Multiple sequence alignment - TraesCS1A01G127400

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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 TraesCS1A01G127400 chr1A 100.000 4551 0 0 1 4551 154573688 154578238 0.000000e+00 8405.0
1 TraesCS1A01G127400 chr1A 93.333 90 6 0 3091 3180 350017095 350017184 2.860000e-27 134.0
2 TraesCS1A01G127400 chr1A 87.952 83 6 3 3199 3281 66445594 66445516 1.350000e-15 95.3
3 TraesCS1A01G127400 chr1D 93.371 4390 187 55 7 4348 138344122 138348455 0.000000e+00 6399.0
4 TraesCS1A01G127400 chr1D 92.222 90 7 0 3091 3180 277362519 277362608 1.330000e-25 128.0
5 TraesCS1A01G127400 chr1D 78.906 128 22 4 421 545 415398335 415398210 1.050000e-11 82.4
6 TraesCS1A01G127400 chr1B 93.627 2542 129 24 2022 4551 212750046 212747526 0.000000e+00 3766.0
7 TraesCS1A01G127400 chr1B 93.891 1244 38 14 794 2023 212751348 212750129 0.000000e+00 1842.0
8 TraesCS1A01G127400 chr1B 89.249 493 39 7 7 495 212797181 212796699 5.040000e-169 604.0
9 TraesCS1A01G127400 chr4B 97.674 86 2 0 3094 3179 41531501 41531416 1.020000e-31 148.0
10 TraesCS1A01G127400 chr7D 94.444 90 5 0 3091 3180 59711291 59711380 6.140000e-29 139.0
11 TraesCS1A01G127400 chr7D 92.958 71 5 0 3199 3269 383900900 383900830 2.240000e-18 104.0
12 TraesCS1A01G127400 chr6D 94.382 89 5 0 3092 3180 88776583 88776495 2.210000e-28 137.0
13 TraesCS1A01G127400 chr6D 80.247 81 15 1 491 571 296823667 296823588 4.920000e-05 60.2
14 TraesCS1A01G127400 chr2B 95.294 85 4 0 3094 3178 139072831 139072915 7.940000e-28 135.0
15 TraesCS1A01G127400 chr2B 92.958 71 5 0 3199 3269 308719690 308719760 2.240000e-18 104.0
16 TraesCS1A01G127400 chr2B 76.000 150 27 7 428 572 769270837 769270692 8.170000e-08 69.4
17 TraesCS1A01G127400 chr2B 74.468 141 31 4 421 557 726082084 726081945 6.360000e-04 56.5
18 TraesCS1A01G127400 chr4A 93.182 88 6 0 3094 3181 27643610 27643523 3.690000e-26 130.0
19 TraesCS1A01G127400 chr2D 94.366 71 4 0 3199 3269 491950184 491950114 4.810000e-20 110.0
20 TraesCS1A01G127400 chr2D 78.344 157 24 10 421 572 627350906 627350755 4.850000e-15 93.5
21 TraesCS1A01G127400 chr3B 92.958 71 5 0 3199 3269 352239662 352239732 2.240000e-18 104.0
22 TraesCS1A01G127400 chr3B 92.958 71 5 0 3199 3269 578772875 578772945 2.240000e-18 104.0
23 TraesCS1A01G127400 chr5B 90.667 75 6 1 3199 3272 248393993 248393919 1.040000e-16 99.0
24 TraesCS1A01G127400 chr3A 78.873 142 22 6 421 557 83981309 83981171 6.270000e-14 89.8
25 TraesCS1A01G127400 chr3A 87.500 48 3 2 421 468 80223705 80223661 8.000000e-03 52.8
26 TraesCS1A01G127400 chr5D 77.778 153 27 5 421 568 213478019 213477869 2.260000e-13 87.9
27 TraesCS1A01G127400 chr5D 88.235 51 3 3 421 468 510601088 510601038 1.770000e-04 58.4
