Multiple sequence alignment - TraesCS5D01G381800

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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 TraesCS5D01G381800 chr5D 100.000 4421 0 0 1 4421 451904431 451908851 0.000000e+00 8165.0
1 TraesCS5D01G381800 chr5D 97.436 39 1 0 4283 4321 451908672 451908710 2.850000e-07 67.6
2 TraesCS5D01G381800 chr5D 97.436 39 1 0 4242 4280 451908713 451908751 2.850000e-07 67.6
3 TraesCS5D01G381800 chr5B 93.476 2943 133 21 846 3760 551675295 551678206 0.000000e+00 4316.0
4 TraesCS5D01G381800 chr5B 85.363 813 58 26 62 829 551674448 551675244 0.000000e+00 785.0
5 TraesCS5D01G381800 chr5B 91.703 229 18 1 4036 4264 551678349 551678576 2.570000e-82 316.0
6 TraesCS5D01G381800 chr5B 87.117 163 18 1 2332 2494 60810003 60810162 9.770000e-42 182.0
7 TraesCS5D01G381800 chr5B 90.426 94 7 1 3837 3928 551678255 551678348 6.000000e-24 122.0
8 TraesCS5D01G381800 chr5B 88.298 94 11 0 4328 4421 551678614 551678707 3.610000e-21 113.0
9 TraesCS5D01G381800 chr5A 91.137 2956 185 29 836 3771 570774215 570777113 0.000000e+00 3936.0
10 TraesCS5D01G381800 chr5A 83.774 530 48 19 3773 4280 570777196 570777709 6.700000e-128 468.0
11 TraesCS5D01G381800 chr5A 78.484 488 50 20 2332 2807 45927944 45927500 7.290000e-68 268.0
12 TraesCS5D01G381800 chr5A 81.373 204 31 6 245 445 640684124 640683925 4.580000e-35 159.0
13 TraesCS5D01G381800 chr1A 81.118 519 50 15 2332 2825 82126721 82126226 5.400000e-99 372.0
14 TraesCS5D01G381800 chr1A 89.130 46 5 0 2538 2583 82126413 82126368 1.720000e-04 58.4
15 TraesCS5D01G381800 chr3B 82.921 404 44 7 2332 2732 758404327 758403946 1.520000e-89 340.0
16 TraesCS5D01G381800 chr3A 82.963 405 42 11 2332 2732 53327630 53327249 1.520000e-89 340.0
17 TraesCS5D01G381800 chr7D 81.197 234 25 4 4068 4283 362375945 362375713 2.110000e-38 171.0


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 TraesCS5D01G381800 chr5D 451904431 451908851 4420 False 2766.733333 8165 98.290667 1 4421 3 chr5D.!!$F1 4420
1 TraesCS5D01G381800 chr5B 551674448 551678707 4259 False 1130.400000 4316 89.853200 62 4421 5 chr5B.!!$F2 4359
2 TraesCS5D01G381800 chr5A 570774215 570777709 3494 False 2202.000000 3936 87.455500 836 4280 2 chr5A.!!$F1 3444

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
25 26 0.035152 TATGTGTGCTGCTTGAGGGG 60.035 55.000 0.00 0.00 0.00 4.79 F
537 551 0.037232 GGCTGGTGGTGTCTGACTAC 60.037 60.000 9.51 5.71 35.33 2.73 F
839 883 0.037975 AAAGATGGCAAAAGGCTGCG 60.038 50.000 0.00 0.00 43.60 5.18 F
930 1008 0.461548 CAGACGGCATCTAGGCAGAA 59.538 55.000 0.00 0.00 44.47 3.02 F
1110 1191 0.704664 GTTCCCTTCCCACCCTCAAT 59.295 55.000 0.00 0.00 0.00 2.57 F
1174 1258 0.974010 AGTGGGATCCGTTCGGCTTA 60.974 55.000 5.45 0.00 0.00 3.09 F
1181 1265 1.022451 TCCGTTCGGCTTAATGTGCC 61.022 55.000 6.35 0.00 46.42 5.01 F
1205 1291 2.038426 TGAGATGAATTGACCCGTGTGT 59.962 45.455 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1336 1422 1.130561 GCACGTAGGGCAAAGATTGAC 59.869 52.381 0.00 0.0 38.21 3.18 R
1962 2052 1.340991 ACAAATTATGCGCCCAGTCCT 60.341 47.619 4.18 0.0 0.00 3.85 R
2343 2446 1.792949 CGTCCAGAGTTTGTTCTTCGG 59.207 52.381 0.00 0.0 0.00 4.30 R
2920 3030 0.327924 CAACCACAGGGCATGGAGTA 59.672 55.000 3.46 0.0 39.87 2.59 R
3086 3196 1.069022 ACACTTGCAGCATTAACAGCG 60.069 47.619 0.00 0.0 37.01 5.18 R
3115 3225 2.806244 GTCTGCGCTTCTTAAGGTGAAA 59.194 45.455 9.73 0.0 0.00 2.69 R
3299 3409 2.668457 GCACGACAGAAACATAGACCTG 59.332 50.000 0.00 0.0 0.00 4.00 R
3475 3585 1.002888 ACTCGACCTCCACTCTACGAA 59.997 52.381 0.00 0.0 0.00 3.85 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
18 19 3.455328 CAGAGCTATGTGTGCTGCT 57.545 52.632 0.00 0.00 41.30 4.24
19 20 1.735386 CAGAGCTATGTGTGCTGCTT 58.265 50.000 0.00 0.00 41.30 3.91
20 21 1.397343 CAGAGCTATGTGTGCTGCTTG 59.603 52.381 0.00 0.00 41.30 4.01
21 22 1.277273 AGAGCTATGTGTGCTGCTTGA 59.723 47.619 0.00 0.00 41.30 3.02
22 23 1.664659 GAGCTATGTGTGCTGCTTGAG 59.335 52.381 0.00 0.00 41.30 3.02
