Multiple sequence alignment - TraesCS3D01G004600

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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 TraesCS3D01G004600 chr3D 100.000 2993 0 0 1 2993 1844326 1847318 0.000000e+00 5528.0
1 TraesCS3D01G004600 chr3D 77.037 135 23 6 2817 2947 560945676 560945806 1.490000e-08 71.3
2 TraesCS3D01G004600 chr3A 94.045 1377 51 15 866 2218 7201852 7200483 0.000000e+00 2060.0
3 TraesCS3D01G004600 chr3A 87.148 887 80 18 4 867 7202889 7202014 0.000000e+00 976.0
4 TraesCS3D01G004600 chr3A 92.934 467 19 11 2537 2993 7200490 7200028 0.000000e+00 667.0
5 TraesCS3D01G004600 chr3A 92.027 301 12 1 2227 2515 325451196 325451496 2.150000e-111 412.0
6 TraesCS3D01G004600 chr3A 92.000 300 12 1 2228 2515 167764265 167763966 7.720000e-111 411.0
7 TraesCS3D01G004600 chr3A 91.262 309 15 1 2224 2520 316668044 316668352 7.720000e-111 411.0
8 TraesCS3D01G004600 chr3A 91.749 303 12 2 2230 2519 25110155 25109853 2.780000e-110 409.0
9 TraesCS3D01G004600 chr3A 91.749 303 12 2 2226 2515 444288563 444288261 2.780000e-110 409.0
10 TraesCS3D01G004600 chr3B 92.632 1330 49 16 828 2127 4202045 4203355 0.000000e+00 1868.0
11 TraesCS3D01G004600 chr3B 94.158 1027 33 9 829 1846 5058240 5059248 0.000000e+00 1539.0
12 TraesCS3D01G004600 chr3B 91.962 846 52 8 1 833 5056322 5057164 0.000000e+00 1171.0
13 TraesCS3D01G004600 chr3B 91.145 847 59 7 1 833 4200163 4201007 0.000000e+00 1134.0
14 TraesCS3D01G004600 chr3B 74.038 208 34 12 2547 2752 40170761 40170950 1.930000e-07 67.6
15 TraesCS3D01G004600 chr5B 91.883 308 12 2 2226 2520 26842390 26842083 4.610000e-113 418.0
16 TraesCS3D01G004600 chr5B 80.319 188 33 4 2593 2777 288439959 288439773 4.020000e-29 139.0
17 TraesCS3D01G004600 chr5B 83.333 102 14 2 2517 2616 696578329 696578229 1.140000e-14 91.6
18 TraesCS3D01G004600 chr1A 92.000 300 12 1 2228 2515 315372740 315373039 7.720000e-111 411.0
19 TraesCS3D01G004600 chr1A 91.333 300 14 1 2228 2515 231449848 231450147 1.670000e-107 399.0
20 TraesCS3D01G004600 chr7B 91.749 303 12 2 2227 2516 643379904 643379602 2.780000e-110 409.0
21 TraesCS3D01G004600 chr7B 84.974 193 23 6 2517 2708 91240425 91240238 1.100000e-44 191.0
22 TraesCS3D01G004600 chr2A 91.694 301 13 1 2228 2516 673223895 673223595 9.990000e-110 407.0
23 TraesCS3D01G004600 chr4A 91.667 300 13 1 2228 2515 43385222 43384923 3.590000e-109 405.0
24 TraesCS3D01G004600 chr7A 91.919 297 11 2 2228 2512 568942043 568942338 1.290000e-108 403.0
25 TraesCS3D01G004600 chr7A 83.077 130 21 1 2510 2638 562892725 562892854 1.890000e-22 117.0
26 TraesCS3D01G004600 chr5A 91.176 306 13 3 2230 2521 13350179 13350484 1.290000e-108 403.0
27 TraesCS3D01G004600 chr5A 90.879 307 14 3 2223 2516 574021151 574021456 1.670000e-107 399.0
28 TraesCS3D01G004600 chr5A 78.261 299 54 10 2230 2519 672507999 672508295 6.590000e-42 182.0
29 TraesCS3D01G004600 chr4B 91.216 296 14 1 2229 2512 626075421 626075716 2.800000e-105 392.0
30 TraesCS3D01G004600 chr4B 80.795 151 26 3 2570 2720 588691893 588692040 6.780000e-22 115.0
31 TraesCS3D01G004600 chr6A 87.255 306 27 1 2227 2520 610200901 610201206 3.700000e-89 339.0
32 TraesCS3D01G004600 chr6A 87.097 93 11 1 2549 2640 462253446 462253354 1.470000e-18 104.0
33 TraesCS3D01G004600 chr1B 83.162 291 40 5 2230 2513 480425185 480425473 1.060000e-64 257.0
34 TraesCS3D01G004600 chr6D 82.927 123 17 3 2523 2645 451802534 451802652 1.130000e-19 108.0
35 TraesCS3D01G004600 chr6D 84.956 113 7 5 2560 2671 417695785 417695888 4.080000e-19 106.0
36 TraesCS3D01G004600 chr2B 85.294 102 13 2 2545 2645 153902850 153902750 1.470000e-18 104.0
37 TraesCS3D01G004600 chr2B 77.311 119 23 4 2636 2752 330064346 330064230 1.930000e-07 67.6
38 TraesCS3D01G004600 chr4D 79.167 120 19 6 2636 2752 12511675 12511559 8.900000e-11 78.7
39 TraesCS3D01G004600 chr4D 74.641 209 31 14 2547 2752 298879856 298880045 4.140000e-09 73.1


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 TraesCS3D01G004600 chr3D 1844326 1847318 2992 False 5528.000000 5528 100.000000 1 2993 1 chr3D.!!$F1 2992
1 TraesCS3D01G004600 chr3A 7200028 7202889 2861 True 1234.333333 2060 91.375667 4 2993 3 chr3A.!!$R4 2989
2 TraesCS3D01G004600 chr3B 4200163 4203355 3192 False 1501.000000 1868 91.888500 1 2127 2 chr3B.!!$F2 2126
3 TraesCS3D01G004600 chr3B 5056322 5059248 2926 False 1355.000000 1539 93.060000 1 1846 2 chr3B.!!$F3 1845

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 0.035820 TGGCCTTTTGCTACTACGGG 60.036 55.0 3.32 0.0 40.92 5.28 F
1798 3085 0.247736 CAAGTCCGTGCCTAGCTCTT 59.752 55.0 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1893 3201 0.250234 TCTTGTCCCCGATCAGCTTG 59.750 55.0 0.0 0.0 0.0 4.01 R
2775 4094 0.179040 TTCTTCCACAACCACCGTCC 60.179 55.0 0.0 0.0 0.0 4.79 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
