Multiple sequence alignment - TraesCS4A01G231600

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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 TraesCS4A01G231600 chr4A 100.000 5027 0 0 1 5027 541336582 541341608 0.000000e+00 9284.0
1 TraesCS4A01G231600 chr4A 90.244 164 15 1 4706 4868 541172935 541173098 3.940000e-51 213.0
2 TraesCS4A01G231600 chr4A 92.424 132 9 1 773 903 541324124 541323993 2.390000e-43 187.0
3 TraesCS4A01G231600 chr4B 91.860 2715 141 28 2348 5026 82667089 82664419 0.000000e+00 3716.0
4 TraesCS4A01G231600 chr4B 94.454 1136 39 7 974 2089 82668631 82667500 0.000000e+00 1727.0
5 TraesCS4A01G231600 chr4B 78.657 581 92 19 3101 3667 172356395 172355833 1.720000e-94 357.0
6 TraesCS4A01G231600 chr4B 88.261 230 14 2 2136 2352 82667494 82667265 3.860000e-66 263.0
7 TraesCS4A01G231600 chr4B 84.259 108 11 1 3720 3827 172355846 172355745 3.200000e-17 100.0
8 TraesCS4A01G231600 chr4B 100.000 32 0 0 4531 4562 82664898 82664867 5.430000e-05 60.2
9 TraesCS4A01G231600 chr4D 94.092 2048 94 7 2705 4752 55582985 55580965 0.000000e+00 3086.0
10 TraesCS4A01G231600 chr4D 92.202 1090 36 12 1014 2089 55584933 55583879 0.000000e+00 1496.0
11 TraesCS4A01G231600 chr4D 90.256 585 23 5 2136 2706 55583873 55583309 0.000000e+00 734.0
12 TraesCS4A01G231600 chr4D 80.140 428 64 14 3101 3511 111558744 111558321 2.940000e-77 300.0
13 TraesCS4A01G231600 chr4D 76.638 351 41 24 3751 4080 111555444 111555114 6.740000e-34 156.0
14 TraesCS4A01G231600 chr4D 100.000 34 0 0 4529 4562 55581140 55581107 4.200000e-06 63.9
15 TraesCS4A01G231600 chr4D 100.000 28 0 0 2090 2117 55583888 55583861 9.000000e-03 52.8
16 TraesCS4A01G231600 chr5A 98.336 541 9 0 1 541 419361496 419360956 0.000000e+00 950.0
17 TraesCS4A01G231600 chr5A 96.154 156 6 0 553 708 419360703 419360548 6.460000e-64 255.0
18 TraesCS4A01G231600 chr5A 87.678 211 8 8 711 903 419360499 419360289 3.910000e-56 230.0
19 TraesCS4A01G231600 chr5A 92.754 138 8 2 772 908 419363111 419363247 1.100000e-46 198.0
20 TraesCS4A01G231600 chr5A 88.112 143 13 3 552 694 341873011 341872873 3.110000e-37 167.0
21 TraesCS4A01G231600 chr5A 87.342 79 6 3 2432 2508 661025805 661025729 2.490000e-13 87.9
22 TraesCS4A01G231600 chr5A 100.000 28 0 0 932 959 432030858 432030885 9.000000e-03 52.8
23 TraesCS4A01G231600 chr1B 95.749 541 23 0 1 541 676247032 676246492 0.000000e+00 872.0
24 TraesCS4A01G231600 chr1B 94.286 455 22 2 1 451 491697836 491697382 0.000000e+00 693.0
25 TraesCS4A01G231600 chr1B 84.444 360 43 8 553 904 491545385 491545031 4.820000e-90 342.0
26 TraesCS4A01G231600 chr1B 95.455 154 7 0 555 708 676246238 676246085 3.890000e-61 246.0
27 TraesCS4A01G231600 chr1B 81.690 213 17 11 711 904 676248397 676248606 1.870000e-34 158.0
28 TraesCS4A01G231600 chr1B 80.275 218 20 8 711 908 676246037 676245823 5.250000e-30 143.0
29 TraesCS4A01G231600 chr1B 89.474 95 10 0 447 541 491545732 491545638 2.460000e-23 121.0
30 TraesCS4A01G231600 chr2B 91.563 403 22 5 1 391 608540278 608539876 3.420000e-151 545.0
31 TraesCS4A01G231600 chr2B 82.659 173 15 5 85 257 608802158 608802001 6.790000e-29 139.0
32 TraesCS4A01G231600 chr2B 96.774 31 1 0 929 959 417420434 417420464 9.000000e-03 52.8
33 TraesCS4A01G231600 chr2D 89.673 397 34 5 1 390 516862683 516862287 2.700000e-137 499.0
34 TraesCS4A01G231600 chr2D 79.927 274 36 7 87 346 517086523 517086255 3.090000e-42 183.0
35 TraesCS4A01G231600 chr2D 94.286 35 2 0 829 863 28057527 28057493 3.000000e-03 54.7
36 TraesCS4A01G231600 chr2A 88.586 403 30 4 1 390 661082119 661081720 4.550000e-130 475.0
37 TraesCS4A01G231600 chr2A 81.287 171 17 6 87 257 661394698 661394543 1.900000e-24 124.0
38 TraesCS4A01G231600 chr5D 92.414 145 11 0 397 541 257123453 257123309 1.830000e-49 207.0
39 TraesCS4A01G231600 chr5D 88.079 151 14 4 552 702 257123057 257122911 5.170000e-40 176.0
40 TraesCS4A01G231600 chr5D 84.444 90 13 1 2396 2485 440170372 440170284 2.490000e-13 87.9
41 TraesCS4A01G231600 chr7B 84.834 211 14 4 711 903 667442061 667442271 3.970000e-46 196.0
42 TraesCS4A01G231600 chr7B 90.278 144 12 2 772 914 541491576 541491718 2.390000e-43 187.0
43 TraesCS4A01G231600 chr7B 94.167 120 7 0 555 674 667441580 667441699 3.090000e-42 183.0
44 TraesCS4A01G231600 chr7B 93.671 79 5 0 772 850 667433595 667433517 8.840000e-23 119.0
45 TraesCS4A01G231600 chr5B 91.096 146 12 1 397 541 291378609 291378464 3.970000e-46 196.0
46 TraesCS4A01G231600 chr5B 86.667 150 14 5 553 698 291378212 291378065 1.450000e-35 161.0
47 TraesCS4A01G231600 chr5B 100.000 28 0 0 932 959 604944588 604944561 9.000000e-03 52.8
