Multiple sequence alignment - TraesCS2A01G120400

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 TraesCS2A01G120400 chr2A 100.000 2837 0 0 1 2837 70648364 70651200 0.000000e+00 5240.0
1 TraesCS2A01G120400 chr2A 78.223 1047 173 31 941 1953 70145245 70144220 1.120000e-173 619.0
2 TraesCS2A01G120400 chr2A 85.572 603 69 9 851 1446 70654912 70655503 1.440000e-172 616.0
3 TraesCS2A01G120400 chr2A 80.077 778 100 26 1478 2240 70291288 70290551 6.960000e-146 527.0
4 TraesCS2A01G120400 chr2A 77.744 656 105 17 1979 2612 70144253 70143617 5.780000e-97 364.0
5 TraesCS2A01G120400 chr2A 80.269 446 65 19 2185 2612 70150769 70150329 5.900000e-82 315.0
6 TraesCS2A01G120400 chr2A 84.524 252 21 13 851 1084 70643836 70644087 1.700000e-57 233.0
7 TraesCS2A01G120400 chr2A 80.442 317 47 7 1984 2287 70656149 70656463 7.910000e-56 228.0
8 TraesCS2A01G120400 chr2A 78.916 332 55 12 1104 1432 70271240 70270921 7.960000e-51 211.0
9 TraesCS2A01G120400 chr2A 93.651 63 3 1 1950 2012 70650284 70650345 3.010000e-15 93.5
10 TraesCS2A01G120400 chr2A 93.651 63 3 1 1921 1982 70650313 70650375 3.010000e-15 93.5
11 TraesCS2A01G120400 chr2B 88.512 1149 71 30 888 1982 107789130 107790271 0.000000e+00 1334.0
12 TraesCS2A01G120400 chr2B 87.694 902 87 15 1950 2833 107790210 107791105 0.000000e+00 1029.0
13 TraesCS2A01G120400 chr2B 84.731 930 106 18 24 938 107788220 107789128 0.000000e+00 898.0
14 TraesCS2A01G120400 chr2B 86.372 565 61 10 851 1404 107793138 107793697 1.120000e-168 603.0
15 TraesCS2A01G120400 chr2B 80.421 618 87 25 844 1446 107568465 107569063 9.330000e-120 440.0
16 TraesCS2A01G120400 chr2B 78.744 621 93 22 851 1446 107576783 107577389 2.060000e-101 379.0
17 TraesCS2A01G120400 chr2B 79.365 567 94 15 2066 2612 106961796 106961233 7.420000e-101 377.0
18 TraesCS2A01G120400 chr2B 80.587 443 72 8 999 1440 107039186 107038757 2.110000e-86 329.0
19 TraesCS2A01G120400 chr2B 77.396 553 65 26 1984 2516 107023189 107022677 1.000000e-69 274.0
20 TraesCS2A01G120400 chr2B 82.935 293 41 5 2209 2492 107573936 107574228 3.630000e-64 255.0
21 TraesCS2A01G120400 chr2D 93.981 864 37 11 1979 2833 71595118 71595975 0.000000e+00 1293.0
22 TraesCS2A01G120400 chr2D 85.389 1054 106 27 808 1841 71594065 71595090 0.000000e+00 1050.0
23 TraesCS2A01G120400 chr2D 83.683 619 64 13 851 1452 71598716 71599314 1.490000e-152 549.0
24 TraesCS2A01G120400 chr2D 77.686 968 165 31 960 1899 70642794 70643738 6.910000e-151 544.0
25 TraesCS2A01G120400 chr2D 86.395 441 45 9 385 823 71593623 71594050 4.280000e-128 468.0
26 TraesCS2A01G120400 chr2D 79.185 687 103 22 789 1452 70674435 70673766 9.330000e-120 440.0
27 TraesCS2A01G120400 chr2D 78.964 618 100 20 1999 2601 71471260 71471862 7.370000e-106 394.0
28 TraesCS2A01G120400 chr2D 80.639 501 67 19 1999 2486 71405771 71406254 7.470000e-96 361.0
29 TraesCS2A01G120400 chr2D 81.073 317 45 10 1984 2287 71600203 71600517 3.650000e-59 239.0
30 TraesCS2A01G120400 chr2D 76.749 443 86 11 1008 1446 71565718 71566147 6.110000e-57 231.0
31 TraesCS2A01G120400 chr2D 80.515 272 39 9 1979 2240 71400393 71400660 2.230000e-46 196.0
32 TraesCS2A01G120400 chr2D 80.455 220 37 5 2399 2612 70636914 70637133 2.260000e-36 163.0


