Multiple sequence alignment - TraesCS7A01G116800

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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 TraesCS7A01G116800 chr7A 100.000 2426 0 0 1 2426 74648464 74650889 0.000000e+00 4481.0
1 TraesCS7A01G116800 chr7A 88.745 773 29 25 104 841 70831654 70830905 0.000000e+00 893.0
2 TraesCS7A01G116800 chr7A 83.934 305 36 12 1517 1815 653638250 653638547 1.840000e-71 279.0
3 TraesCS7A01G116800 chr7A 84.615 286 34 9 1535 1815 653622679 653622959 2.380000e-70 276.0
4 TraesCS7A01G116800 chr7A 90.426 94 9 0 399 492 68200421 68200514 9.110000e-25 124.0
5 TraesCS7A01G116800 chr7A 85.600 125 11 2 560 684 68200552 68200669 9.110000e-25 124.0
6 TraesCS7A01G116800 chr4A 97.639 1567 36 1 833 2399 625030502 625028937 0.000000e+00 2687.0
7 TraesCS7A01G116800 chr7D 92.658 1580 90 8 835 2396 254372178 254370607 0.000000e+00 2252.0
8 TraesCS7A01G116800 chr7D 88.198 788 53 20 82 841 68988554 68989329 0.000000e+00 904.0
9 TraesCS7A01G116800 chr7D 86.289 547 36 21 323 841 66400583 66400048 2.110000e-155 558.0
10 TraesCS7A01G116800 chr7D 81.789 313 40 13 198 504 65788195 65787894 1.860000e-61 246.0
11 TraesCS7A01G116800 chr7D 90.123 162 6 8 559 716 65787800 65787645 4.090000e-48 202.0
12 TraesCS7A01G116800 chr7D 81.279 219 38 3 1292 1508 71820291 71820508 8.920000e-40 174.0
13 TraesCS7A01G116800 chr7D 97.959 98 2 0 227 324 66401072 66400975 1.150000e-38 171.0
14 TraesCS7A01G116800 chr7D 96.296 81 3 0 1 81 203173296 203173216 1.510000e-27 134.0
15 TraesCS7A01G116800 chr7D 86.400 125 10 2 560 684 64413678 64413795 1.960000e-26 130.0
16 TraesCS7A01G116800 chr7D 79.878 164 24 7 81 237 66408729 66408568 7.090000e-21 111.0
17 TraesCS7A01G116800 chr7D 90.000 70 7 0 11 80 112056107 112056176 9.240000e-15 91.6
18 TraesCS7A01G116800 chr7B 90.000 1570 120 12 846 2396 231696511 231694960 0.000000e+00 1995.0
19 TraesCS7A01G116800 chr7B 87.980 599 60 12 1807 2400 478838600 478838009 0.000000e+00 697.0
20 TraesCS7A01G116800 chr7B 95.402 348 15 1 82 428 10567135 10567482 9.800000e-154 553.0
21 TraesCS7A01G116800 chr7B 92.120 368 18 7 360 727 7605079 7604723 2.150000e-140 508.0
22 TraesCS7A01G116800 chr7B 93.564 202 13 0 451 652 10567477 10567678 3.920000e-78 302.0
23 TraesCS7A01G116800 chr7B 86.381 257 27 3 237 492 5929926 5930175 8.550000e-70 274.0
24 TraesCS7A01G116800 chr7B 96.190 105 4 0 260 364 7612493 7612389 3.210000e-39 172.0
