Multiple sequence alignment - TraesCS5D01G196100

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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 TraesCS5D01G196100 chr5D 100.000 4935 0 0 1 4935 299809388 299814322 0.000000e+00 9114.0
1 TraesCS5D01G196100 chr5B 94.022 2877 111 32 734 3578 341050962 341053809 0.000000e+00 4303.0
2 TraesCS5D01G196100 chr5B 90.842 1365 80 26 3581 4935 341053912 341055241 0.000000e+00 1786.0
3 TraesCS5D01G196100 chr5B 87.527 457 34 14 244 685 341050430 341050878 1.590000e-139 507.0
4 TraesCS5D01G196100 chr5B 92.188 192 15 0 38 229 341050254 341050445 6.290000e-69 272.0
5 TraesCS5D01G196100 chr5A 93.947 1619 62 11 1770 3381 397144307 397145896 0.000000e+00 2414.0
6 TraesCS5D01G196100 chr5A 90.051 1578 90 27 3380 4935 397146000 397147532 0.000000e+00 1982.0
7 TraesCS5D01G196100 chr5A 90.988 1043 58 20 615 1633 397143280 397144310 0.000000e+00 1373.0
8 TraesCS5D01G196100 chr5A 92.585 472 23 7 1 463 397142803 397143271 0.000000e+00 667.0
9 TraesCS5D01G196100 chr1A 89.971 349 15 9 4541 4889 543638599 543638927 2.730000e-117 433.0
10 TraesCS5D01G196100 chr3A 87.770 139 17 0 1640 1778 488253006 488252868 3.950000e-36 163.0
11 TraesCS5D01G196100 chr6B 82.993 147 21 3 1640 1784 142711887 142712031 4.010000e-26 130.0
12 TraesCS5D01G196100 chr2A 82.895 152 19 4 1640 1786 194551860 194552009 4.010000e-26 130.0
13 TraesCS5D01G196100 chr2D 87.156 109 14 0 1678 1786 400383483 400383375 1.870000e-24 124.0
14 TraesCS5D01G196100 chrUn 82.119 151 17 7 1645 1785 290145904 290145754 2.410000e-23 121.0
15 TraesCS5D01G196100 chr7D 83.721 129 17 4 1654 1779 100740485 100740358 8.680000e-23 119.0
16 TraesCS5D01G196100 chr7D 78.344 157 23 5 1640 1786 55086770 55086615 1.890000e-14 91.6
17 TraesCS5D01G196100 chr4D 81.579 152 21 4 1640 1786 381892715 381892864 8.680000e-23 119.0
18 TraesCS5D01G196100 chr4A 95.000 40 1 1 3074 3113 700532429 700532467 1.480000e-05 62.1


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 TraesCS5D01G196100 chr5D 299809388 299814322 4934 False 9114 9114 100.00000 1 4935 1 chr5D.!!$F1 4934
1 TraesCS5D01G196100 chr5B 341050254 341055241 4987 False 1717 4303 91.14475 38 4935 4 chr5B.!!$F1 4897
2 TraesCS5D01G196100 chr5A 397142803 397147532 4729 False 1609 2414 91.89275 1 4935 4 chr5A.!!$F1 4934

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
549 568 0.104487 TGCGGACGGAACAAGTACAA 59.896 50.0 0.00 0.0 0.00 2.41 F
891 965 0.108774 CTCCGCCTTTATTCCCCCTC 59.891 60.0 0.00 0.0 0.00 4.30 F
1437 1534 0.393402 TCTCTGGGTAGCGCGAAGTA 60.393 55.0 12.10 0.0 0.00 2.24 F
1931 2031 0.605589 ACGTTTTCTGGGGCTGTAGC 60.606 55.0 0.00 0.0 41.14 3.58 F
2889 2993 1.719600 CTCTAGCTGTTGGTGCTGAC 58.280 55.0 0.00 0.0 41.32 3.51 F
3585 3901 0.681733 ACATCAACTCTCGGTGCACT 59.318 50.0 17.98 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1913 2013 0.321653 AGCTACAGCCCCAGAAAACG 60.322 55.000 0.0 0.0 43.38 3.60 R
