Multiple sequence alignment - TraesCS4A01G344000

Loading Multiple Alignment...

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 TraesCS4A01G344000 chr4A 100.000 4243 0 0 1 4243 623983801 623979559 0.000000e+00 7836
1 TraesCS4A01G344000 chr4A 93.057 1109 51 6 1361 2468 22639585 22640668 0.000000e+00 1598
2 TraesCS4A01G344000 chr4A 92.882 857 55 2 3104 3960 723614615 723613765 0.000000e+00 1240
3 TraesCS4A01G344000 chr4A 89.041 292 12 3 2471 2742 517571259 517570968 1.130000e-90 344
4 TraesCS4A01G344000 chr7A 93.786 3138 118 29 1 3105 633798364 633801457 0.000000e+00 4643
5 TraesCS4A01G344000 chr7A 89.384 292 10 4 2471 2741 187793760 187793469 8.730000e-92 348
6 TraesCS4A01G344000 chr7A 89.347 291 11 3 2471 2741 721557887 721558177 8.730000e-92 348
7 TraesCS4A01G344000 chr7A 86.466 266 31 2 858 1119 61494035 61493771 1.930000e-73 287
8 TraesCS4A01G344000 chr7A 94.828 174 9 0 1188 1361 333610166 333609993 5.410000e-69 272
9 TraesCS4A01G344000 chr2D 93.425 1521 53 8 2471 3960 374341203 374339699 0.000000e+00 2211
10 TraesCS4A01G344000 chr2D 95.195 437 16 3 2034 2470 374342081 374341650 0.000000e+00 686
11 TraesCS4A01G344000 chr2D 88.333 180 17 2 1186 1365 312029363 312029538 3.320000e-51 213
12 TraesCS4A01G344000 chr2D 97.115 104 3 0 3966 4069 374339748 374339645 4.360000e-40 176
13 TraesCS4A01G344000 chr5B 92.857 1512 79 7 2471 3960 4576214 4577718 0.000000e+00 2167
14 TraesCS4A01G344000 chr5B 91.507 471 22 4 1361 1831 4575061 4575513 2.150000e-177 632
15 TraesCS4A01G344000 chr5B 89.452 493 46 5 4 495 20353645 20353158 6.030000e-173 617
16 TraesCS4A01G344000 chr5B 89.228 492 49 3 1 492 485519829 485520316 2.800000e-171 612
17 TraesCS4A01G344000 chr5B 88.911 496 51 4 1 495 698970248 698970740 3.630000e-170 608
18 TraesCS4A01G344000 chr5B 90.145 345 24 7 1632 1968 696806108 696805766 1.400000e-119 440
19 TraesCS4A01G344000 chr5B 89.583 288 23 3 1357 1637 476630048 476630335 4.030000e-95 359
20 TraesCS4A01G344000 chr5B 86.466 266 31 2 858 1119 290578272 290578536 1.930000e-73 287
21 TraesCS4A01G344000 chr5B 96.319 163 6 0 4063 4225 468818409 468818247 6.990000e-68 268
22 TraesCS4A01G344000 chr5B 96.319 163 6 0 4063 4225 561792058 561791896 6.990000e-68 268
23 TraesCS4A01G344000 chr3A 92.318 1510 78 8 2471 3960 734195972 734194481 0.000000e+00 2111
24 TraesCS4A01G344000 chr3A 90.546 476 36 6 4 477 171147869 171148337 4.660000e-174 621
25 TraesCS4A01G344000 chr3A 91.325 415 33 3 1361 1774 301802482 301802070 7.960000e-157 564
26 TraesCS4A01G344000 chr3A 89.372 414 34 7 1632 2036 705948685 705949097 2.930000e-141 512
27 TraesCS4A01G344000 chr3A 95.541 314 12 1 2157 2470 511223507 511223818 6.330000e-138 501
28 TraesCS4A01G344000 chr6B 90.439 1548 86 10 2472 3960 663488603 663490147 0.000000e+00 1982
29 TraesCS4A01G344000 chr6B 92.630 1384 56 13 2471 3824 525981086 525979719 0.000000e+00 1949
30 TraesCS4A01G344000 chr6B 89.413 1209 60 16 2471 3624 501360830 501359635 0.000000e+00 1461
31 TraesCS4A01G344000 chr6B 95.422 699 31 1 1361 2059 663487509 663488206 0.000000e+00 1112
32 TraesCS4A01G344000 chr6B 94.904 314 12 2 2157 2470 525981840 525981531 4.930000e-134 488
33 TraesCS4A01G344000 chr6B 96.319 163 6 0 4063 4225 446813695 446813533 6.990000e-68 268
34 TraesCS4A01G344000 chr6B 96.319 163 6 0 4063 4225 689183430 689183592 6.990000e-68 268
35 TraesCS4A01G344000 chr6B 96.330 109 4 0 3961 4069 501358697 501358589 3.370000e-41 180
36 TraesCS4A01G344000 chr6B 98.000 100 2 0 3967 4066 663490099 663490198 1.570000e-39 174
37 TraesCS4A01G344000 chr6B 96.154 104 4 0 3961 4064 505327453 505327556 2.030000e-38 171
38 TraesCS4A01G344000 chr4D 91.150 1209 49 8 2471 3624 189518723 189519928 0.000000e+00 1587
39 TraesCS4A01G344000 chr4D 97.170 106 3 0 3961 4066 189520859 189520964 3.370000e-41 180
40 TraesCS4A01G344000 chr7D 90.586 1211 54 13 2471 3624 569720705 569719498 0.000000e+00 1550
41 TraesCS4A01G344000 chr7D 95.192 104 5 0 3966 4069 569718564 569718461 9.440000e-37 165
42 TraesCS4A01G344000 chr2B 89.661 1209 70 5 2471 3624 64327589 64326381 0.000000e+00 1489
43 TraesCS4A01G344000 chr2B 91.163 860 67 5 3104 3960 127498222 127497369 0.000000e+00 1158
44 TraesCS4A01G344000 chr2B 92.918 706 29 4 2471 3156 216213622 216214326 0.000000e+00 1007
45 TraesCS4A01G344000 chr2B 90.407 344 24 5 1706 2042 12856131 12855790 1.080000e-120 444
46 TraesCS4A01G344000 chr2B 93.578 109 7 0 3961 4069 64325448 64325340 3.390000e-36 163
47 TraesCS4A01G344000 chr3B 91.743 981 49 10 2974 3954 826121412 826122360 0.000000e+00 1334
48 TraesCS4A01G344000 chr3B 94.143 461 23 3 2701 3159 210823585 210824043 0.000000e+00 699
49 TraesCS4A01G344000 chr3B 90.361 415 28 9 1632 2036 761003726 761004138 6.240000e-148 534
50 TraesCS4A01G344000 chr3B 95.541 314 10 2 2157 2470 172152168 172151859 2.280000e-137 499
51 TraesCS4A01G344000 chr1D 91.582 986 38 4 2471 3411 211215822 211214837 0.000000e+00 1319
52 TraesCS4A01G344000 chr1D 82.646 582 68 16 542 1106 403726630 403726065 6.380000e-133 484
53 TraesCS4A01G344000 chr1D 91.667 180 11 2 1186 1365 403725912 403725737 3.280000e-61 246
54 TraesCS4A01G344000 chrUn 91.399 965 45 4 2697 3624 104825294 104826257 0.000000e+00 1288
55 TraesCS4A01G344000 chrUn 91.858 479 36 3 4 480 101649660 101649183 0.000000e+00 665
