Multiple sequence alignment - TraesCS4A01G059000

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 TraesCS4A01G059000 chr4A 100.000 5234 0 0 1 5234 54110986 54105753 0.000000e+00 9666.0
1 TraesCS4A01G059000 chr4A 75.203 617 121 25 2893 3499 532794047 532794641 4.020000e-66 263.0
2 TraesCS4A01G059000 chr4A 78.710 310 62 2 3800 4107 532796841 532797148 2.470000e-48 204.0
3 TraesCS4A01G059000 chr4D 95.036 4150 128 33 829 4938 397097294 397093183 0.000000e+00 6451.0
4 TraesCS4A01G059000 chr4D 91.447 304 13 5 4932 5234 397093152 397092861 6.310000e-109 405.0
5 TraesCS4A01G059000 chr4D 85.950 363 41 7 482 838 397097671 397097313 3.830000e-101 379.0
6 TraesCS4A01G059000 chr4D 76.689 592 97 31 2921 3499 63588252 63587689 1.840000e-74 291.0
7 TraesCS4A01G059000 chr4D 92.903 155 7 3 330 482 397098351 397098199 6.820000e-54 222.0
8 TraesCS4A01G059000 chr4D 78.827 307 59 4 3804 4107 63585447 63585144 8.890000e-48 202.0
9 TraesCS4A01G059000 chr4D 93.636 110 7 0 1 110 397098606 397098497 1.170000e-36 165.0
10 TraesCS4A01G059000 chr4B 94.745 4015 159 25 687 4666 489091260 489087263 0.000000e+00 6198.0
11 TraesCS4A01G059000 chr4B 82.420 785 67 29 3063 3816 496819147 496818403 2.070000e-173 619.0
12 TraesCS4A01G059000 chr4B 94.161 274 11 3 4669 4938 489087128 489086856 3.770000e-111 412.0
13 TraesCS4A01G059000 chr4B 89.206 315 13 6 4934 5234 489086823 489086516 1.780000e-99 374.0
14 TraesCS4A01G059000 chr4B 76.206 622 113 32 2893 3498 94211568 94210966 3.960000e-76 296.0
15 TraesCS4A01G059000 chr7B 80.333 600 96 12 2978 3569 713041560 713042145 8.050000e-118 435.0
16 TraesCS4A01G059000 chr7A 79.602 603 97 16 2978 3570 712179877 712180463 4.880000e-110 409.0
17 TraesCS4A01G059000 chr7A 86.395 147 20 0 3804 3950 712180956 712181102 1.510000e-35 161.0
18 TraesCS4A01G059000 chr2A 73.165 790 184 26 1253 2031 430954582 430953810 5.200000e-65 259.0
19 TraesCS4A01G059000 chr2A 97.059 34 1 0 3261 3294 763869387 763869420 2.040000e-04 58.4
20 TraesCS4A01G059000 chr2D 74.355 620 147 12 1400 2013 308982907 308983520 2.420000e-63 254.0
21 TraesCS4A01G059000 chr1B 74.878 617 123 25 2893 3499 222209123 222209717 8.700000e-63 252.0
22 TraesCS4A01G059000 chr1B 81.977 172 17 9 3800 3962 687276778 687276612 3.290000e-27 134.0
23 TraesCS4A01G059000 chr7D 85.714 147 21 0 3804 3950 618489480 618489626 7.020000e-34 156.0
24 TraesCS4A01G059000 chr1A 80.814 172 19 8 3800 3962 592529385 592529219 7.120000e-24 122.0
25 TraesCS4A01G059000 chr5D 82.759 116 15 3 3806 3920 11950020 11949909 1.200000e-16 99.0


