Multiple sequence alignment - TraesCS2D01G377100

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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 TraesCS2D01G377100 chr2D 100.000 2141 0 0 1 2141 481574209 481576349 0.000000e+00 3954.0
1 TraesCS2D01G377100 chr2D 90.000 50 2 1 1909 1955 385174196 385174147 6.380000e-06 62.1
2 TraesCS2D01G377100 chr2A 90.021 942 56 20 1 918 624312857 624313784 0.000000e+00 1184.0
3 TraesCS2D01G377100 chr2A 89.634 328 22 7 989 1307 624313833 624314157 7.110000e-110 407.0
4 TraesCS2D01G377100 chr2B 85.354 1031 56 37 542 1537 564877794 564878764 0.000000e+00 979.0
5 TraesCS2D01G377100 chr2B 87.500 680 52 22 1480 2141 564878765 564879429 0.000000e+00 754.0
6 TraesCS2D01G377100 chr2B 93.469 490 21 8 1 488 564877309 564877789 0.000000e+00 717.0
7 TraesCS2D01G377100 chr6B 85.526 76 7 2 1952 2025 49542986 49542913 2.280000e-10 76.8


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 TraesCS2D01G377100 chr2D 481574209 481576349 2140 False 3954.000000 3954 100.000000 1 2141 1 chr2D.!!$F1 2140
1 TraesCS2D01G377100 chr2A 624312857 624314157 1300 False 795.500000 1184 89.827500 1 1307 2 chr2A.!!$F1 1306
2 TraesCS2D01G377100 chr2B 564877309 564879429 2120 False 816.666667 979 88.774333 1 2141 3 chr2B.!!$F1 2140

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
951 984 0.038159 GCGTACTGCAGAGTTCCACT 60.038 55.0 23.35 0.0 45.45 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1899 2018 0.104487 TTGACGGACACGCCTAACAA 59.896 50.0 0.0 0.0 46.04 2.83 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 0.927029 GGCTTTATGGAACTCCCCCT 59.073 55.000 0.00 0.00 34.29 4.79
63 64 1.410224 GGCTTTATGGAACTCCCCCTG 60.410 57.143 0.00 0.00 34.29 4.45
64 65 1.285078 GCTTTATGGAACTCCCCCTGT 59.715 52.381 0.00 0.00 34.29 4.00
65 66 2.508300 GCTTTATGGAACTCCCCCTGTA 59.492 50.000 0.00 0.00 34.29 2.74
119 120 7.668492 AGAAACTAGAAAGGAACGACTTATGT 58.332 34.615 0.00 0.00 0.00 2.29
265 266 6.524101 TGCACATCCCTAAACCTAAAATTC 57.476 37.500 0.00 0.00 0.00 2.17
282 284 6.510746 AAAATTCGCAGTTCAACTTTTAGC 57.489 33.333 0.00 0.00 0.00 3.09
304 306 5.047731 AGCCTTCTCATTTTTCTTAGTTGGC 60.048 40.000 0.00 0.00 34.90 4.52
310 312 8.862325 TCTCATTTTTCTTAGTTGGCTTCATA 57.138 30.769 0.00 0.00 0.00 2.15
312 314 8.402798 TCATTTTTCTTAGTTGGCTTCATACA 57.597 30.769 0.00 0.00 0.00 2.29
313 315 8.855110 TCATTTTTCTTAGTTGGCTTCATACAA 58.145 29.630 0.00 0.00 0.00 2.41
395 398 7.841222 AGCCCTCTGTATTTTGGAATTTATCTT 59.159 33.333 0.00 0.00 0.00 2.40
468 471 9.659830 CTGAAGCGTTTTTATTACTAGTTTTGT 57.340 29.630 0.00 0.00 0.00 2.83
488 491 8.511321 GTTTTGTGTGATTTCATACTGGTATCA 58.489 33.333 8.60 0.00 38.56 2.15
499 502 5.822519 TCATACTGGTATCATTGCCTTTGTC 59.177 40.000 0.00 0.00 0.00 3.18
603 606 7.174599 AGTTTTTCTGAATGAGAAGATGACTGG 59.825 37.037 0.00 0.00 41.86 4.00
