Multiple sequence alignment - TraesCS4D01G020100

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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 TraesCS4D01G020100 chr4D 100.000 8285 0 0 1 8285 8661027 8652743 0.000000e+00 15300.0
1 TraesCS4D01G020100 chr4D 84.314 255 33 5 824 1075 390036057 390036307 8.310000e-60 243.0
2 TraesCS4D01G020100 chr4A 96.500 2886 55 18 3902 6772 594682916 594685770 0.000000e+00 4728.0
3 TraesCS4D01G020100 chr4A 97.900 1619 27 2 2288 3900 594681192 594682809 0.000000e+00 2795.0
4 TraesCS4D01G020100 chr4A 98.487 1388 19 2 798 2184 594679807 594681193 0.000000e+00 2446.0
5 TraesCS4D01G020100 chr4A 97.962 834 16 1 1 833 594678815 594679648 0.000000e+00 1445.0
6 TraesCS4D01G020100 chr4A 94.245 695 29 4 6884 7568 594685827 594686520 0.000000e+00 1051.0
7 TraesCS4D01G020100 chr4A 90.722 291 19 3 7995 8285 594700634 594700916 1.690000e-101 381.0
8 TraesCS4D01G020100 chr4A 80.519 385 48 19 7813 8181 594687022 594687395 3.810000e-68 270.0
9 TraesCS4D01G020100 chr4B 96.485 2105 54 9 3617 5710 16060405 16058310 0.000000e+00 3459.0
10 TraesCS4D01G020100 chr4B 97.207 1862 47 5 3617 5477 17040143 17042000 0.000000e+00 3145.0
11 TraesCS4D01G020100 chr4B 91.517 1839 79 24 1 1834 16064107 16062341 0.000000e+00 2460.0
12 TraesCS4D01G020100 chr4B 94.370 1421 56 14 5462 6870 17042197 17043605 0.000000e+00 2159.0
13 TraesCS4D01G020100 chr4B 95.499 1333 59 1 2288 3620 17038618 17039949 0.000000e+00 2128.0
14 TraesCS4D01G020100 chr4B 96.286 1077 40 0 2288 3364 16062035 16060959 0.000000e+00 1768.0
15 TraesCS4D01G020100 chr4B 95.768 1016 40 3 5743 6756 16058320 16057306 0.000000e+00 1635.0
16 TraesCS4D01G020100 chr4B 92.667 941 64 5 881 1818 17037356 17038294 0.000000e+00 1351.0
17 TraesCS4D01G020100 chr4B 90.323 775 48 7 6905 7668 17043681 17044439 0.000000e+00 990.0
18 TraesCS4D01G020100 chr4B 91.457 714 46 3 6919 7631 16057249 16056550 0.000000e+00 966.0
19 TraesCS4D01G020100 chr4B 95.318 299 12 2 1887 2184 16062331 16062034 2.710000e-129 473.0
20 TraesCS4D01G020100 chr4B 94.983 299 14 1 1887 2184 17038321 17038619 1.260000e-127 468.0
21 TraesCS4D01G020100 chr4B 97.287 258 7 0 3363 3620 16060845 16060588 9.870000e-119 438.0
22 TraesCS4D01G020100 chr4B 94.650 243 13 0 8012 8254 17044611 17044853 2.180000e-100 377.0
23 TraesCS4D01G020100 chr4B 95.625 160 7 0 718 877 17037010 17037169 2.970000e-64 257.0
24 TraesCS4D01G020100 chr4B 80.905 199 9 16 8091 8285 16056450 16056277 6.750000e-26 130.0
25 TraesCS4D01G020100 chr3B 85.676 370 41 4 824 1184 268961272 268961638 6.070000e-101 379.0
26 TraesCS4D01G020100 chr3B 98.131 107 2 0 2183 2289 728614942 728614836 3.950000e-43 187.0
27 TraesCS4D01G020100 chr3B 93.333 45 3 0 7691 7735 736305077 736305121 5.370000e-07 67.6
28 TraesCS4D01G020100 chr1B 85.135 370 43 4 824 1184 299264606 299264240 1.310000e-97 368.0
29 TraesCS4D01G020100 chr1B 92.913 127 6 2 2171 2296 88542207 88542083 1.840000e-41 182.0
30 TraesCS4D01G020100 chr5B 84.300 293 46 0 5776 6068 10446112 10445820 3.780000e-73 287.0
31 TraesCS4D01G020100 chr5B 88.136 59 4 2 7693 7748 488254690 488254632 5.370000e-07 67.6
32 TraesCS4D01G020100 chr6A 89.950 199 18 2 987 1184 432569737 432569934 1.070000e-63 255.0
33 TraesCS4D01G020100 chr5D 90.000 190 18 1 995 1184 440911138 440911326 2.310000e-60 244.0
34 TraesCS4D01G020100 chr7B 96.552 116 2 2 2178 2293 741544742 741544855 3.050000e-44 191.0
35 TraesCS4D01G020100 chr7B 96.364 110 4 0 2180 2289 58655895 58656004 1.840000e-41 182.0
36 TraesCS4D01G020100 chr6D 97.297 111 3 0 2180 2290 249445799 249445909 1.100000e-43 189.0
37 TraesCS4D01G020100 chr6D 94.737 114 6 0 2176 2289 456557351 456557464 2.380000e-40 178.0
38 TraesCS4D01G020100 chr2D 97.297 111 3 0 2180 2290 460725348 460725238 1.100000e-43 189.0
39 TraesCS4D01G020100 chr2D 95.455 44 2 0 7692 7735 621124777 621124734 4.150000e-08 71.3
40 TraesCS4D01G020100 chr2B 94.872 117 6 0 2180 2296 770902338 770902454 5.110000e-42 183.0
41 TraesCS4D01G020100 chr1D 96.364 110 4 0 2180 2289 110734933 110734824 1.840000e-41 182.0
42 TraesCS4D01G020100 chr5A 95.455 44 2 0 7692 7735 16043416 16043459 4.150000e-08 71.3
43 TraesCS4D01G020100 chr5A 90.385 52 4 1 7691 7742 11079203 11079253 5.370000e-07 67.6
44 TraesCS4D01G020100 chr3A 93.333 45 3 0 7691 7735 368744940 368744896 5.370000e-07 67.6
45 TraesCS4D01G020100 chrUn 93.182 44 3 0 7692 7735 110700197 110700240 1.930000e-06 65.8
46 TraesCS4D01G020100 chrUn 93.182 44 3 0 7692 7735 143995272 143995229 1.930000e-06 65.8
47 TraesCS4D01G020100 chr3D 85.714 56 7 1 7698 7752 64676126 64676071 3.230000e-04 58.4


