Multiple sequence alignment - TraesCS2B01G397900

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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 TraesCS2B01G397900 chr2B 100.000 2141 0 0 1 2141 564877241 564879381 0.000000e+00 3954.0
1 TraesCS2B01G397900 chr2B 100.000 67 0 0 1525 1591 564878707 564878773 8.020000e-25 124.0
2 TraesCS2B01G397900 chr2B 100.000 67 0 0 1467 1533 564878765 564878831 8.020000e-25 124.0
3 TraesCS2B01G397900 chr2D 85.354 1031 56 37 554 1524 481574750 481575745 0.000000e+00 979.0
4 TraesCS2B01G397900 chr2D 94.086 558 22 8 1 549 481574141 481574696 0.000000e+00 837.0
5 TraesCS2B01G397900 chr2D 86.783 628 51 21 1525 2138 481575688 481576297 0.000000e+00 671.0
6 TraesCS2B01G397900 chr2A 86.182 825 72 24 554 1350 624313391 624314201 0.000000e+00 854.0
7 TraesCS2B01G397900 chr2A 93.514 555 30 6 1 552 624312789 624313340 0.000000e+00 821.0
8 TraesCS2B01G397900 chr1A 82.353 68 8 1 2060 2127 552160684 552160621 2.970000e-04 56.5
9 TraesCS2B01G397900 chr6D 100.000 29 0 0 2012 2040 455755003 455755031 1.000000e-03 54.7
10 TraesCS2B01G397900 chr6B 100.000 29 0 0 2012 2040 693053745 693053773 1.000000e-03 54.7
11 TraesCS2B01G397900 chr6A 94.444 36 1 1 2012 2047 469109096 469109130 1.000000e-03 54.7


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 TraesCS2B01G397900 chr2B 564877241 564879381 2140 False 1400.666667 3954 100.000 1 2141 3 chr2B.!!$F1 2140
1 TraesCS2B01G397900 chr2D 481574141 481576297 2156 False 829.000000 979 88.741 1 2138 3 chr2D.!!$F1 2137
2 TraesCS2B01G397900 chr2A 624312789 624314201 1412 False 837.500000 854 89.848 1 1350 2 chr2A.!!$F1 1349

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
955 1030 0.179121 TGTGCGTGACTGTTCGTTCT 60.179 50.0 7.79 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2010 2149 0.098905 TTCGAGAGATTGAGCCGACG 59.901 55.0 0.0 0.0 41.6 5.12 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
63 64 3.187700 CATCCTACAAGGTGCGAACTAC 58.812 50.000 0.00 0.00 36.53 2.73
117 118 4.380841 AGCACATATGTTGATGGCTTTG 57.619 40.909 5.37 0.00 32.67 2.77
242 245 2.166829 GCATTGTCCATGGTGGTTGTA 58.833 47.619 12.58 0.00 39.03 2.41
243 246 2.560542 GCATTGTCCATGGTGGTTGTAA 59.439 45.455 12.58 0.00 39.03 2.41
285 288 2.703536 TCAGTTGACTGCCTGGAACTTA 59.296 45.455 6.27 0.00 43.46 2.24
331 334 6.926630 TGCACATCCCTAAACCTAAAATTT 57.073 33.333 0.00 0.00 0.00 1.82
337 340 6.584185 TCCCTAAACCTAAAATTTGCAGTC 57.416 37.500 0.00 0.00 0.00 3.51
338 341 5.479027 TCCCTAAACCTAAAATTTGCAGTCC 59.521 40.000 0.00 0.00 0.00 3.85
353 356 3.882888 TGCAGTCCCAACTTTTAGTCTTG 59.117 43.478 0.00 0.00 31.71 3.02
380 383 6.648879 TTTTTCTTAGTTGGGTTCATCCTG 57.351 37.500 0.00 0.00 36.25 3.86
420 423 4.458397 AGGATGTCATGAACTTGGCTATG 58.542 43.478 0.00 0.00 0.00 2.23
461 465 5.127031 GCCCTCTGTATTTTGGAATTTAGCA 59.873 40.000 0.00 0.00 0.00 3.49
552 562 7.269316 TGCGTGATTTCATACTGGTATCTTTA 58.731 34.615 0.00 0.00 0.00 1.85
584 643 8.122952 GCACAAATTTACTGCTAATAGTTCGAT 58.877 33.333 11.18 0.00 32.19 3.59
600 659 6.824305 AGTTCGATTGATGGTTTTTCTGAT 57.176 33.333 0.00 0.00 0.00 2.90
733 792 4.574013 CAGCAGTAATCCTAGCCTTTTCTG 59.426 45.833 0.00 0.00 0.00 3.02
744 803 1.798813 GCCTTTTCTGCACACACACAC 60.799 52.381 0.00 0.00 0.00 3.82