48 TraesCS4A01G231600 chr6D 76.552 145 28 5 2361 2502 394870978 394870837 1.940000e-09 75.0
49 TraesCS4A01G231600 chr6B 100.000 28 0 0 932 959 207606031 207606004 9.000000e-03 52.8
50 TraesCS4A01G231600 chr6B 96.774 31 1 0 929 959 227156763 227156793 9.000000e-03 52.8


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 TraesCS4A01G231600 chr4A 541336582 541341608 5026 False 9284.000000 9284 100.00000 1 5027 1 chr4A.!!$F2 5026
1 TraesCS4A01G231600 chr4B 82664419 82668631 4212 True 1441.550000 3716 93.64375 974 5026 4 chr4B.!!$R1 4052
2 TraesCS4A01G231600 chr4B 172355745 172356395 650 True 228.500000 357 81.45800 3101 3827 2 chr4B.!!$R2 726
3 TraesCS4A01G231600 chr4D 55580965 55584933 3968 True 1086.540000 3086 95.31000 1014 4752 5 chr4D.!!$R1 3738
4 TraesCS4A01G231600 chr4D 111555114 111558744 3630 True 228.000000 300 78.38900 3101 4080 2 chr4D.!!$R2 979
5 TraesCS4A01G231600 chr5A 419360289 419361496 1207 True 478.333333 950 94.05600 1 903 3 chr5A.!!$R3 902
6 TraesCS4A01G231600 chr1B 676245823 676247032 1209 True 420.333333 872 90.49300 1 908 3 chr1B.!!$R3 907
7 TraesCS4A01G231600 chr1B 491545031 491545732 701 True 231.500000 342 86.95900 447 904 2 chr1B.!!$R2 457

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
876 1187 0.179045 AAAGTGTCAGCCGCTCAAGT 60.179 50.000 0.00 0.0 32.07 3.16 F
877 1188 0.179045 AAGTGTCAGCCGCTCAAGTT 60.179 50.000 0.00 0.0 32.07 2.66 F
959 1270 0.554305 TACTCCCCGCTATGACCAGA 59.446 55.000 0.00 0.0 0.00 3.86 F
960 1271 0.757188 ACTCCCCGCTATGACCAGAG 60.757 60.000 0.00 0.0 0.00 3.35 F
964 1275 0.827925 CCCGCTATGACCAGAGGCTA 60.828 60.000 0.00 0.0 34.41 3.93 F
966 1277 1.000283 CCGCTATGACCAGAGGCTAAG 60.000 57.143 0.00 0.0 0.00 2.18 F
1170 1499 1.048724 CCATCGCCAACTCCCTCCTA 61.049 60.000 0.00 0.0 0.00 2.94 F
2079 2414 1.434555 TGGAAGTTTGCGGTGATACG 58.565 50.000 0.00 0.0 0.00 3.06 F
3634 7247 1.144057 GGCGTGCCTGTACAGCTAT 59.856 57.895 17.86 0.0 0.00 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 2283 0.662374 GTCATATACACCCGTCGGCG 60.662 60.000 0.29 0.29 37.95 6.46 R
2086 2421 0.786435 ATAATCTCCCCAATGGCCCC 59.214 55.000 0.00 0.00 0.00 5.80 R
2502 3040 0.826256 ACCGAAAAAGGCTTCCACCC 60.826 55.000 0.00 0.00 33.69 4.61 R
2503 3041 1.900245 TACCGAAAAAGGCTTCCACC 58.100 50.000 0.00 0.00 33.69 4.61 R
2504 3042 3.254903 ACATTACCGAAAAAGGCTTCCAC 59.745 43.478 0.00 0.00 33.69 4.02 R
2505 3043 3.492337 ACATTACCGAAAAAGGCTTCCA 58.508 40.909 0.00 0.00 33.69 3.53 R
3017 3881 2.166821 TTGGCATGGCAAATGTTGAC 57.833 45.000 30.32 0.00 39.85 3.18 R
3931 7549 1.079543 CAGCCGTGTCCTCTTCCAG 60.080 63.158 0.00 0.00 0.00 3.86 R
4799 8444 0.454196 AGAACACAAACAACGTGCCC 59.546 50.000 0.00 0.00 37.93 5.36 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
272 273 5.220989 GCATGATTAAGCACATCTCACACAT 60.221 40.000 0.00 0.00 0.00 3.21
812 1123 1.897802 GACCGAAGTGAACCCCTAGAA 59.102 52.381 0.00 0.00 0.00 2.10
827 1138 9.268282 GAACCCCTAGAATAAGTATATGGATGA 57.732 37.037 0.00 0.00 0.00 2.92
868 1179 3.113260 ACAGTGACTAAAGTGTCAGCC 57.887 47.619 0.00 0.00 46.09 4.85
869 1180 2.061773 CAGTGACTAAAGTGTCAGCCG 58.938 52.381 0.00 0.00 46.09 5.52
870 1181 0.790814 GTGACTAAAGTGTCAGCCGC 59.209 55.000 0.00 0.00 46.09 6.53
871 1182 0.679505 TGACTAAAGTGTCAGCCGCT 59.320 50.000 0.00 0.00 41.43 5.52
872 1183 1.336887 TGACTAAAGTGTCAGCCGCTC 60.337 52.381 0.00 0.00 41.43 5.03
873 1184 0.679505 ACTAAAGTGTCAGCCGCTCA 59.320 50.000 0.00 0.00 32.07 4.26
874 1185 1.070134 ACTAAAGTGTCAGCCGCTCAA 59.930 47.619 0.00 0.00 32.07 3.02
875 1186 1.728971 CTAAAGTGTCAGCCGCTCAAG 59.271 52.381 0.00 0.00 32.07 3.02
876 1187 0.179045 AAAGTGTCAGCCGCTCAAGT 60.179 50.000 0.00 0.00 32.07 3.16
877 1188 0.179045 AAGTGTCAGCCGCTCAAGTT 60.179 50.000 0.00 0.00 32.07 2.66
878 1189 0.179045 AGTGTCAGCCGCTCAAGTTT 60.179 50.000 0.00 0.00 0.00 2.66
879 1190 0.663153 GTGTCAGCCGCTCAAGTTTT 59.337 50.000 0.00 0.00 0.00 2.43
880 1191 0.662619 TGTCAGCCGCTCAAGTTTTG 59.337 50.000 0.00 0.00 0.00 2.44
881 1192 0.944386 GTCAGCCGCTCAAGTTTTGA 59.056 50.000 0.00 0.00 38.17 2.69
922 1233 9.651913 TTTTCTCATAAATTAAATTGCCCTGAC 57.348 29.630 0.00 0.00 0.00 3.51
923 1234 7.953005 TCTCATAAATTAAATTGCCCTGACA 57.047 32.000 0.00 0.00 0.00 3.58
924 1235 7.771183 TCTCATAAATTAAATTGCCCTGACAC 58.229 34.615 0.00 0.00 0.00 3.67
925 1236 7.615365 TCTCATAAATTAAATTGCCCTGACACT 59.385 33.333 0.00 0.00 0.00 3.55
926 1237 8.815565 TCATAAATTAAATTGCCCTGACACTA 57.184 30.769 0.00 0.00 0.00 2.74
927 1238 9.249053 TCATAAATTAAATTGCCCTGACACTAA 57.751 29.630 0.00 0.00 0.00 2.24
931 1242 9.474313 AAATTAAATTGCCCTGACACTAATAGA 57.526 29.630 0.00 0.00 0.00 1.98
