Multiple sequence alignment - TraesCS7A01G344100

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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 TraesCS7A01G344100 chr7A 100.000 4379 0 0 1 4379 506133157 506128779 0.000000e+00 8087.0
1 TraesCS7A01G344100 chr7A 95.000 80 4 0 3094 3173 506129982 506129903 4.600000e-25 126.0
2 TraesCS7A01G344100 chr7A 95.000 80 4 0 3176 3255 506130064 506129985 4.600000e-25 126.0
3 TraesCS7A01G344100 chr7D 93.137 3803 160 46 4 3771 426846150 426849886 0.000000e+00 5483.0
4 TraesCS7A01G344100 chr7D 93.853 423 24 2 3958 4379 426850225 426850646 1.720000e-178 636.0
5 TraesCS7A01G344100 chr7D 92.337 261 10 5 3770 4028 426849983 426850235 3.220000e-96 363.0
6 TraesCS7A01G344100 chr7D 95.000 80 4 0 3094 3173 426849285 426849364 4.600000e-25 126.0
7 TraesCS7A01G344100 chr7B 96.135 2717 78 11 900 3609 444475006 444477702 0.000000e+00 4410.0
8 TraesCS7A01G344100 chr7B 90.691 752 46 6 4 755 444473999 444474726 0.000000e+00 979.0
9 TraesCS7A01G344100 chr7B 92.229 489 34 2 3893 4379 444478014 444478500 0.000000e+00 689.0
10 TraesCS7A01G344100 chr7B 89.057 265 5 5 3621 3862 444477752 444478015 1.530000e-79 307.0
11 TraesCS7A01G344100 chr7B 95.968 124 4 1 756 879 444474807 444474929 2.670000e-47 200.0
12 TraesCS7A01G344100 chr7B 95.000 80 4 0 3094 3173 444477268 444477347 4.600000e-25 126.0
13 TraesCS7A01G344100 chr6B 84.893 1218 152 17 1368 2574 688780999 688779803 0.000000e+00 1201.0
14 TraesCS7A01G344100 chr6A 89.372 621 66 0 1954 2574 599165860 599166480 0.000000e+00 782.0
15 TraesCS7A01G344100 chr6A 83.629 507 60 10 1379 1878 599165336 599165826 5.160000e-124 455.0
16 TraesCS7A01G344100 chr6A 83.882 304 32 11 3884 4181 46977358 46977650 1.550000e-69 274.0
17 TraesCS7A01G344100 chr6A 86.765 68 8 1 4310 4376 46977820 46977887 1.690000e-09 75.0
18 TraesCS7A01G344100 chr6D 89.966 588 56 2 1990 2574 453170711 453171298 0.000000e+00 756.0
19 TraesCS7A01G344100 chr6D 82.616 627 75 13 1377 1992 453170016 453170619 1.400000e-144 523.0
20 TraesCS7A01G344100 chr3A 80.628 191 21 9 3884 4068 737369759 737369579 2.750000e-27 134.0
21 TraesCS7A01G344100 chr4B 95.161 62 3 0 2507 2568 270806447 270806386 1.000000e-16 99.0
22 TraesCS7A01G344100 chr4A 95.238 42 1 1 3569 3609 741428932 741428891 1.020000e-06 65.8
23 TraesCS7A01G344100 chr2D 100.000 32 0 0 3573 3604 92739162 92739193 4.730000e-05 60.2


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 TraesCS7A01G344100 chr7A 506128779 506133157 4378 True 2779.666667 8087 96.666667 1 4379 3 chr7A.!!$R1 4378
