Multiple sequence alignment - TraesCS5B01G353400

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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 TraesCS5B01G353400 chr5B 100.000 5426 0 0 1 5426 532936307 532930882 0.000000e+00 10021.0
1 TraesCS5B01G353400 chr5B 86.404 1346 162 13 999 2341 532895617 532894290 0.000000e+00 1452.0
2 TraesCS5B01G353400 chr5B 89.344 976 78 7 4467 5425 615002660 615003626 0.000000e+00 1203.0
3 TraesCS5B01G353400 chr5B 83.718 909 108 24 2981 3859 532892620 532891722 0.000000e+00 822.0
4 TraesCS5B01G353400 chr5B 80.569 844 131 20 991 1825 532890113 532889294 2.150000e-173 619.0
5 TraesCS5B01G353400 chr5B 85.405 555 66 11 3297 3842 532878938 532878390 3.670000e-156 562.0
6 TraesCS5B01G353400 chr5B 76.465 1092 160 47 1813 2885 532888353 532887340 2.260000e-138 503.0
7 TraesCS5B01G353400 chr5B 82.729 469 56 14 3990 4447 532891609 532891155 1.420000e-105 394.0
8 TraesCS5B01G353400 chr5B 91.667 252 21 0 2994 3245 532879271 532879020 3.110000e-92 350.0
9 TraesCS5B01G353400 chr5B 86.503 163 17 4 2728 2889 532893941 532893783 2.010000e-39 174.0
10 TraesCS5B01G353400 chr5B 88.496 113 13 0 2483 2595 532894181 532894069 2.640000e-28 137.0
11 TraesCS5B01G353400 chr5B 86.047 86 12 0 270 355 525619585 525619670 5.790000e-15 93.5
12 TraesCS5B01G353400 chr5B 95.122 41 2 0 215 255 315152937 315152897 1.260000e-06 65.8
13 TraesCS5B01G353400 chr5A 94.142 1946 103 9 1009 2951 553465102 553463165 0.000000e+00 2952.0
14 TraesCS5B01G353400 chr5A 83.756 1342 169 17 1005 2341 553426316 553425019 0.000000e+00 1225.0
15 TraesCS5B01G353400 chr5A 88.421 950 79 13 2963 3909 553462913 553461992 0.000000e+00 1116.0
16 TraesCS5B01G353400 chr5A 89.255 577 54 4 357 933 553465711 553465143 0.000000e+00 715.0
17 TraesCS5B01G353400 chr5A 90.737 475 32 5 3973 4447 553458507 553458045 1.660000e-174 623.0
18 TraesCS5B01G353400 chr5A 83.434 495 60 10 3377 3864 553424254 553423775 1.790000e-119 440.0
19 TraesCS5B01G353400 chr5A 83.156 469 55 13 3990 4447 553423663 553423208 1.820000e-109 407.0
20 TraesCS5B01G353400 chr5A 79.861 432 64 20 2731 3159 553424661 553424250 1.480000e-75 294.0
21 TraesCS5B01G353400 chr5A 81.757 148 19 3 118 257 553466771 553466624 3.430000e-22 117.0
22 TraesCS5B01G353400 chr5A 89.655 58 6 0 197 254 366177329 366177272 2.100000e-09 75.0
23 TraesCS5B01G353400 chr5D 91.981 2095 138 13 269 2352 438391300 438389225 0.000000e+00 2911.0
24 TraesCS5B01G353400 chr5D 91.584 2020 114 25 2446 4447 438389140 438387159 0.000000e+00 2737.0
25 TraesCS5B01G353400 chr5D 86.212 1349 153 20 999 2341 438372513 438371192 0.000000e+00 1430.0
26 TraesCS5B01G353400 chr5D 82.542 1180 141 44 3305 4447 438370258 438369107 0.000000e+00 977.0
27 TraesCS5B01G353400 chr5D 81.142 753 88 18 1291 2043 438364930 438364232 6.140000e-154 555.0
28 TraesCS5B01G353400 chr5D 83.962 530 71 12 3318 3843 438362296 438361777 3.770000e-136 496.0
29 TraesCS5B01G353400 chr5D 83.333 486 60 11 3983 4450 438361623 438361141 3.880000e-116 429.0
30 TraesCS5B01G353400 chr5D 90.146 274 26 1 2976 3248 438370636 438370363 6.680000e-94 355.0
31 TraesCS5B01G353400 chr5D 97.143 35 1 0 3734 3768 319145911 319145877 5.870000e-05 60.2
32 TraesCS5B01G353400 chr3D 90.769 975 67 6 4467 5423 482860246 482861215 0.000000e+00 1280.0
33 TraesCS5B01G353400 chr3D 100.000 35 0 0 3735 3769 48365673 48365639 1.260000e-06 65.8
34 TraesCS5B01G353400 chr1B 90.418 981 65 13 4462 5425 338013423 338012455 0.000000e+00 1264.0
35 TraesCS5B01G353400 chr1B 80.679 1061 173 21 1291 2338 569566186 569565145 0.000000e+00 795.0
36 TraesCS5B01G353400 chr1B 83.694 601 79 14 3254 3842 569561992 569561399 2.860000e-152 549.0
37 TraesCS5B01G353400 chr1B 82.759 232 38 1 3009 3238 569562543 569562312 7.120000e-49 206.0
38 TraesCS5B01G353400 chr1B 95.000 40 2 0 3730 3769 535384575 535384536 4.540000e-06 63.9
39 TraesCS5B01G353400 chr6B 89.613 982 69 8 4467 5425 149166933 149165962 0.000000e+00 1218.0
40 TraesCS5B01G353400 chr6B 80.892 157 30 0 3075 3231 544403646 544403802 2.050000e-24 124.0
41 TraesCS5B01G353400 chr6B 75.956 183 39 4 3375 3553 544404633 544404814 7.490000e-14 89.8
42 TraesCS5B01G353400 chr7D 91.148 915 53 16 4529 5425 631606495 631607399 0.000000e+00 1216.0
43 TraesCS5B01G353400 chr7D 100.000 32 0 0 1466 1497 566014426 566014457 5.870000e-05 60.2
44 TraesCS5B01G353400 chr7B 89.340 985 80 13 4458 5424 639786261 639785284 0.000000e+00 1214.0
45 TraesCS5B01G353400 chr7B 89.570 930 75 4 4514 5426 740230203 740229279 0.000000e+00 1160.0
46 TraesCS5B01G353400 chr7B 84.091 264 23 8 4452 4699 740471339 740471079 2.530000e-58 237.0
47 TraesCS5B01G353400 chr7B 100.000 34 0 0 3735 3768 57633388 57633355 4.540000e-06 63.9
48 TraesCS5B01G353400 chr2D 89.286 980 77 6 4467 5425 452373935 452372963 0.000000e+00 1203.0
49 TraesCS5B01G353400 chr2D 92.500 120 9 0 4467 4586 284603042 284603161 7.230000e-39 172.0
50 TraesCS5B01G353400 chr4B 88.325 985 85 11 4459 5425 417353486 417354458 0.000000e+00 1155.0
51 TraesCS5B01G353400 chr1D 81.775 1059 161 22 1291 2336 420860418 420859379 0.000000e+00 857.0
52 TraesCS5B01G353400 chr1D 83.193 595 84 12 3258 3843 420856873 420856286 1.030000e-146 531.0
