Multiple sequence alignment - TraesCS2A01G579900

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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 TraesCS2A01G579900 chr2A 100.000 4970 0 0 1 4970 772370145 772375114 0.000000e+00 9178.0
1 TraesCS2A01G579900 chr2A 93.663 2083 102 15 2900 4970 779977619 779975555 0.000000e+00 3088.0
2 TraesCS2A01G579900 chr2A 94.265 1081 38 12 883 1954 779991716 779990651 0.000000e+00 1631.0
3 TraesCS2A01G579900 chr2A 84.856 383 30 10 292 649 779992097 779991718 1.320000e-95 361.0
4 TraesCS2A01G579900 chr2B 89.138 2145 197 17 1481 3592 787952219 787954360 0.000000e+00 2638.0
5 TraesCS2A01G579900 chr2B 82.087 709 107 8 3884 4587 787954373 787955066 5.540000e-164 588.0
6 TraesCS2A01G579900 chr2B 86.301 511 59 6 604 1114 787951347 787951846 3.380000e-151 545.0
7 TraesCS2A01G579900 chr2B 91.228 57 5 0 141 197 110139740 110139684 1.480000e-10 78.7
8 TraesCS2A01G579900 chr2D 91.065 1578 106 12 2332 3888 650748167 650749730 0.000000e+00 2100.0
9 TraesCS2A01G579900 chr2D 92.254 1291 77 9 3694 4970 650749473 650750754 0.000000e+00 1808.0
10 TraesCS2A01G579900 chr2D 91.275 1043 66 10 1305 2337 650724864 650725891 0.000000e+00 1399.0
11 TraesCS2A01G579900 chr2D 89.385 650 53 7 341 977 650717326 650717972 0.000000e+00 804.0
12 TraesCS2A01G579900 chr2D 81.522 920 151 11 3727 4645 650826825 650825924 0.000000e+00 739.0
13 TraesCS2A01G579900 chr2D 81.735 657 91 9 3319 3951 650827627 650826976 5.700000e-144 521.0
14 TraesCS2A01G579900 chr2D 71.245 1012 242 36 1658 2647 635808421 635807437 1.400000e-50 211.0
15 TraesCS2A01G579900 chr2D 93.590 78 5 0 4752 4829 650825869 650825792 3.140000e-22 117.0
16 TraesCS2A01G579900 chrUn 73.732 1222 246 64 1484 2658 312470625 312469432 4.630000e-110 409.0
17 TraesCS2A01G579900 chrUn 89.062 64 6 1 3334 3397 47543511 47543573 1.480000e-10 78.7
18 TraesCS2A01G579900 chr7D 73.468 1240 266 50 1658 2865 608085661 608086869 4.630000e-110 409.0
19 TraesCS2A01G579900 chr7B 73.732 1222 246 64 1484 2658 693340250 693339057 4.630000e-110 409.0
20 TraesCS2A01G579900 chr7B 72.376 1448 304 76 1487 2868 697607212 697605795 2.190000e-98 370.0
21 TraesCS2A01G579900 chr7B 72.815 1247 262 60 1670 2865 697519015 697520235 2.200000e-93 353.0
22 TraesCS2A01G579900 chr7B 73.255 1017 202 59 1670 2648 695373518 695372534 1.740000e-79 307.0
23 TraesCS2A01G579900 chr7B 73.981 319 68 13 647 959 697432770 697432461 1.130000e-21 115.0
24 TraesCS2A01G579900 chr7B 77.368 190 33 9 775 959 695917274 695917090 2.450000e-18 104.0
25 TraesCS2A01G579900 chr7B 73.118 279 61 13 674 945 685087613 685087342 2.460000e-13 87.9
26 TraesCS2A01G579900 chr4A 75.662 793 165 24 1976 2754 729292887 729292109 2.190000e-98 370.0
27 TraesCS2A01G579900 chr4A 77.706 619 112 23 2019 2622 731043557 731042950 6.120000e-94 355.0
28 TraesCS2A01G579900 chr4A 74.648 781 174 20 2030 2798 730353210 730352442 1.730000e-84 324.0
29 TraesCS2A01G579900 chr7A 77.414 580 102 22 2307 2866 700062599 700063169 8.030000e-83 318.0
30 TraesCS2A01G579900 chr7A 74.460 278 55 13 674 944 700055286 700055554 6.800000e-19 106.0
31 TraesCS2A01G579900 chr7A 73.448 290 69 8 674 959 700112418 700112133 8.800000e-18 102.0
32 TraesCS2A01G579900 chr5B 80.597 268 48 3 690 955 711391673 711391938 2.350000e-48 204.0
33 TraesCS2A01G579900 chr3A 85.057 87 12 1 108 193 128134504 128134590 2.460000e-13 87.9


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 TraesCS2A01G579900 chr2A 772370145 772375114 4969 False 9178 9178 100.000000 1 4970 1 chr2A.!!$F1 4969
1 TraesCS2A01G579900 chr2A 779975555 779977619 2064 True 3088 3088 93.663000 2900 4970 1 chr2A.!!$R1 2070
2 TraesCS2A01G579900 chr2A 779990651 779992097 1446 True 996 1631 89.560500 292 1954 2 chr2A.!!$R2 1662
3 TraesCS2A01G579900 chr2B 787951347 787955066 3719 False 1257 2638 85.842000 604 4587 3 chr2B.!!$F1 3983
4 TraesCS2A01G579900 chr2D 650748167 650750754 2587 False 1954 2100 91.659500 2332 4970 2 chr2D.!!$F3 2638
5 TraesCS2A01G579900 chr2D 650724864 650725891 1027 False 1399 1399 91.275000 1305 2337 1 chr2D.!!$F2 1032
6 TraesCS2A01G579900 chr2D 650717326 650717972 646 False 804 804 89.385000 341 977 1 chr2D.!!$F1 636
7 TraesCS2A01G579900 chr2D 650825792 650827627 1835 True 459 739 85.615667 3319 4829 3 chr2D.!!$R2 1510
8 TraesCS2A01G579900 chr2D 635807437 635808421 984 True 211 211 71.245000 1658 2647 1 chr2D.!!$R1 989
9 TraesCS2A01G579900 chrUn 312469432 312470625 1193 True 409 409 73.732000 1484 2658 1 chrUn.!!$R1 1174
10 TraesCS2A01G579900 chr7D 608085661 608086869 1208 False 409 409 73.468000 1658 2865 1 chr7D.!!$F1 1207
11 TraesCS2A01G579900 chr7B 693339057 693340250 1193 True 409 409 73.732000 1484 2658 1 chr7B.!!$R2 1174
12 TraesCS2A01G579900 chr7B 697605795 697607212 1417 True 370 370 72.376000 1487 2868 1 chr7B.!!$R6 1381
13 TraesCS2A01G579900 chr7B 697519015 697520235 1220 False 353 353 72.815000 1670 2865 1 chr7B.!!$F1 1195
