Multiple sequence alignment - TraesCS4A01G041400

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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 TraesCS4A01G041400 chr4A 100.000 3462 0 0 948 4409 34788018 34784557 0.000000e+00 6394.0
1 TraesCS4A01G041400 chr4A 85.494 779 77 18 2859 3636 454846632 454847375 0.000000e+00 780.0
2 TraesCS4A01G041400 chr4A 100.000 411 0 0 1 411 34788965 34788555 0.000000e+00 760.0
3 TraesCS4A01G041400 chr4D 89.909 2973 168 62 948 3865 433393813 433390918 0.000000e+00 3707.0
4 TraesCS4A01G041400 chr4D 91.245 811 50 12 2413 3218 374099396 374098602 0.000000e+00 1085.0
5 TraesCS4A01G041400 chr4D 85.253 495 32 16 3863 4346 433390881 433390417 5.160000e-129 472.0
6 TraesCS4A01G041400 chr4D 86.236 356 15 13 60 411 433394461 433394136 5.420000e-94 355.0
7 TraesCS4A01G041400 chr4D 96.491 57 2 0 1770 1826 374099456 374099400 1.310000e-15 95.3
8 TraesCS4A01G041400 chr4B 88.874 3020 162 74 948 3863 531581167 531578218 0.000000e+00 3555.0
9 TraesCS4A01G041400 chr4B 83.294 419 28 20 1 411 531581868 531581484 9.080000e-92 348.0
10 TraesCS4A01G041400 chr4B 81.349 252 23 13 3982 4223 531578092 531577855 2.710000e-42 183.0
11 TraesCS4A01G041400 chr7D 88.554 1293 90 24 2356 3636 495879794 495878548 0.000000e+00 1515.0
12 TraesCS4A01G041400 chr7D 89.357 498 43 3 1770 2267 495880276 495879789 6.270000e-173 617.0
13 TraesCS4A01G041400 chr1D 88.682 1237 87 23 2413 3636 468993674 468994870 0.000000e+00 1459.0
14 TraesCS4A01G041400 chr1D 83.704 270 14 7 3864 4125 468995000 468995247 1.230000e-55 228.0
15 TraesCS4A01G041400 chr1D 95.000 60 3 0 1767 1826 468993611 468993670 1.310000e-15 95.3
16 TraesCS4A01G041400 chr7B 88.384 1188 86 21 2487 3654 137024046 137025201 0.000000e+00 1382.0
17 TraesCS4A01G041400 chr5B 87.595 1185 95 22 2487 3654 417341132 417342281 0.000000e+00 1327.0
18 TraesCS4A01G041400 chr5B 93.846 65 4 0 1612 1676 538547306 538547370 1.010000e-16 99.0
19 TraesCS4A01G041400 chr7A 86.780 1233 102 31 2413 3636 239764528 239763348 0.000000e+00 1317.0
20 TraesCS4A01G041400 chr7A 82.222 270 16 10 3865 4125 239763187 239762941 2.080000e-48 204.0
21 TraesCS4A01G041400 chr6B 87.089 1185 101 24 2487 3654 668977089 668978238 0.000000e+00 1293.0
22 TraesCS4A01G041400 chr6B 89.663 416 36 6 1108 1518 487835473 487835060 1.410000e-144 523.0
23 TraesCS4A01G041400 chr6A 86.776 915 77 17 2735 3636 581455933 581455050 0.000000e+00 979.0
24 TraesCS4A01G041400 chr6A 89.681 407 37 4 1108 1510 471800552 471800957 8.460000e-142 514.0
25 TraesCS4A01G041400 chr6A 90.854 328 23 4 2413 2739 581456978 581456657 2.440000e-117 433.0
26 TraesCS4A01G041400 chr6A 83.704 270 14 7 3864 4125 581454920 581454673 1.230000e-55 228.0
27 TraesCS4A01G041400 chr2A 85.090 778 83 19 2859 3636 219084836 219084092 0.000000e+00 763.0
28 TraesCS4A01G041400 chr3A 84.821 784 83 19 2859 3636 391191713 391190960 0.000000e+00 756.0
29 TraesCS4A01G041400 chr3A 89.681 407 41 1 1104 1509 178987294 178986888 6.540000e-143 518.0
30 TraesCS4A01G041400 chr2B 88.133 573 55 6 1776 2346 159848449 159849010 0.000000e+00 669.0
31 TraesCS4A01G041400 chr2B 85.185 594 41 22 1990 2581 30248671 30249219 2.300000e-157 566.0
32 TraesCS4A01G041400 chr2B 89.655 406 39 3 1108 1510 605381365 605380960 8.460000e-142 514.0
33 TraesCS4A01G041400 chr2B 90.351 228 20 2 1776 2003 30243163 30243388 9.270000e-77 298.0
34 TraesCS4A01G041400 chr6D 89.806 412 35 6 1108 1514 332499021 332499430 5.050000e-144 521.0
35 TraesCS4A01G041400 chr3D 89.851 404 40 1 1104 1506 151901737 151902140 6.540000e-143 518.0
36 TraesCS4A01G041400 chr3B 89.724 399 41 0 1108 1506 222318457 222318855 1.090000e-140 510.0
37 TraesCS4A01G041400 chr5D 95.385 65 3 0 1612 1676 442337554 442337618 2.170000e-18 104.0
38 TraesCS4A01G041400 chr5A 95.385 65 3 0 1612 1676 558548326 558548390 2.170000e-18 104.0


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 TraesCS4A01G041400 chr4A 34784557 34788965 4408 True 3577.000000 6394 100.000000 1 4409 2 chr4A.!!$R1 4408
1 TraesCS4A01G041400 chr4A 454846632 454847375 743 False 780.000000 780 85.494000 2859 3636 1 chr4A.!!$F1 777
2 TraesCS4A01G041400 chr4D 433390417 433394461 4044 True 1511.333333 3707 87.132667 60 4346 3 chr4D.!!$R2 4286
3 TraesCS4A01G041400 chr4D 374098602 374099456 854 True 590.150000 1085 93.868000 1770 3218 2 chr4D.!!$R1 1448
4 TraesCS4A01G041400 chr4B 531577855 531581868 4013 True 1362.000000 3555 84.505667 1 4223 3 chr4B.!!$R1 4222
5 TraesCS4A01G041400 chr7D 495878548 495880276 1728 True 1066.000000 1515 88.955500 1770 3636 2 chr7D.!!$R1 1866
6 TraesCS4A01G041400 chr1D 468993611 468995247 1636 False 594.100000 1459 89.128667 1767 4125 3 chr1D.!!$F1 2358
7 TraesCS4A01G041400 chr7B 137024046 137025201 1155 False 1382.000000 1382 88.384000 2487 3654 1 chr7B.!!$F1 1167
8 TraesCS4A01G041400 chr5B 417341132 417342281 1149 False 1327.000000 1327 87.595000 2487 3654 1 chr5B.!!$F1 1167
9 TraesCS4A01G041400 chr7A 239762941 239764528 1587 True 760.500000 1317 84.501000 2413 4125 2 chr7A.!!$R1 1712
