Multiple sequence alignment - TraesCS1D01G382600

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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 TraesCS1D01G382600 chr1D 100.000 3939 0 0 1 3939 457549958 457546020 0.000000e+00 7275.0
1 TraesCS1D01G382600 chr1D 82.980 2074 218 69 1945 3939 457844632 457846649 0.000000e+00 1749.0
2 TraesCS1D01G382600 chr1D 86.312 621 74 6 3319 3928 457584233 457584853 0.000000e+00 665.0
3 TraesCS1D01G382600 chr1D 82.701 659 81 22 3067 3703 457821365 457822012 4.450000e-154 555.0
4 TraesCS1D01G382600 chr1D 82.870 648 57 19 2265 2881 457583264 457583888 2.080000e-147 532.0
5 TraesCS1D01G382600 chr1D 87.467 375 36 4 1392 1756 457582377 457582750 4.710000e-114 422.0
6 TraesCS1D01G382600 chr1D 84.777 381 38 9 2054 2420 226467834 226468208 8.040000e-97 364.0
7 TraesCS1D01G382600 chr1D 82.033 423 42 17 1761 2157 457812513 457812927 2.930000e-86 329.0
8 TraesCS1D01G382600 chr1D 84.983 293 33 8 1474 1756 457812138 457812429 1.790000e-73 287.0
9 TraesCS1D01G382600 chr1D 85.017 287 33 7 1474 1751 457811626 457811911 2.320000e-72 283.0
10 TraesCS1D01G382600 chr1D 85.593 236 30 2 3706 3939 457822189 457822422 1.090000e-60 244.0
11 TraesCS1D01G382600 chr1D 85.714 224 21 8 889 1108 457581582 457581798 3.960000e-55 226.0
12 TraesCS1D01G382600 chr1D 87.879 198 14 5 1761 1955 457582829 457583019 1.420000e-54 224.0
13 TraesCS1D01G382600 chr1D 85.915 142 17 3 3569 3707 457822013 457822154 8.820000e-32 148.0
14 TraesCS1D01G382600 chr1D 82.979 141 15 4 1008 1143 457806983 457807119 6.910000e-23 119.0
15 TraesCS1D01G382600 chr1A 95.396 3171 78 19 800 3939 550138354 550135221 0.000000e+00 4985.0
16 TraesCS1D01G382600 chr1A 82.331 1862 201 59 1761 3544 550298585 550300396 0.000000e+00 1498.0
17 TraesCS1D01G382600 chr1A 84.555 1528 153 45 2463 3939 550217983 550219478 0.000000e+00 1437.0
18 TraesCS1D01G382600 chr1A 88.117 547 62 2 3279 3822 550210996 550211542 0.000000e+00 647.0
19 TraesCS1D01G382600 chr1A 82.861 706 84 21 2265 2950 550209993 550210681 2.030000e-167 599.0
20 TraesCS1D01G382600 chr1A 87.297 370 29 12 1392 1745 550298128 550298495 1.320000e-109 407.0
21 TraesCS1D01G382600 chr1A 86.704 361 21 12 78 431 550139055 550138715 3.720000e-100 375.0
22 TraesCS1D01G382600 chr1A 88.745 231 26 0 1526 1756 550216957 550217187 2.320000e-72 283.0
23 TraesCS1D01G382600 chr1A 84.429 289 35 3 1474 1753 550203602 550203889 3.880000e-70 276.0
24 TraesCS1D01G382600 chr1A 83.955 268 43 0 1928 2195 550209382 550209649 1.400000e-64 257.0
25 TraesCS1D01G382600 chr1A 89.510 143 12 1 638 777 550138598 550138456 1.120000e-40 178.0
26 TraesCS1D01G382600 chr1A 82.123 179 22 7 967 1143 550297414 550297584 1.140000e-30 145.0
27 TraesCS1D01G382600 chr1A 84.800 125 16 2 999 1123 550216569 550216690 5.350000e-24 122.0
