Multiple sequence alignment - TraesCS7D01G446000

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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 TraesCS7D01G446000 chr7D 100.000 3099 0 0 1 3099 566554969 566551871 0.000000e+00 5723.0
1 TraesCS7D01G446000 chr7A 87.433 1305 105 25 1 1260 652725550 652724260 0.000000e+00 1447.0
2 TraesCS7D01G446000 chr7A 86.646 951 71 20 1760 2686 652723216 652722298 0.000000e+00 1002.0
3 TraesCS7D01G446000 chr7A 92.373 354 13 6 2727 3080 652722210 652721871 2.780000e-135 492.0
4 TraesCS7D01G446000 chr7A 86.598 194 24 2 1503 1695 652724014 652723822 2.420000e-51 213.0
5 TraesCS7D01G446000 chr7A 100.000 38 0 0 3062 3099 652721874 652721837 1.540000e-08 71.3
6 TraesCS7D01G446000 chr7B 86.683 1254 92 35 1 1202 620656584 620657814 0.000000e+00 1321.0
7 TraesCS7D01G446000 chr7B 90.936 673 56 5 1766 2437 620658635 620659303 0.000000e+00 900.0
8 TraesCS7D01G446000 chr7B 90.252 318 21 7 2787 3099 620659805 620660117 1.030000e-109 407.0
9 TraesCS7D01G446000 chr6B 90.031 321 27 4 1 317 452991688 452991369 8.000000e-111 411.0
10 TraesCS7D01G446000 chr6B 93.220 177 12 0 2923 3099 179991768 179991592 8.520000e-66 261.0
11 TraesCS7D01G446000 chr5B 90.031 321 27 4 1 317 337799881 337799562 8.000000e-111 411.0
12 TraesCS7D01G446000 chr6D 93.820 178 9 2 2923 3099 96827411 96827235 1.830000e-67 267.0
13 TraesCS7D01G446000 chr6A 93.785 177 11 0 2923 3099 115831441 115831265 1.830000e-67 267.0
14 TraesCS7D01G446000 chr3A 88.136 59 7 0 2289 2347 532041322 532041264 1.540000e-08 71.3
15 TraesCS7D01G446000 chr3A 88.136 59 7 0 2289 2347 532066809 532066751 1.540000e-08 71.3
16 TraesCS7D01G446000 chr3A 88.136 59 7 0 2289 2347 532092613 532092555 1.540000e-08 71.3


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 TraesCS7D01G446000 chr7D 566551871 566554969 3098 True 5723.00 5723 100.000000 1 3099 1 chr7D.!!$R1 3098
1 TraesCS7D01G446000 chr7A 652721837 652725550 3713 True 645.06 1447 90.610000 1 3099 5 chr7A.!!$R1 3098
2 TraesCS7D01G446000 chr7B 620656584 620660117 3533 False 876.00 1321 89.290333 1 3099 3 chr7B.!!$F1 3098

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
396 416 0.251474 AACCATGGCTGACAGCACAT 60.251 50.0 27.87 23.15 44.75 3.21 F
1066 1137 0.038526 CGCCAAGTTAGTCACTCGGT 60.039 55.0 0.00 0.00 32.94 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1322 0.100503 GTGCGAAACAGGTTTGTGCT 59.899 50.0 15.42 0.00 37.67 4.40 R
2402 3200 0.178984 ACACACCCTTAAAACCCGGG 60.179 55.0 22.25 22.25 43.79 5.73 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
45 47 2.362717 CTCTACTACCTAGCAACAGGGC 59.637 54.545 4.31 0.00 40.29 5.19
66 68 3.144506 CAATCCTGCAGTCTCTTGTTGT 58.855 45.455 13.81 0.00 0.00 3.32
78 80 3.111098 CTCTTGTTGTTTGCTGCAAGAC 58.889 45.455 15.39 15.66 41.33 3.01
104 106 7.254795 CGAAACTTATTAAGCATTCCACCTAGG 60.255 40.741 7.41 7.41 39.47 3.02
145 147 8.298854 CAACCAAACTGAATCTTCAATCACATA 58.701 33.333 0.00 0.00 36.64 2.29
163 165 0.331278 TACATTGCACCTTCCCTGGG 59.669 55.000 6.33 6.33 0.00 4.45
205 207 4.764050 TTACCACCTCAGAAAGTTCACA 57.236 40.909 0.00 0.00 0.00 3.58
207 209 3.963129 ACCACCTCAGAAAGTTCACAAA 58.037 40.909 0.00 0.00 0.00 2.83
239 242 1.354031 TCCCAGGCTGAGCAATAACAA 59.646 47.619 17.94 0.00 0.00 2.83
264 267 0.824109 TCCCATGTTCACCGCTAGAG 59.176 55.000 0.00 0.00 0.00 2.43
284 287 4.898861 AGAGAGTAGAAACATCCCATCTCC 59.101 45.833 0.00 0.00 33.94 3.71
293 296 6.670902 AGAAACATCCCATCTCCAATGAAAAT 59.329 34.615 0.00 0.00 0.00 1.82
298 301 8.672329 ACATCCCATCTCCAATGAAAATATAGA 58.328 33.333 0.00 0.00 0.00 1.98
309 312 8.863049 CCAATGAAAATATAGAACAGTTGCAAC 58.137 33.333 22.17 22.17 0.00 4.17
312 315 8.795786 TGAAAATATAGAACAGTTGCAACAAC 57.204 30.769 30.11 17.26 0.00 3.32
363 383 2.348218 CCTAAGCGCGCTTTATAAACCG 60.348 50.000 46.40 24.15 37.47 4.44
374 394 6.736853 GCGCTTTATAAACCGATGAATGATAC 59.263 38.462 15.38 0.00 0.00 2.24
384 404 3.364267 CGATGAATGATACGCAACCATGG 60.364 47.826 11.19 11.19 0.00 3.66
396 416 0.251474 AACCATGGCTGACAGCACAT 60.251 50.000 27.87 23.15 44.75 3.21
397 417 0.620030 ACCATGGCTGACAGCACATA 59.380 50.000 27.87 11.89 44.75 2.29
398 418 1.306148 CCATGGCTGACAGCACATAG 58.694 55.000 27.87 17.00 44.75 2.23
399 419 1.134310 CCATGGCTGACAGCACATAGA 60.134 52.381 27.87 5.50 44.75 1.98
400 420 2.635714 CATGGCTGACAGCACATAGAA 58.364 47.619 27.87 5.46 44.75 2.10
401 421 2.391616 TGGCTGACAGCACATAGAAG 57.608 50.000 27.87 0.00 44.75 2.85
