Multiple sequence alignment - TraesCS7B01G118100

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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 TraesCS7B01G118100 chr7B 100.000 5493 0 0 1 5493 137783654 137789146 0.000000e+00 10144
1 TraesCS7B01G118100 chr7D 95.839 4879 99 29 647 5491 171302652 171307460 0.000000e+00 7790
2 TraesCS7B01G118100 chr7D 90.838 382 19 7 268 647 171302243 171302610 1.060000e-136 497
3 TraesCS7B01G118100 chr7A 94.367 4882 183 32 647 5493 174195038 174199862 0.000000e+00 7408
4 TraesCS7B01G118100 chr7A 88.764 623 43 8 13 631 174194386 174194985 0.000000e+00 737
5 TraesCS7B01G118100 chr6A 84.356 326 49 2 4169 4493 521459143 521458819 8.880000e-83 318
6 TraesCS7B01G118100 chr6B 83.129 326 53 2 4169 4493 567408352 567408028 4.160000e-76 296


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 TraesCS7B01G118100 chr7B 137783654 137789146 5492 False 10144.0 10144 100.0000 1 5493 1 chr7B.!!$F1 5492
1 TraesCS7B01G118100 chr7D 171302243 171307460 5217 False 4143.5 7790 93.3385 268 5491 2 chr7D.!!$F1 5223
2 TraesCS7B01G118100 chr7A 174194386 174199862 5476 False 4072.5 7408 91.5655 13 5493 2 chr7A.!!$F1 5480

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
485 488 0.188342 AGGAAAGGAAAGGGCAAGCA 59.812 50.0 0.00 0.00 0.0 3.91 F
489 492 0.251519 AAGGAAAGGGCAAGCAGGAG 60.252 55.0 0.00 0.00 0.0 3.69 F
1534 1634 0.251916 CCTGTAAGCGAATCACCCCA 59.748 55.0 0.00 0.00 0.0 4.96 F
2191 2292 1.016627 TTCTCACTGTGCACTTGTGC 58.983 50.0 27.01 17.73 0.0 4.57 F
3730 3832 0.247460 TCCACAGAGATGTCAAGGCG 59.753 55.0 0.00 0.00 0.0 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1865 0.037326 TGCAGCCAAGAGAACGGTAG 60.037 55.0 0.00 0.0 0.00 3.18 R
2165 2265 0.320683 TGCACAGTGAGAACATCCCG 60.321 55.0 4.15 0.0 0.00 5.14 R
3183 3284 0.036875 GGTAAGACAACCCTGCTGCT 59.963 55.0 0.00 0.0 33.02 4.24 R
3946 4048 0.693049 ATGCCTTTCCGAACTCCAGT 59.307 50.0 0.00 0.0 0.00 4.00 R
5320 5434 0.944311 GTGGCGACGACAACATCAGT 60.944 55.0 4.13 0.0 0.00 3.41 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
45 46 3.798954 CTCCCGCTGGAATCGCCTC 62.799 68.421 0.00 0.00 41.17 4.70
58 59 0.539669 TCGCCTCAGGTGACAGAGAA 60.540 55.000 1.57 0.00 46.14 2.87
59 60 0.389166 CGCCTCAGGTGACAGAGAAC 60.389 60.000 0.00 0.00 46.14 3.01
80 81 7.691890 GAACTTCAGTTCGAATCAAATTACG 57.308 36.000 0.00 0.00 43.97 3.18