745 804 1.472082 CCTTTTCTGCACACACACACA 59.528 47.619 0.00 0.00 0.00 3.72
746 805 2.099592 CCTTTTCTGCACACACACACAT 59.900 45.455 0.00 0.00 0.00 3.21
747 806 3.365832 CTTTTCTGCACACACACACATC 58.634 45.455 0.00 0.00 0.00 3.06
837 896 1.219393 GCTGAAGTAAGGCTCGGCT 59.781 57.895 0.00 0.00 0.00 5.52
955 1030 0.179121 TGTGCGTGACTGTTCGTTCT 60.179 50.000 7.79 0.00 0.00 3.01
971 1064 2.408704 CGTTCTTTGCGTACAAGGAGAG 59.591 50.000 0.00 0.00 42.18 3.20
994 1095 1.446272 CAAGAGGGTCGCTTCGGTC 60.446 63.158 0.00 0.00 0.00 4.79
1160 1267 0.649475 CAGCAGCGAGGAAATCTTCG 59.351 55.000 10.20 10.20 46.37 3.79
1181 1288 5.666423 CGTCAGTAACGCTATATGTATGC 57.334 43.478 0.00 0.00 45.76 3.14
1182 1289 4.557690 CGTCAGTAACGCTATATGTATGCC 59.442 45.833 0.00 0.00 45.76 4.40
1183 1290 4.557690 GTCAGTAACGCTATATGTATGCCG 59.442 45.833 0.00 0.00 0.00 5.69
1184 1291 3.857665 CAGTAACGCTATATGTATGCCGG 59.142 47.826 0.00 0.00 0.00 6.13
1188 1295 4.524316 ACGCTATATGTATGCCGGTTTA 57.476 40.909 1.90 0.00 0.00 2.01
1197 1306 0.106217 ATGCCGGTTTATTCCCCTGG 60.106 55.000 1.90 0.00 0.00 4.45
1205 1314 3.326588 GGTTTATTCCCCTGGTTTGCTTT 59.673 43.478 0.00 0.00 0.00 3.51
1277 1389 4.213270 TGTTCTTTATCTTGCAACGAGTGG 59.787 41.667 0.00 0.00 0.00 4.00
1278 1390 2.742053 TCTTTATCTTGCAACGAGTGGC 59.258 45.455 0.00 0.00 0.00 5.01
1279 1391 2.177394 TTATCTTGCAACGAGTGGCA 57.823 45.000 0.39 0.39 38.46 4.92
1285 1397 1.438651 TGCAACGAGTGGCAATAGTC 58.561 50.000 2.31 0.00 37.03 2.59
1303 1415 1.380380 CCAGCCAGGATGTTTCCCC 60.380 63.158 3.45 0.00 43.76 4.81
1318 1438 7.342026 GGATGTTTCCCCTGTAATCAGTAAAAT 59.658 37.037 0.00 0.00 35.84 1.82
1323 1443 4.644685 CCCCTGTAATCAGTAAAATGGGTG 59.355 45.833 0.00 0.00 39.82 4.61
1327 1447 6.659242 CCTGTAATCAGTAAAATGGGTGAAGT 59.341 38.462 0.00 0.00 39.82 3.01
1329 1449 5.391312 AATCAGTAAAATGGGTGAAGTGC 57.609 39.130 0.00 0.00 0.00 4.40
1345 1465 3.413846 AGTGCTCTTCTTCTTGATGCA 57.586 42.857 0.00 0.00 0.00 3.96
1359 1479 6.270156 TCTTGATGCAAATGTATTGCTTGA 57.730 33.333 13.59 0.06 45.13 3.02
1360 1480 6.094719 TCTTGATGCAAATGTATTGCTTGAC 58.905 36.000 13.59 4.37 45.13 3.18
1361 1481 4.746729 TGATGCAAATGTATTGCTTGACC 58.253 39.130 13.59 0.00 45.13 4.02
1362 1482 4.463539 TGATGCAAATGTATTGCTTGACCT 59.536 37.500 13.59 0.00 45.13 3.85
1363 1483 4.870123 TGCAAATGTATTGCTTGACCTT 57.130 36.364 13.59 0.00 45.13 3.50
1364 1484 4.558178 TGCAAATGTATTGCTTGACCTTG 58.442 39.130 13.59 0.00 45.13 3.61
1365 1485 4.280425 TGCAAATGTATTGCTTGACCTTGA 59.720 37.500 13.59 0.00 45.13 3.02
1374 1494 2.294233 TGCTTGACCTTGATGCAACTTC 59.706 45.455 0.00 0.00 0.00 3.01
1376 1496 1.522668 TGACCTTGATGCAACTTCGG 58.477 50.000 0.00 0.00 0.00 4.30
1382 1502 2.634982 TGATGCAACTTCGGAAATGC 57.365 45.000 16.86 16.86 39.22 3.56
1394 1514 1.729149 CGGAAATGCGTTTGCTCTTCC 60.729 52.381 19.06 7.86 43.43 3.46
1413 1544 1.800681 GTCACAATAGCCGGTTGCC 59.199 57.895 1.90 0.00 42.71 4.52
1416 1547 1.075836 ACAATAGCCGGTTGCCCAA 59.924 52.632 1.90 0.00 42.71 4.12
1419 1550 0.679960 AATAGCCGGTTGCCCAAGTC 60.680 55.000 1.90 0.00 42.71 3.01
1447 1578 5.183331 AGTCTCAGATCGCTTACAGTTACAA 59.817 40.000 0.00 0.00 0.00 2.41
1527 1658 8.055402 CGTTCATTTGTTTCTGTTTTGTTATGG 58.945 33.333 0.00 0.00 0.00 2.74