28 TraesCS1D01G382600 chr1B 92.722 2116 106 23 72 2154 627159498 627157398 0.000000e+00 3011.0
29 TraesCS1D01G382600 chr1B 94.170 1801 44 20 2176 3939 627157407 627155631 0.000000e+00 2687.0
30 TraesCS1D01G382600 chr1B 81.713 2078 226 69 1962 3939 627923420 627925443 0.000000e+00 1591.0
31 TraesCS1D01G382600 chr1B 82.394 1420 154 52 2463 3843 627782562 627783924 0.000000e+00 1149.0
32 TraesCS1D01G382600 chr1B 84.217 792 84 21 3067 3822 627887265 627888051 0.000000e+00 732.0
33 TraesCS1D01G382600 chr1B 85.172 580 58 16 1392 1955 627922876 627923443 1.590000e-158 569.0
34 TraesCS1D01G382600 chr1B 80.656 610 91 20 3251 3842 322475666 322476266 7.760000e-122 448.0
35 TraesCS1D01G382600 chr1B 81.132 424 41 10 1761 2161 627885894 627886301 1.780000e-78 303.0
36 TraesCS1D01G382600 chr1B 85.473 296 32 8 1468 1753 627885354 627885648 8.270000e-77 298.0
37 TraesCS1D01G382600 chr1B 82.464 211 25 9 940 1143 627884685 627884890 1.450000e-39 174.0
38 TraesCS1D01G382600 chr1B 85.217 115 9 2 3830 3937 627888090 627888203 1.160000e-20 111.0
39 TraesCS1D01G382600 chr1B 96.721 61 2 0 3879 3939 627785294 627785354 6.960000e-18 102.0
40 TraesCS1D01G382600 chr3A 84.177 474 61 7 1960 2420 668583194 668583666 7.760000e-122 448.0
41 TraesCS1D01G382600 chr3A 84.770 348 40 6 2084 2420 668225508 668225853 1.750000e-88 337.0
42 TraesCS1D01G382600 chr3B 82.672 479 63 9 1960 2420 705148047 705148523 1.320000e-109 407.0
43 TraesCS1D01G382600 chr7D 100.000 50 0 0 1 50 635687661 635687612 4.190000e-15 93.5
44 TraesCS1D01G382600 chr7D 100.000 50 0 0 1 50 636311476 636311525 4.190000e-15 93.5
45 TraesCS1D01G382600 chrUn 91.228 57 4 1 1 56 68520319 68520375 4.220000e-10 76.8
46 TraesCS1D01G382600 chrUn 93.617 47 3 0 5 51 284723830 284723876 1.960000e-08 71.3
47 TraesCS1D01G382600 chr7B 88.889 63 6 1 1 63 721074600 721074661 4.220000e-10 76.8
48 TraesCS1D01G382600 chr6B 95.745 47 2 0 4 50 39341638 39341592 4.220000e-10 76.8
49 TraesCS1D01G382600 chr4A 92.157 51 4 0 1 51 602246739 602246789 5.460000e-09 73.1
50 TraesCS1D01G382600 chr4A 92.157 51 3 1 5 55 742139509 742139460 1.960000e-08 71.3
51 TraesCS1D01G382600 chr5B 92.157 51 2 2 1 50 526735591 526735640 1.960000e-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 TraesCS1D01G382600 chr1D 457546020 457549958 3938 True 7275.000000 7275 100.000000 1 3939 1 chr1D.!!$R1 3938
1 TraesCS1D01G382600 chr1D 457844632 457846649 2017 False 1749.000000 1749 82.980000 1945 3939 1 chr1D.!!$F3 1994
2 TraesCS1D01G382600 chr1D 457581582 457584853 3271 False 413.800000 665 86.048400 889 3928 5 chr1D.!!$F4 3039
3 TraesCS1D01G382600 chr1D 457821365 457822422 1057 False 315.666667 555 84.736333 3067 3939 3 chr1D.!!$F6 872
4 TraesCS1D01G382600 chr1D 457811626 457812927 1301 False 299.666667 329 84.011000 1474 2157 3 chr1D.!!$F5 683