704 707 2.665777 TTCGTATCGAAGCAGCAGC 58.334 52.632 0.00 0.00 41.05 5.25
719 722 2.097825 AGCAGCAATCCTAGCCTTTTG 58.902 47.619 0.00 0.00 0.00 2.44
721 724 3.016736 GCAGCAATCCTAGCCTTTTGTA 58.983 45.455 0.00 0.00 0.00 2.41
729 732 3.389983 TCCTAGCCTTTTGTACACACACT 59.610 43.478 0.00 0.00 33.30 3.55
730 733 3.498397 CCTAGCCTTTTGTACACACACTG 59.502 47.826 0.00 0.00 33.30 3.66
732 735 3.820557 AGCCTTTTGTACACACACTGAT 58.179 40.909 0.00 0.00 33.30 2.90
733 736 3.565482 AGCCTTTTGTACACACACTGATG 59.435 43.478 0.00 0.00 33.30 3.07
734 737 3.563808 GCCTTTTGTACACACACTGATGA 59.436 43.478 0.00 0.00 33.30 2.92
735 738 4.319766 GCCTTTTGTACACACACTGATGAG 60.320 45.833 0.00 0.00 33.30 2.90
896 925 2.259618 GTTGAGCGCTCATCGTTTCTA 58.740 47.619 38.40 19.84 39.64 2.10
897 926 2.194800 TGAGCGCTCATCGTTTCTAG 57.805 50.000 35.30 0.00 41.07 2.43
898 927 1.472878 TGAGCGCTCATCGTTTCTAGT 59.527 47.619 35.30 0.00 41.07 2.57
899 928 2.113289 GAGCGCTCATCGTTTCTAGTC 58.887 52.381 31.91 0.00 41.07 2.59
900 929 1.746220 AGCGCTCATCGTTTCTAGTCT 59.254 47.619 2.64 0.00 41.07 3.24
936 969 1.000233 GACTGCTCGTTCGTTGCGTA 61.000 55.000 0.00 0.00 0.00 4.42
937 970 1.273455 ACTGCTCGTTCGTTGCGTAC 61.273 55.000 0.00 0.00 0.00 3.67
938 971 1.002250 CTGCTCGTTCGTTGCGTACT 61.002 55.000 0.00 0.00 0.00 2.73
939 972 1.272784 TGCTCGTTCGTTGCGTACTG 61.273 55.000 0.00 0.00 0.00 2.74
940 973 1.411089 CTCGTTCGTTGCGTACTGC 59.589 57.895 3.22 3.22 46.70 4.40
950 983 2.446341 GCGTACTGCAGAGTTCCAC 58.554 57.895 23.35 6.95 45.45 4.02
951 984 0.038159 GCGTACTGCAGAGTTCCACT 60.038 55.000 23.35 0.00 45.45 4.00
952 985 1.201647 GCGTACTGCAGAGTTCCACTA 59.798 52.381 23.35 0.00 45.45 2.74
953 986 2.732597 GCGTACTGCAGAGTTCCACTAG 60.733 54.545 23.35 0.64 45.45 2.57
963 996 4.524714 CAGAGTTCCACTAGACAAGGAGAA 59.475 45.833 0.00 0.00 32.11 2.87
976 1009 1.748500 GGAGAAGCAGCAAGAGGGC 60.749 63.158 0.00 0.00 0.00 5.19
977 1010 1.748500 GAGAAGCAGCAAGAGGGCC 60.749 63.158 0.00 0.00 0.00 5.80
978 1011 3.130160 GAAGCAGCAAGAGGGCCG 61.130 66.667 0.00 0.00 0.00 6.13
982 1015 4.399395 CAGCAAGAGGGCCGCTCA 62.399 66.667 11.17 0.00 32.48 4.26
983 1016 4.093291 AGCAAGAGGGCCGCTCAG 62.093 66.667 11.17 7.81 0.00 3.35
1047 1080 0.803768 CGATCCTCCTGTTGCTCGTG 60.804 60.000 0.00 0.00 0.00 4.35
1148 1181 2.360350 GCCCAAGTAGCAGCAGCA 60.360 61.111 3.17 0.00 45.49 4.41
1191 1227 7.311364 TCAGTAAAGTTATATGCCGGTTTTC 57.689 36.000 1.90 0.00 0.00 2.29
1228 1269 5.221048 GCTTCCAGCAGTACTTTTTCTTTCA 60.221 40.000 0.00 0.00 41.89 2.69
1300 1343 0.326264 ACAGTTCAGCCTGGATGTCC 59.674 55.000 12.27 3.78 36.75 4.02
1307 1350 2.616458 GCCTGGATGTCCCCCTTGT 61.616 63.158 0.00 0.00 34.29 3.16
1308 1351 1.279025 GCCTGGATGTCCCCCTTGTA 61.279 60.000 0.00 0.00 34.29 2.41
1309 1352 1.295020 CCTGGATGTCCCCCTTGTAA 58.705 55.000 0.00 0.00 34.29 2.41
