Multiple sequence alignment - TraesCS7D01G228200

Loading Multiple Alignment...

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 TraesCS7D01G228200 chr7D 100.000 2510 0 0 1 2510 188367733 188365224 0.000000e+00 4636.0
1 TraesCS7D01G228200 chr3D 94.994 879 37 3 1638 2510 105425473 105424596 0.000000e+00 1373.0
2 TraesCS7D01G228200 chr2D 94.671 882 38 5 1637 2510 390711785 390710905 0.000000e+00 1360.0
3 TraesCS7D01G228200 chr2D 88.547 1039 59 23 1 989 81290500 81291528 0.000000e+00 1205.0
4 TraesCS7D01G228200 chr2D 89.588 826 40 13 187 989 622909450 622910252 0.000000e+00 1007.0
5 TraesCS7D01G228200 chr2A 92.605 879 58 3 1638 2510 115749800 115748923 0.000000e+00 1256.0
6 TraesCS7D01G228200 chr2A 88.816 608 58 4 1681 2282 703548792 703548189 0.000000e+00 737.0
7 TraesCS7D01G228200 chr7B 92.378 879 59 4 1638 2510 44606881 44606005 0.000000e+00 1245.0
8 TraesCS7D01G228200 chr7B 84.103 390 32 10 989 1374 332259312 332258949 1.430000e-92 350.0
9 TraesCS7D01G228200 chr7B 87.681 138 9 2 1416 1545 332258677 332258540 1.200000e-33 154.0
10 TraesCS7D01G228200 chr7B 97.436 39 1 0 1416 1454 332258788 332258750 1.610000e-07 67.6
11 TraesCS7D01G228200 chrUn 89.406 1010 56 17 25 990 10203187 10202185 0.000000e+00 1225.0
12 TraesCS7D01G228200 chrUn 90.413 824 54 15 189 989 438149962 438150783 0.000000e+00 1061.0
13 TraesCS7D01G228200 chr6D 91.753 873 65 3 1644 2510 119277909 119277038 0.000000e+00 1206.0
14 TraesCS7D01G228200 chr5A 91.299 885 54 5 1635 2510 651571636 651572506 0.000000e+00 1186.0
15 TraesCS7D01G228200 chr5A 88.830 949 58 19 64 989 617957015 617956092 0.000000e+00 1122.0
16 TraesCS7D01G228200 chr5A 89.907 644 41 9 373 993 436269128 436269770 0.000000e+00 808.0
17 TraesCS7D01G228200 chr5A 92.788 208 13 1 784 989 25020937 25020730 1.460000e-77 300.0
18 TraesCS7D01G228200 chr5A 91.943 211 14 2 781 989 617976862 617977071 2.440000e-75 292.0
19 TraesCS7D01G228200 chr4B 89.989 889 76 8 1633 2510 558137420 558136534 0.000000e+00 1136.0
20 TraesCS7D01G228200 chr4B 91.052 827 49 15 187 990 610554216 610555040 0.000000e+00 1094.0
21 TraesCS7D01G228200 chr4B 89.359 827 64 8 187 990 634472233 634473058 0.000000e+00 1018.0
22 TraesCS7D01G228200 chr4B 89.238 827 64 10 187 990 634956374 634955550 0.000000e+00 1011.0
23 TraesCS7D01G228200 chr4B 90.909 297 24 1 2217 2510 22916220 22916516 1.810000e-106 396.0
24 TraesCS7D01G228200 chr3B 90.678 826 53 14 187 989 31142096 31142920 0.000000e+00 1077.0
25 TraesCS7D01G228200 chr3B 90.436 826 54 15 187 989 544834383 544835206 0.000000e+00 1064.0
26 TraesCS7D01G228200 chr3B 90.219 685 57 4 1832 2510 146891715 146892395 0.000000e+00 885.0
27 TraesCS7D01G228200 chr4A 90.436 826 55 11 187 989 722381939 722381115 0.000000e+00 1066.0
28 TraesCS7D01G228200 chr5D 90.206 827 55 14 187 989 292693135 292693959 0.000000e+00 1055.0
29 TraesCS7D01G228200 chr6B 90.158 823 60 14 187 990 468255867 468255047 0.000000e+00 1051.0
30 TraesCS7D01G228200 chr7A 90.476 546 23 5 989 1514 195516457 195516993 0.000000e+00 693.0
31 TraesCS7D01G228200 chr3A 92.077 467 36 1 2044 2510 552756227 552755762 0.000000e+00 656.0


