Multiple sequence alignment - TraesCS6A01G217500

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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 TraesCS6A01G217500 chr6A 100.000 5344 0 0 1 5344 400119258 400124601 0.000000e+00 9869.0
1 TraesCS6A01G217500 chr6D 97.359 2007 44 1 3347 5344 277671570 277673576 0.000000e+00 3404.0
2 TraesCS6A01G217500 chr6D 96.149 1714 52 2 1634 3347 277669805 277671504 0.000000e+00 2787.0
3 TraesCS6A01G217500 chr6D 92.618 1436 68 16 1 1430 277668392 277669795 0.000000e+00 2030.0
4 TraesCS6A01G217500 chr6D 87.607 234 27 2 3109 3341 2867063 2867295 2.450000e-68 270.0
5 TraesCS6A01G217500 chr6D 84.211 152 18 5 1422 1569 363384205 363384354 5.580000e-30 143.0
6 TraesCS6A01G217500 chr6B 96.605 1826 47 4 3520 5344 439401655 439403466 0.000000e+00 3014.0
7 TraesCS6A01G217500 chr6B 95.727 1334 41 4 1634 2966 439398392 439399710 0.000000e+00 2134.0
8 TraesCS6A01G217500 chr6B 93.056 720 36 8 1 718 439396986 439397693 0.000000e+00 1040.0
9 TraesCS6A01G217500 chr6B 90.774 607 32 8 833 1429 439397794 439398386 0.000000e+00 789.0
10 TraesCS6A01G217500 chr6B 96.684 392 13 0 2956 3347 439399886 439400277 0.000000e+00 652.0
11 TraesCS6A01G217500 chr6B 93.956 182 2 1 3347 3519 439400309 439400490 3.170000e-67 267.0
12 TraesCS6A01G217500 chr4D 89.496 238 23 2 3110 3347 233099226 233098991 3.130000e-77 300.0
13 TraesCS6A01G217500 chrUn 90.625 224 21 0 3110 3333 53802989 53802766 1.130000e-76 298.0
14 TraesCS6A01G217500 chr1A 90.583 223 21 0 3110 3332 181770853 181770631 4.050000e-76 296.0
15 TraesCS6A01G217500 chr1A 93.636 110 3 3 1424 1530 247338854 247338962 1.540000e-35 161.0
16 TraesCS6A01G217500 chr1A 86.301 146 16 4 1428 1569 409855022 409855167 7.170000e-34 156.0
17 TraesCS6A01G217500 chr1D 90.698 215 20 0 3115 3329 178459244 178459030 2.440000e-73 287.0
18 TraesCS6A01G217500 chr1D 92.920 113 4 3 1423 1533 450216789 450216679 1.540000e-35 161.0
19 TraesCS6A01G217500 chr5D 87.137 241 28 1 3110 3347 281028538 281028778 2.450000e-68 270.0
20 TraesCS6A01G217500 chr5D 90.184 163 13 3 401 563 546657083 546657242 5.420000e-50 209.0
21 TraesCS6A01G217500 chr5D 94.495 109 3 2 1424 1530 151671544 151671651 1.190000e-36 165.0
22 TraesCS6A01G217500 chr5D 79.412 170 12 7 1428 1575 429977845 429978013 1.220000e-16 99.0
23 TraesCS6A01G217500 chr3D 87.083 240 25 3 3109 3347 239612381 239612615 3.170000e-67 267.0
24 TraesCS6A01G217500 chr4A 91.946 149 12 0 404 552 622281996 622281848 5.420000e-50 209.0
25 TraesCS6A01G217500 chr5B 91.275 149 13 0 401 549 689858026 689858174 2.520000e-48 204.0
26 TraesCS6A01G217500 chr3B 92.414 145 8 2 1428 1570 752682931 752683074 2.520000e-48 204.0
27 TraesCS6A01G217500 chr3B 84.000 150 22 2 1426 1574 815372927 815372779 5.580000e-30 143.0
28 TraesCS6A01G217500 chr7D 88.356 146 11 5 1429 1569 600508673 600508529 2.560000e-38 171.0
29 TraesCS6A01G217500 chr2B 87.075 147 14 4 1428 1569 757065031 757065177 1.540000e-35 161.0
30 TraesCS6A01G217500 chr2B 79.096 177 10 11 1428 1579 26101921 26101747 4.410000e-16 97.1
31 TraesCS6A01G217500 chr7B 77.841 176 15 8 1428 1581 24997680 24997507 2.650000e-13 87.9


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 TraesCS6A01G217500 chr6A 400119258 400124601 5343 False 9869.000000 9869 100.000000 1 5344 1 chr6A.!!$F1 5343
1 TraesCS6A01G217500 chr6D 277668392 277673576 5184 False 2740.333333 3404 95.375333 1 5344 3 chr6D.!!$F3 5343
2 TraesCS6A01G217500 chr6B 439396986 439403466 6480 False 1316.000000 3014 94.467000 1 5344 6 chr6B.!!$F1 5343


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
775 778 0.034477 GATTGTCCCCACGGTCCAAT 60.034 55.0 0.0 0.0 35.71 3.16 F
815 818 0.035820 GGTCCAAATAGACGTGGCCA 60.036 55.0 0.0 0.0 37.66 5.36 F
2369 2422 0.332632 CCCAGGATGAAAGGAAGGCA 59.667 55.0 0.0 0.0 39.69 4.75 F
2817 2870 0.394938 TCAACGGCTGCAACTCCTTA 59.605 50.0 0.5 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1619 1671 0.034756 TTCCAGTCACATGGTCGTGG 59.965 55.000 0.00 0.00 41.43 4.94 R
2453 2506 0.953727 TGCATTGACTTGTGTGCTCC 59.046 50.000 0.00 0.00 38.37 4.70 R
3366 3671 0.326264 ACTTGGGTGGAGCTCATGAC 59.674 55.000 17.19 8.57 0.00 3.06 R
4621 6100 1.619827 CAAGATTTTGGAGGCTGCCAA 59.380 47.619 22.65 12.50 45.77 4.52 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