28 TraesCS1A01G127400 chr5A 76.471 153 29 5 421 568 277726086 277725936 4.880000e-10 76.8
29 TraesCS1A01G127400 chr6A 85.075 67 10 0 502 568 499639184 499639118 8.170000e-08 69.4
30 TraesCS1A01G127400 chr7A 94.595 37 2 0 415 451 547102782 547102818 1.770000e-04 58.4


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 TraesCS1A01G127400 chr1A 154573688 154578238 4550 False 8405 8405 100.000 1 4551 1 chr1A.!!$F1 4550
1 TraesCS1A01G127400 chr1D 138344122 138348455 4333 False 6399 6399 93.371 7 4348 1 chr1D.!!$F1 4341
2 TraesCS1A01G127400 chr1B 212747526 212751348 3822 True 2804 3766 93.759 794 4551 2 chr1B.!!$R2 3757

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
700 707 0.109342 CTCCCACAAGCAACTCCTGT 59.891 55.0 0.00 0.0 0.00 4.00 F
1334 1363 0.036732 CAAGAAGCAGCAGGGTGGTA 59.963 55.0 3.43 0.0 0.00 3.25 F
1460 1489 0.105453 ATCCATGTAGGCCCTCGAGT 60.105 55.0 12.31 0.0 37.29 4.18 F
1514 1548 0.179089 ACCAGAGTGATGCGAGATGC 60.179 55.0 0.00 0.0 46.70 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1541 1.914051 CAACTCGTACAGTGCATCTCG 59.086 52.381 0.00 0.0 34.56 4.04 R
3223 3347 1.039856 ATGGTCACAAGGCAACAACC 58.960 50.000 0.00 0.0 41.41 3.77 R
3501 3625 4.671831 TGAAGCCTTTGGGTTATCATCAA 58.328 39.130 0.75 0.0 43.92 2.57 R
3667 3791 8.336235 TCTATGGGATGTTGTCTTTTATCCTTT 58.664 33.333 0.00 0.0 39.21 3.11 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
153 154 3.074412 ACGAGTTCATGCCTAAACCTTG 58.926 45.455 0.00 0.00 0.00 3.61
166 168 5.299531 GCCTAAACCTTGAGTTTTGAGAAGT 59.700 40.000 0.00 0.00 46.79 3.01
172 174 5.127682 ACCTTGAGTTTTGAGAAGTGCATTT 59.872 36.000 0.00 0.00 0.00 2.32
175 177 5.350633 TGAGTTTTGAGAAGTGCATTTTGG 58.649 37.500 0.00 0.00 0.00 3.28
197 199 3.306019 GGTACATTGAGCAAAGTTTGGGG 60.306 47.826 17.11 0.00 0.00 4.96
202 204 0.679505 GAGCAAAGTTTGGGGGTTCC 59.320 55.000 17.11 0.00 0.00 3.62
215 217 1.835494 GGGTTCCTGCCCTTTAACTC 58.165 55.000 0.00 0.00 45.22 3.01
216 218 1.450025 GGTTCCTGCCCTTTAACTCG 58.550 55.000 0.00 0.00 0.00 4.18
217 219 1.271217 GGTTCCTGCCCTTTAACTCGT 60.271 52.381 0.00 0.00 0.00 4.18
218 220 1.804748 GTTCCTGCCCTTTAACTCGTG 59.195 52.381 0.00 0.00 0.00 4.35
219 221 0.323629 TCCTGCCCTTTAACTCGTGG 59.676 55.000 0.00 0.00 0.00 4.94
220 222 1.305930 CCTGCCCTTTAACTCGTGGC 61.306 60.000 0.00 0.00 42.49 5.01
221 223 0.321653 CTGCCCTTTAACTCGTGGCT 60.322 55.000 0.00 0.00 42.62 4.75
224 226 1.068541 GCCCTTTAACTCGTGGCTTTG 60.069 52.381 0.00 0.00 39.05 2.77
304 308 6.481644 GGCTGCTAGGCTAATACATTATCATC 59.518 42.308 0.00 0.00 37.85 2.92
312 316 8.043710 AGGCTAATACATTATCATCAACTAGCC 58.956 37.037 0.00 0.00 45.21 3.93
336 342 8.704234 GCCGTGACATGTTTATTTTCAATTTTA 58.296 29.630 0.00 0.00 0.00 1.52
427 433 2.611225 GGATATCATCCGCTCCATCC 57.389 55.000 4.83 0.00 40.13 3.51