1528 1659 7.475771 TCATTTGTTTCTGTTTTGTTATGGC 57.524 32.000 0.00 0.00 0.00 4.40
1529 1660 7.271511 TCATTTGTTTCTGTTTTGTTATGGCT 58.728 30.769 0.00 0.00 0.00 4.75
1530 1661 7.768120 TCATTTGTTTCTGTTTTGTTATGGCTT 59.232 29.630 0.00 0.00 0.00 4.35
1531 1662 6.900568 TTGTTTCTGTTTTGTTATGGCTTG 57.099 33.333 0.00 0.00 0.00 4.01
1533 1664 5.127845 TGTTTCTGTTTTGTTATGGCTTGGA 59.872 36.000 0.00 0.00 0.00 3.53
1534 1665 6.183360 TGTTTCTGTTTTGTTATGGCTTGGAT 60.183 34.615 0.00 0.00 0.00 3.41
1535 1666 5.389859 TCTGTTTTGTTATGGCTTGGATG 57.610 39.130 0.00 0.00 0.00 3.51
1536 1667 4.832266 TCTGTTTTGTTATGGCTTGGATGT 59.168 37.500 0.00 0.00 0.00 3.06
1537 1668 5.304101 TCTGTTTTGTTATGGCTTGGATGTT 59.696 36.000 0.00 0.00 0.00 2.71
1538 1669 6.491745 TCTGTTTTGTTATGGCTTGGATGTTA 59.508 34.615 0.00 0.00 0.00 2.41
1539 1670 6.686630 TGTTTTGTTATGGCTTGGATGTTAG 58.313 36.000 0.00 0.00 0.00 2.34
1540 1671 4.981806 TTGTTATGGCTTGGATGTTAGC 57.018 40.909 0.00 0.00 36.66 3.09
1548 1679 3.820557 GCTTGGATGTTAGCCTATTCCA 58.179 45.455 0.00 0.00 0.00 3.53
1549 1680 4.207165 GCTTGGATGTTAGCCTATTCCAA 58.793 43.478 9.60 9.60 34.96 3.53
1550 1681 4.829492 GCTTGGATGTTAGCCTATTCCAAT 59.171 41.667 10.15 0.00 35.56 3.16
1551 1682 5.048434 GCTTGGATGTTAGCCTATTCCAATC 60.048 44.000 10.15 5.00 35.56 2.67
1552 1683 5.912149 TGGATGTTAGCCTATTCCAATCT 57.088 39.130 0.00 0.00 0.00 2.40
1553 1684 5.624159 TGGATGTTAGCCTATTCCAATCTG 58.376 41.667 0.00 0.00 0.00 2.90
1554 1685 4.457257 GGATGTTAGCCTATTCCAATCTGC 59.543 45.833 0.00 0.00 0.00 4.26
1555 1686 4.502105 TGTTAGCCTATTCCAATCTGCA 57.498 40.909 0.00 0.00 0.00 4.41
1556 1687 4.854173 TGTTAGCCTATTCCAATCTGCAA 58.146 39.130 0.00 0.00 0.00 4.08
1557 1688 4.883585 TGTTAGCCTATTCCAATCTGCAAG 59.116 41.667 0.00 0.00 0.00 4.01
1571 1702 4.630894 TCTGCAAGACGTTCATTTGTTT 57.369 36.364 0.00 0.00 38.67 2.83
1572 1703 4.597079 TCTGCAAGACGTTCATTTGTTTC 58.403 39.130 0.00 0.00 38.67 2.78
1573 1704 4.335315 TCTGCAAGACGTTCATTTGTTTCT 59.665 37.500 0.00 0.00 38.67 2.52
1574 1705 4.350346 TGCAAGACGTTCATTTGTTTCTG 58.650 39.130 0.00 0.00 0.00 3.02
1575 1706 4.142491 TGCAAGACGTTCATTTGTTTCTGT 60.142 37.500 0.00 0.00 0.00 3.41
1576 1707 4.798387 GCAAGACGTTCATTTGTTTCTGTT 59.202 37.500 0.00 0.00 0.00 3.16
1577 1708 5.288472 GCAAGACGTTCATTTGTTTCTGTTT 59.712 36.000 0.00 0.00 0.00 2.83
1578 1709 6.183360 GCAAGACGTTCATTTGTTTCTGTTTT 60.183 34.615 0.00 0.00 0.00 2.43
1579 1710 6.869421 AGACGTTCATTTGTTTCTGTTTTG 57.131 33.333 0.00 0.00 0.00 2.44
1580 1711 6.386654 AGACGTTCATTTGTTTCTGTTTTGT 58.613 32.000 0.00 0.00 0.00 2.83
1581 1712 6.866248 AGACGTTCATTTGTTTCTGTTTTGTT 59.134 30.769 0.00 0.00 0.00 2.83
1582 1713 8.024285 AGACGTTCATTTGTTTCTGTTTTGTTA 58.976 29.630 0.00 0.00 0.00 2.41
1583 1714 8.696410 ACGTTCATTTGTTTCTGTTTTGTTAT 57.304 26.923 0.00 0.00 0.00 1.89
1584 1715 8.591312 ACGTTCATTTGTTTCTGTTTTGTTATG 58.409 29.630 0.00 0.00 0.00 1.90
1596 1727 4.234574 GTTTTGTTATGGCTTGGTAGTGC 58.765 43.478 0.00 0.00 0.00 4.40
1604 1735 1.072505 CTTGGTAGTGCAACCCGGT 59.927 57.895 5.11 0.00 38.90 5.28
1614 1745 0.320334 GCAACCCGGTCCATTTTTGG 60.320 55.000 0.00 0.00 0.00 3.28
1615 1746 1.044611 CAACCCGGTCCATTTTTGGT 58.955 50.000 0.00 0.00 0.00 3.67
1619 1750 1.476488 CCCGGTCCATTTTTGGTGATC 59.524 52.381 0.00 0.00 0.00 2.92
