Multiple sequence alignment - TraesCS4B01G291600

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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 TraesCS4B01G291600 chr4B 100.000 1513 0 0 695 2207 576745295 576746807 0.000000e+00 2795.0
1 TraesCS4B01G291600 chr4B 100.000 588 0 0 1 588 576744601 576745188 0.000000e+00 1086.0
2 TraesCS4B01G291600 chr4B 91.713 362 25 4 1 361 601297303 601297660 4.230000e-137 497.0
3 TraesCS4B01G291600 chr4A 91.218 1002 38 18 695 1650 7177355 7176358 0.000000e+00 1317.0
4 TraesCS4B01G291600 chr4A 91.935 186 14 1 404 588 7177599 7177414 2.170000e-65 259.0
5 TraesCS4B01G291600 chr4D 92.078 669 31 8 994 1644 461465772 461466436 0.000000e+00 922.0
6 TraesCS4B01G291600 chr4D 91.736 363 22 5 1 362 206664627 206664982 4.230000e-137 497.0
7 TraesCS4B01G291600 chr4D 90.500 200 16 2 392 588 461465346 461465545 6.040000e-66 261.0
8 TraesCS4B01G291600 chr4D 94.505 91 5 0 909 999 461465658 461465748 8.220000e-30 141.0
9 TraesCS4B01G291600 chr4D 96.386 83 3 0 695 777 461465575 461465657 1.060000e-28 137.0
10 TraesCS4B01G291600 chr4D 80.000 165 22 10 396 552 437288270 437288431 6.440000e-21 111.0
11 TraesCS4B01G291600 chr2D 84.602 565 73 5 1651 2206 99729237 99728678 1.150000e-152 549.0
12 TraesCS4B01G291600 chr2D 89.498 219 14 2 992 1210 527393522 527393731 3.610000e-68 268.0
13 TraesCS4B01G291600 chr2D 88.235 102 7 2 1811 1908 46712415 46712515 1.380000e-22 117.0
14 TraesCS4B01G291600 chr7D 84.063 571 68 9 1648 2207 586773032 586773590 1.500000e-146 529.0
15 TraesCS4B01G291600 chr7D 83.051 177 17 10 392 558 602100912 602100739 4.910000e-32 148.0
16 TraesCS4B01G291600 chr1A 91.233 365 26 4 1 364 362063667 362063308 1.970000e-135 492.0
17 TraesCS4B01G291600 chr2B 83.243 555 69 10 1645 2184 74043799 74044344 2.550000e-134 488.0
18 TraesCS4B01G291600 chr2B 84.384 365 29 14 1 363 183431753 183432091 1.260000e-87 333.0
19 TraesCS4B01G291600 chr2B 89.954 219 13 2 992 1210 624541434 624541643 7.760000e-70 274.0
20 TraesCS4B01G291600 chr2A 84.242 495 64 5 1724 2207 66794835 66795326 9.230000e-129 470.0
21 TraesCS4B01G291600 chr2A 88.038 209 16 2 1000 1208 672348793 672348992 2.830000e-59 239.0
22 TraesCS4B01G291600 chr2A 78.378 111 17 5 1851 1958 711551133 711551027 5.090000e-07 65.8
23 TraesCS4B01G291600 chrUn 81.961 571 82 7 1648 2207 108923649 108923089 4.290000e-127 464.0
24 TraesCS4B01G291600 chrUn 83.161 386 53 5 1760 2136 108955754 108955372 2.100000e-90 342.0
25 TraesCS4B01G291600 chr5A 89.560 364 31 4 1 361 505422467 505422826 2.580000e-124 455.0
26 TraesCS4B01G291600 chr5A 82.749 342 45 11 35 372 58468733 58468402 2.140000e-75 292.0
27 TraesCS4B01G291600 chr5A 87.705 122 14 1 438 558 659886778 659886657 8.220000e-30 141.0
28 TraesCS4B01G291600 chr5A 77.465 213 42 6 1685 1894 47451835 47451626 2.980000e-24 122.0
29 TraesCS4B01G291600 chr7A 77.817 568 103 17 1651 2207 156321629 156322184 1.630000e-86 329.0
30 TraesCS4B01G291600 chr6B 82.609 368 43 15 1 364 2780836 2780486 2.750000e-79 305.0
31 TraesCS4B01G291600 chr7B 85.377 212 20 8 361 563 20425633 20425424 2.220000e-50 209.0
32 TraesCS4B01G291600 chr3D 89.231 130 11 2 429 555 463187053 463187182 2.270000e-35 159.0
33 TraesCS4B01G291600 chr1D 87.302 126 15 1 244 368 431326064 431326189 2.280000e-30 143.0