25 TraesCS7A01G116800 chr7B 83.060 183 19 5 560 742 5930213 5930383 3.230000e-34 156.0
26 TraesCS7A01G116800 chr7B 94.318 88 2 2 756 841 10569212 10569298 5.440000e-27 132.0
27 TraesCS7A01G116800 chr7B 90.625 96 5 3 750 841 7604666 7604571 9.110000e-25 124.0
28 TraesCS7A01G116800 chr7B 93.750 80 5 0 1 80 71380612 71380691 1.180000e-23 121.0
29 TraesCS7A01G116800 chr2D 90.244 1066 64 8 837 1863 533092136 533093200 0.000000e+00 1356.0
30 TraesCS7A01G116800 chr4B 88.391 603 61 9 1807 2404 636043493 636042895 0.000000e+00 717.0
31 TraesCS7A01G116800 chr4B 88.481 599 60 9 1807 2400 96629507 96630101 0.000000e+00 715.0
32 TraesCS7A01G116800 chr1D 88.284 606 54 17 1807 2403 249621233 249620636 0.000000e+00 710.0
33 TraesCS7A01G116800 chr3B 87.980 599 62 10 1807 2400 267228697 267228104 0.000000e+00 699.0
34 TraesCS7A01G116800 chr3B 83.553 304 34 15 1521 1814 662540279 662539982 1.110000e-68 270.0
35 TraesCS7A01G116800 chr3D 90.654 535 25 7 1327 1861 360642092 360641583 0.000000e+00 688.0
36 TraesCS7A01G116800 chr3D 94.207 397 22 1 837 1233 360690840 360690445 2.670000e-169 604.0
37 TraesCS7A01G116800 chr3D 85.069 288 37 5 1492 1778 553871184 553871466 3.050000e-74 289.0
38 TraesCS7A01G116800 chr3D 96.250 80 3 0 1 80 385425285 385425206 5.440000e-27 132.0
39 TraesCS7A01G116800 chr6A 86.745 596 70 9 1807 2397 589510145 589510736 0.000000e+00 654.0
40 TraesCS7A01G116800 chr6A 85.098 255 33 3 234 487 1752497 1752747 3.100000e-64 255.0
41 TraesCS7A01G116800 chr2A 79.938 643 96 17 933 1557 227536837 227537464 2.210000e-120 442.0
42 TraesCS7A01G116800 chr3A 94.505 91 4 1 1 90 714422560 714422650 3.250000e-29 139.0
43 TraesCS7A01G116800 chr6B 93.671 79 5 0 1 79 22076667 22076745 4.240000e-23 119.0
44 TraesCS7A01G116800 chr6B 92.500 80 6 0 1 80 636179522 636179601 5.480000e-22 115.0
45 TraesCS7A01G116800 chr6B 92.405 79 6 0 1 79 655311058 655310980 1.970000e-21 113.0
46 TraesCS7A01G116800 chr6B 91.250 80 7 0 1 80 636205607 636205686 2.550000e-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 TraesCS7A01G116800 chr7A 74648464 74650889 2425 False 4481.0 4481 100.0000 1 2426 1 chr7A.!!$F1 2425
1 TraesCS7A01G116800 chr7A 70830905 70831654 749 True 893.0 893 88.7450 104 841 1 chr7A.!!$R1 737
2 TraesCS7A01G116800 chr4A 625028937 625030502 1565 True 2687.0 2687 97.6390 833 2399 1 chr4A.!!$R1 1566
3 TraesCS7A01G116800 chr7D 254370607 254372178 1571 True 2252.0 2252 92.6580 835 2396 1 chr7D.!!$R3 1561
