Multiple sequence alignment - TraesCS6B01G372900

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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 TraesCS6B01G372900 chr6B 100.000 3512 0 0 1 3512 646239407 646242918 0.000000e+00 6486.0
1 TraesCS6B01G372900 chr6B 85.294 374 29 6 2473 2843 646254179 646254529 2.580000e-96 363.0
2 TraesCS6B01G372900 chr6B 83.271 269 42 2 3055 3323 646256191 646256456 9.740000e-61 244.0
3 TraesCS6B01G372900 chr6A 91.775 3380 230 22 1 3357 574241066 574244420 0.000000e+00 4658.0
4 TraesCS6B01G372900 chr6A 85.128 390 25 9 2464 2843 574263277 574263643 5.540000e-98 368.0
5 TraesCS6B01G372900 chr6A 93.182 44 3 0 2884 2927 436115381 436115338 8.140000e-07 65.8
6 TraesCS6B01G372900 chr6D 94.173 2849 121 15 1 2843 429009199 429012008 0.000000e+00 4300.0
7 TraesCS6B01G372900 chr6D 87.313 536 50 12 2837 3355 429012046 429012580 6.490000e-167 597.0
8 TraesCS6B01G372900 chr6D 86.559 372 24 7 2473 2843 429020497 429020843 1.530000e-103 387.0
9 TraesCS6B01G372900 chr3A 81.219 1592 277 12 883 2468 689502205 689500630 0.000000e+00 1264.0
10 TraesCS6B01G372900 chr3A 100.000 29 0 0 2979 3007 510299868 510299896 2.000000e-03 54.7
11 TraesCS6B01G372900 chr3D 80.256 1722 300 27 762 2468 553233635 553231939 0.000000e+00 1260.0
12 TraesCS6B01G372900 chr3D 100.000 28 0 0 2979 3006 288550584 288550611 6.000000e-03 52.8
13 TraesCS6B01G372900 chr7D 90.000 60 5 1 2952 3010 447053559 447053500 3.760000e-10 76.8
14 TraesCS6B01G372900 chr7D 93.333 45 3 0 2884 2928 124529305 124529261 2.260000e-07 67.6
15 TraesCS6B01G372900 chr7B 91.837 49 4 0 2880 2928 606587800 606587752 6.290000e-08 69.4
16 TraesCS6B01G372900 chr7B 93.182 44 3 0 2884 2927 46995502 46995459 8.140000e-07 65.8
17 TraesCS6B01G372900 chr4A 83.750 80 6 7 2893 2965 84537489 84537410 6.290000e-08 69.4
18 TraesCS6B01G372900 chr3B 93.333 45 3 0 2884 2928 611177619 611177575 2.260000e-07 67.6
19 TraesCS6B01G372900 chr1A 90.000 50 4 1 2880 2928 117188302 117188253 2.930000e-06 63.9
20 TraesCS6B01G372900 chr7A 83.077 65 8 3 2884 2945 105506375 105506439 4.900000e-04 56.5
21 TraesCS6B01G372900 chr7A 96.774 31 1 0 2976 3006 512336489 512336519 6.000000e-03 52.8


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 TraesCS6B01G372900 chr6B 646239407 646242918 3511 False 6486.0 6486 100.0000 1 3512 1 chr6B.!!$F1 3511
1 TraesCS6B01G372900 chr6B 646254179 646256456 2277 False 303.5 363 84.2825 2473 3323 2 chr6B.!!$F2 850
2 TraesCS6B01G372900 chr6A 574241066 574244420 3354 False 4658.0 4658 91.7750 1 3357 1 chr6A.!!$F1 3356
3 TraesCS6B01G372900 chr6D 429009199 429012580 3381 False 2448.5 4300 90.7430 1 3355 2 chr6D.!!$F2 3354
4 TraesCS6B01G372900 chr3A 689500630 689502205 1575 True 1264.0 1264 81.2190 883 2468 1 chr3A.!!$R1 1585
5 TraesCS6B01G372900 chr3D 553231939 553233635 1696 True 1260.0 1260 80.2560 762 2468 1 chr3D.!!$R1 1706

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
180 189 1.019278 GCAGGTTCGGAATTCGCAGA 61.019 55.0 0.00 0.0 39.05 4.26 F
1122 1155 0.398696 TTTTGGTAGCAAGGCTCGGA 59.601 50.0 7.51 0.0 40.44 4.55 F
2124 2157 0.690762 TACCCAACTTCCTCACAGCC 59.309 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2115 0.250166 ACACTTTAGAACGCCCGCTT 60.250 50.0 0.0 0.0 0.00 4.68 R
2183 2216 0.034059 CTCGTTGGACAAGCTGAGGT 59.966 55.0 0.0 0.0 0.00 3.85 R
3393 4972 0.033796 CCCATGCAATGTCCCACTCT 60.034 55.0 0.0 0.0 44.81 3.24 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
180 189 1.019278 GCAGGTTCGGAATTCGCAGA 61.019 55.000 0.00 0.00 39.05 4.26
