGAACG 57.446 37.500 0.00 0.00 0.00 3.95
161 173 5.317808 TCGGTGTTAAATTCCTCCATTCAA 58.682 37.500 0.00 0.00 0.00 2.69
182 194 6.957984 TCTTCTCTGAAATTGAGTGATTCG 57.042 37.500 0.00 0.00 33.59 3.34
207 219 0.748729 ACCCTAGTTCGAGCTCTCCG 60.749 60.000 12.85 0.00 0.00 4.63
229 241 4.013050 ACTCTGCCCTTTTCTAAGCAATC 58.987 43.478 0.00 0.00 34.26 2.67
248 260 1.477295 AGTGGCGAGCTAAACCTACTC 59.523 52.381 0.00 0.00 0.00 2.59
287 300 3.945285 GGACCATGTTGATTTGTATCGGT 59.055 43.478 0.00 0.00 33.23 4.69
381 399 8.342634 GCTCTATAATTTTTCGACAAAGCCATA 58.657 33.333 2.86 0.43 0.00 2.74
421 446 1.671328 TCTTCGATCTGACGGCTACTG 59.329 52.381 0.00 0.00 0.00 2.74
447 472 1.408340 CAGCGATGACTGTCCTCATCT 59.592 52.381 12.51 6.50 43.09 2.90
463 488 2.901051 AAGATACCGGTTCGCCAGCG 62.901 60.000 15.04 5.50 46.41 5.18
506 531 1.156736 CGGAAAGTCAGGCGTTGATT 58.843 50.000 0.00 0.00 38.29 2.57
517 542 3.423154 CCTGCGTGCCGGAAAGTC 61.423 66.667 5.05 0.00 0.00 3.01
518 543 3.469863 TTCCTGCGTGCCGGAAAGT 62.470 57.895 14.30 0.00 36.42 2.66
519 544 2.668212 TTCCTGCGTGCCGGAAAG 60.668 61.111 14.30 0.00 36.42 2.62
520 545 2.975799 GTTCCTGCGTGCCGGAAA 60.976 61.111 17.62 2.06 40.71 3.13
522 547 4.680237 CTGTTCCTGCGTGCCGGA 62.680 66.667 5.05 0.43 0.00 5.14
540 569 8.758633 TTTCTGAAGAACTAGAGTTAATTCCG 57.241 34.615 0.00 9.44 38.56 4.30
584 614 5.359194 TGGGACCTTGATGAGTTAAGATC 57.641 43.478 0.00 0.00 0.00 2.75
598 948 0.042131 TCACGGTATCCTGGGACCTT 59.958 55.000 14.34 4.92 33.21 3.50
633 983 1.122632 TCAGCTTAACACCCGACCCA 61.123 55.000 0.00 0.00 0.00 4.51
655 1005 6.347725 CGTGCCTATATTCAGCCTGTTTATTC 60.348 42.308 0.00 0.00 0.00 1.75
658 1008 4.100344 TCGTGCCTATATTCAGCCTGTTTA 59.900 41.667 0.00 0.00 0.00 2.01
659 1009 3.118408 TCGTGCCTATATTCAGCCTGTTT 60.118 43.478 0.00 0.00 0.00 2.83
660 1010 2.434336 TCGTGCCTATATTCAGCCTGTT 59.566 45.455 0.00 0.00 0.00 3.16
661 1011 2.036475 CTCGTGCCTATATTCAGCCTGT 59.964 50.000 0.00 0.00 0.00 4.00
703 1053 2.754552 TGCTCTCTGCTCTCTTCTCTTC 59.245 50.000 0.00 0.00 43.37 2.87
704 1054 2.756760 CTGCTCTCTGCTCTCTTCTCTT 59.243 50.000 0.00 0.00 43.37 2.85
705 1055 2.025981 TCTGCTCTCTGCTCTCTTCTCT 60.026 50.000 0.00 0.00 43.37 3.10
706 1056 2.368439 TCTGCTCTCTGCTCTCTTCTC 58.632 52.381 0.00 0.00 43.37 2.87
707 1057 2.512692 TCTGCTCTCTGCTCTCTTCT 57.487 50.000 0.00 0.00 43.37 2.85
826 1176 2.372040 AATAGCGGCGCGGGAATGTA 62.372 55.000 27.59 11.89 0.00 2.29
886 1236 4.772100 TGATGAGTGGTGAGTGATGAGTAA 59.228 41.667 0.00 0.00 0.00 2.24