83 84 7.950236 ACTTCAGTTCGAATCAAATTACGTAG 58.050 34.615 0.00 0.00 31.69 3.51
149 150 1.550072 CATACTTTGGGCCTTGGGTTG 59.450 52.381 4.53 0.00 0.00 3.77
157 158 2.612493 GCCTTGGGTTGGGCCTAGA 61.612 63.158 4.53 0.00 42.30 2.43
173 174 3.797184 GCCTAGACTAGACTTTGCGATGG 60.797 52.174 11.27 0.00 0.00 3.51
192 193 4.564782 TGGCCAATATGAAAAATGCCAA 57.435 36.364 0.61 0.00 43.85 4.52
201 202 0.831711 AAAAATGCCAAGCCCGGACT 60.832 50.000 0.73 0.00 0.00 3.85
208 209 1.073199 CAAGCCCGGACTCAAACCT 59.927 57.895 0.73 0.00 0.00 3.50
218 219 3.628646 CTCAAACCTGAGGCCCGGG 62.629 68.421 19.09 19.09 44.72 5.73
254 255 6.127479 TGCCTTCATGTCTGTAACAAAACTTT 60.127 34.615 0.00 0.00 42.37 2.66
255 256 6.198966 GCCTTCATGTCTGTAACAAAACTTTG 59.801 38.462 0.60 0.60 42.37 2.77
338 341 0.666913 CCAGTCATTGCATGCCTAGC 59.333 55.000 16.68 1.67 0.00 3.42
399 402 4.280677 TGTGTGGGGTCAATCATTTTTCTC 59.719 41.667 0.00 0.00 0.00 2.87
409 412 5.243730 TCAATCATTTTTCTCTGGTGGGTTC 59.756 40.000 0.00 0.00 0.00 3.62
412 415 3.943671 TTTTTCTCTGGTGGGTTCAGA 57.056 42.857 0.00 0.00 38.75 3.27
424 427 3.433615 GTGGGTTCAGATTTCAGAAGACG 59.566 47.826 0.00 0.00 0.00 4.18
455 458 0.531974 AAAGAAACGACGAGCCAGCA 60.532 50.000 0.00 0.00 0.00 4.41
464 467 2.042259 CGAGCCAGCAAGCAATGGA 61.042 57.895 4.68 0.00 39.02 3.41
465 468 1.381928 CGAGCCAGCAAGCAATGGAT 61.382 55.000 4.68 0.00 39.02 3.41
474 477 3.053395 AGCAAGCAATGGATAGGAAAGGA 60.053 43.478 0.00 0.00 0.00 3.36
476 479 4.160252 GCAAGCAATGGATAGGAAAGGAAA 59.840 41.667 0.00 0.00 0.00 3.13
477 480 5.680665 GCAAGCAATGGATAGGAAAGGAAAG 60.681 44.000 0.00 0.00 0.00 2.62
478 481 4.540715 AGCAATGGATAGGAAAGGAAAGG 58.459 43.478 0.00 0.00 0.00 3.11
479 482 3.638627 GCAATGGATAGGAAAGGAAAGGG 59.361 47.826 0.00 0.00 0.00 3.95
480 483 3.602205 ATGGATAGGAAAGGAAAGGGC 57.398 47.619 0.00 0.00 0.00 5.19
481 484 2.283834 TGGATAGGAAAGGAAAGGGCA 58.716 47.619 0.00 0.00 0.00 5.36
482 485 2.652348 TGGATAGGAAAGGAAAGGGCAA 59.348 45.455 0.00 0.00 0.00 4.52
483 486 3.291584 GGATAGGAAAGGAAAGGGCAAG 58.708 50.000 0.00 0.00 0.00 4.01
484 487 2.215942 TAGGAAAGGAAAGGGCAAGC 57.784 50.000 0.00 0.00 0.00 4.01
485 488 0.188342 AGGAAAGGAAAGGGCAAGCA 59.812 50.000 0.00 0.00 0.00 3.91
486 489 0.605083 GGAAAGGAAAGGGCAAGCAG 59.395 55.000 0.00 0.00 0.00 4.24
487 490 0.605083 GAAAGGAAAGGGCAAGCAGG 59.395 55.000 0.00 0.00 0.00 4.85
488 491 0.188342 AAAGGAAAGGGCAAGCAGGA 59.812 50.000 0.00 0.00 0.00 3.86
