Multiple sequence alignment - TraesCS5B01G332900

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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 TraesCS5B01G332900 chr5B 100.000 2423 0 0 1 2423 517195963 517198385 0.000000e+00 4475.0
1 TraesCS5B01G332900 chr5B 91.082 684 39 7 1762 2423 655086797 655087480 0.000000e+00 905.0
2 TraesCS5B01G332900 chr5A 91.419 1783 116 17 1 1755 541938989 541940762 0.000000e+00 2410.0
3 TraesCS5B01G332900 chr4B 91.266 687 38 3 1759 2423 614117073 614117759 0.000000e+00 917.0
4 TraesCS5B01G332900 chr4B 91.082 684 38 4 1762 2423 47497357 47496675 0.000000e+00 904.0
5 TraesCS5B01G332900 chr4B 89.119 386 21 9 2059 2423 429673202 429672817 6.100000e-126 460.0
6 TraesCS5B01G332900 chr3B 91.108 686 39 11 1760 2423 715069039 715068354 0.000000e+00 909.0
7 TraesCS5B01G332900 chr3B 91.095 685 40 2 1760 2423 592298989 592298305 0.000000e+00 907.0
8 TraesCS5B01G332900 chr3B 98.592 142 2 0 2282 2423 23767969 23768110 4.000000e-63 252.0
9 TraesCS5B01G332900 chr2B 90.684 687 43 2 1758 2423 148863702 148863016 0.000000e+00 894.0
10 TraesCS5B01G332900 chr2B 90.205 684 45 3 1762 2423 526998587 526997904 0.000000e+00 872.0
11 TraesCS5B01G332900 chr6B 90.630 683 43 10 1762 2423 507914100 507913418 0.000000e+00 887.0
12 TraesCS5B01G332900 chr6B 88.355 687 53 13 1762 2423 577360140 577360824 0.000000e+00 800.0
13 TraesCS5B01G332900 chr7B 88.730 701 43 18 1759 2423 602024451 602025151 0.000000e+00 824.0
14 TraesCS5B01G332900 chr4A 88.839 663 62 8 1762 2423 597339928 597339277 0.000000e+00 804.0
15 TraesCS5B01G332900 chr7D 88.012 684 56 12 1762 2423 9000353 8999674 0.000000e+00 785.0
16 TraesCS5B01G332900 chr3D 94.318 264 15 0 980 1243 571996170 571996433 2.900000e-109 405.0
17 TraesCS5B01G332900 chr5D 93.561 264 17 0 980 1243 329259824 329260087 6.280000e-106 394.0
18 TraesCS5B01G332900 chr5D 80.376 479 68 15 1 456 427522938 427523413 8.300000e-90 340.0
19 TraesCS5B01G332900 chr6A 85.849 212 29 1 2212 2422 153347873 153347662 8.720000e-55 224.0
20 TraesCS5B01G332900 chr1A 87.805 82 9 1 543 623 374572215 374572134 7.130000e-16 95.3
21 TraesCS5B01G332900 chr2A 73.171 287 65 9 224 502 11034796 11034514 2.570000e-15 93.5
22 TraesCS5B01G332900 chr3A 76.190 168 31 5 505 668 686856472 686856634 2.000000e-11 80.5


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 TraesCS5B01G332900 chr5B 517195963 517198385 2422 False 4475 4475 100.000 1 2423 1 chr5B.!!$F1 2422