437 443 1.086696 CGCTCCATCCGTTCACAAAT 58.913 50.000 0.00 0.00 0.00 2.32
520 527 9.701098 TTAACTCATTTCAGTTCGTATGTAGTT 57.299 29.630 0.00 0.00 37.75 2.24
559 566 6.311200 CCGAAGCATCTTAAAATTTTGAAGGG 59.689 38.462 13.76 9.60 0.00 3.95
561 568 7.598493 CGAAGCATCTTAAAATTTTGAAGGGAA 59.402 33.333 13.76 0.00 0.00 3.97
563 570 7.389232 AGCATCTTAAAATTTTGAAGGGAAGG 58.611 34.615 13.76 0.00 0.00 3.46
578 585 6.154706 TGAAGGGAAGGAGTAGTTAGCTAAAG 59.845 42.308 7.99 0.00 0.00 1.85
583 590 6.535865 GGAAGGAGTAGTTAGCTAAAGAAAGC 59.464 42.308 7.99 0.00 43.11 3.51
596 603 6.668323 GCTAAAGAAAGCTGTATGTGTCAAA 58.332 36.000 0.00 0.00 39.50 2.69
597 604 6.578919 GCTAAAGAAAGCTGTATGTGTCAAAC 59.421 38.462 0.00 0.00 39.50 2.93
598 605 5.438761 AAGAAAGCTGTATGTGTCAAACC 57.561 39.130 0.00 0.00 0.00 3.27
604 611 7.524717 AAGCTGTATGTGTCAAACCTTTTAT 57.475 32.000 0.00 0.00 0.00 1.40
605 612 7.145932 AGCTGTATGTGTCAAACCTTTTATC 57.854 36.000 0.00 0.00 0.00 1.75
606 613 6.714810 AGCTGTATGTGTCAAACCTTTTATCA 59.285 34.615 0.00 0.00 0.00 2.15
607 614 7.394359 AGCTGTATGTGTCAAACCTTTTATCAT 59.606 33.333 0.00 0.00 0.00 2.45
608 615 8.028938 GCTGTATGTGTCAAACCTTTTATCATT 58.971 33.333 0.00 0.00 0.00 2.57
628 635 3.347958 TTTTTCTGCGCGTGAATCTTT 57.652 38.095 8.43 0.00 0.00 2.52
629 636 3.347958 TTTTCTGCGCGTGAATCTTTT 57.652 38.095 8.43 0.00 0.00 2.27
657 664 7.614124 TTTTATCAATTACGGTTGGGTAGTC 57.386 36.000 0.00 0.00 0.00 2.59
669 676 4.335037 GGTTGGGTAGTCACAAAACGTTTA 59.665 41.667 15.03 0.00 38.79 2.01
670 677 5.008911 GGTTGGGTAGTCACAAAACGTTTAT 59.991 40.000 15.03 2.69 38.79 1.40
675 682 5.697633 GGTAGTCACAAAACGTTTATCTCCA 59.302 40.000 15.03 0.00 0.00 3.86
685 692 3.896272 ACGTTTATCTCCATACTCCTCCC 59.104 47.826 0.00 0.00 0.00 4.30
697 704 0.322008 CTCCTCCCACAAGCAACTCC 60.322 60.000 0.00 0.00 0.00 3.85
700 707 0.109342 CTCCCACAAGCAACTCCTGT 59.891 55.000 0.00 0.00 0.00 4.00
704 711 3.585289 TCCCACAAGCAACTCCTGTATTA 59.415 43.478 0.00 0.00 0.00 0.98
742 752 2.887568 GGCAGCGGTGTCGATCTG 60.888 66.667 17.07 0.00 39.00 2.90
743 753 3.558411 GCAGCGGTGTCGATCTGC 61.558 66.667 17.07 13.93 42.11 4.26
744 754 2.887568 CAGCGGTGTCGATCTGCC 60.888 66.667 16.85 4.61 37.86 4.85
745 755 3.071206 AGCGGTGTCGATCTGCCT 61.071 61.111 16.85 5.93 37.86 4.75
747 757 2.456119 GCGGTGTCGATCTGCCTTG 61.456 63.158 11.62 0.00 39.00 3.61
915 935 2.046217 GGCACCGGAACCCTCTTC 60.046 66.667 9.46 0.00 0.00 2.87
916 936 2.593956 GGCACCGGAACCCTCTTCT 61.594 63.158 9.46 0.00 0.00 2.85
1122 1142 0.460109 TCTCCATCACACGCCGATTG 60.460 55.000 0.00 0.00 0.00 2.67
1334 1363 0.036732 CAAGAAGCAGCAGGGTGGTA 59.963 55.000 3.43 0.00 0.00 3.25
1438 1467 4.397103 TCTCTTGGCTATTTCAATGTGCAG 59.603 41.667 0.00 0.00 0.00 4.41
1460 1489 0.105453 ATCCATGTAGGCCCTCGAGT 60.105 55.000 12.31 0.00 37.29 4.18