23 24 0.731417 GCTATGTGTGCTGCTTGAGG 59.269 55.000 0.00 0.00 0.00 3.86
24 25 1.376543 CTATGTGTGCTGCTTGAGGG 58.623 55.000 0.00 0.00 0.00 4.30
25 26 0.035152 TATGTGTGCTGCTTGAGGGG 60.035 55.000 0.00 0.00 0.00 4.79
26 27 2.072874 ATGTGTGCTGCTTGAGGGGT 62.073 55.000 0.00 0.00 0.00 4.95
27 28 2.113774 TGTGCTGCTTGAGGGGTG 59.886 61.111 0.00 0.00 0.00 4.61
28 29 2.674380 GTGCTGCTTGAGGGGTGG 60.674 66.667 0.00 0.00 0.00 4.61
29 30 3.970410 TGCTGCTTGAGGGGTGGG 61.970 66.667 0.00 0.00 0.00 4.61
30 31 4.748144 GCTGCTTGAGGGGTGGGG 62.748 72.222 0.00 0.00 0.00 4.96
31 32 4.052518 CTGCTTGAGGGGTGGGGG 62.053 72.222 0.00 0.00 0.00 5.40
32 33 4.938756 TGCTTGAGGGGTGGGGGT 62.939 66.667 0.00 0.00 0.00 4.95
33 34 4.366684 GCTTGAGGGGTGGGGGTG 62.367 72.222 0.00 0.00 0.00 4.61
34 35 3.661648 CTTGAGGGGTGGGGGTGG 61.662 72.222 0.00 0.00 0.00 4.61
108 109 8.749696 AGGAAGGCCTAGATTAGATTATTCTT 57.250 34.615 5.16 0.00 44.74 2.52
109 110 9.176751 AGGAAGGCCTAGATTAGATTATTCTTT 57.823 33.333 5.16 0.00 44.74 2.52
112 113 9.952030 AAGGCCTAGATTAGATTATTCTTTAGC 57.048 33.333 5.16 0.00 33.17 3.09
113 114 9.105844 AGGCCTAGATTAGATTATTCTTTAGCA 57.894 33.333 1.29 0.00 33.17 3.49
132 137 1.892474 CACCCCAAACACCGATGATTT 59.108 47.619 0.00 0.00 0.00 2.17
139 144 1.821216 ACACCGATGATTTGTGTCCC 58.179 50.000 0.00 0.00 38.83 4.46
140 145 1.094785 CACCGATGATTTGTGTCCCC 58.905 55.000 0.00 0.00 0.00 4.81
160 165 2.603008 CCCCTCGCCCCAAATGAT 59.397 61.111 0.00 0.00 0.00 2.45
167 172 2.099405 TCGCCCCAAATGATTTTCCTC 58.901 47.619 0.00 0.00 0.00 3.71
170 175 3.316308 CGCCCCAAATGATTTTCCTCTAG 59.684 47.826 0.00 0.00 0.00 2.43
171 176 3.068732 GCCCCAAATGATTTTCCTCTAGC 59.931 47.826 0.00 0.00 0.00 3.42
172 177 4.540715 CCCCAAATGATTTTCCTCTAGCT 58.459 43.478 0.00 0.00 0.00 3.32
173 178 4.582240 CCCCAAATGATTTTCCTCTAGCTC 59.418 45.833 0.00 0.00 0.00 4.09
174 179 4.582240 CCCAAATGATTTTCCTCTAGCTCC 59.418 45.833 0.00 0.00 0.00 4.70
175 180 5.195940 CCAAATGATTTTCCTCTAGCTCCA 58.804 41.667 0.00 0.00 0.00 3.86
176 181 5.067023 CCAAATGATTTTCCTCTAGCTCCAC 59.933 44.000 0.00 0.00 0.00 4.02
177 182 5.441718 AATGATTTTCCTCTAGCTCCACA 57.558 39.130 0.00 0.00 0.00 4.17
178 183 4.908601 TGATTTTCCTCTAGCTCCACAA 57.091 40.909 0.00 0.00 0.00 3.33
179 184 4.579869 TGATTTTCCTCTAGCTCCACAAC 58.420 43.478 0.00 0.00 0.00 3.32
180 185 2.743636 TTTCCTCTAGCTCCACAACG 57.256 50.000 0.00 0.00 0.00 4.10
215 220 2.835156 TGGATAACATGGTCCGACTCAA 59.165 45.455 0.00 0.00 37.32 3.02
276 281 4.523943 ACAACAGCATCTTTCCAAATAGCA 59.476 37.500 0.00 0.00 0.00 3.49
279 284 4.951715 ACAGCATCTTTCCAAATAGCATCA 59.048 37.500 0.00 0.00 0.00 3.07
284 289 7.889073 AGCATCTTTCCAAATAGCATCATCTAT 59.111 33.333 0.00 0.00 0.00 1.98
300 305 9.289782 GCATCATCTATGGTAGGAATTTTTAGT 57.710 33.333 0.00 0.00 35.99 2.24
470 482 3.732048 TTGAGGGGAACAATCCTAACC 57.268 47.619 0.00 0.00 45.77 2.85
492 504 7.458409 ACCAATGCTTATGCTATCATAAAGG 57.542 36.000 1.96 1.91 42.66 3.11
499 513 7.068593 TGCTTATGCTATCATAAAGGCTGTTTT 59.931 33.333 10.22 0.00 42.66 2.43
532 546 1.134580 CATAGAGGCTGGTGGTGTCTG 60.135 57.143 0.00 0.00 0.00 3.51
533 547 0.114364 TAGAGGCTGGTGGTGTCTGA 59.886 55.000 0.00 0.00 0.00 3.27
534 548 1.004440 GAGGCTGGTGGTGTCTGAC 60.004 63.158 0.00 0.00 0.00 3.51
536 550 0.178932 AGGCTGGTGGTGTCTGACTA 60.179 55.000 9.51 0.00 0.00 2.59
537 551 0.037232 GGCTGGTGGTGTCTGACTAC 60.037 60.000 9.51 5.71 35.33 2.73
539 553 1.067495 GCTGGTGGTGTCTGACTACTC 60.067 57.143 9.51 3.11 36.33 2.59
540 554 1.546476 CTGGTGGTGTCTGACTACTCC 59.454 57.143 9.51 11.66 36.33 3.85
541 555 0.896226 GGTGGTGTCTGACTACTCCC 59.104 60.000 9.51 6.33 36.33 4.30
542 556 1.550409 GGTGGTGTCTGACTACTCCCT 60.550 57.143 9.51 0.00 36.33 4.20
543 557 2.249139 GTGGTGTCTGACTACTCCCTT 58.751 52.381 9.51 0.00 33.32 3.95
545 559 1.550976 GGTGTCTGACTACTCCCTTGG 59.449 57.143 9.51 0.00 0.00 3.61
546 560 1.066787 GTGTCTGACTACTCCCTTGGC 60.067 57.143 9.51 0.00 0.00 4.52
547 561 0.537653 GTCTGACTACTCCCTTGGCC 59.462 60.000 0.00 0.00 0.00 5.36
548 562 0.617820 TCTGACTACTCCCTTGGCCC 60.618 60.000 0.00 0.00 0.00 5.80
