Multiple sequence alignment - TraesCS3B01G420500

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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 TraesCS3B01G420500 chr3B 100.000 4052 0 0 1 4052 657645164 657649215 0.000000e+00 7483
1 TraesCS3B01G420500 chr3A 93.537 4100 206 23 1 4052 637116610 637112522 0.000000e+00 6048
2 TraesCS3B01G420500 chr3D 92.484 4058 208 45 39 4027 497597680 497601709 0.000000e+00 5714
3 TraesCS3B01G420500 chr2B 88.783 526 59 0 2231 2756 34038452 34038977 0.000000e+00 645
4 TraesCS3B01G420500 chr2B 84.184 392 47 10 3673 4052 407887265 407886877 2.300000e-97 366
5 TraesCS3B01G420500 chr2B 84.539 304 35 8 2799 3100 34038985 34039278 1.420000e-74 291
6 TraesCS3B01G420500 chr1D 88.095 378 32 6 3685 4052 348125156 348124782 1.730000e-118 436
7 TraesCS3B01G420500 chr5B 85.979 378 40 6 3685 4052 176793093 176793467 3.800000e-105 392
8 TraesCS3B01G420500 chr5B 84.224 393 45 11 3673 4052 204615178 204615566 2.300000e-97 366
9 TraesCS3B01G420500 chr6D 85.979 378 36 8 3685 4052 77328580 77328210 4.910000e-104 388
10 TraesCS3B01G420500 chr2D 85.204 392 41 8 3673 4052 244754967 244754581 1.770000e-103 387
11 TraesCS3B01G420500 chr1B 84.949 392 44 8 3673 4052 177159289 177158901 2.280000e-102 383
12 TraesCS3B01G420500 chr1B 85.286 367 39 8 3673 4027 192674573 192674210 8.280000e-97 364
13 TraesCS3B01G420500 chr6B 84.694 392 45 9 3673 4052 570080281 570079893 1.060000e-100 377
14 TraesCS3B01G420500 chr6B 83.929 392 44 10 3673 4052 308977826 308977442 1.380000e-94 357


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 TraesCS3B01G420500 chr3B 657645164 657649215 4051 False 7483 7483 100.000 1 4052 1 chr3B.!!$F1 4051
1 TraesCS3B01G420500 chr3A 637112522 637116610 4088 True 6048 6048 93.537 1 4052 1 chr3A.!!$R1 4051
2 TraesCS3B01G420500 chr3D 497597680 497601709 4029 False 5714 5714 92.484 39 4027 1 chr3D.!!$F1 3988
3 TraesCS3B01G420500 chr2B 34038452 34039278 826 False 468 645 86.661 2231 3100 2 chr2B.!!$F1 869

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
693 784 0.251916 TAGCTTGGTCCCCACGATTG 59.748 55.0 0.0 0.0 30.78 2.67 F
1283 1391 0.249868 TCTGTTCTCCACCAGTTGCG 60.250 55.0 0.0 0.0 0.00 4.85 F
2781 2889 0.622665 CAGAAGGGTGGAGGCAATCT 59.377 55.0 0.0 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1503 1611 0.041386 AACGGTTCTCTCCTAGGCCT 59.959 55.000 11.78 11.78 0.00 5.19 R
