Multiple sequence alignment - TraesCS2D01G000600

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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 TraesCS2D01G000600 chr2D 100.000 9437 0 0 1 9437 287007 277571 0.000000e+00 17427.0
1 TraesCS2D01G000600 chr2D 84.225 355 23 21 1872 2213 616018335 616018001 1.980000e-81 315.0
2 TraesCS2D01G000600 chr2D 82.379 227 34 6 348 569 76633540 76633315 9.670000e-45 193.0
3 TraesCS2D01G000600 chr2D 94.286 70 4 0 1606 1675 616018504 616018435 3.600000e-19 108.0
4 TraesCS2D01G000600 chr2A 95.971 6677 84 41 957 7559 249781 256346 0.000000e+00 10669.0
5 TraesCS2D01G000600 chr2A 92.593 1242 51 19 7510 8731 256353 257573 0.000000e+00 1746.0
6 TraesCS2D01G000600 chr2A 96.607 943 24 4 1 936 245519 246460 0.000000e+00 1557.0
7 TraesCS2D01G000600 chr2A 86.957 667 56 16 8792 9435 257608 258266 0.000000e+00 721.0
8 TraesCS2D01G000600 chr2A 83.750 240 33 6 1 237 472431205 472431441 1.230000e-53 222.0
9 TraesCS2D01G000600 chr2A 100.000 28 0 0 1857 1884 616202872 616202899 1.700000e-02 52.8
10 TraesCS2D01G000600 chr2B 89.875 2084 113 34 4464 6489 11086370 11084327 0.000000e+00 2590.0
11 TraesCS2D01G000600 chr2B 94.891 1233 13 6 6488 7703 11084203 11083004 0.000000e+00 1882.0
12 TraesCS2D01G000600 chr2B 85.477 964 65 31 2590 3522 11088619 11087700 0.000000e+00 935.0
13 TraesCS2D01G000600 chr2B 89.333 450 24 13 3635 4062 11087683 11087236 2.320000e-150 544.0
14 TraesCS2D01G000600 chr2B 83.877 552 42 29 7731 8252 11082919 11082385 5.120000e-132 483.0
15 TraesCS2D01G000600 chr2B 90.778 347 18 4 4072 4415 11087083 11086748 1.450000e-122 451.0
16 TraesCS2D01G000600 chr2B 82.773 476 34 24 1770 2213 11089526 11089067 1.920000e-101 381.0
17 TraesCS2D01G000600 chr2B 87.162 296 33 3 9143 9437 11080879 11080588 1.960000e-86 331.0
18 TraesCS2D01G000600 chr2B 87.442 215 20 4 8522 8732 11081081 11080870 3.410000e-59 241.0
19 TraesCS2D01G000600 chr2B 81.858 226 31 7 357 574 402717402 402717179 2.090000e-41 182.0
20 TraesCS2D01G000600 chr2B 83.230 161 17 7 8271 8430 11082284 11082133 1.280000e-28 139.0
21 TraesCS2D01G000600 chr3B 94.426 1525 66 11 2895 4414 1797390 1795880 0.000000e+00 2327.0
22 TraesCS2D01G000600 chr3B 92.740 730 26 5 4848 5551 1792134 1791406 0.000000e+00 1029.0
23 TraesCS2D01G000600 chr3B 89.959 727 41 20 2183 2892 1798593 1797882 0.000000e+00 909.0
24 TraesCS2D01G000600 chr3B 94.945 455 20 1 4414 4868 1795853 1795402 0.000000e+00 710.0
25 TraesCS2D01G000600 chr3B 87.535 361 33 5 8793 9144 42738818 42739175 3.170000e-109 407.0
26 TraesCS2D01G000600 chr3B 83.258 442 53 17 3318 3749 778414991 778415421 4.130000e-103 387.0
27 TraesCS2D01G000600 chr3B 77.961 608 110 18 2992 3587 44660961 44660366 9.010000e-95 359.0
28 TraesCS2D01G000600 chr3B 77.759 607 114 13 2992 3587 44945890 44946486 4.190000e-93 353.0
29 TraesCS2D01G000600 chr3B 77.430 607 116 14 2992 3587 44741448 44740852 9.070000e-90 342.0
30 TraesCS2D01G000600 chr3B 81.633 343 51 7 2602 2937 44393382 44393045 3.360000e-69 274.0
31 TraesCS2D01G000600 chr3B 79.300 343 58 8 2602 2937 44936701 44937037 2.650000e-55 228.0
32 TraesCS2D01G000600 chr3B 79.300 343 53 9 2602 2937 44662059 44661728 3.430000e-54 224.0
33 TraesCS2D01G000600 chr3B 74.584 421 79 19 4494 4895 44653093 44652682 9.810000e-35 159.0
34 TraesCS2D01G000600 chr3B 75.424 354 51 21 241 574 659714932 659715269 1.280000e-28 139.0
35 TraesCS2D01G000600 chr3B 77.586 232 44 5 4494 4718 44645775 44645545 5.950000e-27 134.0
36 TraesCS2D01G000600 chr3B 83.486 109 14 4 1884 1990 44934421 44934527 2.170000e-16 99.0
37 TraesCS2D01G000600 chr5D 82.435 575 80 16 5206 5766 285655047 285655614 5.120000e-132 483.0
38 TraesCS2D01G000600 chr5D 77.680 681 125 21 2992 3660 285651307 285651972 3.200000e-104 390.0
39 TraesCS2D01G000600 chr5D 82.732 388 47 8 3694 4062 285652471 285652857 2.540000e-85 327.0
40 TraesCS2D01G000600 chr5D 81.871 342 50 8 2603 2937 285650288 285650624 2.600000e-70 278.0
41 TraesCS2D01G000600 chr5D 80.106 377 50 14 5828 6190 285656633 285656998 3.380000e-64 257.0
42 TraesCS2D01G000600 chr5D 76.858 471 79 20 4494 4946 285653899 285654357 1.220000e-58 239.0
43 TraesCS2D01G000600 chr5D 92.517 147 10 1 1872 2018 531280312 531280457 9.600000e-50 209.0
44 TraesCS2D01G000600 chr5D 78.994 338 37 19 6608 6945 285657222 285657525 5.780000e-47 200.0
45 TraesCS2D01G000600 chr5D 79.130 230 39 6 348 574 327461730 327461953 5.900000e-32 150.0
46 TraesCS2D01G000600 chr5D 94.118 68 4 0 2117 2184 285648285 285648352 4.660000e-18 104.0
47 TraesCS2D01G000600 chr5A 82.261 575 81 16 5206 5766 377922098 377922665 2.380000e-130 477.0
48 TraesCS2D01G000600 chr5A 85.011 447 50 11 3308 3745 436604575 436605013 1.130000e-118 438.0
49 TraesCS2D01G000600 chr5A 87.606 355 38 5 8792 9144 499056067 499056417 3.170000e-109 407.0
50 TraesCS2D01G000600 chr5A 77.353 680 127 21 2992 3659 377918362 377919026 2.490000e-100 377.0
51 TraesCS2D01G000600 chr5A 82.732 388 47 8 3694 4062 377919525 377919911 2.540000e-85 327.0
52 TraesCS2D01G000600 chr5A 79.946 369 49 14 5828 6182 377923709 377924066 2.040000e-61 248.0
53 TraesCS2D01G000600 chr5A 76.824 466 77 21 4500 4946 377920957 377921410 5.700000e-57 233.0