549 563 0.909610 CTGACTACTCCCTTGGCCCA 60.910 60.000 0.00 0.00 0.00 5.36
550 564 0.909610 TGACTACTCCCTTGGCCCAG 60.910 60.000 0.00 0.00 0.00 4.45
554 568 0.696501 TACTCCCTTGGCCCAGTTTC 59.303 55.000 0.00 0.00 0.00 2.78
590 623 1.885887 CAAAAGAACCATCGGGCTTGA 59.114 47.619 0.00 0.00 37.90 3.02
642 682 1.380403 CGTCACCAAGGCACCAACAA 61.380 55.000 0.00 0.00 0.00 2.83
801 845 4.410400 CCGCAGGTCAACCTCCCC 62.410 72.222 0.00 0.00 46.65 4.81
818 862 2.443016 CCCCTCCCTCGGTCTGAG 60.443 72.222 1.20 1.20 44.83 3.35
829 873 1.623311 TCGGTCTGAGAAAAGATGGCA 59.377 47.619 0.00 0.00 0.00 4.92
832 876 3.253188 CGGTCTGAGAAAAGATGGCAAAA 59.747 43.478 0.00 0.00 0.00 2.44
835 879 3.256631 TCTGAGAAAAGATGGCAAAAGGC 59.743 43.478 0.00 0.00 43.74 4.35
836 880 3.233507 TGAGAAAAGATGGCAAAAGGCT 58.766 40.909 0.00 0.00 44.01 4.58
838 882 2.071540 GAAAAGATGGCAAAAGGCTGC 58.928 47.619 0.00 0.00 44.01 5.25
839 883 0.037975 AAAGATGGCAAAAGGCTGCG 60.038 50.000 0.00 0.00 43.60 5.18
840 884 1.181098 AAGATGGCAAAAGGCTGCGT 61.181 50.000 0.00 0.00 43.60 5.24
886 964 0.771755 CCCATCCCTAAACCCTAGCC 59.228 60.000 0.00 0.00 0.00 3.93
930 1008 0.461548 CAGACGGCATCTAGGCAGAA 59.538 55.000 0.00 0.00 44.47 3.02
1101 1182 1.002502 CGAGGTTGGTTCCCTTCCC 60.003 63.158 0.00 0.00 30.60 3.97
1110 1191 0.704664 GTTCCCTTCCCACCCTCAAT 59.295 55.000 0.00 0.00 0.00 2.57
1170 1254 1.153628 GTGAGTGGGATCCGTTCGG 60.154 63.158 5.45 4.74 0.00 4.30
1174 1258 0.974010 AGTGGGATCCGTTCGGCTTA 60.974 55.000 5.45 0.00 0.00 3.09
1181 1265 1.022451 TCCGTTCGGCTTAATGTGCC 61.022 55.000 6.35 0.00 46.42 5.01
1198 1282 2.424956 GTGCCCTTGAGATGAATTGACC 59.575 50.000 0.00 0.00 0.00 4.02
1204 1290 2.698803 TGAGATGAATTGACCCGTGTG 58.301 47.619 0.00 0.00 0.00 3.82
1205 1291 2.038426 TGAGATGAATTGACCCGTGTGT 59.962 45.455 0.00 0.00 0.00 3.72
1298 1384 5.124457 ACCAAATGTTCATCTATGTGAGTGC 59.876 40.000 0.00 0.00 0.00 4.40
1308 1394 5.016051 TCTATGTGAGTGCTCCAATCTTC 57.984 43.478 0.00 0.00 29.32 2.87
1321 1407 2.490718 CCAATCTTCCCCCAGTTCACAA 60.491 50.000 0.00 0.00 0.00 3.33
1325 1411 4.946160 TCTTCCCCCAGTTCACAATTAT 57.054 40.909 0.00 0.00 0.00 1.28
1336 1422 7.703621 CCCAGTTCACAATTATTGCTAAATCTG 59.296 37.037 4.68 6.65 0.00 2.90
1380 1467 3.742882 AGTCCTACGCCGTTAAAAGTTTC 59.257 43.478 0.00 0.00 0.00 2.78
1425 1512 5.698545 ACTGAACACTTAACTTCTGATCTGC 59.301 40.000 0.00 0.00 0.00 4.26
1488 1576 7.148407 GCATGGCAATATAGTGGTACAGTTATC 60.148 40.741 1.88 0.00 40.27 1.75
1573 1661 8.903820 ACTTAATTTTCAGCAGAGTTTAACTGT 58.096 29.630 0.93 0.00 37.64 3.55
1576 1664 6.604735 TTTTCAGCAGAGTTTAACTGTCTC 57.395 37.500 0.93 0.00 37.64 3.36
1582 1670 5.931146 AGCAGAGTTTAACTGTCTCATCAAG 59.069 40.000 0.93 0.00 37.64 3.02
1645 1733 5.891551 TCTAGATATGTGTGGTGCTAACTGA 59.108 40.000 0.00 0.00 0.00 3.41
1773 1862 5.351465 AGTGTCATTTCACTTTACTATGCGG 59.649 40.000 0.00 0.00 44.92 5.69
1774 1863 5.121768 GTGTCATTTCACTTTACTATGCGGT 59.878 40.000 0.00 0.00 35.68 5.68
1775 1864 6.311935 GTGTCATTTCACTTTACTATGCGGTA 59.688 38.462 0.00 0.00 35.68 4.02
1776 1865 7.011109 GTGTCATTTCACTTTACTATGCGGTAT 59.989 37.037 0.00 0.00 35.68 2.73
1777 1866 7.011016 TGTCATTTCACTTTACTATGCGGTATG 59.989 37.037 0.00 0.00 0.00 2.39
1778 1867 5.728351 TTTCACTTTACTATGCGGTATGC 57.272 39.130 0.00 0.00 46.70 3.14
1789 1878 2.044352 GGTATGCGCCTTGGGGTT 60.044 61.111 4.18 0.00 34.45 4.11
1829 1918 5.023533 TGTCTAGGCTATCAAACACCATC 57.976 43.478 0.00 0.00 0.00 3.51
1861 1950 8.523658 GGTTAAAAAGAAGGTGATGAGCTAATT 58.476 33.333 0.00 0.00 0.00 1.40
1962 2052 4.873827 GTGCCTAACCACGATATTTTGAGA 59.126 41.667 0.00 0.00 0.00 3.27
2153 2243 2.482142 GGAGTTCCGAAATCTCTGCGAT 60.482 50.000 8.38 0.00 0.00 4.58
2343 2446 4.154918 CCTTGACAAGGTAGATCAGTTTGC 59.845 45.833 23.92 0.00 43.95 3.68
2416 2520 5.241506 CCTTTGCCTTTGAGATTCTGTTGTA 59.758 40.000 0.00 0.00 0.00 2.41
2583 2689 6.240894 TGTTCTTTCTGGAAATCTAGCACAT 58.759 36.000 0.00 0.00 0.00 3.21
2920 3030 3.644966 TTATCGAAATGGGCCTTCAGT 57.355 42.857 4.53 0.00 0.00 3.41
