Multiple sequence alignment - TraesCS3A01G114900

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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 TraesCS3A01G114900 chr3A 100.000 5047 0 0 1 5047 82438909 82443955 0.000000e+00 9321
1 TraesCS3A01G114900 chr3A 91.840 1348 76 16 1884 3205 83725477 83724138 0.000000e+00 1849
2 TraesCS3A01G114900 chr3A 88.487 608 67 3 4352 4957 443172842 443172236 0.000000e+00 732
3 TraesCS3A01G114900 chr3D 91.129 3100 136 55 1229 4263 70725466 70728491 0.000000e+00 4072
4 TraesCS3A01G114900 chr3D 94.105 1357 49 14 2475 3813 510300220 510301563 0.000000e+00 2034
5 TraesCS3A01G114900 chr3D 90.929 1400 82 18 1884 3249 71496668 71495280 0.000000e+00 1840
6 TraesCS3A01G114900 chr3D 86.694 1210 87 27 17 1178 70724264 70725447 0.000000e+00 1275
7 TraesCS3A01G114900 chr3D 82.258 186 21 7 4502 4681 8723897 8724076 3.150000e-32 150
8 TraesCS3A01G114900 chr3B 93.520 1960 73 19 1932 3865 116191294 116193225 0.000000e+00 2867
9 TraesCS3A01G114900 chr3B 86.729 1507 100 49 2368 3836 117553667 117552223 0.000000e+00 1583
10 TraesCS3A01G114900 chr3B 87.201 1172 89 28 43 1178 116189342 116190488 0.000000e+00 1277
11 TraesCS3A01G114900 chr3B 83.930 1033 104 27 4027 5047 116193386 116194368 0.000000e+00 931
12 TraesCS3A01G114900 chr3B 90.028 712 67 4 4338 5047 425683088 425682379 0.000000e+00 918
13 TraesCS3A01G114900 chr3B 87.844 691 74 6 4355 5040 52660127 52660812 0.000000e+00 802
14 TraesCS3A01G114900 chr3B 86.908 718 64 13 1242 1944 116190510 116191212 0.000000e+00 778
15 TraesCS3A01G114900 chr3B 88.095 462 22 7 1884 2344 117554078 117553649 7.490000e-143 518
16 TraesCS3A01G114900 chr4D 94.000 1350 53 13 2478 3813 497616139 497614804 0.000000e+00 2019
17 TraesCS3A01G114900 chr4D 89.858 562 53 3 4344 4903 16612976 16612417 0.000000e+00 719
18 TraesCS3A01G114900 chr4D 94.792 96 2 3 4178 4271 507672767 507672673 4.070000e-31 147
19 TraesCS3A01G114900 chr4D 93.684 95 4 2 4175 4267 334968058 334968152 1.890000e-29 141
20 TraesCS3A01G114900 chr1B 88.976 508 46 2 4344 4850 489241712 489241214 2.000000e-173 619
21 TraesCS3A01G114900 chr1B 92.929 99 6 1 4166 4263 665492997 665493095 5.270000e-30 143
22 TraesCS3A01G114900 chr4A 86.348 564 61 5 4344 4904 583918591 583919141 7.230000e-168 601
23 TraesCS3A01G114900 chrUn 87.137 482 53 5 4563 5040 16712740 16712264 5.750000e-149 538
24 TraesCS3A01G114900 chr2D 84.412 340 43 7 1369 1705 6722815 6723147 4.870000e-85 326
25 TraesCS3A01G114900 chr4B 82.353 340 48 9 1369 1705 579786560 579786890 8.270000e-73 285
26 TraesCS3A01G114900 chr4B 94.565 92 5 0 4173 4264 413113544 413113635 5.270000e-30 143
27 TraesCS3A01G114900 chr4B 92.079 101 5 3 4166 4264 656304549 656304648 6.810000e-29 139
28 TraesCS3A01G114900 chr1A 95.745 94 1 3 4177 4269 132795547 132795456 1.130000e-31 148
29 TraesCS3A01G114900 chr1A 92.157 102 4 4 4168 4268 490796165 490796263 1.890000e-29 141
30 TraesCS3A01G114900 chr6D 93.814 97 4 2 4173 4268 23419711 23419806 1.460000e-30 145


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 TraesCS3A01G114900 chr3A 82438909 82443955 5046 False 9321.00 9321 100.00000 1 5047 1 chr3A.!!$F1 5046
1 TraesCS3A01G114900 chr3A 83724138 83725477 1339 True 1849.00 1849 91.84000 1884 3205 1 chr3A.!!$R1 1321
2 TraesCS3A01G114900 chr3A 443172236 443172842 606 True 732.00 732 88.48700 4352 4957 1 chr3A.!!$R2 605
3 TraesCS3A01G114900 chr3D 70724264 70728491 4227 False 2673.50 4072 88.91150 17 4263 2 chr3D.!!$F3 4246
4 TraesCS3A01G114900 chr3D 510300220 510301563 1343 False 2034.00 2034 94.10500 2475 3813 1 chr3D.!!$F2 1338
5 TraesCS3A01G114900 chr3D 71495280 71496668 1388 True 1840.00 1840 90.92900 1884 3249 1 chr3D.!!$R1 1365
6 TraesCS3A01G114900 chr3B 116189342 116194368 5026 False 1463.25 2867 87.88975 43 5047 4 chr3B.!!$F2 5004
7 TraesCS3A01G114900 chr3B 117552223 117554078 1855 True 1050.50 1583 87.41200 1884 3836 2 chr3B.!!$R2 1952
8 TraesCS3A01G114900 chr3B 425682379 425683088 709 True 918.00 918 90.02800 4338 5047 1 chr3B.!!$R1 709
9 TraesCS3A01G114900 chr3B 52660127 52660812 685 False 802.00 802 87.84400 4355 5040 1 chr3B.!!$F1 685
10 TraesCS3A01G114900 chr4D 497614804 497616139 1335 True 2019.00 2019 94.00000 2478 3813 1 chr4D.!!$R2 1335
11 TraesCS3A01G114900 chr4D 16612417 16612976 559 True 719.00 719 89.85800 4344 4903 1 chr4D.!!$R1 559
12 TraesCS3A01G114900 chr4A 583918591 583919141 550 False 601.00 601 86.34800 4344 4904 1 chr4A.!!$F1 560

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
33 34 0.040204 AAAGCCTAGCCATTGCACCT 59.960 50.0 0.0 0.0 41.13 4.00 F
283 285 0.251742 TTTCAAGGGGGTCCATGCTG 60.252 55.0 0.0 0.0 32.17 4.41 F
1516 1589 0.250234 TCCTCATTTCGGGCTCTGTG 59.750 55.0 0.0 0.0 0.00 3.66 F
2031 2205 0.177836 AGCCACCCTGTTTTTGTTGC 59.822 50.0 0.0 0.0 0.00 4.17 F
3909 4198 0.110688 CGAACACTTGACATGCACCG 60.111 55.0 0.0 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1213 1271 0.105778 CTCCCTTTCTCTCCGATGCC 59.894 60.0 0.00 0.0 0.00 4.40 R