1620 1751 2.166829 CCGGTCCATTTTTGGTGATCA 58.833 47.619 0.00 0.00 0.00 2.92
1622 1753 3.006323 CCGGTCCATTTTTGGTGATCAAA 59.994 43.478 0.00 0.00 42.98 2.69
1680 1813 8.893727 GTTAGATTTACACTTCATGCTTGGTAT 58.106 33.333 0.00 0.00 0.00 2.73
1681 1814 7.944729 AGATTTACACTTCATGCTTGGTATT 57.055 32.000 0.00 0.00 0.00 1.89
1682 1815 7.765307 AGATTTACACTTCATGCTTGGTATTG 58.235 34.615 0.00 0.00 0.00 1.90
1683 1816 5.895636 TTACACTTCATGCTTGGTATTGG 57.104 39.130 0.00 0.00 0.00 3.16
1684 1817 3.766545 ACACTTCATGCTTGGTATTGGT 58.233 40.909 0.00 0.00 0.00 3.67
1685 1818 4.917385 ACACTTCATGCTTGGTATTGGTA 58.083 39.130 0.00 0.00 0.00 3.25
1686 1819 4.943705 ACACTTCATGCTTGGTATTGGTAG 59.056 41.667 0.00 0.00 0.00 3.18
1687 1820 5.185454 CACTTCATGCTTGGTATTGGTAGA 58.815 41.667 0.00 0.00 0.00 2.59
1688 1821 5.295292 CACTTCATGCTTGGTATTGGTAGAG 59.705 44.000 0.00 0.00 0.00 2.43
1689 1822 5.045578 ACTTCATGCTTGGTATTGGTAGAGT 60.046 40.000 0.00 0.00 0.00 3.24
1690 1823 5.023533 TCATGCTTGGTATTGGTAGAGTC 57.976 43.478 0.00 0.00 0.00 3.36
1694 1827 5.185454 TGCTTGGTATTGGTAGAGTCAATG 58.815 41.667 0.00 0.00 36.40 2.82
1712 1845 7.584987 AGTCAATGTTCAAGCTACATTACAAC 58.415 34.615 11.96 10.69 42.63 3.32
1725 1858 3.679980 ACATTACAACATGACTCGTGCTC 59.320 43.478 0.00 0.00 0.00 4.26
1727 1860 1.502231 ACAACATGACTCGTGCTCAC 58.498 50.000 0.00 0.00 0.00 3.51
1740 1873 3.056607 TCGTGCTCACTGAAATCTCATCA 60.057 43.478 0.00 0.00 0.00 3.07
1744 1877 4.634443 TGCTCACTGAAATCTCATCATGTG 59.366 41.667 0.00 0.00 32.28 3.21
1816 1951 5.243207 ACGTGTAGGTTTTTCTAGGGATTG 58.757 41.667 0.00 0.00 0.00 2.67
1828 1963 4.546674 TCTAGGGATTGTACTGCATGAGA 58.453 43.478 0.00 0.00 0.00 3.27
1867 2002 5.310409 TCCCCTTAGAATAAGCATCCAAG 57.690 43.478 0.00 0.00 0.00 3.61
1881 2016 5.021458 AGCATCCAAGGACATTTCAGATTT 58.979 37.500 0.00 0.00 0.00 2.17
1886 2021 6.487828 TCCAAGGACATTTCAGATTTGATCT 58.512 36.000 0.00 0.00 41.15 2.75
1935 2070 7.271511 AGATAGCTAGATTCCTTGTGTGAAAG 58.728 38.462 0.00 0.00 0.00 2.62
1951 2086 3.057526 GTGAAAGCAACCCACCACTATTC 60.058 47.826 0.00 0.00 0.00 1.75
1955 2090 2.084546 GCAACCCACCACTATTCTGTC 58.915 52.381 0.00 0.00 0.00 3.51
1957 2092 3.338249 CAACCCACCACTATTCTGTCAG 58.662 50.000 0.00 0.00 0.00 3.51
1958 2093 2.621070 ACCCACCACTATTCTGTCAGT 58.379 47.619 0.00 0.00 0.00 3.41
1959 2094 2.303022 ACCCACCACTATTCTGTCAGTG 59.697 50.000 0.00 0.00 41.51 3.66
1967 2102 3.774766 ACTATTCTGTCAGTGGTATGGCA 59.225 43.478 0.00 0.00 32.88 4.92
1971 2106 2.305635 TCTGTCAGTGGTATGGCATGTT 59.694 45.455 10.98 0.00 33.58 2.71
1973 2108 2.017049 GTCAGTGGTATGGCATGTTCC 58.983 52.381 10.98 10.36 0.00 3.62
1997 2136 1.337823 ACTATGAGGCGTTGCGACTTT 60.338 47.619 1.84 0.00 46.07 2.66
2010 2149 6.411652 CGTTGCGACTTTAATCTTAAGATCC 58.588 40.000 18.19 3.83 32.75 3.36
2018 2157 3.372660 AATCTTAAGATCCGTCGGCTC 57.627 47.619 18.19 6.72 32.75 4.70
2028 2167 1.715862 CCGTCGGCTCAATCTCTCGA 61.716 60.000 0.00 0.00 0.00 4.04
2040 2179 5.767269 TCAATCTCTCGAAGATGCTCATAC 58.233 41.667 9.79 0.00 44.26 2.39
2056 2195 2.687935 TCATACGAGTAGAGCATGTGCA 59.312 45.455 7.83 0.00 45.16 4.57
2086 2225 4.568956 TCATAGGGATGAATGTGCGTATG 58.431 43.478 0.00 0.00 39.20 2.39
2087 2226 4.040339 TCATAGGGATGAATGTGCGTATGT 59.960 41.667 7.59 0.00 39.20 2.29