3115 3225 5.395682 AATGCTGCAAGTGTTACATGATT 57.604 34.783 6.36 0.00 35.30 2.57
3299 3409 4.868067 TGTTCTCACGAAGGTCTTACTTC 58.132 43.478 0.00 0.00 42.63 3.01
3436 3546 4.187694 CCATTGAGCTTCTCTGGTTACTC 58.812 47.826 0.00 0.00 0.00 2.59
3477 3587 2.987046 GCTGTGTAGCTTTGTGTGTTC 58.013 47.619 0.00 0.00 46.57 3.18
3500 3610 1.304547 AGTGGAGGTCGAGTCAGGG 60.305 63.158 0.00 0.00 0.00 4.45
3550 3660 5.028375 GCTAACCAATTGTAGCGTGATTTC 58.972 41.667 11.12 0.00 0.00 2.17
3557 3667 5.607119 ATTGTAGCGTGATTTCGTTTCTT 57.393 34.783 0.00 0.00 0.00 2.52
3558 3668 4.640805 TGTAGCGTGATTTCGTTTCTTC 57.359 40.909 0.00 0.00 0.00 2.87
3567 3677 2.748461 TTCGTTTCTTCGTTGCAAGG 57.252 45.000 12.91 12.91 0.00 3.61
3569 3679 0.028770 CGTTTCTTCGTTGCAAGGCA 59.971 50.000 14.22 2.59 36.47 4.75
3596 3706 4.520078 TGTTGCGTTTCTGTATTTTCGTC 58.480 39.130 0.00 0.00 0.00 4.20
3598 3708 2.155802 GCGTTTCTGTATTTTCGTCGC 58.844 47.619 0.00 0.00 34.93 5.19
3602 3712 3.306917 TTCTGTATTTTCGTCGCCTCA 57.693 42.857 0.00 0.00 0.00 3.86
3663 3773 2.338809 TCCAGATGACACTCCTGGTTT 58.661 47.619 15.77 0.00 45.71 3.27
3684 3794 6.462909 GGTTTCATGTTCTCCCTTGACATTTT 60.463 38.462 0.00 0.00 0.00 1.82
3762 3873 2.099405 CCGTTCCCCAAATTACTGCAT 58.901 47.619 0.00 0.00 0.00 3.96
3771 3882 8.330466 TCCCCAAATTACTGCATTTATATACG 57.670 34.615 0.00 0.00 0.00 3.06
3782 3974 7.604164 ACTGCATTTATATACGAGGAAATCTGG 59.396 37.037 0.00 0.00 0.00 3.86
3797 3989 7.744733 AGGAAATCTGGCAAAAAGGAAATAAA 58.255 30.769 0.00 0.00 0.00 1.40
3819 4011 9.918630 ATAAAGAACACATTTTGAATCTGAAGG 57.081 29.630 0.00 0.00 0.00 3.46
3821 4013 7.352079 AGAACACATTTTGAATCTGAAGGTT 57.648 32.000 0.00 0.00 0.00 3.50
3831 4023 7.928307 TTGAATCTGAAGGTTAAATCTCAGG 57.072 36.000 8.36 0.00 0.00 3.86
3849 4042 2.133641 GGGGGTTGCTGCAACACTT 61.134 57.895 37.50 0.00 45.90 3.16
3850 4043 1.685355 GGGGGTTGCTGCAACACTTT 61.685 55.000 37.50 0.00 45.90 2.66
3874 4083 8.848474 TTATAGCATAGCCATTTTACCTCTTC 57.152 34.615 0.00 0.00 0.00 2.87
3923 4134 2.230992 GGTGCCAATACTGAATGTTGCA 59.769 45.455 0.00 0.00 0.00 4.08
3934 4145 5.776744 ACTGAATGTTGCATCCTTTTCTTC 58.223 37.500 0.00 0.00 0.00 2.87
3936 4147 4.518590 TGAATGTTGCATCCTTTTCTTCGA 59.481 37.500 0.00 0.00 0.00 3.71
3973 4184 8.708378 TGATCTGAATCATGACATAGGTTTAGT 58.292 33.333 0.00 0.00 36.98 2.24
3978 4189 7.611467 TGAATCATGACATAGGTTTAGTTGCTT 59.389 33.333 0.00 0.00 0.00 3.91
3982 4193 5.865085 TGACATAGGTTTAGTTGCTTCTGT 58.135 37.500 0.00 0.00 0.00 3.41
3983 4194 5.700832 TGACATAGGTTTAGTTGCTTCTGTG 59.299 40.000 0.00 0.00 0.00 3.66
3986 4197 6.372659 ACATAGGTTTAGTTGCTTCTGTGATG 59.627 38.462 0.00 0.00 0.00 3.07
3988 4199 5.865085 AGGTTTAGTTGCTTCTGTGATGTA 58.135 37.500 0.00 0.00 0.00 2.29
3996 4207 6.434652 AGTTGCTTCTGTGATGTACTACTAGT 59.565 38.462 0.00 0.00 0.00 2.57
4030 4242 4.660789 AAACATTCAAAGAACAGCTGCT 57.339 36.364 15.27 0.00 0.00 4.24
4034 4246 0.588252 TCAAAGAACAGCTGCTTCGC 59.412 50.000 15.27 0.00 0.00 4.70
4128 4340 1.355720 GGGATCTAATCATGGTGGGGG 59.644 57.143 0.00 0.00 0.00 5.40
4155 4367 0.323178 CTGGAGGGAATGCAGCAAGT 60.323 55.000 0.00 0.00 40.79 3.16
4156 4368 0.322816 TGGAGGGAATGCAGCAAGTC 60.323 55.000 0.00 0.00 0.00 3.01
4196 4408 2.719426 CAAAGCAGCTTCTTTGGAGG 57.281 50.000 25.55 5.42 45.50 4.30
4236 4449 1.966451 GCTGGGGTTCACCAAGACG 60.966 63.158 0.00 0.00 43.78 4.18
4251 4464 0.036010 AGACGGTCATCCAGGCAAAG 60.036 55.000 11.27 0.00 0.00 2.77
4268 4481 3.187432 GCAAAGCCAGACTCTGTTTACTC 59.813 47.826 5.32 0.00 0.00 2.59
4273 4486 3.583806 CCAGACTCTGTTTACTCTGCAG 58.416 50.000 7.63 7.63 30.60 4.41
4274 4487 3.006323 CCAGACTCTGTTTACTCTGCAGT 59.994 47.826 14.67 0.00 36.55 4.40
4277 4490 5.861251 CAGACTCTGTTTACTCTGCAGTAAG 59.139 44.000 14.67 7.28 44.33 2.34
4278 4491 4.561105 ACTCTGTTTACTCTGCAGTAAGC 58.439 43.478 14.67 9.44 44.33 3.09
4288 4501 2.175236 GCAGTAAGCAAGTCCAGGC 58.825 57.895 0.00 0.00 44.79 4.85
4290 4503 1.896220 CAGTAAGCAAGTCCAGGCAA 58.104 50.000 0.00 0.00 0.00 4.52
4293 4506 1.068264 GTAAGCAAGTCCAGGCAAAGC 60.068 52.381 0.00 0.00 0.00 3.51
