Multiple sequence alignment - TraesCS2A01G283800

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 TraesCS2A01G283800 chr2A 100.000 9606 0 0 1 9606 475869231 475878836 0.000000e+00 17740.0
1 TraesCS2A01G283800 chr2A 88.889 81 9 0 6582 6662 733795757 733795837 6.140000e-17 100.0
2 TraesCS2A01G283800 chr2A 95.745 47 1 1 9189 9235 475878375 475878420 3.720000e-09 75.0
3 TraesCS2A01G283800 chr2A 95.745 47 1 1 9145 9190 475878419 475878465 3.720000e-09 75.0
4 TraesCS2A01G283800 chr2D 98.163 5389 86 5 3468 8851 355679454 355684834 0.000000e+00 9391.0
5 TraesCS2A01G283800 chr2D 94.345 3519 134 32 1 3469 355675685 355679188 0.000000e+00 5336.0
6 TraesCS2A01G283800 chr2D 95.778 758 28 3 8850 9606 355684916 355685670 0.000000e+00 1219.0
7 TraesCS2A01G283800 chr2D 89.474 76 8 0 6581 6656 433507290 433507365 7.940000e-16 97.1
8 TraesCS2A01G283800 chr2D 89.041 73 8 0 6590 6662 4322466 4322394 3.690000e-14 91.6
9 TraesCS2A01G283800 chr2D 89.041 73 8 0 6590 6662 4348244 4348172 3.690000e-14 91.6
10 TraesCS2A01G283800 chr2D 89.041 73 8 0 6590 6662 4379189 4379117 3.690000e-14 91.6
11 TraesCS2A01G283800 chr2D 95.745 47 0 1 9189 9235 355685211 355685255 3.720000e-09 75.0
12 TraesCS2A01G283800 chr2D 95.745 47 1 1 9145 9190 355685254 355685300 3.720000e-09 75.0
13 TraesCS2A01G283800 chr2B 96.565 4046 115 10 5155 9190 423662806 423666837 0.000000e+00 6680.0
14 TraesCS2A01G283800 chr2B 91.338 2736 139 40 68 2726 423656972 423659686 0.000000e+00 3650.0
15 TraesCS2A01G283800 chr2B 96.930 1694 41 5 3468 5158 423660999 423662684 0.000000e+00 2830.0
16 TraesCS2A01G283800 chr2B 97.227 649 17 1 2821 3469 423660086 423660733 0.000000e+00 1098.0
17 TraesCS2A01G283800 chr2B 92.048 415 19 6 9190 9597 423666792 423667199 1.080000e-158 571.0
18 TraesCS2A01G283800 chr2B 98.750 80 1 0 2743 2822 423659893 423659972 1.010000e-29 143.0
19 TraesCS2A01G283800 chr6A 90.530 792 67 4 5795 6579 395249328 395250118 0.000000e+00 1040.0
20 TraesCS2A01G283800 chr6A 83.669 845 88 25 6672 7477 395250124 395250957 0.000000e+00 750.0
21 TraesCS2A01G283800 chr6A 87.349 332 34 5 2626 2955 395240920 395241245 3.280000e-99 374.0
22 TraesCS2A01G283800 chr6A 87.747 253 28 3 3974 4225 395248636 395248886 9.440000e-75 292.0
23 TraesCS2A01G283800 chr6A 90.341 176 16 1 3162 3337 395241445 395241619 7.500000e-56 230.0
24 TraesCS2A01G283800 chr6A 82.418 273 16 10 3467 3727 395248375 395248627 9.780000e-50 209.0
25 TraesCS2A01G283800 chr6A 92.857 112 7 1 5685 5796 395249002 395249112 2.780000e-35 161.0
26 TraesCS2A01G283800 chr6A 96.629 89 3 0 3056 3144 538097832 538097744 2.160000e-31 148.0
27 TraesCS2A01G283800 chrUn 88.251 732 61 15 1587 2298 360626222 360625496 0.000000e+00 852.0
28 TraesCS2A01G283800 chrUn 86.353 447 47 10 2512 2955 385732732 385732297 8.730000e-130 475.0
29 TraesCS2A01G283800 chrUn 90.503 179 16 1 3162 3340 385732097 385731920 1.610000e-57 235.0
30 TraesCS2A01G283800 chrUn 86.792 106 13 1 2297 2401 385732847 385732742 6.100000e-22 117.0
31 TraesCS2A01G283800 chrUn 80.368 163 12 6 1303 1453 360626501 360626347 1.320000e-18 106.0