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 TraesCS2A01G120400 chr2A 70648364 70651200 2836 False 1809.0 5240 95.767333 1 2837 3 chr2A.!!$F2 2836
1 TraesCS2A01G120400 chr2A 70290551 70291288 737 True 527.0 527 80.077000 1478 2240 1 chr2A.!!$R3 762
2 TraesCS2A01G120400 chr2A 70143617 70145245 1628 True 491.5 619 77.983500 941 2612 2 chr2A.!!$R4 1671
3 TraesCS2A01G120400 chr2A 70654912 70656463 1551 False 422.0 616 83.007000 851 2287 2 chr2A.!!$F3 1436
4 TraesCS2A01G120400 chr2B 107788220 107793697 5477 False 966.0 1334 86.827250 24 2833 4 chr2B.!!$F3 2809
5 TraesCS2A01G120400 chr2B 107568465 107569063 598 False 440.0 440 80.421000 844 1446 1 chr2B.!!$F1 602
6 TraesCS2A01G120400 chr2B 106961233 106961796 563 True 377.0 377 79.365000 2066 2612 1 chr2B.!!$R1 546
7 TraesCS2A01G120400 chr2B 107573936 107577389 3453 False 317.0 379 80.839500 851 2492 2 chr2B.!!$F2 1641
8 TraesCS2A01G120400 chr2B 107022677 107023189 512 True 274.0 274 77.396000 1984 2516 1 chr2B.!!$R2 532
9 TraesCS2A01G120400 chr2D 71593623 71600517 6894 False 719.8 1293 86.104200 385 2833 5 chr2D.!!$F7 2448
10 TraesCS2A01G120400 chr2D 70642794 70643738 944 False 544.0 544 77.686000 960 1899 1 chr2D.!!$F2 939
11 TraesCS2A01G120400 chr2D 70673766 70674435 669 True 440.0 440 79.185000 789 1452 1 chr2D.!!$R1 663
12 TraesCS2A01G120400 chr2D 71471260 71471862 602 False 394.0 394 78.964000 1999 2601 1 chr2D.!!$F5 602

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
205 208 0.329596 AGAAAGACATGGCACCTCCC 59.67 55.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2108 9288 0.036732 GATCGATGCCAGCCCCAATA 59.963 55.0 0.54 0.0 0.0 1.9 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
42 43 3.989817 GGAAAATGACATGTGCTGGTTTC 59.010 43.478 1.15 5.88 0.00 2.78
43 44 4.501229 GGAAAATGACATGTGCTGGTTTCA 60.501 41.667 1.15 0.00 0.00 2.69
44 45 4.877378 AAATGACATGTGCTGGTTTCAT 57.123 36.364 1.15 0.00 0.00 2.57
45 46 4.877378 AATGACATGTGCTGGTTTCATT 57.123 36.364 1.15 0.83 0.00 2.57
46 47 4.877378 ATGACATGTGCTGGTTTCATTT 57.123 36.364 1.15 0.00 0.00 2.32
47 48 4.241590 TGACATGTGCTGGTTTCATTTC 57.758 40.909 1.15 0.00 0.00 2.17
97 98 3.243501 GCCAAAAGTGAAGCACAAGATCA 60.244 43.478 0.00 0.00 36.74 2.92
115 116 9.512588 ACAAGATCATTGGGTTATCTGATATTC 57.487 33.333 0.00 0.00 29.68 1.75
132 133 9.852091 TCTGATATTCATACATCTTCAGAATCG 57.148 33.333 0.00 0.00 36.22 3.34
147 150 5.175859 TCAGAATCGTTGGTGGATAAACTC 58.824 41.667 0.00 0.00 0.00 3.01
160 163 3.619038 GGATAAACTCGCAGGAGAACAAG 59.381 47.826 0.00 0.00 43.27 3.16
173 176 4.410555 AGGAGAACAAGAACAGAGGAAAGT 59.589 41.667 0.00 0.00 0.00 2.66
192 195 7.401493 AGGAAAGTAGATTGATCCAGAGAAAGA 59.599 37.037 0.00 0.00 32.47 2.52
205 208 0.329596 AGAAAGACATGGCACCTCCC 59.670 55.000 0.00 0.00 0.00 4.30
227 230 2.929641 TCACTGATGGCTTCACAACAA 58.070 42.857 0.00 0.00 0.00 2.83
230 233 1.603802 CTGATGGCTTCACAACAACGT 59.396 47.619 0.00 0.00 0.00 3.99
232 235 1.601903 GATGGCTTCACAACAACGTGA 59.398 47.619 0.00 0.00 44.05 4.35
243 246 5.082059 CACAACAACGTGATATCAAGCTTC 58.918 41.667 17.25 0.00 39.34 3.86
263 267 4.685169 TCGAAATGAGAGAAAATGCCAC 57.315 40.909 0.00 0.00 0.00 5.01
286 290 6.093495 CACGAAAAGGCTCTAAAATGTATGGA 59.907 38.462 0.00 0.00 0.00 3.41
287 291 6.828785 ACGAAAAGGCTCTAAAATGTATGGAT 59.171 34.615 0.00 0.00 0.00 3.41
