Multiple sequence alignment - TraesCS1B01G062300

Loading Multiple Alignment...

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 TraesCS1B01G062300 chr1B 100.000 4004 0 0 1 4004 47179510 47183513 0.000000e+00 7395.0
1 TraesCS1B01G062300 chr1B 94.286 35 2 0 3817 3851 6540656 6540690 2.000000e-03 54.7
2 TraesCS1B01G062300 chr1B 94.286 35 2 0 3817 3851 7117985 7118019 2.000000e-03 54.7
3 TraesCS1B01G062300 chr1A 93.113 3412 162 21 601 4004 29800010 29803356 0.000000e+00 4931.0
4 TraesCS1B01G062300 chr1A 88.055 586 33 12 1 559 29799431 29800006 0.000000e+00 660.0
5 TraesCS1B01G062300 chr1D 96.274 2684 86 6 601 3271 28573855 28576537 0.000000e+00 4390.0
6 TraesCS1B01G062300 chr1D 88.476 1371 103 25 2613 3977 28658935 28660256 0.000000e+00 1605.0
7 TraesCS1B01G062300 chr1D 85.164 519 46 13 71 572 28572685 28573189 1.660000e-138 503.0
8 TraesCS1B01G062300 chr1D 94.118 272 16 0 3295 3566 28577062 28577333 8.010000e-112 414.0
9 TraesCS1B01G062300 chr1D 89.720 214 21 1 3764 3977 28577732 28577944 5.100000e-69 272.0
10 TraesCS1B01G062300 chr1D 92.308 91 7 0 599 689 28573766 28573856 3.250000e-26 130.0
11 TraesCS1B01G062300 chr2B 74.576 354 73 11 1963 2305 243003939 243003592 5.400000e-29 139.0


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 TraesCS1B01G062300 chr1B 47179510 47183513 4003 False 7395.0 7395 100.0000 1 4004 1 chr1B.!!$F3 4003
1 TraesCS1B01G062300 chr1A 29799431 29803356 3925 False 2795.5 4931 90.5840 1 4004 2 chr1A.!!$F1 4003
2 TraesCS1B01G062300 chr1D 28658935 28660256 1321 False 1605.0 1605 88.4760 2613 3977 1 chr1D.!!$F1 1364
3 TraesCS1B01G062300 chr1D 28572685 28577944 5259 False 1141.8 4390 91.5168 71 3977 5 chr1D.!!$F2 3906

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
34 36 0.436150 CATATCGCCTCGATGCAACG 59.564 55.000 10.48 10.48 46.43 4.10 F
1158 1831 0.039798 CGTCGAACGGACTCCTTGAA 60.040 55.000 0.00 0.00 43.79 2.69 F
1209 1882 0.981183 ATGCGTTCTACCCAACTCCA 59.019 50.000 0.00 0.00 0.00 3.86 F
2148 2821 1.222936 CCATGACTCCAGACAGGGC 59.777 63.158 0.00 0.00 35.28 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1504 2177 0.984230 CCTGCAGGGTTGGACTCTAA 59.016 55.000 26.14 0.0 0.00 2.10 R
2847 3520 0.248215 GGAGTTGCAAATCGCCATCG 60.248 55.000 19.59 0.0 41.33 3.84 R
2956 3629 1.265635 TGTGCCAATGCTCGTGTTTAC 59.734 47.619 0.00 0.0 38.71 2.01 R
3953 5394 0.473755 TTTCTGTGAAGCCAGCCAGA 59.526 50.000 0.00 0.0 32.32 3.86 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
