Multiple sequence alignment - TraesCS4A01G233200

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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 TraesCS4A01G233200 chr4A 100.000 3873 0 0 1 3873 542260581 542264453 0.000000e+00 7153.0
1 TraesCS4A01G233200 chr4D 96.520 1983 48 6 913 2892 54810906 54808942 0.000000e+00 3260.0
2 TraesCS4A01G233200 chr4D 89.331 956 66 17 1 932 54811858 54810915 0.000000e+00 1168.0
3 TraesCS4A01G233200 chr4D 85.191 601 57 9 3299 3873 54808649 54808055 4.310000e-164 588.0
4 TraesCS4A01G233200 chr4D 88.754 329 24 8 2961 3287 54808943 54808626 1.300000e-104 390.0
5 TraesCS4A01G233200 chr4D 83.221 149 24 1 3424 3572 2831052 2830905 6.750000e-28 135.0
6 TraesCS4A01G233200 chr4B 92.130 2211 104 24 1 2182 81359161 81361330 0.000000e+00 3055.0
7 TraesCS4A01G233200 chr4B 97.050 1017 20 3 2215 3231 81361329 81362335 0.000000e+00 1703.0
8 TraesCS4A01G233200 chr4B 81.575 597 37 26 3306 3873 81363337 81363889 3.580000e-115 425.0
9 TraesCS4A01G233200 chr2B 90.000 150 12 1 3638 3787 206749320 206749174 1.420000e-44 191.0
10 TraesCS4A01G233200 chr2B 100.000 29 0 0 3324 3352 369221819 369221847 2.000000e-03 54.7
11 TraesCS4A01G233200 chr1D 85.714 161 22 1 3412 3572 465990874 465991033 6.650000e-38 169.0
12 TraesCS4A01G233200 chr1D 82.500 160 25 3 3413 3572 303075568 303075724 1.880000e-28 137.0
13 TraesCS4A01G233200 chr1D 88.889 54 0 4 293 340 175819839 175819892 1.160000e-05 62.1
14 TraesCS4A01G233200 chr7B 83.333 162 25 2 3411 3572 698649538 698649697 8.670000e-32 148.0
15 TraesCS4A01G233200 chr7B 82.822 163 25 3 3412 3572 498088976 498089137 4.030000e-30 143.0
16 TraesCS4A01G233200 chr7B 88.889 54 0 5 293 340 152467610 152467663 1.160000e-05 62.1
17 TraesCS4A01G233200 chr7D 83.133 166 23 4 3412 3574 474009747 474009910 3.120000e-31 147.0
18 TraesCS4A01G233200 chr7D 88.889 54 0 5 293 340 183723542 183723595 1.160000e-05 62.1
19 TraesCS4A01G233200 chr5B 84.615 143 21 1 3427 3569 377695596 377695737 1.450000e-29 141.0
20 TraesCS4A01G233200 chr5B 81.188 101 13 3 3259 3353 232292397 232292297 4.150000e-10 76.8
21 TraesCS4A01G233200 chr5D 84.783 138 19 2 3424 3560 73499641 73499777 1.880000e-28 137.0
22 TraesCS4A01G233200 chr6A 81.481 162 28 2 3412 3572 578513159 578513319 8.730000e-27 132.0
23 TraesCS4A01G233200 chr2A 83.929 112 12 2 3248 3353 566852253 566852142 6.850000e-18 102.0
24 TraesCS4A01G233200 chr3B 83.019 106 12 1 3254 3353 29779463 29779358 1.480000e-14 91.6
25 TraesCS4A01G233200 chr3B 100.000 29 0 0 3324 3352 155888539 155888567 2.000000e-03 54.7
26 TraesCS4A01G233200 chr3D 81.579 114 9 5 3248 3353 515186822 515186931 2.480000e-12 84.2
27 TraesCS4A01G233200 chr3D 88.889 54 0 4 293 340 338923994 338924047 1.160000e-05 62.1
28 TraesCS4A01G233200 chr1B 87.097 62 7 1 3255 3316 613421477 613421417 6.940000e-08 69.4
