Multiple sequence alignment - TraesCS5B01G525400

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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 TraesCS5B01G525400 chr5B 100.000 3444 0 0 1 3444 685324075 685320632 0.000000e+00 6360.0
1 TraesCS5B01G525400 chr5B 94.578 1826 65 14 559 2373 685503339 685505141 0.000000e+00 2793.0
2 TraesCS5B01G525400 chr5B 95.400 413 19 0 3032 3444 685505560 685505972 0.000000e+00 658.0
3 TraesCS5B01G525400 chr5B 93.500 400 22 2 2397 2793 685505138 685505536 2.960000e-165 592.0
4 TraesCS5B01G525400 chr5B 75.582 1159 221 49 1019 2137 703529390 703530526 1.830000e-142 516.0
5 TraesCS5B01G525400 chr5B 74.549 1163 211 62 1017 2138 703610485 703611603 2.460000e-116 429.0
6 TraesCS5B01G525400 chr5B 76.327 735 149 17 1448 2176 700229171 700228456 1.510000e-98 370.0
7 TraesCS5B01G525400 chr5B 90.821 207 12 4 357 562 451189916 451189716 1.580000e-68 270.0
8 TraesCS5B01G525400 chr5B 86.058 208 24 4 985 1191 699597081 699597284 5.790000e-53 219.0
9 TraesCS5B01G525400 chr5B 86.058 208 24 4 985 1191 700006965 700007168 5.790000e-53 219.0
10 TraesCS5B01G525400 chr5B 79.856 139 23 1 2357 2490 703530722 703530860 2.830000e-16 97.1
11 TraesCS5B01G525400 chr5D 87.330 1760 148 32 876 2619 543503824 543502124 0.000000e+00 1945.0
12 TraesCS5B01G525400 chr5D 86.250 960 104 7 2276 3230 551058894 551059830 0.000000e+00 1016.0
13 TraesCS5B01G525400 chr5D 88.540 637 64 7 1581 2210 551058241 551058875 0.000000e+00 763.0
14 TraesCS5B01G525400 chr5D 93.333 525 16 5 357 878 543504380 543503872 0.000000e+00 758.0
15 TraesCS5B01G525400 chr5D 87.812 640 76 2 984 1622 551057608 551058246 0.000000e+00 749.0
16 TraesCS5B01G525400 chr5D 90.424 543 46 3 2688 3230 543502125 543501589 0.000000e+00 710.0
17 TraesCS5B01G525400 chr5D 76.490 1208 210 50 981 2136 552051662 552050477 1.060000e-164 590.0
18 TraesCS5B01G525400 chr5D 75.821 1187 232 35 983 2144 552458397 552457241 5.020000e-153 551.0
19 TraesCS5B01G525400 chr5D 96.209 211 7 1 3234 3444 543501538 543501329 9.150000e-91 344.0
20 TraesCS5B01G525400 chr5D 76.143 503 103 13 1652 2144 552443447 552442952 7.380000e-62 248.0
21 TraesCS5B01G525400 chr5D 77.494 431 68 17 988 1399 551738698 551739118 7.430000e-57 231.0
22 TraesCS5B01G525400 chr5D 90.184 163 8 2 3228 3390 551059876 551060030 4.510000e-49 206.0
23 TraesCS5B01G525400 chr5D 81.553 103 10 5 1312 1405 543536472 543536370 3.690000e-10 76.8
24 TraesCS5B01G525400 chr5D 83.582 67 11 0 2268 2334 551987975 551987909 2.870000e-06 63.9
25 TraesCS5B01G525400 chr4A 84.346 856 98 13 2173 3019 616896339 616895511 0.000000e+00 806.0
26 TraesCS5B01G525400 chr4A 89.252 642 66 2 984 1622 616897532 616896891 0.000000e+00 800.0
27 TraesCS5B01G525400 chr4A 88.948 561 60 2 1581 2140 616896896 616896337 0.000000e+00 691.0
28 TraesCS5B01G525400 chr4A 73.591 1242 221 71 966 2163 705639152 705640330 9.020000e-101 377.0
29 TraesCS5B01G525400 chr4A 78.413 542 103 11 1643 2176 616229895 616229360 1.180000e-89 340.0
30 TraesCS5B01G525400 chr4A 81.173 324 52 9 1019 1336 616885943 616885623 5.710000e-63 252.0
31 TraesCS5B01G525400 chr4A 72.556 849 161 41 1017 1842 616835427 616834628 9.680000e-51 211.0
32 TraesCS5B01G525400 chr4A 75.772 421 65 24 1017 1405 616754838 616754423 9.820000e-41 178.0
33 TraesCS5B01G525400 chr4A 80.769 156 24 4 2368 2518 624482055 624481901 2.170000e-22 117.0
34 TraesCS5B01G525400 chr4A 80.128 156 25 4 2368 2518 624451278 624451124 1.010000e-20 111.0
35 TraesCS5B01G525400 chr4A 77.698 139 21 8 2268 2405 616211486 616211357 3.690000e-10 76.8
36 TraesCS5B01G525400 chr4A 100.000 30 0 0 1604 1633 616871298 616871269 4.800000e-04 56.5
37 TraesCS5B01G525400 chr6B 97.241 290 7 1 1 290 189131934 189131646 1.110000e-134 490.0
38 TraesCS5B01G525400 chr6B 92.989 271 19 0 1 271 80770249 80770519 2.490000e-106 396.0
39 TraesCS5B01G525400 chr2B 96.296 297 10 1 1 297 731073273 731073568 1.440000e-133 486.0
40 TraesCS5B01G525400 chr2B 93.137 204 7 3 357 559 280486022 280485825 3.360000e-75 292.0
41 TraesCS5B01G525400 chr2B 95.192 104 5 0 254 357 731073579 731073682 7.650000e-37 165.0
42 TraesCS5B01G525400 chr2A 94.276 297 17 0 1 297 741092436 741092732 4.050000e-124 455.0
43 TraesCS5B01G525400 chr2A 95.745 94 4 0 264 357 741092726 741092819 5.950000e-33 152.0
44 TraesCS5B01G525400 chr1D 94.295 298 13 1 1 298 265699155 265699448 1.460000e-123 453.0
45 TraesCS5B01G525400 chr1D 79.727 587 83 20 1008 1575 22968934 22968365 3.220000e-105 392.0
46 TraesCS5B01G525400 chr1D 79.059 425 84 5 1721 2143 227868183 227868604 1.560000e-73 287.0
47 TraesCS5B01G525400 chr1D 96.512 86 3 0 272 357 265699449 265699534 3.580000e-30 143.0
48 TraesCS5B01G525400 chr6D 96.310 271 10 0 1 271 455670283 455670553 2.440000e-121 446.0
49 TraesCS5B01G525400 chr6D 88.626 211 15 6 350 559 273913690 273913892 7.380000e-62 248.0
50 TraesCS5B01G525400 chr7A 75.654 764 140 33 1424 2163 23198083 23198824 4.260000e-89 339.0
51 TraesCS5B01G525400 chr3B 92.453 212 7 5 357 567 578285336 578285539 9.350000e-76 294.0
52 TraesCS5B01G525400 chr1A 73.312 948 191 45 976 1883 569738561 569739486 3.360000e-75 292.0
53 TraesCS5B01G525400 chr1A 91.626 203 10 4 357 559 278788745 278788940 1.220000e-69 274.0