10 TraesCS4A01G041400 chr6B 668977089 668978238 1149 False 1293.000000 1293 87.089000 2487 3654 1 chr6B.!!$F1 1167
11 TraesCS4A01G041400 chr6A 581454673 581456978 2305 True 546.666667 979 87.111333 2413 4125 3 chr6A.!!$R1 1712
12 TraesCS4A01G041400 chr2A 219084092 219084836 744 True 763.000000 763 85.090000 2859 3636 1 chr2A.!!$R1 777
13 TraesCS4A01G041400 chr3A 391190960 391191713 753 True 756.000000 756 84.821000 2859 3636 1 chr3A.!!$R2 777
14 TraesCS4A01G041400 chr2B 159848449 159849010 561 False 669.000000 669 88.133000 1776 2346 1 chr2B.!!$F3 570
15 TraesCS4A01G041400 chr2B 30248671 30249219 548 False 566.000000 566 85.185000 1990 2581 1 chr2B.!!$F2 591

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
157 161 0.033504 AACCAACAGCGTCTCGTCAT 59.966 50.0 0.0 0.0 0.0 3.06 F
159 163 0.388520 CCAACAGCGTCTCGTCATCA 60.389 55.0 0.0 0.0 0.0 3.07 F
2097 2178 0.029167 CACACATGTTCTTGCACGCA 59.971 50.0 0.0 0.0 0.0 5.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1549 1582 0.038343 TGGAAGAAGCAAATTGGCGC 60.038 50.0 0.00 0.0 39.27 6.53 R
2104 2185 0.810031 ATTGGATTTCGAGACGCGGG 60.810 55.0 12.47 0.0 41.33 6.13 R
3589 4491 0.028637 GGCAGGCGTCGTACTACTAC 59.971 60.0 0.00 0.0 0.00 2.73 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
17 18 3.196648 CAAAATTCCGGCCCCGAG 58.803 61.111 8.54 0.00 42.83 4.63
21 22 2.831894 AAATTCCGGCCCCGAGAACC 62.832 60.000 8.54 0.00 42.83 3.62
29 30 0.036306 GCCCCGAGAACCTGAGAAAA 59.964 55.000 0.00 0.00 0.00 2.29
33 34 2.290323 CCCGAGAACCTGAGAAAACCAT 60.290 50.000 0.00 0.00 0.00 3.55
35 36 3.557054 CCGAGAACCTGAGAAAACCATCA 60.557 47.826 0.00 0.00 0.00 3.07
36 37 4.256920 CGAGAACCTGAGAAAACCATCAT 58.743 43.478 0.00 0.00 0.00 2.45
37 38 4.331168 CGAGAACCTGAGAAAACCATCATC 59.669 45.833 0.00 0.00 0.00 2.92
38 39 5.246981 AGAACCTGAGAAAACCATCATCA 57.753 39.130 0.00 0.00 0.00 3.07
39 40 5.251764 AGAACCTGAGAAAACCATCATCAG 58.748 41.667 0.00 0.00 37.68 2.90
40 41 4.916041 ACCTGAGAAAACCATCATCAGA 57.084 40.909 2.20 0.00 39.80 3.27
41 42 5.447778 ACCTGAGAAAACCATCATCAGAT 57.552 39.130 2.20 0.00 39.80 2.90
42 43 5.435291 ACCTGAGAAAACCATCATCAGATC 58.565 41.667 2.20 0.00 39.80 2.75
43 44 5.045359 ACCTGAGAAAACCATCATCAGATCA 60.045 40.000 0.00 0.00 39.80 2.92
44 45 5.527951 CCTGAGAAAACCATCATCAGATCAG 59.472 44.000 0.00 0.00 39.80 2.90
68 69 7.333174 CAGATCAGATGAGATTCATTCAGATGG 59.667 40.741 0.00 0.00 37.20 3.51
73 74 7.386573 CAGATGAGATTCATTCAGATGGAAGAG 59.613 40.741 0.00 0.00 37.20 2.85
83 84 3.118112 TCAGATGGAAGAGGAAGGCAATC 60.118 47.826 0.00 0.00 0.00 2.67
85 86 3.267812 AGATGGAAGAGGAAGGCAATCAA 59.732 43.478 0.00 0.00 0.00 2.57
86 87 3.524095 TGGAAGAGGAAGGCAATCAAA 57.476 42.857 0.00 0.00 0.00 2.69
87 88 3.157087 TGGAAGAGGAAGGCAATCAAAC 58.843 45.455 0.00 0.00 0.00 2.93
88 89 2.493675 GGAAGAGGAAGGCAATCAAACC 59.506 50.000 0.00 0.00 0.00 3.27
90 91 3.463048 AGAGGAAGGCAATCAAACCAT 57.537 42.857 0.00 0.00 0.00 3.55
93 94 2.827921 AGGAAGGCAATCAAACCATCAC 59.172 45.455 0.00 0.00 0.00 3.06
94 95 2.094026 GGAAGGCAATCAAACCATCACC 60.094 50.000 0.00 0.00 0.00 4.02
95 96 2.307496 AGGCAATCAAACCATCACCA 57.693 45.000 0.00 0.00 0.00 4.17
105 109 4.821805 TCAAACCATCACCAGACTTCTTTC 59.178 41.667 0.00 0.00 0.00 2.62
128 132 4.271016 GGCGTCCCATCCCATCCC 62.271 72.222 0.00 0.00 0.00 3.85
130 134 2.833913 GCGTCCCATCCCATCCCAT 61.834 63.158 0.00 0.00 0.00 4.00
131 135 1.376466 CGTCCCATCCCATCCCATC 59.624 63.158 0.00 0.00 0.00 3.51
132 136 1.770324 GTCCCATCCCATCCCATCC 59.230 63.158 0.00 0.00 0.00 3.51
133 137 1.847506 TCCCATCCCATCCCATCCG 60.848 63.158 0.00 0.00 0.00 4.18
134 138 2.759114 CCATCCCATCCCATCCGG 59.241 66.667 0.00 0.00 0.00 5.14
157 161 0.033504 AACCAACAGCGTCTCGTCAT 59.966 50.000 0.00 0.00 0.00 3.06
159 163 0.388520 CCAACAGCGTCTCGTCATCA 60.389 55.000 0.00 0.00 0.00 3.07
161 165 0.734253 AACAGCGTCTCGTCATCAGC 60.734 55.000 0.00 0.00 0.00 4.26
162 166 1.138459 CAGCGTCTCGTCATCAGCT 59.862 57.895 0.00 0.00 35.06 4.24
163 167 0.865218 CAGCGTCTCGTCATCAGCTC 60.865 60.000 0.00 0.00 32.05 4.09
165 169 1.136872 GCGTCTCGTCATCAGCTCAC 61.137 60.000 0.00 0.00 0.00 3.51
169 173 3.059884 GTCTCGTCATCAGCTCACAAAA 58.940 45.455 0.00 0.00 0.00 2.44
171 175 4.153117 GTCTCGTCATCAGCTCACAAAAAT 59.847 41.667 0.00 0.00 0.00 1.82
172 176 5.348724 GTCTCGTCATCAGCTCACAAAAATA 59.651 40.000 0.00 0.00 0.00 1.40
173 177 6.036517 GTCTCGTCATCAGCTCACAAAAATAT 59.963 38.462 0.00 0.00 0.00 1.28
174 178 7.222805 GTCTCGTCATCAGCTCACAAAAATATA 59.777 37.037 0.00 0.00 0.00 0.86
176 180 8.437360 TCGTCATCAGCTCACAAAAATATAAT 57.563 30.769 0.00 0.00 0.00 1.28
177 181 8.337532 TCGTCATCAGCTCACAAAAATATAATG 58.662 33.333 0.00 0.00 0.00 1.90
186 190 7.521261 GCTCACAAAAATATAATGGAGAGAGCC 60.521 40.741 0.00 0.00 37.02 4.70
1027 1036 5.823045 CCAGGTGATTACTCAATTAACCTCC 59.177 44.000 0.00 0.00 38.50 4.30
1071 1084 2.614057 CTGAGGCTGCTTAATTTACCGG 59.386 50.000 0.00 0.00 0.00 5.28
1082 1115 2.588856 ATTTACCGGGCGAGGCTGAC 62.589 60.000 6.32 0.00 33.69 3.51
1100 1133 2.778679 GATCTTGGTGTCGCACGC 59.221 61.111 4.33 0.00 34.83 5.34
1101 1134 3.071459 GATCTTGGTGTCGCACGCG 62.071 63.158 3.53 3.53 41.35 6.01
1406 1439 2.062519 GAGAAGAAGTGGAAGTGCGAC 58.937 52.381 0.00 0.00 0.00 5.19