1820 1893 0.109781 CTTTTGACGGCGGGAATGTG 60.110 55.0 13.24 0.0 0.00 3.21 R
3432 3696 0.318529 CGGAGGTGATGATGAGCGAG 60.319 60.0 0.00 0.0 0.00 5.03 R
4008 4297 0.249699 TGCCAGTAACACCGTCACAG 60.250 55.0 0.00 0.0 0.00 3.66 R
4780 5122 1.180029 CAGGAAACTTGGCTCATGGG 58.820 55.0 0.00 0.0 40.21 4.00 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
28 29 3.385755 AGCCATAAAAAGCCTAGCCATTG 59.614 43.478 0.00 0.00 0.00 2.82
33 34 0.040204 AAAGCCTAGCCATTGCACCT 59.960 50.000 0.00 0.00 41.13 4.00
39 40 2.224161 CCTAGCCATTGCACCTCTCTAC 60.224 54.545 0.00 0.00 41.13 2.59
45 46 1.204146 TTGCACCTCTCTACCCATCC 58.796 55.000 0.00 0.00 0.00 3.51
56 57 6.142259 TCTCTACCCATCCCTATTCTCTAC 57.858 45.833 0.00 0.00 0.00 2.59
57 58 5.615692 TCTCTACCCATCCCTATTCTCTACA 59.384 44.000 0.00 0.00 0.00 2.74
78 79 0.394565 AGCCGAGCAATGTAGATCCC 59.605 55.000 0.00 0.00 0.00 3.85
88 89 4.686554 GCAATGTAGATCCCGACTAATCAC 59.313 45.833 0.00 0.00 0.00 3.06
89 90 5.509840 GCAATGTAGATCCCGACTAATCACT 60.510 44.000 0.00 0.00 0.00 3.41
110 111 2.675772 AGCAGAGCCCAAGCAAGC 60.676 61.111 0.00 0.00 43.56 4.01
111 112 2.675772 GCAGAGCCCAAGCAAGCT 60.676 61.111 0.00 0.00 43.56 3.74
149 150 2.751806 AGCAGCTAATCAAGAAGCAACC 59.248 45.455 0.00 0.00 41.32 3.77
155 156 4.218417 GCTAATCAAGAAGCAACCAAAGGA 59.782 41.667 0.00 0.00 38.63 3.36
158 160 4.385358 TCAAGAAGCAACCAAAGGAAAC 57.615 40.909 0.00 0.00 0.00 2.78
160 162 3.801114 AGAAGCAACCAAAGGAAACAC 57.199 42.857 0.00 0.00 0.00 3.32
176 178 5.298276 AGGAAACACAAAAGTCTTAATCGCA 59.702 36.000 0.00 0.00 0.00 5.10
226 228 3.771160 GATCACGACACGCCCCCT 61.771 66.667 0.00 0.00 0.00 4.79
239 241 1.228063 CCCCCTCCATCATTGCTCG 60.228 63.158 0.00 0.00 0.00 5.03
283 285 0.251742 TTTCAAGGGGGTCCATGCTG 60.252 55.000 0.00 0.00 32.17 4.41
284 286 2.757099 CAAGGGGGTCCATGCTGC 60.757 66.667 0.00 0.00 34.83 5.25
285 287 2.943265 AAGGGGGTCCATGCTGCT 60.943 61.111 0.00 0.00 34.83 4.24
311 313 1.209261 TGCCACACGGTGATATGATGT 59.791 47.619 16.29 0.00 35.23 3.06
335 347 2.035321 ACACCACGTTTAAAATGCAGGG 59.965 45.455 0.00 0.00 0.00 4.45
366 378 2.516930 GGTGATGCCATGACCCCG 60.517 66.667 1.30 0.00 37.17 5.73
382 394 0.676782 CCCGTGGCTTTTACAGGGAG 60.677 60.000 5.79 0.00 44.45 4.30
388 400 1.272490 GGCTTTTACAGGGAGTTTGCC 59.728 52.381 0.00 0.00 0.00 4.52
414 429 0.392998 ATTAGCCAGTGCGGGACAAG 60.393 55.000 1.61 0.00 44.33 3.16
439 454 2.040009 ATCGGGTGGGTTATGCTCCG 62.040 60.000 0.00 0.00 38.92 4.63
480 497 2.614983 GTGATCAGGAGACGACCTACTC 59.385 54.545 0.00 0.00 38.32 2.59
513 530 3.544684 TCATGTGGCATAGATTGTGGTC 58.455 45.455 0.00 0.00 0.00 4.02
538 555 2.685897 TGGCAACCAACAAGAAGTACAC 59.314 45.455 0.00 0.00 0.00 2.90
541 558 4.202111 GGCAACCAACAAGAAGTACACAAT 60.202 41.667 0.00 0.00 0.00 2.71
543 560 5.449862 GCAACCAACAAGAAGTACACAATCA 60.450 40.000 0.00 0.00 0.00 2.57
546 563 6.299141 ACCAACAAGAAGTACACAATCATCT 58.701 36.000 0.00 0.00 0.00 2.90
579 597 2.481952 CGGAAGAGGAACAAGAAAGCAG 59.518 50.000 0.00 0.00 0.00 4.24
580 598 2.816672 GGAAGAGGAACAAGAAAGCAGG 59.183 50.000 0.00 0.00 0.00 4.85
587 607 4.022849 AGGAACAAGAAAGCAGGAAAATCG 60.023 41.667 0.00 0.00 0.00 3.34
590 610 3.240069 CAAGAAAGCAGGAAAATCGCAG 58.760 45.455 0.00 0.00 0.00 5.18
681 701 3.773418 ATCCCATTCTGATCAGCTGAG 57.227 47.619 22.96 8.88 0.00 3.35
721 744 0.529337 CTGCACTATCAGACGCCCAG 60.529 60.000 0.00 0.00 36.19 4.45
785 815 7.673926 ACACCACTCCAAAAATGAATAGGTTAT 59.326 33.333 0.00 0.00 0.00 1.89
786 816 9.184523 CACCACTCCAAAAATGAATAGGTTATA 57.815 33.333 0.00 0.00 0.00 0.98
787 817 9.936329 ACCACTCCAAAAATGAATAGGTTATAT 57.064 29.630 0.00 0.00 0.00 0.86
869 899 3.878699 TCCGTGATGATGGATCAAATGTG 59.121 43.478 0.00 0.00 42.96 3.21
1150 1208 4.749310 CAGTTGGCGCTCGGAGCT 62.749 66.667 25.96 4.90 39.60 4.09
1178 1236 1.349357 GCACAGGGGAGAAGAAGAAGT 59.651 52.381 0.00 0.00 0.00 3.01
1179 1237 2.873649 GCACAGGGGAGAAGAAGAAGTG 60.874 54.545 0.00 0.00 0.00 3.16
1181 1239 2.370189 ACAGGGGAGAAGAAGAAGTGTG 59.630 50.000 0.00 0.00 0.00 3.82
1182 1240 2.370189 CAGGGGAGAAGAAGAAGTGTGT 59.630 50.000 0.00 0.00 0.00 3.72
1183 1241 3.578716 CAGGGGAGAAGAAGAAGTGTGTA 59.421 47.826 0.00 0.00 0.00 2.90
1186 1244 4.468153 GGGGAGAAGAAGAAGTGTGTAGAT 59.532 45.833 0.00 0.00 0.00 1.98
1187 1245 5.046231 GGGGAGAAGAAGAAGTGTGTAGATT 60.046 44.000 0.00 0.00 0.00 2.40
1188 1246 6.103330 GGGAGAAGAAGAAGTGTGTAGATTC 58.897 44.000 0.00 0.00 0.00 2.52
1189 1247 6.103330 GGAGAAGAAGAAGTGTGTAGATTCC 58.897 44.000 0.00 0.00 0.00 3.01
1190 1248 6.071051 GGAGAAGAAGAAGTGTGTAGATTCCT 60.071 42.308 0.00 0.00 0.00 3.36
1191 1249 6.930731 AGAAGAAGAAGTGTGTAGATTCCTC 58.069 40.000 0.00 0.00 0.00 3.71
1192 1250 6.723977 AGAAGAAGAAGTGTGTAGATTCCTCT 59.276 38.462 0.00 0.00 35.39 3.69
1193 1251 7.891183 AGAAGAAGAAGTGTGTAGATTCCTCTA 59.109 37.037 0.00 0.00 32.66 2.43
1194 1252 7.639113 AGAAGAAGTGTGTAGATTCCTCTAG 57.361 40.000 0.00 0.00 34.63 2.43
1195 1253 6.605594 AGAAGAAGTGTGTAGATTCCTCTAGG 59.394 42.308 0.00 0.00 34.63 3.02
