Multiple sequence alignment - TraesCS4D01G237500

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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 TraesCS4D01G237500 chr4D 100.000 6057 0 0 1 6057 399722637 399728693 0.000000e+00 11186.0
1 TraesCS4D01G237500 chr4D 98.246 57 0 1 3753 3808 399726306 399726362 1.390000e-16 99.0
2 TraesCS4D01G237500 chr4D 98.246 57 0 1 3670 3726 399726389 399726444 1.390000e-16 99.0
3 TraesCS4D01G237500 chr4B 97.180 2872 62 9 1 2862 493764251 493767113 0.000000e+00 4837.0
4 TraesCS4D01G237500 chr4B 95.521 1987 63 10 3670 5643 493782674 493784647 0.000000e+00 3153.0
5 TraesCS4D01G237500 chr4B 93.525 556 19 4 2896 3450 493781796 493782335 0.000000e+00 811.0
6 TraesCS4D01G237500 chr4B 96.986 365 8 3 3446 3808 493782367 493782730 1.440000e-170 610.0
7 TraesCS4D01G237500 chr4B 83.468 248 21 9 5811 6057 493785099 493785327 4.760000e-51 213.0
8 TraesCS4D01G237500 chr4B 98.246 57 1 0 3670 3726 493782757 493782813 3.860000e-17 100.0
9 TraesCS4D01G237500 chr4B 98.246 57 0 1 3753 3808 493782591 493782647 1.390000e-16 99.0
10 TraesCS4D01G237500 chr4B 100.000 37 0 0 2860 2896 493781672 493781708 1.090000e-07 69.4
11 TraesCS4D01G237500 chr4A 88.558 1914 103 51 4182 6057 57519806 57521641 0.000000e+00 2215.0
12 TraesCS4D01G237500 chr4A 91.102 753 40 13 769 1499 57516927 57517674 0.000000e+00 994.0
13 TraesCS4D01G237500 chr4A 92.616 474 23 7 2106 2578 57519206 57519668 0.000000e+00 671.0
14 TraesCS4D01G237500 chr4A 87.332 371 40 5 1575 1943 57518563 57518928 9.390000e-113 418.0
15 TraesCS4D01G237500 chr4A 90.580 138 13 0 1933 2070 57519069 57519206 3.730000e-42 183.0
16 TraesCS4D01G237500 chr4A 84.466 103 13 3 2034 2136 89724740 89724839 1.390000e-16 99.0
17 TraesCS4D01G237500 chr4A 91.667 48 4 0 3511 3558 607262118 607262165 3.920000e-07 67.6
18 TraesCS4D01G237500 chr6D 88.889 198 17 4 421 615 377544111 377544306 7.850000e-59 239.0
19 TraesCS4D01G237500 chr6D 93.333 45 3 0 3514 3558 68970699 68970743 3.920000e-07 67.6
20 TraesCS4D01G237500 chr6D 93.333 45 3 0 3514 3558 345315683 345315639 3.920000e-07 67.6
21 TraesCS4D01G237500 chr7A 84.746 118 14 2 3513 3630 441097584 441097697 1.380000e-21 115.0
22 TraesCS4D01G237500 chr7A 84.466 103 14 2 2034 2136 116899177 116899077 3.860000e-17 100.0
23 TraesCS4D01G237500 chr7A 83.654 104 14 3 2034 2136 690703201 690703302 1.800000e-15 95.3
24 TraesCS4D01G237500 chr7D 83.810 105 14 3 2034 2136 3731881 3731984 5.000000e-16 97.1
25 TraesCS4D01G237500 chr6A 83.654 104 14 3 2034 2136 322540722 322540823 1.800000e-15 95.3
26 TraesCS4D01G237500 chr6A 89.286 56 6 0 3514 3569 55548659 55548714 3.030000e-08 71.3