250 262 6.530019 AGTTTGTTGAAGTGTCAAAGGAAT 57.470 33.333 0.00 0.00 45.29 3.01
286 299 6.662865 ACACATGGATTGGTTGATAACAAA 57.337 33.333 0.00 0.00 37.77 2.83
389 404 2.331451 GTGCACGCCCAGAAACAC 59.669 61.111 0.00 0.00 0.00 3.32
407 422 3.952675 AAACACAGGTGCGCGCAG 61.953 61.111 37.44 25.69 0.00 5.18
1045 1078 7.013750 GGAAGAACCTCAAATTTCTCTTCAAGT 59.986 37.037 16.97 0.00 40.23 3.16
1047 1080 8.298729 AGAACCTCAAATTTCTCTTCAAGTTT 57.701 30.769 0.00 0.00 0.00 2.66
1069 1102 6.446781 TTGTAGTAGACAACTTCCTATCCG 57.553 41.667 0.00 0.00 43.30 4.18
1105 1138 0.609131 AGCGGCAGCCACTATTGTTT 60.609 50.000 13.30 0.00 46.67 2.83
1122 1155 0.398696 TTTTGGTAGCAAGGCTCGGA 59.601 50.000 7.51 0.00 40.44 4.55
1125 1158 2.656069 GGTAGCAAGGCTCGGACCA 61.656 63.158 0.00 0.00 40.44 4.02
1238 1271 2.111043 ACAGCCACGGAAGGTGTG 59.889 61.111 5.76 1.14 45.52 3.82
1497 1530 4.870426 GTCTTCTCAGCCATTGACGAATTA 59.130 41.667 0.00 0.00 0.00 1.40
1537 1570 5.239744 GTCTGTCCTGACACTATCGACATAT 59.760 44.000 10.15 0.00 36.21 1.78
1563 1596 0.889994 TCAATTGCAGCGGCTTCAAT 59.110 45.000 19.78 19.78 41.91 2.57
1581 1614 3.011595 TCAATCCCACACCATCCTTCATT 59.988 43.478 0.00 0.00 0.00 2.57
1584 1617 2.582172 TCCCACACCATCCTTCATTGAT 59.418 45.455 0.00 0.00 0.00 2.57
1671 1704 1.069765 CGCTGGGCTGATATCGGTT 59.930 57.895 13.12 0.00 0.00 4.44
1837 1870 1.663739 GTGCTACTGTCCACGTCCA 59.336 57.895 0.00 0.00 0.00 4.02
1902 1935 2.792290 CGCTGCGGATGACAACTCG 61.792 63.158 15.40 0.00 0.00 4.18
1907 1940 1.000052 TGCGGATGACAACTCGTACAA 60.000 47.619 0.00 0.00 0.00 2.41
1914 1947 3.462982 TGACAACTCGTACAAGTGCATT 58.537 40.909 0.00 0.00 0.00 3.56
2023 2056 2.440147 CCACCCTTGCACCCATCA 59.560 61.111 0.00 0.00 0.00 3.07
2037 2070 2.060275 CCCATCATCCTCCCAATCTCA 58.940 52.381 0.00 0.00 0.00 3.27
2041 2074 4.141321 CCATCATCCTCCCAATCTCAGAAA 60.141 45.833 0.00 0.00 0.00 2.52
2082 2115 0.746204 TCGTGGCACAAAAGCTGTCA 60.746 50.000 19.09 0.00 44.16 3.58
2093 2126 4.090057 GCTGTCAAGCGGGCGTTC 62.090 66.667 0.00 0.00 40.27 3.95
2104 2137 1.936203 GCGGGCGTTCTAAAGTGTACA 60.936 52.381 0.00 0.00 0.00 2.90
2106 2139 3.772932 CGGGCGTTCTAAAGTGTACATA 58.227 45.455 0.00 0.00 0.00 2.29
2124 2157 0.690762 TACCCAACTTCCTCACAGCC 59.309 55.000 0.00 0.00 0.00 4.85
2125 2158 1.352622 ACCCAACTTCCTCACAGCCA 61.353 55.000 0.00 0.00 0.00 4.75
2148 2181 1.578915 GAGCATTTTTGCATACACGCG 59.421 47.619 3.53 3.53 37.25 6.01
2183 2216 1.731709 CATCGATGAGGTTCAACGCAA 59.268 47.619 21.02 0.00 41.51 4.85
2214 2247 3.566261 AACGAGCATGTTGAGCCG 58.434 55.556 0.00 0.00 33.79 5.52
2316 2349 0.038251 ATATGCATCGCGGTGATCGT 60.038 50.000 26.37 10.37 41.72 3.73
2337 2370 2.437651 TGTATGGATGATCGGCTTTGGA 59.562 45.455 0.00 0.00 0.00 3.53
2355 2388 5.943349 TTGGATCAGGATTCAAATGCAAT 57.057 34.783 0.45 0.00 33.57 3.56
2378 2411 1.965930 TGGTGTGGAAGTGCATCGC 60.966 57.895 0.00 0.00 0.00 4.58
2385 2418 1.449246 GAAGTGCATCGCTCCAGCT 60.449 57.895 0.00 0.00 39.32 4.24
2571 2604 8.943909 TTTTTACCCGCTTTGATTTCTAAAAA 57.056 26.923 0.00 0.00 0.00 1.94
2617 2650 6.458342 GGCAAAGCCTCACTGTTATAATGTAC 60.458 42.308 0.00 0.00 46.69 2.90
2655 2688 5.347620 ACCTGTACACCGCAGAAAATATA 57.652 39.130 0.00 0.00 36.12 0.86
2771 2805 8.158169 TGATATGATTATTGGTCTGCTTGTTC 57.842 34.615 0.00 0.00 0.00 3.18
2896 2979 4.706962 GCTTACATTTCTCCCTTGGTTCAT 59.293 41.667 0.00 0.00 0.00 2.57
2959 3069 6.675413 AGTGTGTTTGTTCCCTATGTAGTA 57.325 37.500 0.00 0.00 0.00 1.82
2967 3077 9.052759 GTTTGTTCCCTATGTAGTACATATTGG 57.947 37.037 20.65 21.44 40.01 3.16
2998 3109 6.377327 AAGCATCTTATATTTGTGAACGGG 57.623 37.500 0.00 0.00 0.00 5.28
