Multiple sequence alignment - TraesCS2A01G143800

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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 TraesCS2A01G143800 chr2A 100.000 1998 0 0 1 1998 88740738 88738741 0.000000e+00 3690.0
1 TraesCS2A01G143800 chr2A 100.000 154 0 0 2377 2530 88738362 88738209 4.120000e-73 285.0
2 TraesCS2A01G143800 chr1A 89.560 1705 146 15 1 1700 525042144 525040467 0.000000e+00 2134.0
3 TraesCS2A01G143800 chr1A 92.142 1438 106 4 1 1435 488623169 488621736 0.000000e+00 2023.0
4 TraesCS2A01G143800 chr1A 91.969 1407 107 3 1 1404 590651521 590652924 0.000000e+00 1967.0
5 TraesCS2A01G143800 chr1A 89.157 249 21 4 1455 1701 590671469 590671713 3.160000e-79 305.0
6 TraesCS2A01G143800 chr1A 88.755 249 22 4 1455 1701 488621744 488621500 1.470000e-77 300.0
7 TraesCS2A01G143800 chr7A 91.933 1438 109 4 1 1435 92422392 92423825 0.000000e+00 2006.0
8 TraesCS2A01G143800 chr7A 87.550 249 24 5 1455 1701 92423817 92424060 5.330000e-72 281.0
9 TraesCS2A01G143800 chr3A 91.655 1438 108 6 1 1435 732976656 732975228 0.000000e+00 1980.0
10 TraesCS2A01G143800 chr3A 88.755 249 22 4 1455 1701 732975236 732974992 1.470000e-77 300.0
11 TraesCS2A01G143800 chr4A 89.910 1328 112 7 1 1325 723795473 723794165 0.000000e+00 1690.0
12 TraesCS2A01G143800 chr4A 92.715 151 11 0 2377 2527 581115423 581115573 4.240000e-53 219.0
13 TraesCS2A01G143800 chr4A 88.435 147 15 2 2379 2525 420526679 420526535 2.590000e-40 176.0
14 TraesCS2A01G143800 chr4A 89.474 57 3 1 1725 1778 450868048 450867992 4.520000e-08 69.4
15 TraesCS2A01G143800 chr5A 90.742 1091 94 4 348 1435 41388046 41389132 0.000000e+00 1448.0
16 TraesCS2A01G143800 chr5A 88.755 249 22 4 1455 1701 41389124 41389368 1.470000e-77 300.0
17 TraesCS2A01G143800 chr5A 87.550 249 23 5 1455 1701 41391286 41391528 5.330000e-72 281.0
18 TraesCS2A01G143800 chr5A 91.463 164 14 0 1272 1435 41391131 41391294 2.530000e-55 226.0
19 TraesCS2A01G143800 chr2B 94.507 710 36 2 1 707 748163516 748164225 0.000000e+00 1092.0
20 TraesCS2A01G143800 chr2B 90.210 286 22 2 1719 1998 543546875 543546590 3.980000e-98 368.0
21 TraesCS2A01G143800 chr2B 94.805 154 8 0 2377 2530 543546090 543545937 9.040000e-60 241.0
22 TraesCS2A01G143800 chr6B 88.732 852 85 7 585 1435 351230068 351229227 0.000000e+00 1031.0
23 TraesCS2A01G143800 chr6B 95.593 590 23 1 1 587 351230962 351230373 0.000000e+00 942.0
24 TraesCS2A01G143800 chr6B 89.157 249 21 4 1455 1701 351229235 351228991 3.160000e-79 305.0