1196 1254 6.080969 AGAAGTGTGTAGATTCCTCTAGGA 57.919 41.667 0.00 0.00 43.73 2.94
1214 1272 3.942130 GGAATTGTCCTGGAGTTTTGG 57.058 47.619 0.00 0.00 41.24 3.28
1215 1273 2.029020 GGAATTGTCCTGGAGTTTTGGC 60.029 50.000 0.00 0.00 41.24 4.52
1216 1274 2.380064 ATTGTCCTGGAGTTTTGGCA 57.620 45.000 0.00 0.00 0.00 4.92
1217 1275 2.380064 TTGTCCTGGAGTTTTGGCAT 57.620 45.000 0.00 0.00 0.00 4.40
1218 1276 1.909700 TGTCCTGGAGTTTTGGCATC 58.090 50.000 0.00 0.00 0.00 3.91
1219 1277 0.804989 GTCCTGGAGTTTTGGCATCG 59.195 55.000 0.00 0.00 0.00 3.84
1220 1278 0.322456 TCCTGGAGTTTTGGCATCGG 60.322 55.000 0.00 0.00 0.00 4.18
1221 1279 0.322456 CCTGGAGTTTTGGCATCGGA 60.322 55.000 0.00 0.00 0.00 4.55
1222 1280 1.089920 CTGGAGTTTTGGCATCGGAG 58.910 55.000 0.00 0.00 0.00 4.63
1223 1281 0.690192 TGGAGTTTTGGCATCGGAGA 59.310 50.000 0.00 0.00 45.75 3.71
1224 1282 1.339055 TGGAGTTTTGGCATCGGAGAG 60.339 52.381 0.00 0.00 43.63 3.20
1225 1283 1.066143 GGAGTTTTGGCATCGGAGAGA 60.066 52.381 0.00 0.00 43.63 3.10
1226 1284 2.615493 GGAGTTTTGGCATCGGAGAGAA 60.615 50.000 0.00 0.00 43.63 2.87
1227 1285 3.074412 GAGTTTTGGCATCGGAGAGAAA 58.926 45.455 0.00 0.00 43.63 2.52
1235 1293 2.660572 CATCGGAGAGAAAGGGAGAGA 58.339 52.381 0.00 0.00 43.63 3.10
1239 1297 1.289530 GGAGAGAAAGGGAGAGAGGGA 59.710 57.143 0.00 0.00 0.00 4.20
1240 1298 2.292587 GGAGAGAAAGGGAGAGAGGGAA 60.293 54.545 0.00 0.00 0.00 3.97
1249 1307 2.192263 GGAGAGAGGGAAAGATGGTGT 58.808 52.381 0.00 0.00 0.00 4.16
1251 1309 2.169561 GAGAGAGGGAAAGATGGTGTCC 59.830 54.545 0.00 0.00 0.00 4.02
1365 1438 2.912025 GGTGTGTTGTGGGCTGGG 60.912 66.667 0.00 0.00 0.00 4.45
1366 1439 2.912025 GTGTGTTGTGGGCTGGGG 60.912 66.667 0.00 0.00 0.00 4.96
1367 1440 4.912395 TGTGTTGTGGGCTGGGGC 62.912 66.667 0.00 0.00 37.82 5.80
1480 1553 2.283388 ACGACGGGGAGCAAGGTA 60.283 61.111 0.00 0.00 0.00 3.08
1481 1554 2.183555 CGACGGGGAGCAAGGTAC 59.816 66.667 0.00 0.00 0.00 3.34
1483 1556 4.078516 ACGGGGAGCAAGGTACGC 62.079 66.667 0.00 0.00 0.00 4.42
1484 1557 4.077184 CGGGGAGCAAGGTACGCA 62.077 66.667 0.00 0.00 0.00 5.24
1486 1559 2.820037 GGGAGCAAGGTACGCAGC 60.820 66.667 0.00 0.00 0.00 5.25
1487 1560 2.047274 GGAGCAAGGTACGCAGCA 60.047 61.111 0.00 0.00 0.00 4.41
1489 1562 2.046892 AGCAAGGTACGCAGCAGG 60.047 61.111 0.00 0.00 0.00 4.85
1490 1563 3.804193 GCAAGGTACGCAGCAGGC 61.804 66.667 0.00 0.00 39.90 4.85
1491 1564 3.127533 CAAGGTACGCAGCAGGCC 61.128 66.667 0.00 0.00 40.31 5.19
1504 1577 2.366167 AGGCCGAGGCTCCTCATT 60.366 61.111 14.33 0.00 42.86 2.57
1505 1578 1.997874 AGGCCGAGGCTCCTCATTT 60.998 57.895 14.33 0.00 42.86 2.32
1506 1579 1.524849 GGCCGAGGCTCCTCATTTC 60.525 63.158 14.33 1.95 42.86 2.17
1508 1581 1.227380 CCGAGGCTCCTCATTTCGG 60.227 63.158 15.52 7.77 43.90 4.30
1509 1582 1.227380 CGAGGCTCCTCATTTCGGG 60.227 63.158 15.52 0.00 42.86 5.14
1511 1584 1.977293 GAGGCTCCTCATTTCGGGCT 61.977 60.000 10.90 0.00 42.31 5.19
1513 1586 1.524482 GCTCCTCATTTCGGGCTCT 59.476 57.895 0.00 0.00 0.00 4.09
1515 1588 0.539051 CTCCTCATTTCGGGCTCTGT 59.461 55.000 0.00 0.00 0.00 3.41
1516 1589 0.250234 TCCTCATTTCGGGCTCTGTG 59.750 55.000 0.00 0.00 0.00 3.66
1517 1590 0.250234 CCTCATTTCGGGCTCTGTGA 59.750 55.000 0.00 0.00 0.00 3.58
1523 1596 0.606096 TTCGGGCTCTGTGATTCGAA 59.394 50.000 0.00 0.00 34.85 3.71
1525 1598 1.202417 TCGGGCTCTGTGATTCGAATC 60.202 52.381 27.59 27.59 35.97 2.52
1574 1647 2.562214 CCTTCCTCCCCTTCTCACCTTA 60.562 54.545 0.00 0.00 0.00 2.69
1580 1653 2.025321 TCCCCTTCTCACCTTATTTGCC 60.025 50.000 0.00 0.00 0.00 4.52
1674 1747 1.021390 CATCGCCGGTGAGCTCTTTT 61.021 55.000 24.04 0.94 0.00 2.27
1682 1755 2.854777 CGGTGAGCTCTTTTACATCTCG 59.145 50.000 16.19 0.01 0.00 4.04
1693 1766 2.933495 TACATCTCGGTTTCACCTCG 57.067 50.000 0.00 0.00 35.66 4.63
1720 1793 1.134848 TGTTTGGAAAGTTGGCTGTGC 60.135 47.619 0.00 0.00 0.00 4.57
1755 1828 5.144832 TCCATGAGGTGTTCTTATCCGATA 58.855 41.667 0.00 0.00 35.89 2.92
1781 1854 2.962569 GGGGAAAAGTGCGGCTTC 59.037 61.111 0.00 0.00 36.17 3.86
1790 1863 2.357034 TGCGGCTTCGGACTGTTC 60.357 61.111 0.00 0.00 0.00 3.18
1820 1893 2.106511 TGGGGAAAGCATAGCTGATACC 59.893 50.000 0.00 0.00 39.62 2.73
1829 1905 3.329386 CATAGCTGATACCACATTCCCG 58.671 50.000 0.00 0.00 0.00 5.14
1847 1923 2.550978 CCGCCGTCAAAAGTAGATCAT 58.449 47.619 0.00 0.00 0.00 2.45
1868 1944 4.582701 TTGCCAGTACTTGATTTTGGTG 57.417 40.909 0.00 0.00 0.00 4.17
1881 1957 1.981256 TTTGGTGGAGGACTTCTTGC 58.019 50.000 0.00 0.00 0.00 4.01
1909 1985 1.253545 GCGCATTTTCACAATGATCGC 59.746 47.619 0.30 2.05 34.13 4.58
1978 2149 5.520649 GCATTCTGAACTGCTAGTAAGTACC 59.479 44.000 13.78 0.00 35.49 3.34
2001 2172 4.691860 ATCGGAAGCAAAATTCAGAGTG 57.308 40.909 0.00 0.00 36.93 3.51
2027 2201 1.962807 TCATGAGCCACCCTGTTTTTG 59.037 47.619 0.00 0.00 0.00 2.44
2031 2205 0.177836 AGCCACCCTGTTTTTGTTGC 59.822 50.000 0.00 0.00 0.00 4.17
2932 3150 1.430632 GCCGTTCGTGAGGATCGTA 59.569 57.895 5.13 0.00 38.61 3.43
3184 3410 4.222847 GAGATCCACCGGCGGACC 62.223 72.222 35.78 3.23 38.07 4.46