402 422 1.901833 TGGCTGACAGCACATAGAAGA 59.098 47.619 27.87 0.00 44.75 2.87
453 473 0.252467 ACAGGGAAGAGAGACAGGGG 60.252 60.000 0.00 0.00 0.00 4.79
572 592 2.203126 CCCTTCTCCATCGCCTGC 60.203 66.667 0.00 0.00 0.00 4.85
819 874 2.364448 GGTTCGGCCTCCTCCTCT 60.364 66.667 0.00 0.00 0.00 3.69
1066 1137 0.038526 CGCCAAGTTAGTCACTCGGT 60.039 55.000 0.00 0.00 32.94 4.69
1079 1150 0.708802 ACTCGGTTCTCCCTTCCCTA 59.291 55.000 0.00 0.00 0.00 3.53
1084 1155 0.455005 GTTCTCCCTTCCCTACGTCG 59.545 60.000 0.00 0.00 0.00 5.12
1089 1160 1.514553 CCTTCCCTACGTCGAACCC 59.485 63.158 0.00 0.00 0.00 4.11
1091 1162 0.893447 CTTCCCTACGTCGAACCCTT 59.107 55.000 0.00 0.00 0.00 3.95
1092 1163 0.890683 TTCCCTACGTCGAACCCTTC 59.109 55.000 0.00 0.00 0.00 3.46
1121 1195 1.872679 GCTTCGGTCACGGTCGATC 60.873 63.158 0.00 0.00 41.39 3.69
1130 1204 1.134310 TCACGGTCGATCTAGTGGCTA 60.134 52.381 4.21 0.00 35.50 3.93
1131 1205 1.264557 CACGGTCGATCTAGTGGCTAG 59.735 57.143 0.00 0.00 35.57 3.42
1146 1220 1.229359 CTAGTGCCTAGGTCGGGGA 59.771 63.158 11.31 0.00 31.03 4.81
1150 1224 1.049289 GTGCCTAGGTCGGGGATTCT 61.049 60.000 11.31 0.00 0.00 2.40
1151 1225 1.048724 TGCCTAGGTCGGGGATTCTG 61.049 60.000 11.31 0.00 0.00 3.02
1202 1276 0.610785 GAACGCCAGGAATTCCCCAA 60.611 55.000 21.22 0.00 36.42 4.12
1205 1279 0.106519 CGCCAGGAATTCCCCAATCT 60.107 55.000 21.22 0.00 36.42 2.40
1207 1281 2.034878 GCCAGGAATTCCCCAATCTTC 58.965 52.381 21.22 0.00 36.42 2.87
1234 1313 4.608170 TTTTTCCTTGAGGGGCATAGAT 57.392 40.909 0.00 0.00 35.41 1.98
1243 1322 4.492646 TGAGGGGCATAGATGTCAGAATA 58.507 43.478 0.00 0.00 33.08 1.75
1254 1333 4.940046 AGATGTCAGAATAGCACAAACCTG 59.060 41.667 0.00 0.00 0.00 4.00
1256 1335 4.460263 TGTCAGAATAGCACAAACCTGTT 58.540 39.130 0.00 0.00 31.64 3.16
1260 1339 2.989422 ATAGCACAAACCTGTTTCGC 57.011 45.000 5.84 5.84 31.64 4.70
1261 1340 1.669604 TAGCACAAACCTGTTTCGCA 58.330 45.000 13.27 1.57 31.64 5.10
1262 1341 0.100503 AGCACAAACCTGTTTCGCAC 59.899 50.000 13.27 0.00 31.64 5.34
1264 1343 0.738389 CACAAACCTGTTTCGCACCT 59.262 50.000 0.00 0.00 31.64 4.00
1266 1345 1.134175 ACAAACCTGTTTCGCACCTTG 59.866 47.619 0.00 0.00 28.57 3.61
1267 1346 0.744281 AAACCTGTTTCGCACCTTGG 59.256 50.000 0.00 0.00 0.00 3.61
1268 1347 0.106918 AACCTGTTTCGCACCTTGGA 60.107 50.000 0.00 0.00 0.00 3.53
1269 1348 0.110486 ACCTGTTTCGCACCTTGGAT 59.890 50.000 0.00 0.00 0.00 3.41
1270 1349 0.804989 CCTGTTTCGCACCTTGGATC 59.195 55.000 0.00 0.00 0.00 3.36
1271 1350 1.611673 CCTGTTTCGCACCTTGGATCT 60.612 52.381 0.00 0.00 0.00 2.75
1272 1351 2.354704 CCTGTTTCGCACCTTGGATCTA 60.355 50.000 0.00 0.00 0.00 1.98
1273 1352 2.932614 CTGTTTCGCACCTTGGATCTAG 59.067 50.000 0.00 0.00 0.00 2.43
1274 1353 1.666189 GTTTCGCACCTTGGATCTAGC 59.334 52.381 0.00 0.00 0.00 3.42
1275 1354 0.901827 TTCGCACCTTGGATCTAGCA 59.098 50.000 0.00 0.00 0.00 3.49
1276 1355 0.461548 TCGCACCTTGGATCTAGCAG 59.538 55.000 0.00 0.00 0.00 4.24
1277 1356 0.176680 CGCACCTTGGATCTAGCAGT 59.823 55.000 0.00 0.00 0.00 4.40
1278 1357 1.661341 GCACCTTGGATCTAGCAGTG 58.339 55.000 0.00 0.00 0.00 3.66
1279 1358 1.745141 GCACCTTGGATCTAGCAGTGG 60.745 57.143 0.00 0.00 0.00 4.00
1280 1359 0.543749 ACCTTGGATCTAGCAGTGGC 59.456 55.000 0.00 0.00 41.61 5.01
1281 1360 0.543277 CCTTGGATCTAGCAGTGGCA 59.457 55.000 0.00 0.00 44.61 4.92
1282 1361 1.661341 CTTGGATCTAGCAGTGGCAC 58.339 55.000 10.29 10.29 44.61 5.01
1297 1376 3.708013 GCACTATGCCTAGTTCCCC 57.292 57.895 0.00 0.00 35.99 4.81
1298 1377 0.108774 GCACTATGCCTAGTTCCCCC 59.891 60.000 0.00 0.00 35.99 5.40
1299 1378 0.393077 CACTATGCCTAGTTCCCCCG 59.607 60.000 0.00 0.00 35.99 5.73
1306 1385 1.078426 CTAGTTCCCCCGCTGTTGG 60.078 63.158 0.00 0.00 0.00 3.77
1324 1403 7.041167 CGCTGTTGGGATGATATTTCTTGATAA 60.041 37.037 0.00 0.00 0.00 1.75
1325 1404 8.295288 GCTGTTGGGATGATATTTCTTGATAAG 58.705 37.037 0.00 0.00 0.00 1.73
1326 1405 8.696043 TGTTGGGATGATATTTCTTGATAAGG 57.304 34.615 0.00 0.00 0.00 2.69
1327 1406 8.281531 TGTTGGGATGATATTTCTTGATAAGGT 58.718 33.333 0.00 0.00 0.00 3.50
1329 1408 8.044574 TGGGATGATATTTCTTGATAAGGTCA 57.955 34.615 0.00 0.00 34.25 4.02
1330 1409 7.939039 TGGGATGATATTTCTTGATAAGGTCAC 59.061 37.037 0.00 0.00 36.32 3.67
1331 1410 7.939039 GGGATGATATTTCTTGATAAGGTCACA 59.061 37.037 0.00 0.00 36.32 3.58
1332 1411 9.342308 GGATGATATTTCTTGATAAGGTCACAA 57.658 33.333 0.00 0.00 36.32 3.33
1354 1443 7.538678 CACAACTACTGTAAAATCAGAAATGGC 59.461 37.037 0.65 0.00 36.10 4.40