1515 1548 2.362120 TCTTCTCCCGGTCCGTCC 60.362 66.667 11.06 0.00 0.00 4.79
1537 1570 4.862823 CTCCGTCCCTCCCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
1570 1603 1.669795 CGCCAATTTGCTTCTTCCACC 60.670 52.381 0.00 0.00 0.00 4.61
1579 1612 2.827322 TGCTTCTTCCACCATCCATTTG 59.173 45.455 0.00 0.00 0.00 2.32
1737 1797 4.537433 CTGCCCCGCCTGCTCTAC 62.537 72.222 0.00 0.00 0.00 2.59
1834 1906 3.555956 GGTAATGATGGTCAACGCACTAG 59.444 47.826 0.00 0.00 0.00 2.57
1847 1919 0.240411 GCACTAGTGTTCGTCCGTCT 59.760 55.000 23.44 0.00 0.00 4.18
1943 2015 3.945285 AGTATGTTTTGGAGCGTTATGGG 59.055 43.478 0.00 0.00 0.00 4.00
1947 2019 1.828979 TTTGGAGCGTTATGGGGTTC 58.171 50.000 0.00 0.00 0.00 3.62
1952 2024 1.877367 GCGTTATGGGGTTCGCAAA 59.123 52.632 0.00 0.00 46.40 3.68
2007 2080 5.010922 TGGTGGATTTTTGTCTGGAATGAAG 59.989 40.000 0.00 0.00 0.00 3.02
2028 2102 1.826487 GAGACCGAGAGAGCTCCCC 60.826 68.421 10.93 2.49 37.91 4.81
2056 2130 1.016653 GCAGTCTTTGTCCGAGAGCC 61.017 60.000 0.00 0.00 0.00 4.70
2080 2157 0.037232 GGAGCAGTGACCCAGTACAC 60.037 60.000 0.00 0.00 37.30 2.90
2097 2178 0.029167 CACACATGTTCTTGCACGCA 59.971 50.000 0.00 0.00 0.00 5.24
2098 2179 0.029300 ACACATGTTCTTGCACGCAC 59.971 50.000 0.00 0.00 0.00 5.34
2099 2180 0.993251 CACATGTTCTTGCACGCACG 60.993 55.000 0.00 0.00 0.00 5.34
2100 2181 2.076628 CATGTTCTTGCACGCACGC 61.077 57.895 0.00 0.00 0.00 5.34
2101 2182 2.542013 ATGTTCTTGCACGCACGCA 61.542 52.632 0.00 0.00 41.03 5.24
2102 2183 2.715864 ATGTTCTTGCACGCACGCAC 62.716 55.000 0.00 0.00 42.87 5.34
2103 2184 4.292208 TTCTTGCACGCACGCACG 62.292 61.111 0.00 0.00 42.87 5.34
2130 2215 5.333339 CGCGTCTCGAAATCCAATCAATTAT 60.333 40.000 0.00 0.00 41.67 1.28
2170 2255 4.064388 CTCATACAGAGCGAGAGATGAGA 58.936 47.826 12.77 0.00 41.76 3.27
2206 2297 0.256752 TGATGAGGGATGCCACTTGG 59.743 55.000 5.86 0.00 38.53 3.61
2227 2318 3.312697 GGTGGATTCTTTTAGGATCGTGC 59.687 47.826 0.00 0.00 0.00 5.34
2290 2381 3.433343 TGTGATGCAATCCCAGTTGAAT 58.567 40.909 0.00 0.00 44.73 2.57
2297 2388 3.675228 GCAATCCCAGTTGAATTGCAGAG 60.675 47.826 18.78 0.00 44.79 3.35
2402 2493 0.319728 CCCATCATGACTAGGCTCGG 59.680 60.000 0.00 0.00 0.00 4.63
2403 2494 0.320247 CCATCATGACTAGGCTCGGC 60.320 60.000 0.00 0.00 0.00 5.54
2404 2495 0.665670 CATCATGACTAGGCTCGGCG 60.666 60.000 0.00 0.00 0.00 6.46
2405 2496 2.427540 ATCATGACTAGGCTCGGCGC 62.428 60.000 0.00 0.00 38.13 6.53
2485 2587 7.288672 AGCGCTTAACGTTTATTATCTTATGC 58.711 34.615 2.64 0.00 46.11 3.14
2501 2606 5.851720 TCTTATGCCTGTGATCTGAATCTC 58.148 41.667 0.00 0.00 32.75 2.75
2994 3845 4.338539 ACGTCGTCCGGTCAGCAC 62.339 66.667 0.00 0.00 42.24 4.40
2997 3848 3.986006 TCGTCCGGTCAGCACCAC 61.986 66.667 0.00 0.00 44.02 4.16
3009 3869 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
3012 3872 2.518349 CACCACCACCACCACCAC 60.518 66.667 0.00 0.00 0.00 4.16
3225 4097 1.609501 AGCCACGCTGGACTTCCTA 60.610 57.895 8.04 0.00 40.96 2.94
3228 4100 0.970937 CCACGCTGGACTTCCTAGGA 60.971 60.000 7.62 7.62 40.96 2.94
3288 4174 3.803082 CCCGTGTTCATGCAGCCG 61.803 66.667 0.00 0.00 0.00 5.52
3409 4295 0.596083 CAGCTCGCCGATCCTGTAAG 60.596 60.000 6.72 0.00 0.00 2.34
3410 4296 1.951631 GCTCGCCGATCCTGTAAGC 60.952 63.158 0.00 0.00 0.00 3.09
3413 4299 4.827481 GCCGATCCTGTAAGCGAA 57.173 55.556 0.00 0.00 0.00 4.70
3414 4300 3.059603 GCCGATCCTGTAAGCGAAA 57.940 52.632 0.00 0.00 0.00 3.46
3416 4302 1.940613 GCCGATCCTGTAAGCGAAAAT 59.059 47.619 0.00 0.00 0.00 1.82
3417 4303 2.286418 GCCGATCCTGTAAGCGAAAATG 60.286 50.000 0.00 0.00 0.00 2.32
3418 4304 2.286418 CCGATCCTGTAAGCGAAAATGC 60.286 50.000 0.00 0.00 0.00 3.56
3420 4306 3.802139 CGATCCTGTAAGCGAAAATGCTA 59.198 43.478 0.00 0.00 46.60 3.49
3421 4307 4.318121 CGATCCTGTAAGCGAAAATGCTAC 60.318 45.833 0.00 0.00 46.60 3.58
3423 4309 2.030457 CCTGTAAGCGAAAATGCTACCG 59.970 50.000 0.00 0.00 46.60 4.02
3424 4310 1.395608 TGTAAGCGAAAATGCTACCGC 59.604 47.619 0.00 0.00 46.60 5.68
3440 4326 1.437986 CGCAGGGTAGTAGCACTCC 59.562 63.158 1.13 0.00 0.00 3.85
3478 4364 0.109132 AGCTGTAAAATGCCGCTTGC 60.109 50.000 0.00 0.00 41.77 4.01
3479 4365 1.405469 GCTGTAAAATGCCGCTTGCG 61.405 55.000 8.14 8.14 45.60 4.85
3480 4366 0.109781 CTGTAAAATGCCGCTTGCGT 60.110 50.000 13.97 0.00 45.60 5.24
3481 4367 0.109964 TGTAAAATGCCGCTTGCGTC 60.110 50.000 13.97 1.20 45.60 5.19
3482 4368 1.125847 GTAAAATGCCGCTTGCGTCG 61.126 55.000 13.97 0.77 45.60 5.12
3533 4420 2.116366 CTTGGCCGTTCTTTTGTTTCG 58.884 47.619 0.00 0.00 0.00 3.46
3577 4479 6.040504 AGCAAGTTACTTTTGTTCCTTTAGGG 59.959 38.462 0.00 0.00 35.41 3.53
3585 4487 3.418684 TGTTCCTTTAGGGTTCAGCTC 57.581 47.619 0.00 0.00 36.25 4.09
3586 4488 2.979678 TGTTCCTTTAGGGTTCAGCTCT 59.020 45.455 0.00 0.00 36.25 4.09
3587 4489 3.394606 TGTTCCTTTAGGGTTCAGCTCTT 59.605 43.478 0.00 0.00 36.25 2.85
3588 4490 4.595781 TGTTCCTTTAGGGTTCAGCTCTTA 59.404 41.667 0.00 0.00 36.25 2.10
3589 4491 5.179533 GTTCCTTTAGGGTTCAGCTCTTAG 58.820 45.833 0.00 0.00 36.25 2.18
3590 4492 4.426704 TCCTTTAGGGTTCAGCTCTTAGT 58.573 43.478 0.00 0.00 36.25 2.24
3591 4493 5.586877 TCCTTTAGGGTTCAGCTCTTAGTA 58.413 41.667 0.00 0.00 36.25 1.82
