Multiple sequence alignment - TraesCS4D01G078500

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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 TraesCS4D01G078500 chr4D 100.000 1259 0 0 1522 2780 52748851 52747593 0.000000e+00 2326.0
1 TraesCS4D01G078500 chr4D 100.000 1170 0 0 1 1170 52750372 52749203 0.000000e+00 2161.0
2 TraesCS4D01G078500 chr4D 88.208 636 67 7 2153 2780 173566654 173566019 0.000000e+00 752.0
3 TraesCS4D01G078500 chr4D 87.025 632 69 11 2154 2776 313456063 313455436 0.000000e+00 701.0
4 TraesCS4D01G078500 chr4D 89.116 294 31 1 1522 1814 52497172 52496879 5.660000e-97 364.0
5 TraesCS4D01G078500 chr4D 84.783 184 19 8 1953 2134 367049453 367049629 2.850000e-40 176.0
6 TraesCS4D01G078500 chr7A 93.729 590 37 0 1 590 219166800 219167389 0.000000e+00 885.0
7 TraesCS4D01G078500 chr1D 93.266 594 37 3 1 593 137644810 137645401 0.000000e+00 872.0
8 TraesCS4D01G078500 chr7B 92.797 597 41 2 1 596 110879741 110879146 0.000000e+00 863.0
9 TraesCS4D01G078500 chr7B 92.573 579 42 1 1 579 40184697 40185274 0.000000e+00 830.0
10 TraesCS4D01G078500 chr6B 92.667 600 42 2 1 600 560790207 560790804 0.000000e+00 863.0
11 TraesCS4D01G078500 chr3D 90.794 630 53 5 2154 2780 72311389 72312016 0.000000e+00 837.0
12 TraesCS4D01G078500 chr3D 86.709 632 77 6 2154 2780 401497401 401496772 0.000000e+00 695.0
13 TraesCS4D01G078500 chr2B 92.268 582 43 2 1 581 626105898 626105318 0.000000e+00 824.0
14 TraesCS4D01G078500 chr2B 81.600 125 20 2 1992 2115 132863587 132863465 1.760000e-17 100.0
15 TraesCS4D01G078500 chr2B 78.226 124 23 4 1991 2112 670940769 670940648 2.970000e-10 76.8
16 TraesCS4D01G078500 chr4B 91.737 593 48 1 1 593 599822844 599823435 0.000000e+00 822.0
17 TraesCS4D01G078500 chr4B 89.765 469 32 10 1697 2153 77509026 77508562 1.110000e-163 586.0
18 TraesCS4D01G078500 chr4B 89.964 279 24 1 1536 1814 77007499 77007225 9.470000e-95 357.0
19 TraesCS4D01G078500 chr4B 95.322 171 8 0 1000 1170 77007678 77007508 3.530000e-69 272.0
20 TraesCS4D01G078500 chr4B 94.737 171 9 0 1000 1170 77509353 77509183 1.640000e-67 267.0
21 TraesCS4D01G078500 chr4B 95.862 145 5 1 1522 1665 77509167 77509023 1.660000e-57 233.0
22 TraesCS4D01G078500 chr4B 84.483 232 28 5 1905 2134 451912779 451913004 3.600000e-54 222.0
23 TraesCS4D01G078500 chr4B 83.682 239 13 12 640 877 77509691 77509478 4.690000e-48 202.0
24 TraesCS4D01G078500 chr4B 92.063 63 4 1 939 1001 77509458 77509397 1.370000e-13 87.9
25 TraesCS4D01G078500 chr4A 91.582 594 49 1 1 593 686557000 686556407 0.000000e+00 819.0
26 TraesCS4D01G078500 chr4A 88.214 543 41 13 1522 2050 544067729 544068262 6.540000e-176 627.0
