Multiple sequence alignment - TraesCS5A01G092900

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 TraesCS5A01G092900 chr5A 100.000 9573 0 0 1 9573 129118199 129108627 0.000000e+00 17679.0
1 TraesCS5A01G092900 chr5A 89.024 82 6 3 7373 7452 129110749 129110669 2.200000e-16 99.0
2 TraesCS5A01G092900 chr5A 89.024 82 6 3 7451 7531 129110827 129110748 2.200000e-16 99.0
3 TraesCS5A01G092900 chr5B 96.459 8021 228 32 1565 9573 131324105 131316129 0.000000e+00 13188.0
4 TraesCS5A01G092900 chr5B 90.135 1186 73 15 394 1572 131325363 131324215 0.000000e+00 1502.0
5 TraesCS5A01G092900 chr5B 90.000 390 30 2 9 390 131337924 131337536 6.680000e-136 496.0
6 TraesCS5A01G092900 chr5B 87.805 82 7 3 7373 7452 131318248 131318168 1.020000e-14 93.5
7 TraesCS5A01G092900 chr5D 96.300 7972 242 17 1607 9573 119010115 119002192 0.000000e+00 13038.0
8 TraesCS5A01G092900 chr5D 90.822 1569 107 23 7 1564 119011772 119010230 0.000000e+00 2065.0
9 TraesCS5A01G092900 chr5D 80.174 459 77 7 1 456 386852058 386852505 1.990000e-86 331.0
10 TraesCS5A01G092900 chr5D 82.432 296 49 2 1 296 108577526 108577818 1.230000e-63 255.0
11 TraesCS5A01G092900 chr5D 89.024 82 6 3 7373 7452 119004300 119004220 2.200000e-16 99.0
12 TraesCS5A01G092900 chr5D 88.889 81 8 1 7451 7531 119004378 119004299 2.200000e-16 99.0
13 TraesCS5A01G092900 chr6D 85.879 779 93 10 10 782 268679690 268678923 0.000000e+00 813.0
14 TraesCS5A01G092900 chr6B 92.658 395 24 2 3436 3830 720950610 720950221 1.800000e-156 564.0
15 TraesCS5A01G092900 chr6B 87.147 389 46 2 1 386 417141824 417141437 1.140000e-118 438.0
16 TraesCS5A01G092900 chr1B 80.482 789 110 16 7 781 299795631 299796389 1.800000e-156 564.0
17 TraesCS5A01G092900 chr2B 82.561 453 62 12 331 776 597778782 597778340 5.420000e-102 383.0
18 TraesCS5A01G092900 chr2B 85.075 335 42 3 9 335 597807499 597807165 1.540000e-87 335.0
19 TraesCS5A01G092900 chr4B 75.000 804 167 28 4746 5533 161554453 161553668 3.310000e-89 340.0
20 TraesCS5A01G092900 chr2A 77.997 609 82 22 4928 5503 760765901 760766490 1.540000e-87 335.0
21 TraesCS5A01G092900 chr4A 74.969 807 160 34 4746 5533 428156163 428155380 5.540000e-87 333.0
22 TraesCS5A01G092900 chr4D 77.413 518 99 15 5025 5533 133477739 133478247 9.400000e-75 292.0
23 TraesCS5A01G092900 chr7B 79.861 288 42 8 18 296 89976665 89976385 7.580000e-46 196.0


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 TraesCS5A01G092900 chr5A 129108627 129118199 9572 True 17679 17679 100.000 1 9573 1 chr5A.!!$R1 9572
1 TraesCS5A01G092900 chr5B 131316129 131324105 7976 True 13188 13188 96.459 1565 9573 1 chr5B.!!$R1 8008
2 TraesCS5A01G092900 chr5B 131324215 131325363 1148 True 1502 1502 90.135 394 1572 1 chr5B.!!$R3 1178
3 TraesCS5A01G092900 chr5D 119002192 119010115 7923 True 13038 13038 96.300 1607 9573 1 chr5D.!!$R1 7966
4 TraesCS5A01G092900 chr5D 119010230 119011772 1542 True 2065 2065 90.822 7 1564 1 chr5D.!!$R2 1557
5 TraesCS5A01G092900 chr6D 268678923 268679690 767 True 813 813 85.879 10 782 1 chr6D.!!$R1 772
6 TraesCS5A01G092900 chr1B 299795631 299796389 758 False 564 564 80.482 7 781 1 chr1B.!!$F1 774
7 TraesCS5A01G092900 chr4B 161553668 161554453 785 True 340 340 75.000 4746 5533 1 chr4B.!!$R1 787
8 TraesCS5A01G092900 chr2A 760765901 760766490 589 False 335 335 77.997 4928 5503 1 chr2A.!!$F1 575
9 TraesCS5A01G092900 chr4A 428155380 428156163 783 True 333 333 74.969 4746 5533 1 chr4A.!!$R1 787
10 TraesCS5A01G092900 chr4D 133477739 133478247 508 False 292 292 77.413 5025 5533 1 chr4D.!!$F1 508

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
95 96 0.034574 TTGTTGACACTGCCACCACT 60.035 50.000 0.00 0.00 0.00 4.00 F
1065 1083 0.249911 ACTGCAGACGAGTTCAACCC 60.250 55.000 23.35 0.00 0.00 4.11 F
1068 1086 0.534203 GCAGACGAGTTCAACCCCAA 60.534 55.000 0.00 0.00 0.00 4.12 F
1912 1934 1.502163 GACGGTATGATGCAGCCAGC 61.502 60.000 0.00 0.00 45.96 4.85 F
