Multiple sequence alignment - TraesCS2A01G023100

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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 TraesCS2A01G023100 chr2A 100.000 3682 0 0 1 3682 11310749 11307068 0.000000e+00 6800
1 TraesCS2A01G023100 chr2A 90.056 3057 238 28 677 3682 11045361 11042320 0.000000e+00 3901
2 TraesCS2A01G023100 chr2D 92.637 3368 184 12 337 3682 10801046 10797721 0.000000e+00 4787
3 TraesCS2A01G023100 chr2D 92.209 2503 173 6 155 2637 10512341 10509841 0.000000e+00 3522
4 TraesCS2A01G023100 chr2D 92.050 2503 177 6 155 2637 10495290 10492790 0.000000e+00 3500
5 TraesCS2A01G023100 chr2D 91.890 2503 174 7 155 2637 10293184 10295677 0.000000e+00 3470
6 TraesCS2A01G023100 chr2B 90.986 2973 234 23 731 3682 15638814 15635855 0.000000e+00 3975
7 TraesCS2A01G023100 chr2B 91.493 2786 192 16 579 3333 15883327 15880556 0.000000e+00 3790
8 TraesCS2A01G023100 chr2B 90.257 2874 239 16 824 3682 15119809 15116962 0.000000e+00 3718
9 TraesCS2A01G023100 chr2B 88.923 2898 266 22 747 3623 15382573 15379710 0.000000e+00 3522
10 TraesCS2A01G023100 chr2B 91.107 2429 191 14 731 3141 15818710 15816289 0.000000e+00 3265
11 TraesCS2A01G023100 chr2B 91.066 2429 192 14 731 3141 15917681 15915260 0.000000e+00 3260
12 TraesCS2A01G023100 chr2B 90.902 2429 196 14 731 3141 15695404 15692983 0.000000e+00 3238
13 TraesCS2A01G023100 chr2B 92.458 1432 101 6 1712 3141 15756769 15755343 0.000000e+00 2039
14 TraesCS2A01G023100 chr2B 90.108 556 50 5 3126 3680 15692700 15692149 0.000000e+00 717
15 TraesCS2A01G023100 chr2B 89.928 556 51 5 3126 3680 15914977 15914426 0.000000e+00 712
16 TraesCS2A01G023100 chr2B 89.748 556 52 5 3126 3680 15816006 15815455 0.000000e+00 706
17 TraesCS2A01G023100 chr2B 89.568 556 53 5 3126 3680 15755060 15754509 0.000000e+00 701
18 TraesCS2A01G023100 chr2B 93.007 143 10 0 4 146 417774544 417774402 3.730000e-50 209
19 TraesCS2A01G023100 chrUn 91.833 2412 160 15 579 2966 339546441 339548839 0.000000e+00 3328
20 TraesCS2A01G023100 chrUn 91.708 2412 163 13 579 2966 339561602 339559204 0.000000e+00 3312
21 TraesCS2A01G023100 chrUn 92.289 2049 133 8 579 2614 349087491 349085455 0.000000e+00 2885
22 TraesCS2A01G023100 chrUn 92.180 2046 135 8 579 2611 349092566 349094599 0.000000e+00 2868
23 TraesCS2A01G023100 chrUn 86.975 238 18 7 579 815 328699764 328699989 4.720000e-64 255
24 TraesCS2A01G023100 chrUn 86.975 238 18 7 579 815 433700886 433700661 4.720000e-64 255
25 TraesCS2A01G023100 chr6B 85.476 420 49 9 156 573 205121040 205120631 9.450000e-116 427