932 1243 8.682936 ATTAAATTGCCCTGACACTAATAGAG 57.317 34.615 0.00 0.00 0.00 2.43
933 1244 5.700402 AATTGCCCTGACACTAATAGAGT 57.300 39.130 0.00 0.00 39.82 3.24
934 1245 6.808321 AATTGCCCTGACACTAATAGAGTA 57.192 37.500 0.00 0.00 35.64 2.59
935 1246 7.380423 AATTGCCCTGACACTAATAGAGTAT 57.620 36.000 0.00 0.00 35.64 2.12
936 1247 8.492415 AATTGCCCTGACACTAATAGAGTATA 57.508 34.615 0.00 0.00 35.64 1.47
937 1248 7.907841 TTGCCCTGACACTAATAGAGTATAA 57.092 36.000 0.00 0.00 35.64 0.98
938 1249 7.526142 TGCCCTGACACTAATAGAGTATAAG 57.474 40.000 0.00 0.00 35.64 1.73
939 1250 7.067421 TGCCCTGACACTAATAGAGTATAAGT 58.933 38.462 0.00 0.00 35.64 2.24
940 1251 7.563924 TGCCCTGACACTAATAGAGTATAAGTT 59.436 37.037 0.00 0.00 35.64 2.66
941 1252 9.075678 GCCCTGACACTAATAGAGTATAAGTTA 57.924 37.037 0.00 0.00 35.64 2.24
947 1258 9.585369 ACACTAATAGAGTATAAGTTACTCCCC 57.415 37.037 8.71 0.00 43.61 4.81
948 1259 8.728833 CACTAATAGAGTATAAGTTACTCCCCG 58.271 40.741 8.71 0.00 43.61 5.73
949 1260 6.587206 AATAGAGTATAAGTTACTCCCCGC 57.413 41.667 8.71 0.00 43.61 6.13
950 1261 4.181799 AGAGTATAAGTTACTCCCCGCT 57.818 45.455 8.71 0.00 43.61 5.52
951 1262 5.316158 AGAGTATAAGTTACTCCCCGCTA 57.684 43.478 8.71 0.00 43.61 4.26
952 1263 5.890049 AGAGTATAAGTTACTCCCCGCTAT 58.110 41.667 8.71 0.00 43.61 2.97
953 1264 5.711036 AGAGTATAAGTTACTCCCCGCTATG 59.289 44.000 8.71 0.00 43.61 2.23
954 1265 5.638133 AGTATAAGTTACTCCCCGCTATGA 58.362 41.667 0.00 0.00 0.00 2.15
955 1266 4.868314 ATAAGTTACTCCCCGCTATGAC 57.132 45.455 0.00 0.00 0.00 3.06
956 1267 1.411041 AGTTACTCCCCGCTATGACC 58.589 55.000 0.00 0.00 0.00 4.02
957 1268 1.117150 GTTACTCCCCGCTATGACCA 58.883 55.000 0.00 0.00 0.00 4.02
958 1269 1.068741 GTTACTCCCCGCTATGACCAG 59.931 57.143 0.00 0.00 0.00 4.00
959 1270 0.554305 TACTCCCCGCTATGACCAGA 59.446 55.000 0.00 0.00 0.00 3.86
960 1271 0.757188 ACTCCCCGCTATGACCAGAG 60.757 60.000 0.00 0.00 0.00 3.35
961 1272 1.457643 TCCCCGCTATGACCAGAGG 60.458 63.158 0.00 0.00 35.43 3.69
962 1273 2.423446 CCCGCTATGACCAGAGGC 59.577 66.667 0.00 0.00 34.41 4.70
963 1274 2.136878 CCCGCTATGACCAGAGGCT 61.137 63.158 0.00 0.00 34.41 4.58
964 1275 0.827925 CCCGCTATGACCAGAGGCTA 60.828 60.000 0.00 0.00 34.41 3.93
965 1276 1.040646 CCGCTATGACCAGAGGCTAA 58.959 55.000 0.00 0.00 0.00 3.09
966 1277 1.000283 CCGCTATGACCAGAGGCTAAG 60.000 57.143 0.00 0.00 0.00 2.18
967 1278 1.957177 CGCTATGACCAGAGGCTAAGA 59.043 52.381 0.00 0.00 0.00 2.10
968 1279 2.362397 CGCTATGACCAGAGGCTAAGAA 59.638 50.000 0.00 0.00 0.00 2.52
969 1280 3.551863 CGCTATGACCAGAGGCTAAGAAG 60.552 52.174 0.00 0.00 0.00 2.85
970 1281 3.639094 GCTATGACCAGAGGCTAAGAAGA 59.361 47.826 0.00 0.00 0.00 2.87
971 1282 4.261994 GCTATGACCAGAGGCTAAGAAGAG 60.262 50.000 0.00 0.00 0.00 2.85
972 1283 2.461695 TGACCAGAGGCTAAGAAGAGG 58.538 52.381 0.00 0.00 0.00 3.69
1019 1341 2.585247 GACGTGTCCCTATGCGGC 60.585 66.667 0.00 0.00 0.00 6.53
1170 1499 1.048724 CCATCGCCAACTCCCTCCTA 61.049 60.000 0.00 0.00 0.00 2.94
1305 1634 3.966543 CACCGGTTCCAGGGCCTT 61.967 66.667 2.97 0.00 0.00 4.35
1516 1845 3.834799 GGGCTACCGAGGACGTGG 61.835 72.222 0.00 0.00 37.88 4.94
1596 1925 4.808238 GACGACGCGGACTCGGAC 62.808 72.222 19.67 10.72 35.37 4.79
1610 1939 3.408851 GGACGGTTCGTGCGTTCC 61.409 66.667 0.00 0.00 41.37 3.62
1613 1942 1.883725 GACGGTTCGTGCGTTCCTTC 61.884 60.000 0.00 0.00 41.37 3.46
1650 1982 7.330208 CCTTTCGTCTTCGTAAATCCTTCTTTA 59.670 37.037 0.00 0.00 38.33 1.85
1651 1983 7.572502 TTCGTCTTCGTAAATCCTTCTTTAC 57.427 36.000 0.00 0.00 37.94 2.01
1678 2010 8.827832 ATCTTAATTGATTTGTGATTCTCCCA 57.172 30.769 0.00 0.00 0.00 4.37
1679 2011 8.827832 TCTTAATTGATTTGTGATTCTCCCAT 57.172 30.769 0.00 0.00 0.00 4.00
1680 2012 8.689061 TCTTAATTGATTTGTGATTCTCCCATG 58.311 33.333 0.00 0.00 0.00 3.66
1681 2013 6.862469 AATTGATTTGTGATTCTCCCATGT 57.138 33.333 0.00 0.00 0.00 3.21
2010 2345 5.070446 TCAGATTAGTTGTCACTTGTCAGGT 59.930 40.000 0.00 0.00 34.06 4.00
2013 2348 1.837439 AGTTGTCACTTGTCAGGTGGA 59.163 47.619 14.49 0.11 35.61 4.02
2068 2403 7.016072 TGTTGTATTTGGGAATCATGGAAGTTT 59.984 33.333 0.00 0.00 0.00 2.66
2076 2411 2.198827 TCATGGAAGTTTGCGGTGAT 57.801 45.000 0.00 0.00 0.00 3.06
2079 2414 1.434555 TGGAAGTTTGCGGTGATACG 58.565 50.000 0.00 0.00 0.00 3.06
2087 2422 3.731136 CGGTGATACGCCATTGGG 58.269 61.111 4.53 0.00 32.88 4.12
2088 2423 1.891919 CGGTGATACGCCATTGGGG 60.892 63.158 17.57 17.57 41.67 4.96
2117 2452 5.505780 TGGGGAGATTATGTTGTTACCTTG 58.494 41.667 0.00 0.00 0.00 3.61
2118 2453 5.014755 TGGGGAGATTATGTTGTTACCTTGT 59.985 40.000 0.00 0.00 0.00 3.16
2119 2454 5.949952 GGGGAGATTATGTTGTTACCTTGTT 59.050 40.000 0.00 0.00 0.00 2.83
