Multiple sequence alignment - TraesCS3A01G134400

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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 TraesCS3A01G134400 chr3A 100.000 3139 0 0 1 3139 111809289 111806151 0.000000e+00 5797.0
1 TraesCS3A01G134400 chr3A 86.813 546 33 8 2592 3137 747520474 747519968 9.770000e-160 573.0
2 TraesCS3A01G134400 chr3A 99.592 245 1 0 1 245 111816079 111815835 6.180000e-122 448.0
3 TraesCS3A01G134400 chr3A 86.856 388 34 13 2212 2586 747520900 747520517 4.840000e-113 418.0
4 TraesCS3A01G134400 chr5A 94.130 1908 105 2 244 2144 3881426 3879519 0.000000e+00 2896.0
5 TraesCS3A01G134400 chr5A 87.805 123 14 1 2212 2333 610379765 610379643 3.260000e-30 143.0
6 TraesCS3A01G134400 chr1D 93.927 1910 105 6 244 2144 484742224 484740317 0.000000e+00 2874.0
7 TraesCS3A01G134400 chr1D 93.381 423 27 1 2715 3137 6745909 6745488 2.660000e-175 625.0
8 TraesCS3A01G134400 chr2D 93.750 1904 109 5 244 2140 630027113 630025213 0.000000e+00 2848.0
9 TraesCS3A01G134400 chr1A 93.911 1823 103 3 330 2145 497587822 497586001 0.000000e+00 2745.0
10 TraesCS3A01G134400 chr1A 92.938 1671 92 5 244 1904 581883135 581881481 0.000000e+00 2409.0
11 TraesCS3A01G134400 chr1A 91.775 231 18 1 2906 3136 8185282 8185053 1.400000e-83 320.0
12 TraesCS3A01G134400 chr1A 91.775 231 18 1 2906 3136 8214251 8214022 1.400000e-83 320.0
13 TraesCS3A01G134400 chrUn 93.300 1582 89 6 244 1814 354809589 354808014 0.000000e+00 2318.0
14 TraesCS3A01G134400 chrUn 91.775 231 18 1 2906 3136 307262686 307262457 1.400000e-83 320.0
15 TraesCS3A01G134400 chr3B 87.620 1874 203 17 244 2102 23037457 23035598 0.000000e+00 2148.0
16 TraesCS3A01G134400 chr2A 92.979 1467 91 7 244 1702 193777618 193779080 0.000000e+00 2128.0
17 TraesCS3A01G134400 chr2A 83.595 1914 294 14 244 2144 31817080 31815174 0.000000e+00 1777.0
18 TraesCS3A01G134400 chr2A 98.599 928 11 2 2213 3139 191917200 191918126 0.000000e+00 1640.0
19 TraesCS3A01G134400 chr2A 94.200 1069 60 2 1076 2144 161937615 161938681 0.000000e+00 1629.0
20 TraesCS3A01G134400 chr2A 94.444 810 38 2 244 1046 161936812 161937621 0.000000e+00 1240.0
21 TraesCS3A01G134400 chr2A 91.383 441 36 2 1701 2140 193783006 193783445 1.250000e-168 603.0
22 TraesCS3A01G134400 chr2A 88.068 528 24 8 2592 3119 424512234 424511746 9.700000e-165 590.0
23 TraesCS3A01G134400 chr2A 100.000 245 0 0 1 245 445421791 445421547 1.330000e-123 453.0
24 TraesCS3A01G134400 chr2A 100.000 245 0 0 1 245 473391374 473391618 1.330000e-123 453.0
25 TraesCS3A01G134400 chr2A 99.590 244 1 0 1 244 445413499 445413256 2.220000e-121 446.0
26 TraesCS3A01G134400 chr2A 86.701 391 37 9 2224 2601 424512651 424512263 1.350000e-113 420.0
27 TraesCS3A01G134400 chr2A 91.262 103 8 1 2209 2310 611699466 611699568 4.220000e-29 139.0
28 TraesCS3A01G134400 chr2A 79.470 151 27 4 2216 2363 679228621 679228770 1.540000e-18 104.0
29 TraesCS3A01G134400 chr2A 96.774 31 1 0 2190 2220 444016408 444016378 6.000000e-03 52.8
30 TraesCS3A01G134400 chr7A 98.922 928 8 2 2213 3139 269097721 269098647 0.000000e+00 1657.0
31 TraesCS3A01G134400 chr7A 93.519 972 56 4 1173 2144 543443149 543444113 0.000000e+00 1439.0
32 TraesCS3A01G134400 chr7A 86.579 380 43 7 2214 2586 153054014 153053636 2.250000e-111 412.0
33 TraesCS3A01G134400 chr7A 85.455 385 43 8 2214 2586 153076256 153075873 3.800000e-104 388.0
34 TraesCS3A01G134400 chr7A 88.034 117 9 4 2213 2327 37004467 37004580 1.960000e-27 134.0
35 TraesCS3A01G134400 chr4B 98.624 654 8 1 2487 3139 142771221 142771874 0.000000e+00 1157.0
36 TraesCS3A01G134400 chr4B 99.590 244 1 0 1 244 491491136 491490893 2.220000e-121 446.0
37 TraesCS3A01G134400 chr4B 98.507 201 3 0 2224 2424 142770587 142770787 3.850000e-94 355.0
38 TraesCS3A01G134400 chr1B 85.220 1069 144 7 244 1303 657197073 657196010 0.000000e+00 1086.0
39 TraesCS3A01G134400 chr1B 87.597 516 25 9 2592 3107 321679053 321678577 2.110000e-156 562.0
40 TraesCS3A01G134400 chr1B 95.556 45 2 0 2188 2232 643365552 643365596 4.340000e-09 73.1
41 TraesCS3A01G134400 chr5B 89.617 549 50 2 2592 3134 573575489 573576036 0.000000e+00 691.0
42 TraesCS3A01G134400 chr6D 87.546 546 29 8 2592 3137 313019985 313019479 2.080000e-166 595.0
43 TraesCS3A01G134400 chr7D 87.179 546 31 8 2592 3137 249448129 249448635 4.510000e-163 584.0
44 TraesCS3A01G134400 chr6B 87.879 528 25 8 2592 3119 560641453 560641941 4.510000e-163 584.0
45 TraesCS3A01G134400 chr6B 99.592 245 1 0 1 245 29182156 29182400 6.180000e-122 448.0
