Multiple sequence alignment - TraesCS3D01G434000

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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 TraesCS3D01G434000 chr3D 100.000 2357 0 0 1 2357 546696326 546698682 0.000000e+00 4353.0
1 TraesCS3D01G434000 chr3D 94.611 1336 58 7 633 1954 584701386 584700051 0.000000e+00 2056.0
2 TraesCS3D01G434000 chr3D 94.679 1090 45 3 631 1707 613711274 613712363 0.000000e+00 1679.0
3 TraesCS3D01G434000 chr3D 86.341 205 16 6 382 575 500002345 500002142 1.830000e-51 213.0
4 TraesCS3D01G434000 chr3D 88.793 116 9 3 443 554 420810455 420810340 3.160000e-29 139.0
5 TraesCS3D01G434000 chr3D 79.769 173 21 7 202 366 420810880 420810714 1.910000e-21 113.0
6 TraesCS3D01G434000 chr2D 95.138 1337 51 7 633 1955 73126866 73125530 0.000000e+00 2097.0
7 TraesCS3D01G434000 chr2D 94.170 1355 60 10 630 1967 621748805 621750157 0.000000e+00 2047.0
8 TraesCS3D01G434000 chr2D 94.300 1193 52 7 781 1958 36804621 36803430 0.000000e+00 1812.0
9 TraesCS3D01G434000 chr1D 95.075 1340 51 5 633 1958 60171809 60170471 0.000000e+00 2095.0
10 TraesCS3D01G434000 chr1D 94.498 1345 56 6 633 1961 247505752 247504410 0.000000e+00 2058.0
11 TraesCS3D01G434000 chr1D 94.520 1332 54 8 633 1950 205134691 205133365 0.000000e+00 2037.0
12 TraesCS3D01G434000 chr1D 93.745 1343 67 7 630 1958 461539162 461540501 0.000000e+00 1999.0
13 TraesCS3D01G434000 chr1D 82.857 105 9 4 381 476 493604696 493604800 4.170000e-13 86.1
14 TraesCS3D01G434000 chr1D 86.441 59 2 2 486 544 493604790 493604842 2.530000e-05 60.2
15 TraesCS3D01G434000 chr7D 94.461 1336 58 9 630 1951 497560910 497562243 0.000000e+00 2043.0
16 TraesCS3D01G434000 chr4A 93.467 1347 71 7 630 1962 66588366 66589709 0.000000e+00 1984.0
17 TraesCS3D01G434000 chr4A 91.026 156 14 0 381 536 383538341 383538496 6.600000e-51 211.0
18 TraesCS3D01G434000 chr4A 85.577 104 12 2 423 525 13764476 13764577 3.200000e-19 106.0
19 TraesCS3D01G434000 chr7B 93.939 1320 63 7 633 1937 720163383 720162066 0.000000e+00 1978.0
20 TraesCS3D01G434000 chr1A 93.145 1342 71 7 633 1958 497343319 497341983 0.000000e+00 1949.0
21 TraesCS3D01G434000 chr1A 86.441 59 2 2 486 544 591927132 591927184 2.530000e-05 60.2
22 TraesCS3D01G434000 chr6A 93.829 1183 60 3 633 1802 13879205 13878023 0.000000e+00 1768.0
23 TraesCS3D01G434000 chr6A 87.571 177 19 3 381 554 430502114 430502290 3.970000e-48 202.0
24 TraesCS3D01G434000 chr6A 85.897 78 10 1 307 384 430501989 430502065 5.400000e-12 82.4
25 TraesCS3D01G434000 chr3A 94.637 634 20 7 1 631 683434600 683435222 0.000000e+00 970.0