25 TraesCS2A01G143800 chr1B 83.724 854 133 4 1 848 107524733 107523880 0.000000e+00 802.0
26 TraesCS2A01G143800 chr7B 83.489 854 135 4 1 848 29633861 29633008 0.000000e+00 791.0
27 TraesCS2A01G143800 chr5D 94.937 158 6 2 1547 1703 228504028 228504184 1.940000e-61 246.0


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 TraesCS2A01G143800 chr2A 88738209 88740738 2529 True 1987.500000 3690 100.000000 1 2530 2 chr2A.!!$R1 2529
1 TraesCS2A01G143800 chr1A 525040467 525042144 1677 True 2134.000000 2134 89.560000 1 1700 1 chr1A.!!$R1 1699
2 TraesCS2A01G143800 chr1A 590651521 590652924 1403 False 1967.000000 1967 91.969000 1 1404 1 chr1A.!!$F1 1403
3 TraesCS2A01G143800 chr1A 488621500 488623169 1669 True 1161.500000 2023 90.448500 1 1701 2 chr1A.!!$R2 1700
4 TraesCS2A01G143800 chr7A 92422392 92424060 1668 False 1143.500000 2006 89.741500 1 1701 2 chr7A.!!$F1 1700
5 TraesCS2A01G143800 chr3A 732974992 732976656 1664 True 1140.000000 1980 90.205000 1 1701 2 chr3A.!!$R1 1700
6 TraesCS2A01G143800 chr4A 723794165 723795473 1308 True 1690.000000 1690 89.910000 1 1325 1 chr4A.!!$R3 1324
7 TraesCS2A01G143800 chr5A 41388046 41391528 3482 False 563.750000 1448 89.627500 348 1701 4 chr5A.!!$F1 1353
8 TraesCS2A01G143800 chr2B 748163516 748164225 709 False 1092.000000 1092 94.507000 1 707 1 chr2B.!!$F1 706
9 TraesCS2A01G143800 chr2B 543545937 543546875 938 True 304.500000 368 92.507500 1719 2530 2 chr2B.!!$R1 811
10 TraesCS2A01G143800 chr6B 351228991 351230962 1971 True 759.333333 1031 91.160667 1 1701 3 chr6B.!!$R1 1700
11 TraesCS2A01G143800 chr1B 107523880 107524733 853 True 802.000000 802 83.724000 1 848 1 chr1B.!!$R1 847
12 TraesCS2A01G143800 chr7B 29633008 29633861 853 True 791.000000 791 83.489000 1 848 1 chr7B.!!$R1 847

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
406 411 1.149148 GTGCTTCGGACCTTGAACTC 58.851 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 4200 0.392998 GCGCCTCATCTCCTCCAAAA 60.393 55.0 0.0 0.0 0.0 2.44 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
104 105 4.767409 AGGTTATTTGAGAAAAGGGAGCAC 59.233 41.667 0.00 0.00 0.00 4.40
281 283 6.310764 AGATTTGAAGAGGTGAGATGTGAT 57.689 37.500 0.00 0.00 0.00 3.06
301 303 6.751425 TGTGATTTCAAAGCAACACAAAGTAG 59.249 34.615 0.00 0.00 35.77 2.57
329 334 5.815233 AGCTGAAGGCAGAAAGCTATATA 57.185 39.130 1.80 0.00 44.00 0.86
406 411 1.149148 GTGCTTCGGACCTTGAACTC 58.851 55.000 0.00 0.00 0.00 3.01
415 420 3.056821 CGGACCTTGAACTCTGACACATA 60.057 47.826 0.00 0.00 0.00 2.29