68 69 1.745141 GCAGGTAGCCCAGACAATCAG 60.745 57.143 0.00 0.00 37.23 2.90
73 74 3.307762 GGTAGCCCAGACAATCAGAAGTT 60.308 47.826 0.00 0.00 0.00 2.66
94 95 5.604650 AGTTCCTCCAATCTATTCTACCCTG 59.395 44.000 0.00 0.00 0.00 4.45
133 134 6.094881 ACTCAAAACTTCTTCGATTCAAACCA 59.905 34.615 0.00 0.00 0.00 3.67
234 235 4.320421 CGCACAAAATTGAGATGGAACTCA 60.320 41.667 0.00 0.00 43.83 3.41
280 281 3.514777 CAACGAGTGCAGCTTAGGA 57.485 52.632 0.00 0.00 0.00 2.94
312 313 2.290367 TGTCCATCTTCTGCAAAACACG 59.710 45.455 0.00 0.00 0.00 4.49
368 371 4.181578 CGCCTAATCCCGATCGAAATTAT 58.818 43.478 18.66 0.00 0.00 1.28
378 381 4.449068 CCGATCGAAATTATAGCAGCAGTT 59.551 41.667 18.66 0.00 0.00 3.16
381 384 5.484173 TCGAAATTATAGCAGCAGTTTGG 57.516 39.130 0.00 0.00 0.00 3.28
525 528 4.783621 GCGCCCATGAGCTGGTCA 62.784 66.667 12.41 12.41 44.30 4.02
606 609 2.609921 GTTCCGGGAGAAGGGGGT 60.610 66.667 0.00 0.00 34.29 4.95
611 614 2.454941 GGGAGAAGGGGGTGGAGA 59.545 66.667 0.00 0.00 0.00 3.71
671 674 0.402121 GAAGGAAGCTGGAACCTGGT 59.598 55.000 0.00 0.00 34.03 4.00
763 766 2.667137 GATCCGATCGACAGATTGTCC 58.333 52.381 18.66 0.00 44.20 4.02
764 767 0.744874 TCCGATCGACAGATTGTCCC 59.255 55.000 18.66 0.00 44.20 4.46
765 768 0.249489 CCGATCGACAGATTGTCCCC 60.249 60.000 18.66 0.00 44.20 4.81
766 769 0.459899 CGATCGACAGATTGTCCCCA 59.540 55.000 10.26 0.00 44.20 4.96
767 770 1.802880 CGATCGACAGATTGTCCCCAC 60.803 57.143 10.26 0.00 44.20 4.61
768 771 0.175760 ATCGACAGATTGTCCCCACG 59.824 55.000 3.81 0.00 44.20 4.94
769 772 1.447838 CGACAGATTGTCCCCACGG 60.448 63.158 3.81 0.00 44.20 4.94
770 773 1.677552 GACAGATTGTCCCCACGGT 59.322 57.895 0.00 0.00 41.37 4.83
771 774 0.391263 GACAGATTGTCCCCACGGTC 60.391 60.000 0.00 0.00 41.37 4.79
772 775 1.078426 CAGATTGTCCCCACGGTCC 60.078 63.158 0.00 0.00 0.00 4.46
773 776 1.537889 AGATTGTCCCCACGGTCCA 60.538 57.895 0.00 0.00 0.00 4.02
774 777 1.131303 AGATTGTCCCCACGGTCCAA 61.131 55.000 0.00 0.00 0.00 3.53
775 778 0.034477 GATTGTCCCCACGGTCCAAT 60.034 55.000 0.00 0.00 35.71 3.16
776 779 0.407918 ATTGTCCCCACGGTCCAATT 59.592 50.000 0.00 0.00 31.81 2.32
777 780 0.186386 TTGTCCCCACGGTCCAATTT 59.814 50.000 0.00 0.00 0.00 1.82
778 781 0.186386 TGTCCCCACGGTCCAATTTT 59.814 50.000 0.00 0.00 0.00 1.82
779 782 1.334160 GTCCCCACGGTCCAATTTTT 58.666 50.000 0.00 0.00 0.00 1.94
815 818 0.035820 GGTCCAAATAGACGTGGCCA 60.036 55.000 0.00 0.00 37.66 5.36
865 910 2.997897 GGGCTCACGGGACAGAGT 60.998 66.667 0.00 0.00 33.46 3.24
889 934 4.440829 TCCCCAATTGCTCCCGGC 62.441 66.667 0.00 0.00 42.22 6.13
979 1025 4.069232 CTGCAGTCTTCCCGCCGA 62.069 66.667 5.25 0.00 0.00 5.54
981 1027 2.125106 GCAGTCTTCCCGCCGATT 60.125 61.111 0.00 0.00 0.00 3.34
1001 1047 5.567623 CGATTGTTTCCCTATCTCCATCGAT 60.568 44.000 0.00 0.00 0.00 3.59
1056 1107 2.171448 CTCTGATTTCCGGTGGATCCTT 59.829 50.000 14.23 0.00 0.00 3.36
1231 1283 6.412214 TGAGTGATGATCATTGACTCAACAT 58.588 36.000 30.64 10.81 37.51 2.71
1249 1301 4.927978 ACATTTTGTCCATTCGGTTTGA 57.072 36.364 0.00 0.00 0.00 2.69
1252 1304 6.287525 ACATTTTGTCCATTCGGTTTGATTT 58.712 32.000 0.00 0.00 0.00 2.17
1281 1333 6.250104 CGTAGTACTGTAGTTGGAATTTCGTC 59.750 42.308 5.39 0.00 0.00 4.20
1320 1372 5.789574 AGGATTCACACCTATACCCAAAA 57.210 39.130 0.00 0.00 35.84 2.44
1361 1413 2.168728 GGTGTGGGAGTTAGATGAGACC 59.831 54.545 0.00 0.00 0.00 3.85
1403 1455 0.413832 AGACCTAGCCACTCCCAAGA 59.586 55.000 0.00 0.00 0.00 3.02
1432 1484 7.865706 ACATTCTGTTGTTCCAATATACTCC 57.134 36.000 0.00 0.00 0.00 3.85
1433 1485 6.828785 ACATTCTGTTGTTCCAATATACTCCC 59.171 38.462 0.00 0.00 0.00 4.30
1434 1486 6.636454 TTCTGTTGTTCCAATATACTCCCT 57.364 37.500 0.00 0.00 0.00 4.20
1435 1487 6.235231 TCTGTTGTTCCAATATACTCCCTC 57.765 41.667 0.00 0.00 0.00 4.30
1436 1488 5.130477 TCTGTTGTTCCAATATACTCCCTCC 59.870 44.000 0.00 0.00 0.00 4.30
1437 1489 4.141801 TGTTGTTCCAATATACTCCCTCCG 60.142 45.833 0.00 0.00 0.00 4.63
1438 1490 3.649843 TGTTCCAATATACTCCCTCCGT 58.350 45.455 0.00 0.00 0.00 4.69
1439 1491 4.035112 TGTTCCAATATACTCCCTCCGTT 58.965 43.478 0.00 0.00 0.00 4.44
1440 1492 4.100498 TGTTCCAATATACTCCCTCCGTTC 59.900 45.833 0.00 0.00 0.00 3.95
1441 1493 3.236896 TCCAATATACTCCCTCCGTTCC 58.763 50.000 0.00 0.00 0.00 3.62
