Multiple sequence alignment - TraesCS1D01G103700

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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 TraesCS1D01G103700 chr1D 100.000 8270 0 0 1 8270 93121024 93112755 0.000000e+00 15272
1 TraesCS1D01G103700 chr1D 88.104 807 82 13 28 827 326281834 326281035 0.000000e+00 946
2 TraesCS1D01G103700 chr1D 93.248 622 39 3 20 640 415984362 415984981 0.000000e+00 913
3 TraesCS1D01G103700 chr1B 95.177 7526 245 46 796 8267 148442507 148435046 0.000000e+00 11779
4 TraesCS1D01G103700 chr1A 95.594 5742 182 25 824 6521 91051988 91057702 0.000000e+00 9136
5 TraesCS1D01G103700 chr1A 93.750 1792 73 16 6508 8267 91057746 91059530 0.000000e+00 2652
6 TraesCS1D01G103700 chr6D 94.364 621 35 0 20 640 14615521 14616141 0.000000e+00 953
7 TraesCS1D01G103700 chr6D 94.069 607 36 0 34 640 464465369 464465975 0.000000e+00 922
8 TraesCS1D01G103700 chr6B 93.720 621 39 0 20 640 31939443 31940063 0.000000e+00 931
9 TraesCS1D01G103700 chr7B 93.559 621 40 0 20 640 138474832 138475452 0.000000e+00 926
10 TraesCS1D01G103700 chr5B 93.559 621 40 0 20 640 680927229 680927849 0.000000e+00 926
11 TraesCS1D01G103700 chrUn 93.559 621 39 1 20 640 83929057 83928438 0.000000e+00 924
12 TraesCS1D01G103700 chrUn 94.805 77 3 1 1856 1932 348740503 348740578 1.460000e-22 119
13 TraesCS1D01G103700 chrUn 94.805 77 3 1 1856 1932 364369455 364369530 1.460000e-22 119
14 TraesCS1D01G103700 chrUn 94.805 77 3 1 1856 1932 374196432 374196357 1.460000e-22 119
15 TraesCS1D01G103700 chrUn 94.805 77 3 1 1856 1932 374198290 374198215 1.460000e-22 119
16 TraesCS1D01G103700 chrUn 94.805 77 3 1 1856 1932 374285593 374285518 1.460000e-22 119
17 TraesCS1D01G103700 chr4D 93.237 621 40 2 20 640 47729352 47728734 0.000000e+00 913
18 TraesCS1D01G103700 chr4D 95.152 165 8 0 639 803 468208806 468208642 2.290000e-65 261
19 TraesCS1D01G103700 chr2D 96.364 165 6 0 639 803 475083494 475083658 1.060000e-68 272
20 TraesCS1D01G103700 chr7D 96.319 163 6 0 639 801 363554546 363554708 1.370000e-67 268
21 TraesCS1D01G103700 chr7D 95.732 164 7 0 639 802 224070887 224070724 1.770000e-66 265
22 TraesCS1D01G103700 chr7D 93.678 174 10 1 629 802 595914522 595914694 8.230000e-65 259
23 TraesCS1D01G103700 chr5D 95.706 163 7 0 639 801 127451980 127452142 6.370000e-66 263
24 TraesCS1D01G103700 chr5D 95.732 164 6 1 638 801 293426995 293426833 6.370000e-66 263
25 TraesCS1D01G103700 chr3D 93.605 172 10 1 639 810 612710145 612709975 1.070000e-63 255
26 TraesCS1D01G103700 chr3D 94.805 77 3 1 1856 1932 536588303 536588228 1.460000e-22 119
27 TraesCS1D01G103700 chr3D 94.805 77 3 1 1856 1932 536878815 536878740 1.460000e-22 119
28 TraesCS1D01G103700 chr3A 81.716 268 30 9 2994 3243 174379836 174379570 1.090000e-48 206
29 TraesCS1D01G103700 chr7A 82.329 249 29 7 2994 3228 722273939 722274186 1.410000e-47 202


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 TraesCS1D01G103700 chr1D 93112755 93121024 8269 True 15272 15272 100.000 1 8270 1 chr1D.!!$R1 8269
1 TraesCS1D01G103700 chr1D 326281035 326281834 799 True 946 946 88.104 28 827 1 chr1D.!!$R2 799
2 TraesCS1D01G103700 chr1D 415984362 415984981 619 False 913 913 93.248 20 640 1 chr1D.!!$F1 620
3 TraesCS1D01G103700 chr1B 148435046 148442507 7461 True 11779 11779 95.177 796 8267 1 chr1B.!!$R1 7471
4 TraesCS1D01G103700 chr1A 91051988 91059530 7542 False 5894 9136 94.672 824 8267 2 chr1A.!!$F1 7443