2820 2928 0.249657 GCCTCCGTGAGAAGCTATGG 60.250 60.000 2.84 0.00 0.00 2.74 R
3682 3795 1.064654 GCTGCCGGCTTTTAGATCAAG 59.935 52.381 29.70 13.44 38.06 3.02 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 3.388841 CTGCGACTGGTTAGGGGT 58.611 61.111 0.00 0.00 0.00 4.95
68 69 0.392706 TGGTTCATGTCGCTGACAGT 59.607 50.000 14.80 3.77 46.04 3.55
115 124 5.235850 TGACAAAACATAGGTTAGCTCCA 57.764 39.130 0.00 0.00 35.82 3.86
178 217 6.202937 CGTTTGGAGATCATGTAGTAGAGTC 58.797 44.000 0.00 0.00 0.00 3.36
183 222 4.069304 AGATCATGTAGTAGAGTCTCGCC 58.931 47.826 0.00 0.00 0.00 5.54
185 224 1.941294 CATGTAGTAGAGTCTCGCCGT 59.059 52.381 0.00 0.00 0.00 5.68
188 227 0.392060 TAGTAGAGTCTCGCCGTGCA 60.392 55.000 0.00 0.00 0.00 4.57
237 276 1.063174 GCAACGATCTGCTGTTGATCC 59.937 52.381 13.40 0.00 46.45 3.36
292 331 3.059044 CGTGTGACGCAATACTAGACAAC 59.941 47.826 0.00 0.00 33.65 3.32
300 339 4.124238 GCAATACTAGACAACGGCCATAA 58.876 43.478 2.24 0.00 0.00 1.90
377 428 1.140312 AGGACCTTTGTTCTGCTCCA 58.860 50.000 0.00 0.00 0.00 3.86
382 433 2.108952 ACCTTTGTTCTGCTCCAGGAAT 59.891 45.455 0.00 0.00 31.51 3.01
383 434 2.751806 CCTTTGTTCTGCTCCAGGAATC 59.248 50.000 0.00 0.00 31.51 2.52
384 435 2.099141 TTGTTCTGCTCCAGGAATCG 57.901 50.000 0.00 0.00 31.51 3.34
385 436 1.266178 TGTTCTGCTCCAGGAATCGA 58.734 50.000 0.00 0.00 31.51 3.59
386 437 1.623311 TGTTCTGCTCCAGGAATCGAA 59.377 47.619 0.00 0.00 31.51 3.71
387 438 2.237143 TGTTCTGCTCCAGGAATCGAAT 59.763 45.455 0.00 0.00 31.51 3.34
388 439 3.274288 GTTCTGCTCCAGGAATCGAATT 58.726 45.455 0.00 0.00 31.51 2.17
389 440 2.910199 TCTGCTCCAGGAATCGAATTG 58.090 47.619 0.00 0.00 31.51 2.32
390 441 2.237143 TCTGCTCCAGGAATCGAATTGT 59.763 45.455 0.00 0.00 31.51 2.71
391 442 3.012518 CTGCTCCAGGAATCGAATTGTT 58.987 45.455 0.00 0.00 0.00 2.83
392 443 3.009723 TGCTCCAGGAATCGAATTGTTC 58.990 45.455 0.00 0.00 0.00 3.18
393 444 3.274288 GCTCCAGGAATCGAATTGTTCT 58.726 45.455 0.00 0.00 0.00 3.01
394 445 3.064545 GCTCCAGGAATCGAATTGTTCTG 59.935 47.826 0.00 0.00 0.00 3.02
395 446 4.256920 CTCCAGGAATCGAATTGTTCTGT 58.743 43.478 0.00 0.00 0.00 3.41
396 447 4.002982 TCCAGGAATCGAATTGTTCTGTG 58.997 43.478 0.00 0.00 0.00 3.66
397 448 3.426695 CCAGGAATCGAATTGTTCTGTGC 60.427 47.826 0.00 0.00 0.00 4.57