32 TraesCS2A01G283800 chr6B 88.251 732 61 15 1587 2298 8331666 8330940 0.000000e+00 852.0
33 TraesCS2A01G283800 chr6B 88.251 732 61 15 1587 2298 8342635 8341909 0.000000e+00 852.0
34 TraesCS2A01G283800 chr6B 88.251 732 61 15 1587 2298 8352279 8351553 0.000000e+00 852.0
35 TraesCS2A01G283800 chr6B 88.251 732 61 15 1587 2298 8361926 8361200 0.000000e+00 852.0
36 TraesCS2A01G283800 chr6B 88.251 732 61 15 1587 2298 8371572 8370846 0.000000e+00 852.0
37 TraesCS2A01G283800 chr6B 86.771 446 46 9 2512 2955 8351278 8350844 1.450000e-132 484.0
38 TraesCS2A01G283800 chr6B 86.577 447 46 10 2512 2955 8341634 8341199 1.880000e-131 481.0
39 TraesCS2A01G283800 chr6B 86.607 448 45 10 2512 2955 8370571 8370135 1.880000e-131 481.0
40 TraesCS2A01G283800 chr6B 86.353 447 47 10 2512 2955 8360925 8360490 8.730000e-130 475.0
41 TraesCS2A01G283800 chr6B 78.973 409 78 8 1 406 200323498 200323901 1.230000e-68 272.0
42 TraesCS2A01G283800 chr6B 90.503 179 16 1 3162 3340 8350644 8350467 1.610000e-57 235.0
43 TraesCS2A01G283800 chr6B 90.503 179 16 1 3162 3340 8360290 8360113 1.610000e-57 235.0
44 TraesCS2A01G283800 chr6B 90.503 179 16 1 3162 3340 8369935 8369758 1.610000e-57 235.0
45 TraesCS2A01G283800 chr6B 89.944 179 17 1 3162 3340 8340999 8340822 7.500000e-56 230.0
46 TraesCS2A01G283800 chr6B 86.792 106 13 1 2297 2401 8341749 8341644 6.100000e-22 117.0
47 TraesCS2A01G283800 chr6B 86.792 106 13 1 2297 2401 8351393 8351288 6.100000e-22 117.0
48 TraesCS2A01G283800 chr6B 86.792 106 13 1 2297 2401 8361040 8360935 6.100000e-22 117.0
49 TraesCS2A01G283800 chr6B 86.792 106 13 1 2297 2401 8370686 8370581 6.100000e-22 117.0
50 TraesCS2A01G283800 chr6B 80.368 163 12 6 1303 1453 8331945 8331791 1.320000e-18 106.0
51 TraesCS2A01G283800 chr6B 80.368 163 12 6 1303 1453 8342914 8342760 1.320000e-18 106.0
52 TraesCS2A01G283800 chr6B 80.368 163 12 6 1303 1453 8352558 8352404 1.320000e-18 106.0
53 TraesCS2A01G283800 chr6B 80.368 163 12 6 1303 1453 8362205 8362051 1.320000e-18 106.0
54 TraesCS2A01G283800 chr6B 80.368 163 12 6 1303 1453 8371851 8371697 1.320000e-18 106.0
55 TraesCS2A01G283800 chr6B 88.608 79 8 1 6579 6656 142478856 142478934 2.860000e-15 95.3
56 TraesCS2A01G283800 chr1D 80.544 478 70 15 1 472 235581730 235582190 7.140000e-91 346.0
57 TraesCS2A01G283800 chr5B 81.592 402 67 7 1 398 507652745 507653143 9.300000e-85 326.0
58 TraesCS2A01G283800 chr7D 79.404 403 74 7 1 396 372910464 372910864 9.500000e-70 276.0
59 TraesCS2A01G283800 chr7D 81.493 335 59 3 82 415 167589234 167589566 1.230000e-68 272.0
60 TraesCS2A01G283800 chr7D 78.554 415 79 8 3 415 571238219 571237813 2.060000e-66 265.0
61 TraesCS2A01G283800 chr7D 78.870 407 73 7 68 471 386352691 386352295 7.400000e-66 263.0
62 TraesCS2A01G283800 chr7D 93.939 99 4 2 3052 3149 34756860 34756957 2.160000e-31 148.0
63 TraesCS2A01G283800 chr7D 87.805 123 14 1 3057 3179 638458225 638458104 1.010000e-29 143.0
64 TraesCS2A01G283800 chr7A 80.769 338 57 7 1 334 497585860 497586193 3.440000e-64 257.0