14 TraesCS2A01G579900 chr7B 695372534 695373518 984 True 307 307 73.255000 1670 2648 1 chr7B.!!$R3 978
15 TraesCS2A01G579900 chr4A 729292109 729292887 778 True 370 370 75.662000 1976 2754 1 chr4A.!!$R1 778
16 TraesCS2A01G579900 chr4A 731042950 731043557 607 True 355 355 77.706000 2019 2622 1 chr4A.!!$R3 603
17 TraesCS2A01G579900 chr4A 730352442 730353210 768 True 324 324 74.648000 2030 2798 1 chr4A.!!$R2 768
18 TraesCS2A01G579900 chr7A 700062599 700063169 570 False 318 318 77.414000 2307 2866 1 chr7A.!!$F2 559

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
226 227 0.037326 CAGGTATGCCACACGACACT 60.037 55.000 1.54 0.0 37.19 3.55 F
1078 1111 0.449388 CGTTTGCCATCCTCAAGCTC 59.551 55.000 0.00 0.0 0.00 4.09 F
2262 2449 1.945394 CATGCACTTGGAGATAGGCAC 59.055 52.381 0.00 0.0 33.67 5.01 F
3546 3786 0.846693 GGATGGTGGGTAGGCAGAAT 59.153 55.000 0.00 0.0 0.00 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1826 1974 3.025322 TGTCTTTTTCTTCCTGGGCAA 57.975 42.857 0.00 0.0 0.00 4.52 R
2276 2463 1.067295 ATTCCAGAGTGTGCTCCCAA 58.933 50.000 0.00 0.0 42.59 4.12 R
3960 4580 0.859232 GCGCTCGAGTTCAAACTTCA 59.141 50.000 15.13 0.0 39.88 3.02 R
4666 5309 0.036105 TCAGGCATGCTCACGTCATT 60.036 50.000 18.92 0.0 0.00 2.57 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
24 25 2.032981 GCCCGAAGCACATATTGGG 58.967 57.895 0.00 0.00 42.97 4.12
25 26 1.455383 GCCCGAAGCACATATTGGGG 61.455 60.000 1.74 1.74 45.72 4.96
26 27 1.455383 CCCGAAGCACATATTGGGGC 61.455 60.000 0.00 0.00 38.62 5.80
27 28 1.648720 CGAAGCACATATTGGGGCG 59.351 57.895 0.00 0.00 0.00 6.13
28 29 1.785041 CGAAGCACATATTGGGGCGG 61.785 60.000 0.00 0.00 0.00 6.13
29 30 1.455383 GAAGCACATATTGGGGCGGG 61.455 60.000 0.00 0.00 0.00 6.13
30 31 3.605664 GCACATATTGGGGCGGGC 61.606 66.667 0.00 0.00 0.00 6.13
31 32 2.912025 CACATATTGGGGCGGGCC 60.912 66.667 13.01 13.01 0.00 5.80
32 33 3.103213 ACATATTGGGGCGGGCCT 61.103 61.111 20.88 3.09 36.10 5.19
33 34 1.772567 ACATATTGGGGCGGGCCTA 60.773 57.895 20.88 12.21 36.10 3.93
34 35 1.002134 CATATTGGGGCGGGCCTAG 60.002 63.158 20.88 0.00 36.10 3.02
35 36 2.231380 ATATTGGGGCGGGCCTAGG 61.231 63.158 20.88 3.67 36.10 3.02
43 44 2.766651 CGGGCCTAGGCTTGGGTA 60.767 66.667 32.18 0.00 41.60 3.69
44 45 2.147387 CGGGCCTAGGCTTGGGTAT 61.147 63.158 32.18 0.00 41.60 2.73
45 46 1.705997 CGGGCCTAGGCTTGGGTATT 61.706 60.000 32.18 0.00 41.60 1.89
46 47 0.556258 GGGCCTAGGCTTGGGTATTT 59.444 55.000 32.18 0.00 41.60 1.40
47 48 1.692411 GGCCTAGGCTTGGGTATTTG 58.308 55.000 32.18 0.00 41.60 2.32
48 49 1.692411 GCCTAGGCTTGGGTATTTGG 58.308 55.000 27.17 0.00 38.26 3.28
49 50 1.063942 GCCTAGGCTTGGGTATTTGGT 60.064 52.381 27.17 0.00 38.26 3.67
50 51 2.654863 CCTAGGCTTGGGTATTTGGTG 58.345 52.381 7.14 0.00 0.00 4.17
51 52 2.025321 CCTAGGCTTGGGTATTTGGTGT 60.025 50.000 7.14 0.00 0.00 4.16
52 53 2.694616 AGGCTTGGGTATTTGGTGTT 57.305 45.000 0.00 0.00 0.00 3.32
53 54 2.970987 AGGCTTGGGTATTTGGTGTTT 58.029 42.857 0.00 0.00 0.00 2.83
54 55 3.313791 AGGCTTGGGTATTTGGTGTTTT 58.686 40.909 0.00 0.00 0.00 2.43
55 56 4.484912 AGGCTTGGGTATTTGGTGTTTTA 58.515 39.130 0.00 0.00 0.00 1.52
56 57 4.902448 AGGCTTGGGTATTTGGTGTTTTAA 59.098 37.500 0.00 0.00 0.00 1.52
57 58 5.367060 AGGCTTGGGTATTTGGTGTTTTAAA 59.633 36.000 0.00 0.00 0.00 1.52
58 59 5.699001 GGCTTGGGTATTTGGTGTTTTAAAG 59.301 40.000 0.00 0.00 0.00 1.85
59 60 6.463190 GGCTTGGGTATTTGGTGTTTTAAAGA 60.463 38.462 0.00 0.00 0.00 2.52
60 61 6.987404 GCTTGGGTATTTGGTGTTTTAAAGAA 59.013 34.615 0.00 0.00 0.00 2.52
61 62 7.496263 GCTTGGGTATTTGGTGTTTTAAAGAAA 59.504 33.333 0.00 0.00 0.00 2.52
62 63 8.950208 TTGGGTATTTGGTGTTTTAAAGAAAG 57.050 30.769 0.00 0.00 0.00 2.62
63 64 7.501844 TGGGTATTTGGTGTTTTAAAGAAAGG 58.498 34.615 0.00 0.00 0.00 3.11
64 65 6.932400 GGGTATTTGGTGTTTTAAAGAAAGGG 59.068 38.462 0.00 0.00 0.00 3.95
65 66 6.425721 GGTATTTGGTGTTTTAAAGAAAGGGC 59.574 38.462 0.00 0.00 0.00 5.19
66 67 4.409718 TTGGTGTTTTAAAGAAAGGGCC 57.590 40.909 0.00 0.00 0.00 5.80
67 68 3.648739 TGGTGTTTTAAAGAAAGGGCCT 58.351 40.909 0.00 0.00 0.00 5.19
68 69 3.386402 TGGTGTTTTAAAGAAAGGGCCTG 59.614 43.478 6.92 0.00 0.00 4.85
69 70 3.244078 GGTGTTTTAAAGAAAGGGCCTGG 60.244 47.826 6.92 0.00 0.00 4.45
70 71 2.367241 TGTTTTAAAGAAAGGGCCTGGC 59.633 45.455 6.92 11.05 0.00 4.85
94 95 4.404691 CCCAGCGGCTTTTTCTCT 57.595 55.556 0.00 0.00 0.00 3.10
95 96 1.878775 CCCAGCGGCTTTTTCTCTG 59.121 57.895 0.00 0.00 0.00 3.35
96 97 0.606401 CCCAGCGGCTTTTTCTCTGA 60.606 55.000 0.00 0.00 0.00 3.27
97 98 0.519077 CCAGCGGCTTTTTCTCTGAC 59.481 55.000 0.00 0.00 0.00 3.51
98 99 0.164647 CAGCGGCTTTTTCTCTGACG 59.835 55.000 0.00 0.00 35.02 4.35
99 100 0.951040 AGCGGCTTTTTCTCTGACGG 60.951 55.000 0.00 0.00 32.16 4.79
100 101 1.912371 GCGGCTTTTTCTCTGACGGG 61.912 60.000 0.00 0.00 32.16 5.28
101 102 1.876664 GGCTTTTTCTCTGACGGGC 59.123 57.895 0.00 0.00 0.00 6.13
102 103 0.606673 GGCTTTTTCTCTGACGGGCT 60.607 55.000 0.00 0.00 0.00 5.19
103 104 0.519077 GCTTTTTCTCTGACGGGCTG 59.481 55.000 0.00 0.00 0.00 4.85
104 105 1.160137 CTTTTTCTCTGACGGGCTGG 58.840 55.000 0.00 0.00 0.00 4.85