288 292 7.134815 CGAAAAGGCTCTAAAATGTATGGATG 58.865 38.462 0.00 0.00 0.00 3.51
302 306 5.630121 TGTATGGATGGTTATTTAGGCTGG 58.370 41.667 0.00 0.00 0.00 4.85
303 307 3.593442 TGGATGGTTATTTAGGCTGGG 57.407 47.619 0.00 0.00 0.00 4.45
309 313 6.954102 GGATGGTTATTTAGGCTGGGATAATT 59.046 38.462 0.00 0.00 0.00 1.40
320 324 3.817647 GCTGGGATAATTGAGCTAACCAG 59.182 47.826 0.00 0.00 45.29 4.00
335 339 0.839946 ACCAGGGCATAGACACCATC 59.160 55.000 0.00 0.00 0.00 3.51
336 340 0.839277 CCAGGGCATAGACACCATCA 59.161 55.000 0.00 0.00 0.00 3.07
337 341 1.212688 CCAGGGCATAGACACCATCAA 59.787 52.381 0.00 0.00 0.00 2.57
371 375 1.747355 GATGCCAAGGACAACCATGAG 59.253 52.381 0.00 0.00 37.08 2.90
405 409 2.543238 CCTCTAATCCGACGGTAAGCAC 60.543 54.545 14.79 0.00 0.00 4.40
459 463 6.294397 GGAACTATCCTATTACCACCACTACG 60.294 46.154 0.00 0.00 42.93 3.51
471 475 3.945921 CCACCACTACGAGAGATCTACAA 59.054 47.826 0.00 0.00 0.00 2.41
495 499 6.502074 AAATCTATAAGAAGGGACCCTCAC 57.498 41.667 15.27 11.47 30.89 3.51
507 512 3.141488 CCTCACCTAGCTCGCCGT 61.141 66.667 0.00 0.00 0.00 5.68
542 548 1.677552 GAGAGTTGAGGGGCCGAAA 59.322 57.895 0.00 0.00 0.00 3.46
543 549 0.673956 GAGAGTTGAGGGGCCGAAAC 60.674 60.000 0.00 1.69 0.00 2.78
558 564 3.001939 GCCGAAACGAAGAAACAGAAAGA 59.998 43.478 0.00 0.00 0.00 2.52
598 613 3.157087 GGATCAAGGCACTGGAAAAAGA 58.843 45.455 0.00 0.00 44.39 2.52
648 663 8.814038 ATGTATCAAACTTCTAGCAGGAAATT 57.186 30.769 0.00 0.00 0.00 1.82
680 696 9.772973 ATTACAAAAATAAACCCCAACTTCTTC 57.227 29.630 0.00 0.00 0.00 2.87
681 697 7.432148 ACAAAAATAAACCCCAACTTCTTCT 57.568 32.000 0.00 0.00 0.00 2.85
730 746 1.668751 TCTGAATATTTCGCCCGTTGC 59.331 47.619 0.00 0.00 0.00 4.17
739 755 2.594592 GCCCGTTGCCTTGACAGT 60.595 61.111 0.00 0.00 0.00 3.55
842 888 8.232513 CCACTTTAGATTACGGGTTAAGAAAAC 58.767 37.037 0.00 0.00 0.00 2.43
966 7637 2.837291 CTCCTCCCAGGGCGAGAG 60.837 72.222 14.69 9.94 35.59 3.20
1170 7870 0.250124 CTGTGTGGTTTACCTCCGCA 60.250 55.000 0.00 3.43 42.18 5.69
1266 7966 2.030958 GTACGGGGCTTTCACGGTG 61.031 63.158 0.56 0.56 0.00 4.94
1362 8062 2.585247 GCTGTACGTGGATCCCGC 60.585 66.667 18.87 7.75 0.00 6.13
1364 8064 3.768185 CTGTACGTGGATCCCGCCG 62.768 68.421 18.87 15.69 0.00 6.46
1432 8140 5.791336 TCCTGATCGAATTACAGCAGTAT 57.209 39.130 0.00 0.00 0.00 2.12
1483 8331 1.938577 CTTCGTCTGCATCCTTCCATG 59.061 52.381 0.00 0.00 0.00 3.66
1497 8361 3.329386 CTTCCATGTATACTCATGCCCG 58.671 50.000 4.17 0.00 42.44 6.13
1629 8496 3.697542 TCATGGCAGATGTTCCTTTCATG 59.302 43.478 0.00 0.00 34.00 3.07
1765 8641 3.299281 CGCGATATCTTGCTCTGTTATCG 59.701 47.826 0.00 14.32 42.63 2.92
1776 8652 3.677424 GCTCTGTTATCGTTCCAGCTCTT 60.677 47.826 0.00 0.00 0.00 2.85
1786 8662 3.142174 GTTCCAGCTCTTGCACTTAGTT 58.858 45.455 0.00 0.00 42.74 2.24
1793 8669 3.815401 GCTCTTGCACTTAGTTTCTGGAA 59.185 43.478 0.00 0.00 39.41 3.53
1843 8719 5.123186 CCATCGCAGTTTTGTTGAGGTATAA 59.877 40.000 0.00 0.00 0.00 0.98
1880 9047 4.248859 TCCTCTCTTCTTTGAAAGATGCG 58.751 43.478 8.64 6.47 37.38 4.73
1948 9122 9.905713 TGAATCATTTATCTTAGTTTACTGCCT 57.094 29.630 0.00 0.00 0.00 4.75
1952 9126 9.778741 TCATTTATCTTAGTTTACTGCCTATGG 57.221 33.333 0.00 0.00 0.00 2.74
1953 9127 9.778741 CATTTATCTTAGTTTACTGCCTATGGA 57.221 33.333 0.00 0.00 0.00 3.41
1955 9129 9.609346 TTTATCTTAGTTTACTGCCTATGGAAC 57.391 33.333 0.00 0.00 0.00 3.62