65 TraesCS2A01G283800 chr1B 97.701 87 2 0 3057 3143 632020927 632021013 6.010000e-32 150.0
66 TraesCS2A01G283800 chr4A 96.629 89 3 0 3056 3144 48905991 48905903 2.160000e-31 148.0
67 TraesCS2A01G283800 chr4A 85.897 78 10 1 6579 6656 612373937 612373861 2.220000e-11 82.4
68 TraesCS2A01G283800 chr3B 96.629 89 3 0 3056 3144 521797770 521797858 2.160000e-31 148.0
69 TraesCS2A01G283800 chr3B 89.535 86 9 0 6579 6664 830296641 830296556 1.020000e-19 110.0
70 TraesCS2A01G283800 chr3B 89.535 86 9 0 6579 6664 830570606 830570521 1.020000e-19 110.0
71 TraesCS2A01G283800 chr4D 88.000 125 10 4 3057 3180 4772132 4772252 1.010000e-29 143.0
72 TraesCS2A01G283800 chr7B 88.372 86 10 0 6573 6658 740993871 740993956 4.750000e-18 104.0
73 TraesCS2A01G283800 chr7B 88.000 75 8 1 6582 6656 120452089 120452016 4.780000e-13 87.9
74 TraesCS2A01G283800 chr3D 88.608 79 9 0 6591 6669 591606766 591606844 7.940000e-16 97.1
75 TraesCS2A01G283800 chr4B 85.000 60 9 0 482 541 163799314 163799373 2.900000e-05 62.1


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 TraesCS2A01G283800 chr2A 475869231 475878836 9605 False 5963.333333 17740 97.163333 1 9606 3 chr2A.!!$F2 9605
1 TraesCS2A01G283800 chr2D 355675685 355685670 9985 False 3219.200000 9391 95.955200 1 9606 5 chr2D.!!$F2 9605
2 TraesCS2A01G283800 chr2B 423656972 423667199 10227 False 2495.333333 6680 95.476333 68 9597 6 chr2B.!!$F1 9529
3 TraesCS2A01G283800 chr6A 395248375 395250957 2582 False 490.400000 1040 87.444200 3467 7477 5 chr6A.!!$F2 4010
4 TraesCS2A01G283800 chr6A 395240920 395241619 699 False 302.000000 374 88.845000 2626 3337 2 chr6A.!!$F1 711
5 TraesCS2A01G283800 chrUn 360625496 360626501 1005 True 479.000000 852 84.309500 1303 2298 2 chrUn.!!$R1 995
6 TraesCS2A01G283800 chrUn 385731920 385732847 927 True 275.666667 475 87.882667 2297 3340 3 chrUn.!!$R2 1043
7 TraesCS2A01G283800 chr6B 8330940 8331945 1005 True 479.000000 852 84.309500 1303 2298 2 chr6B.!!$R1 995
8 TraesCS2A01G283800 chr6B 8350467 8352558 2091 True 358.800000 852 86.537000 1303 3340 5 chr6B.!!$R3 2037
9 TraesCS2A01G283800 chr6B 8369758 8371851 2093 True 358.200000 852 86.504200 1303 3340 5 chr6B.!!$R5 2037
10 TraesCS2A01G283800 chr6B 8340822 8342914 2092 True 357.200000 852 86.386400 1303 3340 5 chr6B.!!$R2 2037
11 TraesCS2A01G283800 chr6B 8360113 8362205 2092 True 357.000000 852 86.453400 1303 3340 5 chr6B.!!$R4 2037

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
494 505 0.389166 CCTGACTTGAGGCGTCTGTC 60.389 60.000 18.94 18.94 32.70 3.51 F
770 819 0.951040 CTCGGGTCACAGCAACTTCC 60.951 60.000 0.00 0.00 0.00 3.46 F
826 875 0.961753 GGAAAGAACCCTTGGTGCTG 59.038 55.000 0.00 0.00 41.57 4.41 F
2135 2238 0.038159 GTCAGGACTTGTCGGGTCAG 60.038 60.000 0.00 0.00 35.61 3.51 F
2394 2665 2.031120 TGGGACAAGGCAACAAGAAAG 58.969 47.619 0.00 0.00 41.41 2.62 F
4498 5405 3.771216 ACAGGGAAATCAGACAAGCAAT 58.229 40.909 0.00 0.00 0.00 3.56 F
5400 6432 2.427245 CCACCAGGAGGCCTAGACG 61.427 68.421 4.42 0.00 39.06 4.18 F
6061 7310 1.668751 GAGTTCCGTGCAAAGTCAACA 59.331 47.619 0.00 0.00 0.00 3.33 F