26 TraesCS2A01G023100 chr4B 84.773 440 50 14 157 592 59852126 59852552 3.400000e-115 425
27 TraesCS2A01G023100 chr1B 84.010 419 59 6 155 570 231624346 231624759 2.660000e-106 396
28 TraesCS2A01G023100 chr7D 83.816 414 55 11 157 569 169836705 169836303 2.070000e-102 383
29 TraesCS2A01G023100 chr7D 77.471 435 64 11 155 571 249619100 249619518 2.860000e-56 230
30 TraesCS2A01G023100 chr3D 76.735 533 74 35 1 492 11562711 11563234 6.100000e-63 252
31 TraesCS2A01G023100 chr3D 83.521 267 38 6 309 571 498726646 498726382 1.020000e-60 244
32 TraesCS2A01G023100 chr3D 88.742 151 17 0 4 154 68915111 68914961 6.280000e-43 185
33 TraesCS2A01G023100 chr5A 78.153 444 61 21 155 571 355372443 355372877 2.200000e-62 250
34 TraesCS2A01G023100 chr6D 86.598 194 24 2 155 347 62131029 62131221 2.880000e-51 213
35 TraesCS2A01G023100 chr3B 88.202 178 16 4 155 331 783421245 783421418 1.340000e-49 207
36 TraesCS2A01G023100 chr7A 90.909 154 13 1 1 154 690678674 690678826 4.820000e-49 206
37 TraesCS2A01G023100 chr3A 90.260 154 15 0 1 154 388799479 388799632 6.230000e-48 202
38 TraesCS2A01G023100 chr3A 90.323 155 13 2 1 154 505234201 505234354 6.230000e-48 202
39 TraesCS2A01G023100 chr1D 91.216 148 12 1 1 147 70581526 70581673 2.240000e-47 200
40 TraesCS2A01G023100 chr5B 89.404 151 16 0 4 154 387899227 387899077 1.350000e-44 191
41 TraesCS2A01G023100 chr4A 87.662 154 19 0 1 154 468601158 468601311 2.920000e-41 180


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 TraesCS2A01G023100 chr2A 11307068 11310749 3681 True 6800.0 6800 100.0000 1 3682 1 chr2A.!!$R2 3681
1 TraesCS2A01G023100 chr2A 11042320 11045361 3041 True 3901.0 3901 90.0560 677 3682 1 chr2A.!!$R1 3005
2 TraesCS2A01G023100 chr2D 10797721 10801046 3325 True 4787.0 4787 92.6370 337 3682 1 chr2D.!!$R3 3345
3 TraesCS2A01G023100 chr2D 10509841 10512341 2500 True 3522.0 3522 92.2090 155 2637 1 chr2D.!!$R2 2482
4 TraesCS2A01G023100 chr2D 10492790 10495290 2500 True 3500.0 3500 92.0500 155 2637 1 chr2D.!!$R1 2482
5 TraesCS2A01G023100 chr2D 10293184 10295677 2493 False 3470.0 3470 91.8900 155 2637 1 chr2D.!!$F1 2482
6 TraesCS2A01G023100 chr2B 15635855 15638814 2959 True 3975.0 3975 90.9860 731 3682 1 chr2B.!!$R3 2951
7 TraesCS2A01G023100 chr2B 15880556 15883327 2771 True 3790.0 3790 91.4930 579 3333 1 chr2B.!!$R4 2754
8 TraesCS2A01G023100 chr2B 15116962 15119809 2847 True 3718.0 3718 90.2570 824 3682 1 chr2B.!!$R1 2858
9 TraesCS2A01G023100 chr2B 15379710 15382573 2863 True 3522.0 3522 88.9230 747 3623 1 chr2B.!!$R2 2876
