Multiple sequence alignment - TraesCS5A01G544700

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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 TraesCS5A01G544700 chr5A 100.000 5415 0 0 1 5415 700212993 700207579 0.000000e+00 10000.0
1 TraesCS5A01G544700 chr4B 93.864 4808 210 40 673 5415 660479007 660483794 0.000000e+00 7166.0
2 TraesCS5A01G544700 chr4B 86.441 59 7 1 5041 5099 414593998 414593941 4.530000e-06 63.9
3 TraesCS5A01G544700 chrUn 96.755 3513 93 8 650 4147 110382138 110385644 0.000000e+00 5836.0
4 TraesCS5A01G544700 chrUn 96.482 739 14 4 4172 4900 110385640 110386376 0.000000e+00 1210.0
5 TraesCS5A01G544700 chrUn 87.430 358 23 7 5077 5415 110386380 110386734 5.080000e-105 392.0
6 TraesCS5A01G544700 chr6D 93.197 588 36 4 33 618 94777587 94778172 0.000000e+00 861.0
7 TraesCS5A01G544700 chr6D 91.653 599 44 6 26 621 381976432 381975837 0.000000e+00 824.0
8 TraesCS5A01G544700 chr5B 92.893 591 38 4 33 621 56579548 56578960 0.000000e+00 856.0
9 TraesCS5A01G544700 chr7A 91.806 598 45 4 26 621 487623675 487624270 0.000000e+00 830.0
10 TraesCS5A01G544700 chr6B 91.792 597 43 5 26 620 72403261 72402669 0.000000e+00 826.0
11 TraesCS5A01G544700 chr6B 90.196 51 4 1 5032 5082 263007303 263007254 1.260000e-06 65.8
12 TraesCS5A01G544700 chr7B 91.639 598 46 4 24 619 547275194 547275789 0.000000e+00 824.0
13 TraesCS5A01G544700 chr7B 92.308 39 3 0 2 40 69409387 69409349 7.580000e-04 56.5
14 TraesCS5A01G544700 chr7B 100.000 28 0 0 2 29 700556018 700556045 1.000000e-02 52.8
15 TraesCS5A01G544700 chr2D 91.556 604 41 8 24 621 616122397 616122996 0.000000e+00 824.0
16 TraesCS5A01G544700 chr2D 91.653 599 42 8 26 620 645052675 645053269 0.000000e+00 822.0
17 TraesCS5A01G544700 chr2B 90.939 607 50 5 26 630 747813691 747814294 0.000000e+00 811.0
18 TraesCS5A01G544700 chr1B 82.175 331 47 8 2394 2721 623112888 623112567 1.920000e-69 274.0
19 TraesCS5A01G544700 chr1A 81.873 331 48 8 2394 2721 320514461 320514140 8.940000e-68 268.0
20 TraesCS5A01G544700 chr3B 97.826 46 1 0 2 47 599102448 599102493 4.500000e-11 80.5
21 TraesCS5A01G544700 chr3A 95.652 46 2 0 2 47 597972647 597972692 2.090000e-09 75.0


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 TraesCS5A01G544700 chr5A 700207579 700212993 5414 True 10000.000000 10000 100.000000 1 5415 1 chr5A.!!$R1 5414
1 TraesCS5A01G544700 chr4B 660479007 660483794 4787 False 7166.000000 7166 93.864000 673 5415 1 chr4B.!!$F1 4742
2 TraesCS5A01G544700 chrUn 110382138 110386734 4596 False 2479.333333 5836 93.555667 650 5415 3 chrUn.!!$F1 4765
