Multiple sequence alignment - TraesCS4B01G308300

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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 TraesCS4B01G308300 chr4B 100.000 3527 0 0 1 3527 599171552 599168026 0.000000e+00 6514.0
1 TraesCS4B01G308300 chr4B 96.202 1290 43 3 938 2224 598914020 598912734 0.000000e+00 2106.0
2 TraesCS4B01G308300 chr4B 94.482 888 43 5 1 887 598914911 598914029 0.000000e+00 1363.0
3 TraesCS4B01G308300 chr4B 90.377 1060 61 20 1 1054 598604260 598603236 0.000000e+00 1354.0
4 TraesCS4B01G308300 chr4B 93.313 658 32 3 2341 2996 598601821 598601174 0.000000e+00 961.0
5 TraesCS4B01G308300 chr4B 85.533 788 82 12 1369 2136 598458866 598458091 0.000000e+00 795.0
6 TraesCS4B01G308300 chr4B 94.978 458 21 2 1889 2345 598602368 598601912 0.000000e+00 717.0
7 TraesCS4B01G308300 chr4B 88.946 588 46 7 2577 3160 598911621 598911049 0.000000e+00 708.0
8 TraesCS4B01G308300 chr4B 95.685 394 17 0 1044 1437 598603090 598602697 5.630000e-178 634.0
9 TraesCS4B01G308300 chr4B 91.500 400 29 4 946 1342 598459257 598458860 2.710000e-151 545.0
10 TraesCS4B01G308300 chr4B 96.386 332 8 2 1524 1852 598602700 598602370 9.760000e-151 544.0
11 TraesCS4B01G308300 chr4B 88.889 342 29 5 42 381 306583179 306583513 2.870000e-111 412.0
12 TraesCS4B01G308300 chr4B 100.000 193 0 0 3803 3995 599167750 599167558 1.370000e-94 357.0
13 TraesCS4B01G308300 chr4B 95.833 168 7 0 2993 3160 598599068 598598901 5.090000e-69 272.0
14 TraesCS4B01G308300 chr4B 88.618 123 8 6 688 805 598459601 598459480 1.160000e-30 145.0
15 TraesCS4B01G308300 chr4B 87.209 86 9 2 2227 2311 2571100 2571184 3.290000e-16 97.1
16 TraesCS4B01G308300 chr4D 95.115 2211 87 12 29 2224 474702305 474700101 0.000000e+00 3465.0
17 TraesCS4B01G308300 chr4D 85.940 1202 107 25 946 2137 474603215 474602066 0.000000e+00 1227.0
18 TraesCS4B01G308300 chr4D 88.994 527 38 8 2638 3160 474698971 474698461 5.630000e-178 634.0
19 TraesCS4B01G308300 chr4D 87.727 220 20 6 592 805 474603614 474603396 2.380000e-62 250.0
20 TraesCS4B01G308300 chr4A 90.728 1704 119 22 460 2137 681592495 681594185 0.000000e+00 2235.0
21 TraesCS4B01G308300 chr4A 89.345 1511 103 29 643 2137 681652845 681654313 0.000000e+00 1845.0
22 TraesCS4B01G308300 chr4A 87.209 86 9 2 2227 2311 733848544 733848628 3.290000e-16 97.1
23 TraesCS4B01G308300 chr4A 82.979 94 11 2 523 615 681652757 681652846 3.310000e-11 80.5
24 TraesCS4B01G308300 chr7D 89.674 368 31 6 3163 3527 94818182 94818545 2.810000e-126 462.0
25 TraesCS4B01G308300 chr7D 89.431 369 34 3 3162 3527 637601059 637600693 1.010000e-125 460.0
26 TraesCS4B01G308300 chr3D 90.251 359 27 2 3163 3519 423008933 423008581 2.810000e-126 462.0
27 TraesCS4B01G308300 chr3D 82.410 415 62 6 1694 2101 5175705 5175295 6.350000e-93 351.0
28 TraesCS4B01G308300 chr3D 90.816 196 16 2 2326 2520 460120992 460120798 1.100000e-65 261.0
29 TraesCS4B01G308300 chr3D 78.440 436 67 13 1171 1603 9543511 9543922 3.960000e-65 259.0
30 TraesCS4B01G308300 chr3B 89.646 367 29 4 3163 3527 743134078 743134437 3.640000e-125 459.0
31 TraesCS4B01G308300 chr3B 78.662 628 82 27 988 1603 13731867 13732454 1.750000e-98 370.0
32 TraesCS4B01G308300 chr3B 91.623 191 13 3 2326 2514 538630825 538630636 1.100000e-65 261.0
33 TraesCS4B01G308300 chr3B 90.476 105 7 2 3888 3992 624146066 624145965 6.960000e-28 135.0
34 TraesCS4B01G308300 chr3B 88.462 104 9 2 3889 3992 731021307 731021207 5.420000e-24 122.0
35 TraesCS4B01G308300 chr3B 87.013 77 6 3 3886 3962 318398637 318398565 2.560000e-12 84.2
36 TraesCS4B01G308300 chr3B 91.837 49 1 2 3889 3937 498496993 498496948 9.270000e-07 65.8
37 TraesCS4B01G308300 chr2B 89.674 368 27 5 3162 3527 718352116 718351758 3.640000e-125 459.0
38 TraesCS4B01G308300 chr2B 89.189 370 28 6 3163 3527 792719456 792719818 6.090000e-123 451.0
39 TraesCS4B01G308300 chr2B 93.717 191 10 1 3807 3995 339233522 339233332 6.530000e-73 285.0
40 TraesCS4B01G308300 chr2B 91.710 193 13 3 2326 2516 133123143 133122952 8.510000e-67 265.0
41 TraesCS4B01G308300 chr2B 91.710 193 13 3 2326 2516 377923650 377923459 8.510000e-67 265.0
42 TraesCS4B01G308300 chr2B 97.297 37 1 0 2536 2572 751257168 751257204 3.330000e-06 63.9
43 TraesCS4B01G308300 chr6D 88.978 372 36 3 3159 3527 431324491 431324860 4.710000e-124 455.0
44 TraesCS4B01G308300 chr5D 89.037 374 31 8 3162 3527 59202082 59201711 4.710000e-124 455.0
45 TraesCS4B01G308300 chr5D 89.160 369 30 5 3162 3527 449217351 449216990 6.090000e-123 451.0
46 TraesCS4B01G308300 chr5B 89.150 341 31 4 41 380 229823157 229822822 1.720000e-113 420.0
47 TraesCS4B01G308300 chr5B 93.194 191 11 1 3807 3995 58004000 58003810 3.040000e-71 279.0
48 TraesCS4B01G308300 chr5B 91.667 192 13 3 2327 2516 164458149 164457959 3.060000e-66 263.0
49 TraesCS4B01G308300 chr5B 88.889 99 10 1 3894 3992 166723225 166723322 1.950000e-23 121.0
50 TraesCS4B01G308300 chr6B 89.086 339 31 4 44 381 526777437 526777104 2.220000e-112 416.0
51 TraesCS4B01G308300 chr6B 88.663 344 32 4 39 380 84861319 84860981 2.870000e-111 412.0
52 TraesCS4B01G308300 chr1B 88.663 344 32 5 39 380 521185095 521185433 2.870000e-111 412.0
53 TraesCS4B01G308300 chr1B 86.047 86 10 2 2227 2311 76786030 76785946 1.530000e-14 91.6
54 TraesCS4B01G308300 chrUn 88.068 352 35 5 33 381 103351189 103351536 1.030000e-110 411.0
