Multiple sequence alignment - TraesCS2A01G464600

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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 TraesCS2A01G464600 chr2A 100.000 7102 0 0 1 7102 709856790 709863891 0.000000e+00 13116.0
1 TraesCS2A01G464600 chr2A 90.648 2438 198 19 1622 4041 710095661 710098086 0.000000e+00 3212.0
2 TraesCS2A01G464600 chr2A 84.825 2458 351 13 1622 4063 710038808 710041259 0.000000e+00 2453.0
3 TraesCS2A01G464600 chr2A 82.635 334 47 10 5037 5367 710045995 710046320 1.170000e-72 285.0
4 TraesCS2A01G464600 chr2A 82.007 289 20 8 5989 6268 710087618 710087883 4.310000e-52 217.0
5 TraesCS2A01G464600 chr2A 82.422 256 27 8 4949 5203 710193983 710194221 2.600000e-49 207.0
6 TraesCS2A01G464600 chr2A 81.349 252 29 5 5738 5989 710046480 710046713 9.400000e-44 189.0
7 TraesCS2A01G464600 chr2A 77.711 332 47 16 5879 6195 710099863 710100182 2.040000e-40 178.0
8 TraesCS2A01G464600 chr2A 87.402 127 14 1 6454 6580 710100313 710100437 2.060000e-30 145.0
9 TraesCS2A01G464600 chr2A 94.828 58 3 0 6268 6325 751242440 751242383 2.730000e-14 91.6
10 TraesCS2A01G464600 chr2A 93.103 58 4 0 6268 6325 751273019 751272962 1.270000e-12 86.1
11 TraesCS2A01G464600 chr2A 95.455 44 2 0 6219 6262 710100174 710100217 3.550000e-08 71.3
12 TraesCS2A01G464600 chr2D 95.123 3957 141 30 1622 5567 571197797 571201712 0.000000e+00 6191.0
13 TraesCS2A01G464600 chr2D 81.748 3238 463 71 1622 4769 571211594 571214793 0.000000e+00 2588.0
14 TraesCS2A01G464600 chr2D 81.277 2772 437 59 1622 4332 571529659 571532409 0.000000e+00 2169.0
15 TraesCS2A01G464600 chr2D 85.620 911 117 9 1622 2524 571445863 571446767 0.000000e+00 944.0
16 TraesCS2A01G464600 chr2D 91.679 661 41 4 5595 6255 571201703 571202349 0.000000e+00 904.0
17 TraesCS2A01G464600 chr2D 83.549 541 49 18 5747 6268 571219301 571219820 3.000000e-128 470.0
18 TraesCS2A01G464600 chr2D 81.238 517 76 17 4863 5367 571216926 571217433 1.440000e-106 398.0
19 TraesCS2A01G464600 chr2D 87.171 304 24 6 6349 6641 571202787 571203086 1.480000e-86 331.0
20 TraesCS2A01G464600 chr2D 81.266 395 63 8 6714 7102 77178449 77178838 6.920000e-80 309.0
21 TraesCS2A01G464600 chr2D 94.388 196 11 0 6907 7102 571203576 571203771 1.160000e-77 302.0
22 TraesCS2A01G464600 chr2B 94.026 4051 188 28 1622 5649 683045586 683049605 0.000000e+00 6091.0
23 TraesCS2A01G464600 chr2B 84.417 2631 366 32 1622 4225 683070287 683072900 0.000000e+00 2547.0
24 TraesCS2A01G464600 chr2B 81.734 2053 309 42 2229 4235 794691227 794689195 0.000000e+00 1653.0
25 TraesCS2A01G464600 chr2B 81.734 2053 309 42 2229 4235 794800128 794798096 0.000000e+00 1653.0
26 TraesCS2A01G464600 chr2B 82.788 1743 264 23 2509 4225 683057571 683059303 0.000000e+00 1524.0
27 TraesCS2A01G464600 chr2B 87.694 1227 137 8 1622 2837 683130846 683132069 0.000000e+00 1417.0
28 TraesCS2A01G464600 chr2B 85.165 910 118 9 1622 2524 683162179 683163078 0.000000e+00 917.0
29 TraesCS2A01G464600 chr2B 91.009 634 50 4 6470 7102 683051181 683051808 0.000000e+00 848.0
30 TraesCS2A01G464600 chr2B 87.861 692 50 12 5602 6268 683062178 683062860 0.000000e+00 782.0
31 TraesCS2A01G464600 chr2B 90.200 449 18 8 5646 6076 683050424 683050864 4.810000e-156 562.0
32 TraesCS2A01G464600 chr2B 85.127 511 51 10 5594 6092 683135010 683135507 3.830000e-137 499.0
