Multiple sequence alignment - TraesCS3D01G422300

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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 TraesCS3D01G422300 chr3D 100.000 4301 0 0 1 4301 534234224 534238524 0.000000e+00 7943.0
1 TraesCS3D01G422300 chr3D 95.960 99 4 0 3197 3295 534237323 534237421 1.240000e-35 161.0
2 TraesCS3D01G422300 chr3D 95.960 99 4 0 3100 3198 534237420 534237518 1.240000e-35 161.0
3 TraesCS3D01G422300 chr3D 91.667 60 5 0 761 820 534234932 534234991 2.760000e-12 84.2
4 TraesCS3D01G422300 chr3D 91.667 60 5 0 709 768 534234984 534235043 2.760000e-12 84.2
5 TraesCS3D01G422300 chr3B 96.932 3227 85 10 556 3779 706355582 706358797 0.000000e+00 5398.0
6 TraesCS3D01G422300 chr3B 91.360 544 21 5 3784 4301 706360263 706360806 0.000000e+00 721.0
7 TraesCS3D01G422300 chr3B 96.970 99 3 0 3197 3295 706358129 706358227 2.660000e-37 167.0
8 TraesCS3D01G422300 chr3B 96.970 99 3 0 3100 3198 706358226 706358324 2.660000e-37 167.0
9 TraesCS3D01G422300 chr3B 91.667 60 5 0 761 820 706355735 706355794 2.760000e-12 84.2
10 TraesCS3D01G422300 chr3B 91.667 60 5 0 709 768 706355787 706355846 2.760000e-12 84.2
11 TraesCS3D01G422300 chr3A 96.628 1038 29 5 556 1589 669954048 669955083 0.000000e+00 1718.0
12 TraesCS3D01G422300 chr3A 91.977 511 15 5 3817 4301 669972482 669972992 0.000000e+00 693.0
13 TraesCS3D01G422300 chr3A 91.389 511 18 5 3817 4301 669955173 669955683 0.000000e+00 676.0
14 TraesCS3D01G422300 chr3A 91.389 511 18 5 3817 4301 669983786 669983276 0.000000e+00 676.0
15 TraesCS3D01G422300 chr3A 88.333 60 7 0 761 820 669954202 669954261 5.970000e-09 73.1
16 TraesCS3D01G422300 chr7D 98.564 557 8 0 1 557 596029218 596029774 0.000000e+00 985.0
17 TraesCS3D01G422300 chr7D 98.561 556 8 0 1 556 69677088 69677643 0.000000e+00 983.0
18 TraesCS3D01G422300 chr7D 98.561 556 8 0 1 556 529968436 529967881 0.000000e+00 983.0
19 TraesCS3D01G422300 chr1D 98.227 564 9 1 1 564 7745865 7745303 0.000000e+00 985.0
20 TraesCS3D01G422300 chr1D 98.561 556 8 0 1 556 457628117 457628672 0.000000e+00 983.0
21 TraesCS3D01G422300 chr1D 98.561 556 8 0 1 556 492622826 492622271 0.000000e+00 983.0
22 TraesCS3D01G422300 chr1D 98.384 557 9 0 1 557 447842987 447843543 0.000000e+00 979.0
23 TraesCS3D01G422300 chr6D 98.561 556 8 0 1 556 46008947 46009502 0.000000e+00 983.0