26 TraesCS3D01G434000 chr3A 97.668 343 8 0 2015 2357 683435207 683435549 7.260000e-165 590.0
27 TraesCS3D01G434000 chr3A 85.366 205 18 6 382 575 639501707 639501504 3.970000e-48 202.0
28 TraesCS3D01G434000 chr3A 83.598 189 25 1 197 379 600924253 600924065 3.110000e-39 172.0
29 TraesCS3D01G434000 chr3A 86.111 144 12 7 441 577 530190834 530190976 5.250000e-32 148.0
30 TraesCS3D01G434000 chr3A 80.851 188 20 10 197 384 116532097 116532268 1.470000e-27 134.0
31 TraesCS3D01G434000 chr3B 91.236 639 21 11 1 633 723788679 723789288 0.000000e+00 837.0
32 TraesCS3D01G434000 chr3B 97.391 345 9 0 2013 2357 723789275 723789619 2.610000e-164 588.0
33 TraesCS3D01G434000 chr3B 87.006 177 13 4 382 549 661342862 661342687 8.600000e-45 191.0
34 TraesCS3D01G434000 chr3B 85.106 188 19 5 197 384 149469504 149469682 1.440000e-42 183.0
35 TraesCS3D01G434000 chr4D 91.026 156 14 0 381 536 253777243 253777398 6.600000e-51 211.0
36 TraesCS3D01G434000 chr4D 83.193 119 12 7 411 523 453312445 453312329 4.140000e-18 102.0
37 TraesCS3D01G434000 chr6D 83.938 193 22 7 199 388 432451053 432451239 2.410000e-40 176.0
38 TraesCS3D01G434000 chr2B 83.069 189 29 2 198 384 26564799 26564612 4.030000e-38 169.0
39 TraesCS3D01G434000 chr5B 81.915 188 27 5 202 384 294131694 294131509 4.060000e-33 152.0
40 TraesCS3D01G434000 chr2A 81.818 187 23 5 198 384 16861762 16861587 1.890000e-31 147.0
41 TraesCS3D01G434000 chr5D 83.333 144 15 8 441 577 471427190 471427049 8.840000e-25 124.0
42 TraesCS3D01G434000 chr6B 94.366 71 4 0 202 272 455077963 455077893 2.480000e-20 110.0
43 TraesCS3D01G434000 chr1B 86.441 59 2 2 486 544 685720830 685720882 2.530000e-05 60.2
44 TraesCS3D01G434000 chr4B 92.500 40 3 0 326 365 652317296 652317335 9.100000e-05 58.4


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 TraesCS3D01G434000 chr3D 546696326 546698682 2356 False 4353.0 4353 100.0000 1 2357 1 chr3D.!!$F1 2356
1 TraesCS3D01G434000 chr3D 584700051 584701386 1335 True 2056.0 2056 94.6110 633 1954 1 chr3D.!!$R2 1321
2 TraesCS3D01G434000 chr3D 613711274 613712363 1089 False 1679.0 1679 94.6790 631 1707 1 chr3D.!!$F2 1076
3 TraesCS3D01G434000 chr2D 73125530 73126866 1336 True 2097.0 2097 95.1380 633 1955 1 chr2D.!!$R2 1322
4 TraesCS3D01G434000 chr2D 621748805 621750157 1352 False 2047.0 2047 94.1700 630 1967 1 chr2D.!!$F1 1337
5 TraesCS3D01G434000 chr2D 36803430 36804621 1191 True 1812.0 1812 94.3000 781 1958 1 chr2D.!!$R1 1177
6 TraesCS3D01G434000 chr1D 60170471 60171809 1338 True 2095.0 2095 95.0750 633 1958 1 chr1D.!!$R1 1325
7 TraesCS3D01G434000 chr1D 247504410 247505752 1342 True 2058.0 2058 94.4980 633 1961 1 chr1D.!!$R3 1328