1466 1495 0.395448 GTAGGCCCTCGAGTACTGGT 60.395 60.000 12.31 0.00 0.00 4.00
1470 1499 1.180029 GCCCTCGAGTACTGGTGTTA 58.820 55.000 12.31 0.00 0.00 2.41
1507 1541 3.273434 TCTGCATAAACCAGAGTGATGC 58.727 45.455 0.00 0.00 42.49 3.91
1514 1548 0.179089 ACCAGAGTGATGCGAGATGC 60.179 55.000 0.00 0.00 46.70 3.91
2070 2193 6.385649 TCTTTCGGGGCAATGTATAATTTC 57.614 37.500 0.00 0.00 0.00 2.17
2075 2198 4.340950 CGGGGCAATGTATAATTTCCACTT 59.659 41.667 0.00 0.00 0.00 3.16
2156 2279 5.923733 ACATTTTTGGTGAGTTTGGTACA 57.076 34.783 0.00 0.00 0.00 2.90
2283 2406 7.066284 GCACTGTGGATGTCTTATATTTTGACT 59.934 37.037 10.21 0.00 0.00 3.41
2607 2731 3.191371 CCTCTATTTGTTGTTGCCTGACC 59.809 47.826 0.00 0.00 0.00 4.02
2612 2736 2.280524 TTGTTGCCTGACCCGACG 60.281 61.111 0.00 0.00 0.00 5.12
2862 2986 7.008440 CATTCACAATGTCACGAATCACTAT 57.992 36.000 0.00 0.00 34.18 2.12
2863 2987 8.130307 CATTCACAATGTCACGAATCACTATA 57.870 34.615 0.00 0.00 34.18 1.31
3233 3357 1.609208 CAGCAGTAAGGTTGTTGCCT 58.391 50.000 0.00 0.00 41.41 4.75
3501 3625 7.878621 TCAACAGAATCCCCTTATCATCTAT 57.121 36.000 0.00 0.00 0.00 1.98
3586 3710 4.306600 CGCCATGCTAACACACTATATCA 58.693 43.478 0.00 0.00 0.00 2.15
3760 3884 7.433708 TCTGTACCTTTGTAACAATGTCATG 57.566 36.000 0.00 0.00 0.00 3.07
3801 3925 3.073144 GAGTCAGACTCGGTAGCAATC 57.927 52.381 14.96 0.00 35.28 2.67
3802 3926 1.402259 AGTCAGACTCGGTAGCAATCG 59.598 52.381 0.00 0.00 0.00 3.34
3803 3927 0.738975 TCAGACTCGGTAGCAATCGG 59.261 55.000 0.00 0.00 0.00 4.18
3804 3928 0.456221 CAGACTCGGTAGCAATCGGT 59.544 55.000 0.00 0.00 0.00 4.69
3805 3929 1.674441 CAGACTCGGTAGCAATCGGTA 59.326 52.381 0.00 0.00 0.00 4.02
3806 3930 1.948145 AGACTCGGTAGCAATCGGTAG 59.052 52.381 0.00 0.00 0.00 3.18
3807 3931 0.384669 ACTCGGTAGCAATCGGTAGC 59.615 55.000 0.00 0.00 39.62 3.58
3808 3932 0.384309 CTCGGTAGCAATCGGTAGCA 59.616 55.000 0.00 0.00 42.39 3.49
3809 3933 0.818938 TCGGTAGCAATCGGTAGCAA 59.181 50.000 0.00 0.00 42.39 3.91
3833 3957 8.789762 CAATTCATGATTTATAGCTCACATCCA 58.210 33.333 0.00 0.00 0.00 3.41
3871 3995 1.335496 GTGTTTGGTTACATGCACCGT 59.665 47.619 9.56 0.00 37.07 4.83
3894 4018 1.250328 TTTGCCTCCTTGCATCTGTG 58.750 50.000 0.00 0.00 41.70 3.66
4020 4149 2.066340 TGGTGGGTCCACTTAGCTG 58.934 57.895 18.32 0.00 45.52 4.24
4044 4174 3.388345 TGATGCACTGTACGGTGTTTA 57.612 42.857 30.46 19.65 39.21 2.01
4095 4225 8.165239 AGTTAACAATTACACATGACACACAT 57.835 30.769 8.61 0.00 40.17 3.21
4110 4240 5.891551 TGACACACATAGTTATCCTAGAGCA 59.108 40.000 0.00 0.00 0.00 4.26
4165 4295 1.361668 GCGTCCAACGTGATGAGCAT 61.362 55.000 0.00 0.00 44.73 3.79
4192 4322 4.148825 GGCGAGCATCCTGTCGGT 62.149 66.667 0.00 0.00 36.67 4.69
4213 4343 4.719616 GCGTCGAACCAGTTGCGC 62.720 66.667 0.00 0.00 38.15 6.09
4219 4349 1.063488 GAACCAGTTGCGCGTTGTT 59.937 52.632 8.43 1.24 0.00 2.83