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 TraesCS4D01G020100 chr4D 8652743 8661027 8284 True 15300.000 15300 100.000000 1 8285 1 chr4D.!!$R1 8284
1 TraesCS4D01G020100 chr4A 594678815 594687395 8580 False 2122.500 4728 94.268833 1 8181 6 chr4A.!!$F2 8180
2 TraesCS4D01G020100 chr4B 16056277 16064107 7830 True 1416.125 3459 93.127875 1 8285 8 chr4B.!!$R1 8284
3 TraesCS4D01G020100 chr4B 17037010 17044853 7843 False 1359.375 3145 94.415500 718 8254 8 chr4B.!!$F1 7536

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
582 584 0.179034 AGCATCGCCCCATCTTCTTC 60.179 55.000 0.00 0.00 0.00 2.87 F
1092 1471 1.630244 CCGTTCTGAGAAAGCAGCCG 61.630 60.000 0.00 0.00 35.86 5.52 F
2199 2584 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30 F
2622 3007 0.881159 CAACGACCAACCGTAGCCAA 60.881 55.000 0.00 0.00 42.54 4.52 F
3400 3906 1.455248 CGGTCTTTCTCTCCTCGTCT 58.545 55.000 0.00 0.00 0.00 4.18 F
3551 4057 7.836183 AGGTTTTGCTTATCACTATCCTTCATT 59.164 33.333 0.00 0.00 0.00 2.57 F
4344 5153 8.257306 TGCATGTTCATAGTACTATCTGTTTGA 58.743 33.333 12.62 5.07 0.00 2.69 F
5485 6506 3.772025 AGGGACCTATTTCTCACAGTGAG 59.228 47.826 22.94 22.94 45.59 3.51 F
6546 7628 3.636300 GTGGTCTATATTGGCCAATTGCA 59.364 43.478 34.85 18.73 43.89 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2184 2569 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30 R
2698 3083 1.135315 GTAACTCGGTGCATGGTACGA 60.135 52.381 0.00 0.00 0.00 3.43 R
3388 3894 2.168936 GGTCAGTCTAGACGAGGAGAGA 59.831 54.545 17.07 5.48 39.42 3.10 R
3912 4720 4.622260 ATAAAGGTGGTTTGCATTGCTT 57.378 36.364 10.49 0.00 0.00 3.91 R
4260 5069 7.850935 TCCCTCGTGATATAGGAAAAATAGT 57.149 36.000 0.00 0.00 34.58 2.12 R
5485 6506 2.952310 ACAACAGGCACTTTTCTTCCTC 59.048 45.455 0.00 0.00 34.60 3.71 R
5727 6757 2.046507 GCAGTGAGCACCTGGAGG 60.047 66.667 0.00 0.00 44.79 4.30 R
6612 7694 0.179034 CTGCAGCTACTGGGGATTCC 60.179 60.000 0.00 0.00 31.21 3.01 R
7829 9250 0.179215 GCTCTTCGTTTGGCATCGTG 60.179 55.000 11.18 7.06 0.00 4.35 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
27 29 4.136341 TCTCCAGACCTAGTTTTGGGTA 57.864 45.455 0.00 0.00 38.45 3.69
416 418 2.759191 TGTCATCTGAGCCATATTCGC 58.241 47.619 0.00 0.00 0.00 4.70
582 584 0.179034 AGCATCGCCCCATCTTCTTC 60.179 55.000 0.00 0.00 0.00 2.87
598 600 4.655649 TCTTCTTCTATATTGGGCTGCTCA 59.344 41.667 0.00 0.00 0.00 4.26
626 628 3.502211 AGTCAATCACGTGGGTTTGATTC 59.498 43.478 22.90 15.35 39.86 2.52
831 1027 4.470334 AGTTTCTTTTGTGCACATTGGT 57.530 36.364 22.39 0.00 0.00 3.67
1092 1471 1.630244 CCGTTCTGAGAAAGCAGCCG 61.630 60.000 0.00 0.00 35.86 5.52
1332 1711 5.252547 TGCCTCTGCAATATTTACTGTTCA 58.747 37.500 0.00 0.00 46.66 3.18
1998 2382 3.628942 GGACAAGATATGCAGCATGAACA 59.371 43.478 18.81 0.00 39.69 3.18
2184 2569 5.068198 TGTTCCGGTGTTACCTATGATCTAC 59.932 44.000 0.00 0.00 35.66 2.59
2185 2570 5.057843 TCCGGTGTTACCTATGATCTACT 57.942 43.478 0.00 0.00 35.66 2.57
2186 2571 5.068636 TCCGGTGTTACCTATGATCTACTC 58.931 45.833 0.00 0.00 35.66 2.59
2187 2572 4.217983 CCGGTGTTACCTATGATCTACTCC 59.782 50.000 0.00 0.00 35.66 3.85
2188 2573 4.217983 CGGTGTTACCTATGATCTACTCCC 59.782 50.000 0.00 0.00 35.66 4.30
2189 2574 5.395611 GGTGTTACCTATGATCTACTCCCT 58.604 45.833 0.00 0.00 34.73 4.20
2190 2575 5.477637 GGTGTTACCTATGATCTACTCCCTC 59.522 48.000 0.00 0.00 34.73 4.30
2191 2576 5.477637 GTGTTACCTATGATCTACTCCCTCC 59.522 48.000 0.00 0.00 0.00 4.30
2192 2577 3.443145 ACCTATGATCTACTCCCTCCG 57.557 52.381 0.00 0.00 0.00 4.63
2193 2578 2.717515 ACCTATGATCTACTCCCTCCGT 59.282 50.000 0.00 0.00 0.00 4.69
2194 2579 3.140519 ACCTATGATCTACTCCCTCCGTT 59.859 47.826 0.00 0.00 0.00 4.44
2195 2580 3.759618 CCTATGATCTACTCCCTCCGTTC 59.240 52.174 0.00 0.00 0.00 3.95
2196 2581 1.676746 TGATCTACTCCCTCCGTTCG 58.323 55.000 0.00 0.00 0.00 3.95
2197 2582 0.953003 GATCTACTCCCTCCGTTCGG 59.047 60.000 4.74 4.74 0.00 4.30
2198 2583 0.549950 ATCTACTCCCTCCGTTCGGA 59.450 55.000 13.34 13.34 0.00 4.55
2199 2584 0.329261 TCTACTCCCTCCGTTCGGAA 59.671 55.000 14.79 0.04 33.41 4.30
2200 2585 1.064166 TCTACTCCCTCCGTTCGGAAT 60.064 52.381 14.79 2.09 33.41 3.01
2201 2586 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
2202 2587 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2203 2588 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2204 2589 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2205 2590 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2206 2591 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2207 2592 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2208 2593 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2209 2594 2.597305 CTCCGTTCGGAATTACTTGTCG 59.403 50.000 14.79 0.00 33.41 4.35
2210 2595 2.030007 TCCGTTCGGAATTACTTGTCGT 60.030 45.455 11.66 0.00 0.00 4.34