8 TraesCS3D01G434000 chr1D 205133365 205134691 1326 True 2037.0 2037 94.5200 633 1950 1 chr1D.!!$R2 1317
9 TraesCS3D01G434000 chr1D 461539162 461540501 1339 False 1999.0 1999 93.7450 630 1958 1 chr1D.!!$F1 1328
10 TraesCS3D01G434000 chr7D 497560910 497562243 1333 False 2043.0 2043 94.4610 630 1951 1 chr7D.!!$F1 1321
11 TraesCS3D01G434000 chr4A 66588366 66589709 1343 False 1984.0 1984 93.4670 630 1962 1 chr4A.!!$F2 1332
12 TraesCS3D01G434000 chr7B 720162066 720163383 1317 True 1978.0 1978 93.9390 633 1937 1 chr7B.!!$R1 1304
13 TraesCS3D01G434000 chr1A 497341983 497343319 1336 True 1949.0 1949 93.1450 633 1958 1 chr1A.!!$R1 1325
14 TraesCS3D01G434000 chr6A 13878023 13879205 1182 True 1768.0 1768 93.8290 633 1802 1 chr6A.!!$R1 1169
15 TraesCS3D01G434000 chr3A 683434600 683435549 949 False 780.0 970 96.1525 1 2357 2 chr3A.!!$F3 2356
16 TraesCS3D01G434000 chr3B 723788679 723789619 940 False 712.5 837 94.3135 1 2357 2 chr3B.!!$F2 2356

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
624 642 0.108138 ATTAGTGCTTCCGCTTCGCT 60.108 50.0 0.0 0.0 36.97 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1992 2038 0.108585 TTTGACTGCACCAGGACCTC 59.891 55.0 0.0 0.0 35.51 3.85 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
55 56 5.567623 GCTGTCTCCTTGTATTGACTCTTCA 60.568 44.000 0.00 0.00 0.00 3.02
60 61 8.200792 GTCTCCTTGTATTGACTCTTCATGTAT 58.799 37.037 0.00 0.00 0.00 2.29
116 118 7.769044 AGTTGTGTTTAGTGTTGACTCTACATT 59.231 33.333 0.00 0.00 31.79 2.71
223 225 7.275560 GCACTGTTCATGAAAGTGTTTTTAAGT 59.724 33.333 30.07 14.23 42.65 2.24
554 560 7.127686 CAGTCAAATTCTGGCATTTTGAAAAC 58.872 34.615 16.86 9.37 40.08 2.43
560 566 4.545610 TCTGGCATTTTGAAAACGCTTAG 58.454 39.130 8.64 7.69 0.00 2.18
561 567 4.037446 TCTGGCATTTTGAAAACGCTTAGT 59.963 37.500 8.64 0.00 0.00 2.24
562 568 4.047822 TGGCATTTTGAAAACGCTTAGTG 58.952 39.130 8.64 0.00 0.00 2.74
563 569 3.121025 GGCATTTTGAAAACGCTTAGTGC 60.121 43.478 8.64 5.29 38.57 4.40
564 570 3.489047 GCATTTTGAAAACGCTTAGTGCA 59.511 39.130 1.02 0.00 43.06 4.57
565 571 4.375305 GCATTTTGAAAACGCTTAGTGCAG 60.375 41.667 1.02 0.00 43.06 4.41
566 572 2.399396 TTGAAAACGCTTAGTGCAGC 57.601 45.000 0.00 0.00 43.06 5.25
567 573 1.593196 TGAAAACGCTTAGTGCAGCT 58.407 45.000 0.00 0.00 43.06 4.24
568 574 1.946768 TGAAAACGCTTAGTGCAGCTT 59.053 42.857 0.00 0.00 43.06 3.74
569 575 3.135225 TGAAAACGCTTAGTGCAGCTTA 58.865 40.909 0.00 0.00 43.06 3.09
570 576 3.562141 TGAAAACGCTTAGTGCAGCTTAA 59.438 39.130 0.00 0.00 43.06 1.85
571 577 3.813529 AAACGCTTAGTGCAGCTTAAG 57.186 42.857 0.00 0.00 43.06 1.85
