Multiple sequence alignment - TraesCS2A01G055600

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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 TraesCS2A01G055600 chr2A 100.000 2690 0 0 1 2690 23877852 23880541 0.000000e+00 4968.0
1 TraesCS2A01G055600 chr2A 94.580 1513 57 16 546 2040 23827985 23829490 0.000000e+00 2316.0
2 TraesCS2A01G055600 chr2A 91.770 243 17 3 2146 2387 23829599 23829839 4.290000e-88 335.0
3 TraesCS2A01G055600 chr2A 98.876 89 1 0 2059 2147 23829474 23829562 2.770000e-35 159.0
4 TraesCS2A01G055600 chr2A 96.429 84 1 2 4 87 773234761 773234680 1.300000e-28 137.0
5 TraesCS2A01G055600 chr2A 100.000 41 0 0 708 748 23828190 23828230 2.870000e-10 76.8
6 TraesCS2A01G055600 chr2D 93.661 1972 117 7 75 2040 21680389 21682358 0.000000e+00 2942.0
7 TraesCS2A01G055600 chr2D 93.266 1975 117 13 75 2038 21641575 21643544 0.000000e+00 2896.0
8 TraesCS2A01G055600 chr2D 93.383 1209 69 8 831 2038 21620839 21622037 0.000000e+00 1779.0
9 TraesCS2A01G055600 chr2D 92.675 1174 78 7 75 1242 21663974 21665145 0.000000e+00 1685.0
10 TraesCS2A01G055600 chr2D 91.291 643 23 8 2059 2688 21682342 21682964 0.000000e+00 846.0
11 TraesCS2A01G055600 chr2D 86.081 546 39 12 2146 2690 21622148 21622657 1.090000e-153 553.0
12 TraesCS2A01G055600 chr2D 97.573 206 5 0 2483 2688 21666141 21666346 1.180000e-93 353.0
13 TraesCS2A01G055600 chr2D 84.426 366 38 14 152 502 579001946 579002307 2.560000e-90 342.0
14 TraesCS2A01G055600 chr2D 89.961 259 20 3 2392 2649 21643870 21644123 2.000000e-86 329.0
15 TraesCS2A01G055600 chr2D 89.520 229 22 2 2146 2373 21643655 21643882 3.390000e-74 289.0
16 TraesCS2A01G055600 chr2D 91.558 154 12 1 539 692 21619298 21619450 7.550000e-51 211.0
17 TraesCS2A01G055600 chr2D 93.043 115 8 0 727 841 21619518 21619632 4.610000e-38 169.0
18 TraesCS2A01G055600 chr2D 96.629 89 3 0 2059 2147 21622023 21622111 6.000000e-32 148.0
19 TraesCS2A01G055600 chr2D 96.629 89 3 0 2059 2147 21643530 21643618 6.000000e-32 148.0
20 TraesCS2A01G055600 chr2D 87.838 74 9 0 75 148 21619231 21619304 1.330000e-13 87.9
21 TraesCS2A01G055600 chr2D 90.164 61 4 1 2405 2465 21666083 21666141 7.980000e-11 78.7
22 TraesCS2A01G055600 chr2B 91.578 1983 146 11 75 2040 34865389 34863411 0.000000e+00 2717.0
23 TraesCS2A01G055600 chr2B 91.797 1597 110 15 456 2040 34890328 34888741 0.000000e+00 2204.0
24 TraesCS2A01G055600 chr2B 89.687 543 54 2 2149 2690 34863305 34862764 0.000000e+00 691.0
25 TraesCS2A01G055600 chr2B 89.340 394 35 6 75 463 34952535 34952144 3.110000e-134 488.0
26 TraesCS2A01G055600 chr2B 90.456 241 21 2 2148 2387 34888630 34888391 1.550000e-82 316.0
27 TraesCS2A01G055600 chr2B 98.913 92 1 0 2059 2150 34888757 34888666 5.960000e-37 165.0
28 TraesCS2A01G055600 chr2B 100.000 30 0 0 2561 2590 93442956 93442927 3.740000e-04 56.5