1 TraesCS7A01G344100 chr7D 426846150 426850646 4496 False 1652.000000 5483 93.581750 4 4379 4 chr7D.!!$F1 4375
2 TraesCS7A01G344100 chr7B 444473999 444478500 4501 False 1118.500000 4410 93.180000 4 4379 6 chr7B.!!$F1 4375
3 TraesCS7A01G344100 chr6B 688779803 688780999 1196 True 1201.000000 1201 84.893000 1368 2574 1 chr6B.!!$R1 1206
4 TraesCS7A01G344100 chr6A 599165336 599166480 1144 False 618.500000 782 86.500500 1379 2574 2 chr6A.!!$F2 1195
5 TraesCS7A01G344100 chr6D 453170016 453171298 1282 False 639.500000 756 86.291000 1377 2574 2 chr6D.!!$F1 1197

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
346 347 0.106819 GGGCTGATGAGCTTCCATGT 60.107 55.0 3.6 0.0 45.44 3.21 F
1060 1225 0.035458 CGCACACCTCTTTCCTTCCT 59.965 55.0 0.0 0.0 0.00 3.36 F
1698 1869 0.320508 GGTCTTTGAGGGTGACGACC 60.321 60.0 0.0 0.0 42.27 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1690 1861 0.938168 GACAACGTCTGGGTCGTCAC 60.938 60.000 0.0 0.0 40.69 3.67 R
2697 2974 1.004918 ACTTCCTTGAACGAGGCCG 60.005 57.895 0.0 0.0 42.50 6.13 R
3603 3887 1.136500 GTAATCCCTCCGTCCAGTGTC 59.864 57.143 0.0 0.0 0.00 3.67 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
53 54 1.081840 GCAGCTGAAGAACCAACGC 60.082 57.895 20.43 0.00 0.00 4.84
56 57 2.556287 CTGAAGAACCAACGCGCC 59.444 61.111 5.73 0.00 0.00 6.53
59 60 1.959226 GAAGAACCAACGCGCCTCA 60.959 57.895 5.73 0.00 0.00 3.86
62 63 1.154225 GAACCAACGCGCCTCATTG 60.154 57.895 5.73 2.09 0.00 2.82
86 87 3.639094 ACTACCAGATATCTGAGTGTGCC 59.361 47.826 30.40 0.00 46.59 5.01
122 123 2.045926 AACCTGCGCAGTCCATCC 60.046 61.111 33.75 0.00 0.00 3.51
123 124 2.596851 AACCTGCGCAGTCCATCCT 61.597 57.895 33.75 8.73 0.00 3.24
209 210 2.476997 GTCTCTCGGCTCAAAAGACAAC 59.523 50.000 0.00 0.00 37.04 3.32
304 305 2.211806 GATCAGCACAAGGAGATGAGC 58.788 52.381 0.00 0.00 37.20 4.26
309 310 1.446907 CACAAGGAGATGAGCACACC 58.553 55.000 0.00 0.00 0.00 4.16
333 334 3.970410 CTGGCACCCTTGGGCTGA 61.970 66.667 5.46 0.00 32.62 4.26
334 335 3.267233 TGGCACCCTTGGGCTGAT 61.267 61.111 5.46 0.00 0.00 2.90
335 336 2.757099 GGCACCCTTGGGCTGATG 60.757 66.667 5.46 0.00 0.00 3.07
346 347 0.106819 GGGCTGATGAGCTTCCATGT 60.107 55.000 3.60 0.00 45.44 3.21
369 370 1.095807 GGTTTCCTACGGCATGGAGC 61.096 60.000 0.00 0.00 44.65 4.70
376 377 3.203442 CGGCATGGAGCTGCATTT 58.797 55.556 19.19 0.00 43.88 2.32
411 416 8.128582 TGTGACTTGATGTGTTTAGAATTTCAC 58.871 33.333 0.00 0.00 0.00 3.18
477 482 2.256156 TAGCTGCATGGGGGAGGAGA 62.256 60.000 1.02 0.00 35.12 3.71
478 483 3.117452 GCTGCATGGGGGAGGAGAG 62.117 68.421 0.00 0.00 35.12 3.20