53 TraesCS5B01G353400 chr1D 86.111 468 46 8 4451 4901 260314692 260315157 2.270000e-133 486.0
54 TraesCS5B01G353400 chr1D 83.871 465 52 16 4444 4891 476413234 476413692 6.500000e-114 422.0
55 TraesCS5B01G353400 chr1D 82.875 473 62 9 4467 4922 6521929 6521459 1.820000e-109 407.0
56 TraesCS5B01G353400 chr1D 83.226 310 44 6 3990 4298 420856189 420855887 1.490000e-70 278.0
57 TraesCS5B01G353400 chr1D 84.052 232 35 1 3009 3238 420857430 420857199 7.070000e-54 222.0
58 TraesCS5B01G353400 chr1D 84.810 158 24 0 3702 3859 420752338 420752181 5.630000e-35 159.0
59 TraesCS5B01G353400 chr1D 97.500 40 1 0 3730 3769 399188632 399188593 9.750000e-08 69.4
60 TraesCS5B01G353400 chrUn 83.034 501 66 12 4452 4936 132113391 132112894 2.320000e-118 436.0
61 TraesCS5B01G353400 chr6D 82.669 502 64 12 4461 4944 32369961 32369465 1.810000e-114 424.0
62 TraesCS5B01G353400 chr6D 91.045 134 10 2 4454 4586 447279843 447279975 4.320000e-41 180.0
63 TraesCS5B01G353400 chr6D 80.892 157 30 0 3075 3231 362987998 362988154 2.050000e-24 124.0
64 TraesCS5B01G353400 chr6D 80.952 126 22 2 3375 3499 362988682 362988806 1.240000e-16 99.0
65 TraesCS5B01G353400 chr6D 100.000 33 0 0 3736 3768 470961823 470961791 1.630000e-05 62.1
66 TraesCS5B01G353400 chr4D 85.149 404 41 13 4457 4843 132948655 132949056 3.940000e-106 396.0
67 TraesCS5B01G353400 chr6A 80.892 157 30 0 3075 3231 503426259 503426415 2.050000e-24 124.0
68 TraesCS5B01G353400 chr6A 77.095 179 36 4 3375 3549 503426901 503427078 1.240000e-16 99.0
69 TraesCS5B01G353400 chr1A 90.385 52 5 0 202 253 298600203 298600152 9.750000e-08 69.4
70 TraesCS5B01G353400 chr3A 100.000 28 0 0 1379 1406 743201346 743201373 1.000000e-02 52.8


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 TraesCS5B01G353400 chr5B 532930882 532936307 5425 True 10021.000000 10021 100.000000 1 5426 1 chr5B.!!$R2 5425
1 TraesCS5B01G353400 chr5B 615002660 615003626 966 False 1203.000000 1203 89.344000 4467 5425 1 chr5B.!!$F2 958
2 TraesCS5B01G353400 chr5B 532887340 532895617 8277 True 585.857143 1452 83.554857 991 4447 7 chr5B.!!$R4 3456
3 TraesCS5B01G353400 chr5B 532878390 532879271 881 True 456.000000 562 88.536000 2994 3842 2 chr5B.!!$R3 848
4 TraesCS5B01G353400 chr5A 553458045 553466771 8726 True 1104.600000 2952 88.862400 118 4447 5 chr5A.!!$R3 4329
5 TraesCS5B01G353400 chr5A 553423208 553426316 3108 True 591.500000 1225 82.551750 1005 4447 4 chr5A.!!$R2 3442
6 TraesCS5B01G353400 chr5D 438387159 438391300 4141 True 2824.000000 2911 91.782500 269 4447 2 chr5D.!!$R4 4178
7 TraesCS5B01G353400 chr5D 438369107 438372513 3406 True 920.666667 1430 86.300000 999 4447 3 chr5D.!!$R3 3448
8 TraesCS5B01G353400 chr5D 438361141 438364930 3789 True 493.333333 555 82.812333 1291 4450 3 chr5D.!!$R2 3159
9 TraesCS5B01G353400 chr3D 482860246 482861215 969 False 1280.000000 1280 90.769000 4467 5423 1 chr3D.!!$F1 956
10 TraesCS5B01G353400 chr1B 338012455 338013423 968 True 1264.000000 1264 90.418000 4462 5425 1 chr1B.!!$R1 963
11 TraesCS5B01G353400 chr1B 569561399 569566186 4787 True 516.666667 795 82.377333 1291 3842 3 chr1B.!!$R3 2551
12 TraesCS5B01G353400 chr6B 149165962 149166933 971 True 1218.000000 1218 89.613000 4467 5425 1 chr6B.!!$R1 958
13 TraesCS5B01G353400 chr7D 631606495 631607399 904 False 1216.000000 1216 91.148000 4529 5425 1 chr7D.!!$F2 896
14 TraesCS5B01G353400 chr7B 639785284 639786261 977 True 1214.000000 1214 89.340000 4458 5424 1 chr7B.!!$R2 966
15 TraesCS5B01G353400 chr7B 740229279 740230203 924 True 1160.000000 1160 89.570000 4514 5426 1 chr7B.!!$R3 912
16 TraesCS5B01G353400 chr2D 452372963 452373935 972 True 1203.000000 1203 89.286000 4467 5425 1 chr2D.!!$R1 958
17 TraesCS5B01G353400 chr4B 417353486 417354458 972 False 1155.000000 1155 88.325000 4459 5425 1 chr4B.!!$F1 966
18 TraesCS5B01G353400 chr1D 420855887 420860418 4531 True 472.000000 857 83.061500 1291 4298 4 chr1D.!!$R4 3007

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
246 259 0.035458 CGAAGAGCTTGAACCTGGGT 59.965 55.000 0.00 0.00 0.0 4.51 F
413 1272 0.045008 TGGAACCCTAGCACCCCATA 59.955 55.000 0.00 0.00 0.0 2.74 F
973 1860 0.100682 TACCTTCACTGATCGCGCTC 59.899 55.000 5.56 0.53 0.0 5.03 F
1147 2039 0.687354 AGCAAACCCTCGTGTCTGAT 59.313 50.000 0.00 0.00 0.0 2.90 F
2347 3275 0.745845 CTGATGCTTCCACTTCCCCG 60.746 60.000 0.00 0.00 0.0 5.73 F
2354 3282 1.415289 CTTCCACTTCCCCGGGTATAC 59.585 57.143 21.85 0.00 0.0 1.47 F
3415 9486 1.194781 ACTCCAGGCTGACGGTGATT 61.195 55.000 17.94 0.00 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1122 2014 1.227853 ACGAGGGTTTGCTCCACAC 60.228 57.895 0.00 0.0 0.00 3.82 R
2331 3259 2.677228 CCGGGGAAGTGGAAGCAT 59.323 61.111 0.00 0.0 0.00 3.79 R
2615 6493 0.108041 GAAATGGTTGGGCATGGCAG 60.108 55.000 22.06 0.0 0.00 4.85 R
3054 8786 0.107993 TCTGAATCCTTGCTCAGCCG 60.108 55.000 0.00 0.0 39.17 5.52 R
3347 9413 0.554865 ACCCCCTTGATGATCCCCAA 60.555 55.000 0.00 0.0 0.00 4.12 R
3769 9889 1.613317 TACCCTGATGCCACTCACGG 61.613 60.000 0.00 0.0 0.00 4.94 R
5177 15668 0.248289 CCTGGTATTCGGTCGTTGGT 59.752 55.000 0.00 0.0 0.00 3.67 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
17 18 2.901840 CAATGACGATGGCCCCGG 60.902 66.667 17.25 0.00 0.00 5.73
