Multiple sequence alignment - TraesCS4B01G245300

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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 TraesCS4B01G245300 chr4B 100.000 6205 0 0 1 6205 507242695 507248899 0.000000e+00 11459.0
1 TraesCS4B01G245300 chr4B 100.000 31 0 0 157 187 15965585 15965615 2.420000e-04 58.4
2 TraesCS4B01G245300 chr4B 100.000 31 0 0 157 187 15994807 15994837 2.420000e-04 58.4
3 TraesCS4B01G245300 chr4B 100.000 31 0 0 157 187 16024009 16024039 2.420000e-04 58.4
4 TraesCS4B01G245300 chr4D 94.869 3995 162 22 2248 6205 408795803 408791815 0.000000e+00 6202.0
5 TraesCS4B01G245300 chr4D 90.057 2283 140 37 1 2252 408803234 408801008 0.000000e+00 2878.0
6 TraesCS4B01G245300 chr4A 96.093 2073 79 2 3519 5590 80169175 80167104 0.000000e+00 3378.0
7 TraesCS4B01G245300 chr4A 90.581 2442 162 31 1191 3589 80171583 80169167 0.000000e+00 3173.0
8 TraesCS4B01G245300 chr4A 90.596 638 31 10 5587 6205 80166944 80166317 0.000000e+00 819.0
9 TraesCS4B01G245300 chr4A 82.025 968 129 25 251 1201 80172538 80171599 0.000000e+00 782.0
10 TraesCS4B01G245300 chr4A 90.141 71 7 0 3519 3589 80169206 80169136 6.620000e-15 93.5
11 TraesCS4B01G245300 chr4A 80.508 118 20 2 378 493 627571146 627571030 3.080000e-13 87.9
12 TraesCS4B01G245300 chr1A 79.319 382 65 9 1 368 449845976 449845595 7.980000e-64 255.0
13 TraesCS4B01G245300 chr1A 75.123 406 86 12 380 777 432763428 432763826 6.390000e-40 176.0
14 TraesCS4B01G245300 chr6A 80.000 255 46 3 1 251 615274406 615274659 3.820000e-42 183.0
15 TraesCS4B01G245300 chr6A 76.571 175 40 1 625 799 534935994 534935821 1.840000e-15 95.3
16 TraesCS4B01G245300 chr6A 73.664 262 54 5 125 371 65660216 65659955 3.080000e-13 87.9
17 TraesCS4B01G245300 chr7D 75.448 391 79 15 1 380 634289376 634289760 2.300000e-39 174.0
18 TraesCS4B01G245300 chr7D 83.721 86 13 1 284 369 524867335 524867419 5.160000e-11 80.5
19 TraesCS4B01G245300 chr3B 75.194 387 77 14 10 380 101811883 101811500 1.380000e-36 165.0
20 TraesCS4B01G245300 chr3B 77.016 248 54 3 6 251 178311133 178311379 8.390000e-29 139.0
21 TraesCS4B01G245300 chr3B 85.135 74 8 3 309 380 367476051 367476123 8.630000e-09 73.1
22 TraesCS4B01G245300 chr1B 77.083 288 61 5 402 687 629921323 629921039 1.790000e-35 161.0
23 TraesCS4B01G245300 chr1B 74.157 356 69 18 40 379 317444681 317445029 6.530000e-25 126.0
24 TraesCS4B01G245300 chr1B 79.570 93 19 0 685 777 583906937 583907029 4.010000e-07 67.6
25 TraesCS4B01G245300 chr6B 80.189 212 38 4 6 216 523208149 523207941 8.330000e-34 156.0
26 TraesCS4B01G245300 chr5B 74.278 381 88 7 399 775 546323281 546323655 1.080000e-32 152.0
27 TraesCS4B01G245300 chr5B 74.257 404 72 22 380 777 703850383 703850006 2.330000e-29 141.0
28 TraesCS4B01G245300 chr5B 82.677 127 18 2 378 502 26884041 26884165 6.580000e-20 110.0
29 TraesCS4B01G245300 chr5B 92.208 77 6 0 978 1054 387898396 387898472 6.580000e-20 110.0
30 TraesCS4B01G245300 chr5B 77.632 152 34 0 466 617 544325174 544325325 6.620000e-15 93.5
31 TraesCS4B01G245300 chr2D 75.585 299 70 3 395 692 589507033 589507329 1.800000e-30 145.0
32 TraesCS4B01G245300 chr5A 75.224 335 64 14 401 732 290514943 290514625 2.330000e-29 141.0
33 TraesCS4B01G245300 chr5A 76.970 165 37 1 396 560 9467391 9467554 6.620000e-15 93.5
34 TraesCS4B01G245300 chr7B 74.133 375 80 9 10 380 509563240 509562879 8.390000e-29 139.0
35 TraesCS4B01G245300 chr1D 75.497 302 58 7 84 371 456173909 456174208 3.900000e-27 134.0
36 TraesCS4B01G245300 chr3A 80.405 148 25 4 72 217 636854044 636853899 6.580000e-20 110.0
37 TraesCS4B01G245300 chr5D 71.209 455 104 16 376 827 377173758 377173328 8.570000e-14 89.8
38 TraesCS4B01G245300 chr2B 94.000 50 2 1 6 55 581463321 581463369 2.400000e-09 75.0


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 TraesCS4B01G245300 chr4B 507242695 507248899 6204 False 11459.0 11459 100.0000 1 6205 1 chr4B.!!$F4 6204
1 TraesCS4B01G245300 chr4D 408791815 408795803 3988 True 6202.0 6202 94.8690 2248 6205 1 chr4D.!!$R1 3957
2 TraesCS4B01G245300 chr4D 408801008 408803234 2226 True 2878.0 2878 90.0570 1 2252 1 chr4D.!!$R2 2251
3 TraesCS4B01G245300 chr4A 80166317 80172538 6221 True 1649.1 3378 89.8872 251 6205 5 chr4A.!!$R2 5954

