Multiple sequence alignment - TraesCS6B01G317600

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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 TraesCS6B01G317600 chr6B 100.000 4643 0 0 1 4643 565422917 565418275 0.000000e+00 8575
1 TraesCS6B01G317600 chr6B 98.837 86 1 0 1864 1949 191540714 191540629 2.240000e-33 154
2 TraesCS6B01G317600 chr6D 95.266 2535 98 9 2127 4643 380445494 380448024 0.000000e+00 3997
3 TraesCS6B01G317600 chr6D 88.859 754 40 16 523 1242 380443942 380444685 0.000000e+00 887
4 TraesCS6B01G317600 chr6D 89.834 541 22 15 1 520 380443380 380443908 0.000000e+00 664
5 TraesCS6B01G317600 chr6D 86.089 496 46 13 1352 1834 380444753 380445238 3.200000e-141 512
6 TraesCS6B01G317600 chr6D 95.082 183 9 0 1947 2129 380445255 380445437 5.880000e-74 289
7 TraesCS6B01G317600 chr6A 94.917 2538 101 14 2128 4643 520541977 520539446 0.000000e+00 3947
8 TraesCS6B01G317600 chr6A 92.818 738 30 10 523 1242 520543478 520542746 0.000000e+00 1048
9 TraesCS6B01G317600 chr6A 84.211 551 52 23 1286 1834 520542730 520542213 1.930000e-138 503
10 TraesCS6B01G317600 chr6A 84.843 508 15 26 24 520 520543968 520543512 5.480000e-124 455
11 TraesCS6B01G317600 chr6A 96.739 184 6 0 1947 2130 520542193 520542010 1.620000e-79 307
12 TraesCS6B01G317600 chr2A 98.876 89 1 0 1861 1949 692531012 692531100 4.810000e-35 159
13 TraesCS6B01G317600 chr4A 100.000 85 0 0 1865 1949 675138554 675138638 1.730000e-34 158
14 TraesCS6B01G317600 chr5A 96.774 93 3 0 1861 1953 401726805 401726897 6.220000e-34 156
15 TraesCS6B01G317600 chr5A 98.837 86 1 0 1864 1949 19256088 19256003 2.240000e-33 154
16 TraesCS6B01G317600 chr3B 96.739 92 3 0 1864 1955 762449757 762449848 2.240000e-33 154
17 TraesCS6B01G317600 chr1B 95.833 96 3 1 1862 1957 686756521 686756427 2.240000e-33 154
18 TraesCS6B01G317600 chr4D 96.739 92 2 1 1862 1953 76446898 76446808 8.050000e-33 152
19 TraesCS6B01G317600 chr7D 90.000 120 7 3 1831 1950 405908522 405908636 2.890000e-32 150


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 TraesCS6B01G317600 chr6B 565418275 565422917 4642 True 8575.0 8575 100.0000 1 4643 1 chr6B.!!$R2 4642
1 TraesCS6B01G317600 chr6D 380443380 380448024 4644 False 1269.8 3997 91.0260 1 4643 5 chr6D.!!$F1 4642
2 TraesCS6B01G317600 chr6A 520539446 520543968 4522 True 1252.0 3947 90.7056 24 4643 5 chr6A.!!$R1 4619

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
702 755 0.393808 AGACGTGGAGGAGAGAGAGC 60.394 60.0 0.00 0.00 0.00 4.09 F
1337 1433 0.107268 ACGCCGGTGTTCTTTTACCT 59.893 50.0 16.69 0.00 34.77 3.08 F
1458 1555 0.172578 CCACCTGAGCATGCATGTTG 59.827 55.0 26.79 12.52 0.00 3.33 F
1533 1630 0.320858 TTGAACCATCTAACGGCGCA 60.321 50.0 10.83 0.00 0.00 6.09 F
1875 1996 0.492276 AACCCAGGTACTCCCTCTGT 59.508 55.0 0.00 0.00 43.86 3.41 F
2928 3129 0.034670 GAGAAATCAGCACAGCCCCT 60.035 55.0 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2526 0.603707 AACCTGTGGACTGATGTGCG 60.604 55.000 0.00 0.00 37.34 5.34 R
2798 2996 1.419387 CTGATAAGCCTCCTCCTTGGG 59.581 57.143 0.00 0.00 36.20 4.12 R
2904 3105 1.465354 GCTGTGCTGATTTCTCTTGCG 60.465 52.381 0.00 0.00 0.00 4.85 R
2928 3129 1.559682 GCTATGTTCTGGGAGGAACCA 59.440 52.381 5.15 0.00 43.31 3.67 R
3603 3808 0.539438 TGGCAACATGGACAGGTTCC 60.539 55.000 0.00 5.61 46.17 3.62 R
4114 4323 0.984230 ACACCCGAACATCTCCATGT 59.016 50.000 0.00 0.00 45.89 3.21 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
39 40 1.689233 CTTGATCTCCCGGGTCCCA 60.689 63.158 22.86 11.78 0.00 4.37
109 110 2.584236 GGTAGGTAGATCTTCTCCGCA 58.416 52.381 0.00 0.00 0.00 5.69
112 113 2.303175 AGGTAGATCTTCTCCGCACTC 58.697 52.381 0.00 0.00 0.00 3.51
115 116 1.034838 AGATCTTCTCCGCACTCGCT 61.035 55.000 0.00 0.00 35.30 4.93
116 117 0.869454 GATCTTCTCCGCACTCGCTG 60.869 60.000 0.00 0.00 35.30 5.18
117 118 2.290122 ATCTTCTCCGCACTCGCTGG 62.290 60.000 0.00 0.00 35.30 4.85
125 126 4.079850 CACTCGCTGGCTGGCTCT 62.080 66.667 2.00 0.00 0.00 4.09
126 127 3.768922 ACTCGCTGGCTGGCTCTC 61.769 66.667 2.00 0.00 0.00 3.20
127 128 3.459965 CTCGCTGGCTGGCTCTCT 61.460 66.667 2.00 0.00 0.00 3.10
128 129 3.429080 CTCGCTGGCTGGCTCTCTC 62.429 68.421 2.00 0.00 0.00 3.20
129 130 3.459965 CGCTGGCTGGCTCTCTCT 61.460 66.667 2.00 0.00 0.00 3.10
130 131 2.500646 GCTGGCTGGCTCTCTCTC 59.499 66.667 2.00 0.00 0.00 3.20
131 132 2.059786 GCTGGCTGGCTCTCTCTCT 61.060 63.158 2.00 0.00 0.00 3.10
132 133 2.019897 GCTGGCTGGCTCTCTCTCTC 62.020 65.000 2.00 0.00 0.00 3.20
133 134 1.727511 CTGGCTGGCTCTCTCTCTCG 61.728 65.000 2.00 0.00 0.00 4.04
134 135 1.453015 GGCTGGCTCTCTCTCTCGA 60.453 63.158 0.00 0.00 0.00 4.04
