Multiple sequence alignment - TraesCS6A01G386600

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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 TraesCS6A01G386600 chr6A 100.000 4294 0 0 987 5280 603279456 603283749 0.000000e+00 7930
1 TraesCS6A01G386600 chr6A 95.103 776 37 1 4505 5280 603295674 603296448 0.000000e+00 1221
2 TraesCS6A01G386600 chr6A 100.000 623 0 0 1 623 603278470 603279092 0.000000e+00 1151
3 TraesCS6A01G386600 chr6A 92.737 771 54 2 4511 5280 154977410 154976641 0.000000e+00 1112
4 TraesCS6A01G386600 chr6A 92.397 776 58 1 4506 5280 204249014 204249789 0.000000e+00 1105
5 TraesCS6A01G386600 chr6A 83.168 404 59 5 1562 1964 617386577 617386182 1.400000e-95 361
6 TraesCS6A01G386600 chr6A 85.623 313 30 11 1120 1432 561947732 561948029 1.100000e-81 315
7 TraesCS6A01G386600 chr6B 89.572 2148 119 45 2385 4489 694403474 694405559 0.000000e+00 2628
8 TraesCS6A01G386600 chr6B 89.707 991 77 17 1387 2359 694402315 694403298 0.000000e+00 1242
9 TraesCS6A01G386600 chr6B 93.291 313 8 8 988 1297 694401980 694402282 2.900000e-122 449
10 TraesCS6A01G386600 chr6D 92.669 1255 54 13 3259 4489 456557594 456558834 0.000000e+00 1773
11 TraesCS6A01G386600 chr6D 90.764 812 47 13 2426 3212 456556551 456557359 0.000000e+00 1059
12 TraesCS6A01G386600 chr6D 91.713 724 48 4 1638 2359 456555580 456556293 0.000000e+00 994
13 TraesCS6A01G386600 chr6D 86.124 627 37 27 988 1603 456554852 456555439 9.650000e-177 630
14 TraesCS6A01G386600 chr6D 84.844 640 46 22 1 623 456554192 456554797 9.790000e-167 597
15 TraesCS6A01G386600 chr3A 92.655 776 55 2 4506 5280 501298232 501299006 0.000000e+00 1116
16 TraesCS6A01G386600 chr3A 92.746 772 54 2 4510 5280 487784669 487785439 0.000000e+00 1114
17 TraesCS6A01G386600 chr3A 92.526 776 57 1 4506 5280 614418875 614419650 0.000000e+00 1110
18 TraesCS6A01G386600 chr3A 92.416 778 57 2 4505 5280 23744877 23744100 0.000000e+00 1109
19 TraesCS6A01G386600 chr3A 92.407 777 58 1 4505 5280 662454819 662454043 0.000000e+00 1107
20 TraesCS6A01G386600 chr3A 83.416 404 58 5 1562 1964 712416411 712416806 3.000000e-97 366
21 TraesCS6A01G386600 chr3A 85.623 313 34 9 1120 1432 712416071 712416372 8.530000e-83 318
22 TraesCS6A01G386600 chr3A 83.801 321 31 17 1120 1432 695988816 695989123 8.650000e-73 285
23 TraesCS6A01G386600 chr3A 83.178 321 31 17 1120 1432 15024769 15025074 6.740000e-69 272
24 TraesCS6A01G386600 chr2A 92.535 777 56 2 4505 5280 507920129 507919354 0.000000e+00 1112
25 TraesCS6A01G386600 chr2A 84.984 313 32 11 1120 1432 68473455 68473752 2.390000e-78 303
26 TraesCS6A01G386600 chr3B 84.264 394 53 5 1572 1964 47168528 47168143 4.990000e-100 375
27 TraesCS6A01G386600 chr3B 84.665 313 32 8 1120 1432 704100425 704100129 1.110000e-76 298
28 TraesCS6A01G386600 chr4B 82.716 405 59 8 1562 1964 639461974 639462369 3.030000e-92 350
29 TraesCS6A01G386600 chr7A 83.801 321 30 17 1120 1432 732040103 732040409 8.650000e-73 285
30 TraesCS6A01G386600 chr1B 82.243 321 34 17 1120 1432 96193047 96193352 6.790000e-64 255


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 TraesCS6A01G386600 chr6A 603278470 603283749 5279 False 4540.500000 7930 100.000000 1 5280 2 chr6A.!!$F4 5279
1 TraesCS6A01G386600 chr6A 603295674 603296448 774 False 1221.000000 1221 95.103000 4505 5280 1 chr6A.!!$F3 775
2 TraesCS6A01G386600 chr6A 154976641 154977410 769 True 1112.000000 1112 92.737000 4511 5280 1 chr6A.!!$R1 769
3 TraesCS6A01G386600 chr6A 204249014 204249789 775 False 1105.000000 1105 92.397000 4506 5280 1 chr6A.!!$F1 774
4 TraesCS6A01G386600 chr6B 694401980 694405559 3579 False 1439.666667 2628 90.856667 988 4489 3 chr6B.!!$F1 3501
5 TraesCS6A01G386600 chr6D 456554192 456558834 4642 False 1010.600000 1773 89.222800 1 4489 5 chr6D.!!$F1 4488
6 TraesCS6A01G386600 chr3A 501298232 501299006 774 False 1116.000000 1116 92.655000 4506 5280 1 chr3A.!!$F3 774
7 TraesCS6A01G386600 chr3A 487784669 487785439 770 False 1114.000000 1114 92.746000 4510 5280 1 chr3A.!!$F2 770
8 TraesCS6A01G386600 chr3A 614418875 614419650 775 False 1110.000000 1110 92.526000 4506 5280 1 chr3A.!!$F4 774
9 TraesCS6A01G386600 chr3A 23744100 23744877 777 True 1109.000000 1109 92.416000 4505 5280 1 chr3A.!!$R1 775
10 TraesCS6A01G386600 chr3A 662454043 662454819 776 True 1107.000000 1107 92.407000 4505 5280 1 chr3A.!!$R2 775
11 TraesCS6A01G386600 chr3A 712416071 712416806 735 False 342.000000 366 84.519500 1120 1964 2 chr3A.!!$F6 844
12 TraesCS6A01G386600 chr2A 507919354 507920129 775 True 1112.000000 1112 92.535000 4505 5280 1 chr2A.!!$R1 775

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
484 500 0.030908 CCGTTAGGATCTCAGACCGC 59.969 60.000 0.00 0.00 41.02 5.68 F
520 536 0.106519 AGCCTGGCCTCGCAATAATT 60.107 50.000 16.57 0.00 0.00 1.40 F
