Multiple sequence alignment - TraesCS4D01G292100

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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 TraesCS4D01G292100 chr4D 100.000 2600 0 0 1 2600 463400506 463403105 0.000000e+00 4802.0
1 TraesCS4D01G292100 chr4D 86.885 427 32 20 1771 2183 477914171 477914587 8.480000e-125 457.0
2 TraesCS4D01G292100 chr4D 84.259 432 47 17 1787 2211 456124202 456124619 4.030000e-108 401.0
3 TraesCS4D01G292100 chr4B 88.827 1611 111 43 1033 2600 579389775 579391359 0.000000e+00 1914.0
4 TraesCS4D01G292100 chr4B 94.512 492 27 0 1019 1510 579102441 579102932 0.000000e+00 760.0
5 TraesCS4D01G292100 chr4B 92.391 460 27 8 1771 2228 579103347 579103800 0.000000e+00 649.0
6 TraesCS4D01G292100 chr4B 97.351 302 8 0 1 302 579101402 579101703 4.960000e-142 514.0
7 TraesCS4D01G292100 chr4B 92.517 294 19 2 325 616 579101693 579101985 4.000000e-113 418.0
8 TraesCS4D01G292100 chr4B 92.361 288 15 6 325 610 579105389 579105671 1.120000e-108 403.0
9 TraesCS4D01G292100 chr4B 91.096 292 23 3 1787 2076 604141371 604141661 2.430000e-105 392.0
10 TraesCS4D01G292100 chr4B 85.761 309 31 7 1 302 579105097 579105399 5.400000e-82 315.0
11 TraesCS4D01G292100 chr4B 83.628 226 19 12 2376 2595 579103904 579104117 2.040000e-46 196.0
12 TraesCS4D01G292100 chr4B 90.323 62 6 0 734 795 579102093 579102154 5.960000e-12 82.4
13 TraesCS4D01G292100 chr4A 86.251 931 80 32 1700 2600 6033760 6032848 0.000000e+00 966.0
14 TraesCS4D01G292100 chr4A 85.746 891 47 36 759 1610 6034795 6033946 0.000000e+00 869.0
15 TraesCS4D01G292100 chr4A 85.242 454 46 13 1770 2218 21844250 21844687 5.100000e-122 448.0
16 TraesCS4D01G292100 chr4A 86.500 400 38 12 1793 2188 11622990 11622603 2.390000e-115 425.0
17 TraesCS4D01G292100 chr4A 92.982 285 18 2 1793 2076 684615227 684615510 5.180000e-112 414.0
18 TraesCS4D01G292100 chr4A 88.889 306 29 4 1 302 6035615 6035311 3.160000e-99 372.0
19 TraesCS4D01G292100 chr4A 81.879 298 16 6 325 616 6035321 6035056 1.570000e-52 217.0
20 TraesCS4D01G292100 chr5D 90.625 64 5 1 558 621 564548404 564548342 1.660000e-12 84.2
21 TraesCS4D01G292100 chr5B 91.667 60 4 1 558 617 706838079 706838021 5.960000e-12 82.4
22 TraesCS4D01G292100 chr2D 90.741 54 2 2 1376 1429 343164749 343164799 4.640000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G292100 chr4D 463400506 463403105 2599 False 4802.000 4802 100.00000 1 2600 1 chr4D.!!$F2 2599
1 TraesCS4D01G292100 chr4B 579389775 579391359 1584 False 1914.000 1914 88.82700 1033 2600 1 chr4B.!!$F1 1567
2 TraesCS4D01G292100 chr4B 579101402 579105671 4269 False 417.175 760 91.10550 1 2595 8 chr4B.!!$F3 2594
3 TraesCS4D01G292100 chr4A 6032848 6035615 2767 True 606.000 966 85.69125 1 2600 4 chr4A.!!$R2 2599

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
689 699 0.031043 TCATACGCCCGTCCGTTATG 59.969 55.0 0.0 0.0 42.2 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1951 0.517316 ATGCAAAGAAAGCGACCGAC 59.483 50.0 0.0 0.0 33.85 4.79 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
