Multiple sequence alignment - TraesCS4D01G071900

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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 TraesCS4D01G071900 chr4D 100.000 6729 0 0 1 6729 46652764 46659492 0.000000e+00 12427.0
1 TraesCS4D01G071900 chr4D 86.131 137 19 0 975 1111 46633051 46633187 1.510000e-31 148.0
2 TraesCS4D01G071900 chr4D 77.778 198 37 5 6495 6690 393249741 393249933 1.530000e-21 115.0
3 TraesCS4D01G071900 chr4D 95.652 69 3 0 3340 3408 46656046 46656114 1.980000e-20 111.0
4 TraesCS4D01G071900 chr4D 95.652 69 3 0 3283 3351 46656103 46656171 1.980000e-20 111.0
5 TraesCS4D01G071900 chr4D 85.263 95 8 5 3082 3173 46655788 46655879 7.190000e-15 93.5
6 TraesCS4D01G071900 chr4D 85.263 95 8 5 3025 3116 46655845 46655936 7.190000e-15 93.5
7 TraesCS4D01G071900 chr4B 94.686 3105 115 10 1844 4906 68401815 68404911 0.000000e+00 4774.0
8 TraesCS4D01G071900 chr4B 95.412 1068 46 3 4188 5254 68412290 68413355 0.000000e+00 1698.0
9 TraesCS4D01G071900 chr4B 95.353 1033 45 3 4188 5219 68420806 68421836 0.000000e+00 1639.0
10 TraesCS4D01G071900 chr4B 86.426 1164 93 24 1 1133 68400111 68401240 0.000000e+00 1214.0
11 TraesCS4D01G071900 chr4B 91.949 857 50 7 4188 5043 68512878 68513716 0.000000e+00 1182.0
12 TraesCS4D01G071900 chr4B 86.039 967 67 11 5766 6690 68622673 68623613 0.000000e+00 976.0
13 TraesCS4D01G071900 chr4B 89.163 729 33 14 5257 5969 68405288 68405986 0.000000e+00 867.0
14 TraesCS4D01G071900 chr4B 95.983 473 16 2 5322 5791 68413349 68413821 0.000000e+00 765.0
15 TraesCS4D01G071900 chr4B 95.983 473 16 2 5322 5791 68423220 68423692 0.000000e+00 765.0
16 TraesCS4D01G071900 chr4B 87.526 481 39 6 5299 5768 68614563 68615033 2.760000e-148 536.0
17 TraesCS4D01G071900 chr4B 87.363 364 23 4 1455 1803 68401454 68401809 4.890000e-106 396.0
18 TraesCS4D01G071900 chr4B 78.044 501 95 13 2679 3173 68359743 68360234 1.100000e-77 302.0
19 TraesCS4D01G071900 chr4B 84.783 230 23 7 6379 6605 17259427 17259207 3.160000e-53 220.0
20 TraesCS4D01G071900 chr4B 82.653 196 20 7 5008 5192 68405105 68405297 1.940000e-35 161.0
21 TraesCS4D01G071900 chr4B 75.538 372 55 26 3007 3351 68403056 68403418 4.200000e-32 150.0
22 TraesCS4D01G071900 chr4B 89.744 117 11 1 5113 5228 68363165 68363281 1.510000e-31 148.0
23 TraesCS4D01G071900 chr4B 94.118 68 4 0 3341 3408 68403294 68403361 3.320000e-18 104.0
24 TraesCS4D01G071900 chr4B 86.022 93 11 2 3082 3173 68403017 68403108 1.540000e-16 99.0
25 TraesCS4D01G071900 chr4B 97.674 43 1 0 5212 5254 68423184 68423226 2.600000e-09 75.0
26 TraesCS4D01G071900 chr4B 97.561 41 1 0 6648 6688 17259139 17259099 3.370000e-08 71.3
27 TraesCS4D01G071900 chr4A 95.012 2025 60 17 3956 5969 552149408 552147414 0.000000e+00 3142.0
28 TraesCS4D01G071900 chr4A 94.363 1632 81 3 2327 3957 552151092 552149471 0.000000e+00 2494.0
29 TraesCS4D01G071900 chr4A 89.504 1229 80 16 1 1198 552153383 552152173 0.000000e+00 1509.0
30 TraesCS4D01G071900 chr4A 88.498 852 60 15 1455 2289 552151922 552151092 0.000000e+00 996.0
31 TraesCS4D01G071900 chr4A 79.604 505 92 6 2682 3176 552198472 552197969 1.070000e-92 351.0
32 TraesCS4D01G071900 chr4A 80.556 324 30 15 5971 6291 552147321 552147028 1.140000e-52 219.0
33 TraesCS4D01G071900 chr4A 84.279 229 26 5 6386 6611 594161232 594161453 1.470000e-51 215.0
34 TraesCS4D01G071900 chr4A 83.799 179 15 8 1238 1411 552152096 552151927 2.510000e-34 158.0
35 TraesCS4D01G071900 chr4A 91.837 98 5 1 4803 4900 552195676 552195582 4.230000e-27 134.0
36 TraesCS4D01G071900 chr4A 95.652 69 3 0 3283 3351 552150086 552150018 1.980000e-20 111.0
37 TraesCS4D01G071900 chr4A 86.022 93 11 2 3082 3173 552150401 552150310 1.540000e-16 99.0
38 TraesCS4D01G071900 chr4A 90.141 71 7 0 1392 1462 502902653 502902723 7.190000e-15 93.5
39 TraesCS4D01G071900 chr4A 85.263 95 8 5 3025 3116 552150344 552150253 7.190000e-15 93.5
40 TraesCS4D01G071900 chr4A 89.189 74 6 2 1402 1475 476748152 476748081 2.580000e-14 91.6
41 TraesCS4D01G071900 chr4A 95.122 41 2 0 6648 6688 594161634 594161674 1.570000e-06 65.8
42 TraesCS4D01G071900 chr7A 84.615 234 29 4 6379 6611 217550669 217550896 6.790000e-55 226.0
43 TraesCS4D01G071900 chr7D 88.462 182 20 1 6430 6611 615601174 615601354 1.140000e-52 219.0
44 TraesCS4D01G071900 chr6D 79.793 193 22 7 6379 6569 418687833 418687656 2.550000e-24 124.0
45 TraesCS4D01G071900 chr6D 90.000 70 6 1 1392 1461 95896032 95896100 9.290000e-14 89.8
46 TraesCS4D01G071900 chrUn 98.276 58 1 0 1402 1459 362854020 362854077 1.190000e-17 102.0
47 TraesCS4D01G071900 chrUn 98.276 58 1 0 1402 1459 376190083 376190026 1.190000e-17 102.0
48 TraesCS4D01G071900 chr7B 93.846 65 3 1 1402 1466 678632430 678632493 5.550000e-16 97.1
49 TraesCS4D01G071900 chr6B 89.474 76 5 3 1403 1476 258143299 258143225 7.190000e-15 93.5
50 TraesCS4D01G071900 chr5B 91.304 69 5 1 1403 1471 119500270 119500337 7.190000e-15 93.5
51 TraesCS4D01G071900 chr1B 85.227 88 10 3 1405 1492 14866895 14866979 3.340000e-13 87.9


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G071900 chr4D 46652764 46659492 6728 False 2567.200000 12427 92.366000 1 6729 5 chr4D.!!$F3 6728
1 TraesCS4D01G071900 chr4B 68412290 68413821 1531 False 1231.500000 1698 95.697500 4188 5791 2 chr4B.!!$F6 1603
2 TraesCS4D01G071900 chr4B 68512878 68513716 838 False 1182.000000 1182 91.949000 4188 5043 1 chr4B.!!$F1 855