33 TraesCS2A01G464600 chr2B 80.731 602 84 26 4786 5367 683073573 683074162 2.350000e-119 440.0
34 TraesCS2A01G464600 chr2B 80.426 516 83 15 4863 5367 683074592 683075100 1.870000e-100 377.0
35 TraesCS2A01G464600 chr2B 82.993 441 32 10 5718 6136 683075364 683075783 6.770000e-95 359.0
36 TraesCS2A01G464600 chr2B 77.486 533 98 18 6581 7102 606610630 606611151 4.160000e-77 300.0
37 TraesCS2A01G464600 chr2B 82.596 339 49 7 5060 5394 683061782 683062114 2.510000e-74 291.0
38 TraesCS2A01G464600 chr2B 81.432 377 37 19 6096 6457 683135778 683136136 1.950000e-70 278.0
39 TraesCS2A01G464600 chr2B 92.453 159 8 4 6090 6246 683051025 683051181 2.580000e-54 224.0
40 TraesCS2A01G464600 chr2B 82.845 239 34 5 5158 5394 683134706 683134939 2.600000e-49 207.0
41 TraesCS2A01G464600 chr2B 92.254 142 6 5 6444 6583 683137461 683137599 5.620000e-46 196.0
42 TraesCS2A01G464600 chr2B 85.714 126 14 2 5446 5567 683075137 683075262 5.780000e-26 130.0
43 TraesCS2A01G464600 chr2B 82.353 119 21 0 3990 4108 683074161 683074279 3.500000e-18 104.0
44 TraesCS2A01G464600 chr2B 84.884 86 8 3 6401 6486 683078313 683078393 1.640000e-11 82.4
45 TraesCS2A01G464600 chr3B 98.766 1621 18 2 1 1621 806117526 806115908 0.000000e+00 2881.0
46 TraesCS2A01G464600 chr3B 98.591 1632 12 1 1 1621 175769324 175770955 0.000000e+00 2876.0
47 TraesCS2A01G464600 chr3B 97.409 1621 40 2 1 1621 125859695 125858077 0.000000e+00 2760.0
48 TraesCS2A01G464600 chr3B 94.136 324 6 6 1324 1636 810125629 810125308 1.390000e-131 481.0
49 TraesCS2A01G464600 chr6A 98.354 1640 14 5 1 1627 387979522 387977883 0.000000e+00 2867.0
50 TraesCS2A01G464600 chr6A 85.961 869 112 5 1622 2481 617079338 617080205 0.000000e+00 920.0
51 TraesCS2A01G464600 chr7B 98.581 1621 18 3 1 1621 296336575 296334960 0.000000e+00 2861.0
52 TraesCS2A01G464600 chr7B 98.165 1635 18 5 1 1623 559542735 559544369 0.000000e+00 2843.0
53 TraesCS2A01G464600 chr5B 98.335 1622 26 1 1 1622 22525237 22526857 0.000000e+00 2844.0
54 TraesCS2A01G464600 chr5B 97.574 1649 13 4 1 1625 457996261 457997906 0.000000e+00 2798.0
55 TraesCS2A01G464600 chr5B 92.063 63 3 1 6263 6325 390710575 390710515 3.530000e-13 87.9
56 TraesCS2A01G464600 chr5B 93.220 59 2 1 6267 6325 591828456 591828400 1.270000e-12 86.1
57 TraesCS2A01G464600 chr5B 90.476 63 5 1 6263 6325 589996983 589996922 1.640000e-11 82.4
58 TraesCS2A01G464600 chr4A 97.812 1645 12 2 1 1621 342425572 342423928 0.000000e+00 2817.0
59 TraesCS2A01G464600 chr4A 97.812 1645 12 2 1 1621 715756661 715755017 0.000000e+00 2817.0
60 TraesCS2A01G464600 chr4A 85.753 372 43 7 6739 7102 688766042 688765673 1.120000e-102 385.0
61 TraesCS2A01G464600 chr4A 84.946 372 43 8 6740 7102 688854059 688853692 1.460000e-96 364.0
62 TraesCS2A01G464600 chr1A 98.437 1599 14 4 37 1624 557476180 557474582 0.000000e+00 2804.0
63 TraesCS2A01G464600 chr1A 84.577 402 58 4 6702 7102 248877458 248877060 5.160000e-106 396.0
64 TraesCS2A01G464600 chr1B 97.325 1645 11 3 1 1621 341515670 341517305 0.000000e+00 2763.0
65 TraesCS2A01G464600 chr1B 80.272 294 51 5 6815 7102 564001074 564001366 1.550000e-51 215.0
66 TraesCS2A01G464600 chrUn 85.928 803 98 9 1622 2415 307301045 307301841 0.000000e+00 843.0
67 TraesCS2A01G464600 chrUn 79.363 722 101 31 4864 5560 307301891 307302589 1.400000e-126 464.0
