Multiple sequence alignment - TraesCS3D01G058100

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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 TraesCS3D01G058100 chr3D 100.000 3221 0 0 1 3221 24503865 24500645 0.000000e+00 5949.0
1 TraesCS3D01G058100 chr3D 95.328 792 29 6 1775 2564 24335779 24334994 0.000000e+00 1251.0
2 TraesCS3D01G058100 chr3D 95.202 792 30 6 1775 2564 24385954 24385169 0.000000e+00 1245.0
3 TraesCS3D01G058100 chr3D 95.076 792 31 6 1775 2564 24288491 24287706 0.000000e+00 1240.0
4 TraesCS3D01G058100 chr3D 94.540 641 30 4 2583 3221 581981497 581980860 0.000000e+00 985.0
5 TraesCS3D01G058100 chr3D 93.789 322 20 0 1422 1743 24288811 24288490 4.830000e-133 484.0
6 TraesCS3D01G058100 chr3D 93.478 322 21 0 1422 1743 24386274 24385953 2.250000e-131 479.0
7 TraesCS3D01G058100 chr3D 93.168 322 22 0 1422 1743 24336099 24335778 1.050000e-129 473.0
8 TraesCS3D01G058100 chr3D 90.461 304 16 4 573 865 24336442 24336141 3.900000e-104 388.0
9 TraesCS3D01G058100 chr3D 90.461 304 16 4 573 865 24386617 24386316 3.900000e-104 388.0
10 TraesCS3D01G058100 chr3D 90.099 303 18 6 573 865 24289153 24288853 1.810000e-102 383.0
11 TraesCS3D01G058100 chr3D 100.000 29 0 0 1397 1425 24288857 24288829 2.000000e-03 54.7
12 TraesCS3D01G058100 chr3D 100.000 29 0 0 1397 1425 24336145 24336117 2.000000e-03 54.7
13 TraesCS3D01G058100 chr3D 100.000 29 0 0 1397 1425 24386320 24386292 2.000000e-03 54.7
14 TraesCS3D01G058100 chr3B 90.749 1989 121 29 620 2564 42370567 42368598 0.000000e+00 2595.0
15 TraesCS3D01G058100 chr3A 91.117 1925 113 19 590 2478 34250148 34248246 0.000000e+00 2555.0
16 TraesCS3D01G058100 chr3A 90.706 1926 112 19 589 2478 34052345 34050451 0.000000e+00 2503.0
17 TraesCS3D01G058100 chr3A 94.241 573 29 4 1 570 737965654 737966225 0.000000e+00 872.0
18 TraesCS3D01G058100 chr3A 91.453 234 10 2 589 812 34151518 34151285 2.410000e-81 313.0
19 TraesCS3D01G058100 chr3A 89.494 257 10 2 570 824 34250391 34250150 3.120000e-80 309.0
20 TraesCS3D01G058100 chr3A 88.550 262 12 3 571 829 34151759 34151513 5.220000e-78 302.0
21 TraesCS3D01G058100 chr3A 88.213 263 12 7 570 829 34052586 34052340 2.430000e-76 296.0
22 TraesCS3D01G058100 chr5D 94.817 656 27 7 2567 3221 496312707 496313356 0.000000e+00 1016.0
23 TraesCS3D01G058100 chr5D 94.393 642 33 2 2583 3221 468084263 468084904 0.000000e+00 983.0
24 TraesCS3D01G058100 chr5D 94.056 572 30 4 1 569 496923253 496923823 0.000000e+00 865.0
25 TraesCS3D01G058100 chr5D 94.035 570 29 5 1 567 51072340 51071773 0.000000e+00 859.0
