Multiple sequence alignment - TraesCS6A01G407400

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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 TraesCS6A01G407400 chr6A 100.000 2273 0 0 1 2273 612193841 612191569 0.000000e+00 4198
1 TraesCS6A01G407400 chr6A 94.872 273 14 0 1990 2262 612175439 612175711 5.800000e-116 427
2 TraesCS6A01G407400 chr6A 96.429 112 3 1 1875 1986 612175196 612175306 1.390000e-42 183
3 TraesCS6A01G407400 chr5D 95.158 1301 62 1 1 1301 332802660 332803959 0.000000e+00 2052
4 TraesCS6A01G407400 chr5D 95.435 1161 53 0 1 1161 459244251 459243091 0.000000e+00 1851
5 TraesCS6A01G407400 chr2D 95.008 1302 62 2 1 1302 132690767 132689469 0.000000e+00 2041
6 TraesCS6A01G407400 chr1A 94.240 1302 74 1 1 1302 492268559 492269859 0.000000e+00 1988
7 TraesCS6A01G407400 chr3D 91.776 1301 105 1 2 1302 553376258 553374960 0.000000e+00 1808
8 TraesCS6A01G407400 chr4B 91.603 1310 105 3 1 1307 661249021 661247714 0.000000e+00 1805
9 TraesCS6A01G407400 chr1D 91.321 1302 111 1 1 1302 354513889 354515188 0.000000e+00 1777
10 TraesCS6A01G407400 chr3B 89.695 1310 133 1 1 1308 33098932 33097623 0.000000e+00 1670
11 TraesCS6A01G407400 chr2B 89.748 1307 131 2 1 1306 1653178 1651874 0.000000e+00 1668
12 TraesCS6A01G407400 chr2B 90.551 127 12 0 1324 1450 792724574 792724448 3.880000e-38 169
13 TraesCS6A01G407400 chr2B 90.000 130 12 1 1324 1453 792722227 792722099 1.400000e-37 167
14 TraesCS6A01G407400 chr2B 89.764 127 13 0 1324 1450 792723371 792723245 1.810000e-36 163
15 TraesCS6A01G407400 chr6D 90.376 426 23 10 1574 1986 466313470 466313050 5.520000e-151 544
16 TraesCS6A01G407400 chr6D 90.545 275 25 1 1992 2266 466266468 466266741 1.660000e-96 363
17 TraesCS6A01G407400 chr6D 94.253 87 5 0 1990 2076 466312917 466312831 1.420000e-27 134
18 TraesCS6A01G407400 chr6B 96.703 273 9 0 1990 2262 711343493 711343765 2.660000e-124 455
19 TraesCS6A01G407400 chr6B 95.238 273 13 0 1990 2262 711377421 711377149 1.250000e-117 433
20 TraesCS6A01G407400 chr6B 95.279 233 8 2 1574 1806 711342783 711343012 1.280000e-97 366
21 TraesCS6A01G407400 chr6B 90.171 234 13 7 1761 1986 711377785 711377554 1.710000e-76 296
22 TraesCS6A01G407400 chr6B 94.565 184 7 3 1803 1986 711343180 711343360 4.780000e-72 281
23 TraesCS6A01G407400 chr7A 94.355 124 7 0 1450 1573 558673527 558673404 8.290000e-45 191


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 TraesCS6A01G407400 chr6A 612191569 612193841 2272 True 4198.000000 4198 100.000000 1 2273 1 chr6A.!!$R1 2272
1 TraesCS6A01G407400 chr6A 612175196 612175711 515 False 305.000000 427 95.650500 1875 2262 2 chr6A.!!$F1 387
2 TraesCS6A01G407400 chr5D 332802660 332803959 1299 False 2052.000000 2052 95.158000 1 1301 1 chr5D.!!$F1 1300
3 TraesCS6A01G407400 chr5D 459243091 459244251 1160 True 1851.000000 1851 95.435000 1 1161 1 chr5D.!!$R1 1160
4 TraesCS6A01G407400 chr2D 132689469 132690767 1298 True 2041.000000 2041 95.008000 1 1302 1 chr2D.!!$R1 1301
5 TraesCS6A01G407400 chr1A 492268559 492269859 1300 False 1988.000000 1988 94.240000 1 1302 1 chr1A.!!$F1 1301
6 TraesCS6A01G407400 chr3D 553374960 553376258 1298 True 1808.000000 1808 91.776000 2 1302 1 chr3D.!!$R1 1300
7 TraesCS6A01G407400 chr4B 661247714 661249021 1307 True 1805.000000 1805 91.603000 1 1307 1 chr4B.!!$R1 1306
8 TraesCS6A01G407400 chr1D 354513889 354515188 1299 False 1777.000000 1777 91.321000 1 1302 1 chr1D.!!$F1 1301
9 TraesCS6A01G407400 chr3B 33097623 33098932 1309 True 1670.000000 1670 89.695000 1 1308 1 chr3B.!!$R1 1307
10 TraesCS6A01G407400 chr2B 1651874 1653178 1304 True 1668.000000 1668 89.748000 1 1306 1 chr2B.!!$R1 1305
11 TraesCS6A01G407400 chr6D 466312831 466313470 639 True 339.000000 544 92.314500 1574 2076 2 chr6D.!!$R1 502
12 TraesCS6A01G407400 chr6B 711342783 711343765 982 False 367.333333 455 95.515667 1574 2262 3 chr6B.!!$F1 688
13 TraesCS6A01G407400 chr6B 711377149 711377785 636 True 364.500000 433 92.704500 1761 2262 2 chr6B.!!$R1 501

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
555 556 0.60864 AGGTCAAGCTACCGGAGTTG 59.391 55.0 9.46 5.97 44.77 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1425 1431 0.253044 GTAGGAAGCCATGCCTGTGA 59.747 55.0 0.0 0.0 35.73 3.58 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
51 52 4.755411 CACAGATCGGTACAACACCTATT 58.245 43.478 0.00 0.00 46.19 1.73
68 69 6.884836 ACACCTATTAATCTTGTTTCAGACCC 59.115 38.462 0.00 0.00 0.00 4.46
72 73 7.499232 CCTATTAATCTTGTTTCAGACCCGATT 59.501 37.037 0.00 0.00 33.49 3.34
90 91 4.336153 CCGATTGATGATGTGAATTGGTCA 59.664 41.667 0.00 0.00 32.09 4.02
103 104 1.619654 TTGGTCATGGAAAGCTGGTG 58.380 50.000 0.00 0.00 0.00 4.17
