Multiple sequence alignment - TraesCS6A01G324800

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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 TraesCS6A01G324800 chr6A 100.000 4077 0 0 1 4077 558925019 558920943 0.000000e+00 7529.0
1 TraesCS6A01G324800 chr6A 90.739 2516 140 39 1599 4077 558936341 558933882 0.000000e+00 3269.0
2 TraesCS6A01G324800 chr6A 87.634 558 43 13 3083 3624 558951413 558950866 3.460000e-175 625.0
3 TraesCS6A01G324800 chr6A 80.556 648 75 31 965 1585 558937027 558936404 6.210000e-123 451.0
4 TraesCS6A01G324800 chr6A 90.805 87 6 2 3937 4022 558933755 558933670 9.260000e-22 115.0
5 TraesCS6A01G324800 chr6D 94.695 2507 88 19 1599 4077 413386357 413383868 0.000000e+00 3851.0
6 TraesCS6A01G324800 chr6D 87.654 1944 156 36 1601 3509 413397781 413395887 0.000000e+00 2183.0
7 TraesCS6A01G324800 chr6D 91.339 254 17 2 1336 1585 413386672 413386420 3.900000e-90 342.0
8 TraesCS6A01G324800 chr6D 89.340 197 16 2 965 1161 413387042 413386851 4.070000e-60 243.0
9 TraesCS6A01G324800 chr6D 92.593 81 6 0 3946 4026 413383600 413383520 2.570000e-22 117.0
10 TraesCS6A01G324800 chr6D 94.737 38 2 0 1285 1322 413398168 413398205 4.400000e-05 60.2
11 TraesCS6A01G324800 chr6B 90.758 2521 136 42 1599 4077 623448275 623445810 0.000000e+00 3275.0
12 TraesCS6A01G324800 chr6B 95.119 1639 65 7 1599 3236 623390324 623388700 0.000000e+00 2569.0
13 TraesCS6A01G324800 chr6B 86.548 959 73 24 1 904 623431405 623430448 0.000000e+00 1005.0
14 TraesCS6A01G324800 chr6B 97.441 508 12 1 3571 4077 623369836 623369329 0.000000e+00 865.0
15 TraesCS6A01G324800 chr6B 89.513 677 47 5 930 1585 623391059 623390386 0.000000e+00 835.0
16 TraesCS6A01G324800 chr6B 81.395 645 66 30 965 1585 623448952 623448338 1.030000e-130 477.0
17 TraesCS6A01G324800 chr6B 93.358 271 10 3 3306 3569 623382004 623381735 1.060000e-105 394.0
18 TraesCS6A01G324800 chr6B 83.249 197 10 9 3495 3684 623443947 623443767 4.220000e-35 159.0
19 TraesCS6A01G324800 chr6B 95.181 83 3 1 3232 3313 623382296 623382214 3.310000e-26 130.0
20 TraesCS6A01G324800 chr6B 89.655 87 7 2 3937 4022 623369202 623369117 4.310000e-20 110.0
21 TraesCS6A01G324800 chr6B 89.655 87 7 2 3937 4022 623445683 623445598 4.310000e-20 110.0


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 TraesCS6A01G324800 chr6A 558920943 558925019 4076 True 7529.000000 7529 100.000000 1 4077 1 chr6A.!!$R1 4076
