Multiple sequence alignment - TraesCS4A01G462600

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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 TraesCS4A01G462600 chr4A 100.000 2225 0 0 1 2225 726671051 726673275 0.000000e+00 4109
1 TraesCS4A01G462600 chr4A 90.111 900 71 6 581 1470 726719636 726720527 0.000000e+00 1153
2 TraesCS4A01G462600 chr4A 83.549 1003 127 26 868 1856 726683597 726684575 0.000000e+00 904
3 TraesCS4A01G462600 chr4A 90.270 555 46 6 1560 2112 726720523 726721071 0.000000e+00 719
4 TraesCS4A01G462600 chr7A 90.956 1548 125 10 650 2193 10634419 10632883 0.000000e+00 2069
5 TraesCS4A01G462600 chr7A 90.956 1548 125 10 650 2193 10641617 10640081 0.000000e+00 2069
6 TraesCS4A01G462600 chr7A 90.956 1548 125 10 650 2193 10647488 10645952 0.000000e+00 2069
7 TraesCS4A01G462600 chr7A 80.080 1757 278 45 158 1893 10857203 10855498 0.000000e+00 1240
8 TraesCS4A01G462600 chr7A 80.104 1739 263 52 161 1856 10620879 10619181 0.000000e+00 1218
9 TraesCS4A01G462600 chr7A 80.587 886 148 15 685 1565 10802904 10802038 0.000000e+00 662
10 TraesCS4A01G462600 chr7A 83.146 534 72 11 1016 1545 10412483 10413002 2.590000e-129 472
11 TraesCS4A01G462600 chr7D 81.019 1786 247 52 161 1893 11321414 11319668 0.000000e+00 1336
12 TraesCS4A01G462600 chr7D 77.804 847 169 13 161 1001 11255565 11254732 2.550000e-139 505
13 TraesCS4A01G462600 chr2A 74.092 633 133 21 673 1289 17474280 17473663 4.780000e-57 231
14 TraesCS4A01G462600 chr2D 72.955 758 153 36 490 1226 15471723 15470997 1.340000e-52 217
15 TraesCS4A01G462600 chr2B 74.619 394 70 22 573 957 27581615 27581243 1.780000e-31 147


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 TraesCS4A01G462600 chr4A 726671051 726673275 2224 False 4109 4109 100.0000 1 2225 1 chr4A.!!$F1 2224
1 TraesCS4A01G462600 chr4A 726719636 726721071 1435 False 936 1153 90.1905 581 2112 2 chr4A.!!$F3 1531
2 TraesCS4A01G462600 chr4A 726683597 726684575 978 False 904 904 83.5490 868 1856 1 chr4A.!!$F2 988
3 TraesCS4A01G462600 chr7A 10632883 10634419 1536 True 2069 2069 90.9560 650 2193 1 chr7A.!!$R2 1543
4 TraesCS4A01G462600 chr7A 10640081 10641617 1536 True 2069 2069 90.9560 650 2193 1 chr7A.!!$R3 1543
5 TraesCS4A01G462600 chr7A 10645952 10647488 1536 True 2069 2069 90.9560 650 2193 1 chr7A.!!$R4 1543
6 TraesCS4A01G462600 chr7A 10855498 10857203 1705 True 1240 1240 80.0800 158 1893 1 chr7A.!!$R6 1735
7 TraesCS4A01G462600 chr7A 10619181 10620879 1698 True 1218 1218 80.1040 161 1856 1 chr7A.!!$R1 1695
8 TraesCS4A01G462600 chr7A 10802038 10802904 866 True 662 662 80.5870 685 1565 1 chr7A.!!$R5 880
9 TraesCS4A01G462600 chr7A 10412483 10413002 519 False 472 472 83.1460 1016 1545 1 chr7A.!!$F1 529
10 TraesCS4A01G462600 chr7D 11319668 11321414 1746 True 1336 1336 81.0190 161 1893 1 chr7D.!!$R2 1732
11 TraesCS4A01G462600 chr7D 11254732 11255565 833 True 505 505 77.8040 161 1001 1 chr7D.!!$R1 840
12 TraesCS4A01G462600 chr2A 17473663 17474280 617 True 231 231 74.0920 673 1289 1 chr2A.!!$R1 616
13 TraesCS4A01G462600 chr2D 15470997 15471723 726 True 217 217 72.9550 490 1226 1 chr2D.!!$R1 736

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
86 87 0.033405 TCCTTAGGTCGCTAGTGCCT 60.033 55.0 18.92 18.92 35.36 4.75 F
116 117 0.039618 ATTTCTGCGGGGTTGGACAT 59.960 50.0 0.00 0.00 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1206 0.326264 AGTGCCTTGGCTTGTAGAGG 59.674 55.0 13.18 0.0 0.00 3.69 R
2108 2201 0.895530 TAGGGAACTTCGTGGAGCAG 59.104 55.0 0.00 0.0 43.67 4.24 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
26 27 5.051891 CATTTGCTGCTACAAAACTAGCT 57.948 39.130 8.45 0.00 42.45 3.32
27 28 4.488126 TTTGCTGCTACAAAACTAGCTG 57.512 40.909 0.00 1.10 40.02 4.24
31 32 4.270178 CTGCTACAAAACTAGCTGCATC 57.730 45.455 1.02 0.00 40.02 3.91
32 33 3.009723 TGCTACAAAACTAGCTGCATCC 58.990 45.455 1.02 0.00 40.02 3.51
33 34 3.274288 GCTACAAAACTAGCTGCATCCT 58.726 45.455 1.02 0.00 36.88 3.24
34 35 3.691609 GCTACAAAACTAGCTGCATCCTT 59.308 43.478 1.02 0.00 36.88 3.36
35 36 4.156739 GCTACAAAACTAGCTGCATCCTTT 59.843 41.667 1.02 0.00 36.88 3.11
36 37 5.354234 GCTACAAAACTAGCTGCATCCTTTA 59.646 40.000 1.02 0.00 36.88 1.85
37 38 6.128007 GCTACAAAACTAGCTGCATCCTTTAA 60.128 38.462 1.02 0.00 36.88 1.52
38 39 6.840780 ACAAAACTAGCTGCATCCTTTAAT 57.159 33.333 1.02 0.00 0.00 1.40
39 40 7.232118 ACAAAACTAGCTGCATCCTTTAATT 57.768 32.000 1.02 0.00 0.00 1.40
40 41 7.092716 ACAAAACTAGCTGCATCCTTTAATTG 58.907 34.615 1.02 0.00 0.00 2.32
41 42 5.841957 AACTAGCTGCATCCTTTAATTGG 57.158 39.130 1.02 0.00 0.00 3.16
42 43 4.860022 ACTAGCTGCATCCTTTAATTGGT 58.140 39.130 1.02 0.00 0.00 3.67
43 44 6.001449 ACTAGCTGCATCCTTTAATTGGTA 57.999 37.500 1.02 0.00 0.00 3.25
44 45 5.823045 ACTAGCTGCATCCTTTAATTGGTAC 59.177 40.000 1.02 0.00 0.00 3.34