2889 2993 0.735978 TGGCTGTATCAAGCGACACG 60.736 55.000 0.0 0.0 44.52 4.49 R
3396 3610 1.749634 ACCTGTATTCTTCGAGGGACG 59.250 52.381 0.0 0.0 44.09 4.79 R
3585 3901 0.978151 TTAGCGGGAACTAGCCAACA 59.022 50.000 0.0 0.0 33.10 3.33 R
3793 4109 1.068055 GCCTTGCCAGAGTTGTTGATG 60.068 52.381 0.0 0.0 0.00 3.07 R
4846 5180 2.203070 GCGCCATTGACGAGGGAT 60.203 61.111 0.0 0.0 0.00 3.85 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 2.028484 GCTGTCCGGACAACACGA 59.972 61.111 35.36 14.05 41.33 4.35
32 33 0.665369 GTCCGGACAACACGATTCGT 60.665 55.000 29.75 5.75 42.36 3.85
316 318 7.619698 TGATTCTCTCTGTATTCCAAAGGACTA 59.380 37.037 0.00 0.00 0.00 2.59
347 352 6.654793 TGTATGCAACTTTGAAAAACCAAC 57.345 33.333 0.00 0.00 0.00 3.77
418 423 1.881973 ACATCACATGTCCACTTGTGC 59.118 47.619 16.99 0.00 45.82 4.57
424 437 2.223479 ACATGTCCACTTGTGCGTTTTC 60.223 45.455 0.00 0.00 33.67 2.29
443 456 7.148755 GCGTTTTCTTATCTCAAATTGCACATT 60.149 33.333 0.00 0.00 0.00 2.71
485 498 7.903995 AACCACAATAAGCCAAATTAACATG 57.096 32.000 0.00 0.00 0.00 3.21
490 503 6.591062 ACAATAAGCCAAATTAACATGTGCTG 59.409 34.615 0.00 0.00 0.00 4.41
494 507 2.620242 CAAATTAACATGTGCTGCCCC 58.380 47.619 0.00 0.00 0.00 5.80
508 521 2.184830 GCCCCGGTCCGAAATTAGC 61.185 63.158 14.39 2.15 0.00 3.09
516 529 2.740447 GGTCCGAAATTAGCTGACGTTT 59.260 45.455 0.00 0.00 0.00 3.60
517 530 3.187842 GGTCCGAAATTAGCTGACGTTTT 59.812 43.478 0.00 0.00 0.00 2.43
518 531 4.392216 GTCCGAAATTAGCTGACGTTTTC 58.608 43.478 0.00 0.00 0.00 2.29
519 532 4.151867 GTCCGAAATTAGCTGACGTTTTCT 59.848 41.667 0.00 0.00 0.00 2.52
535 554 4.181578 GTTTTCTTATCTAGCACTGCGGA 58.818 43.478 0.00 0.00 0.00 5.54
541 560 1.805945 CTAGCACTGCGGACGGAAC 60.806 63.158 0.00 0.00 0.00 3.62
549 568 0.104487 TGCGGACGGAACAAGTACAA 59.896 50.000 0.00 0.00 0.00 2.41
557 576 5.294050 ACGGAACAAGTACAAAACGAAAA 57.706 34.783 0.00 0.00 0.00 2.29
558 577 5.697826 ACGGAACAAGTACAAAACGAAAAA 58.302 33.333 0.00 0.00 0.00 1.94
566 585 5.333513 AGTACAAAACGAAAAACATCGCAA 58.666 33.333 0.00 0.00 46.51 4.85
570 589 2.013286 ACGAAAAACATCGCAACGAC 57.987 45.000 0.00 0.00 46.51 4.34
572 591 1.333347 CGAAAAACATCGCAACGACCA 60.333 47.619 0.00 0.00 39.18 4.02
575 594 3.363341 AAAACATCGCAACGACCAAAT 57.637 38.095 0.00 0.00 39.18 2.32
577 596 3.465122 AACATCGCAACGACCAAATAC 57.535 42.857 0.00 0.00 39.18 1.89
580 599 1.149987 TCGCAACGACCAAATACACC 58.850 50.000 0.00 0.00 0.00 4.16
582 601 1.149987 GCAACGACCAAATACACCGA 58.850 50.000 0.00 0.00 0.00 4.69
616 635 0.655733 GGTGTGTATATGCGTGCACC 59.344 55.000 12.15 13.15 39.38 5.01
674 695 6.891908 AGACCTGCATATATGTTGGTTTTTCT 59.108 34.615 23.17 16.28 36.31 2.52
698 719 6.696441 AAACATGATTTTGCCAAAACATGT 57.304 29.167 26.97 26.97 44.80 3.21
722 745 4.148563 GCATGAGCATAGCATGAAAGAG 57.851 45.455 7.68 0.00 44.49 2.85
