Multiple sequence alignment - TraesCS6B01G318000

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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 TraesCS6B01G318000 chr6B 100.000 3023 0 0 1 3023 566039983 566036961 0.000000e+00 5583.0
1 TraesCS6B01G318000 chr6B 91.600 1119 83 5 946 2055 566122444 566121328 0.000000e+00 1535.0
2 TraesCS6B01G318000 chr6B 93.960 1010 60 1 1203 2212 566027192 566026184 0.000000e+00 1526.0
3 TraesCS6B01G318000 chr6B 95.918 392 14 2 818 1208 566028065 566027675 4.250000e-178 634.0
4 TraesCS6B01G318000 chr6B 95.593 295 13 0 2385 2679 35095710 35096004 9.810000e-130 473.0
5 TraesCS6B01G318000 chr6D 94.505 2311 109 12 1 2300 380253870 380256173 0.000000e+00 3548.0
6 TraesCS6B01G318000 chr6D 92.888 1631 83 11 703 2300 380366256 380367886 0.000000e+00 2338.0
7 TraesCS6B01G318000 chr6D 91.266 1122 87 8 943 2055 380177548 380178667 0.000000e+00 1519.0
8 TraesCS6B01G318000 chr6D 89.655 348 28 7 2676 3020 6753340 6753682 1.290000e-118 436.0
9 TraesCS6B01G318000 chr6A 94.760 1355 69 2 767 2119 520650593 520649239 0.000000e+00 2108.0
10 TraesCS6B01G318000 chr6A 90.772 1127 88 12 947 2061 520670613 520669491 0.000000e+00 1491.0
11 TraesCS6B01G318000 chr6A 91.892 74 6 0 3 76 552709903 552709976 1.480000e-18 104.0
12 TraesCS6B01G318000 chr7D 92.264 349 19 4 2678 3023 9205458 9205801 3.500000e-134 488.0
13 TraesCS6B01G318000 chr7D 83.900 441 59 10 81 514 64492110 64491675 7.800000e-111 411.0
14 TraesCS6B01G318000 chr7D 80.350 514 84 11 86 592 39221474 39221977 1.020000e-99 374.0
15 TraesCS6B01G318000 chr7D 90.598 117 10 1 2383 2499 627857645 627857530 1.450000e-33 154.0
16 TraesCS6B01G318000 chr7D 90.598 117 10 1 2383 2499 628013170 628013055 1.450000e-33 154.0
17 TraesCS6B01G318000 chr7D 88.889 117 12 1 2383 2499 628092796 628092681 3.140000e-30 143.0
18 TraesCS6B01G318000 chr1B 91.354 347 25 3 2680 3023 26583941 26584285 1.270000e-128 470.0
19 TraesCS6B01G318000 chr1B 81.180 356 53 12 2675 3021 473228816 473228466 1.070000e-69 274.0
20 TraesCS6B01G318000 chr1B 92.308 91 7 0 2295 2385 373606318 373606228 2.450000e-26 130.0
21 TraesCS6B01G318000 chr3A 90.476 357 29 5 2667 3020 674492978 674493332 1.640000e-127 466.0
22 TraesCS6B01G318000 chr3A 90.625 352 24 6 2680 3023 23900088 23899738 2.750000e-125 459.0
23 TraesCS6B01G318000 chr3A 83.046 348 46 9 2686 3023 91307502 91307158 1.360000e-78 303.0
24 TraesCS6B01G318000 chr3A 83.721 86 14 0 2 87 309335850 309335935 6.950000e-12 82.4
25 TraesCS6B01G318000 chr2B 94.613 297 14 2 2383 2679 798557277 798557571 2.750000e-125 459.0
26 TraesCS6B01G318000 chr2B 93.898 295 16 2 2385 2679 798553536 798553828 7.690000e-121 444.0
27 TraesCS6B01G318000 chr2B 76.736 576 96 21 86 654 554913113 554912569 1.370000e-73 287.0
28 TraesCS6B01G318000 chr2B 75.092 546 90 35 130 661 721364505 721363992 2.360000e-51 213.0
29 TraesCS6B01G318000 chr2B 82.432 148 21 4 2384 2528 703574314 703574169 1.140000e-24 124.0
30 TraesCS6B01G318000 chr5D 89.914 347 28 4 2680 3023 447418562 447418904 9.950000e-120 440.0
31 TraesCS6B01G318000 chr2A 81.250 544 80 14 88 620 374445167 374444635 1.300000e-113 420.0
32 TraesCS6B01G318000 chr2A 78.673 211 43 2 412 620 480027833 480028043 4.060000e-29 139.0
33 TraesCS6B01G318000 chr2A 81.818 143 16 8 2385 2525 100927795 100927661 8.860000e-21 111.0
34 TraesCS6B01G318000 chr1D 94.531 256 14 0 2426 2681 487353688 487353433 2.180000e-106 396.0
35 TraesCS6B01G318000 chr1D 77.734 512 100 8 85 590 468694946 468694443 4.900000e-78 302.0
36 TraesCS6B01G318000 chr1D 97.059 34 1 0 1184 1217 72498134 72498167 1.170000e-04 58.4
37 TraesCS6B01G318000 chr3D 79.961 509 77 19 88 591 333004338 333003850 4.800000e-93 351.0
38 TraesCS6B01G318000 chr3D 81.149 435 59 15 87 514 13551259 13551677 8.080000e-86 327.0
39 TraesCS6B01G318000 chr3D 87.805 82 10 0 9 90 501047954 501047873 2.480000e-16 97.1
40 TraesCS6B01G318000 chr2D 81.481 432 72 4 87 514 634115183 634115610 6.200000e-92 348.0
41 TraesCS6B01G318000 chr2D 92.391 92 6 1 2295 2385 428554878 428554969 2.450000e-26 130.0
42 TraesCS6B01G318000 chr2D 92.135 89 7 0 2297 2385 433716927 433717015 3.160000e-25 126.0
43 TraesCS6B01G318000 chr2D 87.356 87 11 0 1 87 641254428 641254342 1.920000e-17 100.0
44 TraesCS6B01G318000 chr4D 77.778 594 85 18 1 568 367949335 367948763 3.760000e-84 322.0
45 TraesCS6B01G318000 chr4D 91.304 92 7 1 2295 2385 64390469 64390560 1.140000e-24 124.0
46 TraesCS6B01G318000 chr3B 78.895 507 83 17 87 589 432014935 432014449 3.760000e-84 322.0
47 TraesCS6B01G318000 chr3B 91.489 94 7 1 2293 2385 18828145 18828238 8.800000e-26 128.0
48 TraesCS6B01G318000 chr1A 83.815 346 38 13 2685 3023 265032321 265031987 2.260000e-81 313.0
49 TraesCS6B01G318000 chr1A 91.304 92 7 1 2295 2385 295587974 295588065 1.140000e-24 124.0
50 TraesCS6B01G318000 chr7A 76.267 434 76 19 206 634 256069669 256070080 3.950000e-49 206.0
51 TraesCS6B01G318000 chr7A 90.411 73 7 0 2 74 14212289 14212217 2.480000e-16 97.1
52 TraesCS6B01G318000 chr4A 78.884 251 32 8 1 230 97296724 97296974 1.880000e-32 150.0
53 TraesCS6B01G318000 chr7B 92.308 91 7 0 2295 2385 444539487 444539577 2.450000e-26 130.0