123 124 5.176223 TGGTGTCGTTCGAGAAAACTTTATC 59.824 40.000 0.00 0.00 0.00 1.75
139 140 2.910360 TCCCACCGGATGCTGATG 59.090 61.111 9.46 0.00 31.13 3.07
298 299 3.392616 AGGGGCGATTACAGAATCTTCAT 59.607 43.478 0.00 0.00 39.56 2.57
468 469 1.307097 GCATGGGAGCTGATGAAGAC 58.693 55.000 0.00 0.00 0.00 3.01
532 533 4.532126 TCTGGACAGAAGCTAGAAAATGGA 59.468 41.667 0.00 0.00 33.91 3.41
555 556 0.608640 AGGTCAAGCTACCGGAGTTG 59.391 55.000 9.46 5.97 44.77 3.16
582 583 6.287589 CCTATGACTTGGTGTAGGGATATC 57.712 45.833 0.00 0.00 31.99 1.63
632 633 3.019933 TCGGGCAAAAATTGTTACTGC 57.980 42.857 0.00 0.00 0.00 4.40
671 672 3.918591 ACCTCTCGCAATAATATAACGCG 59.081 43.478 3.53 3.53 46.92 6.01
768 769 2.298163 GGAACAGACGAAGGTTCTACCA 59.702 50.000 14.09 0.00 41.95 3.25
848 849 4.098416 GTTTCAGTGCTTGAACACAGAAC 58.902 43.478 2.51 0.00 45.22 3.01
1046 1047 2.202743 GCTATGGCACTCGCGACA 60.203 61.111 3.71 1.07 39.92 4.35
1154 1157 4.819105 TGAGAAACTCCAATATGTCGGT 57.181 40.909 0.00 0.00 0.00 4.69
1177 1180 3.501828 CCACTTGTGTGCTAAACATGCTA 59.498 43.478 0.00 0.00 41.97 3.49
1210 1213 1.327690 TACCGACTGCTGGATGGACC 61.328 60.000 5.30 0.00 39.54 4.46
1214 1218 4.181010 CTGCTGGATGGACCCCCG 62.181 72.222 0.00 0.00 38.00 5.73
1215 1219 4.731853 TGCTGGATGGACCCCCGA 62.732 66.667 0.00 0.00 38.00 5.14
1236 1242 0.617413 CTGGCTTCCTCATGACCAGT 59.383 55.000 17.28 0.00 42.42 4.00
1324 1330 6.481954 AAAAAGGATCACTACACGATCAAC 57.518 37.500 0.00 0.00 40.93 3.18
1325 1331 4.801330 AAGGATCACTACACGATCAACA 57.199 40.909 0.00 0.00 40.93 3.33
1326 1332 4.111375 AGGATCACTACACGATCAACAC 57.889 45.455 0.00 0.00 40.93 3.32
1327 1333 3.509967 AGGATCACTACACGATCAACACA 59.490 43.478 0.00 0.00 40.93 3.72
1328 1334 3.612860 GGATCACTACACGATCAACACAC 59.387 47.826 0.00 0.00 40.93 3.82
1329 1335 3.719173 TCACTACACGATCAACACACA 57.281 42.857 0.00 0.00 0.00 3.72
1330 1336 3.377439 TCACTACACGATCAACACACAC 58.623 45.455 0.00 0.00 0.00 3.82
1331 1337 2.475111 CACTACACGATCAACACACACC 59.525 50.000 0.00 0.00 0.00 4.16
1332 1338 2.066262 CTACACGATCAACACACACCC 58.934 52.381 0.00 0.00 0.00 4.61
1333 1339 0.534203 ACACGATCAACACACACCCC 60.534 55.000 0.00 0.00 0.00 4.95
1334 1340 0.250295 CACGATCAACACACACCCCT 60.250 55.000 0.00 0.00 0.00 4.79
1335 1341 1.001520 CACGATCAACACACACCCCTA 59.998 52.381 0.00 0.00 0.00 3.53
1336 1342 1.001633 ACGATCAACACACACCCCTAC 59.998 52.381 0.00 0.00 0.00 3.18
1337 1343 1.001520 CGATCAACACACACCCCTACA 59.998 52.381 0.00 0.00 0.00 2.74
1338 1344 2.354704 CGATCAACACACACCCCTACAT 60.355 50.000 0.00 0.00 0.00 2.29
1339 1345 2.559698 TCAACACACACCCCTACATG 57.440 50.000 0.00 0.00 0.00 3.21
1340 1346 0.881118 CAACACACACCCCTACATGC 59.119 55.000 0.00 0.00 0.00 4.06
1341 1347 0.476338 AACACACACCCCTACATGCA 59.524 50.000 0.00 0.00 0.00 3.96
1342 1348 0.250727 ACACACACCCCTACATGCAC 60.251 55.000 0.00 0.00 0.00 4.57
1343 1349 0.960364 CACACACCCCTACATGCACC 60.960 60.000 0.00 0.00 0.00 5.01
1344 1350 1.378514 CACACCCCTACATGCACCC 60.379 63.158 0.00 0.00 0.00 4.61
1345 1351 1.850289 ACACCCCTACATGCACCCA 60.850 57.895 0.00 0.00 0.00 4.51
1346 1352 1.378514 CACCCCTACATGCACCCAC 60.379 63.158 0.00 0.00 0.00 4.61
1347 1353 2.124736 CCCCTACATGCACCCACG 60.125 66.667 0.00 0.00 0.00 4.94
1348 1354 2.824041 CCCTACATGCACCCACGC 60.824 66.667 0.00 0.00 0.00 5.34
1349 1355 2.824041 CCTACATGCACCCACGCC 60.824 66.667 0.00 0.00 0.00 5.68
1350 1356 2.046411 CTACATGCACCCACGCCA 60.046 61.111 0.00 0.00 0.00 5.69
1351 1357 2.359354 TACATGCACCCACGCCAC 60.359 61.111 0.00 0.00 0.00 5.01
1352 1358 3.910914 TACATGCACCCACGCCACC 62.911 63.158 0.00 0.00 0.00 4.61
1354 1360 4.594854 ATGCACCCACGCCACCAA 62.595 61.111 0.00 0.00 0.00 3.67
1380 1386 4.907034 CGTCCGACTCGCCCGATG 62.907 72.222 0.00 0.00 0.00 3.84
1408 1414 4.954970 CACGCCCCTGGTGCACTT 62.955 66.667 17.98 0.00 36.54 3.16
1409 1415 4.954970 ACGCCCCTGGTGCACTTG 62.955 66.667 17.98 9.60 36.54 3.16
1410 1416 4.641645 CGCCCCTGGTGCACTTGA 62.642 66.667 17.98 0.00 0.00 3.02
1411 1417 2.985847 GCCCCTGGTGCACTTGAC 60.986 66.667 17.98 0.00 0.00 3.18
1412 1418 2.669569 CCCCTGGTGCACTTGACG 60.670 66.667 17.98 0.74 0.00 4.35
1413 1419 3.357079 CCCTGGTGCACTTGACGC 61.357 66.667 17.98 0.00 0.00 5.19
1414 1420 3.716006 CCTGGTGCACTTGACGCG 61.716 66.667 17.98 3.53 0.00 6.01
1415 1421 2.661537 CTGGTGCACTTGACGCGA 60.662 61.111 15.93 0.00 0.00 5.87
1416 1422 2.202946 TGGTGCACTTGACGCGAA 60.203 55.556 15.93 0.00 0.00 4.70
1417 1423 2.248431 GGTGCACTTGACGCGAAC 59.752 61.111 15.93 7.16 0.00 3.95
1419 1425 3.995669 TGCACTTGACGCGAACGC 61.996 61.111 15.93 9.20 45.53 4.84
1420 1426 3.702555 GCACTTGACGCGAACGCT 61.703 61.111 15.93 4.47 45.53 5.07