18 19 3.087253 AATGACGATGGCCCCGGA 61.087 61.111 17.25 5.56 0.00 5.14
19 20 3.400599 AATGACGATGGCCCCGGAC 62.401 63.158 17.25 11.61 0.00 4.79
21 22 4.530857 GACGATGGCCCCGGACTG 62.531 72.222 17.25 0.00 0.00 3.51
29 30 4.263572 CCCCGGACTGGCACACAA 62.264 66.667 0.73 0.00 35.87 3.33
30 31 2.034066 CCCGGACTGGCACACAAT 59.966 61.111 0.73 0.00 35.87 2.71
31 32 2.040544 CCCGGACTGGCACACAATC 61.041 63.158 0.73 0.00 35.87 2.67
32 33 2.040544 CCGGACTGGCACACAATCC 61.041 63.158 0.00 0.00 0.00 3.01
33 34 1.302431 CGGACTGGCACACAATCCA 60.302 57.895 0.00 0.00 31.31 3.41
34 35 0.677731 CGGACTGGCACACAATCCAT 60.678 55.000 0.00 0.00 31.31 3.41
35 36 1.098050 GGACTGGCACACAATCCATC 58.902 55.000 0.00 0.00 31.95 3.51
36 37 1.098050 GACTGGCACACAATCCATCC 58.902 55.000 0.00 0.00 0.00 3.51
37 38 0.405198 ACTGGCACACAATCCATCCA 59.595 50.000 0.00 0.00 0.00 3.41
38 39 1.006281 ACTGGCACACAATCCATCCAT 59.994 47.619 0.00 0.00 0.00 3.41
39 40 1.679680 CTGGCACACAATCCATCCATC 59.320 52.381 0.00 0.00 0.00 3.51
40 41 1.005687 TGGCACACAATCCATCCATCA 59.994 47.619 0.00 0.00 0.00 3.07
41 42 2.313317 GGCACACAATCCATCCATCAT 58.687 47.619 0.00 0.00 0.00 2.45
42 43 2.696707 GGCACACAATCCATCCATCATT 59.303 45.455 0.00 0.00 0.00 2.57
43 44 3.890756 GGCACACAATCCATCCATCATTA 59.109 43.478 0.00 0.00 0.00 1.90
44 45 4.341806 GGCACACAATCCATCCATCATTAA 59.658 41.667 0.00 0.00 0.00 1.40
45 46 5.284079 GCACACAATCCATCCATCATTAAC 58.716 41.667 0.00 0.00 0.00 2.01
46 47 5.163530 GCACACAATCCATCCATCATTAACA 60.164 40.000 0.00 0.00 0.00 2.41
47 48 6.627731 GCACACAATCCATCCATCATTAACAA 60.628 38.462 0.00 0.00 0.00 2.83
48 49 7.494211 CACACAATCCATCCATCATTAACAAT 58.506 34.615 0.00 0.00 0.00 2.71
49 50 7.650504 CACACAATCCATCCATCATTAACAATC 59.349 37.037 0.00 0.00 0.00 2.67
50 51 7.149973 CACAATCCATCCATCATTAACAATCC 58.850 38.462 0.00 0.00 0.00 3.01
51 52 6.840181 ACAATCCATCCATCATTAACAATCCA 59.160 34.615 0.00 0.00 0.00 3.41
52 53 7.511371 ACAATCCATCCATCATTAACAATCCAT 59.489 33.333 0.00 0.00 0.00 3.41
53 54 7.713734 ATCCATCCATCATTAACAATCCATC 57.286 36.000 0.00 0.00 0.00 3.51
54 55 6.855667 TCCATCCATCATTAACAATCCATCT 58.144 36.000 0.00 0.00 0.00 2.90
55 56 6.717997 TCCATCCATCATTAACAATCCATCTG 59.282 38.462 0.00 0.00 0.00 2.90
56 57 6.071560 CCATCCATCATTAACAATCCATCTGG 60.072 42.308 0.00 0.00 0.00 3.86
57 58 5.387788 TCCATCATTAACAATCCATCTGGG 58.612 41.667 0.00 0.00 35.41 4.45
58 59 5.103558 TCCATCATTAACAATCCATCTGGGT 60.104 40.000 0.00 0.00 38.11 4.51
59 60 5.242393 CCATCATTAACAATCCATCTGGGTC 59.758 44.000 0.00 0.00 38.11 4.46
60 61 4.792068 TCATTAACAATCCATCTGGGTCC 58.208 43.478 0.00 0.00 38.11 4.46
61 62 3.275617 TTAACAATCCATCTGGGTCCG 57.724 47.619 0.00 0.00 38.11 4.79
62 63 1.285280 AACAATCCATCTGGGTCCGA 58.715 50.000 0.00 0.00 38.11 4.55
63 64 0.833287 ACAATCCATCTGGGTCCGAG 59.167 55.000 0.00 0.00 38.11 4.63
64 65 0.533755 CAATCCATCTGGGTCCGAGC 60.534 60.000 0.00 0.00 38.11 5.03
65 66 1.700042 AATCCATCTGGGTCCGAGCC 61.700 60.000 9.85 9.85 38.11 4.70
66 67 4.227134 CCATCTGGGTCCGAGCCG 62.227 72.222 11.95 7.06 38.98 5.52
67 68 3.461773 CATCTGGGTCCGAGCCGT 61.462 66.667 11.95 0.00 38.98 5.68
68 69 3.148279 ATCTGGGTCCGAGCCGTC 61.148 66.667 11.95 0.00 38.98 4.79
77 78 4.351938 CGAGCCGTCGGGTGAACA 62.352 66.667 22.86 0.00 42.87 3.18
78 79 2.737376 GAGCCGTCGGGTGAACAC 60.737 66.667 22.86 1.48 31.55 3.32
79 80 3.509137 GAGCCGTCGGGTGAACACA 62.509 63.158 22.86 0.00 31.55 3.72
80 81 3.343421 GCCGTCGGGTGAACACAC 61.343 66.667 14.38 2.11 34.97 3.82
87 88 4.043168 GGTGAACACACCGACAGG 57.957 61.111 7.25 0.00 43.39 4.00
97 98 4.436998 CCGACAGGTGGGCTCGAC 62.437 72.222 0.00 0.00 0.00 4.20
98 99 3.374402 CGACAGGTGGGCTCGACT 61.374 66.667 0.00 0.00 0.00 4.18
99 100 2.044555 CGACAGGTGGGCTCGACTA 61.045 63.158 0.00 0.00 0.00 2.59
100 101 1.810532 GACAGGTGGGCTCGACTAG 59.189 63.158 0.00 0.00 0.00 2.57
101 102 0.680280 GACAGGTGGGCTCGACTAGA 60.680 60.000 0.00 0.00 0.00 2.43
102 103 0.251653 ACAGGTGGGCTCGACTAGAA 60.252 55.000 0.00 0.00 0.00 2.10
103 104 1.115467 CAGGTGGGCTCGACTAGAAT 58.885 55.000 0.00 0.00 0.00 2.40
104 105 1.115467 AGGTGGGCTCGACTAGAATG 58.885 55.000 0.00 0.00 0.00 2.67
105 106 0.824759 GGTGGGCTCGACTAGAATGT 59.175 55.000 0.00 0.00 0.00 2.71
106 107 2.029623 GGTGGGCTCGACTAGAATGTA 58.970 52.381 0.00 0.00 0.00 2.29
107 108 2.429610 GGTGGGCTCGACTAGAATGTAA 59.570 50.000 0.00 0.00 0.00 2.41
108 109 3.445857 GTGGGCTCGACTAGAATGTAAC 58.554 50.000 0.00 0.00 0.00 2.50
109 110 2.098607 TGGGCTCGACTAGAATGTAACG 59.901 50.000 0.00 0.00 0.00 3.18
110 111 2.357009 GGGCTCGACTAGAATGTAACGA 59.643 50.000 0.00 0.00 0.00 3.85
111 112 3.361414 GGCTCGACTAGAATGTAACGAC 58.639 50.000 0.00 0.00 0.00 4.34
112 113 3.181503 GGCTCGACTAGAATGTAACGACA 60.182 47.826 0.00 0.00 40.72 4.35
113 114 4.029704 GCTCGACTAGAATGTAACGACAG 58.970 47.826 0.00 0.00 39.50 3.51
114 115 4.589252 CTCGACTAGAATGTAACGACAGG 58.411 47.826 0.00 0.00 39.50 4.00
115 116 4.005650 TCGACTAGAATGTAACGACAGGT 58.994 43.478 0.00 0.00 39.50 4.00
116 117 4.096311 CGACTAGAATGTAACGACAGGTG 58.904 47.826 0.00 0.00 39.50 4.00
167 173 4.902443 TCGAAGATCTAGTAGCAACCTG 57.098 45.455 0.00 0.00 0.00 4.00
176 182 5.779922 TCTAGTAGCAACCTGTACTTTGTG 58.220 41.667 0.00 0.00 31.79 3.33
181 187 2.851195 CAACCTGTACTTTGTGCTCCT 58.149 47.619 0.00 0.00 0.00 3.69