45 46 4.599041 AGCTGCATCCTTTAATTGGTACA 58.401 39.130 1.02 0.00 0.00 2.90
46 47 5.203528 AGCTGCATCCTTTAATTGGTACAT 58.796 37.500 1.02 0.00 39.30 2.29
47 48 5.300286 AGCTGCATCCTTTAATTGGTACATC 59.700 40.000 1.02 0.00 39.30 3.06
48 49 5.300286 GCTGCATCCTTTAATTGGTACATCT 59.700 40.000 0.00 0.00 39.30 2.90
49 50 6.514048 GCTGCATCCTTTAATTGGTACATCTC 60.514 42.308 0.00 0.00 39.30 2.75
50 51 6.662755 TGCATCCTTTAATTGGTACATCTCT 58.337 36.000 0.00 0.00 39.30 3.10
51 52 6.543465 TGCATCCTTTAATTGGTACATCTCTG 59.457 38.462 0.00 0.00 39.30 3.35
52 53 6.543831 GCATCCTTTAATTGGTACATCTCTGT 59.456 38.462 0.00 0.00 39.30 3.41
53 54 7.715249 GCATCCTTTAATTGGTACATCTCTGTA 59.285 37.037 0.00 0.00 39.30 2.74
54 55 9.613428 CATCCTTTAATTGGTACATCTCTGTAA 57.387 33.333 0.00 0.00 39.51 2.41
55 56 9.838339 ATCCTTTAATTGGTACATCTCTGTAAG 57.162 33.333 0.00 0.00 39.51 2.34
56 57 8.265055 TCCTTTAATTGGTACATCTCTGTAAGG 58.735 37.037 0.00 0.00 39.51 2.69
57 58 8.265055 CCTTTAATTGGTACATCTCTGTAAGGA 58.735 37.037 0.00 0.00 39.51 3.36
58 59 9.667107 CTTTAATTGGTACATCTCTGTAAGGAA 57.333 33.333 0.00 0.00 39.51 3.36
60 61 9.613428 TTAATTGGTACATCTCTGTAAGGAATG 57.387 33.333 0.00 0.00 39.51 2.67
61 62 5.023533 TGGTACATCTCTGTAAGGAATGC 57.976 43.478 0.00 0.00 39.51 3.56
62 63 4.469586 TGGTACATCTCTGTAAGGAATGCA 59.530 41.667 0.00 0.00 39.51 3.96
63 64 5.045942 TGGTACATCTCTGTAAGGAATGCAA 60.046 40.000 0.00 0.00 39.51 4.08
64 65 5.525378 GGTACATCTCTGTAAGGAATGCAAG 59.475 44.000 0.00 0.00 39.51 4.01
65 66 4.521146 ACATCTCTGTAAGGAATGCAAGG 58.479 43.478 0.00 0.00 32.49 3.61
66 67 2.991250 TCTCTGTAAGGAATGCAAGGC 58.009 47.619 0.00 0.00 0.00 4.35
67 68 2.573462 TCTCTGTAAGGAATGCAAGGCT 59.427 45.455 0.00 0.00 0.00 4.58
68 69 2.941720 CTCTGTAAGGAATGCAAGGCTC 59.058 50.000 0.00 0.00 0.00 4.70
69 70 2.019984 CTGTAAGGAATGCAAGGCTCC 58.980 52.381 0.00 0.00 0.00 4.70
70 71 1.635487 TGTAAGGAATGCAAGGCTCCT 59.365 47.619 0.00 0.00 41.51 3.69
72 73 3.265737 TGTAAGGAATGCAAGGCTCCTTA 59.734 43.478 18.69 18.69 45.69 2.69
73 74 2.725221 AGGAATGCAAGGCTCCTTAG 57.275 50.000 0.11 0.00 36.06 2.18
74 75 1.213926 AGGAATGCAAGGCTCCTTAGG 59.786 52.381 0.11 0.00 36.06 2.69
75 76 1.064389 GGAATGCAAGGCTCCTTAGGT 60.064 52.381 0.11 0.00 34.50 3.08
76 77 2.293170 GAATGCAAGGCTCCTTAGGTC 58.707 52.381 0.11 0.00 34.50 3.85
77 78 0.179000 ATGCAAGGCTCCTTAGGTCG 59.821 55.000 0.11 0.00 34.50 4.79
78 79 1.815840 GCAAGGCTCCTTAGGTCGC 60.816 63.158 0.11 2.42 34.50 5.19
79 80 1.901085 CAAGGCTCCTTAGGTCGCT 59.099 57.895 13.00 0.54 34.50 4.93
80 81 1.112113 CAAGGCTCCTTAGGTCGCTA 58.888 55.000 13.00 0.00 34.50 4.26
81 82 1.067821 CAAGGCTCCTTAGGTCGCTAG 59.932 57.143 13.00 0.00 34.50 3.42
82 83 0.259356 AGGCTCCTTAGGTCGCTAGT 59.741 55.000 13.00 0.00 0.00 2.57
83 84 0.386113 GGCTCCTTAGGTCGCTAGTG 59.614 60.000 13.00 0.00 0.00 2.74
84 85 0.249114 GCTCCTTAGGTCGCTAGTGC 60.249 60.000 0.00 0.00 0.00 4.40
85 86 0.386113 CTCCTTAGGTCGCTAGTGCC 59.614 60.000 0.00 3.57 35.36 5.01
86 87 0.033405 TCCTTAGGTCGCTAGTGCCT 60.033 55.000 18.92 18.92 35.36 4.75
87 88 0.103208 CCTTAGGTCGCTAGTGCCTG 59.897 60.000 22.06 11.15 35.36 4.85
88 89 0.818296 CTTAGGTCGCTAGTGCCTGT 59.182 55.000 22.06 6.63 35.36 4.00
89 90 0.815734 TTAGGTCGCTAGTGCCTGTC 59.184 55.000 22.06 2.58 35.36 3.51
90 91 0.323087 TAGGTCGCTAGTGCCTGTCA 60.323 55.000 22.06 6.59 35.36 3.58
91 92 1.185618 AGGTCGCTAGTGCCTGTCAA 61.186 55.000 15.64 0.00 35.36 3.18
92 93 0.320421 GGTCGCTAGTGCCTGTCAAA 60.320 55.000 0.00 0.00 35.36 2.69
93 94 1.071605 GTCGCTAGTGCCTGTCAAAG 58.928 55.000 0.00 0.00 35.36 2.77
94 95 0.966179 TCGCTAGTGCCTGTCAAAGA 59.034 50.000 0.00 0.00 35.36 2.52
95 96 1.343142 TCGCTAGTGCCTGTCAAAGAA 59.657 47.619 0.00 0.00 35.36 2.52
96 97 2.028112 TCGCTAGTGCCTGTCAAAGAAT 60.028 45.455 0.00 0.00 35.36 2.40
97 98 3.194755 TCGCTAGTGCCTGTCAAAGAATA 59.805 43.478 0.00 0.00 35.36 1.75
98 99 4.122776 CGCTAGTGCCTGTCAAAGAATAT 58.877 43.478 0.00 0.00 35.36 1.28
99 100 4.572389 CGCTAGTGCCTGTCAAAGAATATT 59.428 41.667 0.00 0.00 35.36 1.28
100 101 5.065218 CGCTAGTGCCTGTCAAAGAATATTT 59.935 40.000 0.00 0.00 35.36 1.40
101 102 6.490534 GCTAGTGCCTGTCAAAGAATATTTC 58.509 40.000 0.00 0.00 0.00 2.17
102 103 6.317391 GCTAGTGCCTGTCAAAGAATATTTCT 59.683 38.462 0.00 0.00 43.15 2.52
103 104 6.506500 AGTGCCTGTCAAAGAATATTTCTG 57.493 37.500 0.00 0.00 40.59 3.02
104 105 5.098211 GTGCCTGTCAAAGAATATTTCTGC 58.902 41.667 0.00 0.00 40.59 4.26
105 106 4.142622 TGCCTGTCAAAGAATATTTCTGCG 60.143 41.667 0.00 0.00 40.59 5.18
106 107 4.731773 GCCTGTCAAAGAATATTTCTGCGG 60.732 45.833 0.00 0.00 40.59 5.69
107 108 4.201950 CCTGTCAAAGAATATTTCTGCGGG 60.202 45.833 0.00 0.00 40.59 6.13
108 109 3.694072 TGTCAAAGAATATTTCTGCGGGG 59.306 43.478 0.00 0.00 40.59 5.73
109 110 3.694566 GTCAAAGAATATTTCTGCGGGGT 59.305 43.478 0.00 0.00 40.59 4.95