489 492 0.251519 AAGGAAAGGGCAAGCAGGAG 60.252 55.000 0.00 0.00 0.00 3.69
490 493 1.680314 GGAAAGGGCAAGCAGGAGG 60.680 63.158 0.00 0.00 0.00 4.30
491 494 2.283460 AAAGGGCAAGCAGGAGGC 60.283 61.111 0.00 0.00 45.30 4.70
522 525 2.354656 GACGCTGTCTGTCACGCA 60.355 61.111 2.10 0.00 36.37 5.24
617 622 3.616219 TGTTTATCATTCCGGTTCCCTG 58.384 45.455 0.00 0.00 0.00 4.45
721 768 4.471025 TGTCATCTGTCTCTCTCTCTCTCT 59.529 45.833 0.00 0.00 0.00 3.10
722 769 5.053145 GTCATCTGTCTCTCTCTCTCTCTC 58.947 50.000 0.00 0.00 0.00 3.20
723 770 3.801114 TCTGTCTCTCTCTCTCTCTCG 57.199 52.381 0.00 0.00 0.00 4.04
724 771 2.159099 TCTGTCTCTCTCTCTCTCTCGC 60.159 54.545 0.00 0.00 0.00 5.03
725 772 1.831106 TGTCTCTCTCTCTCTCTCGCT 59.169 52.381 0.00 0.00 0.00 4.93
726 773 2.159099 TGTCTCTCTCTCTCTCTCGCTC 60.159 54.545 0.00 0.00 0.00 5.03
872 919 2.250939 CGCCTGCTCCGTGTTTGAA 61.251 57.895 0.00 0.00 0.00 2.69
897 956 0.882927 GTTACACTCCACGCAGCCAA 60.883 55.000 0.00 0.00 0.00 4.52
1126 1210 3.753294 ACATTGAAGGTTCGTGTCTCT 57.247 42.857 0.00 0.00 0.00 3.10
1174 1259 3.557264 GGGGTGTACTGGTTCTTCTTCTG 60.557 52.174 0.00 0.00 0.00 3.02
1267 1352 4.276926 GCCTCTGATGTTGTTTCTTCAGTT 59.723 41.667 0.00 0.00 39.24 3.16
1375 1475 0.964358 GAAACATCTGCCTGCCTGCT 60.964 55.000 0.00 0.00 0.00 4.24
1376 1476 0.541296 AAACATCTGCCTGCCTGCTT 60.541 50.000 0.00 0.00 0.00 3.91
1377 1477 1.248785 AACATCTGCCTGCCTGCTTG 61.249 55.000 0.00 0.00 0.00 4.01
1378 1478 2.754658 ATCTGCCTGCCTGCTTGC 60.755 61.111 0.00 0.00 0.00 4.01
1534 1634 0.251916 CCTGTAAGCGAATCACCCCA 59.748 55.000 0.00 0.00 0.00 4.96
1553 1653 3.891366 CCCATTTCCTGTTTCACTTCACT 59.109 43.478 0.00 0.00 0.00 3.41
1556 1656 4.981806 TTTCCTGTTTCACTTCACTTGG 57.018 40.909 0.00 0.00 0.00 3.61
1757 1857 5.240121 AGTTCCATTTTCCATTTGTGATGC 58.760 37.500 0.00 0.00 0.00 3.91
1765 1865 6.395426 TTTCCATTTGTGATGCAGATATCC 57.605 37.500 0.00 0.00 0.00 2.59
1809 1909 6.370994 AGTCTTCTGCAGAACAACATCATAAG 59.629 38.462 25.16 10.88 31.28 1.73
1954 2054 4.218635 TGAGCTCTACTGTACAAACCTCTG 59.781 45.833 16.19 0.00 0.00 3.35
1980 2080 4.754372 CACTTCTTGTGCATATGTGTGT 57.246 40.909 4.29 0.00 40.06 3.72
2079 2179 1.486726 CTGTCTGGTCCATTCCCTACC 59.513 57.143 0.00 0.00 0.00 3.18
2191 2292 1.016627 TTCTCACTGTGCACTTGTGC 58.983 50.000 27.01 17.73 0.00 4.57
2540 2641 1.068333 GTGCTGTAACTGGTTGCATGG 60.068 52.381 4.87 0.00 34.80 3.66
2627 2728 3.759527 TCGATGACGAAGGTAAGTGAG 57.240 47.619 0.00 0.00 45.74 3.51
