Multiple sequence alignment - TraesCS2D01G264600

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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 TraesCS2D01G264600 chr2D 100.000 8450 0 0 1 8450 323639764 323648213 0.000000e+00 15605.0
1 TraesCS2D01G264600 chr2D 95.556 90 4 0 6622 6711 449513577 449513666 2.460000e-30 145.0
2 TraesCS2D01G264600 chr2A 96.425 4392 108 27 1 4355 406776820 406772441 0.000000e+00 7195.0
3 TraesCS2D01G264600 chr2A 96.221 4128 101 18 4352 8450 406772284 406768183 0.000000e+00 6708.0
4 TraesCS2D01G264600 chr2B 94.723 2937 109 23 1 2916 391759182 391762093 0.000000e+00 4523.0
5 TraesCS2D01G264600 chr2B 94.393 1516 60 10 5084 6596 391766299 391767792 0.000000e+00 2305.0
6 TraesCS2D01G264600 chr2B 96.880 1282 36 2 6704 7981 391767804 391769085 0.000000e+00 2143.0
7 TraesCS2D01G264600 chr2B 95.636 1077 33 5 2932 3994 391762415 391763491 0.000000e+00 1716.0
8 TraesCS2D01G264600 chr2B 98.103 738 13 1 4352 5088 391763944 391764681 0.000000e+00 1284.0
9 TraesCS2D01G264600 chr2B 87.738 473 24 13 8011 8450 391769179 391769650 9.720000e-144 521.0
10 TraesCS2D01G264600 chr2B 97.351 302 8 0 4054 4355 391763486 391763787 1.630000e-141 514.0
11 TraesCS2D01G264600 chr2B 92.683 82 5 1 5126 5206 706924055 706923974 5.360000e-22 117.0
12 TraesCS2D01G264600 chr7B 96.552 87 3 0 6620 6706 228390849 228390935 2.460000e-30 145.0
13 TraesCS2D01G264600 chr7B 88.073 109 13 0 5098 5206 587669021 587668913 6.880000e-26 130.0
14 TraesCS2D01G264600 chr4D 94.565 92 5 0 6615 6706 371926807 371926898 8.840000e-30 143.0
15 TraesCS2D01G264600 chr4B 90.741 108 8 2 6613 6718 507357679 507357786 8.840000e-30 143.0
16 TraesCS2D01G264600 chr6B 94.505 91 5 0 6619 6709 353557877 353557967 3.180000e-29 141.0
17 TraesCS2D01G264600 chr3B 93.478 92 5 1 6620 6711 526495895 526495805 1.480000e-27 135.0
18 TraesCS2D01G264600 chr5A 87.288 118 14 1 5090 5206 634053882 634053765 5.320000e-27 134.0
19 TraesCS2D01G264600 chr5A 80.000 90 17 1 2729 2817 554217412 554217323 1.970000e-06 65.8
20 TraesCS2D01G264600 chr3D 93.333 90 6 0 6622 6711 570848752 570848663 5.320000e-27 134.0
21 TraesCS2D01G264600 chr7D 90.291 103 7 3 6615 6715 561192213 561192112 1.910000e-26 132.0
22 TraesCS2D01G264600 chr1D 87.850 107 13 0 5098 5204 437730851 437730957 8.900000e-25 126.0
23 TraesCS2D01G264600 chr7A 87.619 105 13 0 5102 5206 67729531 67729635 1.150000e-23 122.0
24 TraesCS2D01G264600 chr1B 87.387 111 9 4 5098 5206 593144982 593145089 1.150000e-23 122.0
25 TraesCS2D01G264600 chr5D 79.856 139 25 3 5097 5233 220689543 220689680 1.940000e-16 99.0
26 TraesCS2D01G264600 chr6A 81.111 90 16 1 2729 2817 227099490 227099579 4.230000e-08 71.3