167 172 3.570926 GGTTGTAAAGCCTAAAGCCAC 57.429 47.619 0.00 0.00 45.47 5.01
171 176 2.159382 GTAAAGCCTAAAGCCACAGCA 58.841 47.619 0.00 0.00 45.47 4.41
362 379 4.007644 TGCAGCGGTGGAGACAGG 62.008 66.667 17.54 0.00 44.46 4.00
370 387 0.840722 GGTGGAGACAGGGGGAAAGA 60.841 60.000 0.00 0.00 44.46 2.52
446 464 0.519792 CACGTGATCGACTACGCGAA 60.520 55.000 15.93 0.00 44.22 4.70
448 466 1.510524 CGTGATCGACTACGCGAACG 61.511 60.000 15.93 12.68 44.22 3.95
449 467 1.581912 TGATCGACTACGCGAACGC 60.582 57.895 15.93 9.20 44.22 4.84
583 636 6.527722 CGTAGTACTATTACTTTTTGCCGACA 59.472 38.462 5.75 0.00 39.43 4.35
599 652 1.202154 CGACACGTAATTCTCCGCTCT 60.202 52.381 0.00 0.00 0.00 4.09
642 695 1.055338 GCGTCAAATTGCTTGCTGTC 58.945 50.000 0.00 0.00 34.76 3.51
702 755 0.393808 AGACGTGGAGGAGAGAGAGC 60.394 60.000 0.00 0.00 0.00 4.09
743 803 9.601971 GCGTATAAACTTTTGAAGATACAACAA 57.398 29.630 0.00 0.00 0.00 2.83
794 854 7.255942 CCCACTTTGTTAAATCCTTGTCAATCT 60.256 37.037 0.00 0.00 0.00 2.40
801 861 1.561643 TCCTTGTCAATCTCCTCGCT 58.438 50.000 0.00 0.00 0.00 4.93
926 1000 2.119655 GCCAGCAGCAAGATCCAGG 61.120 63.158 0.00 0.00 42.97 4.45
1050 1127 0.244178 GAGAAACTCCGCCGTCTTCT 59.756 55.000 0.00 0.00 0.00 2.85
1068 1145 3.314541 TCTTCCGTGTCTCTTTTAGCC 57.685 47.619 0.00 0.00 0.00 3.93
1139 1235 3.564218 GAGGAGCCGGCCCATGAT 61.564 66.667 28.68 9.95 0.00 2.45
1182 1278 3.767230 CGTCAGCGTTCCAGCACG 61.767 66.667 0.00 0.00 43.36 5.34
1210 1306 4.388499 CGGCCAGCAAGGTACCGT 62.388 66.667 6.18 0.00 37.99 4.83
1211 1307 2.436115 GGCCAGCAAGGTACCGTC 60.436 66.667 6.18 0.00 40.61 4.79
1212 1308 2.436115 GCCAGCAAGGTACCGTCC 60.436 66.667 6.18 0.00 40.61 4.79
1213 1309 2.125673 CCAGCAAGGTACCGTCCG 60.126 66.667 6.18 0.00 0.00 4.79
1218 1314 2.674380 AAGGTACCGTCCGTCGCT 60.674 61.111 6.18 0.00 38.35 4.93
1223 1319 1.376424 TACCGTCCGTCGCTTCTCT 60.376 57.895 0.00 0.00 38.35 3.10
1230 1326 1.355066 CCGTCGCTTCTCTTTGCCTC 61.355 60.000 0.00 0.00 0.00 4.70
1234 1330 0.742635 CGCTTCTCTTTGCCTCTCCC 60.743 60.000 0.00 0.00 0.00 4.30
1236 1332 1.284313 CTTCTCTTTGCCTCTCCCCT 58.716 55.000 0.00 0.00 0.00 4.79
1242 1338 0.540365 TTTGCCTCTCCCCTTGCAAG 60.540 55.000 19.93 19.93 43.76 4.01
1243 1339 2.753446 GCCTCTCCCCTTGCAAGC 60.753 66.667 21.43 3.99 0.00 4.01
1265 1361 4.681978 GCGGCCTCGGTGTTCACT 62.682 66.667 0.00 0.00 36.79 3.41
1266 1362 2.432628 CGGCCTCGGTGTTCACTC 60.433 66.667 0.00 0.00 0.00 3.51
1267 1363 2.741092 GGCCTCGGTGTTCACTCA 59.259 61.111 0.00 0.00 0.00 3.41
1268 1364 1.296715 GGCCTCGGTGTTCACTCAT 59.703 57.895 0.00 0.00 0.00 2.90
1269 1365 0.321653 GGCCTCGGTGTTCACTCATT 60.322 55.000 0.00 0.00 0.00 2.57
1270 1366 1.523758 GCCTCGGTGTTCACTCATTT 58.476 50.000 2.98 0.00 0.00 2.32
1271 1367 1.197721 GCCTCGGTGTTCACTCATTTG 59.802 52.381 2.98 0.00 0.00 2.32
1272 1368 2.494059 CCTCGGTGTTCACTCATTTGT 58.506 47.619 2.98 0.00 0.00 2.83
1273 1369 2.224079 CCTCGGTGTTCACTCATTTGTG 59.776 50.000 2.98 0.00 39.15 3.33
1274 1370 3.130633 CTCGGTGTTCACTCATTTGTGA 58.869 45.455 2.98 0.00 44.17 3.58
1297 1393 1.095600 GTGATTCTTCCTTTCCCCGC 58.904 55.000 0.00 0.00 0.00 6.13
1305 1401 1.451387 CCTTTCCCCGCGTATGCTT 60.451 57.895 4.92 0.00 39.65 3.91
1308 1404 1.302383 TTTCCCCGCGTATGCTTGTG 61.302 55.000 4.92 0.00 39.65 3.33
1317 1413 1.390123 CGTATGCTTGTGTCTCCGTTG 59.610 52.381 0.00 0.00 0.00 4.10
1319 1415 1.512926 ATGCTTGTGTCTCCGTTGAC 58.487 50.000 0.00 0.00 37.47 3.18
1329 1425 3.708734 CCGTTGACGCCGGTGTTC 61.709 66.667 23.85 15.52 40.59 3.18
1331 1427 2.241880 CGTTGACGCCGGTGTTCTT 61.242 57.895 23.85 0.00 0.00 2.52
1332 1428 1.768112 CGTTGACGCCGGTGTTCTTT 61.768 55.000 23.85 0.00 0.00 2.52
1334 1430 1.598601 GTTGACGCCGGTGTTCTTTTA 59.401 47.619 23.85 2.21 0.00 1.52
1335 1431 1.219646 TGACGCCGGTGTTCTTTTAC 58.780 50.000 23.85 8.00 0.00 2.01
1336 1432 0.514255 GACGCCGGTGTTCTTTTACC 59.486 55.000 23.85 2.41 0.00 2.85
1337 1433 0.107268 ACGCCGGTGTTCTTTTACCT 59.893 50.000 16.69 0.00 34.77 3.08
1338 1434 1.232119 CGCCGGTGTTCTTTTACCTT 58.768 50.000 6.91 0.00 34.77 3.50
1339 1435 1.605232 CGCCGGTGTTCTTTTACCTTT 59.395 47.619 6.91 0.00 34.77 3.11
1340 1436 2.033675 CGCCGGTGTTCTTTTACCTTTT 59.966 45.455 6.91 0.00 34.77 2.27
1344 1440 5.680408 GCCGGTGTTCTTTTACCTTTTCTTT 60.680 40.000 1.90 0.00 34.77 2.52
1345 1441 6.334989 CCGGTGTTCTTTTACCTTTTCTTTT 58.665 36.000 0.00 0.00 34.77 2.27
1346 1442 6.474427 CCGGTGTTCTTTTACCTTTTCTTTTC 59.526 38.462 0.00 0.00 34.77 2.29
1348 1444 7.220108 CGGTGTTCTTTTACCTTTTCTTTTCTG 59.780 37.037 0.00 0.00 34.77 3.02
1349 1445 8.033038 GGTGTTCTTTTACCTTTTCTTTTCTGT 58.967 33.333 0.00 0.00 34.11 3.41