3025 3136 3.057626 AGGTGACAGAGGGATGATCAT 57.942 47.619 8.25 8.25 0.00 2.45
3067 4645 6.493458 AGGCCACATTCAAACTACACTAAAAT 59.507 34.615 5.01 0.00 0.00 1.82
3113 4691 6.475504 TCACAAGATGGCTTAGAAAGAATCA 58.524 36.000 0.00 0.00 31.81 2.57
3145 4724 2.272146 CCACCCCATTCACCCTCG 59.728 66.667 0.00 0.00 0.00 4.63
3150 4729 1.133294 ACCCCATTCACCCTCGTTTTT 60.133 47.619 0.00 0.00 0.00 1.94
3216 4795 1.457643 CCGTCTCCATAGGGCCTGA 60.458 63.158 18.53 3.76 0.00 3.86
3238 4817 1.228737 AACGGGTTTCCATGGTGGG 60.229 57.895 12.58 0.00 38.32 4.61
3325 4904 2.670229 CGGTGCTCGTACAATAGTGTGT 60.670 50.000 5.98 0.00 38.82 3.72
3331 4910 4.552355 CTCGTACAATAGTGTGTTGGTCA 58.448 43.478 5.98 0.00 38.82 4.02
3337 4916 5.385198 ACAATAGTGTGTTGGTCATCCTTT 58.615 37.500 0.00 0.00 36.31 3.11
3362 4941 1.185315 GGTGACCCATGTCCAAATGG 58.815 55.000 0.00 0.00 45.82 3.16
3363 4942 0.532115 GTGACCCATGTCCAAATGGC 59.468 55.000 0.00 0.00 45.03 4.40
3364 4943 0.614415 TGACCCATGTCCAAATGGCC 60.614 55.000 0.00 0.00 45.03 5.36
3365 4944 0.614415 GACCCATGTCCAAATGGCCA 60.614 55.000 8.56 8.56 45.03 5.36
3366 4945 0.904394 ACCCATGTCCAAATGGCCAC 60.904 55.000 8.16 0.00 45.03 5.01
3367 4946 1.616091 CCCATGTCCAAATGGCCACC 61.616 60.000 8.16 0.00 45.03 4.61
3368 4947 0.615544 CCATGTCCAAATGGCCACCT 60.616 55.000 8.16 0.00 40.74 4.00
3369 4948 0.819582 CATGTCCAAATGGCCACCTC 59.180 55.000 8.16 0.00 34.44 3.85
3370 4949 0.324645 ATGTCCAAATGGCCACCTCC 60.325 55.000 8.16 0.00 34.44 4.30
3371 4950 1.076549 GTCCAAATGGCCACCTCCA 59.923 57.895 8.16 0.00 40.97 3.86
3372 4951 1.076549 TCCAAATGGCCACCTCCAC 59.923 57.895 8.16 0.00 39.25 4.02
3373 4952 1.984026 CCAAATGGCCACCTCCACC 60.984 63.158 8.16 0.00 39.25 4.61
3374 4953 2.035626 AAATGGCCACCTCCACCG 59.964 61.111 8.16 0.00 39.25 4.94
3375 4954 2.534396 AAATGGCCACCTCCACCGA 61.534 57.895 8.16 0.00 39.25 4.69
3376 4955 2.764637 AAATGGCCACCTCCACCGAC 62.765 60.000 8.16 0.00 39.25 4.79
3377 4956 4.954118 TGGCCACCTCCACCGACT 62.954 66.667 0.00 0.00 0.00 4.18
3378 4957 4.083862 GGCCACCTCCACCGACTC 62.084 72.222 0.00 0.00 0.00 3.36
3379 4958 4.436998 GCCACCTCCACCGACTCG 62.437 72.222 0.00 0.00 0.00 4.18
3389 4968 3.068691 CCGACTCGGGCTCCTTCA 61.069 66.667 9.85 0.00 44.15 3.02
3390 4969 2.182030 CGACTCGGGCTCCTTCAC 59.818 66.667 0.00 0.00 0.00 3.18
3391 4970 2.182030 GACTCGGGCTCCTTCACG 59.818 66.667 0.00 0.00 0.00 4.35
3392 4971 3.358076 GACTCGGGCTCCTTCACGG 62.358 68.421 0.00 0.00 0.00 4.94
3393 4972 3.068691 CTCGGGCTCCTTCACGGA 61.069 66.667 0.00 0.00 40.30 4.69
3406 4985 3.143675 CACGGAGAGTGGGACATTG 57.856 57.895 0.00 0.00 46.77 2.82
3407 4986 1.021390 CACGGAGAGTGGGACATTGC 61.021 60.000 0.00 0.00 46.77 3.56
3408 4987 1.296392 CGGAGAGTGGGACATTGCA 59.704 57.895 0.00 0.00 44.52 4.08
3409 4988 0.107508 CGGAGAGTGGGACATTGCAT 60.108 55.000 0.00 0.00 44.52 3.96
3410 4989 1.386533 GGAGAGTGGGACATTGCATG 58.613 55.000 0.00 0.00 44.52 4.06
3411 4990 1.386533 GAGAGTGGGACATTGCATGG 58.613 55.000 0.00 0.00 44.52 3.66
3412 4991 0.033796 AGAGTGGGACATTGCATGGG 60.034 55.000 0.00 0.00 44.52 4.00
3413 4992 1.000739 AGTGGGACATTGCATGGGG 59.999 57.895 0.00 0.00 44.52 4.96
3414 4993 1.305213 GTGGGACATTGCATGGGGT 60.305 57.895 0.00 0.00 44.52 4.95
3415 4994 1.305129 TGGGACATTGCATGGGGTG 60.305 57.895 0.00 0.00 33.60 4.61
3416 4995 1.305213 GGGACATTGCATGGGGTGT 60.305 57.895 0.00 0.00 33.60 4.16
3417 4996 1.606885 GGGACATTGCATGGGGTGTG 61.607 60.000 0.00 0.00 33.60 3.82
3418 4997 0.899717 GGACATTGCATGGGGTGTGT 60.900 55.000 0.00 0.00 33.60 3.72
3419 4998 0.968405 GACATTGCATGGGGTGTGTT 59.032 50.000 0.00 0.00 33.60 3.32