29 TraesCS4A01G233200 chr1A 77.600 125 15 9 3239 3354 574489558 574489438 3.230000e-06 63.9
30 TraesCS4A01G233200 chr1A 88.889 54 0 4 293 340 218526844 218526897 1.160000e-05 62.1
31 TraesCS4A01G233200 chr7A 88.889 54 0 5 293 340 187460832 187460779 1.160000e-05 62.1
32 TraesCS4A01G233200 chr3A 88.889 54 0 4 293 340 465834114 465834061 1.160000e-05 62.1
33 TraesCS4A01G233200 chr5A 100.000 30 0 0 3324 3353 488629205 488629234 5.410000e-04 56.5
34 TraesCS4A01G233200 chr5A 100.000 30 0 0 3324 3353 674828901 674828930 5.410000e-04 56.5
35 TraesCS4A01G233200 chr5A 100.000 30 0 0 3324 3353 674870302 674870331 5.410000e-04 56.5


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 TraesCS4A01G233200 chr4A 542260581 542264453 3872 False 7153.000000 7153 100.000000 1 3873 1 chr4A.!!$F1 3872
1 TraesCS4A01G233200 chr4D 54808055 54811858 3803 True 1351.500000 3260 89.949000 1 3873 4 chr4D.!!$R2 3872
2 TraesCS4A01G233200 chr4B 81359161 81363889 4728 False 1727.666667 3055 90.251667 1 3873 3 chr4B.!!$F1 3872

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
322 338 0.321671 GTGCTAGAAGCTCCCACACA 59.678 55.000 0.0 0.0 42.97 3.72 F
661 688 1.276989 AGCAGGAATTGGTTTGCATGG 59.723 47.619 0.0 0.0 38.97 3.66 F
1390 1448 0.036732 TCACACCATGTCTCCTTGGC 59.963 55.000 0.0 0.0 39.04 4.52 F
2201 2260 0.107214 TAGCAATACAGCACCCTGGC 60.107 55.000 0.0 0.0 43.53 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1238 1296 0.179062 CGAGGGAGAAGCCTTCCATG 60.179 60.000 0.0 0.0 40.81 3.66 R
1462 1520 1.974265 TGGAATGAAGTGGCAAACGA 58.026 45.000 0.0 0.0 0.00 3.85 R
2828 2888 1.156736 CTTTCAGAAACGACCGCCAT 58.843 50.000 0.0 0.0 0.00 4.40 R
3757 4833 2.300152 TCTGTTTGTGTTTGTTGCCCAA 59.700 40.909 0.0 0.0 0.00 4.12 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
81 82 1.694693 GCCTCAGGGGGTGGTTAGATA 60.695 57.143 0.00 0.00 35.12 1.98
113 117 3.805207 AGTAATCTGGTCGGTTTATGGC 58.195 45.455 0.00 0.00 0.00 4.40
121 125 2.156098 GTCGGTTTATGGCCAACAGAA 58.844 47.619 10.96 0.00 31.37 3.02
122 126 2.554893 GTCGGTTTATGGCCAACAGAAA 59.445 45.455 10.96 5.40 37.90 2.52
125 129 4.282195 TCGGTTTATGGCCAACAGAAATTT 59.718 37.500 10.96 0.00 41.75 1.82
131 135 3.571590 TGGCCAACAGAAATTTGGTAGT 58.428 40.909 0.61 0.00 44.77 2.73
142 146 7.084486 CAGAAATTTGGTAGTTTTGGTCTAGC 58.916 38.462 0.00 0.00 36.71 3.42
151 155 1.899437 TTTGGTCTAGCTGCTCCCCG 61.899 60.000 4.91 0.00 0.00 5.73
152 156 4.228567 GGTCTAGCTGCTCCCCGC 62.229 72.222 4.91 0.00 39.77 6.13
153 157 4.228567 GTCTAGCTGCTCCCCGCC 62.229 72.222 4.91 0.00 38.05 6.13
154 158 4.777854 TCTAGCTGCTCCCCGCCA 62.778 66.667 4.91 0.00 38.05 5.69
155 159 3.785859 CTAGCTGCTCCCCGCCAA 61.786 66.667 4.91 0.00 38.05 4.52
165 180 1.075482 CCCCGCCAATATCTGCCAT 59.925 57.895 0.00 0.00 0.00 4.40
171 186 3.079578 CGCCAATATCTGCCATGAGAAT 58.920 45.455 0.00 0.00 0.00 2.40
177 192 6.150641 CCAATATCTGCCATGAGAATCGATTT 59.849 38.462 12.81 2.33 38.61 2.17
