Multiple sequence alignment - TraesCS2D01G314500

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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 TraesCS2D01G314500 chr2D 100.000 3464 0 0 1 3464 404118955 404122418 0.000000e+00 6397.0
1 TraesCS2D01G314500 chr2A 90.787 3506 227 39 1 3452 542548905 542552368 0.000000e+00 4597.0
2 TraesCS2D01G314500 chr2B 91.643 2489 148 18 1 2467 478183272 478185722 0.000000e+00 3389.0
3 TraesCS2D01G314500 chr2B 88.469 980 86 13 2488 3452 478187929 478188896 0.000000e+00 1158.0
4 TraesCS2D01G314500 chr2B 90.881 329 26 3 2560 2887 478185785 478186110 4.100000e-119 438.0
5 TraesCS2D01G314500 chr2B 89.899 99 8 2 3024 3122 478187829 478187925 3.630000e-25 126.0
6 TraesCS2D01G314500 chr7D 90.000 50 3 2 696 744 439632502 439632550 2.890000e-06 63.9
7 TraesCS2D01G314500 chr7D 97.297 37 1 0 701 737 534703744 534703708 2.890000e-06 63.9
8 TraesCS2D01G314500 chr4D 89.583 48 5 0 702 749 122173651 122173604 1.040000e-05 62.1
9 TraesCS2D01G314500 chr4A 94.595 37 2 0 701 737 631960105 631960141 1.340000e-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 TraesCS2D01G314500 chr2D 404118955 404122418 3463 False 6397.00 6397 100.000 1 3464 1 chr2D.!!$F1 3463
1 TraesCS2D01G314500 chr2A 542548905 542552368 3463 False 4597.00 4597 90.787 1 3452 1 chr2A.!!$F1 3451
2 TraesCS2D01G314500 chr2B 478183272 478188896 5624 False 1277.75 3389 90.223 1 3452 4 chr2B.!!$F1 3451

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
83 84 0.392998 AAGGAGAACGGCGATGCAAT 60.393 50.0 16.62 0.00 0.00 3.56 F
222 223 0.522626 CATGGATCTTGCGTGCAACA 59.477 50.0 2.58 0.62 35.74 3.33 F
1990 2024 0.613853 TCCAGGTACTTCAGACCCCG 60.614 60.0 0.00 0.00 37.73 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1955 1983 1.154093 GGAGTCGTCGCGTTCATGA 60.154 57.895 5.77 0.0 0.0 3.07 R
2361 2407 0.750850 GCTGGTAGTTGCCGAGGATA 59.249 55.000 0.00 0.0 0.0 2.59 R
3067 5327 0.770499 TGGCAGGAGTTGTGGATCAA 59.230 50.000 0.00 0.0 0.0 2.57 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
26 27 3.207669 GATGGAAGCGCCTGCCTG 61.208 66.667 2.29 0.00 44.31 4.85
41 42 1.586154 GCCTGGAACACCATTCACGG 61.586 60.000 0.00 0.00 32.90 4.94
54 55 0.753867 TTCACGGTCAGCTTGGTACA 59.246 50.000 0.00 0.00 0.00 2.90
67 68 2.172851 TGGTACACGCCAAGTAAAGG 57.827 50.000 0.00 0.00 35.25 3.11
79 80 2.295253 AGTAAAGGAGAACGGCGATG 57.705 50.000 16.62 0.00 0.00 3.84
83 84 0.392998 AAGGAGAACGGCGATGCAAT 60.393 50.000 16.62 0.00 0.00 3.56
84 85 1.091771 AGGAGAACGGCGATGCAATG 61.092 55.000 16.62 0.00 0.00 2.82