2032 2054 1.337703 TGCAATGCACTGAACAAGGTC 59.662 47.619 2.72 0.00 31.71 3.85 F
2939 2965 1.409427 AGCCGCTCTTGGTAGACATAC 59.591 52.381 0.00 0.00 0.00 2.39 F
3030 3056 1.891060 GAGTGTCGAGCTGCAAACCG 61.891 60.000 1.02 0.00 0.00 4.44 F
3538 3568 2.292267 AGGTCGGAATGATGATTGTGC 58.708 47.619 0.00 0.00 0.00 4.57 F
4953 4984 1.869767 CGCTCTCATAGGTTTGGCATC 59.130 52.381 0.00 0.00 0.00 3.91 F
5590 5658 1.261938 TGTAGGTAGCACCGTGCCAT 61.262 55.000 19.96 6.05 46.52 4.40 F
6490 6561 1.079543 CAGCTGTTCCTCGGACCAG 60.080 63.158 5.25 6.17 37.65 4.00 F
6908 6982 0.098200 CTCGTCTGTGCATGGCATTG 59.902 55.000 0.00 0.00 41.91 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1400 0.443869 CATCCAGCGAACCAAGAACG 59.556 55.000 0.00 0.00 0.00 3.95 R
1912 1934 0.508641 CGACTGTTCTTCGCAACCAG 59.491 55.000 0.00 0.00 0.00 4.00 R
1981 2003 0.677731 CATTTCTCAGCCCAAGCCGA 60.678 55.000 0.00 0.00 41.25 5.54 R
3030 3056 1.467342 GAACGGAACATACCAAGTGCC 59.533 52.381 0.00 0.00 0.00 5.01 R
3538 3568 1.605710 CTGGTTGGAACTGTTCAGCTG 59.394 52.381 21.01 7.63 0.00 4.24 R
4588 4618 1.494721 TGTCCCCTTTCTCTGTGCTTT 59.505 47.619 0.00 0.00 0.00 3.51 R
4625 4655 5.981174 TGTAGATCTCAATCATCTGCACAA 58.019 37.500 0.00 0.00 37.87 3.33 R
5480 5548 3.365969 CCTTCTTTATTCGCTTTTGCCGT 60.366 43.478 0.00 0.00 43.93 5.68 R
6427 6498 0.033011 ACTCCTCGCCTGGTACTGAT 60.033 55.000 0.00 0.00 0.00 2.90 R
6908 6982 0.599558 TTGCTCTGATTTGCCAGCAC 59.400 50.000 0.00 0.00 41.56 4.40 R
7717 7793 1.927569 TAGGGCGACTCTCCAGAGCT 61.928 60.000 3.33 0.00 45.79 4.09 R
8865 8942 2.162408 GTGCTTCTGGGTTGAGTAATGC 59.838 50.000 0.00 0.00 0.00 3.56 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
84 85 4.098914 AGTAGCCTTCCATTTGTTGACA 57.901 40.909 0.00 0.00 0.00 3.58
95 96 0.034574 TTGTTGACACTGCCACCACT 60.035 50.000 0.00 0.00 0.00 4.00
150 151 8.480066 CAATAGCGTATTAGTGTAATGTCACTG 58.520 37.037 11.69 0.00 46.36 3.66
163 164 0.855349 GTCACTGTGTCAGTTCGCTG 59.145 55.000 7.79 0.00 42.59 5.18
210 211 7.972832 AGAACGTGGTTATTCAGTTTTATCA 57.027 32.000 0.00 0.00 0.00 2.15
267 276 3.114065 CCGCCACGTTCTATCTTTCTAC 58.886 50.000 0.00 0.00 0.00 2.59
273 283 6.565234 CCACGTTCTATCTTTCTACTGTCAT 58.435 40.000 0.00 0.00 0.00 3.06
290 300 1.185315 CATTGATTCGTGGGCCCTTT 58.815 50.000 25.70 2.39 0.00 3.11
307 317 4.023021 GCCCTTTTGTAACATAAACACCGA 60.023 41.667 0.00 0.00 0.00 4.69
308 318 5.336134 GCCCTTTTGTAACATAAACACCGAT 60.336 40.000 0.00 0.00 0.00 4.18
310 320 6.294286 CCCTTTTGTAACATAAACACCGATGT 60.294 38.462 0.00 0.00 42.46 3.06
325 335 3.161067 CCGATGTGTCCTATCTCTCCAT 58.839 50.000 0.00 0.00 0.00 3.41
338 348 1.761198 CTCTCCATCATCACTGGCTCA 59.239 52.381 0.00 0.00 33.56 4.26
353 363 0.475906 GCTCATGGGCCCTTCTGTAT 59.524 55.000 25.70 3.22 0.00 2.29
391 401 4.006319 GACAAAAAGGCTCAGCTATGACT 58.994 43.478 0.00 0.00 0.00 3.41
396 406 7.829211 ACAAAAAGGCTCAGCTATGACTATAAA 59.171 33.333 0.00 0.00 0.00 1.40
407 417 7.275779 CAGCTATGACTATAAACAAACAGACGT 59.724 37.037 0.00 0.00 0.00 4.34
413 423 8.136800 TGACTATAAACAAACAGACGTACTCAA 58.863 33.333 0.00 0.00 0.00 3.02
509 526 2.684881 GTCCACATAAATCAGCCACTGG 59.315 50.000 0.00 0.00 31.51 4.00
551 568 5.297029 GTCCCAGGCTTCTGTATATTTCAAC 59.703 44.000 0.00 0.00 36.81 3.18
556 573 8.902806 CCAGGCTTCTGTATATTTCAACATTTA 58.097 33.333 0.00 0.00 36.81 1.40
598 615 2.072487 CAGGTGGGTCCCGGATGAT 61.072 63.158 0.73 0.00 36.75 2.45
621 638 2.324215 GCATGAGTGTATGCGGCAT 58.676 52.632 20.57 20.57 43.36 4.40
657 674 3.366883 GCATTGACCCAACGAAAATGCTA 60.367 43.478 10.55 0.00 46.03 3.49
691 708 2.916502 TTTGAGTGTGCGGCGACTGT 62.917 55.000 12.98 0.00 0.00 3.55
705 722 1.248486 GACTGTTGGAGGGGAAAAGC 58.752 55.000 0.00 0.00 0.00 3.51
737 754 6.293955 CGTTTGTTGGATGAGGTAAAACTGAT 60.294 38.462 0.00 0.00 0.00 2.90
744 761 5.749109 GGATGAGGTAAAACTGATGAGTACG 59.251 44.000 0.00 0.00 0.00 3.67