22 24 4.550422 TGAACTCTATGCAGTCATATCGC 58.450 43.478 0.00 0.00 34.88 4.58
34 36 0.436150 CATATCGCCTCGATGCAACG 59.564 55.000 10.48 10.48 46.43 4.10
44 46 0.865111 CGATGCAACGTTGGAGTCAA 59.135 50.000 28.33 4.69 30.13 3.18
53 55 3.335579 ACGTTGGAGTCAATAAAGCTCC 58.664 45.455 0.00 0.00 46.61 4.70
70 78 2.232208 GCTCCCATTGAGAAAAGGGTTG 59.768 50.000 0.00 0.00 44.42 3.77
94 102 3.189287 CCTACAACAGTTCCTGACAATGC 59.811 47.826 0.00 0.00 35.18 3.56
225 240 2.434884 AAGGCCGACGCACATGAG 60.435 61.111 0.00 0.00 36.38 2.90
289 304 3.304928 CGCAGAGCAAAGATTTTTCCACT 60.305 43.478 0.00 0.00 0.00 4.00
398 430 4.385358 TGACTGCACGCATTTATCTAGA 57.615 40.909 0.00 0.00 0.00 2.43
399 431 4.363138 TGACTGCACGCATTTATCTAGAG 58.637 43.478 0.00 0.00 0.00 2.43
400 432 4.142160 TGACTGCACGCATTTATCTAGAGT 60.142 41.667 0.00 0.00 0.00 3.24
401 433 5.067283 TGACTGCACGCATTTATCTAGAGTA 59.933 40.000 0.00 0.00 0.00 2.59
402 434 5.524284 ACTGCACGCATTTATCTAGAGTAG 58.476 41.667 0.00 0.00 0.00 2.57
407 439 7.808381 TGCACGCATTTATCTAGAGTAGTAATC 59.192 37.037 0.00 0.00 0.00 1.75
489 521 2.627699 ACAGGCTGTGTAAATTTGGGTG 59.372 45.455 21.37 0.00 37.75 4.61
500 532 6.695713 GTGTAAATTTGGGTGTCAGTTCTTTC 59.304 38.462 0.00 0.00 0.00 2.62
572 604 6.639632 AAAACATGGTAGCAGCCATTATAG 57.360 37.500 9.04 2.21 46.33 1.31
574 606 4.899502 ACATGGTAGCAGCCATTATAGAC 58.100 43.478 9.04 0.00 46.33 2.59
575 607 3.660501 TGGTAGCAGCCATTATAGACG 57.339 47.619 0.00 0.00 32.81 4.18
576 608 2.963101 TGGTAGCAGCCATTATAGACGT 59.037 45.455 0.00 0.00 32.81 4.34
577 609 4.146564 TGGTAGCAGCCATTATAGACGTA 58.853 43.478 0.00 0.00 32.81 3.57
578 610 4.022589 TGGTAGCAGCCATTATAGACGTAC 60.023 45.833 0.00 0.00 32.81 3.67
579 611 4.217983 GGTAGCAGCCATTATAGACGTACT 59.782 45.833 0.00 0.00 0.00 2.73
580 612 4.244425 AGCAGCCATTATAGACGTACTG 57.756 45.455 0.00 0.00 0.00 2.74
581 613 3.889538 AGCAGCCATTATAGACGTACTGA 59.110 43.478 0.00 0.00 0.00 3.41
582 614 4.341235 AGCAGCCATTATAGACGTACTGAA 59.659 41.667 0.00 0.00 0.00 3.02
583 615 5.047847 GCAGCCATTATAGACGTACTGAAA 58.952 41.667 0.00 0.00 0.00 2.69
584 616 5.696724 GCAGCCATTATAGACGTACTGAAAT 59.303 40.000 0.00 0.00 0.00 2.17
586 618 6.923508 CAGCCATTATAGACGTACTGAAATGA 59.076 38.462 16.49 0.00 35.75 2.57
587 619 6.924060 AGCCATTATAGACGTACTGAAATGAC 59.076 38.462 16.49 10.59 35.75 3.06
588 620 6.700081 GCCATTATAGACGTACTGAAATGACA 59.300 38.462 16.49 0.00 35.75 3.58
589 621 7.306632 GCCATTATAGACGTACTGAAATGACAC 60.307 40.741 16.49 8.73 35.75 3.67