27 TraesCS4D01G078500 chr4A 90.816 392 16 9 618 1001 544061776 544062155 8.880000e-140 507.0
28 TraesCS4D01G078500 chr4A 90.136 294 24 2 1522 1814 544172476 544172765 7.270000e-101 377.0
29 TraesCS4D01G078500 chr4A 98.246 171 3 0 1000 1170 544172290 544172460 1.620000e-77 300.0
30 TraesCS4D01G078500 chr4A 81.385 231 32 9 1905 2134 97868198 97867978 7.910000e-41 178.0
31 TraesCS4D01G078500 chr4A 98.611 72 1 0 1099 1170 544067641 544067712 8.080000e-26 128.0
32 TraesCS4D01G078500 chr4A 87.850 107 4 1 1000 1106 544062198 544062295 1.750000e-22 117.0
33 TraesCS4D01G078500 chr4A 83.582 67 11 0 1612 1678 527004297 527004363 2.310000e-06 63.9
34 TraesCS4D01G078500 chrUn 91.568 593 49 1 1 593 346714886 346714295 0.000000e+00 817.0
35 TraesCS4D01G078500 chrUn 84.397 141 22 0 1620 1760 54297118 54297258 3.730000e-29 139.0
36 TraesCS4D01G078500 chr5D 89.082 632 61 8 2154 2780 270912905 270913533 0.000000e+00 778.0
37 TraesCS4D01G078500 chr5D 87.778 630 70 7 2154 2780 528998150 528997525 0.000000e+00 730.0
38 TraesCS4D01G078500 chr5D 86.984 630 74 7 2156 2780 267122423 267123049 0.000000e+00 702.0
39 TraesCS4D01G078500 chr7D 88.978 626 66 3 2154 2776 271089381 271090006 0.000000e+00 771.0
40 TraesCS4D01G078500 chr2D 87.695 642 64 14 2154 2780 341927091 341926450 0.000000e+00 734.0
41 TraesCS4D01G078500 chr6A 81.857 237 35 8 1904 2138 595989881 595989651 2.830000e-45 193.0
42 TraesCS4D01G078500 chr3A 81.739 230 31 9 1867 2090 672624135 672624359 6.120000e-42 182.0
43 TraesCS4D01G078500 chr5B 82.297 209 29 7 1892 2093 484636572 484636365 1.020000e-39 174.0
44 TraesCS4D01G078500 chr1A 81.481 216 33 7 1867 2078 300833685 300833897 1.320000e-38 171.0


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 TraesCS4D01G078500 chr4D 52747593 52750372 2779 True 2243.50 2326 100.0000 1 2780 2 chr4D.!!$R4 2779
1 TraesCS4D01G078500 chr4D 173566019 173566654 635 True 752.00 752 88.2080 2153 2780 1 chr4D.!!$R2 627
2 TraesCS4D01G078500 chr4D 313455436 313456063 627 True 701.00 701 87.0250 2154 2776 1 chr4D.!!$R3 622
3 TraesCS4D01G078500 chr7A 219166800 219167389 589 False 885.00 885 93.7290 1 590 1 chr7A.!!$F1 589
4 TraesCS4D01G078500 chr1D 137644810 137645401 591 False 872.00 872 93.2660 1 593 1 chr1D.!!$F1 592
5 TraesCS4D01G078500 chr7B 110879146 110879741 595 True 863.00 863 92.7970 1 596 1 chr7B.!!$R1 595
6 TraesCS4D01G078500 chr7B 40184697 40185274 577 False 830.00 830 92.5730 1 579 1 chr7B.!!$F1 578
7 TraesCS4D01G078500 chr6B 560790207 560790804 597 False 863.00 863 92.6670 1 600 1 chr6B.!!$F1 599
8 TraesCS4D01G078500 chr3D 72311389 72312016 627 False 837.00 837 90.7940 2154 2780 1 chr3D.!!$F1 626
