Multiple sequence alignment - TraesCS4A01G002700

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 TraesCS4A01G002700 chr4A 100.000 6782 0 0 1 6782 2419050 2412269 0.000000e+00 12525
1 TraesCS4A01G002700 chr4D 95.673 6609 215 32 210 6782 469298038 469304611 0.000000e+00 10554
2 TraesCS4A01G002700 chr4D 92.308 117 7 1 3 117 469297610 469297726 1.510000e-36 165
3 TraesCS4A01G002700 chr4B 95.860 5677 181 29 812 6474 589174368 589180004 0.000000e+00 9132
4 TraesCS4A01G002700 chr4B 91.130 823 65 7 1 820 589173401 589174218 0.000000e+00 1109
5 TraesCS4A01G002700 chr4B 91.277 321 16 8 6462 6782 589180021 589180329 1.750000e-115 427


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 TraesCS4A01G002700 chr4A 2412269 2419050 6781 True 12525.0 12525 100.000000 1 6782 1 chr4A.!!$R1 6781
1 TraesCS4A01G002700 chr4D 469297610 469304611 7001 False 5359.5 10554 93.990500 3 6782 2 chr4D.!!$F1 6779
2 TraesCS4A01G002700 chr4B 589173401 589180329 6928 False 3556.0 9132 92.755667 1 6782 3 chr4B.!!$F1 6781

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
472 695 0.035439 ACGGGAAATGCGGACAAGAT 60.035 50.000 0.0 0.0 0.00 2.40 F
1221 1604 1.081840 GCGACCAAGAAACTGCTGC 60.082 57.895 0.0 0.0 0.00 5.25 F
2007 2393 0.035458 CCTCCCTGACTGTGGTGAAC 59.965 60.000 0.0 0.0 0.00 3.18 F
3045 3431 0.244450 CCAATGCCGTTGTTGCTGAT 59.756 50.000 0.0 0.0 36.01 2.90 F
3436 3823 2.286563 TGTAACACATGCCATTATCGCG 59.713 45.455 0.0 0.0 0.00 5.87 F
4302 4691 0.471617 CAAATCCGAGATCCCCAGCT 59.528 55.000 0.0 0.0 0.00 4.24 F
5223 5613 0.303493 CACCGTTGTCACCGAGTTTG 59.697 55.000 0.0 0.0 0.00 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1426 1809 0.251519 AAGGAAGCCCTGCAAGAAGG 60.252 55.000 0.00 0.0 43.48 3.46 R
3030 3416 0.592637 CAGAATCAGCAACAACGGCA 59.407 50.000 0.00 0.0 0.00 5.69 R
3819 4208 0.393132 TGCACGACAGGAAACACCAA 60.393 50.000 0.00 0.0 42.04 3.67 R
4100 4489 1.135315 CACATGCACCGATTTGAAGGG 60.135 52.381 0.00 0.0 0.00 3.95 R
5223 5613 0.404426 ACCAGCCTTGTTTAGGGGTC 59.596 55.000 0.00 0.0 44.91 4.46 R
5458 5848 0.032217 GGGGCAATTGGGGAAGATGA 60.032 55.000 7.72 0.0 0.00 2.92 R
6630 7063 1.208614 CCTGCGAGTGCTGCTTTTC 59.791 57.895 0.00 0.0 43.34 2.29 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
75 78 7.861629 ACAAGAGAACCAATCATCACCTTATA 58.138 34.615 0.00 0.00 0.00 0.98
135 138 0.341258 TCATCTCCTCAGCCCTTCCT 59.659 55.000 0.00 0.00 0.00 3.36
158 161 7.567250 TCCTTTCCTTTTTACCCATCTTCTTTT 59.433 33.333 0.00 0.00 0.00 2.27
