Multiple sequence alignment - TraesCS2A01G063800

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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 TraesCS2A01G063800 chr2A 100.000 3343 0 0 1 3343 28659360 28656018 0.000000e+00 6174.0
1 TraesCS2A01G063800 chr2A 96.684 392 13 0 2952 3343 28581274 28580883 0.000000e+00 652.0
2 TraesCS2A01G063800 chr2A 96.429 392 13 1 2952 3343 28566033 28565643 0.000000e+00 645.0
3 TraesCS2A01G063800 chr2A 95.408 392 17 1 2952 3343 28607779 28607389 1.020000e-174 623.0
4 TraesCS2A01G063800 chr2A 98.069 259 5 0 2952 3210 28562450 28562192 5.090000e-123 451.0
5 TraesCS2A01G063800 chr2A 85.714 196 22 3 829 1018 28680599 28680404 5.660000e-48 202.0
6 TraesCS2A01G063800 chr2A 91.200 125 11 0 1 125 28694875 28694751 1.590000e-38 171.0
7 TraesCS2A01G063800 chr2A 80.203 197 23 13 339 533 28693998 28693816 2.090000e-27 134.0
8 TraesCS2A01G063800 chr2A 100.000 29 0 0 2005 2033 28211504 28211476 2.000000e-03 54.7
9 TraesCS2A01G063800 chr2A 100.000 29 0 0 2005 2033 28692153 28692125 2.000000e-03 54.7
10 TraesCS2A01G063800 chr2B 91.417 1666 81 19 1326 2946 41438242 41439890 0.000000e+00 2228.0
11 TraesCS2A01G063800 chr2B 87.521 593 36 21 1 578 41437383 41437952 0.000000e+00 651.0
12 TraesCS2A01G063800 chr2B 88.710 372 24 9 169 533 41416426 41416786 3.960000e-119 438.0
13 TraesCS2A01G063800 chr2B 83.747 443 50 13 881 1314 41437998 41438427 1.870000e-107 399.0
14 TraesCS2A01G063800 chr2B 90.244 82 4 1 2646 2723 41606463 41606544 1.640000e-18 104.0
15 TraesCS2A01G063800 chr2B 82.558 86 9 2 2005 2089 41152543 41152463 1.660000e-08 71.3
16 TraesCS2A01G063800 chr2B 91.837 49 3 1 717 764 41416955 41417003 2.150000e-07 67.6
17 TraesCS2A01G063800 chr2B 96.875 32 1 0 2002 2033 41418195 41418226 2.000000e-03 54.7
18 TraesCS2A01G063800 chr2D 90.199 704 36 18 1 690 26346071 26345387 0.000000e+00 887.0
19 TraesCS2A01G063800 chr2D 91.220 615 40 5 1326 1940 26344940 26344340 0.000000e+00 824.0
20 TraesCS2A01G063800 chr2D 91.340 612 34 9 2056 2663 26344299 26343703 0.000000e+00 819.0
21 TraesCS2A01G063800 chr2D 83.367 493 59 13 829 1321 26345229 26344760 5.120000e-118 435.0
22 TraesCS2A01G063800 chr2D 86.508 378 24 18 169 533 26470714 26470351 1.120000e-104 390.0
23 TraesCS2A01G063800 chr2D 92.308 208 10 1 2748 2949 26343708 26343501 1.170000e-74 291.0
24 TraesCS2A01G063800 chr2D 84.000 200 22 4 829 1018 26422563 26422364 2.050000e-42 183.0
25 TraesCS2A01G063800 chr2D 88.800 125 13 1 1 125 26470851 26470728 5.780000e-33 152.0
26 TraesCS2A01G063800 chr2D 77.049 305 43 18 2452 2749 26468518 26468234 2.080000e-32 150.0
27 TraesCS2A01G063800 chr2D 88.182 110 9 3 2474 2583 25929827 25929722 9.740000e-26 128.0
28 TraesCS2A01G063800 chr2D 84.091 88 9 1 2002 2089 25654394 25654476 2.760000e-11 80.5
29 TraesCS2A01G063800 chr2D 91.837 49 3 1 717 764 26470188 26470140 2.150000e-07 67.6
30 TraesCS2A01G063800 chr2D 89.796 49 5 0 723 771 25926233 25926185 2.780000e-06 63.9
31 TraesCS2A01G063800 chr7D 95.000 400 15 3 2942 3341 240906437 240906831 1.020000e-174 623.0
32 TraesCS2A01G063800 chr7B 94.373 391 20 2 2952 3341 478908552 478908163 1.720000e-167 599.0
33 TraesCS2A01G063800 chrUn 87.013 385 39 10 2952 3331 82087798 82087420 1.110000e-114 424.0
34 TraesCS2A01G063800 chr5B 95.817 263 9 2 2952 3213 712205838 712206099 1.110000e-114 424.0
35 TraesCS2A01G063800 chr4B 91.696 289 22 2 3054 3341 567656161 567656448 1.870000e-107 399.0
36 TraesCS2A01G063800 chr1B 83.843 229 27 10 3111 3335 591360542 591360764 3.380000e-50 209.0
37 TraesCS2A01G063800 chr3A 78.788 297 46 15 2952 3235 619092991 619093283 2.050000e-42 183.0


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 TraesCS2A01G063800 chr2A 28656018 28659360 3342 True 6174.000000 6174 100.000000 1 3343 1 chr2A.!!$R4 3342
1 TraesCS2A01G063800 chr2A 28562192 28566033 3841 True 548.000000 645 97.249000 2952 3343 2 chr2A.!!$R6 391
2 TraesCS2A01G063800 chr2B 41437383 41439890 2507 False 1092.666667 2228 87.561667 1 2946 3 chr2B.!!$F3 2945
3 TraesCS2A01G063800 chr2D 26343501 26346071 2570 True 651.200000 887 89.686800 1 2949 5 chr2D.!!$R3 2948

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
826 903 0.109086 ACTCAGACAATCACGGCGAG 60.109 55.0 16.62 5.72 0.0 5.03 F
1307 1386 0.034059 GGAGTGGGCCGATCATACAG 59.966 60.0 9.69 0.00 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1931 2010 0.606096 TATCACCAGTCACCACACCG 59.394 55.0 0.0 0.0 0.0 4.94 R
3119 3258 1.567357 AAGCAGAGGAAGGAGGAGAC 58.433 55.0 0.0 0.0 0.0 3.36 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
35 36 1.014564 CGTCTTGGTTCCTTCTCCGC 61.015 60.000 0.00 0.00 0.00 5.54