56 TraesCS4A01G344000 chrUn 92.520 254 17 1 1384 1637 415418419 415418168 3.120000e-96 363
57 TraesCS4A01G344000 chr1B 92.692 821 44 3 3140 3960 623471830 623471026 0.000000e+00 1170
58 TraesCS4A01G344000 chr1B 92.707 809 53 2 3152 3960 10898125 10898927 0.000000e+00 1162
59 TraesCS4A01G344000 chr1B 92.461 703 22 5 2471 3143 623485764 623485063 0.000000e+00 976
60 TraesCS4A01G344000 chr1B 90.254 472 27 7 1361 1831 10896489 10896942 2.180000e-167 599
61 TraesCS4A01G344000 chr1B 92.453 212 14 2 1981 2192 10896950 10897159 6.890000e-78 302
62 TraesCS4A01G344000 chr1B 96.319 163 6 0 4063 4225 406223126 406223288 6.990000e-68 268
63 TraesCS4A01G344000 chr1B 96.319 163 6 0 4063 4225 563480674 563480512 6.990000e-68 268
64 TraesCS4A01G344000 chr1B 96.154 104 4 0 3961 4064 76954728 76954831 2.030000e-38 171
65 TraesCS4A01G344000 chr1B 96.040 101 4 0 3966 4066 10898878 10898978 9.440000e-37 165
66 TraesCS4A01G344000 chr4B 94.583 720 35 2 3235 3954 117427715 117428430 0.000000e+00 1110
67 TraesCS4A01G344000 chr4B 89.452 493 47 4 4 495 146189498 146189010 6.030000e-173 617
68 TraesCS4A01G344000 chr7B 94.488 508 28 0 3104 3611 236937438 236936931 0.000000e+00 784
69 TraesCS4A01G344000 chr7B 87.594 266 28 3 858 1119 40952851 40953115 1.920000e-78 303
70 TraesCS4A01G344000 chr7B 96.319 163 6 0 4063 4225 419494737 419494575 6.990000e-68 268
71 TraesCS4A01G344000 chr5A 90.121 496 44 4 1 495 144654030 144654521 1.290000e-179 640
72 TraesCS4A01G344000 chr5A 94.268 314 14 2 2157 2470 540933166 540933475 1.070000e-130 477
73 TraesCS4A01G344000 chr5A 89.691 291 10 3 2471 2741 540933922 540934212 1.880000e-93 353
74 TraesCS4A01G344000 chr5A 96.933 163 5 0 4063 4225 374022273 374022111 1.500000e-69 274
75 TraesCS4A01G344000 chr5A 96.319 163 6 0 4063 4225 595668081 595667919 6.990000e-68 268
76 TraesCS4A01G344000 chr6A 89.516 496 49 3 1 495 24638288 24638781 3.600000e-175 625
77 TraesCS4A01G344000 chr6A 94.586 314 13 2 2157 2470 49437696 49437387 2.290000e-132 483
78 TraesCS4A01G344000 chr6A 90.598 351 11 4 2471 2801 603767895 603767547 3.010000e-121 446
79 TraesCS4A01G344000 chr1A 89.249 493 46 4 4 495 41798779 41798293 1.010000e-170 610
80 TraesCS4A01G344000 chr1A 83.660 612 60 18 542 1119 499445489 499444884 1.340000e-149 540
81 TraesCS4A01G344000 chr1A 94.603 315 11 4 2157 2470 422208383 422208692 2.290000e-132 483
82 TraesCS4A01G344000 chr1A 81.068 618 74 19 542 1124 584982857 584982248 1.800000e-123 453
83 TraesCS4A01G344000 chr1A 88.660 291 13 3 2471 2741 422209139 422209429 1.890000e-88 337
84 TraesCS4A01G344000 chr1A 88.525 183 14 3 1186 1365 499444726 499444548 9.240000e-52 215
85 TraesCS4A01G344000 chr1A 90.625 96 9 0 1186 1281 584982094 584981999 1.240000e-25 128
86 TraesCS4A01G344000 chr5D 92.226 283 20 1 1357 1637 396687843 396688125 2.380000e-107 399
87 TraesCS4A01G344000 chr6D 87.970 266 27 2 858 1119 454304794 454304530 4.120000e-80 309
88 TraesCS4A01G344000 chr6D 88.333 180 17 2 1186 1365 454304385 454304210 3.320000e-51 213
89 TraesCS4A01G344000 chr3D 86.090 266 32 2 858 1119 67534304 67534568 8.980000e-72 281
90 TraesCS4A01G344000 chr3D 87.778 180 18 2 1186 1365 67534713 67534888 1.550000e-49 207


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 TraesCS4A01G344000 chr4A 623979559 623983801 4242 True 7836.000000 7836 100.000000 1 4243 1 chr4A.!!$R2 4242
1 TraesCS4A01G344000 chr4A 22639585 22640668 1083 False 1598.000000 1598 93.057000 1361 2468 1 chr4A.!!$F1 1107
2 TraesCS4A01G344000 chr4A 723613765 723614615 850 True 1240.000000 1240 92.882000 3104 3960 1 chr4A.!!$R3 856
3 TraesCS4A01G344000 chr7A 633798364 633801457 3093 False 4643.000000 4643 93.786000 1 3105 1 chr7A.!!$F1 3104
4 TraesCS4A01G344000 chr2D 374339645 374342081 2436 True 1024.333333 2211 95.245000 2034 4069 3 chr2D.!!$R1 2035
5 TraesCS4A01G344000 chr5B 4575061 4577718 2657 False 1399.500000 2167 92.182000 1361 3960 2 chr5B.!!$F5 2599
6 TraesCS4A01G344000 chr3A 734194481 734195972 1491 True 2111.000000 2111 92.318000 2471 3960 1 chr3A.!!$R2 1489
7 TraesCS4A01G344000 chr6B 525979719 525981840 2121 True 1218.500000 1949 93.767000 2157 3824 2 chr6B.!!$R3 1667
8 TraesCS4A01G344000 chr6B 663487509 663490198 2689 False 1089.333333 1982 94.620333 1361 4066 3 chr6B.!!$F3 2705
9 TraesCS4A01G344000 chr6B 501358589 501360830 2241 True 820.500000 1461 92.871500 2471 4069 2 chr6B.!!$R2 1598
10 TraesCS4A01G344000 chr4D 189518723 189520964 2241 False 883.500000 1587 94.160000 2471 4066 2 chr4D.!!$F1 1595
11 TraesCS4A01G344000 chr7D 569718461 569720705 2244 True 857.500000 1550 92.889000 2471 4069 2 chr7D.!!$R1 1598
12 TraesCS4A01G344000 chr2B 127497369 127498222 853 True 1158.000000 1158 91.163000 3104 3960 1 chr2B.!!$R2 856
13 TraesCS4A01G344000 chr2B 216213622 216214326 704 False 1007.000000 1007 92.918000 2471 3156 1 chr2B.!!$F1 685
14 TraesCS4A01G344000 chr2B 64325340 64327589 2249 True 826.000000 1489 91.619500 2471 4069 2 chr2B.!!$R3 1598
15 TraesCS4A01G344000 chr3B 826121412 826122360 948 False 1334.000000 1334 91.743000 2974 3954 1 chr3B.!!$F3 980
16 TraesCS4A01G344000 chr1D 211214837 211215822 985 True 1319.000000 1319 91.582000 2471 3411 1 chr1D.!!$R1 940
17 TraesCS4A01G344000 chr1D 403725737 403726630 893 True 365.000000 484 87.156500 542 1365 2 chr1D.!!$R2 823