3254 3505 1.284657 CGAGTCAGTGATCATGCACC 58.715 55.000 0.00 0.00 39.59 5.01
3255 3506 1.404583 CGAGTCAGTGATCATGCACCA 60.405 52.381 0.00 0.00 39.59 4.17
3256 3507 2.005451 GAGTCAGTGATCATGCACCAC 58.995 52.381 0.00 0.00 39.59 4.16
3432 3696 3.060895 CGAAAAAGATCAGGTACGCAGTC 59.939 47.826 0.00 0.00 43.93 3.51
3446 3710 1.207390 GCAGTCTCGCTCATCATCAC 58.793 55.000 0.00 0.00 0.00 3.06
3494 3758 1.664016 GCTGATGCTCCGTTTGTTGTG 60.664 52.381 0.00 0.00 36.03 3.33
3496 3760 2.290367 CTGATGCTCCGTTTGTTGTGAA 59.710 45.455 0.00 0.00 0.00 3.18
3778 4062 3.112709 GTCGAGGTGTTCTGCGGC 61.113 66.667 0.00 0.00 0.00 6.53
3865 4149 0.603975 ACCTCGAGTTTTGAGCTGGC 60.604 55.000 12.31 0.00 31.98 4.85
3866 4150 1.301677 CCTCGAGTTTTGAGCTGGCC 61.302 60.000 12.31 0.00 31.98 5.36
3904 4193 3.753774 GTGCCGAACACTTGACATG 57.246 52.632 0.00 0.00 46.41 3.21
3907 4196 0.385974 GCCGAACACTTGACATGCAC 60.386 55.000 0.00 0.00 0.00 4.57
3908 4197 0.238289 CCGAACACTTGACATGCACC 59.762 55.000 0.00 0.00 0.00 5.01
3909 4198 0.110688 CGAACACTTGACATGCACCG 60.111 55.000 0.00 0.00 0.00 4.94
3910 4199 0.238289 GAACACTTGACATGCACCGG 59.762 55.000 0.00 0.00 0.00 5.28
3911 4200 1.795170 AACACTTGACATGCACCGGC 61.795 55.000 0.00 0.00 41.68 6.13
3912 4201 1.968017 CACTTGACATGCACCGGCT 60.968 57.895 0.00 0.00 41.91 5.52
3913 4202 1.968017 ACTTGACATGCACCGGCTG 60.968 57.895 0.00 0.00 41.91 4.85
3914 4203 1.672030 CTTGACATGCACCGGCTGA 60.672 57.895 0.00 0.00 41.91 4.26
3915 4204 1.228094 TTGACATGCACCGGCTGAA 60.228 52.632 0.00 0.00 41.91 3.02
3916 4205 1.236616 TTGACATGCACCGGCTGAAG 61.237 55.000 0.00 0.00 41.91 3.02
3917 4206 3.044059 GACATGCACCGGCTGAAGC 62.044 63.158 0.00 0.00 41.91 3.86
3918 4207 3.057548 CATGCACCGGCTGAAGCA 61.058 61.111 13.12 13.12 44.36 3.91
3919 4208 2.044650 ATGCACCGGCTGAAGCAT 60.045 55.556 16.03 16.03 44.36 3.79
3920 4209 1.679977 ATGCACCGGCTGAAGCATT 60.680 52.632 16.03 4.35 44.63 3.56
3921 4210 1.252904 ATGCACCGGCTGAAGCATTT 61.253 50.000 16.03 0.35 44.63 2.32
3922 4211 1.444895 GCACCGGCTGAAGCATTTG 60.445 57.895 0.00 0.00 44.36 2.32
3923 4212 1.213537 CACCGGCTGAAGCATTTGG 59.786 57.895 0.00 2.96 44.36 3.28
3924 4213 1.074775 ACCGGCTGAAGCATTTGGA 59.925 52.632 0.00 0.00 44.36 3.53
3925 4214 0.323725 ACCGGCTGAAGCATTTGGAT 60.324 50.000 0.00 0.00 44.36 3.41
3926 4215 1.064758 ACCGGCTGAAGCATTTGGATA 60.065 47.619 0.00 0.00 44.36 2.59
3927 4216 1.334869 CCGGCTGAAGCATTTGGATAC 59.665 52.381 4.43 0.00 44.36 2.24
3928 4217 2.016318 CGGCTGAAGCATTTGGATACA 58.984 47.619 4.43 0.00 45.46 2.29
3933 4222 5.694229 GCTGAAGCATTTGGATACAGCAGA 61.694 45.833 0.00 0.00 45.26 4.26
3969 4258 1.453155 CTGACAAATCTTGGACGGGG 58.547 55.000 0.00 0.00 34.12 5.73
3991 4280 1.301637 TGTCGTGTGGGTGATGCTG 60.302 57.895 0.00 0.00 0.00 4.41
4008 4297 0.368227 CTGCGCTCTGACGAAACATC 59.632 55.000 9.73 0.00 34.06 3.06
4020 4309 1.864711 CGAAACATCTGTGACGGTGTT 59.135 47.619 6.57 6.57 36.43 3.32
4070 4395 5.399991 TCCCTCTTCACCTTTGAGTTAGTA 58.600 41.667 0.00 0.00 31.71 1.82
4098 4436 0.904865 CCCCTGTCAGGCTGTCAGTA 60.905 60.000 30.45 4.97 32.84 2.74
4160 4499 8.527567 AAAAACACAAAGAATGAGACGAAAAA 57.472 26.923 0.00 0.00 0.00 1.94
4166 4505 7.061673 CACAAAGAATGAGACGAAAAACAACAA 59.938 33.333 0.00 0.00 0.00 2.83
4170 4509 6.526674 AGAATGAGACGAAAAACAACAACAAC 59.473 34.615 0.00 0.00 0.00 3.32
4171 4510 5.109662 TGAGACGAAAAACAACAACAACA 57.890 34.783 0.00 0.00 0.00 3.33
4172 4511 5.520632 TGAGACGAAAAACAACAACAACAA 58.479 33.333 0.00 0.00 0.00 2.83
4173 4512 5.977725 TGAGACGAAAAACAACAACAACAAA 59.022 32.000 0.00 0.00 0.00 2.83
4174 4513 6.475727 TGAGACGAAAAACAACAACAACAAAA 59.524 30.769 0.00 0.00 0.00 2.44
4175 4514 7.010183 TGAGACGAAAAACAACAACAACAAAAA 59.990 29.630 0.00 0.00 0.00 1.94
4176 4515 7.120634 AGACGAAAAACAACAACAACAAAAAC 58.879 30.769 0.00 0.00 0.00 2.43
4177 4516 6.772078 ACGAAAAACAACAACAACAAAAACA 58.228 28.000 0.00 0.00 0.00 2.83
4178 4517 7.241376 ACGAAAAACAACAACAACAAAAACAA 58.759 26.923 0.00 0.00 0.00 2.83
4179 4518 7.749126 ACGAAAAACAACAACAACAAAAACAAA 59.251 25.926 0.00 0.00 0.00 2.83
4180 4519 8.575454 CGAAAAACAACAACAACAAAAACAAAA 58.425 25.926 0.00 0.00 0.00 2.44
4185 4524 8.162906 ACAACAACAACAAAAACAAAAACAAC 57.837 26.923 0.00 0.00 0.00 3.32
4208 4547 2.497792 AATGCACCAGCCGGGAATCA 62.498 55.000 2.18 0.00 41.13 2.57
4267 4606 3.055819 CACTAGACCACTGGTGCTTATGT 60.056 47.826 5.10 1.47 45.52 2.29
4270 4609 2.106511 AGACCACTGGTGCTTATGTTGT 59.893 45.455 5.10 0.00 35.25 3.32
4273 4612 4.072131 ACCACTGGTGCTTATGTTGTTAG 58.928 43.478 0.00 0.00 32.98 2.34
4275 4614 5.221762 ACCACTGGTGCTTATGTTGTTAGTA 60.222 40.000 0.00 0.00 32.98 1.82
4276 4615 5.351465 CCACTGGTGCTTATGTTGTTAGTAG 59.649 44.000 0.00 0.00 0.00 2.57
4280 4619 7.717875 ACTGGTGCTTATGTTGTTAGTAGAAAA 59.282 33.333 0.00 0.00 0.00 2.29
4282 4621 7.174253 TGGTGCTTATGTTGTTAGTAGAAAAGG 59.826 37.037 0.00 0.00 0.00 3.11
4285 4624 8.780249 TGCTTATGTTGTTAGTAGAAAAGGAAC 58.220 33.333 0.00 0.00 0.00 3.62
4289 4628 8.691661 ATGTTGTTAGTAGAAAAGGAACATGT 57.308 30.769 0.00 0.00 32.87 3.21