1 TraesCS5B01G332900 chr5B 655086797 655087480 683 False 905 905 91.082 1762 2423 1 chr5B.!!$F2 661
2 TraesCS5B01G332900 chr5A 541938989 541940762 1773 False 2410 2410 91.419 1 1755 1 chr5A.!!$F1 1754
3 TraesCS5B01G332900 chr4B 614117073 614117759 686 False 917 917 91.266 1759 2423 1 chr4B.!!$F1 664
4 TraesCS5B01G332900 chr4B 47496675 47497357 682 True 904 904 91.082 1762 2423 1 chr4B.!!$R1 661
5 TraesCS5B01G332900 chr3B 715068354 715069039 685 True 909 909 91.108 1760 2423 1 chr3B.!!$R2 663
6 TraesCS5B01G332900 chr3B 592298305 592298989 684 True 907 907 91.095 1760 2423 1 chr3B.!!$R1 663
7 TraesCS5B01G332900 chr2B 148863016 148863702 686 True 894 894 90.684 1758 2423 1 chr2B.!!$R1 665
8 TraesCS5B01G332900 chr2B 526997904 526998587 683 True 872 872 90.205 1762 2423 1 chr2B.!!$R2 661
9 TraesCS5B01G332900 chr6B 507913418 507914100 682 True 887 887 90.630 1762 2423 1 chr6B.!!$R1 661
10 TraesCS5B01G332900 chr6B 577360140 577360824 684 False 800 800 88.355 1762 2423 1 chr6B.!!$F1 661
11 TraesCS5B01G332900 chr7B 602024451 602025151 700 False 824 824 88.730 1759 2423 1 chr7B.!!$F1 664
12 TraesCS5B01G332900 chr4A 597339277 597339928 651 True 804 804 88.839 1762 2423 1 chr4A.!!$R1 661
13 TraesCS5B01G332900 chr7D 8999674 9000353 679 True 785 785 88.012 1762 2423 1 chr7D.!!$R1 661

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
544 563 0.040958 GTTGTTCTTCTGGTGCGCTG 60.041 55.0 9.73 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1437 1464 0.462375 TCTCGTCTCTCCTCTCCTCG 59.538 60.0 0.0 0.0 0.0 4.63 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
54 58 8.478775 ACTACATACCATGACATATGTGTAGT 57.521 34.615 22.60 22.60 43.43 2.73
61 75 8.250143 ACCATGACATATGTGTAGTGATAGAA 57.750 34.615 14.43 0.00 39.09 2.10
67 81 8.948401 ACATATGTGTAGTGATAGAAGGAGAT 57.052 34.615 7.78 0.00 36.63 2.75
105 119 6.459066 TCTAATGTACTGCATCAAGCTATCC 58.541 40.000 0.00 0.00 45.94 2.59
116 130 2.938451 TCAAGCTATCCGCATGAACTTG 59.062 45.455 0.00 0.00 42.75 3.16
169 183 1.450211 CCAGGTGTCCGGTGTTTCT 59.550 57.895 0.00 0.00 0.00 2.52
179 193 0.605589 CGGTGTTTCTTCCTCCCCAC 60.606 60.000 0.00 0.00 0.00 4.61
184 198 1.004394 GTTTCTTCCTCCCCACGGAAT 59.996 52.381 0.00 0.00 39.64 3.01
187 201 0.107654 CTTCCTCCCCACGGAATGTC 60.108 60.000 0.00 0.00 39.64 3.06
188 202 0.546747 TTCCTCCCCACGGAATGTCT 60.547 55.000 0.00 0.00 37.86 3.41
