Multiple sequence alignment - TraesCS2B01G117500

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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 TraesCS2B01G117500 chr2B 100.000 4286 0 0 1 4286 80554541 80558826 0.000000e+00 7915.0
1 TraesCS2B01G117500 chr2B 85.314 1212 125 34 703 1896 77496286 77495110 0.000000e+00 1203.0
2 TraesCS2B01G117500 chr2D 88.961 2763 142 81 675 3363 52041033 52043706 0.000000e+00 3262.0
3 TraesCS2B01G117500 chr2D 91.248 2388 131 55 943 3309 42718057 42715727 0.000000e+00 3181.0
4 TraesCS2B01G117500 chr2D 91.401 314 20 1 475 781 42721024 42720711 1.420000e-114 424.0
5 TraesCS2B01G117500 chr2D 87.302 63 7 1 802 864 42720708 42720647 2.140000e-08 71.3
6 TraesCS2B01G117500 chr2A 91.814 1588 97 15 2 1577 53440195 53441761 0.000000e+00 2182.0
7 TraesCS2B01G117500 chr2A 89.470 1396 60 40 1996 3363 53442182 53443518 0.000000e+00 1683.0
8 TraesCS2B01G117500 chr2A 90.296 371 22 7 1614 1977 53441759 53442122 1.390000e-129 473.0
9 TraesCS2B01G117500 chr5B 95.833 816 33 1 3471 4286 470015777 470016591 0.000000e+00 1317.0
10 TraesCS2B01G117500 chr3B 96.237 691 25 1 3482 4172 448564202 448563513 0.000000e+00 1131.0
11 TraesCS2B01G117500 chr3B 96.639 119 4 0 4167 4285 448561827 448561709 9.400000e-47 198.0
12 TraesCS2B01G117500 chr4A 91.955 808 39 4 3482 4286 500771289 500770505 0.000000e+00 1109.0
13 TraesCS2B01G117500 chr4A 95.429 175 8 0 1991 2165 594126049 594126223 3.260000e-71 279.0
14 TraesCS2B01G117500 chr4B 89.481 675 60 4 3614 4286 131363428 131362763 0.000000e+00 843.0
15 TraesCS2B01G117500 chr4B 91.429 175 15 0 1991 2165 17389696 17389522 1.540000e-59 241.0
16 TraesCS2B01G117500 chr4B 94.245 139 8 0 3482 3620 131368230 131368092 3.360000e-51 213.0
17 TraesCS2B01G117500 chr4B 90.625 128 12 0 1769 1896 17389929 17389802 2.050000e-38 171.0
18 TraesCS2B01G117500 chr5D 91.522 578 35 4 3719 4286 308847367 308847940 0.000000e+00 784.0
19 TraesCS2B01G117500 chr5D 94.215 242 13 1 3482 3723 308843384 308843624 6.770000e-98 368.0
20 TraesCS2B01G117500 chr7D 80.783 843 97 31 3482 4286 410944682 410943867 2.210000e-167 599.0
21 TraesCS2B01G117500 chr4D 79.369 824 98 36 3483 4283 6569050 6569824 8.220000e-142 514.0
22 TraesCS2B01G117500 chr1A 84.200 481 62 12 2731 3209 531241330 531241798 5.050000e-124 455.0
23 TraesCS2B01G117500 chr1A 80.202 495 82 13 1737 2222 531239793 531240280 1.470000e-94 357.0
24 TraesCS2B01G117500 chr1D 83.200 500 60 17 2731 3207 432800698 432801196 1.830000e-118 436.0
25 TraesCS2B01G117500 chr1D 79.317 498 78 18 1737 2216 432798446 432798936 4.130000e-85 326.0
26 TraesCS2B01G117500 chr6D 91.176 272 24 0 1091 1362 449117087 449116816 1.880000e-98 370.0
27 TraesCS2B01G117500 chr1B 79.615 520 81 15 1737 2237 584158569 584159082 2.450000e-92 350.0
28 TraesCS2B01G117500 chr1B 91.165 249 21 1 2730 2977 584160193 584160441 1.910000e-88 337.0
29 TraesCS2B01G117500 chr1B 86.842 152 19 1 3058 3209 584160499 584160649 7.370000e-38 169.0
30 TraesCS2B01G117500 chr7A 91.837 49 4 0 1176 1224 635649579 635649531 7.690000e-08 69.4


