Multiple sequence alignment - TraesCS5B01G231200

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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 TraesCS5B01G231200 chr5B 100.000 2252 0 0 1 2252 407642011 407639760 0.000000e+00 4159
1 TraesCS5B01G231200 chr5B 96.324 136 4 1 1505 1640 107739089 107739223 2.910000e-54 222
2 TraesCS5B01G231200 chr3D 95.971 1514 44 3 1 1504 69660226 69661732 0.000000e+00 2442
3 TraesCS5B01G231200 chr3D 95.588 136 5 1 1505 1640 69661678 69661812 1.350000e-52 217
4 TraesCS5B01G231200 chr6A 95.839 1514 43 6 1 1504 502339089 502340592 0.000000e+00 2429
5 TraesCS5B01G231200 chr7B 95.707 1514 46 5 1 1504 84527063 84528567 0.000000e+00 2418
6 TraesCS5B01G231200 chr7B 95.620 137 5 1 1505 1641 458347673 458347808 3.770000e-53 219
7 TraesCS5B01G231200 chr3A 95.112 1514 56 4 1 1504 681101070 681099565 0.000000e+00 2370
8 TraesCS5B01G231200 chr2B 95.297 1467 52 3 1 1457 137904054 137902595 0.000000e+00 2311
9 TraesCS5B01G231200 chr2B 95.297 1467 52 3 1 1457 137913988 137915447 0.000000e+00 2311
10 TraesCS5B01G231200 chr2B 96.619 1272 26 3 243 1504 717931261 717929997 0.000000e+00 2095
11 TraesCS5B01G231200 chr2B 93.103 145 10 0 1505 1649 717930051 717929907 1.750000e-51 213
12 TraesCS5B01G231200 chr4A 94.320 1514 69 10 1 1504 107232487 107230981 0.000000e+00 2303
13 TraesCS5B01G231200 chr4A 94.078 895 34 4 620 1504 652267991 652267106 0.000000e+00 1341
14 TraesCS5B01G231200 chr6B 93.923 1514 75 3 1 1504 695056450 695057956 0.000000e+00 2270
15 TraesCS5B01G231200 chr6B 95.748 1411 41 5 1 1400 88884751 88886153 0.000000e+00 2255
16 TraesCS5B01G231200 chr6B 92.231 399 15 2 1115 1503 262478729 262478337 3.270000e-153 551
17 TraesCS5B01G231200 chr1A 95.005 1001 34 2 514 1504 493003985 493004979 0.000000e+00 1557
18 TraesCS5B01G231200 chr2A 93.301 821 39 2 693 1503 608610740 608609926 0.000000e+00 1197
19 TraesCS5B01G231200 chr2A 93.714 525 17 3 990 1504 762776021 762775503 0.000000e+00 773
20 TraesCS5B01G231200 chr2A 96.377 138 3 2 1505 1642 762775557 762775422 2.250000e-55 226
21 TraesCS5B01G231200 chr5D 93.524 525 28 3 1734 2252 344427199 344427723 0.000000e+00 776
22 TraesCS5B01G231200 chr5A 91.607 560 35 8 1705 2252 448109129 448109688 0.000000e+00 763
23 TraesCS5B01G231200 chr3B 92.946 482 18 2 1033 1504 476080276 476080751 0.000000e+00 688
24 TraesCS5B01G231200 chrUn 96.350 137 4 1 1505 1641 214936117 214936252 8.090000e-55 224
25 TraesCS5B01G231200 chrUn 96.350 137 4 1 1505 1641 331442366 331442501 8.090000e-55 224
26 TraesCS5B01G231200 chr4B 94.928 138 7 0 1505 1642 9427895 9428032 1.350000e-52 217
27 TraesCS5B01G231200 chr1B 94.964 139 6 1 1505 1642 17752901 17753039 1.350000e-52 217


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 TraesCS5B01G231200 chr5B 407639760 407642011 2251 True 4159.0 4159 100.0000 1 2252 1 chr5B.!!$R1 2251
