Multiple sequence alignment - TraesCS6B01G326900

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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 TraesCS6B01G326900 chr6B 100.000 3786 0 0 1 3786 576575025 576571240 0.000000e+00 6992.0
1 TraesCS6B01G326900 chr6B 92.418 2295 158 8 1244 3526 436208032 436205742 0.000000e+00 3260.0
2 TraesCS6B01G326900 chr6B 92.988 599 36 5 331 926 467168883 467168288 0.000000e+00 869.0
3 TraesCS6B01G326900 chr6B 85.007 727 84 9 332 1054 516269706 516270411 0.000000e+00 715.0
4 TraesCS6B01G326900 chr6B 84.669 724 88 10 333 1054 162103192 162102490 0.000000e+00 701.0
5 TraesCS6B01G326900 chr6B 94.922 256 13 0 3529 3784 436205693 436205438 5.890000e-108 401.0
6 TraesCS6B01G326900 chr6B 91.216 296 11 1 54 334 73372648 73372943 4.590000e-104 388.0
7 TraesCS6B01G326900 chr6B 89.600 250 8 4 102 334 506783199 506783447 6.150000e-78 302.0
8 TraesCS6B01G326900 chr6B 81.720 279 46 4 334 609 356819061 356818785 1.060000e-55 228.0
9 TraesCS6B01G326900 chr6B 89.051 137 11 2 1139 1274 373760621 373760488 2.340000e-37 167.0
10 TraesCS6B01G326900 chr6B 84.496 129 13 4 1065 1187 356839598 356839471 1.850000e-23 121.0
11 TraesCS6B01G326900 chr3B 95.697 3463 140 1 333 3786 422525306 422521844 0.000000e+00 5561.0
12 TraesCS6B01G326900 chr3B 95.455 3234 126 8 562 3786 589967431 589964210 0.000000e+00 5138.0
13 TraesCS6B01G326900 chr3B 92.230 296 8 1 54 334 474946430 474946135 4.550000e-109 405.0
14 TraesCS6B01G326900 chr3B 92.070 227 18 0 333 559 589973163 589972937 1.700000e-83 320.0
15 TraesCS6B01G326900 chr5D 95.248 3472 115 18 326 3786 172590933 172594365 0.000000e+00 5452.0
16 TraesCS6B01G326900 chr3A 94.113 3465 168 13 333 3786 276940668 276944107 0.000000e+00 5236.0
17 TraesCS6B01G326900 chr5B 92.610 3207 167 30 54 3221 245670934 245667759 0.000000e+00 4545.0
18 TraesCS6B01G326900 chr5B 97.208 573 15 1 3214 3786 245663152 245662581 0.000000e+00 968.0
19 TraesCS6B01G326900 chr5B 91.092 348 9 4 3 334 288762199 288761858 5.770000e-123 451.0
20 TraesCS6B01G326900 chr5B 81.293 294 44 8 332 618 570948533 570948822 1.060000e-55 228.0
21 TraesCS6B01G326900 chr4B 91.969 2291 166 8 1249 3526 249881858 249884143 0.000000e+00 3195.0
22 TraesCS6B01G326900 chr4B 82.831 763 98 14 2764 3524 422781915 422781184 0.000000e+00 652.0
23 TraesCS6B01G326900 chr4B 92.507 347 9 2 3 334 136587567 136587911 7.360000e-132 481.0
24 TraesCS6B01G326900 chr4B 93.357 286 9 4 54 331 292324653 292324936 7.570000e-112 414.0
25 TraesCS6B01G326900 chr4B 92.230 296 8 1 54 334 92380025 92380320 4.550000e-109 405.0
26 TraesCS6B01G326900 chr4B 91.554 296 10 2 54 334 460146208 460146503 9.860000e-106 394.0
27 TraesCS6B01G326900 chr4B 91.844 282 18 2 54 334 44128082 44127805 4.590000e-104 388.0
28 TraesCS6B01G326900 chr4B 91.156 294 10 6 54 331 292356494 292356787 5.930000e-103 385.0
29 TraesCS6B01G326900 chr4B 90.508 295 11 4 55 334 503239814 503240106 1.280000e-99 374.0
30 TraesCS6B01G326900 chr4B 92.430 251 19 0 3534 3784 249884193 249884443 3.600000e-95 359.0
31 TraesCS6B01G326900 chr4B 91.339 254 7 1 3 241 374895901 374896154 2.180000e-87 333.0
32 TraesCS6B01G326900 chr4B 86.786 280 29 4 2764 3035 10736653 10736374 4.750000e-79 305.0
33 TraesCS6B01G326900 chr4B 86.522 230 31 0 3529 3758 134119779 134119550 1.750000e-63 254.0
34 TraesCS6B01G326900 chr4B 92.683 82 6 0 3445 3526 10720563 10720482 6.640000e-23 119.0
35 TraesCS6B01G326900 chr4B 82.609 138 19 5 333 468 241457305 241457171 2.390000e-22 117.0
36 TraesCS6B01G326900 chr4B 91.429 70 4 2 333 401 401273568 401273636 1.120000e-15 95.3
37 TraesCS6B01G326900 chr4B 87.500 80 6 3 331 408 233241728 233241651 5.210000e-14 89.8