2088 2227 5.245075 TCATAGGGATGAATGTGCGTATGTA 59.755 40.000 7.59 0.00 39.20 2.29
2100 2245 3.734231 GTGCGTATGTATATGTGAGCGTT 59.266 43.478 0.00 0.00 0.00 4.84
2101 2246 4.913345 GTGCGTATGTATATGTGAGCGTTA 59.087 41.667 0.00 0.00 0.00 3.18
2116 2261 4.083217 TGAGCGTTAGTTTTTGTGTTGTGT 60.083 37.500 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 2.197465 AGATTACAGGGGGAGTTCCAC 58.803 52.381 0.00 0.00 39.99 4.02
156 159 5.302313 AGTCGTTCCTTTCTAGTTTCTCAGT 59.698 40.000 0.00 0.00 0.00 3.41
285 288 3.350833 ACCGAGGTGACTAGATTTACGT 58.649 45.455 0.00 0.00 44.43 3.57
331 334 3.857157 AGACTAAAAGTTGGGACTGCA 57.143 42.857 0.00 0.00 35.91 4.41
337 340 8.197439 AGAAAAATGACAAGACTAAAAGTTGGG 58.803 33.333 0.00 0.00 0.00 4.12
338 341 9.586435 AAGAAAAATGACAAGACTAAAAGTTGG 57.414 29.630 0.00 0.00 0.00 3.77
353 356 7.039714 AGGATGAACCCAACTAAGAAAAATGAC 60.040 37.037 0.00 0.00 40.05 3.06
380 383 8.421784 TGACATCCTCTTACATAATTACTGGAC 58.578 37.037 0.00 0.00 0.00 4.02
420 423 4.221703 AGAGGGCTATACATATGACAGTGC 59.778 45.833 10.38 6.80 0.00 4.40
557 616 7.118535 TCGAACTATTAGCAGTAAATTTGTGCA 59.881 33.333 22.32 9.02 39.80 4.57
572 631 9.708222 CAGAAAAACCATCAATCGAACTATTAG 57.292 33.333 0.00 0.00 0.00 1.73
578 637 7.083858 TCAATCAGAAAAACCATCAATCGAAC 58.916 34.615 0.00 0.00 0.00 3.95
584 643 7.822161 TCTTCTCAATCAGAAAAACCATCAA 57.178 32.000 0.00 0.00 40.83 2.57
589 648 7.173907 TCAGTCATCTTCTCAATCAGAAAAACC 59.826 37.037 0.00 0.00 40.83 3.27
600 659 4.617067 GCTCGACTTCAGTCATCTTCTCAA 60.617 45.833 7.71 0.00 44.99 3.02
733 792 1.778334 TACTCGATGTGTGTGTGTGC 58.222 50.000 0.00 0.00 0.00 4.57
744 803 2.920227 GCTCGCTCTGGATTACTCGATG 60.920 54.545 0.00 0.00 0.00 3.84
745 804 1.268352 GCTCGCTCTGGATTACTCGAT 59.732 52.381 0.00 0.00 0.00 3.59
746 805 0.663688 GCTCGCTCTGGATTACTCGA 59.336 55.000 0.00 0.00 0.00 4.04
747 806 0.665835 AGCTCGCTCTGGATTACTCG 59.334 55.000 0.00 0.00 0.00 4.18
846 905 3.948719 TGCCCCGACAGGTGGAAC 61.949 66.667 0.00 0.00 35.12 3.62
955 1030 0.394938 TGCCTCTCCTTGTACGCAAA 59.605 50.000 0.00 0.00 33.73 3.68
971 1064 3.909086 AAGCGACCCTCTTGCTGCC 62.909 63.158 0.00 0.00 38.89 4.85
994 1095 1.468520 CACGAGGTAAAACATGGCTGG 59.531 52.381 0.00 0.00 0.00 4.85
1160 1267 4.557690 CGGCATACATATAGCGTTACTGAC 59.442 45.833 0.00 0.00 0.00 3.51
1177 1284 1.144093 CCAGGGGAATAAACCGGCATA 59.856 52.381 0.00 0.00 0.00 3.14
1178 1285 0.106217 CCAGGGGAATAAACCGGCAT 60.106 55.000 0.00 0.00 0.00 4.40
1179 1286 1.304952 CCAGGGGAATAAACCGGCA 59.695 57.895 0.00 0.00 0.00 5.69
1181 1288 1.822371 CAAACCAGGGGAATAAACCGG 59.178 52.381 0.00 0.00 0.00 5.28
1182 1289 1.203758 GCAAACCAGGGGAATAAACCG 59.796 52.381 0.00 0.00 0.00 4.44
1183 1290 2.536066 AGCAAACCAGGGGAATAAACC 58.464 47.619 0.00 0.00 0.00 3.27
1184 1291 4.039852 TGAAAGCAAACCAGGGGAATAAAC 59.960 41.667 0.00 0.00 0.00 2.01
1188 1295 2.250924 CTGAAAGCAAACCAGGGGAAT 58.749 47.619 0.00 0.00 0.00 3.01
1211 1320 9.736023 ACAAAAGTAAGAAAGAAAATACAGCAG 57.264 29.630 0.00 0.00 0.00 4.24
1213 1322 9.952188 AGACAAAAGTAAGAAAGAAAATACAGC 57.048 29.630 0.00 0.00 0.00 4.40
1253 1364 5.140177 CACTCGTTGCAAGATAAAGAACAC 58.860 41.667 0.00 0.00 0.00 3.32
1285 1397 1.380380 GGGGAAACATCCTGGCTGG 60.380 63.158 3.65 3.65 37.10 4.85