34 TraesCS4B01G291600 chr1D 80.460 174 21 10 398 561 423268544 423268374 1.070000e-23 121.0
35 TraesCS4B01G291600 chr5B 87.500 120 14 1 244 362 281628249 281628130 1.060000e-28 137.0
36 TraesCS4B01G291600 chr1B 81.609 174 19 10 392 555 572646863 572646693 4.940000e-27 132.0


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 TraesCS4B01G291600 chr4B 576744601 576746807 2206 False 1940.50 2795 100.00000 1 2207 2 chr4B.!!$F2 2206
1 TraesCS4B01G291600 chr4A 7176358 7177599 1241 True 788.00 1317 91.57650 404 1650 2 chr4A.!!$R1 1246
2 TraesCS4B01G291600 chr4D 461465346 461466436 1090 False 365.25 922 93.36725 392 1644 4 chr4D.!!$F3 1252
3 TraesCS4B01G291600 chr2D 99728678 99729237 559 True 549.00 549 84.60200 1651 2206 1 chr2D.!!$R1 555
4 TraesCS4B01G291600 chr7D 586773032 586773590 558 False 529.00 529 84.06300 1648 2207 1 chr7D.!!$F1 559
5 TraesCS4B01G291600 chr2B 74043799 74044344 545 False 488.00 488 83.24300 1645 2184 1 chr2B.!!$F1 539
6 TraesCS4B01G291600 chrUn 108923089 108923649 560 True 464.00 464 81.96100 1648 2207 1 chrUn.!!$R1 559
7 TraesCS4B01G291600 chr7A 156321629 156322184 555 False 329.00 329 77.81700 1651 2207 1 chr7A.!!$F1 556

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
335 336 0.593263 GCTTGCACTATGAATGCCGC 60.593 55.0 0.0 0.0 42.69 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1337 1372 0.179 CAATTACTGGGAGCTCCGCT 59.821 55.0 26.36 13.13 43.88 5.52 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
29 30 4.882671 ACATGGATTTATGTTCGTCAGC 57.117 40.909 0.00 0.00 38.05 4.26
30 31 4.517285 ACATGGATTTATGTTCGTCAGCT 58.483 39.130 0.00 0.00 38.05 4.24
31 32 4.943705 ACATGGATTTATGTTCGTCAGCTT 59.056 37.500 0.00 0.00 38.05 3.74
32 33 6.112734 ACATGGATTTATGTTCGTCAGCTTA 58.887 36.000 0.00 0.00 38.05 3.09
33 34 6.767902 ACATGGATTTATGTTCGTCAGCTTAT 59.232 34.615 0.00 0.00 38.05 1.73
34 35 7.931407 ACATGGATTTATGTTCGTCAGCTTATA 59.069 33.333 0.00 0.00 38.05 0.98
35 36 8.939929 CATGGATTTATGTTCGTCAGCTTATAT 58.060 33.333 0.00 0.00 0.00 0.86
85 86 7.692460 TTTTGTTGTGCTCAGATAATCATCT 57.308 32.000 0.00 0.00 42.52 2.90
86 87 6.915544 TTGTTGTGCTCAGATAATCATCTC 57.084 37.500 0.00 0.00 39.62 2.75
87 88 5.981174 TGTTGTGCTCAGATAATCATCTCA 58.019 37.500 0.00 0.00 39.62 3.27
88 89 6.408869 TGTTGTGCTCAGATAATCATCTCAA 58.591 36.000 0.00 0.00 39.62 3.02
89 90 6.537660 TGTTGTGCTCAGATAATCATCTCAAG 59.462 38.462 0.00 0.00 39.62 3.02
90 91 6.231258 TGTGCTCAGATAATCATCTCAAGT 57.769 37.500 0.00 0.00 39.62 3.16
91 92 6.279123 TGTGCTCAGATAATCATCTCAAGTC 58.721 40.000 0.00 0.00 39.62 3.01
92 93 5.401972 GTGCTCAGATAATCATCTCAAGTCG 59.598 44.000 0.00 0.00 39.62 4.18
93 94 5.068329 TGCTCAGATAATCATCTCAAGTCGT 59.932 40.000 0.00 0.00 39.62 4.34
94 95 5.982516 GCTCAGATAATCATCTCAAGTCGTT 59.017 40.000 0.00 0.00 39.62 3.85
95 96 6.478344 GCTCAGATAATCATCTCAAGTCGTTT 59.522 38.462 0.00 0.00 39.62 3.60
96 97 7.516470 GCTCAGATAATCATCTCAAGTCGTTTG 60.516 40.741 0.00 0.00 39.62 2.93
97 98 7.547227 TCAGATAATCATCTCAAGTCGTTTGA 58.453 34.615 5.32 5.32 43.40 2.69
98 99 8.200120 TCAGATAATCATCTCAAGTCGTTTGAT 58.800 33.333 5.77 0.00 44.48 2.57
99 100 9.468532 CAGATAATCATCTCAAGTCGTTTGATA 57.531 33.333 5.77 0.79 44.48 2.15
100 101 9.469807 AGATAATCATCTCAAGTCGTTTGATAC 57.530 33.333 5.77 0.00 44.48 2.24
