Multiple sequence alignment - TraesCS7A01G568700

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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 TraesCS7A01G568700 chr7A 100.000 4819 0 0 1 4819 736430025 736425207 0.000000e+00 8900.0
1 TraesCS7A01G568700 chr7A 81.502 2211 342 44 2207 4367 735962494 735964687 0.000000e+00 1755.0
2 TraesCS7A01G568700 chr7A 80.931 2276 374 36 2142 4367 736006616 736004351 0.000000e+00 1744.0
3 TraesCS7A01G568700 chr7A 81.200 2234 356 44 2145 4328 736094420 736092201 0.000000e+00 1740.0
4 TraesCS7A01G568700 chr7A 80.417 2303 374 47 2142 4393 735822320 735820044 0.000000e+00 1683.0
5 TraesCS7A01G568700 chr7A 81.224 1438 227 28 2988 4393 736071392 736069966 0.000000e+00 1120.0
6 TraesCS7A01G568700 chr7A 83.263 1183 172 9 435 1595 736329586 736328408 0.000000e+00 1064.0
7 TraesCS7A01G568700 chr7A 83.602 1116 163 12 534 1633 736008354 736007243 0.000000e+00 1029.0
8 TraesCS7A01G568700 chr7A 82.919 644 90 9 3762 4393 736000347 735999712 3.260000e-156 562.0
9 TraesCS7A01G568700 chr7A 76.092 435 75 19 4401 4816 736089816 736089392 2.940000e-47 200.0
10 TraesCS7A01G568700 chr7A 75.339 442 84 15 4392 4816 735839955 735839522 6.370000e-44 189.0
11 TraesCS7A01G568700 chr7D 95.632 2335 65 6 2096 4393 632020392 632022726 0.000000e+00 3712.0
12 TraesCS7A01G568700 chr7D 92.673 1747 78 16 225 1951 632018100 632019816 0.000000e+00 2471.0
13 TraesCS7A01G568700 chr7D 83.225 2307 315 51 2139 4393 621261059 621263345 0.000000e+00 2050.0
14 TraesCS7A01G568700 chr7D 81.922 2268 329 47 2180 4393 555049539 555051779 0.000000e+00 1842.0
15 TraesCS7A01G568700 chr7D 81.519 2278 353 41 2171 4395 632143037 632145299 0.000000e+00 1812.0
16 TraesCS7A01G568700 chr7D 81.170 2257 353 50 2193 4393 632035145 632037385 0.000000e+00 1748.0
17 TraesCS7A01G568700 chr7D 81.354 2215 353 37 2226 4393 632098423 632100624 0.000000e+00 1748.0
18 TraesCS7A01G568700 chr7D 79.844 2302 400 32 2144 4393 632081071 632083360 0.000000e+00 1622.0
19 TraesCS7A01G568700 chr7D 84.964 1104 148 9 534 1621 632033223 632034324 0.000000e+00 1103.0
20 TraesCS7A01G568700 chr7D 83.085 1141 169 12 501 1621 555047293 555048429 0.000000e+00 1016.0
21 TraesCS7A01G568700 chr7D 82.821 1106 174 6 478 1572 632096459 632097559 0.000000e+00 976.0
22 TraesCS7A01G568700 chr7D 80.978 1125 180 25 3298 4395 632046385 632047502 0.000000e+00 861.0
23 TraesCS7A01G568700 chr7D 93.224 428 29 0 4392 4819 632023464 632023891 8.800000e-177 630.0
24 TraesCS7A01G568700 chr7D 81.986 433 54 11 4401 4815 555053812 555054238 3.570000e-91 346.0
25 TraesCS7A01G568700 chr7D 79.345 397 65 6 4417 4803 621264130 621264519 3.700000e-66 263.0
26 TraesCS7A01G568700 chr7D 97.802 91 1 1 139 228 632010748 632010838 6.460000e-34 156.0
27 TraesCS7A01G568700 chr7D 94.030 67 2 2 1960 2025 632020128 632020193 3.070000e-17 100.0
28 TraesCS7A01G568700 chr7D 91.667 48 1 1 356 400 579763974 579763927 4.030000e-06 63.9
29 TraesCS7A01G568700 chr1B 83.155 2244 329 30 2192 4394 577925968 577923733 0.000000e+00 2004.0
30 TraesCS7A01G568700 chr1B 84.707 1347 164 19 328 1653 577928990 577927665 0.000000e+00 1308.0
31 TraesCS7A01G568700 chr7B 81.957 2167 330 41 2180 4295 747526070 747523914 0.000000e+00 1779.0
32 TraesCS7A01G568700 chr7B 80.741 2295 383 30 2149 4395 744249757 744252040 0.000000e+00 1735.0
33 TraesCS7A01G568700 chr7B 80.519 2310 364 44 2136 4393 744209495 744211770 0.000000e+00 1694.0
34 TraesCS7A01G568700 chr7B 80.320 2251 382 35 2189 4393 745232105 745234340 0.000000e+00 1646.0
35 TraesCS7A01G568700 chr7B 80.458 2139 365 32 2226 4319 744293266 744291136 0.000000e+00 1585.0
36 TraesCS7A01G568700 chr7B 83.718 1474 210 18 2230 3682 744337222 744335758 0.000000e+00 1365.0
37 TraesCS7A01G568700 chr7B 84.897 1119 139 10 534 1637 743709480 743710583 0.000000e+00 1103.0
38 TraesCS7A01G568700 chr7B 84.093 1119 148 10 534 1637 744269347 744270450 0.000000e+00 1053.0
39 TraesCS7A01G568700 chr7B 83.275 1142 159 20 538 1654 743999258 743998124 0.000000e+00 1022.0
40 TraesCS7A01G568700 chr7B 82.912 1147 171 16 534 1661 744339378 744338238 0.000000e+00 1009.0
41 TraesCS7A01G568700 chr7B 83.244 1116 167 12 479 1577 743650547 743651659 0.000000e+00 1007.0
42 TraesCS7A01G568700 chr7B 80.986 1278 207 23 2142 3399 744329031 744327770 0.000000e+00 981.0
43 TraesCS7A01G568700 chr7B 82.963 1080 170 8 534 1601 744248066 744249143 0.000000e+00 963.0
44 TraesCS7A01G568700 chr7B 77.431 802 144 24 3355 4125 743727171 743727966 1.230000e-120 444.0