3420 4999 0.680618 ACATTGCATGGGGTGTGTTG 59.319 50.000 0.00 0.00 33.60 3.33
3421 5000 0.967662 CATTGCATGGGGTGTGTTGA 59.032 50.000 0.00 0.00 0.00 3.18
3422 5001 0.968405 ATTGCATGGGGTGTGTTGAC 59.032 50.000 0.00 0.00 0.00 3.18
3423 5002 0.106268 TTGCATGGGGTGTGTTGACT 60.106 50.000 0.00 0.00 0.00 3.41
3424 5003 0.767998 TGCATGGGGTGTGTTGACTA 59.232 50.000 0.00 0.00 0.00 2.59
3425 5004 1.165270 GCATGGGGTGTGTTGACTAC 58.835 55.000 0.00 0.00 0.00 2.73
3426 5005 1.821216 CATGGGGTGTGTTGACTACC 58.179 55.000 0.00 0.00 0.00 3.18
3427 5006 0.323629 ATGGGGTGTGTTGACTACCG 59.676 55.000 0.00 0.00 35.31 4.02
3428 5007 1.004200 GGGGTGTGTTGACTACCGG 60.004 63.158 0.00 0.00 35.31 5.28
3429 5008 1.670083 GGGTGTGTTGACTACCGGC 60.670 63.158 0.00 0.00 35.31 6.13
3430 5009 1.370064 GGTGTGTTGACTACCGGCT 59.630 57.895 0.00 0.00 0.00 5.52
3431 5010 0.250166 GGTGTGTTGACTACCGGCTT 60.250 55.000 0.00 0.00 0.00 4.35
3432 5011 1.145803 GTGTGTTGACTACCGGCTTC 58.854 55.000 0.00 0.00 0.00 3.86
3433 5012 0.753867 TGTGTTGACTACCGGCTTCA 59.246 50.000 0.00 0.00 0.00 3.02
3434 5013 1.145803 GTGTTGACTACCGGCTTCAC 58.854 55.000 0.00 0.00 0.00 3.18
3435 5014 0.753867 TGTTGACTACCGGCTTCACA 59.246 50.000 0.00 0.41 0.00 3.58
3436 5015 1.145803 GTTGACTACCGGCTTCACAC 58.854 55.000 0.00 0.00 0.00 3.82
3437 5016 0.753867 TTGACTACCGGCTTCACACA 59.246 50.000 0.00 0.00 0.00 3.72
3438 5017 0.973632 TGACTACCGGCTTCACACAT 59.026 50.000 0.00 0.00 0.00 3.21
3439 5018 1.346395 TGACTACCGGCTTCACACATT 59.654 47.619 0.00 0.00 0.00 2.71
3440 5019 1.732259 GACTACCGGCTTCACACATTG 59.268 52.381 0.00 0.00 0.00 2.82
3441 5020 1.071699 ACTACCGGCTTCACACATTGT 59.928 47.619 0.00 0.00 0.00 2.71
3442 5021 2.300723 ACTACCGGCTTCACACATTGTA 59.699 45.455 0.00 0.00 0.00 2.41
3443 5022 2.489938 ACCGGCTTCACACATTGTAT 57.510 45.000 0.00 0.00 0.00 2.29
3444 5023 3.620427 ACCGGCTTCACACATTGTATA 57.380 42.857 0.00 0.00 0.00 1.47
3445 5024 3.267483 ACCGGCTTCACACATTGTATAC 58.733 45.455 0.00 0.00 0.00 1.47
3446 5025 3.266636 CCGGCTTCACACATTGTATACA 58.733 45.455 0.08 0.08 0.00 2.29
3447 5026 3.063452 CCGGCTTCACACATTGTATACAC 59.937 47.826 4.68 0.00 0.00 2.90
3448 5027 3.241963 CGGCTTCACACATTGTATACACG 60.242 47.826 4.68 2.41 0.00 4.49
3449 5028 3.063452 GGCTTCACACATTGTATACACGG 59.937 47.826 4.68 3.23 0.00 4.94
3450 5029 3.930229 GCTTCACACATTGTATACACGGA 59.070 43.478 4.68 0.00 0.00 4.69
3451 5030 4.570772 GCTTCACACATTGTATACACGGAT 59.429 41.667 4.68 0.00 0.00 4.18
3452 5031 5.502382 GCTTCACACATTGTATACACGGATG 60.502 44.000 4.68 9.56 0.00 3.51
3453 5032 5.079689 TCACACATTGTATACACGGATGT 57.920 39.130 13.54 13.54 43.30 3.06
3454 5033 5.483811 TCACACATTGTATACACGGATGTT 58.516 37.500 15.78 7.86 40.48 2.71
3455 5034 5.579119 TCACACATTGTATACACGGATGTTC 59.421 40.000 15.78 0.00 40.48 3.18
3456 5035 5.580691 CACACATTGTATACACGGATGTTCT 59.419 40.000 15.78 5.18 40.48 3.01
3457 5036 6.754675 CACACATTGTATACACGGATGTTCTA 59.245 38.462 15.78 0.00 40.48 2.10
3458 5037 6.755141 ACACATTGTATACACGGATGTTCTAC 59.245 38.462 15.78 0.00 40.48 2.59
3459 5038 6.754675 CACATTGTATACACGGATGTTCTACA 59.245 38.462 15.78 0.00 40.48 2.74
3460 5039 7.438160 CACATTGTATACACGGATGTTCTACAT 59.562 37.037 15.78 0.00 42.43 2.29
3461 5040 7.438160 ACATTGTATACACGGATGTTCTACATG 59.562 37.037 13.54 8.97 39.27 3.21
3462 5041 5.838529 TGTATACACGGATGTTCTACATGG 58.161 41.667 0.08 0.00 39.27 3.66
3463 5042 2.024176 ACACGGATGTTCTACATGGC 57.976 50.000 0.00 0.00 39.27 4.40
3464 5043 0.930310 CACGGATGTTCTACATGGCG 59.070 55.000 0.00 0.00 39.27 5.69
3465 5044 0.179084 ACGGATGTTCTACATGGCGG 60.179 55.000 0.00 0.00 39.27 6.13