1 TraesCS5B01G231200 chr3D 69660226 69661812 1586 False 1329.5 2442 95.7795 1 1640 2 chr3D.!!$F1 1639
2 TraesCS5B01G231200 chr6A 502339089 502340592 1503 False 2429.0 2429 95.8390 1 1504 1 chr6A.!!$F1 1503
3 TraesCS5B01G231200 chr7B 84527063 84528567 1504 False 2418.0 2418 95.7070 1 1504 1 chr7B.!!$F1 1503
4 TraesCS5B01G231200 chr3A 681099565 681101070 1505 True 2370.0 2370 95.1120 1 1504 1 chr3A.!!$R1 1503
5 TraesCS5B01G231200 chr2B 137902595 137904054 1459 True 2311.0 2311 95.2970 1 1457 1 chr2B.!!$R1 1456
6 TraesCS5B01G231200 chr2B 137913988 137915447 1459 False 2311.0 2311 95.2970 1 1457 1 chr2B.!!$F1 1456
7 TraesCS5B01G231200 chr2B 717929907 717931261 1354 True 1154.0 2095 94.8610 243 1649 2 chr2B.!!$R2 1406
8 TraesCS5B01G231200 chr4A 107230981 107232487 1506 True 2303.0 2303 94.3200 1 1504 1 chr4A.!!$R1 1503
9 TraesCS5B01G231200 chr4A 652267106 652267991 885 True 1341.0 1341 94.0780 620 1504 1 chr4A.!!$R2 884
10 TraesCS5B01G231200 chr6B 695056450 695057956 1506 False 2270.0 2270 93.9230 1 1504 1 chr6B.!!$F2 1503
11 TraesCS5B01G231200 chr6B 88884751 88886153 1402 False 2255.0 2255 95.7480 1 1400 1 chr6B.!!$F1 1399
12 TraesCS5B01G231200 chr1A 493003985 493004979 994 False 1557.0 1557 95.0050 514 1504 1 chr1A.!!$F1 990
13 TraesCS5B01G231200 chr2A 608609926 608610740 814 True 1197.0 1197 93.3010 693 1503 1 chr2A.!!$R1 810
14 TraesCS5B01G231200 chr2A 762775422 762776021 599 True 499.5 773 95.0455 990 1642 2 chr2A.!!$R2 652
15 TraesCS5B01G231200 chr5D 344427199 344427723 524 False 776.0 776 93.5240 1734 2252 1 chr5D.!!$F1 518
16 TraesCS5B01G231200 chr5A 448109129 448109688 559 False 763.0 763 91.6070 1705 2252 1 chr5A.!!$F1 547

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
116 117 1.271108 TGTGCGTTGATCCTTAAGGCA 60.271 47.619 17.32 7.19 43.88 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1492 1505 0.029834 GCTAGTTCGGGCGTTATCGA 59.97 55.0 0.0 0.0 39.71 3.59 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
116 117 1.271108 TGTGCGTTGATCCTTAAGGCA 60.271 47.619 17.32 7.19 43.88 4.75
138 139 8.006564 AGGCAAAATATTTTCCTGATGGAGATA 58.993 33.333 21.35 0.00 44.24 1.98
140 141 9.635520 GCAAAATATTTTCCTGATGGAGATATG 57.364 33.333 10.53 0.00 44.24 1.78
226 228 3.633525 ACGCTCAGACGTGGGTATATTTA 59.366 43.478 0.00 0.00 46.28 1.40
269 271 7.706674 AGAAAATTAGCATATGGGATGATCCT 58.293 34.615 11.87 0.00 36.57 3.24
662 664 2.300152 CGCTCCAGAATGCTATTCCCTA 59.700 50.000 5.57 0.00 31.97 3.53
952 955 5.417580 GCTTGGTATTTGTGGTATGAAAGGA 59.582 40.000 0.00 0.00 0.00 3.36
969 972 7.528996 TGAAAGGAGAAAATTGACACATGAT 57.471 32.000 0.00 0.00 0.00 2.45
979 982 9.252962 GAAAATTGACACATGATGAAGAAACTT 57.747 29.630 0.00 0.00 0.00 2.66
1224 1227 5.330455 AGATAGACATTTGCTTCGACTCA 57.670 39.130 0.00 0.00 0.00 3.41
1258 1271 5.280654 AGCAATTGTGGTTTGAATCTTGT 57.719 34.783 7.40 0.00 28.67 3.16