105 106 0.250727 TTTTTCTCTGACGGGCTGGG 60.251 55.000 0.00 0.00 0.00 4.45
106 107 1.415672 TTTTCTCTGACGGGCTGGGT 61.416 55.000 0.00 0.00 0.00 4.51
107 108 1.415672 TTTCTCTGACGGGCTGGGTT 61.416 55.000 0.00 0.00 0.00 4.11
108 109 1.415672 TTCTCTGACGGGCTGGGTTT 61.416 55.000 0.00 0.00 0.00 3.27
109 110 1.672356 CTCTGACGGGCTGGGTTTG 60.672 63.158 0.00 0.00 0.00 2.93
110 111 2.672996 CTGACGGGCTGGGTTTGG 60.673 66.667 0.00 0.00 0.00 3.28
111 112 4.278513 TGACGGGCTGGGTTTGGG 62.279 66.667 0.00 0.00 0.00 4.12
116 117 4.299796 GGCTGGGTTTGGGCCTGA 62.300 66.667 4.53 0.00 42.31 3.86
117 118 2.203625 GCTGGGTTTGGGCCTGAA 60.204 61.111 4.53 0.00 0.00 3.02
118 119 1.836604 GCTGGGTTTGGGCCTGAAA 60.837 57.895 4.53 0.00 0.00 2.69
119 120 1.406860 GCTGGGTTTGGGCCTGAAAA 61.407 55.000 4.53 0.00 0.00 2.29
120 121 0.392706 CTGGGTTTGGGCCTGAAAAC 59.607 55.000 16.25 16.25 35.89 2.43
123 124 3.986970 GTTTGGGCCTGAAAACCAG 57.013 52.632 4.53 0.00 42.55 4.00
130 131 4.743018 CTGAAAACCAGGCCCGAT 57.257 55.556 0.00 0.00 39.23 4.18
131 132 2.183409 CTGAAAACCAGGCCCGATG 58.817 57.895 0.00 0.00 39.23 3.84
132 133 0.322456 CTGAAAACCAGGCCCGATGA 60.322 55.000 0.00 0.00 39.23 2.92
133 134 0.608035 TGAAAACCAGGCCCGATGAC 60.608 55.000 0.00 0.00 0.00 3.06
134 135 1.304134 AAAACCAGGCCCGATGACC 60.304 57.895 0.00 0.00 0.00 4.02
135 136 3.622060 AAACCAGGCCCGATGACCG 62.622 63.158 0.00 0.00 38.18 4.79
137 138 4.227134 CCAGGCCCGATGACCGAG 62.227 72.222 0.00 0.00 41.76 4.63
138 139 4.899239 CAGGCCCGATGACCGAGC 62.899 72.222 0.00 0.00 41.56 5.03
140 141 4.899239 GGCCCGATGACCGAGCTG 62.899 72.222 0.00 0.00 41.99 4.24
141 142 4.899239 GCCCGATGACCGAGCTGG 62.899 72.222 0.00 0.00 39.05 4.85
142 143 4.227134 CCCGATGACCGAGCTGGG 62.227 72.222 14.03 14.03 44.64 4.45
162 163 4.043100 GGGCCCAGGCGTAGGTTT 62.043 66.667 19.95 0.00 43.06 3.27
163 164 2.035155 GGCCCAGGCGTAGGTTTT 59.965 61.111 1.86 0.00 43.06 2.43
164 165 2.044555 GGCCCAGGCGTAGGTTTTC 61.045 63.158 1.86 0.00 43.06 2.29
165 166 1.002502 GCCCAGGCGTAGGTTTTCT 60.003 57.895 0.00 0.00 0.00 2.52
166 167 1.305930 GCCCAGGCGTAGGTTTTCTG 61.306 60.000 0.00 0.00 0.00 3.02
167 168 1.305930 CCCAGGCGTAGGTTTTCTGC 61.306 60.000 0.00 0.00 0.00 4.26
168 169 1.305930 CCAGGCGTAGGTTTTCTGCC 61.306 60.000 0.00 0.00 46.07 4.85
169 170 4.716003 GGCGTAGGTTTTCTGCCT 57.284 55.556 0.00 0.00 42.44 4.75
170 171 2.467962 GGCGTAGGTTTTCTGCCTC 58.532 57.895 0.00 0.00 42.44 4.70
171 172 1.359459 GGCGTAGGTTTTCTGCCTCG 61.359 60.000 0.00 0.00 42.44 4.63
172 173 1.359459 GCGTAGGTTTTCTGCCTCGG 61.359 60.000 0.00 0.00 37.54 4.63
173 174 0.739813 CGTAGGTTTTCTGCCTCGGG 60.740 60.000 0.00 0.00 37.54 5.14
183 184 2.124695 GCCTCGGGCTTGGTTAGG 60.125 66.667 7.58 0.00 46.69 2.69
212 213 2.994699 CCAACGGATGGCCAGGTA 59.005 61.111 13.05 0.00 43.80 3.08
213 214 1.531748 CCAACGGATGGCCAGGTAT 59.468 57.895 13.05 0.00 43.80 2.73
214 215 0.819259 CCAACGGATGGCCAGGTATG 60.819 60.000 13.05 6.47 43.80 2.39
215 216 1.152963 AACGGATGGCCAGGTATGC 60.153 57.895 13.05 0.00 0.00 3.14
222 223 2.267642 GCCAGGTATGCCACACGA 59.732 61.111 1.54 0.00 37.19 4.35
223 224 2.106683 GCCAGGTATGCCACACGAC 61.107 63.158 1.54 0.00 37.19 4.34
224 225 1.295101 CCAGGTATGCCACACGACA 59.705 57.895 1.54 0.00 37.19 4.35
225 226 1.019278 CCAGGTATGCCACACGACAC 61.019 60.000 1.54 0.00 37.19 3.67
226 227 0.037326 CAGGTATGCCACACGACACT 60.037 55.000 1.54 0.00 37.19 3.55
227 228 0.685097 AGGTATGCCACACGACACTT 59.315 50.000 1.54 0.00 37.19 3.16
228 229 1.897133 AGGTATGCCACACGACACTTA 59.103 47.619 1.54 0.00 37.19 2.24
229 230 2.500098 AGGTATGCCACACGACACTTAT 59.500 45.455 1.54 0.00 37.19 1.73
230 231 2.864343 GGTATGCCACACGACACTTATC 59.136 50.000 0.00 0.00 34.09 1.75
231 232 2.760634 ATGCCACACGACACTTATCA 57.239 45.000 0.00 0.00 0.00 2.15
232 233 2.760634 TGCCACACGACACTTATCAT 57.239 45.000 0.00 0.00 0.00 2.45
233 234 3.052455 TGCCACACGACACTTATCATT 57.948 42.857 0.00 0.00 0.00 2.57
234 235 3.407698 TGCCACACGACACTTATCATTT 58.592 40.909 0.00 0.00 0.00 2.32
235 236 3.188254 TGCCACACGACACTTATCATTTG 59.812 43.478 0.00 0.00 0.00 2.32
236 237 3.435327 GCCACACGACACTTATCATTTGA 59.565 43.478 0.00 0.00 0.00 2.69
237 238 4.436050 GCCACACGACACTTATCATTTGAG 60.436 45.833 0.00 0.00 0.00 3.02
238 239 4.929211 CCACACGACACTTATCATTTGAGA 59.071 41.667 0.00 0.00 0.00 3.27
239 240 5.408299 CCACACGACACTTATCATTTGAGAA 59.592 40.000 0.00 0.00 0.00 2.87
240 241 6.073276 CCACACGACACTTATCATTTGAGAAA 60.073 38.462 0.00 0.00 0.00 2.52
241 242 7.351981 CACACGACACTTATCATTTGAGAAAA 58.648 34.615 0.00 0.00 0.00 2.29
242 243 7.531871 CACACGACACTTATCATTTGAGAAAAG 59.468 37.037 0.00 0.00 0.00 2.27
243 244 7.441157 ACACGACACTTATCATTTGAGAAAAGA 59.559 33.333 0.00 0.00 0.00 2.52
244 245 8.282592 CACGACACTTATCATTTGAGAAAAGAA 58.717 33.333 0.00 0.00 0.00 2.52
245 246 8.836413 ACGACACTTATCATTTGAGAAAAGAAA 58.164 29.630 0.00 0.00 0.00 2.52
246 247 9.663904 CGACACTTATCATTTGAGAAAAGAAAA 57.336 29.630 6.95 0.00 0.00 2.29
253 254 7.951530 TCATTTGAGAAAAGAAAATTGCCTC 57.048 32.000 0.00 0.00 0.00 4.70