1361 1450 6.855836 TGTAAAATCAGAAATGGCATCAGAC 58.144 36.000 0.00 0.00 0.00 3.51
1365 1454 4.290711 TCAGAAATGGCATCAGACTCAA 57.709 40.909 0.00 0.00 0.00 3.02
1373 1462 2.485814 GGCATCAGACTCAAGAAACCAC 59.514 50.000 0.00 0.00 0.00 4.16
1390 1479 3.420893 ACCACAACTTATGGACATGGTG 58.579 45.455 0.00 0.00 39.87 4.17
1396 1485 2.170397 ACTTATGGACATGGTGCGATGA 59.830 45.455 0.00 0.00 0.00 2.92
1400 1489 0.451783 GGACATGGTGCGATGAAACC 59.548 55.000 0.00 0.00 36.96 3.27
1407 1496 1.243902 GTGCGATGAAACCTTTCCCA 58.756 50.000 0.00 0.00 36.36 4.37
1408 1497 1.818674 GTGCGATGAAACCTTTCCCAT 59.181 47.619 0.00 0.00 36.36 4.00
1410 1499 3.065371 GTGCGATGAAACCTTTCCCATAG 59.935 47.826 0.00 0.00 36.36 2.23
1411 1500 3.279434 GCGATGAAACCTTTCCCATAGT 58.721 45.455 0.00 0.00 36.36 2.12
1412 1501 4.080807 TGCGATGAAACCTTTCCCATAGTA 60.081 41.667 0.00 0.00 36.36 1.82
1413 1502 4.879545 GCGATGAAACCTTTCCCATAGTAA 59.120 41.667 0.00 0.00 36.36 2.24
1414 1503 5.531287 GCGATGAAACCTTTCCCATAGTAAT 59.469 40.000 0.00 0.00 36.36 1.89
1425 2150 9.442047 CCTTTCCCATAGTAATTAGATGTGATC 57.558 37.037 6.56 0.00 0.00 2.92
1434 2159 6.939163 AGTAATTAGATGTGATCTGGGCATTC 59.061 38.462 0.00 0.00 40.51 2.67
1436 2169 3.878237 AGATGTGATCTGGGCATTCAT 57.122 42.857 0.00 0.00 38.44 2.57
1437 2170 3.487372 AGATGTGATCTGGGCATTCATG 58.513 45.455 0.00 0.00 38.44 3.07
1459 2236 6.463995 TGCTGAAACTTTTCTGGTACATTT 57.536 33.333 9.75 0.00 38.20 2.32
1465 2246 8.474025 TGAAACTTTTCTGGTACATTTTGTGAT 58.526 29.630 3.48 0.00 38.20 3.06
1473 2254 6.602803 TCTGGTACATTTTGTGATATGTGCAT 59.397 34.615 0.00 0.00 38.58 3.96
1488 2269 1.430632 GCATCGGCATGTTGTCCTG 59.569 57.895 0.00 0.00 40.72 3.86
1494 2275 0.804989 GGCATGTTGTCCTGTGCTAC 59.195 55.000 0.00 0.00 37.70 3.58
1505 2294 3.384789 GTCCTGTGCTACTGGATGTCATA 59.615 47.826 14.60 0.00 45.85 2.15
1511 2300 6.986250 TGTGCTACTGGATGTCATATTAGAG 58.014 40.000 0.00 0.00 0.00 2.43
1543 2332 7.978975 AGTTGTGTAAACAATGTGCAGTTAAAT 59.021 29.630 0.83 0.00 31.79 1.40
1544 2333 9.239002 GTTGTGTAAACAATGTGCAGTTAAATA 57.761 29.630 0.83 0.00 31.79 1.40
1546 2335 9.973450 TGTGTAAACAATGTGCAGTTAAATATT 57.027 25.926 0.00 0.00 0.00 1.28
1583 2372 6.310197 GCTGTAGATTTGTAGACTTTGCTTG 58.690 40.000 0.00 0.00 0.00 4.01
1599 2388 6.832384 ACTTTGCTTGGAATATGTGAGATGAT 59.168 34.615 0.00 0.00 0.00 2.45
1600 2389 6.628919 TTGCTTGGAATATGTGAGATGATG 57.371 37.500 0.00 0.00 0.00 3.07
1603 2392 6.261603 TGCTTGGAATATGTGAGATGATGAAC 59.738 38.462 0.00 0.00 0.00 3.18
1608 2397 8.485392 TGGAATATGTGAGATGATGAACTTACA 58.515 33.333 0.00 0.00 37.13 2.41
1641 2430 7.775397 AAGTTTGCACCAATAAATGATATGC 57.225 32.000 0.00 0.00 34.61 3.14
1644 2433 4.857799 TGCACCAATAAATGATATGCGTG 58.142 39.130 0.00 0.00 35.92 5.34
1694 2485 8.648693 TGTCTAGAAAAGGATAAGGCTATTACC 58.351 37.037 0.00 0.00 0.00 2.85
1695 2486 8.648693 GTCTAGAAAAGGATAAGGCTATTACCA 58.351 37.037 0.00 0.00 0.00 3.25
1696 2487 8.648693 TCTAGAAAAGGATAAGGCTATTACCAC 58.351 37.037 0.00 0.00 0.00 4.16
1697 2488 6.602278 AGAAAAGGATAAGGCTATTACCACC 58.398 40.000 0.00 0.00 0.00 4.61
1698 2489 5.987019 AAAGGATAAGGCTATTACCACCA 57.013 39.130 0.00 0.00 0.00 4.17
1699 2490 5.568620 AAGGATAAGGCTATTACCACCAG 57.431 43.478 0.00 0.00 0.00 4.00
1700 2491 3.328050 AGGATAAGGCTATTACCACCAGC 59.672 47.826 0.00 0.00 34.48 4.85
1701 2492 3.072476 GGATAAGGCTATTACCACCAGCA 59.928 47.826 0.00 0.00 37.02 4.41
1702 2493 2.717639 AAGGCTATTACCACCAGCAG 57.282 50.000 0.00 0.00 37.02 4.24
1703 2494 1.584724 AGGCTATTACCACCAGCAGT 58.415 50.000 0.00 0.00 37.02 4.40
1704 2495 1.916181 AGGCTATTACCACCAGCAGTT 59.084 47.619 0.00 0.00 37.02 3.16
1705 2496 2.308866 AGGCTATTACCACCAGCAGTTT 59.691 45.455 0.00 0.00 37.02 2.66
1706 2497 3.089284 GGCTATTACCACCAGCAGTTTT 58.911 45.455 0.00 0.00 37.02 2.43
1707 2498 3.128764 GGCTATTACCACCAGCAGTTTTC 59.871 47.826 0.00 0.00 37.02 2.29
1708 2499 3.128764 GCTATTACCACCAGCAGTTTTCC 59.871 47.826 0.00 0.00 35.35 3.13
1709 2500 3.525800 ATTACCACCAGCAGTTTTCCT 57.474 42.857 0.00 0.00 0.00 3.36
1710 2501 3.306472 TTACCACCAGCAGTTTTCCTT 57.694 42.857 0.00 0.00 0.00 3.36
1711 2502 1.402787 ACCACCAGCAGTTTTCCTTG 58.597 50.000 0.00 0.00 0.00 3.61
1712 2503 1.064017 ACCACCAGCAGTTTTCCTTGA 60.064 47.619 0.00 0.00 0.00 3.02
1713 2504 2.031120 CCACCAGCAGTTTTCCTTGAA 58.969 47.619 0.00 0.00 0.00 2.69
1714 2505 2.430332 CCACCAGCAGTTTTCCTTGAAA 59.570 45.455 0.00 0.00 0.00 2.69
1715 2506 3.070015 CCACCAGCAGTTTTCCTTGAAAT 59.930 43.478 0.00 0.00 31.34 2.17