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
218 220 0.311790 TAGTCGTCGCCGTTGAACTT 59.688 50.000 0.00 0.0 35.01 2.66 F
1057 1083 0.249398 ACGGCCTAGCTGGTAAAGTG 59.751 55.000 0.00 0.0 39.57 3.16 F
1058 1084 0.462047 CGGCCTAGCTGGTAAAGTGG 60.462 60.000 0.00 0.0 38.35 4.00 F
1059 1085 0.618981 GGCCTAGCTGGTAAAGTGGT 59.381 55.000 0.00 0.0 38.35 4.16 F
1622 1691 0.913924 TTGGCTGGCAGATGAGATGA 59.086 50.000 20.86 0.0 0.00 2.92 F
2347 2439 0.919710 GGGAAGGTGGAGTAGGCAAT 59.080 55.000 0.00 0.0 0.00 3.56 F
3326 3445 1.073763 ACAGAACAACATGGCCTGCTA 59.926 47.619 3.32 0.0 0.00 3.49 F
4250 4432 0.179048 CTCACTGGCAGGTGTGTTGA 60.179 55.000 20.34 11.0 38.28 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1084 1110 0.108472 TCAGCGCTGAACCAGATCTG 60.108 55.000 36.62 16.24 36.53 2.90 R
2322 2402 0.253020 TACTCCACCTTCCCCTTCCC 60.253 60.000 0.00 0.00 0.00 3.97 R
2325 2405 0.914902 GCCTACTCCACCTTCCCCTT 60.915 60.000 0.00 0.00 0.00 3.95 R
2326 2406 1.307084 GCCTACTCCACCTTCCCCT 60.307 63.158 0.00 0.00 0.00 4.79 R
3362 3481 0.679002 ATGCGTGCCTCTCTGCAATT 60.679 50.000 0.00 0.00 44.11 2.32 R
3399 3518 0.749091 TCATACAGGTGCAGCATGGC 60.749 55.000 19.63 0.00 35.86 4.40 R
5028 5210 0.099259 CCATGTATGTGCAGCCAACG 59.901 55.000 0.00 0.00 0.00 4.10 R
5410 5592 0.178950 AGGCATCGCTCAGGAGGATA 60.179 55.000 0.00 0.00 0.00 2.59 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
70 71 1.303317 GAGGCCACCAAACGACCAT 60.303 57.895 5.01 0.00 0.00 3.55
76 77 3.181494 GGCCACCAAACGACCATTAATAC 60.181 47.826 0.00 0.00 0.00 1.89
77 78 3.692593 GCCACCAAACGACCATTAATACT 59.307 43.478 0.00 0.00 0.00 2.12
85 86 6.613755 AACGACCATTAATACTGGCATAAC 57.386 37.500 0.00 0.00 37.27 1.89
119 120 1.586541 CGATATCGCTGCTGCCCTA 59.413 57.895 12.95 2.31 35.36 3.53
122 123 1.121407 ATATCGCTGCTGCCCTACCA 61.121 55.000 10.24 0.00 35.36 3.25
123 124 1.334384 TATCGCTGCTGCCCTACCAA 61.334 55.000 10.24 0.00 35.36 3.67
151 153 2.839486 TGACCTTGTCGATGAAAGCT 57.161 45.000 0.00 0.00 34.95 3.74
155 157 1.089920 CTTGTCGATGAAAGCTGGGG 58.910 55.000 0.00 0.00 0.00 4.96
162 164 2.637947 GATGAAAGCTGGGGAGTCTTC 58.362 52.381 0.00 0.00 0.00 2.87
163 165 0.321671 TGAAAGCTGGGGAGTCTTCG 59.678 55.000 0.00 0.00 0.00 3.79
173 175 1.639298 GGAGTCTTCGTGCATGTGCC 61.639 60.000 5.68 0.00 41.18 5.01
189 191 3.458163 CCCCTAAGGACGAGCGCA 61.458 66.667 11.47 0.00 38.24 6.09
192 194 1.517257 CCTAAGGACGAGCGCACTG 60.517 63.158 11.47 0.02 0.00 3.66
204 206 2.202623 GCACTGGAGCCGTAGTCG 60.203 66.667 0.00 0.00 0.00 4.18
218 220 0.311790 TAGTCGTCGCCGTTGAACTT 59.688 50.000 0.00 0.00 35.01 2.66
229 231 4.485163 GCCGTTGAACTTTTGCATAGATT 58.515 39.130 3.58 0.00 0.00 2.40
240 242 5.871465 TTTGCATAGATTTGAAGCACGTA 57.129 34.783 0.00 0.00 34.56 3.57
251 253 4.320667 TGAAGCACGTAACATCAAATCG 57.679 40.909 0.00 0.00 0.00 3.34
252 254 3.991121 TGAAGCACGTAACATCAAATCGA 59.009 39.130 0.00 0.00 0.00 3.59
257 272 4.027556 GCACGTAACATCAAATCGAAAACG 59.972 41.667 0.00 0.00 0.00 3.60
280 296 3.542969 AACCTAGCCACCCAAGAAAAT 57.457 42.857 0.00 0.00 0.00 1.82
298 314 5.774690 AGAAAATGGCAGGAATCTACAACAA 59.225 36.000 0.00 0.00 0.00 2.83
455 472 2.928396 CCCCCTGTCTCGGTGGTT 60.928 66.667 0.00 0.00 0.00 3.67
463 480 2.163815 CTGTCTCGGTGGTTCGTCTATT 59.836 50.000 0.00 0.00 0.00 1.73
464 481 3.346315 TGTCTCGGTGGTTCGTCTATTA 58.654 45.455 0.00 0.00 0.00 0.98
493 510 0.814010 GGCGTGTGAAGGTGTGTCTT 60.814 55.000 0.00 0.00 0.00 3.01
507 524 4.098960 GGTGTGTCTTCGGTGGATCTTATA 59.901 45.833 0.00 0.00 0.00 0.98
529 546 2.159037 GGATTCGGTCGGTTTTTGTCTC 59.841 50.000 0.00 0.00 0.00 3.36
554 571 2.111384 GGATCTGCTTGGACCTAGTCA 58.889 52.381 4.81 2.98 33.68 3.41
579 596 1.742900 CGCCTGCGTTCGTGTATCTG 61.743 60.000 2.83 0.00 34.35 2.90
581 598 0.458543 CCTGCGTTCGTGTATCTGCT 60.459 55.000 0.00 0.00 0.00 4.24
582 599 1.202256 CCTGCGTTCGTGTATCTGCTA 60.202 52.381 0.00 0.00 0.00 3.49
583 600 2.112522 CTGCGTTCGTGTATCTGCTAG 58.887 52.381 0.00 0.00 0.00 3.42
596 613 4.686191 ATCTGCTAGTTGGATCCTTCTG 57.314 45.455 14.23 7.36 0.00 3.02
620 640 2.405357 CGACGCTTCTATTTATCGGCAG 59.595 50.000 0.00 0.00 0.00 4.85
666 686 5.272283 TCCTTTAGGACCTAAGCATAACG 57.728 43.478 13.65 0.00 39.78 3.18
671 691 4.820894 AGGACCTAAGCATAACGACTTT 57.179 40.909 0.00 0.00 0.00 2.66
