Multiple sequence alignment - TraesCS4A01G420400

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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 TraesCS4A01G420400 chr4A 100.000 2683 0 0 1 2683 690993618 690990936 0.000000e+00 4955.0
1 TraesCS4A01G420400 chr4A 98.955 1722 17 1 56 1777 690984435 690982715 0.000000e+00 3079.0
2 TraesCS4A01G420400 chr4A 99.199 1249 10 0 56 1304 691009919 691008671 0.000000e+00 2252.0
3 TraesCS4A01G420400 chr4A 99.449 907 5 0 1777 2683 691008448 691007542 0.000000e+00 1648.0
4 TraesCS4A01G420400 chr4A 97.309 706 18 1 1777 2481 691016968 691016263 0.000000e+00 1197.0
5 TraesCS4A01G420400 chr4A 98.456 583 9 0 1195 1777 691017579 691016997 0.000000e+00 1027.0
6 TraesCS4A01G420400 chr4A 92.193 602 45 2 1880 2481 690981363 690980764 0.000000e+00 850.0
7 TraesCS4A01G420400 chr4A 93.050 259 14 1 703 957 691017836 691017578 2.520000e-100 375.0
8 TraesCS4A01G420400 chr4A 99.490 196 1 0 1582 1777 691008672 691008477 9.130000e-95 357.0
9 TraesCS4A01G420400 chr4A 98.020 202 4 0 2482 2683 691015967 691015766 4.250000e-93 351.0
10 TraesCS4A01G420400 chr4A 86.429 280 22 11 426 704 691018183 691017919 2.610000e-75 292.0
11 TraesCS4A01G420400 chr4A 90.594 202 19 0 2482 2683 690980468 690980267 4.400000e-68 268.0
12 TraesCS4A01G420400 chr4A 84.127 189 22 3 1009 1193 691050321 691050137 2.750000e-40 176.0
13 TraesCS4A01G420400 chr4A 84.127 189 22 3 1009 1193 691107248 691107064 2.750000e-40 176.0
14 TraesCS4A01G420400 chr4A 95.413 109 5 0 1777 1885 690982686 690982578 9.870000e-40 174.0
15 TraesCS4A01G420400 chr4A 93.023 86 6 0 56 141 691018267 691018182 2.800000e-25 126.0
16 TraesCS4A01G420400 chr7D 80.376 372 61 5 1033 1392 34312174 34312545 3.400000e-69 272.0
17 TraesCS4A01G420400 chr7D 87.000 100 9 3 1520 1618 34331974 34332070 2.820000e-20 110.0
18 TraesCS4A01G420400 chr7D 79.310 145 26 3 502 644 34311858 34312000 6.110000e-17 99.0
19 TraesCS4A01G420400 chr4D 81.407 199 23 5 1064 1249 506283587 506283390 1.660000e-32 150.0
20 TraesCS4A01G420400 chr4D 85.870 92 10 2 1519 1608 506283164 506283074 7.910000e-16 95.3
21 TraesCS4A01G420400 chr3B 79.397 199 27 6 1064 1249 799773955 799773758 7.800000e-26 128.0
22 TraesCS4A01G420400 chr3B 95.588 68 1 2 1 66 661407852 661407785 1.020000e-19 108.0
23 TraesCS4A01G420400 chr3B 85.870 92 10 3 1519 1608 799757328 799757238 7.910000e-16 95.3
24 TraesCS4A01G420400 chr3B 87.654 81 5 4 56 135 4320160 4320236 3.680000e-14 89.8
25 TraesCS4A01G420400 chr6B 98.462 65 0 1 1 64 645368691 645368755 2.180000e-21 113.0
26 TraesCS4A01G420400 chr6B 96.970 66 0 2 1 64 64173111 64173046 2.820000e-20 110.0
27 TraesCS4A01G420400 chr6B 96.923 65 1 1 1 64 495758438 495758502 1.020000e-19 108.0
28 TraesCS4A01G420400 chr5B 98.438 64 0 1 1 63 121663017 121662954 7.850000e-21 111.0
29 TraesCS4A01G420400 chr2A 98.438 64 0 1 1 63 738190104 738190167 7.850000e-21 111.0
30 TraesCS4A01G420400 chr3D 96.923 65 0 2 1 63 475116340 475116404 1.020000e-19 108.0
31 TraesCS4A01G420400 chr3D 89.412 85 5 4 1 82 108652988 108653071 1.310000e-18 104.0
32 TraesCS4A01G420400 chr1A 96.923 65 1 1 1 64 581950150 581950214 1.020000e-19 108.0
33 TraesCS4A01G420400 chr6A 83.908 87 8 4 56 138 123504674 123504590 7.960000e-11 78.7


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 TraesCS4A01G420400 chr4A 690990936 690993618 2682 True 4955.000000 4955 100.000000 1 2683 1 chr4A.!!$R1 2682
1 TraesCS4A01G420400 chr4A 691007542 691009919 2377 True 1419.000000 2252 99.379333 56 2683 3 chr4A.!!$R5 2627
2 TraesCS4A01G420400 chr4A 690980267 690984435 4168 True 1092.750000 3079 94.288750 56 2683 4 chr4A.!!$R4 2627
3 TraesCS4A01G420400 chr4A 691015766 691018267 2501 True 561.333333 1197 94.381167 56 2683 6 chr4A.!!$R6 2627

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
33 34 0.035317 GAGCACATGGACACCACTGA 59.965 55.0 0.0 0.0 35.8 3.41 F
34 35 0.035881 AGCACATGGACACCACTGAG 59.964 55.0 0.0 0.0 35.8 3.35 F
1381 1491 0.108138 AACATGTGCGAGCCCTAGAC 60.108 55.0 0.0 0.0 0.0 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1535 1645 0.038251 GACCAGTGATGCGTGACAGA 60.038 55.000 0.00 0.0 0.00 3.41 R
1540 1650 0.170339 TAGACGACCAGTGATGCGTG 59.830 55.000 9.09 0.0 37.07 5.34 R
2234 3872 2.699846 ACCACCACCGTAAGAGTGTTAA 59.300 45.455 0.00 0.0 43.02 2.01 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
19 20 1.597742 TCTGAGGCAAAACTGAGCAC 58.402 50.000 0.00 0.00 0.00 4.40
20 21 1.134128 TCTGAGGCAAAACTGAGCACA 60.134 47.619 0.00 0.00 0.00 4.57
21 22 1.884579 CTGAGGCAAAACTGAGCACAT 59.115 47.619 0.00 0.00 0.00 3.21
22 23 1.610038 TGAGGCAAAACTGAGCACATG 59.390 47.619 0.00 0.00 0.00 3.21
23 24 0.963962 AGGCAAAACTGAGCACATGG 59.036 50.000 0.00 0.00 0.00 3.66
24 25 0.961019 GGCAAAACTGAGCACATGGA 59.039 50.000 0.00 0.00 0.00 3.41
25 26 1.336240 GGCAAAACTGAGCACATGGAC 60.336 52.381 0.00 0.00 0.00 4.02