24 TraesCS3D01G422300 chr5D 97.557 573 10 4 1 572 52606153 52605584 0.000000e+00 977.0


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 TraesCS3D01G422300 chr3D 534234224 534238524 4300 False 1686.680000 7943 95.050800 1 4301 5 chr3D.!!$F1 4300
1 TraesCS3D01G422300 chr3B 706355582 706360806 5224 False 1103.566667 5398 94.261000 556 4301 6 chr3B.!!$F1 3745
2 TraesCS3D01G422300 chr3A 669954048 669955683 1635 False 822.366667 1718 92.116667 556 4301 3 chr3A.!!$F2 3745
3 TraesCS3D01G422300 chr3A 669972482 669972992 510 False 693.000000 693 91.977000 3817 4301 1 chr3A.!!$F1 484
4 TraesCS3D01G422300 chr3A 669983276 669983786 510 True 676.000000 676 91.389000 3817 4301 1 chr3A.!!$R1 484
5 TraesCS3D01G422300 chr7D 596029218 596029774 556 False 985.000000 985 98.564000 1 557 1 chr7D.!!$F2 556
6 TraesCS3D01G422300 chr7D 69677088 69677643 555 False 983.000000 983 98.561000 1 556 1 chr7D.!!$F1 555
7 TraesCS3D01G422300 chr7D 529967881 529968436 555 True 983.000000 983 98.561000 1 556 1 chr7D.!!$R1 555
8 TraesCS3D01G422300 chr1D 7745303 7745865 562 True 985.000000 985 98.227000 1 564 1 chr1D.!!$R1 563
9 TraesCS3D01G422300 chr1D 457628117 457628672 555 False 983.000000 983 98.561000 1 556 1 chr1D.!!$F2 555
10 TraesCS3D01G422300 chr1D 492622271 492622826 555 True 983.000000 983 98.561000 1 556 1 chr1D.!!$R2 555
11 TraesCS3D01G422300 chr1D 447842987 447843543 556 False 979.000000 979 98.384000 1 557 1 chr1D.!!$F1 556
12 TraesCS3D01G422300 chr6D 46008947 46009502 555 False 983.000000 983 98.561000 1 556 1 chr6D.!!$F1 555
13 TraesCS3D01G422300 chr5D 52605584 52606153 569 True 977.000000 977 97.557000 1 572 1 chr5D.!!$R1 571

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
336 337 0.037734 CTTTAGTCCCGGTTGGCCTT 59.962 55.000 3.32 0.0 0.00 4.35 F
488 489 1.271656 CCGAACCGTGACTAAAGACCT 59.728 52.381 0.00 0.0 0.00 3.85 F
1899 1904 1.590525 CGTGCATCATGGCAATGGC 60.591 57.895 0.00 0.0 46.93 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2092 2097 0.179029 CCCACCCCGTCACCAATATC 60.179 60.0 0.0 0.0 0.0 1.63 R
2103 2108 1.637724 TATAACCCAAGCCCACCCCG 61.638 60.0 0.0 0.0 0.0 5.73 R
3676 3682 0.183971 CCCCAAACACCACCACTACA 59.816 55.0 0.0 0.0 0.0 2.74 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
91 92 0.464373 GGCTCTCGGGCATTTCATCA 60.464 55.000 0.00 0.00 40.53 3.07