732 753 1.137872 GGAAGGAGCGATGATGACAGT 59.862 52.381 0.00 0.00 0.00 3.55
786 807 1.944024 CGTTAGGTGGTTTGCAGACAA 59.056 47.619 9.87 0.00 0.00 3.18
788 809 2.270352 TAGGTGGTTTGCAGACAAGG 57.730 50.000 9.87 0.00 37.04 3.61
795 816 3.568007 TGGTTTGCAGACAAGGATGTAAC 59.432 43.478 9.87 0.00 40.74 2.50
885 906 3.409026 AACAGATGAGTGTCTTCACCC 57.591 47.619 0.00 0.00 44.83 4.61
886 907 2.329267 ACAGATGAGTGTCTTCACCCA 58.671 47.619 0.00 0.00 44.83 4.51
887 908 2.705658 ACAGATGAGTGTCTTCACCCAA 59.294 45.455 0.00 0.00 44.83 4.12
1054 1080 2.148446 TCTACGGCCTAGCTGGTAAA 57.852 50.000 0.00 0.00 39.57 2.01
1055 1081 2.029623 TCTACGGCCTAGCTGGTAAAG 58.970 52.381 0.00 0.00 39.57 1.85
1056 1082 1.755380 CTACGGCCTAGCTGGTAAAGT 59.245 52.381 0.00 0.00 39.57 2.66
1057 1083 0.249398 ACGGCCTAGCTGGTAAAGTG 59.751 55.000 0.00 0.00 39.57 3.16
1058 1084 0.462047 CGGCCTAGCTGGTAAAGTGG 60.462 60.000 0.00 0.00 38.35 4.00
1059 1085 0.618981 GGCCTAGCTGGTAAAGTGGT 59.381 55.000 0.00 0.00 38.35 4.16
1060 1086 1.835531 GGCCTAGCTGGTAAAGTGGTA 59.164 52.381 0.00 0.00 38.35 3.25
1061 1087 2.237893 GGCCTAGCTGGTAAAGTGGTAA 59.762 50.000 0.00 0.00 38.35 2.85
1080 1106 4.408821 GCACCTCGTCCCATGCCA 62.409 66.667 0.00 0.00 31.71 4.92
1084 1110 1.144057 CCTCGTCCCATGCCAGTAC 59.856 63.158 0.00 0.00 0.00 2.73
1128 1163 3.609373 TGTAGCTAATTCGTGCGTGTTAC 59.391 43.478 0.00 0.00 0.00 2.50
1129 1164 2.679450 AGCTAATTCGTGCGTGTTACA 58.321 42.857 0.00 0.00 0.00 2.41
1380 1443 4.978083 ATACAAGCAATTGCAAGGAGAG 57.022 40.909 30.89 14.36 45.16 3.20
1456 1522 1.530013 CCTCACTTGCCCAGCTTTGG 61.530 60.000 0.00 0.00 0.00 3.28
1491 1557 3.704800 AGGCTAGGAAGAGAACCAAAC 57.295 47.619 0.00 0.00 0.00 2.93
1493 1559 3.589288 AGGCTAGGAAGAGAACCAAACAT 59.411 43.478 0.00 0.00 0.00 2.71
1494 1560 4.043435 AGGCTAGGAAGAGAACCAAACATT 59.957 41.667 0.00 0.00 0.00 2.71
1495 1561 4.156739 GGCTAGGAAGAGAACCAAACATTG 59.843 45.833 0.00 0.00 0.00 2.82
1517 1586 3.983988 GCTTTGCCAAGAAGTAGAAAAGC 59.016 43.478 0.86 0.00 40.62 3.51
1527 1596 8.706035 CCAAGAAGTAGAAAAGCATGAAATTTG 58.294 33.333 0.00 0.00 0.00 2.32
1556 1625 6.839124 ATTAACTCACAATGCTGGATTTGA 57.161 33.333 0.00 0.07 0.00 2.69
1563 1632 5.412594 TCACAATGCTGGATTTGAGTAGAAC 59.587 40.000 0.00 0.00 0.00 3.01
1570 1639 3.325425 TGGATTTGAGTAGAACCCGTGAA 59.675 43.478 0.00 0.00 0.00 3.18
1572 1641 3.396260 TTTGAGTAGAACCCGTGAAGG 57.604 47.619 0.00 0.00 40.63 3.46
1573 1642 2.005370 TGAGTAGAACCCGTGAAGGT 57.995 50.000 0.00 0.00 44.00 3.50
1622 1691 0.913924 TTGGCTGGCAGATGAGATGA 59.086 50.000 20.86 0.00 0.00 2.92
1633 1702 5.274718 GCAGATGAGATGAATTTGCTTGAG 58.725 41.667 0.00 0.00 33.55 3.02
1693 1762 4.179361 CAGTGGCCTGCTTTTCCA 57.821 55.556 3.32 0.00 0.00 3.53
1758 1827 4.465305 GCACTAATAGGGTACGGGATATGT 59.535 45.833 0.00 0.00 0.00 2.29
1760 1829 5.021458 ACTAATAGGGTACGGGATATGTGG 58.979 45.833 0.00 0.00 0.00 4.17
1765 1839 1.068417 TACGGGATATGTGGCGTGC 59.932 57.895 0.00 0.00 0.00 5.34
1787 1861 1.456705 TTGCACCCCTGGAAACCAC 60.457 57.895 0.00 0.00 0.00 4.16
1801 1875 6.045072 TGGAAACCACGATACTTCTGTTAT 57.955 37.500 0.00 0.00 0.00 1.89
1878 1957 6.149474 AGCTGTATGTTAAACTCATGGTGTTC 59.851 38.462 5.69 0.00 0.00 3.18
1970 2049 3.208594 ACATCGATGTTCATGTGGATGG 58.791 45.455 25.18 0.00 37.90 3.51
2004 2084 4.675976 TTATGTATGGGTTCTACCACCG 57.324 45.455 0.00 0.00 44.72 4.94
2048 2128 5.856126 TGTTCCTTTCATGTTACGATGTC 57.144 39.130 0.00 0.00 0.00 3.06
2103 2183 3.624326 TTGCAAGGAAACAACATCTCG 57.376 42.857 0.00 0.00 0.00 4.04
2126 2206 5.112686 GCTCCTTTGTCAGGTATTAGTCAG 58.887 45.833 0.00 0.00 44.37 3.51
2177 2257 2.575735 TGGGTTCCTTGCTGTCATATCA 59.424 45.455 0.00 0.00 0.00 2.15
2221 2301 2.891580 ACATATACTCCGCGATGAAGGT 59.108 45.455 8.23 0.00 0.00 3.50
2321 2401 5.240891 TCTCAAGTGAGTGATGATTCCAAC 58.759 41.667 8.14 0.00 42.60 3.77
2322 2402 3.996363 TCAAGTGAGTGATGATTCCAACG 59.004 43.478 0.00 0.00 0.00 4.10
2323 2403 2.977914 AGTGAGTGATGATTCCAACGG 58.022 47.619 0.00 0.00 0.00 4.44
2324 2404 2.009774 GTGAGTGATGATTCCAACGGG 58.990 52.381 0.00 0.00 0.00 5.28
2325 2405 1.905894 TGAGTGATGATTCCAACGGGA 59.094 47.619 0.00 0.00 43.03 5.14
2346 2438 1.205460 GGGGAAGGTGGAGTAGGCAA 61.205 60.000 0.00 0.00 0.00 4.52