38 TraesCS6B01G326900 chr4B 90.625 64 6 0 333 396 373348004 373348067 6.740000e-13 86.1
39 TraesCS6B01G326900 chr4B 86.765 68 9 0 333 400 404627424 404627357 4.060000e-10 76.8
40 TraesCS6B01G326900 chr6A 93.235 1552 91 6 1984 3526 233245045 233246591 0.000000e+00 2272.0
41 TraesCS6B01G326900 chr6A 91.790 743 53 3 1244 1986 233244150 233244884 0.000000e+00 1027.0
42 TraesCS6B01G326900 chr6A 87.116 683 78 7 2762 3441 579825067 579825742 0.000000e+00 765.0
43 TraesCS6B01G326900 chr6A 93.798 258 16 0 3529 3786 233246640 233246897 4.590000e-104 388.0
44 TraesCS6B01G326900 chr6A 98.058 103 2 0 1244 1346 390199694 390199796 3.000000e-41 180.0
45 TraesCS6B01G326900 chr2A 92.402 1553 104 6 1984 3526 499392375 499390827 0.000000e+00 2202.0
46 TraesCS6B01G326900 chr2A 91.923 260 21 0 3527 3786 499390780 499390521 7.730000e-97 364.0
47 TraesCS6B01G326900 chr4A 92.209 1553 96 10 1984 3526 360503113 360504650 0.000000e+00 2174.0
48 TraesCS6B01G326900 chr4A 92.328 743 56 1 1244 1986 360502211 360502952 0.000000e+00 1055.0
49 TraesCS6B01G326900 chr4A 89.962 528 46 4 333 859 371047838 371047317 0.000000e+00 675.0
50 TraesCS6B01G326900 chr4A 94.574 258 14 0 3529 3786 360504699 360504956 2.120000e-107 399.0
51 TraesCS6B01G326900 chr1D 88.498 1165 99 17 2366 3526 195770196 195771329 0.000000e+00 1376.0
52 TraesCS6B01G326900 chr1D 88.469 1006 82 18 1051 2024 195768708 195769711 0.000000e+00 1184.0
53 TraesCS6B01G326900 chr1D 87.597 258 29 2 3529 3786 195771377 195771631 2.860000e-76 296.0
54 TraesCS6B01G326900 chr1B 88.755 1076 89 18 2452 3526 269575150 269574106 0.000000e+00 1288.0
55 TraesCS6B01G326900 chr1B 93.659 757 48 0 1244 2000 334537334 334536578 0.000000e+00 1133.0
56 TraesCS6B01G326900 chr1B 87.177 1006 91 18 1051 2033 269643669 269642679 0.000000e+00 1109.0
57 TraesCS6B01G326900 chr1B 88.689 557 61 2 1792 2346 269642819 269642263 0.000000e+00 678.0
58 TraesCS6B01G326900 chr1B 89.914 347 11 6 3 334 154089810 154090147 3.500000e-115 425.0
59 TraesCS6B01G326900 chr1B 91.864 295 8 5 55 334 141972056 141971763 7.620000e-107 398.0
60 TraesCS6B01G326900 chr1B 89.535 258 26 1 3529 3786 269574058 269573802 3.650000e-85 326.0
61 TraesCS6B01G326900 chr1B 86.260 131 18 0 3628 3758 425361440 425361310 3.940000e-30 143.0
62 TraesCS6B01G326900 chr1B 89.773 88 9 0 2366 2453 269642203 269642116 3.090000e-21 113.0
63 TraesCS6B01G326900 chr4D 86.736 769 85 11 2764 3526 6146284 6145527 0.000000e+00 839.0
64 TraesCS6B01G326900 chr4D 87.773 229 27 1 3530 3758 6145479 6145252 2.240000e-67 267.0
65 TraesCS6B01G326900 chr4D 81.761 159 24 1 3628 3786 280773989 280774142 1.100000e-25 128.0
66 TraesCS6B01G326900 chr6D 87.848 683 77 6 2762 3441 448409693 448409014 0.000000e+00 797.0
67 TraesCS6B01G326900 chr1A 87.243 682 78 6 2762 3441 561312136 561311462 0.000000e+00 769.0
68 TraesCS6B01G326900 chr1A 87.671 292 24 12 771 1054 200579670 200579383 2.820000e-86 329.0
69 TraesCS6B01G326900 chr1A 83.704 270 27 10 3257 3526 424801245 424801497 4.890000e-59 239.0
70 TraesCS6B01G326900 chr1A 84.332 217 32 2 2997 3212 546249567 546249782 1.070000e-50 211.0
71 TraesCS6B01G326900 chr1A 82.270 141 25 0 3628 3768 345714646 345714786 5.140000e-24 122.0
72 TraesCS6B01G326900 chr1A 76.136 264 28 21 3223 3483 546250087 546250318 5.170000e-19 106.0
73 TraesCS6B01G326900 chr1A 91.892 74 6 0 328 401 179448361 179448434 1.860000e-18 104.0
74 TraesCS6B01G326900 chr1A 92.000 75 5 1 327 401 272644923 272644996 1.860000e-18 104.0
75 TraesCS6B01G326900 chr1A 94.231 52 3 0 333 384 244185099 244185048 3.130000e-11 80.5
76 TraesCS6B01G326900 chr7B 92.219 347 8 2 3 334 224172422 224172764 1.230000e-129 473.0
