Multiple sequence alignment - TraesCS2B01G028100

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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 TraesCS2B01G028100 chr2B 100.000 6194 0 0 1 6194 13180954 13187147 0.000000e+00 11439.0
1 TraesCS2B01G028100 chr2B 93.592 1545 72 18 4672 6194 485691267 485692806 0.000000e+00 2279.0
2 TraesCS2B01G028100 chr2B 93.126 611 21 6 4 597 13315021 13315627 0.000000e+00 876.0
3 TraesCS2B01G028100 chr2B 85.517 290 34 6 1169 1454 13437627 13437342 4.690000e-76 296.0
4 TraesCS2B01G028100 chr1D 94.472 1628 81 6 3050 4671 235547575 235545951 0.000000e+00 2499.0
5 TraesCS2B01G028100 chr1D 93.871 1550 63 11 4672 6194 25464747 25466291 0.000000e+00 2307.0
6 TraesCS2B01G028100 chr1D 90.909 913 63 14 1029 1933 235549509 235548609 0.000000e+00 1208.0
7 TraesCS2B01G028100 chr5D 94.161 1627 81 8 3053 4673 462907869 462909487 0.000000e+00 2466.0
8 TraesCS2B01G028100 chr5D 93.839 1542 66 17 4672 6194 114516767 114518298 0.000000e+00 2294.0
9 TraesCS2B01G028100 chr5D 93.672 1280 56 8 4672 5932 275162756 275161483 0.000000e+00 1892.0
10 TraesCS2B01G028100 chr5D 92.230 1287 57 10 4672 5937 482331711 482330447 0.000000e+00 1783.0
11 TraesCS2B01G028100 chr5D 92.200 1282 55 13 4672 5932 520497084 520495827 0.000000e+00 1772.0
12 TraesCS2B01G028100 chr5D 91.757 1286 64 8 4672 5937 336310518 336309255 0.000000e+00 1749.0
13 TraesCS2B01G028100 chr5D 93.737 990 39 6 4672 5643 473071624 473072608 0.000000e+00 1463.0
14 TraesCS2B01G028100 chr5D 94.279 437 22 2 596 1029 84221157 84220721 0.000000e+00 665.0
15 TraesCS2B01G028100 chr5D 92.906 437 26 2 598 1029 473071190 473071626 1.130000e-176 630.0
16 TraesCS2B01G028100 chr5D 92.890 436 28 2 597 1029 517036312 517036747 1.130000e-176 630.0
17 TraesCS2B01G028100 chr7A 92.905 1635 93 15 3050 4671 439031072 439032696 0.000000e+00 2355.0
18 TraesCS2B01G028100 chr7A 91.841 1336 79 13 3050 4362 639884909 639883581 0.000000e+00 1836.0
19 TraesCS2B01G028100 chr7A 95.263 190 7 1 2436 2623 639885130 639884941 3.630000e-77 300.0
20 TraesCS2B01G028100 chr7A 95.858 169 5 1 2436 2602 439030649 439030817 7.910000e-69 272.0
21 TraesCS2B01G028100 chr3D 94.049 1546 64 15 4672 6194 546486426 546487966 0.000000e+00 2320.0
22 TraesCS2B01G028100 chr3D 94.094 1270 61 8 3050 4310 143483348 143482084 0.000000e+00 1917.0
23 TraesCS2B01G028100 chr3D 95.481 509 19 3 2428 2934 143484604 143484098 0.000000e+00 809.0
24 TraesCS2B01G028100 chr3D 94.050 437 23 2 596 1029 527509675 527510111 0.000000e+00 660.0
25 TraesCS2B01G028100 chr3D 94.023 435 24 2 597 1029 546485994 546486428 0.000000e+00 658.0
26 TraesCS2B01G028100 chr3D 92.517 294 19 2 2644 2934 43023417 43023124 9.600000e-113 418.0
27 TraesCS2B01G028100 chr3D 89.888 178 8 5 2431 2599 43023605 43023429 2.910000e-53 220.0
28 TraesCS2B01G028100 chr3D 98.374 123 2 0 2929 3051 143483734 143483612 3.760000e-52 217.0
29 TraesCS2B01G028100 chr3D 92.800 125 8 1 2929 3052 43022761 43022637 4.930000e-41 180.0
30 TraesCS2B01G028100 chr1B 92.617 1639 82 19 3050 4671 253825459 253823843 0.000000e+00 2320.0
31 TraesCS2B01G028100 chr1B 92.000 300 24 0 1030 1329 253827599 253827300 7.420000e-114 422.0
32 TraesCS2B01G028100 chr1B 88.930 271 16 4 1665 1922 253826773 253826504 7.750000e-84 322.0
33 TraesCS2B01G028100 chr7D 93.798 1548 64 17 4672 6194 90563175 90561635 0.000000e+00 2298.0
34 TraesCS2B01G028100 chr7D 93.484 1550 66 19 4672 6194 605600285 605601826 0.000000e+00 2270.0
35 TraesCS2B01G028100 chr7D 94.630 1434 68 7 3241 4672 635929327 635927901 0.000000e+00 2213.0
36 TraesCS2B01G028100 chr7D 93.531 1283 58 8 4672 5932 94497057 94495778 0.000000e+00 1886.0
37 TraesCS2B01G028100 chr7D 93.289 447 27 3 585 1029 246983063 246982618 0.000000e+00 656.0
38 TraesCS2B01G028100 chr7D 92.906 437 26 2 594 1029 63995386 63995818 1.130000e-176 630.0
39 TraesCS2B01G028100 chr7D 88.926 298 24 5 1128 1425 635931676 635931388 5.900000e-95 359.0
40 TraesCS2B01G028100 chr7B 93.722 1545 64 15 4672 6194 58797818 58799351 0.000000e+00 2285.0
41 TraesCS2B01G028100 chr7B 92.787 1012 50 11 3670 4671 634824607 634825605 0.000000e+00 1443.0
42 TraesCS2B01G028100 chr7B 83.448 290 40 6 1169 1454 611350482 611350197 4.760000e-66 263.0
43 TraesCS2B01G028100 chr7B 92.405 158 12 0 1030 1187 17503469 17503312 6.250000e-55 226.0
44 TraesCS2B01G028100 chr7B 97.500 120 3 0 2929 3048 634824171 634824290 8.140000e-49 206.0
45 TraesCS2B01G028100 chr2A 94.171 1441 76 4 3238 4673 441110111 441111548 0.000000e+00 2189.0
46 TraesCS2B01G028100 chr2A 90.268 709 65 4 3966 4671 23539852 23539145 0.000000e+00 924.0
47 TraesCS2B01G028100 chr2A 92.662 586 28 8 1 573 9122068 9122651 0.000000e+00 830.0
48 TraesCS2B01G028100 chr2A 92.513 187 12 2 1239 1425 441107857 441108041 3.680000e-67 267.0