1310 1353 1.852965 CCTGGATGTCCCCCTTGTAAT 59.147 52.381 0.00 0.00 34.29 1.89
1311 1354 2.158608 CCTGGATGTCCCCCTTGTAATC 60.159 54.545 0.00 0.00 34.29 1.75
1312 1355 2.509548 CTGGATGTCCCCCTTGTAATCA 59.490 50.000 0.00 0.00 34.29 2.57
1313 1356 2.509548 TGGATGTCCCCCTTGTAATCAG 59.490 50.000 0.00 0.00 34.29 2.90
1327 1370 8.674607 CCCTTGTAATCAGGTAATCAGTAAAAC 58.325 37.037 0.00 0.00 0.00 2.43
1332 1375 5.999205 TCAGGTAATCAGTAAAACGGGTA 57.001 39.130 0.00 0.00 0.00 3.69
1336 1379 5.645067 AGGTAATCAGTAAAACGGGTAAAGC 59.355 40.000 0.00 0.00 0.00 3.51
1338 1381 3.110447 TCAGTAAAACGGGTAAAGCGT 57.890 42.857 0.00 0.00 0.00 5.07
1349 1392 4.240096 CGGGTAAAGCGTTCTTCTTCTTA 58.760 43.478 0.00 0.00 0.00 2.10
1409 1459 1.929836 GCTCTTCAGTCACAATAGCCG 59.070 52.381 0.00 0.00 0.00 5.52
1410 1460 2.544685 CTCTTCAGTCACAATAGCCGG 58.455 52.381 0.00 0.00 0.00 6.13
1411 1461 1.899814 TCTTCAGTCACAATAGCCGGT 59.100 47.619 1.90 0.00 0.00 5.28
1412 1462 2.301870 TCTTCAGTCACAATAGCCGGTT 59.698 45.455 1.90 0.00 0.00 4.44
1413 1463 2.093306 TCAGTCACAATAGCCGGTTG 57.907 50.000 1.90 1.91 0.00 3.77
1414 1464 1.086696 CAGTCACAATAGCCGGTTGG 58.913 55.000 1.90 0.00 38.77 3.77
1415 1465 0.981183 AGTCACAATAGCCGGTTGGA 59.019 50.000 1.90 0.00 37.49 3.53
1416 1466 1.066143 AGTCACAATAGCCGGTTGGAG 60.066 52.381 1.90 0.00 37.49 3.86
1417 1467 1.066430 GTCACAATAGCCGGTTGGAGA 60.066 52.381 1.90 0.01 37.49 3.71
1418 1468 1.207089 TCACAATAGCCGGTTGGAGAG 59.793 52.381 1.90 0.00 37.49 3.20
1419 1469 1.066143 CACAATAGCCGGTTGGAGAGT 60.066 52.381 1.90 0.00 37.49 3.24
1426 1476 2.317609 CGGTTGGAGAGTGGTTGCG 61.318 63.158 0.00 0.00 0.00 4.85
1429 1479 1.597854 TTGGAGAGTGGTTGCGCAG 60.598 57.895 11.31 0.00 0.00 5.18
1432 1482 1.292223 GAGAGTGGTTGCGCAGGTA 59.708 57.895 11.31 0.00 0.00 3.08
1460 1510 5.031578 GTCTCAGATCGCTTACAGTTACAG 58.968 45.833 0.00 0.00 0.00 2.74
1504 1612 3.817647 GCTTGGATGTTAGCCTATTCCAG 59.182 47.826 0.00 0.00 0.00 3.86
1510 1618 2.159099 TGTTAGCCTATTCCAGTCTGCG 60.159 50.000 0.00 0.00 0.00 5.18
1513 1621 0.249657 GCCTATTCCAGTCTGCGAGG 60.250 60.000 0.00 0.00 0.00 4.63
1532 1640 3.964909 AGGCGTTCATTTGTTTCTGTTC 58.035 40.909 0.00 0.00 0.00 3.18
1537 1645 5.275881 GCGTTCATTTGTTTCTGTTCTGTTG 60.276 40.000 0.00 0.00 0.00 3.33
1538 1646 5.275881 CGTTCATTTGTTTCTGTTCTGTTGC 60.276 40.000 0.00 0.00 0.00 4.17
1539 1647 4.681744 TCATTTGTTTCTGTTCTGTTGCC 58.318 39.130 0.00 0.00 0.00 4.52
1559 1667 1.376812 CTTGGTAGTGGAACCCGGC 60.377 63.158 0.00 0.00 38.90 6.13
1569 1677 1.476845 GGAACCCGGCCCATTTTTGT 61.477 55.000 0.00 0.00 0.00 2.83
1570 1678 0.320334 GAACCCGGCCCATTTTTGTG 60.320 55.000 0.00 0.00 0.00 3.33
1574 1682 0.108233 CCGGCCCATTTTTGTGGATG 60.108 55.000 0.00 0.00 42.02 3.51
1575 1683 0.108233 CGGCCCATTTTTGTGGATGG 60.108 55.000 0.00 0.00 42.02 3.51
1577 1685 1.066215 GGCCCATTTTTGTGGATGGAC 60.066 52.381 4.02 0.00 44.49 4.02