159 162 8.210946 CCTTTCCTTTTTACCCATCTTCTTTTT 58.789 33.333 0.00 0.00 0.00 1.94
166 169 3.001086 ACCCATCTTCTTTTTACCCCCT 58.999 45.455 0.00 0.00 0.00 4.79
218 439 0.179140 CCGCCGCATGCACTATTTTT 60.179 50.000 19.57 0.00 41.33 1.94
312 534 9.814899 TCGTATGGATTCATTTTAAAAATGCAT 57.185 25.926 17.06 17.06 42.03 3.96
390 612 5.643777 AGTAGCGAAAATGGGATATGTATGC 59.356 40.000 0.00 0.00 0.00 3.14
443 665 8.621286 ACCGAAGTGAATAATGATCAATAAACC 58.379 33.333 0.00 0.00 0.00 3.27
462 685 2.289444 ACCACACAGTAGACGGGAAATG 60.289 50.000 0.00 0.00 0.00 2.32
470 693 0.673644 AGACGGGAAATGCGGACAAG 60.674 55.000 0.00 0.00 0.00 3.16
472 695 0.035439 ACGGGAAATGCGGACAAGAT 60.035 50.000 0.00 0.00 0.00 2.40
487 710 2.154462 CAAGATGAGGTGAAACGGCTT 58.846 47.619 0.00 0.00 38.12 4.35
493 716 2.335011 GTGAAACGGCTTGGTGGC 59.665 61.111 0.00 0.00 37.94 5.01
500 723 1.221840 CGGCTTGGTGGCTATGAGT 59.778 57.895 0.00 0.00 39.32 3.41
686 909 9.906660 GAGAACATTTATATTTGTTGTTGGTGA 57.093 29.630 5.74 0.00 36.25 4.02
719 942 4.688879 TGTTTGGACTAGATTTGTAGCACG 59.311 41.667 0.00 0.00 0.00 5.34
939 1321 3.760035 CACCTCCGTCCCTGTCCG 61.760 72.222 0.00 0.00 0.00 4.79
954 1337 3.756783 CCGTCTCCCCCTCCCTCT 61.757 72.222 0.00 0.00 0.00 3.69
1221 1604 1.081840 GCGACCAAGAAACTGCTGC 60.082 57.895 0.00 0.00 0.00 5.25
1254 1637 1.515952 CCAGCGCTCTCGAGTTCTG 60.516 63.158 7.13 13.93 38.10 3.02
1426 1809 2.159296 ACCTCTTTTGTGGTGTTTTCGC 60.159 45.455 0.00 0.00 43.84 4.70
1540 1926 1.439644 GAGAGCCATGAGGACGGTC 59.560 63.158 0.00 0.00 36.89 4.79
1800 2186 2.487934 GATGTTGCGAGGTATGATGCT 58.512 47.619 0.00 0.00 0.00 3.79
1941 2327 4.060900 CCATGAATGTGGAGATAAGTCCG 58.939 47.826 0.00 0.00 42.02 4.79
2007 2393 0.035458 CCTCCCTGACTGTGGTGAAC 59.965 60.000 0.00 0.00 0.00 3.18
2024 2410 4.096382 GGTGAACTTGAACAATGACAGTGT 59.904 41.667 1.98 1.98 0.00 3.55
2085 2471 7.653713 CAGTTCTATGTGTATGGTTATGAGGAC 59.346 40.741 0.00 0.00 0.00 3.85
2154 2540 2.310538 CCAAAGTTGTTGGGCTCTTCT 58.689 47.619 0.00 0.00 35.96 2.85
2404 2790 2.861147 AGTTTGTCAGTTAGGCCCTC 57.139 50.000 0.00 0.00 0.00 4.30
2754 3140 7.039011 GGAAATGGGTCAATATATTCCCTTTCC 60.039 40.741 26.10 26.10 42.51 3.13
2871 3257 3.196685 GCTTGATACTCTTCCCTGACACT 59.803 47.826 0.00 0.00 0.00 3.55
3019 3405 6.591834 AGATATAATGCGTGCACCTATTTCTC 59.408 38.462 12.15 9.17 0.00 2.87
3030 3416 6.095440 GTGCACCTATTTCTCATACAACCAAT 59.905 38.462 5.22 0.00 0.00 3.16
3033 3419 5.594317 ACCTATTTCTCATACAACCAATGCC 59.406 40.000 0.00 0.00 0.00 4.40