521 537 0.312102 GCCTGGCCTCGCAATAATTC 59.688 55.000 7.66 0.00 0.00 2.17 F
1054 1071 0.399075 CAAAGGTAACCCCGTCCACT 59.601 55.000 0.00 0.00 38.74 4.00 F
1636 1783 0.682852 ACGGGTCATTCGTTCCTCAA 59.317 50.000 0.00 0.00 37.61 3.02 F
2181 2337 1.154599 GCATGACGTCAGTGTTGCG 60.155 57.895 24.41 6.99 0.00 4.85 F
3939 4516 0.179070 TTGTCGTTGGTGTAGCTGCA 60.179 50.000 0.00 0.00 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1512 1542 0.536006 AGCAACAGCCTCAGTTGTCC 60.536 55.000 7.74 0.0 46.09 4.02 R
1636 1783 1.346395 TCTACAGCAATTCCCACACGT 59.654 47.619 0.00 0.0 0.00 4.49 R
1784 1938 1.434188 TGCAAGGAAAGAGACCCTCA 58.566 50.000 0.00 0.0 32.06 3.86 R
2721 3086 0.033109 GCCCCCTCAGCAACCTAAAT 60.033 55.000 0.00 0.0 0.00 1.40 R
3048 3417 0.390124 TTTCCGTTCGCCACACTAGT 59.610 50.000 0.00 0.0 0.00 2.57 R
4008 4585 1.118965 TCCGACTCTTGAAGCCACCA 61.119 55.000 0.00 0.0 0.00 4.17 R
5022 5618 1.134580 CACGACCTCATGATCAAGCCT 60.135 52.381 0.00 0.0 0.00 4.58 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 2.506544 CGTTCGTCGCCATATGGAG 58.493 57.895 26.47 22.44 37.39 3.86
37 38 9.101828 GCCATATGGAGCATTTTGTACAAATGC 62.102 40.741 28.98 28.98 46.69 3.56
47 49 7.710273 CATTTTGTACAAATGCTAAAGTGTCG 58.290 34.615 21.17 0.00 31.82 4.35
60 62 1.999048 AGTGTCGTTTGTTCGTGTGA 58.001 45.000 0.00 0.00 0.00 3.58
68 70 3.062369 CGTTTGTTCGTGTGAAACTGGTA 59.938 43.478 0.00 0.00 38.04 3.25
69 71 4.584394 GTTTGTTCGTGTGAAACTGGTAG 58.416 43.478 0.00 0.00 38.04 3.18
70 72 3.804786 TGTTCGTGTGAAACTGGTAGA 57.195 42.857 0.00 0.00 38.04 2.59
71 73 3.450578 TGTTCGTGTGAAACTGGTAGAC 58.549 45.455 0.00 0.00 38.04 2.59
72 74 3.131577 TGTTCGTGTGAAACTGGTAGACT 59.868 43.478 0.00 0.00 38.04 3.24
73 75 3.364889 TCGTGTGAAACTGGTAGACTG 57.635 47.619 0.00 0.00 38.04 3.51
74 76 2.035449 TCGTGTGAAACTGGTAGACTGG 59.965 50.000 0.00 0.00 38.04 4.00
75 77 2.223971 CGTGTGAAACTGGTAGACTGGT 60.224 50.000 0.00 0.00 38.04 4.00
76 78 3.005050 CGTGTGAAACTGGTAGACTGGTA 59.995 47.826 0.00 0.00 38.04 3.25
88 90 1.768870 AGACTGGTAGTGTTGCCTTGT 59.231 47.619 0.00 0.00 0.00 3.16
98 100 3.129287 AGTGTTGCCTTGTTGAAGTGAAG 59.871 43.478 0.00 0.00 0.00 3.02
122 124 0.182537 TGAAACACCCTGGGACTGTG 59.817 55.000 22.23 9.82 36.11 3.66
156 158 6.039047 AGCTTATGCCATCAATTGTTCTACTG 59.961 38.462 5.13 0.00 40.80 2.74
159 161 4.018490 TGCCATCAATTGTTCTACTGCAT 58.982 39.130 5.13 0.00 0.00 3.96
163 165 6.369615 GCCATCAATTGTTCTACTGCATTTTT 59.630 34.615 5.13 0.00 0.00 1.94
199 201 9.224267 ACTGTTATTATGGTCAGATTATGATGC 57.776 33.333 0.00 0.00 40.92 3.91
201 203 9.743581 TGTTATTATGGTCAGATTATGATGCAT 57.256 29.630 0.00 0.00 40.92 3.96
205 207 9.743581 ATTATGGTCAGATTATGATGCATTACA 57.256 29.630 0.00 0.00 40.92 2.41
207 209 7.500720 TGGTCAGATTATGATGCATTACAAG 57.499 36.000 0.00 0.00 40.92 3.16
213 216 9.976511 CAGATTATGATGCATTACAAGGAAATT 57.023 29.630 0.00 0.00 0.00 1.82
214 217 9.976511 AGATTATGATGCATTACAAGGAAATTG 57.023 29.630 0.00 0.00 45.01 2.32
223 226 2.046285 AAGGAAATTGGCGAGGGCG 61.046 57.895 0.00 0.00 41.24 6.13
249 252 2.202690 CACGGCGCGTTCATAGGA 60.203 61.111 6.90 0.00 38.32 2.94
268 283 2.290134 GGAGCCGAACCCTAGTCTTTTT 60.290 50.000 0.00 0.00 0.00 1.94
296 312 4.777896 TCTTAGGTAAATCAGCTGACCAGT 59.222 41.667 20.97 7.03 36.15 4.00
301 317 1.856539 AATCAGCTGACCAGTGGGGG 61.857 60.000 20.97 4.02 42.91 5.40
306 322 0.681243 GCTGACCAGTGGGGGATTTC 60.681 60.000 15.21 0.78 42.91 2.17
310 326 0.255890 ACCAGTGGGGGATTTCATCG 59.744 55.000 15.21 0.00 42.91 3.84
313 329 0.181350 AGTGGGGGATTTCATCGCTC 59.819 55.000 1.34 0.00 42.56 5.03
350 366 5.738909 TCCAATGCTCTTTGTTTGGAAAAA 58.261 33.333 0.92 0.00 43.41 1.94
389 405 8.139989 ACATGAGTTTTTCTCTGAAATTCCAAG 58.860 33.333 0.00 0.00 43.13 3.61
434 450 2.614983 GGCTCTGTTTTGTTTGGTACGA 59.385 45.455 0.00 0.00 0.00 3.43
447 463 1.580815 GGTACGAGACCTCTACTCCG 58.419 60.000 4.30 0.00 45.89 4.63
452 468 2.487372 ACGAGACCTCTACTCCGTTTTC 59.513 50.000 0.00 0.00 0.00 2.29
453 469 2.475852 CGAGACCTCTACTCCGTTTTCG 60.476 54.545 0.00 0.00 43.67 3.46
484 500 0.030908 CCGTTAGGATCTCAGACCGC 59.969 60.000 0.00 0.00 41.02 5.68
485 501 0.030908 CGTTAGGATCTCAGACCGCC 59.969 60.000 0.00 0.00 0.00 6.13
486 502 0.030908 GTTAGGATCTCAGACCGCCG 59.969 60.000 0.00 0.00 0.00 6.46
487 503 0.106868 TTAGGATCTCAGACCGCCGA 60.107 55.000 0.00 0.00 0.00 5.54
488 504 0.110678 TAGGATCTCAGACCGCCGAT 59.889 55.000 0.00 0.00 0.00 4.18
489 505 1.175983 AGGATCTCAGACCGCCGATC 61.176 60.000 0.00 0.00 33.31 3.69
490 506 1.287503 GATCTCAGACCGCCGATCC 59.712 63.158 0.00 0.00 0.00 3.36
491 507 2.465097 GATCTCAGACCGCCGATCCG 62.465 65.000 0.00 0.00 0.00 4.18
492 508 4.933064 CTCAGACCGCCGATCCGC 62.933 72.222 0.00 0.00 0.00 5.54
520 536 0.106519 AGCCTGGCCTCGCAATAATT 60.107 50.000 16.57 0.00 0.00 1.40