110 111 3.571401 CCAACTTGAGCCAAAGACTTCAT 59.429 43.478 3.14 0.00 0.00 2.57
132 133 3.234596 CGTGAGGACTTCGAACAAAAC 57.765 47.619 0.00 0.00 0.00 2.43
136 137 3.203716 GAGGACTTCGAACAAAACAGGT 58.796 45.455 0.00 0.00 0.00 4.00
141 142 3.243068 ACTTCGAACAAAACAGGTCATGC 60.243 43.478 0.00 0.00 0.00 4.06
159 160 4.512944 TCATGCGAGAGAATTAAATGCCTC 59.487 41.667 0.00 0.00 0.00 4.70
182 183 6.524734 TCTGTAATGTCAAGCTTCAAGAAGA 58.475 36.000 13.70 0.00 40.79 2.87
183 184 6.648310 TCTGTAATGTCAAGCTTCAAGAAGAG 59.352 38.462 13.70 3.09 40.79 2.85
222 223 0.522626 CATGGATCTTGCGTGCAACA 59.477 50.000 2.58 0.62 35.74 3.33
307 308 4.899457 TCCCTACTATTTCCGACATGTGAT 59.101 41.667 1.15 0.00 0.00 3.06
364 365 2.320781 TGTAGAAGCTATGAGGGAGGC 58.679 52.381 0.00 0.00 0.00 4.70
448 449 3.303406 GCACAGTTGAGCTTGTGAAATC 58.697 45.455 18.27 0.00 34.50 2.17
464 465 1.298906 AATCCCCTGCCATCACCCAT 61.299 55.000 0.00 0.00 0.00 4.00
504 507 3.199677 CGCCATGATGCCATTTTTGATT 58.800 40.909 0.00 0.00 0.00 2.57
518 524 6.822676 CCATTTTTGATTGCCCAAGCTTTATA 59.177 34.615 0.00 0.00 40.80 0.98
574 581 2.898705 CTCTGTCCGGGATCTCTTTTG 58.101 52.381 0.00 0.00 0.00 2.44
579 586 3.772572 TGTCCGGGATCTCTTTTGTGATA 59.227 43.478 0.00 0.00 33.36 2.15
592 599 9.396022 TCTCTTTTGTGATATTTTCATAGGGTC 57.604 33.333 0.00 0.00 36.54 4.46
623 631 2.233922 TCCTCCCAGATCAAACTCGTTC 59.766 50.000 0.00 0.00 0.00 3.95
630 638 0.673644 ATCAAACTCGTTCGCTGGGG 60.674 55.000 0.00 0.00 0.00 4.96
634 642 0.883370 AACTCGTTCGCTGGGGTTTC 60.883 55.000 0.00 0.00 0.00 2.78
646 655 3.349879 GGGTTTCCCCGATCAAACA 57.650 52.632 8.22 0.00 42.41 2.83
651 675 1.750193 TTCCCCGATCAAACATGAGC 58.250 50.000 0.00 0.00 0.00 4.26
660 684 6.427853 CCCGATCAAACATGAGCTTGATATTA 59.572 38.462 16.78 0.00 39.85 0.98
661 685 7.360691 CCCGATCAAACATGAGCTTGATATTAG 60.361 40.741 16.78 11.24 39.85 1.73
666 690 6.506538 AACATGAGCTTGATATTAGGGTCT 57.493 37.500 0.00 0.00 0.00 3.85
676 700 7.449704 GCTTGATATTAGGGTCTTTGATCCATT 59.550 37.037 0.00 0.00 34.77 3.16
692 716 6.303054 TGATCCATTTGTTGTTTGTCTCCTA 58.697 36.000 0.00 0.00 0.00 2.94
733 758 9.480053 AAATCAACAACACTTATTTTGAGATGG 57.520 29.630 0.00 0.00 30.07 3.51
736 761 6.824305 ACAACACTTATTTTGAGATGGAGG 57.176 37.500 0.00 0.00 0.00 4.30
737 762 6.542821 ACAACACTTATTTTGAGATGGAGGA 58.457 36.000 0.00 0.00 0.00 3.71
739 764 7.505585 ACAACACTTATTTTGAGATGGAGGAAA 59.494 33.333 0.00 0.00 0.00 3.13
914 942 2.643551 CCTTTATGTGCTCCCGAACAT 58.356 47.619 0.00 0.00 42.22 2.71
941 969 3.057526 GGAACAAAGAATTACCGCTGCTT 60.058 43.478 0.00 0.00 0.00 3.91