723 746 3.564644 GCATGAGCATAGCATGAAAGAGT 59.435 43.478 7.68 0.00 44.49 3.24
724 747 4.319622 GCATGAGCATAGCATGAAAGAGTC 60.320 45.833 7.68 0.00 44.49 3.36
725 748 4.750021 TGAGCATAGCATGAAAGAGTCT 57.250 40.909 0.00 0.00 0.00 3.24
726 749 5.095145 TGAGCATAGCATGAAAGAGTCTT 57.905 39.130 0.00 0.00 0.00 3.01
727 750 5.114780 TGAGCATAGCATGAAAGAGTCTTC 58.885 41.667 5.70 0.86 0.00 2.87
728 751 5.105023 TGAGCATAGCATGAAAGAGTCTTCT 60.105 40.000 5.70 1.05 34.29 2.85
731 754 6.760770 AGCATAGCATGAAAGAGTCTTCTAAC 59.239 38.462 5.70 0.93 31.96 2.34
732 755 6.760770 GCATAGCATGAAAGAGTCTTCTAACT 59.239 38.462 5.70 3.58 31.96 2.24
890 964 0.327191 TCTCCGCCTTTATTCCCCCT 60.327 55.000 0.00 0.00 0.00 4.79
891 965 0.108774 CTCCGCCTTTATTCCCCCTC 59.891 60.000 0.00 0.00 0.00 4.30
892 966 1.150764 CCGCCTTTATTCCCCCTCC 59.849 63.158 0.00 0.00 0.00 4.30
893 967 1.353394 CCGCCTTTATTCCCCCTCCT 61.353 60.000 0.00 0.00 0.00 3.69
894 968 0.108774 CGCCTTTATTCCCCCTCCTC 59.891 60.000 0.00 0.00 0.00 3.71
1049 1129 2.935740 GCAAGAAGGCCAAGGGTGC 61.936 63.158 5.01 3.86 0.00 5.01
1051 1131 3.133365 AAGAAGGCCAAGGGTGCGT 62.133 57.895 5.01 0.00 0.00 5.24
1052 1132 2.597510 GAAGGCCAAGGGTGCGTT 60.598 61.111 5.01 0.00 39.31 4.84
1062 1142 2.428925 GGGTGCGTTCCCGATCCTA 61.429 63.158 1.62 0.00 37.93 2.94
1071 1151 1.457079 CCCGATCCTACGACCCCTT 60.457 63.158 0.00 0.00 35.09 3.95
1076 1156 2.584873 ATCCTACGACCCCTTCCGCT 62.585 60.000 0.00 0.00 0.00 5.52
1099 1179 1.577421 CCGCGTTCGTGGGATTTTT 59.423 52.632 15.77 0.00 32.56 1.94
1145 1226 3.939592 CTGTGAGATGTGCTGATTGATGT 59.060 43.478 0.00 0.00 0.00 3.06
1150 1231 3.377485 AGATGTGCTGATTGATGTTGCTC 59.623 43.478 0.00 0.00 0.00 4.26
1200 1281 1.342174 GACTACCAGACCGACCACAAA 59.658 52.381 0.00 0.00 0.00 2.83
1209 1290 1.133606 ACCGACCACAAATTCACCCTT 60.134 47.619 0.00 0.00 0.00 3.95
1268 1350 2.563179 GACACCTTGTCTCTTCCTGCTA 59.437 50.000 0.00 0.00 43.73 3.49
1386 1483 0.963225 TTCCGTGTGATCCGAGTGAA 59.037 50.000 0.00 0.00 0.00 3.18
1418 1515 1.120530 AGTGGTTTGACGACCTCTGT 58.879 50.000 0.00 0.00 40.85 3.41
1434 1531 1.934220 CTGTCTCTGGGTAGCGCGAA 61.934 60.000 12.10 0.00 0.00 4.70
1436 1533 1.677966 TCTCTGGGTAGCGCGAAGT 60.678 57.895 12.10 0.00 0.00 3.01
1437 1534 0.393402 TCTCTGGGTAGCGCGAAGTA 60.393 55.000 12.10 0.00 0.00 2.24
1440 1537 1.202371 TCTGGGTAGCGCGAAGTATTG 60.202 52.381 12.10 0.00 0.00 1.90
1441 1538 0.808453 TGGGTAGCGCGAAGTATTGC 60.808 55.000 12.10 0.00 0.00 3.56
1502 1601 1.603326 GGTTTGCATTTGTTTGGCTGG 59.397 47.619 0.00 0.00 0.00 4.85
1521 1620 5.009110 GGCTGGTAGAAGAATTTATTCCTGC 59.991 44.000 0.27 0.00 37.51 4.85
1524 1623 6.721318 TGGTAGAAGAATTTATTCCTGCTGT 58.279 36.000 0.27 0.00 37.51 4.40
1525 1624 6.823689 TGGTAGAAGAATTTATTCCTGCTGTC 59.176 38.462 0.27 0.00 37.51 3.51
1683 1783 1.296727 GCCCTAAGTATTGCACGTCC 58.703 55.000 0.00 0.00 0.00 4.79
1700 1800 3.576982 ACGTCCAAGTCCTAAGTCATTGA 59.423 43.478 0.00 0.00 0.00 2.57