1421 1427 2.168621 CACTTGACGCGAACGCTG 59.831 61.111 15.93 12.27 45.53 5.18
1422 1428 3.702555 ACTTGACGCGAACGCTGC 61.703 61.111 15.93 8.98 45.53 5.25
1423 1429 4.430423 CTTGACGCGAACGCTGCC 62.430 66.667 15.93 6.53 45.53 4.85
1426 1432 4.210304 GACGCGAACGCTGCCATC 62.210 66.667 15.93 0.00 45.53 3.51
1428 1434 4.505217 CGCGAACGCTGCCATCAC 62.505 66.667 16.66 0.00 39.32 3.06
1429 1435 3.422303 GCGAACGCTGCCATCACA 61.422 61.111 11.97 0.00 38.26 3.58
1430 1436 2.780643 CGAACGCTGCCATCACAG 59.219 61.111 0.00 0.00 40.80 3.66
1431 1437 2.743752 CGAACGCTGCCATCACAGG 61.744 63.158 0.00 0.00 38.16 4.00
1439 1445 4.349682 CCATCACAGGCATGGCTT 57.650 55.556 20.85 8.55 34.59 4.35
1440 1446 2.112898 CCATCACAGGCATGGCTTC 58.887 57.895 20.85 0.00 34.59 3.86
1441 1447 1.389609 CCATCACAGGCATGGCTTCC 61.390 60.000 20.85 0.00 34.59 3.46
1442 1448 0.395311 CATCACAGGCATGGCTTCCT 60.395 55.000 20.85 0.60 0.00 3.36
1443 1449 1.134007 CATCACAGGCATGGCTTCCTA 60.134 52.381 20.85 5.94 0.00 2.94
1444 1450 0.253044 TCACAGGCATGGCTTCCTAC 59.747 55.000 20.85 0.00 0.00 3.18
1445 1451 0.254178 CACAGGCATGGCTTCCTACT 59.746 55.000 20.85 0.00 0.00 2.57
1446 1452 1.486310 CACAGGCATGGCTTCCTACTA 59.514 52.381 20.85 0.00 0.00 1.82
1447 1453 2.092968 CACAGGCATGGCTTCCTACTAA 60.093 50.000 20.85 0.00 0.00 2.24
1448 1454 2.092914 ACAGGCATGGCTTCCTACTAAC 60.093 50.000 20.85 0.00 0.00 2.34
1449 1455 2.092968 CAGGCATGGCTTCCTACTAACA 60.093 50.000 20.85 0.00 0.00 2.41
1450 1456 2.576191 AGGCATGGCTTCCTACTAACAA 59.424 45.455 17.44 0.00 0.00 2.83
1451 1457 3.010138 AGGCATGGCTTCCTACTAACAAA 59.990 43.478 17.44 0.00 0.00 2.83
1452 1458 3.128764 GGCATGGCTTCCTACTAACAAAC 59.871 47.826 12.86 0.00 0.00 2.93
1453 1459 3.756434 GCATGGCTTCCTACTAACAAACA 59.244 43.478 0.00 0.00 0.00 2.83
1454 1460 4.217550 GCATGGCTTCCTACTAACAAACAA 59.782 41.667 0.00 0.00 0.00 2.83
1455 1461 5.619981 GCATGGCTTCCTACTAACAAACAAG 60.620 44.000 0.00 0.00 0.00 3.16
1456 1462 5.298989 TGGCTTCCTACTAACAAACAAGA 57.701 39.130 0.00 0.00 0.00 3.02
1457 1463 5.061179 TGGCTTCCTACTAACAAACAAGAC 58.939 41.667 0.00 0.00 0.00 3.01
1458 1464 4.454847 GGCTTCCTACTAACAAACAAGACC 59.545 45.833 0.00 0.00 0.00 3.85
1459 1465 5.061179 GCTTCCTACTAACAAACAAGACCA 58.939 41.667 0.00 0.00 0.00 4.02
1460 1466 5.179555 GCTTCCTACTAACAAACAAGACCAG 59.820 44.000 0.00 0.00 0.00 4.00
1461 1467 5.223449 TCCTACTAACAAACAAGACCAGG 57.777 43.478 0.00 0.00 0.00 4.45
1462 1468 4.041198 TCCTACTAACAAACAAGACCAGGG 59.959 45.833 0.00 0.00 0.00 4.45
1463 1469 3.945640 ACTAACAAACAAGACCAGGGT 57.054 42.857 0.00 0.00 0.00 4.34
1464 1470 4.245251 ACTAACAAACAAGACCAGGGTT 57.755 40.909 0.00 0.00 0.00 4.11
1465 1471 3.951680 ACTAACAAACAAGACCAGGGTTG 59.048 43.478 2.81 2.81 0.00 3.77
1466 1472 2.525105 ACAAACAAGACCAGGGTTGT 57.475 45.000 3.99 3.99 38.56 3.32
1467 1473 2.375146 ACAAACAAGACCAGGGTTGTC 58.625 47.619 9.38 0.00 35.83 3.18
1468 1474 2.025321 ACAAACAAGACCAGGGTTGTCT 60.025 45.455 9.38 0.00 44.75 3.41
1476 1482 5.125367 AGACCAGGGTTGTCTTTTAAACT 57.875 39.130 0.00 0.00 40.06 2.66
1477 1483 5.516044 AGACCAGGGTTGTCTTTTAAACTT 58.484 37.500 0.00 0.00 40.06 2.66
1478 1484 5.955959 AGACCAGGGTTGTCTTTTAAACTTT 59.044 36.000 0.00 0.00 40.06 2.66
1479 1485 5.972935 ACCAGGGTTGTCTTTTAAACTTTG 58.027 37.500 0.00 0.00 0.00 2.77
1480 1486 5.482526 ACCAGGGTTGTCTTTTAAACTTTGT 59.517 36.000 0.00 0.00 0.00 2.83
1481 1487 6.014070 ACCAGGGTTGTCTTTTAAACTTTGTT 60.014 34.615 0.00 0.00 0.00 2.83
1482 1488 6.312672 CCAGGGTTGTCTTTTAAACTTTGTTG 59.687 38.462 0.00 0.00 0.00 3.33
1483 1489 5.872617 AGGGTTGTCTTTTAAACTTTGTTGC 59.127 36.000 0.00 0.00 0.00 4.17
1484 1490 5.639931 GGGTTGTCTTTTAAACTTTGTTGCA 59.360 36.000 0.00 0.00 0.00 4.08
1485 1491 6.147985 GGGTTGTCTTTTAAACTTTGTTGCAA 59.852 34.615 0.00 0.00 0.00 4.08
1486 1492 7.233689 GGTTGTCTTTTAAACTTTGTTGCAAG 58.766 34.615 0.00 0.00 0.00 4.01
1487 1493 7.095397 GGTTGTCTTTTAAACTTTGTTGCAAGT 60.095 33.333 0.00 0.00 0.00 3.16
1488 1494 7.954788 TGTCTTTTAAACTTTGTTGCAAGTT 57.045 28.000 0.00 0.00 40.63 2.66
1489 1495 7.791949 TGTCTTTTAAACTTTGTTGCAAGTTG 58.208 30.769 0.00 0.00 39.03 3.16
1490 1496 7.653713 TGTCTTTTAAACTTTGTTGCAAGTTGA 59.346 29.630 7.16 0.00 39.03 3.18
1491 1497 8.162245 GTCTTTTAAACTTTGTTGCAAGTTGAG 58.838 33.333 7.16 0.00 39.03 3.02
1492 1498 6.959671 TTTAAACTTTGTTGCAAGTTGAGG 57.040 33.333 7.16 0.00 39.03 3.86
1493 1499 3.525268 AACTTTGTTGCAAGTTGAGGG 57.475 42.857 7.16 0.00 37.79 4.30
1494 1500 2.456577 ACTTTGTTGCAAGTTGAGGGT 58.543 42.857 7.16 0.00 0.00 4.34
1495 1501 2.166254 ACTTTGTTGCAAGTTGAGGGTG 59.834 45.455 7.16 0.00 0.00 4.61
1496 1502 0.459489 TTGTTGCAAGTTGAGGGTGC 59.541 50.000 7.16 0.00 38.78 5.01
1497 1503 0.682532 TGTTGCAAGTTGAGGGTGCA 60.683 50.000 7.16 0.00 46.11 4.57