1 TraesCS6A01G324800 chr6A 558933670 558937027 3357 True 1278.333333 3269 87.366667 965 4077 3 chr6A.!!$R3 3112
2 TraesCS6A01G324800 chr6A 558950866 558951413 547 True 625.000000 625 87.634000 3083 3624 1 chr6A.!!$R2 541
3 TraesCS6A01G324800 chr6D 413395887 413397781 1894 True 2183.000000 2183 87.654000 1601 3509 1 chr6D.!!$R1 1908
4 TraesCS6A01G324800 chr6D 413383520 413387042 3522 True 1138.250000 3851 91.991750 965 4077 4 chr6D.!!$R2 3112
5 TraesCS6A01G324800 chr6B 623388700 623391059 2359 True 1702.000000 2569 92.316000 930 3236 2 chr6B.!!$R4 2306
6 TraesCS6A01G324800 chr6B 623443767 623448952 5185 True 1005.250000 3275 86.264250 965 4077 4 chr6B.!!$R5 3112
7 TraesCS6A01G324800 chr6B 623430448 623431405 957 True 1005.000000 1005 86.548000 1 904 1 chr6B.!!$R1 903
8 TraesCS6A01G324800 chr6B 623369117 623369836 719 True 487.500000 865 93.548000 3571 4077 2 chr6B.!!$R2 506
9 TraesCS6A01G324800 chr6B 623381735 623382296 561 True 262.000000 394 94.269500 3232 3569 2 chr6B.!!$R3 337

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
912 967 0.033781 TTGTACACCGGCGCTTAGTT 59.966 50.0 7.64 0.0 0.0 2.24 F
918 973 0.034337 ACCGGCGCTTAGTTTCTCAA 59.966 50.0 7.64 0.0 0.0 3.02 F
1591 1692 0.036732 AGAGAAGCGGCAATGTTCCA 59.963 50.0 1.45 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2109 2276 0.387622 GGCATGTCACATGTGCACAC 60.388 55.000 24.37 17.33 40.53 3.82 R
2484 2667 3.610619 CTGTCAGCATCACGGCCCA 62.611 63.158 0.00 0.00 0.00 5.36 R
3217 3409 2.928116 GGTAGAACCACAGTCGTATTGC 59.072 50.000 0.00 0.00 38.42 3.56 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
68 69 3.181461 CCTCCCATAGCAGTCTCGATTTT 60.181 47.826 0.00 0.00 0.00 1.82
110 111 3.024431 GCTACGCTCTAGCCTAGGT 57.976 57.895 11.31 0.00 37.91 3.08
208 209 1.322442 GCAAAGGTTCTCAACTGGCT 58.678 50.000 0.00 0.00 0.00 4.75
235 236 2.557490 GGTAGATCGGACGGCTATTTCT 59.443 50.000 0.00 0.00 0.00 2.52
239 240 3.635373 AGATCGGACGGCTATTTCTTACA 59.365 43.478 0.00 0.00 0.00 2.41
243 244 3.467803 GGACGGCTATTTCTTACAGCAT 58.532 45.455 0.00 0.00 37.02 3.79
280 281 4.906618 ACCGGCCGATCTAATTGATTTAT 58.093 39.130 30.73 0.00 35.14 1.40
281 282 4.935808 ACCGGCCGATCTAATTGATTTATC 59.064 41.667 30.73 0.00 35.14 1.75
286 287 6.825721 GGCCGATCTAATTGATTTATCATCCT 59.174 38.462 0.00 0.00 36.56 3.24
289 290 9.224267 CCGATCTAATTGATTTATCATCCTGTT 57.776 33.333 0.00 0.00 36.56 3.16