20 21 0.035820 TGGCCTTTTGCTACTACGGG 60.036 55.000 3.32 0.00 40.92 5.28
64 65 0.802222 GCAGCGAGTCAAGCGATGTA 60.802 55.000 0.00 0.00 45.81 2.29
141 142 4.503123 CGGTAATTGCTACATCCATCTCCA 60.503 45.833 0.00 0.00 31.45 3.86
259 261 6.373779 AGATCGTTTTGCTACATTGAAACTG 58.626 36.000 0.00 0.00 31.58 3.16
275 277 6.522625 TGAAACTGTTTTGGAGATTGTTGA 57.477 33.333 7.28 0.00 0.00 3.18
420 430 2.835701 GATGGCGGCGACTGTGAGAA 62.836 60.000 16.45 0.00 0.00 2.87
488 498 1.067084 AGGCGTCAGAGATGCATCG 59.933 57.895 20.67 9.81 45.37 3.84
503 513 3.426117 ATCGATGGTGACCGCGGTC 62.426 63.158 43.88 43.88 44.77 4.79
519 529 1.396653 GGTCTGGGATTCATTGGCAG 58.603 55.000 0.00 0.00 0.00 4.85
609 629 1.421646 CACCTCTTGAGGGTTGGAAGT 59.578 52.381 19.51 0.00 34.44 3.01
610 630 2.637872 CACCTCTTGAGGGTTGGAAGTA 59.362 50.000 19.51 0.00 34.44 2.24
660 680 2.430367 GGCGTGTGGGTCTTTCCT 59.570 61.111 0.00 0.00 36.25 3.36
700 720 3.157881 AGTGAGGAAGAAGACGACATGA 58.842 45.455 0.00 0.00 0.00 3.07
784 808 2.635443 CGAAATTTGGGCTGGCGGT 61.635 57.895 0.00 0.00 0.00 5.68
798 822 4.524318 CGGTCCGGCGCCTAACAT 62.524 66.667 26.68 0.00 0.00 2.71
930 2199 3.397482 CAGGCCATACACTTGAGATAGC 58.603 50.000 5.01 0.00 0.00 2.97
1785 3066 0.460459 GCTCGGCCTACTTCAAGTCC 60.460 60.000 0.00 0.00 0.00 3.85
1790 3071 1.019805 GCCTACTTCAAGTCCGTGCC 61.020 60.000 0.00 0.00 0.00 5.01
1791 3072 0.608640 CCTACTTCAAGTCCGTGCCT 59.391 55.000 0.00 0.00 0.00 4.75
1798 3085 0.247736 CAAGTCCGTGCCTAGCTCTT 59.752 55.000 0.00 0.00 0.00 2.85
1893 3201 1.293179 GTGATTTTGCAGGGTGGCC 59.707 57.895 0.00 0.00 0.00 5.36
2050 3364 2.025605 TCATGCATGGCTTCCTTTCTCT 60.026 45.455 25.97 0.00 0.00 3.10
2101 3415 4.201891 GCAACCAGTCTTAGATCATGCAAG 60.202 45.833 0.00 0.00 0.00 4.01
2103 3417 3.776969 ACCAGTCTTAGATCATGCAAGGA 59.223 43.478 0.00 0.00 0.00 3.36
2105 3419 4.383444 CCAGTCTTAGATCATGCAAGGACA 60.383 45.833 0.00 0.00 0.00 4.02
2121 3435 2.158623 AGGACATGCAAGAACAGTGGAA 60.159 45.455 0.00 0.00 0.00 3.53
2123 3437 3.366679 GGACATGCAAGAACAGTGGAATG 60.367 47.826 0.00 0.00 0.00 2.67
2124 3438 3.225104 ACATGCAAGAACAGTGGAATGT 58.775 40.909 0.00 0.00 33.96 2.71
2126 3440 3.713858 TGCAAGAACAGTGGAATGTTG 57.286 42.857 0.00 0.00 43.32 3.33
2127 3441 2.223782 TGCAAGAACAGTGGAATGTTGC 60.224 45.455 15.92 15.92 43.32 4.17
2128 3442 2.223782 GCAAGAACAGTGGAATGTTGCA 60.224 45.455 17.13 0.00 43.32 4.08
2129 3443 7.960400 ATGCAAGAACAGTGGAATGTTGCAC 62.960 44.000 23.09 9.06 43.43 4.57
2137 3453 2.596346 TGGAATGTTGCACATGGAGTT 58.404 42.857 0.00 0.00 37.97 3.01
2148 3464 4.081752 TGCACATGGAGTTGAGTTTTGTTT 60.082 37.500 0.00 0.00 0.00 2.83
2151 3467 6.672836 GCACATGGAGTTGAGTTTTGTTTTTG 60.673 38.462 0.00 0.00 0.00 2.44
2152 3468 6.589523 CACATGGAGTTGAGTTTTGTTTTTGA 59.410 34.615 0.00 0.00 0.00 2.69
2153 3469 7.278424 CACATGGAGTTGAGTTTTGTTTTTGAT 59.722 33.333 0.00 0.00 0.00 2.57
2156 3472 8.925161 TGGAGTTGAGTTTTGTTTTTGATAAG 57.075 30.769 0.00 0.00 0.00 1.73
2188 3506 1.691434 CTCCTGGCTTCTAGATCCACC 59.309 57.143 9.48 2.83 0.00 4.61
2195 3513 2.615912 GCTTCTAGATCCACCAATGCAC 59.384 50.000 0.00 0.00 0.00 4.57
2205 3523 2.421775 CCACCAATGCACGCAACTATAA 59.578 45.455 0.00 0.00 0.00 0.98
2217 3535 8.708742 TGCACGCAACTATAATATTATTCTCAC 58.291 33.333 13.09 1.42 0.00 3.51
2218 3536 8.708742 GCACGCAACTATAATATTATTCTCACA 58.291 33.333 13.09 0.00 0.00 3.58
2220 3538 9.758651 ACGCAACTATAATATTATTCTCACACA 57.241 29.630 13.09 0.00 0.00 3.72
2231 3549 9.950496 ATATTATTCTCACACAATAGCCTAAGG 57.050 33.333 0.00 0.00 0.00 2.69
2244 3562 2.130272 CCTAAGGCCTCCTTTGGTTC 57.870 55.000 5.23 0.00 46.36 3.62
2245 3563 1.354368 CCTAAGGCCTCCTTTGGTTCA 59.646 52.381 5.23 0.00 46.36 3.18
2246 3564 2.024941 CCTAAGGCCTCCTTTGGTTCAT 60.025 50.000 5.23 0.00 46.36 2.57
2247 3565 3.202151 CCTAAGGCCTCCTTTGGTTCATA 59.798 47.826 5.23 0.00 46.36 2.15
2248 3566 3.372440 AAGGCCTCCTTTGGTTCATAG 57.628 47.619 5.23 0.00 41.69 2.23
2249 3567 1.566231 AGGCCTCCTTTGGTTCATAGG 59.434 52.381 0.00 0.00 34.61 2.57
2250 3568 1.564348 GGCCTCCTTTGGTTCATAGGA 59.436 52.381 0.00 6.86 38.81 2.94
2251 3569 2.175715 GGCCTCCTTTGGTTCATAGGAT 59.824 50.000 0.00 0.00 39.94 3.24
2252 3570 3.394606 GGCCTCCTTTGGTTCATAGGATA 59.605 47.826 0.00 0.00 39.94 2.59
2253 3571 4.505742 GGCCTCCTTTGGTTCATAGGATAG 60.506 50.000 0.00 4.66 39.94 2.08
2254 3572 4.348168 GCCTCCTTTGGTTCATAGGATAGA 59.652 45.833 7.38 0.00 39.94 1.98
2255 3573 5.163195 GCCTCCTTTGGTTCATAGGATAGAA 60.163 44.000 7.38 0.00 39.94 2.10
2256 3574 6.634955 GCCTCCTTTGGTTCATAGGATAGAAA 60.635 42.308 7.38 0.00 39.94 2.52
2257 3575 7.521669 CCTCCTTTGGTTCATAGGATAGAAAT 58.478 38.462 7.38 0.00 39.94 2.17
2258 3576 8.001292 CCTCCTTTGGTTCATAGGATAGAAATT 58.999 37.037 7.38 0.00 39.94 1.82
2259 3577 9.413734 CTCCTTTGGTTCATAGGATAGAAATTT 57.586 33.333 7.38 0.00 39.94 1.82