258 274 9.941664 CAAGACTAATCATTACTAATGCTTTGG 57.058 33.333 4.13 5.45 38.77 3.28
284 300 2.984562 TGCCGCTAATCAATCAGTGAA 58.015 42.857 0.00 0.00 40.50 3.18
322 338 0.321671 GTGCTAGAAGCTCCCACACA 59.678 55.000 0.00 0.00 42.97 3.72
352 373 4.444876 GGGAAGGATTAGTGAGCTGCATTA 60.445 45.833 1.02 0.00 0.00 1.90
354 375 5.363939 GAAGGATTAGTGAGCTGCATTAGT 58.636 41.667 1.02 0.00 0.00 2.24
368 389 6.425114 AGCTGCATTAGTAGATGGTTAAATCG 59.575 38.462 1.02 0.00 0.00 3.34
379 400 6.299141 AGATGGTTAAATCGGATAACATGCT 58.701 36.000 6.10 0.00 35.44 3.79
389 410 5.269459 CGGATAACATGCTTAAAGATCCG 57.731 43.478 6.06 6.06 45.72 4.18
393 414 7.875971 GGATAACATGCTTAAAGATCCGATTT 58.124 34.615 0.00 0.00 0.00 2.17
394 415 7.805071 GGATAACATGCTTAAAGATCCGATTTG 59.195 37.037 0.00 0.00 0.00 2.32
395 416 4.925068 ACATGCTTAAAGATCCGATTTGC 58.075 39.130 0.00 0.00 0.00 3.68
403 424 8.224437 GCTTAAAGATCCGATTTGCTATTACTC 58.776 37.037 0.00 0.00 0.00 2.59
434 455 8.903059 TTTTGGGTGGTGGATTAATAAGTAAT 57.097 30.769 0.00 0.00 34.97 1.89
437 458 7.751646 TGGGTGGTGGATTAATAAGTAATAGG 58.248 38.462 0.00 0.00 32.26 2.57
475 496 3.165875 AGACATGTGTAGGTGCTGTAGT 58.834 45.455 1.15 0.00 0.00 2.73
518 539 5.242393 CCATTGATTTCTTGGTGAGTGTCTT 59.758 40.000 0.00 0.00 0.00 3.01
519 540 5.756195 TTGATTTCTTGGTGAGTGTCTTG 57.244 39.130 0.00 0.00 0.00 3.02
618 643 9.183368 TGTGCAACATAGATATTTTGGTGATAA 57.817 29.630 0.00 0.00 45.67 1.75
659 686 3.834231 AGTAAGCAGGAATTGGTTTGCAT 59.166 39.130 0.00 0.00 44.75 3.96
661 688 1.276989 AGCAGGAATTGGTTTGCATGG 59.723 47.619 0.00 0.00 38.97 3.66
678 705 5.689835 TGCATGGCTATAGGAATGTTGTTA 58.310 37.500 1.04 0.00 0.00 2.41
679 706 5.530915 TGCATGGCTATAGGAATGTTGTTAC 59.469 40.000 1.04 0.00 0.00 2.50
777 804 3.052329 TCTGCTCCAGAGAGATAGAGGA 58.948 50.000 0.00 0.00 43.39 3.71
807 834 6.037172 GCATGACGAACCACTGTTTCTATATT 59.963 38.462 0.00 0.00 33.97 1.28
808 835 7.621991 CATGACGAACCACTGTTTCTATATTC 58.378 38.462 0.00 0.00 33.97 1.75
815 844 5.071250 ACCACTGTTTCTATATTCGCCCATA 59.929 40.000 0.00 0.00 0.00 2.74
820 849 5.071250 TGTTTCTATATTCGCCCATAGTGGT 59.929 40.000 0.00 0.00 35.17 4.16
864 893 4.763594 TTTTGTTTGATTCGGCGTTTTC 57.236 36.364 6.85 3.11 0.00 2.29
871 900 2.543012 TGATTCGGCGTTTTCGTGTTAA 59.457 40.909 6.85 0.00 46.03 2.01
882 912 7.745594 GGCGTTTTCGTGTTAATTTGAATAGTA 59.254 33.333 0.00 0.00 46.03 1.82
884 914 9.257865 CGTTTTCGTGTTAATTTGAATAGTAGG 57.742 33.333 0.00 0.00 38.65 3.18
982 1040 2.554462 TCCTCGACAACAGACTCTTCAG 59.446 50.000 0.00 0.00 0.00 3.02
1238 1296 7.240674 TCACTGTTTTATTTCGATGTATGCAC 58.759 34.615 0.00 0.00 0.00 4.57
1279 1337 9.332502 CCTCGCAGTAGTATATATCTAGAATGT 57.667 37.037 0.00 0.00 0.00 2.71
1298 1356 6.954073 AGAATGTTTTCTCTTTGCTGACAAGC 60.954 38.462 0.00 0.00 43.19 4.01
1384 1442 2.277969 CTCAGCATCACACCATGTCTC 58.722 52.381 0.00 0.00 0.00 3.36