318 319 3.352648 AGCGCTGCCCTTTATTTTTCTA 58.647 40.909 10.39 0.00 0.00 2.10
371 373 5.586339 TGCGAACAGTTTTTGAATTCATGA 58.414 33.333 9.40 0.00 0.00 3.07
573 581 3.809234 TGACGAAGATTGTTTGCATTCG 58.191 40.909 13.22 13.22 46.03 3.34
582 590 5.403166 AGATTGTTTGCATTCGTGAACATTG 59.597 36.000 0.52 0.00 32.64 2.82
595 603 9.689976 ATTCGTGAACATTGTTTTGAATTCATA 57.310 25.926 9.40 1.04 0.00 2.15
641 651 7.171167 ACGATTGATTTTCAAATGCATGAACAA 59.829 29.630 0.00 3.67 40.12 2.83
642 652 8.172484 CGATTGATTTTCAAATGCATGAACAAT 58.828 29.630 13.18 13.18 40.12 2.71
643 653 9.272901 GATTGATTTTCAAATGCATGAACAATG 57.727 29.630 16.15 5.00 40.12 2.82
649 679 6.528014 TCAAATGCATGAACAATGTCAAAC 57.472 33.333 0.00 0.00 38.65 2.93
660 690 8.164058 TGAACAATGTCAAACTCATGAACATA 57.836 30.769 9.75 0.00 0.00 2.29
663 693 7.031372 ACAATGTCAAACTCATGAACATATGC 58.969 34.615 9.75 0.00 0.00 3.14
747 780 3.910648 AGGAAAAAGAACGTAGGTCTCG 58.089 45.455 0.00 0.00 0.00 4.04
765 800 3.465753 CGTGCGGCGCTAGTTTTA 58.534 55.556 33.26 7.71 0.00 1.52
770 805 2.844223 GTGCGGCGCTAGTTTTATTTTC 59.156 45.455 33.26 0.00 0.00 2.29
776 811 3.339695 CGCTAGTTTTATTTTCGGCGTC 58.660 45.455 6.85 0.00 37.21 5.19
779 814 3.177605 AGTTTTATTTTCGGCGTCACG 57.822 42.857 6.85 0.00 0.00 4.35
806 841 3.744660 GAACAGATCCATACCATCACCC 58.255 50.000 0.00 0.00 0.00 4.61
849 904 2.190578 GGATCTGGAGGCCCAACG 59.809 66.667 0.00 0.00 42.98 4.10
902 957 2.244000 CAAGCACCCTTGTACACCG 58.756 57.895 0.00 0.00 42.76 4.94
903 958 1.072505 AAGCACCCTTGTACACCGG 59.927 57.895 0.00 0.00 0.00 5.28
904 959 3.053896 GCACCCTTGTACACCGGC 61.054 66.667 0.00 0.00 0.00 6.13
905 960 2.740826 CACCCTTGTACACCGGCG 60.741 66.667 0.00 0.00 0.00 6.46
906 961 4.692475 ACCCTTGTACACCGGCGC 62.692 66.667 0.00 0.00 0.00 6.53
907 962 4.388499 CCCTTGTACACCGGCGCT 62.388 66.667 7.64 0.00 0.00 5.92
908 963 2.358247 CCTTGTACACCGGCGCTT 60.358 61.111 7.64 0.00 0.00 4.68
909 964 1.079681 CCTTGTACACCGGCGCTTA 60.080 57.895 7.64 0.00 0.00 3.09
910 965 1.082117 CCTTGTACACCGGCGCTTAG 61.082 60.000 7.64 0.00 0.00 2.18
911 966 0.389426 CTTGTACACCGGCGCTTAGT 60.389 55.000 7.64 3.86 0.00 2.24
912 967 0.033781 TTGTACACCGGCGCTTAGTT 59.966 50.000 7.64 0.00 0.00 2.24
913 968 0.033781 TGTACACCGGCGCTTAGTTT 59.966 50.000 7.64 0.00 0.00 2.66
914 969 0.717784 GTACACCGGCGCTTAGTTTC 59.282 55.000 7.64 0.00 0.00 2.78
915 970 0.604578 TACACCGGCGCTTAGTTTCT 59.395 50.000 7.64 0.00 0.00 2.52