4307 4520 3.544356 GCAAAGCCAGACTCTGTTTAC 57.456 47.619 5.32 0.00 0.00 2.01
4308 4521 3.142174 GCAAAGCCAGACTCTGTTTACT 58.858 45.455 5.32 0.00 0.00 2.24
4309 4522 3.187432 GCAAAGCCAGACTCTGTTTACTC 59.813 47.826 5.32 0.00 0.00 2.59
4310 4523 4.636249 CAAAGCCAGACTCTGTTTACTCT 58.364 43.478 5.32 0.00 0.00 3.24
4311 4524 3.951775 AGCCAGACTCTGTTTACTCTG 57.048 47.619 5.32 0.00 0.00 3.35
4312 4525 2.028567 AGCCAGACTCTGTTTACTCTGC 60.029 50.000 5.32 0.00 30.60 4.26
4313 4526 2.289072 GCCAGACTCTGTTTACTCTGCA 60.289 50.000 5.32 0.00 30.60 4.41
4314 4527 3.583806 CCAGACTCTGTTTACTCTGCAG 58.416 50.000 7.63 7.63 30.60 4.41
4315 4528 2.992543 CAGACTCTGTTTACTCTGCAGC 59.007 50.000 9.47 0.00 0.00 5.25
4316 4529 2.630098 AGACTCTGTTTACTCTGCAGCA 59.370 45.455 9.47 0.00 0.00 4.41
4317 4530 3.070159 AGACTCTGTTTACTCTGCAGCAA 59.930 43.478 9.47 0.00 0.00 3.91
4318 4531 3.397482 ACTCTGTTTACTCTGCAGCAAG 58.603 45.455 9.47 4.66 0.00 4.01
4319 4532 2.146342 TCTGTTTACTCTGCAGCAAGC 58.854 47.619 9.47 5.70 45.96 4.01
4349 4562 1.268386 CGCCTTCTGCATGCATAGTTG 60.268 52.381 22.97 9.36 41.33 3.16
4355 4568 3.156293 TCTGCATGCATAGTTGGTTTGT 58.844 40.909 22.97 0.00 0.00 2.83
4358 4571 2.916716 GCATGCATAGTTGGTTTGTTCG 59.083 45.455 14.21 0.00 0.00 3.95
4366 4579 3.815809 AGTTGGTTTGTTCGGAGATCAA 58.184 40.909 0.00 0.00 43.45 2.57
4389 4602 5.567037 TCTCAGGTCTGAATTTCAGGAAA 57.433 39.130 22.86 4.62 44.39 3.13
4390 4603 5.940617 TCTCAGGTCTGAATTTCAGGAAAA 58.059 37.500 22.86 4.28 44.39 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.277273 TCAAGCAGCACACATAGCTCT 59.723 47.619 0.00 0.00 41.14 4.09
3 4 1.678123 CCTCAAGCAGCACACATAGCT 60.678 52.381 0.00 0.00 44.62 3.32
4 5 0.731417 CCTCAAGCAGCACACATAGC 59.269 55.000 0.00 0.00 0.00 2.97
6 7 0.035152 CCCCTCAAGCAGCACACATA 60.035 55.000 0.00 0.00 0.00 2.29
7 8 1.303888 CCCCTCAAGCAGCACACAT 60.304 57.895 0.00 0.00 0.00 3.21
8 9 2.113774 CCCCTCAAGCAGCACACA 59.886 61.111 0.00 0.00 0.00 3.72
9 10 2.113986 ACCCCTCAAGCAGCACAC 59.886 61.111 0.00 0.00 0.00 3.82
10 11 2.113774 CACCCCTCAAGCAGCACA 59.886 61.111 0.00 0.00 0.00 4.57
11 12 2.674380 CCACCCCTCAAGCAGCAC 60.674 66.667 0.00 0.00 0.00 4.40
12 13 3.970410 CCCACCCCTCAAGCAGCA 61.970 66.667 0.00 0.00 0.00 4.41
13 14 4.748144 CCCCACCCCTCAAGCAGC 62.748 72.222 0.00 0.00 0.00 5.25
14 15 4.052518 CCCCCACCCCTCAAGCAG 62.053 72.222 0.00 0.00 0.00 4.24
15 16 4.938756 ACCCCCACCCCTCAAGCA 62.939 66.667 0.00 0.00 0.00 3.91
16 17 4.366684 CACCCCCACCCCTCAAGC 62.367 72.222 0.00 0.00 0.00 4.01
17 18 3.661648 CCACCCCCACCCCTCAAG 61.662 72.222 0.00 0.00 0.00 3.02
52 53 5.010922 TCCTTCACAAATTGATCCAAGGTTG 59.989 40.000 0.00 0.00 32.27 3.77
53 54 5.147032 TCCTTCACAAATTGATCCAAGGTT 58.853 37.500 0.00 0.00 32.27 3.50
54 55 4.739793 TCCTTCACAAATTGATCCAAGGT 58.260 39.130 0.00 0.00 32.27 3.50
55 56 5.927281 ATCCTTCACAAATTGATCCAAGG 57.073 39.130 0.00 5.49 32.84 3.61
56 57 8.611654 AAAAATCCTTCACAAATTGATCCAAG 57.388 30.769 0.00 0.00 32.84 3.61
87 88 9.105844 TGCTAAAGAATAATCTAATCTAGGCCT 57.894 33.333 11.78 11.78 33.77 5.19
89 90 9.157104 GGTGCTAAAGAATAATCTAATCTAGGC 57.843 37.037 0.00 0.00 33.77 3.93
91 92 9.660180 GGGGTGCTAAAGAATAATCTAATCTAG 57.340 37.037 0.00 0.00 33.77 2.43
98 99 6.152831 GTGTTTGGGGTGCTAAAGAATAATCT 59.847 38.462 0.00 0.00 37.57 2.40
99 100 6.330278 GTGTTTGGGGTGCTAAAGAATAATC 58.670 40.000 0.00 0.00 0.00 1.75
100 101 5.186992 GGTGTTTGGGGTGCTAAAGAATAAT 59.813 40.000 0.00 0.00 0.00 1.28
103 104 2.897326 GGTGTTTGGGGTGCTAAAGAAT 59.103 45.455 0.00 0.00 0.00 2.40
106 107 0.596082 CGGTGTTTGGGGTGCTAAAG 59.404 55.000 0.00 0.00 0.00 1.85
107 108 0.183014 TCGGTGTTTGGGGTGCTAAA 59.817 50.000 0.00 0.00 0.00 1.85
108 109 0.402504 ATCGGTGTTTGGGGTGCTAA 59.597 50.000 0.00 0.00 0.00 3.09
109 110 0.322098 CATCGGTGTTTGGGGTGCTA 60.322 55.000 0.00 0.00 0.00 3.49
110 111 1.603455 CATCGGTGTTTGGGGTGCT 60.603 57.895 0.00 0.00 0.00 4.40
111 112 0.965363 ATCATCGGTGTTTGGGGTGC 60.965 55.000 0.00 0.00 0.00 5.01
112 113 1.544724 AATCATCGGTGTTTGGGGTG 58.455 50.000 0.00 0.00 0.00 4.61