398 449 2.416547 AGGAATCGAATTGTTCTGTGCG 59.583 45.455 0.00 0.00 0.00 5.34
399 450 2.415168 GGAATCGAATTGTTCTGTGCGA 59.585 45.455 0.00 0.00 0.00 5.10
463 536 3.775316 ACATCCAAGATCCGGTTCTAGTT 59.225 43.478 15.38 3.40 0.00 2.24
471 544 2.579873 TCCGGTTCTAGTTATCCGAGG 58.420 52.381 0.00 0.00 44.86 4.63
472 545 2.092212 TCCGGTTCTAGTTATCCGAGGT 60.092 50.000 0.00 0.00 44.86 3.85
575 657 6.310224 GCAGTGCTTAGAAACTTAGAAGAGAG 59.690 42.308 8.18 0.00 0.00 3.20
645 733 6.810911 TGAGAAGACTGATATTTGCTAGGAC 58.189 40.000 0.00 0.00 0.00 3.85
651 739 5.468658 ACTGATATTTGCTAGGACCCTAGT 58.531 41.667 20.69 6.97 45.67 2.57
693 784 0.251916 TAGCTTGGTCCCCACGATTG 59.748 55.000 0.00 0.00 30.78 2.67
716 807 8.958175 TTGTTCGGTACAATGATTTAATTGTC 57.042 30.769 5.87 0.07 45.47 3.18
718 809 8.788806 TGTTCGGTACAATGATTTAATTGTCTT 58.211 29.630 5.87 0.00 45.47 3.01
719 810 9.061610 GTTCGGTACAATGATTTAATTGTCTTG 57.938 33.333 5.87 0.00 45.47 3.02
849 948 7.094805 GCAGTGTCTACTTTTGTGGAAATATCA 60.095 37.037 0.00 0.00 41.57 2.15
1052 1160 2.961062 GGTGCATTCTCCTATTTGCCAT 59.039 45.455 0.00 0.00 34.20 4.40
1059 1167 4.314522 TCTCCTATTTGCCATTGTTGGA 57.685 40.909 0.00 0.00 46.92 3.53
1089 1197 6.660949 CCACATCTTTACCTCTGGAAAAAGAT 59.339 38.462 17.38 17.38 42.94 2.40
1104 1212 4.471904 AAAAGATGCACTCCTCGACATA 57.528 40.909 0.00 0.00 0.00 2.29
1205 1313 3.882888 ACGTGTGATGAAATTTCTGGTGT 59.117 39.130 18.64 6.07 0.00 4.16
1218 1326 1.133294 TCTGGTGTGGTCACAGGAGTA 60.133 52.381 3.80 0.00 45.45 2.59
1283 1391 0.249868 TCTGTTCTCCACCAGTTGCG 60.250 55.000 0.00 0.00 0.00 4.85
1372 1480 9.640974 CAAATTTGCAAGTTCTTAATTTGTCAG 57.359 29.630 16.82 0.00 39.52 3.51
1485 1593 2.094390 CCCTGTGTGGATCAGCAAATTG 60.094 50.000 0.00 0.00 38.35 2.32
1519 1627 3.967987 TGAATTAGGCCTAGGAGAGAACC 59.032 47.826 14.75 2.36 0.00 3.62
1590 1698 1.325355 CATGGCTATTCTTGGGGCAG 58.675 55.000 0.00 0.00 38.81 4.85
1623 1731 3.704061 GAGGAGAGATACCAGCTTCAGTT 59.296 47.826 0.00 0.00 0.00 3.16
2120 2228 2.307098 ACTTCTCAGGTGAATTCCCCAG 59.693 50.000 9.79 1.13 0.00 4.45
2229 2337 3.628942 TGCCTAATGCTGTGATCATTGAC 59.371 43.478 0.00 0.00 42.00 3.18
2451 2559 5.345702 CAATTGTCATACCTGCATTTGGAG 58.654 41.667 0.00 0.00 0.00 3.86
2598 2706 5.296151 TGGATTCACTCAATCTATCCCAC 57.704 43.478 0.00 0.00 40.90 4.61
2781 2889 0.622665 CAGAAGGGTGGAGGCAATCT 59.377 55.000 0.00 0.00 0.00 2.40