254 255 7.499292 TCATTTGAGAAAAGAAAATTGCCTCA 58.501 30.769 0.00 0.00 0.00 3.86
255 256 7.986320 TCATTTGAGAAAAGAAAATTGCCTCAA 59.014 29.630 0.00 0.00 37.38 3.02
256 257 8.614346 CATTTGAGAAAAGAAAATTGCCTCAAA 58.386 29.630 14.37 14.37 46.38 2.69
257 258 8.558973 TTTGAGAAAAGAAAATTGCCTCAAAA 57.441 26.923 0.00 0.00 42.50 2.44
258 259 8.558973 TTGAGAAAAGAAAATTGCCTCAAAAA 57.441 26.923 0.00 0.00 36.58 1.94
331 332 0.819259 AGGCCACACATGTGTCACAC 60.819 55.000 28.38 17.76 42.83 3.82
335 343 2.159254 GCCACACATGTGTCACACTTTT 60.159 45.455 28.38 0.86 42.83 2.27
348 356 1.300853 ACTTTTGGCCGCAATGCAC 60.301 52.632 5.91 0.00 0.00 4.57
355 363 3.891400 CCGCAATGCACCCCATCG 61.891 66.667 5.91 0.00 31.43 3.84
406 423 2.280797 GCACACCGACTCCAGCAA 60.281 61.111 0.00 0.00 0.00 3.91
418 435 1.194781 TCCAGCAACCTCCTCCAGTC 61.195 60.000 0.00 0.00 0.00 3.51
454 471 1.512201 TACCTCCTCCTCCCACGGAA 61.512 60.000 0.00 0.00 31.44 4.30
477 494 3.402681 CCCCCATCAGCCGAGTGT 61.403 66.667 0.00 0.00 0.00 3.55
495 517 4.148825 CTCCCCCGACCTGCTTCG 62.149 72.222 0.00 0.00 38.80 3.79
566 588 4.698575 GGATTTGACTCTGTAGATCCACC 58.301 47.826 0.00 0.00 34.57 4.61
607 636 4.552355 TCCATGCGTATTATTAGTGACCG 58.448 43.478 0.00 0.00 0.00 4.79
610 639 4.834357 TGCGTATTATTAGTGACCGCTA 57.166 40.909 0.00 0.00 40.24 4.26
621 654 3.722147 AGTGACCGCTATTCAGCTAATG 58.278 45.455 0.00 0.00 46.26 1.90
624 657 2.802816 GACCGCTATTCAGCTAATGGTG 59.197 50.000 0.00 0.00 46.26 4.17
676 709 2.668889 GTGACTGCTGCTGCTGCT 60.669 61.111 27.67 12.31 41.07 4.24
799 832 1.517242 AGCTGAGAAAACTTGAGCCG 58.483 50.000 0.00 0.00 0.00 5.52
808 841 6.149129 AGAAAACTTGAGCCGAAGATTTTT 57.851 33.333 0.00 0.00 30.55 1.94
833 866 1.402896 GGAGCGGGTGATGGAGATGA 61.403 60.000 0.00 0.00 0.00 2.92
838 871 0.604780 GGGTGATGGAGATGATGGCG 60.605 60.000 0.00 0.00 0.00 5.69
947 980 3.068732 TGAGTATCATCGCCTCAAGAAGG 59.931 47.826 0.00 0.00 42.56 3.46
969 1002 2.166664 AGGTCCAAGATTACGAGCTCAC 59.833 50.000 15.40 0.00 28.47 3.51
971 1004 2.166664 GTCCAAGATTACGAGCTCACCT 59.833 50.000 15.40 0.00 0.00 4.00
972 1005 2.427453 TCCAAGATTACGAGCTCACCTC 59.573 50.000 15.40 4.58 37.22 3.85
973 1006 2.166459 CCAAGATTACGAGCTCACCTCA 59.834 50.000 15.40 0.00 40.78 3.86
974 1007 3.443037 CAAGATTACGAGCTCACCTCAG 58.557 50.000 15.40 0.00 40.78 3.35
975 1008 3.006112 AGATTACGAGCTCACCTCAGA 57.994 47.619 15.40 0.00 40.78 3.27
976 1009 2.685897 AGATTACGAGCTCACCTCAGAC 59.314 50.000 15.40 0.00 40.78 3.51
977 1010 1.174783 TTACGAGCTCACCTCAGACC 58.825 55.000 15.40 0.00 40.78 3.85
978 1011 1.025113 TACGAGCTCACCTCAGACCG 61.025 60.000 15.40 0.00 40.78 4.79
1078 1111 0.449388 CGTTTGCCATCCTCAAGCTC 59.551 55.000 0.00 0.00 0.00 4.09
1449 1537 2.632512 CCCCCAAAATGTGTTAGCACTT 59.367 45.455 11.22 1.65 45.44 3.16
1450 1538 3.829601 CCCCCAAAATGTGTTAGCACTTA 59.170 43.478 11.22 0.00 45.44 2.24
1451 1539 4.082245 CCCCCAAAATGTGTTAGCACTTAG 60.082 45.833 11.22 0.00 45.44 2.18
1452 1540 4.485163 CCCAAAATGTGTTAGCACTTAGC 58.515 43.478 11.22 0.00 45.44 3.09
1565 1701 6.659668 AGCCTGGAGAAAATAGAAAAGGTTAC 59.340 38.462 0.00 0.00 0.00 2.50
1623 1768 3.279434 GCCCACTGTAAATAAGGGACAG 58.721 50.000 0.00 0.00 44.98 3.51
1628 1773 5.360591 CACTGTAAATAAGGGACAGCCTAG 58.639 45.833 1.29 0.00 43.60 3.02
1735 1883 5.917415 CTTCATGAGAATGCCAGTCATGGTA 60.917 44.000 10.74 0.00 45.13 3.25
1826 1974 3.007398 TCAACCCTTGCACAGTTTGTTTT 59.993 39.130 0.00 0.00 0.00 2.43
1874 2022 3.002102 CCGAAAAAGATGGCCATTTTGG 58.998 45.455 21.84 19.28 41.55 3.28
1906 2054 5.712152 ATGGGTTCATGTCTCTCAAAAAC 57.288 39.130 0.00 0.00 31.34 2.43
1948 2096 1.994779 GGCGAATGTTTGAGGCAATTG 59.005 47.619 0.00 0.00 0.00 2.32
2184 2371 2.093288 TCTTGGTCCTGATGTGAGATGC 60.093 50.000 0.00 0.00 0.00 3.91
2242 2429 5.428253 TGTTCCTTGAGCTATTCATGTACC 58.572 41.667 0.00 0.00 35.27 3.34
2257 2444 4.408596 TCATGTACCATGCACTTGGAGATA 59.591 41.667 13.35 0.00 39.25 1.98
2262 2449 1.945394 CATGCACTTGGAGATAGGCAC 59.055 52.381 0.00 0.00 33.67 5.01
2276 2463 2.125912 GCACGCAGACGATGGAGT 60.126 61.111 0.00 0.00 43.93 3.85
2303 2490 2.357154 GCACACTCTGGAATATTGGGGT 60.357 50.000 0.00 0.00 0.00 4.95
2525 2717 2.295885 CAGAGGGCATCATTTCAGACC 58.704 52.381 0.58 0.00 0.00 3.85
2583 2775 7.991460 GGGTTTATAAGAAGTACTAATGCAGGT 59.009 37.037 0.00 0.00 0.00 4.00
3031 3241 4.084287 ACGTCACCTTACTTACAGGATCA 58.916 43.478 0.00 0.00 35.14 2.92
3042 3252 5.503927 ACTTACAGGATCAGCAAATCACAT 58.496 37.500 0.00 0.00 0.00 3.21
3048 3258 3.314635 GGATCAGCAAATCACATGGTCTC 59.685 47.826 0.00 0.00 0.00 3.36
3131 3342 1.340248 ACGTCTTTCGCTCTCCAAAGA 59.660 47.619 0.00 0.00 44.19 2.52
3263 3477 6.522054 TCACAGTAAGTAAGGAAAGAGGTTG 58.478 40.000 0.00 0.00 0.00 3.77
3267 3481 6.431234 CAGTAAGTAAGGAAAGAGGTTGCAAT 59.569 38.462 0.59 0.00 0.00 3.56
3341 3555 6.980397 AGAGGTGTTGAAAATGTTAAAAGCAG 59.020 34.615 0.00 0.00 0.00 4.24
3380 3594 2.103771 CCAAGCTAGCTGATAAGGAGCA 59.896 50.000 20.16 0.00 39.05 4.26
3387 3601 2.093235 AGCTGATAAGGAGCAACTCACC 60.093 50.000 0.00 0.00 39.05 4.02