55 TraesCS4B01G308300 chr3A 76.329 621 88 23 994 1603 11677520 11676948 1.090000e-70 278.0
56 TraesCS4B01G308300 chr3A 76.167 621 89 23 994 1603 11704966 11704394 5.090000e-69 272.0
57 TraesCS4B01G308300 chr3A 84.874 238 30 2 1866 2100 11704121 11703887 6.670000e-58 235.0
58 TraesCS4B01G308300 chr3A 100.000 28 0 0 2306 2333 28475831 28475804 7.000000e-03 52.8
59 TraesCS4B01G308300 chr7B 91.795 195 12 4 2326 2518 706164755 706164947 6.580000e-68 268.0
60 TraesCS4B01G308300 chr7B 91.710 193 13 3 2326 2516 313088023 313087832 8.510000e-67 265.0
61 TraesCS4B01G308300 chr7B 89.268 205 19 2 2326 2529 274230017 274230219 1.840000e-63 254.0
62 TraesCS4B01G308300 chr1D 89.286 140 13 2 3854 3992 443541278 443541140 1.480000e-39 174.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G308300 chr4B 599167558 599171552 3994 True 3435.500000 6514 100.000000 1 3995 2 chr4B.!!$R4 3994
1 TraesCS4B01G308300 chr4B 598911049 598914911 3862 True 1392.333333 2106 93.210000 1 3160 3 chr4B.!!$R3 3159
2 TraesCS4B01G308300 chr4B 598598901 598604260 5359 True 747.000000 1354 94.428667 1 3160 6 chr4B.!!$R2 3159
3 TraesCS4B01G308300 chr4B 598458091 598459601 1510 True 495.000000 795 88.550333 688 2136 3 chr4B.!!$R1 1448
4 TraesCS4B01G308300 chr4D 474698461 474702305 3844 True 2049.500000 3465 92.054500 29 3160 2 chr4D.!!$R2 3131
5 TraesCS4B01G308300 chr4D 474602066 474603614 1548 True 738.500000 1227 86.833500 592 2137 2 chr4D.!!$R1 1545
6 TraesCS4B01G308300 chr4A 681592495 681594185 1690 False 2235.000000 2235 90.728000 460 2137 1 chr4A.!!$F1 1677
7 TraesCS4B01G308300 chr4A 681652757 681654313 1556 False 962.750000 1845 86.162000 523 2137 2 chr4A.!!$F3 1614
8 TraesCS4B01G308300 chr3B 13731867 13732454 587 False 370.000000 370 78.662000 988 1603 1 chr3B.!!$F1 615
9 TraesCS4B01G308300 chr3A 11676948 11677520 572 True 278.000000 278 76.329000 994 1603 1 chr3A.!!$R1 609
10 TraesCS4B01G308300 chr3A 11703887 11704966 1079 True 253.500000 272 80.520500 994 2100 2 chr3A.!!$R3 1106

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
977 1079 1.070843 CGGTGTCACGTGTGCTTTAAG 60.071 52.381 16.51 0.0 0.00 1.85 F
2235 2617 0.108281 GCAAGGTAGTCCTCCGTTCC 60.108 60.000 0.00 0.0 44.35 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2966 4475 1.615883 TGTTGTTGCCACTGTTGTTGT 59.384 42.857 0.0 0.0 0.00 3.32 R
3334 6953 0.035176 GGTGTTACCAACCGGCACTA 59.965 55.000 0.0 0.0 38.42 2.74 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
68 69 7.012661 TCCCTTCGTTTCTTTATCTAAGGTT 57.987 36.000 0.00 0.00 34.46 3.50
100 101 1.659794 GCACGGTGAACAAGGCAAT 59.340 52.632 13.29 0.00 0.00 3.56
330 336 5.789643 AAGAAATGCACCTTACATTGTGT 57.210 34.783 0.00 0.00 37.78 3.72
542 556 8.601476 GCATCAATACGTAGCTATATAAAACCC 58.399 37.037 0.08 0.00 0.00 4.11
586 600 4.072839 CCTTGGTACTTTGGAAGGAAGAC 58.927 47.826 0.00 0.00 37.74 3.01
974 1076 2.819552 GCGGTGTCACGTGTGCTTT 61.820 57.895 16.51 0.00 35.98 3.51
977 1079 1.070843 CGGTGTCACGTGTGCTTTAAG 60.071 52.381 16.51 0.00 0.00 1.85
1004 1108 7.653647 ACTCTTACCATTTCTATCTCGATGTC 58.346 38.462 0.00 0.00 0.00 3.06
1191 1460 3.031495 CGCGATTCCTCGGAGCTA 58.969 61.111 0.00 0.00 45.15 3.32
1390 1689 4.143333 GCTGGGACTTCGGCGCTA 62.143 66.667 7.64 0.00 0.00 4.26
1499 1798 1.676967 GGGCCTCCACAAAGAGCAG 60.677 63.158 0.84 0.00 32.17 4.24
1885 2254 1.267574 TTCTTCTCGGCAGCTGGGAT 61.268 55.000 17.12 0.00 0.00 3.85
2010 2386 2.095252 GTTCTTGCGGAGGTCGAGC 61.095 63.158 6.48 6.48 42.43 5.03
2235 2617 0.108281 GCAAGGTAGTCCTCCGTTCC 60.108 60.000 0.00 0.00 44.35 3.62
2247 3655 6.193504 AGTCCTCCGTTCCTAAGTATAAGTT 58.806 40.000 0.00 0.00 0.00 2.66
2248 3656 6.666980 AGTCCTCCGTTCCTAAGTATAAGTTT 59.333 38.462 0.00 0.00 0.00 2.66
2278 3688 7.907214 AAAGATTTCACTGTGGACTACATAC 57.093 36.000 8.11 0.00 38.92 2.39
2279 3689 5.651530 AGATTTCACTGTGGACTACATACG 58.348 41.667 8.11 0.00 38.92 3.06
2292 3702 6.370442 TGGACTACATACGAAACAAAATGAGG 59.630 38.462 0.00 0.00 0.00 3.86
2304 3714 7.114811 CGAAACAAAATGAGGGAATTTACACTG 59.885 37.037 0.00 0.00 0.00 3.66
2305 3715 6.976934 ACAAAATGAGGGAATTTACACTGT 57.023 33.333 0.00 0.00 0.00 3.55
2309 3719 9.757227 CAAAATGAGGGAATTTACACTGTAAAA 57.243 29.630 16.48 1.43 0.00 1.52
2313 3723 8.561738 TGAGGGAATTTACACTGTAAAATCTC 57.438 34.615 21.27 19.27 0.00 2.75
2378 3884 3.470709 ACCATGCATGACACATAGTAGC 58.529 45.455 28.31 0.00 0.00 3.58
2453 3959 9.527157 TTTCTTCATTTAATTCTATGACACCCA 57.473 29.630 2.75 0.00 30.89 4.51
2491 3998 7.679783 AGTTGGCATGCATGATACTAAGTATA 58.320 34.615 30.64 0.00 0.00 1.47
2493 4000 8.783093 GTTGGCATGCATGATACTAAGTATAAA 58.217 33.333 30.64 4.56 0.00 1.40
2530 4037 2.373502 AGCCTTAAGATATGCTCCCACC 59.626 50.000 3.36 0.00 0.00 4.61
2533 4040 4.689983 GCCTTAAGATATGCTCCCACCTTT 60.690 45.833 3.36 0.00 0.00 3.11
2550 4057 5.354234 CCACCTTTTCATAATACAAGAGCGT 59.646 40.000 0.00 0.00 0.00 5.07
2722 4231 2.829120 ACAGAGGAACTTCCAGACTAGC 59.171 50.000 10.57 0.00 41.55 3.42
2858 4367 7.716998 CACATCACTTAGGGCTATAACTTCAAT 59.283 37.037 0.00 0.00 0.00 2.57
2901 4410 0.916358 CCATTCAGGTGGAGGAGGGT 60.916 60.000 0.00 0.00 42.02 4.34
2966 4475 3.119531 GCATTGTACCAACATAGCAGCAA 60.120 43.478 0.00 0.00 36.38 3.91
3015 6633 5.888982 AAGACTGGAGAAACAGGAAACTA 57.111 39.130 0.00 0.00 42.75 2.24