4 TraesCS7A01G116800 chr7D 68988554 68989329 775 False 904.0 904 88.1980 82 841 1 chr7D.!!$F2 759
5 TraesCS7A01G116800 chr7D 66400048 66401072 1024 True 364.5 558 92.1240 227 841 2 chr7D.!!$R5 614
6 TraesCS7A01G116800 chr7D 65787645 65788195 550 True 224.0 246 85.9560 198 716 2 chr7D.!!$R4 518
7 TraesCS7A01G116800 chr7B 231694960 231696511 1551 True 1995.0 1995 90.0000 846 2396 1 chr7B.!!$R2 1550
8 TraesCS7A01G116800 chr7B 478838009 478838600 591 True 697.0 697 87.9800 1807 2400 1 chr7B.!!$R3 593
9 TraesCS7A01G116800 chr7B 10567135 10569298 2163 False 329.0 553 94.4280 82 841 3 chr7B.!!$F3 759
10 TraesCS7A01G116800 chr7B 7604571 7605079 508 True 316.0 508 91.3725 360 841 2 chr7B.!!$R4 481
11 TraesCS7A01G116800 chr2D 533092136 533093200 1064 False 1356.0 1356 90.2440 837 1863 1 chr2D.!!$F1 1026
12 TraesCS7A01G116800 chr4B 636042895 636043493 598 True 717.0 717 88.3910 1807 2404 1 chr4B.!!$R1 597
13 TraesCS7A01G116800 chr4B 96629507 96630101 594 False 715.0 715 88.4810 1807 2400 1 chr4B.!!$F1 593
14 TraesCS7A01G116800 chr1D 249620636 249621233 597 True 710.0 710 88.2840 1807 2403 1 chr1D.!!$R1 596
15 TraesCS7A01G116800 chr3B 267228104 267228697 593 True 699.0 699 87.9800 1807 2400 1 chr3B.!!$R1 593
16 TraesCS7A01G116800 chr3D 360641583 360642092 509 True 688.0 688 90.6540 1327 1861 1 chr3D.!!$R1 534
17 TraesCS7A01G116800 chr6A 589510145 589510736 591 False 654.0 654 86.7450 1807 2397 1 chr6A.!!$F2 590
18 TraesCS7A01G116800 chr2A 227536837 227537464 627 False 442.0 442 79.9380 933 1557 1 chr2A.!!$F1 624

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
44 45 0.034574 ATGGACGGTTTAGCCATGCA 60.035 50.0 0.0 0.0 40.72 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 3960 0.391661 GAGCTCCGCCAGTGAATTCA 60.392 55.0 3.38 3.38 0.0 2.57 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
22 23 4.824479 TGGCATGAGTGAATCTCTAACA 57.176 40.909 0.00 0.00 43.13 2.41
23 24 5.164620 TGGCATGAGTGAATCTCTAACAA 57.835 39.130 0.00 0.00 43.13 2.83
24 25 5.181009 TGGCATGAGTGAATCTCTAACAAG 58.819 41.667 0.00 0.00 43.13 3.16
25 26 5.046376 TGGCATGAGTGAATCTCTAACAAGA 60.046 40.000 0.00 0.00 43.13 3.02
26 27 6.054295 GGCATGAGTGAATCTCTAACAAGAT 58.946 40.000 0.00 0.00 43.13 2.40
27 28 6.018098 GGCATGAGTGAATCTCTAACAAGATG 60.018 42.308 0.00 0.00 43.13 2.90
28 29 6.018098 GCATGAGTGAATCTCTAACAAGATGG 60.018 42.308 0.00 0.00 43.13 3.51
29 30 6.857437 TGAGTGAATCTCTAACAAGATGGA 57.143 37.500 0.00 0.00 43.13 3.41