1291 1403 4.510167 CTGATTACAGGGGAAACATCCT 57.490 45.455 0.00 0.00 40.14 3.24
1327 1447 4.521639 ACATTTGCATCAAGAAGAAGAGCA 59.478 37.500 0.00 0.00 32.93 4.26
1329 1449 7.220300 GCAATACATTTGCATCAAGAAGAAGAG 59.780 37.037 5.49 0.00 44.34 2.85
1345 1465 5.047164 TGCATCAAGGTCAAGCAATACATTT 60.047 36.000 0.00 0.00 31.42 2.32
1359 1479 2.270352 TTCCGAAGTTGCATCAAGGT 57.730 45.000 0.00 0.00 0.00 3.50
1360 1480 3.504863 CATTTCCGAAGTTGCATCAAGG 58.495 45.455 0.00 0.00 0.00 3.61
1361 1481 2.919229 GCATTTCCGAAGTTGCATCAAG 59.081 45.455 11.33 0.00 35.22 3.02
1362 1482 2.668001 CGCATTTCCGAAGTTGCATCAA 60.668 45.455 14.78 0.00 34.80 2.57
1363 1483 1.135717 CGCATTTCCGAAGTTGCATCA 60.136 47.619 14.78 0.00 34.80 3.07
1364 1484 1.135689 ACGCATTTCCGAAGTTGCATC 60.136 47.619 14.78 0.00 34.80 3.91
1365 1485 0.881118 ACGCATTTCCGAAGTTGCAT 59.119 45.000 14.78 1.40 34.80 3.96
1374 1494 1.606606 GAAGAGCAAACGCATTTCCG 58.393 50.000 0.00 0.00 0.00 4.30
1376 1496 1.069227 ACGGAAGAGCAAACGCATTTC 60.069 47.619 0.00 0.00 0.00 2.17
1382 1502 0.934496 TTGTGACGGAAGAGCAAACG 59.066 50.000 0.00 0.00 0.00 3.60
1394 1514 1.423845 GCAACCGGCTATTGTGACG 59.576 57.895 0.00 0.00 40.25 4.35
1413 1544 2.477021 CGATCTGAGACTGTCGACTTGG 60.477 54.545 17.92 9.41 36.25 3.61
1416 1547 0.730265 GCGATCTGAGACTGTCGACT 59.270 55.000 17.92 0.00 36.25 4.18
1419 1550 2.096013 TGTAAGCGATCTGAGACTGTCG 59.904 50.000 1.52 0.00 37.17 4.35
1447 1578 7.025520 AGCCATCATACCAGATAATTTAGCT 57.974 36.000 0.00 0.00 0.00 3.32
1527 1658 3.820557 TGGAATAGGCTAACATCCAAGC 58.179 45.455 18.99 0.00 37.24 4.01
1530 1661 5.624159 CAGATTGGAATAGGCTAACATCCA 58.376 41.667 17.94 17.94 38.36 3.41
1531 1662 4.457257 GCAGATTGGAATAGGCTAACATCC 59.543 45.833 14.22 14.22 0.00 3.51
1533 1664 5.052693 TGCAGATTGGAATAGGCTAACAT 57.947 39.130 0.00 0.00 0.00 2.71
1534 1665 4.502105 TGCAGATTGGAATAGGCTAACA 57.498 40.909 0.00 0.00 0.00 2.41
1535 1666 5.008118 GTCTTGCAGATTGGAATAGGCTAAC 59.992 44.000 0.00 0.00 0.00 2.34
1536 1667 5.126067 GTCTTGCAGATTGGAATAGGCTAA 58.874 41.667 0.00 0.00 0.00 3.09
1537 1668 4.708177 GTCTTGCAGATTGGAATAGGCTA 58.292 43.478 0.00 0.00 0.00 3.93
1538 1669 3.549794 GTCTTGCAGATTGGAATAGGCT 58.450 45.455 0.00 0.00 0.00 4.58
1539 1670 2.289002 CGTCTTGCAGATTGGAATAGGC 59.711 50.000 0.00 0.00 0.00 3.93
1540 1671 3.535561 ACGTCTTGCAGATTGGAATAGG 58.464 45.455 0.00 0.00 0.00 2.57
1541 1672 4.631377 TGAACGTCTTGCAGATTGGAATAG 59.369 41.667 0.00 0.00 0.00 1.73
1542 1673 4.574892 TGAACGTCTTGCAGATTGGAATA 58.425 39.130 0.00 0.00 0.00 1.75
1543 1674 3.411446 TGAACGTCTTGCAGATTGGAAT 58.589 40.909 0.00 0.00 0.00 3.01
1544 1675 2.844946 TGAACGTCTTGCAGATTGGAA 58.155 42.857 0.00 0.00 0.00 3.53
1545 1676 2.542020 TGAACGTCTTGCAGATTGGA 57.458 45.000 0.00 0.00 0.00 3.53
1546 1677 3.837213 AATGAACGTCTTGCAGATTGG 57.163 42.857 0.00 0.00 0.00 3.16
1547 1678 4.539870 ACAAATGAACGTCTTGCAGATTG 58.460 39.130 0.00 0.00 0.00 2.67
1548 1679 4.836125 ACAAATGAACGTCTTGCAGATT 57.164 36.364 0.00 0.00 0.00 2.40
1549 1680 4.836125 AACAAATGAACGTCTTGCAGAT 57.164 36.364 0.00 0.00 0.00 2.90
1550 1681 4.335315 AGAAACAAATGAACGTCTTGCAGA 59.665 37.500 0.00 0.00 0.00 4.26
1551 1682 4.438797 CAGAAACAAATGAACGTCTTGCAG 59.561 41.667 0.00 0.00 0.00 4.41