110 111 4.157840 GTCAAAGAATATTTCTGCGGGGTT 59.842 41.667 0.00 0.00 40.59 4.11
111 112 4.157656 TCAAAGAATATTTCTGCGGGGTTG 59.842 41.667 0.00 0.00 40.59 3.77
112 113 2.654863 AGAATATTTCTGCGGGGTTGG 58.345 47.619 0.00 0.00 38.91 3.77
113 114 2.241176 AGAATATTTCTGCGGGGTTGGA 59.759 45.455 0.00 0.00 38.91 3.53
114 115 2.052782 ATATTTCTGCGGGGTTGGAC 57.947 50.000 0.00 0.00 0.00 4.02
115 116 0.693622 TATTTCTGCGGGGTTGGACA 59.306 50.000 0.00 0.00 0.00 4.02
116 117 0.039618 ATTTCTGCGGGGTTGGACAT 59.960 50.000 0.00 0.00 0.00 3.06
117 118 0.893270 TTTCTGCGGGGTTGGACATG 60.893 55.000 0.00 0.00 0.00 3.21
118 119 2.034066 CTGCGGGGTTGGACATGT 59.966 61.111 0.00 0.00 0.00 3.21
119 120 2.282110 TGCGGGGTTGGACATGTG 60.282 61.111 1.15 0.00 0.00 3.21
120 121 3.061848 GCGGGGTTGGACATGTGG 61.062 66.667 1.15 0.00 0.00 4.17
121 122 2.753701 CGGGGTTGGACATGTGGA 59.246 61.111 1.15 0.00 0.00 4.02
122 123 1.674322 CGGGGTTGGACATGTGGAC 60.674 63.158 1.15 0.00 0.00 4.02
123 124 1.458486 GGGGTTGGACATGTGGACA 59.542 57.895 1.15 0.00 0.00 4.02
124 125 0.893727 GGGGTTGGACATGTGGACAC 60.894 60.000 1.15 0.00 0.00 3.67
125 126 0.179004 GGGTTGGACATGTGGACACA 60.179 55.000 1.15 7.68 46.44 3.72
138 139 5.488262 TGTGGACACATGGATATATGGAG 57.512 43.478 0.13 0.00 36.21 3.86
139 140 5.154418 TGTGGACACATGGATATATGGAGA 58.846 41.667 0.13 0.00 36.21 3.71
140 141 5.606329 TGTGGACACATGGATATATGGAGAA 59.394 40.000 0.13 0.00 36.21 2.87
141 142 6.169094 GTGGACACATGGATATATGGAGAAG 58.831 44.000 0.00 0.00 32.32 2.85
142 143 6.014242 GTGGACACATGGATATATGGAGAAGA 60.014 42.308 0.00 0.00 32.32 2.87
143 144 6.558394 TGGACACATGGATATATGGAGAAGAA 59.442 38.462 0.00 0.00 32.32 2.52
144 145 7.238305 TGGACACATGGATATATGGAGAAGAAT 59.762 37.037 0.00 0.00 32.32 2.40
145 146 8.762645 GGACACATGGATATATGGAGAAGAATA 58.237 37.037 0.00 0.00 32.32 1.75
156 157 5.677319 TGGAGAAGAATATTTCTGGTCGT 57.323 39.130 0.00 0.00 40.59 4.34
179 180 1.701847 GGTGGACATATGGAGATGGCT 59.298 52.381 7.80 0.00 34.98 4.75
202 203 3.141398 CATCACCTGCAAGTAGTGTTGT 58.859 45.455 0.00 0.00 33.21 3.32
223 224 0.802494 GTTGGTGGTAGCGAATGTGG 59.198 55.000 0.00 0.00 0.00 4.17
249 250 6.994496 TCAAGGAATTAGACAGCCTAATCATG 59.006 38.462 0.00 0.00 44.94 3.07
278 279 9.631452 TTATACGCAAGAGATATCATCTTTCAG 57.369 33.333 5.32 7.24 40.38 3.02
312 313 1.812571 CCGTTGCTGCTAATGAAGGTT 59.187 47.619 0.00 0.00 0.00 3.50
313 314 2.228822 CCGTTGCTGCTAATGAAGGTTT 59.771 45.455 0.00 0.00 0.00 3.27
317 318 6.092748 CGTTGCTGCTAATGAAGGTTTAATT 58.907 36.000 0.00 0.00 0.00 1.40
319 320 6.832520 TGCTGCTAATGAAGGTTTAATTGA 57.167 33.333 0.00 0.00 0.00 2.57
333 334 5.362430 GGTTTAATTGAATGGATGTGGGCTA 59.638 40.000 0.00 0.00 0.00 3.93
396 397 4.507710 TGTCCACATACAAGATGAAGAGC 58.492 43.478 0.00 0.00 0.00 4.09
404 408 6.538021 ACATACAAGATGAAGAGCAGATGAAC 59.462 38.462 0.00 0.00 0.00 3.18
406 410 5.311265 ACAAGATGAAGAGCAGATGAACAA 58.689 37.500 0.00 0.00 0.00 2.83
413 417 5.124936 TGAAGAGCAGATGAACAATGGATTG 59.875 40.000 0.00 0.00 43.26 2.67
418 422 4.337555 GCAGATGAACAATGGATTGCTACT 59.662 41.667 0.00 0.00 41.38 2.57
435 439 3.368843 GCTACTGCAAGAGGACAGAATCA 60.369 47.826 0.00 0.00 39.41 2.57
439 443 4.202398 ACTGCAAGAGGACAGAATCAAAGA 60.202 41.667 0.00 0.00 37.35 2.52
448 452 9.041354 AGAGGACAGAATCAAAGAAACTAGTAT 57.959 33.333 0.00 0.00 0.00 2.12
452 456 8.045176 ACAGAATCAAAGAAACTAGTATTGGC 57.955 34.615 0.00 0.00 0.00 4.52
454 458 6.316390 AGAATCAAAGAAACTAGTATTGGCGG 59.684 38.462 0.00 0.00 0.00 6.13
462 466 6.592994 AGAAACTAGTATTGGCGGTTCTTTAC 59.407 38.462 0.00 0.00 0.00 2.01
468 472 1.061546 TGGCGGTTCTTTACTCCCTT 58.938 50.000 0.00 0.00 0.00 3.95
472 476 3.626217 GGCGGTTCTTTACTCCCTTATTG 59.374 47.826 0.00 0.00 0.00 1.90
473 477 3.626217 GCGGTTCTTTACTCCCTTATTGG 59.374 47.826 0.00 0.00 0.00 3.16
474 478 3.626217 CGGTTCTTTACTCCCTTATTGGC 59.374 47.826 0.00 0.00 0.00 4.52
517 524 3.917329 GCATGTGCATGATAGCTTGAT 57.083 42.857 15.53 0.00 41.20 2.57
530 537 3.834489 AGCTTGATGTCCATCACTAGG 57.166 47.619 9.41 2.88 46.49 3.02
534 541 4.554292 CTTGATGTCCATCACTAGGATCG 58.446 47.826 9.41 0.00 46.49 3.69
535 542 3.832527 TGATGTCCATCACTAGGATCGA 58.167 45.455 5.88 0.00 42.42 3.59
538 545 4.855715 TGTCCATCACTAGGATCGAATC 57.144 45.455 0.00 0.00 37.52 2.52
540 547 7.971569 GATGTCCATCACTAGGATCGAATCCA 61.972 46.154 13.95 2.88 43.31 3.41
548 555 2.762360 GATCGAATCCACACGGCAA 58.238 52.632 0.00 0.00 0.00 4.52
552 559 1.579429 GAATCCACACGGCAACCAC 59.421 57.895 0.00 0.00 0.00 4.16
563 570 2.600173 CAACCACGTTGGCCCCAT 60.600 61.111 0.00 0.00 42.67 4.00
570 598 1.472480 CACGTTGGCCCCATCTTAAAG 59.528 52.381 0.00 0.00 0.00 1.85
600 628 1.267574 TGAGAGGTGCCCCAAGCTAG 61.268 60.000 0.00 0.00 44.23 3.42
602 630 2.204151 AGGTGCCCCAAGCTAGGT 60.204 61.111 2.24 0.00 44.23 3.08
624 652 2.161855 CTGTATTTGCTGCTCCCACAA 58.838 47.619 0.00 0.00 0.00 3.33