289 290 4.826248 GGCCAACCGGGACTAAAA 57.174 55.556 6.32 0.00 43.78 1.52
336 337 0.037734 CTTTAGTCCCGGTTGGCCTT 59.962 55.000 3.32 0.00 0.00 4.35
476 477 2.679287 GGTCTCCTCCCGAACCGT 60.679 66.667 0.00 0.00 0.00 4.83
488 489 1.271656 CCGAACCGTGACTAAAGACCT 59.728 52.381 0.00 0.00 0.00 3.85
857 859 6.831664 ATTATACACCATCCTCCTCTTTGT 57.168 37.500 0.00 0.00 0.00 2.83
994 998 9.652114 AATATGAAAAGGCATCTAGGATTTCTT 57.348 29.630 0.00 0.00 0.00 2.52
1180 1185 4.574892 TCGTGAGATAATTTTGGCTGTCA 58.425 39.130 0.00 0.00 33.31 3.58
1211 1216 4.096833 TGAGCAGTTGGATTATGTTGATGC 59.903 41.667 0.00 0.00 0.00 3.91
1213 1218 4.337555 AGCAGTTGGATTATGTTGATGCTC 59.662 41.667 0.00 0.00 36.85 4.26
1252 1257 3.237628 GAGCAGGACGCAAAATTTTCTC 58.762 45.455 0.00 0.00 46.13 2.87
1509 1514 6.405538 TGAAGGTTTCTGCTTTTTGAACAAT 58.594 32.000 0.00 0.00 0.00 2.71
1721 1726 5.627780 CCGGCAAGTAAACTACAAAAATCAC 59.372 40.000 0.00 0.00 0.00 3.06
1899 1904 1.590525 CGTGCATCATGGCAATGGC 60.591 57.895 0.00 0.00 46.93 4.40
1906 1911 3.454573 ATGGCAATGGCACGCAGG 61.455 61.111 12.83 0.00 41.84 4.85
1942 1947 6.934083 TGGAAGCAAACAAGTTCTTTTCTTTT 59.066 30.769 0.00 0.00 0.00 2.27
1943 1948 7.117667 TGGAAGCAAACAAGTTCTTTTCTTTTC 59.882 33.333 0.00 0.00 0.00 2.29
2054 2059 4.394920 ACCGTTAATTATTGTGTGCAGGAG 59.605 41.667 0.00 0.00 0.00 3.69
2055 2060 4.634004 CCGTTAATTATTGTGTGCAGGAGA 59.366 41.667 0.00 0.00 0.00 3.71
2062 2067 2.228545 TGTGTGCAGGAGAGATCTCT 57.771 50.000 25.39 25.39 42.48 3.10
2081 2086 5.678583 TCTCTCCTATCCTGCATCAAAAAG 58.321 41.667 0.00 0.00 0.00 2.27
2092 2097 4.459606 TGCATCAAAAAGTAGCGTAAACG 58.540 39.130 0.00 0.00 43.27 3.60
2103 2108 5.039333 AGTAGCGTAAACGATATTGGTGAC 58.961 41.667 6.71 0.00 42.35 3.67
2124 2129 1.219469 GGGGTGGGCTTGGGTTATAAT 59.781 52.381 0.00 0.00 0.00 1.28
2130 2135 6.957606 GGGTGGGCTTGGGTTATAATATAAAT 59.042 38.462 0.00 0.00 0.00 1.40
2172 2177 7.218204 GGTTTTAATGATGTCGACATGCTTTAC 59.782 37.037 34.48 19.08 36.57 2.01
2192 2197 1.781429 CGTATGCGATCAACTTCTCGG 59.219 52.381 0.00 0.00 41.33 4.63
2273 2278 9.601217 TGCTGGTAAGAAATCTAATTCTAGTTC 57.399 33.333 0.00 0.00 38.69 3.01
2300 2305 6.264292 TGGTTTTGTGTTTGCTATCTACATGT 59.736 34.615 2.69 2.69 0.00 3.21
2434 2439 4.514441 CCTCTATTGTAAATGCTGCTCTGG 59.486 45.833 0.00 0.00 0.00 3.86
2531 2536 7.339466 GGAAAAATGGTATTAGCTCTTGAAGGA 59.661 37.037 0.00 0.00 0.00 3.36