521 537 0.312102 GCCTGGCCTCGCAATAATTC 59.688 55.000 7.66 0.00 0.00 2.17
522 538 1.972872 CCTGGCCTCGCAATAATTCT 58.027 50.000 3.32 0.00 0.00 2.40
524 540 1.605710 CTGGCCTCGCAATAATTCTGG 59.394 52.381 3.32 0.00 0.00 3.86
601 617 4.596585 AACCCCCACCACCGCTTG 62.597 66.667 0.00 0.00 0.00 4.01
616 632 3.991725 CTTGCCCTCCTGCTGCTCC 62.992 68.421 0.00 0.00 0.00 4.70
618 634 4.173924 GCCCTCCTGCTGCTCCTC 62.174 72.222 0.00 0.00 0.00 3.71
1048 1064 1.074248 ACCTGCAAAGGTAACCCCG 59.926 57.895 0.00 0.00 41.04 5.73
1054 1071 0.399075 CAAAGGTAACCCCGTCCACT 59.601 55.000 0.00 0.00 38.74 4.00
1057 1074 2.663075 GGTAACCCCGTCCACTCCC 61.663 68.421 0.00 0.00 0.00 4.30
1092 1109 1.621301 GCTGCTGTGCGTAGAGTGTG 61.621 60.000 0.00 0.00 0.00 3.82
1140 1157 0.768622 TGATCTGGGGTTTCGTGGTT 59.231 50.000 0.00 0.00 0.00 3.67
1187 1207 2.906897 AACAAGCCGCTGGTGGTG 60.907 61.111 0.00 0.00 0.00 4.17
1292 1312 3.997064 CTGGAGCGGCAAGGTCTCG 62.997 68.421 1.45 0.00 46.05 4.04
1300 1320 1.985116 GCAAGGTCTCGTCCCCTCT 60.985 63.158 0.00 0.00 0.00 3.69
1312 1332 2.040359 CCCTCTTCCCTCCCCCTC 60.040 72.222 0.00 0.00 0.00 4.30
1323 1343 4.150454 CCCCCTCTCTCCCTCGCT 62.150 72.222 0.00 0.00 0.00 4.93
1350 1370 2.865343 TCCTCGAATCTAGGTTTCGC 57.135 50.000 18.25 0.00 44.20 4.70
1358 1378 3.950794 CTAGGTTTCGCTGGCCGCA 62.951 63.158 17.57 4.54 39.08 5.69
1373 1393 2.671963 GCAGTTTCCCGGTGACCC 60.672 66.667 0.00 0.00 0.00 4.46
1469 1495 3.396260 TTTTCCTCCCGTCAGTGTTAG 57.604 47.619 0.00 0.00 0.00 2.34
1512 1542 2.852748 CGTCTTGACGAGTTAGACTGG 58.147 52.381 17.00 0.00 36.90 4.00
1578 1610 5.484173 TTATGAATTGTCGCAATGAGACC 57.516 39.130 14.22 0.00 37.80 3.85
1594 1630 4.460263 TGAGACCGAATAATTGGGGATTG 58.540 43.478 0.00 0.00 33.93 2.67
1603 1639 8.584157 CCGAATAATTGGGGATTGATTGAATTA 58.416 33.333 0.00 0.00 0.00 1.40
1622 1769 4.475051 TTATGTGTAGCATTGTACGGGT 57.525 40.909 0.00 0.00 38.94 5.28
1623 1770 2.373540 TGTGTAGCATTGTACGGGTC 57.626 50.000 0.00 0.00 0.00 4.46
1624 1771 1.619332 TGTGTAGCATTGTACGGGTCA 59.381 47.619 0.00 0.00 0.00 4.02
1625 1772 2.235155 TGTGTAGCATTGTACGGGTCAT 59.765 45.455 0.00 0.00 0.00 3.06
1636 1783 0.682852 ACGGGTCATTCGTTCCTCAA 59.317 50.000 0.00 0.00 37.61 3.02
1648 1795 2.227194 GTTCCTCAACGTGTGGGAATT 58.773 47.619 15.88 0.00 38.24 2.17
1662 1809 2.637382 TGGGAATTGCTGTAGAGTGACA 59.363 45.455 0.00 0.00 0.00 3.58
1670 1817 2.417924 GCTGTAGAGTGACATGACCTGG 60.418 54.545 0.00 0.00 0.00 4.45
1761 1915 5.995282 TGTAGTCGTGTCATGAAAGGATTTT 59.005 36.000 11.32 4.09 39.27 1.82
1762 1916 7.156000 TGTAGTCGTGTCATGAAAGGATTTTA 58.844 34.615 11.32 3.25 39.27 1.52
1763 1917 7.822334 TGTAGTCGTGTCATGAAAGGATTTTAT 59.178 33.333 11.32 0.07 39.27 1.40
1764 1918 7.687941 AGTCGTGTCATGAAAGGATTTTATT 57.312 32.000 11.32 0.00 39.27 1.40
1765 1919 8.786826 AGTCGTGTCATGAAAGGATTTTATTA 57.213 30.769 11.32 0.00 39.27 0.98
1784 1938 8.710749 TTTATTAATTTGCTATGCAGGATCCT 57.289 30.769 9.02 9.02 40.61 3.24
1814 1968 2.787473 TTCCTTGCATTCTCGGTCAT 57.213 45.000 0.00 0.00 0.00 3.06
1882 2038 4.454678 TCAAGCATAGCCAAGATAACTGG 58.545 43.478 0.00 0.00 0.00 4.00
1897 2053 7.195374 AGATAACTGGGCACTGATAAGTTTA 57.805 36.000 0.00 0.00 33.37 2.01
1920 2076 3.361794 TCTGTCGCTGCTGATAGAATC 57.638 47.619 14.61 0.00 33.80 2.52
2049 2205 1.961277 CCTCTGCGGCAAAGTTCGT 60.961 57.895 3.44 0.00 0.00 3.85
2181 2337 1.154599 GCATGACGTCAGTGTTGCG 60.155 57.895 24.41 6.99 0.00 4.85
2238 2394 2.617274 GCTCGGCTGTGGTGTTTCC 61.617 63.158 0.00 0.00 0.00 3.13
2254 2410 4.753610 GTGTTTCCACTGGTAGGTTCTAAC 59.246 45.833 0.00 0.00 38.61 2.34
2334 2490 9.019764 CGTCACACAAGATTTTTCTGTAATTTT 57.980 29.630 0.00 0.00 0.00 1.82
2358 2514 9.928236 TTTACATGCTTTTAAACAAATTTCTGC 57.072 25.926 0.00 0.00 0.00 4.26
2360 2516 8.212317 ACATGCTTTTAAACAAATTTCTGCTT 57.788 26.923 0.00 0.00 0.00 3.91
2361 2517 8.676401 ACATGCTTTTAAACAAATTTCTGCTTT 58.324 25.926 0.00 0.00 0.00 3.51
2362 2518 9.505995 CATGCTTTTAAACAAATTTCTGCTTTT 57.494 25.926 0.00 0.00 0.00 2.27
2378 2534 9.995957 TTTCTGCTTTTAAACAAATTTTTAGCC 57.004 25.926 0.00 0.00 0.00 3.93
2379 2535 7.846485 TCTGCTTTTAAACAAATTTTTAGCCG 58.154 30.769 0.00 0.00 0.00 5.52
2381 2537 7.622880 TGCTTTTAAACAAATTTTTAGCCGTC 58.377 30.769 0.00 0.00 0.00 4.79
2382 2538 7.277981 TGCTTTTAAACAAATTTTTAGCCGTCA 59.722 29.630 0.00 0.00 0.00 4.35
2383 2539 7.581241 GCTTTTAAACAAATTTTTAGCCGTCAC 59.419 33.333 0.00 0.00 0.00 3.67
2397 2751 2.414161 GCCGTCACACTCTTTTATTGGC 60.414 50.000 0.00 0.00 0.00 4.52
2406 2760 7.277539 TCACACTCTTTTATTGGCAAACTTTTG 59.722 33.333 3.01 0.00 41.03 2.44
2417 2771 4.462483 TGGCAAACTTTTGTTCTGAGAGTT 59.538 37.500 3.74 0.00 42.67 3.01
2424 2778 8.682936 AACTTTTGTTCTGAGAGTTGATACAT 57.317 30.769 0.00 0.00 38.45 2.29
2425 2779 8.092521 ACTTTTGTTCTGAGAGTTGATACATG 57.907 34.615 0.00 0.00 0.00 3.21