49 TraesCS2B01G028100 chr6D 92.636 1548 56 15 4672 6194 28980847 28979333 0.000000e+00 2174.0
50 TraesCS2B01G028100 chr6D 92.111 938 58 8 3616 4552 298130733 298129811 0.000000e+00 1308.0
51 TraesCS2B01G028100 chr6D 94.965 576 23 3 3050 3620 298139893 298139319 0.000000e+00 898.0
52 TraesCS2B01G028100 chr6D 95.874 509 17 3 2428 2934 298141148 298140642 0.000000e+00 821.0
53 TraesCS2B01G028100 chr6D 92.644 435 31 1 596 1029 5447442 5447008 5.270000e-175 625.0
54 TraesCS2B01G028100 chr6D 81.789 615 53 26 1850 2429 30098985 30098395 1.570000e-125 460.0
55 TraesCS2B01G028100 chr6D 83.005 406 41 13 2024 2413 31470833 31471226 5.950000e-90 342.0
56 TraesCS2B01G028100 chr6D 95.122 123 6 0 2929 3051 298140278 298140156 1.760000e-45 195.0
57 TraesCS2B01G028100 chr5B 93.398 1439 82 8 3238 4671 89745418 89746848 0.000000e+00 2119.0
58 TraesCS2B01G028100 chr5B 90.955 398 32 4 1030 1425 89692132 89692527 3.290000e-147 532.0
59 TraesCS2B01G028100 chr5B 94.340 53 3 0 191 243 485912336 485912388 1.430000e-11 82.4
60 TraesCS2B01G028100 chr4B 91.925 1548 64 22 4672 6194 251639450 251640961 0.000000e+00 2109.0
61 TraesCS2B01G028100 chr4A 93.036 1436 86 5 3241 4670 281593802 281592375 0.000000e+00 2085.0
62 TraesCS2B01G028100 chr4A 90.123 405 32 5 1025 1425 281594916 281594516 2.560000e-143 520.0
63 TraesCS2B01G028100 chr4A 81.897 232 26 11 1173 1392 730354191 730354418 1.370000e-41 182.0
64 TraesCS2B01G028100 chr3B 93.018 1246 55 18 4972 6194 707161582 707162818 0.000000e+00 1790.0
65 TraesCS2B01G028100 chr3B 93.542 511 27 4 2428 2934 66955551 66955043 0.000000e+00 756.0
66 TraesCS2B01G028100 chr3B 92.063 126 8 2 2929 3052 66954679 66954554 6.380000e-40 176.0
67 TraesCS2B01G028100 chr6B 92.035 1268 78 8 4672 5937 347768202 347766956 0.000000e+00 1760.0
68 TraesCS2B01G028100 chr6B 86.696 451 36 7 1980 2429 79876338 79876765 4.340000e-131 479.0
69 TraesCS2B01G028100 chr6B 83.900 441 35 15 2004 2429 57416260 57416679 7.530000e-104 388.0
70 TraesCS2B01G028100 chr6B 92.453 159 10 2 1030 1187 339800634 339800791 6.250000e-55 226.0
71 TraesCS2B01G028100 chr6B 87.019 208 12 5 2226 2429 50410277 50410081 2.910000e-53 220.0
72 TraesCS2B01G028100 chr6B 92.517 147 10 1 1777 1922 1495471 1495325 6.290000e-50 209.0
73 TraesCS2B01G028100 chr2D 91.972 1283 57 17 4672 5932 331197633 331198891 0.000000e+00 1757.0
74 TraesCS2B01G028100 chr2D 92.857 434 28 2 598 1028 645082453 645082020 1.470000e-175 627.0
75 TraesCS2B01G028100 chr2D 83.759 431 34 11 2003 2413 48563126 48563540 5.860000e-100 375.0
76 TraesCS2B01G028100 chr3A 90.944 519 33 9 2428 2934 55047598 55047082 0.000000e+00 686.0
77 TraesCS2B01G028100 chr3A 92.353 170 12 1 1018 1187 221514473 221514641 2.230000e-59 241.0
78 TraesCS2B01G028100 chr3A 92.742 124 8 1 2929 3051 55046717 55046594 1.770000e-40 178.0
79 TraesCS2B01G028100 chrUn 87.805 451 39 9 1980 2429 27472008 27472443 1.190000e-141 514.0
80 TraesCS2B01G028100 chrUn 85.185 297 35 8 1980 2270 68355994 68356287 4.690000e-76 296.0
81 TraesCS2B01G028100 chrUn 80.353 397 35 21 2065 2429 137914298 137913913 1.710000e-65 261.0
82 TraesCS2B01G028100 chrUn 81.648 267 30 10 1588 1836 312454888 312454623 2.930000e-48 204.0
83 TraesCS2B01G028100 chrUn 81.273 267 31 11 1588 1836 268239023 268239288 1.360000e-46 198.0
84 TraesCS2B01G028100 chr6A 85.841 452 29 13 1980 2429 46700395 46699977 1.220000e-121 448.0
85 TraesCS2B01G028100 chr6A 84.247 438 41 12 2004 2429 32740317 32740738 9.670000e-108 401.0
86 TraesCS2B01G028100 chr6A 78.557 485 46 26 1976 2429 45353289 45353746 3.680000e-67 267.0
87 TraesCS2B01G028100 chr6A 92.208 154 11 1 1030 1182 353573245 353573398 3.760000e-52 217.0
88 TraesCS2B01G028100 chr5A 85.065 308 34 9 1980 2283 655642487 655642786 2.810000e-78 303.0
89 TraesCS2B01G028100 chr5A 87.037 270 24 7 2006 2270 655640962 655641225 1.690000e-75 294.0
90 TraesCS2B01G028100 chr5A 84.848 297 36 7 1981 2270 655640544 655640838 2.180000e-74 291.0
91 TraesCS2B01G028100 chr5A 84.848 297 35 5 1980 2270 655872843 655873135 2.180000e-74 291.0
92 TraesCS2B01G028100 chr5A 78.182 440 43 17 1588 1975 655640057 655640495 1.340000e-56 231.0
93 TraesCS2B01G028100 chr5A 91.720 157 13 0 1031 1187 70133530 70133686 1.050000e-52 219.0
94 TraesCS2B01G028100 chr5A 79.323 266 38 11 1588 1836 655641988 655642253 2.970000e-38 171.0


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 TraesCS2B01G028100 chr2B 13180954 13187147 6193 False 11439.000000 11439 100.000000 1 6194 1 chr2B.!!$F1 6193
1 TraesCS2B01G028100 chr2B 485691267 485692806 1539 False 2279.000000 2279 93.592000 4672 6194 1 chr2B.!!$F3 1522
2 TraesCS2B01G028100 chr2B 13315021 13315627 606 False 876.000000 876 93.126000 4 597 1 chr2B.!!$F2 593