84 87 2.101415 AGCAGATTCGACATCGGAATCA 59.899 45.455 19.28 0.00 37.83 2.57
128 132 7.707893 ACATATTCTGCCACTCATTTAAAATGC 59.292 33.333 0.00 0.00 0.00 3.56
209 213 2.866085 ATCGCAGGCTCCTTGCTGAC 62.866 60.000 0.00 0.00 42.39 3.51
222 226 2.707849 GCTGACATGGCCCAAGCAG 61.708 63.158 0.00 4.22 42.56 4.24
273 277 1.915266 CTGTCCTGGGTGCTCTCCA 60.915 63.158 0.00 0.00 0.00 3.86
302 306 5.244626 TCGTTCCTAGTTTAGGTTACTGCTT 59.755 40.000 2.30 0.00 46.32 3.91
303 307 5.930569 CGTTCCTAGTTTAGGTTACTGCTTT 59.069 40.000 2.30 0.00 46.32 3.51
304 308 6.426025 CGTTCCTAGTTTAGGTTACTGCTTTT 59.574 38.462 2.30 0.00 46.32 2.27
305 309 7.041576 CGTTCCTAGTTTAGGTTACTGCTTTTT 60.042 37.037 2.30 0.00 46.32 1.94
331 335 2.368311 TTTTTGCGGGGAAGGTTACT 57.632 45.000 0.00 0.00 0.00 2.24
332 336 1.611519 TTTTGCGGGGAAGGTTACTG 58.388 50.000 0.00 0.00 0.00 2.74
333 337 0.891904 TTTGCGGGGAAGGTTACTGC 60.892 55.000 0.00 0.00 37.04 4.40
334 338 1.774894 TTGCGGGGAAGGTTACTGCT 61.775 55.000 0.00 0.00 37.40 4.24
385 395 7.345914 ACTGCTAACCCTCAGAAACTAGATTAT 59.654 37.037 0.00 0.00 34.57 1.28
443 453 8.685257 ATTATGTATGATCTTAGATGACCCCA 57.315 34.615 0.00 0.00 0.00 4.96
498 508 2.322355 TTTTGTTGGTGTTGCATGGG 57.678 45.000 0.00 0.00 0.00 4.00
523 533 2.385803 CCTAGGGATGTAAGTGGACGT 58.614 52.381 0.00 0.00 0.00 4.34
543 553 1.677576 TGTCCGTCAAGTGTACGAACT 59.322 47.619 0.00 0.00 42.90 3.01
573 583 5.811399 TCATGGTTTTTGTATTAGCTCGG 57.189 39.130 0.00 0.00 0.00 4.63
574 584 5.250200 TCATGGTTTTTGTATTAGCTCGGT 58.750 37.500 0.00 0.00 0.00 4.69
616 626 8.865090 TGATTAGTTTATTTTTGCCTTCTTGGA 58.135 29.630 0.00 0.00 38.35 3.53
618 628 9.657419 ATTAGTTTATTTTTGCCTTCTTGGATG 57.343 29.630 0.00 0.00 38.35 3.51
621 631 4.541973 ATTTTTGCCTTCTTGGATGGTC 57.458 40.909 0.00 0.00 38.35 4.02
622 632 1.533625 TTTGCCTTCTTGGATGGTCG 58.466 50.000 0.00 0.00 38.35 4.79
623 633 0.400213 TTGCCTTCTTGGATGGTCGT 59.600 50.000 0.00 0.00 38.35 4.34
624 634 0.321564 TGCCTTCTTGGATGGTCGTG 60.322 55.000 0.00 0.00 38.35 4.35
625 635 1.026718 GCCTTCTTGGATGGTCGTGG 61.027 60.000 0.00 0.00 38.35 4.94
626 636 0.392998 CCTTCTTGGATGGTCGTGGG 60.393 60.000 0.00 0.00 38.35 4.61
627 637 0.613260 CTTCTTGGATGGTCGTGGGA 59.387 55.000 0.00 0.00 0.00 4.37
628 638 1.210478 CTTCTTGGATGGTCGTGGGAT 59.790 52.381 0.00 0.00 0.00 3.85
629 639 2.168458 TCTTGGATGGTCGTGGGATA 57.832 50.000 0.00 0.00 0.00 2.59
630 640 2.039418 TCTTGGATGGTCGTGGGATAG 58.961 52.381 0.00 0.00 0.00 2.08
631 641 1.762957 CTTGGATGGTCGTGGGATAGT 59.237 52.381 0.00 0.00 0.00 2.12
632 642 1.119684 TGGATGGTCGTGGGATAGTG 58.880 55.000 0.00 0.00 0.00 2.74
633 643 1.120530 GGATGGTCGTGGGATAGTGT 58.879 55.000 0.00 0.00 0.00 3.55
637 647 2.527497 TGGTCGTGGGATAGTGTGTAA 58.473 47.619 0.00 0.00 0.00 2.41
639 649 3.118920 TGGTCGTGGGATAGTGTGTAATG 60.119 47.826 0.00 0.00 0.00 1.90