3466 5045 1.498865 CGGATGTTCTACATGGCGGC 61.499 60.000 0.00 0.00 39.27 6.53
3467 5046 0.463654 GGATGTTCTACATGGCGGCA 60.464 55.000 16.34 16.34 39.27 5.69
3468 5047 1.597742 GATGTTCTACATGGCGGCAT 58.402 50.000 20.18 20.18 39.27 4.40
3469 5048 1.265095 GATGTTCTACATGGCGGCATG 59.735 52.381 40.61 40.61 39.27 4.06
3470 5049 1.356624 GTTCTACATGGCGGCATGC 59.643 57.895 41.72 26.15 45.38 4.06
3493 5072 4.310672 GCTCAGGTAGCGTCGATG 57.689 61.111 0.00 0.00 42.53 3.84
3494 5073 1.433879 GCTCAGGTAGCGTCGATGT 59.566 57.895 6.48 0.00 42.53 3.06
3495 5074 0.179134 GCTCAGGTAGCGTCGATGTT 60.179 55.000 6.48 2.37 42.53 2.71
3496 5075 1.065102 GCTCAGGTAGCGTCGATGTTA 59.935 52.381 6.48 1.23 42.53 2.41
3497 5076 2.287668 GCTCAGGTAGCGTCGATGTTAT 60.288 50.000 6.48 0.00 42.53 1.89
3498 5077 3.556513 CTCAGGTAGCGTCGATGTTATC 58.443 50.000 6.48 5.01 0.00 1.75
3499 5078 3.211865 TCAGGTAGCGTCGATGTTATCT 58.788 45.455 8.34 8.34 0.00 1.98
3500 5079 4.383173 TCAGGTAGCGTCGATGTTATCTA 58.617 43.478 13.20 0.36 0.00 1.98
3501 5080 5.001874 TCAGGTAGCGTCGATGTTATCTAT 58.998 41.667 13.20 0.00 0.00 1.98
3502 5081 5.121925 TCAGGTAGCGTCGATGTTATCTATC 59.878 44.000 13.20 3.54 0.00 2.08
3503 5082 5.001874 AGGTAGCGTCGATGTTATCTATCA 58.998 41.667 12.10 0.00 0.00 2.15
3504 5083 5.648526 AGGTAGCGTCGATGTTATCTATCAT 59.351 40.000 12.10 0.00 0.00 2.45
3505 5084 6.822170 AGGTAGCGTCGATGTTATCTATCATA 59.178 38.462 12.10 0.00 0.00 2.15
3506 5085 7.011576 AGGTAGCGTCGATGTTATCTATCATAG 59.988 40.741 12.10 0.00 0.00 2.23
3507 5086 6.125327 AGCGTCGATGTTATCTATCATAGG 57.875 41.667 6.48 0.00 0.00 2.57
3508 5087 5.880887 AGCGTCGATGTTATCTATCATAGGA 59.119 40.000 6.48 0.00 0.00 2.94
3509 5088 6.374613 AGCGTCGATGTTATCTATCATAGGAA 59.625 38.462 6.48 0.00 0.00 3.36
3510 5089 7.027760 GCGTCGATGTTATCTATCATAGGAAA 58.972 38.462 6.48 0.00 0.00 3.13
3511 5090 7.008447 GCGTCGATGTTATCTATCATAGGAAAC 59.992 40.741 6.48 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
168 177 4.858692 ACATTTTTCAATCTGCGAATTCCG 59.141 37.500 0.00 0.00 42.21 4.30
286 299 6.014584 GGGGAAGTTCAAACCAACTGATTTAT 60.015 38.462 5.01 0.00 36.69 1.40
382 397 1.132262 CGCACCTGTGTTTGTGTTTCT 59.868 47.619 0.00 0.00 34.94 2.52
383 398 1.544686 CGCACCTGTGTTTGTGTTTC 58.455 50.000 0.00 0.00 34.94 2.78
384 399 0.457681 GCGCACCTGTGTTTGTGTTT 60.458 50.000 0.30 0.00 34.94 2.83
389 404 4.249020 TGCGCGCACCTGTGTTTG 62.249 61.111 33.09 0.00 0.00 2.93
407 422 3.088532 TGTTCACATATTTGAGGTGGCC 58.911 45.455 0.00 0.00 40.34 5.36
734 759 8.201464 TGATAACGTGTAACATGATACTTGGAT 58.799 33.333 13.55 5.18 35.74 3.41
1047 1080 5.356190 CACGGATAGGAAGTTGTCTACTACA 59.644 44.000 0.00 0.00 35.54 2.74
1105 1138 1.295423 GTCCGAGCCTTGCTACCAA 59.705 57.895 0.00 0.00 39.88 3.67
1122 1155 1.799933 GACCCAGGATCTCATCTGGT 58.200 55.000 12.93 3.16 46.75 4.00
1125 1158 1.118356 GCCGACCCAGGATCTCATCT 61.118 60.000 0.00 0.00 0.00 2.90
1537 1570 1.075542 CCGCTGCAATTGACGACTAA 58.924 50.000 10.34 0.00 0.00 2.24
1548 1581 2.342650 GGGATTGAAGCCGCTGCAA 61.343 57.895 16.39 16.39 41.13 4.08
1563 1596 1.991813 TCAATGAAGGATGGTGTGGGA 59.008 47.619 0.00 0.00 0.00 4.37
1671 1704 2.172483 GAAGGTTCCTCGCAGCCTCA 62.172 60.000 0.00 0.00 0.00 3.86
1818 1851 1.080025 GGACGTGGACAGTAGCACC 60.080 63.158 0.00 0.00 0.00 5.01
1854 1887 1.964290 GCACGACAGACATGAGCTGC 61.964 60.000 16.51 0.00 36.86 5.25
1856 1889 1.445066 CGCACGACAGACATGAGCT 60.445 57.895 0.00 0.00 0.00 4.09
1887 1920 0.599060 TGTACGAGTTGTCATCCGCA 59.401 50.000 0.00 0.00 0.00 5.69
1896 1929 4.641954 GATGAATGCACTTGTACGAGTTG 58.358 43.478 13.39 10.05 0.00 3.16
