Multiple sequence alignment - TraesCS2D01G585700

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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 TraesCS2D01G585700 chr2D 100.000 8269 0 0 1 8269 644582177 644590445 0.000000e+00 15271.0
1 TraesCS2D01G585700 chr2D 98.852 8273 85 9 1 8269 587585982 587594248 0.000000e+00 14742.0
2 TraesCS2D01G585700 chr2D 80.999 1021 162 17 3734 4747 18195990 18194995 0.000000e+00 782.0
3 TraesCS2D01G585700 chr2D 82.218 568 65 20 7690 8237 587367739 587368290 2.720000e-124 457.0
4 TraesCS2D01G585700 chr2D 84.314 459 30 14 210 642 587575772 587576214 2.150000e-110 411.0
5 TraesCS2D01G585700 chr2D 87.611 226 20 1 2974 3191 577622624 577622849 1.070000e-63 255.0
6 TraesCS2D01G585700 chr2D 92.000 100 7 1 3431 3530 577624567 577624665 1.120000e-28 139.0
7 TraesCS2D01G585700 chr2D 87.097 124 11 4 4627 4749 22100279 22100160 1.450000e-27 135.0
8 TraesCS2D01G585700 chr2D 89.773 88 6 3 2163 2248 33773731 33773817 8.770000e-20 110.0
9 TraesCS2D01G585700 chr3A 80.876 1004 160 17 3733 4731 738951711 738950735 0.000000e+00 761.0
10 TraesCS2D01G585700 chr3A 92.357 157 12 0 2297 2453 576272252 576272408 3.000000e-54 224.0
11 TraesCS2D01G585700 chr3A 85.646 209 25 5 7 211 277439936 277439729 1.810000e-51 215.0
12 TraesCS2D01G585700 chr3A 77.202 193 36 7 4400 4589 740879295 740879482 1.140000e-18 106.0
13 TraesCS2D01G585700 chr3A 91.892 74 5 1 2159 2231 64340829 64340756 1.470000e-17 102.0
14 TraesCS2D01G585700 chr3A 89.024 82 7 2 2159 2240 88852909 88852988 5.280000e-17 100.0
15 TraesCS2D01G585700 chrUn 100.000 391 0 0 6012 6402 479894315 479894705 0.000000e+00 723.0
16 TraesCS2D01G585700 chrUn 100.000 256 0 0 8014 8269 480359012 480358757 2.700000e-129 473.0
17 TraesCS2D01G585700 chrUn 84.026 457 38 10 2981 3414 215552413 215551969 2.780000e-109 407.0
18 TraesCS2D01G585700 chrUn 84.035 451 37 10 2981 3408 2784328 2784766 1.290000e-107 401.0
19 TraesCS2D01G585700 chrUn 79.897 194 29 9 4400 4589 63338838 63339025 5.210000e-27 134.0
20 TraesCS2D01G585700 chr3B 76.057 1324 286 25 4863 6172 20452421 20451115 0.000000e+00 660.0
21 TraesCS2D01G585700 chr3B 76.835 695 147 12 623 1309 20459994 20459306 6.060000e-101 379.0
22 TraesCS2D01G585700 chr3B 83.256 215 30 6 1 211 345020136 345020348 8.470000e-45 193.0
23 TraesCS2D01G585700 chr3B 83.178 214 31 5 1 210 75071849 75072061 3.050000e-44 191.0
24 TraesCS2D01G585700 chr3B 77.143 105 15 8 1457 1552 413835568 413835672 1.500000e-02 52.8
25 TraesCS2D01G585700 chr6B 77.818 1118 209 33 4859 5955 662031089 662029990 0.000000e+00 654.0
26 TraesCS2D01G585700 chr6B 75.962 624 117 21 4131 4744 35820267 35820867 2.920000e-74 291.0