1581 1689 2.234414 CCATTTTTGTGGATGGACTGGG 59.766 50.000 0.00 0.00 44.49 4.45
1582 1690 3.164268 CATTTTTGTGGATGGACTGGGA 58.836 45.455 0.00 0.00 0.00 4.37
1637 1745 6.992063 AGATTTACACTTCATGCTTGGTAG 57.008 37.500 0.00 1.12 0.00 3.18
1641 1759 6.985188 TTACACTTCATGCTTGGTAGAATC 57.015 37.500 0.00 0.00 0.00 2.52
1659 1777 9.331282 GGTAGAATCTTCAAGCTACATTACAAT 57.669 33.333 0.00 0.00 35.97 2.71
1672 1790 6.861572 GCTACATTACAATATGACTCGTGCTA 59.138 38.462 0.00 0.00 0.00 3.49
1674 1792 9.411801 CTACATTACAATATGACTCGTGCTAAT 57.588 33.333 0.00 0.00 0.00 1.73
1687 1805 5.525378 ACTCGTGCTAATTGAAATCTCATCC 59.475 40.000 0.00 0.00 0.00 3.51
1691 1809 6.183360 CGTGCTAATTGAAATCTCATCCTGTT 60.183 38.462 0.00 0.00 0.00 3.16
1755 1873 6.062434 TGGTAAATGACGTGTAGGTTTTTG 57.938 37.500 0.00 0.00 0.00 2.44
1765 1883 5.180271 CGTGTAGGTTTTTGCTAGGGATTA 58.820 41.667 0.00 0.00 0.00 1.75
1777 1895 4.223700 TGCTAGGGATTATACTGCATGAGG 59.776 45.833 0.00 0.00 0.00 3.86
1815 1934 8.429237 TTTTTCCCTTAGAATAAGCATCCAAA 57.571 30.769 0.00 0.00 33.44 3.28
1829 1948 6.205101 AGCATCCAAAGACATTTCAGATTC 57.795 37.500 0.00 0.00 0.00 2.52
1834 1953 5.586243 TCCAAAGACATTTCAGATTCGATCC 59.414 40.000 0.00 0.00 0.00 3.36
1840 1959 5.416083 ACATTTCAGATTCGATCCGTGTTA 58.584 37.500 0.00 0.00 0.00 2.41
1841 1960 5.291128 ACATTTCAGATTCGATCCGTGTTAC 59.709 40.000 0.00 0.00 0.00 2.50
1869 1988 2.569404 AGCATGGCTTAGATAGGTAGGC 59.431 50.000 0.00 0.00 33.89 3.93
1883 2002 2.152016 GGTAGGCTCCTTGTGTGAAAC 58.848 52.381 0.00 0.00 37.35 2.78
1899 2018 3.639561 GTGAAACCAACCCACCACTATTT 59.360 43.478 0.00 0.00 0.00 1.40
1903 2022 3.648739 ACCAACCCACCACTATTTTGTT 58.351 40.909 0.00 0.00 0.00 2.83
1908 2034 2.422127 CCCACCACTATTTTGTTAGGCG 59.578 50.000 0.00 0.00 0.00 5.52
1912 2038 3.749609 ACCACTATTTTGTTAGGCGTGTC 59.250 43.478 0.00 0.00 0.00 3.67
1914 2040 2.997986 ACTATTTTGTTAGGCGTGTCCG 59.002 45.455 0.00 0.00 40.77 4.79
1930 2056 0.454600 TCCGTCAACTATGAGGCGTC 59.545 55.000 0.00 0.00 39.54 5.19
1931 2057 0.456221 CCGTCAACTATGAGGCGTCT 59.544 55.000 8.06 0.00 39.54 4.18
1932 2058 1.674441 CCGTCAACTATGAGGCGTCTA 59.326 52.381 8.06 0.00 39.54 2.59
1933 2059 2.293677 CCGTCAACTATGAGGCGTCTAT 59.706 50.000 8.06 2.71 39.54 1.98
1934 2060 3.300857 CGTCAACTATGAGGCGTCTATG 58.699 50.000 8.06 0.35 35.88 2.23
1935 2061 3.003378 CGTCAACTATGAGGCGTCTATGA 59.997 47.826 8.06 2.67 35.88 2.15
1955 2081 9.126151 TCTATGACGACTTCAATCTTAAGATCT 57.874 33.333 18.19 6.41 37.92 2.75
1963 2089 5.344743 TCAATCTTAAGATCTGTCGGCTT 57.655 39.130 18.19 0.00 32.75 4.35
1973 2099 1.676529 TCTGTCGGCTTAATCTCTCGG 59.323 52.381 0.00 0.00 0.00 4.63
2001 2127 3.611293 CTCATAGGAGTAGAGCATGTGCG 60.611 52.174 0.00 0.00 40.19 5.34
2017 2143 2.621763 GCGAGTGCATTCATAGGGG 58.378 57.895 10.08 0.00 42.15 4.79
2031 2157 2.902705 TAGGGGTGAATGTGCGTATC 57.097 50.000 0.00 0.00 0.00 2.24