5 TraesCS1D01G103700 chr6D 14615521 14616141 620 False 953 953 94.364 20 640 1 chr6D.!!$F1 620
6 TraesCS1D01G103700 chr6D 464465369 464465975 606 False 922 922 94.069 34 640 1 chr6D.!!$F2 606
7 TraesCS1D01G103700 chr6B 31939443 31940063 620 False 931 931 93.720 20 640 1 chr6B.!!$F1 620
8 TraesCS1D01G103700 chr7B 138474832 138475452 620 False 926 926 93.559 20 640 1 chr7B.!!$F1 620
9 TraesCS1D01G103700 chr5B 680927229 680927849 620 False 926 926 93.559 20 640 1 chr5B.!!$F1 620
10 TraesCS1D01G103700 chrUn 83928438 83929057 619 True 924 924 93.559 20 640 1 chrUn.!!$R1 620
11 TraesCS1D01G103700 chr4D 47728734 47729352 618 True 913 913 93.237 20 640 1 chr4D.!!$R1 620

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
237 238 0.460311 CGACGGCTCCCTAAAGATGT 59.540 55.000 0.0 0.0 0.00 3.06 F
581 583 1.086067 CGTCGCTAGGTGGTCTACGA 61.086 60.000 0.0 0.0 32.96 3.43 F
1204 1211 0.679640 CGAGACCTCTCCTCTGCTGT 60.680 60.000 0.0 0.0 39.79 4.40 F
1520 1527 1.167851 CCATGATTGACCGTGCTGTT 58.832 50.000 0.0 0.0 0.00 3.16 F
2553 2577 1.399440 CCTGTTGTCAGATCCATTGCG 59.601 52.381 0.0 0.0 43.76 4.85 F
3511 3558 1.133025 CGCCCCTTAATCAGCAAACAG 59.867 52.381 0.0 0.0 0.00 3.16 F
4222 4277 0.447801 GGTGCTACATTGCTGGAACG 59.552 55.000 0.0 0.0 0.00 3.95 F
4931 4991 2.813754 TCTTGAGGAAAGCCGTCAATTG 59.186 45.455 0.0 0.0 45.26 2.32 F
6462 6549 3.197265 GGTTTCATTGCATATTGGTGCC 58.803 45.455 0.0 0.0 44.43 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1204 1211 0.319083 ACGGCGTGGTTACAGATTCA 59.681 50.000 13.76 0.0 0.00 2.57 R
1795 1813 0.320073 TTGGGTAGACACGGAAAGCG 60.320 55.000 0.00 0.0 0.00 4.68 R
2553 2577 1.202498 GGGTTACTGTCGCCAGGATAC 60.202 57.143 0.00 0.0 43.36 2.24 R
3491 3538 1.133025 CTGTTTGCTGATTAAGGGGCG 59.867 52.381 0.00 0.0 0.00 6.13 R
3570 3617 2.029649 GCTCCAAGCAAGCAAATTCTCA 60.030 45.455 0.00 0.0 41.89 3.27 R
4815 4875 1.080093 CTAGCGCAACCACGGAGAA 60.080 57.895 11.47 0.0 0.00 2.87 R
5965 6032 0.322816 AAACGCCATGCACATCCTCT 60.323 50.000 0.00 0.0 0.00 3.69 R
6694 6838 2.223641 CCGACAAATAGCTGCAATGCAT 60.224 45.455 8.91 0.0 38.13 3.96 R
7462 7627 0.591170 GGCAAGCAAGCAAAGACGTA 59.409 50.000 0.00 0.0 35.83 3.57 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
237 238 0.460311 CGACGGCTCCCTAAAGATGT 59.540 55.000 0.00 0.00 0.00 3.06
299 300 2.486966 GCATCGTTGCTGGGCTTC 59.513 61.111 11.21 0.00 45.77 3.86
307 308 1.719063 TTGCTGGGCTTCTGGAGGTT 61.719 55.000 0.00 0.00 0.00 3.50
313 314 1.202940 GGGCTTCTGGAGGTTTGTCTT 60.203 52.381 0.00 0.00 0.00 3.01
335 336 1.543429 GGCGGATCTATCTTTGGTGGG 60.543 57.143 0.00 0.00 0.00 4.61
413 414 5.350640 CCTTCCAACCTACGTTATTCTTCAC 59.649 44.000 0.00 0.00 0.00 3.18
414 415 5.733620 TCCAACCTACGTTATTCTTCACT 57.266 39.130 0.00 0.00 0.00 3.41
444 445 1.893808 CTGTTCTGGTGCGCTGGTT 60.894 57.895 9.73 0.00 0.00 3.67
488 490 4.342359 ACTTCCCGACTGTCTACTACAAT 58.658 43.478 6.21 0.00 37.74 2.71
581 583 1.086067 CGTCGCTAGGTGGTCTACGA 61.086 60.000 0.00 0.00 32.96 3.43
648 650 4.672587 TTGAAGATGAATACTCCCTCCG 57.327 45.455 0.00 0.00 0.00 4.63
651 653 4.099573 TGAAGATGAATACTCCCTCCGTTC 59.900 45.833 0.00 0.00 0.00 3.95
660 662 7.951806 TGAATACTCCCTCCGTTCCTAAATATA 59.048 37.037 0.00 0.00 0.00 0.86
661 663 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
662 664 8.731591 ATACTCCCTCCGTTCCTAAATATAAA 57.268 34.615 0.00 0.00 0.00 1.40
663 665 7.628501 ACTCCCTCCGTTCCTAAATATAAAT 57.371 36.000 0.00 0.00 0.00 1.40