54 TraesCS6B01G318000 chr5B 90.000 100 8 2 2288 2385 536228879 536228780 8.800000e-26 128.0
55 TraesCS6B01G318000 chr5B 89.474 76 8 0 1 76 339928875 339928950 2.480000e-16 97.1
56 TraesCS6B01G318000 chrUn 91.209 91 8 0 2295 2385 86671315 86671405 1.140000e-24 124.0
57 TraesCS6B01G318000 chrUn 88.235 51 6 0 1187 1237 24657901 24657851 9.050000e-06 62.1


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 TraesCS6B01G318000 chr6B 566036961 566039983 3022 True 5583.0 5583 100.0000 1 3023 1 chr6B.!!$R1 3022
1 TraesCS6B01G318000 chr6B 566121328 566122444 1116 True 1535.0 1535 91.6000 946 2055 1 chr6B.!!$R2 1109
2 TraesCS6B01G318000 chr6B 566026184 566028065 1881 True 1080.0 1526 94.9390 818 2212 2 chr6B.!!$R3 1394
3 TraesCS6B01G318000 chr6D 380253870 380256173 2303 False 3548.0 3548 94.5050 1 2300 1 chr6D.!!$F3 2299
4 TraesCS6B01G318000 chr6D 380366256 380367886 1630 False 2338.0 2338 92.8880 703 2300 1 chr6D.!!$F4 1597
5 TraesCS6B01G318000 chr6D 380177548 380178667 1119 False 1519.0 1519 91.2660 943 2055 1 chr6D.!!$F2 1112
6 TraesCS6B01G318000 chr6A 520649239 520650593 1354 True 2108.0 2108 94.7600 767 2119 1 chr6A.!!$R1 1352
7 TraesCS6B01G318000 chr6A 520669491 520670613 1122 True 1491.0 1491 90.7720 947 2061 1 chr6A.!!$R2 1114
8 TraesCS6B01G318000 chr7D 39221474 39221977 503 False 374.0 374 80.3500 86 592 1 chr7D.!!$F2 506
9 TraesCS6B01G318000 chr2B 798553536 798557571 4035 False 451.5 459 94.2555 2383 2679 2 chr2B.!!$F1 296
10 TraesCS6B01G318000 chr2B 554912569 554913113 544 True 287.0 287 76.7360 86 654 1 chr2B.!!$R1 568
11 TraesCS6B01G318000 chr2B 721363992 721364505 513 True 213.0 213 75.0920 130 661 1 chr2B.!!$R3 531
12 TraesCS6B01G318000 chr2A 374444635 374445167 532 True 420.0 420 81.2500 88 620 1 chr2A.!!$R2 532
13 TraesCS6B01G318000 chr1D 468694443 468694946 503 True 302.0 302 77.7340 85 590 1 chr1D.!!$R1 505
14 TraesCS6B01G318000 chr4D 367948763 367949335 572 True 322.0 322 77.7780 1 568 1 chr4D.!!$R1 567

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
277 312 0.246360 CTGCCGTGATGTACCACAGA 59.754 55.0 3.62 0.0 36.89 3.41 F
591 655 0.687354 GCTCCCATATCCGTGTCCAT 59.313 55.0 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1174 1288 1.348036 CTGGAAGAAACCGAACTCCCT 59.652 52.381 0.00 0.0 34.07 4.20 R
2423 3783 0.095245 TTCGTCGTCGGTCGTATCAC 59.905 55.000 1.55 0.0 40.80 3.06 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
36 37 1.226101 CGCGTGCATGATTCGCTTT 60.226 52.632 10.93 0.00 46.31 3.51
76 77 1.134699 ACCCTACGACATGCACATCAG 60.135 52.381 0.00 0.00 0.00 2.90
173 194 0.869454 GCGACAGCTGAAGAGATCGG 60.869 60.000 23.35 4.23 41.01 4.18
200 221 7.382898 AGTTTTGCTTCTTTTTGTCCAACTTA 58.617 30.769 0.00 0.00 0.00 2.24
277 312 0.246360 CTGCCGTGATGTACCACAGA 59.754 55.000 3.62 0.00 36.89 3.41
290 325 2.389715 ACCACAGACTAGAGGGCATAC 58.610 52.381 0.00 0.00 0.00 2.39
340 375 2.236146 AGCTCACGGGAAATCATGTGTA 59.764 45.455 0.00 0.00 34.08 2.90
515 577 4.094294 TGAATTTCGTCGGGTTTGATGATC 59.906 41.667 0.00 0.00 34.06 2.92
522 584 2.837591 TCGGGTTTGATGATCTTCTCCA 59.162 45.455 9.75 0.00 0.00 3.86
556 620 2.032550 CAGGCTTGAAATGTATGCGGAG 59.967 50.000 0.00 0.00 0.00 4.63
569 633 1.227380 GCGGAGAGCGTTGGATGAT 60.227 57.895 0.00 0.00 35.41 2.45
591 655 0.687354 GCTCCCATATCCGTGTCCAT 59.313 55.000 0.00 0.00 0.00 3.41
603 667 8.637099 CATATCCGTGTCCATATAATGATCTCT 58.363 37.037 0.00 0.00 0.00 3.10
642 707 1.611491 GAAGGAAATTTGCGGTGACCA 59.389 47.619 1.11 0.00 0.00 4.02
654 719 1.838112 GGTGACCATTTGAGATGCCA 58.162 50.000 0.00 0.00 0.00 4.92
681 746 7.867445 ATTGTCTAATTTGCTTAAACAACCG 57.133 32.000 0.00 0.00 34.07 4.44
686 751 2.941453 TTGCTTAAACAACCGCAACA 57.059 40.000 0.00 0.00 37.45 3.33
687 752 3.444703 TTGCTTAAACAACCGCAACAT 57.555 38.095 0.00 0.00 37.45 2.71
688 753 2.736978 TGCTTAAACAACCGCAACATG 58.263 42.857 0.00 0.00 0.00 3.21
697 762 1.512522 CCGCAACATGCATGTCACG 60.513 57.895 31.83 31.83 45.36 4.35
714 779 5.357257 TGTCACGCTCTAAAAGAAAGAACT 58.643 37.500 0.00 0.00 0.00 3.01
887 989 4.133078 GGTTGCAATCAAAACCCAAATGA 58.867 39.130 4.39 0.00 40.03 2.57
974 1078 3.319137 TGAACTGACCAGTCTATGCAC 57.681 47.619 2.84 0.00 41.58 4.57
1050 1155 2.033141 CACCTGTCAGTGCCTGGG 59.967 66.667 2.00 0.00 31.51 4.45
1174 1288 2.362503 AGATCGTCCGTGCAGGGA 60.363 61.111 23.92 23.92 41.52 4.20
1338 1940 2.915659 TTCCACACGAGCCTCCGT 60.916 61.111 0.00 0.00 44.43 4.69
1581 2183 3.230522 GAACCACTACCCGCCGTGT 62.231 63.158 0.00 0.00 0.00 4.49
1938 2544 1.980052 CGAGGGGCCTCTGTACAAA 59.020 57.895 11.93 0.00 40.69 2.83
2075 2681 5.467735 GCATTTCTTCTTCCAGCAAATTTGT 59.532 36.000 19.03 3.98 0.00 2.83
2190 2797 2.166829 TGGTGTAATGGTGGATGCAAC 58.833 47.619 0.00 0.00 0.00 4.17
2193 2800 3.377172 GGTGTAATGGTGGATGCAACTAC 59.623 47.826 3.18 1.58 0.00 2.73
2228 2835 3.136763 AGAATGACATTATCAGCGCTGG 58.863 45.455 35.36 21.75 41.91 4.85
2247 2854 4.708177 CTGGGAGGTGATTATTTCGTCAT 58.292 43.478 0.00 0.00 0.00 3.06
2263 2870 4.463209 TCGTCATTTTCAAGATTTGTCGC 58.537 39.130 0.00 0.00 0.00 5.19
2280 2887 2.946329 GTCGCCTCAGTCTCTTCTCATA 59.054 50.000 0.00 0.00 0.00 2.15
2300 2907 9.258826 TCTCATACATTCGTAGTTCTACTACTC 57.741 37.037 13.37 0.00 46.68 2.59