45 TraesCS7A01G568700 chr7B 80.995 221 26 9 4596 4805 743716331 743716546 1.390000e-35 161.0
46 TraesCS7A01G568700 chr3B 81.832 1299 204 22 360 1639 788258864 788257579 0.000000e+00 1062.0
47 TraesCS7A01G568700 chr3B 82.172 746 104 12 917 1637 778534216 778534957 2.460000e-172 616.0
48 TraesCS7A01G568700 chrUn 83.175 737 104 11 917 1637 219093772 219093040 0.000000e+00 656.0


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 TraesCS7A01G568700 chr7A 736425207 736430025 4818 True 8900.00 8900 100.00000 1 4819 1 chr7A.!!$R6 4818
1 TraesCS7A01G568700 chr7A 735962494 735964687 2193 False 1755.00 1755 81.50200 2207 4367 1 chr7A.!!$F1 2160
2 TraesCS7A01G568700 chr7A 735820044 735822320 2276 True 1683.00 1683 80.41700 2142 4393 1 chr7A.!!$R1 2251
3 TraesCS7A01G568700 chr7A 736004351 736008354 4003 True 1386.50 1744 82.26650 534 4367 2 chr7A.!!$R7 3833
4 TraesCS7A01G568700 chr7A 736069966 736071392 1426 True 1120.00 1120 81.22400 2988 4393 1 chr7A.!!$R4 1405
5 TraesCS7A01G568700 chr7A 736328408 736329586 1178 True 1064.00 1064 83.26300 435 1595 1 chr7A.!!$R5 1160
6 TraesCS7A01G568700 chr7A 736089392 736094420 5028 True 970.00 1740 78.64600 2145 4816 2 chr7A.!!$R8 2671
7 TraesCS7A01G568700 chr7A 735999712 736000347 635 True 562.00 562 82.91900 3762 4393 1 chr7A.!!$R3 631
8 TraesCS7A01G568700 chr7D 632143037 632145299 2262 False 1812.00 1812 81.51900 2171 4395 1 chr7D.!!$F4 2224
9 TraesCS7A01G568700 chr7D 632018100 632023891 5791 False 1728.25 3712 93.88975 225 4819 4 chr7D.!!$F7 4594
10 TraesCS7A01G568700 chr7D 632081071 632083360 2289 False 1622.00 1622 79.84400 2144 4393 1 chr7D.!!$F3 2249
11 TraesCS7A01G568700 chr7D 632033223 632037385 4162 False 1425.50 1748 83.06700 534 4393 2 chr7D.!!$F8 3859
12 TraesCS7A01G568700 chr7D 632096459 632100624 4165 False 1362.00 1748 82.08750 478 4393 2 chr7D.!!$F9 3915
13 TraesCS7A01G568700 chr7D 621261059 621264519 3460 False 1156.50 2050 81.28500 2139 4803 2 chr7D.!!$F6 2664
14 TraesCS7A01G568700 chr7D 555047293 555054238 6945 False 1068.00 1842 82.33100 501 4815 3 chr7D.!!$F5 4314
15 TraesCS7A01G568700 chr7D 632046385 632047502 1117 False 861.00 861 80.97800 3298 4395 1 chr7D.!!$F2 1097
16 TraesCS7A01G568700 chr1B 577923733 577928990 5257 True 1656.00 2004 83.93100 328 4394 2 chr1B.!!$R1 4066
17 TraesCS7A01G568700 chr7B 747523914 747526070 2156 True 1779.00 1779 81.95700 2180 4295 1 chr7B.!!$R4 2115
18 TraesCS7A01G568700 chr7B 744209495 744211770 2275 False 1694.00 1694 80.51900 2136 4393 1 chr7B.!!$F5 2257
19 TraesCS7A01G568700 chr7B 745232105 745234340 2235 False 1646.00 1646 80.32000 2189 4393 1 chr7B.!!$F7 2204
20 TraesCS7A01G568700 chr7B 744291136 744293266 2130 True 1585.00 1585 80.45800 2226 4319 1 chr7B.!!$R2 2093
21 TraesCS7A01G568700 chr7B 744248066 744252040 3974 False 1349.00 1735 81.85200 534 4395 2 chr7B.!!$F8 3861
22 TraesCS7A01G568700 chr7B 744335758 744339378 3620 True 1187.00 1365 83.31500 534 3682 2 chr7B.!!$R5 3148
23 TraesCS7A01G568700 chr7B 743709480 743710583 1103 False 1103.00 1103 84.89700 534 1637 1 chr7B.!!$F2 1103
24 TraesCS7A01G568700 chr7B 744269347 744270450 1103 False 1053.00 1053 84.09300 534 1637 1 chr7B.!!$F6 1103
25 TraesCS7A01G568700 chr7B 743998124 743999258 1134 True 1022.00 1022 83.27500 538 1654 1 chr7B.!!$R1 1116
26 TraesCS7A01G568700 chr7B 743650547 743651659 1112 False 1007.00 1007 83.24400 479 1577 1 chr7B.!!$F1 1098
27 TraesCS7A01G568700 chr7B 744327770 744329031 1261 True 981.00 981 80.98600 2142 3399 1 chr7B.!!$R3 1257
28 TraesCS7A01G568700 chr7B 743727171 743727966 795 False 444.00 444 77.43100 3355 4125 1 chr7B.!!$F4 770
29 TraesCS7A01G568700 chr3B 788257579 788258864 1285 True 1062.00 1062 81.83200 360 1639 1 chr3B.!!$R1 1279
30 TraesCS7A01G568700 chr3B 778534216 778534957 741 False 616.00 616 82.17200 917 1637 1 chr3B.!!$F1 720
31 TraesCS7A01G568700 chrUn 219093040 219093772 732 True 656.00 656 83.17500 917 1637 1 chrUn.!!$R1 720

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
154 155 0.036010 ACACCCAGCTACTGTGCATC 60.036 55.000 8.81 0.0 33.30 3.91 F
242 243 0.179184 GACGTCTTCTCTCTGCCGTC 60.179 60.000 8.70 0.0 38.03 4.79 F
283 284 0.931005 GGAGCAGGCGATTTAGTTCG 59.069 55.000 0.00 0.0 41.99 3.95 F
352 353 0.976641 TTCACCAGGATCGAGTTGCT 59.023 50.000 0.00 0.0 0.00 3.91 F
1148 1231 1.287425 GCTATCGTAGGTGTTGGTGC 58.713 55.000 0.00 0.0 0.00 5.01 F
2365 4613 1.135333 CTTGCGTAGAAGAGGGGAGTC 59.865 57.143 0.00 0.0 0.00 3.36 F