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 TraesCS2B01G117500 chr2B 80554541 80558826 4285 False 7915.000000 7915 100.000000 1 4286 1 chr2B.!!$F1 4285
1 TraesCS2B01G117500 chr2B 77495110 77496286 1176 True 1203.000000 1203 85.314000 703 1896 1 chr2B.!!$R1 1193
2 TraesCS2B01G117500 chr2D 52041033 52043706 2673 False 3262.000000 3262 88.961000 675 3363 1 chr2D.!!$F1 2688
3 TraesCS2B01G117500 chr2D 42715727 42721024 5297 True 1225.433333 3181 89.983667 475 3309 3 chr2D.!!$R1 2834
4 TraesCS2B01G117500 chr2A 53440195 53443518 3323 False 1446.000000 2182 90.526667 2 3363 3 chr2A.!!$F1 3361
5 TraesCS2B01G117500 chr5B 470015777 470016591 814 False 1317.000000 1317 95.833000 3471 4286 1 chr5B.!!$F1 815
6 TraesCS2B01G117500 chr3B 448561709 448564202 2493 True 664.500000 1131 96.438000 3482 4285 2 chr3B.!!$R1 803
7 TraesCS2B01G117500 chr4A 500770505 500771289 784 True 1109.000000 1109 91.955000 3482 4286 1 chr4A.!!$R1 804
8 TraesCS2B01G117500 chr4B 131362763 131363428 665 True 843.000000 843 89.481000 3614 4286 1 chr4B.!!$R1 672
9 TraesCS2B01G117500 chr5D 308843384 308847940 4556 False 576.000000 784 92.868500 3482 4286 2 chr5D.!!$F1 804
10 TraesCS2B01G117500 chr7D 410943867 410944682 815 True 599.000000 599 80.783000 3482 4286 1 chr7D.!!$R1 804
11 TraesCS2B01G117500 chr4D 6569050 6569824 774 False 514.000000 514 79.369000 3483 4283 1 chr4D.!!$F1 800
12 TraesCS2B01G117500 chr1A 531239793 531241798 2005 False 406.000000 455 82.201000 1737 3209 2 chr1A.!!$F1 1472
13 TraesCS2B01G117500 chr1D 432798446 432801196 2750 False 381.000000 436 81.258500 1737 3207 2 chr1D.!!$F1 1470
14 TraesCS2B01G117500 chr1B 584158569 584160649 2080 False 285.333333 350 85.874000 1737 3209 3 chr1B.!!$F1 1472

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
809 829 0.105401 TCACCCCACTACACTCCACA 60.105 55.0 0.0 0.0 0.0 4.17 F
875 1840 0.108774 GCTCCTTAAATCCCCCTCCG 59.891 60.0 0.0 0.0 0.0 4.63 F
2557 6320 0.313987 TACGCCCACATGCTCGATAG 59.686 55.0 0.0 0.0 0.0 2.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2701 6913 0.041926 CACACACGCACACAGTCATG 60.042 55.0 0.0 0.0 0.0 3.07 R
3055 7611 0.324614 ACACCGTCCTGCATCATCAA 59.675 50.0 0.0 0.0 0.0 2.57 R
3390 7979 0.246635 TAGAGTCCGCAAACCTGAGC 59.753 55.0 0.0 0.0 0.0 4.26 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
59 60 7.765695 AAATGTAACTCCAAACAGATGATGT 57.234 32.000 0.00 0.00 46.97 3.06
86 87 9.461312 AAATGAAGATGTAAACTAGTTATGCCA 57.539 29.630 8.92 3.92 0.00 4.92
89 90 5.681639 AGATGTAAACTAGTTATGCCACCC 58.318 41.667 8.92 0.63 0.00 4.61
128 129 3.056328 GTGCCTCGGGTTTGCTCC 61.056 66.667 0.00 0.00 0.00 4.70
131 132 2.429930 CCTCGGGTTTGCTCCACA 59.570 61.111 0.00 0.00 0.00 4.17
146 147 1.172180 CCACAGGTGACGGTTTGCAT 61.172 55.000 0.00 0.00 36.26 3.96
215 216 0.471211 AACGAGAGGAGTTGGGGTGA 60.471 55.000 0.00 0.00 0.00 4.02
239 240 0.394565 AACTTGACAGGAGCGAGCTT 59.605 50.000 0.00 0.00 0.00 3.74
307 308 2.768344 GGGAGGCCGGATGAAGGA 60.768 66.667 5.05 0.00 0.00 3.36
321 322 3.959329 AAGGACGCTACGGGCTCCT 62.959 63.158 13.41 13.41 44.48 3.69
326 327 3.541713 GCTACGGGCTCCTGGGAG 61.542 72.222 11.97 11.97 44.56 4.30
338 339 4.136978 TGGGAGCTCCAGGAGTTC 57.863 61.111 33.29 22.32 41.46 3.01