572 578 1.079503 ACGCTTAGTGCAGCTTAAGC 58.920 50.000 20.09 20.09 43.06 3.09
621 639 2.317530 AGGATTAGTGCTTCCGCTTC 57.682 50.000 0.00 0.00 37.10 3.86
622 640 0.931005 GGATTAGTGCTTCCGCTTCG 59.069 55.000 0.00 0.00 36.97 3.79
623 641 0.301987 GATTAGTGCTTCCGCTTCGC 59.698 55.000 0.00 0.00 36.97 4.70
624 642 0.108138 ATTAGTGCTTCCGCTTCGCT 60.108 50.000 0.00 0.00 36.97 4.93
625 643 0.320421 TTAGTGCTTCCGCTTCGCTT 60.320 50.000 0.00 0.00 36.97 4.68
626 644 0.320421 TAGTGCTTCCGCTTCGCTTT 60.320 50.000 0.00 0.00 36.97 3.51
627 645 1.441016 GTGCTTCCGCTTCGCTTTG 60.441 57.895 0.00 0.00 36.97 2.77
628 646 2.502726 GCTTCCGCTTCGCTTTGC 60.503 61.111 0.00 0.00 0.00 3.68
640 658 5.739161 CGCTTCGCTTTGCTTATTAGAAAAT 59.261 36.000 0.00 0.00 28.42 1.82
730 748 9.623000 ACAAAAGACCTTACAAAGTAGTACATT 57.377 29.630 2.52 0.00 0.00 2.71
766 784 3.614092 CACCATCTAGGCAACATCTGTT 58.386 45.455 0.00 0.00 43.14 3.16
833 851 2.831685 TACCAAACAGACATCGCACT 57.168 45.000 0.00 0.00 0.00 4.40
1065 1085 0.952280 ATCCGTCGTCGATATGCAGT 59.048 50.000 2.98 0.00 39.71 4.40
1081 1101 4.424566 GTTGCACCATGCCGCCAG 62.425 66.667 0.00 0.00 44.23 4.85
1307 1328 3.992641 GAGGGGTTTGGGGGTGGG 61.993 72.222 0.00 0.00 0.00 4.61
1311 1333 2.164967 GGGTTTGGGGGTGGGTAGT 61.165 63.158 0.00 0.00 0.00 2.73
1343 1365 1.262640 TTCGCCTCCAGGAAGGGTAC 61.263 60.000 2.14 0.00 36.88 3.34
1383 1418 1.153168 ATGCCGGACCTTGGATTCG 60.153 57.895 5.05 0.00 0.00 3.34
1384 1419 2.513897 GCCGGACCTTGGATTCGG 60.514 66.667 5.05 12.59 43.13 4.30
1396 1431 3.415650 GATTCGGCCGGTCCCCATT 62.416 63.158 27.83 0.06 0.00 3.16
1492 1527 0.110486 GGCTCAACCCACCAGAAAGA 59.890 55.000 0.00 0.00 0.00 2.52
1542 1577 0.108329 AGACGCCGAATCCAACGATT 60.108 50.000 0.00 0.00 41.57 3.34
1553 1588 1.736645 CAACGATTCGACGTGGCCT 60.737 57.895 13.95 0.00 45.83 5.19
1765 1806 2.281276 GTTCGCCCGGTGTTCCTT 60.281 61.111 0.00 0.00 0.00 3.36
1967 2013 2.125512 CGAGGGGCGAGACCAAAG 60.126 66.667 0.00 0.00 44.57 2.77
1968 2014 2.436824 GAGGGGCGAGACCAAAGC 60.437 66.667 0.00 0.00 42.05 3.51
1972 2018 2.665603 GGCGAGACCAAAGCCTCT 59.334 61.111 0.00 0.00 46.83 3.69
1973 2019 1.743252 GGCGAGACCAAAGCCTCTG 60.743 63.158 0.00 0.00 46.83 3.35
1974 2020 1.743252 GCGAGACCAAAGCCTCTGG 60.743 63.158 0.00 0.00 40.05 3.86
1975 2021 1.975327 CGAGACCAAAGCCTCTGGA 59.025 57.895 0.00 0.00 37.40 3.86
1976 2022 0.321671 CGAGACCAAAGCCTCTGGAA 59.678 55.000 0.00 0.00 37.40 3.53
1977 2023 1.270839 CGAGACCAAAGCCTCTGGAAA 60.271 52.381 0.00 0.00 37.40 3.13
1978 2024 2.431454 GAGACCAAAGCCTCTGGAAAG 58.569 52.381 0.00 0.00 37.40 2.62