1706 1806 9.178758 GTCCAAGTCCTAAGTCATTGATTTTAT 57.821 33.333 0.00 0.00 0.00 1.40
1798 1898 1.226974 CACATCGGCAGACCCTACG 60.227 63.158 0.00 0.00 0.00 3.51
1876 1976 3.815962 TGAGGTAGCTATCTTGCGAGTAG 59.184 47.826 8.21 3.85 38.13 2.57
1931 2031 0.605589 ACGTTTTCTGGGGCTGTAGC 60.606 55.000 0.00 0.00 41.14 3.58
1988 2088 7.027778 ACAGTCATTTGTTAGACCAAAAGAC 57.972 36.000 11.81 11.81 45.97 3.01
2080 2181 2.162681 GGAGGTGTGGGTTCTGATTTG 58.837 52.381 0.00 0.00 0.00 2.32
2216 2317 2.311542 TGCCACCCCATTCTTAGAACAT 59.688 45.455 0.00 0.00 0.00 2.71
2271 2373 3.020984 TGATAGTGTCACCGATGCAGTA 58.979 45.455 0.00 0.00 0.00 2.74
2339 2441 5.783100 CAACTGCTGTTGTTTTGACATTT 57.217 34.783 23.89 0.00 46.08 2.32
2588 2692 5.546621 TTCCAGCTTTTAGTACTGACTGT 57.453 39.130 5.39 0.00 36.28 3.55
2589 2693 5.135508 TCCAGCTTTTAGTACTGACTGTC 57.864 43.478 5.39 0.00 36.28 3.51
2591 2695 6.008331 TCCAGCTTTTAGTACTGACTGTCTA 58.992 40.000 5.39 0.00 36.28 2.59
2623 2727 5.190925 TGGGCAGGTCATTACTACAATTACT 59.809 40.000 0.00 0.00 0.00 2.24
2729 2833 6.994421 AACCCTCAATGTAATGGTTTCTTT 57.006 33.333 0.00 0.00 35.87 2.52
2889 2993 1.719600 CTCTAGCTGTTGGTGCTGAC 58.280 55.000 0.00 0.00 41.32 3.51
3045 3149 8.265055 AGTACTATTACTTTGCCAATCTTAGCA 58.735 33.333 0.00 0.00 34.66 3.49
3087 3191 8.861086 ACATCTTCATAGGTACGTGATCTAAAT 58.139 33.333 0.00 0.00 0.00 1.40
3095 3199 7.291411 AGGTACGTGATCTAAATGCTCTTAT 57.709 36.000 0.00 0.00 0.00 1.73
3098 3202 9.077674 GGTACGTGATCTAAATGCTCTTATATG 57.922 37.037 0.00 0.00 0.00 1.78
3113 3217 6.071278 GCTCTTATATGTCTTTACGGAGGGAT 60.071 42.308 0.00 0.00 0.00 3.85
3311 3415 5.757320 TCATTGCAACCACAAATAAAACTGG 59.243 36.000 0.00 0.00 32.27 4.00
3396 3610 8.824159 TTCTCAACTAGCTAATATTGATCAGC 57.176 34.615 12.66 0.00 31.00 4.26
3398 3612 6.749139 TCAACTAGCTAATATTGATCAGCGT 58.251 36.000 9.57 0.00 39.04 5.07
3422 3636 3.927142 CCTCGAAGAATACAGGTTGTGAC 59.073 47.826 0.00 0.00 34.09 3.67
3438 3652 7.365840 GGTTGTGACCTGTTAGATTCTTTAG 57.634 40.000 0.00 0.00 42.99 1.85
3541 3757 7.710907 TCCTCAGAAGAATCAAAATGTATACGG 59.289 37.037 0.00 0.00 0.00 4.02
3585 3901 0.681733 ACATCAACTCTCGGTGCACT 59.318 50.000 17.98 0.00 0.00 4.40
3600 3916 1.298859 GCACTGTTGGCTAGTTCCCG 61.299 60.000 0.00 0.00 0.00 5.14
3611 3927 2.934553 GCTAGTTCCCGCTAACGATTTT 59.065 45.455 0.00 0.00 43.93 1.82
3840 4156 1.638133 CTGATCCAGCACGAGTTCAG 58.362 55.000 0.00 0.00 0.00 3.02
3910 4226 0.322636 AGAAGAGCTCGAAGGTCGGA 60.323 55.000 8.37 0.00 46.62 4.55
3913 4229 0.741915 AGAGCTCGAAGGTCGGAATC 59.258 55.000 8.37 0.00 46.62 2.52
3916 4232 1.939785 CTCGAAGGTCGGAATCGCG 60.940 63.158 0.00 0.00 40.88 5.87
4181 4504 6.578163 TGAACTTGATTCAGCATTCATTCA 57.422 33.333 5.63 0.00 42.62 2.57
4190 4513 5.106876 TCAGCATTCATTCATCTCTTCCA 57.893 39.130 0.00 0.00 0.00 3.53
4197 4520 5.455392 TCATTCATCTCTTCCATTTCCCA 57.545 39.130 0.00 0.00 0.00 4.37