27 TraesCS4D01G237500 chr3B 82.243 107 16 2 3566 3671 78581585 78581481 8.360000e-14 89.8
28 TraesCS4D01G237500 chr1A 82.524 103 17 1 2034 2136 117904299 117904400 8.360000e-14 89.8
29 TraesCS4D01G237500 chr2B 82.828 99 14 3 2034 2131 784372430 784372526 1.080000e-12 86.1
30 TraesCS4D01G237500 chr2B 82.828 99 14 3 2034 2131 784448512 784448608 1.080000e-12 86.1
31 TraesCS4D01G237500 chr2B 93.333 45 3 0 3514 3558 593647339 593647295 3.920000e-07 67.6
32 TraesCS4D01G237500 chrUn 90.909 55 5 0 3514 3568 21201552 21201498 2.340000e-09 75.0
33 TraesCS4D01G237500 chr6B 93.333 45 3 0 3514 3558 28223328 28223284 3.920000e-07 67.6


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 TraesCS4D01G237500 chr4D 399722637 399728693 6056 False 3794.666667 11186 98.830667 1 6057 3 chr4D.!!$F1 6056
1 TraesCS4D01G237500 chr4B 493764251 493767113 2862 False 4837.000000 4837 97.180000 1 2862 1 chr4B.!!$F1 2861
2 TraesCS4D01G237500 chr4B 493781672 493785327 3655 False 722.200000 3153 95.141714 2860 6057 7 chr4B.!!$F2 3197
3 TraesCS4D01G237500 chr4A 57516927 57521641 4714 False 896.200000 2215 90.037600 769 6057 5 chr4A.!!$F3 5288

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
62 63 0.030773 GCGACACAGTCACAGACTCA 59.969 55.000 0.0 0.0 41.37 3.41 F
508 510 1.150536 GTTGGTGCCCTCACTGGAA 59.849 57.895 0.0 0.0 42.72 3.53 F
1057 1081 1.536662 ACACCGCTTCCCTTCTCCT 60.537 57.895 0.0 0.0 0.00 3.69 F
2131 3121 1.832167 GCCCAACCACTGAGCCAAA 60.832 57.895 0.0 0.0 0.00 3.28 F
3370 4480 0.254747 TTCCAACATAGGGGCTTCGG 59.745 55.000 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2048 3038 0.462759 GACTAGTGATGCACAGGGGC 60.463 60.000 0.00 0.0 36.74 5.80 R
2089 3079 3.888460 TTGTGCAGCCTGCCCAGA 61.888 61.111 15.29 0.0 44.23 3.86 R
2920 4029 0.907704 TGGCGGGACAAGTAGGATGT 60.908 55.000 0.00 0.0 0.00 3.06 R
3501 4647 0.109723 ACACACCCGTATTGGCAAGT 59.890 50.000 5.96 0.0 35.87 3.16 R
5062 6304 0.250901 GTCCCAAGCCTGAAGAAGCA 60.251 55.000 0.00 0.0 0.00 3.91 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
62 63 0.030773 GCGACACAGTCACAGACTCA 59.969 55.000 0.00 0.00 41.37 3.41
80 81 2.034066 CAGCAACCACCCATCCGT 59.966 61.111 0.00 0.00 0.00 4.69
81 82 1.298340 CAGCAACCACCCATCCGTA 59.702 57.895 0.00 0.00 0.00 4.02
171 173 2.728817 CCCTACCATCGTCGCTCC 59.271 66.667 0.00 0.00 0.00 4.70
271 273 3.775654 CTCCCAGGAGCCGGTCAC 61.776 72.222 1.90 0.00 35.31 3.67
390 392 2.651361 CCGCTCGGTTCAGTGAGT 59.349 61.111 0.00 0.00 34.67 3.41
426 428 1.434188 TGGTATAGCCCCAGATGTGG 58.566 55.000 0.75 0.75 44.56 4.17
469 471 5.042463 TCTGTTGTTGTCCTGGTCATTTA 57.958 39.130 0.00 0.00 0.00 1.40
506 508 1.601759 CTGTTGGTGCCCTCACTGG 60.602 63.158 0.00 0.00 42.72 4.00
