Multiple sequence alignment - TraesCS2D01G434300

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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 TraesCS2D01G434300 chr2D 100.000 4715 0 0 1 4715 545497549 545502263 0.000000e+00 8708.0
1 TraesCS2D01G434300 chr2D 90.074 1491 112 16 2465 3928 583232606 583231125 0.000000e+00 1901.0
2 TraesCS2D01G434300 chr2D 88.802 1286 108 26 968 2244 583234039 583232781 0.000000e+00 1544.0
3 TraesCS2D01G434300 chr2D 87.049 1274 130 19 2464 3718 581524904 581526161 0.000000e+00 1406.0
4 TraesCS2D01G434300 chr2D 83.739 1439 189 23 968 2381 581523463 581524881 0.000000e+00 1319.0
5 TraesCS2D01G434300 chr2D 82.920 1007 135 15 1 972 68809564 68808560 0.000000e+00 872.0
6 TraesCS2D01G434300 chr2D 94.755 286 10 2 3832 4114 545501285 545501568 1.560000e-119 440.0
7 TraesCS2D01G434300 chr2D 94.755 286 10 2 3737 4020 545501380 545501662 1.560000e-119 440.0
8 TraesCS2D01G434300 chr2D 86.598 291 24 8 3932 4209 583231315 583231027 1.650000e-79 307.0
9 TraesCS2D01G434300 chr2D 93.229 192 9 2 3927 4114 545501285 545501476 3.590000e-71 279.0
10 TraesCS2D01G434300 chr2D 93.229 192 9 2 3737 3928 545501475 545501662 3.590000e-71 279.0
11 TraesCS2D01G434300 chr2D 88.718 195 7 5 3837 4020 583231315 583231125 1.710000e-54 224.0
12 TraesCS2D01G434300 chr2D 92.784 97 5 2 3737 3833 583231219 583231125 6.360000e-29 139.0
13 TraesCS2D01G434300 chr2D 90.722 97 8 1 4019 4114 545501285 545501381 1.380000e-25 128.0
14 TraesCS2D01G434300 chr2D 94.444 54 2 1 4093 4145 581526519 581526572 1.090000e-11 82.4
15 TraesCS2D01G434300 chr2D 100.000 39 0 0 2397 2435 545499918 545499956 6.540000e-09 73.1
16 TraesCS2D01G434300 chr2D 100.000 39 0 0 2370 2408 545499945 545499983 6.540000e-09 73.1
17 TraesCS2D01G434300 chr2A 98.319 2082 25 3 2397 4478 687505367 687503296 0.000000e+00 3642.0
18 TraesCS2D01G434300 chr2A 98.166 1418 20 3 997 2408 687506746 687505329 0.000000e+00 2470.0
19 TraesCS2D01G434300 chr2A 82.785 1034 130 17 2464 3462 718378689 718377669 0.000000e+00 880.0
20 TraesCS2D01G434300 chr2A 94.406 286 11 2 3737 4020 687503932 687503650 7.250000e-118 435.0
21 TraesCS2D01G434300 chr2A 93.357 286 14 2 3832 4114 687504027 687503744 7.300000e-113 418.0
22 TraesCS2D01G434300 chr2A 95.142 247 7 2 4469 4715 687497532 687497291 7.400000e-103 385.0
23 TraesCS2D01G434300 chr2A 78.234 657 99 21 1751 2381 718379353 718378715 9.570000e-102 381.0
24 TraesCS2D01G434300 chr2A 93.750 192 8 2 3737 3928 687503837 687503650 7.720000e-73 285.0
25 TraesCS2D01G434300 chr2A 91.146 192 13 2 3927 4114 687504027 687503836 1.680000e-64 257.0
26 TraesCS2D01G434300 chr2A 96.639 119 3 1 968 1086 687506811 687506694 3.720000e-46 196.0
27 TraesCS2D01G434300 chr2B 89.608 2425 198 19 1033 3441 702727607 702725221 0.000000e+00 3033.0
28 TraesCS2D01G434300 chr2B 87.184 1264 137 14 2464 3718 699828711 699827464 0.000000e+00 1413.0
29 TraesCS2D01G434300 chr2B 83.761 1404 191 16 999 2381 699830121 699828734 0.000000e+00 1295.0
30 TraesCS2D01G434300 chr2B 88.596 456 37 6 3483 3928 702724938 702724488 1.490000e-149 540.0
31 TraesCS2D01G434300 chr2B 86.301 292 24 9 3932 4209 702724678 702724389 2.130000e-78 303.0
32 TraesCS2D01G434300 chr2B 88.718 195 7 5 3837 4020 702724678 702724488 1.710000e-54 224.0
33 TraesCS2D01G434300 chr2B 93.333 60 3 1 4093 4151 699827106 699827047 2.340000e-13 87.9
34 TraesCS2D01G434300 chr2B 100.000 37 0 0 3468 3504 702724974 702724938 8.470000e-08 69.4
35 TraesCS2D01G434300 chr1D 95.035 1007 12 10 1 971 382251704 382252708 0.000000e+00 1548.0
36 TraesCS2D01G434300 chr1D 94.747 990 17 7 1 955 92252002 92252991 0.000000e+00 1507.0
37 TraesCS2D01G434300 chr7D 94.711 1002 17 8 1 968 134840177 134841176 0.000000e+00 1524.0
38 TraesCS2D01G434300 chr3D 94.240 1007 22 8 1 971 520425082 520424076 0.000000e+00 1506.0
39 TraesCS2D01G434300 chr4B 92.563 995 47 8 1 968 520395026 520396020 0.000000e+00 1402.0
40 TraesCS2D01G434300 chr5B 90.358 1006 59 10 1 970 657435402 657434399 0.000000e+00 1286.0
41 TraesCS2D01G434300 chr5D 87.000 1000 91 6 2 966 370591357 370592352 0.000000e+00 1090.0
42 TraesCS2D01G434300 chr5D 86.613 1001 99 8 2 967 536749632 536750632 0.000000e+00 1074.0
43 TraesCS2D01G434300 chr5D 94.437 701 4 7 303 968 494779633 494780333 0.000000e+00 1046.0
44 TraesCS2D01G434300 chr5D 97.297 37 0 1 4348 4383 217944797 217944833 1.420000e-05 62.1
45 TraesCS2D01G434300 chr5A 85.672 1005 105 8 1 966 707465490 707466494 0.000000e+00 1022.0
46 TraesCS2D01G434300 chr5A 90.976 410 13 7 583 968 703467642 703467233 8.980000e-147 531.0