26 TraesCS3D01G058100 chr6D 94.073 658 33 5 2567 3221 19618523 19619177 0.000000e+00 994.0
27 TraesCS3D01G058100 chr6D 94.844 640 27 4 2587 3221 452453077 452452439 0.000000e+00 994.0
28 TraesCS3D01G058100 chr6D 93.892 573 28 7 1 569 446734849 446734280 0.000000e+00 857.0
29 TraesCS3D01G058100 chr7D 94.696 641 31 2 2583 3221 93942904 93942265 0.000000e+00 992.0
30 TraesCS3D01G058100 chr7D 94.219 640 31 4 2583 3221 633915426 633914792 0.000000e+00 972.0
31 TraesCS3D01G058100 chr7D 93.860 570 30 5 3 569 608455968 608455401 0.000000e+00 854.0
32 TraesCS3D01G058100 chr7D 93.860 570 30 5 3 569 608474417 608473850 0.000000e+00 854.0
33 TraesCS3D01G058100 chr4D 94.929 631 25 5 2596 3221 296707203 296706575 0.000000e+00 981.0
34 TraesCS3D01G058100 chr4D 87.097 62 8 0 2320 2381 487119501 487119440 1.600000e-08 71.3
35 TraesCS3D01G058100 chr2B 92.998 657 43 3 2567 3221 786255775 786256430 0.000000e+00 955.0
36 TraesCS3D01G058100 chrUn 94.046 571 28 6 3 569 74786583 74787151 0.000000e+00 861.0
37 TraesCS3D01G058100 chr6A 93.576 576 32 5 1 572 10484607 10485181 0.000000e+00 854.0
38 TraesCS3D01G058100 chr1D 93.576 576 32 5 3 575 439355137 439354564 0.000000e+00 854.0
39 TraesCS3D01G058100 chr5A 82.667 150 26 0 2070 2219 668168452 668168303 2.020000e-27 134.0


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 TraesCS3D01G058100 chr3D 24500645 24503865 3220 True 5949.000 5949 100.00000 1 3221 1 chr3D.!!$R1 3220
1 TraesCS3D01G058100 chr3D 581980860 581981497 637 True 985.000 985 94.54000 2583 3221 1 chr3D.!!$R2 638
2 TraesCS3D01G058100 chr3D 24334994 24336442 1448 True 541.675 1251 94.73925 573 2564 4 chr3D.!!$R4 1991
3 TraesCS3D01G058100 chr3D 24385169 24386617 1448 True 541.675 1245 94.78525 573 2564 4 chr3D.!!$R5 1991
4 TraesCS3D01G058100 chr3D 24287706 24289153 1447 True 540.425 1240 94.74100 573 2564 4 chr3D.!!$R3 1991
5 TraesCS3D01G058100 chr3B 42368598 42370567 1969 True 2595.000 2595 90.74900 620 2564 1 chr3B.!!$R1 1944
6 TraesCS3D01G058100 chr3A 34248246 34250391 2145 True 1432.000 2555 90.30550 570 2478 2 chr3A.!!$R3 1908
7 TraesCS3D01G058100 chr3A 34050451 34052586 2135 True 1399.500 2503 89.45950 570 2478 2 chr3A.!!$R1 1908
8 TraesCS3D01G058100 chr3A 737965654 737966225 571 False 872.000 872 94.24100 1 570 1 chr3A.!!$F1 569
9 TraesCS3D01G058100 chr5D 496312707 496313356 649 False 1016.000 1016 94.81700 2567 3221 1 chr5D.!!$F2 654
10 TraesCS3D01G058100 chr5D 468084263 468084904 641 False 983.000 983 94.39300 2583 3221 1 chr5D.!!$F1 638
11 TraesCS3D01G058100 chr5D 496923253 496923823 570 False 865.000 865 94.05600 1 569 1 chr5D.!!$F3 568