2347 2439 0.919710 GGGAAGGTGGAGTAGGCAAT 59.080 55.000 0.00 0.00 0.00 3.56
2408 2500 8.077991 CACATGTTATTCAGAATCAGTTGTGTT 58.922 33.333 0.00 0.00 31.04 3.32
2419 2511 8.022550 CAGAATCAGTTGTGTTATGTGCATAAA 58.977 33.333 6.24 0.00 35.30 1.40
2421 2513 5.698832 TCAGTTGTGTTATGTGCATAAAGC 58.301 37.500 6.24 3.95 45.96 3.51
2434 2526 2.094597 GCATAAAGCAACATCACTGCCA 60.095 45.455 0.00 0.00 44.79 4.92
2449 2541 2.954318 ACTGCCATTCATTAGATGCACC 59.046 45.455 0.00 0.00 0.00 5.01
2457 2549 1.596260 CATTAGATGCACCGCTGTCAG 59.404 52.381 0.00 0.00 0.00 3.51
2467 2559 1.940613 ACCGCTGTCAGTTTTGAGAAC 59.059 47.619 0.93 0.00 32.98 3.01
2482 2574 4.890158 TGAGAACTATGAAGCCAGAACA 57.110 40.909 0.00 0.00 0.00 3.18
2511 2603 2.671396 CCGTATGTTTAACTCTGCGCTT 59.329 45.455 9.73 0.00 0.00 4.68
2522 2614 3.020026 CTGCGCTTGCCTGAACTCG 62.020 63.158 9.73 0.00 38.03 4.18
2525 2617 1.956620 GCGCTTGCCTGAACTCGTAC 61.957 60.000 0.00 0.00 0.00 3.67
2584 2676 7.199766 TGCAAACCTTAACTAGTGAATTTGTG 58.800 34.615 15.76 4.63 0.00 3.33
2620 2712 9.049523 TGAAACAACTATCTCTCATATCATTGC 57.950 33.333 0.00 0.00 0.00 3.56
2639 2731 3.937814 TGCTGTGTATTCTTTCGGTGAT 58.062 40.909 0.00 0.00 0.00 3.06
2641 2733 4.759693 TGCTGTGTATTCTTTCGGTGATTT 59.240 37.500 0.00 0.00 0.00 2.17
2643 2735 5.334879 GCTGTGTATTCTTTCGGTGATTTGT 60.335 40.000 0.00 0.00 0.00 2.83
2651 2743 2.442212 TCGGTGATTTGTCGCTGTTA 57.558 45.000 0.00 0.00 0.00 2.41
2689 2781 8.469309 TGATTATCATTGGAAGGGAAAGATTC 57.531 34.615 0.00 0.00 0.00 2.52
2697 2789 5.644188 TGGAAGGGAAAGATTCATCTTGTT 58.356 37.500 2.74 0.00 45.83 2.83
2708 2800 9.688592 AAAGATTCATCTTGTTCTTGCTTTTAG 57.311 29.630 2.74 0.00 45.83 1.85
2715 2807 4.053469 TGTTCTTGCTTTTAGTTTGCCC 57.947 40.909 0.00 0.00 0.00 5.36
2731 2823 3.788227 TGCCCTGTACTCATTTTGTCT 57.212 42.857 0.00 0.00 0.00 3.41
2752 2844 4.015084 CTCCAGAGAGCCATTTCATTGTT 58.985 43.478 0.00 0.00 32.13 2.83
2753 2845 4.410099 TCCAGAGAGCCATTTCATTGTTT 58.590 39.130 0.00 0.00 0.00 2.83
2755 2847 4.381292 CCAGAGAGCCATTTCATTGTTTCC 60.381 45.833 0.00 0.00 0.00 3.13
2768 2860 5.269189 TCATTGTTTCCTATTTTCCCTCCC 58.731 41.667 0.00 0.00 0.00 4.30
2769 2861 3.359695 TGTTTCCTATTTTCCCTCCCG 57.640 47.619 0.00 0.00 0.00 5.14
2772 2864 3.639672 TTCCTATTTTCCCTCCCGTTC 57.360 47.619 0.00 0.00 0.00 3.95
2807 2899 5.122869 GCACATCTCATAGTTTCTGCTTTCA 59.877 40.000 0.00 0.00 0.00 2.69
2923 3015 5.410439 GCCAATGAGCACTTTTCATTTTCAT 59.590 36.000 0.00 0.00 41.91 2.57
2926 3018 7.333423 CCAATGAGCACTTTTCATTTTCATGAT 59.667 33.333 0.00 0.00 41.91 2.45
2931 3023 7.857569 AGCACTTTTCATTTTCATGATGTTTG 58.142 30.769 0.00 0.00 39.28 2.93
2932 3024 7.496591 AGCACTTTTCATTTTCATGATGTTTGT 59.503 29.630 0.00 0.00 39.28 2.83
3024 3133 6.581171 AACAGAGAAATTCCACAAGAATCC 57.419 37.500 0.00 0.00 44.75 3.01
3072 3189 7.638444 TCCATTTTTATAAGGGACAGTGATGA 58.362 34.615 0.00 0.00 0.00 2.92
3074 3191 8.917088 CCATTTTTATAAGGGACAGTGATGAAT 58.083 33.333 0.00 0.00 0.00 2.57
3075 3192 9.956720 CATTTTTATAAGGGACAGTGATGAATC 57.043 33.333 0.00 0.00 0.00 2.52
3080 3197 3.033909 AGGGACAGTGATGAATCGATCA 58.966 45.455 0.00 0.00 43.67 2.92
3190 3307 6.472887 CCTTCTCTTTGTATTGTTCCCAGTA 58.527 40.000 0.00 0.00 0.00 2.74
3200 3317 7.406916 TGTATTGTTCCCAGTACCATTACATT 58.593 34.615 0.00 0.00 33.97 2.71
3210 3327 5.645929 CAGTACCATTACATTAGCACCAACA 59.354 40.000 0.00 0.00 0.00 3.33
3308 3427 7.931407 TGCTGTACAAGAGAGAATAAAGAAACA 59.069 33.333 0.00 0.00 0.00 2.83
3318 3437 9.604626 GAGAGAATAAAGAAACAGAACAACATG 57.395 33.333 0.00 0.00 0.00 3.21
3326 3445 1.073763 ACAGAACAACATGGCCTGCTA 59.926 47.619 3.32 0.00 0.00 3.49
3362 3481 6.379703 TCAAACAATCTCCCAAGTTGAAGAAA 59.620 34.615 3.87 0.00 0.00 2.52
3378 3497 1.808945 AGAAAATTGCAGAGAGGCACG 59.191 47.619 0.00 0.00 44.86 5.34
3399 3518 7.253750 GGCACGCATGTTCTTAGAAATAAATTG 60.254 37.037 0.00 0.00 0.00 2.32
3431 3550 5.634859 GCACCTGTATGAAACAAAGAAATGG 59.365 40.000 0.00 0.00 37.74 3.16
3433 3552 7.432869 CACCTGTATGAAACAAAGAAATGGAA 58.567 34.615 0.00 0.00 37.74 3.53
3434 3553 7.925483 CACCTGTATGAAACAAAGAAATGGAAA 59.075 33.333 0.00 0.00 37.74 3.13
3460 3579 9.807921 AATTTTAGATCCAAAGAAGTTCAGGTA 57.192 29.630 5.50 0.00 0.00 3.08
3462 3581 9.807921 TTTTAGATCCAAAGAAGTTCAGGTATT 57.192 29.630 5.50 0.00 0.00 1.89