2260 3578 9.768215 TCCTTTGGTTCATAGGATAGAAATTTT 57.232 29.630 3.54 0.00 36.84 1.82
2294 3612 8.286191 AGGAAAATCATAGGAAGTGAAATGAC 57.714 34.615 0.00 0.00 31.56 3.06
2295 3613 7.890127 AGGAAAATCATAGGAAGTGAAATGACA 59.110 33.333 0.00 0.00 31.56 3.58
2296 3614 8.689972 GGAAAATCATAGGAAGTGAAATGACAT 58.310 33.333 0.00 0.00 31.56 3.06
2297 3615 9.512435 GAAAATCATAGGAAGTGAAATGACATG 57.488 33.333 0.00 0.00 31.56 3.21
2298 3616 6.630444 ATCATAGGAAGTGAAATGACATGC 57.370 37.500 0.00 0.00 31.56 4.06
2299 3617 5.499313 TCATAGGAAGTGAAATGACATGCA 58.501 37.500 0.00 0.00 0.00 3.96
2300 3618 6.124340 TCATAGGAAGTGAAATGACATGCAT 58.876 36.000 0.00 0.00 39.43 3.96
2301 3619 4.978083 AGGAAGTGAAATGACATGCATC 57.022 40.909 0.00 0.00 35.78 3.91
2302 3620 4.597004 AGGAAGTGAAATGACATGCATCT 58.403 39.130 0.00 0.00 35.78 2.90
2303 3621 4.639310 AGGAAGTGAAATGACATGCATCTC 59.361 41.667 0.00 0.00 35.78 2.75
2304 3622 4.397103 GGAAGTGAAATGACATGCATCTCA 59.603 41.667 7.13 7.13 35.78 3.27
2305 3623 5.106038 GGAAGTGAAATGACATGCATCTCAA 60.106 40.000 8.81 0.00 35.82 3.02
2306 3624 6.405508 GGAAGTGAAATGACATGCATCTCAAT 60.406 38.462 8.81 0.00 35.82 2.57
2307 3625 6.525578 AGTGAAATGACATGCATCTCAATT 57.474 33.333 8.81 6.85 35.82 2.32
2308 3626 6.561614 AGTGAAATGACATGCATCTCAATTC 58.438 36.000 19.97 19.97 35.82 2.17
2309 3627 5.747197 GTGAAATGACATGCATCTCAATTCC 59.253 40.000 22.40 13.88 35.82 3.01
2310 3628 4.563337 AATGACATGCATCTCAATTCCG 57.437 40.909 8.81 0.00 35.78 4.30
2311 3629 3.264998 TGACATGCATCTCAATTCCGA 57.735 42.857 1.73 0.00 0.00 4.55
2312 3630 3.812262 TGACATGCATCTCAATTCCGAT 58.188 40.909 1.73 0.00 0.00 4.18
2313 3631 3.562557 TGACATGCATCTCAATTCCGATG 59.437 43.478 1.73 8.47 39.91 3.84
2314 3632 3.548770 ACATGCATCTCAATTCCGATGT 58.451 40.909 0.00 0.00 39.30 3.06
2315 3633 3.562973 ACATGCATCTCAATTCCGATGTC 59.437 43.478 0.00 7.60 39.30 3.06
2316 3634 3.264998 TGCATCTCAATTCCGATGTCA 57.735 42.857 12.58 9.34 39.30 3.58
2317 3635 3.812262 TGCATCTCAATTCCGATGTCAT 58.188 40.909 12.58 0.00 39.30 3.06
2318 3636 4.201657 TGCATCTCAATTCCGATGTCATT 58.798 39.130 12.58 0.00 39.30 2.57
2319 3637 4.641541 TGCATCTCAATTCCGATGTCATTT 59.358 37.500 12.58 0.00 39.30 2.32
2320 3638 4.974275 GCATCTCAATTCCGATGTCATTTG 59.026 41.667 12.58 0.00 39.30 2.32
2321 3639 5.220912 GCATCTCAATTCCGATGTCATTTGA 60.221 40.000 12.58 0.00 39.30 2.69
2322 3640 6.514541 GCATCTCAATTCCGATGTCATTTGAT 60.515 38.462 12.58 0.00 39.30 2.57
2323 3641 6.367686 TCTCAATTCCGATGTCATTTGATG 57.632 37.500 0.00 0.00 0.00 3.07
2324 3642 4.923893 TCAATTCCGATGTCATTTGATGC 58.076 39.130 0.00 0.00 0.00 3.91
2325 3643 4.398673 TCAATTCCGATGTCATTTGATGCA 59.601 37.500 0.00 0.00 0.00 3.96
2326 3644 5.068067 TCAATTCCGATGTCATTTGATGCAT 59.932 36.000 0.00 0.00 32.43 3.96
2327 3645 6.262720 TCAATTCCGATGTCATTTGATGCATA 59.737 34.615 0.00 0.00 30.80 3.14
2328 3646 5.678132 TTCCGATGTCATTTGATGCATAG 57.322 39.130 0.00 0.00 30.80 2.23
2329 3647 4.067192 TCCGATGTCATTTGATGCATAGG 58.933 43.478 0.00 13.10 38.99 2.57
2330 3648 4.067192 CCGATGTCATTTGATGCATAGGA 58.933 43.478 0.00 0.00 39.45 2.94
2331 3649 4.698780 CCGATGTCATTTGATGCATAGGAT 59.301 41.667 0.00 0.00 39.45 3.24
2332 3650 5.876460 CCGATGTCATTTGATGCATAGGATA 59.124 40.000 0.00 0.00 39.45 2.59
2333 3651 6.036844 CCGATGTCATTTGATGCATAGGATAG 59.963 42.308 0.00 0.00 39.45 2.08
2334 3652 6.815142 CGATGTCATTTGATGCATAGGATAGA 59.185 38.462 0.00 0.00 30.80 1.98
2335 3653 7.332678 CGATGTCATTTGATGCATAGGATAGAA 59.667 37.037 0.00 0.00 30.80 2.10
2336 3654 9.175312 GATGTCATTTGATGCATAGGATAGAAT 57.825 33.333 0.00 0.00 30.80 2.40
2337 3655 8.929260 TGTCATTTGATGCATAGGATAGAATT 57.071 30.769 0.00 0.00 0.00 2.17
2338 3656 9.358406 TGTCATTTGATGCATAGGATAGAATTT 57.642 29.630 0.00 0.00 0.00 1.82
2363 3681 8.635765 TTTTTCATTGAGTCTAGGCTAATGTT 57.364 30.769 18.08 0.00 32.22 2.71
2364 3682 8.635765 TTTTCATTGAGTCTAGGCTAATGTTT 57.364 30.769 18.08 0.00 32.22 2.83
2365 3683 8.635765 TTTCATTGAGTCTAGGCTAATGTTTT 57.364 30.769 18.08 0.00 32.22 2.43
2366 3684 8.635765 TTCATTGAGTCTAGGCTAATGTTTTT 57.364 30.769 18.08 0.00 32.22 1.94
2385 3703 4.379339 TTTTTCCTCCAAAACGTGAAGG 57.621 40.909 0.00 0.00 33.47 3.46
2386 3704 3.284793 TTTCCTCCAAAACGTGAAGGA 57.715 42.857 0.00 0.00 0.00 3.36
2387 3705 3.502123 TTCCTCCAAAACGTGAAGGAT 57.498 42.857 3.90 0.00 0.00 3.24
2388 3706 3.502123 TCCTCCAAAACGTGAAGGATT 57.498 42.857 3.90 0.00 0.00 3.01
2389 3707 3.146066 TCCTCCAAAACGTGAAGGATTG 58.854 45.455 3.90 0.40 0.00 2.67
2390 3708 3.146066 CCTCCAAAACGTGAAGGATTGA 58.854 45.455 3.90 0.00 0.00 2.57
2391 3709 3.758554 CCTCCAAAACGTGAAGGATTGAT 59.241 43.478 3.90 0.00 0.00 2.57
2392 3710 4.218417 CCTCCAAAACGTGAAGGATTGATT 59.782 41.667 3.90 0.00 0.00 2.57
2393 3711 5.371115 TCCAAAACGTGAAGGATTGATTC 57.629 39.130 0.00 0.00 0.00 2.52
