Multiple sequence alignment - TraesCS7A01G156200

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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 TraesCS7A01G156200 chr7A 100.000 2219 0 0 1 2219 108869840 108872058 0.000000e+00 4098.0
1 TraesCS7A01G156200 chr5A 96.247 1439 14 5 1 1439 666111102 666109704 0.000000e+00 2322.0
2 TraesCS7A01G156200 chr5A 81.287 513 37 24 365 838 443290609 443290117 5.820000e-96 361.0
3 TraesCS7A01G156200 chr5A 97.297 37 1 0 1508 1544 666109706 666109670 1.840000e-06 63.9
4 TraesCS7A01G156200 chr1D 93.730 1276 41 20 331 1592 451052550 451053800 0.000000e+00 1877.0
5 TraesCS7A01G156200 chr1D 91.716 338 8 3 1 338 451051302 451051619 3.360000e-123 451.0
6 TraesCS7A01G156200 chr1D 82.658 444 46 15 916 1341 295962326 295961896 4.500000e-97 364.0
7 TraesCS7A01G156200 chr5D 95.470 861 19 3 1 861 557974439 557973599 0.000000e+00 1356.0
8 TraesCS7A01G156200 chr5D 93.372 513 33 1 1708 2219 443763000 443763512 0.000000e+00 758.0
9 TraesCS7A01G156200 chr5D 90.909 418 12 12 958 1375 557955980 557955589 2.510000e-149 538.0
10 TraesCS7A01G156200 chr5D 84.034 476 42 18 382 838 342176308 342175848 5.660000e-116 427.0
11 TraesCS7A01G156200 chr5D 94.262 122 5 2 857 978 557964857 557964738 3.760000e-43 185.0
12 TraesCS7A01G156200 chr7D 93.567 513 32 1 1708 2219 22649167 22649679 0.000000e+00 763.0
13 TraesCS7A01G156200 chr6D 93.372 513 33 1 1708 2219 17497186 17496674 0.000000e+00 758.0
14 TraesCS7A01G156200 chr6D 92.773 512 37 0 1708 2219 45667549 45667038 0.000000e+00 741.0
15 TraesCS7A01G156200 chr2B 93.320 509 34 0 1708 2216 745724705 745725213 0.000000e+00 752.0
16 TraesCS7A01G156200 chr7B 92.969 512 36 0 1708 2219 741980540 741980029 0.000000e+00 747.0
17 TraesCS7A01G156200 chr7B 97.619 42 1 0 916 957 612845460 612845419 3.060000e-09 73.1
18 TraesCS7A01G156200 chr3D 92.982 513 35 1 1708 2219 520151700 520151188 0.000000e+00 747.0
19 TraesCS7A01G156200 chr3D 92.955 511 35 1 1709 2219 552916025 552915516 0.000000e+00 743.0
20 TraesCS7A01G156200 chr2D 92.788 513 36 1 1708 2219 43967925 43967413 0.000000e+00 741.0
21 TraesCS7A01G156200 chr2D 94.595 74 4 0 1494 1567 590672121 590672194 5.010000e-22 115.0
22 TraesCS7A01G156200 chr5B 83.878 490 48 14 365 838 401668794 401668320 2.620000e-119 438.0
23 TraesCS7A01G156200 chr1A 84.768 453 48 12 905 1341 368820408 368819961 3.380000e-118 435.0
24 TraesCS7A01G156200 chr1B 83.372 433 53 14 916 1341 397442640 397442220 1.240000e-102 383.0
25 TraesCS7A01G156200 chr6A 93.407 91 5 1 1 90 97773744 97773834 1.380000e-27 134.0
26 TraesCS7A01G156200 chr6A 89.873 79 8 0 1315 1393 97775103 97775181 3.900000e-18 102.0
27 TraesCS7A01G156200 chr6B 90.698 86 8 0 913 998 279013713 279013798 5.010000e-22 115.0


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 TraesCS7A01G156200 chr7A 108869840 108872058 2218 False 4098.00 4098 100.000 1 2219 1 chr7A.!!$F1 2218