437 442 4.464008 ACCTTTGTGATGACAGTGACAAT 58.536 39.130 0.00 0.00 32.26 2.71
618 933 4.655649 AGCACATCCCTCAACAGTATATCA 59.344 41.667 0.00 0.00 0.00 2.15
670 985 5.565592 TTGGATATAACAAGCAACTGCAG 57.434 39.130 13.48 13.48 45.16 4.41
672 987 3.378112 GGATATAACAAGCAACTGCAGCA 59.622 43.478 15.27 0.00 45.16 4.41
716 1031 4.445452 ACTGACGAAACGCTATAAGGAA 57.555 40.909 0.00 0.00 0.00 3.36
776 1091 4.084118 GCAGAGGCTGACGAATCATATTTC 60.084 45.833 0.00 0.00 36.96 2.17
781 1096 4.516698 GGCTGACGAATCATATTTCATGGT 59.483 41.667 0.00 0.00 33.22 3.55
794 1109 9.081204 TCATATTTCATGGTTGCTAATTATGCT 57.919 29.630 0.00 0.00 0.00 3.79
800 1115 6.774170 TCATGGTTGCTAATTATGCTGAGAAT 59.226 34.615 0.00 0.00 0.00 2.40
878 1193 7.119407 GGTAACTTCCTTTGTTCAGAAGGTATC 59.881 40.741 0.55 0.00 40.78 2.24
884 1199 8.603898 TCCTTTGTTCAGAAGGTATCTACATA 57.396 34.615 3.11 0.00 43.35 2.29
913 1228 9.201127 AGTTTTATACTCTCGTCAGGTTTAAAC 57.799 33.333 9.98 9.98 28.23 2.01
914 1229 8.981647 GTTTTATACTCTCGTCAGGTTTAAACA 58.018 33.333 19.57 0.00 0.00 2.83
949 1264 7.566760 TTTATAGTTGCAGACCCATACAATG 57.433 36.000 0.00 0.00 0.00 2.82
952 1267 2.022764 TGCAGACCCATACAATGTCG 57.977 50.000 0.00 0.00 34.24 4.35
954 1269 1.743772 GCAGACCCATACAATGTCGCT 60.744 52.381 0.00 0.00 34.24 4.93
955 1270 1.935873 CAGACCCATACAATGTCGCTG 59.064 52.381 0.00 0.00 34.24 5.18
971 1286 2.035961 TCGCTGCTACAAGTTCAGAACT 59.964 45.455 10.27 10.27 45.46 3.01
977 1292 6.073003 GCTGCTACAAGTTCAGAACTAAATGT 60.073 38.462 16.46 17.84 41.91 2.71
984 1299 3.350219 TCAGAACTAAATGTGAGGCCC 57.650 47.619 0.00 0.00 0.00 5.80
985 1300 2.009774 CAGAACTAAATGTGAGGCCCG 58.990 52.381 0.00 0.00 0.00 6.13
1051 1366 7.905265 AGGATCAAACAGACATCCAGATATAG 58.095 38.462 0.00 0.00 38.95 1.31
1072 1387 2.488347 GGTAACTCCCTTGGCTCACAAA 60.488 50.000 0.00 0.00 38.91 2.83
1083 1398 4.948341 TGGCTCACAAAGTCTGTAAGTA 57.052 40.909 0.00 0.00 36.10 2.24
1087 1402 5.520649 GGCTCACAAAGTCTGTAAGTATAGC 59.479 44.000 0.00 0.00 36.10 2.97
1173 1488 8.450578 TCATCTACAAGTTCAGAACAAAATGT 57.549 30.769 15.85 15.05 0.00 2.71
1177 1492 5.894807 ACAAGTTCAGAACAAAATGTGGAG 58.105 37.500 15.85 0.00 0.00 3.86
1185 1500 3.457610 ACAAAATGTGGAGTTTGCCAG 57.542 42.857 0.00 0.00 40.13 4.85
1196 1511 1.756538 AGTTTGCCAGTCCAAAAGGTG 59.243 47.619 0.00 0.00 36.55 4.00
1197 1512 1.480545 GTTTGCCAGTCCAAAAGGTGT 59.519 47.619 0.00 0.00 36.55 4.16
1220 1535 8.850452 GTGTCAAGTTTAAAAAGAAGACTGTTG 58.150 33.333 0.00 0.00 0.00 3.33