68 TraesCS2A01G464600 chrUn 79.363 722 101 31 4864 5560 316029933 316030631 1.400000e-126 464.0
69 TraesCS2A01G464600 chrUn 78.924 669 93 31 4864 5507 347761989 347762634 1.840000e-110 411.0
70 TraesCS2A01G464600 chrUn 80.932 236 28 9 5330 5560 361998903 361999126 3.410000e-38 171.0
71 TraesCS2A01G464600 chrUn 80.932 236 28 9 5330 5560 400349777 400350000 3.410000e-38 171.0
72 TraesCS2A01G464600 chrUn 92.500 40 2 1 6156 6195 307302964 307303002 1.000000e-03 56.5
73 TraesCS2A01G464600 chrUn 92.500 40 2 1 6156 6195 316031006 316031044 1.000000e-03 56.5
74 TraesCS2A01G464600 chr6B 84.914 643 95 2 2622 3263 717745534 717744893 0.000000e+00 649.0
75 TraesCS2A01G464600 chr6B 83.505 97 16 0 6101 6197 717703661 717703565 2.730000e-14 91.6
76 TraesCS2A01G464600 chr4B 95.894 341 3 4 1295 1624 66625088 66624748 6.270000e-150 542.0
77 TraesCS2A01G464600 chr3A 86.880 343 42 3 6762 7102 23246723 23247064 1.450000e-101 381.0
78 TraesCS2A01G464600 chr3A 91.803 61 4 1 6265 6325 594362664 594362723 4.570000e-12 84.2
79 TraesCS2A01G464600 chr1D 94.915 59 1 1 6267 6325 351255322 351255378 2.730000e-14 91.6
80 TraesCS2A01G464600 chr4D 93.443 61 3 1 6266 6325 73330326 73330386 9.810000e-14 89.8
81 TraesCS2A01G464600 chr5D 93.220 59 2 2 6265 6322 133864685 133864742 1.270000e-12 86.1


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 TraesCS2A01G464600 chr2A 709856790 709863891 7101 False 13116.000000 13116 100.000000 1 7102 1 chr2A.!!$F1 7101
1 TraesCS2A01G464600 chr2A 710038808 710041259 2451 False 2453.000000 2453 84.825000 1622 4063 1 chr2A.!!$F2 2441
2 TraesCS2A01G464600 chr2A 710095661 710100437 4776 False 901.575000 3212 87.804000 1622 6580 4 chr2A.!!$F6 4958
3 TraesCS2A01G464600 chr2A 710045995 710046713 718 False 237.000000 285 81.992000 5037 5989 2 chr2A.!!$F5 952
4 TraesCS2A01G464600 chr2D 571529659 571532409 2750 False 2169.000000 2169 81.277000 1622 4332 1 chr2D.!!$F3 2710
5 TraesCS2A01G464600 chr2D 571197797 571203771 5974 False 1932.000000 6191 92.090250 1622 7102 4 chr2D.!!$F4 5480
6 TraesCS2A01G464600 chr2D 571211594 571219820 8226 False 1152.000000 2588 82.178333 1622 6268 3 chr2D.!!$F5 4646
7 TraesCS2A01G464600 chr2D 571445863 571446767 904 False 944.000000 944 85.620000 1622 2524 1 chr2D.!!$F2 902
8 TraesCS2A01G464600 chr2B 683045586 683051808 6222 False 1931.250000 6091 91.922000 1622 7102 4 chr2B.!!$F3 5480
9 TraesCS2A01G464600 chr2B 794689195 794691227 2032 True 1653.000000 1653 81.734000 2229 4235 1 chr2B.!!$R1 2006
10 TraesCS2A01G464600 chr2B 794798096 794800128 2032 True 1653.000000 1653 81.734000 2229 4235 1 chr2B.!!$R2 2006
11 TraesCS2A01G464600 chr2B 683162179 683163078 899 False 917.000000 917 85.165000 1622 2524 1 chr2B.!!$F2 902
12 TraesCS2A01G464600 chr2B 683057571 683062860 5289 False 865.666667 1524 84.415000 2509 6268 3 chr2B.!!$F4 3759
13 TraesCS2A01G464600 chr2B 683070287 683078393 8106 False 577.057143 2547 83.074000 1622 6486 7 chr2B.!!$F5 4864
14 TraesCS2A01G464600 chr2B 683130846 683137599 6753 False 519.400000 1417 85.870400 1622 6583 5 chr2B.!!$F6 4961
15 TraesCS2A01G464600 chr2B 606610630 606611151 521 False 300.000000 300 77.486000 6581 7102 1 chr2B.!!$F1 521
16 TraesCS2A01G464600 chr3B 806115908 806117526 1618 True 2881.000000 2881 98.766000 1 1621 1 chr3B.!!$R2 1620