2426 2780 7.933577 ACTTTTGTTCTGAGAGTTGATACATGA 59.066 33.333 0.00 0.00 0.00 3.07
2427 2781 8.853077 TTTTGTTCTGAGAGTTGATACATGAT 57.147 30.769 0.00 0.00 0.00 2.45
2428 2782 8.853077 TTTGTTCTGAGAGTTGATACATGATT 57.147 30.769 0.00 0.00 0.00 2.57
2429 2783 8.484641 TTGTTCTGAGAGTTGATACATGATTC 57.515 34.615 0.00 0.00 0.00 2.52
2430 2784 7.845037 TGTTCTGAGAGTTGATACATGATTCT 58.155 34.615 0.00 0.00 0.00 2.40
2456 2810 7.681679 TGATTCCATACTGTTGTTTACACCTA 58.318 34.615 0.00 0.00 32.10 3.08
2489 2843 5.767665 TGACAACAATATGTGTAGCACCTTT 59.232 36.000 0.00 0.00 40.60 3.11
2490 2844 6.012658 ACAACAATATGTGTAGCACCTTTG 57.987 37.500 0.00 1.80 40.60 2.77
2491 2845 5.767665 ACAACAATATGTGTAGCACCTTTGA 59.232 36.000 10.60 0.00 40.60 2.69
2492 2846 5.880054 ACAATATGTGTAGCACCTTTGAC 57.120 39.130 10.60 0.00 39.29 3.18
2493 2847 5.312895 ACAATATGTGTAGCACCTTTGACA 58.687 37.500 10.60 0.00 39.29 3.58
2503 2865 5.184892 AGCACCTTTGACATTATCCTCTT 57.815 39.130 0.00 0.00 0.00 2.85
2610 2972 1.408702 GCAAAGGTTGAAGCAGGTTCA 59.591 47.619 11.11 11.11 43.82 3.18
2611 2973 2.544486 GCAAAGGTTGAAGCAGGTTCAG 60.544 50.000 14.53 4.21 46.09 3.02
2704 3069 5.681639 ACCTGAGTGTGTAAACTAAGCTTT 58.318 37.500 3.20 0.00 28.26 3.51
2705 3070 5.527582 ACCTGAGTGTGTAAACTAAGCTTTG 59.472 40.000 3.20 5.03 28.26 2.77
2721 3086 2.687935 GCTTTGACACCTGAACTTCCAA 59.312 45.455 0.00 0.00 0.00 3.53
2784 3150 5.631929 CGGATTATTGGCATTGACATTGATG 59.368 40.000 0.00 0.00 0.00 3.07
2827 3193 9.832445 TGGTATGATTATAGTTTCTGTCCTTTC 57.168 33.333 0.00 0.00 0.00 2.62
2854 3221 1.340600 TGTAAATTCCGCCCCCTGAAG 60.341 52.381 0.00 0.00 0.00 3.02
2901 3268 5.967674 CGTAATTTTCCTCTTAAGCTGCATG 59.032 40.000 1.02 0.00 0.00 4.06
2902 3269 3.855689 TTTTCCTCTTAAGCTGCATGC 57.144 42.857 11.82 11.82 43.29 4.06
2932 3300 7.750229 TGTTCAATTGCTGAAAGAGAGTAAT 57.250 32.000 0.00 0.00 45.67 1.89
2953 3322 4.456280 TTCACATTCGTGTCTCTGCTAT 57.544 40.909 0.00 0.00 44.02 2.97
2959 3328 4.634184 TTCGTGTCTCTGCTATAAGACC 57.366 45.455 0.00 0.00 40.98 3.85
3048 3417 3.179443 ACTGAAACTGTTCTTCTGCGA 57.821 42.857 0.00 0.00 34.60 5.10
3058 3427 0.243907 TCTTCTGCGACTAGTGTGGC 59.756 55.000 0.00 1.23 46.07 5.01
3068 3437 1.001633 ACTAGTGTGGCGAACGGAAAT 59.998 47.619 0.00 0.00 0.00 2.17
3182 3561 2.419574 GCACAGGGCTCCTTAACGAATA 60.420 50.000 0.00 0.00 40.25 1.75
3186 3565 3.621715 CAGGGCTCCTTAACGAATAACAC 59.378 47.826 0.00 0.00 0.00 3.32
3190 3569 3.063588 GCTCCTTAACGAATAACACTGGC 59.936 47.826 0.00 0.00 0.00 4.85
3246 3730 5.401674 GTGTACTTTTGTTCTCTCGTGGTAG 59.598 44.000 0.00 0.00 0.00 3.18
3304 3872 6.935741 ACTTGATGTGCTGTACTTGTTAAA 57.064 33.333 0.00 0.00 0.00 1.52
3480 4055 1.668826 AACCAATCCAGCAGGTCCTA 58.331 50.000 0.00 0.00 33.74 2.94
3616 4191 7.263100 TGTATATGGCATGTTCATGAACTTC 57.737 36.000 32.57 22.14 41.67 3.01
3666 4241 5.385628 ACTCTTCGTAGGATACCTTACCT 57.614 43.478 0.00 0.00 38.71 3.08
3692 4267 5.172205 GCCAGTTTAGAGTCCTGACTTAAG 58.828 45.833 0.00 0.00 42.66 1.85
3701 4276 6.132658 AGAGTCCTGACTTAAGCTATCATCA 58.867 40.000 1.29 0.00 42.66 3.07
3739 4314 9.859427 CTAAATAAATGAAAGATGTTTGAGCCA 57.141 29.630 0.00 0.00 0.00 4.75
3745 4320 4.202243 TGAAAGATGTTTGAGCCAAAAGGG 60.202 41.667 0.00 0.00 35.03 3.95
3761 4336 6.765989 GCCAAAAGGGAAAAGAGTTTAAATGT 59.234 34.615 0.00 0.00 40.01 2.71
3888 4464 7.472334 ACAATATCTTGCCTTGACTGATTTT 57.528 32.000 0.00 0.00 35.69 1.82
3890 4466 7.816031 ACAATATCTTGCCTTGACTGATTTTTG 59.184 33.333 0.00 0.00 35.69 2.44
3930 4507 1.069668 GGTACCTCTGTTGTCGTTGGT 59.930 52.381 4.06 0.00 0.00 3.67
3939 4516 0.179070 TTGTCGTTGGTGTAGCTGCA 60.179 50.000 0.00 0.00 0.00 4.41
3975 4552 1.973281 CACACGGCCATTCCAGCTT 60.973 57.895 2.24 0.00 34.01 3.74
4008 4585 2.091885 TGTCTGGAAGGGAACAGCTTTT 60.092 45.455 0.00 0.00 34.76 2.27
4011 4588 1.063266 TGGAAGGGAACAGCTTTTGGT 60.063 47.619 0.00 0.00 0.00 3.67
4023 4600 1.683385 GCTTTTGGTGGCTTCAAGAGT 59.317 47.619 0.00 0.00 31.48 3.24
4086 4663 6.015856 ACAAGGTATCAATCATACTCTCTCGG 60.016 42.308 0.00 0.00 38.00 4.63
4105 4682 3.340337 GGACAGAAATAATCCGCAAGC 57.660 47.619 0.00 0.00 0.00 4.01
4210 4792 3.343617 CCACAACATGAACCTTACCGAT 58.656 45.455 0.00 0.00 0.00 4.18
4302 4884 1.227380 CCTGCTATGTGTCTCGCCC 60.227 63.158 0.00 0.00 0.00 6.13
4306 4888 1.227380 CTATGTGTCTCGCCCTGCC 60.227 63.158 0.00 0.00 0.00 4.85
4309 4891 4.803426 GTGTCTCGCCCTGCCTCG 62.803 72.222 0.00 0.00 0.00 4.63
4336 4918 1.665679 AGCAGTTTGTGTCGTGTGAAG 59.334 47.619 0.00 0.00 0.00 3.02
4445 5037 1.000274 GTTGTGTTGGATGGTTGCCTC 60.000 52.381 0.00 0.00 0.00 4.70
4446 5038 0.478072 TGTGTTGGATGGTTGCCTCT 59.522 50.000 0.00 0.00 0.00 3.69
4447 5039 0.883833 GTGTTGGATGGTTGCCTCTG 59.116 55.000 0.00 0.00 0.00 3.35
4448 5040 0.251297 TGTTGGATGGTTGCCTCTGG 60.251 55.000 0.00 0.00 0.00 3.86
