Multiple sequence alignment - TraesCS1B01G143800

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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 TraesCS1B01G143800 chr1B 100.000 4495 0 0 2628 7122 195556964 195561458 0.000000e+00 8301.0
1 TraesCS1B01G143800 chr1B 100.000 2335 0 0 1 2335 195554337 195556671 0.000000e+00 4313.0
2 TraesCS1B01G143800 chr1B 95.766 1299 41 7 4 1295 283126644 283125353 0.000000e+00 2082.0
3 TraesCS1B01G143800 chr1B 87.913 786 79 13 518 1295 406349465 406348688 0.000000e+00 911.0
4 TraesCS1B01G143800 chr1B 83.721 86 14 0 6309 6394 629568161 629568246 1.650000e-11 82.4
5 TraesCS1B01G143800 chr1B 90.164 61 5 1 6332 6391 629906898 629906958 2.130000e-10 78.7
6 TraesCS1B01G143800 chr1D 96.737 2482 65 11 2628 5102 141545332 141547804 0.000000e+00 4120.0
7 TraesCS1B01G143800 chr1D 94.766 1624 65 10 5103 6721 141547839 141549447 0.000000e+00 2510.0
8 TraesCS1B01G143800 chr1D 87.897 818 82 13 489 1295 301241086 301240275 0.000000e+00 946.0
9 TraesCS1B01G143800 chr1D 91.071 560 35 5 1371 1929 141523945 141524490 0.000000e+00 743.0
10 TraesCS1B01G143800 chr1D 91.787 414 11 5 6732 7122 141549823 141550236 8.070000e-154 555.0
11 TraesCS1B01G143800 chr1D 91.711 374 16 8 1944 2313 141544729 141545091 8.250000e-139 505.0
12 TraesCS1B01G143800 chr1D 77.895 95 20 1 6502 6595 493761333 493761239 2.770000e-04 58.4
13 TraesCS1B01G143800 chr1A 96.094 1920 55 15 2628 4535 149356170 149354259 0.000000e+00 3112.0
14 TraesCS1B01G143800 chr1A 95.137 1501 54 8 4534 6026 149353903 149352414 0.000000e+00 2350.0
15 TraesCS1B01G143800 chr1A 87.500 632 67 11 489 1113 376146574 376145948 0.000000e+00 719.0
16 TraesCS1B01G143800 chr1A 87.073 410 35 5 6714 7122 149351293 149350901 1.410000e-121 448.0
17 TraesCS1B01G143800 chr1A 94.017 234 14 0 1981 2214 149356655 149356422 8.790000e-94 355.0
18 TraesCS1B01G143800 chr1A 89.922 258 26 0 6144 6401 149352399 149352142 4.120000e-87 333.0
19 TraesCS1B01G143800 chr1A 90.860 186 14 2 1112 1295 376145844 376145660 5.520000e-61 246.0
20 TraesCS1B01G143800 chr1A 94.375 160 8 1 1767 1925 149356812 149356653 1.980000e-60 244.0
21 TraesCS1B01G143800 chr1A 94.245 139 6 2 2198 2335 149356406 149356269 2.010000e-50 211.0
22 TraesCS1B01G143800 chr2D 92.195 1230 79 12 75 1295 28643138 28644359 0.000000e+00 1724.0
23 TraesCS1B01G143800 chr2B 85.956 591 65 8 622 1200 71347250 71347834 3.650000e-172 616.0
24 TraesCS1B01G143800 chr2B 85.135 592 68 11 622 1200 71338119 71338703 7.960000e-164 588.0
25 TraesCS1B01G143800 chr2B 83.198 494 66 10 816 1295 719799681 719800171 3.050000e-118 436.0
26 TraesCS1B01G143800 chrUn 81.107 524 68 13 681 1200 409764007 409764503 2.410000e-104 390.0
27 TraesCS1B01G143800 chr5B 100.000 29 0 0 6502 6530 672809060 672809032 4.000000e-03 54.7


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 TraesCS1B01G143800 chr1B 195554337 195561458 7121 False 6307.000000 8301 100.000000 1 7122 2 chr1B.!!$F3 7121
1 TraesCS1B01G143800 chr1B 283125353 283126644 1291 True 2082.000000 2082 95.766000 4 1295 1 chr1B.!!$R1 1291
2 TraesCS1B01G143800 chr1B 406348688 406349465 777 True 911.000000 911 87.913000 518 1295 1 chr1B.!!$R2 777
3 TraesCS1B01G143800 chr1D 141544729 141550236 5507 False 1922.500000 4120 93.750250 1944 7122 4 chr1D.!!$F2 5178
4 TraesCS1B01G143800 chr1D 301240275 301241086 811 True 946.000000 946 87.897000 489 1295 1 chr1D.!!$R1 806
5 TraesCS1B01G143800 chr1D 141523945 141524490 545 False 743.000000 743 91.071000 1371 1929 1 chr1D.!!$F1 558
6 TraesCS1B01G143800 chr1A 149350901 149356812 5911 True 1007.571429 3112 92.980429 1767 7122 7 chr1A.!!$R1 5355
7 TraesCS1B01G143800 chr1A 376145660 376146574 914 True 482.500000 719 89.180000 489 1295 2 chr1A.!!$R2 806
8 TraesCS1B01G143800 chr2D 28643138 28644359 1221 False 1724.000000 1724 92.195000 75 1295 1 chr2D.!!$F1 1220
9 TraesCS1B01G143800 chr2B 71347250 71347834 584 False 616.000000 616 85.956000 622 1200 1 chr2B.!!$F2 578
10 TraesCS1B01G143800 chr2B 71338119 71338703 584 False 588.000000 588 85.135000 622 1200 1 chr2B.!!$F1 578

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
211 212 1.550976 GGACCTGACAGGGACTACAAG 59.449 57.143 25.34 0.0 40.58 3.16 F
298 304 2.029623 GCATGATGGAGGTTTGCTCAT 58.970 47.619 0.00 0.0 0.00 2.90 F