17 TraesCS2A01G464600 chr3B 175769324 175770955 1631 False 2876.000000 2876 98.591000 1 1621 1 chr3B.!!$F1 1620
18 TraesCS2A01G464600 chr3B 125858077 125859695 1618 True 2760.000000 2760 97.409000 1 1621 1 chr3B.!!$R1 1620
19 TraesCS2A01G464600 chr6A 387977883 387979522 1639 True 2867.000000 2867 98.354000 1 1627 1 chr6A.!!$R1 1626
20 TraesCS2A01G464600 chr6A 617079338 617080205 867 False 920.000000 920 85.961000 1622 2481 1 chr6A.!!$F1 859
21 TraesCS2A01G464600 chr7B 296334960 296336575 1615 True 2861.000000 2861 98.581000 1 1621 1 chr7B.!!$R1 1620
22 TraesCS2A01G464600 chr7B 559542735 559544369 1634 False 2843.000000 2843 98.165000 1 1623 1 chr7B.!!$F1 1622
23 TraesCS2A01G464600 chr5B 22525237 22526857 1620 False 2844.000000 2844 98.335000 1 1622 1 chr5B.!!$F1 1621
24 TraesCS2A01G464600 chr5B 457996261 457997906 1645 False 2798.000000 2798 97.574000 1 1625 1 chr5B.!!$F2 1624
25 TraesCS2A01G464600 chr4A 342423928 342425572 1644 True 2817.000000 2817 97.812000 1 1621 1 chr4A.!!$R1 1620
26 TraesCS2A01G464600 chr4A 715755017 715756661 1644 True 2817.000000 2817 97.812000 1 1621 1 chr4A.!!$R4 1620
27 TraesCS2A01G464600 chr1A 557474582 557476180 1598 True 2804.000000 2804 98.437000 37 1624 1 chr1A.!!$R2 1587
28 TraesCS2A01G464600 chr1B 341515670 341517305 1635 False 2763.000000 2763 97.325000 1 1621 1 chr1B.!!$F1 1620
29 TraesCS2A01G464600 chrUn 307301045 307303002 1957 False 454.500000 843 85.930333 1622 6195 3 chrUn.!!$F4 4573
30 TraesCS2A01G464600 chrUn 347761989 347762634 645 False 411.000000 411 78.924000 4864 5507 1 chrUn.!!$F1 643
31 TraesCS2A01G464600 chrUn 316029933 316031044 1111 False 260.250000 464 85.931500 4864 6195 2 chrUn.!!$F5 1331
32 TraesCS2A01G464600 chr6B 717744893 717745534 641 True 649.000000 649 84.914000 2622 3263 1 chr6B.!!$R2 641

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
225 226 1.361993 GATCGAGCGAGCCATCTGT 59.638 57.895 0.00 0.00 0.00 3.41 F
557 558 1.420514 TCGATCCTCTAGGTGGTCGAT 59.579 52.381 12.00 0.00 38.56 3.59 F
1466 1468 4.502950 GCTAAGATGCCAGTCTAAGATGCT 60.503 45.833 0.00 0.00 0.00 3.79 F
2795 3141 3.415212 CAAAGCCTGGATCTGAAGTTCA 58.585 45.455 5.25 5.25 0.00 3.18 F
3268 3617 3.531538 TGATAAACTTGAGATCACGGCC 58.468 45.455 0.00 0.00 0.00 6.13 F
4147 4546 1.269936 CCTTTGGCTTTCCACAAGCTG 60.270 52.381 6.53 0.00 43.33 4.24 F
5572 10019 0.742281 CAGCAGCGCAGTGGATAGTT 60.742 55.000 11.47 0.00 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1188 1190 0.494551 TGGTTACCTTCCTCCCTCCA 59.505 55.000 2.07 0.0 0.00 3.86 R
1466 1468 6.319152 GGACTGTCAGTTAGCATCTTAGACTA 59.681 42.308 7.00 0.0 0.00 2.59 R
2826 3172 1.395262 GGAAAAGCTGCGTAAGAGAGC 59.605 52.381 0.00 0.0 42.72 4.09 R
4147 4546 1.331756 CATCCCACATGCGACTAAAGC 59.668 52.381 0.00 0.0 0.00 3.51 R
4930 7731 3.126514 GGTGCAACAGATGAATCAGACAG 59.873 47.826 0.00 0.0 39.98 3.51 R
5590 10037 0.036164 TGTCACCCACTGCGCTAATT 59.964 50.000 9.73 0.0 0.00 1.40 R
6705 18047 1.003223 AGTAAACTCGTGCCGCAAAAC 60.003 47.619 0.00 0.0 0.00 2.43 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
225 226 1.361993 GATCGAGCGAGCCATCTGT 59.638 57.895 0.00 0.00 0.00 3.41
507 508 3.371097 GAACTGCATCTCGGGCGGA 62.371 63.158 0.00 0.00 40.08 5.54
557 558 1.420514 TCGATCCTCTAGGTGGTCGAT 59.579 52.381 12.00 0.00 38.56 3.59
