Multiple sequence alignment - TraesCS7D01G027600

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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 TraesCS7D01G027600 chr7D 100.000 8336 0 0 1 8336 13504170 13512505 0.000000e+00 15394.0
1 TraesCS7D01G027600 chr7D 84.863 1460 165 29 5978 7394 13660431 13658985 0.000000e+00 1421.0
2 TraesCS7D01G027600 chr7D 84.725 1401 177 12 3038 4410 535409326 535407935 0.000000e+00 1367.0
3 TraesCS7D01G027600 chr7D 97.285 663 17 1 4401 5063 112414762 112415423 0.000000e+00 1123.0
4 TraesCS7D01G027600 chr7D 97.546 652 13 2 4409 5059 95103676 95104325 0.000000e+00 1112.0
5 TraesCS7D01G027600 chr7D 83.447 1178 155 21 3263 4410 500783824 500782657 0.000000e+00 1059.0
6 TraesCS7D01G027600 chr7D 86.918 902 79 25 1499 2382 13663044 13662164 0.000000e+00 976.0
7 TraesCS7D01G027600 chr7D 79.502 844 97 39 606 1412 13663952 13663148 1.590000e-146 531.0
8 TraesCS7D01G027600 chr7D 82.689 543 80 8 5321 5856 13661007 13660472 3.520000e-128 470.0
9 TraesCS7D01G027600 chr7D 80.213 470 68 20 6364 6826 13611254 13610803 6.240000e-86 329.0
10 TraesCS7D01G027600 chr7D 81.163 361 34 18 2606 2939 13505805 13506158 8.300000e-65 259.0
11 TraesCS7D01G027600 chr7D 81.163 361 34 18 1636 1989 13506775 13507108 8.300000e-65 259.0
12 TraesCS7D01G027600 chr7D 81.232 357 36 13 2607 2939 13662914 13662565 8.300000e-65 259.0
13 TraesCS7D01G027600 chr7D 79.577 284 55 2 2098 2380 13613955 13613674 5.100000e-47 200.0
14 TraesCS7D01G027600 chr7D 77.624 362 54 21 4 363 63646386 63646050 2.370000e-45 195.0
15 TraesCS7D01G027600 chr7D 94.175 103 6 0 5215 5317 13662446 13662344 3.110000e-34 158.0
16 TraesCS7D01G027600 chr7D 89.320 103 11 0 5215 5317 13506270 13506372 6.790000e-26 130.0
17 TraesCS7D01G027600 chr7D 89.320 103 11 0 2101 2203 13509384 13509486 6.790000e-26 130.0
18 TraesCS7D01G027600 chr7D 86.747 83 11 0 5215 5297 13613952 13613870 8.910000e-15 93.5
19 TraesCS7D01G027600 chr7D 79.114 158 14 15 2423 2566 13663281 13663129 3.200000e-14 91.6
20 TraesCS7D01G027600 chr3D 97.241 2356 52 3 5992 8336 585226964 585224611 0.000000e+00 3978.0
21 TraesCS7D01G027600 chr3D 96.078 2422 56 10 2027 4410 585230353 585227933 0.000000e+00 3910.0
22 TraesCS7D01G027600 chr3D 90.938 938 59 11 5058 5981 585227941 585227016 0.000000e+00 1238.0
23 TraesCS7D01G027600 chr3D 83.725 1192 169 16 3237 4410 19930965 19929781 0.000000e+00 1103.0
24 TraesCS7D01G027600 chr3D 88.186 711 65 11 123 829 585233635 585232940 0.000000e+00 830.0
25 TraesCS7D01G027600 chr3D 97.968 443 8 1 1542 1984 585230788 585230347 0.000000e+00 767.0
26 TraesCS7D01G027600 chr3D 80.342 468 69 19 6364 6826 585088755 585089204 4.820000e-87 333.0
27 TraesCS7D01G027600 chr3D 81.053 380 46 17 1 378 277140332 277140687 6.370000e-71 279.0
28 TraesCS7D01G027600 chr3D 80.508 354 37 16 2607 2935 585230693 585230347 8.360000e-60 243.0
29 TraesCS7D01G027600 chr3D 79.890 363 36 18 1636 1989 585229753 585229419 1.810000e-56 231.0
30 TraesCS7D01G027600 chr3D 92.500 160 6 2 815 968 585230958 585230799 3.030000e-54 224.0
31 TraesCS7D01G027600 chr3D 88.288 111 12 1 2093 2203 585227789 585227680 1.890000e-26 132.0
32 TraesCS7D01G027600 chr7A 90.333 2462 152 35 123 2542 13047124 13049541 0.000000e+00 3149.0
33 TraesCS7D01G027600 chr7A 94.876 1815 50 17 5722 7521 13053330 13055116 0.000000e+00 2796.0
34 TraesCS7D01G027600 chr7A 85.975 1861 209 20 2592 4410 13050124 13051974 0.000000e+00 1943.0
35 TraesCS7D01G027600 chr7A 83.345 1441 200 26 2999 4410 721124026 721122597 0.000000e+00 1295.0
36 TraesCS7D01G027600 chr7A 82.532 1414 188 26 3029 4409 43134208 43132821 0.000000e+00 1188.0
37 TraesCS7D01G027600 chr7A 83.577 1297 162 25 6144 7394 13115534 13114243 0.000000e+00 1168.0
38 TraesCS7D01G027600 chr7A 91.884 653 33 12 5055 5706 13051963 13052596 0.000000e+00 894.0
39 TraesCS7D01G027600 chr7A 94.965 576 15 5 7773 8336 13055125 13055698 0.000000e+00 891.0
40 TraesCS7D01G027600 chr7A 80.606 990 144 32 6366 7337 13101801 13100842 0.000000e+00 721.0
41 TraesCS7D01G027600 chr7A 79.110 517 50 24 1501 1989 13049994 13050480 3.780000e-78 303.0
42 TraesCS7D01G027600 chr7A 80.743 296 25 16 2606 2876 13048640 13048928 1.420000e-47 202.0
43 TraesCS7D01G027600 chr7A 96.629 89 1 2 1423 1511 13048396 13048482 6.740000e-31 147.0
44 TraesCS7D01G027600 chr7A 89.320 103 11 0 5215 5317 13049090 13049192 6.790000e-26 130.0
45 TraesCS7D01G027600 chr7A 95.588 68 3 0 990 1057 13116730 13116663 8.850000e-20 110.0
46 TraesCS7D01G027600 chr4A 90.657 1584 101 20 5993 7534 723019706 723018128 0.000000e+00 2061.0
47 TraesCS7D01G027600 chr4A 82.288 1451 198 29 5995 7393 722885717 722887160 0.000000e+00 1201.0
48 TraesCS7D01G027600 chr4A 88.672 821 66 10 7540 8336 722937372 722936555 0.000000e+00 976.0