2537 2542 5.544562 GGTATTAGCTCTTGAAGGAGGGTAT 59.455 44.000 0.00 0.00 34.21 2.73
2609 2614 2.420687 GGGAGATGAAGATGCGTTCCTT 60.421 50.000 0.00 0.00 0.00 3.36
2657 2662 1.632422 CATTCAAAAGCACCATCCGC 58.368 50.000 0.00 0.00 0.00 5.54
2669 2674 1.299541 CCATCCGCACAGTCAATACC 58.700 55.000 0.00 0.00 0.00 2.73
2670 2675 1.406751 CCATCCGCACAGTCAATACCA 60.407 52.381 0.00 0.00 0.00 3.25
2705 2710 8.193953 ACTTGAGATTATGTTGGGATGTTTTT 57.806 30.769 0.00 0.00 0.00 1.94
2878 2884 4.379082 GGTTCACAGGGTTTAGTTATTGCG 60.379 45.833 0.00 0.00 0.00 4.85
2879 2885 3.340034 TCACAGGGTTTAGTTATTGCGG 58.660 45.455 0.00 0.00 0.00 5.69
2929 2935 4.705507 ACACCATCGTTGTGAGATACTAGT 59.294 41.667 0.00 0.00 37.18 2.57
2976 2982 5.882557 AGTTTATCAGTGCTGTATTTGAGGG 59.117 40.000 0.00 0.00 0.00 4.30
3041 3047 2.882927 TCCTTGTATTCGATGACCCG 57.117 50.000 0.00 0.00 0.00 5.28
3125 3131 8.519492 GCTTTTTGCTTGACATCTTATTTGTA 57.481 30.769 0.00 0.00 38.95 2.41
3190 3196 8.624776 GGCTTATACTCTAGTTTCATTTTGCAT 58.375 33.333 0.00 0.00 0.00 3.96
3240 3246 9.685276 TTATTTGTGTGATTTCTACCATCTGAT 57.315 29.630 0.00 0.00 0.00 2.90
3318 3324 2.264120 GAGGCCCAAGCTCCTCTTCC 62.264 65.000 11.12 0.00 44.19 3.46
3373 3379 1.446792 CAGTGGTGCTCCAGCTACG 60.447 63.158 7.99 0.00 45.24 3.51
3382 3388 0.457443 CTCCAGCTACGTCATGAGCA 59.543 55.000 10.48 0.00 41.36 4.26
3383 3389 0.894835 TCCAGCTACGTCATGAGCAA 59.105 50.000 10.48 0.00 41.36 3.91
3398 3404 5.410746 TCATGAGCAATTGAGAGTGAACTTC 59.589 40.000 10.34 0.00 0.00 3.01
3400 3406 4.067896 GAGCAATTGAGAGTGAACTTCCA 58.932 43.478 10.34 0.00 0.00 3.53
3403 3409 4.456911 GCAATTGAGAGTGAACTTCCATGA 59.543 41.667 10.34 0.00 0.00 3.07
3404 3410 5.618640 GCAATTGAGAGTGAACTTCCATGAC 60.619 44.000 10.34 0.00 0.00 3.06
3406 3412 4.263018 TGAGAGTGAACTTCCATGACTG 57.737 45.455 0.00 0.00 0.00 3.51
3407 3413 3.643320 TGAGAGTGAACTTCCATGACTGT 59.357 43.478 0.00 0.00 0.00 3.55
3409 3415 3.070018 GAGTGAACTTCCATGACTGTGG 58.930 50.000 0.00 0.00 40.76 4.17
3410 3416 2.439507 AGTGAACTTCCATGACTGTGGT 59.560 45.455 0.00 0.00 40.27 4.16
3411 3417 3.117888 AGTGAACTTCCATGACTGTGGTT 60.118 43.478 0.00 0.00 40.27 3.67
3413 3419 4.097892 GTGAACTTCCATGACTGTGGTTTT 59.902 41.667 0.00 0.00 40.27 2.43
3414 3420 4.097741 TGAACTTCCATGACTGTGGTTTTG 59.902 41.667 0.00 0.00 40.27 2.44
3415 3421 2.958355 ACTTCCATGACTGTGGTTTTGG 59.042 45.455 0.00 0.00 40.27 3.28