942 1292 2.843701 ACTGAACTGGAGCAAACTGAG 58.156 47.619 0.00 0.00 0.00 3.35
949 1299 2.170397 TGAACTCAACTGAACTGGAGCA 59.830 45.455 0.00 0.00 0.00 4.26
1266 1616 3.518998 CAGAGGTCCCGCGACGAT 61.519 66.667 8.23 0.00 40.17 3.73
1397 1760 1.639722 TTCATCGTGGAAGGGACTGA 58.360 50.000 0.00 0.00 40.86 3.41
1441 1804 4.645535 AGTGCTCTGAGTTCTGCAAATTA 58.354 39.130 6.53 0.00 37.17 1.40
1510 1873 3.822607 CCTCTCGGAGGTCAACTTG 57.177 57.895 4.96 0.00 44.25 3.16
1562 1925 1.274728 AGCAGTCAGAGCGAAACAGAT 59.725 47.619 0.00 0.00 37.01 2.90
1627 2003 7.045126 TCATTTTGTTGTTTTTATCTCCCGT 57.955 32.000 0.00 0.00 0.00 5.28
1657 2033 2.045926 ATGCCGGGAGTCAACAGC 60.046 61.111 2.18 0.00 0.00 4.40
1694 2070 1.135489 TGCTTAACAGTAGCCTCGTCG 60.135 52.381 0.00 0.00 37.85 5.12
1766 2142 1.121257 GCACGTCGTACAGTACAAACG 59.879 52.381 24.00 24.00 40.88 3.60
1890 2266 1.658596 CGCCATGATTTTCGTTCGAGA 59.341 47.619 0.00 0.00 0.00 4.04
1931 2307 8.689069 CGTCGTAAAGAGCCTTATTAAATACTC 58.311 37.037 0.00 0.00 0.00 2.59
1962 2338 5.818136 ATTAATTGGAGTGGTTGATCACG 57.182 39.130 0.00 0.00 42.10 4.35
2074 2450 7.605691 AGAAATCCTTGTGTCTGAAGATAACAG 59.394 37.037 0.00 0.00 36.80 3.16
2109 2485 3.525537 CTCTCTTGTGCGTGTATGGATT 58.474 45.455 0.00 0.00 0.00 3.01
2120 2496 0.673644 TTTAGGCCGCTCTCTTGTGC 60.674 55.000 0.00 0.00 0.00 4.57
2122 2498 2.561478 TTTTTAGGCCGCTCTCTTGT 57.439 45.000 0.00 0.00 0.00 3.16
2147 2523 0.543749 AGGATAGCACCTCTGCAACC 59.456 55.000 0.00 0.00 46.97 3.77
2151 2527 1.272212 GCTCTAGGATAGCACCTCTGC 59.728 57.143 0.00 0.00 44.63 4.26
2193 2569 9.355215 CTAACTACGACTTATCAAGTGTGAATT 57.645 33.333 0.00 0.00 43.03 2.17
2769 3177 4.227134 CAGGCAGGGGATCGACCG 62.227 72.222 0.00 0.00 40.11 4.79
2770 3178 1.335132 TTACAGGCAGGGGATCGACC 61.335 60.000 0.00 0.00 38.08 4.79
2771 3179 0.759346 ATTACAGGCAGGGGATCGAC 59.241 55.000 0.00 0.00 0.00 4.20
2772 3180 1.507140 AATTACAGGCAGGGGATCGA 58.493 50.000 0.00 0.00 0.00 3.59
2942 3361 5.405571 ACGTGCAAACTATCTTCAAGTGTAG 59.594 40.000 0.00 0.00 0.00 2.74
2946 3365 5.050091 CAGAACGTGCAAACTATCTTCAAGT 60.050 40.000 0.00 0.00 0.00 3.16
2980 3399 2.425773 CTTGCAGTTCGTGTGCGC 60.426 61.111 0.00 0.00 44.35 6.09
3027 3458 3.808726 GTCGGTCGACATAGATAGACTGT 59.191 47.826 18.91 0.00 44.02 3.55
3030 3461 4.650545 GAGTCGGTCGACATAGATAGAC 57.349 50.000 22.81 13.19 46.76 2.59
3102 4924 7.839680 ACAAGTTTCAGGATTATTTTGGACT 57.160 32.000 0.00 0.00 0.00 3.85
3114 4936 5.667466 AGTTTTCGTCTACAAGTTTCAGGA 58.333 37.500 0.00 0.00 0.00 3.86