30 31 6.634805 TGAGTGAATCTCTAACAAGATGGAC 58.365 40.000 0.00 0.00 43.13 4.02
31 32 5.655488 AGTGAATCTCTAACAAGATGGACG 58.345 41.667 0.00 0.00 36.14 4.79
32 33 4.806247 GTGAATCTCTAACAAGATGGACGG 59.194 45.833 0.00 0.00 36.14 4.79
33 34 4.466370 TGAATCTCTAACAAGATGGACGGT 59.534 41.667 0.00 0.00 36.14 4.83
34 35 5.046591 TGAATCTCTAACAAGATGGACGGTT 60.047 40.000 0.00 0.00 36.14 4.44
35 36 4.884668 TCTCTAACAAGATGGACGGTTT 57.115 40.909 0.00 0.00 0.00 3.27
36 37 5.988310 TCTCTAACAAGATGGACGGTTTA 57.012 39.130 0.00 0.00 0.00 2.01
37 38 5.962433 TCTCTAACAAGATGGACGGTTTAG 58.038 41.667 0.00 0.00 0.00 1.85
38 39 4.501071 TCTAACAAGATGGACGGTTTAGC 58.499 43.478 0.00 0.00 0.00 3.09
39 40 2.109425 ACAAGATGGACGGTTTAGCC 57.891 50.000 0.00 0.00 0.00 3.93
40 41 1.349688 ACAAGATGGACGGTTTAGCCA 59.650 47.619 0.00 0.00 36.97 4.75
41 42 2.026262 ACAAGATGGACGGTTTAGCCAT 60.026 45.455 0.00 0.00 44.70 4.40
42 43 2.332063 AGATGGACGGTTTAGCCATG 57.668 50.000 4.01 0.00 42.22 3.66
43 44 0.663153 GATGGACGGTTTAGCCATGC 59.337 55.000 4.01 0.00 42.22 4.06
44 45 0.034574 ATGGACGGTTTAGCCATGCA 60.035 50.000 0.00 0.00 40.72 3.96
45 46 0.958382 TGGACGGTTTAGCCATGCAC 60.958 55.000 0.00 0.00 36.97 4.57
46 47 0.676782 GGACGGTTTAGCCATGCACT 60.677 55.000 0.00 0.00 36.97 4.40
47 48 0.447801 GACGGTTTAGCCATGCACTG 59.552 55.000 0.00 0.00 36.97 3.66
59 60 3.375782 CATGCACTGGATATCTCGTGA 57.624 47.619 21.22 11.38 0.00 4.35
60 61 3.721035 CATGCACTGGATATCTCGTGAA 58.279 45.455 21.22 14.91 0.00 3.18
61 62 4.313282 CATGCACTGGATATCTCGTGAAT 58.687 43.478 21.22 16.10 0.00 2.57
62 63 3.721035 TGCACTGGATATCTCGTGAATG 58.279 45.455 21.22 6.32 0.00 2.67
63 64 3.062763 GCACTGGATATCTCGTGAATGG 58.937 50.000 21.22 3.40 0.00 3.16
64 65 3.493350 GCACTGGATATCTCGTGAATGGT 60.493 47.826 21.22 1.00 0.00 3.55
65 66 4.262036 GCACTGGATATCTCGTGAATGGTA 60.262 45.833 21.22 0.00 0.00 3.25
66 67 5.465051 CACTGGATATCTCGTGAATGGTAG 58.535 45.833 15.39 0.00 0.00 3.18
67 68 5.241728 CACTGGATATCTCGTGAATGGTAGA 59.758 44.000 15.39 0.00 0.00 2.59
68 69 5.833667 ACTGGATATCTCGTGAATGGTAGAA 59.166 40.000 2.05 0.00 0.00 2.10
69 70 6.495181 ACTGGATATCTCGTGAATGGTAGAAT 59.505 38.462 2.05 0.00 0.00 2.40
70 71 6.925211 TGGATATCTCGTGAATGGTAGAATC 58.075 40.000 2.05 0.00 0.00 2.52
71 72 6.493458 TGGATATCTCGTGAATGGTAGAATCA 59.507 38.462 2.05 0.00 0.00 2.57
72 73 6.809196 GGATATCTCGTGAATGGTAGAATCAC 59.191 42.308 2.05 0.00 39.98 3.06
