Multiple sequence alignment - TraesCS3A01G039600

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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 TraesCS3A01G039600 chr3A 100.000 3668 0 0 1 3668 20949910 20953577 0.000000e+00 6774.0
1 TraesCS3A01G039600 chr3A 83.352 889 118 11 1062 1938 20942603 20943473 0.000000e+00 795.0
2 TraesCS3A01G039600 chr3A 96.212 132 4 1 1 132 696395322 696395192 7.980000e-52 215.0
3 TraesCS3A01G039600 chr3A 86.792 53 5 2 2343 2394 46567584 46567635 1.420000e-04 58.4
4 TraesCS3A01G039600 chr3D 89.585 2698 194 39 119 2764 15337144 15334482 0.000000e+00 3345.0
5 TraesCS3A01G039600 chr3D 88.254 2205 156 47 529 2665 489744239 489746408 0.000000e+00 2542.0
6 TraesCS3A01G039600 chr3D 85.214 886 104 12 1062 1938 15338370 15337503 0.000000e+00 885.0
7 TraesCS3A01G039600 chr3D 82.192 949 100 39 2763 3668 15334437 15333515 0.000000e+00 752.0
8 TraesCS3A01G039600 chr3D 82.767 412 43 11 3154 3554 489746648 489747042 3.510000e-90 342.0
9 TraesCS3A01G039600 chr3B 90.264 2609 161 39 119 2682 22455160 22452600 0.000000e+00 3325.0
10 TraesCS3A01G039600 chr3B 83.389 602 62 24 3096 3668 22451636 22451044 1.170000e-144 523.0
11 TraesCS3A01G039600 chr3B 83.989 356 36 13 2763 3110 22452004 22451662 4.570000e-84 322.0
12 TraesCS3A01G039600 chr2A 74.851 1511 291 70 1086 2566 415063763 415062312 1.460000e-168 603.0
13 TraesCS3A01G039600 chr2A 74.261 1523 308 64 1086 2566 750148319 750149799 6.880000e-157 564.0
14 TraesCS3A01G039600 chr2D 76.518 873 165 31 1086 1952 317940863 317941701 1.210000e-119 440.0
15 TraesCS3A01G039600 chr7D 75.369 881 166 38 1086 1957 498273591 498274429 9.610000e-101 377.0
16 TraesCS3A01G039600 chr7D 78.107 169 23 7 169 335 509695420 509695576 1.080000e-15 95.3
17 TraesCS3A01G039600 chr4B 89.404 302 28 4 154 452 644487434 644487734 9.610000e-101 377.0
18 TraesCS3A01G039600 chr1D 84.021 388 51 7 154 533 451779865 451780249 2.690000e-96 363.0
19 TraesCS3A01G039600 chr1A 78.552 373 58 13 170 533 22244092 22244451 3.690000e-55 226.0
20 TraesCS3A01G039600 chr1A 96.875 128 3 1 1 128 41908174 41908048 2.870000e-51 213.0
21 TraesCS3A01G039600 chr7A 99.180 122 1 0 1 122 696203595 696203474 1.710000e-53 220.0
22 TraesCS3A01G039600 chr7A 98.374 123 2 0 1 123 98415782 98415904 2.220000e-52 217.0
23 TraesCS3A01G039600 chr7A 77.976 168 25 4 169 335 580660968 580660812 1.080000e-15 95.3
24 TraesCS3A01G039600 chr5A 98.374 123 2 0 1 123 71275928 71275806 2.220000e-52 217.0
25 TraesCS3A01G039600 chr5A 97.600 125 3 0 1 125 550248310 550248434 7.980000e-52 215.0
26 TraesCS3A01G039600 chr6A 97.600 125 3 0 1 125 268172086 268171962 7.980000e-52 215.0
27 TraesCS3A01G039600 chr6A 96.850 127 4 0 1 127 44407678 44407804 2.870000e-51 213.0
28 TraesCS3A01G039600 chr6A 96.154 130 5 0 1 130 613144734 613144863 2.870000e-51 213.0
29 TraesCS3A01G039600 chr5B 83.475 236 34 4 171 403 700844105 700843872 7.980000e-52 215.0
30 TraesCS3A01G039600 chr1B 87.195 164 14 3 176 332 621319369 621319532 2.910000e-41 180.0
31 TraesCS3A01G039600 chr5D 80.455 220 37 4 171 388 549226374 549226159 2.930000e-36 163.0


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 TraesCS3A01G039600 chr3A 20949910 20953577 3667 False 6774.000000 6774 100.000000 1 3668 1 chr3A.!!$F2 3667
1 TraesCS3A01G039600 chr3A 20942603 20943473 870 False 795.000000 795 83.352000 1062 1938 1 chr3A.!!$F1 876
2 TraesCS3A01G039600 chr3D 15333515 15338370 4855 True 1660.666667 3345 85.663667 119 3668 3 chr3D.!!$R1 3549
3 TraesCS3A01G039600 chr3D 489744239 489747042 2803 False 1442.000000 2542 85.510500 529 3554 2 chr3D.!!$F1 3025
4 TraesCS3A01G039600 chr3B 22451044 22455160 4116 True 1390.000000 3325 85.880667 119 3668 3 chr3B.!!$R1 3549
5 TraesCS3A01G039600 chr2A 415062312 415063763 1451 True 603.000000 603 74.851000 1086 2566 1 chr2A.!!$R1 1480
6 TraesCS3A01G039600 chr2A 750148319 750149799 1480 False 564.000000 564 74.261000 1086 2566 1 chr2A.!!$F1 1480
7 TraesCS3A01G039600 chr2D 317940863 317941701 838 False 440.000000 440 76.518000 1086 1952 1 chr2D.!!$F1 866