2120 2455 6.436218 GGGGAGATTATGTTGTTACCTTGTTT 59.564 38.462 0.00 0.00 0.00 2.83
2121 2456 7.039293 GGGGAGATTATGTTGTTACCTTGTTTT 60.039 37.037 0.00 0.00 0.00 2.43
2122 2457 8.364894 GGGAGATTATGTTGTTACCTTGTTTTT 58.635 33.333 0.00 0.00 0.00 1.94
2176 2511 4.291540 TGGCATTTGATTGTCTAATCGC 57.708 40.909 0.00 0.00 44.55 4.58
2184 2519 3.119280 TGATTGTCTAATCGCCGTCTCAA 60.119 43.478 0.00 0.00 44.55 3.02
2185 2520 2.561733 TGTCTAATCGCCGTCTCAAG 57.438 50.000 0.00 0.00 0.00 3.02
2379 2917 6.688073 ATACTACTCCCTTGTCCCATAATG 57.312 41.667 0.00 0.00 0.00 1.90
2383 2921 4.631234 ACTCCCTTGTCCCATAATGTAGA 58.369 43.478 0.00 0.00 0.00 2.59
2504 3042 9.546909 CGAAAATATATTTCAAGATGAATCGGG 57.453 33.333 11.08 0.00 36.11 5.14
2507 3045 7.928307 ATATATTTCAAGATGAATCGGGTGG 57.072 36.000 0.00 0.00 36.11 4.61
2508 3046 3.712016 TTTCAAGATGAATCGGGTGGA 57.288 42.857 0.00 0.00 36.11 4.02
2509 3047 3.712016 TTCAAGATGAATCGGGTGGAA 57.288 42.857 0.00 0.00 30.26 3.53
2510 3048 3.266510 TCAAGATGAATCGGGTGGAAG 57.733 47.619 0.00 0.00 0.00 3.46
2511 3049 1.672881 CAAGATGAATCGGGTGGAAGC 59.327 52.381 0.00 0.00 0.00 3.86
2694 3232 2.297597 GTGATCGAGTGGCTAGCCTAAT 59.702 50.000 33.07 19.13 36.94 1.73
2795 3659 5.993055 TCCATGTCTAAAATGAGCAGATGA 58.007 37.500 0.00 0.00 0.00 2.92
3017 3881 2.856222 AGGAGTCTTCTTGGTTTGCTG 58.144 47.619 0.00 0.00 0.00 4.41
3030 3894 2.548875 GTTTGCTGTCAACATTTGCCA 58.451 42.857 0.00 0.00 30.75 4.92
3076 3940 6.875948 AATGTTTGGCTTCAAAATTTACCC 57.124 33.333 0.00 0.00 41.43 3.69
3089 3953 8.507524 TCAAAATTTACCCGTTTGGAAATTTT 57.492 26.923 14.56 14.56 44.16 1.82
3277 4141 5.648178 TGCTCATGATTGCACAATAAAGT 57.352 34.783 5.58 0.00 33.94 2.66
3356 4226 3.376546 GCACAGATTTTGGAAGCTAGAGG 59.623 47.826 0.00 0.00 28.70 3.69
3383 4260 3.295785 TGTCACAAAATTCGCAACATCG 58.704 40.909 0.00 0.00 0.00 3.84
3434 4317 3.686726 GTGGCTCTGACTTTCAGTAATGG 59.313 47.826 3.19 0.00 44.58 3.16
3633 7246 2.279810 TGGCGTGCCTGTACAGCTA 61.280 57.895 17.86 5.29 36.94 3.32
3634 7247 1.144057 GGCGTGCCTGTACAGCTAT 59.856 57.895 17.86 0.00 0.00 2.97
3667 7280 2.496871 AGAGATGCCACTGAGTTCTCAG 59.503 50.000 23.12 23.12 43.03 3.35
3669 7282 2.233431 AGATGCCACTGAGTTCTCAGTC 59.767 50.000 26.29 18.65 46.96 3.51
3670 7283 1.709578 TGCCACTGAGTTCTCAGTCT 58.290 50.000 26.29 9.22 46.96 3.24
3671 7284 1.615883 TGCCACTGAGTTCTCAGTCTC 59.384 52.381 26.29 20.93 46.96 3.36
3672 7285 1.615883 GCCACTGAGTTCTCAGTCTCA 59.384 52.381 26.29 5.76 46.96 3.27
3686 7299 3.054875 TCAGTCTCACAATCAAGGATGGG 60.055 47.826 0.00 0.00 0.00 4.00
3718 7331 5.407407 TCACACTCCCTCTAAAGAACATC 57.593 43.478 0.00 0.00 0.00 3.06
3725 7338 3.370953 CCCTCTAAAGAACATCCCACTGG 60.371 52.174 0.00 0.00 0.00 4.00
3847 7465 6.414732 TCGGAAGAAGATCAACATAAATGGT 58.585 36.000 0.00 0.00 37.03 3.55
3884 7502 2.412065 GCGAGCAATCAAGAGTTGTCAC 60.412 50.000 0.00 0.00 0.00 3.67
3905 7523 4.094887 CACTCAAAAGTCCCATAACGATGG 59.905 45.833 0.00 0.00 42.45 3.51
3920 7538 1.804748 CGATGGCACTGATGATGATGG 59.195 52.381 0.00 0.00 0.00 3.51
3931 7549 2.297698 TGATGATGGGGATGAATGGC 57.702 50.000 0.00 0.00 0.00 4.40
3947 7565 2.435059 GCTGGAAGAGGACACGGC 60.435 66.667 0.00 0.00 34.07 5.68
4008 7634 8.359875 ACGATGAGGATATATCTTTCAGTGAT 57.640 34.615 18.61 8.11 0.00 3.06
4081 7717 0.868406 CGTCTTGGTGCTTCTGGTTC 59.132 55.000 0.00 0.00 0.00 3.62
4085 7721 1.532868 CTTGGTGCTTCTGGTTCGAAG 59.467 52.381 0.00 0.00 42.52 3.79
4103 7739 4.461431 TCGAAGCGATATGTATATGTGGGT 59.539 41.667 0.00 0.00 0.00 4.51
4183 7819 2.373169 AGGATTGTTCACCTTCTGCTCA 59.627 45.455 0.00 0.00 31.95 4.26
4210 7846 0.598065 GTGCCGCCAAGATCAGTTTT 59.402 50.000 0.00 0.00 0.00 2.43
4220 7856 3.963428 AGATCAGTTTTGCGGTCTAGT 57.037 42.857 0.00 0.00 0.00 2.57
4237 7873 0.846693 AGTTCTCCCTTGTGGCAACT 59.153 50.000 0.00 0.00 34.04 3.16
4238 7874 2.054799 AGTTCTCCCTTGTGGCAACTA 58.945 47.619 0.00 0.00 36.00 2.24
4300 7942 3.766591 TGTGGTTGTTTGGATCAACACTT 59.233 39.130 10.21 0.00 44.53 3.16
4349 7991 3.801698 ACAATGATGATGGGAACTCGAG 58.198 45.455 11.84 11.84 0.00 4.04
4368 8010 6.127814 ACTCGAGTATTCTTATGTTTCGGTGA 60.128 38.462 18.46 0.00 0.00 4.02
4369 8011 6.623486 TCGAGTATTCTTATGTTTCGGTGAA 58.377 36.000 0.00 0.00 0.00 3.18
4370 8012 7.092079 TCGAGTATTCTTATGTTTCGGTGAAA 58.908 34.615 0.00 0.00 0.00 2.69
4475 8117 2.030946 GCCAAGTCTGCGATAACATGAC 59.969 50.000 0.00 0.00 0.00 3.06
4517 8159 0.779997 AGCAGGGACCACATTTTCCT 59.220 50.000 0.00 0.00 31.90 3.36
4518 8160 1.147817 AGCAGGGACCACATTTTCCTT 59.852 47.619 0.00 0.00 31.90 3.36
4632 8274 2.016318 TGCGGCTTGATCCATAGTTTG 58.984 47.619 0.00 0.00 0.00 2.93
4694 8339 2.817665 TGATTTTGGTGCATCATGGGA 58.182 42.857 0.00 0.00 0.00 4.37