10 TraesCS2A01G023100 chr2B 15914426 15917681 3255 True 1986.0 3260 90.4970 731 3680 2 chr2B.!!$R9 2949
11 TraesCS2A01G023100 chr2B 15815455 15818710 3255 True 1985.5 3265 90.4275 731 3680 2 chr2B.!!$R8 2949
12 TraesCS2A01G023100 chr2B 15692149 15695404 3255 True 1977.5 3238 90.5050 731 3680 2 chr2B.!!$R6 2949
13 TraesCS2A01G023100 chr2B 15754509 15756769 2260 True 1370.0 2039 91.0130 1712 3680 2 chr2B.!!$R7 1968
14 TraesCS2A01G023100 chrUn 339546441 339548839 2398 False 3328.0 3328 91.8330 579 2966 1 chrUn.!!$F2 2387
15 TraesCS2A01G023100 chrUn 339559204 339561602 2398 True 3312.0 3312 91.7080 579 2966 1 chrUn.!!$R1 2387
16 TraesCS2A01G023100 chrUn 349085455 349087491 2036 True 2885.0 2885 92.2890 579 2614 1 chrUn.!!$R2 2035
17 TraesCS2A01G023100 chrUn 349092566 349094599 2033 False 2868.0 2868 92.1800 579 2611 1 chrUn.!!$F3 2032
18 TraesCS2A01G023100 chr3D 11562711 11563234 523 False 252.0 252 76.7350 1 492 1 chr3D.!!$F1 491

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
434 472 0.176680 GAGGTGATGTCGTCTGCCAT 59.823 55.0 8.32 0.0 0.0 4.40 F
592 637 0.935898 GGCTCGCTCATGAAGATGTG 59.064 55.0 0.00 0.0 0.0 3.21 F
1698 1780 0.109412 GTGTGTCCGACTACTTCCCG 60.109 60.0 0.00 0.0 0.0 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1407 0.547471 TGGTGAGAAGATGGAGCCCA 60.547 55.0 0.00 0.00 38.19 5.36 R
2447 2533 0.174845 TGAAACGTAGGCCTGGATCG 59.825 55.0 17.99 16.65 0.00 3.69 R
3599 4022 0.878416 TTGCCCGTGTAATTCAGCAC 59.122 50.0 0.00 0.00 0.00 4.40 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 0.731514 ACAGTTACACGACGATGCCG 60.732 55.000 0.00 0.00 42.50 5.69
76 77 3.238903 GATGCCGTCATCAATGTAACG 57.761 47.619 0.68 0.00 46.44 3.18
80 81 0.315059 CGTCATCAATGTAACGGCGC 60.315 55.000 6.90 0.00 0.00 6.53
84 85 1.910819 CATCAATGTAACGGCGCAAAC 59.089 47.619 10.83 2.99 0.00 2.93
121 122 2.554272 CGGCTCGTTTTTCACCGG 59.446 61.111 0.00 0.00 40.18 5.28
131 132 3.561503 GTTTTTCACCGGCAACTATGTC 58.438 45.455 0.00 0.00 0.00 3.06
134 135 1.557099 TCACCGGCAACTATGTCTCT 58.443 50.000 0.00 0.00 0.00 3.10
141 142 2.223618 GGCAACTATGTCTCTCCGACTC 60.224 54.545 0.00 0.00 43.25 3.36
147 148 0.249676 TGTCTCTCCGACTCGTAGCT 59.750 55.000 0.00 0.00 43.25 3.32
148 149 1.479730 TGTCTCTCCGACTCGTAGCTA 59.520 52.381 0.00 0.00 43.25 3.32
192 204 0.458543 CGGAAGAGATGACCACCACG 60.459 60.000 0.00 0.00 0.00 4.94
290 302 0.749454 GATCCAAAGGCAGATGGCGT 60.749 55.000 0.26 0.00 46.16 5.68
426 464 1.730487 CGGGAGAGAGGTGATGTCG 59.270 63.158 0.00 0.00 0.00 4.35
429 467 1.683629 GGGAGAGAGGTGATGTCGTCT 60.684 57.143 0.00 0.00 35.65 4.18
