Multiple sequence alignment - TraesCS4A01G329900

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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 TraesCS4A01G329900 chr4A 100.000 3495 0 0 1 3495 615098611 615102105 0.000000e+00 6455.0
1 TraesCS4A01G329900 chr4A 97.221 2555 63 5 1 2553 615080685 615083233 0.000000e+00 4318.0
2 TraesCS4A01G329900 chr4A 97.143 2555 66 4 1 2553 615057888 615060437 0.000000e+00 4307.0
3 TraesCS4A01G329900 chr4A 94.816 2141 83 10 918 3041 614906861 614908990 0.000000e+00 3314.0
4 TraesCS4A01G329900 chr4A 95.212 2005 60 16 1 1991 614962094 614964076 0.000000e+00 3138.0
5 TraesCS4A01G329900 chr4A 92.450 808 35 4 1986 2793 614982742 614983523 0.000000e+00 1131.0
6 TraesCS4A01G329900 chr4A 95.277 614 23 2 1940 2553 615044510 615045117 0.000000e+00 968.0
7 TraesCS4A01G329900 chr4A 95.181 415 14 2 1940 2354 615052221 615052629 0.000000e+00 651.0
8 TraesCS4A01G329900 chr4A 85.577 624 35 16 18 615 614906283 614906877 1.390000e-168 603.0
9 TraesCS4A01G329900 chr4A 92.342 222 11 1 3253 3468 614909532 614909753 9.420000e-81 311.0
10 TraesCS4A01G329900 chr4A 88.506 87 8 1 3147 3231 614909453 614909539 1.720000e-18 104.0
11 TraesCS4A01G329900 chr4A 87.500 80 8 2 3147 3224 614984439 614984518 1.340000e-14 91.6
12 TraesCS4A01G329900 chr5B 93.258 2136 92 13 918 3041 697172709 697174804 0.000000e+00 3099.0
13 TraesCS4A01G329900 chr5B 75.242 1656 314 55 965 2568 6603142 6601531 0.000000e+00 699.0
14 TraesCS4A01G329900 chr5B 93.425 365 23 1 2430 2793 697333101 697333465 1.100000e-149 540.0
15 TraesCS4A01G329900 chr5B 88.043 276 26 6 21 293 697171989 697172260 1.570000e-83 320.0
16 TraesCS4A01G329900 chr5B 91.558 154 4 3 3255 3399 697174898 697175051 1.640000e-48 204.0
17 TraesCS4A01G329900 chr5B 84.951 206 15 5 411 615 697172535 697172725 9.900000e-46 195.0
18 TraesCS4A01G329900 chr5B 95.000 120 2 2 293 408 697172292 697172411 5.960000e-43 185.0
19 TraesCS4A01G329900 chr5B 88.889 99 4 1 3133 3231 697174812 697174903 7.930000e-22 115.0
20 TraesCS4A01G329900 chr5D 94.121 1786 59 16 918 2694 553627110 553625362 0.000000e+00 2675.0
21 TraesCS4A01G329900 chr5D 75.584 1626 309 46 965 2531 5567690 5569286 0.000000e+00 723.0
22 TraesCS4A01G329900 chr5D 77.126 1329 219 38 1029 2313 6355848 6354561 0.000000e+00 691.0
23 TraesCS4A01G329900 chr5D 78.269 1063 166 36 1518 2534 6373488 6372445 1.070000e-174 623.0
24 TraesCS4A01G329900 chr5D 90.783 434 12 10 77 493 553627599 553627177 3.940000e-154 555.0
25 TraesCS4A01G329900 chr5D 94.340 106 4 1 3127 3230 553476120 553476015 1.000000e-35 161.0
26 TraesCS4A01G329900 chr5D 80.723 166 23 5 2372 2529 5795075 5795239 1.700000e-23 121.0
27 TraesCS4A01G329900 chr5D 90.805 87 6 2 3147 3231 553624114 553624028 7.930000e-22 115.0
28 TraesCS4A01G329900 chr5D 95.238 63 3 0 553 615 553627156 553627094 2.220000e-17 100.0
29 TraesCS4A01G329900 chr5D 85.567 97 11 3 3030 3123 292161309 292161405 7.980000e-17 99.0
30 TraesCS4A01G329900 chr5D 86.154 65 8 1 2975 3038 553476188 553476124 6.260000e-08 69.4