4449 5041 0.251341 GTTGGATGGTTGCCTCTGGT 60.251 55.000 0.00 0.00 0.00 4.00
4450 5042 0.482446 TTGGATGGTTGCCTCTGGTT 59.518 50.000 0.00 0.00 0.00 3.67
4453 5045 0.967380 GATGGTTGCCTCTGGTTGGG 60.967 60.000 0.00 0.00 0.00 4.12
4454 5046 2.283173 GGTTGCCTCTGGTTGGGG 60.283 66.667 0.00 0.00 0.00 4.96
4455 5047 2.520968 GTTGCCTCTGGTTGGGGT 59.479 61.111 0.00 0.00 0.00 4.95
4456 5048 1.603739 GTTGCCTCTGGTTGGGGTC 60.604 63.158 0.00 0.00 0.00 4.46
4457 5049 2.081787 TTGCCTCTGGTTGGGGTCA 61.082 57.895 0.00 0.00 0.00 4.02
4469 5061 3.270877 GTTGGGGTCATTACTGCTAGTG 58.729 50.000 0.00 0.00 0.00 2.74
4489 5081 5.250200 AGTGTGTTTTACTTGTTGACTCCA 58.750 37.500 0.00 0.00 0.00 3.86
4490 5082 5.123344 AGTGTGTTTTACTTGTTGACTCCAC 59.877 40.000 0.00 0.00 0.00 4.02
4491 5083 5.004448 TGTGTTTTACTTGTTGACTCCACA 58.996 37.500 0.00 0.00 0.00 4.17
4492 5084 5.473846 TGTGTTTTACTTGTTGACTCCACAA 59.526 36.000 0.00 0.00 0.00 3.33
4493 5085 6.016192 TGTGTTTTACTTGTTGACTCCACAAA 60.016 34.615 0.00 0.00 0.00 2.83
4494 5086 7.033185 GTGTTTTACTTGTTGACTCCACAAAT 58.967 34.615 0.00 0.00 0.00 2.32
4495 5087 8.185505 GTGTTTTACTTGTTGACTCCACAAATA 58.814 33.333 0.00 0.00 0.00 1.40
4496 5088 8.908903 TGTTTTACTTGTTGACTCCACAAATAT 58.091 29.630 0.00 0.00 0.00 1.28
4497 5089 9.180678 GTTTTACTTGTTGACTCCACAAATATG 57.819 33.333 0.00 0.00 0.00 1.78
4498 5090 8.458573 TTTACTTGTTGACTCCACAAATATGT 57.541 30.769 0.00 0.00 41.61 2.29
4524 5116 1.906333 GTTGGGGGTTTGGTGCGAT 60.906 57.895 0.00 0.00 0.00 4.58
4624 5218 2.106332 CGCCGGCGAATCTTACCT 59.894 61.111 44.86 0.00 42.83 3.08
4633 5227 2.034305 GCGAATCTTACCTAGCTTCGGA 59.966 50.000 8.58 0.00 46.96 4.55
4665 5259 4.140663 AGGAGATAATACCCCTACTGCTGT 60.141 45.833 0.66 0.66 0.00 4.40
4667 5261 5.071923 GGAGATAATACCCCTACTGCTGTTT 59.928 44.000 0.09 0.00 0.00 2.83
4678 5272 1.454847 TGCTGTTTTGCGGGGTCTT 60.455 52.632 0.00 0.00 35.36 3.01
4694 5288 4.454678 GGGTCTTTGCATGATCACTATGA 58.545 43.478 0.00 0.00 0.00 2.15
4797 5391 4.362677 TCTGGTCTAGAGCTAATGGGTTT 58.637 43.478 21.80 0.00 0.00 3.27
4800 5394 4.162320 TGGTCTAGAGCTAATGGGTTTCAG 59.838 45.833 21.80 0.00 0.00 3.02
4914 5510 1.228894 TGGCCTCCGTCTTCTCTGT 60.229 57.895 3.32 0.00 0.00 3.41
4968 5564 4.657824 CCGACAGGCCGTGTTCGT 62.658 66.667 14.49 0.26 40.56 3.85
5009 5605 1.548719 TGCTGATTACTGTAGCCGTGT 59.451 47.619 0.00 0.00 36.64 4.49
5022 5618 1.565156 GCCGTGTTTCTGATGACGCA 61.565 55.000 0.00 0.00 0.00 5.24
5086 5683 0.036952 CGATCACTGTTGCCACTCCT 60.037 55.000 0.00 0.00 0.00 3.69
5192 5790 3.976490 TTCTCCTGCCGTCCCCGAT 62.976 63.158 0.00 0.00 35.63 4.18
5213 5811 2.122413 TCACTGACTGGTGGGGCT 60.122 61.111 0.00 0.00 37.75 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.392706 ATGCTCCATATGGCGACGAA 59.607 50.000 17.58 0.28 34.44 3.85
37 38 4.031991 TCACACGAACAAACGACACTTTAG 59.968 41.667 0.00 0.00 37.03 1.85
42 43 2.791417 TTCACACGAACAAACGACAC 57.209 45.000 0.00 0.00 37.03 3.67
43 44 2.737783 AGTTTCACACGAACAAACGACA 59.262 40.909 0.00 0.00 35.55 4.35
47 49 3.481112 ACCAGTTTCACACGAACAAAC 57.519 42.857 0.00 0.00 0.00 2.93
60 62 4.742743 GCAACACTACCAGTCTACCAGTTT 60.743 45.833 0.00 0.00 0.00 2.66
68 70 1.768870 ACAAGGCAACACTACCAGTCT 59.231 47.619 0.00 0.00 41.41 3.24
69 71 2.256117 ACAAGGCAACACTACCAGTC 57.744 50.000 0.00 0.00 41.41 3.51
70 72 2.092646 TCAACAAGGCAACACTACCAGT 60.093 45.455 0.00 0.00 41.41 4.00
71 73 2.571212 TCAACAAGGCAACACTACCAG 58.429 47.619 0.00 0.00 41.41 4.00
72 74 2.719531 TCAACAAGGCAACACTACCA 57.280 45.000 0.00 0.00 41.41 3.25
73 75 2.949644 ACTTCAACAAGGCAACACTACC 59.050 45.455 0.00 0.00 41.41 3.18
74 76 3.625764 TCACTTCAACAAGGCAACACTAC 59.374 43.478 0.00 0.00 41.41 2.73
75 77 3.879998 TCACTTCAACAAGGCAACACTA 58.120 40.909 0.00 0.00 41.41 2.74
76 78 2.722094 TCACTTCAACAAGGCAACACT 58.278 42.857 0.00 0.00 41.41 3.55
88 90 2.024846 TGTTTCACCCCCTTCACTTCAA 60.025 45.455 0.00 0.00 0.00 2.69
163 165 6.768381 TGACCATAATAACAGTCACACACAAA 59.232 34.615 0.00 0.00 34.44 2.83
166 168 6.163476 TCTGACCATAATAACAGTCACACAC 58.837 40.000 0.00 0.00 35.50 3.82
167 169 6.353404 TCTGACCATAATAACAGTCACACA 57.647 37.500 0.00 0.00 35.50 3.72
168 170 7.849804 AATCTGACCATAATAACAGTCACAC 57.150 36.000 0.00 0.00 35.50 3.82
199 201 3.181487 CCCTCGCCAATTTCCTTGTAATG 60.181 47.826 0.00 0.00 32.61 1.90
201 203 2.442413 CCCTCGCCAATTTCCTTGTAA 58.558 47.619 0.00 0.00 32.61 2.41
205 207 2.046285 CGCCCTCGCCAATTTCCTT 61.046 57.895 0.00 0.00 0.00 3.36
207 209 3.518068 CCGCCCTCGCCAATTTCC 61.518 66.667 0.00 0.00 0.00 3.13
236 239 3.330853 CGGCTCCTATGAACGCGC 61.331 66.667 5.73 0.00 0.00 6.86
239 242 0.529992 GGGTTCGGCTCCTATGAACG 60.530 60.000 0.00 0.00 42.18 3.95
274 289 4.872691 CACTGGTCAGCTGATTTACCTAAG 59.127 45.833 21.47 12.94 32.99 2.18
275 290 4.323485 CCACTGGTCAGCTGATTTACCTAA 60.323 45.833 21.47 1.01 32.99 2.69