2820 2928 1.617850 TGCCAATGGATTGACAACCAC 59.382 47.619 2.05 1.81 40.14 4.16
2901 3011 3.748083 TCTCTTATCTGGATTGGCATGC 58.252 45.455 9.90 9.90 0.00 4.06
2907 3017 1.076559 TGGATTGGCATGCCTGAGG 60.077 57.895 35.53 0.00 36.94 3.86
2952 3062 4.370364 TTTCAACAGAAAGCAAGACACC 57.630 40.909 0.00 0.00 0.00 4.16
3010 3120 2.825836 CCTTCCATGTGCGAGGGC 60.826 66.667 0.00 0.00 40.52 5.19
3042 3152 2.670592 GCTTTGCCGGTACCCGTT 60.671 61.111 6.25 0.00 46.80 4.44
3195 3308 1.813513 CCAGTGCTACCCAAACTCAG 58.186 55.000 0.00 0.00 0.00 3.35
3235 3348 4.196626 TGTCCTGTCCTGGTAAATAACG 57.803 45.455 0.00 0.00 0.00 3.18
3249 3362 4.531659 AAATAACGCCGTCTAATGAAGC 57.468 40.909 0.00 0.00 0.00 3.86
3250 3363 2.658373 TAACGCCGTCTAATGAAGCA 57.342 45.000 0.00 0.00 0.00 3.91
3253 3366 2.356135 ACGCCGTCTAATGAAGCAAAT 58.644 42.857 0.00 0.00 0.00 2.32
3254 3367 3.527533 ACGCCGTCTAATGAAGCAAATA 58.472 40.909 0.00 0.00 0.00 1.40
3351 3464 7.951530 AAATGGATGCAGTTTGTCTTTTAAG 57.048 32.000 0.00 0.00 0.00 1.85
3356 3469 6.858478 GGATGCAGTTTGTCTTTTAAGTTCTC 59.142 38.462 0.00 0.00 0.00 2.87
3498 3611 7.984617 ACCTTAAAGATAGCAGTCTGAAGATTC 59.015 37.037 3.32 0.00 29.69 2.52
3508 3621 5.928839 GCAGTCTGAAGATTCAAGTCTTACA 59.071 40.000 3.32 0.00 38.51 2.41
3547 3660 4.898265 ACTGCAGAGCTTCCATATTCTCTA 59.102 41.667 23.35 0.00 34.45 2.43
3554 3667 4.345257 AGCTTCCATATTCTCTAAAGGCGA 59.655 41.667 0.00 0.00 0.00 5.54
3569 3682 1.964223 AGGCGAGAGAAAAGAGTGACA 59.036 47.619 0.00 0.00 0.00 3.58
3573 3686 3.611986 GCGAGAGAAAAGAGTGACATGAG 59.388 47.826 0.00 0.00 0.00 2.90
3581 3694 4.717233 AAGAGTGACATGAGCTCTAGTG 57.283 45.455 16.19 13.20 38.50 2.74
3585 3698 2.670414 GTGACATGAGCTCTAGTGTTGC 59.330 50.000 16.19 9.86 0.00 4.17
3656 3769 1.597663 GTGAACTGGAAACTGTGTCCG 59.402 52.381 12.27 9.40 42.21 4.79
3667 3780 0.036164 CTGTGTCCGGGGTTTGATCA 59.964 55.000 0.00 0.00 0.00 2.92
3675 3788 3.009695 TCCGGGGTTTGATCACATAACTT 59.990 43.478 0.00 0.00 0.00 2.66
3680 3793 4.437390 GGGTTTGATCACATAACTTCAGCG 60.437 45.833 8.31 0.00 0.00 5.18
3682 3795 2.279741 TGATCACATAACTTCAGCGGC 58.720 47.619 0.00 0.00 0.00 6.53
3691 3804 3.334583 AACTTCAGCGGCTTGATCTAA 57.665 42.857 0.00 0.00 0.00 2.10
3701 3814 1.064654 GCTTGATCTAAAAGCCGGCAG 59.935 52.381 31.54 17.75 43.45 4.85
3742 3856 7.716799 ATAATAAAGGTCTTGAACATTGCCA 57.283 32.000 0.00 0.00 30.97 4.92