508 510 1.150536 GTTGGTGCCCTCACTGGAA 59.849 57.895 0.00 0.00 42.72 3.53
538 540 2.852449 TGGTTTTGGCAGATACAACGA 58.148 42.857 0.00 0.00 0.00 3.85
568 570 9.529325 TCGTGATCGAATATTTTCTAAACATCT 57.471 29.630 0.00 0.00 43.34 2.90
677 679 7.009179 ACCATTGGAGGAGTATGTATGTATG 57.991 40.000 10.37 0.00 0.00 2.39
743 745 6.340522 TCACTCGCTCAATTCTATGAATTCA 58.659 36.000 11.26 11.26 0.00 2.57
858 867 4.459337 GGCTAGCAAATGTCTTGGTTACTT 59.541 41.667 18.24 0.00 0.00 2.24
1057 1081 1.536662 ACACCGCTTCCCTTCTCCT 60.537 57.895 0.00 0.00 0.00 3.69
1425 1449 4.047822 GCAAGTCCTCTCTCATCAATACG 58.952 47.826 0.00 0.00 0.00 3.06
1573 1639 5.858581 GCTAGTGGTTAAAATTGCTGAAGTG 59.141 40.000 0.00 0.00 0.00 3.16
1816 2655 3.115390 TCCTGGATTTAAGCTACTGCCT 58.885 45.455 0.00 0.00 40.80 4.75
1853 2692 4.561326 CGAAAAGGACGGTAAACCCTCTAA 60.561 45.833 0.00 0.00 0.00 2.10
1954 2944 5.396484 CACACAGCCTTTGAATTATGAGTG 58.604 41.667 0.00 0.00 0.00 3.51
2089 3079 7.684529 AGTCTATTTCTGAGAATTGAACCTGT 58.315 34.615 0.00 0.00 0.00 4.00
2131 3121 1.832167 GCCCAACCACTGAGCCAAA 60.832 57.895 0.00 0.00 0.00 3.28
2672 3693 6.529220 AGAATAGGATATGCCACAAGTCTTC 58.471 40.000 0.00 0.00 40.02 2.87
2808 3829 3.640967 GGCAACTTTATCCATTGGGCATA 59.359 43.478 2.09 0.00 0.00 3.14
2809 3830 4.262164 GGCAACTTTATCCATTGGGCATAG 60.262 45.833 2.09 0.00 0.00 2.23
2858 3879 3.321039 AGATTGCATCAGGTGGATCCTA 58.679 45.455 14.23 0.00 46.24 2.94
2896 3917 4.701651 CAGATGGTCCAACAGAATTGCTAA 59.298 41.667 0.00 0.00 0.00 3.09
2898 3919 3.153919 TGGTCCAACAGAATTGCTAACC 58.846 45.455 0.00 0.00 0.00 2.85
2900 3921 3.191371 GGTCCAACAGAATTGCTAACCAG 59.809 47.826 0.00 0.00 0.00 4.00
2901 3922 4.072131 GTCCAACAGAATTGCTAACCAGA 58.928 43.478 0.00 0.00 0.00 3.86
2902 3923 4.154918 GTCCAACAGAATTGCTAACCAGAG 59.845 45.833 0.00 0.00 0.00 3.35
2920 4029 5.958380 ACCAGAGTTGACCATGAATCTAGTA 59.042 40.000 0.00 0.00 0.00 1.82
2943 4052 0.879090 CCTACTTGTCCCGCCAAAAC 59.121 55.000 0.00 0.00 0.00 2.43
2965 4074 1.965754 GACCATCCCGCAGAGCTCTT 61.966 60.000 15.27 0.00 0.00 2.85
3031 4140 7.930325 CAGTTTCTAGCTGATATGAAATCTCCA 59.070 37.037 0.00 0.00 36.12 3.86
3041 4150 7.166167 TGATATGAAATCTCCATGGTCATCAG 58.834 38.462 15.91 4.73 31.58 2.90
3182 4291 6.145338 TCTTCTTAGCTCTACCGTAATTGG 57.855 41.667 0.00 0.00 0.00 3.16
3212 4321 1.471119 CAGGATGGCTTGTGCTGAAT 58.529 50.000 1.68 0.00 37.22 2.57
3245 4354 4.188247 TGAACTGGTTCAGATCGGTTAG 57.812 45.455 11.53 0.00 43.90 2.34
3256 4365 1.403687 ATCGGTTAGCCTGCCTCCTC 61.404 60.000 0.00 0.00 0.00 3.71
3259 4368 1.691195 GGTTAGCCTGCCTCCTCTCC 61.691 65.000 0.00 0.00 0.00 3.71
3262 4371 2.880629 TAGCCTGCCTCCTCTCCCAC 62.881 65.000 0.00 0.00 0.00 4.61