12 TraesCS3D01G058100 chr5D 51071773 51072340 567 True 859.000 859 94.03500 1 567 1 chr5D.!!$R1 566
13 TraesCS3D01G058100 chr6D 19618523 19619177 654 False 994.000 994 94.07300 2567 3221 1 chr6D.!!$F1 654
14 TraesCS3D01G058100 chr6D 452452439 452453077 638 True 994.000 994 94.84400 2587 3221 1 chr6D.!!$R2 634
15 TraesCS3D01G058100 chr6D 446734280 446734849 569 True 857.000 857 93.89200 1 569 1 chr6D.!!$R1 568
16 TraesCS3D01G058100 chr7D 93942265 93942904 639 True 992.000 992 94.69600 2583 3221 1 chr7D.!!$R1 638
17 TraesCS3D01G058100 chr7D 633914792 633915426 634 True 972.000 972 94.21900 2583 3221 1 chr7D.!!$R4 638
18 TraesCS3D01G058100 chr7D 608455401 608455968 567 True 854.000 854 93.86000 3 569 1 chr7D.!!$R2 566
19 TraesCS3D01G058100 chr7D 608473850 608474417 567 True 854.000 854 93.86000 3 569 1 chr7D.!!$R3 566
20 TraesCS3D01G058100 chr4D 296706575 296707203 628 True 981.000 981 94.92900 2596 3221 1 chr4D.!!$R1 625
21 TraesCS3D01G058100 chr2B 786255775 786256430 655 False 955.000 955 92.99800 2567 3221 1 chr2B.!!$F1 654
22 TraesCS3D01G058100 chrUn 74786583 74787151 568 False 861.000 861 94.04600 3 569 1 chrUn.!!$F1 566
23 TraesCS3D01G058100 chr6A 10484607 10485181 574 False 854.000 854 93.57600 1 572 1 chr6A.!!$F1 571
24 TraesCS3D01G058100 chr1D 439354564 439355137 573 True 854.000 854 93.57600 3 575 1 chr1D.!!$R1 572

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
504 512 1.064003 TGGGCTTCTGCACCTCTTTA 58.936 50.0 0.0 0.0 43.18 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2633 0.374758 CGTGAATGGACATTGGCGAG 59.625 55.0 1.69 0.0 31.0 5.03 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
45 48 3.570550 CAGATTTTACGTGGAAAACCCCA 59.429 43.478 0.00 0.00 31.35 4.96
104 108 7.995488 ACCAAAATCCTCTTCCACTATTATCAG 59.005 37.037 0.00 0.00 0.00 2.90
163 167 9.421806 CACTAGAGGATTTCATACATCAAGATC 57.578 37.037 0.00 0.00 0.00 2.75
166 170 7.377398 AGAGGATTTCATACATCAAGATCTCG 58.623 38.462 0.00 0.00 0.00 4.04
168 172 5.641209 GGATTTCATACATCAAGATCTCGGG 59.359 44.000 0.00 0.00 0.00 5.14
197 201 4.280677 GGATGAACACAACAAGATTTGGGA 59.719 41.667 0.00 0.00 33.76 4.37
313 320 1.450360 AGGAGCTCCCTTGGTTCTTT 58.550 50.000 29.54 3.28 44.85 2.52
327 334 6.266330 CCTTGGTTCTTTCTTCAATCTTCCTT 59.734 38.462 0.00 0.00 0.00 3.36
433 441 1.217942 GGAGGGTAAAGCATCCCCATT 59.782 52.381 1.48 0.00 44.40 3.16
459 467 5.011329 ACTCATGTGCAAAGTCCAAAATGAT 59.989 36.000 0.00 0.00 0.00 2.45
504 512 1.064003 TGGGCTTCTGCACCTCTTTA 58.936 50.000 0.00 0.00 43.18 1.85