4696 8341 3.775866 TGATTTTGGTGCATCATGGGAAT 59.224 39.130 0.00 0.00 0.00 3.01
4721 8366 3.406764 GCTGTGTGTCTTCTTTCTGGAT 58.593 45.455 0.00 0.00 0.00 3.41
4790 8435 8.629158 TGTTCTGTTAGTGATGCAAGTTTAAAT 58.371 29.630 0.00 0.00 0.00 1.40
4797 8442 4.627035 GTGATGCAAGTTTAAATTCCAGGC 59.373 41.667 0.00 0.00 0.00 4.85
4798 8443 3.676291 TGCAAGTTTAAATTCCAGGCC 57.324 42.857 0.00 0.00 0.00 5.19
4799 8444 2.029470 TGCAAGTTTAAATTCCAGGCCG 60.029 45.455 0.00 0.00 0.00 6.13
4800 8445 2.673893 GCAAGTTTAAATTCCAGGCCGG 60.674 50.000 0.00 0.00 0.00 6.13
4801 8446 1.847328 AGTTTAAATTCCAGGCCGGG 58.153 50.000 17.03 17.03 34.36 5.73
4802 8447 0.174845 GTTTAAATTCCAGGCCGGGC 59.825 55.000 22.67 22.67 34.36 6.13
4803 8448 0.251832 TTTAAATTCCAGGCCGGGCA 60.252 50.000 31.59 6.95 34.36 5.36
4804 8449 0.968393 TTAAATTCCAGGCCGGGCAC 60.968 55.000 31.59 10.38 34.36 5.01
4818 8463 0.454196 GGGCACGTTGTTTGTGTTCT 59.546 50.000 0.00 0.00 39.53 3.01
4845 8490 7.307694 CACTTCAGCTTACAATGCTAATTTCA 58.692 34.615 0.00 0.00 38.92 2.69
4850 8495 6.862608 CAGCTTACAATGCTAATTTCACACAA 59.137 34.615 0.00 0.00 38.92 3.33
4855 8506 5.068987 ACAATGCTAATTTCACACAACTGGT 59.931 36.000 0.00 0.00 0.00 4.00
4869 8520 2.629617 CAACTGGTTGGAAGCAAGGAAT 59.370 45.455 5.64 0.00 36.95 3.01
4879 8530 4.834496 TGGAAGCAAGGAATGAAACAAGAT 59.166 37.500 0.00 0.00 0.00 2.40
4880 8531 5.305128 TGGAAGCAAGGAATGAAACAAGATT 59.695 36.000 0.00 0.00 0.00 2.40
4927 8578 1.676006 CTTCTTGGTTTGGTCTTGCGT 59.324 47.619 0.00 0.00 0.00 5.24
4928 8579 2.623878 TCTTGGTTTGGTCTTGCGTA 57.376 45.000 0.00 0.00 0.00 4.42
4974 8633 1.013596 TTGTGTTGGCTTGTCTGTCG 58.986 50.000 0.00 0.00 0.00 4.35
4975 8634 0.107897 TGTGTTGGCTTGTCTGTCGT 60.108 50.000 0.00 0.00 0.00 4.34
4978 8637 1.400142 TGTTGGCTTGTCTGTCGTTTG 59.600 47.619 0.00 0.00 0.00 2.93
4979 8638 1.400494 GTTGGCTTGTCTGTCGTTTGT 59.600 47.619 0.00 0.00 0.00 2.83
4980 8639 1.013596 TGGCTTGTCTGTCGTTTGTG 58.986 50.000 0.00 0.00 0.00 3.33
4981 8640 1.014352 GGCTTGTCTGTCGTTTGTGT 58.986 50.000 0.00 0.00 0.00 3.72
4982 8641 1.400494 GGCTTGTCTGTCGTTTGTGTT 59.600 47.619 0.00 0.00 0.00 3.32
4983 8642 2.440501 GCTTGTCTGTCGTTTGTGTTG 58.559 47.619 0.00 0.00 0.00 3.33
4985 8644 0.730265 TGTCTGTCGTTTGTGTTGGC 59.270 50.000 0.00 0.00 0.00 4.52
5008 8675 2.488836 TGACCCCTCCCTTTATTCTCC 58.511 52.381 0.00 0.00 0.00 3.71
5009 8676 2.047296 TGACCCCTCCCTTTATTCTCCT 59.953 50.000 0.00 0.00 0.00 3.69
5010 8677 3.124066 GACCCCTCCCTTTATTCTCCTT 58.876 50.000 0.00 0.00 0.00 3.36
5011 8678 3.124066 ACCCCTCCCTTTATTCTCCTTC 58.876 50.000 0.00 0.00 0.00 3.46
5012 8679 3.246908 ACCCCTCCCTTTATTCTCCTTCT 60.247 47.826 0.00 0.00 0.00 2.85
5013 8680 3.392947 CCCCTCCCTTTATTCTCCTTCTC 59.607 52.174 0.00 0.00 0.00 2.87
5015 8682 4.724293 CCCTCCCTTTATTCTCCTTCTCTT 59.276 45.833 0.00 0.00 0.00 2.85
5017 8684 6.560687 CCCTCCCTTTATTCTCCTTCTCTTAT 59.439 42.308 0.00 0.00 0.00 1.73
5018 8685 7.735321 CCCTCCCTTTATTCTCCTTCTCTTATA 59.265 40.741 0.00 0.00 0.00 0.98
5019 8686 9.332713 CCTCCCTTTATTCTCCTTCTCTTATAT 57.667 37.037 0.00 0.00 0.00 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
272 273 1.720805 GACGACCATGCATGTGTGTA 58.279 50.000 24.58 0.00 0.00 2.90
487 488 2.032860 GCCTCTGCGCCCTCAATCTA 62.033 60.000 4.18 0.00 0.00 1.98
544 545 2.331805 CTACGCCGACCATCTCCG 59.668 66.667 0.00 0.00 0.00 4.63
545 546 2.027751 GCTACGCCGACCATCTCC 59.972 66.667 0.00 0.00 0.00 3.71
546 547 2.027751 GGCTACGCCGACCATCTC 59.972 66.667 0.00 0.00 39.62 2.75
681 924 0.321122 GTTGCTGCTAGTCCTGCTGT 60.321 55.000 0.00 0.00 0.00 4.40
708 951 5.841783 AGTTAGGGGAGAAGGAATACTCATC 59.158 44.000 0.00 0.00 35.17 2.92
709 952 5.793967 AGTTAGGGGAGAAGGAATACTCAT 58.206 41.667 0.00 0.00 35.17 2.90
770 1064 7.595875 CGGTCCATATATACGATTTTGTGTACA 59.404 37.037 0.00 0.00 0.00 2.90
896 1207 9.651913 GTCAGGGCAATTTAATTTATGAGAAAA 57.348 29.630 0.00 0.00 0.00 2.29
897 1208 8.811017 TGTCAGGGCAATTTAATTTATGAGAAA 58.189 29.630 0.00 0.00 0.00 2.52
898 1209 8.250332 GTGTCAGGGCAATTTAATTTATGAGAA 58.750 33.333 0.00 0.00 0.00 2.87
899 1210 7.615365 AGTGTCAGGGCAATTTAATTTATGAGA 59.385 33.333 0.00 0.00 0.00 3.27
900 1211 7.775120 AGTGTCAGGGCAATTTAATTTATGAG 58.225 34.615 0.00 0.00 0.00 2.90
901 1212 7.716799 AGTGTCAGGGCAATTTAATTTATGA 57.283 32.000 0.00 0.00 0.00 2.15
905 1216 9.474313 TCTATTAGTGTCAGGGCAATTTAATTT 57.526 29.630 0.00 0.00 0.00 1.82
906 1217 9.125026 CTCTATTAGTGTCAGGGCAATTTAATT 57.875 33.333 0.00 0.00 0.00 1.40
907 1218 8.275040 ACTCTATTAGTGTCAGGGCAATTTAAT 58.725 33.333 0.00 0.00 36.93 1.40
908 1219 7.630082 ACTCTATTAGTGTCAGGGCAATTTAA 58.370 34.615 0.00 0.00 36.93 1.52