745 762 5.717078 TGAGGTAAAACTGATGAGTACGT 57.283 39.130 0.00 0.00 0.00 3.57
747 764 6.615088 TGAGGTAAAACTGATGAGTACGTAC 58.385 40.000 18.10 18.10 0.00 3.67
748 765 6.432162 TGAGGTAAAACTGATGAGTACGTACT 59.568 38.462 27.71 27.71 39.71 2.73
751 768 8.457261 AGGTAAAACTGATGAGTACGTACTAAG 58.543 37.037 27.44 21.95 36.50 2.18
752 769 7.219726 GGTAAAACTGATGAGTACGTACTAAGC 59.780 40.741 27.44 23.29 36.50 3.09
753 770 5.892160 AACTGATGAGTACGTACTAAGCA 57.108 39.130 25.61 25.61 36.50 3.91
754 771 5.892160 ACTGATGAGTACGTACTAAGCAA 57.108 39.130 26.74 13.94 33.01 3.91
755 772 5.638783 ACTGATGAGTACGTACTAAGCAAC 58.361 41.667 26.74 19.45 33.01 4.17
776 793 2.643551 CCGAGGGCACACAAATAGAAT 58.356 47.619 0.00 0.00 0.00 2.40
859 876 1.280421 GTGGTCTGGCCTTCTCATCTT 59.720 52.381 3.32 0.00 38.35 2.40
860 877 1.556911 TGGTCTGGCCTTCTCATCTTC 59.443 52.381 3.32 0.00 38.35 2.87
861 878 1.836802 GGTCTGGCCTTCTCATCTTCT 59.163 52.381 3.32 0.00 0.00 2.85
863 880 3.530535 GTCTGGCCTTCTCATCTTCTTC 58.469 50.000 3.32 0.00 0.00 2.87
864 881 3.197549 GTCTGGCCTTCTCATCTTCTTCT 59.802 47.826 3.32 0.00 0.00 2.85
865 882 3.450457 TCTGGCCTTCTCATCTTCTTCTC 59.550 47.826 3.32 0.00 0.00 2.87
867 884 3.197333 TGGCCTTCTCATCTTCTTCTCAG 59.803 47.826 3.32 0.00 0.00 3.35
868 885 3.197549 GGCCTTCTCATCTTCTTCTCAGT 59.802 47.826 0.00 0.00 0.00 3.41
869 886 4.323409 GGCCTTCTCATCTTCTTCTCAGTT 60.323 45.833 0.00 0.00 0.00 3.16
870 887 5.105146 GGCCTTCTCATCTTCTTCTCAGTTA 60.105 44.000 0.00 0.00 0.00 2.24
908 925 9.449719 CATGAGTATCTACATTTATTTACCCCC 57.550 37.037 0.00 0.00 34.92 5.40
915 932 7.631933 TCTACATTTATTTACCCCCTCGAAAA 58.368 34.615 0.00 0.00 0.00 2.29
916 933 6.769134 ACATTTATTTACCCCCTCGAAAAG 57.231 37.500 0.00 0.00 0.00 2.27
921 938 4.796495 CCCCCTCGAAAAGCCCGG 62.796 72.222 0.00 0.00 0.00 5.73
950 968 1.234615 CCACCCCACGTCATCAACAC 61.235 60.000 0.00 0.00 0.00 3.32
1062 1080 0.464036 ACCACTGCAGACGAGTTCAA 59.536 50.000 23.35 0.00 0.00 2.69
1065 1083 0.249911 ACTGCAGACGAGTTCAACCC 60.250 55.000 23.35 0.00 0.00 4.11
1066 1084 0.951040 CTGCAGACGAGTTCAACCCC 60.951 60.000 8.42 0.00 0.00 4.95
1067 1085 1.070786 GCAGACGAGTTCAACCCCA 59.929 57.895 0.00 0.00 0.00 4.96
1068 1086 0.534203 GCAGACGAGTTCAACCCCAA 60.534 55.000 0.00 0.00 0.00 4.12
1069 1087 1.961793 CAGACGAGTTCAACCCCAAA 58.038 50.000 0.00 0.00 0.00 3.28
1094 1112 4.426313 CCAACCCGGCCTTCCTCC 62.426 72.222 0.00 0.00 0.00 4.30
1162 1180 2.903855 GGTCGGCTCGTCGGGATA 60.904 66.667 0.00 0.00 0.00 2.59
1233 1255 2.046864 CGACGAAGAGGGAGCTGGA 61.047 63.158 0.00 0.00 0.00 3.86
1378 1400 3.181490 GGGCGGGAATTTAGTGATTTGAC 60.181 47.826 0.00 0.00 0.00 3.18
1579 1601 5.002516 AGTGGATAGTACCAGTAGTATCGC 58.997 45.833 19.35 15.88 44.01 4.58
1812 1834 6.560003 TGTATGATGGTGATGGTTCTTAGT 57.440 37.500 0.00 0.00 0.00 2.24
1912 1934 1.502163 GACGGTATGATGCAGCCAGC 61.502 60.000 0.00 0.00 45.96 4.85
1970 1992 1.521616 CTGCCAGAAGAGCCCTCTC 59.478 63.158 0.00 0.00 39.39 3.20
2032 2054 1.337703 TGCAATGCACTGAACAAGGTC 59.662 47.619 2.72 0.00 31.71 3.85
2109 2131 2.619646 CTGCCATGCATGCTAATACACA 59.380 45.455 21.69 7.13 38.13 3.72
2124 2146 7.147637 TGCTAATACACAGTGATGTTATACCCA 60.148 37.037 7.81 0.00 33.85 4.51
2164 2186 1.497991 CCCGCACAGATACCGTTATG 58.502 55.000 0.00 0.00 0.00 1.90
2283 2305 4.323104 GCTGTCTGACTTGGAGAAGGTATT 60.323 45.833 9.51 0.00 32.95 1.89
2284 2306 5.799213 CTGTCTGACTTGGAGAAGGTATTT 58.201 41.667 9.51 0.00 32.95 1.40
2323 2345 3.198417 TGAGAGCTCATGCCATAAGTTCA 59.802 43.478 17.77 3.05 40.80 3.18
2420 2442 5.325239 AGTAAATGCTTGGGCTACTTTTCT 58.675 37.500 0.00 0.00 39.59 2.52
2687 2710 7.630242 AGTTTTAATAGCAGAGCAAAGCATA 57.370 32.000 0.00 0.00 0.00 3.14
2688 2711 7.701445 AGTTTTAATAGCAGAGCAAAGCATAG 58.299 34.615 0.00 0.00 0.00 2.23
2689 2712 7.554118 AGTTTTAATAGCAGAGCAAAGCATAGA 59.446 33.333 0.00 0.00 0.00 1.98