1498 1504 4.674306 TGCAAGTTGAGGGTGCAA 57.326 50.000 7.16 0.00 44.88 4.08
1499 1505 3.130264 TGCAAGTTGAGGGTGCAAT 57.870 47.368 7.16 0.00 44.88 3.56
1500 1506 2.284754 TGCAAGTTGAGGGTGCAATA 57.715 45.000 7.16 0.00 44.88 1.90
1501 1507 1.885887 TGCAAGTTGAGGGTGCAATAC 59.114 47.619 7.16 0.00 44.88 1.89
1502 1508 1.135689 GCAAGTTGAGGGTGCAATACG 60.136 52.381 7.16 0.00 38.19 3.06
1503 1509 2.151202 CAAGTTGAGGGTGCAATACGT 58.849 47.619 0.00 0.00 0.00 3.57
1504 1510 2.094762 AGTTGAGGGTGCAATACGTC 57.905 50.000 0.00 0.00 0.00 4.34
1505 1511 1.084289 GTTGAGGGTGCAATACGTCC 58.916 55.000 0.00 0.00 0.00 4.79
1506 1512 0.390603 TTGAGGGTGCAATACGTCCG 60.391 55.000 0.00 0.00 0.00 4.79
1507 1513 1.520787 GAGGGTGCAATACGTCCGG 60.521 63.158 0.00 0.00 0.00 5.14
1508 1514 2.234913 GAGGGTGCAATACGTCCGGT 62.235 60.000 0.00 0.00 0.00 5.28
1509 1515 1.376295 GGGTGCAATACGTCCGGTT 60.376 57.895 0.00 0.00 0.00 4.44
1510 1516 0.956902 GGGTGCAATACGTCCGGTTT 60.957 55.000 0.00 0.00 0.00 3.27
1511 1517 0.445043 GGTGCAATACGTCCGGTTTC 59.555 55.000 0.00 0.00 0.00 2.78
1512 1518 1.149987 GTGCAATACGTCCGGTTTCA 58.850 50.000 0.00 0.00 0.00 2.69
1513 1519 1.532007 GTGCAATACGTCCGGTTTCAA 59.468 47.619 0.00 0.00 0.00 2.69
1514 1520 2.031857 GTGCAATACGTCCGGTTTCAAA 60.032 45.455 0.00 0.00 0.00 2.69
1515 1521 2.224549 TGCAATACGTCCGGTTTCAAAG 59.775 45.455 0.00 0.00 0.00 2.77
1516 1522 2.481185 GCAATACGTCCGGTTTCAAAGA 59.519 45.455 0.00 0.00 0.00 2.52
1517 1523 3.126343 GCAATACGTCCGGTTTCAAAGAT 59.874 43.478 0.00 0.00 0.00 2.40
1518 1524 4.647964 CAATACGTCCGGTTTCAAAGATG 58.352 43.478 0.00 0.00 0.00 2.90
1519 1525 2.536761 ACGTCCGGTTTCAAAGATGA 57.463 45.000 0.00 0.00 0.00 2.92
1520 1526 2.413837 ACGTCCGGTTTCAAAGATGAG 58.586 47.619 0.00 0.00 36.78 2.90
1521 1527 2.036733 ACGTCCGGTTTCAAAGATGAGA 59.963 45.455 0.00 0.00 36.78 3.27
1522 1528 2.668457 CGTCCGGTTTCAAAGATGAGAG 59.332 50.000 0.00 0.00 36.78 3.20
1523 1529 3.665190 GTCCGGTTTCAAAGATGAGAGT 58.335 45.455 0.00 0.00 36.78 3.24
1524 1530 4.065789 GTCCGGTTTCAAAGATGAGAGTT 58.934 43.478 0.00 0.00 36.78 3.01
1525 1531 5.235516 GTCCGGTTTCAAAGATGAGAGTTA 58.764 41.667 0.00 0.00 36.78 2.24
1526 1532 5.875359 GTCCGGTTTCAAAGATGAGAGTTAT 59.125 40.000 0.00 0.00 36.78 1.89
1527 1533 7.039882 GTCCGGTTTCAAAGATGAGAGTTATA 58.960 38.462 0.00 0.00 36.78 0.98
1528 1534 7.548075 GTCCGGTTTCAAAGATGAGAGTTATAA 59.452 37.037 0.00 0.00 36.78 0.98
1529 1535 8.098286 TCCGGTTTCAAAGATGAGAGTTATAAA 58.902 33.333 0.00 0.00 36.78 1.40
1530 1536 8.893727 CCGGTTTCAAAGATGAGAGTTATAAAT 58.106 33.333 0.00 0.00 36.78 1.40
1531 1537 9.922305 CGGTTTCAAAGATGAGAGTTATAAATC 57.078 33.333 4.76 4.76 36.78 2.17
1537 1543 9.708222 CAAAGATGAGAGTTATAAATCAAACCG 57.292 33.333 14.80 0.00 0.00 4.44
1538 1544 9.667107 AAAGATGAGAGTTATAAATCAAACCGA 57.333 29.630 14.80 0.00 0.00 4.69
1539 1545 8.879342 AGATGAGAGTTATAAATCAAACCGAG 57.121 34.615 14.80 0.00 0.00 4.63
1540 1546 6.903883 TGAGAGTTATAAATCAAACCGAGC 57.096 37.500 14.80 0.00 0.00 5.03
1541 1547 5.518847 TGAGAGTTATAAATCAAACCGAGCG 59.481 40.000 14.80 0.00 0.00 5.03
1542 1548 4.809426 AGAGTTATAAATCAAACCGAGCGG 59.191 41.667 14.80 7.48 42.03 5.52
1554 1560 2.976356 GAGCGGTTAGTTCGGGGT 59.024 61.111 0.00 0.00 0.00 4.95
1555 1561 1.294459 GAGCGGTTAGTTCGGGGTT 59.706 57.895 0.00 0.00 0.00 4.11
1556 1562 1.004200 AGCGGTTAGTTCGGGGTTG 60.004 57.895 0.00 0.00 0.00 3.77
1557 1563 1.004679 GCGGTTAGTTCGGGGTTGA 60.005 57.895 0.00 0.00 0.00 3.18
1558 1564 0.603439 GCGGTTAGTTCGGGGTTGAA 60.603 55.000 0.00 0.00 0.00 2.69
1559 1565 1.881591 CGGTTAGTTCGGGGTTGAAA 58.118 50.000 0.00 0.00 0.00 2.69
1560 1566 2.220313 CGGTTAGTTCGGGGTTGAAAA 58.780 47.619 0.00 0.00 0.00 2.29
1561 1567 2.617774 CGGTTAGTTCGGGGTTGAAAAA 59.382 45.455 0.00 0.00 0.00 1.94
1562 1568 3.253921 CGGTTAGTTCGGGGTTGAAAAAT 59.746 43.478 0.00 0.00 0.00 1.82
1563 1569 4.552355 GGTTAGTTCGGGGTTGAAAAATG 58.448 43.478 0.00 0.00 0.00 2.32
1564 1570 4.552355 GTTAGTTCGGGGTTGAAAAATGG 58.448 43.478 0.00 0.00 0.00 3.16
1565 1571 2.952116 AGTTCGGGGTTGAAAAATGGA 58.048 42.857 0.00 0.00 0.00 3.41
1566 1572 2.626266 AGTTCGGGGTTGAAAAATGGAC 59.374 45.455 0.00 0.00 0.00 4.02
1567 1573 2.626266 GTTCGGGGTTGAAAAATGGACT 59.374 45.455 0.00 0.00 0.00 3.85
1568 1574 2.952116 TCGGGGTTGAAAAATGGACTT 58.048 42.857 0.00 0.00 0.00 3.01
1569 1575 3.301274 TCGGGGTTGAAAAATGGACTTT 58.699 40.909 0.00 0.00 0.00 2.66
1570 1576 3.707102 TCGGGGTTGAAAAATGGACTTTT 59.293 39.130 0.00 0.00 38.73 2.27
1571 1577 4.055360 CGGGGTTGAAAAATGGACTTTTC 58.945 43.478 2.57 2.57 42.93 2.29
1572 1578 4.202212 CGGGGTTGAAAAATGGACTTTTCT 60.202 41.667 9.49 0.00 43.01 2.52