2394 3712 4.217550 TCCAAAACGTGAAGGATTGATTCC 59.782 41.667 0.00 0.00 45.85 3.01
2437 3755 7.290110 GAATCCATTCCTATAAACCAAAGGG 57.710 40.000 0.00 0.00 41.29 3.95
2438 3756 4.542697 TCCATTCCTATAAACCAAAGGGC 58.457 43.478 0.00 0.00 37.90 5.19
2439 3757 4.231890 TCCATTCCTATAAACCAAAGGGCT 59.768 41.667 0.00 0.00 37.90 5.19
2440 3758 4.962362 CCATTCCTATAAACCAAAGGGCTT 59.038 41.667 0.00 0.00 37.90 4.35
2441 3759 5.069119 CCATTCCTATAAACCAAAGGGCTTC 59.931 44.000 0.00 0.00 37.90 3.86
2442 3760 4.938575 TCCTATAAACCAAAGGGCTTCA 57.061 40.909 0.00 0.00 37.90 3.02
2443 3761 5.263872 TCCTATAAACCAAAGGGCTTCAA 57.736 39.130 0.00 0.00 37.90 2.69
2444 3762 5.646215 TCCTATAAACCAAAGGGCTTCAAA 58.354 37.500 0.00 0.00 37.90 2.69
2445 3763 5.714806 TCCTATAAACCAAAGGGCTTCAAAG 59.285 40.000 0.00 0.00 37.90 2.77
2446 3764 4.890158 ATAAACCAAAGGGCTTCAAAGG 57.110 40.909 0.00 0.00 37.90 3.11
2447 3765 2.470057 AACCAAAGGGCTTCAAAGGA 57.530 45.000 0.00 0.00 37.90 3.36
2448 3766 2.470057 ACCAAAGGGCTTCAAAGGAA 57.530 45.000 0.00 0.00 37.90 3.36
2449 3767 2.976440 ACCAAAGGGCTTCAAAGGAAT 58.024 42.857 0.00 0.00 37.90 3.01
2450 3768 3.317406 ACCAAAGGGCTTCAAAGGAATT 58.683 40.909 0.00 0.00 37.90 2.17
2451 3769 3.716353 ACCAAAGGGCTTCAAAGGAATTT 59.284 39.130 0.00 0.00 37.90 1.82
2452 3770 4.165950 ACCAAAGGGCTTCAAAGGAATTTT 59.834 37.500 0.00 0.00 37.90 1.82
2453 3771 5.132502 CCAAAGGGCTTCAAAGGAATTTTT 58.867 37.500 0.00 0.00 31.34 1.94
2454 3772 5.239306 CCAAAGGGCTTCAAAGGAATTTTTC 59.761 40.000 0.00 0.00 31.34 2.29
2455 3773 9.962289 ACCAAAGGGCTTCAAAGGAATTTTTCC 62.962 40.741 0.00 0.00 44.02 3.13
2470 3788 8.201554 GGAATTTTTCCTTTGCAAATCCTATC 57.798 34.615 13.23 4.40 46.57 2.08
2471 3789 7.280876 GGAATTTTTCCTTTGCAAATCCTATCC 59.719 37.037 13.23 9.41 46.57 2.59
2472 3790 6.933514 TTTTTCCTTTGCAAATCCTATCCT 57.066 33.333 13.23 0.00 0.00 3.24
2473 3791 8.608185 ATTTTTCCTTTGCAAATCCTATCCTA 57.392 30.769 13.23 0.00 0.00 2.94
2474 3792 8.608185 TTTTTCCTTTGCAAATCCTATCCTAT 57.392 30.769 13.23 0.00 0.00 2.57
2475 3793 9.707957 TTTTTCCTTTGCAAATCCTATCCTATA 57.292 29.630 13.23 0.00 0.00 1.31
2476 3794 8.924511 TTTCCTTTGCAAATCCTATCCTATAG 57.075 34.615 13.23 0.00 0.00 1.31
2477 3795 7.872061 TCCTTTGCAAATCCTATCCTATAGA 57.128 36.000 13.23 0.00 0.00 1.98
2478 3796 8.275187 TCCTTTGCAAATCCTATCCTATAGAA 57.725 34.615 13.23 0.00 0.00 2.10
2479 3797 8.894592 TCCTTTGCAAATCCTATCCTATAGAAT 58.105 33.333 13.23 0.00 0.00 2.40
2480 3798 9.525826 CCTTTGCAAATCCTATCCTATAGAATT 57.474 33.333 13.23 0.00 0.00 2.17
2482 3800 9.520515 TTTGCAAATCCTATCCTATAGAATTCC 57.479 33.333 8.05 0.00 0.00 3.01
2483 3801 8.454859 TGCAAATCCTATCCTATAGAATTCCT 57.545 34.615 0.00 0.00 0.00 3.36
2484 3802 9.560860 TGCAAATCCTATCCTATAGAATTCCTA 57.439 33.333 0.00 0.00 0.00 2.94
2506 3824 9.250246 TCCTATAAAATTCCTACAAACCAAAGG 57.750 33.333 0.00 0.00 0.00 3.11
2507 3825 9.250246 CCTATAAAATTCCTACAAACCAAAGGA 57.750 33.333 0.00 0.00 37.64 3.36
2509 3827 6.419484 AAAATTCCTACAAACCAAAGGAGG 57.581 37.500 0.00 0.00 40.43 4.30
2510 3828 2.579410 TCCTACAAACCAAAGGAGGC 57.421 50.000 0.00 0.00 34.46 4.70
2511 3829 1.074889 TCCTACAAACCAAAGGAGGCC 59.925 52.381 0.00 0.00 34.46 5.19
2512 3830 1.075536 CCTACAAACCAAAGGAGGCCT 59.924 52.381 3.86 3.86 33.87 5.19
2513 3831 2.307686 CCTACAAACCAAAGGAGGCCTA 59.692 50.000 4.42 0.00 31.13 3.93
2514 3832 3.245122 CCTACAAACCAAAGGAGGCCTAA 60.245 47.826 4.42 0.00 31.13 2.69
2515 3833 2.876581 ACAAACCAAAGGAGGCCTAAG 58.123 47.619 4.42 0.00 31.13 2.18
2516 3834 2.177016 ACAAACCAAAGGAGGCCTAAGT 59.823 45.455 4.42 0.00 31.13 2.24
2517 3835 3.230976 CAAACCAAAGGAGGCCTAAGTT 58.769 45.455 4.42 0.00 31.13 2.66
2518 3836 3.612795 AACCAAAGGAGGCCTAAGTTT 57.387 42.857 4.42 2.47 31.13 2.66
2519 3837 3.612795 ACCAAAGGAGGCCTAAGTTTT 57.387 42.857 4.42 0.91 31.13 2.43
2520 3838 3.230976 ACCAAAGGAGGCCTAAGTTTTG 58.769 45.455 4.42 13.75 31.13 2.44
2521 3839 3.117284 ACCAAAGGAGGCCTAAGTTTTGA 60.117 43.478 22.45 0.00 31.13 2.69
2522 3840 3.895041 CCAAAGGAGGCCTAAGTTTTGAA 59.105 43.478 22.45 0.00 31.13 2.69
2523 3841 4.528206 CCAAAGGAGGCCTAAGTTTTGAAT 59.472 41.667 22.45 0.00 31.13 2.57
2524 3842 5.012046 CCAAAGGAGGCCTAAGTTTTGAATT 59.988 40.000 22.45 1.66 31.13 2.17
2525 3843 6.464322 CCAAAGGAGGCCTAAGTTTTGAATTT 60.464 38.462 22.45 5.70 31.13 1.82
2526 3844 5.728637 AGGAGGCCTAAGTTTTGAATTTG 57.271 39.130 4.42 0.00 28.47 2.32
2527 3845 4.528206 AGGAGGCCTAAGTTTTGAATTTGG 59.472 41.667 4.42 0.00 28.47 3.28
2528 3846 4.283467 GGAGGCCTAAGTTTTGAATTTGGT 59.717 41.667 4.42 0.00 0.00 3.67
2529 3847 5.221641 GGAGGCCTAAGTTTTGAATTTGGTT 60.222 40.000 4.42 0.00 0.00 3.67
2530 3848 5.853936 AGGCCTAAGTTTTGAATTTGGTTC 58.146 37.500 1.29 0.00 37.35 3.62
2531 3849 5.365314 AGGCCTAAGTTTTGAATTTGGTTCA 59.635 36.000 1.29 0.00 44.87 3.18
2532 3850 5.696270 GGCCTAAGTTTTGAATTTGGTTCAG 59.304 40.000 0.00 0.00 46.85 3.02