1552 1683 4.142491 ACAGAAACAAATGAACGTCTTGCA 60.142 37.500 0.00 0.00 0.00 4.08
1553 1684 4.351192 ACAGAAACAAATGAACGTCTTGC 58.649 39.130 0.00 0.00 0.00 4.01
1554 1685 6.869421 AAACAGAAACAAATGAACGTCTTG 57.131 33.333 0.00 0.00 0.00 3.02
1555 1686 6.866248 ACAAAACAGAAACAAATGAACGTCTT 59.134 30.769 0.00 0.00 0.00 3.01
1556 1687 6.386654 ACAAAACAGAAACAAATGAACGTCT 58.613 32.000 0.00 0.00 0.00 4.18
1557 1688 6.626199 ACAAAACAGAAACAAATGAACGTC 57.374 33.333 0.00 0.00 0.00 4.34
1558 1689 8.591312 CATAACAAAACAGAAACAAATGAACGT 58.409 29.630 0.00 0.00 0.00 3.99
1559 1690 8.055402 CCATAACAAAACAGAAACAAATGAACG 58.945 33.333 0.00 0.00 0.00 3.95
1560 1691 7.850492 GCCATAACAAAACAGAAACAAATGAAC 59.150 33.333 0.00 0.00 0.00 3.18
1561 1692 7.768120 AGCCATAACAAAACAGAAACAAATGAA 59.232 29.630 0.00 0.00 0.00 2.57
1562 1693 7.271511 AGCCATAACAAAACAGAAACAAATGA 58.728 30.769 0.00 0.00 0.00 2.57
1563 1694 7.481275 AGCCATAACAAAACAGAAACAAATG 57.519 32.000 0.00 0.00 0.00 2.32
1564 1695 7.012232 CCAAGCCATAACAAAACAGAAACAAAT 59.988 33.333 0.00 0.00 0.00 2.32
1565 1696 6.314896 CCAAGCCATAACAAAACAGAAACAAA 59.685 34.615 0.00 0.00 0.00 2.83
1566 1697 5.814705 CCAAGCCATAACAAAACAGAAACAA 59.185 36.000 0.00 0.00 0.00 2.83
1567 1698 5.105146 ACCAAGCCATAACAAAACAGAAACA 60.105 36.000 0.00 0.00 0.00 2.83
1568 1699 5.356426 ACCAAGCCATAACAAAACAGAAAC 58.644 37.500 0.00 0.00 0.00 2.78
1569 1700 5.606348 ACCAAGCCATAACAAAACAGAAA 57.394 34.783 0.00 0.00 0.00 2.52
1570 1701 5.830991 ACTACCAAGCCATAACAAAACAGAA 59.169 36.000 0.00 0.00 0.00 3.02
1571 1702 5.240623 CACTACCAAGCCATAACAAAACAGA 59.759 40.000 0.00 0.00 0.00 3.41
1572 1703 5.460646 CACTACCAAGCCATAACAAAACAG 58.539 41.667 0.00 0.00 0.00 3.16
1573 1704 4.261825 GCACTACCAAGCCATAACAAAACA 60.262 41.667 0.00 0.00 0.00 2.83
1574 1705 4.234574 GCACTACCAAGCCATAACAAAAC 58.765 43.478 0.00 0.00 0.00 2.43
1575 1706 3.891977 TGCACTACCAAGCCATAACAAAA 59.108 39.130 0.00 0.00 0.00 2.44
1576 1707 3.491342 TGCACTACCAAGCCATAACAAA 58.509 40.909 0.00 0.00 0.00 2.83
1577 1708 3.147553 TGCACTACCAAGCCATAACAA 57.852 42.857 0.00 0.00 0.00 2.83
1578 1709 2.817258 GTTGCACTACCAAGCCATAACA 59.183 45.455 0.00 0.00 0.00 2.41
1579 1710 2.163613 GGTTGCACTACCAAGCCATAAC 59.836 50.000 2.53 0.00 37.27 1.89
1580 1711 2.442413 GGTTGCACTACCAAGCCATAA 58.558 47.619 2.53 0.00 37.27 1.90
1581 1712 2.122783 GGTTGCACTACCAAGCCATA 57.877 50.000 2.53 0.00 37.27 2.74
1582 1713 2.961424 GGTTGCACTACCAAGCCAT 58.039 52.632 2.53 0.00 37.27 4.40
1583 1714 4.492604 GGTTGCACTACCAAGCCA 57.507 55.556 2.53 0.00 37.27 4.75
1596 1727 1.044611 ACCAAAAATGGACCGGGTTG 58.955 50.000 6.32 0.00 0.00 3.77
1632 1765 6.707440 ACATTCCTAACACAAATGAACACA 57.293 33.333 1.65 0.00 35.03 3.72
1649 1782 7.989826 AGCATGAAGTGTAAATCTAACATTCC 58.010 34.615 0.00 0.00 0.00 3.01
1650 1783 9.282247 CAAGCATGAAGTGTAAATCTAACATTC 57.718 33.333 0.00 0.00 0.00 2.67
1653 1786 6.714810 ACCAAGCATGAAGTGTAAATCTAACA 59.285 34.615 0.00 0.00 0.00 2.41
1680 1813 4.973168 AGCTTGAACATTGACTCTACCAA 58.027 39.130 0.00 0.00 0.00 3.67
1681 1814 4.623932 AGCTTGAACATTGACTCTACCA 57.376 40.909 0.00 0.00 0.00 3.25
1682 1815 5.479306 TGTAGCTTGAACATTGACTCTACC 58.521 41.667 0.00 0.00 0.00 3.18
1683 1816 7.602517 AATGTAGCTTGAACATTGACTCTAC 57.397 36.000 11.64 0.00 43.96 2.59