3045 3431 0.244450 CCAATGCCGTTGTTGCTGAT 59.756 50.000 0.00 0.00 36.01 2.90
3436 3823 2.286563 TGTAACACATGCCATTATCGCG 59.713 45.455 0.00 0.00 0.00 5.87
3458 3845 5.506815 GCGTTAAAGAAAGTTTGTAAGGCCT 60.507 40.000 0.00 0.00 32.27 5.19
3506 3893 5.324409 ACCATCTGTTTGGAAGAATAAGCA 58.676 37.500 6.44 0.00 39.25 3.91
3729 4118 7.647318 TGTAATATAATTTGCAGCCAACAATCG 59.353 33.333 0.00 0.00 0.00 3.34
3737 4126 2.824041 CCAACAATCGGGGGAGCG 60.824 66.667 0.00 0.00 0.00 5.03
3746 4135 3.157252 GGGGGAGCGATCAGAGCA 61.157 66.667 1.84 0.00 37.01 4.26
3819 4208 7.094463 GGATTTCTGTTCTCACAAATCATGAGT 60.094 37.037 0.09 0.00 43.47 3.41
4001 4390 4.224594 AGCAGATCTCCAGAAATTGACTCA 59.775 41.667 0.00 0.00 0.00 3.41
4010 4399 4.453819 CCAGAAATTGACTCAACAGAGACC 59.546 45.833 0.00 0.00 33.55 3.85
4019 4408 3.808618 ACTCAACAGAGACCAGATTTGGC 60.809 47.826 1.27 0.00 39.17 4.52
4100 4489 0.676736 TTGGTCCCATTGTTTTCCGC 59.323 50.000 0.00 0.00 0.00 5.54
4236 4625 0.846693 ACCTGAGGCTGTTTGGAAGT 59.153 50.000 0.00 0.00 0.00 3.01
4241 4630 3.999663 CTGAGGCTGTTTGGAAGTTAGAG 59.000 47.826 0.00 0.00 0.00 2.43
4253 4642 6.256643 TGGAAGTTAGAGTTTAACCTTGGT 57.743 37.500 0.12 0.00 0.00 3.67
4302 4691 0.471617 CAAATCCGAGATCCCCAGCT 59.528 55.000 0.00 0.00 0.00 4.24
4379 4768 2.035961 TCCTCTTCGAGTCACAAAGGTG 59.964 50.000 0.00 0.00 46.66 4.00
4436 4825 1.795170 CGGTGAACAACTGCAAGGGG 61.795 60.000 0.00 0.00 39.30 4.79
4646 5035 8.653338 CATTGGAAAGCATTGATACTCTTTTTG 58.347 33.333 0.00 0.00 0.00 2.44
4657 5046 5.763204 TGATACTCTTTTTGGGAACTGTGTC 59.237 40.000 0.00 0.00 0.00 3.67
4847 5237 6.908825 TCGTCCTTTTATCACATTTTTCCAG 58.091 36.000 0.00 0.00 0.00 3.86
4987 5377 5.793952 CGAAAGAAAGATGACAAGAGCAATG 59.206 40.000 0.00 0.00 0.00 2.82
5003 5393 5.123502 AGAGCAATGCAGATAAACAACAGAG 59.876 40.000 8.35 0.00 0.00 3.35
5005 5395 5.939883 AGCAATGCAGATAAACAACAGAGTA 59.060 36.000 8.35 0.00 0.00 2.59
5032 5422 3.653164 TCAGCTATATCTGTGTCCCCAA 58.347 45.455 3.63 0.00 35.63 4.12
5104 5494 6.466885 GGAACCTTACTATCAGAGTTGCTA 57.533 41.667 0.00 0.00 39.81 3.49
5142 5532 1.729484 GAAGCGAAAAGTTGGCGGC 60.729 57.895 0.00 0.00 39.55 6.53
5223 5613 0.303493 CACCGTTGTCACCGAGTTTG 59.697 55.000 0.00 0.00 0.00 2.93
5514 5904 2.087646 GGCTCCAACCTGATGAAAGAC 58.912 52.381 0.00 0.00 0.00 3.01
5709 6099 1.164662 CCCTCATGATGAAGCAGCCG 61.165 60.000 0.00 0.00 0.00 5.52
5833 6223 1.476085 CGTCTCTCCTCTGCATCTTGT 59.524 52.381 0.00 0.00 0.00 3.16
5884 6274 2.930040 CACTAACTGCACTACCATTCCG 59.070 50.000 0.00 0.00 0.00 4.30