5 TraesCS1D01G382600 chr1A 550135221 550139055 3834 True 1846.000000 4985 90.536667 78 3939 3 chr1A.!!$R1 3861
6 TraesCS1D01G382600 chr1A 550297414 550300396 2982 False 683.333333 1498 83.917000 967 3544 3 chr1A.!!$F4 2577
7 TraesCS1D01G382600 chr1A 550216569 550219478 2909 False 614.000000 1437 86.033333 999 3939 3 chr1A.!!$F3 2940
8 TraesCS1D01G382600 chr1A 550209382 550211542 2160 False 501.000000 647 84.977667 1928 3822 3 chr1A.!!$F2 1894
9 TraesCS1D01G382600 chr1B 627155631 627159498 3867 True 2849.000000 3011 93.446000 72 3939 2 chr1B.!!$R1 3867
10 TraesCS1D01G382600 chr1B 627922876 627925443 2567 False 1080.000000 1591 83.442500 1392 3939 2 chr1B.!!$F4 2547
11 TraesCS1D01G382600 chr1B 627782562 627785354 2792 False 625.500000 1149 89.557500 2463 3939 2 chr1B.!!$F2 1476
12 TraesCS1D01G382600 chr1B 322475666 322476266 600 False 448.000000 448 80.656000 3251 3842 1 chr1B.!!$F1 591
13 TraesCS1D01G382600 chr1B 627884685 627888203 3518 False 323.600000 732 83.700600 940 3937 5 chr1B.!!$F3 2997

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
20 21 0.525761 CGGCAAAAATGGACGGTCAT 59.474 50.000 10.76 0.0 31.77 3.06 F
696 721 0.609151 CCAAGCCATTGTGCAATCCA 59.391 50.000 0.00 0.0 34.39 3.41 F
1282 1659 1.541310 CCGGTGGTTAGGTGAGCAGA 61.541 60.000 0.00 0.0 0.00 4.26 F
1819 3058 2.285083 CGAACCCATGAAAATAGCCGA 58.715 47.619 0.00 0.0 0.00 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1219 1596 0.037303 TCCGCTAGGGTACTATCCGG 59.963 60.000 6.02 0.00 41.50 5.14 R
1620 2612 0.110328 CAAGCAGCGCTGAGAAGTTG 60.110 55.000 40.21 26.23 39.62 3.16 R
2723 4407 4.729868 ACTGTGGTAGCCTTTTTCTGAAT 58.270 39.130 0.00 0.00 0.00 2.57 R
3422 5341 2.725008 CTCATCCGAGGACTCCGC 59.275 66.667 0.00 0.00 35.44 5.54 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
17 18 4.484987 TCGGCAAAAATGGACGGT 57.515 50.000 0.00 0.00 37.38 4.83
18 19 2.249692 TCGGCAAAAATGGACGGTC 58.750 52.632 0.00 0.00 37.38 4.79
19 20 0.535328 TCGGCAAAAATGGACGGTCA 60.535 50.000 10.76 0.00 37.38 4.02
20 21 0.525761 CGGCAAAAATGGACGGTCAT 59.474 50.000 10.76 0.00 31.77 3.06
21 22 1.067915 CGGCAAAAATGGACGGTCATT 60.068 47.619 10.76 5.38 38.84 2.57
22 23 2.162608 CGGCAAAAATGGACGGTCATTA 59.837 45.455 10.76 0.00 36.45 1.90
23 24 3.181491 CGGCAAAAATGGACGGTCATTAT 60.181 43.478 10.76 0.00 36.45 1.28
24 25 4.676723 CGGCAAAAATGGACGGTCATTATT 60.677 41.667 10.76 4.79 36.45 1.40
25 26 5.175127 GGCAAAAATGGACGGTCATTATTT 58.825 37.500 10.76 10.18 36.45 1.40
26 27 6.334202 GGCAAAAATGGACGGTCATTATTTA 58.666 36.000 10.76 0.00 36.45 1.40
27 28 6.983890 GGCAAAAATGGACGGTCATTATTTAT 59.016 34.615 10.76 3.26 36.45 1.40
28 29 7.169140 GGCAAAAATGGACGGTCATTATTTATC 59.831 37.037 10.76 6.44 36.45 1.75
29 30 7.920682 GCAAAAATGGACGGTCATTATTTATCT 59.079 33.333 10.76 0.00 36.45 1.98