3592 4494 5.657302 TCCTTTAGGGTTCAGCTCTTAGTAG 59.343 44.000 0.00 0.00 36.25 2.57
3637 4561 5.572896 AGCAAAGTTTCTTTTGAAGTTCACG 59.427 36.000 4.68 0.00 39.79 4.35
3639 4563 4.965119 AGTTTCTTTTGAAGTTCACGCT 57.035 36.364 4.68 0.00 39.88 5.07
3665 4589 3.584406 AGTCAGTGTCTTTCTCCATCG 57.416 47.619 0.00 0.00 0.00 3.84
3673 4597 1.135139 TCTTTCTCCATCGGCTCTTCG 59.865 52.381 0.00 0.00 0.00 3.79
3678 4602 2.202851 CATCGGCTCTTCGCTGCT 60.203 61.111 0.00 0.00 44.92 4.24
3759 4695 4.147701 CCCCCTGCATTTAGAGCG 57.852 61.111 0.00 0.00 33.85 5.03
3766 4702 1.063166 GCATTTAGAGCGGCACAGC 59.937 57.895 1.45 0.00 37.41 4.40
3802 4739 2.746279 ATTTTGTGACCACCTGACCA 57.254 45.000 0.00 0.00 0.00 4.02
3804 4741 1.208706 TTTGTGACCACCTGACCAGA 58.791 50.000 0.00 0.00 0.00 3.86
3805 4742 0.468226 TTGTGACCACCTGACCAGAC 59.532 55.000 0.00 0.00 0.00 3.51
3806 4743 1.371558 GTGACCACCTGACCAGACC 59.628 63.158 0.00 0.00 0.00 3.85
3807 4744 1.122019 GTGACCACCTGACCAGACCT 61.122 60.000 0.00 0.00 0.00 3.85
3808 4745 1.121407 TGACCACCTGACCAGACCTG 61.121 60.000 0.00 0.00 0.00 4.00
3809 4746 2.348998 CCACCTGACCAGACCTGC 59.651 66.667 0.00 0.00 0.00 4.85
3810 4747 2.348998 CACCTGACCAGACCTGCC 59.651 66.667 0.00 0.00 0.00 4.85
3811 4748 2.930562 ACCTGACCAGACCTGCCC 60.931 66.667 0.00 0.00 0.00 5.36
3888 4897 0.947244 CCCAGCTTGCGATGGTTATC 59.053 55.000 0.00 0.00 45.24 1.75
3891 4900 2.223340 CCAGCTTGCGATGGTTATCAAC 60.223 50.000 0.00 0.00 41.77 3.18
3901 4910 3.328382 TGGTTATCAACGCTGCTAACT 57.672 42.857 11.15 0.00 35.43 2.24
3902 4911 3.670625 TGGTTATCAACGCTGCTAACTT 58.329 40.909 11.15 0.00 35.43 2.66
3903 4912 3.435327 TGGTTATCAACGCTGCTAACTTG 59.565 43.478 11.15 0.00 35.43 3.16
3904 4913 3.435671 GGTTATCAACGCTGCTAACTTGT 59.564 43.478 11.15 0.00 35.43 3.16
3905 4914 4.394795 GTTATCAACGCTGCTAACTTGTG 58.605 43.478 5.53 0.00 33.33 3.33
3906 4915 1.948104 TCAACGCTGCTAACTTGTGT 58.052 45.000 0.00 0.00 0.00 3.72
3907 4916 1.597195 TCAACGCTGCTAACTTGTGTG 59.403 47.619 0.00 0.00 0.00 3.82
3908 4917 0.944386 AACGCTGCTAACTTGTGTGG 59.056 50.000 0.00 0.00 0.00 4.17
3909 4918 0.884704 ACGCTGCTAACTTGTGTGGG 60.885 55.000 0.00 0.00 0.00 4.61
3970 4979 7.778083 TCGATGCTTTAAGTAGGTTATCTCAA 58.222 34.615 0.00 0.00 0.00 3.02
3971 4980 7.705325 TCGATGCTTTAAGTAGGTTATCTCAAC 59.295 37.037 0.00 0.00 0.00 3.18
3972 4981 7.707035 CGATGCTTTAAGTAGGTTATCTCAACT 59.293 37.037 0.00 0.00 0.00 3.16
3973 4982 8.950208 ATGCTTTAAGTAGGTTATCTCAACTC 57.050 34.615 0.00 0.00 0.00 3.01
3974 4983 7.033791 TGCTTTAAGTAGGTTATCTCAACTCG 58.966 38.462 0.00 0.00 0.00 4.18
3999 5008 1.382522 CTTGGTCAGGCGTTGCATAT 58.617 50.000 0.00 0.00 0.00 1.78
4014 5023 6.607689 CGTTGCATATTTTTGTGGAAGTAGA 58.392 36.000 0.00 0.00 0.00 2.59
4019 5028 9.290988 TGCATATTTTTGTGGAAGTAGAAGTAA 57.709 29.630 0.00 0.00 0.00 2.24
4020 5029 9.774742 GCATATTTTTGTGGAAGTAGAAGTAAG 57.225 33.333 0.00 0.00 0.00 2.34
4073 5089 0.392998 GGCGGCCTCATCTTTCAGAA 60.393 55.000 12.87 0.00 0.00 3.02
4079 5095 4.676196 CGGCCTCATCTTTCAGAAAATTGG 60.676 45.833 0.00 0.00 0.00 3.16
4083 5102 5.300969 TCATCTTTCAGAAAATTGGAGCG 57.699 39.130 0.00 0.00 0.00 5.03
4103 5122 7.656137 TGGAGCGTCCTAAATTTCATAGTATTC 59.344 37.037 0.00 0.00 37.46 1.75
4115 5134 9.699410 AATTTCATAGTATTCTGGTGGAAATGA 57.301 29.630 0.00 0.00 37.49 2.57
4127 5146 7.405292 TCTGGTGGAAATGATGACTTAAATCT 58.595 34.615 0.00 0.00 0.00 2.40
4144 5163 7.445402 ACTTAAATCTATTATTGGCGATGTGCT 59.555 33.333 0.00 0.00 45.43 4.40
4171 5190 1.102154 TTTAATGTGATGGCGCTGGG 58.898 50.000 7.64 0.00 0.00 4.45
4216 5245 0.108756 GGTACACGTCCTCTTCCAGC 60.109 60.000 0.00 0.00 0.00 4.85
4238 5267 6.095300 CAGCACAATGTCACCCTGAATAATTA 59.905 38.462 0.00 0.00 0.00 1.40
4240 5269 6.095440 GCACAATGTCACCCTGAATAATTAGT 59.905 38.462 0.00 0.00 0.00 2.24
4243 5272 8.325787 ACAATGTCACCCTGAATAATTAGTACA 58.674 33.333 0.00 0.00 0.00 2.90
4244 5273 8.830580 CAATGTCACCCTGAATAATTAGTACAG 58.169 37.037 0.00 8.45 0.00 2.74
4245 5274 7.727578 TGTCACCCTGAATAATTAGTACAGA 57.272 36.000 13.99 0.00 0.00 3.41
4246 5275 7.782049 TGTCACCCTGAATAATTAGTACAGAG 58.218 38.462 13.99 6.95 0.00 3.35
4247 5276 7.399191 TGTCACCCTGAATAATTAGTACAGAGT 59.601 37.037 13.99 7.41 0.00 3.24
4248 5277 8.910944 GTCACCCTGAATAATTAGTACAGAGTA 58.089 37.037 13.99 0.00 0.00 2.59
4249 5278 8.910944 TCACCCTGAATAATTAGTACAGAGTAC 58.089 37.037 13.99 0.00 0.00 2.73
4250 5279 8.142551 CACCCTGAATAATTAGTACAGAGTACC 58.857 40.741 13.99 0.00 0.00 3.34
4251 5280 7.842743 ACCCTGAATAATTAGTACAGAGTACCA 59.157 37.037 13.99 0.00 0.00 3.25
4252 5281 8.701895 CCCTGAATAATTAGTACAGAGTACCAA 58.298 37.037 13.99 0.00 0.00 3.67
4289 5318 1.349627 CAAATACTCTGCAGCGGCG 59.650 57.895 9.47 0.51 45.35 6.46
4312 5341 3.061697 GGTCGTGTTCACGTGGAATAATC 59.938 47.826 21.61 0.00 37.93 1.75
4320 5349 4.066490 TCACGTGGAATAATCGGTTGTTT 58.934 39.130 17.00 0.00 0.00 2.83
4329 5358 2.774439 ATCGGTTGTTTGAACAGTGC 57.226 45.000 0.00 0.00 40.50 4.40
4346 5375 2.413112 AGTGCGATTCTGTGAAACGATG 59.587 45.455 12.73 0.00 42.39 3.84
4347 5376 1.731709 TGCGATTCTGTGAAACGATGG 59.268 47.619 12.73 0.00 42.39 3.51