1597 1603 2.404215 CAGCTATAACCGATGGTTCCG 58.596 52.381 4.16 0.00 43.05 4.30
1698 1704 5.810587 TGCAGATACAAAGTAGGAATCGTTC 59.189 40.000 0.00 0.00 0.00 3.95
1783 1793 7.768120 TGTTGTTGGAAATCAGCAAAAATTACT 59.232 29.630 0.00 0.00 45.67 2.24
1784 1794 9.255304 GTTGTTGGAAATCAGCAAAAATTACTA 57.745 29.630 0.00 0.00 45.67 1.82
1785 1795 8.810652 TGTTGGAAATCAGCAAAAATTACTAC 57.189 30.769 0.00 0.00 33.63 2.73
1828 2020 7.728532 TGTATAAACATAGCATCCAGGAGACTA 59.271 37.037 0.00 0.00 40.21 2.59
1838 2030 6.556495 AGCATCCAGGAGACTATAAGAAATCA 59.444 38.462 0.00 0.00 40.21 2.57
1844 2036 7.713073 CCAGGAGACTATAAGAAATCAAACTCC 59.287 40.741 0.00 0.00 40.21 3.85
1904 2096 2.238646 TCAATTGGACCGGCTCAGTAAT 59.761 45.455 0.00 0.00 0.00 1.89
1986 2178 1.513158 CAGAATCCTCGCCAGACGT 59.487 57.895 0.00 0.00 44.19 4.34
1987 2179 0.738975 CAGAATCCTCGCCAGACGTA 59.261 55.000 0.00 0.00 44.19 3.57
1988 2180 1.338337 CAGAATCCTCGCCAGACGTAT 59.662 52.381 0.00 0.00 44.19 3.06
2041 2362 2.441750 ACCATTAACCTCCTGTGTGTGT 59.558 45.455 0.00 0.00 0.00 3.72
2048 2369 2.224378 ACCTCCTGTGTGTGTGATTCTG 60.224 50.000 0.00 0.00 0.00 3.02
2093 2414 1.181098 GGCCAGACTGTTGCCAACAT 61.181 55.000 11.26 1.51 44.70 2.71
2128 2449 0.252197 GGTTGGGTCAGCGGAGTTAT 59.748 55.000 0.00 0.00 0.00 1.89
2184 2505 7.040548 TGCACAAATGATGATGTTCTCACTTAA 60.041 33.333 0.00 0.00 36.48 1.85
2262 2583 4.083271 GCACGACTCCAGCTAGAAAATTTT 60.083 41.667 2.28 2.28 0.00 1.82
2263 2584 5.622378 CACGACTCCAGCTAGAAAATTTTC 58.378 41.667 21.00 21.00 37.45 2.29
2264 2585 5.179368 CACGACTCCAGCTAGAAAATTTTCA 59.821 40.000 28.00 15.37 39.61 2.69
2265 2586 5.409826 ACGACTCCAGCTAGAAAATTTTCAG 59.590 40.000 28.00 22.54 39.61 3.02
2266 2587 5.635417 ACTCCAGCTAGAAAATTTTCAGC 57.365 39.130 28.82 28.82 39.61 4.26
2267 2588 5.072741 ACTCCAGCTAGAAAATTTTCAGCA 58.927 37.500 32.77 22.04 40.50 4.41
2268 2589 5.713861 ACTCCAGCTAGAAAATTTTCAGCAT 59.286 36.000 32.77 23.43 40.50 3.79
2269 2590 6.886459 ACTCCAGCTAGAAAATTTTCAGCATA 59.114 34.615 32.77 23.73 40.50 3.14
2270 2591 7.559170 ACTCCAGCTAGAAAATTTTCAGCATAT 59.441 33.333 32.77 21.44 40.50 1.78
2271 2592 7.709947 TCCAGCTAGAAAATTTTCAGCATATG 58.290 34.615 32.77 26.61 40.50 1.78
2272 2593 6.420008 CCAGCTAGAAAATTTTCAGCATATGC 59.580 38.462 32.77 20.36 40.50 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.224185 TGTTGTACCGATCTGTGCAGTT 60.224 45.455 7.98 0.00 32.39 3.16
51 52 5.800296 TCAATCGGGTCTGAAACAAGATTA 58.200 37.500 0.00 0.00 35.28 1.75
68 69 5.488645 TGACCAATTCACATCATCAATCG 57.511 39.130 0.00 0.00 0.00 3.34
72 73 4.857679 TCCATGACCAATTCACATCATCA 58.142 39.130 0.00 0.00 36.92 3.07
90 91 1.523758 GAACGACACCAGCTTTCCAT 58.476 50.000 0.00 0.00 0.00 3.41
103 104 4.687483 TGGGATAAAGTTTTCTCGAACGAC 59.313 41.667 0.00 0.00 34.74 4.34
123 124 2.043604 TAGCATCAGCATCCGGTGGG 62.044 60.000 0.00 0.00 45.49 4.61
139 140 7.212976 TGTCTGAGTGGAATATTCAAGATAGC 58.787 38.462 17.07 0.00 0.00 2.97
298 299 6.978659 CGAGTCCATAACTGCTTGTTATTCTA 59.021 38.462 11.21 1.32 46.40 2.10
306 307 3.238108 AGACGAGTCCATAACTGCTTG 57.762 47.619 0.00 0.00 38.74 4.01
468 469 4.562789 CACTTGATCAAAGCATGCATCAAG 59.437 41.667 34.51 34.51 46.05 3.02
532 533 1.221840 CCGGTAGCTTGACCTGCAT 59.778 57.895 4.18 0.00 37.34 3.96
582 583 1.470890 GAGAACCGAGAGTCACAGAGG 59.529 57.143 0.00 0.00 0.00 3.69
632 633 1.063717 AGGTCCAAATAGCCCACATGG 60.064 52.381 0.00 0.00 37.09 3.66
671 672 3.003480 GGGTTCATACTTGCTCTGTCAC 58.997 50.000 0.00 0.00 0.00 3.67
729 730 1.133513 TCCAAAGGAAGCTCCAGCAAA 60.134 47.619 0.48 0.00 45.16 3.68
848 849 3.028921 GCCACTCCTCCAGCTCCAG 62.029 68.421 0.00 0.00 0.00 3.86
1046 1047 2.717530 CTACGATAGAGCGCGAAAACT 58.282 47.619 12.10 5.09 41.38 2.66
1154 1157 2.293122 GCATGTTTAGCACACAAGTGGA 59.707 45.455 5.08 0.00 45.98 4.02
1177 1180 0.912487 TCGGTAATCCCCAAGGTGCT 60.912 55.000 0.00 0.00 0.00 4.40
1210 1213 3.787001 GAGGAAGCCAGGTCGGGG 61.787 72.222 0.00 0.00 34.06 5.73
1214 1218 0.107459 GGTCATGAGGAAGCCAGGTC 60.107 60.000 0.00 0.00 0.00 3.85
1215 1219 0.842030 TGGTCATGAGGAAGCCAGGT 60.842 55.000 0.00 0.00 0.00 4.00
1236 1242 1.573932 CGCACGATCAGCCAAAACA 59.426 52.632 0.00 0.00 0.00 2.83
1308 1314 3.987868 GTGTGTGTTGATCGTGTAGTGAT 59.012 43.478 0.00 0.00 0.00 3.06
1309 1315 3.377439 GTGTGTGTTGATCGTGTAGTGA 58.623 45.455 0.00 0.00 0.00 3.41
1310 1316 2.475111 GGTGTGTGTTGATCGTGTAGTG 59.525 50.000 0.00 0.00 0.00 2.74
1311 1317 2.547218 GGGTGTGTGTTGATCGTGTAGT 60.547 50.000 0.00 0.00 0.00 2.73
1312 1318 2.066262 GGGTGTGTGTTGATCGTGTAG 58.934 52.381 0.00 0.00 0.00 2.74
1313 1319 1.270412 GGGGTGTGTGTTGATCGTGTA 60.270 52.381 0.00 0.00 0.00 2.90
1314 1320 0.534203 GGGGTGTGTGTTGATCGTGT 60.534 55.000 0.00 0.00 0.00 4.49