29 TraesCS2A01G055600 chr6A 83.428 1231 137 35 776 1969 604573922 604572722 0.000000e+00 1081.0
30 TraesCS2A01G055600 chr6A 96.512 86 2 1 4 88 574900852 574900767 1.000000e-29 141.0
31 TraesCS2A01G055600 chr6A 98.750 80 0 1 4 83 609071328 609071250 1.000000e-29 141.0
32 TraesCS2A01G055600 chr6A 97.368 38 1 0 2653 2690 558034811 558034774 6.220000e-07 65.8
33 TraesCS2A01G055600 chr6D 82.510 1235 145 38 776 1969 457636689 457635485 0.000000e+00 1018.0
34 TraesCS2A01G055600 chr6D 80.838 1289 180 38 708 1969 457591154 457589906 0.000000e+00 950.0
35 TraesCS2A01G055600 chr6D 97.297 37 1 0 2654 2690 412358529 412358493 2.240000e-06 63.9
36 TraesCS2A01G055600 chr6B 82.163 1239 142 42 776 1969 696100180 696098976 0.000000e+00 990.0
37 TraesCS2A01G055600 chr6B 85.332 859 95 16 774 1625 695947353 695948187 0.000000e+00 859.0
38 TraesCS2A01G055600 chr6B 91.667 72 6 0 708 779 695947151 695947222 1.700000e-17 100.0
39 TraesCS2A01G055600 chr3D 85.559 367 40 9 152 506 454744146 454744511 3.270000e-99 372.0
40 TraesCS2A01G055600 chr3D 94.737 38 2 0 2653 2690 529837890 529837927 2.890000e-05 60.2
41 TraesCS2A01G055600 chrUn 84.765 361 41 10 155 502 61736691 61736332 1.530000e-92 350.0
42 TraesCS2A01G055600 chrUn 91.379 58 5 0 2633 2690 455757067 455757010 2.220000e-11 80.5
43 TraesCS2A01G055600 chr1A 83.702 362 38 17 152 502 437723987 437724338 3.340000e-84 322.0
44 TraesCS2A01G055600 chr1A 97.561 82 2 0 4 85 539988774 539988693 1.000000e-29 141.0
45 TraesCS2A01G055600 chr5A 97.590 83 1 1 1 83 30985362 30985443 1.000000e-29 141.0
46 TraesCS2A01G055600 chr5A 98.750 80 0 1 4 83 31004341 31004263 1.000000e-29 141.0
47 TraesCS2A01G055600 chr5A 97.590 83 1 1 1 83 31048063 31048144 1.000000e-29 141.0
48 TraesCS2A01G055600 chr5A 96.429 84 3 0 4 87 424368063 424367980 3.610000e-29 139.0
49 TraesCS2A01G055600 chr5A 95.402 87 4 0 1 87 425566728 425566814 3.610000e-29 139.0
50 TraesCS2A01G055600 chr3A 91.379 58 5 0 2633 2690 725161880 725161823 2.220000e-11 80.5
51 TraesCS2A01G055600 chr3A 91.379 58 5 0 2633 2690 725177273 725177216 2.220000e-11 80.5
52 TraesCS2A01G055600 chr1B 92.727 55 4 0 2633 2687 334246993 334247047 2.220000e-11 80.5
53 TraesCS2A01G055600 chr7B 91.071 56 5 0 2635 2690 600840648 600840703 2.870000e-10 76.8
54 TraesCS2A01G055600 chr7B 100.000 33 0 0 2558 2590 505470104 505470072 8.040000e-06 62.1
55 TraesCS2A01G055600 chr1D 93.878 49 3 0 2640 2688 441199004 441199052 1.030000e-09 75.0
56 TraesCS2A01G055600 chr3B 89.655 58 3 1 2633 2690 78654636 78654690 1.340000e-08 71.3


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 TraesCS2A01G055600 chr2A 23877852 23880541 2689 False 4968.000000 4968 100.000000 1 2690 1 chr2A.!!$F1 2689