49 TraesCS7D01G027600 chr4A 87.529 850 85 11 5138 5981 723020593 723019759 0.000000e+00 963.0
50 TraesCS7D01G027600 chr4A 87.912 819 72 10 7542 8335 722966196 722965380 0.000000e+00 939.0
51 TraesCS7D01G027600 chr4A 88.356 730 67 13 7540 8257 723000480 722999757 0.000000e+00 861.0
52 TraesCS7D01G027600 chr4A 87.873 536 52 8 1829 2359 722883476 722884003 1.190000e-172 617.0
53 TraesCS7D01G027600 chr4A 90.065 463 46 0 6106 6568 722940095 722939633 1.200000e-167 601.0
54 TraesCS7D01G027600 chr4A 89.201 463 49 1 6106 6568 722968668 722968207 2.020000e-160 577.0
55 TraesCS7D01G027600 chr4A 90.842 404 37 0 6106 6509 722965156 722964753 7.360000e-150 542.0
56 TraesCS7D01G027600 chr4A 84.264 591 54 19 862 1430 723023269 723022696 2.650000e-149 540.0
57 TraesCS7D01G027600 chr4A 80.597 603 70 24 1502 2094 723021063 723020498 1.000000e-113 422.0
58 TraesCS7D01G027600 chr4A 81.496 508 79 8 6839 7337 722904657 722905158 3.620000e-108 403.0
59 TraesCS7D01G027600 chr4A 89.865 296 17 5 1501 1785 722883185 722883478 1.320000e-97 368.0
60 TraesCS7D01G027600 chr4A 85.559 367 27 5 2621 2972 723022540 723022185 2.210000e-95 361.0
61 TraesCS7D01G027600 chr4A 80.363 331 27 10 1032 1361 722882701 722882994 5.070000e-52 217.0
62 TraesCS7D01G027600 chr4A 79.279 333 45 15 2628 2939 723020929 723020600 2.360000e-50 211.0
63 TraesCS7D01G027600 chr4A 93.204 103 7 0 5215 5317 722883741 722883843 1.450000e-32 152.0
64 TraesCS7D01G027600 chr4A 84.277 159 18 6 8101 8258 741030289 741030441 1.870000e-31 148.0
65 TraesCS7D01G027600 chr4A 91.089 101 9 0 2103 2203 723020516 723020416 4.060000e-28 137.0
66 TraesCS7D01G027600 chr4A 88.889 72 7 1 2423 2493 723021337 723021266 4.140000e-13 87.9
67 TraesCS7D01G027600 chr4A 88.732 71 7 1 1580 1650 741618100 741618169 1.490000e-12 86.1
68 TraesCS7D01G027600 chr4A 97.826 46 1 0 8291 8336 722940361 722940316 6.940000e-11 80.5
69 TraesCS7D01G027600 chr1B 86.185 1426 163 14 3016 4410 161984544 161983122 0.000000e+00 1511.0
70 TraesCS7D01G027600 chr1B 74.603 504 96 21 6716 7194 286976859 286977355 8.540000e-45 193.0
71 TraesCS7D01G027600 chr2D 83.587 1444 197 21 2995 4410 204107891 204109322 0.000000e+00 1317.0
72 TraesCS7D01G027600 chr2D 97.692 650 12 2 4410 5059 532160373 532161019 0.000000e+00 1114.0
73 TraesCS7D01G027600 chr2D 85.022 227 21 7 1005 1231 574660268 574660055 1.410000e-52 219.0
74 TraesCS7D01G027600 chr2D 85.714 98 10 4 270 367 413944351 413944444 5.320000e-17 100.0
75 TraesCS7D01G027600 chr6D 97.297 666 12 4 4411 5075 73502326 73502986 0.000000e+00 1125.0
76 TraesCS7D01G027600 chr6D 96.078 663 23 3 4411 5071 344800407 344799746 0.000000e+00 1077.0
77 TraesCS7D01G027600 chr6D 91.742 666 41 9 4407 5059 466542238 466542902 0.000000e+00 913.0
78 TraesCS7D01G027600 chr5D 96.861 669 15 6 4406 5073 479784273 479784936 0.000000e+00 1114.0
79 TraesCS7D01G027600 chr4D 97.385 650 17 0 4409 5058 495300420 495299771 0.000000e+00 1107.0
80 TraesCS7D01G027600 chr4D 97.231 650 17 1 4411 5059 438434662 438434013 0.000000e+00 1099.0
81 TraesCS7D01G027600 chr3A 83.905 1137 153 15 3300 4410 681068052 681066920 0.000000e+00 1059.0
82 TraesCS7D01G027600 chr3A 83.451 1136 156 14 3301 4410 681085223 681084094 0.000000e+00 1027.0
83 TraesCS7D01G027600 chr2B 80.890 921 133 23 2992 3881 416841840 416840932 0.000000e+00 686.0
84 TraesCS7D01G027600 chr2B 84.051 627 72 7 3038 3636 66413561 66412935 5.610000e-161 579.0
85 TraesCS7D01G027600 chr2B 83.663 404 45 8 3004 3395 237342822 237342428 2.210000e-95 361.0
86 TraesCS7D01G027600 chr2B 80.109 367 44 14 1 367 487227868 487228205 6.460000e-61 246.0
87 TraesCS7D01G027600 chr2B 74.803 254 38 10 3260 3489 71686029 71686280 3.200000e-14 91.6
88 TraesCS7D01G027600 chr1D 81.783 774 102 11 2995 3734 426615557 426614789 5.530000e-171 612.0
89 TraesCS7D01G027600 chr3B 82.341 504 65 8 3024 3505 456917986 456917485 4.650000e-112 416.0
90 TraesCS7D01G027600 chr3B 91.228 57 4 1 1603 1659 417174176 417174231 8.970000e-10 76.8
91 TraesCS7D01G027600 chr2A 83.444 151 20 3 6438 6587 655659527 655659673 1.460000e-27 135.0
92 TraesCS7D01G027600 chr5B 75.433 289 51 14 29 309 636887981 636887705 1.140000e-23 122.0
93 TraesCS7D01G027600 chr7B 86.726 113 8 5 6682 6791 708501045 708500937 1.470000e-22 119.0
94 TraesCS7D01G027600 chr4B 93.056 72 5 0 1580 1651 184592365 184592436 1.140000e-18 106.0


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G027600 chr7D 13504170 13512505 8335 False 15394.000000 15394 100.000000 1 8336 1 chr7D.!!$F1 8335
1 TraesCS7D01G027600 chr7D 535407935 535409326 1391 True 1367.000000 1367 84.725000 3038 4410 1 chr7D.!!$R3 1372
2 TraesCS7D01G027600 chr7D 112414762 112415423 661 False 1123.000000 1123 97.285000 4401 5063 1 chr7D.!!$F3 662