434 472 0.176680 GAGGTGATGTCGTCTGCCAT 59.823 55.000 8.32 0.00 0.00 4.40
439 477 2.906182 GATGTCGTCTGCCATCGCCA 62.906 60.000 0.00 0.00 0.00 5.69
505 543 1.613630 GAGGGGAAGAGGGAGTGCA 60.614 63.158 0.00 0.00 0.00 4.57
592 637 0.935898 GGCTCGCTCATGAAGATGTG 59.064 55.000 0.00 0.00 0.00 3.21
703 748 3.159213 TGGACTGTCCAGAATGCAATT 57.841 42.857 25.12 0.00 42.67 2.32
839 906 2.635915 CCCGGCTGTCCTATAAATACCA 59.364 50.000 0.00 0.00 0.00 3.25
994 1064 5.872070 CCAAAGATGACTCTTGGTACTCTTC 59.128 44.000 0.00 0.00 40.93 2.87
1064 1134 1.098050 CTATTGTCCCAGCAGCAACC 58.902 55.000 0.00 0.00 0.00 3.77
1137 1207 2.211250 ACATGCACCAGCTGATTCTT 57.789 45.000 17.39 0.00 42.74 2.52
1176 1246 1.826921 GTGGATCCATGGCCTGCTG 60.827 63.158 19.62 0.00 0.00 4.41
1337 1407 2.699954 CTTGTTCAGCTTCGGGTACAT 58.300 47.619 0.00 0.00 0.00 2.29
1424 1494 2.249413 CTTGCCTCGTCCATGGAGCT 62.249 60.000 16.81 0.00 0.00 4.09
1462 1544 0.537653 GGAAGAGGAGTACAGCCACC 59.462 60.000 7.43 0.00 0.00 4.61
1527 1609 3.996480 TGTCAACATCCGTCATGTAACA 58.004 40.909 0.00 4.04 45.77 2.41
1572 1654 2.767505 AGAAGGCTTGTGTTCGGTAAG 58.232 47.619 3.46 0.00 0.00 2.34
1671 1753 1.051812 CGGCCCTCAACCATCTCTAT 58.948 55.000 0.00 0.00 0.00 1.98
1698 1780 0.109412 GTGTGTCCGACTACTTCCCG 60.109 60.000 0.00 0.00 0.00 5.14
1788 1870 5.003160 CGGTTGCATGATCCCATTATAGAA 58.997 41.667 0.00 0.00 0.00 2.10
1799 1881 3.772025 CCCATTATAGAAGAGCGGATCCT 59.228 47.826 10.75 0.00 0.00 3.24
1812 1894 1.409064 CGGATCCTCGAAAGGTCATCA 59.591 52.381 10.75 0.00 43.82 3.07
1814 1896 3.462021 GGATCCTCGAAAGGTCATCAAG 58.538 50.000 3.84 0.00 43.82 3.02
1821 1903 4.307432 TCGAAAGGTCATCAAGTCTTGAC 58.693 43.478 17.49 6.04 43.48 3.18
1840 1922 5.066968 TGACAAAGGTGGTGAAAAGAAAC 57.933 39.130 0.00 0.00 0.00 2.78
1852 1934 2.910688 AAAGAAACAGGCGAGAGACA 57.089 45.000 0.00 0.00 46.78 3.41
1955 2041 4.441079 GGTTAGTATGTCGCCTTAAGCTCA 60.441 45.833 0.00 0.00 40.39 4.26
2131 2217 3.189910 GCACTTGCTGAGATGATGAACAA 59.810 43.478 0.00 0.00 38.21 2.83
2132 2218 4.320714 GCACTTGCTGAGATGATGAACAAA 60.321 41.667 0.00 0.00 38.21 2.83
2213 2299 3.242867 AGTCCAAGAGTCTGACATTCCA 58.757 45.455 10.88 0.00 0.00 3.53
2234 2320 5.105106 TCCACGGCTAAACTATCTCAAATCA 60.105 40.000 0.00 0.00 0.00 2.57
2339 2425 3.646637 GCTACACCATACCCAAGGATAGT 59.353 47.826 0.00 0.00 0.00 2.12
2349 2435 5.615925 ACCCAAGGATAGTCACATACTTC 57.384 43.478 0.00 0.00 39.80 3.01
2371 2457 4.659172 CCGGCTTGGACTTGGCCA 62.659 66.667 0.00 0.00 45.50 5.36
2399 2485 4.808414 CAAGATCTGGACTGAACCACTA 57.192 45.455 0.00 0.00 35.91 2.74