7202 8481 2.036256 GGACATGTGGGCCTTGCT 59.964 61.111 1.15 0.00 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1913 2.307392 TGCTTACTGGGTGGCTTATTCA 59.693 45.455 0.00 0.00 0.00 2.57 R
1959 2058 2.358582 TCGCCATGCATAACCATCTTTG 59.641 45.455 0.00 0.00 0.00 2.77 R
3151 3737 7.341256 ACTTCCTCCGTTCACTATTATAAGACA 59.659 37.037 0.00 0.00 0.00 3.41 R
4279 5186 0.898320 TACTCTGGTCAAGCTCTGGC 59.102 55.000 0.00 0.00 39.06 4.85 R
4637 5544 3.452990 TCACAAAGGTGTACTGTGAGGAA 59.547 43.478 10.01 0.00 43.36 3.36 R
5830 7078 0.251354 TGACCTGCATTGAGAGAGGC 59.749 55.000 0.00 0.00 0.00 4.70 R
7290 8583 0.891373 TCTACTGCTCGCTCTGCTTT 59.109 50.000 0.00 0.00 0.00 3.51 R
7415 8715 1.064654 GCACGGAAGGCATTCTGAATC 59.935 52.381 25.67 10.30 43.45 2.52 R
8955 10343 0.032130 TTCTCGAAGTTGCGCAGACT 59.968 50.000 11.31 14.44 0.00 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
31 32 1.548357 GGCTCCAGCAAGTCCAGAGA 61.548 60.000 0.03 0.00 44.36 3.10
39 40 1.228894 AAGTCCAGAGACAGCCCGA 60.229 57.895 0.00 0.00 46.15 5.14
46 47 3.973267 GAGACAGCCCGACAGCGAC 62.973 68.421 0.00 0.00 40.82 5.19
89 90 0.972471 TCGCTTGGATCTCCTGCTCA 60.972 55.000 11.08 0.00 35.31 4.26
134 135 2.737467 GCATAGTGTGCGTGGTTATG 57.263 50.000 0.00 0.00 45.23 1.90
141 142 1.156736 GTGCGTGGTTATGTTCTGCT 58.843 50.000 0.00 0.00 0.00 4.24
147 148 1.702401 TGGTTATGTTCTGCTGGACCA 59.298 47.619 0.00 0.00 33.62 4.02
148 149 2.308570 TGGTTATGTTCTGCTGGACCAT 59.691 45.455 0.00 0.00 31.26 3.55
156 159 1.486310 TCTGCTGGACCATAGCGAAAT 59.514 47.619 0.00 0.00 44.01 2.17
259 262 2.612746 GGCTAGGGTTGGGGGACA 60.613 66.667 0.00 0.00 0.00 4.02
267 270 4.938074 TTGGGGGACACCGACCGA 62.938 66.667 0.00 0.00 41.60 4.69
268 271 4.938074 TGGGGGACACCGACCGAA 62.938 66.667 0.00 0.00 41.60 4.30
353 356 2.094026 CCACATGAGAAGATGTCCGTCA 60.094 50.000 0.00 0.00 34.18 4.35
360 363 3.882888 GAGAAGATGTCCGTCAGATCTCT 59.117 47.826 0.00 0.00 33.80 3.10
363 366 2.028130 GATGTCCGTCAGATCTCTGGT 58.972 52.381 7.33 0.00 43.91 4.00
404 408 1.051812 GACCCCATCATCAGTCCGAT 58.948 55.000 0.00 0.00 33.27 4.18
422 426 1.204704 GATGTGATGGACGTGTCAGGA 59.795 52.381 0.00 0.00 0.00 3.86
447 451 0.677731 CCGATGCCCCATATTCGCAT 60.678 55.000 0.00 0.00 45.62 4.73
458 462 4.706476 CCCATATTCGCATCATATTTGGGT 59.294 41.667 0.00 0.00 36.41 4.51
477 488 1.344953 TTGGATATGCGGGTCAGCCT 61.345 55.000 0.00 0.00 36.02 4.58
482 493 1.264749 TATGCGGGTCAGCCTGACTT 61.265 55.000 23.23 7.27 46.19 3.01
483 494 2.743928 GCGGGTCAGCCTGACTTG 60.744 66.667 23.23 16.53 46.19 3.16
484 495 3.059982 CGGGTCAGCCTGACTTGA 58.940 61.111 23.23 0.00 46.19 3.02
485 496 1.079543 CGGGTCAGCCTGACTTGAG 60.080 63.158 23.23 9.36 46.19 3.02
492 503 4.586618 CCTGACTTGAGGCGTCTG 57.413 61.111 8.06 3.46 32.70 3.51
494 505 0.389166 CCTGACTTGAGGCGTCTGTC 60.389 60.000 18.94 18.94 32.70 3.51
496 507 1.813178 CTGACTTGAGGCGTCTGTCTA 59.187 52.381 22.99 14.11 32.06 2.59
522 548 6.344572 TCGAATTTTTATGATCGGTCAGTG 57.655 37.500 3.97 0.00 37.87 3.66
526 552 5.966636 TTTTTATGATCGGTCAGTGATCG 57.033 39.130 19.87 19.87 44.13 3.69