635 643 5.406780 GCTCTACATCACCTGATATTTTCCG 59.593 44.000 0.00 0.00 32.63 4.30
645 653 5.418840 ACCTGATATTTTCCGAGCAAATGTT 59.581 36.000 0.00 0.00 0.00 2.71
719 956 2.151202 GCTCTCGGTTTTGTTCCATGA 58.849 47.619 0.00 0.00 0.00 3.07
827 1079 3.952811 GTTCTCAAACGGCTCGCT 58.047 55.556 0.00 0.00 0.00 4.93
869 1121 2.024871 GTCGCCAGGTCTCGATCG 59.975 66.667 9.36 9.36 37.06 3.69
915 1168 1.156645 AGCAGAATTCAGGCGATCGC 61.157 55.000 31.52 31.52 41.06 4.58
978 1233 3.511477 TGGGCCTGGCTAATTAAAAACA 58.489 40.909 19.68 0.11 0.00 2.83
1014 1269 3.152341 CATTCTCAGGTTTTGTCTGCCT 58.848 45.455 0.00 0.00 32.63 4.75
1023 1278 2.866156 GTTTTGTCTGCCTTTTTCTGCC 59.134 45.455 0.00 0.00 0.00 4.85
1034 1289 3.476552 CTTTTTCTGCCTGACCAGTACA 58.523 45.455 0.00 0.00 34.47 2.90
1045 1301 1.685224 CCAGTACATGGCCACACCT 59.315 57.895 8.16 0.00 43.83 4.00
1049 1305 3.009723 CAGTACATGGCCACACCTAAAG 58.990 50.000 8.16 0.00 40.22 1.85
1097 1358 1.947456 GGTGCCGAGGAATTATTGTCC 59.053 52.381 0.00 0.00 35.17 4.02
1100 1361 2.158813 TGCCGAGGAATTATTGTCCCTC 60.159 50.000 0.00 0.00 41.25 4.30
1106 1367 2.949644 GGAATTATTGTCCCTCGGGTTG 59.050 50.000 1.18 0.00 36.47 3.77
1141 1417 1.497309 CCCTCCAAGTTGGGCCTGTA 61.497 60.000 21.85 0.09 38.32 2.74
1142 1418 0.404040 CCTCCAAGTTGGGCCTGTAA 59.596 55.000 21.85 0.00 38.32 2.41
1175 1452 2.564975 CAAGCGCAAGGGAAGCAG 59.435 61.111 11.47 0.00 38.28 4.24
1193 1470 7.333174 GGGAAGCAGTCATATTCTAAATCTAGC 59.667 40.741 0.00 0.00 0.00 3.42
1207 1488 8.873215 TCTAAATCTAGCAGCATAACACTAAC 57.127 34.615 0.00 0.00 0.00 2.34
1208 1489 8.696374 TCTAAATCTAGCAGCATAACACTAACT 58.304 33.333 0.00 0.00 0.00 2.24
1209 1490 9.967346 CTAAATCTAGCAGCATAACACTAACTA 57.033 33.333 0.00 0.00 0.00 2.24
1211 1492 8.649973 AATCTAGCAGCATAACACTAACTAAC 57.350 34.615 0.00 0.00 0.00 2.34
1269 1550 3.512516 GCTCATGCCGCTTCACCC 61.513 66.667 0.00 0.00 0.00 4.61
1383 1664 2.680352 GGAGAGGAGTGGCGTGGA 60.680 66.667 0.00 0.00 0.00 4.02
1391 1672 1.557443 GAGTGGCGTGGACTTTGTCG 61.557 60.000 0.00 0.00 32.65 4.35
1392 1673 1.885850 GTGGCGTGGACTTTGTCGT 60.886 57.895 0.00 0.00 32.65 4.34
1396 1677 2.935955 GTGGACTTTGTCGTGCCG 59.064 61.111 0.00 0.00 32.65 5.69
1481 1786 3.880033 AACCCCTGGAGGAGCTGCT 62.880 63.158 7.79 7.79 38.24 4.24
1549 1854 2.022625 TCTCACTCTTCCCCTCCATGAT 60.023 50.000 0.00 0.00 0.00 2.45
1580 1885 1.193644 CTCGTCAACGTTCGTGTTCA 58.806 50.000 0.00 0.00 40.80 3.18
1628 1933 4.802051 GAAGCATGCCGGCCTCCA 62.802 66.667 26.77 4.98 0.00 3.86
1655 1960 1.004560 CCGGAGAGCAAGCTCAACA 60.005 57.895 22.68 0.00 44.99 3.33