54 TraesCS2D01G000600 chr5A 86.127 173 21 2 6608 6780 377924298 377924467 5.820000e-42 183.0
55 TraesCS2D01G000600 chr5A 80.631 222 31 8 348 564 429429288 429429074 2.730000e-35 161.0
56 TraesCS2D01G000600 chr5A 94.118 68 4 0 2117 2184 377915325 377915392 4.660000e-18 104.0
57 TraesCS2D01G000600 chr5B 81.597 576 82 19 5206 5766 323865478 323866044 1.120000e-123 455.0
58 TraesCS2D01G000600 chr5B 87.989 358 28 8 8796 9144 664879977 664879626 8.820000e-110 409.0
59 TraesCS2D01G000600 chr5B 78.418 607 110 16 2992 3587 323861763 323862359 8.950000e-100 375.0
60 TraesCS2D01G000600 chr5B 82.732 388 46 11 3694 4062 323862866 323863251 9.140000e-85 326.0
61 TraesCS2D01G000600 chr5B 80.052 381 58 10 2564 2937 323860634 323861003 5.620000e-67 267.0
62 TraesCS2D01G000600 chr5B 80.105 382 51 14 5823 6190 323867165 323867535 2.610000e-65 261.0
63 TraesCS2D01G000600 chr5B 76.809 470 78 20 4494 4946 323864312 323864767 1.580000e-57 235.0
64 TraesCS2D01G000600 chr5B 75.657 571 64 38 6414 6945 323867611 323868145 2.060000e-51 215.0
65 TraesCS2D01G000600 chr5B 81.308 214 33 5 365 573 145814584 145814795 5.860000e-37 167.0
66 TraesCS2D01G000600 chr6A 85.301 449 45 16 3308 3745 315405536 315405974 2.420000e-120 444.0
67 TraesCS2D01G000600 chr6A 77.871 357 48 22 241 569 375092328 375092681 9.670000e-45 193.0
68 TraesCS2D01G000600 chr6A 75.676 333 49 15 241 543 532233142 532233472 4.600000e-28 137.0
69 TraesCS2D01G000600 chr1D 89.014 355 33 5 8793 9144 469388600 469388249 1.460000e-117 435.0
70 TraesCS2D01G000600 chr1D 76.744 344 59 11 242 565 383726625 383726967 1.260000e-38 172.0
71 TraesCS2D01G000600 chrUn 80.870 575 88 16 5206 5766 292664585 292665151 5.230000e-117 433.0
72 TraesCS2D01G000600 chrUn 80.870 575 88 16 5206 5766 292670059 292670625 5.230000e-117 433.0
73 TraesCS2D01G000600 chrUn 80.870 575 88 16 5206 5766 350312916 350313482 5.230000e-117 433.0
74 TraesCS2D01G000600 chrUn 81.299 385 50 12 3697 4062 67405300 67404919 9.270000e-75 292.0
75 TraesCS2D01G000600 chrUn 79.843 382 52 14 5823 6190 292666147 292666517 1.220000e-63 255.0
76 TraesCS2D01G000600 chrUn 79.843 382 52 14 5823 6190 292671621 292671991 1.220000e-63 255.0
77 TraesCS2D01G000600 chrUn 79.843 382 52 14 5823 6190 350314478 350314848 1.220000e-63 255.0
78 TraesCS2D01G000600 chrUn 80.588 340 50 12 5462 5790 11867021 11866687 2.040000e-61 248.0
79 TraesCS2D01G000600 chrUn 76.522 460 79 18 4504 4946 67403860 67403413 3.430000e-54 224.0
80 TraesCS2D01G000600 chrUn 75.826 575 63 39 6411 6945 292666588 292667126 1.230000e-53 222.0
81 TraesCS2D01G000600 chrUn 75.652 575 64 38 6411 6945 292672062 292672600 5.740000e-52 217.0
82 TraesCS2D01G000600 chrUn 77.561 410 46 22 6411 6780 476671087 476671490 1.240000e-48 206.0
83 TraesCS2D01G000600 chrUn 88.298 94 11 0 6852 6945 291550555 291550648 7.750000e-21 113.0
84 TraesCS2D01G000600 chrUn 88.298 94 11 0 6852 6945 291556168 291556261 7.750000e-21 113.0
85 TraesCS2D01G000600 chrUn 88.298 94 11 0 6852 6945 330833141 330833048 7.750000e-21 113.0
86 TraesCS2D01G000600 chrUn 84.000 100 14 2 1922 2020 67413842 67413744 2.810000e-15 95.3
87 TraesCS2D01G000600 chr4D 83.174 523 39 26 1872 2369 320589563 320590061 5.230000e-117 433.0
88 TraesCS2D01G000600 chr4D 84.583 240 34 3 1 238 443202298 443202060 1.580000e-57 235.0
89 TraesCS2D01G000600 chr4D 90.217 184 13 3 1872 2055 507397629 507397807 1.580000e-57 235.0
90 TraesCS2D01G000600 chr4D 83.613 238 38 1 2 238 368421132 368421369 1.230000e-53 222.0
91 TraesCS2D01G000600 chr4D 77.364 349 62 12 311 647 368421459 368421802 3.480000e-44 191.0
92 TraesCS2D01G000600 chr4D 92.537 67 5 0 1606 1672 320589396 320589462 7.800000e-16 97.1
93 TraesCS2D01G000600 chr4D 92.537 67 5 0 1606 1672 507397464 507397530 7.800000e-16 97.1
94 TraesCS2D01G000600 chr4B 84.598 448 50 13 3308 3745 633179873 633179435 2.440000e-115 427.0
95 TraesCS2D01G000600 chr4B 84.615 325 21 19 1872 2183 419681145 419680837 7.170000e-76 296.0
96 TraesCS2D01G000600 chr4B 92.857 70 5 0 1606 1675 419681315 419681246 1.680000e-17 102.0
97 TraesCS2D01G000600 chr7D 89.318 337 32 4 8809 9144 607049223 607048890 4.080000e-113 420.0
98 TraesCS2D01G000600 chr7D 84.362 243 35 3 1 242 228540091 228539851 1.580000e-57 235.0
99 TraesCS2D01G000600 chr3A 88.418 354 33 6 8792 9144 716129763 716130109 4.080000e-113 420.0
100 TraesCS2D01G000600 chr6D 88.757 338 33 5 8809 9144 28655220 28655554 8.820000e-110 409.0
101 TraesCS2D01G000600 chr6D 76.744 301 39 17 241 513 265212499 265212796 1.280000e-28 139.0
102 TraesCS2D01G000600 chr7A 87.079 356 40 5 8792 9144 64475077 64474725 1.910000e-106 398.0
103 TraesCS2D01G000600 chr7A 79.630 378 42 19 3308 3660 512247061 512247428 1.220000e-58 239.0
104 TraesCS2D01G000600 chr7A 81.818 220 32 6 3420 3636 47400123 47400337 2.710000e-40 178.0
105 TraesCS2D01G000600 chr1B 87.288 354 35 8 8792 9144 278613526 278613182 6.870000e-106 396.0
106 TraesCS2D01G000600 chr1B 82.579 442 55 15 3318 3749 10137945 10137516 4.160000e-98 370.0
107 TraesCS2D01G000600 chr1B 83.898 236 31 5 7 238 434758232 434758000 1.600000e-52 219.0
108 TraesCS2D01G000600 chr1B 95.714 70 3 0 1606 1675 6237067 6236998 7.750000e-21 113.0