4305 4644 9.696917 AAGGAACATGTGATTATTTCTTTTGTC 57.303 29.630 0.00 0.00 0.00 3.18
4321 4660 7.464830 TCTTTTGTCTTCTAAACAGAGAACG 57.535 36.000 0.00 0.00 32.05 3.95
4322 4661 6.479001 TCTTTTGTCTTCTAAACAGAGAACGG 59.521 38.462 0.00 0.00 32.05 4.44
4394 4733 9.482627 GGAGAATTACATAGAGGTTGAATACAG 57.517 37.037 0.00 0.00 0.00 2.74
4396 4735 7.653713 AGAATTACATAGAGGTTGAATACAGCG 59.346 37.037 0.00 0.00 0.00 5.18
4402 4741 5.599999 AGAGGTTGAATACAGCGTAGAAT 57.400 39.130 0.00 0.00 0.00 2.40
4404 4743 6.740110 AGAGGTTGAATACAGCGTAGAATAG 58.260 40.000 0.00 0.00 0.00 1.73
4416 4755 4.579753 AGCGTAGAATAGAAGAGGGTACAC 59.420 45.833 0.00 0.00 0.00 2.90
4418 4757 5.163581 GCGTAGAATAGAAGAGGGTACACAA 60.164 44.000 0.00 0.00 0.00 3.33
4472 4811 2.111669 TGCCTGGCGCATCTATGG 59.888 61.111 14.98 2.33 44.64 2.74
4524 4864 4.025229 CACGAGAACGAAGGAATCAAAACA 60.025 41.667 0.00 0.00 42.66 2.83
4543 4883 4.120244 GAGCTCACCTCCTGGACA 57.880 61.111 9.40 0.00 34.35 4.02
4579 4920 6.071320 GGAAGCAATATCCACCCTCTTAAAT 58.929 40.000 0.00 0.00 36.92 1.40
4587 4928 6.625532 ATCCACCCTCTTAAATTTTGCAAT 57.374 33.333 0.00 0.00 0.00 3.56
4632 4973 4.511617 ACGCATCACTCTCGATGATAAT 57.488 40.909 5.13 0.00 44.67 1.28
4689 5030 2.438434 CCGGATCGCCAAGGCTTT 60.438 61.111 9.73 0.00 39.32 3.51
4780 5122 2.161012 TCGAATCACTACTCACGTGTCC 59.839 50.000 16.51 0.00 34.14 4.02
4815 5157 3.870538 TCCTGAATAGCTGGCATCAAT 57.129 42.857 0.00 0.00 35.69 2.57
4842 5185 4.972514 CCTTGATAAAGGTTTCCTCTGC 57.027 45.455 0.00 0.00 35.22 4.26
4855 5198 1.296715 CTCTGCCGGTAACCAGCTT 59.703 57.895 1.90 0.00 33.62 3.74
4877 5220 2.906691 ATTCTCTCTCAGCATTCGGG 57.093 50.000 0.00 0.00 0.00 5.14
4879 5222 0.033109 TCTCTCTCAGCATTCGGGGA 60.033 55.000 0.00 0.00 0.00 4.81
4895 5239 2.419297 CGGGGATTCTCACTTCTTCCAG 60.419 54.545 0.00 0.00 0.00 3.86
4940 5284 6.588719 ATCAATTTCCCATTCGACAAAAGA 57.411 33.333 0.00 0.00 0.00 2.52
4995 5342 4.819105 ATTGTTCCGTTCTATCCAGACA 57.181 40.909 0.00 0.00 0.00 3.41
5008 5359 1.004080 CAGACAGTCCAGCACCCAG 60.004 63.158 0.00 0.00 0.00 4.45
5035 5386 5.933617 AGATAATGGCAGCAAGTGATTCTA 58.066 37.500 0.00 0.00 0.00 2.10
5042 5393 5.068987 TGGCAGCAAGTGATTCTAAAACTTT 59.931 36.000 0.00 0.00 31.88 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 3.943671 TGGCTAGGCTTTTTATGGCTA 57.056 42.857 18.18 0.00 40.79 3.93
6 7 2.826674 TGGCTAGGCTTTTTATGGCT 57.173 45.000 18.18 0.00 42.95 4.75
7 8 3.721035 CAATGGCTAGGCTTTTTATGGC 58.279 45.455 18.18 0.00 0.00 4.40
8 9 3.132646 TGCAATGGCTAGGCTTTTTATGG 59.867 43.478 18.18 6.38 41.91 2.74
9 10 4.114794 GTGCAATGGCTAGGCTTTTTATG 58.885 43.478 18.18 7.45 41.91 1.90
10 11 3.132824 GGTGCAATGGCTAGGCTTTTTAT 59.867 43.478 18.18 0.00 41.91 1.40
11 12 2.495669 GGTGCAATGGCTAGGCTTTTTA 59.504 45.455 18.18 5.91 41.91 1.52
12 13 1.276138 GGTGCAATGGCTAGGCTTTTT 59.724 47.619 18.18 5.92 41.91 1.94
13 14 0.897621 GGTGCAATGGCTAGGCTTTT 59.102 50.000 18.18 8.42 41.91 2.27
14 15 0.040204 AGGTGCAATGGCTAGGCTTT 59.960 50.000 18.18 14.47 41.91 3.51
15 16 0.394899 GAGGTGCAATGGCTAGGCTT 60.395 55.000 18.18 8.48 41.91 4.35
28 29 0.399233 AGGGATGGGTAGAGAGGTGC 60.399 60.000 0.00 0.00 0.00 5.01
33 34 5.615692 TGTAGAGAATAGGGATGGGTAGAGA 59.384 44.000 0.00 0.00 0.00 3.10
39 40 3.513515 GCTCTGTAGAGAATAGGGATGGG 59.486 52.174 12.89 0.00 44.74 4.00
45 46 2.227865 GCTCGGCTCTGTAGAGAATAGG 59.772 54.545 12.89 0.36 44.74 2.57
56 57 2.402305 GATCTACATTGCTCGGCTCTG 58.598 52.381 0.00 0.00 0.00 3.35
57 58 1.342819 GGATCTACATTGCTCGGCTCT 59.657 52.381 0.00 0.00 0.00 4.09
78 79 3.626977 CTCTGCTGCTAGTGATTAGTCG 58.373 50.000 0.00 0.00 0.00 4.18
88 89 1.818785 GCTTGGGCTCTGCTGCTAG 60.819 63.158 0.00 0.00 35.22 3.42
89 90 2.128290 TTGCTTGGGCTCTGCTGCTA 62.128 55.000 0.00 0.00 39.59 3.49
110 111 3.381045 TGCTGTTCACGTCACTTTCTAG 58.619 45.455 0.00 0.00 0.00 2.43
111 112 3.381045 CTGCTGTTCACGTCACTTTCTA 58.619 45.455 0.00 0.00 0.00 2.10
149 150 7.305993 GCGATTAAGACTTTTGTGTTTCCTTTG 60.306 37.037 0.00 0.00 37.16 2.77
155 156 6.857964 CAGATGCGATTAAGACTTTTGTGTTT 59.142 34.615 0.00 0.00 37.16 2.83
158 160 5.931532 ACAGATGCGATTAAGACTTTTGTG 58.068 37.500 0.00 0.00 0.00 3.33
160 162 6.169419 TGACAGATGCGATTAAGACTTTTG 57.831 37.500 0.00 0.00 0.00 2.44
176 178 2.766263 TCCTGATTACGGCTTGACAGAT 59.234 45.455 0.00 0.00 0.00 2.90
225 227 1.799403 GATCTGCGAGCAATGATGGAG 59.201 52.381 4.83 0.00 0.00 3.86
226 228 1.870993 CGATCTGCGAGCAATGATGGA 60.871 52.381 4.83 0.00 44.57 3.41
228 230 1.070776 CACGATCTGCGAGCAATGATG 60.071 52.381 4.83 1.76 44.57 3.07
254 256 2.429250 ACCCCCTTGAAAGTTTGAAACG 59.571 45.455 1.97 0.00 36.23 3.60
283 285 2.355009 CCGTGTGGCAAGCAAAGC 60.355 61.111 0.00 0.00 0.00 3.51
284 286 1.299316 CACCGTGTGGCAAGCAAAG 60.299 57.895 0.00 0.00 39.70 2.77
285 287 1.106351 ATCACCGTGTGGCAAGCAAA 61.106 50.000 0.00 0.00 39.70 3.68
311 313 2.688446 TGCATTTTAAACGTGGTGTGGA 59.312 40.909 0.00 0.00 0.00 4.02
335 347 0.881118 ATCACCGTGTGGCACATTTC 59.119 50.000 24.95 10.19 44.52 2.17