2301 2908 8.375608 TCATACATTCGTAGTTCTACTACTCC 57.624 38.462 13.37 0.00 46.68 3.85
2303 2910 5.753716 ACATTCGTAGTTCTACTACTCCCT 58.246 41.667 13.37 0.00 46.68 4.20
2304 2911 5.821995 ACATTCGTAGTTCTACTACTCCCTC 59.178 44.000 13.37 0.00 46.68 4.30
2306 2913 3.129871 CGTAGTTCTACTACTCCCTCCG 58.870 54.545 13.37 0.00 46.68 4.63
2307 2914 3.431486 CGTAGTTCTACTACTCCCTCCGT 60.431 52.174 13.37 0.00 46.68 4.69
2308 2915 3.735720 AGTTCTACTACTCCCTCCGTT 57.264 47.619 0.00 0.00 0.00 4.44
2309 2916 3.619419 AGTTCTACTACTCCCTCCGTTC 58.381 50.000 0.00 0.00 0.00 3.95
2310 2917 2.687425 GTTCTACTACTCCCTCCGTTCC 59.313 54.545 0.00 0.00 0.00 3.62
2311 2918 2.203584 TCTACTACTCCCTCCGTTCCT 58.796 52.381 0.00 0.00 0.00 3.36
2312 2919 3.387962 TCTACTACTCCCTCCGTTCCTA 58.612 50.000 0.00 0.00 0.00 2.94
2313 2920 3.782523 TCTACTACTCCCTCCGTTCCTAA 59.217 47.826 0.00 0.00 0.00 2.69
2314 2921 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
2315 2922 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
2316 2923 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
2317 2924 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
2318 2925 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
2319 2926 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
2320 2927 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
2321 2928 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
2322 2929 7.300658 ACTCCCTCCGTTCCTAAATATAAGTA 58.699 38.462 0.00 0.00 0.00 2.24
2323 2930 7.954620 ACTCCCTCCGTTCCTAAATATAAGTAT 59.045 37.037 0.00 0.00 0.00 2.12
2324 2931 8.731591 TCCCTCCGTTCCTAAATATAAGTATT 57.268 34.615 0.00 0.00 31.89 1.89
2325 2932 9.162733 TCCCTCCGTTCCTAAATATAAGTATTT 57.837 33.333 0.00 0.00 41.92 1.40
2327 2934 9.991906 CCTCCGTTCCTAAATATAAGTATTTCA 57.008 33.333 0.00 0.00 40.21 2.69
2393 3753 6.157994 AGTTTAGAGTATAGATTGTTGGCCCA 59.842 38.462 0.00 0.00 0.00 5.36
2395 3755 4.040755 AGAGTATAGATTGTTGGCCCAGT 58.959 43.478 0.00 0.00 0.00 4.00
2410 3770 1.035932 CCAGTCCCGACACCGAGTAT 61.036 60.000 0.00 0.00 38.22 2.12
2414 3774 2.301009 AGTCCCGACACCGAGTATTTTT 59.699 45.455 0.00 0.00 38.22 1.94
2444 3804 0.095245 GATACGACCGACGACGAACA 59.905 55.000 9.28 6.18 45.77 3.18
2452 3812 0.357894 CGACGACGAACAACGATGAC 59.642 55.000 0.00 0.00 45.77 3.06
2467 3827 1.064208 GATGACAGACGAAGCTCGCTA 59.936 52.381 5.63 0.00 45.12 4.26
2506 3866 2.074230 TTTACGCCGAGACACACCGT 62.074 55.000 0.00 0.00 36.07 4.83
2553 3913 1.451028 GCGATGCTCCTCCAAAGCT 60.451 57.895 0.00 0.00 40.50 3.74
2612 3972 1.148273 AGCAGCCGGAACTCAAACA 59.852 52.632 5.05 0.00 0.00 2.83
2679 4039 8.477709 GTGTCGTTCCTCGTATATTTCTTTATG 58.522 37.037 0.00 0.00 40.80 1.90
2680 4040 7.650504 TGTCGTTCCTCGTATATTTCTTTATGG 59.349 37.037 0.00 0.00 40.80 2.74
2681 4041 7.864379 GTCGTTCCTCGTATATTTCTTTATGGA 59.136 37.037 0.00 0.00 40.80 3.41
2682 4042 7.864379 TCGTTCCTCGTATATTTCTTTATGGAC 59.136 37.037 0.00 0.00 40.80 4.02
2683 4043 7.650504 CGTTCCTCGTATATTTCTTTATGGACA 59.349 37.037 0.00 0.00 34.52 4.02
2684 4044 8.762426 GTTCCTCGTATATTTCTTTATGGACAC 58.238 37.037 0.00 0.00 0.00 3.67
2685 4045 7.143340 TCCTCGTATATTTCTTTATGGACACG 58.857 38.462 0.00 0.00 0.00 4.49
2686 4046 7.013559 TCCTCGTATATTTCTTTATGGACACGA 59.986 37.037 0.00 0.00 34.06 4.35
2687 4047 7.114529 CCTCGTATATTTCTTTATGGACACGAC 59.885 40.741 0.00 0.00 32.07 4.34
2688 4048 7.709947 TCGTATATTTCTTTATGGACACGACT 58.290 34.615 0.00 0.00 30.60 4.18
2689 4049 8.839343 TCGTATATTTCTTTATGGACACGACTA 58.161 33.333 0.00 0.00 30.60 2.59
2690 4050 9.454585 CGTATATTTCTTTATGGACACGACTAA 57.545 33.333 0.00 0.00 0.00 2.24
2713 4073 5.610908 CGTCCTAACGTACGGAATTTAAG 57.389 43.478 21.06 3.14 43.94 1.85
2714 4074 5.331902 CGTCCTAACGTACGGAATTTAAGA 58.668 41.667 21.06 5.49 43.94 2.10
2715 4075 5.453587 CGTCCTAACGTACGGAATTTAAGAG 59.546 44.000 21.06 0.00 43.94 2.85
2716 4076 6.555315 GTCCTAACGTACGGAATTTAAGAGA 58.445 40.000 21.06 3.82 0.00 3.10
2717 4077 7.199078 GTCCTAACGTACGGAATTTAAGAGAT 58.801 38.462 21.06 0.00 0.00 2.75
2718 4078 8.345565 GTCCTAACGTACGGAATTTAAGAGATA 58.654 37.037 21.06 0.00 0.00 1.98
2719 4079 9.071276 TCCTAACGTACGGAATTTAAGAGATAT 57.929 33.333 21.06 0.00 0.00 1.63
2720 4080 9.339492 CCTAACGTACGGAATTTAAGAGATATC 57.661 37.037 21.06 0.00 0.00 1.63
2721 4081 9.339492 CTAACGTACGGAATTTAAGAGATATCC 57.661 37.037 21.06 0.00 0.00 2.59
2730 4090 9.974980 GGAATTTAAGAGATATCCGATAGATCC 57.025 37.037 0.00 0.00 36.33 3.36
2734 4094 9.983024 TTTAAGAGATATCCGATAGATCCTTCT 57.017 33.333 0.00 0.00 36.33 2.85
2735 4095 9.983024 TTAAGAGATATCCGATAGATCCTTCTT 57.017 33.333 0.00 0.45 36.33 2.52
2738 4098 9.793259 AGAGATATCCGATAGATCCTTCTTATC 57.207 37.037 0.00 0.00 36.33 1.75
2739 4099 9.793259 GAGATATCCGATAGATCCTTCTTATCT 57.207 37.037 0.00 0.00 36.33 1.98
2740 4100 9.793259 AGATATCCGATAGATCCTTCTTATCTC 57.207 37.037 0.00 0.00 36.33 2.75
2741 4101 8.934023 ATATCCGATAGATCCTTCTTATCTCC 57.066 38.462 0.00 0.00 36.33 3.71
2742 4102 5.511363 TCCGATAGATCCTTCTTATCTCCC 58.489 45.833 0.00 0.00 35.36 4.30
2743 4103 5.254267 TCCGATAGATCCTTCTTATCTCCCT 59.746 44.000 0.00 0.00 35.36 4.20
2744 4104 5.592688 CCGATAGATCCTTCTTATCTCCCTC 59.407 48.000 0.00 0.00 35.36 4.30