8 TraesCS3A01G039600 chr7D 498273591 498274429 838 False 377.000000 377 75.369000 1086 1957 1 chr7D.!!$F1 871

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
41 42 0.028902 GCACGAACCGGGATAAATGC 59.971 55.0 6.32 4.0 28.17 3.56 F
67 68 0.105194 TGGTCCTGGTTCTGGACTGA 60.105 55.0 18.71 7.6 46.87 3.41 F
433 1546 0.249911 GGACAACGCCTCACTTGAGT 60.250 55.0 5.53 0.0 40.48 3.41 F
2208 3503 0.031917 TCCCTTACCTCCGGTGCATA 60.032 55.0 0.00 0.0 36.19 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1058 2234 1.216122 GCGTCTCATCATCAAGAGGC 58.784 55.000 1.88 1.88 43.53 4.70 R
1277 2460 1.227031 TTGGCGAAGTTGACGTCGT 60.227 52.632 17.90 0.00 46.66 4.34 R
2367 3665 0.115152 TCTCTGGCCTGAACTCCTCA 59.885 55.000 13.89 0.00 0.00 3.86 R
3140 5091 0.036388 GAATGAACCGGGTGCTCTGA 60.036 55.000 6.32 0.00 0.00 3.27 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
20 21 3.283259 AACCAGGACTAATGCCTTAGC 57.717 47.619 8.50 2.56 38.33 3.09
21 22 1.490910 ACCAGGACTAATGCCTTAGCC 59.509 52.381 8.50 10.27 38.33 3.93
23 24 0.106894 AGGACTAATGCCTTAGCCGC 59.893 55.000 8.50 0.00 38.33 6.53
24 25 0.179056 GGACTAATGCCTTAGCCGCA 60.179 55.000 8.50 0.00 38.33 5.69
25 26 0.938008 GACTAATGCCTTAGCCGCAC 59.062 55.000 8.50 0.00 39.49 5.34
26 27 0.810031 ACTAATGCCTTAGCCGCACG 60.810 55.000 8.50 0.00 39.49 5.34
27 28 0.529773 CTAATGCCTTAGCCGCACGA 60.530 55.000 0.00 0.00 39.49 4.35
28 29 0.108089 TAATGCCTTAGCCGCACGAA 60.108 50.000 0.00 0.00 39.49 3.85
31 32 3.186047 CCTTAGCCGCACGAACCG 61.186 66.667 0.00 0.00 0.00 4.44
33 34 4.745751 TTAGCCGCACGAACCGGG 62.746 66.667 6.32 0.00 45.66 5.73
36 37 4.517815 GCCGCACGAACCGGGATA 62.518 66.667 6.32 0.00 45.66 2.59
37 38 2.184836 CCGCACGAACCGGGATAA 59.815 61.111 6.32 0.00 41.99 1.75
38 39 1.448189 CCGCACGAACCGGGATAAA 60.448 57.895 6.32 0.00 41.99 1.40
39 40 0.812412 CCGCACGAACCGGGATAAAT 60.812 55.000 6.32 0.00 41.99 1.40
40 41 0.303493 CGCACGAACCGGGATAAATG 59.697 55.000 6.32 0.00 28.17 2.32
41 42 0.028902 GCACGAACCGGGATAAATGC 59.971 55.000 6.32 4.00 28.17 3.56
42 43 1.374560 CACGAACCGGGATAAATGCA 58.625 50.000 6.32 0.00 28.17 3.96
44 45 0.661020 CGAACCGGGATAAATGCACC 59.339 55.000 6.32 0.00 0.00 5.01
45 46 1.029681 GAACCGGGATAAATGCACCC 58.970 55.000 6.32 0.00 40.17 4.61
46 47 0.333312 AACCGGGATAAATGCACCCA 59.667 50.000 6.32 0.00 43.40 4.51
47 48 0.555769 ACCGGGATAAATGCACCCAT 59.444 50.000 6.32 0.00 43.40 4.00
48 49 1.063266 ACCGGGATAAATGCACCCATT 60.063 47.619 6.32 0.00 43.32 3.16
49 50 1.340889 CCGGGATAAATGCACCCATTG 59.659 52.381 9.80 0.00 40.69 2.82
50 51 1.340889 CGGGATAAATGCACCCATTGG 59.659 52.381 9.80 0.00 40.69 3.16
56 57 0.615544 AATGCACCCATTGGTCCTGG 60.616 55.000 1.20 0.00 45.57 4.45
58 59 1.228862 GCACCCATTGGTCCTGGTT 60.229 57.895 1.20 0.00 45.57 3.67
59 60 1.250840 GCACCCATTGGTCCTGGTTC 61.251 60.000 1.20 0.00 45.57 3.62
63 64 0.698238 CCATTGGTCCTGGTTCTGGA 59.302 55.000 0.00 0.00 0.00 3.86
65 66 1.352352 CATTGGTCCTGGTTCTGGACT 59.648 52.381 18.71 2.44 46.87 3.85
66 67 0.764890 TTGGTCCTGGTTCTGGACTG 59.235 55.000 18.71 0.00 46.87 3.51
67 68 0.105194 TGGTCCTGGTTCTGGACTGA 60.105 55.000 18.71 7.60 46.87 3.41
68 69 1.056660 GGTCCTGGTTCTGGACTGAA 58.943 55.000 18.71 0.00 46.87 3.02
69 70 1.270893 GGTCCTGGTTCTGGACTGAAC 60.271 57.143 18.71 12.04 46.87 3.18
73 74 4.695560 GTTCTGGACTGAACCGGG 57.304 61.111 6.32 0.00 40.10 5.73
74 75 2.055299 GTTCTGGACTGAACCGGGA 58.945 57.895 6.32 0.00 40.10 5.14
75 76 0.320508 GTTCTGGACTGAACCGGGAC 60.321 60.000 6.32 0.00 40.10 4.46
76 77 0.471211 TTCTGGACTGAACCGGGACT 60.471 55.000 6.32 0.00 36.97 3.85
77 78 0.406750 TCTGGACTGAACCGGGACTA 59.593 55.000 6.32 0.00 36.97 2.59
78 79 1.203087 TCTGGACTGAACCGGGACTAA 60.203 52.381 6.32 0.00 36.97 2.24
79 80 1.831736 CTGGACTGAACCGGGACTAAT 59.168 52.381 6.32 0.00 33.06 1.73
80 81 1.553248 TGGACTGAACCGGGACTAATG 59.447 52.381 6.32 0.00 0.00 1.90
82 83 0.909623 ACTGAACCGGGACTAATGGG 59.090 55.000 6.32 0.00 0.00 4.00
83 84 0.463833 CTGAACCGGGACTAATGGGC 60.464 60.000 6.32 0.00 0.00 5.36
84 85 0.912487 TGAACCGGGACTAATGGGCT 60.912 55.000 6.32 0.00 0.00 5.19