109 TraesCS2D01G000600 chr1B 95.714 70 3 0 1606 1675 7483013 7482944 7.750000e-21 113.0
110 TraesCS2D01G000600 chr1A 83.102 432 56 13 3326 3749 578007442 578007020 2.490000e-100 377.0
111 TraesCS2D01G000600 chr1A 82.703 185 27 5 384 565 87247476 87247658 9.810000e-35 159.0
112 TraesCS2D01G000600 chr4A 75.399 626 90 26 1 569 562415940 562416558 2.630000e-60 244.0
113 TraesCS2D01G000600 chr4A 85.345 232 33 1 8 238 138432555 138432786 1.220000e-58 239.0
114 TraesCS2D01G000600 chr3D 84.100 239 36 2 1 238 488570958 488571195 7.370000e-56 230.0
115 TraesCS2D01G000600 chr3D 83.951 243 33 6 1 238 104687558 104687799 2.650000e-55 228.0
116 TraesCS2D01G000600 chr3D 88.608 79 6 3 244 321 348938225 348938301 1.010000e-14 93.5
117 TraesCS2D01G000600 chr6B 77.871 357 46 20 241 569 412135188 412134837 3.480000e-44 191.0


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 TraesCS2D01G000600 chr2D 277571 287007 9436 True 17427.000000 17427 100.000000 1 9437 1 chr2D.!!$R1 9436
1 TraesCS2D01G000600 chr2D 616018001 616018504 503 True 211.500000 315 89.255500 1606 2213 2 chr2D.!!$R3 607
2 TraesCS2D01G000600 chr2A 245519 258266 12747 False 3673.250000 10669 93.032000 1 9435 4 chr2A.!!$F3 9434
3 TraesCS2D01G000600 chr2B 11080588 11089526 8938 True 797.700000 2590 87.483800 1770 9437 10 chr2B.!!$R2 7667
4 TraesCS2D01G000600 chr3B 1791406 1798593 7187 True 1243.750000 2327 93.017500 2183 5551 4 chr3B.!!$R5 3368
5 TraesCS2D01G000600 chr3B 44945890 44946486 596 False 353.000000 353 77.759000 2992 3587 1 chr3B.!!$F2 595
6 TraesCS2D01G000600 chr3B 44740852 44741448 596 True 342.000000 342 77.430000 2992 3587 1 chr3B.!!$R4 595
7 TraesCS2D01G000600 chr3B 44660366 44662059 1693 True 291.500000 359 78.630500 2602 3587 2 chr3B.!!$R6 985
8 TraesCS2D01G000600 chr5D 285648285 285657525 9240 False 284.750000 483 81.849250 2117 6945 8 chr5D.!!$F3 4828
9 TraesCS2D01G000600 chr5A 377915325 377924467 9142 False 278.428571 477 82.765857 2117 6780 7 chr5A.!!$F3 4663
10 TraesCS2D01G000600 chr5B 323860634 323868145 7511 False 304.857143 455 79.338571 2564 6945 7 chr5B.!!$F2 4381
11 TraesCS2D01G000600 chrUn 350312916 350314848 1932 False 344.000000 433 80.356500 5206 6190 2 chrUn.!!$F5 984
12 TraesCS2D01G000600 chrUn 292664585 292672600 8015 False 302.500000 433 78.817333 5206 6945 6 chrUn.!!$F4 1739
13 TraesCS2D01G000600 chrUn 67403413 67405300 1887 True 258.000000 292 78.910500 3697 4946 2 chrUn.!!$R4 1249
14 TraesCS2D01G000600 chr4D 320589396 320590061 665 False 265.050000 433 87.855500 1606 2369 2 chr4D.!!$F1 763
15 TraesCS2D01G000600 chr4D 368421132 368421802 670 False 206.500000 222 80.488500 2 647 2 chr4D.!!$F2 645
16 TraesCS2D01G000600 chr4A 562415940 562416558 618 False 244.000000 244 75.399000 1 569 1 chr4A.!!$F2 568

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
621 685 0.680061 AGGTCGTGGTTTCAGTCCTC 59.320 55.000 0.0 0.0 0.00 3.71 F
1281 4667 0.391130 TGATCCAACCCGAAGCGAAG 60.391 55.000 0.0 0.0 0.00 3.79 F
1313 4699 0.394216 CAGGCGGGATTGATTGGTGA 60.394 55.000 0.0 0.0 0.00 4.02 F
1314 4700 0.552848 AGGCGGGATTGATTGGTGAT 59.447 50.000 0.0 0.0 0.00 3.06 F
1599 5011 1.453155 ATGAATGGTCTGTCGCAACC 58.547 50.000 0.0 0.0 36.03 3.77 F
3036 9421 1.529226 TTGTGGGGTTATTGAGTGCG 58.471 50.000 0.0 0.0 0.00 5.34 F
7002 25158 1.270625 TGGAACTAACAAGAGCACCGG 60.271 52.381 0.0 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1590 5002 0.533085 TGAATTCCACGGTTGCGACA 60.533 50.000 6.39 0.0 0.00 4.35 R
2085 5514 7.306515 CCATTGTATTGTTGTAGTTGTTGTTGC 60.307 37.037 0.00 0.0 0.00 4.17 R
3036 9421 8.903723 GCATCACGTAAATGATAGTAAGTAGTC 58.096 37.037 12.85 0.0 37.20 2.59 R
5275 22111 4.753107 TCAAACTTTACCTTGTAGCTTCCG 59.247 41.667 0.00 0.0 0.00 4.30 R
5777 22631 7.436376 TCAGAACACTCAGCTCATTTATTATCG 59.564 37.037 0.00 0.0 0.00 2.92 R
7004 25160 0.897863 TTTTGGATGCCCGGTCTTGG 60.898 55.000 0.00 0.0 34.29 3.61 R
8766 28135 0.179073 GCATAGGCACAGTGACGGAT 60.179 55.000 4.15 0.0 40.72 4.18 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
621 685 0.680061 AGGTCGTGGTTTCAGTCCTC 59.320 55.000 0.00 0.00 0.00 3.71
650 714 1.762222 GATCGTTTGTGGGCGGATCG 61.762 60.000 0.00 0.00 0.00 3.69
664 728 2.805845 CGGATCGTTCATCTACGGTTT 58.194 47.619 0.00 0.00 41.67 3.27
726 792 5.074584 AGCTGCTACTTGGAGTTAGTAAC 57.925 43.478 0.00 4.78 36.43 2.50
745 811 7.040473 AGTAACGATCGTTATCCTCATCTTT 57.960 36.000 35.52 13.65 41.77 2.52
936 1007 4.646040 GGTGGGCGGGTTTTATTTTACTAT 59.354 41.667 0.00 0.00 0.00 2.12
937 1008 5.827267 GGTGGGCGGGTTTTATTTTACTATA 59.173 40.000 0.00 0.00 0.00 1.31
938 1009 6.320926 GGTGGGCGGGTTTTATTTTACTATAA 59.679 38.462 0.00 0.00 0.00 0.98
940 1011 6.039605 TGGGCGGGTTTTATTTTACTATAAGC 59.960 38.462 0.00 0.00 0.00 3.09
941 1012 6.039605 GGGCGGGTTTTATTTTACTATAAGCA 59.960 38.462 0.00 0.00 0.00 3.91
942 1013 7.136772 GGCGGGTTTTATTTTACTATAAGCAG 58.863 38.462 0.00 0.00 0.00 4.24
943 1014 6.635641 GCGGGTTTTATTTTACTATAAGCAGC 59.364 38.462 0.00 0.00 29.95 5.25
944 1015 7.680113 GCGGGTTTTATTTTACTATAAGCAGCA 60.680 37.037 0.00 0.00 34.29 4.41
945 1016 8.185505 CGGGTTTTATTTTACTATAAGCAGCAA 58.814 33.333 0.00 0.00 0.00 3.91
957 1028 8.930846 ACTATAAGCAGCAATATGAATCCTTT 57.069 30.769 0.00 0.00 0.00 3.11