47 TraesCS2D01G434300 chr3B 84.811 981 130 10 1 966 260139287 260140263 0.000000e+00 968.0
48 TraesCS2D01G434300 chr3B 95.122 82 4 0 886 967 736739531 736739612 3.830000e-26 130.0
49 TraesCS2D01G434300 chr1A 81.369 1213 187 23 2522 3716 566586548 566585357 0.000000e+00 952.0
50 TraesCS2D01G434300 chrUn 100.000 392 0 0 1176 1567 479739906 479739515 0.000000e+00 725.0
51 TraesCS2D01G434300 chr1B 82.323 792 109 18 2523 3304 657282593 657281823 0.000000e+00 658.0
52 TraesCS2D01G434300 chr6B 97.059 34 1 0 4354 4387 422568246 422568279 1.830000e-04 58.4
53 TraesCS2D01G434300 chr6B 87.273 55 2 4 4354 4408 703356151 703356200 1.830000e-04 58.4


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G434300 chr2D 545497549 545502263 4714 False 1302.525000 8708 95.836250 1 4715 8 chr2D.!!$F1 4714
1 TraesCS2D01G434300 chr2D 581523463 581526572 3109 False 935.800000 1406 88.410667 968 4145 3 chr2D.!!$F2 3177
2 TraesCS2D01G434300 chr2D 68808560 68809564 1004 True 872.000000 872 82.920000 1 972 1 chr2D.!!$R1 971
3 TraesCS2D01G434300 chr2D 583231027 583234039 3012 True 823.000000 1901 89.395200 968 4209 5 chr2D.!!$R2 3241
4 TraesCS2D01G434300 chr2A 687503296 687506811 3515 True 1100.428571 3642 95.111857 968 4478 7 chr2A.!!$R2 3510
5 TraesCS2D01G434300 chr2A 718377669 718379353 1684 True 630.500000 880 80.509500 1751 3462 2 chr2A.!!$R3 1711
6 TraesCS2D01G434300 chr2B 699827047 699830121 3074 True 931.966667 1413 88.092667 999 4151 3 chr2B.!!$R1 3152
7 TraesCS2D01G434300 chr2B 702724389 702727607 3218 True 833.880000 3033 90.644600 1033 4209 5 chr2B.!!$R2 3176
8 TraesCS2D01G434300 chr1D 382251704 382252708 1004 False 1548.000000 1548 95.035000 1 971 1 chr1D.!!$F2 970
9 TraesCS2D01G434300 chr1D 92252002 92252991 989 False 1507.000000 1507 94.747000 1 955 1 chr1D.!!$F1 954
10 TraesCS2D01G434300 chr7D 134840177 134841176 999 False 1524.000000 1524 94.711000 1 968 1 chr7D.!!$F1 967
11 TraesCS2D01G434300 chr3D 520424076 520425082 1006 True 1506.000000 1506 94.240000 1 971 1 chr3D.!!$R1 970
12 TraesCS2D01G434300 chr4B 520395026 520396020 994 False 1402.000000 1402 92.563000 1 968 1 chr4B.!!$F1 967
13 TraesCS2D01G434300 chr5B 657434399 657435402 1003 True 1286.000000 1286 90.358000 1 970 1 chr5B.!!$R1 969
14 TraesCS2D01G434300 chr5D 370591357 370592352 995 False 1090.000000 1090 87.000000 2 966 1 chr5D.!!$F2 964
15 TraesCS2D01G434300 chr5D 536749632 536750632 1000 False 1074.000000 1074 86.613000 2 967 1 chr5D.!!$F4 965
16 TraesCS2D01G434300 chr5D 494779633 494780333 700 False 1046.000000 1046 94.437000 303 968 1 chr5D.!!$F3 665
17 TraesCS2D01G434300 chr5A 707465490 707466494 1004 False 1022.000000 1022 85.672000 1 966 1 chr5A.!!$F1 965
18 TraesCS2D01G434300 chr3B 260139287 260140263 976 False 968.000000 968 84.811000 1 966 1 chr3B.!!$F1 965
19 TraesCS2D01G434300 chr1A 566585357 566586548 1191 True 952.000000 952 81.369000 2522 3716 1 chr1A.!!$R1 1194
20 TraesCS2D01G434300 chr1B 657281823 657282593 770 True 658.000000 658 82.323000 2523 3304 1 chr1B.!!$R1 781

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
37 38 4.156739 GGTCGAAGCTTTGGAAGATTGATT 59.843 41.667 13.87 0.0 37.23 2.57 F
946 1023 5.741388 ATGTGACGGATCAATAAAGCTTC 57.259 39.130 0.00 0.0 36.31 3.86 F
2408 2606 1.980765 TGCAGAGGAAGTCCATGAAGT 59.019 47.619 0.00 0.0 38.89 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2580 1.137675 TCATGGACTTCCTCTGCATCG 59.862 52.381 0.0 0.0 36.82 3.84 R
2410 2608 0.247460 TGGACTTCCTCTGCATCGTG 59.753 55.000 0.0 0.0 36.82 4.35 R
4658 5399 0.034896 GGTCGTCCCATGTGAACAGT 59.965 55.000 0.0 0.0 0.00 3.55 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
37 38 4.156739 GGTCGAAGCTTTGGAAGATTGATT 59.843 41.667 13.87 0.00 37.23 2.57
946 1023 5.741388 ATGTGACGGATCAATAAAGCTTC 57.259 39.130 0.00 0.00 36.31 3.86
2286 2450 8.047911 TGACCATTAATCCATGCATTCATTTTT 58.952 29.630 0.00 0.00 0.00 1.94
2385 2580 2.704572 CCTCAAGTCCATGAAGTCCAC 58.295 52.381 0.00 0.00 0.00 4.02
2407 2605 2.775911 TGCAGAGGAAGTCCATGAAG 57.224 50.000 0.00 0.00 38.89 3.02
2408 2606 1.980765 TGCAGAGGAAGTCCATGAAGT 59.019 47.619 0.00 0.00 38.89 3.01
2409 2607 2.027745 TGCAGAGGAAGTCCATGAAGTC 60.028 50.000 0.00 0.00 38.89 3.01
2410 2608 2.679349 GCAGAGGAAGTCCATGAAGTCC 60.679 54.545 0.00 0.00 38.89 3.85
2411 2609 2.568956 CAGAGGAAGTCCATGAAGTCCA 59.431 50.000 0.00 0.00 38.89 4.02
2412 2610 2.569404 AGAGGAAGTCCATGAAGTCCAC 59.431 50.000 0.00 0.00 38.89 4.02
2413 2611 1.276421 AGGAAGTCCATGAAGTCCACG 59.724 52.381 0.00 0.00 38.89 4.94
2414 2612 1.275291 GGAAGTCCATGAAGTCCACGA 59.725 52.381 0.00 0.00 35.64 4.35