3463 3582 9.807921 TTTAGATCCAAAGAAGTTCAGGTATTT 57.192 29.630 5.50 0.00 0.00 1.40
3464 3583 7.929941 AGATCCAAAGAAGTTCAGGTATTTC 57.070 36.000 5.50 2.21 0.00 2.17
3465 3584 6.595716 AGATCCAAAGAAGTTCAGGTATTTCG 59.404 38.462 5.50 0.00 0.00 3.46
3466 3585 5.001232 TCCAAAGAAGTTCAGGTATTTCGG 58.999 41.667 5.50 2.28 0.00 4.30
3467 3586 4.156008 CCAAAGAAGTTCAGGTATTTCGGG 59.844 45.833 5.50 0.00 0.00 5.14
3469 3588 4.203654 AGAAGTTCAGGTATTTCGGGTC 57.796 45.455 5.50 0.00 0.00 4.46
3470 3589 3.055312 AGAAGTTCAGGTATTTCGGGTCC 60.055 47.826 5.50 0.00 0.00 4.46
3472 3591 2.910977 AGTTCAGGTATTTCGGGTCCTT 59.089 45.455 0.00 0.00 0.00 3.36
3473 3592 3.329814 AGTTCAGGTATTTCGGGTCCTTT 59.670 43.478 0.00 0.00 0.00 3.11
3488 3608 4.836175 GGGTCCTTTTTGTATCCCTTGAAA 59.164 41.667 0.00 0.00 32.89 2.69
3493 3613 8.244113 GTCCTTTTTGTATCCCTTGAAACATAG 58.756 37.037 0.00 0.00 0.00 2.23
3613 3795 7.383102 TCTGCAAATAATTTTCTCAGAGTCC 57.617 36.000 0.00 0.00 31.64 3.85
3659 3841 9.027202 TCACTTACCAGTACATGATAACTGTTA 57.973 33.333 19.08 2.26 41.25 2.41
3716 3898 4.741928 ATTCCTTAGTTTCCCCTGTTGT 57.258 40.909 0.00 0.00 0.00 3.32
3719 3901 3.655777 TCCTTAGTTTCCCCTGTTGTCAT 59.344 43.478 0.00 0.00 0.00 3.06
3818 4000 0.601311 GCGCTGAACTCCACAGTCTT 60.601 55.000 0.00 0.00 37.64 3.01
3934 4116 2.275134 TGTTCTCTTTGCCAGCATCA 57.725 45.000 0.00 0.00 0.00 3.07
4004 4186 2.567169 TCCTTTCTAGCAGCAGCAGTTA 59.433 45.455 3.17 0.00 45.49 2.24
4144 4326 3.819368 TCTCTTGTCAACAATGCCTTCA 58.181 40.909 0.00 0.00 35.02 3.02
4250 4432 0.179048 CTCACTGGCAGGTGTGTTGA 60.179 55.000 20.34 11.00 38.28 3.18
4255 4437 3.317711 CACTGGCAGGTGTGTTGAATTTA 59.682 43.478 20.34 0.00 33.04 1.40
4372 4554 0.397564 TGAGTGCTCATGGTTGCTCA 59.602 50.000 0.00 0.00 34.14 4.26
4610 4792 4.891168 ACTGGCATCAATTTATCAGCATCA 59.109 37.500 0.00 0.00 0.00 3.07
4637 4819 3.119316 TCCATTCGTTTGCTGTTGTTGTT 60.119 39.130 0.00 0.00 0.00 2.83
4652 4834 0.960861 TTGTTGCCACACGGTTGACA 60.961 50.000 0.00 0.00 30.32 3.58
4706 4888 3.131400 GCGTCTTCTTCTCCTCCTACAAT 59.869 47.826 0.00 0.00 0.00 2.71
4791 4973 5.050499 CGATCTCACTTACATTCAATCTGGC 60.050 44.000 0.00 0.00 0.00 4.85
4813 4995 1.348036 GCCTGGTTCTGGTAGAAGTGT 59.652 52.381 0.00 0.00 34.42 3.55
5028 5210 3.005554 CCTGCCATGTCGATAATGGATC 58.994 50.000 26.07 14.15 46.44 3.36
5066 5248 5.163258 ACATGGTAGATCTCCATCTGTTTCC 60.163 44.000 18.41 2.37 42.92 3.13
5176 5358 1.612726 GCCTCATTGAGCTTCAGGTGT 60.613 52.381 8.23 0.00 0.00 4.16
5219 5401 0.463295 CTGGAGCACCGCAATCTGAT 60.463 55.000 0.00 0.00 39.42 2.90
5222 5404 2.288666 GGAGCACCGCAATCTGATAAA 58.711 47.619 0.00 0.00 0.00 1.40
5230 5412 5.345741 CACCGCAATCTGATAAAAACCAAAG 59.654 40.000 0.00 0.00 0.00 2.77
5410 5592 1.000993 ATCTCTCTGGGCCGAGTGT 59.999 57.895 15.09 9.46 32.83 3.55
5523 5705 8.961634 TCATATCAAATTGAATTTACCCGTCAA 58.038 29.630 2.42 0.00 35.83 3.18
5542 5725 5.049267 CGTCAATAACCGGAAAAGGAAGAAA 60.049 40.000 9.46 0.00 34.73 2.52
5678 6024 1.103803 CCTTGCTCAGCTGAATGCAT 58.896 50.000 25.85 0.00 45.94 3.96
5754 6114 6.168270 ACTTAAGCTCAGAAGAAACAGAGT 57.832 37.500 1.29 0.00 0.00 3.24
5935 6295 4.829064 TTTAAAACGAAGTGCAGCATCT 57.171 36.364 0.00 0.00 45.00 2.90
5994 6354 6.319141 AGAAGAAAGACAGTATTTTGGTGC 57.681 37.500 0.00 0.00 0.00 5.01
6007 6367 5.559148 ATTTTGGTGCAAAACATTAGGGA 57.441 34.783 0.00 0.00 44.40 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 115 3.938637 AAGCCGGCTTTGGTAGGGC 62.939 63.158 35.84 0.00 44.07 5.19
119 120 2.597510 GGTCAAGCCGGCTTTGGT 60.598 61.111 38.60 16.80 33.42 3.67
122 123 1.152756 ACAAGGTCAAGCCGGCTTT 60.153 52.632 38.60 22.21 43.70 3.51
123 124 1.600916 GACAAGGTCAAGCCGGCTT 60.601 57.895 35.84 35.84 43.70 4.35
151 153 1.296392 CATGCACGAAGACTCCCCA 59.704 57.895 0.00 0.00 0.00 4.96
155 157 1.639298 GGGCACATGCACGAAGACTC 61.639 60.000 6.15 0.00 44.36 3.36
163 165 1.032114 GTCCTTAGGGGCACATGCAC 61.032 60.000 6.15 0.93 45.53 4.57
173 175 2.202756 GTGCGCTCGTCCTTAGGG 60.203 66.667 9.73 0.00 0.00 3.53
189 191 2.396955 CGACGACTACGGCTCCAGT 61.397 63.158 0.00 0.00 46.46 4.00
192 194 4.549516 GGCGACGACTACGGCTCC 62.550 72.222 0.00 0.00 45.12 4.70
204 206 0.248296 TGCAAAAGTTCAACGGCGAC 60.248 50.000 16.62 0.00 0.00 5.19