3 TraesCS5A01G544700 chr6D 94777587 94778172 585 False 861.000000 861 93.197000 33 618 1 chr6D.!!$F1 585
4 TraesCS5A01G544700 chr6D 381975837 381976432 595 True 824.000000 824 91.653000 26 621 1 chr6D.!!$R1 595
5 TraesCS5A01G544700 chr5B 56578960 56579548 588 True 856.000000 856 92.893000 33 621 1 chr5B.!!$R1 588
6 TraesCS5A01G544700 chr7A 487623675 487624270 595 False 830.000000 830 91.806000 26 621 1 chr7A.!!$F1 595
7 TraesCS5A01G544700 chr6B 72402669 72403261 592 True 826.000000 826 91.792000 26 620 1 chr6B.!!$R1 594
8 TraesCS5A01G544700 chr7B 547275194 547275789 595 False 824.000000 824 91.639000 24 619 1 chr7B.!!$F1 595
9 TraesCS5A01G544700 chr2D 616122397 616122996 599 False 824.000000 824 91.556000 24 621 1 chr2D.!!$F1 597
10 TraesCS5A01G544700 chr2D 645052675 645053269 594 False 822.000000 822 91.653000 26 620 1 chr2D.!!$F2 594
11 TraesCS5A01G544700 chr2B 747813691 747814294 603 False 811.000000 811 90.939000 26 630 1 chr2B.!!$F1 604

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
970 1009 0.322187 CCACCGACCTTCCCGATTTT 60.322 55.000 0.00 0.0 0.00 1.82 F
1074 1113 0.107312 ATGGCTCGCTGCTGAAGATT 60.107 50.000 0.00 0.0 42.39 2.40 F
1477 1520 0.915364 GGGAGAGGGAGAGCAAATGT 59.085 55.000 0.00 0.0 0.00 2.71 F
2105 2148 0.615331 ACCCAGACGCAATCATCACT 59.385 50.000 0.00 0.0 0.00 3.41 F
2285 2328 1.499007 TCTTTGAAGCCCCCAGAGTTT 59.501 47.619 0.00 0.0 0.00 2.66 F
3287 3330 1.745141 GCAGAAACTGATCCGGATGCT 60.745 52.381 24.82 0.0 32.44 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1835 1878 1.449778 GTTCCTTAGACGCCCCTGC 60.450 63.158 0.00 0.0 0.00 4.85 R
2009 2052 1.664659 CTGAGATCTGAAAGCAAGCCG 59.335 52.381 0.00 0.0 0.00 5.52 R
2285 2328 1.988107 ACCTTCTTCCAATCAGCCTCA 59.012 47.619 0.00 0.0 0.00 3.86 R
4051 4094 1.229927 GGGGCATAAGCATGGACCA 59.770 57.895 0.00 0.0 44.61 4.02 R
4198 4241 9.812347 AATCATAATATATCAGGCTGGAAAACA 57.188 29.630 15.73 0.0 0.00 2.83 R
5282 5374 0.036010 AAGCTGTAGTGGCATTCGCT 60.036 50.000 0.00 0.0 39.84 4.93 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
17 18 4.546637 ACAACTAGTTCGCCGACG 57.453 55.556 4.77 0.00 42.01 5.12
18 19 1.080974 ACAACTAGTTCGCCGACGG 60.081 57.895 10.29 10.29 40.63 4.79
19 20 1.080974 CAACTAGTTCGCCGACGGT 60.081 57.895 16.73 0.00 40.63 4.83
20 21 1.080974 AACTAGTTCGCCGACGGTG 60.081 57.895 21.48 21.48 40.63 4.94
21 22 1.799258 AACTAGTTCGCCGACGGTGT 61.799 55.000 25.69 10.58 40.63 4.16
22 23 1.513586 CTAGTTCGCCGACGGTGTC 60.514 63.158 25.69 19.10 40.63 3.67