942 970 3.559238 ACAAAGAATTACCGCTGCTTG 57.441 42.857 0.00 0.00 0.00 4.01
943 971 2.884639 ACAAAGAATTACCGCTGCTTGT 59.115 40.909 0.00 0.00 0.00 3.16
944 972 3.236816 CAAAGAATTACCGCTGCTTGTG 58.763 45.455 0.00 0.00 0.00 3.33
991 1019 1.299773 CCAACACGCAAATTGCCGT 60.300 52.632 12.80 10.63 41.12 5.68
996 1024 2.501650 CGCAAATTGCCGTCGTGG 60.502 61.111 12.80 0.00 41.12 4.94
1013 1041 2.034879 GGTGCATGTCAGTCCACCG 61.035 63.158 2.69 0.00 38.45 4.94
1990 2024 0.613853 TCCAGGTACTTCAGACCCCG 60.614 60.000 0.00 0.00 37.73 5.73
2211 2257 1.153005 CCTCTGCTTCATCCTGCCC 60.153 63.158 0.00 0.00 0.00 5.36
2358 2404 3.384532 GGCAAGACGGACGGGGTA 61.385 66.667 0.00 0.00 0.00 3.69
2361 2407 1.673808 GCAAGACGGACGGGGTATCT 61.674 60.000 0.00 0.00 0.00 1.98
2449 2495 1.148310 CGTCAAGACCAACTGCGAAT 58.852 50.000 0.00 0.00 0.00 3.34
2471 2517 6.821616 ATCCATGACTCACTAGGATTTCTT 57.178 37.500 0.00 0.00 35.65 2.52
2538 4771 1.224075 CGGTATGGCATTGAGCTCTG 58.776 55.000 16.19 6.96 44.79 3.35
2539 4772 0.950116 GGTATGGCATTGAGCTCTGC 59.050 55.000 17.36 17.36 44.79 4.26
2540 4773 0.585357 GTATGGCATTGAGCTCTGCG 59.415 55.000 18.55 7.08 44.79 5.18
2541 4774 0.178767 TATGGCATTGAGCTCTGCGT 59.821 50.000 18.55 13.29 44.79 5.24
2542 4775 0.679002 ATGGCATTGAGCTCTGCGTT 60.679 50.000 18.55 8.21 44.79 4.84
2543 4776 0.890542 TGGCATTGAGCTCTGCGTTT 60.891 50.000 18.55 0.00 44.79 3.60
2544 4777 1.086696 GGCATTGAGCTCTGCGTTTA 58.913 50.000 18.55 0.00 44.79 2.01
2545 4778 1.202076 GGCATTGAGCTCTGCGTTTAC 60.202 52.381 18.55 4.20 44.79 2.01
2546 4779 1.202076 GCATTGAGCTCTGCGTTTACC 60.202 52.381 16.19 0.00 41.15 2.85
2547 4780 2.350522 CATTGAGCTCTGCGTTTACCT 58.649 47.619 16.19 0.00 0.00 3.08
2548 4781 3.521560 CATTGAGCTCTGCGTTTACCTA 58.478 45.455 16.19 0.00 0.00 3.08
2597 4830 1.214175 TGGACAGTGAGGGCAGAAAAA 59.786 47.619 0.00 0.00 0.00 1.94
2605 4839 1.270826 GAGGGCAGAAAAAGAGCAACC 59.729 52.381 0.00 0.00 0.00 3.77
2610 4844 2.358898 GCAGAAAAAGAGCAACCACTCA 59.641 45.455 0.00 0.00 39.26 3.41
2694 4929 4.973168 TGATACAATGGTCTAAGGGCATC 58.027 43.478 0.00 0.00 0.00 3.91
2723 4960 5.695851 TCTTTCTCCTTTTGCAGATTGTC 57.304 39.130 0.00 0.00 0.00 3.18
2748 4987 7.328982 TCAATGAATGAAATTTGTGAATCCACG 59.671 33.333 0.00 0.00 40.89 4.94
2766 5005 8.915871 AATCCACGAAGAATGTGAATTTTATG 57.084 30.769 0.00 0.00 39.73 1.90
2784 5023 1.974265 TGTTCGCACAAGGGAATTCA 58.026 45.000 7.93 0.00 46.53 2.57
2788 5033 4.520874 TGTTCGCACAAGGGAATTCATTTA 59.479 37.500 7.93 0.00 46.53 1.40
2793 5038 7.158021 TCGCACAAGGGAATTCATTTATTTTT 58.842 30.769 7.93 0.00 33.30 1.94