31 TraesCS4A01G329900 chr7A 96.452 310 11 0 614 923 4784765 4785074 2.410000e-141 512.0
32 TraesCS4A01G329900 chr7A 86.957 92 7 1 3040 3126 82512402 82512311 7.980000e-17 99.0
33 TraesCS4A01G329900 chr3B 96.721 305 10 0 614 918 606376353 606376049 3.110000e-140 508.0
34 TraesCS4A01G329900 chr5A 96.417 307 11 0 611 917 563891628 563891934 1.120000e-139 507.0
35 TraesCS4A01G329900 chr5A 95.584 317 11 3 613 927 148835882 148835567 4.030000e-139 505.0
36 TraesCS4A01G329900 chr5A 77.133 844 133 34 1735 2548 3314369 3315182 5.360000e-118 435.0
37 TraesCS4A01G329900 chr5A 89.655 87 4 1 3038 3119 533835104 533835190 4.770000e-19 106.0
38 TraesCS4A01G329900 chr6A 95.000 320 16 0 608 927 181909843 181910162 1.450000e-138 503.0
39 TraesCS4A01G329900 chr4D 96.117 309 11 1 614 922 459568658 459568965 1.450000e-138 503.0
40 TraesCS4A01G329900 chrUn 82.639 144 24 1 2077 2219 31311893 31311750 3.660000e-25 126.0
41 TraesCS4A01G329900 chrUn 71.954 435 89 18 2057 2484 31370247 31369839 2.870000e-16 97.1
42 TraesCS4A01G329900 chr2D 88.764 89 7 1 3039 3124 76898754 76898666 4.770000e-19 106.0
43 TraesCS4A01G329900 chr2D 86.598 97 8 1 3039 3130 302248098 302248002 6.170000e-18 102.0
44 TraesCS4A01G329900 chr2D 88.372 86 5 1 3039 3119 382456025 382455940 7.980000e-17 99.0
45 TraesCS4A01G329900 chr7B 88.372 86 6 2 3038 3119 7562504 7562419 2.220000e-17 100.0
46 TraesCS4A01G329900 chr2A 87.640 89 6 1 3040 3123 432581713 432581625 7.980000e-17 99.0
47 TraesCS4A01G329900 chr2B 84.112 107 9 4 3030 3131 136175707 136175810 2.870000e-16 97.1


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 TraesCS4A01G329900 chr4A 615098611 615102105 3494 False 6455.000000 6455 100.000000 1 3495 1 chr4A.!!$F6 3494
1 TraesCS4A01G329900 chr4A 615080685 615083233 2548 False 4318.000000 4318 97.221000 1 2553 1 chr4A.!!$F5 2552
2 TraesCS4A01G329900 chr4A 615057888 615060437 2549 False 4307.000000 4307 97.143000 1 2553 1 chr4A.!!$F4 2552
3 TraesCS4A01G329900 chr4A 614962094 614964076 1982 False 3138.000000 3138 95.212000 1 1991 1 chr4A.!!$F1 1990
4 TraesCS4A01G329900 chr4A 614906283 614909753 3470 False 1083.000000 3314 90.310250 18 3468 4 chr4A.!!$F7 3450
5 TraesCS4A01G329900 chr4A 615044510 615045117 607 False 968.000000 968 95.277000 1940 2553 1 chr4A.!!$F2 613
6 TraesCS4A01G329900 chr4A 614982742 614984518 1776 False 611.300000 1131 89.975000 1986 3224 2 chr4A.!!$F8 1238
7 TraesCS4A01G329900 chr5B 6601531 6603142 1611 True 699.000000 699 75.242000 965 2568 1 chr5B.!!$R1 1603
8 TraesCS4A01G329900 chr5B 697171989 697175051 3062 False 686.333333 3099 90.283167 21 3399 6 chr5B.!!$F2 3378
9 TraesCS4A01G329900 chr5D 553624028 553627599 3571 True 861.250000 2675 92.736750 77 3231 4 chr5D.!!$R4 3154
10 TraesCS4A01G329900 chr5D 5567690 5569286 1596 False 723.000000 723 75.584000 965 2531 1 chr5D.!!$F1 1566
11 TraesCS4A01G329900 chr5D 6354561 6355848 1287 True 691.000000 691 77.126000 1029 2313 1 chr5D.!!$R1 1284
12 TraesCS4A01G329900 chr5D 6372445 6373488 1043 True 623.000000 623 78.269000 1518 2534 1 chr5D.!!$R2 1016