1729 2034 2.995872 GCTCAACGACCGCCTCTCT 61.996 63.158 0.00 0.00 0.00 3.10
1744 2049 0.106469 TCTCTATGCTCCGCTCCACT 60.106 55.000 0.00 0.00 0.00 4.00
1941 2289 1.411074 GGGCGGATTAAAACCCTGGAT 60.411 52.381 0.00 0.00 39.42 3.41
2004 2352 0.539438 ATTTCTCCAGCGGTGGCAAA 60.539 50.000 28.72 25.98 44.60 3.68
2067 2415 4.070552 GAGAACCGAGGCGCAGGT 62.071 66.667 10.83 13.02 43.68 4.00
2090 2438 4.180057 GACACGAAGATTGAGATCTGCTT 58.820 43.478 0.00 0.00 41.78 3.91
2128 2476 1.374125 CTGATCGCAACGGTGACCA 60.374 57.895 3.55 0.00 36.14 4.02
2209 2557 3.040206 ATGCAGGCCTCGTGCTCAT 62.040 57.895 15.70 4.57 44.26 2.90
2248 2596 8.235230 TCCTTCTGAAATAGTACCCATCTCTAT 58.765 37.037 0.00 0.00 0.00 1.98
2283 2631 5.112220 TGCATGCTAATGAAATTCGATCC 57.888 39.130 20.33 0.00 37.87 3.36
2284 2632 4.579753 TGCATGCTAATGAAATTCGATCCA 59.420 37.500 20.33 0.00 37.87 3.41
2285 2633 4.913924 GCATGCTAATGAAATTCGATCCAC 59.086 41.667 11.37 0.00 37.87 4.02
2286 2634 5.278169 GCATGCTAATGAAATTCGATCCACT 60.278 40.000 11.37 0.00 37.87 4.00
2287 2635 5.991328 TGCTAATGAAATTCGATCCACTC 57.009 39.130 0.00 0.00 37.87 3.51
2382 2730 1.246056 GCAGGCATTGTTGAGGAGCA 61.246 55.000 0.00 0.00 0.00 4.26
2398 2747 4.003788 CACAGGCGACGGGGAAGT 62.004 66.667 0.00 0.00 0.00 3.01
2473 2822 6.966632 TGAATACGTGCTAGATTTGCATTTTC 59.033 34.615 0.00 0.00 42.69 2.29
2551 2901 7.361457 TGGGACTATCTTCGATGAGTATTTT 57.639 36.000 7.14 0.00 0.00 1.82
2687 3039 8.103305 TCACTGCTCAATTTAACCTCTAATCTT 58.897 33.333 0.00 0.00 0.00 2.40
2758 3110 2.206223 TCCTCTCACTACTCCAGCCTA 58.794 52.381 0.00 0.00 0.00 3.93
2800 3152 4.467198 TCTATTCTCCCTCGTTTCCAAC 57.533 45.455 0.00 0.00 0.00 3.77
2870 3223 3.589288 ACCCTCAGGAATTTAGCTTGAGT 59.411 43.478 0.00 0.00 37.67 3.41
2895 3248 5.879237 TGAAGTCACACATTTCACTGTTTC 58.121 37.500 0.00 0.00 0.00 2.78
2971 3326 7.416154 TTCTTGAATAAGTAGTTTGACCACG 57.584 36.000 0.00 0.00 35.38 4.94
2997 3354 8.360390 GGTTTGACTAGATTTGACCAAAATTCT 58.640 33.333 0.00 2.28 38.64 2.40
2998 3355 9.185192 GTTTGACTAGATTTGACCAAAATTCTG 57.815 33.333 0.00 3.32 38.64 3.02
3081 3439 2.849942 TGACCACAGTTTGACCAGATG 58.150 47.619 0.00 0.00 0.00 2.90
3093 3451 4.852134 TGACCAGATGTGACCAAAATTG 57.148 40.909 0.00 0.00 0.00 2.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.999431 GTAAAATCTGGTGTCTCTTTGTTGATA 58.001 33.333 0.00 0.00 0.00 2.15
81 85 9.790344 CATCTGATAATAGTGGAAGAGGATTTT 57.210 33.333 0.00 0.00 0.00 1.82
104 108 5.940470 AGAAGAACTTGTTGTATCCCACATC 59.060 40.000 0.00 0.00 36.90 3.06
148 152 6.030548 GATCCCGAGATCTTGATGTATGAA 57.969 41.667 11.89 0.00 44.78 2.57