635 681 1.890876 ACGCAGCACCACTTTATTCA 58.109 45.000 0.00 0.00 0.00 2.57
770 819 0.951040 CTCGGGTCACAGCAACTTCC 60.951 60.000 0.00 0.00 0.00 3.46
793 842 2.759973 CCTCCTGCGTCCCAGCTA 60.760 66.667 0.00 0.00 40.36 3.32
826 875 0.961753 GGAAAGAACCCTTGGTGCTG 59.038 55.000 0.00 0.00 41.57 4.41
888 937 2.203480 TTCACCCACTTGCCTGCC 60.203 61.111 0.00 0.00 0.00 4.85
1030 1079 1.065401 GTGAGTGGAGCTCTCTCATCG 59.935 57.143 29.49 0.00 44.41 3.84
1091 1140 2.971452 GGCGGGACTCGACTTCTT 59.029 61.111 0.00 0.00 45.10 2.52
1092 1141 1.446272 GGCGGGACTCGACTTCTTG 60.446 63.158 0.00 0.00 45.10 3.02
1093 1142 1.289380 GCGGGACTCGACTTCTTGT 59.711 57.895 0.00 0.00 42.43 3.16
1162 1211 3.493503 GGGACGTTCTTGTTCTTGTGTAG 59.506 47.826 0.00 0.00 0.00 2.74
1346 1397 2.717580 TGGTCGTAACTGCTACAGTG 57.282 50.000 0.15 0.00 44.62 3.66
1571 1661 6.653526 AACATTGGATCATGTTTGACTTCA 57.346 33.333 5.76 0.00 37.71 3.02
1639 1729 7.395190 TGCTTCAACTCATGCATAACTAAAT 57.605 32.000 0.00 0.00 0.00 1.40
1823 1913 1.610673 AGATCACCCACGAGCCACT 60.611 57.895 0.00 0.00 0.00 4.00
2135 2238 0.038159 GTCAGGACTTGTCGGGTCAG 60.038 60.000 0.00 0.00 35.61 3.51
2212 2322 4.119136 TGTACAGTCTGTGTGATGTTGTG 58.881 43.478 16.03 0.00 40.69 3.33
2285 2395 5.826586 TGAATTGCGTTGAACATTTGTACT 58.173 33.333 0.00 0.00 0.00 2.73
2394 2665 2.031120 TGGGACAAGGCAACAAGAAAG 58.969 47.619 0.00 0.00 41.41 2.62
2503 2774 7.994425 TTATTTGGTGTTCTCTGCAGATAAA 57.006 32.000 18.63 12.06 0.00 1.40
2615 2886 5.826601 TGTTCTTGCAAACAGTGTATTGA 57.173 34.783 17.11 0.00 34.31 2.57
3369 3996 4.999950 GGGAGCAAGTATAGATTGTCATGG 59.000 45.833 0.00 0.00 0.00 3.66
3387 4014 5.888161 GTCATGGTATCCTTTCCTGTGAATT 59.112 40.000 0.00 0.00 0.00 2.17
3388 4015 6.378280 GTCATGGTATCCTTTCCTGTGAATTT 59.622 38.462 0.00 0.00 0.00 1.82
3421 4048 7.716560 TGGTATTATCTGGTCAAATCATCTGTG 59.283 37.037 0.00 0.00 0.00 3.66
4279 5186 3.956199 AGCAATCAACTGTAATGGGGATG 59.044 43.478 0.00 0.00 0.00 3.51
4498 5405 3.771216 ACAGGGAAATCAGACAAGCAAT 58.229 40.909 0.00 0.00 0.00 3.56
4637 5544 5.065090 GTGCTTGATTTGCCAAAAGTTTCTT 59.935 36.000 0.00 0.00 0.00 2.52
5027 5934 9.778741 TTGTGAAGAATCTACTGTGTTATTCTT 57.221 29.630 18.52 18.52 46.24 2.52
5400 6432 2.427245 CCACCAGGAGGCCTAGACG 61.427 68.421 4.42 0.00 39.06 4.18
5429 6461 3.509388 GCAGCTGCAAATTTCTGCT 57.491 47.368 33.36 15.11 46.00 4.24
5819 7067 9.798994 CTACGTCTTAACACCAACTAATCTTAT 57.201 33.333 0.00 0.00 0.00 1.73
5830 7078 8.017373 CACCAACTAATCTTATGTCTTGTTGTG 58.983 37.037 0.00 0.00 33.81 3.33
6061 7310 1.668751 GAGTTCCGTGCAAAGTCAACA 59.331 47.619 0.00 0.00 0.00 3.33
6343 7598 8.862325 AATTACAACAGTGGTTATCATTGAGA 57.138 30.769 0.00 0.00 36.69 3.27
6478 7733 4.446994 TGGCATAAATTTGCGTGATTCA 57.553 36.364 0.00 0.00 43.71 2.57
6579 7834 6.708285 AGATTACGTTTTGACTAACCAGGAT 58.292 36.000 0.00 0.00 0.00 3.24
6618 7873 8.854614 AAATCAATGGTATAGGACTTAGATGC 57.145 34.615 0.00 0.00 0.00 3.91
7039 8318 5.991933 TTTATTGGCATGGAACTAGCAAA 57.008 34.783 0.00 0.00 0.00 3.68
7202 8481 2.036256 GGACATGTGGGCCTTGCT 59.964 61.111 1.15 0.00 0.00 3.91