668 670 8.784043 CCCTCCGTTCCTAAATATAAATCTTTG 58.216 37.037 0.00 0.00 0.00 2.77
708 712 8.589701 TGAACCACATACGGATGTATATAGAT 57.410 34.615 14.23 0.00 44.82 1.98
709 713 8.466798 TGAACCACATACGGATGTATATAGATG 58.533 37.037 14.23 0.00 44.82 2.90
710 714 6.806751 ACCACATACGGATGTATATAGATGC 58.193 40.000 14.23 0.00 44.82 3.91
752 757 4.439057 TCAATTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
753 758 4.081365 TCAATTTGCTCCGTATGTAGTCCA 60.081 41.667 0.00 0.00 0.00 4.02
755 760 3.728076 TTGCTCCGTATGTAGTCCATC 57.272 47.619 0.00 0.00 34.86 3.51
756 761 2.945456 TGCTCCGTATGTAGTCCATCT 58.055 47.619 0.00 0.00 34.86 2.90
757 762 4.094830 TGCTCCGTATGTAGTCCATCTA 57.905 45.455 0.00 0.00 34.86 1.98
758 763 4.072839 TGCTCCGTATGTAGTCCATCTAG 58.927 47.826 0.00 0.00 34.86 2.43
759 764 4.073549 GCTCCGTATGTAGTCCATCTAGT 58.926 47.826 0.00 0.00 34.86 2.57
760 765 4.083217 GCTCCGTATGTAGTCCATCTAGTG 60.083 50.000 0.00 0.00 34.86 2.74
810 815 4.473477 ACGGAAGAAGTAGATTGGAAGG 57.527 45.455 0.00 0.00 0.00 3.46
815 820 6.128254 CGGAAGAAGTAGATTGGAAGGTTTTC 60.128 42.308 0.00 0.00 0.00 2.29
816 821 6.943146 GGAAGAAGTAGATTGGAAGGTTTTCT 59.057 38.462 0.00 0.00 33.68 2.52
817 822 7.094592 GGAAGAAGTAGATTGGAAGGTTTTCTG 60.095 40.741 0.00 0.00 33.68 3.02
821 826 8.533569 AAGTAGATTGGAAGGTTTTCTGAAAA 57.466 30.769 11.33 11.33 33.68 2.29
822 827 8.533569 AGTAGATTGGAAGGTTTTCTGAAAAA 57.466 30.769 16.47 0.82 33.68 1.94
953 960 2.965147 CTCTCCTTCCCATTCTCTCTCC 59.035 54.545 0.00 0.00 0.00 3.71
1167 1174 3.003763 ACCTTCCTCCAGCCGTCC 61.004 66.667 0.00 0.00 0.00 4.79
1204 1211 0.679640 CGAGACCTCTCCTCTGCTGT 60.680 60.000 0.00 0.00 39.79 4.40
1257 1264 2.897969 CTGTGGTGTAGTTAGGTGGTCT 59.102 50.000 0.00 0.00 0.00 3.85
1295 1302 2.608546 GCACAAGCAAGCAAACATGAAA 59.391 40.909 0.00 0.00 41.58 2.69
1303 1310 2.041701 AGCAAACATGAAAAGCCAGGT 58.958 42.857 0.00 0.00 31.86 4.00
1329 1336 2.007608 GTTTCCCTGGTCGTATTGCTC 58.992 52.381 0.00 0.00 0.00 4.26
1389 1396 4.261801 GCTGCCTAAATCAGAGTTAACCA 58.738 43.478 0.88 0.00 33.54 3.67
1394 1401 6.719370 TGCCTAAATCAGAGTTAACCACAATT 59.281 34.615 0.88 0.00 0.00 2.32
1469 1476 3.834799 CCTACCAGTCGGTCCGCC 61.835 72.222 6.34 0.00 44.71 6.13
1486 1493 3.641436 TCCGCCAGTGTATCAGTTGATAT 59.359 43.478 5.22 0.00 39.03 1.63
1520 1527 1.167851 CCATGATTGACCGTGCTGTT 58.832 50.000 0.00 0.00 0.00 3.16
1521 1528 1.541147 CCATGATTGACCGTGCTGTTT 59.459 47.619 0.00 0.00 0.00 2.83
1538 1545 3.164268 TGTTTGAACATTGGGATGGAGG 58.836 45.455 0.00 0.00 37.60 4.30
1561 1568 4.913335 AGACATTGGCACATGATGAATC 57.087 40.909 13.95 0.00 39.30 2.52
1563 1570 4.338400 AGACATTGGCACATGATGAATCTG 59.662 41.667 13.95 0.00 39.30 2.90
1764 1782 1.884579 CACCTCAGAAGCAAGCACATT 59.115 47.619 0.00 0.00 0.00 2.71
1795 1813 4.114794 GGTTCATCCATTGCACATTTAGC 58.885 43.478 0.00 0.00 35.97 3.09
2217 2241 2.157738 GCCTGGCAAGCAAGATATAGG 58.842 52.381 15.17 0.00 0.00 2.57
2431 2455 8.144478 TCACCTAATGCTGATATTACTCTGAAC 58.856 37.037 0.00 0.00 0.00 3.18
2553 2577 1.399440 CCTGTTGTCAGATCCATTGCG 59.601 52.381 0.00 0.00 43.76 4.85
3085 3109 4.395854 TGCCACTACTTCACTGCATATTTG 59.604 41.667 0.00 0.00 0.00 2.32
3495 3542 9.797556 ACTTACTTTATTTCATAAATTTCGCCC 57.202 29.630 0.00 0.00 34.50 6.13
3496 3543 9.244799 CTTACTTTATTTCATAAATTTCGCCCC 57.755 33.333 0.00 0.00 34.50 5.80
3497 3544 7.418337 ACTTTATTTCATAAATTTCGCCCCT 57.582 32.000 0.00 0.00 34.50 4.79