54 TraesCS5B01G525400 chr1A 72.881 944 199 42 976 1883 569656820 569657742 4.380000e-69 272.0
55 TraesCS5B01G525400 chr1A 72.584 952 197 44 976 1883 569698599 569699530 1.590000e-63 254.0
56 TraesCS5B01G525400 chr1A 80.128 156 25 4 2368 2518 569702574 569702728 1.010000e-20 111.0
57 TraesCS5B01G525400 chr1A 80.128 156 25 4 2368 2518 569742512 569742666 1.010000e-20 111.0
58 TraesCS5B01G525400 chr1A 78.846 156 27 4 2368 2518 569660764 569660918 2.190000e-17 100.0
59 TraesCS5B01G525400 chr7D 92.647 204 8 4 357 559 75808821 75808624 1.560000e-73 287.0
60 TraesCS5B01G525400 chr5A 91.346 208 10 4 350 556 639100097 639099897 9.410000e-71 278.0
61 TraesCS5B01G525400 chrUn 90.521 211 12 5 350 559 80784236 80784439 4.380000e-69 272.0
62 TraesCS5B01G525400 chr1B 76.091 573 99 23 961 1498 115748942 115749511 7.330000e-67 265.0
63 TraesCS5B01G525400 chr4B 82.971 276 32 12 920 1190 581073658 581073393 5.750000e-58 235.0


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 TraesCS5B01G525400 chr5B 685320632 685324075 3443 True 6360.000000 6360 100.000000 1 3444 1 chr5B.!!$R2 3443
1 TraesCS5B01G525400 chr5B 685503339 685505972 2633 False 1347.666667 2793 94.492667 559 3444 3 chr5B.!!$F4 2885
2 TraesCS5B01G525400 chr5B 703610485 703611603 1118 False 429.000000 429 74.549000 1017 2138 1 chr5B.!!$F3 1121
3 TraesCS5B01G525400 chr5B 700228456 700229171 715 True 370.000000 370 76.327000 1448 2176 1 chr5B.!!$R3 728
4 TraesCS5B01G525400 chr5B 703529390 703530860 1470 False 306.550000 516 77.719000 1019 2490 2 chr5B.!!$F5 1471
5 TraesCS5B01G525400 chr5D 543501329 543504380 3051 True 939.250000 1945 91.824000 357 3444 4 chr5D.!!$R6 3087
6 TraesCS5B01G525400 chr5D 551057608 551060030 2422 False 683.500000 1016 88.196500 984 3390 4 chr5D.!!$F2 2406
7 TraesCS5B01G525400 chr5D 552050477 552051662 1185 True 590.000000 590 76.490000 981 2136 1 chr5D.!!$R3 1155
8 TraesCS5B01G525400 chr5D 552457241 552458397 1156 True 551.000000 551 75.821000 983 2144 1 chr5D.!!$R5 1161
9 TraesCS5B01G525400 chr4A 616895511 616897532 2021 True 765.666667 806 87.515333 984 3019 3 chr4A.!!$R9 2035
10 TraesCS5B01G525400 chr4A 705639152 705640330 1178 False 377.000000 377 73.591000 966 2163 1 chr4A.!!$F1 1197
11 TraesCS5B01G525400 chr4A 616229360 616229895 535 True 340.000000 340 78.413000 1643 2176 1 chr4A.!!$R2 533
12 TraesCS5B01G525400 chr4A 616834628 616835427 799 True 211.000000 211 72.556000 1017 1842 1 chr4A.!!$R4 825
13 TraesCS5B01G525400 chr1D 22968365 22968934 569 True 392.000000 392 79.727000 1008 1575 1 chr1D.!!$R1 567
14 TraesCS5B01G525400 chr7A 23198083 23198824 741 False 339.000000 339 75.654000 1424 2163 1 chr7A.!!$F1 739
15 TraesCS5B01G525400 chr1A 569738561 569742666 4105 False 201.500000 292 76.720000 976 2518 2 chr1A.!!$F4 1542
16 TraesCS5B01G525400 chr1B 115748942 115749511 569 False 265.000000 265 76.091000 961 1498 1 chr1B.!!$F1 537

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
43 44 0.035317 TGATTGTCGCTGTTGCCTCT 59.965 50.000 0.00 0.00 35.36 3.69 F
136 137 0.036732 AACTTCATTCGCCTCCAGCA 59.963 50.000 0.00 0.00 44.04 4.41 F
150 151 0.107312 CCAGCAGGTCTCCCAATCTG 60.107 60.000 0.00 0.00 0.00 2.90 F
425 426 0.248215 CTCGTTTCGATGGCAATGGC 60.248 55.000 0.00 0.00 34.61 4.40 F
426 427 0.957888 TCGTTTCGATGGCAATGGCA 60.958 50.000 12.96 12.96 43.71 4.92 F
736 741 1.615392 AGTTTCAAGCAGTTGGATGGC 59.385 47.619 0.00 0.00 34.09 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1870 2091 4.324254 GGAACCCATCTGTCTTGACCATAA 60.324 45.833 0.00 0.00 0.00 1.90 R
2176 4985 6.016527 TCCGCCAACTAGTATACTCATTACTG 60.017 42.308 9.12 0.16 0.00 2.74 R
2185 4994 6.673154 AAATTGTTCCGCCAACTAGTATAC 57.327 37.500 0.00 0.00 35.79 1.47 R
2250 5064 4.935205 TCGAGCATATATTCCCGAAAATGG 59.065 41.667 0.00 0.00 0.00 3.16 R
2353 5185 5.772825 TCCAAAAAGAAGAAGACATGGTG 57.227 39.130 0.00 0.00 0.00 4.17 R
2697 5537 1.347221 GCGGTACATTTTCGAGCGG 59.653 57.895 0.00 0.00 34.79 5.52 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.472686 CTCCTAATATATGGCAGTACCTCC 57.527 45.833 0.00 0.00 40.22 4.30
24 25 6.167061 TCCTAATATATGGCAGTACCTCCT 57.833 41.667 0.00 0.00 40.22 3.69
25 26 5.958380 TCCTAATATATGGCAGTACCTCCTG 59.042 44.000 0.00 0.00 40.22 3.86
26 27 5.958380 CCTAATATATGGCAGTACCTCCTGA 59.042 44.000 0.00 0.00 40.22 3.86
27 28 6.613271 CCTAATATATGGCAGTACCTCCTGAT 59.387 42.308 0.00 0.09 40.22 2.90
28 29 6.959606 AATATATGGCAGTACCTCCTGATT 57.040 37.500 0.00 0.00 40.22 2.57
29 30 4.630644 ATATGGCAGTACCTCCTGATTG 57.369 45.455 0.00 0.00 40.22 2.67
30 31 1.656587 TGGCAGTACCTCCTGATTGT 58.343 50.000 3.10 0.00 40.22 2.71
31 32 1.555075 TGGCAGTACCTCCTGATTGTC 59.445 52.381 3.10 0.00 40.22 3.18
32 33 1.471676 GGCAGTACCTCCTGATTGTCG 60.472 57.143 0.00 0.00 34.23 4.35
33 34 1.927895 CAGTACCTCCTGATTGTCGC 58.072 55.000 0.00 0.00 34.23 5.19
34 35 1.478510 CAGTACCTCCTGATTGTCGCT 59.521 52.381 0.00 0.00 34.23 4.93
35 36 1.478510 AGTACCTCCTGATTGTCGCTG 59.521 52.381 0.00 0.00 0.00 5.18
36 37 1.204941 GTACCTCCTGATTGTCGCTGT 59.795 52.381 0.00 0.00 0.00 4.40
37 38 0.687354 ACCTCCTGATTGTCGCTGTT 59.313 50.000 0.00 0.00 0.00 3.16
38 39 1.081892 CCTCCTGATTGTCGCTGTTG 58.918 55.000 0.00 0.00 0.00 3.33
39 40 0.445436 CTCCTGATTGTCGCTGTTGC 59.555 55.000 0.00 0.00 0.00 4.17
