Multiple sequence alignment - TraesCS5A01G147100

Loading Multiple Alignment...

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 TraesCS5A01G147100 chr5A 100.000 5162 0 0 1 5162 324482649 324487810 0.000000e+00 9533.0
1 TraesCS5A01G147100 chr5A 86.214 457 33 16 1989 2437 362790918 362790484 7.830000e-128 468.0
2 TraesCS5A01G147100 chr5A 83.149 362 28 14 2435 2793 362789370 362789039 3.020000e-77 300.0
3 TraesCS5A01G147100 chr5A 86.434 258 21 7 64 307 530895858 530895601 2.370000e-68 270.0
4 TraesCS5A01G147100 chr5A 82.375 261 28 8 2894 3150 129617718 129617472 1.460000e-50 211.0
5 TraesCS5A01G147100 chr5A 90.000 130 13 0 904 1033 530895531 530895402 8.890000e-38 169.0
6 TraesCS5A01G147100 chr5A 88.281 128 9 4 4536 4657 367133292 367133165 1.160000e-31 148.0
7 TraesCS5A01G147100 chr5A 86.607 112 8 3 4537 4641 417902826 417902715 3.270000e-22 117.0
8 TraesCS5A01G147100 chr4A 93.394 2740 129 21 2 2696 407208662 407211394 0.000000e+00 4010.0
9 TraesCS5A01G147100 chr4A 92.837 2457 126 18 2682 5124 407213010 407215430 0.000000e+00 3517.0
10 TraesCS5A01G147100 chr4A 91.509 106 8 1 4320 4424 708630003 708630108 1.500000e-30 145.0
11 TraesCS5A01G147100 chr4A 86.000 100 11 3 4874 4971 661974547 661974449 2.540000e-18 104.0
12 TraesCS5A01G147100 chr4A 100.000 33 0 0 2525 2557 407211253 407211285 1.550000e-05 62.1
13 TraesCS5A01G147100 chr4A 84.615 65 5 5 5065 5126 402267136 402267074 5.580000e-05 60.2
14 TraesCS5A01G147100 chr1A 93.258 2729 121 20 2 2686 537933865 537931156 0.000000e+00 3962.0
15 TraesCS5A01G147100 chr1A 93.984 1230 60 5 3700 4922 537893282 537892060 0.000000e+00 1849.0
16 TraesCS5A01G147100 chr1A 93.804 1033 33 10 2681 3710 537910060 537909056 0.000000e+00 1524.0
17 TraesCS5A01G147100 chr1A 100.000 33 0 0 2525 2557 537931287 537931255 1.550000e-05 62.1
18 TraesCS5A01G147100 chr4D 89.601 1529 131 17 2826 4336 252217224 252218742 0.000000e+00 1917.0
19 TraesCS5A01G147100 chr4D 90.158 823 63 9 1986 2795 252215634 252216451 0.000000e+00 1055.0
20 TraesCS5A01G147100 chr4D 88.857 350 28 9 4417 4764 252218740 252219080 2.220000e-113 420.0
21 TraesCS5A01G147100 chr4D 94.898 98 4 1 4324 4421 436376811 436376715 8.950000e-33 152.0
22 TraesCS5A01G147100 chr4D 82.677 127 12 5 4537 4655 456266856 456266732 2.540000e-18 104.0
23 TraesCS5A01G147100 chr4D 92.537 67 4 1 4811 4876 252219074 252219140 1.530000e-15 95.3
24 TraesCS5A01G147100 chr2B 86.941 1095 121 15 3251 4336 424317241 424318322 0.000000e+00 1210.0
25 TraesCS5A01G147100 chr2B 89.714 350 23 8 4417 4764 424318320 424318658 7.940000e-118 435.0
26 TraesCS5A01G147100 chr2B 87.121 132 15 1 904 1033 132843316 132843447 1.160000e-31 148.0
27 TraesCS5A01G147100 chr2B 91.765 85 6 1 4887 4970 338737507 338737591 3.270000e-22 117.0
28 TraesCS5A01G147100 chr2B 90.385 52 2 2 5075 5125 403417189 403417238 1.200000e-06 65.8
29 TraesCS5A01G147100 chr2B 82.857 70 9 3 5056 5124 588398335 588398402 5.580000e-05 60.2