5905 6295 3.813724 CGGGGCTTTAGAGGCTTAATTAC 59.186 47.826 6.79 0.00 46.98 1.89
6171 6566 4.022589 CACTGAACAAACTTGATCTGCCAT 60.023 41.667 0.00 0.00 34.04 4.40
6188 6584 6.053650 TCTGCCATTCTAACATTCTGATCTG 58.946 40.000 0.00 0.00 0.00 2.90
6195 6591 9.491675 CATTCTAACATTCTGATCTGAAGCTAT 57.508 33.333 18.38 8.78 0.00 2.97
6260 6656 3.717707 TGATATCTCACTTTACTGCCGC 58.282 45.455 3.98 0.00 0.00 6.53
6264 6660 0.669318 CTCACTTTACTGCCGCCGAA 60.669 55.000 0.00 0.00 0.00 4.30
6265 6661 0.036765 TCACTTTACTGCCGCCGAAT 60.037 50.000 0.00 0.00 0.00 3.34
6266 6662 0.373716 CACTTTACTGCCGCCGAATC 59.626 55.000 0.00 0.00 0.00 2.52
6297 6693 6.605471 TTAGGTACTGGACATATATGCCTG 57.395 41.667 20.90 20.90 41.52 4.85
6317 6713 3.445008 TGTCTAAAGCAGGAGAGGTGAT 58.555 45.455 0.00 0.00 0.00 3.06
6343 6739 9.461312 TTGATGCTAACTAATCCTGTTTAACAT 57.539 29.630 0.00 0.00 0.00 2.71
6347 6743 6.967199 GCTAACTAATCCTGTTTAACATGTGC 59.033 38.462 0.00 0.00 0.00 4.57
6348 6744 6.892658 AACTAATCCTGTTTAACATGTGCA 57.107 33.333 0.00 0.00 0.00 4.57
6349 6745 6.892658 ACTAATCCTGTTTAACATGTGCAA 57.107 33.333 0.00 0.00 0.00 4.08
6350 6746 7.283625 ACTAATCCTGTTTAACATGTGCAAA 57.716 32.000 0.00 0.00 0.00 3.68
6351 6747 7.370383 ACTAATCCTGTTTAACATGTGCAAAG 58.630 34.615 0.00 0.00 0.00 2.77
6352 6748 4.582701 TCCTGTTTAACATGTGCAAAGG 57.417 40.909 0.00 3.82 0.00 3.11
6412 6808 9.699410 TTCTAATCATGTTCTATTTGTTCCCAT 57.301 29.630 0.00 0.00 0.00 4.00
6425 6828 4.202245 TGTTCCCATTAGTCACTAGCAC 57.798 45.455 0.00 0.00 0.00 4.40
6426 6829 3.580895 TGTTCCCATTAGTCACTAGCACA 59.419 43.478 0.00 0.00 0.00 4.57
6429 6832 4.093743 TCCCATTAGTCACTAGCACAGAA 58.906 43.478 0.00 0.00 0.00 3.02
6435 6838 4.513198 AGTCACTAGCACAGAAGTTCTC 57.487 45.455 1.26 0.00 0.00 2.87
6438 6841 1.903183 ACTAGCACAGAAGTTCTCCCC 59.097 52.381 1.26 0.00 0.00 4.81
6469 6902 2.084610 TGATCGACAGGTGCTTCTTG 57.915 50.000 0.00 0.00 0.00 3.02
6485 6918 7.362401 GGTGCTTCTTGAAGAACATCATAACAT 60.362 37.037 19.63 0.00 29.89 2.71
6488 6921 8.668353 GCTTCTTGAAGAACATCATAACATACA 58.332 33.333 13.87 0.00 29.89 2.29
6495 6928 9.736023 GAAGAACATCATAACATACATTTTCCC 57.264 33.333 0.00 0.00 0.00 3.97
6496 6929 8.237811 AGAACATCATAACATACATTTTCCCC 57.762 34.615 0.00 0.00 0.00 4.81
6497 6930 6.976934 ACATCATAACATACATTTTCCCCC 57.023 37.500 0.00 0.00 0.00 5.40
6551 6984 2.557924 CCAGTGGCTGATTTACTTGCAA 59.442 45.455 0.00 0.00 32.44 4.08
6554 6987 2.819608 GTGGCTGATTTACTTGCAAGGA 59.180 45.455 29.18 20.21 0.00 3.36