1315 1321 0.250295 AGGGGTGTGTGTTGATCGTG 60.250 55.000 0.00 0.00 0.00 4.35
1316 1322 1.001633 GTAGGGGTGTGTGTTGATCGT 59.998 52.381 0.00 0.00 0.00 3.73
1317 1323 1.001520 TGTAGGGGTGTGTGTTGATCG 59.998 52.381 0.00 0.00 0.00 3.69
1318 1324 2.851263 TGTAGGGGTGTGTGTTGATC 57.149 50.000 0.00 0.00 0.00 2.92
1319 1325 2.879756 GCATGTAGGGGTGTGTGTTGAT 60.880 50.000 0.00 0.00 0.00 2.57
1320 1326 1.544537 GCATGTAGGGGTGTGTGTTGA 60.545 52.381 0.00 0.00 0.00 3.18
1321 1327 0.881118 GCATGTAGGGGTGTGTGTTG 59.119 55.000 0.00 0.00 0.00 3.33
1322 1328 0.476338 TGCATGTAGGGGTGTGTGTT 59.524 50.000 0.00 0.00 0.00 3.32
1323 1329 0.250727 GTGCATGTAGGGGTGTGTGT 60.251 55.000 0.00 0.00 0.00 3.72
1324 1330 0.960364 GGTGCATGTAGGGGTGTGTG 60.960 60.000 0.00 0.00 0.00 3.82
1325 1331 1.378762 GGTGCATGTAGGGGTGTGT 59.621 57.895 0.00 0.00 0.00 3.72
1326 1332 1.378514 GGGTGCATGTAGGGGTGTG 60.379 63.158 0.00 0.00 0.00 3.82
1327 1333 1.850289 TGGGTGCATGTAGGGGTGT 60.850 57.895 0.00 0.00 0.00 4.16
1328 1334 1.378514 GTGGGTGCATGTAGGGGTG 60.379 63.158 0.00 0.00 0.00 4.61
1329 1335 2.966732 CGTGGGTGCATGTAGGGGT 61.967 63.158 0.00 0.00 0.00 4.95
1330 1336 2.124736 CGTGGGTGCATGTAGGGG 60.125 66.667 0.00 0.00 0.00 4.79
1331 1337 2.824041 GCGTGGGTGCATGTAGGG 60.824 66.667 0.00 0.00 34.15 3.53
1332 1338 2.824041 GGCGTGGGTGCATGTAGG 60.824 66.667 0.00 0.00 36.28 3.18
1333 1339 2.046411 TGGCGTGGGTGCATGTAG 60.046 61.111 0.00 0.00 36.28 2.74
1334 1340 2.359354 GTGGCGTGGGTGCATGTA 60.359 61.111 0.00 0.00 36.28 2.29
1337 1343 4.594854 TTGGTGGCGTGGGTGCAT 62.595 61.111 0.00 0.00 36.28 3.96
1363 1369 4.907034 CATCGGGCGAGTCGGACG 62.907 72.222 15.52 4.29 0.00 4.79
1391 1397 4.954970 AAGTGCACCAGGGGCGTG 62.955 66.667 14.63 0.00 0.00 5.34
1392 1398 4.954970 CAAGTGCACCAGGGGCGT 62.955 66.667 14.63 0.00 0.00 5.68
1393 1399 4.641645 TCAAGTGCACCAGGGGCG 62.642 66.667 14.63 0.00 0.00 6.13
1394 1400 2.985847 GTCAAGTGCACCAGGGGC 60.986 66.667 14.63 6.79 0.00 5.80
1395 1401 2.669569 CGTCAAGTGCACCAGGGG 60.670 66.667 14.63 0.00 0.00 4.79
1396 1402 3.357079 GCGTCAAGTGCACCAGGG 61.357 66.667 14.63 0.36 0.00 4.45
1397 1403 3.716006 CGCGTCAAGTGCACCAGG 61.716 66.667 14.63 3.19 0.00 4.45
1398 1404 2.243957 TTCGCGTCAAGTGCACCAG 61.244 57.895 14.63 6.50 0.00 4.00
1399 1405 2.202946 TTCGCGTCAAGTGCACCA 60.203 55.556 14.63 0.00 0.00 4.17
1400 1406 2.248431 GTTCGCGTCAAGTGCACC 59.752 61.111 14.63 0.00 0.00 5.01
1401 1407 2.128128 CGTTCGCGTCAAGTGCAC 60.128 61.111 9.40 9.40 35.57 4.57
1402 1408 3.995669 GCGTTCGCGTCAAGTGCA 61.996 61.111 5.77 0.00 43.62 4.57
1403 1409 3.702555 AGCGTTCGCGTCAAGTGC 61.703 61.111 5.77 3.14 43.62 4.40
1404 1410 2.168621 CAGCGTTCGCGTCAAGTG 59.831 61.111 5.77 0.00 43.62 3.16
1405 1411 3.702555 GCAGCGTTCGCGTCAAGT 61.703 61.111 5.77 0.00 43.62 3.16
1406 1412 4.430423 GGCAGCGTTCGCGTCAAG 62.430 66.667 5.77 0.00 43.62 3.02
1409 1415 4.210304 GATGGCAGCGTTCGCGTC 62.210 66.667 5.77 8.72 43.62 5.19
1411 1417 4.505217 GTGATGGCAGCGTTCGCG 62.505 66.667 11.40 0.00 44.73 5.87
1412 1418 3.372676 CTGTGATGGCAGCGTTCGC 62.373 63.158 9.24 9.24 0.00 4.70
1413 1419 2.743752 CCTGTGATGGCAGCGTTCG 61.744 63.158 0.00 0.00 35.28 3.95
1414 1420 3.181367 CCTGTGATGGCAGCGTTC 58.819 61.111 0.00 0.00 35.28 3.95
1422 1428 1.389609 GGAAGCCATGCCTGTGATGG 61.390 60.000 0.00 0.00 43.01 3.51
1423 1429 0.395311 AGGAAGCCATGCCTGTGATG 60.395 55.000 0.00 0.00 32.06 3.07
1424 1430 1.133976 GTAGGAAGCCATGCCTGTGAT 60.134 52.381 0.00 0.00 35.73 3.06
1425 1431 0.253044 GTAGGAAGCCATGCCTGTGA 59.747 55.000 0.00 0.00 35.73 3.58
1426 1432 0.254178 AGTAGGAAGCCATGCCTGTG 59.746 55.000 0.00 0.00 35.73 3.66
1427 1433 1.879575 TAGTAGGAAGCCATGCCTGT 58.120 50.000 0.00 0.00 35.73 4.00
1428 1434 2.092968 TGTTAGTAGGAAGCCATGCCTG 60.093 50.000 0.00 0.00 35.73 4.85
1429 1435 2.196595 TGTTAGTAGGAAGCCATGCCT 58.803 47.619 0.00 0.00 38.31 4.75
1430 1436 2.710096 TGTTAGTAGGAAGCCATGCC 57.290 50.000 0.00 0.00 0.00 4.40
1431 1437 3.756434 TGTTTGTTAGTAGGAAGCCATGC 59.244 43.478 0.00 0.00 0.00 4.06
1432 1438 5.705441 TCTTGTTTGTTAGTAGGAAGCCATG 59.295 40.000 0.00 0.00 0.00 3.66
1433 1439 5.705905 GTCTTGTTTGTTAGTAGGAAGCCAT 59.294 40.000 0.00 0.00 0.00 4.40
1434 1440 5.061179 GTCTTGTTTGTTAGTAGGAAGCCA 58.939 41.667 0.00 0.00 0.00 4.75
1435 1441 4.454847 GGTCTTGTTTGTTAGTAGGAAGCC 59.545 45.833 0.00 0.00 0.00 4.35
1436 1442 5.061179 TGGTCTTGTTTGTTAGTAGGAAGC 58.939 41.667 0.00 0.00 0.00 3.86
1437 1443 5.701290 CCTGGTCTTGTTTGTTAGTAGGAAG 59.299 44.000 0.00 0.00 0.00 3.46
1438 1444 5.455612 CCCTGGTCTTGTTTGTTAGTAGGAA 60.456 44.000 0.00 0.00 0.00 3.36
1439 1445 4.041198 CCCTGGTCTTGTTTGTTAGTAGGA 59.959 45.833 0.00 0.00 0.00 2.94