2982 5233 0.675083 TGTGGCTGCATTGGTTGAAG 59.325 50.000 0.50 0.0 33.57 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1315 1398 0.236711 CTTCTGTGAAGCGTTGCCTG 59.763 55.000 0.00 0.00 0.00 4.85 R
2095 3362 2.863809 ACTAGCTCAAAACTGTTGGGG 58.136 47.619 0.00 0.00 0.00 4.96 R
2096 3363 6.385649 TTTTACTAGCTCAAAACTGTTGGG 57.614 37.500 0.00 0.00 0.00 4.12 R
2097 3364 6.438763 CCTTTTACTAGCTCAAAACTGTTGG 58.561 40.000 0.00 0.00 0.00 3.77 R
2982 5233 2.292569 CCACATATCTCAGGTGCAATGC 59.707 50.000 0.00 0.00 37.62 3.56 R
3258 5521 0.695347 CTGAGTTGGGAAAGAGGCCT 59.305 55.000 3.86 3.86 0.00 5.19 R
4481 10450 0.539051 ATGCTACCTGACAGCCAGAC 59.461 55.000 0.00 0.00 45.78 3.51 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
22 23 5.320549 AGCAAAGCAAAGGAATGTATCAG 57.679 39.130 0.00 0.00 0.00 2.90
23 24 5.012239 AGCAAAGCAAAGGAATGTATCAGA 58.988 37.500 0.00 0.00 0.00 3.27
24 25 5.477984 AGCAAAGCAAAGGAATGTATCAGAA 59.522 36.000 0.00 0.00 0.00 3.02
25 26 6.154021 AGCAAAGCAAAGGAATGTATCAGAAT 59.846 34.615 0.00 0.00 0.00 2.40
26 27 7.340232 AGCAAAGCAAAGGAATGTATCAGAATA 59.660 33.333 0.00 0.00 0.00 1.75
27 28 7.975616 GCAAAGCAAAGGAATGTATCAGAATAA 59.024 33.333 0.00 0.00 0.00 1.40
28 29 9.859427 CAAAGCAAAGGAATGTATCAGAATAAA 57.141 29.630 0.00 0.00 0.00 1.40
30 31 7.710896 AGCAAAGGAATGTATCAGAATAAAGC 58.289 34.615 0.00 0.00 0.00 3.51
31 32 7.559170 AGCAAAGGAATGTATCAGAATAAAGCT 59.441 33.333 0.00 0.00 0.00 3.74
32 33 7.646922 GCAAAGGAATGTATCAGAATAAAGCTG 59.353 37.037 0.00 0.00 34.71 4.24
33 34 6.874288 AGGAATGTATCAGAATAAAGCTGC 57.126 37.500 0.00 0.00 33.45 5.25
34 35 6.359804 AGGAATGTATCAGAATAAAGCTGCA 58.640 36.000 1.02 0.00 33.45 4.41
35 36 6.485984 AGGAATGTATCAGAATAAAGCTGCAG 59.514 38.462 10.11 10.11 33.45 4.41
36 37 5.686159 ATGTATCAGAATAAAGCTGCAGC 57.314 39.130 31.53 31.53 42.49 5.25
70 71 3.663176 GCAGCAGCGCACTGGAAA 61.663 61.111 25.78 0.00 44.63 3.13
71 72 3.033184 CAGCAGCGCACTGGAAAA 58.967 55.556 19.51 0.00 44.63 2.29
72 73 1.359833 CAGCAGCGCACTGGAAAAA 59.640 52.632 19.51 0.00 44.63 1.94
92 93 5.966742 AAAAGTAATGAGCAAAGGTCCTC 57.033 39.130 0.00 0.00 0.00 3.71
93 94 4.917906 AAGTAATGAGCAAAGGTCCTCT 57.082 40.909 0.00 0.00 0.00 3.69
94 95 4.479786 AGTAATGAGCAAAGGTCCTCTC 57.520 45.455 0.00 0.00 0.00 3.20
95 96 3.840666 AGTAATGAGCAAAGGTCCTCTCA 59.159 43.478 10.39 10.39 39.54 3.27
96 97 4.472833 AGTAATGAGCAAAGGTCCTCTCAT 59.527 41.667 13.45 13.45 45.21 2.90
97 98 3.557228 ATGAGCAAAGGTCCTCTCATC 57.443 47.619 13.45 2.49 41.01 2.92
98 99 1.556911 TGAGCAAAGGTCCTCTCATCC 59.443 52.381 4.94 0.00 31.35 3.51
99 100 1.556911 GAGCAAAGGTCCTCTCATCCA 59.443 52.381 0.00 0.00 0.00 3.41
100 101 1.280421 AGCAAAGGTCCTCTCATCCAC 59.720 52.381 0.00 0.00 0.00 4.02
101 102 1.003580 GCAAAGGTCCTCTCATCCACA 59.996 52.381 0.00 0.00 0.00 4.17
102 103 2.356535 GCAAAGGTCCTCTCATCCACAT 60.357 50.000 0.00 0.00 0.00 3.21
103 104 3.539604 CAAAGGTCCTCTCATCCACATC 58.460 50.000 0.00 0.00 0.00 3.06
104 105 1.799933 AGGTCCTCTCATCCACATCC 58.200 55.000 0.00 0.00 0.00 3.51
105 106 1.293458 AGGTCCTCTCATCCACATCCT 59.707 52.381 0.00 0.00 0.00 3.24
106 107 2.122768 GGTCCTCTCATCCACATCCTT 58.877 52.381 0.00 0.00 0.00 3.36
107 108 2.507471 GGTCCTCTCATCCACATCCTTT 59.493 50.000 0.00 0.00 0.00 3.11
108 109 3.054065 GGTCCTCTCATCCACATCCTTTT 60.054 47.826 0.00 0.00 0.00 2.27
109 110 3.944015 GTCCTCTCATCCACATCCTTTTG 59.056 47.826 0.00 0.00 0.00 2.44
110 111 2.686915 CCTCTCATCCACATCCTTTTGC 59.313 50.000 0.00 0.00 0.00 3.68
111 112 2.686915 CTCTCATCCACATCCTTTTGCC 59.313 50.000 0.00 0.00 0.00 4.52
112 113 2.309755 TCTCATCCACATCCTTTTGCCT 59.690 45.455 0.00 0.00 0.00 4.75
113 114 3.094572 CTCATCCACATCCTTTTGCCTT 58.905 45.455 0.00 0.00 0.00 4.35
114 115 3.509442 TCATCCACATCCTTTTGCCTTT 58.491 40.909 0.00 0.00 0.00 3.11
115 116 3.258872 TCATCCACATCCTTTTGCCTTTG 59.741 43.478 0.00 0.00 0.00 2.77
116 117 2.676748 TCCACATCCTTTTGCCTTTGT 58.323 42.857 0.00 0.00 0.00 2.83
117 118 2.627699 TCCACATCCTTTTGCCTTTGTC 59.372 45.455 0.00 0.00 0.00 3.18
118 119 2.364970 CCACATCCTTTTGCCTTTGTCA 59.635 45.455 0.00 0.00 0.00 3.58
119 120 3.553508 CCACATCCTTTTGCCTTTGTCAG 60.554 47.826 0.00 0.00 0.00 3.51
120 121 3.318839 CACATCCTTTTGCCTTTGTCAGA 59.681 43.478 0.00 0.00 0.00 3.27
121 122 3.571401 ACATCCTTTTGCCTTTGTCAGAG 59.429 43.478 0.00 0.00 0.00 3.35
122 123 3.576078 TCCTTTTGCCTTTGTCAGAGA 57.424 42.857 0.00 0.00 0.00 3.10
123 124 3.480470 TCCTTTTGCCTTTGTCAGAGAG 58.520 45.455 0.00 0.00 0.00 3.20
124 125 2.030451 CCTTTTGCCTTTGTCAGAGAGC 60.030 50.000 0.00 0.00 0.00 4.09
125 126 2.346766 TTTGCCTTTGTCAGAGAGCA 57.653 45.000 3.43 3.43 0.00 4.26