3 TraesCS7D01G027600 chr7D 95103676 95104325 649 False 1112.000000 1112 97.546000 4409 5059 1 chr7D.!!$F2 650
4 TraesCS7D01G027600 chr7D 500782657 500783824 1167 True 1059.000000 1059 83.447000 3263 4410 1 chr7D.!!$R2 1147
5 TraesCS7D01G027600 chr7D 13658985 13663952 4967 True 558.085714 1421 84.070429 606 7394 7 chr7D.!!$R5 6788
6 TraesCS7D01G027600 chr7D 13610803 13613955 3152 True 207.500000 329 82.179000 2098 6826 3 chr7D.!!$R4 4728
7 TraesCS7D01G027600 chr3D 585224611 585233635 9024 True 1283.666667 3978 90.177444 123 8336 9 chr3D.!!$R2 8213
8 TraesCS7D01G027600 chr3D 19929781 19930965 1184 True 1103.000000 1103 83.725000 3237 4410 1 chr3D.!!$R1 1173
9 TraesCS7D01G027600 chr7A 721122597 721124026 1429 True 1295.000000 1295 83.345000 2999 4410 1 chr7A.!!$R3 1411
10 TraesCS7D01G027600 chr7A 43132821 43134208 1387 True 1188.000000 1188 82.532000 3029 4409 1 chr7A.!!$R2 1380
11 TraesCS7D01G027600 chr7A 13047124 13055698 8574 False 1161.666667 3149 89.315000 123 8336 9 chr7A.!!$F1 8213
12 TraesCS7D01G027600 chr7A 13100842 13101801 959 True 721.000000 721 80.606000 6366 7337 1 chr7A.!!$R1 971
13 TraesCS7D01G027600 chr7A 13114243 13116730 2487 True 639.000000 1168 89.582500 990 7394 2 chr7A.!!$R4 6404
14 TraesCS7D01G027600 chr4A 722999757 723000480 723 True 861.000000 861 88.356000 7540 8257 1 chr4A.!!$R1 717
15 TraesCS7D01G027600 chr4A 722964753 722968668 3915 True 686.000000 939 89.318333 6106 8335 3 chr4A.!!$R3 2229
16 TraesCS7D01G027600 chr4A 723018128 723023269 5141 True 597.862500 2061 85.982875 862 7534 8 chr4A.!!$R4 6672
17 TraesCS7D01G027600 chr4A 722936555 722940361 3806 True 552.500000 976 92.187667 6106 8336 3 chr4A.!!$R2 2230
18 TraesCS7D01G027600 chr4A 722882701 722887160 4459 False 511.000000 1201 86.718600 1032 7393 5 chr4A.!!$F4 6361
19 TraesCS7D01G027600 chr4A 722904657 722905158 501 False 403.000000 403 81.496000 6839 7337 1 chr4A.!!$F1 498
20 TraesCS7D01G027600 chr1B 161983122 161984544 1422 True 1511.000000 1511 86.185000 3016 4410 1 chr1B.!!$R1 1394
21 TraesCS7D01G027600 chr2D 204107891 204109322 1431 False 1317.000000 1317 83.587000 2995 4410 1 chr2D.!!$F1 1415
22 TraesCS7D01G027600 chr2D 532160373 532161019 646 False 1114.000000 1114 97.692000 4410 5059 1 chr2D.!!$F3 649
23 TraesCS7D01G027600 chr6D 73502326 73502986 660 False 1125.000000 1125 97.297000 4411 5075 1 chr6D.!!$F1 664
24 TraesCS7D01G027600 chr6D 344799746 344800407 661 True 1077.000000 1077 96.078000 4411 5071 1 chr6D.!!$R1 660
25 TraesCS7D01G027600 chr6D 466542238 466542902 664 False 913.000000 913 91.742000 4407 5059 1 chr6D.!!$F2 652
26 TraesCS7D01G027600 chr5D 479784273 479784936 663 False 1114.000000 1114 96.861000 4406 5073 1 chr5D.!!$F1 667
27 TraesCS7D01G027600 chr4D 495299771 495300420 649 True 1107.000000 1107 97.385000 4409 5058 1 chr4D.!!$R2 649
28 TraesCS7D01G027600 chr4D 438434013 438434662 649 True 1099.000000 1099 97.231000 4411 5059 1 chr4D.!!$R1 648
29 TraesCS7D01G027600 chr3A 681066920 681068052 1132 True 1059.000000 1059 83.905000 3300 4410 1 chr3A.!!$R1 1110
30 TraesCS7D01G027600 chr3A 681084094 681085223 1129 True 1027.000000 1027 83.451000 3301 4410 1 chr3A.!!$R2 1109
31 TraesCS7D01G027600 chr2B 416840932 416841840 908 True 686.000000 686 80.890000 2992 3881 1 chr2B.!!$R3 889
32 TraesCS7D01G027600 chr2B 66412935 66413561 626 True 579.000000 579 84.051000 3038 3636 1 chr2B.!!$R1 598
33 TraesCS7D01G027600 chr1D 426614789 426615557 768 True 612.000000 612 81.783000 2995 3734 1 chr1D.!!$R1 739
34 TraesCS7D01G027600 chr3B 456917485 456917986 501 True 416.000000 416 82.341000 3024 3505 1 chr3B.!!$R1 481

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
232 233 0.035820 GTTGGGGATGGCAACGTAGA 60.036 55.000 0.00 0.00 42.51 2.59 F
433 434 0.179081 GGACCGGGCATGAAGAGTAC 60.179 60.000 11.00 0.00 0.00 2.73 F
503 506 0.741221 ATTTCCCGTTCGAGCAGAGC 60.741 55.000 0.00 0.00 0.00 4.09 F
2419 6143 0.759060 GAGGAGAAGGAGGAGGAGGC 60.759 65.000 0.00 0.00 0.00 4.70 F
3439 7817 0.533755 GATCTTGGGATCCCGCACTG 60.534 60.000 26.03 13.18 41.70 3.66 F
4843 9737 0.454600 TGACATCGAACGGGCTCTAC 59.545 55.000 0.00 0.00 0.00 2.59 F
5278 10183 0.527817 GATTGGACGTACCGCCTGAG 60.528 60.000 0.00 0.00 42.61 3.35 F
5437 10359 2.072298 GCTTCGTTTCATCAGCTGAGT 58.928 47.619 22.96 7.66 34.68 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1324 3376 0.731417 CCTTTGGCTGCATCGAAGAG 59.269 55.000 15.06 4.15 43.63 2.85 R
2420 6144 0.604780 GCAGCTGCTGTTCTTCAGGA 60.605 55.000 31.33 0.00 43.78 3.86 R
2437 6182 1.550524 AGAAGATACTCTTGTGCCGCA 59.449 47.619 0.00 0.00 36.73 5.69 R
3546 7927 3.124921 GAACCCACCGTCATGCCG 61.125 66.667 0.00 0.00 0.00 5.69 R
5295 10200 0.039074 CCTCGATGATCTACGGTGCC 60.039 60.000 10.90 0.00 0.00 5.01 R