1466 1468 4.502950 GCTAAGATGCCAGTCTAAGATGCT 60.503 45.833 0.00 0.00 0.00 3.79
1660 1701 5.221722 GGTAGAGTTGATCCTGATTGGCATA 60.222 44.000 0.00 0.00 35.26 3.14
2795 3141 3.415212 CAAAGCCTGGATCTGAAGTTCA 58.585 45.455 5.25 5.25 0.00 3.18
2808 3154 5.751586 TCTGAAGTTCATTGGGGGTAATAC 58.248 41.667 5.91 0.00 0.00 1.89
2826 3172 6.926272 GGTAATACAGGCTCTACAAGATTCAG 59.074 42.308 0.00 0.00 0.00 3.02
3268 3617 3.531538 TGATAAACTTGAGATCACGGCC 58.468 45.455 0.00 0.00 0.00 6.13
3750 4115 5.757320 CGAATCTCTTATCACTTCCTGCAAT 59.243 40.000 0.00 0.00 0.00 3.56
3997 4363 5.768164 ACATTCGGAACATTTTTCCTACAGT 59.232 36.000 0.00 0.00 36.45 3.55
4147 4546 1.269936 CCTTTGGCTTTCCACAAGCTG 60.270 52.381 6.53 0.00 43.33 4.24
4774 5382 3.582714 ATTTTGCTCTAGGTTTGCTGC 57.417 42.857 0.00 0.00 0.00 5.25
4930 7731 1.227674 CCTTCATCGCTAGGCACCC 60.228 63.158 0.00 0.00 0.00 4.61
5114 9429 5.183228 GCCTCTGTAGCCAACTGTATAAAA 58.817 41.667 0.00 0.00 0.00 1.52
5118 9436 8.739972 CCTCTGTAGCCAACTGTATAAAATTTT 58.260 33.333 8.75 8.75 0.00 1.82
5375 9750 2.032302 CGGTGACAATCTCTCCTACGAG 59.968 54.545 0.00 0.00 37.48 4.18
5539 9935 0.989602 TCTCACGACCTCCTCTACCA 59.010 55.000 0.00 0.00 0.00 3.25
5566 10013 2.357881 TTCTCAGCAGCGCAGTGG 60.358 61.111 11.47 0.00 0.00 4.00
5567 10014 2.776670 CTTCTCAGCAGCGCAGTGGA 62.777 60.000 11.47 2.53 0.00 4.02
5568 10015 2.125229 CTCAGCAGCGCAGTGGAT 60.125 61.111 11.47 0.00 0.00 3.41
5569 10016 1.142531 CTCAGCAGCGCAGTGGATA 59.857 57.895 11.47 0.00 0.00 2.59
5570 10017 0.875040 CTCAGCAGCGCAGTGGATAG 60.875 60.000 11.47 0.00 0.00 2.08
5571 10018 1.153489 CAGCAGCGCAGTGGATAGT 60.153 57.895 11.47 0.00 0.00 2.12
5572 10019 0.742281 CAGCAGCGCAGTGGATAGTT 60.742 55.000 11.47 0.00 0.00 2.24
5573 10020 0.824109 AGCAGCGCAGTGGATAGTTA 59.176 50.000 11.47 0.00 0.00 2.24
5574 10021 1.207089 AGCAGCGCAGTGGATAGTTAA 59.793 47.619 11.47 0.00 0.00 2.01
5575 10022 2.006888 GCAGCGCAGTGGATAGTTAAA 58.993 47.619 11.47 0.00 0.00 1.52
5576 10023 2.418628 GCAGCGCAGTGGATAGTTAAAA 59.581 45.455 11.47 0.00 0.00 1.52
5577 10024 3.065371 GCAGCGCAGTGGATAGTTAAAAT 59.935 43.478 11.47 0.00 0.00 1.82
5578 10025 4.272504 GCAGCGCAGTGGATAGTTAAAATA 59.727 41.667 11.47 0.00 0.00 1.40
5579 10026 5.220777 GCAGCGCAGTGGATAGTTAAAATAA 60.221 40.000 11.47 0.00 0.00 1.40
5580 10027 6.513393 GCAGCGCAGTGGATAGTTAAAATAAT 60.513 38.462 11.47 0.00 0.00 1.28
5581 10028 6.852853 CAGCGCAGTGGATAGTTAAAATAATG 59.147 38.462 11.47 0.00 0.00 1.90
5582 10029 6.542370 AGCGCAGTGGATAGTTAAAATAATGT 59.458 34.615 11.47 0.00 0.00 2.71
5583 10030 7.067008 AGCGCAGTGGATAGTTAAAATAATGTT 59.933 33.333 11.47 0.00 0.00 2.71
5584 10031 7.700656 GCGCAGTGGATAGTTAAAATAATGTTT 59.299 33.333 0.30 0.00 0.00 2.83
5585 10032 9.221775 CGCAGTGGATAGTTAAAATAATGTTTC 57.778 33.333 0.00 0.00 0.00 2.78
5659 10957 7.214467 TGGGTCATCACTAAATTTGAAGTTC 57.786 36.000 0.00 0.00 0.00 3.01
5729 11028 3.290948 TTTAGTTTGAGGCACCTGTGT 57.709 42.857 0.00 0.00 0.00 3.72
5730 11029 3.290948 TTAGTTTGAGGCACCTGTGTT 57.709 42.857 0.00 0.00 0.00 3.32
5731 11030 1.680338 AGTTTGAGGCACCTGTGTTC 58.320 50.000 0.00 0.00 0.00 3.18
5732 11031 1.064758 AGTTTGAGGCACCTGTGTTCA 60.065 47.619 0.00 1.49 0.00 3.18
5733 11032 1.334869 GTTTGAGGCACCTGTGTTCAG 59.665 52.381 0.00 0.00 41.01 3.02
5734 11033 0.836606 TTGAGGCACCTGTGTTCAGA 59.163 50.000 0.00 0.00 43.76 3.27