3496 3717 5.946486 AGGATCTTGAAAAACTGGAACTCT 58.054 37.500 0.00 0.00 0.00 3.24
3546 3786 0.846693 GGATGGTGGGTAGGCAGAAT 59.153 55.000 0.00 0.00 0.00 2.40
3699 3944 0.955428 TGGTGCGCCTGAAATCACTC 60.955 55.000 18.96 0.00 35.27 3.51
3974 4594 4.570772 TGAGGAGTTTGAAGTTTGAACTCG 59.429 41.667 18.35 0.00 46.33 4.18
4084 4720 2.371841 TGGACCAAGTAACTGCATGAGT 59.628 45.455 0.00 0.00 35.94 3.41
4085 4721 2.744202 GGACCAAGTAACTGCATGAGTG 59.256 50.000 0.00 0.00 34.02 3.51
4086 4722 3.557054 GGACCAAGTAACTGCATGAGTGA 60.557 47.826 0.00 0.00 34.02 3.41
4087 4723 4.256920 GACCAAGTAACTGCATGAGTGAT 58.743 43.478 0.00 0.00 34.02 3.06
4088 4724 4.655963 ACCAAGTAACTGCATGAGTGATT 58.344 39.130 0.00 0.00 34.02 2.57
4089 4725 4.456911 ACCAAGTAACTGCATGAGTGATTG 59.543 41.667 0.00 4.23 34.02 2.67
4190 4826 5.191426 AGTACGAGCCATTACTAGTTCTGA 58.809 41.667 0.00 0.00 0.00 3.27
4274 4913 1.872952 TGTTTCCAGCATCTGAACACG 59.127 47.619 0.00 0.00 32.44 4.49
4391 5030 2.086869 CAGAATGCCATGTCCGAAGTT 58.913 47.619 0.00 0.00 0.00 2.66
4400 5039 3.125829 CCATGTCCGAAGTTGATGAACAG 59.874 47.826 0.00 0.00 34.17 3.16
4401 5040 3.469008 TGTCCGAAGTTGATGAACAGT 57.531 42.857 0.00 0.00 34.17 3.55
4446 5085 6.141527 TGTTTGCGAAATCGTTGAATGTTAAG 59.858 34.615 4.59 0.00 42.22 1.85
4460 5099 9.624697 GTTGAATGTTAAGTGCTGAATTTATGA 57.375 29.630 0.00 0.00 0.00 2.15
4477 5116 8.826293 AATTTATGAATTGCCCATGGATTTTT 57.174 26.923 15.22 1.15 34.26 1.94
4481 5120 9.745018 TTATGAATTGCCCATGGATTTTTAAAA 57.255 25.926 15.22 0.00 0.00 1.52
4505 5148 3.319755 TGGGACGACGAACAATAGTTTC 58.680 45.455 0.00 0.00 38.30 2.78
4649 5292 1.329906 GATGTGAGCAAGCCTGATTCG 59.670 52.381 0.00 0.00 0.00 3.34
4666 5309 7.117092 GCCTGATTCGCAAAAAGGTAAAAATAA 59.883 33.333 0.00 0.00 0.00 1.40
4691 5334 1.469703 CGTGAGCATGCCTGAATTTGA 59.530 47.619 15.66 0.00 0.00 2.69
4699 5342 6.513180 AGCATGCCTGAATTTGATAAGATTG 58.487 36.000 15.66 0.00 0.00 2.67
4715 5358 0.467290 ATTGTGCTGGTCGTTTGGGT 60.467 50.000 0.00 0.00 0.00 4.51
4717 5360 0.398696 TGTGCTGGTCGTTTGGGTAT 59.601 50.000 0.00 0.00 0.00 2.73
4732 5375 0.947244 GGTATGAAGGAATGGCTGCG 59.053 55.000 0.00 0.00 0.00 5.18
4734 5377 2.017049 GTATGAAGGAATGGCTGCGTT 58.983 47.619 0.00 0.00 0.00 4.84
4741 5384 1.000274 GGAATGGCTGCGTTTTCTGTT 60.000 47.619 0.00 0.00 0.00 3.16
4742 5385 2.319472 GAATGGCTGCGTTTTCTGTTC 58.681 47.619 0.00 0.00 0.00 3.18
4744 5387 1.092921 TGGCTGCGTTTTCTGTTCGT 61.093 50.000 0.00 0.00 0.00 3.85
4745 5388 0.384353 GGCTGCGTTTTCTGTTCGTC 60.384 55.000 0.00 0.00 0.00 4.20
4746 5389 0.582005 GCTGCGTTTTCTGTTCGTCT 59.418 50.000 0.00 0.00 0.00 4.18
4747 5390 1.397315 GCTGCGTTTTCTGTTCGTCTC 60.397 52.381 0.00 0.00 0.00 3.36
4748 5391 1.858458 CTGCGTTTTCTGTTCGTCTCA 59.142 47.619 0.00 0.00 0.00 3.27
4749 5392 2.272678 TGCGTTTTCTGTTCGTCTCAA 58.727 42.857 0.00 0.00 0.00 3.02
4750 5393 2.029970 TGCGTTTTCTGTTCGTCTCAAC 59.970 45.455 0.00 0.00 0.00 3.18
4884 5527 3.057969 TCTGCGTGTCCATTCATCTTT 57.942 42.857 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.418368 ATATGTGCTTCGGGCTCAAA 57.582 45.000 9.27 0.00 45.58 2.69
3 4 1.667236 CAATATGTGCTTCGGGCTCA 58.333 50.000 8.05 8.05 46.32 4.26
7 8 1.455383 GCCCCAATATGTGCTTCGGG 61.455 60.000 0.00 0.00 0.00 5.14
8 9 1.785041 CGCCCCAATATGTGCTTCGG 61.785 60.000 0.00 0.00 0.00 4.30
9 10 1.648720 CGCCCCAATATGTGCTTCG 59.351 57.895 0.00 0.00 0.00 3.79
10 11 1.455383 CCCGCCCCAATATGTGCTTC 61.455 60.000 0.00 0.00 0.00 3.86
11 12 1.455587 CCCGCCCCAATATGTGCTT 60.456 57.895 0.00 0.00 0.00 3.91
12 13 2.195683 CCCGCCCCAATATGTGCT 59.804 61.111 0.00 0.00 0.00 4.40
13 14 3.605664 GCCCGCCCCAATATGTGC 61.606 66.667 0.00 0.00 0.00 4.57
14 15 2.063015 TAGGCCCGCCCCAATATGTG 62.063 60.000 0.00 0.00 36.58 3.21
15 16 1.772567 TAGGCCCGCCCCAATATGT 60.773 57.895 0.00 0.00 36.58 2.29
16 17 1.002134 CTAGGCCCGCCCCAATATG 60.002 63.158 0.00 0.00 36.58 1.78
17 18 2.231380 CCTAGGCCCGCCCCAATAT 61.231 63.158 0.00 0.00 36.58 1.28
18 19 2.852075 CCTAGGCCCGCCCCAATA 60.852 66.667 0.00 0.00 36.58 1.90
26 27 1.705997 AATACCCAAGCCTAGGCCCG 61.706 60.000 30.42 20.61 43.17 6.13
27 28 0.556258 AAATACCCAAGCCTAGGCCC 59.444 55.000 30.42 3.93 43.17 5.80
28 29 1.692411 CAAATACCCAAGCCTAGGCC 58.308 55.000 30.42 12.55 43.17 5.19
29 30 1.063942 ACCAAATACCCAAGCCTAGGC 60.064 52.381 27.19 27.19 42.33 3.93
30 31 2.025321 ACACCAAATACCCAAGCCTAGG 60.025 50.000 3.67 3.67 0.00 3.02
31 32 3.366052 ACACCAAATACCCAAGCCTAG 57.634 47.619 0.00 0.00 0.00 3.02
32 33 3.818295 AACACCAAATACCCAAGCCTA 57.182 42.857 0.00 0.00 0.00 3.93
33 34 2.694616 AACACCAAATACCCAAGCCT 57.305 45.000 0.00 0.00 0.00 4.58
34 35 3.762407 AAAACACCAAATACCCAAGCC 57.238 42.857 0.00 0.00 0.00 4.35
35 36 6.517605 TCTTTAAAACACCAAATACCCAAGC 58.482 36.000 0.00 0.00 0.00 4.01
36 37 8.950208 TTTCTTTAAAACACCAAATACCCAAG 57.050 30.769 0.00 0.00 0.00 3.61
37 38 7.988028 CCTTTCTTTAAAACACCAAATACCCAA 59.012 33.333 0.00 0.00 0.00 4.12
38 39 7.419172 CCCTTTCTTTAAAACACCAAATACCCA 60.419 37.037 0.00 0.00 0.00 4.51
39 40 6.932400 CCCTTTCTTTAAAACACCAAATACCC 59.068 38.462 0.00 0.00 0.00 3.69