77 TraesCS6B01G326900 chr7B 84.375 128 9 7 1065 1184 571571389 571571265 8.590000e-22 115.0
78 TraesCS6B01G326900 chrUn 91.066 347 10 2 3 334 466888269 466887929 2.070000e-122 449.0
79 TraesCS6B01G326900 chr5A 89.041 292 20 10 771 1054 220457913 220457626 6.020000e-93 351.0
80 TraesCS6B01G326900 chr5A 84.074 270 26 9 3257 3526 365326903 365327155 1.050000e-60 244.0
81 TraesCS6B01G326900 chr2B 86.120 317 38 6 729 1044 268009348 268009037 1.680000e-88 337.0
82 TraesCS6B01G326900 chr7D 82.353 323 41 8 1140 1449 436397064 436397383 2.240000e-67 267.0
83 TraesCS6B01G326900 chr7D 80.385 260 36 7 1140 1388 436395500 436395755 2.320000e-42 183.0


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 TraesCS6B01G326900 chr6B 576571240 576575025 3785 True 6992.000000 6992 100.000000 1 3786 1 chr6B.!!$R6 3785
1 TraesCS6B01G326900 chr6B 436205438 436208032 2594 True 1830.500000 3260 93.670000 1244 3784 2 chr6B.!!$R7 2540
2 TraesCS6B01G326900 chr6B 467168288 467168883 595 True 869.000000 869 92.988000 331 926 1 chr6B.!!$R5 595
3 TraesCS6B01G326900 chr6B 516269706 516270411 705 False 715.000000 715 85.007000 332 1054 1 chr6B.!!$F3 722
4 TraesCS6B01G326900 chr6B 162102490 162103192 702 True 701.000000 701 84.669000 333 1054 1 chr6B.!!$R1 721
5 TraesCS6B01G326900 chr3B 422521844 422525306 3462 True 5561.000000 5561 95.697000 333 3786 1 chr3B.!!$R1 3453
6 TraesCS6B01G326900 chr3B 589964210 589967431 3221 True 5138.000000 5138 95.455000 562 3786 1 chr3B.!!$R3 3224
7 TraesCS6B01G326900 chr5D 172590933 172594365 3432 False 5452.000000 5452 95.248000 326 3786 1 chr5D.!!$F1 3460
8 TraesCS6B01G326900 chr3A 276940668 276944107 3439 False 5236.000000 5236 94.113000 333 3786 1 chr3A.!!$F1 3453
9 TraesCS6B01G326900 chr5B 245667759 245670934 3175 True 4545.000000 4545 92.610000 54 3221 1 chr5B.!!$R2 3167
10 TraesCS6B01G326900 chr5B 245662581 245663152 571 True 968.000000 968 97.208000 3214 3786 1 chr5B.!!$R1 572
11 TraesCS6B01G326900 chr4B 249881858 249884443 2585 False 1777.000000 3195 92.199500 1249 3784 2 chr4B.!!$F10 2535
12 TraesCS6B01G326900 chr4B 422781184 422781915 731 True 652.000000 652 82.831000 2764 3524 1 chr4B.!!$R8 760
13 TraesCS6B01G326900 chr6A 233244150 233246897 2747 False 1229.000000 2272 92.941000 1244 3786 3 chr6A.!!$F3 2542
14 TraesCS6B01G326900 chr6A 579825067 579825742 675 False 765.000000 765 87.116000 2762 3441 1 chr6A.!!$F2 679
15 TraesCS6B01G326900 chr2A 499390521 499392375 1854 True 1283.000000 2202 92.162500 1984 3786 2 chr2A.!!$R1 1802
16 TraesCS6B01G326900 chr4A 360502211 360504956 2745 False 1209.333333 2174 93.037000 1244 3786 3 chr4A.!!$F1 2542
17 TraesCS6B01G326900 chr4A 371047317 371047838 521 True 675.000000 675 89.962000 333 859 1 chr4A.!!$R1 526
18 TraesCS6B01G326900 chr1D 195768708 195771631 2923 False 952.000000 1376 88.188000 1051 3786 3 chr1D.!!$F1 2735
19 TraesCS6B01G326900 chr1B 334536578 334537334 756 True 1133.000000 1133 93.659000 1244 2000 1 chr1B.!!$R2 756
20 TraesCS6B01G326900 chr1B 269573802 269575150 1348 True 807.000000 1288 89.145000 2452 3786 2 chr1B.!!$R4 1334
21 TraesCS6B01G326900 chr1B 269642116 269643669 1553 True 633.333333 1109 88.546333 1051 2453 3 chr1B.!!$R5 1402
22 TraesCS6B01G326900 chr4D 6145252 6146284 1032 True 553.000000 839 87.254500 2764 3758 2 chr4D.!!$R1 994
23 TraesCS6B01G326900 chr6D 448409014 448409693 679 True 797.000000 797 87.848000 2762 3441 1 chr6D.!!$R1 679
24 TraesCS6B01G326900 chr1A 561311462 561312136 674 True 769.000000 769 87.243000 2762 3441 1 chr1A.!!$R3 679
25 TraesCS6B01G326900 chr7D 436395500 436397383 1883 False 225.000000 267 81.369000 1140 1449 2 chr7D.!!$F1 309