1 TraesCS2A01G055600 chr2A 23827985 23829839 1854 False 721.700000 2316 96.306500 546 2387 4 chr2A.!!$F2 1841
2 TraesCS2A01G055600 chr2D 21680389 21682964 2575 False 1894.000000 2942 92.476000 75 2688 2 chr2D.!!$F5 2613
3 TraesCS2A01G055600 chr2D 21641575 21644123 2548 False 915.500000 2896 92.344000 75 2649 4 chr2D.!!$F3 2574
4 TraesCS2A01G055600 chr2D 21663974 21666346 2372 False 705.566667 1685 93.470667 75 2688 3 chr2D.!!$F4 2613
5 TraesCS2A01G055600 chr2D 21619231 21622657 3426 False 491.316667 1779 91.422000 75 2690 6 chr2D.!!$F2 2615
6 TraesCS2A01G055600 chr2B 34862764 34865389 2625 True 1704.000000 2717 90.632500 75 2690 2 chr2B.!!$R3 2615
7 TraesCS2A01G055600 chr2B 34888391 34890328 1937 True 895.000000 2204 93.722000 456 2387 3 chr2B.!!$R4 1931
8 TraesCS2A01G055600 chr6A 604572722 604573922 1200 True 1081.000000 1081 83.428000 776 1969 1 chr6A.!!$R3 1193
9 TraesCS2A01G055600 chr6D 457635485 457636689 1204 True 1018.000000 1018 82.510000 776 1969 1 chr6D.!!$R3 1193
10 TraesCS2A01G055600 chr6D 457589906 457591154 1248 True 950.000000 950 80.838000 708 1969 1 chr6D.!!$R2 1261
11 TraesCS2A01G055600 chr6B 696098976 696100180 1204 True 990.000000 990 82.163000 776 1969 1 chr6B.!!$R1 1193
12 TraesCS2A01G055600 chr6B 695947151 695948187 1036 False 479.500000 859 88.499500 708 1625 2 chr6B.!!$F1 917

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
64 65 0.030399 AACCGGGACTATAGGCCCTT 60.03 55.0 36.19 24.27 42.4 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1791 3291 1.286354 GCGGTGTCGTCAAATCCGAA 61.286 55.0 12.89 0.0 43.22 4.3 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
21 22 4.056092 GATACTTTAGTCCCGGTTCAGG 57.944 50.000 0.00 0.00 0.00 3.86
22 23 2.019807 ACTTTAGTCCCGGTTCAGGA 57.980 50.000 0.00 0.00 0.00 3.86
23 24 2.332117 ACTTTAGTCCCGGTTCAGGAA 58.668 47.619 0.00 0.00 34.43 3.36
24 25 2.038164 ACTTTAGTCCCGGTTCAGGAAC 59.962 50.000 0.00 3.58 40.45 3.62
34 35 2.845363 GTTCAGGAACCGGGACTAAA 57.155 50.000 6.32 0.00 35.36 1.85
35 36 2.696506 GTTCAGGAACCGGGACTAAAG 58.303 52.381 6.32 0.00 35.36 1.85
36 37 1.272807 TCAGGAACCGGGACTAAAGG 58.727 55.000 6.32 0.00 0.00 3.11
37 38 0.392595 CAGGAACCGGGACTAAAGGC 60.393 60.000 6.32 0.00 0.00 4.35
38 39 1.077930 GGAACCGGGACTAAAGGCC 60.078 63.158 6.32 0.00 0.00 5.19
39 40 1.077930 GAACCGGGACTAAAGGCCC 60.078 63.158 11.29 11.29 41.11 5.80
40 41 1.540617 AACCGGGACTAAAGGCCCT 60.541 57.895 18.97 0.00 42.40 5.19
41 42 1.138228 AACCGGGACTAAAGGCCCTT 61.138 55.000 18.97 4.45 42.40 3.95
42 43 0.252835 ACCGGGACTAAAGGCCCTTA 60.253 55.000 18.97 0.00 42.40 2.69
43 44 0.179702 CCGGGACTAAAGGCCCTTAC 59.820 60.000 18.97 0.00 42.40 2.34
44 45 0.179092 CGGGACTAAAGGCCCTTACG 60.179 60.000 18.97 1.56 42.40 3.18
45 46 1.197812 GGGACTAAAGGCCCTTACGA 58.802 55.000 14.19 0.00 41.31 3.43