73 74 5.860941 ATCTCGTGAATGGTAGAATCACT 57.139 39.130 3.94 0.00 40.95 3.41
74 75 5.661056 TCTCGTGAATGGTAGAATCACTT 57.339 39.130 3.94 0.00 40.95 3.16
75 76 6.037786 TCTCGTGAATGGTAGAATCACTTT 57.962 37.500 3.94 0.00 40.95 2.66
76 77 6.464222 TCTCGTGAATGGTAGAATCACTTTT 58.536 36.000 3.94 0.00 40.95 2.27
77 78 6.590292 TCTCGTGAATGGTAGAATCACTTTTC 59.410 38.462 3.94 0.00 40.95 2.29
78 79 6.464222 TCGTGAATGGTAGAATCACTTTTCT 58.536 36.000 3.94 0.00 40.95 2.52
79 80 6.590292 TCGTGAATGGTAGAATCACTTTTCTC 59.410 38.462 3.94 0.00 40.95 2.87
80 81 6.368791 CGTGAATGGTAGAATCACTTTTCTCA 59.631 38.462 3.94 0.00 40.95 3.27
98 99 9.693739 CTTTTCTCATAGATATAGAGCCCTCTA 57.306 37.037 7.42 7.42 45.24 2.43
115 116 7.908453 AGCCCTCTATGTTAATATGTAAGACC 58.092 38.462 0.00 0.00 0.00 3.85
230 233 3.436817 TCCGTACGCAAAACAATTACG 57.563 42.857 10.49 0.00 36.22 3.18
483 880 2.673200 GGATGAGGCCCTGCTGTGA 61.673 63.158 0.00 0.00 0.00 3.58
511 908 3.191637 GACCTACGTCCCGATCCGC 62.192 68.421 0.00 0.00 32.40 5.54
652 1097 3.104766 TCGACGCCGATGTCCTAC 58.895 61.111 0.00 0.00 40.30 3.18
653 1098 2.352001 CGACGCCGATGTCCTACG 60.352 66.667 0.00 0.00 38.22 3.51
654 1099 2.796651 GACGCCGATGTCCTACGT 59.203 61.111 0.00 0.00 40.11 3.57
655 1100 1.298190 GACGCCGATGTCCTACGTC 60.298 63.158 0.00 0.00 45.10 4.34
656 1101 2.025727 CGCCGATGTCCTACGTCC 59.974 66.667 0.00 0.00 30.49 4.79
657 1102 2.478890 CGCCGATGTCCTACGTCCT 61.479 63.158 0.00 0.00 30.49 3.85
658 1103 1.162181 CGCCGATGTCCTACGTCCTA 61.162 60.000 0.00 0.00 30.49 2.94
718 1601 5.032846 TCCTGACCAACTTTCATCTAGGAT 58.967 41.667 0.00 0.00 0.00 3.24
727 1610 4.813161 ACTTTCATCTAGGATGTTGCATCG 59.187 41.667 7.30 0.00 0.00 3.84
729 1612 3.982475 TCATCTAGGATGTTGCATCGAC 58.018 45.455 7.30 0.00 0.00 4.20
731 1614 3.717400 TCTAGGATGTTGCATCGACTC 57.283 47.619 0.00 0.00 0.00 3.36
733 1616 4.461198 TCTAGGATGTTGCATCGACTCTA 58.539 43.478 0.00 0.00 0.00 2.43
734 1617 4.887655 TCTAGGATGTTGCATCGACTCTAA 59.112 41.667 0.00 0.00 0.00 2.10
736 1619 5.028549 AGGATGTTGCATCGACTCTAATT 57.971 39.130 0.00 0.00 0.00 1.40
738 1621 5.986135 AGGATGTTGCATCGACTCTAATTAC 59.014 40.000 0.00 0.00 0.00 1.89
741 1624 7.041780 GGATGTTGCATCGACTCTAATTACATT 60.042 37.037 0.00 0.00 0.00 2.71
742 1625 8.887036 ATGTTGCATCGACTCTAATTACATTA 57.113 30.769 0.00 0.00 0.00 1.90
1021 2957 1.153989 CTCTCCTCTGCCCCGGATA 59.846 63.158 0.73 0.00 0.00 2.59
1022 2958 1.152525 TCTCCTCTGCCCCGGATAC 60.153 63.158 0.73 0.00 0.00 2.24