2211 2596 3.190327 TCCGTTCGGAATTACTTGTCGTA 59.810 43.478 11.66 0.00 0.00 3.43
2212 2597 3.545078 CCGTTCGGAATTACTTGTCGTAG 59.455 47.826 5.19 0.00 0.00 3.51
2213 2598 3.545078 CGTTCGGAATTACTTGTCGTAGG 59.455 47.826 0.00 0.00 0.00 3.18
2214 2599 4.672542 CGTTCGGAATTACTTGTCGTAGGA 60.673 45.833 0.00 0.00 0.00 2.94
2215 2600 5.163513 GTTCGGAATTACTTGTCGTAGGAA 58.836 41.667 0.00 0.00 0.00 3.36
2216 2601 5.587388 TCGGAATTACTTGTCGTAGGAAT 57.413 39.130 0.00 0.00 29.73 3.01
2217 2602 5.345702 TCGGAATTACTTGTCGTAGGAATG 58.654 41.667 0.00 0.00 29.07 2.67
2218 2603 4.506654 CGGAATTACTTGTCGTAGGAATGG 59.493 45.833 0.00 0.00 29.07 3.16
2219 2604 5.667466 GGAATTACTTGTCGTAGGAATGGA 58.333 41.667 0.00 0.00 29.07 3.41
2220 2605 6.289064 GGAATTACTTGTCGTAGGAATGGAT 58.711 40.000 0.00 0.00 29.07 3.41
2221 2606 6.202954 GGAATTACTTGTCGTAGGAATGGATG 59.797 42.308 0.00 0.00 29.07 3.51
2222 2607 5.670792 TTACTTGTCGTAGGAATGGATGT 57.329 39.130 0.00 0.00 0.00 3.06
2223 2608 6.778834 TTACTTGTCGTAGGAATGGATGTA 57.221 37.500 0.00 0.00 0.00 2.29
2224 2609 5.871396 ACTTGTCGTAGGAATGGATGTAT 57.129 39.130 0.00 0.00 0.00 2.29
2225 2610 5.844004 ACTTGTCGTAGGAATGGATGTATC 58.156 41.667 0.00 0.00 0.00 2.24
2226 2611 5.598830 ACTTGTCGTAGGAATGGATGTATCT 59.401 40.000 0.00 0.00 0.00 1.98
2227 2612 6.776116 ACTTGTCGTAGGAATGGATGTATCTA 59.224 38.462 0.00 0.00 0.00 1.98
2228 2613 6.819397 TGTCGTAGGAATGGATGTATCTAG 57.181 41.667 0.00 0.00 0.00 2.43
2229 2614 6.540083 TGTCGTAGGAATGGATGTATCTAGA 58.460 40.000 0.00 0.00 0.00 2.43
2230 2615 6.430308 TGTCGTAGGAATGGATGTATCTAGAC 59.570 42.308 0.00 0.00 0.00 2.59
2231 2616 6.430308 GTCGTAGGAATGGATGTATCTAGACA 59.570 42.308 0.00 0.00 0.00 3.41
2232 2617 7.121463 GTCGTAGGAATGGATGTATCTAGACAT 59.879 40.741 0.00 0.00 42.82 3.06
2233 2618 7.670140 TCGTAGGAATGGATGTATCTAGACATT 59.330 37.037 0.00 0.00 40.18 2.71
2234 2619 8.307483 CGTAGGAATGGATGTATCTAGACATTT 58.693 37.037 0.00 0.00 40.18 2.32
2261 2646 9.547753 TTTAGTTCTAGATACATCCATTTCTGC 57.452 33.333 0.00 0.00 0.00 4.26
2262 2647 6.219473 AGTTCTAGATACATCCATTTCTGCG 58.781 40.000 0.00 0.00 0.00 5.18
2263 2648 6.040955 AGTTCTAGATACATCCATTTCTGCGA 59.959 38.462 0.00 0.00 0.00 5.10
2264 2649 5.773575 TCTAGATACATCCATTTCTGCGAC 58.226 41.667 0.00 0.00 0.00 5.19
2265 2650 4.406648 AGATACATCCATTTCTGCGACA 57.593 40.909 0.00 0.00 0.00 4.35
2266 2651 4.769688 AGATACATCCATTTCTGCGACAA 58.230 39.130 0.00 0.00 0.00 3.18
2267 2652 4.813161 AGATACATCCATTTCTGCGACAAG 59.187 41.667 0.00 0.00 0.00 3.16
2268 2653 2.783135 ACATCCATTTCTGCGACAAGT 58.217 42.857 0.00 0.00 0.00 3.16
2269 2654 3.937814 ACATCCATTTCTGCGACAAGTA 58.062 40.909 0.00 0.00 0.00 2.24
2270 2655 4.323417 ACATCCATTTCTGCGACAAGTAA 58.677 39.130 0.00 0.00 0.00 2.24
2271 2656 4.943705 ACATCCATTTCTGCGACAAGTAAT 59.056 37.500 0.00 0.00 0.00 1.89
2272 2657 5.415701 ACATCCATTTCTGCGACAAGTAATT 59.584 36.000 0.00 0.00 0.00 1.40
2273 2658 5.957842 TCCATTTCTGCGACAAGTAATTT 57.042 34.783 0.00 0.00 0.00 1.82
2274 2659 5.698832 TCCATTTCTGCGACAAGTAATTTG 58.301 37.500 0.00 0.00 42.68 2.32
2275 2660 4.858692 CCATTTCTGCGACAAGTAATTTGG 59.141 41.667 0.00 0.00 41.25 3.28
2276 2661 5.335583 CCATTTCTGCGACAAGTAATTTGGA 60.336 40.000 0.00 0.00 41.25 3.53
2277 2662 5.759506 TTTCTGCGACAAGTAATTTGGAA 57.240 34.783 0.00 0.00 41.25 3.53
2278 2663 4.742438 TCTGCGACAAGTAATTTGGAAC 57.258 40.909 0.00 0.00 41.25 3.62
2279 2664 3.185594 TCTGCGACAAGTAATTTGGAACG 59.814 43.478 0.00 0.00 41.25 3.95
2280 2665 2.224549 TGCGACAAGTAATTTGGAACGG 59.775 45.455 0.00 0.00 41.25 4.44
2281 2666 2.481185 GCGACAAGTAATTTGGAACGGA 59.519 45.455 0.00 0.00 41.25 4.69
2282 2667 3.424433 GCGACAAGTAATTTGGAACGGAG 60.424 47.826 0.00 0.00 41.25 4.63
2283 2668 3.124636 CGACAAGTAATTTGGAACGGAGG 59.875 47.826 0.00 0.00 41.25 4.30
2284 2669 3.418047 ACAAGTAATTTGGAACGGAGGG 58.582 45.455 0.00 0.00 41.25 4.30
2285 2670 3.073356 ACAAGTAATTTGGAACGGAGGGA 59.927 43.478 0.00 0.00 41.25 4.20
2286 2671 3.629142 AGTAATTTGGAACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
2287 2672 2.910977 AGTAATTTGGAACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
2288 2673 4.098894 AGTAATTTGGAACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
2622 3007 0.881159 CAACGACCAACCGTAGCCAA 60.881 55.000 0.00 0.00 42.54 4.52
2698 3083 4.083802 GCGCTGTTGAGAGTTTCTTTACAT 60.084 41.667 0.00 0.00 0.00 2.29
2895 3286 4.726583 TGTACTTATCTCCGCACTATCCT 58.273 43.478 0.00 0.00 0.00 3.24
3388 3894 2.227194 CCAAAGTTACTGGCGGTCTTT 58.773 47.619 0.06 4.67 0.00 2.52
3400 3906 1.455248 CGGTCTTTCTCTCCTCGTCT 58.545 55.000 0.00 0.00 0.00 4.18
3551 4057 7.836183 AGGTTTTGCTTATCACTATCCTTCATT 59.164 33.333 0.00 0.00 0.00 2.57