2406 2492 5.391256 TCTGGACTGAACCACTAGAGTTTA 58.609 41.667 0.00 0.00 35.91 2.01
2407 2493 5.477291 TCTGGACTGAACCACTAGAGTTTAG 59.523 44.000 15.50 15.50 37.00 1.85
2447 2533 1.278238 CCGCGAATGTACTTCTCACC 58.722 55.000 8.23 0.00 0.00 4.02
2477 2563 5.944007 AGGCCTACGTTTCATTTCATTTAGT 59.056 36.000 1.29 0.00 0.00 2.24
2495 2581 1.615424 TAGTGGGAGGAGGGGTTGC 60.615 63.158 0.00 0.00 0.00 4.17
2574 2660 3.321968 GGGATTCACTTGGACAAAGCTTT 59.678 43.478 5.69 5.69 39.76 3.51
2599 2685 3.548415 GGCGTTAAGAGTATCAGTCTCCG 60.548 52.174 0.00 0.00 37.82 4.63
2611 2697 1.066573 CAGTCTCCGAGAAGGCAATGT 60.067 52.381 0.00 0.00 40.77 2.71
2830 2920 5.458779 GTGTGTACAAACAAAGAAGCAATCC 59.541 40.000 11.49 0.00 37.36 3.01
2833 2923 7.013750 TGTGTACAAACAAAGAAGCAATCCATA 59.986 33.333 0.00 0.00 37.36 2.74
2967 3076 7.880160 ATGTTTATGTTGTATACATGCCTGT 57.120 32.000 6.36 0.00 46.81 4.00
3011 3120 6.042781 AGCTTTGATCCCGTCTTACCATTATA 59.957 38.462 0.00 0.00 0.00 0.98
3064 3173 6.204688 TGCCAACTTGTTGTTCTATGAACTAG 59.795 38.462 11.82 0.00 36.63 2.57
3066 3175 6.934645 CCAACTTGTTGTTCTATGAACTAGGA 59.065 38.462 11.82 0.00 36.63 2.94
3101 3211 9.720769 CTCTATTAACTAGGGTTTCTTTTGTCA 57.279 33.333 0.00 0.00 36.92 3.58
3188 3599 1.396996 ACACAATGATTAACGAGCCGC 59.603 47.619 0.00 0.00 0.00 6.53
3189 3604 1.014352 ACAATGATTAACGAGCCGCC 58.986 50.000 0.00 0.00 0.00 6.13
3204 3619 2.359975 GCCAAGGTTCCCCGTCAG 60.360 66.667 0.00 0.00 35.12 3.51
3211 3626 1.167781 GGTTCCCCGTCAGCGAAAAA 61.168 55.000 0.00 0.00 41.33 1.94
3262 3680 0.966179 GTTCAAGGCCCGGTTCATTT 59.034 50.000 0.00 0.00 0.00 2.32
3277 3696 5.582665 CGGTTCATTTTCCCTTTGAAACAAA 59.417 36.000 0.00 0.00 42.56 2.83
3286 3705 6.993786 TCCCTTTGAAACAAACAAAATTCC 57.006 33.333 0.00 0.00 36.91 3.01
3303 3722 2.049433 CGAAGAACTGGACCGCGT 60.049 61.111 4.92 0.00 0.00 6.01
3307 3726 2.432628 GAACTGGACCGCGTCAGG 60.433 66.667 20.08 10.54 33.68 3.86
3321 3740 3.844099 CGCGTCAGGTTTTGCTTAATAAC 59.156 43.478 0.00 0.00 0.00 1.89
3367 3786 1.484038 TGGCTTGGTGCTTGAAAACT 58.516 45.000 0.00 0.00 42.39 2.66
3370 3789 4.402829 TGGCTTGGTGCTTGAAAACTATA 58.597 39.130 0.00 0.00 42.39 1.31
3513 3933 3.211045 TGTTTGGTTTGTACTCTCAGCC 58.789 45.455 0.00 0.00 0.00 4.85
3524 3947 7.435068 TTGTACTCTCAGCCTTTTCATTTAC 57.565 36.000 0.00 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.353836 TGCTGCTTCGGGCGAAAC 61.354 61.111 0.00 0.00 45.43 2.78
62 63 0.724549 TGCGCCGTTACATTGATGAC 59.275 50.000 4.18 0.00 0.00 3.06
111 112 3.482436 AGACATAGTTGCCGGTGAAAAA 58.518 40.909 1.90 0.00 0.00 1.94