1902 1935 2.609459 CTCCCGATGAATGCACTTGTAC 59.391 50.000 0.00 0.00 0.00 2.90
1907 1940 0.467384 CTCCTCCCGATGAATGCACT 59.533 55.000 0.00 0.00 0.00 4.40
1914 1947 0.261696 TGTCATCCTCCTCCCGATGA 59.738 55.000 0.00 0.00 41.94 2.92
1986 2019 2.887152 GGTGATGTTGGCTTTGAGAGTT 59.113 45.455 0.00 0.00 0.00 3.01
2023 2056 5.527026 AGTTTTTCTGAGATTGGGAGGAT 57.473 39.130 0.00 0.00 0.00 3.24
2037 2070 6.654582 AGGACATTGCAAACAAAAGTTTTTCT 59.345 30.769 1.71 0.00 39.77 2.52
2041 2074 5.063312 CGAAGGACATTGCAAACAAAAGTTT 59.937 36.000 1.71 0.00 39.77 2.66
2082 2115 0.250166 ACACTTTAGAACGCCCGCTT 60.250 50.000 0.00 0.00 0.00 4.68
2093 2126 6.708285 AGGAAGTTGGGTATGTACACTTTAG 58.292 40.000 0.00 0.00 0.00 1.85
2104 2137 1.282157 GGCTGTGAGGAAGTTGGGTAT 59.718 52.381 0.00 0.00 0.00 2.73
2106 2139 1.352622 TGGCTGTGAGGAAGTTGGGT 61.353 55.000 0.00 0.00 0.00 4.51
2124 2157 4.491280 GCGTGTATGCAAAAATGCTCAATG 60.491 41.667 0.00 0.00 35.49 2.82
2125 2158 3.613737 GCGTGTATGCAAAAATGCTCAAT 59.386 39.130 0.00 0.00 35.49 2.57
2148 2181 1.078143 GATGACTGCAGTCCCACCC 60.078 63.158 37.23 20.48 44.15 4.61
2160 2193 2.881074 CGTTGAACCTCATCGATGACT 58.119 47.619 23.99 11.39 40.81 3.41
2183 2216 0.034059 CTCGTTGGACAAGCTGAGGT 59.966 55.000 0.00 0.00 0.00 3.85
2214 2247 0.249657 GATGCAGGGTCATCCTCGAC 60.250 60.000 0.00 0.00 46.12 4.20
2232 2265 0.034198 TGGATGTGTTTCCGAAGCGA 59.966 50.000 0.00 0.00 38.74 4.93
2297 2330 0.038251 ACGATCACCGCGATGCATAT 60.038 50.000 8.23 0.00 43.32 1.78
2316 2349 2.437651 TCCAAAGCCGATCATCCATACA 59.562 45.455 0.00 0.00 0.00 2.29
2337 2370 6.183360 CCACACTATTGCATTTGAATCCTGAT 60.183 38.462 0.00 0.00 0.00 2.90
2355 2388 0.833949 TGCACTTCCACACCACACTA 59.166 50.000 0.00 0.00 0.00 2.74
2378 2411 0.038744 ATTGGTGTTGGGAGCTGGAG 59.961 55.000 0.00 0.00 0.00 3.86
2385 2418 0.783206 ATGGTCCATTGGTGTTGGGA 59.217 50.000 0.00 0.00 34.85 4.37
2571 2604 4.325109 GCCTTCCCTTGTACTCCCTATTTT 60.325 45.833 0.00 0.00 0.00 1.82
2617 2650 6.706270 GTGTACAGGTACAATAATGGAGATGG 59.294 42.308 13.41 0.00 46.33 3.51
2734 2767 8.795513 CCAATAATCATATCAGCAACCACATTA 58.204 33.333 0.00 0.00 0.00 1.90
2735 2768 7.288389 ACCAATAATCATATCAGCAACCACATT 59.712 33.333 0.00 0.00 0.00 2.71
2736 2769 6.779049 ACCAATAATCATATCAGCAACCACAT 59.221 34.615 0.00 0.00 0.00 3.21
2737 2770 6.128486 ACCAATAATCATATCAGCAACCACA 58.872 36.000 0.00 0.00 0.00 4.17
2874 2957 7.938140 TTATGAACCAAGGGAGAAATGTAAG 57.062 36.000 0.00 0.00 0.00 2.34
2977 3088 4.023193 CCCCCGTTCACAAATATAAGATGC 60.023 45.833 0.00 0.00 0.00 3.91
2998 3109 0.688087 CCCTCTGTCACCTACTCCCC 60.688 65.000 0.00 0.00 0.00 4.81
3025 3136 7.865530 TGTGGCCTGTTATCTATCCTATTTA 57.134 36.000 3.32 0.00 0.00 1.40
3067 4645 6.819284 TGATATGTCACTTGTGCATATCTGA 58.181 36.000 30.05 20.85 45.55 3.27
3093 4671 6.705381 CGATCTGATTCTTTCTAAGCCATCTT 59.295 38.462 0.00 0.00 36.35 2.40
3126 4705 2.863484 AGGGTGAATGGGGTGGCA 60.863 61.111 0.00 0.00 0.00 4.92
3150 4729 1.068333 GCACCCGTCGTGTAGTCTTAA 60.068 52.381 2.30 0.00 44.97 1.85
3157 4736 1.233950 TTCGTAGCACCCGTCGTGTA 61.234 55.000 2.30 0.00 44.97 2.90
3167 4746 2.380410 CGGCAGGTGTTCGTAGCAC 61.380 63.158 0.00 0.00 36.22 4.40
3216 4795 1.892474 CACCATGGAAACCCGTTGAAT 59.108 47.619 21.47 0.00 0.00 2.57
3248 4827 4.961511 GCACGCTGTCACGACCCA 62.962 66.667 0.00 0.00 36.70 4.51
3325 4904 0.704076 CCCCCAGAAAGGATGACCAA 59.296 55.000 0.00 0.00 41.22 3.67
3331 4910 2.398919 GGTCACCCCCAGAAAGGAT 58.601 57.895 0.00 0.00 41.22 3.24
3357 4936 2.035626 CGGTGGAGGTGGCCATTT 59.964 61.111 9.72 0.00 40.68 2.32
3358 4937 2.933287 TCGGTGGAGGTGGCCATT 60.933 61.111 9.72 0.00 40.68 3.16