1225 1540 7.116736 AGTTTAAAAAGAAGACTGTTGGAGGA 58.883 34.615 0.00 0.00 0.00 3.71
1314 1629 8.632679 ACTTATATATTTGCAGACCCAAACATG 58.367 33.333 0.00 0.00 37.51 3.21
1342 1657 9.520204 ACTCATCTACAAGTTCAAAACAAAATG 57.480 29.630 0.00 0.00 0.00 2.32
1351 1666 4.335400 TCAAAACAAAATGAGGGGCTTC 57.665 40.909 0.00 0.00 0.00 3.86
1408 1723 3.685139 TTCAAGGAGCAAGTAGACCTG 57.315 47.619 0.00 0.00 32.73 4.00
1439 1754 5.957798 CTTAGAGAAAGCAAAATCATGGCA 58.042 37.500 0.00 0.00 0.00 4.92
1440 1755 4.184079 AGAGAAAGCAAAATCATGGCAC 57.816 40.909 0.00 0.00 0.00 5.01
1441 1756 3.056322 AGAGAAAGCAAAATCATGGCACC 60.056 43.478 0.00 0.00 0.00 5.01
1442 1757 2.901839 AGAAAGCAAAATCATGGCACCT 59.098 40.909 0.00 0.00 0.00 4.00
1443 1758 3.056322 AGAAAGCAAAATCATGGCACCTC 60.056 43.478 0.00 0.00 0.00 3.85
1444 1759 1.927487 AGCAAAATCATGGCACCTCA 58.073 45.000 0.00 0.00 0.00 3.86
1445 1760 2.250031 AGCAAAATCATGGCACCTCAA 58.750 42.857 0.00 0.00 0.00 3.02
1446 1761 2.028748 AGCAAAATCATGGCACCTCAAC 60.029 45.455 0.00 0.00 0.00 3.18
1447 1762 2.598589 CAAAATCATGGCACCTCAACG 58.401 47.619 0.00 0.00 0.00 4.10
1448 1763 1.176527 AAATCATGGCACCTCAACGG 58.823 50.000 0.00 0.00 39.35 4.44
1450 1765 0.908910 ATCATGGCACCTCAACGGTA 59.091 50.000 0.00 0.00 46.94 4.02
1451 1766 0.908910 TCATGGCACCTCAACGGTAT 59.091 50.000 0.00 0.00 46.94 2.73
1452 1767 1.016627 CATGGCACCTCAACGGTATG 58.983 55.000 0.00 0.00 46.94 2.39
1453 1768 0.107214 ATGGCACCTCAACGGTATGG 60.107 55.000 0.00 0.00 46.94 2.74
1454 1769 1.451387 GGCACCTCAACGGTATGGG 60.451 63.158 0.00 0.00 46.94 4.00
1455 1770 2.112815 GCACCTCAACGGTATGGGC 61.113 63.158 0.00 0.00 46.94 5.36
1456 1771 1.298340 CACCTCAACGGTATGGGCA 59.702 57.895 0.00 0.00 46.94 5.36
1457 1772 0.322098 CACCTCAACGGTATGGGCAA 60.322 55.000 0.00 0.00 46.94 4.52
1458 1773 0.402504 ACCTCAACGGTATGGGCAAA 59.597 50.000 0.00 0.00 46.73 3.68
1459 1774 1.202952 ACCTCAACGGTATGGGCAAAA 60.203 47.619 0.00 0.00 46.73 2.44
1460 1775 2.099405 CCTCAACGGTATGGGCAAAAT 58.901 47.619 0.00 0.00 0.00 1.82
1461 1776 2.099098 CCTCAACGGTATGGGCAAAATC 59.901 50.000 0.00 0.00 0.00 2.17
1462 1777 2.752354 CTCAACGGTATGGGCAAAATCA 59.248 45.455 0.00 0.00 0.00 2.57
1463 1778 3.157881 TCAACGGTATGGGCAAAATCAA 58.842 40.909 0.00 0.00 0.00 2.57
1464 1779 3.192422 TCAACGGTATGGGCAAAATCAAG 59.808 43.478 0.00 0.00 0.00 3.02
1465 1780 2.099405 ACGGTATGGGCAAAATCAAGG 58.901 47.619 0.00 0.00 0.00 3.61
1466 1781 2.291282 ACGGTATGGGCAAAATCAAGGA 60.291 45.455 0.00 0.00 0.00 3.36