41 42 2.048222 TTCCTTCTCCGCTGCACG 60.048 61.111 0.00 2.27 43.15 5.34
68 69 0.874607 GCCGGGCATACTGTAGTTCG 60.875 60.000 15.62 0.00 0.00 3.95
87 89 2.372074 TAGTTGATCCGCCACCCCC 61.372 63.158 0.00 0.00 0.00 5.40
89 91 2.938798 TTGATCCGCCACCCCCTT 60.939 61.111 0.00 0.00 0.00 3.95
115 117 3.446570 GCCGCTGCCATTTGAGCT 61.447 61.111 0.00 0.00 32.70 4.09
117 119 2.402388 CGCTGCCATTTGAGCTCG 59.598 61.111 9.64 0.00 32.70 5.03
118 120 2.796651 GCTGCCATTTGAGCTCGG 59.203 61.111 9.64 5.06 32.12 4.63
119 121 2.768492 GCTGCCATTTGAGCTCGGG 61.768 63.158 9.64 9.06 32.12 5.14
120 122 1.377725 CTGCCATTTGAGCTCGGGT 60.378 57.895 9.64 0.00 0.00 5.28
187 189 3.207669 CCTCCGGGACCGTAGTCG 61.208 72.222 10.17 0.00 44.54 4.18
203 205 2.374184 AGTCGATGAGGAACAGAGGAG 58.626 52.381 0.00 0.00 0.00 3.69
332 343 4.399395 CCTTGAGCGGGCAGAGCA 62.399 66.667 0.00 0.00 37.01 4.26
438 453 4.090057 GGCAGGCGCGTTCAGTTC 62.090 66.667 8.43 0.00 39.92 3.01
439 454 3.345808 GCAGGCGCGTTCAGTTCA 61.346 61.111 8.43 0.00 0.00 3.18
440 455 2.856032 CAGGCGCGTTCAGTTCAG 59.144 61.111 8.43 0.00 0.00 3.02
466 481 4.509737 GGTGGACGACCTAGCGGC 62.510 72.222 5.33 0.00 42.25 6.53
518 535 3.315949 GGTACGGCAGTGTGGGGA 61.316 66.667 0.00 0.00 0.00 4.81
521 538 0.953960 GTACGGCAGTGTGGGGAAAG 60.954 60.000 0.00 0.00 0.00 2.62
531 548 3.142174 GTGTGGGGAAAGTTCAGAGAAG 58.858 50.000 0.00 0.00 0.00 2.85
534 551 2.639839 TGGGGAAAGTTCAGAGAAGAGG 59.360 50.000 0.00 0.00 0.00 3.69
535 552 2.616765 GGGGAAAGTTCAGAGAAGAGGC 60.617 54.545 0.00 0.00 0.00 4.70
536 553 2.342179 GGAAAGTTCAGAGAAGAGGCG 58.658 52.381 0.00 0.00 0.00 5.52
537 554 2.028930 GGAAAGTTCAGAGAAGAGGCGA 60.029 50.000 0.00 0.00 0.00 5.54
539 556 1.181786 AGTTCAGAGAAGAGGCGAGG 58.818 55.000 0.00 0.00 0.00 4.63
540 557 0.174617 GTTCAGAGAAGAGGCGAGGG 59.825 60.000 0.00 0.00 0.00 4.30
575 592 2.203394 CCCATTGGCGGATCAGGG 60.203 66.667 0.00 0.00 0.00 4.45
609 626 1.299468 CCATAGCGTCGAGAGTGCC 60.299 63.158 0.00 0.00 34.89 5.01
610 627 1.729470 CCATAGCGTCGAGAGTGCCT 61.729 60.000 0.00 0.00 34.89 4.75
667 689 6.462552 TCAGTGAGATTCTGAGATAACCTG 57.537 41.667 0.00 0.00 37.07 4.00
719 741 4.988598 CGGCCAGGTGCGTTCAGT 62.989 66.667 2.24 0.00 42.61 3.41
770 831 2.593026 GGAAGTGTGGGGAAATGTCAA 58.407 47.619 0.00 0.00 0.00 3.18
810 887 3.993103 CGTTGGCGGATCGTACTC 58.007 61.111 0.00 0.00 0.00 2.59
811 888 1.138036 CGTTGGCGGATCGTACTCA 59.862 57.895 0.00 0.00 0.00 3.41
812 889 0.866061 CGTTGGCGGATCGTACTCAG 60.866 60.000 0.00 0.00 0.00 3.35
813 890 0.454600 GTTGGCGGATCGTACTCAGA 59.545 55.000 0.00 0.00 0.00 3.27
814 891 0.454600 TTGGCGGATCGTACTCAGAC 59.545 55.000 0.00 0.00 0.00 3.51
815 892 0.678684 TGGCGGATCGTACTCAGACA 60.679 55.000 0.00 0.00 0.00 3.41
816 893 0.454600 GGCGGATCGTACTCAGACAA 59.545 55.000 0.00 0.00 0.00 3.18
821 898 3.364062 GGATCGTACTCAGACAATCACG 58.636 50.000 0.00 0.00 0.00 4.35
822 899 2.913777 TCGTACTCAGACAATCACGG 57.086 50.000 0.00 0.00 0.00 4.94
823 900 1.135489 TCGTACTCAGACAATCACGGC 60.135 52.381 0.00 0.00 0.00 5.68
824 901 1.269166 GTACTCAGACAATCACGGCG 58.731 55.000 4.80 4.80 0.00 6.46
825 902 1.135489 GTACTCAGACAATCACGGCGA 60.135 52.381 16.62 0.00 0.00 5.54
826 903 0.109086 ACTCAGACAATCACGGCGAG 60.109 55.000 16.62 5.72 0.00 5.03
827 904 0.171231 CTCAGACAATCACGGCGAGA 59.829 55.000 16.62 12.96 0.00 4.04
858 935 3.133542 TGAGCATACTGAGACAATCTGGG 59.866 47.826 0.00 0.00 0.00 4.45
866 943 4.080129 ACTGAGACAATCTGGGCACAATAT 60.080 41.667 0.00 0.00 0.00 1.28
883 960 4.586001 ACAATATGGGTCCATGAGCAAATC 59.414 41.667 12.42 0.00 37.82 2.17
944 1021 4.397420 TCTGACACAATGGTTATGCAGTT 58.603 39.130 0.00 0.00 0.00 3.16
945 1022 4.455533 TCTGACACAATGGTTATGCAGTTC 59.544 41.667 0.00 0.00 0.00 3.01
946 1023 3.505680 TGACACAATGGTTATGCAGTTCC 59.494 43.478 0.00 0.00 0.00 3.62
947 1024 3.495331 ACACAATGGTTATGCAGTTCCA 58.505 40.909 8.57 8.57 0.00 3.53
1003 1082 4.068599 TCATTGTTGTTAACGGCAGATGA 58.931 39.130 0.26 10.42 0.00 2.92
1004 1083 4.517075 TCATTGTTGTTAACGGCAGATGAA 59.483 37.500 0.26 0.00 0.00 2.57
1005 1084 3.889196 TGTTGTTAACGGCAGATGAAC 57.111 42.857 0.26 0.00 0.00 3.18
1006 1085 3.206964 TGTTGTTAACGGCAGATGAACA 58.793 40.909 0.26 0.76 0.00 3.18
1007 1086 3.002862 TGTTGTTAACGGCAGATGAACAC 59.997 43.478 0.26 0.00 30.11 3.32
1008 1087 2.147958 TGTTAACGGCAGATGAACACC 58.852 47.619 0.26 0.00 0.00 4.16
1122 1201 6.312426 CGATGCTAGTTTGTTCTTCTCTGAAT 59.688 38.462 0.00 0.00 0.00 2.57
1186 1265 8.873215 ATTATCGACATTACAAAAGAGATCGT 57.127 30.769 0.00 0.00 0.00 3.73
1187 1266 6.814076 ATCGACATTACAAAAGAGATCGTC 57.186 37.500 0.00 0.00 0.00 4.20
1188 1267 5.950883 TCGACATTACAAAAGAGATCGTCT 58.049 37.500 0.00 0.00 36.94 4.18