3 TraesCS4D01G071900 chr4B 68622673 68623613 940 False 976.000000 976 86.039000 5766 6690 1 chr4B.!!$F3 924
4 TraesCS4D01G071900 chr4B 68400111 68405986 5875 False 970.625000 4774 86.996125 1 5969 8 chr4B.!!$F5 5968
5 TraesCS4D01G071900 chr4B 68420806 68423692 2886 False 826.333333 1639 96.336667 4188 5791 3 chr4B.!!$F7 1603
6 TraesCS4D01G071900 chr4B 68359743 68363281 3538 False 225.000000 302 83.894000 2679 5228 2 chr4B.!!$F4 2549
7 TraesCS4D01G071900 chr4A 552147028 552153383 6355 True 980.166667 3142 88.741000 1 6291 9 chr4A.!!$R2 6290
8 TraesCS4D01G071900 chr4A 552195582 552198472 2890 True 242.500000 351 85.720500 2682 4900 2 chr4A.!!$R3 2218

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
897 934 0.395586 CCCCCAAATGCGGAGATTCA 60.396 55.000 0.00 0.00 0.00 2.57 F
1310 1449 0.534873 TACCTGCTTGATGTAGCGCA 59.465 50.000 11.47 0.00 44.18 6.09 F
1311 1450 0.742281 ACCTGCTTGATGTAGCGCAG 60.742 55.000 11.47 0.00 46.97 5.18 F
1314 1453 1.086067 TGCTTGATGTAGCGCAGAGC 61.086 55.000 11.47 8.33 44.18 4.09 F
1366 1513 1.202651 CCATCCATCGGTCAAGGGTAC 60.203 57.143 0.00 0.00 0.00 3.34 F
1930 2121 1.394917 GGAATACTCTGTGCACTTGCG 59.605 52.381 19.41 8.50 45.83 4.85 F
3074 3297 1.955778 CAACTGCCAACCATTCTGACA 59.044 47.619 0.00 0.00 0.00 3.58 F
4109 4481 2.134789 AGAGGTGGGATGTGCAATTC 57.865 50.000 0.00 0.00 0.00 2.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1966 2157 0.094046 CACGCGTATGTTTTCGACCC 59.906 55.000 13.44 0.00 0.00 4.46 R
2677 2891 2.003301 GGGACGATCTGCAGAAAGAAC 58.997 52.381 22.50 11.22 0.00 3.01 R
2736 2950 2.854777 CGTGTTTCTAGCTTGATCTCCG 59.145 50.000 0.00 0.00 0.00 4.63 R
3074 3297 3.790437 CATGGGCTGAGGACGCCT 61.790 66.667 0.71 0.00 46.73 5.52 R
3533 3838 7.587037 TTGATTGGAATGGAATTGTATCTCC 57.413 36.000 0.00 0.00 36.07 3.71 R
3741 4049 3.119352 GCCACAAAGATTGGATTGTCCTC 60.119 47.826 0.00 0.00 37.66 3.71 R
4926 6106 2.146342 GCGATCATCCCCACATAACAG 58.854 52.381 0.00 0.00 0.00 3.16 R
5883 8734 0.100325 TGTTTCAGCAAACACCTGCG 59.900 50.000 0.00 0.00 45.73 5.18 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
79 80 5.694006 CGGTTCAATGAAAGGCAAATGTTAA 59.306 36.000 0.00 0.00 0.00 2.01
84 85 8.755696 TCAATGAAAGGCAAATGTTAACATAC 57.244 30.769 21.07 13.27 35.10 2.39
88 89 7.151308 TGAAAGGCAAATGTTAACATACTTGG 58.849 34.615 24.34 11.16 35.10 3.61
90 91 6.515272 AGGCAAATGTTAACATACTTGGAG 57.485 37.500 24.34 11.90 35.10 3.86
126 127 3.582647 TCTTGGTTGCAGTTCCTCATAGA 59.417 43.478 6.30 0.00 0.00 1.98
129 130 3.126831 GGTTGCAGTTCCTCATAGATCG 58.873 50.000 0.00 0.00 0.00 3.69
146 147 4.318332 AGATCGAGTTGCACAAGATTTGA 58.682 39.130 0.00 0.00 0.00 2.69
158 159 3.254166 ACAAGATTTGACAGTCCATGCAC 59.746 43.478 0.00 0.00 0.00 4.57
186 187 8.624776 CCATATTCTTTCACTAGGGAATGTTTC 58.375 37.037 17.52 0.00 31.89 2.78
197 198 3.197766 AGGGAATGTTTCTGTCGATAGCA 59.802 43.478 3.98 0.00 0.00 3.49
212 213 2.238942 TAGCAAGACGCATATGGTGG 57.761 50.000 4.56 0.00 46.13 4.61
217 218 0.541392 AGACGCATATGGTGGCTTCA 59.459 50.000 4.56 0.00 45.26 3.02
220 221 0.514255 CGCATATGGTGGCTTCATCG 59.486 55.000 4.56 0.00 0.00 3.84
225 226 2.540265 ATGGTGGCTTCATCGATCTC 57.460 50.000 0.00 0.00 0.00 2.75
256 262 1.680207 GGCTCGGAAGGTACTCGTAAT 59.320 52.381 0.00 0.00 38.49 1.89
257 263 2.100418 GGCTCGGAAGGTACTCGTAATT 59.900 50.000 0.00 0.00 38.49 1.40
258 264 3.114065 GCTCGGAAGGTACTCGTAATTG 58.886 50.000 0.00 0.00 38.49 2.32
261 267 5.506982 GCTCGGAAGGTACTCGTAATTGTAT 60.507 44.000 0.00 0.00 38.49 2.29
272 278 4.177783 TCGTAATTGTATGATGTGCGTGT 58.822 39.130 0.00 0.00 0.00 4.49
276 282 6.623353 CGTAATTGTATGATGTGCGTGTTTAG 59.377 38.462 0.00 0.00 0.00 1.85
288 296 4.494410 GTGCGTGTTTAGTGTTTCTCAAAC 59.506 41.667 0.00 0.00 41.73 2.93
344 352 3.613299 GTGAAAAACGAGGTAGCTCTAGC 59.387 47.826 19.17 0.00 42.49 3.42
356 364 1.730487 CTCTAGCGAGCGGTGACAT 59.270 57.895 4.69 0.00 0.00 3.06
406 416 1.433053 CGGAATTTATCGCCGCACCA 61.433 55.000 0.00 0.00 38.46 4.17
523 537 0.534412 ACTCACTCCATCGCCTCTTG 59.466 55.000 0.00 0.00 0.00 3.02
631 659 0.565674 GAGATTCTCCCCCTCTCCCT 59.434 60.000 1.97 0.00 31.25 4.20
656 684 2.759973 TCGGCACCTCCTAGGCTG 60.760 66.667 2.96 0.00 39.63 4.85
657 685 2.759973 CGGCACCTCCTAGGCTGA 60.760 66.667 2.96 0.00 39.63 4.26
687 715 1.219124 GAGTTCCAGCAGCATCCGA 59.781 57.895 0.00 0.00 0.00 4.55
806 842 2.978946 TTCCCGTTGGCCAGGATCC 61.979 63.158 12.72 2.48 0.00 3.36
835 871 1.797933 CGTCGACTCGCTCAAGGTG 60.798 63.158 14.70 0.00 0.00 4.00
896 933 0.395724 ACCCCCAAATGCGGAGATTC 60.396 55.000 0.00 0.00 0.00 2.52
897 934 0.395586 CCCCCAAATGCGGAGATTCA 60.396 55.000 0.00 0.00 0.00 2.57
921 958 9.304335 TCATATCTAATCATACTCAACGGGTTA 57.696 33.333 0.00 0.00 0.00 2.85
931 968 4.181578 ACTCAACGGGTTATCATTTCTCG 58.818 43.478 0.00 0.00 0.00 4.04
932 969 2.933906 TCAACGGGTTATCATTTCTCGC 59.066 45.455 0.00 0.00 0.00 5.03
941 978 1.428448 TCATTTCTCGCGTTCCAGTG 58.572 50.000 5.77 0.00 0.00 3.66
949 986 1.577328 CGCGTTCCAGTGCCAAATCT 61.577 55.000 0.00 0.00 0.00 2.40
954 991 0.968405 TCCAGTGCCAAATCTTTGCC 59.032 50.000 0.00 0.00 36.86 4.52
1126 1169 6.404734 GGAGATGGTAAATCACATTCAACCAC 60.405 42.308 0.00 0.00 39.52 4.16
1127 1170 4.757799 TGGTAAATCACATTCAACCACG 57.242 40.909 0.00 0.00 34.90 4.94
1182 1242 3.669939 CCCCCATTATTCTGTGGAGTT 57.330 47.619 0.00 0.00 37.72 3.01
1190 1250 7.331026 CCATTATTCTGTGGAGTTTAGAGTCA 58.669 38.462 0.00 0.00 37.72 3.41