85 86 0.255033 GAACCGGGACTAATGGGCTT 59.745 55.000 6.32 0.00 0.00 4.35
87 88 0.835276 ACCGGGACTAATGGGCTTAC 59.165 55.000 6.32 0.00 0.00 2.34
89 90 1.129058 CGGGACTAATGGGCTTACCT 58.871 55.000 0.00 0.00 41.11 3.08
90 91 1.202651 CGGGACTAATGGGCTTACCTG 60.203 57.143 0.00 0.00 41.11 4.00
98 99 2.272471 GGCTTACCTGGCCTGGAC 59.728 66.667 33.43 18.61 45.57 4.02
100 101 2.602676 GCTTACCTGGCCTGGACCA 61.603 63.158 33.43 15.66 38.29 4.02
102 103 0.404040 CTTACCTGGCCTGGACCAAA 59.596 55.000 33.43 19.14 39.86 3.28
105 106 2.677875 CTGGCCTGGACCAAAGCC 60.678 66.667 22.94 22.94 45.96 4.35
109 110 3.268032 CCTGGACCAAAGCCCCCT 61.268 66.667 0.00 0.00 0.00 4.79
110 111 2.854076 CTGGACCAAAGCCCCCTT 59.146 61.111 0.00 0.00 0.00 3.95
111 112 1.156095 CTGGACCAAAGCCCCCTTT 59.844 57.895 0.00 0.00 41.86 3.11
112 113 0.471780 CTGGACCAAAGCCCCCTTTT 60.472 55.000 0.00 0.00 39.20 2.27
113 114 0.471022 TGGACCAAAGCCCCCTTTTC 60.471 55.000 0.00 0.00 39.20 2.29
115 116 1.076513 GGACCAAAGCCCCCTTTTCTA 59.923 52.381 0.00 0.00 39.20 2.10
116 117 2.168496 GACCAAAGCCCCCTTTTCTAC 58.832 52.381 0.00 0.00 39.20 2.59
117 118 1.787058 ACCAAAGCCCCCTTTTCTACT 59.213 47.619 0.00 0.00 39.20 2.57
118 119 2.990998 ACCAAAGCCCCCTTTTCTACTA 59.009 45.455 0.00 0.00 39.20 1.82
119 120 3.010250 ACCAAAGCCCCCTTTTCTACTAG 59.990 47.826 0.00 0.00 39.20 2.57
120 121 3.010250 CCAAAGCCCCCTTTTCTACTAGT 59.990 47.826 0.00 0.00 39.20 2.57
121 122 4.010349 CAAAGCCCCCTTTTCTACTAGTG 58.990 47.826 5.39 0.00 39.20 2.74
122 123 3.200958 AGCCCCCTTTTCTACTAGTGA 57.799 47.619 5.39 0.00 0.00 3.41
124 125 2.838813 GCCCCCTTTTCTACTAGTGAGT 59.161 50.000 5.39 0.00 39.92 3.41
126 127 4.654724 GCCCCCTTTTCTACTAGTGAGTAT 59.345 45.833 5.39 0.00 37.53 2.12
127 128 5.130643 GCCCCCTTTTCTACTAGTGAGTATT 59.869 44.000 5.39 0.00 37.53 1.89
128 129 6.325804 GCCCCCTTTTCTACTAGTGAGTATTA 59.674 42.308 5.39 0.00 37.53 0.98
253 1365 2.282391 TGGTGCATCCACACAGCC 60.282 61.111 0.00 0.00 43.88 4.85
282 1395 6.677431 GCACACTAGTACGACTATACTTTGCT 60.677 42.308 0.00 0.00 36.74 3.91
284 1397 8.393366 CACACTAGTACGACTATACTTTGCTAA 58.607 37.037 0.00 0.00 36.74 3.09
357 1470 8.341892 ACTCCTTGATTTTTATCAACTCCTTC 57.658 34.615 0.00 0.00 35.80 3.46
373 1486 4.020218 ACTCCTTCATTTCATCCACGAGAA 60.020 41.667 0.00 0.00 0.00 2.87
388 1501 4.245660 CACGAGAAGACCATAAGCAGAAA 58.754 43.478 0.00 0.00 0.00 2.52
433 1546 0.249911 GGACAACGCCTCACTTGAGT 60.250 55.000 5.53 0.00 40.48 3.41
435 1548 0.753262 ACAACGCCTCACTTGAGTCT 59.247 50.000 5.53 0.00 40.48 3.24
437 1550 0.601311 AACGCCTCACTTGAGTCTGC 60.601 55.000 5.53 1.37 40.48 4.26
452 1565 2.369860 AGTCTGCTTGGACAATGACTGA 59.630 45.455 11.73 2.13 38.57 3.41
459 1572 4.518970 GCTTGGACAATGACTGAAAGGTTA 59.481 41.667 0.00 0.00 39.30 2.85
460 1573 5.335191 GCTTGGACAATGACTGAAAGGTTAG 60.335 44.000 0.00 0.00 39.30 2.34
461 1574 5.304686 TGGACAATGACTGAAAGGTTAGT 57.695 39.130 0.00 0.00 39.30 2.24
548 1661 8.465999 TCATTGCAATTTAAGTATGGTTAGTGG 58.534 33.333 9.83 0.00 0.00 4.00
594 1707 4.137116 TGATTTATGTCTTGGTCCCTCG 57.863 45.455 0.00 0.00 0.00 4.63
625 1739 2.727544 GCTCCGCCAAAGCAAACA 59.272 55.556 0.00 0.00 39.61 2.83
645 1759 5.845985 ACATGATCAAACACAAGTACTCG 57.154 39.130 0.00 0.00 0.00 4.18
652 1766 5.860641 TCAAACACAAGTACTCGTCAAAAC 58.139 37.500 0.00 0.00 0.00 2.43
654 1770 3.864243 ACACAAGTACTCGTCAAAACCA 58.136 40.909 0.00 0.00 0.00 3.67
661 1777 4.689345 AGTACTCGTCAAAACCAACTATGC 59.311 41.667 0.00 0.00 0.00 3.14
764 1880 9.128107 CACCAATATAACAATGAACAACTTGAC 57.872 33.333 0.00 0.00 0.00 3.18
842 1960 8.404107 TGATTGTACCTTCTTTTTCCTAAAGG 57.596 34.615 0.00 0.00 43.22 3.11
845 1963 4.471078 ACCTTCTTTTTCCTAAAGGCCT 57.529 40.909 0.00 0.00 41.65 5.19
846 1964 5.594199 ACCTTCTTTTTCCTAAAGGCCTA 57.406 39.130 5.16 0.00 41.65 3.93
847 1965 5.960704 ACCTTCTTTTTCCTAAAGGCCTAA 58.039 37.500 5.16 0.00 41.65 2.69
848 1966 6.562228 ACCTTCTTTTTCCTAAAGGCCTAAT 58.438 36.000 5.16 0.00 41.65 1.73
1036 2212 2.153645 TGATGCTTGTGCTAACAGTGG 58.846 47.619 0.00 0.00 37.67 4.00