1189 1268 5.800438 TCGACATTACAAAAGAGATCGTCTG 59.200 40.000 0.00 0.00 34.84 3.51
1190 1269 5.573282 CGACATTACAAAAGAGATCGTCTGT 59.427 40.000 0.00 0.00 34.84 3.41
1191 1270 6.237332 CGACATTACAAAAGAGATCGTCTGTC 60.237 42.308 0.00 0.00 34.84 3.51
1192 1271 6.692486 ACATTACAAAAGAGATCGTCTGTCT 58.308 36.000 0.00 0.00 34.84 3.41
1193 1272 7.827701 ACATTACAAAAGAGATCGTCTGTCTA 58.172 34.615 0.00 0.00 34.84 2.59
1194 1273 8.470805 ACATTACAAAAGAGATCGTCTGTCTAT 58.529 33.333 0.00 0.00 34.84 1.98
1195 1274 8.750416 CATTACAAAAGAGATCGTCTGTCTATG 58.250 37.037 0.00 0.00 34.84 2.23
1196 1275 5.655488 ACAAAAGAGATCGTCTGTCTATGG 58.345 41.667 0.00 0.00 34.84 2.74
1197 1276 5.186021 ACAAAAGAGATCGTCTGTCTATGGT 59.814 40.000 0.00 0.00 34.84 3.55
1198 1277 5.923733 AAAGAGATCGTCTGTCTATGGTT 57.076 39.130 0.00 0.00 34.84 3.67
1199 1278 5.923733 AAGAGATCGTCTGTCTATGGTTT 57.076 39.130 0.00 0.00 34.84 3.27
1200 1279 5.508200 AGAGATCGTCTGTCTATGGTTTC 57.492 43.478 0.00 0.00 32.57 2.78
1201 1280 4.950475 AGAGATCGTCTGTCTATGGTTTCA 59.050 41.667 0.00 0.00 32.57 2.69
1202 1281 5.067153 AGAGATCGTCTGTCTATGGTTTCAG 59.933 44.000 0.00 0.00 32.57 3.02
1203 1282 3.868757 TCGTCTGTCTATGGTTTCAGG 57.131 47.619 0.00 0.00 0.00 3.86
1204 1283 2.094182 TCGTCTGTCTATGGTTTCAGGC 60.094 50.000 0.00 0.00 0.00 4.85
1205 1284 2.093973 CGTCTGTCTATGGTTTCAGGCT 60.094 50.000 0.00 0.00 31.43 4.58
1206 1285 3.617531 CGTCTGTCTATGGTTTCAGGCTT 60.618 47.826 0.00 0.00 31.43 4.35
1207 1286 4.327680 GTCTGTCTATGGTTTCAGGCTTT 58.672 43.478 0.00 0.00 31.03 3.51
1208 1287 4.154918 GTCTGTCTATGGTTTCAGGCTTTG 59.845 45.833 0.00 0.00 31.03 2.77
1209 1288 3.420893 TGTCTATGGTTTCAGGCTTTGG 58.579 45.455 0.00 0.00 0.00 3.28
1210 1289 3.073798 TGTCTATGGTTTCAGGCTTTGGA 59.926 43.478 0.00 0.00 0.00 3.53
1211 1290 3.691609 GTCTATGGTTTCAGGCTTTGGAG 59.308 47.826 0.00 0.00 0.00 3.86
1220 1299 4.009015 GCTTTGGAGCCAAGGGAG 57.991 61.111 12.51 4.62 43.29 4.30
1221 1300 1.680314 GCTTTGGAGCCAAGGGAGG 60.680 63.158 12.51 0.00 43.29 4.30
1229 1308 4.102113 CCAAGGGAGGCCAACTTG 57.898 61.111 20.75 20.75 40.85 3.16
1230 1309 2.278330 CCAAGGGAGGCCAACTTGC 61.278 63.158 21.74 1.03 40.08 4.01
1231 1310 1.531365 CAAGGGAGGCCAACTTGCA 60.531 57.895 17.43 0.00 35.70 4.08
1232 1311 1.228675 AAGGGAGGCCAACTTGCAG 60.229 57.895 5.01 0.00 0.00 4.41
1233 1312 3.376918 GGGAGGCCAACTTGCAGC 61.377 66.667 5.01 0.00 0.00 5.25
1234 1313 2.282745 GGAGGCCAACTTGCAGCT 60.283 61.111 5.01 0.00 0.00 4.24
1235 1314 2.338785 GGAGGCCAACTTGCAGCTC 61.339 63.158 5.01 0.00 0.00 4.09
1236 1315 2.282745 AGGCCAACTTGCAGCTCC 60.283 61.111 5.01 0.00 0.00 4.70
1237 1316 3.376918 GGCCAACTTGCAGCTCCC 61.377 66.667 0.00 0.00 0.00 4.30
1238 1317 2.282745 GCCAACTTGCAGCTCCCT 60.283 61.111 0.00 0.00 0.00 4.20
1239 1318 1.002134 GCCAACTTGCAGCTCCCTA 60.002 57.895 0.00 0.00 0.00 3.53
1240 1319 0.394899 GCCAACTTGCAGCTCCCTAT 60.395 55.000 0.00 0.00 0.00 2.57
1241 1320 1.957113 GCCAACTTGCAGCTCCCTATT 60.957 52.381 0.00 0.00 0.00 1.73
1242 1321 2.450476 CCAACTTGCAGCTCCCTATTT 58.550 47.619 0.00 0.00 0.00 1.40
1243 1322 2.827921 CCAACTTGCAGCTCCCTATTTT 59.172 45.455 0.00 0.00 0.00 1.82
1244 1323 3.119352 CCAACTTGCAGCTCCCTATTTTC 60.119 47.826 0.00 0.00 0.00 2.29
1245 1324 2.728007 ACTTGCAGCTCCCTATTTTCC 58.272 47.619 0.00 0.00 0.00 3.13
1246 1325 2.310052 ACTTGCAGCTCCCTATTTTCCT 59.690 45.455 0.00 0.00 0.00 3.36
1247 1326 3.245407 ACTTGCAGCTCCCTATTTTCCTT 60.245 43.478 0.00 0.00 0.00 3.36
1248 1327 3.004752 TGCAGCTCCCTATTTTCCTTC 57.995 47.619 0.00 0.00 0.00 3.46
1249 1328 2.578021 TGCAGCTCCCTATTTTCCTTCT 59.422 45.455 0.00 0.00 0.00 2.85
1250 1329 3.780294 TGCAGCTCCCTATTTTCCTTCTA 59.220 43.478 0.00 0.00 0.00 2.10
1251 1330 4.130857 GCAGCTCCCTATTTTCCTTCTAC 58.869 47.826 0.00 0.00 0.00 2.59
1252 1331 4.141597 GCAGCTCCCTATTTTCCTTCTACT 60.142 45.833 0.00 0.00 0.00 2.57
1253 1332 5.606505 CAGCTCCCTATTTTCCTTCTACTC 58.393 45.833 0.00 0.00 0.00 2.59
1254 1333 5.129485 CAGCTCCCTATTTTCCTTCTACTCA 59.871 44.000 0.00 0.00 0.00 3.41
1255 1334 5.129650 AGCTCCCTATTTTCCTTCTACTCAC 59.870 44.000 0.00 0.00 0.00 3.51
1256 1335 5.593010 CTCCCTATTTTCCTTCTACTCACG 58.407 45.833 0.00 0.00 0.00 4.35
1257 1336 5.266788 TCCCTATTTTCCTTCTACTCACGA 58.733 41.667 0.00 0.00 0.00 4.35
1258 1337 5.897824 TCCCTATTTTCCTTCTACTCACGAT 59.102 40.000 0.00 0.00 0.00 3.73
1259 1338 5.986135 CCCTATTTTCCTTCTACTCACGATG 59.014 44.000 0.00 0.00 0.00 3.84
1260 1339 6.183360 CCCTATTTTCCTTCTACTCACGATGA 60.183 42.308 0.00 0.00 0.00 2.92
1269 1348 3.996614 TCACGATGAGACGCCAGA 58.003 55.556 0.00 0.00 36.70 3.86
1270 1349 2.493547 TCACGATGAGACGCCAGAT 58.506 52.632 0.00 0.00 36.70 2.90