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 TraesCS7D01G228200 chr7D 188365224 188367733 2509 True 4636 4636 100.000 1 2510 1 chr7D.!!$R1 2509
1 TraesCS7D01G228200 chr3D 105424596 105425473 877 True 1373 1373 94.994 1638 2510 1 chr3D.!!$R1 872
2 TraesCS7D01G228200 chr2D 390710905 390711785 880 True 1360 1360 94.671 1637 2510 1 chr2D.!!$R1 873
3 TraesCS7D01G228200 chr2D 81290500 81291528 1028 False 1205 1205 88.547 1 989 1 chr2D.!!$F1 988
4 TraesCS7D01G228200 chr2D 622909450 622910252 802 False 1007 1007 89.588 187 989 1 chr2D.!!$F2 802
5 TraesCS7D01G228200 chr2A 115748923 115749800 877 True 1256 1256 92.605 1638 2510 1 chr2A.!!$R1 872
6 TraesCS7D01G228200 chr2A 703548189 703548792 603 True 737 737 88.816 1681 2282 1 chr2A.!!$R2 601
7 TraesCS7D01G228200 chr7B 44606005 44606881 876 True 1245 1245 92.378 1638 2510 1 chr7B.!!$R1 872
8 TraesCS7D01G228200 chrUn 10202185 10203187 1002 True 1225 1225 89.406 25 990 1 chrUn.!!$R1 965
9 TraesCS7D01G228200 chrUn 438149962 438150783 821 False 1061 1061 90.413 189 989 1 chrUn.!!$F1 800
10 TraesCS7D01G228200 chr6D 119277038 119277909 871 True 1206 1206 91.753 1644 2510 1 chr6D.!!$R1 866
11 TraesCS7D01G228200 chr5A 651571636 651572506 870 False 1186 1186 91.299 1635 2510 1 chr5A.!!$F3 875
12 TraesCS7D01G228200 chr5A 617956092 617957015 923 True 1122 1122 88.830 64 989 1 chr5A.!!$R2 925
13 TraesCS7D01G228200 chr5A 436269128 436269770 642 False 808 808 89.907 373 993 1 chr5A.!!$F1 620
14 TraesCS7D01G228200 chr4B 558136534 558137420 886 True 1136 1136 89.989 1633 2510 1 chr4B.!!$R1 877
15 TraesCS7D01G228200 chr4B 610554216 610555040 824 False 1094 1094 91.052 187 990 1 chr4B.!!$F2 803
16 TraesCS7D01G228200 chr4B 634472233 634473058 825 False 1018 1018 89.359 187 990 1 chr4B.!!$F3 803
17 TraesCS7D01G228200 chr4B 634955550 634956374 824 True 1011 1011 89.238 187 990 1 chr4B.!!$R2 803
18 TraesCS7D01G228200 chr3B 31142096 31142920 824 False 1077 1077 90.678 187 989 1 chr3B.!!$F1 802
19 TraesCS7D01G228200 chr3B 544834383 544835206 823 False 1064 1064 90.436 187 989 1 chr3B.!!$F3 802
20 TraesCS7D01G228200 chr3B 146891715 146892395 680 False 885 885 90.219 1832 2510 1 chr3B.!!$F2 678
21 TraesCS7D01G228200 chr4A 722381115 722381939 824 True 1066 1066 90.436 187 989 1 chr4A.!!$R1 802
22 TraesCS7D01G228200 chr5D 292693135 292693959 824 False 1055 1055 90.206 187 989 1 chr5D.!!$F1 802
23 TraesCS7D01G228200 chr6B 468255047 468255867 820 True 1051 1051 90.158 187 990 1 chr6B.!!$R1 803
24 TraesCS7D01G228200 chr7A 195516457 195516993 536 False 693 693 90.476 989 1514 1 chr7A.!!$F1 525

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
426 457 0.535797 GGAGGGGGACAACTTACTCG 59.464 60.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1601 1676 0.235665 GAACACGTCACACTGCATGG 59.764 55.0 0.0 0.0 0.0 3.66 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
61 63 4.406456 TGCAATTAGTGGGTGAAACTGAT 58.594 39.130 0.00 0.00 36.74 2.90
68 70 9.561069 AATTAGTGGGTGAAACTGATACATATC 57.439 33.333 0.00 0.00 36.74 1.63
94 96 7.973388 CCAGTTAACTGAAATCTTTTGAACACA 59.027 33.333 32.50 0.00 46.59 3.72