13 TraesCS4A01G329900 chr5A 3314369 3315182 813 False 435.000000 435 77.133000 1735 2548 1 chr5A.!!$F1 813

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
851 1059 0.947244 GAATAATGCGAGCACCAGGG 59.053 55.0 0.0 0.0 0.00 4.45 F
2165 2435 1.579964 CTGCTTCGCATTGTCCAGCA 61.580 55.0 5.9 5.9 38.13 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2440 2744 1.574428 GACAATCGGTTGCAACGCT 59.426 52.632 22.67 7.38 38.96 5.07 R
2968 4729 0.188342 AAGATGGTGGCACCCTGTTT 59.812 50.000 32.61 18.46 37.50 2.83 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
179 216 3.561313 GCCTGTTTTCCTTGATGGACCTA 60.561 47.826 0.00 0.00 46.14 3.08
550 758 1.227147 TGATTCGATCGGCCGTTCC 60.227 57.895 27.15 13.57 0.00 3.62
582 790 3.937814 TGGAATCTTGTCTTGTACGCAT 58.062 40.909 0.00 0.00 0.00 4.73
670 878 2.184322 CGCGCATACACTCACCCT 59.816 61.111 8.75 0.00 0.00 4.34
796 1004 3.277962 GGAACGTCTCCTCCCACTA 57.722 57.895 8.87 0.00 41.61 2.74
851 1059 0.947244 GAATAATGCGAGCACCAGGG 59.053 55.000 0.00 0.00 0.00 4.45
1636 1855 4.332543 TGATTTGTGCTAGCAATCTTACCG 59.667 41.667 21.29 0.00 0.00 4.02
2165 2435 1.579964 CTGCTTCGCATTGTCCAGCA 61.580 55.000 5.90 5.90 38.13 4.41
2440 2744 2.280797 GTCAGTGCGCTGGTGGAA 60.281 61.111 26.23 4.37 42.78 3.53
2699 3791 9.794719 GGGTAATTAATCTGTAATTTAGCTCCT 57.205 33.333 0.00 0.00 0.00 3.69
2754 3846 4.798387 GGGCTTAAATTCATGCGTAGTTTG 59.202 41.667 0.00 0.00 0.00 2.93
2814 4555 4.240096 CATGTTTCCATTTGCCAAGTCTC 58.760 43.478 0.00 0.00 0.00 3.36
2824 4566 1.089920 GCCAAGTCTCGCATGATTGT 58.910 50.000 0.00 0.00 0.00 2.71
2841 4583 6.556974 TGATTGTCCTCAGAGATTCAGAAT 57.443 37.500 0.00 0.00 0.00 2.40
2843 4585 8.260099 TGATTGTCCTCAGAGATTCAGAATAT 57.740 34.615 0.00 0.00 0.00 1.28
2914 4674 7.920160 TTCTTTCACACTGTAATATCATGCA 57.080 32.000 0.00 0.00 0.00 3.96
2989 4750 0.620556 ACAGGGTGCCACCATCTTAG 59.379 55.000 17.22 0.00 41.02 2.18
2991 4752 1.207488 AGGGTGCCACCATCTTAGCA 61.207 55.000 17.22 0.00 41.02 3.49
3043 4804 9.530633 CCCAACATAATAGTTACTCTTGTACTC 57.469 37.037 0.00 0.00 0.00 2.59
3047 4808 8.693625 ACATAATAGTTACTCTTGTACTCCCAC 58.306 37.037 0.00 0.00 0.00 4.61
3048 4809 8.915036 CATAATAGTTACTCTTGTACTCCCACT 58.085 37.037 0.00 0.00 0.00 4.00
3049 4810 6.777213 ATAGTTACTCTTGTACTCCCACTG 57.223 41.667 0.00 0.00 0.00 3.66
3050 4811 4.481072 AGTTACTCTTGTACTCCCACTGT 58.519 43.478 0.00 0.00 0.00 3.55
3051 4812 5.638133 AGTTACTCTTGTACTCCCACTGTA 58.362 41.667 0.00 0.00 0.00 2.74
3053 4814 6.552350 AGTTACTCTTGTACTCCCACTGTAAA 59.448 38.462 0.00 0.00 0.00 2.01
3054 4815 5.470047 ACTCTTGTACTCCCACTGTAAAG 57.530 43.478 0.00 0.00 0.00 1.85
3056 4817 5.601313 ACTCTTGTACTCCCACTGTAAAGAA 59.399 40.000 0.00 0.00 0.00 2.52
3058 4819 6.522054 TCTTGTACTCCCACTGTAAAGAAAG 58.478 40.000 0.00 0.00 0.00 2.62
3059 4820 6.325545 TCTTGTACTCCCACTGTAAAGAAAGA 59.674 38.462 0.00 0.00 0.00 2.52
3060 4821 6.097915 TGTACTCCCACTGTAAAGAAAGAG 57.902 41.667 0.00 0.00 0.00 2.85
3061 4822 5.601313 TGTACTCCCACTGTAAAGAAAGAGT 59.399 40.000 8.05 8.05 37.18 3.24
3062 4823 4.962155 ACTCCCACTGTAAAGAAAGAGTG 58.038 43.478 0.00 0.00 39.74 3.51