1191 1251 7.989741 CCATTATTCTGTGGAGTTTAGAGTCAT 59.010 37.037 0.00 0.00 37.72 3.06
1198 1258 3.444034 TGGAGTTTAGAGTCATGGAGTCG 59.556 47.826 0.00 0.00 37.12 4.18
1199 1259 3.695060 GGAGTTTAGAGTCATGGAGTCGA 59.305 47.826 0.00 0.00 37.12 4.20
1200 1260 4.339814 GGAGTTTAGAGTCATGGAGTCGAT 59.660 45.833 0.00 0.00 37.12 3.59
1202 1262 4.950475 AGTTTAGAGTCATGGAGTCGATGA 59.050 41.667 13.26 13.26 37.12 2.92
1203 1263 5.419155 AGTTTAGAGTCATGGAGTCGATGAA 59.581 40.000 18.15 1.66 37.12 2.57
1204 1264 3.791973 AGAGTCATGGAGTCGATGAAC 57.208 47.619 18.15 14.78 37.12 3.18
1205 1265 3.092301 AGAGTCATGGAGTCGATGAACA 58.908 45.455 18.15 0.00 37.12 3.18
1206 1266 3.511540 AGAGTCATGGAGTCGATGAACAA 59.488 43.478 18.15 0.00 37.12 2.83
1212 1291 3.804036 TGGAGTCGATGAACAAAGTTGT 58.196 40.909 0.00 0.00 44.72 3.32
1260 1396 6.494893 TGGTTTATCAGATTTTTCCGTCAG 57.505 37.500 0.00 0.00 0.00 3.51
1278 1414 5.923114 CCGTCAGATTCTATTGTTCGATGAT 59.077 40.000 0.00 0.00 0.00 2.45
1289 1428 4.563337 TGTTCGATGATAACTAGGTCGG 57.437 45.455 0.00 0.00 33.46 4.79
1308 1447 1.933853 GGTTACCTGCTTGATGTAGCG 59.066 52.381 0.00 0.00 44.18 4.26
1309 1448 1.327764 GTTACCTGCTTGATGTAGCGC 59.672 52.381 0.00 0.00 44.18 5.92
1310 1449 0.534873 TACCTGCTTGATGTAGCGCA 59.465 50.000 11.47 0.00 44.18 6.09
1311 1450 0.742281 ACCTGCTTGATGTAGCGCAG 60.742 55.000 11.47 0.00 46.97 5.18
1313 1452 3.055144 TGCTTGATGTAGCGCAGAG 57.945 52.632 11.47 0.00 44.18 3.35
1314 1453 1.086067 TGCTTGATGTAGCGCAGAGC 61.086 55.000 11.47 8.33 44.18 4.09
1326 1465 2.888447 GCAGAGCCACAGACACCCT 61.888 63.158 0.00 0.00 0.00 4.34
1366 1513 1.202651 CCATCCATCGGTCAAGGGTAC 60.203 57.143 0.00 0.00 0.00 3.34
1381 1556 7.051623 GTCAAGGGTACATTTGACCATACATA 58.948 38.462 21.81 0.00 43.68 2.29
1387 1562 6.542370 GGTACATTTGACCATACATACTTGCT 59.458 38.462 0.00 0.00 36.91 3.91
1388 1563 6.441093 ACATTTGACCATACATACTTGCTG 57.559 37.500 0.00 0.00 0.00 4.41
1389 1564 5.945784 ACATTTGACCATACATACTTGCTGT 59.054 36.000 0.00 0.00 0.00 4.40
1390 1565 6.434028 ACATTTGACCATACATACTTGCTGTT 59.566 34.615 0.00 0.00 0.00 3.16
1391 1566 6.892658 TTTGACCATACATACTTGCTGTTT 57.107 33.333 0.00 0.00 0.00 2.83
1392 1567 6.892658 TTGACCATACATACTTGCTGTTTT 57.107 33.333 0.00 0.00 0.00 2.43
1393 1568 6.892658 TGACCATACATACTTGCTGTTTTT 57.107 33.333 0.00 0.00 0.00 1.94
1412 1587 4.560136 TTTTTGTGTGTGATACATGCGT 57.440 36.364 0.00 0.00 42.24 5.24
1413 1588 5.674933 TTTTTGTGTGTGATACATGCGTA 57.325 34.783 0.00 0.00 42.24 4.42
1414 1589 5.871465 TTTTGTGTGTGATACATGCGTAT 57.129 34.783 0.00 0.00 42.24 3.06
1415 1590 5.871465 TTTGTGTGTGATACATGCGTATT 57.129 34.783 0.00 0.00 42.24 1.89
1416 1591 5.871465 TTGTGTGTGATACATGCGTATTT 57.129 34.783 0.00 0.00 42.24 1.40
1417 1592 6.969828 TTGTGTGTGATACATGCGTATTTA 57.030 33.333 0.00 0.00 42.24 1.40
1418 1593 6.582437 TGTGTGTGATACATGCGTATTTAG 57.418 37.500 0.00 0.00 42.24 1.85
1419 1594 6.334202 TGTGTGTGATACATGCGTATTTAGA 58.666 36.000 0.00 0.00 42.24 2.10
1420 1595 6.254804 TGTGTGTGATACATGCGTATTTAGAC 59.745 38.462 0.00 0.00 42.24 2.59
1421 1596 6.254804 GTGTGTGATACATGCGTATTTAGACA 59.745 38.462 0.00 0.00 42.24 3.41
1422 1597 6.814146 TGTGTGATACATGCGTATTTAGACAA 59.186 34.615 0.00 0.00 38.48 3.18
1423 1598 7.332182 TGTGTGATACATGCGTATTTAGACAAA 59.668 33.333 0.00 0.00 38.48 2.83
1424 1599 8.335356 GTGTGATACATGCGTATTTAGACAAAT 58.665 33.333 0.00 0.00 38.48 2.32
1425 1600 8.547894 TGTGATACATGCGTATTTAGACAAATC 58.452 33.333 0.00 0.00 38.48 2.17
1426 1601 8.765219 GTGATACATGCGTATTTAGACAAATCT 58.235 33.333 0.00 0.00 38.48 2.40
1427 1602 9.974980 TGATACATGCGTATTTAGACAAATCTA 57.025 29.630 0.00 0.00 38.48 1.98
1430 1605 8.942338 ACATGCGTATTTAGACAAATCTAAGA 57.058 30.769 0.00 0.00 45.93 2.10
1431 1606 8.818057 ACATGCGTATTTAGACAAATCTAAGAC 58.182 33.333 0.00 0.83 45.93 3.01
1432 1607 8.817100 CATGCGTATTTAGACAAATCTAAGACA 58.183 33.333 9.81 0.00 45.93 3.41
1433 1608 8.766000 TGCGTATTTAGACAAATCTAAGACAA 57.234 30.769 9.81 0.00 45.93 3.18
1434 1609 8.869897 TGCGTATTTAGACAAATCTAAGACAAG 58.130 33.333 9.81 0.00 45.93 3.16
1435 1610 9.084164 GCGTATTTAGACAAATCTAAGACAAGA 57.916 33.333 9.81 0.00 45.93 3.02
1443 1618 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
1444 1619 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
1445 1620 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
1446 1621 8.359642 CAAATCTAAGACAAGAATTTTGGGACA 58.640 33.333 5.68 0.00 28.49 4.02
1447 1622 7.693969 ATCTAAGACAAGAATTTTGGGACAG 57.306 36.000 5.68 0.00 42.39 3.51
1448 1623 6.837312 TCTAAGACAAGAATTTTGGGACAGA 58.163 36.000 5.68 0.00 42.39 3.41
1449 1624 6.936900 TCTAAGACAAGAATTTTGGGACAGAG 59.063 38.462 5.68 0.00 42.39 3.35
1450 1625 4.401925 AGACAAGAATTTTGGGACAGAGG 58.598 43.478 5.68 0.00 42.39 3.69
1451 1626 3.500343 ACAAGAATTTTGGGACAGAGGG 58.500 45.455 5.68 0.00 42.39 4.30
1452 1627 3.140144 ACAAGAATTTTGGGACAGAGGGA 59.860 43.478 5.68 0.00 42.39 4.20
1453 1628 3.728385 AGAATTTTGGGACAGAGGGAG 57.272 47.619 0.00 0.00 42.39 4.30
1475 1650 5.805728 AGTACATATGGTTAGCTATTGGCC 58.194 41.667 7.80 0.00 43.05 5.36
1600 1776 5.253330 ACACTGAAAAGACAACTTTCCTCA 58.747 37.500 0.00 0.00 44.32 3.86
1601 1777 5.710099 ACACTGAAAAGACAACTTTCCTCAA 59.290 36.000 0.00 0.00 44.32 3.02
1616 1792 7.298374 ACTTTCCTCAATTCCTCTACCTTTTT 58.702 34.615 0.00 0.00 0.00 1.94
1774 1964 2.551032 CTCAACCGTTTTACTTCCACCC 59.449 50.000 0.00 0.00 0.00 4.61