3744 3858 4.525912 AAAGGTCTTGAACATTGCCATC 57.474 40.909 0.00 0.00 30.97 3.51
3749 3863 2.743664 TCTTGAACATTGCCATCGTCTG 59.256 45.455 0.00 0.00 0.00 3.51
3754 3868 4.940654 TGAACATTGCCATCGTCTGAATTA 59.059 37.500 0.00 0.00 0.00 1.40
3755 3869 4.882671 ACATTGCCATCGTCTGAATTAC 57.117 40.909 0.00 0.00 0.00 1.89
3778 3892 4.148825 CCCCTTCTGAGCGACCGG 62.149 72.222 0.00 0.00 0.00 5.28
3789 3903 2.329690 CGACCGGCGATGAGAGAG 59.670 66.667 9.30 0.00 44.57 3.20
3825 3939 8.791327 TGCTTATTGACATTGATTCTACTTCA 57.209 30.769 0.00 0.00 0.00 3.02
3947 4061 3.733337 AGCAACAACACTCTGAAGTAGG 58.267 45.455 0.00 0.00 33.25 3.18
3961 4083 9.127277 ACTCTGAAGTAGGAGATTAGAATGTAC 57.873 37.037 0.00 0.00 32.59 2.90
4044 4168 2.158385 CCTCTGGTAGCCTCATAGGTCT 60.158 54.545 0.00 0.00 37.80 3.85
4048 4172 3.450904 TGGTAGCCTCATAGGTCTTGTT 58.549 45.455 0.00 0.00 37.80 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.371526 GAATGCTGATTCCTCTGTCCAATA 58.628 41.667 0.00 0.00 33.05 1.90
68 69 6.263516 GTACTGATGTACACTAACAGGTCA 57.736 41.667 18.47 8.17 46.06 4.02
82 91 7.224297 ACCTATGTTTTGTCAAGTACTGATGT 58.776 34.615 0.00 0.00 36.14 3.06
188 227 1.079127 CGATCGAAAGGTGCAGGGT 60.079 57.895 10.26 0.00 0.00 4.34
191 230 0.439985 CACACGATCGAAAGGTGCAG 59.560 55.000 24.34 1.85 35.11 4.41
198 237 0.665068 CCGACCACACACGATCGAAA 60.665 55.000 24.34 0.00 36.70 3.46
237 276 0.820891 AGTTCTGGTGCCTGCAGTTG 60.821 55.000 13.81 0.00 0.00 3.16
337 382 4.932799 CCTTATTACCGTTGTCACATGTGA 59.067 41.667 24.56 24.56 37.24 3.58
339 384 4.933400 GTCCTTATTACCGTTGTCACATGT 59.067 41.667 0.00 0.00 0.00 3.21
340 385 4.331717 GGTCCTTATTACCGTTGTCACATG 59.668 45.833 0.00 0.00 0.00 3.21
377 428 2.416547 CGCACAGAACAATTCGATTCCT 59.583 45.455 0.00 0.00 34.02 3.36
382 433 1.144969 GGTCGCACAGAACAATTCGA 58.855 50.000 0.00 0.00 36.33 3.71
383 434 0.865111 TGGTCGCACAGAACAATTCG 59.135 50.000 0.00 0.00 44.92 3.34
388 439 1.436195 GCAAGTGGTCGCACAGAACA 61.436 55.000 0.00 0.00 45.88 3.18
389 440 1.160329 AGCAAGTGGTCGCACAGAAC 61.160 55.000 0.00 0.00 37.00 3.01
390 441 1.146041 AGCAAGTGGTCGCACAGAA 59.854 52.632 0.00 0.00 0.00 3.02
391 442 1.595109 CAGCAAGTGGTCGCACAGA 60.595 57.895 0.00 0.00 0.00 3.41
392 443 1.159713 TTCAGCAAGTGGTCGCACAG 61.160 55.000 0.00 0.00 0.00 3.66