1442 1494 3.116862 TCCAATATACTCCCTCCGTTCCT 60.117 47.826 0.00 0.00 0.00 3.36
1443 1495 4.106825 TCCAATATACTCCCTCCGTTCCTA 59.893 45.833 0.00 0.00 0.00 2.94
1444 1496 4.836736 CCAATATACTCCCTCCGTTCCTAA 59.163 45.833 0.00 0.00 0.00 2.69
1445 1497 5.306160 CCAATATACTCCCTCCGTTCCTAAA 59.694 44.000 0.00 0.00 0.00 1.85
1446 1498 6.013639 CCAATATACTCCCTCCGTTCCTAAAT 60.014 42.308 0.00 0.00 0.00 1.40
1447 1499 7.179694 CCAATATACTCCCTCCGTTCCTAAATA 59.820 40.741 0.00 0.00 0.00 1.40
1448 1500 8.759782 CAATATACTCCCTCCGTTCCTAAATAT 58.240 37.037 0.00 0.00 0.00 1.28
1451 1503 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1452 1504 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1453 1505 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1454 1506 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1455 1507 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1456 1508 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1457 1509 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
1458 1510 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
1459 1511 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
1460 1512 8.202137 TCCGTTCCTAAATATAAGTCTTTGGAG 58.798 37.037 0.00 0.00 0.00 3.86
1461 1513 8.202137 CCGTTCCTAAATATAAGTCTTTGGAGA 58.798 37.037 0.00 0.00 0.00 3.71
1462 1514 9.250624 CGTTCCTAAATATAAGTCTTTGGAGAG 57.749 37.037 0.00 0.00 31.07 3.20
1478 1530 4.769859 GGAGAGATTCCACTATACCGAC 57.230 50.000 0.00 0.00 46.01 4.79
1479 1531 4.142790 GGAGAGATTCCACTATACCGACA 58.857 47.826 0.00 0.00 46.01 4.35
1480 1532 4.767928 GGAGAGATTCCACTATACCGACAT 59.232 45.833 0.00 0.00 46.01 3.06
1481 1533 5.944599 GGAGAGATTCCACTATACCGACATA 59.055 44.000 0.00 0.00 46.01 2.29
1482 1534 6.127952 GGAGAGATTCCACTATACCGACATAC 60.128 46.154 0.00 0.00 46.01 2.39
1483 1535 5.411977 AGAGATTCCACTATACCGACATACG 59.588 44.000 0.00 0.00 42.18 3.06
1497 1549 4.822107 CGACATACGGAGCAAAATAAGTG 58.178 43.478 0.00 0.00 38.46 3.16
1498 1550 4.565166 CGACATACGGAGCAAAATAAGTGA 59.435 41.667 0.00 0.00 38.46 3.41
1499 1551 5.062934 CGACATACGGAGCAAAATAAGTGAA 59.937 40.000 0.00 0.00 38.46 3.18
1500 1552 6.401688 CGACATACGGAGCAAAATAAGTGAAA 60.402 38.462 0.00 0.00 38.46 2.69
1501 1553 6.608610 ACATACGGAGCAAAATAAGTGAAAC 58.391 36.000 0.00 0.00 0.00 2.78
1558 1610 9.924650 TCTCTACAAAGACTTACATTTAGGAAC 57.075 33.333 0.00 0.00 0.00 3.62
1559 1611 8.752766 TCTACAAAGACTTACATTTAGGAACG 57.247 34.615 0.00 0.00 0.00 3.95
1560 1612 6.796705 ACAAAGACTTACATTTAGGAACGG 57.203 37.500 0.00 0.00 0.00 4.44
1561 1613 6.527423 ACAAAGACTTACATTTAGGAACGGA 58.473 36.000 0.00 0.00 0.00 4.69
1562 1614 6.649557 ACAAAGACTTACATTTAGGAACGGAG 59.350 38.462 0.00 0.00 0.00 4.63
1563 1615 5.340439 AGACTTACATTTAGGAACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
1564 1616 4.161754 AGACTTACATTTAGGAACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
1565 1617 4.098894 ACTTACATTTAGGAACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
1566 1618 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
1567 1619 2.547990 ACATTTAGGAACGGAGGGAGT 58.452 47.619 0.00 0.00 0.00 3.85
1568 1620 3.716431 ACATTTAGGAACGGAGGGAGTA 58.284 45.455 0.00 0.00 0.00 2.59
1569 1621 3.705072 ACATTTAGGAACGGAGGGAGTAG 59.295 47.826 0.00 0.00 0.00 2.57
1570 1622 3.463048 TTTAGGAACGGAGGGAGTAGT 57.537 47.619 0.00 0.00 0.00 2.73
1571 1623 3.463048 TTAGGAACGGAGGGAGTAGTT 57.537 47.619 0.00 0.00 0.00 2.24
1572 1624 4.591321 TTAGGAACGGAGGGAGTAGTTA 57.409 45.455 0.00 0.00 0.00 2.24
1573 1625 2.732763 AGGAACGGAGGGAGTAGTTAC 58.267 52.381 0.00 0.00 0.00 2.50
1574 1626 2.311243 AGGAACGGAGGGAGTAGTTACT 59.689 50.000 0.00 0.00 39.71 2.24
1587 1639 5.078411 AGTAGTTACTCATGGCAAGACTG 57.922 43.478 0.00 0.00 0.00 3.51
1588 1640 3.340814 AGTTACTCATGGCAAGACTGG 57.659 47.619 0.00 0.00 0.00 4.00
1589 1641 2.639839 AGTTACTCATGGCAAGACTGGT 59.360 45.455 0.00 0.00 0.00 4.00
1590 1642 3.838317 AGTTACTCATGGCAAGACTGGTA 59.162 43.478 0.00 0.00 0.00 3.25
1591 1643 4.081420 AGTTACTCATGGCAAGACTGGTAG 60.081 45.833 0.00 0.00 0.00 3.18
1592 1644 2.540383 ACTCATGGCAAGACTGGTAGA 58.460 47.619 0.00 0.00 0.00 2.59
1593 1645 2.499289 ACTCATGGCAAGACTGGTAGAG 59.501 50.000 0.00 0.00 0.00 2.43
1594 1646 2.762887 CTCATGGCAAGACTGGTAGAGA 59.237 50.000 0.00 0.00 0.00 3.10