3296 4405 1.219393 GCTACCGCCAGAAGCTCTT 59.781 57.895 0.00 0.00 40.39 2.85
3316 4425 1.433199 TCCCATCCGATATCTGGAGGT 59.567 52.381 19.52 5.98 39.30 3.85
3368 4478 5.833131 TCATAATTTCCAACATAGGGGCTTC 59.167 40.000 0.00 0.00 0.00 3.86
3369 4479 2.122783 TTTCCAACATAGGGGCTTCG 57.877 50.000 0.00 0.00 0.00 3.79
3370 4480 0.254747 TTCCAACATAGGGGCTTCGG 59.745 55.000 0.00 0.00 0.00 4.30
3371 4481 1.823899 CCAACATAGGGGCTTCGGC 60.824 63.158 0.00 0.00 40.88 5.54
3372 4482 1.224592 CAACATAGGGGCTTCGGCT 59.775 57.895 0.00 0.00 41.44 5.52
3373 4483 0.815615 CAACATAGGGGCTTCGGCTC 60.816 60.000 0.00 0.00 41.58 4.70
3374 4484 2.029666 CATAGGGGCTTCGGCTCG 59.970 66.667 0.00 0.00 43.67 5.03
3375 4485 3.234730 ATAGGGGCTTCGGCTCGG 61.235 66.667 0.00 0.00 43.67 4.63
3376 4486 4.772231 TAGGGGCTTCGGCTCGGT 62.772 66.667 0.00 0.00 43.67 4.69
3380 4490 4.388499 GGCTTCGGCTCGGTCCAA 62.388 66.667 0.00 0.00 41.44 3.53
3381 4491 3.119096 GCTTCGGCTCGGTCCAAC 61.119 66.667 0.00 0.00 38.08 3.77
3382 4492 2.342279 CTTCGGCTCGGTCCAACA 59.658 61.111 0.00 0.00 0.00 3.33
3383 4493 1.301401 CTTCGGCTCGGTCCAACAA 60.301 57.895 0.00 0.00 0.00 2.83
3386 4496 1.890041 CGGCTCGGTCCAACAAACA 60.890 57.895 0.00 0.00 0.00 2.83
3476 4622 3.753272 ACATTCAACAGCACATAGTGGAC 59.247 43.478 0.00 0.00 33.64 4.02
3500 4646 4.116782 TGGCCATTTGTATCATATGCCT 57.883 40.909 0.00 0.00 0.00 4.75
3501 4647 5.253991 TGGCCATTTGTATCATATGCCTA 57.746 39.130 0.00 0.00 0.00 3.93
3502 4648 5.009631 TGGCCATTTGTATCATATGCCTAC 58.990 41.667 0.00 3.37 0.00 3.18
3542 4689 0.251165 GGTTTGAGCCCCAACTAGCA 60.251 55.000 0.00 0.00 33.85 3.49
3749 4896 6.847792 CAGACGTGCTGCACATATTTAAATAG 59.152 38.462 29.86 12.87 37.90 1.73
3819 5050 5.163447 ACAAGATAATACACAGCCGCTTAGA 60.163 40.000 0.00 0.00 0.00 2.10
3890 5121 2.126463 GCTGTCAGCGCGTAGTCA 60.126 61.111 9.53 3.83 0.00 3.41
3891 5122 2.155194 GCTGTCAGCGCGTAGTCAG 61.155 63.158 9.53 14.43 0.00 3.51
3902 5133 3.508762 CGCGTAGTCAGTTGGTTAATCT 58.491 45.455 0.00 0.00 0.00 2.40
3993 5224 2.732289 TTTTTGGTGCCCTCTGCTC 58.268 52.632 0.00 0.00 42.00 4.26
3994 5225 0.106268 TTTTTGGTGCCCTCTGCTCA 60.106 50.000 0.00 0.00 42.00 4.26
4171 5410 1.930251 CTCCTTCACCACTCTCCAGA 58.070 55.000 0.00 0.00 0.00 3.86
4239 5478 4.712122 TGGTTTTCTTGTCAACTCCAAC 57.288 40.909 0.00 0.00 0.00 3.77
4330 5570 8.706322 TGAGGATATAGCAATTCTACACACTA 57.294 34.615 0.00 0.00 0.00 2.74
4509 5749 6.114089 ACATGATCAGATCAAGTTCTTCCTG 58.886 40.000 17.24 9.75 43.50 3.86
4649 5889 5.163561 TGTTCCAACTCAACAAATTGACCTC 60.164 40.000 0.00 0.00 40.01 3.85
4694 5934 5.693104 TCGTAACAATGTGAGACAACTTACC 59.307 40.000 0.00 0.00 32.66 2.85
4696 5936 4.706842 ACAATGTGAGACAACTTACCCT 57.293 40.909 0.00 0.00 32.66 4.34