18 TraesCS4A01G344000 chrUn 104825294 104826257 963 False 1288.000000 1288 91.399000 2697 3624 1 chrUn.!!$F1 927
19 TraesCS4A01G344000 chr1B 623471026 623471830 804 True 1170.000000 1170 92.692000 3140 3960 1 chr1B.!!$R2 820
20 TraesCS4A01G344000 chr1B 623485063 623485764 701 True 976.000000 976 92.461000 2471 3143 1 chr1B.!!$R3 672
21 TraesCS4A01G344000 chr1B 10896489 10898978 2489 False 557.000000 1162 92.863500 1361 4066 4 chr1B.!!$F3 2705
22 TraesCS4A01G344000 chr4B 117427715 117428430 715 False 1110.000000 1110 94.583000 3235 3954 1 chr4B.!!$F1 719
23 TraesCS4A01G344000 chr7B 236936931 236937438 507 True 784.000000 784 94.488000 3104 3611 1 chr7B.!!$R1 507
24 TraesCS4A01G344000 chr5A 540933166 540934212 1046 False 415.000000 477 91.979500 2157 2741 2 chr5A.!!$F2 584
25 TraesCS4A01G344000 chr1A 422208383 422209429 1046 False 410.000000 483 91.631500 2157 2741 2 chr1A.!!$F1 584
26 TraesCS4A01G344000 chr1A 499444548 499445489 941 True 377.500000 540 86.092500 542 1365 2 chr1A.!!$R2 823
27 TraesCS4A01G344000 chr1A 584981999 584982857 858 True 290.500000 453 85.846500 542 1281 2 chr1A.!!$R3 739
28 TraesCS4A01G344000 chr6D 454304210 454304794 584 True 261.000000 309 88.151500 858 1365 2 chr6D.!!$R1 507
29 TraesCS4A01G344000 chr3D 67534304 67534888 584 False 244.000000 281 86.934000 858 1365 2 chr3D.!!$F1 507

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
366 367 0.392706 CCATCCATCCGTCGATCCAA 59.607 55.000 0.00 0.00 0.0 3.53 F
843 876 0.680618 CCCTTTTGTTGAGCATGGCA 59.319 50.000 0.00 0.00 0.0 4.92 F
880 916 1.152247 TGAGGAGGCAGTCAGGTGT 60.152 57.895 0.00 0.00 0.0 4.16 F
2434 2788 0.533755 CAACCTCCGGCTGATCATCC 60.534 60.000 5.46 5.46 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1268 1415 3.196207 TTGCTCAGGGGAGGCACAC 62.196 63.158 0.00 0.00 41.67 3.82 R
2267 2621 4.502105 TGCCTGAACCATACATGTACAT 57.498 40.909 7.96 1.41 0.00 2.29 R
2671 3496 7.086230 AGTTGAGTTCTACTGATAACCTACG 57.914 40.000 0.00 0.00 31.08 3.51 R
3973 5550 0.249868 CAACAGTCGGCAAGGACTCA 60.250 55.000 1.78 0.00 45.20 3.41 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
88 89 2.568623 AGAACTCAATTCGGGCACTT 57.431 45.000 0.00 0.00 42.69 3.16
90 91 3.600388 AGAACTCAATTCGGGCACTTAG 58.400 45.455 0.00 0.00 42.69 2.18
145 146 7.552050 AAATGAAAACTCCCCATATCAACAA 57.448 32.000 0.00 0.00 0.00 2.83
154 155 5.328565 TCCCCATATCAACAATGTTTGTCA 58.671 37.500 0.00 0.00 44.59 3.58
168 169 5.590104 TGTTTGTCATCACAAGATACACG 57.410 39.130 0.00 0.00 43.54 4.49
233 234 7.095910 TGTTAATATGTTGAATGTTTGCCCTG 58.904 34.615 0.00 0.00 0.00 4.45
289 290 5.021458 AGCTGAATTCTGATTGGTGGAATT 58.979 37.500 15.79 0.00 40.80 2.17
311 312 1.331756 GTTGTGGCATGGATCGATGAC 59.668 52.381 20.59 18.43 0.00 3.06
340 341 0.470080 ATCCGTCCATCCGTCCATCT 60.470 55.000 0.00 0.00 0.00 2.90
342 343 1.203013 TCCGTCCATCCGTCCATCTAT 60.203 52.381 0.00 0.00 0.00 1.98
343 344 2.040679 TCCGTCCATCCGTCCATCTATA 59.959 50.000 0.00 0.00 0.00 1.31
354 355 4.406972 CCGTCCATCTATACATCCATCCAT 59.593 45.833 0.00 0.00 0.00 3.41
355 356 5.452496 CCGTCCATCTATACATCCATCCATC 60.452 48.000 0.00 0.00 0.00 3.51
356 357 5.452496 CGTCCATCTATACATCCATCCATCC 60.452 48.000 0.00 0.00 0.00 3.51
357 358 4.651045 TCCATCTATACATCCATCCATCCG 59.349 45.833 0.00 0.00 0.00 4.18
358 359 4.406972 CCATCTATACATCCATCCATCCGT 59.593 45.833 0.00 0.00 0.00 4.69
359 360 5.452496 CCATCTATACATCCATCCATCCGTC 60.452 48.000 0.00 0.00 0.00 4.79
360 361 3.694566 TCTATACATCCATCCATCCGTCG 59.305 47.826 0.00 0.00 0.00 5.12
361 362 1.989706 TACATCCATCCATCCGTCGA 58.010 50.000 0.00 0.00 0.00 4.20
362 363 1.342074 ACATCCATCCATCCGTCGAT 58.658 50.000 0.00 0.00 0.00 3.59
363 364 1.273606 ACATCCATCCATCCGTCGATC 59.726 52.381 0.00 0.00 0.00 3.69
364 365 0.898320 ATCCATCCATCCGTCGATCC 59.102 55.000 0.00 0.00 0.00 3.36
365 366 0.469144 TCCATCCATCCGTCGATCCA 60.469 55.000 0.00 0.00 0.00 3.41
366 367 0.392706 CCATCCATCCGTCGATCCAA 59.607 55.000 0.00 0.00 0.00 3.53
367 368 1.502231 CATCCATCCGTCGATCCAAC 58.498 55.000 0.00 0.00 0.00 3.77
374 375 2.100631 CGTCGATCCAACCCACTGC 61.101 63.158 0.00 0.00 0.00 4.40
450 451 1.834822 CAGTCCTCTCCCCCGATCC 60.835 68.421 0.00 0.00 0.00 3.36
527 529 1.690985 CTTCCCTCCCCTCCACTCC 60.691 68.421 0.00 0.00 0.00 3.85
617 634 2.261361 CACACGATCTCCACCGCA 59.739 61.111 0.00 0.00 0.00 5.69
798 830 1.154338 CTTGCTCGCTTTGCTTCGG 60.154 57.895 0.00 0.00 0.00 4.30
843 876 0.680618 CCCTTTTGTTGAGCATGGCA 59.319 50.000 0.00 0.00 0.00 4.92
870 906 4.687215 TGCTGCACGTGAGGAGGC 62.687 66.667 22.23 14.64 0.00 4.70
880 916 1.152247 TGAGGAGGCAGTCAGGTGT 60.152 57.895 0.00 0.00 0.00 4.16
1125 1165 4.161565 AGACCAGAACGCATTGGAGTATAA 59.838 41.667 6.67 0.00 37.89 0.98
1268 1415 4.568359 CCAATGGTGAGAATTCAGTACTCG 59.432 45.833 8.44 0.00 32.98 4.18
1375 1525 9.826574 AATAGCAATCATTTTGAAAGCATATGT 57.173 25.926 4.29 0.00 34.17 2.29
1729 1880 6.758416 TCAGTTGTGATCTTAGTATCATGTGC 59.242 38.462 0.00 0.00 38.13 4.57
1734 1885 6.695713 TGTGATCTTAGTATCATGTGCGTAAC 59.304 38.462 0.00 0.00 38.13 2.50
1979 2131 5.976458 TCATTTTTGAATATGGCCAACTCC 58.024 37.500 10.96 0.00 0.00 3.85
2265 2619 6.373005 TTCAGAGAGAAAGAGAGAGAGAGA 57.627 41.667 0.00 0.00 32.05 3.10
2266 2620 6.566079 TCAGAGAGAAAGAGAGAGAGAGAT 57.434 41.667 0.00 0.00 0.00 2.75
2267 2621 7.675161 TCAGAGAGAAAGAGAGAGAGAGATA 57.325 40.000 0.00 0.00 0.00 1.98
2434 2788 0.533755 CAACCTCCGGCTGATCATCC 60.534 60.000 5.46 5.46 0.00 3.51