1979 2025 1.777272 AGACCAAAGCCTCTGGAAAGT 59.223 47.619 0.00 0.00 37.40 2.66
1980 2026 2.155279 GACCAAAGCCTCTGGAAAGTC 58.845 52.381 0.00 0.00 37.40 3.01
1981 2027 1.202940 ACCAAAGCCTCTGGAAAGTCC 60.203 52.381 0.00 0.00 37.40 3.85
1982 2028 1.074566 CCAAAGCCTCTGGAAAGTCCT 59.925 52.381 0.00 0.00 37.46 3.85
1983 2029 2.431454 CAAAGCCTCTGGAAAGTCCTC 58.569 52.381 0.00 0.00 37.46 3.71
1984 2030 1.734655 AAGCCTCTGGAAAGTCCTCA 58.265 50.000 0.00 0.00 37.46 3.86
1985 2031 1.274712 AGCCTCTGGAAAGTCCTCAG 58.725 55.000 0.00 0.00 37.46 3.35
1986 2032 0.980423 GCCTCTGGAAAGTCCTCAGT 59.020 55.000 0.00 0.00 37.46 3.41
1987 2033 2.180276 GCCTCTGGAAAGTCCTCAGTA 58.820 52.381 0.00 0.00 37.46 2.74
1988 2034 2.769095 GCCTCTGGAAAGTCCTCAGTAT 59.231 50.000 0.00 0.00 37.46 2.12
1989 2035 3.431486 GCCTCTGGAAAGTCCTCAGTATG 60.431 52.174 0.00 0.00 37.46 2.39
1990 2036 3.431486 CCTCTGGAAAGTCCTCAGTATGC 60.431 52.174 0.00 0.00 37.46 3.14
1991 2037 2.166459 TCTGGAAAGTCCTCAGTATGCG 59.834 50.000 0.00 0.00 37.46 4.73
1992 2038 1.207089 TGGAAAGTCCTCAGTATGCGG 59.793 52.381 0.00 0.00 43.99 5.69
1997 2043 2.808598 TCCTCAGTATGCGGAGGTC 58.191 57.895 24.75 0.00 46.76 3.85
1998 2044 0.755698 TCCTCAGTATGCGGAGGTCC 60.756 60.000 24.75 0.00 46.76 4.46
1999 2045 0.757188 CCTCAGTATGCGGAGGTCCT 60.757 60.000 19.39 0.00 46.02 3.85
2000 2046 0.387202 CTCAGTATGCGGAGGTCCTG 59.613 60.000 0.00 0.00 34.07 3.86
2001 2047 1.043116 TCAGTATGCGGAGGTCCTGG 61.043 60.000 0.00 0.00 34.76 4.45
2002 2048 1.001760 AGTATGCGGAGGTCCTGGT 59.998 57.895 0.00 0.00 0.00 4.00
2003 2049 1.144057 GTATGCGGAGGTCCTGGTG 59.856 63.158 0.00 0.00 0.00 4.17
2004 2050 2.731571 TATGCGGAGGTCCTGGTGC 61.732 63.158 0.00 0.00 0.00 5.01
2006 2052 4.767255 GCGGAGGTCCTGGTGCAG 62.767 72.222 0.00 0.00 0.00 4.41
2007 2053 3.314331 CGGAGGTCCTGGTGCAGT 61.314 66.667 0.00 0.00 0.00 4.40
2008 2054 2.665603 GGAGGTCCTGGTGCAGTC 59.334 66.667 0.00 0.00 0.00 3.51
2009 2055 2.217038 GGAGGTCCTGGTGCAGTCA 61.217 63.158 0.00 0.00 0.00 3.41
2010 2056 1.754745 GAGGTCCTGGTGCAGTCAA 59.245 57.895 0.00 0.00 0.00 3.18
2011 2057 0.108585 GAGGTCCTGGTGCAGTCAAA 59.891 55.000 0.00 0.00 0.00 2.69
2012 2058 0.773644 AGGTCCTGGTGCAGTCAAAT 59.226 50.000 0.00 0.00 0.00 2.32
2013 2059 1.145738 AGGTCCTGGTGCAGTCAAATT 59.854 47.619 0.00 0.00 0.00 1.82
2019 2065 1.680735 TGGTGCAGTCAAATTCGCTTT 59.319 42.857 0.00 0.00 0.00 3.51
2032 2078 4.708726 ATTCGCTTTGCTTATGCTTTCT 57.291 36.364 1.96 0.00 40.48 2.52
2129 2175 3.897239 CTGGGTGCAATTGTAATCCCTA 58.103 45.455 18.86 5.86 36.23 3.53
2214 2260 8.654230 TGATTCATGCTAGAGTAGAATTTGTC 57.346 34.615 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 7.148272 ACAGCGGTTTGTTACTTAAGTTTTGTA 60.148 33.333 14.49 0.00 0.00 2.41