46 TraesCS3A01G134400 chr6B 99.590 244 1 0 1 244 29189050 29189293 2.220000e-121 446.0
47 TraesCS3A01G134400 chr6B 87.154 397 33 13 2212 2595 560641027 560641418 4.810000e-118 435.0
48 TraesCS3A01G134400 chr4A 83.978 543 40 10 2595 3137 344733126 344732631 7.880000e-131 477.0
49 TraesCS3A01G134400 chr4A 99.592 245 1 0 1 245 441972440 441972196 6.180000e-122 448.0
50 TraesCS3A01G134400 chr4A 86.047 387 39 8 2214 2586 344733557 344733172 4.880000e-108 401.0
51 TraesCS3A01G134400 chr4A 79.874 159 16 12 2212 2358 16878723 16878569 5.540000e-18 102.0
52 TraesCS3A01G134400 chr4A 79.747 158 15 13 2212 2358 16872458 16872307 7.160000e-17 99.0
53 TraesCS3A01G134400 chr6A 100.000 245 0 0 1 245 156831157 156831401 1.330000e-123 453.0
54 TraesCS3A01G134400 chr6A 79.747 158 17 12 2212 2358 53916286 53916439 1.990000e-17 100.0
55 TraesCS3A01G134400 chr6A 79.730 148 18 10 2220 2358 78987114 78987258 2.580000e-16 97.1
56 TraesCS3A01G134400 chr5D 89.426 331 18 2 2592 2921 43199703 43199389 4.880000e-108 401.0
57 TraesCS3A01G134400 chr4D 85.237 359 33 12 2226 2571 98534779 98535130 4.980000e-93 351.0


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 TraesCS3A01G134400 chr3A 111806151 111809289 3138 True 5797.0 5797 100.0000 1 3139 1 chr3A.!!$R1 3138
1 TraesCS3A01G134400 chr3A 747519968 747520900 932 True 495.5 573 86.8345 2212 3137 2 chr3A.!!$R3 925
2 TraesCS3A01G134400 chr5A 3879519 3881426 1907 True 2896.0 2896 94.1300 244 2144 1 chr5A.!!$R1 1900
3 TraesCS3A01G134400 chr1D 484740317 484742224 1907 True 2874.0 2874 93.9270 244 2144 1 chr1D.!!$R2 1900
4 TraesCS3A01G134400 chr2D 630025213 630027113 1900 True 2848.0 2848 93.7500 244 2140 1 chr2D.!!$R1 1896
5 TraesCS3A01G134400 chr1A 497586001 497587822 1821 True 2745.0 2745 93.9110 330 2145 1 chr1A.!!$R3 1815
6 TraesCS3A01G134400 chr1A 581881481 581883135 1654 True 2409.0 2409 92.9380 244 1904 1 chr1A.!!$R4 1660
7 TraesCS3A01G134400 chrUn 354808014 354809589 1575 True 2318.0 2318 93.3000 244 1814 1 chrUn.!!$R2 1570
8 TraesCS3A01G134400 chr3B 23035598 23037457 1859 True 2148.0 2148 87.6200 244 2102 1 chr3B.!!$R1 1858
9 TraesCS3A01G134400 chr2A 31815174 31817080 1906 True 1777.0 1777 83.5950 244 2144 1 chr2A.!!$R1 1900
10 TraesCS3A01G134400 chr2A 191917200 191918126 926 False 1640.0 1640 98.5990 2213 3139 1 chr2A.!!$F1 926
11 TraesCS3A01G134400 chr2A 161936812 161938681 1869 False 1434.5 1629 94.3220 244 2144 2 chr2A.!!$F5 1900
12 TraesCS3A01G134400 chr2A 193777618 193783445 5827 False 1365.5 2128 92.1810 244 2140 2 chr2A.!!$F6 1896
13 TraesCS3A01G134400 chr2A 424511746 424512651 905 True 505.0 590 87.3845 2224 3119 2 chr2A.!!$R5 895
14 TraesCS3A01G134400 chr7A 269097721 269098647 926 False 1657.0 1657 98.9220 2213 3139 1 chr7A.!!$F2 926
15 TraesCS3A01G134400 chr7A 543443149 543444113 964 False 1439.0 1439 93.5190 1173 2144 1 chr7A.!!$F3 971
16 TraesCS3A01G134400 chr4B 142770587 142771874 1287 False 756.0 1157 98.5655 2224 3139 2 chr4B.!!$F1 915
17 TraesCS3A01G134400 chr1B 657196010 657197073 1063 True 1086.0 1086 85.2200 244 1303 1 chr1B.!!$R2 1059
18 TraesCS3A01G134400 chr5B 573575489 573576036 547 False 691.0 691 89.6170 2592 3134 1 chr5B.!!$F1 542
19 TraesCS3A01G134400 chr6D 313019479 313019985 506 True 595.0 595 87.5460 2592 3137 1 chr6D.!!$R1 545
20 TraesCS3A01G134400 chr7D 249448129 249448635 506 False 584.0 584 87.1790 2592 3137 1 chr7D.!!$F1 545
21 TraesCS3A01G134400 chr6B 560641027 560641941 914 False 509.5 584 87.5165 2212 3119 2 chr6B.!!$F3 907
22 TraesCS3A01G134400 chr4A 344732631 344733557 926 True 439.0 477 85.0125 2214 3137 2 chr4A.!!$R4 923

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
54 55 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.0 0.0 0.0 36.80 3.67 F
1171 1189 0.517316 CTGCGTCTAACAGTTTGGCC 59.483 55.0 0.0 0.0 0.00 5.36 F
1431 1449 0.969409 ATGCTTTGGAGAGCTTGGCC 60.969 55.0 0.0 0.0 43.11 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1583 1602 1.014352 GCGATTGGTGTGATGTACCC 58.986 55.000 0.0 0.0 37.40 3.69 R
2060 6012 0.107703 CCAAAGATAGCCACGCAGGA 60.108 55.000 0.0 0.0 41.22 3.86 R
2680 7061 1.302832 CCGCTCCTTTGCTCAACCT 60.303 57.895 0.0 0.0 0.00 3.50 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
23 24 5.793817 CCTAATGATGTGATCCCGTTATCA 58.206 41.667 0.00 0.00 33.48 2.15
24 25 6.230472 CCTAATGATGTGATCCCGTTATCAA 58.770 40.000 0.00 0.00 37.61 2.57
25 26 6.147821 CCTAATGATGTGATCCCGTTATCAAC 59.852 42.308 0.00 0.00 37.61 3.18