3359 4938 3.717294 GTCGGTGGAGGTGGCCAT 61.717 66.667 9.72 0.00 40.68 4.40
3360 4939 4.954118 AGTCGGTGGAGGTGGCCA 62.954 66.667 0.00 0.00 35.02 5.36
3361 4940 4.083862 GAGTCGGTGGAGGTGGCC 62.084 72.222 0.00 0.00 0.00 5.36
3362 4941 4.436998 CGAGTCGGTGGAGGTGGC 62.437 72.222 4.10 0.00 0.00 5.01
3363 4942 3.760035 CCGAGTCGGTGGAGGTGG 61.760 72.222 23.83 0.00 42.73 4.61
3364 4943 3.760035 CCCGAGTCGGTGGAGGTG 61.760 72.222 28.98 9.02 46.80 4.00
3367 4946 3.827898 GAGCCCGAGTCGGTGGAG 61.828 72.222 28.98 15.31 46.80 3.86
3370 4949 3.358076 GAAGGAGCCCGAGTCGGTG 62.358 68.421 28.98 20.78 46.80 4.94
3371 4950 3.069318 GAAGGAGCCCGAGTCGGT 61.069 66.667 28.98 12.83 46.80 4.69
3373 4952 2.182030 GTGAAGGAGCCCGAGTCG 59.818 66.667 5.29 5.29 0.00 4.18
3374 4953 2.182030 CGTGAAGGAGCCCGAGTC 59.818 66.667 0.00 0.00 0.00 3.36
3375 4954 3.382832 CCGTGAAGGAGCCCGAGT 61.383 66.667 0.00 0.00 45.00 4.18
3376 4955 3.068691 TCCGTGAAGGAGCCCGAG 61.069 66.667 0.00 0.00 45.98 4.63
3384 4963 1.185618 TGTCCCACTCTCCGTGAAGG 61.186 60.000 0.00 0.00 46.81 3.46
3385 4964 0.898320 ATGTCCCACTCTCCGTGAAG 59.102 55.000 0.00 0.00 46.81 3.02
3386 4965 1.001974 CAATGTCCCACTCTCCGTGAA 59.998 52.381 0.00 0.00 46.81 3.18
3387 4966 0.608130 CAATGTCCCACTCTCCGTGA 59.392 55.000 0.00 0.00 46.81 4.35
3388 4967 1.021390 GCAATGTCCCACTCTCCGTG 61.021 60.000 0.00 0.00 43.41 4.94
3389 4968 1.296715 GCAATGTCCCACTCTCCGT 59.703 57.895 0.00 0.00 0.00 4.69
3390 4969 0.107508 ATGCAATGTCCCACTCTCCG 60.108 55.000 0.00 0.00 0.00 4.63
3391 4970 1.386533 CATGCAATGTCCCACTCTCC 58.613 55.000 0.00 0.00 40.20 3.71
3392 4971 1.386533 CCATGCAATGTCCCACTCTC 58.613 55.000 0.00 0.00 44.81 3.20
3393 4972 0.033796 CCCATGCAATGTCCCACTCT 60.034 55.000 0.00 0.00 44.81 3.24
3394 4973 1.039233 CCCCATGCAATGTCCCACTC 61.039 60.000 0.00 0.00 44.81 3.51
3395 4974 1.000739 CCCCATGCAATGTCCCACT 59.999 57.895 0.00 0.00 44.81 4.00
3396 4975 1.305213 ACCCCATGCAATGTCCCAC 60.305 57.895 0.00 0.00 44.81 4.61
3397 4976 1.305129 CACCCCATGCAATGTCCCA 60.305 57.895 0.00 0.00 44.81 4.37
3398 4977 1.305213 ACACCCCATGCAATGTCCC 60.305 57.895 0.00 0.00 44.81 4.46
3399 4978 0.899717 ACACACCCCATGCAATGTCC 60.900 55.000 0.00 0.00 44.81 4.02
3400 4979 0.968405 AACACACCCCATGCAATGTC 59.032 50.000 0.00 0.00 44.81 3.06
3401 4980 0.680618 CAACACACCCCATGCAATGT 59.319 50.000 0.00 0.00 44.81 2.71
3402 4981 0.967662 TCAACACACCCCATGCAATG 59.032 50.000 0.00 0.00 46.21 2.82
3403 4982 0.968405 GTCAACACACCCCATGCAAT 59.032 50.000 0.00 0.00 0.00 3.56
3404 4983 0.106268 AGTCAACACACCCCATGCAA 60.106 50.000 0.00 0.00 0.00 4.08
3405 4984 0.767998 TAGTCAACACACCCCATGCA 59.232 50.000 0.00 0.00 0.00 3.96
3406 4985 1.165270 GTAGTCAACACACCCCATGC 58.835 55.000 0.00 0.00 0.00 4.06
3407 4986 1.821216 GGTAGTCAACACACCCCATG 58.179 55.000 0.00 0.00 0.00 3.66
3408 4987 0.323629 CGGTAGTCAACACACCCCAT 59.676 55.000 0.00 0.00 0.00 4.00
3409 4988 1.749665 CGGTAGTCAACACACCCCA 59.250 57.895 0.00 0.00 0.00 4.96
3410 4989 1.004200 CCGGTAGTCAACACACCCC 60.004 63.158 0.00 0.00 0.00 4.95
3411 4990 1.670083 GCCGGTAGTCAACACACCC 60.670 63.158 1.90 0.00 0.00 4.61
3412 4991 0.250166 AAGCCGGTAGTCAACACACC 60.250 55.000 1.90 0.00 0.00 4.16
3413 4992 1.145803 GAAGCCGGTAGTCAACACAC 58.854 55.000 1.90 0.00 0.00 3.82
3414 4993 0.753867 TGAAGCCGGTAGTCAACACA 59.246 50.000 1.90 0.00 0.00 3.72
3415 4994 1.145803 GTGAAGCCGGTAGTCAACAC 58.854 55.000 1.90 0.98 0.00 3.32
3416 4995 0.753867 TGTGAAGCCGGTAGTCAACA 59.246 50.000 1.90 0.00 0.00 3.33
3417 4996 1.145803 GTGTGAAGCCGGTAGTCAAC 58.854 55.000 1.90 2.71 0.00 3.18