218 220 4.764679 ACGTGCTTCAAATCTATGCAAA 57.235 36.364 0.00 0.00 35.34 3.68
229 231 4.449405 TCGATTTGATGTTACGTGCTTCAA 59.551 37.500 14.58 14.58 0.00 2.69
280 296 2.819608 GCTTTGTTGTAGATTCCTGCCA 59.180 45.455 0.00 0.00 0.00 4.92
455 472 2.295349 GCCCTCCAACGATAATAGACGA 59.705 50.000 0.00 0.00 0.00 4.20
463 480 1.216977 CACACGCCCTCCAACGATA 59.783 57.895 0.00 0.00 0.00 2.92
464 481 2.047274 CACACGCCCTCCAACGAT 60.047 61.111 0.00 0.00 0.00 3.73
493 510 3.762288 CCGAATCCTATAAGATCCACCGA 59.238 47.826 0.00 0.00 0.00 4.69
507 524 2.148768 GACAAAAACCGACCGAATCCT 58.851 47.619 0.00 0.00 0.00 3.24
529 546 1.450312 GTCCAAGCAGATCCACCGG 60.450 63.158 0.00 0.00 0.00 5.28
554 571 3.179265 CGAACGCAGGCGAACGAT 61.179 61.111 21.62 0.73 42.83 3.73
596 613 3.301116 GCCGATAAATAGAAGCGTCGATC 59.699 47.826 0.00 0.00 0.00 3.69
620 640 1.334054 CACAGCAGAAAAGCAATCGC 58.666 50.000 0.00 0.00 36.85 4.58
694 714 3.051940 TCCTCACTGGAGCTGGATAAT 57.948 47.619 0.00 0.00 40.56 1.28
749 770 1.311859 ACGACGACTACAACCACTGA 58.688 50.000 0.00 0.00 0.00 3.41
786 807 8.680903 CATAAGAAGCAATGAAAGTTACATCCT 58.319 33.333 0.00 0.00 0.00 3.24
788 809 9.846248 AACATAAGAAGCAATGAAAGTTACATC 57.154 29.630 0.00 0.00 0.00 3.06
795 816 9.467258 TTGAAAGAACATAAGAAGCAATGAAAG 57.533 29.630 0.00 0.00 0.00 2.62
862 883 4.580580 GGGTGAAGACACTCATCTGTTTTT 59.419 41.667 0.00 0.00 45.87 1.94
863 884 4.137543 GGGTGAAGACACTCATCTGTTTT 58.862 43.478 0.00 0.00 45.87 2.43
864 885 3.744660 GGGTGAAGACACTCATCTGTTT 58.255 45.455 0.00 0.00 45.87 2.83
865 886 3.409026 GGGTGAAGACACTCATCTGTT 57.591 47.619 0.00 0.00 45.87 3.16
915 936 4.616181 ACACCACGTTTTTCTCTTCTTG 57.384 40.909 0.00 0.00 0.00 3.02
918 939 4.351131 ACAACACCACGTTTTTCTCTTC 57.649 40.909 0.00 0.00 34.86 2.87
1058 1084 0.462047 CATGGGACGAGGTGCCTTAC 60.462 60.000 7.81 0.00 44.53 2.34
1059 1085 1.904771 CATGGGACGAGGTGCCTTA 59.095 57.895 7.81 0.00 44.53 2.69
1060 1086 2.671070 CATGGGACGAGGTGCCTT 59.329 61.111 7.81 0.00 44.53 4.35
1061 1087 4.101448 GCATGGGACGAGGTGCCT 62.101 66.667 7.81 0.00 44.53 4.75
1070 1096 1.765314 AGATCTGTACTGGCATGGGAC 59.235 52.381 0.00 0.00 0.00 4.46
1080 1106 1.134965 GCGCTGAACCAGATCTGTACT 60.135 52.381 21.11 5.12 32.44 2.73
1084 1110 0.108472 TCAGCGCTGAACCAGATCTG 60.108 55.000 36.62 16.24 36.53 2.90
1092 1118 2.748605 AGCTACATATCAGCGCTGAAC 58.251 47.619 40.83 23.28 43.58 3.18
1282 1343 9.748708 AAATACAAAATCATCCCATCAAATACG 57.251 29.630 0.00 0.00 0.00 3.06
1323 1385 0.330267 ACCAAACATTAGGTCCCCGG 59.670 55.000 0.00 0.00 30.79 5.73
1456 1522 3.563390 CCTAGCCTAGATTTTGAGCAAGC 59.437 47.826 0.00 0.00 0.00 4.01
1462 1528 6.127026 GGTTCTCTTCCTAGCCTAGATTTTGA 60.127 42.308 0.00 0.00 0.00 2.69
1491 1557 4.771590 TCTACTTCTTGGCAAAGCAATG 57.228 40.909 0.00 0.00 33.06 2.82
1493 1559 5.590530 TTTTCTACTTCTTGGCAAAGCAA 57.409 34.783 0.00 0.00 33.06 3.91
1494 1560 4.499696 GCTTTTCTACTTCTTGGCAAAGCA 60.500 41.667 0.00 0.00 42.65 3.91
1495 1561 3.983988 GCTTTTCTACTTCTTGGCAAAGC 59.016 43.478 0.00 0.00 38.27 3.51
1529 1598 8.776470 CAAATCCAGCATTGTGAGTTAATTTTT 58.224 29.630 0.00 0.00 0.00 1.94
1531 1600 7.669427 TCAAATCCAGCATTGTGAGTTAATTT 58.331 30.769 0.00 0.00 0.00 1.82
1556 1625 1.346722 CCAACCTTCACGGGTTCTACT 59.653 52.381 0.00 0.00 46.58 2.57
1563 1632 2.209690 AATTACCCAACCTTCACGGG 57.790 50.000 0.00 0.00 46.22 5.28
1570 1639 3.653836 TGACACTGGTAATTACCCAACCT 59.346 43.478 28.00 9.80 45.87 3.50
1572 1641 5.067954 AGTTGACACTGGTAATTACCCAAC 58.932 41.667 28.47 28.47 45.87 3.77
1573 1642 5.072600 AGAGTTGACACTGGTAATTACCCAA 59.927 40.000 28.00 21.05 45.87 4.12
1622 1691 5.105997 GCTCAACATCCTACTCAAGCAAATT 60.106 40.000 0.00 0.00 0.00 1.82
1633 1702 5.447818 GCAGTTATTGTGCTCAACATCCTAC 60.448 44.000 2.82 0.00 38.99 3.18
1693 1762 1.068333 CGCCAGTTGCATAGTTTTGCT 60.068 47.619 0.00 0.00 43.18 3.91
1712 1781 0.881159 TTTTGCCGTCCACTACCACG 60.881 55.000 0.00 0.00 35.72 4.94
1715 1784 2.096980 GCTAATTTTGCCGTCCACTACC 59.903 50.000 0.00 0.00 0.00 3.18
1765 1839 1.531365 TTTCCAGGGGTGCAAGCAG 60.531 57.895 0.00 0.00 34.77 4.24
1801 1875 9.916360 TGATCTTGTAAGACAGGTAGAACTATA 57.084 33.333 0.00 0.00 37.98 1.31
1970 2049 3.243839 CCATACATAATTGCAACTGGGGC 60.244 47.826 0.00 0.00 0.00 5.80