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
724 752 0.037882 CACACTGTCGCACCATCTCT 60.038 55.0 0.00 0.0 0.0 3.10 F
791 819 0.644380 TCCCCTCCTCCATCATCACT 59.356 55.0 0.00 0.0 0.0 3.41 F
1938 3576 0.032678 AGAGCGAGTGTTCACAGGTG 59.967 55.0 5.74 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 3455 0.240145 TACCTGTGAACACTCGCTCG 59.760 55.000 6.51 0.0 32.95 5.03 R
2716 4685 1.004918 CCTCGTGTTCCTCCGCTTT 60.005 57.895 0.00 0.0 0.00 3.51 R
3702 5734 3.791353 GCAGCAAAACAGAGTTACAACAC 59.209 43.478 0.00 0.0 0.00 3.32 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
25 26 8.499514 GAAAACTTCATTCTCAGTCATCAAAC 57.500 34.615 0.00 0.00 0.00 2.93
26 27 7.572523 AAACTTCATTCTCAGTCATCAAACA 57.427 32.000 0.00 0.00 0.00 2.83
27 28 7.572523 AACTTCATTCTCAGTCATCAAACAA 57.427 32.000 0.00 0.00 0.00 2.83
28 29 7.756395 ACTTCATTCTCAGTCATCAAACAAT 57.244 32.000 0.00 0.00 0.00 2.71
29 30 8.174733 ACTTCATTCTCAGTCATCAAACAATT 57.825 30.769 0.00 0.00 0.00 2.32
30 31 8.080417 ACTTCATTCTCAGTCATCAAACAATTG 58.920 33.333 3.24 3.24 37.92 2.32
31 32 6.384224 TCATTCTCAGTCATCAAACAATTGC 58.616 36.000 5.05 0.00 36.45 3.56
32 33 5.771153 TTCTCAGTCATCAAACAATTGCA 57.229 34.783 5.05 0.00 36.45 4.08
33 34 5.771153 TCTCAGTCATCAAACAATTGCAA 57.229 34.783 5.05 0.00 36.45 4.08
34 35 6.335471 TCTCAGTCATCAAACAATTGCAAT 57.665 33.333 5.99 5.99 36.45 3.56
35 36 6.751157 TCTCAGTCATCAAACAATTGCAATT 58.249 32.000 18.99 18.99 36.45 2.32
36 37 6.864685 TCTCAGTCATCAAACAATTGCAATTC 59.135 34.615 21.70 7.56 36.45 2.17
37 38 6.514063 TCAGTCATCAAACAATTGCAATTCA 58.486 32.000 21.70 4.47 36.45 2.57
38 39 7.156000 TCAGTCATCAAACAATTGCAATTCAT 58.844 30.769 21.70 10.41 36.45 2.57
39 40 7.329962 TCAGTCATCAAACAATTGCAATTCATC 59.670 33.333 21.70 5.62 36.45 2.92
40 41 7.330946 CAGTCATCAAACAATTGCAATTCATCT 59.669 33.333 21.70 4.42 36.45 2.90
41 42 7.876068 AGTCATCAAACAATTGCAATTCATCTT 59.124 29.630 21.70 9.65 36.45 2.40
42 43 9.142515 GTCATCAAACAATTGCAATTCATCTTA 57.857 29.630 21.70 6.86 36.45 2.10
43 44 9.878667 TCATCAAACAATTGCAATTCATCTTAT 57.121 25.926 21.70 8.74 36.45 1.73
50 51 9.158233 ACAATTGCAATTCATCTTATTTTCAGG 57.842 29.630 21.70 7.46 0.00 3.86
51 52 9.373603 CAATTGCAATTCATCTTATTTTCAGGA 57.626 29.630 21.70 0.00 0.00 3.86
52 53 9.947433 AATTGCAATTCATCTTATTTTCAGGAA 57.053 25.926 18.99 0.00 0.00 3.36
56 57 9.189723 GCAATTCATCTTATTTTCAGGAATAGC 57.810 33.333 0.00 0.00 0.00 2.97
75 76 4.357918 AGCAAACTCCACATACTCAACT 57.642 40.909 0.00 0.00 0.00 3.16
109 110 7.332926 AGTCTTCTACAATTGCTAACACTCATG 59.667 37.037 5.05 0.00 0.00 3.07
110 111 5.801350 TCTACAATTGCTAACACTCATGC 57.199 39.130 5.05 0.00 0.00 4.06
111 112 5.244755 TCTACAATTGCTAACACTCATGCA 58.755 37.500 5.05 0.00 0.00 3.96
122 123 7.716560 TGCTAACACTCATGCAATACTAATGAT 59.283 33.333 0.00 0.00 32.12 2.45
123 124 8.562892 GCTAACACTCATGCAATACTAATGATT 58.437 33.333 0.00 0.00 30.31 2.57
128 129 9.223099 CACTCATGCAATACTAATGATTATGGA 57.777 33.333 0.00 0.00 30.31 3.41
144 145 7.335627 TGATTATGGAGTTTTAATCGGACACT 58.664 34.615 0.00 0.00 37.54 3.55
145 146 6.978343 TTATGGAGTTTTAATCGGACACTG 57.022 37.500 0.00 0.00 0.00 3.66
147 148 4.566004 TGGAGTTTTAATCGGACACTGAG 58.434 43.478 0.00 0.00 0.00 3.35
161 162 3.185455 ACACTGAGAAAGATAGGGGCTT 58.815 45.455 0.00 0.00 0.00 4.35
167 168 6.268847 ACTGAGAAAGATAGGGGCTTATAGTG 59.731 42.308 0.00 0.00 0.00 2.74
169 170 6.615726 TGAGAAAGATAGGGGCTTATAGTGTT 59.384 38.462 0.00 0.00 0.00 3.32
170 171 7.068686 AGAAAGATAGGGGCTTATAGTGTTC 57.931 40.000 0.00 0.00 0.00 3.18
171 172 6.615726 AGAAAGATAGGGGCTTATAGTGTTCA 59.384 38.462 0.00 0.00 0.00 3.18
173 174 4.593634 AGATAGGGGCTTATAGTGTTCACC 59.406 45.833 0.00 0.00 0.00 4.02