479 484 1.383664 CTGCATGGGGGAGGAGAGA 60.384 63.158 0.00 0.00 0.00 3.10
480 485 1.690633 TGCATGGGGGAGGAGAGAC 60.691 63.158 0.00 0.00 0.00 3.36
503 508 2.239907 GACCCCCTTGAGTAGATTTGCT 59.760 50.000 0.00 0.00 0.00 3.91
504 509 2.025887 ACCCCCTTGAGTAGATTTGCTG 60.026 50.000 0.00 0.00 0.00 4.41
505 510 2.019984 CCCCTTGAGTAGATTTGCTGC 58.980 52.381 0.00 0.00 0.00 5.25
515 520 2.376109 AGATTTGCTGCATCCTTCAGG 58.624 47.619 1.84 0.00 32.41 3.86
519 524 1.077930 GCTGCATCCTTCAGGCTCA 60.078 57.895 0.00 0.00 34.44 4.26
554 559 9.810545 TGATTGAATGATTGAATGTACGTAGTA 57.189 29.630 0.00 0.00 45.11 1.82
598 603 8.001881 TCACCTGTTGTTGTAATGTTTGTATT 57.998 30.769 0.00 0.00 0.00 1.89
600 605 7.704472 CACCTGTTGTTGTAATGTTTGTATTGT 59.296 33.333 0.00 0.00 0.00 2.71
601 606 8.904834 ACCTGTTGTTGTAATGTTTGTATTGTA 58.095 29.630 0.00 0.00 0.00 2.41
602 607 9.906660 CCTGTTGTTGTAATGTTTGTATTGTAT 57.093 29.630 0.00 0.00 0.00 2.29
646 654 5.713389 TCGATGTAGAAGTAGGAACCTGAAA 59.287 40.000 3.36 0.00 0.00 2.69
648 656 6.571731 CGATGTAGAAGTAGGAACCTGAAACA 60.572 42.308 3.36 0.85 0.00 2.83
753 780 6.389906 TGCAACGATCGTCTGATTATATGAT 58.610 36.000 22.98 0.00 34.09 2.45
754 781 7.535139 TGCAACGATCGTCTGATTATATGATA 58.465 34.615 22.98 3.02 34.09 2.15
755 782 7.698130 TGCAACGATCGTCTGATTATATGATAG 59.302 37.037 22.98 0.00 34.09 2.08
756 783 7.698550 GCAACGATCGTCTGATTATATGATAGT 59.301 37.037 22.98 0.00 34.09 2.12
829 941 0.386113 TTACGTGCCCAAACCAAAGC 59.614 50.000 0.00 0.00 0.00 3.51
911 1045 4.065110 GAGGCAACCTCGCAAAGT 57.935 55.556 0.00 0.00 41.08 2.66
949 1114 1.210155 GTTGTCCAGCGTTGCCATC 59.790 57.895 0.00 0.00 0.00 3.51
971 1136 1.041447 GGCCTGCCATTTCTGCATCT 61.041 55.000 2.58 0.00 38.22 2.90
1011 1176 0.602905 GCGCACGGGGATAATAAGCT 60.603 55.000 0.30 0.00 0.00 3.74
1015 1180 1.045407 ACGGGGATAATAAGCTGCGA 58.955 50.000 0.00 0.00 0.00 5.10
1017 1182 1.429463 GGGGATAATAAGCTGCGACG 58.571 55.000 0.00 0.00 0.00 5.12
1020 1185 2.480845 GGATAATAAGCTGCGACGGTT 58.519 47.619 0.00 0.00 0.00 4.44
1057 1222 1.600916 GCCGCACACCTCTTTCCTT 60.601 57.895 0.00 0.00 0.00 3.36
1058 1223 1.578206 GCCGCACACCTCTTTCCTTC 61.578 60.000 0.00 0.00 0.00 3.46
1059 1224 0.955919 CCGCACACCTCTTTCCTTCC 60.956 60.000 0.00 0.00 0.00 3.46
1060 1225 0.035458 CGCACACCTCTTTCCTTCCT 59.965 55.000 0.00 0.00 0.00 3.36
1072 1237 6.821160 CCTCTTTCCTTCCTGAGAAATAGAAC 59.179 42.308 0.00 0.00 31.37 3.01
1251 1416 3.240770 GGCAAGCCCAAGCCCAAA 61.241 61.111 0.00 0.00 45.18 3.28
1307 1478 1.662044 CCAAGCACAAACCAGAGCC 59.338 57.895 0.00 0.00 0.00 4.70