126 127 1.597742 TTGCCTTTGTCAGAGAGCAC 58.402 50.000 6.18 0.00 0.00 4.40
127 128 0.250467 TGCCTTTGTCAGAGAGCACC 60.250 55.000 3.43 0.00 0.00 5.01
128 129 0.036022 GCCTTTGTCAGAGAGCACCT 59.964 55.000 0.00 0.00 0.00 4.00
129 130 1.805869 CCTTTGTCAGAGAGCACCTG 58.194 55.000 0.00 0.00 0.00 4.00
130 131 1.155042 CTTTGTCAGAGAGCACCTGC 58.845 55.000 0.00 0.00 42.49 4.85
140 141 2.747855 GCACCTGCTGCTACACCC 60.748 66.667 0.00 0.00 43.33 4.61
141 142 2.749682 CACCTGCTGCTACACCCA 59.250 61.111 0.00 0.00 0.00 4.51
142 143 1.376424 CACCTGCTGCTACACCCAG 60.376 63.158 0.00 0.00 0.00 4.45
148 149 3.748863 CTGCTACACCCAGCTACTG 57.251 57.895 0.00 0.00 42.30 2.74
149 150 0.898320 CTGCTACACCCAGCTACTGT 59.102 55.000 0.00 0.00 42.30 3.55
150 151 0.608130 TGCTACACCCAGCTACTGTG 59.392 55.000 7.64 7.64 42.30 3.66
151 152 0.741221 GCTACACCCAGCTACTGTGC 60.741 60.000 8.81 0.00 38.57 4.57
152 153 0.608130 CTACACCCAGCTACTGTGCA 59.392 55.000 8.81 0.00 33.30 4.57
153 154 1.208052 CTACACCCAGCTACTGTGCAT 59.792 52.381 8.81 0.00 33.30 3.96
154 155 0.036010 ACACCCAGCTACTGTGCATC 60.036 55.000 8.81 0.00 33.30 3.91
155 156 0.745845 CACCCAGCTACTGTGCATCC 60.746 60.000 0.00 0.00 34.99 3.51
156 157 0.911525 ACCCAGCTACTGTGCATCCT 60.912 55.000 0.00 0.00 34.99 3.24
157 158 0.463295 CCCAGCTACTGTGCATCCTG 60.463 60.000 0.00 0.00 34.99 3.86
158 159 1.094073 CCAGCTACTGTGCATCCTGC 61.094 60.000 0.00 0.00 45.29 4.85
168 169 2.584064 CATCCTGCGGCTGGTGTA 59.416 61.111 22.96 6.98 0.00 2.90
169 170 1.522355 CATCCTGCGGCTGGTGTAG 60.522 63.158 22.96 9.67 0.00 2.74
182 183 3.600388 CTGGTGTAGCTTAACAGGAAGG 58.400 50.000 7.61 0.00 0.00 3.46
183 184 2.304761 TGGTGTAGCTTAACAGGAAGGG 59.695 50.000 0.00 0.00 0.00 3.95
184 185 2.570302 GGTGTAGCTTAACAGGAAGGGA 59.430 50.000 0.00 0.00 0.00 4.20
185 186 3.597255 GTGTAGCTTAACAGGAAGGGAC 58.403 50.000 0.00 0.00 0.00 4.46
186 187 3.007614 GTGTAGCTTAACAGGAAGGGACA 59.992 47.826 0.00 0.00 0.00 4.02
187 188 2.861147 AGCTTAACAGGAAGGGACAC 57.139 50.000 0.00 0.00 0.00 3.67
188 189 1.351350 AGCTTAACAGGAAGGGACACC 59.649 52.381 0.00 0.00 0.00 4.16
189 190 1.613520 GCTTAACAGGAAGGGACACCC 60.614 57.143 0.00 0.00 45.90 4.61
199 200 2.450243 GGACACCCCAGAGGAGGA 59.550 66.667 0.00 0.00 39.89 3.71
200 201 1.687493 GGACACCCCAGAGGAGGAG 60.687 68.421 0.00 0.00 39.89 3.69
201 202 2.284995 ACACCCCAGAGGAGGAGC 60.285 66.667 0.00 0.00 39.89 4.70
202 203 2.284921 CACCCCAGAGGAGGAGCA 60.285 66.667 0.00 0.00 39.89 4.26
203 204 2.040278 ACCCCAGAGGAGGAGCAG 59.960 66.667 0.00 0.00 39.89 4.24
204 205 2.366167 CCCCAGAGGAGGAGCAGA 59.634 66.667 0.00 0.00 38.24 4.26
205 206 1.761667 CCCCAGAGGAGGAGCAGAG 60.762 68.421 0.00 0.00 38.24 3.35
206 207 2.433994 CCCAGAGGAGGAGCAGAGC 61.434 68.421 0.00 0.00 33.47 4.09
207 208 1.381599 CCAGAGGAGGAGCAGAGCT 60.382 63.158 0.00 0.00 43.88 4.09
208 209 1.678598 CCAGAGGAGGAGCAGAGCTG 61.679 65.000 0.00 0.00 39.88 4.24
238 239 0.885196 AGGTGACGTCTTCTCTCTGC 59.115 55.000 17.92 0.00 0.00 4.26
241 242 0.889638 TGACGTCTTCTCTCTGCCGT 60.890 55.000 17.92 0.00 0.00 5.68
242 243 0.179184 GACGTCTTCTCTCTGCCGTC 60.179 60.000 8.70 0.00 38.03 4.79
243 244 1.226156 CGTCTTCTCTCTGCCGTCG 60.226 63.158 0.00 0.00 0.00 5.12
244 245 1.636570 CGTCTTCTCTCTGCCGTCGA 61.637 60.000 0.00 0.00 0.00 4.20
246 247 1.133407 GTCTTCTCTCTGCCGTCGATT 59.867 52.381 0.00 0.00 0.00 3.34
278 279 1.441729 CTCGGGAGCAGGCGATTTA 59.558 57.895 0.00 0.00 0.00 1.40
283 284 0.931005 GGAGCAGGCGATTTAGTTCG 59.069 55.000 0.00 0.00 41.99 3.95
291 292 2.853003 GGCGATTTAGTTCGACTGAGAC 59.147 50.000 0.00 0.00 43.89 3.36
301 302 3.577649 TCGACTGAGACTCACAAATCC 57.422 47.619 0.00 0.00 0.00 3.01
302 303 2.890945 TCGACTGAGACTCACAAATCCA 59.109 45.455 0.00 0.00 0.00 3.41
344 345 2.834549 TGAGTTCCTCTTCACCAGGATC 59.165 50.000 0.00 0.00 39.91 3.36
352 353 0.976641 TTCACCAGGATCGAGTTGCT 59.023 50.000 0.00 0.00 0.00 3.91
358 359 1.394917 CAGGATCGAGTTGCTTTTCCG 59.605 52.381 0.00 0.00 0.00 4.30
405 406 3.834231 CCATCCATCTCAAAGGTTGGTTT 59.166 43.478 0.00 0.00 39.09 3.27
443 444 2.715763 TGTCCCTCTCCTTACACCTT 57.284 50.000 0.00 0.00 0.00 3.50
452 459 6.042208 CCCTCTCCTTACACCTTCCTAATTAG 59.958 46.154 5.43 5.43 0.00 1.73
522 541 9.474313 ACCTTTATTATTACAGCAAAATCCAGA 57.526 29.630 0.00 0.00 0.00 3.86
968 999 2.359981 TCAATCTCGGGTCCTACGAT 57.640 50.000 0.00 0.00 39.89 3.73
1020 1075 2.187946 GTGATCCCAGCCACGAGG 59.812 66.667 0.00 0.00 38.23 4.63
1109 1170 1.738030 GCCCAGATCATGCAAACAAGC 60.738 52.381 0.00 0.00 0.00 4.01
1148 1231 1.287425 GCTATCGTAGGTGTTGGTGC 58.713 55.000 0.00 0.00 0.00 5.01