40 41 6.425721 GCCCTTTCTTTAAAACACCAAATACC 59.574 38.462 0.00 0.00 0.00 2.73
41 42 6.425721 GGCCCTTTCTTTAAAACACCAAATAC 59.574 38.462 0.00 0.00 0.00 1.89
42 43 6.327887 AGGCCCTTTCTTTAAAACACCAAATA 59.672 34.615 0.00 0.00 0.00 1.40
43 44 5.131977 AGGCCCTTTCTTTAAAACACCAAAT 59.868 36.000 0.00 0.00 0.00 2.32
44 45 4.471747 AGGCCCTTTCTTTAAAACACCAAA 59.528 37.500 0.00 0.00 0.00 3.28
45 46 4.034410 AGGCCCTTTCTTTAAAACACCAA 58.966 39.130 0.00 0.00 0.00 3.67
46 47 3.386402 CAGGCCCTTTCTTTAAAACACCA 59.614 43.478 0.00 0.00 0.00 4.17
47 48 3.244078 CCAGGCCCTTTCTTTAAAACACC 60.244 47.826 0.00 0.00 0.00 4.16
48 49 3.802329 GCCAGGCCCTTTCTTTAAAACAC 60.802 47.826 0.00 0.00 0.00 3.32
49 50 2.367241 GCCAGGCCCTTTCTTTAAAACA 59.633 45.455 0.00 0.00 0.00 2.83
50 51 2.289444 GGCCAGGCCCTTTCTTTAAAAC 60.289 50.000 21.62 0.00 44.06 2.43
51 52 1.974957 GGCCAGGCCCTTTCTTTAAAA 59.025 47.619 21.62 0.00 44.06 1.52
52 53 1.639722 GGCCAGGCCCTTTCTTTAAA 58.360 50.000 21.62 0.00 44.06 1.52
53 54 3.374318 GGCCAGGCCCTTTCTTTAA 57.626 52.632 21.62 0.00 44.06 1.52
77 78 0.606401 TCAGAGAAAAAGCCGCTGGG 60.606 55.000 0.00 0.00 33.24 4.45
78 79 0.519077 GTCAGAGAAAAAGCCGCTGG 59.481 55.000 0.00 0.00 33.24 4.85
79 80 0.164647 CGTCAGAGAAAAAGCCGCTG 59.835 55.000 0.00 0.00 33.61 5.18
80 81 0.951040 CCGTCAGAGAAAAAGCCGCT 60.951 55.000 0.00 0.00 0.00 5.52
81 82 1.497722 CCGTCAGAGAAAAAGCCGC 59.502 57.895 0.00 0.00 0.00 6.53
82 83 1.912371 GCCCGTCAGAGAAAAAGCCG 61.912 60.000 0.00 0.00 0.00 5.52
83 84 0.606673 AGCCCGTCAGAGAAAAAGCC 60.607 55.000 0.00 0.00 0.00 4.35
84 85 0.519077 CAGCCCGTCAGAGAAAAAGC 59.481 55.000 0.00 0.00 0.00 3.51
85 86 1.160137 CCAGCCCGTCAGAGAAAAAG 58.840 55.000 0.00 0.00 0.00 2.27
86 87 0.250727 CCCAGCCCGTCAGAGAAAAA 60.251 55.000 0.00 0.00 0.00 1.94
87 88 1.374947 CCCAGCCCGTCAGAGAAAA 59.625 57.895 0.00 0.00 0.00 2.29
88 89 1.415672 AACCCAGCCCGTCAGAGAAA 61.416 55.000 0.00 0.00 0.00 2.52
89 90 1.415672 AAACCCAGCCCGTCAGAGAA 61.416 55.000 0.00 0.00 0.00 2.87
90 91 1.841556 AAACCCAGCCCGTCAGAGA 60.842 57.895 0.00 0.00 0.00 3.10
91 92 1.672356 CAAACCCAGCCCGTCAGAG 60.672 63.158 0.00 0.00 0.00 3.35
92 93 2.429930 CAAACCCAGCCCGTCAGA 59.570 61.111 0.00 0.00 0.00 3.27
93 94 2.672996 CCAAACCCAGCCCGTCAG 60.673 66.667 0.00 0.00 0.00 3.51
94 95 4.278513 CCCAAACCCAGCCCGTCA 62.279 66.667 0.00 0.00 0.00 4.35
100 101 1.406860 TTTTCAGGCCCAAACCCAGC 61.407 55.000 0.00 0.00 0.00 4.85
101 102 0.392706 GTTTTCAGGCCCAAACCCAG 59.607 55.000 0.00 0.00 0.00 4.45
102 103 1.051556 GGTTTTCAGGCCCAAACCCA 61.052 55.000 23.03 0.00 44.32 4.51
103 104 1.752198 GGTTTTCAGGCCCAAACCC 59.248 57.895 23.03 11.72 44.32 4.11
105 106 3.986970 CTGGTTTTCAGGCCCAAAC 57.013 52.632 12.42 12.42 39.76 2.93
113 114 0.322456 TCATCGGGCCTGGTTTTCAG 60.322 55.000 12.87 0.00 43.00 3.02
114 115 0.608035 GTCATCGGGCCTGGTTTTCA 60.608 55.000 12.87 0.00 0.00 2.69
115 116 1.313091 GGTCATCGGGCCTGGTTTTC 61.313 60.000 12.87 0.00 0.00 2.29
116 117 1.304134 GGTCATCGGGCCTGGTTTT 60.304 57.895 12.87 0.00 0.00 2.43
117 118 2.355115 GGTCATCGGGCCTGGTTT 59.645 61.111 12.87 0.00 0.00 3.27
118 119 4.096003 CGGTCATCGGGCCTGGTT 62.096 66.667 12.87 0.00 34.75 3.67
120 121 4.227134 CTCGGTCATCGGGCCTGG 62.227 72.222 12.87 0.00 39.77 4.45
125 126 4.227134 CCCAGCTCGGTCATCGGG 62.227 72.222 0.00 0.00 43.49 5.14
126 127 4.899239 GCCCAGCTCGGTCATCGG 62.899 72.222 0.00 0.00 39.77 4.18
127 128 4.899239 GGCCCAGCTCGGTCATCG 62.899 72.222 0.00 0.00 40.90 3.84
128 129 4.899239 CGGCCCAGCTCGGTCATC 62.899 72.222 2.00 0.00 0.00 2.92
145 146 3.578968 AAAACCTACGCCTGGGCCC 62.579 63.158 17.59 17.59 37.98 5.80
146 147 2.035155 AAAACCTACGCCTGGGCC 59.965 61.111 5.99 0.00 37.98 5.80
147 148 1.002502 AGAAAACCTACGCCTGGGC 60.003 57.895 0.82 0.82 37.85 5.36
148 149 1.305930 GCAGAAAACCTACGCCTGGG 61.306 60.000 0.00 0.00 0.00 4.45
149 150 1.305930 GGCAGAAAACCTACGCCTGG 61.306 60.000 0.00 0.00 39.73 4.45
150 151 2.171635 GGCAGAAAACCTACGCCTG 58.828 57.895 0.00 0.00 39.73 4.85
151 152 4.716003 GGCAGAAAACCTACGCCT 57.284 55.556 0.00 0.00 39.73 5.52
152 153 1.359459 CGAGGCAGAAAACCTACGCC 61.359 60.000 0.00 0.00 43.31 5.68
153 154 1.359459 CCGAGGCAGAAAACCTACGC 61.359 60.000 0.00 0.00 37.77 4.42
154 155 0.739813 CCCGAGGCAGAAAACCTACG 60.740 60.000 0.00 0.00 37.77 3.51
155 156 3.154589 CCCGAGGCAGAAAACCTAC 57.845 57.895 0.00 0.00 37.77 3.18
167 168 2.124695 GCCTAACCAAGCCCGAGG 60.125 66.667 0.00 0.00 0.00 4.63
168 169 2.124695 GGCCTAACCAAGCCCGAG 60.125 66.667 0.00 0.00 43.76 4.63
194 195 1.994885 ATACCTGGCCATCCGTTGGG 61.995 60.000 5.51 4.26 46.55 4.12
196 197 1.447317 GCATACCTGGCCATCCGTTG 61.447 60.000 5.51 1.90 34.14 4.10
197 198 1.152963 GCATACCTGGCCATCCGTT 60.153 57.895 5.51 0.00 34.14 4.44
198 199 2.510906 GCATACCTGGCCATCCGT 59.489 61.111 5.51 5.61 34.14 4.69
206 207 1.019278 GTGTCGTGTGGCATACCTGG 61.019 60.000 8.89 0.00 36.63 4.45
207 208 0.037326 AGTGTCGTGTGGCATACCTG 60.037 55.000 8.89 0.00 36.63 4.00
208 209 0.685097 AAGTGTCGTGTGGCATACCT 59.315 50.000 8.89 0.00 36.63 3.08