27 TraesCS2D01G264600 chrUn 80.000 90 17 1 2729 2817 105614382 105614293 1.970000e-06 65.8


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 TraesCS2D01G264600 chr2D 323639764 323648213 8449 False 15605.0 15605 100.000000 1 8450 1 chr2D.!!$F1 8449
1 TraesCS2D01G264600 chr2A 406768183 406776820 8637 True 6951.5 7195 96.323000 1 8450 2 chr2A.!!$R1 8449
2 TraesCS2D01G264600 chr2B 391759182 391769650 10468 False 1858.0 4523 94.974857 1 8450 7 chr2B.!!$F1 8449

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
347 357 0.393944 AGTGGGATGCTGTGATGCAG 60.394 55.000 0.00 0.00 46.71 4.41 F
439 450 1.352114 TTTTATCGTCCCTTCGCGTG 58.648 50.000 5.77 0.00 0.00 5.34 F
1808 1838 1.708341 ATCTTGCTGTGCCCAAAAGT 58.292 45.000 0.00 0.00 0.00 2.66 F
2413 2446 0.416231 TTGGTACTCAGGGTAGGGCT 59.584 55.000 0.00 0.00 0.00 5.19 F
2778 2812 1.014352 GGAAAACATCCCGGTCGATG 58.986 55.000 16.49 16.49 43.00 3.84 F
3762 4124 3.104519 TGTAGGTATCCGAACCCTTCA 57.895 47.619 0.00 0.00 40.71 3.02 F
5126 7272 2.668144 TGTTCGGTTGGAAGGGATTT 57.332 45.000 0.00 0.00 34.69 2.17 F
6509 8658 0.951040 CTTTGACGTCCCAGAGGTGC 60.951 60.000 14.12 0.00 30.56 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 2253 4.142708 TGGAATAAAACATGCACTGCGTAG 60.143 41.667 0.00 0.0 0.00 3.51 R
2413 2446 4.471386 ACCTAAATTGCTGGAGCTTAGAGA 59.529 41.667 0.00 0.0 42.66 3.10 R
2778 2812 1.177401 GAGCAATGTGGGAAAGGGTC 58.823 55.000 0.00 0.0 0.00 4.46 R
3998 4360 2.184533 ACATACTTGACATCGGGTCCA 58.815 47.619 5.83 0.0 46.38 4.02 R
4001 4363 4.028131 TCCTTACATACTTGACATCGGGT 58.972 43.478 0.00 0.0 0.00 5.28 R
5130 7276 0.929244 CCCAATCCACTCCAATCCCT 59.071 55.000 0.00 0.0 0.00 4.20 R
6689 8839 1.384643 GGTACTCCCTCTGCCCCAT 60.385 63.158 0.00 0.0 0.00 4.00 R
8056 10276 0.983378 AAGGCGTAGGAATCAGGGCT 60.983 55.000 0.00 0.0 38.19 5.19 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
41 42 2.472695 TCTTGCATTGCGTTACTCCT 57.527 45.000 3.84 0.00 0.00 3.69
76 77 2.507992 CGGCTTCACTCGCTCCTG 60.508 66.667 0.00 0.00 0.00 3.86
84 85 1.986757 ACTCGCTCCTGCTCCATGT 60.987 57.895 0.00 0.00 36.97 3.21
186 187 2.091333 TCTTTTGGTGCCCTTTCTTCCT 60.091 45.455 0.00 0.00 0.00 3.36
268 269 2.742053 GCTTGCACTTTCCTGTCGAATA 59.258 45.455 0.00 0.00 0.00 1.75
283 284 6.263842 CCTGTCGAATACCATGGTTACTAGTA 59.736 42.308 25.38 2.58 0.00 1.82
347 357 0.393944 AGTGGGATGCTGTGATGCAG 60.394 55.000 0.00 0.00 46.71 4.41
366 376 9.241919 TGATGCAGTTTAAGAATCCTTTAATCA 57.758 29.630 0.00 0.00 33.94 2.57
369 379 9.295825 TGCAGTTTAAGAATCCTTTAATCAGAA 57.704 29.630 0.00 0.00 33.94 3.02
392 403 4.763073 TGAATCTGCATCAACTAGTCCTG 58.237 43.478 0.00 0.00 0.00 3.86