3498 3545 7.847096 ACTTTATTTCATAAATTTCGCCCCTT 58.153 30.769 0.00 0.00 34.50 3.95
3499 3546 8.973182 ACTTTATTTCATAAATTTCGCCCCTTA 58.027 29.630 0.00 0.00 34.50 2.69
3500 3547 9.810545 CTTTATTTCATAAATTTCGCCCCTTAA 57.189 29.630 0.00 0.00 34.50 1.85
3502 3549 9.974980 TTATTTCATAAATTTCGCCCCTTAATC 57.025 29.630 0.00 0.00 32.38 1.75
3503 3550 7.411486 TTTCATAAATTTCGCCCCTTAATCA 57.589 32.000 0.00 0.00 0.00 2.57
3504 3551 6.633500 TCATAAATTTCGCCCCTTAATCAG 57.367 37.500 0.00 0.00 0.00 2.90
3505 3552 3.801114 AAATTTCGCCCCTTAATCAGC 57.199 42.857 0.00 0.00 0.00 4.26
3506 3553 2.435372 ATTTCGCCCCTTAATCAGCA 57.565 45.000 0.00 0.00 0.00 4.41
3507 3554 2.208132 TTTCGCCCCTTAATCAGCAA 57.792 45.000 0.00 0.00 0.00 3.91
3508 3555 2.208132 TTCGCCCCTTAATCAGCAAA 57.792 45.000 0.00 0.00 0.00 3.68
3509 3556 1.459450 TCGCCCCTTAATCAGCAAAC 58.541 50.000 0.00 0.00 0.00 2.93
3510 3557 1.173043 CGCCCCTTAATCAGCAAACA 58.827 50.000 0.00 0.00 0.00 2.83
3511 3558 1.133025 CGCCCCTTAATCAGCAAACAG 59.867 52.381 0.00 0.00 0.00 3.16
3512 3559 2.171003 GCCCCTTAATCAGCAAACAGT 58.829 47.619 0.00 0.00 0.00 3.55
3513 3560 2.562738 GCCCCTTAATCAGCAAACAGTT 59.437 45.455 0.00 0.00 0.00 3.16
3514 3561 3.761752 GCCCCTTAATCAGCAAACAGTTA 59.238 43.478 0.00 0.00 0.00 2.24
3570 3617 6.488006 GTCTAATATTGTCAACTGATGGGCAT 59.512 38.462 0.00 0.00 0.00 4.40
3809 3856 1.149101 AACCCCAGAGGAGCTTGAAA 58.851 50.000 0.00 0.00 39.89 2.69
4072 4127 4.682860 GCATGTGTATGAGGCAATAAATGC 59.317 41.667 0.00 0.00 44.67 3.56
4222 4277 0.447801 GGTGCTACATTGCTGGAACG 59.552 55.000 0.00 0.00 0.00 3.95
4461 4518 6.007076 TGTATGCATCTTTCCCTGTTTTGTA 58.993 36.000 0.19 0.00 0.00 2.41
4464 4521 4.176271 GCATCTTTCCCTGTTTTGTATGC 58.824 43.478 0.00 0.00 0.00 3.14
4477 4534 7.307337 CCTGTTTTGTATGCCAAAGTTTTCATC 60.307 37.037 4.00 0.00 43.63 2.92
4812 4872 6.103997 TCCGTATTCCTTCTTTCACATGTAC 58.896 40.000 0.00 0.00 0.00 2.90
4815 4875 6.090358 CGTATTCCTTCTTTCACATGTACGTT 59.910 38.462 0.00 0.00 0.00 3.99
4931 4991 2.813754 TCTTGAGGAAAGCCGTCAATTG 59.186 45.455 0.00 0.00 45.26 2.32
5503 5563 5.871396 ACAACTCTTCTTTACTCCTGACA 57.129 39.130 0.00 0.00 0.00 3.58
5927 5994 5.421374 ACCTACAGTTCTACATCCAGGTAAC 59.579 44.000 0.00 0.00 33.46 2.50
5979 6046 6.072286 GGTAATAATTCAGAGGATGTGCATGG 60.072 42.308 0.00 0.00 0.00 3.66
6236 6303 5.992829 TCATCAAGAGTAAGCAACCGTTTTA 59.007 36.000 0.00 0.00 0.00 1.52
6249 6322 5.972382 GCAACCGTTTTACACTTTATGAACA 59.028 36.000 0.00 0.00 0.00 3.18
6339 6412 4.260497 CCATGCTACGACATGTTCATCTTG 60.260 45.833 0.00 0.00 44.88 3.02
6462 6549 3.197265 GGTTTCATTGCATATTGGTGCC 58.803 45.455 0.00 0.00 44.43 5.01
6694 6838 5.304614 GGTATCTTGGCTGACTATAACCTCA 59.695 44.000 0.00 0.00 0.00 3.86
6905 7049 4.273318 GCCTTCTGTGAACAAATAGGGAT 58.727 43.478 0.00 0.00 0.00 3.85
6907 7051 4.641989 CCTTCTGTGAACAAATAGGGATGG 59.358 45.833 0.00 0.00 0.00 3.51
6908 7052 3.620488 TCTGTGAACAAATAGGGATGGC 58.380 45.455 0.00 0.00 0.00 4.40
6909 7053 3.010027 TCTGTGAACAAATAGGGATGGCA 59.990 43.478 0.00 0.00 0.00 4.92
7156 7315 6.165700 TCCAATTAGGGATCGGTTAACTAC 57.834 41.667 5.42 0.00 38.24 2.73
7218 7382 1.019805 GTTAGACAACTGCGAGGGGC 61.020 60.000 0.00 0.00 43.96 5.80
7230 7394 1.490693 CGAGGGGCGTGATGAATTCG 61.491 60.000 0.04 0.00 34.64 3.34
7326 7490 2.193447 CACGACAATGCTGCTACGTAT 58.807 47.619 0.00 0.00 32.04 3.06
7327 7491 2.216488 CACGACAATGCTGCTACGTATC 59.784 50.000 0.00 0.00 32.04 2.24