916 971 0.669625 ACACCGGCGCTTAGTTTCTC 60.670 55.000 7.64 0.00 0.00 2.87
917 972 0.669318 CACCGGCGCTTAGTTTCTCA 60.669 55.000 7.64 0.00 0.00 3.27
918 973 0.034337 ACCGGCGCTTAGTTTCTCAA 59.966 50.000 7.64 0.00 0.00 3.02
919 974 1.153353 CCGGCGCTTAGTTTCTCAAA 58.847 50.000 7.64 0.00 0.00 2.69
920 975 1.533731 CCGGCGCTTAGTTTCTCAAAA 59.466 47.619 7.64 0.00 0.00 2.44
921 976 2.031508 CCGGCGCTTAGTTTCTCAAAAA 60.032 45.455 7.64 0.00 0.00 1.94
922 977 3.226347 CGGCGCTTAGTTTCTCAAAAAG 58.774 45.455 7.64 0.00 0.00 2.27
923 978 3.059188 CGGCGCTTAGTTTCTCAAAAAGA 60.059 43.478 7.64 0.00 0.00 2.52
924 979 4.553938 CGGCGCTTAGTTTCTCAAAAAGAA 60.554 41.667 7.64 0.00 42.35 2.52
942 997 7.821595 AAAAGAAAAAGAAAAAGTACACCGG 57.178 32.000 0.00 0.00 0.00 5.28
1119 1174 1.141858 GCTTCCTCTTGTATCCCCCAG 59.858 57.143 0.00 0.00 0.00 4.45
1125 1180 3.605054 TTGTATCCCCCAGCCCCCA 62.605 63.158 0.00 0.00 0.00 4.96
1133 1188 4.480476 CCAGCCCCCATTTCCCCC 62.480 72.222 0.00 0.00 0.00 5.40
1183 1249 4.799419 TGTTTTAGTTTAGTCACGGCAC 57.201 40.909 0.00 0.00 0.00 5.01
1186 1252 1.340088 TAGTTTAGTCACGGCACCCA 58.660 50.000 0.00 0.00 0.00 4.51
1188 1254 1.134037 AGTTTAGTCACGGCACCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
1273 1360 1.676529 TCCGCGGAAACATGTTGAAAA 59.323 42.857 28.99 0.00 0.00 2.29
1283 1370 5.738118 AACATGTTGAAAATTGGTTGCAG 57.262 34.783 11.07 0.00 0.00 4.41
1324 1419 0.698818 AGGATTCGGTGCCTTTTCCT 59.301 50.000 0.00 0.00 0.00 3.36
1391 1491 5.590259 TCCAGCTGTTTTTAAGATGATAGCC 59.410 40.000 13.81 0.00 32.79 3.93
1429 1530 4.015084 AGCATTTGAAGAGAACTGATGGG 58.985 43.478 0.00 0.00 0.00 4.00
1434 1535 2.040278 TGAAGAGAACTGATGGGGGTTG 59.960 50.000 0.00 0.00 0.00 3.77
1435 1536 0.329596 AGAGAACTGATGGGGGTTGC 59.670 55.000 0.00 0.00 0.00 4.17
1548 1649 0.302890 GTGAAGGATCATCTTGCGCG 59.697 55.000 0.00 0.00 38.01 6.86
1582 1683 3.639538 TCATAAATACGAGAGAAGCGGC 58.360 45.455 0.00 0.00 0.00 6.53
1585 1686 2.604046 AATACGAGAGAAGCGGCAAT 57.396 45.000 1.45 0.00 0.00 3.56
1586 1687 1.858091 ATACGAGAGAAGCGGCAATG 58.142 50.000 1.45 0.00 0.00 2.82
1588 1689 0.320771 ACGAGAGAAGCGGCAATGTT 60.321 50.000 1.45 0.00 0.00 2.71
1590 1691 0.729690 GAGAGAAGCGGCAATGTTCC 59.270 55.000 1.45 0.00 0.00 3.62
1591 1692 0.036732 AGAGAAGCGGCAATGTTCCA 59.963 50.000 1.45 0.00 0.00 3.53
1594 1695 1.474077 AGAAGCGGCAATGTTCCATTC 59.526 47.619 1.45 0.00 0.00 2.67
1595 1696 0.171007 AAGCGGCAATGTTCCATTCG 59.829 50.000 1.45 0.00 0.00 3.34