101 102 9.249457 GATAATCATCTCAAGTCGTTTGATACA 57.751 33.333 5.77 0.00 44.48 2.29
102 103 9.770097 ATAATCATCTCAAGTCGTTTGATACAT 57.230 29.630 5.77 0.00 44.48 2.29
103 104 8.498054 AATCATCTCAAGTCGTTTGATACATT 57.502 30.769 5.77 1.77 44.48 2.71
104 105 7.294676 TCATCTCAAGTCGTTTGATACATTG 57.705 36.000 5.77 0.00 44.48 2.82
105 106 7.096551 TCATCTCAAGTCGTTTGATACATTGA 58.903 34.615 5.77 0.00 44.48 2.57
106 107 7.765819 TCATCTCAAGTCGTTTGATACATTGAT 59.234 33.333 5.77 2.76 44.48 2.57
107 108 7.905604 TCTCAAGTCGTTTGATACATTGATT 57.094 32.000 5.77 0.00 44.48 2.57
108 109 8.996024 TCTCAAGTCGTTTGATACATTGATTA 57.004 30.769 5.77 0.00 44.48 1.75
109 110 9.430623 TCTCAAGTCGTTTGATACATTGATTAA 57.569 29.630 5.77 0.00 44.48 1.40
115 116 9.781834 GTCGTTTGATACATTGATTAATTTCCA 57.218 29.630 0.00 0.00 0.00 3.53
137 138 9.921637 TTCCATTTGTTGTCTCAATATTAAACC 57.078 29.630 0.00 0.00 0.00 3.27
138 139 9.308000 TCCATTTGTTGTCTCAATATTAAACCT 57.692 29.630 0.00 0.00 0.00 3.50
159 160 7.625828 ACCTAACATAACCAAACTTATCAGC 57.374 36.000 0.00 0.00 0.00 4.26
160 161 7.402862 ACCTAACATAACCAAACTTATCAGCT 58.597 34.615 0.00 0.00 0.00 4.24
161 162 7.888546 ACCTAACATAACCAAACTTATCAGCTT 59.111 33.333 0.00 0.00 0.00 3.74
162 163 8.184192 CCTAACATAACCAAACTTATCAGCTTG 58.816 37.037 0.00 0.00 0.00 4.01
163 164 7.524717 AACATAACCAAACTTATCAGCTTGT 57.475 32.000 0.00 0.00 0.00 3.16
164 165 6.913170 ACATAACCAAACTTATCAGCTTGTG 58.087 36.000 0.00 0.00 0.00 3.33
165 166 3.923017 ACCAAACTTATCAGCTTGTGC 57.077 42.857 0.00 0.00 40.05 4.57
199 200 7.865706 ATTAAATACGAACATTTCTGCCTCT 57.134 32.000 0.00 0.00 30.84 3.69
200 201 8.958119 ATTAAATACGAACATTTCTGCCTCTA 57.042 30.769 0.00 0.00 30.84 2.43
201 202 8.958119 TTAAATACGAACATTTCTGCCTCTAT 57.042 30.769 0.00 0.00 30.84 1.98
203 204 7.948278 AATACGAACATTTCTGCCTCTATAC 57.052 36.000 0.00 0.00 0.00 1.47
204 205 4.694339 ACGAACATTTCTGCCTCTATACC 58.306 43.478 0.00 0.00 0.00 2.73
205 206 4.058817 CGAACATTTCTGCCTCTATACCC 58.941 47.826 0.00 0.00 0.00 3.69
206 207 4.202264 CGAACATTTCTGCCTCTATACCCT 60.202 45.833 0.00 0.00 0.00 4.34
207 208 5.685075 CGAACATTTCTGCCTCTATACCCTT 60.685 44.000 0.00 0.00 0.00 3.95
208 209 5.717119 ACATTTCTGCCTCTATACCCTTT 57.283 39.130 0.00 0.00 0.00 3.11
209 210 6.079712 ACATTTCTGCCTCTATACCCTTTT 57.920 37.500 0.00 0.00 0.00 2.27
210 211 6.494059 ACATTTCTGCCTCTATACCCTTTTT 58.506 36.000 0.00 0.00 0.00 1.94
322 323 9.616156 ATTAATATTGAATCCAAATTGCTTGCA 57.384 25.926 0.00 0.00 35.67 4.08
323 324 6.913873 ATATTGAATCCAAATTGCTTGCAC 57.086 33.333 0.00 0.00 35.67 4.57
324 325 4.339872 TTGAATCCAAATTGCTTGCACT 57.660 36.364 0.00 0.00 33.27 4.40
325 326 5.465532 TTGAATCCAAATTGCTTGCACTA 57.534 34.783 0.00 0.00 33.27 2.74
326 327 5.664294 TGAATCCAAATTGCTTGCACTAT 57.336 34.783 0.00 0.00 33.27 2.12
327 328 5.412640 TGAATCCAAATTGCTTGCACTATG 58.587 37.500 0.00 0.00 33.27 2.23
328 329 5.185442 TGAATCCAAATTGCTTGCACTATGA 59.815 36.000 0.00 0.00 33.27 2.15
329 330 5.664294 ATCCAAATTGCTTGCACTATGAA 57.336 34.783 0.00 0.00 33.27 2.57
330 331 5.664294 TCCAAATTGCTTGCACTATGAAT 57.336 34.783 0.00 0.00 33.27 2.57
331 332 5.412640 TCCAAATTGCTTGCACTATGAATG 58.587 37.500 0.00 0.00 33.27 2.67
332 333 4.033587 CCAAATTGCTTGCACTATGAATGC 59.966 41.667 0.00 0.00 43.68 3.56
333 334 2.945447 TTGCTTGCACTATGAATGCC 57.055 45.000 0.00 0.00 42.69 4.40