7290 8583 7.886629 ATTTCAGAAGGATTAGCTGCAATTA 57.113 32.000 1.02 0.00 0.00 1.40
7749 9053 3.950397 TGGGCTTTGAACTAGTACATGG 58.050 45.455 0.00 0.00 0.00 3.66
7788 9092 9.522804 TGTGTTTTACTTTGCTAACATTAAAGG 57.477 29.630 0.00 0.00 36.11 3.11
7836 9140 4.164221 AGAGGTCACCAAGTGAGAAAGAAA 59.836 41.667 0.00 0.00 43.57 2.52
7908 9212 2.824041 CGCCGGAAAGGACATGGG 60.824 66.667 5.05 0.00 45.00 4.00
7986 9290 3.444034 AGGAAGACGATGATGACTTCGAA 59.556 43.478 11.24 0.00 43.25 3.71
8070 9374 3.389656 TGTCAAGAGTGTTGTCCATGGTA 59.610 43.478 12.58 0.00 0.00 3.25
8189 9493 1.334869 GATCATAAGCCAAGTTGCCCG 59.665 52.381 0.00 0.00 0.00 6.13
8261 9566 8.776376 AGAGCAATTTCTCAAAAGAACAAAAA 57.224 26.923 7.86 0.00 41.23 1.94
8536 9841 2.879907 CAGGCTGAATTGGGTGCG 59.120 61.111 9.42 0.00 0.00 5.34
8588 9893 6.092955 ACAACGACTTACTGGTAGAAATCA 57.907 37.500 0.00 0.00 0.00 2.57
8955 10343 7.339976 TCTTTCATTTCCACTGAATGATGCATA 59.660 33.333 0.00 0.00 41.61 3.14
8957 10345 6.124340 TCATTTCCACTGAATGATGCATAGT 58.876 36.000 0.00 0.00 38.29 2.12
9026 10414 5.943416 ACTAAATTGGTTGTTCGATGATCCA 59.057 36.000 0.00 0.00 0.00 3.41
9029 10417 7.403312 AAATTGGTTGTTCGATGATCCATTA 57.597 32.000 0.00 0.00 0.00 1.90
9030 10418 7.403312 AATTGGTTGTTCGATGATCCATTAA 57.597 32.000 0.00 0.00 0.00 1.40
9110 10498 5.904984 TTGTATGGCATATCTACTGGGTT 57.095 39.130 10.92 0.00 0.00 4.11
9179 10567 7.048629 TGCATGAAGATGTTTCTTGGTTAAA 57.951 32.000 0.00 0.00 42.34 1.52
9363 10758 8.607713 TCCTACAAAACTCCCTGAATAAATACA 58.392 33.333 0.00 0.00 0.00 2.29
9372 10767 8.210946 ACTCCCTGAATAAATACAATCGAATGA 58.789 33.333 7.64 0.00 0.00 2.57
9406 10802 6.677781 TGCACAGCTAATGGACTAAAATAC 57.322 37.500 0.00 0.00 0.00 1.89
9424 10820 6.861065 AAATACTTTACAGGCATATCACGG 57.139 37.500 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.053264 AGGAGATCCAAGCGAGGCAT 61.053 55.000 0.92 0.00 38.89 4.40
74 75 2.172082 CCAGATTGAGCAGGAGATCCAA 59.828 50.000 0.92 0.00 38.89 3.53
89 90 2.499685 GAGCGCCGGTACCAGATT 59.500 61.111 13.54 0.00 0.00 2.40
121 122 0.871722 GCAGAACATAACCACGCACA 59.128 50.000 0.00 0.00 0.00 4.57
124 125 0.447801 CCAGCAGAACATAACCACGC 59.552 55.000 0.00 0.00 0.00 5.34
134 135 0.175760 TCGCTATGGTCCAGCAGAAC 59.824 55.000 7.34 0.00 39.04 3.01
141 142 2.503765 TCTCCAATTTCGCTATGGTCCA 59.496 45.455 0.00 0.00 35.66 4.02
147 148 2.205074 CACGCTCTCCAATTTCGCTAT 58.795 47.619 0.00 0.00 0.00 2.97
148 149 1.640428 CACGCTCTCCAATTTCGCTA 58.360 50.000 0.00 0.00 0.00 4.26
156 159 1.975327 CTCTTCCCACGCTCTCCAA 59.025 57.895 0.00 0.00 0.00 3.53
185 188 1.422161 CCCATCCACCCCATCTCTCC 61.422 65.000 0.00 0.00 0.00 3.71
259 262 2.476821 CGGCTATTTAATTCGGTCGGT 58.523 47.619 0.00 0.00 0.00 4.69
312 315 4.101790 GGTGTGAATGCCGCGTGG 62.102 66.667 11.67 11.67 38.77 4.94
341 344 2.692557 CCAGAGATCTGACGGACATCTT 59.307 50.000 11.44 0.00 46.59 2.40
371 374 2.598787 GGGTCCCACACGGAATGGA 61.599 63.158 1.78 0.00 44.47 3.41
373 376 2.045340 GGGGTCCCACACGGAATG 60.045 66.667 10.98 0.00 44.47 2.67
404 408 0.317160 GTCCTGACACGTCCATCACA 59.683 55.000 0.00 0.00 0.00 3.58