113 114 1.892474 CAAATCATCGGTGTTTGGGGT 59.108 47.619 12.90 0.00 31.08 4.95
142 147 2.588029 AATCATTTGGGGCGAGGGGG 62.588 60.000 0.00 0.00 0.00 5.40
143 148 0.687427 AAATCATTTGGGGCGAGGGG 60.687 55.000 0.00 0.00 0.00 4.79
145 150 1.136891 GGAAAATCATTTGGGGCGAGG 59.863 52.381 0.00 0.00 0.00 4.63
146 151 2.099756 GAGGAAAATCATTTGGGGCGAG 59.900 50.000 0.00 0.00 0.00 5.03
147 152 2.099405 GAGGAAAATCATTTGGGGCGA 58.901 47.619 0.00 0.00 0.00 5.54
148 153 2.102578 AGAGGAAAATCATTTGGGGCG 58.897 47.619 0.00 0.00 0.00 6.13
149 154 3.068732 GCTAGAGGAAAATCATTTGGGGC 59.931 47.826 0.00 0.00 0.00 5.80
160 165 2.289444 CCGTTGTGGAGCTAGAGGAAAA 60.289 50.000 0.00 0.00 42.00 2.29
167 172 0.176680 ATGAGCCGTTGTGGAGCTAG 59.823 55.000 0.00 0.00 42.00 3.42
170 175 1.639298 GACATGAGCCGTTGTGGAGC 61.639 60.000 0.00 0.00 42.00 4.70
171 176 1.021390 GGACATGAGCCGTTGTGGAG 61.021 60.000 0.00 0.00 42.00 3.86
172 177 1.003839 GGACATGAGCCGTTGTGGA 60.004 57.895 0.00 0.00 42.00 4.02
173 178 0.249120 TAGGACATGAGCCGTTGTGG 59.751 55.000 0.00 0.00 42.50 4.17
174 179 2.315925 ATAGGACATGAGCCGTTGTG 57.684 50.000 0.00 0.00 0.00 3.33
175 180 2.632377 CAATAGGACATGAGCCGTTGT 58.368 47.619 0.00 0.00 0.00 3.32
176 181 1.942657 CCAATAGGACATGAGCCGTTG 59.057 52.381 0.00 10.67 36.89 4.10
177 182 1.837439 TCCAATAGGACATGAGCCGTT 59.163 47.619 0.00 0.00 39.61 4.44
178 183 1.496060 TCCAATAGGACATGAGCCGT 58.504 50.000 0.00 0.00 39.61 5.68
239 244 4.968259 TGCTGTTGTGTTACTACTTCCAT 58.032 39.130 0.00 0.00 0.00 3.41
245 250 5.468746 TGGAAAGATGCTGTTGTGTTACTAC 59.531 40.000 0.00 0.00 0.00 2.73
254 259 5.063180 TGCTATTTGGAAAGATGCTGTTG 57.937 39.130 0.00 0.00 0.00 3.33
255 260 5.419788 TGATGCTATTTGGAAAGATGCTGTT 59.580 36.000 0.00 0.00 0.00 3.16
257 262 5.509716 TGATGCTATTTGGAAAGATGCTG 57.490 39.130 0.00 0.00 0.00 4.41
258 263 6.069331 AGATGATGCTATTTGGAAAGATGCT 58.931 36.000 0.00 0.00 0.00 3.79
259 264 6.328641 AGATGATGCTATTTGGAAAGATGC 57.671 37.500 0.00 0.00 0.00 3.91
359 364 5.702670 TGTTCAAGCTAGAACCAGAAATGAG 59.297 40.000 0.00 0.00 45.62 2.90
455 467 3.365472 AGCATTGGTTAGGATTGTTCCC 58.635 45.455 0.00 0.00 43.76 3.97
470 482 7.027760 CAGCCTTTATGATAGCATAAGCATTG 58.972 38.462 20.47 11.31 45.07 2.82
499 513 7.121168 CACCAGCCTCTATGATTTGTCTAAAAA 59.879 37.037 0.00 0.00 0.00 1.94
503 517 4.101585 CCACCAGCCTCTATGATTTGTCTA 59.898 45.833 0.00 0.00 0.00 2.59
516 530 1.004440 GTCAGACACCACCAGCCTC 60.004 63.158 0.00 0.00 0.00 4.70
532 546 0.910088 ACTGGGCCAAGGGAGTAGTC 60.910 60.000 13.11 0.00 0.00 2.59
533 547 0.475828 AACTGGGCCAAGGGAGTAGT 60.476 55.000 13.11 0.00 0.00 2.73
534 548 0.698818 AAACTGGGCCAAGGGAGTAG 59.301 55.000 13.11 0.00 0.00 2.57
536 550 1.460699 GAAACTGGGCCAAGGGAGT 59.539 57.895 13.11 0.00 0.00 3.85
537 551 1.304464 GGAAACTGGGCCAAGGGAG 60.304 63.158 13.11 0.00 0.00 4.30
539 553 0.334676 TATGGAAACTGGGCCAAGGG 59.665 55.000 13.11 0.00 37.78 3.95
540 554 1.474330 GTATGGAAACTGGGCCAAGG 58.526 55.000 13.11 0.00 37.78 3.61
541 555 1.094785 CGTATGGAAACTGGGCCAAG 58.905 55.000 8.04 5.25 37.78 3.61
542 556 0.693622 TCGTATGGAAACTGGGCCAA 59.306 50.000 8.04 0.00 37.78 4.52
543 557 0.251916 CTCGTATGGAAACTGGGCCA 59.748 55.000 5.85 5.85 38.78 5.36
545 559 1.095807 GCCTCGTATGGAAACTGGGC 61.096 60.000 0.00 0.00 0.00 5.36
546 560 0.463833 GGCCTCGTATGGAAACTGGG 60.464 60.000 0.00 0.00 0.00 4.45
547 561 0.463833 GGGCCTCGTATGGAAACTGG 60.464 60.000 0.84 0.00 0.00 4.00
548 562 0.810031 CGGGCCTCGTATGGAAACTG 60.810 60.000 0.84 0.00 0.00 3.16
549 563 0.974010 TCGGGCCTCGTATGGAAACT 60.974 55.000 0.84 0.00 40.32 2.66
550 564 0.808847 GTCGGGCCTCGTATGGAAAC 60.809 60.000 0.84 0.00 40.32 2.78
554 568 2.246761 TTTGGTCGGGCCTCGTATGG 62.247 60.000 0.84 0.00 40.32 2.74
590 623 3.855524 GCCGATGTTCCGACACAAAATTT 60.856 43.478 0.00 0.00 38.91 1.82
801 845 2.443016 CTCAGACCGAGGGAGGGG 60.443 72.222 0.00 0.00 38.18 4.79
812 856 4.802999 CCTTTTGCCATCTTTTCTCAGAC 58.197 43.478 0.00 0.00 0.00 3.51
818 862 2.071540 GCAGCCTTTTGCCATCTTTTC 58.928 47.619 0.00 0.00 42.71 2.29