3040 6658 6.490566 AAAGCCTAACTACGGTTTTGTATG 57.509 37.500 0.00 0.00 34.30 2.39
3114 6732 8.465999 CAACTACCATTAATTGATGCAAAGGTA 58.534 33.333 4.71 1.38 0.00 3.08
3160 6779 0.248621 GCGCAACAACCTGATATGGC 60.249 55.000 0.30 0.00 0.00 4.40
3161 6780 1.382522 CGCAACAACCTGATATGGCT 58.617 50.000 0.00 0.00 0.00 4.75
3162 6781 1.331756 CGCAACAACCTGATATGGCTC 59.668 52.381 0.00 0.00 0.00 4.70
3163 6782 2.368439 GCAACAACCTGATATGGCTCA 58.632 47.619 0.00 0.00 0.00 4.26
3164 6783 2.098117 GCAACAACCTGATATGGCTCAC 59.902 50.000 0.00 0.00 0.00 3.51
3165 6784 3.614092 CAACAACCTGATATGGCTCACT 58.386 45.455 0.00 0.00 0.00 3.41
3166 6785 4.769688 CAACAACCTGATATGGCTCACTA 58.230 43.478 0.00 0.00 0.00 2.74
3167 6786 4.679373 ACAACCTGATATGGCTCACTAG 57.321 45.455 0.00 0.00 0.00 2.57
3176 6795 4.816990 GCTCACTAGCGGAGAACC 57.183 61.111 14.43 0.00 39.39 3.62
3188 6807 2.816204 GGAGAACCGGGCTATAACTC 57.184 55.000 6.32 3.49 0.00 3.01
3189 6808 1.343789 GGAGAACCGGGCTATAACTCC 59.656 57.143 6.32 8.99 36.23 3.85
3190 6809 1.000496 GAGAACCGGGCTATAACTCCG 60.000 57.143 6.32 0.00 43.05 4.63
3194 6813 3.582743 CGGGCTATAACTCCGGTTC 57.417 57.895 0.00 0.00 40.07 3.62
3195 6814 0.318445 CGGGCTATAACTCCGGTTCG 60.318 60.000 0.00 0.00 40.07 3.95
3196 6815 0.749049 GGGCTATAACTCCGGTTCGT 59.251 55.000 0.00 0.00 36.92 3.85
3197 6816 1.956477 GGGCTATAACTCCGGTTCGTA 59.044 52.381 0.00 0.00 36.92 3.43
3198 6817 2.362077 GGGCTATAACTCCGGTTCGTAA 59.638 50.000 0.00 0.00 36.92 3.18
3199 6818 3.551659 GGGCTATAACTCCGGTTCGTAAG 60.552 52.174 0.00 0.00 36.92 2.34
3200 6819 3.551659 GGCTATAACTCCGGTTCGTAAGG 60.552 52.174 0.00 0.00 36.92 2.69
3201 6820 2.591571 ATAACTCCGGTTCGTAAGGC 57.408 50.000 0.00 0.00 36.92 4.35
3202 6821 0.532115 TAACTCCGGTTCGTAAGGCC 59.468 55.000 0.00 0.00 36.92 5.19
3203 6822 2.176314 AACTCCGGTTCGTAAGGCCC 62.176 60.000 0.00 0.00 38.47 5.80
3204 6823 2.284112 TCCGGTTCGTAAGGCCCT 60.284 61.111 0.00 0.00 38.47 5.19
3205 6824 1.896122 CTCCGGTTCGTAAGGCCCTT 61.896 60.000 0.00 0.00 38.47 3.95
3206 6825 1.002990 CCGGTTCGTAAGGCCCTTT 60.003 57.895 0.00 0.00 38.47 3.11
3207 6826 0.249955 CCGGTTCGTAAGGCCCTTTA 59.750 55.000 0.00 0.00 38.47 1.85
3208 6827 1.648504 CGGTTCGTAAGGCCCTTTAG 58.351 55.000 0.00 0.00 38.47 1.85
3209 6828 1.066645 CGGTTCGTAAGGCCCTTTAGT 60.067 52.381 0.00 0.00 38.47 2.24
3210 6829 2.353323 GGTTCGTAAGGCCCTTTAGTG 58.647 52.381 0.00 0.00 38.47 2.74
3211 6830 1.736126 GTTCGTAAGGCCCTTTAGTGC 59.264 52.381 0.00 0.00 38.47 4.40
3216 6835 2.035155 GGCCCTTTAGTGCCGGTT 59.965 61.111 1.90 0.00 38.00 4.44
3217 6836 2.044555 GGCCCTTTAGTGCCGGTTC 61.045 63.158 1.90 0.00 38.00 3.62
3218 6837 1.002502 GCCCTTTAGTGCCGGTTCT 60.003 57.895 1.90 4.41 0.00 3.01
3219 6838 1.305930 GCCCTTTAGTGCCGGTTCTG 61.306 60.000 1.90 0.00 0.00 3.02
3220 6839 0.036306 CCCTTTAGTGCCGGTTCTGT 59.964 55.000 1.90 0.00 0.00 3.41
3221 6840 1.276989 CCCTTTAGTGCCGGTTCTGTA 59.723 52.381 1.90 0.00 0.00 2.74
3222 6841 2.289819 CCCTTTAGTGCCGGTTCTGTAA 60.290 50.000 1.90 1.06 0.00 2.41
3223 6842 3.606687 CCTTTAGTGCCGGTTCTGTAAT 58.393 45.455 1.90 0.00 0.00 1.89
3224 6843 3.621715 CCTTTAGTGCCGGTTCTGTAATC 59.378 47.826 1.90 0.00 0.00 1.75
3225 6844 2.572191 TAGTGCCGGTTCTGTAATCG 57.428 50.000 1.90 0.00 38.99 3.34
3233 6852 4.868450 CGGTTCTGTAATCGGCATTAAA 57.132 40.909 0.00 0.00 35.52 1.52
3234 6853 5.224562 CGGTTCTGTAATCGGCATTAAAA 57.775 39.130 0.00 0.00 35.52 1.52
3235 6854 5.263185 CGGTTCTGTAATCGGCATTAAAAG 58.737 41.667 0.00 0.00 35.52 2.27
3236 6855 5.064198 CGGTTCTGTAATCGGCATTAAAAGA 59.936 40.000 0.00 0.00 35.52 2.52
3237 6856 6.238374 CGGTTCTGTAATCGGCATTAAAAGAT 60.238 38.462 0.00 0.00 35.52 2.40
3238 6857 6.912591 GGTTCTGTAATCGGCATTAAAAGATG 59.087 38.462 0.00 0.00 0.00 2.90
3239 6858 6.618287 TCTGTAATCGGCATTAAAAGATGG 57.382 37.500 0.00 0.00 0.00 3.51
3240 6859 5.530915 TCTGTAATCGGCATTAAAAGATGGG 59.469 40.000 0.00 0.00 0.00 4.00
3241 6860 4.582656 TGTAATCGGCATTAAAAGATGGGG 59.417 41.667 0.00 0.00 0.00 4.96
3242 6861 3.593442 ATCGGCATTAAAAGATGGGGA 57.407 42.857 0.00 0.00 0.00 4.81
3243 6862 2.650322 TCGGCATTAAAAGATGGGGAC 58.350 47.619 0.00 0.00 0.00 4.46
3244 6863 2.241176 TCGGCATTAAAAGATGGGGACT 59.759 45.455 0.00 0.00 0.00 3.85
3245 6864 3.456644 TCGGCATTAAAAGATGGGGACTA 59.543 43.478 0.00 0.00 0.00 2.59
3246 6865 4.080243 TCGGCATTAAAAGATGGGGACTAA 60.080 41.667 0.00 0.00 0.00 2.24
3247 6866 4.642885 CGGCATTAAAAGATGGGGACTAAA 59.357 41.667 0.00 0.00 0.00 1.85
3248 6867 5.301805 CGGCATTAAAAGATGGGGACTAAAT 59.698 40.000 0.00 0.00 0.00 1.40
3249 6868 6.515832 GGCATTAAAAGATGGGGACTAAATG 58.484 40.000 0.00 0.00 0.00 2.32
3250 6869 6.098266 GGCATTAAAAGATGGGGACTAAATGT 59.902 38.462 0.00 0.00 0.00 2.71
3251 6870 7.203218 GCATTAAAAGATGGGGACTAAATGTC 58.797 38.462 0.00 0.00 44.63 3.06
3265 6884 6.218108 ACTAAATGTCCTCCTTTAGTACCG 57.782 41.667 6.03 0.00 43.08 4.02
3266 6885 4.482952 AAATGTCCTCCTTTAGTACCGG 57.517 45.455 0.00 0.00 0.00 5.28
3267 6886 2.610438 TGTCCTCCTTTAGTACCGGT 57.390 50.000 13.98 13.98 0.00 5.28
3268 6887 2.893424 TGTCCTCCTTTAGTACCGGTT 58.107 47.619 15.04 0.00 0.00 4.44
3269 6888 2.827921 TGTCCTCCTTTAGTACCGGTTC 59.172 50.000 15.04 8.12 0.00 3.62
3270 6889 3.095332 GTCCTCCTTTAGTACCGGTTCT 58.905 50.000 15.04 17.06 0.00 3.01
3271 6890 3.094572 TCCTCCTTTAGTACCGGTTCTG 58.905 50.000 22.71 6.94 0.00 3.02