3 TraesCS2B01G028100 chr1D 25464747 25466291 1544 False 2307.000000 2307 93.871000 4672 6194 1 chr1D.!!$F1 1522
4 TraesCS2B01G028100 chr1D 235545951 235549509 3558 True 1853.500000 2499 92.690500 1029 4671 2 chr1D.!!$R1 3642
5 TraesCS2B01G028100 chr5D 462907869 462909487 1618 False 2466.000000 2466 94.161000 3053 4673 1 chr5D.!!$F2 1620
6 TraesCS2B01G028100 chr5D 114516767 114518298 1531 False 2294.000000 2294 93.839000 4672 6194 1 chr5D.!!$F1 1522
7 TraesCS2B01G028100 chr5D 275161483 275162756 1273 True 1892.000000 1892 93.672000 4672 5932 1 chr5D.!!$R2 1260
8 TraesCS2B01G028100 chr5D 482330447 482331711 1264 True 1783.000000 1783 92.230000 4672 5937 1 chr5D.!!$R4 1265
9 TraesCS2B01G028100 chr5D 520495827 520497084 1257 True 1772.000000 1772 92.200000 4672 5932 1 chr5D.!!$R5 1260
10 TraesCS2B01G028100 chr5D 336309255 336310518 1263 True 1749.000000 1749 91.757000 4672 5937 1 chr5D.!!$R3 1265
11 TraesCS2B01G028100 chr5D 473071190 473072608 1418 False 1046.500000 1463 93.321500 598 5643 2 chr5D.!!$F4 5045
12 TraesCS2B01G028100 chr7A 439030649 439032696 2047 False 1313.500000 2355 94.381500 2436 4671 2 chr7A.!!$F1 2235
13 TraesCS2B01G028100 chr7A 639883581 639885130 1549 True 1068.000000 1836 93.552000 2436 4362 2 chr7A.!!$R1 1926
14 TraesCS2B01G028100 chr3D 546485994 546487966 1972 False 1489.000000 2320 94.036000 597 6194 2 chr3D.!!$F2 5597
15 TraesCS2B01G028100 chr3D 143482084 143484604 2520 True 981.000000 1917 95.983000 2428 4310 3 chr3D.!!$R2 1882
16 TraesCS2B01G028100 chr3D 43022637 43023605 968 True 272.666667 418 91.735000 2431 3052 3 chr3D.!!$R1 621
17 TraesCS2B01G028100 chr1B 253823843 253827599 3756 True 1021.333333 2320 91.182333 1030 4671 3 chr1B.!!$R1 3641
18 TraesCS2B01G028100 chr7D 90561635 90563175 1540 True 2298.000000 2298 93.798000 4672 6194 1 chr7D.!!$R1 1522
19 TraesCS2B01G028100 chr7D 605600285 605601826 1541 False 2270.000000 2270 93.484000 4672 6194 1 chr7D.!!$F2 1522
20 TraesCS2B01G028100 chr7D 94495778 94497057 1279 True 1886.000000 1886 93.531000 4672 5932 1 chr7D.!!$R2 1260
21 TraesCS2B01G028100 chr7D 635927901 635931676 3775 True 1286.000000 2213 91.778000 1128 4672 2 chr7D.!!$R4 3544
22 TraesCS2B01G028100 chr7B 58797818 58799351 1533 False 2285.000000 2285 93.722000 4672 6194 1 chr7B.!!$F1 1522
23 TraesCS2B01G028100 chr7B 634824171 634825605 1434 False 824.500000 1443 95.143500 2929 4671 2 chr7B.!!$F2 1742
24 TraesCS2B01G028100 chr2A 441107857 441111548 3691 False 1228.000000 2189 93.342000 1239 4673 2 chr2A.!!$F2 3434
25 TraesCS2B01G028100 chr2A 23539145 23539852 707 True 924.000000 924 90.268000 3966 4671 1 chr2A.!!$R1 705
26 TraesCS2B01G028100 chr2A 9122068 9122651 583 False 830.000000 830 92.662000 1 573 1 chr2A.!!$F1 572
27 TraesCS2B01G028100 chr6D 28979333 28980847 1514 True 2174.000000 2174 92.636000 4672 6194 1 chr6D.!!$R2 1522
28 TraesCS2B01G028100 chr6D 298129811 298130733 922 True 1308.000000 1308 92.111000 3616 4552 1 chr6D.!!$R4 936
29 TraesCS2B01G028100 chr6D 298139319 298141148 1829 True 638.000000 898 95.320333 2428 3620 3 chr6D.!!$R5 1192
30 TraesCS2B01G028100 chr6D 30098395 30098985 590 True 460.000000 460 81.789000 1850 2429 1 chr6D.!!$R3 579
31 TraesCS2B01G028100 chr5B 89745418 89746848 1430 False 2119.000000 2119 93.398000 3238 4671 1 chr5B.!!$F2 1433
32 TraesCS2B01G028100 chr4B 251639450 251640961 1511 False 2109.000000 2109 91.925000 4672 6194 1 chr4B.!!$F1 1522
33 TraesCS2B01G028100 chr4A 281592375 281594916 2541 True 1302.500000 2085 91.579500 1025 4670 2 chr4A.!!$R1 3645
34 TraesCS2B01G028100 chr3B 707161582 707162818 1236 False 1790.000000 1790 93.018000 4972 6194 1 chr3B.!!$F1 1222
35 TraesCS2B01G028100 chr3B 66954554 66955551 997 True 466.000000 756 92.802500 2428 3052 2 chr3B.!!$R1 624
36 TraesCS2B01G028100 chr6B 347766956 347768202 1246 True 1760.000000 1760 92.035000 4672 5937 1 chr6B.!!$R3 1265
37 TraesCS2B01G028100 chr2D 331197633 331198891 1258 False 1757.000000 1757 91.972000 4672 5932 1 chr2D.!!$F2 1260
38 TraesCS2B01G028100 chr3A 55046594 55047598 1004 True 432.000000 686 91.843000 2428 3051 2 chr3A.!!$R1 623
39 TraesCS2B01G028100 chr5A 655640057 655642786 2729 False 258.000000 303 82.891000 1588 2283 5 chr5A.!!$F3 695

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
838 869 0.037882 CAGAGAGCCGTTGAGCAGAA 60.038 55.0 0.00 0.0 34.23 3.02 F
1318 1358 0.109689 CACCACCGAACTCTCTCGTC 60.110 60.0 0.00 0.0 37.11 4.20 F
1470 1816 0.912486 CCCATCTCCTTTCCCGACTT 59.088 55.0 0.00 0.0 0.00 3.01 F
2844 5963 0.984230 TGGATCGGAGTCCAAAAGCT 59.016 50.0 10.49 0.0 45.03 3.74 F
3620 7657 1.631405 TCATTCCCAAAGGTGCCTTG 58.369 50.0 4.00 0.0 36.26 3.61 F
4468 8548 2.224793 GGGTCAAAAGTGAGGGCTACTT 60.225 50.0 0.00 0.0 39.92 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2055 3588 0.331278 TCCCGAACATTTGCCCAGAT 59.669 50.000 0.00 0.0 0.00 2.90 R