6555 6988 3.084039 TGGCTGATTTACTTGCAAGGAG 58.916 45.455 29.18 10.77 0.00 3.69
6556 6989 3.084786 GGCTGATTTACTTGCAAGGAGT 58.915 45.455 29.18 14.34 0.00 3.85
6557 6990 3.119708 GGCTGATTTACTTGCAAGGAGTG 60.120 47.826 29.18 13.39 0.00 3.51
6558 6991 3.753272 GCTGATTTACTTGCAAGGAGTGA 59.247 43.478 29.18 12.09 0.00 3.41
6580 7013 2.487934 TGAAGCAACTCAGAGTTCTGC 58.512 47.619 16.61 16.61 43.46 4.26
6585 7018 2.614987 GCAACTCAGAGTTCTGCTGGAT 60.615 50.000 13.27 0.00 43.46 3.41
6604 7037 5.455872 TGGATACTCAGGGGTCTACTAAAG 58.544 45.833 0.00 0.00 37.61 1.85
6606 7039 3.476485 ACTCAGGGGTCTACTAAAGCT 57.524 47.619 0.00 0.00 0.00 3.74
6630 7063 2.347490 CACAGGACAAGGACGGGG 59.653 66.667 0.00 0.00 0.00 5.73
6635 7068 0.400594 AGGACAAGGACGGGGAAAAG 59.599 55.000 0.00 0.00 0.00 2.27
6639 7072 1.603739 AAGGACGGGGAAAAGCAGC 60.604 57.895 0.00 0.00 0.00 5.25
6641 7074 2.626780 GGACGGGGAAAAGCAGCAC 61.627 63.158 0.00 0.00 0.00 4.40
6642 7075 1.600916 GACGGGGAAAAGCAGCACT 60.601 57.895 0.00 0.00 0.00 4.40
6643 7076 1.578206 GACGGGGAAAAGCAGCACTC 61.578 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 7.181569 TGGTTCTCTTGTTTGGAAAAGATTT 57.818 32.000 0.00 0.00 32.20 2.17
39 40 6.790232 TTGGTTCTCTTGTTTGGAAAAGAT 57.210 33.333 0.00 0.00 32.20 2.40
158 161 5.292550 ACCATGGAATTTTAAGGGGGTAA 57.707 39.130 21.47 0.00 0.00 2.85
159 162 4.976870 ACCATGGAATTTTAAGGGGGTA 57.023 40.909 21.47 0.00 0.00 3.69
166 169 9.535878 GTTCACTTTGTAACCATGGAATTTTAA 57.464 29.630 21.47 4.40 0.00 1.52
218 439 7.710475 TGTAATCGAAGCAATAACTGATCATGA 59.290 33.333 0.00 0.00 0.00 3.07
232 454 6.595326 AGATGAAAGTCAATGTAATCGAAGCA 59.405 34.615 0.00 0.00 0.00 3.91
350 572 4.041049 CGCTACTTTTGCACATTTGTTGA 58.959 39.130 0.00 0.00 0.00 3.18
390 612 3.379372 ACCGCTTGATGAGGAATTGATTG 59.621 43.478 0.00 0.00 39.07 2.67
432 654 5.291128 CCGTCTACTGTGTGGTTTATTGATC 59.709 44.000 0.00 0.00 0.00 2.92
443 665 1.732259 GCATTTCCCGTCTACTGTGTG 59.268 52.381 0.00 0.00 0.00 3.82
453 676 0.035439 ATCTTGTCCGCATTTCCCGT 60.035 50.000 0.00 0.00 0.00 5.28
462 685 1.464997 GTTTCACCTCATCTTGTCCGC 59.535 52.381 0.00 0.00 0.00 5.54
470 693 0.804989 CCAAGCCGTTTCACCTCATC 59.195 55.000 0.00 0.00 0.00 2.92
472 695 0.817634 CACCAAGCCGTTTCACCTCA 60.818 55.000 0.00 0.00 0.00 3.86
487 710 4.323417 CTGTTTACAACTCATAGCCACCA 58.677 43.478 0.00 0.00 0.00 4.17
493 716 3.307242 GCCTCGCTGTTTACAACTCATAG 59.693 47.826 0.00 0.00 0.00 2.23
512 735 2.867855 TTCTCGGTTGCGTCAGCCT 61.868 57.895 10.06 0.00 44.33 4.58