1693 1787 7.078851 TGTTTCGAATTAATATGCGTTGTTGT 58.921 30.769 0.00 0.00 34.26 3.32
1783 1885 9.071276 CCATAAGAGGCTGTCAATAATTTGTAT 57.929 33.333 0.00 0.00 34.32 2.29
1786 1889 6.662755 AGAGGCTGTCAATAATTTGTATGGA 58.337 36.000 0.00 0.00 34.32 3.41
1861 2667 2.927553 GCATGGTGCTAAACAAGGAG 57.072 50.000 0.00 0.00 40.96 3.69
1921 2733 8.792830 ATTTATTGCTACATAACACTGACACT 57.207 30.769 0.00 0.00 0.00 3.55
1926 2760 5.221441 TGCTACATAACACTGACACTCAAGT 60.221 40.000 0.00 0.00 0.00 3.16
1930 2764 6.785191 ACATAACACTGACACTCAAGTTTTG 58.215 36.000 0.00 0.00 33.75 2.44
1931 2765 6.374333 ACATAACACTGACACTCAAGTTTTGT 59.626 34.615 0.00 0.00 34.82 2.83
1951 2785 9.089601 GTTTTGTTTTTGCTAAGCCTAAGTAAA 57.910 29.630 0.00 0.00 0.00 2.01
2074 3215 3.674682 GCACTTTTGCCAACACTTGTACA 60.675 43.478 0.00 0.00 43.66 2.90
2077 3218 1.740297 TTGCCAACACTTGTACACGT 58.260 45.000 0.00 0.00 0.00 4.49
2079 3220 2.902523 TGCCAACACTTGTACACGTTA 58.097 42.857 1.60 0.00 0.00 3.18
2096 3363 9.811655 GTACACGTTACTTTTCTTAATAAACCC 57.188 33.333 0.00 0.00 0.00 4.11
2097 3364 7.874940 ACACGTTACTTTTCTTAATAAACCCC 58.125 34.615 0.00 0.00 0.00 4.95
2158 4286 4.742012 TGGTCCTCTTGTCTCTTAAGAGT 58.258 43.478 27.59 0.00 46.12 3.24
2185 4419 8.823220 AAATTAGAATGCCTTAAAGGAGCTTA 57.177 30.769 0.00 0.00 37.67 3.09
2365 4613 1.135333 CTTGCGTAGAAGAGGGGAGTC 59.865 57.143 0.00 0.00 0.00 3.36
2646 4894 8.275758 AGCTGATATATCGGAACCTTATAGAGA 58.724 37.037 23.25 0.00 35.13 3.10
2773 5024 8.740906 TGGAGACATCGATAATCTAACTAATCC 58.259 37.037 10.52 7.41 33.40 3.01
2913 5164 3.272574 TCAAGATGAAGCCCAGTGATC 57.727 47.619 0.00 0.00 0.00 2.92
2982 5233 0.675083 TGTGGCTGCATTGGTTGAAG 59.325 50.000 0.50 0.00 33.57 3.02
3075 5338 6.418057 TGAAATTGTTGCAATTCCTTAGGT 57.582 33.333 0.59 0.00 0.00 3.08
3258 5521 1.295792 GTGCAGTTTGGACGAGTTGA 58.704 50.000 0.00 0.00 0.00 3.18
3327 5590 4.516323 TGTATCTGCTGCTTCATTTGCTA 58.484 39.130 0.00 0.00 0.00 3.49
3339 5602 5.581126 TTCATTTGCTACAAATGCTAGGG 57.419 39.130 22.27 4.44 37.50 3.53
3650 5916 1.990060 TCAGCTCCCCTACCTGCAC 60.990 63.158 0.00 0.00 0.00 4.57
3733 5999 1.468914 GGCAACTCCATTTCCGAGTTC 59.531 52.381 0.34 0.00 45.28 3.01
3794 6075 4.536687 GTACAAGCCATGCGCCGC 62.537 66.667 4.18 0.00 38.78 6.53
3904 6195 1.002430 CAGCACCTCAGCTACCTTGAA 59.998 52.381 0.00 0.00 44.54 2.69
3921 6212 7.096884 ACCTTGAAAACTTTCCTTCTGTTAC 57.903 36.000 0.00 0.00 36.36 2.50
4026 6317 0.178990 AAGTTGAAGGTGCTGGGGAC 60.179 55.000 0.00 0.00 0.00 4.46
4070 6361 1.618837 TCCTAGAGGATTACGCCATGC 59.381 52.381 0.00 0.00 39.78 4.06
4154 6445 0.460459 GTTGCTCTCTTCGGTAGCCC 60.460 60.000 0.00 0.00 35.33 5.19
4271 6562 4.873827 TGTTGTACACAAGAAGAGACAACC 59.126 41.667 11.84 0.00 43.73 3.77
4369 6669 5.452078 TTAATTTGTTTGGGCACTCTCAG 57.548 39.130 0.00 0.00 0.00 3.35
4395 10364 3.242016 GGCAGTTTGTAAGTTCGTTTTGC 59.758 43.478 0.00 0.00 0.00 3.68
4432 10401 1.136891 CATGAGGAGTATGCCGACACA 59.863 52.381 0.00 0.00 0.00 3.72
4443 10412 1.156736 GCCGACACACTAATGCAAGT 58.843 50.000 0.00 0.00 0.00 3.16
4475 10444 5.762179 TCCAGATATGAGGTTCACAAACT 57.238 39.130 0.00 0.00 35.61 2.66
4481 10450 2.930950 TGAGGTTCACAAACTCTTGGG 58.069 47.619 3.09 0.00 37.29 4.12
4484 10453 2.509964 AGGTTCACAAACTCTTGGGTCT 59.490 45.455 0.00 0.00 37.24 3.85
4501 10470 1.757118 GTCTGGCTGTCAGGTAGCATA 59.243 52.381 9.73 0.00 43.53 3.14
4511 10480 4.941263 TGTCAGGTAGCATAATGAACCAAC 59.059 41.667 0.00 0.00 34.29 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.012239 TCTGATACATTCCTTTGCTTTGCT 58.988 37.500 0.00 0.00 0.00 3.91
1 2 5.314923 TCTGATACATTCCTTTGCTTTGC 57.685 39.130 0.00 0.00 0.00 3.68
2 3 9.859427 TTTATTCTGATACATTCCTTTGCTTTG 57.141 29.630 0.00 0.00 0.00 2.77
4 5 8.193438 GCTTTATTCTGATACATTCCTTTGCTT 58.807 33.333 0.00 0.00 0.00 3.91
5 6 7.559170 AGCTTTATTCTGATACATTCCTTTGCT 59.441 33.333 0.00 0.00 0.00 3.91
6 7 7.646922 CAGCTTTATTCTGATACATTCCTTTGC 59.353 37.037 0.00 0.00 33.54 3.68
7 8 7.646922 GCAGCTTTATTCTGATACATTCCTTTG 59.353 37.037 0.00 0.00 33.54 2.77
8 9 7.340232 TGCAGCTTTATTCTGATACATTCCTTT 59.660 33.333 0.00 0.00 33.54 3.11
9 10 6.830324 TGCAGCTTTATTCTGATACATTCCTT 59.170 34.615 0.00 0.00 33.54 3.36
10 11 6.359804 TGCAGCTTTATTCTGATACATTCCT 58.640 36.000 0.00 0.00 33.54 3.36
11 12 6.624352 TGCAGCTTTATTCTGATACATTCC 57.376 37.500 0.00 0.00 33.54 3.01
12 13 6.141462 GCTGCAGCTTTATTCTGATACATTC 58.859 40.000 31.33 0.00 38.21 2.67
13 14 5.277683 CGCTGCAGCTTTATTCTGATACATT 60.278 40.000 34.22 0.00 39.32 2.71
14 15 4.212847 CGCTGCAGCTTTATTCTGATACAT 59.787 41.667 34.22 0.00 39.32 2.29