1054 2230 3.024547 GTGGTCATGGTCTCTGCTACTA 58.975 50.000 0.00 0.00 0.00 1.82
1055 2231 3.024547 TGGTCATGGTCTCTGCTACTAC 58.975 50.000 0.00 0.00 0.00 2.73
1056 2232 2.033550 GGTCATGGTCTCTGCTACTACG 59.966 54.545 0.00 0.00 0.00 3.51
1057 2233 2.683867 GTCATGGTCTCTGCTACTACGT 59.316 50.000 0.00 0.00 0.00 3.57
1058 2234 2.683362 TCATGGTCTCTGCTACTACGTG 59.317 50.000 0.00 0.00 0.00 4.49
1277 2460 1.228894 AGTGCTTCTCCTCCGACCA 60.229 57.895 0.00 0.00 0.00 4.02
1340 2523 0.739561 GAGGTCTCGTTCGGCTACAT 59.260 55.000 0.00 0.00 0.00 2.29
1626 2829 2.710902 CGACATGTCCGAGGAGGCA 61.711 63.158 20.03 0.00 40.77 4.75
1882 3088 1.301244 ATGATCGGCGTGATGCTCC 60.301 57.895 6.85 0.00 45.43 4.70
1883 3089 2.031674 ATGATCGGCGTGATGCTCCA 62.032 55.000 6.85 0.00 45.43 3.86
2011 3221 4.022935 ACCAAAATGCATATATCCACGCTG 60.023 41.667 0.00 0.00 0.00 5.18
2028 3310 0.816373 CTGCTCTGCTCTGCTCTGTA 59.184 55.000 0.00 0.00 0.00 2.74
2103 3385 2.357881 TCGCTGCTGCTCAACCAG 60.358 61.111 14.03 0.00 36.97 4.00
2208 3503 0.031917 TCCCTTACCTCCGGTGCATA 60.032 55.000 0.00 0.00 36.19 3.14
2395 3693 1.228894 AGGCCAGAGAGGTTCGACA 60.229 57.895 5.01 0.00 40.61 4.35
2396 3694 1.216710 GGCCAGAGAGGTTCGACAG 59.783 63.158 0.00 0.00 40.61 3.51
2448 3746 1.815421 GATGATGCTGCCGTTCGGT 60.815 57.895 12.81 0.00 0.00 4.69
2621 3919 1.552337 TCCTTTGGTAGCTCTCTGCAG 59.448 52.381 7.63 7.63 45.94 4.41
2683 3983 3.445008 AGCTAGTCCATCAAGTCTCCAA 58.555 45.455 0.00 0.00 0.00 3.53
2698 4001 2.029020 TCTCCAACAGATCACCAAGACG 60.029 50.000 0.00 0.00 0.00 4.18
2700 4003 2.104111 TCCAACAGATCACCAAGACGTT 59.896 45.455 0.00 0.00 0.00 3.99
2723 4027 7.804600 CGTTCATGCTTATATATGCATTGTTGT 59.195 33.333 25.63 9.09 46.29 3.32
2797 4692 6.012658 TCAACAAACCATACAATTGCTCTC 57.987 37.500 5.05 0.00 0.00 3.20
2812 4707 9.301897 ACAATTGCTCTCCTAAGTAAAAGAAAT 57.698 29.630 5.05 0.00 0.00 2.17
2814 4709 9.746457 AATTGCTCTCCTAAGTAAAAGAAATCT 57.254 29.630 0.00 0.00 0.00 2.40
2815 4710 8.779354 TTGCTCTCCTAAGTAAAAGAAATCTC 57.221 34.615 0.00 0.00 0.00 2.75
2816 4711 7.907389 TGCTCTCCTAAGTAAAAGAAATCTCA 58.093 34.615 0.00 0.00 0.00 3.27
2817 4712 8.375506 TGCTCTCCTAAGTAAAAGAAATCTCAA 58.624 33.333 0.00 0.00 0.00 3.02
2818 4713 9.389755 GCTCTCCTAAGTAAAAGAAATCTCAAT 57.610 33.333 0.00 0.00 0.00 2.57
2825 4720 8.884124 AAGTAAAAGAAATCTCAATGATGGGA 57.116 30.769 0.00 0.00 41.26 4.37
2826 4721 8.517062 AGTAAAAGAAATCTCAATGATGGGAG 57.483 34.615 0.00 0.00 40.06 4.30
2827 4722 8.331740 AGTAAAAGAAATCTCAATGATGGGAGA 58.668 33.333 0.00 0.00 40.06 3.71
2838 4733 5.474532 TCAATGATGGGAGAGTTCAAACTTG 59.525 40.000 0.00 0.00 39.88 3.16
2891 4794 4.849883 TGCGCGTTTTTCTATCTTTCAAA 58.150 34.783 8.43 0.00 0.00 2.69
2899 4802 8.342634 CGTTTTTCTATCTTTCAAACTTCCTCA 58.657 33.333 0.00 0.00 0.00 3.86
2934 4840 2.237392 GACTAGCCAACTGTCCTTGGAT 59.763 50.000 2.01 0.00 43.19 3.41
3062 4969 4.976224 TGATCCAAACTGAATGATGCAG 57.024 40.909 0.00 0.00 39.26 4.41
3070 4977 2.161012 ACTGAATGATGCAGTTTGAGCG 59.839 45.455 0.00 0.00 43.67 5.03
3071 4978 2.153645 TGAATGATGCAGTTTGAGCGT 58.846 42.857 0.00 0.00 33.85 5.07
3074 4981 2.404265 TGATGCAGTTTGAGCGTTTG 57.596 45.000 0.00 0.00 33.85 2.93
3076 4987 1.266718 GATGCAGTTTGAGCGTTTGGA 59.733 47.619 0.00 0.00 33.85 3.53
3080 4991 2.030805 GCAGTTTGAGCGTTTGGAGAAT 60.031 45.455 0.00 0.00 0.00 2.40
3083 4994 5.619981 GCAGTTTGAGCGTTTGGAGAATATT 60.620 40.000 0.00 0.00 0.00 1.28
3104 5015 8.774546 ATATTGTCCTCAACTGAGAGAGAATA 57.225 34.615 18.82 18.82 44.74 1.75
3107 5018 5.954752 TGTCCTCAACTGAGAGAGAATATGT 59.045 40.000 8.33 0.00 44.74 2.29
3110 5021 7.918562 GTCCTCAACTGAGAGAGAATATGTAAC 59.081 40.741 8.33 0.00 44.74 2.50
3128 5079 0.527565 ACTGATGCAAATGGTTCGGC 59.472 50.000 0.00 0.00 0.00 5.54
3129 5080 0.523968 CTGATGCAAATGGTTCGGCG 60.524 55.000 0.00 0.00 0.00 6.46
3140 5091 0.177373 GGTTCGGCGAATAGGTTCCT 59.823 55.000 26.42 0.00 0.00 3.36
3141 5092 1.568606 GTTCGGCGAATAGGTTCCTC 58.431 55.000 26.42 5.45 0.00 3.71
3151 5102 0.970937 TAGGTTCCTCAGAGCACCCG 60.971 60.000 11.79 0.00 0.00 5.28
3152 5103 2.266055 GTTCCTCAGAGCACCCGG 59.734 66.667 0.00 0.00 0.00 5.73