2714 2740 4.202503 ACTGATTGTTGTCTGGAATCCACT 60.203 41.667 0.00 0.00 0.00 4.00
2811 2837 8.688151 ACATGTATCTCTTCCTTTGTAGACTAC 58.312 37.037 5.62 5.62 0.00 2.73
2842 2868 2.482336 CCTTAACATGCTTGTGCGTACA 59.518 45.455 0.82 0.82 43.34 2.90
2870 2896 7.518188 ACTCTTGGATAAGAAACCAGAAGAAA 58.482 34.615 0.00 0.00 42.11 2.52
2896 2922 5.339695 CCCATTGGTTAGCCTACTTTCCTTA 60.340 44.000 1.20 0.00 35.27 2.69
2939 2965 1.409427 AGCCGCTCTTGGTAGACATAC 59.591 52.381 0.00 0.00 0.00 2.39
3030 3056 1.891060 GAGTGTCGAGCTGCAAACCG 61.891 60.000 1.02 0.00 0.00 4.44
3116 3142 7.011482 GGGCACTTTCTTAGTTGTATCACATAG 59.989 40.741 0.00 0.00 33.85 2.23
3204 3234 5.450818 TTGCATAGGTGACCTTAAAGGAT 57.549 39.130 10.53 0.00 37.67 3.24
3477 3507 5.634118 ACAAAATGAAGATGGGTGAAGAGA 58.366 37.500 0.00 0.00 0.00 3.10
3500 3530 3.149196 GCCAAATCTCTTGAAGGTGACA 58.851 45.455 0.00 0.00 0.00 3.58
3520 3550 2.426738 CAGAAGAGGTCAGCTCTGTAGG 59.573 54.545 7.27 0.00 0.00 3.18
3538 3568 2.292267 AGGTCGGAATGATGATTGTGC 58.708 47.619 0.00 0.00 0.00 4.57
3579 3609 4.827284 CAGGGGCGGAAATAAGTATTGAAT 59.173 41.667 0.00 0.00 0.00 2.57
3631 3661 7.550906 TCCTTTTGTTTTACATTCCTTGTTTGG 59.449 33.333 0.00 0.00 39.87 3.28
3651 3681 2.879026 GGTCTTCCCTAATCCGCATTTC 59.121 50.000 0.00 0.00 0.00 2.17
3830 3860 9.851686 AACCTATAACTGATTTTGCATCTATCA 57.148 29.630 0.00 0.00 0.00 2.15
4006 4036 4.690280 GGTAACCATTTTTGGTGCTCAATG 59.310 41.667 0.00 0.00 42.20 2.82
4078 4108 9.838339 ACTTTATCACCAGGAAATATTAGAGTG 57.162 33.333 0.00 0.00 0.00 3.51
4172 4202 5.586243 AGAACAATCACAATAATCACTCCCG 59.414 40.000 0.00 0.00 0.00 5.14
4286 4316 8.668353 TGCTTACTCATAATTAGCTTGACTTTG 58.332 33.333 0.00 0.00 33.15 2.77
4287 4317 8.883731 GCTTACTCATAATTAGCTTGACTTTGA 58.116 33.333 0.00 0.00 0.00 2.69
4306 4336 4.866508 TGATTGAGTACCGAACTTCAGT 57.133 40.909 0.00 0.00 39.07 3.41
4447 4477 9.695155 ACCTATACAATGGTAATAAGCTTTGTT 57.305 29.630 3.20 2.97 44.42 2.83
4490 4520 4.927425 CGTAGCACAAAGGTAAAAGAGCTA 59.073 41.667 0.00 0.00 33.71 3.32
4621 4651 6.187682 AGAAAGGGGACAATCAATTACGAAT 58.812 36.000 0.00 0.00 0.00 3.34
4625 4655 7.239763 AGGGGACAATCAATTACGAATTTTT 57.760 32.000 0.00 0.00 0.00 1.94
4953 4984 1.869767 CGCTCTCATAGGTTTGGCATC 59.130 52.381 0.00 0.00 0.00 3.91
5290 5345 4.268884 GCAAGATTCTCTAGGTACTTTGCG 59.731 45.833 0.00 0.00 41.75 4.85
5326 5381 7.780745 TCCTAAATTTCACTTTCTTGGTACCAA 59.219 33.333 25.58 25.58 0.00 3.67
5480 5548 2.752358 CCTCTGTTGAGCTGGGCA 59.248 61.111 0.00 0.00 38.93 5.36
5482 5550 2.031012 TCTGTTGAGCTGGGCACG 59.969 61.111 0.00 0.00 0.00 5.34
5526 5594 1.909302 TGAGGTTAGGGAGCTGAAAGG 59.091 52.381 0.00 0.00 35.91 3.11
5590 5658 1.261938 TGTAGGTAGCACCGTGCCAT 61.262 55.000 19.96 6.05 46.52 4.40
5885 5953 6.597672 AGAATTCATGTGTTCTAATTGCGGTA 59.402 34.615 8.44 0.00 33.15 4.02
6243 6314 1.284111 ATTCCTGGCTCTGGCATCCA 61.284 55.000 0.00 0.00 40.87 3.41
6346 6417 3.329386 CAATTCTGTTCGAGAGCAGGAA 58.671 45.455 15.18 9.57 39.67 3.36
6427 6498 1.611519 CGCAAAAGGGTAGGGTTGAA 58.388 50.000 0.00 0.00 0.00 2.69
6437 6508 3.118371 GGGTAGGGTTGAATCAGTACCAG 60.118 52.174 6.46 0.00 33.00 4.00
6440 6511 1.369625 GGTTGAATCAGTACCAGGCG 58.630 55.000 0.00 0.00 32.12 5.52
6490 6561 1.079543 CAGCTGTTCCTCGGACCAG 60.080 63.158 5.25 6.17 37.65 4.00
6566 6637 6.015772 AGGCGTTTCAAATAAAAAGAAGCCTA 60.016 34.615 0.00 0.00 38.90 3.93
6570 6641 7.308951 CGTTTCAAATAAAAAGAAGCCTAGGGA 60.309 37.037 11.72 0.00 0.00 4.20
6804 6875 1.933181 GGCAAACAACTTTTGAGTGGC 59.067 47.619 0.91 0.00 36.80 5.01
6812 6883 2.233271 ACTTTTGAGTGGCACAGATGG 58.767 47.619 21.41 7.60 41.80 3.51
6813 6884 2.158623 ACTTTTGAGTGGCACAGATGGA 60.159 45.455 21.41 0.00 41.80 3.41
6814 6885 2.655090 TTTGAGTGGCACAGATGGAA 57.345 45.000 21.41 2.81 41.80 3.53
6863 6937 8.970691 AACACTGTAAAGTAATGAATCAATGC 57.029 30.769 0.00 0.00 0.00 3.56
6895 6969 1.489481 TTCTGCCATCATCCTCGTCT 58.511 50.000 0.00 0.00 0.00 4.18