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 TraesCS4A01G059000 chr4A 54105753 54110986 5233 True 9666.0 9666 100.0000 1 5234 1 chr4A.!!$R1 5233
1 TraesCS4A01G059000 chr4A 532794047 532797148 3101 False 233.5 263 76.9565 2893 4107 2 chr4A.!!$F1 1214
2 TraesCS4A01G059000 chr4D 397092861 397098606 5745 True 1524.4 6451 91.7944 1 5234 5 chr4D.!!$R2 5233
3 TraesCS4A01G059000 chr4D 63585144 63588252 3108 True 246.5 291 77.7580 2921 4107 2 chr4D.!!$R1 1186
4 TraesCS4A01G059000 chr4B 489086516 489091260 4744 True 2328.0 6198 92.7040 687 5234 3 chr4B.!!$R3 4547
5 TraesCS4A01G059000 chr4B 496818403 496819147 744 True 619.0 619 82.4200 3063 3816 1 chr4B.!!$R2 753
6 TraesCS4A01G059000 chr4B 94210966 94211568 602 True 296.0 296 76.2060 2893 3498 1 chr4B.!!$R1 605
7 TraesCS4A01G059000 chr7B 713041560 713042145 585 False 435.0 435 80.3330 2978 3569 1 chr7B.!!$F1 591
8 TraesCS4A01G059000 chr7A 712179877 712181102 1225 False 285.0 409 82.9985 2978 3950 2 chr7A.!!$F1 972
9 TraesCS4A01G059000 chr2A 430953810 430954582 772 True 259.0 259 73.1650 1253 2031 1 chr2A.!!$R1 778
10 TraesCS4A01G059000 chr2D 308982907 308983520 613 False 254.0 254 74.3550 1400 2013 1 chr2D.!!$F1 613
11 TraesCS4A01G059000 chr1B 222209123 222209717 594 False 252.0 252 74.8780 2893 3499 1 chr1B.!!$F1 606

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
318 325 0.032815 TTTGCTCGTGTCACGGATGA 59.967 50.0 24.33 4.95 42.81 2.92 F
540 1074 0.102300 AGCAAAAACAGGGCACGTTC 59.898 50.0 0.00 0.00 0.00 3.95 F
1044 1629 0.115745 ACACCTTTCTCCTCCCCGTA 59.884 55.0 0.00 0.00 0.00 4.02 F
2353 2938 0.178950 ATCGATAGGGGAGCTGAGCA 60.179 55.0 7.39 0.00 0.00 4.26 F
3786 6634 1.460504 ATGTGGCTGCATTCTCTGTG 58.539 50.0 0.50 0.00 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1246 1831 1.820481 CGGAGAGGTCGAGGGAGAC 60.820 68.421 0.00 0.0 40.25 3.36 R
2332 2917 0.246086 CTCAGCTCCCCTATCGATGC 59.754 60.000 8.54 1.1 0.00 3.91 R
2712 3297 0.038526 ACAGGCGGTTGTACGAGAAG 60.039 55.000 0.00 0.0 35.47 2.85 R
3810 6659 1.292223 GACCTTCAGCGTGTAGGCA 59.708 57.895 9.46 0.0 38.34 4.75 R
4971 8036 0.037697 TGCCTGCCTTGTACGTAGTG 60.038 55.000 0.00 0.0 45.73 2.74 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
95 96 9.635404 AGTAATATCTATAGTGTAGCTCCCATC 57.365 37.037 0.00 0.00 0.00 3.51
96 97 9.409918 GTAATATCTATAGTGTAGCTCCCATCA 57.590 37.037 0.00 0.00 0.00 3.07
100 101 7.704578 TCTATAGTGTAGCTCCCATCATAAC 57.295 40.000 0.00 0.00 0.00 1.89
101 102 7.238710 TCTATAGTGTAGCTCCCATCATAACA 58.761 38.462 0.00 0.00 0.00 2.41
102 103 6.942163 ATAGTGTAGCTCCCATCATAACAT 57.058 37.500 0.00 0.00 0.00 2.71