4255 5064 9.180551 TGATGCAGGATCATTCGTATATCACGA 62.181 40.741 0.00 0.00 45.86 4.35
4344 5153 8.257306 TGCATGTTCATAGTACTATCTGTTTGA 58.743 33.333 12.62 5.07 0.00 2.69
5485 6506 3.772025 AGGGACCTATTTCTCACAGTGAG 59.228 47.826 22.94 22.94 45.59 3.51
5646 6667 4.438744 GGCAATTCCTTTACAGGTGAATCG 60.439 45.833 0.00 0.00 41.69 3.34
5664 6685 7.587757 GGTGAATCGCATATTTATGTTCTGTTC 59.412 37.037 0.00 0.00 36.11 3.18
5859 6931 5.938125 GGAAGTTATGCAACTCTTTGGTCTA 59.062 40.000 0.00 0.00 44.41 2.59
6297 7374 5.827797 TGCAATCTTTGTCTTGGATATACCC 59.172 40.000 0.00 0.00 38.00 3.69
6443 7525 8.450964 ACTACAAAATATTCGTGGAAGAATGTG 58.549 33.333 7.92 0.00 40.66 3.21
6519 7601 7.811653 TCAATGTTTATTGCACAAGATACGAA 58.188 30.769 0.00 0.00 42.71 3.85
6546 7628 3.636300 GTGGTCTATATTGGCCAATTGCA 59.364 43.478 34.85 18.73 43.89 4.08
6612 7694 2.558359 CCTTGGTGTCTTTGGCCTTAAG 59.442 50.000 3.32 8.11 0.00 1.85
6678 7760 8.547967 TCATCACTCTTTTATTCAACCAGTAC 57.452 34.615 0.00 0.00 0.00 2.73
6699 7781 1.275010 TGTAGAATGCGTCTTCTGCCA 59.725 47.619 10.66 5.86 37.14 4.92
6789 7871 2.391678 ACATTCAAAGGGATCCATGGC 58.608 47.619 15.23 0.00 0.00 4.40
6791 7873 2.619697 TTCAAAGGGATCCATGGCAA 57.380 45.000 15.23 0.00 0.00 4.52
6797 7879 2.906568 AGGGATCCATGGCAAAACTTT 58.093 42.857 15.23 0.00 0.00 2.66
6805 7887 7.148423 GGATCCATGGCAAAACTTTTTATTCAC 60.148 37.037 6.96 0.00 0.00 3.18
6809 7891 6.917217 TGGCAAAACTTTTTATTCACCTTG 57.083 33.333 0.00 0.00 0.00 3.61
6813 7895 6.714492 CAAAACTTTTTATTCACCTTGGTGC 58.286 36.000 14.49 0.00 0.00 5.01
6815 7897 3.964031 ACTTTTTATTCACCTTGGTGCCA 59.036 39.130 14.49 4.67 0.00 4.92
6820 7902 1.619654 TTCACCTTGGTGCCAATCTG 58.380 50.000 14.49 3.39 35.20 2.90
6827 7912 3.404899 CTTGGTGCCAATCTGCATTTTT 58.595 40.909 3.91 0.00 44.30 1.94
6847 7932 6.569179 TTTTATGCTTTCAACTGGGAGTAC 57.431 37.500 0.00 0.00 0.00 2.73
6854 7939 4.942761 TTCAACTGGGAGTACGTAACTT 57.057 40.909 0.00 0.00 39.07 2.66
6855 7940 4.247267 TCAACTGGGAGTACGTAACTTG 57.753 45.455 0.00 0.00 39.07 3.16
6856 7941 2.735134 CAACTGGGAGTACGTAACTTGC 59.265 50.000 0.00 0.00 39.07 4.01
6857 7942 1.965643 ACTGGGAGTACGTAACTTGCA 59.034 47.619 0.00 0.00 39.07 4.08
6858 7943 2.565834 ACTGGGAGTACGTAACTTGCAT 59.434 45.455 0.00 0.00 39.07 3.96
6859 7944 3.765511 ACTGGGAGTACGTAACTTGCATA 59.234 43.478 0.00 0.00 39.07 3.14
6860 7945 4.142227 ACTGGGAGTACGTAACTTGCATAG 60.142 45.833 0.00 0.00 39.07 2.23
6861 7946 3.765511 TGGGAGTACGTAACTTGCATAGT 59.234 43.478 0.00 0.00 39.07 2.12
6953 8087 1.745232 TGTTGGACACACACAGGTTC 58.255 50.000 0.00 0.00 0.00 3.62
7006 8140 3.764218 GGGCAGAATGGATGAGATTCAT 58.236 45.455 0.00 0.00 36.68 2.57
7018 8152 2.092753 TGAGATTCATGAGGGCCTTCAC 60.093 50.000 21.34 7.02 0.00 3.18
7019 8153 1.134280 AGATTCATGAGGGCCTTCACG 60.134 52.381 21.34 12.95 0.00 4.35
7161 8295 2.814280 AGTGTCGGACAACCAGTAAG 57.186 50.000 13.23 0.00 35.59 2.34
7438 8576 1.209019 TGTTTGCCTGTTTGGTTGCAT 59.791 42.857 0.00 0.00 38.35 3.96
7524 8667 0.247460 GGACCCTTGAATTGCTTGCC 59.753 55.000 0.00 0.00 0.00 4.52
7556 8699 4.671766 GCTGCATTGTAACCTCGGTTAAAG 60.672 45.833 9.96 2.87 41.51 1.85
7560 8703 5.410439 GCATTGTAACCTCGGTTAAAGAAGA 59.590 40.000 9.96 0.00 41.51 2.87
7561 8704 6.072893 GCATTGTAACCTCGGTTAAAGAAGAA 60.073 38.462 9.96 0.00 41.51 2.52
7568 8711 5.054477 CCTCGGTTAAAGAAGAAGTTGTGA 58.946 41.667 0.00 0.00 0.00 3.58
7577 8944 5.162000 AGAAGAAGTTGTGAAAGAAAGCG 57.838 39.130 0.00 0.00 0.00 4.68
7578 8945 3.971032 AGAAGTTGTGAAAGAAAGCGG 57.029 42.857 0.00 0.00 0.00 5.52
7628 9000 0.719465 GTTCGACTGTTATGTGCCCG 59.281 55.000 0.00 0.00 0.00 6.13
7651 9023 1.421646 GCCCTGGGCTGAACTATGTAT 59.578 52.381 30.42 0.00 46.69 2.29
7652 9024 2.811873 GCCCTGGGCTGAACTATGTATG 60.812 54.545 30.42 0.00 46.69 2.39
7663 9035 7.365741 GCTGAACTATGTATGCATGCTTTTAT 58.634 34.615 20.33 12.27 36.58 1.40
7694 9066 2.299297 CTCCGTCCCAACTTACTTGTCT 59.701 50.000 0.00 0.00 0.00 3.41
7695 9067 3.499338 TCCGTCCCAACTTACTTGTCTA 58.501 45.455 0.00 0.00 0.00 2.59
7696 9068 4.091549 TCCGTCCCAACTTACTTGTCTAT 58.908 43.478 0.00 0.00 0.00 1.98
7718 9091 8.147704 TCTATATACATCCATTTCTGCGACAAA 58.852 33.333 0.00 0.00 0.00 2.83
7735 9108 4.514401 GACAAATAATTCTGGACGGAGGT 58.486 43.478 0.00 0.00 0.00 3.85
7750 9124 5.293569 GGACGGAGGTGTATAATTTTGAGTG 59.706 44.000 0.00 0.00 0.00 3.51
7778 9152 1.800655 CGAATCGAGCAGAGGAAGGTG 60.801 57.143 0.00 0.00 0.00 4.00
7779 9153 0.539051 AATCGAGCAGAGGAAGGTGG 59.461 55.000 0.00 0.00 0.00 4.61
7782 9161 1.821061 CGAGCAGAGGAAGGTGGTGT 61.821 60.000 0.00 0.00 0.00 4.16
7802 9181 0.392336 TGCTGTTGGGAATTGGCAAC 59.608 50.000 0.00 0.00 0.00 4.17
7847 9268 1.148310 ACACGATGCCAAACGAAGAG 58.852 50.000 0.00 0.00 0.00 2.85