960 1031 8.882415 ATAAGCAGCAATATGAATCCTTTTTG 57.118 30.769 0.00 0.00 0.00 2.44
1014 4385 3.530265 ACAAAACACCACTCACTCGTA 57.470 42.857 0.00 0.00 0.00 3.43
1041 4412 2.909662 CTCTTCTTGTTCTTCCTCCCCT 59.090 50.000 0.00 0.00 0.00 4.79
1042 4413 2.907042 TCTTCTTGTTCTTCCTCCCCTC 59.093 50.000 0.00 0.00 0.00 4.30
1043 4414 1.657804 TCTTGTTCTTCCTCCCCTCC 58.342 55.000 0.00 0.00 0.00 4.30
1084 4455 1.352083 TCCCTTCCTTCCTGTGTCTG 58.648 55.000 0.00 0.00 0.00 3.51
1273 4659 1.740025 GCTTCTTCTTGATCCAACCCG 59.260 52.381 0.00 0.00 0.00 5.28
1281 4667 0.391130 TGATCCAACCCGAAGCGAAG 60.391 55.000 0.00 0.00 0.00 3.79
1311 4697 1.076777 CCAGGCGGGATTGATTGGT 60.077 57.895 0.00 0.00 40.01 3.67
1312 4698 1.386525 CCAGGCGGGATTGATTGGTG 61.387 60.000 0.00 0.00 40.01 4.17
1313 4699 0.394216 CAGGCGGGATTGATTGGTGA 60.394 55.000 0.00 0.00 0.00 4.02
1314 4700 0.552848 AGGCGGGATTGATTGGTGAT 59.447 50.000 0.00 0.00 0.00 3.06
1315 4701 1.774254 AGGCGGGATTGATTGGTGATA 59.226 47.619 0.00 0.00 0.00 2.15
1316 4702 1.880027 GGCGGGATTGATTGGTGATAC 59.120 52.381 0.00 0.00 0.00 2.24
1321 4707 4.864806 CGGGATTGATTGGTGATACGATAG 59.135 45.833 0.00 0.00 46.19 2.08
1399 4789 9.784531 TCTACTCTACTCTACTCTACTCTACTC 57.215 40.741 0.00 0.00 0.00 2.59
1448 4838 2.909217 AGCTCTACTCCTTTCCTGGTT 58.091 47.619 0.00 0.00 0.00 3.67
1449 4839 4.062490 AGCTCTACTCCTTTCCTGGTTA 57.938 45.455 0.00 0.00 0.00 2.85
1450 4840 4.625963 AGCTCTACTCCTTTCCTGGTTAT 58.374 43.478 0.00 0.00 0.00 1.89
1451 4841 4.407296 AGCTCTACTCCTTTCCTGGTTATG 59.593 45.833 0.00 0.00 0.00 1.90
1452 4842 4.162509 GCTCTACTCCTTTCCTGGTTATGT 59.837 45.833 0.00 0.00 0.00 2.29
1453 4843 5.363005 GCTCTACTCCTTTCCTGGTTATGTA 59.637 44.000 0.00 0.00 0.00 2.29
1454 4844 6.042208 GCTCTACTCCTTTCCTGGTTATGTAT 59.958 42.308 0.00 0.00 0.00 2.29
1455 4845 7.361457 TCTACTCCTTTCCTGGTTATGTATG 57.639 40.000 0.00 0.00 0.00 2.39
1456 4846 6.901300 TCTACTCCTTTCCTGGTTATGTATGT 59.099 38.462 0.00 0.00 0.00 2.29
1457 4847 8.063153 TCTACTCCTTTCCTGGTTATGTATGTA 58.937 37.037 0.00 0.00 0.00 2.29
1458 4848 7.691993 ACTCCTTTCCTGGTTATGTATGTAT 57.308 36.000 0.00 0.00 0.00 2.29
1459 4849 7.509546 ACTCCTTTCCTGGTTATGTATGTATG 58.490 38.462 0.00 0.00 0.00 2.39
1590 5002 8.699130 AGAAAAGAAAACAAGAATGAATGGTCT 58.301 29.630 0.00 0.00 0.00 3.85
1596 5008 2.743664 CAAGAATGAATGGTCTGTCGCA 59.256 45.455 0.00 0.00 0.00 5.10
1599 5011 1.453155 ATGAATGGTCTGTCGCAACC 58.547 50.000 0.00 0.00 36.03 3.77
1672 5084 2.121291 TGTTATGCGGCATCTGGAAA 57.879 45.000 20.34 4.79 0.00 3.13
1675 5087 3.202906 GTTATGCGGCATCTGGAAACTA 58.797 45.455 20.34 0.00 0.00 2.24
1676 5088 2.418368 ATGCGGCATCTGGAAACTAA 57.582 45.000 10.23 0.00 0.00 2.24
1677 5089 2.192664 TGCGGCATCTGGAAACTAAA 57.807 45.000 0.00 0.00 0.00 1.85
1678 5090 2.509569 TGCGGCATCTGGAAACTAAAA 58.490 42.857 0.00 0.00 0.00 1.52
1680 5092 3.509575 TGCGGCATCTGGAAACTAAAATT 59.490 39.130 0.00 0.00 0.00 1.82
1681 5093 4.105486 GCGGCATCTGGAAACTAAAATTC 58.895 43.478 0.00 0.00 0.00 2.17
1682 5094 4.142381 GCGGCATCTGGAAACTAAAATTCT 60.142 41.667 0.00 0.00 0.00 2.40
1683 5095 5.573146 CGGCATCTGGAAACTAAAATTCTC 58.427 41.667 0.00 0.00 0.00 2.87
1727 5139 3.380954 TCTCTTCTCTGATAGCAGCACAG 59.619 47.826 2.24 1.44 42.01 3.66
1832 5246 8.383318 TCTAGATTCCTCTTTTGTTTGACTTG 57.617 34.615 0.00 0.00 32.66 3.16
2085 5514 7.010738 AGCTGTTTTCATTTCATTTCACACAAG 59.989 33.333 0.00 0.00 0.00 3.16
2213 5721 9.305555 CTCATTCATTCAGGTCCCATATTTATT 57.694 33.333 0.00 0.00 0.00 1.40
2218 5726 9.739276 TCATTCAGGTCCCATATTTATTATGTC 57.261 33.333 0.00 0.00 36.69 3.06
2223 5731 9.436957 CAGGTCCCATATTTATTATGTCAGTAC 57.563 37.037 0.00 0.00 36.69 2.73
3036 9421 1.529226 TTGTGGGGTTATTGAGTGCG 58.471 50.000 0.00 0.00 0.00 5.34
3872 10744 5.818678 AGGGCAACGGATTATATTGTAGA 57.181 39.130 0.00 0.00 37.60 2.59
3873 10745 5.548406 AGGGCAACGGATTATATTGTAGAC 58.452 41.667 0.00 0.00 37.60 2.59
3874 10746 4.694037 GGGCAACGGATTATATTGTAGACC 59.306 45.833 0.00 0.00 37.60 3.85
5275 22111 2.135139 GCCTTTTGCTTGGTAAAGTGC 58.865 47.619 0.00 0.00 35.69 4.40
5777 22631 5.880332 TGATACAGAACTTGCAGAATTACCC 59.120 40.000 0.00 0.00 0.00 3.69
7000 25156 4.575885 TGTATGGAACTAACAAGAGCACC 58.424 43.478 0.00 0.00 0.00 5.01
7001 25157 2.163818 TGGAACTAACAAGAGCACCG 57.836 50.000 0.00 0.00 0.00 4.94
7002 25158 1.270625 TGGAACTAACAAGAGCACCGG 60.271 52.381 0.00 0.00 0.00 5.28
7003 25159 0.796927 GAACTAACAAGAGCACCGGC 59.203 55.000 0.00 0.00 41.61 6.13
7004 25160 0.605589 AACTAACAAGAGCACCGGCC 60.606 55.000 0.00 0.00 42.56 6.13
7005 25161 1.745489 CTAACAAGAGCACCGGCCC 60.745 63.158 0.00 0.00 42.56 5.80
7006 25162 2.463589 CTAACAAGAGCACCGGCCCA 62.464 60.000 0.00 0.00 42.56 5.36
7007 25163 2.058125 TAACAAGAGCACCGGCCCAA 62.058 55.000 0.00 0.00 42.56 4.12
7008 25164 3.058160 CAAGAGCACCGGCCCAAG 61.058 66.667 0.00 0.00 42.56 3.61
7009 25165 3.249189 AAGAGCACCGGCCCAAGA 61.249 61.111 0.00 0.00 42.56 3.02
7010 25166 3.553095 AAGAGCACCGGCCCAAGAC 62.553 63.158 0.00 0.00 42.56 3.01
7373 25541 5.141568 GCTGTTTTGTTTGCATGCATAAAG 58.858 37.500 23.37 12.12 0.00 1.85
7374 25542 5.050227 GCTGTTTTGTTTGCATGCATAAAGA 60.050 36.000 23.37 15.67 0.00 2.52
7375 25543 6.511444 GCTGTTTTGTTTGCATGCATAAAGAA 60.511 34.615 23.37 15.47 0.00 2.52
7376 25544 7.493743 TGTTTTGTTTGCATGCATAAAGAAT 57.506 28.000 23.37 0.00 0.00 2.40