46 47 1.556451 GGGACTAAAGGCCCTTACGAA 59.444 52.381 14.19 0.00 41.31 3.85
47 48 2.625737 GGACTAAAGGCCCTTACGAAC 58.374 52.381 0.00 0.00 0.00 3.95
48 49 2.625737 GACTAAAGGCCCTTACGAACC 58.374 52.381 0.00 0.00 0.00 3.62
49 50 1.066645 ACTAAAGGCCCTTACGAACCG 60.067 52.381 0.00 0.00 0.00 4.44
50 51 0.249955 TAAAGGCCCTTACGAACCGG 59.750 55.000 0.00 0.00 0.00 5.28
51 52 2.473891 AAAGGCCCTTACGAACCGGG 62.474 60.000 6.32 0.00 41.06 5.73
52 53 3.393106 GGCCCTTACGAACCGGGA 61.393 66.667 6.32 0.00 40.55 5.14
53 54 2.125391 GCCCTTACGAACCGGGAC 60.125 66.667 6.32 0.00 40.55 4.46
54 55 2.653087 GCCCTTACGAACCGGGACT 61.653 63.158 6.32 0.00 40.55 3.85
55 56 1.322538 GCCCTTACGAACCGGGACTA 61.323 60.000 6.32 0.00 40.55 2.59
56 57 1.406903 CCCTTACGAACCGGGACTAT 58.593 55.000 6.32 0.00 40.55 2.12
57 58 2.586425 CCCTTACGAACCGGGACTATA 58.414 52.381 6.32 0.00 40.55 1.31
58 59 2.555757 CCCTTACGAACCGGGACTATAG 59.444 54.545 6.32 0.00 40.55 1.31
59 60 2.555757 CCTTACGAACCGGGACTATAGG 59.444 54.545 6.32 1.59 0.00 2.57
60 61 1.609208 TACGAACCGGGACTATAGGC 58.391 55.000 6.32 0.00 0.00 3.93
61 62 1.111715 ACGAACCGGGACTATAGGCC 61.112 60.000 17.25 17.25 0.00 5.19
62 63 1.813728 CGAACCGGGACTATAGGCCC 61.814 65.000 31.77 31.77 41.11 5.80
63 64 0.471401 GAACCGGGACTATAGGCCCT 60.471 60.000 36.19 21.66 42.40 5.19
64 65 0.030399 AACCGGGACTATAGGCCCTT 60.030 55.000 36.19 24.27 42.40 3.95
65 66 0.030399 ACCGGGACTATAGGCCCTTT 60.030 55.000 36.19 22.52 42.40 3.11
66 67 1.137697 CCGGGACTATAGGCCCTTTT 58.862 55.000 36.19 0.00 42.40 2.27
67 68 1.493446 CCGGGACTATAGGCCCTTTTT 59.507 52.381 36.19 0.00 42.40 1.94
68 69 2.486727 CCGGGACTATAGGCCCTTTTTC 60.487 54.545 36.19 13.48 42.40 2.29
69 70 2.438392 CGGGACTATAGGCCCTTTTTCT 59.562 50.000 36.19 0.00 42.40 2.52
70 71 3.644738 CGGGACTATAGGCCCTTTTTCTA 59.355 47.826 36.19 0.00 42.40 2.10
71 72 4.502777 CGGGACTATAGGCCCTTTTTCTAC 60.503 50.000 36.19 11.37 42.40 2.59
72 73 4.202440 GGGACTATAGGCCCTTTTTCTACC 60.202 50.000 33.73 5.44 41.31 3.18
73 74 4.411212 GGACTATAGGCCCTTTTTCTACCA 59.589 45.833 14.46 0.00 0.00 3.25
106 107 7.264373 AGAAAAATTATATCCTTGTCGCCAG 57.736 36.000 0.00 0.00 0.00 4.85
115 116 2.832129 TCCTTGTCGCCAGAAGTTCTAT 59.168 45.455 4.74 0.00 0.00 1.98
137 138 5.667539 TGGTTCCAAAATTTTCACAGACA 57.332 34.783 0.00 0.00 0.00 3.41
141 142 6.538381 GGTTCCAAAATTTTCACAGACATGTT 59.462 34.615 0.00 0.00 37.65 2.71
153 154 1.691976 AGACATGTTGTTCCTCACGGA 59.308 47.619 0.00 0.00 37.60 4.69
185 186 7.556275 CACTTTGGAACCTGGTTGTATATACAT 59.444 37.037 18.42 0.00 35.89 2.29
187 188 7.446106 TTGGAACCTGGTTGTATATACATCT 57.554 36.000 18.42 0.07 35.89 2.90
269 272 7.706607 AGAATAAACTTGACTTTCTTTTGCACC 59.293 33.333 0.00 0.00 0.00 5.01
422 430 6.375736 GGGGTTTCTTTTTGTGGAATTTTTCA 59.624 34.615 0.00 0.00 0.00 2.69