276 291 3.197766 CCACTGGTCAGCTGATTTACCTA 59.802 47.826 21.47 3.28 32.99 3.08
277 292 2.026822 CCACTGGTCAGCTGATTTACCT 60.027 50.000 21.47 0.00 32.99 3.08
278 293 2.359900 CCACTGGTCAGCTGATTTACC 58.640 52.381 21.47 17.18 0.00 2.85
279 294 2.359900 CCCACTGGTCAGCTGATTTAC 58.640 52.381 21.47 7.25 0.00 2.01
280 295 1.281867 CCCCACTGGTCAGCTGATTTA 59.718 52.381 21.47 8.44 0.00 1.40
285 301 1.856539 AATCCCCCACTGGTCAGCTG 61.857 60.000 7.63 7.63 0.00 4.24
292 308 1.103398 GCGATGAAATCCCCCACTGG 61.103 60.000 0.00 0.00 41.39 4.00
296 312 0.181114 CAGAGCGATGAAATCCCCCA 59.819 55.000 0.00 0.00 41.39 4.96
301 317 5.755375 TCTGGAATTACAGAGCGATGAAATC 59.245 40.000 16.79 0.00 42.26 2.17
313 329 5.826737 AGAGCATTGGAATCTGGAATTACAG 59.173 40.000 11.83 11.83 39.84 2.74
348 364 9.671279 AAAAACTCATGTCCATTTCTTTCTTTT 57.329 25.926 0.00 0.00 0.00 2.27
350 366 8.699130 AGAAAAACTCATGTCCATTTCTTTCTT 58.301 29.630 11.04 0.00 33.62 2.52
351 367 8.242729 AGAAAAACTCATGTCCATTTCTTTCT 57.757 30.769 11.04 0.00 33.62 2.52
352 368 8.512800 GAGAAAAACTCATGTCCATTTCTTTC 57.487 34.615 15.26 6.71 44.36 2.62
370 386 5.011023 GGAGCCTTGGAATTTCAGAGAAAAA 59.989 40.000 0.00 0.00 0.00 1.94
434 450 1.201880 GCGAAAACGGAGTAGAGGTCT 59.798 52.381 0.00 0.00 45.00 3.85
440 456 1.201647 TCCTCTGCGAAAACGGAGTAG 59.798 52.381 10.40 7.14 45.00 2.57
441 457 1.250328 TCCTCTGCGAAAACGGAGTA 58.750 50.000 10.40 0.00 45.00 2.59
447 463 2.225727 ACGGAAAATCCTCTGCGAAAAC 59.774 45.455 0.00 0.00 33.30 2.43
452 468 1.933853 CCTAACGGAAAATCCTCTGCG 59.066 52.381 0.00 0.00 33.30 5.18
453 469 3.261981 TCCTAACGGAAAATCCTCTGC 57.738 47.619 0.00 0.00 36.03 4.26
522 538 1.064017 GCTGTGGGTTTGGGATATCCA 60.064 52.381 23.27 6.92 45.43 3.41
524 540 1.134220 TCGCTGTGGGTTTGGGATATC 60.134 52.381 0.00 0.00 0.00 1.63
559 575 0.037046 CTTTGTGAAATGGGCTGGGC 60.037 55.000 0.00 0.00 0.00 5.36
560 576 0.037046 GCTTTGTGAAATGGGCTGGG 60.037 55.000 0.00 0.00 0.00 4.45
601 617 4.173924 GAGGAGCAGCAGGAGGGC 62.174 72.222 0.00 0.00 0.00 5.19
986 1002 2.182842 GCCATTGCCGATCGCTTCT 61.183 57.895 10.32 0.00 38.78 2.85
1048 1064 1.990614 GGAGTGGAGGGGAGTGGAC 60.991 68.421 0.00 0.00 0.00 4.02
1083 1100 5.542779 ACCAGAATTCAAGACACACTCTAC 58.457 41.667 8.44 0.00 0.00 2.59
1085 1102 4.696479 ACCAGAATTCAAGACACACTCT 57.304 40.909 8.44 0.00 0.00 3.24
1092 1109 7.382218 CCAAACAACAATACCAGAATTCAAGAC 59.618 37.037 8.44 0.00 0.00 3.01
1292 1312 2.367107 GGGGAGGGAAGAGGGGAC 60.367 72.222 0.00 0.00 0.00 4.46
1300 1320 2.647949 GGGAGAGAGGGGGAGGGAA 61.648 68.421 0.00 0.00 0.00 3.97
1323 1343 1.335182 CTAGATTCGAGGAAGCGCAGA 59.665 52.381 11.47 0.00 32.82 4.26
1469 1495 3.357079 CAAGCGCACCCAGTGGAC 61.357 66.667 11.95 0.00 33.64 4.02
1498 1527 2.557490 AGTTGTCCCAGTCTAACTCGTC 59.443 50.000 0.00 0.00 0.00 4.20
1500 1529 2.557056 TCAGTTGTCCCAGTCTAACTCG 59.443 50.000 0.00 0.00 31.47 4.18
1512 1542 0.536006 AGCAACAGCCTCAGTTGTCC 60.536 55.000 7.74 0.00 46.09 4.02
1564 1596 2.951457 TATTCGGTCTCATTGCGACA 57.049 45.000 8.88 0.00 33.11 4.35
1594 1630 7.798516 CCGTACAATGCTACACATAATTCAATC 59.201 37.037 0.00 0.00 38.34 2.67
1603 1639 2.235155 TGACCCGTACAATGCTACACAT 59.765 45.455 0.00 0.00 42.30 3.21
1605 1752 2.373540 TGACCCGTACAATGCTACAC 57.626 50.000 0.00 0.00 0.00 2.90
1636 1783 1.346395 TCTACAGCAATTCCCACACGT 59.654 47.619 0.00 0.00 0.00 4.49
1648 1795 2.232208 CAGGTCATGTCACTCTACAGCA 59.768 50.000 0.00 0.00 31.70 4.41
1662 1809 4.974645 TTTCTTCTGTACACCAGGTCAT 57.025 40.909 0.00 0.00 41.83 3.06
1670 1817 9.562583 TTTGTACAAACATTTTCTTCTGTACAC 57.437 29.630 17.01 0.00 45.16 2.90
1740 1889 7.687941 AATAAAATCCTTTCATGACACGACT 57.312 32.000 0.00 0.00 0.00 4.18
1761 1915 7.460910 TCAGGATCCTGCATAGCAAATTAATA 58.539 34.615 33.39 10.40 43.31 0.98
1762 1916 6.309357 TCAGGATCCTGCATAGCAAATTAAT 58.691 36.000 33.39 0.00 43.31 1.40
1763 1917 5.693961 TCAGGATCCTGCATAGCAAATTAA 58.306 37.500 33.39 11.48 43.31 1.40
1764 1918 5.308976 TCAGGATCCTGCATAGCAAATTA 57.691 39.130 33.39 11.68 43.31 1.40
1765 1919 4.142790 CTCAGGATCCTGCATAGCAAATT 58.857 43.478 33.39 0.00 43.31 1.82
1784 1938 1.434188 TGCAAGGAAAGAGACCCTCA 58.566 50.000 0.00 0.00 32.06 3.86
1845 2000 7.120873 GGCTATGCTTGATGATACATGAAATCT 59.879 37.037 0.00 0.00 0.00 2.40
1858 2013 5.048921 CCAGTTATCTTGGCTATGCTTGATG 60.049 44.000 0.00 0.00 0.00 3.07
1863 2018 2.487986 GCCCAGTTATCTTGGCTATGCT 60.488 50.000 8.35 0.00 45.53 3.79
1882 2038 5.062308 CGACAGAAGTAAACTTATCAGTGCC 59.938 44.000 0.00 0.00 36.11 5.01
1897 2053 2.095461 TCTATCAGCAGCGACAGAAGT 58.905 47.619 0.00 0.00 0.00 3.01
1920 2076 2.215478 CTTCGCCAACGCTCTCAACG 62.215 60.000 0.00 0.00 39.84 4.10
2181 2337 2.464459 CGCCTGCGGGTTGATCTTC 61.464 63.158 14.55 0.00 35.56 2.87
2254 2410 2.163818 TCTGTACAAGGAAAGTGCGG 57.836 50.000 0.00 0.00 0.00 5.69