1467 1782 2.358898 CGGTATGGGCAAAATCAAGGAG 59.641 50.000 0.00 0.00 0.00 3.69
1468 1783 2.101415 GGTATGGGCAAAATCAAGGAGC 59.899 50.000 0.00 0.00 0.00 4.70
1469 1784 1.941377 ATGGGCAAAATCAAGGAGCA 58.059 45.000 0.00 0.00 0.00 4.26
1488 1812 5.124617 GGAGCAAGGAAAAGGAAAGTAGATG 59.875 44.000 0.00 0.00 0.00 2.90
1492 1816 6.375455 GCAAGGAAAAGGAAAGTAGATGATCA 59.625 38.462 0.00 0.00 0.00 2.92
1522 1846 0.883833 CAACCTCATGGCACCTCAAC 59.116 55.000 0.00 0.00 36.63 3.18
1533 1857 4.699637 TGGCACCTCAACGGTATAAATAG 58.300 43.478 0.00 0.00 46.94 1.73
1544 1868 9.661563 TCAACGGTATAAATAGATTCACACTTT 57.338 29.630 0.00 0.00 0.00 2.66
1583 1908 9.871238 ACTGAAGTTATACAACATTTATCTCGT 57.129 29.630 0.00 0.00 37.10 4.18
1616 1941 4.810345 AGGGTCATTTGGAGGTTTTTACA 58.190 39.130 0.00 0.00 0.00 2.41
1619 1944 5.756347 GGGTCATTTGGAGGTTTTTACAAAC 59.244 40.000 0.00 0.00 41.57 2.93
1620 1945 5.460748 GGTCATTTGGAGGTTTTTACAAACG 59.539 40.000 0.00 0.00 43.01 3.60
1642 4127 4.392940 GAAATGCCTGCATATCTACCACT 58.607 43.478 4.84 0.00 35.31 4.00
1679 4164 3.634397 AATCCTATGGCGATGTATGGG 57.366 47.619 0.00 0.00 0.00 4.00
1696 4182 2.064573 GGGCAAACCAAAGATTGTCG 57.935 50.000 0.00 0.00 39.85 4.35
1701 4187 1.247567 AACCAAAGATTGTCGGCTGG 58.752 50.000 0.00 0.00 0.00 4.85
1702 4188 0.400213 ACCAAAGATTGTCGGCTGGA 59.600 50.000 0.00 0.00 0.00 3.86
1703 4189 0.804989 CCAAAGATTGTCGGCTGGAC 59.195 55.000 0.00 0.00 46.27 4.02
1710 4196 2.741092 GTCGGCTGGACAAGGTCA 59.259 61.111 0.00 0.00 45.36 4.02
1711 4197 1.296715 GTCGGCTGGACAAGGTCAT 59.703 57.895 0.00 0.00 45.36 3.06
1712 4198 0.321653 GTCGGCTGGACAAGGTCATT 60.322 55.000 0.00 0.00 45.36 2.57
1713 4199 0.400213 TCGGCTGGACAAGGTCATTT 59.600 50.000 0.00 0.00 33.68 2.32
1714 4200 1.202879 TCGGCTGGACAAGGTCATTTT 60.203 47.619 0.00 0.00 33.68 1.82
1715 4201 1.613437 CGGCTGGACAAGGTCATTTTT 59.387 47.619 0.00 0.00 33.68 1.94
1873 4365 2.034376 ACGACCTCGACCTCAGCT 59.966 61.111 0.78 0.00 43.02 4.24
1874 4366 1.984321 GACGACCTCGACCTCAGCTC 61.984 65.000 0.78 0.00 43.02 4.09
1875 4367 2.766400 CGACCTCGACCTCAGCTCC 61.766 68.421 0.00 0.00 43.02 4.70
1907 4399 4.803426 CTGGCTGGAGTCCGACGC 62.803 72.222 4.30 7.02 0.00 5.19
2518 5131 1.226802 CAGCTCGCGTGACTGCTAT 60.227 57.895 13.13 0.00 34.10 2.97
2523 5136 2.286831 GCTCGCGTGACTGCTATAAGTA 60.287 50.000 13.13 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 7.864686 TCCATGCACTTATAAATTCATCTTCG 58.135 34.615 0.00 0.00 0.00 3.79
104 105 0.541392 TGCCATACACTAGTGCCCAG 59.459 55.000 22.90 10.58 0.00 4.45