30 31 9.236691 CAAAAATGGACGGTCATTATTTATCTG 57.763 33.333 10.76 8.08 36.45 2.90
31 32 8.746052 AAAATGGACGGTCATTATTTATCTGA 57.254 30.769 10.76 0.00 36.45 3.27
32 33 8.924511 AAATGGACGGTCATTATTTATCTGAT 57.075 30.769 10.76 0.00 36.45 2.90
33 34 7.912056 ATGGACGGTCATTATTTATCTGATG 57.088 36.000 10.76 0.00 0.00 3.07
34 35 6.826668 TGGACGGTCATTATTTATCTGATGT 58.173 36.000 10.76 0.00 0.00 3.06
35 36 7.958088 TGGACGGTCATTATTTATCTGATGTA 58.042 34.615 10.76 0.00 0.00 2.29
36 37 7.870954 TGGACGGTCATTATTTATCTGATGTAC 59.129 37.037 10.76 0.00 0.00 2.90
37 38 7.331193 GGACGGTCATTATTTATCTGATGTACC 59.669 40.741 10.76 0.00 0.00 3.34
38 39 6.866770 ACGGTCATTATTTATCTGATGTACCG 59.133 38.462 16.78 16.78 42.29 4.02
39 40 6.866770 CGGTCATTATTTATCTGATGTACCGT 59.133 38.462 0.00 0.00 37.81 4.83
40 41 8.024865 CGGTCATTATTTATCTGATGTACCGTA 58.975 37.037 0.00 0.00 37.81 4.02
41 42 9.701098 GGTCATTATTTATCTGATGTACCGTAA 57.299 33.333 0.00 0.00 0.00 3.18
47 48 8.658499 ATTTATCTGATGTACCGTAAAAGGTC 57.342 34.615 0.00 0.00 44.68 3.85
48 49 5.934402 ATCTGATGTACCGTAAAAGGTCT 57.066 39.130 0.00 0.00 44.68 3.85
49 50 5.320549 TCTGATGTACCGTAAAAGGTCTC 57.679 43.478 0.00 0.00 44.68 3.36
50 51 4.768448 TCTGATGTACCGTAAAAGGTCTCA 59.232 41.667 0.00 0.00 44.68 3.27
51 52 5.244402 TCTGATGTACCGTAAAAGGTCTCAA 59.756 40.000 0.00 0.00 44.68 3.02
52 53 6.045072 TGATGTACCGTAAAAGGTCTCAAT 57.955 37.500 0.00 0.00 44.68 2.57
53 54 7.123098 TCTGATGTACCGTAAAAGGTCTCAATA 59.877 37.037 0.00 0.00 44.68 1.90
54 55 7.613585 TGATGTACCGTAAAAGGTCTCAATAA 58.386 34.615 0.00 0.00 44.68 1.40
55 56 8.095792 TGATGTACCGTAAAAGGTCTCAATAAA 58.904 33.333 0.00 0.00 44.68 1.40
56 57 7.894376 TGTACCGTAAAAGGTCTCAATAAAG 57.106 36.000 0.00 0.00 44.68 1.85
57 58 5.874895 ACCGTAAAAGGTCTCAATAAAGC 57.125 39.130 0.00 0.00 41.46 3.51
58 59 5.310451 ACCGTAAAAGGTCTCAATAAAGCA 58.690 37.500 0.00 0.00 41.46 3.91
59 60 5.944007 ACCGTAAAAGGTCTCAATAAAGCAT 59.056 36.000 0.00 0.00 41.46 3.79
60 61 6.433093 ACCGTAAAAGGTCTCAATAAAGCATT 59.567 34.615 0.00 0.00 41.46 3.56
61 62 6.747280 CCGTAAAAGGTCTCAATAAAGCATTG 59.253 38.462 0.00 0.00 44.69 2.82
62 63 7.305474 CGTAAAAGGTCTCAATAAAGCATTGT 58.695 34.615 0.00 0.00 43.88 2.71
63 64 7.271223 CGTAAAAGGTCTCAATAAAGCATTGTG 59.729 37.037 0.00 0.00 43.88 3.33
64 65 6.655078 AAAGGTCTCAATAAAGCATTGTGT 57.345 33.333 0.00 0.00 43.88 3.72
65 66 5.633830 AGGTCTCAATAAAGCATTGTGTG 57.366 39.130 0.00 0.00 43.88 3.82
66 67 5.072741 AGGTCTCAATAAAGCATTGTGTGT 58.927 37.500 0.00 0.00 43.88 3.72
67 68 5.182001 AGGTCTCAATAAAGCATTGTGTGTC 59.818 40.000 0.00 0.00 43.88 3.67
68 69 5.048782 GGTCTCAATAAAGCATTGTGTGTCA 60.049 40.000 0.00 0.00 43.88 3.58
69 70 6.437928 GTCTCAATAAAGCATTGTGTGTCAA 58.562 36.000 0.00 0.00 43.88 3.18