651 661 7.119116 GGATAGTGTGTAATGTGAAATGTGACA 59.881 37.037 0.00 0.00 0.00 3.58
655 665 5.050431 TGTGTAATGTGAAATGTGACAGACG 60.050 40.000 0.00 0.00 0.00 4.18
661 671 0.250727 AAATGTGACAGACGGGTGGG 60.251 55.000 0.00 0.00 0.00 4.61
662 672 2.124507 AATGTGACAGACGGGTGGGG 62.125 60.000 0.00 0.00 0.00 4.96
663 673 3.239253 GTGACAGACGGGTGGGGT 61.239 66.667 0.00 0.00 0.00 4.95
664 674 3.238497 TGACAGACGGGTGGGGTG 61.238 66.667 0.00 0.00 0.00 4.61
670 680 4.358181 ACGGGTGGGGTGGGGTAT 62.358 66.667 0.00 0.00 0.00 2.73
671 681 3.485745 CGGGTGGGGTGGGGTATC 61.486 72.222 0.00 0.00 0.00 2.24
672 682 2.286578 GGGTGGGGTGGGGTATCA 60.287 66.667 0.00 0.00 0.00 2.15
673 683 1.699930 GGGTGGGGTGGGGTATCAT 60.700 63.158 0.00 0.00 0.00 2.45
674 684 0.402272 GGGTGGGGTGGGGTATCATA 60.402 60.000 0.00 0.00 0.00 2.15
675 685 0.769247 GGTGGGGTGGGGTATCATAC 59.231 60.000 0.00 0.00 0.00 2.39
676 686 0.395312 GTGGGGTGGGGTATCATACG 59.605 60.000 0.00 0.00 0.00 3.06
677 687 1.373812 GGGGTGGGGTATCATACGC 59.626 63.158 3.19 3.19 40.51 4.42
682 692 4.981415 GGGTATCATACGCCCGTC 57.019 61.111 0.17 0.00 35.79 4.79
683 693 1.291272 GGGTATCATACGCCCGTCC 59.709 63.158 0.17 0.00 35.79 4.79
684 694 1.080974 GGTATCATACGCCCGTCCG 60.081 63.158 0.00 0.00 0.00 4.79
685 695 1.656441 GTATCATACGCCCGTCCGT 59.344 57.895 0.00 3.17 44.62 4.69
686 696 0.031178 GTATCATACGCCCGTCCGTT 59.969 55.000 0.00 0.00 42.20 4.44
687 697 1.266718 GTATCATACGCCCGTCCGTTA 59.733 52.381 0.00 0.00 42.20 3.18
688 698 0.963962 ATCATACGCCCGTCCGTTAT 59.036 50.000 0.00 0.00 42.20 1.89
689 699 0.031043 TCATACGCCCGTCCGTTATG 59.969 55.000 0.00 0.00 42.20 1.90
690 700 0.249155 CATACGCCCGTCCGTTATGT 60.249 55.000 0.00 0.00 42.20 2.29
691 701 0.249155 ATACGCCCGTCCGTTATGTG 60.249 55.000 0.00 0.00 42.20 3.21
692 702 1.311651 TACGCCCGTCCGTTATGTGA 61.312 55.000 0.00 0.00 42.20 3.58
693 703 1.446445 CGCCCGTCCGTTATGTGAA 60.446 57.895 0.00 0.00 0.00 3.18
711 721 0.898326 AATGTGTTTTCCCCTCGGCC 60.898 55.000 0.00 0.00 0.00 6.13
712 722 2.075355 ATGTGTTTTCCCCTCGGCCA 62.075 55.000 2.24 0.00 0.00 5.36
715 725 1.674651 GTTTTCCCCTCGGCCAGTC 60.675 63.158 2.24 0.00 0.00 3.51
725 735 0.250295 TCGGCCAGTCACCTTTCTTG 60.250 55.000 2.24 0.00 0.00 3.02
726 736 0.535102 CGGCCAGTCACCTTTCTTGT 60.535 55.000 2.24 0.00 0.00 3.16
728 738 1.239347 GCCAGTCACCTTTCTTGTCC 58.761 55.000 0.00 0.00 0.00 4.02
729 739 1.476833 GCCAGTCACCTTTCTTGTCCA 60.477 52.381 0.00 0.00 0.00 4.02
731 741 3.490348 CCAGTCACCTTTCTTGTCCATT 58.510 45.455 0.00 0.00 0.00 3.16
732 742 3.503748 CCAGTCACCTTTCTTGTCCATTC 59.496 47.826 0.00 0.00 0.00 2.67
735 778 3.058914 GTCACCTTTCTTGTCCATTCACG 60.059 47.826 0.00 0.00 0.00 4.35
742 785 5.828299 TTCTTGTCCATTCACGTTTCTTT 57.172 34.783 0.00 0.00 0.00 2.52
757 800 0.108804 TCTTTCTGGACGGATGCGAC 60.109 55.000 15.49 7.18 0.00 5.19
762 805 0.039074 CTGGACGGATGCGACTATCC 60.039 60.000 15.49 10.49 42.62 2.59
766 809 2.483188 GGACGGATGCGACTATCCTTTT 60.483 50.000 15.49 0.00 43.64 2.27