1596 1697 1.226660 GCGGCAATGTTCCATTCGG 60.227 57.895 0.00 0.00 0.00 4.30
1597 1698 1.653094 GCGGCAATGTTCCATTCGGA 61.653 55.000 0.00 0.00 40.60 4.55
1610 1759 3.625764 TCCATTCGGAATTTCGGATTCAC 59.374 43.478 6.24 4.06 38.83 3.18
1631 1782 1.348036 GGCACCTACTGTCTTTCCTGT 59.652 52.381 0.00 0.00 0.00 4.00
1830 1981 1.065273 GCATGGCAATCAGCTTCCG 59.935 57.895 0.00 0.00 44.79 4.30
1876 2043 6.294675 CCAAAATCTTCTCAAGGTTGCATACA 60.295 38.462 0.00 0.00 30.76 2.29
2109 2276 0.622665 AGCAAGATTCAGGGGTGGAG 59.377 55.000 0.00 0.00 0.00 3.86
2167 2334 7.499563 TGCTTGGTTTTGTACACTACAGATTTA 59.500 33.333 0.00 0.00 40.24 1.40
2242 2409 2.941025 CCCAAGGGAAGGGGCTGA 60.941 66.667 0.00 0.00 42.90 4.26
2244 2411 2.234296 CCAAGGGAAGGGGCTGAGT 61.234 63.158 0.00 0.00 0.00 3.41
2368 2535 2.283298 CATAGAGTGTCATGGTGTGGC 58.717 52.381 0.00 0.00 0.00 5.01
2799 2983 6.536582 CGTATGTTGACTCCTTCATTTCTCAT 59.463 38.462 0.00 0.00 32.84 2.90
3217 3409 0.675522 AACTAATGCACGGGGGAACG 60.676 55.000 0.00 0.00 40.31 3.95
3375 3788 5.571357 CCGTACCAAACTTGTGAATATTTGC 59.429 40.000 0.00 0.00 31.95 3.68
3378 3791 6.403866 ACCAAACTTGTGAATATTTGCTCA 57.596 33.333 0.00 0.00 31.95 4.26
3502 3936 8.864069 TTGGTTAGTGTGTTAATGAATTTGTG 57.136 30.769 0.00 0.00 0.00 3.33
3544 3978 3.942748 ACACTTTAGGAAACAAGCACGAA 59.057 39.130 0.00 0.00 0.00 3.85
3628 4066 2.132762 CGGACCAGTACACAAGTTGTC 58.867 52.381 5.27 0.00 39.91 3.18
3713 4153 2.344093 TCCTAGGGCTTTCTCCTTGT 57.656 50.000 9.46 0.00 35.92 3.16
3908 4351 4.215613 CCTGATATTCTCCATGTCGTCGTA 59.784 45.833 0.00 0.00 0.00 3.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.043116 TGCTATGGGAGGACAGACCG 61.043 60.000 0.00 0.00 44.74 4.79
68 69 2.356382 CCGTGCCACTGTTGTAAAGAAA 59.644 45.455 0.00 0.00 0.00 2.52
78 79 3.238497 TAGCCACCGTGCCACTGT 61.238 61.111 0.00 0.00 0.00 3.55
121 122 0.393077 ACAAAGGTCCACCGAGACAG 59.607 55.000 0.00 0.00 42.08 3.51
127 128 1.810151 CCATGTTACAAAGGTCCACCG 59.190 52.381 0.00 0.00 42.08 4.94
172 173 4.370917 CTTTGCAACTGCTATTTTGGTGT 58.629 39.130 0.00 0.00 42.66 4.16
179 180 4.144297 TGAGAACCTTTGCAACTGCTATT 58.856 39.130 0.00 0.00 42.66 1.73
208 209 2.184830 CGTCCGATCTACCGCCTCA 61.185 63.158 0.00 0.00 0.00 3.86
235 236 4.827692 ACAATAACCGTCAGATGCTGTAA 58.172 39.130 0.00 0.00 32.61 2.41
239 240 3.793559 GGTACAATAACCGTCAGATGCT 58.206 45.455 0.00 0.00 0.00 3.79
261 262 6.825721 AGGATGATAAATCAATTAGATCGGCC 59.174 38.462 0.00 0.00 40.69 6.13