3063 4824 4.409247 ACTCCCACTGTAAAGAAAGAGTGT 59.591 41.667 0.00 0.00 38.70 3.55
3064 4825 5.104485 ACTCCCACTGTAAAGAAAGAGTGTT 60.104 40.000 0.00 0.00 38.70 3.32
3065 4826 5.751586 TCCCACTGTAAAGAAAGAGTGTTT 58.248 37.500 0.00 0.00 38.70 2.83
3066 4827 6.891388 TCCCACTGTAAAGAAAGAGTGTTTA 58.109 36.000 0.00 0.00 38.70 2.01
3067 4828 6.990349 TCCCACTGTAAAGAAAGAGTGTTTAG 59.010 38.462 0.00 0.00 38.70 1.85
3068 4829 6.990349 CCCACTGTAAAGAAAGAGTGTTTAGA 59.010 38.462 0.00 0.00 38.70 2.10
3069 4830 7.661847 CCCACTGTAAAGAAAGAGTGTTTAGAT 59.338 37.037 0.00 0.00 38.70 1.98
3070 4831 8.713271 CCACTGTAAAGAAAGAGTGTTTAGATC 58.287 37.037 0.00 0.00 38.70 2.75
3071 4832 9.261180 CACTGTAAAGAAAGAGTGTTTAGATCA 57.739 33.333 0.00 0.00 36.33 2.92
3072 4833 9.262358 ACTGTAAAGAAAGAGTGTTTAGATCAC 57.738 33.333 0.00 0.00 36.22 3.06
3073 4834 9.482627 CTGTAAAGAAAGAGTGTTTAGATCACT 57.517 33.333 0.00 0.00 46.86 3.41
3078 4839 9.482627 AAGAAAGAGTGTTTAGATCACTACTTG 57.517 33.333 0.00 0.00 44.68 3.16
3079 4840 8.861086 AGAAAGAGTGTTTAGATCACTACTTGA 58.139 33.333 0.00 0.00 44.68 3.02
3080 4841 9.477484 GAAAGAGTGTTTAGATCACTACTTGAA 57.523 33.333 0.00 0.00 44.68 2.69
3082 4843 8.994429 AGAGTGTTTAGATCACTACTTGAATG 57.006 34.615 0.00 0.00 44.68 2.67
3083 4844 8.807118 AGAGTGTTTAGATCACTACTTGAATGA 58.193 33.333 0.00 0.00 44.68 2.57
3084 4845 9.593134 GAGTGTTTAGATCACTACTTGAATGAT 57.407 33.333 0.00 0.00 44.68 2.45
3091 4852 8.978564 AGATCACTACTTGAATGATATAAGCG 57.021 34.615 0.00 0.00 37.92 4.68
3092 4853 7.543868 AGATCACTACTTGAATGATATAAGCGC 59.456 37.037 0.00 0.00 37.92 5.92
3093 4854 6.749139 TCACTACTTGAATGATATAAGCGCT 58.251 36.000 2.64 2.64 0.00 5.92
3094 4855 6.863645 TCACTACTTGAATGATATAAGCGCTC 59.136 38.462 12.06 0.00 0.00 5.03
3095 4856 6.865726 CACTACTTGAATGATATAAGCGCTCT 59.134 38.462 12.06 3.59 0.00 4.09
3096 4857 7.383572 CACTACTTGAATGATATAAGCGCTCTT 59.616 37.037 12.06 3.37 36.35 2.85
3097 4858 8.577296 ACTACTTGAATGATATAAGCGCTCTTA 58.423 33.333 12.06 5.99 38.97 2.10
3098 4859 9.579768 CTACTTGAATGATATAAGCGCTCTTAT 57.420 33.333 12.06 13.21 45.02 1.73
3110 4871 6.526566 AAGCGCTCTTATATTTCTTTACGG 57.473 37.500 12.06 0.00 0.00 4.02
3111 4872 5.839621 AGCGCTCTTATATTTCTTTACGGA 58.160 37.500 2.64 0.00 0.00 4.69
3112 4873 5.921408 AGCGCTCTTATATTTCTTTACGGAG 59.079 40.000 2.64 0.00 0.00 4.63
3113 4874 5.118817 GCGCTCTTATATTTCTTTACGGAGG 59.881 44.000 0.00 0.00 0.00 4.30
3114 4875 5.634020 CGCTCTTATATTTCTTTACGGAGGG 59.366 44.000 0.00 0.00 0.00 4.30
3115 4876 6.516194 CGCTCTTATATTTCTTTACGGAGGGA 60.516 42.308 0.00 0.00 34.63 4.20
3116 4877 6.869388 GCTCTTATATTTCTTTACGGAGGGAG 59.131 42.308 0.00 0.00 0.00 4.30
3117 4878 7.471679 GCTCTTATATTTCTTTACGGAGGGAGT 60.472 40.741 0.00 0.00 0.00 3.85
3118 4879 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
3119 4880 9.597681 TCTTATATTTCTTTACGGAGGGAGTAT 57.402 33.333 0.00 0.00 0.00 2.12
3120 4881 9.857957 CTTATATTTCTTTACGGAGGGAGTATC 57.142 37.037 0.00 0.00 0.00 2.24
3121 4882 7.850935 ATATTTCTTTACGGAGGGAGTATCA 57.149 36.000 0.00 0.00 36.25 2.15
3122 4883 6.749036 ATTTCTTTACGGAGGGAGTATCAT 57.251 37.500 0.00 0.00 36.25 2.45