1716 2507 4.280677 CCACCAGCAGTTTTCCTTGAAATA 59.719 41.667 0.00 0.00 31.34 1.40
1717 2508 5.047092 CCACCAGCAGTTTTCCTTGAAATAT 60.047 40.000 0.00 0.00 31.34 1.28
1718 2509 5.865552 CACCAGCAGTTTTCCTTGAAATATG 59.134 40.000 0.00 0.00 31.34 1.78
1719 2510 5.539955 ACCAGCAGTTTTCCTTGAAATATGT 59.460 36.000 0.00 0.00 31.34 2.29
1731 2522 6.929049 TCCTTGAAATATGTCTATAACCAGCG 59.071 38.462 0.00 0.00 0.00 5.18
1737 2528 3.520290 TGTCTATAACCAGCGGTTCTG 57.480 47.619 14.79 8.03 43.05 3.02
1747 2538 2.103042 GCGGTTCTGTAGGCAGCAG 61.103 63.158 0.00 2.48 42.29 4.24
1748 2539 1.293498 CGGTTCTGTAGGCAGCAGT 59.707 57.895 0.00 0.00 42.29 4.40
1749 2540 0.320771 CGGTTCTGTAGGCAGCAGTT 60.321 55.000 0.00 0.00 42.29 3.16
1750 2541 1.443802 GGTTCTGTAGGCAGCAGTTC 58.556 55.000 0.00 3.75 42.29 3.01
1751 2542 1.002544 GGTTCTGTAGGCAGCAGTTCT 59.997 52.381 0.00 0.00 42.29 3.01
1752 2543 2.072298 GTTCTGTAGGCAGCAGTTCTG 58.928 52.381 0.00 0.00 45.62 3.02
1764 2555 5.808042 CAGCAGTTCTGCTTGTAATATGT 57.192 39.130 22.40 0.00 43.52 2.29
1765 2556 5.804173 CAGCAGTTCTGCTTGTAATATGTC 58.196 41.667 22.40 0.00 43.52 3.06
1766 2557 5.583854 CAGCAGTTCTGCTTGTAATATGTCT 59.416 40.000 22.40 0.00 43.52 3.41
1767 2558 6.758416 CAGCAGTTCTGCTTGTAATATGTCTA 59.242 38.462 22.40 0.00 43.52 2.59
1768 2559 7.440556 CAGCAGTTCTGCTTGTAATATGTCTAT 59.559 37.037 22.40 0.00 43.52 1.98
1769 2560 8.642432 AGCAGTTCTGCTTGTAATATGTCTATA 58.358 33.333 19.80 0.00 43.52 1.31
1770 2561 9.261180 GCAGTTCTGCTTGTAATATGTCTATAA 57.739 33.333 16.29 0.00 0.00 0.98
1775 2566 9.764363 TCTGCTTGTAATATGTCTATAAACCAG 57.236 33.333 0.00 0.00 0.00 4.00
1776 2567 8.378172 TGCTTGTAATATGTCTATAAACCAGC 57.622 34.615 0.00 0.00 33.16 4.85
1777 2568 7.990314 TGCTTGTAATATGTCTATAAACCAGCA 59.010 33.333 0.00 0.00 36.38 4.41
1778 2569 8.499162 GCTTGTAATATGTCTATAAACCAGCAG 58.501 37.037 0.00 0.00 32.99 4.24
1779 2570 7.962964 TGTAATATGTCTATAAACCAGCAGC 57.037 36.000 0.00 0.00 0.00 5.25
1780 2571 7.735917 TGTAATATGTCTATAAACCAGCAGCT 58.264 34.615 0.00 0.00 0.00 4.24
1781 2572 7.872993 TGTAATATGTCTATAAACCAGCAGCTC 59.127 37.037 0.00 0.00 0.00 4.09
1782 2573 6.678568 ATATGTCTATAAACCAGCAGCTCT 57.321 37.500 0.00 0.00 0.00 4.09
1783 2574 4.826274 TGTCTATAAACCAGCAGCTCTT 57.174 40.909 0.00 0.00 0.00 2.85
1784 2575 5.165961 TGTCTATAAACCAGCAGCTCTTT 57.834 39.130 0.00 0.00 0.00 2.52
1785 2576 6.294361 TGTCTATAAACCAGCAGCTCTTTA 57.706 37.500 0.00 0.00 0.00 1.85
1786 2577 6.341316 TGTCTATAAACCAGCAGCTCTTTAG 58.659 40.000 0.00 0.00 0.00 1.85
1787 2578 6.070767 TGTCTATAAACCAGCAGCTCTTTAGT 60.071 38.462 0.00 0.00 0.00 2.24
1788 2579 6.477360 GTCTATAAACCAGCAGCTCTTTAGTC 59.523 42.308 0.00 0.00 0.00 2.59
1789 2580 3.492102 AAACCAGCAGCTCTTTAGTCA 57.508 42.857 0.00 0.00 0.00 3.41
1790 2581 3.492102 AACCAGCAGCTCTTTAGTCAA 57.508 42.857 0.00 0.00 0.00 3.18
1791 2582 3.051081 ACCAGCAGCTCTTTAGTCAAG 57.949 47.619 0.00 0.00 0.00 3.02
1792 2583 1.736681 CCAGCAGCTCTTTAGTCAAGC 59.263 52.381 0.00 0.00 36.27 4.01
1793 2584 2.420642 CAGCAGCTCTTTAGTCAAGCA 58.579 47.619 0.00 0.00 38.51 3.91
1794 2585 2.415857 CAGCAGCTCTTTAGTCAAGCAG 59.584 50.000 0.00 0.00 38.51 4.24
1795 2586 2.038295 AGCAGCTCTTTAGTCAAGCAGT 59.962 45.455 0.00 0.00 38.51 4.40
1824 2615 6.404623 GCTTGGAACATGTTATGCTGATACAA 60.405 38.462 11.95 0.00 39.30 2.41
1833 2624 7.489574 TGTTATGCTGATACAATTTCGCATA 57.510 32.000 0.00 0.00 36.01 3.14
1879 2670 0.250467 TCTTCTCTGTTGCTGGTGCC 60.250 55.000 0.00 0.00 38.71 5.01
1942 2733 1.723608 CGCTGGTGTTCTTTGGCACA 61.724 55.000 0.00 0.00 37.35 4.57
1957 2748 1.740025 GGCACAACTGGAACTATGCTC 59.260 52.381 0.00 0.00 33.57 4.26
2092 2883 3.443052 TGATTCCTTTGCCAATGTGGAT 58.557 40.909 0.00 0.00 40.96 3.41
2117 2908 0.555769 AAATGTGTCCTGGTGTGGGT 59.444 50.000 0.00 0.00 0.00 4.51
2132 2925 5.130145 TGGTGTGGGTTTTTCTTTCATGAAT 59.870 36.000 9.40 0.00 0.00 2.57
2150 2943 7.751732 TCATGAATTCCTGAGTTTAATTGTCG 58.248 34.615 9.12 0.00 0.00 4.35
2230 3023 3.982475 TGATCAGTGTGAGTCAGTGTTC 58.018 45.455 0.00 0.00 45.01 3.18
2282 3080 2.719705 TCCCTAATGTGTTCTTGGGGTT 59.280 45.455 4.65 0.00 35.56 4.11
2284 3082 2.231235 CCTAATGTGTTCTTGGGGTTGC 59.769 50.000 0.00 0.00 0.00 4.17
2316 3114 8.875803 TGTGATTATGTTGGACTAACGATTTAC 58.124 33.333 0.00 0.00 42.34 2.01
2326 3124 9.932207 TTGGACTAACGATTTACTTGAGAATAA 57.068 29.630 0.00 0.00 0.00 1.40
2367 3165 3.733709 GGTCAGGGCCCATTATCAG 57.266 57.895 27.56 4.33 0.00 2.90