190 204 0.978146 CCTCCCCACGGAATGTCTCT 60.978 60.000 0.00 0.00 37.86 3.10
203 217 6.483640 ACGGAATGTCTCTTAAATGATTAGGC 59.516 38.462 0.00 0.00 0.00 3.93
206 220 8.563732 GGAATGTCTCTTAAATGATTAGGCTTC 58.436 37.037 0.00 0.00 0.00 3.86
210 224 7.126421 TGTCTCTTAAATGATTAGGCTTCCTCT 59.874 37.037 0.00 0.00 34.61 3.69
212 226 7.989741 TCTCTTAAATGATTAGGCTTCCTCTTG 59.010 37.037 0.00 0.00 34.61 3.02
213 227 7.633789 TCTTAAATGATTAGGCTTCCTCTTGT 58.366 34.615 0.00 0.00 34.61 3.16
214 228 7.770897 TCTTAAATGATTAGGCTTCCTCTTGTC 59.229 37.037 0.00 0.00 34.61 3.18
215 229 3.526931 TGATTAGGCTTCCTCTTGTCG 57.473 47.619 0.00 0.00 34.61 4.35
307 324 3.164977 TTGGCACGAGGGACCACA 61.165 61.111 0.00 0.00 31.83 4.17
313 330 2.878429 CGAGGGACCACACTCTCG 59.122 66.667 0.00 0.00 43.73 4.04
329 346 7.275123 CCACACTCTCGTTCTTATTAGGTTTAC 59.725 40.741 0.00 0.00 0.00 2.01
347 364 3.531821 CCCTCTTTGTTGGGGTTGT 57.468 52.632 0.00 0.00 39.76 3.32
348 365 1.039856 CCCTCTTTGTTGGGGTTGTG 58.960 55.000 0.00 0.00 39.76 3.33
352 369 1.190643 CTTTGTTGGGGTTGTGTGGT 58.809 50.000 0.00 0.00 0.00 4.16
358 375 4.887190 GGGTTGTGTGGTGGCGGT 62.887 66.667 0.00 0.00 0.00 5.68
361 378 2.515057 TTGTGTGGTGGCGGTGAC 60.515 61.111 0.00 0.00 0.00 3.67
362 379 3.330992 TTGTGTGGTGGCGGTGACA 62.331 57.895 0.00 0.00 0.00 3.58
364 381 2.281414 TGTGGTGGCGGTGACATG 60.281 61.111 0.00 0.00 0.00 3.21
365 382 3.737172 GTGGTGGCGGTGACATGC 61.737 66.667 0.00 0.00 0.00 4.06
366 383 3.952508 TGGTGGCGGTGACATGCT 61.953 61.111 0.00 0.00 0.00 3.79
385 402 8.353423 ACATGCTTTTGTAGGAATAATGTCTT 57.647 30.769 0.00 0.00 0.00 3.01
387 404 8.680903 CATGCTTTTGTAGGAATAATGTCTTCT 58.319 33.333 0.00 0.00 0.00 2.85
389 406 9.905713 TGCTTTTGTAGGAATAATGTCTTCTAT 57.094 29.630 0.00 0.00 0.00 1.98
396 413 7.609097 AGGAATAATGTCTTCTATGCTCAGA 57.391 36.000 0.00 0.00 0.00 3.27
413 430 0.326264 AGACCCTTCACTGATGGTGC 59.674 55.000 9.54 2.45 44.98 5.01
415 432 1.555075 GACCCTTCACTGATGGTGCTA 59.445 52.381 9.54 0.00 44.98 3.49
417 434 1.556911 CCCTTCACTGATGGTGCTAGT 59.443 52.381 9.54 0.00 44.98 2.57
456 473 2.420687 GGAAGTGCTTCTCCATCGGATT 60.421 50.000 11.18 0.00 39.45 3.01
473 490 2.038033 GGATTATCCGGGATTTGGTCGA 59.962 50.000 15.98 0.00 0.00 4.20
492 511 1.404391 GATGCTGCTTTGATGGACCTG 59.596 52.381 0.00 0.00 0.00 4.00
501 520 2.806945 TGATGGACCTGGTTTGGATC 57.193 50.000 0.00 1.42 0.00 3.36