5735 11034 0.836606 TGAGGCACCTGTGTTCAGAA 59.163 50.000 0.00 0.00 43.76 3.02
5736 11035 1.230324 GAGGCACCTGTGTTCAGAAC 58.770 55.000 6.32 6.32 43.76 3.01
5840 12740 4.578871 AGGCAACAAATATTTCCAAAGCC 58.421 39.130 14.25 14.25 41.41 4.35
5934 12852 2.953648 TGACGACACCACTCAGTAAGAA 59.046 45.455 0.00 0.00 0.00 2.52
6270 16151 9.046296 CACATTATCTTACCCTTCATTGTACTC 57.954 37.037 0.00 0.00 0.00 2.59
6279 16160 1.481871 TCATTGTACTCCCTCCGTCC 58.518 55.000 0.00 0.00 0.00 4.79
6283 16164 0.928505 TGTACTCCCTCCGTCCCATA 59.071 55.000 0.00 0.00 0.00 2.74
6284 16165 1.288633 TGTACTCCCTCCGTCCCATAA 59.711 52.381 0.00 0.00 0.00 1.90
6285 16166 2.090943 TGTACTCCCTCCGTCCCATAAT 60.091 50.000 0.00 0.00 0.00 1.28
6286 16167 1.424638 ACTCCCTCCGTCCCATAATG 58.575 55.000 0.00 0.00 0.00 1.90
6288 16169 2.090943 ACTCCCTCCGTCCCATAATGTA 60.091 50.000 0.00 0.00 0.00 2.29
6289 16170 2.969950 CTCCCTCCGTCCCATAATGTAA 59.030 50.000 0.00 0.00 0.00 2.41
6290 16171 2.969950 TCCCTCCGTCCCATAATGTAAG 59.030 50.000 0.00 0.00 0.00 2.34
6293 16174 4.563580 CCCTCCGTCCCATAATGTAAGATG 60.564 50.000 0.00 0.00 0.00 2.90
6294 16175 4.040461 CCTCCGTCCCATAATGTAAGATGT 59.960 45.833 0.00 0.00 0.00 3.06
6295 16176 5.454755 CCTCCGTCCCATAATGTAAGATGTT 60.455 44.000 0.00 0.00 0.00 2.71
6321 16202 8.642908 TTTTGACACTATACATTATGAGACGG 57.357 34.615 0.00 0.00 0.00 4.79
6322 16203 7.576861 TTGACACTATACATTATGAGACGGA 57.423 36.000 0.00 0.00 0.00 4.69
6338 16219 1.614160 GGAGGACGGAGGGAGTACT 59.386 63.158 0.00 0.00 35.04 2.73
6339 16220 0.842635 GGAGGACGGAGGGAGTACTA 59.157 60.000 0.00 0.00 31.89 1.82
6340 16221 1.424684 GGAGGACGGAGGGAGTACTAT 59.575 57.143 0.00 0.00 31.89 2.12
6341 16222 2.552809 GGAGGACGGAGGGAGTACTATC 60.553 59.091 0.00 0.00 31.89 2.08
6345 16226 4.602732 AGGACGGAGGGAGTACTATCTAAT 59.397 45.833 0.00 0.00 29.47 1.73
6346 16227 5.789575 AGGACGGAGGGAGTACTATCTAATA 59.210 44.000 0.00 0.00 29.47 0.98
6347 16228 6.274200 AGGACGGAGGGAGTACTATCTAATAA 59.726 42.308 0.00 0.00 29.47 1.40
6348 16229 7.036717 AGGACGGAGGGAGTACTATCTAATAAT 60.037 40.741 0.00 0.00 29.47 1.28
6349 16230 8.270744 GGACGGAGGGAGTACTATCTAATAATA 58.729 40.741 0.00 0.00 0.00 0.98
6350 16231 9.678260 GACGGAGGGAGTACTATCTAATAATAA 57.322 37.037 0.00 0.00 0.00 1.40
6378 16362 4.610536 GCGTCGTCGATACTATAAAACTCC 59.389 45.833 6.17 0.00 39.71 3.85
6398 16382 1.757118 CCATGATAGACCGTCACCTGT 59.243 52.381 0.40 0.00 0.00 4.00
6417 16417 7.021196 CACCTGTGAAAACCGTTATCAATTAG 58.979 38.462 0.00 0.00 0.00 1.73
6444 16444 2.034305 GTGAGACAGTACACTCGTGGTT 59.966 50.000 1.77 0.00 36.11 3.67
6446 16446 3.050619 GAGACAGTACACTCGTGGTTTG 58.949 50.000 1.77 0.00 34.19 2.93
6641 17983 3.849953 CGTTTACGAGCGGCCTGC 61.850 66.667 11.02 11.02 46.98 4.85
6663 18005 0.582960 AAAAGTTTACGGTGTCGCGG 59.417 50.000 6.13 0.00 40.63 6.46
6705 18047 3.181497 CCCATAAACTCGTCCTGCAAATG 60.181 47.826 0.00 0.00 0.00 2.32
6764 18106 2.171725 GCCTCGTGGTACCGCAATC 61.172 63.158 24.65 7.18 35.27 2.67
6778 18120 5.329035 ACCGCAATCTTTTCATAGCATTT 57.671 34.783 0.00 0.00 0.00 2.32
6998 18603 2.569059 CCATAGAGTTGCCAGTGATGG 58.431 52.381 0.00 0.00 0.00 3.51
7050 18655 2.165437 GAGGCACTGTTCTCGATCTTCT 59.835 50.000 0.00 0.00 41.55 2.85
7082 18687 5.171147 CAAGAAATGCAGTGATCTCATCC 57.829 43.478 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 226 3.071479 GTGCATTCCCGAGAAGTACAAA 58.929 45.455 0.00 0.00 34.86 2.83