26 27 1.337703 GCAAAACTGAGCACATGGACA 59.662 47.619 0.00 0.00 0.00 4.02
27 28 2.859806 GCAAAACTGAGCACATGGACAC 60.860 50.000 0.00 0.00 0.00 3.67
28 29 1.609208 AAACTGAGCACATGGACACC 58.391 50.000 0.00 0.00 0.00 4.16
29 30 0.473755 AACTGAGCACATGGACACCA 59.526 50.000 0.00 0.00 38.19 4.17
30 31 0.250467 ACTGAGCACATGGACACCAC 60.250 55.000 0.00 0.00 35.80 4.16
31 32 0.035881 CTGAGCACATGGACACCACT 59.964 55.000 0.00 0.00 35.80 4.00
32 33 0.250424 TGAGCACATGGACACCACTG 60.250 55.000 0.00 0.00 35.80 3.66
33 34 0.035317 GAGCACATGGACACCACTGA 59.965 55.000 0.00 0.00 35.80 3.41
34 35 0.035881 AGCACATGGACACCACTGAG 59.964 55.000 0.00 0.00 35.80 3.35
35 36 0.957395 GCACATGGACACCACTGAGG 60.957 60.000 0.00 0.00 45.67 3.86
36 37 0.321919 CACATGGACACCACTGAGGG 60.322 60.000 0.00 0.00 43.89 4.30
37 38 1.377725 CATGGACACCACTGAGGGC 60.378 63.158 0.00 0.00 43.89 5.19
38 39 1.847506 ATGGACACCACTGAGGGCA 60.848 57.895 0.00 0.00 43.89 5.36
39 40 1.426251 ATGGACACCACTGAGGGCAA 61.426 55.000 0.00 0.00 43.89 4.52
40 41 1.150536 GGACACCACTGAGGGCAAA 59.849 57.895 0.00 0.00 43.89 3.68
41 42 0.467290 GGACACCACTGAGGGCAAAA 60.467 55.000 0.00 0.00 43.89 2.44
42 43 0.954452 GACACCACTGAGGGCAAAAG 59.046 55.000 0.00 0.00 43.89 2.27
43 44 0.468029 ACACCACTGAGGGCAAAAGG 60.468 55.000 0.00 0.00 43.89 3.11
44 45 0.178992 CACCACTGAGGGCAAAAGGA 60.179 55.000 0.00 0.00 43.89 3.36
45 46 0.779997 ACCACTGAGGGCAAAAGGAT 59.220 50.000 0.00 0.00 43.89 3.24
46 47 1.992557 ACCACTGAGGGCAAAAGGATA 59.007 47.619 0.00 0.00 43.89 2.59
47 48 2.378547 ACCACTGAGGGCAAAAGGATAA 59.621 45.455 0.00 0.00 43.89 1.75
48 49 3.011708 ACCACTGAGGGCAAAAGGATAAT 59.988 43.478 0.00 0.00 43.89 1.28
49 50 4.026052 CCACTGAGGGCAAAAGGATAATT 58.974 43.478 0.00 0.00 0.00 1.40
50 51 5.200483 CCACTGAGGGCAAAAGGATAATTA 58.800 41.667 0.00 0.00 0.00 1.40
51 52 5.656416 CCACTGAGGGCAAAAGGATAATTAA 59.344 40.000 0.00 0.00 0.00 1.40
52 53 6.405842 CCACTGAGGGCAAAAGGATAATTAAC 60.406 42.308 0.00 0.00 0.00 2.01
53 54 5.656859 ACTGAGGGCAAAAGGATAATTAACC 59.343 40.000 3.60 3.60 0.00 2.85
54 55 4.959839 TGAGGGCAAAAGGATAATTAACCC 59.040 41.667 8.09 3.96 34.91 4.11
145 146 0.109723 GCACACCCTACCCACTGAAA 59.890 55.000 0.00 0.00 0.00 2.69
194 195 6.639632 AATCTATAAAAATGTGAGCGCCAT 57.360 33.333 2.29 0.00 0.00 4.40
222 223 1.203087 TCTAGGACTTGAACCCCGACA 60.203 52.381 0.00 0.00 0.00 4.35
228 229 3.190738 TTGAACCCCGACAGGCTGG 62.191 63.158 20.34 2.42 35.76 4.85
307 308 7.627088 GCAACTTGATATGCAGTCTACAACAAT 60.627 37.037 0.00 0.00 42.12 2.71
1307 1417 4.821589 CCTTCAGGGCTCGGCGTC 62.822 72.222 6.85 0.00 0.00 5.19
1316 1426 2.805353 CTCGGCGTCGTGGACAAG 60.805 66.667 10.18 0.00 37.69 3.16
1317 1427 4.351938 TCGGCGTCGTGGACAAGG 62.352 66.667 10.18 0.00 37.69 3.61
1320 1430 4.681978 GCGTCGTGGACAAGGCCT 62.682 66.667 0.00 0.00 32.09 5.19
1321 1431 2.738521 CGTCGTGGACAAGGCCTG 60.739 66.667 5.69 2.82 32.09 4.85
1322 1432 3.050275 GTCGTGGACAAGGCCTGC 61.050 66.667 5.69 0.00 32.09 4.85
1323 1433 4.680237 TCGTGGACAAGGCCTGCG 62.680 66.667 5.69 2.72 0.00 5.18
1324 1434 4.988598 CGTGGACAAGGCCTGCGT 62.989 66.667 5.69 6.98 0.00 5.24
1325 1435 3.357079 GTGGACAAGGCCTGCGTG 61.357 66.667 5.69 2.95 0.00 5.34
1326 1436 4.641645 TGGACAAGGCCTGCGTGG 62.642 66.667 5.69 0.00 39.35 4.94
1327 1437 4.329545 GGACAAGGCCTGCGTGGA 62.330 66.667 5.69 0.00 38.35 4.02
1333 1443 2.676471 GGCCTGCGTGGACCATTT 60.676 61.111 0.00 0.00 38.13 2.32
1334 1444 2.700773 GGCCTGCGTGGACCATTTC 61.701 63.158 0.00 0.00 38.13 2.17
1335 1445 1.675641 GCCTGCGTGGACCATTTCT 60.676 57.895 0.00 0.00 38.35 2.52
1336 1446 1.244019 GCCTGCGTGGACCATTTCTT 61.244 55.000 0.00 0.00 38.35 2.52
1337 1447 0.804989 CCTGCGTGGACCATTTCTTC 59.195 55.000 0.00 0.00 38.35 2.87
1338 1448 1.522668 CTGCGTGGACCATTTCTTCA 58.477 50.000 0.00 0.00 0.00 3.02
1339 1449 1.197721 CTGCGTGGACCATTTCTTCAC 59.802 52.381 0.00 0.00 0.00 3.18
1340 1450 1.234821 GCGTGGACCATTTCTTCACA 58.765 50.000 0.00 0.00 0.00 3.58
1341 1451 1.197721 GCGTGGACCATTTCTTCACAG 59.802 52.381 0.00 0.00 0.00 3.66
1342 1452 1.197721 CGTGGACCATTTCTTCACAGC 59.802 52.381 0.00 0.00 0.00 4.40
1343 1453 2.508526 GTGGACCATTTCTTCACAGCT 58.491 47.619 0.00 0.00 0.00 4.24
1344 1454 2.887152 GTGGACCATTTCTTCACAGCTT 59.113 45.455 0.00 0.00 0.00 3.74
1345 1455 2.886523 TGGACCATTTCTTCACAGCTTG 59.113 45.455 0.00 0.00 0.00 4.01
1346 1456 2.352127 GGACCATTTCTTCACAGCTTGC 60.352 50.000 0.00 0.00 0.00 4.01
1347 1457 2.294233 GACCATTTCTTCACAGCTTGCA 59.706 45.455 0.00 0.00 0.00 4.08
1348 1458 2.895404 ACCATTTCTTCACAGCTTGCAT 59.105 40.909 0.00 0.00 0.00 3.96
1349 1459 3.250744 CCATTTCTTCACAGCTTGCATG 58.749 45.455 0.00 0.00 0.00 4.06
1350 1460 3.250744 CATTTCTTCACAGCTTGCATGG 58.749 45.455 1.34 0.00 0.00 3.66
1351 1461 0.599558 TTCTTCACAGCTTGCATGGC 59.400 50.000 1.34 2.93 0.00 4.40