27 TraesCS2D01G585700 chr6B 78.986 138 25 4 3818 3953 345211443 345211578 3.180000e-14 91.6
28 TraesCS2D01G585700 chr6B 94.737 38 2 0 2716 2753 687865255 687865292 8.960000e-05 60.2
29 TraesCS2D01G585700 chr4A 77.525 1099 220 18 4872 5955 589334104 589335190 3.260000e-178 636.0
30 TraesCS2D01G585700 chr4A 85.238 210 28 3 4 210 740674031 740673822 6.500000e-51 213.0
31 TraesCS2D01G585700 chr4A 77.727 220 38 9 4400 4614 739786323 739786536 3.130000e-24 124.0
32 TraesCS2D01G585700 chr7D 77.220 1115 212 35 4859 5955 630503814 630504904 1.530000e-171 614.0
33 TraesCS2D01G585700 chr7D 97.156 211 6 0 3524 3734 578394906 578394696 2.840000e-94 357.0
34 TraesCS2D01G585700 chr7D 85.024 207 28 3 4 207 617980250 617980044 3.020000e-49 207.0
35 TraesCS2D01G585700 chr7D 83.810 210 31 3 4 210 539698638 539698429 6.550000e-46 196.0
36 TraesCS2D01G585700 chr7D 93.421 76 4 1 2159 2233 540860179 540860254 2.440000e-20 111.0
37 TraesCS2D01G585700 chr7D 81.481 108 15 3 3814 3917 34971352 34971246 5.320000e-12 84.2
38 TraesCS2D01G585700 chr7B 75.246 1321 278 41 4859 6154 733142547 733143843 4.300000e-162 582.0
39 TraesCS2D01G585700 chr7B 77.047 745 133 25 5227 5955 733037947 733038669 2.160000e-105 394.0
40 TraesCS2D01G585700 chr7B 97.156 211 6 0 3524 3734 243206700 243206910 2.840000e-94 357.0
41 TraesCS2D01G585700 chr7B 97.156 211 6 0 3524 3734 706059567 706059357 2.840000e-94 357.0
42 TraesCS2D01G585700 chr7B 88.525 122 14 0 644 765 733535289 733535168 1.860000e-31 148.0
43 TraesCS2D01G585700 chr7B 78.832 137 21 8 4457 4589 244593613 244593481 1.480000e-12 86.1
44 TraesCS2D01G585700 chr7B 87.755 49 6 0 2702 2750 24127757 24127805 3.220000e-04 58.4
45 TraesCS2D01G585700 chr7B 91.892 37 3 0 1457 1493 612297830 612297794 1.500000e-02 52.8
46 TraesCS2D01G585700 chr1B 75.482 1142 237 31 4875 5993 660997242 660996121 1.230000e-142 518.0
47 TraesCS2D01G585700 chr1B 75.524 1144 231 39 4875 5992 661055181 661054061 4.420000e-142 516.0
48 TraesCS2D01G585700 chr1B 75.482 1089 236 22 4875 5952 660723251 660722183 3.440000e-138 503.0
49 TraesCS2D01G585700 chr1B 74.978 1151 248 36 4875 6005 660684179 660683049 2.070000e-135 494.0
50 TraesCS2D01G585700 chr1B 74.978 1131 252 26 4876 5992 661122506 661121393 7.460000e-135 492.0
51 TraesCS2D01G585700 chr1B 74.498 1145 258 27 4865 5992 660880778 660879651 4.520000e-127 466.0
52 TraesCS2D01G585700 chr1B 84.026 457 38 10 2981 3414 36815945 36816389 2.780000e-109 407.0
53 TraesCS2D01G585700 chr1B 78.723 517 91 15 4867 5372 660915142 660914634 2.230000e-85 327.0
54 TraesCS2D01G585700 chr1B 81.414 382 44 7 3054 3414 35961577 35961202 3.780000e-73 287.0