1271 1350 0.101219 TCACGATGAGACGCCAGATG 59.899 55.000 0.00 0.00 36.70 2.90
1272 1351 1.227089 ACGATGAGACGCCAGATGC 60.227 57.895 0.00 0.00 36.70 3.91
1273 1352 1.953138 CGATGAGACGCCAGATGCC 60.953 63.158 0.00 0.00 36.24 4.40
1274 1353 1.144716 GATGAGACGCCAGATGCCA 59.855 57.895 0.00 0.00 36.24 4.92
1275 1354 1.153289 ATGAGACGCCAGATGCCAC 60.153 57.895 0.00 0.00 36.24 5.01
1276 1355 1.902765 ATGAGACGCCAGATGCCACA 61.903 55.000 0.00 0.00 36.24 4.17
1277 1356 1.153289 GAGACGCCAGATGCCACAT 60.153 57.895 0.00 0.00 36.24 3.21
1278 1357 1.153289 AGACGCCAGATGCCACATC 60.153 57.895 0.00 0.00 36.24 3.06
1279 1358 2.512286 ACGCCAGATGCCACATCG 60.512 61.111 2.12 0.00 36.24 3.84
1280 1359 3.945434 CGCCAGATGCCACATCGC 61.945 66.667 2.12 0.59 36.24 4.58
1281 1360 3.589881 GCCAGATGCCACATCGCC 61.590 66.667 2.12 0.00 0.00 5.54
1282 1361 2.124612 CCAGATGCCACATCGCCA 60.125 61.111 2.12 0.00 0.00 5.69
1283 1362 2.184830 CCAGATGCCACATCGCCAG 61.185 63.158 2.12 0.00 0.00 4.85
1284 1363 1.153309 CAGATGCCACATCGCCAGA 60.153 57.895 2.12 0.00 0.00 3.86
1285 1364 1.145598 AGATGCCACATCGCCAGAG 59.854 57.895 2.12 0.00 0.00 3.35
1286 1365 1.144716 GATGCCACATCGCCAGAGA 59.855 57.895 0.00 0.00 0.00 3.10
1287 1366 1.153289 ATGCCACATCGCCAGAGAC 60.153 57.895 0.00 0.00 0.00 3.36
1288 1367 2.887568 GCCACATCGCCAGAGACG 60.888 66.667 0.00 0.00 0.00 4.18
1289 1368 2.202797 CCACATCGCCAGAGACGG 60.203 66.667 0.00 0.00 0.00 4.79
1290 1369 2.710902 CCACATCGCCAGAGACGGA 61.711 63.158 0.00 0.00 0.00 4.69
1291 1370 1.226802 CACATCGCCAGAGACGGAG 60.227 63.158 0.00 0.00 0.00 4.63
1306 1385 2.133195 GGAGTGGGCCGATCATACA 58.867 57.895 9.69 0.00 0.00 2.29
1307 1386 0.034059 GGAGTGGGCCGATCATACAG 59.966 60.000 9.69 0.00 0.00 2.74
1308 1387 0.753262 GAGTGGGCCGATCATACAGT 59.247 55.000 0.00 0.00 0.00 3.55
1309 1388 0.465705 AGTGGGCCGATCATACAGTG 59.534 55.000 0.00 0.00 0.00 3.66
1310 1389 0.532862 GTGGGCCGATCATACAGTGG 60.533 60.000 0.00 0.00 0.00 4.00
1311 1390 0.689412 TGGGCCGATCATACAGTGGA 60.689 55.000 0.00 0.00 0.00 4.02
1312 1391 0.687354 GGGCCGATCATACAGTGGAT 59.313 55.000 0.00 0.00 0.00 3.41
1313 1392 1.609061 GGGCCGATCATACAGTGGATG 60.609 57.143 9.27 9.27 0.00 3.51
1314 1393 1.609061 GGCCGATCATACAGTGGATGG 60.609 57.143 15.54 0.06 0.00 3.51
1315 1394 1.070758 GCCGATCATACAGTGGATGGT 59.929 52.381 15.54 8.38 0.00 3.55
1316 1395 2.299013 GCCGATCATACAGTGGATGGTA 59.701 50.000 15.54 0.00 0.00 3.25
1317 1396 3.861131 GCCGATCATACAGTGGATGGTAC 60.861 52.174 15.54 6.41 0.00 3.34
1318 1397 3.306088 CCGATCATACAGTGGATGGTACC 60.306 52.174 15.54 4.43 0.00 3.34
1319 1398 3.320826 CGATCATACAGTGGATGGTACCA 59.679 47.826 18.99 18.99 37.63 3.25
1320 1399 4.559502 CGATCATACAGTGGATGGTACCAG 60.560 50.000 21.41 7.90 40.85 4.00
1321 1400 2.434336 TCATACAGTGGATGGTACCAGC 59.566 50.000 22.17 22.17 40.85 4.85
1322 1401 1.945580 TACAGTGGATGGTACCAGCA 58.054 50.000 30.05 14.46 40.85 4.41
1323 1402 1.064003 ACAGTGGATGGTACCAGCAA 58.936 50.000 30.05 18.53 40.85 3.91
1324 1403 1.635487 ACAGTGGATGGTACCAGCAAT 59.365 47.619 30.05 13.66 40.85 3.56
1339 1418 6.506500 ACCAGCAATACAAAAGAGATCAAG 57.493 37.500 0.00 0.00 0.00 3.02
1341 1420 7.168219 ACCAGCAATACAAAAGAGATCAAGTA 58.832 34.615 0.00 0.00 0.00 2.24
1379 1458 4.012374 ACATAGGAAACCAAGTGCATCTG 58.988 43.478 0.00 0.00 0.00 2.90
1382 1461 2.887152 AGGAAACCAAGTGCATCTGTTC 59.113 45.455 0.00 0.00 0.00 3.18
1403 1482 5.178096 TCATCTATGGTTTCAGGCTTTGA 57.822 39.130 0.00 0.00 0.00 2.69
1452 1531 1.825474 CACTGTCCTTCTACCCACGAT 59.175 52.381 0.00 0.00 0.00 3.73
1456 1535 1.409427 GTCCTTCTACCCACGATGAGG 59.591 57.143 0.00 0.00 0.00 3.86
1503 1582 1.741401 GTGCGCCACTCATACAGCA 60.741 57.895 4.18 0.00 0.00 4.41
1559 1638 3.471620 TCGCAAGAGAAGGGTGCT 58.528 55.556 0.00 0.00 45.01 4.40
1667 1746 9.504710 AGTTAATTATCTCGCACATATATCGAC 57.495 33.333 0.00 0.00 0.00 4.20
1775 1854 2.779471 CGTCGTTGGTTGTTTTAACAGC 59.221 45.455 1.36 1.36 40.50 4.40
1913 1992 4.394078 CGTCGGTCCGAACTGCGA 62.394 66.667 17.32 0.00 44.57 5.10
1931 2010 2.223135 GCGAGCAATCTCAAGGTAAAGC 60.223 50.000 0.00 0.00 39.30 3.51
1940 2019 0.591170 CAAGGTAAAGCGGTGTGGTG 59.409 55.000 0.00 0.00 0.00 4.17
1980 2061 2.037772 GAGATACCGCCATCCACTGAAT 59.962 50.000 0.00 0.00 0.00 2.57
1996 2077 6.040247 CCACTGAATGAATGAATGATGGTTG 58.960 40.000 0.00 0.00 0.00 3.77
2025 2106 6.581712 AGTTTTATGTTTGGTGCATTTGTCT 58.418 32.000 0.00 0.00 0.00 3.41
2102 2202 1.670811 GCCACTAACACCAATCCATCG 59.329 52.381 0.00 0.00 0.00 3.84
2182 2303 6.820656 AGACATGCCACTTCAAAGATAACTAG 59.179 38.462 0.00 0.00 0.00 2.57
2450 2571 1.691434 AGCTTGTATCTCCTGCCTAGC 59.309 52.381 0.00 0.00 0.00 3.42