30 TraesCS5A01G147100 chr2A 90.000 250 20 3 63 307 471723593 471723344 8.340000e-83 318.0
31 TraesCS5A01G147100 chr2A 80.822 292 34 12 2865 3150 241459237 241459512 5.240000e-50 209.0
32 TraesCS5A01G147100 chr2A 88.281 128 14 1 907 1033 471723272 471723145 8.950000e-33 152.0
33 TraesCS5A01G147100 chr2A 97.778 45 0 1 5088 5131 753819751 753819795 5.540000e-10 76.8
34 TraesCS5A01G147100 chr5B 89.113 248 22 3 65 307 493636568 493636815 2.340000e-78 303.0
35 TraesCS5A01G147100 chr5B 87.903 248 25 3 65 307 475666508 475666755 2.350000e-73 287.0
36 TraesCS5A01G147100 chr5B 78.400 375 58 13 925 1294 661530007 661529651 6.730000e-54 222.0
37 TraesCS5A01G147100 chr5B 93.836 146 9 0 1 146 637396238 637396383 2.420000e-53 220.0
38 TraesCS5A01G147100 chr5B 94.681 94 4 1 4330 4422 432174696 432174789 1.500000e-30 145.0
39 TraesCS5A01G147100 chr5B 87.200 125 14 1 904 1026 475666825 475666949 1.940000e-29 141.0
40 TraesCS5A01G147100 chr5B 84.615 65 10 0 969 1033 493651543 493651607 1.200000e-06 65.8
41 TraesCS5A01G147100 chr5B 91.489 47 2 2 5080 5124 570986014 570986060 4.320000e-06 63.9
42 TraesCS5A01G147100 chr3B 78.400 375 58 13 925 1294 536431380 536431024 6.730000e-54 222.0
43 TraesCS5A01G147100 chr1D 78.400 375 58 13 925 1294 53255079 53254723 6.730000e-54 222.0
44 TraesCS5A01G147100 chr4B 93.836 146 9 0 1 146 117037496 117037351 2.420000e-53 220.0
45 TraesCS5A01G147100 chr4B 75.196 383 58 15 919 1294 636692358 636692710 4.170000e-31 147.0
46 TraesCS5A01G147100 chr4B 88.764 89 8 2 4883 4970 640017272 640017359 1.970000e-19 108.0
47 TraesCS5A01G147100 chr1B 77.394 376 61 14 925 1294 110792588 110792231 8.760000e-48 202.0
48 TraesCS5A01G147100 chr1B 77.843 343 48 18 959 1294 332164886 332165207 2.450000e-43 187.0
49 TraesCS5A01G147100 chr2D 91.803 122 6 4 186 303 550641933 550641812 3.200000e-37 167.0
50 TraesCS5A01G147100 chr2D 86.923 130 17 0 904 1033 550641732 550641603 4.170000e-31 147.0
51 TraesCS5A01G147100 chrUn 92.233 103 7 1 4320 4422 244923798 244923899 1.500000e-30 145.0
52 TraesCS5A01G147100 chrUn 92.233 103 7 1 4320 4422 287095686 287095787 1.500000e-30 145.0
53 TraesCS5A01G147100 chr5D 94.624 93 5 0 4327 4419 15905596 15905688 1.500000e-30 145.0
54 TraesCS5A01G147100 chr5D 87.500 120 8 3 4543 4655 322389155 322389036 1.170000e-26 132.0
55 TraesCS5A01G147100 chr5D 87.368 95 10 2 4886 4979 23010576 23010483 1.970000e-19 108.0
56 TraesCS5A01G147100 chr7A 95.349 86 4 0 4335 4420 422475068 422475153 2.510000e-28 137.0
57 TraesCS5A01G147100 chr7A 91.489 47 2 1 5079 5125 734047808 734047764 4.320000e-06 63.9
58 TraesCS5A01G147100 chr3A 83.969 131 13 4 4536 4658 137914535 137914405 9.080000e-23 119.0
59 TraesCS5A01G147100 chr3A 97.436 39 1 0 5088 5126 393189500 393189462 3.340000e-07 67.6
60 TraesCS5A01G147100 chr6D 89.247 93 9 1 4881 4972 469612204 469612296 1.170000e-21 115.0
61 TraesCS5A01G147100 chr7D 89.011 91 9 1 4887 4976 34494520 34494610 1.520000e-20 111.0