70 71 6.580041 GTCTCAATAAAGCATTGTGTGTCAAG 59.420 38.462 0.00 0.00 43.88 3.02
139 147 4.383649 GCTACATGTTACGAACTCACGAAA 59.616 41.667 2.30 0.00 37.03 3.46
231 240 3.800506 CCGGACGTGGCTTATAAAAGTAG 59.199 47.826 0.00 0.00 34.99 2.57
233 242 3.558829 GGACGTGGCTTATAAAAGTAGGC 59.441 47.826 0.00 0.00 34.99 3.93
251 261 6.850555 AGTAGGCGTAAGATAATTATCCGAC 58.149 40.000 19.67 17.82 43.02 4.79
258 268 8.333186 GCGTAAGATAATTATCCGACTGTTTTT 58.667 33.333 19.67 8.44 43.02 1.94
289 304 4.075682 TCCTAGATTGATAGGTCTCGCAG 58.924 47.826 0.00 0.00 42.63 5.18
490 507 2.533266 AGATTTCGTCTGTGCACTGT 57.467 45.000 19.41 0.00 35.31 3.55
516 533 3.762288 GTCCAGAGTGGTTTTAAATCCCC 59.238 47.826 11.89 1.73 39.03 4.81
527 544 4.475051 TTTAAATCCCCGAATCGTCTGA 57.525 40.909 0.82 0.00 0.00 3.27
532 549 2.662866 TCCCCGAATCGTCTGATTACT 58.337 47.619 0.82 0.00 44.79 2.24
551 568 3.759581 ACTGGAAACTACTCCTACGTCA 58.240 45.455 0.00 0.00 36.35 4.35
559 576 8.235905 GGAAACTACTCCTACGTCATGATATAC 58.764 40.741 0.00 0.00 32.21 1.47
576 594 5.245301 TGATATACATCCCCGAGTTGGTTAG 59.755 44.000 0.00 0.00 35.15 2.34
577 595 1.946984 ACATCCCCGAGTTGGTTAGA 58.053 50.000 0.00 0.00 35.15 2.10
579 597 2.844348 ACATCCCCGAGTTGGTTAGAAT 59.156 45.455 0.00 0.00 35.15 2.40
580 598 3.118371 ACATCCCCGAGTTGGTTAGAATC 60.118 47.826 0.00 0.00 35.15 2.52
581 599 1.835531 TCCCCGAGTTGGTTAGAATCC 59.164 52.381 0.00 0.00 35.15 3.01
591 613 6.238648 AGTTGGTTAGAATCCAAACTGTAGG 58.761 40.000 0.00 0.00 44.91 3.18
696 721 0.609151 CCAAGCCATTGTGCAATCCA 59.391 50.000 0.00 0.00 34.39 3.41
707 732 1.675641 GCAATCCACGCCCAAGTCT 60.676 57.895 0.00 0.00 0.00 3.24
993 1107 6.439375 TCTTCTTCATTGTGCCCTTACTACTA 59.561 38.462 0.00 0.00 0.00 1.82
994 1108 6.808321 TCTTCATTGTGCCCTTACTACTAT 57.192 37.500 0.00 0.00 0.00 2.12
995 1109 6.582636 TCTTCATTGTGCCCTTACTACTATG 58.417 40.000 0.00 0.00 0.00 2.23
1176 1548 2.026169 AGTACACGGTGAGATCTCTCCA 60.026 50.000 32.60 17.47 41.88 3.86
1219 1596 3.243434 TGAGATCTCTCCGCGAATAAACC 60.243 47.826 22.95 0.00 42.20 3.27
1242 1619 2.224719 GGATAGTACCCTAGCGGACTCA 60.225 54.545 0.00 0.00 30.09 3.41
1282 1659 1.541310 CCGGTGGTTAGGTGAGCAGA 61.541 60.000 0.00 0.00 0.00 4.26
1323 1719 7.272978 TCCTGCCACTTTATCACTATTAGTTC 58.727 38.462 0.00 0.00 0.00 3.01
1620 2612 4.096984 CCAGATTTAGAATGGAAGGTGCAC 59.903 45.833 8.80 8.80 36.09 4.57
1621 2613 4.701651 CAGATTTAGAATGGAAGGTGCACA 59.298 41.667 20.43 0.00 0.00 4.57
1819 3058 2.285083 CGAACCCATGAAAATAGCCGA 58.715 47.619 0.00 0.00 0.00 5.54
1922 3164 2.569853 TCTTCAATTCCCTTCGCAGGTA 59.430 45.455 0.00 0.00 38.79 3.08
2082 3397 6.804677 TGCAGTGTTTGAGTTGTCAATATTT 58.195 32.000 0.00 0.00 42.41 1.40
2461 4112 8.378565 AGATGGATTTCTCTACTTTGAACTCAA 58.621 33.333 0.00 0.00 0.00 3.02
2624 4308 4.897509 TGCTTGATTCCTCTTGAAGAGA 57.102 40.909 23.05 4.90 45.07 3.10