95 97 8.798153 CAGTTAACTGAAATCTTTTGAACACAC 58.202 33.333 28.17 0.00 46.59 3.82
96 98 8.739972 AGTTAACTGAAATCTTTTGAACACACT 58.260 29.630 7.48 0.00 0.00 3.55
97 99 8.798153 GTTAACTGAAATCTTTTGAACACACTG 58.202 33.333 0.00 0.00 0.00 3.66
100 102 7.775120 ACTGAAATCTTTTGAACACACTGAAT 58.225 30.769 0.00 0.00 0.00 2.57
133 136 8.850156 AGTTAAGTTCATACACTGAAGCAAATT 58.150 29.630 0.00 0.00 44.44 1.82
156 159 8.747538 ATTCATTTAACTTCATACACTACCCC 57.252 34.615 0.00 0.00 0.00 4.95
157 160 7.260387 TCATTTAACTTCATACACTACCCCA 57.740 36.000 0.00 0.00 0.00 4.96
270 274 9.827411 GAGAAAATTCAGTTAACTTCATACACC 57.173 33.333 5.07 0.00 0.00 4.16
277 281 4.689345 AGTTAACTTCATACACCGAAGCAC 59.311 41.667 1.12 0.00 43.02 4.40
398 429 4.748277 TTGAACCCTAACCCTAGAATCG 57.252 45.455 0.00 0.00 0.00 3.34
426 457 0.535797 GGAGGGGGACAACTTACTCG 59.464 60.000 0.00 0.00 0.00 4.18
588 620 1.133792 CACACCTCCTCCACTTGGTTT 60.134 52.381 0.00 0.00 36.34 3.27
602 634 4.829518 GTTTGATTCGCCGCCGCC 62.830 66.667 0.00 0.00 0.00 6.13
712 744 0.820871 CGGGGAGAAAGAGAGACAGG 59.179 60.000 0.00 0.00 0.00 4.00
766 798 3.456105 GATAAGGGACCCGTGCCGG 62.456 68.421 9.54 0.00 46.59 6.13
770 802 4.960866 GGGACCCGTGCCGGTTTT 62.961 66.667 1.90 0.00 46.80 2.43
771 803 3.666253 GGACCCGTGCCGGTTTTG 61.666 66.667 1.90 0.69 46.80 2.44
776 808 2.670251 CGTGCCGGTTTTGCCCTA 60.670 61.111 1.90 0.00 0.00 3.53
866 918 7.350382 TGTCATAATAGAGGTTAAAATGCCCA 58.650 34.615 0.00 0.00 0.00 5.36
880 932 1.765230 TGCCCAAACAAACGGTTAGT 58.235 45.000 0.00 0.00 39.29 2.24
924 976 3.052036 CCAAAATCAGTGTTTTCTGGCG 58.948 45.455 11.54 0.00 36.25 5.69
968 1022 2.795329 CAACCCTAGGCTTCAATGTGT 58.205 47.619 2.05 0.00 0.00 3.72
1088 1143 1.376037 GAGTTAAGGTGCAGGCGCT 60.376 57.895 7.64 0.00 39.64 5.92
1090 1145 1.671054 GTTAAGGTGCAGGCGCTGA 60.671 57.895 7.64 0.00 39.64 4.26
1116 1171 1.525306 GGGCGGTACCTACAATGGC 60.525 63.158 10.90 5.27 39.10 4.40
1120 1175 0.107897 CGGTACCTACAATGGCAGCA 60.108 55.000 10.90 0.00 0.00 4.41
1121 1176 1.379527 GGTACCTACAATGGCAGCAC 58.620 55.000 4.06 0.00 0.00 4.40
1145 1200 0.664466 GTTGGCCGAAAGCAAGAAGC 60.664 55.000 0.00 0.00 46.50 3.86
1162 1217 2.124570 CCATGGGAAGCGGTGGAG 60.125 66.667 2.85 0.00 33.53 3.86
1163 1218 2.669133 CCATGGGAAGCGGTGGAGA 61.669 63.158 2.85 0.00 33.53 3.71
1175 1236 2.038813 TGGAGATGGTGGAGGCGA 59.961 61.111 0.00 0.00 0.00 5.54
1479 1554 1.469940 CCTTGCTTCTACGACTGCGAT 60.470 52.381 0.00 0.00 41.64 4.58
1514 1589 0.249657 CACTGCCGATTCTAGCTCCC 60.250 60.000 0.00 0.00 0.00 4.30
1515 1590 0.397816 ACTGCCGATTCTAGCTCCCT 60.398 55.000 0.00 0.00 0.00 4.20
1516 1591 0.316841 CTGCCGATTCTAGCTCCCTC 59.683 60.000 0.00 0.00 0.00 4.30
1517 1592 1.115930 TGCCGATTCTAGCTCCCTCC 61.116 60.000 0.00 0.00 0.00 4.30
1518 1593 1.822114 GCCGATTCTAGCTCCCTCCC 61.822 65.000 0.00 0.00 0.00 4.30
1519 1594 0.470080 CCGATTCTAGCTCCCTCCCA 60.470 60.000 0.00 0.00 0.00 4.37
1520 1595 1.638529 CGATTCTAGCTCCCTCCCAT 58.361 55.000 0.00 0.00 0.00 4.00
1521 1596 1.274728 CGATTCTAGCTCCCTCCCATG 59.725 57.143 0.00 0.00 0.00 3.66
1522 1597 1.003003 GATTCTAGCTCCCTCCCATGC 59.997 57.143 0.00 0.00 0.00 4.06