823 867 1.444895 CACGCAGCCTTTTGCCATC 60.445 57.895 0.00 0.00 42.71 3.51
854 932 3.553095 GATGGGGATGGTAGGCGGC 62.553 68.421 0.00 0.00 0.00 6.53
886 964 3.760684 GCCTGCAATAAGAGGGGATAATG 59.239 47.826 0.00 0.00 0.00 1.90
930 1008 2.602676 CGGTGGAATGGTGGGAGGT 61.603 63.158 0.00 0.00 0.00 3.85
933 1011 1.848431 TTCCGGTGGAATGGTGGGA 60.848 57.895 0.00 0.00 36.71 4.37
1101 1182 2.819595 CCGGCGTCATTGAGGGTG 60.820 66.667 6.01 0.00 0.00 4.61
1120 1201 2.411547 CGAAGCTTTTTCACTAGGCACG 60.412 50.000 0.00 0.00 0.00 5.34
1121 1202 2.095718 CCGAAGCTTTTTCACTAGGCAC 60.096 50.000 0.00 0.00 0.00 5.01
1122 1203 2.151202 CCGAAGCTTTTTCACTAGGCA 58.849 47.619 0.00 0.00 0.00 4.75
1170 1254 3.282021 TCATCTCAAGGGCACATTAAGC 58.718 45.455 0.00 0.00 0.00 3.09
1174 1258 4.159135 GTCAATTCATCTCAAGGGCACATT 59.841 41.667 0.00 0.00 0.00 2.71
1181 1265 2.679837 CACGGGTCAATTCATCTCAAGG 59.320 50.000 0.00 0.00 0.00 3.61
1198 1282 4.685169 AAGATGCAAGAATAACACACGG 57.315 40.909 0.00 0.00 0.00 4.94
1298 1384 1.635487 TGAACTGGGGGAAGATTGGAG 59.365 52.381 0.00 0.00 0.00 3.86
1308 1394 3.099141 AGCAATAATTGTGAACTGGGGG 58.901 45.455 0.00 0.00 0.00 5.40
1321 1407 9.525409 GCAAAGATTGACAGATTTAGCAATAAT 57.475 29.630 0.00 0.00 31.65 1.28
1325 1411 5.336690 GGGCAAAGATTGACAGATTTAGCAA 60.337 40.000 0.00 0.00 41.76 3.91
1336 1422 1.130561 GCACGTAGGGCAAAGATTGAC 59.869 52.381 0.00 0.00 38.21 3.18
1380 1467 7.196331 TCAGTTCAGATACAGATACACAATCG 58.804 38.462 0.00 0.00 39.79 3.34
1471 1559 3.058016 GGCGCGATAACTGTACCACTATA 60.058 47.826 12.10 0.00 0.00 1.31
1488 1576 4.404654 GAAACCAGCTTGGGCGCG 62.405 66.667 0.00 0.00 43.37 6.86
1538 1626 6.318648 TCTGCTGAAAATTAAGTGTTCAGTGT 59.681 34.615 19.05 0.00 46.50 3.55
1573 1661 5.104817 TCAACATATGCAGGACTTGATGAGA 60.105 40.000 1.58 0.00 0.00 3.27
1576 1664 5.823209 TTCAACATATGCAGGACTTGATG 57.177 39.130 1.58 0.00 0.00 3.07
1645 1733 6.014242 TCTGAAGATAAGATTGTGTCACCAGT 60.014 38.462 0.00 0.00 0.00 4.00
1723 1812 6.299023 TGTGAGTAATTGCACAGTTTACAG 57.701 37.500 6.54 0.00 39.86 2.74
1773 1862 1.510844 CAAACCCCAAGGCGCATAC 59.489 57.895 10.83 0.00 36.11 2.39
1774 1863 1.680651 CCAAACCCCAAGGCGCATA 60.681 57.895 10.83 0.00 36.11 3.14
1775 1864 2.996734 CCAAACCCCAAGGCGCAT 60.997 61.111 10.83 0.00 36.11 4.73
1829 1918 7.885297 TCATCACCTTCTTTTTAACCATTGAG 58.115 34.615 0.00 0.00 0.00 3.02
1962 2052 1.340991 ACAAATTATGCGCCCAGTCCT 60.341 47.619 4.18 0.00 0.00 3.85
2145 2235 9.039870 AGAAATTACTTCTATTTCATCGCAGAG 57.960 33.333 10.02 0.00 42.90 3.35
2343 2446 1.792949 CGTCCAGAGTTTGTTCTTCGG 59.207 52.381 0.00 0.00 0.00 4.30
2416 2520 9.588096 AAACACTATTTAGAACCCAGAAATTCT 57.412 29.630 0.00 0.00 38.67 2.40
2583 2689 7.010339 TGGAGAAAGGAAAAACAAGGAAAAA 57.990 32.000 0.00 0.00 0.00 1.94
2920 3030 0.327924 CAACCACAGGGCATGGAGTA 59.672 55.000 3.46 0.00 39.87 2.59
3042 3152 6.055588 TGTTTTGTTTTCTTTTTGTGGTGGA 58.944 32.000 0.00 0.00 0.00 4.02
3074 3184 4.319405 GCATTAACAGCGCCACAAATTTTT 60.319 37.500 2.29 0.00 0.00 1.94
3086 3196 1.069022 ACACTTGCAGCATTAACAGCG 60.069 47.619 0.00 0.00 37.01 5.18
3115 3225 2.806244 GTCTGCGCTTCTTAAGGTGAAA 59.194 45.455 9.73 0.00 0.00 2.69
3299 3409 2.668457 GCACGACAGAAACATAGACCTG 59.332 50.000 0.00 0.00 0.00 4.00
3475 3585 1.002888 ACTCGACCTCCACTCTACGAA 59.997 52.381 0.00 0.00 0.00 3.85
3477 3587 1.008329 GACTCGACCTCCACTCTACG 58.992 60.000 0.00 0.00 0.00 3.51
3500 3610 0.753111 GTTCATGGGGGAGCATGACC 60.753 60.000 0.00 0.00 37.53 4.02
3550 3660 0.028770 TGCCTTGCAACGAAGAAACG 59.971 50.000 0.00 0.00 34.76 3.60
3557 3667 0.321564 ACAGCTATGCCTTGCAACGA 60.322 50.000 0.00 0.00 43.62 3.85
3558 3668 0.523072 AACAGCTATGCCTTGCAACG 59.477 50.000 0.00 0.00 43.62 4.10
3567 3677 1.197721 ACAGAAACGCAACAGCTATGC 59.802 47.619 12.46 12.46 40.41 3.14
3569 3679 5.880054 AAATACAGAAACGCAACAGCTAT 57.120 34.783 0.00 0.00 0.00 2.97
3596 3706 1.503542 GTGCAGGAAACATGAGGCG 59.496 57.895 0.00 0.00 0.00 5.52
3598 3708 0.251297 TGGGTGCAGGAAACATGAGG 60.251 55.000 0.00 0.00 0.00 3.86