1355 1368 3.256879 ACTCTTCTTCAGTCGCTTCATCA 59.743 43.478 0.00 0.00 0.00 3.07
1356 1369 4.081752 ACTCTTCTTCAGTCGCTTCATCAT 60.082 41.667 0.00 0.00 0.00 2.45
1357 1370 4.428209 TCTTCTTCAGTCGCTTCATCATC 58.572 43.478 0.00 0.00 0.00 2.92
1358 1371 3.874392 TCTTCAGTCGCTTCATCATCA 57.126 42.857 0.00 0.00 0.00 3.07
1359 1372 4.397481 TCTTCAGTCGCTTCATCATCAT 57.603 40.909 0.00 0.00 0.00 2.45
1360 1373 4.366586 TCTTCAGTCGCTTCATCATCATC 58.633 43.478 0.00 0.00 0.00 2.92
1486 1499 3.133183 GCTAGGTTTTCTTCTCCGAGGAT 59.867 47.826 0.00 0.00 0.00 3.24
1487 1500 4.383226 GCTAGGTTTTCTTCTCCGAGGATT 60.383 45.833 0.00 0.00 0.00 3.01
1488 1501 4.642466 AGGTTTTCTTCTCCGAGGATTT 57.358 40.909 0.00 0.00 0.00 2.17
1489 1502 4.327680 AGGTTTTCTTCTCCGAGGATTTG 58.672 43.478 0.00 0.00 0.00 2.32
1490 1503 3.440522 GGTTTTCTTCTCCGAGGATTTGG 59.559 47.826 0.00 0.00 0.00 3.28
1491 1504 4.324267 GTTTTCTTCTCCGAGGATTTGGA 58.676 43.478 0.00 0.00 35.48 3.53
1492 1505 4.844349 TTTCTTCTCCGAGGATTTGGAT 57.156 40.909 0.00 0.00 36.26 3.41
1493 1506 4.408182 TTCTTCTCCGAGGATTTGGATC 57.592 45.455 0.00 0.00 36.26 3.36
1494 1507 2.362397 TCTTCTCCGAGGATTTGGATCG 59.638 50.000 0.00 0.00 36.26 3.69
1495 1508 2.067365 TCTCCGAGGATTTGGATCGA 57.933 50.000 0.00 0.00 38.72 3.59
1496 1509 2.598565 TCTCCGAGGATTTGGATCGAT 58.401 47.619 0.00 0.00 38.72 3.59
1497 1510 3.763057 TCTCCGAGGATTTGGATCGATA 58.237 45.455 0.00 0.00 38.72 2.92
1498 1511 4.149598 TCTCCGAGGATTTGGATCGATAA 58.850 43.478 0.00 0.00 38.72 1.75
1499 1512 4.022242 TCTCCGAGGATTTGGATCGATAAC 60.022 45.833 0.00 0.00 38.72 1.89
1500 1513 2.987149 CCGAGGATTTGGATCGATAACG 59.013 50.000 0.00 0.00 38.72 3.18
1501 1514 2.408704 CGAGGATTTGGATCGATAACGC 59.591 50.000 0.00 0.00 38.72 4.84
1502 1515 2.737252 GAGGATTTGGATCGATAACGCC 59.263 50.000 0.00 0.00 39.58 5.68
1503 1516 1.804748 GGATTTGGATCGATAACGCCC 59.195 52.381 0.00 0.00 39.58 6.13
1504 1517 1.459592 GATTTGGATCGATAACGCCCG 59.540 52.381 0.00 0.00 39.58 6.13
1505 1518 0.460722 TTTGGATCGATAACGCCCGA 59.539 50.000 0.00 0.00 39.58 5.14
1506 1519 0.460722 TTGGATCGATAACGCCCGAA 59.539 50.000 0.00 0.00 38.36 4.30
1507 1520 0.249155 TGGATCGATAACGCCCGAAC 60.249 55.000 0.00 0.00 38.36 3.95
1508 1521 0.031721 GGATCGATAACGCCCGAACT 59.968 55.000 0.00 0.00 38.36 3.01
1509 1522 1.267806 GGATCGATAACGCCCGAACTA 59.732 52.381 0.00 0.00 38.36 2.24
1510 1523 2.582687 GATCGATAACGCCCGAACTAG 58.417 52.381 0.00 0.00 38.36 2.57
1511 1524 0.029834 TCGATAACGCCCGAACTAGC 59.970 55.000 0.00 0.00 39.58 3.42
1512 1525 0.248743 CGATAACGCCCGAACTAGCA 60.249 55.000 0.00 0.00 0.00 3.49
1513 1526 1.799917 CGATAACGCCCGAACTAGCAA 60.800 52.381 0.00 0.00 0.00 3.91
1514 1527 1.859080 GATAACGCCCGAACTAGCAAG 59.141 52.381 0.00 0.00 0.00 4.01
1515 1528 0.889994 TAACGCCCGAACTAGCAAGA 59.110 50.000 0.00 0.00 0.00 3.02
1516 1529 0.249398 AACGCCCGAACTAGCAAGAT 59.751 50.000 0.00 0.00 0.00 2.40