3220 5175 8.783660 TCATATTCTGTTAGGAGTAGGTTGAT 57.216 34.615 0.00 0.00 0.00 2.57
3221 5176 8.861086 TCATATTCTGTTAGGAGTAGGTTGATC 58.139 37.037 0.00 0.00 0.00 2.92
3288 5243 7.551974 ACCAGACATTTGATAAGATCTTGACAG 59.448 37.037 18.47 8.51 0.00 3.51
3302 5261 3.761218 TCTTGACAGGTTCAACAGCAAAA 59.239 39.130 0.00 0.00 39.45 2.44
3361 5321 2.416836 CGAATCGCTTGGGAGACTTGTA 60.417 50.000 0.00 0.00 0.00 2.41
3374 5334 6.327365 TGGGAGACTTGTATCACATCATGTAT 59.673 38.462 0.00 0.00 0.00 2.29
3478 5443 5.010112 TCTGAACCAACTTGTCAAACAAACA 59.990 36.000 0.00 0.00 37.69 2.83
3486 5452 7.405769 CAACTTGTCAAACAAACAAACAAAGT 58.594 30.769 0.00 0.00 37.69 2.66
3487 5453 8.543774 CAACTTGTCAAACAAACAAACAAAGTA 58.456 29.630 0.00 0.00 37.69 2.24
3488 5454 8.649973 ACTTGTCAAACAAACAAACAAAGTAA 57.350 26.923 0.00 0.00 37.69 2.24
3490 5456 8.649973 TTGTCAAACAAACAAACAAAGTAAGT 57.350 26.923 0.00 0.00 34.76 2.24
3491 5457 8.066668 TGTCAAACAAACAAACAAAGTAAGTG 57.933 30.769 0.00 0.00 0.00 3.16
3492 5458 7.921214 TGTCAAACAAACAAACAAAGTAAGTGA 59.079 29.630 0.00 0.00 0.00 3.41
3493 5459 8.756864 GTCAAACAAACAAACAAAGTAAGTGAA 58.243 29.630 0.00 0.00 0.00 3.18
3495 5461 7.883229 AACAAACAAACAAAGTAAGTGAAGG 57.117 32.000 0.00 0.00 0.00 3.46
3496 5462 6.988522 ACAAACAAACAAAGTAAGTGAAGGT 58.011 32.000 0.00 0.00 0.00 3.50
3499 5465 5.258051 ACAAACAAAGTAAGTGAAGGTGGA 58.742 37.500 0.00 0.00 0.00 4.02
3504 5470 5.163088 ACAAAGTAAGTGAAGGTGGAGGAAT 60.163 40.000 0.00 0.00 0.00 3.01
3533 5503 7.775120 ACAATAATTCGGCAGATTCTTTTGAT 58.225 30.769 0.00 0.00 0.00 2.57
3537 5507 3.673902 TCGGCAGATTCTTTTGATCACA 58.326 40.909 0.00 0.00 0.00 3.58
3559 5541 7.888021 TCACATGGGATTAAAAAGCTAGAAAGA 59.112 33.333 0.00 0.00 0.00 2.52
3568 5550 8.671384 TTAAAAAGCTAGAAAGAAGTAGCACA 57.329 30.769 0.00 0.00 43.55 4.57
3570 5552 3.839293 AGCTAGAAAGAAGTAGCACACG 58.161 45.455 0.00 0.00 43.55 4.49
3572 5554 3.614390 GCTAGAAAGAAGTAGCACACGGT 60.614 47.826 0.00 0.00 41.21 4.83
3573 5555 3.027974 AGAAAGAAGTAGCACACGGTC 57.972 47.619 0.00 0.00 0.00 4.79
3578 5560 2.563179 AGAAGTAGCACACGGTCTGAAT 59.437 45.455 0.00 0.00 0.00 2.57
3584 5566 5.593095 AGTAGCACACGGTCTGAATAATAGA 59.407 40.000 0.00 0.00 0.00 1.98
3593 5575 5.652518 GGTCTGAATAATAGAGTATCCGCC 58.347 45.833 0.00 0.00 33.66 6.13
3596 5578 5.073311 TGAATAATAGAGTATCCGCCAGC 57.927 43.478 0.00 0.00 33.66 4.85
3597 5579 4.081642 TGAATAATAGAGTATCCGCCAGCC 60.082 45.833 0.00 0.00 33.66 4.85
3629 5611 4.474394 AGAAAAAGAAAAGCAGTAGCCCT 58.526 39.130 0.00 0.00 43.56 5.19
3634 5616 4.855715 AGAAAAGCAGTAGCCCTTTTTC 57.144 40.909 0.00 0.00 40.31 2.29
3641 5626 8.595362 AAAGCAGTAGCCCTTTTTCTAATTAT 57.405 30.769 0.00 0.00 43.56 1.28
3642 5627 7.573968 AGCAGTAGCCCTTTTTCTAATTATG 57.426 36.000 0.00 0.00 43.56 1.90
3644 5629 7.067494 AGCAGTAGCCCTTTTTCTAATTATGTG 59.933 37.037 0.00 0.00 43.56 3.21
3646 5631 8.956426 CAGTAGCCCTTTTTCTAATTATGTGAA 58.044 33.333 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 1.490910 GGCTAAGGCATTAGTCCTGGT 59.509 52.381 18.55 0.00 40.55 4.00
2 3 1.541233 CGGCTAAGGCATTAGTCCTGG 60.541 57.143 16.40 0.00 39.96 4.45
3 4 1.871080 CGGCTAAGGCATTAGTCCTG 58.129 55.000 16.40 11.23 39.96 3.86
4 5 0.106894 GCGGCTAAGGCATTAGTCCT 59.893 55.000 16.40 0.00 39.96 3.85
5 6 0.179056 TGCGGCTAAGGCATTAGTCC 60.179 55.000 16.40 16.54 39.96 3.85
6 7 0.938008 GTGCGGCTAAGGCATTAGTC 59.062 55.000 18.55 15.72 43.19 2.59
7 8 0.810031 CGTGCGGCTAAGGCATTAGT 60.810 55.000 18.55 0.00 43.19 2.24
8 9 0.529773 TCGTGCGGCTAAGGCATTAG 60.530 55.000 13.70 13.70 43.19 1.73
10 11 1.376683 TTCGTGCGGCTAAGGCATT 60.377 52.632 0.00 0.00 43.19 3.56
12 13 2.740826 GTTCGTGCGGCTAAGGCA 60.741 61.111 0.00 0.00 40.87 4.75
13 14 3.497031 GGTTCGTGCGGCTAAGGC 61.497 66.667 0.00 0.00 37.82 4.35
15 16 3.186047 CCGGTTCGTGCGGCTAAG 61.186 66.667 0.00 0.00 0.00 2.18
16 17 4.745751 CCCGGTTCGTGCGGCTAA 62.746 66.667 0.00 0.00 0.00 3.09
20 21 0.812412 ATTTATCCCGGTTCGTGCGG 60.812 55.000 0.00 0.00 0.00 5.69
21 22 0.303493 CATTTATCCCGGTTCGTGCG 59.697 55.000 0.00 0.00 0.00 5.34