1780 1970 2.160813 CGTTTTACTTCCACCCCATTCG 59.839 50.000 0.00 0.00 0.00 3.34
1792 1982 2.080693 CCCCATTCGTCGATTGTTGAA 58.919 47.619 14.21 0.00 0.00 2.69
1804 1994 7.584847 TCGTCGATTGTTGAACTTTGATTTTAC 59.415 33.333 0.00 0.00 0.00 2.01
1855 2045 3.810373 CGTCATGTCTGCAAGTTTTACC 58.190 45.455 0.00 0.00 33.76 2.85
1930 2121 1.394917 GGAATACTCTGTGCACTTGCG 59.605 52.381 19.41 8.50 45.83 4.85
1966 2157 9.143631 TGTAATGATATGCATGAGAACTATTCG 57.856 33.333 10.16 0.00 37.28 3.34
2015 2206 8.760980 ACTAATGGCTTATAGTAAAATTGGCA 57.239 30.769 0.00 0.00 0.00 4.92
2022 2214 2.723124 AGTAAAATTGGCACGCCTTG 57.277 45.000 9.92 0.00 36.94 3.61
2039 2231 5.475909 ACGCCTTGGAATCTACGAGATAATA 59.524 40.000 0.00 0.00 32.89 0.98
2212 2418 4.989279 AATCCAAGCGATGCAATACTTT 57.011 36.364 0.00 0.00 0.00 2.66
2310 2516 6.827727 TCATAACTGAGATTTAACCTAGGGC 58.172 40.000 14.81 0.00 0.00 5.19
2319 2525 5.836358 AGATTTAACCTAGGGCTGAGAGTAG 59.164 44.000 14.81 0.00 0.00 2.57
2443 2649 8.861086 AGTGTACTATTGTAGGGATATGAACAG 58.139 37.037 0.00 0.00 0.00 3.16
2544 2750 2.685897 CCGGAGAGTGAAGGTAGAGAAG 59.314 54.545 0.00 0.00 0.00 2.85
2553 2759 6.486941 AGTGAAGGTAGAGAAGTAAGCTAGT 58.513 40.000 0.00 0.00 0.00 2.57
2563 2769 5.870706 AGAAGTAAGCTAGTGCCTTTTCTT 58.129 37.500 0.00 0.00 40.80 2.52
2936 3150 3.562869 CGATTTGGTCGCGAGAAAC 57.437 52.632 10.24 0.00 44.33 2.78
3074 3297 1.955778 CAACTGCCAACCATTCTGACA 59.044 47.619 0.00 0.00 0.00 3.58
3282 3580 3.087031 CTGAGGCTGTGGATCATTTTGT 58.913 45.455 0.00 0.00 0.00 2.83
3632 3940 4.163427 TCACAGGAGATTCTTTGTCCTCT 58.837 43.478 2.77 0.00 38.75 3.69
3641 3949 5.936956 AGATTCTTTGTCCTCTGAACATGAC 59.063 40.000 0.00 0.00 0.00 3.06
3678 3986 5.434352 TTCACCTAGATACACGCTCATAC 57.566 43.478 0.00 0.00 0.00 2.39
3683 3991 7.393515 TCACCTAGATACACGCTCATACATAAT 59.606 37.037 0.00 0.00 0.00 1.28
3684 3992 7.486232 CACCTAGATACACGCTCATACATAATG 59.514 40.741 0.00 0.00 36.88 1.90
3741 4049 8.672823 TGATGAGAAGGTCAAATCTATTCATG 57.327 34.615 0.00 0.00 39.19 3.07
3850 4158 5.247110 TGAAGGAGCATTCTTCTAGAACTGT 59.753 40.000 0.00 0.00 37.00 3.55
3864 4172 6.409704 TCTAGAACTGTGCATCAAGCTTATT 58.590 36.000 0.00 0.00 45.94 1.40
3865 4173 7.555965 TCTAGAACTGTGCATCAAGCTTATTA 58.444 34.615 0.00 0.00 45.94 0.98
3866 4174 6.674694 AGAACTGTGCATCAAGCTTATTAG 57.325 37.500 0.00 0.00 45.94 1.73
3938 4246 6.128363 CGTTAACCCTTCCATGACTAAACTTC 60.128 42.308 0.00 0.00 0.00 3.01
3944 4252 6.183347 CCTTCCATGACTAAACTTCCAGATT 58.817 40.000 0.00 0.00 0.00 2.40
3951 4259 9.482627 CATGACTAAACTTCCAGATTCTATACC 57.517 37.037 0.00 0.00 0.00 2.73
3973 4345 9.914834 ATACCTCCTATTATTTTGCACTTTACA 57.085 29.630 0.00 0.00 0.00 2.41
4109 4481 2.134789 AGAGGTGGGATGTGCAATTC 57.865 50.000 0.00 0.00 0.00 2.17
4235 4607 3.275999 TGATGAGATGTGCACAATGGAG 58.724 45.455 25.72 0.00 0.00 3.86
4264 4636 4.475051 TCATCCATGCAAAGGATTTTGG 57.525 40.909 18.49 6.82 43.21 3.28
4797 5197 6.380079 AGACCAATGTTACAGGAAGATTCT 57.620 37.500 0.00 0.00 28.75 2.40
4901 6081 6.178239 ACGGTAGTGCATTTCTTATGTTTC 57.822 37.500 0.00 0.00 0.00 2.78
4926 6106 6.737254 TTTAGAACTAGGTAGTGCATTTGC 57.263 37.500 0.00 0.00 36.50 3.68
4939 6119 1.824230 GCATTTGCTGTTATGTGGGGA 59.176 47.619 0.00 0.00 38.21 4.81
5066 6309 6.407202 TGCTATTTCCTTCTGGAGTTTAGAC 58.593 40.000 0.00 0.00 44.24 2.59
5764 8608 2.105821 TCTGTTTCCACCGATCCTTTGT 59.894 45.455 0.00 0.00 0.00 2.83
5769 8616 1.635663 CCACCGATCCTTTGTGTCGC 61.636 60.000 0.00 0.00 34.25 5.19
5791 8638 4.378149 GCCGTTAAGACTTTAAGAAGGTGC 60.378 45.833 0.00 0.00 37.19 5.01
5815 8662 4.743151 TGTTTACTCTCAGTTTAGCGTGTG 59.257 41.667 0.00 0.00 0.00 3.82
5855 8702 0.178992 TTGGAGGTCCTTGTTGGCTG 60.179 55.000 0.00 0.00 36.82 4.85
5898 8749 3.648982 CGCGCAGGTGTTTGCTGA 61.649 61.111 8.75 0.00 41.90 4.26
5992 8961 1.344803 TGCCTGGGATGAGATTCCTCT 60.345 52.381 0.00 0.00 40.10 3.69
6017 8989 3.193267 TGCATTTTCCTTGGTATCTGCAC 59.807 43.478 0.00 0.00 33.80 4.57
6040 9012 8.946935 GCACTTTAAATTTTCTTTGCATTGTTC 58.053 29.630 0.00 0.00 0.00 3.18
6041 9013 9.146270 CACTTTAAATTTTCTTTGCATTGTTCG 57.854 29.630 0.00 0.00 0.00 3.95
6084 9056 4.912897 AGGTGTTCCCTACCTCCC 57.087 61.111 0.00 0.00 45.19 4.30
6085 9057 1.400941 TAGGTGTTCCCTACCTCCCT 58.599 55.000 0.00 0.00 45.19 4.20
6086 9058 0.252742 AGGTGTTCCCTACCTCCCTG 60.253 60.000 0.00 0.00 45.19 4.45
6109 9081 4.935808 GGTAAAAGCTCGGAAGAATTGAGA 59.064 41.667 0.00 0.00 41.32 3.27
6119 9091 4.081972 CGGAAGAATTGAGAGGAGAAGTGA 60.082 45.833 0.00 0.00 0.00 3.41
6149 9121 0.883833 AGCGGAGATTTGCCAAGTTG 59.116 50.000 0.00 0.00 0.00 3.16
6152 9125 1.401931 CGGAGATTTGCCAAGTTGCTG 60.402 52.381 0.00 0.00 0.00 4.41
6263 9236 1.443872 CGCGAGCCTCGTGTAGTTT 60.444 57.895 19.03 0.00 44.47 2.66
6265 9238 1.956620 GCGAGCCTCGTGTAGTTTGC 61.957 60.000 16.50 0.00 42.81 3.68
6266 9239 1.352156 CGAGCCTCGTGTAGTTTGCC 61.352 60.000 5.82 0.00 34.72 4.52
6329 9302 3.110178 GCTGGTCGGTTCGGTTCG 61.110 66.667 0.00 0.00 0.00 3.95
6330 9303 2.431942 CTGGTCGGTTCGGTTCGG 60.432 66.667 0.00 0.00 0.00 4.30
6331 9304 3.216944 CTGGTCGGTTCGGTTCGGT 62.217 63.158 0.00 0.00 0.00 4.69
6332 9305 2.029518 GGTCGGTTCGGTTCGGTT 59.970 61.111 0.00 0.00 0.00 4.44
6333 9306 2.023771 GGTCGGTTCGGTTCGGTTC 61.024 63.158 0.00 0.00 0.00 3.62
6374 9347 6.289064 GTGATCGGGTATTTAGGTCATTTCT 58.711 40.000 0.00 0.00 0.00 2.52
6382 9355 4.864704 TTTAGGTCATTTCTGTTTGGGC 57.135 40.909 0.00 0.00 0.00 5.36