3123 4884 7.850935 ATTTCTTTACGGAGGGAGTATCATA 57.149 36.000 0.00 0.00 36.25 2.15
3124 4885 6.645790 TTCTTTACGGAGGGAGTATCATAC 57.354 41.667 0.00 0.00 36.25 2.39
3125 4886 5.698104 TCTTTACGGAGGGAGTATCATACA 58.302 41.667 0.00 0.00 36.25 2.29
3126 4887 5.768662 TCTTTACGGAGGGAGTATCATACAG 59.231 44.000 0.00 0.00 36.25 2.74
3127 4888 3.596940 ACGGAGGGAGTATCATACAGT 57.403 47.619 0.00 0.00 36.25 3.55
3128 4889 4.719026 ACGGAGGGAGTATCATACAGTA 57.281 45.455 0.00 0.00 36.25 2.74
3129 4890 5.258216 ACGGAGGGAGTATCATACAGTAT 57.742 43.478 0.00 0.00 36.25 2.12
3130 4891 6.384342 ACGGAGGGAGTATCATACAGTATA 57.616 41.667 0.00 0.00 36.25 1.47
3149 4914 8.978539 ACAGTATAATACAGTACAATGCATTCG 58.021 33.333 9.53 8.06 0.00 3.34
3159 5378 6.037062 CAGTACAATGCATTCGGAGTAAATCA 59.963 38.462 9.53 0.00 0.00 2.57
3160 5379 5.490139 ACAATGCATTCGGAGTAAATCAG 57.510 39.130 9.53 0.00 0.00 2.90
3161 5380 5.185454 ACAATGCATTCGGAGTAAATCAGA 58.815 37.500 9.53 0.00 0.00 3.27
3162 5381 5.824624 ACAATGCATTCGGAGTAAATCAGAT 59.175 36.000 9.53 0.00 31.83 2.90
3163 5382 6.992123 ACAATGCATTCGGAGTAAATCAGATA 59.008 34.615 9.53 0.00 31.83 1.98
3164 5383 7.498900 ACAATGCATTCGGAGTAAATCAGATAA 59.501 33.333 9.53 0.00 31.83 1.75
3165 5384 7.664082 ATGCATTCGGAGTAAATCAGATAAG 57.336 36.000 0.00 0.00 31.83 1.73
3223 5442 2.306847 ACATGTTTTCTCCCACGCTTT 58.693 42.857 0.00 0.00 0.00 3.51
3224 5443 2.034558 ACATGTTTTCTCCCACGCTTTG 59.965 45.455 0.00 0.00 0.00 2.77
3225 5444 1.757682 TGTTTTCTCCCACGCTTTGT 58.242 45.000 0.00 0.00 0.00 2.83
3226 5445 1.673920 TGTTTTCTCCCACGCTTTGTC 59.326 47.619 0.00 0.00 0.00 3.18
3227 5446 1.673920 GTTTTCTCCCACGCTTTGTCA 59.326 47.619 0.00 0.00 0.00 3.58
3228 5447 1.305201 TTTCTCCCACGCTTTGTCAC 58.695 50.000 0.00 0.00 0.00 3.67
3229 5448 0.179234 TTCTCCCACGCTTTGTCACA 59.821 50.000 0.00 0.00 0.00 3.58
3230 5449 0.531974 TCTCCCACGCTTTGTCACAC 60.532 55.000 0.00 0.00 0.00 3.82
3231 5450 1.507141 CTCCCACGCTTTGTCACACC 61.507 60.000 0.00 0.00 0.00 4.16
3232 5451 2.631428 CCACGCTTTGTCACACCG 59.369 61.111 0.00 0.00 0.00 4.94
3233 5452 2.177580 CCACGCTTTGTCACACCGT 61.178 57.895 0.00 0.00 0.00 4.83
3234 5453 1.711060 CCACGCTTTGTCACACCGTT 61.711 55.000 0.00 0.00 0.00 4.44
3235 5454 0.098025 CACGCTTTGTCACACCGTTT 59.902 50.000 0.00 0.00 0.00 3.60
3236 5455 0.806241 ACGCTTTGTCACACCGTTTT 59.194 45.000 0.00 0.00 0.00 2.43
3237 5456 1.200484 ACGCTTTGTCACACCGTTTTT 59.800 42.857 0.00 0.00 0.00 1.94
3317 5539 2.912956 ACCAAGTTGAAGGCATCCTCTA 59.087 45.455 3.87 0.00 30.89 2.43
3369 5597 4.643387 AGGCGGCAGGGTCAACAC 62.643 66.667 13.08 0.00 0.00 3.32
3416 5644 7.384115 GCTAGAACATGTACGGCTGAATTTATA 59.616 37.037 0.00 0.00 0.00 0.98
3419 5647 9.772973 AGAACATGTACGGCTGAATTTATAATA 57.227 29.630 0.00 0.00 0.00 0.98
3444 5672 3.674682 GCACATCGTTCACTAAGAGAGCT 60.675 47.826 0.00 0.00 0.00 4.09
3468 5696 2.575532 TGCTTTCTCTGGTGTTTCCTG 58.424 47.619 0.00 0.00 37.07 3.86
3469 5697 1.268079 GCTTTCTCTGGTGTTTCCTGC 59.732 52.381 0.00 0.00 37.07 4.85
3470 5698 2.575532 CTTTCTCTGGTGTTTCCTGCA 58.424 47.619 0.00 0.00 37.07 4.41