334 335 0.734309 TGCTTGCACTATGAATGCCG 59.266 50.000 0.00 0.00 42.69 5.69
335 336 0.593263 GCTTGCACTATGAATGCCGC 60.593 55.000 0.00 0.00 42.69 6.53
336 337 0.734309 CTTGCACTATGAATGCCGCA 59.266 50.000 0.00 0.00 42.69 5.69
337 338 0.734309 TTGCACTATGAATGCCGCAG 59.266 50.000 0.00 0.00 42.69 5.18
338 339 1.009222 GCACTATGAATGCCGCAGC 60.009 57.895 0.00 0.00 37.08 5.25
351 352 2.281208 GCAGCAACGTGTGGGGTA 60.281 61.111 0.00 0.00 0.00 3.69
352 353 1.674322 GCAGCAACGTGTGGGGTAT 60.674 57.895 0.00 0.00 0.00 2.73
353 354 1.241315 GCAGCAACGTGTGGGGTATT 61.241 55.000 0.00 0.00 0.00 1.89
354 355 1.946747 GCAGCAACGTGTGGGGTATTA 60.947 52.381 0.00 0.00 0.00 0.98
355 356 2.639065 CAGCAACGTGTGGGGTATTAT 58.361 47.619 0.00 0.00 0.00 1.28
356 357 2.612212 CAGCAACGTGTGGGGTATTATC 59.388 50.000 0.00 0.00 0.00 1.75
357 358 2.504175 AGCAACGTGTGGGGTATTATCT 59.496 45.455 0.00 0.00 0.00 1.98
358 359 3.707611 AGCAACGTGTGGGGTATTATCTA 59.292 43.478 0.00 0.00 0.00 1.98
359 360 4.056050 GCAACGTGTGGGGTATTATCTAG 58.944 47.826 0.00 0.00 0.00 2.43
360 361 4.442472 GCAACGTGTGGGGTATTATCTAGT 60.442 45.833 0.00 0.00 0.00 2.57
361 362 5.667466 CAACGTGTGGGGTATTATCTAGTT 58.333 41.667 0.00 0.00 0.00 2.24
362 363 5.945144 ACGTGTGGGGTATTATCTAGTTT 57.055 39.130 0.00 0.00 0.00 2.66
363 364 7.267128 CAACGTGTGGGGTATTATCTAGTTTA 58.733 38.462 0.00 0.00 0.00 2.01
364 365 7.422465 ACGTGTGGGGTATTATCTAGTTTAA 57.578 36.000 0.00 0.00 0.00 1.52
365 366 8.026396 ACGTGTGGGGTATTATCTAGTTTAAT 57.974 34.615 0.00 0.00 0.00 1.40
366 367 9.146586 ACGTGTGGGGTATTATCTAGTTTAATA 57.853 33.333 0.00 0.00 0.00 0.98
367 368 9.985730 CGTGTGGGGTATTATCTAGTTTAATAA 57.014 33.333 8.51 0.00 0.00 1.40
436 437 9.988350 CTATACAACCAAATCTCATTACACAAC 57.012 33.333 0.00 0.00 0.00 3.32
569 574 9.354673 GGGTTTCATCTAATTAATCAATCCTCA 57.645 33.333 0.00 0.00 0.00 3.86
742 748 7.374754 TCGTCGTGAAAAATAAACATTTCTGTG 59.625 33.333 0.00 0.00 35.22 3.66
804 810 4.186856 TCAGTTCATAACGCACTGATGA 57.813 40.909 0.00 0.00 41.60 2.92
805 811 3.926527 TCAGTTCATAACGCACTGATGAC 59.073 43.478 0.00 0.00 41.60 3.06
806 812 3.679502 CAGTTCATAACGCACTGATGACA 59.320 43.478 0.00 0.00 40.43 3.58
820 826 5.236695 CACTGATGACAGCAATCATTAGAGG 59.763 44.000 21.47 12.78 46.95 3.69
844 850 4.095782 GGATGTAAACTAAGCGCCATTGAA 59.904 41.667 2.29 0.00 0.00 2.69
955 961 1.461127 CTCTACAAGGCAAAGCGACAC 59.539 52.381 0.00 0.00 0.00 3.67
959 965 1.602377 ACAAGGCAAAGCGACACTTAC 59.398 47.619 0.00 0.00 37.75 2.34
970 976 1.071071 CGACACTTACCCAAGGAACCA 59.929 52.381 0.00 0.00 35.97 3.67
1058 1093 2.125512 GCTCATCTTCGTGCCGGT 60.126 61.111 1.90 0.00 0.00 5.28
1185 1220 2.893895 CGCATGTCGAGCCTGCAT 60.894 61.111 12.59 0.00 41.67 3.96
1278 1313 3.397613 GATTCCTGCGCTGGAGGCT 62.398 63.158 31.08 21.36 37.43 4.58
1305 1340 2.409948 GTGGGGACAGGATTCTTCAG 57.590 55.000 0.00 0.00 44.46 3.02
1337 1372 4.379813 GGCTGATTCTCAAATTTCTGCGAA 60.380 41.667 0.00 0.00 0.00 4.70
1432 1477 8.131100 TGTCAAATTGTTTCTTCAGACATCTTC 58.869 33.333 0.00 0.00 30.64 2.87
1433 1478 8.131100 GTCAAATTGTTTCTTCAGACATCTTCA 58.869 33.333 0.00 0.00 0.00 3.02
1438 1483 7.658179 TGTTTCTTCAGACATCTTCATGTAC 57.342 36.000 0.00 0.00 43.79 2.90
1443 1488 6.875726 TCTTCAGACATCTTCATGTACCAAAG 59.124 38.462 0.00 0.00 43.79 2.77
1482 1527 0.312102 GGTTCAGGCTTTGTGTGCTC 59.688 55.000 0.00 0.00 0.00 4.26