1308 1479 1.283793 CAAGCACAAACCAGAGCCG 59.716 57.895 0.00 0.00 0.00 5.52
1309 1480 1.898574 AAGCACAAACCAGAGCCGG 60.899 57.895 0.00 0.00 0.00 6.13
1310 1481 2.281484 GCACAAACCAGAGCCGGA 60.281 61.111 5.05 0.00 0.00 5.14
1311 1482 2.328099 GCACAAACCAGAGCCGGAG 61.328 63.158 5.05 0.00 0.00 4.63
1312 1483 2.032681 ACAAACCAGAGCCGGAGC 59.967 61.111 5.05 0.00 40.32 4.70
1408 1579 4.175489 ACGCGATGGAGACCGACG 62.175 66.667 15.93 0.00 0.00 5.12
1644 1815 1.186267 AGGTGGACTTGGAGGTCGAC 61.186 60.000 7.13 7.13 41.82 4.20
1690 1861 1.425448 AGGTTTCTGGGTCTTTGAGGG 59.575 52.381 0.00 0.00 0.00 4.30
1698 1869 0.320508 GGTCTTTGAGGGTGACGACC 60.321 60.000 0.00 0.00 42.27 4.79
1891 2068 0.480690 AAATGGTGGTGGTGCTGGTA 59.519 50.000 0.00 0.00 0.00 3.25
1908 2085 1.383523 GTAGCAAGGCTGTTCCATCC 58.616 55.000 0.07 0.00 40.10 3.51
2097 2374 4.717233 TTATGCATTGTCATTGTGTCCC 57.283 40.909 3.54 0.00 0.00 4.46
2314 2591 1.654023 GCGTGGTTTATGGGTCTGCC 61.654 60.000 0.00 0.00 0.00 4.85
2466 2743 4.641396 TGATATTGAATCCGCTGGGTAAG 58.359 43.478 0.00 0.00 33.83 2.34
2475 2752 1.123928 CGCTGGGTAAGAGAAGGGAT 58.876 55.000 0.00 0.00 0.00 3.85
2697 2974 4.514401 CAGTAATGGGTAAGACCAAGGAC 58.486 47.826 0.00 0.00 45.13 3.85
2840 3117 3.540314 CTCTGACAGGAAAGATGGAGG 57.460 52.381 1.81 0.00 0.00 4.30
3342 3623 8.836413 TGGTAAATAACTATTCTAGCATTGCAC 58.164 33.333 11.91 0.00 0.00 4.57
3377 3658 7.891498 AAAAATAGTTGGGTGTGTTCTTAGT 57.109 32.000 0.00 0.00 0.00 2.24
3508 3792 1.344763 ACCTGTGTTGTAGCTGGTCTC 59.655 52.381 0.00 0.00 32.60 3.36
3546 3830 1.802960 CTCAGGTGTTGATGTGCTGTC 59.197 52.381 0.00 0.00 34.68 3.51
3597 3881 8.689054 ACTCCCTCCTTCCTATAATATAAGACA 58.311 37.037 0.00 0.00 0.00 3.41
3768 4172 8.762481 AAAACCATTTACCTCTATTATGGTCC 57.238 34.615 0.00 0.00 46.10 4.46
3807 4234 1.850345 TGGTTTGGTTCAAGGAGAGGT 59.150 47.619 0.00 0.00 0.00 3.85
3839 4266 6.201997 GGATTTACATTTGTTTTGGTGTGGTC 59.798 38.462 0.00 0.00 0.00 4.02
3963 4390 7.548075 ACATGAAAGAATTGATCTGATTTTGCC 59.452 33.333 0.00 0.00 38.79 4.52
3982 4409 3.006430 TGCCATCGTTTGTCTCTGTAGAA 59.994 43.478 0.00 0.00 32.16 2.10
3992 4419 6.545504 TTGTCTCTGTAGAATTTTGCTCAC 57.454 37.500 0.00 0.00 32.16 3.51
4042 4521 0.036732 TCATGTGTGGAAGCTGGACC 59.963 55.000 0.00 0.00 0.00 4.46
4208 4687 9.926158 AAATTTTATTGTGTAGATGCATGTTCA 57.074 25.926 2.46 0.18 0.00 3.18
4211 4690 5.808042 ATTGTGTAGATGCATGTTCACTC 57.192 39.130 26.40 11.82 0.00 3.51
4238 4717 1.152694 TGCTTGAGCCTGTTGCCTT 60.153 52.632 0.00 0.00 42.71 4.35
4252 4731 1.986210 GCCTTGCCATGAAGCCCTT 60.986 57.895 0.00 0.00 0.00 3.95