3471 5699 2.260844 TTCTCTGGTGTTTCCTGCAG 57.739 50.000 6.78 6.78 37.07 4.41
3472 5700 1.131638 TCTCTGGTGTTTCCTGCAGT 58.868 50.000 13.81 0.00 37.07 4.40
3473 5701 1.490490 TCTCTGGTGTTTCCTGCAGTT 59.510 47.619 13.81 0.00 37.07 3.16
3474 5702 1.876156 CTCTGGTGTTTCCTGCAGTTC 59.124 52.381 13.81 0.51 37.07 3.01
3475 5703 1.490490 TCTGGTGTTTCCTGCAGTTCT 59.510 47.619 13.81 0.00 37.07 3.01
3476 5704 1.605710 CTGGTGTTTCCTGCAGTTCTG 59.394 52.381 13.81 0.00 37.07 3.02
3477 5705 0.312102 GGTGTTTCCTGCAGTTCTGC 59.688 55.000 13.81 16.65 0.00 4.26
3478 5706 1.024271 GTGTTTCCTGCAGTTCTGCA 58.976 50.000 23.14 23.14 43.22 4.41
3479 5707 1.024271 TGTTTCCTGCAGTTCTGCAC 58.976 50.000 21.30 12.85 40.23 4.57
3480 5708 1.312815 GTTTCCTGCAGTTCTGCACT 58.687 50.000 21.30 0.00 40.23 4.40
3481 5709 2.158827 TGTTTCCTGCAGTTCTGCACTA 60.159 45.455 21.30 10.86 40.23 2.74
3482 5710 3.077359 GTTTCCTGCAGTTCTGCACTAT 58.923 45.455 21.30 0.00 40.23 2.12
3483 5711 3.423539 TTCCTGCAGTTCTGCACTATT 57.576 42.857 21.30 0.00 40.23 1.73
3484 5712 4.551702 TTCCTGCAGTTCTGCACTATTA 57.448 40.909 21.30 2.26 40.23 0.98
3485 5713 4.551702 TCCTGCAGTTCTGCACTATTAA 57.448 40.909 21.30 1.59 40.23 1.40
3486 5714 5.102953 TCCTGCAGTTCTGCACTATTAAT 57.897 39.130 21.30 0.00 40.23 1.40
3487 5715 5.500234 TCCTGCAGTTCTGCACTATTAATT 58.500 37.500 21.30 0.00 40.23 1.40
3488 5716 5.355071 TCCTGCAGTTCTGCACTATTAATTG 59.645 40.000 21.30 9.84 40.23 2.32
3489 5717 5.124457 CCTGCAGTTCTGCACTATTAATTGT 59.876 40.000 21.30 0.00 40.23 2.71
3490 5718 6.349611 CCTGCAGTTCTGCACTATTAATTGTT 60.350 38.462 21.30 0.00 40.23 2.83
3491 5719 6.980593 TGCAGTTCTGCACTATTAATTGTTT 58.019 32.000 21.30 0.00 40.23 2.83
3492 5720 6.862608 TGCAGTTCTGCACTATTAATTGTTTG 59.137 34.615 21.30 0.00 40.23 2.93
3493 5721 6.183360 GCAGTTCTGCACTATTAATTGTTTGC 60.183 38.462 18.26 3.17 32.76 3.68
3494 5722 7.086376 CAGTTCTGCACTATTAATTGTTTGCT 58.914 34.615 11.65 0.17 32.76 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 216 9.634163 CCAGTTTTGTTTCTTAAGTAGTTGTTT 57.366 29.630 1.63 0.00 0.00 2.83
409 616 3.871594 CGATCTGGTGCCCTTTTAAGTAG 59.128 47.826 0.00 0.00 0.00 2.57
410 617 3.516300 TCGATCTGGTGCCCTTTTAAGTA 59.484 43.478 0.00 0.00 0.00 2.24
550 758 4.872691 AGACAAGATTCCAATCTAGCAACG 59.127 41.667 2.17 0.00 44.67 4.10
582 790 7.984422 AATCACATATGAATCGAGCCATTTA 57.016 32.000 10.38 0.00 38.69 1.40
670 878 0.233590 GTGCGTGTGTGCGTTCATAA 59.766 50.000 0.00 0.00 37.81 1.90
796 1004 0.887933 ATTTCCGGTGATGCGCTTTT 59.112 45.000 9.73 0.00 0.00 2.27
2165 2435 2.177594 CTCCTTCAGCTTGGGCGAGT 62.178 60.000 0.00 0.00 44.37 4.18
2440 2744 1.574428 GACAATCGGTTGCAACGCT 59.426 52.632 22.67 7.38 38.96 5.07
2754 3846 7.303998 GCATAAGATATTGACATTCAAGAGGC 58.696 38.462 0.00 0.00 40.05 4.70
2814 4555 2.591571 TCTCTGAGGACAATCATGCG 57.408 50.000 4.59 0.00 0.00 4.73
2824 4566 4.903649 TGGCATATTCTGAATCTCTGAGGA 59.096 41.667 6.10 0.00 0.00 3.71
2841 4583 5.945784 GGAACATATTCATTAGCCTGGCATA 59.054 40.000 22.65 8.98 36.46 3.14
2843 4585 4.141181 AGGAACATATTCATTAGCCTGGCA 60.141 41.667 22.65 0.22 36.46 4.92