3272 6891 2.418334 CCTCCTTTAGTACCGGTTCTGC 60.418 54.545 22.71 6.98 0.00 4.26
3273 6892 2.232941 CTCCTTTAGTACCGGTTCTGCA 59.767 50.000 22.71 7.36 0.00 4.41
3274 6893 2.028748 TCCTTTAGTACCGGTTCTGCAC 60.029 50.000 22.71 10.16 0.00 4.57
3275 6894 1.990563 CTTTAGTACCGGTTCTGCACG 59.009 52.381 22.71 4.46 0.00 5.34
3276 6895 1.246649 TTAGTACCGGTTCTGCACGA 58.753 50.000 22.71 3.53 0.00 4.35
3277 6896 1.246649 TAGTACCGGTTCTGCACGAA 58.753 50.000 22.71 0.00 0.00 3.85
3283 6902 4.072088 GTTCTGCACGAACCGCCG 62.072 66.667 14.47 0.00 45.00 6.46
3287 6906 4.666397 TGCACGAACCGCCGCTAA 62.666 61.111 0.00 0.00 31.41 3.09
3288 6907 3.416382 GCACGAACCGCCGCTAAA 61.416 61.111 0.00 0.00 0.00 1.85
3289 6908 2.776072 CACGAACCGCCGCTAAAG 59.224 61.111 0.00 0.00 0.00 1.85
3290 6909 2.433664 ACGAACCGCCGCTAAAGG 60.434 61.111 0.00 0.00 0.00 3.11
3291 6910 3.192922 CGAACCGCCGCTAAAGGG 61.193 66.667 0.00 0.00 0.00 3.95
3297 6916 4.733542 GCCGCTAAAGGGCCACCA 62.734 66.667 6.18 0.00 44.97 4.17
3298 6917 2.750237 CCGCTAAAGGGCCACCAC 60.750 66.667 6.18 0.00 40.13 4.16
3299 6918 3.124921 CGCTAAAGGGCCACCACG 61.125 66.667 6.18 0.00 40.13 4.94
3300 6919 2.033602 GCTAAAGGGCCACCACGT 59.966 61.111 6.18 0.00 40.13 4.49
3301 6920 2.332654 GCTAAAGGGCCACCACGTG 61.333 63.158 9.08 9.08 40.13 4.49
3338 6957 2.124695 GCGGGGAGCCCTTTAGTG 60.125 66.667 5.38 0.00 42.67 2.74
3339 6958 2.124695 CGGGGAGCCCTTTAGTGC 60.125 66.667 5.38 0.00 42.67 4.40
3340 6959 2.275748 GGGGAGCCCTTTAGTGCC 59.724 66.667 5.38 0.00 41.34 5.01
3341 6960 2.124695 GGGAGCCCTTTAGTGCCG 60.125 66.667 0.00 0.00 0.00 5.69
3342 6961 2.124695 GGAGCCCTTTAGTGCCGG 60.125 66.667 0.00 0.00 0.00 6.13
3343 6962 2.669240 GAGCCCTTTAGTGCCGGT 59.331 61.111 1.90 0.00 0.00 5.28
3344 6963 1.002502 GAGCCCTTTAGTGCCGGTT 60.003 57.895 1.90 0.00 0.00 4.44
3345 6964 1.303317 AGCCCTTTAGTGCCGGTTG 60.303 57.895 1.90 0.00 0.00 3.77
3346 6965 2.340328 GCCCTTTAGTGCCGGTTGG 61.340 63.158 1.90 0.00 38.77 3.77
3347 6966 1.074248 CCCTTTAGTGCCGGTTGGT 59.926 57.895 1.90 0.00 37.67 3.67
3348 6967 0.325602 CCCTTTAGTGCCGGTTGGTA 59.674 55.000 1.90 0.00 37.67 3.25
3349 6968 1.271488 CCCTTTAGTGCCGGTTGGTAA 60.271 52.381 1.90 0.00 37.67 2.85
3350 6969 1.808343 CCTTTAGTGCCGGTTGGTAAC 59.192 52.381 1.90 0.00 37.67 2.50
3368 6987 6.799926 GGTAACACCAATCGGTACTAAAAA 57.200 37.500 0.00 0.00 46.94 1.94
3369 6988 6.834876 GGTAACACCAATCGGTACTAAAAAG 58.165 40.000 0.00 0.00 46.94 2.27
3370 6989 6.427853 GGTAACACCAATCGGTACTAAAAAGT 59.572 38.462 0.00 0.00 46.94 2.66
3371 6990 6.947644 AACACCAATCGGTACTAAAAAGTT 57.052 33.333 0.00 0.00 46.94 2.66
3372 6991 6.947644 ACACCAATCGGTACTAAAAAGTTT 57.052 33.333 0.00 0.00 46.94 2.66
3373 6992 7.337480 ACACCAATCGGTACTAAAAAGTTTT 57.663 32.000 0.00 0.00 46.94 2.43
3374 6993 7.197703 ACACCAATCGGTACTAAAAAGTTTTG 58.802 34.615 0.61 0.00 46.94 2.44
3375 6994 6.639279 CACCAATCGGTACTAAAAAGTTTTGG 59.361 38.462 0.61 1.17 46.94 3.28
3376 6995 6.153756 CCAATCGGTACTAAAAAGTTTTGGG 58.846 40.000 0.61 0.82 33.54 4.12
3377 6996 5.970317 ATCGGTACTAAAAAGTTTTGGGG 57.030 39.130 0.61 0.00 33.54 4.96
3378 6997 4.143543 TCGGTACTAAAAAGTTTTGGGGG 58.856 43.478 0.61 0.00 33.54 5.40
3379 6998 3.890756 CGGTACTAAAAAGTTTTGGGGGT 59.109 43.478 0.61 2.06 33.54 4.95
3380 6999 4.341806 CGGTACTAAAAAGTTTTGGGGGTT 59.658 41.667 0.61 0.00 33.54 4.11
3381 7000 5.163426 CGGTACTAAAAAGTTTTGGGGGTTT 60.163 40.000 0.61 0.00 33.54 3.27
3382 7001 6.629963 CGGTACTAAAAAGTTTTGGGGGTTTT 60.630 38.462 0.61 0.00 33.54 2.43
3383 7002 6.539464 GGTACTAAAAAGTTTTGGGGGTTTTG 59.461 38.462 0.61 0.00 33.54 2.44
3384 7003 6.129414 ACTAAAAAGTTTTGGGGGTTTTGT 57.871 33.333 0.61 0.00 33.54 2.83
3385 7004 6.544650 ACTAAAAAGTTTTGGGGGTTTTGTT 58.455 32.000 0.61 0.00 33.54 2.83
3386 7005 7.005296 ACTAAAAAGTTTTGGGGGTTTTGTTT 58.995 30.769 0.61 0.00 33.54 2.83
3387 7006 6.732896 AAAAAGTTTTGGGGGTTTTGTTTT 57.267 29.167 0.61 0.00 0.00 2.43
3388 7007 6.732896 AAAAGTTTTGGGGGTTTTGTTTTT 57.267 29.167 0.00 0.00 0.00 1.94
3389 7008 7.834881 AAAAGTTTTGGGGGTTTTGTTTTTA 57.165 28.000 0.00 0.00 0.00 1.52
3390 7009 8.423906 AAAAGTTTTGGGGGTTTTGTTTTTAT 57.576 26.923 0.00 0.00 0.00 1.40
3391 7010 8.423906 AAAGTTTTGGGGGTTTTGTTTTTATT 57.576 26.923 0.00 0.00 0.00 1.40
3392 7011 9.529823 AAAGTTTTGGGGGTTTTGTTTTTATTA 57.470 25.926 0.00 0.00 0.00 0.98
3393 7012 9.702253 AAGTTTTGGGGGTTTTGTTTTTATTAT 57.298 25.926 0.00 0.00 0.00 1.28
3394 7013 9.702253 AGTTTTGGGGGTTTTGTTTTTATTATT 57.298 25.926 0.00 0.00 0.00 1.40
3458 7077 9.757859 TTTTCGTTTGATGGTATTTTACGATAC 57.242 29.630 0.00 0.00 36.58 2.24
3459 7078 8.706492 TTCGTTTGATGGTATTTTACGATACT 57.294 30.769 0.00 0.00 36.58 2.12
3460 7079 9.800433 TTCGTTTGATGGTATTTTACGATACTA 57.200 29.630 0.00 0.00 36.58 1.82
3461 7080 9.236691 TCGTTTGATGGTATTTTACGATACTAC 57.763 33.333 0.00 0.00 33.86 2.73
3462 7081 9.022915 CGTTTGATGGTATTTTACGATACTACA 57.977 33.333 0.00 0.00 33.86 2.74
3520 7139 9.877178 AAATAGAATTTCTCGTAGAACTGATGT 57.123 29.630 1.27 0.00 33.26 3.06
3840 7459 9.953697 AACTATTTAGATCACGATCAACTCTAC 57.046 33.333 9.60 0.00 40.22 2.59
3841 7460 9.121658 ACTATTTAGATCACGATCAACTCTACA 57.878 33.333 9.60 0.00 40.22 2.74
3842 7461 9.605955 CTATTTAGATCACGATCAACTCTACAG 57.394 37.037 9.60 0.00 40.22 2.74
3843 7462 4.909696 AGATCACGATCAACTCTACAGG 57.090 45.455 9.60 0.00 40.22 4.00