59 63 0.994241 CGAGGTCGATCATCTTCGCG 60.994 60.000 0.00 0.00 43.02 5.87
70 74 1.452145 ATCTTCGCGCTCCTCTCTCC 61.452 60.000 5.56 0.00 0.00 3.71
171 175 1.807755 GCGAGCACTGCATTATCCTCA 60.808 52.381 3.30 0.00 0.00 3.86
180 184 4.350225 ACTGCATTATCCTCATCTGTCCAT 59.650 41.667 0.00 0.00 0.00 3.41
300 304 2.111878 GCGCCATGGCCACTATCT 59.888 61.111 30.79 0.00 37.98 1.98
340 344 0.730494 GCGCACACTGCATTTCTTCC 60.730 55.000 0.30 0.00 45.36 3.46
358 364 1.144936 CCCCCTTTCTCTGCTAGCG 59.855 63.158 10.77 5.22 0.00 4.26
405 411 6.538742 GCAAGTGCTAACTCTTAATCATACCA 59.461 38.462 0.00 0.00 34.77 3.25
454 461 2.039974 ATGCGCCGAGACAATGCAA 61.040 52.632 4.18 0.00 39.26 4.08
539 546 3.243401 ACAACTCGCAGATGTCGCATATA 60.243 43.478 0.00 0.00 33.89 0.86
555 563 5.870433 TCGCATATAAGGTTGTTTTCGAGAA 59.130 36.000 0.00 0.00 0.00 2.87
621 629 1.591327 GCAACCAAACACGCCCTTG 60.591 57.895 0.00 0.00 0.00 3.61
623 631 0.457851 CAACCAAACACGCCCTTGAA 59.542 50.000 0.00 0.00 0.00 2.69
646 654 6.835819 AAAAAGTAGGATTAAAGTGCCTCC 57.164 37.500 0.00 0.00 33.28 4.30
647 655 3.821421 AGTAGGATTAAAGTGCCTCCG 57.179 47.619 0.00 0.00 33.28 4.63
648 656 2.434702 AGTAGGATTAAAGTGCCTCCGG 59.565 50.000 0.00 0.00 33.28 5.14
696 704 7.342799 ACATATTCAAAGTGGGCAAATATCTGT 59.657 33.333 0.00 0.00 0.00 3.41
737 760 3.142838 GGTCTACCACGCGCCCTA 61.143 66.667 5.73 0.00 35.64 3.53
738 761 2.103736 GTCTACCACGCGCCCTAC 59.896 66.667 5.73 0.00 0.00 3.18
753 776 4.735132 TACTGCTGCCGTCGTGCC 62.735 66.667 0.00 0.00 0.00 5.01
794 827 3.011517 CCTCCACACCCCTGGGAG 61.012 72.222 16.20 9.05 46.24 4.30
863 896 2.993264 TCGGGACTCCACGTTCCC 60.993 66.667 12.34 12.34 38.12 3.97
907 946 1.380112 AGTCAGGGGCTCGAGGTAC 60.380 63.158 15.58 0.00 0.00 3.34
955 994 2.478292 TCTCCTAGTCAAATCCCCACC 58.522 52.381 0.00 0.00 0.00 4.61
970 1009 0.322187 CCACCGACCTTCCCGATTTT 60.322 55.000 0.00 0.00 0.00 1.82
1012 1051 4.284860 CGCCGATGCCGATGGAGA 62.285 66.667 0.00 0.00 38.22 3.71
1050 1089 1.548357 GGAAGAGCTCAGAGCCACCA 61.548 60.000 19.40 0.00 43.77 4.17
1067 1106 3.406200 AGGGAATGGCTCGCTGCT 61.406 61.111 0.00 0.00 45.21 4.24
1074 1113 0.107312 ATGGCTCGCTGCTGAAGATT 60.107 50.000 0.00 0.00 42.39 2.40
1096 1139 1.571919 CGAGAAATCCCAGGTTAGCG 58.428 55.000 0.00 0.00 0.00 4.26
1118 1161 1.352622 TGCTTTGGGTCACTCCAGGT 61.353 55.000 0.00 0.00 38.17 4.00
1184 1227 3.260632 GCTTTCCTATTTTTGGCCAGGAA 59.739 43.478 15.91 15.91 34.12 3.36
1186 1229 5.571454 GCTTTCCTATTTTTGGCCAGGAATT 60.571 40.000 19.43 11.51 35.67 2.17
1265 1308 2.688507 GTCGATGACAATGACAGTGGT 58.311 47.619 7.92 0.00 32.91 4.16