900 1124 2.701951 TCAGTATTTAAGCCTACCCCGG 59.298 50.000 0.00 0.00 0.00 5.73
933 1157 3.835395 ACCCCTTGTCAAAGAACAAACAA 59.165 39.130 0.00 0.00 38.60 2.83
934 1158 4.081697 ACCCCTTGTCAAAGAACAAACAAG 60.082 41.667 7.03 7.03 45.15 3.16
935 1159 4.081697 CCCCTTGTCAAAGAACAAACAAGT 60.082 41.667 11.76 0.00 44.45 3.16
944 1168 6.797995 TCAAAGAACAAACAAGTAACAACGTC 59.202 34.615 0.00 0.00 0.00 4.34
956 1180 2.203015 AACGTCGCAACACCAGCT 60.203 55.556 0.00 0.00 0.00 4.24
958 1182 0.531090 AACGTCGCAACACCAGCTAA 60.531 50.000 0.00 0.00 0.00 3.09
959 1183 0.944311 ACGTCGCAACACCAGCTAAG 60.944 55.000 0.00 0.00 0.00 2.18
960 1184 1.497722 GTCGCAACACCAGCTAAGC 59.502 57.895 0.00 0.00 0.00 3.09
961 1185 1.070615 TCGCAACACCAGCTAAGCA 59.929 52.632 0.00 0.00 0.00 3.91
962 1186 1.207593 CGCAACACCAGCTAAGCAC 59.792 57.895 0.00 0.00 0.00 4.40
963 1187 1.506309 CGCAACACCAGCTAAGCACA 61.506 55.000 0.00 0.00 0.00 4.57
1009 1236 2.965147 GCAAGTGCAATGGCGTCGA 61.965 57.895 0.00 0.00 45.35 4.20
1010 1237 1.133253 CAAGTGCAATGGCGTCGAG 59.867 57.895 0.00 0.00 45.35 4.04
1011 1238 2.680913 AAGTGCAATGGCGTCGAGC 61.681 57.895 0.00 0.00 45.35 5.03
1185 1413 4.735132 GTGCACGCCGCCACTCTA 62.735 66.667 0.00 0.00 41.33 2.43
1194 1422 2.809010 GCCACTCTACTCTCCGCC 59.191 66.667 0.00 0.00 0.00 6.13
1212 1440 1.872234 CCTCGCGTCCATGTACACG 60.872 63.158 5.77 0.00 39.09 4.49
1410 1653 2.413142 GCTGCTGGCCATGTTCCTC 61.413 63.158 5.51 0.00 34.27 3.71
1555 1840 3.771160 CCGTGGACGAGAAGGGGG 61.771 72.222 0.00 0.00 43.02 5.40
1631 1951 3.435327 TGCCGTGTGTTTAAATAGAGCTG 59.565 43.478 0.00 0.00 0.00 4.24
1645 1965 0.667792 GAGCTGTCGGTCGCTTTCTT 60.668 55.000 0.00 0.00 36.45 2.52
1647 1967 0.110644 GCTGTCGGTCGCTTTCTTTG 60.111 55.000 0.00 0.00 0.00 2.77
1666 1996 4.952262 TTGCATATTGTCTGAACAGCTC 57.048 40.909 0.00 0.00 36.57 4.09
1681 2011 5.926542 TGAACAGCTCTCACAAATACAGTAC 59.073 40.000 0.00 0.00 0.00 2.73
1682 2012 5.468540 ACAGCTCTCACAAATACAGTACA 57.531 39.130 0.00 0.00 0.00 2.90
1684 2014 5.011125 ACAGCTCTCACAAATACAGTACAGT 59.989 40.000 0.00 0.00 0.00 3.55
1686 2016 7.090808 CAGCTCTCACAAATACAGTACAGTAA 58.909 38.462 1.93 0.00 0.00 2.24
1691 2021 9.214957 TCTCACAAATACAGTACAGTAATTTGG 57.785 33.333 22.16 16.24 32.74 3.28
1735 2209 4.646492 ACAGAAACCAAGCTCAGTTTTCAT 59.354 37.500 13.52 3.46 36.36 2.57
1747 2221 9.651913 AAGCTCAGTTTTCATTTTGTTCTAAAA 57.348 25.926 0.00 0.00 0.00 1.52
1779 2255 5.185635 CCAAAGCCATCAGGAAGAACAAATA 59.814 40.000 0.00 0.00 36.89 1.40
1791 2267 8.792633 CAGGAAGAACAAATATTCCACTTGTTA 58.207 33.333 6.02 0.00 44.11 2.41
2002 2479 2.969628 AAGGTATGCTTCTCTCCGTG 57.030 50.000 0.00 0.00 0.00 4.94
2155 2638 3.601685 CCGTTTGCTTGGGCCGTT 61.602 61.111 0.00 0.00 37.74 4.44
2281 2781 5.902981 TCTTTTGTTTTCACGCGTACATTAC 59.097 36.000 13.44 7.58 0.00 1.89
2283 2783 4.377911 TGTTTTCACGCGTACATTACTG 57.622 40.909 13.44 0.00 0.00 2.74