55 TraesCS2D01G585700 chr1B 76.818 220 40 9 4400 4614 12838675 12838888 6.780000e-21 113.0
56 TraesCS2D01G585700 chr1D 75.386 1101 225 37 4875 5952 475178390 475177313 2.680000e-134 490.0
57 TraesCS2D01G585700 chr1D 84.651 215 30 3 4 215 223179188 223178974 2.340000e-50 211.0
58 TraesCS2D01G585700 chr1D 83.654 208 32 2 1 206 182046370 182046577 2.350000e-45 195.0
59 TraesCS2D01G585700 chr1D 80.808 99 19 0 3818 3916 24567847 24567749 2.470000e-10 78.7
60 TraesCS2D01G585700 chr1D 87.879 66 8 0 3851 3916 222729647 222729582 2.470000e-10 78.7
61 TraesCS2D01G585700 chr1A 76.404 801 158 18 4875 5666 570878505 570877727 3.590000e-108 403.0
62 TraesCS2D01G585700 chr1A 89.831 177 14 2 2281 2453 542369957 542370133 3.000000e-54 224.0
63 TraesCS2D01G585700 chr1A 94.667 75 4 0 7300 7374 551985734 551985660 5.240000e-22 117.0
64 TraesCS2D01G585700 chr5D 98.578 211 3 0 3524 3734 7044201 7044411 2.820000e-99 374.0
65 TraesCS2D01G585700 chr5D 97.642 212 4 1 3524 3734 164651734 164651523 6.100000e-96 363.0
66 TraesCS2D01G585700 chr5D 97.156 211 6 0 3524 3734 439659559 439659349 2.840000e-94 357.0
67 TraesCS2D01G585700 chr5D 90.000 160 14 2 2294 2453 276547796 276547639 1.090000e-48 206.0
68 TraesCS2D01G585700 chr5D 95.775 71 3 0 7297 7367 21789112 21789182 1.890000e-21 115.0
69 TraesCS2D01G585700 chr5D 92.500 80 5 1 4670 4749 479353790 479353868 6.780000e-21 113.0
70 TraesCS2D01G585700 chr3D 97.630 211 5 0 3524 3734 554681770 554681560 6.100000e-96 363.0
71 TraesCS2D01G585700 chr3D 87.500 168 19 2 2294 2460 511056875 511056709 8.470000e-45 193.0
72 TraesCS2D01G585700 chr3D 88.235 136 13 2 4596 4731 606791561 606791429 8.590000e-35 159.0
73 TraesCS2D01G585700 chr3D 93.421 76 5 0 7292 7367 505557401 505557326 6.780000e-21 113.0
74 TraesCS2D01G585700 chr3D 90.361 83 6 1 7287 7367 263991625 263991707 3.160000e-19 108.0
75 TraesCS2D01G585700 chr3D 80.292 137 25 2 3818 3953 601126992 601127127 1.470000e-17 102.0
76 TraesCS2D01G585700 chr6D 97.156 211 6 0 3524 3734 469559266 469559056 2.840000e-94 357.0
77 TraesCS2D01G585700 chr6D 86.325 117 16 0 2974 3090 256111747 256111863 2.420000e-25 128.0
78 TraesCS2D01G585700 chr6D 83.562 73 8 4 4703 4774 457749828 457749897 1.930000e-06 65.8
79 TraesCS2D01G585700 chr6D 95.000 40 2 0 1458 1497 448027328 448027289 6.930000e-06 63.9
80 TraesCS2D01G585700 chr2B 74.485 776 169 28 3834 4593 772493824 772493062 8.060000e-80 309.0
81 TraesCS2D01G585700 chr2B 83.382 343 36 5 2975 3297 705358148 705358489 1.740000e-76 298.0
82 TraesCS2D01G585700 chr2B 83.942 274 25 11 7982 8237 709997200 709997472 2.310000e-60 244.0