4198 4521 5.195940 TCATTCATCTCTTCCATTTCCCAC 58.804 41.667 0.00 0.00 0.00 4.61
4209 4532 3.073650 TCCATTTCCCACCCCAAATTTTG 59.926 43.478 1.99 1.99 0.00 2.44
4215 4538 3.389656 TCCCACCCCAAATTTTGAACTTC 59.610 43.478 10.72 0.00 0.00 3.01
4223 4546 5.069781 CCCAAATTTTGAACTTCCTGTGGTA 59.930 40.000 10.72 0.00 0.00 3.25
4233 4558 5.470047 ACTTCCTGTGGTAGTCTACTTTG 57.530 43.478 9.85 0.00 26.81 2.77
4239 4564 3.194968 TGTGGTAGTCTACTTTGCTAGGC 59.805 47.826 9.85 0.00 0.00 3.93
4250 4579 8.361139 GTCTACTTTGCTAGGCAGAAGATATTA 58.639 37.037 15.51 3.86 40.61 0.98
4269 4598 8.223330 AGATATTAATGCCTGAATTGAGTCCTT 58.777 33.333 0.00 0.00 0.00 3.36
4271 4600 2.957402 TGCCTGAATTGAGTCCTTGT 57.043 45.000 0.00 0.00 0.00 3.16
4278 4607 1.632589 ATTGAGTCCTTGTTTGGGCC 58.367 50.000 0.00 0.00 30.64 5.80
4312 4641 1.573829 TTGAACTGCGATGAACGGCC 61.574 55.000 0.00 0.00 42.83 6.13
4329 4658 3.041940 CGACTGGTTGGCCACGTC 61.042 66.667 3.88 9.26 40.46 4.34
4331 4660 4.619227 ACTGGTTGGCCACGTCGG 62.619 66.667 3.88 5.62 40.46 4.79
4336 4665 1.890510 GTTGGCCACGTCGGAAAGT 60.891 57.895 3.88 0.00 36.56 2.66
4346 4675 0.653636 GTCGGAAAGTGTCGTGCAAA 59.346 50.000 0.00 0.00 0.00 3.68
4351 4680 1.061421 GAAAGTGTCGTGCAAACGTGA 59.939 47.619 0.00 0.00 0.00 4.35
4436 4765 6.241207 GAGAATCGTCTCTTATCTCCTCTG 57.759 45.833 0.00 0.00 45.99 3.35
4516 4845 3.369451 TCTCGCTCGAGATCATATCTTCG 59.631 47.826 18.75 6.00 45.26 3.79
4545 4874 0.667487 CGTCAGCAATGTCACCGTCT 60.667 55.000 0.00 0.00 0.00 4.18
4572 4901 4.772231 TACTCCGGCCGCCTCCTT 62.772 66.667 22.85 2.11 0.00 3.36
4574 4903 4.410400 CTCCGGCCGCCTCCTTTT 62.410 66.667 22.85 0.00 0.00 2.27
4581 4910 2.663196 CGCCTCCTTTTCTCCCGT 59.337 61.111 0.00 0.00 0.00 5.28
4668 4997 0.824759 GCTCCCTGTCTATGAACGGT 59.175 55.000 0.00 0.00 0.00 4.83
4674 5003 0.319986 TGTCTATGAACGGTTGCGCA 60.320 50.000 5.66 5.66 0.00 6.09
4717 5046 1.080772 GTGACCATGTGCGAGACGA 60.081 57.895 0.00 0.00 0.00 4.20
4846 5180 3.603158 TCGAGGTAGCAAAAGCACATA 57.397 42.857 0.00 0.00 0.00 2.29
4898 5232 4.168014 ACTGCGTTTGATCGTATTCGTAA 58.832 39.130 0.00 0.00 38.33 3.18
4899 5233 4.802039 ACTGCGTTTGATCGTATTCGTAAT 59.198 37.500 0.00 0.00 38.33 1.89
4900 5234 5.060884 TGCGTTTGATCGTATTCGTAATG 57.939 39.130 0.00 0.00 38.33 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 0.808453 CCCGCAACCATACGAATCGT 60.808 55.000 14.28 14.28 44.35 3.73
27 28 0.463116 GGACCCGCAACCATACGAAT 60.463 55.000 0.00 0.00 0.00 3.34
55 56 5.901276 AGATGTTGGATTGATTAAGGGCATT 59.099 36.000 0.00 0.00 0.00 3.56
242 244 6.509418 TGTGGCCTAAATAACATGTCTTTC 57.491 37.500 3.32 0.00 0.00 2.62
243 245 6.663093 TCATGTGGCCTAAATAACATGTCTTT 59.337 34.615 23.51 5.22 46.39 2.52
316 318 9.539825 TTTTTCAAAGTTGCATACATTATGTGT 57.460 25.926 8.26 0.00 44.95 3.72
347 352 7.167468 GCTTGTGTTGTGTCCTTAGTATTTTTG 59.833 37.037 0.00 0.00 0.00 2.44
418 423 7.801547 ATGTGCAATTTGAGATAAGAAAACG 57.198 32.000 0.00 0.00 0.00 3.60