591 623 8.746751 CATTATAGACGTACTGAAATGACACTG 58.253 37.037 0.00 0.00 35.75 3.66
592 624 3.318017 AGACGTACTGAAATGACACTGC 58.682 45.455 0.00 0.00 0.00 4.40
594 626 3.664107 ACGTACTGAAATGACACTGCAT 58.336 40.909 0.00 0.00 0.00 3.96
595 627 4.816392 ACGTACTGAAATGACACTGCATA 58.184 39.130 0.00 0.00 0.00 3.14
597 629 5.120208 ACGTACTGAAATGACACTGCATAAC 59.880 40.000 0.00 0.00 0.00 1.89
598 630 5.120053 CGTACTGAAATGACACTGCATAACA 59.880 40.000 0.00 0.00 0.00 2.41
599 631 6.347321 CGTACTGAAATGACACTGCATAACAA 60.347 38.462 0.00 0.00 0.00 2.83
622 1291 3.758023 TGACCAATGTGGAAAGCTACATG 59.242 43.478 0.18 0.00 44.28 3.21
674 1343 3.244284 TGTGTAACCACCGAAAGCTACAT 60.244 43.478 0.00 0.00 41.09 2.29
676 1345 5.114081 GTGTAACCACCGAAAGCTACATAT 58.886 41.667 0.00 0.00 35.44 1.78
679 1348 7.278424 GTGTAACCACCGAAAGCTACATATAAA 59.722 37.037 0.00 0.00 35.44 1.40
804 1477 7.363705 CCTGCAAATAAATTACAACCATGAGGA 60.364 37.037 0.00 0.00 38.69 3.71
834 1507 2.236893 TGCACTGAAGTCATGCCTATCA 59.763 45.455 10.94 0.00 38.63 2.15
921 1594 3.054361 GTGGAAAAGAGAGGGCAGGATAA 60.054 47.826 0.00 0.00 0.00 1.75
959 1632 9.787532 TCACTGCAAATTAAGTTAAATAGCATC 57.212 29.630 15.21 0.00 32.79 3.91
1034 1707 1.206849 CCTCTGTTTCCTCCTCTGCTC 59.793 57.143 0.00 0.00 0.00 4.26
1068 1741 1.798813 GCGTTTTTCACTGCAGCAAGT 60.799 47.619 15.27 0.00 0.00 3.16
1158 1831 0.039798 CGTCGAACGGACTCCTTGAA 60.040 55.000 0.00 0.00 43.79 2.69
1209 1882 0.981183 ATGCGTTCTACCCAACTCCA 59.019 50.000 0.00 0.00 0.00 3.86
1243 1916 3.385193 AATCGCATGATGATACCGTGA 57.615 42.857 0.00 0.00 34.24 4.35
1290 1963 2.034799 GCCATCCACTCTAGCTACCCA 61.035 57.143 0.00 0.00 0.00 4.51
1323 1996 2.258726 GGGCTTGGCTTTCGTCGTT 61.259 57.895 0.00 0.00 0.00 3.85
1504 2177 1.701847 ACATCAACAGCCTCCAGTCTT 59.298 47.619 0.00 0.00 0.00 3.01
1572 2245 3.754188 CAAGACATGGTTCTTGCTAGC 57.246 47.619 8.10 8.10 44.53 3.42
1596 2269 2.557924 TGATGCAATTCAAGTGTGGGTC 59.442 45.455 0.00 0.00 0.00 4.46
1704 2377 7.039011 ACAGATTATGACCTCTCAAGTGTGTTA 60.039 37.037 0.00 0.00 0.00 2.41
1887 2560 6.493802 TGAAAATCATCCTACCTATAGCGAGT 59.506 38.462 0.00 0.00 0.00 4.18
2064 2737 1.604378 CCTACTTGGTGCAGGAGGG 59.396 63.158 0.00 0.00 30.54 4.30
2086 2759 5.134850 GGGTTTGGGAAGGTATATAAAGGGA 59.865 44.000 0.00 0.00 0.00 4.20
2100 2773 1.760405 AAGGGACCCTTCCATCAACT 58.240 50.000 20.95 0.00 40.17 3.16
2130 2803 2.633488 GTTGCTGTGAAGAGGGTATCC 58.367 52.381 0.00 0.00 0.00 2.59