1388 3363 1.762957 CCAGGACGACCCATATCTTGT 59.237 52.381 0.00 0.00 37.41 3.16
1816 3793 1.754226 GTGTGGTTGATGGTGGTGTTT 59.246 47.619 0.00 0.00 0.00 2.83
1983 3960 0.541863 CCCAACCTGCTAATCGTCCT 59.458 55.000 0.00 0.00 0.00 3.85
2218 4197 5.344743 TGTTGAGTGTCTTGTTCTTCTCT 57.655 39.130 0.00 0.00 0.00 3.10
2313 4295 5.556006 TCGATCCGGTTTCCCTTATAAAT 57.444 39.130 0.00 0.00 0.00 1.40
2316 4298 5.761234 CGATCCGGTTTCCCTTATAAATTGA 59.239 40.000 0.00 0.00 0.00 2.57
2318 4300 7.201750 CGATCCGGTTTCCCTTATAAATTGAAA 60.202 37.037 0.00 0.00 0.00 2.69
2360 4342 7.801104 TGGCCACTTTGAGTAATATATTCAGA 58.199 34.615 0.00 0.00 0.00 3.27
2418 4400 6.663944 AAAAAGATACATCTACTGAACGCC 57.336 37.500 0.00 0.00 35.76 5.68
2419 4401 4.323553 AAGATACATCTACTGAACGCCC 57.676 45.455 0.00 0.00 35.76 6.13
2420 4402 3.567397 AGATACATCTACTGAACGCCCT 58.433 45.455 0.00 0.00 34.85 5.19
2421 4403 3.570550 AGATACATCTACTGAACGCCCTC 59.429 47.826 0.00 0.00 34.85 4.30
2422 4404 0.824759 ACATCTACTGAACGCCCTCC 59.175 55.000 0.00 0.00 0.00 4.30
2423 4405 1.115467 CATCTACTGAACGCCCTCCT 58.885 55.000 0.00 0.00 0.00 3.69
2424 4406 1.067821 CATCTACTGAACGCCCTCCTC 59.932 57.143 0.00 0.00 0.00 3.71
2425 4407 1.030488 TCTACTGAACGCCCTCCTCG 61.030 60.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.394663 CCGTCCATCTTGTTAGAGATTCACT 60.395 44.000 0.00 0.00 34.20 3.41
9 10 4.806247 CCGTCCATCTTGTTAGAGATTCAC 59.194 45.833 0.00 0.00 34.20 3.18
10 11 4.466370 ACCGTCCATCTTGTTAGAGATTCA 59.534 41.667 0.00 0.00 34.20 2.57
11 12 5.012328 ACCGTCCATCTTGTTAGAGATTC 57.988 43.478 0.00 0.00 34.20 2.52
12 13 5.422214 AACCGTCCATCTTGTTAGAGATT 57.578 39.130 0.00 0.00 34.20 2.40
13 14 5.422214 AAACCGTCCATCTTGTTAGAGAT 57.578 39.130 0.00 0.00 36.84 2.75
14 15 4.884668 AAACCGTCCATCTTGTTAGAGA 57.115 40.909 0.00 0.00 32.92 3.10
15 16 4.567159 GCTAAACCGTCCATCTTGTTAGAG 59.433 45.833 0.00 0.00 32.92 2.43
16 17 4.501071 GCTAAACCGTCCATCTTGTTAGA 58.499 43.478 0.00 0.00 34.21 2.10
17 18 3.621715 GGCTAAACCGTCCATCTTGTTAG 59.378 47.826 0.00 0.00 0.00 2.34
18 19 3.008157 TGGCTAAACCGTCCATCTTGTTA 59.992 43.478 0.00 0.00 43.94 2.41
19 20 2.224670 TGGCTAAACCGTCCATCTTGTT 60.225 45.455 0.00 0.00 43.94 2.83
20 21 1.349688 TGGCTAAACCGTCCATCTTGT 59.650 47.619 0.00 0.00 43.94 3.16
21 22 2.107950 TGGCTAAACCGTCCATCTTG 57.892 50.000 0.00 0.00 43.94 3.02
22 23 2.643551 CATGGCTAAACCGTCCATCTT 58.356 47.619 0.00 0.00 43.94 2.40
23 24 1.747206 GCATGGCTAAACCGTCCATCT 60.747 52.381 0.00 0.00 43.94 2.90