2636 4320 9.877178 TTCCTCTTGAAGAGATACTAAAATCAC 57.123 33.333 23.05 0.00 45.07 3.06
2723 4407 1.428448 CGAAATGAAGTCTGCCGTGA 58.572 50.000 0.00 0.00 0.00 4.35
2877 4561 1.899142 AGTTTGCGGGCATAAATGGTT 59.101 42.857 0.00 0.00 0.00 3.67
3235 5069 7.118101 GTCGTGTTCAAAGTTAATGGGTATACA 59.882 37.037 5.01 0.00 0.00 2.29
3422 5341 1.296056 CCTCGCCTTGGGTTTGTACG 61.296 60.000 0.00 0.00 0.00 3.67
3530 5449 6.679327 ACTTCACAAGAACTTCAGGTTAAC 57.321 37.500 0.00 0.00 38.41 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.535328 TGACCGTCCATTTTTGCCGA 60.535 50.000 0.00 0.00 0.00 5.54
1 2 0.525761 ATGACCGTCCATTTTTGCCG 59.474 50.000 0.00 0.00 0.00 5.69
2 3 2.741759 AATGACCGTCCATTTTTGCC 57.258 45.000 0.00 0.00 33.29 4.52
3 4 7.920682 AGATAAATAATGACCGTCCATTTTTGC 59.079 33.333 5.10 0.00 37.81 3.68
4 5 9.236691 CAGATAAATAATGACCGTCCATTTTTG 57.763 33.333 5.10 0.00 37.81 2.44
5 6 9.184523 TCAGATAAATAATGACCGTCCATTTTT 57.815 29.630 5.10 7.89 37.81 1.94
6 7 8.746052 TCAGATAAATAATGACCGTCCATTTT 57.254 30.769 5.10 0.00 37.81 1.82
7 8 8.786898 CATCAGATAAATAATGACCGTCCATTT 58.213 33.333 5.10 2.76 37.81 2.32
8 9 7.939039 ACATCAGATAAATAATGACCGTCCATT 59.061 33.333 0.00 5.14 39.76 3.16
9 10 7.453393 ACATCAGATAAATAATGACCGTCCAT 58.547 34.615 0.00 0.00 0.00 3.41
10 11 6.826668 ACATCAGATAAATAATGACCGTCCA 58.173 36.000 0.00 0.00 0.00 4.02
11 12 7.331193 GGTACATCAGATAAATAATGACCGTCC 59.669 40.741 0.00 0.00 0.00 4.79
12 13 7.061905 CGGTACATCAGATAAATAATGACCGTC 59.938 40.741 0.00 0.00 37.65 4.79
13 14 6.866770 CGGTACATCAGATAAATAATGACCGT 59.133 38.462 0.00 0.00 37.65 4.83
14 15 6.866770 ACGGTACATCAGATAAATAATGACCG 59.133 38.462 16.36 16.36 42.20 4.79
15 16 9.701098 TTACGGTACATCAGATAAATAATGACC 57.299 33.333 0.00 0.00 0.00 4.02
21 22 9.754382 GACCTTTTACGGTACATCAGATAAATA 57.246 33.333 0.00 0.00 37.42 1.40
22 23 8.483758 AGACCTTTTACGGTACATCAGATAAAT 58.516 33.333 0.00 0.00 37.42 1.40
23 24 7.844009 AGACCTTTTACGGTACATCAGATAAA 58.156 34.615 0.00 0.00 37.42 1.40
24 25 7.123098 TGAGACCTTTTACGGTACATCAGATAA 59.877 37.037 0.00 0.00 37.42 1.75
25 26 6.604396 TGAGACCTTTTACGGTACATCAGATA 59.396 38.462 0.00 0.00 37.42 1.98
26 27 5.421056 TGAGACCTTTTACGGTACATCAGAT 59.579 40.000 0.00 0.00 37.42 2.90
27 28 4.768448 TGAGACCTTTTACGGTACATCAGA 59.232 41.667 0.00 0.00 37.42 3.27
28 29 5.068234 TGAGACCTTTTACGGTACATCAG 57.932 43.478 0.00 0.00 37.42 2.90
29 30 5.471556 TTGAGACCTTTTACGGTACATCA 57.528 39.130 0.00 0.00 37.42 3.07
30 31 8.483307 TTTATTGAGACCTTTTACGGTACATC 57.517 34.615 0.00 0.00 37.42 3.06
31 32 7.065443 GCTTTATTGAGACCTTTTACGGTACAT 59.935 37.037 0.00 0.00 37.42 2.29
32 33 6.369615 GCTTTATTGAGACCTTTTACGGTACA 59.630 38.462 0.00 0.00 37.42 2.90
33 34 6.369615 TGCTTTATTGAGACCTTTTACGGTAC 59.630 38.462 0.00 0.00 37.42 3.34
34 35 6.465948 TGCTTTATTGAGACCTTTTACGGTA 58.534 36.000 0.00 0.00 37.42 4.02