4264 4743 4.348857 GCCCTTTGCTGCAACTTG 57.651 55.556 15.72 8.26 36.87 3.16
4275 4754 2.016318 CTGCAACTTGTCACTTCACCA 58.984 47.619 0.00 0.00 0.00 4.17
4292 4771 1.134877 ACCATCGATGACACTCTGCTG 60.135 52.381 26.86 8.10 0.00 4.41
4299 4778 1.227943 GACACTCTGCTGCAACCCA 60.228 57.895 3.02 0.00 0.00 4.51
4300 4779 1.228063 ACACTCTGCTGCAACCCAG 60.228 57.895 3.02 0.00 44.67 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 2.507102 CTACGCAGACCACGCAGG 60.507 66.667 0.00 0.00 45.67 4.85
10 11 2.257371 GACTACGCAGACCACGCA 59.743 61.111 0.00 0.00 0.00 5.24
11 12 2.506438 GGACTACGCAGACCACGC 60.506 66.667 0.00 0.00 36.70 5.34
12 13 2.959372 TGGACTACGCAGACCACG 59.041 61.111 2.48 0.00 40.97 4.94
53 54 0.824109 TCTGGTAGTCCAATGAGGCG 59.176 55.000 0.00 0.00 43.81 5.52
56 57 6.493115 ACTCAGATATCTGGTAGTCCAATGAG 59.507 42.308 28.30 17.32 43.81 2.90
59 60 6.041409 CACACTCAGATATCTGGTAGTCCAAT 59.959 42.308 28.30 10.59 43.81 3.16
62 63 4.261825 GCACACTCAGATATCTGGTAGTCC 60.262 50.000 28.30 13.29 43.91 3.85
122 123 2.640184 TGATGATTCTTCAGCTGCCAG 58.360 47.619 9.47 7.65 39.07 4.85
123 124 2.793288 TGATGATTCTTCAGCTGCCA 57.207 45.000 9.47 0.00 39.07 4.92
304 305 4.624364 TGCCAGCCAGTCGGTGTG 62.624 66.667 0.00 0.00 38.36 3.82
309 310 4.335647 AAGGGTGCCAGCCAGTCG 62.336 66.667 16.48 0.00 38.48 4.18
369 370 9.630098 ATCAAGTCACATTAACTTAAAATGCAG 57.370 29.630 0.00 0.00 37.77 4.41
477 482 1.717077 TCTACTCAAGGGGGTCTGTCT 59.283 52.381 0.00 0.00 0.00 3.41
478 483 2.233305 TCTACTCAAGGGGGTCTGTC 57.767 55.000 0.00 0.00 0.00 3.51
479 484 2.950990 ATCTACTCAAGGGGGTCTGT 57.049 50.000 0.00 0.00 0.00 3.41
480 485 3.878778 CAAATCTACTCAAGGGGGTCTG 58.121 50.000 0.00 0.00 0.00 3.51
503 508 0.182061 GGATGAGCCTGAAGGATGCA 59.818 55.000 0.00 0.00 37.39 3.96
504 509 0.883814 CGGATGAGCCTGAAGGATGC 60.884 60.000 0.00 0.00 37.39 3.91
505 510 0.250209 CCGGATGAGCCTGAAGGATG 60.250 60.000 0.00 0.00 37.39 3.51
515 520 2.462456 TCAATCATAGCCGGATGAGC 57.538 50.000 5.05 0.00 39.18 4.26
519 524 5.563592 TCAATCATTCAATCATAGCCGGAT 58.436 37.500 5.05 0.00 0.00 4.18
553 558 5.068723 GGTGATTACCGAAAGTCCATCTCTA 59.931 44.000 0.00 0.00 37.19 2.43
554 559 4.141914 GGTGATTACCGAAAGTCCATCTCT 60.142 45.833 0.00 0.00 37.19 3.10
555 560 4.120589 GGTGATTACCGAAAGTCCATCTC 58.879 47.826 0.00 0.00 37.19 2.75
646 654 0.251165 ATTAGCTTTGCCACGGGTGT 60.251 50.000 0.00 0.00 0.00 4.16
648 656 0.965363 CCATTAGCTTTGCCACGGGT 60.965 55.000 0.00 0.00 0.00 5.28
753 780 6.553953 TGCTTTCATTCATGGGTAGTACTA 57.446 37.500 0.00 0.00 0.00 1.82