185 191 2.427506 CTGTACTTTGTGCTCCTTCCC 58.572 52.381 0.00 0.00 0.00 3.97
198 204 4.021192 TGCTCCTTCCCAAATCAATTCAAC 60.021 41.667 0.00 0.00 0.00 3.18
199 205 4.021192 GCTCCTTCCCAAATCAATTCAACA 60.021 41.667 0.00 0.00 0.00 3.33
200 206 5.467035 TCCTTCCCAAATCAATTCAACAC 57.533 39.130 0.00 0.00 0.00 3.32
201 207 4.898265 TCCTTCCCAAATCAATTCAACACA 59.102 37.500 0.00 0.00 0.00 3.72
213 219 6.380995 TCAATTCAACACAAGCATGACATAC 58.619 36.000 0.00 0.00 0.00 2.39
214 220 4.403015 TTCAACACAAGCATGACATACG 57.597 40.909 0.00 0.00 0.00 3.06
215 221 2.741517 TCAACACAAGCATGACATACGG 59.258 45.455 0.00 0.00 0.00 4.02
229 242 4.641541 TGACATACGGTTTTATCTCCTCGA 59.358 41.667 0.00 0.00 0.00 4.04
246 259 0.035458 CGAAGAGCTTGAACCTGGGT 59.965 55.000 0.00 0.00 0.00 4.51
254 267 4.740902 AGCTTGAACCTGGGTAAAATCTT 58.259 39.130 0.00 0.00 0.00 2.40
257 270 6.099701 AGCTTGAACCTGGGTAAAATCTTTTT 59.900 34.615 0.00 0.00 0.00 1.94
285 298 3.814316 GCTGGTGAACCTGGGTAAAATCT 60.814 47.826 8.28 0.00 35.73 2.40
286 299 4.010349 CTGGTGAACCTGGGTAAAATCTC 58.990 47.826 0.00 0.00 36.82 2.75
293 306 5.584551 ACCTGGGTAAAATCTCTTGTCTT 57.415 39.130 0.00 0.00 0.00 3.01
318 331 3.417690 ACCATCGCGTCTAAACTACTC 57.582 47.619 5.77 0.00 0.00 2.59
323 336 1.825077 GCGTCTAAACTACTCGCTCC 58.175 55.000 0.00 0.00 42.88 4.70
331 344 3.122250 CTACTCGCTCCGAACCCCG 62.122 68.421 0.00 0.00 34.74 5.73
335 348 3.751246 CGCTCCGAACCCCGTACA 61.751 66.667 0.00 0.00 36.31 2.90
353 1212 1.278985 ACACAAGATCTGCCGGAATCA 59.721 47.619 5.05 0.00 0.00 2.57
355 1214 2.749076 CACAAGATCTGCCGGAATCAAA 59.251 45.455 5.05 0.00 0.00 2.69
370 1229 0.899019 TCAAATCCGTCATCCGTCCA 59.101 50.000 0.00 0.00 33.66 4.02
372 1231 1.867233 CAAATCCGTCATCCGTCCATC 59.133 52.381 0.00 0.00 33.66 3.51
373 1232 0.393077 AATCCGTCATCCGTCCATCC 59.607 55.000 0.00 0.00 33.66 3.51
396 1255 1.102978 CGCTAAAATGGGAAGGGTGG 58.897 55.000 0.00 0.00 0.00 4.61
412 1271 1.230149 TGGAACCCTAGCACCCCAT 60.230 57.895 0.00 0.00 0.00 4.00
413 1272 0.045008 TGGAACCCTAGCACCCCATA 59.955 55.000 0.00 0.00 0.00 2.74
414 1273 1.346046 TGGAACCCTAGCACCCCATAT 60.346 52.381 0.00 0.00 0.00 1.78
422 1281 1.059913 AGCACCCCATATACTGCCTC 58.940 55.000 0.00 0.00 0.00 4.70
442 1301 2.046700 GGTTGCCACCGAATCCGA 60.047 61.111 0.00 0.00 38.22 4.55
476 1335 1.089112 CTGCCGATGAACTGAATGCA 58.911 50.000 0.00 0.00 0.00 3.96
484 1343 1.888512 TGAACTGAATGCAGGAAAGGC 59.111 47.619 5.47 0.00 46.60 4.35
489 1348 3.963124 AATGCAGGAAAGGCCCCCG 62.963 63.158 0.00 0.00 37.37 5.73
541 1403 1.194781 AACGACATGAGGAGCCCAGT 61.195 55.000 0.00 0.00 0.00 4.00
557 1419 4.737826 CCCAGTGTGGCAGGTAAAACCT 62.738 54.545 0.00 0.00 41.66 3.50
617 1483 1.019278 GGCGAGAACAGCGAAATCCA 61.019 55.000 0.00 0.00 35.00 3.41
621 1487 2.151202 GAGAACAGCGAAATCCAACCA 58.849 47.619 0.00 0.00 0.00 3.67
675 1542 0.181587 ACAATCCACCGTGTCAACCA 59.818 50.000 0.00 0.00 0.00 3.67
742 1609 1.012486 GTTGGACAAGGTAGGTCGCG 61.012 60.000 0.00 0.00 36.12 5.87
743 1610 2.162338 TTGGACAAGGTAGGTCGCGG 62.162 60.000 6.13 0.00 36.12 6.46
744 1611 2.643232 GGACAAGGTAGGTCGCGGT 61.643 63.158 6.13 0.00 36.12 5.68
745 1612 1.315257 GGACAAGGTAGGTCGCGGTA 61.315 60.000 6.13 0.00 36.12 4.02
791 1658 2.300152 CACACACAGTAGACCAGACCAT 59.700 50.000 0.00 0.00 0.00 3.55
871 1738 5.877012 AGTCAATATGAATTCACAAGCTCGT 59.123 36.000 11.07 0.00 0.00 4.18
883 1750 3.702555 GCTCGTGTCACCGTGTGC 61.703 66.667 0.00 0.00 32.98 4.57
886 1753 2.587753 CGTGTCACCGTGTGCCTT 60.588 61.111 0.00 0.00 32.98 4.35
944 1831 4.012374 ACGAATGATCAAATGTCAAGGCT 58.988 39.130 0.00 0.00 0.00 4.58
956 1843 2.427453 TGTCAAGGCTGTAGCTAGCTAC 59.573 50.000 37.26 37.26 46.56 3.58
973 1860 0.100682 TACCTTCACTGATCGCGCTC 59.899 55.000 5.56 0.53 0.00 5.03
993 1880 2.954868 CGCGTCGCCGAAGCTAAT 60.955 61.111 21.76 0.00 35.07 1.73
994 1881 2.621000 GCGTCGCCGAAGCTAATG 59.379 61.111 17.65 0.00 34.45 1.90
997 1884 1.348594 GTCGCCGAAGCTAATGTGC 59.651 57.895 0.00 0.00 36.60 4.57
1144 2036 1.371558 GGAGCAAACCCTCGTGTCT 59.628 57.895 0.00 0.00 32.57 3.41
1147 2039 0.687354 AGCAAACCCTCGTGTCTGAT 59.313 50.000 0.00 0.00 0.00 2.90
1398 2296 2.462782 CGTCCTCCTCGTCCTCGTC 61.463 68.421 0.00 0.00 38.33 4.20
1399 2297 2.125229 TCCTCCTCGTCCTCGTCG 60.125 66.667 0.00 0.00 38.33 5.12
1400 2298 3.878519 CCTCCTCGTCCTCGTCGC 61.879 72.222 0.00 0.00 38.33 5.19
1486 2387 3.059982 CAGAGCTTCGACCACCCA 58.940 61.111 0.00 0.00 0.00 4.51
1939 2846 2.126189 GGGTACTGCGACGTCACC 60.126 66.667 17.16 14.48 0.00 4.02
2347 3275 0.745845 CTGATGCTTCCACTTCCCCG 60.746 60.000 0.00 0.00 0.00 5.73
2354 3282 1.415289 CTTCCACTTCCCCGGGTATAC 59.585 57.143 21.85 0.00 0.00 1.47
2357 3285 1.772453 CCACTTCCCCGGGTATACAAT 59.228 52.381 21.85 0.00 0.00 2.71
2390 3318 6.591448 ACCAAACTTTTCAGAGCTTTTTCAAG 59.409 34.615 0.00 0.00 0.00 3.02
2412 3546 6.546972 AGAAAAGATTTTCAGAGTTCCGTC 57.453 37.500 17.72 0.00 46.81 4.79
2413 5842 6.292150 AGAAAAGATTTTCAGAGTTCCGTCT 58.708 36.000 17.72 0.00 46.81 4.18
2429 5858 3.125146 TCCGTCTGATTTTGCTGAATTCG 59.875 43.478 0.04 0.00 0.00 3.34
2467 5913 5.486526 TGTTGTTTCATCAAACTTTTGCCT 58.513 33.333 0.00 0.00 42.29 4.75
2581 6039 3.785486 TCTTCGTATGGTTCTGCAGATG 58.215 45.455 19.04 0.00 0.00 2.90