2148 2821 1.222936 CCATGACTCCAGACAGGGC 59.777 63.158 0.00 0.00 35.28 5.19
2214 2887 4.376008 CGACATCGTAACCTTGTTCAGTTG 60.376 45.833 0.00 0.00 34.11 3.16
2659 3332 1.725641 TAACAGCAATGCACGAGGAG 58.274 50.000 8.35 0.00 0.00 3.69
2675 3348 3.619038 CGAGGAGATCAACCTTTGTTAGC 59.381 47.826 11.77 0.00 37.93 3.09
2713 3386 4.166725 AGCATTGGAATAAGGGATCACTGA 59.833 41.667 0.00 0.00 0.00 3.41
2802 3475 1.470979 GGACTACTATGTGCACACCCG 60.471 57.143 24.37 15.49 0.00 5.28
2847 3520 2.608261 GCAGAGTATCATGCGGTACCTC 60.608 54.545 10.90 1.76 37.82 3.85
2956 3629 6.122782 CGTTACGCATTGTCATATCTTTCAG 58.877 40.000 0.00 0.00 0.00 3.02
3006 3679 5.129485 TGGTCTTTCAGGAGGAAGATGATAC 59.871 44.000 0.00 0.00 36.72 2.24
3052 3731 0.245539 GTGAGCTTGCATGCCACATT 59.754 50.000 26.54 10.78 35.63 2.71
3055 3734 1.730064 GAGCTTGCATGCCACATTTTG 59.270 47.619 19.99 0.00 0.00 2.44
3060 3741 4.611130 GCTTGCATGCCACATTTTGTTTAC 60.611 41.667 16.68 0.00 0.00 2.01
3147 3828 5.539582 AGTGCGTAATTGCTTTTCGAATA 57.460 34.783 0.00 0.00 35.36 1.75
3149 3830 4.728608 GTGCGTAATTGCTTTTCGAATAGG 59.271 41.667 15.97 3.48 35.36 2.57
3248 3933 5.539582 TCAATTGCTTATTACGTGGTGTC 57.460 39.130 0.00 0.00 0.00 3.67
3359 4545 9.358872 AGCTCACAAACATATATGTATATGACG 57.641 33.333 18.56 14.40 45.23 4.35
3414 4600 5.221843 TGGAGGAGGCTGCGTTTATATATTT 60.222 40.000 0.00 0.00 0.00 1.40
3508 4694 2.216898 GCGATTCTGCAGCCTATCTTT 58.783 47.619 9.47 0.00 34.15 2.52
3580 4766 2.039137 ACCTCCTTCCCTCCCGTC 59.961 66.667 0.00 0.00 0.00 4.79
3602 4797 1.077501 GCTCAGCAGCCCCACAATA 60.078 57.895 0.00 0.00 40.14 1.90
3610 4805 0.627469 AGCCCCACAATACCATCCCT 60.627 55.000 0.00 0.00 0.00 4.20
3636 4831 1.190178 GGACCGAGTGTTACCACCCT 61.190 60.000 0.00 0.00 42.88 4.34
3638 4833 0.761702 ACCGAGTGTTACCACCCTGT 60.762 55.000 0.00 0.00 42.88 4.00
3680 5094 2.770164 TTCTTTCCAGCCTGACTAGC 57.230 50.000 0.00 0.00 0.00 3.42
3693 5107 1.870055 GACTAGCCGTCGGTTGTGGA 61.870 60.000 13.94 0.00 32.04 4.02
3727 5141 3.099905 CTCCTCTCATCACCACCACTTA 58.900 50.000 0.00 0.00 0.00 2.24
3734 5148 0.322456 TCACCACCACTTATGCTGCC 60.322 55.000 0.00 0.00 0.00 4.85
3736 5150 0.112218 ACCACCACTTATGCTGCCAA 59.888 50.000 0.00 0.00 0.00 4.52
3737 5151 0.813184 CCACCACTTATGCTGCCAAG 59.187 55.000 8.93 8.93 0.00 3.61
3746 5160 2.181021 GCTGCCAAGCTGATGTGC 59.819 61.111 0.00 0.00 46.60 4.57
3747 5161 2.483745 CTGCCAAGCTGATGTGCG 59.516 61.111 0.00 0.00 38.13 5.34
3748 5162 2.032376 TGCCAAGCTGATGTGCGA 59.968 55.556 0.00 0.00 38.13 5.10