1 TraesCS7A01G156200 chr5A 666109670 666111102 1432 True 1192.95 2322 96.772 1 1544 2 chr5A.!!$R2 1543
2 TraesCS7A01G156200 chr1D 451051302 451053800 2498 False 1164.00 1877 92.723 1 1592 2 chr1D.!!$F1 1591
3 TraesCS7A01G156200 chr5D 557973599 557974439 840 True 1356.00 1356 95.470 1 861 1 chr5D.!!$R4 860
4 TraesCS7A01G156200 chr5D 443763000 443763512 512 False 758.00 758 93.372 1708 2219 1 chr5D.!!$F1 511
5 TraesCS7A01G156200 chr7D 22649167 22649679 512 False 763.00 763 93.567 1708 2219 1 chr7D.!!$F1 511
6 TraesCS7A01G156200 chr6D 17496674 17497186 512 True 758.00 758 93.372 1708 2219 1 chr6D.!!$R1 511
7 TraesCS7A01G156200 chr6D 45667038 45667549 511 True 741.00 741 92.773 1708 2219 1 chr6D.!!$R2 511
8 TraesCS7A01G156200 chr2B 745724705 745725213 508 False 752.00 752 93.320 1708 2216 1 chr2B.!!$F1 508
9 TraesCS7A01G156200 chr7B 741980029 741980540 511 True 747.00 747 92.969 1708 2219 1 chr7B.!!$R2 511
10 TraesCS7A01G156200 chr3D 520151188 520151700 512 True 747.00 747 92.982 1708 2219 1 chr3D.!!$R1 511
11 TraesCS7A01G156200 chr3D 552915516 552916025 509 True 743.00 743 92.955 1709 2219 1 chr3D.!!$R2 510
12 TraesCS7A01G156200 chr2D 43967413 43967925 512 True 741.00 741 92.788 1708 2219 1 chr2D.!!$R1 511

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
231 232 1.194781 ACTGGGCGGATCAAGTCACT 61.195 55.0 0.0 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 2619 0.03213 TGGAGCAGTTGACACGAGAC 59.968 55.0 0.0 0.0 0.0 3.36 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
90 91 5.852282 ACAAGTTGTGGCAGTAAGAAATT 57.148 34.783 7.96 0.00 0.00 1.82
231 232 1.194781 ACTGGGCGGATCAAGTCACT 61.195 55.000 0.00 0.00 0.00 3.41
275 276 2.672098 AGAAGGATGTGTATCTCGGCT 58.328 47.619 0.00 0.00 33.68 5.52
393 1332 4.889995 GGCCCATTATTCTAGCAGAAAAGT 59.110 41.667 0.00 0.00 37.82 2.66
575 1514 4.404640 TCTTCTATTACGGACGGATGGAT 58.595 43.478 0.00 0.00 0.00 3.41
900 1839 4.978099 ACTTCAGTGACATCAAATCCAGT 58.022 39.130 0.00 0.00 0.00 4.00
1021 1960 2.040606 CGGGGAGGAAGGGAGGAA 59.959 66.667 0.00 0.00 0.00 3.36
1022 1961 2.368011 CGGGGAGGAAGGGAGGAAC 61.368 68.421 0.00 0.00 0.00 3.62
1023 1962 2.001838 GGGGAGGAAGGGAGGAACC 61.002 68.421 0.00 0.00 38.08 3.62
1024 1963 1.229853 GGGAGGAAGGGAGGAACCA 60.230 63.158 0.00 0.00 41.20 3.67
1025 1964 1.275421 GGGAGGAAGGGAGGAACCAG 61.275 65.000 0.00 0.00 41.20 4.00
1026 1965 1.275421 GGAGGAAGGGAGGAACCAGG 61.275 65.000 0.00 0.00 41.20 4.45
1027 1966 1.229984 AGGAAGGGAGGAACCAGGG 60.230 63.158 0.00 0.00 41.20 4.45
1028 1967 2.309504 GGAAGGGAGGAACCAGGGG 61.310 68.421 0.00 0.00 41.20 4.79
1029 1968 1.229853 GAAGGGAGGAACCAGGGGA 60.230 63.158 0.00 0.00 41.20 4.81
1030 1969 1.229984 AAGGGAGGAACCAGGGGAG 60.230 63.158 0.00 0.00 41.20 4.30
1031 1970 2.692741 GGGAGGAACCAGGGGAGG 60.693 72.222 0.00 0.00 41.20 4.30
1032 1971 2.454941 GGAGGAACCAGGGGAGGA 59.545 66.667 0.00 0.00 38.79 3.71
1425 2364 0.314935 CAGCTGGCCAATGAAAACGT 59.685 50.000 7.01 0.00 0.00 3.99