2032 2158 0.908910 AGGGGTGAATGTGCGTATCA 59.091 50.000 0.00 0.00 0.00 2.15
2033 2159 1.134401 AGGGGTGAATGTGCGTATCAG 60.134 52.381 0.00 0.00 0.00 2.90
2034 2160 0.657840 GGGTGAATGTGCGTATCAGC 59.342 55.000 0.00 0.00 40.03 4.26
2035 2161 0.301687 GGTGAATGTGCGTATCAGCG 59.698 55.000 0.00 0.00 40.67 5.18
2036 2162 0.999406 GTGAATGTGCGTATCAGCGT 59.001 50.000 0.00 0.00 40.67 5.07
2037 2163 2.190161 GTGAATGTGCGTATCAGCGTA 58.810 47.619 0.00 0.00 40.67 4.42
2038 2164 2.794910 GTGAATGTGCGTATCAGCGTAT 59.205 45.455 0.00 0.00 40.67 3.06
2039 2165 2.794350 TGAATGTGCGTATCAGCGTATG 59.206 45.455 0.00 0.00 40.67 2.39
2051 2177 1.781429 CAGCGTATGTATGTGAGCGTC 59.219 52.381 0.00 0.00 0.00 5.19
2052 2178 1.676529 AGCGTATGTATGTGAGCGTCT 59.323 47.619 0.00 0.00 0.00 4.18
2067 2193 1.320259 GCGTCTGTTTTTGTGTTGTGC 59.680 47.619 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 3.119849 ACATATGTGCTTTTGCCTTCGAC 60.120 43.478 7.78 0.00 46.87 4.20
90 91 4.386350 GTCGTTCCTTTCTAGTTTCTCAGC 59.614 45.833 0.00 0.00 0.00 4.26
119 120 2.085320 ACGGCTACAAACACAACAACA 58.915 42.857 0.00 0.00 0.00 3.33
265 266 3.251004 AGAAGGCTAAAAGTTGAACTGCG 59.749 43.478 0.00 0.00 0.00 5.18
282 284 6.581171 AGCCAACTAAGAAAAATGAGAAGG 57.419 37.500 0.00 0.00 0.00 3.46
310 312 9.784531 CATCCTCTTACATAATTACTGGATTGT 57.215 33.333 0.00 0.00 30.37 2.71
313 315 9.159254 TGACATCCTCTTACATAATTACTGGAT 57.841 33.333 0.00 0.00 32.69 3.41
468 471 6.262944 GGCAATGATACCAGTATGAAATCACA 59.737 38.462 0.00 0.00 38.98 3.58
488 491 1.176527 CCACGGATGACAAAGGCAAT 58.823 50.000 0.00 0.00 0.00 3.56
499 502 1.800586 CAGTCAGTTTGTCCACGGATG 59.199 52.381 0.00 0.00 0.00 3.51
538 541 8.716619 TTAACAGTATATTTGTGCGTTTTCAC 57.283 30.769 0.00 0.00 37.48 3.18
574 577 9.985318 GTCATCTTCTCATTCAGAAAAACTATG 57.015 33.333 0.00 0.00 40.83 2.23
603 606 1.725164 CTAACCAAAACCGCTCGACTC 59.275 52.381 0.00 0.00 0.00 3.36
689 692 1.262683 GGATTGCTGCTGCTTCGATAC 59.737 52.381 17.00 3.22 40.48 2.24
704 707 4.759693 TGTGTGTACAAAAGGCTAGGATTG 59.240 41.667 0.00 0.00 32.88 2.67
719 722 3.255888 TGGACTCTCATCAGTGTGTGTAC 59.744 47.826 0.00 0.00 30.62 2.90
721 724 2.298446 CTGGACTCTCATCAGTGTGTGT 59.702 50.000 0.00 0.00 0.00 3.72
729 732 1.649321 ACAAGCCTGGACTCTCATCA 58.351 50.000 0.00 0.00 0.00 3.07
730 733 2.480416 CGTACAAGCCTGGACTCTCATC 60.480 54.545 0.00 0.00 33.75 2.92
732 735 0.888619 CGTACAAGCCTGGACTCTCA 59.111 55.000 0.00 0.00 33.75 3.27
733 736 0.889306 ACGTACAAGCCTGGACTCTC 59.111 55.000 0.00 0.00 33.75 3.20
734 737 0.889306 GACGTACAAGCCTGGACTCT 59.111 55.000 0.00 0.00 33.75 3.24
735 738 0.601558 TGACGTACAAGCCTGGACTC 59.398 55.000 0.00 0.00 33.75 3.36
896 925 2.258591 CACACGGCGTGCTAGACT 59.741 61.111 37.21 16.26 39.19 3.24
922 951 1.411089 GCAGTACGCAACGAACGAG 59.589 57.895 0.14 0.00 41.79 4.18
944 977 3.006967 TGCTTCTCCTTGTCTAGTGGAAC 59.993 47.826 0.00 0.00 0.00 3.62