7851 9272 1.725931 CGATGCCAAACGAAGAGCAAC 60.726 52.381 0.00 0.00 38.99 4.17
7858 9279 3.473367 CAAACGAAGAGCAACGAATGAG 58.527 45.455 0.00 0.00 0.00 2.90
7860 9281 2.329379 ACGAAGAGCAACGAATGAGTC 58.671 47.619 0.00 0.00 0.00 3.36
7902 9323 9.928618 TTCCAATCCAGAATTATTATTACACCA 57.071 29.630 0.00 0.00 0.00 4.17
7917 9338 9.609346 ATTATTACACCATACAAACTGGAGTAC 57.391 33.333 0.00 0.00 38.85 2.73
7918 9339 4.967084 ACACCATACAAACTGGAGTACA 57.033 40.909 0.00 0.00 36.07 2.90
7919 9340 5.298989 ACACCATACAAACTGGAGTACAA 57.701 39.130 0.00 0.00 36.07 2.41
7920 9341 5.686753 ACACCATACAAACTGGAGTACAAA 58.313 37.500 0.00 0.00 36.07 2.83
7921 9342 5.763204 ACACCATACAAACTGGAGTACAAAG 59.237 40.000 0.00 0.00 36.07 2.77
7922 9343 5.995282 CACCATACAAACTGGAGTACAAAGA 59.005 40.000 0.00 0.00 37.22 2.52
7923 9344 6.147821 CACCATACAAACTGGAGTACAAAGAG 59.852 42.308 0.00 0.00 37.22 2.85
7924 9345 6.042781 ACCATACAAACTGGAGTACAAAGAGA 59.957 38.462 0.00 0.00 37.22 3.10
7925 9346 7.106239 CCATACAAACTGGAGTACAAAGAGAT 58.894 38.462 0.00 0.00 35.70 2.75
7926 9347 8.258007 CCATACAAACTGGAGTACAAAGAGATA 58.742 37.037 0.00 0.00 35.70 1.98
7927 9348 9.088512 CATACAAACTGGAGTACAAAGAGATAC 57.911 37.037 0.00 0.00 0.00 2.24
7928 9349 7.304497 ACAAACTGGAGTACAAAGAGATACT 57.696 36.000 0.00 0.00 34.28 2.12
7929 9350 8.418597 ACAAACTGGAGTACAAAGAGATACTA 57.581 34.615 0.00 0.00 31.69 1.82
7930 9351 8.524487 ACAAACTGGAGTACAAAGAGATACTAG 58.476 37.037 0.00 0.00 31.69 2.57
7931 9352 8.524487 CAAACTGGAGTACAAAGAGATACTAGT 58.476 37.037 0.00 0.00 31.69 2.57
7932 9353 9.750783 AAACTGGAGTACAAAGAGATACTAGTA 57.249 33.333 4.77 4.77 31.69 1.82
7933 9354 8.735692 ACTGGAGTACAAAGAGATACTAGTAC 57.264 38.462 4.31 0.00 38.92 2.73
7934 9355 8.550585 ACTGGAGTACAAAGAGATACTAGTACT 58.449 37.037 4.31 0.00 44.97 2.73
7937 9358 8.992073 GGAGTACAAAGAGATACTAGTACTAGC 58.008 40.741 26.54 12.76 43.71 3.42
7964 9446 3.659089 AAGTCAACGATCGGCCGGG 62.659 63.158 27.83 17.46 0.00 5.73
8232 9714 1.279271 ACTTCACCTGGTAGCACATCC 59.721 52.381 0.00 0.00 0.00 3.51
8255 9741 3.267860 CTCGGCCGATTGCTCTGC 61.268 66.667 31.19 0.00 40.92 4.26
8256 9742 3.729965 CTCGGCCGATTGCTCTGCT 62.730 63.158 31.19 0.00 40.92 4.24
8257 9743 3.570638 CGGCCGATTGCTCTGCTG 61.571 66.667 24.07 0.00 40.92 4.41
8258 9744 3.885521 GGCCGATTGCTCTGCTGC 61.886 66.667 0.00 0.00 40.92 5.25
8270 9756 4.405671 TGCTGCTGCTGGCTCTCC 62.406 66.667 17.00 0.00 42.39 3.71
8280 9766 4.593864 GGCTCTCCGGTGGCGATC 62.594 72.222 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 29 3.198417 GGCCAAACAAATGATGGATCCTT 59.802 43.478 14.23 6.57 36.27 3.36
416 418 2.892852 TCCAAACTCAAATCAAGCCCAG 59.107 45.455 0.00 0.00 0.00 4.45
551 553 2.362077 GGGCGATGCTAAATGAATGGTT 59.638 45.455 0.00 0.00 0.00 3.67
582 584 6.058183 ACTTAAAGTGAGCAGCCCAATATAG 58.942 40.000 0.00 0.00 0.00 1.31
598 600 4.081322 ACCCACGTGATTGACTTAAAGT 57.919 40.909 19.30 0.00 0.00 2.66
626 628 9.956720 AACAGATCAATTTTACAAAGACTGAAG 57.043 29.630 0.00 0.00 0.00 3.02
1092 1471 6.377146 TCCCAAAATAGACCTTAACATTCTGC 59.623 38.462 0.00 0.00 0.00 4.26
1288 1667 8.956533 AGGCAAAGAAAGCAAAAGTAAAAATA 57.043 26.923 0.00 0.00 0.00 1.40
1432 1813 9.485206 CATGTCACTCACATATCAATGATTAGA 57.515 33.333 0.00 0.00 44.60 2.10
1812 2195 5.538433 AGGAGTATAGCAAAGAGGCTTCTAG 59.462 44.000 0.00 0.00 42.71 2.43
1818 2201 2.103941 AGCAGGAGTATAGCAAAGAGGC 59.896 50.000 0.00 0.00 0.00 4.70
1998 2382 4.165565 TCTCCAATGATGCTGAAGGAATCT 59.834 41.667 0.00 0.00 31.22 2.40
2184 2569 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
2185 2570 1.856629 AGTAATTCCGAACGGAGGGA 58.143 50.000 15.34 2.49 46.06 4.20
2186 2571 2.277084 CAAGTAATTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
2187 2572 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2188 2573 2.597305 CGACAAGTAATTCCGAACGGAG 59.403 50.000 15.34 5.60 46.06 4.63
2189 2574 2.030007 ACGACAAGTAATTCCGAACGGA 60.030 45.455 12.04 12.04 43.52 4.69
2190 2575 2.331194 ACGACAAGTAATTCCGAACGG 58.669 47.619 6.94 6.94 0.00 4.44
2191 2576 3.545078 CCTACGACAAGTAATTCCGAACG 59.455 47.826 0.00 0.00 34.45 3.95
2192 2577 4.737054 TCCTACGACAAGTAATTCCGAAC 58.263 43.478 0.00 0.00 34.45 3.95
2193 2578 5.389859 TTCCTACGACAAGTAATTCCGAA 57.610 39.130 0.00 0.00 34.45 4.30
2194 2579 5.345702 CATTCCTACGACAAGTAATTCCGA 58.654 41.667 0.00 0.00 34.45 4.55
2195 2580 4.506654 CCATTCCTACGACAAGTAATTCCG 59.493 45.833 0.00 0.00 34.45 4.30
2196 2581 5.667466 TCCATTCCTACGACAAGTAATTCC 58.333 41.667 0.00 0.00 34.45 3.01
2197 2582 6.761714 ACATCCATTCCTACGACAAGTAATTC 59.238 38.462 0.00 0.00 34.45 2.17
2198 2583 6.650120 ACATCCATTCCTACGACAAGTAATT 58.350 36.000 0.00 0.00 34.45 1.40
2199 2584 6.235231 ACATCCATTCCTACGACAAGTAAT 57.765 37.500 0.00 0.00 34.45 1.89