4224 4354 4.897856 GTTGCGCGTTGTTGCCGT 62.898 61.111 8.43 0.00 0.00 5.68
4266 4400 0.253020 GGGGTAGAGGTTGGGAGGAA 60.253 60.000 0.00 0.00 0.00 3.36
4269 4403 2.290768 GGGTAGAGGTTGGGAGGAAAAC 60.291 54.545 0.00 0.00 0.00 2.43
4272 4406 2.136026 AGAGGTTGGGAGGAAAACTGT 58.864 47.619 0.00 0.00 0.00 3.55
4309 4443 0.819582 GGCGTTAGTGTACTAGGCCA 59.180 55.000 21.45 0.00 43.47 5.36
4310 4444 1.411612 GGCGTTAGTGTACTAGGCCAT 59.588 52.381 21.45 0.00 43.47 4.40
4364 4498 2.819595 GCGGCGGTCATGACATGT 60.820 61.111 26.47 0.00 0.00 3.21
4366 4500 1.447663 CGGCGGTCATGACATGTCA 60.448 57.895 29.67 29.67 44.59 3.58
4395 4529 2.083774 GGCAAGGTTGACGATGATCAA 58.916 47.619 0.00 0.00 36.23 2.57
4402 4536 5.678583 AGGTTGACGATGATCAATGAGAAT 58.321 37.500 0.00 0.00 40.60 2.40
4404 4538 6.927936 AGGTTGACGATGATCAATGAGAATAG 59.072 38.462 0.00 0.00 40.60 1.73
4406 4540 7.439356 GGTTGACGATGATCAATGAGAATAGAA 59.561 37.037 0.00 0.00 40.60 2.10
4421 4555 7.461749 TGAGAATAGAAAGAAACCACTCCAAT 58.538 34.615 0.00 0.00 0.00 3.16
4436 4571 5.185635 CCACTCCAATTGTAAACCATCACAT 59.814 40.000 4.43 0.00 0.00 3.21
4446 4581 7.340122 TGTAAACCATCACATGAAACAGAAA 57.660 32.000 0.00 0.00 0.00 2.52
4455 4590 5.351740 TCACATGAAACAGAAACGTACAACA 59.648 36.000 0.00 0.00 0.00 3.33
4456 4591 5.451023 CACATGAAACAGAAACGTACAACAC 59.549 40.000 0.00 0.00 0.00 3.32
4497 4632 7.707624 AATGAGATTGTTAAGGCATGAGAAA 57.292 32.000 0.00 0.00 0.00 2.52
4498 4633 6.500684 TGAGATTGTTAAGGCATGAGAAAC 57.499 37.500 0.00 0.00 0.00 2.78
4500 4635 5.245531 AGATTGTTAAGGCATGAGAAACGA 58.754 37.500 0.00 0.00 0.00 3.85
4507 4642 1.424493 GCATGAGAAACGAGAGGCGG 61.424 60.000 0.00 0.00 46.49 6.13
4509 4644 0.173708 ATGAGAAACGAGAGGCGGTC 59.826 55.000 0.00 0.00 40.51 4.79
4514 4649 3.606065 AACGAGAGGCGGTCGAACG 62.606 63.158 20.73 20.73 46.49 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
153 154 4.746611 CCCAAAATGCACTTCTCAAAACTC 59.253 41.667 0.00 0.00 0.00 3.01
166 168 2.896044 TGCTCAATGTACCCAAAATGCA 59.104 40.909 0.00 0.00 0.00 3.96
172 174 4.202202 CCAAACTTTGCTCAATGTACCCAA 60.202 41.667 0.00 0.00 0.00 4.12
175 177 3.306019 CCCCAAACTTTGCTCAATGTACC 60.306 47.826 0.00 0.00 0.00 3.34
197 199 1.271217 ACGAGTTAAAGGGCAGGAACC 60.271 52.381 0.00 0.00 0.00 3.62
202 204 0.321653 AGCCACGAGTTAAAGGGCAG 60.322 55.000 0.00 0.00 46.96 4.85
214 216 3.904800 TGAGATAATCCAAAGCCACGA 57.095 42.857 0.00 0.00 0.00 4.35
215 217 5.505173 AATTGAGATAATCCAAAGCCACG 57.495 39.130 0.00 0.00 0.00 4.94
216 218 6.866480 TGAAATTGAGATAATCCAAAGCCAC 58.134 36.000 0.00 0.00 0.00 5.01
217 219 7.178983 ACTTGAAATTGAGATAATCCAAAGCCA 59.821 33.333 0.00 0.00 0.00 4.75
218 220 7.550712 ACTTGAAATTGAGATAATCCAAAGCC 58.449 34.615 0.00 0.00 0.00 4.35