1350 1446 9.073368 GTGTTCTTTTACCTTTTCTTTTCTGTC 57.927 33.333 0.00 0.00 0.00 3.51
1351 1447 8.248253 TGTTCTTTTACCTTTTCTTTTCTGTCC 58.752 33.333 0.00 0.00 0.00 4.02
1352 1448 7.948034 TCTTTTACCTTTTCTTTTCTGTCCA 57.052 32.000 0.00 0.00 0.00 4.02
1353 1449 8.356000 TCTTTTACCTTTTCTTTTCTGTCCAA 57.644 30.769 0.00 0.00 0.00 3.53
1354 1450 8.977412 TCTTTTACCTTTTCTTTTCTGTCCAAT 58.023 29.630 0.00 0.00 0.00 3.16
1355 1451 9.249457 CTTTTACCTTTTCTTTTCTGTCCAATC 57.751 33.333 0.00 0.00 0.00 2.67
1363 1459 0.620556 TTCTGTCCAATCCTCCTGCC 59.379 55.000 0.00 0.00 0.00 4.85
1384 1480 2.535331 TGTTCGCTTTGAAAACCAAGC 58.465 42.857 0.00 0.00 38.60 4.01
1413 1510 2.767445 GCGAGCAGAATGGCATGCA 61.767 57.895 21.36 6.13 45.01 3.96
1414 1511 2.030551 CGAGCAGAATGGCATGCAT 58.969 52.632 21.36 8.40 45.01 3.96
1415 1512 0.317854 CGAGCAGAATGGCATGCATG 60.318 55.000 22.70 22.70 45.01 4.06
1416 1513 1.029681 GAGCAGAATGGCATGCATGA 58.970 50.000 30.64 10.92 45.01 3.07
1417 1514 1.001268 GAGCAGAATGGCATGCATGAG 60.001 52.381 30.64 5.13 45.01 2.90
1428 1525 1.337384 ATGCATGAGCCGGTACCTGA 61.337 55.000 10.90 0.00 41.13 3.86
1432 1529 1.115467 ATGAGCCGGTACCTGAAGAG 58.885 55.000 10.90 0.00 0.00 2.85
1433 1530 0.251653 TGAGCCGGTACCTGAAGAGT 60.252 55.000 10.90 0.00 0.00 3.24
1434 1531 0.173708 GAGCCGGTACCTGAAGAGTG 59.826 60.000 10.90 0.00 0.00 3.51
1435 1532 1.448013 GCCGGTACCTGAAGAGTGC 60.448 63.158 10.90 0.00 0.00 4.40
1436 1533 1.153823 CCGGTACCTGAAGAGTGCG 60.154 63.158 10.90 0.00 0.00 5.34
1437 1534 1.805945 CGGTACCTGAAGAGTGCGC 60.806 63.158 10.90 0.00 0.00 6.09
1438 1535 1.292223 GGTACCTGAAGAGTGCGCA 59.708 57.895 5.66 5.66 0.00 6.09
1439 1536 1.014564 GGTACCTGAAGAGTGCGCAC 61.015 60.000 32.79 32.79 0.00 5.34
1456 1553 0.963856 CACCACCTGAGCATGCATGT 60.964 55.000 26.79 14.24 0.00 3.21
1457 1554 0.251474 ACCACCTGAGCATGCATGTT 60.251 50.000 26.79 22.13 0.00 2.71
1458 1555 0.172578 CCACCTGAGCATGCATGTTG 59.827 55.000 26.79 12.52 0.00 3.33
1459 1556 0.885879 CACCTGAGCATGCATGTTGT 59.114 50.000 26.79 13.16 0.00 3.32
1460 1557 0.885879 ACCTGAGCATGCATGTTGTG 59.114 50.000 26.79 15.16 0.00 3.33
1461 1558 0.885879 CCTGAGCATGCATGTTGTGT 59.114 50.000 26.79 7.82 0.00 3.72
1462 1559 1.402325 CCTGAGCATGCATGTTGTGTG 60.402 52.381 26.79 12.60 0.00 3.82
1463 1560 1.538075 CTGAGCATGCATGTTGTGTGA 59.462 47.619 26.79 4.82 0.00 3.58
1469 1566 3.612241 GCATGCATGTTGTGTGAAGCTTA 60.612 43.478 26.79 0.00 0.00 3.09
1518 1615 0.603707 CAGGCCTGAAGTCGCTTGAA 60.604 55.000 29.88 0.00 34.22 2.69
1522 1619 1.813513 CCTGAAGTCGCTTGAACCAT 58.186 50.000 0.00 0.00 0.00 3.55
1524 1621 2.613977 CCTGAAGTCGCTTGAACCATCT 60.614 50.000 0.00 0.00 0.00 2.90
1532 1629 0.373716 CTTGAACCATCTAACGGCGC 59.626 55.000 6.90 0.00 0.00 6.53
1533 1630 0.320858 TTGAACCATCTAACGGCGCA 60.321 50.000 10.83 0.00 0.00 6.09
1536 1633 2.588877 CCATCTAACGGCGCAGGG 60.589 66.667 13.26 1.15 0.00 4.45
1538 1635 1.153449 CATCTAACGGCGCAGGGAA 60.153 57.895 13.26 0.00 0.00 3.97
1539 1636 0.532862 CATCTAACGGCGCAGGGAAT 60.533 55.000 13.26 0.00 0.00 3.01
1540 1637 0.532862 ATCTAACGGCGCAGGGAATG 60.533 55.000 13.26 0.00 0.00 2.67
1549 1646 3.831883 CAGGGAATGCCGGTGATG 58.168 61.111 1.90 0.00 33.83 3.07
1550 1647 1.825191 CAGGGAATGCCGGTGATGG 60.825 63.158 1.90 0.00 33.83 3.51
1584 1705 2.772924 CCAGGTTTGGGGGAGCAT 59.227 61.111 0.00 0.00 41.05 3.79
1658 1779 3.004951 CAGGGAAGAGGCTGGCAT 58.995 61.111 3.38 0.00 0.00 4.40
1804 1925 6.711194 CACCGACAATAAGAGATCTAGAGGTA 59.289 42.308 0.00 0.00 0.00 3.08
1831 1952 7.647715 AGACGATTGGTTCAAAATGTTTTGTAG 59.352 33.333 15.51 2.02 45.77 2.74
1834 1955 8.901748 CGATTGGTTCAAAATGTTTTGTAGTAG 58.098 33.333 15.51 1.78 45.77 2.57
1835 1956 9.191995 GATTGGTTCAAAATGTTTTGTAGTAGG 57.808 33.333 15.51 0.00 45.77 3.18
1836 1957 7.883391 TGGTTCAAAATGTTTTGTAGTAGGA 57.117 32.000 15.51 0.00 45.77 2.94
1837 1958 7.936584 TGGTTCAAAATGTTTTGTAGTAGGAG 58.063 34.615 15.51 0.00 45.77 3.69
1838 1959 7.558444 TGGTTCAAAATGTTTTGTAGTAGGAGT 59.442 33.333 15.51 0.00 45.77 3.85
1839 1960 9.059260 GGTTCAAAATGTTTTGTAGTAGGAGTA 57.941 33.333 15.51 0.00 45.77 2.59
1858 1979 6.016443 AGGAGTATTACGTACCAGATAGCAAC 60.016 42.308 0.00 0.00 33.58 4.17
1865 1986 2.263895 ACCAGATAGCAACCCAGGTA 57.736 50.000 0.00 0.00 0.00 3.08
1866 1987 1.838077 ACCAGATAGCAACCCAGGTAC 59.162 52.381 0.00 0.00 0.00 3.34
1867 1988 2.119495 CCAGATAGCAACCCAGGTACT 58.881 52.381 0.00 0.00 43.88 2.73
1868 1989 2.103263 CCAGATAGCAACCCAGGTACTC 59.897 54.545 0.00 0.00 34.60 2.59
1869 1990 2.103263 CAGATAGCAACCCAGGTACTCC 59.897 54.545 0.00 0.00 34.60 3.85