518 526 6.783708 AATTTTTCTCACAAGTACACCCAA 57.216 33.333 0.00 0.00 0.00 4.12
556 571 2.092321 TCCGGTTCCTCACTTCCAAAAA 60.092 45.455 0.00 0.00 0.00 1.94
680 724 7.040686 GGAAATTAACTTGAGTAGAAAGTGGCA 60.041 37.037 0.00 0.00 37.90 4.92
705 797 1.219522 ACGTGCAAGCCGTTGACTAC 61.220 55.000 0.00 0.00 35.46 2.73
706 798 1.218875 CGTGCAAGCCGTTGACTACA 61.219 55.000 0.00 0.00 35.46 2.74
816 1045 4.040936 AGCTAGAGAGTTGAAGTCCAGA 57.959 45.455 0.00 0.00 0.00 3.86
829 1058 3.815856 AGTCCAGATACATGCACTCAG 57.184 47.619 0.00 0.00 0.00 3.35
1791 3291 7.781324 AATTCCACAGGAAATTTGTACTCAT 57.219 32.000 2.16 0.00 45.41 2.90
2068 3587 3.994204 TTTTGCGGGAAAGGACTAAAC 57.006 42.857 0.00 0.00 0.00 2.01
2069 3588 2.943036 TTGCGGGAAAGGACTAAACT 57.057 45.000 0.00 0.00 0.00 2.66
2070 3589 2.467566 TGCGGGAAAGGACTAAACTC 57.532 50.000 0.00 0.00 0.00 3.01
2071 3590 1.695242 TGCGGGAAAGGACTAAACTCA 59.305 47.619 0.00 0.00 0.00 3.41
2072 3591 2.304761 TGCGGGAAAGGACTAAACTCAT 59.695 45.455 0.00 0.00 0.00 2.90
2205 3763 4.725556 TTGTTGCTAACGACTTGCTTAG 57.274 40.909 0.00 0.00 0.00 2.18
2238 3796 1.186200 AGAATGTGCTAGGCTGTCGA 58.814 50.000 0.00 0.00 0.00 4.20
2240 3798 0.460987 AATGTGCTAGGCTGTCGAGC 60.461 55.000 7.46 7.46 45.40 5.03
2394 3956 3.003275 TCTTGATCGGAAAAATATGGCGC 59.997 43.478 0.00 0.00 0.00 6.53
2395 3957 2.293170 TGATCGGAAAAATATGGCGCA 58.707 42.857 10.83 0.00 0.00 6.09
2465 4051 2.028420 TAGCAGATGCACATTTCGCT 57.972 45.000 7.68 0.00 45.16 4.93
2466 4052 0.450583 AGCAGATGCACATTTCGCTG 59.549 50.000 7.68 0.00 45.16 5.18
2467 4053 1.138047 GCAGATGCACATTTCGCTGC 61.138 55.000 0.00 0.00 41.38 5.25
2468 4054 0.450583 CAGATGCACATTTCGCTGCT 59.549 50.000 0.00 0.00 34.29 4.24
2469 4055 0.731417 AGATGCACATTTCGCTGCTC 59.269 50.000 0.00 0.00 34.29 4.26
2470 4056 0.448990 GATGCACATTTCGCTGCTCA 59.551 50.000 0.00 0.00 34.29 4.26
2471 4057 0.450583 ATGCACATTTCGCTGCTCAG 59.549 50.000 0.00 0.00 34.29 3.35
2472 4058 1.136147 GCACATTTCGCTGCTCAGG 59.864 57.895 0.00 0.00 0.00 3.86
2473 4059 1.798735 CACATTTCGCTGCTCAGGG 59.201 57.895 7.53 7.53 42.08 4.45
2474 4060 0.957395 CACATTTCGCTGCTCAGGGT 60.957 55.000 12.64 0.00 41.52 4.34
2475 4061 0.674895 ACATTTCGCTGCTCAGGGTC 60.675 55.000 12.64 0.00 41.52 4.46
2476 4062 0.674581 CATTTCGCTGCTCAGGGTCA 60.675 55.000 12.64 2.96 41.52 4.02
2477 4063 0.674895 ATTTCGCTGCTCAGGGTCAC 60.675 55.000 12.64 0.00 41.52 3.67
2478 4064 2.038814 TTTCGCTGCTCAGGGTCACA 62.039 55.000 12.64 0.00 41.52 3.58
2479 4065 2.031012 CGCTGCTCAGGGTCACAA 59.969 61.111 5.86 0.00 36.72 3.33
2480 4066 1.376424 CGCTGCTCAGGGTCACAAT 60.376 57.895 5.86 0.00 36.72 2.71
2481 4067 0.108186 CGCTGCTCAGGGTCACAATA 60.108 55.000 5.86 0.00 36.72 1.90
2482 4068 1.373570 GCTGCTCAGGGTCACAATAC 58.626 55.000 0.00 0.00 0.00 1.89