2745 4105 5.592688 CGATAGATCCTTCTTATCTCCCTCC 59.407 48.000 0.00 0.00 35.36 4.30
2746 4106 4.140575 AGATCCTTCTTATCTCCCTCCC 57.859 50.000 0.00 0.00 0.00 4.30
2747 4107 2.383442 TCCTTCTTATCTCCCTCCCG 57.617 55.000 0.00 0.00 0.00 5.14
2748 4108 1.574339 TCCTTCTTATCTCCCTCCCGT 59.426 52.381 0.00 0.00 0.00 5.28
2749 4109 1.689273 CCTTCTTATCTCCCTCCCGTG 59.311 57.143 0.00 0.00 0.00 4.94
2750 4110 2.667470 CTTCTTATCTCCCTCCCGTGA 58.333 52.381 0.00 0.00 0.00 4.35
2751 4111 2.068834 TCTTATCTCCCTCCCGTGAC 57.931 55.000 0.00 0.00 0.00 3.67
2752 4112 1.041437 CTTATCTCCCTCCCGTGACC 58.959 60.000 0.00 0.00 0.00 4.02
2753 4113 0.635009 TTATCTCCCTCCCGTGACCT 59.365 55.000 0.00 0.00 0.00 3.85
2754 4114 0.635009 TATCTCCCTCCCGTGACCTT 59.365 55.000 0.00 0.00 0.00 3.50
2755 4115 0.688087 ATCTCCCTCCCGTGACCTTC 60.688 60.000 0.00 0.00 0.00 3.46
2756 4116 2.284405 TCCCTCCCGTGACCTTCC 60.284 66.667 0.00 0.00 0.00 3.46
2757 4117 2.606519 CCCTCCCGTGACCTTCCA 60.607 66.667 0.00 0.00 0.00 3.53
2758 4118 1.995626 CCCTCCCGTGACCTTCCAT 60.996 63.158 0.00 0.00 0.00 3.41
2759 4119 1.221840 CCTCCCGTGACCTTCCATG 59.778 63.158 0.00 0.00 0.00 3.66
2760 4120 1.450312 CTCCCGTGACCTTCCATGC 60.450 63.158 0.00 0.00 0.00 4.06
2761 4121 2.184020 CTCCCGTGACCTTCCATGCA 62.184 60.000 0.00 0.00 0.00 3.96
2762 4122 1.077501 CCCGTGACCTTCCATGCAT 60.078 57.895 0.00 0.00 0.00 3.96
2763 4123 1.378882 CCCGTGACCTTCCATGCATG 61.379 60.000 20.19 20.19 0.00 4.06
2764 4124 1.430632 CGTGACCTTCCATGCATGC 59.569 57.895 21.69 11.82 0.00 4.06
2765 4125 1.430632 GTGACCTTCCATGCATGCG 59.569 57.895 21.69 14.24 0.00 4.73
2766 4126 1.002257 TGACCTTCCATGCATGCGT 60.002 52.632 21.69 10.53 0.00 5.24
2767 4127 1.307355 TGACCTTCCATGCATGCGTG 61.307 55.000 29.36 29.36 0.00 5.34
2768 4128 1.303561 ACCTTCCATGCATGCGTGT 60.304 52.632 32.28 15.35 0.00 4.49
2769 4129 0.035534 ACCTTCCATGCATGCGTGTA 60.036 50.000 32.28 19.20 0.00 2.90
2770 4130 1.311859 CCTTCCATGCATGCGTGTAT 58.688 50.000 32.28 10.59 0.00 2.29
2771 4131 1.677576 CCTTCCATGCATGCGTGTATT 59.322 47.619 32.28 3.50 0.00 1.89
2772 4132 2.099592 CCTTCCATGCATGCGTGTATTT 59.900 45.455 32.28 1.79 0.00 1.40
2773 4133 3.429272 CCTTCCATGCATGCGTGTATTTT 60.429 43.478 32.28 0.43 0.00 1.82
2774 4134 3.865011 TCCATGCATGCGTGTATTTTT 57.135 38.095 32.28 0.00 0.00 1.94
2857 4217 9.932207 AAAAATAAAATTGATGATGTCAGCAGA 57.068 25.926 1.00 0.00 43.59 4.26
2860 4220 9.745880 AATAAAATTGATGATGTCAGCAGATTC 57.254 29.630 1.00 0.00 43.59 2.52
2861 4221 7.406031 AAAATTGATGATGTCAGCAGATTCT 57.594 32.000 1.00 0.00 43.59 2.40
2862 4222 7.406031 AAATTGATGATGTCAGCAGATTCTT 57.594 32.000 1.00 0.00 43.59 2.52
2863 4223 7.406031 AATTGATGATGTCAGCAGATTCTTT 57.594 32.000 1.00 0.00 43.59 2.52
2864 4224 6.829229 TTGATGATGTCAGCAGATTCTTTT 57.171 33.333 1.00 0.00 43.59 2.27
2865 4225 6.829229 TGATGATGTCAGCAGATTCTTTTT 57.171 33.333 0.00 0.00 37.34 1.94
2866 4226 6.849502 TGATGATGTCAGCAGATTCTTTTTC 58.150 36.000 0.00 0.00 37.34 2.29
2867 4227 6.431852 TGATGATGTCAGCAGATTCTTTTTCA 59.568 34.615 0.00 0.00 37.34 2.69
2868 4228 6.638096 TGATGTCAGCAGATTCTTTTTCAA 57.362 33.333 0.00 0.00 0.00 2.69
2869 4229 7.041635 TGATGTCAGCAGATTCTTTTTCAAA 57.958 32.000 0.00 0.00 0.00 2.69
2870 4230 7.490840 TGATGTCAGCAGATTCTTTTTCAAAA 58.509 30.769 0.00 0.00 0.00 2.44
2871 4231 7.436080 TGATGTCAGCAGATTCTTTTTCAAAAC 59.564 33.333 0.00 0.00 0.00 2.43
2872 4232 6.866480 TGTCAGCAGATTCTTTTTCAAAACT 58.134 32.000 0.00 0.00 0.00 2.66
2873 4233 6.974622 TGTCAGCAGATTCTTTTTCAAAACTC 59.025 34.615 0.00 0.00 0.00 3.01
2874 4234 6.974622 GTCAGCAGATTCTTTTTCAAAACTCA 59.025 34.615 0.00 0.00 0.00 3.41
2875 4235 7.489113 GTCAGCAGATTCTTTTTCAAAACTCAA 59.511 33.333 0.00 0.00 0.00 3.02
2876 4236 8.034215 TCAGCAGATTCTTTTTCAAAACTCAAA 58.966 29.630 0.00 0.00 0.00 2.69
2877 4237 8.658609 CAGCAGATTCTTTTTCAAAACTCAAAA 58.341 29.630 0.00 0.00 0.00 2.44
2878 4238 9.387257 AGCAGATTCTTTTTCAAAACTCAAAAT 57.613 25.926 0.00 0.00 0.00 1.82
2879 4239 9.992910 GCAGATTCTTTTTCAAAACTCAAAATT 57.007 25.926 0.00 0.00 0.00 1.82
2903 4263 8.833231 TTCAAAATGTTTTGTAACTCAAACCA 57.167 26.923 15.51 0.00 45.77 3.67
2904 4264 9.442047 TTCAAAATGTTTTGTAACTCAAACCAT 57.558 25.926 15.51 0.00 46.12 3.55
2905 4265 9.092876 TCAAAATGTTTTGTAACTCAAACCATC 57.907 29.630 15.51 0.00 44.39 3.51
2906 4266 8.877779 CAAAATGTTTTGTAACTCAAACCATCA 58.122 29.630 9.48 0.00 44.39 3.07
2907 4267 8.647143 AAATGTTTTGTAACTCAAACCATCAG 57.353 30.769 4.42 0.00 44.39 2.90
2908 4268 5.587289 TGTTTTGTAACTCAAACCATCAGC 58.413 37.500 0.00 0.00 44.39 4.26
2909 4269 4.846779 TTTGTAACTCAAACCATCAGCC 57.153 40.909 0.00 0.00 40.56 4.85
2910 4270 2.422597 TGTAACTCAAACCATCAGCCG 58.577 47.619 0.00 0.00 0.00 5.52
2911 4271 1.737793 GTAACTCAAACCATCAGCCGG 59.262 52.381 0.00 0.00 0.00 6.13
2912 4272 0.400213 AACTCAAACCATCAGCCGGA 59.600 50.000 5.05 0.00 0.00 5.14
2913 4273 0.620556 ACTCAAACCATCAGCCGGAT 59.379 50.000 5.05 0.00 36.39 4.18
2914 4274 1.004745 ACTCAAACCATCAGCCGGATT 59.995 47.619 5.05 0.00 32.57 3.01
2915 4275 1.402968 CTCAAACCATCAGCCGGATTG 59.597 52.381 5.05 2.05 37.58 2.67
2916 4276 1.004161 TCAAACCATCAGCCGGATTGA 59.996 47.619 5.05 8.87 41.44 2.57