1517 1530 0.249398 ACGCCCGAACTAGCAAGATT 59.751 50.000 0.00 0.00 0.00 2.40
1518 1531 1.479323 ACGCCCGAACTAGCAAGATTA 59.521 47.619 0.00 0.00 0.00 1.75
1519 1532 2.128035 CGCCCGAACTAGCAAGATTAG 58.872 52.381 0.00 0.00 0.00 1.73
1520 1533 1.867865 GCCCGAACTAGCAAGATTAGC 59.132 52.381 0.00 0.00 0.00 3.09
1521 1534 2.483889 GCCCGAACTAGCAAGATTAGCT 60.484 50.000 0.00 0.00 45.77 3.32
1522 1535 3.243771 GCCCGAACTAGCAAGATTAGCTA 60.244 47.826 0.00 0.00 43.25 3.32
1532 1545 6.993786 AGCAAGATTAGCTAGGTTTTCTTC 57.006 37.500 13.23 9.87 41.32 2.87
1533 1546 6.716284 AGCAAGATTAGCTAGGTTTTCTTCT 58.284 36.000 13.23 11.27 41.32 2.85
1534 1547 6.821160 AGCAAGATTAGCTAGGTTTTCTTCTC 59.179 38.462 13.23 9.74 41.32 2.87
1535 1548 6.037720 GCAAGATTAGCTAGGTTTTCTTCTCC 59.962 42.308 13.23 5.17 0.00 3.71
1536 1549 5.908341 AGATTAGCTAGGTTTTCTTCTCCG 58.092 41.667 0.00 0.00 0.00 4.63
1537 1550 5.657302 AGATTAGCTAGGTTTTCTTCTCCGA 59.343 40.000 0.00 0.00 0.00 4.55
1538 1551 3.878160 AGCTAGGTTTTCTTCTCCGAG 57.122 47.619 0.00 0.00 0.00 4.63
1539 1552 2.498078 AGCTAGGTTTTCTTCTCCGAGG 59.502 50.000 0.00 0.00 0.00 4.63
1540 1553 2.496470 GCTAGGTTTTCTTCTCCGAGGA 59.504 50.000 0.00 0.00 0.00 3.71
1610 1623 8.682936 AAGGATGCTACTTTACTTATGAATGG 57.317 34.615 0.00 0.00 0.00 3.16
1665 1680 9.971922 AAATATATGAAATAGAACCAGCAAAGC 57.028 29.630 0.00 0.00 28.50 3.51
1666 1681 8.696043 ATATATGAAATAGAACCAGCAAAGCA 57.304 30.769 0.00 0.00 28.50 3.91
1667 1682 4.503741 TGAAATAGAACCAGCAAAGCAC 57.496 40.909 0.00 0.00 0.00 4.40
1668 1683 3.058293 TGAAATAGAACCAGCAAAGCACG 60.058 43.478 0.00 0.00 0.00 5.34
1669 1684 0.804989 ATAGAACCAGCAAAGCACGC 59.195 50.000 0.00 0.00 0.00 5.34
1670 1685 1.234615 TAGAACCAGCAAAGCACGCC 61.235 55.000 0.00 0.00 0.00 5.68
1671 1686 3.879351 GAACCAGCAAAGCACGCCG 62.879 63.158 0.00 0.00 0.00 6.46
1672 1687 4.927782 ACCAGCAAAGCACGCCGA 62.928 61.111 0.00 0.00 0.00 5.54
1673 1688 3.434319 CCAGCAAAGCACGCCGAT 61.434 61.111 0.00 0.00 0.00 4.18
1674 1689 2.106074 CCAGCAAAGCACGCCGATA 61.106 57.895 0.00 0.00 0.00 2.92
1675 1690 1.643868 CCAGCAAAGCACGCCGATAA 61.644 55.000 0.00 0.00 0.00 1.75
1676 1691 0.167908 CAGCAAAGCACGCCGATAAA 59.832 50.000 0.00 0.00 0.00 1.40
1677 1692 0.447801 AGCAAAGCACGCCGATAAAG 59.552 50.000 0.00 0.00 0.00 1.85
1678 1693 1.133946 GCAAAGCACGCCGATAAAGC 61.134 55.000 0.00 0.00 0.00 3.51
1679 1694 0.447801 CAAAGCACGCCGATAAAGCT 59.552 50.000 0.00 0.00 37.08 3.74
1680 1695 0.727398 AAAGCACGCCGATAAAGCTC 59.273 50.000 0.00 0.00 33.83 4.09
1681 1696 0.391130 AAGCACGCCGATAAAGCTCA 60.391 50.000 0.00 0.00 33.83 4.26
1682 1697 0.391130 AGCACGCCGATAAAGCTCAA 60.391 50.000 0.00 0.00 0.00 3.02
1683 1698 0.247695 GCACGCCGATAAAGCTCAAC 60.248 55.000 0.00 0.00 0.00 3.18
1684 1699 1.075542 CACGCCGATAAAGCTCAACA 58.924 50.000 0.00 0.00 0.00 3.33
1685 1700 1.665679 CACGCCGATAAAGCTCAACAT 59.334 47.619 0.00 0.00 0.00 2.71