3749 5163 2.249557 CTGCCAAGCTGATGTGCGAC 62.250 60.000 0.00 0.00 38.13 5.19
3750 5164 2.780643 CCAAGCTGATGTGCGACG 59.219 61.111 0.00 0.00 38.13 5.12
3751 5165 2.029288 CCAAGCTGATGTGCGACGT 61.029 57.895 0.00 0.00 38.13 4.34
3752 5166 1.417592 CAAGCTGATGTGCGACGTC 59.582 57.895 5.18 5.18 38.13 4.34
3753 5167 1.010935 CAAGCTGATGTGCGACGTCT 61.011 55.000 14.70 0.00 35.24 4.18
3754 5168 0.526211 AAGCTGATGTGCGACGTCTA 59.474 50.000 14.70 0.00 35.24 2.59
3755 5169 0.526211 AGCTGATGTGCGACGTCTAA 59.474 50.000 14.70 0.00 35.24 2.10
3756 5170 1.135139 AGCTGATGTGCGACGTCTAAT 59.865 47.619 14.70 1.45 35.24 1.73
3757 5171 1.518929 GCTGATGTGCGACGTCTAATC 59.481 52.381 14.70 11.03 35.24 1.75
3758 5172 2.796383 GCTGATGTGCGACGTCTAATCT 60.796 50.000 14.70 0.00 35.24 2.40
3759 5173 3.039405 CTGATGTGCGACGTCTAATCTC 58.961 50.000 14.70 5.75 35.24 2.75
3760 5174 2.422127 TGATGTGCGACGTCTAATCTCA 59.578 45.455 14.70 8.27 35.24 3.27
3761 5175 3.066760 TGATGTGCGACGTCTAATCTCAT 59.933 43.478 14.70 11.45 35.24 2.90
3762 5176 3.066369 TGTGCGACGTCTAATCTCATC 57.934 47.619 14.70 0.00 0.00 2.92
3792 5233 3.577805 AAAGGCTACACAAGTGGAGTT 57.422 42.857 13.61 0.00 43.47 3.01
3813 5254 0.540365 CAAACACTGCCCCCACTGAT 60.540 55.000 0.00 0.00 0.00 2.90
3829 5270 4.825634 CCACTGATACGACCCTAGATGTAA 59.174 45.833 0.00 0.00 0.00 2.41
3851 5292 4.412060 TTAATCTTTCAACCCCACCCAT 57.588 40.909 0.00 0.00 0.00 4.00
3852 5293 3.274281 AATCTTTCAACCCCACCCATT 57.726 42.857 0.00 0.00 0.00 3.16
3858 5299 4.691326 TTCAACCCCACCCATTTTTAAC 57.309 40.909 0.00 0.00 0.00 2.01
3863 5304 2.831526 CCCCACCCATTTTTAACTCCAG 59.168 50.000 0.00 0.00 0.00 3.86
3950 5391 6.127619 GGCAACTTAGCAAGGACTGAAAATAT 60.128 38.462 0.00 0.00 35.83 1.28
3953 5394 9.167311 CAACTTAGCAAGGACTGAAAATATAGT 57.833 33.333 0.00 0.00 0.00 2.12
3970 5411 1.123861 AGTCTGGCTGGCTTCACAGA 61.124 55.000 2.00 0.00 40.97 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.436150 CGTTGCATCGAGGCGATATG 59.564 55.000 16.06 5.91 45.19 1.78
16 17 0.032130 ACGTTGCATCGAGGCGATAT 59.968 50.000 23.12 3.82 45.19 1.63
19 21 2.048597 AACGTTGCATCGAGGCGA 60.049 55.556 23.12 13.46 41.13 5.54
22 24 0.670546 ACTCCAACGTTGCATCGAGG 60.671 55.000 25.84 21.25 34.70 4.63
44 46 4.958581 CCCTTTTCTCAATGGGAGCTTTAT 59.041 41.667 0.46 0.00 46.43 1.40
53 55 3.500343 AGGACAACCCTTTTCTCAATGG 58.500 45.455 0.00 0.00 44.85 3.16
94 102 7.227156 AGGAGTATGTAGCATTCTAAATTGGG 58.773 38.462 0.00 0.00 0.00 4.12