909 1220 7.195374 ACTCTATTAGTGTCAGGGCAATTTA 57.805 36.000 0.00 0.00 36.93 1.40
910 1221 6.067217 ACTCTATTAGTGTCAGGGCAATTT 57.933 37.500 0.00 0.00 36.93 1.82
911 1222 5.700402 ACTCTATTAGTGTCAGGGCAATT 57.300 39.130 0.00 0.00 36.93 2.32
912 1223 8.492415 TTATACTCTATTAGTGTCAGGGCAAT 57.508 34.615 1.83 0.00 39.39 3.56
913 1224 7.563924 ACTTATACTCTATTAGTGTCAGGGCAA 59.436 37.037 1.83 0.00 39.39 4.52
914 1225 7.067421 ACTTATACTCTATTAGTGTCAGGGCA 58.933 38.462 1.83 0.00 39.39 5.36
915 1226 7.527568 ACTTATACTCTATTAGTGTCAGGGC 57.472 40.000 1.83 0.00 39.39 5.19
921 1232 9.585369 GGGGAGTAACTTATACTCTATTAGTGT 57.415 37.037 13.55 4.05 42.54 3.55
922 1233 8.728833 CGGGGAGTAACTTATACTCTATTAGTG 58.271 40.741 13.55 0.00 42.54 2.74
923 1234 7.392953 GCGGGGAGTAACTTATACTCTATTAGT 59.607 40.741 13.55 0.00 42.54 2.24
924 1235 7.611079 AGCGGGGAGTAACTTATACTCTATTAG 59.389 40.741 13.55 4.94 42.54 1.73
925 1236 7.465116 AGCGGGGAGTAACTTATACTCTATTA 58.535 38.462 13.55 0.00 42.54 0.98
926 1237 6.313324 AGCGGGGAGTAACTTATACTCTATT 58.687 40.000 13.55 0.00 42.54 1.73
927 1238 5.890049 AGCGGGGAGTAACTTATACTCTAT 58.110 41.667 13.55 0.00 42.54 1.98
928 1239 5.316158 AGCGGGGAGTAACTTATACTCTA 57.684 43.478 13.55 0.00 42.54 2.43
929 1240 4.181799 AGCGGGGAGTAACTTATACTCT 57.818 45.455 13.55 0.00 42.54 3.24
930 1241 5.709164 TCATAGCGGGGAGTAACTTATACTC 59.291 44.000 7.01 7.01 42.28 2.59
931 1242 5.476254 GTCATAGCGGGGAGTAACTTATACT 59.524 44.000 0.00 0.00 0.00 2.12
932 1243 5.336293 GGTCATAGCGGGGAGTAACTTATAC 60.336 48.000 0.00 0.00 0.00 1.47
933 1244 4.768968 GGTCATAGCGGGGAGTAACTTATA 59.231 45.833 0.00 0.00 0.00 0.98
934 1245 3.577415 GGTCATAGCGGGGAGTAACTTAT 59.423 47.826 0.00 0.00 0.00 1.73
935 1246 2.961062 GGTCATAGCGGGGAGTAACTTA 59.039 50.000 0.00 0.00 0.00 2.24
936 1247 1.761198 GGTCATAGCGGGGAGTAACTT 59.239 52.381 0.00 0.00 0.00 2.66
937 1248 1.342674 TGGTCATAGCGGGGAGTAACT 60.343 52.381 0.00 0.00 0.00 2.24
938 1249 1.068741 CTGGTCATAGCGGGGAGTAAC 59.931 57.143 0.00 0.00 0.00 2.50
939 1250 1.063492 TCTGGTCATAGCGGGGAGTAA 60.063 52.381 0.00 0.00 0.00 2.24
940 1251 0.554305 TCTGGTCATAGCGGGGAGTA 59.446 55.000 0.00 0.00 0.00 2.59
941 1252 0.757188 CTCTGGTCATAGCGGGGAGT 60.757 60.000 0.00 0.00 0.00 3.85
942 1253 1.467678 CCTCTGGTCATAGCGGGGAG 61.468 65.000 0.00 0.00 0.00 4.30
943 1254 1.457643 CCTCTGGTCATAGCGGGGA 60.458 63.158 0.00 0.00 0.00 4.81
944 1255 3.142393 CCTCTGGTCATAGCGGGG 58.858 66.667 0.00 0.00 0.00 5.73
945 1256 0.827925 TAGCCTCTGGTCATAGCGGG 60.828 60.000 0.00 0.00 0.00 6.13
946 1257 1.000283 CTTAGCCTCTGGTCATAGCGG 60.000 57.143 0.00 0.00 0.00 5.52
947 1258 1.957177 TCTTAGCCTCTGGTCATAGCG 59.043 52.381 0.00 0.00 0.00 4.26
948 1259 3.639094 TCTTCTTAGCCTCTGGTCATAGC 59.361 47.826 0.00 0.00 0.00 2.97
949 1260 4.280677 CCTCTTCTTAGCCTCTGGTCATAG 59.719 50.000 0.00 0.00 0.00 2.23
950 1261 4.079154 TCCTCTTCTTAGCCTCTGGTCATA 60.079 45.833 0.00 0.00 0.00 2.15
951 1262 3.037549 CCTCTTCTTAGCCTCTGGTCAT 58.962 50.000 0.00 0.00 0.00 3.06
952 1263 2.043115 TCCTCTTCTTAGCCTCTGGTCA 59.957 50.000 0.00 0.00 0.00 4.02
953 1264 2.741145 TCCTCTTCTTAGCCTCTGGTC 58.259 52.381 0.00 0.00 0.00 4.02
954 1265 2.930109 TCCTCTTCTTAGCCTCTGGT 57.070 50.000 0.00 0.00 0.00 4.00
955 1266 4.559862 TTTTCCTCTTCTTAGCCTCTGG 57.440 45.455 0.00 0.00 0.00 3.86
1019 1341 4.514577 CTGTCGGGTGGCGCCTAG 62.515 72.222 29.70 15.80 37.43 3.02
1260 1589 1.021920 CGTCAGTGAGCTCCGAGAGA 61.022 60.000 12.15 0.00 0.00 3.10
1449 1778 1.668101 CCGGGTGCAGTAGAGAGGAC 61.668 65.000 0.00 0.00 0.00 3.85
1596 1925 2.851104 GAAGGAACGCACGAACCG 59.149 61.111 0.00 0.00 0.00 4.44
1610 1939 1.443802 GAAAGGTCTTGGAGGCGAAG 58.556 55.000 0.00 0.00 0.00 3.79
1613 1942 1.004918 ACGAAAGGTCTTGGAGGCG 60.005 57.895 0.00 0.00 0.00 5.52
1651 1983 9.525409 GGGAGAATCACAAATCAATTAAGATTG 57.475 33.333 0.00 0.00 39.41 2.67
1678 2010 6.804677 TCTGCACTTAAATCAACAACAACAT 58.195 32.000 0.00 0.00 0.00 2.71
1679 2011 6.201226 TCTGCACTTAAATCAACAACAACA 57.799 33.333 0.00 0.00 0.00 3.33
1680 2012 7.698836 AATCTGCACTTAAATCAACAACAAC 57.301 32.000 0.00 0.00 0.00 3.32
1681 2013 8.602328 CAAAATCTGCACTTAAATCAACAACAA 58.398 29.630 0.00 0.00 0.00 2.83
1948 2283 0.662374 GTCATATACACCCGTCGGCG 60.662 60.000 0.29 0.29 37.95 6.46
2010 2345 9.241919 CAAAATATATGCCCATAATAGTGTCCA 57.758 33.333 0.00 0.00 0.00 4.02
2044 2379 7.385267 CAAACTTCCATGATTCCCAAATACAA 58.615 34.615 0.00 0.00 0.00 2.41
2079 2414 3.481999 CCAATGGCCCCCAATGGC 61.482 66.667 0.00 0.00 45.99 4.40
2081 2416 2.769195 CCCCAATGGCCCCCAATG 60.769 66.667 0.00 0.00 36.95 2.82
2082 2417 2.957572 TCCCCAATGGCCCCCAAT 60.958 61.111 0.00 0.00 36.95 3.16