3844 7463 3.634448 AGATCACGATCAACTCTACAGGG 59.366 47.826 9.60 0.00 40.22 4.45
3845 7464 1.476891 TCACGATCAACTCTACAGGGC 59.523 52.381 0.00 0.00 0.00 5.19
3846 7465 0.456221 ACGATCAACTCTACAGGGCG 59.544 55.000 0.00 0.00 0.00 6.13
3847 7466 0.872021 CGATCAACTCTACAGGGCGC 60.872 60.000 0.00 0.00 0.00 6.53
3848 7467 0.872021 GATCAACTCTACAGGGCGCG 60.872 60.000 0.00 0.00 0.00 6.86
3849 7468 1.605058 ATCAACTCTACAGGGCGCGT 61.605 55.000 8.43 0.00 0.00 6.01
3850 7469 1.374252 CAACTCTACAGGGCGCGTT 60.374 57.895 8.43 0.00 0.00 4.84
3851 7470 1.374252 AACTCTACAGGGCGCGTTG 60.374 57.895 8.43 4.56 0.00 4.10
3852 7471 3.188786 CTCTACAGGGCGCGTTGC 61.189 66.667 8.43 0.00 45.38 4.17
3864 7483 2.355363 CGTTGCAGACGTTCCCGA 60.355 61.111 11.62 0.00 46.49 5.14
3865 7484 1.952133 CGTTGCAGACGTTCCCGAA 60.952 57.895 11.62 0.00 46.49 4.30
3866 7485 1.568025 GTTGCAGACGTTCCCGAAC 59.432 57.895 0.00 0.00 37.88 3.95
3867 7486 0.878961 GTTGCAGACGTTCCCGAACT 60.879 55.000 6.06 0.00 39.08 3.01
3868 7487 0.599204 TTGCAGACGTTCCCGAACTC 60.599 55.000 6.06 3.31 39.08 3.01
3869 7488 1.737008 GCAGACGTTCCCGAACTCC 60.737 63.158 6.06 0.00 39.08 3.85
3870 7489 1.080025 CAGACGTTCCCGAACTCCC 60.080 63.158 6.06 0.00 39.08 4.30
3871 7490 2.126189 GACGTTCCCGAACTCCCG 60.126 66.667 6.06 0.00 39.08 5.14
3872 7491 2.598394 ACGTTCCCGAACTCCCGA 60.598 61.111 6.06 0.00 39.08 5.14
3873 7492 2.146073 GACGTTCCCGAACTCCCGAA 62.146 60.000 6.06 0.00 39.08 4.30
3874 7493 1.735559 CGTTCCCGAACTCCCGAAC 60.736 63.158 6.06 0.00 39.08 3.95
3875 7494 1.375140 GTTCCCGAACTCCCGAACC 60.375 63.158 0.22 0.00 38.25 3.62
3876 7495 2.934570 TTCCCGAACTCCCGAACCG 61.935 63.158 0.00 0.00 0.00 4.44
3887 7506 2.260434 CGAACCGGCGGAGAAGAA 59.740 61.111 35.78 0.00 0.00 2.52
3888 7507 1.373748 CGAACCGGCGGAGAAGAAA 60.374 57.895 35.78 0.00 0.00 2.52
3889 7508 0.947180 CGAACCGGCGGAGAAGAAAA 60.947 55.000 35.78 0.00 0.00 2.29
3890 7509 1.232119 GAACCGGCGGAGAAGAAAAA 58.768 50.000 35.78 0.00 0.00 1.94
3907 7526 2.375014 AAAAGAAAAAGCCCTCCCGA 57.625 45.000 0.00 0.00 0.00 5.14
3908 7527 1.617322 AAAGAAAAAGCCCTCCCGAC 58.383 50.000 0.00 0.00 0.00 4.79
3909 7528 0.251209 AAGAAAAAGCCCTCCCGACC 60.251 55.000 0.00 0.00 0.00 4.79
3910 7529 1.134438 AGAAAAAGCCCTCCCGACCT 61.134 55.000 0.00 0.00 0.00 3.85
3911 7530 0.251209 GAAAAAGCCCTCCCGACCTT 60.251 55.000 0.00 0.00 0.00 3.50
3912 7531 1.003928 GAAAAAGCCCTCCCGACCTTA 59.996 52.381 0.00 0.00 0.00 2.69
3913 7532 1.296002 AAAAGCCCTCCCGACCTTAT 58.704 50.000 0.00 0.00 0.00 1.73
3914 7533 0.837940 AAAGCCCTCCCGACCTTATC 59.162 55.000 0.00 0.00 0.00 1.75
3915 7534 1.054978 AAGCCCTCCCGACCTTATCC 61.055 60.000 0.00 0.00 0.00 2.59
3916 7535 2.517798 GCCCTCCCGACCTTATCCC 61.518 68.421 0.00 0.00 0.00 3.85
3917 7536 1.842010 CCCTCCCGACCTTATCCCC 60.842 68.421 0.00 0.00 0.00 4.81
3918 7537 1.074775 CCTCCCGACCTTATCCCCA 60.075 63.158 0.00 0.00 0.00 4.96
3919 7538 1.408453 CCTCCCGACCTTATCCCCAC 61.408 65.000 0.00 0.00 0.00 4.61
3920 7539 1.745320 CTCCCGACCTTATCCCCACG 61.745 65.000 0.00 0.00 0.00 4.94
3921 7540 2.108362 CCGACCTTATCCCCACGC 59.892 66.667 0.00 0.00 0.00 5.34
3922 7541 2.108362 CGACCTTATCCCCACGCC 59.892 66.667 0.00 0.00 0.00 5.68
3923 7542 2.509422 GACCTTATCCCCACGCCC 59.491 66.667 0.00 0.00 0.00 6.13
3924 7543 3.456105 GACCTTATCCCCACGCCCG 62.456 68.421 0.00 0.00 0.00 6.13
3925 7544 4.929707 CCTTATCCCCACGCCCGC 62.930 72.222 0.00 0.00 0.00 6.13
3926 7545 3.861797 CTTATCCCCACGCCCGCT 61.862 66.667 0.00 0.00 0.00 5.52
3927 7546 3.809374 CTTATCCCCACGCCCGCTC 62.809 68.421 0.00 0.00 0.00 5.03
3928 7547 4.853142 TATCCCCACGCCCGCTCT 62.853 66.667 0.00 0.00 0.00 4.09
3929 7548 2.932569 TTATCCCCACGCCCGCTCTA 62.933 60.000 0.00 0.00 0.00 2.43
3937 7556 4.971125 GCCCGCTCTACGCCATCC 62.971 72.222 0.00 0.00 41.76 3.51
3938 7557 4.301027 CCCGCTCTACGCCATCCC 62.301 72.222 0.00 0.00 41.76 3.85
3939 7558 4.301027 CCGCTCTACGCCATCCCC 62.301 72.222 0.00 0.00 41.76 4.81
3940 7559 4.647615 CGCTCTACGCCATCCCCG 62.648 72.222 0.00 0.00 34.21 5.73
3941 7560 4.971125 GCTCTACGCCATCCCCGC 62.971 72.222 0.00 0.00 0.00 6.13
3942 7561 4.301027 CTCTACGCCATCCCCGCC 62.301 72.222 0.00 0.00 0.00 6.13
3960 7579 4.101448 CCCTCGGCACCTTCCCAG 62.101 72.222 0.00 0.00 0.00 4.45
3962 7581 4.785453 CTCGGCACCTTCCCAGGC 62.785 72.222 0.00 0.00 45.56 4.85
3966 7585 4.666253 GCACCTTCCCAGGCAGCA 62.666 66.667 0.00 0.00 45.56 4.41
3967 7586 2.360852 CACCTTCCCAGGCAGCAG 60.361 66.667 0.00 0.00 45.56 4.24
3968 7587 3.655211 ACCTTCCCAGGCAGCAGG 61.655 66.667 0.00 0.00 45.56 4.85
3993 7612 3.334054 GCAGGCACCTCCCTCCTT 61.334 66.667 0.00 0.00 31.24 3.36
3994 7613 2.673523 CAGGCACCTCCCTCCTTG 59.326 66.667 0.00 0.00 31.24 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
297 303 6.436843 AGGTGCATTTCTTTTAATACCTCG 57.563 37.500 0.00 0.00 32.09 4.63
307 313 6.160576 ACACAATGTAAGGTGCATTTCTTT 57.839 33.333 0.00 0.00 38.57 2.52
445 457 7.844493 AAGGGCATGTACAATGATTGATAAT 57.156 32.000 12.80 0.00 0.00 1.28
564 578 4.072839 GTCTTCCTTCCAAAGTACCAAGG 58.927 47.826 0.00 0.00 37.36 3.61
827 859 0.037975 GAGCGTTAAGGTCCCGTCAA 60.038 55.000 0.00 0.00 41.28 3.18
974 1076 9.842775 TCGAGATAGAAATGGTAAGAGTACTTA 57.157 33.333 0.00 0.00 37.53 2.24
977 1079 8.569641 ACATCGAGATAGAAATGGTAAGAGTAC 58.430 37.037 0.00 0.00 0.00 2.73