467 474 2.033372 CTTGCATATCATGGCCCAACA 58.967 47.619 0.00 0.0 0.00 3.33 F
1364 1498 0.104090 AGGGGGCGGGGTATTCTTAT 60.104 55.000 0.00 0.0 0.00 1.73 F
1365 1499 0.775542 GGGGGCGGGGTATTCTTATT 59.224 55.000 0.00 0.0 0.00 1.40 F
2839 3009 1.072505 GGCCAGTCCAAGGTTTCGA 59.927 57.895 0.00 0.0 34.01 3.71 F
4354 4533 1.067516 CTGCCATTTTATGCCTTCGGG 59.932 52.381 0.00 0.0 38.37 5.14 F
5150 5721 2.301870 TCAAAATACCTGACGGTGCTCT 59.698 45.455 0.00 0.0 45.18 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1345 1479 0.104090 ATAAGAATACCCCGCCCCCT 60.104 55.0 0.00 0.00 0.00 4.79 R
1346 1480 0.775542 AATAAGAATACCCCGCCCCC 59.224 55.0 0.00 0.00 0.00 5.40 R
2225 2392 1.040646 TCTATGGCACGATCACCCTC 58.959 55.0 0.00 0.00 0.00 4.30 R
2672 2840 0.034337 GGTTTACACCTCGCCAGACA 59.966 55.0 0.00 0.00 40.44 3.41 R
3284 3460 0.454957 CAGCCGGCTGAAATGAAACG 60.455 55.0 46.72 19.48 46.30 3.60 R
4794 5331 1.104577 TGCACAAGAACCCCGGTTTC 61.105 55.0 0.00 2.43 38.60 2.78 R
5239 5810 0.108804 ACATCGGTGAGGCTAACGTG 60.109 55.0 0.65 0.00 0.00 4.49 R
6355 6938 0.249155 CTCTTTATCGGCGGCGGTTA 60.249 55.0 31.73 16.60 0.00 2.85 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
25 26 8.168681 CTTCGCAAATTTATTACGACCAATTT 57.831 30.769 0.00 0.00 31.18 1.82
34 35 7.867305 TTATTACGACCAATTTTCATAGCCA 57.133 32.000 0.00 0.00 0.00 4.75
56 57 2.555757 GCTATGGTTGCTTCATGATCCC 59.444 50.000 0.00 0.00 0.00 3.85
78 79 6.266786 TCCCTTGTCTTGAACTTTATTTTCCC 59.733 38.462 0.00 0.00 0.00 3.97
123 124 9.722056 GGATTAATATGTCATTTTGTGAGTGTC 57.278 33.333 0.00 0.00 37.56 3.67
150 151 9.034544 GTGTGCTTGTTTAAAATTGATTCTCTT 57.965 29.630 0.00 0.00 0.00 2.85
152 153 9.248291 GTGCTTGTTTAAAATTGATTCTCTTGA 57.752 29.630 0.00 0.00 0.00 3.02
191 192 2.417787 GCAGGCTGCTTGAATTTTAGGG 60.418 50.000 31.37 0.00 40.96 3.53
211 212 1.550976 GGACCTGACAGGGACTACAAG 59.449 57.143 25.34 0.00 40.58 3.16
246 247 6.704937 GCATTCATGAATCTCTCATACACAGA 59.295 38.462 18.16 0.00 43.28 3.41
298 304 2.029623 GCATGATGGAGGTTTGCTCAT 58.970 47.619 0.00 0.00 0.00 2.90
344 350 8.664798 GTTAGAAAATATTTTCCATTGTTGGGC 58.335 33.333 29.00 8.11 45.84 5.36
467 474 2.033372 CTTGCATATCATGGCCCAACA 58.967 47.619 0.00 0.00 0.00 3.33
499 506 4.631813 AGCAATCCGACATTGTTTACTCTC 59.368 41.667 8.35 0.00 0.00 3.20
767 784 3.904800 TGGATGTTGCTTCGGATAAGA 57.095 42.857 0.00 0.00 0.00 2.10
857 874 6.013293 AGGAGTTTACTCTTAAGGTGAATGCT 60.013 38.462 9.56 1.58 42.48 3.79
912 929 4.144297 AGCCATTTTTCTTGCTGTAGTCA 58.856 39.130 0.00 0.00 31.70 3.41
944 962 4.637483 AACATGCTGTCATATTTTCCCG 57.363 40.909 0.00 0.00 0.00 5.14
978 996 9.797642 TTGGCAATATAATCTGATGATAGTGTT 57.202 29.630 18.74 0.60 31.70 3.32
991 1009 6.697455 TGATGATAGTGTTTTATCTCACGCTC 59.303 38.462 0.00 0.00 39.25 5.03
1069 1087 9.606631 AGGTATTTTTGCATAAGTCTCTTAGAG 57.393 33.333 2.23 2.23 0.00 2.43
1268 1402 4.751600 CCGCTGAGCAGATTGTTCATATTA 59.248 41.667 4.88 0.00 37.00 0.98
1295 1429 8.204160 TGATAAATGACAAATCTAGATCGTGGT 58.796 33.333 5.51 2.16 0.00 4.16
1296 1430 6.668541 AAATGACAAATCTAGATCGTGGTG 57.331 37.500 5.51 2.72 0.00 4.17
1297 1431 3.521560 TGACAAATCTAGATCGTGGTGC 58.478 45.455 5.51 3.25 0.00 5.01
1298 1432 3.195610 TGACAAATCTAGATCGTGGTGCT 59.804 43.478 5.51 0.00 0.00 4.40
1299 1433 4.401202 TGACAAATCTAGATCGTGGTGCTA 59.599 41.667 5.51 0.00 0.00 3.49
1300 1434 5.105513 TGACAAATCTAGATCGTGGTGCTAA 60.106 40.000 5.51 0.00 0.00 3.09
1301 1435 5.918608 ACAAATCTAGATCGTGGTGCTAAT 58.081 37.500 5.51 0.00 0.00 1.73
1302 1436 7.050970 ACAAATCTAGATCGTGGTGCTAATA 57.949 36.000 5.51 0.00 0.00 0.98
1303 1437 7.671302 ACAAATCTAGATCGTGGTGCTAATAT 58.329 34.615 5.51 0.00 0.00 1.28
1304 1438 8.803235 ACAAATCTAGATCGTGGTGCTAATATA 58.197 33.333 5.51 0.00 0.00 0.86
1305 1439 9.809096 CAAATCTAGATCGTGGTGCTAATATAT 57.191 33.333 5.51 0.00 0.00 0.86
1307 1441 7.569639 TCTAGATCGTGGTGCTAATATATCC 57.430 40.000 0.00 0.00 0.00 2.59
1308 1442 7.116736 TCTAGATCGTGGTGCTAATATATCCA 58.883 38.462 0.00 0.00 0.00 3.41
1309 1443 6.798427 AGATCGTGGTGCTAATATATCCAT 57.202 37.500 0.00 0.00 0.00 3.41
1310 1444 6.577103 AGATCGTGGTGCTAATATATCCATG 58.423 40.000 4.06 4.06 36.76 3.66
1311 1445 4.503910 TCGTGGTGCTAATATATCCATGC 58.496 43.478 5.20 0.45 35.79 4.06
1312 1446 4.020662 TCGTGGTGCTAATATATCCATGCA 60.021 41.667 0.00 0.00 35.79 3.96
1313 1447 4.694982 CGTGGTGCTAATATATCCATGCAA 59.305 41.667 0.00 0.00 32.10 4.08