3602 3712 3.091545 CAACTATGGGTGCAGGAAACAT 58.908 45.455 0.00 0.00 0.00 2.71
3691 3801 2.297701 GAAGACTTGGACAGCAAACCA 58.702 47.619 0.00 0.00 0.00 3.67
3693 3803 3.565482 TCATGAAGACTTGGACAGCAAAC 59.435 43.478 0.00 0.00 0.00 2.93
3698 3808 5.334724 GCTTTTCTCATGAAGACTTGGACAG 60.335 44.000 0.00 0.00 32.27 3.51
3735 3846 1.312371 ATTTGGGGAACGGATGCACG 61.312 55.000 0.00 0.00 40.31 5.34
3736 3847 0.894835 AATTTGGGGAACGGATGCAC 59.105 50.000 0.00 0.00 0.00 4.57
3742 3853 1.540267 TGCAGTAATTTGGGGAACGG 58.460 50.000 0.00 0.00 0.00 4.44
3743 3854 3.866883 AATGCAGTAATTTGGGGAACG 57.133 42.857 0.00 0.00 0.00 3.95
3762 3873 8.740123 TTTTGCCAGATTTCCTCGTATATAAA 57.260 30.769 0.00 0.00 0.00 1.40
3771 3882 4.871933 TTCCTTTTTGCCAGATTTCCTC 57.128 40.909 0.00 0.00 0.00 3.71
3797 3989 6.966534 ACCTTCAGATTCAAAATGTGTTCT 57.033 33.333 0.00 0.00 0.00 3.01
3831 4023 1.685355 AAAGTGTTGCAGCAACCCCC 61.685 55.000 31.05 20.02 42.96 5.40
3849 4042 8.660435 AGAAGAGGTAAAATGGCTATGCTATAA 58.340 33.333 0.00 0.00 0.00 0.98
3850 4043 8.207350 AGAAGAGGTAAAATGGCTATGCTATA 57.793 34.615 0.00 0.00 0.00 1.31
3886 4097 4.678256 TGGCACCATATTAGGTTGGAAAA 58.322 39.130 0.00 0.00 40.77 2.29
3893 4104 5.904984 TCAGTATTGGCACCATATTAGGT 57.095 39.130 0.00 0.00 44.48 3.08
3944 4155 7.556416 ACCTATGTCATGATTCAGATCAGAT 57.444 36.000 0.00 0.00 45.01 2.90
3961 4172 5.865085 TCACAGAAGCAACTAAACCTATGT 58.135 37.500 0.00 0.00 0.00 2.29
3973 4184 6.835819 ACTAGTAGTACATCACAGAAGCAA 57.164 37.500 0.00 0.00 0.00 3.91
4030 4242 4.635324 TCAGTTTATCATTCAGCATGCGAA 59.365 37.500 21.32 21.32 34.76 4.70
4034 4246 8.804743 GTTCAATTCAGTTTATCATTCAGCATG 58.195 33.333 0.00 0.00 37.54 4.06
4084 4296 3.584834 ACCAACCAATTTTAATCGCAGC 58.415 40.909 0.00 0.00 0.00 5.25
4088 4300 5.542779 TCCCAAACCAACCAATTTTAATCG 58.457 37.500 0.00 0.00 0.00 3.34
4128 4340 0.543749 CATTCCCTCCAGACTCCACC 59.456 60.000 0.00 0.00 0.00 4.61
4155 4367 1.618837 GTAGAGCACTTGGTCACCTGA 59.381 52.381 10.86 0.00 44.42 3.86
4156 4368 1.344438 TGTAGAGCACTTGGTCACCTG 59.656 52.381 10.86 0.00 44.42 4.00
4178 4390 1.959282 CACCTCCAAAGAAGCTGCTTT 59.041 47.619 14.40 14.40 38.57 3.51
4196 4408 2.811317 CTGCCGGCGAGAGTTCAC 60.811 66.667 23.90 0.00 0.00 3.18
4236 4449 3.608432 GGCTTTGCCTGGATGACC 58.392 61.111 0.00 0.00 46.69 4.02
4251 4464 2.289072 TGCAGAGTAAACAGAGTCTGGC 60.289 50.000 23.79 14.55 44.09 4.85
4273 4486 1.068264 GCTTTGCCTGGACTTGCTTAC 60.068 52.381 0.00 0.00 0.00 2.34
4274 4487 1.247567 GCTTTGCCTGGACTTGCTTA 58.752 50.000 0.00 0.00 0.00 3.09
4277 4490 2.653115 GGCTTTGCCTGGACTTGC 59.347 61.111 0.00 0.00 46.69 4.01
4287 4500 3.142174 AGTAAACAGAGTCTGGCTTTGC 58.858 45.455 23.79 17.69 35.51 3.68
4288 4501 4.450419 CAGAGTAAACAGAGTCTGGCTTTG 59.550 45.833 23.79 15.58 41.41 2.77
4290 4503 3.556004 GCAGAGTAAACAGAGTCTGGCTT 60.556 47.826 23.79 17.58 44.09 4.35
4293 4506 3.583806 CTGCAGAGTAAACAGAGTCTGG 58.416 50.000 23.79 6.57 44.09 3.86
4294 4507 2.992543 GCTGCAGAGTAAACAGAGTCTG 59.007 50.000 20.43 18.83 45.87 3.51
4295 4508 2.630098 TGCTGCAGAGTAAACAGAGTCT 59.370 45.455 20.43 0.00 33.10 3.24
4296 4509 3.032017 TGCTGCAGAGTAAACAGAGTC 57.968 47.619 20.43 0.00 33.10 3.36
4297 4510 3.397482 CTTGCTGCAGAGTAAACAGAGT 58.603 45.455 20.43 0.00 33.10 3.24
4311 4524 3.319926 GAGAACGCCTGCTTGCTGC 62.320 63.158 0.00 0.00 43.25 5.25
4312 4525 2.866028 GAGAACGCCTGCTTGCTG 59.134 61.111 0.00 0.00 0.00 4.41
4313 4526 2.740055 CGAGAACGCCTGCTTGCT 60.740 61.111 0.00 0.00 0.00 3.91
4335 4548 3.581024 ACAAACCAACTATGCATGCAG 57.419 42.857 26.69 15.79 0.00 4.41
4338 4551 3.190327 TCCGAACAAACCAACTATGCATG 59.810 43.478 10.16 1.82 0.00 4.06
4339 4552 3.417101 TCCGAACAAACCAACTATGCAT 58.583 40.909 3.79 3.79 0.00 3.96
4349 4562 4.866682 GAGATTGATCTCCGAACAAACC 57.133 45.455 9.39 0.00 45.88 3.27
4389 4602 7.062957 CCACTCCATCTTACAGGGAAATTATT 58.937 38.462 0.00 0.00 0.00 1.40
4390 4603 6.410853 CCCACTCCATCTTACAGGGAAATTAT 60.411 42.308 0.00 0.00 36.96 1.28


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

AutoCloner maintained by Alex Coulton.