1870 1991 1.416772 GATAGCAACCCAGGTACTCCC 59.583 57.143 0.00 0.00 34.60 4.30
1872 1993 0.910088 AGCAACCCAGGTACTCCCTC 60.910 60.000 0.00 0.00 43.86 4.30
1873 1994 0.910088 GCAACCCAGGTACTCCCTCT 60.910 60.000 0.00 0.00 43.86 3.69
1874 1995 0.905357 CAACCCAGGTACTCCCTCTG 59.095 60.000 0.00 0.00 43.86 3.35
1875 1996 0.492276 AACCCAGGTACTCCCTCTGT 59.508 55.000 0.00 0.00 43.86 3.41
1876 1997 1.390287 ACCCAGGTACTCCCTCTGTA 58.610 55.000 0.00 0.00 43.86 2.74
1877 1998 1.720533 ACCCAGGTACTCCCTCTGTAA 59.279 52.381 0.00 0.00 43.86 2.41
1878 1999 2.113052 ACCCAGGTACTCCCTCTGTAAA 59.887 50.000 0.00 0.00 43.86 2.01
1879 2000 2.500504 CCCAGGTACTCCCTCTGTAAAC 59.499 54.545 0.00 0.00 43.86 2.01
1880 2001 3.442076 CCAGGTACTCCCTCTGTAAACT 58.558 50.000 0.00 0.00 43.86 2.66
1881 2002 4.571362 CCCAGGTACTCCCTCTGTAAACTA 60.571 50.000 0.00 0.00 43.86 2.24
1882 2003 5.021458 CCAGGTACTCCCTCTGTAAACTAA 58.979 45.833 0.00 0.00 43.86 2.24
1883 2004 5.661759 CCAGGTACTCCCTCTGTAAACTAAT 59.338 44.000 0.00 0.00 43.86 1.73
1884 2005 6.407074 CCAGGTACTCCCTCTGTAAACTAATG 60.407 46.154 0.00 0.00 43.86 1.90
1885 2006 6.154706 CAGGTACTCCCTCTGTAAACTAATGT 59.845 42.308 0.00 0.00 43.86 2.71
1886 2007 7.341256 CAGGTACTCCCTCTGTAAACTAATGTA 59.659 40.741 0.00 0.00 43.86 2.29
1887 2008 7.897565 AGGTACTCCCTCTGTAAACTAATGTAA 59.102 37.037 0.00 0.00 40.71 2.41
1888 2009 8.196103 GGTACTCCCTCTGTAAACTAATGTAAG 58.804 40.741 0.00 0.00 0.00 2.34
1889 2010 8.964772 GTACTCCCTCTGTAAACTAATGTAAGA 58.035 37.037 0.00 0.00 0.00 2.10
1890 2011 8.068892 ACTCCCTCTGTAAACTAATGTAAGAG 57.931 38.462 0.00 0.00 0.00 2.85
1891 2012 7.674772 ACTCCCTCTGTAAACTAATGTAAGAGT 59.325 37.037 0.00 0.00 0.00 3.24
1892 2013 7.837863 TCCCTCTGTAAACTAATGTAAGAGTG 58.162 38.462 0.00 0.00 0.00 3.51
1893 2014 7.453752 TCCCTCTGTAAACTAATGTAAGAGTGT 59.546 37.037 0.00 0.00 0.00 3.55
1894 2015 8.095169 CCCTCTGTAAACTAATGTAAGAGTGTT 58.905 37.037 0.00 0.00 0.00 3.32
1895 2016 9.490379 CCTCTGTAAACTAATGTAAGAGTGTTT 57.510 33.333 0.00 0.00 0.00 2.83
1943 2064 9.490379 AAATGCTCTTATATTAGTTTACGGAGG 57.510 33.333 0.00 0.00 0.00 4.30
1944 2065 6.989659 TGCTCTTATATTAGTTTACGGAGGG 58.010 40.000 0.00 0.00 0.00 4.30
1945 2066 6.779049 TGCTCTTATATTAGTTTACGGAGGGA 59.221 38.462 0.00 0.00 0.00 4.20
1946 2067 7.039923 TGCTCTTATATTAGTTTACGGAGGGAG 60.040 40.741 0.00 0.00 0.00 4.30
1947 2068 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
2041 2162 1.383109 TGCCGATCAGGATCCCAGT 60.383 57.895 8.55 0.00 45.00 4.00
2111 2232 5.500234 AGATAAATGACAGGCAAGCTAACA 58.500 37.500 0.00 0.00 0.00 2.41
2186 2366 1.522676 CACGTGCTGCATACTATTCCG 59.477 52.381 5.27 4.44 0.00 4.30
2189 2369 2.408050 GTGCTGCATACTATTCCGGAG 58.592 52.381 5.27 0.00 0.00 4.63
2214 2394 9.209175 AGTAATTTGTTCTTAGGATATGATCGC 57.791 33.333 0.00 0.00 0.00 4.58
2231 2414 3.026630 TCGCAACCTTCTAAGTGTCTG 57.973 47.619 0.00 0.00 0.00 3.51
2315 2498 5.750524 AGGGATAAAGCTTCTTTCCTTCTC 58.249 41.667 17.13 5.64 0.00 2.87
2324 2507 3.662247 TCTTTCCTTCTCGAGGTTCAC 57.338 47.619 13.56 0.00 46.39 3.18
2326 2509 3.005897 TCTTTCCTTCTCGAGGTTCACAG 59.994 47.826 13.56 3.08 46.39 3.66
2355 2538 4.678509 TGTAAATTTCGCACATCAGTCC 57.321 40.909 0.00 0.00 0.00 3.85
2356 2539 4.068599 TGTAAATTTCGCACATCAGTCCA 58.931 39.130 0.00 0.00 0.00 4.02
2377 2560 7.942341 AGTCCACAGGTTATACTTCAAAATTCA 59.058 33.333 0.00 0.00 0.00 2.57
2391 2575 4.401519 TCAAAATTCACACCCCGTAAACAA 59.598 37.500 0.00 0.00 0.00 2.83
2472 2656 2.957402 AGGCATTCCTGAACAGAACA 57.043 45.000 3.19 0.00 42.34 3.18
2518 2709 6.811665 CCATGGGTATGTATAGACATTGTACG 59.188 42.308 8.52 0.00 44.18 3.67
2526 2717 6.319399 TGTATAGACATTGTACGATATGCGG 58.681 40.000 0.00 0.00 46.49 5.69
2529 2720 1.864711 ACATTGTACGATATGCGGTGC 59.135 47.619 0.00 0.00 46.49 5.01
2698 2896 8.012241 CAGAGAGCACAAAGTTGTATTTTACTC 58.988 37.037 0.00 0.00 39.91 2.59
2724 2922 9.243637 CGTGATAAATTCCTTTTTGAAGTGAAA 57.756 29.630 0.00 0.00 0.00 2.69
2745 2943 8.143193 GTGAAACCATCATATATCAATGCCAAA 58.857 33.333 0.77 0.00 40.97 3.28
2761 2959 5.581126 TGCCAAAGTGCCTTCATTTATAG 57.419 39.130 0.00 0.00 0.00 1.31
2762 2960 5.016173 TGCCAAAGTGCCTTCATTTATAGT 58.984 37.500 0.00 0.00 0.00 2.12
2763 2961 6.184068 TGCCAAAGTGCCTTCATTTATAGTA 58.816 36.000 0.00 0.00 0.00 1.82
2764 2962 6.661377 TGCCAAAGTGCCTTCATTTATAGTAA 59.339 34.615 0.00 0.00 0.00 2.24
2798 2996 4.818534 TTTCACAGAACATCAGTCAAGC 57.181 40.909 0.00 0.00 0.00 4.01
2904 3105 4.787882 GCTTCTCTCTTCAACACACAAAGC 60.788 45.833 0.00 0.00 0.00 3.51
2928 3129 0.034670 GAGAAATCAGCACAGCCCCT 60.035 55.000 0.00 0.00 0.00 4.79
2988 3190 6.699575 AGTCATATGCTTTTATGTTCACCC 57.300 37.500 0.00 0.00 32.49 4.61