1314 1448 5.181056 CGTGGTGCTAATATATCCATGCAAA 59.819 40.000 0.00 0.00 32.10 3.68
1315 1449 6.293900 CGTGGTGCTAATATATCCATGCAAAA 60.294 38.462 0.00 0.00 32.10 2.44
1316 1450 7.432869 GTGGTGCTAATATATCCATGCAAAAA 58.567 34.615 0.00 0.00 32.10 1.94
1317 1451 7.382218 GTGGTGCTAATATATCCATGCAAAAAC 59.618 37.037 0.00 0.00 32.10 2.43
1318 1452 7.287466 TGGTGCTAATATATCCATGCAAAAACT 59.713 33.333 0.00 0.00 32.10 2.66
1319 1453 7.809806 GGTGCTAATATATCCATGCAAAAACTC 59.190 37.037 0.00 0.00 32.10 3.01
1320 1454 7.809806 GTGCTAATATATCCATGCAAAAACTCC 59.190 37.037 0.00 0.00 32.10 3.85
1321 1455 7.505248 TGCTAATATATCCATGCAAAAACTCCA 59.495 33.333 0.00 0.00 0.00 3.86
1322 1456 8.359642 GCTAATATATCCATGCAAAAACTCCAA 58.640 33.333 0.00 0.00 0.00 3.53
1323 1457 9.903682 CTAATATATCCATGCAAAAACTCCAAG 57.096 33.333 0.00 0.00 0.00 3.61
1324 1458 2.818130 TCCATGCAAAAACTCCAAGC 57.182 45.000 0.00 0.00 0.00 4.01
1325 1459 2.037901 TCCATGCAAAAACTCCAAGCA 58.962 42.857 0.00 0.00 39.79 3.91
1326 1460 2.633967 TCCATGCAAAAACTCCAAGCAT 59.366 40.909 0.00 0.00 45.92 3.79
1327 1461 3.071312 TCCATGCAAAAACTCCAAGCATT 59.929 39.130 0.00 0.00 42.76 3.56
1328 1462 3.434299 CCATGCAAAAACTCCAAGCATTC 59.566 43.478 0.00 0.00 42.76 2.67
1329 1463 4.312443 CATGCAAAAACTCCAAGCATTCT 58.688 39.130 0.00 0.00 42.76 2.40
1330 1464 4.405116 TGCAAAAACTCCAAGCATTCTT 57.595 36.364 0.00 0.00 0.00 2.52
1331 1465 4.768583 TGCAAAAACTCCAAGCATTCTTT 58.231 34.783 0.00 0.00 0.00 2.52
1332 1466 4.571580 TGCAAAAACTCCAAGCATTCTTTG 59.428 37.500 0.00 0.00 0.00 2.77
1333 1467 4.571984 GCAAAAACTCCAAGCATTCTTTGT 59.428 37.500 0.00 0.00 0.00 2.83
1334 1468 5.752955 GCAAAAACTCCAAGCATTCTTTGTA 59.247 36.000 0.00 0.00 0.00 2.41
1335 1469 6.074142 GCAAAAACTCCAAGCATTCTTTGTAG 60.074 38.462 0.00 0.00 0.00 2.74
1336 1470 4.773323 AACTCCAAGCATTCTTTGTAGC 57.227 40.909 0.00 0.00 0.00 3.58
1337 1471 4.026356 ACTCCAAGCATTCTTTGTAGCT 57.974 40.909 0.00 0.00 39.37 3.32
1338 1472 3.755378 ACTCCAAGCATTCTTTGTAGCTG 59.245 43.478 0.00 0.00 37.41 4.24
1339 1473 3.754965 TCCAAGCATTCTTTGTAGCTGT 58.245 40.909 0.00 0.00 37.41 4.40
1340 1474 3.503363 TCCAAGCATTCTTTGTAGCTGTG 59.497 43.478 0.00 0.00 37.41 3.66
1341 1475 3.503363 CCAAGCATTCTTTGTAGCTGTGA 59.497 43.478 0.00 0.00 37.41 3.58
1342 1476 4.470462 CAAGCATTCTTTGTAGCTGTGAC 58.530 43.478 0.00 0.00 37.41 3.67
1343 1477 4.013267 AGCATTCTTTGTAGCTGTGACT 57.987 40.909 0.00 0.00 35.72 3.41
1344 1478 3.999663 AGCATTCTTTGTAGCTGTGACTC 59.000 43.478 0.00 0.00 35.72 3.36
1345 1479 3.748048 GCATTCTTTGTAGCTGTGACTCA 59.252 43.478 0.00 0.00 0.00 3.41
1346 1480 4.142945 GCATTCTTTGTAGCTGTGACTCAG 60.143 45.833 0.00 0.00 46.12 3.35
1347 1481 3.667497 TCTTTGTAGCTGTGACTCAGG 57.333 47.619 0.00 0.00 43.78 3.86
1348 1482 2.300152 TCTTTGTAGCTGTGACTCAGGG 59.700 50.000 0.00 0.00 43.78 4.45
1349 1483 0.976641 TTGTAGCTGTGACTCAGGGG 59.023 55.000 0.00 0.00 43.78 4.79
1350 1484 0.904865 TGTAGCTGTGACTCAGGGGG 60.905 60.000 0.00 0.00 43.78 5.40
1351 1485 1.990060 TAGCTGTGACTCAGGGGGC 60.990 63.158 0.00 0.00 43.78 5.80
1352 1486 4.767255 GCTGTGACTCAGGGGGCG 62.767 72.222 6.65 0.00 43.78 6.13
1353 1487 4.087892 CTGTGACTCAGGGGGCGG 62.088 72.222 0.00 0.00 40.23 6.13
1357 1491 4.791069 GACTCAGGGGGCGGGGTA 62.791 72.222 0.00 0.00 0.00 3.69
1358 1492 4.103928 ACTCAGGGGGCGGGGTAT 62.104 66.667 0.00 0.00 0.00 2.73
1359 1493 2.772622 CTCAGGGGGCGGGGTATT 60.773 66.667 0.00 0.00 0.00 1.89
1360 1494 2.770904 TCAGGGGGCGGGGTATTC 60.771 66.667 0.00 0.00 0.00 1.75
1361 1495 2.772622 CAGGGGGCGGGGTATTCT 60.773 66.667 0.00 0.00 0.00 2.40
1362 1496 2.043941 AGGGGGCGGGGTATTCTT 59.956 61.111 0.00 0.00 0.00 2.52
1363 1497 1.057851 CAGGGGGCGGGGTATTCTTA 61.058 60.000 0.00 0.00 0.00 2.10
1364 1498 0.104090 AGGGGGCGGGGTATTCTTAT 60.104 55.000 0.00 0.00 0.00 1.73
1365 1499 0.775542 GGGGGCGGGGTATTCTTATT 59.224 55.000 0.00 0.00 0.00 1.40
1366 1500 1.146359 GGGGGCGGGGTATTCTTATTT 59.854 52.381 0.00 0.00 0.00 1.40
1367 1501 2.425247 GGGGGCGGGGTATTCTTATTTT 60.425 50.000 0.00 0.00 0.00 1.82
1368 1502 3.302161 GGGGCGGGGTATTCTTATTTTT 58.698 45.455 0.00 0.00 0.00 1.94
1369 1503 3.319972 GGGGCGGGGTATTCTTATTTTTC 59.680 47.826 0.00 0.00 0.00 2.29
1422 1556 7.090953 AGTACTTCTCTATGTGTGACTAAGC 57.909 40.000 0.00 0.00 0.00 3.09
1501 1635 6.121776 TCATGACTTTGGTATTGTAGGTGT 57.878 37.500 0.00 0.00 0.00 4.16