3002 3103 3.090037 TGCCACAGAGAGGTTACTAGTC 58.910 50.000 0.00 0.00 0.00 2.59
3017 3118 7.390996 AGGTTACTAGTCTATCCATACATGTCG 59.609 40.741 0.00 0.00 0.00 4.35
3026 3127 4.753516 TCCATACATGTCGAATGGAAGT 57.246 40.909 21.47 0.00 44.75 3.01
3183 3284 2.203337 GTGTGGCAGTTGGAGGCA 60.203 61.111 0.00 0.00 39.41 4.75
3190 3291 2.033757 AGTTGGAGGCAGCAGCAG 59.966 61.111 2.65 0.00 44.61 4.24
3191 3292 3.060615 GTTGGAGGCAGCAGCAGG 61.061 66.667 2.65 0.00 44.61 4.85
3210 3311 0.881796 GGTTGTCTTACCTTGCCTGC 59.118 55.000 0.00 0.00 35.23 4.85
3211 3312 1.545651 GGTTGTCTTACCTTGCCTGCT 60.546 52.381 0.00 0.00 35.23 4.24
3212 3313 1.537202 GTTGTCTTACCTTGCCTGCTG 59.463 52.381 0.00 0.00 0.00 4.41
3222 3323 2.046507 GCCTGCTGAGTGGGAGTG 60.047 66.667 0.00 0.00 0.00 3.51
3223 3324 2.667418 CCTGCTGAGTGGGAGTGG 59.333 66.667 0.00 0.00 0.00 4.00
3227 3328 1.347707 CTGCTGAGTGGGAGTGGTTAA 59.652 52.381 0.00 0.00 0.00 2.01
3230 3331 3.010420 GCTGAGTGGGAGTGGTTAATTC 58.990 50.000 0.00 0.00 0.00 2.17
3231 3332 3.559171 GCTGAGTGGGAGTGGTTAATTCA 60.559 47.826 0.00 0.00 0.00 2.57
3245 3346 1.885049 AATTCAGCTAGCCTCCTCCA 58.115 50.000 12.13 0.00 0.00 3.86
3268 3369 6.267070 CACGTTTTGGTTGTGGTTATTAGTT 58.733 36.000 0.00 0.00 0.00 2.24
3294 3395 4.753516 AGCCAAGCAAAGTAAACCTTTT 57.246 36.364 0.00 0.00 41.51 2.27
3344 3445 7.125792 CCTAACAAGGCTAGGAGAATCTTAA 57.874 40.000 0.00 0.00 38.63 1.85
3349 3450 3.970640 AGGCTAGGAGAATCTTAACCTGG 59.029 47.826 0.00 0.00 41.13 4.45
3468 3569 4.088823 AGAACGATGCAGAATTGAAAGC 57.911 40.909 0.00 0.00 0.00 3.51
3488 3589 0.676466 TGCAATCCGACAAGCCGAAT 60.676 50.000 0.00 0.00 0.00 3.34
3565 3667 6.456181 GCACAAAGACTTATCACAGAGCATAC 60.456 42.308 0.00 0.00 0.00 2.39
3622 3724 4.515567 GGTCTAATTATTCCAGGAAAGCCG 59.484 45.833 5.81 0.00 39.96 5.52
3703 3805 0.320683 TTCATGAGCAGTGTGACCCG 60.321 55.000 0.00 0.00 0.00 5.28
3721 3823 2.632028 CCCGAAGATCATCCACAGAGAT 59.368 50.000 0.00 0.00 0.00 2.75
3730 3832 0.247460 TCCACAGAGATGTCAAGGCG 59.753 55.000 0.00 0.00 0.00 5.52
3946 4048 3.315142 GATCACCGGCCAGACAGCA 62.315 63.158 0.00 0.00 0.00 4.41
4034 4136 6.437928 CAATTTACTTGACTAAACTGCTGCA 58.562 36.000 0.88 0.88 36.97 4.41
4113 4215 6.636850 GCACTTTTGTCGAAACTGTTCATAAT 59.363 34.615 0.00 0.00 32.89 1.28
4318 4424 3.770040 CACCGGCCGAGGATGTCA 61.770 66.667 30.73 0.00 34.73 3.58
4441 4547 0.179150 GCTGCTACTCTGACCTGACG 60.179 60.000 0.00 0.00 0.00 4.35