2917 4277 1.818060 CAAACCATCAGCCGGATTGAA 59.182 47.619 5.05 0.00 38.27 2.69
2918 4278 2.214376 AACCATCAGCCGGATTGAAA 57.786 45.000 5.05 0.00 32.57 2.69
2919 4279 2.214376 ACCATCAGCCGGATTGAAAA 57.786 45.000 5.05 0.00 32.57 2.29
2920 4280 2.524306 ACCATCAGCCGGATTGAAAAA 58.476 42.857 5.05 0.00 32.57 1.94
2921 4281 2.231235 ACCATCAGCCGGATTGAAAAAC 59.769 45.455 5.05 0.00 32.57 2.43
2922 4282 2.493278 CCATCAGCCGGATTGAAAAACT 59.507 45.455 5.05 0.00 32.57 2.66
2923 4283 3.504863 CATCAGCCGGATTGAAAAACTG 58.495 45.455 5.05 0.00 32.57 3.16
2924 4284 2.582052 TCAGCCGGATTGAAAAACTGT 58.418 42.857 5.05 0.00 0.00 3.55
2925 4285 2.552315 TCAGCCGGATTGAAAAACTGTC 59.448 45.455 5.05 0.00 0.00 3.51
2926 4286 2.554032 CAGCCGGATTGAAAAACTGTCT 59.446 45.455 5.05 0.00 0.00 3.41
2927 4287 3.004734 CAGCCGGATTGAAAAACTGTCTT 59.995 43.478 5.05 0.00 0.00 3.01
2928 4288 3.253432 AGCCGGATTGAAAAACTGTCTTC 59.747 43.478 5.05 0.00 0.00 2.87
2929 4289 3.004315 GCCGGATTGAAAAACTGTCTTCA 59.996 43.478 5.05 2.20 0.00 3.02
2930 4290 4.537015 CCGGATTGAAAAACTGTCTTCAC 58.463 43.478 0.00 0.00 31.41 3.18
2931 4291 4.036262 CCGGATTGAAAAACTGTCTTCACA 59.964 41.667 0.00 0.00 31.41 3.58
2932 4292 5.278463 CCGGATTGAAAAACTGTCTTCACAT 60.278 40.000 0.00 3.76 31.41 3.21
2933 4293 6.072728 CCGGATTGAAAAACTGTCTTCACATA 60.073 38.462 0.00 0.00 31.41 2.29
2934 4294 7.359595 CGGATTGAAAAACTGTCTTCACATAA 58.640 34.615 5.14 0.00 31.41 1.90
2935 4295 7.860373 CGGATTGAAAAACTGTCTTCACATAAA 59.140 33.333 5.14 0.00 31.41 1.40
2936 4296 9.528018 GGATTGAAAAACTGTCTTCACATAAAA 57.472 29.630 5.14 0.00 31.41 1.52
2942 4302 9.450807 AAAAACTGTCTTCACATAAAAGATTCG 57.549 29.630 0.00 0.00 35.35 3.34
2943 4303 7.730364 AACTGTCTTCACATAAAAGATTCGT 57.270 32.000 0.00 0.00 35.35 3.85
2944 4304 7.352719 ACTGTCTTCACATAAAAGATTCGTC 57.647 36.000 0.00 0.00 35.35 4.20
2945 4305 6.929049 ACTGTCTTCACATAAAAGATTCGTCA 59.071 34.615 0.00 0.00 35.35 4.35
2946 4306 7.095607 ACTGTCTTCACATAAAAGATTCGTCAC 60.096 37.037 0.00 0.00 35.35 3.67
2947 4307 6.128929 TGTCTTCACATAAAAGATTCGTCACG 60.129 38.462 0.00 0.00 35.35 4.35
2948 4308 6.089016 GTCTTCACATAAAAGATTCGTCACGA 59.911 38.462 0.00 0.00 35.35 4.35
2949 4309 5.756950 TCACATAAAAGATTCGTCACGAC 57.243 39.130 0.00 0.00 34.89 4.34
2971 4331 4.310357 GAGACCTTCGAAACTAGATCCC 57.690 50.000 0.00 0.00 0.00 3.85
2972 4332 3.700038 GAGACCTTCGAAACTAGATCCCA 59.300 47.826 0.00 0.00 0.00 4.37
2973 4333 4.290942 AGACCTTCGAAACTAGATCCCAT 58.709 43.478 0.00 0.00 0.00 4.00
2974 4334 4.100189 AGACCTTCGAAACTAGATCCCATG 59.900 45.833 0.00 0.00 0.00 3.66
2975 4335 3.775316 ACCTTCGAAACTAGATCCCATGT 59.225 43.478 0.00 0.00 0.00 3.21
2976 4336 4.960469 ACCTTCGAAACTAGATCCCATGTA 59.040 41.667 0.00 0.00 0.00 2.29
2977 4337 5.069251 ACCTTCGAAACTAGATCCCATGTAG 59.931 44.000 0.00 0.00 32.78 2.74
2978 4338 5.509840 CCTTCGAAACTAGATCCCATGTAGG 60.510 48.000 0.00 0.00 30.91 3.18
2979 4339 4.543689 TCGAAACTAGATCCCATGTAGGT 58.456 43.478 0.00 0.00 34.66 3.08
2980 4340 5.698104 TCGAAACTAGATCCCATGTAGGTA 58.302 41.667 0.00 0.00 34.66 3.08
2981 4341 6.312529 TCGAAACTAGATCCCATGTAGGTAT 58.687 40.000 0.00 0.00 34.66 2.73
2982 4342 6.208797 TCGAAACTAGATCCCATGTAGGTATG 59.791 42.308 0.00 0.00 34.66 2.39
2983 4343 6.015350 CGAAACTAGATCCCATGTAGGTATGT 60.015 42.308 0.00 0.00 34.66 2.29
2984 4344 7.471539 CGAAACTAGATCCCATGTAGGTATGTT 60.472 40.741 0.00 0.00 34.66 2.71
2985 4345 6.919775 ACTAGATCCCATGTAGGTATGTTC 57.080 41.667 0.00 0.00 34.66 3.18
2986 4346 5.780793 ACTAGATCCCATGTAGGTATGTTCC 59.219 44.000 0.00 0.00 34.66 3.62
2987 4347 3.578716 AGATCCCATGTAGGTATGTTCCG 59.421 47.826 0.00 0.00 34.66 4.30
2988 4348 3.035055 TCCCATGTAGGTATGTTCCGA 57.965 47.619 0.00 0.00 34.66 4.55
2989 4349 2.696707 TCCCATGTAGGTATGTTCCGAC 59.303 50.000 0.00 0.00 34.66 4.79
2990 4350 2.432874 CCCATGTAGGTATGTTCCGACA 59.567 50.000 1.70 1.70 44.47 4.35
2991 4351 3.118555 CCCATGTAGGTATGTTCCGACAA 60.119 47.826 3.19 0.00 43.82 3.18
2992 4352 3.869246 CCATGTAGGTATGTTCCGACAAC 59.131 47.826 3.19 0.00 43.82 3.32
2993 4353 4.382685 CCATGTAGGTATGTTCCGACAACT 60.383 45.833 3.19 0.00 43.82 3.16
2994 4354 4.877378 TGTAGGTATGTTCCGACAACTT 57.123 40.909 0.00 0.00 39.43 2.66
2995 4355 5.217978 TGTAGGTATGTTCCGACAACTTT 57.782 39.130 0.00 0.00 39.43 2.66
2996 4356 5.613329 TGTAGGTATGTTCCGACAACTTTT 58.387 37.500 0.00 0.00 39.43 2.27
2997 4357 6.056884 TGTAGGTATGTTCCGACAACTTTTT 58.943 36.000 0.00 0.00 39.43 1.94
3021 4381 4.603231 TTCCGATAAAATGTTACCACGC 57.397 40.909 0.00 0.00 0.00 5.34
3022 4382 3.597255 TCCGATAAAATGTTACCACGCA 58.403 40.909 0.00 0.00 0.00 5.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.521291 GCAATGTGCTTTCACGCCTA 59.479 50.000 0.00 0.00 46.01 3.93
42 43 1.885887 GTAGGGTGCAATGTGCTTTCA 59.114 47.619 1.43 0.00 45.31 2.69
290 325 6.016693 TCCAATAATGTATGTGCGTAAATGGG 60.017 38.462 0.00 0.00 0.00 4.00
340 375 1.182667 TGAACGGATCATGTCGTCCT 58.817 50.000 10.64 0.00 38.78 3.85
515 577 3.202906 TGGTTTCGACAAACTGGAGAAG 58.797 45.455 0.35 0.00 41.61 2.85
522 584 1.676006 CAAGCCTGGTTTCGACAAACT 59.324 47.619 0.00 0.00 41.61 2.66
556 620 1.218230 GAGCCGATCATCCAACGCTC 61.218 60.000 0.00 0.00 0.00 5.03
591 655 5.278315 CGTCCACGGACAAGAGATCATTATA 60.278 44.000 16.23 0.00 44.77 0.98