946 979 2.828520 CTGCTTCTCCTTGTCTAGTGGA 59.171 50.000 0.00 0.00 0.00 4.02
950 983 3.056250 TCTTGCTGCTTCTCCTTGTCTAG 60.056 47.826 0.00 0.00 0.00 2.43
951 984 2.899900 TCTTGCTGCTTCTCCTTGTCTA 59.100 45.455 0.00 0.00 0.00 2.59
952 985 1.696336 TCTTGCTGCTTCTCCTTGTCT 59.304 47.619 0.00 0.00 0.00 3.41
953 986 2.075338 CTCTTGCTGCTTCTCCTTGTC 58.925 52.381 0.00 0.00 0.00 3.18
977 1010 4.785512 AGCCGAAGCGACTGAGCG 62.786 66.667 0.00 0.00 46.67 5.03
978 1011 2.883253 GAGCCGAAGCGACTGAGC 60.883 66.667 0.00 0.00 46.67 4.26
979 1012 1.515952 CTGAGCCGAAGCGACTGAG 60.516 63.158 0.00 0.00 46.67 3.35
980 1013 2.568612 CTGAGCCGAAGCGACTGA 59.431 61.111 0.00 0.00 46.67 3.41
981 1014 3.184683 GCTGAGCCGAAGCGACTG 61.185 66.667 0.00 0.00 46.67 3.51
982 1015 4.443266 GGCTGAGCCGAAGCGACT 62.443 66.667 8.16 0.00 46.67 4.18
993 1026 2.416547 CACGAGGTAAAACATGGCTGAG 59.583 50.000 0.00 0.00 0.00 3.35
1128 1161 3.612247 CTGCTGCTACTTGGGCGGT 62.612 63.158 0.00 0.00 38.25 5.68
1174 1207 4.204799 GGGAAGAAAACCGGCATATAACT 58.795 43.478 0.00 0.00 0.00 2.24
1176 1209 3.203487 AGGGGAAGAAAACCGGCATATAA 59.797 43.478 0.00 0.00 0.00 0.98
1191 1227 0.540365 TGGAAGCAAAGCAGGGGAAG 60.540 55.000 0.00 0.00 0.00 3.46
1255 1298 5.965334 CACGCTCGTTGCAAGATAAAAATAT 59.035 36.000 0.00 0.00 43.06 1.28
1257 1300 4.158384 CACGCTCGTTGCAAGATAAAAAT 58.842 39.130 0.00 0.00 43.06 1.82
1258 1301 3.550561 CACGCTCGTTGCAAGATAAAAA 58.449 40.909 0.00 0.00 43.06 1.94
1259 1302 2.095969 CCACGCTCGTTGCAAGATAAAA 60.096 45.455 0.00 0.00 43.06 1.52
1276 1319 1.669115 CCAGGCTGAACTGTCCACG 60.669 63.158 17.94 0.00 36.75 4.94
1279 1322 0.326264 ACATCCAGGCTGAACTGTCC 59.674 55.000 17.94 0.00 36.75 4.02
1282 1325 0.393537 GGGACATCCAGGCTGAACTG 60.394 60.000 17.94 12.25 37.91 3.16
1300 1343 5.373812 ACTGATTACCTGATTACAAGGGG 57.626 43.478 0.00 0.00 0.00 4.79
1307 1350 6.949715 ACCCGTTTTACTGATTACCTGATTA 58.050 36.000 0.00 0.00 0.00 1.75
1308 1351 5.812286 ACCCGTTTTACTGATTACCTGATT 58.188 37.500 0.00 0.00 0.00 2.57
1309 1352 5.431179 ACCCGTTTTACTGATTACCTGAT 57.569 39.130 0.00 0.00 0.00 2.90
1310 1353 4.895668 ACCCGTTTTACTGATTACCTGA 57.104 40.909 0.00 0.00 0.00 3.86
1311 1354 6.402875 GCTTTACCCGTTTTACTGATTACCTG 60.403 42.308 0.00 0.00 0.00 4.00
1312 1355 5.645067 GCTTTACCCGTTTTACTGATTACCT 59.355 40.000 0.00 0.00 0.00 3.08
1313 1356 5.446340 CGCTTTACCCGTTTTACTGATTACC 60.446 44.000 0.00 0.00 0.00 2.85
1327 1370 2.685100 AGAAGAAGAACGCTTTACCCG 58.315 47.619 0.00 0.00 33.61 5.28
1332 1375 5.689383 TGCATTAAGAAGAAGAACGCTTT 57.311 34.783 0.00 0.00 33.61 3.51
1336 1379 9.003112 CAATACATTGCATTAAGAAGAAGAACG 57.997 33.333 0.00 0.00 0.00 3.95
1378 1428 5.210715 GTGACTGAAGAGCAAACTCATTTG 58.789 41.667 0.00 0.00 46.09 2.32
1384 1434 4.453819 GCTATTGTGACTGAAGAGCAAACT 59.546 41.667 0.00 0.00 37.55 2.66