2200 2585 5.670792 ACATCCATTCCTACGACAAGTAA 57.329 39.130 0.00 0.00 34.45 2.24
2201 2586 6.776116 AGATACATCCATTCCTACGACAAGTA 59.224 38.462 0.00 0.00 0.00 2.24
2202 2587 5.598830 AGATACATCCATTCCTACGACAAGT 59.401 40.000 0.00 0.00 0.00 3.16
2203 2588 6.090483 AGATACATCCATTCCTACGACAAG 57.910 41.667 0.00 0.00 0.00 3.16
2204 2589 7.002276 TCTAGATACATCCATTCCTACGACAA 58.998 38.462 0.00 0.00 0.00 3.18
2205 2590 6.430308 GTCTAGATACATCCATTCCTACGACA 59.570 42.308 0.00 0.00 0.00 4.35
2206 2591 6.430308 TGTCTAGATACATCCATTCCTACGAC 59.570 42.308 0.00 0.00 0.00 4.34
2207 2592 6.540083 TGTCTAGATACATCCATTCCTACGA 58.460 40.000 0.00 0.00 0.00 3.43
2208 2593 6.819397 TGTCTAGATACATCCATTCCTACG 57.181 41.667 0.00 0.00 0.00 3.51
2235 2620 9.547753 GCAGAAATGGATGTATCTAGAACTAAA 57.452 33.333 0.00 0.00 0.00 1.85
2236 2621 7.867909 CGCAGAAATGGATGTATCTAGAACTAA 59.132 37.037 0.00 0.00 0.00 2.24
2237 2622 7.230712 TCGCAGAAATGGATGTATCTAGAACTA 59.769 37.037 0.00 0.00 0.00 2.24
2238 2623 6.040955 TCGCAGAAATGGATGTATCTAGAACT 59.959 38.462 0.00 0.00 0.00 3.01
2239 2624 6.144724 GTCGCAGAAATGGATGTATCTAGAAC 59.855 42.308 0.00 0.00 39.69 3.01
2240 2625 6.183360 TGTCGCAGAAATGGATGTATCTAGAA 60.183 38.462 0.00 0.00 39.69 2.10
2241 2626 5.301805 TGTCGCAGAAATGGATGTATCTAGA 59.698 40.000 0.00 0.00 39.69 2.43
2242 2627 5.532557 TGTCGCAGAAATGGATGTATCTAG 58.467 41.667 0.00 0.00 39.69 2.43
2243 2628 5.529581 TGTCGCAGAAATGGATGTATCTA 57.470 39.130 0.00 0.00 39.69 1.98
2244 2629 4.406648 TGTCGCAGAAATGGATGTATCT 57.593 40.909 0.00 0.00 39.69 1.98
2245 2630 4.572389 ACTTGTCGCAGAAATGGATGTATC 59.428 41.667 0.00 0.00 39.69 2.24
2246 2631 4.517285 ACTTGTCGCAGAAATGGATGTAT 58.483 39.130 0.00 0.00 39.69 2.29
2247 2632 3.937814 ACTTGTCGCAGAAATGGATGTA 58.062 40.909 0.00 0.00 39.69 2.29
2248 2633 2.783135 ACTTGTCGCAGAAATGGATGT 58.217 42.857 0.00 0.00 39.69 3.06
2249 2634 4.944962 TTACTTGTCGCAGAAATGGATG 57.055 40.909 0.00 0.00 39.69 3.51
2250 2635 6.324819 CAAATTACTTGTCGCAGAAATGGAT 58.675 36.000 0.00 0.00 39.69 3.41
2251 2636 5.335583 CCAAATTACTTGTCGCAGAAATGGA 60.336 40.000 0.00 0.00 39.69 3.41
2252 2637 4.858692 CCAAATTACTTGTCGCAGAAATGG 59.141 41.667 0.00 0.00 39.69 3.16
2253 2638 5.698832 TCCAAATTACTTGTCGCAGAAATG 58.301 37.500 0.00 0.00 39.69 2.32
2254 2639 5.957842 TCCAAATTACTTGTCGCAGAAAT 57.042 34.783 0.00 0.00 39.69 2.17
2255 2640 5.516090 GTTCCAAATTACTTGTCGCAGAAA 58.484 37.500 0.00 0.00 39.69 2.52
2256 2641 4.319190 CGTTCCAAATTACTTGTCGCAGAA 60.319 41.667 0.00 0.00 39.69 3.02
2257 2642 3.185594 CGTTCCAAATTACTTGTCGCAGA 59.814 43.478 0.00 0.00 32.65 4.26
2258 2643 3.479006 CGTTCCAAATTACTTGTCGCAG 58.521 45.455 0.00 0.00 32.65 5.18
2259 2644 2.224549 CCGTTCCAAATTACTTGTCGCA 59.775 45.455 0.00 0.00 32.65 5.10
2260 2645 2.481185 TCCGTTCCAAATTACTTGTCGC 59.519 45.455 0.00 0.00 32.65 5.19
2261 2646 3.124636 CCTCCGTTCCAAATTACTTGTCG 59.875 47.826 0.00 0.00 32.65 4.35
2262 2647 3.439129 CCCTCCGTTCCAAATTACTTGTC 59.561 47.826 0.00 0.00 32.65 3.18
2263 2648 3.073356 TCCCTCCGTTCCAAATTACTTGT 59.927 43.478 0.00 0.00 32.65 3.16
2264 2649 3.681593 TCCCTCCGTTCCAAATTACTTG 58.318 45.455 0.00 0.00 34.52 3.16
2265 2650 3.329814 ACTCCCTCCGTTCCAAATTACTT 59.670 43.478 0.00 0.00 0.00 2.24
2266 2651 2.910977 ACTCCCTCCGTTCCAAATTACT 59.089 45.455 0.00 0.00 0.00 2.24
2267 2652 3.345508 ACTCCCTCCGTTCCAAATTAC 57.654 47.619 0.00 0.00 0.00 1.89
2268 2653 4.533311 ACTTACTCCCTCCGTTCCAAATTA 59.467 41.667 0.00 0.00 0.00 1.40
2269 2654 3.329814 ACTTACTCCCTCCGTTCCAAATT 59.670 43.478 0.00 0.00 0.00 1.82
2270 2655 2.910977 ACTTACTCCCTCCGTTCCAAAT 59.089 45.455 0.00 0.00 0.00 2.32
2271 2656 2.332117 ACTTACTCCCTCCGTTCCAAA 58.668 47.619 0.00 0.00 0.00 3.28
2272 2657 2.019807 ACTTACTCCCTCCGTTCCAA 57.980 50.000 0.00 0.00 0.00 3.53
2273 2658 2.019807 AACTTACTCCCTCCGTTCCA 57.980 50.000 0.00 0.00 0.00 3.53
2274 2659 4.750021 AATAACTTACTCCCTCCGTTCC 57.250 45.455 0.00 0.00 0.00 3.62
2275 2660 6.462552 ACTAATAACTTACTCCCTCCGTTC 57.537 41.667 0.00 0.00 0.00 3.95
2276 2661 6.666980 AGAACTAATAACTTACTCCCTCCGTT 59.333 38.462 0.00 0.00 0.00 4.44
2277 2662 6.096564 CAGAACTAATAACTTACTCCCTCCGT 59.903 42.308 0.00 0.00 0.00 4.69
2278 2663 6.096564 ACAGAACTAATAACTTACTCCCTCCG 59.903 42.308 0.00 0.00 0.00 4.63
2279 2664 7.093421 ACACAGAACTAATAACTTACTCCCTCC 60.093 40.741 0.00 0.00 0.00 4.30
2280 2665 7.838884 ACACAGAACTAATAACTTACTCCCTC 58.161 38.462 0.00 0.00 0.00 4.30
2281 2666 7.793948 ACACAGAACTAATAACTTACTCCCT 57.206 36.000 0.00 0.00 0.00 4.20
2282 2667 8.718734 CAAACACAGAACTAATAACTTACTCCC 58.281 37.037 0.00 0.00 0.00 4.30
2283 2668 9.269453 ACAAACACAGAACTAATAACTTACTCC 57.731 33.333 0.00 0.00 0.00 3.85
2622 3007 2.290071 CCCACGGACAAGGACAGTAAAT 60.290 50.000 0.00 0.00 0.00 1.40