2415 2613 2.093447 GGAAGTCCATGAAGTCCACGAT 60.093 50.000 0.00 0.00 35.64 3.73
2416 2614 2.680312 AGTCCATGAAGTCCACGATG 57.320 50.000 0.00 0.00 0.00 3.84
2417 2615 1.009829 GTCCATGAAGTCCACGATGC 58.990 55.000 0.00 0.00 0.00 3.91
2418 2616 0.612744 TCCATGAAGTCCACGATGCA 59.387 50.000 0.00 0.00 0.00 3.96
2419 2617 1.012086 CCATGAAGTCCACGATGCAG 58.988 55.000 0.00 0.00 0.00 4.41
2420 2618 1.405933 CCATGAAGTCCACGATGCAGA 60.406 52.381 0.00 0.00 0.00 4.26
2421 2619 1.931841 CATGAAGTCCACGATGCAGAG 59.068 52.381 0.00 0.00 0.00 3.35
2422 2620 0.247460 TGAAGTCCACGATGCAGAGG 59.753 55.000 0.00 0.00 0.00 3.69
2423 2621 0.532573 GAAGTCCACGATGCAGAGGA 59.467 55.000 0.00 0.00 0.00 3.71
2424 2622 0.976641 AAGTCCACGATGCAGAGGAA 59.023 50.000 0.00 0.00 32.85 3.36
2425 2623 0.534412 AGTCCACGATGCAGAGGAAG 59.466 55.000 0.00 0.00 32.85 3.46
2426 2624 0.247736 GTCCACGATGCAGAGGAAGT 59.752 55.000 0.00 0.00 32.85 3.01
2427 2625 0.532573 TCCACGATGCAGAGGAAGTC 59.467 55.000 0.00 0.00 0.00 3.01
2428 2626 0.460987 CCACGATGCAGAGGAAGTCC 60.461 60.000 0.00 0.00 0.00 3.85
2429 2627 0.247460 CACGATGCAGAGGAAGTCCA 59.753 55.000 0.00 0.00 38.89 4.02
2430 2628 1.134580 CACGATGCAGAGGAAGTCCAT 60.135 52.381 0.00 0.00 38.89 3.41
2431 2629 1.134580 ACGATGCAGAGGAAGTCCATG 60.135 52.381 0.00 0.00 38.89 3.66
2432 2630 1.137675 CGATGCAGAGGAAGTCCATGA 59.862 52.381 0.00 0.00 38.89 3.07
2433 2631 2.419159 CGATGCAGAGGAAGTCCATGAA 60.419 50.000 0.00 0.00 38.89 2.57
2678 2902 5.495926 AAACAAGTCTCATGGATCTGAGT 57.504 39.130 10.76 0.00 42.68 3.41
2679 2903 4.734398 ACAAGTCTCATGGATCTGAGTC 57.266 45.455 10.76 6.51 42.68 3.36
2680 2904 3.450457 ACAAGTCTCATGGATCTGAGTCC 59.550 47.826 10.76 4.78 42.68 3.85
3120 3383 7.272244 TCTCACATGTTCTTGTCTTCACTTTA 58.728 34.615 0.00 0.00 0.00 1.85
3723 4233 2.072298 GTCTCTTTCTGATGCGCTTGT 58.928 47.619 9.73 0.00 0.00 3.16
3892 4629 1.270305 GCACCAGCTAGTGACAAGTGA 60.270 52.381 16.93 0.00 40.34 3.41
3893 4630 2.806745 GCACCAGCTAGTGACAAGTGAA 60.807 50.000 16.93 0.00 40.34 3.18
3894 4631 2.802816 CACCAGCTAGTGACAAGTGAAC 59.197 50.000 6.41 0.00 40.34 3.18
3895 4632 2.700897 ACCAGCTAGTGACAAGTGAACT 59.299 45.455 0.00 0.00 0.00 3.01
3896 4633 3.134804 ACCAGCTAGTGACAAGTGAACTT 59.865 43.478 0.00 0.00 36.45 2.66
3911 4648 5.181748 AGTGAACTTGTATGATCCTCTTGC 58.818 41.667 0.00 0.00 0.00 4.01
3914 4651 5.877012 TGAACTTGTATGATCCTCTTGCTTC 59.123 40.000 0.00 0.00 0.00 3.86
3928 4665 5.122082 CCTCTTGCTTCTTCTGTGAATTCTC 59.878 44.000 7.05 3.61 0.00 2.87
3929 4666 5.614308 TCTTGCTTCTTCTGTGAATTCTCA 58.386 37.500 7.05 8.51 0.00 3.27
3958 4695 9.841295 AGTCAACTTGTACTTTATTTTGGTAGA 57.159 29.630 0.00 0.00 0.00 2.59
3959 4696 9.874215 GTCAACTTGTACTTTATTTTGGTAGAC 57.126 33.333 0.00 0.00 0.00 2.59
3960 4697 9.841295 TCAACTTGTACTTTATTTTGGTAGACT 57.159 29.630 0.00 0.00 0.00 3.24
3963 4700 9.708092 ACTTGTACTTTATTTTGGTAGACTCTC 57.292 33.333 0.00 0.00 0.00 3.20
3964 4701 9.706691 CTTGTACTTTATTTTGGTAGACTCTCA 57.293 33.333 0.00 0.00 0.00 3.27
4047 4784 8.614994 CAAGTCAACTTGTTCTTTATTTTCGT 57.385 30.769 13.54 0.00 46.11 3.85
4108 4845 5.163713 GGATGATACTCTTGGTTTTCTGTGC 60.164 44.000 0.00 0.00 0.00 4.57
4285 5026 7.136772 CAGAACGCAAATCATATGAATCATGT 58.863 34.615 9.99 3.65 0.00 3.21
4393 5134 2.096268 TCTGCAAATTTTCTCTCGTGCG 60.096 45.455 0.00 0.00 34.73 5.34
4427 5168 6.089551 CGCTTTATTCCTGTATATGTTCCTCG 59.910 42.308 0.00 0.00 0.00 4.63
4478 5219 1.728074 CCATAGCGCGCGTTCGATA 60.728 57.895 32.35 12.04 38.10 2.92
4479 5220 1.272784 CCATAGCGCGCGTTCGATAA 61.273 55.000 32.35 10.47 38.10 1.75
4480 5221 0.179307 CATAGCGCGCGTTCGATAAC 60.179 55.000 32.35 11.90 38.10 1.89
4481 5222 0.593008 ATAGCGCGCGTTCGATAACA 60.593 50.000 32.35 8.77 38.10 2.41
4482 5223 0.797629 TAGCGCGCGTTCGATAACAA 60.798 50.000 32.35 4.24 38.10 2.83
4483 5224 1.921757 GCGCGCGTTCGATAACAAC 60.922 57.895 32.35 5.70 38.10 3.32
4484 5225 1.412987 CGCGCGTTCGATAACAACA 59.587 52.632 24.19 0.00 38.10 3.33
4485 5226 0.179270 CGCGCGTTCGATAACAACAA 60.179 50.000 24.19 0.00 38.10 2.83
4486 5227 1.235695 GCGCGTTCGATAACAACAAC 58.764 50.000 8.43 0.00 38.10 3.32
4487 5228 1.397441 GCGCGTTCGATAACAACAACA 60.397 47.619 8.43 0.00 38.10 3.33
4488 5229 2.893837 CGCGTTCGATAACAACAACAA 58.106 42.857 0.00 0.00 38.10 2.83
4489 5230 3.281601 CGCGTTCGATAACAACAACAAA 58.718 40.909 0.00 0.00 38.10 2.83
4490 5231 3.719840 CGCGTTCGATAACAACAACAAAA 59.280 39.130 0.00 0.00 38.10 2.44
4491 5232 4.202558 CGCGTTCGATAACAACAACAAAAA 59.797 37.500 0.00 0.00 38.10 1.94
4512 5253 7.466746 AAAAAGAAGCTATTGCCTTGTATGA 57.533 32.000 0.00 0.00 40.80 2.15