2460 2581 1.741525 CTGCCTAGCTCTCCTGCTC 59.258 63.158 0.00 0.00 42.97 4.26
2471 2592 3.386402 GCTCTCCTGCTCCAGTTTAGTAT 59.614 47.826 0.00 0.00 0.00 2.12
2503 2624 8.243426 TGTTAAGCTAACATTATTTGAAGGCTG 58.757 33.333 0.00 0.00 43.23 4.85
2559 2681 3.261137 GTGTGGCTACCTTCCTAGTCTTT 59.739 47.826 0.00 0.00 0.00 2.52
2677 2805 2.147958 CACAAGCATGGCAAGCAAAAT 58.852 42.857 17.75 0.00 0.00 1.82
2697 2825 8.246180 GCAAAATGATCTTAAGGATGACTCAAA 58.754 33.333 1.85 0.00 34.33 2.69
2728 2857 8.429237 TTCTACATTTTGGTTCCAAATGGTAT 57.571 30.769 16.25 5.80 36.09 2.73
2729 2858 7.835822 TCTACATTTTGGTTCCAAATGGTATG 58.164 34.615 16.25 17.13 36.09 2.39
2810 2945 2.629656 GCCCATCACCAGTGCACAC 61.630 63.158 21.04 0.00 0.00 3.82
2854 2993 4.641541 TGCTGTCCAACATAAATCATCCAG 59.358 41.667 0.00 0.00 0.00 3.86
2900 3039 2.029964 TCAGAAACGACACCCGGC 59.970 61.111 0.00 0.00 43.93 6.13
2924 3063 2.821969 ACAATTGAGCCCTGAATCACAC 59.178 45.455 13.59 0.00 0.00 3.82
2949 3088 6.857964 CGATCACAAGCTTTTGACTAAACAAT 59.142 34.615 17.19 0.00 0.00 2.71
2950 3089 7.149080 CGATCACAAGCTTTTGACTAAACAATG 60.149 37.037 17.19 0.00 0.00 2.82
2961 3100 2.475111 ACTAAACAATGTGTCAGCGACG 59.525 45.455 0.00 0.00 34.95 5.12
3062 3201 2.391389 CGAAAGAGGCGGCTTGGAC 61.391 63.158 14.76 0.00 0.00 4.02
3096 3235 2.733945 GCTGGCGATCTCCCTCTC 59.266 66.667 0.00 0.00 0.00 3.20
3119 3258 2.447244 AGCGTGTTCTTCCTCTTCTG 57.553 50.000 0.00 0.00 0.00 3.02
3121 3260 2.062519 GCGTGTTCTTCCTCTTCTGTC 58.937 52.381 0.00 0.00 0.00 3.51
3139 3278 1.905894 GTCTCCTCCTTCCTCTGCTTT 59.094 52.381 0.00 0.00 0.00 3.51
3156 3295 5.249393 TCTGCTTTCTCCTCCTGTAATTCTT 59.751 40.000 0.00 0.00 0.00 2.52
3159 3298 6.118852 GCTTTCTCCTCCTGTAATTCTTGAT 58.881 40.000 0.00 0.00 0.00 2.57
3163 3302 7.020827 TCTCCTCCTGTAATTCTTGATTTGT 57.979 36.000 0.00 0.00 0.00 2.83
3299 3438 3.814268 CCGCTTGCACCCCATTCG 61.814 66.667 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 3.427233 GCGGATCAACTACGAACTACAGT 60.427 47.826 0.00 0.00 0.00 3.55
68 69 1.153229 GGGGTGGCGGATCAACTAC 60.153 63.158 0.00 0.00 0.00 2.73
87 89 2.178890 GCAGCGGCATCCAGAGAAG 61.179 63.158 3.18 0.00 40.72 2.85
89 91 4.166888 GGCAGCGGCATCCAGAGA 62.167 66.667 11.88 0.00 43.71 3.10
187 189 1.134551 GTGCCTCCTCTGTTCCTCATC 60.135 57.143 0.00 0.00 0.00 2.92
422 437 3.300667 CTGAACTGAACGCGCCTGC 62.301 63.158 5.73 0.00 37.91 4.85
436 451 2.144078 TCCACCTTCCCGCACTGAA 61.144 57.895 0.00 0.00 0.00 3.02
437 452 2.525629 TCCACCTTCCCGCACTGA 60.526 61.111 0.00 0.00 0.00 3.41
438 453 2.358737 GTCCACCTTCCCGCACTG 60.359 66.667 0.00 0.00 0.00 3.66
439 454 4.003788 CGTCCACCTTCCCGCACT 62.004 66.667 0.00 0.00 0.00 4.40
440 455 3.998672 TCGTCCACCTTCCCGCAC 61.999 66.667 0.00 0.00 0.00 5.34
511 527 3.045634 TCTTCTCTGAACTTTCCCCACA 58.954 45.455 0.00 0.00 0.00 4.17
518 535 2.028567 CCTCGCCTCTTCTCTGAACTTT 60.029 50.000 0.00 0.00 0.00 2.66
521 538 0.174617 CCCTCGCCTCTTCTCTGAAC 59.825 60.000 0.00 0.00 0.00 3.18
589 606 0.100682 GCACTCTCGACGCTATGGAA 59.899 55.000 0.00 0.00 0.00 3.53
704 726 3.357079 CCACTGAACGCACCTGGC 61.357 66.667 0.00 0.00 39.90 4.85
705 727 3.357079 GCCACTGAACGCACCTGG 61.357 66.667 0.00 0.00 0.00 4.45
706 728 3.357079 GGCCACTGAACGCACCTG 61.357 66.667 0.00 0.00 0.00 4.00
707 729 3.832237 CTGGCCACTGAACGCACCT 62.832 63.158 0.00 0.00 0.00 4.00
756 817 1.584495 GCCGTTGACATTTCCCCAC 59.416 57.895 0.00 0.00 0.00 4.61
805 882 1.135489 TCGCCGTGATTGTCTGAGTAC 60.135 52.381 0.00 0.00 0.00 2.73
806 883 1.132453 CTCGCCGTGATTGTCTGAGTA 59.868 52.381 0.00 0.00 0.00 2.59
807 884 0.109086 CTCGCCGTGATTGTCTGAGT 60.109 55.000 0.00 0.00 0.00 3.41
808 885 0.171231 TCTCGCCGTGATTGTCTGAG 59.829 55.000 0.00 0.00 0.00 3.35
810 887 0.109086 ACTCTCGCCGTGATTGTCTG 60.109 55.000 0.00 0.00 0.00 3.51
811 888 0.109086 CACTCTCGCCGTGATTGTCT 60.109 55.000 0.00 0.00 34.35 3.41
812 889 1.687494 GCACTCTCGCCGTGATTGTC 61.687 60.000 8.05 0.00 34.35 3.18
813 890 1.738099 GCACTCTCGCCGTGATTGT 60.738 57.895 8.05 0.00 34.35 2.71
814 891 1.416813 GAGCACTCTCGCCGTGATTG 61.417 60.000 2.62 2.62 34.35 2.67
815 892 1.153745 GAGCACTCTCGCCGTGATT 60.154 57.895 0.00 0.00 34.35 2.57
816 893 2.276863 CTGAGCACTCTCGCCGTGAT 62.277 60.000 0.00 0.00 42.26 3.06
821 898 1.153862 CTCACTGAGCACTCTCGCC 60.154 63.158 0.00 0.00 42.26 5.54
822 899 4.474530 CTCACTGAGCACTCTCGC 57.525 61.111 0.00 0.00 42.26 5.03
858 935 1.610522 GCTCATGGACCCATATTGTGC 59.389 52.381 0.55 0.90 34.91 4.57
866 943 1.341285 CCAGATTTGCTCATGGACCCA 60.341 52.381 0.00 0.00 34.60 4.51
883 960 9.499479 AATAGAACTATGATCACATTAAGCCAG 57.501 33.333 0.00 0.00 37.87 4.85
992 1069 0.250124 TTCGGTGTTCATCTGCCGTT 60.250 50.000 0.00 0.00 44.07 4.44