62 TraesCS5A01G147100 chr7D 86.154 65 6 3 5061 5124 87751535 87751473 3.340000e-07 67.6
63 TraesCS5A01G147100 chr6B 93.151 73 5 0 4886 4958 543229241 543229313 1.970000e-19 108.0
64 TraesCS5A01G147100 chr6B 85.106 94 10 3 4881 4971 42318596 42318504 5.500000e-15 93.5
65 TraesCS5A01G147100 chr6B 81.481 81 11 4 4516 4593 713938458 713938379 4.320000e-06 63.9


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 TraesCS5A01G147100 chr5A 324482649 324487810 5161 False 9533.000 9533 100.000000 1 5162 1 chr5A.!!$F1 5161
1 TraesCS5A01G147100 chr5A 362789039 362790918 1879 True 384.000 468 84.681500 1989 2793 2 chr5A.!!$R4 804
2 TraesCS5A01G147100 chr4A 407208662 407215430 6768 False 2529.700 4010 95.410333 2 5124 3 chr4A.!!$F2 5122
3 TraesCS5A01G147100 chr1A 537931156 537933865 2709 True 2012.050 3962 96.629000 2 2686 2 chr1A.!!$R3 2684
4 TraesCS5A01G147100 chr1A 537892060 537893282 1222 True 1849.000 1849 93.984000 3700 4922 1 chr1A.!!$R1 1222
5 TraesCS5A01G147100 chr1A 537909056 537910060 1004 True 1524.000 1524 93.804000 2681 3710 1 chr1A.!!$R2 1029
6 TraesCS5A01G147100 chr4D 252215634 252219140 3506 False 871.825 1917 90.288250 1986 4876 4 chr4D.!!$F1 2890
7 TraesCS5A01G147100 chr2B 424317241 424318658 1417 False 822.500 1210 88.327500 3251 4764 2 chr2B.!!$F5 1513

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
937 951 0.769873 ATATTCTGCCCTGCCTGGAG 59.230 55.0 0.00 0.00 38.35 3.86 F
1764 1784 0.251787 ACAAGGTGGGAAAGGATGGC 60.252 55.0 0.00 0.00 0.00 4.40 F
1824 1844 0.603975 GAAGCTCCGGATGGTATGCC 60.604 60.0 3.57 0.00 36.30 4.40 F
3041 6598 1.327690 AAGCTGATGCATGCTTGGGG 61.328 55.0 20.11 6.57 46.25 4.96 F
3237 6797 1.608055 CAAACCACAGACTCATGCCA 58.392 50.0 0.00 0.00 0.00 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1820 1840 0.316204 GAGCTGCAGTTTGTTGGCAT 59.684 50.0 16.64 0.0 36.87 4.40 R
3320 6882 1.904287 TGGTTTGTAGTCATGGCACC 58.096 50.0 0.00 0.0 0.00 5.01 R
3813 7380 2.351350 GGGACTGGTACAAATGTTTGCG 60.351 50.0 5.44 0.0 41.79 4.85 R
4146 7716 0.468214 CCTCCTATGCTCGTCCCAGA 60.468 60.0 0.00 0.0 0.00 3.86 R
4194 7764 0.533032 GTTCCTCCACTTCTCTCGGG 59.467 60.0 0.00 0.0 0.00 5.14 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
32 33 2.997897 GTGGCCGGACCTGAGACT 60.998 66.667 3.83 0.00 40.22 3.24
148 149 3.118112 TCCCTCTCAATCCATTCTTCTGC 60.118 47.826 0.00 0.00 0.00 4.26
150 151 3.878103 CCTCTCAATCCATTCTTCTGCTG 59.122 47.826 0.00 0.00 0.00 4.41
179 180 7.336427 TGTTTTTCAACTGGAGCAAAATTCATT 59.664 29.630 0.00 0.00 33.58 2.57
198 199 8.743085 ATTCATTGTACTCTGCTTGTGATTAT 57.257 30.769 0.00 0.00 0.00 1.28
222 223 8.722480 ATCTTCATCATCGTCACTAATTTTGA 57.278 30.769 0.00 0.00 0.00 2.69
259 262 8.853469 ACTAACAGCTAAGAATACGTACAATC 57.147 34.615 0.00 0.00 0.00 2.67
303 306 6.035112 GTCAACGTCCAATTTTAGAGCTCTAG 59.965 42.308 22.19 11.16 0.00 2.43
612 616 8.053355 TGAGACTGTAGTGAAGAGGTTATATGA 58.947 37.037 0.00 0.00 0.00 2.15