630 661 2.356665 TGCTGCTCCCACAAAAAGTA 57.643 45.000 0.00 0.00 0.00 2.24
665 702 7.811236 AGTAATGAAGTTGAATACTTTCGTCGA 59.189 33.333 0.00 0.00 47.00 4.20
677 714 4.562082 ACTTTCGTCGATTGACCACATTA 58.438 39.130 7.54 0.00 42.37 1.90
697 734 2.873797 GGGCATCCCAACTCTCAAC 58.126 57.895 0.00 0.00 44.65 3.18
729 766 9.088512 GCTATATATGCAACTGGAGTACAATAC 57.911 37.037 0.00 0.00 0.00 1.89
806 843 2.477825 CCGAGGCTCATACATGTTCTG 58.522 52.381 15.95 2.43 0.00 3.02
981 1021 2.607442 TCCCTAGGCTGCAGTGCA 60.607 61.111 18.58 18.58 36.92 4.57
982 1022 1.980784 CTCCCTAGGCTGCAGTGCAT 61.981 60.000 20.10 6.60 38.13 3.96
983 1023 0.690744 TCCCTAGGCTGCAGTGCATA 60.691 55.000 20.10 7.53 38.13 3.14
984 1024 0.399454 CCCTAGGCTGCAGTGCATAT 59.601 55.000 20.10 10.06 38.13 1.78
1155 1206 2.671963 GCGAACCACCACCCTTCC 60.672 66.667 0.00 0.00 0.00 3.46
1247 1302 6.127507 TGAGATATATCTGGCTCCATCTTTCG 60.128 42.308 20.05 0.00 37.25 3.46
1289 1346 9.646427 ATTCAGTGTTCTAGTCATCTTAGTTTC 57.354 33.333 0.00 0.00 0.00 2.78
1290 1347 8.410673 TCAGTGTTCTAGTCATCTTAGTTTCT 57.589 34.615 0.00 0.00 0.00 2.52
1291 1348 8.861086 TCAGTGTTCTAGTCATCTTAGTTTCTT 58.139 33.333 0.00 0.00 0.00 2.52
1311 1375 3.981071 TGTTTCTTCATCATCGTCCCT 57.019 42.857 0.00 0.00 0.00 4.20
1335 1399 7.096884 TGTACTAGTCTACTGCCAGTAATTG 57.903 40.000 5.98 0.00 29.00 2.32
1343 1407 8.361139 AGTCTACTGCCAGTAATTGATGTATAC 58.639 37.037 5.98 0.00 29.00 1.47
1462 1533 4.127171 TGTCAGCCTACAAAGTTGAAGAC 58.873 43.478 0.00 0.00 0.00 3.01
1486 1558 7.624549 ACTTCTCTGTGATATATGGTTGTGTT 58.375 34.615 0.00 0.00 0.00 3.32
1579 1653 0.249447 TCTGCGCCTGTATCAATCCG 60.249 55.000 4.18 0.00 0.00 4.18
1838 1929 4.702131 GGTTTGTCAGCTATGGACTGATTT 59.298 41.667 4.51 0.00 45.40 2.17
1883 1975 4.270566 TGTGATTTTGCAGCAATTGTTGAC 59.729 37.500 24.50 15.79 0.00 3.18
1944 2036 8.936864 GCAAGCTTCTAGTTATTACTTCTGAAA 58.063 33.333 0.00 0.00 35.78 2.69
1960 2052 4.944048 TCTGAAACATCTCACGACTGAAA 58.056 39.130 0.00 0.00 0.00 2.69
1966 2058 4.631131 ACATCTCACGACTGAAATGTGAA 58.369 39.130 0.00 0.00 41.65 3.18
1968 2060 5.702670 ACATCTCACGACTGAAATGTGAAAT 59.297 36.000 0.00 0.00 41.65 2.17
1975 2067 5.049405 ACGACTGAAATGTGAAATCACCTTC 60.049 40.000 10.83 12.80 45.88 3.46
1983 2075 5.514274 TGTGAAATCACCTTCAAACTTCC 57.486 39.130 10.83 0.00 45.88 3.46
1991 2083 3.625764 CACCTTCAAACTTCCAAACGAGA 59.374 43.478 0.00 0.00 0.00 4.04
2027 2119 6.816640 CCGATACTTGGAGACATTTGAAGTAA 59.183 38.462 0.00 0.00 42.32 2.24
2055 2147 8.366401 TGCAAGATTATTTTCTGTTCCATTTGA 58.634 29.630 0.00 0.00 0.00 2.69
2070 2163 8.805175 TGTTCCATTTGATATTGTCAATCTGTT 58.195 29.630 0.07 0.00 45.77 3.16
2080 2173 9.167311 GATATTGTCAATCTGTTGAGGTTACTT 57.833 33.333 0.07 0.00 44.58 2.24
2093 2186 1.675116 GGTTACTTCACCTCCGCCTTC 60.675 57.143 0.00 0.00 33.50 3.46
2094 2187 1.275573 GTTACTTCACCTCCGCCTTCT 59.724 52.381 0.00 0.00 0.00 2.85
2095 2188 2.494870 GTTACTTCACCTCCGCCTTCTA 59.505 50.000 0.00 0.00 0.00 2.10
2108 2201 3.006003 CCGCCTTCTAAGGGAGTCTATTC 59.994 52.174 10.69 0.00 46.56 1.75
2112 2205 4.898861 CCTTCTAAGGGAGTCTATTCTGCT 59.101 45.833 0.42 0.00 42.66 4.24
2126 2219 0.832135 TCTGCTCCACGAAGTTCCCT 60.832 55.000 0.00 0.00 41.61 4.20
2127 2220 0.895530 CTGCTCCACGAAGTTCCCTA 59.104 55.000 0.00 0.00 41.61 3.53
2141 2234 5.606348 AGTTCCCTACATGACATCTCTTC 57.394 43.478 0.00 0.00 0.00 2.87
2146 2239 2.749280 ACATGACATCTCTTCGCACA 57.251 45.000 0.00 0.00 0.00 4.57
2149 2242 3.193479 ACATGACATCTCTTCGCACACTA 59.807 43.478 0.00 0.00 0.00 2.74
2151 2244 3.081804 TGACATCTCTTCGCACACTAGA 58.918 45.455 0.00 0.00 0.00 2.43
2189 2282 4.151157 GCCATTGCTCACAAGAAATTTGAC 59.849 41.667 0.00 0.00 39.69 3.18
2193 2286 5.534207 TGCTCACAAGAAATTTGACCAAT 57.466 34.783 0.00 0.00 0.00 3.16
2194 2287 5.531634 TGCTCACAAGAAATTTGACCAATC 58.468 37.500 0.00 0.00 0.00 2.67
2195 2288 5.302568 TGCTCACAAGAAATTTGACCAATCT 59.697 36.000 0.00 0.00 0.00 2.40
2196 2289 5.860716 GCTCACAAGAAATTTGACCAATCTC 59.139 40.000 0.00 0.00 0.00 2.75
2197 2290 6.331369 TCACAAGAAATTTGACCAATCTCC 57.669 37.500 0.00 0.00 0.00 3.71
2198 2291 5.048782 TCACAAGAAATTTGACCAATCTCCG 60.049 40.000 0.00 0.00 0.00 4.63
2199 2292 4.827284 ACAAGAAATTTGACCAATCTCCGT 59.173 37.500 0.00 0.00 0.00 4.69
2200 2293 5.156355 CAAGAAATTTGACCAATCTCCGTG 58.844 41.667 0.00 0.00 0.00 4.94
2201 2294 4.651778 AGAAATTTGACCAATCTCCGTGA 58.348 39.130 0.00 0.00 0.00 4.35
2202 2295 5.256474 AGAAATTTGACCAATCTCCGTGAT 58.744 37.500 0.00 0.00 36.89 3.06
2203 2296 5.355350 AGAAATTTGACCAATCTCCGTGATC 59.645 40.000 0.00 0.00 33.57 2.92
2204 2297 3.981071 TTTGACCAATCTCCGTGATCT 57.019 42.857 0.00 0.00 33.57 2.75
2205 2298 3.981071 TTGACCAATCTCCGTGATCTT 57.019 42.857 0.00 0.00 33.57 2.40
2206 2299 3.526931 TGACCAATCTCCGTGATCTTC 57.473 47.619 0.00 0.00 33.57 2.87