4513 5254 7.466746 AAAAGAAGCTATTGCCTTGTATGAA 57.533 32.000 0.00 0.00 40.80 2.57
4514 5255 7.651027 AAAGAAGCTATTGCCTTGTATGAAT 57.349 32.000 0.00 0.00 40.80 2.57
4515 5256 6.630444 AGAAGCTATTGCCTTGTATGAATG 57.370 37.500 0.00 0.00 40.80 2.67
4516 5257 5.533903 AGAAGCTATTGCCTTGTATGAATGG 59.466 40.000 0.00 0.00 40.80 3.16
4517 5258 4.147321 AGCTATTGCCTTGTATGAATGGG 58.853 43.478 0.00 0.00 40.80 4.00
4518 5259 3.305608 GCTATTGCCTTGTATGAATGGGC 60.306 47.826 0.00 0.00 42.73 5.36
4519 5260 2.530460 TTGCCTTGTATGAATGGGCT 57.470 45.000 0.00 0.00 42.84 5.19
4520 5261 3.660970 TTGCCTTGTATGAATGGGCTA 57.339 42.857 0.00 0.00 42.84 3.93
4521 5262 3.660970 TGCCTTGTATGAATGGGCTAA 57.339 42.857 0.00 0.00 42.84 3.09
4522 5263 3.974719 TGCCTTGTATGAATGGGCTAAA 58.025 40.909 0.00 0.00 42.84 1.85
4523 5264 4.545678 TGCCTTGTATGAATGGGCTAAAT 58.454 39.130 0.00 0.00 42.84 1.40
4524 5265 4.341806 TGCCTTGTATGAATGGGCTAAATG 59.658 41.667 0.00 0.00 42.84 2.32
4525 5266 4.262164 GCCTTGTATGAATGGGCTAAATGG 60.262 45.833 0.00 0.00 39.68 3.16
4526 5267 4.281688 CCTTGTATGAATGGGCTAAATGGG 59.718 45.833 0.00 0.00 0.00 4.00
4527 5268 3.230134 TGTATGAATGGGCTAAATGGGC 58.770 45.455 0.00 0.00 0.00 5.36
4536 5277 2.747177 GGCTAAATGGGCCTTTAAGGT 58.253 47.619 13.03 0.00 45.57 3.50
4537 5278 3.104512 GGCTAAATGGGCCTTTAAGGTT 58.895 45.455 13.03 1.12 45.57 3.50
4538 5279 3.517901 GGCTAAATGGGCCTTTAAGGTTT 59.482 43.478 13.03 7.59 45.57 3.27
4539 5280 4.019681 GGCTAAATGGGCCTTTAAGGTTTT 60.020 41.667 13.03 9.85 45.57 2.43
4540 5281 5.188163 GGCTAAATGGGCCTTTAAGGTTTTA 59.812 40.000 13.03 10.37 45.57 1.52
4541 5282 6.126883 GGCTAAATGGGCCTTTAAGGTTTTAT 60.127 38.462 13.03 0.26 45.57 1.40
4542 5283 7.335627 GCTAAATGGGCCTTTAAGGTTTTATT 58.664 34.615 13.03 6.08 37.80 1.40
4543 5284 8.479689 GCTAAATGGGCCTTTAAGGTTTTATTA 58.520 33.333 13.03 6.68 37.80 0.98
4545 5286 7.432148 AATGGGCCTTTAAGGTTTTATTAGG 57.568 36.000 13.03 0.00 37.80 2.69
4546 5287 6.155247 TGGGCCTTTAAGGTTTTATTAGGA 57.845 37.500 13.03 0.00 37.80 2.94
4547 5288 6.563163 TGGGCCTTTAAGGTTTTATTAGGAA 58.437 36.000 13.03 0.00 37.80 3.36
4548 5289 7.193338 TGGGCCTTTAAGGTTTTATTAGGAAT 58.807 34.615 13.03 0.00 37.80 3.01
4549 5290 7.680739 TGGGCCTTTAAGGTTTTATTAGGAATT 59.319 33.333 13.03 0.00 37.80 2.17
4550 5291 8.202137 GGGCCTTTAAGGTTTTATTAGGAATTC 58.798 37.037 13.03 0.00 37.80 2.17
4551 5292 8.978472 GGCCTTTAAGGTTTTATTAGGAATTCT 58.022 33.333 13.03 0.00 37.80 2.40
4552 5293 9.803315 GCCTTTAAGGTTTTATTAGGAATTCTG 57.197 33.333 13.03 0.00 37.80 3.02
4568 5309 8.281529 AGGAATTCTGAAAATACTATAGGGCT 57.718 34.615 5.23 0.00 0.00 5.19
4569 5310 8.160106 AGGAATTCTGAAAATACTATAGGGCTG 58.840 37.037 5.23 0.00 0.00 4.85
4570 5311 7.391833 GGAATTCTGAAAATACTATAGGGCTGG 59.608 40.741 5.23 0.00 0.00 4.85
4571 5312 5.228945 TCTGAAAATACTATAGGGCTGGC 57.771 43.478 4.43 0.00 0.00 4.85
4572 5313 4.041691 TCTGAAAATACTATAGGGCTGGCC 59.958 45.833 13.15 13.15 0.00 5.36
4573 5314 3.719479 TGAAAATACTATAGGGCTGGCCA 59.281 43.478 23.25 4.71 37.98 5.36
4574 5315 4.167113 TGAAAATACTATAGGGCTGGCCAA 59.833 41.667 23.25 6.42 37.98 4.52
4575 5316 4.806952 AAATACTATAGGGCTGGCCAAA 57.193 40.909 23.25 10.40 37.98 3.28
4576 5317 4.806952 AATACTATAGGGCTGGCCAAAA 57.193 40.909 23.25 7.72 37.98 2.44
4577 5318 4.806952 ATACTATAGGGCTGGCCAAAAA 57.193 40.909 23.25 5.08 37.98 1.94
4602 5343 7.721286 ATAGACTAAATTCAAGCAGAATCCG 57.279 36.000 5.08 1.07 46.09 4.18
4603 5344 4.333926 AGACTAAATTCAAGCAGAATCCGC 59.666 41.667 5.08 0.00 46.09 5.54
4604 5345 2.947448 AAATTCAAGCAGAATCCGCC 57.053 45.000 5.08 0.00 46.09 6.13
4605 5346 0.734889 AATTCAAGCAGAATCCGCCG 59.265 50.000 5.08 0.00 46.09 6.46
4606 5347 1.097547 ATTCAAGCAGAATCCGCCGG 61.098 55.000 0.00 0.00 43.42 6.13
4607 5348 3.880846 CAAGCAGAATCCGCCGGC 61.881 66.667 19.07 19.07 0.00 6.13
4610 5351 4.235762 GCAGAATCCGCCGGCCTA 62.236 66.667 23.46 9.76 0.00 3.93
4611 5352 2.743718 CAGAATCCGCCGGCCTAT 59.256 61.111 23.46 12.01 0.00 2.57
4612 5353 1.071471 CAGAATCCGCCGGCCTATT 59.929 57.895 23.46 20.35 0.00 1.73
4613 5354 0.951040 CAGAATCCGCCGGCCTATTC 60.951 60.000 28.58 28.58 0.00 1.75
4614 5355 1.671379 GAATCCGCCGGCCTATTCC 60.671 63.158 26.81 15.08 0.00 3.01
4623 5364 4.977393 GCCTATTCCGGCTTTCCA 57.023 55.556 0.00 0.00 46.63 3.53
4624 5365 2.707902 GCCTATTCCGGCTTTCCAG 58.292 57.895 0.00 0.00 46.63 3.86
4625 5366 1.448119 GCCTATTCCGGCTTTCCAGC 61.448 60.000 0.00 0.00 46.63 4.85
4626 5367 0.181350 CCTATTCCGGCTTTCCAGCT 59.819 55.000 0.00 0.00 46.44 4.24
4631 5372 2.359107 CGGCTTTCCAGCTGCTCA 60.359 61.111 8.66 0.00 45.64 4.26