836 846 6.054860 ACACTGCACAAATTATAGAGTCCT 57.945 37.500 0.00 0.00 0.00 3.85
867 881 6.418819 GTGTGTTTCATGATCCTCTGTTTTTG 59.581 38.462 0.00 0.00 0.00 2.44
934 948 1.315690 CACATATTCTGCCCTGCCTG 58.684 55.000 0.00 0.00 0.00 4.85
937 951 0.769873 ATATTCTGCCCTGCCTGGAG 59.230 55.000 0.00 0.00 38.35 3.86
1166 1180 5.807011 GGAAAAGTGTTCAATCATGGTATGC 59.193 40.000 0.00 0.00 0.00 3.14
1248 1262 4.566426 AAAGAAGGTTGCAGCTCTAGAT 57.434 40.909 0.00 0.00 0.00 1.98
1278 1292 3.069443 GCCAGGACCAATTCTCACAAAAA 59.931 43.478 0.00 0.00 0.00 1.94
1318 1332 2.670019 AGTACAACCAACCCCTTTCC 57.330 50.000 0.00 0.00 0.00 3.13
1320 1334 0.845337 TACAACCAACCCCTTTCCGT 59.155 50.000 0.00 0.00 0.00 4.69
1373 1387 5.652014 TCCAATTGTCCATCCACTTGTTATC 59.348 40.000 4.43 0.00 0.00 1.75
1406 1421 9.546909 CTGACATGACATTTACTCATTGTTTAC 57.453 33.333 0.00 0.00 0.00 2.01
1486 1504 2.624838 CCTCAAATGCACACTTCAGGTT 59.375 45.455 0.00 0.00 0.00 3.50
1516 1534 9.791820 TCACATTCTTGCTACATTCATTAATTG 57.208 29.630 0.00 0.00 0.00 2.32
1609 1629 6.850752 TTTCAGATACATGTGTGACCTCTA 57.149 37.500 9.11 0.00 0.00 2.43
1611 1631 4.335594 TCAGATACATGTGTGACCTCTACG 59.664 45.833 9.11 0.00 0.00 3.51
1643 1663 4.203226 TCTGCAAATACACCTCAAACACA 58.797 39.130 0.00 0.00 0.00 3.72
1644 1664 4.036262 TCTGCAAATACACCTCAAACACAC 59.964 41.667 0.00 0.00 0.00 3.82
1678 1698 6.284475 GTGAGATCACATTCTTGCTACATC 57.716 41.667 8.09 0.00 45.75 3.06
1684 1704 5.687780 TCACATTCTTGCTACATCCATGAT 58.312 37.500 0.00 0.00 0.00 2.45
1688 1708 8.573885 CACATTCTTGCTACATCCATGATTTAT 58.426 33.333 0.00 0.00 0.00 1.40
1712 1732 3.583806 TGGCAAAATTGTTTATGCTCCG 58.416 40.909 0.00 0.00 38.79 4.63
1758 1778 2.741553 GCCAACAAACAAGGTGGGAAAG 60.742 50.000 0.00 0.00 30.31 2.62
1759 1779 2.158971 CCAACAAACAAGGTGGGAAAGG 60.159 50.000 0.00 0.00 30.31 3.11
1764 1784 0.251787 ACAAGGTGGGAAAGGATGGC 60.252 55.000 0.00 0.00 0.00 4.40
1819 1839 1.123928 CTAAGGAAGCTCCGGATGGT 58.876 55.000 3.57 1.64 42.75 3.55
1820 1840 2.317040 CTAAGGAAGCTCCGGATGGTA 58.683 52.381 3.57 0.00 42.75 3.25
1821 1841 1.807814 AAGGAAGCTCCGGATGGTAT 58.192 50.000 3.57 0.00 42.75 2.73
1824 1844 0.603975 GAAGCTCCGGATGGTATGCC 60.604 60.000 3.57 0.00 36.30 4.40
1919 1945 4.886579 ACATCAATCTTTCTTTTGTGGCC 58.113 39.130 0.00 0.00 0.00 5.36
1964 1990 6.564312 CGTCCAACGTGTTTGTACATCAATTA 60.564 38.462 0.00 0.00 36.74 1.40
2041 2067 2.289002 CAGCGAGGTAAATCAATCCTGC 59.711 50.000 0.00 0.00 0.00 4.85
2168 2195 8.681486 ACATATTCTTGCAGCATATGAAGTTA 57.319 30.769 20.45 5.41 34.96 2.24
2223 2250 7.502120 ACTCTTATGCCATTTGTCATGTATC 57.498 36.000 0.00 0.00 0.00 2.24
2468 3618 2.948979 TGTGTGACCAAACCATTCAGAC 59.051 45.455 0.00 0.00 34.84 3.51
2508 3661 2.015736 ATGAGTCGAATGTGCAGTCC 57.984 50.000 0.00 0.00 0.00 3.85
2648 3825 2.205022 CCTTCTGCAAGGGACATTCA 57.795 50.000 0.00 0.00 45.27 2.57
2650 3827 3.094572 CCTTCTGCAAGGGACATTCATT 58.905 45.455 0.00 0.00 45.27 2.57
2721 5530 6.753180 TGCCAGTTTTAATGCTGAAACATTA 58.247 32.000 7.98 0.00 40.64 1.90