2207 2300 2.831526 TGACCAATCTCCGTGATCTTCA 59.168 45.455 0.00 0.00 33.57 3.02
2208 2301 3.118992 TGACCAATCTCCGTGATCTTCAG 60.119 47.826 0.00 0.00 33.57 3.02
2209 2302 2.208431 CCAATCTCCGTGATCTTCAGC 58.792 52.381 0.00 0.00 33.57 4.26
2210 2303 2.158986 CCAATCTCCGTGATCTTCAGCT 60.159 50.000 0.00 0.00 33.57 4.24
2211 2304 3.122297 CAATCTCCGTGATCTTCAGCTC 58.878 50.000 0.00 0.00 33.57 4.09
2212 2305 1.107114 TCTCCGTGATCTTCAGCTCC 58.893 55.000 0.00 0.00 0.00 4.70
2213 2306 0.103937 CTCCGTGATCTTCAGCTCCC 59.896 60.000 0.00 0.00 0.00 4.30
2214 2307 1.144936 CCGTGATCTTCAGCTCCCC 59.855 63.158 0.00 0.00 0.00 4.81
2215 2308 1.333636 CCGTGATCTTCAGCTCCCCT 61.334 60.000 0.00 0.00 0.00 4.79
2216 2309 0.179089 CGTGATCTTCAGCTCCCCTG 60.179 60.000 0.00 0.00 43.17 4.45
2217 2310 0.908198 GTGATCTTCAGCTCCCCTGT 59.092 55.000 0.00 0.00 42.38 4.00
2218 2311 1.280421 GTGATCTTCAGCTCCCCTGTT 59.720 52.381 0.00 0.00 42.38 3.16
2219 2312 1.556911 TGATCTTCAGCTCCCCTGTTC 59.443 52.381 0.00 0.00 42.38 3.18
2220 2313 1.836802 GATCTTCAGCTCCCCTGTTCT 59.163 52.381 0.00 0.00 42.38 3.01
2221 2314 2.623418 TCTTCAGCTCCCCTGTTCTA 57.377 50.000 0.00 0.00 42.38 2.10
2222 2315 3.121929 TCTTCAGCTCCCCTGTTCTAT 57.878 47.619 0.00 0.00 42.38 1.98
2223 2316 2.768527 TCTTCAGCTCCCCTGTTCTATG 59.231 50.000 0.00 0.00 42.38 2.23
2224 2317 0.833287 TCAGCTCCCCTGTTCTATGC 59.167 55.000 0.00 0.00 42.38 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.855388 CAGCTAGTTTTGTAGCAGCAAATG 59.145 41.667 5.72 0.00 46.81 2.32
5 6 5.051891 CAGCTAGTTTTGTAGCAGCAAAT 57.948 39.130 5.72 0.00 46.81 2.32
6 7 4.488126 CAGCTAGTTTTGTAGCAGCAAA 57.512 40.909 5.72 2.22 46.81 3.68
9 10 2.534231 GCAGCTAGTTTTGTAGCAGC 57.466 50.000 4.77 4.77 46.95 5.25
10 11 3.064545 GGATGCAGCTAGTTTTGTAGCAG 59.935 47.826 0.22 0.00 46.81 4.24
11 12 3.009723 GGATGCAGCTAGTTTTGTAGCA 58.990 45.455 0.22 0.00 46.81 3.49
12 13 3.274288 AGGATGCAGCTAGTTTTGTAGC 58.726 45.455 0.22 0.00 45.06 3.58
13 14 5.886960 AAAGGATGCAGCTAGTTTTGTAG 57.113 39.130 0.22 0.00 0.00 2.74
14 15 7.938140 ATTAAAGGATGCAGCTAGTTTTGTA 57.062 32.000 0.22 0.00 0.00 2.41
15 16 6.840780 ATTAAAGGATGCAGCTAGTTTTGT 57.159 33.333 0.22 0.00 0.00 2.83
16 17 6.532657 CCAATTAAAGGATGCAGCTAGTTTTG 59.467 38.462 0.22 0.00 0.00 2.44
17 18 6.211384 ACCAATTAAAGGATGCAGCTAGTTTT 59.789 34.615 0.22 1.05 0.00 2.43
18 19 5.716703 ACCAATTAAAGGATGCAGCTAGTTT 59.283 36.000 0.22 2.42 0.00 2.66
19 20 5.264395 ACCAATTAAAGGATGCAGCTAGTT 58.736 37.500 0.22 0.00 0.00 2.24
20 21 4.860022 ACCAATTAAAGGATGCAGCTAGT 58.140 39.130 0.22 0.00 0.00 2.57
21 22 5.822519 TGTACCAATTAAAGGATGCAGCTAG 59.177 40.000 0.22 0.00 0.00 3.42
22 23 5.750524 TGTACCAATTAAAGGATGCAGCTA 58.249 37.500 0.22 0.00 0.00 3.32
23 24 4.599041 TGTACCAATTAAAGGATGCAGCT 58.401 39.130 0.22 0.00 0.00 4.24
24 25 4.981806 TGTACCAATTAAAGGATGCAGC 57.018 40.909 0.00 0.00 0.00 5.25
25 26 6.769822 AGAGATGTACCAATTAAAGGATGCAG 59.230 38.462 4.48 0.00 0.00 4.41
26 27 6.543465 CAGAGATGTACCAATTAAAGGATGCA 59.457 38.462 4.48 0.00 0.00 3.96
27 28 6.543831 ACAGAGATGTACCAATTAAAGGATGC 59.456 38.462 4.48 0.00 0.00 3.91
28 29 9.613428 TTACAGAGATGTACCAATTAAAGGATG 57.387 33.333 4.48 0.00 0.00 3.51
29 30 9.838339 CTTACAGAGATGTACCAATTAAAGGAT 57.162 33.333 4.48 0.00 0.00 3.24
30 31 8.265055 CCTTACAGAGATGTACCAATTAAAGGA 58.735 37.037 4.48 0.00 0.00 3.36
31 32 8.265055 TCCTTACAGAGATGTACCAATTAAAGG 58.735 37.037 0.00 0.00 0.00 3.11
32 33 9.667107 TTCCTTACAGAGATGTACCAATTAAAG 57.333 33.333 0.00 0.00 0.00 1.85
34 35 9.613428 CATTCCTTACAGAGATGTACCAATTAA 57.387 33.333 0.00 0.00 0.00 1.40
35 36 7.715249 GCATTCCTTACAGAGATGTACCAATTA 59.285 37.037 0.00 0.00 0.00 1.40
36 37 6.543831 GCATTCCTTACAGAGATGTACCAATT 59.456 38.462 0.00 0.00 0.00 2.32
37 38 6.058183 GCATTCCTTACAGAGATGTACCAAT 58.942 40.000 0.00 0.00 0.00 3.16
38 39 5.045942 TGCATTCCTTACAGAGATGTACCAA 60.046 40.000 0.00 0.00 0.00 3.67
39 40 4.469586 TGCATTCCTTACAGAGATGTACCA 59.530 41.667 0.00 0.00 0.00 3.25
40 41 5.023533 TGCATTCCTTACAGAGATGTACC 57.976 43.478 0.00 0.00 0.00 3.34
41 42 5.525378 CCTTGCATTCCTTACAGAGATGTAC 59.475 44.000 0.00 0.00 0.00 2.90
42 43 5.674525 CCTTGCATTCCTTACAGAGATGTA 58.325 41.667 0.00 0.00 0.00 2.29
43 44 4.521146 CCTTGCATTCCTTACAGAGATGT 58.479 43.478 0.00 0.00 0.00 3.06
44 45 3.314635 GCCTTGCATTCCTTACAGAGATG 59.685 47.826 0.00 0.00 0.00 2.90
45 46 3.201708 AGCCTTGCATTCCTTACAGAGAT 59.798 43.478 0.00 0.00 0.00 2.75
46 47 2.573462 AGCCTTGCATTCCTTACAGAGA 59.427 45.455 0.00 0.00 0.00 3.10
47 48 2.941720 GAGCCTTGCATTCCTTACAGAG 59.058 50.000 0.00 0.00 0.00 3.35
48 49 2.356125 GGAGCCTTGCATTCCTTACAGA 60.356 50.000 0.00 0.00 0.00 3.41
49 50 2.019984 GGAGCCTTGCATTCCTTACAG 58.980 52.381 0.00 0.00 0.00 2.74
50 51 1.635487 AGGAGCCTTGCATTCCTTACA 59.365 47.619 4.32 0.00 38.13 2.41