1390 1448 0.036732 TCACACCATGTCTCCTTGGC 59.963 55.000 0.00 0.00 39.04 4.52
1409 1467 1.066143 GCTGCCCTCAGTAAGTAGCAA 60.066 52.381 0.00 0.00 42.29 3.91
1426 1484 3.308401 AGCAAGACCTTGGGTTCATTTT 58.692 40.909 11.26 0.00 40.74 1.82
1448 1506 4.786507 TCATCACTTGATTTTTGTCTGCG 58.213 39.130 0.00 0.00 31.21 5.18
1455 1513 6.249893 CACTTGATTTTTGTCTGCGACATATG 59.750 38.462 11.23 0.00 42.40 1.78
1460 1518 8.337532 TGATTTTTGTCTGCGACATATGATTAG 58.662 33.333 10.38 2.54 42.40 1.73
1461 1519 7.609760 TTTTTGTCTGCGACATATGATTAGT 57.390 32.000 10.38 0.00 42.40 2.24
1462 1520 7.609760 TTTTGTCTGCGACATATGATTAGTT 57.390 32.000 10.38 0.00 42.40 2.24
1713 1772 8.391075 TGGTATATCTTACTTATTGGCTTTGC 57.609 34.615 0.00 0.00 0.00 3.68
2098 2157 7.925483 TGTTTTATGCACTGCTTACATTTTTCT 59.075 29.630 1.98 0.00 0.00 2.52
2196 2255 4.155826 TCAACACATTAGCAATACAGCACC 59.844 41.667 0.00 0.00 36.85 5.01
2197 2256 3.016736 ACACATTAGCAATACAGCACCC 58.983 45.455 0.00 0.00 36.85 4.61
2198 2257 3.282021 CACATTAGCAATACAGCACCCT 58.718 45.455 0.00 0.00 36.85 4.34
2199 2258 3.065786 CACATTAGCAATACAGCACCCTG 59.934 47.826 0.00 0.00 44.80 4.45
2200 2259 2.418368 TTAGCAATACAGCACCCTGG 57.582 50.000 0.00 0.00 43.53 4.45
2201 2260 0.107214 TAGCAATACAGCACCCTGGC 60.107 55.000 0.00 0.00 43.53 4.85
2203 2262 0.967380 GCAATACAGCACCCTGGCTT 60.967 55.000 0.00 0.00 42.71 4.35
2204 2263 1.098050 CAATACAGCACCCTGGCTTC 58.902 55.000 0.00 0.00 42.71 3.86
2205 2264 0.995024 AATACAGCACCCTGGCTTCT 59.005 50.000 0.00 0.00 42.71 2.85
2206 2265 0.995024 ATACAGCACCCTGGCTTCTT 59.005 50.000 0.00 0.00 42.71 2.52
2207 2266 0.324943 TACAGCACCCTGGCTTCTTC 59.675 55.000 0.00 0.00 42.71 2.87
2208 2267 1.676967 CAGCACCCTGGCTTCTTCC 60.677 63.158 0.00 0.00 42.71 3.46
2209 2268 2.156098 AGCACCCTGGCTTCTTCCA 61.156 57.895 0.00 0.00 42.71 3.53
2210 2269 1.000396 GCACCCTGGCTTCTTCCAT 60.000 57.895 0.00 0.00 35.22 3.41
2211 2270 0.613012 GCACCCTGGCTTCTTCCATT 60.613 55.000 0.00 0.00 35.22 3.16
2255 2314 9.643735 TTCTTCCCATTTTACTTACCTTTGTTA 57.356 29.630 0.00 0.00 0.00 2.41
2312 2371 8.777865 TGTCGATGATTCTTTGTTTCTATTCT 57.222 30.769 0.00 0.00 0.00 2.40
2350 2409 5.276536 GCAATTTCACTTCAGTGTTTGCTTC 60.277 40.000 22.99 8.00 44.16 3.86
2516 2575 5.683770 GCCACTGGTGTTTTCTTATTTGGTT 60.684 40.000 0.00 0.00 0.00 3.67
2531 2590 8.477256 TCTTATTTGGTTGGAATCATGGATTTC 58.523 33.333 0.00 0.00 31.89 2.17
2535 2594 3.638627 GGTTGGAATCATGGATTTCCCTC 59.361 47.826 15.80 10.64 31.89 4.30
2655 2714 9.388506 CTCTTTTTACATGACATCCAGAACTAT 57.611 33.333 0.00 0.00 0.00 2.12
2828 2888 1.002576 CTTCAAGCACACACGATGCAA 60.003 47.619 0.00 0.00 45.92 4.08
2956 3016 2.611473 GGTCAGTCATCTGTGGTCTGTG 60.611 54.545 0.00 0.00 41.91 3.66
3206 3269 2.214216 GGGGGTGGTTTTGCCCTTC 61.214 63.158 0.00 0.00 44.25 3.46
3293 4262 9.247861 ACAATACCTTTTAGAGATTTCAATGCT 57.752 29.630 0.00 0.00 0.00 3.79
3294 4263 9.512435 CAATACCTTTTAGAGATTTCAATGCTG 57.488 33.333 0.00 0.00 0.00 4.41