1522 1656 9.744468 AGGTGTTGATGTTGTTTTAATAAACTC 57.256 29.630 0.00 0.00 43.25 3.01
1601 1735 8.943594 AGGAGGGAGTATACTAAATCTGTAAG 57.056 38.462 5.09 0.00 0.00 2.34
1730 1864 1.225475 GCTGCGTTTGACATCGTCG 60.225 57.895 0.00 0.00 34.95 5.12
1755 1889 8.208560 CGTAGCTTTTAAATGATCTGATACGAC 58.791 37.037 5.33 0.00 34.61 4.34
1779 1913 4.207891 ACCTCTGTACTAGCACATTTGG 57.792 45.455 0.00 2.49 0.00 3.28
1782 1916 3.599343 TCTGTACTAGCACATTTGGCTG 58.401 45.455 0.00 0.00 42.62 4.85
1914 2049 8.486210 AGGTATCTAATTGTATGTTCTCTTGCA 58.514 33.333 0.00 0.00 0.00 4.08
1922 2057 5.551233 TGTATGTTCTCTTGCAAGTAAGCT 58.449 37.500 25.19 12.79 34.99 3.74
1923 2058 5.639506 TGTATGTTCTCTTGCAAGTAAGCTC 59.360 40.000 25.19 12.50 34.99 4.09
1924 2059 4.071961 TGTTCTCTTGCAAGTAAGCTCA 57.928 40.909 25.19 14.53 34.99 4.26
1925 2060 4.450976 TGTTCTCTTGCAAGTAAGCTCAA 58.549 39.130 25.19 5.22 34.99 3.02
1926 2061 5.065914 TGTTCTCTTGCAAGTAAGCTCAAT 58.934 37.500 25.19 0.00 34.99 2.57
1927 2062 5.532406 TGTTCTCTTGCAAGTAAGCTCAATT 59.468 36.000 25.19 0.00 34.99 2.32
1928 2063 6.710295 TGTTCTCTTGCAAGTAAGCTCAATTA 59.290 34.615 25.19 1.23 34.99 1.40
1929 2064 7.391554 TGTTCTCTTGCAAGTAAGCTCAATTAT 59.608 33.333 25.19 0.00 34.99 1.28
1930 2065 8.883731 GTTCTCTTGCAAGTAAGCTCAATTATA 58.116 33.333 25.19 0.58 34.99 0.98
1931 2066 9.618890 TTCTCTTGCAAGTAAGCTCAATTATAT 57.381 29.630 25.19 0.00 34.99 0.86
1932 2067 9.618890 TCTCTTGCAAGTAAGCTCAATTATATT 57.381 29.630 25.19 0.00 34.99 1.28
1935 2070 9.793252 CTTGCAAGTAAGCTCAATTATATTTGT 57.207 29.630 18.65 0.00 34.99 2.83
1944 2079 9.860898 AAGCTCAATTATATTTGTTTTCAGGAC 57.139 29.630 7.13 0.00 0.00 3.85
1945 2080 9.023962 AGCTCAATTATATTTGTTTTCAGGACA 57.976 29.630 7.13 0.00 0.00 4.02
1946 2081 9.638239 GCTCAATTATATTTGTTTTCAGGACAA 57.362 29.630 7.13 0.00 35.36 3.18
2190 2325 5.243060 GGGGTTACAAAGCTAAGTTGTCAAT 59.757 40.000 5.55 0.00 39.80 2.57
2194 2329 7.704899 GGTTACAAAGCTAAGTTGTCAATGTTT 59.295 33.333 5.55 0.00 39.80 2.83
2196 2331 6.862209 ACAAAGCTAAGTTGTCAATGTTTCA 58.138 32.000 0.00 0.00 34.02 2.69
2225 2392 5.864474 GCTATGAAGACCTACGAATGTATGG 59.136 44.000 0.00 0.00 0.00 2.74
2262 2429 6.611381 CCATAGAATGTGTCGTTTTTGTCAT 58.389 36.000 0.00 0.00 0.00 3.06
2326 2494 8.201464 ACCAGGTGAAAGTTTTACAAAATAAGG 58.799 33.333 12.08 5.57 0.00 2.69
2672 2840 4.104738 TCAGGACCTGTTTGGAAAAGAGAT 59.895 41.667 21.06 0.00 39.71 2.75
2815 2984 4.506288 GTCCCTCAAAAACAAAATTGACGG 59.494 41.667 0.00 0.00 34.79 4.79
2839 3009 1.072505 GGCCAGTCCAAGGTTTCGA 59.927 57.895 0.00 0.00 34.01 3.71
3210 3385 6.412362 TCTAGAGCTCAAATATTGGTCTCC 57.588 41.667 17.77 0.00 39.03 3.71
3259 3435 2.935201 CACTCATCTTGTTAGAGCTGCC 59.065 50.000 0.00 0.00 32.92 4.85
3277 3453 1.814248 GCCGTGGAGTTCCTGAAAGTT 60.814 52.381 0.00 0.00 36.82 2.66
3287 3463 3.300711 CTGAAAGTTCGGGGTCGTT 57.699 52.632 0.00 0.00 37.69 3.85
3361 3537 3.504906 ACCATGTCACAAGAGCAGATTTG 59.495 43.478 0.00 0.00 0.00 2.32
3445 3621 8.381636 AGATTCTCTCAAATTTTCAGGAGAAGA 58.618 33.333 18.22 11.18 41.16 2.87
3703 3879 5.157940 TCAGAATAAGAGCAAACAGAGCT 57.842 39.130 0.00 0.00 46.82 4.09
3885 4061 5.949354 AGAGGAGCTATGGTATGTATCAGTC 59.051 44.000 0.00 0.00 0.00 3.51
3929 4105 7.575414 TTGGAACAGCTAGTTTAACATTCAA 57.425 32.000 0.00 0.00 41.51 2.69
4145 4321 7.648908 TGTATTTTCATCAAACTTGCAGTTGAG 59.351 33.333 13.03 0.00 38.66 3.02
4354 4533 1.067516 CTGCCATTTTATGCCTTCGGG 59.932 52.381 0.00 0.00 38.37 5.14
4449 4628 3.264964 ACGGAGCCCTTTTTCTATTGGTA 59.735 43.478 0.00 0.00 0.00 3.25
4498 4677 6.260050 CCTATTGTCTAGGCTTTAAATTCGCA 59.740 38.462 0.00 0.00 0.00 5.10
4506 4685 6.226988 AGGCTTTAAATTCGCACAAATTTG 57.773 33.333 16.67 16.67 38.82 2.32
4509 4688 5.178438 GCTTTAAATTCGCACAAATTTGGGA 59.822 36.000 24.58 13.67 38.82 4.37
4513 4692 3.526931 TTCGCACAAATTTGGGAAACA 57.473 38.095 24.58 1.37 43.30 2.83
4597 5134 9.440773 GGGCAAAGAAATAAATCTTGAGAATTT 57.559 29.630 0.00 0.00 39.54 1.82
4773 5310 7.308589 GGCAACACTATGAAGTTGTTATTGAGT 60.309 37.037 7.08 0.00 45.16 3.41
4791 5328 3.568007 TGAGTGTGGCAAACTTATGTTCC 59.432 43.478 12.49 0.00 34.96 3.62
4794 5331 4.037923 AGTGTGGCAAACTTATGTTCCAAG 59.962 41.667 3.96 0.00 33.61 3.61
4948 5485 7.342769 TCCTAGTCAAAGATACAATTCGCTA 57.657 36.000 0.00 0.00 0.00 4.26
4949 5486 7.778083 TCCTAGTCAAAGATACAATTCGCTAA 58.222 34.615 0.00 0.00 0.00 3.09