4632 5373 2.684843 CGGCTTTCCAGCTGCTCAC 61.685 63.158 8.66 0.00 45.64 3.51
4633 5374 1.601759 GGCTTTCCAGCTGCTCACA 60.602 57.895 8.66 0.00 46.44 3.58
4634 5375 0.964358 GGCTTTCCAGCTGCTCACAT 60.964 55.000 8.66 0.00 46.44 3.21
4635 5376 0.170561 GCTTTCCAGCTGCTCACATG 59.829 55.000 8.66 0.00 43.51 3.21
4636 5377 0.809385 CTTTCCAGCTGCTCACATGG 59.191 55.000 8.66 0.00 0.00 3.66
4637 5378 0.609957 TTTCCAGCTGCTCACATGGG 60.610 55.000 8.66 0.00 33.45 4.00
4638 5379 1.491274 TTCCAGCTGCTCACATGGGA 61.491 55.000 8.66 0.00 33.45 4.37
4639 5380 1.226542 CCAGCTGCTCACATGGGAT 59.773 57.895 8.66 0.00 0.00 3.85
4640 5381 0.818445 CCAGCTGCTCACATGGGATC 60.818 60.000 8.66 0.00 0.00 3.36
4641 5382 0.180642 CAGCTGCTCACATGGGATCT 59.819 55.000 0.00 0.00 0.00 2.75
4642 5383 0.917533 AGCTGCTCACATGGGATCTT 59.082 50.000 0.00 0.00 0.00 2.40
4643 5384 1.134159 AGCTGCTCACATGGGATCTTC 60.134 52.381 0.00 0.00 0.00 2.87
4644 5385 1.134159 GCTGCTCACATGGGATCTTCT 60.134 52.381 0.00 0.00 0.00 2.85
4645 5386 2.836262 CTGCTCACATGGGATCTTCTC 58.164 52.381 0.00 0.00 0.00 2.87
4646 5387 2.169978 CTGCTCACATGGGATCTTCTCA 59.830 50.000 0.00 0.00 0.00 3.27
4647 5388 2.573009 TGCTCACATGGGATCTTCTCAA 59.427 45.455 0.00 0.00 26.19 3.02
4648 5389 3.009363 TGCTCACATGGGATCTTCTCAAA 59.991 43.478 0.00 0.00 26.19 2.69
4649 5390 4.012374 GCTCACATGGGATCTTCTCAAAA 58.988 43.478 0.00 0.00 26.19 2.44
4650 5391 4.460382 GCTCACATGGGATCTTCTCAAAAA 59.540 41.667 0.00 0.00 26.19 1.94
4674 5415 3.708563 AAAAACTGTTCACATGGGACG 57.291 42.857 0.00 0.00 0.00 4.79
4675 5416 2.631160 AAACTGTTCACATGGGACGA 57.369 45.000 0.00 0.00 0.00 4.20
4676 5417 1.878953 AACTGTTCACATGGGACGAC 58.121 50.000 0.00 0.00 0.00 4.34
4677 5418 0.034896 ACTGTTCACATGGGACGACC 59.965 55.000 0.00 0.00 40.81 4.79
4678 5419 0.321671 CTGTTCACATGGGACGACCT 59.678 55.000 0.00 0.00 41.11 3.85
4679 5420 0.320374 TGTTCACATGGGACGACCTC 59.680 55.000 0.00 0.00 41.11 3.85
4680 5421 0.391263 GTTCACATGGGACGACCTCC 60.391 60.000 0.00 0.00 41.11 4.30
4681 5422 0.544357 TTCACATGGGACGACCTCCT 60.544 55.000 0.00 0.00 39.39 3.69
4682 5423 0.970937 TCACATGGGACGACCTCCTC 60.971 60.000 3.44 0.00 39.39 3.71
4691 5432 3.920144 CGACCTCCTCGTATGTGAC 57.080 57.895 0.00 0.00 37.64 3.67
4692 5433 1.092348 CGACCTCCTCGTATGTGACA 58.908 55.000 0.00 0.00 37.64 3.58
4693 5434 1.676529 CGACCTCCTCGTATGTGACAT 59.323 52.381 2.65 2.65 37.64 3.06
4694 5435 2.099263 CGACCTCCTCGTATGTGACATT 59.901 50.000 2.29 0.00 37.64 2.71
4695 5436 3.707793 GACCTCCTCGTATGTGACATTC 58.292 50.000 2.29 0.00 0.00 2.67
4696 5437 2.099263 ACCTCCTCGTATGTGACATTCG 59.901 50.000 16.83 16.83 0.00 3.34
4697 5438 2.099263 CCTCCTCGTATGTGACATTCGT 59.901 50.000 20.90 0.00 0.00 3.85
4698 5439 3.364062 CTCCTCGTATGTGACATTCGTC 58.636 50.000 20.90 2.94 42.93 4.20
4707 5448 3.661745 GACATTCGTCACCGCCTAT 57.338 52.632 0.00 0.00 42.13 2.57
4708 5449 1.209128 GACATTCGTCACCGCCTATG 58.791 55.000 0.00 0.00 42.13 2.23
4709 5450 0.821517 ACATTCGTCACCGCCTATGA 59.178 50.000 0.00 0.00 0.00 2.15
4710 5451 1.206132 ACATTCGTCACCGCCTATGAA 59.794 47.619 0.00 0.00 0.00 2.57
4711 5452 1.860950 CATTCGTCACCGCCTATGAAG 59.139 52.381 0.00 0.00 0.00 3.02
4712 5453 0.174845 TTCGTCACCGCCTATGAAGG 59.825 55.000 0.00 0.00 46.76 3.46
4713 5454 0.968901 TCGTCACCGCCTATGAAGGT 60.969 55.000 0.00 0.00 45.64 3.50
4714 5455 0.527817 CGTCACCGCCTATGAAGGTC 60.528 60.000 0.00 0.00 45.64 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 8.359642 CAGGAACATTTTCAGTTTAGATGGAAA 58.640 33.333 0.00 0.00 32.80 3.13
2385 2580 1.137675 TCATGGACTTCCTCTGCATCG 59.862 52.381 0.00 0.00 36.82 3.84
2407 2605 0.247736 ACTTCCTCTGCATCGTGGAC 59.752 55.000 0.00 0.00 0.00 4.02
2408 2606 0.532573 GACTTCCTCTGCATCGTGGA 59.467 55.000 0.00 0.00 0.00 4.02
2409 2607 0.460987 GGACTTCCTCTGCATCGTGG 60.461 60.000 0.00 0.00 0.00 4.94
2410 2608 0.247460 TGGACTTCCTCTGCATCGTG 59.753 55.000 0.00 0.00 36.82 4.35
2411 2609 1.134580 CATGGACTTCCTCTGCATCGT 60.135 52.381 0.00 0.00 36.82 3.73
2412 2610 1.137675 TCATGGACTTCCTCTGCATCG 59.862 52.381 0.00 0.00 36.82 3.84
2413 2611 2.996249 TCATGGACTTCCTCTGCATC 57.004 50.000 0.00 0.00 36.82 3.91
2414 2612 2.842496 TCTTCATGGACTTCCTCTGCAT 59.158 45.455 0.00 0.00 36.82 3.96
2415 2613 2.235650 CTCTTCATGGACTTCCTCTGCA 59.764 50.000 0.00 0.00 36.82 4.41
2416 2614 2.499289 TCTCTTCATGGACTTCCTCTGC 59.501 50.000 0.00 0.00 36.82 4.26
2417 2615 4.815533 TTCTCTTCATGGACTTCCTCTG 57.184 45.455 0.00 0.00 36.82 3.35
2418 2616 4.323409 GCTTTCTCTTCATGGACTTCCTCT 60.323 45.833 0.00 0.00 36.82 3.69
2419 2617 3.938334 GCTTTCTCTTCATGGACTTCCTC 59.062 47.826 0.00 0.00 36.82 3.71