40 41 0.955428 TCCTGATTGTCGCTGTTGCC 60.955 55.000 0.00 0.00 35.36 4.52
41 42 0.957395 CCTGATTGTCGCTGTTGCCT 60.957 55.000 0.00 0.00 35.36 4.75
42 43 0.445436 CTGATTGTCGCTGTTGCCTC 59.555 55.000 0.00 0.00 35.36 4.70
43 44 0.035317 TGATTGTCGCTGTTGCCTCT 59.965 50.000 0.00 0.00 35.36 3.69
44 45 1.160137 GATTGTCGCTGTTGCCTCTT 58.840 50.000 0.00 0.00 35.36 2.85
45 46 1.537202 GATTGTCGCTGTTGCCTCTTT 59.463 47.619 0.00 0.00 35.36 2.52
46 47 0.944386 TTGTCGCTGTTGCCTCTTTC 59.056 50.000 0.00 0.00 35.36 2.62
47 48 1.221466 TGTCGCTGTTGCCTCTTTCG 61.221 55.000 0.00 0.00 35.36 3.46
48 49 1.667830 TCGCTGTTGCCTCTTTCGG 60.668 57.895 0.00 0.00 35.36 4.30
56 57 4.394712 CCTCTTTCGGCCGCCACT 62.395 66.667 23.51 0.00 0.00 4.00
57 58 2.815647 CTCTTTCGGCCGCCACTC 60.816 66.667 23.51 0.00 0.00 3.51
58 59 3.302347 CTCTTTCGGCCGCCACTCT 62.302 63.158 23.51 0.00 0.00 3.24
59 60 2.815647 CTTTCGGCCGCCACTCTC 60.816 66.667 23.51 0.00 0.00 3.20
60 61 4.388499 TTTCGGCCGCCACTCTCC 62.388 66.667 23.51 0.00 0.00 3.71
65 66 4.475135 GCCGCCACTCTCCCCTTC 62.475 72.222 0.00 0.00 0.00 3.46
66 67 2.685380 CCGCCACTCTCCCCTTCT 60.685 66.667 0.00 0.00 0.00 2.85
67 68 2.581354 CGCCACTCTCCCCTTCTG 59.419 66.667 0.00 0.00 0.00 3.02
68 69 1.984570 CGCCACTCTCCCCTTCTGA 60.985 63.158 0.00 0.00 0.00 3.27
69 70 1.333636 CGCCACTCTCCCCTTCTGAT 61.334 60.000 0.00 0.00 0.00 2.90
70 71 0.179936 GCCACTCTCCCCTTCTGATG 59.820 60.000 0.00 0.00 0.00 3.07
71 72 0.835941 CCACTCTCCCCTTCTGATGG 59.164 60.000 2.69 2.69 0.00 3.51
72 73 1.623557 CCACTCTCCCCTTCTGATGGA 60.624 57.143 10.93 1.60 0.00 3.41
73 74 2.191400 CACTCTCCCCTTCTGATGGAA 58.809 52.381 10.93 0.00 0.00 3.53
83 84 3.790091 CTTCTGATGGAAGCGAATCTCA 58.210 45.455 0.00 0.00 43.88 3.27
84 85 3.170791 TCTGATGGAAGCGAATCTCAC 57.829 47.619 0.00 0.00 0.00 3.51
85 86 2.159043 TCTGATGGAAGCGAATCTCACC 60.159 50.000 0.00 0.00 0.00 4.02
86 87 1.833630 TGATGGAAGCGAATCTCACCT 59.166 47.619 0.00 0.00 0.00 4.00
87 88 2.208431 GATGGAAGCGAATCTCACCTG 58.792 52.381 0.00 0.00 0.00 4.00
88 89 0.250234 TGGAAGCGAATCTCACCTGG 59.750 55.000 0.00 0.00 0.00 4.45
89 90 0.462759 GGAAGCGAATCTCACCTGGG 60.463 60.000 0.00 0.00 0.00 4.45
90 91 0.537188 GAAGCGAATCTCACCTGGGA 59.463 55.000 0.00 0.00 0.00 4.37
91 92 1.139853 GAAGCGAATCTCACCTGGGAT 59.860 52.381 0.00 0.00 0.00 3.85
92 93 0.755686 AGCGAATCTCACCTGGGATC 59.244 55.000 0.00 0.00 0.00 3.36
93 94 0.250081 GCGAATCTCACCTGGGATCC 60.250 60.000 1.92 1.92 0.00 3.36
94 95 0.394565 CGAATCTCACCTGGGATCCC 59.605 60.000 25.22 25.22 0.00 3.85
95 96 0.394565 GAATCTCACCTGGGATCCCG 59.605 60.000 26.03 19.24 39.42 5.14
96 97 0.326618 AATCTCACCTGGGATCCCGT 60.327 55.000 26.03 15.70 39.42 5.28
97 98 0.760945 ATCTCACCTGGGATCCCGTC 60.761 60.000 26.03 2.63 39.42 4.79
105 106 3.555967 GGATCCCGTCCATCAGCT 58.444 61.111 0.00 0.00 46.96 4.24
106 107 1.369321 GGATCCCGTCCATCAGCTC 59.631 63.158 0.00 0.00 46.96 4.09
107 108 1.369321 GATCCCGTCCATCAGCTCC 59.631 63.158 0.00 0.00 0.00 4.70
108 109 1.074926 ATCCCGTCCATCAGCTCCT 60.075 57.895 0.00 0.00 0.00 3.69
109 110 0.692419 ATCCCGTCCATCAGCTCCTT 60.692 55.000 0.00 0.00 0.00 3.36
110 111 0.909610 TCCCGTCCATCAGCTCCTTT 60.910 55.000 0.00 0.00 0.00 3.11
111 112 0.745845 CCCGTCCATCAGCTCCTTTG 60.746 60.000 0.00 0.00 0.00 2.77
112 113 1.372087 CCGTCCATCAGCTCCTTTGC 61.372 60.000 0.00 0.00 0.00 3.68
113 114 0.674581 CGTCCATCAGCTCCTTTGCA 60.675 55.000 0.00 0.00 34.99 4.08
114 115 0.807496 GTCCATCAGCTCCTTTGCAC 59.193 55.000 0.00 0.00 34.99 4.57
115 116 0.674581 TCCATCAGCTCCTTTGCACG 60.675 55.000 0.00 0.00 34.99 5.34
116 117 1.136147 CATCAGCTCCTTTGCACGC 59.864 57.895 0.00 0.00 34.99 5.34
117 118 1.302752 ATCAGCTCCTTTGCACGCA 60.303 52.632 0.00 0.00 34.99 5.24
118 119 0.890542 ATCAGCTCCTTTGCACGCAA 60.891 50.000 0.00 0.00 34.99 4.85
119 120 1.370900 CAGCTCCTTTGCACGCAAC 60.371 57.895 3.45 0.00 35.46 4.17
120 121 1.526917 AGCTCCTTTGCACGCAACT 60.527 52.632 3.45 0.00 35.46 3.16
121 122 1.103398 AGCTCCTTTGCACGCAACTT 61.103 50.000 3.45 0.00 35.46 2.66
122 123 0.661483 GCTCCTTTGCACGCAACTTC 60.661 55.000 3.45 0.00 35.46 3.01
123 124 0.662619 CTCCTTTGCACGCAACTTCA 59.337 50.000 3.45 0.00 35.46 3.02
124 125 1.267806 CTCCTTTGCACGCAACTTCAT 59.732 47.619 3.45 0.00 35.46 2.57
125 126 1.680735 TCCTTTGCACGCAACTTCATT 59.319 42.857 3.45 0.00 35.46 2.57
126 127 2.053627 CCTTTGCACGCAACTTCATTC 58.946 47.619 3.45 0.00 35.46 2.67
127 128 1.710249 CTTTGCACGCAACTTCATTCG 59.290 47.619 3.45 0.00 35.46 3.34
128 129 0.660005 TTGCACGCAACTTCATTCGC 60.660 50.000 0.00 0.00 0.00 4.70
129 130 1.797537 GCACGCAACTTCATTCGCC 60.798 57.895 0.00 0.00 0.00 5.54
130 131 1.868997 CACGCAACTTCATTCGCCT 59.131 52.632 0.00 0.00 0.00 5.52
131 132 0.179215 CACGCAACTTCATTCGCCTC 60.179 55.000 0.00 0.00 0.00 4.70
132 133 1.298859 ACGCAACTTCATTCGCCTCC 61.299 55.000 0.00 0.00 0.00 4.30
133 134 1.298157 CGCAACTTCATTCGCCTCCA 61.298 55.000 0.00 0.00 0.00 3.86
134 135 0.449388 GCAACTTCATTCGCCTCCAG 59.551 55.000 0.00 0.00 0.00 3.86
135 136 0.449388 CAACTTCATTCGCCTCCAGC 59.551 55.000 0.00 0.00 38.52 4.85
136 137 0.036732 AACTTCATTCGCCTCCAGCA 59.963 50.000 0.00 0.00 44.04 4.41
137 138 0.392193 ACTTCATTCGCCTCCAGCAG 60.392 55.000 0.00 0.00 44.04 4.24
138 139 1.078214 TTCATTCGCCTCCAGCAGG 60.078 57.895 0.00 0.00 46.82 4.85