23 24 1.063469 GTGCATTTATCCCGGTTCGTG 59.937 52.381 0.00 0.00 0.00 4.35
24 25 1.375551 GTGCATTTATCCCGGTTCGT 58.624 50.000 0.00 0.00 0.00 3.85
25 26 0.661020 GGTGCATTTATCCCGGTTCG 59.339 55.000 0.00 0.00 0.00 3.95
26 27 1.029681 GGGTGCATTTATCCCGGTTC 58.970 55.000 0.00 0.00 0.00 3.62
27 28 0.333312 TGGGTGCATTTATCCCGGTT 59.667 50.000 0.00 0.00 43.75 4.44
28 29 0.555769 ATGGGTGCATTTATCCCGGT 59.444 50.000 0.00 0.00 43.75 5.28
44 45 0.698238 TCCAGAACCAGGACCAATGG 59.302 55.000 0.00 0.00 43.87 3.16
56 57 0.320508 GTCCCGGTTCAGTCCAGAAC 60.321 60.000 0.00 0.00 45.50 3.01
58 59 0.406750 TAGTCCCGGTTCAGTCCAGA 59.593 55.000 0.00 0.00 0.00 3.86
59 60 1.263356 TTAGTCCCGGTTCAGTCCAG 58.737 55.000 0.00 0.00 0.00 3.86
63 64 0.909623 CCCATTAGTCCCGGTTCAGT 59.090 55.000 0.00 0.00 0.00 3.41
65 66 0.912487 AGCCCATTAGTCCCGGTTCA 60.912 55.000 0.00 0.00 0.00 3.18
66 67 0.255033 AAGCCCATTAGTCCCGGTTC 59.745 55.000 0.00 0.00 0.00 3.62
67 68 1.211212 GTAAGCCCATTAGTCCCGGTT 59.789 52.381 0.00 0.00 0.00 4.44
68 69 0.835276 GTAAGCCCATTAGTCCCGGT 59.165 55.000 0.00 0.00 0.00 5.28
69 70 0.108019 GGTAAGCCCATTAGTCCCGG 59.892 60.000 0.00 0.00 0.00 5.73
71 72 1.143073 CCAGGTAAGCCCATTAGTCCC 59.857 57.143 0.00 0.00 34.66 4.46
72 73 1.477014 GCCAGGTAAGCCCATTAGTCC 60.477 57.143 0.00 0.00 34.66 3.85
73 74 1.477014 GGCCAGGTAAGCCCATTAGTC 60.477 57.143 0.00 0.00 45.16 2.59
74 75 0.551396 GGCCAGGTAAGCCCATTAGT 59.449 55.000 0.00 0.00 45.16 2.24
75 76 3.421567 GGCCAGGTAAGCCCATTAG 57.578 57.895 0.00 0.00 45.16 1.73
82 83 2.137177 TTGGTCCAGGCCAGGTAAGC 62.137 60.000 14.79 6.09 40.01 3.09
83 84 0.404040 TTTGGTCCAGGCCAGGTAAG 59.596 55.000 14.79 0.00 40.01 2.34
84 85 0.404040 CTTTGGTCCAGGCCAGGTAA 59.596 55.000 14.79 5.69 40.01 2.85
85 86 2.074967 CTTTGGTCCAGGCCAGGTA 58.925 57.895 14.79 0.00 40.01 3.08
87 88 2.677875 GCTTTGGTCCAGGCCAGG 60.678 66.667 8.15 8.15 40.01 4.45
93 94 0.471780 AAAAGGGGGCTTTGGTCCAG 60.472 55.000 0.00 0.00 39.39 3.86
94 95 0.471022 GAAAAGGGGGCTTTGGTCCA 60.471 55.000 0.00 0.00 39.39 4.02
95 96 0.178932 AGAAAAGGGGGCTTTGGTCC 60.179 55.000 0.00 0.00 36.26 4.46
96 97 2.168496 GTAGAAAAGGGGGCTTTGGTC 58.832 52.381 0.00 0.00 0.00 4.02
98 99 2.604912 AGTAGAAAAGGGGGCTTTGG 57.395 50.000 0.00 0.00 0.00 3.28
100 101 3.914435 TCACTAGTAGAAAAGGGGGCTTT 59.086 43.478 3.59 0.00 0.00 3.51
102 103 3.108376 CTCACTAGTAGAAAAGGGGGCT 58.892 50.000 3.59 0.00 0.00 5.19
115 116 9.502091 TTGTTCTTGCAAATAATACTCACTAGT 57.498 29.630 0.00 0.00 39.91 2.57
128 129 9.777297 AACCATACTTAAATTGTTCTTGCAAAT 57.223 25.926 0.00 0.00 31.63 2.32
197 1309 4.781775 AGGATCTTTCTCCTCTCGACTA 57.218 45.455 0.00 0.00 42.12 2.59
208 1320 5.192522 ACCACCATGTATTGAGGATCTTTCT 59.807 40.000 0.00 0.00 34.92 2.52
209 1321 5.440610 ACCACCATGTATTGAGGATCTTTC 58.559 41.667 0.00 0.00 34.92 2.62
253 1365 0.520404 AGTCGTACTAGTGTGCCACG 59.480 55.000 5.39 7.24 39.64 4.94
269 1382 5.456173 GTCGACTGCTTAGCAAAGTATAGTC 59.544 44.000 8.68 9.18 38.41 2.59
282 1395 6.452242 TCAAAATAGAGTTGTCGACTGCTTA 58.548 36.000 17.92 9.67 39.19 3.09
284 1397 4.883083 TCAAAATAGAGTTGTCGACTGCT 58.117 39.130 17.92 14.13 39.19 4.24
341 1454 9.087871 TGGATGAAATGAAGGAGTTGATAAAAA 57.912 29.630 0.00 0.00 0.00 1.94
345 1458 5.817296 CGTGGATGAAATGAAGGAGTTGATA 59.183 40.000 0.00 0.00 0.00 2.15
357 1470 3.599343 TGGTCTTCTCGTGGATGAAATG 58.401 45.455 0.00 0.00 31.35 2.32
373 1486 5.221621 GGCTAGATCTTTCTGCTTATGGTCT 60.222 44.000 0.00 0.00 33.17 3.85
388 1501 1.794714 ACAACGGATGGGCTAGATCT 58.205 50.000 0.00 0.00 0.00 2.75
433 1546 3.490439 TTCAGTCATTGTCCAAGCAGA 57.510 42.857 0.00 0.00 0.00 4.26
435 1548 2.886523 CCTTTCAGTCATTGTCCAAGCA 59.113 45.455 0.00 0.00 0.00 3.91
437 1550 5.765182 ACTAACCTTTCAGTCATTGTCCAAG 59.235 40.000 0.00 0.00 0.00 3.61
452 1565 5.825679 TGCTATTCAACACACACTAACCTTT 59.174 36.000 0.00 0.00 0.00 3.11
459 1572 3.003689 GTGCTTGCTATTCAACACACACT 59.996 43.478 0.00 0.00 36.97 3.55
460 1573 3.300009 GTGCTTGCTATTCAACACACAC 58.700 45.455 0.00 0.00 36.97 3.82
461 1574 2.293122 GGTGCTTGCTATTCAACACACA 59.707 45.455 0.00 0.00 37.92 3.72
625 1739 5.538118 TGACGAGTACTTGTGTTTGATCAT 58.462 37.500 20.77 0.00 0.00 2.45