4970 5507 7.201182 CGCTAAATTGATTCTGACGTTTTCTTG 60.201 37.037 0.00 0.00 0.00 3.02
5018 5555 3.748568 AGAAGAAAGGATCGTTTCAGCAC 59.251 43.478 31.61 21.69 38.66 4.40
5150 5721 2.301870 TCAAAATACCTGACGGTGCTCT 59.698 45.455 0.00 0.00 45.18 4.09
5151 5722 2.386661 AAATACCTGACGGTGCTCTG 57.613 50.000 0.00 0.00 45.18 3.35
5230 5801 4.633126 TCAGAGATTTCATTCGCTTCCTTG 59.367 41.667 0.00 0.00 0.00 3.61
5239 5810 0.608640 TCGCTTCCTTGAGGAGAACC 59.391 55.000 0.00 0.00 46.36 3.62
5390 5968 4.870426 TCAGAAATCTGCTATCGACAAACC 59.130 41.667 5.53 0.00 43.46 3.27
5423 6001 2.330440 TTGCTGAGCAACTCTGACAA 57.670 45.000 17.04 0.00 43.99 3.18
5451 6029 5.446473 GCCTGAACATGTTGAGAATAACGAG 60.446 44.000 24.45 7.77 33.28 4.18
5452 6030 5.446473 CCTGAACATGTTGAGAATAACGAGC 60.446 44.000 24.45 2.69 33.28 5.03
5508 6086 0.107116 AGATAGACGGCGTCCTCACT 60.107 55.000 34.04 23.99 32.18 3.41
5613 6191 1.684983 ACCGACACCGAAGAAGAAGAA 59.315 47.619 0.00 0.00 38.22 2.52
5614 6192 2.288273 ACCGACACCGAAGAAGAAGAAG 60.288 50.000 0.00 0.00 38.22 2.85
5615 6193 2.030185 CCGACACCGAAGAAGAAGAAGA 60.030 50.000 0.00 0.00 38.22 2.87
5616 6194 3.552273 CCGACACCGAAGAAGAAGAAGAA 60.552 47.826 0.00 0.00 38.22 2.52
5617 6195 3.670991 CGACACCGAAGAAGAAGAAGAAG 59.329 47.826 0.00 0.00 38.22 2.85
5618 6196 4.556898 CGACACCGAAGAAGAAGAAGAAGA 60.557 45.833 0.00 0.00 38.22 2.87
5619 6197 5.277857 ACACCGAAGAAGAAGAAGAAGAA 57.722 39.130 0.00 0.00 0.00 2.52
5620 6198 5.293560 ACACCGAAGAAGAAGAAGAAGAAG 58.706 41.667 0.00 0.00 0.00 2.85
5621 6199 5.069251 ACACCGAAGAAGAAGAAGAAGAAGA 59.931 40.000 0.00 0.00 0.00 2.87
6084 6665 2.749076 CAATCGGGCAGTGATTCTTTGA 59.251 45.455 0.00 0.00 33.91 2.69
6273 6856 3.056821 CGCCGTTATCATCCCTCTATCAA 60.057 47.826 0.00 0.00 0.00 2.57
6294 6877 2.158871 ACGGAGTCAGGCAAAACTTACA 60.159 45.455 0.00 0.00 29.74 2.41
6315 6898 9.099454 CTTACAGTAGAAGACAACAGAAAAGTT 57.901 33.333 0.00 0.00 0.00 2.66
6355 6938 2.106511 AGGACCAACACACTAGCACAAT 59.893 45.455 0.00 0.00 0.00 2.71
6377 6960 0.808453 CCGCCGCCGATAAAGAGAAA 60.808 55.000 0.00 0.00 36.29 2.52
6379 6962 1.365699 GCCGCCGATAAAGAGAAACA 58.634 50.000 0.00 0.00 0.00 2.83
6411 6994 8.616076 CGAAATGATTCAAACTAGGCTTCTAAT 58.384 33.333 0.00 0.00 35.15 1.73
6427 7010 9.920946 AGGCTTCTAATAAAATGATCCAAACTA 57.079 29.630 0.00 0.00 0.00 2.24
6441 7024 5.456548 TCCAAACTATAGACACACGAACA 57.543 39.130 6.78 0.00 0.00 3.18
6446 7029 8.879759 CCAAACTATAGACACACGAACAAATAT 58.120 33.333 6.78 0.00 0.00 1.28
6457 7040 6.860539 CACACGAACAAATATTGAATCCACAA 59.139 34.615 0.00 0.00 0.00 3.33
6597 7367 8.414629 AACTTATTTCTTCTTCAAGGAGCAAT 57.585 30.769 0.00 0.00 0.00 3.56
6635 7405 8.506168 TCCTGAATAAGACGCAAAATCTAATT 57.494 30.769 0.00 0.00 0.00 1.40
6644 7414 7.752695 AGACGCAAAATCTAATTGTCCTTAAG 58.247 34.615 0.00 0.00 0.00 1.85
6648 7418 9.065871 CGCAAAATCTAATTGTCCTTAAGAAAG 57.934 33.333 3.36 0.00 0.00 2.62
6676 7446 6.072673 ACCTAAAAATGAAGCAGTAACCTTCG 60.073 38.462 0.00 0.00 41.16 3.79
6694 7464 1.080093 GCGTCACCATCGGTCAAGA 60.080 57.895 0.00 0.00 31.02 3.02
6707 7477 1.553704 GGTCAAGATCCACCGTACCTT 59.446 52.381 0.00 0.00 0.00 3.50
6728 7876 1.972660 ATGGTCCTTAGCTCGCCCAC 61.973 60.000 0.00 0.00 0.00 4.61
6902 8074 3.434319 ATCGGTTGCCTTGCAGCG 61.434 61.111 0.00 1.30 40.59 5.18
6922 8094 1.936203 GCCAACAATGACATGTGGTGC 60.936 52.381 1.15 0.00 32.81 5.01
7055 8227 1.876799 CCATGCCACACACGTAAAGAA 59.123 47.619 0.00 0.00 0.00 2.52
7086 8258 2.370349 ACTGACATAGCAGAGCGTACT 58.630 47.619 0.00 0.00 39.20 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.734538 AATTGGTCGTAATAAATTTGCGAAG 57.265 32.000 0.00 0.00 33.30 3.79
1 2 8.522178 AAAATTGGTCGTAATAAATTTGCGAA 57.478 26.923 0.00 0.00 33.65 4.70
2 3 7.808381 TGAAAATTGGTCGTAATAAATTTGCGA 59.192 29.630 0.00 3.23 32.42 5.10
34 35 3.484407 GGATCATGAAGCAACCATAGCT 58.516 45.455 0.00 0.00 45.97 3.32
56 57 8.940768 TTTGGGAAAATAAAGTTCAAGACAAG 57.059 30.769 0.00 0.00 0.00 3.16
78 79 3.655486 TCCATCACAAGCAAGCAATTTG 58.345 40.909 0.00 0.00 39.88 2.32
123 124 7.379529 AGAGAATCAATTTTAAACAAGCACACG 59.620 33.333 0.00 0.00 37.82 4.49
150 151 3.181482 TGCTCAAAAGAAAAACGGCATCA 60.181 39.130 0.00 0.00 0.00 3.07
152 153 3.383761 CTGCTCAAAAGAAAAACGGCAT 58.616 40.909 0.00 0.00 0.00 4.40
191 192 1.550976 CTTGTAGTCCCTGTCAGGTCC 59.449 57.143 17.85 7.46 31.93 4.46