1523 1598 0.030705 TTCTAGCTCCCTCCCATGCT 60.031 55.000 0.00 0.00 39.30 3.79
1524 1599 0.030705 TCTAGCTCCCTCCCATGCTT 60.031 55.000 0.00 0.00 37.02 3.91
1525 1600 0.108207 CTAGCTCCCTCCCATGCTTG 59.892 60.000 0.00 0.00 37.02 4.01
1526 1601 0.621571 TAGCTCCCTCCCATGCTTGT 60.622 55.000 0.00 0.00 37.02 3.16
1527 1602 0.621571 AGCTCCCTCCCATGCTTGTA 60.622 55.000 0.00 0.00 30.96 2.41
1528 1603 0.464554 GCTCCCTCCCATGCTTGTAC 60.465 60.000 0.00 0.00 0.00 2.90
1529 1604 0.181350 CTCCCTCCCATGCTTGTACC 59.819 60.000 0.00 0.00 0.00 3.34
1530 1605 0.253160 TCCCTCCCATGCTTGTACCT 60.253 55.000 0.00 0.00 0.00 3.08
1531 1606 0.107017 CCCTCCCATGCTTGTACCTG 60.107 60.000 0.00 0.00 0.00 4.00
1532 1607 0.911769 CCTCCCATGCTTGTACCTGA 59.088 55.000 0.00 0.00 0.00 3.86
1533 1608 1.134280 CCTCCCATGCTTGTACCTGAG 60.134 57.143 0.00 0.00 0.00 3.35
1534 1609 0.253044 TCCCATGCTTGTACCTGAGC 59.747 55.000 6.15 6.15 39.33 4.26
1535 1610 1.091771 CCCATGCTTGTACCTGAGCG 61.092 60.000 8.02 0.00 41.75 5.03
1536 1611 1.709147 CCATGCTTGTACCTGAGCGC 61.709 60.000 0.00 0.00 41.75 5.92
1537 1612 1.450312 ATGCTTGTACCTGAGCGCC 60.450 57.895 2.29 0.00 41.75 6.53
1538 1613 3.188786 GCTTGTACCTGAGCGCCG 61.189 66.667 2.29 0.00 0.00 6.46
1539 1614 2.509336 CTTGTACCTGAGCGCCGG 60.509 66.667 2.29 4.89 0.00 6.13
1540 1615 4.752879 TTGTACCTGAGCGCCGGC 62.753 66.667 19.07 19.07 40.37 6.13
1552 1627 4.382320 GCCGGCCGTTACCACTCA 62.382 66.667 26.12 0.00 0.00 3.41
1553 1628 2.433664 CCGGCCGTTACCACTCAC 60.434 66.667 26.12 0.00 0.00 3.51
1554 1629 2.807895 CGGCCGTTACCACTCACG 60.808 66.667 19.50 0.00 36.12 4.35
1555 1630 3.116531 GGCCGTTACCACTCACGC 61.117 66.667 0.00 0.00 34.98 5.34
1556 1631 3.475774 GCCGTTACCACTCACGCG 61.476 66.667 3.53 3.53 34.98 6.01
1557 1632 3.475774 CCGTTACCACTCACGCGC 61.476 66.667 5.73 0.00 34.98 6.86
1558 1633 3.823421 CGTTACCACTCACGCGCG 61.823 66.667 30.96 30.96 0.00 6.86
1559 1634 3.475774 GTTACCACTCACGCGCGG 61.476 66.667 35.22 22.52 0.00 6.46
1560 1635 3.980989 TTACCACTCACGCGCGGT 61.981 61.111 35.22 22.48 35.46 5.68
1561 1636 3.502990 TTACCACTCACGCGCGGTT 62.503 57.895 35.22 11.70 32.81 4.44
1562 1637 2.974935 TTACCACTCACGCGCGGTTT 62.975 55.000 35.22 10.79 32.81 3.27
1563 1638 4.368808 CCACTCACGCGCGGTTTG 62.369 66.667 35.22 23.24 0.00 2.93
1564 1639 3.636043 CACTCACGCGCGGTTTGT 61.636 61.111 35.22 22.52 0.00 2.83
1565 1640 2.893404 ACTCACGCGCGGTTTGTT 60.893 55.556 35.22 8.98 0.00 2.83
1566 1641 2.326550 CTCACGCGCGGTTTGTTT 59.673 55.556 35.22 8.09 0.00 2.83
1567 1642 2.003443 CTCACGCGCGGTTTGTTTG 61.003 57.895 35.22 20.89 0.00 2.93
1568 1643 2.277628 CACGCGCGGTTTGTTTGT 60.278 55.556 35.22 6.31 0.00 2.83
1569 1644 1.870016 CACGCGCGGTTTGTTTGTT 60.870 52.632 35.22 5.42 0.00 2.83
1570 1645 1.870016 ACGCGCGGTTTGTTTGTTG 60.870 52.632 35.22 0.99 0.00 3.33
1571 1646 2.572448 CGCGCGGTTTGTTTGTTGG 61.572 57.895 24.84 0.00 0.00 3.77
1572 1647 1.226717 GCGCGGTTTGTTTGTTGGA 60.227 52.632 8.83 0.00 0.00 3.53
1573 1648 0.596341 GCGCGGTTTGTTTGTTGGAT 60.596 50.000 8.83 0.00 0.00 3.41
1574 1649 1.846541 CGCGGTTTGTTTGTTGGATT 58.153 45.000 0.00 0.00 0.00 3.01