603 667 0.037697 CCTCATTCGTCCACGGACAA 60.038 55.000 16.23 9.64 44.77 3.18
681 746 0.795735 GAGCGTGACATGCATGTTGC 60.796 55.000 31.82 30.65 45.29 4.17
686 751 3.599343 TCTTTTAGAGCGTGACATGCAT 58.401 40.909 21.34 11.80 31.07 3.96
687 752 3.038788 TCTTTTAGAGCGTGACATGCA 57.961 42.857 21.34 0.00 31.07 3.96
688 753 4.152402 TCTTTCTTTTAGAGCGTGACATGC 59.848 41.667 11.89 11.89 0.00 4.06
697 762 5.215903 GTGGCAAGTTCTTTCTTTTAGAGC 58.784 41.667 0.00 0.00 0.00 4.09
714 779 2.668212 CGCCCTTCTTCGTGGCAA 60.668 61.111 0.00 0.00 45.63 4.52
731 796 3.761752 TGTAGGCAAAAGTATTGAAGGGC 59.238 43.478 0.00 0.00 0.00 5.19
887 989 5.507637 AGAAGCATCTTTGGATTCAGACAT 58.492 37.500 0.00 0.00 29.15 3.06
974 1078 6.155136 TCGAGATATAGCTTTGCTTGAGATG 58.845 40.000 0.00 0.00 40.44 2.90
1050 1155 2.967615 GCCGGGAGAATGTAGCGC 60.968 66.667 2.18 0.00 0.00 5.92
1174 1288 1.348036 CTGGAAGAAACCGAACTCCCT 59.652 52.381 0.00 0.00 34.07 4.20
2075 2681 6.366340 TGACACCATAAGAAAACCCTTTACA 58.634 36.000 0.00 0.00 0.00 2.41
2131 2738 4.882671 ACCATTTGAGTTACGATCATGC 57.117 40.909 0.00 0.00 0.00 4.06
2190 2797 5.285607 GTCATTCTCCACTAAACGAACGTAG 59.714 44.000 0.00 0.00 0.00 3.51
2193 2800 3.985279 TGTCATTCTCCACTAAACGAACG 59.015 43.478 0.00 0.00 0.00 3.95
2228 2835 7.083875 TGAAAATGACGAAATAATCACCTCC 57.916 36.000 0.00 0.00 0.00 4.30
2247 2854 3.882888 ACTGAGGCGACAAATCTTGAAAA 59.117 39.130 0.00 0.00 0.00 2.29
2263 2870 5.067153 ACGAATGTATGAGAAGAGACTGAGG 59.933 44.000 0.00 0.00 0.00 3.86
2300 2907 9.433153 GAAATACTTATATTTAGGAACGGAGGG 57.567 37.037 0.00 0.00 40.42 4.30
2301 2908 9.991906 TGAAATACTTATATTTAGGAACGGAGG 57.008 33.333 0.00 0.00 40.42 4.30
2350 2957 8.349568 TCTAAACTACGTCTATATGCATCCAT 57.650 34.615 0.19 0.00 35.44 3.41
2351 2958 7.447545 ACTCTAAACTACGTCTATATGCATCCA 59.552 37.037 0.19 0.00 0.00 3.41
2352 2959 7.818642 ACTCTAAACTACGTCTATATGCATCC 58.181 38.462 0.19 0.00 0.00 3.51
2363 2970 9.448294 CCAACAATCTATACTCTAAACTACGTC 57.552 37.037 0.00 0.00 0.00 4.34
2364 2971 7.919621 GCCAACAATCTATACTCTAAACTACGT 59.080 37.037 0.00 0.00 0.00 3.57
2365 2972 7.381678 GGCCAACAATCTATACTCTAAACTACG 59.618 40.741 0.00 0.00 0.00 3.51
2367 2974 7.346175 TGGGCCAACAATCTATACTCTAAACTA 59.654 37.037 2.13 0.00 0.00 2.24
2368 2975 6.157994 TGGGCCAACAATCTATACTCTAAACT 59.842 38.462 2.13 0.00 0.00 2.66
2369 2976 6.354130 TGGGCCAACAATCTATACTCTAAAC 58.646 40.000 2.13 0.00 0.00 2.01
2370 2977 6.157994 ACTGGGCCAACAATCTATACTCTAAA 59.842 38.462 8.04 0.00 0.00 1.85
2372 2979 5.216622 ACTGGGCCAACAATCTATACTCTA 58.783 41.667 8.04 0.00 0.00 2.43
2373 2980 4.040755 ACTGGGCCAACAATCTATACTCT 58.959 43.478 8.04 0.00 0.00 3.24
2374 2981 4.381411 GACTGGGCCAACAATCTATACTC 58.619 47.826 8.04 0.00 0.00 2.59
2375 2982 3.136626 GGACTGGGCCAACAATCTATACT 59.863 47.826 8.04 0.00 0.00 2.12
2376 2983 3.477530 GGACTGGGCCAACAATCTATAC 58.522 50.000 8.04 0.00 0.00 1.47
2378 2985 1.215423 GGGACTGGGCCAACAATCTAT 59.785 52.381 8.04 0.00 0.00 1.98
2379 2986 0.623723 GGGACTGGGCCAACAATCTA 59.376 55.000 8.04 0.00 0.00 1.98
2381 2988 2.046285 CGGGACTGGGCCAACAATC 61.046 63.158 8.04 2.80 0.00 2.67
2382 2989 2.035626 CGGGACTGGGCCAACAAT 59.964 61.111 8.04 0.00 0.00 2.71
2383 2990 3.172106 TCGGGACTGGGCCAACAA 61.172 61.111 8.04 0.00 0.00 2.83
2384 2991 3.948719 GTCGGGACTGGGCCAACA 61.949 66.667 8.04 0.00 0.00 3.33
2385 2992 3.948719 TGTCGGGACTGGGCCAAC 61.949 66.667 8.04 1.58 0.00 3.77
2386 2993 3.948719 GTGTCGGGACTGGGCCAA 61.949 66.667 8.04 0.00 0.00 4.52
2393 3753 1.553706 AAATACTCGGTGTCGGGACT 58.446 50.000 0.00 0.00 39.73 3.85
2395 3755 2.671914 CGAAAAATACTCGGTGTCGGGA 60.672 50.000 0.00 0.00 39.73 5.14
2410 3770 1.194997 CGTATCACCGTTGCCGAAAAA 59.805 47.619 0.00 0.00 35.63 1.94
2414 3774 1.153978 GTCGTATCACCGTTGCCGA 60.154 57.895 0.00 0.00 35.63 5.54
2423 3783 0.095245 TTCGTCGTCGGTCGTATCAC 59.905 55.000 1.55 0.00 40.80 3.06
2424 3784 0.095245 GTTCGTCGTCGGTCGTATCA 59.905 55.000 1.55 0.00 40.80 2.15
2425 3785 0.095245 TGTTCGTCGTCGGTCGTATC 59.905 55.000 1.55 4.35 40.80 2.24
2428 3788 1.655350 GTTGTTCGTCGTCGGTCGT 60.655 57.895 1.55 0.00 40.80 4.34
2429 3789 2.690817 CGTTGTTCGTCGTCGGTCG 61.691 63.158 1.55 0.00 41.41 4.79
2444 3804 1.729472 CGAGCTTCGTCTGTCATCGTT 60.729 52.381 0.00 0.00 34.72 3.85
2452 3812 0.179197 TCGTTAGCGAGCTTCGTCTG 60.179 55.000 1.86 0.00 42.81 3.51
2467 3827 5.895216 AAAAGTAATTCGTCGAGTTCGTT 57.105 34.783 6.23 0.00 40.80 3.85
2506 3866 7.857404 AGGATTGAAGGCTAGCTTTATACTA 57.143 36.000 12.63 0.00 0.00 1.82
2553 3913 7.201776 GCTAATCGATCAGGATAGATTGAGCTA 60.202 40.741 20.77 6.27 41.22 3.32
2612 3972 2.554462 AGCGATCTCTGTGCATACGTAT 59.446 45.455 1.14 1.14 0.00 3.06
2692 4052 6.555315 TCTCTTAAATTCCGTACGTTAGGAC 58.445 40.000 15.21 0.00 36.06 3.85
2693 4053 6.757897 TCTCTTAAATTCCGTACGTTAGGA 57.242 37.500 15.21 10.58 34.19 2.94
2694 4054 9.339492 GATATCTCTTAAATTCCGTACGTTAGG 57.661 37.037 15.21 6.81 0.00 2.69
2695 4055 9.339492 GGATATCTCTTAAATTCCGTACGTTAG 57.661 37.037 15.21 0.00 0.00 2.34
2696 4056 8.017373 CGGATATCTCTTAAATTCCGTACGTTA 58.983 37.037 15.21 3.20 40.82 3.18
2697 4057 6.860023 CGGATATCTCTTAAATTCCGTACGTT 59.140 38.462 15.21 4.25 40.82 3.99