1349 1392 1.472276 CCTATGACGACGCGCTCAAC 61.472 60.000 5.73 1.00 0.00 3.18
1467 1510 2.239439 AGTCGGTCAGGGAGAGGGA 61.239 63.158 0.00 0.00 0.00 4.20
1477 1520 0.915364 GGGAGAGGGAGAGCAAATGT 59.085 55.000 0.00 0.00 0.00 2.71
1508 1551 7.468141 TCTGTCTAGAGAAACAGCAAAGATA 57.532 36.000 0.00 0.00 42.10 1.98
1517 1560 2.875296 ACAGCAAAGATAAACTGCCCA 58.125 42.857 0.00 0.00 36.73 5.36
1526 1569 3.718956 AGATAAACTGCCCAGCTAGGATT 59.281 43.478 0.85 0.00 41.22 3.01
1673 1716 1.339929 GTGGAAAATGGTTCACGGCTT 59.660 47.619 0.00 0.00 0.00 4.35
1739 1782 4.031611 ACTTTACCGAGATAGGAAGGCTT 58.968 43.478 0.00 0.00 34.73 4.35
1835 1878 2.292828 ACCTGGTGGATTTGGACAAG 57.707 50.000 0.00 0.00 37.04 3.16
1886 1929 2.510238 GCTAGGTCACAGGCAGCG 60.510 66.667 0.00 0.00 0.00 5.18
2009 2052 2.101750 CCACCCTGTTTTGTTTGGTACC 59.898 50.000 4.43 4.43 0.00 3.34
2027 2070 1.012841 CCGGCTTGCTTTCAGATCTC 58.987 55.000 0.00 0.00 0.00 2.75
2105 2148 0.615331 ACCCAGACGCAATCATCACT 59.385 50.000 0.00 0.00 0.00 3.41
2111 2154 1.938577 GACGCAATCATCACTGAGCAT 59.061 47.619 0.00 0.00 34.12 3.79
2285 2328 1.499007 TCTTTGAAGCCCCCAGAGTTT 59.501 47.619 0.00 0.00 0.00 2.66
2405 2448 5.567138 ATCTTAAAGACAAATTCTGGGCG 57.433 39.130 0.00 0.00 33.46 6.13
2903 2946 5.614324 TGTTTGAGATCCCGTCAAGATAT 57.386 39.130 0.00 0.00 35.39 1.63
3287 3330 1.745141 GCAGAAACTGATCCGGATGCT 60.745 52.381 24.82 0.00 32.44 3.79
3372 3415 3.338249 AGCATTCATACGTCAGTTTGCT 58.662 40.909 8.80 8.80 34.56 3.91
3380 3423 3.386768 ACGTCAGTTTGCTGTATGACT 57.613 42.857 9.77 0.00 43.05 3.41
3466 3509 8.677300 GCCAACTGAAACTAATATGATTCAAGA 58.323 33.333 0.00 0.00 31.94 3.02
3565 3608 2.466846 TGGTCTGCTTCTGCTACCATA 58.533 47.619 10.24 0.00 44.73 2.74
3702 3745 2.026641 CAACCAAGGATGATGCCGAAT 58.973 47.619 0.00 0.00 0.00 3.34
3727 3770 5.723295 ACTTTATGCAGGTTTTTGCTATGG 58.277 37.500 0.00 0.00 44.38 2.74
4026 4069 3.826236 CATGCTACTCCATGCTTATGC 57.174 47.619 0.00 0.00 36.52 3.14
4051 4094 5.244626 CCCCTGTTCACATTTTCTTCTTCAT 59.755 40.000 0.00 0.00 0.00 2.57
4198 4241 4.268359 GTTCAGGGATTCTCTTGCTCATT 58.732 43.478 0.00 0.00 0.00 2.57
4467 4519 7.617041 AGAATTTTAGGTATGCTGTCTGTTC 57.383 36.000 0.00 0.00 0.00 3.18
4480 4532 4.338879 CTGTCTGTTCCTCCAAATCCATT 58.661 43.478 0.00 0.00 0.00 3.16
4695 4748 8.724229 CATGTAATACTTGTCACCATCCATATG 58.276 37.037 0.00 0.00 0.00 1.78
4806 4879 1.194781 AGGGTGGCGACTCTGATGTT 61.195 55.000 0.00 0.00 28.66 2.71
4808 4881 1.066430 GGGTGGCGACTCTGATGTTTA 60.066 52.381 0.00 0.00 0.00 2.01