2533 3851 6.280643 GCCTAAGTTTTGAATTTGGTTCAGT 58.719 36.000 0.00 0.00 46.85 3.41
2534 3852 6.420903 GCCTAAGTTTTGAATTTGGTTCAGTC 59.579 38.462 0.00 0.00 46.85 3.51
2535 3853 7.488322 CCTAAGTTTTGAATTTGGTTCAGTCA 58.512 34.615 0.00 0.00 46.85 3.41
2536 3854 7.978975 CCTAAGTTTTGAATTTGGTTCAGTCAA 59.021 33.333 0.00 0.00 46.85 3.18
2537 3855 9.533253 CTAAGTTTTGAATTTGGTTCAGTCAAT 57.467 29.630 0.00 0.00 46.85 2.57
2538 3856 8.791327 AAGTTTTGAATTTGGTTCAGTCAATT 57.209 26.923 0.00 0.00 46.85 2.32
2539 3857 8.791327 AGTTTTGAATTTGGTTCAGTCAATTT 57.209 26.923 0.00 0.00 46.85 1.82
2540 3858 9.230122 AGTTTTGAATTTGGTTCAGTCAATTTT 57.770 25.926 0.00 0.00 46.85 1.82
2541 3859 9.489393 GTTTTGAATTTGGTTCAGTCAATTTTC 57.511 29.630 0.00 0.00 46.85 2.29
2542 3860 8.783833 TTTGAATTTGGTTCAGTCAATTTTCA 57.216 26.923 0.00 0.00 46.85 2.69
2583 3901 2.660064 GGGGAGGAAGAAGCTCGCA 61.660 63.158 0.00 0.00 32.66 5.10
2588 3906 2.105466 GGAAGAAGCTCGCAGGCAG 61.105 63.158 0.00 0.00 34.17 4.85
2677 3995 4.206943 AAAAACCGGTCCCCGCCA 62.207 61.111 8.04 0.00 46.86 5.69
2694 4012 0.842635 CCAAGGCTAGAGGAATGGCT 59.157 55.000 0.00 0.00 38.25 4.75
2738 4057 2.125225 GGAGGTTGAGGGGAGGGT 59.875 66.667 0.00 0.00 0.00 4.34
2746 4065 4.423209 AGGGGAGGGTGAGGAGGC 62.423 72.222 0.00 0.00 0.00 4.70
2829 4157 3.680196 GCTGGAGGTAGATGAACAGGAAC 60.680 52.174 0.00 0.00 0.00 3.62
2855 4183 4.287067 TGTTCAGAGGTGGAAGAAAGCTAT 59.713 41.667 0.00 0.00 0.00 2.97
2856 4184 5.483937 TGTTCAGAGGTGGAAGAAAGCTATA 59.516 40.000 0.00 0.00 0.00 1.31
2857 4185 5.599999 TCAGAGGTGGAAGAAAGCTATAC 57.400 43.478 0.00 0.00 0.00 1.47
2858 4186 4.406003 TCAGAGGTGGAAGAAAGCTATACC 59.594 45.833 0.00 0.00 0.00 2.73
2859 4187 3.385111 AGAGGTGGAAGAAAGCTATACCG 59.615 47.826 0.00 0.00 30.94 4.02
2870 4198 0.508641 GCTATACCGCGTTGCATCTG 59.491 55.000 4.92 0.00 0.00 2.90
2943 4271 1.931345 TACCCCTAGCCTCTCCCTTA 58.069 55.000 0.00 0.00 0.00 2.69
2951 4279 4.843516 CCTAGCCTCTCCCTTATTCTCAAT 59.156 45.833 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.340034 TGGATGTACCAAATTGTCGTCC 58.660 45.455 11.51 11.51 46.75 4.79
33 34 0.941463 CTCGCTGCGGATGGATGTAC 60.941 60.000 23.03 0.00 0.00 2.90
141 142 0.992072 CGTTCGATTGTGACATCGCT 59.008 50.000 10.92 0.00 39.86 4.93
164 165 4.718961 GGTGATGGATGTAGCAATTACCT 58.281 43.478 0.00 0.00 0.00 3.08
259 261 7.538303 AAAACACATCAACAATCTCCAAAAC 57.462 32.000 0.00 0.00 0.00 2.43
420 430 1.792949 GCAACATCTCTCGTGTCGTTT 59.207 47.619 0.00 0.00 0.00 3.60
503 513 0.685131 TGGCTGCCAATGAATCCCAG 60.685 55.000 21.08 0.00 0.00 4.45
519 529 3.908081 CCGGGATTGCAGCATGGC 61.908 66.667 0.00 0.00 35.86 4.40
575 585 2.835895 GGTGGTGTTTGCCCCGTT 60.836 61.111 0.00 0.00 0.00 4.44
576 586 3.785122 GAGGTGGTGTTTGCCCCGT 62.785 63.158 0.00 0.00 0.00 5.28
637 657 4.344865 GACCCACACGCCCACCAT 62.345 66.667 0.00 0.00 0.00 3.55
700 720 6.725101 ATTAGATCTGATCCTCTCTCTCCT 57.275 41.667 13.83 0.00 0.00 3.69
784 808 2.822255 GCAATGTTAGGCGCCGGA 60.822 61.111 23.20 10.93 0.00 5.14
798 822 5.592688 GCAATAGTATTTGTCTAAGGGGCAA 59.407 40.000 0.00 0.00 0.00 4.52
912 2181 5.278169 CCATTTGCTATCTCAAGTGTATGGC 60.278 44.000 0.00 0.00 33.50 4.40
930 2199 3.385755 GGATGAGGACCCAAATCCATTTG 59.614 47.826 11.22 5.21 45.04 2.32
969 2241 4.530857 GCGGGATGGAGTGGACGG 62.531 72.222 0.00 0.00 0.00 4.79
970 2242 3.723235 CTGCGGGATGGAGTGGACG 62.723 68.421 0.00 0.00 0.00 4.79
971 2243 2.187946 CTGCGGGATGGAGTGGAC 59.812 66.667 0.00 0.00 0.00 4.02
1798 3085 0.313043 GCTTGCAGCAAGAAAGAGCA 59.687 50.000 34.93 0.00 43.42 4.26
1811 3098 4.039488 AGAAGATTGGTGATTTTGCTTGCA 59.961 37.500 0.00 0.00 0.00 4.08
1817 3105 5.710513 TGGACAGAAGATTGGTGATTTTG 57.289 39.130 0.00 0.00 0.00 2.44
1821 3109 4.916041 TCTTGGACAGAAGATTGGTGAT 57.084 40.909 0.00 0.00 0.00 3.06
1867 3175 3.055675 ACCCTGCAAAATCACATCCATTG 60.056 43.478 0.00 0.00 0.00 2.82
1872 3180 1.404583 GCCACCCTGCAAAATCACATC 60.405 52.381 0.00 0.00 0.00 3.06
1893 3201 0.250234 TCTTGTCCCCGATCAGCTTG 59.750 55.000 0.00 0.00 0.00 4.01
1947 3255 6.499350 AGTTGGTTACTAGGATCTTGGTGTAA 59.501 38.462 3.97 0.94 34.56 2.41
1978 3286 4.890581 CCACTACTACTACTGCTCAAGGAT 59.109 45.833 0.00 0.00 0.00 3.24
2050 3364 4.884744 TGGACGACAGGAAAGAATGAAAAA 59.115 37.500 0.00 0.00 0.00 1.94
2101 3415 1.896220 TCCACTGTTCTTGCATGTCC 58.104 50.000 0.00 0.00 0.00 4.02
2103 3417 3.225104 ACATTCCACTGTTCTTGCATGT 58.775 40.909 0.00 0.00 0.00 3.21
2105 3419 3.553508 GCAACATTCCACTGTTCTTGCAT 60.554 43.478 0.00 0.00 37.25 3.96
2107 3421 2.223782 TGCAACATTCCACTGTTCTTGC 60.224 45.455 0.00 0.00 37.25 4.01
2123 3437 3.715628 AAACTCAACTCCATGTGCAAC 57.284 42.857 0.00 0.00 37.35 4.17
2124 3438 3.446873 ACAAAACTCAACTCCATGTGCAA 59.553 39.130 0.00 0.00 0.00 4.08
2126 3440 3.715628 ACAAAACTCAACTCCATGTGC 57.284 42.857 0.00 0.00 0.00 4.57