1575 1650 1.520590 CGCGGTTTGTTTGTTGGATTG 59.479 47.619 0.00 0.00 0.00 2.67
1576 1651 1.864082 GCGGTTTGTTTGTTGGATTGG 59.136 47.619 0.00 0.00 0.00 3.16
1577 1652 2.482142 GCGGTTTGTTTGTTGGATTGGA 60.482 45.455 0.00 0.00 0.00 3.53
1578 1653 3.380142 CGGTTTGTTTGTTGGATTGGAG 58.620 45.455 0.00 0.00 0.00 3.86
1579 1654 3.067461 CGGTTTGTTTGTTGGATTGGAGA 59.933 43.478 0.00 0.00 0.00 3.71
1580 1655 4.620982 GGTTTGTTTGTTGGATTGGAGAG 58.379 43.478 0.00 0.00 0.00 3.20
1581 1656 4.501400 GGTTTGTTTGTTGGATTGGAGAGG 60.501 45.833 0.00 0.00 0.00 3.69
1582 1657 3.874383 TGTTTGTTGGATTGGAGAGGA 57.126 42.857 0.00 0.00 0.00 3.71
1583 1658 4.387026 TGTTTGTTGGATTGGAGAGGAT 57.613 40.909 0.00 0.00 0.00 3.24
1584 1659 4.081406 TGTTTGTTGGATTGGAGAGGATG 58.919 43.478 0.00 0.00 0.00 3.51
1585 1660 2.425143 TGTTGGATTGGAGAGGATGC 57.575 50.000 0.00 0.00 0.00 3.91
1586 1661 1.303309 GTTGGATTGGAGAGGATGCG 58.697 55.000 0.00 0.00 0.00 4.73
1587 1662 0.911769 TTGGATTGGAGAGGATGCGT 59.088 50.000 0.00 0.00 0.00 5.24
1588 1663 0.465705 TGGATTGGAGAGGATGCGTC 59.534 55.000 0.00 0.00 0.00 5.19
1589 1664 0.598680 GGATTGGAGAGGATGCGTCG 60.599 60.000 0.00 0.00 0.00 5.12
1590 1665 1.218230 GATTGGAGAGGATGCGTCGC 61.218 60.000 11.10 11.10 0.00 5.19
1591 1666 1.680522 ATTGGAGAGGATGCGTCGCT 61.681 55.000 19.50 3.67 0.00 4.93
1592 1667 2.279120 GGAGAGGATGCGTCGCTG 60.279 66.667 19.50 0.00 0.00 5.18
1593 1668 2.959071 GAGAGGATGCGTCGCTGC 60.959 66.667 19.50 9.93 0.00 5.25
1616 1691 2.110835 TGCCATGCAGTGTGACGT 59.889 55.556 0.00 0.00 33.32 4.34
1617 1692 2.253051 TGCCATGCAGTGTGACGTG 61.253 57.895 0.00 0.00 33.32 4.49
1618 1693 2.253758 GCCATGCAGTGTGACGTGT 61.254 57.895 0.00 0.00 0.00 4.49
1619 1694 1.785041 GCCATGCAGTGTGACGTGTT 61.785 55.000 0.00 0.00 0.00 3.32
1620 1695 0.235665 CCATGCAGTGTGACGTGTTC 59.764 55.000 0.00 0.00 0.00 3.18
1621 1696 1.220529 CATGCAGTGTGACGTGTTCT 58.779 50.000 0.00 0.00 0.00 3.01
1622 1697 1.599071 CATGCAGTGTGACGTGTTCTT 59.401 47.619 0.00 0.00 0.00 2.52
1623 1698 1.006086 TGCAGTGTGACGTGTTCTTG 58.994 50.000 0.00 0.00 0.00 3.02
1624 1699 1.006832 GCAGTGTGACGTGTTCTTGT 58.993 50.000 0.00 0.00 0.00 3.16
1625 1700 1.396996 GCAGTGTGACGTGTTCTTGTT 59.603 47.619 0.00 0.00 0.00 2.83
1626 1701 2.536928 GCAGTGTGACGTGTTCTTGTTC 60.537 50.000 0.00 0.00 0.00 3.18
1627 1702 2.930040 CAGTGTGACGTGTTCTTGTTCT 59.070 45.455 0.00 0.00 0.00 3.01
1628 1703 3.000322 CAGTGTGACGTGTTCTTGTTCTC 60.000 47.826 0.00 0.00 0.00 2.87
1629 1704 3.119101 AGTGTGACGTGTTCTTGTTCTCT 60.119 43.478 0.00 0.00 0.00 3.10
1630 1705 3.000322 GTGTGACGTGTTCTTGTTCTCTG 60.000 47.826 0.00 0.00 0.00 3.35
1631 1706 3.119280 TGTGACGTGTTCTTGTTCTCTGA 60.119 43.478 0.00 0.00 0.00 3.27
1632 1707 4.051922 GTGACGTGTTCTTGTTCTCTGAT 58.948 43.478 0.00 0.00 0.00 2.90
1633 1708 4.508124 GTGACGTGTTCTTGTTCTCTGATT 59.492 41.667 0.00 0.00 0.00 2.57
1634 1709 5.006746 GTGACGTGTTCTTGTTCTCTGATTT 59.993 40.000 0.00 0.00 0.00 2.17
1635 1710 5.006649 TGACGTGTTCTTGTTCTCTGATTTG 59.993 40.000 0.00 0.00 0.00 2.32
1636 1711 4.876107 ACGTGTTCTTGTTCTCTGATTTGT 59.124 37.500 0.00 0.00 0.00 2.83
1742 1818 1.266175 CTCTGAAGCCAAACAGCAGTG 59.734 52.381 0.00 0.00 34.57 3.66