1956 9130 5.985911 TCTTAGTTTACTGCCTATGGAACC 58.014 41.667 0.00 0.00 0.00 3.62
1957 9131 5.486063 TCTTAGTTTACTGCCTATGGAACCA 59.514 40.000 0.00 0.00 0.00 3.67
1958 9132 4.862641 AGTTTACTGCCTATGGAACCAT 57.137 40.909 11.20 11.20 40.19 3.55
1959 9133 5.193099 AGTTTACTGCCTATGGAACCATT 57.807 39.130 11.68 0.00 37.82 3.16
1960 9134 5.580022 AGTTTACTGCCTATGGAACCATTT 58.420 37.500 11.68 0.00 37.82 2.32
1961 9135 6.727394 AGTTTACTGCCTATGGAACCATTTA 58.273 36.000 11.68 0.00 37.82 1.40
1962 9136 7.354312 AGTTTACTGCCTATGGAACCATTTAT 58.646 34.615 11.68 0.00 37.82 1.40
1963 9137 7.502561 AGTTTACTGCCTATGGAACCATTTATC 59.497 37.037 11.68 1.03 37.82 1.75
1964 9138 5.653255 ACTGCCTATGGAACCATTTATCT 57.347 39.130 11.68 0.00 37.82 1.98
1965 9139 6.018433 ACTGCCTATGGAACCATTTATCTT 57.982 37.500 11.68 0.00 37.82 2.40
1966 9140 7.149202 ACTGCCTATGGAACCATTTATCTTA 57.851 36.000 11.68 0.00 37.82 2.10
2034 9214 6.379703 TGGTGTTGATATTTGTTAAGATGGGG 59.620 38.462 0.00 0.00 0.00 4.96
2035 9215 6.183360 GGTGTTGATATTTGTTAAGATGGGGG 60.183 42.308 0.00 0.00 0.00 5.40
2217 9432 5.587388 AATGAGCAATTCCACACATTAGG 57.413 39.130 0.00 0.00 0.00 2.69
2289 9511 4.507710 TCTTTGCAGCGAGTGAGATTATT 58.492 39.130 0.00 0.00 0.00 1.40
2319 9544 3.641437 TGCTTCCATACTGTTTGCAAC 57.359 42.857 0.00 0.00 0.00 4.17
2338 9566 4.749976 CAACCACCTTCTAGAGCTCTTAC 58.250 47.826 23.84 0.00 0.00 2.34
2363 9591 7.040062 ACCATTGATAATTTCTCCGTTGAAACA 60.040 33.333 2.83 0.00 38.54 2.83
2418 9648 8.409358 TGCTATTGCATATGAGTCTAGTCTAA 57.591 34.615 6.97 0.00 45.31 2.10
2528 9763 8.607459 CATGACAGTAAAATATCACACCTCTTC 58.393 37.037 0.00 0.00 0.00 2.87
2541 9782 4.752101 CACACCTCTTCTCCTTTAACAGTG 59.248 45.833 0.00 0.00 0.00 3.66
2542 9783 4.202367 ACACCTCTTCTCCTTTAACAGTGG 60.202 45.833 0.00 0.00 0.00 4.00
2544 9785 5.011738 CACCTCTTCTCCTTTAACAGTGGTA 59.988 44.000 0.00 0.00 31.62 3.25
2596 9838 0.447801 GGTAGAAGTGCCATTGTGCG 59.552 55.000 0.00 0.00 0.00 5.34
2605 9847 1.805428 GCCATTGTGCGTTTGTCCCT 61.805 55.000 0.00 0.00 0.00 4.20
2617 9859 4.739195 CGTTTGTCCCTTGTTCTTTTTGA 58.261 39.130 0.00 0.00 0.00 2.69
2619 9861 4.729227 TTGTCCCTTGTTCTTTTTGACC 57.271 40.909 0.00 0.00 0.00 4.02
2620 9862 3.702792 TGTCCCTTGTTCTTTTTGACCA 58.297 40.909 0.00 0.00 0.00 4.02
2629 9871 5.437060 TGTTCTTTTTGACCAGAACTAGCT 58.563 37.500 12.09 0.00 40.67 3.32
2641 9886 3.817647 CAGAACTAGCTGGACTGCTTTTT 59.182 43.478 3.17 3.42 43.74 1.94
2654 9899 5.278463 GGACTGCTTTTTCATCAGCTAACAA 60.278 40.000 0.00 0.00 36.92 2.83
2655 9900 6.336842 ACTGCTTTTTCATCAGCTAACAAT 57.663 33.333 0.00 0.00 36.92 2.71
2656 9901 6.154445 ACTGCTTTTTCATCAGCTAACAATG 58.846 36.000 0.00 0.00 36.92 2.82
2657 9902 6.016024 ACTGCTTTTTCATCAGCTAACAATGA 60.016 34.615 0.00 0.00 36.92 2.57
2658 9903 6.151691 TGCTTTTTCATCAGCTAACAATGAC 58.848 36.000 0.00 0.00 36.92 3.06
2662 9907 6.882610 TTTCATCAGCTAACAATGACAGTT 57.117 33.333 0.00 0.00 0.00 3.16
2665 9910 6.108687 TCATCAGCTAACAATGACAGTTAGG 58.891 40.000 13.55 2.46 45.31 2.69
2674 9919 6.681729 ACAATGACAGTTAGGAGGAAGTAA 57.318 37.500 0.00 0.00 0.00 2.24
2678 9923 7.973048 ATGACAGTTAGGAGGAAGTAATGTA 57.027 36.000 0.00 0.00 0.00 2.29
2679 9924 7.166691 TGACAGTTAGGAGGAAGTAATGTAC 57.833 40.000 0.00 0.00 0.00 2.90