2406 2939 3.835790 TTTGGTTCCTCGCGGTGGG 62.836 63.158 6.13 6.82 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 87 0.037605 GTTGTGCCTACACCGCTAGT 60.038 55.000 0.00 0.00 46.86 2.57
128 132 5.882557 AGTGATAGCTTGAATTGGTTAGGTG 59.117 40.000 0.00 0.00 0.00 4.00
312 316 1.957877 CAGTAACCTTCCCCGCAAAAA 59.042 47.619 0.00 0.00 0.00 1.94
313 317 1.611519 CAGTAACCTTCCCCGCAAAA 58.388 50.000 0.00 0.00 0.00 2.44
314 318 0.891904 GCAGTAACCTTCCCCGCAAA 60.892 55.000 0.00 0.00 0.00 3.68
315 319 1.302993 GCAGTAACCTTCCCCGCAA 60.303 57.895 0.00 0.00 0.00 4.85
316 320 0.905809 TAGCAGTAACCTTCCCCGCA 60.906 55.000 0.00 0.00 0.00 5.69
317 321 0.461516 GTAGCAGTAACCTTCCCCGC 60.462 60.000 0.00 0.00 0.00 6.13
318 322 0.177373 GGTAGCAGTAACCTTCCCCG 59.823 60.000 0.00 0.00 33.97 5.73
319 323 0.545171 GGGTAGCAGTAACCTTCCCC 59.455 60.000 0.00 0.00 34.75 4.81
320 324 1.209747 CAGGGTAGCAGTAACCTTCCC 59.790 57.143 0.00 0.00 44.96 3.97
321 325 2.185387 TCAGGGTAGCAGTAACCTTCC 58.815 52.381 0.00 0.00 44.96 3.46
322 326 3.975168 TTCAGGGTAGCAGTAACCTTC 57.025 47.619 0.00 0.00 44.96 3.46
323 327 3.651423 ACTTTCAGGGTAGCAGTAACCTT 59.349 43.478 0.00 0.00 44.96 3.50
325 329 3.697619 ACTTTCAGGGTAGCAGTAACC 57.302 47.619 0.00 0.00 36.03 2.85
326 330 5.581085 CACATACTTTCAGGGTAGCAGTAAC 59.419 44.000 0.00 0.00 0.00 2.50
327 331 5.482526 TCACATACTTTCAGGGTAGCAGTAA 59.517 40.000 0.00 0.00 0.00 2.24
328 332 5.020795 TCACATACTTTCAGGGTAGCAGTA 58.979 41.667 0.00 0.00 0.00 2.74
329 333 3.838317 TCACATACTTTCAGGGTAGCAGT 59.162 43.478 0.00 0.00 0.00 4.40
330 334 4.471904 TCACATACTTTCAGGGTAGCAG 57.528 45.455 0.00 0.00 0.00 4.24
331 335 4.901197 TTCACATACTTTCAGGGTAGCA 57.099 40.909 0.00 0.00 0.00 3.49
332 336 7.819900 CCTATATTCACATACTTTCAGGGTAGC 59.180 40.741 0.00 0.00 0.00 3.58
333 337 9.090103 TCCTATATTCACATACTTTCAGGGTAG 57.910 37.037 0.00 0.00 0.00 3.18
334 338 8.867097 GTCCTATATTCACATACTTTCAGGGTA 58.133 37.037 0.00 0.00 0.00 3.69
443 453 1.937191 AATTCCGGGCCAAAGTTCAT 58.063 45.000 4.39 0.00 0.00 2.57
498 508 2.035576 CCACTTACATCCCTAGGCGTAC 59.964 54.545 2.05 0.00 0.00 3.67
523 533 2.124011 GTTCGTACACTTGACGGACA 57.876 50.000 1.84 0.00 46.11 4.02
530 540 0.319211 TGCGGGAGTTCGTACACTTG 60.319 55.000 0.00 0.00 0.00 3.16
543 553 1.967066 ACAAAAACCATGAATGCGGGA 59.033 42.857 0.00 0.00 0.00 5.14
605 615 0.321564 CACGACCATCCAAGAAGGCA 60.322 55.000 0.00 0.00 37.29 4.75
616 626 1.568504 ACACACTATCCCACGACCAT 58.431 50.000 0.00 0.00 0.00 3.55
618 628 3.118884 ACATTACACACTATCCCACGACC 60.119 47.826 0.00 0.00 0.00 4.79
621 631 4.118093 TCACATTACACACTATCCCACG 57.882 45.455 0.00 0.00 0.00 4.94
622 632 6.374333 ACATTTCACATTACACACTATCCCAC 59.626 38.462 0.00 0.00 0.00 4.61
623 633 6.374053 CACATTTCACATTACACACTATCCCA 59.626 38.462 0.00 0.00 0.00 4.37
624 634 6.597672 TCACATTTCACATTACACACTATCCC 59.402 38.462 0.00 0.00 0.00 3.85
625 635 7.119116 TGTCACATTTCACATTACACACTATCC 59.881 37.037 0.00 0.00 0.00 2.59
626 636 8.028540 TGTCACATTTCACATTACACACTATC 57.971 34.615 0.00 0.00 0.00 2.08