1440 2379 1.986698 AACGTGTTCCTAATCCGACG 58.013 50.000 0.00 0.00 0.00 5.12
1582 2535 2.423185 CCCATGATGCACACGTTAATGT 59.577 45.455 0.00 0.00 0.00 2.71
1592 2545 4.377022 GCACACGTTAATGTTTCTCGATGT 60.377 41.667 0.00 0.00 0.00 3.06
1593 2546 5.305812 CACACGTTAATGTTTCTCGATGTC 58.694 41.667 0.00 0.00 0.00 3.06
1594 2547 4.089493 ACACGTTAATGTTTCTCGATGTCG 59.911 41.667 0.00 0.00 41.45 4.35
1595 2548 3.060363 ACGTTAATGTTTCTCGATGTCGC 59.940 43.478 0.00 0.00 39.60 5.19
1596 2549 3.303495 CGTTAATGTTTCTCGATGTCGCT 59.697 43.478 0.00 0.00 39.60 4.93
1597 2550 4.569029 GTTAATGTTTCTCGATGTCGCTG 58.431 43.478 0.00 0.00 39.60 5.18
1598 2551 1.002366 ATGTTTCTCGATGTCGCTGC 58.998 50.000 0.00 0.00 39.60 5.25
1599 2552 0.038251 TGTTTCTCGATGTCGCTGCT 60.038 50.000 0.00 0.00 39.60 4.24
1600 2553 0.368227 GTTTCTCGATGTCGCTGCTG 59.632 55.000 0.00 0.00 39.60 4.41
1601 2554 1.354337 TTTCTCGATGTCGCTGCTGC 61.354 55.000 5.34 5.34 39.60 5.25
1602 2555 2.202716 CTCGATGTCGCTGCTGCT 60.203 61.111 14.03 0.00 39.60 4.24
1603 2556 1.808799 CTCGATGTCGCTGCTGCTT 60.809 57.895 14.03 0.00 39.60 3.91
1604 2557 2.021964 CTCGATGTCGCTGCTGCTTG 62.022 60.000 14.03 0.00 39.60 4.01
1605 2558 2.385875 CGATGTCGCTGCTGCTTGT 61.386 57.895 14.03 0.00 36.97 3.16
1606 2559 1.134075 GATGTCGCTGCTGCTTGTG 59.866 57.895 14.03 0.78 36.97 3.33
1607 2560 2.249557 GATGTCGCTGCTGCTTGTGG 62.250 60.000 14.03 0.00 36.97 4.17
1608 2561 2.974698 GTCGCTGCTGCTTGTGGT 60.975 61.111 14.03 0.00 36.97 4.16
1609 2562 2.203195 TCGCTGCTGCTTGTGGTT 60.203 55.556 14.03 0.00 36.97 3.67
1610 2563 1.823470 TCGCTGCTGCTTGTGGTTT 60.823 52.632 14.03 0.00 36.97 3.27
1611 2564 1.066257 CGCTGCTGCTTGTGGTTTT 59.934 52.632 14.03 0.00 36.97 2.43
1612 2565 0.936297 CGCTGCTGCTTGTGGTTTTC 60.936 55.000 14.03 0.00 36.97 2.29
1613 2566 0.386838 GCTGCTGCTTGTGGTTTTCT 59.613 50.000 8.53 0.00 36.03 2.52
1614 2567 1.608590 GCTGCTGCTTGTGGTTTTCTA 59.391 47.619 8.53 0.00 36.03 2.10
1615 2568 2.351157 GCTGCTGCTTGTGGTTTTCTAG 60.351 50.000 8.53 0.00 36.03 2.43
1616 2569 1.608590 TGCTGCTTGTGGTTTTCTAGC 59.391 47.619 0.00 0.00 35.10 3.42
1617 2570 1.068264 GCTGCTTGTGGTTTTCTAGCC 60.068 52.381 0.00 0.00 34.01 3.93
1618 2571 2.229792 CTGCTTGTGGTTTTCTAGCCA 58.770 47.619 0.00 0.00 34.01 4.75
1619 2572 2.622942 CTGCTTGTGGTTTTCTAGCCAA 59.377 45.455 0.00 0.00 36.41 4.52
1620 2573 2.360801 TGCTTGTGGTTTTCTAGCCAAC 59.639 45.455 0.00 0.00 36.41 3.77
1621 2574 2.623416 GCTTGTGGTTTTCTAGCCAACT 59.377 45.455 4.45 0.00 36.41 3.16
1622 2575 3.550842 GCTTGTGGTTTTCTAGCCAACTG 60.551 47.826 4.45 0.00 36.41 3.16
1623 2576 1.953686 TGTGGTTTTCTAGCCAACTGC 59.046 47.619 4.45 0.00 36.41 4.40
1624 2577 1.269723 GTGGTTTTCTAGCCAACTGCC 59.730 52.381 4.45 0.00 42.71 4.85
1625 2578 1.144913 TGGTTTTCTAGCCAACTGCCT 59.855 47.619 4.45 0.00 42.71 4.75
1626 2579 1.813178 GGTTTTCTAGCCAACTGCCTC 59.187 52.381 4.45 0.00 42.71 4.70