1352 1462 1.214589 CTTCACAGCTTGCATGGCC 59.785 57.895 0.00 0.00 0.00 5.36
1353 1463 1.529152 CTTCACAGCTTGCATGGCCA 61.529 55.000 8.56 8.56 0.00 5.36
1354 1464 0.901114 TTCACAGCTTGCATGGCCAT 60.901 50.000 14.09 14.09 0.00 4.40
1355 1465 1.141019 CACAGCTTGCATGGCCATC 59.859 57.895 17.61 11.64 0.00 3.51
1356 1466 1.000019 ACAGCTTGCATGGCCATCT 60.000 52.632 17.61 6.67 0.00 2.90
1357 1467 1.320344 ACAGCTTGCATGGCCATCTG 61.320 55.000 23.22 23.22 0.00 2.90
1358 1468 2.106332 GCTTGCATGGCCATCTGC 59.894 61.111 22.05 22.05 38.87 4.26
1359 1469 2.717044 GCTTGCATGGCCATCTGCA 61.717 57.895 26.47 26.47 46.08 4.41
1361 1471 3.610976 TGCATGGCCATCTGCAAG 58.389 55.556 27.69 12.33 44.87 4.01
1372 1482 3.304041 TCTGCAAGAACATGTGCGA 57.696 47.368 0.00 0.00 42.31 5.10
1373 1483 1.150827 TCTGCAAGAACATGTGCGAG 58.849 50.000 0.00 0.00 42.31 5.03
1374 1484 0.453950 CTGCAAGAACATGTGCGAGC 60.454 55.000 14.49 14.49 43.93 5.03
1375 1485 1.154150 GCAAGAACATGTGCGAGCC 60.154 57.895 11.28 0.00 0.00 4.70
1376 1486 1.503542 CAAGAACATGTGCGAGCCC 59.496 57.895 0.00 0.00 0.00 5.19
1377 1487 0.957395 CAAGAACATGTGCGAGCCCT 60.957 55.000 0.00 0.00 0.00 5.19
1378 1488 0.613260 AAGAACATGTGCGAGCCCTA 59.387 50.000 0.00 0.00 0.00 3.53
1379 1489 0.176680 AGAACATGTGCGAGCCCTAG 59.823 55.000 0.00 0.00 0.00 3.02
1380 1490 0.175760 GAACATGTGCGAGCCCTAGA 59.824 55.000 0.00 0.00 0.00 2.43
1381 1491 0.108138 AACATGTGCGAGCCCTAGAC 60.108 55.000 0.00 0.00 0.00 2.59
1382 1492 0.972983 ACATGTGCGAGCCCTAGACT 60.973 55.000 0.00 0.00 0.00 3.24
1383 1493 0.249238 CATGTGCGAGCCCTAGACTC 60.249 60.000 0.00 0.00 0.00 3.36
1384 1494 1.395826 ATGTGCGAGCCCTAGACTCC 61.396 60.000 7.04 2.38 0.00 3.85
1385 1495 2.442272 TGCGAGCCCTAGACTCCC 60.442 66.667 7.04 0.34 0.00 4.30
1386 1496 2.123640 GCGAGCCCTAGACTCCCT 60.124 66.667 7.04 0.00 0.00 4.20
1387 1497 2.494530 GCGAGCCCTAGACTCCCTG 61.495 68.421 7.04 0.00 0.00 4.45
1388 1498 1.227664 CGAGCCCTAGACTCCCTGA 59.772 63.158 7.04 0.00 0.00 3.86
1389 1499 0.178975 CGAGCCCTAGACTCCCTGAT 60.179 60.000 7.04 0.00 0.00 2.90
1390 1500 1.627864 GAGCCCTAGACTCCCTGATC 58.372 60.000 0.00 0.00 0.00 2.92
1391 1501 0.178975 AGCCCTAGACTCCCTGATCG 60.179 60.000 0.00 0.00 0.00 3.69
1392 1502 1.182385 GCCCTAGACTCCCTGATCGG 61.182 65.000 0.00 0.00 0.00 4.18
1393 1503 1.182385 CCCTAGACTCCCTGATCGGC 61.182 65.000 0.00 0.00 0.00 5.54
1394 1504 1.519751 CCTAGACTCCCTGATCGGCG 61.520 65.000 0.00 0.00 0.00 6.46
1395 1505 2.136196 CTAGACTCCCTGATCGGCGC 62.136 65.000 0.00 0.00 0.00 6.53
1396 1506 4.593864 GACTCCCTGATCGGCGCC 62.594 72.222 19.07 19.07 0.00 6.53
1415 1525 4.722700 GGTGACTGCCACGGCCAT 62.723 66.667 2.24 0.00 46.62 4.40
1416 1526 3.434319 GTGACTGCCACGGCCATG 61.434 66.667 2.24 0.00 41.09 3.66
1419 1529 4.746309 ACTGCCACGGCCATGCAT 62.746 61.111 10.85 0.00 41.09 3.96
1420 1530 4.201679 CTGCCACGGCCATGCATG 62.202 66.667 20.19 20.19 41.09 4.06
1423 1533 3.761140 CCACGGCCATGCATGCAA 61.761 61.111 26.68 8.49 0.00 4.08
1424 1534 2.507547 CACGGCCATGCATGCAAC 60.508 61.111 26.68 16.80 0.00 4.17
1425 1535 2.677524 ACGGCCATGCATGCAACT 60.678 55.556 26.68 6.15 0.00 3.16
1426 1536 2.277591 ACGGCCATGCATGCAACTT 61.278 52.632 26.68 5.25 0.00 2.66
1427 1537 1.517694 CGGCCATGCATGCAACTTC 60.518 57.895 26.68 13.64 0.00 3.01
1428 1538 1.592743 GGCCATGCATGCAACTTCA 59.407 52.632 26.68 0.00 0.00 3.02
1429 1539 0.459585 GGCCATGCATGCAACTTCAG 60.460 55.000 26.68 10.69 0.00 3.02
1430 1540 0.528924 GCCATGCATGCAACTTCAGA 59.471 50.000 26.68 0.00 0.00 3.27
1431 1541 1.469251 GCCATGCATGCAACTTCAGAG 60.469 52.381 26.68 8.22 0.00 3.35
1432 1542 2.089201 CCATGCATGCAACTTCAGAGA 58.911 47.619 26.68 0.00 0.00 3.10
1433 1543 2.688446 CCATGCATGCAACTTCAGAGAT 59.312 45.455 26.68 0.00 0.00 2.75
1434 1544 3.130516 CCATGCATGCAACTTCAGAGATT 59.869 43.478 26.68 0.00 0.00 2.40
1435 1545 4.381612 CCATGCATGCAACTTCAGAGATTT 60.382 41.667 26.68 0.00 0.00 2.17
1436 1546 4.430137 TGCATGCAACTTCAGAGATTTC 57.570 40.909 20.30 0.00 0.00 2.17
1437 1547 4.077108 TGCATGCAACTTCAGAGATTTCT 58.923 39.130 20.30 0.00 0.00 2.52
1438 1548 4.521639 TGCATGCAACTTCAGAGATTTCTT 59.478 37.500 20.30 0.00 0.00 2.52
1439 1549 5.706833 TGCATGCAACTTCAGAGATTTCTTA 59.293 36.000 20.30 0.00 0.00 2.10
1440 1550 6.026513 GCATGCAACTTCAGAGATTTCTTAC 58.973 40.000 14.21 0.00 0.00 2.34
1441 1551 6.549952 CATGCAACTTCAGAGATTTCTTACC 58.450 40.000 0.00 0.00 0.00 2.85
1442 1552 5.620206 TGCAACTTCAGAGATTTCTTACCA 58.380 37.500 0.00 0.00 0.00 3.25
1443 1553 6.240894 TGCAACTTCAGAGATTTCTTACCAT 58.759 36.000 0.00 0.00 0.00 3.55
1444 1554 6.372659 TGCAACTTCAGAGATTTCTTACCATC 59.627 38.462 0.00 0.00 0.00 3.51
1445 1555 6.456181 GCAACTTCAGAGATTTCTTACCATCG 60.456 42.308 0.00 0.00 0.00 3.84
1446 1556 5.112686 ACTTCAGAGATTTCTTACCATCGC 58.887 41.667 0.00 0.00 0.00 4.58
1447 1557 3.706698 TCAGAGATTTCTTACCATCGCG 58.293 45.455 0.00 0.00 0.00 5.87
1448 1558 2.219674 CAGAGATTTCTTACCATCGCGC 59.780 50.000 0.00 0.00 0.00 6.86