24 25 0.663153 GCATGGCTAAACCGTCCATC 59.337 55.000 0.00 0.00 43.94 3.51
25 26 0.034574 TGCATGGCTAAACCGTCCAT 60.035 50.000 0.00 0.00 43.94 3.41
26 27 0.958382 GTGCATGGCTAAACCGTCCA 60.958 55.000 0.00 0.00 43.94 4.02
27 28 0.676782 AGTGCATGGCTAAACCGTCC 60.677 55.000 0.00 0.00 43.94 4.79
28 29 0.447801 CAGTGCATGGCTAAACCGTC 59.552 55.000 0.00 0.00 43.94 4.79
29 30 0.960364 CCAGTGCATGGCTAAACCGT 60.960 55.000 0.00 0.00 43.83 4.83
30 31 1.802636 CCAGTGCATGGCTAAACCG 59.197 57.895 0.00 0.00 43.83 4.44
39 40 3.375782 TCACGAGATATCCAGTGCATG 57.624 47.619 18.22 0.00 34.84 4.06
40 41 4.313282 CATTCACGAGATATCCAGTGCAT 58.687 43.478 18.22 12.81 34.84 3.96
41 42 3.493176 CCATTCACGAGATATCCAGTGCA 60.493 47.826 18.22 11.41 34.84 4.57
42 43 3.062763 CCATTCACGAGATATCCAGTGC 58.937 50.000 18.22 0.00 34.84 4.40
43 44 4.327982 ACCATTCACGAGATATCCAGTG 57.672 45.455 17.37 17.37 36.06 3.66
44 45 5.386060 TCTACCATTCACGAGATATCCAGT 58.614 41.667 0.00 0.00 0.00 4.00
45 46 5.966742 TCTACCATTCACGAGATATCCAG 57.033 43.478 0.00 0.00 0.00 3.86
46 47 6.493458 TGATTCTACCATTCACGAGATATCCA 59.507 38.462 0.00 0.00 0.00 3.41
47 48 6.809196 GTGATTCTACCATTCACGAGATATCC 59.191 42.308 0.00 0.00 31.40 2.59
48 49 7.598278 AGTGATTCTACCATTCACGAGATATC 58.402 38.462 0.00 0.00 43.49 1.63
49 50 7.531857 AGTGATTCTACCATTCACGAGATAT 57.468 36.000 0.00 0.00 43.49 1.63
50 51 6.961360 AGTGATTCTACCATTCACGAGATA 57.039 37.500 0.00 0.00 43.49 1.98
51 52 5.860941 AGTGATTCTACCATTCACGAGAT 57.139 39.130 0.00 0.00 43.49 2.75
52 53 5.661056 AAGTGATTCTACCATTCACGAGA 57.339 39.130 0.00 0.00 43.49 4.04
53 54 6.591834 AGAAAAGTGATTCTACCATTCACGAG 59.408 38.462 0.00 0.00 43.49 4.18
54 55 6.464222 AGAAAAGTGATTCTACCATTCACGA 58.536 36.000 0.00 0.00 43.49 4.35
55 56 6.368791 TGAGAAAAGTGATTCTACCATTCACG 59.631 38.462 0.00 0.00 43.49 4.35
56 57 7.672983 TGAGAAAAGTGATTCTACCATTCAC 57.327 36.000 0.00 0.00 39.70 3.18
57 58 9.605275 CTATGAGAAAAGTGATTCTACCATTCA 57.395 33.333 0.00 0.00 39.70 2.57
58 59 9.823647 TCTATGAGAAAAGTGATTCTACCATTC 57.176 33.333 0.00 0.00 39.70 2.67
68 69 8.757877 GGGCTCTATATCTATGAGAAAAGTGAT 58.242 37.037 0.00 0.00 0.00 3.06
69 70 7.952930 AGGGCTCTATATCTATGAGAAAAGTGA 59.047 37.037 0.00 0.00 0.00 3.41
70 71 8.133024 AGGGCTCTATATCTATGAGAAAAGTG 57.867 38.462 0.00 0.00 0.00 3.16
71 72 8.176780 AGAGGGCTCTATATCTATGAGAAAAGT 58.823 37.037 0.00 0.00 38.35 2.66
72 73 8.593945 AGAGGGCTCTATATCTATGAGAAAAG 57.406 38.462 0.00 0.00 38.35 2.27