4348 5377 1.062587 GCGATTCTGTGAAACGATGGG 59.937 52.381 12.73 0.00 42.39 4.00
4349 5378 2.616960 CGATTCTGTGAAACGATGGGA 58.383 47.619 4.38 0.00 42.39 4.37
4350 5379 3.198068 CGATTCTGTGAAACGATGGGAT 58.802 45.455 4.38 0.00 42.39 3.85
4351 5380 3.001634 CGATTCTGTGAAACGATGGGATG 59.998 47.826 4.38 0.00 42.39 3.51
4352 5381 3.417069 TTCTGTGAAACGATGGGATGT 57.583 42.857 0.00 0.00 42.39 3.06
4353 5382 2.972625 TCTGTGAAACGATGGGATGTC 58.027 47.619 0.00 0.00 42.39 3.06
4354 5383 2.301583 TCTGTGAAACGATGGGATGTCA 59.698 45.455 0.00 0.00 42.39 3.58
4355 5384 2.416547 CTGTGAAACGATGGGATGTCAC 59.583 50.000 0.00 0.00 42.39 3.67
4356 5385 1.737793 GTGAAACGATGGGATGTCACC 59.262 52.381 0.00 0.00 31.32 4.02
4357 5386 5.993605 TGTGAAACGATGGGATGTCACCC 62.994 52.174 0.00 0.00 45.54 4.61
4366 5395 1.276421 GGGATGTCACCCTGGATATCG 59.724 57.143 0.00 0.00 45.90 2.92
4367 5396 1.971357 GGATGTCACCCTGGATATCGT 59.029 52.381 0.00 0.00 36.57 3.73
4368 5397 2.368875 GGATGTCACCCTGGATATCGTT 59.631 50.000 0.00 0.00 36.57 3.85
4369 5398 3.576982 GGATGTCACCCTGGATATCGTTA 59.423 47.826 0.00 0.00 36.57 3.18
4370 5399 4.557205 GATGTCACCCTGGATATCGTTAC 58.443 47.826 0.00 0.00 0.00 2.50
4371 5400 2.359848 TGTCACCCTGGATATCGTTACG 59.640 50.000 0.00 0.00 0.00 3.18
4372 5401 2.360165 GTCACCCTGGATATCGTTACGT 59.640 50.000 4.24 0.00 0.00 3.57
4373 5402 2.359848 TCACCCTGGATATCGTTACGTG 59.640 50.000 4.24 0.15 0.00 4.49
4374 5403 1.068127 ACCCTGGATATCGTTACGTGC 59.932 52.381 4.24 0.00 0.00 5.34
4375 5404 1.067974 CCCTGGATATCGTTACGTGCA 59.932 52.381 4.24 0.00 0.00 4.57
4376 5405 2.482316 CCCTGGATATCGTTACGTGCAA 60.482 50.000 4.24 0.00 0.00 4.08
4377 5406 2.538449 CCTGGATATCGTTACGTGCAAC 59.462 50.000 4.24 0.00 0.00 4.17
4378 5407 3.444916 CTGGATATCGTTACGTGCAACT 58.555 45.455 4.24 0.00 31.75 3.16
4379 5408 3.441163 TGGATATCGTTACGTGCAACTC 58.559 45.455 4.24 0.00 31.75 3.01
4380 5409 2.793232 GGATATCGTTACGTGCAACTCC 59.207 50.000 4.24 0.00 31.75 3.85
4381 5410 3.441163 GATATCGTTACGTGCAACTCCA 58.559 45.455 4.24 0.00 31.75 3.86
4382 5411 2.157834 ATCGTTACGTGCAACTCCAA 57.842 45.000 4.24 0.00 31.75 3.53
4383 5412 1.210870 TCGTTACGTGCAACTCCAAC 58.789 50.000 4.24 0.00 31.75 3.77
4384 5413 0.111442 CGTTACGTGCAACTCCAACG 60.111 55.000 0.00 0.00 36.88 4.10
4385 5414 0.233848 GTTACGTGCAACTCCAACGG 59.766 55.000 0.00 0.00 31.75 4.44
4386 5415 0.179078 TTACGTGCAACTCCAACGGT 60.179 50.000 0.00 0.00 31.75 4.83
4387 5416 0.876777 TACGTGCAACTCCAACGGTG 60.877 55.000 0.00 0.00 31.75 4.94
4388 5417 2.331451 GTGCAACTCCAACGGTGC 59.669 61.111 0.00 0.00 0.00 5.01
4389 5418 2.124529 TGCAACTCCAACGGTGCA 60.125 55.556 0.00 0.00 0.00 4.57
4390 5419 1.750780 TGCAACTCCAACGGTGCAA 60.751 52.632 0.42 0.00 0.00 4.08
4391 5420 1.008538 GCAACTCCAACGGTGCAAG 60.009 57.895 0.00 0.00 0.00 4.01
4392 5421 1.008538 CAACTCCAACGGTGCAAGC 60.009 57.895 0.00 0.00 0.00 4.01
4393 5422 1.453015 AACTCCAACGGTGCAAGCA 60.453 52.632 0.00 0.00 0.00 3.91
4394 5423 1.034838 AACTCCAACGGTGCAAGCAA 61.035 50.000 0.00 0.00 0.00 3.91
4395 5424 1.034838 ACTCCAACGGTGCAAGCAAA 61.035 50.000 0.00 0.00 0.00 3.68
4396 5425 0.318107 CTCCAACGGTGCAAGCAAAG 60.318 55.000 0.00 0.00 0.00 2.77
4397 5426 1.950630 CCAACGGTGCAAGCAAAGC 60.951 57.895 0.00 0.00 0.00 3.51
4398 5427 1.066257 CAACGGTGCAAGCAAAGCT 59.934 52.632 0.00 0.00 42.56 3.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.248640 TCTGATGATGGTTTTCTCAGGTTC 58.751 41.667 0.00 0.00 35.24 3.62
21 22 6.346896 TCTGATCTGATGATGGTTTTCTCAG 58.653 40.000 0.00 0.00 35.71 3.35
35 36 7.784470 TGAATCTCATCTGATCTGATCTGAT 57.216 36.000 25.42 25.42 45.25 2.90
36 37 7.784470 ATGAATCTCATCTGATCTGATCTGA 57.216 36.000 23.67 23.67 40.72 3.27
37 38 8.091449 TGAATGAATCTCATCTGATCTGATCTG 58.909 37.037 17.82 16.82 35.76 2.90
38 39 8.196378 TGAATGAATCTCATCTGATCTGATCT 57.804 34.615 17.82 0.00 35.76 2.75
39 40 8.308207 TCTGAATGAATCTCATCTGATCTGATC 58.692 37.037 11.82 10.72 35.76 2.92
40 41 8.196378 TCTGAATGAATCTCATCTGATCTGAT 57.804 34.615 9.15 9.15 35.76 2.90
41 42 7.598759 TCTGAATGAATCTCATCTGATCTGA 57.401 36.000 4.63 4.63 35.76 3.27
42 43 7.333174 CCATCTGAATGAATCTCATCTGATCTG 59.667 40.741 0.00 0.00 35.76 2.90
43 44 7.235812 TCCATCTGAATGAATCTCATCTGATCT 59.764 37.037 0.00 0.00 35.76 2.75
44 45 7.387643 TCCATCTGAATGAATCTCATCTGATC 58.612 38.462 0.00 0.00 35.76 2.92
55 56 5.692928 CCTTCCTCTTCCATCTGAATGAAT 58.307 41.667 0.00 0.00 34.61 2.57
56 57 4.627255 GCCTTCCTCTTCCATCTGAATGAA 60.627 45.833 0.00 0.00 34.61 2.57
57 58 3.118112 GCCTTCCTCTTCCATCTGAATGA 60.118 47.826 0.00 0.00 34.61 2.57
58 59 3.212685 GCCTTCCTCTTCCATCTGAATG 58.787 50.000 0.00 0.00 31.06 2.67
68 69 3.157087 TGGTTTGATTGCCTTCCTCTTC 58.843 45.455 0.00 0.00 0.00 2.87
73 74 2.094026 GGTGATGGTTTGATTGCCTTCC 60.094 50.000 0.00 0.00 0.00 3.46
83 84 4.022849 GGAAAGAAGTCTGGTGATGGTTTG 60.023 45.833 0.00 0.00 0.00 2.93
85 86 3.498661 GGGAAAGAAGTCTGGTGATGGTT 60.499 47.826 0.00 0.00 0.00 3.67
86 87 2.040412 GGGAAAGAAGTCTGGTGATGGT 59.960 50.000 0.00 0.00 0.00 3.55
87 88 2.619074 GGGGAAAGAAGTCTGGTGATGG 60.619 54.545 0.00 0.00 0.00 3.51
88 89 2.307098 AGGGGAAAGAAGTCTGGTGATG 59.693 50.000 0.00 0.00 0.00 3.07