754 781 5.435686 TGCTTTCATTCATGGGTAGTACT 57.564 39.130 0.00 0.00 0.00 2.73
755 782 5.590259 ACATGCTTTCATTCATGGGTAGTAC 59.410 40.000 7.08 0.00 43.11 2.73
756 783 5.589855 CACATGCTTTCATTCATGGGTAGTA 59.410 40.000 7.08 0.00 43.11 1.82
757 784 4.400251 CACATGCTTTCATTCATGGGTAGT 59.600 41.667 7.08 0.00 43.11 2.73
758 785 4.202080 CCACATGCTTTCATTCATGGGTAG 60.202 45.833 7.08 0.00 41.29 3.18
921 1086 1.813862 CGCTGGACAACTCCCTCAAAA 60.814 52.381 0.00 0.00 35.34 2.44
936 1101 3.136123 CCTGGATGGCAACGCTGG 61.136 66.667 0.00 0.00 42.51 4.85
949 1114 2.718073 GCAGAAATGGCAGGCCTGG 61.718 63.158 33.46 15.41 36.94 4.45
992 1157 0.602905 AGCTTATTATCCCCGTGCGC 60.603 55.000 0.00 0.00 0.00 6.09
1001 1166 2.348591 GCAACCGTCGCAGCTTATTATC 60.349 50.000 0.00 0.00 0.00 1.75
1015 1180 3.692406 GGGGAGACGAGCAACCGT 61.692 66.667 0.00 0.00 46.43 4.83
1017 1182 4.452733 CGGGGGAGACGAGCAACC 62.453 72.222 0.00 0.00 0.00 3.77
1057 1222 5.576563 TTTGGGTGTTCTATTTCTCAGGA 57.423 39.130 0.00 0.00 0.00 3.86
1058 1223 5.358160 GGATTTGGGTGTTCTATTTCTCAGG 59.642 44.000 0.00 0.00 0.00 3.86
1059 1224 5.358160 GGGATTTGGGTGTTCTATTTCTCAG 59.642 44.000 0.00 0.00 0.00 3.35
1060 1225 5.261216 GGGATTTGGGTGTTCTATTTCTCA 58.739 41.667 0.00 0.00 0.00 3.27
1072 1237 2.440247 GCCGAGGGGATTTGGGTG 60.440 66.667 0.00 0.00 34.06 4.61
1094 1259 3.127533 GGCGTGCTGCTAGGGTTG 61.128 66.667 0.00 0.00 45.43 3.77
1129 1294 4.471726 GATGTCGCCGTCGGTCGT 62.472 66.667 21.64 11.31 37.94 4.34
1251 1416 3.901797 CTTCGGCTTCGGCTTGGGT 62.902 63.158 0.00 0.00 41.44 4.51
1294 1459 2.328099 GCTCCGGCTCTGGTTTGTG 61.328 63.158 0.00 0.00 35.22 3.33
1690 1861 0.938168 GACAACGTCTGGGTCGTCAC 60.938 60.000 0.00 0.00 40.69 3.67
1698 1869 1.135112 TCCGATGATGACAACGTCTGG 60.135 52.381 3.74 6.46 39.91 3.86
1908 2085 1.017387 GGTGCTGATTTCCCTTAGCG 58.983 55.000 0.00 0.00 38.96 4.26
2314 2591 6.963242 CCATCATCATACAACAAAGAACTTCG 59.037 38.462 0.00 0.00 0.00 3.79
2466 2743 5.351948 AGTCTTGAAGCTTATCCCTTCTC 57.648 43.478 0.00 0.00 39.47 2.87
2697 2974 1.004918 ACTTCCTTGAACGAGGCCG 60.005 57.895 0.00 0.00 42.50 6.13
2840 3117 5.638783 CATTTGACAGAGCTTGGAATCTTC 58.361 41.667 0.00 0.00 0.00 2.87
2883 3160 4.627467 GCATCAAGCTCTTTACGAGAAAGA 59.373 41.667 13.87 13.87 42.62 2.52
3327 3608 3.159353 ACGACGTGCAATGCTAGAATA 57.841 42.857 6.82 0.00 0.00 1.75
3342 3623 5.636543 ACCCAACTATTTTTAGAGAACGACG 59.363 40.000 0.00 0.00 0.00 5.12
3377 3658 5.719085 ACACAACCAATGCCCATCTTTATTA 59.281 36.000 0.00 0.00 0.00 0.98
3483 3767 3.135895 ACCAGCTACAACACAGGTTTAGT 59.864 43.478 0.00 0.00 34.21 2.24