2982 6539 7.243604 TGAAAGTTTAAATTGCATCCATCCT 57.756 32.000 0.00 0.00 0.00 3.24
3041 6598 1.327690 AAGCTGATGCATGCTTGGGG 61.328 55.000 20.11 6.57 46.25 4.96
3051 6608 2.738743 CATGCTTGGGGACATTAGGTT 58.261 47.619 0.00 0.00 42.32 3.50
3189 6749 2.399396 ATTGACCGTCTTTTGTTGCG 57.601 45.000 0.00 0.00 0.00 4.85
3197 6757 2.650608 GTCTTTTGTTGCGTCATCACC 58.349 47.619 0.00 0.00 0.00 4.02
3237 6797 1.608055 CAAACCACAGACTCATGCCA 58.392 50.000 0.00 0.00 0.00 4.92
3288 6848 4.703379 TTGGCCTCAAACCAAATGAAAT 57.297 36.364 3.32 0.00 44.11 2.17
3315 6877 5.132897 TGATTGCCAACAAAGAATGGTAC 57.867 39.130 0.00 0.00 39.77 3.34
3316 6878 4.832266 TGATTGCCAACAAAGAATGGTACT 59.168 37.500 0.00 0.00 39.77 2.73
3317 6879 4.582701 TTGCCAACAAAGAATGGTACTG 57.417 40.909 0.00 0.00 39.00 2.74
3318 6880 3.561143 TGCCAACAAAGAATGGTACTGT 58.439 40.909 0.00 0.00 39.00 3.55
3320 6882 4.759693 TGCCAACAAAGAATGGTACTGTAG 59.240 41.667 0.00 0.00 39.00 2.74
3321 6883 4.156008 GCCAACAAAGAATGGTACTGTAGG 59.844 45.833 0.00 0.00 39.00 3.18
3324 6886 4.324267 ACAAAGAATGGTACTGTAGGTGC 58.676 43.478 0.00 0.00 0.00 5.01
3414 6978 5.163311 GCCAATTTTTATCAGGGCTAATGGT 60.163 40.000 0.00 0.00 38.37 3.55
3662 7227 4.706035 ACAATACACACCAACTACGGAAA 58.294 39.130 0.00 0.00 0.00 3.13
3742 7309 2.159531 TCGCAGCATTGAGTAATTGTGC 60.160 45.455 0.00 0.00 36.11 4.57
3804 7371 4.455606 GGCTTAGCTACTGTTTCATCCAT 58.544 43.478 3.59 0.00 0.00 3.41
3813 7380 8.844244 AGCTACTGTTTCATCCATTTTATCATC 58.156 33.333 0.00 0.00 0.00 2.92
3904 7471 6.464222 CCCTTCTACAATTCAGTTAGTCACA 58.536 40.000 0.00 0.00 0.00 3.58
3939 7506 5.368145 TCTGTTTCTGCAGATACACAAGTT 58.632 37.500 29.08 0.00 40.23 2.66
4112 7679 2.045536 GGTGCCTGGGAGAAGCAG 60.046 66.667 0.00 0.00 37.15 4.24
4146 7716 0.331954 TAGAGGAGCGGAAGAGGTGT 59.668 55.000 0.00 0.00 0.00 4.16
4190 7760 3.357079 GCAACAGTCGGGTGCAGG 61.357 66.667 8.23 0.00 0.00 4.85
4244 7815 0.249826 AGCAAAATTGTTGGCGGTGG 60.250 50.000 0.00 0.00 38.86 4.61
4342 7913 5.598417 GGCAATTTTATCCATGTAGTCCCTT 59.402 40.000 0.00 0.00 0.00 3.95
4343 7914 6.098266 GGCAATTTTATCCATGTAGTCCCTTT 59.902 38.462 0.00 0.00 0.00 3.11
4720 8299 7.744087 TCTCTGTAAAATTACACAGTGCAAT 57.256 32.000 15.34 0.00 42.28 3.56
4765 8344 8.844244 CATATTTCCTTCTATAGCATTATGGGC 58.156 37.037 0.00 0.00 0.00 5.36
4783 8362 0.466189 GCCCGTTGATCACCATCCAT 60.466 55.000 0.00 0.00 0.00 3.41
4879 8458 9.502091 TTCAGCTAATTCAATAACTTGTACTGT 57.498 29.630 0.00 0.00 33.87 3.55
4990 8570 7.646922 GGAGTACTACAACTATATTTGACGGTG 59.353 40.741 9.59 0.00 0.00 4.94
5009 8589 5.068591 ACGGTGAATAAAAGAAAGCCTTTGT 59.931 36.000 0.00 0.00 43.90 2.83
5046 8626 6.471233 TTAGTCTGATGGAGAATTCGTCAT 57.529 37.500 13.74 13.74 29.85 3.06
5124 8708 1.730121 GCACGTGCACGCTTACTAGTA 60.730 52.381 37.35 0.00 44.43 1.82
5125 8709 2.793933 CACGTGCACGCTTACTAGTAT 58.206 47.619 37.35 12.57 44.43 2.12
5126 8710 3.176708 CACGTGCACGCTTACTAGTATT 58.823 45.455 37.35 12.01 44.43 1.89