490 503 2.184830 GCTAATTTCGGACCGGGGC 61.185 63.158 15.25 0.00 0.00 5.80
494 507 0.921347 CGTCAGCTAATTTCGGACCG 59.079 55.000 7.84 7.84 0.00 4.79
501 514 8.604890 GCTAGATAAGAAAACGTCAGCTAATTT 58.395 33.333 0.00 0.00 0.00 1.82
508 521 5.220303 GCAGTGCTAGATAAGAAAACGTCAG 60.220 44.000 8.18 0.00 0.00 3.51
516 529 2.223502 CGTCCGCAGTGCTAGATAAGAA 60.224 50.000 14.33 0.00 0.00 2.52
517 530 1.333931 CGTCCGCAGTGCTAGATAAGA 59.666 52.381 14.33 0.00 0.00 2.10
518 531 1.600663 CCGTCCGCAGTGCTAGATAAG 60.601 57.143 14.33 5.98 0.00 1.73
519 532 0.384309 CCGTCCGCAGTGCTAGATAA 59.616 55.000 14.33 0.00 0.00 1.75
526 545 2.954753 CTTGTTCCGTCCGCAGTGC 61.955 63.158 4.58 4.58 0.00 4.40
535 554 4.943142 TTTCGTTTTGTACTTGTTCCGT 57.057 36.364 0.00 0.00 0.00 4.69
541 560 5.228220 TGCGATGTTTTTCGTTTTGTACTTG 59.772 36.000 0.00 0.00 41.16 3.16
549 568 2.779471 GTCGTTGCGATGTTTTTCGTTT 59.221 40.909 0.00 0.00 41.16 3.60
557 576 2.809119 TGTATTTGGTCGTTGCGATGTT 59.191 40.909 0.00 0.00 38.42 2.71
558 577 2.158841 GTGTATTTGGTCGTTGCGATGT 59.841 45.455 0.00 0.00 38.42 3.06
563 582 1.149987 TCGGTGTATTTGGTCGTTGC 58.850 50.000 0.00 0.00 0.00 4.17
566 585 3.048337 ACAATCGGTGTATTTGGTCGT 57.952 42.857 0.00 0.00 39.29 4.34
593 612 1.740585 GCACGCATATACACACCCAAA 59.259 47.619 0.00 0.00 0.00 3.28
594 613 1.339151 TGCACGCATATACACACCCAA 60.339 47.619 0.00 0.00 0.00 4.12
595 614 0.250513 TGCACGCATATACACACCCA 59.749 50.000 0.00 0.00 0.00 4.51
596 615 0.655733 GTGCACGCATATACACACCC 59.344 55.000 0.00 0.00 33.23 4.61
597 616 0.655733 GGTGCACGCATATACACACC 59.344 55.000 11.45 0.00 40.64 4.16
611 630 7.613801 AGAAAAACATATATACAGGTTGGTGCA 59.386 33.333 0.00 0.00 0.00 4.57
650 671 7.100458 AGAAAAACCAACATATATGCAGGTC 57.900 36.000 22.79 14.01 37.29 3.85
715 738 9.078990 TGTCATTCTAGTTAGAAGACTCTTTCA 57.921 33.333 19.92 7.37 44.67 2.69
731 754 9.208022 TCCTGCGATATTATTTTGTCATTCTAG 57.792 33.333 0.00 0.00 0.00 2.43
732 755 9.208022 CTCCTGCGATATTATTTTGTCATTCTA 57.792 33.333 0.00 0.00 0.00 2.10
745 819 2.034179 CCACACGACTCCTGCGATATTA 59.966 50.000 0.00 0.00 0.00 0.98
785 859 8.432110 AACCCTAGCTTAATGTTTTGTTTTTG 57.568 30.769 0.00 0.00 0.00 2.44
890 964 4.798682 GGAAGGAGCGGGGGAGGA 62.799 72.222 0.00 0.00 0.00 3.71
892 966 4.806339 AGGGAAGGAGCGGGGGAG 62.806 72.222 0.00 0.00 0.00 4.30
893 967 4.798682 GAGGGAAGGAGCGGGGGA 62.799 72.222 0.00 0.00 0.00 4.81
1051 1131 1.456331 GGGGTCGTAGGATCGGGAA 60.456 63.158 0.00 0.00 0.00 3.97
1052 1132 1.941403 AAGGGGTCGTAGGATCGGGA 61.941 60.000 0.00 0.00 0.00 5.14
1099 1179 1.705873 GAATCTAGCTCGGAGGGGAA 58.294 55.000 7.20 0.00 0.00 3.97
1101 1181 0.178947 AGGAATCTAGCTCGGAGGGG 60.179 60.000 7.20 0.00 0.00 4.79
1200 1281 2.574824 GGTGTAGGTGGTAAGGGTGAAT 59.425 50.000 0.00 0.00 0.00 2.57
1209 1290 0.250793 CATTGGCGGTGTAGGTGGTA 59.749 55.000 0.00 0.00 0.00 3.25