412 423 9.113838 AGTCCTGTCAGTTTATTTATTATGCAG 57.886 33.333 0.00 0.00 0.00 4.41
422 433 9.492973 GTTTATTTATTATGCAGCATGGGATTT 57.507 29.630 18.81 1.89 35.86 2.17
428 439 2.653726 TGCAGCATGGGATTTTATCGT 58.346 42.857 0.00 0.00 35.86 3.73
439 450 1.352114 TTTTATCGTCCCTTCGCGTG 58.648 50.000 5.77 0.00 0.00 5.34
486 497 4.392940 CCTTCCACTGTGAATTGACTCTT 58.607 43.478 9.86 0.00 0.00 2.85
497 508 9.390795 CTGTGAATTGACTCTTAATTGTTTCAG 57.609 33.333 0.00 0.00 0.00 3.02
531 542 8.014322 TGTTAATCTAGCTGTTAAACGAGTTG 57.986 34.615 0.00 0.00 0.00 3.16
536 547 2.287915 AGCTGTTAAACGAGTTGCACAG 59.712 45.455 17.07 17.07 36.90 3.66
537 548 2.639751 CTGTTAAACGAGTTGCACAGC 58.360 47.619 12.15 0.00 31.12 4.40
581 592 2.047061 TGGTTCTTGACTACAGGCACT 58.953 47.619 0.00 0.00 43.88 4.40
642 653 4.078537 TGCCATGCTAAGTTCTTGCTTAA 58.921 39.130 0.00 0.00 31.43 1.85
643 654 4.706476 TGCCATGCTAAGTTCTTGCTTAAT 59.294 37.500 0.00 0.00 31.43 1.40
644 655 5.163622 TGCCATGCTAAGTTCTTGCTTAATC 60.164 40.000 0.00 0.00 31.43 1.75
645 656 5.163622 GCCATGCTAAGTTCTTGCTTAATCA 60.164 40.000 0.00 0.00 31.43 2.57
646 657 6.460676 GCCATGCTAAGTTCTTGCTTAATCAT 60.461 38.462 0.00 0.00 31.43 2.45
647 658 7.255242 GCCATGCTAAGTTCTTGCTTAATCATA 60.255 37.037 0.00 0.00 31.43 2.15
648 659 8.072567 CCATGCTAAGTTCTTGCTTAATCATAC 58.927 37.037 0.00 0.00 31.43 2.39
650 661 7.039270 TGCTAAGTTCTTGCTTAATCATACGA 58.961 34.615 0.00 0.00 31.43 3.43
652 663 8.058915 GCTAAGTTCTTGCTTAATCATACGAAG 58.941 37.037 0.00 0.00 31.43 3.79
653 664 9.088512 CTAAGTTCTTGCTTAATCATACGAAGT 57.911 33.333 0.00 0.00 36.06 3.01
654 665 7.295952 AGTTCTTGCTTAATCATACGAAGTG 57.704 36.000 0.00 0.00 45.73 3.16
655 666 6.874134 AGTTCTTGCTTAATCATACGAAGTGT 59.126 34.615 0.00 0.00 45.73 3.55
737 762 2.689658 TGGTCCAGAACTTCAAGAGGA 58.310 47.619 0.00 0.00 0.00 3.71
936 965 2.797156 CAGACTCGAAGGAACACTTGTG 59.203 50.000 0.00 0.00 40.21 3.33
1089 1119 2.612972 CCTGACACATACGCCATATCCC 60.613 54.545 0.00 0.00 0.00 3.85
1414 1444 7.607991 CCACATTAAGTTGTTAGGAGAACTGAT 59.392 37.037 0.00 0.00 38.32 2.90
1808 1838 1.708341 ATCTTGCTGTGCCCAAAAGT 58.292 45.000 0.00 0.00 0.00 2.66
2223 2253 2.884639 ACTGGGTGTGTGCTTATTGTTC 59.115 45.455 0.00 0.00 0.00 3.18
2413 2446 0.416231 TTGGTACTCAGGGTAGGGCT 59.584 55.000 0.00 0.00 0.00 5.19
2449 2482 4.578105 GCAATTTAGGTTCCAGATGAGAGG 59.422 45.833 0.00 0.00 0.00 3.69
2612 2645 6.657541 TGTTTGGTGAGGAATTAACTACCATC 59.342 38.462 0.00 0.00 37.95 3.51
2615 2648 5.104527 TGGTGAGGAATTAACTACCATCCAG 60.105 44.000 0.00 0.00 33.60 3.86
2778 2812 1.014352 GGAAAACATCCCGGTCGATG 58.986 55.000 16.49 16.49 43.00 3.84
2842 2876 4.978388 AGGGGTTATTAGGAGATGAGCTTT 59.022 41.667 0.00 0.00 0.00 3.51