543 766 1.153369 ACTGGCGATTGCGTATGCT 60.153 52.632 8.69 0.00 44.10 3.79
678 901 6.266330 TCCAAACAACATTATCATCACCAACA 59.734 34.615 0.00 0.00 0.00 3.33
683 906 8.492673 TCTAGTCCAAACAACATTATCATCAC 57.507 34.615 0.00 0.00 0.00 3.06
691 914 7.230510 TGCTACAAATCTAGTCCAAACAACATT 59.769 33.333 0.00 0.00 0.00 2.71
692 915 6.714810 TGCTACAAATCTAGTCCAAACAACAT 59.285 34.615 0.00 0.00 0.00 2.71
719 942 3.726291 TTTAGCCCTTTCAGTGTTTGC 57.274 42.857 0.00 0.00 0.00 3.68
758 982 6.115446 TCACATGACTATTTAGCCCTTTCAG 58.885 40.000 0.00 0.00 0.00 3.02
939 1321 2.284151 GGAGAGGGAGGGGGAGAC 59.716 72.222 0.00 0.00 0.00 3.36
1238 1621 1.653094 CTCCAGAACTCGAGAGCGCT 61.653 60.000 21.68 11.27 37.46 5.92
1254 1637 2.812591 CAGCATAAGCATGGATCACTCC 59.187 50.000 0.00 0.00 45.49 3.85
1305 1688 2.433436 ACCCCAAGAAAATAGTCACGC 58.567 47.619 0.00 0.00 0.00 5.34
1426 1809 0.251519 AAGGAAGCCCTGCAAGAAGG 60.252 55.000 0.00 0.00 43.48 3.46
1569 1955 2.669240 CAGAAGGAACCCCCGTCC 59.331 66.667 0.00 0.00 43.39 4.79
1638 2024 0.611896 AAACCCCCAAATCAGGCTCG 60.612 55.000 0.00 0.00 0.00 5.03
1941 2327 2.054453 GCCCCAATCCAAGACTGGC 61.054 63.158 0.00 0.00 43.17 4.85
2007 2393 4.285292 GCAAGACACTGTCATTGTTCAAG 58.715 43.478 11.80 0.00 34.60 3.02
2024 2410 0.894835 TGGCTCATAGACACGCAAGA 59.105 50.000 0.00 0.00 43.62 3.02
2154 2540 3.118847 TCTGCAAAACCAAATGTGCTGAA 60.119 39.130 2.17 0.00 40.54 3.02
2404 2790 0.617413 AACTCCACTGCCTCATCCAG 59.383 55.000 0.00 0.00 36.41 3.86
2754 3140 3.935203 ACTCTGTTGCATCATTCCGTAAG 59.065 43.478 0.00 0.00 0.00 2.34
2794 3180 3.657727 CCATCCCTGTTATCCCCAGTTAT 59.342 47.826 0.00 0.00 0.00 1.89
3030 3416 0.592637 CAGAATCAGCAACAACGGCA 59.407 50.000 0.00 0.00 0.00 5.69
3033 3419 3.727079 GCTCATCAGAATCAGCAACAACG 60.727 47.826 0.00 0.00 0.00 4.10
3293 3680 8.642935 TGATGAAATTAATGAACAGGGTAACA 57.357 30.769 0.00 0.00 39.74 2.41
3436 3823 9.976511 ATAAAGGCCTTACAAACTTTCTTTAAC 57.023 29.630 20.84 0.00 35.11 2.01
3506 3893 2.092158 GCCTGCTTTTCTCTATTCCCCT 60.092 50.000 0.00 0.00 0.00 4.79
3699 4088 9.664332 TGTTGGCTGCAAATTATATTACAAAAT 57.336 25.926 0.50 0.00 0.00 1.82
3729 4118 3.157252 TGCTCTGATCGCTCCCCC 61.157 66.667 0.00 0.00 0.00 5.40
3737 4126 3.472283 ACCATGTCATCTGCTCTGATC 57.528 47.619 0.00 0.00 0.00 2.92
3746 4135 6.386927 TCCAATTCCTAAGTACCATGTCATCT 59.613 38.462 0.00 0.00 0.00 2.90
3819 4208 0.393132 TGCACGACAGGAAACACCAA 60.393 50.000 0.00 0.00 42.04 3.67
4001 4390 3.073650 AGAAGCCAAATCTGGTCTCTGTT 59.926 43.478 0.00 0.00 45.53 3.16