557 558 1.227943 GCAGTCCAGGACAGCAACA 60.228 57.895 27.71 0.00 43.05 3.33
1188 1190 0.494551 TGGTTACCTTCCTCCCTCCA 59.505 55.000 2.07 0.00 0.00 3.86
1453 1455 7.040478 AGCATCTTAGACTAGCATCTTAGACTG 60.040 40.741 2.27 4.18 37.24 3.51
1454 1456 7.004086 AGCATCTTAGACTAGCATCTTAGACT 58.996 38.462 2.27 0.00 37.24 3.24
1455 1457 7.214467 AGCATCTTAGACTAGCATCTTAGAC 57.786 40.000 2.27 0.00 37.24 2.59
1456 1458 8.788806 GTTAGCATCTTAGACTAGCATCTTAGA 58.211 37.037 2.62 2.62 38.40 2.10
1466 1468 6.319152 GGACTGTCAGTTAGCATCTTAGACTA 59.681 42.308 7.00 0.00 0.00 2.59
2795 3141 2.789219 AGAGCCTGTATTACCCCCAAT 58.211 47.619 0.00 0.00 0.00 3.16
2808 3154 3.132646 AGAGCTGAATCTTGTAGAGCCTG 59.867 47.826 0.00 0.00 0.00 4.85
2826 3172 1.395262 GGAAAAGCTGCGTAAGAGAGC 59.605 52.381 0.00 0.00 42.72 4.09
3750 4115 3.269906 GAGGGAGGTCAGGCTATATAGGA 59.730 52.174 11.72 0.00 0.00 2.94
3997 4363 3.441101 AGGGTGAGCATGTAGACTAACA 58.559 45.455 0.00 0.00 0.00 2.41
4147 4546 1.331756 CATCCCACATGCGACTAAAGC 59.668 52.381 0.00 0.00 0.00 3.51
4580 5131 5.485662 AGTACGAGCCAATTTAATGCTTC 57.514 39.130 0.00 0.00 34.99 3.86
4774 5382 3.809279 TGCCGTGATGTATATTGCTGAAG 59.191 43.478 0.00 0.00 0.00 3.02
4930 7731 3.126514 GGTGCAACAGATGAATCAGACAG 59.873 47.826 0.00 0.00 39.98 3.51
5539 9935 1.550072 GCTGCTGAGAAGAGAGAAGGT 59.450 52.381 0.00 0.00 0.00 3.50
5587 10034 2.030274 GTCACCCACTGCGCTAATTTTT 60.030 45.455 9.73 0.00 0.00 1.94
5588 10035 1.539827 GTCACCCACTGCGCTAATTTT 59.460 47.619 9.73 0.00 0.00 1.82
5589 10036 1.165270 GTCACCCACTGCGCTAATTT 58.835 50.000 9.73 0.00 0.00 1.82
5590 10037 0.036164 TGTCACCCACTGCGCTAATT 59.964 50.000 9.73 0.00 0.00 1.40
5591 10038 0.673644 GTGTCACCCACTGCGCTAAT 60.674 55.000 9.73 0.00 41.11 1.73
5592 10039 1.301401 GTGTCACCCACTGCGCTAA 60.301 57.895 9.73 0.00 41.11 3.09
5593 10040 2.342279 GTGTCACCCACTGCGCTA 59.658 61.111 9.73 0.00 41.11 4.26
5600 10047 1.597027 CGGGTTGAGTGTCACCCAC 60.597 63.158 8.11 0.00 44.89 4.61
5601 10048 2.067605 ACGGGTTGAGTGTCACCCA 61.068 57.895 8.11 0.00 37.48 4.51
5602 10049 1.597027 CACGGGTTGAGTGTCACCC 60.597 63.158 0.00 0.00 35.63 4.61
5729 11028 5.273208 AGGCCTAGTATCTGAAGTTCTGAA 58.727 41.667 15.40 4.15 0.00 3.02
5730 11029 4.873010 AGGCCTAGTATCTGAAGTTCTGA 58.127 43.478 1.29 14.02 0.00 3.27
5731 11030 4.261405 CGAGGCCTAGTATCTGAAGTTCTG 60.261 50.000 4.42 3.79 0.00 3.02
5732 11031 3.886505 CGAGGCCTAGTATCTGAAGTTCT 59.113 47.826 4.42 0.00 0.00 3.01
5733 11032 3.633065 ACGAGGCCTAGTATCTGAAGTTC 59.367 47.826 17.89 0.00 0.00 3.01
5734 11033 3.633418 ACGAGGCCTAGTATCTGAAGTT 58.367 45.455 17.89 0.00 0.00 2.66
5735 11034 3.300239 ACGAGGCCTAGTATCTGAAGT 57.700 47.619 17.89 0.00 0.00 3.01
5736 11035 4.643463 TCTACGAGGCCTAGTATCTGAAG 58.357 47.826 23.94 14.24 0.00 3.02
5840 12740 2.900122 CCACAAATGGTAGCACTTCG 57.100 50.000 0.00 0.00 41.64 3.79
5934 12852 6.747280 GTCGCATAGCAAAGTACAAATTCAAT 59.253 34.615 0.00 0.00 0.00 2.57
6270 16151 2.969950 TCTTACATTATGGGACGGAGGG 59.030 50.000 0.00 0.00 0.00 4.30
6295 16176 9.093970 CCGTCTCATAATGTATAGTGTCAAAAA 57.906 33.333 0.00 0.00 0.00 1.94
6302 16183 6.613233 GTCCTCCGTCTCATAATGTATAGTG 58.387 44.000 0.00 0.00 0.00 2.74
6303 16184 5.411977 CGTCCTCCGTCTCATAATGTATAGT 59.588 44.000 0.00 0.00 0.00 2.12