1595 1647 3.378512 TCATGGCAAGACTGGTAGAGAT 58.621 45.455 0.00 0.00 0.00 2.75
1596 1648 3.133542 TCATGGCAAGACTGGTAGAGATG 59.866 47.826 0.00 0.00 0.00 2.90
1597 1649 2.540383 TGGCAAGACTGGTAGAGATGT 58.460 47.619 0.00 0.00 0.00 3.06
1598 1650 2.497675 TGGCAAGACTGGTAGAGATGTC 59.502 50.000 0.00 0.00 0.00 3.06
1599 1651 2.159028 GGCAAGACTGGTAGAGATGTCC 60.159 54.545 0.00 0.00 0.00 4.02
1600 1652 2.159028 GCAAGACTGGTAGAGATGTCCC 60.159 54.545 0.00 0.00 0.00 4.46
1601 1653 3.370104 CAAGACTGGTAGAGATGTCCCT 58.630 50.000 0.00 0.00 0.00 4.20
1602 1654 3.767309 AGACTGGTAGAGATGTCCCTT 57.233 47.619 0.00 0.00 0.00 3.95
1603 1655 3.637769 AGACTGGTAGAGATGTCCCTTC 58.362 50.000 0.00 0.00 0.00 3.46
1604 1656 2.696187 GACTGGTAGAGATGTCCCTTCC 59.304 54.545 0.00 0.00 0.00 3.46
1605 1657 1.683917 CTGGTAGAGATGTCCCTTCCG 59.316 57.143 0.00 0.00 0.00 4.30
1606 1658 1.041437 GGTAGAGATGTCCCTTCCGG 58.959 60.000 0.00 0.00 0.00 5.14
1615 1667 2.040254 CCCTTCCGGGTGGGGATA 60.040 66.667 20.65 0.00 46.12 2.59
1616 1668 2.449450 CCCTTCCGGGTGGGGATAC 61.449 68.421 20.65 0.00 46.12 2.24
1617 1669 1.691337 CCTTCCGGGTGGGGATACA 60.691 63.158 0.00 0.00 35.62 2.29
1618 1670 1.060163 CCTTCCGGGTGGGGATACAT 61.060 60.000 0.00 0.00 35.62 2.29
1619 1671 0.396811 CTTCCGGGTGGGGATACATC 59.603 60.000 0.00 0.00 35.62 3.06
1620 1672 1.057851 TTCCGGGTGGGGATACATCC 61.058 60.000 0.00 0.00 46.41 3.51
1630 1682 2.910688 GGATACATCCACGACCATGT 57.089 50.000 3.26 0.00 46.38 3.21
1631 1683 2.483876 GGATACATCCACGACCATGTG 58.516 52.381 3.26 0.00 46.38 3.21
1632 1684 2.102420 GGATACATCCACGACCATGTGA 59.898 50.000 3.26 0.00 46.38 3.58
1653 1705 7.722363 TGTGACTGGAAATAAGCTAATCGATA 58.278 34.615 0.00 0.00 0.00 2.92
1668 1720 8.556194 AGCTAATCGATATTAAATCGTGCAAAA 58.444 29.630 0.00 0.00 41.77 2.44
1771 1824 4.932200 GGATCTTAGATTGCATTAGGGTCG 59.068 45.833 0.00 0.00 0.00 4.79
1825 1878 5.109903 ACACCTAATAGATCGCTTCACAAC 58.890 41.667 0.00 0.00 0.00 3.32
1828 1881 6.923508 CACCTAATAGATCGCTTCACAACATA 59.076 38.462 0.00 0.00 0.00 2.29
1896 1949 3.006940 GGATGCCGTTGTACTGATTCAA 58.993 45.455 0.00 0.00 0.00 2.69
1897 1950 3.181510 GGATGCCGTTGTACTGATTCAAC 60.182 47.826 0.00 0.00 40.02 3.18
1898 1951 2.147958 TGCCGTTGTACTGATTCAACC 58.852 47.619 0.00 0.00 40.22 3.77
1899 1952 2.147958 GCCGTTGTACTGATTCAACCA 58.852 47.619 0.00 0.00 40.22 3.67
1900 1953 2.747446 GCCGTTGTACTGATTCAACCAT 59.253 45.455 0.00 0.00 40.22 3.55
1901 1954 3.936453 GCCGTTGTACTGATTCAACCATA 59.064 43.478 0.00 0.00 40.22 2.74
1902 1955 4.201783 GCCGTTGTACTGATTCAACCATAC 60.202 45.833 0.00 0.00 40.22 2.39
1903 1956 5.175859 CCGTTGTACTGATTCAACCATACT 58.824 41.667 0.00 0.00 40.22 2.12
1904 1957 5.063438 CCGTTGTACTGATTCAACCATACTG 59.937 44.000 0.00 0.00 40.22 2.74
1905 1958 5.445939 CGTTGTACTGATTCAACCATACTGC 60.446 44.000 0.00 0.00 40.22 4.40
1906 1959 5.420725 TGTACTGATTCAACCATACTGCT 57.579 39.130 0.00 0.00 0.00 4.24
1907 1960 5.804639 TGTACTGATTCAACCATACTGCTT 58.195 37.500 0.00 0.00 0.00 3.91
1908 1961 5.643348 TGTACTGATTCAACCATACTGCTTG 59.357 40.000 0.00 0.00 0.00 4.01
1939 1992 2.285977 GGACAACCTTGAGAACACGTT 58.714 47.619 0.00 0.00 0.00 3.99
1989 2042 6.015519 GTGCAATCTATCTGACATAGAGGTCT 60.016 42.308 0.00 0.00 39.20 3.85
2099 2152 4.406972 TCTGTAGCTATTGGCATGAAGACT 59.593 41.667 0.00 0.00 44.79 3.24
2163 2216 1.002430 GCGAATCTATGGATGGAGGCA 59.998 52.381 0.00 0.00 31.75 4.75
2234 2287 3.956848 TCCTGTCAGACTTGATCGATGAT 59.043 43.478 0.54 0.00 35.39 2.45
2306 2359 1.207593 CGAAAGCCGCCTGAACAAG 59.792 57.895 0.00 0.00 0.00 3.16
2369 2422 0.332632 CCCAGGATGAAAGGAAGGCA 59.667 55.000 0.00 0.00 39.69 4.75
2410 2463 5.012664 TGGAGAACATAGACAGTAAAGGCAA 59.987 40.000 0.00 0.00 0.00 4.52
2453 2506 2.064762 GACATGCCAGATAAGCTAGCG 58.935 52.381 9.55 0.00 33.62 4.26
2522 2575 3.338249 TGGATGTGTAGCTTCTTTCTGC 58.662 45.455 0.00 0.00 0.00 4.26
2534 2587 5.178996 AGCTTCTTTCTGCGCTATTCATATG 59.821 40.000 9.73 0.00 0.00 1.78
2542 2595 3.058983 TGCGCTATTCATATGGAAAAGCG 60.059 43.478 27.57 27.57 44.60 4.68
2782 2835 4.200092 GGGATTACAAGACAGGGTGATTC 58.800 47.826 0.00 0.00 0.00 2.52
2794 2847 7.275920 AGACAGGGTGATTCTGTTAATGATAC 58.724 38.462 0.00 0.00 44.51 2.24
2817 2870 0.394938 TCAACGGCTGCAACTCCTTA 59.605 50.000 0.50 0.00 0.00 2.69