139 140 1.841302 TTCATTCGCCTCCAGCAGGT 61.841 55.000 0.00 0.00 45.61 4.00
140 141 1.817099 CATTCGCCTCCAGCAGGTC 60.817 63.158 0.00 0.00 45.61 3.85
141 142 1.992277 ATTCGCCTCCAGCAGGTCT 60.992 57.895 0.00 0.00 45.61 3.85
142 143 1.965754 ATTCGCCTCCAGCAGGTCTC 61.966 60.000 0.00 0.00 45.61 3.36
143 144 4.154347 CGCCTCCAGCAGGTCTCC 62.154 72.222 0.00 0.00 45.61 3.71
144 145 3.791586 GCCTCCAGCAGGTCTCCC 61.792 72.222 0.00 0.00 45.61 4.30
145 146 2.284921 CCTCCAGCAGGTCTCCCA 60.285 66.667 0.00 0.00 37.53 4.37
146 147 1.920325 CCTCCAGCAGGTCTCCCAA 60.920 63.158 0.00 0.00 37.53 4.12
147 148 1.277580 CCTCCAGCAGGTCTCCCAAT 61.278 60.000 0.00 0.00 37.53 3.16
148 149 0.179936 CTCCAGCAGGTCTCCCAATC 59.820 60.000 0.00 0.00 35.89 2.67
149 150 0.252881 TCCAGCAGGTCTCCCAATCT 60.253 55.000 0.00 0.00 35.89 2.40
150 151 0.107312 CCAGCAGGTCTCCCAATCTG 60.107 60.000 0.00 0.00 0.00 2.90
151 152 0.107312 CAGCAGGTCTCCCAATCTGG 60.107 60.000 0.00 0.00 37.25 3.86
152 153 0.252881 AGCAGGTCTCCCAATCTGGA 60.253 55.000 0.00 0.00 40.96 3.86
159 160 2.136791 TCCCAATCTGGAGATCGCC 58.863 57.895 8.81 8.81 40.96 5.54
160 161 1.301244 CCCAATCTGGAGATCGCCG 60.301 63.158 11.16 6.04 40.96 6.46
161 162 1.301244 CCAATCTGGAGATCGCCGG 60.301 63.158 17.70 17.70 40.96 6.13
162 163 1.742146 CAATCTGGAGATCGCCGGA 59.258 57.895 26.79 26.79 46.82 5.14
163 164 0.319383 CAATCTGGAGATCGCCGGAG 60.319 60.000 27.96 14.58 46.02 4.63
164 165 1.467678 AATCTGGAGATCGCCGGAGG 61.468 60.000 27.96 11.13 46.02 4.30
165 166 3.833224 AATCTGGAGATCGCCGGAGGA 62.833 57.143 27.96 15.40 46.02 3.71
167 168 5.723045 AATCTGGAGATCGCCGGAGGATA 62.723 52.174 27.96 8.88 46.02 2.59
179 180 4.160928 AGGATACGCCTCGACTCC 57.839 61.111 0.00 0.00 46.97 3.85
180 181 1.892862 AGGATACGCCTCGACTCCG 60.893 63.158 0.00 0.00 46.97 4.63
181 182 2.185494 GGATACGCCTCGACTCCGT 61.185 63.158 5.71 5.71 38.84 4.69
182 183 1.279238 GATACGCCTCGACTCCGTC 59.721 63.158 3.86 0.00 36.51 4.79
183 184 1.153208 ATACGCCTCGACTCCGTCT 60.153 57.895 3.86 0.00 36.51 4.18
184 185 0.747283 ATACGCCTCGACTCCGTCTT 60.747 55.000 3.86 0.00 36.51 3.01
185 186 1.642037 TACGCCTCGACTCCGTCTTG 61.642 60.000 3.86 0.00 36.51 3.02
186 187 2.687805 CGCCTCGACTCCGTCTTGA 61.688 63.158 0.00 0.00 37.05 3.02
187 188 1.810532 GCCTCGACTCCGTCTTGAT 59.189 57.895 0.00 0.00 37.05 2.57
188 189 0.526524 GCCTCGACTCCGTCTTGATG 60.527 60.000 0.00 0.00 37.05 3.07
189 190 1.095600 CCTCGACTCCGTCTTGATGA 58.904 55.000 0.00 0.00 37.05 2.92
190 191 1.472878 CCTCGACTCCGTCTTGATGAA 59.527 52.381 0.00 0.00 37.05 2.57
191 192 2.099921 CCTCGACTCCGTCTTGATGAAT 59.900 50.000 0.00 0.00 37.05 2.57
192 193 3.429547 CCTCGACTCCGTCTTGATGAATT 60.430 47.826 0.00 0.00 37.05 2.17
193 194 3.770666 TCGACTCCGTCTTGATGAATTC 58.229 45.455 0.00 0.00 37.05 2.17
194 195 2.860735 CGACTCCGTCTTGATGAATTCC 59.139 50.000 2.27 0.00 0.00 3.01
195 196 3.198872 GACTCCGTCTTGATGAATTCCC 58.801 50.000 2.27 0.00 0.00 3.97
196 197 2.571653 ACTCCGTCTTGATGAATTCCCA 59.428 45.455 2.27 0.00 0.00 4.37
197 198 3.009033 ACTCCGTCTTGATGAATTCCCAA 59.991 43.478 2.27 6.60 0.00 4.12
198 199 4.202441 CTCCGTCTTGATGAATTCCCAAT 58.798 43.478 2.27 0.00 0.00 3.16
199 200 4.199310 TCCGTCTTGATGAATTCCCAATC 58.801 43.478 2.27 0.18 0.00 2.67
200 201 3.316308 CCGTCTTGATGAATTCCCAATCC 59.684 47.826 2.27 1.16 0.00 3.01
201 202 3.947196 CGTCTTGATGAATTCCCAATCCA 59.053 43.478 2.27 0.00 0.00 3.41
202 203 4.036027 CGTCTTGATGAATTCCCAATCCAG 59.964 45.833 2.27 1.52 0.00 3.86
203 204 3.956199 TCTTGATGAATTCCCAATCCAGC 59.044 43.478 2.27 0.00 0.00 4.85
204 205 3.675348 TGATGAATTCCCAATCCAGCT 57.325 42.857 2.27 0.00 0.00 4.24
205 206 3.985127 TGATGAATTCCCAATCCAGCTT 58.015 40.909 2.27 0.00 0.00 3.74
206 207 3.702548 TGATGAATTCCCAATCCAGCTTG 59.297 43.478 2.27 0.00 0.00 4.01
207 208 1.826720 TGAATTCCCAATCCAGCTTGC 59.173 47.619 2.27 0.00 0.00 4.01
208 209 2.105766 GAATTCCCAATCCAGCTTGCT 58.894 47.619 0.00 0.00 0.00 3.91
209 210 1.481871 ATTCCCAATCCAGCTTGCTG 58.518 50.000 15.02 15.02 0.00 4.41
210 211 0.612732 TTCCCAATCCAGCTTGCTGG 60.613 55.000 29.89 29.89 45.53 4.85
211 212 2.718073 CCCAATCCAGCTTGCTGGC 61.718 63.158 30.64 1.46 43.90 4.85
212 213 1.681327 CCAATCCAGCTTGCTGGCT 60.681 57.895 30.64 21.82 43.90 4.75
228 229 3.431725 CTGGGCCGCCGAAGAAAC 61.432 66.667 2.55 0.00 0.00 2.78
246 247 3.801997 CCCCCTCGCTCATGGCTT 61.802 66.667 0.00 0.00 39.13 4.35
247 248 2.203126 CCCCTCGCTCATGGCTTC 60.203 66.667 0.00 0.00 39.13 3.86
248 249 2.586245 CCCTCGCTCATGGCTTCA 59.414 61.111 0.00 0.00 39.13 3.02
249 250 1.817099 CCCTCGCTCATGGCTTCAC 60.817 63.158 0.00 0.00 39.13 3.18
250 251 1.220206 CCTCGCTCATGGCTTCACT 59.780 57.895 0.00 0.00 39.13 3.41
251 252 0.461548 CCTCGCTCATGGCTTCACTA 59.538 55.000 0.00 0.00 39.13 2.74
252 253 1.537776 CCTCGCTCATGGCTTCACTAG 60.538 57.143 0.00 0.00 39.13 2.57
261 262 3.458163 CTTCACTAGCCGCCGGGA 61.458 66.667 4.77 0.00 34.06 5.14
262 263 2.998480 TTCACTAGCCGCCGGGAA 60.998 61.111 4.77 0.00 34.06 3.97
263 264 3.305177 TTCACTAGCCGCCGGGAAC 62.305 63.158 4.77 0.00 34.06 3.62
264 265 3.771160 CACTAGCCGCCGGGAACT 61.771 66.667 4.77 0.00 34.06 3.01
265 266 3.459063 ACTAGCCGCCGGGAACTC 61.459 66.667 4.77 0.00 34.06 3.01
266 267 4.222847 CTAGCCGCCGGGAACTCC 62.223 72.222 4.77 0.00 34.06 3.85
302 303 4.778143 GGGTTCGCCGCCATCACT 62.778 66.667 0.00 0.00 38.45 3.41