3055 6556 0.108019 AGGGTCAAAGTTCCACGACC 59.892 55.000 0.00 0.0 45.95 4.79 R
3340 7377 1.003580 ACACGAGGCAACATTGGATCT 59.996 47.619 0.00 0.0 41.41 2.75 R
3677 7714 0.237498 GGGCGTCCTTCAAAAGTTCG 59.763 55.000 0.00 0.0 0.00 3.95 R
4791 8878 2.025037 TCTTACCCCATTCTTGCTGCAT 60.025 45.455 1.84 0.0 0.00 3.96 R
5831 9979 1.967066 CCTAAATGCCACAAACCCACA 59.033 47.619 0.00 0.0 0.00 4.17 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
27 28 5.997129 GGAGATTCTTGGCAAAATGGAAAAA 59.003 36.000 0.00 0.00 0.00 1.94
106 107 2.493278 AGCATGGAAAATGCACCAGTAC 59.507 45.455 12.44 0.00 46.77 2.73
142 154 8.839310 TGGTGGGTCAAAATTAATTATTGTTG 57.161 30.769 0.01 2.80 0.00 3.33
218 231 3.907474 TCTTCCAGAGGACATGTAACCAA 59.093 43.478 0.00 0.00 0.00 3.67
393 406 8.548721 GTTTCGTCTTTGAATCAAAAGTCTCTA 58.451 33.333 9.85 0.00 38.16 2.43
449 463 5.104776 TCAGATAGACTCTTTCCAATGTGGG 60.105 44.000 0.00 0.00 32.49 4.61
505 535 7.572759 ACACACAAATACTTGTCTAAATGTCG 58.427 34.615 0.00 0.00 44.15 4.35
560 590 3.365969 CCGGCATGAAAAGGTTTGACTAC 60.366 47.826 0.00 0.00 0.00 2.73
599 629 9.905713 ATTCAGTAGCTATGTTCAAATTAAGGA 57.094 29.630 0.00 0.00 0.00 3.36
629 659 0.550914 TTTTGCCCTCAGTGGTGTCT 59.449 50.000 0.00 0.00 0.00 3.41
637 667 0.104855 TCAGTGGTGTCTGTGTGCTC 59.895 55.000 0.00 0.00 36.85 4.26
668 698 2.417586 CTCAGATGCGAATTGTGCTCAA 59.582 45.455 3.31 3.31 37.98 3.02
751 782 2.223745 GTTTTGACTCGGCCCTTACAA 58.776 47.619 0.00 0.00 0.00 2.41
763 794 1.064825 CCTTACAAGTGGGACCAGGT 58.935 55.000 0.00 0.00 0.00 4.00
801 832 0.319986 TATTCAGACCGTTGCACGCA 60.320 50.000 0.00 0.00 40.91 5.24
818 849 1.228831 CATGGCTTGTGGGACCCAA 60.229 57.895 16.98 0.00 34.18 4.12
838 869 0.037882 CAGAGAGCCGTTGAGCAGAA 60.038 55.000 0.00 0.00 34.23 3.02
911 947 3.749064 GACAGAGAGCACGGCGGA 61.749 66.667 13.24 0.00 0.00 5.54
935 971 2.881266 CGGCGAGAGAGAGAGAGCG 61.881 68.421 0.00 0.00 0.00 5.03
986 1022 1.003233 GACGGTGTTGAGATCCCCTTT 59.997 52.381 0.00 0.00 0.00 3.11
1052 1092 7.431249 TCCACTACTAGGAAAATGCTTATACG 58.569 38.462 0.00 0.00 30.71 3.06
1070 1110 7.378194 GCTTATACGTAGAAGTTTACCAGTAGC 59.622 40.741 25.95 8.67 0.00 3.58
1083 1123 0.951558 CAGTAGCGTTTGTTTGGGCT 59.048 50.000 0.00 0.00 39.44 5.19
1096 1136 3.075005 GGGCTCCCACGCTACTGA 61.075 66.667 0.00 0.00 35.81 3.41
1251 1291 4.932799 TGCGCTATTACTAAGTGAAAAGCA 59.067 37.500 9.73 0.00 0.00 3.91
1318 1358 0.109689 CACCACCGAACTCTCTCGTC 60.110 60.000 0.00 0.00 37.11 4.20
1329 1369 4.181309 ACTCTCTCGTCAATTCCTCAAC 57.819 45.455 0.00 0.00 0.00 3.18
1331 1371 4.039245 ACTCTCTCGTCAATTCCTCAACAA 59.961 41.667 0.00 0.00 0.00 2.83
1332 1372 4.307432 TCTCTCGTCAATTCCTCAACAAC 58.693 43.478 0.00 0.00 0.00 3.32
1372 1412 2.603473 CCACCCCTCTGTCGACCA 60.603 66.667 14.12 0.00 0.00 4.02
1392 1588 1.075970 CTCTCCCCCACGATCTCCA 60.076 63.158 0.00 0.00 0.00 3.86
1399 1595 3.770040 CACGATCTCCACCCCGCA 61.770 66.667 0.00 0.00 0.00 5.69
1470 1816 0.912486 CCCATCTCCTTTCCCGACTT 59.088 55.000 0.00 0.00 0.00 3.01
1478 1824 1.301677 CTTTCCCGACTTGCCTCTGC 61.302 60.000 0.00 0.00 38.26 4.26
1514 1860 1.870580 CGCCCGATGGATTTAACGCTA 60.871 52.381 0.00 0.00 0.00 4.26
1576 1922 1.139256 GGCTAACCCTAGAAGAGGCAC 59.861 57.143 0.00 0.00 45.17 5.01
1577 1923 2.112190 GCTAACCCTAGAAGAGGCACT 58.888 52.381 0.00 0.00 45.17 4.40
1870 2961 2.068821 AGGTGATGGCCTCTGCGAT 61.069 57.895 3.32 0.00 38.78 4.58
1905 2996 5.365605 TGTTTCTTGGAGTTCTTGGAGTCTA 59.634 40.000 0.00 0.00 0.00 2.59
1917 3009 2.376109 TGGAGTCTATGGAGTCGTTCC 58.624 52.381 7.73 2.35 46.98 3.62
1922 3014 3.018149 GTCTATGGAGTCGTTCCTGAGT 58.982 50.000 9.52 0.00 46.92 3.41
1932 3024 1.264288 CGTTCCTGAGTGTTTCTTGGC 59.736 52.381 0.00 0.00 0.00 4.52
1953 3047 1.328279 TCCTCGAGCAGTTCAACTCA 58.672 50.000 6.99 0.00 32.98 3.41
1958 3052 1.532437 CGAGCAGTTCAACTCATTGCA 59.468 47.619 2.65 0.00 37.24 4.08
1960 3054 2.291465 GAGCAGTTCAACTCATTGCACA 59.709 45.455 2.65 0.00 34.74 4.57
1962 3056 2.859806 GCAGTTCAACTCATTGCACACC 60.860 50.000 0.00 0.00 34.74 4.16
1976 3070 1.079819 ACACCGAAGAGGCGATGTG 60.080 57.895 0.00 0.00 46.52 3.21
1977 3071 1.079819 CACCGAAGAGGCGATGTGT 60.080 57.895 0.00 0.00 46.52 3.72
2003 3140 7.052873 AGGAATGTGGAATTGTGATCTCTAAG 58.947 38.462 0.00 0.00 0.00 2.18
2009 3146 6.876257 GTGGAATTGTGATCTCTAAGTCTGTT 59.124 38.462 0.00 0.00 0.00 3.16
2010 3147 7.064016 GTGGAATTGTGATCTCTAAGTCTGTTC 59.936 40.741 0.00 0.00 0.00 3.18
2025 3558 3.636764 GTCTGTTCAAATCTTGGGGTTGT 59.363 43.478 0.00 0.00 0.00 3.32
2038 3571 5.949354 TCTTGGGGTTGTGGATAATTTAGTG 59.051 40.000 0.00 0.00 0.00 2.74
2053 3586 9.321562 GATAATTTAGTGGTAGAAACGGAATCA 57.678 33.333 0.00 0.00 0.00 2.57
2054 3587 7.989416 AATTTAGTGGTAGAAACGGAATCAA 57.011 32.000 0.00 0.00 0.00 2.57
2055 3588 7.989416 ATTTAGTGGTAGAAACGGAATCAAA 57.011 32.000 0.00 0.00 0.00 2.69