209 210 2.373540 TAAGTGTCGTGTGGCATACC 57.626 50.000 8.89 0.00 0.00 2.73
210 211 3.517602 TGATAAGTGTCGTGTGGCATAC 58.482 45.455 4.05 4.05 0.00 2.39
211 212 3.878160 TGATAAGTGTCGTGTGGCATA 57.122 42.857 0.00 0.00 0.00 3.14
212 213 2.760634 TGATAAGTGTCGTGTGGCAT 57.239 45.000 0.00 0.00 0.00 4.40
213 214 2.760634 ATGATAAGTGTCGTGTGGCA 57.239 45.000 0.00 0.00 0.00 4.92
214 215 3.435327 TCAAATGATAAGTGTCGTGTGGC 59.565 43.478 0.00 0.00 0.00 5.01
215 216 4.929211 TCTCAAATGATAAGTGTCGTGTGG 59.071 41.667 0.00 0.00 0.00 4.17
216 217 6.466308 TTCTCAAATGATAAGTGTCGTGTG 57.534 37.500 0.00 0.00 0.00 3.82
217 218 7.441157 TCTTTTCTCAAATGATAAGTGTCGTGT 59.559 33.333 0.00 0.00 0.00 4.49
218 219 7.796838 TCTTTTCTCAAATGATAAGTGTCGTG 58.203 34.615 0.00 0.00 0.00 4.35
219 220 7.962964 TCTTTTCTCAAATGATAAGTGTCGT 57.037 32.000 0.00 0.00 0.00 4.34
220 221 9.663904 TTTTCTTTTCTCAAATGATAAGTGTCG 57.336 29.630 0.00 0.00 0.00 4.35
227 228 9.643693 GAGGCAATTTTCTTTTCTCAAATGATA 57.356 29.630 0.00 0.00 0.00 2.15
228 229 8.152246 TGAGGCAATTTTCTTTTCTCAAATGAT 58.848 29.630 0.00 0.00 0.00 2.45
229 230 7.499292 TGAGGCAATTTTCTTTTCTCAAATGA 58.501 30.769 0.00 0.00 0.00 2.57
230 231 7.718272 TGAGGCAATTTTCTTTTCTCAAATG 57.282 32.000 0.00 0.00 0.00 2.32
231 232 8.735692 TTTGAGGCAATTTTCTTTTCTCAAAT 57.264 26.923 10.35 0.00 41.67 2.32
232 233 8.558973 TTTTGAGGCAATTTTCTTTTCTCAAA 57.441 26.923 10.35 10.35 43.48 2.69
233 234 8.558973 TTTTTGAGGCAATTTTCTTTTCTCAA 57.441 26.923 0.00 0.00 37.80 3.02
274 275 6.155049 CCCAGATTCAGTATTGATGGGTTTTT 59.845 38.462 14.41 0.00 42.50 1.94
275 276 5.658190 CCCAGATTCAGTATTGATGGGTTTT 59.342 40.000 14.41 0.00 42.50 2.43
276 277 5.044179 TCCCAGATTCAGTATTGATGGGTTT 60.044 40.000 19.45 0.00 45.48 3.27
277 278 4.478317 TCCCAGATTCAGTATTGATGGGTT 59.522 41.667 19.45 0.00 45.48 4.11
278 279 4.047166 TCCCAGATTCAGTATTGATGGGT 58.953 43.478 19.45 0.00 45.48 4.51
279 280 4.712051 TCCCAGATTCAGTATTGATGGG 57.288 45.455 15.88 15.88 46.16 4.00
280 281 7.226441 TGTTATCCCAGATTCAGTATTGATGG 58.774 38.462 0.49 0.49 32.91 3.51
281 282 8.859236 ATGTTATCCCAGATTCAGTATTGATG 57.141 34.615 0.00 0.00 32.27 3.07
282 283 9.872684 AAATGTTATCCCAGATTCAGTATTGAT 57.127 29.630 0.00 0.00 32.27 2.57
283 284 9.342308 GAAATGTTATCCCAGATTCAGTATTGA 57.658 33.333 0.00 0.00 0.00 2.57
284 285 8.571336 GGAAATGTTATCCCAGATTCAGTATTG 58.429 37.037 0.00 0.00 0.00 1.90
285 286 8.281531 TGGAAATGTTATCCCAGATTCAGTATT 58.718 33.333 0.00 0.00 36.04 1.89
286 287 7.815383 TGGAAATGTTATCCCAGATTCAGTAT 58.185 34.615 0.00 0.00 36.04 2.12
287 288 7.206789 TGGAAATGTTATCCCAGATTCAGTA 57.793 36.000 0.00 0.00 36.04 2.74
288 289 6.078456 TGGAAATGTTATCCCAGATTCAGT 57.922 37.500 0.00 0.00 36.04 3.41
289 290 6.040166 CCTTGGAAATGTTATCCCAGATTCAG 59.960 42.308 0.00 0.00 36.04 3.02
290 291 5.893255 CCTTGGAAATGTTATCCCAGATTCA 59.107 40.000 0.00 0.00 36.04 2.57
295 296 2.695147 GGCCTTGGAAATGTTATCCCAG 59.305 50.000 0.00 0.00 36.04 4.45
331 332 2.028733 GGTGCATTGCGGCCAAAAG 61.029 57.895 14.68 0.00 34.05 2.27
377 394 1.361668 CGGTGTGCCTCGATTTCTGG 61.362 60.000 0.00 0.00 0.00 3.86
393 410 2.584391 GGAGGTTGCTGGAGTCGGT 61.584 63.158 0.00 0.00 0.00 4.69
406 423 0.907230 GCTCAAGGACTGGAGGAGGT 60.907 60.000 5.90 0.00 0.00 3.85
454 471 3.564218 GGCTGATGGGGGCTCGAT 61.564 66.667 0.00 0.00 0.00 3.59
477 494 2.683933 GAAGCAGGTCGGGGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
504 526 0.536460 GGAAGCGGTGAGGGTCAAAA 60.536 55.000 0.00 0.00 0.00 2.44
566 588 3.826157 TGGAAATGAAAGCTTACACTGGG 59.174 43.478 0.00 0.00 0.00 4.45
610 639 2.133281 TGCTGCACCATTAGCTGAAT 57.867 45.000 0.00 0.00 40.52 2.57
642 675 0.319900 CACCGGATCCGCCATTAGAG 60.320 60.000 29.12 14.51 38.24 2.43
799 832 2.159462 CCGCTCCAGCAGAAAAATCTTC 60.159 50.000 0.00 0.00 42.21 2.87
808 841 2.685017 ATCACCCGCTCCAGCAGA 60.685 61.111 0.00 0.00 42.21 4.26
941 974 4.094476 TCGTAATCTTGGACCTCCTTCTT 58.906 43.478 0.00 0.00 36.82 2.52
947 980 2.427453 TGAGCTCGTAATCTTGGACCTC 59.573 50.000 9.64 0.00 0.00 3.85
977 1010 3.649277 CTTGGAGGCCCGTCTGACG 62.649 68.421 22.49 22.49 42.11 4.35
978 1011 1.255667 TACTTGGAGGCCCGTCTGAC 61.256 60.000 0.00 0.00 34.29 3.51
1078 1111 6.400940 GCGAGAGAGAAATCTGAAAACAGAAG 60.401 42.308 4.09 0.00 34.56 2.85
1423 1511 4.020662 TGCTAACACATTTTGGGGGAAATC 60.021 41.667 0.00 0.00 0.00 2.17
1449 1537 9.252962 GCTTAATAACGAAAATAGGTAGTGCTA 57.747 33.333 0.00 0.00 0.00 3.49
1450 1538 7.042925 CGCTTAATAACGAAAATAGGTAGTGCT 60.043 37.037 0.00 0.00 0.00 4.40
1451 1539 7.061634 CGCTTAATAACGAAAATAGGTAGTGC 58.938 38.462 0.00 0.00 0.00 4.40
1452 1540 8.054236 CACGCTTAATAACGAAAATAGGTAGTG 58.946 37.037 0.00 0.00 0.00 2.74
1453 1541 7.223387 CCACGCTTAATAACGAAAATAGGTAGT 59.777 37.037 0.00 0.00 0.00 2.73
1454 1542 7.436080 TCCACGCTTAATAACGAAAATAGGTAG 59.564 37.037 0.00 0.00 0.00 3.18
1455 1543 7.264221 TCCACGCTTAATAACGAAAATAGGTA 58.736 34.615 0.00 0.00 0.00 3.08
1464 1552 4.116961 CAAGGATCCACGCTTAATAACGA 58.883 43.478 15.82 0.00 0.00 3.85