2615 6493 7.881751 ACAGTTACATTTCCTTACCTCTAAACC 59.118 37.037 0.00 0.00 0.00 3.27
2665 6572 5.123502 AGACAAGATGCTCATCACAACAATC 59.876 40.000 11.90 1.12 40.22 2.67
2679 6587 5.991606 TCACAACAATCTTACAGACAAGAGG 59.008 40.000 0.00 0.00 37.93 3.69
2705 6622 2.202676 CGAGAGCCAGAAGACGCC 60.203 66.667 0.00 0.00 0.00 5.68
2957 8669 3.565063 GCACAAAATTCAGTGGCCAAATT 59.435 39.130 7.24 7.65 36.29 1.82
2958 8670 4.036616 GCACAAAATTCAGTGGCCAAATTT 59.963 37.500 17.27 17.27 36.29 1.82
2959 8671 5.450274 GCACAAAATTCAGTGGCCAAATTTT 60.450 36.000 24.27 24.27 41.07 1.82
2960 8672 6.238593 GCACAAAATTCAGTGGCCAAATTTTA 60.239 34.615 27.21 7.33 39.38 1.52
2961 8673 7.680588 GCACAAAATTCAGTGGCCAAATTTTAA 60.681 33.333 27.21 11.26 39.38 1.52
3000 8732 2.289002 GTCTCACTCCACTGCTTGTTTG 59.711 50.000 0.00 0.00 0.00 2.93
3054 8786 2.031163 AGGTGGTCGCTGTGAAGC 59.969 61.111 0.00 0.00 0.00 3.86
3415 9486 1.194781 ACTCCAGGCTGACGGTGATT 61.195 55.000 17.94 0.00 0.00 2.57
3573 9644 5.741011 AGTAACCTGAACACTTGACTGAAA 58.259 37.500 0.00 0.00 0.00 2.69
3769 9889 3.117171 CGTGCTGCTGCTGGAGAC 61.117 66.667 16.29 9.75 40.48 3.36
3911 10110 5.993441 GCCCAAATCCATATTCATCTTTTGG 59.007 40.000 0.00 0.00 40.66 3.28
3929 10140 9.691362 ATCTTTTGGAAAATATAACACACACAC 57.309 29.630 0.00 0.00 0.00 3.82
3931 10142 8.635877 TTTTGGAAAATATAACACACACACAC 57.364 30.769 0.00 0.00 0.00 3.82
3933 10144 6.730175 TGGAAAATATAACACACACACACAC 58.270 36.000 0.00 0.00 0.00 3.82
3934 10145 6.318900 TGGAAAATATAACACACACACACACA 59.681 34.615 0.00 0.00 0.00 3.72
3935 10146 6.635239 GGAAAATATAACACACACACACACAC 59.365 38.462 0.00 0.00 0.00 3.82
3940 10151 1.336980 ACACACACACACACACACGTA 60.337 47.619 0.00 0.00 0.00 3.57
3941 10152 1.059979 CACACACACACACACACGTAC 59.940 52.381 0.00 0.00 0.00 3.67
3942 10153 1.336980 ACACACACACACACACGTACA 60.337 47.619 0.00 0.00 0.00 2.90
3943 10154 1.059979 CACACACACACACACGTACAC 59.940 52.381 0.00 0.00 0.00 2.90
3944 10155 1.336980 ACACACACACACACGTACACA 60.337 47.619 0.00 0.00 0.00 3.72
3945 10156 1.059979 CACACACACACACGTACACAC 59.940 52.381 0.00 0.00 0.00 3.82
3959 10170 4.782252 GTACACACGTACACACACAAAT 57.218 40.909 0.00 0.00 46.18 2.32
3960 10171 3.666883 ACACACGTACACACACAAATG 57.333 42.857 0.00 0.00 0.00 2.32
3962 10173 2.353269 CACACGTACACACACAAATGGT 59.647 45.455 0.00 0.00 0.00 3.55
4036 13664 2.360475 GCAGGGAAGCTGGTGGAC 60.360 66.667 0.00 0.00 0.00 4.02
4141 13769 1.944676 GAGGCCGCTAATGTCGTCG 60.945 63.158 0.00 0.00 0.00 5.12
4147 13775 1.192436 CGCTAATGTCGTCGGTCGTC 61.192 60.000 0.00 0.00 40.80 4.20
4300 13958 1.136500 GTTCTTCAGGGCCGGTAGTAG 59.864 57.143 1.90 1.82 0.00 2.57
4307 13965 1.133853 AGGGCCGGTAGTAGAGTAGTG 60.134 57.143 1.90 0.00 0.00 2.74
4392 14063 2.403252 AACCCCAGATTTGTAGAGCG 57.597 50.000 0.00 0.00 0.00 5.03
4393 14064 0.107654 ACCCCAGATTTGTAGAGCGC 60.108 55.000 0.00 0.00 0.00 5.92
4441 14112 7.695820 AGACGTATATACAAGAGTGTTGAGTC 58.304 38.462 13.22 7.21 39.30 3.36
4447 14118 4.527509 ACAAGAGTGTTGAGTCGATCAT 57.472 40.909 7.07 0.00 37.89 2.45
4450 14121 4.790765 AGAGTGTTGAGTCGATCATTGA 57.209 40.909 0.00 0.00 37.89 2.57
4452 14123 5.728471 AGAGTGTTGAGTCGATCATTGATT 58.272 37.500 0.00 0.00 37.89 2.57
4453 14124 6.169094 AGAGTGTTGAGTCGATCATTGATTT 58.831 36.000 0.00 0.00 37.89 2.17
4454 14125 6.652481 AGAGTGTTGAGTCGATCATTGATTTT 59.348 34.615 0.00 0.00 37.89 1.82
4455 14126 7.173907 AGAGTGTTGAGTCGATCATTGATTTTT 59.826 33.333 0.00 0.00 37.89 1.94
4456 14127 8.322906 AGTGTTGAGTCGATCATTGATTTTTA 57.677 30.769 0.00 0.00 37.89 1.52
4457 14128 8.950210 AGTGTTGAGTCGATCATTGATTTTTAT 58.050 29.630 0.00 0.00 37.89 1.40
4458 14129 9.559958 GTGTTGAGTCGATCATTGATTTTTATT 57.440 29.630 0.00 0.00 37.89 1.40
4512 14183 0.585357 GCATGTGCATCTGGACGATC 59.415 55.000 0.00 0.00 39.39 3.69
4635 14491 6.351711 GGATGCTGATAGTCTGTGCCTAATAT 60.352 42.308 0.00 0.00 0.00 1.28
4666 14899 3.367292 CCTCGCAGCCAAACATAAACATT 60.367 43.478 0.00 0.00 0.00 2.71
4739 15055 2.281484 GGCGTGCTCCTCAACCAA 60.281 61.111 0.00 0.00 0.00 3.67
4748 15064 0.468226 TCCTCAACCAAGACGCTTGT 59.532 50.000 15.28 4.67 0.00 3.16
4750 15066 1.581934 CTCAACCAAGACGCTTGTCA 58.418 50.000 15.28 0.50 45.40 3.58
4822 15312 1.522092 CTGCATCTACCTTGCCCGA 59.478 57.895 0.00 0.00 39.39 5.14
4962 15452 7.279981 CCATGAATATGTAGAAAGAAACACCGA 59.720 37.037 0.00 0.00 32.21 4.69
4983 15473 0.391130 CCATCGAAGAAGCCAACCGA 60.391 55.000 0.00 0.00 43.58 4.69
5076 15566 6.006449 TCATCATCCGATCAACTGATCTAGA 58.994 40.000 15.79 12.73 46.58 2.43
5108 15599 1.778309 GTATTGGGTGGGGTTGGGT 59.222 57.895 0.00 0.00 0.00 4.51
5202 15694 2.235402 ACGACCGAATACCAGGTTTCAT 59.765 45.455 0.00 0.00 41.51 2.57
5262 15754 2.358247 TCTCGGCCGCCTTCAAAC 60.358 61.111 23.51 0.00 0.00 2.93
5263 15755 2.668212 CTCGGCCGCCTTCAAACA 60.668 61.111 23.51 0.00 0.00 2.83
5275 15767 3.307762 GCCTTCAAACACCCAGATCTAGT 60.308 47.826 0.00 0.00 0.00 2.57
5292 15784 0.178987 AGTCACCTAGATCCGGCGAT 60.179 55.000 9.30 0.00 0.00 4.58
5376 16058 3.615811 TGGAGCCTGGGAGGAGGT 61.616 66.667 0.00 0.00 37.67 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.901840 CCGGGGCCATCGTCATTG 60.902 66.667 4.39 0.00 0.00 2.82
1 2 3.087253 TCCGGGGCCATCGTCATT 61.087 61.111 4.39 0.00 0.00 2.57
2 3 3.861797 GTCCGGGGCCATCGTCAT 61.862 66.667 4.39 0.00 0.00 3.06