1449 1559 1.190323 GAGATTTCTTACCATCGCGCG 59.810 52.381 26.76 26.76 0.00 6.86
1450 1560 0.232303 GATTTCTTACCATCGCGCGG 59.768 55.000 31.69 16.94 0.00 6.46
1451 1561 0.461339 ATTTCTTACCATCGCGCGGT 60.461 50.000 31.69 23.12 40.73 5.68
1452 1562 1.355796 TTTCTTACCATCGCGCGGTG 61.356 55.000 35.04 35.04 37.33 4.94
1453 1563 2.202690 CTTACCATCGCGCGGTGA 60.203 61.111 42.16 22.76 37.33 4.02
1454 1564 1.807981 CTTACCATCGCGCGGTGAA 60.808 57.895 42.16 27.93 37.33 3.18
1455 1565 2.020836 CTTACCATCGCGCGGTGAAC 62.021 60.000 42.16 0.00 37.33 3.18
1467 1577 2.501650 GTGAACGCGGCGTACGTA 60.502 61.111 29.63 12.28 44.30 3.57
1468 1578 1.869132 GTGAACGCGGCGTACGTAT 60.869 57.895 29.63 12.92 44.30 3.06
1469 1579 1.868692 TGAACGCGGCGTACGTATG 60.869 57.895 29.63 10.54 44.30 2.39
1470 1580 1.869132 GAACGCGGCGTACGTATGT 60.869 57.895 29.63 11.24 44.30 2.29
1471 1581 1.405469 GAACGCGGCGTACGTATGTT 61.405 55.000 29.63 10.40 44.30 2.71
1472 1582 1.676438 AACGCGGCGTACGTATGTTG 61.676 55.000 29.63 9.77 44.30 3.33
1473 1583 2.852087 CGCGGCGTACGTATGTTGG 61.852 63.158 17.90 7.00 46.52 3.77
1474 1584 3.000266 CGGCGTACGTATGTTGGC 59.000 61.111 17.90 9.49 37.93 4.52
1475 1585 1.806351 CGGCGTACGTATGTTGGCA 60.806 57.895 17.90 0.00 37.93 4.92
1476 1586 1.352882 CGGCGTACGTATGTTGGCAA 61.353 55.000 17.90 0.00 37.93 4.52
1477 1587 1.011333 GGCGTACGTATGTTGGCAAT 58.989 50.000 17.90 0.00 0.00 3.56
1478 1588 2.203401 GGCGTACGTATGTTGGCAATA 58.797 47.619 17.90 0.00 0.00 1.90
1479 1589 2.220133 GGCGTACGTATGTTGGCAATAG 59.780 50.000 17.90 0.00 0.00 1.73
1480 1590 2.348218 GCGTACGTATGTTGGCAATAGC 60.348 50.000 17.90 0.00 41.10 2.97
1494 1604 4.708726 GCAATAGCCAACTCTTTGATGT 57.291 40.909 0.00 0.00 34.24 3.06
1495 1605 5.064441 GCAATAGCCAACTCTTTGATGTT 57.936 39.130 0.00 0.00 34.24 2.71
1496 1606 5.473039 GCAATAGCCAACTCTTTGATGTTT 58.527 37.500 0.00 0.00 34.24 2.83
1497 1607 5.574443 GCAATAGCCAACTCTTTGATGTTTC 59.426 40.000 0.00 0.00 34.24 2.78
1498 1608 5.904362 ATAGCCAACTCTTTGATGTTTCC 57.096 39.130 0.00 0.00 34.24 3.13
1499 1609 3.837355 AGCCAACTCTTTGATGTTTCCT 58.163 40.909 0.00 0.00 34.24 3.36
1500 1610 4.218312 AGCCAACTCTTTGATGTTTCCTT 58.782 39.130 0.00 0.00 34.24 3.36
1501 1611 4.279420 AGCCAACTCTTTGATGTTTCCTTC 59.721 41.667 0.00 0.00 34.24 3.46
1502 1612 4.559502 GCCAACTCTTTGATGTTTCCTTCC 60.560 45.833 0.00 0.00 34.24 3.46
1503 1613 4.829492 CCAACTCTTTGATGTTTCCTTCCT 59.171 41.667 0.00 0.00 34.24 3.36
1504 1614 5.048434 CCAACTCTTTGATGTTTCCTTCCTC 60.048 44.000 0.00 0.00 34.24 3.71
1505 1615 5.310409 ACTCTTTGATGTTTCCTTCCTCA 57.690 39.130 0.00 0.00 0.00 3.86
1506 1616 5.694995 ACTCTTTGATGTTTCCTTCCTCAA 58.305 37.500 0.00 0.00 0.00 3.02
1507 1617 6.310149 ACTCTTTGATGTTTCCTTCCTCAAT 58.690 36.000 0.00 0.00 0.00 2.57
1508 1618 6.779539 ACTCTTTGATGTTTCCTTCCTCAATT 59.220 34.615 0.00 0.00 0.00 2.32
1509 1619 7.288621 ACTCTTTGATGTTTCCTTCCTCAATTT 59.711 33.333 0.00 0.00 0.00 1.82
1510 1620 8.021898 TCTTTGATGTTTCCTTCCTCAATTTT 57.978 30.769 0.00 0.00 0.00 1.82
1511 1621 8.485392 TCTTTGATGTTTCCTTCCTCAATTTTT 58.515 29.630 0.00 0.00 0.00 1.94
1531 1641 5.523438 TTTTTACACTTCCTTCCGCAATT 57.477 34.783 0.00 0.00 0.00 2.32
1532 1642 6.636562 TTTTTACACTTCCTTCCGCAATTA 57.363 33.333 0.00 0.00 0.00 1.40
1533 1643 6.827586 TTTTACACTTCCTTCCGCAATTAT 57.172 33.333 0.00 0.00 0.00 1.28
1534 1644 6.827586 TTTACACTTCCTTCCGCAATTATT 57.172 33.333 0.00 0.00 0.00 1.40
1535 1645 6.827586 TTACACTTCCTTCCGCAATTATTT 57.172 33.333 0.00 0.00 0.00 1.40
1536 1646 5.310720 ACACTTCCTTCCGCAATTATTTC 57.689 39.130 0.00 0.00 0.00 2.17
1537 1647 5.010282 ACACTTCCTTCCGCAATTATTTCT 58.990 37.500 0.00 0.00 0.00 2.52
1538 1648 5.106157 ACACTTCCTTCCGCAATTATTTCTG 60.106 40.000 0.00 0.00 0.00 3.02
1539 1649 5.010282 ACTTCCTTCCGCAATTATTTCTGT 58.990 37.500 0.00 0.00 0.00 3.41
1540 1650 5.123979 ACTTCCTTCCGCAATTATTTCTGTC 59.876 40.000 0.00 0.00 0.00 3.51
1541 1651 4.584874 TCCTTCCGCAATTATTTCTGTCA 58.415 39.130 0.00 0.00 0.00 3.58
1542 1652 4.394920 TCCTTCCGCAATTATTTCTGTCAC 59.605 41.667 0.00 0.00 0.00 3.67
1543 1653 4.334443 CTTCCGCAATTATTTCTGTCACG 58.666 43.478 0.00 0.00 0.00 4.35
1544 1654 2.095213 TCCGCAATTATTTCTGTCACGC 59.905 45.455 0.00 0.00 0.00 5.34
1545 1655 2.159585 CCGCAATTATTTCTGTCACGCA 60.160 45.455 0.00 0.00 0.00 5.24
1546 1656 3.487376 CCGCAATTATTTCTGTCACGCAT 60.487 43.478 0.00 0.00 0.00 4.73
1547 1657 3.720818 CGCAATTATTTCTGTCACGCATC 59.279 43.478 0.00 0.00 0.00 3.91
1548 1658 4.661125 GCAATTATTTCTGTCACGCATCA 58.339 39.130 0.00 0.00 0.00 3.07
1549 1659 4.496895 GCAATTATTTCTGTCACGCATCAC 59.503 41.667 0.00 0.00 0.00 3.06
1550 1660 5.674569 GCAATTATTTCTGTCACGCATCACT 60.675 40.000 0.00 0.00 0.00 3.41
1551 1661 4.926860 TTATTTCTGTCACGCATCACTG 57.073 40.909 0.00 0.00 0.00 3.66
1552 1662 1.511850 TTTCTGTCACGCATCACTGG 58.488 50.000 0.00 0.00 0.00 4.00