344 345 1.346068 GAGCTCCAGGAGTTCAAGTGT 59.654 52.381 24.75 0.00 39.23 3.55
345 346 2.563179 GAGCTCCAGGAGTTCAAGTGTA 59.437 50.000 24.75 0.00 39.23 2.90
443 451 8.649973 AATATGTTAACAAGAGTCCTTCGATC 57.350 34.615 13.23 0.00 0.00 3.69
457 465 2.134201 TCGATCCATGCGTACATCAC 57.866 50.000 0.00 0.00 32.87 3.06
459 467 2.100749 TCGATCCATGCGTACATCACTT 59.899 45.455 0.00 0.00 32.87 3.16
495 503 4.156455 TCCTATTTGTGGGAGCAGATTC 57.844 45.455 0.00 0.00 0.00 2.52
504 512 4.041567 TGTGGGAGCAGATTCTTAAACTCA 59.958 41.667 0.00 0.00 0.00 3.41
568 576 0.914644 ATGTCACCTGGATGTCTGGG 59.085 55.000 0.00 0.00 38.62 4.45
809 829 0.105401 TCACCCCACTACACTCCACA 60.105 55.000 0.00 0.00 0.00 4.17
830 850 4.929808 ACATACAATCTTCTCGTTTTCGCT 59.070 37.500 0.00 0.00 43.73 4.93
872 1837 1.132500 CGAGCTCCTTAAATCCCCCT 58.868 55.000 8.47 0.00 0.00 4.79
873 1838 1.070914 CGAGCTCCTTAAATCCCCCTC 59.929 57.143 8.47 0.00 0.00 4.30
874 1839 1.422024 GAGCTCCTTAAATCCCCCTCC 59.578 57.143 0.87 0.00 0.00 4.30
875 1840 0.108774 GCTCCTTAAATCCCCCTCCG 59.891 60.000 0.00 0.00 0.00 4.63
876 1841 1.802553 CTCCTTAAATCCCCCTCCGA 58.197 55.000 0.00 0.00 0.00 4.55
975 3513 2.575789 CGCGCCGGCATTGTTTAC 60.576 61.111 28.98 3.46 39.92 2.01
978 3516 1.136565 CGCCGGCATTGTTTACCAG 59.863 57.895 28.98 0.37 0.00 4.00
1285 3865 2.116772 TCGTCGACAAGGACCCCT 59.883 61.111 17.16 0.00 33.30 4.79
1359 3939 2.705220 CTCGTCCGCGTCGTCATA 59.295 61.111 17.50 1.60 39.49 2.15
1400 3980 2.461110 CGTACGTGCATTGCCCCTC 61.461 63.158 7.22 0.00 0.00 4.30
1401 3981 2.125310 TACGTGCATTGCCCCTCG 60.125 61.111 6.12 8.36 0.00 4.63
1441 4021 0.317160 GTTGCCAAGCCCTGTTTACC 59.683 55.000 0.00 0.00 0.00 2.85
1505 4093 1.227764 CCAGCCGTCCATGATCAGG 60.228 63.158 0.09 0.00 0.00 3.86
1547 4135 1.741770 GCGCTTCCTGGAATCGTGT 60.742 57.895 27.24 0.00 34.34 4.49
1558 4146 1.078759 GAATCGTGTGCGTCAGGGAG 61.079 60.000 2.55 0.00 39.49 4.30
1684 4275 8.181573 TGAAAACTTCGAACTATTATGGCATTC 58.818 33.333 4.78 0.00 0.00 2.67
1692 4283 6.204688 CGAACTATTATGGCATTCTGGCTAAA 59.795 38.462 4.78 0.00 44.10 1.85
1694 4285 7.896383 ACTATTATGGCATTCTGGCTAAAAA 57.104 32.000 4.78 0.00 44.10 1.94
1879 4470 3.449227 CTCGGCACCTACGGCTCA 61.449 66.667 0.00 0.00 0.00 4.26
1998 4639 3.531538 CCATGTCCTAATACACGCTTGT 58.468 45.455 0.05 0.05 40.02 3.16
2303 5459 2.352686 CAATACCGCGCATGCTGC 60.353 61.111 17.13 18.82 40.69 5.25
2318 5474 3.413846 TGCTGCACAGAGAGAGAAAAT 57.586 42.857 0.00 0.00 0.00 1.82
2350 5523 1.599071 CGAGCAGCACAAAAACAGAGA 59.401 47.619 0.00 0.00 0.00 3.10
2352 5525 3.487376 CGAGCAGCACAAAAACAGAGAAA 60.487 43.478 0.00 0.00 0.00 2.52
2353 5526 4.423732 GAGCAGCACAAAAACAGAGAAAA 58.576 39.130 0.00 0.00 0.00 2.29
2357 5530 5.445010 GCAGCACAAAAACAGAGAAAAACAG 60.445 40.000 0.00 0.00 0.00 3.16
2358 5531 5.863397 CAGCACAAAAACAGAGAAAAACAGA 59.137 36.000 0.00 0.00 0.00 3.41
2360 5533 5.220284 GCACAAAAACAGAGAAAAACAGAGC 60.220 40.000 0.00 0.00 0.00 4.09
2362 5535 6.532657 CACAAAAACAGAGAAAAACAGAGCAT 59.467 34.615 0.00 0.00 0.00 3.79
2366 5539 3.004106 ACAGAGAAAAACAGAGCATGCAC 59.996 43.478 21.98 14.59 0.00 4.57
2367 5540 2.225019 AGAGAAAAACAGAGCATGCACG 59.775 45.455 21.98 12.39 0.00 5.34