366 378 2.288213 GCAAACTCCCTGTAAAAGCCAC 60.288 50.000 0.00 0.00 0.00 5.01
370 382 3.056607 CCATGGCAAACTCCCTGTAAAAG 60.057 47.826 0.00 0.00 0.00 2.27
414 429 3.454812 AGCATAACCCACCCGATATATCC 59.545 47.826 7.15 0.00 0.00 2.59
439 454 2.621526 ACTTTGAACCCAACCGAATCAC 59.378 45.455 0.00 0.00 30.88 3.06
480 497 1.605710 GCCACATGATGAAGGGAATCG 59.394 52.381 0.00 0.00 0.00 3.34
572 590 1.733718 GCCTGCGATTTTCCTGCTTTC 60.734 52.381 0.00 0.00 0.00 2.62
579 597 0.729140 CGTTGTGCCTGCGATTTTCC 60.729 55.000 0.00 0.00 0.00 3.13
580 598 1.337110 GCGTTGTGCCTGCGATTTTC 61.337 55.000 0.00 0.00 37.76 2.29
681 701 2.017559 ATAAGGCCGAGCAGACGACC 62.018 60.000 0.00 0.00 36.12 4.79
691 711 2.698274 TGATAGTGCAGAATAAGGCCGA 59.302 45.455 0.00 0.00 0.00 5.54
721 744 0.968405 TTCATTTTGTGGCTGGGAGC 59.032 50.000 0.00 0.00 41.46 4.70
785 815 4.141344 CCGGAAAGGAACCTCCCATTAATA 60.141 45.833 0.00 0.00 45.00 0.98
786 816 3.372675 CCGGAAAGGAACCTCCCATTAAT 60.373 47.826 0.00 0.00 45.00 1.40
787 817 2.025699 CCGGAAAGGAACCTCCCATTAA 60.026 50.000 0.00 0.00 45.00 1.40
788 818 1.562475 CCGGAAAGGAACCTCCCATTA 59.438 52.381 0.00 0.00 45.00 1.90
789 819 0.331616 CCGGAAAGGAACCTCCCATT 59.668 55.000 0.00 0.00 45.00 3.16
790 820 0.845102 ACCGGAAAGGAACCTCCCAT 60.845 55.000 9.46 0.00 45.00 4.00
791 821 0.178897 TACCGGAAAGGAACCTCCCA 60.179 55.000 9.46 0.00 45.00 4.37
792 822 0.986527 TTACCGGAAAGGAACCTCCC 59.013 55.000 9.46 0.00 45.00 4.30
831 861 2.581354 GAGACGCCATGACCTGCT 59.419 61.111 0.00 0.00 0.00 4.24
832 862 2.512515 GGAGACGCCATGACCTGC 60.513 66.667 0.00 0.00 36.34 4.85
869 899 2.688446 GCCTAATTAGCCCAACCTGTTC 59.312 50.000 6.99 0.00 0.00 3.18
959 989 5.076598 AGCGGTGGATATATATAGGGGAGAT 59.923 44.000 0.00 0.00 0.00 2.75
1150 1208 0.115152 TCTCCCCTGTGCTCTTCAGA 59.885 55.000 0.00 0.00 35.20 3.27
1166 1224 6.930731 AGGAATCTACACACTTCTTCTTCTC 58.069 40.000 0.00 0.00 0.00 2.87
1194 1252 2.029020 GCCAAAACTCCAGGACAATTCC 60.029 50.000 0.00 0.00 43.22 3.01
1195 1253 2.627699 TGCCAAAACTCCAGGACAATTC 59.372 45.455 0.00 0.00 0.00 2.17
1196 1254 2.676748 TGCCAAAACTCCAGGACAATT 58.323 42.857 0.00 0.00 0.00 2.32
1197 1255 2.380064 TGCCAAAACTCCAGGACAAT 57.620 45.000 0.00 0.00 0.00 2.71
1198 1256 2.238521 GATGCCAAAACTCCAGGACAA 58.761 47.619 0.00 0.00 0.00 3.18
1199 1257 1.881925 CGATGCCAAAACTCCAGGACA 60.882 52.381 0.00 0.00 0.00 4.02
1200 1258 0.804989 CGATGCCAAAACTCCAGGAC 59.195 55.000 0.00 0.00 0.00 3.85
1201 1259 0.322456 CCGATGCCAAAACTCCAGGA 60.322 55.000 0.00 0.00 0.00 3.86
1202 1260 0.322456 TCCGATGCCAAAACTCCAGG 60.322 55.000 0.00 0.00 0.00 4.45
1203 1261 1.089920 CTCCGATGCCAAAACTCCAG 58.910 55.000 0.00 0.00 0.00 3.86
1204 1262 0.690192 TCTCCGATGCCAAAACTCCA 59.310 50.000 0.00 0.00 0.00 3.86
1205 1263 1.066143 TCTCTCCGATGCCAAAACTCC 60.066 52.381 0.00 0.00 0.00 3.85
1206 1264 2.386661 TCTCTCCGATGCCAAAACTC 57.613 50.000 0.00 0.00 0.00 3.01
1207 1265 2.859165 TTCTCTCCGATGCCAAAACT 57.141 45.000 0.00 0.00 0.00 2.66
1208 1266 2.162408 CCTTTCTCTCCGATGCCAAAAC 59.838 50.000 0.00 0.00 0.00 2.43
1209 1267 2.436417 CCTTTCTCTCCGATGCCAAAA 58.564 47.619 0.00 0.00 0.00 2.44
1210 1268 1.340017 CCCTTTCTCTCCGATGCCAAA 60.340 52.381 0.00 0.00 0.00 3.28
1211 1269 0.253044 CCCTTTCTCTCCGATGCCAA 59.747 55.000 0.00 0.00 0.00 4.52
1212 1270 0.617535 TCCCTTTCTCTCCGATGCCA 60.618 55.000 0.00 0.00 0.00 4.92
1213 1271 0.105778 CTCCCTTTCTCTCCGATGCC 59.894 60.000 0.00 0.00 0.00 4.40
1214 1272 1.068434 CTCTCCCTTTCTCTCCGATGC 59.932 57.143 0.00 0.00 0.00 3.91
1215 1273 2.622942 CTCTCTCCCTTTCTCTCCGATG 59.377 54.545 0.00 0.00 0.00 3.84
1216 1274 2.424234 CCTCTCTCCCTTTCTCTCCGAT 60.424 54.545 0.00 0.00 0.00 4.18
1217 1275 1.064314 CCTCTCTCCCTTTCTCTCCGA 60.064 57.143 0.00 0.00 0.00 4.55
1218 1276 1.398692 CCTCTCTCCCTTTCTCTCCG 58.601 60.000 0.00 0.00 0.00 4.63
1219 1277 1.289530 TCCCTCTCTCCCTTTCTCTCC 59.710 57.143 0.00 0.00 0.00 3.71
1220 1278 2.838637 TCCCTCTCTCCCTTTCTCTC 57.161 55.000 0.00 0.00 0.00 3.20
1221 1279 3.078305 TCTTTCCCTCTCTCCCTTTCTCT 59.922 47.826 0.00 0.00 0.00 3.10
1222 1280 3.445987 TCTTTCCCTCTCTCCCTTTCTC 58.554 50.000 0.00 0.00 0.00 2.87
1223 1281 3.569135 TCTTTCCCTCTCTCCCTTTCT 57.431 47.619 0.00 0.00 0.00 2.52
1224 1282 3.118075 CCATCTTTCCCTCTCTCCCTTTC 60.118 52.174 0.00 0.00 0.00 2.62
1225 1283 2.849318 CCATCTTTCCCTCTCTCCCTTT 59.151 50.000 0.00 0.00 0.00 3.11
1226 1284 2.226013 ACCATCTTTCCCTCTCTCCCTT 60.226 50.000 0.00 0.00 0.00 3.95
1227 1285 1.367848 ACCATCTTTCCCTCTCTCCCT 59.632 52.381 0.00 0.00 0.00 4.20
1249 1307 1.330655 GGCGTCCTCTGATTCTGGGA 61.331 60.000 0.00 0.00 0.00 4.37
1251 1309 1.227089 CGGCGTCCTCTGATTCTGG 60.227 63.158 0.00 0.00 0.00 3.86
1324 1382 5.850557 AATCAATCACCAAGAACACAACA 57.149 34.783 0.00 0.00 0.00 3.33
1326 1384 5.128499 ACCAAATCAATCACCAAGAACACAA 59.872 36.000 0.00 0.00 0.00 3.33
1365 1438 2.401766 CCAGAACACCTGCATCGCC 61.402 63.158 0.00 0.00 41.57 5.54
1366 1439 3.044059 GCCAGAACACCTGCATCGC 62.044 63.158 0.00 0.00 41.57 4.58
1367 1440 2.401766 GGCCAGAACACCTGCATCG 61.402 63.158 0.00 0.00 41.57 3.84