2538 4124 1.546589 TTGCCGTCGTGGGGTAATCT 61.547 55.000 0.00 0.00 38.63 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.703052 TCCTGAACCGGGACTAAAGTATC 59.297 47.826 6.32 0.00 33.41 2.24
2 3 3.173953 TCCTGAACCGGGACTAAAGTA 57.826 47.619 6.32 0.00 33.41 2.24
3 4 2.019807 TCCTGAACCGGGACTAAAGT 57.980 50.000 6.32 0.00 33.41 2.66
4 5 2.696506 GTTCCTGAACCGGGACTAAAG 58.303 52.381 6.32 0.00 38.83 1.85
5 6 2.845363 GTTCCTGAACCGGGACTAAA 57.155 50.000 6.32 0.00 38.83 1.85
15 16 2.614734 CCTTTAGTCCCGGTTCCTGAAC 60.615 54.545 0.00 1.33 40.45 3.18
16 17 1.626825 CCTTTAGTCCCGGTTCCTGAA 59.373 52.381 0.00 0.00 0.00 3.02
17 18 1.272807 CCTTTAGTCCCGGTTCCTGA 58.727 55.000 0.00 0.00 0.00 3.86
18 19 0.392595 GCCTTTAGTCCCGGTTCCTG 60.393 60.000 0.00 0.00 0.00 3.86
19 20 1.559965 GGCCTTTAGTCCCGGTTCCT 61.560 60.000 0.00 0.00 0.00 3.36
20 21 1.077930 GGCCTTTAGTCCCGGTTCC 60.078 63.158 0.00 0.00 0.00 3.62
21 22 1.077930 GGGCCTTTAGTCCCGGTTC 60.078 63.158 0.84 0.00 32.00 3.62
22 23 3.084304 GGGCCTTTAGTCCCGGTT 58.916 61.111 0.84 0.00 32.00 4.44
26 27 1.197812 TCGTAAGGGCCTTTAGTCCC 58.802 55.000 26.29 5.03 42.94 4.46
27 28 2.625737 GTTCGTAAGGGCCTTTAGTCC 58.374 52.381 26.29 6.64 38.47 3.85
28 29 2.625737 GGTTCGTAAGGGCCTTTAGTC 58.374 52.381 26.29 14.62 38.47 2.59
29 30 1.066645 CGGTTCGTAAGGGCCTTTAGT 60.067 52.381 26.29 1.50 38.47 2.24
30 31 1.648504 CGGTTCGTAAGGGCCTTTAG 58.351 55.000 26.29 18.30 38.47 1.85
31 32 0.249955 CCGGTTCGTAAGGGCCTTTA 59.750 55.000 26.29 2.60 38.47 1.85
32 33 1.002990 CCGGTTCGTAAGGGCCTTT 60.003 57.895 26.29 5.08 38.47 3.11
33 34 2.666812 CCGGTTCGTAAGGGCCTT 59.333 61.111 24.44 24.44 38.47 4.35
34 35 3.396570 CCCGGTTCGTAAGGGCCT 61.397 66.667 0.00 0.00 38.51 5.19
35 36 3.393106 TCCCGGTTCGTAAGGGCC 61.393 66.667 0.00 0.00 44.70 5.80
36 37 1.322538 TAGTCCCGGTTCGTAAGGGC 61.323 60.000 0.00 0.00 44.70 5.19
37 38 1.406903 ATAGTCCCGGTTCGTAAGGG 58.593 55.000 0.00 0.00 46.40 3.95
38 39 2.555757 CCTATAGTCCCGGTTCGTAAGG 59.444 54.545 0.00 0.00 38.47 2.69
39 40 2.030451 GCCTATAGTCCCGGTTCGTAAG 60.030 54.545 0.00 0.00 0.00 2.34
40 41 1.956477 GCCTATAGTCCCGGTTCGTAA 59.044 52.381 0.00 0.00 0.00 3.18
41 42 1.609208 GCCTATAGTCCCGGTTCGTA 58.391 55.000 0.00 0.00 0.00 3.43
42 43 1.111715 GGCCTATAGTCCCGGTTCGT 61.112 60.000 0.00 0.00 0.00 3.85
43 44 1.664306 GGCCTATAGTCCCGGTTCG 59.336 63.158 0.00 0.00 0.00 3.95
44 45 2.056141 GGGCCTATAGTCCCGGTTC 58.944 63.158 2.38 0.00 32.00 3.62
45 46 4.308061 GGGCCTATAGTCCCGGTT 57.692 61.111 2.38 0.00 32.00 4.44
49 50 4.202440 GGTAGAAAAAGGGCCTATAGTCCC 60.202 50.000 11.13 11.13 42.94 4.46
50 51 4.411212 TGGTAGAAAAAGGGCCTATAGTCC 59.589 45.833 6.41 4.84 0.00 3.85
51 52 5.130643 ACTGGTAGAAAAAGGGCCTATAGTC 59.869 44.000 6.41 2.06 0.00 2.59
52 53 5.037598 ACTGGTAGAAAAAGGGCCTATAGT 58.962 41.667 6.41 0.00 0.00 2.12