3309 3511 3.347216 ACTGAACACTGCTTTGACTTGT 58.653 40.909 0.00 0.00 0.00 3.16
3456 3659 6.015180 ACAGTTCAAAGGTACAATGATGCATT 60.015 34.615 0.00 0.00 34.04 3.56
3482 3685 7.758076 TGATGTACCTACGTTTACTGATCAAAG 59.242 37.037 0.00 0.00 0.00 2.77
3574 3779 6.211384 AGAGCAAGCATTTACCCAGTATTTTT 59.789 34.615 0.00 0.00 0.00 1.94
3593 3798 9.237846 GTATTTTTGCTTCATTTCATAGGCTAC 57.762 33.333 0.00 0.00 0.00 3.58
3654 3859 2.095461 TGCGACTGAAGCTACATCTCT 58.905 47.619 0.00 0.00 35.28 3.10
3658 3863 3.127721 CGACTGAAGCTACATCTCTGTCA 59.872 47.826 17.35 2.02 36.79 3.58
3660 3865 3.829026 ACTGAAGCTACATCTCTGTCACA 59.171 43.478 0.00 0.00 36.79 3.58
3667 3872 4.439426 GCTACATCTCTGTCACACACTAGG 60.439 50.000 0.00 0.00 36.79 3.02
3671 3876 2.698274 TCTCTGTCACACACTAGGCAAA 59.302 45.455 0.00 0.00 0.00 3.68
3682 3887 3.313526 ACACTAGGCAAATCATTCATCGC 59.686 43.478 0.00 0.00 0.00 4.58
3695 3900 1.982612 TCATCGCGAAGTTCAGACAG 58.017 50.000 15.24 0.00 0.00 3.51
3710 3915 1.228367 ACAGGGACTTTGCAGCAGG 60.228 57.895 0.00 0.00 34.60 4.85
3712 3917 0.538057 CAGGGACTTTGCAGCAGGAA 60.538 55.000 0.00 0.00 34.60 3.36
3713 3918 0.185901 AGGGACTTTGCAGCAGGAAA 59.814 50.000 0.00 0.00 27.25 3.13
3717 3922 1.408702 GACTTTGCAGCAGGAAAACCA 59.591 47.619 0.00 0.00 34.53 3.67
3796 4001 6.662755 TCATTCATATACCAAGGAAAGCTGT 58.337 36.000 0.00 0.00 0.00 4.40
4060 4269 9.009327 CCATTGAATTTACAACTAAATGCGTAG 57.991 33.333 0.00 0.00 32.22 3.51
4416 4626 3.672255 CTGCATGGCGTTGAAGCGG 62.672 63.158 0.00 0.00 38.18 5.52
4560 4770 1.012486 CGTTGAAGACCGGGTACTGC 61.012 60.000 6.32 1.06 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.103755 AGCAGATCGATCATGCGTGT 59.896 50.000 28.24 17.37 44.64 4.49
109 110 3.768922 GAGAGCCAGCCAGCGAGT 61.769 66.667 0.00 0.00 38.01 4.18
112 113 3.429080 GAGAGAGAGCCAGCCAGCG 62.429 68.421 0.00 0.00 38.01 5.18
115 116 1.752310 CGAGAGAGAGAGCCAGCCA 60.752 63.158 0.00 0.00 0.00 4.75
116 117 1.453015 TCGAGAGAGAGAGCCAGCC 60.453 63.158 0.00 0.00 34.84 4.85
117 118 4.234019 TCGAGAGAGAGAGCCAGC 57.766 61.111 0.00 0.00 34.84 4.85
133 134 2.802787 ACAACCTCCATCGATCGATC 57.197 50.000 27.20 15.68 31.62 3.69
134 135 4.621991 CTTTACAACCTCCATCGATCGAT 58.378 43.478 24.60 24.60 34.81 3.59
167 172 2.713770 GTCGCCATGATGCTGCTG 59.286 61.111 0.00 0.00 0.00 4.41
242 254 0.106569 GATCCCATGTCATGTGCCCA 60.107 55.000 11.84 0.00 0.00 5.36
362 379 2.908796 CTAGCCCGGTCTTTCCCC 59.091 66.667 0.00 0.00 0.00 4.81
446 464 3.217743 GGCTAGGCTAGGTCGCGT 61.218 66.667 22.40 0.00 0.00 6.01
448 466 0.822532 TACTGGCTAGGCTAGGTCGC 60.823 60.000 22.40 9.17 41.48 5.19
449 467 1.240256 CTACTGGCTAGGCTAGGTCG 58.760 60.000 22.40 5.30 41.48 4.79
451 469 3.135027 GCTACTGGCTAGGCTAGGT 57.865 57.895 22.40 14.12 41.48 3.08
520 542 1.444250 GGTGGATCGCCGGTAATCA 59.556 57.895 16.75 2.39 36.79 2.57
521 543 4.355925 GGTGGATCGCCGGTAATC 57.644 61.111 1.90 6.48 36.79 1.75
564 617 4.060205 ACGTGTCGGCAAAAAGTAATAGT 58.940 39.130 0.00 0.00 0.00 2.12
565 618 4.657075 ACGTGTCGGCAAAAAGTAATAG 57.343 40.909 0.00 0.00 0.00 1.73
583 636 0.381089 CGGAGAGCGGAGAATTACGT 59.619 55.000 0.00 0.00 0.00 3.57
702 755 1.163420 TACGCACAACAGCAAGGGTG 61.163 55.000 0.00 0.00 37.06 4.61
743 803 0.533755 GCCTGTCTGTCTGCTTGTGT 60.534 55.000 0.00 0.00 0.00 3.72
744 804 0.533531 TGCCTGTCTGTCTGCTTGTG 60.534 55.000 0.00 0.00 0.00 3.33
745 805 0.250209 CTGCCTGTCTGTCTGCTTGT 60.250 55.000 0.00 0.00 0.00 3.16
801 861 4.507916 CGGGGAGGAGAGGCGAGA 62.508 72.222 0.00 0.00 0.00 4.04
892 966 2.099427 GCTGGCTGGTACTCTGTACTAC 59.901 54.545 7.64 0.00 0.00 2.73
926 1000 3.044059 GCAGCAGGAATGACGGTGC 62.044 63.158 0.00 0.00 45.55 5.01
1050 1127 2.897969 AGAGGCTAAAAGAGACACGGAA 59.102 45.455 0.00 0.00 34.40 4.30
1068 1145 0.814410 TCGATCGACGGAAGGGAGAG 60.814 60.000 15.15 0.00 42.82 3.20
1210 1306 1.374252 GGCAAAGAGAAGCGACGGA 60.374 57.895 0.00 0.00 0.00 4.69
1211 1307 1.355066 GAGGCAAAGAGAAGCGACGG 61.355 60.000 0.00 0.00 0.00 4.79
1212 1308 0.389166 AGAGGCAAAGAGAAGCGACG 60.389 55.000 0.00 0.00 0.00 5.12
1213 1309 1.355005 GAGAGGCAAAGAGAAGCGAC 58.645 55.000 0.00 0.00 0.00 5.19
1218 1314 1.352352 CAAGGGGAGAGGCAAAGAGAA 59.648 52.381 0.00 0.00 0.00 2.87
1223 1319 0.540365 CTTGCAAGGGGAGAGGCAAA 60.540 55.000 19.14 0.00 44.65 3.68
1249 1345 2.432628 GAGTGAACACCGAGGCCG 60.433 66.667 0.00 0.00 0.00 6.13
1250 1346 0.321653 AATGAGTGAACACCGAGGCC 60.322 55.000 0.00 0.00 0.00 5.19
1251 1347 1.197721 CAAATGAGTGAACACCGAGGC 59.802 52.381 1.11 0.00 0.00 4.70
1252 1348 2.224079 CACAAATGAGTGAACACCGAGG 59.776 50.000 1.11 0.00 42.05 4.63