225 240 6.024049 GCTACGCATGCCTTCATAATTTATC 58.976 40.000 13.15 0.00 0.00 1.75
289 304 8.612486 TTTCAGGATACATGGTTAGGTAAGTA 57.388 34.615 0.00 0.00 41.41 2.24
468 500 2.627699 CACCCAAATTTACACAGCCTGT 59.372 45.455 0.00 0.00 36.82 4.00
489 521 4.200092 ACTGTTTCCTGGAAAGAACTGAC 58.800 43.478 21.68 9.83 31.87 3.51
559 591 3.889538 TCAGTACGTCTATAATGGCTGCT 59.110 43.478 0.00 0.00 0.00 4.24
568 600 6.127842 TGCAGTGTCATTTCAGTACGTCTATA 60.128 38.462 0.00 0.00 0.00 1.31
572 604 3.057019 TGCAGTGTCATTTCAGTACGTC 58.943 45.455 0.00 0.00 0.00 4.34
574 606 5.120053 TGTTATGCAGTGTCATTTCAGTACG 59.880 40.000 5.55 0.00 0.00 3.67
575 607 6.480524 TGTTATGCAGTGTCATTTCAGTAC 57.519 37.500 5.55 0.00 0.00 2.73
576 608 7.390162 TCATTGTTATGCAGTGTCATTTCAGTA 59.610 33.333 5.55 0.00 36.38 2.74
577 609 6.207221 TCATTGTTATGCAGTGTCATTTCAGT 59.793 34.615 5.55 1.78 36.38 3.41
578 610 6.525628 GTCATTGTTATGCAGTGTCATTTCAG 59.474 38.462 5.55 0.00 36.38 3.02
579 611 6.380995 GTCATTGTTATGCAGTGTCATTTCA 58.619 36.000 5.55 3.93 36.38 2.69
580 612 5.801947 GGTCATTGTTATGCAGTGTCATTTC 59.198 40.000 5.55 1.93 36.38 2.17
581 613 5.243507 TGGTCATTGTTATGCAGTGTCATTT 59.756 36.000 5.55 0.00 36.38 2.32
582 614 4.766373 TGGTCATTGTTATGCAGTGTCATT 59.234 37.500 5.55 0.00 36.38 2.57
583 615 4.334552 TGGTCATTGTTATGCAGTGTCAT 58.665 39.130 0.00 5.56 36.38 3.06
584 616 3.749226 TGGTCATTGTTATGCAGTGTCA 58.251 40.909 0.00 0.00 36.38 3.58
586 618 4.523943 ACATTGGTCATTGTTATGCAGTGT 59.476 37.500 0.00 0.00 36.38 3.55
587 619 4.860352 CACATTGGTCATTGTTATGCAGTG 59.140 41.667 0.00 0.00 36.31 3.66
588 620 4.082081 CCACATTGGTCATTGTTATGCAGT 60.082 41.667 0.00 0.00 31.35 4.40
589 621 4.158209 TCCACATTGGTCATTGTTATGCAG 59.842 41.667 0.00 0.00 39.03 4.41
591 623 4.717233 TCCACATTGGTCATTGTTATGC 57.283 40.909 0.00 0.00 39.03 3.14
592 624 5.577945 GCTTTCCACATTGGTCATTGTTATG 59.422 40.000 0.00 0.00 39.03 1.90
594 626 4.832266 AGCTTTCCACATTGGTCATTGTTA 59.168 37.500 0.00 0.00 39.03 2.41
595 627 3.642848 AGCTTTCCACATTGGTCATTGTT 59.357 39.130 0.00 0.00 39.03 2.83
597 629 3.947910 AGCTTTCCACATTGGTCATTG 57.052 42.857 0.00 0.00 39.03 2.82
598 630 4.406456 TGTAGCTTTCCACATTGGTCATT 58.594 39.130 0.00 0.00 39.03 2.57
599 631 4.032960 TGTAGCTTTCCACATTGGTCAT 57.967 40.909 0.00 0.00 39.03 3.06
679 1348 7.761704 CACTACACATAGCTTCACAAGTCTATT 59.238 37.037 0.00 0.00 30.63 1.73
695 1368 7.347222 ACTTTCCCATATTCTCCACTACACATA 59.653 37.037 0.00 0.00 0.00 2.29