5871 11574 2.862674 TATTGGTTCAGGCCGGCGTC 62.863 60.000 20.79 6.63 0.00 5.19 R
6987 13470 0.988832 TTGGTGGAAGTAGCCCGAAT 59.011 50.000 0.00 0.00 0.00 3.34 R
7702 15068 4.663389 GCTCAAGTTTTACGCAGAACTACG 60.663 45.833 0.00 0.00 35.17 3.51 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
21 22 2.731976 GCTATCATTCCACGACGAATCC 59.268 50.000 0.00 0.00 29.85 3.01
23 24 2.979814 TCATTCCACGACGAATCCAT 57.020 45.000 0.00 0.00 29.85 3.41
25 26 2.935849 TCATTCCACGACGAATCCATTG 59.064 45.455 0.00 0.00 29.85 2.82
26 27 2.753055 TTCCACGACGAATCCATTGA 57.247 45.000 0.00 0.00 0.00 2.57
27 28 2.004583 TCCACGACGAATCCATTGAC 57.995 50.000 0.00 0.00 0.00 3.18
28 29 0.645355 CCACGACGAATCCATTGACG 59.355 55.000 0.00 0.00 0.00 4.35
29 30 1.624487 CACGACGAATCCATTGACGA 58.376 50.000 0.00 0.00 0.00 4.20
30 31 1.320555 CACGACGAATCCATTGACGAC 59.679 52.381 0.00 0.00 0.00 4.34
31 32 0.921347 CGACGAATCCATTGACGACC 59.079 55.000 0.00 0.00 0.00 4.79
32 33 1.469251 CGACGAATCCATTGACGACCT 60.469 52.381 0.00 0.00 0.00 3.85
33 34 2.223409 CGACGAATCCATTGACGACCTA 60.223 50.000 0.00 0.00 0.00 3.08
34 35 3.372954 GACGAATCCATTGACGACCTAG 58.627 50.000 0.00 0.00 0.00 3.02
35 36 3.021695 ACGAATCCATTGACGACCTAGA 58.978 45.455 0.00 0.00 0.00 2.43
36 37 3.446161 ACGAATCCATTGACGACCTAGAA 59.554 43.478 0.00 0.00 0.00 2.10
37 38 4.045104 CGAATCCATTGACGACCTAGAAG 58.955 47.826 0.00 0.00 0.00 2.85
38 39 4.440250 CGAATCCATTGACGACCTAGAAGT 60.440 45.833 0.00 0.00 0.00 3.01
40 41 6.540438 AATCCATTGACGACCTAGAAGTAA 57.460 37.500 0.00 0.00 0.00 2.24
41 42 6.732896 ATCCATTGACGACCTAGAAGTAAT 57.267 37.500 0.00 0.00 0.00 1.89
42 43 5.902681 TCCATTGACGACCTAGAAGTAATG 58.097 41.667 0.00 0.00 0.00 1.90
43 44 5.655090 TCCATTGACGACCTAGAAGTAATGA 59.345 40.000 0.00 0.00 0.00 2.57
44 45 5.749109 CCATTGACGACCTAGAAGTAATGAC 59.251 44.000 0.00 0.00 0.00 3.06
46 47 3.376234 TGACGACCTAGAAGTAATGACCG 59.624 47.826 0.00 0.00 0.00 4.79
47 48 3.614092 ACGACCTAGAAGTAATGACCGA 58.386 45.455 0.00 0.00 0.00 4.69
48 49 4.012374 ACGACCTAGAAGTAATGACCGAA 58.988 43.478 0.00 0.00 0.00 4.30
52 53 6.600882 ACCTAGAAGTAATGACCGAAAGAA 57.399 37.500 0.00 0.00 0.00 2.52
53 54 7.184067 ACCTAGAAGTAATGACCGAAAGAAT 57.816 36.000 0.00 0.00 0.00 2.40
56 57 9.595823 CCTAGAAGTAATGACCGAAAGAATAAA 57.404 33.333 0.00 0.00 0.00 1.40
65 66 8.801882 ATGACCGAAAGAATAAAAATACCAGA 57.198 30.769 0.00 0.00 0.00 3.86
66 67 8.801882 TGACCGAAAGAATAAAAATACCAGAT 57.198 30.769 0.00 0.00 0.00 2.90
67 68 9.893634 TGACCGAAAGAATAAAAATACCAGATA 57.106 29.630 0.00 0.00 0.00 1.98
69 70 9.338622 ACCGAAAGAATAAAAATACCAGATAGG 57.661 33.333 0.00 0.00 45.67 2.57
70 71 9.555727 CCGAAAGAATAAAAATACCAGATAGGA 57.444 33.333 0.00 0.00 41.22 2.94
82 83 9.699410 AAATACCAGATAGGACATTTCATTGAA 57.301 29.630 0.00 0.00 41.22 2.69
83 84 8.682936 ATACCAGATAGGACATTTCATTGAAC 57.317 34.615 0.00 0.00 41.22 3.18
85 86 6.375455 ACCAGATAGGACATTTCATTGAACAC 59.625 38.462 0.00 0.00 41.22 3.32
86 87 6.457392 CCAGATAGGACATTTCATTGAACACG 60.457 42.308 0.00 0.00 41.22 4.49
88 89 7.277760 CAGATAGGACATTTCATTGAACACGTA 59.722 37.037 0.00 0.00 0.00 3.57
89 90 5.862924 AGGACATTTCATTGAACACGTAG 57.137 39.130 0.00 0.00 0.00 3.51
90 91 5.547465 AGGACATTTCATTGAACACGTAGA 58.453 37.500 0.00 0.00 0.00 2.59
91 92 5.639506 AGGACATTTCATTGAACACGTAGAG 59.360 40.000 0.00 0.00 0.00 2.43
92 93 5.283060 ACATTTCATTGAACACGTAGAGC 57.717 39.130 0.00 0.00 0.00 4.09
94 95 1.346365 TCATTGAACACGTAGAGCGC 58.654 50.000 0.00 0.00 46.11 5.92
95 96 1.067693 CATTGAACACGTAGAGCGCA 58.932 50.000 11.47 0.00 46.11 6.09
96 97 1.459209 CATTGAACACGTAGAGCGCAA 59.541 47.619 11.47 0.00 46.11 4.85
111 112 3.065019 GCGCAAGGTGTAAATATGGTG 57.935 47.619 0.30 0.00 38.28 4.17
112 113 2.223479 GCGCAAGGTGTAAATATGGTGG 60.223 50.000 0.30 0.00 38.28 4.61
113 114 3.275143 CGCAAGGTGTAAATATGGTGGA 58.725 45.455 0.00 0.00 0.00 4.02
115 116 4.270008 GCAAGGTGTAAATATGGTGGAGT 58.730 43.478 0.00 0.00 0.00 3.85
116 117 4.705023 GCAAGGTGTAAATATGGTGGAGTT 59.295 41.667 0.00 0.00 0.00 3.01
117 118 5.185056 GCAAGGTGTAAATATGGTGGAGTTT 59.815 40.000 0.00 0.00 0.00 2.66
118 119 6.620678 CAAGGTGTAAATATGGTGGAGTTTG 58.379 40.000 0.00 0.00 0.00 2.93
119 120 6.134535 AGGTGTAAATATGGTGGAGTTTGA 57.865 37.500 0.00 0.00 0.00 2.69
121 122 5.163794 GGTGTAAATATGGTGGAGTTTGACG 60.164 44.000 0.00 0.00 0.00 4.35
193 194 3.977244 GTGCTGTGGTTTGGGGCG 61.977 66.667 0.00 0.00 0.00 6.13
225 226 2.444696 CTTGGGTTGGGGATGGCA 59.555 61.111 0.00 0.00 0.00 4.92
232 233 0.035820 GTTGGGGATGGCAACGTAGA 60.036 55.000 0.00 0.00 42.51 2.59
273 274 2.625823 CGGCGGTTGTGCAAAGGAT 61.626 57.895 0.00 0.00 36.28 3.24
362 363 1.946475 GCCCTAGTGGTCAGTCCGAC 61.946 65.000 0.00 0.00 44.57 4.79
367 368 2.520020 TGGTCAGTCCGACGTGGT 60.520 61.111 0.00 0.00 46.42 4.16
369 370 1.239296 TGGTCAGTCCGACGTGGTAG 61.239 60.000 0.00 0.00 46.42 3.18