51 52 2.426842 AGGAGCCTTGCATTCCTTAC 57.573 50.000 4.32 0.00 38.13 2.34
52 53 3.117888 CCTAAGGAGCCTTGCATTCCTTA 60.118 47.826 19.74 19.74 46.66 2.69
54 55 1.213926 CCTAAGGAGCCTTGCATTCCT 59.786 52.381 11.94 4.32 43.05 3.36
55 56 1.064389 ACCTAAGGAGCCTTGCATTCC 60.064 52.381 11.94 0.00 37.47 3.01
56 57 2.293170 GACCTAAGGAGCCTTGCATTC 58.707 52.381 11.94 0.19 37.47 2.67
57 58 1.407437 CGACCTAAGGAGCCTTGCATT 60.407 52.381 11.94 0.00 37.47 3.56
58 59 0.179000 CGACCTAAGGAGCCTTGCAT 59.821 55.000 11.94 0.00 37.47 3.96
59 60 1.596934 CGACCTAAGGAGCCTTGCA 59.403 57.895 11.94 0.00 37.47 4.08
60 61 1.815840 GCGACCTAAGGAGCCTTGC 60.816 63.158 11.94 2.68 37.47 4.01
61 62 1.067821 CTAGCGACCTAAGGAGCCTTG 59.932 57.143 11.94 0.00 37.47 3.61
62 63 1.342175 ACTAGCGACCTAAGGAGCCTT 60.342 52.381 7.01 7.01 39.83 4.35
63 64 0.259356 ACTAGCGACCTAAGGAGCCT 59.741 55.000 0.00 0.00 32.55 4.58
64 65 0.386113 CACTAGCGACCTAAGGAGCC 59.614 60.000 0.00 0.00 32.55 4.70
65 66 0.249114 GCACTAGCGACCTAAGGAGC 60.249 60.000 0.00 0.00 0.00 4.70
66 67 0.386113 GGCACTAGCGACCTAAGGAG 59.614 60.000 0.00 0.00 43.41 3.69
67 68 0.033405 AGGCACTAGCGACCTAAGGA 60.033 55.000 0.00 0.00 43.41 3.36
68 69 0.103208 CAGGCACTAGCGACCTAAGG 59.897 60.000 0.00 0.00 43.41 2.69
69 70 0.818296 ACAGGCACTAGCGACCTAAG 59.182 55.000 0.00 0.00 43.41 2.18
70 71 0.815734 GACAGGCACTAGCGACCTAA 59.184 55.000 0.00 0.00 43.41 2.69
71 72 0.323087 TGACAGGCACTAGCGACCTA 60.323 55.000 0.00 0.00 43.41 3.08
72 73 1.185618 TTGACAGGCACTAGCGACCT 61.186 55.000 0.00 0.00 43.41 3.85
73 74 0.320421 TTTGACAGGCACTAGCGACC 60.320 55.000 0.00 0.00 43.41 4.79
74 75 1.071605 CTTTGACAGGCACTAGCGAC 58.928 55.000 0.00 0.00 43.41 5.19
75 76 0.966179 TCTTTGACAGGCACTAGCGA 59.034 50.000 0.00 0.00 43.41 4.93
76 77 1.795768 TTCTTTGACAGGCACTAGCG 58.204 50.000 0.00 0.00 43.41 4.26
77 78 6.317391 AGAAATATTCTTTGACAGGCACTAGC 59.683 38.462 0.00 0.00 36.36 3.42
78 79 7.678218 GCAGAAATATTCTTTGACAGGCACTAG 60.678 40.741 0.00 0.00 38.11 2.57
79 80 6.094048 GCAGAAATATTCTTTGACAGGCACTA 59.906 38.462 0.00 0.00 38.11 2.74
80 81 5.105997 GCAGAAATATTCTTTGACAGGCACT 60.106 40.000 0.00 0.00 38.11 4.40
81 82 5.098211 GCAGAAATATTCTTTGACAGGCAC 58.902 41.667 0.00 0.00 38.11 5.01
82 83 4.142622 CGCAGAAATATTCTTTGACAGGCA 60.143 41.667 0.00 0.00 38.11 4.75
83 84 4.346129 CGCAGAAATATTCTTTGACAGGC 58.654 43.478 0.00 0.00 38.11 4.85
84 85 4.201950 CCCGCAGAAATATTCTTTGACAGG 60.202 45.833 0.00 0.00 38.11 4.00
85 86 4.201950 CCCCGCAGAAATATTCTTTGACAG 60.202 45.833 0.00 0.00 38.11 3.51
86 87 3.694072 CCCCGCAGAAATATTCTTTGACA 59.306 43.478 0.00 0.00 38.11 3.58
87 88 3.694566 ACCCCGCAGAAATATTCTTTGAC 59.305 43.478 0.00 0.00 38.11 3.18
88 89 3.963129 ACCCCGCAGAAATATTCTTTGA 58.037 40.909 0.00 0.00 38.11 2.69
89 90 4.423732 CAACCCCGCAGAAATATTCTTTG 58.576 43.478 0.00 0.00 38.11 2.77
90 91 3.447229 CCAACCCCGCAGAAATATTCTTT 59.553 43.478 0.00 0.00 38.11 2.52
91 92 3.023832 CCAACCCCGCAGAAATATTCTT 58.976 45.455 0.00 0.00 38.11 2.52
92 93 2.241176 TCCAACCCCGCAGAAATATTCT 59.759 45.455 0.00 0.00 41.70 2.40
93 94 2.357952 GTCCAACCCCGCAGAAATATTC 59.642 50.000 0.00 0.00 0.00 1.75
94 95 2.291282 TGTCCAACCCCGCAGAAATATT 60.291 45.455 0.00 0.00 0.00 1.28
95 96 1.283613 TGTCCAACCCCGCAGAAATAT 59.716 47.619 0.00 0.00 0.00 1.28
96 97 0.693622 TGTCCAACCCCGCAGAAATA 59.306 50.000 0.00 0.00 0.00 1.40
97 98 0.039618 ATGTCCAACCCCGCAGAAAT 59.960 50.000 0.00 0.00 0.00 2.17
98 99 0.893270 CATGTCCAACCCCGCAGAAA 60.893 55.000 0.00 0.00 0.00 2.52
99 100 1.303236 CATGTCCAACCCCGCAGAA 60.303 57.895 0.00 0.00 0.00 3.02
100 101 2.350895 CATGTCCAACCCCGCAGA 59.649 61.111 0.00 0.00 0.00 4.26
101 102 2.034066 ACATGTCCAACCCCGCAG 59.966 61.111 0.00 0.00 0.00 5.18
102 103 2.282110 CACATGTCCAACCCCGCA 60.282 61.111 0.00 0.00 0.00 5.69
103 104 3.061848 CCACATGTCCAACCCCGC 61.062 66.667 0.00 0.00 0.00 6.13
104 105 1.674322 GTCCACATGTCCAACCCCG 60.674 63.158 0.00 0.00 0.00 5.73
105 106 0.893727 GTGTCCACATGTCCAACCCC 60.894 60.000 0.00 0.00 0.00 4.95
106 107 0.179004 TGTGTCCACATGTCCAACCC 60.179 55.000 0.00 0.00 36.21 4.11
107 108 3.412722 TGTGTCCACATGTCCAACC 57.587 52.632 0.00 0.00 36.21 3.77
116 117 5.154418 TCTCCATATATCCATGTGTCCACA 58.846 41.667 2.09 2.09 46.44 4.17
117 118 5.745312 TCTCCATATATCCATGTGTCCAC 57.255 43.478 0.00 0.00 0.00 4.02
118 119 6.084060 TCTTCTCCATATATCCATGTGTCCA 58.916 40.000 0.00 0.00 0.00 4.02
119 120 6.611613 TCTTCTCCATATATCCATGTGTCC 57.388 41.667 0.00 0.00 0.00 4.02
130 131 9.090103 ACGACCAGAAATATTCTTCTCCATATA 57.910 33.333 0.00 0.00 38.11 0.86
131 132 7.875041 CACGACCAGAAATATTCTTCTCCATAT 59.125 37.037 0.00 0.00 38.11 1.78
132 133 7.210174 CACGACCAGAAATATTCTTCTCCATA 58.790 38.462 0.00 0.00 38.11 2.74
133 134 6.051717 CACGACCAGAAATATTCTTCTCCAT 58.948 40.000 0.00 0.00 38.11 3.41