1756 1832 3.822735 ACAGCAGTGCATGATTTTGTACT 59.177 39.130 19.20 0.00 42.34 2.73
1855 1931 1.698532 CAGGGCCTTGATCTCAGCTAT 59.301 52.381 9.80 0.00 0.00 2.97
1921 1997 4.038271 TGGACAGAGCCTCAATTGAATT 57.962 40.909 9.88 0.00 0.00 2.17
2079 2161 2.026641 GTACCACCATACCAGTCGCTA 58.973 52.381 0.00 0.00 0.00 4.26
2097 2179 2.905075 CTACGGAGCCATCATGAACAA 58.095 47.619 0.00 0.00 0.00 2.83
2120 2202 1.645710 AAGAACCATCCACCGAGAGT 58.354 50.000 0.00 0.00 0.00 3.24
2171 2255 1.733041 CACACACTGTCCGCTACCG 60.733 63.158 0.00 0.00 0.00 4.02
2228 2312 9.922305 GTCATTTTACCTTTGATAATCTCTTCG 57.078 33.333 0.00 0.00 0.00 3.79
2258 2342 2.109128 TCTCCGAGCAAGATCTAGGGAT 59.891 50.000 0.00 0.00 34.45 3.85
2273 2357 9.661954 AGATCTAGGGATTTTAGATAACTGACA 57.338 33.333 0.00 0.00 37.85 3.58
2357 2441 5.497474 AGACTCCAAATACGCCAAATAAGT 58.503 37.500 0.00 0.00 0.00 2.24
2398 2482 6.420306 CGAACTTGATCAGAACATCCAGATAG 59.580 42.308 0.00 0.00 0.00 2.08
2440 2524 3.346315 TGCCATTGTCTATCAGTTGGTG 58.654 45.455 0.00 0.00 35.18 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 8.374743 AGTTTCACCCACTAATTGCAATATTTT 58.625 29.630 13.39 0.00 0.00 1.82
40 41 5.414454 TGTATCAGTTTCACCCACTAATTGC 59.586 40.000 0.00 0.00 0.00 3.56
47 49 5.680619 TGGATATGTATCAGTTTCACCCAC 58.319 41.667 2.74 0.00 34.40 4.61
49 51 5.930135 ACTGGATATGTATCAGTTTCACCC 58.070 41.667 2.74 0.00 34.40 4.61
68 70 7.973388 TGTGTTCAAAAGATTTCAGTTAACTGG 59.027 33.333 30.35 15.22 43.91 4.00
106 109 8.896320 TTTGCTTCAGTGTATGAACTTAACTA 57.104 30.769 0.00 0.00 43.09 2.24
133 136 7.260387 TGGGGTAGTGTATGAAGTTAAATGA 57.740 36.000 0.00 0.00 0.00 2.57
156 159 4.452455 AGCGTCTGAAGTTAACTGGATTTG 59.548 41.667 9.34 0.05 0.00 2.32
157 160 4.452455 CAGCGTCTGAAGTTAACTGGATTT 59.548 41.667 9.34 0.00 32.44 2.17
270 274 5.980698 ATCAGTTAGATGAATGTGCTTCG 57.019 39.130 0.00 0.00 36.60 3.79
331 335 5.351465 GGCTTCGATTTGAATGAACTGTAGA 59.649 40.000 0.00 0.00 35.63 2.59
398 429 1.652947 TGTCCCCCTCCTTTACTGTC 58.347 55.000 0.00 0.00 0.00 3.51
426 457 1.982073 CTTCTGGATTTGGCGGCGTC 61.982 60.000 3.62 3.62 0.00 5.19
712 744 2.112190 CTTTCCCCACTCTACTCTCCC 58.888 57.143 0.00 0.00 0.00 4.30
866 918 5.346551 GCAGAAAACAACTAACCGTTTGTTT 59.653 36.000 8.16 7.37 37.89 2.83
880 932 5.237048 GGCCTAATCATTTGCAGAAAACAA 58.763 37.500 0.00 0.00 0.00 2.83
924 976 5.622378 CAGAAAAGACTCCTACGATTTTGC 58.378 41.667 0.00 0.00 0.00 3.68
968 1022 3.795150 GCGAGTGAATTGCAGAAAACCAA 60.795 43.478 0.00 0.00 38.31 3.67
1023 1078 1.580815 GCACTAGCAAGAGAGCCATC 58.419 55.000 0.00 0.00 41.58 3.51
1128 1183 2.268076 GGCTTCTTGCTTTCGGCCA 61.268 57.895 2.24 0.00 42.39 5.36
1145 1200 1.987807 ATCTCCACCGCTTCCCATGG 61.988 60.000 4.14 4.14 0.00 3.66
1152 1207 1.903877 CTCCACCATCTCCACCGCTT 61.904 60.000 0.00 0.00 0.00 4.68
1153 1208 2.284625 TCCACCATCTCCACCGCT 60.285 61.111 0.00 0.00 0.00 5.52
1162 1217 3.866582 CCCCTCGCCTCCACCATC 61.867 72.222 0.00 0.00 0.00 3.51
1163 1218 4.414956 TCCCCTCGCCTCCACCAT 62.415 66.667 0.00 0.00 0.00 3.55
1201 1262 3.873812 CCACCCCCAGCCGTATCC 61.874 72.222 0.00 0.00 0.00 2.59
1247 1308 3.775654 CTCCTCCACCGCCTCCAC 61.776 72.222 0.00 0.00 0.00 4.02