2384 5634 1.866601 CACGAGCAAACATCTGTGTGA 59.133 47.619 4.66 0.00 38.92 3.58
2557 6320 0.313987 TACGCCCACATGCTCGATAG 59.686 55.000 0.00 0.00 0.00 2.08
2584 6748 4.103357 CAAATATTTCGGTCTCGTCTCGT 58.897 43.478 0.00 0.00 37.69 4.18
2585 6749 3.605743 ATATTTCGGTCTCGTCTCGTC 57.394 47.619 0.00 0.00 37.69 4.20
2639 6834 8.480853 CGTGTTTTCTGTTTTGTTTTTCTACAA 58.519 29.630 0.00 0.00 36.30 2.41
2701 6913 3.425525 CGTGTGACGAGGAATGTATATGC 59.574 47.826 0.00 0.00 46.05 3.14
2722 6934 1.348250 GACTGTGTGCGTGTGTGTG 59.652 57.895 0.00 0.00 0.00 3.82
2735 7231 4.974721 GTGTGGTGGGTGCAGGGG 62.975 72.222 0.00 0.00 0.00 4.79
3022 7577 2.045242 CGTCTCCGTCCTCTCCCA 60.045 66.667 0.00 0.00 0.00 4.37
3055 7611 2.967887 TCTGACGGTGGATGATGATGAT 59.032 45.455 0.00 0.00 0.00 2.45
3243 7802 0.862490 CGTTCCATGTAACACGCACA 59.138 50.000 1.87 0.00 0.00 4.57
3244 7803 1.397945 CGTTCCATGTAACACGCACAC 60.398 52.381 1.87 0.00 0.00 3.82
3245 7804 1.600013 GTTCCATGTAACACGCACACA 59.400 47.619 0.00 0.00 0.00 3.72
3246 7805 1.222300 TCCATGTAACACGCACACAC 58.778 50.000 0.00 0.00 0.00 3.82
3247 7806 0.110867 CCATGTAACACGCACACACG 60.111 55.000 0.00 0.00 39.50 4.49
3249 7808 1.004398 CATGTAACACGCACACACGTT 60.004 47.619 0.00 0.00 45.75 3.99
3250 7809 0.646381 TGTAACACGCACACACGTTC 59.354 50.000 0.00 0.00 45.75 3.95
3251 7810 0.646381 GTAACACGCACACACGTTCA 59.354 50.000 0.00 0.00 45.75 3.18
3252 7811 1.259507 GTAACACGCACACACGTTCAT 59.740 47.619 0.00 0.00 45.75 2.57
3254 7813 1.087202 ACACGCACACACGTTCATGT 61.087 50.000 0.00 0.00 45.75 3.21
3255 7814 0.855995 CACGCACACACGTTCATGTA 59.144 50.000 0.00 0.00 45.75 2.29
3256 7815 1.459209 CACGCACACACGTTCATGTAT 59.541 47.619 0.00 0.00 45.75 2.29
3258 7817 1.459209 CGCACACACGTTCATGTATGT 59.541 47.619 0.00 0.00 29.38 2.29
3260 7819 3.122111 CGCACACACGTTCATGTATGTAA 59.878 43.478 0.00 0.00 29.38 2.41
3262 7821 5.444983 GCACACACGTTCATGTATGTAAAA 58.555 37.500 0.00 0.00 29.38 1.52
3354 7943 3.612247 GACAGGGTCCGTGCAGCAT 62.612 63.158 11.55 0.00 0.00 3.79
3363 7952 2.167219 CGTGCAGCATGGTACTCGG 61.167 63.158 6.73 0.00 35.86 4.63
3364 7953 1.218047 GTGCAGCATGGTACTCGGA 59.782 57.895 0.00 0.00 35.86 4.55
3365 7954 1.084370 GTGCAGCATGGTACTCGGAC 61.084 60.000 0.00 0.00 35.86 4.79
3366 7955 1.218047 GCAGCATGGTACTCGGACA 59.782 57.895 0.00 0.00 35.86 4.02
3367 7956 0.807667 GCAGCATGGTACTCGGACAG 60.808 60.000 0.00 0.00 35.86 3.51
3368 7957 0.179100 CAGCATGGTACTCGGACAGG 60.179 60.000 0.00 0.00 0.00 4.00
3369 7958 1.144057 GCATGGTACTCGGACAGGG 59.856 63.158 0.00 0.00 0.00 4.45
3370 7959 1.614241 GCATGGTACTCGGACAGGGT 61.614 60.000 0.00 0.00 37.34 4.34
3371 7960 0.460311 CATGGTACTCGGACAGGGTC 59.540 60.000 0.00 0.00 33.93 4.46
3372 7961 1.035932 ATGGTACTCGGACAGGGTCG 61.036 60.000 0.00 0.00 33.93 4.79
3373 7962 2.413142 GGTACTCGGACAGGGTCGG 61.413 68.421 0.00 0.00 33.93 4.79
3374 7963 2.044650 TACTCGGACAGGGTCGGG 60.045 66.667 4.44 0.00 33.93 5.14
3375 7964 3.650298 TACTCGGACAGGGTCGGGG 62.650 68.421 2.68 2.68 38.94 5.73
3376 7965 4.753662 CTCGGACAGGGTCGGGGA 62.754 72.222 0.00 0.00 35.76 4.81
3377 7966 4.070265 TCGGACAGGGTCGGGGAT 62.070 66.667 4.44 0.00 34.39 3.85