393 444 0.534877 ATTCAGCAAGTGGTCGCACA 60.535 50.000 0.00 0.00 0.00 4.57
394 445 0.110056 CATTCAGCAAGTGGTCGCAC 60.110 55.000 0.00 0.00 0.00 5.34
395 446 0.250252 TCATTCAGCAAGTGGTCGCA 60.250 50.000 0.00 0.00 0.00 5.10
396 447 0.445436 CTCATTCAGCAAGTGGTCGC 59.555 55.000 0.00 0.00 0.00 5.19
397 448 1.728971 GACTCATTCAGCAAGTGGTCG 59.271 52.381 0.00 0.00 0.00 4.79
398 449 1.728971 CGACTCATTCAGCAAGTGGTC 59.271 52.381 0.00 0.00 0.00 4.02
399 450 1.344438 TCGACTCATTCAGCAAGTGGT 59.656 47.619 0.00 0.00 0.00 4.16
463 536 0.535328 CAGCCTCTCGACCTCGGATA 60.535 60.000 0.00 0.00 40.29 2.59
471 544 0.608640 TCTTTTCCCAGCCTCTCGAC 59.391 55.000 0.00 0.00 0.00 4.20
472 545 1.573108 ATCTTTTCCCAGCCTCTCGA 58.427 50.000 0.00 0.00 0.00 4.04
575 657 8.660373 CAGAAATGTACTCTCTGAATACCAAAC 58.340 37.037 11.68 0.00 39.15 2.93
645 733 8.528044 AAGAGATAGTTCTTGTTAGACTAGGG 57.472 38.462 0.00 0.00 36.12 3.53
693 784 9.061610 CAAGACAATTAAATCATTGTACCGAAC 57.938 33.333 0.00 0.00 45.55 3.95
697 788 9.573133 CTTCCAAGACAATTAAATCATTGTACC 57.427 33.333 0.00 0.00 45.55 3.34
704 795 9.965824 GAAAAGACTTCCAAGACAATTAAATCA 57.034 29.630 0.00 0.00 0.00 2.57
711 802 5.888161 AGTGTGAAAAGACTTCCAAGACAAT 59.112 36.000 0.00 0.00 0.00 2.71
713 804 4.843728 AGTGTGAAAAGACTTCCAAGACA 58.156 39.130 0.00 0.00 0.00 3.41
714 805 5.354234 TGAAGTGTGAAAAGACTTCCAAGAC 59.646 40.000 11.77 0.00 45.05 3.01
715 806 5.496556 TGAAGTGTGAAAAGACTTCCAAGA 58.503 37.500 11.77 0.00 45.05 3.02
716 807 5.818136 TGAAGTGTGAAAAGACTTCCAAG 57.182 39.130 11.77 0.00 45.05 3.61
718 809 6.773976 AATTGAAGTGTGAAAAGACTTCCA 57.226 33.333 11.77 3.38 45.05 3.53
719 810 6.697455 GGAAATTGAAGTGTGAAAAGACTTCC 59.303 38.462 11.77 0.00 45.05 3.46
881 980 5.346270 TCCTAAAATTAGTTTGGGCCCATT 58.654 37.500 29.23 16.99 45.28 3.16
882 981 4.954089 TCCTAAAATTAGTTTGGGCCCAT 58.046 39.130 29.23 14.47 45.28 4.00
1059 1167 7.451731 TTCCAGAGGTAAAGATGTGGATATT 57.548 36.000 0.00 0.00 34.12 1.28
1089 1197 5.000591 TGAATTTTTATGTCGAGGAGTGCA 58.999 37.500 0.00 0.00 0.00 4.57
1128 1236 3.806949 TCCCAGTTGCTCAGGTAATTT 57.193 42.857 0.00 0.00 0.00 1.82
1188 1296 4.278170 GTGACCACACCAGAAATTTCATCA 59.722 41.667 19.99 7.41 40.74 3.07
1205 1313 3.245264 TGAGAGTGATACTCCTGTGACCA 60.245 47.826 5.41 0.00 46.18 4.02
1218 1326 1.209019 AGCGAGGCATTTGAGAGTGAT 59.791 47.619 0.00 0.00 0.00 3.06