6908 6982 0.098200 CTCGTCTGTGCATGGCATTG 59.902 55.000 0.00 0.00 41.91 2.82
6948 7022 7.819644 AGCAACAAAAAGCTTTTCAAAAGAAT 58.180 26.923 24.04 3.83 38.01 2.40
7200 7274 4.394300 CAGGCTAGCCATGTTTATAGCATC 59.606 45.833 34.70 2.35 41.92 3.91
7301 7376 9.354673 TCACTTCATTTTAAAAGGATTGTCTCT 57.645 29.630 15.37 0.00 0.00 3.10
7338 7413 4.280174 AGCAAGAGTGAAGAAATTGCATGT 59.720 37.500 10.44 0.00 46.66 3.21
7339 7414 4.620184 GCAAGAGTGAAGAAATTGCATGTC 59.380 41.667 3.51 0.00 44.32 3.06
7362 7437 5.778241 TCTTTTACATGGTCTGACTCCTGTA 59.222 40.000 7.85 9.87 0.00 2.74
7635 7711 2.375110 CGCACATTGTTCTGTCACAAC 58.625 47.619 0.00 0.00 39.48 3.32
7717 7793 1.757118 CTATGCAGACCCCTTCTCGAA 59.243 52.381 0.00 0.00 28.96 3.71
7777 7853 3.420893 TGCCTTGATCTTAACCCACTTG 58.579 45.455 0.00 0.00 0.00 3.16
7917 7993 7.520937 GCCAGCAAAAACTTGATTTGATTGATT 60.521 33.333 3.37 0.00 39.56 2.57
7992 8068 6.463472 CCTGCAGATGTCATCCAGAACTAATA 60.463 42.308 17.39 0.00 0.00 0.98
8044 8120 8.959705 ATCAGGTAATTAGCAGTAAAGGTAAC 57.040 34.615 16.53 0.00 34.67 2.50
8063 8139 6.589139 AGGTAACGTTTCAGAGTAATTACTGC 59.411 38.462 22.68 13.45 46.39 4.40
8319 8395 5.633830 TTGTTCAGAGAAATGAGAATGGC 57.366 39.130 0.00 0.00 0.00 4.40
8412 8488 3.614092 TCAGCATCTGGACCAAAATCTC 58.386 45.455 0.00 0.00 31.51 2.75
8494 8570 4.460263 TGGCTTGGATCATATGGTGTAAC 58.540 43.478 2.13 0.00 0.00 2.50
8498 8574 6.460123 GGCTTGGATCATATGGTGTAACTTTG 60.460 42.308 2.13 0.00 36.74 2.77
8500 8576 7.362920 GCTTGGATCATATGGTGTAACTTTGTT 60.363 37.037 2.13 0.00 36.74 2.83
8590 8666 3.863424 GCCTGCATGAAAATTGATGACAG 59.137 43.478 0.00 4.14 31.42 3.51
8593 8669 3.057386 TGCATGAAAATTGATGACAGCGT 60.057 39.130 0.00 0.00 0.00 5.07
8601 8677 2.568696 TGATGACAGCGTCTTAGAGC 57.431 50.000 9.49 0.00 33.15 4.09
8623 8699 8.928448 AGAGCAACCTCTATATGTTTCTTATCA 58.072 33.333 0.00 0.00 46.45 2.15
8672 8749 7.148407 GCATTACTACTTACATCAGTTGCTTGT 60.148 37.037 0.00 0.00 0.00 3.16
8684 8761 4.402155 TCAGTTGCTTGTTGGAAAGAACAT 59.598 37.500 0.00 0.00 35.77 2.71
8716 8793 6.043243 TCCTTTGATTGAAGTCCTTGACTAGT 59.957 38.462 0.00 0.00 42.59 2.57
8762 8839 1.271108 TGCTGACCTGCCAACGAATTA 60.271 47.619 0.00 0.00 0.00 1.40
8770 8847 4.165779 CCTGCCAACGAATTAACATCAAC 58.834 43.478 0.00 0.00 0.00 3.18
8772 8849 3.498777 TGCCAACGAATTAACATCAACGA 59.501 39.130 0.00 0.00 0.00 3.85
8865 8942 7.606858 TTCAGTATCTGCTGATTTTGAAGAG 57.393 36.000 19.33 3.77 43.99 2.85
8908 8985 5.865552 CACCCTTTGCATGAAACTTATGAAG 59.134 40.000 0.00 0.00 0.00 3.02
8910 8987 5.865552 CCCTTTGCATGAAACTTATGAAGTG 59.134 40.000 0.00 0.00 41.91 3.16
8920 8997 5.818678 AACTTATGAAGTGGTACAGGACA 57.181 39.130 0.00 0.00 41.91 4.02
8927 9004 3.194005 AGTGGTACAGGACAGTTGTTG 57.806 47.619 0.00 0.00 41.80 3.33
8935 9012 6.823689 GGTACAGGACAGTTGTTGATCATAAT 59.176 38.462 0.00 0.00 0.00 1.28
9328 9407 5.733676 AGTCCAATTTCAGCAACTTTGTTT 58.266 33.333 0.00 0.00 0.00 2.83
9332 9411 7.064016 GTCCAATTTCAGCAACTTTGTTTTACA 59.936 33.333 0.00 0.00 0.00 2.41
9339 9418 6.090628 TCAGCAACTTTGTTTTACAAAAGCAG 59.909 34.615 17.97 13.37 46.15 4.24
9422 9503 9.598517 AGCTTCTCTTCATTCTTTACATAAGAG 57.401 33.333 0.00 0.00 40.69 2.85
9464 9545 6.857964 CAGTATCAATTCCACTGTTTGACAAC 59.142 38.462 0.00 0.00 35.91 3.32
9499 9580 3.838317 GCCCCTTTCCTACCAATCTTTTT 59.162 43.478 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.148348 CGTTGTTTTAGTCTTCGTCAGAGG 59.852 45.833 0.00 0.00 29.34 3.69
3 4 4.373717 CGTCGTTGTTTTAGTCTTCGTCAG 60.374 45.833 0.00 0.00 0.00 3.51
5 6 3.725740 TCGTCGTTGTTTTAGTCTTCGTC 59.274 43.478 0.00 0.00 0.00 4.20
35 36 3.378112 TCATCATCCAAAAAGACGATGGC 59.622 43.478 0.00 0.00 35.22 4.40
44 45 6.071952 GGCTACTTGTCTTCATCATCCAAAAA 60.072 38.462 0.00 0.00 0.00 1.94
95 96 1.667236 CGACATTAGATTGCTGGCCA 58.333 50.000 4.71 4.71 0.00 5.36
100 101 2.717639 AAGGGCGACATTAGATTGCT 57.282 45.000 0.00 0.00 28.79 3.91