15 16 3.557185 CGCTGCAGCTTTATTCTGATACA 59.443 43.478 34.22 0.00 39.32 2.29
16 17 3.059325 CCGCTGCAGCTTTATTCTGATAC 60.059 47.826 34.22 2.64 39.32 2.24
17 18 3.133691 CCGCTGCAGCTTTATTCTGATA 58.866 45.455 34.22 0.00 39.32 2.15
18 19 1.945394 CCGCTGCAGCTTTATTCTGAT 59.055 47.619 34.22 0.00 39.32 2.90
19 20 1.066215 TCCGCTGCAGCTTTATTCTGA 60.066 47.619 34.22 15.05 39.32 3.27
20 21 1.329906 CTCCGCTGCAGCTTTATTCTG 59.670 52.381 34.22 17.01 39.32 3.02
21 22 1.661341 CTCCGCTGCAGCTTTATTCT 58.339 50.000 34.22 0.00 39.32 2.40
22 23 0.028637 GCTCCGCTGCAGCTTTATTC 59.971 55.000 34.22 15.45 39.32 1.75
23 24 0.393537 AGCTCCGCTGCAGCTTTATT 60.394 50.000 34.22 15.58 45.34 1.40
24 25 1.222936 AGCTCCGCTGCAGCTTTAT 59.777 52.632 34.22 14.92 45.34 1.40
25 26 2.665000 AGCTCCGCTGCAGCTTTA 59.335 55.556 34.22 18.88 45.34 1.85
48 49 1.299620 CAGTGCGCTGCTGCTTTTT 60.300 52.632 15.44 0.00 35.77 1.94
49 50 2.333938 CAGTGCGCTGCTGCTTTT 59.666 55.556 15.44 0.00 35.77 2.27
50 51 3.667282 CCAGTGCGCTGCTGCTTT 61.667 61.111 22.03 3.72 41.26 3.51
51 52 4.631247 TCCAGTGCGCTGCTGCTT 62.631 61.111 22.03 4.01 41.26 3.91
52 53 4.631247 TTCCAGTGCGCTGCTGCT 62.631 61.111 22.03 5.38 41.26 4.24
53 54 2.682256 TTTTTCCAGTGCGCTGCTGC 62.682 55.000 22.03 5.34 41.26 5.25
54 55 1.359833 TTTTTCCAGTGCGCTGCTG 59.640 52.632 22.03 20.38 41.26 4.41
55 56 3.840437 TTTTTCCAGTGCGCTGCT 58.160 50.000 22.03 3.76 41.26 4.24
69 70 6.071320 AGAGGACCTTTGCTCATTACTTTTT 58.929 36.000 0.00 0.00 42.60 1.94
70 71 5.635120 AGAGGACCTTTGCTCATTACTTTT 58.365 37.500 0.00 0.00 42.60 2.27
71 72 5.221925 TGAGAGGACCTTTGCTCATTACTTT 60.222 40.000 7.19 0.00 42.60 2.66
72 73 4.287067 TGAGAGGACCTTTGCTCATTACTT 59.713 41.667 7.19 0.00 42.60 2.24
73 74 3.840666 TGAGAGGACCTTTGCTCATTACT 59.159 43.478 7.19 0.00 42.60 2.24
74 75 4.207891 TGAGAGGACCTTTGCTCATTAC 57.792 45.455 7.19 0.00 42.60 1.89
75 76 4.141620 GGATGAGAGGACCTTTGCTCATTA 60.142 45.833 19.90 0.00 45.30 1.90
76 77 3.371380 GGATGAGAGGACCTTTGCTCATT 60.371 47.826 19.90 8.59 45.30 2.57
78 79 1.556911 GGATGAGAGGACCTTTGCTCA 59.443 52.381 12.47 12.47 42.60 4.26
79 80 1.556911 TGGATGAGAGGACCTTTGCTC 59.443 52.381 0.00 0.00 40.48 4.26
80 81 1.280421 GTGGATGAGAGGACCTTTGCT 59.720 52.381 0.00 0.00 0.00 3.91
81 82 1.003580 TGTGGATGAGAGGACCTTTGC 59.996 52.381 0.00 0.00 0.00 3.68
82 83 3.539604 GATGTGGATGAGAGGACCTTTG 58.460 50.000 0.00 0.00 0.00 2.77
83 84 2.507471 GGATGTGGATGAGAGGACCTTT 59.493 50.000 0.00 0.00 0.00 3.11
84 85 2.122768 GGATGTGGATGAGAGGACCTT 58.877 52.381 0.00 0.00 0.00 3.50
85 86 1.293458 AGGATGTGGATGAGAGGACCT 59.707 52.381 0.00 0.00 0.00 3.85
86 87 1.799933 AGGATGTGGATGAGAGGACC 58.200 55.000 0.00 0.00 0.00 4.46
87 88 3.922171 AAAGGATGTGGATGAGAGGAC 57.078 47.619 0.00 0.00 0.00 3.85
88 89 3.623203 GCAAAAGGATGTGGATGAGAGGA 60.623 47.826 0.00 0.00 0.00 3.71
89 90 2.686915 GCAAAAGGATGTGGATGAGAGG 59.313 50.000 0.00 0.00 0.00 3.69
90 91 2.686915 GGCAAAAGGATGTGGATGAGAG 59.313 50.000 0.00 0.00 0.00 3.20
91 92 2.309755 AGGCAAAAGGATGTGGATGAGA 59.690 45.455 0.00 0.00 0.00 3.27
92 93 2.731572 AGGCAAAAGGATGTGGATGAG 58.268 47.619 0.00 0.00 0.00 2.90
93 94 2.905415 AGGCAAAAGGATGTGGATGA 57.095 45.000 0.00 0.00 0.00 2.92
94 95 3.007182 ACAAAGGCAAAAGGATGTGGATG 59.993 43.478 0.00 0.00 0.00 3.51
95 96 3.242011 ACAAAGGCAAAAGGATGTGGAT 58.758 40.909 0.00 0.00 0.00 3.41
96 97 2.627699 GACAAAGGCAAAAGGATGTGGA 59.372 45.455 0.00 0.00 0.00 4.02
97 98 2.364970 TGACAAAGGCAAAAGGATGTGG 59.635 45.455 0.00 0.00 0.00 4.17
98 99 3.318839 TCTGACAAAGGCAAAAGGATGTG 59.681 43.478 0.00 0.00 0.00 3.21
99 100 3.565307 TCTGACAAAGGCAAAAGGATGT 58.435 40.909 0.00 0.00 0.00 3.06
100 101 3.822735 TCTCTGACAAAGGCAAAAGGATG 59.177 43.478 0.00 0.00 0.00 3.51
101 102 4.077822 CTCTCTGACAAAGGCAAAAGGAT 58.922 43.478 0.00 0.00 0.00 3.24
102 103 3.480470 CTCTCTGACAAAGGCAAAAGGA 58.520 45.455 0.00 0.00 0.00 3.36
103 104 2.030451 GCTCTCTGACAAAGGCAAAAGG 60.030 50.000 0.00 0.00 0.00 3.11
104 105 2.620115 TGCTCTCTGACAAAGGCAAAAG 59.380 45.455 0.00 0.00 0.00 2.27
105 106 2.358898 GTGCTCTCTGACAAAGGCAAAA 59.641 45.455 0.00 0.00 0.00 2.44
106 107 1.949525 GTGCTCTCTGACAAAGGCAAA 59.050 47.619 0.00 0.00 0.00 3.68
107 108 1.597742 GTGCTCTCTGACAAAGGCAA 58.402 50.000 0.00 0.00 0.00 4.52
108 109 0.250467 GGTGCTCTCTGACAAAGGCA 60.250 55.000 0.00 0.00 0.00 4.75
109 110 0.036022 AGGTGCTCTCTGACAAAGGC 59.964 55.000 0.00 0.00 0.00 4.35
110 111 1.805869 CAGGTGCTCTCTGACAAAGG 58.194 55.000 0.00 0.00 34.36 3.11
111 112 1.155042 GCAGGTGCTCTCTGACAAAG 58.845 55.000 8.01 0.00 38.21 2.77