219 221 8.992835 AACTTGAAATTGAGATAATCCAAAGC 57.007 30.769 0.00 0.00 0.00 3.51
279 283 5.734720 TGATAATGTATTAGCCTAGCAGCC 58.265 41.667 0.00 0.00 0.00 4.85
304 308 5.545658 AATAAACATGTCACGGCTAGTTG 57.454 39.130 0.00 0.00 0.00 3.16
419 425 5.758296 TCTTATATTTGTGAACGGATGGAGC 59.242 40.000 0.00 0.00 0.00 4.70
427 433 9.825972 AGTCAAAACATCTTATATTTGTGAACG 57.174 29.630 0.00 0.00 35.01 3.95
487 494 7.703328 ACGAACTGAAATGAGTTAACAAATGT 58.297 30.769 8.61 0.00 36.27 2.71
488 495 9.825972 ATACGAACTGAAATGAGTTAACAAATG 57.174 29.630 8.61 0.00 36.27 2.32
489 496 9.825972 CATACGAACTGAAATGAGTTAACAAAT 57.174 29.630 8.61 0.00 36.27 2.32
496 503 7.870954 TGAACTACATACGAACTGAAATGAGTT 59.129 33.333 0.00 0.00 38.94 3.01
559 566 7.528481 GCTTTCTTTAGCTAACTACTCCTTC 57.472 40.000 5.45 0.00 38.15 3.46
578 585 5.438761 AAGGTTTGACACATACAGCTTTC 57.561 39.130 0.00 0.00 0.00 2.62
583 590 9.912634 AAATGATAAAAGGTTTGACACATACAG 57.087 29.630 0.00 0.00 0.00 2.74
608 615 3.347958 AAAGATTCACGCGCAGAAAAA 57.652 38.095 16.89 0.00 0.00 1.94
646 653 2.291365 ACGTTTTGTGACTACCCAACC 58.709 47.619 0.00 0.00 0.00 3.77
657 664 6.594159 AGGAGTATGGAGATAAACGTTTTGTG 59.406 38.462 20.19 0.00 0.00 3.33
669 676 3.312890 CTTGTGGGAGGAGTATGGAGAT 58.687 50.000 0.00 0.00 0.00 2.75
670 677 2.752030 CTTGTGGGAGGAGTATGGAGA 58.248 52.381 0.00 0.00 0.00 3.71
675 682 2.237392 GAGTTGCTTGTGGGAGGAGTAT 59.763 50.000 0.00 0.00 0.00 2.12
731 741 1.204941 AGTACAAGGCAGATCGACACC 59.795 52.381 0.00 0.00 0.00 4.16
734 744 2.094700 TGACAGTACAAGGCAGATCGAC 60.095 50.000 0.00 0.00 0.00 4.20
735 745 2.167662 TGACAGTACAAGGCAGATCGA 58.832 47.619 0.00 0.00 0.00 3.59
742 752 4.455533 TCAAACATCATGACAGTACAAGGC 59.544 41.667 0.00 0.00 0.00 4.35
743 753 5.122869 CCTCAAACATCATGACAGTACAAGG 59.877 44.000 0.00 4.24 0.00 3.61
744 754 5.934043 TCCTCAAACATCATGACAGTACAAG 59.066 40.000 0.00 0.00 0.00 3.16
745 755 5.863965 TCCTCAAACATCATGACAGTACAA 58.136 37.500 0.00 0.00 0.00 2.41
747 757 6.992063 ATTCCTCAAACATCATGACAGTAC 57.008 37.500 0.00 0.00 0.00 2.73
794 806 4.204012 TCGTGGAAACATTCTGTCCTTTT 58.796 39.130 0.00 0.00 46.14 2.27
827 847 7.016268 GGAGGTCAGGAATGTATAGGAACATAA 59.984 40.741 0.00 0.00 39.16 1.90
836 856 3.258372 GCGATGGAGGTCAGGAATGTATA 59.742 47.826 0.00 0.00 0.00 1.47
837 857 2.037772 GCGATGGAGGTCAGGAATGTAT 59.962 50.000 0.00 0.00 0.00 2.29
915 935 5.010112 TCGAGATGAGGGACTTATTAGCAAG 59.990 44.000 0.00 0.00 41.55 4.01
916 936 4.893524 TCGAGATGAGGGACTTATTAGCAA 59.106 41.667 0.00 0.00 41.55 3.91
954 974 1.768265 TCCCCCTTTTTCTTAGCCCT 58.232 50.000 0.00 0.00 0.00 5.19
1334 1363 2.313317 CCAGAATATGGCATTGGCACT 58.687 47.619 15.84 5.16 43.83 4.40
1438 1467 1.416401 TCGAGGGCCTACATGGATTTC 59.584 52.381 5.73 0.00 38.35 2.17
1460 1489 8.756486 TGTTCTACTAGCATATAACACCAGTA 57.244 34.615 0.00 0.00 0.00 2.74