3418 4997 0.753867 TGTGTGAAGCCGGTAGTCAA 59.246 50.000 1.90 0.00 0.00 3.18
3419 4998 0.973632 ATGTGTGAAGCCGGTAGTCA 59.026 50.000 1.90 0.97 0.00 3.41
3420 4999 1.732259 CAATGTGTGAAGCCGGTAGTC 59.268 52.381 1.90 0.00 0.00 2.59
3421 5000 1.071699 ACAATGTGTGAAGCCGGTAGT 59.928 47.619 1.90 0.00 0.00 2.73
3422 5001 1.808411 ACAATGTGTGAAGCCGGTAG 58.192 50.000 1.90 0.00 0.00 3.18
3423 5002 3.620427 ATACAATGTGTGAAGCCGGTA 57.380 42.857 1.90 0.00 0.00 4.02
3424 5003 2.489938 ATACAATGTGTGAAGCCGGT 57.510 45.000 1.90 0.00 0.00 5.28
3425 5004 3.063452 GTGTATACAATGTGTGAAGCCGG 59.937 47.826 7.25 0.00 0.00 6.13
3426 5005 3.241963 CGTGTATACAATGTGTGAAGCCG 60.242 47.826 7.25 0.00 0.00 5.52
3427 5006 3.063452 CCGTGTATACAATGTGTGAAGCC 59.937 47.826 7.25 0.00 0.00 4.35
3428 5007 3.930229 TCCGTGTATACAATGTGTGAAGC 59.070 43.478 7.25 0.00 0.00 3.86
3429 5008 5.580691 ACATCCGTGTATACAATGTGTGAAG 59.419 40.000 17.07 5.16 36.63 3.02
3430 5009 5.483811 ACATCCGTGTATACAATGTGTGAA 58.516 37.500 17.07 0.00 36.63 3.18
3431 5010 5.079689 ACATCCGTGTATACAATGTGTGA 57.920 39.130 17.07 5.62 36.63 3.58
3432 5011 5.580691 AGAACATCCGTGTATACAATGTGTG 59.419 40.000 18.06 11.61 37.67 3.82
3433 5012 5.730550 AGAACATCCGTGTATACAATGTGT 58.269 37.500 18.06 12.93 37.67 3.72
3434 5013 6.754675 TGTAGAACATCCGTGTATACAATGTG 59.245 38.462 18.06 12.43 37.54 3.21
3435 5014 6.869695 TGTAGAACATCCGTGTATACAATGT 58.130 36.000 13.54 13.54 37.54 2.71
3436 5015 7.095649 CCATGTAGAACATCCGTGTATACAATG 60.096 40.741 7.25 10.49 40.77 2.82
3437 5016 6.929049 CCATGTAGAACATCCGTGTATACAAT 59.071 38.462 7.25 0.00 40.77 2.71
3438 5017 6.277605 CCATGTAGAACATCCGTGTATACAA 58.722 40.000 7.25 0.00 40.77 2.41
3439 5018 5.737922 GCCATGTAGAACATCCGTGTATACA 60.738 44.000 0.08 0.08 41.22 2.29
3440 5019 4.684703 GCCATGTAGAACATCCGTGTATAC 59.315 45.833 0.00 0.00 36.53 1.47
3441 5020 4.557895 CGCCATGTAGAACATCCGTGTATA 60.558 45.833 0.00 0.00 36.53 1.47
3442 5021 3.728845 GCCATGTAGAACATCCGTGTAT 58.271 45.455 0.00 0.00 36.53 2.29
3443 5022 2.480587 CGCCATGTAGAACATCCGTGTA 60.481 50.000 0.00 0.00 36.53 2.90
3444 5023 1.739035 CGCCATGTAGAACATCCGTGT 60.739 52.381 0.00 0.00 36.53 4.49
3445 5024 0.930310 CGCCATGTAGAACATCCGTG 59.070 55.000 0.00 0.00 36.53 4.94
3446 5025 0.179084 CCGCCATGTAGAACATCCGT 60.179 55.000 0.00 0.00 36.53 4.69
3447 5026 1.498865 GCCGCCATGTAGAACATCCG 61.499 60.000 0.00 0.00 36.53 4.18
3448 5027 0.463654 TGCCGCCATGTAGAACATCC 60.464 55.000 0.00 0.00 36.53 3.51
3449 5028 1.265095 CATGCCGCCATGTAGAACATC 59.735 52.381 0.00 0.00 43.07 3.06
3450 5029 1.311859 CATGCCGCCATGTAGAACAT 58.688 50.000 0.00 0.00 43.07 2.71
3451 5030 2.779282 CATGCCGCCATGTAGAACA 58.221 52.632 0.00 0.00 43.07 3.18
3477 5056 3.251245 AGATAACATCGACGCTACCTGAG 59.749 47.826 0.00 0.00 0.00 3.35
3478 5057 3.211865 AGATAACATCGACGCTACCTGA 58.788 45.455 0.00 0.00 0.00 3.86
3479 5058 3.627732 AGATAACATCGACGCTACCTG 57.372 47.619 0.00 0.00 0.00 4.00
3480 5059 5.001874 TGATAGATAACATCGACGCTACCT 58.998 41.667 0.00 0.00 0.00 3.08
3481 5060 5.292671 TGATAGATAACATCGACGCTACC 57.707 43.478 0.00 0.00 0.00 3.18
3482 5061 7.011202 TCCTATGATAGATAACATCGACGCTAC 59.989 40.741 0.00 0.00 0.00 3.58
3483 5062 7.046033 TCCTATGATAGATAACATCGACGCTA 58.954 38.462 0.00 0.00 0.00 4.26
3484 5063 5.880887 TCCTATGATAGATAACATCGACGCT 59.119 40.000 0.00 0.00 0.00 5.07
3485 5064 6.120378 TCCTATGATAGATAACATCGACGC 57.880 41.667 0.00 0.00 0.00 5.19
3486 5065 8.383264 GTTTCCTATGATAGATAACATCGACG 57.617 38.462 0.00 0.00 0.00 5.12


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

AutoCloner maintained by Alex Coulton.