627 637 7.877612 TCTGTCACATTTCACATTACACACTAT 59.122 33.333 0.00 0.00 0.00 2.12
628 638 7.170828 GTCTGTCACATTTCACATTACACACTA 59.829 37.037 0.00 0.00 0.00 2.74
629 639 6.017934 GTCTGTCACATTTCACATTACACACT 60.018 38.462 0.00 0.00 0.00 3.55
630 640 6.136071 GTCTGTCACATTTCACATTACACAC 58.864 40.000 0.00 0.00 0.00 3.82
631 641 5.050431 CGTCTGTCACATTTCACATTACACA 60.050 40.000 0.00 0.00 0.00 3.72
632 642 5.374080 CGTCTGTCACATTTCACATTACAC 58.626 41.667 0.00 0.00 0.00 2.90
633 643 4.450757 CCGTCTGTCACATTTCACATTACA 59.549 41.667 0.00 0.00 0.00 2.41
637 647 2.224523 ACCCGTCTGTCACATTTCACAT 60.225 45.455 0.00 0.00 0.00 3.21
639 649 1.531149 CACCCGTCTGTCACATTTCAC 59.469 52.381 0.00 0.00 0.00 3.18
655 665 0.402272 TATGATACCCCACCCCACCC 60.402 60.000 0.00 0.00 0.00 4.61
661 671 1.373812 GGGCGTATGATACCCCACC 59.626 63.158 18.53 7.02 38.38 4.61
662 672 1.005394 CGGGCGTATGATACCCCAC 60.005 63.158 21.36 5.40 40.86 4.61
663 673 1.458020 ACGGGCGTATGATACCCCA 60.458 57.895 21.36 0.00 40.86 4.96
664 674 1.291272 GACGGGCGTATGATACCCC 59.709 63.158 15.25 15.25 40.86 4.95
666 676 1.080974 CGGACGGGCGTATGATACC 60.081 63.158 0.00 0.00 0.00 2.73
667 677 0.031178 AACGGACGGGCGTATGATAC 59.969 55.000 0.00 0.00 0.00 2.24
668 678 1.603456 TAACGGACGGGCGTATGATA 58.397 50.000 0.00 0.00 0.00 2.15
669 679 0.963962 ATAACGGACGGGCGTATGAT 59.036 50.000 0.00 0.00 0.00 2.45
670 680 0.031043 CATAACGGACGGGCGTATGA 59.969 55.000 0.00 0.00 0.00 2.15
671 681 0.249155 ACATAACGGACGGGCGTATG 60.249 55.000 0.00 1.86 0.00 2.39
672 682 0.249155 CACATAACGGACGGGCGTAT 60.249 55.000 0.00 0.00 0.00 3.06
673 683 1.139308 CACATAACGGACGGGCGTA 59.861 57.895 0.00 0.00 0.00 4.42
674 684 2.125832 CACATAACGGACGGGCGT 60.126 61.111 0.00 0.00 0.00 5.68
675 685 0.808453 ATTCACATAACGGACGGGCG 60.808 55.000 0.00 0.00 0.00 6.13
676 686 0.655733 CATTCACATAACGGACGGGC 59.344 55.000 0.00 0.00 0.00 6.13
677 687 1.663643 CACATTCACATAACGGACGGG 59.336 52.381 0.00 0.00 0.00 5.28
678 688 2.343101 ACACATTCACATAACGGACGG 58.657 47.619 0.00 0.00 0.00 4.79
679 689 4.398549 AAACACATTCACATAACGGACG 57.601 40.909 0.00 0.00 0.00 4.79
680 690 5.151389 GGAAAACACATTCACATAACGGAC 58.849 41.667 0.00 0.00 0.00 4.79
681 691 4.216687 GGGAAAACACATTCACATAACGGA 59.783 41.667 0.00 0.00 32.82 4.69
682 692 4.481463 GGGAAAACACATTCACATAACGG 58.519 43.478 0.00 0.00 32.82 4.44
683 693 4.217550 AGGGGAAAACACATTCACATAACG 59.782 41.667 0.00 0.00 34.29 3.18
684 694 5.619086 CGAGGGGAAAACACATTCACATAAC 60.619 44.000 0.00 0.00 34.29 1.89
685 695 4.457603 CGAGGGGAAAACACATTCACATAA 59.542 41.667 0.00 0.00 34.29 1.90
686 696 4.006989 CGAGGGGAAAACACATTCACATA 58.993 43.478 0.00 0.00 34.29 2.29
687 697 2.819608 CGAGGGGAAAACACATTCACAT 59.180 45.455 0.00 0.00 34.29 3.21
688 698 2.226330 CGAGGGGAAAACACATTCACA 58.774 47.619 0.00 0.00 34.29 3.58
689 699 1.539827 CCGAGGGGAAAACACATTCAC 59.460 52.381 0.00 0.00 34.06 3.18
690 700 1.904287 CCGAGGGGAAAACACATTCA 58.096 50.000 0.00 0.00 34.06 2.57