2855 2889 7.606073 AGGAGATGAGCTTTTAGAAAAGAAGAC 59.394 37.037 17.00 6.49 46.39 3.01
3762 4124 3.104519 TGTAGGTATCCGAACCCTTCA 57.895 47.619 0.00 0.00 40.71 3.02
3891 4253 5.880332 TCCGGGAGTATCAAAGATGAAAAAG 59.120 40.000 0.00 0.00 39.49 2.27
3995 4357 8.753497 AATATGTCTCATTTTACCTCCTTTCC 57.247 34.615 0.00 0.00 0.00 3.13
3996 4358 5.843019 TGTCTCATTTTACCTCCTTTCCT 57.157 39.130 0.00 0.00 0.00 3.36
3997 4359 6.945636 TGTCTCATTTTACCTCCTTTCCTA 57.054 37.500 0.00 0.00 0.00 2.94
3998 4360 7.510675 TGTCTCATTTTACCTCCTTTCCTAT 57.489 36.000 0.00 0.00 0.00 2.57
4000 4362 6.768381 GTCTCATTTTACCTCCTTTCCTATGG 59.232 42.308 0.00 0.00 0.00 2.74
4001 4363 6.676632 TCTCATTTTACCTCCTTTCCTATGGA 59.323 38.462 0.00 0.00 0.00 3.41
4002 4364 6.659824 TCATTTTACCTCCTTTCCTATGGAC 58.340 40.000 0.00 0.00 0.00 4.02
4003 4365 5.446260 TTTTACCTCCTTTCCTATGGACC 57.554 43.478 0.00 0.00 0.00 4.46
4073 4435 4.817318 TTCCTTTGTTTGTTTCCTTGCT 57.183 36.364 0.00 0.00 0.00 3.91
4297 4659 3.445805 TCGGAATAAGGTGCATTTTTCCC 59.554 43.478 13.43 0.00 37.12 3.97
4361 4883 9.778993 CATTACTTCTGTTTCCTGTTATCATTG 57.221 33.333 0.00 0.00 0.00 2.82
5126 7272 2.668144 TGTTCGGTTGGAAGGGATTT 57.332 45.000 0.00 0.00 34.69 2.17
5130 7276 3.231207 TCGGTTGGAAGGGATTTGAAA 57.769 42.857 0.00 0.00 0.00 2.69
5351 7497 7.270047 CCGACTTATTACTTGGAAGGTCATAA 58.730 38.462 0.00 0.00 0.00 1.90
5413 7560 5.986135 GTGACACTAAGCACCTATATTCCTG 59.014 44.000 0.00 0.00 0.00 3.86
5455 7603 7.654022 AGGGAGTTTTTATTGACTCAAAACA 57.346 32.000 8.89 0.00 43.14 2.83
5893 8041 5.424757 GCATATTGTACTCCCAACTACACA 58.575 41.667 0.00 0.00 0.00 3.72
5899 8047 2.890814 ACTCCCAACTACACAGCTACT 58.109 47.619 0.00 0.00 0.00 2.57
5900 8048 4.043608 ACTCCCAACTACACAGCTACTA 57.956 45.455 0.00 0.00 0.00 1.82
6093 8241 6.003326 TCAATCAAATTGAAGTGGCTAGACA 58.997 36.000 0.00 0.00 45.57 3.41
6242 8390 3.997681 GCTCCACTCCAGAAAAGTTCTAC 59.002 47.826 0.00 0.00 38.11 2.59
6264 8412 4.100189 ACCTAAGCTTATGTGCCTAGTCTG 59.900 45.833 12.91 0.00 0.00 3.51
6509 8658 0.951040 CTTTGACGTCCCAGAGGTGC 60.951 60.000 14.12 0.00 30.56 5.01
6625 8775 9.872757 TTTTCGAATTTTGTGTATGAAGTACTC 57.127 29.630 0.00 0.00 34.27 2.59
6626 8776 7.591006 TCGAATTTTGTGTATGAAGTACTCC 57.409 36.000 0.00 0.00 34.27 3.85
6646 8796 4.359105 TCCCTCCGTCCCATAATATAAGG 58.641 47.826 0.00 0.00 0.00 2.69
6648 8798 3.118371 CCTCCGTCCCATAATATAAGGGC 60.118 52.174 0.00 0.00 42.52 5.19
6662 8812 6.673154 ATATAAGGGCGTTTTTGACACTAC 57.327 37.500 0.00 0.00 0.00 2.73
6663 8813 2.335316 AGGGCGTTTTTGACACTACA 57.665 45.000 0.00 0.00 0.00 2.74
6664 8814 1.944709 AGGGCGTTTTTGACACTACAC 59.055 47.619 0.00 0.00 0.00 2.90