1249 1310 4.779733 TCCTCCTCCACCGCCTCC 62.780 72.222 0.00 0.00 0.00 4.30
1250 1311 3.151022 CTCCTCCTCCACCGCCTC 61.151 72.222 0.00 0.00 0.00 4.70
1251 1312 4.787280 CCTCCTCCTCCACCGCCT 62.787 72.222 0.00 0.00 0.00 5.52
1386 1447 2.570581 GTGCAACGCGCGTACATG 60.571 61.111 37.93 30.36 46.97 3.21
1514 1589 1.745141 GCTCAGGTACAAGCATGGGAG 60.745 57.143 8.71 0.00 38.89 4.30
1515 1590 0.253044 GCTCAGGTACAAGCATGGGA 59.747 55.000 8.71 0.00 38.89 4.37
1516 1591 1.091771 CGCTCAGGTACAAGCATGGG 61.092 60.000 12.72 0.00 38.97 4.00
1517 1592 1.709147 GCGCTCAGGTACAAGCATGG 61.709 60.000 0.00 1.00 38.97 3.66
1518 1593 1.709147 GGCGCTCAGGTACAAGCATG 61.709 60.000 7.64 0.00 38.97 4.06
1519 1594 1.450312 GGCGCTCAGGTACAAGCAT 60.450 57.895 7.64 0.00 38.97 3.79
1520 1595 2.047274 GGCGCTCAGGTACAAGCA 60.047 61.111 7.64 0.00 38.97 3.91
1521 1596 3.188786 CGGCGCTCAGGTACAAGC 61.189 66.667 7.64 0.00 36.29 4.01
1522 1597 2.509336 CCGGCGCTCAGGTACAAG 60.509 66.667 7.64 0.00 0.00 3.16
1523 1598 4.752879 GCCGGCGCTCAGGTACAA 62.753 66.667 12.58 0.00 0.00 2.41
1535 1610 4.382320 TGAGTGGTAACGGCCGGC 62.382 66.667 31.76 21.18 42.51 6.13
1536 1611 2.433664 GTGAGTGGTAACGGCCGG 60.434 66.667 31.76 11.88 42.51 6.13
1537 1612 2.807895 CGTGAGTGGTAACGGCCG 60.808 66.667 26.86 26.86 42.51 6.13
1538 1613 3.116531 GCGTGAGTGGTAACGGCC 61.117 66.667 0.00 0.00 40.12 6.13
1539 1614 3.475774 CGCGTGAGTGGTAACGGC 61.476 66.667 0.00 0.00 40.12 5.68
1540 1615 3.475774 GCGCGTGAGTGGTAACGG 61.476 66.667 8.43 0.00 43.14 4.44
1541 1616 3.823421 CGCGCGTGAGTGGTAACG 61.823 66.667 24.19 0.00 43.14 3.18
1542 1617 3.475774 CCGCGCGTGAGTGGTAAC 61.476 66.667 29.95 0.00 43.14 2.50
1546 1621 4.368808 CAAACCGCGCGTGAGTGG 62.369 66.667 29.95 14.69 46.65 4.00
1547 1622 2.640736 AAACAAACCGCGCGTGAGTG 62.641 55.000 29.95 21.58 46.39 3.51
1548 1623 2.466140 AAACAAACCGCGCGTGAGT 61.466 52.632 29.95 17.06 0.00 3.41
1549 1624 2.003443 CAAACAAACCGCGCGTGAG 61.003 57.895 29.95 16.31 0.00 3.51
1550 1625 2.023461 CAAACAAACCGCGCGTGA 59.977 55.556 29.95 0.00 0.00 4.35
1551 1626 1.870016 AACAAACAAACCGCGCGTG 60.870 52.632 29.95 22.56 0.00 5.34
1552 1627 1.870016 CAACAAACAAACCGCGCGT 60.870 52.632 29.95 14.24 0.00 6.01
1553 1628 2.572448 CCAACAAACAAACCGCGCG 61.572 57.895 25.67 25.67 0.00 6.86
1554 1629 0.596341 ATCCAACAAACAAACCGCGC 60.596 50.000 0.00 0.00 0.00 6.86
1555 1630 1.520590 CAATCCAACAAACAAACCGCG 59.479 47.619 0.00 0.00 0.00 6.46
1556 1631 1.864082 CCAATCCAACAAACAAACCGC 59.136 47.619 0.00 0.00 0.00 5.68
1557 1632 3.067461 TCTCCAATCCAACAAACAAACCG 59.933 43.478 0.00 0.00 0.00 4.44
1558 1633 4.501400 CCTCTCCAATCCAACAAACAAACC 60.501 45.833 0.00 0.00 0.00 3.27
1559 1634 4.340950 TCCTCTCCAATCCAACAAACAAAC 59.659 41.667 0.00 0.00 0.00 2.93
1560 1635 4.541705 TCCTCTCCAATCCAACAAACAAA 58.458 39.130 0.00 0.00 0.00 2.83
1561 1636 4.177537 TCCTCTCCAATCCAACAAACAA 57.822 40.909 0.00 0.00 0.00 2.83
1562 1637 3.874383 TCCTCTCCAATCCAACAAACA 57.126 42.857 0.00 0.00 0.00 2.83
1563 1638 3.119352 GCATCCTCTCCAATCCAACAAAC 60.119 47.826 0.00 0.00 0.00 2.93
1564 1639 3.091545 GCATCCTCTCCAATCCAACAAA 58.908 45.455 0.00 0.00 0.00 2.83