3378 7967 2.123597 CGGACAGGGTCGGGGATA 60.124 66.667 0.00 0.00 32.65 2.59
3379 7968 1.533273 CGGACAGGGTCGGGGATAT 60.533 63.158 0.00 0.00 32.65 1.63
3380 7969 1.119574 CGGACAGGGTCGGGGATATT 61.120 60.000 0.00 0.00 32.65 1.28
3381 7970 1.137697 GGACAGGGTCGGGGATATTT 58.862 55.000 0.00 0.00 32.65 1.40
3382 7971 1.493446 GGACAGGGTCGGGGATATTTT 59.507 52.381 0.00 0.00 32.65 1.82
3383 7972 2.092049 GGACAGGGTCGGGGATATTTTT 60.092 50.000 0.00 0.00 32.65 1.94
3407 7996 3.567473 GCTCAGGTTTGCGGACTC 58.433 61.111 0.00 0.00 0.00 3.36
3408 7997 1.004440 GCTCAGGTTTGCGGACTCT 60.004 57.895 0.00 0.00 0.00 3.24
3409 7998 0.246635 GCTCAGGTTTGCGGACTCTA 59.753 55.000 0.00 0.00 0.00 2.43
3410 7999 1.134670 GCTCAGGTTTGCGGACTCTAT 60.135 52.381 0.00 0.00 0.00 1.98
3411 8000 2.678190 GCTCAGGTTTGCGGACTCTATT 60.678 50.000 0.00 0.00 0.00 1.73
3412 8001 3.190874 CTCAGGTTTGCGGACTCTATTC 58.809 50.000 0.00 0.00 0.00 1.75
3413 8002 2.093658 TCAGGTTTGCGGACTCTATTCC 60.094 50.000 0.00 0.00 0.00 3.01
3419 8008 2.812499 GGACTCTATTCCGCCGCA 59.188 61.111 0.00 0.00 0.00 5.69
3420 8009 1.300233 GGACTCTATTCCGCCGCAG 60.300 63.158 0.00 0.00 0.00 5.18
3421 8010 1.951631 GACTCTATTCCGCCGCAGC 60.952 63.158 0.00 0.00 0.00 5.25
3422 8011 2.663188 CTCTATTCCGCCGCAGCC 60.663 66.667 0.00 0.00 34.57 4.85
3423 8012 4.585526 TCTATTCCGCCGCAGCCG 62.586 66.667 0.00 0.00 34.57 5.52
3424 8013 4.585526 CTATTCCGCCGCAGCCGA 62.586 66.667 0.00 0.00 36.29 5.54
3425 8014 3.865929 CTATTCCGCCGCAGCCGAT 62.866 63.158 0.00 0.00 36.29 4.18
3426 8015 3.858868 TATTCCGCCGCAGCCGATC 62.859 63.158 0.00 0.00 36.29 3.69
3432 8021 4.514577 CCGCAGCCGATCGGTCTT 62.515 66.667 33.33 17.72 40.72 3.01
3433 8022 2.509336 CGCAGCCGATCGGTCTTT 60.509 61.111 33.33 15.26 37.65 2.52
3434 8023 2.100631 CGCAGCCGATCGGTCTTTT 61.101 57.895 33.33 12.84 37.65 2.27
3435 8024 1.635663 CGCAGCCGATCGGTCTTTTT 61.636 55.000 33.33 11.14 37.65 1.94
3457 8046 4.953940 TTTTGAATTTTCACAGGGGGAG 57.046 40.909 0.00 0.00 36.83 4.30
3458 8047 2.603075 TGAATTTTCACAGGGGGAGG 57.397 50.000 0.00 0.00 31.01 4.30
3459 8048 1.077005 TGAATTTTCACAGGGGGAGGG 59.923 52.381 0.00 0.00 31.01 4.30
3460 8049 0.413434 AATTTTCACAGGGGGAGGGG 59.587 55.000 0.00 0.00 0.00 4.79
3461 8050 1.518431 ATTTTCACAGGGGGAGGGGG 61.518 60.000 0.00 0.00 0.00 5.40
3478 8067 4.115199 GCCCTCCGCCACCTGAAT 62.115 66.667 0.00 0.00 0.00 2.57
3479 8068 2.742116 GCCCTCCGCCACCTGAATA 61.742 63.158 0.00 0.00 0.00 1.75
3480 8069 2.056906 GCCCTCCGCCACCTGAATAT 62.057 60.000 0.00 0.00 0.00 1.28
3575 8164 0.703488 TGAACATTCCTGGCCATCCA 59.297 50.000 5.51 0.00 40.85 3.41
3625 8230 2.779755 TACGGGTCATCATTGTTGCT 57.220 45.000 0.00 0.00 0.00 3.91
3697 8302 4.752101 CAGATTCTGGCTTATTCGGGTTAG 59.248 45.833 5.73 0.00 0.00 2.34
3703 8308 4.228824 TGGCTTATTCGGGTTAGAGGTAT 58.771 43.478 0.00 0.00 0.00 2.73
3731 12083 0.249398 ACCCGTTAAAGCTGAGCGAT 59.751 50.000 0.00 0.00 0.00 4.58
3892 12253 2.173669 CGACGCCGCATCATTCCTT 61.174 57.895 0.00 0.00 0.00 3.36
4149 12535 3.589288 AGGGTTCAGTAAAAGAGGAGCAT 59.411 43.478 0.00 0.00 0.00 3.79
4164 12550 3.487202 CATGCGGCGCTGTTACGT 61.487 61.111 33.26 7.10 34.88 3.57
4205 14288 7.295952 TCTCTCGTTTTTAGAATTGCTGATC 57.704 36.000 0.00 0.00 0.00 2.92