47 48 3.219176 ACATCCAATGTCCATAGCCAG 57.781 47.619 0.00 0.00 39.92 4.85
48 49 2.158564 ACATCCAATGTCCATAGCCAGG 60.159 50.000 0.00 0.00 39.92 4.45
49 50 1.891933 TCCAATGTCCATAGCCAGGA 58.108 50.000 0.00 0.00 0.00 3.86
50 51 2.204463 TCCAATGTCCATAGCCAGGAA 58.796 47.619 0.00 0.00 36.80 3.36
51 52 2.580322 TCCAATGTCCATAGCCAGGAAA 59.420 45.455 0.00 0.00 36.80 3.13
52 53 2.689983 CCAATGTCCATAGCCAGGAAAC 59.310 50.000 0.00 0.00 36.80 2.78
53 54 2.689983 CAATGTCCATAGCCAGGAAACC 59.310 50.000 0.00 0.00 36.80 3.27
54 55 1.367346 TGTCCATAGCCAGGAAACCA 58.633 50.000 0.00 0.00 36.80 3.67
55 56 1.922447 TGTCCATAGCCAGGAAACCAT 59.078 47.619 0.00 0.00 36.80 3.55
56 57 2.301346 GTCCATAGCCAGGAAACCATG 58.699 52.381 0.00 0.00 36.80 3.66
57 58 2.092429 GTCCATAGCCAGGAAACCATGA 60.092 50.000 0.00 0.00 36.80 3.07
58 59 2.092429 TCCATAGCCAGGAAACCATGAC 60.092 50.000 0.00 0.00 30.71 3.06
59 60 2.092212 CCATAGCCAGGAAACCATGACT 60.092 50.000 0.00 0.00 0.00 3.41
60 61 3.136443 CCATAGCCAGGAAACCATGACTA 59.864 47.826 0.00 0.00 0.00 2.59
61 62 4.202503 CCATAGCCAGGAAACCATGACTAT 60.203 45.833 0.00 0.00 0.00 2.12
62 63 3.567478 AGCCAGGAAACCATGACTATC 57.433 47.619 0.00 0.00 0.00 2.08
63 64 3.118531 AGCCAGGAAACCATGACTATCT 58.881 45.455 0.00 0.00 0.00 1.98
64 65 3.118112 AGCCAGGAAACCATGACTATCTG 60.118 47.826 0.00 0.00 0.00 2.90
65 66 3.370953 GCCAGGAAACCATGACTATCTGT 60.371 47.826 0.00 0.00 0.00 3.41
66 67 4.848357 CCAGGAAACCATGACTATCTGTT 58.152 43.478 0.00 0.00 0.00 3.16
67 68 4.637534 CCAGGAAACCATGACTATCTGTTG 59.362 45.833 0.00 0.00 0.00 3.33
68 69 5.491070 CAGGAAACCATGACTATCTGTTGA 58.509 41.667 0.00 0.00 0.00 3.18
69 70 6.118170 CAGGAAACCATGACTATCTGTTGAT 58.882 40.000 0.00 0.00 36.74 2.57
70 71 6.259608 CAGGAAACCATGACTATCTGTTGATC 59.740 42.308 0.00 0.00 34.32 2.92
71 72 6.070021 AGGAAACCATGACTATCTGTTGATCA 60.070 38.462 0.00 0.00 34.32 2.92
72 73 6.037610 GGAAACCATGACTATCTGTTGATCAC 59.962 42.308 0.00 0.00 34.32 3.06
73 74 5.682234 ACCATGACTATCTGTTGATCACA 57.318 39.130 0.00 0.00 34.32 3.58
74 75 6.053632 ACCATGACTATCTGTTGATCACAA 57.946 37.500 0.00 0.00 33.87 3.33
85 86 3.575630 GTTGATCACAACGAGCTAGTCA 58.424 45.455 0.00 0.00 45.06 3.41
86 87 3.934457 TGATCACAACGAGCTAGTCAA 57.066 42.857 0.00 0.00 0.00 3.18
87 88 3.575630 TGATCACAACGAGCTAGTCAAC 58.424 45.455 0.00 0.00 0.00 3.18
88 89 3.255888 TGATCACAACGAGCTAGTCAACT 59.744 43.478 0.00 0.00 0.00 3.16
89 90 4.457949 TGATCACAACGAGCTAGTCAACTA 59.542 41.667 0.00 0.00 0.00 2.24
90 91 4.421033 TCACAACGAGCTAGTCAACTAG 57.579 45.455 11.99 11.99 46.63 2.57
91 92 4.070009 TCACAACGAGCTAGTCAACTAGA 58.930 43.478 19.03 0.00 46.80 2.43
92 93 4.154375 TCACAACGAGCTAGTCAACTAGAG 59.846 45.833 19.03 11.89 46.80 2.43
93 94 3.440872 ACAACGAGCTAGTCAACTAGAGG 59.559 47.826 19.03 10.05 46.80 3.69
94 95 2.018515 ACGAGCTAGTCAACTAGAGGC 58.981 52.381 19.03 6.58 46.80 4.70
95 96 2.294074 CGAGCTAGTCAACTAGAGGCT 58.706 52.381 19.03 10.84 46.80 4.58
96 97 2.685897 CGAGCTAGTCAACTAGAGGCTT 59.314 50.000 19.03 1.20 46.80 4.35
97 98 3.878103 CGAGCTAGTCAACTAGAGGCTTA 59.122 47.826 19.03 0.00 46.80 3.09
98 99 4.260866 CGAGCTAGTCAACTAGAGGCTTAC 60.261 50.000 19.03 1.96 46.80 2.34
99 100 4.862371 AGCTAGTCAACTAGAGGCTTACT 58.138 43.478 19.03 3.99 46.80 2.24
100 101 6.003859 AGCTAGTCAACTAGAGGCTTACTA 57.996 41.667 19.03 0.00 46.80 1.82
101 102 6.059484 AGCTAGTCAACTAGAGGCTTACTAG 58.941 44.000 19.03 8.32 46.80 2.57
102 103 5.239963 GCTAGTCAACTAGAGGCTTACTAGG 59.760 48.000 19.03 0.00 46.80 3.02
103 104 4.538738 AGTCAACTAGAGGCTTACTAGGG 58.461 47.826 13.13 6.54 40.86 3.53
104 105 4.230041 AGTCAACTAGAGGCTTACTAGGGA 59.770 45.833 13.13 8.30 40.86 4.20
105 106 4.338964 GTCAACTAGAGGCTTACTAGGGAC 59.661 50.000 13.13 14.30 40.86 4.46
106 107 4.017775 TCAACTAGAGGCTTACTAGGGACA 60.018 45.833 13.13 0.00 40.86 4.02
107 108 4.817874 ACTAGAGGCTTACTAGGGACAT 57.182 45.455 13.13 0.00 40.86 3.06
108 109 4.475345 ACTAGAGGCTTACTAGGGACATG 58.525 47.826 13.13 0.00 40.86 3.21
109 110 2.683768 AGAGGCTTACTAGGGACATGG 58.316 52.381 0.00 0.00 0.00 3.66
110 111 2.022918 AGAGGCTTACTAGGGACATGGT 60.023 50.000 0.00 0.00 0.00 3.55
111 112 2.103263 GAGGCTTACTAGGGACATGGTG 59.897 54.545 0.00 0.00 0.00 4.17
112 113 1.838077 GGCTTACTAGGGACATGGTGT 59.162 52.381 0.00 0.00 0.00 4.16
113 114 2.238898 GGCTTACTAGGGACATGGTGTT 59.761 50.000 0.00 0.00 0.00 3.32
114 115 3.270877 GCTTACTAGGGACATGGTGTTG 58.729 50.000 0.00 0.00 0.00 3.33
115 116 3.307480 GCTTACTAGGGACATGGTGTTGT 60.307 47.826 0.00 0.00 0.00 3.32