1686 1701 1.933853 ACGCCGATAAAGCTCAACATC 59.066 47.619 0.00 0.00 0.00 3.06
1687 1702 1.933181 CGCCGATAAAGCTCAACATCA 59.067 47.619 0.00 0.00 0.00 3.07
1688 1703 2.351418 CGCCGATAAAGCTCAACATCAA 59.649 45.455 0.00 0.00 0.00 2.57
1689 1704 3.181511 CGCCGATAAAGCTCAACATCAAA 60.182 43.478 0.00 0.00 0.00 2.69
1690 1705 4.098416 GCCGATAAAGCTCAACATCAAAC 58.902 43.478 0.00 0.00 0.00 2.93
1691 1706 4.142600 GCCGATAAAGCTCAACATCAAACT 60.143 41.667 0.00 0.00 0.00 2.66
1692 1707 5.619981 GCCGATAAAGCTCAACATCAAACTT 60.620 40.000 0.00 0.00 0.00 2.66
1693 1708 6.024049 CCGATAAAGCTCAACATCAAACTTC 58.976 40.000 0.00 0.00 0.00 3.01
1694 1709 6.348458 CCGATAAAGCTCAACATCAAACTTCA 60.348 38.462 0.00 0.00 0.00 3.02
1695 1710 6.521133 CGATAAAGCTCAACATCAAACTTCAC 59.479 38.462 0.00 0.00 0.00 3.18
1696 1711 4.574599 AAGCTCAACATCAAACTTCACC 57.425 40.909 0.00 0.00 0.00 4.02
1697 1712 3.554934 AGCTCAACATCAAACTTCACCA 58.445 40.909 0.00 0.00 0.00 4.17
1698 1713 3.953612 AGCTCAACATCAAACTTCACCAA 59.046 39.130 0.00 0.00 0.00 3.67
1699 1714 4.402155 AGCTCAACATCAAACTTCACCAAA 59.598 37.500 0.00 0.00 0.00 3.28
1700 1715 5.105392 AGCTCAACATCAAACTTCACCAAAA 60.105 36.000 0.00 0.00 0.00 2.44
1701 1716 5.580297 GCTCAACATCAAACTTCACCAAAAA 59.420 36.000 0.00 0.00 0.00 1.94
1746 1761 2.296471 AGGAACACGAACAGAGTACAGG 59.704 50.000 0.00 0.00 0.00 4.00
1761 1776 3.583086 AGTACAGGCAGACACTATGGTTT 59.417 43.478 0.00 0.00 0.00 3.27
1788 1803 7.402054 ACCAAATCTACATCCATCAAGTTACA 58.598 34.615 0.00 0.00 0.00 2.41
1839 1856 2.586425 CCACCGATGAGGCCATTATTT 58.414 47.619 5.01 0.00 46.52 1.40
1840 1857 3.750371 CCACCGATGAGGCCATTATTTA 58.250 45.455 5.01 0.00 46.52 1.40
1891 1909 1.000052 TGAAACTGCACACGGTCGATA 60.000 47.619 0.00 0.00 32.87 2.92
1919 1942 2.776526 ACAGGACCACCAGCCCAA 60.777 61.111 0.00 0.00 38.94 4.12
1930 1953 2.443016 AGCCCAAAAACGGTGCCA 60.443 55.556 0.00 0.00 0.00 4.92
1932 1955 2.028925 CCCAAAAACGGTGCCAGC 59.971 61.111 0.00 0.00 0.00 4.85
1933 1956 2.498056 CCCAAAAACGGTGCCAGCT 61.498 57.895 0.00 0.00 0.00 4.24
1956 1980 1.745141 GCTCATGACAGACCCATGACC 60.745 57.143 0.00 0.00 43.67 4.02
2055 2079 0.174845 CGAGCGGGTAGATGAAACCA 59.825 55.000 0.00 0.00 38.87 3.67
2100 2124 2.076100 CTTATCGGCAGCACAAAGTCA 58.924 47.619 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 228 2.894731 TCTCACCATCACCAACTCTCT 58.105 47.619 0.00 0.00 0.00 3.10
269 271 3.119319 TGTTGGGCTATGAGGTATCCAA 58.881 45.455 0.00 0.00 32.60 3.53
466 468 2.162681 CCCTGACTTTGTCATGTTCCC 58.837 52.381 0.65 0.00 41.94 3.97
547 549 1.168714 GAAGCTCCAGCCGTTGATTT 58.831 50.000 0.00 0.00 43.38 2.17
650 652 6.493115 CAGGATAGATCGATAGGGAATAGCAT 59.507 42.308 0.00 0.00 0.00 3.79
662 664 6.155475 GCTTATTAGCCAGGATAGATCGAT 57.845 41.667 0.00 0.00 41.74 3.59
770 772 1.078759 GAGCATCTTCCACACGTCCG 61.079 60.000 0.00 0.00 0.00 4.79