4240 14323 3.001634 CACTGGCAATACGCAACTCATAG 59.998 47.826 0.00 0.00 45.17 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 9.912634 CTGTTTGGAGTTACATTTTTACATCAT 57.087 29.630 0.00 0.00 0.00 2.45
37 38 8.862325 TTTACATCATCTGTTTGGAGTTACAT 57.138 30.769 0.00 0.00 39.39 2.29
40 41 9.513906 TTCATTTACATCATCTGTTTGGAGTTA 57.486 29.630 0.00 0.00 39.39 2.24
43 44 8.272545 TCTTCATTTACATCATCTGTTTGGAG 57.727 34.615 0.00 0.00 39.39 3.86
86 87 3.965258 TGCTTGATGGCCACGGGT 61.965 61.111 8.16 0.00 0.00 5.28
89 90 3.027170 GACGTGCTTGATGGCCACG 62.027 63.158 8.16 8.06 40.06 4.94
93 94 2.434185 TCCGACGTGCTTGATGGC 60.434 61.111 0.00 0.00 0.00 4.40
118 119 1.150536 TCACCTGTGGAGCAAACCC 59.849 57.895 0.00 0.00 0.00 4.11
128 129 0.238289 GATGCAAACCGTCACCTGTG 59.762 55.000 0.00 0.00 0.00 3.66
131 132 0.949105 GTCGATGCAAACCGTCACCT 60.949 55.000 0.00 0.00 0.00 4.00
146 147 1.210931 CCGTAGAGCCAAACGTCGA 59.789 57.895 0.00 0.00 37.40 4.20
183 184 2.154462 CTCTCGTTTGCACCAAAGGAT 58.846 47.619 11.86 0.00 43.77 3.24
192 193 0.250295 CCCAACTCCTCTCGTTTGCA 60.250 55.000 0.00 0.00 0.00 4.08
193 194 0.955919 CCCCAACTCCTCTCGTTTGC 60.956 60.000 0.00 0.00 0.00 3.68
215 216 0.600255 CGCTCCTGTCAAGTTTCGGT 60.600 55.000 0.00 0.00 0.00 4.69
218 219 0.793250 GCTCGCTCCTGTCAAGTTTC 59.207 55.000 0.00 0.00 0.00 2.78
224 225 1.290324 GTCAAGCTCGCTCCTGTCA 59.710 57.895 0.00 0.00 0.00 3.58
321 322 0.473694 TTGAACTCCTGGAGCTCCCA 60.474 55.000 29.95 15.48 44.25 4.37
324 325 1.346068 ACACTTGAACTCCTGGAGCTC 59.654 52.381 23.43 20.59 32.04 4.09
326 327 3.265791 CATACACTTGAACTCCTGGAGC 58.734 50.000 23.43 8.91 32.04 4.70
338 339 1.742900 CGCGTCCGAGCATACACTTG 61.743 60.000 0.00 0.00 36.85 3.16
344 345 3.650907 TTTGCCGCGTCCGAGCATA 62.651 57.895 4.92 0.00 39.27 3.14
377 378 2.349580 TGGTAAGTCATCGACGTACTCG 59.650 50.000 16.18 8.00 43.39 4.18
380 388 6.238610 AGATATGGTAAGTCATCGACGTAC 57.761 41.667 10.53 10.53 43.23 3.67
417 425 9.745880 GATCGAAGGACTCTTGTTAACATATTA 57.254 33.333 9.56 0.00 32.52 0.98
443 451 2.159531 CCAACAAGTGATGTACGCATGG 60.160 50.000 0.00 0.00 42.99 3.66
495 503 8.519526 AGAGATGTCTTGTAGACTGAGTTTAAG 58.480 37.037 8.18 0.00 45.27 1.85
504 512 4.323569 TCCCAGAGATGTCTTGTAGACT 57.676 45.455 8.18 0.00 45.27 3.24
568 576 1.128147 GTGCTATGCTTTGTTCGCGC 61.128 55.000 0.00 0.00 0.00 6.86
594 602 3.228017 TGACAGCGACGTCCCCAA 61.228 61.111 10.58 0.00 34.88 4.12
595 603 3.986006 GTGACAGCGACGTCCCCA 61.986 66.667 10.58 0.00 34.88 4.96
697 717 3.578272 TGGTTTGTGGCGCGTGTC 61.578 61.111 8.43 0.00 0.00 3.67
809 829 6.369065 AGAAAGCGAAAACGAGAAGATTGTAT 59.631 34.615 0.00 0.00 0.00 2.29
830 850 0.248907 GATCGATCACGGGCGAGAAA 60.249 55.000 20.52 0.00 40.14 2.52
872 1837 1.607612 GAAAAGGCAGGGGATCGGA 59.392 57.895 0.00 0.00 0.00 4.55
873 1838 1.819632 CGAAAAGGCAGGGGATCGG 60.820 63.158 0.00 0.00 0.00 4.18
874 1839 2.472909 GCGAAAAGGCAGGGGATCG 61.473 63.158 0.00 0.00 0.00 3.69
875 1840 2.121538 GGCGAAAAGGCAGGGGATC 61.122 63.158 0.00 0.00 45.92 3.36
876 1841 2.043953 GGCGAAAAGGCAGGGGAT 60.044 61.111 0.00 0.00 45.92 3.85
937 1904 1.153823 GGTGACTGGACGGACGATG 60.154 63.158 0.00 0.00 0.00 3.84