116 117 4.504858 CTTACTAGGGACATGGTGTTGTC 58.495 47.826 0.00 0.00 44.27 3.18
117 118 2.621070 ACTAGGGACATGGTGTTGTCT 58.379 47.619 0.00 0.00 44.39 3.41
118 119 3.786553 ACTAGGGACATGGTGTTGTCTA 58.213 45.455 0.00 0.00 44.39 2.59
119 120 4.362677 ACTAGGGACATGGTGTTGTCTAT 58.637 43.478 0.00 0.00 44.39 1.98
120 121 3.634397 AGGGACATGGTGTTGTCTATG 57.366 47.619 0.00 0.00 44.39 2.23
121 122 2.912956 AGGGACATGGTGTTGTCTATGT 59.087 45.455 0.00 0.00 44.39 2.29
122 123 4.101114 AGGGACATGGTGTTGTCTATGTA 58.899 43.478 0.00 0.00 44.39 2.29
123 124 4.721776 AGGGACATGGTGTTGTCTATGTAT 59.278 41.667 0.00 0.00 44.39 2.29
124 125 5.057149 GGGACATGGTGTTGTCTATGTATC 58.943 45.833 0.00 0.00 44.39 2.24
125 126 5.057149 GGACATGGTGTTGTCTATGTATCC 58.943 45.833 0.00 0.00 44.39 2.59
126 127 5.396324 GGACATGGTGTTGTCTATGTATCCA 60.396 44.000 0.00 0.00 44.39 3.41
127 128 5.428253 ACATGGTGTTGTCTATGTATCCAC 58.572 41.667 0.00 0.00 32.41 4.02
128 129 5.045942 ACATGGTGTTGTCTATGTATCCACA 60.046 40.000 0.00 0.00 39.52 4.17
129 130 4.827692 TGGTGTTGTCTATGTATCCACAC 58.172 43.478 0.00 0.00 37.54 3.82
130 131 4.284746 TGGTGTTGTCTATGTATCCACACA 59.715 41.667 0.00 0.00 37.54 3.72
131 132 5.045942 TGGTGTTGTCTATGTATCCACACAT 60.046 40.000 0.00 0.00 41.88 3.21
132 133 5.294306 GGTGTTGTCTATGTATCCACACATG 59.706 44.000 0.00 0.00 39.46 3.21
133 134 5.874810 GTGTTGTCTATGTATCCACACATGT 59.125 40.000 0.00 0.00 39.46 3.21
134 135 7.039270 GTGTTGTCTATGTATCCACACATGTA 58.961 38.462 0.00 0.00 39.46 2.29
135 136 7.710907 GTGTTGTCTATGTATCCACACATGTAT 59.289 37.037 0.00 0.00 39.46 2.29
136 137 7.926018 TGTTGTCTATGTATCCACACATGTATC 59.074 37.037 0.00 0.00 39.46 2.24
137 138 7.839680 TGTCTATGTATCCACACATGTATCT 57.160 36.000 0.00 0.00 39.46 1.98
138 139 7.661040 TGTCTATGTATCCACACATGTATCTG 58.339 38.462 0.00 0.00 39.46 2.90
139 140 7.505585 TGTCTATGTATCCACACATGTATCTGA 59.494 37.037 0.00 0.00 39.46 3.27
140 141 8.026026 GTCTATGTATCCACACATGTATCTGAG 58.974 40.741 0.00 0.00 39.46 3.35
141 142 6.737720 ATGTATCCACACATGTATCTGAGT 57.262 37.500 0.00 0.00 37.74 3.41
142 143 6.544928 TGTATCCACACATGTATCTGAGTT 57.455 37.500 0.00 0.00 0.00 3.01
143 144 6.946340 TGTATCCACACATGTATCTGAGTTT 58.054 36.000 0.00 0.00 0.00 2.66
144 145 7.041721 TGTATCCACACATGTATCTGAGTTTC 58.958 38.462 0.00 0.00 0.00 2.78
145 146 4.832248 TCCACACATGTATCTGAGTTTCC 58.168 43.478 0.00 0.00 0.00 3.13
146 147 4.532126 TCCACACATGTATCTGAGTTTCCT 59.468 41.667 0.00 0.00 0.00 3.36
147 148 5.719563 TCCACACATGTATCTGAGTTTCCTA 59.280 40.000 0.00 0.00 0.00 2.94
148 149 6.384015 TCCACACATGTATCTGAGTTTCCTAT 59.616 38.462 0.00 0.00 0.00 2.57
149 150 6.703607 CCACACATGTATCTGAGTTTCCTATC 59.296 42.308 0.00 0.00 0.00 2.08
150 151 7.267857 CACACATGTATCTGAGTTTCCTATCA 58.732 38.462 0.00 0.00 0.00 2.15
151 152 7.765819 CACACATGTATCTGAGTTTCCTATCAA 59.234 37.037 0.00 0.00 0.00 2.57
152 153 8.489489 ACACATGTATCTGAGTTTCCTATCAAT 58.511 33.333 0.00 0.00 0.00 2.57
153 154 9.987272 CACATGTATCTGAGTTTCCTATCAATA 57.013 33.333 0.00 0.00 0.00 1.90
154 155 9.988815 ACATGTATCTGAGTTTCCTATCAATAC 57.011 33.333 0.00 0.00 0.00 1.89
155 156 9.987272 CATGTATCTGAGTTTCCTATCAATACA 57.013 33.333 0.00 0.00 35.88 2.29
163 164 9.547753 TGAGTTTCCTATCAATACAATTCTAGC 57.452 33.333 0.00 0.00 0.00 3.42
164 165 9.547753 GAGTTTCCTATCAATACAATTCTAGCA 57.452 33.333 0.00 0.00 0.00 3.49
167 168 8.853077 TTCCTATCAATACAATTCTAGCATGG 57.147 34.615 0.00 0.00 0.00 3.66
168 169 8.206126 TCCTATCAATACAATTCTAGCATGGA 57.794 34.615 0.00 0.00 0.00 3.41
169 170 8.829746 TCCTATCAATACAATTCTAGCATGGAT 58.170 33.333 0.00 0.00 0.00 3.41
178 179 8.902540 ACAATTCTAGCATGGATAATAAACGA 57.097 30.769 0.00 0.00 0.00 3.85
179 180 9.507329 ACAATTCTAGCATGGATAATAAACGAT 57.493 29.630 0.00 0.00 0.00 3.73
305 306 5.182001 GGCATTAAAAAGAGCTTCAGACTGA 59.818 40.000 0.00 0.00 0.00 3.41
307 308 6.580416 GCATTAAAAAGAGCTTCAGACTGAAC 59.420 38.462 13.99 10.89 32.21 3.18
328 329 5.825593 ACTGAAAAATAGGTCTCCAGTGA 57.174 39.130 0.00 0.00 32.85 3.41
371 372 2.429069 GTTTTGCAAGCGCTCCCG 60.429 61.111 12.06 3.28 39.64 5.14
399 400 8.746530 TGTACGCCATGGGTATTTTTAAATTTA 58.253 29.630 15.13 0.00 33.77 1.40
753 761 3.570125 GTCATATGGAGAGTGGTCGATGA 59.430 47.826 2.13 0.00 0.00 2.92
936 954 2.820178 TGATGCTGAGGAGAGGTTACA 58.180 47.619 0.00 0.00 0.00 2.41
964 982 5.374154 TCAGACTATAGGTGAGGGAGATCTT 59.626 44.000 4.43 0.00 0.00 2.40
1046 1064 1.260544 AAACCTTCAGGATGGCAAGC 58.739 50.000 0.00 0.00 38.94 4.01
1082 1100 5.016831 TGTCTAGTTATGCTCCTGACAAGA 58.983 41.667 0.00 0.00 32.94 3.02