6455 9428 7.432148 AAGAAAACCTGAACCCAAATTACTT 57.568 32.000 0.00 0.00 0.00 2.24
6459 9432 6.800072 AACCTGAACCCAAATTACTTGAAA 57.200 33.333 0.00 0.00 37.17 2.69
6464 9437 7.116233 CCTGAACCCAAATTACTTGAAATTTCG 59.884 37.037 13.34 2.86 37.03 3.46
6503 9476 6.376299 AGGTACCCAAAAAGTCCGAAATATTC 59.624 38.462 8.74 0.00 0.00 1.75
6632 9623 4.833938 TGGGTATTTTGGGTTTTACAGACC 59.166 41.667 0.00 0.00 36.41 3.85
6667 9658 5.124297 GCTTAACCTAAAAACCGAATAGCCA 59.876 40.000 0.00 0.00 0.00 4.75
6680 9671 3.561725 CGAATAGCCAGGAAATGAGAACC 59.438 47.826 0.00 0.00 0.00 3.62
6690 9681 4.227527 AGGAAATGAGAACCGAACCCTAAT 59.772 41.667 0.00 0.00 0.00 1.73
6691 9682 4.948004 GGAAATGAGAACCGAACCCTAATT 59.052 41.667 0.00 0.00 0.00 1.40
6692 9683 6.069847 AGGAAATGAGAACCGAACCCTAATTA 60.070 38.462 0.00 0.00 0.00 1.40
6693 9684 6.037940 GGAAATGAGAACCGAACCCTAATTAC 59.962 42.308 0.00 0.00 0.00 1.89
6694 9685 5.687166 ATGAGAACCGAACCCTAATTACA 57.313 39.130 0.00 0.00 0.00 2.41
6695 9686 4.824289 TGAGAACCGAACCCTAATTACAC 58.176 43.478 0.00 0.00 0.00 2.90
6696 9687 4.283978 TGAGAACCGAACCCTAATTACACA 59.716 41.667 0.00 0.00 0.00 3.72
6697 9688 5.221682 TGAGAACCGAACCCTAATTACACAA 60.222 40.000 0.00 0.00 0.00 3.33
6698 9689 4.999311 AGAACCGAACCCTAATTACACAAC 59.001 41.667 0.00 0.00 0.00 3.32
6699 9690 4.354893 ACCGAACCCTAATTACACAACA 57.645 40.909 0.00 0.00 0.00 3.33
6700 9691 4.716794 ACCGAACCCTAATTACACAACAA 58.283 39.130 0.00 0.00 0.00 2.83
6701 9692 5.318630 ACCGAACCCTAATTACACAACAAT 58.681 37.500 0.00 0.00 0.00 2.71
6702 9693 5.771165 ACCGAACCCTAATTACACAACAATT 59.229 36.000 0.00 0.00 0.00 2.32
6703 9694 6.072342 ACCGAACCCTAATTACACAACAATTC 60.072 38.462 0.00 0.00 0.00 2.17
6704 9695 6.019152 CGAACCCTAATTACACAACAATTCG 58.981 40.000 0.00 0.00 0.00 3.34
6705 9696 5.890424 ACCCTAATTACACAACAATTCGG 57.110 39.130 0.00 0.00 31.33 4.30
6706 9697 4.703093 ACCCTAATTACACAACAATTCGGG 59.297 41.667 13.14 13.14 46.46 5.14
6707 9698 4.944930 CCCTAATTACACAACAATTCGGGA 59.055 41.667 10.40 0.00 45.05 5.14
6708 9699 5.416326 CCCTAATTACACAACAATTCGGGAA 59.584 40.000 10.40 0.00 45.05 3.97
6709 9700 6.096282 CCCTAATTACACAACAATTCGGGAAT 59.904 38.462 10.40 0.00 45.05 3.01
6710 9701 7.363443 CCCTAATTACACAACAATTCGGGAATT 60.363 37.037 10.40 0.89 45.05 2.17
6711 9702 7.700656 CCTAATTACACAACAATTCGGGAATTC 59.299 37.037 3.74 0.00 38.84 2.17
6712 9703 3.552604 ACACAACAATTCGGGAATTCG 57.447 42.857 3.74 3.66 38.84 3.34
6713 9704 2.227865 ACACAACAATTCGGGAATTCGG 59.772 45.455 3.74 0.00 38.84 4.30
6714 9705 2.227865 CACAACAATTCGGGAATTCGGT 59.772 45.455 3.74 0.00 38.84 4.69
6715 9706 2.888414 ACAACAATTCGGGAATTCGGTT 59.112 40.909 3.74 4.36 38.84 4.44
6716 9707 3.057806 ACAACAATTCGGGAATTCGGTTC 60.058 43.478 3.74 0.00 38.84 3.62
6717 9708 1.735571 ACAATTCGGGAATTCGGTTCG 59.264 47.619 3.74 1.51 38.84 3.95
6718 9709 1.063469 CAATTCGGGAATTCGGTTCGG 59.937 52.381 3.74 0.00 38.84 4.30
6719 9710 0.463116 ATTCGGGAATTCGGTTCGGG 60.463 55.000 0.00 0.00 37.73 5.14
6720 9711 1.829523 TTCGGGAATTCGGTTCGGGT 61.830 55.000 0.00 0.00 37.73 5.28
6721 9712 1.376295 CGGGAATTCGGTTCGGGTT 60.376 57.895 0.00 0.00 37.73 4.11
6722 9713 1.363885 CGGGAATTCGGTTCGGGTTC 61.364 60.000 0.00 0.00 37.73 3.62
6723 9714 1.363885 GGGAATTCGGTTCGGGTTCG 61.364 60.000 0.00 0.00 37.73 3.95
6724 9715 0.390209 GGAATTCGGTTCGGGTTCGA 60.390 55.000 0.00 0.00 44.44 3.71
6725 9716 0.997196 GAATTCGGTTCGGGTTCGAG 59.003 55.000 0.00 0.00 46.75 4.04
6726 9717 0.319405 AATTCGGTTCGGGTTCGAGT 59.681 50.000 0.00 0.00 46.75 4.18
6727 9718 1.176527 ATTCGGTTCGGGTTCGAGTA 58.823 50.000 0.00 0.00 46.75 2.59
6728 9719 0.523072 TTCGGTTCGGGTTCGAGTAG 59.477 55.000 0.00 0.00 46.75 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 3.138098 TGCCTCCCATTATGCTAACATCA 59.862 43.478 0.00 0.00 37.74 3.07
9 10 3.882102 TGCCTCCCATTATGCTAACAT 57.118 42.857 0.00 0.00 40.49 2.71
79 80 4.019174 CTGGATTTTGCCTCCAAGTATGT 58.981 43.478 0.00 0.00 42.12 2.29
84 85 4.530875 AGATACTGGATTTTGCCTCCAAG 58.469 43.478 0.00 0.00 42.12 3.61
88 89 4.273318 ACCAAGATACTGGATTTTGCCTC 58.727 43.478 0.00 0.00 38.96 4.70
90 91 4.747810 CAACCAAGATACTGGATTTTGCC 58.252 43.478 0.00 0.00 38.96 4.52
101 102 3.674997 TGAGGAACTGCAACCAAGATAC 58.325 45.455 6.94 0.00 41.55 2.24
126 127 3.814842 TGTCAAATCTTGTGCAACTCGAT 59.185 39.130 0.00 0.00 38.04 3.59
129 130 4.531332 GACTGTCAAATCTTGTGCAACTC 58.469 43.478 2.24 0.00 38.04 3.01
146 147 3.054139 AGAATATGGTGTGCATGGACTGT 60.054 43.478 18.75 4.52 0.00 3.55
158 159 7.056635 ACATTCCCTAGTGAAAGAATATGGTG 58.943 38.462 0.00 0.00 0.00 4.17
186 187 1.845266 ATGCGTCTTGCTATCGACAG 58.155 50.000 0.00 0.00 46.63 3.51
197 198 1.065491 TGAAGCCACCATATGCGTCTT 60.065 47.619 0.00 0.00 36.99 3.01
212 213 3.042189 CGAGTCTTGAGATCGATGAAGC 58.958 50.000 0.54 0.00 38.72 3.86
217 218 1.600013 CCGACGAGTCTTGAGATCGAT 59.400 52.381 0.00 0.00 39.66 3.59
220 221 0.736053 AGCCGACGAGTCTTGAGATC 59.264 55.000 0.00 0.00 0.00 2.75
225 226 2.196382 TTCCGAGCCGACGAGTCTTG 62.196 60.000 0.00 0.00 35.09 3.02
256 262 4.752604 ACACTAAACACGCACATCATACAA 59.247 37.500 0.00 0.00 0.00 2.41
257 263 4.311606 ACACTAAACACGCACATCATACA 58.688 39.130 0.00 0.00 0.00 2.29
258 264 4.921470 ACACTAAACACGCACATCATAC 57.079 40.909 0.00 0.00 0.00 2.39
261 267 3.874543 AGAAACACTAAACACGCACATCA 59.125 39.130 0.00 0.00 0.00 3.07