4817 4890 4.363999 GACTCTGATGTTTAGATCCCACG 58.636 47.826 0.00 0.00 0.00 4.94
4827 4900 0.107508 AGATCCCACGCACAATGGAG 60.108 55.000 0.00 0.00 39.87 3.86
4841 4914 1.566298 ATGGAGGTGAAGTGGGGAGC 61.566 60.000 0.00 0.00 0.00 4.70
4852 4925 0.034670 GTGGGGAGCAGAGATGCTTT 60.035 55.000 3.97 0.00 46.36 3.51
4853 4926 0.700564 TGGGGAGCAGAGATGCTTTT 59.299 50.000 3.97 0.00 46.36 2.27
4903 4976 9.634163 GGGTAACAAACTTTACATATTTGAAGG 57.366 33.333 3.13 0.00 36.91 3.46
4905 4978 7.867445 AACAAACTTTACATATTTGAAGGCG 57.133 32.000 3.13 0.00 36.91 5.52
4906 4979 6.386654 ACAAACTTTACATATTTGAAGGCGG 58.613 36.000 3.13 0.00 36.91 6.13
4997 5070 3.454812 TGGCAAATCTAGGGAAGTACTCC 59.545 47.826 0.00 0.00 44.54 3.85
5007 5080 1.020437 GAAGTACTCCCTCCGTACCG 58.980 60.000 0.00 0.00 38.34 4.02
5038 5111 9.319143 AGTTGATGTATCTAGACATGTTTTAGC 57.681 33.333 0.00 0.00 40.18 3.09
5040 5113 7.489160 TGATGTATCTAGACATGTTTTAGCGT 58.511 34.615 0.00 1.51 40.18 5.07
5047 5120 8.630278 TCTAGACATGTTTTAGCGTTAGATTC 57.370 34.615 0.00 0.00 0.00 2.52
5056 5129 7.168637 TGTTTTAGCGTTAGATTCATCCGTATC 59.831 37.037 0.00 0.00 0.00 2.24
5058 5131 5.455056 AGCGTTAGATTCATCCGTATCTT 57.545 39.130 0.00 0.00 32.18 2.40
5071 5144 8.007405 TCATCCGTATCTTGACAAATCTAAGA 57.993 34.615 0.00 0.00 35.19 2.10
5072 5145 8.474831 TCATCCGTATCTTGACAAATCTAAGAA 58.525 33.333 0.00 0.00 34.47 2.52
5114 5190 7.739825 AGGTAATACTACAGAGTACGTGGATA 58.260 38.462 0.00 0.00 41.01 2.59
5125 5201 6.530534 CAGAGTACGTGGATACTGGTTAAAAG 59.469 42.308 0.00 0.00 35.48 2.27
5181 5257 2.096980 CACAACAGACGAGTAGCCGATA 59.903 50.000 0.00 0.00 0.00 2.92
5194 5270 0.593128 GCCGATATTGTGATGGGCAC 59.407 55.000 4.74 0.00 46.77 5.01
5229 5308 2.660189 ATTATGTTGCTGTTGCTGCC 57.340 45.000 0.00 0.00 40.48 4.85
5248 5327 2.419851 GCCAGTGCTATCTCTTCTGCTT 60.420 50.000 0.00 0.00 33.53 3.91
5260 5352 0.112995 TTCTGCTTGCTGGATGGGTT 59.887 50.000 0.00 0.00 0.00 4.11
5310 5405 2.744741 GCCACTACAGCTTCTTTCTTCC 59.255 50.000 0.00 0.00 0.00 3.46
5320 5415 2.951229 TCTTTCTTCCCAGGGTTGTC 57.049 50.000 5.01 0.00 0.00 3.18
5337 5432 5.163550 GGGTTGTCCAATACTAAAATCTGGC 60.164 44.000 0.00 0.00 35.00 4.85
5341 5436 6.349300 TGTCCAATACTAAAATCTGGCTCTC 58.651 40.000 0.00 0.00 0.00 3.20
5359 5454 2.051345 GTTTGGTGCTTGGCGTCG 60.051 61.111 0.00 0.00 0.00 5.12
5375 5473 1.196808 CGTCGGGGTCTGTGATTTTTG 59.803 52.381 0.00 0.00 0.00 2.44
5376 5474 2.227194 GTCGGGGTCTGTGATTTTTGT 58.773 47.619 0.00 0.00 0.00 2.83
5377 5475 2.621526 GTCGGGGTCTGTGATTTTTGTT 59.378 45.455 0.00 0.00 0.00 2.83