1006 1085 5.977725 CGTCATACACTGAATAGAATTCGGT 59.022 40.000 8.05 8.05 38.47 4.69
1007 1086 5.977725 ACGTCATACACTGAATAGAATTCGG 59.022 40.000 0.00 6.87 35.07 4.30
1008 1087 6.560433 GCACGTCATACACTGAATAGAATTCG 60.560 42.308 0.00 0.00 35.07 3.34
1082 1161 0.734889 CATCGCACCTTCCCAACATC 59.265 55.000 0.00 0.00 0.00 3.06
1160 1239 9.961265 ACGATCTCTTTTGTAATGTCGATAATA 57.039 29.630 0.00 0.00 0.00 0.98
1161 1240 8.873215 ACGATCTCTTTTGTAATGTCGATAAT 57.127 30.769 0.00 0.00 0.00 1.28
1162 1241 8.188799 AGACGATCTCTTTTGTAATGTCGATAA 58.811 33.333 0.00 0.00 0.00 1.75
1163 1242 7.644157 CAGACGATCTCTTTTGTAATGTCGATA 59.356 37.037 0.00 0.00 0.00 2.92
1164 1243 6.473778 CAGACGATCTCTTTTGTAATGTCGAT 59.526 38.462 0.00 0.00 0.00 3.59
1165 1244 5.800438 CAGACGATCTCTTTTGTAATGTCGA 59.200 40.000 0.00 0.00 0.00 4.20
1166 1245 5.573282 ACAGACGATCTCTTTTGTAATGTCG 59.427 40.000 0.00 0.00 0.00 4.35
1167 1246 6.809196 AGACAGACGATCTCTTTTGTAATGTC 59.191 38.462 0.00 0.00 33.74 3.06
1168 1247 6.692486 AGACAGACGATCTCTTTTGTAATGT 58.308 36.000 0.00 0.00 0.00 2.71
1169 1248 8.750416 CATAGACAGACGATCTCTTTTGTAATG 58.250 37.037 0.00 0.00 0.00 1.90
1170 1249 7.923344 CCATAGACAGACGATCTCTTTTGTAAT 59.077 37.037 0.00 0.00 0.00 1.89
1171 1250 7.093902 ACCATAGACAGACGATCTCTTTTGTAA 60.094 37.037 0.00 0.00 0.00 2.41
1172 1251 6.377429 ACCATAGACAGACGATCTCTTTTGTA 59.623 38.462 0.00 0.00 0.00 2.41
1173 1252 5.186021 ACCATAGACAGACGATCTCTTTTGT 59.814 40.000 0.00 0.00 0.00 2.83
1174 1253 5.655488 ACCATAGACAGACGATCTCTTTTG 58.345 41.667 0.00 0.00 0.00 2.44
1175 1254 5.923733 ACCATAGACAGACGATCTCTTTT 57.076 39.130 0.00 0.00 0.00 2.27
1176 1255 5.923733 AACCATAGACAGACGATCTCTTT 57.076 39.130 0.00 0.00 0.00 2.52
1177 1256 5.419155 TGAAACCATAGACAGACGATCTCTT 59.581 40.000 0.00 0.00 0.00 2.85
1178 1257 4.950475 TGAAACCATAGACAGACGATCTCT 59.050 41.667 0.00 0.00 0.00 3.10
1179 1258 5.250235 TGAAACCATAGACAGACGATCTC 57.750 43.478 0.00 0.00 0.00 2.75
1180 1259 4.098654 CCTGAAACCATAGACAGACGATCT 59.901 45.833 0.00 0.00 32.90 2.75
1181 1260 4.363999 CCTGAAACCATAGACAGACGATC 58.636 47.826 0.00 0.00 32.90 3.69
1182 1261 3.430929 GCCTGAAACCATAGACAGACGAT 60.431 47.826 0.00 0.00 32.90 3.73
1183 1262 2.094182 GCCTGAAACCATAGACAGACGA 60.094 50.000 0.00 0.00 32.90 4.20
1184 1263 2.093973 AGCCTGAAACCATAGACAGACG 60.094 50.000 0.00 0.00 32.90 4.18
1185 1264 3.618690 AGCCTGAAACCATAGACAGAC 57.381 47.619 0.00 0.00 32.90 3.51
1186 1265 4.326826 CAAAGCCTGAAACCATAGACAGA 58.673 43.478 0.00 0.00 32.90 3.41
1187 1266 3.441572 CCAAAGCCTGAAACCATAGACAG 59.558 47.826 0.00 0.00 0.00 3.51
1188 1267 3.073798 TCCAAAGCCTGAAACCATAGACA 59.926 43.478 0.00 0.00 0.00 3.41
1189 1268 3.686016 TCCAAAGCCTGAAACCATAGAC 58.314 45.455 0.00 0.00 0.00 2.59
1190 1269 3.873801 GCTCCAAAGCCTGAAACCATAGA 60.874 47.826 0.00 0.00 43.10 1.98
1191 1270 2.424956 GCTCCAAAGCCTGAAACCATAG 59.575 50.000 0.00 0.00 43.10 2.23
1192 1271 2.446435 GCTCCAAAGCCTGAAACCATA 58.554 47.619 0.00 0.00 43.10 2.74
1193 1272 1.260544 GCTCCAAAGCCTGAAACCAT 58.739 50.000 0.00 0.00 43.10 3.55
1194 1273 2.732289 GCTCCAAAGCCTGAAACCA 58.268 52.632 0.00 0.00 43.10 3.67
1204 1283 4.751431 CCTCCCTTGGCTCCAAAG 57.249 61.111 2.69 0.00 35.33 2.77
1212 1291 2.278330 GCAAGTTGGCCTCCCTTGG 61.278 63.158 22.53 10.78 36.84 3.61
1213 1292 1.530013 CTGCAAGTTGGCCTCCCTTG 61.530 60.000 19.17 19.17 38.83 3.61
1214 1293 1.228675 CTGCAAGTTGGCCTCCCTT 60.229 57.895 3.32 0.00 0.00 3.95
1215 1294 2.437897 CTGCAAGTTGGCCTCCCT 59.562 61.111 3.32 0.00 0.00 4.20
1216 1295 3.376918 GCTGCAAGTTGGCCTCCC 61.377 66.667 3.32 0.00 35.30 4.30
1217 1296 2.282745 AGCTGCAAGTTGGCCTCC 60.283 61.111 3.32 0.00 35.30 4.30
1218 1297 2.338785 GGAGCTGCAAGTTGGCCTC 61.339 63.158 3.32 0.00 35.30 4.70
1219 1298 2.282745 GGAGCTGCAAGTTGGCCT 60.283 61.111 3.32 0.00 35.30 5.19
1220 1299 2.484287 TAGGGAGCTGCAAGTTGGCC 62.484 60.000 7.79 0.00 35.30 5.36
1221 1300 0.394899 ATAGGGAGCTGCAAGTTGGC 60.395 55.000 7.79 0.18 35.30 4.52
1222 1301 2.134789 AATAGGGAGCTGCAAGTTGG 57.865 50.000 7.79 0.00 35.30 3.77
1223 1302 3.119352 GGAAAATAGGGAGCTGCAAGTTG 60.119 47.826 7.79 0.00 35.30 3.16
1224 1303 3.092301 GGAAAATAGGGAGCTGCAAGTT 58.908 45.455 7.79 0.00 35.30 2.66
1225 1304 2.310052 AGGAAAATAGGGAGCTGCAAGT 59.690 45.455 7.79 0.00 35.30 3.16
1226 1305 3.010200 AGGAAAATAGGGAGCTGCAAG 57.990 47.619 7.79 0.00 0.00 4.01
1227 1306 3.010584 AGAAGGAAAATAGGGAGCTGCAA 59.989 43.478 7.79 0.00 0.00 4.08
1228 1307 2.578021 AGAAGGAAAATAGGGAGCTGCA 59.422 45.455 7.79 0.00 0.00 4.41
1229 1308 3.289407 AGAAGGAAAATAGGGAGCTGC 57.711 47.619 0.00 0.00 0.00 5.25
1230 1309 5.129485 TGAGTAGAAGGAAAATAGGGAGCTG 59.871 44.000 0.00 0.00 0.00 4.24