2849 5094 6.428083 TTGGTCCTCAGTGTGAGTAAAATA 57.572 37.500 3.35 0.00 42.80 1.40
2850 5095 5.790593 TGGTCCTCAGTGTGAGTAAAATAC 58.209 41.667 3.35 0.00 42.80 1.89
2856 5101 6.369065 CCTCAGTGTGAGTAAAATACAAGGAC 59.631 42.308 3.35 0.00 42.80 3.85
2858 5103 6.929049 TCAGTGTGAGTAAAATACAAGGACAG 59.071 38.462 0.00 0.00 0.00 3.51
2923 5179 2.573462 GCCATCTATAGAGGGGCATGAA 59.427 50.000 29.55 0.00 45.47 2.57
2952 5208 2.866762 ACGACTCACAAGCTTTTCAGAC 59.133 45.455 0.00 0.00 0.00 3.51
2959 5215 5.376625 TCACAAGCTTTTCAGACCTTACAT 58.623 37.500 0.00 0.00 0.00 2.29
2967 5223 8.734386 AGCTTTTCAGACCTTACATGAATAAAG 58.266 33.333 0.00 0.00 33.26 1.85
2968 5224 8.730680 GCTTTTCAGACCTTACATGAATAAAGA 58.269 33.333 0.00 0.00 33.26 2.52
2971 5227 9.739276 TTTCAGACCTTACATGAATAAAGATGT 57.261 29.630 0.00 0.00 36.72 3.06
3014 5271 6.877855 CCACCTTCATGTGATCCTATAATGAG 59.122 42.308 0.00 0.00 38.55 2.90
3067 5327 2.198827 TCGCCAAATCCTGAACATGT 57.801 45.000 0.00 0.00 0.00 3.21
3102 5362 3.376234 CCTGCCATGAACACATAACTGAG 59.624 47.826 0.00 0.00 0.00 3.35
3116 5376 1.668419 ACTGAGGAACACACTTGCAC 58.332 50.000 0.00 0.00 0.00 4.57
3117 5377 1.210478 ACTGAGGAACACACTTGCACT 59.790 47.619 0.00 0.00 0.00 4.40
3122 5382 4.702612 TGAGGAACACACTTGCACTTTTTA 59.297 37.500 0.00 0.00 0.00 1.52
3131 5392 9.893305 ACACACTTGCACTTTTTATATAAGAAC 57.107 29.630 0.00 0.00 0.00 3.01
3178 5441 2.649140 TTTTGTTTAACGCGTCCTCG 57.351 45.000 14.44 0.00 40.37 4.63
3181 5444 1.005294 TGTTTAACGCGTCCTCGAGC 61.005 55.000 14.44 0.00 40.29 5.03
3189 5452 0.944311 GCGTCCTCGAGCTTGAACAA 60.944 55.000 6.99 0.00 39.71 2.83
3211 5474 9.668497 AACAAATACTCTTTATTAGGTCCAGTC 57.332 33.333 0.00 0.00 0.00 3.51
3223 5486 4.020617 CCAGTCGGGCCTTCAGCA 62.021 66.667 0.84 0.00 46.50 4.41
3244 5507 4.439289 GCAAGGTAGATTTGCCTGAACATC 60.439 45.833 0.00 0.00 43.88 3.06
3251 5514 4.885907 AGATTTGCCTGAACATCACATAGG 59.114 41.667 0.00 0.00 0.00 2.57
3259 5522 6.072838 GCCTGAACATCACATAGGTTATCATG 60.073 42.308 0.00 0.00 30.81 3.07
3270 5533 8.289618 CACATAGGTTATCATGGAAATTAACCG 58.710 37.037 0.00 0.00 41.14 4.44
3284 5547 4.749245 ATTAACCGCAGTTTCAGTTCAG 57.251 40.909 0.00 0.00 37.42 3.02
3310 5574 8.635765 ACAAAATAATGCTGAAGTTAAGGAGA 57.364 30.769 0.00 0.00 0.00 3.71
3445 5709 6.737254 TTAAGGAATTTTACCAAGAGCTCG 57.263 37.500 8.37 0.00 0.00 5.03
3452 5716 8.027189 GGAATTTTACCAAGAGCTCGTTTTAAT 58.973 33.333 8.37 1.36 0.00 1.40
3458 5722 7.549615 ACCAAGAGCTCGTTTTAATAATACC 57.450 36.000 8.37 0.00 0.00 2.73
3459 5723 7.107542 ACCAAGAGCTCGTTTTAATAATACCA 58.892 34.615 8.37 0.00 0.00 3.25