370 371 1.505353 GTCAGTCCGACGTGGTAGG 59.495 63.158 0.00 0.00 39.52 3.18
381 382 2.203728 TGGTAGGCACGTCCAGGT 60.204 61.111 6.78 0.00 37.29 4.00
382 383 2.264794 GGTAGGCACGTCCAGGTG 59.735 66.667 6.78 0.00 40.89 4.00
403 404 3.238497 CCGGGCGGTCCATATCCA 61.238 66.667 0.00 0.00 34.36 3.41
407 408 1.299976 GGCGGTCCATATCCATCCC 59.700 63.158 0.00 0.00 0.00 3.85
422 423 1.201429 ATCCCAGATATGGACCGGGC 61.201 60.000 8.28 0.21 36.79 6.13
432 433 0.616395 TGGACCGGGCATGAAGAGTA 60.616 55.000 11.00 0.00 0.00 2.59
433 434 0.179081 GGACCGGGCATGAAGAGTAC 60.179 60.000 11.00 0.00 0.00 2.73
434 435 0.824759 GACCGGGCATGAAGAGTACT 59.175 55.000 0.00 0.00 0.00 2.73
458 459 2.030007 CGGTCAGTCTAACGTTTGGGTA 60.030 50.000 5.91 0.00 0.00 3.69
469 472 3.948004 TTTGGGTATGGTGGGGCGC 62.948 63.158 0.00 0.00 0.00 6.53
472 475 4.875713 GGTATGGTGGGGCGCCTG 62.876 72.222 28.56 0.00 34.70 4.85
493 496 1.275010 GTTGGATGGCAATTTCCCGTT 59.725 47.619 3.27 0.00 0.00 4.44
501 504 1.438651 CAATTTCCCGTTCGAGCAGA 58.561 50.000 0.00 0.00 0.00 4.26
502 505 1.394917 CAATTTCCCGTTCGAGCAGAG 59.605 52.381 0.00 0.00 0.00 3.35
503 506 0.741221 ATTTCCCGTTCGAGCAGAGC 60.741 55.000 0.00 0.00 0.00 4.09
504 507 2.094757 TTTCCCGTTCGAGCAGAGCA 62.095 55.000 0.00 0.00 0.00 4.26
505 508 2.492449 TTCCCGTTCGAGCAGAGCAG 62.492 60.000 0.00 0.00 0.00 4.24
506 509 2.259818 CCGTTCGAGCAGAGCAGT 59.740 61.111 0.00 0.00 0.00 4.40
507 510 2.091112 CCGTTCGAGCAGAGCAGTG 61.091 63.158 0.00 0.00 0.00 3.66
508 511 1.081175 CGTTCGAGCAGAGCAGTGA 60.081 57.895 0.00 0.00 0.00 3.41
509 512 1.340657 CGTTCGAGCAGAGCAGTGAC 61.341 60.000 0.00 0.00 0.00 3.67
510 513 1.011451 GTTCGAGCAGAGCAGTGACC 61.011 60.000 0.00 0.00 0.00 4.02
531 534 1.377725 CCGAGCAGCCTGTCCAAAT 60.378 57.895 0.00 0.00 0.00 2.32
590 593 0.829182 ACGGGTATATGGGTCGGGTC 60.829 60.000 0.00 0.00 0.00 4.46
874 2889 0.979665 GGGCTGCTAGCATGGAGATA 59.020 55.000 19.72 0.00 44.75 1.98
877 2892 2.500910 GGCTGCTAGCATGGAGATAGAT 59.499 50.000 19.72 0.00 44.75 1.98
891 2906 3.147629 AGATAGATGTTACGCCTACGCT 58.852 45.455 0.00 0.00 45.53 5.07
1237 3289 2.487986 CCAGAGGAGCTCAAGGTTGTTT 60.488 50.000 17.19 0.00 32.06 2.83
1324 3376 0.813210 GCACCTGCAGCAGACTATCC 60.813 60.000 24.90 2.13 41.59 2.59
1345 3397 0.883833 CTTCGATGCAGCCAAAGGTT 59.116 50.000 0.00 0.00 0.00 3.50
1412 5010 6.214208 TCATCTCATGGGAAGAAGAAGAAGAA 59.786 38.462 0.00 0.00 0.00 2.52
1413 5011 6.047511 TCTCATGGGAAGAAGAAGAAGAAG 57.952 41.667 0.00 0.00 0.00 2.85
1414 5012 5.782331 TCTCATGGGAAGAAGAAGAAGAAGA 59.218 40.000 0.00 0.00 0.00 2.87
1415 5013 6.270927 TCTCATGGGAAGAAGAAGAAGAAGAA 59.729 38.462 0.00 0.00 0.00 2.52
1416 5014 6.471146 TCATGGGAAGAAGAAGAAGAAGAAG 58.529 40.000 0.00 0.00 0.00 2.85
1417 5015 6.270927 TCATGGGAAGAAGAAGAAGAAGAAGA 59.729 38.462 0.00 0.00 0.00 2.87
1418 5016 6.500589 TGGGAAGAAGAAGAAGAAGAAGAA 57.499 37.500 0.00 0.00 0.00 2.52
1419 5017 6.529220 TGGGAAGAAGAAGAAGAAGAAGAAG 58.471 40.000 0.00 0.00 0.00 2.85
1420 5018 6.327626 TGGGAAGAAGAAGAAGAAGAAGAAGA 59.672 38.462 0.00 0.00 0.00 2.87
1421 5019 7.147479 TGGGAAGAAGAAGAAGAAGAAGAAGAA 60.147 37.037 0.00 0.00 0.00 2.52
1936 5638 1.406069 GGCAGATGATGACGGTGACTT 60.406 52.381 0.00 0.00 0.00 3.01
2035 5742 3.065925 GCTTTCTGTTGCTTCACTGAAGT 59.934 43.478 18.16 0.00 41.27 3.01
2105 5816 6.072112 TGCTTTACTGAAAGGTTAGCTTTG 57.928 37.500 14.37 3.60 42.12 2.77
2204 5915 4.096682 GGTACCATAGATCATCGAGGCTAC 59.903 50.000 7.15 0.00 0.00 3.58
2206 5917 2.428890 CCATAGATCATCGAGGCTACCC 59.571 54.545 0.00 0.00 0.00 3.69
2248 5960 4.994852 TCTCGAATCGTTGGTTGAGAAAAT 59.005 37.500 1.52 0.00 30.14 1.82
2419 6143 0.759060 GAGGAGAAGGAGGAGGAGGC 60.759 65.000 0.00 0.00 0.00 4.70
2420 6144 1.228215 AGGAGAAGGAGGAGGAGGCT 61.228 60.000 0.00 0.00 0.00 4.58
2421 6145 0.759060 GGAGAAGGAGGAGGAGGCTC 60.759 65.000 5.78 5.78 0.00 4.70
2437 6182 3.931768 CTCCTGAAGAACAGCAGCT 57.068 52.632 0.00 0.00 44.52 4.24
2626 6906 3.507233 GCTGGATGGTGAAAAATGTGAGA 59.493 43.478 0.00 0.00 0.00 3.27
2687 6967 7.754924 AGTTTTACCTTGTGATTATTGCATTCG 59.245 33.333 0.00 0.00 0.00 3.34
2931 7222 7.742089 CGCAAAGTCTTTCTTACAAGTTATCAG 59.258 37.037 0.00 0.00 35.02 2.90
3439 7817 0.533755 GATCTTGGGATCCCGCACTG 60.534 60.000 26.03 13.18 41.70 3.66
3726 8205 5.065914 CCATCAATAGATTGGGTTCGATGT 58.934 41.667 2.52 0.00 38.30 3.06
3905 8566 0.826715 GCTCTGGCAGAGGTGTCATA 59.173 55.000 37.73 6.61 42.54 2.15
4324 8993 2.338809 CTATCTGGGGAGGTAATGCCA 58.661 52.381 0.00 0.00 42.44 4.92
4843 9737 0.454600 TGACATCGAACGGGCTCTAC 59.545 55.000 0.00 0.00 0.00 2.59
5059 9962 8.002459 AGGGACCAAAAACATACTTTTCTCTTA 58.998 33.333 0.00 0.00 0.00 2.10
5208 10113 9.314321 CTTTCTGGTCGTTTGATAATGTAGTAT 57.686 33.333 0.00 0.00 0.00 2.12
5274 10179 3.259751 GCGATTGGACGTACCGCC 61.260 66.667 8.51 0.00 42.61 6.13