537 556 1.806542 CGGTGATGGTTGTTCTTCTGG 59.193 52.381 0.00 0.00 0.00 3.86
544 563 0.040958 GTTGTTCTTCTGGTGCGCTG 60.041 55.000 9.73 0.00 0.00 5.18
550 569 2.738213 CTTCTGGTGCGCTGGTCCTT 62.738 60.000 9.73 0.00 0.00 3.36
561 580 2.159085 CGCTGGTCCTTTAGGGTCTTAG 60.159 54.545 0.00 0.00 36.25 2.18
574 593 4.327680 AGGGTCTTAGCATGACAACTTTC 58.672 43.478 0.00 0.00 36.26 2.62
583 602 5.720202 AGCATGACAACTTTCGACTATGTA 58.280 37.500 0.00 0.00 0.00 2.29
585 604 5.577164 GCATGACAACTTTCGACTATGTACT 59.423 40.000 0.00 0.00 0.00 2.73
594 613 6.580041 ACTTTCGACTATGTACTACAACAACG 59.420 38.462 0.00 0.00 32.02 4.10
598 617 7.580600 TCGACTATGTACTACAACAACGTTTA 58.419 34.615 0.00 0.00 32.02 2.01
602 621 4.047822 TGTACTACAACAACGTTTACCCG 58.952 43.478 0.00 0.00 0.00 5.28
611 630 0.108329 ACGTTTACCCGGCTCTGATG 60.108 55.000 0.00 0.00 0.00 3.07
620 639 1.074926 GGCTCTGATGAGGGAGGGA 60.075 63.158 0.00 0.00 40.53 4.20
634 653 5.152934 GAGGGAGGGACAATAATGGTAGTA 58.847 45.833 0.00 0.00 0.00 1.82
635 654 5.738401 AGGGAGGGACAATAATGGTAGTAT 58.262 41.667 0.00 0.00 0.00 2.12
644 663 6.431722 ACAATAATGGTAGTATGCCTTTGGT 58.568 36.000 0.00 0.00 43.60 3.67
686 705 8.879759 CAGTCGTCAAACCTGTATAATTGTTAT 58.120 33.333 0.00 0.00 0.00 1.89
695 714 8.603242 ACCTGTATAATTGTTATTTAGCTCCG 57.397 34.615 0.00 0.00 0.00 4.63
703 722 4.945246 TGTTATTTAGCTCCGATGGTCTC 58.055 43.478 0.00 0.00 0.00 3.36
705 724 5.831525 TGTTATTTAGCTCCGATGGTCTCTA 59.168 40.000 0.00 0.00 0.00 2.43
736 755 9.458727 ACCATGATTGATTATGAATAGATGGAC 57.541 33.333 16.29 0.00 32.22 4.02
746 765 6.821616 ATGAATAGATGGACTGTTTCTCCT 57.178 37.500 0.00 0.00 30.33 3.69
777 796 4.348863 AATGCCTATTCGATTCAGAGCT 57.651 40.909 0.00 0.00 0.00 4.09
778 797 5.474578 AATGCCTATTCGATTCAGAGCTA 57.525 39.130 0.00 0.00 0.00 3.32
788 807 6.656632 TCGATTCAGAGCTAGGTTTGATAT 57.343 37.500 15.10 11.37 0.00 1.63
792 811 9.429359 CGATTCAGAGCTAGGTTTGATATTTAT 57.571 33.333 15.10 6.21 0.00 1.40
846 873 0.318699 GGAGACAAAAGTTTGCCCGC 60.319 55.000 3.68 0.00 41.79 6.13
852 879 2.611751 ACAAAAGTTTGCCCGCATTTTC 59.388 40.909 3.68 0.00 41.79 2.29
855 882 2.908688 AGTTTGCCCGCATTTTCTTT 57.091 40.000 0.00 0.00 0.00 2.52
864 891 3.253230 CCGCATTTTCTTTAAAGCCCAG 58.747 45.455 10.51 0.99 0.00 4.45
880 907 4.218312 AGCCCAGCCTAAATAGAAAATGG 58.782 43.478 0.00 0.00 0.00 3.16
907 934 8.026607 CGAAAATTAATAAAGCCAACCTTCTCA 58.973 33.333 0.00 0.00 31.99 3.27