3460 5724 7.773690 ACCAAGAGCTCGTTTTAATAATACCAT 59.226 33.333 8.37 0.00 0.00 3.55
3461 5725 9.268268 CCAAGAGCTCGTTTTAATAATACCATA 57.732 33.333 8.37 0.00 0.00 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.156736 CTGACCGTGAATGGTGTTCC 58.843 55.000 0.00 0.00 44.01 3.62
41 42 0.882927 TTGGCGTGTACCAAGCTGAC 60.883 55.000 0.00 0.00 44.80 3.51
54 55 1.607251 CCGTTCTCCTTTACTTGGCGT 60.607 52.381 0.00 0.00 0.00 5.68
59 60 2.618053 CATCGCCGTTCTCCTTTACTT 58.382 47.619 0.00 0.00 0.00 2.24
67 68 1.258982 CTACATTGCATCGCCGTTCTC 59.741 52.381 0.00 0.00 0.00 2.87
79 80 1.135286 GGCTCAAGTTGGCTACATTGC 60.135 52.381 13.69 0.53 0.00 3.56
83 84 2.158682 TCTTTGGCTCAAGTTGGCTACA 60.159 45.455 13.69 4.51 0.00 2.74
84 85 2.226674 GTCTTTGGCTCAAGTTGGCTAC 59.773 50.000 13.69 0.00 0.00 3.58
110 111 1.034356 TTGTTCGAAGTCCTCACGGA 58.966 50.000 0.00 0.00 36.83 4.69
121 122 2.286713 CGCATGACCTGTTTTGTTCGAA 60.287 45.455 0.00 0.00 0.00 3.71
132 133 5.745514 CATTTAATTCTCTCGCATGACCTG 58.254 41.667 0.00 0.00 0.00 4.00
136 137 4.454678 AGGCATTTAATTCTCTCGCATGA 58.545 39.130 0.00 0.00 0.00 3.07
141 142 7.225538 ACATTACAGAGGCATTTAATTCTCTCG 59.774 37.037 5.10 4.82 34.71 4.04
159 160 6.648310 TCTCTTCTTGAAGCTTGACATTACAG 59.352 38.462 2.10 0.00 0.00 2.74
201 202 1.936436 TTGCACGCAAGATCCATGCC 61.936 55.000 13.72 3.15 40.72 4.40
222 223 6.542821 TCATAACTTCTTGTTGGTTCTCCAT 58.457 36.000 0.00 0.00 43.91 3.41
245 246 2.435372 TAAGGGGCACAACATCCATC 57.565 50.000 0.00 0.00 0.00 3.51
272 273 6.712547 GGAAATAGTAGGGATCAACCAATCTG 59.287 42.308 0.00 0.00 41.20 2.90
273 274 6.464465 CGGAAATAGTAGGGATCAACCAATCT 60.464 42.308 0.00 0.00 41.20 2.40
335 336 5.289675 CCTCATAGCTTCTACAAGTTGTTCG 59.710 44.000 14.90 6.25 31.45 3.95
364 365 5.048507 GGTTGGCGACTTTAGACCTATTAG 58.951 45.833 4.59 0.00 0.00 1.73
409 410 0.603975 GCCCACATCGAGCTAATCCC 60.604 60.000 0.00 0.00 0.00 3.85
448 449 2.123597 CATGGGTGATGGCAGGGG 60.124 66.667 0.00 0.00 0.00 4.79
518 524 6.293081 CGATCGATTCATTGGTGCTTTCTATT 60.293 38.462 10.26 0.00 0.00 1.73
555 561 2.028112 CACAAAAGAGATCCCGGACAGA 60.028 50.000 0.73 0.00 0.00 3.41
561 567 7.320443 TGAAAATATCACAAAAGAGATCCCG 57.680 36.000 0.00 0.00 31.50 5.14
574 581 8.143835 CCCAAAATGACCCTATGAAAATATCAC 58.856 37.037 0.00 0.00 41.93 3.06
579 586 6.070251 GGAACCCAAAATGACCCTATGAAAAT 60.070 38.462 0.00 0.00 0.00 1.82
630 638 2.159379 GCTCATGTTTGATCGGGGAAAC 60.159 50.000 0.00 0.60 33.48 2.78
634 642 1.402968 CAAGCTCATGTTTGATCGGGG 59.597 52.381 0.00 0.00 36.66 5.73
637 646 7.360691 CCCTAATATCAAGCTCATGTTTGATCG 60.361 40.741 18.91 10.74 46.35 3.69