134 135 5.419542 CACGACCAGAAATATTCTTCTCCA 58.580 41.667 0.00 0.00 38.11 3.86
135 136 4.811557 CCACGACCAGAAATATTCTTCTCC 59.188 45.833 0.00 0.00 38.11 3.71
136 137 4.811557 CCCACGACCAGAAATATTCTTCTC 59.188 45.833 0.00 0.00 38.11 2.87
137 138 4.384208 CCCCACGACCAGAAATATTCTTCT 60.384 45.833 0.00 0.00 38.11 2.85
138 139 3.877508 CCCCACGACCAGAAATATTCTTC 59.122 47.826 0.00 0.00 38.11 2.87
139 140 3.265995 ACCCCACGACCAGAAATATTCTT 59.734 43.478 0.00 0.00 38.11 2.52
140 141 2.844348 ACCCCACGACCAGAAATATTCT 59.156 45.455 0.00 0.00 41.70 2.40
141 142 2.943033 CACCCCACGACCAGAAATATTC 59.057 50.000 0.00 0.00 0.00 1.75
142 143 2.356741 CCACCCCACGACCAGAAATATT 60.357 50.000 0.00 0.00 0.00 1.28
143 144 1.211949 CCACCCCACGACCAGAAATAT 59.788 52.381 0.00 0.00 0.00 1.28
144 145 0.616371 CCACCCCACGACCAGAAATA 59.384 55.000 0.00 0.00 0.00 1.40
145 146 1.131303 TCCACCCCACGACCAGAAAT 61.131 55.000 0.00 0.00 0.00 2.17
146 147 1.766864 TCCACCCCACGACCAGAAA 60.767 57.895 0.00 0.00 0.00 2.52
147 148 2.122769 TCCACCCCACGACCAGAA 60.123 61.111 0.00 0.00 0.00 3.02
148 149 2.920912 GTCCACCCCACGACCAGA 60.921 66.667 0.00 0.00 0.00 3.86
149 150 1.261938 TATGTCCACCCCACGACCAG 61.262 60.000 0.00 0.00 0.00 4.00
150 151 0.619255 ATATGTCCACCCCACGACCA 60.619 55.000 0.00 0.00 0.00 4.02
151 152 0.179056 CATATGTCCACCCCACGACC 60.179 60.000 0.00 0.00 0.00 4.79
152 153 0.179056 CCATATGTCCACCCCACGAC 60.179 60.000 1.24 0.00 0.00 4.34
153 154 0.325765 TCCATATGTCCACCCCACGA 60.326 55.000 1.24 0.00 0.00 4.35
154 155 0.106708 CTCCATATGTCCACCCCACG 59.893 60.000 1.24 0.00 0.00 4.94
155 156 1.507140 TCTCCATATGTCCACCCCAC 58.493 55.000 1.24 0.00 0.00 4.61
156 157 2.057140 CATCTCCATATGTCCACCCCA 58.943 52.381 1.24 0.00 0.00 4.96
179 180 3.769739 ACACTACTTGCAGGTGATGAA 57.230 42.857 12.40 0.00 35.28 2.57
202 203 1.876799 CACATTCGCTACCACCAACAA 59.123 47.619 0.00 0.00 0.00 2.83
223 224 6.349300 TGATTAGGCTGTCTAATTCCTTGAC 58.651 40.000 15.11 2.53 45.78 3.18
293 294 3.559238 AAACCTTCATTAGCAGCAACG 57.441 42.857 0.00 0.00 0.00 4.10
312 313 4.584325 GCTAGCCCACATCCATTCAATTAA 59.416 41.667 2.29 0.00 0.00 1.40
313 314 4.144297 GCTAGCCCACATCCATTCAATTA 58.856 43.478 2.29 0.00 0.00 1.40
317 318 0.183492 GGCTAGCCCACATCCATTCA 59.817 55.000 24.19 0.00 0.00 2.57
333 334 3.958860 AGCAAAGTCAGGCGGGCT 61.959 61.111 0.00 0.00 34.54 5.19
344 345 5.632347 GTCCTTGAATTCATCAACAGCAAAG 59.368 40.000 9.40 0.00 43.08 2.77
345 346 5.302568 AGTCCTTGAATTCATCAACAGCAAA 59.697 36.000 9.40 0.00 43.08 3.68
396 397 5.732528 GCAGTAGCAATCCATTGTTCATCTG 60.733 44.000 1.37 6.42 41.58 2.90
413 417 2.751166 TTCTGTCCTCTTGCAGTAGC 57.249 50.000 0.00 0.00 42.57 3.58
418 422 4.356405 TCTTTGATTCTGTCCTCTTGCA 57.644 40.909 0.00 0.00 0.00 4.08
427 431 7.148407 CGCCAATACTAGTTTCTTTGATTCTGT 60.148 37.037 0.00 0.00 0.00 3.41
431 435 5.944007 ACCGCCAATACTAGTTTCTTTGATT 59.056 36.000 0.00 0.00 0.00 2.57
435 439 5.557866 AGAACCGCCAATACTAGTTTCTTT 58.442 37.500 0.00 0.00 0.00 2.52
439 443 6.470278 AGTAAAGAACCGCCAATACTAGTTT 58.530 36.000 0.00 0.00 0.00 2.66
448 452 1.061546 AGGGAGTAAAGAACCGCCAA 58.938 50.000 0.00 0.00 0.00 4.52
452 456 3.626217 GCCAATAAGGGAGTAAAGAACCG 59.374 47.826 0.00 0.00 38.09 4.44
454 458 7.054751 ACATAGCCAATAAGGGAGTAAAGAAC 58.945 38.462 0.00 0.00 38.09 3.01
462 466 6.174720 TCTGTAACATAGCCAATAAGGGAG 57.825 41.667 0.00 0.00 38.09 4.30
468 472 7.434492 GTCTTAGCTCTGTAACATAGCCAATA 58.566 38.462 0.00 0.00 34.73 1.90
472 476 4.202030 ACGTCTTAGCTCTGTAACATAGCC 60.202 45.833 0.00 0.00 34.73 3.93
473 477 4.922719 ACGTCTTAGCTCTGTAACATAGC 58.077 43.478 0.00 0.00 34.46 2.97
474 478 5.230306 GCAACGTCTTAGCTCTGTAACATAG 59.770 44.000 0.00 0.00 0.00 2.23
515 522 4.855715 TTCGATCCTAGTGATGGACATC 57.144 45.455 5.37 5.37 37.86 3.06
516 523 4.221703 GGATTCGATCCTAGTGATGGACAT 59.778 45.833 6.63 0.00 46.19 3.06
517 524 3.574396 GGATTCGATCCTAGTGATGGACA 59.426 47.826 6.63 0.00 46.19 4.02
530 537 0.373716 GTTGCCGTGTGGATTCGATC 59.626 55.000 0.00 0.00 37.49 3.69
534 541 1.579429 GTGGTTGCCGTGTGGATTC 59.421 57.895 0.00 0.00 37.49 2.52
535 542 2.258013 CGTGGTTGCCGTGTGGATT 61.258 57.895 0.00 0.00 37.49 3.01
538 545 3.206246 AACGTGGTTGCCGTGTGG 61.206 61.111 0.00 0.00 38.77 4.17
540 547 3.206246 CCAACGTGGTTGCCGTGT 61.206 61.111 3.03 0.00 41.62 4.49
546 553 2.600173 ATGGGGCCAACGTGGTTG 60.600 61.111 4.39 1.59 42.49 3.77
548 555 1.493854 TAAGATGGGGCCAACGTGGT 61.494 55.000 4.39 0.00 40.46 4.16
552 559 2.017049 CTCTTTAAGATGGGGCCAACG 58.983 52.381 4.39 0.00 0.00 4.10
562 569 4.220821 TCTCAACTCGGCACTCTTTAAGAT 59.779 41.667 0.00 0.00 0.00 2.40
563 570 3.572682 TCTCAACTCGGCACTCTTTAAGA 59.427 43.478 0.00 0.00 0.00 2.10
570 598 0.389166 CACCTCTCAACTCGGCACTC 60.389 60.000 0.00 0.00 0.00 3.51
600 628 1.745653 GGGAGCAGCAAATACAGAACC 59.254 52.381 0.00 0.00 0.00 3.62