74 76 2.750712 ACAACTTGTACAGCGGTTTGTT 59.249 40.909 0.00 0.00 32.56 2.83
116 118 7.599621 GCTGACGACTGTTATACTCTCTAGATA 59.400 40.741 0.00 0.00 0.00 1.98
137 139 1.719780 CGTGAAAAGTAGTCGGCTGAC 59.280 52.381 18.39 18.39 45.86 3.51
385 391 7.933033 ACCAATTAAAATGCAGTTCAGTTCAAT 59.067 29.630 0.00 0.00 30.90 2.57
478 484 6.062095 AGGAAACATAGCACACAAGTAACTT 58.938 36.000 0.00 0.00 0.00 2.66
621 639 6.785191 TCCTCATTTTCTAATAAGCAAAGCG 58.215 36.000 0.00 0.00 0.00 4.68
622 640 7.168804 GCATCCTCATTTTCTAATAAGCAAAGC 59.831 37.037 0.00 0.00 0.00 3.51
623 641 8.192774 TGCATCCTCATTTTCTAATAAGCAAAG 58.807 33.333 0.00 0.00 0.00 2.77
624 642 7.975616 GTGCATCCTCATTTTCTAATAAGCAAA 59.024 33.333 0.00 0.00 0.00 3.68
625 643 7.416664 GGTGCATCCTCATTTTCTAATAAGCAA 60.417 37.037 0.00 0.00 0.00 3.91
626 644 6.039717 GGTGCATCCTCATTTTCTAATAAGCA 59.960 38.462 0.00 0.00 0.00 3.91
627 645 6.442112 GGTGCATCCTCATTTTCTAATAAGC 58.558 40.000 0.00 0.00 0.00 3.09
628 646 6.015940 GGGGTGCATCCTCATTTTCTAATAAG 60.016 42.308 17.44 0.00 36.51 1.73
730 748 1.651737 TGGTGGCTTCAGGCTTACTA 58.348 50.000 1.64 0.00 41.69 1.82
766 784 0.714180 TCAAGGGGGTAGGAGTAGCA 59.286 55.000 0.00 0.00 0.00 3.49
833 851 6.428083 TCCGGCATTAGATGTTAGGATTTA 57.572 37.500 0.00 0.00 0.00 1.40
1099 1119 1.226773 GCGGCGTTGTATCTACCGT 60.227 57.895 9.37 0.00 45.53 4.83
1124 1144 1.678970 GATGGTGTGGAGGTTGCCC 60.679 63.158 0.00 0.00 0.00 5.36
1298 1319 4.686437 CCCCACTACCCACCCCCA 62.686 72.222 0.00 0.00 0.00 4.96
1307 1328 0.035343 GAAGCCAAGGTCCCCACTAC 60.035 60.000 0.00 0.00 0.00 2.73
1375 1410 4.104183 GGGACCGGCCGAATCCAA 62.104 66.667 35.18 0.00 37.63 3.53
1396 1431 0.251916 CGGAGGTTTGGTGGCATAGA 59.748 55.000 0.00 0.00 0.00 1.98
1553 1588 1.153647 GGTGGTGATGATCGTCGCA 60.154 57.895 25.66 12.13 0.00 5.10
1758 1799 0.322456 CAGCGGGATCCAAAGGAACA 60.322 55.000 15.23 0.00 34.34 3.18
1765 1806 3.781307 CGGGACAGCGGGATCCAA 61.781 66.667 15.23 0.00 36.65 3.53
1783 1824 2.922503 TCTCCGTCTTGGCTGGCA 60.923 61.111 0.00 0.00 37.80 4.92
1962 2008 1.074566 AGGACTTTCCAGAGGCTTTGG 59.925 52.381 17.68 17.68 39.61 3.28
1963 2009 2.224621 TGAGGACTTTCCAGAGGCTTTG 60.225 50.000 0.00 0.00 39.61 2.77
1964 2010 2.039613 CTGAGGACTTTCCAGAGGCTTT 59.960 50.000 0.00 0.00 39.61 3.51
1965 2011 1.627834 CTGAGGACTTTCCAGAGGCTT 59.372 52.381 0.00 0.00 39.61 4.35
1967 2013 0.980423 ACTGAGGACTTTCCAGAGGC 59.020 55.000 0.00 0.00 39.61 4.70
1968 2014 3.431486 GCATACTGAGGACTTTCCAGAGG 60.431 52.174 0.00 0.00 39.61 3.69
1969 2015 3.736433 CGCATACTGAGGACTTTCCAGAG 60.736 52.174 0.00 0.00 39.61 3.35