90 91 2.106511 CAAGGGGAAAGAAGTCTGGTGA 59.893 50.000 0.00 0.00 0.00 4.02
93 94 1.888391 GCCAAGGGGAAAGAAGTCTGG 60.888 57.143 0.00 0.00 35.59 3.86
94 95 1.539157 GCCAAGGGGAAAGAAGTCTG 58.461 55.000 0.00 0.00 35.59 3.51
95 96 0.036875 CGCCAAGGGGAAAGAAGTCT 59.963 55.000 0.00 0.00 35.59 3.24
105 109 4.506255 GGATGGGACGCCAAGGGG 62.506 72.222 1.12 1.12 37.18 4.79
128 132 0.734889 GCTGTTGGTTGATCCGGATG 59.265 55.000 24.82 4.83 39.52 3.51
130 134 1.375396 CGCTGTTGGTTGATCCGGA 60.375 57.895 6.61 6.61 39.52 5.14
131 135 1.635663 GACGCTGTTGGTTGATCCGG 61.636 60.000 0.00 0.00 39.52 5.14
132 136 0.670546 AGACGCTGTTGGTTGATCCG 60.671 55.000 0.00 0.00 39.52 4.18
133 137 1.079503 GAGACGCTGTTGGTTGATCC 58.920 55.000 0.00 0.00 0.00 3.36
134 138 0.716108 CGAGACGCTGTTGGTTGATC 59.284 55.000 0.00 0.00 0.00 2.92
157 161 8.267183 TCTCTCCATTATATTTTTGTGAGCTGA 58.733 33.333 0.00 0.00 0.00 4.26
159 163 7.228308 GCTCTCTCCATTATATTTTTGTGAGCT 59.772 37.037 0.00 0.00 38.02 4.09
161 165 7.040823 GGGCTCTCTCCATTATATTTTTGTGAG 60.041 40.741 0.00 0.00 0.00 3.51
162 166 6.772716 GGGCTCTCTCCATTATATTTTTGTGA 59.227 38.462 0.00 0.00 0.00 3.58
163 167 6.293626 CGGGCTCTCTCCATTATATTTTTGTG 60.294 42.308 0.00 0.00 0.00 3.33
165 169 5.182001 CCGGGCTCTCTCCATTATATTTTTG 59.818 44.000 0.00 0.00 0.00 2.44
169 173 2.237392 GCCGGGCTCTCTCCATTATATT 59.763 50.000 12.87 0.00 0.00 1.28
171 175 1.267121 GCCGGGCTCTCTCCATTATA 58.733 55.000 12.87 0.00 0.00 0.98
172 176 1.484444 GGCCGGGCTCTCTCCATTAT 61.484 60.000 22.87 0.00 0.00 1.28
173 177 2.140792 GGCCGGGCTCTCTCCATTA 61.141 63.158 22.87 0.00 0.00 1.90
174 178 3.483869 GGCCGGGCTCTCTCCATT 61.484 66.667 22.87 0.00 0.00 3.16
288 292 3.993584 GTCGTACACGTGGGGGCA 61.994 66.667 21.57 0.00 40.80 5.36
331 335 2.575461 CGGTGAGGTTACCCGGAC 59.425 66.667 0.73 0.00 37.44 4.79
334 338 4.807039 CGCCGGTGAGGTTACCCG 62.807 72.222 10.20 0.00 43.70 5.28
386 390 1.897423 GGTGCATTAAGTTGGGGGC 59.103 57.895 0.00 0.00 0.00 5.80
975 979 1.021920 GGAGGGCACGCTTCTTCTTC 61.022 60.000 0.00 0.00 0.00 2.87
1027 1036 1.059369 CGCTTTCGGTCAATCGCAG 59.941 57.895 0.00 0.00 0.00 5.18
1071 1084 1.880340 CAAGATCGTCAGCCTCGCC 60.880 63.158 0.00 0.00 0.00 5.54
1082 1115 3.071459 GCGTGCGACACCAAGATCG 62.071 63.158 0.00 0.00 41.32 3.69
1406 1439 1.461127 GCGTACTTCTTGGAGCACTTG 59.539 52.381 0.00 0.00 0.00 3.16
1549 1582 0.038343 TGGAAGAAGCAAATTGGCGC 60.038 50.000 0.00 0.00 39.27 6.53
1570 1603 2.159421 GCAGTCAGTCAGCAAATGGATG 60.159 50.000 0.00 0.00 0.00 3.51
1579 1612 1.586422 TTTGTCAGCAGTCAGTCAGC 58.414 50.000 0.00 0.00 0.00 4.26
1729 1789 2.125512 GTGGTGGCGGTAGAGCAG 60.126 66.667 0.00 0.00 39.27 4.24
1730 1790 3.702048 GGTGGTGGCGGTAGAGCA 61.702 66.667 0.00 0.00 39.27 4.26
1732 1792 2.579201 CTGGTGGTGGCGGTAGAG 59.421 66.667 0.00 0.00 0.00 2.43
1733 1793 3.702048 GCTGGTGGTGGCGGTAGA 61.702 66.667 0.00 0.00 0.00 2.59
1734 1794 4.778143 GGCTGGTGGTGGCGGTAG 62.778 72.222 0.00 0.00 0.00 3.18
1810 1882 2.095853 GTGCGTTGACCATCATTACCTG 59.904 50.000 0.00 0.00 0.00 4.00
1834 1906 4.031426 CAGCTAAAATAGACGGACGAACAC 59.969 45.833 0.00 0.00 0.00 3.32
1847 1919 3.857665 CGTGAACGAGAGCAGCTAAAATA 59.142 43.478 0.00 0.00 43.02 1.40
1949 2021 2.465097 TTCCCCGTCGCGCAATTTTG 62.465 55.000 8.75 0.00 0.00 2.44
1952 2024 3.124921 CTTCCCCGTCGCGCAATT 61.125 61.111 8.75 0.00 0.00 2.32
2007 2080 2.826738 AGCTCTCTCGGTCTCGGC 60.827 66.667 0.00 0.00 36.95 5.54
2042 2116 1.078848 CCCTGGCTCTCGGACAAAG 60.079 63.158 0.00 0.00 29.31 2.77
2056 2130 3.721706 GGGTCACTGCTCCCCCTG 61.722 72.222 0.00 0.00 37.89 4.45
2080 2157 0.993251 CGTGCGTGCAAGAACATGTG 60.993 55.000 11.54 0.00 0.00 3.21
2102 2183 3.617538 GATTTCGAGACGCGGGCG 61.618 66.667 12.47 12.04 46.03 6.13
2103 2184 3.262686 GGATTTCGAGACGCGGGC 61.263 66.667 12.47 1.16 41.33 6.13
2104 2185 0.810031 ATTGGATTTCGAGACGCGGG 60.810 55.000 12.47 0.00 41.33 6.13
2146 2231 3.812609 TCATCTCTCGCTCTGTATGAGTC 59.187 47.826 0.00 0.00 44.41 3.36
2148 2233 4.064388 TCTCATCTCTCGCTCTGTATGAG 58.936 47.826 0.00 0.00 45.33 2.90
2166 2251 7.562821 TCATCACCTCTCAAAGATCTAATCTCA 59.437 37.037 0.00 0.00 39.08 3.27
2167 2252 7.950512 TCATCACCTCTCAAAGATCTAATCTC 58.049 38.462 0.00 0.00 39.08 2.75
2170 2255 6.043012 CCCTCATCACCTCTCAAAGATCTAAT 59.957 42.308 0.00 0.00 0.00 1.73
2206 2297 3.938963 TGCACGATCCTAAAAGAATCCAC 59.061 43.478 0.00 0.00 0.00 4.02
2244 2335 5.869579 AGCCACTAATCAGAAGTTCAGAAA 58.130 37.500 5.50 0.00 0.00 2.52
2290 2381 1.003355 CTCCGGAAAGGCTCTGCAA 60.003 57.895 5.23 0.00 40.77 4.08
2297 2388 0.250770 AGTCCAAACTCCGGAAAGGC 60.251 55.000 5.23 2.07 40.77 4.35
2405 2496 3.083997 CAACGGGAGGGAGGAGGG 61.084 72.222 0.00 0.00 0.00 4.30
2406 2497 3.787001 GCAACGGGAGGGAGGAGG 61.787 72.222 0.00 0.00 0.00 4.30
2407 2498 1.842381 AAAGCAACGGGAGGGAGGAG 61.842 60.000 0.00 0.00 0.00 3.69
2408 2499 1.838073 GAAAGCAACGGGAGGGAGGA 61.838 60.000 0.00 0.00 0.00 3.71
2409 2500 1.377333 GAAAGCAACGGGAGGGAGG 60.377 63.158 0.00 0.00 0.00 4.30
2410 2501 0.674895 CAGAAAGCAACGGGAGGGAG 60.675 60.000 0.00 0.00 0.00 4.30
2411 2502 1.374947 CAGAAAGCAACGGGAGGGA 59.625 57.895 0.00 0.00 0.00 4.20
2477 2568 6.436738 AGATTCAGATCACAGGCATAAGAT 57.563 37.500 0.00 0.00 34.60 2.40