2420 2618 3.618507 CGCTTTCTCTTCATGGACTTCCT 60.619 47.826 0.00 0.00 36.82 3.36
2421 2619 2.675348 CGCTTTCTCTTCATGGACTTCC 59.325 50.000 0.00 0.00 0.00 3.46
2422 2620 2.095053 GCGCTTTCTCTTCATGGACTTC 59.905 50.000 0.00 0.00 0.00 3.01
2423 2621 2.079925 GCGCTTTCTCTTCATGGACTT 58.920 47.619 0.00 0.00 0.00 3.01
2424 2622 1.277557 AGCGCTTTCTCTTCATGGACT 59.722 47.619 2.64 0.00 0.00 3.85
2425 2623 1.731720 AGCGCTTTCTCTTCATGGAC 58.268 50.000 2.64 0.00 0.00 4.02
2426 2624 2.289631 TGAAGCGCTTTCTCTTCATGGA 60.290 45.455 25.84 0.00 42.43 3.41
2427 2625 2.079158 TGAAGCGCTTTCTCTTCATGG 58.921 47.619 25.84 0.00 42.43 3.66
2431 2629 3.002144 GGATCATGAAGCGCTTTCTCTTC 59.998 47.826 25.84 17.50 39.20 2.87
2432 2630 2.941720 GGATCATGAAGCGCTTTCTCTT 59.058 45.455 25.84 9.79 36.71 2.85
2433 2631 2.170187 AGGATCATGAAGCGCTTTCTCT 59.830 45.455 25.84 12.86 36.71 3.10
2678 2902 2.630889 ACCTTGGACTCAGATCTGGA 57.369 50.000 22.42 8.56 0.00 3.86
2679 2903 3.133721 CCTAACCTTGGACTCAGATCTGG 59.866 52.174 22.42 15.01 0.00 3.86
2680 2904 4.026744 TCCTAACCTTGGACTCAGATCTG 58.973 47.826 17.07 17.07 0.00 2.90
2681 2905 4.338795 TCCTAACCTTGGACTCAGATCT 57.661 45.455 0.00 0.00 0.00 2.75
2682 2906 5.622346 ATTCCTAACCTTGGACTCAGATC 57.378 43.478 0.00 0.00 32.65 2.75
2683 2907 5.071115 GCTATTCCTAACCTTGGACTCAGAT 59.929 44.000 0.00 0.00 32.65 2.90
2684 2908 4.406003 GCTATTCCTAACCTTGGACTCAGA 59.594 45.833 0.00 0.00 32.65 3.27
2685 2909 4.443598 GGCTATTCCTAACCTTGGACTCAG 60.444 50.000 0.00 0.00 32.65 3.35
2686 2910 3.454812 GGCTATTCCTAACCTTGGACTCA 59.545 47.826 0.00 0.00 32.65 3.41
2687 2911 3.454812 TGGCTATTCCTAACCTTGGACTC 59.545 47.826 0.00 0.00 32.65 3.36
2688 2912 3.200165 GTGGCTATTCCTAACCTTGGACT 59.800 47.826 0.00 0.00 32.65 3.85
2689 2913 3.200165 AGTGGCTATTCCTAACCTTGGAC 59.800 47.826 0.00 0.00 32.65 4.02
3120 3383 1.548582 CCACTTCTTGGCATCCAGGTT 60.549 52.381 0.00 0.00 39.07 3.50
3892 4629 6.059787 AGAAGCAAGAGGATCATACAAGTT 57.940 37.500 0.00 0.00 37.82 2.66
3893 4630 5.690464 AGAAGCAAGAGGATCATACAAGT 57.310 39.130 0.00 0.00 37.82 3.16
3894 4631 6.258287 CAGAAGAAGCAAGAGGATCATACAAG 59.742 42.308 0.00 0.00 37.82 3.16
3895 4632 6.111382 CAGAAGAAGCAAGAGGATCATACAA 58.889 40.000 0.00 0.00 37.82 2.41
3896 4633 5.188555 ACAGAAGAAGCAAGAGGATCATACA 59.811 40.000 0.00 0.00 37.82 2.29
3897 4634 5.523188 CACAGAAGAAGCAAGAGGATCATAC 59.477 44.000 0.00 0.00 37.82 2.39
3902 4639 4.630644 TTCACAGAAGAAGCAAGAGGAT 57.369 40.909 0.00 0.00 0.00 3.24
3903 4640 4.630644 ATTCACAGAAGAAGCAAGAGGA 57.369 40.909 0.00 0.00 0.00 3.71
3932 4669 9.841295 TCTACCAAAATAAAGTACAAGTTGACT 57.159 29.630 10.54 6.04 0.00 3.41
3933 4670 9.874215 GTCTACCAAAATAAAGTACAAGTTGAC 57.126 33.333 10.54 3.70 0.00 3.18
3934 4671 9.841295 AGTCTACCAAAATAAAGTACAAGTTGA 57.159 29.630 10.54 0.00 0.00 3.18
3937 4674 9.708092 GAGAGTCTACCAAAATAAAGTACAAGT 57.292 33.333 0.00 0.00 0.00 3.16
3938 4675 9.706691 TGAGAGTCTACCAAAATAAAGTACAAG 57.293 33.333 0.00 0.00 0.00 3.16
3942 4679 9.162764 GCAATGAGAGTCTACCAAAATAAAGTA 57.837 33.333 0.00 0.00 0.00 2.24
3943 4680 7.665559 TGCAATGAGAGTCTACCAAAATAAAGT 59.334 33.333 0.00 0.00 0.00 2.66
3944 4681 7.965107 GTGCAATGAGAGTCTACCAAAATAAAG 59.035 37.037 0.00 0.00 0.00 1.85
3945 4682 7.094377 GGTGCAATGAGAGTCTACCAAAATAAA 60.094 37.037 0.00 0.00 0.00 1.40
3946 4683 6.374333 GGTGCAATGAGAGTCTACCAAAATAA 59.626 38.462 0.00 0.00 0.00 1.40
3947 4684 5.880332 GGTGCAATGAGAGTCTACCAAAATA 59.120 40.000 0.00 0.00 0.00 1.40
3948 4685 4.702131 GGTGCAATGAGAGTCTACCAAAAT 59.298 41.667 0.00 0.00 0.00 1.82
3949 4686 4.072131 GGTGCAATGAGAGTCTACCAAAA 58.928 43.478 0.00 0.00 0.00 2.44
3950 4687 3.072330 TGGTGCAATGAGAGTCTACCAAA 59.928 43.478 7.60 0.00 34.12 3.28
3951 4688 2.637382 TGGTGCAATGAGAGTCTACCAA 59.363 45.455 7.60 0.00 34.12 3.67
3952 4689 2.234661 CTGGTGCAATGAGAGTCTACCA 59.765 50.000 9.37 9.37 35.61 3.25
3953 4690 2.898705 CTGGTGCAATGAGAGTCTACC 58.101 52.381 0.00 0.00 0.00 3.18
3954 4691 2.093764 AGCTGGTGCAATGAGAGTCTAC 60.094 50.000 0.00 0.00 42.74 2.59
3955 4692 2.182827 AGCTGGTGCAATGAGAGTCTA 58.817 47.619 0.00 0.00 42.74 2.59
3956 4693 0.982704 AGCTGGTGCAATGAGAGTCT 59.017 50.000 0.00 0.00 42.74 3.24
3957 4694 2.093764 ACTAGCTGGTGCAATGAGAGTC 60.094 50.000 0.13 0.00 42.74 3.36
3958 4695 1.905215 ACTAGCTGGTGCAATGAGAGT 59.095 47.619 0.13 0.00 42.74 3.24
3959 4696 2.093816 TCACTAGCTGGTGCAATGAGAG 60.094 50.000 24.24 0.00 42.74 3.20
3960 4697 1.901833 TCACTAGCTGGTGCAATGAGA 59.098 47.619 24.24 3.38 42.74 3.27
3961 4698 2.005451 GTCACTAGCTGGTGCAATGAG 58.995 52.381 24.24 0.08 42.74 2.90
3962 4699 1.347378 TGTCACTAGCTGGTGCAATGA 59.653 47.619 24.24 4.89 42.74 2.57