1231 1310 5.129650 GTGAGTAGAAGGAAAATAGGGAGCT 59.870 44.000 0.00 0.00 0.00 4.09
1232 1311 5.361427 GTGAGTAGAAGGAAAATAGGGAGC 58.639 45.833 0.00 0.00 0.00 4.70
1233 1312 5.360144 TCGTGAGTAGAAGGAAAATAGGGAG 59.640 44.000 0.00 0.00 0.00 4.30
1234 1313 5.266788 TCGTGAGTAGAAGGAAAATAGGGA 58.733 41.667 0.00 0.00 0.00 4.20
1235 1314 5.593679 TCGTGAGTAGAAGGAAAATAGGG 57.406 43.478 0.00 0.00 0.00 3.53
1236 1315 6.806751 TCATCGTGAGTAGAAGGAAAATAGG 58.193 40.000 0.00 0.00 0.00 2.57
1237 1316 7.646130 GTCTCATCGTGAGTAGAAGGAAAATAG 59.354 40.741 12.62 0.00 44.58 1.73
1238 1317 7.481642 GTCTCATCGTGAGTAGAAGGAAAATA 58.518 38.462 12.62 0.00 44.58 1.40
1239 1318 6.334202 GTCTCATCGTGAGTAGAAGGAAAAT 58.666 40.000 12.62 0.00 44.58 1.82
1240 1319 5.619309 CGTCTCATCGTGAGTAGAAGGAAAA 60.619 44.000 12.62 0.00 44.58 2.29
1241 1320 4.142665 CGTCTCATCGTGAGTAGAAGGAAA 60.143 45.833 12.62 0.00 44.58 3.13
1242 1321 3.374367 CGTCTCATCGTGAGTAGAAGGAA 59.626 47.826 12.62 0.00 44.58 3.36
1243 1322 2.937149 CGTCTCATCGTGAGTAGAAGGA 59.063 50.000 12.62 0.00 44.58 3.36
1244 1323 2.539953 GCGTCTCATCGTGAGTAGAAGG 60.540 54.545 12.62 3.68 44.58 3.46
1245 1324 2.539953 GGCGTCTCATCGTGAGTAGAAG 60.540 54.545 12.62 0.00 44.58 2.85
1246 1325 1.400846 GGCGTCTCATCGTGAGTAGAA 59.599 52.381 12.62 0.00 44.58 2.10
1247 1326 1.015109 GGCGTCTCATCGTGAGTAGA 58.985 55.000 12.62 0.00 44.58 2.59
1248 1327 0.733150 TGGCGTCTCATCGTGAGTAG 59.267 55.000 12.62 9.78 44.58 2.57
1249 1328 0.733150 CTGGCGTCTCATCGTGAGTA 59.267 55.000 12.62 1.16 44.58 2.59
1250 1329 0.960861 TCTGGCGTCTCATCGTGAGT 60.961 55.000 12.62 0.00 44.58 3.41
1251 1330 0.383590 ATCTGGCGTCTCATCGTGAG 59.616 55.000 8.24 8.24 45.59 3.51
1252 1331 0.101219 CATCTGGCGTCTCATCGTGA 59.899 55.000 0.00 0.00 0.00 4.35
1253 1332 1.485838 GCATCTGGCGTCTCATCGTG 61.486 60.000 0.00 0.00 0.00 4.35
1254 1333 1.227089 GCATCTGGCGTCTCATCGT 60.227 57.895 0.00 0.00 0.00 3.73
1255 1334 1.953138 GGCATCTGGCGTCTCATCG 60.953 63.158 0.00 0.00 46.16 3.84
1256 1335 1.144716 TGGCATCTGGCGTCTCATC 59.855 57.895 0.00 0.00 46.16 2.92
1257 1336 1.153289 GTGGCATCTGGCGTCTCAT 60.153 57.895 0.00 0.00 46.16 2.90
1258 1337 1.902765 ATGTGGCATCTGGCGTCTCA 61.903 55.000 0.00 0.00 46.16 3.27
1259 1338 1.153289 ATGTGGCATCTGGCGTCTC 60.153 57.895 0.00 0.00 46.16 3.36
1260 1339 1.153289 GATGTGGCATCTGGCGTCT 60.153 57.895 0.00 0.00 46.16 4.18
1261 1340 2.528743 CGATGTGGCATCTGGCGTC 61.529 63.158 7.41 0.00 46.16 5.19
1262 1341 2.512286 CGATGTGGCATCTGGCGT 60.512 61.111 7.41 0.00 46.16 5.68
1263 1342 3.945434 GCGATGTGGCATCTGGCG 61.945 66.667 7.41 0.00 46.16 5.69
1264 1343 3.589881 GGCGATGTGGCATCTGGC 61.590 66.667 7.41 8.83 44.08 4.85
1271 1350 2.887568 CGTCTCTGGCGATGTGGC 60.888 66.667 0.00 0.00 45.12 5.01
1272 1351 2.202797 CCGTCTCTGGCGATGTGG 60.203 66.667 0.00 0.00 0.00 4.17
1273 1352 1.226802 CTCCGTCTCTGGCGATGTG 60.227 63.158 0.00 0.00 0.00 3.21
1274 1353 1.679305 ACTCCGTCTCTGGCGATGT 60.679 57.895 0.00 0.00 0.00 3.06
1275 1354 1.226802 CACTCCGTCTCTGGCGATG 60.227 63.158 0.00 0.00 0.00 3.84
1276 1355 2.418910 CCACTCCGTCTCTGGCGAT 61.419 63.158 0.00 0.00 0.00 4.58
1277 1356 3.062466 CCACTCCGTCTCTGGCGA 61.062 66.667 0.00 0.00 0.00 5.54
1278 1357 4.135153 CCCACTCCGTCTCTGGCG 62.135 72.222 0.00 0.00 0.00 5.69
1279 1358 4.459089 GCCCACTCCGTCTCTGGC 62.459 72.222 0.00 0.00 0.00 4.85
1280 1359 3.775654 GGCCCACTCCGTCTCTGG 61.776 72.222 0.00 0.00 0.00 3.86
1281 1360 4.135153 CGGCCCACTCCGTCTCTG 62.135 72.222 0.00 0.00 44.18 3.35
1288 1367 0.034059 CTGTATGATCGGCCCACTCC 59.966 60.000 0.00 0.00 0.00 3.85
1289 1368 0.753262 ACTGTATGATCGGCCCACTC 59.247 55.000 0.00 0.00 0.00 3.51
1290 1369 0.465705 CACTGTATGATCGGCCCACT 59.534 55.000 0.00 0.00 0.00 4.00
1291 1370 0.532862 CCACTGTATGATCGGCCCAC 60.533 60.000 0.00 0.00 0.00 4.61
1292 1371 0.689412 TCCACTGTATGATCGGCCCA 60.689 55.000 0.00 0.00 0.00 5.36
1293 1372 0.687354 ATCCACTGTATGATCGGCCC 59.313 55.000 0.00 0.00 0.00 5.80
1294 1373 1.609061 CCATCCACTGTATGATCGGCC 60.609 57.143 0.00 0.00 0.00 6.13
1295 1374 1.070758 ACCATCCACTGTATGATCGGC 59.929 52.381 0.00 0.00 0.00 5.54
1296 1375 3.306088 GGTACCATCCACTGTATGATCGG 60.306 52.174 7.15 1.22 0.00 4.18
1297 1376 3.320826 TGGTACCATCCACTGTATGATCG 59.679 47.826 11.60 0.00 31.96 3.69
1298 1377 4.800914 GCTGGTACCATCCACTGTATGATC 60.801 50.000 16.75 0.00 33.55 2.92
1299 1378 3.071602 GCTGGTACCATCCACTGTATGAT 59.928 47.826 16.75 0.00 33.55 2.45
1300 1379 2.434336 GCTGGTACCATCCACTGTATGA 59.566 50.000 16.75 0.00 33.55 2.15
1301 1380 2.170397 TGCTGGTACCATCCACTGTATG 59.830 50.000 16.75 0.10 33.55 2.39
1302 1381 2.477245 TGCTGGTACCATCCACTGTAT 58.523 47.619 16.75 0.00 33.55 2.29