1553 1663 0.392706 TTCTGTCACGCATCACTGGT 59.607 50.000 0.00 0.00 0.00 4.00
1554 1664 0.038251 TCTGTCACGCATCACTGGTC 60.038 55.000 0.00 0.00 0.00 4.02
1555 1665 1.347097 CTGTCACGCATCACTGGTCG 61.347 60.000 0.00 0.00 0.00 4.79
1556 1666 1.372997 GTCACGCATCACTGGTCGT 60.373 57.895 0.00 0.00 35.35 4.34
1557 1667 1.080772 TCACGCATCACTGGTCGTC 60.081 57.895 0.00 0.00 32.38 4.20
1558 1668 1.080501 CACGCATCACTGGTCGTCT 60.081 57.895 0.00 0.00 32.38 4.18
1559 1669 0.170339 CACGCATCACTGGTCGTCTA 59.830 55.000 0.00 0.00 32.38 2.59
1560 1670 1.103803 ACGCATCACTGGTCGTCTAT 58.896 50.000 0.00 0.00 0.00 1.98
1561 1671 1.065701 ACGCATCACTGGTCGTCTATC 59.934 52.381 0.00 0.00 0.00 2.08
1562 1672 1.600663 CGCATCACTGGTCGTCTATCC 60.601 57.143 0.00 0.00 0.00 2.59
1563 1673 1.409064 GCATCACTGGTCGTCTATCCA 59.591 52.381 0.00 0.00 0.00 3.41
1564 1674 2.036475 GCATCACTGGTCGTCTATCCAT 59.964 50.000 0.00 0.00 33.01 3.41
1565 1675 3.493350 GCATCACTGGTCGTCTATCCATT 60.493 47.826 0.00 0.00 33.01 3.16
1566 1676 4.302455 CATCACTGGTCGTCTATCCATTC 58.698 47.826 0.00 0.00 33.01 2.67
1567 1677 3.361786 TCACTGGTCGTCTATCCATTCA 58.638 45.455 0.00 0.00 33.01 2.57
1568 1678 3.960755 TCACTGGTCGTCTATCCATTCAT 59.039 43.478 0.00 0.00 33.01 2.57
1569 1679 4.053983 CACTGGTCGTCTATCCATTCATG 58.946 47.826 0.00 0.00 33.01 3.07
1762 2151 0.592637 CAGATTGCAAACACGCCTCA 59.407 50.000 1.71 0.00 0.00 3.86
1996 3634 4.667519 AAACTCTTAGTGTGGAACGTCT 57.332 40.909 0.00 0.00 42.39 4.18
2161 3799 6.222038 AGAAATTCTACTACTTGCCGATGA 57.778 37.500 0.00 0.00 0.00 2.92
2226 3864 3.827302 TGGTACAATTAACAAACCCGCAT 59.173 39.130 0.00 0.00 31.92 4.73
2234 3872 1.816074 ACAAACCCGCATAACACGAT 58.184 45.000 0.00 0.00 0.00 3.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.134128 TGTGCTCAGTTTTGCCTCAGA 60.134 47.619 0.00 0.00 0.00 3.27
1 2 1.311859 TGTGCTCAGTTTTGCCTCAG 58.688 50.000 0.00 0.00 0.00 3.35
2 3 1.610038 CATGTGCTCAGTTTTGCCTCA 59.390 47.619 0.00 0.00 0.00 3.86
3 4 1.068055 CCATGTGCTCAGTTTTGCCTC 60.068 52.381 0.00 0.00 0.00 4.70
4 5 0.963962 CCATGTGCTCAGTTTTGCCT 59.036 50.000 0.00 0.00 0.00 4.75
5 6 0.961019 TCCATGTGCTCAGTTTTGCC 59.039 50.000 0.00 0.00 0.00 4.52
6 7 1.337703 TGTCCATGTGCTCAGTTTTGC 59.662 47.619 0.00 0.00 0.00 3.68
7 8 2.287788 GGTGTCCATGTGCTCAGTTTTG 60.288 50.000 0.00 0.00 0.00 2.44
8 9 1.956477 GGTGTCCATGTGCTCAGTTTT 59.044 47.619 0.00 0.00 0.00 2.43
9 10 1.133823 TGGTGTCCATGTGCTCAGTTT 60.134 47.619 0.00 0.00 0.00 2.66
10 11 0.473755 TGGTGTCCATGTGCTCAGTT 59.526 50.000 0.00 0.00 0.00 3.16
11 12 0.250467 GTGGTGTCCATGTGCTCAGT 60.250 55.000 0.00 0.00 35.28 3.41
12 13 0.035881 AGTGGTGTCCATGTGCTCAG 59.964 55.000 0.00 0.00 35.28 3.35
13 14 0.250424 CAGTGGTGTCCATGTGCTCA 60.250 55.000 0.00 0.00 35.28 4.26
14 15 0.035317 TCAGTGGTGTCCATGTGCTC 59.965 55.000 0.00 0.00 35.28 4.26
15 16 0.035881 CTCAGTGGTGTCCATGTGCT 59.964 55.000 0.00 0.00 35.28 4.40
16 17 0.957395 CCTCAGTGGTGTCCATGTGC 60.957 60.000 0.00 0.00 35.28 4.57
17 18 0.321919 CCCTCAGTGGTGTCCATGTG 60.322 60.000 0.00 0.00 35.28 3.21
18 19 2.069776 CCCTCAGTGGTGTCCATGT 58.930 57.895 0.00 0.00 35.28 3.21
19 20 1.377725 GCCCTCAGTGGTGTCCATG 60.378 63.158 0.00 0.00 35.28 3.66
20 21 1.426251 TTGCCCTCAGTGGTGTCCAT 61.426 55.000 0.00 0.00 35.28 3.41
21 22 1.640593 TTTGCCCTCAGTGGTGTCCA 61.641 55.000 0.00 0.00 0.00 4.02
22 23 0.467290 TTTTGCCCTCAGTGGTGTCC 60.467 55.000 0.00 0.00 0.00 4.02
23 24 0.954452 CTTTTGCCCTCAGTGGTGTC 59.046 55.000 0.00 0.00 0.00 3.67
24 25 0.468029 CCTTTTGCCCTCAGTGGTGT 60.468 55.000 0.00 0.00 0.00 4.16
25 26 0.178992 TCCTTTTGCCCTCAGTGGTG 60.179 55.000 0.00 0.00 0.00 4.17
26 27 0.779997 ATCCTTTTGCCCTCAGTGGT 59.220 50.000 0.00 0.00 0.00 4.16
27 28 2.806945 TATCCTTTTGCCCTCAGTGG 57.193 50.000 0.00 0.00 0.00 4.00
28 29 6.405842 GGTTAATTATCCTTTTGCCCTCAGTG 60.406 42.308 5.46 0.00 0.00 3.66
29 30 5.656859 GGTTAATTATCCTTTTGCCCTCAGT 59.343 40.000 5.46 0.00 0.00 3.41
30 31 5.069119 GGGTTAATTATCCTTTTGCCCTCAG 59.931 44.000 11.51 0.00 0.00 3.35
31 32 4.959839 GGGTTAATTATCCTTTTGCCCTCA 59.040 41.667 11.51 0.00 0.00 3.86
32 33 5.208890 AGGGTTAATTATCCTTTTGCCCTC 58.791 41.667 11.51 0.00 39.57 4.30
33 34 5.220872 AGGGTTAATTATCCTTTTGCCCT 57.779 39.130 11.51 0.00 38.99 5.19
34 35 5.950544 AAGGGTTAATTATCCTTTTGCCC 57.049 39.130 11.51 0.00 37.60 5.36
145 146 2.515071 GGCCTCCCGATGATGAGCT 61.515 63.158 0.00 0.00 0.00 4.09
194 195 3.496160 GGTTCAAGTCCTAGAGTTGCCAA 60.496 47.826 7.20 0.00 41.27 4.52
222 223 0.912486 GAACAGTGGTATCCCAGCCT 59.088 55.000 0.00 0.00 42.94 4.58
228 229 7.987458 TGAATGATTAGAAGAACAGTGGTATCC 59.013 37.037 0.00 0.00 0.00 2.59
407 408 8.144478 AGTATCTGTACATGCGATTCTGTAATT 58.856 33.333 0.00 0.00 33.09 1.40
413 414 4.202151 TGCAGTATCTGTACATGCGATTCT 60.202 41.667 12.41 5.66 37.57 2.40
1303 1413 4.681978 AGGCCTTGTCCACGACGC 62.682 66.667 0.00 0.00 34.95 5.19