3416 3422 2.746279 TCCATGACTGTGGTTTTGGT 57.254 45.000 0.00 0.00 40.27 3.67
3417 3423 3.866703 TCCATGACTGTGGTTTTGGTA 57.133 42.857 0.00 0.00 40.27 3.25
3418 3424 3.482436 TCCATGACTGTGGTTTTGGTAC 58.518 45.455 0.00 0.00 40.27 3.34
3419 3425 3.137544 TCCATGACTGTGGTTTTGGTACT 59.862 43.478 0.00 0.00 40.27 2.73
3420 3426 3.502211 CCATGACTGTGGTTTTGGTACTC 59.498 47.826 0.00 0.00 34.46 2.59
3473 3479 3.668447 TCTTGTGAGAGCATTTCTGGAC 58.332 45.455 0.00 0.00 35.87 4.02
3490 3496 4.929808 TCTGGACGAGTTCTCTTATTTTGC 59.070 41.667 0.00 0.00 0.00 3.68
3497 3503 5.062809 CGAGTTCTCTTATTTTGCTCACTCC 59.937 44.000 0.00 0.00 0.00 3.85
3538 3544 5.872070 TGTCAAGTGAATATATGTCGCACAA 59.128 36.000 0.00 0.00 32.16 3.33
3593 3599 1.001517 ACATGCGTTATGGTGCCCA 60.002 52.632 0.00 0.00 41.25 5.36
3596 3602 1.136695 CATGCGTTATGGTGCCCAAAT 59.863 47.619 0.00 0.00 36.95 2.32
3597 3603 1.261480 TGCGTTATGGTGCCCAAATT 58.739 45.000 0.00 0.00 36.95 1.82
3675 3681 3.638627 TGATCATGCCGACTCTGTATTCT 59.361 43.478 0.00 0.00 0.00 2.40
3676 3682 4.100035 TGATCATGCCGACTCTGTATTCTT 59.900 41.667 0.00 0.00 0.00 2.52
3703 3709 0.768622 TGGTGTTTGGGGTCGATCTT 59.231 50.000 0.00 0.00 0.00 2.40
3708 3714 2.304470 TGTTTGGGGTCGATCTTGATCA 59.696 45.455 10.69 0.00 0.00 2.92
3711 3717 0.755686 GGGGTCGATCTTGATCAGCT 59.244 55.000 10.69 0.00 0.00 4.24
3733 3739 6.204882 AGCTTGTGGTTTCAGTTGTATCTTAC 59.795 38.462 0.00 0.00 0.00 2.34
3743 3749 1.563924 TGTATCTTACGCAGGGGTGT 58.436 50.000 0.00 0.00 41.49 4.16
3752 3758 1.442148 GCAGGGGTGTATCTCCGAC 59.558 63.158 0.00 0.00 42.70 4.79
3787 5254 4.588899 TGGCACACATTAAGAAGCTGTAT 58.411 39.130 0.00 0.00 0.00 2.29
3815 5282 6.472887 TGTTGTCAGATAAGTTAAGAAGGGG 58.527 40.000 0.00 0.00 0.00 4.79
3840 5307 0.902984 TCCAGTGCTACGGTCCATGT 60.903 55.000 0.00 0.00 0.00 3.21
3988 5455 4.504097 GTCTTTGCAAAATCACAACAGGTC 59.496 41.667 13.84 0.00 0.00 3.85
4011 5479 0.396417 ACATCTCTCCTCCAGACCCG 60.396 60.000 0.00 0.00 0.00 5.28
4023 5491 2.022934 CCAGACCCGTAGTAGTTCTCC 58.977 57.143 0.00 0.00 0.00 3.71
4110 5578 9.083422 TCATACCAACAAAATTCACAGGAATAA 57.917 29.630 0.00 0.00 42.87 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 3.149196 CTCCTATGCACACAAGGTGTTT 58.851 45.455 0.00 0.00 45.08 2.83
336 337 1.669760 CCTTTAGTCGCGGTTGGCA 60.670 57.895 6.13 0.00 43.84 4.92