2056 3589 7.989416 TTTAGTGGTAGAAACGGAATCAAAT 57.011 32.000 0.00 0.00 0.00 2.32
2057 3590 7.605410 TTAGTGGTAGAAACGGAATCAAATC 57.395 36.000 0.00 0.00 0.00 2.17
2058 3591 5.805728 AGTGGTAGAAACGGAATCAAATCT 58.194 37.500 0.00 0.00 0.00 2.40
2070 3603 4.872124 GGAATCAAATCTGGGCAAATGTTC 59.128 41.667 0.00 0.00 0.00 3.18
2077 3610 1.175983 TGGGCAAATGTTCGGGACAC 61.176 55.000 0.00 0.00 42.04 3.67
2091 3624 2.094390 CGGGACACTTTGACGATTAGGA 60.094 50.000 0.00 0.00 0.00 2.94
2096 3629 6.072119 GGGACACTTTGACGATTAGGAATTTT 60.072 38.462 0.00 0.00 0.00 1.82
2125 4046 2.125912 TCGAGCTCTTCTTGCGGC 60.126 61.111 12.85 0.00 35.28 6.53
2147 4068 5.178809 GGCGCGTTATCAAATTTAGAGGTAT 59.821 40.000 8.43 0.00 0.00 2.73
2150 4071 6.071463 GCGTTATCAAATTTAGAGGTATGCG 58.929 40.000 0.00 0.00 0.00 4.73
2165 4086 1.742761 ATGCGAGGATCTTGTTGTGG 58.257 50.000 0.00 0.00 0.00 4.17
2184 4105 4.096532 TGTGGTTATTCGCAACTGTTCAAA 59.903 37.500 0.00 0.00 0.00 2.69
2191 4112 8.964150 GTTATTCGCAACTGTTCAAAATTTAGT 58.036 29.630 0.00 0.00 0.00 2.24
2216 5300 4.082026 GTCCAGGCTTGTGCTAATTGATTT 60.082 41.667 0.00 0.00 39.59 2.17
2219 5303 6.210385 TCCAGGCTTGTGCTAATTGATTTTTA 59.790 34.615 0.00 0.00 39.59 1.52
2220 5304 6.532657 CCAGGCTTGTGCTAATTGATTTTTAG 59.467 38.462 0.00 0.00 39.59 1.85
2221 5305 7.092716 CAGGCTTGTGCTAATTGATTTTTAGT 58.907 34.615 0.00 0.00 39.59 2.24
2222 5306 8.243426 CAGGCTTGTGCTAATTGATTTTTAGTA 58.757 33.333 0.00 0.00 39.59 1.82
2223 5307 8.462016 AGGCTTGTGCTAATTGATTTTTAGTAG 58.538 33.333 0.00 0.00 39.59 2.57
2274 5375 2.823984 TGCTGCAAGTGAAAAATGTGG 58.176 42.857 0.00 0.00 35.30 4.17
2284 5385 4.840115 AGTGAAAAATGTGGGGATCATGTT 59.160 37.500 0.00 0.00 0.00 2.71
2294 5395 1.205417 GGGATCATGTTTTGGCAGTGG 59.795 52.381 0.00 0.00 0.00 4.00
2311 5412 5.125100 CAGTGGTTGCTGTCATATTTTGT 57.875 39.130 0.00 0.00 0.00 2.83
2345 5446 6.839124 TGATGCCAAAATGTATCAGTTTCT 57.161 33.333 0.00 0.00 29.07 2.52
2346 5447 7.936496 TGATGCCAAAATGTATCAGTTTCTA 57.064 32.000 0.00 0.00 29.07 2.10
2347 5448 7.988737 TGATGCCAAAATGTATCAGTTTCTAG 58.011 34.615 0.00 0.00 29.07 2.43
2348 5449 7.611467 TGATGCCAAAATGTATCAGTTTCTAGT 59.389 33.333 0.00 0.00 29.07 2.57
2349 5450 7.759489 TGCCAAAATGTATCAGTTTCTAGTT 57.241 32.000 0.00 0.00 29.07 2.24
2350 5451 8.177119 TGCCAAAATGTATCAGTTTCTAGTTT 57.823 30.769 0.00 0.00 29.07 2.66
2351 5452 8.296713 TGCCAAAATGTATCAGTTTCTAGTTTC 58.703 33.333 0.00 0.00 29.07 2.78
2352 5453 8.515414 GCCAAAATGTATCAGTTTCTAGTTTCT 58.485 33.333 0.00 0.00 29.07 2.52
2382 5483 9.383462 GTAGATGAATGTCGTTATATATAGGCG 57.617 37.037 10.62 10.62 0.00 5.52
2383 5484 8.221965 AGATGAATGTCGTTATATATAGGCGA 57.778 34.615 13.80 13.80 0.00 5.54
2384 5485 8.683615 AGATGAATGTCGTTATATATAGGCGAA 58.316 33.333 17.31 11.30 33.30 4.70
2385 5486 8.858003 ATGAATGTCGTTATATATAGGCGAAG 57.142 34.615 17.31 0.00 33.30 3.79
2387 5488 8.301720 TGAATGTCGTTATATATAGGCGAAGTT 58.698 33.333 17.31 15.11 33.30 2.66
2388 5489 9.778993 GAATGTCGTTATATATAGGCGAAGTTA 57.221 33.333 17.31 9.17 33.30 2.24
2390 5491 8.955061 TGTCGTTATATATAGGCGAAGTTAAC 57.045 34.615 17.31 0.00 33.30 2.01
2401 5502 4.023193 AGGCGAAGTTAACCTGAATGTTTG 60.023 41.667 0.88 0.00 30.82 2.93
2416 5517 3.410631 TGTTTGCTCGGGATTACTTGA 57.589 42.857 0.00 0.00 0.00 3.02
2418 5519 3.244422 TGTTTGCTCGGGATTACTTGACT 60.244 43.478 0.00 0.00 0.00 3.41
2419 5520 3.695830 TTGCTCGGGATTACTTGACTT 57.304 42.857 0.00 0.00 0.00 3.01
2429 5530 5.291128 GGGATTACTTGACTTGACGTACATG 59.709 44.000 0.00 0.00 0.00 3.21
2430 5531 5.220416 GGATTACTTGACTTGACGTACATGC 60.220 44.000 0.00 0.00 0.00 4.06
2431 5532 3.386768 ACTTGACTTGACGTACATGCT 57.613 42.857 0.00 0.00 0.00 3.79
2432 5533 3.059884 ACTTGACTTGACGTACATGCTG 58.940 45.455 0.00 0.00 0.00 4.41
2433 5534 3.243737 ACTTGACTTGACGTACATGCTGA 60.244 43.478 0.00 0.00 0.00 4.26
2434 5535 3.592898 TGACTTGACGTACATGCTGAT 57.407 42.857 0.00 0.00 0.00 2.90
2550 5651 4.142425 GCACTCTGGTAAGTAGTGGAGTAC 60.142 50.000 0.00 0.00 40.76 2.73
2665 5783 8.325046 ACTAAATCTCTTACTCTTTTGCAGGAT 58.675 33.333 0.00 0.00 0.00 3.24
2760 5878 6.423182 AGATTATGTGTTGCTAGCCCTTTTA 58.577 36.000 13.29 0.00 0.00 1.52
2844 5963 0.984230 TGGATCGGAGTCCAAAAGCT 59.016 50.000 10.49 0.00 45.03 3.74
2892 6013 7.750769 AGAATATCTCGTACCTTATTCGCTAC 58.249 38.462 0.00 0.00 36.58 3.58
2920 6041 4.754114 TGCTTGTTTTATTGTGGCCATTTC 59.246 37.500 9.72 0.00 0.00 2.17
2956 6455 3.260128 CAGCCATATCAGCATCAGGACTA 59.740 47.826 0.00 0.00 0.00 2.59
3048 6549 6.911250 TCTTCTTATGGTCTGTTGACACTA 57.089 37.500 0.00 0.00 44.61 2.74
3053 6554 8.589701 TCTTATGGTCTGTTGACACTATCTTA 57.410 34.615 0.00 0.00 44.61 2.10
3055 6556 9.254133 CTTATGGTCTGTTGACACTATCTTATG 57.746 37.037 0.00 0.00 44.61 1.90
3189 7215 6.235231 GAGTATCTTGGTGTATTCAAGGGA 57.765 41.667 0.00 0.00 41.23 4.20