2698 3083 1.135315 GTAACTCGGTGCATGGTACGA 60.135 52.381 0.00 0.00 0.00 3.43
2830 3221 1.587088 GCGGCAGCATTCCATTTCG 60.587 57.895 3.18 0.00 44.35 3.46
3388 3894 2.168936 GGTCAGTCTAGACGAGGAGAGA 59.831 54.545 17.07 5.48 39.42 3.10
3400 3906 4.678256 AGAAGATGAAGGTGGTCAGTCTA 58.322 43.478 0.00 0.00 0.00 2.59
3669 4372 6.528423 GTCATGATAGATGCTACCAACGTATC 59.472 42.308 0.00 0.00 0.00 2.24
3912 4720 4.622260 ATAAAGGTGGTTTGCATTGCTT 57.378 36.364 10.49 0.00 0.00 3.91
4258 5067 8.365647 TCCCTCGTGATATAGGAAAAATAGTTC 58.634 37.037 0.00 0.00 34.58 3.01
4259 5068 8.258850 TCCCTCGTGATATAGGAAAAATAGTT 57.741 34.615 0.00 0.00 34.58 2.24
4260 5069 7.850935 TCCCTCGTGATATAGGAAAAATAGT 57.149 36.000 0.00 0.00 34.58 2.12
4261 5070 8.368668 AGTTCCCTCGTGATATAGGAAAAATAG 58.631 37.037 0.00 0.00 38.30 1.73
4262 5071 8.258850 AGTTCCCTCGTGATATAGGAAAAATA 57.741 34.615 0.00 0.00 38.30 1.40
5485 6506 2.952310 ACAACAGGCACTTTTCTTCCTC 59.048 45.455 0.00 0.00 34.60 3.71
5593 6614 2.167075 CTCCATTGGAATGTCCTTTGGC 59.833 50.000 6.88 0.00 38.40 4.52
5646 6667 5.568482 TGCACGAACAGAACATAAATATGC 58.432 37.500 0.36 0.00 37.19 3.14
5727 6757 2.046507 GCAGTGAGCACCTGGAGG 60.047 66.667 0.00 0.00 44.79 4.30
5768 6840 4.783227 AGAAGGTAGCCTGAAATGGAAGTA 59.217 41.667 0.00 0.00 32.13 2.24
6297 7374 8.103948 ACAAGACCAGAGAAAACATATCAAAG 57.896 34.615 0.00 0.00 0.00 2.77
6443 7525 4.939052 TTAGGTTATAGGAGCACAGAGC 57.061 45.455 0.00 0.00 46.19 4.09
6477 7559 8.816640 AAACATTGATGAACTGAAAATGGTAC 57.183 30.769 0.00 0.00 33.50 3.34
6519 7601 2.849943 TGGCCAATATAGACCACCAGTT 59.150 45.455 0.61 0.00 0.00 3.16
6546 7628 7.776969 ACCAGAGAGAATATTGTTGCATTGTAT 59.223 33.333 0.00 0.00 0.00 2.29
6612 7694 0.179034 CTGCAGCTACTGGGGATTCC 60.179 60.000 0.00 0.00 31.21 3.01
6639 7721 6.567687 AGAGTGATGATGATAAGAGGTACG 57.432 41.667 0.00 0.00 0.00 3.67
6678 7760 1.929836 GGCAGAAGACGCATTCTACAG 59.070 52.381 2.68 0.00 37.43 2.74
6766 7848 5.163001 TGCCATGGATCCCTTTGAATGTATA 60.163 40.000 18.40 0.00 0.00 1.47
6773 7855 2.566724 GTTTTGCCATGGATCCCTTTGA 59.433 45.455 18.40 0.00 0.00 2.69
6774 7856 2.568509 AGTTTTGCCATGGATCCCTTTG 59.431 45.455 18.40 4.37 0.00 2.77
6777 7859 2.629017 AAGTTTTGCCATGGATCCCT 57.371 45.000 18.40 0.00 0.00 4.20
6779 7861 6.878389 TGAATAAAAAGTTTTGCCATGGATCC 59.122 34.615 18.40 4.20 0.00 3.36
6781 7863 6.654582 GGTGAATAAAAAGTTTTGCCATGGAT 59.345 34.615 18.40 0.00 0.00 3.41
6782 7864 5.994668 GGTGAATAAAAAGTTTTGCCATGGA 59.005 36.000 18.40 0.00 0.00 3.41
6783 7865 5.997129 AGGTGAATAAAAAGTTTTGCCATGG 59.003 36.000 7.63 7.63 0.00 3.66
6784 7866 7.354257 CAAGGTGAATAAAAAGTTTTGCCATG 58.646 34.615 0.61 0.00 0.00 3.66
6786 7868 5.819901 CCAAGGTGAATAAAAAGTTTTGCCA 59.180 36.000 0.61 0.00 0.00 4.92
6805 7887 4.100479 TGCAGATTGGCACCAAGG 57.900 55.556 8.30 1.69 39.25 3.61
6827 7912 3.259876 ACGTACTCCCAGTTGAAAGCATA 59.740 43.478 0.00 0.00 0.00 3.14
6856 7941 8.969121 TTCAGAACATAAAACATGCAACTATG 57.031 30.769 0.00 0.00 0.00 2.23
6917 8051 6.040955 TGTCCAACAACAAATAATGGCAAGTA 59.959 34.615 0.00 0.00 0.00 2.24
6953 8087 5.505489 CGTCTTCTCTGTCCATGTCTATCAG 60.505 48.000 0.00 0.00 0.00 2.90
7018 8152 1.805945 GGACTGACAGTAAGCGGCG 60.806 63.158 8.41 0.51 0.00 6.46
7019 8153 1.014564 GTGGACTGACAGTAAGCGGC 61.015 60.000 8.41 0.00 0.00 6.53
7051 8185 1.895798 TCCAGAGATATGTCATCGGCC 59.104 52.381 2.30 0.00 0.00 6.13
7123 8257 2.084546 CTTTCTTTGCCCCTAGGTTCG 58.915 52.381 8.29 0.00 34.57 3.95
7132 8266 0.591659 GTCCGACACTTTCTTTGCCC 59.408 55.000 0.00 0.00 0.00 5.36
7161 8295 0.387929 TGTCGGGTGAGACAAGTCAC 59.612 55.000 2.72 0.00 46.81 3.67
7295 8429 4.201802 TGTTCTATGTGCACATTGTATGCG 60.202 41.667 35.45 15.63 46.49 4.73
7438 8576 5.235186 CGATTTAAACACAAAATTGCACCCA 59.765 36.000 0.00 0.00 0.00 4.51
7524 8667 2.526091 TACAATGCAGCAAAGCCGCG 62.526 55.000 0.00 0.00 36.85 6.46
7556 8699 4.201920 ACCGCTTTCTTTCACAACTTCTTC 60.202 41.667 0.00 0.00 0.00 2.87
7560 8703 2.357952 GGACCGCTTTCTTTCACAACTT 59.642 45.455 0.00 0.00 0.00 2.66
7561 8704 1.947456 GGACCGCTTTCTTTCACAACT 59.053 47.619 0.00 0.00 0.00 3.16
7568 8711 2.094675 CATGGATGGACCGCTTTCTTT 58.905 47.619 0.00 0.00 42.61 2.52
7671 9043 3.233507 ACAAGTAAGTTGGGACGGAGTA 58.766 45.455 0.00 0.00 40.59 2.59
7672 9044 2.036862 GACAAGTAAGTTGGGACGGAGT 59.963 50.000 0.00 0.00 42.69 3.85
7673 9045 2.299297 AGACAAGTAAGTTGGGACGGAG 59.701 50.000 0.00 0.00 40.90 4.63
7694 9066 8.846943 ATTTGTCGCAGAAATGGATGTATATA 57.153 30.769 0.00 0.00 39.69 0.86
7695 9067 7.750229 ATTTGTCGCAGAAATGGATGTATAT 57.250 32.000 0.00 0.00 39.69 0.86
7696 9068 8.669946 TTATTTGTCGCAGAAATGGATGTATA 57.330 30.769 0.00 0.00 39.69 1.47
7718 9091 6.989155 TTATACACCTCCGTCCAGAATTAT 57.011 37.500 0.00 0.00 0.00 1.28