476 477 4.056050 GCGACAAAAGAGGTCTTTAGTCA 58.944 43.478 5.41 0.00 44.69 3.41
488 489 4.734134 TCGAACCGCGACAAAAGA 57.266 50.000 8.23 0.00 45.59 2.52
591 592 9.783256 GTGAATATACACAAACCTAAATTGTCC 57.217 33.333 0.00 0.00 38.90 4.02
638 639 6.618287 TTCCAATATTTCATAAGGTCAGCG 57.382 37.500 0.00 0.00 0.00 5.18
857 859 8.614469 AAAAAGGAAAAATGTGTCAAAGTTCA 57.386 26.923 0.00 0.00 0.00 3.18
1117 1121 3.117888 TCCCTCTCAGTTCTGCAAAAAGT 60.118 43.478 0.00 0.00 0.00 2.66
1171 1176 2.942752 GCTCAGGATCATTGACAGCCAA 60.943 50.000 0.00 0.00 39.41 4.52
1180 1185 3.947612 ATCCAACTGCTCAGGATCATT 57.052 42.857 1.66 0.00 37.61 2.57
1211 1216 2.169978 TCCTCATCTGTCATTGGCAGAG 59.830 50.000 23.93 16.20 44.86 3.35
1213 1218 2.562635 CTCCTCATCTGTCATTGGCAG 58.437 52.381 12.12 12.12 35.43 4.85
1252 1257 1.878953 ACACTAACTCCGGCAACTTG 58.121 50.000 0.00 0.00 0.00 3.16
1615 1620 6.338146 AGCATGTATCTTGAGCTTACGTTTA 58.662 36.000 0.00 0.00 29.98 2.01
1721 1726 9.784531 ACAGGACATTTCTATATAAACTGATGG 57.215 33.333 0.00 0.00 0.00 3.51
1867 1872 0.584396 TGCACGTCGAAATCAACCAC 59.416 50.000 0.00 0.00 0.00 4.16
1899 1904 3.334691 TCCATAAAAGAGTTCCTGCGTG 58.665 45.455 0.00 0.00 0.00 5.34
1906 1911 7.203218 ACTTGTTTGCTTCCATAAAAGAGTTC 58.797 34.615 0.00 0.00 0.00 3.01
1942 1947 6.553476 ACACTAATAGCATACCTATGTGTGGA 59.447 38.462 14.50 0.00 39.89 4.02
1943 1948 6.759272 ACACTAATAGCATACCTATGTGTGG 58.241 40.000 14.50 0.00 39.89 4.17
2054 2059 4.343231 TGATGCAGGATAGGAGAGATCTC 58.657 47.826 15.29 15.29 42.14 2.75
2055 2060 4.401048 TGATGCAGGATAGGAGAGATCT 57.599 45.455 0.00 0.00 0.00 2.75
2062 2067 5.126067 GCTACTTTTTGATGCAGGATAGGA 58.874 41.667 0.00 0.00 0.00 2.94
2081 2086 4.085924 CGTCACCAATATCGTTTACGCTAC 60.086 45.833 0.00 0.00 39.60 3.58
2092 2097 0.179029 CCCACCCCGTCACCAATATC 60.179 60.000 0.00 0.00 0.00 1.63
2103 2108 1.637724 TATAACCCAAGCCCACCCCG 61.638 60.000 0.00 0.00 0.00 5.73
2124 2129 9.807921 AAACCTTTCTTGAGAGGAACATTTATA 57.192 29.630 13.25 0.00 36.84 0.98
2130 2135 7.777910 TCATTAAAACCTTTCTTGAGAGGAACA 59.222 33.333 13.25 0.00 36.84 3.18
2172 2177 1.781429 CCGAGAAGTTGATCGCATACG 59.219 52.381 2.28 0.00 37.61 3.06
2207 2212 4.143389 CGAACACTACTTCTGGCTTAAACG 60.143 45.833 0.00 0.00 0.00 3.60
2273 2278 4.223320 AGATAGCAAACACAAAACCACG 57.777 40.909 0.00 0.00 0.00 4.94
2635 2640 2.230992 CGGATGGTGCTTTTGAATGGAA 59.769 45.455 0.00 0.00 0.00 3.53