937 964 6.404712 AAGAATAAAAACGTAGCCTTCTCG 57.595 37.500 0.00 0.00 0.00 4.04
1154 1181 0.600518 CAGCTCATCCATCTCAGCGG 60.601 60.000 0.00 0.00 36.95 5.52
1283 1310 1.284715 CGGTTTTCCTTGGCGGTTC 59.715 57.895 0.00 0.00 37.95 3.62
1286 1313 1.899534 TTTTCCTTGGCGGTTCCGG 60.900 57.895 13.16 0.00 37.80 5.14
1317 1344 0.617249 AAGAGGAGGAGCAGGAGGTG 60.617 60.000 0.00 0.00 0.00 4.00
1437 1464 2.017559 ATTAGGCGACGAGGTGGAGC 62.018 60.000 0.00 0.00 0.00 4.70
1520 1547 2.206515 CTTCGTGCTCGCAGTCCTCT 62.207 60.000 2.69 0.00 36.96 3.69
1573 1600 9.647797 TCGATCTACTGTAAATTAAAGCTTCAA 57.352 29.630 0.00 0.00 0.00 2.69
1577 1604 9.647797 TCTACTGTAAATTAAAGCTTCAATCGA 57.352 29.630 0.00 0.00 0.00 3.59
1590 1617 4.260375 GCTTCAATCGATGCAATAAGACGT 60.260 41.667 0.00 0.00 40.97 4.34
1591 1618 5.051039 GCTTCAATCGATGCAATAAGACGTA 60.051 40.000 0.00 0.00 40.97 3.57
1592 1619 5.883328 TCAATCGATGCAATAAGACGTAC 57.117 39.130 0.00 0.00 0.00 3.67
1628 1655 3.636764 GAGTTCCATCCCTTGTTTGTGTT 59.363 43.478 0.00 0.00 0.00 3.32
1657 1684 3.461061 TGATCATGACGGCTTCTGATTC 58.539 45.455 0.00 0.00 0.00 2.52
1685 1712 4.954202 ACTGATATTTGTCGTCTCCTACCA 59.046 41.667 0.00 0.00 0.00 3.25
1691 1718 3.587797 TGTCGTCTCCTACCATGTTTC 57.412 47.619 0.00 0.00 0.00 2.78
1697 1724 4.031611 GTCTCCTACCATGTTTCCCTACT 58.968 47.826 0.00 0.00 0.00 2.57
1700 1727 3.449737 TCCTACCATGTTTCCCTACTTCG 59.550 47.826 0.00 0.00 0.00 3.79
1704 1731 3.579586 ACCATGTTTCCCTACTTCGTACA 59.420 43.478 0.00 0.00 0.00 2.90
1728 1755 1.800283 ATCGATGATCTCCGTGCGCT 61.800 55.000 9.73 0.00 0.00 5.92
1755 1782 1.006805 GATCAGATCAGGTCCGGCG 60.007 63.158 5.44 0.00 0.00 6.46
1756 1783 3.157217 ATCAGATCAGGTCCGGCGC 62.157 63.158 0.00 0.00 0.00 6.53
1775 1802 1.765074 GGTTAGGCCAACTCCACCA 59.235 57.895 5.01 0.00 37.30 4.17
1882 1909 1.646540 CGCTTTGTGTCCGCTTTCA 59.353 52.632 0.00 0.00 0.00 2.69
1920 1947 1.399089 GTTTGCGCCGCTTTTAGGATA 59.601 47.619 11.67 0.00 0.00 2.59
1936 1963 2.088423 GGATAAAACGGACACCATGCA 58.912 47.619 0.00 0.00 0.00 3.96
1964 1991 3.973516 TCGTCTGCGCGTGTCCTT 61.974 61.111 8.43 0.00 38.14 3.36
1971 1998 4.003788 CGCGTGTCCTTCCCTGGT 62.004 66.667 0.00 0.00 0.00 4.00
2062 2102 0.043334 CTCTTCCCCTCTCTTCCCCA 59.957 60.000 0.00 0.00 0.00 4.96
2223 2269 4.069232 CGGTCTTGAGCTCGCCCA 62.069 66.667 9.64 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 58 9.379770 TGTATTATCCAACATCTCCTTCTATCA 57.620 33.333 0.00 0.00 0.00 2.15