227 236 3.250040 GCGGAGTACAACACAACAGATTT 59.750 43.478 0.00 0.00 0.00 2.17
267 276 0.734889 GGCCCACGAATCAATGACAG 59.265 55.000 0.00 0.00 0.00 3.51
273 283 0.965439 CAAAAGGGCCCACGAATCAA 59.035 50.000 27.56 0.00 0.00 2.57
307 317 5.245751 GTGATGATGGAGAGATAGGACACAT 59.754 44.000 0.00 0.00 0.00 3.21
308 318 4.586421 GTGATGATGGAGAGATAGGACACA 59.414 45.833 0.00 0.00 0.00 3.72
310 320 4.831710 CAGTGATGATGGAGAGATAGGACA 59.168 45.833 0.00 0.00 0.00 4.02
325 335 1.225426 GCCCATGAGCCAGTGATGA 59.775 57.895 0.00 0.00 0.00 2.92
338 348 1.538666 GCCATACAGAAGGGCCCAT 59.461 57.895 27.56 13.79 41.90 4.00
353 363 6.152661 CCTTTTTGTCCTGATATTTACTGCCA 59.847 38.462 0.00 0.00 0.00 4.92
391 401 7.324322 CGTTGAGTACGTCTGTTTGTTTATA 57.676 36.000 0.00 0.00 45.14 0.98
407 417 2.070783 GCGAACCATTTCCGTTGAGTA 58.929 47.619 0.00 0.00 0.00 2.59
413 423 1.068610 CAACATGCGAACCATTTCCGT 60.069 47.619 0.00 0.00 29.71 4.69
415 425 1.349234 GCAACATGCGAACCATTTCC 58.651 50.000 0.00 0.00 31.71 3.13
482 498 5.048083 GTGGCTGATTTATGTGGACAAAAGA 60.048 40.000 0.00 0.00 0.00 2.52
488 504 2.684881 CCAGTGGCTGATTTATGTGGAC 59.315 50.000 0.00 0.00 32.44 4.02
594 611 3.396560 CATACACTCATGCGTGGATCAT 58.603 45.455 19.38 5.03 36.32 2.45
598 615 3.064079 GCATACACTCATGCGTGGA 57.936 52.632 19.38 12.11 41.73 4.02
621 638 2.839975 TCAATGCAGTTGACCGTTACA 58.160 42.857 7.27 0.00 41.79 2.41
691 708 1.378762 CCTCGCTTTTCCCCTCCAA 59.621 57.895 0.00 0.00 0.00 3.53
705 722 0.796312 CATCCAACAAACGTCCCTCG 59.204 55.000 0.00 0.00 46.00 4.63
737 754 2.162208 CGGGTTGCTTAGTACGTACTCA 59.838 50.000 30.53 19.55 37.73 3.41
744 761 0.461516 GCCCTCGGGTTGCTTAGTAC 60.462 60.000 3.54 0.00 37.65 2.73
745 762 0.905809 TGCCCTCGGGTTGCTTAGTA 60.906 55.000 3.54 0.00 37.65 1.82
747 764 1.745489 GTGCCCTCGGGTTGCTTAG 60.745 63.158 3.54 0.00 37.65 2.18
748 765 2.349755 GTGCCCTCGGGTTGCTTA 59.650 61.111 3.54 0.00 37.65 3.09
751 768 4.947147 TGTGTGCCCTCGGGTTGC 62.947 66.667 3.54 0.00 37.65 4.17
752 769 1.178534 ATTTGTGTGCCCTCGGGTTG 61.179 55.000 3.54 0.00 37.65 3.77
753 770 0.402504 TATTTGTGTGCCCTCGGGTT 59.597 50.000 3.54 0.00 37.65 4.11
754 771 0.035439 CTATTTGTGTGCCCTCGGGT 60.035 55.000 3.54 0.00 37.65 5.28
755 772 0.251916 TCTATTTGTGTGCCCTCGGG 59.748 55.000 0.00 0.00 38.57 5.14
776 793 0.317160 CGCCGATAGTGATTAGGGCA 59.683 55.000 0.50 0.00 40.52 5.36
908 925 1.741770 CTGGACCGGGCTTTTCGAG 60.742 63.158 7.57 0.00 0.00 4.04
1026 1044 1.538135 GTGGGGTGGGGTAGTGAGT 60.538 63.158 0.00 0.00 0.00 3.41
1062 1080 2.647949 TTGGGGTTGGGTTTGGGGT 61.648 57.895 0.00 0.00 0.00 4.95
1065 1083 2.144078 GGGTTGGGGTTGGGTTTGG 61.144 63.158 0.00 0.00 0.00 3.28
1066 1084 2.503382 CGGGTTGGGGTTGGGTTTG 61.503 63.158 0.00 0.00 0.00 2.93
1067 1085 2.123208 CGGGTTGGGGTTGGGTTT 60.123 61.111 0.00 0.00 0.00 3.27
1068 1086 4.227583 CCGGGTTGGGGTTGGGTT 62.228 66.667 0.00 0.00 0.00 4.11
1094 1112 1.144936 GAGAAGATGGAGCGTGGGG 59.855 63.158 0.00 0.00 0.00 4.96
1213 1235 3.816524 AGCTCCCTCTTCGTCGCG 61.817 66.667 0.00 0.00 0.00 5.87
1220 1242 2.685380 CGGGTCCAGCTCCCTCTT 60.685 66.667 7.35 0.00 42.56 2.85
1221 1243 4.787280 CCGGGTCCAGCTCCCTCT 62.787 72.222 7.35 0.00 42.56 3.69
1257 1279 4.444838 CCGTCCCGTGATTCCGCA 62.445 66.667 0.00 0.00 0.00 5.69
1378 1400 0.443869 CATCCAGCGAACCAAGAACG 59.556 55.000 0.00 0.00 0.00 3.95
1579 1601 5.377358 GCACAGTATAATTTGCATAGCGAG 58.623 41.667 6.45 0.00 34.97 5.03
1912 1934 0.508641 CGACTGTTCTTCGCAACCAG 59.491 55.000 0.00 0.00 0.00 4.00
1970 1992 1.098050 CCAAGCCGAAATTCCTCCTG 58.902 55.000 0.00 0.00 0.00 3.86
1981 2003 0.677731 CATTTCTCAGCCCAAGCCGA 60.678 55.000 0.00 0.00 41.25 5.54
2109 2131 9.793259 CCTAAAATGTATGGGTATAACATCACT 57.207 33.333 0.00 0.00 0.00 3.41
2124 2146 4.196971 GGCTTCCACGACCTAAAATGTAT 58.803 43.478 0.00 0.00 0.00 2.29
2297 2319 5.933617 ACTTATGGCATGAGCTCTCAATAA 58.066 37.500 18.20 11.74 43.58 1.40