5127 8711 3.611113 CACGTGCACGCTTACTAGTATTT 59.389 43.478 37.35 11.79 44.43 1.40
5128 8712 3.855950 ACGTGCACGCTTACTAGTATTTC 59.144 43.478 37.35 0.00 44.43 2.17
5129 8713 3.855379 CGTGCACGCTTACTAGTATTTCA 59.145 43.478 28.16 0.00 0.00 2.69
5130 8714 4.325204 CGTGCACGCTTACTAGTATTTCAA 59.675 41.667 28.16 0.00 0.00 2.69
5131 8715 5.498700 CGTGCACGCTTACTAGTATTTCAAG 60.499 44.000 28.16 0.57 0.00 3.02
5132 8716 5.347907 GTGCACGCTTACTAGTATTTCAAGT 59.652 40.000 0.00 0.00 0.00 3.16
5133 8717 5.347635 TGCACGCTTACTAGTATTTCAAGTG 59.652 40.000 12.30 12.30 33.90 3.16
5134 8718 5.347907 GCACGCTTACTAGTATTTCAAGTGT 59.652 40.000 13.35 13.35 39.76 3.55
5135 8719 6.752240 CACGCTTACTAGTATTTCAAGTGTG 58.248 40.000 24.04 24.04 45.61 3.82
5136 8720 5.867716 ACGCTTACTAGTATTTCAAGTGTGG 59.132 40.000 16.83 3.43 38.24 4.17
5137 8721 6.097356 CGCTTACTAGTATTTCAAGTGTGGA 58.903 40.000 2.79 0.00 0.00 4.02
5138 8722 6.757010 CGCTTACTAGTATTTCAAGTGTGGAT 59.243 38.462 2.79 0.00 0.00 3.41
5139 8723 7.919091 CGCTTACTAGTATTTCAAGTGTGGATA 59.081 37.037 2.79 0.00 0.00 2.59
5140 8724 9.595823 GCTTACTAGTATTTCAAGTGTGGATAA 57.404 33.333 2.79 0.00 0.00 1.75
5144 8728 9.787435 ACTAGTATTTCAAGTGTGGATAACAAA 57.213 29.630 0.00 0.00 41.57 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.965219 CGTAGGAGATAAGGCCGGG 59.035 63.158 2.18 0.00 0.00 5.73
120 121 4.165758 AGAATGGATTGAGAGGGAAAGAGG 59.834 45.833 0.00 0.00 0.00 3.69
148 149 4.493547 TGCTCCAGTTGAAAAACAAACAG 58.506 39.130 0.00 0.00 40.36 3.16
150 151 5.854431 TTTGCTCCAGTTGAAAAACAAAC 57.146 34.783 0.00 0.00 40.36 2.93
179 180 6.935167 TGAAGATAATCACAAGCAGAGTACA 58.065 36.000 0.00 0.00 0.00 2.90
198 199 8.546597 TTCAAAATTAGTGACGATGATGAAGA 57.453 30.769 0.00 0.00 0.00 2.87
259 262 7.700656 ACGTTGACAAAATAAAGGAAGAAAGTG 59.299 33.333 0.00 0.00 0.00 3.16
303 306 5.404946 TGCTTCTTTGCTGCAGATTTTATC 58.595 37.500 20.43 0.00 32.55 1.75
427 431 6.974932 TCTATTCTGTCACTCATCTTTTGC 57.025 37.500 0.00 0.00 0.00 3.68
570 574 3.073650 AGTCTCATTCTTCCTTGCTGGTT 59.926 43.478 0.00 0.00 37.07 3.67
571 575 2.641815 AGTCTCATTCTTCCTTGCTGGT 59.358 45.455 0.00 0.00 37.07 4.00
626 630 6.014669 GTCAGTATCTCATTTGCCCTCTATCT 60.015 42.308 0.00 0.00 0.00 1.98
820 830 6.173339 CACACACCAGGACTCTATAATTTGT 58.827 40.000 0.00 0.00 0.00 2.83
836 846 2.884012 GGATCATGAAACACACACACCA 59.116 45.455 0.00 0.00 0.00 4.17
934 948 5.738783 GCATAGAGAGTTGTGAAGATCCTCC 60.739 48.000 0.00 0.00 0.00 4.30
937 951 4.376146 GGCATAGAGAGTTGTGAAGATCC 58.624 47.826 0.00 0.00 0.00 3.36
996 1010 8.112183 ACATCCATTCCTTTCTTAGTCATCTTT 58.888 33.333 0.00 0.00 0.00 2.52
997 1011 7.637511 ACATCCATTCCTTTCTTAGTCATCTT 58.362 34.615 0.00 0.00 0.00 2.40
1166 1180 6.198778 CGCTTTCTTCTCATCTGACATTCTAG 59.801 42.308 0.00 0.00 0.00 2.43
1219 1233 3.675775 GCTGCAACCTTCTTTTGTTGTCA 60.676 43.478 0.00 0.00 42.91 3.58
1248 1262 0.698238 ATTGGTCCTGGCTAGCACAA 59.302 50.000 18.24 11.15 0.00 3.33
1295 1309 4.018688 GGAAAGGGGTTGGTTGTACTATCT 60.019 45.833 0.00 0.00 0.00 1.98