4 5 4.530857 CAGTCCGGGGCCATCGTC 62.531 72.222 4.39 3.76 0.00 4.20
12 13 3.567579 ATTGTGTGCCAGTCCGGGG 62.568 63.158 0.00 0.00 34.06 5.73
13 14 2.034066 ATTGTGTGCCAGTCCGGG 59.966 61.111 0.00 0.00 34.06 5.73
14 15 2.040544 GGATTGTGTGCCAGTCCGG 61.041 63.158 0.00 0.00 39.81 5.14
15 16 3.578456 GGATTGTGTGCCAGTCCG 58.422 61.111 0.00 0.00 39.81 4.79
17 18 1.098050 GGATGGATTGTGTGCCAGTC 58.902 55.000 0.00 0.00 37.64 3.51
18 19 0.405198 TGGATGGATTGTGTGCCAGT 59.595 50.000 0.00 0.00 37.64 4.00
19 20 1.679680 GATGGATGGATTGTGTGCCAG 59.320 52.381 0.00 0.00 37.64 4.85
20 21 1.005687 TGATGGATGGATTGTGTGCCA 59.994 47.619 0.00 0.00 38.78 4.92
21 22 1.766494 TGATGGATGGATTGTGTGCC 58.234 50.000 0.00 0.00 0.00 5.01
22 23 5.163530 TGTTAATGATGGATGGATTGTGTGC 60.164 40.000 0.00 0.00 0.00 4.57
23 24 6.453926 TGTTAATGATGGATGGATTGTGTG 57.546 37.500 0.00 0.00 0.00 3.82
24 25 7.201938 GGATTGTTAATGATGGATGGATTGTGT 60.202 37.037 0.00 0.00 0.00 3.72
25 26 7.149973 GGATTGTTAATGATGGATGGATTGTG 58.850 38.462 0.00 0.00 0.00 3.33
26 27 6.840181 TGGATTGTTAATGATGGATGGATTGT 59.160 34.615 0.00 0.00 0.00 2.71
27 28 7.292713 TGGATTGTTAATGATGGATGGATTG 57.707 36.000 0.00 0.00 0.00 2.67
28 29 7.954056 AGATGGATTGTTAATGATGGATGGATT 59.046 33.333 0.00 0.00 0.00 3.01
29 30 7.396339 CAGATGGATTGTTAATGATGGATGGAT 59.604 37.037 0.00 0.00 0.00 3.41
30 31 6.717997 CAGATGGATTGTTAATGATGGATGGA 59.282 38.462 0.00 0.00 0.00 3.41
31 32 6.071560 CCAGATGGATTGTTAATGATGGATGG 60.072 42.308 0.00 0.00 37.39 3.51
32 33 6.071560 CCCAGATGGATTGTTAATGATGGATG 60.072 42.308 0.00 0.00 37.39 3.51
33 34 6.014647 CCCAGATGGATTGTTAATGATGGAT 58.985 40.000 0.00 0.00 37.39 3.41
34 35 5.103558 ACCCAGATGGATTGTTAATGATGGA 60.104 40.000 0.00 0.00 37.39 3.41
35 36 5.142639 ACCCAGATGGATTGTTAATGATGG 58.857 41.667 0.00 0.00 37.39 3.51
36 37 5.242393 GGACCCAGATGGATTGTTAATGATG 59.758 44.000 0.00 0.00 37.39 3.07
37 38 5.388654 GGACCCAGATGGATTGTTAATGAT 58.611 41.667 0.00 0.00 37.39 2.45
38 39 4.685848 CGGACCCAGATGGATTGTTAATGA 60.686 45.833 0.00 0.00 37.39 2.57
39 40 3.565482 CGGACCCAGATGGATTGTTAATG 59.435 47.826 0.00 0.00 37.39 1.90
40 41 3.458118 TCGGACCCAGATGGATTGTTAAT 59.542 43.478 0.00 0.00 37.39 1.40
41 42 2.841266 TCGGACCCAGATGGATTGTTAA 59.159 45.455 0.00 0.00 37.39 2.01
42 43 2.434336 CTCGGACCCAGATGGATTGTTA 59.566 50.000 0.00 0.00 37.39 2.41
43 44 1.210478 CTCGGACCCAGATGGATTGTT 59.790 52.381 0.00 0.00 37.39 2.83
44 45 0.833287 CTCGGACCCAGATGGATTGT 59.167 55.000 0.00 0.00 37.39 2.71
45 46 0.533755 GCTCGGACCCAGATGGATTG 60.534 60.000 0.00 0.00 37.39 2.67
46 47 1.700042 GGCTCGGACCCAGATGGATT 61.700 60.000 0.00 0.00 37.39 3.01
47 48 2.143419 GGCTCGGACCCAGATGGAT 61.143 63.158 0.00 0.00 37.39 3.41
48 49 2.764128 GGCTCGGACCCAGATGGA 60.764 66.667 0.00 0.00 37.39 3.41
49 50 4.227134 CGGCTCGGACCCAGATGG 62.227 72.222 0.00 0.00 41.37 3.51
50 51 3.432051 GACGGCTCGGACCCAGATG 62.432 68.421 0.00 0.00 0.00 2.90
51 52 3.148279 GACGGCTCGGACCCAGAT 61.148 66.667 0.00 0.00 0.00 2.90
60 61 4.351938 TGTTCACCCGACGGCTCG 62.352 66.667 8.86 0.00 39.83 5.03
61 62 2.737376 GTGTTCACCCGACGGCTC 60.737 66.667 8.86 0.00 0.00 4.70
62 63 3.542676 TGTGTTCACCCGACGGCT 61.543 61.111 8.86 0.00 0.00 5.52
63 64 3.343421 GTGTGTTCACCCGACGGC 61.343 66.667 8.86 0.00 38.51 5.68
71 72 4.848685 ACCTGTCGGTGTGTTCAC 57.151 55.556 0.00 0.00 43.51 3.18
80 81 4.436998 GTCGAGCCCACCTGTCGG 62.437 72.222 0.00 0.00 34.43 4.79
81 82 1.994507 CTAGTCGAGCCCACCTGTCG 61.995 65.000 0.00 0.00 34.98 4.35
82 83 0.680280 TCTAGTCGAGCCCACCTGTC 60.680 60.000 0.00 0.00 0.00 3.51
83 84 0.251653 TTCTAGTCGAGCCCACCTGT 60.252 55.000 0.00 0.00 0.00 4.00
84 85 1.115467 ATTCTAGTCGAGCCCACCTG 58.885 55.000 0.00 0.00 0.00 4.00
85 86 1.115467 CATTCTAGTCGAGCCCACCT 58.885 55.000 0.00 0.00 0.00 4.00
86 87 0.824759 ACATTCTAGTCGAGCCCACC 59.175 55.000 0.00 0.00 0.00 4.61
87 88 3.445857 GTTACATTCTAGTCGAGCCCAC 58.554 50.000 0.00 0.00 0.00 4.61
88 89 2.098607 CGTTACATTCTAGTCGAGCCCA 59.901 50.000 0.00 0.00 0.00 5.36
89 90 2.357009 TCGTTACATTCTAGTCGAGCCC 59.643 50.000 0.00 0.00 0.00 5.19
90 91 3.181503 TGTCGTTACATTCTAGTCGAGCC 60.182 47.826 0.00 0.00 0.00 4.70
91 92 4.012319 TGTCGTTACATTCTAGTCGAGC 57.988 45.455 0.00 0.00 0.00 5.03
92 93 4.094590 ACCTGTCGTTACATTCTAGTCGAG 59.905 45.833 0.00 0.00 34.37 4.04
93 94 4.005650 ACCTGTCGTTACATTCTAGTCGA 58.994 43.478 0.00 0.00 34.37 4.20
94 95 4.096311 CACCTGTCGTTACATTCTAGTCG 58.904 47.826 0.00 0.00 34.37 4.18
95 96 4.157289 TCCACCTGTCGTTACATTCTAGTC 59.843 45.833 0.00 0.00 34.37 2.59
96 97 4.082354 GTCCACCTGTCGTTACATTCTAGT 60.082 45.833 0.00 0.00 34.37 2.57
97 98 4.082408 TGTCCACCTGTCGTTACATTCTAG 60.082 45.833 0.00 0.00 34.37 2.43
98 99 3.827876 TGTCCACCTGTCGTTACATTCTA 59.172 43.478 0.00 0.00 34.37 2.10
99 100 2.631062 TGTCCACCTGTCGTTACATTCT 59.369 45.455 0.00 0.00 34.37 2.40
100 101 3.034721 TGTCCACCTGTCGTTACATTC 57.965 47.619 0.00 0.00 34.37 2.67
101 102 3.135994 GTTGTCCACCTGTCGTTACATT 58.864 45.455 0.00 0.00 34.37 2.71
102 103 2.367567 AGTTGTCCACCTGTCGTTACAT 59.632 45.455 0.00 0.00 34.37 2.29
103 104 1.758280 AGTTGTCCACCTGTCGTTACA 59.242 47.619 0.00 0.00 0.00 2.41
104 105 2.521105 AGTTGTCCACCTGTCGTTAC 57.479 50.000 0.00 0.00 0.00 2.50
105 106 4.669206 TTAAGTTGTCCACCTGTCGTTA 57.331 40.909 0.00 0.00 0.00 3.18