4642 4748 5.571285 AGATGAAGTGTACACAGGAGAGTA 58.429 41.667 27.06 5.62 0.00 2.59
4787 4893 6.980397 CAGTTTGTATTTTCTCTTTGGCAGTT 59.020 34.615 0.00 0.00 0.00 3.16
4833 4944 3.624326 TTTCAGATTGAAACAGGTGCG 57.376 42.857 0.36 0.00 41.02 5.34
4944 5058 9.646522 ATTACTCCATACAGCCAAAATATTTCT 57.353 29.630 0.10 0.00 0.00 2.52
4961 5075 4.746951 TGTGTAGCGCGACGACGG 62.747 66.667 12.10 0.48 40.15 4.79
5029 5143 2.679336 TGCAGACAATCATCAACCATCG 59.321 45.455 0.00 0.00 0.00 3.84
5188 5302 1.809684 GGTCAGCCCAGTACTTGTTC 58.190 55.000 0.00 0.00 0.00 3.18
5290 5404 2.602878 GTCTCGAAATAGGCGTTGTCA 58.397 47.619 0.00 0.00 0.00 3.58
5320 5434 2.282391 GTGTGGCTGTCCATGGCA 60.282 61.111 6.96 7.80 45.62 4.92
5443 5557 3.069158 CGTATATCCTGTCCCGGAAGTTT 59.931 47.826 0.73 0.00 36.49 2.66
5452 5566 4.383602 CGGAAGTTTGCGCACCGG 62.384 66.667 24.14 0.00 39.92 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.682921 CAACAAGCCAACAACATTTTGC 58.317 40.909 0.00 0.00 36.00 3.68
1 2 3.682921 GCAACAAGCCAACAACATTTTG 58.317 40.909 0.00 0.00 36.57 2.44
24 25 2.419198 CGATTCCAGCGGGAGAGG 59.581 66.667 5.52 0.00 46.01 3.69
45 46 3.742433 ACTGAAGTTCTCTGTCACCTG 57.258 47.619 4.17 0.00 30.92 4.00
58 59 6.780706 ACGTAATTTGATTCGAACTGAAGT 57.219 33.333 0.00 0.00 40.65 3.01
59 60 7.063074 ACCTACGTAATTTGATTCGAACTGAAG 59.937 37.037 0.00 0.00 40.65 3.02
83 84 9.083080 GTGTATGCTGGTTAAAAATATTGAACC 57.917 33.333 15.50 15.50 46.63 3.62
102 103 8.227791 CCGGAAAATACATAGTAATGTGTATGC 58.772 37.037 12.44 6.39 45.99 3.14
114 115 6.293955 CCCAAAGTATGCCGGAAAATACATAG 60.294 42.308 5.05 3.78 32.69 2.23
115 116 5.533154 CCCAAAGTATGCCGGAAAATACATA 59.467 40.000 5.05 0.00 32.69 2.29
116 117 4.340950 CCCAAAGTATGCCGGAAAATACAT 59.659 41.667 5.05 0.00 32.69 2.29
149 150 1.202428 CGCAAAGTCTAGTCTAGGCCC 60.202 57.143 7.90 0.00 0.00 5.80
154 155 2.100916 GGCCATCGCAAAGTCTAGTCTA 59.899 50.000 0.00 0.00 36.38 2.59
157 158 0.613260 TGGCCATCGCAAAGTCTAGT 59.387 50.000 0.00 0.00 36.38 2.57
173 174 3.313249 GGCTTGGCATTTTTCATATTGGC 59.687 43.478 0.00 0.00 35.41 4.52
192 193 1.831652 CTCAGGTTTGAGTCCGGGCT 61.832 60.000 9.26 9.26 44.74 5.19
201 202 3.646715 CCCGGGCCTCAGGTTTGA 61.647 66.667 8.08 0.00 0.00 2.69
208 209 1.001393 GAATGTTTCCCGGGCCTCA 60.001 57.895 18.49 14.59 0.00 3.86
291 292 5.039920 TGGATCCAGATTAGTTCCACATG 57.960 43.478 11.44 0.00 31.67 3.21
338 341 2.323959 GTGCTCTCAGACTTGAACGAG 58.676 52.381 0.00 0.00 31.90 4.18