2083 2418 3.682409 CTCCCCAATGGCCCCCAA 61.682 66.667 0.00 0.00 36.95 4.12
2084 2419 4.710904 TCTCCCCAATGGCCCCCA 62.711 66.667 0.00 0.00 38.19 4.96
2085 2420 1.368268 TAATCTCCCCAATGGCCCCC 61.368 60.000 0.00 0.00 0.00 5.40
2086 2421 0.786435 ATAATCTCCCCAATGGCCCC 59.214 55.000 0.00 0.00 0.00 5.80
2087 2422 1.147817 ACATAATCTCCCCAATGGCCC 59.852 52.381 0.00 0.00 0.00 5.80
2088 2423 2.629617 CAACATAATCTCCCCAATGGCC 59.370 50.000 0.00 0.00 0.00 5.36
2123 2458 6.783708 AGGTAACAACATGGTTCTCAAAAA 57.216 33.333 0.00 0.00 41.41 1.94
2124 2459 6.153680 ACAAGGTAACAACATGGTTCTCAAAA 59.846 34.615 0.00 0.00 41.41 2.44
2125 2460 5.654650 ACAAGGTAACAACATGGTTCTCAAA 59.345 36.000 0.00 0.00 41.41 2.69
2126 2461 5.197451 ACAAGGTAACAACATGGTTCTCAA 58.803 37.500 0.00 0.00 41.41 3.02
2127 2462 4.787551 ACAAGGTAACAACATGGTTCTCA 58.212 39.130 0.00 0.00 41.41 3.27
2128 2463 5.067283 ACAACAAGGTAACAACATGGTTCTC 59.933 40.000 0.00 0.00 41.41 2.87
2129 2464 4.953579 ACAACAAGGTAACAACATGGTTCT 59.046 37.500 0.00 0.00 41.41 3.01
2130 2465 5.040635 CACAACAAGGTAACAACATGGTTC 58.959 41.667 0.00 0.00 41.41 3.62
2131 2466 4.464597 ACACAACAAGGTAACAACATGGTT 59.535 37.500 0.00 0.00 41.41 3.67
2132 2467 4.020543 ACACAACAAGGTAACAACATGGT 58.979 39.130 0.00 0.00 41.41 3.55
2133 2468 4.647424 ACACAACAAGGTAACAACATGG 57.353 40.909 0.00 0.00 41.41 3.66
2134 2469 4.803088 CCAACACAACAAGGTAACAACATG 59.197 41.667 0.00 0.00 41.41 3.21
2135 2470 4.679372 GCCAACACAACAAGGTAACAACAT 60.679 41.667 0.00 0.00 41.41 2.71
2136 2471 3.367498 GCCAACACAACAAGGTAACAACA 60.367 43.478 0.00 0.00 41.41 3.33
2137 2472 3.183754 GCCAACACAACAAGGTAACAAC 58.816 45.455 0.00 0.00 41.41 3.32
2138 2473 2.826128 TGCCAACACAACAAGGTAACAA 59.174 40.909 0.00 0.00 41.41 2.83
2139 2474 2.447443 TGCCAACACAACAAGGTAACA 58.553 42.857 0.00 0.00 41.41 2.41
2140 2475 3.726291 ATGCCAACACAACAAGGTAAC 57.274 42.857 0.00 0.00 0.00 2.50
2141 2476 4.160439 TCAAATGCCAACACAACAAGGTAA 59.840 37.500 0.00 0.00 0.00 2.85
2142 2477 3.701542 TCAAATGCCAACACAACAAGGTA 59.298 39.130 0.00 0.00 0.00 3.08
2143 2478 2.499289 TCAAATGCCAACACAACAAGGT 59.501 40.909 0.00 0.00 0.00 3.50
2144 2479 3.176552 TCAAATGCCAACACAACAAGG 57.823 42.857 0.00 0.00 0.00 3.61
2145 2480 4.571580 ACAATCAAATGCCAACACAACAAG 59.428 37.500 0.00 0.00 0.00 3.16
2176 2511 7.976734 ACAGAGTTTAAGAATATCTTGAGACGG 59.023 37.037 2.94 0.00 37.29 4.79
2379 2917 3.831715 AAGAAAACCAATGCGCTCTAC 57.168 42.857 9.73 0.00 0.00 2.59
2383 2921 4.278419 ACTCTTTAAGAAAACCAATGCGCT 59.722 37.500 9.73 0.00 0.00 5.92
2478 3016 9.546909 CCCGATTCATCTTGAAATATATTTTCG 57.453 33.333 11.92 12.42 40.12 3.46
2502 3040 0.826256 ACCGAAAAAGGCTTCCACCC 60.826 55.000 0.00 0.00 33.69 4.61
2503 3041 1.900245 TACCGAAAAAGGCTTCCACC 58.100 50.000 0.00 0.00 33.69 4.61
2504 3042 3.254903 ACATTACCGAAAAAGGCTTCCAC 59.745 43.478 0.00 0.00 33.69 4.02
2505 3043 3.492337 ACATTACCGAAAAAGGCTTCCA 58.508 40.909 0.00 0.00 33.69 3.53
2506 3044 3.504520 TGACATTACCGAAAAAGGCTTCC 59.495 43.478 0.00 0.00 33.69 3.46
2507 3045 4.759516 TGACATTACCGAAAAAGGCTTC 57.240 40.909 0.00 0.00 33.69 3.86
2508 3046 5.242838 TCAATGACATTACCGAAAAAGGCTT 59.757 36.000 0.00 0.00 33.69 4.35
2509 3047 4.764823 TCAATGACATTACCGAAAAAGGCT 59.235 37.500 0.00 0.00 33.69 4.58
2510 3048 5.054390 TCAATGACATTACCGAAAAAGGC 57.946 39.130 0.00 0.00 33.69 4.35
2511 3049 7.063308 CCAAATCAATGACATTACCGAAAAAGG 59.937 37.037 0.00 0.00 37.30 3.11
2512 3050 7.598493 ACCAAATCAATGACATTACCGAAAAAG 59.402 33.333 0.00 0.00 0.00 2.27
2513 3051 7.437748 ACCAAATCAATGACATTACCGAAAAA 58.562 30.769 0.00 0.00 0.00 1.94
2514 3052 6.987386 ACCAAATCAATGACATTACCGAAAA 58.013 32.000 0.00 0.00 0.00 2.29
2515 3053 6.582677 ACCAAATCAATGACATTACCGAAA 57.417 33.333 0.00 0.00 0.00 3.46
2516 3054 7.873719 ATACCAAATCAATGACATTACCGAA 57.126 32.000 0.00 0.00 0.00 4.30
2517 3055 7.773224 AGAATACCAAATCAATGACATTACCGA 59.227 33.333 0.00 0.00 0.00 4.69
2518 3056 7.930217 AGAATACCAAATCAATGACATTACCG 58.070 34.615 0.00 0.00 0.00 4.02
2569 3107 6.982160 TTGCTATGAAAATAGGCCATCAAT 57.018 33.333 5.01 0.00 0.00 2.57
2769 3633 5.809001 TCTGCTCATTTTAGACATGGAACT 58.191 37.500 0.00 0.00 0.00 3.01
3017 3881 2.166821 TTGGCATGGCAAATGTTGAC 57.833 45.000 30.32 0.00 39.85 3.18
3076 3940 6.092748 AGTATGCTAGCAAAATTTCCAAACG 58.907 36.000 23.54 0.00 0.00 3.60
3089 3953 3.706594 AGAGCCTGTTTAGTATGCTAGCA 59.293 43.478 21.85 21.85 31.23 3.49
3277 4141 7.506261 ACCAAAACAATGTAATACCACCAACTA 59.494 33.333 0.00 0.00 0.00 2.24
3356 4226 3.701241 TGCGAATTTTGTGACAACTTCC 58.299 40.909 0.00 0.59 0.00 3.46
3633 7246 3.181445 TGGCATCTCTTAATACCGGCAAT 60.181 43.478 0.00 0.00 0.00 3.56