1500 1545 0.603569 TCTCGCCCTCTTTCTGACAC 59.396 55.000 0.00 0.00 0.00 3.67
1569 1621 9.974980 TTTACTGAATGAAGTGTAATTTTTCCC 57.025 29.630 0.00 0.00 0.00 3.97
1587 1639 1.134280 CCCCTAACAGACCATGCAGAG 60.134 57.143 0.00 0.00 0.00 3.35
1613 1665 1.816863 CGGTAGAGCCATACGCCCAT 61.817 60.000 0.00 0.00 38.78 4.00
1644 1696 4.191544 GTCATTCAGGGAAATGATCGACA 58.808 43.478 2.94 0.00 44.92 4.35
1650 1702 3.758554 CAGGGAAATGATCGACAGGTTTT 59.241 43.478 0.00 0.00 0.00 2.43
1651 1703 4.218417 CAGGGAAATGATCGACAGGTTTTT 59.782 41.667 0.00 0.00 0.00 1.94
1681 1733 1.059913 CGGCCCCTAAGGATCTCAAT 58.940 55.000 0.00 0.00 38.24 2.57
1682 1734 1.421646 CGGCCCCTAAGGATCTCAATT 59.578 52.381 0.00 0.00 38.24 2.32
1710 1763 1.128200 AAAAAGAAGGTGGTTGCCCC 58.872 50.000 0.00 0.00 0.00 5.80
1721 1774 3.952967 GGTGGTTGCCCCGTTAATTAATA 59.047 43.478 0.31 0.00 35.15 0.98
1756 1809 3.359695 AACCGTTACAATAGCCCACAT 57.640 42.857 0.00 0.00 0.00 3.21
1779 1832 2.924101 TAAACCGGCCGACCTGGT 60.924 61.111 30.73 13.24 42.36 4.00
1848 1902 0.108992 GGTCGTCACCAAGCGTCATA 60.109 55.000 0.00 0.00 43.17 2.15
1854 1908 3.262420 GTCACCAAGCGTCATAGTCATT 58.738 45.455 0.00 0.00 0.00 2.57
1868 1922 3.088789 AGTCATTACTCCTCCACGAGT 57.911 47.619 0.00 0.00 45.15 4.18
1891 1949 0.526211 CGACTCCGACTTCACCATCA 59.474 55.000 0.00 0.00 38.22 3.07
1892 1950 1.067846 CGACTCCGACTTCACCATCAA 60.068 52.381 0.00 0.00 38.22 2.57
1910 1968 0.818040 AAACTTCCGCCAACGAAGCT 60.818 50.000 0.00 0.00 43.93 3.74
1934 1992 2.719354 GCCACAAACGCCGAAACT 59.281 55.556 0.00 0.00 0.00 2.66
1942 2000 2.813474 CGCCGAAACTCATGCCGA 60.813 61.111 0.00 0.00 0.00 5.54
1955 2013 4.114997 GCCGACCCATGCCAAACG 62.115 66.667 0.00 0.00 0.00 3.60
1973 2031 4.980805 GTTGACCGCCGGTGCAGA 62.981 66.667 16.53 0.00 35.25 4.26
1991 2049 2.678836 CAGACGTCTAGACAACTCCGAT 59.321 50.000 19.57 0.20 0.00 4.18
2000 2058 5.888724 TCTAGACAACTCCGATTGAGAAGAT 59.111 40.000 0.00 0.00 44.42 2.40
2030 2097 2.435372 TAGAAGAAATGGGCGCCAAT 57.565 45.000 30.85 22.12 36.95 3.16
2039 2106 2.568090 GGCGCCAATCAACACCTG 59.432 61.111 24.80 0.00 0.00 4.00
2044 2111 1.926511 GCCAATCAACACCTGCTCGG 61.927 60.000 0.00 0.00 39.35 4.63
2106 2175 3.127352 GAAGCTCCGACTCCGCGAT 62.127 63.158 8.23 0.00 0.00 4.58
2126 2195 1.065491 TGGCATGGCAAGACGTAGAAT 60.065 47.619 21.13 0.00 0.00 2.40
2136 2205 4.142447 GCAAGACGTAGAATAGACCTGTCA 60.142 45.833 0.00 0.00 0.00 3.58
2145 2214 1.324383 TAGACCTGTCAAGCACGTCA 58.676 50.000 0.00 0.00 36.17 4.35
2172 2241 1.071471 CCGACAACTGAAGCCCTGT 59.929 57.895 0.00 0.00 0.00 4.00
2175 2244 0.951040 GACAACTGAAGCCCTGTCGG 60.951 60.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 7.283127 AGCTGACGAACATAAATCCATGTTTAT 59.717 33.333 3.23 0.00 46.53 1.40
6 7 5.415701 AGCTGACGAACATAAATCCATGTTT 59.584 36.000 3.23 0.00 46.53 2.83
8 9 4.517285 AGCTGACGAACATAAATCCATGT 58.483 39.130 0.00 0.00 40.90 3.21
9 10 5.490139 AAGCTGACGAACATAAATCCATG 57.510 39.130 0.00 0.00 0.00 3.66
60 61 8.114331 AGATGATTATCTGAGCACAACAAAAA 57.886 30.769 0.00 0.00 42.04 1.94
61 62 7.391275 TGAGATGATTATCTGAGCACAACAAAA 59.609 33.333 4.45 0.00 43.63 2.44
62 63 6.880529 TGAGATGATTATCTGAGCACAACAAA 59.119 34.615 4.45 0.00 43.63 2.83
63 64 6.408869 TGAGATGATTATCTGAGCACAACAA 58.591 36.000 4.45 0.00 43.63 2.83
64 65 5.981174 TGAGATGATTATCTGAGCACAACA 58.019 37.500 4.45 0.00 43.63 3.33