3963 4700 1.812235 TGTCACTAGCTGGTGCAATG 58.188 50.000 24.24 1.68 42.74 2.82
3964 4701 2.224621 ACTTGTCACTAGCTGGTGCAAT 60.225 45.455 27.09 18.96 42.74 3.56
3965 4702 1.140852 ACTTGTCACTAGCTGGTGCAA 59.859 47.619 26.04 26.04 42.74 4.08
4047 4784 0.321919 GCTGGTGCAATGAGAGTCCA 60.322 55.000 0.00 0.00 39.41 4.02
4091 4828 4.037208 CAGAATGCACAGAAAACCAAGAGT 59.963 41.667 0.00 0.00 0.00 3.24
4108 4845 4.456911 AGGTGCATACAAGTTCACAGAATG 59.543 41.667 0.00 0.00 46.00 2.67
4174 4912 9.715121 ACAATTCTGAAGCAACAAATTAATCAT 57.285 25.926 0.00 0.00 0.00 2.45
4175 4913 8.980610 CACAATTCTGAAGCAACAAATTAATCA 58.019 29.630 0.00 0.00 0.00 2.57
4176 4914 8.437742 CCACAATTCTGAAGCAACAAATTAATC 58.562 33.333 0.00 0.00 0.00 1.75
4177 4915 7.933033 ACCACAATTCTGAAGCAACAAATTAAT 59.067 29.630 0.00 0.00 0.00 1.40
4317 5058 2.283834 TCCCTTGCCTCCCAAAGAATA 58.716 47.619 0.00 0.00 31.94 1.75
4455 5196 1.487452 GAACGCGCGCTATGGATCAA 61.487 55.000 32.58 0.00 0.00 2.57
4488 5229 7.466746 TCATACAAGGCAATAGCTTCTTTTT 57.533 32.000 0.00 0.00 41.70 1.94
4489 5230 7.466746 TTCATACAAGGCAATAGCTTCTTTT 57.533 32.000 0.00 0.00 41.70 2.27
4490 5231 7.417116 CCATTCATACAAGGCAATAGCTTCTTT 60.417 37.037 0.00 0.00 41.70 2.52
4491 5232 6.040166 CCATTCATACAAGGCAATAGCTTCTT 59.960 38.462 0.00 0.00 41.70 2.52
4492 5233 5.533903 CCATTCATACAAGGCAATAGCTTCT 59.466 40.000 0.00 0.00 41.70 2.85
4493 5234 5.278660 CCCATTCATACAAGGCAATAGCTTC 60.279 44.000 0.00 0.00 41.70 3.86
4494 5235 4.586001 CCCATTCATACAAGGCAATAGCTT 59.414 41.667 0.00 0.00 41.70 3.74
4495 5236 4.147321 CCCATTCATACAAGGCAATAGCT 58.853 43.478 0.00 0.00 41.70 3.32
4496 5237 3.305608 GCCCATTCATACAAGGCAATAGC 60.306 47.826 0.00 0.00 43.32 2.97
4497 5238 4.147321 AGCCCATTCATACAAGGCAATAG 58.853 43.478 1.74 0.00 46.35 1.73
4498 5239 4.183223 AGCCCATTCATACAAGGCAATA 57.817 40.909 1.74 0.00 46.35 1.90
4499 5240 3.036452 AGCCCATTCATACAAGGCAAT 57.964 42.857 1.74 0.00 46.35 3.56
4500 5241 2.530460 AGCCCATTCATACAAGGCAA 57.470 45.000 1.74 0.00 46.35 4.52
4501 5242 3.660970 TTAGCCCATTCATACAAGGCA 57.339 42.857 1.74 0.00 46.35 4.75
4502 5243 4.262164 CCATTTAGCCCATTCATACAAGGC 60.262 45.833 0.00 0.00 44.20 4.35
4503 5244 4.281688 CCCATTTAGCCCATTCATACAAGG 59.718 45.833 0.00 0.00 0.00 3.61
4504 5245 4.262164 GCCCATTTAGCCCATTCATACAAG 60.262 45.833 0.00 0.00 0.00 3.16
4505 5246 3.640967 GCCCATTTAGCCCATTCATACAA 59.359 43.478 0.00 0.00 0.00 2.41
4506 5247 3.230134 GCCCATTTAGCCCATTCATACA 58.770 45.455 0.00 0.00 0.00 2.29
4507 5248 2.562738 GGCCCATTTAGCCCATTCATAC 59.437 50.000 0.00 0.00 45.16 2.39
4508 5249 2.888212 GGCCCATTTAGCCCATTCATA 58.112 47.619 0.00 0.00 45.16 2.15
4509 5250 1.720781 GGCCCATTTAGCCCATTCAT 58.279 50.000 0.00 0.00 45.16 2.57
4510 5251 3.222287 GGCCCATTTAGCCCATTCA 57.778 52.632 0.00 0.00 45.16 2.57
4517 5258 4.819105 AAACCTTAAAGGCCCATTTAGC 57.181 40.909 0.00 0.00 39.63 3.09
4519 5260 8.983789 CCTAATAAAACCTTAAAGGCCCATTTA 58.016 33.333 0.00 0.00 39.63 1.40
4520 5261 7.680739 TCCTAATAAAACCTTAAAGGCCCATTT 59.319 33.333 0.00 0.00 39.63 2.32
4521 5262 7.193338 TCCTAATAAAACCTTAAAGGCCCATT 58.807 34.615 0.00 0.00 39.63 3.16
4522 5263 6.747931 TCCTAATAAAACCTTAAAGGCCCAT 58.252 36.000 0.00 0.00 39.63 4.00
4523 5264 6.155247 TCCTAATAAAACCTTAAAGGCCCA 57.845 37.500 0.00 0.00 39.63 5.36
4524 5265 7.670605 ATTCCTAATAAAACCTTAAAGGCCC 57.329 36.000 0.00 0.00 39.63 5.80
4525 5266 8.978472 AGAATTCCTAATAAAACCTTAAAGGCC 58.022 33.333 0.65 0.00 39.63 5.19
4526 5267 9.803315 CAGAATTCCTAATAAAACCTTAAAGGC 57.197 33.333 0.65 0.00 39.63 4.35
4542 5283 9.393786 AGCCCTATAGTATTTTCAGAATTCCTA 57.606 33.333 0.65 0.00 0.00 2.94
4543 5284 8.160106 CAGCCCTATAGTATTTTCAGAATTCCT 58.840 37.037 0.65 0.00 0.00 3.36
4544 5285 7.391833 CCAGCCCTATAGTATTTTCAGAATTCC 59.608 40.741 0.65 0.00 0.00 3.01
4545 5286 7.094592 GCCAGCCCTATAGTATTTTCAGAATTC 60.095 40.741 0.00 0.00 0.00 2.17
4546 5287 6.717084 GCCAGCCCTATAGTATTTTCAGAATT 59.283 38.462 0.00 0.00 0.00 2.17
4547 5288 6.241645 GCCAGCCCTATAGTATTTTCAGAAT 58.758 40.000 0.00 0.00 0.00 2.40
4548 5289 5.456186 GGCCAGCCCTATAGTATTTTCAGAA 60.456 44.000 0.00 0.00 0.00 3.02
4549 5290 4.041691 GGCCAGCCCTATAGTATTTTCAGA 59.958 45.833 0.00 0.00 0.00 3.27
4550 5291 4.202461 TGGCCAGCCCTATAGTATTTTCAG 60.202 45.833 0.00 0.00 34.56 3.02
4551 5292 3.719479 TGGCCAGCCCTATAGTATTTTCA 59.281 43.478 0.00 0.00 34.56 2.69
4552 5293 4.367039 TGGCCAGCCCTATAGTATTTTC 57.633 45.455 0.00 0.00 34.56 2.29
4553 5294 4.806952 TTGGCCAGCCCTATAGTATTTT 57.193 40.909 5.11 0.00 34.56 1.82
4554 5295 4.806952 TTTGGCCAGCCCTATAGTATTT 57.193 40.909 5.11 0.00 34.56 1.40