5383 5481 5.289595 GGGTCTGTGATTTTTGTTTCCTTC 58.710 41.667 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.080974 CCGTCGGCGAACTAGTTGT 60.081 57.895 12.93 0.00 41.33 3.32
1 2 1.080974 ACCGTCGGCGAACTAGTTG 60.081 57.895 12.93 6.76 41.33 3.16
2 3 1.080974 CACCGTCGGCGAACTAGTT 60.081 57.895 12.93 8.13 41.33 2.24
3 4 2.192608 GACACCGTCGGCGAACTAGT 62.193 60.000 12.93 8.72 41.33 2.57
4 5 1.513586 GACACCGTCGGCGAACTAG 60.514 63.158 12.93 5.05 41.33 2.57
5 6 2.562912 GACACCGTCGGCGAACTA 59.437 61.111 12.93 0.00 41.33 2.24
14 15 4.702081 ACAGCGAGCGACACCGTC 62.702 66.667 0.00 0.00 38.24 4.79
42 43 1.299468 GCGCGAAGATGATCGACCT 60.299 57.895 12.10 0.00 45.48 3.85
59 63 3.438615 TAGGGCGGGAGAGAGGAGC 62.439 68.421 0.00 0.00 0.00 4.70
70 74 0.683504 ACTCCAGTGTAGTAGGGCGG 60.684 60.000 0.00 0.00 0.00 6.13
165 169 5.191426 CAAAGACAATGGACAGATGAGGAT 58.809 41.667 0.00 0.00 0.00 3.24
171 175 1.470098 GCGCAAAGACAATGGACAGAT 59.530 47.619 0.30 0.00 0.00 2.90
300 304 1.509463 GACCATGACGACTGCGGTA 59.491 57.895 0.00 0.00 43.17 4.02
340 344 1.144936 CGCTAGCAGAGAAAGGGGG 59.855 63.158 16.45 0.00 0.00 5.40
358 364 3.746492 CACTTAGCACACAGGGTTAAGAC 59.254 47.826 9.40 0.00 0.00 3.01
390 396 4.380531 CCGCATGTGGTATGATTAAGAGT 58.619 43.478 17.59 0.00 0.00 3.24
405 411 2.086251 CTGTTTGGTTGCCCGCATGT 62.086 55.000 0.00 0.00 0.00 3.21
426 432 2.028766 CTCGGCGCATGCAACTACAG 62.029 60.000 19.57 0.00 45.35 2.74
454 461 1.140804 GGCACGTTGTTTGGTTGCT 59.859 52.632 0.00 0.00 0.00 3.91
539 546 2.949644 CCTGGTTCTCGAAAACAACCTT 59.050 45.455 3.68 0.00 40.37 3.50
555 563 1.197430 CCTTCTCCACTCAGCCTGGT 61.197 60.000 0.00 0.00 0.00 4.00
597 605 2.492090 GTGTTTGGTTGCCGTGCA 59.508 55.556 0.00 0.00 36.47 4.57
623 631 5.414765 CGGAGGCACTTTAATCCTACTTTTT 59.585 40.000 0.00 0.00 41.55 1.94
643 651 7.429636 TCTTTTTGAGTTAAATACACCGGAG 57.570 36.000 9.46 1.26 0.00 4.63
644 652 7.804843 TTCTTTTTGAGTTAAATACACCGGA 57.195 32.000 9.46 0.00 0.00 5.14
645 653 8.748582 GTTTTCTTTTTGAGTTAAATACACCGG 58.251 33.333 0.00 0.00 0.00 5.28
646 654 9.291664 TGTTTTCTTTTTGAGTTAAATACACCG 57.708 29.630 0.00 0.00 0.00 4.94
710 729 3.711849 TGGTAGACCAAGAGGGGAG 57.288 57.895 0.00 0.00 44.35 4.30
735 758 3.181967 GCACGACGGCAGCAGTAG 61.182 66.667 0.00 0.47 0.00 2.57
736 759 4.735132 GGCACGACGGCAGCAGTA 62.735 66.667 0.00 0.00 40.76 2.74
846 879 2.993264 GGGAACGTGGAGTCCCGA 60.993 66.667 22.03 0.00 32.97 5.14
918 957 1.410517 GAGAATCGCTGGATGAGGACA 59.589 52.381 0.00 0.00 31.83 4.02
1029 1068 1.079987 TGGCTCTGAGCTCTTCCCT 59.920 57.895 27.09 0.00 41.99 4.20