2448 3246 8.631480 TTATCTGGTTTTTCTTCTAGGGTTTC 57.369 34.615 0.00 0.00 0.00 2.78
2468 3266 8.332464 GGGTTTCCTTTTTATTTTCAGTTTTCG 58.668 33.333 0.00 0.00 0.00 3.46
2473 3271 8.874816 TCCTTTTTATTTTCAGTTTTCGTTTGG 58.125 29.630 0.00 0.00 0.00 3.28
2480 3278 4.112716 TCAGTTTTCGTTTGGGGTTTTC 57.887 40.909 0.00 0.00 0.00 2.29
2492 3290 6.170506 GTTTGGGGTTTTCTCTTTGTCTTTT 58.829 36.000 0.00 0.00 0.00 2.27
2605 3603 7.865875 TGAACATTTTTCAAATACACGATGG 57.134 32.000 0.00 0.00 0.00 3.51
2648 3646 6.385843 ACAATATTTTCAGCACGCAAACATA 58.614 32.000 0.00 0.00 0.00 2.29
2654 3652 4.700268 TCAGCACGCAAACATATTTCAT 57.300 36.364 0.00 0.00 0.00 2.57
2660 3658 7.842239 CAGCACGCAAACATATTTCATTATTTG 59.158 33.333 0.00 0.00 0.00 2.32
2664 3662 8.868916 ACGCAAACATATTTCATTATTTGAACC 58.131 29.630 0.00 0.00 43.99 3.62
2673 3671 7.945033 TTTCATTATTTGAACCTGTTTCAGC 57.055 32.000 0.00 0.00 45.22 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.381908 CCCTGTTGCTAGGTAGTAGAGTG 59.618 52.174 0.00 0.00 36.02 3.51
45 47 3.144506 ACAACAAGAGACTGCAGGATTG 58.855 45.455 19.93 17.62 0.00 2.67
51 53 2.097954 CAGCAAACAACAAGAGACTGCA 59.902 45.455 0.00 0.00 0.00 4.41
57 59 3.111098 GTCTTGCAGCAAACAACAAGAG 58.889 45.455 9.65 0.00 46.61 2.85
66 68 4.829064 ATAAGTTTCGTCTTGCAGCAAA 57.171 36.364 9.65 0.00 0.00 3.68
78 80 6.436843 AGGTGGAATGCTTAATAAGTTTCG 57.563 37.500 1.68 0.00 0.00 3.46
124 126 9.850628 CAATGTATGTGATTGAAGATTCAGTTT 57.149 29.630 0.00 0.00 38.61 2.66
145 147 1.077265 CCCAGGGAAGGTGCAATGT 59.923 57.895 0.00 0.00 0.00 2.71
264 267 5.359194 TTGGAGATGGGATGTTTCTACTC 57.641 43.478 0.00 0.00 0.00 2.59
284 287 9.409312 TGTTGCAACTGTTCTATATTTTCATTG 57.591 29.630 28.61 0.00 0.00 2.82
293 296 7.990917 TCTTTTGTTGTTGCAACTGTTCTATA 58.009 30.769 28.61 4.49 0.00 1.31
298 301 3.679502 GCTCTTTTGTTGTTGCAACTGTT 59.320 39.130 28.61 0.00 0.00 3.16
305 308 2.187351 TCGTGCTCTTTTGTTGTTGC 57.813 45.000 0.00 0.00 0.00 4.17
309 312 3.309682 TCAGAGTTCGTGCTCTTTTGTTG 59.690 43.478 8.37 0.16 42.69 3.33
312 315 4.739046 AATCAGAGTTCGTGCTCTTTTG 57.261 40.909 8.37 1.29 42.69 2.44
363 383 3.610114 GCCATGGTTGCGTATCATTCATC 60.610 47.826 14.67 0.00 0.00 2.92
374 394 2.872557 CTGTCAGCCATGGTTGCG 59.127 61.111 22.84 10.26 0.00 4.85
384 404 5.193663 TCTATCTTCTATGTGCTGTCAGC 57.806 43.478 18.32 18.32 42.82 4.26
400 420 9.178758 GGTTTCCTTAAATCATGTGTTCTATCT 57.821 33.333 0.00 0.00 0.00 1.98
401 421 8.956426 TGGTTTCCTTAAATCATGTGTTCTATC 58.044 33.333 0.00 0.00 30.64 2.08
402 422 8.877864 TGGTTTCCTTAAATCATGTGTTCTAT 57.122 30.769 0.00 0.00 30.64 1.98
446 466 1.298014 CTTCTGTGAGCCCCCTGTC 59.702 63.158 0.00 0.00 0.00 3.51
453 473 2.749441 GGCCAGCTTCTGTGAGCC 60.749 66.667 0.00 0.00 43.74 4.70
542 562 1.003718 GAAGGGGAAGTCGGTGGTG 60.004 63.158 0.00 0.00 0.00 4.17
819 874 0.684805 GCTCGAGGAAGGGAGGAAGA 60.685 60.000 15.58 0.00 0.00 2.87
930 994 4.139234 GTACGACCGGGTGGAGGC 62.139 72.222 16.56 1.88 39.21 4.70
941 1005 1.589196 GGATCAGCCTGCGTACGAC 60.589 63.158 21.65 11.11 0.00 4.34
1066 1137 0.329261 TCGACGTAGGGAAGGGAGAA 59.671 55.000 0.00 0.00 0.00 2.87
1084 1155 0.727398 CGGCAAGATTCGAAGGGTTC 59.273 55.000 3.35 0.00 0.00 3.62
1089 1160 3.885777 GAAGCGGCAAGATTCGAAG 57.114 52.632 3.35 0.00 35.41 3.79
1130 1204 1.003051 AATCCCCGACCTAGGCACT 59.997 57.895 9.30 0.00 46.37 4.40
1131 1205 1.049289 AGAATCCCCGACCTAGGCAC 61.049 60.000 9.30 2.28 0.00 5.01
1160 1234 2.687935 AGCATTTCAACGAACACCTTGT 59.312 40.909 0.00 0.00 0.00 3.16
1217 1291 2.050144 GACATCTATGCCCCTCAAGGA 58.950 52.381 0.00 0.00 38.24 3.36
1218 1292 1.770658 TGACATCTATGCCCCTCAAGG 59.229 52.381 0.00 0.00 0.00 3.61
1219 1293 2.702478 TCTGACATCTATGCCCCTCAAG 59.298 50.000 0.00 0.00 0.00 3.02
1230 1309 6.108687 CAGGTTTGTGCTATTCTGACATCTA 58.891 40.000 0.00 0.00 0.00 1.98
1234 1313 4.085357 ACAGGTTTGTGCTATTCTGACA 57.915 40.909 0.00 0.00 35.83 3.58
1243 1322 0.100503 GTGCGAAACAGGTTTGTGCT 59.899 50.000 15.42 0.00 37.67 4.40
1254 1333 1.666189 GCTAGATCCAAGGTGCGAAAC 59.334 52.381 0.00 0.00 0.00 2.78
1256 1335 0.901827 TGCTAGATCCAAGGTGCGAA 59.098 50.000 0.00 0.00 0.00 4.70
1260 1339 1.745141 GCCACTGCTAGATCCAAGGTG 60.745 57.143 0.00 0.00 33.53 4.00
1261 1340 0.543749 GCCACTGCTAGATCCAAGGT 59.456 55.000 0.00 0.00 33.53 3.50
1262 1341 0.543277 TGCCACTGCTAGATCCAAGG 59.457 55.000 0.00 0.00 38.71 3.61
1264 1343 1.279496 AGTGCCACTGCTAGATCCAA 58.721 50.000 0.00 0.00 38.71 3.53
1266 1345 2.869636 GCATAGTGCCACTGCTAGATCC 60.870 54.545 7.83 0.00 37.42 3.36