2127 3441 6.589523 TCAAAAACAAAACTCAACTCCATGTG 59.410 34.615 0.00 0.00 0.00 3.21
2128 3442 6.696411 TCAAAAACAAAACTCAACTCCATGT 58.304 32.000 0.00 0.00 0.00 3.21
2129 3443 7.775397 ATCAAAAACAAAACTCAACTCCATG 57.225 32.000 0.00 0.00 0.00 3.66
2137 3453 8.073467 ACCTTCCTTATCAAAAACAAAACTCA 57.927 30.769 0.00 0.00 0.00 3.41
2172 3490 2.421952 GCATTGGTGGATCTAGAAGCCA 60.422 50.000 12.33 12.33 0.00 4.75
2205 3523 9.950496 CCTTAGGCTATTGTGTGAGAATAATAT 57.050 33.333 0.00 0.00 0.00 1.28
2224 3542 0.039764 AACCAAAGGAGGCCTTAGGC 59.960 55.000 16.07 16.07 43.92 3.93
2225 3543 1.354368 TGAACCAAAGGAGGCCTTAGG 59.646 52.381 6.77 7.55 43.92 2.69
2226 3544 2.879103 TGAACCAAAGGAGGCCTTAG 57.121 50.000 6.77 0.00 43.92 2.18
2227 3545 3.202151 CCTATGAACCAAAGGAGGCCTTA 59.798 47.826 6.77 0.00 43.92 2.69
2229 3547 1.566231 CCTATGAACCAAAGGAGGCCT 59.434 52.381 3.86 3.86 33.87 5.19
2230 3548 1.564348 TCCTATGAACCAAAGGAGGCC 59.436 52.381 0.00 0.00 34.46 5.19
2231 3549 3.584733 ATCCTATGAACCAAAGGAGGC 57.415 47.619 0.00 0.00 42.53 4.70
2232 3550 6.500589 TTCTATCCTATGAACCAAAGGAGG 57.499 41.667 0.00 0.00 42.53 4.30
2233 3551 8.986929 AATTTCTATCCTATGAACCAAAGGAG 57.013 34.615 0.00 0.00 42.53 3.69
2234 3552 9.768215 AAAATTTCTATCCTATGAACCAAAGGA 57.232 29.630 0.00 0.00 43.38 3.36
2268 3586 9.396022 GTCATTTCACTTCCTATGATTTTCCTA 57.604 33.333 0.00 0.00 30.51 2.94
2269 3587 7.890127 TGTCATTTCACTTCCTATGATTTTCCT 59.110 33.333 0.00 0.00 30.51 3.36
2270 3588 8.055279 TGTCATTTCACTTCCTATGATTTTCC 57.945 34.615 0.00 0.00 30.51 3.13
2271 3589 9.512435 CATGTCATTTCACTTCCTATGATTTTC 57.488 33.333 0.00 0.00 30.51 2.29
2272 3590 7.977853 GCATGTCATTTCACTTCCTATGATTTT 59.022 33.333 0.00 0.00 30.51 1.82
2273 3591 7.123098 TGCATGTCATTTCACTTCCTATGATTT 59.877 33.333 0.00 0.00 30.51 2.17
2274 3592 6.604396 TGCATGTCATTTCACTTCCTATGATT 59.396 34.615 0.00 0.00 30.51 2.57
2275 3593 6.124340 TGCATGTCATTTCACTTCCTATGAT 58.876 36.000 0.00 0.00 30.51 2.45
2276 3594 5.499313 TGCATGTCATTTCACTTCCTATGA 58.501 37.500 0.00 0.00 0.00 2.15
2277 3595 5.823209 TGCATGTCATTTCACTTCCTATG 57.177 39.130 0.00 0.00 0.00 2.23
2278 3596 6.363065 AGATGCATGTCATTTCACTTCCTAT 58.637 36.000 2.46 0.00 35.05 2.57
2279 3597 5.748402 AGATGCATGTCATTTCACTTCCTA 58.252 37.500 2.46 0.00 35.05 2.94
2280 3598 4.597004 AGATGCATGTCATTTCACTTCCT 58.403 39.130 2.46 0.00 35.05 3.36
2281 3599 4.397103 TGAGATGCATGTCATTTCACTTCC 59.603 41.667 21.70 0.00 40.21 3.46
2282 3600 5.556355 TGAGATGCATGTCATTTCACTTC 57.444 39.130 21.70 0.00 40.21 3.01
2283 3601 5.970317 TTGAGATGCATGTCATTTCACTT 57.030 34.783 25.41 0.00 43.42 3.16
2284 3602 6.405508 GGAATTGAGATGCATGTCATTTCACT 60.406 38.462 36.46 19.63 43.42 3.41
2285 3603 5.747197 GGAATTGAGATGCATGTCATTTCAC 59.253 40.000 36.46 28.44 43.42 3.18
2286 3604 5.449451 CGGAATTGAGATGCATGTCATTTCA 60.449 40.000 36.46 22.91 42.45 2.69
2287 3605 4.974275 CGGAATTGAGATGCATGTCATTTC 59.026 41.667 32.69 32.69 38.57 2.17
2288 3606 4.641541 TCGGAATTGAGATGCATGTCATTT 59.358 37.500 25.41 25.37 35.05 2.32
2289 3607 4.201657 TCGGAATTGAGATGCATGTCATT 58.798 39.130 25.41 19.23 35.05 2.57
2290 3608 3.812262 TCGGAATTGAGATGCATGTCAT 58.188 40.909 25.41 13.07 38.32 3.06
2291 3609 3.264998 TCGGAATTGAGATGCATGTCA 57.735 42.857 21.70 21.70 0.00 3.58
2292 3610 3.562973 ACATCGGAATTGAGATGCATGTC 59.437 43.478 16.63 16.63 45.86 3.06
2293 3611 3.548770 ACATCGGAATTGAGATGCATGT 58.451 40.909 2.46 0.00 45.86 3.21
2294 3612 3.562557 TGACATCGGAATTGAGATGCATG 59.437 43.478 2.46 0.00 45.86 4.06
2295 3613 3.812262 TGACATCGGAATTGAGATGCAT 58.188 40.909 15.70 0.00 45.86 3.96
2296 3614 3.264998 TGACATCGGAATTGAGATGCA 57.735 42.857 15.70 12.64 45.86 3.96
2297 3615 4.825546 AATGACATCGGAATTGAGATGC 57.174 40.909 15.70 10.93 45.86 3.91
2298 3616 6.367686 TCAAATGACATCGGAATTGAGATG 57.632 37.500 14.69 14.69 46.95 2.90
2299 3617 6.514541 GCATCAAATGACATCGGAATTGAGAT 60.515 38.462 5.88 0.00 31.14 2.75
2300 3618 5.220912 GCATCAAATGACATCGGAATTGAGA 60.221 40.000 5.88 0.00 31.14 3.27
2301 3619 4.974275 GCATCAAATGACATCGGAATTGAG 59.026 41.667 5.88 1.27 31.14 3.02
2302 3620 4.398673 TGCATCAAATGACATCGGAATTGA 59.601 37.500 2.76 2.76 0.00 2.57
2303 3621 4.674475 TGCATCAAATGACATCGGAATTG 58.326 39.130 0.00 0.00 0.00 2.32
2304 3622 4.987408 TGCATCAAATGACATCGGAATT 57.013 36.364 0.00 0.00 0.00 2.17
2305 3623 5.182570 CCTATGCATCAAATGACATCGGAAT 59.817 40.000 0.19 0.00 34.59 3.01
2306 3624 4.516321 CCTATGCATCAAATGACATCGGAA 59.484 41.667 0.19 0.00 34.59 4.30
2307 3625 4.067192 CCTATGCATCAAATGACATCGGA 58.933 43.478 0.19 0.00 34.59 4.55
2308 3626 4.067192 TCCTATGCATCAAATGACATCGG 58.933 43.478 0.19 1.24 34.30 4.18
2309 3627 5.874895 ATCCTATGCATCAAATGACATCG 57.125 39.130 0.19 0.00 32.25 3.84
2310 3628 8.557592 TTCTATCCTATGCATCAAATGACATC 57.442 34.615 0.19 0.00 32.25 3.06