1970 2016 2.166459 CGCATACTGAGGACTTTCCAGA 59.834 50.000 0.00 0.00 39.61 3.86
1971 2017 2.544685 CGCATACTGAGGACTTTCCAG 58.455 52.381 0.00 0.00 39.61 3.86
1972 2018 1.207089 CCGCATACTGAGGACTTTCCA 59.793 52.381 0.00 0.00 39.92 3.53
1973 2019 1.480954 TCCGCATACTGAGGACTTTCC 59.519 52.381 0.00 0.00 41.47 3.13
1974 2020 2.815478 CTCCGCATACTGAGGACTTTC 58.185 52.381 0.00 0.00 41.47 2.62
1975 2021 2.969628 CTCCGCATACTGAGGACTTT 57.030 50.000 0.00 0.00 41.47 2.66
1981 2027 0.387202 CAGGACCTCCGCATACTGAG 59.613 60.000 0.00 0.00 42.08 3.35
1982 2028 1.043116 CCAGGACCTCCGCATACTGA 61.043 60.000 0.00 0.00 42.08 3.41
1983 2029 1.330655 ACCAGGACCTCCGCATACTG 61.331 60.000 0.00 0.00 42.08 2.74
1984 2030 1.001760 ACCAGGACCTCCGCATACT 59.998 57.895 0.00 0.00 42.08 2.12
1985 2031 1.144057 CACCAGGACCTCCGCATAC 59.856 63.158 0.00 0.00 42.08 2.39
1986 2032 2.731571 GCACCAGGACCTCCGCATA 61.732 63.158 0.00 0.00 42.08 3.14
1987 2033 4.101448 GCACCAGGACCTCCGCAT 62.101 66.667 0.00 0.00 42.08 4.73
1989 2035 4.767255 CTGCACCAGGACCTCCGC 62.767 72.222 0.00 0.00 42.08 5.54
1990 2036 3.302347 GACTGCACCAGGACCTCCG 62.302 68.421 0.00 0.00 42.08 4.63
1991 2037 1.768684 TTGACTGCACCAGGACCTCC 61.769 60.000 0.00 0.00 35.51 4.30
1992 2038 0.108585 TTTGACTGCACCAGGACCTC 59.891 55.000 0.00 0.00 35.51 3.85
1993 2039 0.773644 ATTTGACTGCACCAGGACCT 59.226 50.000 0.00 0.00 35.51 3.85
1994 2040 1.541588 GAATTTGACTGCACCAGGACC 59.458 52.381 0.00 0.00 35.51 4.46
1995 2041 1.197721 CGAATTTGACTGCACCAGGAC 59.802 52.381 0.00 0.00 35.51 3.85
1996 2042 1.522668 CGAATTTGACTGCACCAGGA 58.477 50.000 0.00 0.00 35.51 3.86
1997 2043 0.109597 GCGAATTTGACTGCACCAGG 60.110 55.000 0.00 0.00 35.51 4.45
1998 2044 0.877071 AGCGAATTTGACTGCACCAG 59.123 50.000 0.00 0.00 37.52 4.00
1999 2045 1.317613 AAGCGAATTTGACTGCACCA 58.682 45.000 0.00 0.00 0.00 4.17
2000 2046 2.422276 AAAGCGAATTTGACTGCACC 57.578 45.000 0.00 0.00 0.00 5.01
2009 2055 5.473039 AGAAAGCATAAGCAAAGCGAATTT 58.527 33.333 0.00 0.00 45.49 1.82
2010 2056 5.064441 AGAAAGCATAAGCAAAGCGAATT 57.936 34.783 0.00 0.00 45.49 2.17
2011 2057 4.156556 TGAGAAAGCATAAGCAAAGCGAAT 59.843 37.500 0.00 0.00 45.49 3.34
2012 2058 3.501828 TGAGAAAGCATAAGCAAAGCGAA 59.498 39.130 0.00 0.00 45.49 4.70
2013 2059 3.073678 TGAGAAAGCATAAGCAAAGCGA 58.926 40.909 0.00 0.00 45.49 4.93
2089 2135 3.126171 CCAGCAAATCAATTCGACGGTTA 59.874 43.478 0.00 0.00 0.00 2.85
2214 2260 7.919091 CCAACAAAACATATGAAGATGATCTGG 59.081 37.037 10.38 8.48 0.00 3.86


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

AutoCloner maintained by Alex Coulton.