1627 2580 2.504367 GTTTTCTAGCCAACTGCCTCA 58.496 47.619 0.00 0.00 42.71 3.86
1628 2581 2.185004 TTTCTAGCCAACTGCCTCAC 57.815 50.000 0.00 0.00 42.71 3.51
1629 2582 1.055849 TTCTAGCCAACTGCCTCACA 58.944 50.000 0.00 0.00 42.71 3.58
1630 2583 0.321671 TCTAGCCAACTGCCTCACAC 59.678 55.000 0.00 0.00 42.71 3.82
1631 2584 0.035317 CTAGCCAACTGCCTCACACA 59.965 55.000 0.00 0.00 42.71 3.72
1632 2585 0.035317 TAGCCAACTGCCTCACACAG 59.965 55.000 0.00 0.00 42.71 3.66
1633 2586 1.227943 GCCAACTGCCTCACACAGA 60.228 57.895 0.00 0.00 38.55 3.41
1634 2587 1.510480 GCCAACTGCCTCACACAGAC 61.510 60.000 0.00 0.00 38.55 3.51
1635 2588 0.107456 CCAACTGCCTCACACAGACT 59.893 55.000 0.00 0.00 38.55 3.24
1636 2589 1.224075 CAACTGCCTCACACAGACTG 58.776 55.000 0.00 0.00 38.55 3.51
1637 2590 0.107456 AACTGCCTCACACAGACTGG 59.893 55.000 7.51 0.00 38.55 4.00
1638 2591 1.670406 CTGCCTCACACAGACTGGC 60.670 63.158 7.51 0.00 43.49 4.85
1639 2592 2.109517 CTGCCTCACACAGACTGGCT 62.110 60.000 7.51 0.00 43.57 4.75
1640 2593 1.072159 GCCTCACACAGACTGGCTT 59.928 57.895 7.51 0.00 40.36 4.35
1641 2594 1.233285 GCCTCACACAGACTGGCTTG 61.233 60.000 7.51 0.00 40.36 4.01
1642 2595 1.233285 CCTCACACAGACTGGCTTGC 61.233 60.000 7.51 0.00 0.00 4.01
1643 2596 0.250209 CTCACACAGACTGGCTTGCT 60.250 55.000 7.51 0.00 0.00 3.91
1644 2597 0.250038 TCACACAGACTGGCTTGCTC 60.250 55.000 7.51 0.00 0.00 4.26
1645 2598 0.250209 CACACAGACTGGCTTGCTCT 60.250 55.000 7.51 0.00 0.00 4.09
1646 2599 1.001293 CACACAGACTGGCTTGCTCTA 59.999 52.381 7.51 0.00 0.00 2.43
1647 2600 1.694150 ACACAGACTGGCTTGCTCTAA 59.306 47.619 7.51 0.00 0.00 2.10
1648 2601 2.072298 CACAGACTGGCTTGCTCTAAC 58.928 52.381 7.51 0.00 0.00 2.34
1649 2602 1.694150 ACAGACTGGCTTGCTCTAACA 59.306 47.619 7.51 0.00 0.00 2.41
1650 2603 2.289320 ACAGACTGGCTTGCTCTAACAG 60.289 50.000 7.51 0.00 35.40 3.16
1659 2612 2.244000 GCTCTAACAGCGGCAAACA 58.756 52.632 1.45 0.00 38.76 2.83
1660 2613 0.110192 GCTCTAACAGCGGCAAACAC 60.110 55.000 1.45 0.00 38.76 3.32
1661 2614 0.163788 CTCTAACAGCGGCAAACACG 59.836 55.000 1.45 0.00 0.00 4.49
1662 2615 0.531090 TCTAACAGCGGCAAACACGT 60.531 50.000 1.45 0.00 0.00 4.49
1663 2616 0.306533 CTAACAGCGGCAAACACGTT 59.693 50.000 1.45 0.00 0.00 3.99
1664 2617 0.733729 TAACAGCGGCAAACACGTTT 59.266 45.000 1.45 0.00 0.00 3.60
1665 2618 0.524604 AACAGCGGCAAACACGTTTC 60.525 50.000 1.45 0.00 0.00 2.78
1666 2619 2.003443 CAGCGGCAAACACGTTTCG 61.003 57.895 1.45 0.00 0.00 3.46
1667 2620 2.023601 GCGGCAAACACGTTTCGT 59.976 55.556 0.00 0.00 42.36 3.85
1668 2621 2.001880 GCGGCAAACACGTTTCGTC 61.002 57.895 0.00 0.00 38.32 4.20
1669 2622 1.639534 CGGCAAACACGTTTCGTCT 59.360 52.632 0.00 0.00 38.32 4.18
1670 2623 0.382636 CGGCAAACACGTTTCGTCTC 60.383 55.000 0.00 0.00 38.32 3.36
1671 2624 0.382636 GGCAAACACGTTTCGTCTCG 60.383 55.000 0.00 0.00 38.32 4.04
1672 2625 0.299597 GCAAACACGTTTCGTCTCGT 59.700 50.000 0.00 0.00 38.32 4.18
1677 2630 3.628005 ACGTTTCGTCTCGTGTCAA 57.372 47.368 0.00 0.00 33.69 3.18