281 283 5.417580 AGGACTACTTTGTGTTGCTTTGAAA 59.582 36.000 0.00 0.00 0.00 2.69
301 303 2.770164 TTCTGCCTTCAGCTTAGGAC 57.230 50.000 14.53 7.27 44.23 3.85
329 334 9.003658 GTATATGTAGTTGATGCTTGCCTTAAT 57.996 33.333 0.00 0.00 0.00 1.40
415 420 3.558931 TGTCACTGTCATCACAAAGGT 57.441 42.857 0.00 0.00 29.82 3.50
618 933 6.288941 TGCATCAATTGTCCATCTTTTCAT 57.711 33.333 5.13 0.00 0.00 2.57
670 985 2.839043 TTTGCGGCCTTCATGCATGC 62.839 55.000 22.25 11.82 38.60 4.06
672 987 1.514087 CTTTGCGGCCTTCATGCAT 59.486 52.632 0.00 0.00 38.60 3.96
682 997 0.521242 CGTCAGTATTGCTTTGCGGC 60.521 55.000 0.00 0.00 0.00 6.53
759 1074 5.679734 ACCATGAAATATGATTCGTCAGC 57.320 39.130 0.00 0.00 31.80 4.26
776 1091 6.381481 TTCTCAGCATAATTAGCAACCATG 57.619 37.500 8.84 0.00 0.00 3.66
781 1096 8.224389 TGCTAAATTCTCAGCATAATTAGCAA 57.776 30.769 13.16 0.60 42.68 3.91
794 1109 5.559770 TCCACATCTTGTGCTAAATTCTCA 58.440 37.500 2.09 0.00 46.51 3.27
800 1115 5.769662 ACATTTCTCCACATCTTGTGCTAAA 59.230 36.000 2.09 3.32 46.51 1.85
850 1165 6.100714 ACCTTCTGAACAAAGGAAGTTACCTA 59.899 38.462 8.81 0.00 45.15 3.08
859 1174 6.928348 TGTAGATACCTTCTGAACAAAGGA 57.072 37.500 8.81 0.00 45.15 3.36
923 1238 8.465999 CATTGTATGGGTCTGCAACTATAAAAA 58.534 33.333 0.00 0.00 0.00 1.94
940 1255 2.549926 TGTAGCAGCGACATTGTATGG 58.450 47.619 3.91 0.00 33.60 2.74
943 1258 3.313012 ACTTGTAGCAGCGACATTGTA 57.687 42.857 9.37 0.00 0.00 2.41
949 1264 2.065993 TCTGAACTTGTAGCAGCGAC 57.934 50.000 0.00 0.00 0.00 5.19
952 1267 5.924475 TTTAGTTCTGAACTTGTAGCAGC 57.076 39.130 26.33 0.00 42.81 5.25
954 1269 6.989759 TCACATTTAGTTCTGAACTTGTAGCA 59.010 34.615 26.33 6.37 42.81 3.49
955 1270 7.360438 CCTCACATTTAGTTCTGAACTTGTAGC 60.360 40.741 26.33 0.00 42.81 3.58
971 1286 0.679640 CTTGGCGGGCCTCACATTTA 60.680 55.000 11.55 0.00 36.94 1.40
984 1299 0.602562 TCATTCCTTTTGGCTTGGCG 59.397 50.000 0.00 0.00 40.12 5.69
985 1300 2.613725 CCTTCATTCCTTTTGGCTTGGC 60.614 50.000 0.00 0.00 40.12 4.52
1051 1366 0.690762 TGTGAGCCAAGGGAGTTACC 59.309 55.000 0.00 0.00 38.08 2.85
1118 1433 6.686630 TGTTTGGGTCTGCAACTATAAAATG 58.313 36.000 0.00 0.00 0.00 2.32
1119 1434 6.909550 TGTTTGGGTCTGCAACTATAAAAT 57.090 33.333 0.00 0.00 0.00 1.82
1173 1488 2.031120 CTTTTGGACTGGCAAACTCCA 58.969 47.619 4.49 4.49 31.94 3.86
1177 1492 1.480545 ACACCTTTTGGACTGGCAAAC 59.519 47.619 0.00 0.00 44.07 2.93
1185 1500 7.815549 TCTTTTTAAACTTGACACCTTTTGGAC 59.184 33.333 0.00 0.00 44.07 4.02