1440 1446 4.202430 ACCCTGGTCTTGTTTGTTAGTAGG 60.202 45.833 0.00 0.00 0.00 3.18
1441 1447 4.969484 ACCCTGGTCTTGTTTGTTAGTAG 58.031 43.478 0.00 0.00 0.00 2.57
1442 1448 5.127491 CAACCCTGGTCTTGTTTGTTAGTA 58.873 41.667 0.00 0.00 0.00 1.82
1443 1449 3.945640 ACCCTGGTCTTGTTTGTTAGT 57.054 42.857 0.00 0.00 0.00 2.24
1444 1450 3.951680 ACAACCCTGGTCTTGTTTGTTAG 59.048 43.478 2.03 0.00 0.00 2.34
1445 1451 3.949113 GACAACCCTGGTCTTGTTTGTTA 59.051 43.478 8.05 0.00 32.54 2.41
1446 1452 2.758423 GACAACCCTGGTCTTGTTTGTT 59.242 45.455 8.05 0.00 32.54 2.83
1447 1453 2.025321 AGACAACCCTGGTCTTGTTTGT 60.025 45.455 8.05 0.00 42.77 2.83
1448 1454 2.654863 AGACAACCCTGGTCTTGTTTG 58.345 47.619 8.05 0.00 42.77 2.93
1455 1461 5.847111 AAGTTTAAAAGACAACCCTGGTC 57.153 39.130 0.00 0.00 35.50 4.02
1456 1462 5.482526 ACAAAGTTTAAAAGACAACCCTGGT 59.517 36.000 0.00 0.00 0.00 4.00
1457 1463 5.972935 ACAAAGTTTAAAAGACAACCCTGG 58.027 37.500 0.00 0.00 0.00 4.45
1458 1464 6.183360 GCAACAAAGTTTAAAAGACAACCCTG 60.183 38.462 0.00 0.00 0.00 4.45
1459 1465 5.872617 GCAACAAAGTTTAAAAGACAACCCT 59.127 36.000 0.00 0.00 0.00 4.34
1460 1466 5.639931 TGCAACAAAGTTTAAAAGACAACCC 59.360 36.000 0.00 0.00 0.00 4.11
1461 1467 6.713792 TGCAACAAAGTTTAAAAGACAACC 57.286 33.333 0.00 0.00 0.00 3.77
1462 1468 7.792925 ACTTGCAACAAAGTTTAAAAGACAAC 58.207 30.769 0.00 0.00 37.05 3.32
1463 1469 7.954788 ACTTGCAACAAAGTTTAAAAGACAA 57.045 28.000 0.00 0.00 37.05 3.18
1464 1470 7.653713 TCAACTTGCAACAAAGTTTAAAAGACA 59.346 29.630 0.00 0.00 45.84 3.41
1465 1471 8.013236 TCAACTTGCAACAAAGTTTAAAAGAC 57.987 30.769 0.00 0.00 45.84 3.01
1466 1472 7.330700 CCTCAACTTGCAACAAAGTTTAAAAGA 59.669 33.333 0.00 0.00 45.84 2.52
1467 1473 7.412891 CCCTCAACTTGCAACAAAGTTTAAAAG 60.413 37.037 0.00 0.00 45.84 2.27
1468 1474 6.370166 CCCTCAACTTGCAACAAAGTTTAAAA 59.630 34.615 0.00 0.00 45.84 1.52
1469 1475 5.872070 CCCTCAACTTGCAACAAAGTTTAAA 59.128 36.000 0.00 0.00 45.84 1.52
1470 1476 5.046950 ACCCTCAACTTGCAACAAAGTTTAA 60.047 36.000 0.00 0.00 45.84 1.52
1471 1477 4.464597 ACCCTCAACTTGCAACAAAGTTTA 59.535 37.500 0.00 0.00 45.84 2.01
1472 1478 3.260632 ACCCTCAACTTGCAACAAAGTTT 59.739 39.130 0.00 0.00 45.84 2.66
1474 1480 2.166254 CACCCTCAACTTGCAACAAAGT 59.834 45.455 0.00 0.00 42.21 2.66
1475 1481 2.813061 CACCCTCAACTTGCAACAAAG 58.187 47.619 0.00 0.00 0.00 2.77
1476 1482 1.134848 GCACCCTCAACTTGCAACAAA 60.135 47.619 0.00 0.00 36.22 2.83
1477 1483 0.459489 GCACCCTCAACTTGCAACAA 59.541 50.000 0.00 0.00 36.22 2.83
1478 1484 0.682532 TGCACCCTCAACTTGCAACA 60.683 50.000 0.00 0.00 43.16 3.33
1479 1485 2.114638 TGCACCCTCAACTTGCAAC 58.885 52.632 0.00 0.00 43.16 4.17
1480 1486 4.674306 TGCACCCTCAACTTGCAA 57.326 50.000 0.00 0.00 43.16 4.08
1481 1487 1.885887 GTATTGCACCCTCAACTTGCA 59.114 47.619 0.00 0.00 44.40 4.08
1482 1488 1.135689 CGTATTGCACCCTCAACTTGC 60.136 52.381 0.00 0.00 36.76 4.01
1483 1489 2.151202 ACGTATTGCACCCTCAACTTG 58.849 47.619 0.00 0.00 0.00 3.16
1484 1490 2.423577 GACGTATTGCACCCTCAACTT 58.576 47.619 0.00 0.00 0.00 2.66
1485 1491 1.338769 GGACGTATTGCACCCTCAACT 60.339 52.381 0.00 0.00 0.00 3.16
1486 1492 1.084289 GGACGTATTGCACCCTCAAC 58.916 55.000 0.00 0.00 0.00 3.18
1487 1493 0.390603 CGGACGTATTGCACCCTCAA 60.391 55.000 0.00 0.00 0.00 3.02
1488 1494 1.216977 CGGACGTATTGCACCCTCA 59.783 57.895 0.00 0.00 0.00 3.86
1489 1495 1.520787 CCGGACGTATTGCACCCTC 60.521 63.158 0.00 0.00 0.00 4.30
1490 1496 1.833787 AACCGGACGTATTGCACCCT 61.834 55.000 9.46 0.00 0.00 4.34
1491 1497 0.956902 AAACCGGACGTATTGCACCC 60.957 55.000 9.46 0.00 0.00 4.61
1492 1498 0.445043 GAAACCGGACGTATTGCACC 59.555 55.000 9.46 0.00 0.00 5.01
1493 1499 1.149987 TGAAACCGGACGTATTGCAC 58.850 50.000 9.46 0.00 0.00 4.57
1494 1500 1.880271 TTGAAACCGGACGTATTGCA 58.120 45.000 9.46 0.00 0.00 4.08
1495 1501 2.481185 TCTTTGAAACCGGACGTATTGC 59.519 45.455 9.46 0.00 0.00 3.56
1496 1502 4.390603 TCATCTTTGAAACCGGACGTATTG 59.609 41.667 9.46 0.00 0.00 1.90
1497 1503 4.571919 TCATCTTTGAAACCGGACGTATT 58.428 39.130 9.46 0.00 0.00 1.89
1498 1504 4.081862 TCTCATCTTTGAAACCGGACGTAT 60.082 41.667 9.46 0.00 0.00 3.06
1499 1505 3.256383 TCTCATCTTTGAAACCGGACGTA 59.744 43.478 9.46 0.00 0.00 3.57
1500 1506 2.036733 TCTCATCTTTGAAACCGGACGT 59.963 45.455 9.46 0.00 0.00 4.34
1501 1507 2.668457 CTCTCATCTTTGAAACCGGACG 59.332 50.000 9.46 0.00 0.00 4.79
1502 1508 3.665190 ACTCTCATCTTTGAAACCGGAC 58.335 45.455 9.46 0.00 0.00 4.79
1503 1509 4.351874 AACTCTCATCTTTGAAACCGGA 57.648 40.909 9.46 0.00 0.00 5.14
1504 1510 7.843490 TTATAACTCTCATCTTTGAAACCGG 57.157 36.000 0.00 0.00 0.00 5.28
1505 1511 9.922305 GATTTATAACTCTCATCTTTGAAACCG 57.078 33.333 0.00 0.00 0.00 4.44
1511 1517 9.708222 CGGTTTGATTTATAACTCTCATCTTTG 57.292 33.333 4.66 0.00 0.00 2.77