2684 9929 7.923344 CAGTTAGGAGGAAGTAATGTACATCAG 59.077 40.741 9.23 0.00 0.00 2.90
2691 9936 9.162764 GAGGAAGTAATGTACATCAGCTAAAAA 57.837 33.333 9.23 0.00 0.00 1.94
2692 9937 9.686683 AGGAAGTAATGTACATCAGCTAAAAAT 57.313 29.630 9.23 0.00 0.00 1.82
2713 9958 9.688592 AAAAATCTTACAGAGAAAGAATTGCAG 57.311 29.630 0.00 0.00 38.06 4.41
2714 9959 7.992754 AATCTTACAGAGAAAGAATTGCAGT 57.007 32.000 0.00 0.00 38.06 4.40
2715 9960 9.507329 AAATCTTACAGAGAAAGAATTGCAGTA 57.493 29.630 0.00 0.00 38.06 2.74
2716 9961 8.715191 ATCTTACAGAGAAAGAATTGCAGTAG 57.285 34.615 0.00 0.00 38.06 2.57
2719 9964 4.287067 ACAGAGAAAGAATTGCAGTAGGGA 59.713 41.667 0.00 0.00 0.00 4.20
2720 9965 5.221925 ACAGAGAAAGAATTGCAGTAGGGAA 60.222 40.000 0.00 0.00 0.00 3.97
2721 9966 5.707298 CAGAGAAAGAATTGCAGTAGGGAAA 59.293 40.000 0.00 0.00 0.00 3.13
2722 9967 5.942826 AGAGAAAGAATTGCAGTAGGGAAAG 59.057 40.000 0.00 0.00 0.00 2.62
2724 9969 6.306987 AGAAAGAATTGCAGTAGGGAAAGAA 58.693 36.000 0.00 0.00 0.00 2.52
2726 9971 6.581171 AAGAATTGCAGTAGGGAAAGAAAG 57.419 37.500 0.00 0.00 0.00 2.62
2727 9972 5.635120 AGAATTGCAGTAGGGAAAGAAAGT 58.365 37.500 0.00 0.00 0.00 2.66
2728 9973 6.779860 AGAATTGCAGTAGGGAAAGAAAGTA 58.220 36.000 0.00 0.00 0.00 2.24
2764 10013 5.760253 CCAAAACACTGACACAACTCTATCT 59.240 40.000 0.00 0.00 0.00 1.98
2779 10028 4.080751 ACTCTATCTATCTCTCCGGGTAGC 60.081 50.000 0.00 0.00 0.00 3.58
2783 10032 0.858369 TATCTCTCCGGGTAGCCCTT 59.142 55.000 5.12 0.00 42.67 3.95
2817 10066 5.485353 ACATCTTCTCTAATCAGGGACAACA 59.515 40.000 0.00 0.00 28.07 3.33
2821 10070 3.515502 TCTCTAATCAGGGACAACACCAG 59.484 47.826 0.00 0.00 0.00 4.00
2833 10082 2.555325 ACAACACCAGTGATGCATTCTG 59.445 45.455 19.34 19.34 36.93 3.02
2834 10083 2.555325 CAACACCAGTGATGCATTCTGT 59.445 45.455 22.30 13.01 0.00 3.41
2835 10084 2.867624 ACACCAGTGATGCATTCTGTT 58.132 42.857 22.30 12.18 0.00 3.16
2836 10085 2.816087 ACACCAGTGATGCATTCTGTTC 59.184 45.455 22.30 4.38 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.205417 CAGCACATGTCATTTTCCCCC 59.795 52.381 0.00 0.00 0.00 5.40
18 19 1.205417 CCAGCACATGTCATTTTCCCC 59.795 52.381 0.00 0.00 0.00 4.81
19 20 1.895131 ACCAGCACATGTCATTTTCCC 59.105 47.619 0.00 0.00 0.00 3.97
20 21 3.665745 AACCAGCACATGTCATTTTCC 57.334 42.857 0.00 0.00 0.00 3.13
21 22 4.619973 TGAAACCAGCACATGTCATTTTC 58.380 39.130 0.00 2.02 0.00 2.29
22 23 4.669206 TGAAACCAGCACATGTCATTTT 57.331 36.364 0.00 0.00 0.00 1.82
42 43 6.261826 AGACTGAAACAGACTCCTTTGAAATG 59.738 38.462 5.76 0.00 31.65 2.32
43 44 6.360618 AGACTGAAACAGACTCCTTTGAAAT 58.639 36.000 5.76 0.00 31.65 2.17
44 45 5.745227 AGACTGAAACAGACTCCTTTGAAA 58.255 37.500 5.76 0.00 31.65 2.69
45 46 5.359194 AGACTGAAACAGACTCCTTTGAA 57.641 39.130 5.76 0.00 31.65 2.69
46 47 4.950050 GAGACTGAAACAGACTCCTTTGA 58.050 43.478 15.99 0.00 43.56 2.69
71 72 0.317854 GTGCTTCACTTTTGGCGTCC 60.318 55.000 0.00 0.00 0.00 4.79
115 116 5.007039 CCACCAACGATTCTGAAGATGTATG 59.993 44.000 0.00 0.00 0.00 2.39
118 119 3.007940 TCCACCAACGATTCTGAAGATGT 59.992 43.478 0.00 0.00 0.00 3.06
125 126 4.032900 CGAGTTTATCCACCAACGATTCTG 59.967 45.833 0.00 0.00 0.00 3.02
126 127 4.181578 CGAGTTTATCCACCAACGATTCT 58.818 43.478 0.00 0.00 0.00 2.40
127 128 3.242316 GCGAGTTTATCCACCAACGATTC 60.242 47.826 0.00 0.00 0.00 2.52
131 132 1.393539 CTGCGAGTTTATCCACCAACG 59.606 52.381 0.00 0.00 0.00 4.10