2914 4674 9.277783 GTGATTAGCAATTGTCCTCTATTACAT 57.722 33.333 7.40 0.00 0.00 2.29
2968 4729 0.188342 AAGATGGTGGCACCCTGTTT 59.812 50.000 32.61 18.46 37.50 2.83
2989 4750 2.409378 CGCATTGTTTTGTTCCTCATGC 59.591 45.455 0.00 0.00 0.00 4.06
2991 4752 2.035704 TGCGCATTGTTTTGTTCCTCAT 59.964 40.909 5.66 0.00 0.00 2.90
3043 4804 6.990349 TCTAAACACTCTTTCTTTACAGTGGG 59.010 38.462 0.00 0.00 40.57 4.61
3047 4808 9.482627 AGTGATCTAAACACTCTTTCTTTACAG 57.517 33.333 0.00 0.00 43.84 2.74
3053 4814 8.861086 TCAAGTAGTGATCTAAACACTCTTTCT 58.139 33.333 0.00 0.00 45.58 2.52
3054 4815 9.477484 TTCAAGTAGTGATCTAAACACTCTTTC 57.523 33.333 0.00 0.00 45.58 2.62
3056 4817 9.429359 CATTCAAGTAGTGATCTAAACACTCTT 57.571 33.333 0.00 0.00 45.58 2.85
3058 4819 8.988064 TCATTCAAGTAGTGATCTAAACACTC 57.012 34.615 0.00 0.00 45.58 3.51
3066 4827 7.543868 GCGCTTATATCATTCAAGTAGTGATCT 59.456 37.037 0.00 0.00 35.70 2.75
3067 4828 7.543868 AGCGCTTATATCATTCAAGTAGTGATC 59.456 37.037 2.64 0.00 35.70 2.92
3068 4829 7.382110 AGCGCTTATATCATTCAAGTAGTGAT 58.618 34.615 2.64 0.00 35.70 3.06
3069 4830 6.749139 AGCGCTTATATCATTCAAGTAGTGA 58.251 36.000 2.64 0.00 0.00 3.41
3070 4831 6.865726 AGAGCGCTTATATCATTCAAGTAGTG 59.134 38.462 13.26 0.00 0.00 2.74
3071 4832 6.987386 AGAGCGCTTATATCATTCAAGTAGT 58.013 36.000 13.26 0.00 0.00 2.73
3072 4833 7.881643 AAGAGCGCTTATATCATTCAAGTAG 57.118 36.000 13.26 0.00 31.07 2.57
3085 4846 8.086522 TCCGTAAAGAAATATAAGAGCGCTTAT 58.913 33.333 23.51 23.51 46.35 1.73
3086 4847 7.428020 TCCGTAAAGAAATATAAGAGCGCTTA 58.572 34.615 13.26 12.50 40.65 3.09
3087 4848 6.278363 TCCGTAAAGAAATATAAGAGCGCTT 58.722 36.000 13.26 8.09 38.15 4.68
3088 4849 5.839621 TCCGTAAAGAAATATAAGAGCGCT 58.160 37.500 11.27 11.27 0.00 5.92
3089 4850 5.118817 CCTCCGTAAAGAAATATAAGAGCGC 59.881 44.000 0.00 0.00 0.00 5.92
3090 4851 5.634020 CCCTCCGTAAAGAAATATAAGAGCG 59.366 44.000 0.00 0.00 0.00 5.03
3091 4852 6.756221 TCCCTCCGTAAAGAAATATAAGAGC 58.244 40.000 0.00 0.00 0.00 4.09
3092 4853 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
3093 4854 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
3094 4855 9.857957 GATACTCCCTCCGTAAAGAAATATAAG 57.142 37.037 0.00 0.00 0.00 1.73
3095 4856 9.370930 TGATACTCCCTCCGTAAAGAAATATAA 57.629 33.333 0.00 0.00 0.00 0.98
3096 4857 8.945195 TGATACTCCCTCCGTAAAGAAATATA 57.055 34.615 0.00 0.00 0.00 0.86
3097 4858 7.850935 TGATACTCCCTCCGTAAAGAAATAT 57.149 36.000 0.00 0.00 0.00 1.28
3098 4859 7.850935 ATGATACTCCCTCCGTAAAGAAATA 57.149 36.000 0.00 0.00 0.00 1.40
3099 4860 6.749036 ATGATACTCCCTCCGTAAAGAAAT 57.251 37.500 0.00 0.00 0.00 2.17
3100 4861 6.608405 TGTATGATACTCCCTCCGTAAAGAAA 59.392 38.462 4.03 0.00 0.00 2.52
3101 4862 6.131264 TGTATGATACTCCCTCCGTAAAGAA 58.869 40.000 4.03 0.00 0.00 2.52
3102 4863 5.698104 TGTATGATACTCCCTCCGTAAAGA 58.302 41.667 4.03 0.00 0.00 2.52
3103 4864 5.535406 ACTGTATGATACTCCCTCCGTAAAG 59.465 44.000 4.03 0.00 0.00 1.85
3104 4865 5.452255 ACTGTATGATACTCCCTCCGTAAA 58.548 41.667 4.03 0.00 0.00 2.01
3105 4866 5.057843 ACTGTATGATACTCCCTCCGTAA 57.942 43.478 4.03 0.00 0.00 3.18
3106 4867 4.719026 ACTGTATGATACTCCCTCCGTA 57.281 45.455 4.03 0.00 0.00 4.02