3295 4264 9.466497 AATACCTTTTAGAGATTTCAATGCTGA 57.534 29.630 0.00 0.00 0.00 4.26
3296 4265 7.150783 ACCTTTTAGAGATTTCAATGCTGAC 57.849 36.000 0.00 0.00 0.00 3.51
3297 4266 6.944862 ACCTTTTAGAGATTTCAATGCTGACT 59.055 34.615 0.00 0.00 0.00 3.41
3298 4267 8.103305 ACCTTTTAGAGATTTCAATGCTGACTA 58.897 33.333 0.00 0.00 0.00 2.59
3299 4268 9.118300 CCTTTTAGAGATTTCAATGCTGACTAT 57.882 33.333 0.00 0.00 0.00 2.12
3305 4274 9.926158 AGAGATTTCAATGCTGACTATATACAG 57.074 33.333 0.00 0.00 37.22 2.74
3306 4275 9.920133 GAGATTTCAATGCTGACTATATACAGA 57.080 33.333 4.88 0.00 36.38 3.41
3307 4276 9.703892 AGATTTCAATGCTGACTATATACAGAC 57.296 33.333 4.88 0.00 36.38 3.51
3346 4315 7.509141 TTGTAGATTCACTCATTTTGCTTCA 57.491 32.000 0.00 0.00 0.00 3.02
3349 4318 8.668353 TGTAGATTCACTCATTTTGCTTCATAC 58.332 33.333 0.00 0.00 0.00 2.39
3353 4384 7.609760 TTCACTCATTTTGCTTCATACGTAT 57.390 32.000 1.14 1.14 0.00 3.06
3358 4389 7.012044 ACTCATTTTGCTTCATACGTATTACCC 59.988 37.037 5.03 0.00 0.00 3.69
3366 4397 4.549668 TCATACGTATTACCCCTGTCCTT 58.450 43.478 5.03 0.00 0.00 3.36
3376 4407 2.449345 ACCCCTGTCCTTGTTTATTGGT 59.551 45.455 0.00 0.00 0.00 3.67
3382 4414 4.810345 TGTCCTTGTTTATTGGTCCCTTT 58.190 39.130 0.00 0.00 0.00 3.11
3582 4658 0.103208 GGAGGTAGTGCTCCATGTCG 59.897 60.000 0.00 0.00 39.45 4.35
3584 4660 0.818296 AGGTAGTGCTCCATGTCGAC 59.182 55.000 9.11 9.11 0.00 4.20
3684 4760 1.686355 CCGATCAGGAGAGCTGTAGT 58.314 55.000 0.00 0.00 45.00 2.73
3715 4791 2.672961 TCGTAGACAATGAGCCAAGG 57.327 50.000 0.00 0.00 0.00 3.61
3757 4833 1.271597 GCACAGTTCAGGGGAGACAAT 60.272 52.381 0.00 0.00 0.00 2.71
3826 4902 1.765904 TCATATACCAGCGAGGGCAAA 59.234 47.619 3.26 0.00 43.89 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.190578 CCCCCTGAGGCGATTGTC 59.809 66.667 0.00 0.00 0.00 3.18
63 64 2.039084 GCATATCTAACCACCCCCTGAG 59.961 54.545 0.00 0.00 0.00 3.35
81 82 3.881688 GACCAGATTACTCAATGCAGCAT 59.118 43.478 0.52 0.52 0.00 3.79
121 125 5.048013 GCAGCTAGACCAAAACTACCAAATT 60.048 40.000 0.00 0.00 0.00 1.82
122 126 4.459337 GCAGCTAGACCAAAACTACCAAAT 59.541 41.667 0.00 0.00 0.00 2.32
125 129 2.637872 AGCAGCTAGACCAAAACTACCA 59.362 45.455 0.00 0.00 0.00 3.25
131 135 0.328258 GGGGAGCAGCTAGACCAAAA 59.672 55.000 11.31 0.00 0.00 2.44
152 156 4.572909 TCGATTCTCATGGCAGATATTGG 58.427 43.478 0.00 0.00 0.00 3.16
153 157 6.738832 AATCGATTCTCATGGCAGATATTG 57.261 37.500 4.39 0.00 0.00 1.90
154 158 7.446319 TGAAAATCGATTCTCATGGCAGATATT 59.554 33.333 10.10 0.00 0.00 1.28
155 159 6.938596 TGAAAATCGATTCTCATGGCAGATAT 59.061 34.615 10.10 0.00 0.00 1.63
165 180 7.697710 GCAAATACATGTGAAAATCGATTCTCA 59.302 33.333 10.10 10.10 37.26 3.27
171 186 6.493449 TCTGCAAATACATGTGAAAATCGA 57.507 33.333 9.11 0.00 0.00 3.59
177 192 7.048629 TCCTTTTTCTGCAAATACATGTGAA 57.951 32.000 9.11 0.00 0.00 3.18
258 274 1.604278 GATTGATTAGCGGCAAGGGAC 59.396 52.381 1.45 0.00 0.00 4.46