4950 6192 2.223829 ACATCGGTTCGCTCTATCCAAG 60.224 50.000 0.00 0.00 0.00 3.61
5062 6304 1.958288 ATGAGGCAACCTAGGTCAGT 58.042 50.000 16.64 0.00 31.76 3.41
5064 6306 0.391793 GAGGCAACCTAGGTCAGTGC 60.392 60.000 23.46 23.46 31.76 4.40
5078 6334 0.879765 CAGTGCTTCTTCAGGCTTGG 59.120 55.000 0.00 0.00 0.00 3.61
5086 6342 0.615331 CTTCAGGCTTGGGACAGCTA 59.385 55.000 0.00 0.00 42.39 3.32
5172 6439 2.632996 TCAGTTTCTGGACTTCACCGAT 59.367 45.455 0.00 0.00 31.51 4.18
5212 6479 4.276926 AGACTTCAGGTTCAGTTTCATTGC 59.723 41.667 0.00 0.00 0.00 3.56
5233 6500 2.421619 GCTGGCCTCTTGATGTATAGC 58.578 52.381 3.32 0.00 0.00 2.97
5248 6515 4.546570 TGTATAGCGGAAGATGATTCACG 58.453 43.478 0.00 0.00 0.00 4.35
5259 6526 2.931512 TGATTCACGATACGCAGACA 57.068 45.000 0.00 0.00 0.00 3.41
5284 6551 0.878961 CAGTAATACCGCGCCCCTTC 60.879 60.000 0.00 0.00 0.00 3.46
5353 6620 4.005650 AGTCTCGTCCACTTGTTACGATA 58.994 43.478 8.06 0.97 43.88 2.92
5400 6667 8.370266 TGGAACTGTACATTTATACCACTACT 57.630 34.615 0.00 0.00 0.00 2.57
5401 6668 8.472413 TGGAACTGTACATTTATACCACTACTC 58.528 37.037 0.00 0.00 0.00 2.59
5441 6708 3.841643 AGCAAATTCAATGTACTGCTGC 58.158 40.909 1.61 0.00 38.64 5.25
5442 6709 3.256383 AGCAAATTCAATGTACTGCTGCA 59.744 39.130 0.88 0.88 38.64 4.41
5556 6823 0.255890 ATCCAGATTTCCGGTGGTGG 59.744 55.000 0.00 2.97 32.73 4.61
5557 6824 1.131303 TCCAGATTTCCGGTGGTGGT 61.131 55.000 0.00 0.00 32.73 4.16
5558 6825 0.616371 CCAGATTTCCGGTGGTGGTA 59.384 55.000 0.00 0.00 0.00 3.25
5559 6826 1.677820 CCAGATTTCCGGTGGTGGTAC 60.678 57.143 0.00 0.00 0.00 3.34
5560 6827 1.278127 CAGATTTCCGGTGGTGGTACT 59.722 52.381 0.00 0.00 0.00 2.73
5561 6828 1.278127 AGATTTCCGGTGGTGGTACTG 59.722 52.381 0.00 0.00 0.00 2.74
5631 6902 0.235926 GCTTTGAACAGCGGAGACAC 59.764 55.000 0.00 0.00 0.00 3.67
5884 7440 2.517875 GCGGCCGGAGTAGGAGTA 60.518 66.667 29.38 0.00 0.00 2.59
5907 7463 2.665000 CCGAGCTCTGAAAGGCCA 59.335 61.111 12.85 0.00 31.60 5.36
6006 7565 4.020617 TTGCTGGGCGAGAGGTGG 62.021 66.667 0.00 0.00 0.00 4.61
6009 7568 3.710722 CTGGGCGAGAGGTGGCTT 61.711 66.667 0.00 0.00 0.00 4.35
6010 7569 3.965539 CTGGGCGAGAGGTGGCTTG 62.966 68.421 0.00 0.00 0.00 4.01
6011 7570 4.785453 GGGCGAGAGGTGGCTTGG 62.785 72.222 0.00 0.00 0.00 3.61
6012 7571 4.785453 GGCGAGAGGTGGCTTGGG 62.785 72.222 0.00 0.00 0.00 4.12
6013 7572 3.706373 GCGAGAGGTGGCTTGGGA 61.706 66.667 0.00 0.00 0.00 4.37
6014 7573 2.581354 CGAGAGGTGGCTTGGGAG 59.419 66.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 2.674380 GCAGTGGGAAGTGGGCTG 60.674 66.667 0.00 0.00 0.00 4.85
62 63 1.485294 TACGGATGGGTGGTTGCTGT 61.485 55.000 0.00 0.00 0.00 4.40
185 187 2.127297 TTTCCTGGAGGGGAGGGG 59.873 66.667 0.00 0.00 36.66 4.79