6304 16185 5.163744 CCGTCCTCCGTCTCATAATGTATAG 60.164 48.000 0.00 0.00 33.66 1.31
6305 16186 4.698780 CCGTCCTCCGTCTCATAATGTATA 59.301 45.833 0.00 0.00 33.66 1.47
6307 16188 2.882761 CCGTCCTCCGTCTCATAATGTA 59.117 50.000 0.00 0.00 33.66 2.29
6308 16189 1.681793 CCGTCCTCCGTCTCATAATGT 59.318 52.381 0.00 0.00 33.66 2.71
6309 16190 1.954382 TCCGTCCTCCGTCTCATAATG 59.046 52.381 0.00 0.00 33.66 1.90
6313 16194 1.454111 CCTCCGTCCTCCGTCTCAT 60.454 63.158 0.00 0.00 33.66 2.90
6315 16196 2.829458 CCCTCCGTCCTCCGTCTC 60.829 72.222 0.00 0.00 33.66 3.36
6316 16197 3.336568 TCCCTCCGTCCTCCGTCT 61.337 66.667 0.00 0.00 33.66 4.18
6317 16198 2.262774 TACTCCCTCCGTCCTCCGTC 62.263 65.000 0.00 0.00 33.66 4.79
6318 16199 2.304056 TACTCCCTCCGTCCTCCGT 61.304 63.158 0.00 0.00 33.66 4.69
6319 16200 1.823041 GTACTCCCTCCGTCCTCCG 60.823 68.421 0.00 0.00 0.00 4.63
6320 16201 0.842635 TAGTACTCCCTCCGTCCTCC 59.157 60.000 0.00 0.00 0.00 4.30
6321 16202 2.372837 AGATAGTACTCCCTCCGTCCTC 59.627 54.545 0.00 0.00 0.00 3.71
6322 16203 2.420705 AGATAGTACTCCCTCCGTCCT 58.579 52.381 0.00 0.00 0.00 3.85
6338 16219 8.872845 TCGACGACGCACTATTATTATTAGATA 58.127 33.333 1.48 0.00 39.58 1.98
6339 16220 7.745972 TCGACGACGCACTATTATTATTAGAT 58.254 34.615 1.48 0.00 39.58 1.98
6340 16221 7.120789 TCGACGACGCACTATTATTATTAGA 57.879 36.000 1.48 0.00 39.58 2.10
6341 16222 7.950108 ATCGACGACGCACTATTATTATTAG 57.050 36.000 0.00 0.00 39.58 1.73
6345 16226 6.471976 AGTATCGACGACGCACTATTATTA 57.528 37.500 0.00 0.00 39.58 0.98
6346 16227 5.354054 AGTATCGACGACGCACTATTATT 57.646 39.130 0.00 0.00 39.58 1.40
6347 16228 6.659361 ATAGTATCGACGACGCACTATTAT 57.341 37.500 19.88 9.39 40.71 1.28
6348 16229 7.581011 TTATAGTATCGACGACGCACTATTA 57.419 36.000 25.68 19.17 42.04 0.98
6349 16230 6.471976 TTATAGTATCGACGACGCACTATT 57.528 37.500 25.68 16.30 42.04 1.73
6350 16231 6.471976 TTTATAGTATCGACGACGCACTAT 57.528 37.500 24.71 24.71 43.13 2.12
6351 16232 5.905480 TTTATAGTATCGACGACGCACTA 57.095 39.130 17.93 17.93 39.27 2.74
6352 16233 4.801147 TTTATAGTATCGACGACGCACT 57.199 40.909 15.52 15.52 39.58 4.40
6353 16234 4.966366 AGTTTTATAGTATCGACGACGCAC 59.034 41.667 0.00 3.19 39.58 5.34
6378 16362 1.757118 ACAGGTGACGGTCTATCATGG 59.243 52.381 9.88 0.00 31.00 3.66
6398 16382 9.173021 ACATCATCTAATTGATAACGGTTTTCA 57.827 29.630 9.51 9.51 34.59 2.69
6417 16417 4.142578 ACGAGTGTACTGTCTCACATCATC 60.143 45.833 14.96 6.13 37.07 2.92
6444 16444 5.422012 AGGAGGCTTTCAAGAAGAAAAACAA 59.578 36.000 0.00 0.00 45.11 2.83
6446 16446 5.521906 AGGAGGCTTTCAAGAAGAAAAAC 57.478 39.130 0.00 0.00 45.11 2.43
6648 17990 3.113979 CCCCGCGACACCGTAAAC 61.114 66.667 8.23 0.00 38.24 2.01
6705 18047 1.003223 AGTAAACTCGTGCCGCAAAAC 60.003 47.619 0.00 0.00 0.00 2.43
6714 18056 4.496010 CGGGTCAGATCTAGTAAACTCGTG 60.496 50.000 0.00 0.00 0.00 4.35
6848 18191 7.392113 TGTTGTATTGTGAATTACCTTTCCGAT 59.608 33.333 0.00 0.00 0.00 4.18
6851 18194 9.353999 GATTGTTGTATTGTGAATTACCTTTCC 57.646 33.333 0.00 0.00 0.00 3.13
6998 18603 5.762218 CCAACTCTGGGATGATCTTATTGAC 59.238 44.000 0.00 0.00 39.30 3.18
7015 18620 1.344763 GTGCCTCACACTACCAACTCT 59.655 52.381 0.00 0.00 46.41 3.24
7050 18655 1.544724 GCATTTCTTGCCACCTACCA 58.455 50.000 0.00 0.00 46.15 3.25


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

AutoCloner maintained by Alex Coulton.