1684 1817 8.311109 TGTAATGTAGCTTGAACATTGACTCTA 58.689 33.333 19.21 0.56 44.94 2.43
1685 1818 7.161404 TGTAATGTAGCTTGAACATTGACTCT 58.839 34.615 19.21 0.00 44.94 3.24
1686 1819 7.364522 TGTAATGTAGCTTGAACATTGACTC 57.635 36.000 19.21 10.05 44.94 3.36
1687 1820 7.228507 TGTTGTAATGTAGCTTGAACATTGACT 59.771 33.333 19.21 0.74 44.94 3.41
1688 1821 7.359595 TGTTGTAATGTAGCTTGAACATTGAC 58.640 34.615 19.21 15.24 44.94 3.18
1689 1822 7.503521 TGTTGTAATGTAGCTTGAACATTGA 57.496 32.000 19.21 6.85 44.94 2.57
1690 1823 8.022550 TCATGTTGTAATGTAGCTTGAACATTG 58.977 33.333 19.21 5.75 44.94 2.82
1694 1827 7.133891 AGTCATGTTGTAATGTAGCTTGAAC 57.866 36.000 0.00 0.00 0.00 3.18
1712 1845 2.070262 TTCAGTGAGCACGAGTCATG 57.930 50.000 0.00 0.00 36.20 3.07
1725 1858 5.820947 TGATCCACATGATGAGATTTCAGTG 59.179 40.000 0.00 0.00 36.61 3.66
1727 1860 6.056236 ACTGATCCACATGATGAGATTTCAG 58.944 40.000 0.00 8.85 36.89 3.02
1770 1904 9.010029 ACGTCATTTACCAAGAAAATTGACTAT 57.990 29.630 0.00 0.00 30.60 2.12
1816 1951 9.846248 AAACATTTTCTTAATCTCATGCAGTAC 57.154 29.630 0.00 0.00 0.00 2.73
1846 1981 4.104738 TCCTTGGATGCTTATTCTAAGGGG 59.895 45.833 13.66 0.00 46.36 4.79
1881 2016 4.702831 TGCTTAGTTCACAACACAGATCA 58.297 39.130 0.00 0.00 0.00 2.92
1886 2021 2.293122 GCCATGCTTAGTTCACAACACA 59.707 45.455 0.00 0.00 0.00 3.72
1916 2051 5.335191 GGTTGCTTTCACACAAGGAATCTAG 60.335 44.000 0.00 0.00 36.60 2.43
1920 2055 2.365293 GGGTTGCTTTCACACAAGGAAT 59.635 45.455 0.00 0.00 36.60 3.01
1921 2056 1.754226 GGGTTGCTTTCACACAAGGAA 59.246 47.619 0.00 0.00 32.20 3.36
1935 2070 2.084546 GACAGAATAGTGGTGGGTTGC 58.915 52.381 0.00 0.00 0.00 4.17
1951 2086 2.408271 ACATGCCATACCACTGACAG 57.592 50.000 0.00 0.00 0.00 3.51
1955 2090 2.292267 GAGGAACATGCCATACCACTG 58.708 52.381 0.00 0.00 0.00 3.66
1957 2092 2.418368 TGAGGAACATGCCATACCAC 57.582 50.000 0.00 0.00 0.00 4.16
1958 2093 2.308570 AGTTGAGGAACATGCCATACCA 59.691 45.455 0.00 0.00 34.17 3.25
1959 2094 3.004752 AGTTGAGGAACATGCCATACC 57.995 47.619 0.00 0.00 34.17 2.73
1960 2095 5.368145 TCATAGTTGAGGAACATGCCATAC 58.632 41.667 0.00 0.00 34.17 2.39
1961 2096 5.614308 CTCATAGTTGAGGAACATGCCATA 58.386 41.667 0.00 0.00 44.78 2.74
1962 2097 4.458397 CTCATAGTTGAGGAACATGCCAT 58.542 43.478 0.00 0.00 44.78 4.40
1963 2098 3.877559 CTCATAGTTGAGGAACATGCCA 58.122 45.455 0.00 0.00 44.78 4.92
1989 2124 5.657474 ACGGATCTTAAGATTAAAGTCGCA 58.343 37.500 18.88 0.00 34.37 5.10
1990 2125 5.108330 CGACGGATCTTAAGATTAAAGTCGC 60.108 44.000 29.79 15.38 38.67 5.19
1997 2136 3.887110 TGAGCCGACGGATCTTAAGATTA 59.113 43.478 30.27 7.06 39.11 1.75
2010 2149 0.098905 TTCGAGAGATTGAGCCGACG 59.901 55.000 0.00 0.00 41.60 5.12
2018 2157 4.616381 CGTATGAGCATCTTCGAGAGATTG 59.384 45.833 7.20 5.58 42.55 2.67
2040 2179 1.657594 CACTTGCACATGCTCTACTCG 59.342 52.381 5.31 0.00 42.66 4.18
2072 2211 6.091305 GCTCACATATACATACGCACATTCAT 59.909 38.462 0.00 0.00 0.00 2.57
2086 2225 7.515643 ACACAAAAACTAACGCTCACATATAC 58.484 34.615 0.00 0.00 0.00 1.47
2087 2226 7.661127 ACACAAAAACTAACGCTCACATATA 57.339 32.000 0.00 0.00 0.00 0.86
2088 2227 6.554334 ACACAAAAACTAACGCTCACATAT 57.446 33.333 0.00 0.00 0.00 1.78


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

AutoCloner maintained by Alex Coulton.