1267 1346 2.411904 GCATAGTGCCACTGCTAGATC 58.588 52.381 7.83 0.00 37.42 2.75
1268 1347 2.540265 GCATAGTGCCACTGCTAGAT 57.460 50.000 7.83 0.00 37.42 1.98
1279 1358 0.108774 GGGGGAACTAGGCATAGTGC 59.891 60.000 12.49 10.21 41.54 4.40
1280 1359 0.393077 CGGGGGAACTAGGCATAGTG 59.607 60.000 12.49 0.00 41.54 2.74
1281 1360 1.408453 GCGGGGGAACTAGGCATAGT 61.408 60.000 4.95 4.95 44.37 2.12
1282 1361 1.122019 AGCGGGGGAACTAGGCATAG 61.122 60.000 3.34 3.34 34.96 2.23
1297 1376 3.480470 AGAAATATCATCCCAACAGCGG 58.520 45.455 0.00 0.00 0.00 5.52
1298 1377 4.576053 TCAAGAAATATCATCCCAACAGCG 59.424 41.667 0.00 0.00 0.00 5.18
1299 1378 6.645790 ATCAAGAAATATCATCCCAACAGC 57.354 37.500 0.00 0.00 0.00 4.40
1306 1385 8.908786 TGTGACCTTATCAAGAAATATCATCC 57.091 34.615 0.00 0.00 39.72 3.51
1324 1403 7.062749 TCTGATTTTACAGTAGTTGTGACCT 57.937 36.000 0.00 0.00 41.10 3.85
1325 1404 7.724305 TTCTGATTTTACAGTAGTTGTGACC 57.276 36.000 0.00 0.00 41.10 4.02
1326 1405 9.599322 CATTTCTGATTTTACAGTAGTTGTGAC 57.401 33.333 0.00 0.00 41.10 3.67
1327 1406 8.783093 CCATTTCTGATTTTACAGTAGTTGTGA 58.217 33.333 0.00 0.00 41.10 3.58
1329 1408 7.230510 TGCCATTTCTGATTTTACAGTAGTTGT 59.769 33.333 0.00 0.00 43.96 3.32
1330 1409 7.592938 TGCCATTTCTGATTTTACAGTAGTTG 58.407 34.615 0.00 0.00 38.79 3.16
1331 1410 7.759489 TGCCATTTCTGATTTTACAGTAGTT 57.241 32.000 0.00 0.00 38.79 2.24
1332 1411 7.611467 TGATGCCATTTCTGATTTTACAGTAGT 59.389 33.333 0.00 0.00 38.79 2.73
1333 1412 7.988737 TGATGCCATTTCTGATTTTACAGTAG 58.011 34.615 0.00 0.00 38.79 2.57
1354 1443 4.818546 AGTTGTGGTTTCTTGAGTCTGATG 59.181 41.667 0.00 0.00 0.00 3.07
1361 1450 5.530915 TGTCCATAAGTTGTGGTTTCTTGAG 59.469 40.000 17.26 0.00 37.96 3.02
1365 1454 4.766891 CCATGTCCATAAGTTGTGGTTTCT 59.233 41.667 17.26 0.35 37.96 2.52
1373 1462 2.355197 TCGCACCATGTCCATAAGTTG 58.645 47.619 0.00 0.00 0.00 3.16
1390 1479 3.279434 ACTATGGGAAAGGTTTCATCGC 58.721 45.455 4.89 0.00 38.92 4.58
1396 1485 9.408648 CACATCTAATTACTATGGGAAAGGTTT 57.591 33.333 7.59 0.00 0.00 3.27
1407 1496 7.559335 TGCCCAGATCACATCTAATTACTAT 57.441 36.000 0.00 0.00 37.58 2.12
1408 1497 6.994421 TGCCCAGATCACATCTAATTACTA 57.006 37.500 0.00 0.00 37.58 1.82
1410 1499 6.712095 TGAATGCCCAGATCACATCTAATTAC 59.288 38.462 0.00 0.00 37.58 1.89
1411 1500 6.840527 TGAATGCCCAGATCACATCTAATTA 58.159 36.000 0.00 0.00 37.58 1.40
1412 1501 5.698104 TGAATGCCCAGATCACATCTAATT 58.302 37.500 0.00 0.00 37.58 1.40
1413 1502 5.314718 TGAATGCCCAGATCACATCTAAT 57.685 39.130 0.00 0.00 37.58 1.73
1414 1503 4.776435 TGAATGCCCAGATCACATCTAA 57.224 40.909 0.00 0.00 37.58 2.10
1434 2159 5.437289 TGTACCAGAAAAGTTTCAGCATG 57.563 39.130 6.56 0.00 39.61 4.06
1436 2169 6.463995 AAATGTACCAGAAAAGTTTCAGCA 57.536 33.333 6.56 0.00 39.61 4.41
1437 2170 6.756542 ACAAAATGTACCAGAAAAGTTTCAGC 59.243 34.615 6.56 0.00 39.61 4.26
1444 2221 9.345517 CACATATCACAAAATGTACCAGAAAAG 57.654 33.333 0.00 0.00 34.61 2.27
1459 2236 2.035530 TGCCGATGCACATATCACAA 57.964 45.000 0.00 0.00 44.23 3.33
1473 2254 1.965930 GCACAGGACAACATGCCGA 60.966 57.895 0.00 0.00 31.71 5.54
1480 2261 2.289694 ACATCCAGTAGCACAGGACAAC 60.290 50.000 3.26 0.00 36.57 3.32
1482 2263 1.550524 GACATCCAGTAGCACAGGACA 59.449 52.381 3.26 0.00 36.57 4.02
1486 2267 6.986250 TCTAATATGACATCCAGTAGCACAG 58.014 40.000 0.00 0.00 0.00 3.66
1488 2269 6.987386 ACTCTAATATGACATCCAGTAGCAC 58.013 40.000 0.00 0.00 0.00 4.40
1511 2300 8.789881 TGCACATTGTTTACACAACTTATTAC 57.210 30.769 0.00 0.00 45.88 1.89
1516 2305 5.323371 ACTGCACATTGTTTACACAACTT 57.677 34.783 0.00 0.00 45.88 2.66
1518 2307 7.513190 TTTAACTGCACATTGTTTACACAAC 57.487 32.000 0.00 0.00 45.88 3.32
1530 2319 8.109705 TGTTCACTGAATATTTAACTGCACAT 57.890 30.769 0.00 0.00 0.00 3.21
1543 2332 2.698803 ACAGCGCATGTTCACTGAATA 58.301 42.857 11.47 0.00 39.96 1.75
1544 2333 1.527034 ACAGCGCATGTTCACTGAAT 58.473 45.000 11.47 0.00 39.96 2.57
1546 2335 1.272212 TCTACAGCGCATGTTCACTGA 59.728 47.619 11.47 3.41 39.96 3.41
1583 2372 8.893219 TGTAAGTTCATCATCTCACATATTCC 57.107 34.615 0.00 0.00 0.00 3.01
1603 2392 8.542497 TGGTGCAAACTTTAGTATACTGTAAG 57.458 34.615 15.90 18.36 42.29 2.34
1622 2411 4.261530 CCACGCATATCATTTATTGGTGCA 60.262 41.667 0.00 0.00 32.05 4.57
1641 2430 4.854399 TCTGCAAAGTTTACAAATCCACG 58.146 39.130 0.00 0.00 0.00 4.94
1679 2470 3.072476 TGCTGGTGGTAATAGCCTTATCC 59.928 47.826 0.00 0.00 36.64 2.59
1684 2475 1.584724 ACTGCTGGTGGTAATAGCCT 58.415 50.000 0.00 0.00 36.64 4.58