204 205 5.178061 TGAATGCAACATCGATCTTGTAGT 58.822 37.500 13.87 9.33 0.00 2.73
206 207 5.816777 TCATGAATGCAACATCGATCTTGTA 59.183 36.000 13.87 10.41 0.00 2.41
211 212 5.998553 AGATTCATGAATGCAACATCGATC 58.001 37.500 25.37 7.36 0.00 3.69
298 304 7.741785 TCTAACCAACAGAAATAGAAAGGACA 58.258 34.615 0.00 0.00 0.00 4.02
767 784 7.844269 ACAGGGCCTATAATTTCTTTAATTGGT 59.156 33.333 5.28 0.00 37.07 3.67
798 815 5.006455 GGGTAGCTATTGTAACGCTTCTTTC 59.994 44.000 0.00 0.00 35.33 2.62
944 962 8.680903 CATCAGATTATATTGCCAAATCCTACC 58.319 37.037 0.00 0.00 31.35 3.18
978 996 4.574892 TCAAATGTGGAGCGTGAGATAAA 58.425 39.130 0.00 0.00 0.00 1.40
991 1009 2.623535 CATGCCAACCATCAAATGTGG 58.376 47.619 0.00 0.00 42.55 4.17
1069 1087 8.877808 ACTGTAACTACAACTACAAAACTACC 57.122 34.615 0.00 0.00 35.50 3.18
1268 1402 9.212641 CCACGATCTAGATTTGTCATTTATCAT 57.787 33.333 6.70 0.00 0.00 2.45
1295 1429 7.505248 TGGAGTTTTTGCATGGATATATTAGCA 59.495 33.333 0.00 0.00 0.00 3.49
1296 1430 7.885297 TGGAGTTTTTGCATGGATATATTAGC 58.115 34.615 0.00 0.00 0.00 3.09
1297 1431 9.903682 CTTGGAGTTTTTGCATGGATATATTAG 57.096 33.333 0.00 0.00 0.00 1.73
1298 1432 8.359642 GCTTGGAGTTTTTGCATGGATATATTA 58.640 33.333 0.00 0.00 0.00 0.98
1299 1433 7.147689 TGCTTGGAGTTTTTGCATGGATATATT 60.148 33.333 0.00 0.00 0.00 1.28
1300 1434 6.324512 TGCTTGGAGTTTTTGCATGGATATAT 59.675 34.615 0.00 0.00 0.00 0.86
1301 1435 5.655974 TGCTTGGAGTTTTTGCATGGATATA 59.344 36.000 0.00 0.00 0.00 0.86
1302 1436 4.467082 TGCTTGGAGTTTTTGCATGGATAT 59.533 37.500 0.00 0.00 0.00 1.63
1303 1437 3.831333 TGCTTGGAGTTTTTGCATGGATA 59.169 39.130 0.00 0.00 0.00 2.59
1304 1438 2.633967 TGCTTGGAGTTTTTGCATGGAT 59.366 40.909 0.00 0.00 0.00 3.41
1305 1439 2.037901 TGCTTGGAGTTTTTGCATGGA 58.962 42.857 0.00 0.00 0.00 3.41
1306 1440 2.529780 TGCTTGGAGTTTTTGCATGG 57.470 45.000 0.00 0.00 0.00 3.66
1307 1441 4.312443 AGAATGCTTGGAGTTTTTGCATG 58.688 39.130 0.00 0.00 42.57 4.06
1308 1442 4.612264 AGAATGCTTGGAGTTTTTGCAT 57.388 36.364 0.00 0.00 44.86 3.96
1309 1443 4.405116 AAGAATGCTTGGAGTTTTTGCA 57.595 36.364 0.00 0.00 38.05 4.08
1310 1444 4.571984 ACAAAGAATGCTTGGAGTTTTTGC 59.428 37.500 0.00 0.00 33.79 3.68
1311 1445 6.074142 GCTACAAAGAATGCTTGGAGTTTTTG 60.074 38.462 0.00 4.63 33.79 2.44
1312 1446 5.985530 GCTACAAAGAATGCTTGGAGTTTTT 59.014 36.000 0.00 0.00 33.79 1.94
1313 1447 5.302823 AGCTACAAAGAATGCTTGGAGTTTT 59.697 36.000 0.00 0.00 33.79 2.43
1314 1448 4.829492 AGCTACAAAGAATGCTTGGAGTTT 59.171 37.500 0.00 0.00 33.79 2.66
1315 1449 4.217118 CAGCTACAAAGAATGCTTGGAGTT 59.783 41.667 0.00 0.00 33.79 3.01
1316 1450 3.755378 CAGCTACAAAGAATGCTTGGAGT 59.245 43.478 0.00 0.00 33.79 3.85
1317 1451 3.755378 ACAGCTACAAAGAATGCTTGGAG 59.245 43.478 0.00 0.00 33.79 3.86
1318 1452 3.503363 CACAGCTACAAAGAATGCTTGGA 59.497 43.478 0.00 0.00 33.79 3.53
1319 1453 3.503363 TCACAGCTACAAAGAATGCTTGG 59.497 43.478 0.00 0.00 33.79 3.61
1320 1454 4.214971 AGTCACAGCTACAAAGAATGCTTG 59.785 41.667 0.00 0.00 33.79 4.01
1321 1455 4.392940 AGTCACAGCTACAAAGAATGCTT 58.607 39.130 0.00 0.00 33.03 3.91
1322 1456 3.999663 GAGTCACAGCTACAAAGAATGCT 59.000 43.478 0.00 0.00 36.04 3.79
1323 1457 3.748048 TGAGTCACAGCTACAAAGAATGC 59.252 43.478 0.00 0.00 0.00 3.56
1324 1458 4.391216 CCTGAGTCACAGCTACAAAGAATG 59.609 45.833 0.00 0.00 44.52 2.67
1325 1459 4.564406 CCCTGAGTCACAGCTACAAAGAAT 60.564 45.833 0.00 0.00 44.52 2.40
1326 1460 3.244215 CCCTGAGTCACAGCTACAAAGAA 60.244 47.826 0.00 0.00 44.52 2.52
1327 1461 2.300152 CCCTGAGTCACAGCTACAAAGA 59.700 50.000 0.00 0.00 44.52 2.52
1328 1462 2.613977 CCCCTGAGTCACAGCTACAAAG 60.614 54.545 0.00 0.00 44.52 2.77
1329 1463 1.347707 CCCCTGAGTCACAGCTACAAA 59.652 52.381 0.00 0.00 44.52 2.83
1330 1464 0.976641 CCCCTGAGTCACAGCTACAA 59.023 55.000 0.00 0.00 44.52 2.41
1331 1465 0.904865 CCCCCTGAGTCACAGCTACA 60.905 60.000 0.00 0.00 44.52 2.74
1332 1466 1.901085 CCCCCTGAGTCACAGCTAC 59.099 63.158 0.00 0.00 44.52 3.58
1333 1467 1.990060 GCCCCCTGAGTCACAGCTA 60.990 63.158 0.00 0.00 44.52 3.32
1334 1468 3.325753 GCCCCCTGAGTCACAGCT 61.326 66.667 0.00 0.00 44.52 4.24
1335 1469 4.767255 CGCCCCCTGAGTCACAGC 62.767 72.222 0.00 0.00 44.52 4.40
1336 1470 4.087892 CCGCCCCCTGAGTCACAG 62.088 72.222 0.00 0.00 45.36 3.66
1340 1474 4.791069 TACCCCGCCCCCTGAGTC 62.791 72.222 0.00 0.00 0.00 3.36
1341 1475 3.653122 AATACCCCGCCCCCTGAGT 62.653 63.158 0.00 0.00 0.00 3.41