2435 2789 0.982852 AACCTCCGGCTGATCATCCA 60.983 55.000 15.63 0.00 0.00 3.41
2671 3496 2.605580 GCAGCACAGTTTTAGTTGCTCC 60.606 50.000 0.00 0.00 36.69 4.70
3333 4246 1.980036 GGTGGTGGTTAGGGTGTTCTA 59.020 52.381 0.00 0.00 0.00 2.10
3342 4255 5.105064 TGGTTAGGGTGTTCTAGTGCTTATC 60.105 44.000 0.00 0.00 0.00 1.75
3414 4331 4.361451 GCAAATGCTGTAGTGCTTATGT 57.639 40.909 0.00 0.00 38.21 2.29
3473 4391 7.940137 TGCTACTGTTTCTAATTTTAGGTTGGA 59.060 33.333 0.00 0.00 0.00 3.53
3484 4402 6.855763 ATTTTAGGTTGGAATGAGATGCAA 57.144 33.333 0.00 0.00 0.00 4.08
3548 4466 5.368145 TGCTATTGTCATATCCTGGTTGTC 58.632 41.667 0.00 0.00 0.00 3.18
3567 4485 7.151976 GGTTGTCTTGTTGCTACCAATATTTT 58.848 34.615 0.00 0.00 32.75 1.82
3648 5223 8.005466 GTGCAAGATGTTCACATGTTAATTTTG 58.995 33.333 0.00 1.22 37.69 2.44
3758 5333 2.948720 GCAGACTCGAAGGTGGCCT 61.949 63.158 3.32 0.00 33.87 5.19
3777 5352 2.620367 CCTTATGCAAGGCACCAAGGTA 60.620 50.000 18.43 0.00 44.90 3.08
3858 5434 1.765314 TGAGCTCCTCCCTTTGCTATC 59.235 52.381 12.15 0.00 35.76 2.08
3881 5457 4.460382 CCTACAACCATGCTCTGTTTCATT 59.540 41.667 0.00 0.00 0.00 2.57
3931 5508 1.070786 GTGGTTGAGTCCTTGCCGA 59.929 57.895 0.00 0.00 0.00 5.54
3932 5509 1.070786 TGGTTGAGTCCTTGCCGAC 59.929 57.895 0.00 0.00 0.00 4.79
3933 5510 1.371558 GGTTGAGTCCTTGCCGACT 59.628 57.895 0.00 0.00 45.86 4.18
3934 5511 0.951040 GGTTGAGTCCTTGCCGACTG 60.951 60.000 3.18 0.00 43.22 3.51
3935 5512 0.249911 GTTGAGTCCTTGCCGACTGT 60.250 55.000 3.18 0.00 43.22 3.55
3936 5513 0.468226 TTGAGTCCTTGCCGACTGTT 59.532 50.000 3.18 0.00 43.22 3.16
3937 5514 0.249868 TGAGTCCTTGCCGACTGTTG 60.250 55.000 3.18 0.00 43.22 3.33
3938 5515 0.249911 GAGTCCTTGCCGACTGTTGT 60.250 55.000 3.18 0.00 43.22 3.32
3939 5516 0.532862 AGTCCTTGCCGACTGTTGTG 60.533 55.000 0.00 0.00 41.60 3.33
3940 5517 0.814010 GTCCTTGCCGACTGTTGTGT 60.814 55.000 0.00 0.00 0.00 3.72
3941 5518 0.531974 TCCTTGCCGACTGTTGTGTC 60.532 55.000 0.00 0.00 0.00 3.67
3949 5526 2.046283 GACTGTTGTGTCGACGATCA 57.954 50.000 11.62 7.40 0.00 2.92
3950 5527 2.390938 GACTGTTGTGTCGACGATCAA 58.609 47.619 11.62 12.91 0.00 2.57
3951 5528 2.394708 ACTGTTGTGTCGACGATCAAG 58.605 47.619 11.62 8.31 0.00 3.02
3952 5529 2.223735 ACTGTTGTGTCGACGATCAAGT 60.224 45.455 11.62 8.95 0.00 3.16
3953 5530 2.124122 TGTTGTGTCGACGATCAAGTG 58.876 47.619 11.62 0.00 0.00 3.16
3954 5531 1.136611 GTTGTGTCGACGATCAAGTGC 60.137 52.381 11.62 2.03 0.00 4.40
3955 5532 0.313987 TGTGTCGACGATCAAGTGCT 59.686 50.000 11.62 0.00 0.00 4.40
3956 5533 0.710567 GTGTCGACGATCAAGTGCTG 59.289 55.000 11.62 0.00 0.00 4.41
3957 5534 0.388520 TGTCGACGATCAAGTGCTGG 60.389 55.000 11.62 0.00 0.00 4.85
3958 5535 0.388649 GTCGACGATCAAGTGCTGGT 60.389 55.000 0.00 0.00 0.00 4.00
3959 5536 0.388520 TCGACGATCAAGTGCTGGTG 60.389 55.000 0.00 0.00 0.00 4.17
3960 5537 0.667487 CGACGATCAAGTGCTGGTGT 60.667 55.000 0.00 0.00 0.00 4.16
3961 5538 1.512926 GACGATCAAGTGCTGGTGTT 58.487 50.000 0.00 0.00 0.00 3.32
3962 5539 1.461127 GACGATCAAGTGCTGGTGTTC 59.539 52.381 0.00 0.00 0.00 3.18
3963 5540 0.439985 CGATCAAGTGCTGGTGTTCG 59.560 55.000 0.00 0.00 32.52 3.95
3964 5541 1.512926 GATCAAGTGCTGGTGTTCGT 58.487 50.000 0.00 0.00 0.00 3.85
3965 5542 1.195448 GATCAAGTGCTGGTGTTCGTG 59.805 52.381 0.00 0.00 0.00 4.35
3966 5543 1.009675 CAAGTGCTGGTGTTCGTGC 60.010 57.895 0.00 0.00 0.00 5.34
3967 5544 2.186826 AAGTGCTGGTGTTCGTGCC 61.187 57.895 0.00 0.00 0.00 5.01
3968 5545 4.012895 GTGCTGGTGTTCGTGCCG 62.013 66.667 0.00 0.00 0.00 5.69
3969 5546 4.539083 TGCTGGTGTTCGTGCCGT 62.539 61.111 0.00 0.00 0.00 5.68
3970 5547 4.012895 GCTGGTGTTCGTGCCGTG 62.013 66.667 0.00 0.00 0.00 4.94
3971 5548 3.345808 CTGGTGTTCGTGCCGTGG 61.346 66.667 0.00 0.00 0.00 4.94
3972 5549 4.164087 TGGTGTTCGTGCCGTGGT 62.164 61.111 0.00 0.00 0.00 4.16
3973 5550 2.898343 GGTGTTCGTGCCGTGGTT 60.898 61.111 0.00 0.00 0.00 3.67
3974 5551 2.326550 GTGTTCGTGCCGTGGTTG 59.673 61.111 0.00 0.00 0.00 3.77
4075 5652 8.434392 AGTAGTATTAGAGTGTCTCTCCTTAGG 58.566 40.741 2.41 0.00 43.71 2.69
4076 5653 6.607019 AGTATTAGAGTGTCTCTCCTTAGGG 58.393 44.000 0.00 0.00 43.71 3.53
4077 5654 2.838637 AGAGTGTCTCTCCTTAGGGG 57.161 55.000 0.00 0.00 43.71 4.79
4078 5655 2.004589 AGAGTGTCTCTCCTTAGGGGT 58.995 52.381 0.00 0.00 43.71 4.95
4079 5656 2.384029 AGAGTGTCTCTCCTTAGGGGTT 59.616 50.000 0.00 0.00 43.71 4.11
4080 5657 2.498078 GAGTGTCTCTCCTTAGGGGTTG 59.502 54.545 0.00 0.00 37.22 3.77
4081 5658 2.158143 AGTGTCTCTCCTTAGGGGTTGT 60.158 50.000 0.00 0.00 36.25 3.32
4082 5659 2.638363 GTGTCTCTCCTTAGGGGTTGTT 59.362 50.000 0.00 0.00 36.25 2.83
4083 5660 3.072622 GTGTCTCTCCTTAGGGGTTGTTT 59.927 47.826 0.00 0.00 36.25 2.83
4084 5661 3.720002 TGTCTCTCCTTAGGGGTTGTTTT 59.280 43.478 0.00 0.00 36.25 2.43
4085 5662 4.909088 TGTCTCTCCTTAGGGGTTGTTTTA 59.091 41.667 0.00 0.00 36.25 1.52
4086 5663 5.370289 TGTCTCTCCTTAGGGGTTGTTTTAA 59.630 40.000 0.00 0.00 36.25 1.52
4087 5664 6.126420 TGTCTCTCCTTAGGGGTTGTTTTAAA 60.126 38.462 0.00 0.00 36.25 1.52
4088 5665 6.206243 GTCTCTCCTTAGGGGTTGTTTTAAAC 59.794 42.308 0.00 0.20 36.25 2.01
4089 5666 6.015991 TCTCCTTAGGGGTTGTTTTAAACA 57.984 37.500 6.41 6.41 40.21 2.83
4135 5712 6.680874 TTTTTGCTGTTCAAAGATTGCAAT 57.319 29.167 12.83 12.83 44.62 3.56
4136 5713 5.910637 TTTGCTGTTCAAAGATTGCAATC 57.089 34.783 28.44 28.44 39.58 2.67
4137 5714 3.916761 TGCTGTTCAAAGATTGCAATCC 58.083 40.909 31.05 17.48 36.04 3.01