405 409 0.732880 CGTCCTGACACGTCCATCAC 60.733 60.000 0.00 0.00 34.95 3.06
447 451 4.078537 CCGCATATCCAACCCAAATATGA 58.921 43.478 5.92 0.00 36.08 2.15
458 462 1.148273 GGCTGACCCGCATATCCAA 59.852 57.895 0.00 0.00 0.00 3.53
477 488 1.905637 TAGACAGACGCCTCAAGTCA 58.094 50.000 9.64 0.00 40.84 3.41
482 493 2.089201 TCGATTTAGACAGACGCCTCA 58.911 47.619 0.00 0.00 0.00 3.86
483 494 2.846039 TCGATTTAGACAGACGCCTC 57.154 50.000 0.00 0.00 0.00 4.70
484 495 3.802948 ATTCGATTTAGACAGACGCCT 57.197 42.857 0.00 0.00 0.00 5.52
485 496 4.859629 AAATTCGATTTAGACAGACGCC 57.140 40.909 0.00 0.00 0.00 5.68
491 502 9.104965 ACCGATCATAAAAATTCGATTTAGACA 57.895 29.630 0.00 0.00 33.59 3.41
492 503 9.582223 GACCGATCATAAAAATTCGATTTAGAC 57.418 33.333 0.00 0.00 33.59 2.59
494 505 9.586150 CTGACCGATCATAAAAATTCGATTTAG 57.414 33.333 0.00 0.00 33.22 1.85
496 507 7.910162 CACTGACCGATCATAAAAATTCGATTT 59.090 33.333 0.00 0.00 33.22 2.17
513 539 3.458163 GGCCCGATCACTGACCGA 61.458 66.667 0.00 0.00 0.00 4.69
635 681 4.715297 CCACCCTCAAAGTATACTGGTACT 59.285 45.833 6.06 0.00 36.50 2.73
652 698 1.536676 CCCTTGTGTTGTCCACCCT 59.463 57.895 0.00 0.00 43.85 4.34
770 819 3.787001 GGACGCAGGAGGGGAAGG 61.787 72.222 0.00 0.00 0.00 3.46
793 842 4.202253 GGTTCTTTCCCAGAAAAGTGCAAT 60.202 41.667 0.00 0.00 43.52 3.56
826 875 1.132500 CTTGGATGGGGAGGTAGGAC 58.868 60.000 0.00 0.00 0.00 3.85
888 937 7.273381 CCAAACAAACAAGAACTGAAACAGTAG 59.727 37.037 4.84 0.00 44.62 2.57
1030 1079 5.106442 ACCAAAGAATCAAACGGAACAAAC 58.894 37.500 0.00 0.00 0.00 2.93
1089 1138 0.037232 GACTCCCGGGTCAAGACAAG 60.037 60.000 22.86 10.44 36.35 3.16
1090 1139 1.812686 CGACTCCCGGGTCAAGACAA 61.813 60.000 22.86 0.00 36.12 3.18
1091 1140 2.273179 CGACTCCCGGGTCAAGACA 61.273 63.158 22.86 0.00 36.12 3.41
1092 1141 1.935327 CTCGACTCCCGGGTCAAGAC 61.935 65.000 22.86 10.27 39.14 3.01
1093 1142 1.677966 CTCGACTCCCGGGTCAAGA 60.678 63.158 22.86 15.07 39.14 3.02
1143 1192 3.463944 CCCTACACAAGAACAAGAACGT 58.536 45.455 0.00 0.00 0.00 3.99
1145 1194 3.211045 TGCCCTACACAAGAACAAGAAC 58.789 45.455 0.00 0.00 0.00 3.01
1162 1211 2.351726 CACAATCTAGCGTTAAGTGCCC 59.648 50.000 0.00 0.00 0.00 5.36
1571 1661 6.764308 AACAATGATGCTACATAAAGCTGT 57.236 33.333 0.00 0.00 43.19 4.40
1639 1729 2.896685 CAGGCCCAAAATGAAGGTAACA 59.103 45.455 0.00 0.00 41.41 2.41
1823 1913 2.307392 TGCTTACTGGGTGGCTTATTCA 59.693 45.455 0.00 0.00 0.00 2.57
1959 2058 2.358582 TCGCCATGCATAACCATCTTTG 59.641 45.455 0.00 0.00 0.00 2.77
3151 3737 7.341256 ACTTCCTCCGTTCACTATTATAAGACA 59.659 37.037 0.00 0.00 0.00 3.41
3388 4015 7.531857 TTTGACCAGATAATACCAGCAAAAA 57.468 32.000 0.00 0.00 0.00 1.94
3393 4020 6.939163 AGATGATTTGACCAGATAATACCAGC 59.061 38.462 0.00 0.00 0.00 4.85
3421 4048 6.184789 TCACTATTTATTTCCCACTTCCCAC 58.815 40.000 0.00 0.00 0.00 4.61
3528 4422 8.584157 TCCATTATGAAAATATTTAAGGCGCAT 58.416 29.630 10.83 0.00 0.00 4.73
3982 4887 7.546358 TGTGCTCCCATTGTATTCAAATTAAG 58.454 34.615 0.00 0.00 37.11 1.85
4279 5186 0.898320 TACTCTGGTCAAGCTCTGGC 59.102 55.000 0.00 0.00 39.06 4.85
4498 5405 7.179160 GGGTTACCAGAAACTTTACCTAGACTA 59.821 40.741 2.98 0.00 36.50 2.59