1171 1189 0.517316 CTGCGTCTAACAGTTTGGCC 59.483 55.000 0.00 0.00 0.00 5.36
1314 1332 3.826524 TCGCTATGAGAGAAGAGTGGAT 58.173 45.455 0.00 0.00 0.00 3.41
1381 1399 7.503230 TGGATGCTTATTCTGCTTGATCAATTA 59.497 33.333 8.96 0.09 0.00 1.40
1431 1449 0.969409 ATGCTTTGGAGAGCTTGGCC 60.969 55.000 0.00 0.00 43.11 5.36
1487 1505 4.861210 AGAATCCTTACGTGCTTCTATCG 58.139 43.478 0.00 0.00 0.00 2.92
1532 1551 7.279758 GGAAATCCTTCACAAATGTCAAAAACA 59.720 33.333 0.00 0.00 36.34 2.83
1583 1602 1.788915 AGGGGGTGATTGATAATGGGG 59.211 52.381 0.00 0.00 0.00 4.96
1686 1708 3.009916 AGGTTTGTGGAGAGCATGAGATT 59.990 43.478 0.00 0.00 0.00 2.40
1820 5769 7.538575 GCTTGCTGGGTTATATATTGGTATTG 58.461 38.462 0.00 0.00 0.00 1.90
1859 5811 2.595124 TTTGAAGACTGACAGCGTGA 57.405 45.000 1.25 0.00 0.00 4.35
1862 5814 2.227194 TGAAGACTGACAGCGTGACTA 58.773 47.619 1.25 0.00 0.00 2.59
1942 5894 2.419297 GGAGGCGATGAGTGTCTCAAAT 60.419 50.000 3.58 0.00 44.04 2.32
1993 5945 5.841267 TTGATAGGCAGGCAAATAGGATA 57.159 39.130 0.00 0.00 0.00 2.59
2007 5959 6.206243 GCAAATAGGATAGTGCATGAGATTGT 59.794 38.462 0.00 0.00 36.05 2.71
2059 6011 8.871629 ATGGTGTTTTATGTAATAGTGTTCCA 57.128 30.769 0.00 0.00 0.00 3.53
2060 6012 8.871629 TGGTGTTTTATGTAATAGTGTTCCAT 57.128 30.769 0.00 0.00 0.00 3.41
2073 6025 0.179045 GTTCCATCCTGCGTGGCTAT 60.179 55.000 0.00 0.00 36.66 2.97
2079 6031 0.107703 TCCTGCGTGGCTATCTTTGG 60.108 55.000 0.00 0.00 35.26 3.28
2170 6123 6.243551 CAAGTGAATTGTACATAGCAGAACG 58.756 40.000 0.00 0.00 33.95 3.95
2171 6124 5.720202 AGTGAATTGTACATAGCAGAACGA 58.280 37.500 0.00 0.00 0.00 3.85
2172 6125 5.577164 AGTGAATTGTACATAGCAGAACGAC 59.423 40.000 0.00 0.00 0.00 4.34
2173 6126 4.561213 TGAATTGTACATAGCAGAACGACG 59.439 41.667 0.00 0.00 0.00 5.12
2174 6127 3.564235 TTGTACATAGCAGAACGACGT 57.436 42.857 0.00 0.00 0.00 4.34
2175 6128 2.858839 TGTACATAGCAGAACGACGTG 58.141 47.619 0.00 0.00 0.00 4.49
2176 6129 2.485038 TGTACATAGCAGAACGACGTGA 59.515 45.455 0.00 0.00 0.00 4.35
2177 6130 2.717580 ACATAGCAGAACGACGTGAA 57.282 45.000 0.00 0.00 0.00 3.18
2178 6131 2.596452 ACATAGCAGAACGACGTGAAG 58.404 47.619 0.00 0.00 0.00 3.02
2179 6132 2.030185 ACATAGCAGAACGACGTGAAGT 60.030 45.455 0.00 0.00 0.00 3.01
2180 6133 2.327081 TAGCAGAACGACGTGAAGTC 57.673 50.000 0.00 0.00 46.16 3.01
2187 6140 2.028484 GACGTGAAGTCGTGCCCA 59.972 61.111 0.00 0.00 44.21 5.36
2188 6141 1.374252 GACGTGAAGTCGTGCCCAT 60.374 57.895 0.00 0.00 44.21 4.00
2189 6142 1.626654 GACGTGAAGTCGTGCCCATG 61.627 60.000 0.00 0.00 44.21 3.66
2190 6143 1.667830 CGTGAAGTCGTGCCCATGT 60.668 57.895 0.00 0.00 0.00 3.21
2191 6144 1.626654 CGTGAAGTCGTGCCCATGTC 61.627 60.000 0.00 0.00 0.00 3.06
2192 6145 0.320771 GTGAAGTCGTGCCCATGTCT 60.321 55.000 0.00 0.00 0.00 3.41
2193 6146 1.067142 GTGAAGTCGTGCCCATGTCTA 60.067 52.381 0.00 0.00 0.00 2.59
2194 6147 1.831106 TGAAGTCGTGCCCATGTCTAT 59.169 47.619 0.00 0.00 0.00 1.98
2195 6148 2.159099 TGAAGTCGTGCCCATGTCTATC 60.159 50.000 0.00 0.00 0.00 2.08
2196 6149 0.753262 AGTCGTGCCCATGTCTATCC 59.247 55.000 0.00 0.00 0.00 2.59
2197 6150 0.249911 GTCGTGCCCATGTCTATCCC 60.250 60.000 0.00 0.00 0.00 3.85
2198 6151 0.398522 TCGTGCCCATGTCTATCCCT 60.399 55.000 0.00 0.00 0.00 4.20
2199 6152 1.133294 TCGTGCCCATGTCTATCCCTA 60.133 52.381 0.00 0.00 0.00 3.53
2200 6153 1.691976 CGTGCCCATGTCTATCCCTAA 59.308 52.381 0.00 0.00 0.00 2.69
2201 6154 2.303022 CGTGCCCATGTCTATCCCTAAT 59.697 50.000 0.00 0.00 0.00 1.73
2202 6155 3.617531 CGTGCCCATGTCTATCCCTAATC 60.618 52.174 0.00 0.00 0.00 1.75
2203 6156 2.912956 TGCCCATGTCTATCCCTAATCC 59.087 50.000 0.00 0.00 0.00 3.01
2204 6157 2.239907 GCCCATGTCTATCCCTAATCCC 59.760 54.545 0.00 0.00 0.00 3.85
2205 6158 3.808189 CCCATGTCTATCCCTAATCCCT 58.192 50.000 0.00 0.00 0.00 4.20
2206 6159 4.821551 GCCCATGTCTATCCCTAATCCCTA 60.822 50.000 0.00 0.00 0.00 3.53
2207 6160 5.350547 CCCATGTCTATCCCTAATCCCTAA 58.649 45.833 0.00 0.00 0.00 2.69
2208 6161 5.973124 CCCATGTCTATCCCTAATCCCTAAT 59.027 44.000 0.00 0.00 0.00 1.73
2209 6162 6.100424 CCCATGTCTATCCCTAATCCCTAATC 59.900 46.154 0.00 0.00 0.00 1.75
2210 6163 6.100424 CCATGTCTATCCCTAATCCCTAATCC 59.900 46.154 0.00 0.00 0.00 3.01
3036 7462 0.749454 GCGCAGAAGATGGGGTGATT 60.749 55.000 0.30 0.00 42.01 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.793817 TGATAACGGGATCACATCATTAGG 58.206 41.667 0.00 0.00 30.75 2.69
1 2 7.121974 GTTGATAACGGGATCACATCATTAG 57.878 40.000 0.00 0.00 35.56 1.73
28 29 2.107031 TCCTGGCTATGGACATTGGATG 59.893 50.000 0.00 0.00 0.00 3.51