284 300 0.037303 CTGGGTCTGTCCAATGCAGT 59.963 55.000 0.00 0.00 36.21 4.40
322 338 3.265489 TCACTAATCCTTCCCCAACCTT 58.735 45.455 0.00 0.00 0.00 3.50
352 373 7.387948 GCATGTTATCCGATTTAACCATCTACT 59.612 37.037 0.00 0.00 0.00 2.57
354 375 7.450074 AGCATGTTATCCGATTTAACCATCTA 58.550 34.615 0.00 0.00 0.00 1.98
368 389 7.440523 AATCGGATCTTTAAGCATGTTATCC 57.559 36.000 0.00 0.00 0.00 2.59
379 400 9.832445 AAGAGTAATAGCAAATCGGATCTTTAA 57.168 29.630 0.00 0.00 0.00 1.52
410 431 9.635404 CTATTACTTATTAATCCACCACCCAAA 57.365 33.333 0.00 0.00 32.31 3.28
411 432 8.221944 CCTATTACTTATTAATCCACCACCCAA 58.778 37.037 0.00 0.00 32.31 4.12
412 433 7.693289 GCCTATTACTTATTAATCCACCACCCA 60.693 40.741 0.00 0.00 32.31 4.51
413 434 6.657966 GCCTATTACTTATTAATCCACCACCC 59.342 42.308 0.00 0.00 32.31 4.61
414 435 7.228590 TGCCTATTACTTATTAATCCACCACC 58.771 38.462 0.00 0.00 32.31 4.61
475 496 3.784178 TGGCCCACAATTTCCTTTATGA 58.216 40.909 0.00 0.00 0.00 2.15
533 554 5.336213 CGCTTCAGTTTTACTAGTGGTAGGA 60.336 44.000 5.39 0.00 0.00 2.94
538 559 4.304110 TCACGCTTCAGTTTTACTAGTGG 58.696 43.478 5.39 0.00 0.00 4.00
618 643 1.478510 CTCTGTTATCACCGCCACTCT 59.521 52.381 0.00 0.00 0.00 3.24
659 686 7.668052 ACAAAAGTAACAACATTCCTATAGCCA 59.332 33.333 0.00 0.00 0.00 4.75
661 688 9.908152 AAACAAAAGTAACAACATTCCTATAGC 57.092 29.630 0.00 0.00 0.00 2.97
678 705 4.020543 TGCCCACTCAGTAAAACAAAAGT 58.979 39.130 0.00 0.00 0.00 2.66
679 706 4.647424 TGCCCACTCAGTAAAACAAAAG 57.353 40.909 0.00 0.00 0.00 2.27
735 762 4.581824 AGAACGATGCATTGCCAATTCTAT 59.418 37.500 14.18 0.00 0.00 1.98
736 763 3.947196 AGAACGATGCATTGCCAATTCTA 59.053 39.130 14.18 0.00 0.00 2.10
740 767 1.470285 GCAGAACGATGCATTGCCAAT 60.470 47.619 14.18 0.00 45.77 3.16
777 804 0.321919 AGTGGTTCGTCATGCATGCT 60.322 50.000 22.25 7.56 0.00 3.79
807 834 5.512404 CCTCAAATAATACCACTATGGGCGA 60.512 44.000 0.00 0.00 43.37 5.54
808 835 4.695455 CCTCAAATAATACCACTATGGGCG 59.305 45.833 0.00 0.00 43.37 6.13
849 878 0.938713 ACACGAAAACGCCGAATCAA 59.061 45.000 0.00 0.00 0.00 2.57
856 885 5.815964 ATTCAAATTAACACGAAAACGCC 57.184 34.783 0.00 0.00 0.00 5.68
859 888 9.550811 CCCTACTATTCAAATTAACACGAAAAC 57.449 33.333 0.00 0.00 0.00 2.43
864 893 7.396419 CGAACCCTACTATTCAAATTAACACG 58.604 38.462 0.00 0.00 0.00 4.49
871 900 5.952347 AGTCCGAACCCTACTATTCAAAT 57.048 39.130 0.00 0.00 0.00 2.32
882 912 6.155247 AGGAGATATATAAGTCCGAACCCT 57.845 41.667 7.70 0.00 33.99 4.34
884 914 8.968969 ACATAAGGAGATATATAAGTCCGAACC 58.031 37.037 7.70 0.00 33.99 3.62
982 1040 2.410730 GCATTGCATGAACTGAACAAGC 59.589 45.455 3.15 0.00 33.48 4.01
1224 1282 3.627123 CCTTCCATGTGCATACATCGAAA 59.373 43.478 0.00 0.00 45.53 3.46
1238 1296 0.179062 CGAGGGAGAAGCCTTCCATG 60.179 60.000 0.00 0.00 40.81 3.66
1384 1442 0.393537 CTTACTGAGGGCAGCCAAGG 60.394 60.000 15.19 2.50 46.26 3.61