1253 1349 3.130633 TCACAAATGAGTGAACACCGAG 58.869 45.455 1.11 0.00 44.92 4.63
1261 1357 7.514784 AGAATCACAATTCACAAATGAGTGA 57.485 32.000 0.00 0.00 46.12 3.41
1262 1358 7.327761 GGAAGAATCACAATTCACAAATGAGTG 59.672 37.037 1.41 0.00 43.21 3.51
1263 1359 7.232127 AGGAAGAATCACAATTCACAAATGAGT 59.768 33.333 1.41 0.00 43.21 3.41
1264 1360 7.600065 AGGAAGAATCACAATTCACAAATGAG 58.400 34.615 1.41 0.00 43.21 2.90
1265 1361 7.528996 AGGAAGAATCACAATTCACAAATGA 57.471 32.000 1.41 0.00 43.21 2.57
1266 1362 8.597662 AAAGGAAGAATCACAATTCACAAATG 57.402 30.769 1.41 0.00 43.21 2.32
1267 1363 7.874528 GGAAAGGAAGAATCACAATTCACAAAT 59.125 33.333 1.41 0.00 43.21 2.32
1268 1364 7.209475 GGAAAGGAAGAATCACAATTCACAAA 58.791 34.615 1.41 0.00 43.21 2.83
1269 1365 6.239289 GGGAAAGGAAGAATCACAATTCACAA 60.239 38.462 1.41 0.00 43.21 3.33
1270 1366 5.243730 GGGAAAGGAAGAATCACAATTCACA 59.756 40.000 1.41 0.00 43.21 3.58
1271 1367 5.336770 GGGGAAAGGAAGAATCACAATTCAC 60.337 44.000 1.41 0.00 43.21 3.18
1272 1368 4.772100 GGGGAAAGGAAGAATCACAATTCA 59.228 41.667 1.41 0.00 43.21 2.57
1273 1369 4.142381 CGGGGAAAGGAAGAATCACAATTC 60.142 45.833 0.00 0.00 41.43 2.17
1274 1370 3.763897 CGGGGAAAGGAAGAATCACAATT 59.236 43.478 0.00 0.00 0.00 2.32
1275 1371 3.356290 CGGGGAAAGGAAGAATCACAAT 58.644 45.455 0.00 0.00 0.00 2.71
1276 1372 2.790433 CGGGGAAAGGAAGAATCACAA 58.210 47.619 0.00 0.00 0.00 3.33
1277 1373 1.613255 GCGGGGAAAGGAAGAATCACA 60.613 52.381 0.00 0.00 0.00 3.58
1278 1374 1.095600 GCGGGGAAAGGAAGAATCAC 58.904 55.000 0.00 0.00 0.00 3.06
1279 1375 0.392461 CGCGGGGAAAGGAAGAATCA 60.392 55.000 0.00 0.00 0.00 2.57
1280 1376 0.392595 ACGCGGGGAAAGGAAGAATC 60.393 55.000 12.47 0.00 0.00 2.52
1281 1377 0.906775 TACGCGGGGAAAGGAAGAAT 59.093 50.000 12.47 0.00 0.00 2.40
1282 1378 0.906775 ATACGCGGGGAAAGGAAGAA 59.093 50.000 12.47 0.00 0.00 2.52
1283 1379 0.177141 CATACGCGGGGAAAGGAAGA 59.823 55.000 12.47 0.00 0.00 2.87
1284 1380 1.436983 GCATACGCGGGGAAAGGAAG 61.437 60.000 12.47 0.00 0.00 3.46
1297 1393 1.390123 CAACGGAGACACAAGCATACG 59.610 52.381 0.00 0.00 0.00 3.06
1305 1401 2.028484 GGCGTCAACGGAGACACA 59.972 61.111 4.54 0.00 38.43 3.72
1317 1413 0.514255 GGTAAAAGAACACCGGCGTC 59.486 55.000 6.01 0.00 0.00 5.19
1319 1415 1.232119 AAGGTAAAAGAACACCGGCG 58.768 50.000 0.00 0.00 39.94 6.46
1329 1425 9.249457 GATTGGACAGAAAAGAAAAGGTAAAAG 57.751 33.333 0.00 0.00 0.00 2.27
1331 1427 7.563556 AGGATTGGACAGAAAAGAAAAGGTAAA 59.436 33.333 0.00 0.00 0.00 2.01
1332 1428 7.066781 AGGATTGGACAGAAAAGAAAAGGTAA 58.933 34.615 0.00 0.00 0.00 2.85
1334 1430 5.458595 AGGATTGGACAGAAAAGAAAAGGT 58.541 37.500 0.00 0.00 0.00 3.50
1335 1431 5.047731 GGAGGATTGGACAGAAAAGAAAAGG 60.048 44.000 0.00 0.00 0.00 3.11
1336 1432 5.772169 AGGAGGATTGGACAGAAAAGAAAAG 59.228 40.000 0.00 0.00 0.00 2.27
1337 1433 5.536161 CAGGAGGATTGGACAGAAAAGAAAA 59.464 40.000 0.00 0.00 0.00 2.29
1338 1434 5.072741 CAGGAGGATTGGACAGAAAAGAAA 58.927 41.667 0.00 0.00 0.00 2.52
1339 1435 4.655963 CAGGAGGATTGGACAGAAAAGAA 58.344 43.478 0.00 0.00 0.00 2.52
1340 1436 3.560025 GCAGGAGGATTGGACAGAAAAGA 60.560 47.826 0.00 0.00 0.00 2.52
1344 1440 0.620556 GGCAGGAGGATTGGACAGAA 59.379 55.000 0.00 0.00 0.00 3.02
1345 1441 0.252881 AGGCAGGAGGATTGGACAGA 60.253 55.000 0.00 0.00 0.00 3.41
1346 1442 0.107312 CAGGCAGGAGGATTGGACAG 60.107 60.000 0.00 0.00 0.00 3.51
1348 1444 0.329596 AACAGGCAGGAGGATTGGAC 59.670 55.000 0.00 0.00 0.00 4.02
1349 1445 0.620556 GAACAGGCAGGAGGATTGGA 59.379 55.000 0.00 0.00 0.00 3.53
1350 1446 0.745845 CGAACAGGCAGGAGGATTGG 60.746 60.000 0.00 0.00 0.00 3.16
1351 1447 1.372087 GCGAACAGGCAGGAGGATTG 61.372 60.000 0.00 0.00 0.00 2.67
1352 1448 1.078143 GCGAACAGGCAGGAGGATT 60.078 57.895 0.00 0.00 0.00 3.01
1353 1449 1.557269 AAGCGAACAGGCAGGAGGAT 61.557 55.000 0.00 0.00 34.64 3.24
1354 1450 1.768684 AAAGCGAACAGGCAGGAGGA 61.769 55.000 0.00 0.00 34.64 3.71
1355 1451 1.302832 AAAGCGAACAGGCAGGAGG 60.303 57.895 0.00 0.00 34.64 4.30
1363 1459 2.535574 GCTTGGTTTTCAAAGCGAACAG 59.464 45.455 0.00 0.00 39.16 3.16
1396 1492 0.317854 CATGCATGCCATTCTGCTCG 60.318 55.000 14.93 0.00 39.16 5.03
1413 1510 1.115467 CTCTTCAGGTACCGGCTCAT 58.885 55.000 7.24 0.00 0.00 2.90
1414 1511 0.251653 ACTCTTCAGGTACCGGCTCA 60.252 55.000 7.24 0.00 0.00 4.26
1415 1512 0.173708 CACTCTTCAGGTACCGGCTC 59.826 60.000 7.24 0.00 0.00 4.70
1416 1513 1.889530 GCACTCTTCAGGTACCGGCT 61.890 60.000 7.24 0.00 0.00 5.52
1417 1514 1.448013 GCACTCTTCAGGTACCGGC 60.448 63.158 7.24 0.00 0.00 6.13
1428 1525 2.281070 CAGGTGGTGCGCACTCTT 60.281 61.111 36.84 23.76 0.00 2.85
1434 1531 3.807538 CATGCTCAGGTGGTGCGC 61.808 66.667 0.00 0.00 38.83 6.09