303 304 3.195698 GGTTCGCCGCCATCACTC 61.196 66.667 0.00 0.00 0.00 3.51
304 305 3.195698 GTTCGCCGCCATCACTCC 61.196 66.667 0.00 0.00 0.00 3.85
305 306 4.467084 TTCGCCGCCATCACTCCC 62.467 66.667 0.00 0.00 0.00 4.30
308 309 4.554036 GCCGCCATCACTCCCCTC 62.554 72.222 0.00 0.00 0.00 4.30
309 310 2.765807 CCGCCATCACTCCCCTCT 60.766 66.667 0.00 0.00 0.00 3.69
310 311 2.801631 CCGCCATCACTCCCCTCTC 61.802 68.421 0.00 0.00 0.00 3.20
311 312 1.760086 CGCCATCACTCCCCTCTCT 60.760 63.158 0.00 0.00 0.00 3.10
312 313 1.743321 CGCCATCACTCCCCTCTCTC 61.743 65.000 0.00 0.00 0.00 3.20
313 314 0.398381 GCCATCACTCCCCTCTCTCT 60.398 60.000 0.00 0.00 0.00 3.10
314 315 1.133325 GCCATCACTCCCCTCTCTCTA 60.133 57.143 0.00 0.00 0.00 2.43
315 316 2.492567 GCCATCACTCCCCTCTCTCTAT 60.493 54.545 0.00 0.00 0.00 1.98
316 317 3.855668 CCATCACTCCCCTCTCTCTATT 58.144 50.000 0.00 0.00 0.00 1.73
317 318 4.230455 CCATCACTCCCCTCTCTCTATTT 58.770 47.826 0.00 0.00 0.00 1.40
318 319 4.283212 CCATCACTCCCCTCTCTCTATTTC 59.717 50.000 0.00 0.00 0.00 2.17
319 320 3.917300 TCACTCCCCTCTCTCTATTTCC 58.083 50.000 0.00 0.00 0.00 3.13
320 321 2.625790 CACTCCCCTCTCTCTATTTCCG 59.374 54.545 0.00 0.00 0.00 4.30
321 322 2.245287 ACTCCCCTCTCTCTATTTCCGT 59.755 50.000 0.00 0.00 0.00 4.69
322 323 2.888414 CTCCCCTCTCTCTATTTCCGTC 59.112 54.545 0.00 0.00 0.00 4.79
323 324 1.609555 CCCCTCTCTCTATTTCCGTCG 59.390 57.143 0.00 0.00 0.00 5.12
324 325 1.001158 CCCTCTCTCTATTTCCGTCGC 60.001 57.143 0.00 0.00 0.00 5.19
325 326 1.001158 CCTCTCTCTATTTCCGTCGCC 60.001 57.143 0.00 0.00 0.00 5.54
326 327 0.661552 TCTCTCTATTTCCGTCGCCG 59.338 55.000 0.00 0.00 0.00 6.46
327 328 0.935366 CTCTCTATTTCCGTCGCCGC 60.935 60.000 0.00 0.00 0.00 6.53
328 329 1.949631 CTCTATTTCCGTCGCCGCC 60.950 63.158 0.00 0.00 0.00 6.13
329 330 2.202824 CTATTTCCGTCGCCGCCA 60.203 61.111 0.00 0.00 0.00 5.69
330 331 2.202824 TATTTCCGTCGCCGCCAG 60.203 61.111 0.00 0.00 0.00 4.85
331 332 2.622903 CTATTTCCGTCGCCGCCAGA 62.623 60.000 0.00 0.00 0.00 3.86
332 333 2.023414 TATTTCCGTCGCCGCCAGAT 62.023 55.000 0.00 0.00 0.00 2.90
333 334 3.870656 TATTTCCGTCGCCGCCAGATC 62.871 57.143 0.00 0.00 0.00 2.75
372 373 4.216708 AGCTCCGTAATAGGCTAGACTTT 58.783 43.478 1.68 0.47 32.94 2.66
415 416 1.673626 GCCCCATAACACTCGTTTCGA 60.674 52.381 0.00 0.00 36.52 3.71
420 421 2.442212 TAACACTCGTTTCGATGGCA 57.558 45.000 0.00 0.00 36.52 4.92
421 422 1.588674 AACACTCGTTTCGATGGCAA 58.411 45.000 0.00 0.00 34.61 4.52
422 423 1.808411 ACACTCGTTTCGATGGCAAT 58.192 45.000 0.00 0.00 34.61 3.56
423 424 1.464608 ACACTCGTTTCGATGGCAATG 59.535 47.619 0.00 0.00 34.61 2.82
424 425 1.086696 ACTCGTTTCGATGGCAATGG 58.913 50.000 0.00 0.00 34.61 3.16
425 426 0.248215 CTCGTTTCGATGGCAATGGC 60.248 55.000 0.00 0.00 34.61 4.40
426 427 0.957888 TCGTTTCGATGGCAATGGCA 60.958 50.000 12.96 12.96 43.71 4.92
496 497 5.844516 TCTTTCCCTTCTCCTGACTTTTCTA 59.155 40.000 0.00 0.00 0.00 2.10
504 505 5.479306 TCTCCTGACTTTTCTATTGGAACG 58.521 41.667 0.00 0.00 33.13 3.95
541 542 5.199982 TCTATGCAATGGAAAGGGGTAAA 57.800 39.130 0.00 0.00 27.55 2.01
542 543 5.200483 TCTATGCAATGGAAAGGGGTAAAG 58.800 41.667 0.00 0.00 27.55 1.85
736 741 1.615392 AGTTTCAAGCAGTTGGATGGC 59.385 47.619 0.00 0.00 34.09 4.40
831 838 3.658757 TTGAAATGTTGCTACTTGGGC 57.341 42.857 0.00 0.00 0.00 5.36
1870 2091 3.393426 TGGACGGGTTAATCCTCTACT 57.607 47.619 2.61 0.00 35.86 2.57
1964 4753 3.386932 TCTCCCCATTCAAAATCCCAG 57.613 47.619 0.00 0.00 0.00 4.45
2176 4985 8.553459 TCTTCTATGATTTGGAACAGTTCTTC 57.447 34.615 13.13 6.27 42.39 2.87
2185 4994 7.496529 TTTGGAACAGTTCTTCAGTAATGAG 57.503 36.000 13.13 0.00 42.39 2.90
2198 5008 8.630917 TCTTCAGTAATGAGTATACTAGTTGGC 58.369 37.037 5.09 2.63 32.47 4.52
2214 5028 4.866921 AGTTGGCGGAACAATTTAGTTTC 58.133 39.130 0.62 0.00 36.98 2.78
2366 5198 8.299570 CAACTTAATTTAGCACCATGTCTTCTT 58.700 33.333 0.00 0.00 0.00 2.52
2534 5371 2.351726 GTGATCGGTGTCAGTATTTGGC 59.648 50.000 0.00 0.00 0.00 4.52
2591 5431 4.023291 AGTGGTGTTGGATTTTGTCAAGT 58.977 39.130 0.00 0.00 0.00 3.16
2674 5514 2.925578 TCCAATTTCTTGCAGCATCG 57.074 45.000 0.00 0.00 0.00 3.84
2716 5556 1.355796 CCGCTCGAAAATGTACCGCA 61.356 55.000 0.00 0.00 0.00 5.69
2717 5557 0.650512 CGCTCGAAAATGTACCGCAT 59.349 50.000 0.00 0.00 40.03 4.73
2719 5559 1.268032 GCTCGAAAATGTACCGCATGG 60.268 52.381 0.00 0.00 37.96 3.66
2734 5574 3.521560 CGCATGGACTAGCTTTGTCTTA 58.478 45.455 15.85 8.59 35.04 2.10
2822 5662 6.374333 TGGCATGTTTAGAGTTAGTGATTTCC 59.626 38.462 0.00 0.00 0.00 3.13
2828 5668 2.993899 AGAGTTAGTGATTTCCGTTGCG 59.006 45.455 0.00 0.00 0.00 4.85
2833 5673 2.489971 AGTGATTTCCGTTGCGAAGAA 58.510 42.857 0.00 0.00 0.00 2.52
2834 5674 2.223377 AGTGATTTCCGTTGCGAAGAAC 59.777 45.455 0.00 0.00 0.00 3.01
2836 5676 2.875933 TGATTTCCGTTGCGAAGAACTT 59.124 40.909 0.00 0.00 0.00 2.66
2837 5677 2.748461 TTTCCGTTGCGAAGAACTTG 57.252 45.000 0.00 0.00 0.00 3.16
2854 5694 1.200716 CTTGCGATGGTTTCTGCATGT 59.799 47.619 0.00 0.00 35.10 3.21
2870 5710 2.689471 GCATGTTGGCTCATTGGTATGA 59.311 45.455 0.00 0.00 38.45 2.15
2914 5755 2.598565 TCAGTGCTAGAGGTCAAGTGT 58.401 47.619 0.00 0.00 0.00 3.55
2919 5760 4.772624 AGTGCTAGAGGTCAAGTGTTGATA 59.227 41.667 0.00 0.00 42.47 2.15
3045 5887 2.918712 AGTTGAGGGAACTGACAGTG 57.081 50.000 9.33 0.00 43.71 3.66