691 701 0.526211 GCCGAGGGGAAAACACATTC 59.474 55.000 0.00 0.00 34.06 2.67
692 702 0.898326 GGCCGAGGGGAAAACACATT 60.898 55.000 0.00 0.00 34.06 2.71
693 703 1.304134 GGCCGAGGGGAAAACACAT 60.304 57.895 0.00 0.00 34.06 3.21
711 721 4.023707 GTGAATGGACAAGAAAGGTGACTG 60.024 45.833 0.00 0.00 42.68 3.51
715 725 2.878406 ACGTGAATGGACAAGAAAGGTG 59.122 45.455 0.00 0.00 0.00 4.00
718 728 5.424121 AGAAACGTGAATGGACAAGAAAG 57.576 39.130 0.00 0.00 0.00 2.62
725 735 3.813166 TCCAGAAAGAAACGTGAATGGAC 59.187 43.478 0.00 0.00 30.85 4.02
726 736 3.813166 GTCCAGAAAGAAACGTGAATGGA 59.187 43.478 0.00 0.00 33.33 3.41
728 738 3.363970 CCGTCCAGAAAGAAACGTGAATG 60.364 47.826 0.00 0.00 33.45 2.67
729 739 2.806244 CCGTCCAGAAAGAAACGTGAAT 59.194 45.455 0.00 0.00 33.45 2.57
731 741 1.409790 TCCGTCCAGAAAGAAACGTGA 59.590 47.619 0.00 0.00 33.45 4.35
732 742 1.860676 TCCGTCCAGAAAGAAACGTG 58.139 50.000 0.00 0.00 33.45 4.49
735 778 1.128692 CGCATCCGTCCAGAAAGAAAC 59.871 52.381 0.00 0.00 0.00 2.78
742 785 0.952280 GATAGTCGCATCCGTCCAGA 59.048 55.000 0.00 0.00 35.54 3.86
757 800 3.119884 TGCGCAACATCACAAAAGGATAG 60.120 43.478 8.16 0.00 0.00 2.08
762 805 0.780002 GCTGCGCAACATCACAAAAG 59.220 50.000 13.05 0.00 0.00 2.27
766 809 3.429925 TTGCTGCGCAACATCACA 58.570 50.000 15.19 0.00 43.99 3.58
838 1061 3.723348 GTTGTCCGTTGGGCGAGC 61.723 66.667 0.00 0.00 44.77 5.03
839 1062 3.411351 CGTTGTCCGTTGGGCGAG 61.411 66.667 0.00 0.00 44.77 5.03
840 1063 4.973055 CCGTTGTCCGTTGGGCGA 62.973 66.667 0.00 0.00 44.77 5.54
849 1072 2.737376 GCGAGGTGACCGTTGTCC 60.737 66.667 0.00 0.00 41.01 4.02
850 1073 2.022129 CTGCGAGGTGACCGTTGTC 61.022 63.158 0.00 0.00 42.12 3.18
851 1074 2.029073 CTGCGAGGTGACCGTTGT 59.971 61.111 0.00 0.00 0.00 3.32
907 1131 1.067060 GTTCTTTGACAAGGGGTGTGC 59.933 52.381 0.00 0.00 41.96 4.57
909 1133 2.818751 TGTTCTTTGACAAGGGGTGT 57.181 45.000 0.00 0.00 45.74 4.16
911 1135 3.436243 TGTTTGTTCTTTGACAAGGGGT 58.564 40.909 0.00 0.00 40.33 4.95
916 1140 7.113684 CGTTGTTACTTGTTTGTTCTTTGACAA 59.886 33.333 0.00 0.00 37.73 3.18
917 1141 6.579292 CGTTGTTACTTGTTTGTTCTTTGACA 59.421 34.615 0.00 0.00 0.00 3.58
918 1142 6.579666 ACGTTGTTACTTGTTTGTTCTTTGAC 59.420 34.615 0.00 0.00 0.00 3.18
919 1143 6.670233 ACGTTGTTACTTGTTTGTTCTTTGA 58.330 32.000 0.00 0.00 0.00 2.69
920 1144 6.236838 CGACGTTGTTACTTGTTTGTTCTTTG 60.237 38.462 0.00 0.00 0.00 2.77
933 1157 0.932399 GGTGTTGCGACGTTGTTACT 59.068 50.000 4.37 0.00 0.00 2.24
934 1158 0.651551 TGGTGTTGCGACGTTGTTAC 59.348 50.000 4.37 3.77 0.00 2.50
935 1159 0.931702 CTGGTGTTGCGACGTTGTTA 59.068 50.000 4.37 0.00 0.00 2.41
944 1168 1.207593 GTGCTTAGCTGGTGTTGCG 59.792 57.895 5.60 0.00 35.28 4.85
956 1180 0.673985 AGCTGTCTGTCGTGTGCTTA 59.326 50.000 0.00 0.00 0.00 3.09
958 1182 1.006805 GAGCTGTCTGTCGTGTGCT 60.007 57.895 0.00 0.00 0.00 4.40
959 1183 2.024319 GGAGCTGTCTGTCGTGTGC 61.024 63.158 0.00 0.00 0.00 4.57
960 1184 0.665670 CTGGAGCTGTCTGTCGTGTG 60.666 60.000 0.00 0.00 0.00 3.82