65 66 6.538021 ACTTGAGATGATTATCTGAGCACAAC 59.462 38.462 4.45 0.00 43.63 3.32
66 67 6.647229 ACTTGAGATGATTATCTGAGCACAA 58.353 36.000 4.45 2.10 43.63 3.33
67 68 6.231258 ACTTGAGATGATTATCTGAGCACA 57.769 37.500 4.45 0.00 43.63 4.57
68 69 5.401972 CGACTTGAGATGATTATCTGAGCAC 59.598 44.000 4.45 1.50 43.63 4.40
69 70 5.068329 ACGACTTGAGATGATTATCTGAGCA 59.932 40.000 4.45 0.00 43.63 4.26
70 71 5.527951 ACGACTTGAGATGATTATCTGAGC 58.472 41.667 4.45 0.00 43.63 4.26
71 72 7.704047 TCAAACGACTTGAGATGATTATCTGAG 59.296 37.037 4.45 5.49 43.63 3.35
72 73 7.547227 TCAAACGACTTGAGATGATTATCTGA 58.453 34.615 4.45 0.00 43.63 3.27
73 74 7.761651 TCAAACGACTTGAGATGATTATCTG 57.238 36.000 4.45 0.00 43.63 2.90
89 90 9.781834 TGGAAATTAATCAATGTATCAAACGAC 57.218 29.630 0.00 0.00 0.00 4.34
111 112 9.921637 GGTTTAATATTGAGACAACAAATGGAA 57.078 29.630 0.00 0.00 33.44 3.53
112 113 9.308000 AGGTTTAATATTGAGACAACAAATGGA 57.692 29.630 0.00 0.00 33.44 3.41
133 134 8.520351 GCTGATAAGTTTGGTTATGTTAGGTTT 58.480 33.333 0.00 0.00 0.00 3.27
134 135 7.888546 AGCTGATAAGTTTGGTTATGTTAGGTT 59.111 33.333 0.00 0.00 0.00 3.50
135 136 7.402862 AGCTGATAAGTTTGGTTATGTTAGGT 58.597 34.615 0.00 0.00 0.00 3.08
136 137 7.865706 AGCTGATAAGTTTGGTTATGTTAGG 57.134 36.000 0.00 0.00 0.00 2.69
137 138 8.730680 ACAAGCTGATAAGTTTGGTTATGTTAG 58.269 33.333 11.07 0.00 34.89 2.34
138 139 8.511321 CACAAGCTGATAAGTTTGGTTATGTTA 58.489 33.333 11.07 0.00 34.89 2.41
139 140 7.370383 CACAAGCTGATAAGTTTGGTTATGTT 58.630 34.615 11.07 0.00 34.89 2.71
140 141 6.570378 GCACAAGCTGATAAGTTTGGTTATGT 60.570 38.462 11.07 0.00 37.91 2.29
141 142 5.801947 GCACAAGCTGATAAGTTTGGTTATG 59.198 40.000 11.07 1.94 37.91 1.90
142 143 5.954335 GCACAAGCTGATAAGTTTGGTTAT 58.046 37.500 11.07 0.00 37.91 1.89
143 144 5.371115 GCACAAGCTGATAAGTTTGGTTA 57.629 39.130 11.07 0.00 37.91 2.85
144 145 4.243007 GCACAAGCTGATAAGTTTGGTT 57.757 40.909 11.07 0.00 37.91 3.67
145 146 3.923017 GCACAAGCTGATAAGTTTGGT 57.077 42.857 11.07 0.00 37.91 3.67
173 174 9.391006 AGAGGCAGAAATGTTCGTATTTAATAA 57.609 29.630 0.00 0.00 30.78 1.40
174 175 8.958119 AGAGGCAGAAATGTTCGTATTTAATA 57.042 30.769 0.00 0.00 30.78 0.98
175 176 7.865706 AGAGGCAGAAATGTTCGTATTTAAT 57.134 32.000 0.00 0.00 30.78 1.40
176 177 8.958119 ATAGAGGCAGAAATGTTCGTATTTAA 57.042 30.769 0.00 0.00 30.78 1.52
177 178 9.472361 GTATAGAGGCAGAAATGTTCGTATTTA 57.528 33.333 0.00 0.00 30.78 1.40
178 179 7.441458 GGTATAGAGGCAGAAATGTTCGTATTT 59.559 37.037 0.00 0.00 33.19 1.40
179 180 6.929606 GGTATAGAGGCAGAAATGTTCGTATT 59.070 38.462 0.00 0.00 34.02 1.89
180 181 6.456501 GGTATAGAGGCAGAAATGTTCGTAT 58.543 40.000 0.00 0.00 34.02 3.06
181 182 5.221382 GGGTATAGAGGCAGAAATGTTCGTA 60.221 44.000 0.00 0.00 34.02 3.43
182 183 4.443034 GGGTATAGAGGCAGAAATGTTCGT 60.443 45.833 0.00 0.00 34.02 3.85
183 184 4.058817 GGGTATAGAGGCAGAAATGTTCG 58.941 47.826 0.00 0.00 34.02 3.95
184 185 5.297569 AGGGTATAGAGGCAGAAATGTTC 57.702 43.478 0.00 0.00 0.00 3.18
185 186 5.717119 AAGGGTATAGAGGCAGAAATGTT 57.283 39.130 0.00 0.00 0.00 2.71
186 187 5.717119 AAAGGGTATAGAGGCAGAAATGT 57.283 39.130 0.00 0.00 0.00 2.71
296 297 9.616156 TGCAAGCAATTTGGATTCAATATTAAT 57.384 25.926 0.00 0.00 37.26 1.40
297 298 8.881743 GTGCAAGCAATTTGGATTCAATATTAA 58.118 29.630 0.00 0.00 39.44 1.40