1678 2631 1.194495 ACGTTTCGTCTCGTGTCAAC 58.806 50.000 0.00 0.00 33.69 3.18
1679 2632 1.202222 ACGTTTCGTCTCGTGTCAACT 60.202 47.619 0.00 0.00 33.69 3.16
1680 2633 1.187271 CGTTTCGTCTCGTGTCAACTG 59.813 52.381 0.00 0.00 0.00 3.16
1681 2634 1.071436 GTTTCGTCTCGTGTCAACTGC 60.071 52.381 0.00 0.00 0.00 4.40
1682 2635 0.384309 TTCGTCTCGTGTCAACTGCT 59.616 50.000 0.00 0.00 0.00 4.24
1683 2636 0.040336 TCGTCTCGTGTCAACTGCTC 60.040 55.000 0.00 0.00 0.00 4.26
1684 2637 1.004277 CGTCTCGTGTCAACTGCTCC 61.004 60.000 0.00 0.00 0.00 4.70
1685 2638 0.032130 GTCTCGTGTCAACTGCTCCA 59.968 55.000 0.00 0.00 0.00 3.86
1686 2639 0.750249 TCTCGTGTCAACTGCTCCAA 59.250 50.000 0.00 0.00 0.00 3.53
1687 2640 0.861837 CTCGTGTCAACTGCTCCAAC 59.138 55.000 0.00 0.00 0.00 3.77
1688 2641 0.464036 TCGTGTCAACTGCTCCAACT 59.536 50.000 0.00 0.00 0.00 3.16
1689 2642 1.134521 TCGTGTCAACTGCTCCAACTT 60.135 47.619 0.00 0.00 0.00 2.66
1690 2643 1.670811 CGTGTCAACTGCTCCAACTTT 59.329 47.619 0.00 0.00 0.00 2.66
1691 2644 2.097466 CGTGTCAACTGCTCCAACTTTT 59.903 45.455 0.00 0.00 0.00 2.27
1692 2645 3.427503 CGTGTCAACTGCTCCAACTTTTT 60.428 43.478 0.00 0.00 0.00 1.94
1693 2646 4.105486 GTGTCAACTGCTCCAACTTTTTC 58.895 43.478 0.00 0.00 0.00 2.29
1694 2647 3.181501 TGTCAACTGCTCCAACTTTTTCG 60.182 43.478 0.00 0.00 0.00 3.46
1695 2648 3.013921 TCAACTGCTCCAACTTTTTCGT 58.986 40.909 0.00 0.00 0.00 3.85
1696 2649 3.064820 TCAACTGCTCCAACTTTTTCGTC 59.935 43.478 0.00 0.00 0.00 4.20
1697 2650 2.639065 ACTGCTCCAACTTTTTCGTCA 58.361 42.857 0.00 0.00 0.00 4.35
1698 2651 2.614057 ACTGCTCCAACTTTTTCGTCAG 59.386 45.455 0.00 0.00 0.00 3.51
1699 2652 1.946768 TGCTCCAACTTTTTCGTCAGG 59.053 47.619 0.00 0.00 0.00 3.86
1700 2653 1.266989 GCTCCAACTTTTTCGTCAGGG 59.733 52.381 0.00 0.00 0.00 4.45
1701 2654 1.266989 CTCCAACTTTTTCGTCAGGGC 59.733 52.381 0.00 0.00 0.00 5.19
1702 2655 0.313987 CCAACTTTTTCGTCAGGGCC 59.686 55.000 0.00 0.00 0.00 5.80
1703 2656 0.040425 CAACTTTTTCGTCAGGGCCG 60.040 55.000 0.00 0.00 0.00 6.13
1704 2657 0.179040 AACTTTTTCGTCAGGGCCGA 60.179 50.000 0.00 0.00 0.00 5.54
1705 2658 0.179040 ACTTTTTCGTCAGGGCCGAA 60.179 50.000 0.00 0.00 42.08 4.30
1706 2659 0.517316 CTTTTTCGTCAGGGCCGAAG 59.483 55.000 0.00 1.21 44.21 3.79
1773 2727 4.457603 TCAAATTACAAGGCACGTAAGCAT 59.542 37.500 0.00 0.00 45.62 3.79
1775 2729 2.753055 TACAAGGCACGTAAGCATCA 57.247 45.000 0.00 0.00 45.62 3.07
1795 2749 6.615088 CATCAACCATACAAGACTGAAAAGG 58.385 40.000 0.00 0.00 0.00 3.11
1798 2752 7.284074 TCAACCATACAAGACTGAAAAGGTAA 58.716 34.615 0.00 0.00 0.00 2.85
1825 2779 6.935741 AATTCTATGCAAAATACCAGCGTA 57.064 33.333 0.00 0.00 0.00 4.42
1835 2789 2.154567 TACCAGCGTATGTCCCTCTT 57.845 50.000 0.00 0.00 0.00 2.85
1944 2898 1.804748 GCTTTACGGACCTCCAAAGTG 59.195 52.381 9.66 0.00 33.78 3.16
2143 3097 1.071605 CTTGCGTAGACAACTGCCTC 58.928 55.000 0.00 0.00 0.00 4.70
2150 3104 1.153628 GACAACTGCCTCCGCGTAT 60.154 57.895 4.92 0.00 38.08 3.06