364 367 2.965147 ACCCCACACAAGGAAGAAATTG 59.035 45.455 0.00 0.00 0.00 2.32
399 402 3.423539 TCTGAAATCTGAACCCACCAG 57.576 47.619 0.00 0.00 0.00 4.00
409 412 6.898912 TGATTGATCGTCTTCTGAAATCTG 57.101 37.500 0.00 0.00 0.00 2.90
412 415 7.912056 TTCTTGATTGATCGTCTTCTGAAAT 57.088 32.000 0.00 0.00 0.00 2.17
424 427 6.590357 TCGTCGTTTCTTTTCTTGATTGATC 58.410 36.000 0.00 0.00 0.00 2.92
455 458 4.958581 CCTTTCCTTTCCTATCCATTGCTT 59.041 41.667 0.00 0.00 0.00 3.91
464 467 2.042979 TGCTTGCCCTTTCCTTTCCTAT 59.957 45.455 0.00 0.00 0.00 2.57
465 468 1.427368 TGCTTGCCCTTTCCTTTCCTA 59.573 47.619 0.00 0.00 0.00 2.94
474 477 2.283460 GCCTCCTGCTTGCCCTTT 60.283 61.111 0.00 0.00 36.87 3.11
480 483 2.086251 TTTTTGCGGCCTCCTGCTTG 62.086 55.000 0.00 0.00 40.92 4.01
481 484 1.187567 ATTTTTGCGGCCTCCTGCTT 61.188 50.000 0.00 0.00 40.92 3.91
482 485 1.598701 GATTTTTGCGGCCTCCTGCT 61.599 55.000 0.00 0.00 40.92 4.24
483 486 1.153765 GATTTTTGCGGCCTCCTGC 60.154 57.895 0.00 0.00 40.16 4.85
484 487 1.512694 GGATTTTTGCGGCCTCCTG 59.487 57.895 0.00 0.00 0.00 3.86
485 488 1.682344 GGGATTTTTGCGGCCTCCT 60.682 57.895 0.00 0.00 0.00 3.69
486 489 2.892640 GGGATTTTTGCGGCCTCC 59.107 61.111 0.00 0.00 0.00 4.30
487 490 2.489751 CGGGATTTTTGCGGCCTC 59.510 61.111 0.00 0.00 0.00 4.70
488 491 3.068064 CCGGGATTTTTGCGGCCT 61.068 61.111 0.00 0.00 0.00 5.19
489 492 3.065567 TCCGGGATTTTTGCGGCC 61.066 61.111 0.00 0.00 0.00 6.13
490 493 2.180769 GTCCGGGATTTTTGCGGC 59.819 61.111 0.00 0.00 0.00 6.53
491 494 2.483288 CGTCCGGGATTTTTGCGG 59.517 61.111 0.00 0.00 0.00 5.69
522 525 0.775542 ACGGGAGGGGTAAAAAGCTT 59.224 50.000 0.00 0.00 0.00 3.74
636 646 0.895559 CACAAAAGGGACCTGAGCCC 60.896 60.000 0.00 0.00 46.40 5.19
637 647 1.527433 GCACAAAAGGGACCTGAGCC 61.527 60.000 0.00 0.00 0.00 4.70
639 649 1.986882 AAGCACAAAAGGGACCTGAG 58.013 50.000 0.00 0.00 0.00 3.35
721 768 1.293179 CCATGTGGTGTGAGAGCGA 59.707 57.895 0.00 0.00 0.00 4.93
722 769 1.742880 CCCATGTGGTGTGAGAGCG 60.743 63.158 0.00 0.00 0.00 5.03
723 770 2.042831 GCCCATGTGGTGTGAGAGC 61.043 63.158 0.00 0.00 36.04 4.09
724 771 1.377725 GGCCCATGTGGTGTGAGAG 60.378 63.158 0.00 0.00 36.04 3.20
725 772 2.756400 GGCCCATGTGGTGTGAGA 59.244 61.111 0.00 0.00 36.04 3.27
726 773 2.361610 GGGCCCATGTGGTGTGAG 60.362 66.667 19.95 0.00 36.04 3.51
765 812 3.268032 AAAGTGGCAGGGGAGGGG 61.268 66.667 0.00 0.00 0.00 4.79