2334 2490 8.885494 AGCAGAAATTTGTTTAAAAGCATGTA 57.115 26.923 0.00 0.00 0.00 2.29
2355 2511 7.626446 ACGGCTAAAAATTTGTTTAAAAGCAG 58.374 30.769 3.17 1.74 30.11 4.24
2356 2512 7.277981 TGACGGCTAAAAATTTGTTTAAAAGCA 59.722 29.630 3.17 0.00 30.11 3.91
2357 2513 7.581241 GTGACGGCTAAAAATTTGTTTAAAAGC 59.419 33.333 0.00 0.00 0.00 3.51
2358 2514 8.596380 TGTGACGGCTAAAAATTTGTTTAAAAG 58.404 29.630 0.00 0.00 0.00 2.27
2360 2516 7.760340 AGTGTGACGGCTAAAAATTTGTTTAAA 59.240 29.630 0.00 0.00 0.00 1.52
2361 2517 7.259161 AGTGTGACGGCTAAAAATTTGTTTAA 58.741 30.769 0.00 0.00 0.00 1.52
2362 2518 6.797454 AGTGTGACGGCTAAAAATTTGTTTA 58.203 32.000 0.00 0.00 0.00 2.01
2365 2521 4.578928 AGAGTGTGACGGCTAAAAATTTGT 59.421 37.500 0.00 0.00 0.00 2.83
2366 2522 5.108385 AGAGTGTGACGGCTAAAAATTTG 57.892 39.130 0.00 0.00 0.00 2.32
2367 2523 5.767816 AAGAGTGTGACGGCTAAAAATTT 57.232 34.783 0.00 0.00 0.00 1.82
2368 2524 5.767816 AAAGAGTGTGACGGCTAAAAATT 57.232 34.783 0.00 0.00 0.00 1.82
2369 2525 5.767816 AAAAGAGTGTGACGGCTAAAAAT 57.232 34.783 0.00 0.00 0.00 1.82
2370 2526 6.870971 ATAAAAGAGTGTGACGGCTAAAAA 57.129 33.333 0.00 0.00 0.00 1.94
2373 2529 4.693566 CCAATAAAAGAGTGTGACGGCTAA 59.306 41.667 0.00 0.00 0.00 3.09
2374 2530 4.250464 CCAATAAAAGAGTGTGACGGCTA 58.750 43.478 0.00 0.00 0.00 3.93
2375 2531 3.074412 CCAATAAAAGAGTGTGACGGCT 58.926 45.455 0.00 0.00 0.00 5.52
2376 2532 2.414161 GCCAATAAAAGAGTGTGACGGC 60.414 50.000 0.00 0.00 0.00 5.68
2377 2533 2.811431 TGCCAATAAAAGAGTGTGACGG 59.189 45.455 0.00 0.00 0.00 4.79
2378 2534 4.481930 TTGCCAATAAAAGAGTGTGACG 57.518 40.909 0.00 0.00 0.00 4.35
2379 2535 5.831997 AGTTTGCCAATAAAAGAGTGTGAC 58.168 37.500 0.00 0.00 0.00 3.67
2381 2537 7.064490 ACAAAAGTTTGCCAATAAAAGAGTGTG 59.936 33.333 3.68 0.00 41.79 3.82
2382 2538 7.102993 ACAAAAGTTTGCCAATAAAAGAGTGT 58.897 30.769 3.68 0.00 41.79 3.55
2383 2539 7.538303 ACAAAAGTTTGCCAATAAAAGAGTG 57.462 32.000 3.68 0.00 41.79 3.51
2397 2751 8.397906 TGTATCAACTCTCAGAACAAAAGTTTG 58.602 33.333 2.22 2.22 43.62 2.93
2406 2760 8.602328 CAAGAATCATGTATCAACTCTCAGAAC 58.398 37.037 0.00 0.00 0.00 3.01
2417 2771 9.498176 CAGTATGGAATCAAGAATCATGTATCA 57.502 33.333 0.00 0.00 0.00 2.15
2424 2778 8.408043 AAACAACAGTATGGAATCAAGAATCA 57.592 30.769 0.00 0.00 43.62 2.57
2425 2779 9.774742 GTAAACAACAGTATGGAATCAAGAATC 57.225 33.333 0.00 0.00 43.62 2.52
2426 2780 9.295825 TGTAAACAACAGTATGGAATCAAGAAT 57.704 29.630 0.00 0.00 43.62 2.40
2427 2781 8.564574 GTGTAAACAACAGTATGGAATCAAGAA 58.435 33.333 0.00 0.00 43.62 2.52
2428 2782 7.174253 GGTGTAAACAACAGTATGGAATCAAGA 59.826 37.037 0.00 0.00 43.62 3.02
2429 2783 7.174946 AGGTGTAAACAACAGTATGGAATCAAG 59.825 37.037 0.28 0.00 43.62 3.02
2430 2784 7.001674 AGGTGTAAACAACAGTATGGAATCAA 58.998 34.615 0.28 0.00 43.62 2.57
2456 2810 7.395190 ACACATATTGTTGTCAGCACATAAT 57.605 32.000 0.00 0.00 33.09 1.28
2459 2813 5.163723 GCTACACATATTGTTGTCAGCACAT 60.164 40.000 0.00 0.00 39.91 3.21
2610 2972 1.554617 AGCCCAAAAACAGCAACAACT 59.445 42.857 0.00 0.00 0.00 3.16
2611 2973 2.022764 AGCCCAAAAACAGCAACAAC 57.977 45.000 0.00 0.00 0.00 3.32
2704 3069 5.070001 CCTAAATTGGAAGTTCAGGTGTCA 58.930 41.667 5.01 0.00 0.00 3.58
2705 3070 5.070685 ACCTAAATTGGAAGTTCAGGTGTC 58.929 41.667 9.01 0.00 33.73 3.67
2721 3086 0.033109 GCCCCCTCAGCAACCTAAAT 60.033 55.000 0.00 0.00 0.00 1.40
2784 3150 3.733443 ACCAACATCAAACTTCTTGGC 57.267 42.857 0.00 0.00 35.70 4.52
2817 3183 7.176690 GGAATTTACAATGAAGGAAAGGACAGA 59.823 37.037 0.00 0.00 0.00 3.41
2827 3193 2.100749 GGGGCGGAATTTACAATGAAGG 59.899 50.000 0.00 0.00 0.00 3.46
2877 3244 5.545658 TGCAGCTTAAGAGGAAAATTACG 57.454 39.130 6.67 0.00 0.00 3.18
2878 3245 5.745769 GCATGCAGCTTAAGAGGAAAATTAC 59.254 40.000 14.21 0.00 41.15 1.89
2915 3283 7.360353 CGAATGTGAATTACTCTCTTTCAGCAA 60.360 37.037 0.00 0.00 34.07 3.91
2953 3322 4.947388 ACAGCACAAGAAACTTTGGTCTTA 59.053 37.500 0.00 0.00 32.79 2.10
2959 3328 2.878580 TGCACAGCACAAGAAACTTTG 58.121 42.857 0.00 0.00 31.71 2.77
3042 3411 1.520600 TTCGCCACACTAGTCGCAGA 61.521 55.000 0.00 0.00 30.66 4.26
3048 3417 0.390124 TTTCCGTTCGCCACACTAGT 59.610 50.000 0.00 0.00 0.00 2.57
3068 3437 8.644374 AACCCAAGCAACAACTATATTAAAGA 57.356 30.769 0.00 0.00 0.00 2.52
3182 3561 1.352083 TGAGCCTAGAAGCCAGTGTT 58.648 50.000 0.00 0.00 0.00 3.32
3186 3565 2.433604 TCTGAATGAGCCTAGAAGCCAG 59.566 50.000 0.00 0.00 0.00 4.85
3224 3708 5.527033 ACTACCACGAGAGAACAAAAGTAC 58.473 41.667 0.00 0.00 0.00 2.73
3316 3884 7.230108 CCAGTTTGCAATCTGATCCAGTAATAT 59.770 37.037 30.40 0.00 34.02 1.28
3319 3887 4.701651 CCAGTTTGCAATCTGATCCAGTAA 59.298 41.667 30.40 0.00 34.02 2.24
3330 3905 4.082571 ACAAGTAGCATCCAGTTTGCAATC 60.083 41.667 0.00 0.00 42.62 2.67
3380 3955 9.944376 ACAGCAAGTAAAGAAGATAGAATTACA 57.056 29.630 0.00 0.00 0.00 2.41