9 TraesCS4D01G078500 chr3D 401496772 401497401 629 True 695.00 695 86.7090 2154 2780 1 chr3D.!!$R1 626
10 TraesCS4D01G078500 chr2B 626105318 626105898 580 True 824.00 824 92.2680 1 581 1 chr2B.!!$R2 580
11 TraesCS4D01G078500 chr4B 599822844 599823435 591 False 822.00 822 91.7370 1 593 1 chr4B.!!$F2 592
12 TraesCS4D01G078500 chr4B 77508562 77509691 1129 True 275.18 586 91.2218 640 2153 5 chr4B.!!$R2 1513
13 TraesCS4D01G078500 chr4A 686556407 686557000 593 True 819.00 819 91.5820 1 593 1 chr4A.!!$R2 592
14 TraesCS4D01G078500 chr4A 544067641 544068262 621 False 377.50 627 93.4125 1099 2050 2 chr4A.!!$F3 951
15 TraesCS4D01G078500 chr4A 544061776 544062295 519 False 312.00 507 89.3330 618 1106 2 chr4A.!!$F2 488
16 TraesCS4D01G078500 chrUn 346714295 346714886 591 True 817.00 817 91.5680 1 593 1 chrUn.!!$R1 592
17 TraesCS4D01G078500 chr5D 270912905 270913533 628 False 778.00 778 89.0820 2154 2780 1 chr5D.!!$F2 626
18 TraesCS4D01G078500 chr5D 528997525 528998150 625 True 730.00 730 87.7780 2154 2780 1 chr5D.!!$R1 626
19 TraesCS4D01G078500 chr5D 267122423 267123049 626 False 702.00 702 86.9840 2156 2780 1 chr5D.!!$F1 624
20 TraesCS4D01G078500 chr7D 271089381 271090006 625 False 771.00 771 88.9780 2154 2776 1 chr7D.!!$F1 622
21 TraesCS4D01G078500 chr2D 341926450 341927091 641 True 734.00 734 87.6950 2154 2780 1 chr2D.!!$R1 626

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
530 537 0.036765 CCGGTGAAGATCGGTGGAAA 60.037 55.0 0.0 0.0 41.39 3.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2411 2490 1.133407 CACCCACGTAGAGAGAAGAGC 59.867 57.143 0.0 0.0 0.0 4.09 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
25 27 1.899437 AACTGACATCCCCACGCGAT 61.899 55.000 15.93 0.00 0.00 4.58
77 80 1.047801 GCCTTCAACCACAAACCCAT 58.952 50.000 0.00 0.00 0.00 4.00
283 286 1.063616 CTAACGTCGCCGATCTGAAGA 59.936 52.381 0.00 0.00 37.88 2.87
297 300 3.411446 TCTGAAGAATCGGCAAACACAT 58.589 40.909 0.00 0.00 31.55 3.21
326 329 3.592814 CTCCGAGACGCCGCCATA 61.593 66.667 0.00 0.00 0.00 2.74
336 339 2.555547 GCCGCCATAATGAGCACCC 61.556 63.158 0.00 0.00 0.00 4.61
457 462 2.609921 GGAGAAACGGGGTCCCCT 60.610 66.667 25.34 6.07 42.67 4.79
472 478 2.365370 CCTCTCCCTCCTGCTGCT 60.365 66.667 0.00 0.00 0.00 4.24
530 537 0.036765 CCGGTGAAGATCGGTGGAAA 60.037 55.000 0.00 0.00 41.39 3.13
600 607 1.381165 AAAACGCCTCGCACCAACTT 61.381 50.000 0.00 0.00 0.00 2.66
601 608 2.058829 AAACGCCTCGCACCAACTTG 62.059 55.000 0.00 0.00 0.00 3.16
602 609 4.389576 CGCCTCGCACCAACTTGC 62.390 66.667 0.00 0.00 39.28 4.01
603 610 3.286751 GCCTCGCACCAACTTGCA 61.287 61.111 0.00 0.00 43.15 4.08