67 81 9.489084 GCAGTACATTAGATGTATTATCCAACA 57.511 33.333 4.29 0.00 46.39 3.33
105 119 3.994392 AGTTACCACTACAAGTTCATGCG 59.006 43.478 0.00 0.00 0.00 4.73
116 130 4.682778 TCATGCCCATAGTTACCACTAC 57.317 45.455 0.00 0.00 38.38 2.73
179 193 6.708054 AGCCTAATCATTTAAGAGACATTCCG 59.292 38.462 0.00 0.00 0.00 4.30
184 198 7.126421 AGAGGAAGCCTAATCATTTAAGAGACA 59.874 37.037 0.00 0.00 31.76 3.41
187 201 7.772757 ACAAGAGGAAGCCTAATCATTTAAGAG 59.227 37.037 0.00 0.00 31.76 2.85
188 202 7.633789 ACAAGAGGAAGCCTAATCATTTAAGA 58.366 34.615 0.00 0.00 31.76 2.10
190 204 6.538742 CGACAAGAGGAAGCCTAATCATTTAA 59.461 38.462 0.00 0.00 31.76 1.52
203 217 1.801913 CGCCGACGACAAGAGGAAG 60.802 63.158 0.00 0.00 43.93 3.46
206 220 2.504244 GACGCCGACGACAAGAGG 60.504 66.667 0.00 0.00 43.93 3.69
259 276 1.674057 GTCCTCCACACCTCCACAG 59.326 63.158 0.00 0.00 0.00 3.66
288 305 3.164977 TGGTCCCTCGTGCCAACA 61.165 61.111 0.00 0.00 0.00 3.33
295 312 1.972223 CGAGAGTGTGGTCCCTCGT 60.972 63.158 0.00 0.00 42.29 4.18
296 313 2.878429 CGAGAGTGTGGTCCCTCG 59.122 66.667 0.00 0.00 41.71 4.63
307 324 6.871844 GGGTAAACCTAATAAGAACGAGAGT 58.128 40.000 0.00 0.00 41.35 3.24
347 364 2.281414 CATGTCACCGCCACCACA 60.281 61.111 0.00 0.00 0.00 4.17
348 365 3.737172 GCATGTCACCGCCACCAC 61.737 66.667 0.00 0.00 0.00 4.16
352 369 1.106351 ACAAAAGCATGTCACCGCCA 61.106 50.000 0.00 0.00 0.00 5.69
358 375 7.611467 AGACATTATTCCTACAAAAGCATGTCA 59.389 33.333 10.25 0.00 40.21 3.58
361 378 8.680903 AGAAGACATTATTCCTACAAAAGCATG 58.319 33.333 0.00 0.00 0.00 4.06
362 379 8.814038 AGAAGACATTATTCCTACAAAAGCAT 57.186 30.769 0.00 0.00 0.00 3.79
366 383 9.905713 AGCATAGAAGACATTATTCCTACAAAA 57.094 29.630 0.00 0.00 0.00 2.44
385 402 2.762887 CAGTGAAGGGTCTGAGCATAGA 59.237 50.000 9.30 0.00 34.02 1.98
387 404 2.820178 TCAGTGAAGGGTCTGAGCATA 58.180 47.619 9.30 0.00 36.04 3.14
389 406 1.277273 CATCAGTGAAGGGTCTGAGCA 59.723 52.381 9.30 0.00 42.67 4.26
390 407 1.406614 CCATCAGTGAAGGGTCTGAGC 60.407 57.143 6.50 0.00 42.67 4.26
413 430 1.107114 ATGCCCTCTGACGACACTAG 58.893 55.000 0.00 0.00 0.00 2.57
415 432 1.188219 ACATGCCCTCTGACGACACT 61.188 55.000 0.00 0.00 0.00 3.55
417 434 1.293179 CACATGCCCTCTGACGACA 59.707 57.895 0.00 0.00 0.00 4.35
456 473 1.270625 GCATCGACCAAATCCCGGATA 60.271 52.381 0.73 0.00 0.00 2.59
473 490 1.471119 CAGGTCCATCAAAGCAGCAT 58.529 50.000 0.00 0.00 0.00 3.79