53 54 5.368989 CACTGGTAGAAAAAGGGCCTATAG 58.631 45.833 6.41 0.00 0.00 1.31
54 55 4.384868 GCACTGGTAGAAAAAGGGCCTATA 60.385 45.833 6.41 0.00 34.14 1.31
55 56 3.624959 GCACTGGTAGAAAAAGGGCCTAT 60.625 47.826 6.41 0.00 34.14 2.57
56 57 2.290705 GCACTGGTAGAAAAAGGGCCTA 60.291 50.000 6.41 0.00 34.14 3.93
57 58 1.547901 GCACTGGTAGAAAAAGGGCCT 60.548 52.381 0.00 0.00 34.14 5.19
58 59 0.888619 GCACTGGTAGAAAAAGGGCC 59.111 55.000 0.00 0.00 34.14 5.80
59 60 1.911057 AGCACTGGTAGAAAAAGGGC 58.089 50.000 0.00 0.00 40.78 5.19
60 61 3.756117 AGAAGCACTGGTAGAAAAAGGG 58.244 45.455 0.00 0.00 0.00 3.95
61 62 5.794894 TCTAGAAGCACTGGTAGAAAAAGG 58.205 41.667 0.00 0.00 0.00 3.11
62 63 7.730364 TTTCTAGAAGCACTGGTAGAAAAAG 57.270 36.000 5.12 0.00 31.72 2.27
63 64 8.514330 TTTTTCTAGAAGCACTGGTAGAAAAA 57.486 30.769 21.93 21.93 42.25 1.94
64 65 8.691661 ATTTTTCTAGAAGCACTGGTAGAAAA 57.308 30.769 16.29 16.29 38.15 2.29
65 66 8.691661 AATTTTTCTAGAAGCACTGGTAGAAA 57.308 30.769 5.12 9.22 32.36 2.52
66 67 9.959721 ATAATTTTTCTAGAAGCACTGGTAGAA 57.040 29.630 5.12 0.00 0.00 2.10
70 71 9.343539 GGATATAATTTTTCTAGAAGCACTGGT 57.656 33.333 5.12 0.00 0.00 4.00
71 72 9.566432 AGGATATAATTTTTCTAGAAGCACTGG 57.434 33.333 5.12 0.00 0.00 4.00
106 107 8.978539 GTGAAAATTTTGGAACCATAGAACTTC 58.021 33.333 8.47 0.00 0.00 3.01
115 116 5.667539 TGTCTGTGAAAATTTTGGAACCA 57.332 34.783 8.47 0.00 0.00 3.67
153 154 5.423931 ACAACCAGGTTCCAAAGTGTATTTT 59.576 36.000 0.12 0.00 0.00 1.82
376 380 8.746052 ACCCCCTTTGATTTCTTTTTAAAAAG 57.254 30.769 27.60 27.60 45.17 2.27
390 396 4.141505 CCACAAAAAGAAACCCCCTTTGAT 60.142 41.667 0.00 0.00 34.42 2.57
422 430 6.377146 ACTTGACCTTTTCATTGTACTTGTGT 59.623 34.615 0.00 0.00 32.84 3.72
493 501 7.266922 TGGGTGTACTTGTGAGAAAAATTAC 57.733 36.000 0.00 0.00 0.00 1.89
513 521 2.649531 TGGACGTTTGATTCTTGGGT 57.350 45.000 0.00 0.00 0.00 4.51
518 526 2.346803 CGGACATGGACGTTTGATTCT 58.653 47.619 0.00 0.00 0.00 2.40
556 571 1.891150 CAGAACAAAAGAGGCCATGCT 59.109 47.619 5.01 0.00 0.00 3.79
614 629 6.237542 GCGTTCCAAATTACATTGCACATAAG 60.238 38.462 0.00 0.00 0.00 1.73
816 1045 2.366916 GGCTCTACCTGAGTGCATGTAT 59.633 50.000 0.00 0.00 44.86 2.29
829 1058 0.817229 GCATGCTGAAGGGCTCTACC 60.817 60.000 11.37 0.00 37.93 3.18
1791 3291 1.286354 GCGGTGTCGTCAAATCCGAA 61.286 55.000 12.89 0.00 43.22 4.30
2047 3566 3.955551 AGTTTAGTCCTTTCCCGCAAAAA 59.044 39.130 0.00 0.00 0.00 1.94
2048 3567 3.558033 AGTTTAGTCCTTTCCCGCAAAA 58.442 40.909 0.00 0.00 0.00 2.44
2049 3568 3.143728 GAGTTTAGTCCTTTCCCGCAAA 58.856 45.455 0.00 0.00 0.00 3.68
2050 3569 2.105134 TGAGTTTAGTCCTTTCCCGCAA 59.895 45.455 0.00 0.00 0.00 4.85
2051 3570 1.695242 TGAGTTTAGTCCTTTCCCGCA 59.305 47.619 0.00 0.00 0.00 5.69
2052 3571 2.467566 TGAGTTTAGTCCTTTCCCGC 57.532 50.000 0.00 0.00 0.00 6.13