3085 5929 6.111382 TGCATGAAGATCTCAGAGGTTTTAG 58.889 40.000 0.00 0.00 37.52 1.85
3150 5994 7.492344 GCTATTTGTTGCATATTTTTAGCCTGT 59.508 33.333 0.00 0.00 0.00 4.00
3158 6002 5.507985 GCATATTTTTAGCCTGTGGTGGATC 60.508 44.000 0.00 0.00 0.00 3.36
3176 6020 7.728532 TGGTGGATCTAATAGTAGACTGCAATA 59.271 37.037 1.27 0.00 39.20 1.90
3230 6074 3.526931 TCACATTCTGCTAGGCTACAC 57.473 47.619 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.478510 AGCGACAATCAGGAGGTACTG 59.521 52.381 0.00 0.00 41.55 2.74
16 17 1.204941 ACAGCGACAATCAGGAGGTAC 59.795 52.381 0.00 0.00 0.00 3.34
17 18 1.557099 ACAGCGACAATCAGGAGGTA 58.443 50.000 0.00 0.00 0.00 3.08
18 19 0.687354 AACAGCGACAATCAGGAGGT 59.313 50.000 0.00 0.00 0.00 3.85
19 20 1.081892 CAACAGCGACAATCAGGAGG 58.918 55.000 0.00 0.00 0.00 4.30
20 21 0.445436 GCAACAGCGACAATCAGGAG 59.555 55.000 0.00 0.00 0.00 3.69
21 22 0.955428 GGCAACAGCGACAATCAGGA 60.955 55.000 0.00 0.00 0.00 3.86
22 23 0.957395 AGGCAACAGCGACAATCAGG 60.957 55.000 0.00 0.00 41.41 3.86
23 24 0.445436 GAGGCAACAGCGACAATCAG 59.555 55.000 0.00 0.00 41.41 2.90
24 25 0.035317 AGAGGCAACAGCGACAATCA 59.965 50.000 0.00 0.00 41.41 2.57
25 26 1.160137 AAGAGGCAACAGCGACAATC 58.840 50.000 0.00 0.00 41.41 2.67
26 27 1.537202 GAAAGAGGCAACAGCGACAAT 59.463 47.619 0.00 0.00 41.41 2.71
27 28 0.944386 GAAAGAGGCAACAGCGACAA 59.056 50.000 0.00 0.00 41.41 3.18
28 29 1.221466 CGAAAGAGGCAACAGCGACA 61.221 55.000 0.00 0.00 41.41 4.35
29 30 1.493311 CGAAAGAGGCAACAGCGAC 59.507 57.895 0.00 0.00 41.41 5.19
30 31 1.667830 CCGAAAGAGGCAACAGCGA 60.668 57.895 0.00 0.00 41.41 4.93
31 32 2.863153 CCGAAAGAGGCAACAGCG 59.137 61.111 0.00 0.00 41.41 5.18
39 40 4.394712 AGTGGCGGCCGAAAGAGG 62.395 66.667 33.48 0.00 0.00 3.69
40 41 2.815647 GAGTGGCGGCCGAAAGAG 60.816 66.667 33.48 0.00 0.00 2.85
41 42 3.296709 GAGAGTGGCGGCCGAAAGA 62.297 63.158 33.48 5.37 0.00 2.52
42 43 2.815647 GAGAGTGGCGGCCGAAAG 60.816 66.667 33.48 0.00 0.00 2.62
43 44 4.388499 GGAGAGTGGCGGCCGAAA 62.388 66.667 33.48 13.68 0.00 3.46
48 49 4.475135 GAAGGGGAGAGTGGCGGC 62.475 72.222 0.00 0.00 0.00 6.53
49 50 2.685380 AGAAGGGGAGAGTGGCGG 60.685 66.667 0.00 0.00 0.00 6.13
50 51 1.333636 ATCAGAAGGGGAGAGTGGCG 61.334 60.000 0.00 0.00 0.00 5.69
51 52 0.179936 CATCAGAAGGGGAGAGTGGC 59.820 60.000 0.00 0.00 0.00 5.01
52 53 0.835941 CCATCAGAAGGGGAGAGTGG 59.164 60.000 0.00 0.00 0.00 4.00
53 54 1.871418 TCCATCAGAAGGGGAGAGTG 58.129 55.000 0.00 0.00 0.00 3.51
54 55 2.649742 TTCCATCAGAAGGGGAGAGT 57.350 50.000 0.00 0.00 31.19 3.24
63 64 3.525537 GTGAGATTCGCTTCCATCAGAA 58.474 45.455 0.00 0.00 0.00 3.02
64 65 2.159043 GGTGAGATTCGCTTCCATCAGA 60.159 50.000 0.00 0.00 0.00 3.27
65 66 2.158986 AGGTGAGATTCGCTTCCATCAG 60.159 50.000 5.45 0.00 0.00 2.90
66 67 1.833630 AGGTGAGATTCGCTTCCATCA 59.166 47.619 5.45 0.00 0.00 3.07
67 68 2.208431 CAGGTGAGATTCGCTTCCATC 58.792 52.381 5.45 0.00 0.00 3.51
68 69 1.134280 CCAGGTGAGATTCGCTTCCAT 60.134 52.381 5.45 0.00 0.00 3.41
69 70 0.250234 CCAGGTGAGATTCGCTTCCA 59.750 55.000 5.45 0.00 0.00 3.53
70 71 0.462759 CCCAGGTGAGATTCGCTTCC 60.463 60.000 0.00 0.00 0.00 3.46
71 72 0.537188 TCCCAGGTGAGATTCGCTTC 59.463 55.000 0.00 0.00 0.00 3.86
72 73 1.139853 GATCCCAGGTGAGATTCGCTT 59.860 52.381 0.00 0.00 0.00 4.68
73 74 0.755686 GATCCCAGGTGAGATTCGCT 59.244 55.000 0.00 0.00 0.00 4.93
74 75 0.250081 GGATCCCAGGTGAGATTCGC 60.250 60.000 0.00 0.00 0.00 4.70
75 76 0.394565 GGGATCCCAGGTGAGATTCG 59.605 60.000 26.95 0.00 35.81 3.34
76 77 0.394565 CGGGATCCCAGGTGAGATTC 59.605 60.000 30.42 0.00 35.37 2.52
77 78 0.326618 ACGGGATCCCAGGTGAGATT 60.327 55.000 30.42 3.06 35.37 2.40
78 79 0.760945 GACGGGATCCCAGGTGAGAT 60.761 60.000 30.42 6.27 35.37 2.75
79 80 1.381327 GACGGGATCCCAGGTGAGA 60.381 63.158 30.42 0.00 35.37 3.27
80 81 2.435693 GGACGGGATCCCAGGTGAG 61.436 68.421 30.42 15.13 42.46 3.51
81 82 2.365105 GGACGGGATCCCAGGTGA 60.365 66.667 30.42 0.00 42.46 4.02
89 90 1.118356 AGGAGCTGATGGACGGGATC 61.118 60.000 0.00 0.00 0.00 3.36
90 91 0.692419 AAGGAGCTGATGGACGGGAT 60.692 55.000 0.00 0.00 0.00 3.85
91 92 0.909610 AAAGGAGCTGATGGACGGGA 60.910 55.000 0.00 0.00 0.00 5.14
92 93 0.745845 CAAAGGAGCTGATGGACGGG 60.746 60.000 0.00 0.00 0.00 5.28
93 94 1.372087 GCAAAGGAGCTGATGGACGG 61.372 60.000 0.00 0.00 0.00 4.79
94 95 0.674581 TGCAAAGGAGCTGATGGACG 60.675 55.000 0.00 0.00 34.99 4.79
95 96 0.807496 GTGCAAAGGAGCTGATGGAC 59.193 55.000 0.00 0.00 34.99 4.02
96 97 0.674581 CGTGCAAAGGAGCTGATGGA 60.675 55.000 0.00 0.00 34.99 3.41
97 98 1.798735 CGTGCAAAGGAGCTGATGG 59.201 57.895 0.00 0.00 34.99 3.51
98 99 1.136147 GCGTGCAAAGGAGCTGATG 59.864 57.895 0.00 0.00 34.99 3.07
99 100 0.890542 TTGCGTGCAAAGGAGCTGAT 60.891 50.000 4.52 0.00 32.44 2.90
100 101 1.525765 TTGCGTGCAAAGGAGCTGA 60.526 52.632 4.52 0.00 32.44 4.26
101 102 1.370900 GTTGCGTGCAAAGGAGCTG 60.371 57.895 9.13 0.00 37.70 4.24
102 103 1.103398 AAGTTGCGTGCAAAGGAGCT 61.103 50.000 9.13 0.00 37.70 4.09
103 104 0.661483 GAAGTTGCGTGCAAAGGAGC 60.661 55.000 9.13 0.00 37.70 4.70
104 105 0.662619 TGAAGTTGCGTGCAAAGGAG 59.337 50.000 9.13 0.00 37.70 3.69
105 106 1.317613 ATGAAGTTGCGTGCAAAGGA 58.682 45.000 9.13 0.00 37.70 3.36
106 107 2.053627 GAATGAAGTTGCGTGCAAAGG 58.946 47.619 9.13 0.00 37.70 3.11
107 108 1.710249 CGAATGAAGTTGCGTGCAAAG 59.290 47.619 9.13 0.00 37.70 2.77