4138 5715 3.575256 TGCTGTTCAAAGATTGCAATCCT 59.425 39.130 31.05 19.28 36.04 3.24
4139 5716 4.766373 TGCTGTTCAAAGATTGCAATCCTA 59.234 37.500 31.05 14.47 36.04 2.94
4140 5717 5.106038 TGCTGTTCAAAGATTGCAATCCTAG 60.106 40.000 31.05 21.54 36.04 3.02
4141 5718 5.105997 GCTGTTCAAAGATTGCAATCCTAGT 60.106 40.000 31.05 13.68 36.04 2.57
4142 5719 6.571150 GCTGTTCAAAGATTGCAATCCTAGTT 60.571 38.462 31.05 18.39 36.04 2.24
4143 5720 6.913170 TGTTCAAAGATTGCAATCCTAGTTC 58.087 36.000 31.05 19.35 36.04 3.01
4144 5721 6.489700 TGTTCAAAGATTGCAATCCTAGTTCA 59.510 34.615 31.05 21.25 36.04 3.18
4145 5722 7.177216 TGTTCAAAGATTGCAATCCTAGTTCAT 59.823 33.333 31.05 11.22 36.04 2.57
4146 5723 7.707624 TCAAAGATTGCAATCCTAGTTCATT 57.292 32.000 31.05 16.09 36.04 2.57
4147 5724 8.125978 TCAAAGATTGCAATCCTAGTTCATTT 57.874 30.769 31.05 20.25 36.04 2.32
4148 5725 8.587608 TCAAAGATTGCAATCCTAGTTCATTTT 58.412 29.630 31.05 19.64 36.04 1.82
4149 5726 8.866956 CAAAGATTGCAATCCTAGTTCATTTTC 58.133 33.333 31.05 7.26 36.04 2.29
4150 5727 7.707624 AGATTGCAATCCTAGTTCATTTTCA 57.292 32.000 31.05 0.00 36.04 2.69
4151 5728 8.125978 AGATTGCAATCCTAGTTCATTTTCAA 57.874 30.769 31.05 0.00 36.04 2.69
4152 5729 8.587608 AGATTGCAATCCTAGTTCATTTTCAAA 58.412 29.630 31.05 0.00 36.04 2.69
4153 5730 8.767478 ATTGCAATCCTAGTTCATTTTCAAAG 57.233 30.769 5.99 0.00 0.00 2.77
4154 5731 7.523293 TGCAATCCTAGTTCATTTTCAAAGA 57.477 32.000 0.00 0.00 0.00 2.52
4155 5732 8.125978 TGCAATCCTAGTTCATTTTCAAAGAT 57.874 30.769 0.00 0.00 0.00 2.40
4156 5733 8.246180 TGCAATCCTAGTTCATTTTCAAAGATC 58.754 33.333 0.00 0.00 0.00 2.75
4157 5734 7.430502 GCAATCCTAGTTCATTTTCAAAGATCG 59.569 37.037 0.00 0.00 0.00 3.69
4158 5735 8.668353 CAATCCTAGTTCATTTTCAAAGATCGA 58.332 33.333 0.00 0.00 0.00 3.59
4159 5736 8.792830 ATCCTAGTTCATTTTCAAAGATCGAA 57.207 30.769 0.00 0.00 0.00 3.71
4160 5737 8.615878 TCCTAGTTCATTTTCAAAGATCGAAA 57.384 30.769 0.00 0.00 0.00 3.46
4161 5738 9.231297 TCCTAGTTCATTTTCAAAGATCGAAAT 57.769 29.630 0.00 0.00 32.66 2.17
4162 5739 9.282247 CCTAGTTCATTTTCAAAGATCGAAATG 57.718 33.333 0.00 11.69 39.58 2.32
4163 5740 9.831737 CTAGTTCATTTTCAAAGATCGAAATGT 57.168 29.630 14.84 5.65 39.37 2.71
4165 5742 8.971321 AGTTCATTTTCAAAGATCGAAATGTTG 58.029 29.630 14.84 0.00 39.37 3.33
4166 5743 8.755018 GTTCATTTTCAAAGATCGAAATGTTGT 58.245 29.630 14.84 0.00 39.37 3.32
4167 5744 8.870160 TCATTTTCAAAGATCGAAATGTTGTT 57.130 26.923 14.84 0.00 39.37 2.83
4168 5745 8.754096 TCATTTTCAAAGATCGAAATGTTGTTG 58.246 29.630 14.84 0.00 39.37 3.33
4169 5746 8.754096 CATTTTCAAAGATCGAAATGTTGTTGA 58.246 29.630 0.00 0.00 35.70 3.18
4170 5747 7.678194 TTTCAAAGATCGAAATGTTGTTGAC 57.322 32.000 0.00 0.00 0.00 3.18
4171 5748 5.757886 TCAAAGATCGAAATGTTGTTGACC 58.242 37.500 0.00 0.00 0.00 4.02
4172 5749 4.766404 AAGATCGAAATGTTGTTGACCC 57.234 40.909 0.00 0.00 0.00 4.46
4173 5750 4.021102 AGATCGAAATGTTGTTGACCCT 57.979 40.909 0.00 0.00 0.00 4.34
4174 5751 3.753272 AGATCGAAATGTTGTTGACCCTG 59.247 43.478 0.00 0.00 0.00 4.45
4175 5752 2.925724 TCGAAATGTTGTTGACCCTGT 58.074 42.857 0.00 0.00 0.00 4.00
4176 5753 3.283751 TCGAAATGTTGTTGACCCTGTT 58.716 40.909 0.00 0.00 0.00 3.16
4177 5754 3.314080 TCGAAATGTTGTTGACCCTGTTC 59.686 43.478 0.00 0.00 0.00 3.18
4178 5755 3.315191 CGAAATGTTGTTGACCCTGTTCT 59.685 43.478 0.00 0.00 0.00 3.01
4179 5756 4.202010 CGAAATGTTGTTGACCCTGTTCTT 60.202 41.667 0.00 0.00 0.00 2.52
4180 5757 4.918810 AATGTTGTTGACCCTGTTCTTC 57.081 40.909 0.00 0.00 0.00 2.87
4181 5758 3.644966 TGTTGTTGACCCTGTTCTTCT 57.355 42.857 0.00 0.00 0.00 2.85
4182 5759 4.764050 TGTTGTTGACCCTGTTCTTCTA 57.236 40.909 0.00 0.00 0.00 2.10
4183 5760 5.304686 TGTTGTTGACCCTGTTCTTCTAT 57.695 39.130 0.00 0.00 0.00 1.98
4184 5761 5.063204 TGTTGTTGACCCTGTTCTTCTATG 58.937 41.667 0.00 0.00 0.00 2.23
4185 5762 3.674997 TGTTGACCCTGTTCTTCTATGC 58.325 45.455 0.00 0.00 0.00 3.14
4186 5763 3.327757 TGTTGACCCTGTTCTTCTATGCT 59.672 43.478 0.00 0.00 0.00 3.79
4187 5764 4.202461 TGTTGACCCTGTTCTTCTATGCTT 60.202 41.667 0.00 0.00 0.00 3.91
4188 5765 5.012664 TGTTGACCCTGTTCTTCTATGCTTA 59.987 40.000 0.00 0.00 0.00 3.09
4189 5766 5.755409 TGACCCTGTTCTTCTATGCTTAA 57.245 39.130 0.00 0.00 0.00 1.85
4190 5767 6.121776 TGACCCTGTTCTTCTATGCTTAAA 57.878 37.500 0.00 0.00 0.00 1.52
4191 5768 6.721318 TGACCCTGTTCTTCTATGCTTAAAT 58.279 36.000 0.00 0.00 0.00 1.40
4192 5769 6.599244 TGACCCTGTTCTTCTATGCTTAAATG 59.401 38.462 0.00 0.00 0.00 2.32
4193 5770 5.888161 ACCCTGTTCTTCTATGCTTAAATGG 59.112 40.000 0.00 0.00 0.00 3.16
4194 5771 5.888161 CCCTGTTCTTCTATGCTTAAATGGT 59.112 40.000 0.00 0.00 0.00 3.55
4195 5772 7.054124 CCCTGTTCTTCTATGCTTAAATGGTA 58.946 38.462 0.00 0.00 0.00 3.25
4196 5773 7.556275 CCCTGTTCTTCTATGCTTAAATGGTAA 59.444 37.037 0.00 0.00 0.00 2.85
4197 5774 8.956426 CCTGTTCTTCTATGCTTAAATGGTAAA 58.044 33.333 0.00 0.00 0.00 2.01
4204 5781 9.781834 TTCTATGCTTAAATGGTAAAAATGTCG 57.218 29.630 0.00 0.00 0.00 4.35
4205 5782 6.885735 ATGCTTAAATGGTAAAAATGTCGC 57.114 33.333 0.00 0.00 0.00 5.19
4206 5783 5.773575 TGCTTAAATGGTAAAAATGTCGCA 58.226 33.333 0.00 0.00 0.00 5.10
4207 5784 6.393990 TGCTTAAATGGTAAAAATGTCGCAT 58.606 32.000 0.00 0.00 0.00 4.73
4208 5785 6.870965 TGCTTAAATGGTAAAAATGTCGCATT 59.129 30.769 0.09 0.09 0.00 3.56
4209 5786 7.386299 TGCTTAAATGGTAAAAATGTCGCATTT 59.614 29.630 10.67 10.67 0.00 2.32