2311 3629 9.529823 AATTCTATCCTATGCATCAAATGACAT 57.470 29.630 0.19 0.00 33.67 3.06
2312 3630 8.929260 AATTCTATCCTATGCATCAAATGACA 57.071 30.769 0.19 0.00 0.00 3.58
2338 3656 8.635765 AACATTAGCCTAGACTCAATGAAAAA 57.364 30.769 12.01 0.00 32.29 1.94
2339 3657 8.635765 AAACATTAGCCTAGACTCAATGAAAA 57.364 30.769 12.01 0.00 32.29 2.29
2340 3658 8.635765 AAAACATTAGCCTAGACTCAATGAAA 57.364 30.769 12.01 0.00 32.29 2.69
2341 3659 8.635765 AAAAACATTAGCCTAGACTCAATGAA 57.364 30.769 12.01 0.00 32.29 2.57
2370 3688 5.376854 AATCAATCCTTCACGTTTTGGAG 57.623 39.130 6.38 0.00 31.59 3.86
2371 3689 4.217550 GGAATCAATCCTTCACGTTTTGGA 59.782 41.667 3.13 3.13 45.56 3.53
2372 3690 4.485163 GGAATCAATCCTTCACGTTTTGG 58.515 43.478 0.00 0.00 45.56 3.28
2413 3731 6.239317 GCCCTTTGGTTTATAGGAATGGATTC 60.239 42.308 0.00 0.00 36.08 2.52
2414 3732 5.602561 GCCCTTTGGTTTATAGGAATGGATT 59.397 40.000 0.00 0.00 0.00 3.01
2415 3733 5.103086 AGCCCTTTGGTTTATAGGAATGGAT 60.103 40.000 0.00 0.00 0.00 3.41
2416 3734 4.231890 AGCCCTTTGGTTTATAGGAATGGA 59.768 41.667 0.00 0.00 0.00 3.41
2417 3735 4.546674 AGCCCTTTGGTTTATAGGAATGG 58.453 43.478 0.00 0.00 0.00 3.16
2418 3736 5.656416 TGAAGCCCTTTGGTTTATAGGAATG 59.344 40.000 0.00 0.00 34.87 2.67
2419 3737 5.837829 TGAAGCCCTTTGGTTTATAGGAAT 58.162 37.500 0.00 0.00 34.87 3.01
2420 3738 5.263872 TGAAGCCCTTTGGTTTATAGGAA 57.736 39.130 0.00 0.00 34.87 3.36
2421 3739 4.938575 TGAAGCCCTTTGGTTTATAGGA 57.061 40.909 0.00 0.00 34.87 2.94
2422 3740 5.105351 CCTTTGAAGCCCTTTGGTTTATAGG 60.105 44.000 0.00 0.00 34.87 2.57
2423 3741 5.714806 TCCTTTGAAGCCCTTTGGTTTATAG 59.285 40.000 0.00 0.00 34.87 1.31
2424 3742 5.646215 TCCTTTGAAGCCCTTTGGTTTATA 58.354 37.500 0.00 0.00 34.87 0.98
2425 3743 4.488770 TCCTTTGAAGCCCTTTGGTTTAT 58.511 39.130 0.00 0.00 34.87 1.40
2426 3744 3.917300 TCCTTTGAAGCCCTTTGGTTTA 58.083 40.909 0.00 0.00 34.87 2.01
2427 3745 2.758130 TCCTTTGAAGCCCTTTGGTTT 58.242 42.857 0.00 0.00 37.85 3.27
2428 3746 2.470057 TCCTTTGAAGCCCTTTGGTT 57.530 45.000 0.00 0.00 37.39 3.67
2429 3747 2.470057 TTCCTTTGAAGCCCTTTGGT 57.530 45.000 0.00 0.00 0.00 3.67
2430 3748 4.356405 AAATTCCTTTGAAGCCCTTTGG 57.644 40.909 0.00 0.00 33.05 3.28
2431 3749 5.239306 GGAAAAATTCCTTTGAAGCCCTTTG 59.761 40.000 1.86 0.00 46.57 2.77
2432 3750 5.376625 GGAAAAATTCCTTTGAAGCCCTTT 58.623 37.500 1.86 0.00 46.57 3.11
2433 3751 4.973168 GGAAAAATTCCTTTGAAGCCCTT 58.027 39.130 1.86 0.00 46.57 3.95
2434 3752 4.623932 GGAAAAATTCCTTTGAAGCCCT 57.376 40.909 1.86 0.00 46.57 5.19
2446 3764 8.043113 AGGATAGGATTTGCAAAGGAAAAATTC 58.957 33.333 18.19 7.27 0.00 2.17
2447 3765 7.921304 AGGATAGGATTTGCAAAGGAAAAATT 58.079 30.769 18.19 0.00 0.00 1.82
2448 3766 7.500629 AGGATAGGATTTGCAAAGGAAAAAT 57.499 32.000 18.19 6.18 0.00 1.82
2449 3767 6.933514 AGGATAGGATTTGCAAAGGAAAAA 57.066 33.333 18.19 1.42 0.00 1.94
2450 3768 9.354673 CTATAGGATAGGATTTGCAAAGGAAAA 57.645 33.333 18.19 2.48 0.00 2.29
2451 3769 8.723365 TCTATAGGATAGGATTTGCAAAGGAAA 58.277 33.333 18.19 3.91 0.00 3.13
2452 3770 8.275187 TCTATAGGATAGGATTTGCAAAGGAA 57.725 34.615 18.19 3.55 0.00 3.36
2453 3771 7.872061 TCTATAGGATAGGATTTGCAAAGGA 57.128 36.000 18.19 2.96 0.00 3.36
2454 3772 9.525826 AATTCTATAGGATAGGATTTGCAAAGG 57.474 33.333 18.19 0.00 0.00 3.11
2456 3774 9.520515 GGAATTCTATAGGATAGGATTTGCAAA 57.479 33.333 15.44 15.44 0.00 3.68
2457 3775 8.894592 AGGAATTCTATAGGATAGGATTTGCAA 58.105 33.333 5.23 0.00 0.00 4.08
2458 3776 8.454859 AGGAATTCTATAGGATAGGATTTGCA 57.545 34.615 5.23 0.00 0.00 4.08
2480 3798 9.250246 CCTTTGGTTTGTAGGAATTTTATAGGA 57.750 33.333 0.00 0.00 0.00 2.94
2481 3799 9.250246 TCCTTTGGTTTGTAGGAATTTTATAGG 57.750 33.333 0.00 0.00 35.20 2.57
2483 3801 9.250246 CCTCCTTTGGTTTGTAGGAATTTTATA 57.750 33.333 0.00 0.00 37.61 0.98
2484 3802 7.310423 GCCTCCTTTGGTTTGTAGGAATTTTAT 60.310 37.037 0.00 0.00 37.61 1.40
2485 3803 6.014925 GCCTCCTTTGGTTTGTAGGAATTTTA 60.015 38.462 0.00 0.00 37.61 1.52
2486 3804 5.221641 GCCTCCTTTGGTTTGTAGGAATTTT 60.222 40.000 0.00 0.00 37.61 1.82
2487 3805 4.283467 GCCTCCTTTGGTTTGTAGGAATTT 59.717 41.667 0.00 0.00 37.61 1.82
2488 3806 3.832490 GCCTCCTTTGGTTTGTAGGAATT 59.168 43.478 0.00 0.00 37.61 2.17
2489 3807 3.431415 GCCTCCTTTGGTTTGTAGGAAT 58.569 45.455 0.00 0.00 37.61 3.01
2490 3808 2.490168 GGCCTCCTTTGGTTTGTAGGAA 60.490 50.000 0.00 0.00 37.61 3.36
2491 3809 1.074889 GGCCTCCTTTGGTTTGTAGGA 59.925 52.381 0.00 0.00 36.65 2.94
2492 3810 1.075536 AGGCCTCCTTTGGTTTGTAGG 59.924 52.381 0.00 0.00 0.00 3.18
2493 3811 2.586648 AGGCCTCCTTTGGTTTGTAG 57.413 50.000 0.00 0.00 0.00 2.74
2494 3812 3.396611 ACTTAGGCCTCCTTTGGTTTGTA 59.603 43.478 9.68 0.00 34.61 2.41
2495 3813 2.177016 ACTTAGGCCTCCTTTGGTTTGT 59.823 45.455 9.68 0.00 34.61 2.83
2496 3814 2.876581 ACTTAGGCCTCCTTTGGTTTG 58.123 47.619 9.68 0.00 34.61 2.93