3190 7216 6.636454 AGTATCTTGGTGTATTCAAGGGAA 57.364 37.500 0.00 0.00 41.23 3.97
3210 7236 8.491045 AGGGAAGTTTTTGAAATCCTATTGAA 57.509 30.769 0.00 0.00 0.00 2.69
3288 7325 7.259290 TGAAGAAGTTGTCTAACCATTTGAC 57.741 36.000 0.00 0.00 37.52 3.18
3403 7440 8.891671 TCTTGCTTCAGCTTTTATTTTTGAAT 57.108 26.923 0.00 0.00 42.66 2.57
3496 7533 3.855255 TTGGTTTCAGACATCTGGACA 57.145 42.857 8.99 1.33 43.91 4.02
3518 7555 5.185828 ACAAGAAGAAAAAGAAGTGCAAGGT 59.814 36.000 0.00 0.00 0.00 3.50
3548 7585 4.142049 GGTCGAGACTCATCTTGAATTCCT 60.142 45.833 2.27 0.00 45.36 3.36
3620 7657 1.631405 TCATTCCCAAAGGTGCCTTG 58.369 50.000 4.00 0.00 36.26 3.61
3636 7673 3.882888 TGCCTTGTCTACTCAAAACCTTG 59.117 43.478 0.00 0.00 0.00 3.61
3641 7678 6.348540 CCTTGTCTACTCAAAACCTTGTATGC 60.349 42.308 0.00 0.00 33.94 3.14
3656 7693 6.998673 ACCTTGTATGCTATTAGATTTGGTCC 59.001 38.462 0.00 0.00 0.00 4.46
3661 7698 8.590204 TGTATGCTATTAGATTTGGTCCGATTA 58.410 33.333 0.00 0.00 0.00 1.75
3662 7699 9.088512 GTATGCTATTAGATTTGGTCCGATTAG 57.911 37.037 0.00 0.00 0.00 1.73
3676 7713 5.221661 GGTCCGATTAGTATGAAGGGTTGAT 60.222 44.000 0.00 0.00 0.00 2.57
3677 7714 5.927115 GTCCGATTAGTATGAAGGGTTGATC 59.073 44.000 0.00 0.00 0.00 2.92
3865 7906 6.916360 ATTTGGTGTACAGGATTTGACAAT 57.084 33.333 0.00 0.00 0.00 2.71
3866 7907 5.703978 TTGGTGTACAGGATTTGACAATG 57.296 39.130 0.00 0.00 0.00 2.82
4015 8063 6.037391 CGTACTAACAAGTTTTCACTTTCCCA 59.963 38.462 0.00 0.00 40.66 4.37
4016 8064 7.255001 CGTACTAACAAGTTTTCACTTTCCCAT 60.255 37.037 0.00 0.00 40.66 4.00
4073 8133 3.782244 GTGGCGCTGTGCTCTTCG 61.782 66.667 13.46 0.00 45.43 3.79
4118 8178 3.454587 AAGCTCGGTTGCCACGTCA 62.455 57.895 0.00 0.00 0.00 4.35
4142 8202 2.760374 GGATGATCGTCCAGGTGATTC 58.240 52.381 26.27 0.00 38.20 2.52
4336 8409 6.319911 TGTGTGTGTCTGATGTTAAATGGAAA 59.680 34.615 0.00 0.00 0.00 3.13
4355 8428 5.006386 GGAAACTTGAGATGGTTCTGTGAT 58.994 41.667 0.00 0.00 30.30 3.06
4468 8548 2.224793 GGGTCAAAAGTGAGGGCTACTT 60.225 50.000 0.00 0.00 39.92 2.24
4552 8632 8.800332 ACTACTACTAACTTTTTAGCTGTAGCA 58.200 33.333 6.65 0.00 41.82 3.49
4563 8644 3.669939 AGCTGTAGCATGGGGTAAAAT 57.330 42.857 6.65 0.00 45.16 1.82
4631 8713 3.886123 GGAACCCATGCTACTTGTATGT 58.114 45.455 0.00 0.00 37.11 2.29
4852 8939 0.036765 TTCGTGGTCGGGATCTTTGG 60.037 55.000 0.00 0.00 37.69 3.28
4891 8978 0.593128 GGTGTTCATGCAGGTGACAC 59.407 55.000 22.91 22.91 33.41 3.67
4896 8983 0.534877 TCATGCAGGTGACACGCTTT 60.535 50.000 0.00 0.00 32.68 3.51
5020 9107 2.028130 GAGCTCCGGAAGAAGAGATGA 58.972 52.381 5.23 0.00 0.00 2.92
5190 9277 5.146010 TGTTGAAAATGTATGGAAAGGCC 57.854 39.130 0.00 0.00 37.10 5.19
5429 9531 3.511934 AGGACAAATTCAGAGCGTAGAGT 59.488 43.478 0.00 0.00 0.00 3.24
5483 9604 1.001706 GGGGTTCTCTTGCGTGTTTTC 60.002 52.381 0.00 0.00 0.00 2.29
5568 9690 7.008941 AGCTAATTGAATTATTCCAGAGCCAT 58.991 34.615 2.22 0.00 0.00 4.40
5731 9875 7.361116 CCTGGTGCCAAAATAAATGAACATTTC 60.361 37.037 14.68 2.14 40.99 2.17
5831 9979 2.203596 ACTCGAACCCAGGACCGT 60.204 61.111 0.00 0.00 0.00 4.83
5852 10000 1.967779 GTGGGTTTGTGGCATTTAGGT 59.032 47.619 0.00 0.00 0.00 3.08
5887 10035 2.166459 CGCTAGGACAGATGGAAAGACA 59.834 50.000 0.00 0.00 0.00 3.41
6160 10319 5.443283 TCTCATCCCCTCTGATTTTCATTG 58.557 41.667 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.389329 AGTCAAAGTCACACATGGAGACT 59.611 43.478 10.12 10.12 43.98 3.24
106 107 7.645058 ATTTTGACCCACCATGAATACTAAG 57.355 36.000 0.00 0.00 0.00 2.18
218 231 3.255642 ACGGAGCAAATGTACAAGCAAAT 59.744 39.130 17.11 1.10 0.00 2.32
393 406 2.558359 GCAGTGGCCACTTAATTTGTCT 59.442 45.455 36.06 8.54 40.20 3.41
457 471 1.302192 TTTAGACACGTGCCCCTGC 60.302 57.895 17.22 0.00 38.26 4.85
505 535 2.863704 GCTTGTCCTTGCCACATGTTTC 60.864 50.000 0.00 0.00 0.00 2.78
532 562 1.185315 CCTTTTCATGCCGGTTGGAT 58.815 50.000 1.90 0.00 37.49 3.41
573 603 9.905713 TCCTTAATTTGAACATAGCTACTGAAT 57.094 29.630 0.00 0.00 0.00 2.57
599 629 7.400052 ACCACTGAGGGCAAAAGAATATTTAAT 59.600 33.333 0.00 0.00 43.89 1.40
604 634 4.019174 CACCACTGAGGGCAAAAGAATAT 58.981 43.478 0.00 0.00 43.89 1.28
608 638 0.550914 ACACCACTGAGGGCAAAAGA 59.449 50.000 0.00 0.00 43.89 2.52
629 659 0.395586 AGGGCAAAACTGAGCACACA 60.396 50.000 0.00 0.00 36.38 3.72
637 667 0.169672 CGCATCTGAGGGCAAAACTG 59.830 55.000 5.18 0.00 0.00 3.16
668 698 1.780503 GCATGGACTAGGGGCAAAAT 58.219 50.000 0.00 0.00 0.00 1.82
751 782 3.252284 CTGCCACCTGGTCCCACT 61.252 66.667 0.00 0.00 37.57 4.00
801 832 1.228862 GTTGGGTCCCACAAGCCAT 60.229 57.895 11.24 0.00 45.69 4.40
818 849 1.181741 TCTGCTCAACGGCTCTCTGT 61.182 55.000 0.00 0.00 0.00 3.41
911 947 1.747367 CTCTCTCTCGCCGTGGTCT 60.747 63.158 0.00 0.00 0.00 3.85
967 1003 1.064825 AAAGGGGATCTCAACACCGT 58.935 50.000 0.00 0.00 35.74 4.83
971 1007 1.075601 AGCCAAAGGGGATCTCAACA 58.924 50.000 0.00 0.00 40.01 3.33