174 175 2.846950 AGGGGCTTATAGTGTTCACCT 58.153 47.619 0.00 0.00 0.00 4.00
175 176 3.190439 AGGGGCTTATAGTGTTCACCTT 58.810 45.455 0.00 0.00 0.00 3.50
176 177 3.591977 AGGGGCTTATAGTGTTCACCTTT 59.408 43.478 0.00 0.00 0.00 3.11
197 214 9.354673 ACCTTTGGGTGATGTCAATAATAATAG 57.645 33.333 0.00 0.00 45.43 1.73
198 215 9.354673 CCTTTGGGTGATGTCAATAATAATAGT 57.645 33.333 0.00 0.00 0.00 2.12
219 236 9.632638 AATAGTTCATGCTAACTTACATCCAAT 57.367 29.630 5.23 0.00 40.20 3.16
222 239 7.611467 AGTTCATGCTAACTTACATCCAATTGA 59.389 33.333 7.12 0.00 36.26 2.57
224 241 8.523915 TCATGCTAACTTACATCCAATTGAAT 57.476 30.769 7.12 0.00 0.00 2.57
258 275 2.698855 ATCAGGATCTTCCCAACACG 57.301 50.000 0.00 0.00 37.19 4.49
259 276 1.639722 TCAGGATCTTCCCAACACGA 58.360 50.000 0.00 0.00 37.19 4.35
261 278 0.905357 AGGATCTTCCCAACACGAGG 59.095 55.000 0.00 0.00 37.19 4.63
273 290 1.283793 CACGAGGTGCTTGCCAAAG 59.716 57.895 0.00 0.00 36.41 2.77
276 293 0.962356 CGAGGTGCTTGCCAAAGGAT 60.962 55.000 0.00 0.00 36.03 3.24
281 298 3.840078 AGGTGCTTGCCAAAGGATAAAAT 59.160 39.130 0.00 0.00 36.03 1.82
282 299 3.934579 GGTGCTTGCCAAAGGATAAAATG 59.065 43.478 0.00 0.00 36.03 2.32
290 307 6.237154 TGCCAAAGGATAAAATGAAAAAGGG 58.763 36.000 0.00 0.00 0.00 3.95
292 309 6.939730 GCCAAAGGATAAAATGAAAAAGGGAA 59.060 34.615 0.00 0.00 0.00 3.97
295 312 9.002600 CAAAGGATAAAATGAAAAAGGGAAAGG 57.997 33.333 0.00 0.00 0.00 3.11
296 313 7.872061 AGGATAAAATGAAAAAGGGAAAGGT 57.128 32.000 0.00 0.00 0.00 3.50
298 315 7.512402 AGGATAAAATGAAAAAGGGAAAGGTGA 59.488 33.333 0.00 0.00 0.00 4.02
300 317 9.208022 GATAAAATGAAAAAGGGAAAGGTGAAG 57.792 33.333 0.00 0.00 0.00 3.02
302 319 7.379059 AAATGAAAAAGGGAAAGGTGAAGAT 57.621 32.000 0.00 0.00 0.00 2.40
303 320 6.596309 ATGAAAAAGGGAAAGGTGAAGATC 57.404 37.500 0.00 0.00 0.00 2.75
317 334 3.434984 GTGAAGATCACCTTGACTCTTGC 59.565 47.826 0.00 0.00 41.37 4.01
318 335 3.071457 TGAAGATCACCTTGACTCTTGCA 59.929 43.478 0.00 0.00 34.68 4.08
319 336 3.996921 AGATCACCTTGACTCTTGCAT 57.003 42.857 0.00 0.00 0.00 3.96
320 337 5.046376 TGAAGATCACCTTGACTCTTGCATA 60.046 40.000 0.00 0.00 34.68 3.14
323 340 5.879223 AGATCACCTTGACTCTTGCATAAAG 59.121 40.000 0.00 0.00 37.22 1.85
324 341 4.973168 TCACCTTGACTCTTGCATAAAGT 58.027 39.130 0.00 0.00 37.18 2.66
325 342 6.109156 TCACCTTGACTCTTGCATAAAGTA 57.891 37.500 0.00 0.00 37.18 2.24
326 343 6.530120 TCACCTTGACTCTTGCATAAAGTAA 58.470 36.000 0.00 0.00 37.18 2.24
329 346 7.805071 CACCTTGACTCTTGCATAAAGTAAAAG 59.195 37.037 0.00 0.21 37.18 2.27
456 476 2.792947 GGCCGTTGGATCCTCGCTA 61.793 63.158 14.23 0.00 0.00 4.26
482 502 0.887247 CATCCGTGCCATTTTCACCA 59.113 50.000 0.00 0.00 0.00 4.17
483 503 1.477700 CATCCGTGCCATTTTCACCAT 59.522 47.619 0.00 0.00 0.00 3.55
622 649 4.682334 TGGGGACGTGCGGGTCTA 62.682 66.667 0.00 0.00 37.12 2.59
654 682 2.687566 CGTGAACCCTAGCCCCCT 60.688 66.667 0.00 0.00 0.00 4.79
724 752 0.037882 CACACTGTCGCACCATCTCT 60.038 55.000 0.00 0.00 0.00 3.10
772 800 1.674322 CGCAACCGGGGATTTGTCT 60.674 57.895 6.32 0.00 0.00 3.41
791 819 0.644380 TCCCCTCCTCCATCATCACT 59.356 55.000 0.00 0.00 0.00 3.41
944 972 3.506096 CTGCTGCTCCACCATGCG 61.506 66.667 0.00 0.00 0.00 4.73
995 1024 2.166050 GACCGGTCCTTAAGGAGAGAAC 59.834 54.545 24.91 12.73 46.49 3.01
996 1025 2.176889 CCGGTCCTTAAGGAGAGAACA 58.823 52.381 24.91 0.00 46.49 3.18
1198 2788 8.770438 TGAAGAGAAGAAGAAGAATTTAGCTC 57.230 34.615 0.00 0.00 0.00 4.09
1347 2948 9.797556 GTTTATGGTTACTGAAATTGGATAACC 57.202 33.333 11.54 11.54 43.37 2.85
1379 2981 6.415867 CACAGCTTCAGTTTTCAATTACAGTG 59.584 38.462 0.00 0.00 0.00 3.66
1380 2982 6.318648 ACAGCTTCAGTTTTCAATTACAGTGA 59.681 34.615 0.00 0.00 0.00 3.41
1424 3028 5.765176 CAATGTGTCATGTGTGTTTGAGAT 58.235 37.500 0.00 0.00 0.00 2.75