1067 1106 2.026356 TGGGATTTCTCGGCAATCTTCA 60.026 45.455 0.00 0.00 32.13 3.02
1074 1113 1.209504 CTAACCTGGGATTTCTCGGCA 59.790 52.381 0.00 0.00 0.00 5.69
1118 1161 4.552355 CAAGCAAGCATGAGAATTTGACA 58.448 39.130 0.00 0.00 0.00 3.58
1167 1210 3.118298 CCCAATTCCTGGCCAAAAATAGG 60.118 47.826 7.01 10.07 44.90 2.57
1265 1308 1.163309 ACCCCCACCATCTTCCTGA 59.837 57.895 0.00 0.00 0.00 3.86
1349 1392 3.116300 CACCGCATACTGCTTGTAGTAG 58.884 50.000 5.01 0.00 42.25 2.57
1389 1432 2.419324 GGTACGACGACTTGAGAGTGAT 59.581 50.000 0.00 0.00 35.88 3.06
1477 1520 5.393569 GCTGTTTCTCTAGACAGATAGCACA 60.394 44.000 12.26 0.73 44.65 4.57
1508 1551 2.728007 GAAATCCTAGCTGGGCAGTTT 58.272 47.619 12.10 11.86 36.20 2.66
1517 1560 4.894784 TCAACTTCAACGAAATCCTAGCT 58.105 39.130 0.00 0.00 0.00 3.32
1526 1569 1.140052 TCCTGCCTCAACTTCAACGAA 59.860 47.619 0.00 0.00 0.00 3.85
1673 1716 2.718563 GGAACATTCCTTCGCCCTTTA 58.281 47.619 3.24 0.00 44.11 1.85
1739 1782 3.110293 TCATCTCCTTCCCCGAACTTA 57.890 47.619 0.00 0.00 0.00 2.24
1784 1827 5.509716 TTGGATTCTTATTCTGCATGCTG 57.490 39.130 20.33 18.97 0.00 4.41
1835 1878 1.449778 GTTCCTTAGACGCCCCTGC 60.450 63.158 0.00 0.00 0.00 4.85
1886 1929 6.140303 ACATCATGACCAAAGTATTCATGC 57.860 37.500 0.00 0.00 44.22 4.06
2009 2052 1.664659 CTGAGATCTGAAAGCAAGCCG 59.335 52.381 0.00 0.00 0.00 5.52
2027 2070 2.035704 CCAGGTATAGCTCTCAGCACTG 59.964 54.545 0.26 0.00 45.56 3.66
2111 2154 2.863740 CGCATCCAGAATAGCGTTGTAA 59.136 45.455 0.00 0.00 44.67 2.41
2159 2202 1.671850 CGATACAGACAAAGGCGGTGT 60.672 52.381 0.00 0.00 0.00 4.16
2285 2328 1.988107 ACCTTCTTCCAATCAGCCTCA 59.012 47.619 0.00 0.00 0.00 3.86
2810 2853 4.970003 GTGAACTGAAAGAAACCACATTCG 59.030 41.667 0.00 0.00 37.43 3.34
2903 2946 2.038426 TCTTTTCCAGCGATCAAGGACA 59.962 45.455 0.00 0.00 0.00 4.02
3287 3330 7.879160 ACCTGTTCTTTATTTGACCGTAATACA 59.121 33.333 0.00 0.00 0.00 2.29
3534 3577 5.181245 GCAGAAGCAGACCAAAATTACTACA 59.819 40.000 0.00 0.00 41.58 2.74
3565 3608 6.601741 AAAATGTTCACACGCATGAAAATT 57.398 29.167 10.47 10.47 44.82 1.82
3702 3745 7.177568 TCCATAGCAAAAACCTGCATAAAGTTA 59.822 33.333 0.00 0.00 45.18 2.24
4026 4069 3.500343 AGAAGAAAATGTGAACAGGGGG 58.500 45.455 0.00 0.00 0.00 5.40
4051 4094 1.229927 GGGGCATAAGCATGGACCA 59.770 57.895 0.00 0.00 44.61 4.02
4198 4241 9.812347 AATCATAATATATCAGGCTGGAAAACA 57.188 29.630 15.73 0.00 0.00 2.83
4467 4519 4.891756 AGCTTGATACAATGGATTTGGAGG 59.108 41.667 0.00 0.00 39.80 4.30
4480 4532 6.882610 AGAACATGTCAAAAGCTTGATACA 57.117 33.333 0.00 5.06 43.39 2.29