1486 1559 2.262774 AAATGAGGAGCCTCGGCCTG 62.263 60.000 11.64 0.00 45.48 4.85
1487 1560 1.977293 GAAATGAGGAGCCTCGGCCT 61.977 60.000 11.64 0.00 45.48 5.19
1489 1562 1.884926 CGAAATGAGGAGCCTCGGC 60.885 63.158 11.64 0.00 45.48 5.54
1490 1563 1.227380 CCGAAATGAGGAGCCTCGG 60.227 63.158 11.64 5.97 45.48 4.63
1491 1564 1.227380 CCCGAAATGAGGAGCCTCG 60.227 63.158 11.64 0.55 45.48 4.63
1493 1566 1.977293 GAGCCCGAAATGAGGAGCCT 61.977 60.000 0.00 0.00 0.00 4.58
1494 1567 1.524849 GAGCCCGAAATGAGGAGCC 60.525 63.158 0.00 0.00 0.00 4.70
1495 1568 0.813210 CAGAGCCCGAAATGAGGAGC 60.813 60.000 0.00 0.00 0.00 4.70
1496 1569 0.539051 ACAGAGCCCGAAATGAGGAG 59.461 55.000 0.00 0.00 0.00 3.69
1497 1570 0.250234 CACAGAGCCCGAAATGAGGA 59.750 55.000 0.00 0.00 0.00 3.71
1499 1572 2.322355 ATCACAGAGCCCGAAATGAG 57.678 50.000 0.00 0.00 0.00 2.90
1500 1573 2.632377 GAATCACAGAGCCCGAAATGA 58.368 47.619 0.00 0.00 0.00 2.57
1501 1574 1.328680 CGAATCACAGAGCCCGAAATG 59.671 52.381 0.00 0.00 0.00 2.32
1504 1577 0.606096 TTCGAATCACAGAGCCCGAA 59.394 50.000 0.00 0.00 34.30 4.30
1505 1578 0.824109 ATTCGAATCACAGAGCCCGA 59.176 50.000 4.39 0.00 0.00 5.14
1506 1579 1.202463 AGATTCGAATCACAGAGCCCG 60.202 52.381 33.42 0.00 37.89 6.13
1508 1581 2.123342 CGAGATTCGAATCACAGAGCC 58.877 52.381 33.42 15.27 43.74 4.70
1509 1582 2.123342 CCGAGATTCGAATCACAGAGC 58.877 52.381 33.42 16.91 43.74 4.09
1511 1584 2.223272 CGACCGAGATTCGAATCACAGA 60.223 50.000 33.42 0.00 43.74 3.41
1513 1586 1.797713 GCGACCGAGATTCGAATCACA 60.798 52.381 33.42 0.00 43.74 3.58
1515 1588 0.248907 GGCGACCGAGATTCGAATCA 60.249 55.000 33.42 0.00 43.74 2.57
1516 1589 2.507643 GGCGACCGAGATTCGAATC 58.492 57.895 27.16 27.16 43.74 2.52
1517 1590 4.732106 GGCGACCGAGATTCGAAT 57.268 55.556 11.20 11.20 43.74 3.34
1574 1647 0.674895 GAGACGGACAGCAGGCAAAT 60.675 55.000 0.00 0.00 0.00 2.32
1580 1653 2.807045 GCACGAGACGGACAGCAG 60.807 66.667 0.00 0.00 0.00 4.24
1693 1766 4.051237 GCCAACTTTCCAAACATGAGAAC 58.949 43.478 0.00 0.00 0.00 3.01
1755 1828 1.814248 GCACTTTTCCCCGTCTTCAGT 60.814 52.381 0.00 0.00 0.00 3.41
1807 1880 3.077359 GGGAATGTGGTATCAGCTATGC 58.923 50.000 0.00 0.00 0.00 3.14
1811 1884 0.179045 GCGGGAATGTGGTATCAGCT 60.179 55.000 0.00 0.00 0.00 4.24
1820 1893 0.109781 CTTTTGACGGCGGGAATGTG 60.110 55.000 13.24 0.00 0.00 3.21
1829 1905 3.487544 GGCAATGATCTACTTTTGACGGC 60.488 47.826 0.00 0.00 0.00 5.68
1847 1923 3.320541 CCACCAAAATCAAGTACTGGCAA 59.679 43.478 0.00 0.00 0.00 4.52
1868 1944 2.115343 AAATCGGCAAGAAGTCCTCC 57.885 50.000 0.00 0.00 0.00 4.30
1881 1957 2.057316 TGTGAAAATGCGCAAAATCGG 58.943 42.857 17.11 0.00 0.00 4.18
1909 1985 3.423154 GACGGGCAGAAGCAACGG 61.423 66.667 8.25 0.00 43.82 4.44
1978 2149 4.855388 CACTCTGAATTTTGCTTCCGATTG 59.145 41.667 0.00 0.00 0.00 2.67
2001 2172 0.842635 AGGGTGGCTCATGAGGAATC 59.157 55.000 23.89 7.16 0.00 2.52
2031 2205 0.248990 GCTCTCCTCTGCAGATCGTG 60.249 60.000 18.63 11.27 0.00 4.35
2801 3013 2.047179 GGCGACCCTGGACTTCAC 60.047 66.667 0.00 0.00 0.00 3.18
2890 3108 2.820037 CCGCCGCCCTTCTTCTTC 60.820 66.667 0.00 0.00 0.00 2.87
2932 3150 1.980772 GCCCACCATCTGCTTGCTT 60.981 57.895 0.00 0.00 0.00 3.91
3254 3505 3.517602 CATTGGTGGATGCAATTCAGTG 58.482 45.455 0.00 0.00 27.53 3.66
3255 3506 3.880047 CATTGGTGGATGCAATTCAGT 57.120 42.857 0.00 0.00 27.53 3.41
3282 3546 2.027385 CATCTCTGTCAGATCACCGGA 58.973 52.381 9.46 0.00 40.20 5.14
3413 3677 3.673594 CGAGACTGCGTACCTGATCTTTT 60.674 47.826 0.00 0.00 0.00 2.27
3432 3696 0.318529 CGGAGGTGATGATGAGCGAG 60.319 60.000 0.00 0.00 0.00 5.03
3494 3758 3.303197 CGCTTCAGCTGATCATCACATTC 60.303 47.826 19.04 0.00 39.32 2.67
3496 3760 2.210961 CGCTTCAGCTGATCATCACAT 58.789 47.619 19.04 0.00 39.32 3.21
3697 3972 3.450115 AGCTCCGACCTGCCGTAC 61.450 66.667 0.00 0.00 0.00 3.67
3763 4041 3.114616 CTGCCGCAGAACACCTCG 61.115 66.667 15.74 0.00 32.44 4.63
3796 4080 4.400109 GCGTCCGTGAGCGTGAGA 62.400 66.667 0.00 0.00 36.15 3.27
3897 4186 1.228094 TTCAGCCGGTGCATGTCAA 60.228 52.632 1.90 0.00 41.13 3.18
3898 4187 1.672030 CTTCAGCCGGTGCATGTCA 60.672 57.895 1.90 0.00 41.13 3.58
3899 4188 3.044059 GCTTCAGCCGGTGCATGTC 62.044 63.158 1.90 0.00 41.13 3.06
3901 4190 1.940883 AATGCTTCAGCCGGTGCATG 61.941 55.000 16.81 6.74 44.15 4.06
3902 4191 1.252904 AAATGCTTCAGCCGGTGCAT 61.253 50.000 1.90 9.09 46.46 3.96
3903 4192 1.902918 AAATGCTTCAGCCGGTGCA 60.903 52.632 1.90 6.99 41.13 4.57
3904 4193 1.444895 CAAATGCTTCAGCCGGTGC 60.445 57.895 1.90 0.76 41.18 5.01
3907 4196 1.334869 GTATCCAAATGCTTCAGCCGG 59.665 52.381 0.00 0.00 41.18 6.13
3908 4197 2.016318 TGTATCCAAATGCTTCAGCCG 58.984 47.619 0.00 0.00 41.18 5.52
3909 4198 2.223665 GCTGTATCCAAATGCTTCAGCC 60.224 50.000 0.00 0.00 40.23 4.85
3910 4199 2.424601 TGCTGTATCCAAATGCTTCAGC 59.575 45.455 0.00 0.00 44.39 4.26
3911 4200 3.943381 TCTGCTGTATCCAAATGCTTCAG 59.057 43.478 0.00 0.00 0.00 3.02
3912 4201 3.954200 TCTGCTGTATCCAAATGCTTCA 58.046 40.909 0.00 0.00 0.00 3.02
3913 4202 5.334724 GCTATCTGCTGTATCCAAATGCTTC 60.335 44.000 0.00 0.00 38.95 3.86