83 TraesCS2D01G585700 chr2B 81.221 213 7 11 8086 8268 698006194 698005985 3.110000e-29 141.0
84 TraesCS2D01G585700 chr2B 93.590 78 3 2 7291 7367 201234357 201234281 1.890000e-21 115.0
85 TraesCS2D01G585700 chr6A 89.076 238 24 1 2974 3211 383079734 383079499 2.260000e-75 294.0
86 TraesCS2D01G585700 chr6A 93.590 78 4 1 2157 2233 256484006 256483929 1.890000e-21 115.0
87 TraesCS2D01G585700 chr6A 97.436 39 1 0 1455 1493 21147599 21147561 5.360000e-07 67.6
88 TraesCS2D01G585700 chr7A 90.341 176 13 2 2281 2452 34048568 34048393 2.320000e-55 228.0
89 TraesCS2D01G585700 chr7A 91.250 160 14 0 2294 2453 539543672 539543831 1.400000e-52 219.0
90 TraesCS2D01G585700 chr7A 90.476 147 14 0 2310 2456 672064628 672064774 2.350000e-45 195.0
91 TraesCS2D01G585700 chr7A 78.238 193 34 7 4400 4589 86100421 86100608 5.240000e-22 117.0
92 TraesCS2D01G585700 chr7A 92.500 80 5 1 2155 2233 115736447 115736368 6.780000e-21 113.0
93 TraesCS2D01G585700 chr7A 91.358 81 6 1 7294 7374 451586796 451586875 8.770000e-20 110.0
94 TraesCS2D01G585700 chr7A 90.789 76 6 1 2159 2233 34048576 34048501 5.280000e-17 100.0
95 TraesCS2D01G585700 chr7A 77.966 118 15 9 4635 4749 287899166 287899275 6.930000e-06 63.9
96 TraesCS2D01G585700 chr2A 89.831 177 11 5 2281 2453 181847608 181847781 3.890000e-53 220.0
97 TraesCS2D01G585700 chr2A 92.453 106 4 4 8083 8187 717554608 717554710 1.860000e-31 148.0
98 TraesCS2D01G585700 chr2A 94.118 51 2 1 4700 4749 16886910 16886860 8.900000e-10 76.8
99 TraesCS2D01G585700 chr2A 84.375 64 5 5 2699 2758 75606774 75606712 3.220000e-04 58.4
100 TraesCS2D01G585700 chr2A 100.000 28 0 0 1457 1484 769033274 769033247 1.500000e-02 52.8
101 TraesCS2D01G585700 chr5B 76.284 409 93 4 625 1031 18711302 18710896 1.810000e-51 215.0
102 TraesCS2D01G585700 chr5B 92.647 136 10 0 2974 3109 645540879 645540744 6.550000e-46 196.0
103 TraesCS2D01G585700 chr5B 97.101 69 2 0 7299 7367 406932658 406932590 5.240000e-22 117.0
104 TraesCS2D01G585700 chr5B 100.000 31 0 0 1454 1484 336209784 336209754 3.220000e-04 58.4
105 TraesCS2D01G585700 chr5A 79.897 194 29 9 4400 4589 553566980 553567167 5.210000e-27 134.0
106 TraesCS2D01G585700 chr5A 91.139 79 6 1 2156 2233 692060225 692060303 1.140000e-18 106.0
107 TraesCS2D01G585700 chr4B 92.500 80 4 2 7289 7367 404771470 404771548 6.780000e-21 113.0


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 TraesCS2D01G585700 chr2D 644582177 644590445 8268 False 15271 15271 100.000 1 8269 1 chr2D.!!$F5 8268
1 TraesCS2D01G585700 chr2D 587585982 587594248 8266 False 14742 14742 98.852 1 8269 1 chr2D.!!$F4 8268