2902 2955 7.770433 TGAATGGAGGTGATCATTAGTAGTTTG 59.230 37.037 0.00 0.00 34.18 2.93
2933 2986 3.745975 ACGCGAAGTCATTTCTCAATTCA 59.254 39.130 15.93 0.00 33.44 2.57
3141 3380 5.414765 CCCGGCTTAATAGGAATGATAAACC 59.585 44.000 0.00 0.00 0.00 3.27
3366 3671 6.477033 CCAGGACTTCTACGAAATTCACTATG 59.523 42.308 0.00 0.00 0.00 2.23
3491 3805 0.403271 AAGTGGCCTGATTGCAGAGT 59.597 50.000 3.32 0.00 45.17 3.24
3524 5002 7.627293 ACCATAATATCCAATGTTTTTCCCCTT 59.373 33.333 0.00 0.00 0.00 3.95
3540 5018 3.639561 TCCCCTTGGTTTTGTCTTAAAGC 59.360 43.478 0.00 0.00 36.36 3.51
3617 5095 4.398044 ACGCACTATCCAAAATAAACCTGG 59.602 41.667 0.00 0.00 0.00 4.45
3840 5318 7.148255 TGTCAATCTTATTACAGGTGCAATCAC 60.148 37.037 0.00 0.00 42.40 3.06
3859 5337 2.342648 GAACGAACTCGCTGGGGT 59.657 61.111 0.00 0.00 44.43 4.95
3882 5360 1.366319 AGATGTCAAGGCCCTCACTT 58.634 50.000 0.00 0.00 0.00 3.16
4049 5527 1.838112 ACCAGGTGGCATACATTGTG 58.162 50.000 0.00 0.00 39.32 3.33
4261 5739 5.540911 TCATCTGCCATTTCCTTTTTGTTC 58.459 37.500 0.00 0.00 0.00 3.18
4262 5740 5.070180 TCATCTGCCATTTCCTTTTTGTTCA 59.930 36.000 0.00 0.00 0.00 3.18
4310 5789 6.316140 CACAGTAATATGCTACTTTGCAGGAA 59.684 38.462 0.00 0.00 46.71 3.36
4363 5842 0.040514 TCGGAAGCATTTTGTGTGCG 60.041 50.000 0.00 0.00 46.86 5.34
4398 5877 4.695396 TGTAGGTCGTTTTAACAGCAAGA 58.305 39.130 0.00 0.00 0.00 3.02
4507 5986 7.775397 AATTTTGCAAATATGTCCTGTATGC 57.225 32.000 13.65 0.00 0.00 3.14
4515 5994 2.908688 TGTCCTGTATGCATGCGTAT 57.091 45.000 21.99 9.26 0.00 3.06
4621 6100 3.544684 TCAGCTTTGACGGCATAATCAT 58.455 40.909 0.00 0.00 0.00 2.45
4662 6141 3.388024 TGCAAACTTCTCTCCTGTACTGT 59.612 43.478 0.00 0.00 0.00 3.55
4750 6229 8.658499 ACAGTTTCCATTTACCTATATCGTTC 57.342 34.615 0.00 0.00 0.00 3.95
4925 6404 7.801716 TTGATCCCTTTAATCTGAATTACGG 57.198 36.000 0.00 0.00 0.00 4.02
5010 6489 9.569122 GGTTAGAATCCTAAACTATGCCATTTA 57.431 33.333 0.00 0.00 39.05 1.40
5084 6563 9.178758 GAGACCTTAAAATGAACAAGATGGTAT 57.821 33.333 0.00 0.00 0.00 2.73
5191 6670 8.453320 ACAAAGTTAAATGTAGTATTTACCCGC 58.547 33.333 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 3.604582 GAGGAACTTCTGATTGTCTGGG 58.395 50.000 0.00 0.00 41.55 4.45
68 69 6.327887 AGGGTAGAATAGATTGGAGGAACTTC 59.672 42.308 0.00 0.00 41.55 3.01
73 74 5.148502 GTCAGGGTAGAATAGATTGGAGGA 58.851 45.833 0.00 0.00 0.00 3.71
94 95 0.032130 TTGAGTGCTCGTGTGAGGTC 59.968 55.000 0.00 0.00 42.79 3.85
133 134 7.037586 TCAGTTTATTTCCCCTTCTCATAGTGT 60.038 37.037 0.00 0.00 0.00 3.55
265 266 1.073216 CGTGTCCTAAGCTGCACTCG 61.073 60.000 1.02 0.00 0.00 4.18
268 269 1.014564 GTCCGTGTCCTAAGCTGCAC 61.015 60.000 1.02 0.00 0.00 4.57
312 313 7.388290 TCGCTGATATGTTTTTGTTTTGTTC 57.612 32.000 0.00 0.00 0.00 3.18
378 381 1.270839 CGTTTCCTCTTCTCCAGCCAA 60.271 52.381 0.00 0.00 0.00 4.52
381 384 0.320771 TGCGTTTCCTCTTCTCCAGC 60.321 55.000 0.00 0.00 0.00 4.85
383 386 0.319555 CGTGCGTTTCCTCTTCTCCA 60.320 55.000 0.00 0.00 0.00 3.86
385 388 0.319641 ACCGTGCGTTTCCTCTTCTC 60.320 55.000 0.00 0.00 0.00 2.87
525 528 2.439156 GCCATCCGGAAGCAGCTT 60.439 61.111 21.49 7.60 0.00 3.74
606 609 1.070786 GCCACCGAAACAGTCTCCA 59.929 57.895 0.00 0.00 0.00 3.86
611 614 0.319083 TATCACGCCACCGAAACAGT 59.681 50.000 0.00 0.00 38.29 3.55
643 646 1.475403 CAGCTTCCTTCGTCCTCCTA 58.525 55.000 0.00 0.00 0.00 2.94
648 651 0.673956 GGTTCCAGCTTCCTTCGTCC 60.674 60.000 0.00 0.00 0.00 4.79
671 674 1.630369 CATCCAGGACCTTCCAGAACA 59.370 52.381 0.00 0.00 39.61 3.18
760 763 1.334160 AAAAATTGGACCGTGGGGAC 58.666 50.000 0.00 0.00 36.97 4.46
761 764 3.852558 AAAAATTGGACCGTGGGGA 57.147 47.368 0.00 0.00 36.97 4.81
777 780 5.163141 TGGACCATGTGGACTCTTCTAAAAA 60.163 40.000 5.96 0.00 38.94 1.94
778 781 4.349636 TGGACCATGTGGACTCTTCTAAAA 59.650 41.667 5.96 0.00 38.94 1.52
779 782 3.907474 TGGACCATGTGGACTCTTCTAAA 59.093 43.478 5.96 0.00 38.94 1.85
780 783 3.516586 TGGACCATGTGGACTCTTCTAA 58.483 45.455 5.96 0.00 38.94 2.10
781 784 3.184382 TGGACCATGTGGACTCTTCTA 57.816 47.619 5.96 0.00 38.94 2.10
782 785 2.030027 TGGACCATGTGGACTCTTCT 57.970 50.000 5.96 0.00 38.94 2.85
783 786 2.859165 TTGGACCATGTGGACTCTTC 57.141 50.000 5.96 0.00 38.94 2.87
784 787 3.814504 ATTTGGACCATGTGGACTCTT 57.185 42.857 5.96 0.00 38.94 2.85
785 788 4.080863 GTCTATTTGGACCATGTGGACTCT 60.081 45.833 5.96 0.00 38.94 3.24