5277 10182 1.514087 GATTGGACGTACCGCCTGA 59.486 57.895 0.00 0.00 42.61 3.86
5278 10183 0.527817 GATTGGACGTACCGCCTGAG 60.528 60.000 0.00 0.00 42.61 3.35
5288 10193 2.341101 CCGCCTGAGTAGTCCGTGT 61.341 63.158 0.00 0.00 0.00 4.49
5358 10263 3.499918 GGCAGTTGAATCATATTCGGAGG 59.500 47.826 0.00 0.00 0.00 4.30
5437 10359 2.072298 GCTTCGTTTCATCAGCTGAGT 58.928 47.619 22.96 7.66 34.68 3.41
5677 10641 2.645838 ACAACCACATCAGCAGAAGT 57.354 45.000 0.00 0.00 0.00 3.01
5727 11409 3.252400 ACATTGCGTGCACCATTATTTG 58.748 40.909 12.15 2.96 0.00 2.32
5741 11424 7.546358 CACCATTATTTGCCTAATGAACTTGA 58.454 34.615 10.64 0.00 40.15 3.02
5789 11474 4.860907 GCTGCAATGGCTATATTTGCATAC 59.139 41.667 9.60 3.05 41.91 2.39
5871 11574 2.961526 AATGGTACTACGTCAGGCTG 57.038 50.000 8.58 8.58 0.00 4.85
5902 11606 7.148656 CGGCCTGAACCAATAAATTAAAAACAG 60.149 37.037 0.00 0.00 0.00 3.16
5910 11614 9.744468 ACCAATAAATTAAAAACAGACTGTGAC 57.256 29.630 9.33 0.00 0.00 3.67
5944 11649 6.471233 TGAGACACAAGAGAGAAAAAGAGA 57.529 37.500 0.00 0.00 0.00 3.10
6076 11835 2.167693 ACATGGCATGCAGGAATCTTTG 59.832 45.455 26.70 0.56 0.00 2.77
6191 11952 4.227300 ACATGAAGGTAGGCCTGATAAACA 59.773 41.667 17.99 9.10 46.33 2.83
6388 12330 3.146783 CGATTTACCAACCTCGCCA 57.853 52.632 0.00 0.00 0.00 5.69
6408 12350 3.311871 CCAATTCCTCAAGCAGAAGATCG 59.688 47.826 0.00 0.00 0.00 3.69
6987 13470 2.891580 GGCCCTTCTCTCATACATCGTA 59.108 50.000 0.00 0.00 0.00 3.43
7702 15068 2.684881 CACACTGATAAATGTCCAGCCC 59.315 50.000 0.00 0.00 0.00 5.19
7824 15197 5.631512 GTGCTTTTGTGTGTGTAAAAGAACA 59.368 36.000 13.11 2.27 45.47 3.18
7950 15333 6.073765 CGAAAATAGCGATAAGTTATGTGCCT 60.074 38.462 0.00 0.00 0.00 4.75
8203 15590 0.833287 GTGCCCCTCTCTGCTAATGA 59.167 55.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.977427 TGGATTCGTCGTGGAATGATAG 58.023 45.455 8.11 0.00 36.79 2.08
4 5 2.935849 CAATGGATTCGTCGTGGAATGA 59.064 45.455 8.11 0.00 36.79 2.57
9 10 0.645355 CGTCAATGGATTCGTCGTGG 59.355 55.000 0.00 0.00 0.00 4.94
10 11 1.320555 GTCGTCAATGGATTCGTCGTG 59.679 52.381 0.00 0.00 0.00 4.35
12 13 0.921347 GGTCGTCAATGGATTCGTCG 59.079 55.000 0.00 0.00 0.00 5.12
13 14 2.295253 AGGTCGTCAATGGATTCGTC 57.705 50.000 0.00 0.00 0.00 4.20
14 15 3.021695 TCTAGGTCGTCAATGGATTCGT 58.978 45.455 0.00 0.00 0.00 3.85
15 16 3.710326 TCTAGGTCGTCAATGGATTCG 57.290 47.619 0.00 0.00 0.00 3.34
16 17 5.012328 ACTTCTAGGTCGTCAATGGATTC 57.988 43.478 0.00 0.00 0.00 2.52
17 18 6.540438 TTACTTCTAGGTCGTCAATGGATT 57.460 37.500 0.00 0.00 0.00 3.01
18 19 6.323996 TCATTACTTCTAGGTCGTCAATGGAT 59.676 38.462 0.00 0.00 0.00 3.41
19 20 5.655090 TCATTACTTCTAGGTCGTCAATGGA 59.345 40.000 0.00 0.00 0.00 3.41
20 21 5.749109 GTCATTACTTCTAGGTCGTCAATGG 59.251 44.000 0.00 0.00 0.00 3.16
21 22 5.749109 GGTCATTACTTCTAGGTCGTCAATG 59.251 44.000 0.00 0.00 0.00 2.82
23 24 4.142534 CGGTCATTACTTCTAGGTCGTCAA 60.143 45.833 0.00 0.00 0.00 3.18
25 26 3.624861 TCGGTCATTACTTCTAGGTCGTC 59.375 47.826 0.00 0.00 0.00 4.20
26 27 3.614092 TCGGTCATTACTTCTAGGTCGT 58.386 45.455 0.00 0.00 0.00 4.34
27 28 4.627611 TTCGGTCATTACTTCTAGGTCG 57.372 45.455 0.00 0.00 0.00 4.79
28 29 6.205101 TCTTTCGGTCATTACTTCTAGGTC 57.795 41.667 0.00 0.00 0.00 3.85
29 30 6.600882 TTCTTTCGGTCATTACTTCTAGGT 57.399 37.500 0.00 0.00 0.00 3.08
30 31 9.595823 TTTATTCTTTCGGTCATTACTTCTAGG 57.404 33.333 0.00 0.00 0.00 3.02
40 41 8.801882 TCTGGTATTTTTATTCTTTCGGTCAT 57.198 30.769 0.00 0.00 0.00 3.06
41 42 8.801882 ATCTGGTATTTTTATTCTTTCGGTCA 57.198 30.769 0.00 0.00 0.00 4.02
43 44 9.338622 CCTATCTGGTATTTTTATTCTTTCGGT 57.661 33.333 0.00 0.00 0.00 4.69
44 45 9.555727 TCCTATCTGGTATTTTTATTCTTTCGG 57.444 33.333 0.00 0.00 37.07 4.30
56 57 9.699410 TTCAATGAAATGTCCTATCTGGTATTT 57.301 29.630 0.00 0.00 36.85 1.40
58 59 8.274322 TGTTCAATGAAATGTCCTATCTGGTAT 58.726 33.333 0.00 0.00 37.07 2.73
59 60 7.552687 GTGTTCAATGAAATGTCCTATCTGGTA 59.447 37.037 0.00 0.00 37.07 3.25
60 61 6.375455 GTGTTCAATGAAATGTCCTATCTGGT 59.625 38.462 0.00 0.00 37.07 4.00
62 63 6.092670 ACGTGTTCAATGAAATGTCCTATCTG 59.907 38.462 0.00 0.00 0.00 2.90
63 64 6.173339 ACGTGTTCAATGAAATGTCCTATCT 58.827 36.000 0.00 0.00 0.00 1.98
64 65 6.422776 ACGTGTTCAATGAAATGTCCTATC 57.577 37.500 0.00 0.00 0.00 2.08
65 66 7.327975 TCTACGTGTTCAATGAAATGTCCTAT 58.672 34.615 0.00 0.00 0.00 2.57
66 67 6.693466 TCTACGTGTTCAATGAAATGTCCTA 58.307 36.000 0.00 0.00 0.00 2.94
67 68 5.547465 TCTACGTGTTCAATGAAATGTCCT 58.453 37.500 0.00 0.00 0.00 3.85
68 69 5.671329 GCTCTACGTGTTCAATGAAATGTCC 60.671 44.000 0.00 0.00 0.00 4.02
69 70 5.316770 GCTCTACGTGTTCAATGAAATGTC 58.683 41.667 0.00 0.00 0.00 3.06
70 71 4.143115 CGCTCTACGTGTTCAATGAAATGT 60.143 41.667 0.00 3.21 36.87 2.71
72 73 3.181520 GCGCTCTACGTGTTCAATGAAAT 60.182 43.478 0.00 0.00 46.11 2.17
73 74 2.156891 GCGCTCTACGTGTTCAATGAAA 59.843 45.455 0.00 0.00 46.11 2.69