492 511 1.636003 AGGGAGAAGTGGATCCAAACC 59.364 52.381 18.20 14.53 37.33 3.27
501 520 0.905357 ACCGATGAAGGGAGAAGTGG 59.095 55.000 0.00 0.00 35.02 4.00
537 556 1.745489 CCCTAAAGGACCAGCGCAC 60.745 63.158 11.47 0.00 38.24 5.34
544 563 3.454812 TCATGCTAAGACCCTAAAGGACC 59.545 47.826 0.00 0.00 39.89 4.46
550 569 5.499004 AAGTTGTCATGCTAAGACCCTAA 57.501 39.130 0.00 0.00 35.15 2.69
561 580 4.928661 ACATAGTCGAAAGTTGTCATGC 57.071 40.909 0.00 0.00 0.00 4.06
574 593 6.680055 AAACGTTGTTGTAGTACATAGTCG 57.320 37.500 0.00 9.70 0.00 4.18
583 602 2.482864 CCGGGTAAACGTTGTTGTAGT 58.517 47.619 0.00 0.00 0.00 2.73
585 604 1.202627 AGCCGGGTAAACGTTGTTGTA 60.203 47.619 3.10 0.00 0.00 2.41
594 613 1.473434 CCTCATCAGAGCCGGGTAAAC 60.473 57.143 5.91 0.00 40.68 2.01
598 617 2.765807 CCCTCATCAGAGCCGGGT 60.766 66.667 5.45 5.45 40.68 5.28
602 621 1.074926 TCCCTCCCTCATCAGAGCC 60.075 63.158 0.00 0.00 40.68 4.70
611 630 3.974642 ACTACCATTATTGTCCCTCCCTC 59.025 47.826 0.00 0.00 0.00 4.30
620 639 6.431722 ACCAAAGGCATACTACCATTATTGT 58.568 36.000 0.00 0.00 0.00 2.71
634 653 4.207891 CACTAGAGTGTACCAAAGGCAT 57.792 45.455 0.00 0.00 40.96 4.40
635 654 3.678056 CACTAGAGTGTACCAAAGGCA 57.322 47.619 0.00 0.00 40.96 4.75
686 705 5.632118 AGTATAGAGACCATCGGAGCTAAA 58.368 41.667 0.00 0.00 0.00 1.85
690 709 3.690628 GGTAGTATAGAGACCATCGGAGC 59.309 52.174 0.00 0.00 33.16 4.70
725 744 6.227298 TCAGGAGAAACAGTCCATCTATTC 57.773 41.667 0.00 0.00 36.43 1.75
758 777 3.256879 CCTAGCTCTGAATCGAATAGGCA 59.743 47.826 0.00 0.00 0.00 4.75
766 785 7.721286 AAATATCAAACCTAGCTCTGAATCG 57.279 36.000 0.00 0.00 0.00 3.34
771 790 8.908786 TTGGATAAATATCAAACCTAGCTCTG 57.091 34.615 0.00 0.00 34.40 3.35
772 791 8.160106 CCTTGGATAAATATCAAACCTAGCTCT 58.840 37.037 0.00 0.00 34.40 4.09
778 797 9.628500 GAAGTACCTTGGATAAATATCAAACCT 57.372 33.333 3.07 0.00 34.40 3.50
792 811 6.183360 GCGAATACTCTTAGAAGTACCTTGGA 60.183 42.308 0.00 0.00 34.68 3.53
793 812 5.978322 GCGAATACTCTTAGAAGTACCTTGG 59.022 44.000 0.00 0.00 34.68 3.61
825 847 2.500229 CGGGCAAACTTTTGTCTCCTA 58.500 47.619 6.28 0.00 42.20 2.94
831 858 2.323968 AAATGCGGGCAAACTTTTGT 57.676 40.000 0.00 0.00 40.24 2.83
846 873 4.541973 AGGCTGGGCTTTAAAGAAAATG 57.458 40.909 19.48 5.53 0.00 2.32
852 879 7.404671 TTTCTATTTAGGCTGGGCTTTAAAG 57.595 36.000 11.02 11.02 0.00 1.85
855 882 6.323739 CCATTTTCTATTTAGGCTGGGCTTTA 59.676 38.462 0.00 0.00 0.00 1.85
864 891 7.770801 AATTTTCGCCATTTTCTATTTAGGC 57.229 32.000 0.00 0.00 38.73 3.93