1342 1476 2.772622 AATACCCCGCCCCCTGAG 60.773 66.667 0.00 0.00 0.00 3.35
1343 1477 2.770904 GAATACCCCGCCCCCTGA 60.771 66.667 0.00 0.00 0.00 3.86
1344 1478 1.057851 TAAGAATACCCCGCCCCCTG 61.058 60.000 0.00 0.00 0.00 4.45
1345 1479 0.104090 ATAAGAATACCCCGCCCCCT 60.104 55.000 0.00 0.00 0.00 4.79
1346 1480 0.775542 AATAAGAATACCCCGCCCCC 59.224 55.000 0.00 0.00 0.00 5.40
1347 1481 2.670019 AAATAAGAATACCCCGCCCC 57.330 50.000 0.00 0.00 0.00 5.80
1348 1482 4.212716 AGAAAAATAAGAATACCCCGCCC 58.787 43.478 0.00 0.00 0.00 6.13
1349 1483 5.451381 CCAAGAAAAATAAGAATACCCCGCC 60.451 44.000 0.00 0.00 0.00 6.13
1350 1484 5.126545 ACCAAGAAAAATAAGAATACCCCGC 59.873 40.000 0.00 0.00 0.00 6.13
1351 1485 6.152154 ACACCAAGAAAAATAAGAATACCCCG 59.848 38.462 0.00 0.00 0.00 5.73
1352 1486 7.476540 ACACCAAGAAAAATAAGAATACCCC 57.523 36.000 0.00 0.00 0.00 4.95
1397 1531 8.047911 AGCTTAGTCACACATAGAGAAGTACTA 58.952 37.037 0.00 0.00 0.00 1.82
1399 1533 7.090953 AGCTTAGTCACACATAGAGAAGTAC 57.909 40.000 0.00 0.00 0.00 2.73
1400 1534 7.704578 AAGCTTAGTCACACATAGAGAAGTA 57.295 36.000 0.00 0.00 0.00 2.24
1475 1609 7.504238 ACACCTACAATACCAAAGTCATGAAAA 59.496 33.333 0.00 0.00 0.00 2.29
1482 1616 6.430000 ACATCAACACCTACAATACCAAAGTC 59.570 38.462 0.00 0.00 0.00 3.01
1483 1617 6.303839 ACATCAACACCTACAATACCAAAGT 58.696 36.000 0.00 0.00 0.00 2.66
1484 1618 6.817765 ACATCAACACCTACAATACCAAAG 57.182 37.500 0.00 0.00 0.00 2.77
1501 1635 8.622157 TGTCCGAGTTTATTAAAACAACATCAA 58.378 29.630 4.04 0.00 46.18 2.57
1722 1856 6.757010 AGATCATTTAAAAGCTACGACGATGT 59.243 34.615 0.00 0.00 0.00 3.06
1730 1864 8.208560 CGTCGTATCAGATCATTTAAAAGCTAC 58.791 37.037 0.00 0.00 0.00 3.58
1755 1889 3.784701 ATGTGCTAGTACAGAGGTTCG 57.215 47.619 18.73 0.00 33.44 3.95
1779 1913 2.648059 AGAAACATACAGCCCATCAGC 58.352 47.619 0.00 0.00 0.00 4.26
1782 1916 4.141711 TGGACTAGAAACATACAGCCCATC 60.142 45.833 0.00 0.00 0.00 3.51
1969 2104 7.458397 AGGTCCAGTCTGTGATTATGTTAAAA 58.542 34.615 0.00 0.00 0.00 1.52
1985 2120 4.755266 TTAAGATGGCTTAGGTCCAGTC 57.245 45.455 0.00 0.00 37.84 3.51
2196 2331 4.383931 TCGTAGGTCTTCATAGCCCTAT 57.616 45.455 0.00 0.00 0.00 2.57
2225 2392 1.040646 TCTATGGCACGATCACCCTC 58.959 55.000 0.00 0.00 0.00 4.30
2285 2452 9.410556 CTTTCACCTGGTTTGTAAGATATTTTG 57.589 33.333 0.00 0.00 0.00 2.44
2643 2811 0.535102 CAAACAGGTCCTGAGCGGTT 60.535 55.000 26.18 5.86 46.05 4.44
2672 2840 0.034337 GGTTTACACCTCGCCAGACA 59.966 55.000 0.00 0.00 40.44 3.41
2815 2984 4.785453 CTTGGACTGGCCCGGAGC 62.785 72.222 0.73 4.32 42.60 4.70
3210 3385 3.728718 GTGCATTTGTGACCTAAACAACG 59.271 43.478 0.00 0.00 37.26 4.10
3259 3435 1.792949 CGAACTTTCAGGAACTCCACG 59.207 52.381 0.00 0.00 34.60 4.94
3277 3453 1.803334 CTGAAATGAAACGACCCCGA 58.197 50.000 0.00 0.00 39.50 5.14
3283 3459 0.605319 AGCCGGCTGAAATGAAACGA 60.605 50.000 32.33 0.00 0.00 3.85
3284 3460 0.454957 CAGCCGGCTGAAATGAAACG 60.455 55.000 46.72 19.48 46.30 3.60
3285 3461 3.406682 CAGCCGGCTGAAATGAAAC 57.593 52.632 46.72 4.68 46.30 2.78
3361 3537 7.043125 GCAACTTGGAAGAGAATTGAAAAGAAC 60.043 37.037 0.00 0.00 0.00 3.01
3427 3603 8.469309 AACTGAATCTTCTCCTGAAAATTTGA 57.531 30.769 0.00 0.00 0.00 2.69
3445 3621 6.423905 CGACGATACAATCCCATAAACTGAAT 59.576 38.462 0.00 0.00 0.00 2.57
3703 3879 3.096092 GGTCTTGGATGCCATTTACCAA 58.904 45.455 0.00 0.00 39.60 3.67
3885 4061 4.470462 CAATGCTCAAGAACCGAAGAAAG 58.530 43.478 0.00 0.00 0.00 2.62
4145 4321 1.778591 CACCAAACAAAATCGCGTCAC 59.221 47.619 5.77 0.00 0.00 3.67
4354 4533 1.875576 CGATGCCTAGGGTCAATCTGC 60.876 57.143 11.72 0.00 0.00 4.26
4472 4651 6.260271 GCGAATTTAAAGCCTAGACAATAGGT 59.740 38.462 3.05 0.00 37.06 3.08
4498 4677 5.659079 TGGTCTACTTGTTTCCCAAATTTGT 59.341 36.000 16.73 0.00 31.20 2.83
4506 4685 8.135529 GCATATTATTTGGTCTACTTGTTTCCC 58.864 37.037 0.00 0.00 0.00 3.97
4544 5081 7.016268 TCCCCAATGTCTAACCTGTAGATTATC 59.984 40.741 0.00 0.00 0.00 1.75
4597 5134 3.568109 CCCCTGAAGTTTACTCCTAGGGA 60.568 52.174 19.54 0.00 40.18 4.20
4689 5226 9.863650 AGGATCAGATGATGTTCTCAATTATTT 57.136 29.630 0.00 0.00 37.44 1.40
4726 5263 4.500375 GCCTCTCTTGCTGTTGTTGAAAAT 60.500 41.667 0.00 0.00 0.00 1.82
4773 5310 4.211125 TCTTGGAACATAAGTTTGCCACA 58.789 39.130 0.00 0.00 39.30 4.17
4791 5328 1.336755 CACAAGAACCCCGGTTTCTTG 59.663 52.381 33.69 33.69 42.21 3.02
4794 5331 1.104577 TGCACAAGAACCCCGGTTTC 61.105 55.000 0.00 2.43 38.60 2.78