3914 4203 4.518211 GCTATCTGCTGTATCCAAATGCTT 59.482 41.667 0.00 0.00 38.95 3.91
3915 4204 4.070716 GCTATCTGCTGTATCCAAATGCT 58.929 43.478 0.00 0.00 38.95 3.79
3916 4205 4.416505 GCTATCTGCTGTATCCAAATGC 57.583 45.455 0.00 0.00 38.95 3.56
3949 4238 0.804989 CCCGTCCAAGATTTGTCAGC 59.195 55.000 0.00 0.00 0.00 4.26
3951 4240 0.768622 ACCCCGTCCAAGATTTGTCA 59.231 50.000 0.00 0.00 0.00 3.58
3969 4258 1.070786 ATCACCCACACGACACCAC 59.929 57.895 0.00 0.00 0.00 4.16
3991 4280 0.368227 CAGATGTTTCGTCAGAGCGC 59.632 55.000 0.00 0.00 0.00 5.92
4008 4297 0.249699 TGCCAGTAACACCGTCACAG 60.250 55.000 0.00 0.00 0.00 3.66
4048 4373 4.625607 ACTAACTCAAAGGTGAAGAGGG 57.374 45.455 0.00 0.00 31.88 4.30
4051 4376 6.742559 AGGTTACTAACTCAAAGGTGAAGA 57.257 37.500 0.00 0.00 31.88 2.87
4052 4377 7.715686 AGAAAGGTTACTAACTCAAAGGTGAAG 59.284 37.037 0.00 0.00 31.88 3.02
4053 4378 7.571025 AGAAAGGTTACTAACTCAAAGGTGAA 58.429 34.615 0.00 0.00 31.88 3.18
4070 4395 1.068121 CCTGACAGGGGAGAAAGGTT 58.932 55.000 14.26 0.00 0.00 3.50
4098 4436 1.608109 TGCGTGTGATTCAAACAGCAT 59.392 42.857 17.01 0.00 31.38 3.79
4160 4499 7.807907 TGTTGTTTTTGTTTTTGTTGTTGTTGT 59.192 25.926 0.00 0.00 0.00 3.32
4170 4509 7.791131 GGTGCATTTTTGTTGTTTTTGTTTTTG 59.209 29.630 0.00 0.00 0.00 2.44
4171 4510 7.492344 TGGTGCATTTTTGTTGTTTTTGTTTTT 59.508 25.926 0.00 0.00 0.00 1.94
4172 4511 6.980397 TGGTGCATTTTTGTTGTTTTTGTTTT 59.020 26.923 0.00 0.00 0.00 2.43
4173 4512 6.507023 TGGTGCATTTTTGTTGTTTTTGTTT 58.493 28.000 0.00 0.00 0.00 2.83
4174 4513 6.076981 TGGTGCATTTTTGTTGTTTTTGTT 57.923 29.167 0.00 0.00 0.00 2.83
4175 4514 5.695851 TGGTGCATTTTTGTTGTTTTTGT 57.304 30.435 0.00 0.00 0.00 2.83
4176 4515 4.558080 GCTGGTGCATTTTTGTTGTTTTTG 59.442 37.500 0.00 0.00 39.41 2.44
4177 4516 4.380339 GGCTGGTGCATTTTTGTTGTTTTT 60.380 37.500 0.00 0.00 41.91 1.94
4178 4517 3.128415 GGCTGGTGCATTTTTGTTGTTTT 59.872 39.130 0.00 0.00 41.91 2.43
4179 4518 2.682352 GGCTGGTGCATTTTTGTTGTTT 59.318 40.909 0.00 0.00 41.91 2.83
4180 4519 2.287769 GGCTGGTGCATTTTTGTTGTT 58.712 42.857 0.00 0.00 41.91 2.83
4181 4520 1.805871 CGGCTGGTGCATTTTTGTTGT 60.806 47.619 0.00 0.00 41.91 3.32
4182 4521 0.860533 CGGCTGGTGCATTTTTGTTG 59.139 50.000 0.00 0.00 41.91 3.33
4185 4524 1.374505 CCCGGCTGGTGCATTTTTG 60.375 57.895 11.58 0.00 41.91 2.44
4208 4547 3.062639 CGGTACAGACCCGGGTTT 58.937 61.111 30.89 21.55 43.64 3.27
4267 4606 8.918202 ATCACATGTTCCTTTTCTACTAACAA 57.082 30.769 0.00 0.00 34.08 2.83
4280 4619 9.082313 AGACAAAAGAAATAATCACATGTTCCT 57.918 29.630 0.00 0.00 0.00 3.36
4295 4634 8.388103 CGTTCTCTGTTTAGAAGACAAAAGAAA 58.612 33.333 0.00 0.00 36.19 2.52
4298 4637 6.479001 TCCGTTCTCTGTTTAGAAGACAAAAG 59.521 38.462 0.00 0.00 36.19 2.27
4299 4638 6.342906 TCCGTTCTCTGTTTAGAAGACAAAA 58.657 36.000 0.00 0.00 36.19 2.44
4305 4644 5.290386 ACTGTTCCGTTCTCTGTTTAGAAG 58.710 41.667 0.00 0.00 36.19 2.85
4334 4673 7.462724 GCAGTAAAGCTTGTGTTTTGTAAACAG 60.463 37.037 0.00 0.00 0.00 3.16
4336 4675 6.530181 AGCAGTAAAGCTTGTGTTTTGTAAAC 59.470 34.615 0.00 0.00 43.70 2.01
4366 4705 7.698163 ATTCAACCTCTATGTAATTCTCCCT 57.302 36.000 0.00 0.00 0.00 4.20
4367 4706 8.429641 TGTATTCAACCTCTATGTAATTCTCCC 58.570 37.037 0.00 0.00 0.00 4.30
4394 4733 4.337555 TGTGTACCCTCTTCTATTCTACGC 59.662 45.833 0.00 0.00 0.00 4.42
4402 4741 6.303903 GGGTTAATTGTGTACCCTCTTCTA 57.696 41.667 0.00 0.00 46.55 2.10
4416 4755 9.104965 TCGTAGAAGATGTTTATGGGTTAATTG 57.895 33.333 0.00 0.00 0.00 2.32
4418 4757 9.490379 GATCGTAGAAGATGTTTATGGGTTAAT 57.510 33.333 0.00 0.00 43.58 1.40
4472 4811 0.109132 CGGGAAGCAAACATTCTGCC 60.109 55.000 0.00 0.00 40.86 4.85
4477 4816 2.959707 TGTAAACCGGGAAGCAAACATT 59.040 40.909 6.32 0.00 0.00 2.71
4543 4883 8.362639 GTGGATATTGCTTCCATTTGTTATGAT 58.637 33.333 0.00 0.00 44.75 2.45
4568 4909 9.822185 GATCAATATTGCAAAATTTAAGAGGGT 57.178 29.630 10.76 0.00 0.00 4.34
4579 4920 9.142515 GTTGTTCAGATGATCAATATTGCAAAA 57.857 29.630 10.76 0.00 36.50 2.44
4587 4928 6.566079 AGGAGGTTGTTCAGATGATCAATA 57.434 37.500 0.00 0.00 36.50 1.90
4598 4939 1.621317 TGATGCGTAGGAGGTTGTTCA 59.379 47.619 0.00 0.00 0.00 3.18
4632 4973 0.887933 GGATTTTGGCTTCCGCAAGA 59.112 50.000 0.00 0.00 43.02 3.02
4689 5030 2.674954 CGCAAAATGCAAGGTTCATGA 58.325 42.857 2.99 0.00 45.36 3.07
4780 5122 1.180029 CAGGAAACTTGGCTCATGGG 58.820 55.000 0.00 0.00 40.21 4.00
4842 5185 3.118738 AGAGAATACAAGCTGGTTACCGG 60.119 47.826 5.73 5.73 0.00 5.28
4855 5198 3.068732 CCCGAATGCTGAGAGAGAATACA 59.931 47.826 0.00 0.00 0.00 2.29
4895 5239 9.481340 TTGATACTATTCATGATCTTGCTACAC 57.519 33.333 0.00 0.00 0.00 2.90
4924 5268 3.762407 TCAGTCTTTTGTCGAATGGGA 57.238 42.857 0.00 0.00 0.00 4.37
4931 5275 3.493129 TCGTTCCATTCAGTCTTTTGTCG 59.507 43.478 0.00 0.00 0.00 4.35
4962 5306 3.104512 ACGGAACAATAGGAGACATGGA 58.895 45.455 0.00 0.00 0.00 3.41
5008 5359 3.879295 TCACTTGCTGCCATTATCTTAGC 59.121 43.478 0.00 0.00 35.06 3.09


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

AutoCloner maintained by Alex Coulton.