220 222 1.276622 GGTGTGAAGCTAGGGGAAGA 58.723 55.000 0.00 0.00 0.00 2.87
271 273 2.270986 GCCACTTCCCACAAGCCAG 61.271 63.158 0.00 0.00 0.00 4.85
390 392 6.596497 GCTATACCAGTACAAAAGCCAGTTAA 59.404 38.462 0.00 0.00 0.00 2.01
426 428 5.347907 CAGATAGACAAACTTACGTCCCAAC 59.652 44.000 0.00 0.00 32.33 3.77
469 471 4.949121 ACAGAGGAACTTAGGAGTATGGT 58.051 43.478 0.00 0.00 41.55 3.55
506 508 6.572519 TCTGCCAAAACCATAAGCATAATTC 58.427 36.000 0.00 0.00 32.11 2.17
508 510 6.736110 ATCTGCCAAAACCATAAGCATAAT 57.264 33.333 0.00 0.00 32.11 1.28
563 565 4.030913 TCTCGGGGAACAAATCTAGATGT 58.969 43.478 5.86 0.00 0.00 3.06
565 567 4.101741 CCTTCTCGGGGAACAAATCTAGAT 59.898 45.833 0.00 0.00 0.00 1.98
566 568 3.451178 CCTTCTCGGGGAACAAATCTAGA 59.549 47.826 0.00 0.00 0.00 2.43
567 569 3.197983 ACCTTCTCGGGGAACAAATCTAG 59.802 47.826 0.00 0.00 36.97 2.43
568 570 3.178865 ACCTTCTCGGGGAACAAATCTA 58.821 45.455 0.00 0.00 36.97 1.98
677 679 3.826157 TCATTCTTGTTCACATTCACCCC 59.174 43.478 0.00 0.00 0.00 4.95
743 745 8.980481 AATGAATGTCGAGAAAGGGTATAATT 57.020 30.769 0.00 0.00 0.00 1.40
787 789 6.422776 ACAATTGCTAAACACCGATCTTAG 57.577 37.500 5.05 0.00 0.00 2.18
799 801 8.043710 TCTCAAAAAGGGAAAACAATTGCTAAA 58.956 29.630 5.05 0.00 0.00 1.85
858 867 1.635487 AGGCCAGAAAGCAGAACCATA 59.365 47.619 5.01 0.00 0.00 2.74
1440 1464 1.112916 TGGAGGTGAGTGCGACTTCA 61.113 55.000 0.00 0.00 0.00 3.02
1573 1639 5.402398 GTGTATCATTGAAAAGGCCAACTC 58.598 41.667 5.01 0.00 0.00 3.01
1839 2678 2.232941 TGCAGAGTTAGAGGGTTTACCG 59.767 50.000 0.00 0.00 46.96 4.02
1853 2692 4.850822 CATCAGCCGATGCAGAGT 57.149 55.556 0.00 0.00 42.54 3.24
1954 2944 5.581874 CACCCATCAAGATAAAAATGTTGGC 59.418 40.000 0.00 0.00 34.19 4.52
2048 3038 0.462759 GACTAGTGATGCACAGGGGC 60.463 60.000 0.00 0.00 36.74 5.80
2089 3079 3.888460 TTGTGCAGCCTGCCCAGA 61.888 61.111 15.29 0.00 44.23 3.86
2206 3196 7.870509 TCCCTGCAAAATATATGATATCAGC 57.129 36.000 11.78 6.93 0.00 4.26
2742 3763 7.548196 ACAAGACGTACTTTCAAAAGAATGA 57.452 32.000 9.39 0.00 39.31 2.57
2759 3780 3.316868 TGGCTTTCCCTAAAAACAAGACG 59.683 43.478 0.00 0.00 0.00 4.18
2808 3829 7.859325 ACAACTAGTGAACAATGTAACAACT 57.141 32.000 0.00 0.00 0.00 3.16
2896 3917 4.780021 ACTAGATTCATGGTCAACTCTGGT 59.220 41.667 0.00 0.00 0.00 4.00
2898 3919 6.867550 TGTACTAGATTCATGGTCAACTCTG 58.132 40.000 0.00 0.00 0.00 3.35
2900 3921 6.926272 GGATGTACTAGATTCATGGTCAACTC 59.074 42.308 0.00 0.00 0.00 3.01
2901 3922 6.613271 AGGATGTACTAGATTCATGGTCAACT 59.387 38.462 0.00 0.00 0.00 3.16
2902 3923 6.821388 AGGATGTACTAGATTCATGGTCAAC 58.179 40.000 0.00 0.00 0.00 3.18
2920 4029 0.907704 TGGCGGGACAAGTAGGATGT 60.908 55.000 0.00 0.00 0.00 3.06