163 167 2.093500 TGTGTTCATCCAAGATCCCGAG 60.093 50.000 0.00 0.00 0.00 4.63
166 170 3.420893 TGTTGTGTTCATCCAAGATCCC 58.579 45.455 0.00 0.00 0.00 3.85
168 172 5.947228 TCTTGTTGTGTTCATCCAAGATC 57.053 39.130 0.00 0.00 37.18 2.75
197 201 5.701224 TGTTCCAATCCCTAGTTTTTGAGT 58.299 37.500 0.00 0.00 0.00 3.41
203 208 5.946377 GTGAGATTGTTCCAATCCCTAGTTT 59.054 40.000 12.13 0.00 0.00 2.66
242 247 1.273606 CTTGTCTCCTTCAAGCTCCGA 59.726 52.381 0.00 0.00 36.38 4.55
245 250 2.849294 ACCTTGTCTCCTTCAAGCTC 57.151 50.000 0.00 0.00 40.35 4.09
307 314 9.457110 GAAGAAAAGGAAGATTGAAGAAAGAAC 57.543 33.333 0.00 0.00 0.00 3.01
313 320 6.206180 AGGGAAGAAAAGGAAGATTGAAGA 57.794 37.500 0.00 0.00 0.00 2.87
327 334 2.443255 ACCAAGAGAGCAAGGGAAGAAA 59.557 45.455 0.00 0.00 0.00 2.52
719 956 0.534873 AAACAAAAACAGTGCGGGCT 59.465 45.000 0.00 0.00 0.00 5.19
811 1063 0.388649 GAGAGCGAGCCGTTTGAGAA 60.389 55.000 0.00 0.00 0.00 2.87
826 1078 1.278337 CGATCGAGCGACAGGAGAG 59.722 63.158 20.02 0.00 0.00 3.20
827 1079 2.180862 CCGATCGAGCGACAGGAGA 61.181 63.158 26.68 0.00 0.00 3.71
886 1139 3.997021 CCTGAATTCTGCTACTGTTTCGT 59.003 43.478 7.05 0.00 0.00 3.85
915 1168 5.509605 TCAATTATCGTCAGTGTCGTTTG 57.490 39.130 9.53 9.38 0.00 2.93
978 1233 4.050037 TGAGAATGGAATGGAATCTCCCT 58.950 43.478 0.00 0.00 36.54 4.20
1014 1269 3.569194 TGTACTGGTCAGGCAGAAAAA 57.431 42.857 2.87 0.00 0.00 1.94
1034 1289 2.505819 CTCCTACTTTAGGTGTGGCCAT 59.494 50.000 9.72 0.00 46.32 4.40
1045 1301 6.324601 AGTAGCTACTCCACTCCTACTTTA 57.675 41.667 20.95 0.00 36.28 1.85
1049 1305 3.067040 GCAAGTAGCTACTCCACTCCTAC 59.933 52.174 26.21 0.49 41.15 3.18
1097 1358 1.971695 GGAAGCAACCAACCCGAGG 60.972 63.158 0.00 0.00 0.00 4.63
1100 1361 2.593436 ACGGAAGCAACCAACCCG 60.593 61.111 0.00 0.00 45.09 5.28
1106 1367 2.671963 GGGGTCACGGAAGCAACC 60.672 66.667 0.00 0.00 38.03 3.77
1193 1470 6.170506 TCCCTTGTTAGTTAGTGTTATGCTG 58.829 40.000 0.00 0.00 0.00 4.41
1205 1486 2.421529 GCGGATCCATCCCTTGTTAGTT 60.422 50.000 13.41 0.00 44.24 2.24
1206 1487 1.141053 GCGGATCCATCCCTTGTTAGT 59.859 52.381 13.41 0.00 44.24 2.24
1207 1488 1.417890 AGCGGATCCATCCCTTGTTAG 59.582 52.381 13.41 0.00 44.24 2.34
1208 1489 1.507140 AGCGGATCCATCCCTTGTTA 58.493 50.000 13.41 0.00 44.24 2.41
1209 1490 0.625849 AAGCGGATCCATCCCTTGTT 59.374 50.000 13.41 0.00 44.24 2.83
1210 1491 0.107017 CAAGCGGATCCATCCCTTGT 60.107 55.000 13.41 0.00 43.10 3.16
1211 1492 0.181114 TCAAGCGGATCCATCCCTTG 59.819 55.000 20.35 20.35 45.92 3.61
1361 1642 3.151022 GCCACTCCTCTCCTCGGG 61.151 72.222 0.00 0.00 0.00 5.14
1391 1672 4.043200 GGGCTGCTGAAACGGCAC 62.043 66.667 0.00 0.00 41.16 5.01