4806 4879 1.557371 TCCATTGTGCGTGGGATCTAA 59.443 47.619 0.00 0.00 37.34 2.10
4808 4881 0.107508 CTCCATTGTGCGTGGGATCT 60.108 55.000 0.00 0.00 37.34 2.75
4817 4890 0.883833 CCACTTCACCTCCATTGTGC 59.116 55.000 0.00 0.00 33.71 4.57
4827 4900 1.194781 TCTCTGCTCCCCACTTCACC 61.195 60.000 0.00 0.00 0.00 4.02
4841 4914 5.049198 TGCACAAACTCTAAAAGCATCTCTG 60.049 40.000 0.00 0.00 0.00 3.35
4852 4925 4.883083 AGTCGAAGATGCACAAACTCTAA 58.117 39.130 0.00 0.00 40.67 2.10
4853 4926 4.521130 AGTCGAAGATGCACAAACTCTA 57.479 40.909 0.00 0.00 40.67 2.43
4905 4978 4.786425 AGATTTATGCCTGGAGAACTTCC 58.214 43.478 0.00 0.00 46.98 3.46
4906 4979 5.067023 CCAAGATTTATGCCTGGAGAACTTC 59.933 44.000 0.00 0.00 0.00 3.01
4956 5029 4.058124 GCCACGTTATATGCTGATTCTCA 58.942 43.478 0.00 0.00 0.00 3.27
4970 5043 3.262405 ACTTCCCTAGATTTGCCACGTTA 59.738 43.478 0.00 0.00 0.00 3.18
4973 5046 2.403252 ACTTCCCTAGATTTGCCACG 57.597 50.000 0.00 0.00 0.00 4.94
5038 5111 6.206498 TGTCAAGATACGGATGAATCTAACG 58.794 40.000 0.00 0.00 32.17 3.18
5040 5113 9.261180 GATTTGTCAAGATACGGATGAATCTAA 57.739 33.333 0.00 0.00 32.17 2.10
5046 5119 8.007405 TCTTAGATTTGTCAAGATACGGATGA 57.993 34.615 0.00 0.00 0.00 2.92
5047 5120 8.648557 TTCTTAGATTTGTCAAGATACGGATG 57.351 34.615 0.00 0.00 0.00 3.51
5071 5144 4.108501 ACCTCCGTCCCAAATTAGTTTT 57.891 40.909 0.00 0.00 0.00 2.43
5072 5145 3.801307 ACCTCCGTCCCAAATTAGTTT 57.199 42.857 0.00 0.00 0.00 2.66
5114 5190 6.238566 GCGTACTCTTTTTCCTTTTAACCAGT 60.239 38.462 0.00 0.00 0.00 4.00
5125 5201 1.062148 GCATCCGCGTACTCTTTTTCC 59.938 52.381 4.92 0.00 0.00 3.13
5137 5213 0.508641 GTTGTATGCTAGCATCCGCG 59.491 55.000 32.76 0.00 45.49 6.46
5229 5308 2.608546 GCAAGCAGAAGAGATAGCACTG 59.391 50.000 0.00 0.00 0.00 3.66
5248 5327 1.607178 CTTGGCAACCCATCCAGCA 60.607 57.895 0.00 0.00 41.78 4.41
5282 5374 0.036010 AAGCTGTAGTGGCATTCGCT 60.036 50.000 0.00 0.00 39.84 4.93
5295 5390 1.074566 CCCTGGGAAGAAAGAAGCTGT 59.925 52.381 7.01 0.00 0.00 4.40
5310 5405 6.095440 CAGATTTTAGTATTGGACAACCCTGG 59.905 42.308 0.00 0.00 35.38 4.45
5320 5415 5.360591 ACGAGAGCCAGATTTTAGTATTGG 58.639 41.667 0.00 0.00 0.00 3.16
5337 5432 1.576421 GCCAAGCACCAAACGAGAG 59.424 57.895 0.00 0.00 0.00 3.20
5341 5436 2.051345 GACGCCAAGCACCAAACG 60.051 61.111 0.00 0.00 0.00 3.60
5359 5454 3.641436 AGGAAACAAAAATCACAGACCCC 59.359 43.478 0.00 0.00 0.00 4.95
5383 5481 1.167851 ACCATGCTTGATCACAACCG 58.832 50.000 0.00 0.00 32.27 4.44


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

AutoCloner maintained by Alex Coulton.