1685 2476 2.420058 AACTGCTGGTGGTAATAGCC 57.580 50.000 0.00 0.00 36.64 3.93
1686 2477 3.128764 GGAAAACTGCTGGTGGTAATAGC 59.871 47.826 0.00 0.00 37.93 2.97
1687 2478 4.589908 AGGAAAACTGCTGGTGGTAATAG 58.410 43.478 0.00 0.00 0.00 1.73
1688 2479 4.650972 AGGAAAACTGCTGGTGGTAATA 57.349 40.909 0.00 0.00 0.00 0.98
1689 2480 3.525800 AGGAAAACTGCTGGTGGTAAT 57.474 42.857 0.00 0.00 0.00 1.89
1690 2481 2.955660 CAAGGAAAACTGCTGGTGGTAA 59.044 45.455 0.00 0.00 0.00 2.85
1691 2482 2.173782 TCAAGGAAAACTGCTGGTGGTA 59.826 45.455 0.00 0.00 0.00 3.25
1692 2483 1.064017 TCAAGGAAAACTGCTGGTGGT 60.064 47.619 0.00 0.00 0.00 4.16
1693 2484 1.691196 TCAAGGAAAACTGCTGGTGG 58.309 50.000 0.00 0.00 0.00 4.61
1694 2485 3.799281 TTTCAAGGAAAACTGCTGGTG 57.201 42.857 0.00 0.00 0.00 4.17
1695 2486 5.539955 ACATATTTCAAGGAAAACTGCTGGT 59.460 36.000 0.00 0.00 35.11 4.00
1696 2487 6.029346 ACATATTTCAAGGAAAACTGCTGG 57.971 37.500 0.00 0.00 35.11 4.85
1697 2488 6.917533 AGACATATTTCAAGGAAAACTGCTG 58.082 36.000 0.00 0.00 35.11 4.41
1698 2489 8.814038 ATAGACATATTTCAAGGAAAACTGCT 57.186 30.769 0.00 2.52 35.11 4.24
1704 2495 9.120538 GCTGGTTATAGACATATTTCAAGGAAA 57.879 33.333 0.00 0.00 35.94 3.13
1705 2496 7.441157 CGCTGGTTATAGACATATTTCAAGGAA 59.559 37.037 0.00 0.00 0.00 3.36
1706 2497 6.929049 CGCTGGTTATAGACATATTTCAAGGA 59.071 38.462 0.00 0.00 0.00 3.36
1707 2498 6.147821 CCGCTGGTTATAGACATATTTCAAGG 59.852 42.308 0.00 0.00 0.00 3.61
1708 2499 6.706270 ACCGCTGGTTATAGACATATTTCAAG 59.294 38.462 0.00 0.00 27.29 3.02
1709 2500 6.588204 ACCGCTGGTTATAGACATATTTCAA 58.412 36.000 0.00 0.00 27.29 2.69
1710 2501 6.169557 ACCGCTGGTTATAGACATATTTCA 57.830 37.500 0.00 0.00 27.29 2.69
1711 2502 6.929606 AGAACCGCTGGTTATAGACATATTTC 59.070 38.462 12.01 0.00 46.95 2.17
1712 2503 6.706270 CAGAACCGCTGGTTATAGACATATTT 59.294 38.462 12.01 0.00 46.95 1.40
1713 2504 6.183360 ACAGAACCGCTGGTTATAGACATATT 60.183 38.462 12.01 0.00 46.95 1.28
1714 2505 5.304614 ACAGAACCGCTGGTTATAGACATAT 59.695 40.000 12.01 0.00 46.95 1.78
1715 2506 4.647853 ACAGAACCGCTGGTTATAGACATA 59.352 41.667 12.01 0.00 46.95 2.29
1716 2507 3.451178 ACAGAACCGCTGGTTATAGACAT 59.549 43.478 12.01 0.00 46.95 3.06
1717 2508 2.829720 ACAGAACCGCTGGTTATAGACA 59.170 45.455 12.01 0.00 46.95 3.41
1718 2509 3.521947 ACAGAACCGCTGGTTATAGAC 57.478 47.619 12.01 1.68 46.95 2.59
1719 2510 3.635373 CCTACAGAACCGCTGGTTATAGA 59.365 47.826 12.01 1.92 46.95 1.98
1749 2540 9.764363 CTGGTTTATAGACATATTACAAGCAGA 57.236 33.333 0.00 0.00 0.00 4.26
1750 2541 8.499162 GCTGGTTTATAGACATATTACAAGCAG 58.501 37.037 0.00 0.00 34.74 4.24
1751 2542 7.990314 TGCTGGTTTATAGACATATTACAAGCA 59.010 33.333 0.00 0.00 38.33 3.91
1752 2543 8.378172 TGCTGGTTTATAGACATATTACAAGC 57.622 34.615 0.00 0.00 34.95 4.01
1753 2544 8.499162 GCTGCTGGTTTATAGACATATTACAAG 58.501 37.037 0.00 0.00 0.00 3.16
1754 2545 8.210946 AGCTGCTGGTTTATAGACATATTACAA 58.789 33.333 0.00 0.00 0.00 2.41
1755 2546 7.735917 AGCTGCTGGTTTATAGACATATTACA 58.264 34.615 0.00 0.00 0.00 2.41
1756 2547 8.091449 AGAGCTGCTGGTTTATAGACATATTAC 58.909 37.037 7.01 0.00 0.00 1.89
1757 2548 8.195165 AGAGCTGCTGGTTTATAGACATATTA 57.805 34.615 7.01 0.00 0.00 0.98
1758 2549 7.072263 AGAGCTGCTGGTTTATAGACATATT 57.928 36.000 7.01 0.00 0.00 1.28
1759 2550 6.678568 AGAGCTGCTGGTTTATAGACATAT 57.321 37.500 7.01 0.00 0.00 1.78
1760 2551 6.485830 AAGAGCTGCTGGTTTATAGACATA 57.514 37.500 7.01 0.00 0.00 2.29
1761 2552 5.365021 AAGAGCTGCTGGTTTATAGACAT 57.635 39.130 7.01 0.00 0.00 3.06
1762 2553 4.826274 AAGAGCTGCTGGTTTATAGACA 57.174 40.909 7.01 0.00 0.00 3.41
1763 2554 6.342111 ACTAAAGAGCTGCTGGTTTATAGAC 58.658 40.000 7.01 0.00 0.00 2.59
1764 2555 6.154534 TGACTAAAGAGCTGCTGGTTTATAGA 59.845 38.462 7.01 0.00 0.00 1.98
1765 2556 6.341316 TGACTAAAGAGCTGCTGGTTTATAG 58.659 40.000 7.01 4.81 0.00 1.31
1766 2557 6.294361 TGACTAAAGAGCTGCTGGTTTATA 57.706 37.500 7.01 0.00 0.00 0.98
1767 2558 5.165961 TGACTAAAGAGCTGCTGGTTTAT 57.834 39.130 7.01 2.13 0.00 1.40
1768 2559 4.617253 TGACTAAAGAGCTGCTGGTTTA 57.383 40.909 7.01 9.97 0.00 2.01
1769 2560 3.492102 TGACTAAAGAGCTGCTGGTTT 57.508 42.857 7.01 9.29 0.00 3.27
1770 2561 3.406764 CTTGACTAAAGAGCTGCTGGTT 58.593 45.455 7.01 3.04 38.24 3.67
1771 2562 2.873649 GCTTGACTAAAGAGCTGCTGGT 60.874 50.000 7.01 0.00 38.24 4.00
1772 2563 1.736681 GCTTGACTAAAGAGCTGCTGG 59.263 52.381 7.01 0.00 38.24 4.85
1773 2564 2.415857 CTGCTTGACTAAAGAGCTGCTG 59.584 50.000 7.01 0.00 38.24 4.41