346 348 6.533012 TCATGAATTCAAAAACTGTTCGCAAA 59.467 30.769 13.09 0.00 0.00 3.68
551 558 4.218265 CGAATGCAAACAATCTTCGTCAA 58.782 39.130 7.92 0.00 35.29 3.18
559 566 5.175491 ACAATGTTCACGAATGCAAACAATC 59.825 36.000 3.68 0.00 0.00 2.67
563 570 5.388225 AAACAATGTTCACGAATGCAAAC 57.612 34.783 0.00 0.00 0.00 2.93
620 630 7.441458 TGACATTGTTCATGCATTTGAAAATCA 59.559 29.630 4.34 0.00 37.36 2.57
621 631 7.798801 TGACATTGTTCATGCATTTGAAAATC 58.201 30.769 4.34 0.00 37.36 2.17
632 642 5.463286 TCATGAGTTTGACATTGTTCATGC 58.537 37.500 17.70 0.00 40.85 4.06
641 651 5.585844 TCGCATATGTTCATGAGTTTGACAT 59.414 36.000 13.12 13.12 0.00 3.06
642 652 4.934602 TCGCATATGTTCATGAGTTTGACA 59.065 37.500 4.29 0.00 0.00 3.58
643 653 5.469373 TCGCATATGTTCATGAGTTTGAC 57.531 39.130 4.29 0.00 0.00 3.18
649 679 2.866156 ACCGTTCGCATATGTTCATGAG 59.134 45.455 4.29 0.00 0.00 2.90
726 759 3.860002 GCGAGACCTACGTTCTTTTTCCT 60.860 47.826 0.00 0.00 0.00 3.36
754 787 2.098870 CGCCGAAAATAAAACTAGCGC 58.901 47.619 0.00 0.00 35.58 5.92
756 789 4.086574 GTGACGCCGAAAATAAAACTAGC 58.913 43.478 0.00 0.00 0.00 3.42
757 790 4.320491 CGTGACGCCGAAAATAAAACTAG 58.680 43.478 0.00 0.00 0.00 2.57
758 791 4.310675 CGTGACGCCGAAAATAAAACTA 57.689 40.909 0.00 0.00 0.00 2.24
759 792 3.177605 CGTGACGCCGAAAATAAAACT 57.822 42.857 0.00 0.00 0.00 2.66
776 811 2.456119 GGATCTGTTCCAGCGCGTG 61.456 63.158 8.43 4.73 44.74 5.34
794 829 1.525995 GGCGTGGGGTGATGGTATG 60.526 63.158 0.00 0.00 0.00 2.39
798 833 4.838152 CTCGGCGTGGGGTGATGG 62.838 72.222 6.85 0.00 0.00 3.51
839 894 1.828979 TGGTAAATTCGTTGGGCCTC 58.171 50.000 4.53 0.00 0.00 4.70
849 904 4.098044 GGCTTTCTAGGCCTTGGTAAATTC 59.902 45.833 12.58 1.94 45.57 2.17
895 950 0.717784 GAAACTAAGCGCCGGTGTAC 59.282 55.000 17.91 0.00 0.00 2.90
896 951 0.604578 AGAAACTAAGCGCCGGTGTA 59.395 50.000 17.91 0.57 0.00 2.90
897 952 0.669625 GAGAAACTAAGCGCCGGTGT 60.670 55.000 17.91 0.00 0.00 4.16
898 953 0.669318 TGAGAAACTAAGCGCCGGTG 60.669 55.000 11.67 11.67 0.00 4.94
899 954 0.034337 TTGAGAAACTAAGCGCCGGT 59.966 50.000 2.29 0.00 0.00 5.28
900 955 1.153353 TTTGAGAAACTAAGCGCCGG 58.847 50.000 2.29 0.00 0.00 6.13
901 956 2.961522 TTTTGAGAAACTAAGCGCCG 57.038 45.000 2.29 0.00 0.00 6.46
902 957 4.483476 TCTTTTTGAGAAACTAAGCGCC 57.517 40.909 2.29 0.00 0.00 6.53
915 970 8.917655 CGGTGTACTTTTTCTTTTTCTTTTTGA 58.082 29.630 0.00 0.00 0.00 2.69