2698 4058 6.205464 TCGGATATCTCTTAAATTCCGTACGT 59.795 38.462 15.21 0.00 44.79 3.57
2699 4059 6.605849 TCGGATATCTCTTAAATTCCGTACG 58.394 40.000 8.69 8.69 44.79 3.67
2700 4060 9.719279 CTATCGGATATCTCTTAAATTCCGTAC 57.281 37.037 8.78 0.00 44.79 3.67
2701 4061 9.676861 TCTATCGGATATCTCTTAAATTCCGTA 57.323 33.333 8.78 1.65 44.79 4.02
2702 4062 8.577048 TCTATCGGATATCTCTTAAATTCCGT 57.423 34.615 8.78 0.66 44.79 4.69
2703 4063 9.672086 GATCTATCGGATATCTCTTAAATTCCG 57.328 37.037 2.05 2.89 45.62 4.30
2704 4064 9.974980 GGATCTATCGGATATCTCTTAAATTCC 57.025 37.037 2.05 0.00 34.33 3.01
2708 4068 9.983024 AGAAGGATCTATCGGATATCTCTTAAA 57.017 33.333 2.05 0.00 34.33 1.52
2709 4069 9.983024 AAGAAGGATCTATCGGATATCTCTTAA 57.017 33.333 2.05 0.00 33.77 1.85
2712 4072 9.793259 GATAAGAAGGATCTATCGGATATCTCT 57.207 37.037 2.05 0.00 33.77 3.10
2713 4073 9.793259 AGATAAGAAGGATCTATCGGATATCTC 57.207 37.037 2.05 0.00 33.77 2.75
2714 4074 9.793259 GAGATAAGAAGGATCTATCGGATATCT 57.207 37.037 2.05 15.32 33.71 1.98
2715 4075 9.010029 GGAGATAAGAAGGATCTATCGGATATC 57.990 40.741 0.00 0.00 33.71 1.63
2716 4076 7.947890 GGGAGATAAGAAGGATCTATCGGATAT 59.052 40.741 0.00 0.00 33.71 1.63
2717 4077 7.129660 AGGGAGATAAGAAGGATCTATCGGATA 59.870 40.741 0.00 0.00 33.71 2.59
2718 4078 6.068498 AGGGAGATAAGAAGGATCTATCGGAT 60.068 42.308 0.00 0.00 33.71 4.18
2719 4079 5.254267 AGGGAGATAAGAAGGATCTATCGGA 59.746 44.000 0.00 0.00 33.71 4.55
2720 4080 5.515106 AGGGAGATAAGAAGGATCTATCGG 58.485 45.833 0.00 0.00 33.71 4.18
2721 4081 5.592688 GGAGGGAGATAAGAAGGATCTATCG 59.407 48.000 0.00 0.00 33.71 2.92
2722 4082 5.897250 GGGAGGGAGATAAGAAGGATCTATC 59.103 48.000 0.00 0.00 33.71 2.08
2723 4083 5.576822 CGGGAGGGAGATAAGAAGGATCTAT 60.577 48.000 0.00 0.00 33.71 1.98
2724 4084 4.263994 CGGGAGGGAGATAAGAAGGATCTA 60.264 50.000 0.00 0.00 33.71 1.98
2725 4085 3.501385 CGGGAGGGAGATAAGAAGGATCT 60.501 52.174 0.00 0.00 36.33 2.75
2726 4086 2.829120 CGGGAGGGAGATAAGAAGGATC 59.171 54.545 0.00 0.00 0.00 3.36
2727 4087 2.180308 ACGGGAGGGAGATAAGAAGGAT 59.820 50.000 0.00 0.00 0.00 3.24
2728 4088 1.574339 ACGGGAGGGAGATAAGAAGGA 59.426 52.381 0.00 0.00 0.00 3.36
2729 4089 1.689273 CACGGGAGGGAGATAAGAAGG 59.311 57.143 0.00 0.00 32.31 3.46
2730 4090 2.667470 TCACGGGAGGGAGATAAGAAG 58.333 52.381 0.00 0.00 37.36 2.85
2731 4091 2.840640 TCACGGGAGGGAGATAAGAA 57.159 50.000 0.00 0.00 37.36 2.52
2739 4099 2.284405 GGAAGGTCACGGGAGGGA 60.284 66.667 0.00 0.00 42.29 4.20
2740 4100 1.995626 ATGGAAGGTCACGGGAGGG 60.996 63.158 0.00 0.00 0.00 4.30
2741 4101 1.221840 CATGGAAGGTCACGGGAGG 59.778 63.158 0.00 0.00 0.00 4.30
2742 4102 1.450312 GCATGGAAGGTCACGGGAG 60.450 63.158 0.00 0.00 0.00 4.30
2743 4103 1.561769 ATGCATGGAAGGTCACGGGA 61.562 55.000 0.00 0.00 0.00 5.14
2744 4104 1.077501 ATGCATGGAAGGTCACGGG 60.078 57.895 0.00 0.00 0.00 5.28
2745 4105 1.996786 GCATGCATGGAAGGTCACGG 61.997 60.000 27.34 0.00 0.00 4.94
2746 4106 1.430632 GCATGCATGGAAGGTCACG 59.569 57.895 27.34 0.00 0.00 4.35
2747 4107 1.308069 ACGCATGCATGGAAGGTCAC 61.308 55.000 27.34 7.64 0.00 3.67
2748 4108 1.002257 ACGCATGCATGGAAGGTCA 60.002 52.632 27.34 0.00 0.00 4.02
2749 4109 1.308069 ACACGCATGCATGGAAGGTC 61.308 55.000 27.34 9.08 0.00 3.85
2750 4110 0.035534 TACACGCATGCATGGAAGGT 60.036 50.000 27.34 17.85 0.00 3.50
2751 4111 1.311859 ATACACGCATGCATGGAAGG 58.688 50.000 27.34 13.99 0.00 3.46
2752 4112 3.425577 AAATACACGCATGCATGGAAG 57.574 42.857 27.34 16.26 0.00 3.46
2753 4113 3.865011 AAAATACACGCATGCATGGAA 57.135 38.095 27.34 6.11 0.00 3.53
2754 4114 3.865011 AAAAATACACGCATGCATGGA 57.135 38.095 27.34 10.58 0.00 3.41
2803 4163 9.634163 CATGCATGCATGTAATTATGTTCTAAT 57.366 29.630 40.30 11.70 46.20 1.73
2831 4191 9.932207 TCTGCTGACATCATCAATTTTATTTTT 57.068 25.926 0.00 0.00 36.69 1.94
2834 4194 9.745880 GAATCTGCTGACATCATCAATTTTATT 57.254 29.630 0.00 0.00 36.69 1.40
2835 4195 9.132923 AGAATCTGCTGACATCATCAATTTTAT 57.867 29.630 0.00 0.00 36.69 1.40
2836 4196 8.515695 AGAATCTGCTGACATCATCAATTTTA 57.484 30.769 0.00 0.00 36.69 1.52
2837 4197 7.406031 AGAATCTGCTGACATCATCAATTTT 57.594 32.000 0.00 0.00 36.69 1.82
2838 4198 7.406031 AAGAATCTGCTGACATCATCAATTT 57.594 32.000 0.00 0.00 36.69 1.82
2839 4199 7.406031 AAAGAATCTGCTGACATCATCAATT 57.594 32.000 0.00 0.00 36.69 2.32
2840 4200 7.406031 AAAAGAATCTGCTGACATCATCAAT 57.594 32.000 0.00 0.00 36.69 2.57
2841 4201 6.829229 AAAAGAATCTGCTGACATCATCAA 57.171 33.333 0.00 0.00 36.69 2.57
2842 4202 6.431852 TGAAAAAGAATCTGCTGACATCATCA 59.568 34.615 0.00 0.27 35.45 3.07
2843 4203 6.849502 TGAAAAAGAATCTGCTGACATCATC 58.150 36.000 0.00 0.00 0.00 2.92
2844 4204 6.829229 TGAAAAAGAATCTGCTGACATCAT 57.171 33.333 0.00 0.00 0.00 2.45
2845 4205 6.638096 TTGAAAAAGAATCTGCTGACATCA 57.362 33.333 0.00 0.00 0.00 3.07
2846 4206 7.650903 AGTTTTGAAAAAGAATCTGCTGACATC 59.349 33.333 0.00 0.00 0.00 3.06
2847 4207 7.495055 AGTTTTGAAAAAGAATCTGCTGACAT 58.505 30.769 0.00 0.00 0.00 3.06
2848 4208 6.866480 AGTTTTGAAAAAGAATCTGCTGACA 58.134 32.000 0.00 0.00 0.00 3.58
2849 4209 6.974622 TGAGTTTTGAAAAAGAATCTGCTGAC 59.025 34.615 0.00 0.00 0.00 3.51
2850 4210 7.099266 TGAGTTTTGAAAAAGAATCTGCTGA 57.901 32.000 0.00 0.00 0.00 4.26