183 186 7.764901 AGAGGAAGTTTATAGATGTTCGGAAAC 59.235 37.037 0.00 0.00 35.85 2.78
230 233 6.661805 CCTCTTCTAATCCATCCTACCTACTC 59.338 46.154 0.00 0.00 0.00 2.59
483 880 0.389426 GACGTAGGTCAATGTGCCGT 60.389 55.000 10.63 0.00 42.91 5.68
511 908 1.801913 CTTCGTGCTCTTCGTCCCG 60.802 63.158 0.00 0.00 0.00 5.14
538 947 4.980805 TGGCAGTTCGTCCCACGC 62.981 66.667 0.00 0.00 42.21 5.34
652 1097 0.463295 TGGCGAGGTAGACTAGGACG 60.463 60.000 0.00 0.00 0.00 4.79
653 1098 1.404748 GTTGGCGAGGTAGACTAGGAC 59.595 57.143 0.00 0.00 0.00 3.85
654 1099 1.005097 TGTTGGCGAGGTAGACTAGGA 59.995 52.381 0.00 0.00 0.00 2.94
655 1100 1.405821 CTGTTGGCGAGGTAGACTAGG 59.594 57.143 0.00 0.00 0.00 3.02
656 1101 1.405821 CCTGTTGGCGAGGTAGACTAG 59.594 57.143 0.00 0.00 0.00 2.57
657 1102 1.471119 CCTGTTGGCGAGGTAGACTA 58.529 55.000 0.00 0.00 0.00 2.59
658 1103 2.277858 CCTGTTGGCGAGGTAGACT 58.722 57.895 0.00 0.00 0.00 3.24
684 1513 0.629596 TGGTCAGGACTCCGGAGTAT 59.370 55.000 36.38 24.74 42.66 2.12
685 1514 0.406750 TTGGTCAGGACTCCGGAGTA 59.593 55.000 36.38 19.00 42.66 2.59
686 1515 1.155390 TTGGTCAGGACTCCGGAGT 59.845 57.895 36.89 36.89 45.84 3.85
687 1516 0.900647 AGTTGGTCAGGACTCCGGAG 60.901 60.000 30.11 30.11 0.00 4.63
718 1601 8.887036 ATAATGTAATTAGAGTCGATGCAACA 57.113 30.769 0.00 0.00 42.97 3.33
752 1635 3.896888 CTGCAGGTGATTAGGAGAGAGAT 59.103 47.826 5.57 0.00 0.00 2.75
781 2715 1.070758 TGACAGAGGTTCCTCAGCAAC 59.929 52.381 19.28 8.51 35.67 4.17
1388 3363 4.020617 CCCGAGCCAGCAAGGACA 62.021 66.667 5.17 0.00 41.22 4.02
1816 3793 2.357760 GCCGCTGAACCCGTACAA 60.358 61.111 0.00 0.00 0.00 2.41
1915 3892 2.702592 AGAACCGAGACAACACCAAA 57.297 45.000 0.00 0.00 0.00 3.28
1983 3960 0.391661 GAGCTCCGCCAGTGAATTCA 60.392 55.000 3.38 3.38 0.00 2.57
2086 4064 1.070134 AGACTTGCGAGCAACCTAACA 59.930 47.619 6.39 0.00 0.00 2.41
2313 4295 2.957402 ATGCCAGGAGAGTGTTTCAA 57.043 45.000 0.00 0.00 0.00 2.69
2316 4298 3.624777 CCATTATGCCAGGAGAGTGTTT 58.375 45.455 0.00 0.00 0.00 2.83
2318 4300 1.133976 GCCATTATGCCAGGAGAGTGT 60.134 52.381 0.00 0.00 0.00 3.55
2404 4386 1.067821 GAGGAGGGCGTTCAGTAGATG 59.932 57.143 0.00 0.00 0.00 2.90
2405 4387 1.404843 GAGGAGGGCGTTCAGTAGAT 58.595 55.000 0.00 0.00 0.00 1.98
2406 4388 1.030488 CGAGGAGGGCGTTCAGTAGA 61.030 60.000 0.00 0.00 0.00 2.59
2407 4389 1.433879 CGAGGAGGGCGTTCAGTAG 59.566 63.158 0.00 0.00 0.00 2.57
2408 4390 3.599584 CGAGGAGGGCGTTCAGTA 58.400 61.111 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.