1466 1495 7.951591 TGCAGATGTTCTACTAGCATATAACA 58.048 34.615 0.00 0.00 0.00 2.41
1470 1499 9.429359 GTTTATGCAGATGTTCTACTAGCATAT 57.571 33.333 0.00 0.00 41.40 1.78
1507 1541 1.914051 CAACTCGTACAGTGCATCTCG 59.086 52.381 0.00 0.00 34.56 4.04
1514 1548 7.117241 ACATAATTCAACAACTCGTACAGTG 57.883 36.000 0.00 0.00 34.56 3.66
1561 1595 7.759489 TTGAACAGCCATAGTACTTGAAAAT 57.241 32.000 0.00 0.00 0.00 1.82
1562 1596 7.759489 ATTGAACAGCCATAGTACTTGAAAA 57.241 32.000 0.00 0.00 0.00 2.29
1563 1597 7.592938 CAATTGAACAGCCATAGTACTTGAAA 58.407 34.615 0.00 0.00 0.00 2.69
1564 1598 6.349280 GCAATTGAACAGCCATAGTACTTGAA 60.349 38.462 10.34 0.00 0.00 2.69
1565 1599 5.123820 GCAATTGAACAGCCATAGTACTTGA 59.876 40.000 10.34 0.00 0.00 3.02
1566 1600 5.106197 TGCAATTGAACAGCCATAGTACTTG 60.106 40.000 10.34 0.00 0.00 3.16
1567 1601 5.009631 TGCAATTGAACAGCCATAGTACTT 58.990 37.500 10.34 0.00 0.00 2.24
1568 1602 4.588899 TGCAATTGAACAGCCATAGTACT 58.411 39.130 10.34 0.00 0.00 2.73
2070 2193 9.784531 ATGGATTACAGATAACTGAATAAGTGG 57.215 33.333 7.05 0.00 46.03 4.00
2235 2358 3.764972 CGAAGTTACCTTCCTCCTCTTCT 59.235 47.826 0.00 0.00 43.52 2.85
2456 2579 5.691754 GGAGCAACACAAAGATTGGTAAAAG 59.308 40.000 0.00 0.00 36.70 2.27
2461 2584 2.949447 AGGAGCAACACAAAGATTGGT 58.051 42.857 0.00 0.00 39.16 3.67
2502 2626 4.594920 ACCTCAAGAATCTTTCTCCAGTCA 59.405 41.667 0.00 0.00 39.61 3.41
2607 2731 7.461107 AGATATGTTCAACAAATAAACGTCGG 58.539 34.615 0.00 0.00 0.00 4.79
2753 2877 8.749354 AGTAAAAATCCAAGGTCAATATGGAAC 58.251 33.333 0.00 0.00 45.75 3.62
2791 2915 7.609760 AATTTTGTGATAGTTCATGACGCTA 57.390 32.000 0.00 1.53 33.56 4.26
2853 2977 8.958119 TGGTTTGTCCTGTAATATAGTGATTC 57.042 34.615 0.00 0.00 37.07 2.52
2862 2986 4.785914 TCCTGGATGGTTTGTCCTGTAATA 59.214 41.667 0.00 0.00 36.68 0.98
2863 2987 3.591527 TCCTGGATGGTTTGTCCTGTAAT 59.408 43.478 0.00 0.00 36.68 1.89
3223 3347 1.039856 ATGGTCACAAGGCAACAACC 58.960 50.000 0.00 0.00 41.41 3.77
3501 3625 4.671831 TGAAGCCTTTGGGTTATCATCAA 58.328 39.130 0.75 0.00 43.92 2.57
3667 3791 8.336235 TCTATGGGATGTTGTCTTTTATCCTTT 58.664 33.333 0.00 0.00 39.21 3.11
3800 3924 7.161404 AGCTATAAATCATGAATTGCTACCGA 58.839 34.615 11.52 0.00 31.44 4.69
3801 3925 7.118245 TGAGCTATAAATCATGAATTGCTACCG 59.882 37.037 12.72 0.00 32.98 4.02
3802 3926 8.233190 GTGAGCTATAAATCATGAATTGCTACC 58.767 37.037 12.72 5.07 32.98 3.18
3803 3927 8.777413 TGTGAGCTATAAATCATGAATTGCTAC 58.223 33.333 12.72 11.61 32.98 3.58
3804 3928 8.907222 TGTGAGCTATAAATCATGAATTGCTA 57.093 30.769 12.72 2.47 32.98 3.49
3805 3929 7.812690 TGTGAGCTATAAATCATGAATTGCT 57.187 32.000 12.63 12.63 35.01 3.91
3806 3930 7.754027 GGATGTGAGCTATAAATCATGAATTGC 59.246 37.037 6.26 5.37 0.00 3.56
3807 3931 8.789762 TGGATGTGAGCTATAAATCATGAATTG 58.210 33.333 6.26 0.00 0.00 2.32