35 36 5.310451 TGCTTTATTGAGACCTTTTACGGT 58.690 37.500 0.00 0.00 40.80 4.83
36 37 5.873179 TGCTTTATTGAGACCTTTTACGG 57.127 39.130 0.00 0.00 0.00 4.02
48 49 7.012799 TGTACTTGACACACAATGCTTTATTGA 59.987 33.333 6.63 0.00 39.95 2.57
49 50 7.138081 TGTACTTGACACACAATGCTTTATTG 58.862 34.615 0.00 0.00 41.67 1.90
50 51 7.270757 TGTACTTGACACACAATGCTTTATT 57.729 32.000 0.00 0.00 37.88 1.40
51 52 6.568462 GCTGTACTTGACACACAATGCTTTAT 60.568 38.462 0.00 0.00 37.88 1.40
52 53 5.277779 GCTGTACTTGACACACAATGCTTTA 60.278 40.000 0.00 0.00 37.88 1.85
53 54 4.498009 GCTGTACTTGACACACAATGCTTT 60.498 41.667 0.00 0.00 37.88 3.51
54 55 3.003689 GCTGTACTTGACACACAATGCTT 59.996 43.478 0.00 0.00 37.88 3.91
55 56 2.549754 GCTGTACTTGACACACAATGCT 59.450 45.455 0.00 0.00 37.88 3.79
56 57 2.549754 AGCTGTACTTGACACACAATGC 59.450 45.455 0.00 0.00 37.88 3.56
57 58 3.561310 ACAGCTGTACTTGACACACAATG 59.439 43.478 20.16 0.00 37.88 2.82
58 59 3.808728 ACAGCTGTACTTGACACACAAT 58.191 40.909 20.16 0.00 37.88 2.71
59 60 3.260475 ACAGCTGTACTTGACACACAA 57.740 42.857 20.16 0.00 33.31 3.33
60 61 2.979814 ACAGCTGTACTTGACACACA 57.020 45.000 20.16 0.00 33.31 3.72
61 62 5.728351 TTTTACAGCTGTACTTGACACAC 57.272 39.130 26.02 0.00 33.31 3.82
62 63 5.295787 CCTTTTTACAGCTGTACTTGACACA 59.704 40.000 26.02 6.30 33.31 3.72
63 64 5.526111 TCCTTTTTACAGCTGTACTTGACAC 59.474 40.000 26.02 0.00 33.31 3.67
64 65 5.676552 TCCTTTTTACAGCTGTACTTGACA 58.323 37.500 26.02 7.85 36.35 3.58
65 66 6.401153 CGATCCTTTTTACAGCTGTACTTGAC 60.401 42.308 26.02 11.44 0.00 3.18
66 67 5.637810 CGATCCTTTTTACAGCTGTACTTGA 59.362 40.000 26.02 17.11 0.00 3.02
67 68 5.408604 ACGATCCTTTTTACAGCTGTACTTG 59.591 40.000 26.02 15.26 0.00 3.16
68 69 5.548406 ACGATCCTTTTTACAGCTGTACTT 58.452 37.500 26.02 2.55 0.00 2.24
69 70 5.148651 ACGATCCTTTTTACAGCTGTACT 57.851 39.130 26.02 2.97 0.00 2.73
70 71 4.927425 TGACGATCCTTTTTACAGCTGTAC 59.073 41.667 26.02 10.98 0.00 2.90
101 102 1.001974 TGTAGCAGCGTCCTGTGAATT 59.998 47.619 0.00 0.00 41.26 2.17
139 147 1.302511 CACGCAAAGGTAGCCCACT 60.303 57.895 0.00 0.00 0.00 4.00
231 240 5.467705 ACAGTCGGATAATTATCTTACGCC 58.532 41.667 21.80 9.68 33.28 5.68
268 278 3.823873 ACTGCGAGACCTATCAATCTAGG 59.176 47.826 0.00 0.00 43.42 3.02
289 304 4.321824 GCGTGAACCCTATATCTCCCTTAC 60.322 50.000 0.00 0.00 0.00 2.34
490 507 3.823281 TTAAAACCACTCTGGACACGA 57.177 42.857 0.00 0.00 40.96 4.35
516 533 5.103000 AGTTTCCAGTAATCAGACGATTCG 58.897 41.667 4.14 4.14 41.09 3.34
527 544 5.948162 TGACGTAGGAGTAGTTTCCAGTAAT 59.052 40.000 0.00 0.00 39.84 1.89
532 549 4.338012 TCATGACGTAGGAGTAGTTTCCA 58.662 43.478 0.00 0.00 39.84 3.53
551 568 4.168101 ACCAACTCGGGGATGTATATCAT 58.832 43.478 1.63 0.00 40.22 2.45
559 576 3.467803 GATTCTAACCAACTCGGGGATG 58.532 50.000 0.00 0.00 40.22 3.51