7735 9108 6.711194 TCGGTTTCACCACTCAAAATTATACA 59.289 34.615 0.00 0.00 38.47 2.29
7750 9124 0.721718 CTGCTCGATTCGGTTTCACC 59.278 55.000 6.18 0.00 34.05 4.02
7758 9132 0.457851 ACCTTCCTCTGCTCGATTCG 59.542 55.000 0.00 0.00 0.00 3.34
7778 9152 1.270252 CCAATTCCCAACAGCAACACC 60.270 52.381 0.00 0.00 0.00 4.16
7779 9153 1.873486 GCCAATTCCCAACAGCAACAC 60.873 52.381 0.00 0.00 0.00 3.32
7782 9161 1.126488 TTGCCAATTCCCAACAGCAA 58.874 45.000 0.00 0.00 37.85 3.91
7802 9181 3.114616 CTCTGTGGAACTGCGCCG 61.115 66.667 4.18 0.00 38.04 6.46
7829 9250 0.179215 GCTCTTCGTTTGGCATCGTG 60.179 55.000 11.18 7.06 0.00 4.35
7860 9281 5.220228 GGATTGGAACTAATAATCGATCGCG 60.220 44.000 11.09 0.00 39.35 5.87
7900 9321 6.464222 TCTCTTTGTACTCCAGTTTGTATGG 58.536 40.000 0.00 0.00 39.33 2.74
7901 9322 9.088512 GTATCTCTTTGTACTCCAGTTTGTATG 57.911 37.037 0.00 0.00 0.00 2.39
7902 9323 9.036980 AGTATCTCTTTGTACTCCAGTTTGTAT 57.963 33.333 0.00 0.00 0.00 2.29
7903 9324 8.418597 AGTATCTCTTTGTACTCCAGTTTGTA 57.581 34.615 0.00 0.00 0.00 2.41
7904 9325 7.304497 AGTATCTCTTTGTACTCCAGTTTGT 57.696 36.000 0.00 0.00 0.00 2.83
7905 9326 8.524487 ACTAGTATCTCTTTGTACTCCAGTTTG 58.476 37.037 0.00 0.00 33.48 2.93
7906 9327 8.653036 ACTAGTATCTCTTTGTACTCCAGTTT 57.347 34.615 0.00 0.00 33.48 2.66
7907 9328 9.176460 GTACTAGTATCTCTTTGTACTCCAGTT 57.824 37.037 5.75 0.00 34.86 3.16
7908 9329 8.550585 AGTACTAGTATCTCTTTGTACTCCAGT 58.449 37.037 5.75 0.00 39.01 4.00
7909 9330 8.967664 AGTACTAGTATCTCTTTGTACTCCAG 57.032 38.462 5.75 0.00 39.01 3.86
7911 9332 8.992073 GCTAGTACTAGTATCTCTTTGTACTCC 58.008 40.741 26.76 4.54 41.10 3.85
7912 9333 9.545105 TGCTAGTACTAGTATCTCTTTGTACTC 57.455 37.037 26.76 8.45 41.10 2.59
7913 9334 9.550406 CTGCTAGTACTAGTATCTCTTTGTACT 57.450 37.037 26.76 0.00 42.18 2.73
7914 9335 9.545105 TCTGCTAGTACTAGTATCTCTTTGTAC 57.455 37.037 26.76 9.37 36.31 2.90
7915 9336 9.545105 GTCTGCTAGTACTAGTATCTCTTTGTA 57.455 37.037 26.76 1.29 35.65 2.41
7916 9337 7.225145 CGTCTGCTAGTACTAGTATCTCTTTGT 59.775 40.741 26.76 0.00 35.65 2.83
7917 9338 7.438757 TCGTCTGCTAGTACTAGTATCTCTTTG 59.561 40.741 26.76 11.89 35.65 2.77
7918 9339 7.499292 TCGTCTGCTAGTACTAGTATCTCTTT 58.501 38.462 26.76 0.00 35.65 2.52
7919 9340 7.053316 TCGTCTGCTAGTACTAGTATCTCTT 57.947 40.000 26.76 0.00 35.65 2.85
7920 9341 6.294899 CCTCGTCTGCTAGTACTAGTATCTCT 60.295 46.154 26.76 1.36 35.65 3.10
7921 9342 5.865552 CCTCGTCTGCTAGTACTAGTATCTC 59.134 48.000 26.76 15.63 35.65 2.75
7922 9343 5.539574 TCCTCGTCTGCTAGTACTAGTATCT 59.460 44.000 26.76 7.87 35.65 1.98
7923 9344 5.782047 TCCTCGTCTGCTAGTACTAGTATC 58.218 45.833 26.76 17.86 35.65 2.24
7924 9345 5.804944 TCCTCGTCTGCTAGTACTAGTAT 57.195 43.478 26.76 0.00 35.65 2.12
7925 9346 5.128499 ACTTCCTCGTCTGCTAGTACTAGTA 59.872 44.000 26.76 22.60 35.65 1.82
7926 9347 4.080975 ACTTCCTCGTCTGCTAGTACTAGT 60.081 45.833 26.76 0.00 35.65 2.57
7927 9348 4.444536 ACTTCCTCGTCTGCTAGTACTAG 58.555 47.826 23.25 23.25 36.29 2.57
7928 9349 4.081254 TGACTTCCTCGTCTGCTAGTACTA 60.081 45.833 1.89 1.89 35.00 1.82
7929 9350 3.272581 GACTTCCTCGTCTGCTAGTACT 58.727 50.000 0.00 0.00 0.00 2.73
7930 9351 3.008330 TGACTTCCTCGTCTGCTAGTAC 58.992 50.000 0.00 0.00 35.00 2.73
7931 9352 3.345508 TGACTTCCTCGTCTGCTAGTA 57.654 47.619 0.00 0.00 35.00 1.82
7932 9353 2.201921 TGACTTCCTCGTCTGCTAGT 57.798 50.000 0.00 0.00 35.00 2.57
7933 9354 2.729467 CGTTGACTTCCTCGTCTGCTAG 60.729 54.545 0.00 0.00 35.00 3.42
7934 9355 1.199327 CGTTGACTTCCTCGTCTGCTA 59.801 52.381 0.00 0.00 35.00 3.49
7937 9358 2.520979 GATCGTTGACTTCCTCGTCTG 58.479 52.381 0.00 0.00 35.00 3.51
7964 9446 3.654020 GCATCGATCGGCCTTGCC 61.654 66.667 16.41 0.00 46.75 4.52
7968 9450 0.320247 GAATCAGCATCGATCGGCCT 60.320 55.000 16.41 6.28 0.00 5.19
7973 9455 0.664466 TCGGCGAATCAGCATCGATC 60.664 55.000 7.35 0.00 42.76 3.69
7974 9456 0.941463 GTCGGCGAATCAGCATCGAT 60.941 55.000 12.92 0.00 42.76 3.59
7975 9457 1.588932 GTCGGCGAATCAGCATCGA 60.589 57.895 12.92 0.00 42.76 3.59
8008 9490 2.742372 GTGGTGTGAGGCGCGATT 60.742 61.111 12.10 0.00 0.00 3.34
8009 9491 3.315142 ATGTGGTGTGAGGCGCGAT 62.315 57.895 12.10 0.00 0.00 4.58
8010 9492 3.932580 GATGTGGTGTGAGGCGCGA 62.933 63.158 12.10 0.00 0.00 5.87
8021 9503 1.078214 CGCCATCCTGTGATGTGGT 60.078 57.895 2.24 0.00 45.78 4.16
8022 9504 2.475466 GCGCCATCCTGTGATGTGG 61.475 63.158 0.00 0.00 45.78 4.17
8036 9518 4.459089 GAGTCCTCCACCTGCGCC 62.459 72.222 4.18 0.00 0.00 6.53
8242 9724 2.823147 AGCAGCAGAGCAATCGGC 60.823 61.111 0.00 0.00 45.30 5.54
8243 9725 3.099438 CAGCAGCAGAGCAATCGG 58.901 61.111 0.00 0.00 36.85 4.18
8258 9744 4.463879 CCACCGGAGAGCCAGCAG 62.464 72.222 9.46 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.