1392 1673 3.866379 ATGGGCTGCTGAAACGGCA 62.866 57.895 0.00 5.18 44.04 5.69
1481 1786 3.003173 CGCAGGAGGGTCAGGGAA 61.003 66.667 0.00 0.00 0.00 3.97
1528 1833 1.362584 TCATGGAGGGGAAGAGTGAGA 59.637 52.381 0.00 0.00 0.00 3.27
1606 1911 2.123428 GGCCGGCATGCTTCTCATT 61.123 57.895 30.85 0.00 31.79 2.57
1677 1982 1.032114 CCTTTCCGCCATGAGGTTCC 61.032 60.000 0.00 0.00 37.19 3.62
1704 2009 2.048127 GGTCGTTGAGCCGCTTCT 60.048 61.111 0.00 0.00 0.00 2.85
1744 2049 1.075374 ACCTTGCTAATCTTGGGCACA 59.925 47.619 0.00 0.00 35.62 4.57
1771 2076 1.002468 CAGAAATTAAGGGCGATGCGG 60.002 52.381 0.00 0.00 0.00 5.69
1849 2197 2.544486 CCATCTGCAGTTCGATCGATCA 60.544 50.000 24.40 15.92 0.00 2.92
1941 2289 3.838271 GTGGCGCCGATCTCCTCA 61.838 66.667 23.90 0.00 0.00 3.86
2004 2352 2.820479 CTCGTCGGCGTCTCCTCT 60.820 66.667 10.18 0.00 39.49 3.69
2063 2411 3.303881 TCTCAATCTTCGTGTCACCTG 57.696 47.619 0.00 0.00 0.00 4.00
2067 2415 3.194329 AGCAGATCTCAATCTTCGTGTCA 59.806 43.478 0.00 0.00 40.38 3.58
2090 2438 2.970639 CTCCGGGCTTTGTCGAGA 59.029 61.111 0.00 0.00 0.00 4.04
2118 2466 3.542676 TCCAGCGTGGTCACCGTT 61.543 61.111 0.00 0.00 39.03 4.44
2283 2631 1.131126 GTGAATGGACATTGGCGAGTG 59.869 52.381 1.69 0.00 0.00 3.51
2284 2632 1.453155 GTGAATGGACATTGGCGAGT 58.547 50.000 1.69 0.00 0.00 4.18
2285 2633 0.374758 CGTGAATGGACATTGGCGAG 59.625 55.000 1.69 0.00 31.00 5.03
2286 2634 1.024046 CCGTGAATGGACATTGGCGA 61.024 55.000 14.94 0.00 31.00 5.54
2287 2635 1.429021 CCGTGAATGGACATTGGCG 59.571 57.895 1.69 6.57 0.00 5.69
2382 2730 3.239253 AACTTCCCCGTCGCCTGT 61.239 61.111 0.00 0.00 0.00 4.00
2388 2736 3.132467 AGCTTATAGACAACTTCCCCGTC 59.868 47.826 0.00 0.00 0.00 4.79
2473 2822 2.231235 GCCCCCACAAAGTCATGTAAAG 59.769 50.000 0.00 0.00 30.84 1.85
2527 2877 6.978674 AAATACTCATCGAAGATAGTCCCA 57.021 37.500 0.00 0.00 45.12 4.37
2551 2901 9.015367 TCATAAAATTTCTTATCCGGTGACAAA 57.985 29.630 0.00 0.00 0.00 2.83
2654 3006 3.726557 AAATTGAGCAGTGATGAGGGA 57.273 42.857 0.00 0.00 0.00 4.20
2687 3039 5.464588 TTGGAATGATGAGGGGTGATTAA 57.535 39.130 0.00 0.00 0.00 1.40
2736 3088 1.960689 GGCTGGAGTAGTGAGAGGATC 59.039 57.143 0.00 0.00 0.00 3.36
2758 3110 0.953960 CCCGGAAGTTAAGCGTGCTT 60.954 55.000 12.30 12.30 39.83 3.91
2800 3152 4.795278 GTCAGAAAAACAACAAGTGCAGAG 59.205 41.667 0.00 0.00 0.00 3.35
2870 3223 7.281999 TGAAACAGTGAAATGTGTGACTTCATA 59.718 33.333 0.00 0.00 32.52 2.15
2971 3326 8.360390 AGAATTTTGGTCAAATCTAGTCAAACC 58.640 33.333 0.00 0.00 33.60 3.27


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

AutoCloner maintained by Alex Coulton.