1513 3143 6.015095 GGTGAAAAAGAAAGGACATGGATTCT 60.015 38.462 0.00 0.00 33.73 2.40
1677 3312 3.837213 AATAGTTGCGCATATGCCATC 57.163 42.857 21.77 17.32 37.91 3.51
1714 3352 7.849804 TTCTAACTGATGCAATTTCTAGGTC 57.150 36.000 0.00 0.00 0.00 3.85
1720 3358 6.100279 ACTGATGCAATTTCTAGGTCTATGGA 59.900 38.462 0.00 0.00 0.00 3.41
1734 3372 4.260170 GTCTATGGATTCTCATGGGATGC 58.740 47.826 0.00 0.00 0.00 3.91
1817 3455 1.527034 TGGTCTGCATTTGTCTCAGC 58.473 50.000 0.00 0.00 0.00 4.26
1938 3576 0.032678 AGAGCGAGTGTTCACAGGTG 59.967 55.000 5.74 0.00 0.00 4.00
2024 3928 3.260884 TGGTCCACATTTGTCCTAGAGAC 59.739 47.826 0.00 0.00 46.51 3.36
2598 4567 8.455682 TCACATTTTTATAACACCGATCCTTTC 58.544 33.333 0.00 0.00 0.00 2.62
2716 4685 0.931468 TCCCTCAGGTTCCCGATCTA 59.069 55.000 0.00 0.00 0.00 1.98
3221 5202 5.355596 TGATTTTGCCAGTTCGACAAAAAT 58.644 33.333 12.93 6.73 43.98 1.82
3285 5267 4.095632 GCTCTTCTCAGATTTTAGGTTGGC 59.904 45.833 0.00 0.00 0.00 4.52
3296 5278 5.625921 TTTTAGGTTGGCGGTATTAACAC 57.374 39.130 0.00 0.00 0.00 3.32
3586 5617 3.149436 TGAACTTGCAAACTGAACTGC 57.851 42.857 0.00 0.00 39.09 4.40
3683 5715 2.175878 ATGCGATCTCCTATGTTGCC 57.824 50.000 0.00 0.00 0.00 4.52
3684 5716 0.829990 TGCGATCTCCTATGTTGCCA 59.170 50.000 0.00 0.00 0.00 4.92
3697 5729 4.877378 ATGTTGCCACATGTTGATCTTT 57.123 36.364 2.00 0.00 42.46 2.52
3702 5734 4.370049 TGCCACATGTTGATCTTTTGTTG 58.630 39.130 0.14 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.131100 TGTTTGATGACTGAGAATGAAGTTTTC 58.869 33.333 0.00 0.00 0.00 2.29
5 6 7.061905 GCAATTGTTTGATGACTGAGAATGAAG 59.938 37.037 7.40 0.00 34.60 3.02
6 7 6.864685 GCAATTGTTTGATGACTGAGAATGAA 59.135 34.615 7.40 0.00 34.60 2.57
7 8 6.016108 TGCAATTGTTTGATGACTGAGAATGA 60.016 34.615 7.40 0.00 34.60 2.57
8 9 6.153756 TGCAATTGTTTGATGACTGAGAATG 58.846 36.000 7.40 0.00 34.60 2.67
9 10 6.335471 TGCAATTGTTTGATGACTGAGAAT 57.665 33.333 7.40 0.00 34.60 2.40
10 11 5.771153 TGCAATTGTTTGATGACTGAGAA 57.229 34.783 7.40 0.00 34.60 2.87
11 12 5.771153 TTGCAATTGTTTGATGACTGAGA 57.229 34.783 7.40 0.00 34.60 3.27
12 13 6.643360 TGAATTGCAATTGTTTGATGACTGAG 59.357 34.615 28.67 0.00 34.60 3.35
13 14 6.514063 TGAATTGCAATTGTTTGATGACTGA 58.486 32.000 28.67 0.00 34.60 3.41
14 15 6.772770 TGAATTGCAATTGTTTGATGACTG 57.227 33.333 28.67 0.00 34.60 3.51
15 16 7.383687 AGATGAATTGCAATTGTTTGATGACT 58.616 30.769 28.67 11.22 34.60 3.41
16 17 7.591006 AGATGAATTGCAATTGTTTGATGAC 57.409 32.000 28.67 11.46 34.60 3.06
17 18 9.878667 ATAAGATGAATTGCAATTGTTTGATGA 57.121 25.926 28.67 7.85 34.60 2.92
24 25 9.158233 CCTGAAAATAAGATGAATTGCAATTGT 57.842 29.630 28.67 16.68 0.00 2.71
25 26 9.373603 TCCTGAAAATAAGATGAATTGCAATTG 57.626 29.630 28.67 9.07 0.00 2.32
26 27 9.947433 TTCCTGAAAATAAGATGAATTGCAATT 57.053 25.926 24.33 24.33 0.00 2.32
30 31 9.189723 GCTATTCCTGAAAATAAGATGAATTGC 57.810 33.333 0.00 0.00 34.34 3.56
35 36 9.466497 AGTTTGCTATTCCTGAAAATAAGATGA 57.534 29.630 0.00 0.00 0.00 2.92
36 37 9.727627 GAGTTTGCTATTCCTGAAAATAAGATG 57.272 33.333 0.00 0.00 0.00 2.90
37 38 8.907885 GGAGTTTGCTATTCCTGAAAATAAGAT 58.092 33.333 0.00 0.00 0.00 2.40
38 39 7.888021 TGGAGTTTGCTATTCCTGAAAATAAGA 59.112 33.333 3.41 0.00 32.12 2.10
39 40 7.970614 GTGGAGTTTGCTATTCCTGAAAATAAG 59.029 37.037 3.41 0.00 32.12 1.73
40 41 7.450014 TGTGGAGTTTGCTATTCCTGAAAATAA 59.550 33.333 3.41 0.00 32.12 1.40
41 42 6.945435 TGTGGAGTTTGCTATTCCTGAAAATA 59.055 34.615 3.41 0.00 32.12 1.40
42 43 5.774690 TGTGGAGTTTGCTATTCCTGAAAAT 59.225 36.000 3.41 0.00 32.12 1.82
43 44 5.136828 TGTGGAGTTTGCTATTCCTGAAAA 58.863 37.500 3.41 0.00 32.12 2.29
44 45 4.724399 TGTGGAGTTTGCTATTCCTGAAA 58.276 39.130 3.41 0.00 32.12 2.69