986 1022 2.685017 ACATGGAGCTCGGAGCCA 60.685 61.111 25.49 17.60 43.77 4.75
1052 1092 5.693555 ACAAACGCTACTGGTAAACTTCTAC 59.306 40.000 0.00 0.00 0.00 2.59
1070 1110 3.849064 TGGGAGCCCAAACAAACG 58.151 55.556 5.60 0.00 44.12 3.60
1083 1123 3.962063 TGGTAATTATCAGTAGCGTGGGA 59.038 43.478 0.00 0.00 0.00 4.37
1096 1136 2.101917 ACCACGCGCTACTGGTAATTAT 59.898 45.455 16.63 0.00 39.11 1.28
1210 1250 2.596575 CGCAGGTTTTACGATATGCACG 60.597 50.000 0.00 0.00 33.33 5.34
1318 1358 6.197096 CGAGAGTTTTTGTTGTTGAGGAATTG 59.803 38.462 0.00 0.00 0.00 2.32
1329 1369 1.597663 AGGTCGCGAGAGTTTTTGTTG 59.402 47.619 10.24 0.00 43.49 3.33
1331 1371 1.202486 TGAGGTCGCGAGAGTTTTTGT 60.202 47.619 10.24 0.00 43.49 2.83
1332 1372 1.192534 GTGAGGTCGCGAGAGTTTTTG 59.807 52.381 10.24 0.00 43.49 2.44
1372 1412 1.075896 GAGATCGTGGGGGAGAGGT 60.076 63.158 0.00 0.00 0.00 3.85
1450 1653 1.153147 GTCGGGAAAGGAGATGGGC 60.153 63.158 0.00 0.00 0.00 5.36
1470 1816 3.461773 GTAGAGCGGGCAGAGGCA 61.462 66.667 0.00 0.00 43.71 4.75
1478 1824 3.043419 CGGAGATGGTAGAGCGGG 58.957 66.667 0.00 0.00 0.00 6.13
1870 2961 1.134753 CCAAGAAACAACAGCAGCACA 59.865 47.619 0.00 0.00 0.00 4.57
1917 3009 2.810852 GAGGAAGCCAAGAAACACTCAG 59.189 50.000 0.00 0.00 0.00 3.35
1922 3014 1.878102 GCTCGAGGAAGCCAAGAAACA 60.878 52.381 15.58 0.00 36.22 2.83
1932 3024 2.288457 TGAGTTGAACTGCTCGAGGAAG 60.288 50.000 15.58 8.12 34.67 3.46
1953 3047 2.034879 CGCCTCTTCGGTGTGCAAT 61.035 57.895 0.00 0.00 38.52 3.56
1960 3054 0.456221 CTACACATCGCCTCTTCGGT 59.544 55.000 0.00 0.00 34.25 4.69
1962 3056 0.738975 TCCTACACATCGCCTCTTCG 59.261 55.000 0.00 0.00 0.00 3.79
1976 3070 6.352516 AGAGATCACAATTCCACATTCCTAC 58.647 40.000 0.00 0.00 0.00 3.18
1977 3071 6.566079 AGAGATCACAATTCCACATTCCTA 57.434 37.500 0.00 0.00 0.00 2.94
2003 3140 3.636764 ACAACCCCAAGATTTGAACAGAC 59.363 43.478 0.00 0.00 0.00 3.51
2009 3146 3.541242 ATCCACAACCCCAAGATTTGA 57.459 42.857 0.00 0.00 0.00 2.69
2010 3147 5.937975 ATTATCCACAACCCCAAGATTTG 57.062 39.130 0.00 0.00 0.00 2.32
2025 3558 7.185318 TCCGTTTCTACCACTAAATTATCCA 57.815 36.000 0.00 0.00 0.00 3.41
2038 3571 4.335594 CCCAGATTTGATTCCGTTTCTACC 59.664 45.833 0.00 0.00 0.00 3.18
2053 3586 1.550072 CCCGAACATTTGCCCAGATTT 59.450 47.619 0.00 0.00 0.00 2.17
2054 3587 1.185315 CCCGAACATTTGCCCAGATT 58.815 50.000 0.00 0.00 0.00 2.40
2055 3588 0.331278 TCCCGAACATTTGCCCAGAT 59.669 50.000 0.00 0.00 0.00 2.90
2056 3589 0.608035 GTCCCGAACATTTGCCCAGA 60.608 55.000 0.00 0.00 0.00 3.86
2057 3590 0.893270 TGTCCCGAACATTTGCCCAG 60.893 55.000 0.00 0.00 31.20 4.45
2058 3591 1.151679 TGTCCCGAACATTTGCCCA 59.848 52.632 0.00 0.00 31.20 5.36
2070 3603 2.094390 TCCTAATCGTCAAAGTGTCCCG 60.094 50.000 0.00 0.00 0.00 5.14
2077 3610 6.417191 TCGGAAAATTCCTAATCGTCAAAG 57.583 37.500 10.31 0.00 45.33 2.77
2091 3624 7.210873 AGAGCTCGAGTAATAATCGGAAAATT 58.789 34.615 15.13 0.00 40.54 1.82
2096 3629 5.064558 AGAAGAGCTCGAGTAATAATCGGA 58.935 41.667 15.13 0.00 40.54 4.55
2098 3631 5.116377 GCAAGAAGAGCTCGAGTAATAATCG 59.884 44.000 15.13 3.54 41.50 3.34
2125 4046 6.071463 GCATACCTCTAAATTTGATAACGCG 58.929 40.000 3.53 3.53 0.00 6.01
2147 4068 0.396435 ACCACAACAAGATCCTCGCA 59.604 50.000 0.00 0.00 0.00 5.10
2150 4071 4.201822 GCGAATAACCACAACAAGATCCTC 60.202 45.833 0.00 0.00 0.00 3.71
2165 4086 8.964150 ACTAAATTTTGAACAGTTGCGAATAAC 58.036 29.630 6.63 0.00 0.00 1.89
2184 4105 3.005791 GCACAAGCCTGGACAACTAAATT 59.994 43.478 0.00 0.00 33.58 1.82
2191 4112 2.557924 CAATTAGCACAAGCCTGGACAA 59.442 45.455 0.00 0.00 43.56 3.18
2274 5375 1.205417 CCACTGCCAAAACATGATCCC 59.795 52.381 0.00 0.00 0.00 3.85
2294 5395 7.928908 TTTCTTGACAAAATATGACAGCAAC 57.071 32.000 0.00 0.00 35.21 4.17
2345 5446 8.277490 ACGACATTCATCTACACTAGAAACTA 57.723 34.615 0.00 0.00 38.50 2.24
2346 5447 7.159322 ACGACATTCATCTACACTAGAAACT 57.841 36.000 0.00 0.00 38.50 2.66
2347 5448 7.813852 AACGACATTCATCTACACTAGAAAC 57.186 36.000 0.00 0.00 38.50 2.78
2375 5476 6.229936 ACATTCAGGTTAACTTCGCCTATA 57.770 37.500 5.42 0.00 0.00 1.31
2376 5477 5.099042 ACATTCAGGTTAACTTCGCCTAT 57.901 39.130 5.42 0.00 0.00 2.57
2377 5478 4.546829 ACATTCAGGTTAACTTCGCCTA 57.453 40.909 5.42 0.00 0.00 3.93
2378 5479 3.418684 ACATTCAGGTTAACTTCGCCT 57.581 42.857 5.42 0.00 0.00 5.52
2379 5480 4.226761 CAAACATTCAGGTTAACTTCGCC 58.773 43.478 5.42 0.00 0.00 5.54
2380 5481 3.668656 GCAAACATTCAGGTTAACTTCGC 59.331 43.478 5.42 0.00 0.00 4.70
2381 5482 5.108385 AGCAAACATTCAGGTTAACTTCG 57.892 39.130 5.42 0.00 0.00 3.79
2382 5483 5.147162 CGAGCAAACATTCAGGTTAACTTC 58.853 41.667 5.42 0.00 0.00 3.01
2383 5484 4.023193 CCGAGCAAACATTCAGGTTAACTT 60.023 41.667 5.42 0.00 0.00 2.66
2384 5485 3.502211 CCGAGCAAACATTCAGGTTAACT 59.498 43.478 5.42 0.00 0.00 2.24
2385 5486 3.365969 CCCGAGCAAACATTCAGGTTAAC 60.366 47.826 0.00 0.00 0.00 2.01