604 611 2.949106 CCTCGCACCAACTTGCAG 59.051 61.111 0.00 0.00 43.15 4.41
605 612 2.253452 CTCGCACCAACTTGCAGC 59.747 61.111 0.00 0.00 43.15 5.25
607 614 3.952675 CGCACCAACTTGCAGCGT 61.953 61.111 14.38 0.00 43.15 5.07
608 615 2.412937 GCACCAACTTGCAGCGTT 59.587 55.556 0.00 0.00 42.49 4.84
609 616 1.658409 GCACCAACTTGCAGCGTTC 60.658 57.895 0.99 0.00 42.49 3.95
610 617 1.369209 CACCAACTTGCAGCGTTCG 60.369 57.895 0.99 0.00 0.00 3.95
611 618 2.427410 CCAACTTGCAGCGTTCGC 60.427 61.111 9.24 9.24 0.00 4.70
612 619 2.792543 CAACTTGCAGCGTTCGCG 60.793 61.111 11.40 0.00 44.73 5.87
613 620 3.269347 AACTTGCAGCGTTCGCGT 61.269 55.556 5.77 0.56 43.62 6.01
614 621 2.819552 AACTTGCAGCGTTCGCGTT 61.820 52.632 5.77 6.57 43.62 4.84
615 622 2.052237 CTTGCAGCGTTCGCGTTT 60.052 55.556 5.77 0.00 43.62 3.60
616 623 2.052590 TTGCAGCGTTCGCGTTTC 60.053 55.556 5.77 0.00 43.62 2.78
630 637 1.792273 GCGTTTCGAAAACTGTGTGCA 60.792 47.619 13.10 0.00 0.00 4.57
631 638 2.510874 CGTTTCGAAAACTGTGTGCAA 58.489 42.857 13.10 0.00 0.00 4.08
635 642 3.773860 TCGAAAACTGTGTGCAAATGT 57.226 38.095 0.00 0.00 0.00 2.71
646 653 2.429971 TGTGCAAATGTGTGTTCATGGT 59.570 40.909 0.00 0.00 0.00 3.55
686 693 7.441836 TCTGTCATTGTATTGTACAGTGTTCT 58.558 34.615 0.00 0.00 44.03 3.01
730 738 9.421399 CCAAGGTTCTGTTTTATTATCCCTTAT 57.579 33.333 0.00 0.00 0.00 1.73
772 780 4.024893 TGCGCGATTTCCTTGATTATCTTC 60.025 41.667 12.10 0.00 0.00 2.87
778 786 7.970614 GCGATTTCCTTGATTATCTTCACTTTT 59.029 33.333 0.00 0.00 0.00 2.27
896 905 2.092291 CACACGGCGCATACGTCTT 61.092 57.895 10.83 0.00 43.29 3.01
927 936 2.943653 CACGCCACGTTTCCTTCC 59.056 61.111 0.00 0.00 38.32 3.46
929 938 1.153127 ACGCCACGTTTCCTTCCAA 60.153 52.632 0.00 0.00 36.35 3.53
931 940 0.040425 CGCCACGTTTCCTTCCAAAG 60.040 55.000 0.00 0.00 0.00 2.77
971 986 2.603560 GCGTCGATTTAGGTTTCCAGAG 59.396 50.000 0.00 0.00 0.00 3.35
1549 1609 2.372040 TAGCAAGTCGTGGTGCGGTT 62.372 55.000 0.40 0.00 45.62 4.44
1683 1745 0.042188 CCTGCGATAATGCCGAAACG 60.042 55.000 0.00 0.00 0.00 3.60
1781 1843 0.250166 GCGTACCCTCCGGCATAATT 60.250 55.000 0.00 0.00 0.00 1.40
1862 1924 4.336932 TCGTCGACGAATAAGTGTACATG 58.663 43.478 36.25 3.87 46.30 3.21
1936 2010 7.444703 AGCTACCATCTTTCTCCTCTTTAAT 57.555 36.000 0.00 0.00 0.00 1.40
1990 2064 6.605471 ATGAAGTGAGTAGACCATGTGTTA 57.395 37.500 0.00 0.00 0.00 2.41
1999 2073 9.378551 TGAGTAGACCATGTGTTAAATGTTATC 57.621 33.333 0.00 0.00 0.00 1.75
2021 2096 2.696707 GGTCTTGATACCGTGGGATGTA 59.303 50.000 0.00 0.00 0.00 2.29
2091 2167 9.840427 AATACACTCTTTTATGGACAAATTTCG 57.160 29.630 0.00 0.00 0.00 3.46