298 299 8.259411 AGTGCAAGCAATTTGGATTCAATATTA 58.741 29.630 0.00 0.00 39.44 0.98
299 300 7.107542 AGTGCAAGCAATTTGGATTCAATATT 58.892 30.769 0.00 0.00 39.44 1.28
300 301 6.646267 AGTGCAAGCAATTTGGATTCAATAT 58.354 32.000 0.00 0.00 39.44 1.28
301 302 6.040209 AGTGCAAGCAATTTGGATTCAATA 57.960 33.333 0.00 0.00 39.44 1.90
302 303 4.901868 AGTGCAAGCAATTTGGATTCAAT 58.098 34.783 0.00 0.00 39.44 2.57
303 304 4.339872 AGTGCAAGCAATTTGGATTCAA 57.660 36.364 0.00 0.00 39.44 2.69
304 305 5.185442 TCATAGTGCAAGCAATTTGGATTCA 59.815 36.000 11.72 0.00 39.44 2.57
305 306 5.653507 TCATAGTGCAAGCAATTTGGATTC 58.346 37.500 11.72 0.00 39.44 2.52
306 307 5.664294 TCATAGTGCAAGCAATTTGGATT 57.336 34.783 11.72 0.00 39.44 3.01
307 308 5.664294 TTCATAGTGCAAGCAATTTGGAT 57.336 34.783 11.72 0.00 39.44 3.41
308 309 5.412640 CATTCATAGTGCAAGCAATTTGGA 58.587 37.500 11.72 5.00 37.26 3.53
309 310 4.033587 GCATTCATAGTGCAAGCAATTTGG 59.966 41.667 11.72 0.05 42.08 3.28
310 311 4.033587 GGCATTCATAGTGCAAGCAATTTG 59.966 41.667 0.00 3.42 44.25 2.32
311 312 4.186159 GGCATTCATAGTGCAAGCAATTT 58.814 39.130 0.00 0.00 44.25 1.82
312 313 3.735820 CGGCATTCATAGTGCAAGCAATT 60.736 43.478 0.00 0.00 44.25 2.32
313 314 2.223641 CGGCATTCATAGTGCAAGCAAT 60.224 45.455 0.00 0.00 44.25 3.56
314 315 1.132834 CGGCATTCATAGTGCAAGCAA 59.867 47.619 0.00 0.00 44.25 3.91
315 316 0.734309 CGGCATTCATAGTGCAAGCA 59.266 50.000 0.00 0.00 44.25 3.91
316 317 0.593263 GCGGCATTCATAGTGCAAGC 60.593 55.000 0.00 1.83 44.25 4.01
317 318 0.734309 TGCGGCATTCATAGTGCAAG 59.266 50.000 0.00 0.00 44.25 4.01
318 319 0.734309 CTGCGGCATTCATAGTGCAA 59.266 50.000 1.75 0.00 44.25 4.08
319 320 1.717791 GCTGCGGCATTCATAGTGCA 61.718 55.000 14.08 0.00 44.25 4.57
320 321 1.009222 GCTGCGGCATTCATAGTGC 60.009 57.895 14.08 0.00 41.78 4.40
321 322 2.396700 TGCTGCGGCATTCATAGTG 58.603 52.632 18.37 0.00 44.28 2.74
322 323 4.961637 TGCTGCGGCATTCATAGT 57.038 50.000 18.37 0.00 44.28 2.12
334 335 1.241315 AATACCCCACACGTTGCTGC 61.241 55.000 0.00 0.00 0.00 5.25
335 336 2.102070 TAATACCCCACACGTTGCTG 57.898 50.000 0.00 0.00 0.00 4.41
336 337 2.504175 AGATAATACCCCACACGTTGCT 59.496 45.455 0.00 0.00 0.00 3.91
337 338 2.914059 AGATAATACCCCACACGTTGC 58.086 47.619 0.00 0.00 0.00 4.17
338 339 5.272283 ACTAGATAATACCCCACACGTTG 57.728 43.478 0.00 0.00 0.00 4.10
339 340 5.945144 AACTAGATAATACCCCACACGTT 57.055 39.130 0.00 0.00 0.00 3.99
340 341 5.945144 AAACTAGATAATACCCCACACGT 57.055 39.130 0.00 0.00 0.00 4.49
341 342 9.985730 TTATTAAACTAGATAATACCCCACACG 57.014 33.333 0.00 0.00 0.00 4.49
530 534 1.336440 TGAAACCCATCAGTTGTTGCG 59.664 47.619 0.00 0.00 0.00 4.85
561 566 2.482664 CGGGTCAGTCTCATGAGGATTG 60.483 54.545 22.42 16.78 0.00 2.67
802 808 3.114606 TCCCCTCTAATGATTGCTGTCA 58.885 45.455 0.00 0.00 0.00 3.58
804 810 3.461085 ACATCCCCTCTAATGATTGCTGT 59.539 43.478 0.00 0.00 0.00 4.40
805 811 4.096190 ACATCCCCTCTAATGATTGCTG 57.904 45.455 0.00 0.00 0.00 4.41
806 812 5.912149 TTACATCCCCTCTAATGATTGCT 57.088 39.130 0.00 0.00 0.00 3.91
820 826 2.032680 TGGCGCTTAGTTTACATCCC 57.967 50.000 7.64 0.00 0.00 3.85
844 850 3.299503 GACCCTGGTTGATTATTGGCAT 58.700 45.455 0.00 0.00 0.00 4.40
894 900 8.690203 TGCTTGCATATATAGCCTTCTTTTTA 57.310 30.769 4.93 0.00 34.03 1.52
955 961 3.255888 GCTTTCTTGGTTCCTTGGGTAAG 59.744 47.826 0.00 0.00 0.00 2.34