2 TraesCS2D01G585700 chr2D 18194995 18195990 995 True 782 782 80.999 3734 4747 1 chr2D.!!$R1 1013
3 TraesCS2D01G585700 chr2D 587367739 587368290 551 False 457 457 82.218 7690 8237 1 chr2D.!!$F2 547
4 TraesCS2D01G585700 chr3A 738950735 738951711 976 True 761 761 80.876 3733 4731 1 chr3A.!!$R3 998
5 TraesCS2D01G585700 chr3B 20451115 20452421 1306 True 660 660 76.057 4863 6172 1 chr3B.!!$R1 1309
6 TraesCS2D01G585700 chr3B 20459306 20459994 688 True 379 379 76.835 623 1309 1 chr3B.!!$R2 686
7 TraesCS2D01G585700 chr6B 662029990 662031089 1099 True 654 654 77.818 4859 5955 1 chr6B.!!$R1 1096
8 TraesCS2D01G585700 chr6B 35820267 35820867 600 False 291 291 75.962 4131 4744 1 chr6B.!!$F1 613
9 TraesCS2D01G585700 chr4A 589334104 589335190 1086 False 636 636 77.525 4872 5955 1 chr4A.!!$F1 1083
10 TraesCS2D01G585700 chr7D 630503814 630504904 1090 False 614 614 77.220 4859 5955 1 chr7D.!!$F2 1096
11 TraesCS2D01G585700 chr7B 733142547 733143843 1296 False 582 582 75.246 4859 6154 1 chr7B.!!$F4 1295
12 TraesCS2D01G585700 chr7B 733037947 733038669 722 False 394 394 77.047 5227 5955 1 chr7B.!!$F3 728
13 TraesCS2D01G585700 chr1B 660996121 660997242 1121 True 518 518 75.482 4875 5993 1 chr1B.!!$R6 1118
14 TraesCS2D01G585700 chr1B 661054061 661055181 1120 True 516 516 75.524 4875 5992 1 chr1B.!!$R7 1117
15 TraesCS2D01G585700 chr1B 660722183 660723251 1068 True 503 503 75.482 4875 5952 1 chr1B.!!$R3 1077
16 TraesCS2D01G585700 chr1B 660683049 660684179 1130 True 494 494 74.978 4875 6005 1 chr1B.!!$R2 1130
17 TraesCS2D01G585700 chr1B 661121393 661122506 1113 True 492 492 74.978 4876 5992 1 chr1B.!!$R8 1116
18 TraesCS2D01G585700 chr1B 660879651 660880778 1127 True 466 466 74.498 4865 5992 1 chr1B.!!$R4 1127
19 TraesCS2D01G585700 chr1B 660914634 660915142 508 True 327 327 78.723 4867 5372 1 chr1B.!!$R5 505
20 TraesCS2D01G585700 chr1D 475177313 475178390 1077 True 490 490 75.386 4875 5952 1 chr1D.!!$R4 1077
21 TraesCS2D01G585700 chr1A 570877727 570878505 778 True 403 403 76.404 4875 5666 1 chr1A.!!$R2 791
22 TraesCS2D01G585700 chr2B 772493062 772493824 762 True 309 309 74.485 3834 4593 1 chr2B.!!$R3 759

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
344 346 0.321564 ATCAAAGGCTAGCACGCACA 60.322 50.000 18.24 0.0 0.00 4.57 F
378 380 2.948979 CAAATCTGGGTATTAGCGCCAA 59.051 45.455 2.29 0.0 0.00 4.52 F
1729 1734 4.635765 CGAAGGCTGGTCAGAAATCAAATA 59.364 41.667 1.65 0.0 0.00 1.40 F
2514 2522 1.000955 CGGACTTGCACCAGTAGAACT 59.999 52.381 0.00 0.0 0.00 3.01 F
4423 4447 0.243636 GGTGAAAACCCATTCTGGCG 59.756 55.000 0.00 0.0 35.79 5.69 F