2420 2442 8.207545 AGATAAAATTGTTACCTTTTTGCCACA 58.792 29.630 3.62 0.00 0.00 4.17
2687 2710 5.474876 GGATTCCAGACAACAATCAGTTTCT 59.525 40.000 0.00 0.00 38.74 2.52
2688 2711 5.241506 TGGATTCCAGACAACAATCAGTTTC 59.758 40.000 0.00 0.00 38.74 2.78
2689 2712 5.010012 GTGGATTCCAGACAACAATCAGTTT 59.990 40.000 5.39 0.00 33.84 2.66
2811 2837 5.416952 ACAAGCATGTTAAGGGATTCTGAAG 59.583 40.000 0.00 0.00 35.91 3.02
2842 2868 7.455008 TCTTCTGGTTTCTTATCCAAGAGTAGT 59.545 37.037 0.00 0.00 41.75 2.73
2870 2896 4.386424 GGAAAGTAGGCTAACCAATGGGAT 60.386 45.833 3.55 0.00 39.06 3.85
2896 2922 6.257411 GCTGCATGACGATCAGCTATATATTT 59.743 38.462 13.16 0.00 46.93 1.40
2902 2928 1.793258 GCTGCATGACGATCAGCTAT 58.207 50.000 13.16 0.00 46.93 2.97
2939 2965 5.353678 TGGCAAAGACTTTGGTTTCATTTTG 59.646 36.000 25.44 1.00 40.94 2.44
3030 3056 1.467342 GAACGGAACATACCAAGTGCC 59.533 52.381 0.00 0.00 0.00 5.01
3089 3115 5.001232 GTGATACAACTAAGAAAGTGCCCA 58.999 41.667 0.00 0.00 38.88 5.36
3204 3234 2.500098 CTGGTCTGGAAAATAGGTCGGA 59.500 50.000 0.00 0.00 0.00 4.55
3477 3507 3.823304 GTCACCTTCAAGAGATTTGGCTT 59.177 43.478 0.00 0.00 0.00 4.35
3520 3550 2.540361 GCTGCACAATCATCATTCCGAC 60.540 50.000 0.00 0.00 0.00 4.79
3538 3568 1.605710 CTGGTTGGAACTGTTCAGCTG 59.394 52.381 21.01 7.63 0.00 4.24
3579 3609 5.217978 ACCTGGATACGTTTCTGTTGTAA 57.782 39.130 0.00 0.00 42.51 2.41
3631 3661 2.544267 CGAAATGCGGATTAGGGAAGAC 59.456 50.000 1.39 0.00 36.03 3.01
3651 3681 7.913297 ACAAATAACGGAAAATATGATCAACCG 59.087 33.333 0.00 10.73 43.61 4.44
3869 3899 7.395617 TGCCTACCTGTTATAATGTGTTGTAA 58.604 34.615 0.00 0.00 0.00 2.41
3878 3908 5.365605 TGTACAGCTGCCTACCTGTTATAAT 59.634 40.000 15.27 0.00 42.02 1.28
4046 4076 8.877864 ATATTTCCTGGTGATAAAGTCAAACA 57.122 30.769 0.00 0.00 38.90 2.83
4078 4108 2.674796 AAGGCCTCACTCGACAATAC 57.325 50.000 5.23 0.00 0.00 1.89
4172 4202 6.108015 TGCTTCCATCTTTTCCATATTTTGC 58.892 36.000 0.00 0.00 0.00 3.68
4286 4316 5.765072 GAACTGAAGTTCGGTACTCAATC 57.235 43.478 17.65 6.95 43.97 2.67
4308 4338 9.883142 AGACTTCCTCTGTATTCATAAAAAGAG 57.117 33.333 0.00 0.00 0.00 2.85
4318 4348 5.721232 TCCGAAAAGACTTCCTCTGTATTC 58.279 41.667 0.00 0.00 0.00 1.75
4322 4352 5.665459 CATATCCGAAAAGACTTCCTCTGT 58.335 41.667 0.00 0.00 0.00 3.41
4405 4435 2.350863 AGGTCTTCCCTGATCCAGTT 57.649 50.000 0.00 0.00 44.08 3.16
4490 4520 3.635373 CACAGCATCATAAGAATGGCCTT 59.365 43.478 3.32 0.00 33.61 4.35
4588 4618 1.494721 TGTCCCCTTTCTCTGTGCTTT 59.505 47.619 0.00 0.00 0.00 3.51
4625 4655 5.981174 TGTAGATCTCAATCATCTGCACAA 58.019 37.500 0.00 0.00 37.87 3.33
4717 4747 8.103305 AGCTAAGATCCAAGATTAACAACAGAA 58.897 33.333 0.00 0.00 0.00 3.02
4727 4757 8.038862 TCCTCAAATAGCTAAGATCCAAGATT 57.961 34.615 0.00 0.00 0.00 2.40
4953 4984 8.475331 AAACTCAGTATAAACAAGGTATGTCG 57.525 34.615 0.00 0.00 42.99 4.35
5330 5385 9.866655 ACACAATGTTTATCCCATAGATTGTAT 57.133 29.630 0.00 0.00 36.33 2.29
5480 5548 3.365969 CCTTCTTTATTCGCTTTTGCCGT 60.366 43.478 0.00 0.00 43.93 5.68
5482 5550 3.920412 CACCTTCTTTATTCGCTTTTGCC 59.080 43.478 0.00 0.00 43.93 4.52
5526 5594 8.699283 AAATCAAGAATAAGTACGTACCTGTC 57.301 34.615 21.80 13.72 0.00 3.51
5590 5658 8.579850 AAGTTTCTTATACATCTCAATGGCAA 57.420 30.769 0.00 0.00 37.19 4.52
5655 5723 2.569404 CTCCTTCCTTCTTAGCCAGTGT 59.431 50.000 0.00 0.00 0.00 3.55
5808 5876 3.641046 AGAGAAAGAGCTGAGATGGCTA 58.359 45.455 0.00 0.00 40.40 3.93
5928 5998 3.248024 TCACTGTCCTCAAGTTATGGGT 58.752 45.455 0.00 0.00 0.00 4.51
6346 6417 2.567615 GGTGTGAGTGGTGAGATTAGGT 59.432 50.000 0.00 0.00 0.00 3.08
6414 6485 3.113043 GGTACTGATTCAACCCTACCCT 58.887 50.000 0.00 0.00 0.00 4.34
6427 6498 0.033011 ACTCCTCGCCTGGTACTGAT 60.033 55.000 0.00 0.00 0.00 2.90
6437 6508 2.280823 AATTCGTCCGACTCCTCGCC 62.281 60.000 0.00 0.00 38.70 5.54
6440 6511 3.802685 CCATTAAATTCGTCCGACTCCTC 59.197 47.826 0.00 0.00 0.00 3.71