45 46 4.365514 TGTGGAGTTTGCTATTCCTGAA 57.634 40.909 3.41 0.00 32.12 3.02
46 47 4.574674 ATGTGGAGTTTGCTATTCCTGA 57.425 40.909 3.41 0.00 32.12 3.86
47 48 5.431765 AGTATGTGGAGTTTGCTATTCCTG 58.568 41.667 3.41 0.00 32.12 3.86
48 49 5.189736 TGAGTATGTGGAGTTTGCTATTCCT 59.810 40.000 3.41 0.00 32.12 3.36
49 50 5.428253 TGAGTATGTGGAGTTTGCTATTCC 58.572 41.667 0.00 0.00 0.00 3.01
50 51 6.595716 AGTTGAGTATGTGGAGTTTGCTATTC 59.404 38.462 0.00 0.00 0.00 1.75
51 52 6.476378 AGTTGAGTATGTGGAGTTTGCTATT 58.524 36.000 0.00 0.00 0.00 1.73
52 53 6.054860 AGTTGAGTATGTGGAGTTTGCTAT 57.945 37.500 0.00 0.00 0.00 2.97
53 54 5.483685 AGTTGAGTATGTGGAGTTTGCTA 57.516 39.130 0.00 0.00 0.00 3.49
54 55 4.357918 AGTTGAGTATGTGGAGTTTGCT 57.642 40.909 0.00 0.00 0.00 3.91
55 56 5.874810 TGATAGTTGAGTATGTGGAGTTTGC 59.125 40.000 0.00 0.00 0.00 3.68
56 57 9.770097 ATATGATAGTTGAGTATGTGGAGTTTG 57.230 33.333 0.00 0.00 0.00 2.93
59 60 9.815306 ACTATATGATAGTTGAGTATGTGGAGT 57.185 33.333 0.00 0.00 0.00 3.85
116 117 9.839817 TGTCCGATTAAAACTCCATAATCATTA 57.160 29.630 6.40 0.00 38.05 1.90
117 118 8.621286 GTGTCCGATTAAAACTCCATAATCATT 58.379 33.333 6.40 0.00 38.05 2.57
122 123 6.703319 TCAGTGTCCGATTAAAACTCCATAA 58.297 36.000 0.00 0.00 0.00 1.90
123 124 6.153851 TCTCAGTGTCCGATTAAAACTCCATA 59.846 38.462 0.00 0.00 0.00 2.74
125 126 4.282449 TCTCAGTGTCCGATTAAAACTCCA 59.718 41.667 0.00 0.00 0.00 3.86
126 127 4.817517 TCTCAGTGTCCGATTAAAACTCC 58.182 43.478 0.00 0.00 0.00 3.85
128 129 6.522054 TCTTTCTCAGTGTCCGATTAAAACT 58.478 36.000 0.00 0.00 0.00 2.66
133 134 5.302059 CCCTATCTTTCTCAGTGTCCGATTA 59.698 44.000 0.00 0.00 0.00 1.75
136 137 3.024547 CCCTATCTTTCTCAGTGTCCGA 58.975 50.000 0.00 0.00 0.00 4.55
144 145 6.143915 ACACTATAAGCCCCTATCTTTCTCA 58.856 40.000 0.00 0.00 0.00 3.27
145 146 6.673839 ACACTATAAGCCCCTATCTTTCTC 57.326 41.667 0.00 0.00 0.00 2.87
147 148 6.706716 GTGAACACTATAAGCCCCTATCTTTC 59.293 42.308 0.00 0.00 0.00 2.62
175 176 9.913310 TGAACTATTATTATTGACATCACCCAA 57.087 29.630 0.00 0.00 0.00 4.12
197 214 7.761409 TCAATTGGATGTAAGTTAGCATGAAC 58.239 34.615 5.42 0.00 0.00 3.18
198 215 7.936496 TCAATTGGATGTAAGTTAGCATGAA 57.064 32.000 5.42 0.00 0.00 2.57
232 249 8.914011 CGTGTTGGGAAGATCCTGATATATATA 58.086 37.037 0.00 0.00 36.57 0.86
233 250 7.619698 TCGTGTTGGGAAGATCCTGATATATAT 59.380 37.037 0.00 0.00 36.57 0.86
241 258 1.406069 CCTCGTGTTGGGAAGATCCTG 60.406 57.143 0.00 0.00 36.57 3.86
242 259 0.905357 CCTCGTGTTGGGAAGATCCT 59.095 55.000 0.00 0.00 36.57 3.24
243 260 0.613777 ACCTCGTGTTGGGAAGATCC 59.386 55.000 0.00 0.00 35.23 3.36
244 261 1.726853 CACCTCGTGTTGGGAAGATC 58.273 55.000 0.00 0.00 0.00 2.75
245 262 0.321653 GCACCTCGTGTTGGGAAGAT 60.322 55.000 0.00 0.00 35.75 2.40
246 263 1.070786 GCACCTCGTGTTGGGAAGA 59.929 57.895 0.00 0.00 35.75 2.87
247 264 0.535102 AAGCACCTCGTGTTGGGAAG 60.535 55.000 0.00 0.00 35.75 3.46
248 265 0.817634 CAAGCACCTCGTGTTGGGAA 60.818 55.000 0.00 0.00 35.75 3.97
249 266 1.227823 CAAGCACCTCGTGTTGGGA 60.228 57.895 0.00 0.00 35.75 4.37
250 267 2.908073 GCAAGCACCTCGTGTTGGG 61.908 63.158 0.00 0.00 35.75 4.12
251 268 2.639286 GCAAGCACCTCGTGTTGG 59.361 61.111 0.00 0.00 35.75 3.77
254 271 1.447317 CTTTGGCAAGCACCTCGTGT 61.447 55.000 0.00 0.00 35.75 4.49
258 275 2.128771 TATCCTTTGGCAAGCACCTC 57.871 50.000 0.00 0.00 0.00 3.85
259 276 2.603075 TTATCCTTTGGCAAGCACCT 57.397 45.000 0.00 0.00 0.00 4.00
261 278 4.819769 TCATTTTATCCTTTGGCAAGCAC 58.180 39.130 0.00 0.00 0.00 4.40
273 290 7.676004 TCACCTTTCCCTTTTTCATTTTATCC 58.324 34.615 0.00 0.00 0.00 2.59
276 293 8.312669 TCTTCACCTTTCCCTTTTTCATTTTA 57.687 30.769 0.00 0.00 0.00 1.52
281 298 5.301805 GTGATCTTCACCTTTCCCTTTTTCA 59.698 40.000 0.00 0.00 41.37 2.69