6402 6458 0.112995 AATGGCTTCCCTGAACAGCA 59.887 50.000 0.00 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1559 1564 2.170607 TGAGACGGGAGATTGGGAATTC 59.829 50.000 0.0 0.0 0.00 2.17 R
2002 2008 4.141779 ACCCACCGTAAAATGTCTCTATCC 60.142 45.833 0.0 0.0 0.00 2.59 R
3065 3073 1.073177 CGCGTTCCCGTCACTAAATT 58.927 50.000 0.0 0.0 36.15 1.82 R
4449 4473 0.673644 AAGAAGGGAACGACGCCATG 60.674 55.000 0.0 0.0 0.00 3.66 R
6455 6511 1.486310 AGACAAGGCATCCGCATAAGA 59.514 47.619 0.0 0.0 41.24 2.10 R
7635 7691 0.467384 CTCCAGTTCATCGCCCTCAT 59.533 55.000 0.0 0.0 0.00 2.90 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
34 35 0.666374 CAACCGGACTTGTGTTTCCC 59.334 55.000 9.46 0.00 0.00 3.97
61 62 2.558359 ACAAGTCTGCAACCAAATAGCC 59.442 45.455 0.00 0.00 0.00 3.93
64 65 1.139520 CTGCAACCAAATAGCCGGC 59.860 57.895 21.89 21.89 0.00 6.13
88 89 3.980646 TCGTTTTAGCACATGCAAACT 57.019 38.095 6.64 0.00 45.16 2.66
100 101 3.199508 ACATGCAAACTAGAGAGGATGCT 59.800 43.478 0.00 0.00 38.51 3.79
101 102 3.988976 TGCAAACTAGAGAGGATGCTT 57.011 42.857 0.00 0.00 38.51 3.91
221 223 1.068753 CGCGCCCTGAATCATCTCT 59.931 57.895 0.00 0.00 0.00 3.10
249 251 0.383949 TTTTGTGCTTTCTGGCCGTC 59.616 50.000 0.00 0.00 0.00 4.79
344 346 0.321564 ATCAAAGGCTAGCACGCACA 60.322 50.000 18.24 0.00 0.00 4.57
378 380 2.948979 CAAATCTGGGTATTAGCGCCAA 59.051 45.455 2.29 0.00 0.00 4.52
1559 1564 4.836825 AGGGAGTACATGTGACTCATTTG 58.163 43.478 24.33 0.00 44.34 2.32
1729 1734 4.635765 CGAAGGCTGGTCAGAAATCAAATA 59.364 41.667 1.65 0.00 0.00 1.40
1911 1916 9.639563 ACAGTTCCCCAAAATGATTAAAATTTT 57.360 25.926 8.75 8.75 37.64 1.82
2047 2053 8.210946 TGGGTAGTATTTAGTTGATCCAATGAG 58.789 37.037 0.00 0.00 0.00 2.90
2075 2081 8.954950 ATACTGATCGATCAAATTTTCACTCT 57.045 30.769 27.09 0.07 36.18 3.24
2182 2188 4.101741 GGTTTGTCTAGGGCACATCTAGAT 59.898 45.833 0.00 0.00 43.25 1.98
2208 2214 4.274459 GCTCTGGTTATTGCACATCTAAGG 59.726 45.833 0.00 0.00 0.00 2.69
2514 2522 1.000955 CGGACTTGCACCAGTAGAACT 59.999 52.381 0.00 0.00 0.00 3.01
2742 2750 7.066163 CGATCCATATTAATTGATGCTGGCTTA 59.934 37.037 0.00 0.00 0.00 3.09
2746 2754 8.454106 CCATATTAATTGATGCTGGCTTAGTAC 58.546 37.037 0.00 0.00 0.00 2.73
3035 3043 1.299926 GGAACATCGACCCGGATCG 60.300 63.158 13.60 13.60 43.63 3.69
3065 3073 1.138036 CGACATAGGGAACGACGCA 59.862 57.895 0.00 0.00 0.00 5.24
3069 3077 2.676342 GACATAGGGAACGACGCAATTT 59.324 45.455 0.00 0.00 0.00 1.82
3161 3169 1.586028 CCAACATGCCAAGGAACGG 59.414 57.895 0.00 0.00 0.00 4.44
3324 3332 2.607892 GCGACGGACTGCAAAAGCT 61.608 57.895 0.00 0.00 0.00 3.74
3496 3504 8.371699 AGTAGATTACTTTCTGCTCTCAAAACT 58.628 33.333 0.00 0.00 34.04 2.66
3548 3556 4.124238 CCTCCGTTTCAGTTTACAAGTCA 58.876 43.478 0.00 0.00 0.00 3.41