646 655 7.141758 TCAAAGACCCTAATATCAAGCTCAT 57.858 36.000 0.00 0.00 0.00 2.90
651 675 8.930846 AATGGATCAAAGACCCTAATATCAAG 57.069 34.615 0.00 0.00 0.00 3.02
660 684 4.482990 ACAACAAATGGATCAAAGACCCT 58.517 39.130 0.00 0.00 0.00 4.34
661 685 4.871933 ACAACAAATGGATCAAAGACCC 57.128 40.909 0.00 0.00 0.00 4.46
666 690 6.098124 AGGAGACAAACAACAAATGGATCAAA 59.902 34.615 0.00 0.00 0.00 2.69
676 700 5.741011 AGTTGAGTAGGAGACAAACAACAA 58.259 37.500 0.00 0.00 39.27 2.83
692 716 8.952278 TGTTGTTGATTTAGTACAAAGTTGAGT 58.048 29.630 0.00 0.00 33.96 3.41
835 863 0.804364 TCGTTGCATGACATCCTTGC 59.196 50.000 0.00 0.00 43.79 4.01
914 942 3.872771 GCGGTAATTCTTTGTTCCCGATA 59.127 43.478 0.00 0.00 36.12 2.92
941 969 8.380099 AGTTAAATGGGTTAAGTAGATCACACA 58.620 33.333 0.00 0.00 34.21 3.72
942 970 8.788325 AGTTAAATGGGTTAAGTAGATCACAC 57.212 34.615 0.00 0.00 34.21 3.82
943 971 9.880157 GTAGTTAAATGGGTTAAGTAGATCACA 57.120 33.333 0.00 0.00 37.97 3.58
991 1019 1.005037 GGACTGACATGCACCACGA 60.005 57.895 0.00 0.00 0.00 4.35
996 1024 0.037697 TACGGTGGACTGACATGCAC 60.038 55.000 0.00 0.00 40.00 4.57
1013 1041 3.094294 GCGCTGTACGTTGTAGTACTAC 58.906 50.000 23.58 23.58 45.23 2.73
1056 1084 2.762043 AGGAGGGCGAGGAAGAGC 60.762 66.667 0.00 0.00 0.00 4.09
1145 1173 3.234630 TTGAGGCTTCCCGTGTCCG 62.235 63.158 0.00 0.00 35.76 4.79
1955 1983 1.154093 GGAGTCGTCGCGTTCATGA 60.154 57.895 5.77 0.00 0.00 3.07
2358 2404 2.894126 CTGGTAGTTGCCGAGGATAGAT 59.106 50.000 0.00 0.00 0.00 1.98
2361 2407 0.750850 GCTGGTAGTTGCCGAGGATA 59.249 55.000 0.00 0.00 0.00 2.59
2449 2495 6.627087 AAAGAAATCCTAGTGAGTCATGGA 57.373 37.500 12.69 12.69 0.00 3.41
2505 2581 3.056749 GCCATACCGTACCTATCCTCTTG 60.057 52.174 0.00 0.00 0.00 3.02
2538 4771 3.505464 TCAGAGAAGCTAGGTAAACGC 57.495 47.619 0.00 0.00 0.00 4.84
2539 4772 4.806330 TGTTCAGAGAAGCTAGGTAAACG 58.194 43.478 0.00 0.00 0.00 3.60
2540 4773 6.874134 TGAATGTTCAGAGAAGCTAGGTAAAC 59.126 38.462 0.00 0.00 32.50 2.01
2541 4774 7.004555 TGAATGTTCAGAGAAGCTAGGTAAA 57.995 36.000 0.00 0.00 32.50 2.01
2542 4775 6.605471 TGAATGTTCAGAGAAGCTAGGTAA 57.395 37.500 0.00 0.00 32.50 2.85
2572 4805 0.764369 TGCCCTCACTGTCCAGTTCT 60.764 55.000 0.00 0.00 40.20 3.01
2597 4830 4.586001 ACAAATTCAATGAGTGGTTGCTCT 59.414 37.500 0.00 0.00 36.51 4.09
2610 4844 8.659925 TGTAAAAATGCACTCACAAATTCAAT 57.340 26.923 0.00 0.00 0.00 2.57
2701 4938 5.132502 TGACAATCTGCAAAAGGAGAAAGA 58.867 37.500 0.00 0.00 0.00 2.52
2706 4943 5.381174 TCATTGACAATCTGCAAAAGGAG 57.619 39.130 0.00 0.00 0.00 3.69
2707 4944 5.787953 TTCATTGACAATCTGCAAAAGGA 57.212 34.783 0.00 0.00 0.00 3.36