2095 2171 8.853345 CACTCTTTTATGGACAAATTTCGATTG 58.147 33.333 0.00 0.00 0.00 2.67
2096 2172 7.542130 ACTCTTTTATGGACAAATTTCGATTGC 59.458 33.333 0.00 0.00 0.00 3.56
2105 2181 6.589907 GGACAAATTTCGATTGCCAAACTTAT 59.410 34.615 0.00 0.00 0.00 1.73
2108 2184 8.085296 ACAAATTTCGATTGCCAAACTTATACA 58.915 29.630 0.00 0.00 0.00 2.29
2109 2185 8.372521 CAAATTTCGATTGCCAAACTTATACAC 58.627 33.333 0.00 0.00 0.00 2.90
2110 2186 6.811253 TTTCGATTGCCAAACTTATACACT 57.189 33.333 0.00 0.00 0.00 3.55
2111 2187 6.811253 TTCGATTGCCAAACTTATACACTT 57.189 33.333 0.00 0.00 0.00 3.16
2112 2188 6.176975 TCGATTGCCAAACTTATACACTTG 57.823 37.500 0.00 0.00 0.00 3.16
2121 2197 7.305474 CCAAACTTATACACTTGTTCATGGAC 58.695 38.462 0.00 0.00 0.00 4.02
2128 2204 2.738846 CACTTGTTCATGGACGAAGAGG 59.261 50.000 17.87 9.28 0.00 3.69
2135 2211 6.072649 TGTTCATGGACGAAGAGGGTATATA 58.927 40.000 0.00 0.00 0.00 0.86
2146 2222 6.127310 CGAAGAGGGTATATAGGATTTGAGGG 60.127 46.154 0.00 0.00 0.00 4.30
2245 2321 1.401905 CCTGGAAACAAGATAAGGCGC 59.598 52.381 0.00 0.00 42.06 6.53
2373 2451 2.873649 GCTACAAGCTTGCTCCTTGAGT 60.874 50.000 26.27 6.02 41.64 3.41
2411 2490 0.463474 GAAGGGCAAGGCTAGCTCTG 60.463 60.000 15.72 12.93 43.32 3.35
2415 2495 1.521616 GCAAGGCTAGCTCTGCTCT 59.478 57.895 25.08 8.37 40.44 4.09
2447 2542 0.608308 GGTGTTGTGTCTAAGGGGCC 60.608 60.000 0.00 0.00 0.00 5.80
2527 2626 3.988050 ATCCGGCCGGGTGTAGGAA 62.988 63.158 42.36 22.50 37.00 3.36
2635 2741 1.371183 CACTTGAGGGTCTTGCCGA 59.629 57.895 0.00 0.00 38.44 5.54
2700 2806 1.592223 GGAGAGCGTGGCTACAGTT 59.408 57.895 0.00 0.00 39.88 3.16
2726 2832 2.203139 TGGTGGGCGTTCACTGTG 60.203 61.111 0.17 0.17 37.75 3.66
2754 2860 4.370776 TCCCCATCTCTTCTGGTTAATGA 58.629 43.478 0.00 0.00 31.44 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 1.066752 CGTCATAATCGCGTGGGGA 59.933 57.895 5.77 0.00 0.00 4.81
25 27 0.685131 TTCCTCCTCCGGCGTCATAA 60.685 55.000 6.01 0.00 0.00 1.90
193 196 2.224992 TGTCTCTCCTTCTGCTCTGTCT 60.225 50.000 0.00 0.00 0.00 3.41
283 286 1.135024 GGCATCATGTGTTTGCCGATT 60.135 47.619 13.19 0.00 45.75 3.34
297 300 1.134699 GTCTCGGAGTTGATGGCATCA 60.135 52.381 25.63 25.63 37.55 3.07
457 462 2.686470 CCAGCAGCAGGAGGGAGA 60.686 66.667 0.00 0.00 0.00 3.71
472 478 3.385384 CCTCCGACTGCTGCTCCA 61.385 66.667 0.00 0.00 0.00 3.86
483 489 4.798682 GGCCCCCTCTTCCTCCGA 62.799 72.222 0.00 0.00 0.00 4.55
573 580 2.332654 CGAGGCGTTTTTCCCCTGG 61.333 63.158 0.00 0.00 0.00 4.45
600 607 4.348427 CGAAACGCGAACGCTGCA 62.348 61.111 15.93 0.00 45.53 4.41
609 616 1.101454 CACACAGTTTTCGAAACGCG 58.899 50.000 10.79 3.53 42.69 6.01
610 617 0.837605 GCACACAGTTTTCGAAACGC 59.162 50.000 10.79 6.81 0.00 4.84