1565 1640 2.726821 GCATCCTCTCCAATCCAACAA 58.273 47.619 0.00 0.00 0.00 2.83
1566 1641 1.407299 CGCATCCTCTCCAATCCAACA 60.407 52.381 0.00 0.00 0.00 3.33
1567 1642 1.303309 CGCATCCTCTCCAATCCAAC 58.697 55.000 0.00 0.00 0.00 3.77
1568 1643 0.911769 ACGCATCCTCTCCAATCCAA 59.088 50.000 0.00 0.00 0.00 3.53
1569 1644 0.465705 GACGCATCCTCTCCAATCCA 59.534 55.000 0.00 0.00 0.00 3.41
1570 1645 0.598680 CGACGCATCCTCTCCAATCC 60.599 60.000 0.00 0.00 0.00 3.01
1571 1646 1.218230 GCGACGCATCCTCTCCAATC 61.218 60.000 16.42 0.00 0.00 2.67
1572 1647 1.227380 GCGACGCATCCTCTCCAAT 60.227 57.895 16.42 0.00 0.00 3.16
1573 1648 2.184322 GCGACGCATCCTCTCCAA 59.816 61.111 16.42 0.00 0.00 3.53
1574 1649 2.755876 AGCGACGCATCCTCTCCA 60.756 61.111 23.70 0.00 0.00 3.86
1575 1650 2.279120 CAGCGACGCATCCTCTCC 60.279 66.667 23.70 0.00 0.00 3.71
1576 1651 2.959071 GCAGCGACGCATCCTCTC 60.959 66.667 23.70 0.00 0.00 3.20
1577 1652 3.763356 TGCAGCGACGCATCCTCT 61.763 61.111 23.70 0.00 36.86 3.69
1599 1674 2.110835 ACGTCACACTGCATGGCA 59.889 55.556 0.00 0.00 36.92 4.92
1600 1675 1.785041 AACACGTCACACTGCATGGC 61.785 55.000 0.00 0.00 0.00 4.40
1601 1676 0.235665 GAACACGTCACACTGCATGG 59.764 55.000 0.00 0.00 0.00 3.66
1602 1677 1.220529 AGAACACGTCACACTGCATG 58.779 50.000 0.00 0.00 0.00 4.06
1603 1678 1.599071 CAAGAACACGTCACACTGCAT 59.401 47.619 0.00 0.00 0.00 3.96
1604 1679 1.006086 CAAGAACACGTCACACTGCA 58.994 50.000 0.00 0.00 0.00 4.41
1605 1680 1.006832 ACAAGAACACGTCACACTGC 58.993 50.000 0.00 0.00 0.00 4.40
1606 1681 2.930040 AGAACAAGAACACGTCACACTG 59.070 45.455 0.00 0.00 0.00 3.66
1607 1682 3.119101 AGAGAACAAGAACACGTCACACT 60.119 43.478 0.00 0.00 0.00 3.55
1608 1683 3.000322 CAGAGAACAAGAACACGTCACAC 60.000 47.826 0.00 0.00 0.00 3.82
1609 1684 3.119280 TCAGAGAACAAGAACACGTCACA 60.119 43.478 0.00 0.00 0.00 3.58
1610 1685 3.444916 TCAGAGAACAAGAACACGTCAC 58.555 45.455 0.00 0.00 0.00 3.67
1611 1686 3.793797 TCAGAGAACAAGAACACGTCA 57.206 42.857 0.00 0.00 0.00 4.35
1612 1687 5.006746 ACAAATCAGAGAACAAGAACACGTC 59.993 40.000 0.00 0.00 0.00 4.34
1613 1688 4.876107 ACAAATCAGAGAACAAGAACACGT 59.124 37.500 0.00 0.00 0.00 4.49
1614 1689 5.409643 ACAAATCAGAGAACAAGAACACG 57.590 39.130 0.00 0.00 0.00 4.49
1615 1690 8.466086 AAAAACAAATCAGAGAACAAGAACAC 57.534 30.769 0.00 0.00 0.00 3.32
1760 1836 6.234177 GGTAGCAGATTGTCTGGCTAATTAT 58.766 40.000 8.85 0.00 44.43 1.28
1855 1931 2.436417 GTTCAGCTTATGGGCACTTGA 58.564 47.619 0.00 0.00 34.17 3.02
1921 1997 1.069978 TGCAAGTGATCGTCCAGTCAA 59.930 47.619 0.00 0.00 0.00 3.18
2079 2161 2.198827 TTTGTTCATGATGGCTCCGT 57.801 45.000 0.00 0.00 0.00 4.69
2162 2246 1.168407 CGGAACCTATCGGTAGCGGA 61.168 60.000 15.23 2.00 44.73 5.54
2228 2312 2.558795 TCTTGCTCGGAGATATAGCACC 59.441 50.000 9.69 0.00 33.78 5.01
2273 2357 9.492973 CCATTGGAAATAAGTGTTGATTTCTTT 57.507 29.630 0.00 0.00 40.43 2.52
2357 2441 7.731882 TCAAGTTCGTGACATGGTTATTTTA 57.268 32.000 0.00 0.00 0.00 1.52
2398 2482 3.059352 AGGAGTGGCTGTTACATGTTC 57.941 47.619 2.30 0.00 0.00 3.18
2454 2538 1.376424 CCATGCGTGAGTTCTGGCT 60.376 57.895 7.72 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.