282 299 5.773575 GTGATCTTCACCTTTCCCTTTTTC 58.226 41.667 0.00 0.00 41.37 2.29
295 312 3.434984 GCAAGAGTCAAGGTGATCTTCAC 59.565 47.826 0.00 0.00 46.23 3.18
296 313 3.071457 TGCAAGAGTCAAGGTGATCTTCA 59.929 43.478 0.00 0.00 32.41 3.02
298 315 3.777106 TGCAAGAGTCAAGGTGATCTT 57.223 42.857 0.00 0.00 35.79 2.40
300 317 5.645497 ACTTTATGCAAGAGTCAAGGTGATC 59.355 40.000 0.00 0.00 36.21 2.92
302 319 4.973168 ACTTTATGCAAGAGTCAAGGTGA 58.027 39.130 0.00 0.00 36.21 4.02
303 320 6.801539 TTACTTTATGCAAGAGTCAAGGTG 57.198 37.500 0.00 0.00 36.21 4.00
306 323 8.559536 TGTCTTTTACTTTATGCAAGAGTCAAG 58.440 33.333 0.00 2.31 36.21 3.02
326 343 9.435688 AGCTTCTGTTTTGTTTTAAATGTCTTT 57.564 25.926 0.00 0.00 0.00 2.52
329 346 8.480066 GCTAGCTTCTGTTTTGTTTTAAATGTC 58.520 33.333 7.70 0.00 0.00 3.06
432 452 2.670148 GGATCCAACGGCCAGGAGT 61.670 63.158 6.95 0.00 37.34 3.85
456 476 2.442236 AATGGCACGGATGAATTCCT 57.558 45.000 2.27 0.00 42.99 3.36
467 487 1.669502 CCACATGGTGAAAATGGCACG 60.670 52.381 0.00 0.00 37.13 5.34
482 502 1.414158 CCGTCCAGGATCTACCACAT 58.586 55.000 0.00 0.00 45.00 3.21
483 503 0.686441 CCCGTCCAGGATCTACCACA 60.686 60.000 0.00 0.00 45.00 4.17
676 704 3.742248 GAGGAGGAGGGAGGGGTCG 62.742 73.684 0.00 0.00 0.00 4.79
724 752 0.631998 ATGAGGGAGGAGGGAGGAGA 60.632 60.000 0.00 0.00 0.00 3.71
772 800 0.644380 AGTGATGATGGAGGAGGGGA 59.356 55.000 0.00 0.00 0.00 4.81
791 819 0.684479 ATCTCCTGGTGCTGCGACTA 60.684 55.000 0.00 0.00 0.00 2.59
847 875 4.680237 CGCGACAAGGCTGACCCA 62.680 66.667 0.00 0.00 36.11 4.51
944 972 0.108520 TCATCCACGAGTTAACCGCC 60.109 55.000 14.00 0.00 0.00 6.13
995 1024 4.029520 TCCTTCTCTCTCCCTCATCTTTG 58.970 47.826 0.00 0.00 0.00 2.77
996 1025 4.344938 TCCTTCTCTCTCCCTCATCTTT 57.655 45.455 0.00 0.00 0.00 2.52
1198 2788 3.897505 ACCTTGATTTTCTTCACCCCTTG 59.102 43.478 0.00 0.00 0.00 3.61
1347 2948 2.430546 AACTGAAGCTGTGACTCTCG 57.569 50.000 0.00 0.00 0.00 4.04
1379 2981 5.162794 TGCAGCAAACATAACACATCAATC 58.837 37.500 0.00 0.00 0.00 2.67
1380 2982 5.136816 TGCAGCAAACATAACACATCAAT 57.863 34.783 0.00 0.00 0.00 2.57
1424 3028 5.045578 CAGTCCCCTCTTTTTCATCCTTCTA 60.046 44.000 0.00 0.00 0.00 2.10
1513 3143 2.200081 CCCCTCTTTTCATCCCTCTCA 58.800 52.381 0.00 0.00 0.00 3.27
1661 3296 1.233019 AGAGATGGCATATGCGCAAC 58.767 50.000 17.11 17.13 43.26 4.17
1677 3312 6.200665 GCATCAGTTAGAAAGACTGCATAGAG 59.799 42.308 0.00 0.00 43.23 2.43
1714 3352 3.055602 TCGCATCCCATGAGAATCCATAG 60.056 47.826 0.00 0.00 36.14 2.23
1720 3358 3.784511 AGAATCGCATCCCATGAGAAT 57.215 42.857 0.00 0.00 42.26 2.40
1734 3372 3.193263 ACAAGCAGCATGACTAGAATCG 58.807 45.455 4.23 0.00 39.69 3.34
1817 3455 0.240145 TACCTGTGAACACTCGCTCG 59.760 55.000 6.51 0.00 32.95 5.03
1938 3576 8.768955 CAGATTAATAACTGACATAAGCACTCC 58.231 37.037 0.00 0.00 36.38 3.85
2716 4685 1.004918 CCTCGTGTTCCTCCGCTTT 60.005 57.895 0.00 0.00 0.00 3.51
3066 5044 8.613060 AAATGCTTATCGATACATGAGTTGAT 57.387 30.769 4.16 4.98 0.00 2.57
3095 5074 9.726438 AGGTAAGTAACAATATATTGAGGATGC 57.274 33.333 28.13 15.28 40.14 3.91
3221 5202 8.221944 TGAGAAAGTTCCCTTGGTTATTCTAAA 58.778 33.333 0.00 0.00 0.00 1.85
3285 5267 4.572795 TGTGTGGCATATGTGTTAATACCG 59.427 41.667 4.29 0.00 0.00 4.02
3296 5278 7.712639 AGATCTAAACTTAGTGTGTGGCATATG 59.287 37.037 0.00 0.00 32.61 1.78
3586 5617 4.710680 CGCCAAGGCATTAAAACATTTTG 58.289 39.130 12.19 0.00 42.06 2.44
3683 5715 6.310956 ACAACACAACAAAAGATCAACATGTG 59.689 34.615 0.00 12.06 41.86 3.21
3684 5716 6.397272 ACAACACAACAAAAGATCAACATGT 58.603 32.000 0.00 0.00 0.00 3.21
3697 5729 5.631512 GCAAAACAGAGTTACAACACAACAA 59.368 36.000 0.00 0.00 0.00 2.83
3702 5734 3.791353 GCAGCAAAACAGAGTTACAACAC 59.209 43.478 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.