2636 2641 1.818060 CGGATGGTGCTTTTGAATGGA 59.182 47.619 0.00 0.00 0.00 3.41
2657 2662 6.317140 AGTTATGCTTGATGGTATTGACTGTG 59.683 38.462 0.00 0.00 0.00 3.66
2803 2809 4.890158 TTGACCTCTCTTCACTGCATAA 57.110 40.909 0.00 0.00 0.00 1.90
2878 2884 4.258543 TGTTGTAACCTATGCTTAGCACC 58.741 43.478 9.82 0.00 43.04 5.01
2879 2885 5.873179 TTGTTGTAACCTATGCTTAGCAC 57.127 39.130 9.82 0.00 43.04 4.40
2976 2982 2.484264 AGAAAACAATCTGTACCGCAGC 59.516 45.455 0.00 0.00 44.66 5.25
3125 3131 3.845781 ACGGCAGATGGTAGAAATCAT 57.154 42.857 0.00 0.00 0.00 2.45
3305 3311 0.540923 CCAGGAGGAAGAGGAGCTTG 59.459 60.000 0.00 0.00 36.83 4.01
3318 3324 1.064825 ACCACCTAAACCACCAGGAG 58.935 55.000 0.00 0.00 38.69 3.69
3369 3375 4.267214 CACTCTCAATTGCTCATGACGTAG 59.733 45.833 0.00 0.00 0.00 3.51
3373 3379 4.694509 AGTTCACTCTCAATTGCTCATGAC 59.305 41.667 0.00 0.00 0.00 3.06
3382 3388 5.704515 CAGTCATGGAAGTTCACTCTCAATT 59.295 40.000 5.01 0.00 0.00 2.32
3383 3389 5.221803 ACAGTCATGGAAGTTCACTCTCAAT 60.222 40.000 5.01 0.00 0.00 2.57
3398 3404 3.486383 AGTACCAAAACCACAGTCATGG 58.514 45.455 0.00 0.00 46.10 3.66
3400 3406 4.431416 TGAGTACCAAAACCACAGTCAT 57.569 40.909 0.00 0.00 0.00 3.06
3403 3409 3.882888 CACATGAGTACCAAAACCACAGT 59.117 43.478 0.00 0.00 0.00 3.55
3404 3410 3.882888 ACACATGAGTACCAAAACCACAG 59.117 43.478 0.00 0.00 0.00 3.66
3406 3412 4.911514 AACACATGAGTACCAAAACCAC 57.088 40.909 0.00 0.00 0.00 4.16
3407 3413 5.067153 CAGAAACACATGAGTACCAAAACCA 59.933 40.000 0.00 0.00 0.00 3.67
3409 3415 6.131544 ACAGAAACACATGAGTACCAAAAC 57.868 37.500 0.00 0.00 0.00 2.43
3410 3416 6.767524 AACAGAAACACATGAGTACCAAAA 57.232 33.333 0.00 0.00 0.00 2.44
3411 3417 6.151985 ACAAACAGAAACACATGAGTACCAAA 59.848 34.615 0.00 0.00 0.00 3.28
3413 3419 5.189928 ACAAACAGAAACACATGAGTACCA 58.810 37.500 0.00 0.00 0.00 3.25
3414 3420 5.751243 ACAAACAGAAACACATGAGTACC 57.249 39.130 0.00 0.00 0.00 3.34
3415 3421 6.551736 ACAACAAACAGAAACACATGAGTAC 58.448 36.000 0.00 0.00 0.00 2.73
3416 3422 6.751514 ACAACAAACAGAAACACATGAGTA 57.248 33.333 0.00 0.00 0.00 2.59
3417 3423 5.643379 ACAACAAACAGAAACACATGAGT 57.357 34.783 0.00 0.00 0.00 3.41
3418 3424 6.949578 AAACAACAAACAGAAACACATGAG 57.050 33.333 0.00 0.00 0.00 2.90
3419 3425 7.116090 CAGAAAACAACAAACAGAAACACATGA 59.884 33.333 0.00 0.00 0.00 3.07
3420 3426 7.228840 CAGAAAACAACAAACAGAAACACATG 58.771 34.615 0.00 0.00 0.00 3.21