327 335 1.671845 CTCGCTAGAGCTACCTCGTTT 59.328 52.381 0.00 0.00 43.05 3.60
344 352 0.740868 ATTGACCATGTCACCGCTCG 60.741 55.000 0.00 0.00 42.60 5.03
356 364 4.326826 GAGTTGTGGAGATTGATTGACCA 58.673 43.478 0.00 0.00 0.00 4.02
406 416 0.912487 TGGCGAGGATGGGGTAGTTT 60.912 55.000 0.00 0.00 0.00 2.66
631 659 4.011517 GAGGTGCCGACGGGGAAA 62.012 66.667 17.22 0.00 38.47 3.13
645 673 1.066573 CAACAGTGTCAGCCTAGGAGG 60.067 57.143 14.75 2.97 38.80 4.30
921 958 2.002586 CACTGGAACGCGAGAAATGAT 58.997 47.619 15.93 0.00 0.00 2.45
931 968 0.598065 AAGATTTGGCACTGGAACGC 59.402 50.000 0.00 0.00 0.00 4.84
932 969 2.664916 CAAAGATTTGGCACTGGAACG 58.335 47.619 0.00 0.00 34.59 3.95
949 986 1.686052 AGAAAAACCATCAGCGGCAAA 59.314 42.857 1.45 0.00 0.00 3.68
954 991 3.976942 CAGTCAAAGAAAAACCATCAGCG 59.023 43.478 0.00 0.00 0.00 5.18
1126 1169 5.049405 ACACAAGGAAATGAAAAGAGTAGCG 60.049 40.000 0.00 0.00 0.00 4.26
1127 1170 6.319141 ACACAAGGAAATGAAAAGAGTAGC 57.681 37.500 0.00 0.00 0.00 3.58
1166 1226 8.824781 CATGACTCTAAACTCCACAGAATAATG 58.175 37.037 0.00 0.00 0.00 1.90
1176 1236 3.444034 CGACTCCATGACTCTAAACTCCA 59.556 47.826 0.00 0.00 0.00 3.86
1182 1242 4.705023 TGTTCATCGACTCCATGACTCTAA 59.295 41.667 0.00 0.00 29.70 2.10
1190 1250 4.389374 ACAACTTTGTTCATCGACTCCAT 58.611 39.130 0.00 0.00 38.47 3.41
1191 1251 3.804036 ACAACTTTGTTCATCGACTCCA 58.196 40.909 0.00 0.00 38.47 3.86
1203 1263 5.581126 TTGATCAGAAGCAACAACTTTGT 57.419 34.783 0.00 0.00 44.72 2.83
1204 1264 7.473027 AATTTGATCAGAAGCAACAACTTTG 57.527 32.000 0.00 0.00 28.70 2.77
1205 1265 8.416329 ACTAATTTGATCAGAAGCAACAACTTT 58.584 29.630 0.00 0.00 28.70 2.66
1206 1266 7.945134 ACTAATTTGATCAGAAGCAACAACTT 58.055 30.769 0.00 0.00 28.70 2.66
1212 1291 6.376299 AGCATGACTAATTTGATCAGAAGCAA 59.624 34.615 0.00 0.00 0.00 3.91
1220 1299 8.623903 TGATAAACCAGCATGACTAATTTGATC 58.376 33.333 0.00 0.00 39.69 2.92
1222 1301 7.828717 TCTGATAAACCAGCATGACTAATTTGA 59.171 33.333 0.00 0.00 39.69 2.69
1260 1396 9.915629 ACCTAGTTATCATCGAACAATAGAATC 57.084 33.333 0.00 0.00 0.00 2.52
1289 1428 1.327764 GCGCTACATCAAGCAGGTAAC 59.672 52.381 0.00 0.00 42.91 2.50
1308 1447 2.359230 GGGTGTCTGTGGCTCTGC 60.359 66.667 0.00 0.00 0.00 4.26
1309 1448 1.294780 GAGGGTGTCTGTGGCTCTG 59.705 63.158 0.00 0.00 0.00 3.35
1310 1449 1.915769 GGAGGGTGTCTGTGGCTCT 60.916 63.158 0.00 0.00 0.00 4.09
1311 1450 1.893919 GAGGAGGGTGTCTGTGGCTC 61.894 65.000 0.00 0.00 0.00 4.70
1312 1451 1.915769 GAGGAGGGTGTCTGTGGCT 60.916 63.158 0.00 0.00 0.00 4.75
1313 1452 1.915769 AGAGGAGGGTGTCTGTGGC 60.916 63.158 0.00 0.00 0.00 5.01
1314 1453 1.978473 CAGAGGAGGGTGTCTGTGG 59.022 63.158 0.00 0.00 36.27 4.17
1326 1465 4.164981 TGGCTAGGACTAAAAACAGAGGA 58.835 43.478 0.00 0.00 0.00 3.71
1366 1513 6.441093 ACAGCAAGTATGTATGGTCAAATG 57.559 37.500 0.00 0.00 0.00 2.32
1391 1566 4.560136 ACGCATGTATCACACACAAAAA 57.440 36.364 0.00 0.00 40.86 1.94
1392 1567 5.871465 ATACGCATGTATCACACACAAAA 57.129 34.783 0.00 0.00 40.86 2.44
1393 1568 5.871465 AATACGCATGTATCACACACAAA 57.129 34.783 0.00 0.00 40.42 2.83
1394 1569 5.871465 AAATACGCATGTATCACACACAA 57.129 34.783 0.00 0.00 40.42 3.33
1395 1570 6.254804 GTCTAAATACGCATGTATCACACACA 59.745 38.462 0.00 0.00 40.42 3.72
1396 1571 6.254804 TGTCTAAATACGCATGTATCACACAC 59.745 38.462 0.00 0.00 40.42 3.82
1397 1572 6.334202 TGTCTAAATACGCATGTATCACACA 58.666 36.000 0.00 0.00 40.42 3.72
1398 1573 6.822073 TGTCTAAATACGCATGTATCACAC 57.178 37.500 0.00 0.00 40.42 3.82
1399 1574 7.835634 TTTGTCTAAATACGCATGTATCACA 57.164 32.000 0.00 0.00 40.42 3.58
1400 1575 8.765219 AGATTTGTCTAAATACGCATGTATCAC 58.235 33.333 0.00 0.00 40.42 3.06
1401 1576 8.887036 AGATTTGTCTAAATACGCATGTATCA 57.113 30.769 0.00 0.00 40.42 2.15
1405 1580 8.818057 GTCTTAGATTTGTCTAAATACGCATGT 58.182 33.333 0.00 0.00 36.66 3.21
1406 1581 8.817100 TGTCTTAGATTTGTCTAAATACGCATG 58.183 33.333 0.00 0.00 36.66 4.06
1407 1582 8.942338 TGTCTTAGATTTGTCTAAATACGCAT 57.058 30.769 0.26 0.00 36.66 4.73
1408 1583 8.766000 TTGTCTTAGATTTGTCTAAATACGCA 57.234 30.769 0.26 0.00 36.66 5.24
1409 1584 9.084164 TCTTGTCTTAGATTTGTCTAAATACGC 57.916 33.333 0.26 0.00 36.66 4.42
1417 1592 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
1418 1593 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
1419 1594 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
1420 1595 8.359642 TGTCCCAAAATTCTTGTCTTAGATTTG 58.640 33.333 0.00 0.00 29.84 2.32
1421 1596 8.477419 TGTCCCAAAATTCTTGTCTTAGATTT 57.523 30.769 0.00 0.00 0.00 2.17
1422 1597 7.944554 TCTGTCCCAAAATTCTTGTCTTAGATT 59.055 33.333 0.00 0.00 0.00 2.40
1423 1598 7.461749 TCTGTCCCAAAATTCTTGTCTTAGAT 58.538 34.615 0.00 0.00 0.00 1.98
1424 1599 6.837312 TCTGTCCCAAAATTCTTGTCTTAGA 58.163 36.000 0.00 0.00 0.00 2.10
1425 1600 6.150140 CCTCTGTCCCAAAATTCTTGTCTTAG 59.850 42.308 0.00 0.00 0.00 2.18
1426 1601 6.003950 CCTCTGTCCCAAAATTCTTGTCTTA 58.996 40.000 0.00 0.00 0.00 2.10
1427 1602 4.829492 CCTCTGTCCCAAAATTCTTGTCTT 59.171 41.667 0.00 0.00 0.00 3.01
1428 1603 4.401925 CCTCTGTCCCAAAATTCTTGTCT 58.598 43.478 0.00 0.00 0.00 3.41
1429 1604 3.507622 CCCTCTGTCCCAAAATTCTTGTC 59.492 47.826 0.00 0.00 0.00 3.18
1430 1605 3.140144 TCCCTCTGTCCCAAAATTCTTGT 59.860 43.478 0.00 0.00 0.00 3.16
1431 1606 3.760684 CTCCCTCTGTCCCAAAATTCTTG 59.239 47.826 0.00 0.00 0.00 3.02
1432 1607 3.399305 ACTCCCTCTGTCCCAAAATTCTT 59.601 43.478 0.00 0.00 0.00 2.52