1565 1701 5.512473 CCAAAATTTGGTGTGCTTCATTTG 58.488 37.500 16.24 0.00 45.93 2.32
1735 1883 7.826252 ACATAGACTGCTATTCATGTTTGTCTT 59.174 33.333 0.00 0.00 35.13 3.01
1826 1974 3.025322 TGTCTTTTTCTTCCTGGGCAA 57.975 42.857 0.00 0.00 0.00 4.52
1874 2022 6.939163 AGAGACATGAACCCATAATAGAATGC 59.061 38.462 0.00 0.00 0.00 3.56
1906 2054 4.302455 CTGTAAATGACCTCGATGCTAGG 58.698 47.826 0.00 0.00 40.20 3.02
1919 2067 4.155826 CCTCAAACATTCGCCTGTAAATGA 59.844 41.667 2.36 1.53 36.57 2.57
2012 2190 7.039313 AGTACCAAGAAAAACCTTTTGCTAG 57.961 36.000 0.00 0.00 34.97 3.42
2014 2192 5.932619 AGTACCAAGAAAAACCTTTTGCT 57.067 34.783 0.00 0.00 37.65 3.91
2184 2371 5.059404 AGTCACTAATTGGAAAATTGGCG 57.941 39.130 0.00 0.00 0.00 5.69
2242 2429 1.945394 GTGCCTATCTCCAAGTGCATG 59.055 52.381 0.00 0.00 0.00 4.06
2257 2444 3.362399 CTCCATCGTCTGCGTGCCT 62.362 63.158 0.00 0.00 39.49 4.75
2262 2449 1.811266 CCCAACTCCATCGTCTGCG 60.811 63.158 0.00 0.00 39.92 5.18
2276 2463 1.067295 ATTCCAGAGTGTGCTCCCAA 58.933 50.000 0.00 0.00 42.59 4.12
2525 2717 7.308348 CCACCCACAACTTAAGTAACACATTAG 60.308 40.741 8.92 0.00 0.00 1.73
2583 2775 5.886609 TGACCAACATCTTCCATTTCCTTA 58.113 37.500 0.00 0.00 0.00 2.69
3031 3241 5.733620 AAAATGAGACCATGTGATTTGCT 57.266 34.783 0.00 0.00 32.36 3.91
3042 3252 3.655777 AGGTCCTTGGTAAAATGAGACCA 59.344 43.478 8.82 0.00 43.81 4.02
3131 3342 7.400052 AGCTAACCAAATTAATCCCAACTTCAT 59.600 33.333 0.00 0.00 0.00 2.57
3263 3477 7.992754 AGATCCCTCAGATGTTTTATATTGC 57.007 36.000 0.00 0.00 34.42 3.56
3267 3481 8.998814 TGGTTTAGATCCCTCAGATGTTTTATA 58.001 33.333 0.00 0.00 34.42 0.98
3292 3506 3.114616 CAGACGGCCACGAAGCTG 61.115 66.667 2.24 8.41 44.60 4.24
3380 3594 3.181485 GCATAGTTCTAGCTCGGTGAGTT 60.181 47.826 0.00 0.00 31.39 3.01
3387 3601 1.957177 TCCCAGCATAGTTCTAGCTCG 59.043 52.381 0.00 0.00 36.26 5.03
3496 3717 2.125310 CGCTCCATTGTACCCGCA 60.125 61.111 0.00 0.00 0.00 5.69
3699 3944 5.586243 ACATAATTCAATGGACAGTTCCTCG 59.414 40.000 0.00 0.00 43.31 4.63
3960 4580 0.859232 GCGCTCGAGTTCAAACTTCA 59.141 50.000 15.13 0.00 39.88 3.02
3974 4594 2.789917 CACCTCATTGCAGCGCTC 59.210 61.111 7.13 2.98 0.00 5.03
4069 4689 4.012374 CCCAATCACTCATGCAGTTACTT 58.988 43.478 0.00 0.00 30.26 2.24
4089 4725 3.798515 TGGGGATCTATATGGTGTACCC 58.201 50.000 7.33 7.33 36.18 3.69
4190 4826 7.607615 AGCCAAGGAATTTAAGATGCATAAT 57.392 32.000 0.00 0.00 0.00 1.28
4231 4867 6.039717 ACATTGTCATCAAACTGTACAGCTTT 59.960 34.615 22.90 17.59 37.11 3.51
4232 4868 5.532406 ACATTGTCATCAAACTGTACAGCTT 59.468 36.000 22.90 14.34 37.11 3.74
4235 4871 6.857964 GGAAACATTGTCATCAAACTGTACAG 59.142 38.462 21.44 21.44 37.11 2.74
4293 4932 2.420022 CCGGTATCAAAGAACCAAGCAG 59.580 50.000 0.00 0.00 35.35 4.24
4387 5026 6.201044 CGAGTAGTTTCACTGTTCATCAACTT 59.799 38.462 0.00 0.00 33.17 2.66
4391 5030 5.196341 ACGAGTAGTTTCACTGTTCATCA 57.804 39.130 0.00 0.00 0.00 3.07
4446 5085 4.757594 TGGGCAATTCATAAATTCAGCAC 58.242 39.130 0.00 0.00 32.69 4.40
4460 5099 9.134055 CCATATTTTAAAAATCCATGGGCAATT 57.866 29.630 13.02 1.10 0.00 2.32
4477 5116 7.267128 ACTATTGTTCGTCGTCCCATATTTTA 58.733 34.615 0.00 0.00 0.00 1.52
4481 5120 4.931661 ACTATTGTTCGTCGTCCCATAT 57.068 40.909 0.00 0.00 0.00 1.78
4505 5148 6.484643 AGCACTGCAAGATATTACAATACAGG 59.515 38.462 3.30 0.00 37.43 4.00
4649 5292 8.756864 TCACGTCATTTATTTTTACCTTTTTGC 58.243 29.630 0.00 0.00 0.00 3.68
4666 5309 0.036105 TCAGGCATGCTCACGTCATT 60.036 50.000 18.92 0.00 0.00 2.57
4671 5314 1.469703 TCAAATTCAGGCATGCTCACG 59.530 47.619 18.92 3.77 0.00 4.35
4691 5334 3.440173 CCAAACGACCAGCACAATCTTAT 59.560 43.478 0.00 0.00 0.00 1.73
4699 5342 0.802494 CATACCCAAACGACCAGCAC 59.198 55.000 0.00 0.00 0.00 4.40
4715 5358 2.418368 AACGCAGCCATTCCTTCATA 57.582 45.000 0.00 0.00 0.00 2.15
4717 5360 1.269448 GAAAACGCAGCCATTCCTTCA 59.731 47.619 0.00 0.00 0.00 3.02
4732 5375 4.804139 TGAGAGTTGAGACGAACAGAAAAC 59.196 41.667 0.00 0.00 0.00 2.43
4734 5377 4.649088 TGAGAGTTGAGACGAACAGAAA 57.351 40.909 0.00 0.00 0.00 2.52
4741 5384 3.477530 TGAGAGTTGAGAGTTGAGACGA 58.522 45.455 0.00 0.00 0.00 4.20
4742 5385 3.906014 TGAGAGTTGAGAGTTGAGACG 57.094 47.619 0.00 0.00 0.00 4.18
4744 5387 5.380900 TCTCTTGAGAGTTGAGAGTTGAGA 58.619 41.667 7.82 0.00 42.60 3.27
4745 5388 5.703978 TCTCTTGAGAGTTGAGAGTTGAG 57.296 43.478 7.82 0.00 42.60 3.02
4746 5389 7.395772 ACATATCTCTTGAGAGTTGAGAGTTGA 59.604 37.037 15.11 0.00 42.60 3.18
4747 5390 7.546358 ACATATCTCTTGAGAGTTGAGAGTTG 58.454 38.462 15.11 0.00 42.60 3.16
4748 5391 7.716799 ACATATCTCTTGAGAGTTGAGAGTT 57.283 36.000 15.11 0.00 42.60 3.01
4749 5392 7.363705 CCAACATATCTCTTGAGAGTTGAGAGT 60.364 40.741 22.00 7.39 42.60 3.24
4750 5393 6.979817 CCAACATATCTCTTGAGAGTTGAGAG 59.020 42.308 22.00 9.94 42.60 3.20
4864 5507 2.743664 CAAAGATGAATGGACACGCAGA 59.256 45.455 0.00 0.00 0.00 4.26
4884 5527 1.065491 AGGCAATATGGTCGCTTGTCA 60.065 47.619 0.00 0.00 0.00 3.58
4946 5597 1.271871 TGAATTGTCGCCCAACATCCT 60.272 47.619 0.00 0.00 35.44 3.24


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

AutoCloner maintained by Alex Coulton.