3462 3468 2.966050 AGAGAACTCGTCCAGAAATGC 58.034 47.619 0.00 0.00 34.09 3.56
3473 3479 5.062809 GGAGTGAGCAAAATAAGAGAACTCG 59.937 44.000 0.00 0.00 33.87 4.18
3490 3496 8.037758 ACAGAAATCTTTATGTAGTGGAGTGAG 58.962 37.037 1.31 0.00 40.45 3.51
3497 3503 9.208022 TCACTTGACAGAAATCTTTATGTAGTG 57.792 33.333 18.47 18.47 43.43 2.74
3571 3577 0.808125 GCACCATAACGCATGTCCAA 59.192 50.000 0.00 0.00 32.21 3.53
3593 3599 3.488778 TGCCATTGCCACTTCAAATTT 57.511 38.095 0.00 0.00 36.33 1.82
3596 3602 1.761784 AGTTGCCATTGCCACTTCAAA 59.238 42.857 0.00 0.00 40.32 2.69
3597 3603 1.340889 GAGTTGCCATTGCCACTTCAA 59.659 47.619 0.00 0.00 43.02 2.69
3618 3624 1.466856 ATAACCACTGTGCATGGCTG 58.533 50.000 4.68 0.00 41.31 4.85
3656 3662 3.195610 ACAAGAATACAGAGTCGGCATGA 59.804 43.478 0.00 0.00 0.00 3.07
3675 3681 1.410365 CCCCAAACACCACCACTACAA 60.410 52.381 0.00 0.00 0.00 2.41
3676 3682 0.183971 CCCCAAACACCACCACTACA 59.816 55.000 0.00 0.00 0.00 2.74
3703 3709 3.213206 ACTGAAACCACAAGCTGATCA 57.787 42.857 0.00 0.00 0.00 2.92
3708 3714 4.718961 AGATACAACTGAAACCACAAGCT 58.281 39.130 0.00 0.00 0.00 3.74
3711 3717 5.049954 GCGTAAGATACAACTGAAACCACAA 60.050 40.000 0.00 0.00 43.02 3.33
3733 3739 2.125326 TCGGAGATACACCCCTGCG 61.125 63.158 0.00 0.00 43.93 5.18
3743 3749 0.467474 AGCACCCATCGTCGGAGATA 60.467 55.000 0.00 0.00 40.67 1.98
3773 3779 8.165239 TGACAACAAACATACAGCTTCTTAAT 57.835 30.769 0.00 0.00 0.00 1.40
3779 3785 7.445402 ACTTATCTGACAACAAACATACAGCTT 59.555 33.333 0.00 0.00 0.00 3.74
3780 3786 6.936900 ACTTATCTGACAACAAACATACAGCT 59.063 34.615 0.00 0.00 0.00 4.24
3781 3787 7.133891 ACTTATCTGACAACAAACATACAGC 57.866 36.000 0.00 0.00 0.00 4.40
3787 5254 8.836413 CCTTCTTAACTTATCTGACAACAAACA 58.164 33.333 0.00 0.00 0.00 2.83
3815 5282 3.181469 TGGACCGTAGCACTGGATATTTC 60.181 47.826 0.00 0.00 0.00 2.17
3840 5307 3.181451 GGTCTTGGAGCATGGTATCATCA 60.181 47.826 0.00 0.00 0.00 3.07
3988 5455 2.031120 GTCTGGAGGAGAGATGTGGAG 58.969 57.143 0.00 0.00 0.00 3.86
4011 5479 5.152804 GTGTGAGAAACGGAGAACTACTAC 58.847 45.833 0.00 0.00 0.00 2.73
4023 5491 4.966850 AGTATTTGTCGTGTGAGAAACG 57.033 40.909 0.00 0.00 39.81 3.60
4110 5578 9.097257 CTTCACATAAATGTTTTGAAGTGGTTT 57.903 29.630 11.08 0.00 39.39 3.27


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

AutoCloner maintained by Alex Coulton.