961 1185 1.662608 CTGGAGCTGTCTGTCGTGT 59.337 57.895 0.00 0.00 0.00 4.49
962 1186 1.735920 GCTGGAGCTGTCTGTCGTG 60.736 63.158 0.00 0.00 38.21 4.35
963 1187 2.653702 GCTGGAGCTGTCTGTCGT 59.346 61.111 0.00 0.00 38.21 4.34
1016 1243 3.388703 CTCAGGCTGGAGCTGGAGC 62.389 68.421 15.73 0.00 41.70 4.70
1017 1244 2.733669 CCTCAGGCTGGAGCTGGAG 61.734 68.421 15.73 2.22 41.70 3.86
1018 1245 2.686470 CCTCAGGCTGGAGCTGGA 60.686 66.667 15.73 0.00 41.70 3.86
1019 1246 2.686470 TCCTCAGGCTGGAGCTGG 60.686 66.667 15.73 9.47 41.70 4.85
1020 1247 2.901813 CTCCTCAGGCTGGAGCTG 59.098 66.667 15.73 0.00 43.67 4.24
1182 1410 2.516460 GCGAGGGCGGAGAGTAGA 60.516 66.667 0.00 0.00 38.16 2.59
1194 1422 4.088421 GTGTACATGGACGCGAGG 57.912 61.111 15.93 0.00 0.00 4.63
1534 1798 4.052229 CTTCTCGTCCACGGGCGT 62.052 66.667 10.29 0.00 40.23 5.68
1537 1801 3.771160 CCCCTTCTCGTCCACGGG 61.771 72.222 0.00 0.00 42.17 5.28
1539 1803 4.452733 GCCCCCTTCTCGTCCACG 62.453 72.222 0.00 0.00 41.45 4.94
1541 1805 4.689549 TCGCCCCCTTCTCGTCCA 62.690 66.667 0.00 0.00 0.00 4.02
1631 1951 0.517316 ATGCAAAGAAAGCGACCGAC 59.483 50.000 0.00 0.00 33.85 4.79
1645 1965 4.582869 AGAGCTGTTCAGACAATATGCAA 58.417 39.130 0.00 0.00 34.85 4.08
1647 1967 4.033817 GTGAGAGCTGTTCAGACAATATGC 59.966 45.833 0.00 0.00 34.85 3.14
1666 1996 8.999431 ACCAAATTACTGTACTGTATTTGTGAG 58.001 33.333 24.90 18.96 0.00 3.51
1681 2011 8.154649 ACAGTAGAACTTGAACCAAATTACTG 57.845 34.615 6.34 6.34 30.52 2.74
1682 2012 8.621286 CAACAGTAGAACTTGAACCAAATTACT 58.379 33.333 0.00 0.00 0.00 2.24
1684 2014 8.740123 TCAACAGTAGAACTTGAACCAAATTA 57.260 30.769 0.00 0.00 0.00 1.40
1686 2016 7.639113 TTCAACAGTAGAACTTGAACCAAAT 57.361 32.000 0.00 0.00 0.00 2.32
1721 2195 9.651913 TTTTAGAACAAAATGAAAACTGAGCTT 57.348 25.926 0.00 0.00 0.00 3.74
1747 2221 3.966665 TCCTGATGGCTTTGGTTTTCTTT 59.033 39.130 0.00 0.00 0.00 2.52
2002 2479 1.068121 ATATAAGCAGACCCAGGGCC 58.932 55.000 4.91 0.00 0.00 5.80
2026 2503 1.612442 CGGAAGGGAGGGGAAGACA 60.612 63.158 0.00 0.00 0.00 3.41
2033 2510 3.474570 CCAGAGCGGAAGGGAGGG 61.475 72.222 0.00 0.00 36.56 4.30
2104 2584 2.434134 CCGAGAAAACGACCGAGCG 61.434 63.158 0.00 0.00 35.09 5.03
2105 2585 1.071567 CTCCGAGAAAACGACCGAGC 61.072 60.000 0.00 0.00 35.09 5.03
2107 2587 1.582968 CCTCCGAGAAAACGACCGA 59.417 57.895 0.00 0.00 35.09 4.69
2109 2589 2.092882 CGCCTCCGAGAAAACGACC 61.093 63.158 0.00 0.00 36.29 4.79
2110 2590 1.080974 TCGCCTCCGAGAAAACGAC 60.081 57.895 0.00 0.00 38.82 4.34
2111 2591 3.357919 TCGCCTCCGAGAAAACGA 58.642 55.556 0.00 0.00 38.82 3.85
2139 2622 2.354539 CAACGGCCCAAGCAAACG 60.355 61.111 0.00 0.00 42.56 3.60
2155 2638 1.366111 GCGCTCGGCCTTATTCAACA 61.366 55.000 0.00 0.00 34.80 3.33
2261 2760 4.270566 ACAGTAATGTACGCGTGAAAACAA 59.729 37.500 24.59 0.64 0.00 2.83
2262 2761 3.803231 ACAGTAATGTACGCGTGAAAACA 59.197 39.130 24.59 18.85 0.00 2.83
2406 2939 2.507324 GCCTCGTCACCTTCTCGC 60.507 66.667 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.