75 76 1.336424 TGCGCTCTACGTGTTCAATGA 60.336 47.619 9.73 0.00 46.11 2.57
76 77 1.067693 TGCGCTCTACGTGTTCAATG 58.932 50.000 9.73 0.00 46.11 2.82
79 80 0.666274 CCTTGCGCTCTACGTGTTCA 60.666 55.000 9.73 0.00 46.11 3.18
80 81 0.666577 ACCTTGCGCTCTACGTGTTC 60.667 55.000 9.73 0.00 46.11 3.18
82 83 1.372997 CACCTTGCGCTCTACGTGT 60.373 57.895 9.73 0.00 46.11 4.49
83 84 0.109458 TACACCTTGCGCTCTACGTG 60.109 55.000 9.73 10.29 46.11 4.49
86 87 4.211374 CCATATTTACACCTTGCGCTCTAC 59.789 45.833 9.73 0.00 0.00 2.59
88 89 3.206150 CCATATTTACACCTTGCGCTCT 58.794 45.455 9.73 0.00 0.00 4.09
89 90 2.943033 ACCATATTTACACCTTGCGCTC 59.057 45.455 9.73 0.00 0.00 5.03
90 91 2.682856 CACCATATTTACACCTTGCGCT 59.317 45.455 9.73 0.00 0.00 5.92
91 92 2.223479 CCACCATATTTACACCTTGCGC 60.223 50.000 0.00 0.00 0.00 6.09
92 93 3.275143 TCCACCATATTTACACCTTGCG 58.725 45.455 0.00 0.00 0.00 4.85
94 95 6.432783 TCAAACTCCACCATATTTACACCTTG 59.567 38.462 0.00 0.00 0.00 3.61
95 96 6.433093 GTCAAACTCCACCATATTTACACCTT 59.567 38.462 0.00 0.00 0.00 3.50
96 97 5.944007 GTCAAACTCCACCATATTTACACCT 59.056 40.000 0.00 0.00 0.00 4.00
99 100 5.553123 ACGTCAAACTCCACCATATTTACA 58.447 37.500 0.00 0.00 0.00 2.41
100 101 6.036408 GGTACGTCAAACTCCACCATATTTAC 59.964 42.308 0.00 0.00 0.00 2.01
101 102 6.108015 GGTACGTCAAACTCCACCATATTTA 58.892 40.000 0.00 0.00 0.00 1.40
102 103 4.939439 GGTACGTCAAACTCCACCATATTT 59.061 41.667 0.00 0.00 0.00 1.40
104 105 3.516300 TGGTACGTCAAACTCCACCATAT 59.484 43.478 0.00 0.00 31.29 1.78
105 106 2.898612 TGGTACGTCAAACTCCACCATA 59.101 45.455 0.00 0.00 31.29 2.74
106 107 1.695242 TGGTACGTCAAACTCCACCAT 59.305 47.619 0.00 0.00 31.29 3.55
107 108 1.069513 CTGGTACGTCAAACTCCACCA 59.930 52.381 0.00 0.00 34.95 4.17
108 109 1.607251 CCTGGTACGTCAAACTCCACC 60.607 57.143 0.00 0.00 0.00 4.61
109 110 1.607251 CCCTGGTACGTCAAACTCCAC 60.607 57.143 0.00 0.00 0.00 4.02
110 111 0.682852 CCCTGGTACGTCAAACTCCA 59.317 55.000 0.00 0.00 0.00 3.86
111 112 0.672711 GCCCTGGTACGTCAAACTCC 60.673 60.000 0.00 0.00 0.00 3.85
112 113 1.012486 CGCCCTGGTACGTCAAACTC 61.012 60.000 0.00 0.00 0.00 3.01
113 114 1.005394 CGCCCTGGTACGTCAAACT 60.005 57.895 0.00 0.00 0.00 2.66
115 116 2.344500 CCGCCCTGGTACGTCAAA 59.656 61.111 0.00 0.00 0.00 2.69
116 117 4.382320 GCCGCCCTGGTACGTCAA 62.382 66.667 0.00 0.00 41.21 3.18
174 175 3.294493 CCCCAAACCACAGCACCG 61.294 66.667 0.00 0.00 0.00 4.94
179 180 1.312371 CCATACGCCCCAAACCACAG 61.312 60.000 0.00 0.00 0.00 3.66
185 186 1.303724 CACCACCATACGCCCCAAA 60.304 57.895 0.00 0.00 0.00 3.28
193 194 1.463674 CCAAGGCTTCACCACCATAC 58.536 55.000 0.00 0.00 43.14 2.39
255 256 2.625823 ATCCTTTGCACAACCGCCG 61.626 57.895 0.00 0.00 0.00 6.46
261 262 0.392336 GTTGGCCATCCTTTGCACAA 59.608 50.000 6.09 0.00 0.00 3.33
267 268 2.376518 TCTTCTCTGTTGGCCATCCTTT 59.623 45.455 6.09 0.00 0.00 3.11
273 274 0.979665 CTCCTCTTCTCTGTTGGCCA 59.020 55.000 0.00 0.00 0.00 5.36
309 310 3.314331 ATATGCGCCCCTCCCTCG 61.314 66.667 4.18 0.00 0.00 4.63
310 311 2.348998 CATATGCGCCCCTCCCTC 59.651 66.667 4.18 0.00 0.00 4.30
385 386 4.699522 GGATATGGACCGCCCGGC 62.700 72.222 6.63 0.00 39.32 6.13
387 388 1.079127 GATGGATATGGACCGCCCG 60.079 63.158 0.00 0.00 37.93 6.13
407 408 0.686789 TCATGCCCGGTCCATATCTG 59.313 55.000 0.00 0.00 0.00 2.90
422 423 3.763902 CTGACCGACAGTACTCTTCATG 58.236 50.000 0.00 0.00 41.30 3.07
434 435 2.544277 CCAAACGTTAGACTGACCGACA 60.544 50.000 0.00 0.00 0.00 4.35
449 450 2.049767 GCCCCACCATACCCAAACG 61.050 63.158 0.00 0.00 0.00 3.60
469 472 1.207811 GGAAATTGCCATCCAACCAGG 59.792 52.381 0.00 0.00 35.99 4.45
471 474 1.274712 GGGAAATTGCCATCCAACCA 58.725 50.000 4.40 0.00 37.46 3.67
472 475 0.175531 CGGGAAATTGCCATCCAACC 59.824 55.000 4.40 0.00 37.46 3.77
478 481 1.094785 CTCGAACGGGAAATTGCCAT 58.905 50.000 4.40 0.00 0.00 4.40
482 485 1.394917 CTCTGCTCGAACGGGAAATTG 59.605 52.381 0.00 0.00 0.00 2.32
493 496 2.965783 GGTCACTGCTCTGCTCGA 59.034 61.111 0.00 0.00 0.00 4.04
501 504 4.057428 GCTCGGTCGGTCACTGCT 62.057 66.667 0.00 0.00 0.00 4.24
502 505 4.357947 TGCTCGGTCGGTCACTGC 62.358 66.667 0.00 0.00 0.00 4.40
503 506 2.126307 CTGCTCGGTCGGTCACTG 60.126 66.667 0.00 0.00 0.00 3.66
504 507 4.057428 GCTGCTCGGTCGGTCACT 62.057 66.667 0.00 0.00 0.00 3.41
507 510 4.803426 CAGGCTGCTCGGTCGGTC 62.803 72.222 0.00 0.00 0.00 4.79
509 512 4.803426 GACAGGCTGCTCGGTCGG 62.803 72.222 15.89 0.00 0.00 4.79
510 513 4.803426 GGACAGGCTGCTCGGTCG 62.803 72.222 15.89 0.00 33.66 4.79
531 534 1.458486 CCTGTACCAGCCCCAAACA 59.542 57.895 0.00 0.00 0.00 2.83
874 2889 2.295885 AGTAGCGTAGGCGTAACATCT 58.704 47.619 1.05 0.00 46.35 2.90
877 2892 2.632377 ACTAGTAGCGTAGGCGTAACA 58.368 47.619 0.00 0.00 46.35 2.41
891 2906 5.392125 GGAGCTGGGGTTCTTATACTAGTA 58.608 45.833 4.77 4.77 0.00 1.82