2053 3572 4.202245 TGATGAGTTTAGTCCTTTCCCG 57.798 45.455 0.00 0.00 0.00 5.14
2054 3573 5.561679 ACTTGATGAGTTTAGTCCTTTCCC 58.438 41.667 0.00 0.00 33.92 3.97
2055 3574 8.669243 CATTACTTGATGAGTTTAGTCCTTTCC 58.331 37.037 0.00 0.00 39.86 3.13
2056 3575 9.220767 ACATTACTTGATGAGTTTAGTCCTTTC 57.779 33.333 0.00 0.00 39.86 2.62
2057 3576 9.574516 AACATTACTTGATGAGTTTAGTCCTTT 57.425 29.630 0.00 0.00 39.86 3.11
2058 3577 9.574516 AAACATTACTTGATGAGTTTAGTCCTT 57.425 29.630 0.00 0.00 39.86 3.36
2059 3578 9.003658 CAAACATTACTTGATGAGTTTAGTCCT 57.996 33.333 0.00 0.00 39.86 3.85
2060 3579 8.784043 ACAAACATTACTTGATGAGTTTAGTCC 58.216 33.333 0.00 0.00 39.86 3.85
2176 3734 5.352643 AGTCGTTAGCAACAATAAACACC 57.647 39.130 0.00 0.00 0.00 4.16
2205 3763 6.199937 AGCACATTCTTCATTAACCATGAC 57.800 37.500 0.00 0.00 41.98 3.06
2238 3796 1.033746 CCATCTTCGGTGCATTGGCT 61.034 55.000 0.00 0.00 41.91 4.75
2240 3798 0.680921 ACCCATCTTCGGTGCATTGG 60.681 55.000 0.00 0.00 30.39 3.16
2335 3897 8.655970 GCTTCGGTTGCAAAAAGAAATAAATAT 58.344 29.630 17.20 0.00 0.00 1.28
2356 3918 6.346120 CCGATCAAGAATAGTATTGTGCTTCG 60.346 42.308 0.00 9.57 0.00 3.79
2423 3985 3.825585 TGCAACACAGAGATTTGGCATTA 59.174 39.130 0.00 0.00 0.00 1.90
2456 4024 0.674895 GACCCTGAGCAGCGAAATGT 60.675 55.000 0.00 0.00 0.00 2.71
2465 4051 1.357137 TGGTATTGTGACCCTGAGCA 58.643 50.000 0.00 0.00 38.89 4.26
2466 4052 2.292267 CATGGTATTGTGACCCTGAGC 58.708 52.381 0.00 0.00 37.31 4.26
2467 4053 2.092753 AGCATGGTATTGTGACCCTGAG 60.093 50.000 0.00 0.00 37.31 3.35
2468 4054 1.915489 AGCATGGTATTGTGACCCTGA 59.085 47.619 0.00 0.00 37.31 3.86
2469 4055 2.425143 AGCATGGTATTGTGACCCTG 57.575 50.000 0.00 0.00 38.89 4.45
2470 4056 3.115390 ACTAGCATGGTATTGTGACCCT 58.885 45.455 4.84 0.00 38.89 4.34
2471 4057 3.206150 CACTAGCATGGTATTGTGACCC 58.794 50.000 15.57 0.00 38.89 4.46
2472 4058 3.873910 ACACTAGCATGGTATTGTGACC 58.126 45.455 22.48 0.00 40.21 4.02
2473 4059 5.880054 AAACACTAGCATGGTATTGTGAC 57.120 39.130 23.44 0.00 0.00 3.67
2474 4060 6.468543 TGTAAACACTAGCATGGTATTGTGA 58.531 36.000 23.44 14.44 0.00 3.58
2475 4061 6.183360 CCTGTAAACACTAGCATGGTATTGTG 60.183 42.308 23.44 20.53 0.00 3.33
2476 4062 5.880332 CCTGTAAACACTAGCATGGTATTGT 59.120 40.000 18.88 18.88 0.00 2.71
2477 4063 5.220854 GCCTGTAAACACTAGCATGGTATTG 60.221 44.000 17.73 17.73 0.00 1.90
2478 4064 4.881850 GCCTGTAAACACTAGCATGGTATT 59.118 41.667 4.84 0.00 0.00 1.89
2479 4065 4.080582 TGCCTGTAAACACTAGCATGGTAT 60.081 41.667 4.84 0.00 0.00 2.73
2480 4066 3.262151 TGCCTGTAAACACTAGCATGGTA 59.738 43.478 4.27 4.27 0.00 3.25
2481 4067 2.039746 TGCCTGTAAACACTAGCATGGT 59.960 45.455 1.62 1.62 0.00 3.55
2482 4068 2.710377 TGCCTGTAAACACTAGCATGG 58.290 47.619 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.