1433 1608 2.989571 ACTCCCTCTGTCCCAAAATTCT 59.010 45.455 0.00 0.00 0.00 2.40
1434 1609 3.441500 ACTCCCTCTGTCCCAAAATTC 57.558 47.619 0.00 0.00 0.00 2.17
1435 1610 3.655777 TGTACTCCCTCTGTCCCAAAATT 59.344 43.478 0.00 0.00 0.00 1.82
1436 1611 3.256704 TGTACTCCCTCTGTCCCAAAAT 58.743 45.455 0.00 0.00 0.00 1.82
1437 1612 2.696775 TGTACTCCCTCTGTCCCAAAA 58.303 47.619 0.00 0.00 0.00 2.44
1438 1613 2.409064 TGTACTCCCTCTGTCCCAAA 57.591 50.000 0.00 0.00 0.00 3.28
1439 1614 2.642171 ATGTACTCCCTCTGTCCCAA 57.358 50.000 0.00 0.00 0.00 4.12
1440 1615 3.576861 CATATGTACTCCCTCTGTCCCA 58.423 50.000 0.00 0.00 0.00 4.37
1441 1616 2.900546 CCATATGTACTCCCTCTGTCCC 59.099 54.545 1.24 0.00 0.00 4.46
1442 1617 3.577919 ACCATATGTACTCCCTCTGTCC 58.422 50.000 1.24 0.00 0.00 4.02
1443 1618 5.279056 GCTAACCATATGTACTCCCTCTGTC 60.279 48.000 1.24 0.00 0.00 3.51
1444 1619 4.589374 GCTAACCATATGTACTCCCTCTGT 59.411 45.833 1.24 0.00 0.00 3.41
1445 1620 4.835615 AGCTAACCATATGTACTCCCTCTG 59.164 45.833 1.24 0.00 0.00 3.35
1446 1621 5.081315 AGCTAACCATATGTACTCCCTCT 57.919 43.478 1.24 0.00 0.00 3.69
1447 1622 7.324178 CAATAGCTAACCATATGTACTCCCTC 58.676 42.308 0.00 0.00 0.00 4.30
1448 1623 6.213600 CCAATAGCTAACCATATGTACTCCCT 59.786 42.308 0.00 0.00 0.00 4.20
1449 1624 6.407202 CCAATAGCTAACCATATGTACTCCC 58.593 44.000 0.00 0.00 0.00 4.30
1450 1625 5.875359 GCCAATAGCTAACCATATGTACTCC 59.125 44.000 0.00 0.00 38.99 3.85
1451 1626 5.875359 GGCCAATAGCTAACCATATGTACTC 59.125 44.000 0.00 0.00 43.05 2.59
1452 1627 5.568825 CGGCCAATAGCTAACCATATGTACT 60.569 44.000 2.24 0.00 43.05 2.73
1453 1628 4.630069 CGGCCAATAGCTAACCATATGTAC 59.370 45.833 2.24 0.00 43.05 2.90
1572 1748 8.190784 AGGAAAGTTGTCTTTTCAGTGTTAATG 58.809 33.333 2.52 0.00 42.99 1.90
1600 1776 6.252995 TGCCATACAAAAAGGTAGAGGAATT 58.747 36.000 0.00 0.00 0.00 2.17
1601 1777 5.826643 TGCCATACAAAAAGGTAGAGGAAT 58.173 37.500 0.00 0.00 0.00 3.01
1616 1792 4.704057 TGCAAACTGTATCAATGCCATACA 59.296 37.500 0.00 0.00 35.77 2.29
1774 1964 4.404507 AAGTTCAACAATCGACGAATGG 57.595 40.909 16.77 5.20 0.00 3.16
1780 1970 8.555166 TGTAAAATCAAAGTTCAACAATCGAC 57.445 30.769 0.00 0.00 0.00 4.20
1823 2013 4.082841 TGCAGACATGACGCAACAAATTAT 60.083 37.500 0.00 0.00 31.46 1.28
1855 2045 7.253750 CGAAATTATTGAAATGCGAGAAAAGGG 60.254 37.037 0.00 0.00 0.00 3.95
1966 2157 0.094046 CACGCGTATGTTTTCGACCC 59.906 55.000 13.44 0.00 0.00 4.46
1980 2171 1.359848 AGCCATTAGTTTCTCACGCG 58.640 50.000 3.53 3.53 0.00 6.01
2015 2206 1.471119 TCTCGTAGATTCCAAGGCGT 58.529 50.000 0.00 0.00 33.89 5.68
2074 2266 4.902443 TCGCACCATTTTTACTGTGAAA 57.098 36.364 0.00 0.00 0.00 2.69
2075 2267 4.902443 TTCGCACCATTTTTACTGTGAA 57.098 36.364 0.00 0.00 32.19 3.18
2087 2279 2.818130 AAAAACTGCATTCGCACCAT 57.182 40.000 0.00 0.00 45.36 3.55
2107 2299 8.778059 ACAGAACATATCAAACTTATTCCCCTA 58.222 33.333 0.00 0.00 0.00 3.53
2109 2301 7.881775 ACAGAACATATCAAACTTATTCCCC 57.118 36.000 0.00 0.00 0.00 4.81
2128 2320 4.161377 TGGCATATGCAGTAGTGTACAGAA 59.839 41.667 28.07 0.00 44.36 3.02
2191 2397 4.989279 AAAGTATTGCATCGCTTGGATT 57.011 36.364 0.00 0.00 31.28 3.01
2192 2398 5.368145 TCTAAAGTATTGCATCGCTTGGAT 58.632 37.500 0.00 0.00 35.09 3.41
2268 2474 7.965107 CAGTTATGAAGACCTTTCAATGCTAAC 59.035 37.037 0.00 0.00 31.55 2.34
2310 2516 5.995282 ACCGATACTCAATCTCTACTCTCAG 59.005 44.000 0.00 0.00 31.87 3.35
2319 2525 5.519206 GGTAACACAACCGATACTCAATCTC 59.481 44.000 0.00 0.00 31.87 2.75
2443 2649 6.036517 CAGAGGTAATGCATACTTTCACAGTC 59.963 42.308 0.00 0.00 36.88 3.51
2544 2750 4.451435 ACGAAAGAAAAGGCACTAGCTTAC 59.549 41.667 0.00 0.00 38.49 2.34
2553 2759 3.882888 AGAACATGACGAAAGAAAAGGCA 59.117 39.130 0.00 0.00 0.00 4.75
2589 2795 7.067008 AGCAAGTGTGGCGTAAATAAGATATTT 59.933 33.333 1.45 1.45 36.08 1.40
2608 2814 3.303132 GGTCAGTAAACAACGAGCAAGTG 60.303 47.826 0.00 0.00 32.82 3.16
2677 2891 2.003301 GGGACGATCTGCAGAAAGAAC 58.997 52.381 22.50 11.22 0.00 3.01
2736 2950 2.854777 CGTGTTTCTAGCTTGATCTCCG 59.145 50.000 0.00 0.00 0.00 4.63
3074 3297 3.790437 CATGGGCTGAGGACGCCT 61.790 66.667 0.71 0.00 46.73 5.52
3533 3838 7.587037 TTGATTGGAATGGAATTGTATCTCC 57.413 36.000 0.00 0.00 36.07 3.71
3610 3918 4.020751 CAGAGGACAAAGAATCTCCTGTGA 60.021 45.833 7.39 0.00 44.59 3.58
3632 3940 4.499526 GCACAACCTTCAATGTCATGTTCA 60.500 41.667 0.00 0.00 0.00 3.18
3678 3986 6.260714 TGCACTGTATTTAGACTGGCATTATG 59.739 38.462 0.00 0.00 0.00 1.90
3683 3991 3.260632 TCTGCACTGTATTTAGACTGGCA 59.739 43.478 0.00 0.00 0.00 4.92
3684 3992 3.861840 TCTGCACTGTATTTAGACTGGC 58.138 45.455 0.00 0.00 0.00 4.85
3741 4049 3.119352 GCCACAAAGATTGGATTGTCCTC 60.119 47.826 0.00 0.00 37.66 3.71
3850 4158 7.880160 ATGGTTTACTAATAAGCTTGATGCA 57.120 32.000 9.86 0.00 45.94 3.96
3865 4173 9.185680 ACTTTCAACAGAAAACTATGGTTTACT 57.814 29.630 7.69 0.00 43.90 2.24
4235 4607 3.508793 CCTTTGCATGGATGATATGGACC 59.491 47.826 0.00 0.00 0.00 4.46
4264 4636 2.620627 CCACCAATTTGGGAGGGTCTAC 60.621 54.545 19.39 0.00 43.37 2.59
4901 6081 7.119846 AGCAAATGCACTACCTAGTTCTAAAAG 59.880 37.037 8.28 0.00 45.16 2.27
4926 6106 2.146342 GCGATCATCCCCACATAACAG 58.854 52.381 0.00 0.00 0.00 3.16
4939 6119 2.873245 GCCTGTGATGGTATGCGATCAT 60.873 50.000 11.36 0.00 40.88 2.45
5127 6591 5.293814 GGCATCATATAGCTATGTGCAAGAG 59.706 44.000 21.99 12.07 45.94 2.85
5241 8065 2.422597 TGATTGGAGTTTGTAGCCACG 58.577 47.619 0.00 0.00 0.00 4.94
5414 8255 5.710513 TGATGGTGTTCAAGGAAATCAAG 57.289 39.130 0.00 0.00 0.00 3.02