3484 3768 3.740115 ACCAGCTACAACACAGGTTTAG 58.260 45.455 0.00 0.00 34.21 1.85
3487 3771 1.768870 AGACCAGCTACAACACAGGTT 59.231 47.619 0.00 0.00 37.87 3.50
3508 3792 2.292016 TGAGCAACACAACAAATACCGG 59.708 45.455 0.00 0.00 0.00 5.28
3562 3846 3.841255 AGGAAGGAGGGAGTACTTTTCAG 59.159 47.826 0.00 0.00 0.00 3.02
3597 3881 2.504367 CCTCCGTCCAGTGTCAAAAAT 58.496 47.619 0.00 0.00 0.00 1.82
3603 3887 1.136500 GTAATCCCTCCGTCCAGTGTC 59.864 57.143 0.00 0.00 0.00 3.67
3604 3888 1.192428 GTAATCCCTCCGTCCAGTGT 58.808 55.000 0.00 0.00 0.00 3.55
3605 3889 1.191535 TGTAATCCCTCCGTCCAGTG 58.808 55.000 0.00 0.00 0.00 3.66
3608 3892 2.168458 TGATGTAATCCCTCCGTCCA 57.832 50.000 0.00 0.00 44.73 4.02
3684 4008 5.049680 GGATTGACGTTGTACACAAAGATGT 60.050 40.000 13.74 0.00 41.61 3.06
3766 4170 1.434513 ATCACCAGGGTTTGCTGGGA 61.435 55.000 0.00 0.00 44.58 4.37
3767 4171 0.542702 AATCACCAGGGTTTGCTGGG 60.543 55.000 0.00 0.00 44.58 4.45
3768 4172 1.001181 CAAATCACCAGGGTTTGCTGG 59.999 52.381 0.00 0.00 45.70 4.85
3807 4234 9.308000 ACCAAAACAAATGTAAATCCAGATCTA 57.692 29.630 0.00 0.00 0.00 1.98
3839 4266 9.358872 GGAGCAATTCCTACAAAATTAAAGAAG 57.641 33.333 0.00 0.00 43.16 2.85
3913 4340 3.270433 ACCATCCATCCAACCTGAAATCT 59.730 43.478 0.00 0.00 0.00 2.40
3963 4390 6.521133 GCAAAATTCTACAGAGACAAACGATG 59.479 38.462 0.00 0.00 0.00 3.84
3992 4419 0.529337 CAGATAGACACAGCCCAGCG 60.529 60.000 0.00 0.00 0.00 5.18
4042 4521 9.158364 GCATGAACAAAATTGTACATATAGACG 57.842 33.333 0.00 0.00 41.31 4.18
4081 4560 9.491675 AGAATAAGATGATCTAATGAGTGCAAG 57.508 33.333 0.00 0.00 0.00 4.01
4084 4563 9.656040 ATGAGAATAAGATGATCTAATGAGTGC 57.344 33.333 0.00 0.00 0.00 4.40
4208 4687 0.689623 CTCAAGCAGAACAGGGGAGT 59.310 55.000 0.00 0.00 0.00 3.85
4211 4690 1.676967 GGCTCAAGCAGAACAGGGG 60.677 63.158 4.13 0.00 44.36 4.79
4238 4717 3.379880 GCAAAGGGCTTCATGGCA 58.620 55.556 0.00 0.00 43.83 4.92
4252 4731 2.090760 TGAAGTGACAAGTTGCAGCAA 58.909 42.857 2.83 2.83 0.00 3.91
4260 4739 3.006859 TCATCGATGGTGAAGTGACAAGT 59.993 43.478 24.61 0.00 0.00 3.16
4264 4743 2.668457 GTGTCATCGATGGTGAAGTGAC 59.332 50.000 24.61 14.16 37.18 3.67
4275 4754 0.533951 TGCAGCAGAGTGTCATCGAT 59.466 50.000 0.00 0.00 0.00 3.59
4292 4771 1.228245 TTGGACAGAGCTGGGTTGC 60.228 57.895 0.00 0.00 34.19 4.17
4299 4778 9.384764 GAATAATTTAAGTACTTGGACAGAGCT 57.615 33.333 18.56 0.00 0.00 4.09
4300 4779 9.162764 TGAATAATTTAAGTACTTGGACAGAGC 57.837 33.333 18.56 3.31 0.00 4.09


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

AutoCloner maintained by Alex Coulton.