1004 1108 1.515088 CACTGACCTAGCTCGTGCG 60.515 63.158 3.48 0.00 45.42 5.34
1191 1460 1.139058 AGACTGTTCTGTGCTTCCGTT 59.861 47.619 0.00 0.00 0.00 4.44
1885 2254 2.124320 GGCTCCTATTTGCCGGCA 60.124 61.111 29.03 29.03 39.71 5.69
2010 2386 2.202987 GATGCGGAGGTGGAGCTG 60.203 66.667 0.00 0.00 0.00 4.24
2224 2606 6.462552 AACTTATACTTAGGAACGGAGGAC 57.537 41.667 0.00 0.00 0.00 3.85
2278 3688 7.114811 CAGTGTAAATTCCCTCATTTTGTTTCG 59.885 37.037 0.00 0.00 0.00 3.46
2279 3689 7.926018 ACAGTGTAAATTCCCTCATTTTGTTTC 59.074 33.333 0.00 0.00 0.00 2.78
2357 3863 3.118298 TGCTACTATGTGTCATGCATGGT 60.118 43.478 25.97 15.83 40.35 3.55
2358 3864 3.469739 TGCTACTATGTGTCATGCATGG 58.530 45.455 25.97 10.76 0.00 3.66
2491 3998 6.724893 AAGGCTGGTTGTAATGTTAGTTTT 57.275 33.333 0.00 0.00 0.00 2.43
2493 4000 7.228590 TCTTAAGGCTGGTTGTAATGTTAGTT 58.771 34.615 1.85 0.00 0.00 2.24
2498 4005 6.263168 GCATATCTTAAGGCTGGTTGTAATGT 59.737 38.462 1.85 0.00 0.00 2.71
2530 4037 9.180678 ACAAAAACGCTCTTGTATTATGAAAAG 57.819 29.630 0.00 0.00 34.04 2.27
2533 4040 7.302524 GGACAAAAACGCTCTTGTATTATGAA 58.697 34.615 0.00 0.00 35.93 2.57
2702 4211 2.159310 CGCTAGTCTGGAAGTTCCTCTG 60.159 54.545 22.41 12.49 37.46 3.35
2713 4222 2.507102 CACACGCCGCTAGTCTGG 60.507 66.667 0.00 0.00 0.00 3.86
2722 4231 2.552585 ATCCTTACGACCACACGCCG 62.553 60.000 0.00 0.00 36.70 6.46
2858 4367 7.776030 TGGTAAAGTCAGTAAGTCCATGAAAAA 59.224 33.333 0.00 0.00 0.00 1.94
2901 4410 3.385433 TCTCCTCTGTGTTGACGGTAAAA 59.615 43.478 0.00 0.00 0.00 1.52
2966 4475 1.615883 TGTTGTTGCCACTGTTGTTGT 59.384 42.857 0.00 0.00 0.00 3.32
3015 6633 5.840243 ACAAAACCGTAGTTAGGCTTTTT 57.160 34.783 0.00 0.00 34.19 1.94
3142 6761 1.331756 GAGCCATATCAGGTTGTTGCG 59.668 52.381 0.00 0.00 0.00 4.85
3169 6788 1.343789 GGAGTTATAGCCCGGTTCTCC 59.656 57.143 0.00 3.10 34.30 3.71
3170 6789 1.000496 CGGAGTTATAGCCCGGTTCTC 60.000 57.143 0.00 0.00 39.59 2.87
3171 6790 1.038280 CGGAGTTATAGCCCGGTTCT 58.962 55.000 0.00 0.00 39.59 3.01
3172 6791 3.582743 CGGAGTTATAGCCCGGTTC 57.417 57.895 0.00 0.00 39.59 3.62
3176 6795 0.318445 CGAACCGGAGTTATAGCCCG 60.318 60.000 9.46 8.76 42.64 6.13
3177 6796 0.749049 ACGAACCGGAGTTATAGCCC 59.251 55.000 9.46 0.00 35.94 5.19
3178 6797 3.551659 CCTTACGAACCGGAGTTATAGCC 60.552 52.174 9.46 0.00 35.94 3.93
3179 6798 3.636381 CCTTACGAACCGGAGTTATAGC 58.364 50.000 9.46 0.00 35.94 2.97
3180 6799 3.551659 GGCCTTACGAACCGGAGTTATAG 60.552 52.174 9.46 0.00 35.94 1.31
3181 6800 2.362077 GGCCTTACGAACCGGAGTTATA 59.638 50.000 9.46 0.00 35.94 0.98
3182 6801 1.137675 GGCCTTACGAACCGGAGTTAT 59.862 52.381 9.46 0.00 35.94 1.89
3183 6802 0.532115 GGCCTTACGAACCGGAGTTA 59.468 55.000 9.46 0.00 35.94 2.24
3184 6803 1.294459 GGCCTTACGAACCGGAGTT 59.706 57.895 9.46 0.00 39.54 3.01
3185 6804 2.653087 GGGCCTTACGAACCGGAGT 61.653 63.158 9.46 7.93 0.00 3.85
3186 6805 1.896122 AAGGGCCTTACGAACCGGAG 61.896 60.000 19.37 0.76 0.00 4.63
3187 6806 1.482748 AAAGGGCCTTACGAACCGGA 61.483 55.000 21.25 0.00 0.00 5.14
3188 6807 0.249955 TAAAGGGCCTTACGAACCGG 59.750 55.000 21.25 0.00 0.00 5.28
3189 6808 1.066645 ACTAAAGGGCCTTACGAACCG 60.067 52.381 21.25 5.60 0.00 4.44
3190 6809 2.353323 CACTAAAGGGCCTTACGAACC 58.647 52.381 21.25 0.00 0.00 3.62
3191 6810 1.736126 GCACTAAAGGGCCTTACGAAC 59.264 52.381 21.25 5.99 0.00 3.95
3192 6811 1.339342 GGCACTAAAGGGCCTTACGAA 60.339 52.381 21.25 4.81 46.74 3.85
3193 6812 0.251073 GGCACTAAAGGGCCTTACGA 59.749 55.000 21.25 7.25 46.74 3.43
3194 6813 2.776659 GGCACTAAAGGGCCTTACG 58.223 57.895 21.25 15.66 46.74 3.18
3199 6818 2.035155 AACCGGCACTAAAGGGCC 59.965 61.111 13.51 13.51 46.80 5.80
3200 6819 1.002502 AGAACCGGCACTAAAGGGC 60.003 57.895 0.00 0.00 0.00 5.19
3201 6820 0.036306 ACAGAACCGGCACTAAAGGG 59.964 55.000 0.00 0.00 0.00 3.95
3202 6821 2.754946 TACAGAACCGGCACTAAAGG 57.245 50.000 0.00 0.00 0.00 3.11
3203 6822 3.306166 CGATTACAGAACCGGCACTAAAG 59.694 47.826 0.00 0.00 0.00 1.85
3204 6823 3.255725 CGATTACAGAACCGGCACTAAA 58.744 45.455 0.00 0.00 0.00 1.85
3205 6824 2.417651 CCGATTACAGAACCGGCACTAA 60.418 50.000 0.00 0.00 35.29 2.24
3206 6825 1.135527 CCGATTACAGAACCGGCACTA 59.864 52.381 0.00 0.00 35.29 2.74
3207 6826 0.108329 CCGATTACAGAACCGGCACT 60.108 55.000 0.00 0.00 35.29 4.40
3208 6827 2.380081 CCGATTACAGAACCGGCAC 58.620 57.895 0.00 0.00 35.29 5.01
3209 6828 4.924019 CCGATTACAGAACCGGCA 57.076 55.556 0.00 0.00 35.29 5.69
3211 6830 1.663695 AATGCCGATTACAGAACCGG 58.336 50.000 0.00 0.00 44.34 5.28
3212 6831 4.868450 TTTAATGCCGATTACAGAACCG 57.132 40.909 0.00 0.00 0.00 4.44
3213 6832 6.431198 TCTTTTAATGCCGATTACAGAACC 57.569 37.500 0.00 0.00 0.00 3.62
3214 6833 6.912591 CCATCTTTTAATGCCGATTACAGAAC 59.087 38.462 0.00 0.00 0.00 3.01
3215 6834 6.039270 CCCATCTTTTAATGCCGATTACAGAA 59.961 38.462 0.00 0.00 0.00 3.02
3216 6835 5.530915 CCCATCTTTTAATGCCGATTACAGA 59.469 40.000 0.00 0.00 0.00 3.41
3217 6836 5.278463 CCCCATCTTTTAATGCCGATTACAG 60.278 44.000 0.00 0.00 0.00 2.74
3218 6837 4.582656 CCCCATCTTTTAATGCCGATTACA 59.417 41.667 0.00 0.00 0.00 2.41
3219 6838 4.825085 TCCCCATCTTTTAATGCCGATTAC 59.175 41.667 0.00 0.00 0.00 1.89
3220 6839 4.825085 GTCCCCATCTTTTAATGCCGATTA 59.175 41.667 0.00 0.00 0.00 1.75
3221 6840 3.636764 GTCCCCATCTTTTAATGCCGATT 59.363 43.478 0.00 0.00 0.00 3.34
3222 6841 3.117512 AGTCCCCATCTTTTAATGCCGAT 60.118 43.478 0.00 0.00 0.00 4.18