916 971 8.166066 CCGGTGTACTTTTTCTTTTTCTTTTTG 58.834 33.333 0.00 0.00 0.00 2.44
917 972 7.148540 GCCGGTGTACTTTTTCTTTTTCTTTTT 60.149 33.333 1.90 0.00 0.00 1.94
918 973 6.311935 GCCGGTGTACTTTTTCTTTTTCTTTT 59.688 34.615 1.90 0.00 0.00 2.27
919 974 5.808540 GCCGGTGTACTTTTTCTTTTTCTTT 59.191 36.000 1.90 0.00 0.00 2.52
920 975 5.345702 GCCGGTGTACTTTTTCTTTTTCTT 58.654 37.500 1.90 0.00 0.00 2.52
921 976 4.496840 CGCCGGTGTACTTTTTCTTTTTCT 60.497 41.667 6.91 0.00 0.00 2.52
922 977 3.727227 CGCCGGTGTACTTTTTCTTTTTC 59.273 43.478 6.91 0.00 0.00 2.29
923 978 3.697982 CGCCGGTGTACTTTTTCTTTTT 58.302 40.909 6.91 0.00 0.00 1.94
924 979 2.542205 GCGCCGGTGTACTTTTTCTTTT 60.542 45.455 17.91 0.00 0.00 2.27
925 980 1.002142 GCGCCGGTGTACTTTTTCTTT 60.002 47.619 17.91 0.00 0.00 2.52
926 981 0.589708 GCGCCGGTGTACTTTTTCTT 59.410 50.000 17.91 0.00 0.00 2.52
927 982 0.250166 AGCGCCGGTGTACTTTTTCT 60.250 50.000 17.91 0.00 0.00 2.52
928 983 0.589708 AAGCGCCGGTGTACTTTTTC 59.410 50.000 17.91 0.00 0.00 2.29
981 1036 4.056125 GCTGCCCCCTTTCGTTGC 62.056 66.667 0.00 0.00 0.00 4.17
1098 1153 0.106894 GGGGGATACAAGAGGAAGCG 59.893 60.000 0.00 0.00 39.74 4.68
1186 1252 7.730364 ATCTATTCGACTATTCGCCAATTTT 57.270 32.000 0.00 0.00 45.46 1.82
1188 1254 6.147821 CCAATCTATTCGACTATTCGCCAATT 59.852 38.462 0.00 0.00 45.46 2.32
1203 1269 3.629398 CCACTGCCAGTTCCAATCTATTC 59.371 47.826 0.00 0.00 0.00 1.75
1213 1279 1.673665 CCTCTGCCACTGCCAGTTC 60.674 63.158 0.00 0.00 36.33 3.01
1273 1360 2.814805 ATCTAGGTGCTGCAACCAAT 57.185 45.000 15.18 2.53 43.20 3.16
1311 1406 1.087501 GCTAAGAGGAAAAGGCACCG 58.912 55.000 0.00 0.00 0.00 4.94
1312 1407 2.200373 TGCTAAGAGGAAAAGGCACC 57.800 50.000 0.00 0.00 0.00 5.01
1324 1419 2.486548 GGTGTTCCCTGTGTTGCTAAGA 60.487 50.000 0.00 0.00 0.00 2.10
1391 1491 1.107945 TGCTGATTCATGGCATGGTG 58.892 50.000 26.15 13.03 0.00 4.17
1429 1530 2.851195 CTCCCAGTATACATGCAACCC 58.149 52.381 5.50 0.00 0.00 4.11
1434 1535 3.332919 CATGAGCTCCCAGTATACATGC 58.667 50.000 12.15 2.03 0.00 4.06
1435 1536 3.244318 TGCATGAGCTCCCAGTATACATG 60.244 47.826 12.15 6.57 42.74 3.21
1548 1649 7.386848 TCTCGTATTTATGAAAATCCGGGAATC 59.613 37.037 0.00 0.67 39.90 2.52
1588 1689 3.625764 GTGAATCCGAAATTCCGAATGGA 59.374 43.478 0.00 0.00 44.61 3.41
1590 1691 3.546020 CCGTGAATCCGAAATTCCGAATG 60.546 47.826 15.69 3.93 0.00 2.67
1591 1692 2.612212 CCGTGAATCCGAAATTCCGAAT 59.388 45.455 15.69 0.00 0.00 3.34