645 1759 5.468746 TGACTACTGCATAGTTGGTTTTGAC 59.531 40.000 9.30 0.00 44.64 3.18
652 1766 5.178061 TGTTGATGACTACTGCATAGTTGG 58.822 41.667 9.30 0.00 44.64 3.77
654 1770 6.643388 TCATGTTGATGACTACTGCATAGTT 58.357 36.000 9.30 0.00 44.64 2.24
789 1906 7.280356 AGGTGTTGTATATGTTGGATTAGGTC 58.720 38.462 0.00 0.00 0.00 3.85
969 2121 3.360867 AGCTCTCAGTTTAGCTCTAGCA 58.639 45.455 4.54 0.00 45.92 3.49
994 2146 0.245266 TTGCTCATTGCCATGCTGTG 59.755 50.000 0.00 0.00 42.00 3.66
1036 2212 2.683867 ACGTAGTAGCAGAGACCATGAC 59.316 50.000 0.00 0.00 41.94 3.06
1054 2230 1.827344 TCTCATCATCAAGAGGCACGT 59.173 47.619 0.00 0.00 32.76 4.49
1055 2231 2.200067 GTCTCATCATCAAGAGGCACG 58.800 52.381 0.00 0.00 36.52 5.34
1056 2232 2.200067 CGTCTCATCATCAAGAGGCAC 58.800 52.381 0.00 0.00 36.30 5.01
1057 2233 2.591571 CGTCTCATCATCAAGAGGCA 57.408 50.000 0.00 0.00 36.30 4.75
1058 2234 1.216122 GCGTCTCATCATCAAGAGGC 58.784 55.000 1.88 1.88 43.53 4.70
1125 2307 3.314331 CGGAGCAGGTGGAGGTGT 61.314 66.667 0.00 0.00 0.00 4.16
1277 2460 1.227031 TTGGCGAAGTTGACGTCGT 60.227 52.632 17.90 0.00 46.66 4.34
1626 2829 2.936498 CACCACTTTCTTGAACTCGTGT 59.064 45.455 0.00 0.00 0.00 4.49
1827 3033 4.742649 AGCTCCTCCTCGTCGGCA 62.743 66.667 0.00 0.00 0.00 5.69
1882 3088 1.227205 GATCGGACTCCTGCAGCTG 60.227 63.158 10.11 10.11 0.00 4.24
1883 3089 2.430610 GGATCGGACTCCTGCAGCT 61.431 63.158 8.66 0.00 32.18 4.24
1982 3189 8.726068 CGTGGATATATGCATTTTGGTTGTATA 58.274 33.333 10.35 0.00 0.00 1.47
1983 3190 7.592938 CGTGGATATATGCATTTTGGTTGTAT 58.407 34.615 10.35 0.00 0.00 2.29
1984 3191 6.514212 GCGTGGATATATGCATTTTGGTTGTA 60.514 38.462 10.35 0.00 32.85 2.41
2011 3221 2.094286 TCTTTACAGAGCAGAGCAGAGC 60.094 50.000 0.00 0.00 0.00 4.09
2028 3310 1.671379 GCCGCCGAAGAGGTTCTTT 60.671 57.895 0.00 0.00 43.70 2.52
2208 3503 2.185350 CGCAGGGTCTCGCTGATT 59.815 61.111 15.93 0.00 45.41 2.57
2367 3665 0.115152 TCTCTGGCCTGAACTCCTCA 59.885 55.000 13.89 0.00 0.00 3.86
2382 3680 2.166664 GCCATTACTGTCGAACCTCTCT 59.833 50.000 0.00 0.00 0.00 3.10
2549 3847 1.071019 CGTCATGTCAACCTCGTCGG 61.071 60.000 0.00 0.00 39.35 4.79
2683 3983 3.329386 CATGAACGTCTTGGTGATCTGT 58.671 45.455 0.00 0.00 0.00 3.41
2774 4665 5.048083 GGAGAGCAATTGTATGGTTTGTTGA 60.048 40.000 7.40 0.00 0.00 3.18
2786 4677 8.691661 TTTCTTTTACTTAGGAGAGCAATTGT 57.308 30.769 7.40 0.00 0.00 2.71
2812 4707 5.013495 AGTTTGAACTCTCCCATCATTGAGA 59.987 40.000 0.00 0.00 32.86 3.27
2814 4709 5.246981 AGTTTGAACTCTCCCATCATTGA 57.753 39.130 0.00 0.00 32.86 2.57
2815 4710 5.474532 TCAAGTTTGAACTCTCCCATCATTG 59.525 40.000 0.00 0.00 38.57 2.82
2816 4711 5.634118 TCAAGTTTGAACTCTCCCATCATT 58.366 37.500 0.00 0.00 38.57 2.57
2817 4712 5.013495 TCTCAAGTTTGAACTCTCCCATCAT 59.987 40.000 0.00 0.00 38.57 2.45
2818 4713 4.347876 TCTCAAGTTTGAACTCTCCCATCA 59.652 41.667 0.00 0.00 38.57 3.07
2821 4716 4.347876 TCATCTCAAGTTTGAACTCTCCCA 59.652 41.667 0.00 0.00 38.57 4.37
2825 4720 9.566432 AATAGTTTCATCTCAAGTTTGAACTCT 57.434 29.630 0.00 0.00 38.57 3.24
2830 4725 9.996554 TGACTAATAGTTTCATCTCAAGTTTGA 57.003 29.630 0.00 0.00 35.57 2.69
2865 4760 5.918011 TGAAAGATAGAAAAACGCGCATTTT 59.082 32.000 19.32 19.32 33.13 1.82
2873 4768 8.342634 TGAGGAAGTTTGAAAGATAGAAAAACG 58.657 33.333 0.00 0.00 36.19 3.60
2891 4794 8.697507 AGTCTGAAAACATTTTATGAGGAAGT 57.302 30.769 0.00 0.00 0.00 3.01
2899 4802 8.299570 CAGTTGGCTAGTCTGAAAACATTTTAT 58.700 33.333 0.00 0.00 0.00 1.40
2998 4905 7.598869 TCCAAATGAGTCATCGCAATATACTAC 59.401 37.037 5.98 0.00 0.00 2.73
2999 4906 7.666623 TCCAAATGAGTCATCGCAATATACTA 58.333 34.615 5.98 0.00 0.00 1.82
3014 4921 5.687166 AATGCATTCCATTCCAAATGAGT 57.313 34.783 5.99 0.00 40.02 3.41
3062 4969 5.699839 ACAATATTCTCCAAACGCTCAAAC 58.300 37.500 0.00 0.00 0.00 2.93
3070 4977 6.655003 TCAGTTGAGGACAATATTCTCCAAAC 59.345 38.462 11.81 13.67 38.32 2.93
3071 4978 6.778821 TCAGTTGAGGACAATATTCTCCAAA 58.221 36.000 11.81 3.77 38.32 3.28
3074 4981 6.097554 TCTCTCAGTTGAGGACAATATTCTCC 59.902 42.308 9.13 1.65 42.30 3.71