804 1477 3.554934 TGACTTCAGTGCACAATCCTTT 58.445 40.909 21.04 0.00 0.00 3.11
876 1549 2.679837 GGCATCGTTGTCTGACATTGAT 59.320 45.455 11.86 14.09 0.00 2.57
921 1594 5.852282 ATTTGCAGTGAGGTAAAAGTTGT 57.148 34.783 0.00 0.00 0.00 3.32
982 1655 2.306805 TCATGTGAGATGGGTGCTTCTT 59.693 45.455 0.00 0.00 0.00 2.52
1034 1707 4.749310 ACGCAAGCTCGAGGCCAG 62.749 66.667 15.58 0.00 43.05 4.85
1158 1831 1.453155 CAAGCGAGCCATTGGTTAGT 58.547 50.000 4.26 0.00 0.00 2.24
1243 1916 2.996621 CGAAGGCGACTGAGAAAGATTT 59.003 45.455 0.00 0.00 42.68 2.17
1504 2177 0.984230 CCTGCAGGGTTGGACTCTAA 59.016 55.000 26.14 0.00 0.00 2.10
1572 2245 2.587956 CACACTTGAATTGCATCACCG 58.412 47.619 0.00 0.00 0.00 4.94
1596 2269 2.093306 TGGCTTCACCATTGTAGTCG 57.907 50.000 0.00 0.00 46.36 4.18
1704 2377 2.037772 GCCGATGTAGGATGGATCTTGT 59.962 50.000 0.00 0.00 0.00 3.16
2064 2737 6.066690 GGTCCCTTTATATACCTTCCCAAAC 58.933 44.000 0.00 0.00 0.00 2.93
2086 2759 5.189934 CCTCTAGTTTAGTTGATGGAAGGGT 59.810 44.000 0.00 0.00 0.00 4.34
2100 2773 5.279506 CCTCTTCACAGCAACCTCTAGTTTA 60.280 44.000 0.00 0.00 36.18 2.01
2130 2803 1.222936 GCCCTGTCTGGAGTCATGG 59.777 63.158 0.00 0.00 38.35 3.66
2136 2809 0.543749 CCTTTAGGCCCTGTCTGGAG 59.456 60.000 0.00 0.00 38.35 3.86
2148 2821 3.503748 CCTCAGCAACAAACTCCTTTAGG 59.496 47.826 0.00 0.00 0.00 2.69
2214 2887 5.186198 TCTTTTCTCCTACAATAGCCAAGC 58.814 41.667 0.00 0.00 0.00 4.01
2306 2979 6.423182 TGAGCCCAGTTTAGTATAAGCATTT 58.577 36.000 0.00 0.00 0.00 2.32
2659 3332 5.393461 CCCAATCAGCTAACAAAGGTTGATC 60.393 44.000 0.00 0.00 37.88 2.92
2675 3348 3.119245 CCAATGCTCAAGAACCCAATCAG 60.119 47.826 0.00 0.00 0.00 2.90
2802 3475 0.972883 TGGGCCTTGCATTGGTAAAC 59.027 50.000 4.53 0.00 0.00 2.01
2847 3520 0.248215 GGAGTTGCAAATCGCCATCG 60.248 55.000 19.59 0.00 41.33 3.84
2937 3610 7.426456 GTGTTTACTGAAAGATATGACAATGCG 59.574 37.037 0.00 0.00 37.43 4.73
2956 3629 1.265635 TGTGCCAATGCTCGTGTTTAC 59.734 47.619 0.00 0.00 38.71 2.01
3052 3731 9.344772 ACATTACATGACTTGGTAGTAAACAAA 57.655 29.630 0.00 0.00 33.84 2.83
3055 3734 9.607285 CAAACATTACATGACTTGGTAGTAAAC 57.393 33.333 0.00 0.00 33.84 2.01
3060 3741 5.125417 CCCCAAACATTACATGACTTGGTAG 59.875 44.000 0.00 7.65 41.21 3.18
3179 3864 2.168496 AGTACGCTGGTAGCTTCTTCA 58.832 47.619 0.00 0.00 39.60 3.02
3192 3877 2.561478 AATCAACCCACAAGTACGCT 57.439 45.000 0.00 0.00 0.00 5.07
3248 3933 7.716998 AGATAGTATTTATTTGTGGGCTGTGAG 59.283 37.037 0.00 0.00 0.00 3.51
3359 4545 6.038997 AGATACACTTCCCACAGTTTCTAC 57.961 41.667 0.00 0.00 0.00 2.59