1304 1414 2.738521 CAGGCCTTGTCCACGACG 60.739 66.667 0.00 0.00 34.95 5.12
1305 1415 3.050275 GCAGGCCTTGTCCACGAC 61.050 66.667 0.00 0.00 0.00 4.34
1306 1416 4.680237 CGCAGGCCTTGTCCACGA 62.680 66.667 0.00 0.00 32.02 4.35
1307 1417 4.988598 ACGCAGGCCTTGTCCACG 62.989 66.667 0.00 2.74 35.12 4.94
1308 1418 3.357079 CACGCAGGCCTTGTCCAC 61.357 66.667 0.00 0.00 0.00 4.02
1309 1419 4.641645 CCACGCAGGCCTTGTCCA 62.642 66.667 0.00 0.00 0.00 4.02
1310 1420 4.329545 TCCACGCAGGCCTTGTCC 62.330 66.667 0.00 0.00 37.29 4.02
1311 1421 3.050275 GTCCACGCAGGCCTTGTC 61.050 66.667 0.00 0.00 37.29 3.18
1312 1422 4.643387 GGTCCACGCAGGCCTTGT 62.643 66.667 0.00 0.76 37.29 3.16
1313 1423 3.925630 ATGGTCCACGCAGGCCTTG 62.926 63.158 0.00 0.00 37.29 3.61
1314 1424 2.713531 AAATGGTCCACGCAGGCCTT 62.714 55.000 0.00 0.00 37.29 4.35
1315 1425 3.210012 AAATGGTCCACGCAGGCCT 62.210 57.895 0.00 0.00 37.29 5.19
1316 1426 2.676471 AAATGGTCCACGCAGGCC 60.676 61.111 0.00 0.00 37.29 5.19
1317 1427 1.244019 AAGAAATGGTCCACGCAGGC 61.244 55.000 0.00 0.00 37.29 4.85
1318 1428 0.804989 GAAGAAATGGTCCACGCAGG 59.195 55.000 0.00 0.00 39.47 4.85
1319 1429 1.197721 GTGAAGAAATGGTCCACGCAG 59.802 52.381 0.00 0.00 0.00 5.18
1320 1430 1.234821 GTGAAGAAATGGTCCACGCA 58.765 50.000 0.00 0.00 0.00 5.24
1321 1431 1.197721 CTGTGAAGAAATGGTCCACGC 59.802 52.381 0.00 0.00 0.00 5.34
1322 1432 1.197721 GCTGTGAAGAAATGGTCCACG 59.802 52.381 0.00 0.00 0.00 4.94
1323 1433 2.508526 AGCTGTGAAGAAATGGTCCAC 58.491 47.619 0.00 0.00 0.00 4.02
1324 1434 2.886523 CAAGCTGTGAAGAAATGGTCCA 59.113 45.455 0.00 0.00 0.00 4.02
1325 1435 2.352127 GCAAGCTGTGAAGAAATGGTCC 60.352 50.000 0.00 0.00 0.00 4.46
1326 1436 2.294233 TGCAAGCTGTGAAGAAATGGTC 59.706 45.455 0.00 0.00 0.00 4.02
1327 1437 2.309613 TGCAAGCTGTGAAGAAATGGT 58.690 42.857 0.00 0.00 0.00 3.55
1328 1438 3.250744 CATGCAAGCTGTGAAGAAATGG 58.749 45.455 0.00 0.00 0.00 3.16
1329 1439 3.250744 CCATGCAAGCTGTGAAGAAATG 58.749 45.455 0.00 0.00 0.00 2.32
1330 1440 2.353406 GCCATGCAAGCTGTGAAGAAAT 60.353 45.455 4.90 0.00 0.00 2.17
1331 1441 1.000060 GCCATGCAAGCTGTGAAGAAA 60.000 47.619 4.90 0.00 0.00 2.52
1332 1442 0.599558 GCCATGCAAGCTGTGAAGAA 59.400 50.000 4.90 0.00 0.00 2.52
1333 1443 1.246056 GGCCATGCAAGCTGTGAAGA 61.246 55.000 11.41 0.00 0.00 2.87
1334 1444 1.214589 GGCCATGCAAGCTGTGAAG 59.785 57.895 11.41 0.00 0.00 3.02
1335 1445 0.901114 ATGGCCATGCAAGCTGTGAA 60.901 50.000 20.04 0.00 0.00 3.18
1336 1446 1.304630 ATGGCCATGCAAGCTGTGA 60.305 52.632 20.04 0.00 0.00 3.58
1337 1447 1.141019 GATGGCCATGCAAGCTGTG 59.859 57.895 26.56 0.00 0.00 3.66
1338 1448 1.000019 AGATGGCCATGCAAGCTGT 60.000 52.632 26.56 0.00 21.82 4.40
1339 1449 1.437573 CAGATGGCCATGCAAGCTG 59.562 57.895 26.56 19.50 39.65 4.24
1340 1450 2.423898 GCAGATGGCCATGCAAGCT 61.424 57.895 26.56 10.91 42.11 3.74
1341 1451 2.106332 GCAGATGGCCATGCAAGC 59.894 61.111 26.56 17.11 42.11 4.01
1345 1455 0.179119 GTTCTTGCAGATGGCCATGC 60.179 55.000 26.56 23.92 43.89 4.06
1346 1456 1.179152 TGTTCTTGCAGATGGCCATG 58.821 50.000 26.56 13.27 43.89 3.66
1347 1457 1.754803 CATGTTCTTGCAGATGGCCAT 59.245 47.619 20.96 20.96 43.89 4.40
1348 1458 1.179152 CATGTTCTTGCAGATGGCCA 58.821 50.000 8.56 8.56 43.89 5.36
1349 1459 1.135199 CACATGTTCTTGCAGATGGCC 60.135 52.381 0.00 0.00 43.89 5.36
1350 1460 1.734707 GCACATGTTCTTGCAGATGGC 60.735 52.381 0.00 0.00 45.13 4.40
1351 1461 1.466866 CGCACATGTTCTTGCAGATGG 60.467 52.381 0.00 0.00 38.76 3.51
1352 1462 1.465777 TCGCACATGTTCTTGCAGATG 59.534 47.619 0.00 0.00 38.76 2.90
1353 1463 1.736126 CTCGCACATGTTCTTGCAGAT 59.264 47.619 0.00 0.00 38.76 2.90
1354 1464 1.150827 CTCGCACATGTTCTTGCAGA 58.849 50.000 0.00 0.00 38.76 4.26
1355 1465 0.453950 GCTCGCACATGTTCTTGCAG 60.454 55.000 0.00 0.00 38.76 4.41
1356 1466 1.575922 GCTCGCACATGTTCTTGCA 59.424 52.632 0.00 0.00 38.76 4.08
1357 1467 1.154150 GGCTCGCACATGTTCTTGC 60.154 57.895 0.00 0.00 35.26 4.01
1358 1468 0.957395 AGGGCTCGCACATGTTCTTG 60.957 55.000 0.00 0.00 0.00 3.02
1359 1469 0.613260 TAGGGCTCGCACATGTTCTT 59.387 50.000 0.00 0.00 0.00 2.52
1360 1470 0.176680 CTAGGGCTCGCACATGTTCT 59.823 55.000 0.00 0.00 0.00 3.01
1361 1471 0.175760 TCTAGGGCTCGCACATGTTC 59.824 55.000 0.00 0.00 0.00 3.18
1362 1472 0.108138 GTCTAGGGCTCGCACATGTT 60.108 55.000 0.00 0.00 0.00 2.71
1363 1473 0.972983 AGTCTAGGGCTCGCACATGT 60.973 55.000 0.00 0.00 0.00 3.21
1364 1474 0.249238 GAGTCTAGGGCTCGCACATG 60.249 60.000 0.00 0.00 0.00 3.21
1365 1475 1.395826 GGAGTCTAGGGCTCGCACAT 61.396 60.000 0.00 0.00 34.00 3.21
1366 1476 2.052690 GGAGTCTAGGGCTCGCACA 61.053 63.158 0.00 0.00 34.00 4.57
1367 1477 2.787567 GGGAGTCTAGGGCTCGCAC 61.788 68.421 19.52 7.14 42.93 5.34
1368 1478 2.442272 GGGAGTCTAGGGCTCGCA 60.442 66.667 19.52 0.00 42.93 5.10
1369 1479 2.123640 AGGGAGTCTAGGGCTCGC 60.124 66.667 17.90 17.90 43.49 5.03
1370 1480 0.178975 ATCAGGGAGTCTAGGGCTCG 60.179 60.000 8.45 0.00 34.00 5.03