132 133 1.737793 CCTGCGAGTTTATCCACCAAC 59.262 52.381 0.00 0.00 0.00 3.77
147 150 2.064762 CTCTGTTCTTGTTCTCCTGCG 58.935 52.381 0.00 0.00 0.00 5.18
160 163 6.644347 TGGATCAATCTACTTTCCTCTGTTC 58.356 40.000 0.00 0.00 0.00 3.18
173 176 6.687393 GCCATGTCTTTCTCTGGATCAATCTA 60.687 42.308 0.00 0.00 0.00 1.98
192 195 1.210204 AGTGATGGGAGGTGCCATGT 61.210 55.000 7.88 0.00 38.95 3.21
205 208 2.815503 TGTTGTGAAGCCATCAGTGATG 59.184 45.455 23.81 23.81 39.19 3.07
221 224 4.143115 CGAAGCTTGATATCACGTTGTTGT 60.143 41.667 2.10 0.00 0.00 3.32
227 230 5.109210 TCATTTCGAAGCTTGATATCACGT 58.891 37.500 2.10 0.00 0.00 4.49
230 233 6.809869 TCTCTCATTTCGAAGCTTGATATCA 58.190 36.000 2.10 0.00 0.00 2.15
232 235 8.498054 TTTTCTCTCATTTCGAAGCTTGATAT 57.502 30.769 2.10 0.00 0.00 1.63
243 246 3.125146 TCGTGGCATTTTCTCTCATTTCG 59.875 43.478 0.00 0.00 0.00 3.46
263 267 6.677781 TCCATACATTTTAGAGCCTTTTCG 57.322 37.500 0.00 0.00 0.00 3.46
286 290 7.534852 TCAATTATCCCAGCCTAAATAACCAT 58.465 34.615 0.00 0.00 0.00 3.55
287 291 6.916909 TCAATTATCCCAGCCTAAATAACCA 58.083 36.000 0.00 0.00 0.00 3.67
288 292 6.071896 GCTCAATTATCCCAGCCTAAATAACC 60.072 42.308 0.00 0.00 0.00 2.85
302 306 3.149981 GCCCTGGTTAGCTCAATTATCC 58.850 50.000 0.00 0.00 0.00 2.59
303 307 3.820557 TGCCCTGGTTAGCTCAATTATC 58.179 45.455 0.00 0.00 0.00 1.75
309 313 1.762957 GTCTATGCCCTGGTTAGCTCA 59.237 52.381 0.00 0.00 0.00 4.26
320 324 4.460263 TGTATTTGATGGTGTCTATGCCC 58.540 43.478 0.00 0.00 0.00 5.36
335 339 1.583404 GCATCGCCGCTTTTGTATTTG 59.417 47.619 0.00 0.00 0.00 2.32
336 340 1.469079 GGCATCGCCGCTTTTGTATTT 60.469 47.619 0.00 0.00 39.62 1.40
337 341 0.100503 GGCATCGCCGCTTTTGTATT 59.899 50.000 0.00 0.00 39.62 1.89
371 375 1.213296 TTAGAGGATCCAGGGGCAAC 58.787 55.000 15.82 0.00 33.66 4.17
376 380 1.896465 GTCGGATTAGAGGATCCAGGG 59.104 57.143 15.82 0.00 44.83 4.45
405 409 3.368843 CGTCCTTGATGGCTAGATATGGG 60.369 52.174 0.00 0.00 35.26 4.00
448 452 2.810870 AGATCTCTCGTAGTGGTGGT 57.189 50.000 0.00 0.00 0.00 4.16
471 475 6.126449 GGTGAGGGTCCCTTCTTATAGATTTT 60.126 42.308 13.13 0.00 31.76 1.82
479 483 2.626149 GCTAGGTGAGGGTCCCTTCTTA 60.626 54.545 13.13 8.55 31.76 2.10
521 526 3.412408 GGCCCCTCAACTCTCCCC 61.412 72.222 0.00 0.00 0.00 4.81
542 548 3.477210 AGCCTCTTTCTGTTTCTTCGT 57.523 42.857 0.00 0.00 0.00 3.85
543 549 3.929610 CCTAGCCTCTTTCTGTTTCTTCG 59.070 47.826 0.00 0.00 0.00 3.79
558 564 0.555769 CCTCCTCTCACTCCTAGCCT 59.444 60.000 0.00 0.00 0.00 4.58
730 746 1.248486 TCGTCTCCTCACTGTCAAGG 58.752 55.000 0.25 0.25 0.00 3.61
739 755 3.181496 CGAGATTGACAATCGTCTCCTCA 60.181 47.826 19.87 0.00 43.06 3.86
758 774 1.372251 CCCGGATCGATTCTGCGAG 60.372 63.158 0.73 0.00 44.26 5.03
842 888 0.179189 GCTGTTCGGCTTTCGGATTG 60.179 55.000 0.00 0.00 39.77 2.67
845 892 1.374252 GAGCTGTTCGGCTTTCGGA 60.374 57.895 7.59 0.00 43.20 4.55
1159 7859 2.577059 CGAGGCTGCGGAGGTAAA 59.423 61.111 5.93 0.00 0.00 2.01
1214 7914 0.973496 GAAGAGGAAGGAGGCGGAGT 60.973 60.000 0.00 0.00 0.00 3.85
1266 7966 1.600916 AAGGAAGACGCAGGCCAAC 60.601 57.895 5.01 0.00 0.00 3.77
1277 7977 0.667487 CGCGAGCAAGACAAGGAAGA 60.667 55.000 0.00 0.00 0.00 2.87
1362 8062 1.664151 GGTACCTCTTTGAATTCGCGG 59.336 52.381 6.13 0.00 0.00 6.46
1364 8064 2.093783 CACGGTACCTCTTTGAATTCGC 59.906 50.000 10.90 0.00 0.00 4.70