1209 3789 1.279840 GTGGAACGTGCTGTGCTTC 59.720 57.895 0.00 0.00 0.00 3.86
1318 3898 3.210528 GGTCGGGAGCGAGTCGAT 61.211 66.667 18.61 10.88 35.35 3.59
1359 3939 3.284449 GTGCCGGCGTTGACCTTT 61.284 61.111 23.90 0.00 0.00 3.11
1400 3980 1.684049 AGAAGGGAGGAGGACAGCG 60.684 63.158 0.00 0.00 0.00 5.18
1401 3981 1.904032 CAGAAGGGAGGAGGACAGC 59.096 63.158 0.00 0.00 0.00 4.40
1402 3982 1.621672 GGCAGAAGGGAGGAGGACAG 61.622 65.000 0.00 0.00 0.00 3.51
1403 3983 1.613630 GGCAGAAGGGAGGAGGACA 60.614 63.158 0.00 0.00 0.00 4.02
1441 4021 2.490165 CTCCAATGGAGGCAGCAAG 58.510 57.895 21.25 0.00 45.43 4.01
1505 4093 1.486145 TTCCTCCTTCCCGTGAACCC 61.486 60.000 0.00 0.00 0.00 4.11
1547 4135 3.706373 GGCCTTCTCCCTGACGCA 61.706 66.667 0.00 0.00 0.00 5.24
1558 4146 0.462759 CTGATCTTCGTGGGGCCTTC 60.463 60.000 0.84 0.00 0.00 3.46
1692 4283 5.622770 ATTCTAAGACACGGCGAAATTTT 57.377 34.783 16.62 3.77 0.00 1.82
1694 4285 4.935808 AGAATTCTAAGACACGGCGAAATT 59.064 37.500 16.62 5.24 0.00 1.82
1695 4286 4.330074 CAGAATTCTAAGACACGGCGAAAT 59.670 41.667 16.62 0.00 0.00 2.17
1998 4639 3.276091 CGCCGTGTTCTGCCAACA 61.276 61.111 0.00 0.00 0.00 3.33
2135 4776 1.518572 CTTGTAGTAGTGGCGCCCG 60.519 63.158 26.77 0.00 0.00 6.13
2222 5366 1.337703 CATCGAGGAAGAGGAGAGCAG 59.662 57.143 0.00 0.00 0.00 4.24
2303 5459 4.818642 TGCTCTGATTTTCTCTCTCTGTG 58.181 43.478 0.00 0.00 0.00 3.66
2318 5474 2.658422 TGCTCGTGCATGCTCTGA 59.342 55.556 20.33 15.01 45.31 3.27
2350 5523 1.335324 GCTCGTGCATGCTCTGTTTTT 60.335 47.619 20.33 0.00 39.41 1.94
2352 5525 0.886043 TGCTCGTGCATGCTCTGTTT 60.886 50.000 20.33 0.00 45.31 2.83
2353 5526 1.301953 TGCTCGTGCATGCTCTGTT 60.302 52.632 20.33 0.00 45.31 3.16
2362 5535 4.193155 CACACAGATGTTTGCTCGTGCA 62.193 50.000 8.30 8.30 42.02 4.57
2366 5539 1.866601 TGTCACACAGATGTTTGCTCG 59.133 47.619 0.00 0.00 36.72 5.03
2367 5540 2.348872 CGTGTCACACAGATGTTTGCTC 60.349 50.000 9.06 0.00 36.72 4.26
2372 5545 1.662517 TTGCGTGTCACACAGATGTT 58.337 45.000 9.06 0.00 36.72 2.71
2373 5546 1.532437 CATTGCGTGTCACACAGATGT 59.468 47.619 9.06 0.00 40.80 3.06
2374 5547 1.726892 GCATTGCGTGTCACACAGATG 60.727 52.381 9.06 9.42 33.40 2.90
2375 5548 0.518636 GCATTGCGTGTCACACAGAT 59.481 50.000 9.06 0.00 33.40 2.90
2376 5549 0.532640 AGCATTGCGTGTCACACAGA 60.533 50.000 9.06 0.00 33.40 3.41
2377 5550 1.127397 CTAGCATTGCGTGTCACACAG 59.873 52.381 9.06 2.00 33.40 3.66
2378 5551 1.147473 CTAGCATTGCGTGTCACACA 58.853 50.000 9.06 0.00 33.40 3.72
2379 5552 0.443869 CCTAGCATTGCGTGTCACAC 59.556 55.000 0.00 0.00 0.00 3.82
2384 5634 2.819608 ACAAAATCCTAGCATTGCGTGT 59.180 40.909 2.38 0.00 0.00 4.49
2557 6320 3.855950 ACGAGACCGAAATATTTGACGTC 59.144 43.478 9.11 9.11 39.50 4.34
2584 6748 2.596338 TGTGGGCACGAGACGAGA 60.596 61.111 0.00 0.00 0.00 4.04
2585 6749 2.430921 GTGTGGGCACGAGACGAG 60.431 66.667 0.00 0.00 35.75 4.18
2701 6913 0.041926 CACACACGCACACAGTCATG 60.042 55.000 0.00 0.00 0.00 3.07
3055 7611 0.324614 ACACCGTCCTGCATCATCAA 59.675 50.000 0.00 0.00 0.00 2.57
3262 7821 9.354673 TCTTTATGGATTCACTTTGTCTCTTTT 57.645 29.630 0.00 0.00 0.00 2.27
3264 7823 9.525826 AATCTTTATGGATTCACTTTGTCTCTT 57.474 29.630 0.00 0.00 31.08 2.85