2387 5488 2.039216 TCCCGAGCAAACATTCAGGTTA 59.961 45.455 0.00 0.00 0.00 2.85
2388 5489 1.202879 TCCCGAGCAAACATTCAGGTT 60.203 47.619 0.00 0.00 0.00 3.50
2389 5490 0.400213 TCCCGAGCAAACATTCAGGT 59.600 50.000 0.00 0.00 0.00 4.00
2390 5491 1.755179 ATCCCGAGCAAACATTCAGG 58.245 50.000 0.00 0.00 0.00 3.86
2401 5502 2.930682 GTCAAGTCAAGTAATCCCGAGC 59.069 50.000 0.00 0.00 0.00 5.03
2416 5517 2.416547 GCAATCAGCATGTACGTCAAGT 59.583 45.455 0.00 0.00 44.79 3.16
2434 5535 9.347934 CCTGTGAAATACGTATTATTTTTGCAA 57.652 29.630 20.62 0.00 39.99 4.08
2465 5566 7.573710 AGGCACTTAGATTTCCATGTATAACA 58.426 34.615 0.00 0.00 27.25 2.41
2665 5783 1.234821 CAAGGCGTCCAAGCTTTGTA 58.765 50.000 0.00 0.00 45.38 2.41
2714 5832 9.574516 AATCTCTATAGAAAAACAAACTGTGGT 57.425 29.630 3.57 0.00 34.73 4.16
2752 5870 8.747538 TCCTAAGATATTTCAGTTAAAAGGGC 57.252 34.615 0.00 0.00 0.00 5.19
2760 5878 9.167311 GTTGTGTGATCCTAAGATATTTCAGTT 57.833 33.333 0.00 0.00 30.90 3.16
2844 5963 3.132289 CGGGACTTGCCTTAAGAGTATCA 59.868 47.826 3.36 0.00 39.76 2.15
2892 6013 3.490526 GCCACAATAAAACAAGCACACTG 59.509 43.478 0.00 0.00 0.00 3.66
2920 6041 0.179076 TGGCTGTAGACGCATCATGG 60.179 55.000 0.00 0.00 0.00 3.66
2956 6455 5.363868 TGATGTAGTTCCAGCTAGCATACTT 59.636 40.000 18.83 7.68 0.00 2.24
3048 6549 4.935808 GTCAAAGTTCCACGACCATAAGAT 59.064 41.667 0.00 0.00 0.00 2.40
3053 6554 1.892209 GGTCAAAGTTCCACGACCAT 58.108 50.000 0.00 0.00 45.96 3.55
3055 6556 0.108019 AGGGTCAAAGTTCCACGACC 59.892 55.000 0.00 0.00 45.95 4.79
3184 7210 8.491045 TCAATAGGATTTCAAAAACTTCCCTT 57.509 30.769 0.00 0.00 0.00 3.95
3210 7236 6.621613 GCCTCGAGTTCCTTGAAAAATATTT 58.378 36.000 12.31 0.00 0.00 1.40
3288 7325 2.291741 GAGTCAAGCAAACCAAGACAGG 59.708 50.000 0.00 0.00 0.00 4.00
3340 7377 1.003580 ACACGAGGCAACATTGGATCT 59.996 47.619 0.00 0.00 41.41 2.75
3403 7440 9.807921 AAGTTCTCTTAGAATATTTTGTCCCAA 57.192 29.630 0.00 0.00 36.50 4.12
3496 7533 5.921962 ACCTTGCACTTCTTTTTCTTCTT 57.078 34.783 0.00 0.00 0.00 2.52
3518 7555 3.698289 AGATGAGTCTCGACCTTACCAA 58.302 45.455 0.00 0.00 0.00 3.67
3548 7585 6.043411 CCAAATTTAACCTTTTCACGTCCAA 58.957 36.000 0.00 0.00 0.00 3.53
3620 7657 8.494016 AATAGCATACAAGGTTTTGAGTAGAC 57.506 34.615 0.00 0.00 37.73 2.59
3636 7673 7.907214 AATCGGACCAAATCTAATAGCATAC 57.093 36.000 0.00 0.00 0.00 2.39
3656 7693 5.769367 TCGATCAACCCTTCATACTAATCG 58.231 41.667 0.00 0.00 35.92 3.34
3661 7698 5.422214 AAGTTCGATCAACCCTTCATACT 57.578 39.130 0.00 0.00 35.28 2.12
3662 7699 6.148811 TCAAAAGTTCGATCAACCCTTCATAC 59.851 38.462 0.00 0.00 35.28 2.39
3676 7713 1.223187 GGCGTCCTTCAAAAGTTCGA 58.777 50.000 0.00 0.00 0.00 3.71
3677 7714 0.237498 GGGCGTCCTTCAAAAGTTCG 59.763 55.000 0.00 0.00 0.00 3.95
3978 8026 6.212955 ACTTGTTAGTACGCAAATTGCATTT 58.787 32.000 18.65 3.97 36.53 2.32
4015 8063 2.599645 GATCACCTCAGCGCCCACAT 62.600 60.000 2.29 0.00 0.00 3.21
4016 8064 3.315142 GATCACCTCAGCGCCCACA 62.315 63.158 2.29 0.00 0.00 4.17
4025 8074 0.960861 AGTCAGCGTCGATCACCTCA 60.961 55.000 0.00 0.00 0.00 3.86
4054 8114 4.254709 AAGAGCACAGCGCCACCA 62.255 61.111 2.29 0.00 44.04 4.17
4073 8133 4.131088 GTCCGCCTCCGAGTGGTC 62.131 72.222 4.35 0.00 38.61 4.02
4104 8164 2.586635 GTGTGACGTGGCAACCGA 60.587 61.111 4.40 0.00 34.83 4.69
4109 8169 2.166130 ATCATCCGTGTGACGTGGCA 62.166 55.000 0.00 0.00 40.58 4.92
4118 8178 0.970937 ACCTGGACGATCATCCGTGT 60.971 55.000 2.91 0.00 43.49 4.49
4336 8409 4.630644 ACATCACAGAACCATCTCAAGT 57.369 40.909 0.00 0.00 32.03 3.16
4355 8428 2.300152 TCCAGTGCAAACAAAACCAACA 59.700 40.909 0.00 0.00 0.00 3.33
4468 8548 6.548622 CCCATGCTACTACTAACCTAACTACA 59.451 42.308 0.00 0.00 0.00 2.74
4552 8632 2.103601 AGTAGCGCGTATTTTACCCCAT 59.896 45.455 8.43 0.00 0.00 4.00
4791 8878 2.025037 TCTTACCCCATTCTTGCTGCAT 60.025 45.455 1.84 0.00 0.00 3.96
4852 8939 3.706086 ACCAAATAGATCAACCCATTGCC 59.294 43.478 0.00 0.00 35.63 4.52
4896 8983 2.813754 CAGAGCATCGACCCAAAGAAAA 59.186 45.455 0.00 0.00 42.67 2.29
5190 9277 8.230472 AGCTTACAAATTCCTCCATAATTCAG 57.770 34.615 0.00 0.00 0.00 3.02
5407 9509 3.511934 ACTCTACGCTCTGAATTTGTCCT 59.488 43.478 0.00 0.00 0.00 3.85
5410 9512 3.258372 TGGACTCTACGCTCTGAATTTGT 59.742 43.478 0.00 0.00 0.00 2.83
5429 9531 2.231716 TAGTCTAGCCTGCACTTGGA 57.768 50.000 0.00 0.00 0.00 3.53
5668 9812 3.054139 AGAGCTGAGGCACATTTTCCATA 60.054 43.478 0.00 0.00 41.70 2.74
5703 9847 5.540337 TGTTCATTTATTTTGGCACCAGGTA 59.460 36.000 0.00 0.00 0.00 3.08
5831 9979 1.967066 CCTAAATGCCACAAACCCACA 59.033 47.619 0.00 0.00 0.00 4.17
5887 10035 4.325344 CCTTCCTTCCCTAACCATGTCAAT 60.325 45.833 0.00 0.00 0.00 2.57
6142 10301 5.455392 TCATCAATGAAAATCAGAGGGGA 57.545 39.130 0.00 0.00 33.08 4.81
6160 10319 5.067805 AGTTGGAGAACTTGTGGTTTTCATC 59.932 40.000 0.00 0.00 39.56 2.92


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

AutoCloner maintained by Alex Coulton.