952 955 8.636213 AGTTTCTTCATCATGTGTCAATTTTCT 58.364 29.630 0.00 0.00 0.00 2.52
969 972 6.735678 TGATATGCGCTTTAAGTTTCTTCA 57.264 33.333 9.73 0.00 0.00 3.02
979 982 8.782144 TGACATATTGATTTGATATGCGCTTTA 58.218 29.630 9.73 0.24 39.82 1.85
1206 1209 4.153117 GTGAATGAGTCGAAGCAAATGTCT 59.847 41.667 0.00 0.00 0.00 3.41
1224 1227 3.305813 CCACAATTGCTTCTGCTGTGAAT 60.306 43.478 5.05 0.00 42.08 2.57
1264 1277 6.811665 CACTTCAATCTTACTACATCCAACGA 59.188 38.462 0.00 0.00 0.00 3.85
1426 1439 3.276857 TGAGCTACTCGATTACGTTCCT 58.723 45.455 0.00 0.00 40.69 3.36
1486 1499 0.460722 TCGGGCGTTATCGATCCAAA 59.539 50.000 0.00 0.00 39.71 3.28
1487 1500 0.460722 TTCGGGCGTTATCGATCCAA 59.539 50.000 0.00 0.00 39.71 3.53
1488 1501 0.249155 GTTCGGGCGTTATCGATCCA 60.249 55.000 0.00 0.00 39.71 3.41
1489 1502 0.031721 AGTTCGGGCGTTATCGATCC 59.968 55.000 0.00 0.00 39.71 3.36
1490 1503 2.582687 CTAGTTCGGGCGTTATCGATC 58.417 52.381 0.00 0.00 39.71 3.69
1491 1504 1.335689 GCTAGTTCGGGCGTTATCGAT 60.336 52.381 2.16 2.16 39.71 3.59
1492 1505 0.029834 GCTAGTTCGGGCGTTATCGA 59.970 55.000 0.00 0.00 39.71 3.59
1493 1506 0.248743 TGCTAGTTCGGGCGTTATCG 60.249 55.000 0.00 0.00 40.37 2.92
1494 1507 1.859080 CTTGCTAGTTCGGGCGTTATC 59.141 52.381 0.00 0.00 0.00 1.75
1495 1508 1.479323 TCTTGCTAGTTCGGGCGTTAT 59.521 47.619 0.00 0.00 0.00 1.89
1496 1509 0.889994 TCTTGCTAGTTCGGGCGTTA 59.110 50.000 0.00 0.00 0.00 3.18
1497 1510 0.249398 ATCTTGCTAGTTCGGGCGTT 59.751 50.000 0.00 0.00 0.00 4.84
1498 1511 0.249398 AATCTTGCTAGTTCGGGCGT 59.751 50.000 0.00 0.00 0.00 5.68
1499 1512 2.128035 CTAATCTTGCTAGTTCGGGCG 58.872 52.381 0.00 0.00 0.00 6.13
1500 1513 1.867865 GCTAATCTTGCTAGTTCGGGC 59.132 52.381 0.00 0.00 0.00 6.13
1501 1514 3.460857 AGCTAATCTTGCTAGTTCGGG 57.539 47.619 0.00 0.00 39.21 5.14
1508 1521 7.852263 AGAAGAAAACCTAGCTAATCTTGCTA 58.148 34.615 0.00 0.00 41.46 3.49
1509 1522 6.716284 AGAAGAAAACCTAGCTAATCTTGCT 58.284 36.000 0.00 0.00 43.79 3.91
1510 1523 6.037720 GGAGAAGAAAACCTAGCTAATCTTGC 59.962 42.308 0.00 0.00 0.00 4.01
1511 1524 6.256757 CGGAGAAGAAAACCTAGCTAATCTTG 59.743 42.308 0.00 0.00 0.00 3.02
1512 1525 6.154706 TCGGAGAAGAAAACCTAGCTAATCTT 59.845 38.462 0.00 0.47 0.00 2.40
1513 1526 5.657302 TCGGAGAAGAAAACCTAGCTAATCT 59.343 40.000 0.00 0.00 0.00 2.40
1514 1527 5.903810 TCGGAGAAGAAAACCTAGCTAATC 58.096 41.667 0.00 0.00 0.00 1.75
1515 1528 5.163395 CCTCGGAGAAGAAAACCTAGCTAAT 60.163 44.000 6.58 0.00 34.09 1.73
1516 1529 4.159879 CCTCGGAGAAGAAAACCTAGCTAA 59.840 45.833 6.58 0.00 34.09 3.09
1517 1530 3.700038 CCTCGGAGAAGAAAACCTAGCTA 59.300 47.826 6.58 0.00 34.09 3.32
1518 1531 2.498078 CCTCGGAGAAGAAAACCTAGCT 59.502 50.000 6.58 0.00 34.09 3.32
1519 1532 2.496470 TCCTCGGAGAAGAAAACCTAGC 59.504 50.000 6.58 0.00 34.09 3.42
1520 1533 5.346181 AATCCTCGGAGAAGAAAACCTAG 57.654 43.478 6.58 0.00 34.09 3.02
1521 1534 5.488341 CAAATCCTCGGAGAAGAAAACCTA 58.512 41.667 6.58 0.00 34.09 3.08