3811 3819 3.503363 GCCTTTCTGCAGCGCGAT 61.503 61.111 12.10 0.00 0.00 4.58
3835 3843 0.900647 AACGGTAGCTCAGTGGCTCT 60.901 55.000 9.08 0.00 42.97 4.09
4423 4447 0.243636 GGTGAAAACCCATTCTGGCG 59.756 55.000 0.00 0.00 35.79 5.69
4662 4687 2.179547 TGCCTTGAGTGCGTGTGTG 61.180 57.895 0.00 0.00 0.00 3.82
6402 6458 0.112995 AATGGCTTCCCTGAACAGCA 59.887 50.000 0.00 0.00 0.00 4.41
6455 6511 2.842496 TGATGAGAAGGACCTGCATCTT 59.158 45.455 22.62 9.88 37.01 2.40
6638 6694 4.363990 CTGCCAGCACTCCGACGT 62.364 66.667 0.00 0.00 0.00 4.34
6754 6810 4.210537 CCATGTCGAAACTAACTGTCGTTT 59.789 41.667 7.58 7.58 36.16 3.60
6880 6936 6.775142 TCAACTGAAAACATCATTAAGGGTGA 59.225 34.615 7.50 0.00 37.44 4.02
6883 6939 6.549364 ACTGAAAACATCATTAAGGGTGACAA 59.451 34.615 7.50 0.00 37.44 3.18
7065 7121 4.980805 TGACTCGCCACCGCCAAC 62.981 66.667 0.00 0.00 0.00 3.77
7093 7149 3.120199 CCTGTTTGCTGGTAATGAACTCG 60.120 47.826 0.00 0.00 0.00 4.18
7106 7162 5.757850 AATGAACTCGAAGTCTGCTTTTT 57.242 34.783 0.00 0.00 34.61 1.94
7462 7518 8.874816 GTTTGGTCTGTTATTCTGAACTAGATC 58.125 37.037 0.00 0.00 34.80 2.75
7508 7564 0.035820 TAGTGGGTGTTTCGATGGCC 60.036 55.000 0.00 0.00 0.00 5.36
7595 7651 7.927092 TGATTTCAGTTGAGCAATTGATGAAAA 59.073 29.630 10.34 0.00 38.31 2.29
7635 7691 3.470868 AGGAATAAGCAGGTAAGGGGAA 58.529 45.455 0.00 0.00 0.00 3.97
8012 8085 0.540830 ACTCCGCTCCTTCTCTGTGT 60.541 55.000 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 0.868406 GGTTGCAGACTTGTTCGAGG 59.132 55.000 0.00 0.00 0.00 4.63
61 62 0.589223 TGTGCTAAAACGAAAGGCCG 59.411 50.000 0.00 0.00 0.00 6.13
64 65 3.281341 TGCATGTGCTAAAACGAAAGG 57.719 42.857 6.55 0.00 42.66 3.11
88 89 1.908619 TGGTTGCAAGCATCCTCTCTA 59.091 47.619 26.54 1.14 36.89 2.43
100 101 5.243507 ACATCTACATGTTGATTGGTTGCAA 59.756 36.000 18.44 0.00 40.66 4.08
101 102 4.766373 ACATCTACATGTTGATTGGTTGCA 59.234 37.500 18.44 0.00 40.66 4.08
132 133 6.549736 TGAGTCTAGTTAACTATATGCAGGCA 59.450 38.462 15.57 0.00 0.00 4.75
181 182 4.085822 CGTTTGGTTACTGCATCGTTTTTG 60.086 41.667 0.00 0.00 0.00 2.44
188 190 0.793104 GCGCGTTTGGTTACTGCATC 60.793 55.000 8.43 0.00 0.00 3.91
344 346 6.399639 ACCCAGATTTGTTGTCGTTTATTT 57.600 33.333 0.00 0.00 0.00 1.40
378 380 3.650647 CCCAGTTGGTAGCATGTGT 57.349 52.632 0.00 0.00 0.00 3.72
617 619 3.034635 CCTACACCAGCCATCTCTTACT 58.965 50.000 0.00 0.00 0.00 2.24
1559 1564 2.170607 TGAGACGGGAGATTGGGAATTC 59.829 50.000 0.00 0.00 0.00 2.17
2002 2008 4.141779 ACCCACCGTAAAATGTCTCTATCC 60.142 45.833 0.00 0.00 0.00 2.59
2019 2025 6.243216 TGGATCAACTAAATACTACCCACC 57.757 41.667 0.00 0.00 0.00 4.61
2047 2053 7.912250 AGTGAAAATTTGATCGATCAGTATTGC 59.088 33.333 25.95 19.61 38.19 3.56