7344 7509 3.361158 CGACATGGCGCAAACCCA 61.361 61.111 8.66 0.00 36.66 4.51
7357 7522 2.622942 GCAAACCCATCACACAAGAAGA 59.377 45.455 0.00 0.00 0.00 2.87
7358 7523 3.550842 GCAAACCCATCACACAAGAAGAC 60.551 47.826 0.00 0.00 0.00 3.01
7364 7529 3.249091 CATCACACAAGAAGACGAGGAG 58.751 50.000 0.00 0.00 0.00 3.69
7462 7627 2.928801 TGGCTAGTGTTGTGATGTGT 57.071 45.000 0.00 0.00 0.00 3.72
7489 7655 1.703411 TGCTTGCTTGCCTACCTTTT 58.297 45.000 0.00 0.00 0.00 2.27
7533 7699 0.314935 GAACATGGTGTGTGGCCTTG 59.685 55.000 3.32 0.00 41.14 3.61
7551 7717 4.272489 CCTTGGATGAAATGGTAGCAGAA 58.728 43.478 0.00 0.00 0.00 3.02
7561 7727 2.752030 TGGTAGCAGAATAGCAGACCT 58.248 47.619 10.17 0.00 41.07 3.85
7677 7844 8.139989 GGATTTACAATAGGTATACTGACGTGT 58.860 37.037 0.00 4.32 0.00 4.49
7687 7854 5.575995 GGTATACTGACGTGTTTCTTCTTCC 59.424 44.000 0.00 0.00 0.00 3.46
7712 7879 4.142447 CGACCTCCGAAATGTTCTAGAAGA 60.142 45.833 5.12 4.84 41.76 2.87
7749 7916 1.974265 TTTGTTCGCCTGGTGATTCA 58.026 45.000 11.31 10.65 0.00 2.57
7756 7923 2.078452 CCTGGTGATTCAGGTGGGT 58.922 57.895 2.93 0.00 46.89 4.51
7757 7924 0.405585 CCTGGTGATTCAGGTGGGTT 59.594 55.000 2.93 0.00 46.89 4.11
7935 8103 3.755628 GGTCGAGCTGTGCCGGTA 61.756 66.667 7.51 0.00 0.00 4.02
7945 8113 0.681887 TGTGCCGGTAGATCCTCGAA 60.682 55.000 1.90 0.00 0.00 3.71
7946 8114 0.458669 GTGCCGGTAGATCCTCGAAA 59.541 55.000 1.90 0.00 0.00 3.46
8005 8173 4.306967 TCGTCCACGGCATGCACA 62.307 61.111 21.36 0.00 40.29 4.57
8176 8344 1.604755 CCAATTGTCGAACGGGTTCAA 59.395 47.619 11.69 0.32 39.46 2.69
8185 8353 1.812571 GAACGGGTTCAAGTCATGCAT 59.187 47.619 6.68 0.00 39.31 3.96
8262 8441 2.529136 GATCTACCCGATCGATCACG 57.471 55.000 24.40 15.36 39.22 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 7.822822 AGGAGCGACTTACAAAATTACTTGTAT 59.177 33.333 4.06 0.00 40.53 2.29
4 5 7.156673 AGGAGCGACTTACAAAATTACTTGTA 58.843 34.615 0.00 0.00 40.08 2.41
5 6 5.995897 AGGAGCGACTTACAAAATTACTTGT 59.004 36.000 1.41 1.41 42.20 3.16
6 7 6.402226 GGAGGAGCGACTTACAAAATTACTTG 60.402 42.308 0.00 0.00 0.00 3.16
7 8 5.642491 GGAGGAGCGACTTACAAAATTACTT 59.358 40.000 0.00 0.00 0.00 2.24
8 9 5.046520 AGGAGGAGCGACTTACAAAATTACT 60.047 40.000 0.00 0.00 0.00 2.24
9 10 5.176592 AGGAGGAGCGACTTACAAAATTAC 58.823 41.667 0.00 0.00 0.00 1.89
10 11 5.416271 AGGAGGAGCGACTTACAAAATTA 57.584 39.130 0.00 0.00 0.00 1.40
11 12 4.254492 GAGGAGGAGCGACTTACAAAATT 58.746 43.478 0.00 0.00 0.00 1.82
12 13 3.369576 GGAGGAGGAGCGACTTACAAAAT 60.370 47.826 0.00 0.00 0.00 1.82
13 14 2.028385 GGAGGAGGAGCGACTTACAAAA 60.028 50.000 0.00 0.00 0.00 2.44
14 15 1.549170 GGAGGAGGAGCGACTTACAAA 59.451 52.381 0.00 0.00 0.00 2.83
15 16 1.183549 GGAGGAGGAGCGACTTACAA 58.816 55.000 0.00 0.00 0.00 2.41
16 17 0.331954 AGGAGGAGGAGCGACTTACA 59.668 55.000 0.00 0.00 0.00 2.41
17 18 1.026584 GAGGAGGAGGAGCGACTTAC 58.973 60.000 0.00 0.00 0.00 2.34
18 19 0.106619 GGAGGAGGAGGAGCGACTTA 60.107 60.000 0.00 0.00 0.00 2.24
175 176 3.949113 GGACACAAACCCTAACAAGACAA 59.051 43.478 0.00 0.00 0.00 3.18
291 292 0.111253 ACAAACCTCCAGAAGCCCAG 59.889 55.000 0.00 0.00 0.00 4.45
297 298 1.542547 GCCGAAGACAAACCTCCAGAA 60.543 52.381 0.00 0.00 0.00 3.02
299 300 1.291877 CGCCGAAGACAAACCTCCAG 61.292 60.000 0.00 0.00 0.00 3.86
307 308 2.307768 AGATAGATCCGCCGAAGACAA 58.692 47.619 0.00 0.00 0.00 3.18
313 314 1.068588 CACCAAAGATAGATCCGCCGA 59.931 52.381 0.00 0.00 0.00 5.54
335 336 0.456312 ACGACGAGATCCGAGCAAAC 60.456 55.000 0.00 0.00 41.76 2.93