786 789 4.192317 GTCTATTTGGACCATGTGGACTC 58.808 47.826 5.96 0.00 38.94 3.36
787 790 3.369471 CGTCTATTTGGACCATGTGGACT 60.369 47.826 16.08 0.00 38.94 3.85
795 798 0.035820 GGCCACGTCTATTTGGACCA 60.036 55.000 0.00 0.00 34.39 4.02
979 1025 5.555017 CATCGATGGAGATAGGGAAACAAT 58.445 41.667 17.96 0.00 0.00 2.71
981 1027 4.607293 CATCGATGGAGATAGGGAAACA 57.393 45.455 17.96 0.00 0.00 2.83
1021 1072 2.550830 TCAGAGGCAAAAGTCCACTC 57.449 50.000 0.00 0.00 0.00 3.51
1022 1073 3.515602 AATCAGAGGCAAAAGTCCACT 57.484 42.857 0.00 0.00 0.00 4.00
1136 1187 6.871562 CATTCGATGCTCTTAACACTACATC 58.128 40.000 0.00 0.00 0.00 3.06
1231 1283 5.007136 GCAAAATCAAACCGAATGGACAAAA 59.993 36.000 0.00 0.00 39.21 2.44
1249 1301 4.933400 CCAACTACAGTACTACGGCAAAAT 59.067 41.667 0.00 0.00 0.00 1.82
1252 1304 3.156293 TCCAACTACAGTACTACGGCAA 58.844 45.455 0.00 0.00 0.00 4.52
1290 1342 6.325286 GGTATAGGTGTGAATCCTTTCTCTCT 59.675 42.308 0.00 0.00 36.60 3.10
1291 1343 6.463190 GGGTATAGGTGTGAATCCTTTCTCTC 60.463 46.154 0.00 0.00 36.60 3.20
1292 1344 5.367060 GGGTATAGGTGTGAATCCTTTCTCT 59.633 44.000 0.00 0.00 36.60 3.10
1293 1345 5.130477 TGGGTATAGGTGTGAATCCTTTCTC 59.870 44.000 0.00 0.00 36.60 2.87
1294 1346 5.036916 TGGGTATAGGTGTGAATCCTTTCT 58.963 41.667 0.00 0.00 36.60 2.52
1295 1347 5.367945 TGGGTATAGGTGTGAATCCTTTC 57.632 43.478 0.00 0.00 36.60 2.62
1296 1348 5.789574 TTGGGTATAGGTGTGAATCCTTT 57.210 39.130 0.00 0.00 36.60 3.11
1297 1349 5.789574 TTTGGGTATAGGTGTGAATCCTT 57.210 39.130 0.00 0.00 36.60 3.36
1320 1372 5.880332 ACACCGTTGTATTTTATGCTGAGAT 59.120 36.000 0.00 0.00 32.60 2.75
1336 1388 2.028476 TCATCTAACTCCCACACCGTTG 60.028 50.000 0.00 0.00 0.00 4.10
1430 1482 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
1431 1483 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
1432 1484 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
1433 1485 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
1434 1486 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
1435 1487 8.202137 TCTCCAAAGACTTATATTTAGGAACGG 58.798 37.037 0.00 0.00 0.00 4.44
1436 1488 9.250624 CTCTCCAAAGACTTATATTTAGGAACG 57.749 37.037 0.00 0.00 0.00 3.95
1457 1509 4.142790 TGTCGGTATAGTGGAATCTCTCC 58.857 47.826 0.00 0.00 45.64 3.71
1458 1510 5.968528 ATGTCGGTATAGTGGAATCTCTC 57.031 43.478 0.00 0.00 0.00 3.20
1459 1511 5.411977 CGTATGTCGGTATAGTGGAATCTCT 59.588 44.000 0.00 0.00 35.71 3.10
1460 1512 5.629097 CGTATGTCGGTATAGTGGAATCTC 58.371 45.833 0.00 0.00 35.71 2.75
1461 1513 5.624344 CGTATGTCGGTATAGTGGAATCT 57.376 43.478 0.00 0.00 35.71 2.40
1475 1527 4.565166 TCACTTATTTTGCTCCGTATGTCG 59.435 41.667 0.00 0.00 39.52 4.35
1476 1528 6.417191 TTCACTTATTTTGCTCCGTATGTC 57.583 37.500 0.00 0.00 0.00 3.06
1477 1529 6.430000 AGTTTCACTTATTTTGCTCCGTATGT 59.570 34.615 0.00 0.00 0.00 2.29
1478 1530 6.842163 AGTTTCACTTATTTTGCTCCGTATG 58.158 36.000 0.00 0.00 0.00 2.39
1479 1531 8.732746 ATAGTTTCACTTATTTTGCTCCGTAT 57.267 30.769 0.00 0.00 0.00 3.06
1480 1532 9.090692 GTATAGTTTCACTTATTTTGCTCCGTA 57.909 33.333 0.00 0.00 0.00 4.02
1481 1533 7.822822 AGTATAGTTTCACTTATTTTGCTCCGT 59.177 33.333 0.00 0.00 0.00 4.69
1482 1534 8.197988 AGTATAGTTTCACTTATTTTGCTCCG 57.802 34.615 0.00 0.00 0.00 4.63
1483 1535 9.384764 AGAGTATAGTTTCACTTATTTTGCTCC 57.615 33.333 0.00 0.00 0.00 4.70
1532 1584 9.924650 GTTCCTAAATGTAAGTCTTTGTAGAGA 57.075 33.333 0.00 0.00 0.00 3.10
1533 1585 8.861101 CGTTCCTAAATGTAAGTCTTTGTAGAG 58.139 37.037 0.00 0.00 0.00 2.43
1534 1586 7.816031 CCGTTCCTAAATGTAAGTCTTTGTAGA 59.184 37.037 0.00 0.00 0.00 2.59
1535 1587 7.816031 TCCGTTCCTAAATGTAAGTCTTTGTAG 59.184 37.037 0.00 0.00 0.00 2.74
1536 1588 7.669427 TCCGTTCCTAAATGTAAGTCTTTGTA 58.331 34.615 0.00 0.00 0.00 2.41
1537 1589 6.527423 TCCGTTCCTAAATGTAAGTCTTTGT 58.473 36.000 0.00 0.00 0.00 2.83
1538 1590 6.092259 CCTCCGTTCCTAAATGTAAGTCTTTG 59.908 42.308 0.00 0.00 0.00 2.77
1539 1591 6.171213 CCTCCGTTCCTAAATGTAAGTCTTT 58.829 40.000 0.00 0.00 0.00 2.52
1540 1592 5.338137 CCCTCCGTTCCTAAATGTAAGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
1541 1593 4.161754 CCCTCCGTTCCTAAATGTAAGTCT 59.838 45.833 0.00 0.00 0.00 3.24
1542 1594 4.161001 TCCCTCCGTTCCTAAATGTAAGTC 59.839 45.833 0.00 0.00 0.00 3.01
1543 1595 4.098894 TCCCTCCGTTCCTAAATGTAAGT 58.901 43.478 0.00 0.00 0.00 2.24