3223 6842 2.241176 AGTCCCCATCTTTTAATGCCGA 59.759 45.455 0.00 0.00 0.00 5.54
3224 6843 2.654863 AGTCCCCATCTTTTAATGCCG 58.345 47.619 0.00 0.00 0.00 5.69
3225 6844 6.098266 ACATTTAGTCCCCATCTTTTAATGCC 59.902 38.462 0.00 0.00 0.00 4.40
3226 6845 7.112452 ACATTTAGTCCCCATCTTTTAATGC 57.888 36.000 0.00 0.00 0.00 3.56
3244 6863 5.025453 ACCGGTACTAAAGGAGGACATTTA 58.975 41.667 4.49 0.00 41.43 1.40
3245 6864 3.842436 ACCGGTACTAAAGGAGGACATTT 59.158 43.478 4.49 0.00 41.43 2.32
3246 6865 3.447950 ACCGGTACTAAAGGAGGACATT 58.552 45.455 4.49 0.00 41.43 2.71
3247 6866 3.111741 ACCGGTACTAAAGGAGGACAT 57.888 47.619 4.49 0.00 41.43 3.06
3248 6867 2.610438 ACCGGTACTAAAGGAGGACA 57.390 50.000 4.49 0.00 41.43 4.02
3249 6868 3.095332 AGAACCGGTACTAAAGGAGGAC 58.905 50.000 8.00 0.00 38.46 3.85
3250 6869 3.094572 CAGAACCGGTACTAAAGGAGGA 58.905 50.000 8.00 0.00 0.00 3.71
3251 6870 2.418334 GCAGAACCGGTACTAAAGGAGG 60.418 54.545 8.00 0.00 0.00 4.30
3252 6871 2.232941 TGCAGAACCGGTACTAAAGGAG 59.767 50.000 8.00 0.00 0.00 3.69
3253 6872 2.028748 GTGCAGAACCGGTACTAAAGGA 60.029 50.000 8.00 0.00 0.00 3.36
3254 6873 2.344025 GTGCAGAACCGGTACTAAAGG 58.656 52.381 8.00 0.00 0.00 3.11
3255 6874 1.990563 CGTGCAGAACCGGTACTAAAG 59.009 52.381 8.00 0.00 0.00 1.85
3256 6875 1.612950 TCGTGCAGAACCGGTACTAAA 59.387 47.619 8.00 0.00 0.00 1.85
3257 6876 1.246649 TCGTGCAGAACCGGTACTAA 58.753 50.000 8.00 0.00 0.00 2.24
3258 6877 1.246649 TTCGTGCAGAACCGGTACTA 58.753 50.000 8.00 0.00 33.14 1.82
3259 6878 2.043625 TTCGTGCAGAACCGGTACT 58.956 52.632 8.00 0.00 33.14 2.73
3260 6879 4.659480 TTCGTGCAGAACCGGTAC 57.341 55.556 8.00 0.00 33.14 3.34
3270 6889 4.666397 TTAGCGGCGGTTCGTGCA 62.666 61.111 19.60 0.00 34.12 4.57
3271 6890 3.362851 CTTTAGCGGCGGTTCGTGC 62.363 63.158 19.60 0.00 0.00 5.34
3272 6891 2.736682 CCTTTAGCGGCGGTTCGTG 61.737 63.158 19.60 5.52 0.00 4.35
3273 6892 2.433664 CCTTTAGCGGCGGTTCGT 60.434 61.111 19.60 0.00 0.00 3.85
3274 6893 3.192922 CCCTTTAGCGGCGGTTCG 61.193 66.667 19.60 5.93 0.00 3.95
3275 6894 3.506096 GCCCTTTAGCGGCGGTTC 61.506 66.667 19.60 0.00 36.47 3.62
3280 6899 4.733542 TGGTGGCCCTTTAGCGGC 62.734 66.667 0.00 0.00 46.29 6.53
3281 6900 2.750237 GTGGTGGCCCTTTAGCGG 60.750 66.667 0.00 0.00 0.00 5.52
3282 6901 3.124921 CGTGGTGGCCCTTTAGCG 61.125 66.667 0.00 0.00 0.00 4.26
3283 6902 2.033602 ACGTGGTGGCCCTTTAGC 59.966 61.111 0.00 0.00 0.00 3.09
3284 6903 3.981308 CACGTGGTGGCCCTTTAG 58.019 61.111 7.95 0.00 0.00 1.85
3323 6942 2.275748 GGCACTAAAGGGCTCCCC 59.724 66.667 3.89 0.00 45.90 4.81
3324 6943 2.124695 CGGCACTAAAGGGCTCCC 60.125 66.667 3.89 0.00 0.00 4.30
3325 6944 2.124695 CCGGCACTAAAGGGCTCC 60.125 66.667 3.89 0.00 0.00 4.70
3326 6945 1.002502 AACCGGCACTAAAGGGCTC 60.003 57.895 0.00 0.00 0.00 4.70
3327 6946 1.303317 CAACCGGCACTAAAGGGCT 60.303 57.895 0.00 0.00 0.00 5.19
3328 6947 2.340328 CCAACCGGCACTAAAGGGC 61.340 63.158 0.00 0.00 0.00 5.19
3329 6948 0.325602 TACCAACCGGCACTAAAGGG 59.674 55.000 0.00 0.00 34.57 3.95
3330 6949 1.808343 GTTACCAACCGGCACTAAAGG 59.192 52.381 0.00 0.00 34.57 3.11
3331 6950 2.224784 GTGTTACCAACCGGCACTAAAG 59.775 50.000 0.00 0.00 34.57 1.85
3332 6951 2.220313 GTGTTACCAACCGGCACTAAA 58.780 47.619 0.00 0.00 34.57 1.85
3333 6952 1.542987 GGTGTTACCAACCGGCACTAA 60.543 52.381 0.00 0.00 38.42 2.24
3334 6953 0.035176 GGTGTTACCAACCGGCACTA 59.965 55.000 0.00 0.00 38.42 2.74
3335 6954 1.228033 GGTGTTACCAACCGGCACT 60.228 57.895 0.00 0.00 38.42 4.40
3336 6955 3.347168 GGTGTTACCAACCGGCAC 58.653 61.111 0.00 0.00 38.42 5.01
3352 6971 6.153756 CCCAAAACTTTTTAGTACCGATTGG 58.846 40.000 0.00 0.00 42.84 3.16
3353 6972 6.153756 CCCCAAAACTTTTTAGTACCGATTG 58.846 40.000 0.00 0.00 0.00 2.67
3354 6973 5.244402 CCCCCAAAACTTTTTAGTACCGATT 59.756 40.000 0.00 0.00 0.00 3.34
3355 6974 4.768448 CCCCCAAAACTTTTTAGTACCGAT 59.232 41.667 0.00 0.00 0.00 4.18
3356 6975 4.143543 CCCCCAAAACTTTTTAGTACCGA 58.856 43.478 0.00 0.00 0.00 4.69
3357 6976 3.890756 ACCCCCAAAACTTTTTAGTACCG 59.109 43.478 0.00 0.00 0.00 4.02
3358 6977 5.874897 AACCCCCAAAACTTTTTAGTACC 57.125 39.130 0.00 0.00 0.00 3.34
3359 6978 7.104939 ACAAAACCCCCAAAACTTTTTAGTAC 58.895 34.615 0.00 0.00 0.00 2.73
3360 6979 7.255199 ACAAAACCCCCAAAACTTTTTAGTA 57.745 32.000 0.00 0.00 0.00 1.82
3361 6980 6.129414 ACAAAACCCCCAAAACTTTTTAGT 57.871 33.333 0.00 0.00 0.00 2.24
3362 6981 7.455641 AAACAAAACCCCCAAAACTTTTTAG 57.544 32.000 0.00 0.00 0.00 1.85
3363 6982 7.834881 AAAACAAAACCCCCAAAACTTTTTA 57.165 28.000 0.00 0.00 0.00 1.52
3364 6983 6.732896 AAAACAAAACCCCCAAAACTTTTT 57.267 29.167 0.00 0.00 0.00 1.94
3365 6984 6.732896 AAAAACAAAACCCCCAAAACTTTT 57.267 29.167 0.00 0.00 0.00 2.27
3366 6985 8.423906 AATAAAAACAAAACCCCCAAAACTTT 57.576 26.923 0.00 0.00 0.00 2.66
3367 6986 9.702253 ATAATAAAAACAAAACCCCCAAAACTT 57.298 25.926 0.00 0.00 0.00 2.66
3368 6987 9.702253 AATAATAAAAACAAAACCCCCAAAACT 57.298 25.926 0.00 0.00 0.00 2.66
3432 7051 9.757859 GTATCGTAAAATACCATCAAACGAAAA 57.242 29.630 0.00 0.00 40.71 2.29
3433 7052 9.153721 AGTATCGTAAAATACCATCAAACGAAA 57.846 29.630 0.00 0.00 40.71 3.46
3434 7053 8.706492 AGTATCGTAAAATACCATCAAACGAA 57.294 30.769 0.00 0.00 40.71 3.85
3435 7054 9.236691 GTAGTATCGTAAAATACCATCAAACGA 57.763 33.333 0.00 0.00 41.45 3.85
3436 7055 9.022915 TGTAGTATCGTAAAATACCATCAAACG 57.977 33.333 0.00 0.00 33.42 3.60