1237 3289 1.000486 CCTTGTCCTCCTCCTCGGA 60.000 63.158 0.00 0.00 40.30 4.55
1324 3376 0.731417 CCTTTGGCTGCATCGAAGAG 59.269 55.000 15.06 4.15 43.63 2.85
1345 3397 5.046591 CAGATGGGTAAGAAACAGAGGTGTA 60.047 44.000 0.00 0.00 35.08 2.90
1412 5010 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1413 5011 9.541143 TTCTTCTTCTTCTTCTTCTTCTTCTTC 57.459 33.333 0.00 0.00 0.00 2.87
1414 5012 9.546428 CTTCTTCTTCTTCTTCTTCTTCTTCTT 57.454 33.333 0.00 0.00 0.00 2.52
1415 5013 8.923270 TCTTCTTCTTCTTCTTCTTCTTCTTCT 58.077 33.333 0.00 0.00 0.00 2.85
1416 5014 9.710900 ATCTTCTTCTTCTTCTTCTTCTTCTTC 57.289 33.333 0.00 0.00 0.00 2.87
1419 5017 9.586435 CCTATCTTCTTCTTCTTCTTCTTCTTC 57.414 37.037 0.00 0.00 0.00 2.87
1420 5018 9.320295 TCCTATCTTCTTCTTCTTCTTCTTCTT 57.680 33.333 0.00 0.00 0.00 2.52
1421 5019 8.893563 TCCTATCTTCTTCTTCTTCTTCTTCT 57.106 34.615 0.00 0.00 0.00 2.85
1495 5129 1.403323 GCCTGAAATAACTGCAGCCTC 59.597 52.381 15.27 3.94 0.00 4.70
1496 5130 1.005215 AGCCTGAAATAACTGCAGCCT 59.995 47.619 15.27 3.55 0.00 4.58
1936 5638 2.367202 GGACATGGGGAGCTTCCGA 61.367 63.158 4.51 0.00 37.43 4.55
2005 5712 5.979517 GTGAAGCAACAGAAAGCTAATTGTT 59.020 36.000 4.38 4.38 40.90 2.83
2105 5816 5.066505 CCATAACCCTTCAGTGAAGCAATAC 59.933 44.000 24.85 0.00 38.24 1.89
2204 5915 1.750399 CTGCTCGATTTGGTGGGGG 60.750 63.158 0.00 0.00 0.00 5.40
2206 5917 1.672881 GATTCTGCTCGATTTGGTGGG 59.327 52.381 0.00 0.00 0.00 4.61
2248 5960 2.415776 GGTGAACCGTAAAACGATCCA 58.584 47.619 0.15 0.00 46.05 3.41
2366 6090 4.021981 GGAGGCTTGAGCAAAGTAACAAAT 60.022 41.667 5.24 0.00 44.36 2.32
2373 6097 0.767375 TGAGGAGGCTTGAGCAAAGT 59.233 50.000 5.24 0.00 44.36 2.66
2420 6144 0.604780 GCAGCTGCTGTTCTTCAGGA 60.605 55.000 31.33 0.00 43.78 3.86
2421 6145 1.874562 GCAGCTGCTGTTCTTCAGG 59.125 57.895 31.33 2.55 43.78 3.86
2430 6175 4.400109 CTTGTGCCGCAGCTGCTG 62.400 66.667 34.22 29.22 40.80 4.41
2437 6182 1.550524 AGAAGATACTCTTGTGCCGCA 59.449 47.619 0.00 0.00 36.73 5.69
2575 6833 5.704515 GCTCTTGCACAACAGATATGGATAT 59.295 40.000 0.00 0.00 39.41 1.63
2576 6834 5.059161 GCTCTTGCACAACAGATATGGATA 58.941 41.667 0.00 0.00 39.41 2.59
2626 6906 5.993441 AGACAGCAGCAGCAAATTAAATTTT 59.007 32.000 3.17 0.00 45.49 1.82
2732 7012 8.844441 TTTTGTCCTTTTTAGTATGTGTTTCG 57.156 30.769 0.00 0.00 0.00 3.46
3546 7927 3.124921 GAACCCACCGTCATGCCG 61.125 66.667 0.00 0.00 0.00 5.69
3726 8205 4.314440 GTGTCACCTGCCGAGCCA 62.314 66.667 0.00 0.00 0.00 4.75
4832 9726 5.766174 TGACAAAATTTTAGTAGAGCCCGTT 59.234 36.000 2.44 0.00 0.00 4.44
5082 9985 2.956333 CCACAGTCCAATGCATCATGAT 59.044 45.455 1.18 1.18 0.00 2.45
5085 9988 2.519771 ACCACAGTCCAATGCATCAT 57.480 45.000 0.00 0.00 0.00 2.45
5123 10028 2.769095 GAGAGAGTTGGTGGCTAATCCT 59.231 50.000 0.00 0.00 35.26 3.24
5124 10029 2.769095 AGAGAGAGTTGGTGGCTAATCC 59.231 50.000 0.00 0.00 0.00 3.01
5208 10113 7.214381 TCAGTAAAGTAACAGAAAGCAAGCTA 58.786 34.615 0.00 0.00 0.00 3.32
5224 10129 6.702329 CACTTCCATAGTCCTTCAGTAAAGT 58.298 40.000 0.00 0.00 33.85 2.66
5274 10179 3.254060 CATTTCCACACGGACTACTCAG 58.746 50.000 0.00 0.00 42.67 3.35
5277 10182 1.338769 GCCATTTCCACACGGACTACT 60.339 52.381 0.00 0.00 42.67 2.57
5278 10183 1.084289 GCCATTTCCACACGGACTAC 58.916 55.000 0.00 0.00 42.67 2.73
5288 10193 1.557371 TGATCTACGGTGCCATTTCCA 59.443 47.619 0.00 0.00 0.00 3.53
5295 10200 0.039074 CCTCGATGATCTACGGTGCC 60.039 60.000 10.90 0.00 0.00 5.01
5297 10202 0.955178 AGCCTCGATGATCTACGGTG 59.045 55.000 10.90 5.39 0.00 4.94
5358 10263 0.536006 ACACCTTCAGCAGCTTGGTC 60.536 55.000 8.20 0.00 0.00 4.02
5421 10343 9.638300 GTAATAAATTACTCAGCTGATGAAACG 57.362 33.333 18.63 6.87 39.53 3.60
5593 10533 3.390135 GTTGTCGTGTTCTGATCTTCCA 58.610 45.455 0.00 0.00 0.00 3.53
5677 10641 3.570125 AGAAGACGATGAGTGAGTTGTCA 59.430 43.478 0.00 0.00 32.31 3.58
5727 11409 6.545298 AGGAATCATCTTCAAGTTCATTAGGC 59.455 38.462 0.00 0.00 0.00 3.93
5741 11424 9.440773 GCTTATTTTTGGAAAAGGAATCATCTT 57.559 29.630 0.00 0.00 0.00 2.40
5871 11574 2.862674 TATTGGTTCAGGCCGGCGTC 62.863 60.000 20.79 6.63 0.00 5.19
5902 11606 6.094061 GTCTCATACCTTTGTAGTCACAGTC 58.906 44.000 0.00 0.00 35.67 3.51
5910 11614 6.925211 TCTCTTGTGTCTCATACCTTTGTAG 58.075 40.000 0.00 0.00 0.00 2.74
6076 11835 5.294306 TCATCCATTCAATTACTTCTGCGTC 59.706 40.000 0.00 0.00 0.00 5.19
6191 11952 3.069300 CAGTAGTCCATGCATACTGCTCT 59.931 47.826 15.00 7.33 45.31 4.09
6388 12330 4.187694 GTCGATCTTCTGCTTGAGGAATT 58.812 43.478 0.00 0.00 34.40 2.17
6408 12350 4.425520 GACTGACACTGCTACATAAGGTC 58.574 47.826 0.00 0.00 0.00 3.85
6987 13470 0.988832 TTGGTGGAAGTAGCCCGAAT 59.011 50.000 0.00 0.00 0.00 3.34
7702 15068 4.663389 GCTCAAGTTTTACGCAGAACTACG 60.663 45.833 0.00 0.00 35.17 3.51
8203 15590 3.576078 TCCTTTGTGACCATGTGTTCT 57.424 42.857 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.