4210 5787 8.227119 GCTTAAATGGTAAAAATGTCGCATTTT 58.773 29.630 18.56 18.56 33.12 1.82
4211 5788 9.527566 CTTAAATGGTAAAAATGTCGCATTTTG 57.472 29.630 22.39 9.22 32.23 2.44
4212 5789 4.981389 TGGTAAAAATGTCGCATTTTGC 57.019 36.364 22.39 18.66 40.69 3.68
4213 5790 4.626042 TGGTAAAAATGTCGCATTTTGCT 58.374 34.783 22.39 14.55 42.25 3.91
4214 5791 5.053145 TGGTAAAAATGTCGCATTTTGCTT 58.947 33.333 22.39 14.06 42.25 3.91
4215 5792 5.050499 TGGTAAAAATGTCGCATTTTGCTTG 60.050 36.000 22.39 0.00 42.25 4.01
4216 5793 5.050431 GGTAAAAATGTCGCATTTTGCTTGT 60.050 36.000 22.39 13.58 42.25 3.16
4217 5794 5.482686 AAAAATGTCGCATTTTGCTTGTT 57.517 30.435 22.39 9.85 42.25 2.83
4218 5795 4.713854 AAATGTCGCATTTTGCTTGTTC 57.286 36.364 10.67 0.00 42.25 3.18
4219 5796 3.648339 ATGTCGCATTTTGCTTGTTCT 57.352 38.095 0.00 0.00 42.25 3.01
4220 5797 4.764679 ATGTCGCATTTTGCTTGTTCTA 57.235 36.364 0.00 0.00 42.25 2.10
4221 5798 4.560136 TGTCGCATTTTGCTTGTTCTAA 57.440 36.364 0.00 0.00 42.25 2.10
4222 5799 4.286910 TGTCGCATTTTGCTTGTTCTAAC 58.713 39.130 0.00 0.00 42.25 2.34
4223 5800 3.668656 GTCGCATTTTGCTTGTTCTAACC 59.331 43.478 0.00 0.00 42.25 2.85
4224 5801 3.316588 TCGCATTTTGCTTGTTCTAACCA 59.683 39.130 0.00 0.00 42.25 3.67
4225 5802 3.425193 CGCATTTTGCTTGTTCTAACCAC 59.575 43.478 0.00 0.00 42.25 4.16
4226 5803 4.367450 GCATTTTGCTTGTTCTAACCACA 58.633 39.130 0.00 0.00 40.96 4.17
4227 5804 4.808364 GCATTTTGCTTGTTCTAACCACAA 59.192 37.500 0.00 0.00 40.96 3.33
4233 5810 2.605837 TGTTCTAACCACAAGACGCA 57.394 45.000 0.00 0.00 0.00 5.24
4234 5811 3.120321 TGTTCTAACCACAAGACGCAT 57.880 42.857 0.00 0.00 0.00 4.73
4235 5812 2.805671 TGTTCTAACCACAAGACGCATG 59.194 45.455 0.00 0.00 0.00 4.06
4236 5813 3.064207 GTTCTAACCACAAGACGCATGA 58.936 45.455 0.00 0.00 0.00 3.07
4237 5814 2.959516 TCTAACCACAAGACGCATGAG 58.040 47.619 0.00 0.00 0.00 2.90
4238 5815 2.002586 CTAACCACAAGACGCATGAGG 58.997 52.381 0.00 0.00 35.03 3.86
4239 5816 1.237285 AACCACAAGACGCATGAGGC 61.237 55.000 0.00 0.00 39.90 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 5.390885 GCGTGTATCTTGTGATGACAAACAT 60.391 40.000 4.68 0.61 41.62 2.71
154 155 2.352651 GCACATGCGTGTATCTTGTGAT 59.647 45.455 12.10 0.00 45.50 3.06
168 169 6.838198 AATGAATGAATATTGTGCACATGC 57.162 33.333 22.39 4.99 42.50 4.06
203 204 9.743937 GCAAACATTCAACATATTAACAATGTG 57.256 29.630 6.14 0.00 37.62 3.21
206 207 8.320617 AGGGCAAACATTCAACATATTAACAAT 58.679 29.630 0.00 0.00 0.00 2.71
208 209 7.039434 TCAGGGCAAACATTCAACATATTAACA 60.039 33.333 0.00 0.00 0.00 2.41
228 229 7.404671 TTGTTTTTATCCTCTTATTCAGGGC 57.595 36.000 0.00 0.00 0.00 5.19
258 259 9.674824 CACCAATCAGAATTCAGCTTATATTTC 57.325 33.333 8.44 0.00 0.00 2.17
275 276 3.366273 CCACAACGAATTCCACCAATCAG 60.366 47.826 0.00 0.00 0.00 2.90
289 290 0.177836 ATCGATCCATGCCACAACGA 59.822 50.000 0.00 0.00 0.00 3.85
311 312 1.305219 ATGGACGGATGTTTGCCACG 61.305 55.000 0.00 0.00 0.00 4.94
340 341 3.692690 TCGACGGATGGATGGATGTATA 58.307 45.455 0.00 0.00 0.00 1.47
342 343 1.989706 TCGACGGATGGATGGATGTA 58.010 50.000 0.00 0.00 0.00 2.29
343 344 1.273606 GATCGACGGATGGATGGATGT 59.726 52.381 0.00 0.00 31.51 3.06
354 355 1.608336 AGTGGGTTGGATCGACGGA 60.608 57.895 0.00 0.00 0.00 4.69
355 356 1.447838 CAGTGGGTTGGATCGACGG 60.448 63.158 0.00 0.00 0.00 4.79
356 357 2.100631 GCAGTGGGTTGGATCGACG 61.101 63.158 0.00 0.00 0.00 5.12
357 358 1.003839 TGCAGTGGGTTGGATCGAC 60.004 57.895 0.00 0.00 0.00 4.20
358 359 1.296392 CTGCAGTGGGTTGGATCGA 59.704 57.895 5.25 0.00 0.00 3.59
359 360 2.401766 GCTGCAGTGGGTTGGATCG 61.402 63.158 16.64 0.00 0.00 3.69
360 361 2.048603 GGCTGCAGTGGGTTGGATC 61.049 63.158 16.64 0.00 0.00 3.36
361 362 2.036256 GGCTGCAGTGGGTTGGAT 59.964 61.111 16.64 0.00 0.00 3.41
362 363 3.177884 AGGCTGCAGTGGGTTGGA 61.178 61.111 16.64 0.00 0.00 3.53
363 364 2.674380 GAGGCTGCAGTGGGTTGG 60.674 66.667 16.64 0.00 0.00 3.77
364 365 1.673665 GAGAGGCTGCAGTGGGTTG 60.674 63.158 16.64 0.00 0.00 3.77
365 366 1.835927 GAGAGAGGCTGCAGTGGGTT 61.836 60.000 16.64 0.00 0.00 4.11
366 367 2.203907 AGAGAGGCTGCAGTGGGT 60.204 61.111 16.64 0.00 0.00 4.51
367 368 1.551908 AAGAGAGAGGCTGCAGTGGG 61.552 60.000 16.64 0.00 0.00 4.61
374 375 1.707632 CGTGTGAAAGAGAGAGGCTG 58.292 55.000 0.00 0.00 0.00 4.85
434 435 1.834822 CTGGATCGGGGGAGAGGAC 60.835 68.421 0.00 0.00 0.00 3.85
439 440 1.915769 GGGATCTGGATCGGGGGAG 60.916 68.421 4.75 0.00 38.69 4.30
450 451 4.598894 CAGCGGCGGAGGGATCTG 62.599 72.222 9.78 0.98 0.00 2.90
843 876 0.826715 ACGTGCAGCAGTAGGATCAT 59.173 50.000 0.00 0.00 0.00 2.45
870 906 1.296715 GCCCTACCACACCTGACTG 59.703 63.158 0.00 0.00 0.00 3.51
1019 1055 1.123861 TCTGGAGAGTTGCAGCACCT 61.124 55.000 2.55 0.00 42.03 4.00
1028 1064 2.355193 GCGAGGGCTCTGGAGAGTT 61.355 63.158 0.00 0.00 43.85 3.01
1125 1165 3.808728 CAACCACAACTATCGGATGGAT 58.191 45.455 8.45 0.00 39.25 3.41
1268 1415 3.196207 TTGCTCAGGGGAGGCACAC 62.196 63.158 0.00 0.00 41.67 3.82
1729 1880 8.520835 ACATCATATAAGCATACACAGTTACG 57.479 34.615 0.00 0.00 0.00 3.18
1734 1885 6.091849 GCCAGACATCATATAAGCATACACAG 59.908 42.308 0.00 0.00 0.00 3.66
1820 1971 9.601217 GAAGAGTATGTACATTACAAGGAACAT 57.399 33.333 14.77 0.00 42.76 2.71
2084 2236 9.709495 CAGATTGGATTGATTGGAACTTAAAAA 57.291 29.630 0.00 0.00 0.00 1.94
2224 2578 6.947733 TCTCTGAAATTGAATTGCCCTCTTAA 59.052 34.615 0.00 0.00 0.00 1.85
2264 2618 6.230472 TGCCTGAACCATACATGTACATATC 58.770 40.000 7.96 5.75 0.00 1.63