576 594 5.272283 TCCGTATCCTACAGTTTGGATTC 57.728 43.478 11.60 7.23 42.47 2.52
577 595 4.443034 GCTCCGTATCCTACAGTTTGGATT 60.443 45.833 11.60 0.30 42.47 3.01
579 597 2.429610 GCTCCGTATCCTACAGTTTGGA 59.570 50.000 0.00 0.00 36.72 3.53
580 598 2.167693 TGCTCCGTATCCTACAGTTTGG 59.832 50.000 0.00 0.00 0.00 3.28
581 599 3.187700 GTGCTCCGTATCCTACAGTTTG 58.812 50.000 0.00 0.00 0.00 2.93
591 613 1.884926 GCTGCCTGTGCTCCGTATC 60.885 63.158 0.00 0.00 38.71 2.24
651 673 2.804090 GACGGACGGCGTCTTGTC 60.804 66.667 32.80 32.80 33.63 3.18
670 695 1.070601 GCACAATGGCTTGGTTTCCTT 59.929 47.619 2.59 0.00 36.64 3.36
696 721 2.660064 CCTGGCTAGACTTGGGCGT 61.660 63.158 0.00 0.00 32.67 5.68
761 786 2.296190 GCCAAACCCTGAAAGTCGAAAT 59.704 45.455 0.00 0.00 0.00 2.17
993 1107 3.559069 AGTGAAATTGATCATCGGCCAT 58.441 40.909 2.24 0.00 0.00 4.40
994 1108 3.003394 AGTGAAATTGATCATCGGCCA 57.997 42.857 2.24 0.00 0.00 5.36
995 1109 3.699067 CAAGTGAAATTGATCATCGGCC 58.301 45.455 0.00 0.00 31.55 6.13
1117 1243 5.092105 TGTTGTGAATTTCGTGTTGACTTG 58.908 37.500 0.00 0.00 0.00 3.16
1219 1596 0.037303 TCCGCTAGGGTACTATCCGG 59.963 60.000 6.02 0.00 41.50 5.14
1242 1619 0.546598 GTTCGAATCCTCCCCATGGT 59.453 55.000 11.73 0.00 0.00 3.55
1277 1654 3.817647 GAGTTCAGGTTGTTGAATCTGCT 59.182 43.478 0.00 0.00 39.81 4.24
1282 1659 2.887152 GCAGGAGTTCAGGTTGTTGAAT 59.113 45.455 0.00 0.00 39.13 2.57
1341 1737 1.774110 TTGCTTGGTTTGAAGAGGCA 58.226 45.000 0.00 0.00 0.00 4.75
1371 1767 5.927030 ACAGATACAGTACATGCGTTTTTG 58.073 37.500 0.00 0.00 0.00 2.44
1620 2612 0.110328 CAAGCAGCGCTGAGAAGTTG 60.110 55.000 40.21 26.23 39.62 3.16
1621 2613 0.250038 TCAAGCAGCGCTGAGAAGTT 60.250 50.000 40.21 20.28 39.62 2.66
1651 2643 4.402056 AAAAAGAAGATATCGCCGAGGA 57.598 40.909 0.00 0.00 0.00 3.71
1819 3058 3.159472 TGCATCCTCAAGCTTCATTGTT 58.841 40.909 0.00 0.00 0.00 2.83
1922 3164 1.972872 CTTTGGAGTCACTTGCAGGT 58.027 50.000 0.00 0.00 0.00 4.00
2461 4112 9.474920 TTTTCGAGCAAAAAGAATACAATCAAT 57.525 25.926 0.00 0.00 30.58 2.57
2620 4304 8.325046 AGAAAAGCAGGTGATTTTAGTATCTCT 58.675 33.333 5.96 0.00 42.78 3.10
2624 4308 9.740710 AACTAGAAAAGCAGGTGATTTTAGTAT 57.259 29.630 5.96 0.00 42.78 2.12
2636 4320 6.018098 CAGCTATCATCAACTAGAAAAGCAGG 60.018 42.308 0.00 0.00 32.43 4.85
2723 4407 4.729868 ACTGTGGTAGCCTTTTTCTGAAT 58.270 39.130 0.00 0.00 0.00 2.57
2936 4692 4.917385 AGGTATGGTAAGCAACAATGTCA 58.083 39.130 0.00 0.00 0.00 3.58
3184 5009 6.266168 TGGTGGCATTACAATTAAGTCTTG 57.734 37.500 0.00 0.00 0.00 3.02
3422 5341 2.725008 CTCATCCGAGGACTCCGC 59.275 66.667 0.00 0.00 35.44 5.54
3530 5449 3.997021 CACTGGTAGTTGCTAAGGACAAG 59.003 47.826 0.00 0.00 0.00 3.16
3703 5783 5.579718 ACGACACAGTTCGATTCTATAAGG 58.420 41.667 10.79 0.00 41.78 2.69


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

AutoCloner maintained by Alex Coulton.