108 109 1.752753 CGAATGAAGTTGCGTGCAAA 58.247 45.000 9.13 0.00 37.70 3.68
109 110 0.660005 GCGAATGAAGTTGCGTGCAA 60.660 50.000 2.58 2.58 0.00 4.08
110 111 1.082169 GCGAATGAAGTTGCGTGCA 60.082 52.632 0.00 0.00 0.00 4.57
111 112 1.797537 GGCGAATGAAGTTGCGTGC 60.798 57.895 0.00 0.00 0.00 5.34
112 113 0.179215 GAGGCGAATGAAGTTGCGTG 60.179 55.000 0.00 0.00 0.00 5.34
113 114 1.298859 GGAGGCGAATGAAGTTGCGT 61.299 55.000 0.00 0.00 0.00 5.24
114 115 1.298157 TGGAGGCGAATGAAGTTGCG 61.298 55.000 0.00 0.00 0.00 4.85
115 116 0.449388 CTGGAGGCGAATGAAGTTGC 59.551 55.000 0.00 0.00 0.00 4.17
116 117 0.449388 GCTGGAGGCGAATGAAGTTG 59.551 55.000 0.00 0.00 0.00 3.16
117 118 0.036732 TGCTGGAGGCGAATGAAGTT 59.963 50.000 0.00 0.00 45.43 2.66
118 119 0.392193 CTGCTGGAGGCGAATGAAGT 60.392 55.000 0.00 0.00 45.43 3.01
119 120 1.094073 CCTGCTGGAGGCGAATGAAG 61.094 60.000 2.92 0.00 45.43 3.02
120 121 1.078214 CCTGCTGGAGGCGAATGAA 60.078 57.895 2.92 0.00 45.43 2.57
121 122 2.586245 CCTGCTGGAGGCGAATGA 59.414 61.111 2.92 0.00 45.43 2.57
141 142 1.748329 CGGCGATCTCCAGATTGGGA 61.748 60.000 0.00 0.00 38.32 4.37
142 143 1.301244 CGGCGATCTCCAGATTGGG 60.301 63.158 0.00 0.00 38.32 4.12
143 144 1.301244 CCGGCGATCTCCAGATTGG 60.301 63.158 9.30 0.00 39.43 3.16
144 145 0.319383 CTCCGGCGATCTCCAGATTG 60.319 60.000 9.30 0.00 38.64 2.67
145 146 1.467678 CCTCCGGCGATCTCCAGATT 61.468 60.000 9.30 0.00 34.37 2.40
146 147 1.905843 CCTCCGGCGATCTCCAGAT 60.906 63.158 9.30 0.00 37.51 2.90
147 148 2.359015 ATCCTCCGGCGATCTCCAGA 62.359 60.000 9.30 0.00 0.00 3.86
148 149 0.609406 TATCCTCCGGCGATCTCCAG 60.609 60.000 9.30 0.00 0.00 3.86
149 150 0.894184 GTATCCTCCGGCGATCTCCA 60.894 60.000 9.30 0.00 0.00 3.86
150 151 1.884444 GTATCCTCCGGCGATCTCC 59.116 63.158 9.30 0.00 0.00 3.71
151 152 1.502640 CGTATCCTCCGGCGATCTC 59.497 63.158 9.30 2.91 0.00 2.75
152 153 2.627737 GCGTATCCTCCGGCGATCT 61.628 63.158 9.30 0.00 0.00 2.75
153 154 2.126424 GCGTATCCTCCGGCGATC 60.126 66.667 9.30 0.68 0.00 3.69
154 155 3.681835 GGCGTATCCTCCGGCGAT 61.682 66.667 9.30 2.41 41.07 4.58
162 163 2.605854 ACGGAGTCGAGGCGTATCCT 62.606 60.000 0.00 0.00 44.71 3.24
163 164 2.185494 ACGGAGTCGAGGCGTATCC 61.185 63.158 0.00 0.00 29.74 2.59
164 165 3.418714 ACGGAGTCGAGGCGTATC 58.581 61.111 0.00 0.00 29.74 2.24
176 177 3.266510 TGGGAATTCATCAAGACGGAG 57.733 47.619 7.93 0.00 0.00 4.63
177 178 3.712016 TTGGGAATTCATCAAGACGGA 57.288 42.857 7.93 0.00 0.00 4.69
178 179 3.316308 GGATTGGGAATTCATCAAGACGG 59.684 47.826 7.93 0.00 0.00 4.79
179 180 3.947196 TGGATTGGGAATTCATCAAGACG 59.053 43.478 7.93 0.00 0.00 4.18
180 181 4.202090 GCTGGATTGGGAATTCATCAAGAC 60.202 45.833 7.93 8.56 0.00 3.01
181 182 3.956199 GCTGGATTGGGAATTCATCAAGA 59.044 43.478 7.93 0.32 0.00 3.02
182 183 3.958798 AGCTGGATTGGGAATTCATCAAG 59.041 43.478 7.93 6.09 0.00 3.02
183 184 3.985127 AGCTGGATTGGGAATTCATCAA 58.015 40.909 7.93 11.26 0.00 2.57
184 185 3.675348 AGCTGGATTGGGAATTCATCA 57.325 42.857 7.93 2.20 0.00 3.07
185 186 3.492137 GCAAGCTGGATTGGGAATTCATC 60.492 47.826 7.93 1.83 0.00 2.92
186 187 2.433239 GCAAGCTGGATTGGGAATTCAT 59.567 45.455 7.93 0.00 0.00 2.57
187 188 1.826720 GCAAGCTGGATTGGGAATTCA 59.173 47.619 7.93 0.00 0.00 2.57
188 189 2.105766 AGCAAGCTGGATTGGGAATTC 58.894 47.619 0.00 0.00 0.00 2.17
189 190 1.829222 CAGCAAGCTGGATTGGGAATT 59.171 47.619 14.10 0.00 40.17 2.17
190 191 1.481871 CAGCAAGCTGGATTGGGAAT 58.518 50.000 14.10 0.00 40.17 3.01
191 192 2.965805 CAGCAAGCTGGATTGGGAA 58.034 52.632 14.10 0.00 40.17 3.97
192 193 4.749323 CAGCAAGCTGGATTGGGA 57.251 55.556 14.10 0.00 40.17 4.37
211 212 3.431725 GTTTCTTCGGCGGCCCAG 61.432 66.667 14.55 10.01 0.00 4.45
244 245 3.014085 TTCCCGGCGGCTAGTGAAG 62.014 63.158 23.20 4.00 0.00 3.02
245 246 2.998480 TTCCCGGCGGCTAGTGAA 60.998 61.111 23.20 15.52 0.00 3.18
246 247 3.766691 GTTCCCGGCGGCTAGTGA 61.767 66.667 23.20 9.37 0.00 3.41
247 248 3.718210 GAGTTCCCGGCGGCTAGTG 62.718 68.421 23.20 6.60 0.00 2.74
248 249 3.459063 GAGTTCCCGGCGGCTAGT 61.459 66.667 23.20 13.16 0.00 2.57
249 250 4.222847 GGAGTTCCCGGCGGCTAG 62.223 72.222 23.20 7.49 0.00 3.42
285 286 4.778143 AGTGATGGCGGCGAACCC 62.778 66.667 12.98 2.29 0.00 4.11
286 287 3.195698 GAGTGATGGCGGCGAACC 61.196 66.667 12.98 3.21 0.00 3.62
287 288 3.195698 GGAGTGATGGCGGCGAAC 61.196 66.667 12.98 2.36 0.00 3.95
288 289 4.467084 GGGAGTGATGGCGGCGAA 62.467 66.667 12.98 0.00 0.00 4.70
291 292 4.554036 GAGGGGAGTGATGGCGGC 62.554 72.222 0.00 0.00 0.00 6.53
292 293 2.765807 AGAGGGGAGTGATGGCGG 60.766 66.667 0.00 0.00 0.00 6.13
293 294 1.743321 GAGAGAGGGGAGTGATGGCG 61.743 65.000 0.00 0.00 0.00 5.69
294 295 0.398381 AGAGAGAGGGGAGTGATGGC 60.398 60.000 0.00 0.00 0.00 4.40
295 296 3.541242 ATAGAGAGAGGGGAGTGATGG 57.459 52.381 0.00 0.00 0.00 3.51
296 297 4.283212 GGAAATAGAGAGAGGGGAGTGATG 59.717 50.000 0.00 0.00 0.00 3.07
297 298 4.488770 GGAAATAGAGAGAGGGGAGTGAT 58.511 47.826 0.00 0.00 0.00 3.06
298 299 3.688702 CGGAAATAGAGAGAGGGGAGTGA 60.689 52.174 0.00 0.00 0.00 3.41
299 300 2.625790 CGGAAATAGAGAGAGGGGAGTG 59.374 54.545 0.00 0.00 0.00 3.51
300 301 2.245287 ACGGAAATAGAGAGAGGGGAGT 59.755 50.000 0.00 0.00 0.00 3.85
301 302 2.888414 GACGGAAATAGAGAGAGGGGAG 59.112 54.545 0.00 0.00 0.00 4.30
302 303 2.748798 CGACGGAAATAGAGAGAGGGGA 60.749 54.545 0.00 0.00 0.00 4.81