131 132 1.068895 TCCTAGCTACGAGTCGGAGAG 59.931 57.143 28.99 16.89 40.79 3.20
134 135 0.829333 AGTCCTAGCTACGAGTCGGA 59.171 55.000 18.30 7.55 0.00 4.55
141 142 2.722487 CCCGCAGTCCTAGCTACG 59.278 66.667 0.00 0.00 0.00 3.51
268 280 1.450531 CCATCTGCCTTTGGATCGGC 61.451 60.000 2.63 2.63 46.46 5.54
426 464 2.969238 CCGATGGCGATGGCAGAC 60.969 66.667 1.01 0.00 42.43 3.51
439 477 1.307517 TCTAAACCCAGGGGCCGAT 60.308 57.895 11.37 0.00 39.32 4.18
448 486 4.397832 GCCGCCGGTCTAAACCCA 62.398 66.667 4.45 0.00 43.21 4.51
452 490 4.440127 GGACGCCGCCGGTCTAAA 62.440 66.667 4.45 0.00 39.22 1.85
484 522 1.040339 CACTCCCTCTTCCCCTCTCG 61.040 65.000 0.00 0.00 0.00 4.04
486 524 1.306568 GCACTCCCTCTTCCCCTCT 60.307 63.158 0.00 0.00 0.00 3.69
658 703 8.201464 CACCTTCTTTTGGTAATTTGGTTAGTT 58.799 33.333 0.00 0.00 35.80 2.24
798 844 3.499737 GCCCGCATCCTTGACGTG 61.500 66.667 0.00 0.00 0.00 4.49
839 906 6.651225 GTGCATCTAAGTTTGTTAGTTCTCCT 59.349 38.462 0.00 0.00 0.00 3.69
994 1064 4.012374 ACCAGCAAAGTCACCATGATAAG 58.988 43.478 0.00 0.00 0.00 1.73
1137 1207 2.032680 GGAATACCGCTGGCTTGTTA 57.967 50.000 0.00 0.00 0.00 2.41
1176 1246 4.825422 TGATGTCTGTGTTCATCTCCTTC 58.175 43.478 0.00 0.00 40.46 3.46
1248 1318 1.137086 CGCAGTACCTCACAGGCTATT 59.863 52.381 0.00 0.00 39.63 1.73
1281 1351 2.031465 GGACGGGAGGCGAAAACA 59.969 61.111 0.00 0.00 40.56 2.83
1320 1390 1.369625 CCATGTACCCGAAGCTGAAC 58.630 55.000 0.00 0.00 0.00 3.18
1337 1407 0.547471 TGGTGAGAAGATGGAGCCCA 60.547 55.000 0.00 0.00 38.19 5.36
1424 1494 1.980052 CGGAGGTGGTGGAGCTTTA 59.020 57.895 0.00 0.00 30.42 1.85
1444 1514 1.562783 AGGTGGCTGTACTCCTCTTC 58.437 55.000 0.00 0.00 0.00 2.87
1456 1526 5.538433 TGCAAAGAGTTTTATTAAGGTGGCT 59.462 36.000 0.00 0.00 0.00 4.75
1462 1544 6.370593 TGTCGCTGCAAAGAGTTTTATTAAG 58.629 36.000 0.00 0.00 0.00 1.85
1572 1654 4.202070 GCTGGTAGGTCACTGAAGTATCTC 60.202 50.000 0.00 0.00 0.00 2.75
1671 1753 1.617322 AGTCGGACACACAGAAGCTA 58.383 50.000 11.27 0.00 0.00 3.32
1728 1810 2.028112 GGCATCCTTGGAAACCTTTTCC 60.028 50.000 10.27 10.27 39.03 3.13
1788 1870 0.684805 ACCTTTCGAGGATCCGCTCT 60.685 55.000 14.01 0.00 0.00 4.09
1799 1881 4.202212 TGTCAAGACTTGATGACCTTTCGA 60.202 41.667 20.43 0.00 44.16 3.71
1812 1894 3.644966 TCACCACCTTTGTCAAGACTT 57.355 42.857 1.53 0.00 30.57 3.01
1814 1896 4.398044 TCTTTTCACCACCTTTGTCAAGAC 59.602 41.667 0.00 0.00 30.57 3.01
1821 1903 4.432712 CCTGTTTCTTTTCACCACCTTTG 58.567 43.478 0.00 0.00 0.00 2.77
1840 1922 1.734465 GTCCAAAATGTCTCTCGCCTG 59.266 52.381 0.00 0.00 0.00 4.85
1852 1934 2.649531 TGAACCAGGACGTCCAAAAT 57.350 45.000 35.00 18.85 38.89 1.82