1318 1332 6.401955 TGTATGTGTGTTGATTATGTCACG 57.598 37.500 0.00 0.00 36.32 4.35
1320 1334 8.296000 CCTTTTGTATGTGTGTTGATTATGTCA 58.704 33.333 0.00 0.00 34.25 3.58
1486 1504 8.969260 AATGAATGTAGCAAGAATGTGATCTA 57.031 30.769 0.00 0.00 0.00 1.98
1536 1554 2.636647 TGGCATTGTTGTCTGTGAGA 57.363 45.000 0.00 0.00 0.00 3.27
1609 1629 2.424842 TTTGCAGAGATTGGGGCCGT 62.425 55.000 0.00 0.00 0.00 5.68
1611 1631 1.683385 GTATTTGCAGAGATTGGGGCC 59.317 52.381 0.00 0.00 0.00 5.80
1643 1663 0.108424 GATCTCACCTGCTGAAGCGT 60.108 55.000 0.00 0.00 45.83 5.07
1644 1664 0.108472 TGATCTCACCTGCTGAAGCG 60.108 55.000 0.00 0.00 45.83 4.68
1688 1708 5.809562 CGGAGCATAAACAATTTTGCCATTA 59.190 36.000 1.29 0.00 35.71 1.90
1712 1732 2.819608 TGCTCCTATTTGTTGTTGGCTC 59.180 45.455 0.00 0.00 0.00 4.70
1759 1779 0.386838 GCTTAGGTTGGCATGCCATC 59.613 55.000 38.78 34.74 46.64 3.51
1764 1784 0.739462 TCGTCGCTTAGGTTGGCATG 60.739 55.000 0.00 0.00 0.00 4.06
1819 1839 1.541147 GAGCTGCAGTTTGTTGGCATA 59.459 47.619 16.64 0.00 36.87 3.14
1820 1840 0.316204 GAGCTGCAGTTTGTTGGCAT 59.684 50.000 16.64 0.00 36.87 4.40
1821 1841 0.752743 AGAGCTGCAGTTTGTTGGCA 60.753 50.000 16.64 0.00 35.96 4.92
1824 1844 2.857592 ACAAGAGCTGCAGTTTGTTG 57.142 45.000 16.64 19.22 30.05 3.33
1829 1849 2.627515 TCAGAACAAGAGCTGCAGTT 57.372 45.000 16.64 9.79 32.27 3.16
1831 1851 2.812591 ACATTCAGAACAAGAGCTGCAG 59.187 45.455 10.11 10.11 32.27 4.41
1832 1852 2.854963 ACATTCAGAACAAGAGCTGCA 58.145 42.857 1.02 0.00 32.27 4.41
1833 1853 3.251729 TCAACATTCAGAACAAGAGCTGC 59.748 43.478 0.00 0.00 32.27 5.25
1916 1942 4.786425 ACATCTCCTTCTAAAAGATGGCC 58.214 43.478 14.18 0.00 46.88 5.36
1964 1990 8.915036 CACTGTTGATCTATAGGTAAAGTAGGT 58.085 37.037 5.95 0.00 0.00 3.08
2204 2231 7.148373 CGATCATGATACATGACAAATGGCATA 60.148 37.037 8.54 0.00 43.11 3.14
2223 2250 5.803461 ACATGAAATTGTTCTTGCGATCATG 59.197 36.000 0.00 10.03 45.12 3.07
2354 2382 5.493809 TGGACTTGGCTATAACCTACAAAC 58.506 41.667 0.00 0.00 0.00 2.93
2468 3618 8.034215 ACTCATTGAGATTTCTACTTCACTGAG 58.966 37.037 20.33 14.95 39.30 3.35
2508 3661 3.026349 GTTTGTCACGTCGTTGTTGATG 58.974 45.455 0.00 0.00 0.00 3.07
2599 3776 3.069586 TCGAGGCAATCCAGTAATAGGTG 59.930 47.826 0.00 0.00 33.74 4.00
2795 5604 8.908786 ACAAGTAGATTTTCTCTGTTGAATGA 57.091 30.769 6.30 0.00 34.86 2.57
2982 6539 2.857186 TCATGTACTGCCAGCAAGAA 57.143 45.000 0.00 0.00 0.00 2.52
3041 6598 8.428186 TCGGTAATAACATCAAACCTAATGTC 57.572 34.615 0.00 0.00 35.10 3.06
3051 6608 5.743714 GCCCATACCTCGGTAATAACATCAA 60.744 44.000 0.00 0.00 33.99 2.57
3189 6749 6.611381 TGAAATTCAGATTTTCGGTGATGAC 58.389 36.000 11.44 0.00 35.65 3.06
3288 6848 6.211184 ACCATTCTTTGTTGGCAATCATAGAA 59.789 34.615 23.26 23.26 36.60 2.10
3315 6877 3.610040 TTGTAGTCATGGCACCTACAG 57.390 47.619 17.57 0.00 41.31 2.74
3316 6878 3.558321 GGTTTGTAGTCATGGCACCTACA 60.558 47.826 15.53 15.53 39.30 2.74
3317 6879 3.007635 GGTTTGTAGTCATGGCACCTAC 58.992 50.000 0.00 11.75 33.32 3.18