7377 25545 7.928103 TGTTTTGTTTGCATGCATAAAGAATT 58.072 26.923 23.37 0.00 0.00 2.17
7378 25546 8.404000 TGTTTTGTTTGCATGCATAAAGAATTT 58.596 25.926 23.37 0.00 43.42 1.82
7379 25547 9.235537 GTTTTGTTTGCATGCATAAAGAATTTT 57.764 25.926 23.37 0.00 40.09 1.82
7380 25548 9.798994 TTTTGTTTGCATGCATAAAGAATTTTT 57.201 22.222 23.37 0.00 40.09 1.94
7508 25681 3.055167 AGGGTTTTTATGCCTGCATTTCC 60.055 43.478 10.27 6.17 37.82 3.13
7859 26146 3.417101 TCGGAAACAAAGGTATGCATGT 58.583 40.909 10.16 0.00 0.00 3.21
7904 26191 1.472188 GGTACTCGCTGAACCCTACT 58.528 55.000 0.00 0.00 0.00 2.57
7906 26193 2.416972 GGTACTCGCTGAACCCTACTTG 60.417 54.545 0.00 0.00 0.00 3.16
7907 26194 1.629043 ACTCGCTGAACCCTACTTGA 58.371 50.000 0.00 0.00 0.00 3.02
7908 26195 2.180276 ACTCGCTGAACCCTACTTGAT 58.820 47.619 0.00 0.00 0.00 2.57
7909 26196 2.093973 ACTCGCTGAACCCTACTTGATG 60.094 50.000 0.00 0.00 0.00 3.07
7910 26197 1.009829 CGCTGAACCCTACTTGATGC 58.990 55.000 0.00 0.00 0.00 3.91
7923 26210 0.602638 TTGATGCGCCTCGTGTCTTT 60.603 50.000 4.18 0.00 0.00 2.52
8237 26564 3.254903 GGATACCAACCCAACAACAAGAC 59.745 47.826 0.00 0.00 0.00 3.01
8248 26643 5.460748 CCCAACAACAAGACGTTTTAATTCC 59.539 40.000 0.00 0.00 34.86 3.01
8249 26644 6.037098 CCAACAACAAGACGTTTTAATTCCA 58.963 36.000 0.00 0.00 34.86 3.53
8251 26646 7.253950 CCAACAACAAGACGTTTTAATTCCAAG 60.254 37.037 0.00 0.00 34.86 3.61
8252 26647 7.090953 ACAACAAGACGTTTTAATTCCAAGA 57.909 32.000 0.00 0.00 34.86 3.02
8253 26648 7.540299 ACAACAAGACGTTTTAATTCCAAGAA 58.460 30.769 0.00 0.00 34.86 2.52
8486 27432 3.846335 GGCGCTTTTCTTTTATTGACTCG 59.154 43.478 7.64 0.00 0.00 4.18
8502 27448 5.268118 TGACTCGAGATGTAGCATCAAAT 57.732 39.130 21.68 0.00 0.00 2.32
8503 27449 5.284864 TGACTCGAGATGTAGCATCAAATC 58.715 41.667 21.68 0.94 0.00 2.17
8504 27450 5.163519 TGACTCGAGATGTAGCATCAAATCA 60.164 40.000 21.68 3.87 0.00 2.57
8506 27452 6.108687 ACTCGAGATGTAGCATCAAATCAAA 58.891 36.000 21.68 0.00 0.00 2.69
8508 27454 7.042187 ACTCGAGATGTAGCATCAAATCAAATC 60.042 37.037 21.68 0.00 0.00 2.17
8511 27457 7.911727 CGAGATGTAGCATCAAATCAAATCAAA 59.088 33.333 11.12 0.00 0.00 2.69
8512 27458 9.745880 GAGATGTAGCATCAAATCAAATCAAAT 57.254 29.630 11.12 0.00 0.00 2.32
8551 27917 1.657556 CACGCGGTCAAACCCAAAT 59.342 52.632 12.47 0.00 33.75 2.32
8563 27929 7.921745 CGGTCAAACCCAAATAAAAAGAAAGTA 59.078 33.333 0.00 0.00 33.75 2.24
8601 27967 3.058293 CGGCAACACAACAGTCATATGTT 60.058 43.478 1.90 0.00 44.12 2.71
8735 28104 8.226543 TCAAATTAGAAAAATGTTCATCACGC 57.773 30.769 0.00 0.00 0.00 5.34
8736 28105 6.853279 AATTAGAAAAATGTTCATCACGCG 57.147 33.333 3.53 3.53 0.00 6.01
8737 28106 2.584791 AGAAAAATGTTCATCACGCGC 58.415 42.857 5.73 0.00 0.00 6.86
8739 28108 0.595588 AAAATGTTCATCACGCGCCA 59.404 45.000 5.73 0.00 0.00 5.69
8744 28113 1.807142 TGTTCATCACGCGCCAAATTA 59.193 42.857 5.73 0.00 0.00 1.40
8746 28115 3.035942 GTTCATCACGCGCCAAATTATC 58.964 45.455 5.73 0.00 0.00 1.75
8747 28116 2.560504 TCATCACGCGCCAAATTATCT 58.439 42.857 5.73 0.00 0.00 1.98
8748 28117 3.723260 TCATCACGCGCCAAATTATCTA 58.277 40.909 5.73 0.00 0.00 1.98
8751 28120 1.937223 CACGCGCCAAATTATCTACCA 59.063 47.619 5.73 0.00 0.00 3.25
8752 28121 2.548057 CACGCGCCAAATTATCTACCAT 59.452 45.455 5.73 0.00 0.00 3.55
8753 28122 2.548057 ACGCGCCAAATTATCTACCATG 59.452 45.455 5.73 0.00 0.00 3.66
8754 28123 2.548057 CGCGCCAAATTATCTACCATGT 59.452 45.455 0.00 0.00 0.00 3.21
8755 28124 3.743911 CGCGCCAAATTATCTACCATGTA 59.256 43.478 0.00 0.00 0.00 2.29
8756 28125 4.212425 CGCGCCAAATTATCTACCATGTAA 59.788 41.667 0.00 0.00 0.00 2.41
8757 28126 5.277586 CGCGCCAAATTATCTACCATGTAAA 60.278 40.000 0.00 0.00 0.00 2.01
8758 28127 6.500041 GCGCCAAATTATCTACCATGTAAAA 58.500 36.000 0.00 0.00 0.00 1.52
8759 28128 6.975772 GCGCCAAATTATCTACCATGTAAAAA 59.024 34.615 0.00 0.00 0.00 1.94
8779 28148 4.946784 AAAAGATTATCCGTCACTGTGC 57.053 40.909 2.12 0.00 0.00 4.57
8780 28149 2.604046 AGATTATCCGTCACTGTGCC 57.396 50.000 2.12 0.00 0.00 5.01
8781 28150 2.111384 AGATTATCCGTCACTGTGCCT 58.889 47.619 2.12 0.00 0.00 4.75
8782 28151 3.296854 AGATTATCCGTCACTGTGCCTA 58.703 45.455 2.12 0.00 0.00 3.93
8783 28152 3.898123 AGATTATCCGTCACTGTGCCTAT 59.102 43.478 2.12 0.00 0.00 2.57
8784 28153 3.452755 TTATCCGTCACTGTGCCTATG 57.547 47.619 2.12 0.00 0.00 2.23
8785 28154 0.179073 ATCCGTCACTGTGCCTATGC 60.179 55.000 2.12 0.00 38.26 3.14
8786 28155 1.815421 CCGTCACTGTGCCTATGCC 60.815 63.158 2.12 0.00 36.33 4.40
8787 28156 1.219124 CGTCACTGTGCCTATGCCT 59.781 57.895 2.12 0.00 36.33 4.75
8788 28157 0.459899 CGTCACTGTGCCTATGCCTA 59.540 55.000 2.12 0.00 36.33 3.93
8789 28158 1.069204 CGTCACTGTGCCTATGCCTAT 59.931 52.381 2.12 0.00 36.33 2.57
8790 28159 2.296190 CGTCACTGTGCCTATGCCTATA 59.704 50.000 2.12 0.00 36.33 1.31
8877 28246 2.664851 CGTGAGGTGCGCTCCAAA 60.665 61.111 28.68 14.40 0.00 3.28
8881 28250 1.000274 GTGAGGTGCGCTCCAAATTTT 60.000 47.619 28.68 8.32 0.00 1.82
8948 28322 9.469807 GATTAGGTCAGAACAGTATATGAACAG 57.530 37.037 0.00 0.00 31.65 3.16
8952 28326 7.396339 AGGTCAGAACAGTATATGAACAGTACA 59.604 37.037 0.00 0.00 31.65 2.90
8968 28342 7.390996 TGAACAGTACACTTTTTAACAGACCAA 59.609 33.333 0.00 0.00 0.00 3.67
8977 28351 9.753669 CACTTTTTAACAGACCAAAAATTTGTC 57.246 29.630 5.27 0.00 34.20 3.18