2265 2619 6.186420 TGCCTGAACCATACATGTACATAT 57.814 37.500 7.96 0.00 0.00 1.78
2266 2620 5.622346 TGCCTGAACCATACATGTACATA 57.378 39.130 7.96 0.00 0.00 2.29
2267 2621 4.502105 TGCCTGAACCATACATGTACAT 57.498 40.909 7.96 1.41 0.00 2.29
2671 3496 7.086230 AGTTGAGTTCTACTGATAACCTACG 57.914 40.000 0.00 0.00 31.08 3.51
3161 4023 1.648467 GCTTGCGGATGGTGTTCTCC 61.648 60.000 0.00 0.00 0.00 3.71
3333 4246 7.281999 GGCTTGAAAGAAGATTAGATAAGCACT 59.718 37.037 0.00 0.00 39.62 4.40
3342 4255 6.591834 TCTCGAAAGGCTTGAAAGAAGATTAG 59.408 38.462 0.00 0.00 0.00 1.73
3356 4269 5.669164 AAAGAACTCTATCTCGAAAGGCT 57.331 39.130 0.00 0.00 0.00 4.58
3548 4466 6.696411 TGGGAAAAATATTGGTAGCAACAAG 58.304 36.000 9.99 0.00 0.00 3.16
3567 4485 3.198635 TGCAAGGAAACAAAACATGGGAA 59.801 39.130 0.00 0.00 0.00 3.97
3618 4536 4.552355 ACATGTGAACATCTTGCACAATG 58.448 39.130 0.00 6.05 44.62 2.82
3648 5223 5.585047 ACGGCATAAGAGATTTTAGTCAACC 59.415 40.000 0.00 0.00 0.00 3.77
3758 5333 2.224892 TGTACCTTGGTGCCTTGCATAA 60.225 45.455 2.03 0.00 41.91 1.90
3858 5434 3.411446 TGAAACAGAGCATGGTTGTAGG 58.589 45.455 0.00 0.00 39.58 3.18
3881 5457 9.691362 GAAAAGCATCAAAATCTTAACTAACCA 57.309 29.630 0.00 0.00 0.00 3.67
3931 5508 2.223735 ACTTGATCGTCGACACAACAGT 60.224 45.455 17.16 8.50 0.00 3.55
3932 5509 2.153817 CACTTGATCGTCGACACAACAG 59.846 50.000 17.16 7.85 0.00 3.16
3933 5510 2.124122 CACTTGATCGTCGACACAACA 58.876 47.619 17.16 6.97 0.00 3.33
3934 5511 1.136611 GCACTTGATCGTCGACACAAC 60.137 52.381 17.16 4.34 0.00 3.32
3935 5512 1.136690 GCACTTGATCGTCGACACAA 58.863 50.000 17.16 16.05 0.00 3.33
3936 5513 0.313987 AGCACTTGATCGTCGACACA 59.686 50.000 17.16 9.52 0.00 3.72
3937 5514 0.710567 CAGCACTTGATCGTCGACAC 59.289 55.000 17.16 6.89 0.00 3.67
3938 5515 0.388520 CCAGCACTTGATCGTCGACA 60.389 55.000 17.16 3.13 0.00 4.35
3939 5516 0.388649 ACCAGCACTTGATCGTCGAC 60.389 55.000 5.18 5.18 0.00 4.20
3940 5517 0.388520 CACCAGCACTTGATCGTCGA 60.389 55.000 0.00 0.00 0.00 4.20
3941 5518 0.667487 ACACCAGCACTTGATCGTCG 60.667 55.000 0.00 0.00 0.00 5.12
3942 5519 1.461127 GAACACCAGCACTTGATCGTC 59.539 52.381 0.00 0.00 0.00 4.20
3943 5520 1.512926 GAACACCAGCACTTGATCGT 58.487 50.000 0.00 0.00 0.00 3.73
3944 5521 0.439985 CGAACACCAGCACTTGATCG 59.560 55.000 0.00 0.00 0.00 3.69
3945 5522 1.195448 CACGAACACCAGCACTTGATC 59.805 52.381 0.00 0.00 0.00 2.92
3946 5523 1.229428 CACGAACACCAGCACTTGAT 58.771 50.000 0.00 0.00 0.00 2.57
3947 5524 1.436195 GCACGAACACCAGCACTTGA 61.436 55.000 0.00 0.00 0.00 3.02
3948 5525 1.009675 GCACGAACACCAGCACTTG 60.010 57.895 0.00 0.00 0.00 3.16
3949 5526 2.186826 GGCACGAACACCAGCACTT 61.187 57.895 0.00 0.00 0.00 3.16
3950 5527 2.591715 GGCACGAACACCAGCACT 60.592 61.111 0.00 0.00 0.00 4.40
3963 5540 1.227853 AAGGACTCAACCACGGCAC 60.228 57.895 0.00 0.00 0.00 5.01
3964 5541 1.227823 CAAGGACTCAACCACGGCA 60.228 57.895 0.00 0.00 0.00 5.69
3965 5542 2.617274 GCAAGGACTCAACCACGGC 61.617 63.158 0.00 0.00 0.00 5.68
3966 5543 1.966451 GGCAAGGACTCAACCACGG 60.966 63.158 0.00 0.00 0.00 4.94
3967 5544 2.317609 CGGCAAGGACTCAACCACG 61.318 63.158 0.00 0.00 0.00 4.94
3968 5545 1.070786 TCGGCAAGGACTCAACCAC 59.929 57.895 0.00 0.00 0.00 4.16
3969 5546 1.070786 GTCGGCAAGGACTCAACCA 59.929 57.895 0.00 0.00 34.09 3.67
3970 5547 0.951040 CAGTCGGCAAGGACTCAACC 60.951 60.000 1.78 0.00 45.20 3.77
3971 5548 0.249911 ACAGTCGGCAAGGACTCAAC 60.250 55.000 1.78 0.00 45.20 3.18
3972 5549 0.468226 AACAGTCGGCAAGGACTCAA 59.532 50.000 1.78 0.00 45.20 3.02
3973 5550 0.249868 CAACAGTCGGCAAGGACTCA 60.250 55.000 1.78 0.00 45.20 3.41
3974 5551 0.249911 ACAACAGTCGGCAAGGACTC 60.250 55.000 1.78 0.00 45.20 3.36
4066 5643 6.015991 TGTTTAAAACAACCCCTAAGGAGA 57.984 37.500 0.00 0.00 38.72 3.71
4112 5689 6.238429 GGATTGCAATCTTTGAACAGCAAAAA 60.238 34.615 32.48 0.00 45.26 1.94
4113 5690 5.236911 GGATTGCAATCTTTGAACAGCAAAA 59.763 36.000 32.48 0.00 45.26 2.44
4114 5691 4.751098 GGATTGCAATCTTTGAACAGCAAA 59.249 37.500 32.48 0.00 43.97 3.68
4115 5692 4.039488 AGGATTGCAATCTTTGAACAGCAA 59.961 37.500 32.48 0.00 44.73 3.91
4116 5693 3.575256 AGGATTGCAATCTTTGAACAGCA 59.425 39.130 32.48 0.00 35.73 4.41
4117 5694 4.184079 AGGATTGCAATCTTTGAACAGC 57.816 40.909 32.48 16.38 35.73 4.40
4118 5695 6.506500 ACTAGGATTGCAATCTTTGAACAG 57.493 37.500 32.48 22.57 35.73 3.16
4119 5696 6.489700 TGAACTAGGATTGCAATCTTTGAACA 59.510 34.615 32.48 25.28 35.73 3.18
4120 5697 6.913170 TGAACTAGGATTGCAATCTTTGAAC 58.087 36.000 32.48 23.65 35.73 3.18
4121 5698 7.707624 ATGAACTAGGATTGCAATCTTTGAA 57.292 32.000 32.48 19.18 35.73 2.69
4122 5699 7.707624 AATGAACTAGGATTGCAATCTTTGA 57.292 32.000 32.48 17.94 35.73 2.69
4123 5700 8.767478 AAAATGAACTAGGATTGCAATCTTTG 57.233 30.769 32.48 28.13 35.73 2.77
4124 5701 8.587608 TGAAAATGAACTAGGATTGCAATCTTT 58.412 29.630 32.48 24.15 35.73 2.52
4125 5702 8.125978 TGAAAATGAACTAGGATTGCAATCTT 57.874 30.769 32.48 28.87 35.73 2.40
4126 5703 7.707624 TGAAAATGAACTAGGATTGCAATCT 57.292 32.000 32.48 22.35 35.73 2.40
4127 5704 8.761575 TTTGAAAATGAACTAGGATTGCAATC 57.238 30.769 27.91 27.91 34.66 2.67
4128 5705 8.587608 TCTTTGAAAATGAACTAGGATTGCAAT 58.412 29.630 12.83 12.83 0.00 3.56
4129 5706 7.950512 TCTTTGAAAATGAACTAGGATTGCAA 58.049 30.769 0.00 0.00 0.00 4.08
4130 5707 7.523293 TCTTTGAAAATGAACTAGGATTGCA 57.477 32.000 0.00 0.00 0.00 4.08
4131 5708 7.430502 CGATCTTTGAAAATGAACTAGGATTGC 59.569 37.037 0.00 0.00 33.45 3.56