880 907 6.811665 AGAAGGTTGGCTTTATTAATTTTCGC 59.188 34.615 0.00 0.00 0.00 4.70
907 934 5.798434 GGCTACGTTTTTATTCTTCGCAAAT 59.202 36.000 0.00 0.00 0.00 2.32
937 964 4.320953 CGTCGGCTAATTTCTTTTGCTTTC 59.679 41.667 0.00 0.00 36.47 2.62
1286 1313 2.764547 CCTCTTCCTCCCGGTCCC 60.765 72.222 0.00 0.00 0.00 4.46
1288 1315 1.758906 CCTCCTCTTCCTCCCGGTC 60.759 68.421 0.00 0.00 0.00 4.79
1302 1329 3.791586 GCCACCTCCTGCTCCTCC 61.792 72.222 0.00 0.00 0.00 4.30
1406 1433 3.596214 GTCGCCTAATCCTTTCTGTTCA 58.404 45.455 0.00 0.00 0.00 3.18
1437 1464 0.462375 TCTCGTCTCTCCTCTCCTCG 59.538 60.000 0.00 0.00 0.00 4.63
1497 1524 3.363875 CTGCGAGCACGAAGTACG 58.636 61.111 8.01 0.00 41.61 3.67
1573 1600 6.315091 AGTAGTACGTCTTATTGCATCGAT 57.685 37.500 0.00 0.00 0.00 3.59
1574 1601 5.746307 AGTAGTACGTCTTATTGCATCGA 57.254 39.130 0.00 0.00 0.00 3.59
1575 1602 8.417928 CAATTAGTAGTACGTCTTATTGCATCG 58.582 37.037 14.13 0.00 0.00 3.84
1576 1603 8.700644 CCAATTAGTAGTACGTCTTATTGCATC 58.299 37.037 17.86 0.00 32.73 3.91
1577 1604 8.202137 ACCAATTAGTAGTACGTCTTATTGCAT 58.798 33.333 17.86 10.66 32.73 3.96
1590 1617 6.938698 TGGAACTCCAACCAATTAGTAGTA 57.061 37.500 0.00 0.00 44.35 1.82
1591 1618 5.836024 TGGAACTCCAACCAATTAGTAGT 57.164 39.130 0.00 0.00 44.35 2.73
1628 1655 2.076100 GCCGTCATGATCAACAGTTCA 58.924 47.619 0.00 0.00 0.00 3.18
1657 1684 4.806247 GGAGACGACAAATATCAGTTCTGG 59.194 45.833 0.00 0.00 0.00 3.86
1668 1695 4.553330 AACATGGTAGGAGACGACAAAT 57.447 40.909 0.00 0.00 37.75 2.32
1669 1696 4.312443 GAAACATGGTAGGAGACGACAAA 58.688 43.478 0.00 0.00 37.75 2.83
1697 1724 5.334957 GGAGATCATCGATAAGCTGTACGAA 60.335 44.000 11.98 0.16 38.22 3.85
1700 1727 4.083217 ACGGAGATCATCGATAAGCTGTAC 60.083 45.833 13.35 0.00 0.00 2.90
1704 1731 2.352225 GCACGGAGATCATCGATAAGCT 60.352 50.000 13.35 0.00 0.00 3.74
1728 1755 0.665298 CTGATCTGATCCTCGTCGCA 59.335 55.000 14.71 0.00 0.00 5.10
1755 1782 2.038837 GTGGAGTTGGCCTAACCGC 61.039 63.158 3.32 6.88 43.94 5.68
1756 1783 1.376812 GGTGGAGTTGGCCTAACCG 60.377 63.158 3.32 0.00 43.94 4.44
1775 1802 2.125961 GGACAGGATAGGGTCGCGT 61.126 63.158 5.77 0.00 34.87 6.01
1840 1867 2.992607 AAAGTCCGTTTACGCCCGCA 62.993 55.000 0.00 0.00 38.18 5.69
1920 1947 0.951558 GTCTGCATGGTGTCCGTTTT 59.048 50.000 0.00 0.00 0.00 2.43
2114 2158 3.192630 AGGAAGGGGCTGGGCAAA 61.193 61.111 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.