3076 4987 6.894654 TCTCTCTCAGTTGAGGACAATATTCT 59.105 38.462 9.13 0.00 42.30 2.40
3080 4991 8.637099 CATATTCTCTCTCAGTTGAGGACAATA 58.363 37.037 9.13 8.99 42.30 1.90
3083 4994 5.954752 ACATATTCTCTCTCAGTTGAGGACA 59.045 40.000 9.13 0.00 42.30 4.02
3104 5015 4.142403 CCGAACCATTTGCATCAGTTACAT 60.142 41.667 0.00 0.00 0.00 2.29
3107 5018 2.163412 GCCGAACCATTTGCATCAGTTA 59.837 45.455 0.00 0.00 0.00 2.24
3110 5021 0.523968 CGCCGAACCATTTGCATCAG 60.524 55.000 0.00 0.00 0.00 2.90
3128 5079 2.482142 GGTGCTCTGAGGAACCTATTCG 60.482 54.545 2.37 0.00 35.48 3.34
3129 5080 2.158885 GGGTGCTCTGAGGAACCTATTC 60.159 54.545 24.25 0.00 40.69 1.75
3140 5091 0.036388 GAATGAACCGGGTGCTCTGA 60.036 55.000 6.32 0.00 0.00 3.27
3141 5092 1.361668 CGAATGAACCGGGTGCTCTG 61.362 60.000 6.32 0.00 0.00 3.35
3151 5102 3.831715 AGCAAAGCTTACGAATGAACC 57.168 42.857 0.00 0.00 33.89 3.62
3191 5143 8.783660 ACCTACTCCTAACAGAATATGATCAA 57.216 34.615 0.00 0.00 0.00 2.57
3197 5149 8.783660 TGATCAACCTACTCCTAACAGAATAT 57.216 34.615 0.00 0.00 0.00 1.28
3220 5175 6.161855 ACAATATCTAGAGCATTCGGTTGA 57.838 37.500 0.00 0.00 0.00 3.18
3221 5176 7.371159 TCTACAATATCTAGAGCATTCGGTTG 58.629 38.462 0.00 0.00 0.00 3.77
3263 5218 7.012138 CCTGTCAAGATCTTATCAAATGTCTGG 59.988 40.741 7.86 2.85 0.00 3.86
3288 5243 2.885502 CGGCTTTTGCTGTTGAACC 58.114 52.632 0.00 0.00 46.30 3.62
3302 5261 5.659440 AATGAATTTATTTGACACCGGCT 57.341 34.783 0.00 0.00 0.00 5.52
3340 5300 1.002366 CAAGTCTCCCAAGCGATTCG 58.998 55.000 0.62 0.62 0.00 3.34
3374 5334 3.961849 TGGCATTGCTTGGTATGTCTAA 58.038 40.909 8.82 0.00 0.00 2.10
3382 5342 2.762665 ACCAATGGCATTGCTTGGT 58.237 47.368 30.21 22.82 45.97 3.67
3383 5343 0.609151 TCACCAATGGCATTGCTTGG 59.391 50.000 30.21 22.31 44.06 3.61
3420 5385 6.070251 TGGCAATTCTAGTTAAGTCATCTGGA 60.070 38.462 0.00 0.00 0.00 3.86
3429 5394 7.441017 AGATAGCTCTGGCAATTCTAGTTAAG 58.559 38.462 0.00 0.00 41.70 1.85
3456 5421 5.201713 TGTTTGTTTGACAAGTTGGTTCA 57.798 34.783 7.96 0.00 39.53 3.18
3478 5443 4.887655 CCTCCACCTTCACTTACTTTGTTT 59.112 41.667 0.00 0.00 0.00 2.83
3486 5452 6.843752 TGTTTAATTCCTCCACCTTCACTTA 58.156 36.000 0.00 0.00 0.00 2.24
3487 5453 5.701224 TGTTTAATTCCTCCACCTTCACTT 58.299 37.500 0.00 0.00 0.00 3.16
3488 5454 5.319043 TGTTTAATTCCTCCACCTTCACT 57.681 39.130 0.00 0.00 0.00 3.41
3490 5456 8.893563 ATTATTGTTTAATTCCTCCACCTTCA 57.106 30.769 0.00 0.00 0.00 3.02
3491 5457 9.803315 GAATTATTGTTTAATTCCTCCACCTTC 57.197 33.333 6.77 0.00 37.74 3.46
3492 5458 8.466798 CGAATTATTGTTTAATTCCTCCACCTT 58.533 33.333 10.79 0.00 39.50 3.50
3493 5459 7.068226 CCGAATTATTGTTTAATTCCTCCACCT 59.932 37.037 10.79 0.00 39.50 4.00
3495 5461 6.695713 GCCGAATTATTGTTTAATTCCTCCAC 59.304 38.462 10.79 0.00 39.50 4.02
3496 5462 6.378564 TGCCGAATTATTGTTTAATTCCTCCA 59.621 34.615 10.79 5.03 39.50 3.86
3499 5465 7.639113 TCTGCCGAATTATTGTTTAATTCCT 57.361 32.000 10.79 0.00 39.50 3.36
3504 5470 9.921637 AAAAGAATCTGCCGAATTATTGTTTAA 57.078 25.926 0.00 0.00 28.33 1.52
3533 5503 7.888021 TCTTTCTAGCTTTTTAATCCCATGTGA 59.112 33.333 0.00 0.00 0.00 3.58
3537 5507 8.885693 ACTTCTTTCTAGCTTTTTAATCCCAT 57.114 30.769 0.00 0.00 0.00 4.00
3559 5541 4.530710 TTATTCAGACCGTGTGCTACTT 57.469 40.909 0.00 0.00 0.00 2.24
3568 5550 5.106237 GCGGATACTCTATTATTCAGACCGT 60.106 44.000 0.00 0.00 38.12 4.83
3570 5552 5.185249 TGGCGGATACTCTATTATTCAGACC 59.815 44.000 0.00 0.00 0.00 3.85
3572 5554 5.105716 GCTGGCGGATACTCTATTATTCAGA 60.106 44.000 0.00 0.00 0.00 3.27
3573 5555 5.105752 GCTGGCGGATACTCTATTATTCAG 58.894 45.833 0.00 0.00 0.00 3.02
3578 5560 2.826128 CTGGCTGGCGGATACTCTATTA 59.174 50.000 3.57 0.00 0.00 0.98
3584 5566 3.083349 TGCTGGCTGGCGGATACT 61.083 61.111 14.97 0.00 34.52 2.12
3593 5575 1.509644 TTTTCTCGTGCTGCTGGCTG 61.510 55.000 0.00 0.00 42.39 4.85
3596 5578 1.229428 TCTTTTTCTCGTGCTGCTGG 58.771 50.000 0.00 0.00 0.00 4.85
3597 5579 3.338818 TTTCTTTTTCTCGTGCTGCTG 57.661 42.857 0.00 0.00 0.00 4.41
3611 5593 5.363868 AGAAAAAGGGCTACTGCTTTTCTTT 59.636 36.000 11.90 0.00 42.89 2.52


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

AutoCloner maintained by Alex Coulton.