1435 1532 3.807538 GCATGCTCAGGTGGTGCG 61.808 66.667 11.37 0.00 38.83 5.34
1436 1533 2.050350 ATGCATGCTCAGGTGGTGC 61.050 57.895 20.33 0.00 36.55 5.01
1437 1534 0.963856 ACATGCATGCTCAGGTGGTG 60.964 55.000 26.53 0.00 29.04 4.17
1438 1535 0.251474 AACATGCATGCTCAGGTGGT 60.251 50.000 26.53 5.83 30.80 4.16
1439 1536 0.172578 CAACATGCATGCTCAGGTGG 59.827 55.000 26.53 0.50 30.80 4.61
1456 1553 4.425180 TGGGTTAGTAAGCTTCACACAA 57.575 40.909 0.00 0.00 0.00 3.33
1457 1554 4.041075 TCATGGGTTAGTAAGCTTCACACA 59.959 41.667 0.00 3.68 0.00 3.72
1458 1555 4.575885 TCATGGGTTAGTAAGCTTCACAC 58.424 43.478 0.00 0.00 0.00 3.82
1459 1556 4.901197 TCATGGGTTAGTAAGCTTCACA 57.099 40.909 0.00 0.00 0.00 3.58
1460 1557 5.351740 GTCTTCATGGGTTAGTAAGCTTCAC 59.648 44.000 0.00 0.00 0.00 3.18
1461 1558 5.012664 TGTCTTCATGGGTTAGTAAGCTTCA 59.987 40.000 0.00 3.17 0.00 3.02
1462 1559 5.488341 TGTCTTCATGGGTTAGTAAGCTTC 58.512 41.667 0.00 0.00 0.00 3.86
1463 1560 5.499004 TGTCTTCATGGGTTAGTAAGCTT 57.501 39.130 11.64 3.48 0.00 3.74
1491 1588 2.359107 TTCAGGCCTGCAGCGAAG 60.359 61.111 28.91 1.31 45.17 3.79
1518 1615 2.186903 CCTGCGCCGTTAGATGGT 59.813 61.111 4.18 0.00 0.00 3.55
1522 1619 1.153449 CATTCCCTGCGCCGTTAGA 60.153 57.895 4.18 0.00 0.00 2.10
1524 1621 2.822255 GCATTCCCTGCGCCGTTA 60.822 61.111 4.18 0.00 41.97 3.18
1532 1629 1.825191 CCATCACCGGCATTCCCTG 60.825 63.158 0.00 0.00 0.00 4.45
1533 1630 2.597340 CCATCACCGGCATTCCCT 59.403 61.111 0.00 0.00 0.00 4.20
1567 1688 1.683365 CATGCTCCCCCAAACCTGG 60.683 63.158 0.00 0.00 43.10 4.45
1640 1761 3.355957 ATGCCAGCCTCTTCCCTGC 62.356 63.158 0.00 0.00 0.00 4.85
1641 1762 1.153005 GATGCCAGCCTCTTCCCTG 60.153 63.158 0.00 0.00 0.00 4.45
1647 1768 4.172512 CTGCCGATGCCAGCCTCT 62.173 66.667 0.00 0.00 36.33 3.69
1674 1795 0.670546 AGCCATGAGACACCGAAACG 60.671 55.000 0.00 0.00 0.00 3.60
1831 1952 6.652481 TGCTATCTGGTACGTAATACTCCTAC 59.348 42.308 0.00 0.00 33.87 3.18
1834 1955 5.954296 TGCTATCTGGTACGTAATACTCC 57.046 43.478 0.00 0.00 33.87 3.85
1835 1956 6.148264 GGTTGCTATCTGGTACGTAATACTC 58.852 44.000 0.00 0.00 33.87 2.59
1836 1957 5.010415 GGGTTGCTATCTGGTACGTAATACT 59.990 44.000 0.00 0.00 33.87 2.12
1837 1958 5.221303 TGGGTTGCTATCTGGTACGTAATAC 60.221 44.000 0.00 0.00 0.00 1.89
1838 1959 4.894705 TGGGTTGCTATCTGGTACGTAATA 59.105 41.667 0.00 0.00 0.00 0.98
1839 1960 3.707611 TGGGTTGCTATCTGGTACGTAAT 59.292 43.478 0.00 0.00 0.00 1.89
1840 1961 3.098377 TGGGTTGCTATCTGGTACGTAA 58.902 45.455 0.00 0.00 0.00 3.18
1841 1962 2.691526 CTGGGTTGCTATCTGGTACGTA 59.308 50.000 0.00 0.00 0.00 3.57
1842 1963 1.480954 CTGGGTTGCTATCTGGTACGT 59.519 52.381 0.00 0.00 0.00 3.57
1843 1964 1.202533 CCTGGGTTGCTATCTGGTACG 60.203 57.143 0.00 0.00 0.00 3.67
1865 1986 7.674772 ACTCTTACATTAGTTTACAGAGGGAGT 59.325 37.037 0.00 0.00 0.00 3.85
1866 1987 7.976734 CACTCTTACATTAGTTTACAGAGGGAG 59.023 40.741 0.00 0.00 0.00 4.30
1867 1988 7.453752 ACACTCTTACATTAGTTTACAGAGGGA 59.546 37.037 2.59 0.00 0.00 4.20
1868 1989 7.612677 ACACTCTTACATTAGTTTACAGAGGG 58.387 38.462 0.00 0.00 0.00 4.30
1869 1990 9.490379 AAACACTCTTACATTAGTTTACAGAGG 57.510 33.333 0.00 0.00 0.00 3.69
1917 2038 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
1918 2039 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
1919 2040 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
1920 2041 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
1921 2042 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1922 2043 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1925 2046 9.592196 ACATACTCCCTCCGTAAACTAATATAA 57.408 33.333 0.00 0.00 0.00 0.98
1926 2047 9.592196 AACATACTCCCTCCGTAAACTAATATA 57.408 33.333 0.00 0.00 0.00 0.86
1927 2048 8.488308 AACATACTCCCTCCGTAAACTAATAT 57.512 34.615 0.00 0.00 0.00 1.28
1928 2049 7.902920 AACATACTCCCTCCGTAAACTAATA 57.097 36.000 0.00 0.00 0.00 0.98
1929 2050 6.803366 AACATACTCCCTCCGTAAACTAAT 57.197 37.500 0.00 0.00 0.00 1.73
1930 2051 7.902920 ATAACATACTCCCTCCGTAAACTAA 57.097 36.000 0.00 0.00 0.00 2.24
1931 2052 7.173218 CGTATAACATACTCCCTCCGTAAACTA 59.827 40.741 0.00 0.00 0.00 2.24
1932 2053 6.016777 CGTATAACATACTCCCTCCGTAAACT 60.017 42.308 0.00 0.00 0.00 2.66
1933 2054 6.145535 CGTATAACATACTCCCTCCGTAAAC 58.854 44.000 0.00 0.00 0.00 2.01
1934 2055 5.241506 CCGTATAACATACTCCCTCCGTAAA 59.758 44.000 0.00 0.00 0.00 2.01
1935 2056 4.761739 CCGTATAACATACTCCCTCCGTAA 59.238 45.833 0.00 0.00 0.00 3.18
1936 2057 4.326826 CCGTATAACATACTCCCTCCGTA 58.673 47.826 0.00 0.00 0.00 4.02
1937 2058 3.152341 CCGTATAACATACTCCCTCCGT 58.848 50.000 0.00 0.00 0.00 4.69