2851 4211 7.760131 TTGAGTTTTGAAAAAGAATCTGCTG 57.240 32.000 0.00 0.00 0.00 4.41
2852 4212 8.776376 TTTTGAGTTTTGAAAAAGAATCTGCT 57.224 26.923 0.00 0.00 0.00 4.24
2853 4213 9.992910 AATTTTGAGTTTTGAAAAAGAATCTGC 57.007 25.926 0.00 0.00 0.00 4.26
2888 4248 3.252215 CGGCTGATGGTTTGAGTTACAAA 59.748 43.478 0.00 0.00 44.79 2.83
2889 4249 2.811431 CGGCTGATGGTTTGAGTTACAA 59.189 45.455 0.00 0.00 36.65 2.41
2890 4250 2.422597 CGGCTGATGGTTTGAGTTACA 58.577 47.619 0.00 0.00 0.00 2.41
2891 4251 1.737793 CCGGCTGATGGTTTGAGTTAC 59.262 52.381 0.00 0.00 0.00 2.50
2892 4252 1.626321 TCCGGCTGATGGTTTGAGTTA 59.374 47.619 0.00 0.00 0.00 2.24
2893 4253 0.400213 TCCGGCTGATGGTTTGAGTT 59.600 50.000 0.00 0.00 0.00 3.01
2894 4254 0.620556 ATCCGGCTGATGGTTTGAGT 59.379 50.000 0.00 0.00 30.54 3.41
2895 4255 1.402968 CAATCCGGCTGATGGTTTGAG 59.597 52.381 0.00 0.00 38.07 3.02
2896 4256 1.004161 TCAATCCGGCTGATGGTTTGA 59.996 47.619 0.00 1.01 40.90 2.69
2897 4257 1.462616 TCAATCCGGCTGATGGTTTG 58.537 50.000 0.00 0.00 37.47 2.93
2898 4258 2.214376 TTCAATCCGGCTGATGGTTT 57.786 45.000 0.00 0.00 32.68 3.27
2899 4259 2.214376 TTTCAATCCGGCTGATGGTT 57.786 45.000 0.00 0.00 32.68 3.67
2900 4260 2.214376 TTTTCAATCCGGCTGATGGT 57.786 45.000 0.00 0.00 32.68 3.55
2901 4261 2.493278 AGTTTTTCAATCCGGCTGATGG 59.507 45.455 0.00 0.00 32.68 3.51
2902 4262 3.057315 ACAGTTTTTCAATCCGGCTGATG 60.057 43.478 0.00 0.00 32.68 3.07
2903 4263 3.157087 ACAGTTTTTCAATCCGGCTGAT 58.843 40.909 0.00 0.00 34.22 2.90
2904 4264 2.552315 GACAGTTTTTCAATCCGGCTGA 59.448 45.455 0.00 0.00 0.00 4.26
2905 4265 2.554032 AGACAGTTTTTCAATCCGGCTG 59.446 45.455 0.00 0.00 0.00 4.85
2906 4266 2.863809 AGACAGTTTTTCAATCCGGCT 58.136 42.857 0.00 0.00 0.00 5.52
2907 4267 3.004315 TGAAGACAGTTTTTCAATCCGGC 59.996 43.478 0.00 0.00 30.84 6.13
2908 4268 4.036262 TGTGAAGACAGTTTTTCAATCCGG 59.964 41.667 0.00 0.00 35.29 5.14
2909 4269 5.168526 TGTGAAGACAGTTTTTCAATCCG 57.831 39.130 3.69 0.00 35.29 4.18
2910 4270 9.528018 TTTTATGTGAAGACAGTTTTTCAATCC 57.472 29.630 3.69 0.00 35.29 3.01
2916 4276 9.450807 CGAATCTTTTATGTGAAGACAGTTTTT 57.549 29.630 0.00 0.00 36.08 1.94
2917 4277 8.621286 ACGAATCTTTTATGTGAAGACAGTTTT 58.379 29.630 0.00 0.00 36.08 2.43
2918 4278 8.154649 ACGAATCTTTTATGTGAAGACAGTTT 57.845 30.769 0.00 0.00 36.08 2.66
2919 4279 7.441157 TGACGAATCTTTTATGTGAAGACAGTT 59.559 33.333 0.00 0.00 36.08 3.16
2920 4280 6.929049 TGACGAATCTTTTATGTGAAGACAGT 59.071 34.615 0.00 0.00 36.08 3.55
2921 4281 7.230222 GTGACGAATCTTTTATGTGAAGACAG 58.770 38.462 0.00 0.00 36.08 3.51
2922 4282 6.128929 CGTGACGAATCTTTTATGTGAAGACA 60.129 38.462 0.00 0.00 36.08 3.41
2923 4283 6.089016 TCGTGACGAATCTTTTATGTGAAGAC 59.911 38.462 4.69 0.00 36.08 3.01
2924 4284 6.089016 GTCGTGACGAATCTTTTATGTGAAGA 59.911 38.462 10.12 0.00 37.72 2.87
2925 4285 6.234213 GTCGTGACGAATCTTTTATGTGAAG 58.766 40.000 10.12 0.00 37.72 3.02
2926 4286 6.148270 GTCGTGACGAATCTTTTATGTGAA 57.852 37.500 10.12 0.00 37.72 3.18
2927 4287 5.756950 GTCGTGACGAATCTTTTATGTGA 57.243 39.130 10.12 0.00 37.72 3.58
2942 4302 4.436653 CGAAGGTCTCGTCGTGAC 57.563 61.111 17.02 17.02 42.89 3.67
2950 4310 3.700038 TGGGATCTAGTTTCGAAGGTCTC 59.300 47.826 0.00 0.00 0.00 3.36
2951 4311 3.709587 TGGGATCTAGTTTCGAAGGTCT 58.290 45.455 0.00 1.62 0.00 3.85
2952 4312 4.141914 ACATGGGATCTAGTTTCGAAGGTC 60.142 45.833 0.00 0.00 0.00 3.85
2953 4313 3.775316 ACATGGGATCTAGTTTCGAAGGT 59.225 43.478 0.00 0.00 0.00 3.50
2954 4314 4.408182 ACATGGGATCTAGTTTCGAAGG 57.592 45.455 0.00 0.00 0.00 3.46
2955 4315 5.069251 ACCTACATGGGATCTAGTTTCGAAG 59.931 44.000 0.00 0.00 41.11 3.79
2956 4316 4.960469 ACCTACATGGGATCTAGTTTCGAA 59.040 41.667 0.00 0.00 41.11 3.71
2957 4317 4.543689 ACCTACATGGGATCTAGTTTCGA 58.456 43.478 0.00 0.00 41.11 3.71
2958 4318 4.939052 ACCTACATGGGATCTAGTTTCG 57.061 45.455 0.00 0.00 41.11 3.46
2959 4319 7.304497 ACATACCTACATGGGATCTAGTTTC 57.696 40.000 0.00 0.00 37.24 2.78
2960 4320 7.202102 GGAACATACCTACATGGGATCTAGTTT 60.202 40.741 0.00 0.00 37.24 2.66
2961 4321 6.270231 GGAACATACCTACATGGGATCTAGTT 59.730 42.308 0.00 0.00 37.24 2.24
2962 4322 5.780793 GGAACATACCTACATGGGATCTAGT 59.219 44.000 0.00 0.00 37.24 2.57
2963 4323 5.105716 CGGAACATACCTACATGGGATCTAG 60.106 48.000 0.00 0.00 37.24 2.43
2964 4324 4.770531 CGGAACATACCTACATGGGATCTA 59.229 45.833 0.00 0.00 37.24 1.98
2965 4325 3.578716 CGGAACATACCTACATGGGATCT 59.421 47.826 0.00 0.00 37.24 2.75
2966 4326 3.576982 TCGGAACATACCTACATGGGATC 59.423 47.826 0.00 0.00 37.24 3.36
2967 4327 3.323979 GTCGGAACATACCTACATGGGAT 59.676 47.826 0.00 0.00 40.99 3.85
2968 4328 2.696707 GTCGGAACATACCTACATGGGA 59.303 50.000 0.00 0.00 41.11 4.37
2969 4329 2.432874 TGTCGGAACATACCTACATGGG 59.567 50.000 0.00 0.00 41.11 4.00
2970 4330 3.812156 TGTCGGAACATACCTACATGG 57.188 47.619 0.00 0.00 42.93 3.66
2971 4331 4.755411 AGTTGTCGGAACATACCTACATG 58.245 43.478 0.00 0.00 35.96 3.21
2972 4332 5.416271 AAGTTGTCGGAACATACCTACAT 57.584 39.130 0.00 0.00 35.96 2.29
2973 4333 4.877378 AAGTTGTCGGAACATACCTACA 57.123 40.909 0.00 0.00 34.73 2.74
2974 4334 6.549912 AAAAAGTTGTCGGAACATACCTAC 57.450 37.500 1.81 0.00 34.73 3.18


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

AutoCloner maintained by Alex Coulton.