1191 1506 8.244113 CAGTCTTCTTTTTAAACTTGACACCTT 58.756 33.333 0.00 0.00 0.00 3.50
1196 1511 8.241367 TCCAACAGTCTTCTTTTTAAACTTGAC 58.759 33.333 0.00 0.00 0.00 3.18
1197 1512 8.343168 TCCAACAGTCTTCTTTTTAAACTTGA 57.657 30.769 0.00 0.00 0.00 3.02
1220 1535 1.777941 ACGGGTCTACTTGATCCTCC 58.222 55.000 0.00 0.00 43.81 4.30
1225 1540 4.040461 CCCATATCAACGGGTCTACTTGAT 59.960 45.833 1.51 1.51 38.08 2.57
1289 1604 8.849168 TCATGTTTGGGTCTGCAAATATATAAG 58.151 33.333 0.00 0.00 0.00 1.73
1290 1605 8.759481 TCATGTTTGGGTCTGCAAATATATAA 57.241 30.769 0.00 0.00 0.00 0.98
1351 1666 2.171003 CTTCACCCCTTTTGGCTTAGG 58.829 52.381 0.00 0.00 38.58 2.69
1365 1680 4.344359 AGTCTTCTCCTTCAACTTCACC 57.656 45.455 0.00 0.00 0.00 4.02
1366 1681 7.155328 TGAATAGTCTTCTCCTTCAACTTCAC 58.845 38.462 0.00 0.00 0.00 3.18
1368 1683 7.333174 CCTTGAATAGTCTTCTCCTTCAACTTC 59.667 40.741 0.00 0.00 34.63 3.01
1441 1756 2.752354 TGATTTTGCCCATACCGTTGAG 59.248 45.455 0.00 0.00 0.00 3.02
1442 1757 2.796557 TGATTTTGCCCATACCGTTGA 58.203 42.857 0.00 0.00 0.00 3.18
1443 1758 3.510719 CTTGATTTTGCCCATACCGTTG 58.489 45.455 0.00 0.00 0.00 4.10
1444 1759 2.495669 CCTTGATTTTGCCCATACCGTT 59.504 45.455 0.00 0.00 0.00 4.44
1445 1760 2.099405 CCTTGATTTTGCCCATACCGT 58.901 47.619 0.00 0.00 0.00 4.83
1446 1761 2.358898 CTCCTTGATTTTGCCCATACCG 59.641 50.000 0.00 0.00 0.00 4.02
1447 1762 2.101415 GCTCCTTGATTTTGCCCATACC 59.899 50.000 0.00 0.00 0.00 2.73
1448 1763 2.760092 TGCTCCTTGATTTTGCCCATAC 59.240 45.455 0.00 0.00 0.00 2.39
1449 1764 3.098774 TGCTCCTTGATTTTGCCCATA 57.901 42.857 0.00 0.00 0.00 2.74
1450 1765 1.941377 TGCTCCTTGATTTTGCCCAT 58.059 45.000 0.00 0.00 0.00 4.00
1451 1766 1.619827 CTTGCTCCTTGATTTTGCCCA 59.380 47.619 0.00 0.00 0.00 5.36
1452 1767 1.066645 CCTTGCTCCTTGATTTTGCCC 60.067 52.381 0.00 0.00 0.00 5.36
1453 1768 1.895131 TCCTTGCTCCTTGATTTTGCC 59.105 47.619 0.00 0.00 0.00 4.52
1454 1769 3.665745 TTCCTTGCTCCTTGATTTTGC 57.334 42.857 0.00 0.00 0.00 3.68
1455 1770 4.992951 CCTTTTCCTTGCTCCTTGATTTTG 59.007 41.667 0.00 0.00 0.00 2.44
1456 1771 4.901250 TCCTTTTCCTTGCTCCTTGATTTT 59.099 37.500 0.00 0.00 0.00 1.82
1457 1772 4.482990 TCCTTTTCCTTGCTCCTTGATTT 58.517 39.130 0.00 0.00 0.00 2.17
1458 1773 4.118168 TCCTTTTCCTTGCTCCTTGATT 57.882 40.909 0.00 0.00 0.00 2.57
1459 1774 3.814504 TCCTTTTCCTTGCTCCTTGAT 57.185 42.857 0.00 0.00 0.00 2.57
1460 1775 3.593442 TTCCTTTTCCTTGCTCCTTGA 57.407 42.857 0.00 0.00 0.00 3.02
1461 1776 3.638627 ACTTTCCTTTTCCTTGCTCCTTG 59.361 43.478 0.00 0.00 0.00 3.61