6665 8815 1.944709 GGGCGTTTTTGACACTACACT 59.055 47.619 0.00 0.00 0.00 3.55
6666 8816 3.132925 GGGCGTTTTTGACACTACACTA 58.867 45.455 0.00 0.00 0.00 2.74
6680 8830 3.805971 ACTACACTAGTGTCAAAAACGCC 59.194 43.478 31.11 0.00 43.74 5.68
6689 8839 8.042515 ACTAGTGTCAAAAACGCCCTTATATTA 58.957 33.333 0.00 0.00 39.30 0.98
6694 8844 5.536916 TCAAAAACGCCCTTATATTATGGGG 59.463 40.000 10.45 10.45 42.04 4.96
6747 8897 7.563906 TGACCTCACAAAATCAAAATTTCCTT 58.436 30.769 0.00 0.00 33.93 3.36
6775 8925 9.871238 TCTGTCCACTTTATGTAGATTTACTTC 57.129 33.333 0.00 0.00 0.00 3.01
7044 9194 7.254084 GCAAACTACAAATCTTTCACAAGGTTG 60.254 37.037 0.00 0.00 33.28 3.77
7168 9318 5.506317 GCATTGCATTGAATGGTACTCCTAC 60.506 44.000 12.66 0.00 34.42 3.18
7398 9554 3.687102 TCGGTGCGGGTCGTTGAT 61.687 61.111 0.00 0.00 0.00 2.57
7617 9773 1.035932 ATCTCCAGCATTGCACAGCC 61.036 55.000 11.91 0.00 0.00 4.85
7854 10010 5.063564 CACTATTTTCTGTAGAAGGAACCGC 59.936 44.000 0.00 0.00 35.21 5.68
7879 10035 7.220108 GCGTTTATTATTTCTGGAATTCGCTTT 59.780 33.333 0.00 0.00 35.66 3.51
7898 10054 2.198827 TGTTACTCTGGTGCCATTGG 57.801 50.000 0.00 0.00 0.00 3.16
7981 10137 6.401394 TCTCATTGCCTGGAGAATATAATCG 58.599 40.000 0.00 0.00 37.23 3.34
8007 10227 8.219769 GTCATTCAGCTATAAAATGATCGACAG 58.780 37.037 13.05 0.00 40.44 3.51
8056 10276 1.419381 TACTTGGGTGTCACTGCAGA 58.581 50.000 23.35 0.00 0.00 4.26
8059 10279 2.359230 GGGTGTCACTGCAGAGCC 60.359 66.667 23.35 13.38 0.00 4.70
8071 10294 0.249657 GCAGAGCCCTGATTCCTACG 60.250 60.000 0.00 0.00 43.02 3.51
8150 10373 3.708631 TCCAATCCTGAAGTCTGGAGATC 59.291 47.826 11.92 0.00 45.24 2.75
8195 10418 2.048222 TCACGGAAGGAGCAAGCG 60.048 61.111 0.00 0.00 0.00 4.68
8275 10508 2.092049 TCGAGGCCAAGGTAGATACAGA 60.092 50.000 5.01 0.00 0.00 3.41
8276 10509 2.693591 CGAGGCCAAGGTAGATACAGAA 59.306 50.000 5.01 0.00 0.00 3.02
8321 10574 3.502572 GGCAACGATCTGAAGGCC 58.497 61.111 0.00 0.00 0.00 5.19
8375 10628 2.359230 GTGGACAGTGAGCTGCCC 60.359 66.667 0.00 0.00 46.30 5.36
8417 10670 1.821332 CTTCCGCATCCTCAAGGCC 60.821 63.158 0.00 0.00 34.44 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.805254 GTGTGCATGGACATGGAGC 59.195 57.895 23.52 6.24 39.83 4.70
156 157 0.951558 GCACCAAAAGAGAAGCGGAA 59.048 50.000 0.00 0.00 0.00 4.30
158 159 1.581447 GGCACCAAAAGAGAAGCGG 59.419 57.895 0.00 0.00 0.00 5.52
215 216 4.445879 GGGTGTATCTCCCCTATTTCAACC 60.446 50.000 0.00 0.00 39.08 3.77
330 340 4.649845 CTGCATCACAGCATCCCA 57.350 55.556 0.00 0.00 44.68 4.37
366 376 6.054295 GGACTAGTTGATGCAGATTCATTCT 58.946 40.000 0.00 0.00 33.90 2.40
369 379 5.104610 ACAGGACTAGTTGATGCAGATTCAT 60.105 40.000 0.00 0.00 0.00 2.57
392 403 7.596248 CCCATGCTGCATAATAAATAAACTGAC 59.404 37.037 15.78 0.00 0.00 3.51