4010 4399 5.238214 GCTACCTAATGAGAAGCCAAATCTG 59.762 44.000 0.00 0.00 0.00 2.90
4019 4408 6.690194 ATTGCTTTGCTACCTAATGAGAAG 57.310 37.500 0.00 0.00 0.00 2.85
4100 4489 1.135315 CACATGCACCGATTTGAAGGG 60.135 52.381 0.00 0.00 0.00 3.95
4241 4630 7.172019 TCGTCAAGATTAGAACCAAGGTTAAAC 59.828 37.037 4.14 0.00 38.60 2.01
4253 4642 6.200286 GTGTTGAGTTGTCGTCAAGATTAGAA 59.800 38.462 0.00 0.00 34.59 2.10
4379 4768 5.067805 ACCACAATCAACTCCAGAAACTTTC 59.932 40.000 0.00 0.00 0.00 2.62
4436 4825 2.073816 TCACTTGGCGCTAAGCTAAAC 58.926 47.619 30.58 0.03 45.72 2.01
4646 5035 2.375146 ACAAACAAGGACACAGTTCCC 58.625 47.619 0.00 0.00 36.12 3.97
4657 5046 4.122143 ACAATGACCACAACAAACAAGG 57.878 40.909 0.00 0.00 0.00 3.61
4987 5377 6.787085 AGTTGTACTCTGTTGTTTATCTGC 57.213 37.500 0.00 0.00 0.00 4.26
5003 5393 6.697892 GGACACAGATATAGCTGAAGTTGTAC 59.302 42.308 24.19 14.26 39.20 2.90
5005 5395 5.395768 GGGACACAGATATAGCTGAAGTTGT 60.396 44.000 24.19 16.82 39.20 3.32
5032 5422 3.910627 ACCTTGTCTTCCACAGGATTAGT 59.089 43.478 0.00 0.00 35.97 2.24
5104 5494 1.003696 CCTTCGCCTCCCTTTTTCTCT 59.996 52.381 0.00 0.00 0.00 3.10
5142 5532 1.870055 ATTTTGCTGCCAGTCCTGCG 61.870 55.000 0.00 0.00 33.01 5.18
5223 5613 0.404426 ACCAGCCTTGTTTAGGGGTC 59.596 55.000 0.00 0.00 44.91 4.46
5458 5848 0.032217 GGGGCAATTGGGGAAGATGA 60.032 55.000 7.72 0.00 0.00 2.92
5514 5904 3.523547 CTCATCTCTCTTCACAGCCTTG 58.476 50.000 0.00 0.00 0.00 3.61
5709 6099 2.433318 GAGTCAGGTGGCGCAGAC 60.433 66.667 10.83 13.03 0.00 3.51
5872 6262 0.034477 AAAGCCCCGGAATGGTAGTG 60.034 55.000 0.73 0.00 35.15 2.74
5878 6268 0.819666 GCCTCTAAAGCCCCGGAATG 60.820 60.000 0.73 0.00 0.00 2.67
5884 6274 5.050126 AGTAATTAAGCCTCTAAAGCCCC 57.950 43.478 0.00 0.00 0.00 5.80
5950 6340 8.859090 AGAAATATTGTTTGTGGTGAGAAATGA 58.141 29.630 0.00 0.00 0.00 2.57
5984 6374 9.773328 TTCGTTCAGATTAATTTTCATTAGCTG 57.227 29.630 0.00 0.00 34.01 4.24
6110 6505 4.804139 CCTGATTCTCTGAATTGCATTTGC 59.196 41.667 0.00 0.00 42.50 3.68
6148 6543 3.316029 TGGCAGATCAAGTTTGTTCAGTG 59.684 43.478 0.00 0.00 31.05 3.66
6260 6656 5.523916 CCAGTACCTAATGTCTTTGATTCGG 59.476 44.000 0.00 0.00 0.00 4.30
6264 6660 6.620877 TGTCCAGTACCTAATGTCTTTGAT 57.379 37.500 0.00 0.00 0.00 2.57
6265 6661 6.620877 ATGTCCAGTACCTAATGTCTTTGA 57.379 37.500 0.00 0.00 0.00 2.69
6297 6693 4.081420 TCAATCACCTCTCCTGCTTTAGAC 60.081 45.833 0.00 0.00 0.00 2.59
6317 6713 8.856153 TGTTAAACAGGATTAGTTAGCATCAA 57.144 30.769 0.00 0.00 0.00 2.57