766 813 2.036256 CAAAGTGGCAGGGGAGGG 59.964 66.667 0.00 0.00 0.00 4.30
767 814 2.036256 CCAAAGTGGCAGGGGAGG 59.964 66.667 0.00 0.00 0.00 4.30
872 919 1.270274 TGCGTGGAGTGTAACGTATGT 59.730 47.619 0.00 0.00 45.86 2.29
1126 1210 2.808919 ACGATTCCAGGACAGAAGAGA 58.191 47.619 0.00 0.00 0.00 3.10
1174 1259 2.003196 CGGAGAAGAAAGACAGAGGC 57.997 55.000 0.00 0.00 0.00 4.70
1301 1386 2.961741 AGAAACAGACAGAGCAGAGACA 59.038 45.455 0.00 0.00 0.00 3.41
1378 1478 4.400109 CAGCGCTTGCACTGCAGG 62.400 66.667 19.93 8.75 40.61 4.85
1379 1479 2.196382 AATCAGCGCTTGCACTGCAG 62.196 55.000 7.50 13.48 40.61 4.41
1380 1480 2.263021 AATCAGCGCTTGCACTGCA 61.263 52.632 7.50 0.00 42.66 4.41
1381 1481 1.800315 CAATCAGCGCTTGCACTGC 60.800 57.895 7.50 0.00 42.66 4.40
1382 1482 1.154093 CCAATCAGCGCTTGCACTG 60.154 57.895 7.50 4.44 42.66 3.66
1534 1634 5.067805 GTCCAAGTGAAGTGAAACAGGAAAT 59.932 40.000 0.00 0.00 41.43 2.17
1553 1653 7.560991 ACATGCAAAGAATATGATTAGGTCCAA 59.439 33.333 0.00 0.00 0.00 3.53
1556 1656 9.807649 AAAACATGCAAAGAATATGATTAGGTC 57.192 29.630 0.00 0.00 0.00 3.85
1757 1857 4.559704 GCCAAGAGAACGGTAGGATATCTG 60.560 50.000 2.05 0.00 0.00 2.90
1765 1865 0.037326 TGCAGCCAAGAGAACGGTAG 60.037 55.000 0.00 0.00 0.00 3.18
1980 2080 3.005261 AGGAACAACAATTATGCAACGCA 59.995 39.130 0.00 0.00 44.86 5.24
2165 2265 0.320683 TGCACAGTGAGAACATCCCG 60.321 55.000 4.15 0.00 0.00 5.14
2191 2292 3.877559 TGTATGACAAATCTCTGCAGGG 58.122 45.455 15.13 11.57 0.00 4.45
2482 2583 3.380320 ACTTGTGGCTTTTAGCTTTCGTT 59.620 39.130 0.00 0.00 41.99 3.85
2540 2641 0.525311 GCAGCAAGAAAGAGGAAGCC 59.475 55.000 0.00 0.00 0.00 4.35
2627 2728 5.645497 AGTACTGCATGGAATTCTTGAAGTC 59.355 40.000 19.59 13.75 39.38 3.01
2966 3067 3.861341 GGCAGTCATACAGAAGCCA 57.139 52.632 0.00 0.00 44.74 4.75
2969 3070 3.599730 TCTGTGGCAGTCATACAGAAG 57.400 47.619 0.00 0.00 45.47 2.85
3060 3161 2.106166 AGGCAGATAATCTTGCTGGGAG 59.894 50.000 0.00 0.00 0.00 4.30
3183 3284 0.036875 GGTAAGACAACCCTGCTGCT 59.963 55.000 0.00 0.00 33.02 4.24
3190 3291 1.534729 CAGGCAAGGTAAGACAACCC 58.465 55.000 0.00 0.00 40.71 4.11
3191 3292 0.881796 GCAGGCAAGGTAAGACAACC 59.118 55.000 0.00 0.00 40.06 3.77
3210 3311 4.256920 CTGAATTAACCACTCCCACTCAG 58.743 47.826 0.00 0.00 0.00 3.35
3211 3312 3.559171 GCTGAATTAACCACTCCCACTCA 60.559 47.826 0.00 0.00 0.00 3.41
3212 3313 3.010420 GCTGAATTAACCACTCCCACTC 58.990 50.000 0.00 0.00 0.00 3.51