8978 28352 9.719355 ACTTTTTAACAGACCAAAAATTTGTCT 57.281 25.926 4.30 4.30 34.20 3.41
9011 28385 6.407412 CCAAGAGCTACTCAGATGTCCAAATA 60.407 42.308 0.00 0.00 32.06 1.40
9036 28410 4.497473 TGAAATTTGGAACGGACATCAC 57.503 40.909 0.00 0.00 0.00 3.06
9063 28437 7.489113 GCACCAAATTATCTACCATGTCAAAAG 59.511 37.037 0.00 0.00 0.00 2.27
9064 28438 7.975616 CACCAAATTATCTACCATGTCAAAAGG 59.024 37.037 0.00 0.00 0.00 3.11
9071 28445 6.078456 TCTACCATGTCAAAAGGAATGGAT 57.922 37.500 7.50 0.00 41.84 3.41
9072 28446 6.493166 TCTACCATGTCAAAAGGAATGGATT 58.507 36.000 7.50 0.00 41.84 3.01
9073 28447 6.953520 TCTACCATGTCAAAAGGAATGGATTT 59.046 34.615 7.50 0.00 41.84 2.17
9134 28508 4.479993 GCGGGTGCAGATGAGCCT 62.480 66.667 0.00 0.00 42.15 4.58
9135 28509 3.094062 GCGGGTGCAGATGAGCCTA 62.094 63.158 0.00 0.00 42.15 3.93
9136 28510 1.068753 CGGGTGCAGATGAGCCTAG 59.931 63.158 0.00 0.00 0.00 3.02
9297 28686 0.537188 ACGCCATGGTACTTCCTCTG 59.463 55.000 14.67 0.00 37.07 3.35
9302 28691 0.978146 ATGGTACTTCCTCTGCGGCT 60.978 55.000 0.00 0.00 37.07 5.52
9365 28756 1.065928 GAGGCGGAATCGTCGTGAT 59.934 57.895 0.00 0.00 46.91 3.06
9368 28759 1.518572 GCGGAATCGTCGTGATGGT 60.519 57.895 0.00 0.00 37.39 3.55
9411 28803 1.299976 GACAAGGACCTTCGGCCAT 59.700 57.895 2.91 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 108 4.142966 CCCGATAAACTCCGAAACACTTTC 60.143 45.833 0.00 0.00 36.32 2.62
157 159 7.113437 TCATCGGAAACATTTTCCACCTATAA 58.887 34.615 16.11 0.00 38.49 0.98
361 415 2.563013 TTAGACGGGAGGAGGGGTCG 62.563 65.000 0.00 0.00 34.68 4.79
406 461 9.267084 GGCTCCAAAATTTGTTTGTTCTAATAA 57.733 29.630 4.92 0.00 0.00 1.40
588 652 3.463944 CACGACCTTTCTACTTGGTTGT 58.536 45.455 0.00 0.00 46.21 3.32
650 714 5.579904 GGAGTCCTTTAAACCGTAGATGAAC 59.420 44.000 0.41 0.00 0.00 3.18
664 728 7.767198 CGGTGTATCTTTAATTGGAGTCCTTTA 59.233 37.037 11.33 5.93 0.00 1.85
769 835 3.854286 AGAAAAACAAGTCGCACTACG 57.146 42.857 0.00 0.00 45.62 3.51
843 914 1.909532 GTTGGTGTAGATCGTTCGTCG 59.090 52.381 0.00 0.00 41.41 5.12
918 989 6.635641 GCTGCTTATAGTAAAATAAAACCCGC 59.364 38.462 0.00 0.00 0.00 6.13
936 1007 7.093377 ACCAAAAAGGATTCATATTGCTGCTTA 60.093 33.333 0.00 0.00 41.22 3.09
937 1008 6.110707 CCAAAAAGGATTCATATTGCTGCTT 58.889 36.000 0.00 0.00 41.22 3.91
938 1009 5.188359 ACCAAAAAGGATTCATATTGCTGCT 59.812 36.000 0.00 0.00 41.22 4.24
940 1011 6.870769 AGACCAAAAAGGATTCATATTGCTG 58.129 36.000 0.00 0.00 41.22 4.41
941 1012 7.486407 AAGACCAAAAAGGATTCATATTGCT 57.514 32.000 0.00 0.00 41.22 3.91
942 1013 7.064966 CCAAAGACCAAAAAGGATTCATATTGC 59.935 37.037 0.00 0.00 41.22 3.56
943 1014 8.313292 TCCAAAGACCAAAAAGGATTCATATTG 58.687 33.333 0.00 0.00 41.22 1.90
944 1015 8.434589 TCCAAAGACCAAAAAGGATTCATATT 57.565 30.769 0.00 0.00 41.22 1.28
945 1016 8.613922 ATCCAAAGACCAAAAAGGATTCATAT 57.386 30.769 0.00 0.00 41.22 1.78
946 1017 8.434589 AATCCAAAGACCAAAAAGGATTCATA 57.565 30.769 0.00 0.00 40.76 2.15
949 1020 7.498900 ACAAAATCCAAAGACCAAAAAGGATTC 59.501 33.333 0.00 0.00 43.09 2.52
950 1021 7.345691 ACAAAATCCAAAGACCAAAAAGGATT 58.654 30.769 0.00 0.00 45.11 3.01
951 1022 6.899089 ACAAAATCCAAAGACCAAAAAGGAT 58.101 32.000 0.00 0.00 41.22 3.24
952 1023 6.306643 ACAAAATCCAAAGACCAAAAAGGA 57.693 33.333 0.00 0.00 41.22 3.36
953 1024 7.389803 AAACAAAATCCAAAGACCAAAAAGG 57.610 32.000 0.00 0.00 45.67 3.11
954 1025 7.754475 CCAAAACAAAATCCAAAGACCAAAAAG 59.246 33.333 0.00 0.00 0.00 2.27
955 1026 7.448469 TCCAAAACAAAATCCAAAGACCAAAAA 59.552 29.630 0.00 0.00 0.00 1.94
956 1027 6.942576 TCCAAAACAAAATCCAAAGACCAAAA 59.057 30.769 0.00 0.00 0.00 2.44
957 1028 6.476378 TCCAAAACAAAATCCAAAGACCAAA 58.524 32.000 0.00 0.00 0.00 3.28
959 1030 5.683876 TCCAAAACAAAATCCAAAGACCA 57.316 34.783 0.00 0.00 0.00 4.02
960 1031 8.669946 TTATTCCAAAACAAAATCCAAAGACC 57.330 30.769 0.00 0.00 0.00 3.85
1014 4385 3.070302 AGGAAGAACAAGAAGAGAACGCT 59.930 43.478 0.00 0.00 0.00 5.07
1041 4412 0.556380 AGGAAGGAGGAGGAGGAGGA 60.556 60.000 0.00 0.00 0.00 3.71
1042 4413 0.341609 AAGGAAGGAGGAGGAGGAGG 59.658 60.000 0.00 0.00 0.00 4.30
1043 4414 1.691163 GGAAGGAAGGAGGAGGAGGAG 60.691 61.905 0.00 0.00 0.00 3.69
1084 4455 1.157870 CGACGAGAGAGGAGGAGAGC 61.158 65.000 0.00 0.00 0.00 4.09
1151 4527 3.303928 GGACCGCCGGATCTAGGG 61.304 72.222 11.71 0.00 0.00 3.53
1254 4636 3.334583 TCGGGTTGGATCAAGAAGAAG 57.665 47.619 0.00 0.00 0.00 2.85
1273 4659 1.225502 GTTCGCTTCGCTTCGCTTC 60.226 57.895 0.00 0.00 0.00 3.86
1296 4682 1.880027 GTATCACCAATCAATCCCGCC 59.120 52.381 0.00 0.00 0.00 6.13
1390 4780 9.669887 GTATATTAGCAGCTAAGGAGTAGAGTA 57.330 37.037 19.60 5.13 30.50 2.59
1391 4781 8.387813 AGTATATTAGCAGCTAAGGAGTAGAGT 58.612 37.037 19.60 5.55 30.50 3.24
1392 4782 8.801882 AGTATATTAGCAGCTAAGGAGTAGAG 57.198 38.462 19.60 0.00 30.50 2.43
1393 4783 9.893634 CTAGTATATTAGCAGCTAAGGAGTAGA 57.106 37.037 19.60 2.81 30.50 2.59
1394 4784 9.675464 ACTAGTATATTAGCAGCTAAGGAGTAG 57.325 37.037 19.60 20.59 29.02 2.57
1396 4786 9.452287 GTACTAGTATATTAGCAGCTAAGGAGT 57.548 37.037 19.60 15.89 29.02 3.85
1397 4787 9.675464 AGTACTAGTATATTAGCAGCTAAGGAG 57.325 37.037 19.60 11.82 29.02 3.69
1565 4977 8.758715 CAGACCATTCATTCTTGTTTTCTTTTC 58.241 33.333 0.00 0.00 0.00 2.29
1590 5002 0.533085 TGAATTCCACGGTTGCGACA 60.533 50.000 6.39 0.00 0.00 4.35