1594 1695 0.027586 GCCGTGAATCCGAAATTCCG 59.972 55.000 7.69 9.60 0.00 4.30
1595 1696 1.091537 TGCCGTGAATCCGAAATTCC 58.908 50.000 7.69 0.88 0.00 3.01
1596 1697 1.202143 GGTGCCGTGAATCCGAAATTC 60.202 52.381 4.17 4.17 0.00 2.17
1597 1698 0.808755 GGTGCCGTGAATCCGAAATT 59.191 50.000 0.00 0.00 0.00 1.82
1598 1699 0.035439 AGGTGCCGTGAATCCGAAAT 60.035 50.000 0.00 0.00 0.00 2.17
1610 1759 0.608640 AGGAAAGACAGTAGGTGCCG 59.391 55.000 0.00 0.00 0.00 5.69
1631 1782 9.322773 CTCACATTGAATTTCTAGAGCTGAATA 57.677 33.333 0.00 0.00 0.00 1.75
1830 1981 3.429960 GGATGTACTTCCTCGTTGGTACC 60.430 52.174 18.30 4.43 35.17 3.34
1876 2043 8.766994 AAGGTACATATGCAAACATCCTAAAT 57.233 30.769 1.58 0.00 37.74 1.40
2109 2276 0.387622 GGCATGTCACATGTGCACAC 60.388 55.000 24.37 17.33 40.53 3.82
2167 2334 4.147321 ACAGGCACATCTTCTTCAACAAT 58.853 39.130 0.00 0.00 0.00 2.71
2178 2345 4.655963 ACACATAAAGAACAGGCACATCT 58.344 39.130 0.00 0.00 0.00 2.90
2242 2409 7.168219 TCAATCAACTGCATTAGGAACTTACT 58.832 34.615 0.00 0.00 41.75 2.24
2244 2411 7.665559 AGTTCAATCAACTGCATTAGGAACTTA 59.334 33.333 0.00 0.00 44.28 2.24
2368 2535 6.446781 AATGCATAAATCAGAAGACACAGG 57.553 37.500 0.00 0.00 0.00 4.00
2402 2583 9.595823 GCTGAGTGTAACCAGAATAGTAATTAA 57.404 33.333 0.00 0.00 37.32 1.40
2419 2600 4.406649 TGATCATCATTCCAGCTGAGTGTA 59.593 41.667 17.39 0.00 32.79 2.90
2484 2667 3.610619 CTGTCAGCATCACGGCCCA 62.611 63.158 0.00 0.00 0.00 5.36
2748 2932 9.606631 GAATATCTTGTTCTTGTGGAGACTATT 57.393 33.333 0.00 0.00 33.02 1.73
2749 2933 7.923344 CGAATATCTTGTTCTTGTGGAGACTAT 59.077 37.037 0.00 0.00 33.02 2.12
3217 3409 2.928116 GGTAGAACCACAGTCGTATTGC 59.072 50.000 0.00 0.00 38.42 3.56
3375 3788 3.731652 TGGTCAAAGTTGCCAATTGAG 57.268 42.857 7.12 0.00 34.02 3.02
3378 3791 5.412286 GCAAATATGGTCAAAGTTGCCAATT 59.588 36.000 10.03 8.75 37.70 2.32
3502 3936 7.133891 AGTGTATCAGCAACAATAGTTTCAC 57.866 36.000 0.00 0.00 35.28 3.18
3566 4000 9.678981 ACTTTAACCAAGTCTACCCCATATATA 57.321 33.333 0.00 0.00 42.62 0.86
3567 4001 8.577164 ACTTTAACCAAGTCTACCCCATATAT 57.423 34.615 0.00 0.00 42.62 0.86
3587 4021 7.599998 GGTCCGATGTACACTTCTTTAACTTTA 59.400 37.037 0.00 0.00 0.00 1.85
3628 4066 5.658468 TGTGAATCTCTTCAGCTATGTGAG 58.342 41.667 0.00 0.00 41.96 3.51
3685 4125 0.689745 AAGCCCTAGGATGCACCGTA 60.690 55.000 11.48 0.00 44.74 4.02
3713 4153 0.401738 CACCAAGGGAAAGAGAGCCA 59.598 55.000 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.