3318 6880 2.640332 TGGTTTGTAGTCATGGCACCTA 59.360 45.455 0.00 0.00 0.00 3.08
3320 6882 1.904287 TGGTTTGTAGTCATGGCACC 58.096 50.000 0.00 0.00 0.00 5.01
3321 6883 3.067461 TGTTTGGTTTGTAGTCATGGCAC 59.933 43.478 0.00 0.00 0.00 5.01
3324 6886 5.010516 TCCATTGTTTGGTTTGTAGTCATGG 59.989 40.000 0.00 0.00 46.52 3.66
3325 6887 6.016360 TCTCCATTGTTTGGTTTGTAGTCATG 60.016 38.462 0.00 0.00 46.52 3.07
3326 6888 6.016276 GTCTCCATTGTTTGGTTTGTAGTCAT 60.016 38.462 0.00 0.00 46.52 3.06
3327 6889 5.298276 GTCTCCATTGTTTGGTTTGTAGTCA 59.702 40.000 0.00 0.00 46.52 3.41
3328 6890 5.531287 AGTCTCCATTGTTTGGTTTGTAGTC 59.469 40.000 0.00 0.00 46.52 2.59
3329 6891 5.445964 AGTCTCCATTGTTTGGTTTGTAGT 58.554 37.500 0.00 0.00 46.52 2.73
3662 7227 4.974645 TGTCATCTCTTAAACACCACCT 57.025 40.909 0.00 0.00 0.00 4.00
3804 7371 7.371159 TGGTACAAATGTTTGCGATGATAAAA 58.629 30.769 5.44 0.00 41.79 1.52
3813 7380 2.351350 GGGACTGGTACAAATGTTTGCG 60.351 50.000 5.44 0.00 41.79 4.85
3904 7471 5.428253 TGCAGAAACAGAAGACACTTTACT 58.572 37.500 0.00 0.00 0.00 2.24
3981 7548 0.963962 CAACAATGGCCAAGAGCAGT 59.036 50.000 10.96 0.00 46.50 4.40
4107 7674 2.596631 CCACTGCCTGCACTGCTT 60.597 61.111 1.98 0.00 0.00 3.91
4146 7716 0.468214 CCTCCTATGCTCGTCCCAGA 60.468 60.000 0.00 0.00 0.00 3.86
4190 7760 3.787001 CCACTTCTCTCGGGCCCC 61.787 72.222 18.66 0.00 0.00 5.80
4194 7764 0.533032 GTTCCTCCACTTCTCTCGGG 59.467 60.000 0.00 0.00 0.00 5.14
4198 7768 1.974236 CACCAGTTCCTCCACTTCTCT 59.026 52.381 0.00 0.00 0.00 3.10
4244 7815 4.323868 GGGCATTATTACCTCCTCTGATCC 60.324 50.000 0.00 0.00 0.00 3.36
4391 7962 8.862085 ACTCCCTCTGTAAACTAATATAAGAGC 58.138 37.037 0.00 0.00 0.00 4.09
4641 8213 3.319972 TCAGATTTCTATTACCCCGTCCG 59.680 47.826 0.00 0.00 0.00 4.79
4765 8344 1.311859 CATGGATGGTGATCAACGGG 58.688 55.000 6.21 0.00 0.00 5.28
4783 8362 1.822990 CTTCGCCCTGTACTAAGGACA 59.177 52.381 0.76 0.00 40.02 4.02
4876 8455 9.575868 TGTTTAGAGAGGGAATACTATCTACAG 57.424 37.037 0.00 0.00 40.04 2.74
4877 8456 9.931698 TTGTTTAGAGAGGGAATACTATCTACA 57.068 33.333 0.00 0.00 40.04 2.74
4941 8520 7.963532 TCCCTTCATAAGAAATATAAGAGCGT 58.036 34.615 0.00 0.00 32.35 5.07
4959 8538 9.483489 TCAAATATAGTTGTAGTACTCCCTTCA 57.517 33.333 12.28 0.00 0.00 3.02
4982 8562 4.825085 AGGCTTTCTTTTATTCACCGTCAA 59.175 37.500 0.00 0.00 0.00 3.18
5078 8658 8.757789 CAACGCACGTCTTTATTAGGATATAAA 58.242 33.333 0.00 0.00 0.00 1.40
5111 8695 6.183360 CCACACTTGAAATACTAGTAAGCGTG 60.183 42.308 6.70 10.83 33.69 5.34
5113 8697 6.097356 TCCACACTTGAAATACTAGTAAGCG 58.903 40.000 6.70 0.00 33.69 4.68
5124 8708 7.581213 TCAGTTTGTTATCCACACTTGAAAT 57.419 32.000 0.00 0.00 31.70 2.17
5125 8709 7.397892 TTCAGTTTGTTATCCACACTTGAAA 57.602 32.000 0.00 0.00 31.70 2.69
5126 8710 7.397892 TTTCAGTTTGTTATCCACACTTGAA 57.602 32.000 0.00 0.00 31.70 2.69
5127 8711 7.581213 ATTTCAGTTTGTTATCCACACTTGA 57.419 32.000 0.00 0.00 31.70 3.02


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

AutoCloner maintained by Alex Coulton.