1596 5008 2.513753 TGCTGAATGAATTCCACGGTT 58.486 42.857 2.27 0.00 35.97 4.44
1599 5011 4.925054 ACATTTTGCTGAATGAATTCCACG 59.075 37.500 16.16 0.00 38.93 4.94
1675 5087 9.710900 GAAGAGAAGAGAAGAGAAGAGAATTTT 57.289 33.333 0.00 0.00 0.00 1.82
1676 5088 9.093458 AGAAGAGAAGAGAAGAGAAGAGAATTT 57.907 33.333 0.00 0.00 0.00 1.82
1677 5089 8.655935 AGAAGAGAAGAGAAGAGAAGAGAATT 57.344 34.615 0.00 0.00 0.00 2.17
1678 5090 8.112183 AGAGAAGAGAAGAGAAGAGAAGAGAAT 58.888 37.037 0.00 0.00 0.00 2.40
1680 5092 7.020827 AGAGAAGAGAAGAGAAGAGAAGAGA 57.979 40.000 0.00 0.00 0.00 3.10
1681 5093 7.609532 AGAAGAGAAGAGAAGAGAAGAGAAGAG 59.390 40.741 0.00 0.00 0.00 2.85
1682 5094 7.461749 AGAAGAGAAGAGAAGAGAAGAGAAGA 58.538 38.462 0.00 0.00 0.00 2.87
1683 5095 7.609532 AGAGAAGAGAAGAGAAGAGAAGAGAAG 59.390 40.741 0.00 0.00 0.00 2.85
1727 5139 3.866651 AGAGACATGGTTGTGTATCTGC 58.133 45.455 3.65 0.00 45.87 4.26
1871 5290 4.416738 GGTCTGGTCCTGCCCTGC 62.417 72.222 0.00 0.00 36.04 4.85
1872 5291 2.930019 TGGTCTGGTCCTGCCCTG 60.930 66.667 0.00 0.00 36.04 4.45
1873 5292 2.930562 GTGGTCTGGTCCTGCCCT 60.931 66.667 0.00 0.00 36.04 5.19
1874 5293 2.606587 ATGTGGTCTGGTCCTGCCC 61.607 63.158 6.72 0.00 36.04 5.36
1875 5294 1.377725 CATGTGGTCTGGTCCTGCC 60.378 63.158 0.00 0.00 37.90 4.85
1876 5295 0.957395 CACATGTGGTCTGGTCCTGC 60.957 60.000 18.51 0.00 0.00 4.85
1877 5296 0.957395 GCACATGTGGTCTGGTCCTG 60.957 60.000 26.55 0.00 0.00 3.86
1878 5297 1.376466 GCACATGTGGTCTGGTCCT 59.624 57.895 26.55 0.00 0.00 3.85
1879 5298 1.675641 GGCACATGTGGTCTGGTCC 60.676 63.158 26.55 13.58 0.00 4.46
1880 5299 2.034879 CGGCACATGTGGTCTGGTC 61.035 63.158 26.55 8.29 0.00 4.02
2085 5514 7.306515 CCATTGTATTGTTGTAGTTGTTGTTGC 60.307 37.037 0.00 0.00 0.00 4.17
3036 9421 8.903723 GCATCACGTAAATGATAGTAAGTAGTC 58.096 37.037 12.85 0.00 37.20 2.59
5275 22111 4.753107 TCAAACTTTACCTTGTAGCTTCCG 59.247 41.667 0.00 0.00 0.00 4.30
5777 22631 7.436376 TCAGAACACTCAGCTCATTTATTATCG 59.564 37.037 0.00 0.00 0.00 2.92
6091 24060 1.272092 CCTGGGCATCTTCAGGTGAAA 60.272 52.381 0.00 0.00 44.03 2.69
7004 25160 0.897863 TTTTGGATGCCCGGTCTTGG 60.898 55.000 0.00 0.00 34.29 3.61
7005 25161 0.965439 TTTTTGGATGCCCGGTCTTG 59.035 50.000 0.00 0.00 34.29 3.02
7006 25162 3.448469 TTTTTGGATGCCCGGTCTT 57.552 47.368 0.00 0.00 34.29 3.01
7281 25449 6.547880 TGAAACCTTGGCAGAAAACTGTATTA 59.452 34.615 0.00 0.00 0.00 0.98
7508 25681 7.589395 ACGTCATGCTAGACTAGATATCAAAG 58.411 38.462 13.91 4.61 36.38 2.77
7757 26044 0.245539 CAAGCATCTGCAACCAAGGG 59.754 55.000 4.79 0.00 45.16 3.95
7859 26146 4.800993 CCGTAAAACACTTGATTTTGCACA 59.199 37.500 0.00 0.00 32.95 4.57
7904 26191 0.602638 AAAGACACGAGGCGCATCAA 60.603 50.000 23.09 0.00 0.00 2.57
7906 26193 0.737715 AGAAAGACACGAGGCGCATC 60.738 55.000 12.96 12.96 0.00 3.91
7907 26194 1.016130 CAGAAAGACACGAGGCGCAT 61.016 55.000 10.83 0.00 0.00 4.73
7908 26195 1.664649 CAGAAAGACACGAGGCGCA 60.665 57.895 10.83 0.00 0.00 6.09
7909 26196 0.944311 TTCAGAAAGACACGAGGCGC 60.944 55.000 0.00 0.00 0.00 6.53
7910 26197 1.457303 CTTTCAGAAAGACACGAGGCG 59.543 52.381 16.92 0.00 41.02 5.52
8237 26564 9.848172 CAACATTTTCTTCTTGGAATTAAAACG 57.152 29.630 0.00 0.00 0.00 3.60
8248 26643 6.562640 CGGCAAACATCAACATTTTCTTCTTG 60.563 38.462 0.00 0.00 0.00 3.02
8249 26644 5.463061 CGGCAAACATCAACATTTTCTTCTT 59.537 36.000 0.00 0.00 0.00 2.52
8251 26646 4.150451 CCGGCAAACATCAACATTTTCTTC 59.850 41.667 0.00 0.00 0.00 2.87
8252 26647 4.057432 CCGGCAAACATCAACATTTTCTT 58.943 39.130 0.00 0.00 0.00 2.52
8253 26648 3.320541 TCCGGCAAACATCAACATTTTCT 59.679 39.130 0.00 0.00 0.00 2.52
8334 26740 8.519799 TTCAAAAGTATGGAGAGTGACTTTTT 57.480 30.769 8.47 0.00 45.30 1.94
8336 26742 7.721399 ACATTCAAAAGTATGGAGAGTGACTTT 59.279 33.333 0.00 0.00 42.45 2.66
8338 26744 6.773638 ACATTCAAAAGTATGGAGAGTGACT 58.226 36.000 0.00 0.00 0.00 3.41
8339 26745 7.440523 AACATTCAAAAGTATGGAGAGTGAC 57.559 36.000 0.00 0.00 0.00 3.67
8340 26746 9.219603 CTAAACATTCAAAAGTATGGAGAGTGA 57.780 33.333 0.00 0.00 0.00 3.41
8341 26747 9.219603 TCTAAACATTCAAAAGTATGGAGAGTG 57.780 33.333 0.00 0.00 0.00 3.51
8342 26748 9.220767 GTCTAAACATTCAAAAGTATGGAGAGT 57.779 33.333 0.00 0.00 0.00 3.24
8343 26749 9.442047 AGTCTAAACATTCAAAAGTATGGAGAG 57.558 33.333 0.00 0.00 0.00 3.20
8355 26761 6.862209 ACAAGTGCAAAGTCTAAACATTCAA 58.138 32.000 0.00 0.00 0.00 2.69
8486 27432 9.745880 ATTTGATTTGATTTGATGCTACATCTC 57.254 29.630 8.87 0.00 0.00 2.75
8511 27457 9.307121 GCGTGCTTCTGAGATATTTGTATATAT 57.693 33.333 0.00 0.00 0.00 0.86
8512 27458 7.484959 CGCGTGCTTCTGAGATATTTGTATATA 59.515 37.037 0.00 0.00 0.00 0.86
8514 27460 5.629435 CGCGTGCTTCTGAGATATTTGTATA 59.371 40.000 0.00 0.00 0.00 1.47
8515 27461 4.445718 CGCGTGCTTCTGAGATATTTGTAT 59.554 41.667 0.00 0.00 0.00 2.29
8516 27462 3.796717 CGCGTGCTTCTGAGATATTTGTA 59.203 43.478 0.00 0.00 0.00 2.41
8520 27466 1.137086 ACCGCGTGCTTCTGAGATATT 59.863 47.619 4.92 0.00 0.00 1.28
8527 27893 1.082756 GTTTGACCGCGTGCTTCTG 60.083 57.895 4.92 0.00 0.00 3.02
8531 27897 4.555709 TGGGTTTGACCGCGTGCT 62.556 61.111 4.92 0.00 39.83 4.40
8536 27902 4.623002 TCTTTTTATTTGGGTTTGACCGC 58.377 39.130 0.00 0.00 39.83 5.68
8566 27932 7.542890 TGTTGTGTTGCCGATATATCAATTTT 58.457 30.769 13.11 0.00 0.00 1.82