2156 3110 2.280186 GCCTCCGCGTATTCCTGG 60.280 66.667 4.92 0.00 0.00 4.45
2204 3158 2.816012 TCGGAGACAACGCCACAA 59.184 55.556 0.00 0.00 35.72 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 232 3.405831 CAAGCAGGAAGACATGAAGACA 58.594 45.455 0.00 0.00 0.00 3.41
295 296 2.159282 CCCTACGAGCAGATTAACGTGT 60.159 50.000 0.00 0.00 39.28 4.49
575 1514 2.761208 GTCCCTGTAAGCTGAGCTTCTA 59.239 50.000 24.63 12.66 46.77 2.10
1021 1960 0.192566 TACTGTGTTCCTCCCCTGGT 59.807 55.000 0.00 0.00 0.00 4.00
1022 1961 0.613777 GTACTGTGTTCCTCCCCTGG 59.386 60.000 0.00 0.00 0.00 4.45
1023 1962 0.613777 GGTACTGTGTTCCTCCCCTG 59.386 60.000 0.00 0.00 0.00 4.45
1024 1963 0.492276 AGGTACTGTGTTCCTCCCCT 59.508 55.000 0.00 0.00 37.18 4.79
1025 1964 0.903236 GAGGTACTGTGTTCCTCCCC 59.097 60.000 10.90 0.00 41.99 4.81
1026 1965 0.531200 CGAGGTACTGTGTTCCTCCC 59.469 60.000 14.70 0.00 43.94 4.30
1027 1966 1.201880 GTCGAGGTACTGTGTTCCTCC 59.798 57.143 14.70 2.32 43.94 4.30
1028 1967 1.884579 TGTCGAGGTACTGTGTTCCTC 59.115 52.381 11.68 11.68 43.57 3.71
1029 1968 1.612463 GTGTCGAGGTACTGTGTTCCT 59.388 52.381 0.00 0.00 41.55 3.36
1030 1969 1.665161 CGTGTCGAGGTACTGTGTTCC 60.665 57.143 0.00 0.00 41.55 3.62
1031 1970 1.665161 CCGTGTCGAGGTACTGTGTTC 60.665 57.143 0.00 0.00 41.55 3.18
1032 1971 0.313043 CCGTGTCGAGGTACTGTGTT 59.687 55.000 0.00 0.00 41.55 3.32
1425 2364 2.797087 GCGATTCGTCGGATTAGGAACA 60.797 50.000 8.03 0.00 0.00 3.18
1464 2403 1.862147 CGATGTCCACGTCGTCGAC 60.862 63.158 15.18 15.18 46.84 4.20
1465 2404 2.477396 CGATGTCCACGTCGTCGA 59.523 61.111 9.47 0.00 46.84 4.20
1470 2409 3.248171 GCTCGCGATGTCCACGTC 61.248 66.667 10.36 0.00 0.00 4.34
1472 2411 3.250323 CTGCTCGCGATGTCCACG 61.250 66.667 10.36 0.00 0.00 4.94
1559 2512 0.322008 TAACGTGTGCATCATGGGCA 60.322 50.000 8.61 8.61 39.32 5.36
1571 2524 4.089493 CGACATCGAGAAACATTAACGTGT 59.911 41.667 0.00 0.00 43.02 4.49
1582 2535 1.354337 GCAGCAGCGACATCGAGAAA 61.354 55.000 5.26 0.00 43.02 2.52
1594 2547 0.386838 AGAAAACCACAAGCAGCAGC 59.613 50.000 0.00 0.00 42.56 5.25
1595 2548 2.351157 GCTAGAAAACCACAAGCAGCAG 60.351 50.000 0.00 0.00 33.38 4.24
1596 2549 1.608590 GCTAGAAAACCACAAGCAGCA 59.391 47.619 0.00 0.00 33.38 4.41
1597 2550 1.068264 GGCTAGAAAACCACAAGCAGC 60.068 52.381 0.00 0.00 34.85 5.25
1598 2551 2.229792 TGGCTAGAAAACCACAAGCAG 58.770 47.619 0.00 0.00 34.85 4.24
1599 2552 2.356665 TGGCTAGAAAACCACAAGCA 57.643 45.000 0.00 0.00 34.85 3.91
1600 2553 2.623416 AGTTGGCTAGAAAACCACAAGC 59.377 45.455 0.00 0.00 35.10 4.01
1601 2554 3.550842 GCAGTTGGCTAGAAAACCACAAG 60.551 47.826 0.00 0.00 40.25 3.16
1602 2555 2.360801 GCAGTTGGCTAGAAAACCACAA 59.639 45.455 0.00 0.00 40.25 3.33
1603 2556 1.953686 GCAGTTGGCTAGAAAACCACA 59.046 47.619 0.00 0.00 40.25 4.17
1604 2557 1.269723 GGCAGTTGGCTAGAAAACCAC 59.730 52.381 0.00 0.00 44.01 4.16
1605 2558 1.616159 GGCAGTTGGCTAGAAAACCA 58.384 50.000 0.00 0.00 44.01 3.67
1615 2568 1.227943 TCTGTGTGAGGCAGTTGGC 60.228 57.895 0.00 0.00 43.74 4.52