406 417 4.397420 ACGATAAAATCCCATGCTGCATA 58.603 39.130 15.78 0.00 0.00 3.14
407 418 3.225104 ACGATAAAATCCCATGCTGCAT 58.775 40.909 9.81 9.81 0.00 3.96
408 419 2.618241 GACGATAAAATCCCATGCTGCA 59.382 45.455 4.13 4.13 0.00 4.41
422 433 0.179156 GACACGCGAAGGGACGATAA 60.179 55.000 15.93 0.00 46.37 1.75
486 497 6.952773 AACAAGTAGTGGCTGAAACAATTA 57.047 33.333 0.00 0.00 0.00 1.40
497 508 5.420409 ACAGCTAGATTAACAAGTAGTGGC 58.580 41.667 0.00 0.00 0.00 5.01
531 542 1.126846 GTCGATATTATGCCGCTGTGC 59.873 52.381 0.00 0.00 0.00 4.57
536 547 2.080286 AGTGGTCGATATTATGCCGC 57.920 50.000 0.00 0.00 0.00 6.53
537 548 4.436242 ACTAGTGGTCGATATTATGCCG 57.564 45.455 0.00 0.00 0.00 5.69
599 610 0.394565 AATGAGCGACCCCAGATAGC 59.605 55.000 0.00 0.00 0.00 2.97
642 653 4.381612 CCAGTACCACACACTTCGTATGAT 60.382 45.833 0.00 0.00 0.00 2.45
643 654 3.057104 CCAGTACCACACACTTCGTATGA 60.057 47.826 0.00 0.00 0.00 2.15
644 655 3.250744 CCAGTACCACACACTTCGTATG 58.749 50.000 0.00 0.00 0.00 2.39
645 656 2.232941 CCCAGTACCACACACTTCGTAT 59.767 50.000 0.00 0.00 0.00 3.06
646 657 1.614903 CCCAGTACCACACACTTCGTA 59.385 52.381 0.00 0.00 0.00 3.43
647 658 0.391597 CCCAGTACCACACACTTCGT 59.608 55.000 0.00 0.00 0.00 3.85
648 659 0.677288 TCCCAGTACCACACACTTCG 59.323 55.000 0.00 0.00 0.00 3.79
650 661 2.224769 CCAATCCCAGTACCACACACTT 60.225 50.000 0.00 0.00 0.00 3.16
652 663 1.349688 TCCAATCCCAGTACCACACAC 59.650 52.381 0.00 0.00 0.00 3.82
653 664 1.735926 TCCAATCCCAGTACCACACA 58.264 50.000 0.00 0.00 0.00 3.72
654 665 2.026262 ACATCCAATCCCAGTACCACAC 60.026 50.000 0.00 0.00 0.00 3.82
655 666 2.274542 ACATCCAATCCCAGTACCACA 58.725 47.619 0.00 0.00 0.00 4.17
1089 1119 2.602257 TATGCCTCGAGTGTTCATGG 57.398 50.000 12.31 0.00 0.00 3.66
1808 1838 7.173907 GGATCAGAACTCTTGTCAAAAGATTCA 59.826 37.037 0.00 0.00 0.00 2.57
2223 2253 4.142708 TGGAATAAAACATGCACTGCGTAG 60.143 41.667 0.00 0.00 0.00 3.51
2413 2446 4.471386 ACCTAAATTGCTGGAGCTTAGAGA 59.529 41.667 0.00 0.00 42.66 3.10
2449 2482 2.814336 AGTCAGGCATTTTCTTCCGTTC 59.186 45.455 0.00 0.00 0.00 3.95
2778 2812 1.177401 GAGCAATGTGGGAAAGGGTC 58.823 55.000 0.00 0.00 0.00 4.46
2817 2851 4.595350 AGCTCATCTCCTAATAACCCCTTC 59.405 45.833 0.00 0.00 0.00 3.46
2855 2889 1.442769 ACACATGCTAAGAAGGTGCG 58.557 50.000 0.00 0.00 32.89 5.34
3030 3372 5.070001 AGTACTTTTCATTGCAGCCTACAA 58.930 37.500 0.00 0.00 0.00 2.41
3391 3742 9.589111 CTTCTTTTTAGGAGAGTTCCATAGTAC 57.411 37.037 0.00 0.00 46.64 2.73
3753 4115 7.509546 TCTCATATGTAAAGGATGAAGGGTTC 58.490 38.462 1.90 0.00 0.00 3.62
3762 4124 6.266558 AGAAGCGTCTCTCATATGTAAAGGAT 59.733 38.462 1.90 0.00 0.00 3.24