6347 6743 3.615224 AATGTATGCCCTTTGCCTTTG 57.385 42.857 0.00 0.00 40.16 2.77
6348 6744 4.639078 AAAATGTATGCCCTTTGCCTTT 57.361 36.364 0.00 0.00 40.16 3.11
6349 6745 4.639078 AAAAATGTATGCCCTTTGCCTT 57.361 36.364 0.00 0.00 40.16 4.35
6412 6808 5.047943 GGAGAACTTCTGTGCTAGTGACTAA 60.048 44.000 0.00 0.00 30.68 2.24
6415 6811 3.580731 GGAGAACTTCTGTGCTAGTGAC 58.419 50.000 0.00 0.00 30.68 3.67
6438 6841 1.486310 TGTCGATCATCCTTTCTGGGG 59.514 52.381 0.00 0.00 36.20 4.96
6453 6856 1.686587 TCTTCAAGAAGCACCTGTCGA 59.313 47.619 4.95 0.00 38.28 4.20
6454 6857 2.154854 TCTTCAAGAAGCACCTGTCG 57.845 50.000 4.95 0.00 38.28 4.35
6469 6902 9.736023 GGGAAAATGTATGTTATGATGTTCTTC 57.264 33.333 0.00 0.00 0.00 2.87
6495 6928 6.796785 ATTGATTTCAACATAAGAAGGGGG 57.203 37.500 0.00 0.00 38.86 5.40
6496 6929 7.869429 GCATATTGATTTCAACATAAGAAGGGG 59.131 37.037 0.00 0.00 38.86 4.79
6497 6930 7.869429 GGCATATTGATTTCAACATAAGAAGGG 59.131 37.037 0.00 0.00 38.86 3.95
6498 6931 8.415553 TGGCATATTGATTTCAACATAAGAAGG 58.584 33.333 0.00 0.00 38.86 3.46
6537 6970 6.149973 TCAATCACTCCTTGCAAGTAAATCAG 59.850 38.462 24.35 12.06 0.00 2.90
6551 6984 3.326006 TCTGAGTTGCTTCAATCACTCCT 59.674 43.478 0.00 0.00 0.00 3.69
6554 6987 4.348863 ACTCTGAGTTGCTTCAATCACT 57.651 40.909 4.06 0.00 0.00 3.41
6555 6988 4.754114 AGAACTCTGAGTTGCTTCAATCAC 59.246 41.667 26.47 8.79 38.80 3.06
6556 6989 4.753610 CAGAACTCTGAGTTGCTTCAATCA 59.246 41.667 26.47 0.00 46.59 2.57
6557 6990 4.378253 GCAGAACTCTGAGTTGCTTCAATC 60.378 45.833 26.47 10.35 46.59 2.67
6558 6991 3.501445 GCAGAACTCTGAGTTGCTTCAAT 59.499 43.478 26.47 0.64 46.59 2.57
6580 7013 3.603965 AGTAGACCCCTGAGTATCCAG 57.396 52.381 0.00 0.00 0.00 3.86
6585 7018 4.604784 AGCTTTAGTAGACCCCTGAGTA 57.395 45.455 0.00 0.00 0.00 2.59
6604 7037 1.537202 CCTTGTCCTGTGCTGTAAAGC 59.463 52.381 0.00 0.00 0.00 3.51
6606 7039 2.805295 CGTCCTTGTCCTGTGCTGTAAA 60.805 50.000 0.00 0.00 0.00 2.01
6630 7063 1.208614 CCTGCGAGTGCTGCTTTTC 59.791 57.895 0.00 0.00 43.34 2.29
6635 7068 1.795286 GATATTACCTGCGAGTGCTGC 59.205 52.381 0.00 0.00 43.34 5.25
6639 7072 6.456988 GGTTCTTTTGATATTACCTGCGAGTG 60.457 42.308 0.00 0.00 0.00 3.51
6641 7074 5.817816 AGGTTCTTTTGATATTACCTGCGAG 59.182 40.000 0.00 0.00 35.33 5.03
6642 7075 5.584649 CAGGTTCTTTTGATATTACCTGCGA 59.415 40.000 0.00 0.00 42.95 5.10
6643 7076 5.810525 CAGGTTCTTTTGATATTACCTGCG 58.189 41.667 0.00 0.00 42.95 5.18


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

AutoCloner maintained by Alex Coulton.