2004 2084 5.645929 ACAACAAACAAACCTGGAAAAATCC 59.354 36.000 0.00 0.00 0.00 3.01
2048 2128 5.419542 TCACTTCCATAGAAACGATGAAGG 58.580 41.667 0.00 0.00 0.00 3.46
2056 2136 5.886960 ATGCACTTCACTTCCATAGAAAC 57.113 39.130 0.00 0.00 0.00 2.78
2126 2206 0.523072 TTTGCGCTGAGGATGAAAGC 59.477 50.000 9.73 0.00 0.00 3.51
2177 2257 9.632638 ATGTAGAAGCCAATCACAATATTAACT 57.367 29.630 0.00 0.00 0.00 2.24
2229 2309 1.529010 CAGGTTGTGGCTCTTGGCA 60.529 57.895 0.00 0.00 46.87 4.92
2321 2401 2.609610 TCCACCTTCCCCTTCCCG 60.610 66.667 0.00 0.00 0.00 5.14
2322 2402 0.253020 TACTCCACCTTCCCCTTCCC 60.253 60.000 0.00 0.00 0.00 3.97
2323 2403 1.205055 CTACTCCACCTTCCCCTTCC 58.795 60.000 0.00 0.00 0.00 3.46
2324 2404 1.205055 CCTACTCCACCTTCCCCTTC 58.795 60.000 0.00 0.00 0.00 3.46
2325 2405 0.914902 GCCTACTCCACCTTCCCCTT 60.915 60.000 0.00 0.00 0.00 3.95
2326 2406 1.307084 GCCTACTCCACCTTCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
2346 2438 6.379988 AGAAAACCCAAGTCAAGTTGTGTTAT 59.620 34.615 2.11 0.00 29.24 1.89
2347 2439 5.712917 AGAAAACCCAAGTCAAGTTGTGTTA 59.287 36.000 2.11 0.00 29.24 2.41
2419 2511 1.913778 TGAATGGCAGTGATGTTGCT 58.086 45.000 0.00 0.00 41.27 3.91
2421 2513 5.823209 TCTAATGAATGGCAGTGATGTTG 57.177 39.130 0.00 0.00 0.00 3.33
2430 2522 1.948834 CGGTGCATCTAATGAATGGCA 59.051 47.619 0.00 0.00 0.00 4.92
2434 2526 2.874701 GACAGCGGTGCATCTAATGAAT 59.125 45.455 15.82 0.00 0.00 2.57
2449 2541 4.686091 TCATAGTTCTCAAAACTGACAGCG 59.314 41.667 1.25 0.00 0.00 5.18
2457 2549 6.017109 TGTTCTGGCTTCATAGTTCTCAAAAC 60.017 38.462 0.00 0.00 0.00 2.43
2467 2559 7.604164 ACGGAATATTATGTTCTGGCTTCATAG 59.396 37.037 13.63 0.00 36.50 2.23
2482 2574 8.922676 CGCAGAGTTAAACATACGGAATATTAT 58.077 33.333 0.00 0.00 0.00 1.28
2504 2596 2.866028 GAGTTCAGGCAAGCGCAG 59.134 61.111 11.47 2.01 41.24 5.18
2511 2603 1.336887 GCTTCAGTACGAGTTCAGGCA 60.337 52.381 0.00 0.00 0.00 4.75
2522 2614 4.410492 CAAGGACACATTGCTTCAGTAC 57.590 45.455 0.00 0.00 32.54 2.73
2620 2712 6.241207 ACAAATCACCGAAAGAATACACAG 57.759 37.500 0.00 0.00 0.00 3.66
2689 2781 6.074142 GGCAAACTAAAAGCAAGAACAAGATG 60.074 38.462 0.00 0.00 0.00 2.90
2697 2789 3.295973 ACAGGGCAAACTAAAAGCAAGA 58.704 40.909 0.00 0.00 0.00 3.02
2708 2800 4.278419 AGACAAAATGAGTACAGGGCAAAC 59.722 41.667 0.00 0.00 0.00 2.93
2715 2807 6.030548 TCTCTGGAGACAAAATGAGTACAG 57.969 41.667 0.00 0.00 42.06 2.74
2731 2823 3.726557 ACAATGAAATGGCTCTCTGGA 57.273 42.857 0.00 0.00 0.00 3.86
2752 2844 3.054655 CAGAACGGGAGGGAAAATAGGAA 60.055 47.826 0.00 0.00 0.00 3.36
2753 2845 2.504175 CAGAACGGGAGGGAAAATAGGA 59.496 50.000 0.00 0.00 0.00 2.94
2755 2847 2.289565 GCAGAACGGGAGGGAAAATAG 58.710 52.381 0.00 0.00 0.00 1.73
2855 2947 6.237901 AGCATAGGAAACATGTAAACTCACA 58.762 36.000 0.00 0.00 0.00 3.58
2856 2948 6.455646 CGAGCATAGGAAACATGTAAACTCAC 60.456 42.308 0.00 0.00 0.00 3.51
2923 3015 9.921637 ACTTCTTTCTTTTTGTTACAAACATCA 57.078 25.926 10.28 0.00 41.79 3.07
3024 3133 9.559732 TGGATTTGAATGTATATTGTAGTCAGG 57.440 33.333 0.00 0.00 0.00 3.86
3051 3168 8.044309 TCGATTCATCACTGTCCCTTATAAAAA 58.956 33.333 0.00 0.00 0.00 1.94
3052 3169 7.561251 TCGATTCATCACTGTCCCTTATAAAA 58.439 34.615 0.00 0.00 0.00 1.52
3053 3170 7.119709 TCGATTCATCACTGTCCCTTATAAA 57.880 36.000 0.00 0.00 0.00 1.40
3055 3172 6.493458 TGATCGATTCATCACTGTCCCTTATA 59.507 38.462 0.00 0.00 0.00 0.98
3072 3189 7.713507 TCCCTTTATTCGTGTAAATGATCGATT 59.286 33.333 0.00 0.00 32.54 3.34
3074 3191 6.575267 TCCCTTTATTCGTGTAAATGATCGA 58.425 36.000 0.00 0.00 0.00 3.59
3075 3192 6.838198 TCCCTTTATTCGTGTAAATGATCG 57.162 37.500 0.00 0.00 0.00 3.69
3080 3197 7.948034 TTTCCATCCCTTTATTCGTGTAAAT 57.052 32.000 0.00 0.00 0.00 1.40
3087 3204 6.463995 TTCCATTTTCCATCCCTTTATTCG 57.536 37.500 0.00 0.00 0.00 3.34
3161 3278 5.163612 GGAACAATACAAAGAGAAGGGATGC 60.164 44.000 0.00 0.00 0.00 3.91
3190 3307 5.951747 AGAATGTTGGTGCTAATGTAATGGT 59.048 36.000 0.00 0.00 0.00 3.55
3200 3317 9.906660 CTGTTTAAAATAAGAATGTTGGTGCTA 57.093 29.630 0.00 0.00 0.00 3.49
3210 3327 9.088987 TGAGGAAAGGCTGTTTAAAATAAGAAT 57.911 29.630 0.00 0.00 0.00 2.40
3308 3427 1.352352 ACTAGCAGGCCATGTTGTTCT 59.648 47.619 5.01 0.00 0.00 3.01
3318 3437 2.360801 TGAACAACAAAACTAGCAGGCC 59.639 45.455 0.00 0.00 0.00 5.19