611 618 2.166741 TGCACACAGTTTTCGAAACG 57.833 45.000 10.79 4.88 0.00 3.60
612 619 4.326009 ACATTTGCACACAGTTTTCGAAAC 59.674 37.500 10.79 6.25 0.00 2.78
613 620 4.325741 CACATTTGCACACAGTTTTCGAAA 59.674 37.500 6.47 6.47 0.00 3.46
614 621 3.856521 CACATTTGCACACAGTTTTCGAA 59.143 39.130 0.00 0.00 0.00 3.71
615 622 3.119673 ACACATTTGCACACAGTTTTCGA 60.120 39.130 0.00 0.00 0.00 3.71
616 623 3.000872 CACACATTTGCACACAGTTTTCG 60.001 43.478 0.00 0.00 0.00 3.46
620 627 3.056962 TGAACACACATTTGCACACAGTT 60.057 39.130 0.00 0.00 0.00 3.16
622 629 3.148026 TGAACACACATTTGCACACAG 57.852 42.857 0.00 0.00 0.00 3.66
630 637 3.030291 ACACCACCATGAACACACATTT 58.970 40.909 0.00 0.00 0.00 2.32
631 638 2.665165 ACACCACCATGAACACACATT 58.335 42.857 0.00 0.00 0.00 2.71
635 642 5.427378 CTCATATACACCACCATGAACACA 58.573 41.667 0.00 0.00 0.00 3.72
646 653 5.813513 ATGACAGATGCTCATATACACCA 57.186 39.130 0.00 0.00 0.00 4.17
730 738 6.072893 TCGCGCAGAACATATACAGAGTATAA 60.073 38.462 8.75 0.00 0.00 0.98
731 739 5.410439 TCGCGCAGAACATATACAGAGTATA 59.590 40.000 8.75 0.00 0.00 1.47
732 740 4.215613 TCGCGCAGAACATATACAGAGTAT 59.784 41.667 8.75 0.00 0.00 2.12
733 741 3.562557 TCGCGCAGAACATATACAGAGTA 59.437 43.478 8.75 0.00 0.00 2.59
734 742 2.357952 TCGCGCAGAACATATACAGAGT 59.642 45.455 8.75 0.00 0.00 3.24
735 743 3.000082 TCGCGCAGAACATATACAGAG 58.000 47.619 8.75 0.00 0.00 3.35
736 744 3.643159 ATCGCGCAGAACATATACAGA 57.357 42.857 8.75 0.00 0.00 3.41
737 745 4.376413 GGAAATCGCGCAGAACATATACAG 60.376 45.833 8.75 0.00 0.00 2.74
738 746 3.493129 GGAAATCGCGCAGAACATATACA 59.507 43.478 8.75 0.00 0.00 2.29
739 747 3.741344 AGGAAATCGCGCAGAACATATAC 59.259 43.478 8.75 0.00 0.00 1.47
772 780 1.069049 CAGGGGCAAACCAGAAAAGTG 59.931 52.381 0.00 0.00 42.91 3.16
778 786 3.551496 CTCGCAGGGGCAAACCAGA 62.551 63.158 0.00 0.00 42.91 3.86
896 905 1.337917 TGGCGTGCGAGTTGGTATTTA 60.338 47.619 0.00 0.00 0.00 1.40
948 963 0.648958 GGAAACCTAAATCGACGCGG 59.351 55.000 12.47 0.00 0.00 6.46
950 965 2.603560 CTCTGGAAACCTAAATCGACGC 59.396 50.000 0.00 0.00 0.00 5.19
971 986 3.484547 CCCACGCGCGAGTTTACC 61.485 66.667 39.36 0.00 0.00 2.85
1065 1125 1.587043 CCTTCTCGACGTCCAGCAGA 61.587 60.000 11.08 4.52 0.00 4.26
1549 1609 4.350368 TTCAGTTTCAGGTAGCACATCA 57.650 40.909 0.00 0.00 0.00 3.07
1584 1644 4.330074 CCCTGCAGAATTCAGTTAGTTACG 59.670 45.833 17.39 0.00 0.00 3.18
1683 1745 3.665675 AAGCGCCATGACCGGTCTC 62.666 63.158 33.39 18.64 35.12 3.36
1781 1843 4.345859 AATCAGTGAAACACGGAGGTAA 57.654 40.909 0.00 0.00 41.23 2.85
1862 1924 7.162082 CCCCACTTCATAATCTGTCCTATTAC 58.838 42.308 0.00 0.00 0.00 1.89
1896 1966 5.500234 TGGTAGCTTGCATCTTTCTTGTAT 58.500 37.500 0.00 0.00 0.00 2.29