2943 4052 2.503061 CTCTGCGGGATGGTCTGG 59.497 66.667 0.00 0.00 0.00 3.86
3010 4119 6.499699 ACCATGGAGATTTCATATCAGCTAGA 59.500 38.462 21.47 0.00 0.00 2.43
3031 4140 2.170397 TGCAATACGTCCTGATGACCAT 59.830 45.455 0.00 0.00 41.18 3.55
3041 4150 1.134788 AGCTACTGGTGCAATACGTCC 60.135 52.381 0.00 0.00 0.00 4.79
3139 4248 1.338136 GGGCAGAAGGGATTCGGAGA 61.338 60.000 0.00 0.00 0.00 3.71
3182 4291 3.733709 CCATCCTGGCCTTATGTCC 57.266 57.895 3.32 0.00 0.00 4.02
3212 4321 0.250295 CCAGTTCAAGCTCCGGTTCA 60.250 55.000 0.00 0.00 0.00 3.18
3245 4354 3.791586 GTGGGAGAGGAGGCAGGC 61.792 72.222 0.00 0.00 0.00 4.85
3256 4365 4.645535 CTTCATGGTATGTATGGTGGGAG 58.354 47.826 0.00 0.00 0.00 4.30
3259 4368 4.090761 AGCTTCATGGTATGTATGGTGG 57.909 45.455 0.00 0.00 0.00 4.61
3262 4371 4.245660 CGGTAGCTTCATGGTATGTATGG 58.754 47.826 0.00 0.00 0.00 2.74
3296 4405 1.433199 ACCTCCAGATATCGGATGGGA 59.567 52.381 19.45 12.48 34.71 4.37
3316 4425 2.656069 GGTCGGTTCAGCTAGGCCA 61.656 63.158 5.01 0.00 0.00 5.36
3368 4478 1.841663 CTGTTTGTTGGACCGAGCCG 61.842 60.000 0.00 0.00 0.00 5.52
3369 4479 0.534203 TCTGTTTGTTGGACCGAGCC 60.534 55.000 0.00 0.00 0.00 4.70
3370 4480 0.586802 GTCTGTTTGTTGGACCGAGC 59.413 55.000 0.00 0.00 0.00 5.03
3371 4481 2.240493 AGTCTGTTTGTTGGACCGAG 57.760 50.000 0.00 0.00 0.00 4.63
3372 4482 2.169769 AGAAGTCTGTTTGTTGGACCGA 59.830 45.455 0.00 0.00 0.00 4.69
3373 4483 2.287915 CAGAAGTCTGTTTGTTGGACCG 59.712 50.000 0.00 0.00 39.09 4.79
3374 4484 2.033424 GCAGAAGTCTGTTTGTTGGACC 59.967 50.000 9.94 0.00 45.45 4.46
3375 4485 2.682856 TGCAGAAGTCTGTTTGTTGGAC 59.317 45.455 9.94 0.00 45.45 4.02
3376 4486 2.997980 TGCAGAAGTCTGTTTGTTGGA 58.002 42.857 9.94 0.00 45.45 3.53
3377 4487 3.781079 TTGCAGAAGTCTGTTTGTTGG 57.219 42.857 9.94 0.00 45.45 3.77
3378 4488 3.970610 CGATTGCAGAAGTCTGTTTGTTG 59.029 43.478 9.94 0.00 45.45 3.33
3379 4489 3.548818 GCGATTGCAGAAGTCTGTTTGTT 60.549 43.478 9.94 0.00 45.45 2.83
3380 4490 2.031682 GCGATTGCAGAAGTCTGTTTGT 60.032 45.455 9.94 0.00 45.45 2.83
3381 4491 2.578495 GCGATTGCAGAAGTCTGTTTG 58.422 47.619 9.94 1.75 45.45 2.93
3382 4492 1.537202 GGCGATTGCAGAAGTCTGTTT 59.463 47.619 7.38 0.00 45.45 2.83
3383 4493 1.160137 GGCGATTGCAGAAGTCTGTT 58.840 50.000 7.38 0.00 45.45 3.16
3386 4496 0.322975 AGTGGCGATTGCAGAAGTCT 59.677 50.000 7.38 0.00 45.35 3.24
3476 4622 4.229096 GCATATGATACAAATGGCCAACG 58.771 43.478 10.96 3.21 0.00 4.10
3500 4646 1.348366 ACACACCCGTATTGGCAAGTA 59.652 47.619 5.96 0.00 35.87 2.24
3501 4647 0.109723 ACACACCCGTATTGGCAAGT 59.890 50.000 5.96 0.00 35.87 3.16
3502 4648 1.243902 AACACACCCGTATTGGCAAG 58.756 50.000 5.96 0.00 35.87 4.01
3568 4715 6.315891 CCAAACAACATCAACTCACCAATTTT 59.684 34.615 0.00 0.00 0.00 1.82