1396 1446 0.981183 TCCAACCGGCTATTGTGACT 59.019 50.000 0.00 0.00 0.00 3.41
1409 1459 2.617274 GCGCAACCACTCTCCAACC 61.617 63.158 0.30 0.00 0.00 3.77
1410 1460 1.845809 CTGCGCAACCACTCTCCAAC 61.846 60.000 13.05 0.00 0.00 3.77
1411 1461 1.597854 CTGCGCAACCACTCTCCAA 60.598 57.895 13.05 0.00 0.00 3.53
1412 1462 2.031012 CTGCGCAACCACTCTCCA 59.969 61.111 13.05 0.00 0.00 3.86
1413 1463 2.167398 TACCTGCGCAACCACTCTCC 62.167 60.000 13.05 0.00 0.00 3.71
1414 1464 0.737715 CTACCTGCGCAACCACTCTC 60.738 60.000 13.05 0.00 0.00 3.20
1415 1465 1.185618 TCTACCTGCGCAACCACTCT 61.186 55.000 13.05 0.00 0.00 3.24
1416 1466 1.014564 GTCTACCTGCGCAACCACTC 61.015 60.000 13.05 0.00 0.00 3.51
1417 1467 1.004918 GTCTACCTGCGCAACCACT 60.005 57.895 13.05 0.00 0.00 4.00
1418 1468 1.291877 CTGTCTACCTGCGCAACCAC 61.292 60.000 13.05 4.60 0.00 4.16
1419 1469 1.005037 CTGTCTACCTGCGCAACCA 60.005 57.895 13.05 0.00 0.00 3.67
1426 1476 2.032799 CGATCTGAGACTGTCTACCTGC 59.967 54.545 10.86 0.00 0.00 4.85
1429 1479 2.294074 AGCGATCTGAGACTGTCTACC 58.706 52.381 10.86 0.00 0.00 3.18
1432 1482 3.348119 TGTAAGCGATCTGAGACTGTCT 58.652 45.455 10.66 10.66 0.00 3.41
1460 1510 6.183347 AGCCATCATACCAGATAATTTAGCC 58.817 40.000 0.00 0.00 0.00 3.93
1504 1612 0.179215 CAAATGAACGCCTCGCAGAC 60.179 55.000 0.00 0.00 0.00 3.51
1510 1618 3.626028 ACAGAAACAAATGAACGCCTC 57.374 42.857 0.00 0.00 0.00 4.70
1513 1621 4.351192 ACAGAACAGAAACAAATGAACGC 58.649 39.130 0.00 0.00 0.00 4.84
1532 1640 1.577328 CCACTACCAAGCGGCAACAG 61.577 60.000 1.45 0.00 34.57 3.16
1537 1645 2.038837 GGTTCCACTACCAAGCGGC 61.039 63.158 0.00 0.00 38.12 6.53
1538 1646 1.376812 GGGTTCCACTACCAAGCGG 60.377 63.158 0.00 0.00 40.09 5.52
1539 1647 1.740296 CGGGTTCCACTACCAAGCG 60.740 63.158 0.00 0.00 40.09 4.68
1551 1659 0.320334 CACAAAAATGGGCCGGGTTC 60.320 55.000 2.18 0.00 0.00 3.62
1559 1667 2.234414 CCAGTCCATCCACAAAAATGGG 59.766 50.000 1.80 0.00 42.31 4.00
1606 1714 7.298122 AGCATGAAGTGTAAATCTAACGTTTG 58.702 34.615 5.91 4.35 0.00 2.93
1607 1715 7.435068 AGCATGAAGTGTAAATCTAACGTTT 57.565 32.000 5.91 0.00 0.00 3.60
1610 1718 6.128282 ACCAAGCATGAAGTGTAAATCTAACG 60.128 38.462 0.00 0.00 0.00 3.18
1641 1759 8.483218 CGAGTCATATTGTAATGTAGCTTGAAG 58.517 37.037 0.00 0.00 0.00 3.02
1659 1777 7.264947 TGAGATTTCAATTAGCACGAGTCATA 58.735 34.615 0.00 0.00 0.00 2.15
1672 1790 7.949690 TGATCAACAGGATGAGATTTCAATT 57.050 32.000 0.00 0.00 39.69 2.32
1674 1792 6.997239 CTGATCAACAGGATGAGATTTCAA 57.003 37.500 0.00 0.00 39.34 2.69
1718 1836 8.287503 ACGTCATTTACCAAGAAAATTGACTAC 58.712 33.333 0.00 0.00 30.60 2.73
1755 1873 4.223923 ACCTCATGCAGTATAATCCCTAGC 59.776 45.833 0.00 0.00 0.00 3.42
1815 1934 4.115516 CACGGATCGAATCTGAAATGTCT 58.884 43.478 9.69 0.00 39.01 3.41
1829 1948 2.529090 GCTTAGTTCGTAACACGGATCG 59.471 50.000 0.00 0.00 42.81 3.69
1834 1953 2.222729 GCCATGCTTAGTTCGTAACACG 60.223 50.000 0.00 0.00 44.19 4.49