1522 1535 4.327680 CAAATCCTCGGAGAAGAAAACCT 58.672 43.478 6.58 0.00 34.09 3.50
1523 1536 3.440522 CCAAATCCTCGGAGAAGAAAACC 59.559 47.826 6.58 0.00 34.09 3.27
1524 1537 4.324267 TCCAAATCCTCGGAGAAGAAAAC 58.676 43.478 6.58 0.00 34.09 2.43
1525 1538 4.634012 TCCAAATCCTCGGAGAAGAAAA 57.366 40.909 6.58 0.00 34.09 2.29
1526 1539 4.517285 CATCCAAATCCTCGGAGAAGAAA 58.483 43.478 6.58 0.00 34.09 2.52
1527 1540 3.118261 CCATCCAAATCCTCGGAGAAGAA 60.118 47.826 6.58 0.00 34.09 2.52
1528 1541 2.435805 CCATCCAAATCCTCGGAGAAGA 59.564 50.000 6.58 0.00 34.09 2.87
1529 1542 2.435805 TCCATCCAAATCCTCGGAGAAG 59.564 50.000 6.58 0.00 34.09 2.85
1530 1543 2.477245 TCCATCCAAATCCTCGGAGAA 58.523 47.619 6.58 0.00 34.09 2.87
1531 1544 2.174685 TCCATCCAAATCCTCGGAGA 57.825 50.000 6.58 0.00 33.97 3.71
1532 1545 4.319177 GTTATCCATCCAAATCCTCGGAG 58.681 47.826 0.00 0.00 33.97 4.63
1533 1546 3.244078 CGTTATCCATCCAAATCCTCGGA 60.244 47.826 0.00 0.00 35.27 4.55
1534 1547 3.067106 CGTTATCCATCCAAATCCTCGG 58.933 50.000 0.00 0.00 0.00 4.63
1535 1548 2.480419 GCGTTATCCATCCAAATCCTCG 59.520 50.000 0.00 0.00 0.00 4.63
1536 1549 2.814336 GGCGTTATCCATCCAAATCCTC 59.186 50.000 0.00 0.00 0.00 3.71
1537 1550 2.489073 GGGCGTTATCCATCCAAATCCT 60.489 50.000 0.00 0.00 0.00 3.24
1538 1551 1.886542 GGGCGTTATCCATCCAAATCC 59.113 52.381 0.00 0.00 0.00 3.01
1539 1552 1.886542 GGGGCGTTATCCATCCAAATC 59.113 52.381 0.00 0.00 0.00 2.17
1540 1553 1.499007 AGGGGCGTTATCCATCCAAAT 59.501 47.619 0.00 0.00 0.00 2.32
1587 1600 8.854614 ATCCATTCATAAGTAAAGTAGCATCC 57.145 34.615 0.00 0.00 0.00 3.51
1640 1655 9.135189 TGCTTTGCTGGTTCTATTTCATATATT 57.865 29.630 0.00 0.00 0.00 1.28
1641 1656 8.571336 GTGCTTTGCTGGTTCTATTTCATATAT 58.429 33.333 0.00 0.00 0.00 0.86
1645 1660 4.379813 CGTGCTTTGCTGGTTCTATTTCAT 60.380 41.667 0.00 0.00 0.00 2.57
1646 1661 3.058293 CGTGCTTTGCTGGTTCTATTTCA 60.058 43.478 0.00 0.00 0.00 2.69
1647 1662 3.492313 CGTGCTTTGCTGGTTCTATTTC 58.508 45.455 0.00 0.00 0.00 2.17
1648 1663 2.351738 GCGTGCTTTGCTGGTTCTATTT 60.352 45.455 0.00 0.00 0.00 1.40
1649 1664 1.200020 GCGTGCTTTGCTGGTTCTATT 59.800 47.619 0.00 0.00 0.00 1.73
1650 1665 0.804989 GCGTGCTTTGCTGGTTCTAT 59.195 50.000 0.00 0.00 0.00 1.98
1651 1666 1.234615 GGCGTGCTTTGCTGGTTCTA 61.235 55.000 0.00 0.00 0.00 2.10
1652 1667 2.555547 GGCGTGCTTTGCTGGTTCT 61.556 57.895 0.00 0.00 0.00 3.01
1653 1668 2.050077 GGCGTGCTTTGCTGGTTC 60.050 61.111 0.00 0.00 0.00 3.62
1654 1669 3.964875 CGGCGTGCTTTGCTGGTT 61.965 61.111 0.00 0.00 35.04 3.67
1655 1670 2.796483 TATCGGCGTGCTTTGCTGGT 62.796 55.000 6.85 0.71 39.23 4.00
1656 1671 1.643868 TTATCGGCGTGCTTTGCTGG 61.644 55.000 6.85 0.00 39.23 4.85
1657 1672 0.167908 TTTATCGGCGTGCTTTGCTG 59.832 50.000 6.85 0.00 40.13 4.41
1658 1673 0.447801 CTTTATCGGCGTGCTTTGCT 59.552 50.000 6.85 0.00 0.00 3.91
1659 1674 1.133946 GCTTTATCGGCGTGCTTTGC 61.134 55.000 6.85 2.27 0.00 3.68