1544 1596 4.161754 ACTCCCTCCGTTCCTAAATGTAAG 59.838 45.833 0.00 0.00 0.00 2.34
1545 1597 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
1546 1598 3.716431 ACTCCCTCCGTTCCTAAATGTA 58.284 45.455 0.00 0.00 0.00 2.29
1547 1599 2.547990 ACTCCCTCCGTTCCTAAATGT 58.452 47.619 0.00 0.00 0.00 2.71
1548 1600 3.705072 ACTACTCCCTCCGTTCCTAAATG 59.295 47.826 0.00 0.00 0.00 2.32
1549 1601 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1550 1602 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1551 1603 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
1552 1604 3.525199 AGTAACTACTCCCTCCGTTCCTA 59.475 47.826 0.00 0.00 0.00 2.94
1553 1605 2.311243 AGTAACTACTCCCTCCGTTCCT 59.689 50.000 0.00 0.00 0.00 3.36
1554 1606 2.687425 GAGTAACTACTCCCTCCGTTCC 59.313 54.545 5.70 0.00 45.33 3.62
1565 1617 4.081420 CCAGTCTTGCCATGAGTAACTACT 60.081 45.833 0.00 0.00 39.71 2.57
1566 1618 4.184629 CCAGTCTTGCCATGAGTAACTAC 58.815 47.826 0.00 0.00 0.00 2.73
1567 1619 3.838317 ACCAGTCTTGCCATGAGTAACTA 59.162 43.478 0.00 0.00 0.00 2.24
1568 1620 2.639839 ACCAGTCTTGCCATGAGTAACT 59.360 45.455 0.00 0.00 0.00 2.24
1569 1621 3.059352 ACCAGTCTTGCCATGAGTAAC 57.941 47.619 0.00 0.00 0.00 2.50
1570 1622 4.093743 TCTACCAGTCTTGCCATGAGTAA 58.906 43.478 0.00 0.00 0.00 2.24
1571 1623 3.701542 CTCTACCAGTCTTGCCATGAGTA 59.298 47.826 0.00 0.00 0.00 2.59
1572 1624 2.499289 CTCTACCAGTCTTGCCATGAGT 59.501 50.000 0.00 0.00 0.00 3.41
1573 1625 2.762887 TCTCTACCAGTCTTGCCATGAG 59.237 50.000 0.00 0.00 0.00 2.90
1574 1626 2.820178 TCTCTACCAGTCTTGCCATGA 58.180 47.619 0.00 0.00 0.00 3.07
1575 1627 3.118482 ACATCTCTACCAGTCTTGCCATG 60.118 47.826 0.00 0.00 0.00 3.66
1576 1628 3.110705 ACATCTCTACCAGTCTTGCCAT 58.889 45.455 0.00 0.00 0.00 4.40
1577 1629 2.497675 GACATCTCTACCAGTCTTGCCA 59.502 50.000 0.00 0.00 0.00 4.92
1578 1630 2.159028 GGACATCTCTACCAGTCTTGCC 60.159 54.545 0.00 0.00 0.00 4.52
1579 1631 2.159028 GGGACATCTCTACCAGTCTTGC 60.159 54.545 0.00 0.00 0.00 4.01
1580 1632 3.370104 AGGGACATCTCTACCAGTCTTG 58.630 50.000 0.00 0.00 0.00 3.02
1581 1633 3.767309 AGGGACATCTCTACCAGTCTT 57.233 47.619 0.00 0.00 0.00 3.01
1582 1634 3.628769 GGAAGGGACATCTCTACCAGTCT 60.629 52.174 0.00 0.00 0.00 3.24
1583 1635 2.696187 GGAAGGGACATCTCTACCAGTC 59.304 54.545 0.00 0.00 0.00 3.51
1584 1636 2.753247 GGAAGGGACATCTCTACCAGT 58.247 52.381 0.00 0.00 0.00 4.00
1585 1637 1.683917 CGGAAGGGACATCTCTACCAG 59.316 57.143 0.00 0.00 0.00 4.00
1586 1638 1.776662 CGGAAGGGACATCTCTACCA 58.223 55.000 0.00 0.00 0.00 3.25
1600 1652 0.396811 GATGTATCCCCACCCGGAAG 59.603 60.000 0.73 0.00 34.93 3.46
1601 1653 1.057851 GGATGTATCCCCACCCGGAA 61.058 60.000 0.73 0.00 41.20 4.30
1602 1654 1.460689 GGATGTATCCCCACCCGGA 60.461 63.158 0.73 0.00 41.20 5.14
1603 1655 1.768482 TGGATGTATCCCCACCCGG 60.768 63.158 8.37 0.00 46.59 5.73
1604 1656 1.450211 GTGGATGTATCCCCACCCG 59.550 63.158 8.37 0.00 46.59 5.28
1607 1659 0.106149 GGTCGTGGATGTATCCCCAC 59.894 60.000 8.37 0.00 46.59 4.61
1608 1660 0.325765 TGGTCGTGGATGTATCCCCA 60.326 55.000 8.37 5.64 46.59 4.96
1609 1661 1.056660 ATGGTCGTGGATGTATCCCC 58.943 55.000 8.37 3.21 46.59 4.81
1610 1662 1.416401 ACATGGTCGTGGATGTATCCC 59.584 52.381 8.37 0.00 46.59 3.85
1612 1664 3.123804 GTCACATGGTCGTGGATGTATC 58.876 50.000 0.00 0.00 37.50 2.24
1613 1665 2.766263 AGTCACATGGTCGTGGATGTAT 59.234 45.455 0.00 0.00 37.50 2.29
1614 1666 2.094234 CAGTCACATGGTCGTGGATGTA 60.094 50.000 0.00 0.00 37.50 2.29
1615 1667 0.976641 AGTCACATGGTCGTGGATGT 59.023 50.000 0.00 0.00 37.50 3.06
1616 1668 1.362768 CAGTCACATGGTCGTGGATG 58.637 55.000 0.00 0.00 37.50 3.51
1617 1669 0.250234 CCAGTCACATGGTCGTGGAT 59.750 55.000 0.00 0.00 37.50 3.41
1618 1670 0.830023 TCCAGTCACATGGTCGTGGA 60.830 55.000 0.00 1.15 41.43 4.02
1619 1671 0.034756 TTCCAGTCACATGGTCGTGG 59.965 55.000 0.00 0.00 41.43 4.94
1620 1672 1.877637 TTTCCAGTCACATGGTCGTG 58.122 50.000 0.00 0.00 41.43 4.35
1621 1673 2.859165 ATTTCCAGTCACATGGTCGT 57.141 45.000 0.00 0.00 41.43 4.34
1622 1674 3.063997 GCTTATTTCCAGTCACATGGTCG 59.936 47.826 0.00 0.00 41.43 4.79
1623 1675 4.265073 AGCTTATTTCCAGTCACATGGTC 58.735 43.478 0.00 0.00 41.43 4.02
1624 1676 4.307032 AGCTTATTTCCAGTCACATGGT 57.693 40.909 0.00 0.00 41.43 3.55
1625 1677 6.293081 CGATTAGCTTATTTCCAGTCACATGG 60.293 42.308 0.00 0.00 42.11 3.66