4132 5709 8.668353 TCGATCTTTGAAAATGAACTAGGATTG 58.332 33.333 0.00 0.00 33.45 2.67
4133 5710 8.792830 TCGATCTTTGAAAATGAACTAGGATT 57.207 30.769 0.00 0.00 33.45 3.01
4134 5711 8.792830 TTCGATCTTTGAAAATGAACTAGGAT 57.207 30.769 0.00 0.00 33.45 3.24
4135 5712 8.615878 TTTCGATCTTTGAAAATGAACTAGGA 57.384 30.769 0.00 0.00 33.45 2.94
4136 5713 9.282247 CATTTCGATCTTTGAAAATGAACTAGG 57.718 33.333 0.00 0.00 38.68 3.02
4137 5714 9.831737 ACATTTCGATCTTTGAAAATGAACTAG 57.168 29.630 12.21 0.00 38.68 2.57
4139 5716 8.971321 CAACATTTCGATCTTTGAAAATGAACT 58.029 29.630 12.21 0.00 38.68 3.01
4140 5717 8.755018 ACAACATTTCGATCTTTGAAAATGAAC 58.245 29.630 12.21 0.00 38.68 3.18
4141 5718 8.870160 ACAACATTTCGATCTTTGAAAATGAA 57.130 26.923 12.21 0.00 38.68 2.57
4142 5719 8.754096 CAACAACATTTCGATCTTTGAAAATGA 58.246 29.630 12.21 0.00 38.68 2.57
4143 5720 8.754096 TCAACAACATTTCGATCTTTGAAAATG 58.246 29.630 5.40 5.40 38.68 2.32
4144 5721 8.755018 GTCAACAACATTTCGATCTTTGAAAAT 58.245 29.630 0.00 0.00 38.68 1.82
4145 5722 7.221838 GGTCAACAACATTTCGATCTTTGAAAA 59.778 33.333 0.00 0.00 38.68 2.29
4146 5723 6.695278 GGTCAACAACATTTCGATCTTTGAAA 59.305 34.615 0.00 0.00 39.45 2.69
4147 5724 6.205784 GGTCAACAACATTTCGATCTTTGAA 58.794 36.000 0.00 0.00 0.00 2.69
4148 5725 5.278266 GGGTCAACAACATTTCGATCTTTGA 60.278 40.000 0.00 0.00 0.00 2.69
4149 5726 4.917415 GGGTCAACAACATTTCGATCTTTG 59.083 41.667 0.00 0.00 0.00 2.77
4150 5727 4.827284 AGGGTCAACAACATTTCGATCTTT 59.173 37.500 0.00 0.00 0.00 2.52
4151 5728 4.216257 CAGGGTCAACAACATTTCGATCTT 59.784 41.667 0.00 0.00 0.00 2.40
4152 5729 3.753272 CAGGGTCAACAACATTTCGATCT 59.247 43.478 0.00 0.00 0.00 2.75
4153 5730 3.502211 ACAGGGTCAACAACATTTCGATC 59.498 43.478 0.00 0.00 0.00 3.69
4154 5731 3.486383 ACAGGGTCAACAACATTTCGAT 58.514 40.909 0.00 0.00 0.00 3.59
4155 5732 2.925724 ACAGGGTCAACAACATTTCGA 58.074 42.857 0.00 0.00 0.00 3.71
4156 5733 3.315191 AGAACAGGGTCAACAACATTTCG 59.685 43.478 0.00 0.00 0.00 3.46
4157 5734 4.918810 AGAACAGGGTCAACAACATTTC 57.081 40.909 0.00 0.00 0.00 2.17
4158 5735 4.956075 AGAAGAACAGGGTCAACAACATTT 59.044 37.500 0.00 0.00 0.00 2.32
4159 5736 4.536765 AGAAGAACAGGGTCAACAACATT 58.463 39.130 0.00 0.00 0.00 2.71
4160 5737 4.170468 AGAAGAACAGGGTCAACAACAT 57.830 40.909 0.00 0.00 0.00 2.71
4161 5738 3.644966 AGAAGAACAGGGTCAACAACA 57.355 42.857 0.00 0.00 0.00 3.33
4162 5739 4.083271 GCATAGAAGAACAGGGTCAACAAC 60.083 45.833 0.00 0.00 0.00 3.32
4163 5740 4.072131 GCATAGAAGAACAGGGTCAACAA 58.928 43.478 0.00 0.00 0.00 2.83
4164 5741 3.327757 AGCATAGAAGAACAGGGTCAACA 59.672 43.478 0.00 0.00 0.00 3.33
4165 5742 3.944087 AGCATAGAAGAACAGGGTCAAC 58.056 45.455 0.00 0.00 0.00 3.18
4166 5743 4.640771 AAGCATAGAAGAACAGGGTCAA 57.359 40.909 0.00 0.00 0.00 3.18
4167 5744 5.755409 TTAAGCATAGAAGAACAGGGTCA 57.245 39.130 0.00 0.00 0.00 4.02
4168 5745 6.038714 CCATTTAAGCATAGAAGAACAGGGTC 59.961 42.308 0.00 0.00 0.00 4.46
4169 5746 5.888161 CCATTTAAGCATAGAAGAACAGGGT 59.112 40.000 0.00 0.00 0.00 4.34
4170 5747 5.888161 ACCATTTAAGCATAGAAGAACAGGG 59.112 40.000 0.00 0.00 0.00 4.45
4171 5748 8.506168 TTACCATTTAAGCATAGAAGAACAGG 57.494 34.615 0.00 0.00 0.00 4.00
4178 5755 9.781834 CGACATTTTTACCATTTAAGCATAGAA 57.218 29.630 0.00 0.00 0.00 2.10
4179 5756 7.913297 GCGACATTTTTACCATTTAAGCATAGA 59.087 33.333 0.00 0.00 0.00 1.98
4180 5757 7.700234 TGCGACATTTTTACCATTTAAGCATAG 59.300 33.333 0.00 0.00 0.00 2.23
4181 5758 7.539436 TGCGACATTTTTACCATTTAAGCATA 58.461 30.769 0.00 0.00 0.00 3.14
4182 5759 6.393990 TGCGACATTTTTACCATTTAAGCAT 58.606 32.000 0.00 0.00 0.00 3.79
4183 5760 5.773575 TGCGACATTTTTACCATTTAAGCA 58.226 33.333 0.00 0.00 0.00 3.91
4184 5761 6.885735 ATGCGACATTTTTACCATTTAAGC 57.114 33.333 0.00 0.00 0.00 3.09
4185 5762 9.527566 CAAAATGCGACATTTTTACCATTTAAG 57.472 29.630 20.50 8.15 33.31 1.85
4186 5763 8.012241 GCAAAATGCGACATTTTTACCATTTAA 58.988 29.630 20.50 0.00 33.31 1.52
4187 5764 7.513968 GCAAAATGCGACATTTTTACCATTTA 58.486 30.769 20.50 0.00 33.31 1.40
4188 5765 6.369799 GCAAAATGCGACATTTTTACCATTT 58.630 32.000 20.50 6.26 35.21 2.32
4189 5766 5.925907 GCAAAATGCGACATTTTTACCATT 58.074 33.333 20.50 1.05 31.71 3.16
4190 5767 5.529014 GCAAAATGCGACATTTTTACCAT 57.471 34.783 20.50 4.38 31.71 3.55
4191 5768 4.981389 GCAAAATGCGACATTTTTACCA 57.019 36.364 20.50 0.00 31.71 3.25
4204 5781 4.367450 TGTGGTTAGAACAAGCAAAATGC 58.633 39.130 0.00 0.00 45.46 3.56
4205 5782 6.515043 CTTGTGGTTAGAACAAGCAAAATG 57.485 37.500 3.60 0.00 45.68 2.32
4213 5790 2.907634 TGCGTCTTGTGGTTAGAACAA 58.092 42.857 0.00 0.00 36.19 2.83
4214 5791 2.605837 TGCGTCTTGTGGTTAGAACA 57.394 45.000 0.00 0.00 0.00 3.18
4215 5792 3.064207 TCATGCGTCTTGTGGTTAGAAC 58.936 45.455 0.00 0.00 0.00 3.01
4216 5793 3.325870 CTCATGCGTCTTGTGGTTAGAA 58.674 45.455 0.00 0.00 0.00 2.10
4217 5794 2.353704 CCTCATGCGTCTTGTGGTTAGA 60.354 50.000 0.00 0.00 0.00 2.10
4218 5795 2.002586 CCTCATGCGTCTTGTGGTTAG 58.997 52.381 0.00 0.00 0.00 2.34
4219 5796 1.943968 GCCTCATGCGTCTTGTGGTTA 60.944 52.381 12.08 0.00 31.79 2.85
4220 5797 1.237285 GCCTCATGCGTCTTGTGGTT 61.237 55.000 12.08 0.00 31.79 3.67
4221 5798 1.672356 GCCTCATGCGTCTTGTGGT 60.672 57.895 12.08 0.00 31.79 4.16
4222 5799 3.181367 GCCTCATGCGTCTTGTGG 58.819 61.111 0.00 8.45 0.00 4.17


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

AutoCloner maintained by Alex Coulton.