2485 2587 2.471818 CAGCGAGATTCAGATCACAGG 58.528 52.381 0.00 0.00 34.60 4.00
2501 2606 0.096628 GTCTCAGCAAATCAGCAGCG 59.903 55.000 0.00 0.00 36.85 5.18
2574 2679 2.646719 GGCGTGTACTGGACGACA 59.353 61.111 8.27 0.00 44.61 4.35
2985 3836 4.248842 TGGTGGTGGTGCTGACCG 62.249 66.667 0.00 0.00 46.62 4.79
2994 3845 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
2997 3848 3.814906 TGGTGGTGGTGGTGGTGG 61.815 66.667 0.00 0.00 0.00 4.61
3009 3869 0.823356 CTTCTTGGTGGTGGTGGTGG 60.823 60.000 0.00 0.00 0.00 4.61
3012 3872 1.903404 GGCTTCTTGGTGGTGGTGG 60.903 63.158 0.00 0.00 0.00 4.61
3160 4032 1.597302 CCATCATCAGCTCCGGCAG 60.597 63.158 0.00 0.00 41.70 4.85
3171 4043 1.233285 GCGATGACTGGCCCATCATC 61.233 60.000 26.03 26.03 45.18 2.92
3365 4251 3.254024 TTCCTCTCCCACGGCTTGC 62.254 63.158 0.00 0.00 0.00 4.01
3419 4305 0.033796 AGTGCTACTACCCTGCGGTA 60.034 55.000 0.00 0.00 42.18 4.02
3421 4307 1.437986 GAGTGCTACTACCCTGCGG 59.562 63.158 0.00 0.00 0.00 5.69
3423 4309 0.461961 CTGGAGTGCTACTACCCTGC 59.538 60.000 0.00 0.00 0.00 4.85
3424 4310 1.853963 ACTGGAGTGCTACTACCCTG 58.146 55.000 0.00 0.00 0.00 4.45
3426 4312 3.094572 TGTTACTGGAGTGCTACTACCC 58.905 50.000 0.00 0.00 0.00 3.69
3429 4315 3.415212 ACGTGTTACTGGAGTGCTACTA 58.585 45.455 0.00 0.00 0.00 1.82
3431 4317 2.719426 ACGTGTTACTGGAGTGCTAC 57.281 50.000 0.00 0.00 0.00 3.58
3432 4318 2.163010 GCTACGTGTTACTGGAGTGCTA 59.837 50.000 0.00 0.00 0.00 3.49
3433 4319 1.067776 GCTACGTGTTACTGGAGTGCT 60.068 52.381 0.00 0.00 0.00 4.40
3434 4320 1.336517 TGCTACGTGTTACTGGAGTGC 60.337 52.381 0.00 0.00 0.00 4.40
3435 4321 2.325761 GTGCTACGTGTTACTGGAGTG 58.674 52.381 0.00 0.00 0.00 3.51
3436 4322 1.068748 CGTGCTACGTGTTACTGGAGT 60.069 52.381 0.00 0.00 36.74 3.85
3437 4323 1.614385 CGTGCTACGTGTTACTGGAG 58.386 55.000 0.00 0.00 36.74 3.86
3438 4324 0.241749 CCGTGCTACGTGTTACTGGA 59.758 55.000 0.00 0.00 40.58 3.86
3439 4325 1.349259 GCCGTGCTACGTGTTACTGG 61.349 60.000 0.00 1.97 40.58 4.00
3440 4326 0.665068 TGCCGTGCTACGTGTTACTG 60.665 55.000 0.00 0.00 40.58 2.74
3478 4364 2.526077 TGCTGCTAATTAGACACGACG 58.474 47.619 16.85 0.00 0.00 5.12
3479 4365 2.282820 GCTGCTGCTAATTAGACACGAC 59.717 50.000 16.85 0.00 36.03 4.34
3480 4366 2.540515 GCTGCTGCTAATTAGACACGA 58.459 47.619 16.85 1.19 36.03 4.35
3533 4420 5.689383 TGCTTTCTTGATTGTGACCTAAC 57.311 39.130 0.00 0.00 0.00 2.34
3577 4479 6.507771 CGTCGTACTACTACTAAGAGCTGAAC 60.508 46.154 0.00 0.00 0.00 3.18
3585 4487 3.303001 GCAGGCGTCGTACTACTACTAAG 60.303 52.174 0.00 0.00 0.00 2.18
3586 4488 2.609459 GCAGGCGTCGTACTACTACTAA 59.391 50.000 0.00 0.00 0.00 2.24
3587 4489 2.205074 GCAGGCGTCGTACTACTACTA 58.795 52.381 0.00 0.00 0.00 1.82
3588 4490 1.012841 GCAGGCGTCGTACTACTACT 58.987 55.000 0.00 0.00 0.00 2.57
3589 4491 0.028637 GGCAGGCGTCGTACTACTAC 59.971 60.000 0.00 0.00 0.00 2.73
3590 4492 1.097547 GGGCAGGCGTCGTACTACTA 61.098 60.000 0.00 0.00 0.00 1.82
3591 4493 2.413142 GGGCAGGCGTCGTACTACT 61.413 63.158 0.00 0.00 0.00 2.57
3592 4494 2.103736 GGGCAGGCGTCGTACTAC 59.896 66.667 0.00 0.00 0.00 2.73
3637 4561 4.376146 AGAAAGACACTGACTTCTGAAGC 58.624 43.478 17.00 10.43 0.00 3.86
3639 4563 4.405680 TGGAGAAAGACACTGACTTCTGAA 59.594 41.667 0.00 0.00 0.00 3.02
3642 4566 4.321601 CGATGGAGAAAGACACTGACTTCT 60.322 45.833 0.00 0.00 0.00 2.85
3643 4567 3.923461 CGATGGAGAAAGACACTGACTTC 59.077 47.826 0.00 0.00 0.00 3.01
3644 4568 3.306364 CCGATGGAGAAAGACACTGACTT 60.306 47.826 0.00 0.00 0.00 3.01
3673 4597 0.572125 GTGCAAACGACAAAAGCAGC 59.428 50.000 0.00 0.00 35.66 5.25
3678 4602 3.362237 CGAAACAAGTGCAAACGACAAAA 59.638 39.130 0.00 0.00 0.00 2.44
3745 4671 1.026182 TGTGCCGCTCTAAATGCAGG 61.026 55.000 0.00 0.00 33.80 4.85
3746 4672 0.376152 CTGTGCCGCTCTAAATGCAG 59.624 55.000 0.00 0.00 33.80 4.41
3747 4673 1.647545 GCTGTGCCGCTCTAAATGCA 61.648 55.000 0.00 0.00 0.00 3.96
3748 4674 1.063166 GCTGTGCCGCTCTAAATGC 59.937 57.895 0.00 0.00 0.00 3.56
3749 4675 1.349627 CGCTGTGCCGCTCTAAATG 59.650 57.895 0.00 0.00 0.00 2.32
3750 4676 3.799753 CGCTGTGCCGCTCTAAAT 58.200 55.556 0.00 0.00 0.00 1.40
3759 4695 3.788766 CCACTTACGCGCTGTGCC 61.789 66.667 5.73 0.00 42.08 5.01
3766 4702 5.285134 CACAAAATTAAATCCCACTTACGCG 59.715 40.000 3.53 3.53 0.00 6.01
3777 4713 6.156519 GGTCAGGTGGTCACAAAATTAAATC 58.843 40.000 3.40 0.00 0.00 2.17
3787 4724 1.407656 GGTCTGGTCAGGTGGTCACA 61.408 60.000 3.40 0.00 0.00 3.58
3888 4897 1.334059 CCACACAAGTTAGCAGCGTTG 60.334 52.381 0.00 0.00 0.00 4.10
3891 4900 0.884704 ACCCACACAAGTTAGCAGCG 60.885 55.000 0.00 0.00 0.00 5.18
3901 4910 2.055042 GCCCACACAACCCACACAA 61.055 57.895 0.00 0.00 0.00 3.33
3902 4911 2.441164 GCCCACACAACCCACACA 60.441 61.111 0.00 0.00 0.00 3.72
3903 4912 3.591835 CGCCCACACAACCCACAC 61.592 66.667 0.00 0.00 0.00 3.82
3970 4979 1.472662 CCTGACCAAGGTGACCGAGT 61.473 60.000 0.00 0.00 41.74 4.18
3971 4980 1.293498 CCTGACCAAGGTGACCGAG 59.707 63.158 0.00 0.00 41.74 4.63
3972 4981 3.466881 CCTGACCAAGGTGACCGA 58.533 61.111 0.00 0.00 41.74 4.69
3990 4999 6.607689 TCTACTTCCACAAAAATATGCAACG 58.392 36.000 0.00 0.00 0.00 4.10