3265 7824 9.171877 GAATCTTTATGGATTCACTTTGTCTCT 57.828 33.333 10.98 0.00 46.26 3.10
3280 7869 7.824672 AGAAGACTGCAAAAGAATCTTTATGG 58.175 34.615 8.83 3.49 29.85 2.74
3281 7870 9.688592 AAAGAAGACTGCAAAAGAATCTTTATG 57.311 29.630 8.83 10.24 35.66 1.90
3354 7943 1.676635 CGACCCTGTCCGAGTACCA 60.677 63.158 0.00 0.00 0.00 3.25
3363 7952 3.292492 AAAAATATCCCCGACCCTGTC 57.708 47.619 0.00 0.00 0.00 3.51
3390 7979 0.246635 TAGAGTCCGCAAACCTGAGC 59.753 55.000 0.00 0.00 0.00 4.26
3391 7980 2.969628 ATAGAGTCCGCAAACCTGAG 57.030 50.000 0.00 0.00 0.00 3.35
3392 7981 2.093658 GGAATAGAGTCCGCAAACCTGA 60.094 50.000 0.00 0.00 0.00 3.86
3393 7982 2.280628 GGAATAGAGTCCGCAAACCTG 58.719 52.381 0.00 0.00 0.00 4.00
3394 7983 2.693267 GGAATAGAGTCCGCAAACCT 57.307 50.000 0.00 0.00 0.00 3.50
3402 7991 1.300233 CTGCGGCGGAATAGAGTCC 60.300 63.158 9.78 0.00 0.00 3.85
3403 7992 1.951631 GCTGCGGCGGAATAGAGTC 60.952 63.158 14.15 0.00 0.00 3.36
3404 7993 2.107141 GCTGCGGCGGAATAGAGT 59.893 61.111 14.15 0.00 0.00 3.24
3405 7994 2.663188 GGCTGCGGCGGAATAGAG 60.663 66.667 14.15 0.00 39.81 2.43
3416 8005 1.635663 AAAAAGACCGATCGGCTGCG 61.636 55.000 33.62 10.51 39.32 5.18
3417 8006 2.171635 AAAAAGACCGATCGGCTGC 58.828 52.632 33.62 22.19 39.32 5.25
3435 8024 4.102367 CCTCCCCCTGTGAAAATTCAAAAA 59.898 41.667 0.00 0.00 39.21 1.94
3436 8025 3.645687 CCTCCCCCTGTGAAAATTCAAAA 59.354 43.478 0.00 0.00 39.21 2.44
3437 8026 3.238597 CCTCCCCCTGTGAAAATTCAAA 58.761 45.455 0.00 0.00 39.21 2.69
3438 8027 2.492567 CCCTCCCCCTGTGAAAATTCAA 60.493 50.000 0.00 0.00 39.21 2.69
3439 8028 1.077005 CCCTCCCCCTGTGAAAATTCA 59.923 52.381 0.00 0.00 34.20 2.57
3440 8029 1.619704 CCCCTCCCCCTGTGAAAATTC 60.620 57.143 0.00 0.00 0.00 2.17
3441 8030 0.413434 CCCCTCCCCCTGTGAAAATT 59.587 55.000 0.00 0.00 0.00 1.82
3442 8031 1.518431 CCCCCTCCCCCTGTGAAAAT 61.518 60.000 0.00 0.00 0.00 1.82
3443 8032 2.167037 CCCCCTCCCCCTGTGAAAA 61.167 63.158 0.00 0.00 0.00 2.29
3444 8033 2.534272 CCCCCTCCCCCTGTGAAA 60.534 66.667 0.00 0.00 0.00 2.69
3461 8050 2.056906 ATATTCAGGTGGCGGAGGGC 62.057 60.000 0.00 0.00 42.51 5.19
3462 8051 0.474184 AATATTCAGGTGGCGGAGGG 59.526 55.000 0.00 0.00 0.00 4.30
3463 8052 2.348411 AAATATTCAGGTGGCGGAGG 57.652 50.000 0.00 0.00 0.00 4.30
3464 8053 5.828299 TTAAAAATATTCAGGTGGCGGAG 57.172 39.130 0.00 0.00 0.00 4.63
3465 8054 6.015350 TGTTTTAAAAATATTCAGGTGGCGGA 60.015 34.615 1.31 0.00 0.00 5.54
3466 8055 6.159988 TGTTTTAAAAATATTCAGGTGGCGG 58.840 36.000 1.31 0.00 0.00 6.13
3467 8056 7.826260 ATGTTTTAAAAATATTCAGGTGGCG 57.174 32.000 1.31 0.00 0.00 5.69
3575 8164 2.639327 GCGGGAAGTGCTGCCAATT 61.639 57.895 0.00 0.00 34.42 2.32
3697 8302 1.361632 GGGTCCGCGTACATACCTC 59.638 63.158 4.92 0.00 32.38 3.85
3703 8308 0.388391 CTTTAACGGGTCCGCGTACA 60.388 55.000 9.85 0.00 44.19 2.90
3954 12315 1.971505 TAGCTTCCATCAGTGCCCCG 61.972 60.000 0.00 0.00 0.00 5.73
4164 12550 3.994392 GAGAGAAGTTGCGTAAACATGGA 59.006 43.478 0.00 0.00 41.61 3.41
4219 14302 2.113860 ATGAGTTGCGTATTGCCAGT 57.886 45.000 0.00 0.00 45.60 4.00
4240 14323 0.454600 TTGTAGTGTCGATCTCGCCC 59.545 55.000 0.00 0.00 39.60 6.13


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

AutoCloner maintained by Alex Coulton.