1365 8065 2.093783 GCACGGTACCTCTTTGAATTCG 59.906 50.000 10.90 0.00 0.00 3.34
1483 8331 2.037251 ACATGGACGGGCATGAGTATAC 59.963 50.000 0.00 0.00 33.38 1.47
1497 8361 5.584251 ACAATTTCAACAAAACCACATGGAC 59.416 36.000 4.53 0.00 38.94 4.02
1540 8404 2.409870 CCGGCTTGATTGCTCCCAC 61.410 63.158 0.00 0.00 0.00 4.61
1629 8496 2.510238 CCAGCGACCACTAGCAGC 60.510 66.667 0.00 0.00 35.48 5.25
1674 8550 2.158249 TCCCTGAGATACTGATCCCTGG 60.158 54.545 0.00 0.00 31.12 4.45
1675 8551 3.164268 CTCCCTGAGATACTGATCCCTG 58.836 54.545 0.00 0.00 31.81 4.45
1765 8641 2.772287 ACTAAGTGCAAGAGCTGGAAC 58.228 47.619 0.00 0.00 42.74 3.62
1776 8652 3.244561 CCTCCTTCCAGAAACTAAGTGCA 60.245 47.826 0.00 0.00 0.00 4.57
1793 8669 4.316823 TGTCCGCCTGGTCCTCCT 62.317 66.667 0.00 0.00 36.30 3.69
1843 8719 7.129425 AGAAGAGAGGAAGAGGTATATGTGTT 58.871 38.462 0.00 0.00 0.00 3.32
1880 9047 7.152645 AGCCATATGATCTTTTCAATTGATGC 58.847 34.615 9.40 0.00 38.03 3.91
1937 9111 4.862641 ATGGTTCCATAGGCAGTAAACT 57.137 40.909 2.14 0.00 0.00 2.66
1938 9112 5.914898 AAATGGTTCCATAGGCAGTAAAC 57.085 39.130 4.67 0.00 0.00 2.01
1939 9113 7.582719 AGATAAATGGTTCCATAGGCAGTAAA 58.417 34.615 4.67 0.00 0.00 2.01
1940 9114 7.149202 AGATAAATGGTTCCATAGGCAGTAA 57.851 36.000 4.67 0.00 0.00 2.24
1941 9115 6.763715 AGATAAATGGTTCCATAGGCAGTA 57.236 37.500 4.67 0.00 0.00 2.74
1942 9116 5.653255 AGATAAATGGTTCCATAGGCAGT 57.347 39.130 4.67 0.00 0.00 4.40
1943 9117 7.227156 ACTAAGATAAATGGTTCCATAGGCAG 58.773 38.462 4.67 0.51 0.00 4.85
1944 9118 7.149202 ACTAAGATAAATGGTTCCATAGGCA 57.851 36.000 4.67 0.00 0.00 4.75
1945 9119 8.465273 AAACTAAGATAAATGGTTCCATAGGC 57.535 34.615 4.67 0.00 0.00 3.93
1949 9123 8.903820 GCAGTAAACTAAGATAAATGGTTCCAT 58.096 33.333 0.00 0.00 0.00 3.41
1950 9124 7.338449 GGCAGTAAACTAAGATAAATGGTTCCA 59.662 37.037 0.00 0.00 0.00 3.53
1951 9125 7.556635 AGGCAGTAAACTAAGATAAATGGTTCC 59.443 37.037 0.00 0.00 0.00 3.62
1952 9126 8.507524 AGGCAGTAAACTAAGATAAATGGTTC 57.492 34.615 0.00 0.00 0.00 3.62
1954 9128 9.561069 CATAGGCAGTAAACTAAGATAAATGGT 57.439 33.333 0.00 0.00 0.00 3.55
1955 9129 9.003658 CCATAGGCAGTAAACTAAGATAAATGG 57.996 37.037 0.00 0.00 0.00 3.16
1956 9130 9.778741 TCCATAGGCAGTAAACTAAGATAAATG 57.221 33.333 0.00 0.00 0.00 2.32
1959 9133 9.998106 GATTCCATAGGCAGTAAACTAAGATAA 57.002 33.333 0.00 0.00 0.00 1.75
1960 9134 9.154632 TGATTCCATAGGCAGTAAACTAAGATA 57.845 33.333 0.00 0.00 0.00 1.98
1961 9135 8.034313 TGATTCCATAGGCAGTAAACTAAGAT 57.966 34.615 0.00 0.00 0.00 2.40
1962 9136 7.432148 TGATTCCATAGGCAGTAAACTAAGA 57.568 36.000 0.00 0.00 0.00 2.10
1963 9137 8.682936 AATGATTCCATAGGCAGTAAACTAAG 57.317 34.615 0.00 0.00 31.59 2.18
1966 9140 9.289782 GATAAATGATTCCATAGGCAGTAAACT 57.710 33.333 0.00 0.00 31.59 2.66
2034 9214 5.517322 TGGTTTTATACACAACAACACCC 57.483 39.130 0.00 0.00 0.00 4.61
2035 9215 5.456173 CGTTGGTTTTATACACAACAACACC 59.544 40.000 0.00 0.00 42.35 4.16
2038 9218 5.910723 CCTCGTTGGTTTTATACACAACAAC 59.089 40.000 0.00 0.00 42.35 3.32
2095 9275 5.718130 CCAGCCCCAATATTATCATGAATGT 59.282 40.000 0.00 0.00 0.00 2.71
2108 9288 0.036732 GATCGATGCCAGCCCCAATA 59.963 55.000 0.54 0.00 0.00 1.90
2115 9295 4.285292 CACAATTTAAGATCGATGCCAGC 58.715 43.478 0.54 0.00 0.00 4.85
2319 9544 3.366396 TGGTAAGAGCTCTAGAAGGTGG 58.634 50.000 18.59 0.00 35.33 4.61