1409 1467 4.524328 GTGATGAAAATGAACCCAAGGTCT 59.476 41.667 0.00 0.00 33.12 3.85
1426 1484 4.514816 TCGCAGACAAAAATCAAGTGATGA 59.485 37.500 0.00 0.00 43.67 2.92
1448 1506 6.037172 AGTGGCAAACGAACTAATCATATGTC 59.963 38.462 1.90 0.00 0.00 3.06
1455 1513 4.742438 TGAAGTGGCAAACGAACTAATC 57.258 40.909 0.00 0.00 0.00 1.75
1460 1518 2.034053 TGGAATGAAGTGGCAAACGAAC 59.966 45.455 0.00 0.00 0.00 3.95
1461 1519 2.302260 TGGAATGAAGTGGCAAACGAA 58.698 42.857 0.00 0.00 0.00 3.85
1462 1520 1.974265 TGGAATGAAGTGGCAAACGA 58.026 45.000 0.00 0.00 0.00 3.85
1749 1808 4.709397 ACCAACTTGATTGTTTTGTCCTCA 59.291 37.500 0.00 0.00 36.47 3.86
1782 1841 2.367241 TCCAAAGGTGTCATCAACTCGA 59.633 45.455 0.00 0.00 41.20 4.04
2131 2190 4.012374 GAGGTCATGTGATCCATTGTGTT 58.988 43.478 0.00 0.00 0.00 3.32
2196 2255 2.692041 GGATCAAATGGAAGAAGCCAGG 59.308 50.000 0.00 0.00 42.15 4.45
2197 2256 2.357009 CGGATCAAATGGAAGAAGCCAG 59.643 50.000 0.00 0.00 42.15 4.85
2198 2257 2.290896 ACGGATCAAATGGAAGAAGCCA 60.291 45.455 0.00 0.00 43.23 4.75
2199 2258 2.369394 ACGGATCAAATGGAAGAAGCC 58.631 47.619 0.00 0.00 0.00 4.35
2200 2259 3.938963 TGTACGGATCAAATGGAAGAAGC 59.061 43.478 0.00 0.00 0.00 3.86
2201 2260 6.683974 ATTGTACGGATCAAATGGAAGAAG 57.316 37.500 0.00 0.00 0.00 2.85
2202 2261 6.624861 GCAATTGTACGGATCAAATGGAAGAA 60.625 38.462 7.40 0.00 0.00 2.52
2203 2262 5.163663 GCAATTGTACGGATCAAATGGAAGA 60.164 40.000 7.40 0.00 0.00 2.87
2204 2263 5.036737 GCAATTGTACGGATCAAATGGAAG 58.963 41.667 7.40 0.00 0.00 3.46
2205 2264 4.704540 AGCAATTGTACGGATCAAATGGAA 59.295 37.500 7.40 0.00 0.00 3.53
2206 2265 4.269183 AGCAATTGTACGGATCAAATGGA 58.731 39.130 7.40 0.00 0.00 3.41
2207 2266 4.637483 AGCAATTGTACGGATCAAATGG 57.363 40.909 7.40 0.00 0.00 3.16
2208 2267 6.324819 AGAAAGCAATTGTACGGATCAAATG 58.675 36.000 7.40 0.00 0.00 2.32
2209 2268 6.515272 AGAAAGCAATTGTACGGATCAAAT 57.485 33.333 7.40 0.00 0.00 2.32
2210 2269 5.957842 AGAAAGCAATTGTACGGATCAAA 57.042 34.783 7.40 0.00 0.00 2.69
2211 2270 5.106317 GGAAGAAAGCAATTGTACGGATCAA 60.106 40.000 7.40 0.00 0.00 2.57
2306 2365 2.941720 GCACTGCCCTCTTGAAGAATAG 59.058 50.000 0.00 0.00 0.00 1.73
2312 2371 1.999648 AATTGCACTGCCCTCTTGAA 58.000 45.000 0.00 0.00 0.00 2.69
2516 2575 4.819702 ATGAGGGAAATCCATGATTCCA 57.180 40.909 19.81 6.56 38.24 3.53
2531 2590 3.710209 AGTGAGACTTTGGAATGAGGG 57.290 47.619 0.00 0.00 0.00 4.30
2700 2760 4.318071 CACGTGCAATCTAAACACAAATCG 59.682 41.667 0.82 0.00 33.89 3.34
2782 2842 4.505566 GCATAAGAGGATCCAACATAGGCA 60.506 45.833 15.82 0.00 33.66 4.75
2828 2888 1.156736 CTTTCAGAAACGACCGCCAT 58.843 50.000 0.00 0.00 0.00 4.40
2956 3016 9.696917 AATCAACAACTTTTGATCTAATGTTCC 57.303 29.630 15.01 0.00 43.95 3.62
2983 3043 9.608617 GGTAAAATCTTAAGAACTTTTTCCTCG 57.391 33.333 21.25 0.00 28.98 4.63
3108 3171 4.292306 ACATACCCAAAGGATGAAAGGAGT 59.708 41.667 0.00 0.00 36.73 3.85
3109 3172 4.860022 ACATACCCAAAGGATGAAAGGAG 58.140 43.478 0.00 0.00 36.73 3.69