3107 4868 3.596940 ACTGTATGATACTCCCTCCGT 57.403 47.619 4.03 0.00 0.00 4.69
3108 4869 7.883391 ATTATACTGTATGATACTCCCTCCG 57.117 40.000 10.51 0.00 0.00 4.63
3109 4870 9.696572 TGTATTATACTGTATGATACTCCCTCC 57.303 37.037 28.23 12.29 38.05 4.30
3123 4884 8.978539 CGAATGCATTGTACTGTATTATACTGT 58.021 33.333 18.59 16.76 42.40 3.55
3124 4885 8.435430 CCGAATGCATTGTACTGTATTATACTG 58.565 37.037 18.59 7.55 32.53 2.74
3125 4886 8.364894 TCCGAATGCATTGTACTGTATTATACT 58.635 33.333 18.59 0.00 32.53 2.12
3126 4887 8.528917 TCCGAATGCATTGTACTGTATTATAC 57.471 34.615 18.59 0.00 32.53 1.47
3127 4888 8.364894 ACTCCGAATGCATTGTACTGTATTATA 58.635 33.333 18.59 0.00 32.53 0.98
3128 4889 7.217200 ACTCCGAATGCATTGTACTGTATTAT 58.783 34.615 18.59 0.00 32.53 1.28
3129 4890 6.578944 ACTCCGAATGCATTGTACTGTATTA 58.421 36.000 18.59 0.00 32.53 0.98
3130 4891 5.428253 ACTCCGAATGCATTGTACTGTATT 58.572 37.500 18.59 0.00 34.67 1.89
3149 4914 7.382759 GGATGACGTTCTTATCTGATTTACTCC 59.617 40.741 0.00 0.00 0.00 3.85
3159 5378 4.537751 TCTCCAGGATGACGTTCTTATCT 58.462 43.478 0.00 0.00 39.69 1.98
3160 5379 4.920640 TCTCCAGGATGACGTTCTTATC 57.079 45.455 0.00 0.00 39.69 1.75
3161 5380 5.878406 AATCTCCAGGATGACGTTCTTAT 57.122 39.130 0.00 0.00 39.69 1.73
3162 5381 5.677319 AAATCTCCAGGATGACGTTCTTA 57.323 39.130 0.00 0.00 39.69 2.10
3163 5382 4.559862 AAATCTCCAGGATGACGTTCTT 57.440 40.909 0.00 0.00 39.69 2.52
3164 5383 4.559862 AAAATCTCCAGGATGACGTTCT 57.440 40.909 0.00 0.00 39.69 3.01
3165 5384 4.455877 ACAAAAATCTCCAGGATGACGTTC 59.544 41.667 0.00 0.00 39.69 3.95
3242 5461 3.694072 CCACTGTGTGACTTCCTCAAAAA 59.306 43.478 7.08 0.00 35.23 1.94
3243 5462 3.278574 CCACTGTGTGACTTCCTCAAAA 58.721 45.455 7.08 0.00 35.23 2.44
3244 5463 2.421388 CCCACTGTGTGACTTCCTCAAA 60.421 50.000 7.08 0.00 35.23 2.69
3245 5464 1.140852 CCCACTGTGTGACTTCCTCAA 59.859 52.381 7.08 0.00 35.23 3.02
3246 5465 0.758734 CCCACTGTGTGACTTCCTCA 59.241 55.000 7.08 0.00 35.23 3.86
3247 5466 0.759346 ACCCACTGTGTGACTTCCTC 59.241 55.000 7.08 0.00 35.23 3.71
3248 5467 1.134098 CAACCCACTGTGTGACTTCCT 60.134 52.381 7.08 0.00 35.23 3.36
3249 5468 1.308998 CAACCCACTGTGTGACTTCC 58.691 55.000 7.08 0.00 35.23 3.46
3250 5469 1.308998 CCAACCCACTGTGTGACTTC 58.691 55.000 7.08 0.00 35.23 3.01
3251 5470 0.623723 ACCAACCCACTGTGTGACTT 59.376 50.000 7.08 0.00 35.23 3.01
3292 5514 2.553028 GGATGCCTTCAACTTGGTCTGA 60.553 50.000 0.00 0.00 0.00 3.27
3317 5539 4.036734 CAGGCCGCATATGTTTTCATAAGT 59.963 41.667 4.29 0.00 44.56 2.24
3369 5597 3.329386 CCCTTGTCTATCGGTATGCATG 58.671 50.000 10.16 0.00 0.00 4.06
3416 5644 5.670485 TCTTAGTGAACGATGTGCCATATT 58.330 37.500 0.00 0.00 0.00 1.28
3419 5647 3.195610 TCTCTTAGTGAACGATGTGCCAT 59.804 43.478 0.00 0.00 0.00 4.40
3444 5672 3.569701 GGAAACACCAGAGAAAGCAATGA 59.430 43.478 0.00 0.00 38.79 2.57
3469 5697 7.086376 AGCAAACAATTAATAGTGCAGAACTG 58.914 34.615 12.39 0.00 40.26 3.16
3470 5698 7.219484 AGCAAACAATTAATAGTGCAGAACT 57.781 32.000 12.39 0.00 43.40 3.01


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

AutoCloner maintained by Alex Coulton.