3480 4055 2.979678 ACCACCATCTGTAAGGTCAACT 59.020 45.455 0.00 0.00 35.52 3.16
3616 4191 7.115520 GTGAATAATATGTGAGATGAGTCCACG 59.884 40.741 0.00 0.00 31.91 4.94
3666 4241 3.097614 GTCAGGACTCTAAACTGGCCTA 58.902 50.000 3.32 0.00 30.94 3.93
3739 4314 9.161629 CAACACATTTAAACTCTTTTCCCTTTT 57.838 29.630 0.00 0.00 0.00 2.27
3888 4464 3.244770 CCCAGCCCTACAGTTAAGAACAA 60.245 47.826 0.00 0.00 0.00 2.83
3890 4466 2.355818 CCCCAGCCCTACAGTTAAGAAC 60.356 54.545 0.00 0.00 0.00 3.01
3930 4507 1.222661 CTGGCCAGATGCAGCTACA 59.777 57.895 29.88 3.43 43.89 2.74
3939 4516 1.535685 GGCAATCTCCTGGCCAGAT 59.464 57.895 34.91 17.34 46.92 2.90
4008 4585 1.118965 TCCGACTCTTGAAGCCACCA 61.119 55.000 0.00 0.00 0.00 4.17
4011 4588 1.293498 GCTCCGACTCTTGAAGCCA 59.707 57.895 0.00 0.00 0.00 4.75
4023 4600 2.669133 CCATGGAACCTGGCTCCGA 61.669 63.158 5.56 1.75 35.55 4.55
4086 4663 5.523916 TCTTAGCTTGCGGATTATTTCTGTC 59.476 40.000 0.00 0.00 32.85 3.51
4105 4682 7.445402 TGTTTCAGATGGAAAAACTCCTCTTAG 59.555 37.037 0.00 0.00 46.53 2.18
4210 4792 1.274167 AGGTCGAACGCCTTGTTGATA 59.726 47.619 0.00 0.00 42.09 2.15
4302 4884 4.441695 TGCTCCGCTTCGAGGCAG 62.442 66.667 20.22 11.18 32.89 4.85
4306 4888 0.946221 ACAAACTGCTCCGCTTCGAG 60.946 55.000 0.00 0.00 0.00 4.04
4309 4891 0.235926 GACACAAACTGCTCCGCTTC 59.764 55.000 0.00 0.00 0.00 3.86
4314 4896 0.304705 CACACGACACAAACTGCTCC 59.695 55.000 0.00 0.00 0.00 4.70
4325 4907 3.198872 TGCATTACAACTTCACACGACA 58.801 40.909 0.00 0.00 0.00 4.35
4336 4918 4.926238 CGGAGGATAGATCTGCATTACAAC 59.074 45.833 5.18 0.00 0.00 3.32
4445 5037 1.004745 AGCAGTAATGACCCCAACCAG 59.995 52.381 0.00 0.00 0.00 4.00
4446 5038 1.072266 AGCAGTAATGACCCCAACCA 58.928 50.000 0.00 0.00 0.00 3.67
4447 5039 2.238898 ACTAGCAGTAATGACCCCAACC 59.761 50.000 0.00 0.00 0.00 3.77
4448 5040 3.270877 CACTAGCAGTAATGACCCCAAC 58.729 50.000 0.00 0.00 0.00 3.77
4449 5041 2.910319 ACACTAGCAGTAATGACCCCAA 59.090 45.455 0.00 0.00 0.00 4.12
4450 5042 2.236146 CACACTAGCAGTAATGACCCCA 59.764 50.000 0.00 0.00 0.00 4.96
4453 5045 5.941948 AAAACACACTAGCAGTAATGACC 57.058 39.130 0.00 0.00 0.00 4.02
4454 5046 7.653767 AGTAAAACACACTAGCAGTAATGAC 57.346 36.000 0.00 0.00 0.00 3.06
4455 5047 7.713507 ACAAGTAAAACACACTAGCAGTAATGA 59.286 33.333 0.00 0.00 0.00 2.57
4456 5048 7.861630 ACAAGTAAAACACACTAGCAGTAATG 58.138 34.615 0.00 0.00 0.00 1.90
4457 5049 8.342634 CAACAAGTAAAACACACTAGCAGTAAT 58.657 33.333 0.00 0.00 0.00 1.89
4469 5061 5.554822 TGTGGAGTCAACAAGTAAAACAC 57.445 39.130 0.00 0.00 0.00 3.32
4489 5081 3.368635 CCCAACATGCAGCACATATTTGT 60.369 43.478 0.00 0.00 36.64 2.83
4490 5082 3.191669 CCCAACATGCAGCACATATTTG 58.808 45.455 0.00 0.00 36.64 2.32
4491 5083 2.168936 CCCCAACATGCAGCACATATTT 59.831 45.455 0.00 0.00 36.64 1.40
4492 5084 1.758280 CCCCAACATGCAGCACATATT 59.242 47.619 0.00 0.00 36.64 1.28
4493 5085 1.405872 CCCCAACATGCAGCACATAT 58.594 50.000 0.00 0.00 36.64 1.78
4494 5086 0.683828 CCCCCAACATGCAGCACATA 60.684 55.000 0.00 0.00 36.64 2.29
4495 5087 1.985662 CCCCCAACATGCAGCACAT 60.986 57.895 0.00 0.00 40.66 3.21
4496 5088 2.601067 CCCCCAACATGCAGCACA 60.601 61.111 0.00 0.00 0.00 4.57
4497 5089 1.757423 AAACCCCCAACATGCAGCAC 61.757 55.000 0.00 0.00 0.00 4.40
4498 5090 1.459158 AAACCCCCAACATGCAGCA 60.459 52.632 0.00 0.00 0.00 4.41
4499 5091 1.004679 CAAACCCCCAACATGCAGC 60.005 57.895 0.00 0.00 0.00 5.25
4500 5092 1.120795 ACCAAACCCCCAACATGCAG 61.121 55.000 0.00 0.00 0.00 4.41
4501 5093 1.074926 ACCAAACCCCCAACATGCA 60.075 52.632 0.00 0.00 0.00 3.96
4502 5094 1.370810 CACCAAACCCCCAACATGC 59.629 57.895 0.00 0.00 0.00 4.06
4503 5095 1.370810 GCACCAAACCCCCAACATG 59.629 57.895 0.00 0.00 0.00 3.21
4508 5100 1.214217 TATATCGCACCAAACCCCCA 58.786 50.000 0.00 0.00 0.00 4.96
4586 5180 1.486310 TGCATGTCTTCGCCTTATCCT 59.514 47.619 0.00 0.00 0.00 3.24
4591 5185 2.680913 GCGTGCATGTCTTCGCCTT 61.681 57.895 7.93 0.00 42.33 4.35
4665 5259 0.033228 CATGCAAAGACCCCGCAAAA 59.967 50.000 0.00 0.00 39.48 2.44
4667 5261 0.611618 ATCATGCAAAGACCCCGCAA 60.612 50.000 0.00 0.00 39.48 4.85
4678 5272 4.637091 CACTTGGTCATAGTGATCATGCAA 59.363 41.667 0.00 0.00 44.52 4.08
4694 5288 1.402613 GCAACCGTGTAAACACTTGGT 59.597 47.619 11.22 8.91 44.34 3.67
4729 5323 0.118346 TGCCCTCTCCTACCTCCAAA 59.882 55.000 0.00 0.00 0.00 3.28
5009 5605 1.159285 CAAGCCTGCGTCATCAGAAA 58.841 50.000 0.00 0.00 36.19 2.52
5022 5618 1.134580 CACGACCTCATGATCAAGCCT 60.135 52.381 0.00 0.00 0.00 4.58
5086 5683 4.023792 GCGCCATTAATCAAGATGTGATGA 60.024 41.667 0.00 0.00 46.80 2.92
5213 5811 2.965831 CTGTATGGCCTAGAGGTAGCAA 59.034 50.000 3.32 0.00 37.57 3.91
5254 5852 2.350895 CACCACAGGGCCGAATCA 59.649 61.111 0.00 0.00 37.90 2.57


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

AutoCloner maintained by Alex Coulton.