3222 3323 3.495276 GGAGGAGGCTAGCTGAATTAACC 60.495 52.174 15.72 6.78 0.00 2.85
3223 3324 3.134804 TGGAGGAGGCTAGCTGAATTAAC 59.865 47.826 15.72 0.00 0.00 2.01
3227 3328 1.127343 GTGGAGGAGGCTAGCTGAAT 58.873 55.000 15.72 0.00 0.00 2.57
3230 3331 1.608717 AACGTGGAGGAGGCTAGCTG 61.609 60.000 15.72 0.00 0.00 4.24
3231 3332 0.905337 AAACGTGGAGGAGGCTAGCT 60.905 55.000 15.72 0.00 0.00 3.32
3245 3346 6.453926 AACTAATAACCACAACCAAAACGT 57.546 33.333 0.00 0.00 0.00 3.99
3268 3369 6.062258 AGGTTTACTTTGCTTGGCTAGATA 57.938 37.500 0.00 0.00 0.00 1.98
3344 3445 3.895704 ACTTACATTTGGTTCCCAGGT 57.104 42.857 0.00 0.00 33.81 4.00
3349 3450 6.371825 CAGTTCTCCTACTTACATTTGGTTCC 59.628 42.308 0.00 0.00 0.00 3.62
3358 3459 4.504340 GGGCAAACAGTTCTCCTACTTACA 60.504 45.833 4.36 0.00 0.00 2.41
3468 3569 1.298157 TTCGGCTTGTCGGATTGCAG 61.298 55.000 0.00 0.00 0.00 4.41
3589 3691 8.373220 CCTGGAATAATTAGACCGGTATAAAGT 58.627 37.037 24.36 17.31 0.00 2.66
3622 3724 2.420687 CCTAGTGATCCAGTCCAAAGGC 60.421 54.545 0.00 0.00 0.00 4.35
3703 3805 5.273674 TGACATCTCTGTGGATGATCTTC 57.726 43.478 15.78 0.00 44.01 2.87
3721 3823 4.555709 ACGTTGGCCGCCTTGACA 62.556 61.111 11.61 0.00 41.42 3.58
3730 3832 2.268076 ATCCAGCAACACGTTGGCC 61.268 57.895 11.64 0.00 45.32 5.36
3946 4048 0.693049 ATGCCTTTCCGAACTCCAGT 59.307 50.000 0.00 0.00 0.00 4.00
4064 4166 3.940209 TCATTTCAGGTTGTTCCATGC 57.060 42.857 0.00 0.00 39.02 4.06
4113 4215 2.916703 ATGGCAGGGCGTTTGCAA 60.917 55.556 0.00 0.00 45.35 4.08
4318 4424 1.376424 CAGCATGCGAACCACCTCT 60.376 57.895 13.01 0.00 0.00 3.69
4378 4484 0.531974 TGAACTTGTGTGAGTCGGCC 60.532 55.000 0.00 0.00 0.00 6.13
4441 4547 1.293924 CCAGCAACGATGAGTCATCC 58.706 55.000 24.23 12.18 37.57 3.51
4642 4748 1.509548 CCATTCCAGGGAGTTGGGGT 61.510 60.000 10.15 0.00 38.81 4.95
4833 4944 6.918569 CAGCAATGGATTCTGATCAGATTTTC 59.081 38.462 25.64 20.27 37.29 2.29
4944 5058 4.746951 CCGTCGTCGCGCTACACA 62.747 66.667 12.90 0.00 35.54 3.72
5029 5143 3.304057 CCTTTGTTTGCGTCTTCTCCTTC 60.304 47.826 0.00 0.00 0.00 3.46
5290 5404 1.597027 CCACACTTCCGCGACCTTT 60.597 57.895 8.23 0.00 0.00 3.11
5320 5434 0.944311 GTGGCGACGACAACATCAGT 60.944 55.000 4.13 0.00 0.00 3.41
5452 5566 2.237751 CCACACGATCGGATTCGCC 61.238 63.158 20.98 0.00 42.82 5.54
5461 5575 2.691409 TTGAAGGATCCCACACGATC 57.309 50.000 8.55 0.00 38.36 3.69


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

AutoCloner maintained by Alex Coulton.