602 630 2.224744 TGTGGGAGCAGCAAATACAGAA 60.225 45.455 0.00 0.00 0.00 3.02
624 652 8.617290 ACTTCATTACTTCCGTCATTACTTTT 57.383 30.769 0.00 0.00 0.00 2.27
630 661 7.687941 ATTCAACTTCATTACTTCCGTCATT 57.312 32.000 0.00 0.00 0.00 2.57
693 730 2.288518 TGCATATATAGCGTGCCGTTGA 60.289 45.455 4.72 0.00 38.06 3.18
697 734 2.092681 CAGTTGCATATATAGCGTGCCG 59.907 50.000 4.72 0.00 38.06 5.69
707 744 8.482943 AGTTGTATTGTACTCCAGTTGCATATA 58.517 33.333 0.00 0.00 0.00 0.86
713 750 6.460781 TGGTAGTTGTATTGTACTCCAGTTG 58.539 40.000 0.00 0.00 0.00 3.16
729 766 7.885297 TGAAAGGAATCTTCATTTGGTAGTTG 58.115 34.615 7.24 0.00 40.75 3.16
731 768 8.477419 TTTGAAAGGAATCTTCATTTGGTAGT 57.523 30.769 7.24 0.00 40.75 2.73
806 843 2.076863 GTCATATGTGCGGATAAGGGC 58.923 52.381 1.90 0.00 0.00 5.19
983 1023 7.545965 GCGCTAACATCTTACTTCCACATATAT 59.454 37.037 0.00 0.00 0.00 0.86
984 1024 6.866770 GCGCTAACATCTTACTTCCACATATA 59.133 38.462 0.00 0.00 0.00 0.86
1067 1109 1.098050 CTCTGGGTATTGCTTGGCAC 58.902 55.000 0.00 0.00 38.71 5.01
1155 1206 0.326264 AGTGCCTTGGCTTGTAGAGG 59.674 55.000 13.18 0.00 0.00 3.69
1264 1319 8.861086 AGAAACTAAGATGACTAGAACACTGAA 58.139 33.333 0.00 0.00 0.00 3.02
1280 1336 8.712363 CGATGATGAAGAAACAAGAAACTAAGA 58.288 33.333 0.00 0.00 0.00 2.10
1288 1345 4.020218 AGGGACGATGATGAAGAAACAAGA 60.020 41.667 0.00 0.00 0.00 3.02
1289 1346 4.093998 CAGGGACGATGATGAAGAAACAAG 59.906 45.833 0.00 0.00 0.00 3.16
1290 1347 4.002982 CAGGGACGATGATGAAGAAACAA 58.997 43.478 0.00 0.00 0.00 2.83
1291 1348 3.007940 ACAGGGACGATGATGAAGAAACA 59.992 43.478 0.00 0.00 0.00 2.83
1311 1375 6.888088 TCAATTACTGGCAGTAGACTAGTACA 59.112 38.462 25.00 9.59 31.47 2.90
1343 1407 7.624360 TGCCAGTTAGATAATTGGTTAACTG 57.376 36.000 19.97 19.97 46.27 3.16
1376 1444 3.214328 GGTGGATTACCTACAATGCAGG 58.786 50.000 0.00 0.00 46.51 4.85
1462 1533 8.498054 AAACACAACCATATATCACAGAGAAG 57.502 34.615 0.00 0.00 0.00 2.85
1486 1558 9.717942 CAACATGATTTTGGGTAGGAAAAATAA 57.282 29.630 0.00 0.00 36.40 1.40
1579 1653 3.254014 AACAGCACGCCGACAATGC 62.254 57.895 0.00 0.00 39.74 3.56
1838 1929 5.163804 ACACGCGCAATCAAATTATTACAGA 60.164 36.000 5.73 0.00 0.00 3.41
1966 2058 4.642885 TCGTTTGGAAGTTTGAAGGTGATT 59.357 37.500 0.00 0.00 0.00 2.57
1968 2060 3.611970 TCGTTTGGAAGTTTGAAGGTGA 58.388 40.909 0.00 0.00 0.00 4.02
1983 2075 4.430007 TCGGATACTTCCAATCTCGTTTG 58.570 43.478 0.00 0.00 42.74 2.93
2000 2092 5.614324 TCAAATGTCTCCAAGTATCGGAT 57.386 39.130 0.00 0.00 0.00 4.18
2055 2147 9.167311 GAAGTAACCTCAACAGATTGACAATAT 57.833 33.333 0.00 0.00 40.01 1.28
2080 2173 0.976073 CCCTTAGAAGGCGGAGGTGA 60.976 60.000 2.50 0.00 45.10 4.02
2093 2186 4.864704 GGAGCAGAATAGACTCCCTTAG 57.135 50.000 0.00 0.00 43.54 2.18
2108 2201 0.895530 TAGGGAACTTCGTGGAGCAG 59.104 55.000 0.00 0.00 43.67 4.24
2112 2205 2.232941 GTCATGTAGGGAACTTCGTGGA 59.767 50.000 0.00 0.00 42.93 4.02
2126 2219 3.193479 AGTGTGCGAAGAGATGTCATGTA 59.807 43.478 0.00 0.00 0.00 2.29
2127 2220 2.028658 AGTGTGCGAAGAGATGTCATGT 60.029 45.455 0.00 0.00 0.00 3.21
2141 2234 4.541779 GGATCAAGATACTCTAGTGTGCG 58.458 47.826 7.70 0.00 0.00 5.34
2146 2239 4.156477 GGCTGGGATCAAGATACTCTAGT 58.844 47.826 0.00 0.00 0.00 2.57
2149 2242 3.051940 TGGCTGGGATCAAGATACTCT 57.948 47.619 0.00 0.00 0.00 3.24
2151 2244 3.749954 GCAATGGCTGGGATCAAGATACT 60.750 47.826 0.00 0.00 36.96 2.12
2169 2262 5.534207 TGGTCAAATTTCTTGTGAGCAAT 57.466 34.783 6.52 0.00 44.35 3.56
2181 2274 5.256474 AGATCACGGAGATTGGTCAAATTT 58.744 37.500 0.00 0.00 37.00 1.82
2182 2275 4.848357 AGATCACGGAGATTGGTCAAATT 58.152 39.130 0.00 0.00 37.00 1.82
2189 2282 2.158986 AGCTGAAGATCACGGAGATTGG 60.159 50.000 0.00 0.00 37.00 3.16
2193 2286 1.107114 GGAGCTGAAGATCACGGAGA 58.893 55.000 0.00 0.00 30.87 3.71
2194 2287 0.103937 GGGAGCTGAAGATCACGGAG 59.896 60.000 0.00 0.00 30.87 4.63
2195 2288 1.330655 GGGGAGCTGAAGATCACGGA 61.331 60.000 0.00 0.00 34.05 4.69
2196 2289 1.144936 GGGGAGCTGAAGATCACGG 59.855 63.158 0.00 0.00 34.05 4.94
2197 2290 0.179089 CAGGGGAGCTGAAGATCACG 60.179 60.000 0.00 0.00 34.05 4.35
2198 2291 0.908198 ACAGGGGAGCTGAAGATCAC 59.092 55.000 0.00 0.00 32.09 3.06
2199 2292 1.556911 GAACAGGGGAGCTGAAGATCA 59.443 52.381 0.00 0.00 30.87 2.92
2200 2293 1.836802 AGAACAGGGGAGCTGAAGATC 59.163 52.381 0.00 0.00 0.00 2.75
2201 2294 1.963985 AGAACAGGGGAGCTGAAGAT 58.036 50.000 0.00 0.00 0.00 2.40
2202 2295 2.623418 TAGAACAGGGGAGCTGAAGA 57.377 50.000 0.00 0.00 0.00 2.87
2203 2296 2.744494 GCATAGAACAGGGGAGCTGAAG 60.744 54.545 0.00 0.00 0.00 3.02
2204 2297 1.210478 GCATAGAACAGGGGAGCTGAA 59.790 52.381 0.00 0.00 0.00 3.02
2205 2298 0.833287 GCATAGAACAGGGGAGCTGA 59.167 55.000 0.00 0.00 0.00 4.26
2206 2299 3.393472 GCATAGAACAGGGGAGCTG 57.607 57.895 0.00 0.00 0.00 4.24


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

AutoCloner maintained by Alex Coulton.