3634 7247 2.171659 TGGCATCTCTTAATACCGGCAA 59.828 45.455 0.00 0.00 0.00 4.52
3667 7280 3.198635 TCTCCCATCCTTGATTGTGAGAC 59.801 47.826 0.00 0.00 0.00 3.36
3668 7281 3.453868 TCTCCCATCCTTGATTGTGAGA 58.546 45.455 0.00 0.00 0.00 3.27
3669 7282 3.920231 TCTCCCATCCTTGATTGTGAG 57.080 47.619 0.00 0.00 0.00 3.51
3670 7283 4.335416 GTTTCTCCCATCCTTGATTGTGA 58.665 43.478 0.00 0.00 0.00 3.58
3671 7284 3.445096 GGTTTCTCCCATCCTTGATTGTG 59.555 47.826 0.00 0.00 0.00 3.33
3672 7285 3.075882 TGGTTTCTCCCATCCTTGATTGT 59.924 43.478 0.00 0.00 34.77 2.71
3686 7299 3.008485 AGAGGGAGTGTGAATGGTTTCTC 59.992 47.826 0.00 0.00 32.78 2.87
3725 7338 5.877012 TCTTCAATGCTAGATTGTGAGAACC 59.123 40.000 0.00 0.00 0.00 3.62
3905 7523 2.160205 CATCCCCATCATCATCAGTGC 58.840 52.381 0.00 0.00 0.00 4.40
3907 7525 4.508584 CCATTCATCCCCATCATCATCAGT 60.509 45.833 0.00 0.00 0.00 3.41
3920 7538 1.478288 CCTCTTCCAGCCATTCATCCC 60.478 57.143 0.00 0.00 0.00 3.85
3931 7549 1.079543 CAGCCGTGTCCTCTTCCAG 60.080 63.158 0.00 0.00 0.00 3.86
3947 7565 2.743928 GCGTGCTTCCTGGACCAG 60.744 66.667 15.15 15.15 33.10 4.00
4008 7634 3.717576 ACATCAGTCATCTTCCTCCAGA 58.282 45.455 0.00 0.00 0.00 3.86
4081 7717 4.744570 ACCCACATATACATATCGCTTCG 58.255 43.478 0.00 0.00 0.00 3.79
4085 7721 4.394920 CCCAAACCCACATATACATATCGC 59.605 45.833 0.00 0.00 0.00 4.58
4103 7739 3.750371 CATACAGTGGACAGAACCCAAA 58.250 45.455 0.00 0.00 35.12 3.28
4183 7819 1.123077 TCTTGGCGGCACAGAGATAT 58.877 50.000 12.92 0.00 0.00 1.63
4210 7846 0.895530 CAAGGGAGAACTAGACCGCA 59.104 55.000 0.00 0.00 0.00 5.69
4220 7856 2.879756 GCATAGTTGCCACAAGGGAGAA 60.880 50.000 0.00 0.00 43.38 2.87
4300 7942 3.189080 CACACGCTTGATCCAAGAATCAA 59.811 43.478 10.55 0.00 43.42 2.57
4405 8047 6.741992 TGACAAGGTTTTAGACATGCTATG 57.258 37.500 0.00 0.00 0.00 2.23
4455 8097 2.282555 CGTCATGTTATCGCAGACTTGG 59.717 50.000 0.00 0.00 42.51 3.61
4517 8159 3.319405 AGAGAAAGACGCTGACTTCTGAA 59.681 43.478 0.00 0.00 0.00 3.02
4518 8160 2.887783 AGAGAAAGACGCTGACTTCTGA 59.112 45.455 0.00 0.00 0.00 3.27
4562 8204 4.686554 CCTAAAGAACAAGAGGAAGACACG 59.313 45.833 0.00 0.00 0.00 4.49
4570 8212 6.884280 ATTTGTCACCTAAAGAACAAGAGG 57.116 37.500 0.00 0.00 35.05 3.69
4694 8339 4.576463 AGAAAGAAGACACACAGCGAAATT 59.424 37.500 0.00 0.00 0.00 1.82
4696 8341 3.309682 CAGAAAGAAGACACACAGCGAAA 59.690 43.478 0.00 0.00 0.00 3.46
4752 8397 4.841246 ACTAACAGAACAGGAAGAGATGGT 59.159 41.667 0.00 0.00 0.00 3.55
4797 8442 2.025441 CACAAACAACGTGCCCGG 59.975 61.111 0.00 0.00 38.78 5.73
4798 8443 0.863957 GAACACAAACAACGTGCCCG 60.864 55.000 0.00 0.00 37.93 6.13
4799 8444 0.454196 AGAACACAAACAACGTGCCC 59.546 50.000 0.00 0.00 37.93 5.36
4800 8445 1.544686 CAGAACACAAACAACGTGCC 58.455 50.000 0.00 0.00 37.93 5.01
4801 8446 0.913876 GCAGAACACAAACAACGTGC 59.086 50.000 0.00 0.00 37.93 5.34
4802 8447 2.254918 TGCAGAACACAAACAACGTG 57.745 45.000 0.00 0.00 40.32 4.49
4818 8463 2.507484 AGCATTGTAAGCTGAAGTGCA 58.493 42.857 11.78 0.00 41.61 4.57
4845 8490 1.750778 CTTGCTTCCAACCAGTTGTGT 59.249 47.619 9.53 0.00 38.85 3.72
4850 8495 2.158475 TCATTCCTTGCTTCCAACCAGT 60.158 45.455 0.00 0.00 0.00 4.00
4855 8506 4.648762 TCTTGTTTCATTCCTTGCTTCCAA 59.351 37.500 0.00 0.00 0.00 3.53
4869 8520 5.825593 ACCTAGACCTCAATCTTGTTTCA 57.174 39.130 0.00 0.00 0.00 2.69
4879 8530 2.488347 GCCAACCAAACCTAGACCTCAA 60.488 50.000 0.00 0.00 0.00 3.02
4880 8531 1.073284 GCCAACCAAACCTAGACCTCA 59.927 52.381 0.00 0.00 0.00 3.86
4910 8561 3.074412 AGATACGCAAGACCAAACCAAG 58.926 45.455 0.00 0.00 43.62 3.61
4914 8565 2.484264 AGCAAGATACGCAAGACCAAAC 59.516 45.455 0.00 0.00 43.62 2.93
4943 8594 1.608590 CCAACACAACATCAGTCACCC 59.391 52.381 0.00 0.00 0.00 4.61
4946 8597 2.346766 AGCCAACACAACATCAGTCA 57.653 45.000 0.00 0.00 0.00 3.41
4947 8598 2.358898 ACAAGCCAACACAACATCAGTC 59.641 45.455 0.00 0.00 0.00 3.51
4974 8633 1.472552 GGGGTCAAAGCCAACACAAAC 60.473 52.381 0.00 0.00 37.54 2.93
4975 8634 0.827368 GGGGTCAAAGCCAACACAAA 59.173 50.000 0.00 0.00 37.54 2.83
4978 8637 1.179174 GGAGGGGTCAAAGCCAACAC 61.179 60.000 0.00 0.00 37.54 3.32
4979 8638 1.152830 GGAGGGGTCAAAGCCAACA 59.847 57.895 0.00 0.00 37.54 3.33
4980 8639 1.606601 GGGAGGGGTCAAAGCCAAC 60.607 63.158 0.00 0.00 37.54 3.77
4981 8640 1.368268 AAGGGAGGGGTCAAAGCCAA 61.368 55.000 0.00 0.00 37.54 4.52
4982 8641 1.368268 AAAGGGAGGGGTCAAAGCCA 61.368 55.000 0.00 0.00 37.54 4.75
4983 8642 0.702316 TAAAGGGAGGGGTCAAAGCC 59.298 55.000 0.00 0.00 34.31 4.35
4985 8644 4.527944 GAGAATAAAGGGAGGGGTCAAAG 58.472 47.826 0.00 0.00 0.00 2.77


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

AutoCloner maintained by Alex Coulton.