6448 6519 5.883503 TGGTAACACCATTAAATTCGTCC 57.116 39.130 0.00 0.00 44.79 4.79
6804 6875 4.277515 TGGAGTTCTTCTTCCATCTGTG 57.722 45.455 0.00 0.00 0.00 3.66
6812 6883 5.237561 GTCTTTCCACTTGGAGTTCTTCTTC 59.762 44.000 0.00 0.00 46.36 2.87
6813 6884 5.104318 AGTCTTTCCACTTGGAGTTCTTCTT 60.104 40.000 0.00 0.00 46.36 2.52
6814 6885 4.410555 AGTCTTTCCACTTGGAGTTCTTCT 59.589 41.667 0.00 0.00 46.36 2.85
6895 6969 1.290639 CAGCACAATGCCATGCACA 59.709 52.632 0.00 0.00 46.52 4.57
6908 6982 0.599558 TTGCTCTGATTTGCCAGCAC 59.400 50.000 0.00 0.00 41.56 4.40
6948 7022 5.762179 TCCAAGGAGCTTCAAGAAGATAA 57.238 39.130 13.70 0.00 40.79 1.75
7104 7178 7.331193 GGTACAACAGTAATTTCTAGTGTGGAG 59.669 40.741 8.99 0.00 32.01 3.86
7301 7376 5.012046 TCACTCTTGCTCCTGAAGTTCATTA 59.988 40.000 5.91 0.00 0.00 1.90
7338 7413 4.593206 ACAGGAGTCAGACCATGTAAAAGA 59.407 41.667 7.35 0.00 0.00 2.52
7339 7414 4.899502 ACAGGAGTCAGACCATGTAAAAG 58.100 43.478 7.35 0.00 0.00 2.27
7635 7711 4.813161 CCTGCTGAATAGTGTGGATAACAG 59.187 45.833 0.00 0.00 40.26 3.16
7717 7793 1.927569 TAGGGCGACTCTCCAGAGCT 61.928 60.000 3.33 0.00 45.79 4.09
7777 7853 3.236618 GACACCTTTGTCGCCACGC 62.237 63.158 0.00 0.00 42.86 5.34
7917 7993 4.085733 ACTATGCAATGGCCAAACACTAA 58.914 39.130 10.96 0.00 40.13 2.24
7992 8068 3.228188 TGGTGACTTGCTTTGGATCTT 57.772 42.857 0.00 0.00 0.00 2.40
8044 8120 4.627467 AGCAGCAGTAATTACTCTGAAACG 59.373 41.667 29.52 15.95 35.44 3.60
8319 8395 2.189594 TTTGGTCAGCATGGACAGAG 57.810 50.000 0.00 0.00 39.59 3.35
8494 8570 5.047802 AGCCATCAAATAGTCACCAACAAAG 60.048 40.000 0.00 0.00 0.00 2.77
8498 8574 5.414454 TGTTAGCCATCAAATAGTCACCAAC 59.586 40.000 0.00 0.00 0.00 3.77
8500 8576 5.172687 TGTTAGCCATCAAATAGTCACCA 57.827 39.130 0.00 0.00 0.00 4.17
8590 8666 3.719173 ATAGAGGTTGCTCTAAGACGC 57.281 47.619 0.00 0.00 39.13 5.19
8593 8669 8.540507 AGAAACATATAGAGGTTGCTCTAAGA 57.459 34.615 0.00 0.00 28.60 2.10
8639 8716 7.278868 ACTGATGTAAGTAGTAATGCTTCAAGC 59.721 37.037 1.04 1.04 42.82 4.01
8640 8717 8.709386 ACTGATGTAAGTAGTAATGCTTCAAG 57.291 34.615 0.00 0.00 0.00 3.02
8652 8729 5.700832 TCCAACAAGCAACTGATGTAAGTAG 59.299 40.000 0.00 0.00 0.00 2.57
8672 8749 8.163408 TCAAAGGAGAGATTATGTTCTTTCCAA 58.837 33.333 14.77 0.88 45.24 3.53
8684 8761 7.502060 AGGACTTCAATCAAAGGAGAGATTA 57.498 36.000 0.00 0.00 33.41 1.75
8770 8847 9.173939 GCAATAATTCCTTAAGAACATCAATCG 57.826 33.333 3.36 0.00 37.29 3.34
8777 8854 9.515226 ACTAACTGCAATAATTCCTTAAGAACA 57.485 29.630 3.36 0.00 37.29 3.18
8787 8864 8.462016 AGTTCCATTCACTAACTGCAATAATTC 58.538 33.333 0.00 0.00 32.38 2.17
8795 8872 6.341316 TCTATGAGTTCCATTCACTAACTGC 58.659 40.000 0.00 0.00 36.71 4.40
8797 8874 7.907389 TGTTCTATGAGTTCCATTCACTAACT 58.093 34.615 0.00 0.00 36.71 2.24
8865 8942 2.162408 GTGCTTCTGGGTTGAGTAATGC 59.838 50.000 0.00 0.00 0.00 3.56
8908 8985 3.188159 TCAACAACTGTCCTGTACCAC 57.812 47.619 0.00 0.00 0.00 4.16
8910 8987 4.002906 TGATCAACAACTGTCCTGTACC 57.997 45.455 0.00 0.00 0.00 3.34
9328 9407 5.389859 AATACTGCATGCTGCTTTTGTAA 57.610 34.783 22.92 0.00 45.31 2.41
9356 9435 9.771915 GCTCTATGTTTATATCGGAGTACTAAC 57.228 37.037 0.00 0.00 0.00 2.34
9363 9442 7.760340 GGTAAAGGCTCTATGTTTATATCGGAG 59.240 40.741 0.00 0.00 0.00 4.63
9364 9443 7.453752 AGGTAAAGGCTCTATGTTTATATCGGA 59.546 37.037 0.00 0.00 0.00 4.55
9365 9444 7.612677 AGGTAAAGGCTCTATGTTTATATCGG 58.387 38.462 0.00 0.00 0.00 4.18
9366 9445 9.141400 GAAGGTAAAGGCTCTATGTTTATATCG 57.859 37.037 0.00 0.00 0.00 2.92
9367 9446 9.998106 TGAAGGTAAAGGCTCTATGTTTATATC 57.002 33.333 0.00 0.00 0.00 1.63
9422 9503 7.827819 TGATACTGTGCAGAAGTTATTACAC 57.172 36.000 7.26 0.00 0.00 2.90
9457 9538 0.180642 TTACCACCAGGCGTTGTCAA 59.819 50.000 0.00 0.00 39.06 3.18
9464 9545 4.796495 GGGGCTTACCACCAGGCG 62.796 72.222 0.00 0.00 42.91 5.52


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

AutoCloner maintained by Alex Coulton.