3362 3481 0.679002 ATGCGTGCCTCTCTGCAATT 60.679 50.000 0.00 0.00 44.11 2.32
3378 3497 8.545420 CATGGCAATTTATTTCTAAGAACATGC 58.455 33.333 0.00 0.00 0.00 4.06
3399 3518 0.749091 TCATACAGGTGCAGCATGGC 60.749 55.000 19.63 0.00 35.86 4.40
3433 3552 9.147732 ACCTGAACTTCTTTGGATCTAAAATTT 57.852 29.630 5.70 0.00 0.00 1.82
3434 3553 8.712228 ACCTGAACTTCTTTGGATCTAAAATT 57.288 30.769 5.70 0.00 0.00 1.82
3452 3571 3.345508 AAGGACCCGAAATACCTGAAC 57.654 47.619 0.00 0.00 32.73 3.18
3453 3572 4.376225 AAAAGGACCCGAAATACCTGAA 57.624 40.909 0.00 0.00 32.73 3.02
3460 3579 4.021229 GGGATACAAAAAGGACCCGAAAT 58.979 43.478 0.00 0.00 39.74 2.17
3462 3581 2.645797 AGGGATACAAAAAGGACCCGAA 59.354 45.455 0.00 0.00 41.81 4.30
3463 3582 2.271777 AGGGATACAAAAAGGACCCGA 58.728 47.619 0.00 0.00 41.81 5.14
3464 3583 2.752903 CAAGGGATACAAAAAGGACCCG 59.247 50.000 0.00 0.00 41.81 5.28
3465 3584 4.042271 TCAAGGGATACAAAAAGGACCC 57.958 45.455 0.00 0.00 37.79 4.46
3466 3585 5.303333 TGTTTCAAGGGATACAAAAAGGACC 59.697 40.000 0.00 0.00 32.99 4.46
3467 3586 6.399639 TGTTTCAAGGGATACAAAAAGGAC 57.600 37.500 0.00 0.00 32.99 3.85
3469 3588 8.122472 ACTATGTTTCAAGGGATACAAAAAGG 57.878 34.615 0.00 0.00 38.26 3.11
3470 3589 9.014297 AGACTATGTTTCAAGGGATACAAAAAG 57.986 33.333 0.00 0.00 38.26 2.27
3472 3591 8.934023 AAGACTATGTTTCAAGGGATACAAAA 57.066 30.769 0.00 0.00 38.26 2.44
3588 3770 7.067981 GGGACTCTGAGAAAATTATTTGCAGAT 59.932 37.037 12.44 0.00 36.64 2.90
3599 3781 3.795688 TTGCAGGGACTCTGAGAAAAT 57.204 42.857 12.44 0.00 46.18 1.82
3607 3789 2.564947 CTCTAGTGTTTGCAGGGACTCT 59.435 50.000 0.00 0.00 34.60 3.24
3612 3794 1.902508 TCTCCTCTAGTGTTTGCAGGG 59.097 52.381 0.00 0.00 0.00 4.45
3613 3795 3.196469 TGATCTCCTCTAGTGTTTGCAGG 59.804 47.826 0.00 0.00 0.00 4.85
3659 3841 4.713321 AGGATGCAAAATACAAGGCTGAAT 59.287 37.500 0.00 0.00 0.00 2.57
3664 3846 4.427312 CAAGAGGATGCAAAATACAAGGC 58.573 43.478 0.00 0.00 0.00 4.35
3719 3901 2.685388 CGAATGCAGAGAGTACTCAGGA 59.315 50.000 24.44 14.81 44.79 3.86
3818 4000 5.359756 AGCTGTAGTATTTGATGCGAATGA 58.640 37.500 0.00 0.00 0.00 2.57
3883 4065 4.799564 TCCAAATTACAAGCCACATTCC 57.200 40.909 0.00 0.00 0.00 3.01
3934 4116 4.369182 CGACAAGAAGTAAAGTGACCAGT 58.631 43.478 0.00 0.00 0.00 4.00
4004 4186 1.220206 CTGACAGCCCAAGAGCGAT 59.780 57.895 0.00 0.00 38.01 4.58
4250 4432 7.340487 GGAAGAGGACATGAGAAATGGTAAATT 59.660 37.037 0.00 0.00 0.00 1.82
4255 4437 3.588842 TGGAAGAGGACATGAGAAATGGT 59.411 43.478 0.00 0.00 0.00 3.55
4372 4554 4.744795 AGAAATTCTGCGTGACTATCCT 57.255 40.909 0.00 0.00 0.00 3.24
4610 4792 2.795329 ACAGCAAACGAATGGAAGGAT 58.205 42.857 0.00 0.00 0.00 3.24
4637 4819 0.682292 TCTATGTCAACCGTGTGGCA 59.318 50.000 0.00 0.00 39.70 4.92
4652 4834 2.035321 GCTGGCTCGAGCTAAAGTCTAT 59.965 50.000 34.46 0.00 41.70 1.98
4706 4888 9.672086 CTGGTTTGTTTCATAACGATCTTTAAA 57.328 29.630 0.00 0.00 37.06 1.52
4791 4973 1.625818 ACTTCTACCAGAACCAGGCTG 59.374 52.381 7.75 7.75 29.89 4.85
4813 4995 1.001974 AGAGATGTTGCCAACGCTGTA 59.998 47.619 7.39 0.00 35.36 2.74
5007 5189 2.549064 TCCATTATCGACATGGCAGG 57.451 50.000 17.38 0.00 41.10 4.85
5028 5210 0.099259 CCATGTATGTGCAGCCAACG 59.901 55.000 0.00 0.00 0.00 4.10
5033 5215 3.993081 GAGATCTACCATGTATGTGCAGC 59.007 47.826 0.00 0.00 0.00 5.25
5034 5216 4.039609 TGGAGATCTACCATGTATGTGCAG 59.960 45.833 1.43 0.00 32.03 4.41
5066 5248 4.815308 CCAGAACCAGAATATTGAGCTGAG 59.185 45.833 0.00 0.00 0.00 3.35
5176 5358 1.155424 ACAAAAAGGCGCTCGAACGA 61.155 50.000 13.23 0.00 34.06 3.85
5219 5401 2.364002 GTGGCTGCTCCTTTGGTTTTTA 59.636 45.455 0.00 0.00 35.26 1.52
5222 5404 0.396974 TGTGGCTGCTCCTTTGGTTT 60.397 50.000 0.00 0.00 35.26 3.27
5230 5412 1.746991 GCTTACCTGTGGCTGCTCC 60.747 63.158 0.00 0.00 0.00 4.70
5277 5459 1.467734 GCACCATTTGAGCAGAGTGAG 59.532 52.381 0.00 0.00 0.00 3.51
5410 5592 0.178950 AGGCATCGCTCAGGAGGATA 60.179 55.000 0.00 0.00 0.00 2.59
5523 5705 6.495526 TCCATTTTTCTTCCTTTTCCGGTTAT 59.504 34.615 0.00 0.00 0.00 1.89
5542 5725 6.947733 TGACATCAAATCAACTACCTCCATTT 59.052 34.615 0.00 0.00 0.00 2.32
5678 6024 5.047802 CCTGGACTTAACTTTACCTGACGTA 60.048 44.000 0.00 0.00 0.00 3.57
5994 6354 6.702329 AGACTCTACACTCCCTAATGTTTTG 58.298 40.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.