1616 2569 0.107456 AGTCTGTGTGAGGCAGTTGG 59.893 55.000 0.00 0.00 35.60 3.77
1617 2570 1.224075 CAGTCTGTGTGAGGCAGTTG 58.776 55.000 0.00 0.00 35.60 3.16
1618 2571 0.107456 CCAGTCTGTGTGAGGCAGTT 59.893 55.000 0.00 0.00 35.60 3.16
1619 2572 1.750930 CCAGTCTGTGTGAGGCAGT 59.249 57.895 0.00 0.00 35.60 4.40
1620 2573 1.670406 GCCAGTCTGTGTGAGGCAG 60.670 63.158 0.00 0.00 44.59 4.85
1621 2574 2.427320 GCCAGTCTGTGTGAGGCA 59.573 61.111 0.00 0.00 44.59 4.75
1622 2575 1.072159 AAGCCAGTCTGTGTGAGGC 59.928 57.895 0.00 0.00 45.54 4.70
1623 2576 1.233285 GCAAGCCAGTCTGTGTGAGG 61.233 60.000 0.00 0.00 0.00 3.86
1624 2577 0.250209 AGCAAGCCAGTCTGTGTGAG 60.250 55.000 0.00 0.00 0.00 3.51
1625 2578 0.250038 GAGCAAGCCAGTCTGTGTGA 60.250 55.000 0.00 0.00 0.00 3.58
1626 2579 0.250209 AGAGCAAGCCAGTCTGTGTG 60.250 55.000 0.00 0.00 0.00 3.82
1627 2580 1.342074 TAGAGCAAGCCAGTCTGTGT 58.658 50.000 0.00 0.00 0.00 3.72
1628 2581 2.072298 GTTAGAGCAAGCCAGTCTGTG 58.928 52.381 0.00 0.00 0.00 3.66
1629 2582 1.694150 TGTTAGAGCAAGCCAGTCTGT 59.306 47.619 0.00 0.00 0.00 3.41
1630 2583 2.344950 CTGTTAGAGCAAGCCAGTCTG 58.655 52.381 0.00 0.00 0.00 3.51
1631 2584 2.758736 CTGTTAGAGCAAGCCAGTCT 57.241 50.000 0.00 0.00 0.00 3.24
1641 2594 0.110192 GTGTTTGCCGCTGTTAGAGC 60.110 55.000 0.00 0.00 45.20 4.09
1642 2595 0.163788 CGTGTTTGCCGCTGTTAGAG 59.836 55.000 0.00 0.00 0.00 2.43
1643 2596 0.531090 ACGTGTTTGCCGCTGTTAGA 60.531 50.000 0.00 0.00 0.00 2.10
1644 2597 0.306533 AACGTGTTTGCCGCTGTTAG 59.693 50.000 0.00 0.00 0.00 2.34
1645 2598 0.733729 AAACGTGTTTGCCGCTGTTA 59.266 45.000 0.00 0.00 0.00 2.41
1646 2599 0.524604 GAAACGTGTTTGCCGCTGTT 60.525 50.000 2.15 0.00 32.11 3.16
1647 2600 1.063488 GAAACGTGTTTGCCGCTGT 59.937 52.632 2.15 0.00 32.11 4.40
1648 2601 2.003443 CGAAACGTGTTTGCCGCTG 61.003 57.895 2.15 0.00 32.11 5.18
1649 2602 2.326550 CGAAACGTGTTTGCCGCT 59.673 55.556 2.15 0.00 32.11 5.52
1650 2603 2.001880 GACGAAACGTGTTTGCCGC 61.002 57.895 2.15 0.00 41.37 6.53
1651 2604 0.382636 GAGACGAAACGTGTTTGCCG 60.383 55.000 2.15 4.08 41.37 5.69
1652 2605 0.382636 CGAGACGAAACGTGTTTGCC 60.383 55.000 2.15 0.00 41.37 4.52
1653 2606 0.299597 ACGAGACGAAACGTGTTTGC 59.700 50.000 2.15 0.00 41.37 3.68
1659 2612 1.194495 GTTGACACGAGACGAAACGT 58.806 50.000 0.00 0.00 45.10 3.99
1660 2613 1.187271 CAGTTGACACGAGACGAAACG 59.813 52.381 0.00 0.00 0.00 3.60
1661 2614 1.071436 GCAGTTGACACGAGACGAAAC 60.071 52.381 0.00 0.00 0.00 2.78
1662 2615 1.202371 AGCAGTTGACACGAGACGAAA 60.202 47.619 0.00 0.00 0.00 3.46
1663 2616 0.384309 AGCAGTTGACACGAGACGAA 59.616 50.000 0.00 0.00 0.00 3.85
1664 2617 0.040336 GAGCAGTTGACACGAGACGA 60.040 55.000 0.00 0.00 0.00 4.20
1665 2618 1.004277 GGAGCAGTTGACACGAGACG 61.004 60.000 0.00 0.00 0.00 4.18
1666 2619 0.032130 TGGAGCAGTTGACACGAGAC 59.968 55.000 0.00 0.00 0.00 3.36
1667 2620 0.750249 TTGGAGCAGTTGACACGAGA 59.250 50.000 0.00 0.00 0.00 4.04