29 30 2.421725 TCCTGGCTATGGACATTGGAT 58.578 47.619 0.00 0.00 0.00 3.41
30 31 1.891933 TCCTGGCTATGGACATTGGA 58.108 50.000 0.00 0.00 0.00 3.53
31 32 2.689983 GTTTCCTGGCTATGGACATTGG 59.310 50.000 0.00 0.00 32.65 3.16
32 33 2.689983 GGTTTCCTGGCTATGGACATTG 59.310 50.000 0.00 0.00 32.65 2.82
33 34 2.311542 TGGTTTCCTGGCTATGGACATT 59.688 45.455 0.00 0.00 32.65 2.71
34 35 1.922447 TGGTTTCCTGGCTATGGACAT 59.078 47.619 0.00 0.00 32.65 3.06
35 36 1.367346 TGGTTTCCTGGCTATGGACA 58.633 50.000 0.00 0.00 32.65 4.02
36 37 2.092429 TCATGGTTTCCTGGCTATGGAC 60.092 50.000 0.00 0.00 32.65 4.02
37 38 2.092429 GTCATGGTTTCCTGGCTATGGA 60.092 50.000 0.00 0.00 0.00 3.41
38 39 2.092212 AGTCATGGTTTCCTGGCTATGG 60.092 50.000 0.00 0.00 0.00 2.74
39 40 3.287867 AGTCATGGTTTCCTGGCTATG 57.712 47.619 0.00 0.00 0.00 2.23
40 41 4.910304 AGATAGTCATGGTTTCCTGGCTAT 59.090 41.667 10.00 10.00 41.67 2.97
41 42 4.101585 CAGATAGTCATGGTTTCCTGGCTA 59.898 45.833 0.00 0.00 34.35 3.93
42 43 3.118112 CAGATAGTCATGGTTTCCTGGCT 60.118 47.826 0.00 0.00 0.00 4.75
43 44 3.209410 CAGATAGTCATGGTTTCCTGGC 58.791 50.000 0.00 0.00 0.00 4.85
44 45 4.494091 ACAGATAGTCATGGTTTCCTGG 57.506 45.455 0.00 0.00 0.00 4.45
45 46 5.491070 TCAACAGATAGTCATGGTTTCCTG 58.509 41.667 0.00 0.00 0.00 3.86
46 47 5.762179 TCAACAGATAGTCATGGTTTCCT 57.238 39.130 0.00 0.00 0.00 3.36
47 48 6.037610 GTGATCAACAGATAGTCATGGTTTCC 59.962 42.308 0.00 0.00 0.00 3.13
48 49 6.595326 TGTGATCAACAGATAGTCATGGTTTC 59.405 38.462 0.00 0.00 33.78 2.78
49 50 6.475504 TGTGATCAACAGATAGTCATGGTTT 58.524 36.000 0.00 0.00 33.78 3.27
50 51 6.053632 TGTGATCAACAGATAGTCATGGTT 57.946 37.500 0.00 0.00 33.78 3.67
51 52 5.682234 TGTGATCAACAGATAGTCATGGT 57.318 39.130 0.00 0.00 33.78 3.55
64 65 8.771523 CTAGTTGACTAGCTCGTTGTGATCAAC 61.772 44.444 0.00 9.17 42.66 3.18
65 66 3.934457 TGACTAGCTCGTTGTGATCAA 57.066 42.857 0.00 0.00 0.00 2.57
66 67 3.255888 AGTTGACTAGCTCGTTGTGATCA 59.744 43.478 0.00 0.00 0.00 2.92
67 68 3.839293 AGTTGACTAGCTCGTTGTGATC 58.161 45.455 0.00 0.00 0.00 2.92
68 69 3.944055 AGTTGACTAGCTCGTTGTGAT 57.056 42.857 0.00 0.00 0.00 3.06
69 70 4.070009 TCTAGTTGACTAGCTCGTTGTGA 58.930 43.478 12.30 0.00 44.24 3.58
70 71 4.407818 CTCTAGTTGACTAGCTCGTTGTG 58.592 47.826 12.30 0.00 44.24 3.33
71 72 3.440872 CCTCTAGTTGACTAGCTCGTTGT 59.559 47.826 12.30 0.00 44.24 3.32
72 73 3.732471 GCCTCTAGTTGACTAGCTCGTTG 60.732 52.174 12.30 0.75 44.24 4.10
73 74 2.424246 GCCTCTAGTTGACTAGCTCGTT 59.576 50.000 12.30 0.00 44.24 3.85
74 75 2.018515 GCCTCTAGTTGACTAGCTCGT 58.981 52.381 12.30 0.00 44.24 4.18
75 76 2.294074 AGCCTCTAGTTGACTAGCTCG 58.706 52.381 12.30 0.00 44.24 5.03
76 77 4.885325 AGTAAGCCTCTAGTTGACTAGCTC 59.115 45.833 12.30 5.16 44.24 4.09
77 78 4.862371 AGTAAGCCTCTAGTTGACTAGCT 58.138 43.478 12.30 5.64 44.24 3.32
78 79 5.239963 CCTAGTAAGCCTCTAGTTGACTAGC 59.760 48.000 12.30 3.61 44.24 3.42
79 80 5.766174 CCCTAGTAAGCCTCTAGTTGACTAG 59.234 48.000 11.14 11.14 45.57 2.57
80 81 5.431073 TCCCTAGTAAGCCTCTAGTTGACTA 59.569 44.000 0.00 0.00 34.72 2.59
81 82 4.230041 TCCCTAGTAAGCCTCTAGTTGACT 59.770 45.833 0.00 0.00 34.72 3.41
82 83 4.338964 GTCCCTAGTAAGCCTCTAGTTGAC 59.661 50.000 0.00 8.18 34.72 3.18
83 84 4.017775 TGTCCCTAGTAAGCCTCTAGTTGA 60.018 45.833 0.00 1.98 34.72 3.18
84 85 4.279145 TGTCCCTAGTAAGCCTCTAGTTG 58.721 47.826 0.00 0.00 34.72 3.16
85 86 4.604784 TGTCCCTAGTAAGCCTCTAGTT 57.395 45.455 0.00 0.00 34.72 2.24
86 87 4.475345 CATGTCCCTAGTAAGCCTCTAGT 58.525 47.826 0.00 0.00 34.72 2.57
87 88 3.829601 CCATGTCCCTAGTAAGCCTCTAG 59.170 52.174 0.00 0.00 35.86 2.43
88 89 3.206866 ACCATGTCCCTAGTAAGCCTCTA 59.793 47.826 0.00 0.00 0.00 2.43
89 90 2.022918 ACCATGTCCCTAGTAAGCCTCT 60.023 50.000 0.00 0.00 0.00 3.69
90 91 2.103263 CACCATGTCCCTAGTAAGCCTC 59.897 54.545 0.00 0.00 0.00 4.70
91 92 2.119495 CACCATGTCCCTAGTAAGCCT 58.881 52.381 0.00 0.00 0.00 4.58
92 93 1.838077 ACACCATGTCCCTAGTAAGCC 59.162 52.381 0.00 0.00 0.00 4.35
93 94 3.270877 CAACACCATGTCCCTAGTAAGC 58.729 50.000 0.00 0.00 0.00 3.09
94 95 4.504858 GACAACACCATGTCCCTAGTAAG 58.495 47.826 0.00 0.00 43.11 2.34
95 96 4.546829 GACAACACCATGTCCCTAGTAA 57.453 45.455 0.00 0.00 43.11 2.24
101 102 8.319752 TGGATACATAGACAACACCATGTCCC 62.320 46.154 3.95 0.00 46.44 4.46
102 103 5.396324 TGGATACATAGACAACACCATGTCC 60.396 44.000 3.95 0.00 46.44 4.02
103 104 5.670485 TGGATACATAGACAACACCATGTC 58.330 41.667 0.00 0.00 45.97 3.06
104 105 5.692115 TGGATACATAGACAACACCATGT 57.308 39.130 0.00 0.00 46.17 3.21