1897 1967 4.905429 TGGTAGCTTGCATCTTTCTTGTA 58.095 39.130 0.00 0.00 0.00 2.41
1898 1968 3.754965 TGGTAGCTTGCATCTTTCTTGT 58.245 40.909 0.00 0.00 0.00 3.16
1899 1969 4.639310 AGATGGTAGCTTGCATCTTTCTTG 59.361 41.667 0.00 0.00 31.04 3.02
1901 1971 4.500499 AGATGGTAGCTTGCATCTTTCT 57.500 40.909 0.00 0.00 31.04 2.52
1907 1981 3.201708 AGGAGAAAGATGGTAGCTTGCAT 59.798 43.478 0.00 0.00 0.00 3.96
1915 1989 9.280456 AGGTAATTAAAGAGGAGAAAGATGGTA 57.720 33.333 0.00 0.00 0.00 3.25
2078 2154 4.533919 TTGGCAATCGAAATTTGTCCAT 57.466 36.364 0.00 0.00 33.43 3.41
2084 2160 8.303876 AGTGTATAAGTTTGGCAATCGAAATTT 58.696 29.630 0.00 0.00 30.63 1.82
2091 2167 7.367285 TGAACAAGTGTATAAGTTTGGCAATC 58.633 34.615 0.00 0.00 0.00 2.67
2095 2171 6.072175 TCCATGAACAAGTGTATAAGTTTGGC 60.072 38.462 0.00 0.00 0.00 4.52
2096 2172 7.305474 GTCCATGAACAAGTGTATAAGTTTGG 58.695 38.462 0.00 0.00 0.00 3.28
2105 2181 4.556233 CTCTTCGTCCATGAACAAGTGTA 58.444 43.478 0.00 0.00 0.00 2.90
2108 2184 2.289694 CCCTCTTCGTCCATGAACAAGT 60.290 50.000 0.00 0.00 0.00 3.16
2109 2185 2.289694 ACCCTCTTCGTCCATGAACAAG 60.290 50.000 0.00 0.00 0.00 3.16
2110 2186 1.697432 ACCCTCTTCGTCCATGAACAA 59.303 47.619 0.00 0.00 0.00 2.83
2111 2187 1.348064 ACCCTCTTCGTCCATGAACA 58.652 50.000 0.00 0.00 0.00 3.18
2112 2188 3.821421 ATACCCTCTTCGTCCATGAAC 57.179 47.619 0.00 0.00 0.00 3.18
2121 2197 6.127310 CCCTCAAATCCTATATACCCTCTTCG 60.127 46.154 0.00 0.00 0.00 3.79
2128 2204 5.489278 AGAAGCCCCTCAAATCCTATATACC 59.511 44.000 0.00 0.00 0.00 2.73
2135 2211 1.713078 ACAAGAAGCCCCTCAAATCCT 59.287 47.619 0.00 0.00 0.00 3.24
2146 2222 1.228459 AAACCCCCGACAAGAAGCC 60.228 57.895 0.00 0.00 0.00 4.35
2245 2321 1.792057 GCGTCGGCGTTCATGTTTG 60.792 57.895 12.58 0.00 40.81 2.93
2325 2401 3.062763 GTTGAGATAGTGATCATGCGGG 58.937 50.000 0.00 0.00 34.17 6.13
2373 2451 4.263068 CCTTCTTCCTCCTCTAGCAAACAA 60.263 45.833 0.00 0.00 0.00 2.83
2411 2490 1.133407 CACCCACGTAGAGAGAAGAGC 59.867 57.143 0.00 0.00 0.00 4.09
2415 2495 2.035449 CACAACACCCACGTAGAGAGAA 59.965 50.000 0.00 0.00 0.00 2.87
2527 2626 3.139810 AGAGACACTGACAGCTGGT 57.860 52.632 19.93 5.35 0.00 4.00
2584 2690 0.038892 GTCGGCCAAGTACGAGACAA 60.039 55.000 2.24 0.00 40.09 3.18
2618 2724 1.371558 GTCGGCAAGACCCTCAAGT 59.628 57.895 0.59 0.00 43.95 3.16
2635 2741 3.338249 CATTGCCACAGTACTAAGCAGT 58.662 45.455 11.93 8.00 38.91 4.40
2726 2832 0.985490 AGAAGAGATGGGGAGTGGCC 60.985 60.000 0.00 0.00 0.00 5.36
2754 2860 1.676006 CCTTCCTTGAAGTTTGTGCGT 59.324 47.619 3.40 0.00 37.92 5.24


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

AutoCloner maintained by Alex Coulton.