112 113 3.312404 GCAGGTGCTCTCTGACAAA 57.688 52.632 8.01 0.00 38.21 2.83
124 125 1.376424 CTGGGTGTAGCAGCAGGTG 60.376 63.158 0.00 0.00 33.07 4.00
125 126 3.072476 CTGGGTGTAGCAGCAGGT 58.928 61.111 0.00 0.00 33.07 4.00
126 127 1.617018 TAGCTGGGTGTAGCAGCAGG 61.617 60.000 0.00 0.00 46.07 4.85
127 128 0.460987 GTAGCTGGGTGTAGCAGCAG 60.461 60.000 0.00 0.00 46.07 4.24
128 129 0.904865 AGTAGCTGGGTGTAGCAGCA 60.905 55.000 0.00 0.00 46.07 4.41
129 130 0.460987 CAGTAGCTGGGTGTAGCAGC 60.461 60.000 0.00 0.00 46.07 5.25
130 131 0.898320 ACAGTAGCTGGGTGTAGCAG 59.102 55.000 0.00 0.00 46.07 4.24
131 132 0.608130 CACAGTAGCTGGGTGTAGCA 59.392 55.000 0.00 0.00 46.07 3.49
132 133 0.741221 GCACAGTAGCTGGGTGTAGC 60.741 60.000 13.47 8.77 44.01 3.58
133 134 0.608130 TGCACAGTAGCTGGGTGTAG 59.392 55.000 13.47 4.15 37.20 2.74
134 135 1.207089 GATGCACAGTAGCTGGGTGTA 59.793 52.381 13.47 10.49 37.20 2.90
135 136 0.036010 GATGCACAGTAGCTGGGTGT 60.036 55.000 13.47 4.33 37.20 4.16
136 137 0.745845 GGATGCACAGTAGCTGGGTG 60.746 60.000 0.00 2.96 37.20 4.61
137 138 0.911525 AGGATGCACAGTAGCTGGGT 60.912 55.000 0.00 0.00 37.20 4.51
138 139 0.463295 CAGGATGCACAGTAGCTGGG 60.463 60.000 0.00 0.00 38.04 4.45
139 140 3.076104 CAGGATGCACAGTAGCTGG 57.924 57.895 0.00 0.00 35.51 4.85
161 162 3.600388 CCTTCCTGTTAAGCTACACCAG 58.400 50.000 0.00 0.00 0.00 4.00
162 163 2.304761 CCCTTCCTGTTAAGCTACACCA 59.695 50.000 0.00 0.00 0.00 4.17
163 164 2.570302 TCCCTTCCTGTTAAGCTACACC 59.430 50.000 0.00 0.00 0.00 4.16
164 165 3.007614 TGTCCCTTCCTGTTAAGCTACAC 59.992 47.826 0.00 0.00 0.00 2.90
165 166 3.007614 GTGTCCCTTCCTGTTAAGCTACA 59.992 47.826 0.00 0.00 0.00 2.74
166 167 3.597255 GTGTCCCTTCCTGTTAAGCTAC 58.403 50.000 0.00 0.00 0.00 3.58
167 168 2.570302 GGTGTCCCTTCCTGTTAAGCTA 59.430 50.000 0.00 0.00 0.00 3.32
168 169 1.351350 GGTGTCCCTTCCTGTTAAGCT 59.649 52.381 0.00 0.00 0.00 3.74
169 170 1.613520 GGGTGTCCCTTCCTGTTAAGC 60.614 57.143 0.00 0.00 41.34 3.09
170 171 2.491675 GGGTGTCCCTTCCTGTTAAG 57.508 55.000 0.00 0.00 41.34 1.85
182 183 1.687493 CTCCTCCTCTGGGGTGTCC 60.687 68.421 0.00 0.00 36.25 4.02
183 184 2.363172 GCTCCTCCTCTGGGGTGTC 61.363 68.421 0.00 0.00 36.25 3.67
184 185 2.284995 GCTCCTCCTCTGGGGTGT 60.285 66.667 0.00 0.00 36.25 4.16
185 186 2.284921 TGCTCCTCCTCTGGGGTG 60.285 66.667 0.00 0.00 36.25 4.61
186 187 2.040278 CTGCTCCTCCTCTGGGGT 59.960 66.667 0.00 0.00 36.25 4.95
187 188 1.761667 CTCTGCTCCTCCTCTGGGG 60.762 68.421 0.00 0.00 0.00 4.96
188 189 2.433994 GCTCTGCTCCTCCTCTGGG 61.434 68.421 0.00 0.00 0.00 4.45
189 190 1.381599 AGCTCTGCTCCTCCTCTGG 60.382 63.158 0.00 0.00 30.62 3.86
190 191 1.817881 CAGCTCTGCTCCTCCTCTG 59.182 63.158 0.00 0.00 36.40 3.35
191 192 4.360643 CAGCTCTGCTCCTCCTCT 57.639 61.111 0.00 0.00 36.40 3.69
205 206 2.033755 CACCTCTGTGAGCAGCAGC 61.034 63.158 0.00 0.00 45.76 5.25
206 207 1.670015 TCACCTCTGTGAGCAGCAG 59.330 57.895 0.00 0.00 46.40 4.24
207 208 3.875390 TCACCTCTGTGAGCAGCA 58.125 55.556 0.00 0.00 46.40 4.41
214 215 1.883275 AGAGAAGACGTCACCTCTGTG 59.117 52.381 27.75 0.00 44.18 3.66
215 216 2.156098 GAGAGAAGACGTCACCTCTGT 58.844 52.381 31.15 21.62 36.25 3.41
216 217 2.161410 CAGAGAGAAGACGTCACCTCTG 59.839 54.545 31.15 28.61 43.55 3.35
217 218 2.432444 CAGAGAGAAGACGTCACCTCT 58.568 52.381 28.32 28.32 38.39 3.69
218 219 1.135517 GCAGAGAGAAGACGTCACCTC 60.136 57.143 19.50 21.07 0.00 3.85
219 220 0.885196 GCAGAGAGAAGACGTCACCT 59.115 55.000 19.50 13.72 0.00 4.00
220 221 0.109039 GGCAGAGAGAAGACGTCACC 60.109 60.000 19.50 8.72 0.00 4.02
221 222 0.455295 CGGCAGAGAGAAGACGTCAC 60.455 60.000 19.50 11.35 0.00 3.67
222 223 0.889638 ACGGCAGAGAGAAGACGTCA 60.890 55.000 19.50 0.00 0.00 4.35
223 224 0.179184 GACGGCAGAGAGAAGACGTC 60.179 60.000 7.70 7.70 42.79 4.34
238 239 2.158959 GCCGTGAGACAATCGACGG 61.159 63.158 14.56 14.56 46.49 4.79
241 242 1.014044 GCTTGCCGTGAGACAATCGA 61.014 55.000 0.00 0.00 0.00 3.59
242 243 1.016130 AGCTTGCCGTGAGACAATCG 61.016 55.000 0.00 0.00 0.00 3.34
243 244 0.723981 GAGCTTGCCGTGAGACAATC 59.276 55.000 0.00 0.00 0.00 2.67
244 245 1.016130 CGAGCTTGCCGTGAGACAAT 61.016 55.000 0.00 0.00 0.00 2.71
246 247 2.049156 CGAGCTTGCCGTGAGACA 60.049 61.111 0.00 0.00 0.00 3.41
278 279 4.551388 GATTTGTGAGTCTCAGTCGAACT 58.449 43.478 1.75 0.00 0.00 3.01
283 284 2.999355 GCTGGATTTGTGAGTCTCAGTC 59.001 50.000 1.75 0.00 0.00 3.51
291 292 4.381292 GGAATTCCTTGCTGGATTTGTGAG 60.381 45.833 17.73 0.00 45.68 3.51
325 326 1.827969 CGATCCTGGTGAAGAGGAACT 59.172 52.381 0.00 0.00 43.01 3.01
326 327 1.825474 TCGATCCTGGTGAAGAGGAAC 59.175 52.381 0.00 0.00 43.01 3.62