3891 4253 4.277476 TGAAACATTGGGGTCCATCATAC 58.723 43.478 0.00 0.00 31.53 2.39
3974 4336 5.843019 AGGAAAGGAGGTAAAATGAGACA 57.157 39.130 0.00 0.00 0.00 3.41
3995 4357 4.039245 ACATACTTGACATCGGGTCCATAG 59.961 45.833 5.83 4.07 46.38 2.23
3996 4358 3.964688 ACATACTTGACATCGGGTCCATA 59.035 43.478 5.83 0.00 46.38 2.74
3997 4359 2.771943 ACATACTTGACATCGGGTCCAT 59.228 45.455 5.83 0.00 46.38 3.41
3998 4360 2.184533 ACATACTTGACATCGGGTCCA 58.815 47.619 5.83 0.00 46.38 4.02
4001 4363 4.028131 TCCTTACATACTTGACATCGGGT 58.972 43.478 0.00 0.00 0.00 5.28
4002 4364 4.665833 TCCTTACATACTTGACATCGGG 57.334 45.455 0.00 0.00 0.00 5.14
4003 4365 5.902681 TCTTCCTTACATACTTGACATCGG 58.097 41.667 0.00 0.00 0.00 4.18
4050 4412 5.744171 AGCAAGGAAACAAACAAAGGAAAT 58.256 33.333 0.00 0.00 0.00 2.17
4073 4435 6.765989 CCCATCGAACCAATCTGTTATAGAAA 59.234 38.462 0.00 0.00 39.30 2.52
4239 4601 7.429340 GCAAAGAACTTGAATTGGTATACATCG 59.571 37.037 5.01 0.00 37.17 3.84
4297 4659 4.576330 AACAGAAGGATAAACAGGGGAG 57.424 45.455 0.00 0.00 0.00 4.30
4361 4883 5.010282 ACTCATCAGGAACCAACCAAATAC 58.990 41.667 0.00 0.00 0.00 1.89
5126 7272 3.564133 CCAATCCACTCCAATCCCTTTCA 60.564 47.826 0.00 0.00 0.00 2.69
5130 7276 0.929244 CCCAATCCACTCCAATCCCT 59.071 55.000 0.00 0.00 0.00 4.20
5273 7419 4.941263 GGAACTTTGTAGTGGCATATGTCA 59.059 41.667 5.74 5.74 34.01 3.58
5526 7674 3.305398 ACGTGAACAAGAGTCAGGATC 57.695 47.619 0.00 0.00 0.00 3.36
5753 7901 1.474332 CCAAAACATGCAGGCCACCT 61.474 55.000 5.01 0.00 0.00 4.00
6054 8202 9.543939 CAATTTGATTGATGCCCTGAGCGATAA 62.544 40.741 0.00 0.00 43.37 1.75
6093 8241 8.935844 GTTTCTCCAACTGAACTTTTCAATTTT 58.064 29.630 0.00 0.00 39.58 1.82
6242 8390 4.626042 CAGACTAGGCACATAAGCTTAGG 58.374 47.826 16.24 16.24 45.37 2.69
6348 8497 9.035890 CATATAGAGGGTGATAACCTATGACAA 57.964 37.037 0.00 0.00 38.79 3.18
6623 8773 4.406003 CCTTATATTATGGGACGGAGGGAG 59.594 50.000 0.00 0.00 0.00 4.30
6624 8774 4.359105 CCTTATATTATGGGACGGAGGGA 58.641 47.826 0.00 0.00 0.00 4.20
6625 8775 3.454812 CCCTTATATTATGGGACGGAGGG 59.545 52.174 0.00 0.00 43.93 4.30
6626 8776 3.118371 GCCCTTATATTATGGGACGGAGG 60.118 52.174 9.14 0.00 43.93 4.30
6646 8796 3.805971 ACTAGTGTAGTGTCAAAAACGCC 59.194 43.478 0.00 0.00 39.30 5.68
6662 8812 2.218603 AGGGCGTTTTTGACACTAGTG 58.781 47.619 21.44 21.44 0.00 2.74
6663 8813 2.632987 AGGGCGTTTTTGACACTAGT 57.367 45.000 0.00 0.00 0.00 2.57
6664 8814 6.920569 ATATAAGGGCGTTTTTGACACTAG 57.079 37.500 0.00 0.00 0.00 2.57
6665 8815 8.832521 CATAATATAAGGGCGTTTTTGACACTA 58.167 33.333 0.00 0.00 0.00 2.74
6666 8816 7.201785 CCATAATATAAGGGCGTTTTTGACACT 60.202 37.037 0.00 0.00 0.00 3.55
6680 8830 4.111577 TCCCTCTGCCCCATAATATAAGG 58.888 47.826 0.00 0.00 0.00 2.69