2338 9566 7.312154 TGTTTCAACGGAGAAATTATCAATGG 58.688 34.615 7.62 0.00 39.46 3.16
2363 9591 6.306643 TGAAAACTTTGGGTCTTTCCATTT 57.693 33.333 0.00 0.00 36.58 2.32
2516 9751 5.308237 ACTGTTAAAGGAGAAGAGGTGTGAT 59.692 40.000 0.00 0.00 0.00 3.06
2517 9752 4.654262 ACTGTTAAAGGAGAAGAGGTGTGA 59.346 41.667 0.00 0.00 0.00 3.58
2528 9763 9.893305 CATAAAAGTTTACCACTGTTAAAGGAG 57.107 33.333 0.00 0.00 38.49 3.69
2541 9782 5.963586 GCATAGCGTCACATAAAAGTTTACC 59.036 40.000 0.00 0.00 0.00 2.85
2542 9783 5.963586 GGCATAGCGTCACATAAAAGTTTAC 59.036 40.000 0.00 0.00 0.00 2.01
2544 9785 4.457603 TGGCATAGCGTCACATAAAAGTTT 59.542 37.500 0.00 0.00 0.00 2.66
2557 9798 1.202114 CAAAATGTGGTGGCATAGCGT 59.798 47.619 0.00 0.00 0.00 5.07
2596 9838 4.868171 GGTCAAAAAGAACAAGGGACAAAC 59.132 41.667 0.00 0.00 32.78 2.93
2619 9861 2.758736 AAGCAGTCCAGCTAGTTCTG 57.241 50.000 0.00 0.00 45.89 3.02
2620 9862 3.778954 AAAAGCAGTCCAGCTAGTTCT 57.221 42.857 0.00 0.00 45.89 3.01
2629 9871 2.867624 AGCTGATGAAAAAGCAGTCCA 58.132 42.857 0.00 0.00 44.50 4.02
2641 9886 6.070824 TCCTAACTGTCATTGTTAGCTGATGA 60.071 38.462 0.00 0.00 43.08 2.92
2654 9899 6.875972 ACATTACTTCCTCCTAACTGTCAT 57.124 37.500 0.00 0.00 0.00 3.06
2655 9900 6.722590 TGTACATTACTTCCTCCTAACTGTCA 59.277 38.462 0.00 0.00 0.00 3.58
2656 9901 7.166691 TGTACATTACTTCCTCCTAACTGTC 57.833 40.000 0.00 0.00 0.00 3.51
2657 9902 7.399191 TGATGTACATTACTTCCTCCTAACTGT 59.601 37.037 10.30 0.00 33.35 3.55
2658 9903 7.782049 TGATGTACATTACTTCCTCCTAACTG 58.218 38.462 10.30 0.00 33.35 3.16
2662 9907 6.136857 AGCTGATGTACATTACTTCCTCCTA 58.863 40.000 10.30 0.00 33.35 2.94
2665 9910 8.718102 TTTTAGCTGATGTACATTACTTCCTC 57.282 34.615 10.30 0.00 33.35 3.71
2674 9919 9.890629 TCTGTAAGATTTTTAGCTGATGTACAT 57.109 29.630 8.43 8.43 38.67 2.29
2678 9923 9.507329 TTTCTCTGTAAGATTTTTAGCTGATGT 57.493 29.630 0.00 0.00 45.62 3.06
2679 9924 9.985318 CTTTCTCTGTAAGATTTTTAGCTGATG 57.015 33.333 0.00 0.00 45.62 3.07
2691 9936 7.768120 CCTACTGCAATTCTTTCTCTGTAAGAT 59.232 37.037 0.00 0.00 45.62 2.40
2692 9937 7.099764 CCTACTGCAATTCTTTCTCTGTAAGA 58.900 38.462 0.00 0.00 43.69 2.10
2708 9953 4.506095 GGGTACTTTCTTTCCCTACTGCAA 60.506 45.833 0.00 0.00 37.18 4.08
2709 9954 3.008704 GGGTACTTTCTTTCCCTACTGCA 59.991 47.826 0.00 0.00 37.18 4.41
2710 9955 3.607741 GGGTACTTTCTTTCCCTACTGC 58.392 50.000 0.00 0.00 37.18 4.40
2716 9961 3.326880 TGAGTGAGGGTACTTTCTTTCCC 59.673 47.826 0.00 0.00 40.16 3.97
2719 9964 3.244596 GGCTGAGTGAGGGTACTTTCTTT 60.245 47.826 0.00 0.00 0.00 2.52
2720 9965 2.303311 GGCTGAGTGAGGGTACTTTCTT 59.697 50.000 0.00 0.00 0.00 2.52
2721 9966 1.903183 GGCTGAGTGAGGGTACTTTCT 59.097 52.381 0.00 0.00 0.00 2.52
2722 9967 1.623811 TGGCTGAGTGAGGGTACTTTC 59.376 52.381 0.00 0.00 0.00 2.62
2724 9969 1.729586 TTGGCTGAGTGAGGGTACTT 58.270 50.000 0.00 0.00 0.00 2.24
2726 9971 2.152016 GTTTTGGCTGAGTGAGGGTAC 58.848 52.381 0.00 0.00 0.00 3.34
2727 9972 1.771854 TGTTTTGGCTGAGTGAGGGTA 59.228 47.619 0.00 0.00 0.00 3.69
2728 9973 0.550914 TGTTTTGGCTGAGTGAGGGT 59.449 50.000 0.00 0.00 0.00 4.34
2779 10028 3.054065 AGAAGATGTTGAGGCCTTAAGGG 60.054 47.826 23.06 5.18 35.18 3.95
2783 10032 6.384015 TGATTAGAGAAGATGTTGAGGCCTTA 59.616 38.462 6.77 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.