344 345 0.951040 AGCTCCGGAAAAGCAACTCG 60.951 55.000 15.74 0.00 42.35 4.18
352 353 1.453155 GCTCATTCAGCTCCGGAAAA 58.547 50.000 5.23 0.00 45.83 2.29
405 406 5.771165 GGGACAAATAAAACTTGGACTACCA 59.229 40.000 0.00 0.00 45.34 3.25
443 444 5.179452 ACAAGCAAGAAGCCTAATTAGGA 57.821 39.130 31.78 0.00 46.63 2.94
522 541 5.410067 CACCATCGCCATTAATTGAACTTT 58.590 37.500 0.00 0.00 0.00 2.66
968 999 3.310501 CGTTCACATTGCTGCTATGATGA 59.689 43.478 26.45 21.34 0.00 2.92
1020 1075 4.500116 GTCGAGCTCCCCTGACGC 62.500 72.222 8.47 0.00 0.00 5.19
1109 1170 0.324943 AACCACCATTGACCTCCTCG 59.675 55.000 0.00 0.00 0.00 4.63
1148 1231 0.804989 GAGGGTTGTCTTGCCAATCG 59.195 55.000 0.00 0.00 0.00 3.34
1315 1398 0.236711 CTTCTGTGAAGCGTTGCCTG 59.763 55.000 0.00 0.00 0.00 4.85
1664 1757 7.428183 ACAACGCATATTAATTCGAAACATCAC 59.572 33.333 0.00 0.00 0.00 3.06
1693 1787 5.242434 ACGAGCCACTGAATTACACATAAA 58.758 37.500 0.00 0.00 0.00 1.40
1915 2727 5.537188 AGCAAAAACAAAACTTGAGTGTCA 58.463 33.333 0.00 0.00 0.00 3.58
1916 2728 7.575332 TTAGCAAAAACAAAACTTGAGTGTC 57.425 32.000 0.00 0.00 0.00 3.67
1918 2730 6.455513 GGCTTAGCAAAAACAAAACTTGAGTG 60.456 38.462 6.53 0.00 0.00 3.51
1919 2731 5.580691 GGCTTAGCAAAAACAAAACTTGAGT 59.419 36.000 6.53 0.00 0.00 3.41
1921 2733 5.729510 AGGCTTAGCAAAAACAAAACTTGA 58.270 33.333 6.53 0.00 0.00 3.02
1926 2760 9.654663 TTTTACTTAGGCTTAGCAAAAACAAAA 57.345 25.926 6.53 3.08 0.00 2.44
1930 2764 9.471084 TGATTTTTACTTAGGCTTAGCAAAAAC 57.529 29.630 20.53 15.87 0.00 2.43
1931 2765 9.691362 CTGATTTTTACTTAGGCTTAGCAAAAA 57.309 29.630 20.44 20.44 0.00 1.94
2037 3178 7.132694 GCAAAAGTGCCTAAAAATTAGCAAT 57.867 32.000 0.00 0.00 45.68 3.56
2074 3215 7.003482 TGGGGGTTTATTAAGAAAAGTAACGT 58.997 34.615 0.00 0.00 0.00 3.99
2077 3218 8.779096 TGTTGGGGGTTTATTAAGAAAAGTAA 57.221 30.769 0.00 0.00 0.00 2.24
2079 3220 6.842280 ACTGTTGGGGGTTTATTAAGAAAAGT 59.158 34.615 0.00 0.00 0.00 2.66
2095 3362 2.863809 ACTAGCTCAAAACTGTTGGGG 58.136 47.619 0.00 0.00 0.00 4.96
2096 3363 6.385649 TTTTACTAGCTCAAAACTGTTGGG 57.614 37.500 0.00 0.00 0.00 4.12
2097 3364 6.438763 CCTTTTACTAGCTCAAAACTGTTGG 58.561 40.000 0.00 0.00 0.00 3.77
2158 4286 8.823220 AGCTCCTTTAAGGCATTCTAATTTAA 57.177 30.769 6.05 0.00 34.61 1.52
2365 4613 4.838486 GCTCCCAGTCTCGACGCG 62.838 72.222 3.53 3.53 36.20 6.01
2771 5022 5.008613 CCGAAGAAACTTTTGTGAATGAGGA 59.991 40.000 0.00 0.00 0.00 3.71
2773 5024 5.821204 ACCGAAGAAACTTTTGTGAATGAG 58.179 37.500 0.00 0.00 0.00 2.90
2913 5164 7.064253 CCGTAGACCAGAAAAAGTAACCAATAG 59.936 40.741 0.00 0.00 0.00 1.73
2982 5233 2.292569 CCACATATCTCAGGTGCAATGC 59.707 50.000 0.00 0.00 37.62 3.56
3258 5521 0.695347 CTGAGTTGGGAAAGAGGCCT 59.305 55.000 3.86 3.86 0.00 5.19
3327 5590 2.375174 TCTCACCAACCCTAGCATTTGT 59.625 45.455 0.00 0.00 0.00 2.83
3339 5602 8.328864 GTCGATAAGATGTATTTTCTCACCAAC 58.671 37.037 0.00 0.00 0.00 3.77
3390 5653 1.078426 CCAACCCGTCATCTCCCAC 60.078 63.158 0.00 0.00 0.00 4.61
3733 5999 7.201626 CCATGTCTCTTAAGCTCATCTCTTTTG 60.202 40.741 0.00 0.00 0.00 2.44
3794 6075 5.927689 TCAGTTTGCAATTAATGAGCCAAAG 59.072 36.000 0.00 3.81 0.00 2.77
3904 6195 5.685728 AGCTCAGTAACAGAAGGAAAGTTT 58.314 37.500 0.00 0.00 0.00 2.66
3921 6212 5.047660 AGACTTCTAACCACTGTAAGCTCAG 60.048 44.000 0.99 0.99 37.60 3.35
4026 6317 3.955291 CTGTCGAGTGCAGGGATAG 57.045 57.895 0.00 0.00 0.00 2.08
4070 6361 4.154015 TCGCATGTATTCTGGAAGTGTTTG 59.846 41.667 0.00 0.00 33.76 2.93
4154 6445 2.304180 ACTCAAGACCAGATTGTCCCAG 59.696 50.000 0.00 0.00 35.83 4.45
4271 6562 6.870769 AGCCAATATTTGAATCCAACTTGAG 58.129 36.000 0.00 0.00 30.88 3.02
4292 6583 4.120589 CCTTCAAATACGGAAGAGTAGCC 58.879 47.826 3.85 0.00 43.46 3.93
4344 6644 3.578282 AGAGTGCCCAAACAAATTAAGGG 59.422 43.478 0.00 0.00 42.55 3.95
4369 6669 2.870411 ACGAACTTACAAACTGCCAGAC 59.130 45.455 0.00 0.00 0.00 3.51
4432 10401 4.572389 GGATCAATGACGACTTGCATTAGT 59.428 41.667 0.00 0.00 33.68 2.24
4443 10412 4.835056 ACCTCATATCTGGATCAATGACGA 59.165 41.667 0.00 0.00 0.00 4.20
4475 10444 1.483595 CCTGACAGCCAGACCCAAGA 61.484 60.000 0.00 0.00 45.78 3.02
4481 10450 0.539051 ATGCTACCTGACAGCCAGAC 59.461 55.000 0.00 0.00 45.78 3.51
4484 10453 2.771372 TCATTATGCTACCTGACAGCCA 59.229 45.455 0.00 0.00 38.29 4.75
4501 10470 4.060205 GCAAAATGCTCAGTTGGTTCATT 58.940 39.130 0.00 0.00 40.96 2.57
4511 10480 3.439129 TCTGAGTCATGCAAAATGCTCAG 59.561 43.478 21.56 21.56 45.31 3.35
4534 10503 1.561643 TCTCGCCCATCTTGAAGAGT 58.438 50.000 0.00 0.00 0.00 3.24


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

AutoCloner maintained by Alex Coulton.