1268 1350 3.645975 CGCGACCTGGCAAAACGT 61.646 61.111 0.00 0.00 0.00 3.99
1386 1483 2.191375 CCACTGCCCAGCGATCAT 59.809 61.111 0.00 0.00 0.00 2.45
1418 1515 0.393402 TACTTCGCGCTACCCAGAGA 60.393 55.000 5.56 0.00 0.00 3.10
1434 1531 5.812642 GCAGCAATATACCTATCGCAATACT 59.187 40.000 0.00 0.00 0.00 2.12
1436 1533 5.977635 AGCAGCAATATACCTATCGCAATA 58.022 37.500 0.00 0.00 0.00 1.90
1437 1534 4.836825 AGCAGCAATATACCTATCGCAAT 58.163 39.130 0.00 0.00 0.00 3.56
1440 1537 5.235186 CCATAAGCAGCAATATACCTATCGC 59.765 44.000 0.00 0.00 0.00 4.58
1441 1538 5.235186 GCCATAAGCAGCAATATACCTATCG 59.765 44.000 0.00 0.00 42.97 2.92
1502 1601 9.255304 CTAGACAGCAGGAATAAATTCTTCTAC 57.745 37.037 2.91 0.00 37.00 2.59
1521 1620 3.067461 CCATTCTCCGAAGTCCTAGACAG 59.933 52.174 0.00 0.00 34.60 3.51
1524 1623 2.243994 TCCCATTCTCCGAAGTCCTAGA 59.756 50.000 0.00 0.00 0.00 2.43
1525 1624 2.667470 TCCCATTCTCCGAAGTCCTAG 58.333 52.381 0.00 0.00 0.00 3.02
1679 1779 4.188247 TCAATGACTTAGGACTTGGACG 57.812 45.455 0.00 0.00 0.00 4.79
1700 1800 6.184789 ACCCACACAAATCTCCGTATAAAAT 58.815 36.000 0.00 0.00 0.00 1.82
1706 1806 4.829872 AATACCCACACAAATCTCCGTA 57.170 40.909 0.00 0.00 0.00 4.02
1749 1849 9.182214 AGTTATTGCACATCTAAATGACTCAAT 57.818 29.630 0.00 0.00 36.67 2.57
1798 1898 3.118261 TCCAGCCCTATGTTGATGACTTC 60.118 47.826 0.00 0.00 0.00 3.01
1912 2012 0.605589 GCTACAGCCCCAGAAAACGT 60.606 55.000 0.00 0.00 34.31 3.99
1913 2013 0.321653 AGCTACAGCCCCAGAAAACG 60.322 55.000 0.00 0.00 43.38 3.60
1931 2031 2.242043 ACAATGACAGAAAAGCCCCAG 58.758 47.619 0.00 0.00 0.00 4.45
1988 2088 3.298619 TGGAACATTGGATAAGCCCATG 58.701 45.455 0.00 0.00 43.66 3.66
1996 2096 9.120538 GTAGAATAGCTTTTGGAACATTGGATA 57.879 33.333 0.00 0.00 39.30 2.59
2109 2210 4.008330 CCAGTTGCATCAGACTGAAGATT 58.992 43.478 16.17 0.00 44.65 2.40
2115 2216 5.732528 GCATAAATCCAGTTGCATCAGACTG 60.733 44.000 8.95 8.95 42.21 3.51
2168 2269 9.691362 TCCACTAAAATGCTAATTTGAAGAAAC 57.309 29.630 0.00 0.00 36.11 2.78
2216 2317 6.488344 TGTGATGGCACTTTACACAAAGATTA 59.512 34.615 4.23 0.00 43.32 1.75
2271 2373 5.378332 AGAGAACGCTAGGATATGTACAGT 58.622 41.667 0.33 0.00 0.00 3.55
2328 2430 6.799925 CACCGTTACCATAGAAATGTCAAAAC 59.200 38.462 0.00 0.00 0.00 2.43
2339 2441 2.760092 GGTACCACACCGTTACCATAGA 59.240 50.000 7.15 0.00 37.63 1.98
2588 2692 2.180276 GACCTGCCCAAGAGAACTAGA 58.820 52.381 0.00 0.00 0.00 2.43
2589 2693 1.902508 TGACCTGCCCAAGAGAACTAG 59.097 52.381 0.00 0.00 0.00 2.57
2591 2695 1.366319 ATGACCTGCCCAAGAGAACT 58.634 50.000 0.00 0.00 0.00 3.01
2729 2833 7.540400 CGAATCAAACATAAGCAACAACCAATA 59.460 33.333 0.00 0.00 0.00 1.90
2889 2993 0.735978 TGGCTGTATCAAGCGACACG 60.736 55.000 0.00 0.00 44.52 4.49
3045 3149 8.991783 ATGAAGATGTCACAAGGATCAAATAT 57.008 30.769 0.00 0.00 39.72 1.28
3087 3191 5.010719 CCCTCCGTAAAGACATATAAGAGCA 59.989 44.000 0.00 0.00 0.00 4.26
3095 3199 6.781014 ACATCTAATCCCTCCGTAAAGACATA 59.219 38.462 0.00 0.00 0.00 2.29