3508 4694 4.562757 CGTCATTAGGTTGTTGGAGAAGGA 60.563 45.833 0.00 0.00 0.00 3.36
3610 4805 2.762327 GGTAACACTCGGTCCCAATAGA 59.238 50.000 0.00 0.00 0.00 1.98
3636 4831 2.046988 CATGGTGGCGAGCTCACA 60.047 61.111 15.40 9.34 36.90 3.58
3638 4833 4.783621 GGCATGGTGGCGAGCTCA 62.784 66.667 15.40 0.00 31.79 4.26
3704 5118 0.618680 TGGTGGTGATGAGAGGAGGG 60.619 60.000 0.00 0.00 0.00 4.30
3734 5148 1.010935 AGACGTCGCACATCAGCTTG 61.011 55.000 10.46 0.00 0.00 4.01
3736 5150 0.526211 TTAGACGTCGCACATCAGCT 59.474 50.000 10.46 0.00 0.00 4.24
3737 5151 1.518929 GATTAGACGTCGCACATCAGC 59.481 52.381 10.46 0.00 0.00 4.26
3738 5152 3.039405 GAGATTAGACGTCGCACATCAG 58.961 50.000 10.46 0.00 0.00 2.90
3739 5153 2.422127 TGAGATTAGACGTCGCACATCA 59.578 45.455 10.46 10.44 0.00 3.07
3740 5154 3.066369 TGAGATTAGACGTCGCACATC 57.934 47.619 10.46 10.07 0.00 3.06
3741 5155 3.066760 TGATGAGATTAGACGTCGCACAT 59.933 43.478 10.46 10.88 0.00 3.21
3742 5156 2.422127 TGATGAGATTAGACGTCGCACA 59.578 45.455 10.46 6.63 0.00 4.57
3743 5157 3.066369 TGATGAGATTAGACGTCGCAC 57.934 47.619 10.46 3.58 0.00 5.34
3744 5158 3.066760 ACATGATGAGATTAGACGTCGCA 59.933 43.478 10.46 0.41 0.00 5.10
3745 5159 3.633235 ACATGATGAGATTAGACGTCGC 58.367 45.455 10.46 1.26 0.00 5.19
3746 5160 6.603095 TCATACATGATGAGATTAGACGTCG 58.397 40.000 10.46 0.00 39.78 5.12
3759 5173 7.967890 TGTGTAGCCTTTATCATACATGATG 57.032 36.000 13.75 0.00 46.34 3.07
3761 5175 7.495606 CACTTGTGTAGCCTTTATCATACATGA 59.504 37.037 0.00 0.00 41.70 3.07
3762 5176 7.254898 CCACTTGTGTAGCCTTTATCATACATG 60.255 40.741 0.00 0.00 31.35 3.21
3773 5214 2.224548 GGAACTCCACTTGTGTAGCCTT 60.225 50.000 0.00 0.00 35.64 4.35
3792 5233 2.197324 GTGGGGGCAGTGTTTGGA 59.803 61.111 0.00 0.00 0.00 3.53
3829 5270 4.412060 TGGGTGGGGTTGAAAGATTAAT 57.588 40.909 0.00 0.00 0.00 1.40
3851 5292 1.613437 GCCTGCTGCTGGAGTTAAAAA 59.387 47.619 27.16 0.00 36.87 1.94
3852 5293 1.247567 GCCTGCTGCTGGAGTTAAAA 58.752 50.000 27.16 0.00 36.87 1.52
3858 5299 1.177256 AAAGTTGCCTGCTGCTGGAG 61.177 55.000 27.16 5.07 42.00 3.86
3863 5304 2.820330 TGTTTTAAAGTTGCCTGCTGC 58.180 42.857 0.00 0.00 41.77 5.25
3920 5361 3.072476 AGTCCTTGCTAAGTTGCCACTTA 59.928 43.478 9.80 9.80 41.81 2.24
3950 5391 0.610174 CTGTGAAGCCAGCCAGACTA 59.390 55.000 0.00 0.00 0.00 2.59
3953 5394 0.473755 TTTCTGTGAAGCCAGCCAGA 59.526 50.000 0.00 0.00 32.32 3.86


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

AutoCloner maintained by Alex Coulton.