444 445 0.397957 TCGTGCTAAGGCCCCATAGA 60.398 55.000 0.00 0.00 37.74 1.98
488 490 1.290955 CGGAGTCGGGCACAACTTA 59.709 57.895 0.00 0.00 0.00 2.24
544 546 1.068588 ACGACTACAAGCACTGAAGCA 59.931 47.619 0.00 0.00 36.85 3.91
615 617 8.162085 AGTATTCATCTTCAATCATGGCAGTAT 58.838 33.333 0.00 0.00 0.00 2.12
661 663 9.606631 GTTCATAGTGGAATCTCTACAAAGATT 57.393 33.333 0.00 0.00 46.23 2.40
662 664 8.207545 GGTTCATAGTGGAATCTCTACAAAGAT 58.792 37.037 0.00 0.00 37.61 2.40
663 665 7.180229 TGGTTCATAGTGGAATCTCTACAAAGA 59.820 37.037 0.00 0.00 29.47 2.52
668 670 6.222038 TGTGGTTCATAGTGGAATCTCTAC 57.778 41.667 0.00 0.00 0.00 2.59
677 679 3.812156 TCCGTATGTGGTTCATAGTGG 57.188 47.619 0.00 0.00 39.36 4.00
680 682 9.952188 CTATATACATCCGTATGTGGTTCATAG 57.048 37.037 3.56 0.80 45.99 2.23
681 683 9.689501 TCTATATACATCCGTATGTGGTTCATA 57.310 33.333 3.56 0.00 45.99 2.15
682 684 8.589701 TCTATATACATCCGTATGTGGTTCAT 57.410 34.615 3.56 0.00 45.99 2.57
683 685 8.466798 CATCTATATACATCCGTATGTGGTTCA 58.533 37.037 3.56 0.00 45.99 3.18
727 732 6.704493 GGACTACATACGGAGCAAATTGAATA 59.296 38.462 0.00 0.00 0.00 1.75
729 734 4.873827 GGACTACATACGGAGCAAATTGAA 59.126 41.667 0.00 0.00 0.00 2.69
733 738 4.345257 AGATGGACTACATACGGAGCAAAT 59.655 41.667 0.00 0.00 40.72 2.32
791 796 6.943146 AGAAAACCTTCCAATCTACTTCTTCC 59.057 38.462 0.00 0.00 31.28 3.46
794 799 7.079451 TCAGAAAACCTTCCAATCTACTTCT 57.921 36.000 0.00 0.00 31.28 2.85
796 801 8.533569 TTTTCAGAAAACCTTCCAATCTACTT 57.466 30.769 4.06 0.00 31.28 2.24
879 885 1.160329 CGGCGGAATTCAGGTGGATC 61.160 60.000 7.93 0.00 0.00 3.36
924 931 2.776913 GGGAAGGAGAGCGACGGAG 61.777 68.421 0.00 0.00 0.00 4.63
925 932 2.754658 GGGAAGGAGAGCGACGGA 60.755 66.667 0.00 0.00 0.00 4.69
1167 1174 1.173444 CGGGTCTCCCATACCTCTCG 61.173 65.000 5.64 0.00 45.83 4.04
1204 1211 0.319083 ACGGCGTGGTTACAGATTCA 59.681 50.000 13.76 0.00 0.00 2.57
1257 1264 0.878086 TGCCGCATCGCATCGAATTA 60.878 50.000 0.00 0.00 39.99 1.40
1295 1302 1.692411 GGAAACAAGTCACCTGGCTT 58.308 50.000 0.00 0.00 41.26 4.35
1303 1310 0.834612 ACGACCAGGGAAACAAGTCA 59.165 50.000 0.00 0.00 0.00 3.41
1329 1336 2.535984 CGGCAGAAACTATGCTTACTCG 59.464 50.000 0.00 0.00 43.35 4.18
1389 1396 3.770933 CCAATCCTCCATTCACCAATTGT 59.229 43.478 4.43 0.00 0.00 2.71
1394 1401 1.284785 GGTCCAATCCTCCATTCACCA 59.715 52.381 0.00 0.00 29.43 4.17
1469 1476 9.264719 TGCAATTCTATATCAACTGATACACTG 57.735 33.333 1.53 0.00 39.57 3.66
1520 1527 3.333381 TCTTCCTCCATCCCAATGTTCAA 59.667 43.478 0.00 0.00 0.00 2.69
1521 1528 2.918934 TCTTCCTCCATCCCAATGTTCA 59.081 45.455 0.00 0.00 0.00 3.18
1538 1545 4.707030 TTCATCATGTGCCAATGTCTTC 57.293 40.909 0.00 0.00 0.00 2.87
1561 1568 3.624861 AGTTGAAGCCATATTTCTCGCAG 59.375 43.478 0.00 0.00 0.00 5.18
1563 1570 5.277538 CCTTAGTTGAAGCCATATTTCTCGC 60.278 44.000 0.00 0.00 33.36 5.03
1764 1782 5.015515 TGCAATGGATGAACCTGTAAATGA 58.984 37.500 0.00 0.00 39.86 2.57
1795 1813 0.320073 TTGGGTAGACACGGAAAGCG 60.320 55.000 0.00 0.00 0.00 4.68
1953 1974 7.667043 TTCAGGTACAATTGTTAAGCAGTAG 57.333 36.000 17.78 1.96 0.00 2.57
2239 2263 8.663167 TGGTGAACCATGATCTAATCATCTAAT 58.337 33.333 0.00 0.00 46.62 1.73
2240 2264 8.033178 TGGTGAACCATGATCTAATCATCTAA 57.967 34.615 0.00 0.00 46.62 2.10
2241 2265 7.616528 TGGTGAACCATGATCTAATCATCTA 57.383 36.000 0.00 0.00 46.62 1.98
2242 2266 6.505048 TGGTGAACCATGATCTAATCATCT 57.495 37.500 0.00 0.00 46.62 2.90