106 107 3.547054 TTAAGTTGTCCACCTGTCGTT 57.453 42.857 0.00 0.00 0.00 3.85
107 108 3.547054 TTTAAGTTGTCCACCTGTCGT 57.453 42.857 0.00 0.00 0.00 4.34
108 109 4.062293 TGATTTAAGTTGTCCACCTGTCG 58.938 43.478 0.00 0.00 0.00 4.35
109 110 5.705441 TGATGATTTAAGTTGTCCACCTGTC 59.295 40.000 0.00 0.00 0.00 3.51
110 111 5.630121 TGATGATTTAAGTTGTCCACCTGT 58.370 37.500 0.00 0.00 0.00 4.00
111 112 5.939883 TCTGATGATTTAAGTTGTCCACCTG 59.060 40.000 0.00 0.00 0.00 4.00
112 113 6.126863 TCTGATGATTTAAGTTGTCCACCT 57.873 37.500 0.00 0.00 0.00 4.00
113 114 6.825721 AGATCTGATGATTTAAGTTGTCCACC 59.174 38.462 0.00 0.00 32.19 4.61
114 115 7.856145 AGATCTGATGATTTAAGTTGTCCAC 57.144 36.000 0.00 0.00 32.19 4.02
115 116 8.981659 TCTAGATCTGATGATTTAAGTTGTCCA 58.018 33.333 5.18 0.00 32.19 4.02
116 117 9.255304 GTCTAGATCTGATGATTTAAGTTGTCC 57.745 37.037 5.18 0.00 32.19 4.02
148 149 6.702716 AGTACAGGTTGCTACTAGATCTTC 57.297 41.667 0.00 0.00 0.00 2.87
150 151 6.437793 ACAAAGTACAGGTTGCTACTAGATCT 59.562 38.462 0.00 0.00 0.00 2.75
156 157 3.139077 GCACAAAGTACAGGTTGCTACT 58.861 45.455 0.00 0.00 0.00 2.57
159 160 2.222027 GAGCACAAAGTACAGGTTGCT 58.778 47.619 10.71 10.71 0.00 3.91
167 173 2.561478 TGGGAAGGAGCACAAAGTAC 57.439 50.000 0.00 0.00 0.00 2.73
176 182 4.021192 TGTTGAATTGATTTGGGAAGGAGC 60.021 41.667 0.00 0.00 0.00 4.70
181 187 5.055812 GCTTGTGTTGAATTGATTTGGGAA 58.944 37.500 0.00 0.00 0.00 3.97
185 191 6.201234 TGTCATGCTTGTGTTGAATTGATTTG 59.799 34.615 0.00 0.00 0.00 2.32
198 204 3.829886 AAACCGTATGTCATGCTTGTG 57.170 42.857 0.00 0.00 0.00 3.33
199 205 5.880332 AGATAAAACCGTATGTCATGCTTGT 59.120 36.000 0.00 0.00 0.00 3.16
200 206 6.363577 AGATAAAACCGTATGTCATGCTTG 57.636 37.500 0.00 0.00 0.00 4.01
201 207 5.527582 GGAGATAAAACCGTATGTCATGCTT 59.472 40.000 0.00 0.00 0.00 3.91
213 219 3.117046 GCTCTTCGAGGAGATAAAACCG 58.883 50.000 27.02 0.00 35.52 4.44
214 220 4.394439 AGCTCTTCGAGGAGATAAAACC 57.606 45.455 27.02 8.19 35.52 3.27
215 221 5.411781 TCAAGCTCTTCGAGGAGATAAAAC 58.588 41.667 27.02 8.88 35.52 2.43
229 242 3.876309 TTTACCCAGGTTCAAGCTCTT 57.124 42.857 0.00 0.00 0.00 2.85
233 246 5.468540 AAAGATTTTACCCAGGTTCAAGC 57.531 39.130 0.00 0.00 0.00 4.01
257 270 1.118838 CCAGGTTCACCAGCCAAAAA 58.881 50.000 0.00 0.00 38.89 1.94
258 271 0.758685 CCCAGGTTCACCAGCCAAAA 60.759 55.000 0.00 0.00 38.89 2.44
259 272 1.152567 CCCAGGTTCACCAGCCAAA 60.153 57.895 0.00 0.00 38.89 3.28
260 273 1.063070 TACCCAGGTTCACCAGCCAA 61.063 55.000 0.00 0.00 38.89 4.52
261 274 1.063070 TTACCCAGGTTCACCAGCCA 61.063 55.000 0.00 0.00 38.89 4.75
262 275 0.111639 TTTACCCAGGTTCACCAGCC 59.888 55.000 0.00 0.00 38.89 4.85
263 276 1.989706 TTTTACCCAGGTTCACCAGC 58.010 50.000 0.00 0.00 38.89 4.85
264 277 4.010349 GAGATTTTACCCAGGTTCACCAG 58.990 47.826 0.00 0.00 38.89 4.00
265 278 3.655777 AGAGATTTTACCCAGGTTCACCA 59.344 43.478 0.00 0.00 38.89 4.17
266 279 4.302559 AGAGATTTTACCCAGGTTCACC 57.697 45.455 0.00 0.00 0.00 4.02
267 280 5.070685 ACAAGAGATTTTACCCAGGTTCAC 58.929 41.667 0.00 0.00 0.00 3.18
275 288 7.591165 GGTAACAAAGACAAGAGATTTTACCC 58.409 38.462 0.00 0.00 0.00 3.69
318 331 3.751246 TGTACGGGGTTCGGAGCG 61.751 66.667 0.00 0.00 44.45 5.03
323 336 1.203994 AGATCTTGTGTACGGGGTTCG 59.796 52.381 0.00 0.00 45.88 3.95
331 344 2.380084 TTCCGGCAGATCTTGTGTAC 57.620 50.000 0.00 0.00 0.00 2.90
335 348 2.787473 TTGATTCCGGCAGATCTTGT 57.213 45.000 0.00 0.00 0.00 3.16
366 1225 2.614057 CCATTTTAGCGTCAGGATGGAC 59.386 50.000 0.00 0.00 36.92 4.02
370 1229 3.545703 CTTCCCATTTTAGCGTCAGGAT 58.454 45.455 0.00 0.00 0.00 3.24
372 1231 2.017049 CCTTCCCATTTTAGCGTCAGG 58.983 52.381 0.00 0.00 0.00 3.86
373 1232 2.017049 CCCTTCCCATTTTAGCGTCAG 58.983 52.381 0.00 0.00 0.00 3.51
381 1240 2.024176 GGTTCCACCCTTCCCATTTT 57.976 50.000 0.00 0.00 30.04 1.82
396 1255 3.008049 CAGTATATGGGGTGCTAGGGTTC 59.992 52.174 0.00 0.00 0.00 3.62
458 1317 1.089112 CTGCATTCAGTTCATCGGCA 58.911 50.000 0.00 0.00 35.61 5.69
469 1328 1.305213 GGGGCCTTTCCTGCATTCA 60.305 57.895 0.84 0.00 34.39 2.57
484 1343 4.832608 GTTGTAGCGAGGCGGGGG 62.833 72.222 0.00 0.00 0.00 5.40
489 1348 1.565305 CAGATCTGTTGTAGCGAGGC 58.435 55.000 14.95 0.00 0.00 4.70
492 1351 1.476891 GGTCCAGATCTGTTGTAGCGA 59.523 52.381 21.11 6.72 0.00 4.93
493 1352 1.799181 CGGTCCAGATCTGTTGTAGCG 60.799 57.143 21.11 18.29 0.00 4.26
557 1419 4.373116 GCTCGTCGAGGGTGGCAA 62.373 66.667 23.09 0.00 0.00 4.52
612 1478 2.046314 CTCGCCGGTGGTTGGATT 60.046 61.111 16.49 0.00 0.00 3.01
617 1483 3.236003 GAGGTTCTCGCCGGTGGTT 62.236 63.158 16.49 0.00 0.00 3.67
675 1542 3.518998 CGAGGGCACGACCGATCT 61.519 66.667 0.00 0.00 40.62 2.75
742 1609 2.003672 CGCAAGTGCATACCGTACC 58.996 57.895 3.87 0.00 42.21 3.34
743 1610 1.347221 GCGCAAGTGCATACCGTAC 59.653 57.895 0.30 0.00 42.21 3.67
744 1611 2.162120 CGCGCAAGTGCATACCGTA 61.162 57.895 8.75 0.00 43.07 4.02
745 1612 3.487202 CGCGCAAGTGCATACCGT 61.487 61.111 8.75 0.00 43.07 4.83
791 1658 2.115052 ACATGGGCGCAGGTGAAA 59.885 55.556 20.80 0.00 0.00 2.69
871 1738 2.034048 TAGCAAGGCACACGGTGACA 62.034 55.000 16.29 0.00 45.35 3.58
883 1750 0.941463 CGCGATGTAGCCTAGCAAGG 60.941 60.000 0.00 0.00 46.76 3.61
886 1753 2.027605 GCGCGATGTAGCCTAGCA 59.972 61.111 12.10 0.00 0.00 3.49