959 965 2.001076 AGCTTTCTTGGTTCCTTGGG 57.999 50.000 0.00 0.00 0.00 4.12
970 976 1.481363 GGCCGTCTAGGTAGCTTTCTT 59.519 52.381 0.00 0.00 43.70 2.52
1278 1313 4.308458 CTGTCCCCACGTTGGCGA 62.308 66.667 0.00 0.00 42.00 5.54
1285 1320 0.613260 TGAAGAATCCTGTCCCCACG 59.387 55.000 0.00 0.00 0.00 4.94
1297 1332 1.277557 AGCCTCACGAAGCTGAAGAAT 59.722 47.619 0.00 0.00 38.11 2.40
1305 1340 1.285578 GAGAATCAGCCTCACGAAGC 58.714 55.000 0.00 0.00 33.17 3.86
1337 1372 0.179000 CAATTACTGGGAGCTCCGCT 59.821 55.000 26.36 13.13 43.88 5.52
1432 1477 5.068234 TCGTAAGTCCTCTTTGGTACATG 57.932 43.478 0.00 0.00 36.89 3.21
1433 1478 5.476614 GTTCGTAAGTCCTCTTTGGTACAT 58.523 41.667 0.00 0.00 36.89 2.29
1438 1483 3.064931 GTGGTTCGTAAGTCCTCTTTGG 58.935 50.000 0.00 0.00 35.36 3.28
1443 1488 2.609737 CCACTGTGGTTCGTAAGTCCTC 60.610 54.545 18.76 0.00 33.06 3.71
1482 1527 0.734253 CGTGTCAGAAAGAGGGCGAG 60.734 60.000 0.00 0.00 0.00 5.03
1500 1545 3.726517 CAGCCGCCTGGAAACACG 61.727 66.667 0.00 0.00 37.49 4.49
1569 1621 1.209019 AGCTCTGCATGGTCTGTTAGG 59.791 52.381 0.00 0.00 0.00 2.69
1613 1665 0.888736 CCCTGAATGACACGTTGGCA 60.889 55.000 0.00 0.00 41.29 4.92
1651 1703 2.660670 TAGGGGCCGAGTTTGAAAAA 57.339 45.000 0.00 0.00 0.00 1.94
1652 1704 2.510613 CTTAGGGGCCGAGTTTGAAAA 58.489 47.619 0.00 0.00 0.00 2.29
1653 1705 1.271707 CCTTAGGGGCCGAGTTTGAAA 60.272 52.381 0.00 0.00 0.00 2.69
1654 1706 0.326927 CCTTAGGGGCCGAGTTTGAA 59.673 55.000 0.00 0.00 0.00 2.69
1655 1707 0.545787 TCCTTAGGGGCCGAGTTTGA 60.546 55.000 0.00 0.00 34.39 2.69
1762 1815 2.924101 ACCAGGTCGGCCGGTTTA 60.924 61.111 27.83 1.61 38.07 2.01
1779 1832 0.179067 GTGTTTCTCCGTGTGGGTGA 60.179 55.000 0.00 0.00 36.54 4.02
1848 1902 3.018149 GACTCGTGGAGGAGTAATGACT 58.982 50.000 2.08 0.00 46.85 3.41
1854 1908 1.025113 CGCTGACTCGTGGAGGAGTA 61.025 60.000 2.08 0.00 46.85 2.59
1868 1922 1.579932 GTGAAGTCGGAGTCGCTGA 59.420 57.895 0.00 0.00 36.13 4.26
1891 1949 0.818040 AGCTTCGTTGGCGGAAGTTT 60.818 50.000 12.37 2.16 38.89 2.66
1892 1950 1.227853 AGCTTCGTTGGCGGAAGTT 60.228 52.632 12.37 5.73 38.89 2.66
1910 1968 3.033764 GCGTTTGTGGCGACGAGA 61.034 61.111 0.00 0.00 41.53 4.04
1934 1992 2.778055 TTTGGCATGGGTCGGCATGA 62.778 55.000 0.00 0.00 38.88 3.07
1942 2000 1.152652 TCAACCGTTTGGCATGGGT 60.153 52.632 0.00 2.84 39.70 4.51
1973 2031 3.079578 TCAATCGGAGTTGTCTAGACGT 58.920 45.455 17.85 5.20 0.00 4.34
1991 2049 8.597167 TCTTCTATCTTTTGGTGATCTTCTCAA 58.403 33.333 0.00 0.00 35.07 3.02
2000 2058 5.418840 GCCCATTTCTTCTATCTTTTGGTGA 59.581 40.000 0.00 0.00 0.00 4.02
2030 2097 1.666011 GTCTCCGAGCAGGTGTTGA 59.334 57.895 0.00 0.00 41.99 3.18
2039 2106 2.047179 GGTTGGTGGTCTCCGAGC 60.047 66.667 0.00 0.00 33.14 5.03
2044 2111 1.134220 TGACAAGTGGTTGGTGGTCTC 60.134 52.381 0.00 0.00 38.07 3.36
2106 2175 0.323302 TTCTACGTCTTGCCATGCCA 59.677 50.000 0.00 0.00 0.00 4.92
2115 2184 5.393243 GCTTGACAGGTCTATTCTACGTCTT 60.393 44.000 0.00 0.00 0.00 3.01
2136 2205 0.250338 GGTTCTTCCCTGACGTGCTT 60.250 55.000 0.00 0.00 0.00 3.91
2145 2214 1.420430 TCAGTTGTCGGTTCTTCCCT 58.580 50.000 0.00 0.00 0.00 4.20
2184 2253 0.963856 CGATGATGATGGCCATGGGG 60.964 60.000 26.56 0.84 35.17 4.96
2187 2256 2.699251 CAACGATGATGATGGCCATG 57.301 50.000 26.56 9.41 35.17 3.66


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

AutoCloner maintained by Alex Coulton.