2075 2081 8.258007 CCGATTGAGAATTACTAATATGCCCTA 58.742 37.037 0.00 0.00 0.00 3.53
2188 2194 4.576463 GTCCCTTAGATGTGCAATAACCAG 59.424 45.833 0.00 0.00 0.00 4.00
2194 2200 4.574674 TTGAGTCCCTTAGATGTGCAAT 57.425 40.909 0.00 0.00 0.00 3.56
2351 2358 8.513774 AGATTTGTGCAAACATTTTCTTTTGTT 58.486 25.926 0.00 0.00 37.66 2.83
2451 2458 4.397103 CGGAAGGGTTGGGATTAACTTAAC 59.603 45.833 0.00 0.00 0.00 2.01
2514 2522 0.038166 GTTCCAGGGATGTGAGGCAA 59.962 55.000 0.00 0.00 0.00 4.52
2733 2741 3.813166 GACAACTTTGTACTAAGCCAGCA 59.187 43.478 15.69 0.00 42.43 4.41
2787 2795 2.104170 CTAGGGTTGTCTCCTGAGGAC 58.896 57.143 0.00 0.00 35.92 3.85
2962 2970 1.501582 GCAACTATGAGGGAGGGAGT 58.498 55.000 0.00 0.00 0.00 3.85
3065 3073 1.073177 CGCGTTCCCGTCACTAAATT 58.927 50.000 0.00 0.00 36.15 1.82
3069 3077 2.562912 GTCGCGTTCCCGTCACTA 59.437 61.111 5.77 0.00 36.15 2.74
3091 3099 2.477375 CGAAGCTGCAAACCTACGTTTA 59.523 45.455 1.02 0.00 40.28 2.01
3161 3169 2.548920 CGATTCCATCCAGTAGGCCTTC 60.549 54.545 12.58 5.68 33.74 3.46
3231 3239 4.293648 TCCGCACGTCCACACCAG 62.294 66.667 0.00 0.00 0.00 4.00
3289 3297 4.758251 CCGAGCACCACATCCGCA 62.758 66.667 0.00 0.00 0.00 5.69
3496 3504 2.677836 GTGTGGAAATATCTCGCTGCAA 59.322 45.455 0.00 0.00 0.00 4.08
3548 3556 3.254903 TGACAACCTAGATATACGCGCAT 59.745 43.478 5.73 0.00 0.00 4.73
3811 3819 2.165030 GCCACTGAGCTACCGTTTAGTA 59.835 50.000 0.00 0.00 0.00 1.82
4423 4447 3.041940 CACCGACGACCTGGCAAC 61.042 66.667 0.00 0.00 0.00 4.17
4449 4473 0.673644 AAGAAGGGAACGACGCCATG 60.674 55.000 0.00 0.00 0.00 3.66
4662 4687 2.551912 CCCACTCCGGCAACACAAC 61.552 63.158 0.00 0.00 0.00 3.32
4733 4758 6.713450 TCCATATTAATACCGAAAAAGGCTCC 59.287 38.462 0.00 0.00 33.69 4.70
6455 6511 1.486310 AGACAAGGCATCCGCATAAGA 59.514 47.619 0.00 0.00 41.24 2.10
6754 6810 1.148273 ACTTCGCCCAGAGTTGCAA 59.852 52.632 0.00 0.00 0.00 4.08
6880 6936 1.181786 CTCCTCGCTTCTCTCCTTGT 58.818 55.000 0.00 0.00 0.00 3.16
6883 6939 0.751643 GCTCTCCTCGCTTCTCTCCT 60.752 60.000 0.00 0.00 0.00 3.69
7065 7121 3.334583 TTACCAGCAAACAGGAGCTAG 57.665 47.619 0.00 0.00 39.50 3.42
7410 7466 4.039124 CAGGGAAAACAGTAGCCAAAACAT 59.961 41.667 0.00 0.00 0.00 2.71
7462 7518 5.124936 GGGCAAAAACCTACTAACACTATGG 59.875 44.000 0.00 0.00 0.00 2.74
7508 7564 1.352156 GAAACCCGCTACGAGTGCTG 61.352 60.000 0.00 0.00 0.00 4.41
7595 7651 4.803452 TCCTTCCAACAGGAAATCAACTT 58.197 39.130 0.00 0.00 40.26 2.66
7635 7691 0.467384 CTCCAGTTCATCGCCCTCAT 59.533 55.000 0.00 0.00 0.00 2.90
8012 8085 4.444876 GCTAGGCCTAAATGGTTCTCATGA 60.445 45.833 14.85 0.00 35.99 3.07


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

AutoCloner maintained by Alex Coulton.