911 1778 1.062587 GATCATTCGTGTTCTTGGCCG 59.937 52.381 0.00 0.00 0.00 6.13
923 1790 4.142534 ACAGCCTTGACATTTGATCATTCG 60.143 41.667 0.00 0.00 0.00 3.34
956 1843 1.880340 GGAGCGCGATCAGTGAAGG 60.880 63.158 27.12 0.00 0.00 3.46
997 1884 0.381801 AAGTTCAAGGTGCGTGCAAG 59.618 50.000 0.00 0.00 0.00 4.01
1122 2014 1.227853 ACGAGGGTTTGCTCCACAC 60.228 57.895 0.00 0.00 0.00 3.82
1165 2057 2.121832 TCCGGGGAGAAGAAGCCA 59.878 61.111 0.00 0.00 0.00 4.75
1240 2132 4.619227 CAGACAACGGTGCGGGGT 62.619 66.667 0.00 0.00 0.00 4.95
2331 3259 2.677228 CCGGGGAAGTGGAAGCAT 59.323 61.111 0.00 0.00 0.00 3.79
2347 3275 8.344446 AGTTTGGTTAACTTGATTGTATACCC 57.656 34.615 5.42 0.00 44.73 3.69
2390 3318 6.202954 TCAGACGGAACTCTGAAAATCTTTTC 59.797 38.462 8.18 8.18 43.06 2.29
2412 3546 6.752335 TTTGTTCGAATTCAGCAAAATCAG 57.248 33.333 0.00 0.00 0.00 2.90
2413 5842 7.277539 ACTTTTTGTTCGAATTCAGCAAAATCA 59.722 29.630 21.57 13.10 38.35 2.57
2429 5858 9.952341 GATGAAACAACAGTAAACTTTTTGTTC 57.048 29.630 15.19 11.23 38.05 3.18
2499 5957 2.288666 TGCTATCTTCACGGCATTTCC 58.711 47.619 0.00 0.00 0.00 3.13
2581 6039 4.833390 AGGAAATGTAACTGTACCTCTGC 58.167 43.478 0.00 0.00 0.00 4.26
2615 6493 0.108041 GAAATGGTTGGGCATGGCAG 60.108 55.000 22.06 0.00 0.00 4.85
2665 6572 4.998033 GGTTTTCCTCCTCTTGTCTGTAAG 59.002 45.833 0.00 0.00 36.94 2.34
2679 6587 0.608640 TCTGGCTCTCGGTTTTCCTC 59.391 55.000 0.00 0.00 37.95 3.71
2705 6622 2.046285 GTCCTTGTCCCGGGCATTG 61.046 63.158 18.49 12.56 0.00 2.82
2856 6774 1.810030 GTAGACCTTGCCGAAGCCG 60.810 63.158 0.00 0.00 38.69 5.52
2914 8059 4.447724 TGCTAAACTGACAGAACATCGAAC 59.552 41.667 10.08 0.00 0.00 3.95
2974 8686 0.322975 GCAGTGGAGTGAGACCATGT 59.677 55.000 0.00 0.00 39.69 3.21
3000 8732 2.243810 TGCCTTCCCAATGGTAAACAC 58.756 47.619 0.00 0.00 0.00 3.32
3054 8786 0.107993 TCTGAATCCTTGCTCAGCCG 60.108 55.000 0.00 0.00 39.17 5.52
3219 8951 6.653320 TGAACATTGTATGTACCAAAGAGGAC 59.347 38.462 0.00 0.00 44.07 3.85
3347 9413 0.554865 ACCCCCTTGATGATCCCCAA 60.555 55.000 0.00 0.00 0.00 4.12
3415 9486 2.224159 GGCCTTGAGGTCCCTGTGA 61.224 63.158 0.00 0.00 37.57 3.58
3769 9889 1.613317 TACCCTGATGCCACTCACGG 61.613 60.000 0.00 0.00 0.00 4.94
3869 10044 2.309613 GGCATGGCATGGACTGAAATA 58.690 47.619 27.48 0.00 0.00 1.40
3911 10110 7.165154 GTGTGTGTGTGTGTGTGTTATATTTTC 59.835 37.037 0.00 0.00 0.00 2.29
3916 10115 3.552294 CGTGTGTGTGTGTGTGTGTTATA 59.448 43.478 0.00 0.00 0.00 0.98
3940 10151 2.353269 CCATTTGTGTGTGTACGTGTGT 59.647 45.455 0.00 0.00 0.00 3.72
3941 10152 2.353269 ACCATTTGTGTGTGTACGTGTG 59.647 45.455 0.00 0.00 0.00 3.82
3942 10153 2.634600 ACCATTTGTGTGTGTACGTGT 58.365 42.857 0.00 0.00 0.00 4.49
3943 10154 3.064134 TCAACCATTTGTGTGTGTACGTG 59.936 43.478 0.00 0.00 34.02 4.49
3944 10155 3.271729 TCAACCATTTGTGTGTGTACGT 58.728 40.909 0.00 0.00 34.02 3.57
3945 10156 3.953874 TCAACCATTTGTGTGTGTACG 57.046 42.857 0.00 0.00 34.02 3.67
3947 10158 5.825151 TCAGATTCAACCATTTGTGTGTGTA 59.175 36.000 0.00 0.00 34.02 2.90
3949 10160 5.185668 TCAGATTCAACCATTTGTGTGTG 57.814 39.130 0.00 0.00 34.02 3.82
3951 10162 8.991243 AATAATCAGATTCAACCATTTGTGTG 57.009 30.769 0.00 0.00 34.02 3.82
4300 13958 5.050490 TGAAGAAAGTTGCAGTCACTACTC 58.950 41.667 0.00 0.00 31.97 2.59
4307 13965 4.130118 TCCTTCTGAAGAAAGTTGCAGTC 58.870 43.478 18.68 0.00 33.07 3.51
4358 14029 3.301274 TGGGGTTTCCACCAGTAAAAAG 58.699 45.455 0.00 0.00 46.43 2.27
4429 14100 4.790765 TCAATGATCGACTCAACACTCT 57.209 40.909 0.00 0.00 37.44 3.24
4487 14158 1.105167 CCAGATGCACATGCCGGAAT 61.105 55.000 5.05 0.00 41.18 3.01
4488 14159 1.750018 CCAGATGCACATGCCGGAA 60.750 57.895 5.05 0.00 41.18 4.30
4572 14247 2.092882 GTAGCGACGGTGGCTTCAC 61.093 63.158 22.50 12.09 41.80 3.18
4635 14491 1.301716 GGCTGCGAGGTCTGTTTGA 60.302 57.895 0.00 0.00 0.00 2.69
4680 14913 2.347490 CAGACGTCCTGGTTGGGG 59.653 66.667 13.01 0.00 39.23 4.96
4739 15055 1.478510 CCTCATACCTGACAAGCGTCT 59.521 52.381 0.00 0.00 43.06 4.18
4748 15064 3.536917 CGGCGGCCTCATACCTGA 61.537 66.667 18.34 0.00 0.00 3.86
4775 15265 4.701651 TCTCTGAAGATGGATTGATGGG 57.298 45.455 0.00 0.00 0.00 4.00
4801 15291 0.680921 GGGCAAGGTAGATGCAGCAA 60.681 55.000 4.07 0.00 45.60 3.91
4822 15312 2.415010 CGTCGGCAGCAGCTAGAT 59.585 61.111 0.00 0.00 41.70 1.98
4855 15345 2.102553 GTAGGAGGTCGACGCTGC 59.897 66.667 9.92 12.81 0.00 5.25
4962 15452 1.743772 CGGTTGGCTTCTTCGATGGAT 60.744 52.381 0.00 0.00 0.00 3.41
4983 15473 4.458829 TCGGGCTCGAGGGACCAT 62.459 66.667 15.58 0.00 40.88 3.55
5076 15566 1.283905 CCAATACCTCCGGGGAAAACT 59.716 52.381 0.37 0.00 38.76 2.66
5108 15599 1.278985 AGGCATCATCGAGGTGAAACA 59.721 47.619 0.00 0.00 39.98 2.83
5176 15667 1.338389 CCTGGTATTCGGTCGTTGGTT 60.338 52.381 0.00 0.00 0.00 3.67
5177 15668 0.248289 CCTGGTATTCGGTCGTTGGT 59.752 55.000 0.00 0.00 0.00 3.67
5178 15669 0.248289 ACCTGGTATTCGGTCGTTGG 59.752 55.000 0.00 0.00 0.00 3.77
5179 15670 2.088950 AACCTGGTATTCGGTCGTTG 57.911 50.000 0.00 0.00 31.87 4.10
5250 15742 2.909965 TGGGTGTTTGAAGGCGGC 60.910 61.111 0.00 0.00 0.00 6.53
5376 16058 4.715130 CGAGGTGGGGGTGGGAGA 62.715 72.222 0.00 0.00 0.00 3.71
5407 16846 1.692395 TGGGATCCATCTTGGCGGA 60.692 57.895 15.23 0.00 37.47 5.54


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

AutoCloner maintained by Alex Coulton.