1371 1481 1.627864 GATCAGGGAGTCTAGGGCTC 58.372 60.000 6.67 6.67 0.00 4.70
1372 1482 0.178975 CGATCAGGGAGTCTAGGGCT 60.179 60.000 0.00 0.00 0.00 5.19
1373 1483 1.182385 CCGATCAGGGAGTCTAGGGC 61.182 65.000 0.00 0.00 35.97 5.19
1374 1484 1.182385 GCCGATCAGGGAGTCTAGGG 61.182 65.000 5.87 0.00 41.48 3.53
1375 1485 1.519751 CGCCGATCAGGGAGTCTAGG 61.520 65.000 5.87 0.00 41.48 3.02
1376 1486 1.953017 CGCCGATCAGGGAGTCTAG 59.047 63.158 5.87 0.00 41.48 2.43
1377 1487 2.194212 GCGCCGATCAGGGAGTCTA 61.194 63.158 0.00 0.00 41.48 2.59
1378 1488 3.532155 GCGCCGATCAGGGAGTCT 61.532 66.667 0.00 0.00 41.48 3.24
1379 1489 4.593864 GGCGCCGATCAGGGAGTC 62.594 72.222 12.58 0.00 41.48 3.36
1398 1508 4.722700 ATGGCCGTGGCAGTCACC 62.723 66.667 13.76 0.00 42.43 4.02
1399 1509 3.434319 CATGGCCGTGGCAGTCAC 61.434 66.667 17.90 0.00 42.43 3.67
1402 1512 4.746309 ATGCATGGCCGTGGCAGT 62.746 61.111 26.22 11.32 42.43 4.40
1403 1513 4.201679 CATGCATGGCCGTGGCAG 62.202 66.667 26.22 13.42 42.43 4.85
1406 1516 3.761140 TTGCATGCATGGCCGTGG 61.761 61.111 27.34 11.02 0.00 4.94
1407 1517 2.495366 AAGTTGCATGCATGGCCGTG 62.495 55.000 27.34 21.33 0.00 4.94
1408 1518 2.216750 GAAGTTGCATGCATGGCCGT 62.217 55.000 27.34 8.19 0.00 5.68
1409 1519 1.517694 GAAGTTGCATGCATGGCCG 60.518 57.895 27.34 2.89 0.00 6.13
1410 1520 0.459585 CTGAAGTTGCATGCATGGCC 60.460 55.000 27.34 12.69 0.00 5.36
1411 1521 0.528924 TCTGAAGTTGCATGCATGGC 59.471 50.000 27.34 19.18 0.00 4.40
1412 1522 2.089201 TCTCTGAAGTTGCATGCATGG 58.911 47.619 27.34 10.03 0.00 3.66
1413 1523 4.371855 AATCTCTGAAGTTGCATGCATG 57.628 40.909 23.37 22.70 0.00 4.06
1414 1524 4.705507 AGAAATCTCTGAAGTTGCATGCAT 59.294 37.500 23.37 6.60 0.00 3.96
1415 1525 4.077108 AGAAATCTCTGAAGTTGCATGCA 58.923 39.130 18.46 18.46 0.00 3.96
1416 1526 4.698583 AGAAATCTCTGAAGTTGCATGC 57.301 40.909 11.82 11.82 0.00 4.06
1417 1527 6.149973 TGGTAAGAAATCTCTGAAGTTGCATG 59.850 38.462 0.00 0.00 30.03 4.06
1418 1528 6.240894 TGGTAAGAAATCTCTGAAGTTGCAT 58.759 36.000 0.00 0.00 30.03 3.96
1419 1529 5.620206 TGGTAAGAAATCTCTGAAGTTGCA 58.380 37.500 0.00 0.00 30.03 4.08
1420 1530 6.456181 CGATGGTAAGAAATCTCTGAAGTTGC 60.456 42.308 0.00 0.00 30.03 4.17
1421 1531 6.456181 GCGATGGTAAGAAATCTCTGAAGTTG 60.456 42.308 0.00 0.00 30.03 3.16
1422 1532 5.582665 GCGATGGTAAGAAATCTCTGAAGTT 59.417 40.000 0.00 0.00 30.03 2.66
1423 1533 5.112686 GCGATGGTAAGAAATCTCTGAAGT 58.887 41.667 0.00 0.00 30.03 3.01
1424 1534 4.208047 CGCGATGGTAAGAAATCTCTGAAG 59.792 45.833 0.00 0.00 30.03 3.02
1425 1535 4.112634 CGCGATGGTAAGAAATCTCTGAA 58.887 43.478 0.00 0.00 30.03 3.02
1426 1536 3.706698 CGCGATGGTAAGAAATCTCTGA 58.293 45.455 0.00 0.00 30.03 3.27
1427 1537 2.219674 GCGCGATGGTAAGAAATCTCTG 59.780 50.000 12.10 0.00 30.03 3.35
1428 1538 2.474816 GCGCGATGGTAAGAAATCTCT 58.525 47.619 12.10 0.00 0.00 3.10
1429 1539 1.190323 CGCGCGATGGTAAGAAATCTC 59.810 52.381 28.94 0.00 0.00 2.75
1430 1540 1.209128 CGCGCGATGGTAAGAAATCT 58.791 50.000 28.94 0.00 0.00 2.40
1431 1541 0.232303 CCGCGCGATGGTAAGAAATC 59.768 55.000 34.63 0.00 0.00 2.17
1432 1542 0.461339 ACCGCGCGATGGTAAGAAAT 60.461 50.000 34.63 0.00 38.15 2.17
1433 1543 1.079681 ACCGCGCGATGGTAAGAAA 60.080 52.632 34.63 0.00 38.15 2.52
1434 1544 1.807981 CACCGCGCGATGGTAAGAA 60.808 57.895 34.63 0.00 37.72 2.52
1435 1545 2.202690 CACCGCGCGATGGTAAGA 60.203 61.111 34.63 0.00 37.72 2.10
1436 1546 1.807981 TTCACCGCGCGATGGTAAG 60.808 57.895 34.63 15.43 37.72 2.34
1437 1547 2.095847 GTTCACCGCGCGATGGTAA 61.096 57.895 34.63 13.67 37.72 2.85
1438 1548 2.507547 GTTCACCGCGCGATGGTA 60.508 61.111 34.63 14.19 37.72 3.25
1449 1559 3.944526 TACGTACGCCGCGTTCACC 62.945 63.158 25.47 8.91 42.85 4.02
1450 1560 1.869132 ATACGTACGCCGCGTTCAC 60.869 57.895 25.47 15.97 42.85 3.18
1451 1561 1.868692 CATACGTACGCCGCGTTCA 60.869 57.895 25.47 3.55 42.85 3.18
1452 1562 1.405469 AACATACGTACGCCGCGTTC 61.405 55.000 25.47 18.19 42.85 3.95
1453 1563 1.444212 AACATACGTACGCCGCGTT 60.444 52.632 25.47 8.92 42.85 4.84
1454 1564 2.153945 CAACATACGTACGCCGCGT 61.154 57.895 23.72 23.72 45.11 6.01
1455 1565 2.611365 CAACATACGTACGCCGCG 59.389 61.111 16.72 12.14 41.42 6.46
1456 1566 3.000266 CCAACATACGTACGCCGC 59.000 61.111 16.72 0.00 41.42 6.53
1457 1567 1.352882 TTGCCAACATACGTACGCCG 61.353 55.000 16.72 6.39 44.03 6.46
1458 1568 1.011333 ATTGCCAACATACGTACGCC 58.989 50.000 16.72 0.00 0.00 5.68
1459 1569 2.348218 GCTATTGCCAACATACGTACGC 60.348 50.000 16.72 0.00 0.00 4.42
1460 1570 3.499072 GCTATTGCCAACATACGTACG 57.501 47.619 15.01 15.01 0.00 3.67
1473 1583 4.708726 ACATCAAAGAGTTGGCTATTGC 57.291 40.909 0.00 0.00 35.29 3.56
1474 1584 6.071728 AGGAAACATCAAAGAGTTGGCTATTG 60.072 38.462 0.00 0.00 35.29 1.90
1475 1585 6.012745 AGGAAACATCAAAGAGTTGGCTATT 58.987 36.000 0.00 0.00 35.29 1.73
1476 1586 5.574188 AGGAAACATCAAAGAGTTGGCTAT 58.426 37.500 0.00 0.00 35.29 2.97