4920 5457 7.224753 GCGAATTGTATCTTTGACTAGGAATCA 59.775 37.037 0.00 0.00 0.00 2.57
4921 5458 7.439655 AGCGAATTGTATCTTTGACTAGGAATC 59.560 37.037 0.00 0.00 0.00 2.52
4948 5485 6.215845 CCCAAGAAAACGTCAGAATCAATTT 58.784 36.000 0.00 0.00 0.00 1.82
4949 5486 5.772521 CCCAAGAAAACGTCAGAATCAATT 58.227 37.500 0.00 0.00 0.00 2.32
4954 5491 2.814336 GAGCCCAAGAAAACGTCAGAAT 59.186 45.455 0.00 0.00 0.00 2.40
4983 5520 5.319453 TCCTTTCTTCTTCTGCACATCATT 58.681 37.500 0.00 0.00 0.00 2.57
4985 5522 4.356405 TCCTTTCTTCTTCTGCACATCA 57.644 40.909 0.00 0.00 0.00 3.07
5120 5691 5.932303 CCGTCAGGTATTTTGAGAAGAAAGA 59.068 40.000 0.00 0.00 0.00 2.52
5121 5692 6.170675 CCGTCAGGTATTTTGAGAAGAAAG 57.829 41.667 0.00 0.00 0.00 2.62
5230 5801 0.896226 AGGCTAACGTGGTTCTCCTC 59.104 55.000 0.00 0.00 34.23 3.71
5239 5810 0.108804 ACATCGGTGAGGCTAACGTG 60.109 55.000 0.65 0.00 0.00 4.49
5304 5882 6.759272 ACTTGCAGTAGTAATTCTTGTCAGA 58.241 36.000 0.00 0.00 0.00 3.27
5307 5885 9.974750 GATTTACTTGCAGTAGTAATTCTTGTC 57.025 33.333 17.86 6.99 39.60 3.18
5390 5968 0.732880 CAGCAACGGGTACTCGTCAG 60.733 60.000 23.18 18.01 43.07 3.51
5423 6001 3.708403 TCTCAACATGTTCAGGCTGAT 57.292 42.857 19.50 0.00 0.00 2.90
5508 6086 0.986527 ATCCATGATATGCCTCGCCA 59.013 50.000 0.00 0.00 0.00 5.69
5616 6194 9.653516 TCTGAGATATTATTGACCTCTTCTTCT 57.346 33.333 0.00 0.00 0.00 2.85
5617 6195 9.912634 CTCTGAGATATTATTGACCTCTTCTTC 57.087 37.037 0.00 0.00 0.00 2.87
5618 6196 8.367156 GCTCTGAGATATTATTGACCTCTTCTT 58.633 37.037 9.28 0.00 0.00 2.52
5619 6197 7.508636 TGCTCTGAGATATTATTGACCTCTTCT 59.491 37.037 9.28 0.00 0.00 2.85
5620 6198 7.665690 TGCTCTGAGATATTATTGACCTCTTC 58.334 38.462 9.28 0.00 0.00 2.87
5621 6199 7.609097 TGCTCTGAGATATTATTGACCTCTT 57.391 36.000 9.28 0.00 0.00 2.85
5892 6470 2.322830 CGTGAGAGACACCGTCCGA 61.323 63.158 0.00 0.00 45.73 4.55
6059 6640 2.083774 GAATCACTGCCCGATTGTTCA 58.916 47.619 0.00 0.00 33.26 3.18
6060 6641 2.359900 AGAATCACTGCCCGATTGTTC 58.640 47.619 0.00 0.00 33.26 3.18
6084 6665 2.032681 GCAGTCGGGTTCCAGCTT 59.967 61.111 0.00 0.00 0.00 3.74
6124 6705 4.456566 TGCCCGTGTAGAAAAAGTAATTCC 59.543 41.667 0.00 0.00 0.00 3.01
6125 6706 5.180680 ACTGCCCGTGTAGAAAAAGTAATTC 59.819 40.000 0.00 0.00 0.00 2.17
6257 6840 4.999310 ACTCCGTTGATAGAGGGATGATA 58.001 43.478 0.00 0.00 33.49 2.15
6273 6856 2.158871 TGTAAGTTTTGCCTGACTCCGT 60.159 45.455 0.00 0.00 0.00 4.69
6315 6898 5.298276 GGTCCTGTGAGATTTTAACACAACA 59.702 40.000 0.00 0.00 42.55 3.33
6318 6901 5.042463 TGGTCCTGTGAGATTTTAACACA 57.958 39.130 0.00 0.00 41.27 3.72
6355 6938 0.249155 CTCTTTATCGGCGGCGGTTA 60.249 55.000 31.73 16.60 0.00 2.85
6377 6960 9.265901 CCTAGTTTGAATCATTTCGATCTATGT 57.734 33.333 0.00 0.00 31.55 2.29
6379 6962 8.153550 AGCCTAGTTTGAATCATTTCGATCTAT 58.846 33.333 0.00 0.00 31.55 1.98
6401 6984 8.829373 AGTTTGGATCATTTTATTAGAAGCCT 57.171 30.769 0.00 0.00 0.00 4.58
6411 6994 9.093970 CGTGTGTCTATAGTTTGGATCATTTTA 57.906 33.333 0.00 0.00 0.00 1.52
6427 7010 8.612619 GGATTCAATATTTGTTCGTGTGTCTAT 58.387 33.333 0.00 0.00 0.00 1.98
6441 7024 6.449698 GCGGATCATTGTGGATTCAATATTT 58.550 36.000 0.00 0.00 36.44 1.40
6446 7029 2.023673 GGCGGATCATTGTGGATTCAA 58.976 47.619 0.00 0.00 0.00 2.69
6457 7040 0.462047 GTTGGTCTTCGGCGGATCAT 60.462 55.000 7.21 0.00 0.00 2.45
6480 7063 4.808364 CGGTGAATTTTGTGGTGTTCAATT 59.192 37.500 0.00 0.00 32.93 2.32
6597 7367 4.020617 CAGGAGGCAAGGCGGTGA 62.021 66.667 0.00 0.00 0.00 4.02
6635 7405 8.846211 CATTTTTAGGTGTCTTTCTTAAGGACA 58.154 33.333 8.46 8.46 32.02 4.02
6644 7414 6.739112 ACTGCTTCATTTTTAGGTGTCTTTC 58.261 36.000 0.00 0.00 0.00 2.62
6648 7418 6.206829 AGGTTACTGCTTCATTTTTAGGTGTC 59.793 38.462 0.00 0.00 0.00 3.67
6676 7446 0.460284 ATCTTGACCGATGGTGACGC 60.460 55.000 0.00 0.00 35.25 5.19
6707 7477 1.686325 GGGCGAGCTAAGGACCATGA 61.686 60.000 0.00 0.00 0.00 3.07
6728 7876 1.228124 TTCTGTTGCAAGGGGGTCG 60.228 57.895 0.00 0.00 0.00 4.79
6795 7943 0.609131 AGTTATGCTGCAAGGGCGTT 60.609 50.000 6.36 0.00 45.35 4.84
6902 8074 1.936203 GCACCACATGTCATTGTTGGC 60.936 52.381 0.00 0.00 0.00 4.52
6935 8107 6.925610 TGAGTCATTGGATATGTTACAAGC 57.074 37.500 0.00 0.00 0.00 4.01
7055 8227 4.847198 TGCTATGTCAGTTTGTGATGGAT 58.153 39.130 0.00 0.00 37.56 3.41


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

AutoCloner maintained by Alex Coulton.