3110 3173 4.946160 ACATACCCAAAGGATGAAAGGA 57.054 40.909 0.00 0.00 36.73 3.36
3111 3174 6.435904 TGTAAACATACCCAAAGGATGAAAGG 59.564 38.462 0.00 0.00 36.73 3.11
3112 3175 7.312899 GTGTAAACATACCCAAAGGATGAAAG 58.687 38.462 0.00 0.00 36.73 2.62
3113 3176 6.072397 CGTGTAAACATACCCAAAGGATGAAA 60.072 38.462 0.00 0.00 36.73 2.69
3114 3177 5.413213 CGTGTAAACATACCCAAAGGATGAA 59.587 40.000 0.00 0.00 36.73 2.57
3115 3178 4.938832 CGTGTAAACATACCCAAAGGATGA 59.061 41.667 0.00 0.00 36.73 2.92
3116 3179 4.095782 CCGTGTAAACATACCCAAAGGATG 59.904 45.833 0.00 0.00 36.73 3.51
3117 3180 4.266714 CCGTGTAAACATACCCAAAGGAT 58.733 43.478 0.00 0.00 36.73 3.24
3206 3269 2.756760 CCAACCCAATGATGTTCAGGAG 59.243 50.000 0.00 0.00 0.00 3.69
3268 4237 9.512435 CAGCATTGAAATCTCTAAAAGGTATTG 57.488 33.333 0.00 0.00 0.00 1.90
3271 4240 8.103305 AGTCAGCATTGAAATCTCTAAAAGGTA 58.897 33.333 0.00 0.00 34.49 3.08
3279 4248 9.926158 CTGTATATAGTCAGCATTGAAATCTCT 57.074 33.333 0.00 0.00 34.49 3.10
3280 4249 9.920133 TCTGTATATAGTCAGCATTGAAATCTC 57.080 33.333 0.00 0.00 34.49 2.75
3281 4250 9.703892 GTCTGTATATAGTCAGCATTGAAATCT 57.296 33.333 0.00 0.00 34.49 2.40
3282 4251 8.642885 CGTCTGTATATAGTCAGCATTGAAATC 58.357 37.037 0.00 0.00 34.49 2.17
3283 4252 8.144478 ACGTCTGTATATAGTCAGCATTGAAAT 58.856 33.333 0.00 0.00 34.49 2.17
3284 4253 7.489160 ACGTCTGTATATAGTCAGCATTGAAA 58.511 34.615 0.00 0.00 34.49 2.69
3285 4254 7.039313 ACGTCTGTATATAGTCAGCATTGAA 57.961 36.000 0.00 0.00 34.49 2.69
3286 4255 6.635030 ACGTCTGTATATAGTCAGCATTGA 57.365 37.500 0.00 0.00 0.00 2.57
3346 4315 4.292643 ACAAGGACAGGGGTAATACGTAT 58.707 43.478 1.14 1.14 0.00 3.06
3349 4318 3.622166 AACAAGGACAGGGGTAATACG 57.378 47.619 0.00 0.00 0.00 3.06
3353 4384 4.106663 ACCAATAAACAAGGACAGGGGTAA 59.893 41.667 0.00 0.00 0.00 2.85
3358 4389 3.089284 GGGACCAATAAACAAGGACAGG 58.911 50.000 0.00 0.00 0.00 4.00
3366 4397 5.559148 AAATGCAAAGGGACCAATAAACA 57.441 34.783 0.00 0.00 0.00 2.83
3509 4558 5.047306 TGGGCCAGACTATAACGATTAGATG 60.047 44.000 0.00 0.00 0.00 2.90
3514 4563 4.497291 TTTGGGCCAGACTATAACGATT 57.503 40.909 6.23 0.00 0.00 3.34
3518 4567 8.793592 CCTTAATATTTTGGGCCAGACTATAAC 58.206 37.037 6.23 0.00 0.00 1.89
3546 4595 4.344104 ACCTCCATTCTGGTTTATTGGTG 58.656 43.478 0.00 0.00 39.03 4.17
3582 4658 6.031751 ACAGATTACTCTTGAGACCTTGTC 57.968 41.667 4.49 0.00 0.00 3.18
3584 4660 7.493971 CCAATACAGATTACTCTTGAGACCTTG 59.506 40.741 4.49 0.00 0.00 3.61
3684 4760 5.300792 TCATTGTCTACGACATATGGTAGCA 59.699 40.000 7.80 0.00 42.40 3.49
3715 4791 3.127548 CCTGTGTGTCATGAATTGTAGCC 59.872 47.826 0.00 0.00 0.00 3.93
3721 4797 2.555325 CTGTGCCTGTGTGTCATGAATT 59.445 45.455 0.00 0.00 0.00 2.17
3757 4833 2.300152 TCTGTTTGTGTTTGTTGCCCAA 59.700 40.909 0.00 0.00 0.00 4.12
3826 4902 6.209192 TGAATTGTTGTTCCTAATGATGCTGT 59.791 34.615 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.