1477 1587 4.985538 AGGAAACATCAAAGAGTTGGCTA 58.014 39.130 0.00 0.00 35.29 3.93
1478 1588 3.837355 AGGAAACATCAAAGAGTTGGCT 58.163 40.909 0.00 0.00 35.29 4.75
1479 1589 4.550422 GAAGGAAACATCAAAGAGTTGGC 58.450 43.478 0.00 0.00 35.29 4.52
1480 1590 4.829492 AGGAAGGAAACATCAAAGAGTTGG 59.171 41.667 0.00 0.00 35.29 3.77
1481 1591 5.532406 TGAGGAAGGAAACATCAAAGAGTTG 59.468 40.000 0.00 0.00 35.95 3.16
1482 1592 5.694995 TGAGGAAGGAAACATCAAAGAGTT 58.305 37.500 0.00 0.00 0.00 3.01
1483 1593 5.310409 TGAGGAAGGAAACATCAAAGAGT 57.690 39.130 0.00 0.00 0.00 3.24
1484 1594 6.830873 ATTGAGGAAGGAAACATCAAAGAG 57.169 37.500 0.00 0.00 40.41 2.85
1485 1595 7.601705 AAATTGAGGAAGGAAACATCAAAGA 57.398 32.000 0.00 0.00 40.41 2.52
1486 1596 8.667076 AAAAATTGAGGAAGGAAACATCAAAG 57.333 30.769 0.00 0.00 40.41 2.77
1519 1629 4.394920 GTGACAGAAATAATTGCGGAAGGA 59.605 41.667 0.00 0.00 0.00 3.36
1520 1630 4.662145 GTGACAGAAATAATTGCGGAAGG 58.338 43.478 0.00 0.00 0.00 3.46
1521 1631 4.334443 CGTGACAGAAATAATTGCGGAAG 58.666 43.478 0.00 0.00 0.00 3.46
1522 1632 3.425625 GCGTGACAGAAATAATTGCGGAA 60.426 43.478 0.00 0.00 0.00 4.30
1523 1633 2.095213 GCGTGACAGAAATAATTGCGGA 59.905 45.455 0.00 0.00 0.00 5.54
1524 1634 2.159585 TGCGTGACAGAAATAATTGCGG 60.160 45.455 0.00 0.00 0.00 5.69
1525 1635 3.116063 TGCGTGACAGAAATAATTGCG 57.884 42.857 0.00 0.00 0.00 4.85
1526 1636 4.496895 GTGATGCGTGACAGAAATAATTGC 59.503 41.667 0.00 0.00 0.00 3.56
1527 1637 5.735892 CAGTGATGCGTGACAGAAATAATTG 59.264 40.000 0.00 0.00 0.00 2.32
1528 1638 5.163723 CCAGTGATGCGTGACAGAAATAATT 60.164 40.000 0.00 0.00 0.00 1.40
1529 1639 4.333649 CCAGTGATGCGTGACAGAAATAAT 59.666 41.667 0.00 0.00 0.00 1.28
1530 1640 3.684305 CCAGTGATGCGTGACAGAAATAA 59.316 43.478 0.00 0.00 0.00 1.40
1531 1641 3.261580 CCAGTGATGCGTGACAGAAATA 58.738 45.455 0.00 0.00 0.00 1.40
1532 1642 2.079158 CCAGTGATGCGTGACAGAAAT 58.921 47.619 0.00 0.00 0.00 2.17
1533 1643 1.202639 ACCAGTGATGCGTGACAGAAA 60.203 47.619 0.00 0.00 0.00 2.52
1534 1644 0.392706 ACCAGTGATGCGTGACAGAA 59.607 50.000 0.00 0.00 0.00 3.02
1535 1645 0.038251 GACCAGTGATGCGTGACAGA 60.038 55.000 0.00 0.00 0.00 3.41
1536 1646 1.347097 CGACCAGTGATGCGTGACAG 61.347 60.000 0.00 0.00 0.00 3.51
1537 1647 1.372872 CGACCAGTGATGCGTGACA 60.373 57.895 0.00 0.00 0.00 3.58
1538 1648 1.344942 GACGACCAGTGATGCGTGAC 61.345 60.000 9.09 0.00 37.07 3.67
1539 1649 1.080772 GACGACCAGTGATGCGTGA 60.081 57.895 9.09 0.00 37.07 4.35
1540 1650 0.170339 TAGACGACCAGTGATGCGTG 59.830 55.000 9.09 0.00 37.07 5.34
1541 1651 1.065701 GATAGACGACCAGTGATGCGT 59.934 52.381 4.90 4.90 39.99 5.24
1542 1652 1.600663 GGATAGACGACCAGTGATGCG 60.601 57.143 0.00 0.00 0.00 4.73
1543 1653 1.409064 TGGATAGACGACCAGTGATGC 59.591 52.381 0.00 0.00 0.00 3.91
1544 1654 4.202151 TGAATGGATAGACGACCAGTGATG 60.202 45.833 0.00 0.00 39.62 3.07
1545 1655 3.960755 TGAATGGATAGACGACCAGTGAT 59.039 43.478 0.00 0.00 39.62 3.06
1546 1656 3.361786 TGAATGGATAGACGACCAGTGA 58.638 45.455 0.00 0.00 39.62 3.41
1547 1657 3.801114 TGAATGGATAGACGACCAGTG 57.199 47.619 0.00 0.00 39.62 3.66
1548 1658 4.327982 CATGAATGGATAGACGACCAGT 57.672 45.455 0.00 0.00 39.62 4.00
1562 1672 3.497262 CACCATCTGTCGATCCATGAATG 59.503 47.826 0.00 0.00 0.00 2.67
1563 1673 3.495629 CCACCATCTGTCGATCCATGAAT 60.496 47.826 0.00 0.00 0.00 2.57
1564 1674 2.158914 CCACCATCTGTCGATCCATGAA 60.159 50.000 0.00 0.00 0.00 2.57
1565 1675 1.413812 CCACCATCTGTCGATCCATGA 59.586 52.381 0.00 0.00 0.00 3.07
1566 1676 1.139654 ACCACCATCTGTCGATCCATG 59.860 52.381 0.00 0.00 0.00 3.66
1567 1677 1.139654 CACCACCATCTGTCGATCCAT 59.860 52.381 0.00 0.00 0.00 3.41
1568 1678 0.536724 CACCACCATCTGTCGATCCA 59.463 55.000 0.00 0.00 0.00 3.41
1569 1679 0.537188 ACACCACCATCTGTCGATCC 59.463 55.000 0.00 0.00 0.00 3.36
1570 1680 2.093973 AGAACACCACCATCTGTCGATC 60.094 50.000 0.00 0.00 0.00 3.69
1571 1681 1.902508 AGAACACCACCATCTGTCGAT 59.097 47.619 0.00 0.00 0.00 3.59
1572 1682 1.000843 CAGAACACCACCATCTGTCGA 59.999 52.381 0.00 0.00 36.64 4.20
1573 1683 1.432514 CAGAACACCACCATCTGTCG 58.567 55.000 0.00 0.00 36.64 4.35
1576 1686 3.127548 GCATAACAGAACACCACCATCTG 59.872 47.826 0.00 0.00 44.77 2.90
1577 1687 3.009473 AGCATAACAGAACACCACCATCT 59.991 43.478 0.00 0.00 0.00 2.90
1578 1688 3.347216 AGCATAACAGAACACCACCATC 58.653 45.455 0.00 0.00 0.00 3.51
1579 1689 3.439857 AGCATAACAGAACACCACCAT 57.560 42.857 0.00 0.00 0.00 3.55
1580 1690 2.949177 AGCATAACAGAACACCACCA 57.051 45.000 0.00 0.00 0.00 4.17
1762 2151 2.688666 TCTTGCCAGCCCGAGGAT 60.689 61.111 0.00 0.00 0.00 3.24
1996 3634 3.003173 CGGGGAGTTGAGGCCTCA 61.003 66.667 32.00 32.00 37.91 3.86
2226 3864 5.858049 CACCGTAAGAGTGTTAATCGTGTTA 59.142 40.000 0.00 0.00 43.02 2.41
2234 3872 2.699846 ACCACCACCGTAAGAGTGTTAA 59.300 45.455 0.00 0.00 43.02 2.01


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

AutoCloner maintained by Alex Coulton.