120 121 6.480320 GGAAACTCAGATACATGTGTGGATAC 59.520 42.308 9.11 0.00 0.00 2.24
121 122 6.384015 AGGAAACTCAGATACATGTGTGGATA 59.616 38.462 9.11 0.00 32.90 2.59
122 123 5.190528 AGGAAACTCAGATACATGTGTGGAT 59.809 40.000 9.11 0.00 32.90 3.41
123 124 4.532126 AGGAAACTCAGATACATGTGTGGA 59.468 41.667 9.11 1.00 32.90 4.02
124 125 4.836825 AGGAAACTCAGATACATGTGTGG 58.163 43.478 9.11 0.00 32.90 4.17
125 126 7.267857 TGATAGGAAACTCAGATACATGTGTG 58.732 38.462 9.11 3.44 43.67 3.82
126 127 7.423844 TGATAGGAAACTCAGATACATGTGT 57.576 36.000 9.11 0.10 43.67 3.72
127 128 8.899427 ATTGATAGGAAACTCAGATACATGTG 57.101 34.615 9.11 0.00 43.67 3.21
128 129 9.988815 GTATTGATAGGAAACTCAGATACATGT 57.011 33.333 2.69 2.69 43.67 3.21
129 130 9.987272 TGTATTGATAGGAAACTCAGATACATG 57.013 33.333 0.00 0.00 43.67 3.21
137 138 9.547753 GCTAGAATTGTATTGATAGGAAACTCA 57.452 33.333 0.00 0.00 43.67 3.41
138 139 9.547753 TGCTAGAATTGTATTGATAGGAAACTC 57.452 33.333 0.00 0.00 43.67 3.01
141 142 9.288576 CCATGCTAGAATTGTATTGATAGGAAA 57.711 33.333 0.00 0.00 0.00 3.13
142 143 8.659527 TCCATGCTAGAATTGTATTGATAGGAA 58.340 33.333 0.00 0.00 0.00 3.36
143 144 8.206126 TCCATGCTAGAATTGTATTGATAGGA 57.794 34.615 0.00 0.00 0.00 2.94
152 153 9.990360 TCGTTTATTATCCATGCTAGAATTGTA 57.010 29.630 0.00 0.00 0.00 2.41
153 154 8.902540 TCGTTTATTATCCATGCTAGAATTGT 57.097 30.769 0.00 0.00 0.00 2.71
222 223 4.103153 TCTGTTGGAAATATGCCCTAGAGG 59.897 45.833 0.00 0.00 39.47 3.69
223 224 5.296151 TCTGTTGGAAATATGCCCTAGAG 57.704 43.478 0.00 0.00 0.00 2.43
224 225 5.708736 TTCTGTTGGAAATATGCCCTAGA 57.291 39.130 0.00 0.00 0.00 2.43
225 226 6.064060 TCATTCTGTTGGAAATATGCCCTAG 58.936 40.000 0.00 0.00 37.49 3.02
226 227 6.012337 TCATTCTGTTGGAAATATGCCCTA 57.988 37.500 0.00 0.00 37.49 3.53
227 228 4.870636 TCATTCTGTTGGAAATATGCCCT 58.129 39.130 0.00 0.00 37.49 5.19
228 229 5.452356 CCTTCATTCTGTTGGAAATATGCCC 60.452 44.000 0.00 0.00 37.49 5.36
229 230 5.127682 ACCTTCATTCTGTTGGAAATATGCC 59.872 40.000 0.00 0.00 37.49 4.40
230 231 6.212888 ACCTTCATTCTGTTGGAAATATGC 57.787 37.500 0.00 0.00 37.49 3.14
239 240 4.398319 ACCTACCAACCTTCATTCTGTTG 58.602 43.478 0.00 0.00 39.20 3.33
240 241 4.724279 ACCTACCAACCTTCATTCTGTT 57.276 40.909 0.00 0.00 0.00 3.16
241 242 4.506802 GGAACCTACCAACCTTCATTCTGT 60.507 45.833 0.00 0.00 0.00 3.41
242 243 4.010349 GGAACCTACCAACCTTCATTCTG 58.990 47.826 0.00 0.00 0.00 3.02
259 260 5.049828 CCTTGTCTTTTGTTGATTGGAACC 58.950 41.667 0.00 0.00 0.00 3.62
305 306 6.187727 TCACTGGAGACCTATTTTTCAGTT 57.812 37.500 0.00 0.00 32.51 3.16
317 318 9.396022 TGATTTTCTTTTATATCACTGGAGACC 57.604 33.333 0.00 0.00 0.00 3.85
371 372 2.047002 AAATACCCATGGCGTACACC 57.953 50.000 6.09 0.00 0.00 4.16
399 400 8.209584 AGATAACTCATCACATAATGAAGCTGT 58.790 33.333 0.00 0.00 41.93 4.40
864 874 2.571653 TCATCCCATCTTCTTGTTCCGT 59.428 45.455 0.00 0.00 0.00 4.69
895 905 4.966168 TCATGGTTATAGAACAGGTGCCTA 59.034 41.667 2.17 0.00 37.29 3.93
936 954 7.350044 TCTCCCTCACCTATAGTCTGAATAT 57.650 40.000 2.96 2.96 0.00 1.28
964 982 8.902806 CCATTTTTCTCATAGTACCAAGCAATA 58.097 33.333 0.00 0.00 0.00 1.90
1148 1166 2.135139 CAAACTGTTAGACGCAGCTCA 58.865 47.619 0.00 0.00 37.47 4.26
1171 1189 5.556915 TGAATAACTCTGTTTACCTGGGTG 58.443 41.667 2.07 0.00 0.00 4.61
1361 1379 7.307632 CGACCCTAATTGATCAAGCAGAATAAG 60.308 40.741 14.54 2.55 0.00 1.73
1381 1399 1.271871 TGATCATGTTTTGGCGACCCT 60.272 47.619 0.00 0.00 0.00 4.34
1431 1449 6.812656 CCCGAAGATCATATCATTTCTGAGAG 59.187 42.308 0.00 0.00 34.12 3.20
1487 1505 4.864704 TCCAGTAATTTCCCACAAAAGC 57.135 40.909 0.00 0.00 0.00 3.51
1532 1551 1.264288 GCTTAAGTCAACTTGCGCACT 59.736 47.619 11.12 0.00 37.40 4.40
1583 1602 1.014352 GCGATTGGTGTGATGTACCC 58.986 55.000 0.00 0.00 37.40 3.69
1661 1683 2.906389 TCATGCTCTCCACAAACCTAGT 59.094 45.455 0.00 0.00 0.00 2.57
1666 1688 4.730657 CAAATCTCATGCTCTCCACAAAC 58.269 43.478 0.00 0.00 0.00 2.93
1686 1708 2.158928 GCAATTATCCCAATGCTGGCAA 60.159 45.455 0.00 0.00 41.99 4.52
1820 5769 6.454795 TCAAAATAACAGGACTTTGGAATGC 58.545 36.000 0.00 0.00 31.20 3.56
1859 5811 5.789643 TTTGCCAGAGAAAAAGCAATAGT 57.210 34.783 0.00 0.00 44.10 2.12
1862 5814 5.280654 TCTTTTGCCAGAGAAAAAGCAAT 57.719 34.783 1.98 0.00 44.10 3.56
1993 5945 8.891671 AACAAAATTTAACAATCTCATGCACT 57.108 26.923 0.00 0.00 0.00 4.40
2059 6011 1.475751 CCAAAGATAGCCACGCAGGAT 60.476 52.381 0.00 0.00 41.22 3.24
2060 6012 0.107703 CCAAAGATAGCCACGCAGGA 60.108 55.000 0.00 0.00 41.22 3.86
2144 6097 7.062956 CGTTCTGCTATGTACAATTCACTTGTA 59.937 37.037 0.00 0.00 46.30 2.41