4555 5296 4.806952 TTTTGGCCAGCCCTATAGTATT 57.193 40.909 5.11 0.00 34.56 1.89
4556 5297 4.806952 TTTTTGGCCAGCCCTATAGTAT 57.193 40.909 5.11 0.00 34.56 2.12
4576 5317 8.616076 CGGATTCTGCTTGAATTTAGTCTATTT 58.384 33.333 6.90 0.00 44.70 1.40
4577 5318 7.254932 GCGGATTCTGCTTGAATTTAGTCTATT 60.255 37.037 10.31 0.00 44.70 1.73
4578 5319 6.203723 GCGGATTCTGCTTGAATTTAGTCTAT 59.796 38.462 10.31 0.00 44.70 1.98
4579 5320 5.523916 GCGGATTCTGCTTGAATTTAGTCTA 59.476 40.000 10.31 0.00 44.70 2.59
4580 5321 4.333926 GCGGATTCTGCTTGAATTTAGTCT 59.666 41.667 10.31 0.00 44.70 3.24
4581 5322 4.496507 GGCGGATTCTGCTTGAATTTAGTC 60.497 45.833 16.73 0.00 44.70 2.59
4582 5323 3.378427 GGCGGATTCTGCTTGAATTTAGT 59.622 43.478 16.73 0.00 44.70 2.24
4583 5324 3.546815 CGGCGGATTCTGCTTGAATTTAG 60.547 47.826 16.73 4.14 44.70 1.85
4584 5325 2.354510 CGGCGGATTCTGCTTGAATTTA 59.645 45.455 16.73 0.00 44.70 1.40
4585 5326 1.133025 CGGCGGATTCTGCTTGAATTT 59.867 47.619 16.73 0.00 44.70 1.82
4586 5327 0.734889 CGGCGGATTCTGCTTGAATT 59.265 50.000 16.73 0.00 44.70 2.17
4588 5329 1.745115 CCGGCGGATTCTGCTTGAA 60.745 57.895 24.41 0.00 39.24 2.69
4589 5330 2.125147 CCGGCGGATTCTGCTTGA 60.125 61.111 24.41 0.00 0.00 3.02
4590 5331 3.880846 GCCGGCGGATTCTGCTTG 61.881 66.667 33.44 9.78 0.00 4.01
4593 5334 3.537206 ATAGGCCGGCGGATTCTGC 62.537 63.158 33.44 13.11 0.00 4.26
4594 5335 0.951040 GAATAGGCCGGCGGATTCTG 60.951 60.000 33.44 1.21 0.00 3.02
4595 5336 1.371558 GAATAGGCCGGCGGATTCT 59.628 57.895 33.44 23.99 0.00 2.40
4596 5337 1.671379 GGAATAGGCCGGCGGATTC 60.671 63.158 33.44 30.11 0.00 2.52
4597 5338 2.430367 GGAATAGGCCGGCGGATT 59.570 61.111 33.44 20.87 0.00 3.01
4607 5348 0.181350 AGCTGGAAAGCCGGAATAGG 59.819 55.000 5.05 0.00 43.76 2.57
4608 5349 1.303309 CAGCTGGAAAGCCGGAATAG 58.697 55.000 5.05 0.00 43.76 1.73
4609 5350 0.748005 GCAGCTGGAAAGCCGGAATA 60.748 55.000 17.12 0.00 43.76 1.75
4610 5351 2.048603 GCAGCTGGAAAGCCGGAAT 61.049 57.895 17.12 0.00 43.76 3.01
4611 5352 2.672996 GCAGCTGGAAAGCCGGAA 60.673 61.111 17.12 0.00 43.76 4.30
4612 5353 3.612247 GAGCAGCTGGAAAGCCGGA 62.612 63.158 17.12 0.00 43.76 5.14
4613 5354 3.130160 GAGCAGCTGGAAAGCCGG 61.130 66.667 17.12 0.00 43.89 6.13
4614 5355 2.359107 TGAGCAGCTGGAAAGCCG 60.359 61.111 17.12 0.00 36.79 5.52
4615 5356 0.964358 ATGTGAGCAGCTGGAAAGCC 60.964 55.000 17.12 0.00 34.90 4.35
4616 5357 0.170561 CATGTGAGCAGCTGGAAAGC 59.829 55.000 17.12 0.00 0.00 3.51
4617 5358 0.809385 CCATGTGAGCAGCTGGAAAG 59.191 55.000 17.12 0.00 28.56 2.62
4618 5359 0.609957 CCCATGTGAGCAGCTGGAAA 60.610 55.000 17.12 0.00 28.56 3.13
4619 5360 1.001764 CCCATGTGAGCAGCTGGAA 60.002 57.895 17.12 0.00 28.56 3.53
4620 5361 1.276859 ATCCCATGTGAGCAGCTGGA 61.277 55.000 17.12 0.00 28.56 3.86
4621 5362 0.818445 GATCCCATGTGAGCAGCTGG 60.818 60.000 17.12 0.00 0.00 4.85
4622 5363 0.180642 AGATCCCATGTGAGCAGCTG 59.819 55.000 10.11 10.11 0.00 4.24
4623 5364 0.917533 AAGATCCCATGTGAGCAGCT 59.082 50.000 0.00 0.00 0.00 4.24
4624 5365 1.134159 AGAAGATCCCATGTGAGCAGC 60.134 52.381 0.00 0.00 0.00 5.25
4625 5366 2.169978 TGAGAAGATCCCATGTGAGCAG 59.830 50.000 0.00 0.00 0.00 4.24
4626 5367 2.190538 TGAGAAGATCCCATGTGAGCA 58.809 47.619 0.00 0.00 0.00 4.26
4627 5368 2.996249 TGAGAAGATCCCATGTGAGC 57.004 50.000 0.00 0.00 0.00 4.26
4654 5395 3.066203 GTCGTCCCATGTGAACAGTTTTT 59.934 43.478 0.00 0.00 0.00 1.94
4655 5396 2.616842 GTCGTCCCATGTGAACAGTTTT 59.383 45.455 0.00 0.00 0.00 2.43
4656 5397 2.218603 GTCGTCCCATGTGAACAGTTT 58.781 47.619 0.00 0.00 0.00 2.66
4657 5398 1.542547 GGTCGTCCCATGTGAACAGTT 60.543 52.381 0.00 0.00 0.00 3.16
4658 5399 0.034896 GGTCGTCCCATGTGAACAGT 59.965 55.000 0.00 0.00 0.00 3.55
4659 5400 0.321671 AGGTCGTCCCATGTGAACAG 59.678 55.000 0.00 0.00 34.66 3.16
4660 5401 0.320374 GAGGTCGTCCCATGTGAACA 59.680 55.000 0.00 0.00 34.66 3.18
4661 5402 0.391263 GGAGGTCGTCCCATGTGAAC 60.391 60.000 0.00 0.00 39.88 3.18
4662 5403 1.980052 GGAGGTCGTCCCATGTGAA 59.020 57.895 0.00 0.00 39.88 3.18
4663 5404 3.708210 GGAGGTCGTCCCATGTGA 58.292 61.111 0.00 0.00 39.88 3.58
4674 5415 3.707793 GAATGTCACATACGAGGAGGTC 58.292 50.000 0.00 0.00 0.00 3.85
4675 5416 2.099263 CGAATGTCACATACGAGGAGGT 59.901 50.000 0.00 0.00 0.00 3.85
4676 5417 2.099263 ACGAATGTCACATACGAGGAGG 59.901 50.000 0.00 0.00 0.00 4.30
4677 5418 3.364062 GACGAATGTCACATACGAGGAG 58.636 50.000 0.00 0.00 44.82 3.69
4678 5419 3.416119 GACGAATGTCACATACGAGGA 57.584 47.619 0.00 0.00 44.82 3.71
4696 5437 3.364277 GACCTTCATAGGCGGTGAC 57.636 57.895 0.00 0.00 46.22 3.67


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

AutoCloner maintained by Alex Coulton.