6689 8839 1.384643 GGTACTCCCTCTGCCCCAT 60.385 63.158 0.00 0.00 0.00 4.00
6694 8844 4.965200 AATTCATAGGTACTCCCTCTGC 57.035 45.455 0.00 0.00 44.81 4.26
6695 8845 5.839063 TGGTAATTCATAGGTACTCCCTCTG 59.161 44.000 0.00 0.00 44.81 3.35
6696 8846 6.039415 TGGTAATTCATAGGTACTCCCTCT 57.961 41.667 0.00 0.00 44.81 3.69
6699 8849 8.258708 GTCATATGGTAATTCATAGGTACTCCC 58.741 40.741 2.13 0.00 41.75 4.30
6721 8871 7.738847 AGGAAATTTTGATTTTGTGAGGTCAT 58.261 30.769 0.00 0.00 0.00 3.06
7044 9194 8.535335 TCTAGATCACCATCCTTCTTAATATGC 58.465 37.037 0.00 0.00 0.00 3.14
7168 9318 7.461749 ACCTGTATCCACCTTATATTGAATGG 58.538 38.462 0.00 0.00 0.00 3.16
7398 9554 5.132502 ACTGTTCTTGTGATGGTGAAATGA 58.867 37.500 0.00 0.00 0.00 2.57
7503 9659 4.022068 GGGATGAAAAACTGACAATCTGCA 60.022 41.667 0.00 0.00 0.00 4.41
7617 9773 6.983307 AGTGCACAAGTAAATCTCTGCTATAG 59.017 38.462 21.04 0.00 33.47 1.31
7778 9934 7.170393 TCTACATCCAGGATATATGTTTCCG 57.830 40.000 0.00 0.00 37.10 4.30
7854 10010 8.523464 CAAAGCGAATTCCAGAAATAATAAACG 58.477 33.333 0.00 0.00 0.00 3.60
7879 10035 1.423541 ACCAATGGCACCAGAGTAACA 59.576 47.619 0.00 0.00 0.00 2.41
7898 10054 9.144747 CATTGCAGATATGTATGTACTAGGAAC 57.855 37.037 0.00 0.00 0.00 3.62
7953 10109 0.986527 TCTCCAGGCAATGAGAAGCA 59.013 50.000 0.00 0.00 34.79 3.91
7981 10137 8.076714 TGTCGATCATTTTATAGCTGAATGAC 57.923 34.615 14.64 7.77 41.14 3.06
7998 10186 1.521457 GGCGCCATTCTGTCGATCA 60.521 57.895 24.80 0.00 0.00 2.92
8002 10190 1.851021 TTTGTGGCGCCATTCTGTCG 61.851 55.000 35.23 0.00 0.00 4.35
8007 10227 1.444895 CTGCTTTGTGGCGCCATTC 60.445 57.895 35.23 21.83 34.52 2.67
8056 10276 0.983378 AAGGCGTAGGAATCAGGGCT 60.983 55.000 0.00 0.00 38.19 5.19
8059 10279 5.890424 TTTTTAAAGGCGTAGGAATCAGG 57.110 39.130 0.00 0.00 0.00 3.86
8095 10318 7.336427 ACAGATTTGCAAACTTTGGAATTTTCA 59.664 29.630 15.41 0.00 40.72 2.69
8150 10373 5.200734 GCGAGATGCTACACATGATTATG 57.799 43.478 0.00 0.00 39.84 1.90
8195 10418 6.422400 GCCTTTATATAGCTGAGTGTTGAGAC 59.578 42.308 0.00 0.00 0.00 3.36
8230 10454 1.221414 GGAGCTTACGCCATTAGCAG 58.779 55.000 0.00 0.00 44.04 4.24
8275 10508 4.063689 CTGCGCCATGATTATCTCTCTTT 58.936 43.478 4.18 0.00 0.00 2.52
8276 10509 3.661944 CTGCGCCATGATTATCTCTCTT 58.338 45.455 4.18 0.00 0.00 2.85
8309 10562 1.068588 TCCATTACGGCCTTCAGATCG 59.931 52.381 0.00 0.00 33.14 3.69
8375 10628 2.930019 TCCAGCACCTCCCTGTGG 60.930 66.667 0.00 0.00 36.73 4.17
8386 10639 1.296392 CGGAAGATGTGGTCCAGCA 59.704 57.895 0.00 0.00 33.10 4.41
8417 10670 4.118410 CCGAGATGATCTTCTCCTTGTTG 58.882 47.826 25.14 14.13 39.19 3.33


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

AutoCloner maintained by Alex Coulton.