3150 4972 9.295825 TGTGTTGATTACATGAATTAGAGGTTT 57.704 29.630 0.00 0.00 39.39 3.27
3154 4976 9.034544 TCGATGTGTTGATTACATGAATTAGAG 57.965 33.333 0.00 0.00 38.78 2.43
3161 4983 4.634004 GGGTTCGATGTGTTGATTACATGA 59.366 41.667 0.00 0.00 38.78 3.07
3163 4985 4.843728 AGGGTTCGATGTGTTGATTACAT 58.156 39.130 0.00 0.00 41.21 2.29
3166 4988 4.221924 TCAGAGGGTTCGATGTGTTGATTA 59.778 41.667 0.00 0.00 0.00 1.75
3167 4989 3.007940 TCAGAGGGTTCGATGTGTTGATT 59.992 43.478 0.00 0.00 0.00 2.57
3170 4992 2.455674 TCAGAGGGTTCGATGTGTTG 57.544 50.000 0.00 0.00 0.00 3.33
3172 4994 1.482593 GGATCAGAGGGTTCGATGTGT 59.517 52.381 0.00 0.00 0.00 3.72
3177 4999 1.938585 AACTGGATCAGAGGGTTCGA 58.061 50.000 1.59 0.00 35.18 3.71
3179 5001 8.575649 TTAAAATAAACTGGATCAGAGGGTTC 57.424 34.615 1.59 0.00 35.18 3.62
3183 5005 8.581253 AGGTTTAAAATAAACTGGATCAGAGG 57.419 34.615 11.51 0.00 35.18 3.69
3195 5017 9.628746 GGAAATACGCTCAAGGTTTAAAATAAA 57.371 29.630 0.00 0.00 0.00 1.40
3228 5051 3.598019 ATGTTGCCACATGAACAATCC 57.402 42.857 2.00 0.00 42.46 3.01
3245 5068 4.383118 CCGAAGATCCTAGGTTCAACATGT 60.383 45.833 19.78 0.00 0.00 3.21
3248 5071 3.437213 TCCGAAGATCCTAGGTTCAACA 58.563 45.455 19.78 0.00 0.00 3.33
3258 5081 1.762460 ACCCGCATCCGAAGATCCT 60.762 57.895 0.00 0.00 36.29 3.24
3275 5098 4.612412 TGGTCCAACCGCGTCCAC 62.612 66.667 4.92 0.00 42.58 4.02
3284 5107 2.282462 CTGGTGGGCTGGTCCAAC 60.282 66.667 1.83 1.83 44.53 3.77
3285 5108 4.284550 GCTGGTGGGCTGGTCCAA 62.285 66.667 0.00 0.00 38.72 3.53
3302 5125 5.905480 AGAAAAATAAAACTTTGCGCCTG 57.095 34.783 4.18 0.00 0.00 4.85
3303 5126 6.508777 TGTAGAAAAATAAAACTTTGCGCCT 58.491 32.000 4.18 0.00 0.00 5.52
3304 5127 6.757026 TGTAGAAAAATAAAACTTTGCGCC 57.243 33.333 4.18 0.00 0.00 6.53
3323 5146 7.061905 ACGTCACATCTTACGAGAAAAATGTAG 59.938 37.037 1.45 0.00 41.55 2.74
3325 5148 5.694910 ACGTCACATCTTACGAGAAAAATGT 59.305 36.000 1.45 0.00 41.55 2.71
3326 5149 6.153212 ACGTCACATCTTACGAGAAAAATG 57.847 37.500 1.45 0.00 41.55 2.32
3327 5150 7.878477 TTACGTCACATCTTACGAGAAAAAT 57.122 32.000 0.00 0.00 41.55 1.82
3372 5198 2.093658 GGTCGCTAGTTTGATTCCCTGA 60.094 50.000 0.00 0.00 0.00 3.86
3411 5238 1.023513 CAGTTAGAGTGGCCAGCAGC 61.024 60.000 5.11 0.00 42.60 5.25
3417 5244 2.224548 ACAAGGTTCAGTTAGAGTGGCC 60.225 50.000 0.00 0.00 0.00 5.36
3434 5261 4.142403 TGCTTCTCTTTTCACACCAACAAG 60.142 41.667 0.00 0.00 0.00 3.16
3619 5447 6.885735 AAAACTGTTCGTGATTCCAAAAAG 57.114 33.333 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.