1283 1391 2.543777 TGCACTGAGGTCCAAAGTAC 57.456 50.000 0.00 0.00 0.00 2.73
1372 1480 0.819259 TGGCCTGTCAAGCTGTTCAC 60.819 55.000 3.32 0.00 0.00 3.18
1447 1555 2.629617 CAGGGAATGCACCAGAAAAACT 59.370 45.455 0.00 0.00 0.00 2.66
1503 1611 0.041386 AACGGTTCTCTCCTAGGCCT 59.959 55.000 11.78 11.78 0.00 5.19
1519 1627 1.508632 ACACCACCTTCATCGAAACG 58.491 50.000 0.00 0.00 0.00 3.60
1590 1698 4.202172 GGTATCTCTCCTCTAAGGTTGCAC 60.202 50.000 0.00 0.00 36.53 4.57
1623 1731 3.053991 TCCCAAGTGACTCCAAGTGAAAA 60.054 43.478 0.00 0.00 0.00 2.29
2120 2228 4.565022 AGTCTTGCAAGAAGAGTAAGAGC 58.435 43.478 29.99 13.67 38.17 4.09
2164 2272 3.565307 TGCTCCCACTGAACTGATTTTT 58.435 40.909 0.00 0.00 0.00 1.94
2229 2337 4.799949 CCAATAAATCCATTGTCAGCAACG 59.200 41.667 0.00 0.00 37.44 4.10
2451 2559 0.610232 ACCCTTCCAGTGCATTCTGC 60.610 55.000 0.00 0.00 45.29 4.26
2598 2706 4.337555 GGGATTTCACCAGAGATCATGTTG 59.662 45.833 0.00 0.00 37.17 3.33
2769 2877 2.048603 GGTGCCAGATTGCCTCCAC 61.049 63.158 0.00 0.00 0.00 4.02
2820 2928 0.249657 GCCTCCGTGAGAAGCTATGG 60.250 60.000 2.84 0.00 0.00 2.74
2901 3011 5.440610 AGCCTGTTATTTTCATACCTCAGG 58.559 41.667 0.00 0.00 42.54 3.86
2907 3017 7.573968 ATCCTCAAGCCTGTTATTTTCATAC 57.426 36.000 0.00 0.00 0.00 2.39
2952 3062 3.191581 AGTCACTGTTATCACCACTCTCG 59.808 47.826 0.00 0.00 0.00 4.04
2965 3075 4.526970 ACAATCCACTTTGAGTCACTGTT 58.473 39.130 0.00 0.00 0.00 3.16
3010 3120 2.479730 GCAAAGCAGCTGATGGATTGAG 60.480 50.000 20.43 0.00 0.00 3.02
3040 3150 4.863131 ACTTACAGCGAGCTATGTAACAAC 59.137 41.667 12.32 0.00 37.06 3.32
3042 3152 4.713824 ACTTACAGCGAGCTATGTAACA 57.286 40.909 12.32 0.00 37.06 2.41
3110 3220 7.823149 AAACCGTTACAGCATTAGTAACTAG 57.177 36.000 12.60 7.67 45.60 2.57
3136 3249 7.599245 ACAGTACTTACACAGAAGACTAAATGC 59.401 37.037 0.00 0.00 0.00 3.56
3195 3308 8.364142 ACAGGACAAGATGAATAATAGAGTAGC 58.636 37.037 0.00 0.00 0.00 3.58
3235 3348 5.485662 AGTTATTTGCTTCATTAGACGGC 57.514 39.130 0.00 0.00 0.00 5.68
3315 3428 8.523915 AACTGCATCCATTTAACAGATATTGA 57.476 30.769 0.00 0.00 32.67 2.57
3351 3464 5.416947 ACGTGTAAGGACATTATGGAGAAC 58.583 41.667 0.00 0.00 38.04 3.01
3356 3469 5.182380 ACCAAAACGTGTAAGGACATTATGG 59.818 40.000 4.26 0.00 38.04 2.74
3363 3476 5.467735 ACTTGATACCAAAACGTGTAAGGAC 59.532 40.000 4.26 0.00 0.00 3.85
3467 3580 8.079211 TCAGACTGCTATCTTTAAGGTGTATT 57.921 34.615 0.00 0.00 0.00 1.89