303 304 1.609555 CGACGGAAATAGAGAGAGGGG 59.390 57.143 0.00 0.00 0.00 4.79
304 305 1.001158 GCGACGGAAATAGAGAGAGGG 60.001 57.143 0.00 0.00 0.00 4.30
305 306 1.001158 GGCGACGGAAATAGAGAGAGG 60.001 57.143 0.00 0.00 0.00 3.69
306 307 2.409152 GGCGACGGAAATAGAGAGAG 57.591 55.000 0.00 0.00 0.00 3.20
334 335 4.708968 CTCCCGCGATCGCTAGGC 62.709 72.222 34.69 8.99 39.32 3.93
335 336 4.708968 GCTCCCGCGATCGCTAGG 62.709 72.222 34.69 32.06 39.32 3.02
336 337 3.602924 GAGCTCCCGCGATCGCTAG 62.603 68.421 34.69 27.64 42.32 3.42
337 338 3.661131 GAGCTCCCGCGATCGCTA 61.661 66.667 34.69 20.08 42.32 4.26
347 348 1.819903 CTAGCCTATTACGGAGCTCCC 59.180 57.143 27.20 10.17 36.79 4.30
348 349 2.488937 GTCTAGCCTATTACGGAGCTCC 59.511 54.545 23.79 23.79 36.79 4.70
349 350 3.414269 AGTCTAGCCTATTACGGAGCTC 58.586 50.000 4.71 4.71 36.79 4.09
350 351 3.512219 AGTCTAGCCTATTACGGAGCT 57.488 47.619 0.00 0.00 39.37 4.09
351 352 4.587584 AAAGTCTAGCCTATTACGGAGC 57.412 45.455 0.00 0.00 0.00 4.70
352 353 8.979574 CAAAATAAAGTCTAGCCTATTACGGAG 58.020 37.037 0.00 0.00 0.00 4.63
353 354 8.480501 ACAAAATAAAGTCTAGCCTATTACGGA 58.519 33.333 0.00 0.00 0.00 4.69
354 355 8.548721 CACAAAATAAAGTCTAGCCTATTACGG 58.451 37.037 0.00 0.00 0.00 4.02
355 356 8.062448 GCACAAAATAAAGTCTAGCCTATTACG 58.938 37.037 0.00 0.00 0.00 3.18
372 373 5.334569 GCGAAAACCTGAGTAGCACAAAATA 60.335 40.000 0.00 0.00 0.00 1.40
415 416 1.679977 ACTCGCTTGCCATTGCCAT 60.680 52.632 0.00 0.00 36.33 4.40
420 421 1.228245 ACCACACTCGCTTGCCATT 60.228 52.632 0.00 0.00 0.00 3.16
421 422 1.968017 CACCACACTCGCTTGCCAT 60.968 57.895 0.00 0.00 0.00 4.40
422 423 2.591429 CACCACACTCGCTTGCCA 60.591 61.111 0.00 0.00 0.00 4.92
423 424 3.357079 CCACCACACTCGCTTGCC 61.357 66.667 0.00 0.00 0.00 4.52
424 425 3.357079 CCCACCACACTCGCTTGC 61.357 66.667 0.00 0.00 0.00 4.01
425 426 1.101049 AAACCCACCACACTCGCTTG 61.101 55.000 0.00 0.00 0.00 4.01
426 427 0.818040 GAAACCCACCACACTCGCTT 60.818 55.000 0.00 0.00 0.00 4.68
496 497 2.750712 CGGAAATACAACCCGTTCCAAT 59.249 45.455 0.00 0.00 39.67 3.16
504 505 3.942748 TGCATAGAACGGAAATACAACCC 59.057 43.478 0.00 0.00 0.00 4.11
828 835 3.483808 TTTCAACATTTTTCAGGGCCC 57.516 42.857 16.46 16.46 0.00 5.80
831 838 7.307573 GCTTTCAGATTTCAACATTTTTCAGGG 60.308 37.037 0.00 0.00 0.00 4.45
1870 2091 4.324254 GGAACCCATCTGTCTTGACCATAA 60.324 45.833 0.00 0.00 0.00 1.90
2176 4985 6.016527 TCCGCCAACTAGTATACTCATTACTG 60.017 42.308 9.12 0.16 0.00 2.74
2185 4994 6.673154 AAATTGTTCCGCCAACTAGTATAC 57.327 37.500 0.00 0.00 35.79 1.47
2198 5008 9.672086 TCTAAACATTGAAACTAAATTGTTCCG 57.328 29.630 0.00 0.00 0.00 4.30
2214 5028 8.964476 ATAACTACCCATCTGTCTAAACATTG 57.036 34.615 0.00 0.00 34.13 2.82
2250 5064 4.935205 TCGAGCATATATTCCCGAAAATGG 59.065 41.667 0.00 0.00 0.00 3.16
2349 5181 6.239008 CCAAAAAGAAGAAGACATGGTGCTAA 60.239 38.462 0.00 0.00 0.00 3.09
2353 5185 5.772825 TCCAAAAAGAAGAAGACATGGTG 57.227 39.130 0.00 0.00 0.00 4.17
2366 5198 8.522830 GGATTTATCAGTGTGATTCCAAAAAGA 58.477 33.333 0.00 0.00 38.26 2.52
2534 5371 3.490526 GCACCACTGCATTAAAACAGTTG 59.509 43.478 10.20 9.81 44.59 3.16
2697 5537 1.347221 GCGGTACATTTTCGAGCGG 59.653 57.895 0.00 0.00 34.79 5.52
2702 5542 2.006888 AGTCCATGCGGTACATTTTCG 58.993 47.619 0.00 0.00 36.64 3.46
2716 5556 5.700402 ATGGTAAGACAAAGCTAGTCCAT 57.300 39.130 13.82 9.12 36.68 3.41
2717 5557 5.221843 ACAATGGTAAGACAAAGCTAGTCCA 60.222 40.000 13.82 7.48 36.68 4.02
2719 5559 7.900782 TTACAATGGTAAGACAAAGCTAGTC 57.099 36.000 10.41 10.41 34.63 2.59
2747 5587 5.148651 AGGTACGAAAGCAAACTGTAGAT 57.851 39.130 0.00 0.00 0.00 1.98
2761 5601 3.280295 TGTTTTGGCTCAAAGGTACGAA 58.720 40.909 0.00 0.00 34.72 3.85
2767 5607 3.381272 TGTTCTCTGTTTTGGCTCAAAGG 59.619 43.478 1.52 0.00 34.72 3.11
2822 5662 0.163788 ATCGCAAGTTCTTCGCAACG 59.836 50.000 0.00 0.00 39.48 4.10
2828 5668 3.814945 CAGAAACCATCGCAAGTTCTTC 58.185 45.455 0.00 0.00 39.48 2.87
2833 5673 1.200716 CATGCAGAAACCATCGCAAGT 59.799 47.619 0.00 0.00 39.65 3.16
2834 5674 1.200716 ACATGCAGAAACCATCGCAAG 59.799 47.619 0.00 0.00 39.65 4.01
2836 5676 1.068402 CAACATGCAGAAACCATCGCA 60.068 47.619 0.00 0.00 40.20 5.10
2837 5677 1.621107 CAACATGCAGAAACCATCGC 58.379 50.000 0.00 0.00 0.00 4.58
2854 5694 8.815565 TTAATTAAGTCATACCAATGAGCCAA 57.184 30.769 0.00 0.00 42.80 4.52
2895 5735 3.062763 CAACACTTGACCTCTAGCACTG 58.937 50.000 0.00 0.00 0.00 3.66
2964 5806 4.136796 TCTTCAGTAACATTGCTTGCTGT 58.863 39.130 12.78 0.00 35.85 4.40
2982 5824 9.026074 GTTTACATGCTATACTCTTCACTCTTC 57.974 37.037 0.00 0.00 0.00 2.87
3045 5887 1.527034 TGCAACTCAGATTCTGCCAC 58.473 50.000 8.89 0.00 33.78 5.01
3052 5894 5.742063 TGAGATCTTCATGCAACTCAGATT 58.258 37.500 0.00 0.00 32.04 2.40
3085 5929 1.593196 TTGTGGAGCAACTGTAGCAC 58.407 50.000 0.00 0.00 31.07 4.40
3144 5988 3.658725 ACTATTAGATCCACCACAGGCT 58.341 45.455 0.00 0.00 0.00 4.58
3150 5994 5.454966 TGCAGTCTACTATTAGATCCACCA 58.545 41.667 0.00 0.00 36.69 4.17
3158 6002 7.671302 ACATGGGTATTGCAGTCTACTATTAG 58.329 38.462 0.00 0.00 0.00 1.73
3176 6020 4.718774 ACATCTTCATCTCACTACATGGGT 59.281 41.667 0.00 0.00 0.00 4.51
3209 6053 3.452264 TGTGTAGCCTAGCAGAATGTGAT 59.548 43.478 0.00 0.00 39.31 3.06
3297 6189 6.769512 TGCCTCTTCCATAAATATAGGTCAC 58.230 40.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.