1303 1382 1.945580 TGCTGGTACCATCCACTGTA 58.054 50.000 16.75 0.00 33.55 2.74
1304 1383 1.064003 TTGCTGGTACCATCCACTGT 58.936 50.000 16.75 0.00 33.55 3.55
1305 1384 2.425143 ATTGCTGGTACCATCCACTG 57.575 50.000 16.75 3.36 33.55 3.66
1306 1385 2.843730 TGTATTGCTGGTACCATCCACT 59.156 45.455 16.75 12.14 33.55 4.00
1307 1386 3.275617 TGTATTGCTGGTACCATCCAC 57.724 47.619 16.75 9.80 33.55 4.02
1308 1387 4.308526 TTTGTATTGCTGGTACCATCCA 57.691 40.909 16.75 13.00 36.00 3.41
1309 1388 4.947388 TCTTTTGTATTGCTGGTACCATCC 59.053 41.667 16.75 10.34 0.00 3.51
1310 1389 5.880332 TCTCTTTTGTATTGCTGGTACCATC 59.120 40.000 16.75 12.51 0.00 3.51
1311 1390 5.815581 TCTCTTTTGTATTGCTGGTACCAT 58.184 37.500 16.75 2.52 0.00 3.55
1312 1391 5.235850 TCTCTTTTGTATTGCTGGTACCA 57.764 39.130 15.39 15.39 0.00 3.25
1313 1392 5.880332 TGATCTCTTTTGTATTGCTGGTACC 59.120 40.000 4.43 4.43 0.00 3.34
1314 1393 6.985188 TGATCTCTTTTGTATTGCTGGTAC 57.015 37.500 0.00 0.00 0.00 3.34
1315 1394 7.168219 ACTTGATCTCTTTTGTATTGCTGGTA 58.832 34.615 0.00 0.00 0.00 3.25
1316 1395 6.006449 ACTTGATCTCTTTTGTATTGCTGGT 58.994 36.000 0.00 0.00 0.00 4.00
1317 1396 6.506500 ACTTGATCTCTTTTGTATTGCTGG 57.493 37.500 0.00 0.00 0.00 4.85
1324 1403 9.411801 GCATCGATATACTTGATCTCTTTTGTA 57.588 33.333 0.00 0.00 0.00 2.41
1341 1420 9.640963 GTTTCCTATGTAAACTAGCATCGATAT 57.359 33.333 0.00 0.00 34.66 1.63
1379 1458 5.415701 TCAAAGCCTGAAACCATAGATGAAC 59.584 40.000 0.00 0.00 0.00 3.18
1382 1461 5.678107 GCTTCAAAGCCTGAAACCATAGATG 60.678 44.000 3.27 0.00 46.20 2.90
1486 1565 1.448365 CTGCTGTATGAGTGGCGCA 60.448 57.895 10.83 0.00 0.00 6.09
1492 1571 2.433604 CTGGTCCATCTGCTGTATGAGT 59.566 50.000 0.00 0.00 0.00 3.41
1503 1582 2.430610 GCCGCTCTCTGGTCCATCT 61.431 63.158 0.00 0.00 0.00 2.90
1559 1638 3.253921 CCAAGATTGATCTGTGCACAACA 59.746 43.478 21.98 17.38 37.19 3.33
1572 1651 3.620488 GTTACCCAGATGCCAAGATTGA 58.380 45.455 0.00 0.00 0.00 2.57
1653 1732 5.232202 ACAGAAAACAGTCGATATATGTGCG 59.768 40.000 0.00 0.00 0.00 5.34
1665 1744 7.822822 AGGGTGTACAATATACAGAAAACAGTC 59.177 37.037 0.00 0.00 0.00 3.51
1667 1746 8.561738 AAGGGTGTACAATATACAGAAAACAG 57.438 34.615 0.00 0.00 0.00 3.16
1734 1813 5.560183 CGACGTAGAATTCTTTGGCTGTTTT 60.560 40.000 14.36 0.00 0.00 2.43
1775 1854 7.485913 GCTATTGTTGGTTCTATGTGATGTTTG 59.514 37.037 0.00 0.00 0.00 2.93
1913 1992 2.290323 ACCGCTTTACCTTGAGATTGCT 60.290 45.455 0.00 0.00 0.00 3.91
1931 2010 0.606096 TATCACCAGTCACCACACCG 59.394 55.000 0.00 0.00 0.00 4.94
1996 2077 9.810231 CAAATGCACCAAACATAAAACTAATTC 57.190 29.630 0.00 0.00 0.00 2.17
2025 2106 5.010719 ACGAGAGAAGGTAAGAACAACATGA 59.989 40.000 0.00 0.00 0.00 3.07
2203 2324 9.537848 GCAATTTGAGAAAATGCAAGAAATAAG 57.462 29.630 0.00 0.00 33.99 1.73
2440 2561 1.760086 GCAGGAGAGCTAGGCAGGA 60.760 63.158 0.00 0.00 0.00 3.86
2450 2571 5.452636 GGAATACTAAACTGGAGCAGGAGAG 60.453 48.000 0.00 0.00 35.51 3.20
2460 2581 6.879458 AGCTTAACACTGGAATACTAAACTGG 59.121 38.462 0.00 0.00 0.00 4.00
2503 2624 5.582689 ATTTAGGCACTGCTAAAACATCC 57.417 39.130 0.00 0.00 41.52 3.51
2559 2681 6.382859 TCAAAGAGCATAGTATCACTACCCAA 59.617 38.462 0.00 0.00 32.84 4.12
2712 2840 4.666412 TCCTCATACCATTTGGAACCAA 57.334 40.909 3.01 1.83 38.94 3.67
2728 2857 3.515104 TGTGTGCAGAAGTCATATCCTCA 59.485 43.478 0.00 0.00 0.00 3.86
2729 2858 4.128925 TGTGTGCAGAAGTCATATCCTC 57.871 45.455 0.00 0.00 0.00 3.71
2783 2912 2.171448 ACTGGTGATGGGCAGAATAGAC 59.829 50.000 0.00 0.00 0.00 2.59
2810 2945 3.189287 CAGTCCTCCATCCTTTGTTTTCG 59.811 47.826 0.00 0.00 0.00 3.46
2854 2993 4.832248 TGGTGTATGATGACTGGTTTCTC 58.168 43.478 0.00 0.00 0.00 2.87
2900 3039 2.821378 TGATTCAGGGCTCAATTGTGTG 59.179 45.455 5.13 0.00 0.00 3.82
2924 3063 5.747565 TGTTTAGTCAAAAGCTTGTGATCG 58.252 37.500 22.04 0.00 33.94 3.69
2949 3088 2.032924 CCATAGTATCGTCGCTGACACA 59.967 50.000 8.91 0.00 32.09 3.72
2950 3089 2.604855 CCCATAGTATCGTCGCTGACAC 60.605 54.545 8.91 1.13 32.09 3.67
3014 3153 2.303175 GTGTGCCCTTTTGTAGTTGGA 58.697 47.619 0.00 0.00 0.00 3.53
3045 3184 2.391389 CGTCCAAGCCGCCTCTTTC 61.391 63.158 0.00 0.00 0.00 2.62
3046 3185 2.358737 CGTCCAAGCCGCCTCTTT 60.359 61.111 0.00 0.00 0.00 2.52
3096 3235 3.057174 AGAAGAGGAAGAACACGCTACAG 60.057 47.826 0.00 0.00 0.00 2.74
3119 3258 1.567357 AAGCAGAGGAAGGAGGAGAC 58.433 55.000 0.00 0.00 0.00 3.36
3121 3260 2.168313 GAGAAAGCAGAGGAAGGAGGAG 59.832 54.545 0.00 0.00 0.00 3.69
3139 3278 7.020827 ACAAATCAAGAATTACAGGAGGAGA 57.979 36.000 0.00 0.00 0.00 3.71
3267 3406 1.799933 AGCGGAGGATGGAGAAGAAT 58.200 50.000 0.00 0.00 0.00 2.40
3299 3438 4.660789 AATTGTGGCTTGGCATTCTATC 57.339 40.909 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.