8580 27946 4.475944 GAACATATGACTGTTGTGTTGCC 58.524 43.478 10.38 0.00 39.40 4.52
8587 27953 4.686091 ACAGTGACGAACATATGACTGTTG 59.314 41.667 16.01 7.01 39.40 3.33
8601 27967 1.218047 GGCATAGGCACAGTGACGA 59.782 57.895 4.15 0.00 43.71 4.20
8732 28101 2.319136 TGGTAGATAATTTGGCGCGT 57.681 45.000 8.43 0.00 0.00 6.01
8733 28102 2.548057 ACATGGTAGATAATTTGGCGCG 59.452 45.455 0.00 0.00 0.00 6.86
8734 28103 5.682943 TTACATGGTAGATAATTTGGCGC 57.317 39.130 0.00 0.00 0.00 6.53
8757 28126 4.156008 GGCACAGTGACGGATAATCTTTTT 59.844 41.667 4.15 0.00 0.00 1.94
8758 28127 3.689649 GGCACAGTGACGGATAATCTTTT 59.310 43.478 4.15 0.00 0.00 2.27
8759 28128 3.055094 AGGCACAGTGACGGATAATCTTT 60.055 43.478 4.15 0.00 0.00 2.52
8760 28129 2.501723 AGGCACAGTGACGGATAATCTT 59.498 45.455 4.15 0.00 0.00 2.40
8761 28130 2.111384 AGGCACAGTGACGGATAATCT 58.889 47.619 4.15 0.00 0.00 2.40
8762 28131 2.604046 AGGCACAGTGACGGATAATC 57.396 50.000 4.15 0.00 0.00 1.75
8763 28132 3.803715 GCATAGGCACAGTGACGGATAAT 60.804 47.826 4.15 0.00 40.72 1.28
8764 28133 2.483013 GCATAGGCACAGTGACGGATAA 60.483 50.000 4.15 0.00 40.72 1.75
8765 28134 1.068588 GCATAGGCACAGTGACGGATA 59.931 52.381 4.15 0.00 40.72 2.59
8766 28135 0.179073 GCATAGGCACAGTGACGGAT 60.179 55.000 4.15 0.00 40.72 4.18
8767 28136 1.218047 GCATAGGCACAGTGACGGA 59.782 57.895 4.15 0.00 40.72 4.69
8768 28137 1.815421 GGCATAGGCACAGTGACGG 60.815 63.158 4.15 0.00 43.71 4.79
8769 28138 0.459899 TAGGCATAGGCACAGTGACG 59.540 55.000 4.15 0.00 43.71 4.35
8770 28139 2.918712 ATAGGCATAGGCACAGTGAC 57.081 50.000 4.15 0.00 43.71 3.67
8771 28140 3.574396 GACTATAGGCATAGGCACAGTGA 59.426 47.826 4.15 0.00 41.79 3.41
8772 28141 3.321968 TGACTATAGGCATAGGCACAGTG 59.678 47.826 3.44 0.00 46.04 3.66
8773 28142 3.576861 TGACTATAGGCATAGGCACAGT 58.423 45.455 3.44 0.00 46.04 3.55
8778 28147 5.611374 TGTTTCTTGACTATAGGCATAGGC 58.389 41.667 9.67 0.23 42.44 3.93
8779 28148 8.682936 AATTGTTTCTTGACTATAGGCATAGG 57.317 34.615 9.67 3.36 38.82 2.57
8780 28149 9.330063 TGAATTGTTTCTTGACTATAGGCATAG 57.670 33.333 9.67 9.92 35.68 2.23
8781 28150 9.851686 ATGAATTGTTTCTTGACTATAGGCATA 57.148 29.630 9.67 0.00 32.78 3.14
8782 28151 8.757982 ATGAATTGTTTCTTGACTATAGGCAT 57.242 30.769 9.67 0.00 32.78 4.40
8783 28152 9.679661 TTATGAATTGTTTCTTGACTATAGGCA 57.320 29.630 3.44 3.44 32.78 4.75
8835 28204 7.035004 GCACCAAATTATCTATCTTGCACAAA 58.965 34.615 0.00 0.00 0.00 2.83
8837 28206 5.220835 CGCACCAAATTATCTATCTTGCACA 60.221 40.000 0.00 0.00 0.00 4.57
8838 28207 5.207768 CGCACCAAATTATCTATCTTGCAC 58.792 41.667 0.00 0.00 0.00 4.57
8840 28209 5.007626 TCACGCACCAAATTATCTATCTTGC 59.992 40.000 0.00 0.00 0.00 4.01
8841 28210 6.293081 CCTCACGCACCAAATTATCTATCTTG 60.293 42.308 0.00 0.00 0.00 3.02
8842 28211 5.760253 CCTCACGCACCAAATTATCTATCTT 59.240 40.000 0.00 0.00 0.00 2.40
8843 28212 5.163301 ACCTCACGCACCAAATTATCTATCT 60.163 40.000 0.00 0.00 0.00 1.98
8844 28213 5.050091 CACCTCACGCACCAAATTATCTATC 60.050 44.000 0.00 0.00 0.00 2.08
8845 28214 4.816385 CACCTCACGCACCAAATTATCTAT 59.184 41.667 0.00 0.00 0.00 1.98
8846 28215 4.188462 CACCTCACGCACCAAATTATCTA 58.812 43.478 0.00 0.00 0.00 1.98
8853 28222 3.276091 CGCACCTCACGCACCAAA 61.276 61.111 0.00 0.00 0.00 3.28
8877 28246 6.815142 GCTCAAATGTCCAAATGCTCTAAAAT 59.185 34.615 0.00 0.00 0.00 1.82
8881 28250 4.334552 TGCTCAAATGTCCAAATGCTCTA 58.665 39.130 0.00 0.00 0.00 2.43
8887 28256 3.428532 AGAGCTGCTCAAATGTCCAAAT 58.571 40.909 29.49 3.19 32.06 2.32
8926 28296 6.859112 ACTGTTCATATACTGTTCTGACCT 57.141 37.500 0.00 0.00 0.00 3.85
8928 28298 8.244802 AGTGTACTGTTCATATACTGTTCTGAC 58.755 37.037 0.00 0.00 33.15 3.51
8930 28300 8.988064 AAGTGTACTGTTCATATACTGTTCTG 57.012 34.615 0.00 0.00 33.15 3.02
8940 28310 9.048446 GGTCTGTTAAAAAGTGTACTGTTCATA 57.952 33.333 0.00 0.00 0.00 2.15
8941 28311 7.554835 TGGTCTGTTAAAAAGTGTACTGTTCAT 59.445 33.333 0.00 0.00 0.00 2.57
8942 28312 6.879993 TGGTCTGTTAAAAAGTGTACTGTTCA 59.120 34.615 0.00 0.00 0.00 3.18
8943 28313 7.311364 TGGTCTGTTAAAAAGTGTACTGTTC 57.689 36.000 0.00 0.00 0.00 3.18
8952 28326 9.719355 AGACAAATTTTTGGTCTGTTAAAAAGT 57.281 25.926 8.44 0.00 42.34 2.66
8985 28359 2.763448 GGACATCTGAGTAGCTCTTGGT 59.237 50.000 0.00 0.00 0.00 3.67
9011 28385 6.423604 GTGATGTCCGTTCCAAATTTCAAATT 59.576 34.615 0.00 0.00 0.00 1.82
9026 28400 0.605319 ATTTGGTGCGTGATGTCCGT 60.605 50.000 0.00 0.00 0.00 4.69
9036 28410 4.574421 TGACATGGTAGATAATTTGGTGCG 59.426 41.667 0.00 0.00 0.00 5.34
9134 28508 4.524802 AATGGATGAACATTGGCTCCTA 57.475 40.909 0.00 0.00 39.47 2.94
9135 28509 3.393426 AATGGATGAACATTGGCTCCT 57.607 42.857 0.00 0.00 39.47 3.69
9136 28510 4.476628 AAAATGGATGAACATTGGCTCC 57.523 40.909 0.00 0.00 40.71 4.70
9164 28552 2.218603 AGCGACGACAAGGACATTTTT 58.781 42.857 0.00 0.00 0.00 1.94
9283 28672 0.978146 AGCCGCAGAGGAAGTACCAT 60.978 55.000 0.00 0.00 45.00 3.55
9302 28691 1.990060 GACCTCCCTAGCTGTGGCA 60.990 63.158 0.00 0.00 41.70 4.92
9309 28698 2.042230 TTCCCCGACCTCCCTAGC 60.042 66.667 0.00 0.00 0.00 3.42
9354 28745 2.028476 TCCTCAAACCATCACGACGATT 60.028 45.455 0.00 0.00 29.21 3.34
9365 28756 1.067142 CGTCGAATCCTCCTCAAACCA 60.067 52.381 0.00 0.00 0.00 3.67
9368 28759 1.552578 TCCGTCGAATCCTCCTCAAA 58.447 50.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.