1462 1777 3.916035 ACTTTCCTTTTCCTTGCTCCTT 58.084 40.909 0.00 0.00 0.00 3.36
1463 1778 3.602205 ACTTTCCTTTTCCTTGCTCCT 57.398 42.857 0.00 0.00 0.00 3.69
1464 1779 4.652822 TCTACTTTCCTTTTCCTTGCTCC 58.347 43.478 0.00 0.00 0.00 4.70
1465 1780 5.940470 TCATCTACTTTCCTTTTCCTTGCTC 59.060 40.000 0.00 0.00 0.00 4.26
1466 1781 5.880901 TCATCTACTTTCCTTTTCCTTGCT 58.119 37.500 0.00 0.00 0.00 3.91
1467 1782 6.375455 TGATCATCTACTTTCCTTTTCCTTGC 59.625 38.462 0.00 0.00 0.00 4.01
1468 1783 7.928307 TGATCATCTACTTTCCTTTTCCTTG 57.072 36.000 0.00 0.00 0.00 3.61
1469 1784 8.112183 ACATGATCATCTACTTTCCTTTTCCTT 58.888 33.333 4.86 0.00 0.00 3.36
1488 1812 5.011090 TGAGGTTGTAGTGCTACATGATC 57.989 43.478 12.18 10.52 44.54 2.92
1492 1816 3.682718 GCCATGAGGTTGTAGTGCTACAT 60.683 47.826 12.18 0.00 39.46 2.29
1603 1928 5.044558 GCATTTCGTTTGTAAAAACCTCCA 58.955 37.500 2.86 0.00 0.00 3.86
1616 1941 4.275936 GGTAGATATGCAGGCATTTCGTTT 59.724 41.667 12.54 1.78 38.70 3.60
1619 1944 3.187227 GTGGTAGATATGCAGGCATTTCG 59.813 47.826 12.54 0.00 38.70 3.46
1620 1945 4.214971 CAGTGGTAGATATGCAGGCATTTC 59.785 45.833 12.54 13.60 37.82 2.17
1642 4127 5.789574 AGGATTTAGGATTGGGTTGTACA 57.210 39.130 0.00 0.00 0.00 2.90
1679 4164 1.000274 AGCCGACAATCTTTGGTTTGC 60.000 47.619 0.00 0.00 34.12 3.68
1694 4180 0.400213 AAATGACCTTGTCCAGCCGA 59.600 50.000 0.00 0.00 0.00 5.54
1713 4199 1.950484 GCGCCTCATCTCCTCCAAAAA 60.950 52.381 0.00 0.00 0.00 1.94
1714 4200 0.392998 GCGCCTCATCTCCTCCAAAA 60.393 55.000 0.00 0.00 0.00 2.44
1715 4201 1.221840 GCGCCTCATCTCCTCCAAA 59.778 57.895 0.00 0.00 0.00 3.28
1716 4202 1.680522 GAGCGCCTCATCTCCTCCAA 61.681 60.000 2.29 0.00 0.00 3.53
1717 4203 2.042537 AGCGCCTCATCTCCTCCA 60.043 61.111 2.29 0.00 0.00 3.86
1718 4204 2.733945 GAGCGCCTCATCTCCTCC 59.266 66.667 2.29 0.00 0.00 4.30
1719 4205 2.733945 GGAGCGCCTCATCTCCTC 59.266 66.667 2.29 0.00 44.19 3.71
1720 4206 3.222855 CGGAGCGCCTCATCTCCT 61.223 66.667 2.29 0.00 45.12 3.69
1856 4348 2.034376 AGCTGAGGTCGAGGTCGT 59.966 61.111 0.00 0.00 40.80 4.34
2391 5004 2.037367 CGGACTCCTCTGGGGACA 59.963 66.667 0.00 0.00 39.58 4.02
2394 5007 3.141488 CGACGGACTCCTCTGGGG 61.141 72.222 0.00 0.00 0.00 4.96
2398 5011 4.049817 AGCCCGACGGACTCCTCT 62.050 66.667 17.49 0.00 0.00 3.69
2404 5017 4.681978 AAGCACAGCCCGACGGAC 62.682 66.667 17.49 2.80 0.00 4.79
2482 5095 2.248248 CTGTGTCCAGGGTAGAGACAA 58.752 52.381 0.00 0.00 41.87 3.18


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

AutoCloner maintained by Alex Coulton.