1938 2059 2.490903 CCCGTATAACATACTCCCTCCG 59.509 54.545 0.00 0.00 0.00 4.63
1939 2060 3.504375 ACCCGTATAACATACTCCCTCC 58.496 50.000 0.00 0.00 0.00 4.30
1940 2061 4.586001 TGAACCCGTATAACATACTCCCTC 59.414 45.833 0.00 0.00 0.00 4.30
1941 2062 4.549668 TGAACCCGTATAACATACTCCCT 58.450 43.478 0.00 0.00 0.00 4.20
1942 2063 4.586001 TCTGAACCCGTATAACATACTCCC 59.414 45.833 0.00 0.00 0.00 4.30
1943 2064 5.068198 TGTCTGAACCCGTATAACATACTCC 59.932 44.000 0.00 0.00 0.00 3.85
1944 2065 5.975939 GTGTCTGAACCCGTATAACATACTC 59.024 44.000 0.00 0.00 0.00 2.59
1945 2066 5.655532 AGTGTCTGAACCCGTATAACATACT 59.344 40.000 0.00 0.00 0.00 2.12
1946 2067 5.747197 CAGTGTCTGAACCCGTATAACATAC 59.253 44.000 0.00 0.00 32.44 2.39
1947 2068 5.653330 TCAGTGTCTGAACCCGTATAACATA 59.347 40.000 0.00 0.00 37.57 2.29
2041 2162 1.000163 GAATGCTTCGATCTCGGGCTA 60.000 52.381 15.19 6.57 40.29 3.93
2068 2189 3.749064 GTCCTCCGTCGCTGCTCA 61.749 66.667 0.00 0.00 0.00 4.26
2189 2369 8.988934 TGCGATCATATCCTAAGAACAAATTAC 58.011 33.333 0.00 0.00 0.00 1.89
2214 2394 4.336889 TGGACAGACACTTAGAAGGTTG 57.663 45.455 0.00 0.00 0.00 3.77
2231 2414 3.205784 AGCCTGAAATAGAGCATGGAC 57.794 47.619 0.00 0.00 0.00 4.02
2315 2498 1.998315 CAAGATGCTCTGTGAACCTCG 59.002 52.381 0.00 0.00 0.00 4.63
2324 2507 4.790140 GTGCGAAATTTACAAGATGCTCTG 59.210 41.667 0.00 0.00 0.00 3.35
2326 2509 4.722194 TGTGCGAAATTTACAAGATGCTC 58.278 39.130 0.00 0.00 0.00 4.26
2343 2526 0.603707 AACCTGTGGACTGATGTGCG 60.604 55.000 0.00 0.00 37.34 5.34
2355 2538 7.807907 GGTGTGAATTTTGAAGTATAACCTGTG 59.192 37.037 0.00 0.00 0.00 3.66
2356 2539 7.039993 GGGTGTGAATTTTGAAGTATAACCTGT 60.040 37.037 0.00 0.00 0.00 4.00
2377 2560 5.221461 TGCAATTAAATTGTTTACGGGGTGT 60.221 36.000 0.00 0.00 42.20 4.16
2472 2656 3.253955 GCAGTTGGCATCGACGTT 58.746 55.556 0.00 0.00 43.97 3.99
2518 2709 3.202906 TCTGGTAAAAGCACCGCATATC 58.797 45.455 0.00 0.00 41.88 1.63
2526 2717 5.646606 TGTCTTTGTTTCTGGTAAAAGCAC 58.353 37.500 0.00 0.00 31.20 4.40
2529 2720 5.067805 AGCCTGTCTTTGTTTCTGGTAAAAG 59.932 40.000 0.00 0.00 0.00 2.27
2698 2896 8.795786 TTCACTTCAAAAAGGAATTTATCACG 57.204 30.769 0.00 0.00 36.78 4.35
2716 2914 8.025445 GGCATTGATATATGATGGTTTCACTTC 58.975 37.037 0.00 0.00 37.11 3.01
2724 2922 6.294899 GCACTTTGGCATTGATATATGATGGT 60.295 38.462 0.00 0.00 0.00 3.55
2798 2996 1.419387 CTGATAAGCCTCCTCCTTGGG 59.581 57.143 0.00 0.00 36.20 4.12
2880 3081 2.473816 TGTGTGTTGAAGAGAGAAGCG 58.526 47.619 0.00 0.00 0.00 4.68
2904 3105 1.465354 GCTGTGCTGATTTCTCTTGCG 60.465 52.381 0.00 0.00 0.00 4.85
2928 3129 1.559682 GCTATGTTCTGGGAGGAACCA 59.440 52.381 5.15 0.00 43.31 3.67
3282 3484 5.294552 AGTCAAAGCAGTGTTCAGTTAGTTC 59.705 40.000 0.00 0.00 0.00 3.01
3309 3511 7.771361 TCTTTCAGTTTATGTAACAACCTGTCA 59.229 33.333 0.00 0.00 39.30 3.58
3456 3659 6.762702 TGATCAGTAAACGTAGGTACATCA 57.237 37.500 0.00 0.00 0.00 3.07
3482 3685 4.277672 ACTTTCTAAAGCGAACTTTTCCCC 59.722 41.667 2.37 0.00 43.74 4.81
3545 3750 4.125703 CTGGGTAAATGCTTGCTCTCTAG 58.874 47.826 0.00 0.00 0.00 2.43
3546 3751 3.519510 ACTGGGTAAATGCTTGCTCTCTA 59.480 43.478 0.00 0.00 0.00 2.43
3574 3779 3.133901 TCGGTAGCCTATGAAATGAAGCA 59.866 43.478 0.00 0.00 0.00 3.91
3593 3798 0.955919 GACAGGTTCCTTGCCTTCGG 60.956 60.000 0.00 0.00 33.31 4.30
3603 3808 0.539438 TGGCAACATGGACAGGTTCC 60.539 55.000 0.00 5.61 46.17 3.62
3654 3859 3.483808 TGATTTGCCTAGTGTGTGACA 57.516 42.857 0.00 0.00 0.00 3.58
3658 3863 4.333649 CGATGAATGATTTGCCTAGTGTGT 59.666 41.667 0.00 0.00 0.00 3.72
3660 3865 3.313526 GCGATGAATGATTTGCCTAGTGT 59.686 43.478 0.00 0.00 0.00 3.55
3667 3872 3.056952 ACTTCGCGATGAATGATTTGC 57.943 42.857 26.56 0.00 35.63 3.68
3671 3876 3.553511 GTCTGAACTTCGCGATGAATGAT 59.446 43.478 26.56 8.46 35.63 2.45
3682 3887 2.802816 CAAAGTCCCTGTCTGAACTTCG 59.197 50.000 0.00 0.00 30.99 3.79
3695 3900 1.039856 TTTTCCTGCTGCAAAGTCCC 58.960 50.000 3.02 0.00 0.00 4.46
3710 3915 5.291971 AGAATTGCATCAGTTGTGGTTTTC 58.708 37.500 0.00 0.00 0.00 2.29
3712 3917 4.942761 AGAATTGCATCAGTTGTGGTTT 57.057 36.364 0.00 0.00 0.00 3.27
3713 3918 4.942761 AAGAATTGCATCAGTTGTGGTT 57.057 36.364 0.00 0.00 0.00 3.67
3796 4001 3.939740 ATTCTGCTGCTCTCCCAATAA 57.060 42.857 0.00 0.00 0.00 1.40
4060 4269 6.471519 CAGGTTTAGTATAGTACAGTCGTTGC 59.528 42.308 0.00 0.00 0.00 4.17
4097 4306 6.930164 TCTCCATGTTTCATTGATGTTTTTGG 59.070 34.615 0.00 0.00 0.00 3.28
4114 4323 0.984230 ACACCCGAACATCTCCATGT 59.016 50.000 0.00 0.00 45.89 3.21
4262 4472 1.999071 CTTCCTGCTCGTCTCCCTCG 61.999 65.000 0.00 0.00 0.00 4.63
4416 4626 2.509561 GCCTTCTCCCGCTTCGTC 60.510 66.667 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.