1864 1983 2.152016 GGTTTCACACAAGGAGCCTAC 58.848 52.381 0.00 0.00 0.00 3.18
1868 1987 1.067060 GGTTGGTTTCACACAAGGAGC 59.933 52.381 0.00 0.00 0.00 4.70
1869 1988 1.681264 GGGTTGGTTTCACACAAGGAG 59.319 52.381 0.00 0.00 0.00 3.69
1883 2002 4.219725 CCTAACAAAATAGTGGTGGGTTGG 59.780 45.833 0.00 0.00 32.35 3.77
1899 2018 0.104487 TTGACGGACACGCCTAACAA 59.896 50.000 0.00 0.00 46.04 2.83
1903 2022 1.133598 CATAGTTGACGGACACGCCTA 59.866 52.381 0.00 0.00 46.04 3.93
1908 2034 1.641577 GCCTCATAGTTGACGGACAC 58.358 55.000 0.00 0.00 0.00 3.67
1912 2038 0.456221 AGACGCCTCATAGTTGACGG 59.544 55.000 0.00 0.00 0.00 4.79
1914 2040 4.291783 GTCATAGACGCCTCATAGTTGAC 58.708 47.826 0.00 0.00 0.00 3.18
1930 2056 9.179552 CAGATCTTAAGATTGAAGTCGTCATAG 57.820 37.037 18.88 0.00 35.70 2.23
1931 2057 8.687242 ACAGATCTTAAGATTGAAGTCGTCATA 58.313 33.333 18.88 0.00 35.70 2.15
1932 2058 7.551585 ACAGATCTTAAGATTGAAGTCGTCAT 58.448 34.615 18.88 0.00 35.70 3.06
1933 2059 6.925211 ACAGATCTTAAGATTGAAGTCGTCA 58.075 36.000 18.88 0.00 34.37 4.35
1934 2060 6.195613 CGACAGATCTTAAGATTGAAGTCGTC 59.804 42.308 29.85 21.37 38.38 4.20
1935 2061 6.030849 CGACAGATCTTAAGATTGAAGTCGT 58.969 40.000 29.85 17.83 38.38 4.34
1942 2068 7.655328 AGATTAAGCCGACAGATCTTAAGATTG 59.345 37.037 18.88 18.53 36.23 2.67
1955 2081 1.676529 CTCCGAGAGATTAAGCCGACA 59.323 52.381 0.00 0.00 0.00 4.35
1963 2089 4.946772 CCTATGAGCATCTCCGAGAGATTA 59.053 45.833 12.13 3.96 45.86 1.75
1985 2111 0.457851 ACTCGCACATGCTCTACTCC 59.542 55.000 1.82 0.00 39.32 3.85
2001 2127 3.281727 TTCACCCCTATGAATGCACTC 57.718 47.619 0.00 0.00 33.62 3.51
2017 2143 0.999406 ACGCTGATACGCACATTCAC 59.001 50.000 0.00 0.00 36.19 3.18
2031 2157 1.781429 GACGCTCACATACATACGCTG 59.219 52.381 0.00 0.00 0.00 5.18
2032 2158 1.676529 AGACGCTCACATACATACGCT 59.323 47.619 0.00 0.00 0.00 5.07
2033 2159 1.781429 CAGACGCTCACATACATACGC 59.219 52.381 0.00 0.00 0.00 4.42
2034 2160 3.066369 ACAGACGCTCACATACATACG 57.934 47.619 0.00 0.00 0.00 3.06
2035 2161 5.779806 AAAACAGACGCTCACATACATAC 57.220 39.130 0.00 0.00 0.00 2.39
2036 2162 5.699001 ACAAAAACAGACGCTCACATACATA 59.301 36.000 0.00 0.00 0.00 2.29
2037 2163 4.515191 ACAAAAACAGACGCTCACATACAT 59.485 37.500 0.00 0.00 0.00 2.29
2038 2164 3.874543 ACAAAAACAGACGCTCACATACA 59.125 39.130 0.00 0.00 0.00 2.29
2039 2165 4.211389 CACAAAAACAGACGCTCACATAC 58.789 43.478 0.00 0.00 0.00 2.39
2051 2177 6.942886 TTTAGAAGCACAACACAAAAACAG 57.057 33.333 0.00 0.00 0.00 3.16
2052 2178 7.715265 TTTTTAGAAGCACAACACAAAAACA 57.285 28.000 0.00 0.00 0.00 2.83
2079 2205 2.025793 TGTTTCCTCCAACACAGGTGAA 60.026 45.455 6.40 0.00 31.48 3.18
2089 2215 6.884295 CACATCCTTACTATTGTTTCCTCCAA 59.116 38.462 0.00 0.00 0.00 3.53
2092 2218 6.258947 GCTCACATCCTTACTATTGTTTCCTC 59.741 42.308 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.