3494 7113 9.877178 ACATCAGTTCTACGAGAAATTCTATTT 57.123 29.630 0.00 0.00 35.75 1.40
3814 7433 9.953697 GTAGAGTTGATCGTGATCTAAATAGTT 57.046 33.333 10.91 0.00 38.60 2.24
3815 7434 9.121658 TGTAGAGTTGATCGTGATCTAAATAGT 57.878 33.333 10.91 0.00 38.60 2.12
3816 7435 9.605955 CTGTAGAGTTGATCGTGATCTAAATAG 57.394 37.037 10.91 0.00 38.60 1.73
3817 7436 8.568794 CCTGTAGAGTTGATCGTGATCTAAATA 58.431 37.037 10.91 0.00 38.60 1.40
3818 7437 7.429633 CCTGTAGAGTTGATCGTGATCTAAAT 58.570 38.462 10.91 3.75 38.60 1.40
3819 7438 6.183360 CCCTGTAGAGTTGATCGTGATCTAAA 60.183 42.308 10.91 0.00 38.60 1.85
3820 7439 5.299531 CCCTGTAGAGTTGATCGTGATCTAA 59.700 44.000 10.91 2.01 38.60 2.10
3821 7440 4.822350 CCCTGTAGAGTTGATCGTGATCTA 59.178 45.833 10.91 0.89 38.60 1.98
3822 7441 3.634448 CCCTGTAGAGTTGATCGTGATCT 59.366 47.826 10.91 0.00 38.60 2.75
3823 7442 3.797184 GCCCTGTAGAGTTGATCGTGATC 60.797 52.174 2.86 2.86 38.29 2.92
3824 7443 2.101582 GCCCTGTAGAGTTGATCGTGAT 59.898 50.000 0.00 0.00 0.00 3.06
3825 7444 1.476891 GCCCTGTAGAGTTGATCGTGA 59.523 52.381 0.00 0.00 0.00 4.35
3826 7445 1.799181 CGCCCTGTAGAGTTGATCGTG 60.799 57.143 0.00 0.00 0.00 4.35
3827 7446 0.456221 CGCCCTGTAGAGTTGATCGT 59.544 55.000 0.00 0.00 0.00 3.73
3828 7447 0.872021 GCGCCCTGTAGAGTTGATCG 60.872 60.000 0.00 0.00 0.00 3.69
3829 7448 0.872021 CGCGCCCTGTAGAGTTGATC 60.872 60.000 0.00 0.00 0.00 2.92
3830 7449 1.141881 CGCGCCCTGTAGAGTTGAT 59.858 57.895 0.00 0.00 0.00 2.57
3831 7450 1.812686 AACGCGCCCTGTAGAGTTGA 61.813 55.000 5.73 0.00 0.00 3.18
3832 7451 1.374252 AACGCGCCCTGTAGAGTTG 60.374 57.895 5.73 0.00 0.00 3.16
3833 7452 1.374252 CAACGCGCCCTGTAGAGTT 60.374 57.895 5.73 0.00 0.00 3.01
3834 7453 2.261671 CAACGCGCCCTGTAGAGT 59.738 61.111 5.73 0.00 0.00 3.24
3835 7454 3.188786 GCAACGCGCCCTGTAGAG 61.189 66.667 5.73 0.00 32.94 2.43
3836 7455 3.932580 CTGCAACGCGCCCTGTAGA 62.933 63.158 5.73 0.00 41.33 2.59
3837 7456 3.490759 CTGCAACGCGCCCTGTAG 61.491 66.667 5.73 6.58 41.33 2.74
3838 7457 3.997397 TCTGCAACGCGCCCTGTA 61.997 61.111 5.73 0.00 41.33 2.74
3857 7476 1.375140 GGTTCGGGAGTTCGGGAAC 60.375 63.158 3.37 3.37 41.45 3.62
3858 7477 2.934570 CGGTTCGGGAGTTCGGGAA 61.935 63.158 0.00 0.00 0.00 3.97
3859 7478 3.376078 CGGTTCGGGAGTTCGGGA 61.376 66.667 0.00 0.00 0.00 5.14
3860 7479 4.446413 CCGGTTCGGGAGTTCGGG 62.446 72.222 0.00 0.00 44.15 5.14
3870 7489 0.947180 TTTTCTTCTCCGCCGGTTCG 60.947 55.000 1.63 0.00 0.00 3.95
3871 7490 1.232119 TTTTTCTTCTCCGCCGGTTC 58.768 50.000 1.63 0.00 0.00 3.62
3872 7491 3.407443 TTTTTCTTCTCCGCCGGTT 57.593 47.368 1.63 0.00 0.00 4.44
3887 7506 2.364324 GTCGGGAGGGCTTTTTCTTTTT 59.636 45.455 0.00 0.00 0.00 1.94
3888 7507 1.961394 GTCGGGAGGGCTTTTTCTTTT 59.039 47.619 0.00 0.00 0.00 2.27
3889 7508 1.617322 GTCGGGAGGGCTTTTTCTTT 58.383 50.000 0.00 0.00 0.00 2.52
3890 7509 0.251209 GGTCGGGAGGGCTTTTTCTT 60.251 55.000 0.00 0.00 0.00 2.52
3891 7510 1.134438 AGGTCGGGAGGGCTTTTTCT 61.134 55.000 0.00 0.00 0.00 2.52
3892 7511 0.251209 AAGGTCGGGAGGGCTTTTTC 60.251 55.000 0.00 0.00 0.00 2.29
3893 7512 1.069775 TAAGGTCGGGAGGGCTTTTT 58.930 50.000 0.00 0.00 0.00 1.94
3894 7513 1.212195 GATAAGGTCGGGAGGGCTTTT 59.788 52.381 0.00 0.00 0.00 2.27
3895 7514 0.837940 GATAAGGTCGGGAGGGCTTT 59.162 55.000 0.00 0.00 0.00 3.51
3896 7515 1.054978 GGATAAGGTCGGGAGGGCTT 61.055 60.000 0.00 0.00 0.00 4.35
3897 7516 1.459730 GGATAAGGTCGGGAGGGCT 60.460 63.158 0.00 0.00 0.00 5.19
3898 7517 2.517798 GGGATAAGGTCGGGAGGGC 61.518 68.421 0.00 0.00 0.00 5.19
3899 7518 1.842010 GGGGATAAGGTCGGGAGGG 60.842 68.421 0.00 0.00 0.00 4.30
3900 7519 1.074775 TGGGGATAAGGTCGGGAGG 60.075 63.158 0.00 0.00 0.00 4.30
3901 7520 1.745320 CGTGGGGATAAGGTCGGGAG 61.745 65.000 0.00 0.00 0.00 4.30
3902 7521 1.759299 CGTGGGGATAAGGTCGGGA 60.759 63.158 0.00 0.00 0.00 5.14
3903 7522 2.819550 CGTGGGGATAAGGTCGGG 59.180 66.667 0.00 0.00 0.00 5.14
3904 7523 2.108362 GCGTGGGGATAAGGTCGG 59.892 66.667 0.00 0.00 0.00 4.79
3905 7524 2.108362 GGCGTGGGGATAAGGTCG 59.892 66.667 0.00 0.00 0.00 4.79
3906 7525 2.509422 GGGCGTGGGGATAAGGTC 59.491 66.667 0.00 0.00 0.00 3.85
3907 7526 3.476419 CGGGCGTGGGGATAAGGT 61.476 66.667 0.00 0.00 0.00 3.50
3908 7527 4.929707 GCGGGCGTGGGGATAAGG 62.930 72.222 0.00 0.00 0.00 2.69
3909 7528 3.809374 GAGCGGGCGTGGGGATAAG 62.809 68.421 0.00 0.00 0.00 1.73
3910 7529 2.932569 TAGAGCGGGCGTGGGGATAA 62.933 60.000 0.00 0.00 0.00 1.75
3911 7530 3.440162 TAGAGCGGGCGTGGGGATA 62.440 63.158 0.00 0.00 0.00 2.59
3912 7531 4.853142 TAGAGCGGGCGTGGGGAT 62.853 66.667 0.00 0.00 0.00 3.85
3925 7544 4.301027 GGCGGGGATGGCGTAGAG 62.301 72.222 0.00 0.00 0.00 2.43
3943 7562 4.101448 CTGGGAAGGTGCCGAGGG 62.101 72.222 0.00 0.00 30.90 4.30
3944 7563 4.101448 CCTGGGAAGGTGCCGAGG 62.101 72.222 0.00 0.00 45.67 4.63
3945 7564 4.785453 GCCTGGGAAGGTGCCGAG 62.785 72.222 0.00 0.00 33.96 4.63
3949 7568 4.666253 TGCTGCCTGGGAAGGTGC 62.666 66.667 0.00 0.00 0.00 5.01
3950 7569 2.360852 CTGCTGCCTGGGAAGGTG 60.361 66.667 0.00 0.00 0.00 4.00
3951 7570 3.655211 CCTGCTGCCTGGGAAGGT 61.655 66.667 0.00 0.00 0.00 3.50
3976 7595 3.334054 AAGGAGGGAGGTGCCTGC 61.334 66.667 0.36 0.36 36.66 4.85
3977 7596 2.673523 CAAGGAGGGAGGTGCCTG 59.326 66.667 0.00 0.00 36.66 4.85


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

AutoCloner maintained by Alex Coulton.