3808 3932 8.929260 TGGATGTGAGCTATAAATCATGAATT 57.071 30.769 0.00 0.00 0.00 2.17
3809 3933 8.162085 ACTGGATGTGAGCTATAAATCATGAAT 58.838 33.333 0.00 0.00 0.00 2.57
3833 3957 4.142609 ACACGCTCCATATCAATCAACT 57.857 40.909 0.00 0.00 0.00 3.16
4020 4149 0.321298 ACCGTACAGTGCATCAACCC 60.321 55.000 0.00 0.00 0.00 4.11
4044 4174 7.607607 TCTTAATGATGTTCAGTGTATGCAACT 59.392 33.333 0.00 0.00 0.00 3.16
4095 4225 4.011023 GCCGAGATGCTCTAGGATAACTA 58.989 47.826 13.73 0.00 41.15 2.24
4110 4240 2.586079 CACCGCAATCGCCGAGAT 60.586 61.111 0.00 0.00 42.43 2.75
4192 4322 4.595538 AACTGGTTCGACGCGCCA 62.596 61.111 5.73 3.69 0.00 5.69
4213 4343 2.744709 CCCCCTACGGCAACAACG 60.745 66.667 0.00 0.00 37.36 4.10
4219 4349 4.000620 TGGACTCCCCCTACGGCA 62.001 66.667 0.00 0.00 0.00 5.69
4224 4354 1.932231 TCCTCGTGGACTCCCCCTA 60.932 63.158 1.10 0.00 37.46 3.53
4230 4360 3.827898 CGCCCTCCTCGTGGACTC 61.828 72.222 1.10 0.00 37.46 3.36
4236 4366 4.835891 CTACCCCGCCCTCCTCGT 62.836 72.222 0.00 0.00 0.00 4.18
4248 4381 1.665137 TTTCCTCCCAACCTCTACCC 58.335 55.000 0.00 0.00 0.00 3.69
4266 4400 0.528901 TCACGCGCACACTACAGTTT 60.529 50.000 5.73 0.00 0.00 2.66
4269 4403 1.686566 CCATCACGCGCACACTACAG 61.687 60.000 5.73 0.00 0.00 2.74
4272 4406 2.813474 GCCATCACGCGCACACTA 60.813 61.111 5.73 0.00 0.00 2.74
4354 4488 4.684214 GCCATAAGGACTGACATGTCATGA 60.684 45.833 28.00 7.83 38.61 3.07
4364 4498 2.642311 TCAACCTTGCCATAAGGACTGA 59.358 45.455 12.32 10.68 39.81 3.41
4366 4500 2.615493 CGTCAACCTTGCCATAAGGACT 60.615 50.000 12.32 0.00 39.81 3.85
4395 4529 7.020827 TGGAGTGGTTTCTTTCTATTCTCAT 57.979 36.000 0.00 0.00 0.00 2.90
4402 4536 8.626526 GTTTACAATTGGAGTGGTTTCTTTCTA 58.373 33.333 10.83 0.00 0.00 2.10
4404 4538 6.700081 GGTTTACAATTGGAGTGGTTTCTTTC 59.300 38.462 10.83 0.00 0.00 2.62
4406 4540 5.659079 TGGTTTACAATTGGAGTGGTTTCTT 59.341 36.000 10.83 0.00 0.00 2.52
4421 4555 6.951062 TCTGTTTCATGTGATGGTTTACAA 57.049 33.333 0.00 0.00 0.00 2.41
4456 4591 9.199184 CAATCTCATTATTTTACACGACTTTCG 57.801 33.333 0.00 0.00 46.93 3.46
4480 4615 4.637276 TCTCGTTTCTCATGCCTTAACAA 58.363 39.130 0.00 0.00 0.00 2.83
4484 4619 2.418746 GCCTCTCGTTTCTCATGCCTTA 60.419 50.000 0.00 0.00 0.00 2.69
4485 4620 1.677217 GCCTCTCGTTTCTCATGCCTT 60.677 52.381 0.00 0.00 0.00 4.35
4497 4632 4.099170 CGTTCGACCGCCTCTCGT 62.099 66.667 0.00 0.00 36.19 4.18
4498 4633 3.318539 TTCGTTCGACCGCCTCTCG 62.319 63.158 0.00 0.00 38.08 4.04
4500 4635 1.970114 TCTTCGTTCGACCGCCTCT 60.970 57.895 0.00 0.00 0.00 3.69
4507 4642 0.179142 GCCCTAGGTCTTCGTTCGAC 60.179 60.000 8.29 0.00 0.00 4.20
4509 4644 1.141234 GGCCCTAGGTCTTCGTTCG 59.859 63.158 8.29 0.00 0.00 3.95
4514 4649 2.187163 GCGTGGCCCTAGGTCTTC 59.813 66.667 8.29 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.