1626 1678 6.479990 TCGATTAGCTTATTTCCAGTCACATG 59.520 38.462 0.00 0.00 0.00 3.21
1627 1679 6.582636 TCGATTAGCTTATTTCCAGTCACAT 58.417 36.000 0.00 0.00 0.00 3.21
1628 1680 5.972935 TCGATTAGCTTATTTCCAGTCACA 58.027 37.500 0.00 0.00 0.00 3.58
1629 1681 8.764524 ATATCGATTAGCTTATTTCCAGTCAC 57.235 34.615 1.71 0.00 0.00 3.67
1653 1705 9.432077 GTCATTTTTGTTTTTGCACGATTTAAT 57.568 25.926 0.00 0.00 0.00 1.40
1663 1715 8.141835 ACCTATGAAGTCATTTTTGTTTTTGC 57.858 30.769 0.00 0.00 37.76 3.68
1668 1720 8.137437 CACAGAACCTATGAAGTCATTTTTGTT 58.863 33.333 0.00 0.00 37.76 2.83
1897 1950 2.787473 TGGAACTCCAAGCAGTATGG 57.213 50.000 0.00 0.00 44.35 2.74
1907 1960 1.780309 AGGTTGTCCATTGGAACTCCA 59.220 47.619 7.05 0.00 39.31 3.86
1908 1961 2.558359 CAAGGTTGTCCATTGGAACTCC 59.442 50.000 7.05 9.68 31.38 3.85
1939 1992 7.724061 ACTGAAAATTTAAGCCTTTGTCCTCTA 59.276 33.333 0.00 0.00 0.00 2.43
1989 2042 4.743057 AGAGCTGTGTCATGCTATGTAA 57.257 40.909 0.00 0.00 39.91 2.41
2099 2152 6.611236 TCTGAATCATGTACCCTGATAGTTCA 59.389 38.462 8.08 8.35 33.08 3.18
2369 2422 1.565759 TCCAGAATAGCCCATGCAGTT 59.434 47.619 0.00 0.00 41.13 3.16
2410 2463 3.967467 ATCTCTCTGGGCAATGGAAAT 57.033 42.857 0.00 0.00 0.00 2.17
2423 2476 4.774660 ATCTGGCATGTCAAATCTCTCT 57.225 40.909 0.00 0.00 0.00 3.10
2453 2506 0.953727 TGCATTGACTTGTGTGCTCC 59.046 50.000 0.00 0.00 38.37 4.70
2534 2587 1.261619 CAGACAGTGTCACGCTTTTCC 59.738 52.381 24.73 0.00 34.60 3.13
2542 2595 1.160137 GAATGGGCAGACAGTGTCAC 58.840 55.000 24.73 15.70 34.60 3.67
2641 2694 3.352648 GGGCAGTTGGTAAGCTTCATAA 58.647 45.455 0.00 0.00 0.00 1.90
2761 2814 4.878397 CAGAATCACCCTGTCTTGTAATCC 59.122 45.833 0.00 0.00 0.00 3.01
2782 2835 4.084537 GCCGTTGATCCGTATCATTAACAG 60.085 45.833 0.00 0.00 41.73 3.16
2794 2847 1.970917 GAGTTGCAGCCGTTGATCCG 61.971 60.000 0.00 0.00 0.00 4.18
2817 2870 8.388656 TCATTCTAATAAGTACCCACCTTCTT 57.611 34.615 0.00 0.00 0.00 2.52
2845 2898 2.650322 TGGAAGGGCCAATAACAGGTTA 59.350 45.455 6.18 0.00 45.87 2.85
2848 2901 3.998560 TGGAAGGGCCAATAACAGG 57.001 52.632 6.18 0.00 45.87 4.00
2902 2955 7.167635 TGAGAAATGACTTCGCGTTATATCTTC 59.832 37.037 5.77 3.65 39.22 2.87
2947 3000 7.500720 TGTACGTTAGATATCAGATCGGAAA 57.499 36.000 5.32 0.00 0.00 3.13
2969 3208 7.375106 CTGAATTATCTTCAGCTGAGTTTGT 57.625 36.000 17.43 5.56 39.36 2.83
2995 3234 5.241506 TCTTTCACCAGTTCAAAGCTATTGG 59.758 40.000 8.23 2.31 0.00 3.16
3044 3283 1.065126 ACTTGAGCAGGGGCATAGAAC 60.065 52.381 0.00 0.00 44.61 3.01
3141 3380 3.304659 GGTGCACCTTGTTGTTATGAGTG 60.305 47.826 29.12 0.00 0.00 3.51
3192 3431 4.497300 CCAAGCACACATAATTTTGAGGG 58.503 43.478 2.69 0.00 0.00 4.30
3200 3439 2.756760 CTCCAAGCCAAGCACACATAAT 59.243 45.455 0.00 0.00 0.00 1.28
3204 3443 2.195567 GCTCCAAGCCAAGCACACA 61.196 57.895 0.00 0.00 38.42 3.72
3366 3671 0.326264 ACTTGGGTGGAGCTCATGAC 59.674 55.000 17.19 8.57 0.00 3.06
3491 3805 5.704354 ACATTGGATATTATGGTGCAAGGA 58.296 37.500 0.00 0.00 32.87 3.36
3524 5002 3.280295 TGGTCGCTTTAAGACAAAACCA 58.720 40.909 0.00 0.00 40.20 3.67
3741 5219 9.664332 CACATTTCCCATTCAAAATTAACCATA 57.336 29.630 0.00 0.00 0.00 2.74
3742 5220 8.162746 ACACATTTCCCATTCAAAATTAACCAT 58.837 29.630 0.00 0.00 0.00 3.55
3840 5318 1.738099 CCCCAGCGAGTTCGTTCAG 60.738 63.158 3.27 0.00 42.22 3.02
3859 5337 3.330701 AGTGAGGGCCTTGACATCTAAAA 59.669 43.478 7.89 0.00 0.00 1.52
3882 5360 9.748708 CTTTGATTCTTGTTCCTTTGTAATCAA 57.251 29.630 0.00 0.00 39.05 2.57
4507 5986 5.409520 ACCTGCATATTTCTGTATACGCATG 59.590 40.000 0.00 0.00 0.00 4.06
4515 5994 6.245408 AGAAAACCACCTGCATATTTCTGTA 58.755 36.000 0.00 0.00 36.19 2.74
4621 6100 1.619827 CAAGATTTTGGAGGCTGCCAA 59.380 47.619 22.65 12.50 45.77 4.52
4750 6229 9.801873 CAACCCTCAATTAATGTAAACAATAGG 57.198 33.333 0.00 0.00 0.00 2.57
4923 6402 5.327091 CAGCATTCAGAAGTTATTTCACCG 58.673 41.667 0.00 0.00 38.31 4.94
4925 6404 6.500684 TCCAGCATTCAGAAGTTATTTCAC 57.499 37.500 0.00 0.00 38.31 3.18
4970 6449 3.985019 TCTAACCATTCGCCCACTTTA 57.015 42.857 0.00 0.00 0.00 1.85
5084 6563 0.253044 GCAACTGAGGAGGTATGCCA 59.747 55.000 1.54 0.00 37.19 4.92
5191 6670 6.932356 ATGTTTATCCAGCACAAGATGTAG 57.068 37.500 0.00 0.00 0.00 2.74



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

AutoCloner maintained by Alex Coulton.