1512 1518 9.667107 TCGGTTTGATTTATAACTCTCATCTTT 57.333 29.630 4.66 0.00 0.00 2.52
1513 1519 9.319143 CTCGGTTTGATTTATAACTCTCATCTT 57.681 33.333 4.66 0.00 0.00 2.40
1514 1520 7.439655 GCTCGGTTTGATTTATAACTCTCATCT 59.560 37.037 4.66 0.00 0.00 2.90
1515 1521 7.567771 CGCTCGGTTTGATTTATAACTCTCATC 60.568 40.741 4.66 0.00 0.00 2.92
1516 1522 6.201044 CGCTCGGTTTGATTTATAACTCTCAT 59.799 38.462 4.66 0.00 0.00 2.90
1517 1523 5.518847 CGCTCGGTTTGATTTATAACTCTCA 59.481 40.000 4.66 0.00 0.00 3.27
1518 1524 5.050972 CCGCTCGGTTTGATTTATAACTCTC 60.051 44.000 0.00 0.00 0.00 3.20
1519 1525 4.809426 CCGCTCGGTTTGATTTATAACTCT 59.191 41.667 0.00 0.00 0.00 3.24
1520 1526 5.079397 CCGCTCGGTTTGATTTATAACTC 57.921 43.478 0.00 0.00 0.00 3.01
1536 1542 2.202703 CCCCGAACTAACCGCTCG 60.203 66.667 0.00 0.00 0.00 5.03
1537 1543 1.017701 CAACCCCGAACTAACCGCTC 61.018 60.000 0.00 0.00 0.00 5.03
1538 1544 1.004200 CAACCCCGAACTAACCGCT 60.004 57.895 0.00 0.00 0.00 5.52
1539 1545 0.603439 TTCAACCCCGAACTAACCGC 60.603 55.000 0.00 0.00 0.00 5.68
1540 1546 1.881591 TTTCAACCCCGAACTAACCG 58.118 50.000 0.00 0.00 0.00 4.44
1541 1547 4.552355 CATTTTTCAACCCCGAACTAACC 58.448 43.478 0.00 0.00 0.00 2.85
1542 1548 4.278919 TCCATTTTTCAACCCCGAACTAAC 59.721 41.667 0.00 0.00 0.00 2.34
1543 1549 4.278919 GTCCATTTTTCAACCCCGAACTAA 59.721 41.667 0.00 0.00 0.00 2.24
1544 1550 3.822167 GTCCATTTTTCAACCCCGAACTA 59.178 43.478 0.00 0.00 0.00 2.24
1545 1551 2.626266 GTCCATTTTTCAACCCCGAACT 59.374 45.455 0.00 0.00 0.00 3.01
1546 1552 2.626266 AGTCCATTTTTCAACCCCGAAC 59.374 45.455 0.00 0.00 0.00 3.95
1547 1553 2.952116 AGTCCATTTTTCAACCCCGAA 58.048 42.857 0.00 0.00 0.00 4.30
1548 1554 2.668144 AGTCCATTTTTCAACCCCGA 57.332 45.000 0.00 0.00 0.00 5.14
1549 1555 3.744238 AAAGTCCATTTTTCAACCCCG 57.256 42.857 0.00 0.00 0.00 5.73
1550 1556 5.290493 AGAAAAGTCCATTTTTCAACCCC 57.710 39.130 12.19 0.00 45.23 4.95
1551 1557 6.345298 TGAAGAAAAGTCCATTTTTCAACCC 58.655 36.000 12.19 1.77 45.23 4.11
1552 1558 6.018751 GCTGAAGAAAAGTCCATTTTTCAACC 60.019 38.462 12.19 3.60 45.23 3.77
1553 1559 6.534793 TGCTGAAGAAAAGTCCATTTTTCAAC 59.465 34.615 12.19 7.12 45.23 3.18
1554 1560 6.638610 TGCTGAAGAAAAGTCCATTTTTCAA 58.361 32.000 12.19 0.00 45.23 2.69
1555 1561 6.219417 TGCTGAAGAAAAGTCCATTTTTCA 57.781 33.333 12.19 1.03 45.23 2.69
1556 1562 5.176406 GCTGCTGAAGAAAAGTCCATTTTTC 59.824 40.000 0.00 3.66 41.24 2.29
1557 1563 5.052481 GCTGCTGAAGAAAAGTCCATTTTT 58.948 37.500 0.00 0.00 41.24 1.94
1558 1564 4.343239 AGCTGCTGAAGAAAAGTCCATTTT 59.657 37.500 0.00 0.00 43.88 1.82
1559 1565 3.893813 AGCTGCTGAAGAAAAGTCCATTT 59.106 39.130 0.00 0.00 0.00 2.32
1560 1566 3.494332 AGCTGCTGAAGAAAAGTCCATT 58.506 40.909 0.00 0.00 0.00 3.16
1561 1567 3.151912 AGCTGCTGAAGAAAAGTCCAT 57.848 42.857 0.00 0.00 0.00 3.41
1562 1568 2.645838 AGCTGCTGAAGAAAAGTCCA 57.354 45.000 0.00 0.00 0.00 4.02
1563 1569 5.065346 GGTTATAGCTGCTGAAGAAAAGTCC 59.935 44.000 13.43 0.00 0.00 3.85
1564 1570 5.220491 CGGTTATAGCTGCTGAAGAAAAGTC 60.220 44.000 13.43 0.00 0.00 3.01
1565 1571 4.631813 CGGTTATAGCTGCTGAAGAAAAGT 59.368 41.667 13.43 0.00 0.00 2.66
1566 1572 4.870426 TCGGTTATAGCTGCTGAAGAAAAG 59.130 41.667 13.43 0.00 0.00 2.27
1567 1573 4.827692 TCGGTTATAGCTGCTGAAGAAAA 58.172 39.130 13.43 0.00 0.00 2.29
1568 1574 4.465632 TCGGTTATAGCTGCTGAAGAAA 57.534 40.909 13.43 0.00 0.00 2.52
1569 1575 4.371786 CATCGGTTATAGCTGCTGAAGAA 58.628 43.478 13.43 0.00 0.00 2.52
1570 1576 3.243873 CCATCGGTTATAGCTGCTGAAGA 60.244 47.826 13.43 3.69 0.00 2.87
1571 1577 3.062763 CCATCGGTTATAGCTGCTGAAG 58.937 50.000 13.43 0.00 0.00 3.02
1572 1578 2.434336 ACCATCGGTTATAGCTGCTGAA 59.566 45.455 13.43 3.46 27.29 3.02
1594 1600 0.824109 CACCAGATTGGCTAGACGGA 59.176 55.000 0.00 0.00 42.67 4.69
1597 1603 5.675538 AGTAAATCACCAGATTGGCTAGAC 58.324 41.667 0.00 0.00 43.52 2.59
1698 1704 5.277825 TGCAATTTTTACCACTCGTTTCTG 58.722 37.500 0.00 0.00 0.00 3.02
1712 1718 3.737266 CGCTCACACAAGATGCAATTTTT 59.263 39.130 0.00 0.00 0.00 1.94
1759 1769 9.255304 GTAGTAATTTTTGCTGATTTCCAACAA 57.745 29.630 0.00 0.00 0.00 2.83
1838 2030 7.639113 TTAGCATGGAATAAAATCGGAGTTT 57.361 32.000 8.57 8.57 0.00 2.66
2041 2362 0.749091 CCATCGCCCAAGCAGAATCA 60.749 55.000 0.00 0.00 39.83 2.57
2048 2369 1.078143 AGAGTTCCATCGCCCAAGC 60.078 57.895 0.00 0.00 0.00 4.01
2093 2414 2.027561 CCAACCTTCTCCGTTACCATGA 60.028 50.000 0.00 0.00 0.00 3.07
2128 2449 5.013079 TGCCTTCCTTCATTGTAAAGAGAGA 59.987 40.000 0.00 0.00 0.00 3.10
2164 2485 6.962182 TCCCTTAAGTGAGAACATCATCATT 58.038 36.000 0.97 0.00 40.92 2.57
2184 2505 5.449553 AGAAATGACTTGAACTGTTTCCCT 58.550 37.500 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.