3569 4716 5.816777 CCAAACAACATCAACTCACCAATTT 59.183 36.000 0.00 0.00 0.00 1.82
3632 4779 4.609301 TGCAAACCAAATAGAGCCCTAAT 58.391 39.130 0.00 0.00 0.00 1.73
3819 5050 1.039068 AGCAGATCTGACGCAGCTAT 58.961 50.000 27.04 0.00 0.00 2.97
3889 5120 6.130298 TGTGAAACACAGATTAACCAACTG 57.870 37.500 0.25 0.00 45.67 3.16
4330 5570 9.260002 CCTACTTAAAACATTGTTGCTTCATTT 57.740 29.630 2.13 0.00 0.00 2.32
4509 5749 0.457337 GCAGCTGCAAACCTACATGC 60.457 55.000 33.36 1.32 42.86 4.06
4649 5889 0.792640 CAAGCCAGTTAGCACAGTCG 59.207 55.000 0.00 0.00 34.23 4.18
4752 5994 8.554528 CACATGTACAATCAATCCTGAAGATAC 58.445 37.037 0.00 0.00 34.49 2.24
5062 6304 0.250901 GTCCCAAGCCTGAAGAAGCA 60.251 55.000 0.00 0.00 0.00 3.91
5064 6306 1.818642 CTGTCCCAAGCCTGAAGAAG 58.181 55.000 0.00 0.00 0.00 2.85
5086 6342 4.319177 CAAGTACTGTTGCTCCTAGCTTT 58.681 43.478 0.00 0.00 42.97 3.51
5172 6439 2.093500 AGTCTATGCAAAGCACGATCCA 60.093 45.455 0.00 0.00 43.04 3.41
5212 6479 2.681706 CTATACATCAAGAGGCCAGCG 58.318 52.381 5.01 0.00 0.00 5.18
5233 6500 2.405357 GCGTATCGTGAATCATCTTCCG 59.595 50.000 0.00 0.00 0.00 4.30
5248 6515 7.485277 GGTATTACTGTATCATGTCTGCGTATC 59.515 40.741 0.00 0.00 0.00 2.24
5259 6526 2.353406 GGGCGCGGTATTACTGTATCAT 60.353 50.000 8.83 0.00 0.00 2.45
5284 6551 6.817765 ATTACTACAACAAACATGGACCAG 57.182 37.500 0.00 0.00 0.00 4.00
5353 6620 2.114670 CGGCCCATTGCGTTCAGAT 61.115 57.895 0.00 0.00 42.61 2.90
5401 6668 3.272334 GGCTGCCTTCGCCATACG 61.272 66.667 12.43 0.00 46.77 3.06
5441 6708 2.702898 TCCGTGCAATTCAATGTGTG 57.297 45.000 0.00 0.00 0.00 3.82
5442 6709 3.724508 TTTCCGTGCAATTCAATGTGT 57.275 38.095 0.00 0.00 0.00 3.72
5671 6942 1.460273 TTTCCGTTTTCCCTGCCTGC 61.460 55.000 0.00 0.00 0.00 4.85
5816 7371 3.880047 AAGAAACACATGGATGGCATG 57.120 42.857 3.81 0.00 36.22 4.06
5870 7426 1.310904 CTCTGTACTCCTACTCCGGC 58.689 60.000 0.00 0.00 0.00 6.13
5879 7435 3.927501 AGCTCGGCTCTGTACTCC 58.072 61.111 0.00 0.00 30.62 3.85
5907 7463 1.841302 TTGACGCTGGCCATTCTCCT 61.841 55.000 5.51 0.00 0.00 3.69
5983 7542 2.664851 CTCGCCCAGCAACGAACA 60.665 61.111 0.00 0.00 37.94 3.18
6006 7565 2.726351 CGGTCTCCCTCTCCCAAGC 61.726 68.421 0.00 0.00 0.00 4.01
6007 7566 2.060980 CCGGTCTCCCTCTCCCAAG 61.061 68.421 0.00 0.00 0.00 3.61
6008 7567 2.038975 CCGGTCTCCCTCTCCCAA 59.961 66.667 0.00 0.00 0.00 4.12
6009 7568 4.075793 CCCGGTCTCCCTCTCCCA 62.076 72.222 0.00 0.00 0.00 4.37
6010 7569 4.862823 CCCCGGTCTCCCTCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
6011 7570 4.862823 CCCCCGGTCTCCCTCTCC 62.863 77.778 0.00 0.00 0.00 3.71
6012 7571 4.077180 ACCCCCGGTCTCCCTCTC 62.077 72.222 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.