2243 2267 7.572523 TTTGGTGAACCATGATCTAATCATC 57.427 36.000 2.34 0.00 46.62 2.92
2245 2269 8.274322 AGTATTTGGTGAACCATGATCTAATCA 58.726 33.333 2.34 0.00 46.97 2.57
2246 2270 8.682936 AGTATTTGGTGAACCATGATCTAATC 57.317 34.615 2.34 0.00 46.97 1.75
2359 2383 2.159310 CCAACTCAGATCACGAGACTCC 60.159 54.545 16.60 0.00 34.47 3.85
2431 2455 1.537202 CTCCCTTTTCTCACTTTGCCG 59.463 52.381 0.00 0.00 0.00 5.69
2553 2577 1.202498 GGGTTACTGTCGCCAGGATAC 60.202 57.143 0.00 0.00 43.36 2.24
2655 2679 8.800370 TGTAAATGCAATAGTTAAGTCCATGA 57.200 30.769 0.00 0.00 0.00 3.07
2749 2773 1.860326 TCACATCAGATAACGCATGCG 59.140 47.619 36.79 36.79 46.03 4.73
2752 2776 5.819379 AGACAAATCACATCAGATAACGCAT 59.181 36.000 0.00 0.00 0.00 4.73
2987 3011 7.667043 TGTCAGTTATATTTCTTCAAACGCT 57.333 32.000 0.00 0.00 0.00 5.07
3085 3109 5.133221 ACAACTGATCATAAGGGGCATAAC 58.867 41.667 0.00 0.00 0.00 1.89
3326 3350 9.360093 GGATATGCCGCTATAATATATCAGAAC 57.640 37.037 0.00 0.00 34.16 3.01
3490 3537 1.271652 TGTTTGCTGATTAAGGGGCGA 60.272 47.619 0.00 0.00 0.00 5.54
3491 3538 1.133025 CTGTTTGCTGATTAAGGGGCG 59.867 52.381 0.00 0.00 0.00 6.13
3492 3539 2.171003 ACTGTTTGCTGATTAAGGGGC 58.829 47.619 0.00 0.00 0.00 5.80
3493 3540 5.418840 ACATAACTGTTTGCTGATTAAGGGG 59.581 40.000 0.00 0.00 28.70 4.79
3494 3541 6.150976 TCACATAACTGTTTGCTGATTAAGGG 59.849 38.462 0.00 0.00 31.62 3.95
3495 3542 7.144722 TCACATAACTGTTTGCTGATTAAGG 57.855 36.000 0.00 0.00 31.62 2.69
3570 3617 2.029649 GCTCCAAGCAAGCAAATTCTCA 60.030 45.455 0.00 0.00 41.89 3.27
3685 3732 4.000325 CCTACGGTCATGTCATGTTCAAA 59.000 43.478 12.54 0.00 0.00 2.69
3686 3733 3.259625 TCCTACGGTCATGTCATGTTCAA 59.740 43.478 12.54 0.00 0.00 2.69
3687 3734 2.829120 TCCTACGGTCATGTCATGTTCA 59.171 45.455 12.54 0.00 0.00 3.18
3696 3743 3.166489 GGAAACTCTCCTACGGTCATG 57.834 52.381 0.00 0.00 41.61 3.07
3792 3839 3.549794 CTTATTTCAAGCTCCTCTGGGG 58.450 50.000 0.00 0.00 0.00 4.96
3809 3856 5.450818 TGATACTTTCTTGGTGCCCTTAT 57.549 39.130 0.00 0.00 0.00 1.73
4072 4127 6.793505 AACGGATATAATTAGCTAGGGGAG 57.206 41.667 0.00 0.00 0.00 4.30
4154 4209 2.992242 GCTTTGCCAGCGAATAGAATC 58.008 47.619 0.00 0.00 39.29 2.52
4222 4277 6.861065 TCAATGTCTGACTTTGGTTAGTTC 57.139 37.500 26.42 0.00 34.96 3.01
4281 4336 4.606071 CTCTTTCAGAGCACCGGG 57.394 61.111 6.32 0.00 35.30 5.73
4461 4518 8.773033 ATAAGGATAGATGAAAACTTTGGCAT 57.227 30.769 0.00 0.00 0.00 4.40
4464 4521 8.986929 AGGATAAGGATAGATGAAAACTTTGG 57.013 34.615 0.00 0.00 0.00 3.28
4477 4534 6.627087 TGCTCCCATAAAGGATAAGGATAG 57.373 41.667 0.00 0.00 41.22 2.08
4680 4740 6.459670 ACAACCACTAACTTTTACCAAAGG 57.540 37.500 0.09 0.00 43.47 3.11
4804 4864 1.724623 CCACGGAGAAACGTACATGTG 59.275 52.381 9.11 0.00 46.75 3.21
4805 4865 1.342174 ACCACGGAGAAACGTACATGT 59.658 47.619 2.69 2.69 46.75 3.21
4812 4872 2.549282 CGCAACCACGGAGAAACG 59.451 61.111 0.00 0.00 40.31 3.60
4815 4875 1.080093 CTAGCGCAACCACGGAGAA 60.080 57.895 11.47 0.00 0.00 2.87
4931 4991 2.279517 CGAGGTGGTAGGCGCATC 60.280 66.667 10.83 0.00 0.00 3.91
5074 5134 6.769822 CAGCAGGATTCTATTAAGTTGGTGAT 59.230 38.462 0.00 0.00 35.49 3.06
5087 5147 5.489792 AAACAGAACTCAGCAGGATTCTA 57.510 39.130 0.00 0.00 30.28 2.10
5177 5237 6.043411 GTCTTCATCGCCTATAGTTTTCAGT 58.957 40.000 0.00 0.00 0.00 3.41
5279 5339 3.124466 TCAATGTACGGCACTGAAATTCG 59.876 43.478 0.00 0.00 29.62 3.34
5701 5768 7.077605 CGAATGAGATACTGAAAAACTTTGCA 58.922 34.615 0.00 0.00 0.00 4.08
5927 5994 8.575649 AAGGTAAATGGTAGTTTATCTGGTTG 57.424 34.615 0.00 0.00 35.69 3.77