3468 3581 7.661536 TCAGACTGCTATCTTTAAGGTGTAT 57.338 36.000 0.00 0.00 0.00 2.29
3484 3597 5.928839 TGTAAGACTTGAATCTTCAGACTGC 59.071 40.000 0.00 0.00 39.65 4.40
3489 3602 6.817641 AGCTGATGTAAGACTTGAATCTTCAG 59.182 38.462 0.00 9.44 39.65 3.02
3498 3611 7.487484 TCAGAGATAAGCTGATGTAAGACTTG 58.513 38.462 0.00 0.00 37.46 3.16
3508 3621 4.405036 TCTGCAGTTCAGAGATAAGCTGAT 59.595 41.667 14.67 0.00 46.34 2.90
3531 3644 4.345257 TCGCCTTTAGAGAATATGGAAGCT 59.655 41.667 0.00 0.00 0.00 3.74
3547 3660 3.181465 TGTCACTCTTTTCTCTCGCCTTT 60.181 43.478 0.00 0.00 0.00 3.11
3554 3667 4.527816 AGAGCTCATGTCACTCTTTTCTCT 59.472 41.667 17.77 0.00 37.50 3.10
3560 3673 4.085733 ACACTAGAGCTCATGTCACTCTT 58.914 43.478 17.77 0.00 41.03 2.85
3569 3682 0.460987 GGCGCAACACTAGAGCTCAT 60.461 55.000 17.77 3.63 0.00 2.90
3573 3686 2.432628 ACGGCGCAACACTAGAGC 60.433 61.111 10.83 0.00 0.00 4.09
3581 3694 1.204312 GAAACTCTGACGGCGCAAC 59.796 57.895 10.83 0.00 0.00 4.17
3585 3698 1.986378 CACTAAGAAACTCTGACGGCG 59.014 52.381 4.80 4.80 0.00 6.46
3656 3769 4.142381 GCTGAAGTTATGTGATCAAACCCC 60.142 45.833 0.00 0.00 0.00 4.95
3667 3780 2.472695 TCAAGCCGCTGAAGTTATGT 57.527 45.000 0.00 0.00 0.00 2.29
3675 3788 2.009774 GCTTTTAGATCAAGCCGCTGA 58.990 47.619 5.20 0.00 40.79 4.26
3682 3795 1.064654 GCTGCCGGCTTTTAGATCAAG 59.935 52.381 29.70 13.44 38.06 3.02
3732 3846 4.361451 AATTCAGACGATGGCAATGTTC 57.639 40.909 0.00 0.00 0.00 3.18
3742 3856 2.034812 GGGCTCGAGTAATTCAGACGAT 59.965 50.000 15.13 0.00 32.81 3.73
3744 3858 1.536284 GGGGCTCGAGTAATTCAGACG 60.536 57.143 15.13 0.00 0.00 4.18
3749 3863 2.431057 TCAGAAGGGGCTCGAGTAATTC 59.569 50.000 15.13 12.83 0.00 2.17
3754 3868 2.355193 GCTCAGAAGGGGCTCGAGT 61.355 63.158 15.13 0.00 0.00 4.18
3755 3869 2.498726 GCTCAGAAGGGGCTCGAG 59.501 66.667 8.45 8.45 0.00 4.04
3778 3892 2.370281 TTCACAACCTCTCTCATCGC 57.630 50.000 0.00 0.00 0.00 4.58
3789 3903 7.384660 TCAATGTCAATAAGCATTTTCACAACC 59.615 33.333 0.00 0.00 33.55 3.77
3825 3939 2.304761 TGTTCTTTGCCCTCCGAATACT 59.695 45.455 0.00 0.00 0.00 2.12
3947 4061 9.280174 AGCTCACTAGTAGTACATTCTAATCTC 57.720 37.037 1.57 0.00 0.00 2.75
3961 4083 3.194542 ACTTGCTTCCAGCTCACTAGTAG 59.805 47.826 0.00 0.00 42.97 2.57


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

AutoCloner maintained by Alex Coulton.