1883 1965 1.985159 ACAGCAATGGTTGTCCCTCTA 59.015 47.619 0.00 0.00 32.53 2.43
2005 2091 4.185394 TCAGTACAACGCAACAGAAAAGA 58.815 39.130 0.00 0.00 0.00 2.52
2059 2145 2.629137 ACTGCTGCAAACATCATTTCCA 59.371 40.909 3.02 0.00 0.00 3.53
2131 2217 4.184079 GCTTTTTGCATGATCTCTGGTT 57.816 40.909 0.00 0.00 42.31 3.67
2132 2218 3.863142 GCTTTTTGCATGATCTCTGGT 57.137 42.857 0.00 0.00 42.31 4.00
2213 2299 5.237344 GCATGATTTGAGATAGTTTAGCCGT 59.763 40.000 0.00 0.00 0.00 5.68
2234 2320 3.099170 AAGGCCTCCCGGATGCAT 61.099 61.111 5.23 0.00 35.76 3.96
2339 2425 2.108168 AGCCGGCTTAGAAGTATGTGA 58.892 47.619 27.08 0.00 0.00 3.58
2349 2435 1.026718 CCAAGTCCAAGCCGGCTTAG 61.027 60.000 39.69 32.91 34.50 2.18
2399 2485 2.903404 CCTCTCGGGCCTAAACTCT 58.097 57.895 0.84 0.00 0.00 3.24
2447 2533 0.174845 TGAAACGTAGGCCTGGATCG 59.825 55.000 17.99 16.65 0.00 3.69
2477 2563 1.615424 GCAACCCCTCCTCCCACTA 60.615 63.158 0.00 0.00 0.00 2.74
2495 2581 2.620627 GGTACCAAGTGAAATCCCAGGG 60.621 54.545 7.15 0.00 0.00 4.45
2547 2633 1.271543 TGTCCAAGTGAATCCCTGCAG 60.272 52.381 6.78 6.78 0.00 4.41
2574 2660 2.357009 GACTGATACTCTTAACGCCGGA 59.643 50.000 5.05 0.00 0.00 5.14
2599 2685 3.608432 GGCCCACATTGCCTTCTC 58.392 61.111 0.00 0.00 45.70 2.87
2611 2697 1.778017 TTCAGCTAGTGCAAGGCCCA 61.778 55.000 0.00 0.00 42.74 5.36
2663 2749 8.883954 AATTGGATCATATATAGAGATGTGCG 57.116 34.615 5.47 0.00 0.00 5.34
2967 3076 2.503331 CTGGGCACACAATTGTACAGA 58.497 47.619 11.53 0.00 35.05 3.41
3030 3139 7.895759 AGAACAACAAGTTGGCAATACATAAT 58.104 30.769 16.45 0.00 44.45 1.28
3033 3142 5.789643 AGAACAACAAGTTGGCAATACAT 57.210 34.783 16.45 0.00 44.45 2.29
3074 3183 9.939802 GACAAAAGAAACCCTAGTTAATAGAGA 57.060 33.333 0.00 0.00 34.19 3.10
3235 3652 1.133792 CCGGGCCTTGAACCTGATTAT 60.134 52.381 0.84 0.00 35.38 1.28
3262 3680 6.092807 CGGAATTTTGTTTGTTTCAAAGGGAA 59.907 34.615 0.00 0.00 36.40 3.97
3277 3696 3.568430 GGTCCAGTTCTTCGGAATTTTGT 59.432 43.478 0.00 0.00 36.27 2.83
3286 3705 2.049433 ACGCGGTCCAGTTCTTCG 60.049 61.111 12.47 0.00 0.00 3.79
3303 3722 6.547880 TCACTTGGTTATTAAGCAAAACCTGA 59.452 34.615 18.61 13.99 46.85 3.86
3307 3726 8.413899 TGTTTCACTTGGTTATTAAGCAAAAC 57.586 30.769 18.61 18.33 46.85 2.43
3321 3740 2.099098 GTGGACAACCTGTTTCACTTGG 59.901 50.000 0.00 0.00 34.42 3.61
3513 3933 4.510038 ACCTGCAGCAGTAAATGAAAAG 57.490 40.909 21.26 4.17 0.00 2.27
3524 3947 2.555325 TGAAATGAAGAACCTGCAGCAG 59.445 45.455 16.23 16.23 0.00 4.24
3599 4022 0.878416 TTGCCCGTGTAATTCAGCAC 59.122 50.000 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.