1774 2565 2.038295 ACTGCTTGACTAAAGAGCTGCT 59.962 45.455 0.00 0.00 38.24 4.24
1775 2566 2.421619 ACTGCTTGACTAAAGAGCTGC 58.578 47.619 0.00 0.00 38.24 5.25
1776 2567 5.210715 CAAAACTGCTTGACTAAAGAGCTG 58.789 41.667 0.00 0.00 38.24 4.24
1777 2568 4.261363 GCAAAACTGCTTGACTAAAGAGCT 60.261 41.667 0.00 0.00 38.24 4.09
1778 2569 3.977579 GCAAAACTGCTTGACTAAAGAGC 59.022 43.478 0.00 0.00 38.24 4.09
1779 2570 5.429957 AGCAAAACTGCTTGACTAAAGAG 57.570 39.130 0.00 0.00 43.52 2.85
1791 2582 2.825205 ACATGTTCCAAGCAAAACTGC 58.175 42.857 0.00 0.00 0.00 4.40
1792 2583 5.107375 GCATAACATGTTCCAAGCAAAACTG 60.107 40.000 15.85 0.00 0.00 3.16
1793 2584 4.990426 GCATAACATGTTCCAAGCAAAACT 59.010 37.500 15.85 0.00 0.00 2.66
1794 2585 4.990426 AGCATAACATGTTCCAAGCAAAAC 59.010 37.500 15.85 0.00 0.00 2.43
1795 2586 4.989797 CAGCATAACATGTTCCAAGCAAAA 59.010 37.500 15.85 0.00 0.00 2.44
1879 2670 0.682209 CCACAGGAATGGCAAGGAGG 60.682 60.000 0.00 0.00 31.52 4.30
1942 2733 3.195610 TGATGTCGAGCATAGTTCCAGTT 59.804 43.478 0.00 0.00 38.06 3.16
1957 2748 2.161012 GCTAATGCCCATGATGATGTCG 59.839 50.000 0.00 0.00 0.00 4.35
2039 2830 2.360165 CACCCTCTATTGAAGCATTGGC 59.640 50.000 0.00 0.00 41.61 4.52
2041 2832 5.678107 GCTTTCACCCTCTATTGAAGCATTG 60.678 44.000 0.00 0.00 33.36 2.82
2051 2842 3.840666 TCAGTCAAGCTTTCACCCTCTAT 59.159 43.478 0.00 0.00 0.00 1.98
2092 2883 4.133820 CACACCAGGACACATTTCACTTA 58.866 43.478 0.00 0.00 0.00 2.24
2132 2925 5.556915 ACCATCGACAATTAAACTCAGGAA 58.443 37.500 0.00 0.00 0.00 3.36
2150 2943 4.871933 ACAATGTTTCCAAAGGACCATC 57.128 40.909 0.00 0.00 0.00 3.51
2206 2999 4.965814 ACACTGACTCACACTGATCATTT 58.034 39.130 0.00 0.00 0.00 2.32
2230 3023 6.446254 GGCCTTTCCATTGTCATCTTGACG 62.446 50.000 0.00 0.00 41.62 4.35
2245 3043 0.681243 GGGACTCACATGGCCTTTCC 60.681 60.000 3.32 0.51 0.00 3.13
2246 3044 0.329596 AGGGACTCACATGGCCTTTC 59.670 55.000 3.32 0.00 0.00 2.62
2247 3045 1.668826 TAGGGACTCACATGGCCTTT 58.331 50.000 3.32 0.00 41.75 3.11
2248 3046 1.668826 TTAGGGACTCACATGGCCTT 58.331 50.000 3.32 0.00 41.75 4.35
2249 3047 1.492176 CATTAGGGACTCACATGGCCT 59.508 52.381 3.32 0.00 41.75 5.19
2282 3080 4.395854 GTCCAACATAATCACATGTCAGCA 59.604 41.667 0.00 0.00 38.19 4.41
2284 3082 7.464577 CGTTAGTCCAACATAATCACATGTCAG 60.465 40.741 0.00 0.00 38.19 3.51
2326 3124 5.227908 CCGTTGGACTAAATATCTGCGTAT 58.772 41.667 0.00 0.00 0.00 3.06
2402 3200 0.178984 ACACACCCTTAAAACCCGGG 60.179 55.000 22.25 22.25 43.79 5.73
2405 3203 6.452242 CAGATAAAACACACCCTTAAAACCC 58.548 40.000 0.00 0.00 0.00 4.11
2448 3246 8.119845 CCCAAACGAAAACTGAAAATAAAAAGG 58.880 33.333 0.00 0.00 0.00 3.11
2468 3266 5.339008 AAGACAAAGAGAAAACCCCAAAC 57.661 39.130 0.00 0.00 0.00 2.93
2471 3269 4.161377 CCAAAAGACAAAGAGAAAACCCCA 59.839 41.667 0.00 0.00 0.00 4.96
2472 3270 4.161565 ACCAAAAGACAAAGAGAAAACCCC 59.838 41.667 0.00 0.00 0.00 4.95
2473 3271 5.339008 ACCAAAAGACAAAGAGAAAACCC 57.661 39.130 0.00 0.00 0.00 4.11
2480 3278 5.835113 TGGAAGAACCAAAAGACAAAGAG 57.165 39.130 0.00 0.00 46.75 2.85
2579 3577 9.566530 CCATCGTGTATTTGAAAAATGTTCATA 57.433 29.630 0.00 0.00 0.00 2.15
2625 3623 5.766702 ATGTTTGCGTGCTGAAAATATTG 57.233 34.783 0.00 0.00 0.00 1.90
2635 3633 7.758980 TCAAATAATGAAATATGTTTGCGTGCT 59.241 29.630 0.00 0.00 34.30 4.40
2648 3646 8.149647 TGCTGAAACAGGTTCAAATAATGAAAT 58.850 29.630 1.66 0.00 45.67 2.17
2789 3855 0.320073 CTTGGGTCGGTGCGAGTTAA 60.320 55.000 0.00 0.00 36.23 2.01
2863 3930 3.518590 GGAGCTTTGATGCCTTGATTTG 58.481 45.455 0.00 0.00 0.00 2.32
2867 3934 0.677731 CGGGAGCTTTGATGCCTTGA 60.678 55.000 0.00 0.00 0.00 3.02
2869 3936 0.678048 GACGGGAGCTTTGATGCCTT 60.678 55.000 0.00 0.00 0.00 4.35
2870 3937 1.078143 GACGGGAGCTTTGATGCCT 60.078 57.895 0.00 0.00 0.00 4.75
2871 3938 0.960364 TTGACGGGAGCTTTGATGCC 60.960 55.000 0.00 0.00 0.00 4.40
2873 3940 3.253188 TCTTTTTGACGGGAGCTTTGATG 59.747 43.478 0.00 0.00 0.00 3.07
2874 3941 3.486383 TCTTTTTGACGGGAGCTTTGAT 58.514 40.909 0.00 0.00 0.00 2.57
2875 3942 2.925724 TCTTTTTGACGGGAGCTTTGA 58.074 42.857 0.00 0.00 0.00 2.69
2876 3943 3.315191 TCTTCTTTTTGACGGGAGCTTTG 59.685 43.478 0.00 0.00 0.00 2.77
2877 3944 3.551846 TCTTCTTTTTGACGGGAGCTTT 58.448 40.909 0.00 0.00 0.00 3.51
2972 4043 0.606401 CACCGCTGGTCCATCAACTT 60.606 55.000 0.00 0.00 31.02 2.66
2975 4046 2.350895 CCACCGCTGGTCCATCAA 59.649 61.111 0.00 0.00 31.02 2.57


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

AutoCloner maintained by Alex Coulton.