1660 1675 0.447801 AGCTTTATCGGCGTGCTTTG 59.552 50.000 6.85 0.00 34.52 2.77
1661 1676 0.727398 GAGCTTTATCGGCGTGCTTT 59.273 50.000 6.85 0.00 33.83 3.51
1662 1677 0.391130 TGAGCTTTATCGGCGTGCTT 60.391 50.000 6.85 0.00 33.83 3.91
1663 1678 0.391130 TTGAGCTTTATCGGCGTGCT 60.391 50.000 6.85 10.07 36.63 4.40
1664 1679 0.247695 GTTGAGCTTTATCGGCGTGC 60.248 55.000 6.85 5.19 34.52 5.34
1665 1680 1.075542 TGTTGAGCTTTATCGGCGTG 58.924 50.000 6.85 0.00 34.52 5.34
1666 1681 1.933853 GATGTTGAGCTTTATCGGCGT 59.066 47.619 6.85 0.00 34.52 5.68
1667 1682 1.933181 TGATGTTGAGCTTTATCGGCG 59.067 47.619 0.00 0.00 34.52 6.46
1668 1683 4.098416 GTTTGATGTTGAGCTTTATCGGC 58.902 43.478 0.00 0.00 0.00 5.54
1669 1684 5.551760 AGTTTGATGTTGAGCTTTATCGG 57.448 39.130 0.00 0.00 0.00 4.18
1670 1685 6.521133 GTGAAGTTTGATGTTGAGCTTTATCG 59.479 38.462 0.00 0.00 0.00 2.92
1671 1686 6.803807 GGTGAAGTTTGATGTTGAGCTTTATC 59.196 38.462 0.00 0.00 0.00 1.75
1672 1687 6.265196 TGGTGAAGTTTGATGTTGAGCTTTAT 59.735 34.615 0.00 0.00 0.00 1.40
1673 1688 5.592282 TGGTGAAGTTTGATGTTGAGCTTTA 59.408 36.000 0.00 0.00 0.00 1.85
1674 1689 4.402155 TGGTGAAGTTTGATGTTGAGCTTT 59.598 37.500 0.00 0.00 0.00 3.51
1675 1690 3.953612 TGGTGAAGTTTGATGTTGAGCTT 59.046 39.130 0.00 0.00 0.00 3.74
1676 1691 3.554934 TGGTGAAGTTTGATGTTGAGCT 58.445 40.909 0.00 0.00 0.00 4.09
1677 1692 3.988379 TGGTGAAGTTTGATGTTGAGC 57.012 42.857 0.00 0.00 0.00 4.26
1707 1722 7.330946 CGTGTTCCTTATAGTTTGATGTTGAGA 59.669 37.037 0.00 0.00 0.00 3.27
1710 1725 7.359262 TCGTGTTCCTTATAGTTTGATGTTG 57.641 36.000 0.00 0.00 0.00 3.33
1720 1735 6.849502 TGTACTCTGTTCGTGTTCCTTATAG 58.150 40.000 0.00 0.00 0.00 1.31
1721 1736 6.127814 CCTGTACTCTGTTCGTGTTCCTTATA 60.128 42.308 0.00 0.00 0.00 0.98
1746 1761 2.778299 TGGTCAAACCATAGTGTCTGC 58.222 47.619 0.00 0.00 44.79 4.26
1761 1776 6.065976 ACTTGATGGATGTAGATTTGGTCA 57.934 37.500 0.00 0.00 0.00 4.02
1788 1803 4.383770 CGATTGTGGGGGTAGTACATTTCT 60.384 45.833 2.06 0.00 0.00 2.52
1839 1856 6.772716 GGGACATTCCTGAAGCAGAATAAATA 59.227 38.462 0.00 0.00 36.57 1.40
1840 1857 5.595952 GGGACATTCCTGAAGCAGAATAAAT 59.404 40.000 0.00 0.00 36.57 1.40
1917 1940 0.318107 CTCAGCTGGCACCGTTTTTG 60.318 55.000 15.13 0.00 0.00 2.44
1919 1942 2.555547 GCTCAGCTGGCACCGTTTT 61.556 57.895 15.13 0.00 0.00 2.43
1930 1953 0.536260 GGTCTGTCATGAGCTCAGCT 59.464 55.000 22.96 0.00 43.88 4.24
1932 1955 0.900421 TGGGTCTGTCATGAGCTCAG 59.100 55.000 22.96 13.90 35.11 3.35
1933 1956 1.208776 CATGGGTCTGTCATGAGCTCA 59.791 52.381 20.79 20.79 43.25 4.26
1956 1980 2.048503 GACACGACCACCGGGAAG 60.049 66.667 6.32 0.00 46.66 3.46
2076 2100 2.988010 TTGTGCTGCCGATAAGAGAT 57.012 45.000 0.00 0.00 0.00 2.75
2100 2124 4.181010 ATGAAGGGCGCGCCATCT 62.181 61.111 46.88 34.25 37.98 2.90


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

AutoCloner maintained by Alex Coulton.