2709 4946 7.646446 TTCATTCATTGACAATCTGCAAAAG 57.354 32.000 0.00 0.00 32.84 2.27
2719 4956 8.991026 GGATTCACAAATTTCATTCATTGACAA 58.009 29.630 0.00 0.00 32.84 3.18
2723 4960 7.328982 TCGTGGATTCACAAATTTCATTCATTG 59.671 33.333 4.68 0.00 43.79 2.82
2748 4987 7.325821 TGTGCGAACATAAAATTCACATTCTTC 59.674 33.333 0.00 0.00 0.00 2.87
2750 4989 6.676950 TGTGCGAACATAAAATTCACATTCT 58.323 32.000 0.00 0.00 0.00 2.40
2766 5005 3.575965 AATGAATTCCCTTGTGCGAAC 57.424 42.857 2.27 0.00 0.00 3.95
2793 5038 7.680730 AGCCTAGAAAAAGTAGAATGAGACAA 58.319 34.615 0.00 0.00 0.00 3.18
2794 5039 7.246171 AGCCTAGAAAAAGTAGAATGAGACA 57.754 36.000 0.00 0.00 0.00 3.41
2798 5043 6.875972 AGGAGCCTAGAAAAAGTAGAATGA 57.124 37.500 0.00 0.00 0.00 2.57
2858 5103 4.904241 AGATGGTAATGAGAGCTATTGGC 58.096 43.478 0.00 0.00 42.19 4.52
2903 5159 6.760440 ATATTCATGCCCCTCTATAGATGG 57.240 41.667 15.29 15.29 0.00 3.51
2923 5179 7.549134 TGAAAAGCTTGTGAGTCGTGAATATAT 59.451 33.333 0.00 0.00 0.00 0.86
2933 5189 3.471680 AGGTCTGAAAAGCTTGTGAGTC 58.528 45.455 0.00 0.00 0.00 3.36
2952 5208 6.912591 GCGGAAACATCTTTATTCATGTAAGG 59.087 38.462 0.00 0.00 32.74 2.69
2959 5215 5.697473 TGTTGCGGAAACATCTTTATTCA 57.303 34.783 0.00 0.00 43.96 2.57
2970 5226 3.428534 GTGGAATTGATTGTTGCGGAAAC 59.571 43.478 0.00 0.00 39.41 2.78
2971 5227 3.553922 GGTGGAATTGATTGTTGCGGAAA 60.554 43.478 0.00 0.00 0.00 3.13
3067 5327 0.770499 TGGCAGGAGTTGTGGATCAA 59.230 50.000 0.00 0.00 0.00 2.57
3079 5339 3.008923 TCAGTTATGTGTTCATGGCAGGA 59.991 43.478 0.00 0.00 35.70 3.86
3102 5362 9.341899 CTTATATAAAAAGTGCAAGTGTGTTCC 57.658 33.333 0.00 0.00 0.00 3.62
3152 5415 5.876460 AGGACGCGTTAAACAAAATAGGTAT 59.124 36.000 15.53 0.00 0.00 2.73
3189 5452 6.041751 CCCGACTGGACCTAATAAAGAGTATT 59.958 42.308 0.00 0.00 37.49 1.89
3223 5486 4.702131 GTGATGTTCAGGCAAATCTACCTT 59.298 41.667 0.00 0.00 32.56 3.50
3244 5507 8.289618 CGGTTAATTTCCATGATAACCTATGTG 58.710 37.037 10.73 0.00 43.22 3.21
3251 5514 6.131544 ACTGCGGTTAATTTCCATGATAAC 57.868 37.500 0.00 0.00 0.00 1.89
3259 5522 4.499037 ACTGAAACTGCGGTTAATTTCC 57.501 40.909 12.24 0.00 34.90 3.13
3270 5533 7.358683 GCATTATTTTGTCTGAACTGAAACTGC 60.359 37.037 0.00 0.00 0.00 4.40
3284 5547 8.730680 TCTCCTTAACTTCAGCATTATTTTGTC 58.269 33.333 0.00 0.00 0.00 3.18
3310 5574 4.829492 GGAAGAAATGGCCAAGTATAGCAT 59.171 41.667 10.96 0.00 0.00 3.79
3427 5691 8.965986 ATTAAAACGAGCTCTTGGTAAAATTC 57.034 30.769 12.85 0.00 0.00 2.17


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

AutoCloner maintained by Alex Coulton.