4014 5023 5.247564 TCATGCACCCAACTACTACTTACTT 59.752 40.000 0.00 0.00 0.00 2.24
4019 5028 2.094182 CGTCATGCACCCAACTACTACT 60.094 50.000 0.00 0.00 0.00 2.57
4020 5029 2.094390 TCGTCATGCACCCAACTACTAC 60.094 50.000 0.00 0.00 0.00 2.73
4055 5064 1.453155 TTTCTGAAAGATGAGGCCGC 58.547 50.000 0.00 0.00 46.36 6.53
4073 5089 5.975693 TGAAATTTAGGACGCTCCAATTT 57.024 34.783 11.39 11.39 39.61 1.82
4079 5095 8.704234 CAGAATACTATGAAATTTAGGACGCTC 58.296 37.037 0.00 0.00 0.00 5.03
4083 5102 9.057089 CCACCAGAATACTATGAAATTTAGGAC 57.943 37.037 0.00 0.00 0.00 3.85
4103 5122 7.636150 AGATTTAAGTCATCATTTCCACCAG 57.364 36.000 0.44 0.00 0.00 4.00
4115 5134 9.507329 ACATCGCCAATAATAGATTTAAGTCAT 57.493 29.630 0.44 0.00 0.00 3.06
4127 5146 4.195416 TCACAAGCACATCGCCAATAATA 58.805 39.130 0.00 0.00 44.04 0.98
4144 5163 4.624882 GCGCCATCACATTAAAAATCACAA 59.375 37.500 0.00 0.00 0.00 3.33
4194 5223 2.683867 CTGGAAGAGGACGTGTACCTAG 59.316 54.545 0.00 0.00 37.93 3.02
4216 5245 7.630242 ACTAATTATTCAGGGTGACATTGTG 57.370 36.000 0.00 0.00 0.00 3.33
4238 5267 5.306394 GCTTCCTTTTTGGTACTCTGTACT 58.694 41.667 7.64 0.00 37.07 2.73
4240 5269 4.202284 ACGCTTCCTTTTTGGTACTCTGTA 60.202 41.667 0.00 0.00 37.07 2.74
4243 5272 3.487120 ACGCTTCCTTTTTGGTACTCT 57.513 42.857 0.00 0.00 37.07 3.24
4244 5273 3.683340 CCTACGCTTCCTTTTTGGTACTC 59.317 47.826 0.00 0.00 37.07 2.59
4245 5274 3.558533 CCCTACGCTTCCTTTTTGGTACT 60.559 47.826 0.00 0.00 37.07 2.73
4246 5275 2.745821 CCCTACGCTTCCTTTTTGGTAC 59.254 50.000 0.00 0.00 37.07 3.34
4247 5276 2.638855 TCCCTACGCTTCCTTTTTGGTA 59.361 45.455 0.00 0.00 37.07 3.25
4248 5277 1.422402 TCCCTACGCTTCCTTTTTGGT 59.578 47.619 0.00 0.00 37.07 3.67
4249 5278 2.194201 TCCCTACGCTTCCTTTTTGG 57.806 50.000 0.00 0.00 37.10 3.28
4250 5279 2.095212 GCTTCCCTACGCTTCCTTTTTG 60.095 50.000 0.00 0.00 0.00 2.44
4251 5280 2.160205 GCTTCCCTACGCTTCCTTTTT 58.840 47.619 0.00 0.00 0.00 1.94
4252 5281 1.073284 TGCTTCCCTACGCTTCCTTTT 59.927 47.619 0.00 0.00 0.00 2.27
4253 5282 0.690762 TGCTTCCCTACGCTTCCTTT 59.309 50.000 0.00 0.00 0.00 3.11
4302 5331 5.764131 TGTTCAAACAACCGATTATTCCAC 58.236 37.500 0.00 0.00 35.67 4.02
4312 5341 0.375454 TCGCACTGTTCAAACAACCG 59.625 50.000 0.00 1.15 38.66 4.44
4320 5349 2.524569 TCACAGAATCGCACTGTTCA 57.475 45.000 0.00 0.00 44.69 3.18
4329 5358 2.616960 TCCCATCGTTTCACAGAATCG 58.383 47.619 4.36 4.36 0.00 3.34
4347 5376 1.971357 ACGATATCCAGGGTGACATCC 59.029 52.381 0.00 0.00 0.00 3.51
4348 5377 3.753294 AACGATATCCAGGGTGACATC 57.247 47.619 0.00 0.00 0.00 3.06
4349 5378 3.005472 CGTAACGATATCCAGGGTGACAT 59.995 47.826 0.00 0.00 0.00 3.06
4350 5379 2.359848 CGTAACGATATCCAGGGTGACA 59.640 50.000 0.00 0.00 0.00 3.58
4351 5380 2.360165 ACGTAACGATATCCAGGGTGAC 59.640 50.000 0.00 0.00 0.00 3.67
4352 5381 2.359848 CACGTAACGATATCCAGGGTGA 59.640 50.000 0.00 0.00 0.00 4.02
4353 5382 2.739292 CACGTAACGATATCCAGGGTG 58.261 52.381 0.00 0.00 0.00 4.61
4354 5383 1.068127 GCACGTAACGATATCCAGGGT 59.932 52.381 0.00 0.00 0.00 4.34
4355 5384 1.067974 TGCACGTAACGATATCCAGGG 59.932 52.381 0.00 0.00 0.00 4.45
4356 5385 2.502213 TGCACGTAACGATATCCAGG 57.498 50.000 0.00 0.00 0.00 4.45
4357 5386 3.444916 AGTTGCACGTAACGATATCCAG 58.555 45.455 0.00 0.00 35.73 3.86
4358 5387 3.441163 GAGTTGCACGTAACGATATCCA 58.559 45.455 0.00 0.00 35.73 3.41
4359 5388 2.793232 GGAGTTGCACGTAACGATATCC 59.207 50.000 0.00 0.00 35.73 2.59
4360 5389 3.441163 TGGAGTTGCACGTAACGATATC 58.559 45.455 0.00 0.00 35.73 1.63
4361 5390 3.513680 TGGAGTTGCACGTAACGATAT 57.486 42.857 0.00 0.00 35.73 1.63
4362 5391 2.988493 GTTGGAGTTGCACGTAACGATA 59.012 45.455 0.00 0.00 35.73 2.92
4363 5392 1.796459 GTTGGAGTTGCACGTAACGAT 59.204 47.619 0.00 0.00 35.73 3.73
4364 5393 1.210870 GTTGGAGTTGCACGTAACGA 58.789 50.000 0.00 0.00 35.73 3.85
4365 5394 0.111442 CGTTGGAGTTGCACGTAACG 60.111 55.000 2.08 2.08 35.73 3.18
4366 5395 0.233848 CCGTTGGAGTTGCACGTAAC 59.766 55.000 0.00 0.00 31.83 2.50
4367 5396 0.179078 ACCGTTGGAGTTGCACGTAA 60.179 50.000 0.00 0.00 31.83 3.18
4368 5397 0.876777 CACCGTTGGAGTTGCACGTA 60.877 55.000 0.00 0.00 31.83 3.57
4369 5398 2.177580 CACCGTTGGAGTTGCACGT 61.178 57.895 0.00 0.00 31.83 4.49
4370 5399 2.631428 CACCGTTGGAGTTGCACG 59.369 61.111 0.00 0.00 0.00 5.34
4371 5400 1.999071 TTGCACCGTTGGAGTTGCAC 61.999 55.000 0.00 0.00 31.68 4.57
4372 5401 1.723608 CTTGCACCGTTGGAGTTGCA 61.724 55.000 0.00 0.00 0.00 4.08
4373 5402 1.008538 CTTGCACCGTTGGAGTTGC 60.009 57.895 0.00 0.00 0.00 4.17
4374 5403 1.008538 GCTTGCACCGTTGGAGTTG 60.009 57.895 0.00 0.00 0.00 3.16
4375 5404 1.034838 TTGCTTGCACCGTTGGAGTT 61.035 50.000 0.00 0.00 0.00 3.01
4376 5405 1.034838 TTTGCTTGCACCGTTGGAGT 61.035 50.000 0.00 0.00 0.00 3.85
4377 5406 0.318107 CTTTGCTTGCACCGTTGGAG 60.318 55.000 0.00 0.00 0.00 3.86
4378 5407 1.732917 CTTTGCTTGCACCGTTGGA 59.267 52.632 0.00 0.00 0.00 3.53
4379 5408 1.950630 GCTTTGCTTGCACCGTTGG 60.951 57.895 0.00 0.00 0.00 3.77
4380 5409 1.066257 AGCTTTGCTTGCACCGTTG 59.934 52.632 0.00 0.00 33.89 4.10
4381 5410 3.525221 AGCTTTGCTTGCACCGTT 58.475 50.000 0.00 0.00 33.89 4.44


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

AutoCloner maintained by Alex Coulton.