4637 5544 3.452990 TCACAAAGGTGTACTGTGAGGAA 59.547 43.478 10.01 0.00 43.36 3.36
5034 5941 4.487714 TTGCAGGTATCCCTCTTACAAG 57.512 45.455 0.00 0.00 39.89 3.16
5819 7067 1.762370 TGAGAGAGGCACAACAAGACA 59.238 47.619 0.00 0.00 0.00 3.41
5830 7078 0.251354 TGACCTGCATTGAGAGAGGC 59.749 55.000 0.00 0.00 0.00 4.70
6061 7310 4.390297 GCGAAATCTGTGAAACTAGAAGCT 59.610 41.667 0.00 0.00 38.04 3.74
6343 7598 3.184628 TGTTCCATCATCTCCTTGGAGT 58.815 45.455 15.44 1.95 40.48 3.85
6478 7733 3.159213 TGAAGTGCAGTCCATCCATTT 57.841 42.857 0.00 0.00 0.00 2.32
6560 7815 4.345859 TCATCCTGGTTAGTCAAAACGT 57.654 40.909 0.00 0.00 0.00 3.99
6618 7873 5.289595 TCTAGATGTGCCTTAAGTATTGCG 58.710 41.667 0.97 0.00 0.00 4.85
6982 8253 8.633561 CACACTAACATATGGAGAGAGATGTAA 58.366 37.037 7.80 0.00 32.31 2.41
7005 8284 5.816258 CCATGCCAATAAATTGCAATACACA 59.184 36.000 13.39 5.15 36.48 3.72
7039 8318 7.891498 AAATGGACTTACTTAACAAGGTTGT 57.109 32.000 0.00 0.00 44.72 3.32
7202 8481 2.677902 CGCCACTTCTGAAAGATAGCCA 60.678 50.000 0.00 0.00 46.36 4.75
7290 8583 0.891373 TCTACTGCTCGCTCTGCTTT 59.109 50.000 0.00 0.00 0.00 3.51
7415 8715 1.064654 GCACGGAAGGCATTCTGAATC 59.935 52.381 25.67 10.30 43.45 2.52
7749 9053 9.659830 CAAAGTAAAACACAACTTACCTGATAC 57.340 33.333 0.00 0.00 34.91 2.24
7836 9140 7.510549 AACAGTGCTTACAAATGTCTTGTAT 57.489 32.000 0.00 0.00 35.15 2.29
7908 9212 2.886124 GCTCGGAAGCCACGTAGC 60.886 66.667 0.00 0.00 43.10 3.58
7986 9290 5.617528 AGATCTTGACTGCTTCATCATCT 57.382 39.130 0.00 0.00 32.84 2.90
8070 9374 2.317371 TCCTTGCTTCAGGAGAGTCT 57.683 50.000 0.00 0.00 38.11 3.24
8189 9493 9.130312 GATCGTGGTATGAACTATAGTTTCATC 57.870 37.037 22.72 12.29 38.56 2.92
8536 9841 4.371786 TCGATGATGTTGCCTTATCAGAC 58.628 43.478 0.00 0.00 36.81 3.51
8588 9893 5.581126 TTCTTTCAGCATGTGAACTTGTT 57.419 34.783 9.36 0.00 45.23 2.83
8616 9921 2.412525 CAAACGCTGCTTGTGCCA 59.587 55.556 0.00 0.00 38.71 4.92
8625 9930 2.174349 GAAGCTCCGCAAACGCTG 59.826 61.111 0.00 0.00 38.22 5.18
8635 9940 4.679373 TCACATCATTCTAGGAAGCTCC 57.321 45.455 0.00 0.00 36.58 4.70
8894 10282 6.127730 CCAAATTCTACCGAGCAACCTTTAAT 60.128 38.462 0.00 0.00 0.00 1.40
8955 10343 0.032130 TTCTCGAAGTTGCGCAGACT 59.968 50.000 11.31 14.44 0.00 3.24
8957 10345 0.944311 GGTTCTCGAAGTTGCGCAGA 60.944 55.000 11.31 2.66 0.00 4.26
8966 10354 4.058124 TGTGAACAATCTGGTTCTCGAAG 58.942 43.478 7.47 0.00 45.74 3.79
9058 10446 6.254589 TGCATTGTTTAGTTTTCCTTGTTTCG 59.745 34.615 0.00 0.00 0.00 3.46
9179 10567 4.446371 GCAATACTGTAGTGCCATTCTCT 58.554 43.478 25.05 0.00 43.36 3.10
9344 10737 8.801882 TTCGATTGTATTTATTCAGGGAGTTT 57.198 30.769 0.00 0.00 0.00 2.66
9363 10758 4.701651 TGCAATTTGGTCTCTCATTCGATT 59.298 37.500 0.00 0.00 0.00 3.34
9372 10767 2.283145 AGCTGTGCAATTTGGTCTCT 57.717 45.000 0.00 0.00 0.00 3.10
9406 10802 4.060038 AGACCGTGATATGCCTGTAAAG 57.940 45.455 0.00 0.00 0.00 1.85
9424 10820 7.472543 TCTTTTAAGTGAAAGTGCTGAAAGAC 58.527 34.615 0.00 0.00 37.76 3.01


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

AutoCloner maintained by Alex Coulton.