2146 6099 6.090763 TCGTTCTGCTATGTACAATTCACTTG 59.909 38.462 0.00 0.00 40.90 3.16
2147 6100 6.090898 GTCGTTCTGCTATGTACAATTCACTT 59.909 38.462 0.00 0.00 0.00 3.16
2148 6101 5.577164 GTCGTTCTGCTATGTACAATTCACT 59.423 40.000 0.00 0.00 0.00 3.41
2149 6102 5.498700 CGTCGTTCTGCTATGTACAATTCAC 60.499 44.000 0.00 0.00 0.00 3.18
2150 6103 4.561213 CGTCGTTCTGCTATGTACAATTCA 59.439 41.667 0.00 0.00 0.00 2.57
2151 6104 4.561606 ACGTCGTTCTGCTATGTACAATTC 59.438 41.667 0.00 0.00 0.00 2.17
2152 6105 4.326278 CACGTCGTTCTGCTATGTACAATT 59.674 41.667 0.00 0.00 0.00 2.32
2153 6106 3.857665 CACGTCGTTCTGCTATGTACAAT 59.142 43.478 0.00 0.00 0.00 2.71
2154 6107 3.058085 TCACGTCGTTCTGCTATGTACAA 60.058 43.478 0.00 0.00 0.00 2.41
2155 6108 2.485038 TCACGTCGTTCTGCTATGTACA 59.515 45.455 0.00 0.00 0.00 2.90
2156 6109 3.127081 TCACGTCGTTCTGCTATGTAC 57.873 47.619 0.00 0.00 0.00 2.90
2157 6110 3.189910 ACTTCACGTCGTTCTGCTATGTA 59.810 43.478 0.00 0.00 0.00 2.29
2158 6111 2.030185 ACTTCACGTCGTTCTGCTATGT 60.030 45.455 0.00 0.00 0.00 2.29
2159 6112 2.594654 GACTTCACGTCGTTCTGCTATG 59.405 50.000 0.00 0.00 32.04 2.23
2160 6113 2.864968 GACTTCACGTCGTTCTGCTAT 58.135 47.619 0.00 0.00 32.04 2.97
2161 6114 2.327081 GACTTCACGTCGTTCTGCTA 57.673 50.000 0.00 0.00 32.04 3.49
2162 6115 3.180984 GACTTCACGTCGTTCTGCT 57.819 52.632 0.00 0.00 32.04 4.24
2170 6123 1.374252 ATGGGCACGACTTCACGTC 60.374 57.895 0.00 0.00 44.76 4.34
2172 6125 1.626654 GACATGGGCACGACTTCACG 61.627 60.000 0.00 0.00 39.31 4.35
2173 6126 0.320771 AGACATGGGCACGACTTCAC 60.321 55.000 0.00 0.00 0.00 3.18
2174 6127 1.262417 TAGACATGGGCACGACTTCA 58.738 50.000 0.00 0.00 0.00 3.02
2175 6128 2.474816 GATAGACATGGGCACGACTTC 58.525 52.381 0.00 0.00 0.00 3.01
2176 6129 1.139058 GGATAGACATGGGCACGACTT 59.861 52.381 0.00 0.00 0.00 3.01
2177 6130 0.753262 GGATAGACATGGGCACGACT 59.247 55.000 0.00 0.00 0.00 4.18
2178 6131 0.249911 GGGATAGACATGGGCACGAC 60.250 60.000 0.00 0.00 0.00 4.34
2179 6132 0.398522 AGGGATAGACATGGGCACGA 60.399 55.000 0.00 0.00 0.00 4.35
2180 6133 1.338107 TAGGGATAGACATGGGCACG 58.662 55.000 0.00 0.00 0.00 5.34
2181 6134 3.307762 GGATTAGGGATAGACATGGGCAC 60.308 52.174 0.00 0.00 0.00 5.01
2182 6135 2.912956 GGATTAGGGATAGACATGGGCA 59.087 50.000 0.00 0.00 0.00 5.36
2183 6136 2.239907 GGGATTAGGGATAGACATGGGC 59.760 54.545 0.00 0.00 0.00 5.36
2184 6137 3.808189 AGGGATTAGGGATAGACATGGG 58.192 50.000 0.00 0.00 0.00 4.00
2185 6138 6.100424 GGATTAGGGATTAGGGATAGACATGG 59.900 46.154 0.00 0.00 0.00 3.66
2186 6139 6.100424 GGGATTAGGGATTAGGGATAGACATG 59.900 46.154 0.00 0.00 0.00 3.21
2187 6140 6.008475 AGGGATTAGGGATTAGGGATAGACAT 60.008 42.308 0.00 0.00 0.00 3.06
2188 6141 5.321625 AGGGATTAGGGATTAGGGATAGACA 59.678 44.000 0.00 0.00 0.00 3.41
2189 6142 5.855988 AGGGATTAGGGATTAGGGATAGAC 58.144 45.833 0.00 0.00 0.00 2.59
2190 6143 7.629757 TTAGGGATTAGGGATTAGGGATAGA 57.370 40.000 0.00 0.00 0.00 1.98
2191 6144 8.300614 AGATTAGGGATTAGGGATTAGGGATAG 58.699 40.741 0.00 0.00 0.00 2.08
2192 6145 8.213458 AGATTAGGGATTAGGGATTAGGGATA 57.787 38.462 0.00 0.00 0.00 2.59
2193 6146 7.033972 AGAGATTAGGGATTAGGGATTAGGGAT 60.034 40.741 0.00 0.00 0.00 3.85
2194 6147 6.283084 AGAGATTAGGGATTAGGGATTAGGGA 59.717 42.308 0.00 0.00 0.00 4.20
2195 6148 6.516696 AGAGATTAGGGATTAGGGATTAGGG 58.483 44.000 0.00 0.00 0.00 3.53
2196 6149 6.613679 GGAGAGATTAGGGATTAGGGATTAGG 59.386 46.154 0.00 0.00 0.00 2.69
2197 6150 6.613679 GGGAGAGATTAGGGATTAGGGATTAG 59.386 46.154 0.00 0.00 0.00 1.73
2198 6151 6.283084 AGGGAGAGATTAGGGATTAGGGATTA 59.717 42.308 0.00 0.00 0.00 1.75
2199 6152 5.080002 AGGGAGAGATTAGGGATTAGGGATT 59.920 44.000 0.00 0.00 0.00 3.01
2200 6153 4.619293 AGGGAGAGATTAGGGATTAGGGAT 59.381 45.833 0.00 0.00 0.00 3.85
2201 6154 4.004862 AGGGAGAGATTAGGGATTAGGGA 58.995 47.826 0.00 0.00 0.00 4.20
2202 6155 4.427956 AGGGAGAGATTAGGGATTAGGG 57.572 50.000 0.00 0.00 0.00 3.53
2203 6156 9.736819 ATTATTAGGGAGAGATTAGGGATTAGG 57.263 37.037 0.00 0.00 0.00 2.69
2208 6161 9.047947 GCTTTATTATTAGGGAGAGATTAGGGA 57.952 37.037 0.00 0.00 0.00 4.20
2209 6162 8.826765 TGCTTTATTATTAGGGAGAGATTAGGG 58.173 37.037 0.00 0.00 0.00 3.53
2210 6163 9.660180 GTGCTTTATTATTAGGGAGAGATTAGG 57.340 37.037 0.00 0.00 0.00 2.69
2680 7061 1.302832 CCGCTCCTTTGCTCAACCT 60.303 57.895 0.00 0.00 0.00 3.50
3036 7462 7.748691 TTCATTGAATCTTGACACTGAATCA 57.251 32.000 0.00 0.00 33.25 2.57


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

AutoCloner maintained by Alex Coulton.