5965 6032 0.322816 AAACGCCATGCACATCCTCT 60.323 50.000 0.00 0.00 0.00 3.69
5979 6046 3.779238 GCTTCTCGTTATTAAGCAAACGC 59.221 43.478 12.94 0.00 46.05 4.84
6267 6340 9.457436 AAATAAAAAGCTTAACCTTCCTATCGA 57.543 29.630 0.00 0.00 0.00 3.59
6439 6526 3.618150 GCACCAATATGCAATGAAACCAC 59.382 43.478 0.00 0.00 45.39 4.16
6498 6585 4.662278 TGTAGAAAGGGCTATGCAAAACT 58.338 39.130 0.00 0.00 0.00 2.66
6694 6838 2.223641 CCGACAAATAGCTGCAATGCAT 60.224 45.455 8.91 0.00 38.13 3.96
6980 7139 9.482627 GAACTCCTGAATATCACCAAATACTAG 57.517 37.037 0.00 0.00 0.00 2.57
6981 7140 8.988060 TGAACTCCTGAATATCACCAAATACTA 58.012 33.333 0.00 0.00 0.00 1.82
6982 7141 7.861629 TGAACTCCTGAATATCACCAAATACT 58.138 34.615 0.00 0.00 0.00 2.12
6983 7142 8.398665 GTTGAACTCCTGAATATCACCAAATAC 58.601 37.037 0.00 0.00 0.00 1.89
6984 7143 8.106462 TGTTGAACTCCTGAATATCACCAAATA 58.894 33.333 0.00 0.00 0.00 1.40
7025 7184 6.765036 CGACTACTCCTTAGGATAGTGTACAA 59.235 42.308 20.19 0.00 31.39 2.41
7156 7315 2.442236 ACAAGGGCAATGTCTATGGG 57.558 50.000 0.00 0.00 0.00 4.00
7218 7382 2.016961 CCTGCCCGAATTCATCACG 58.983 57.895 6.22 0.00 0.00 4.35
7277 7441 3.044305 GAGAACAGCCGCTGCGTT 61.044 61.111 20.56 8.12 44.33 4.84
7326 7490 3.053291 GGGTTTGCGCCATGTCGA 61.053 61.111 4.18 0.00 0.00 4.20
7327 7491 2.597117 GATGGGTTTGCGCCATGTCG 62.597 60.000 4.18 0.00 0.00 4.35
7344 7509 2.232452 CCTCCTCGTCTTCTTGTGTGAT 59.768 50.000 0.00 0.00 0.00 3.06
7357 7522 3.139397 AGATCCTACAGATTCCTCCTCGT 59.861 47.826 0.00 0.00 34.42 4.18
7358 7523 3.505680 CAGATCCTACAGATTCCTCCTCG 59.494 52.174 0.00 0.00 34.42 4.63
7364 7529 8.371699 AGCTAATTTACAGATCCTACAGATTCC 58.628 37.037 0.00 0.00 34.42 3.01
7462 7627 0.591170 GGCAAGCAAGCAAAGACGTA 59.409 50.000 0.00 0.00 35.83 3.57
7489 7655 7.515861 TCCCAATAGAGATACCAATAACATGGA 59.484 37.037 0.00 0.00 43.54 3.41
7533 7699 5.065914 TGCTATTCTGCTACCATTTCATCC 58.934 41.667 0.00 0.00 0.00 3.51
7551 7717 4.772624 TGAAGTACTGAACAGGTCTGCTAT 59.227 41.667 0.00 0.00 0.00 2.97
7561 7727 4.137116 AGTGTTGCTGAAGTACTGAACA 57.863 40.909 0.00 0.00 0.00 3.18
7677 7844 1.000506 CGGAGGTCGTGGAAGAAGAAA 59.999 52.381 0.00 0.00 0.00 2.52
7687 7854 2.080286 AGAACATTTCGGAGGTCGTG 57.920 50.000 0.00 0.00 40.32 4.35
7690 7857 5.326200 TCTTCTAGAACATTTCGGAGGTC 57.674 43.478 0.00 0.00 34.02 3.85
7743 7910 1.071314 ACCCCAACCCACCTGAATCA 61.071 55.000 0.00 0.00 0.00 2.57
7749 7916 2.602676 CGATGACCCCAACCCACCT 61.603 63.158 0.00 0.00 0.00 4.00
7752 7919 1.229561 TACCGATGACCCCAACCCA 60.230 57.895 0.00 0.00 0.00 4.51
7756 7923 1.196911 ATTCGTACCGATGACCCCAA 58.803 50.000 0.00 0.00 35.23 4.12
7757 7924 1.134640 CAATTCGTACCGATGACCCCA 60.135 52.381 0.00 0.00 35.23 4.96
7774 7942 2.515854 GCCATGCTCATGATCTCCAAT 58.484 47.619 11.17 0.00 41.20 3.16
7837 8005 2.743928 CTGGGCAAGGACGTGCTC 60.744 66.667 10.99 6.67 45.83 4.26
7861 8029 2.610859 GGGGGTCCAGAGAAGGCA 60.611 66.667 0.00 0.00 0.00 4.75
7928 8096 1.134907 GTTTTCGAGGATCTACCGGCA 60.135 52.381 0.00 0.00 44.74 5.69
7935 8103 2.112190 GGGAGGAGTTTTCGAGGATCT 58.888 52.381 0.00 0.00 0.00 2.75
7971 8139 1.592223 GAGCCACAACTCTACCGCT 59.408 57.895 0.00 0.00 33.69 5.52
8005 8173 3.241530 TCCAACTGCACCGCCTCT 61.242 61.111 0.00 0.00 0.00 3.69
8185 8353 4.023279 ACACGCACTGATTAATTTGCTTCA 60.023 37.500 12.92 0.00 32.56 3.02


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

AutoCloner maintained by Alex Coulton.