1668 2621 0.861837 GTTGGAGCAGTTGACACGAG 59.138 55.000 0.00 0.00 0.00 4.18
1669 2622 0.464036 AGTTGGAGCAGTTGACACGA 59.536 50.000 0.00 0.00 0.00 4.35
1670 2623 1.299541 AAGTTGGAGCAGTTGACACG 58.700 50.000 0.00 0.00 0.00 4.49
1671 2624 3.782889 AAAAGTTGGAGCAGTTGACAC 57.217 42.857 0.00 0.00 0.00 3.67
1672 2625 3.181501 CGAAAAAGTTGGAGCAGTTGACA 60.182 43.478 0.00 0.00 0.00 3.58
1673 2626 3.181500 ACGAAAAAGTTGGAGCAGTTGAC 60.181 43.478 0.00 0.00 0.00 3.18
1674 2627 3.013921 ACGAAAAAGTTGGAGCAGTTGA 58.986 40.909 0.00 0.00 0.00 3.18
1675 2628 3.181501 TGACGAAAAAGTTGGAGCAGTTG 60.182 43.478 0.00 0.00 0.00 3.16
1676 2629 3.013921 TGACGAAAAAGTTGGAGCAGTT 58.986 40.909 0.00 0.00 0.00 3.16
1677 2630 2.614057 CTGACGAAAAAGTTGGAGCAGT 59.386 45.455 0.00 0.00 0.00 4.40
1678 2631 2.031682 CCTGACGAAAAAGTTGGAGCAG 60.032 50.000 0.00 0.00 0.00 4.24
1679 2632 1.946768 CCTGACGAAAAAGTTGGAGCA 59.053 47.619 0.00 0.00 0.00 4.26
1680 2633 1.266989 CCCTGACGAAAAAGTTGGAGC 59.733 52.381 0.00 0.00 0.00 4.70
1681 2634 1.266989 GCCCTGACGAAAAAGTTGGAG 59.733 52.381 0.00 0.00 0.00 3.86
1682 2635 1.314730 GCCCTGACGAAAAAGTTGGA 58.685 50.000 0.00 0.00 0.00 3.53
1683 2636 0.313987 GGCCCTGACGAAAAAGTTGG 59.686 55.000 0.00 0.00 0.00 3.77
1684 2637 0.040425 CGGCCCTGACGAAAAAGTTG 60.040 55.000 0.00 0.00 35.20 3.16
1685 2638 0.179040 TCGGCCCTGACGAAAAAGTT 60.179 50.000 0.00 0.00 41.42 2.66
1686 2639 1.448497 TCGGCCCTGACGAAAAAGT 59.552 52.632 0.00 0.00 41.42 2.66
1687 2640 4.371975 TCGGCCCTGACGAAAAAG 57.628 55.556 0.00 0.00 41.42 2.27
1692 2645 0.179040 AAAAACTTCGGCCCTGACGA 60.179 50.000 0.00 0.00 43.26 4.20
1693 2646 2.327228 AAAAACTTCGGCCCTGACG 58.673 52.632 0.00 0.00 34.09 4.35
1748 2702 5.048364 TGCTTACGTGCCTTGTAATTTGATT 60.048 36.000 0.00 0.00 31.85 2.57
1754 2708 3.605634 TGATGCTTACGTGCCTTGTAAT 58.394 40.909 0.00 0.00 31.85 1.89
1773 2727 5.690865 ACCTTTTCAGTCTTGTATGGTTGA 58.309 37.500 0.00 0.00 0.00 3.18
1775 2729 8.528044 TTTTACCTTTTCAGTCTTGTATGGTT 57.472 30.769 0.00 0.00 0.00 3.67
1805 2759 5.364778 ACATACGCTGGTATTTTGCATAGA 58.635 37.500 0.00 0.00 37.24 1.98
1821 2775 1.404391 TCGAAGAAGAGGGACATACGC 59.596 52.381 0.00 0.00 0.00 4.42
1825 2779 1.550976 GGTGTCGAAGAAGAGGGACAT 59.449 52.381 0.00 0.00 41.02 3.06
1835 2789 1.006571 GCTTCCGTGGTGTCGAAGA 60.007 57.895 0.00 0.00 0.00 2.87
1915 2869 1.226859 TCCGTAAAGCTGCCGATCG 60.227 57.895 8.51 8.51 0.00 3.69
1920 2874 1.449778 GGAGGTCCGTAAAGCTGCC 60.450 63.158 0.00 0.00 0.00 4.85
1929 2883 0.549469 AAACCACTTTGGAGGTCCGT 59.451 50.000 0.00 0.00 40.96 4.69
2010 2964 4.816385 GGTGTCAGTTCTGAAGTTTGATGA 59.184 41.667 3.99 0.00 0.00 2.92
2060 3014 2.736670 AGGCTGACAGTTCTGGTTTT 57.263 45.000 3.99 0.00 0.00 2.43
2143 3097 1.588139 GTCGTCCAGGAATACGCGG 60.588 63.158 12.47 0.00 0.00 6.46
2150 3104 1.202722 GGAGGTTTTGTCGTCCAGGAA 60.203 52.381 0.00 0.00 40.69 3.36
2156 3110 0.250338 AGCAGGGAGGTTTTGTCGTC 60.250 55.000 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.