2497 3815 3.612795 AACTTAGGCCTCCTTTGGTTT 57.387 42.857 9.68 0.00 34.61 3.27
2498 3816 3.612795 AAACTTAGGCCTCCTTTGGTT 57.387 42.857 9.68 3.79 34.61 3.67
2499 3817 3.117284 TCAAAACTTAGGCCTCCTTTGGT 60.117 43.478 9.68 0.00 34.61 3.67
2500 3818 3.496331 TCAAAACTTAGGCCTCCTTTGG 58.504 45.455 9.68 2.95 34.61 3.28
2501 3819 5.728637 ATTCAAAACTTAGGCCTCCTTTG 57.271 39.130 9.68 14.77 34.61 2.77
2502 3820 6.464322 CCAAATTCAAAACTTAGGCCTCCTTT 60.464 38.462 9.68 1.95 34.61 3.11
2503 3821 5.012046 CCAAATTCAAAACTTAGGCCTCCTT 59.988 40.000 9.68 0.00 34.61 3.36
2504 3822 4.528206 CCAAATTCAAAACTTAGGCCTCCT 59.472 41.667 9.68 0.00 37.71 3.69
2505 3823 4.283467 ACCAAATTCAAAACTTAGGCCTCC 59.717 41.667 9.68 0.00 0.00 4.30
2506 3824 5.468540 ACCAAATTCAAAACTTAGGCCTC 57.531 39.130 9.68 0.00 0.00 4.70
2507 3825 5.365314 TGAACCAAATTCAAAACTTAGGCCT 59.635 36.000 11.78 11.78 44.59 5.19
2508 3826 5.606505 TGAACCAAATTCAAAACTTAGGCC 58.393 37.500 0.00 0.00 44.59 5.19
2509 3827 6.280643 ACTGAACCAAATTCAAAACTTAGGC 58.719 36.000 0.00 0.00 46.80 3.93
2510 3828 7.488322 TGACTGAACCAAATTCAAAACTTAGG 58.512 34.615 0.00 0.00 46.80 2.69
2511 3829 8.925161 TTGACTGAACCAAATTCAAAACTTAG 57.075 30.769 0.00 0.00 46.80 2.18
2512 3830 9.883142 AATTGACTGAACCAAATTCAAAACTTA 57.117 25.926 0.00 0.00 46.80 2.24
2513 3831 8.791327 AATTGACTGAACCAAATTCAAAACTT 57.209 26.923 0.00 0.00 46.80 2.66
2514 3832 8.791327 AAATTGACTGAACCAAATTCAAAACT 57.209 26.923 0.00 0.00 46.80 2.66
2515 3833 9.489393 GAAAATTGACTGAACCAAATTCAAAAC 57.511 29.630 0.00 0.00 46.80 2.43
2516 3834 9.224267 TGAAAATTGACTGAACCAAATTCAAAA 57.776 25.926 0.00 0.00 46.80 2.44
2517 3835 8.663911 GTGAAAATTGACTGAACCAAATTCAAA 58.336 29.630 0.00 0.00 46.80 2.69
2518 3836 8.040132 AGTGAAAATTGACTGAACCAAATTCAA 58.960 29.630 0.00 0.00 46.80 2.69
2519 3837 7.555087 AGTGAAAATTGACTGAACCAAATTCA 58.445 30.769 0.00 0.00 45.39 2.57
2520 3838 9.185192 CTAGTGAAAATTGACTGAACCAAATTC 57.815 33.333 0.00 0.00 37.88 2.17
2521 3839 8.912988 TCTAGTGAAAATTGACTGAACCAAATT 58.087 29.630 0.00 0.00 0.00 1.82
2522 3840 8.463930 TCTAGTGAAAATTGACTGAACCAAAT 57.536 30.769 0.00 0.00 0.00 2.32
2523 3841 7.873719 TCTAGTGAAAATTGACTGAACCAAA 57.126 32.000 0.00 0.00 0.00 3.28
2524 3842 7.013274 CCTTCTAGTGAAAATTGACTGAACCAA 59.987 37.037 0.00 0.00 0.00 3.67
2525 3843 6.486657 CCTTCTAGTGAAAATTGACTGAACCA 59.513 38.462 0.00 0.00 0.00 3.67
2526 3844 6.072452 CCCTTCTAGTGAAAATTGACTGAACC 60.072 42.308 0.00 0.00 0.00 3.62
2527 3845 6.710744 TCCCTTCTAGTGAAAATTGACTGAAC 59.289 38.462 0.00 0.00 0.00 3.18
2528 3846 6.837312 TCCCTTCTAGTGAAAATTGACTGAA 58.163 36.000 0.00 0.00 0.00 3.02
2529 3847 6.270000 TCTCCCTTCTAGTGAAAATTGACTGA 59.730 38.462 0.00 0.00 0.00 3.41
2530 3848 6.467677 TCTCCCTTCTAGTGAAAATTGACTG 58.532 40.000 0.00 0.00 0.00 3.51
2531 3849 6.688073 TCTCCCTTCTAGTGAAAATTGACT 57.312 37.500 0.00 0.00 0.00 3.41
2532 3850 7.228706 TGTTTCTCCCTTCTAGTGAAAATTGAC 59.771 37.037 0.00 0.00 0.00 3.18
2533 3851 7.287061 TGTTTCTCCCTTCTAGTGAAAATTGA 58.713 34.615 0.00 0.00 0.00 2.57
2534 3852 7.510549 TGTTTCTCCCTTCTAGTGAAAATTG 57.489 36.000 0.00 0.00 0.00 2.32
2535 3853 6.207614 GCTGTTTCTCCCTTCTAGTGAAAATT 59.792 38.462 0.00 0.00 0.00 1.82
2536 3854 5.707764 GCTGTTTCTCCCTTCTAGTGAAAAT 59.292 40.000 0.00 0.00 0.00 1.82
2537 3855 5.063880 GCTGTTTCTCCCTTCTAGTGAAAA 58.936 41.667 0.00 0.00 0.00 2.29
2538 3856 4.505039 GGCTGTTTCTCCCTTCTAGTGAAA 60.505 45.833 0.00 0.00 0.00 2.69
2539 3857 3.008049 GGCTGTTTCTCCCTTCTAGTGAA 59.992 47.826 0.00 0.00 0.00 3.18
2540 3858 2.567615 GGCTGTTTCTCCCTTCTAGTGA 59.432 50.000 0.00 0.00 0.00 3.41
2541 3859 2.675317 CGGCTGTTTCTCCCTTCTAGTG 60.675 54.545 0.00 0.00 0.00 2.74
2542 3860 1.550976 CGGCTGTTTCTCCCTTCTAGT 59.449 52.381 0.00 0.00 0.00 2.57
2583 3901 1.386485 ATGATGGGGTAGCCTGCCT 60.386 57.895 11.48 0.00 0.00 4.75
2588 3906 4.407296 CCTAAGATAGATGATGGGGTAGCC 59.593 50.000 1.07 1.07 0.00 3.93
2636 3954 4.719616 GCGAACTTGCACGACCGC 62.720 66.667 14.92 14.92 35.91 5.68
2641 3959 3.777925 CTCCGGCGAACTTGCACG 61.778 66.667 9.30 0.00 36.28 5.34
2673 3991 0.533755 CCATTCCTCTAGCCTTGGCG 60.534 60.000 5.95 0.00 0.00 5.69
2677 3995 2.334023 CCTAGCCATTCCTCTAGCCTT 58.666 52.381 0.00 0.00 32.88 4.35
2738 4057 4.069232 CGTTGCCTCGCCTCCTCA 62.069 66.667 0.00 0.00 0.00 3.86
2775 4094 0.179040 TTCTTCCACAACCACCGTCC 60.179 55.000 0.00 0.00 0.00 4.79
2777 4096 0.834612 TCTTCTTCCACAACCACCGT 59.165 50.000 0.00 0.00 0.00 4.83
2829 4157 3.475566 TTCTTCCACCTCTGAACAGTG 57.524 47.619 1.73 0.00 0.00 3.66
2870 4198 1.204467 TCATTTTTGGCCTTCGGATGC 59.796 47.619 3.32 0.00 0.00 3.91
2943 4271 9.330063 TCGCTTGACTTCAATAATATTGAGAAT 57.670 29.630 14.44 5.80 35.02 2.40
2951 4279 6.345298 TCATGGTCGCTTGACTTCAATAATA 58.655 36.000 0.00 0.00 42.47 0.98


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

AutoCloner maintained by Alex Coulton.