5415 8256 6.012113 AGATGATGGTGTTCAAGGAAATCAA 58.988 36.000 0.00 0.00 0.00 2.57
5422 8264 3.678289 TGTCAGATGATGGTGTTCAAGG 58.322 45.455 0.00 0.00 0.00 3.61
5723 8565 5.589855 ACAGAATGAACACTGTTGATCAACA 59.410 36.000 33.20 33.20 43.92 3.33
5764 8608 4.241590 TCTTAAAGTCTTAACGGCGACA 57.758 40.909 16.62 0.00 32.68 4.35
5769 8616 4.995487 AGCACCTTCTTAAAGTCTTAACGG 59.005 41.667 0.00 0.00 0.00 4.44
5791 8638 4.982916 ACACGCTAAACTGAGAGTAAACAG 59.017 41.667 0.00 0.00 39.65 3.16
5815 8662 5.499047 CAACGAACTGACTAACAAAGGAAC 58.501 41.667 0.00 0.00 0.00 3.62
5855 8702 4.457949 CCATTATGCGACCCCTAATTAACC 59.542 45.833 0.00 0.00 0.00 2.85
5882 8733 3.790899 TGTTTCAGCAAACACCTGCGC 62.791 52.381 0.00 0.00 45.73 6.09
5883 8734 0.100325 TGTTTCAGCAAACACCTGCG 59.900 50.000 0.00 0.00 45.73 5.18
5884 8735 1.405105 TCTGTTTCAGCAAACACCTGC 59.595 47.619 0.00 0.00 45.73 4.85
5885 8736 2.684881 AGTCTGTTTCAGCAAACACCTG 59.315 45.455 0.00 0.00 45.73 4.00
5898 8749 7.285401 ACTGGTTCAAATCACATAAGTCTGTTT 59.715 33.333 0.00 0.00 0.00 2.83
5908 8759 3.190535 GGCGTTACTGGTTCAAATCACAT 59.809 43.478 0.00 0.00 0.00 3.21
5940 8791 3.807622 GTCGACTCAACTGAAATTCACCA 59.192 43.478 8.70 0.00 0.00 4.17
5992 8961 5.221601 TGCAGATACCAAGGAAAATGCAAAA 60.222 36.000 0.00 0.00 39.29 2.44
6017 8989 7.850003 TGCGAACAATGCAAAGAAAATTTAAAG 59.150 29.630 0.00 0.00 39.87 1.85
6079 9051 0.107654 CCGAGCTTTTACCAGGGAGG 60.108 60.000 0.00 0.00 45.67 4.30
6080 9052 0.902531 TCCGAGCTTTTACCAGGGAG 59.097 55.000 0.00 0.00 0.00 4.30
6082 9054 1.278127 TCTTCCGAGCTTTTACCAGGG 59.722 52.381 0.00 0.00 0.00 4.45
6083 9055 2.762535 TCTTCCGAGCTTTTACCAGG 57.237 50.000 0.00 0.00 0.00 4.45
6084 9056 4.695455 TCAATTCTTCCGAGCTTTTACCAG 59.305 41.667 0.00 0.00 0.00 4.00
6085 9057 4.647611 TCAATTCTTCCGAGCTTTTACCA 58.352 39.130 0.00 0.00 0.00 3.25
6086 9058 4.935808 TCTCAATTCTTCCGAGCTTTTACC 59.064 41.667 0.00 0.00 0.00 2.85
6109 9081 3.551635 TCTCCTTCCTTCACTTCTCCT 57.448 47.619 0.00 0.00 0.00 3.69
6119 9091 1.872773 ATCTCCGCTTCTCCTTCCTT 58.127 50.000 0.00 0.00 0.00 3.36
6149 9121 4.471726 GCACATGCCGCTCACAGC 62.472 66.667 0.00 0.00 38.02 4.40
6293 9266 3.839432 GCCTCTCCCGACCCGAAG 61.839 72.222 0.00 0.00 0.00 3.79
6329 9302 0.107848 CAGGGTGACGGGTATGAACC 60.108 60.000 0.00 0.00 45.97 3.62
6330 9303 0.107848 CCAGGGTGACGGGTATGAAC 60.108 60.000 0.00 0.00 0.00 3.18
6331 9304 1.268992 CCCAGGGTGACGGGTATGAA 61.269 60.000 0.00 0.00 37.70 2.57
6332 9305 1.687840 CCCAGGGTGACGGGTATGA 60.688 63.158 0.00 0.00 37.70 2.15
6333 9306 2.908015 CCCAGGGTGACGGGTATG 59.092 66.667 0.00 0.00 37.70 2.39
6374 9347 2.223803 ATACCCGAATTGCCCAAACA 57.776 45.000 0.00 0.00 0.00 2.83
6428 9401 8.325787 AGTAATTTGGGTTCAGGTTTTCTTTTT 58.674 29.630 0.00 0.00 0.00 1.94
6429 9402 7.857456 AGTAATTTGGGTTCAGGTTTTCTTTT 58.143 30.769 0.00 0.00 0.00 2.27
6433 9406 6.811954 TCAAGTAATTTGGGTTCAGGTTTTC 58.188 36.000 0.00 0.00 37.39 2.29
6455 9428 6.072175 CCTGAATTACCAGAACCGAAATTTCA 60.072 38.462 17.99 0.00 36.29 2.69
6459 9432 4.918588 ACCTGAATTACCAGAACCGAAAT 58.081 39.130 0.00 0.00 36.29 2.17
6503 9476 0.877071 AAAAGCTGATGTGTGCTCCG 59.123 50.000 0.00 0.00 38.75 4.63
6601 9592 9.204337 GTAAAACCCAAAATACCCATATTACCT 57.796 33.333 0.00 0.00 30.42 3.08
6606 9597 7.343574 GGTCTGTAAAACCCAAAATACCCATAT 59.656 37.037 0.00 0.00 0.00 1.78
6651 9642 5.946972 TCATTTCCTGGCTATTCGGTTTTTA 59.053 36.000 0.00 0.00 0.00 1.52
6667 9658 1.985895 AGGGTTCGGTTCTCATTTCCT 59.014 47.619 0.00 0.00 0.00 3.36
6680 9671 6.019152 CGAATTGTTGTGTAATTAGGGTTCG 58.981 40.000 0.00 0.00 0.00 3.95
6690 9681 4.083217 CCGAATTCCCGAATTGTTGTGTAA 60.083 41.667 7.39 0.00 40.77 2.41
6691 9682 3.437395 CCGAATTCCCGAATTGTTGTGTA 59.563 43.478 7.39 0.00 40.77 2.90
6692 9683 2.227865 CCGAATTCCCGAATTGTTGTGT 59.772 45.455 7.39 0.00 40.77 3.72
6693 9684 2.227865 ACCGAATTCCCGAATTGTTGTG 59.772 45.455 7.39 0.00 40.77 3.33
6694 9685 2.510613 ACCGAATTCCCGAATTGTTGT 58.489 42.857 7.39 0.02 40.77 3.32
6695 9686 3.498082 GAACCGAATTCCCGAATTGTTG 58.502 45.455 7.39 0.00 40.77 3.33
6696 9687 2.160813 CGAACCGAATTCCCGAATTGTT 59.839 45.455 7.39 6.51 40.77 2.83
6697 9688 1.735571 CGAACCGAATTCCCGAATTGT 59.264 47.619 7.39 0.00 40.77 2.71
6698 9689 1.063469 CCGAACCGAATTCCCGAATTG 59.937 52.381 7.39 0.00 40.77 2.32
6699 9690 1.375551 CCGAACCGAATTCCCGAATT 58.624 50.000 2.32 2.32 43.14 2.17
6700 9691 0.463116 CCCGAACCGAATTCCCGAAT 60.463 55.000 0.00 0.00 33.26 3.34
6701 9692 1.078988 CCCGAACCGAATTCCCGAA 60.079 57.895 0.00 0.00 33.26 4.30
6702 9693 1.829523 AACCCGAACCGAATTCCCGA 61.830 55.000 0.00 0.00 33.26 5.14
6703 9694 1.363885 GAACCCGAACCGAATTCCCG 61.364 60.000 0.00 0.00 33.26 5.14
6704 9695 1.363885 CGAACCCGAACCGAATTCCC 61.364 60.000 0.00 0.00 38.22 3.97
6705 9696 0.390209 TCGAACCCGAACCGAATTCC 60.390 55.000 0.00 0.00 42.51 3.01
6706 9697 0.997196 CTCGAACCCGAACCGAATTC 59.003 55.000 0.00 0.00 45.04 2.17
6707 9698 0.319405 ACTCGAACCCGAACCGAATT 59.681 50.000 0.00 0.00 45.04 2.17
6708 9699 1.133790 CTACTCGAACCCGAACCGAAT 59.866 52.381 0.00 0.00 45.04 3.34
6709 9700 0.523072 CTACTCGAACCCGAACCGAA 59.477 55.000 0.00 0.00 45.04 4.30
6710 9701 2.174334 CTACTCGAACCCGAACCGA 58.826 57.895 0.00 0.00 45.04 4.69
6711 9702 4.779819 CTACTCGAACCCGAACCG 57.220 61.111 0.00 0.00 45.04 4.44


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

AutoCloner maintained by Alex Coulton.