3098 3202 5.532664 ACATCTAATCCCTCCGTAAAGAC 57.467 43.478 0.00 0.00 0.00 3.01
3158 3262 9.319143 GCTATTTGTATACTGTCTCAACTGAAT 57.681 33.333 4.17 0.00 0.00 2.57
3396 3610 1.749634 ACCTGTATTCTTCGAGGGACG 59.250 52.381 0.00 0.00 44.09 4.79
3398 3612 3.056107 CACAACCTGTATTCTTCGAGGGA 60.056 47.826 0.00 0.00 0.00 4.20
3422 3636 6.940298 TGGTTTGGACTAAAGAATCTAACAGG 59.060 38.462 0.00 0.00 0.00 4.00
3438 3652 4.215613 AGAGCTCGTTTAATTGGTTTGGAC 59.784 41.667 8.37 0.00 0.00 4.02
3496 3712 3.525199 AGGATGCTAAAGGAAGTCCATGT 59.475 43.478 0.00 0.00 38.89 3.21
3541 3757 1.009829 CCTCGTTAACTGCATCAGCC 58.990 55.000 3.71 0.00 41.13 4.85
3585 3901 0.978151 TTAGCGGGAACTAGCCAACA 59.022 50.000 0.00 0.00 33.10 3.33
3611 3927 9.638239 GTTGTTCCTGCAAGAATATTTCAATTA 57.362 29.630 0.13 0.00 34.07 1.40
3793 4109 1.068055 GCCTTGCCAGAGTTGTTGATG 60.068 52.381 0.00 0.00 0.00 3.07
3840 4156 3.286751 TGCACAGCGACTTTGGCC 61.287 61.111 0.00 0.00 0.00 5.36
3936 4252 2.436824 GAGGGGCTTGACTTCGCC 60.437 66.667 0.00 0.00 45.55 5.54
3942 4258 2.419436 GCTTAGAGAAGAGGGGCTTGAC 60.419 54.545 0.00 0.00 36.83 3.18
3952 4268 2.313342 ACCCCTGAGAGCTTAGAGAAGA 59.687 50.000 0.00 0.00 34.25 2.87
4181 4504 1.570979 GGGGTGGGAAATGGAAGAGAT 59.429 52.381 0.00 0.00 0.00 2.75
4190 4513 4.415179 AGTTCAAAATTTGGGGTGGGAAAT 59.585 37.500 5.83 0.00 0.00 2.17
4197 4520 4.037222 ACAGGAAGTTCAAAATTTGGGGT 58.963 39.130 5.83 0.00 0.00 4.95
4198 4521 4.379652 CACAGGAAGTTCAAAATTTGGGG 58.620 43.478 5.83 0.00 0.00 4.96
4209 4532 5.725325 AAGTAGACTACCACAGGAAGTTC 57.275 43.478 9.06 0.00 0.00 3.01
4215 4538 3.963428 AGCAAAGTAGACTACCACAGG 57.037 47.619 9.06 0.00 0.00 4.00
4223 4546 4.090090 TCTTCTGCCTAGCAAAGTAGACT 58.910 43.478 9.63 0.00 38.41 3.24
4233 4558 5.809719 GGCATTAATATCTTCTGCCTAGC 57.190 43.478 6.72 0.00 46.97 3.42
4239 4564 9.064706 ACTCAATTCAGGCATTAATATCTTCTG 57.935 33.333 0.00 0.00 0.00 3.02
4250 4579 3.771216 ACAAGGACTCAATTCAGGCATT 58.229 40.909 0.00 0.00 0.00 3.56
4269 4598 6.609876 AGATGTGTATATTATGGCCCAAACA 58.390 36.000 0.00 0.00 0.00 2.83
4271 4600 7.293828 TCAAGATGTGTATATTATGGCCCAAA 58.706 34.615 0.00 0.00 0.00 3.28
4278 4607 8.298030 TCGCAGTTCAAGATGTGTATATTATG 57.702 34.615 0.00 0.00 0.00 1.90
4329 4658 3.142796 GTTTGCACGACACTTTCCG 57.857 52.632 0.00 0.00 0.00 4.30
4346 4675 3.071206 AGCCGATCAGCCTCACGT 61.071 61.111 0.00 0.00 0.00 4.49
4374 4703 2.580966 ACGTAAATCTCCTCTTCCGC 57.419 50.000 0.00 0.00 0.00 5.54
4375 4704 4.091509 CACAAACGTAAATCTCCTCTTCCG 59.908 45.833 0.00 0.00 0.00 4.30
4376 4705 4.142881 GCACAAACGTAAATCTCCTCTTCC 60.143 45.833 0.00 0.00 0.00 3.46
4381 4710 2.812011 GTGGCACAAACGTAAATCTCCT 59.188 45.455 13.86 0.00 44.16 3.69
4545 4874 2.758089 GCCGGAGTAGAGCGACGAA 61.758 63.158 5.05 0.00 0.00 3.85
4846 5180 2.203070 GCGCCATTGACGAGGGAT 60.203 61.111 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.