103 104 4.965814 AGTGTAGCTCCCATCATAACATG 58.034 43.478 0.00 0.00 0.00 3.21
104 105 4.410228 AGTGTAGCTCCCATCATAACATGT 59.590 41.667 0.00 0.00 0.00 3.21
105 106 5.602561 AGTGTAGCTCCCATCATAACATGTA 59.397 40.000 0.00 0.00 0.00 2.29
106 107 6.270927 AGTGTAGCTCCCATCATAACATGTAT 59.729 38.462 0.00 0.00 0.00 2.29
107 108 7.454694 AGTGTAGCTCCCATCATAACATGTATA 59.545 37.037 0.00 0.00 0.00 1.47
108 109 8.094548 GTGTAGCTCCCATCATAACATGTATAA 58.905 37.037 0.00 0.00 0.00 0.98
109 110 8.825774 TGTAGCTCCCATCATAACATGTATAAT 58.174 33.333 0.00 0.00 0.00 1.28
110 111 9.672673 GTAGCTCCCATCATAACATGTATAATT 57.327 33.333 0.00 0.00 0.00 1.40
111 112 8.571461 AGCTCCCATCATAACATGTATAATTG 57.429 34.615 0.00 0.00 0.00 2.32
112 113 8.166061 AGCTCCCATCATAACATGTATAATTGT 58.834 33.333 0.00 0.00 0.00 2.71
113 114 8.454106 GCTCCCATCATAACATGTATAATTGTC 58.546 37.037 0.00 0.00 0.00 3.18
114 115 9.730705 CTCCCATCATAACATGTATAATTGTCT 57.269 33.333 0.00 0.00 0.00 3.41
140 141 4.689612 ATGTAGCTCCCATCATAACGTT 57.310 40.909 5.88 5.88 0.00 3.99
150 151 6.156519 TCCCATCATAACGTTTATCATCTCG 58.843 40.000 5.91 0.00 0.00 4.04
196 199 7.936496 TCATGTGTATGGAATGTGTGTATTT 57.064 32.000 0.00 0.00 34.97 1.40
282 289 4.333926 AGCTCGTCCTCAATTTAGCATTTC 59.666 41.667 0.00 0.00 32.42 2.17
286 293 3.945285 GTCCTCAATTTAGCATTTCCGGA 59.055 43.478 0.00 0.00 0.00 5.14
287 294 4.398044 GTCCTCAATTTAGCATTTCCGGAA 59.602 41.667 14.35 14.35 0.00 4.30
288 295 4.640201 TCCTCAATTTAGCATTTCCGGAAG 59.360 41.667 17.97 8.09 0.00 3.46
290 297 5.588648 CCTCAATTTAGCATTTCCGGAAGTA 59.411 40.000 17.97 3.63 0.00 2.24
291 298 6.094881 CCTCAATTTAGCATTTCCGGAAGTAA 59.905 38.462 17.97 10.94 0.00 2.24
292 299 7.362574 CCTCAATTTAGCATTTCCGGAAGTAAA 60.363 37.037 17.97 17.98 0.00 2.01
293 300 7.309920 TCAATTTAGCATTTCCGGAAGTAAAC 58.690 34.615 17.97 7.63 0.00 2.01
294 301 6.827586 ATTTAGCATTTCCGGAAGTAAACA 57.172 33.333 17.97 1.06 0.00 2.83
295 302 5.616488 TTAGCATTTCCGGAAGTAAACAC 57.384 39.130 17.97 4.34 0.00 3.32
296 303 3.482436 AGCATTTCCGGAAGTAAACACA 58.518 40.909 17.97 0.00 0.00 3.72
297 304 4.079253 AGCATTTCCGGAAGTAAACACAT 58.921 39.130 17.97 2.20 0.00 3.21
298 305 4.522789 AGCATTTCCGGAAGTAAACACATT 59.477 37.500 17.97 0.00 0.00 2.71
299 306 5.010617 AGCATTTCCGGAAGTAAACACATTT 59.989 36.000 17.97 0.00 0.00 2.32
300 307 5.694458 GCATTTCCGGAAGTAAACACATTTT 59.306 36.000 17.97 0.00 0.00 1.82
301 308 6.201997 GCATTTCCGGAAGTAAACACATTTTT 59.798 34.615 17.97 0.00 0.00 1.94
302 309 7.563270 CATTTCCGGAAGTAAACACATTTTTG 58.437 34.615 17.97 0.00 0.00 2.44
303 310 4.612943 TCCGGAAGTAAACACATTTTTGC 58.387 39.130 0.00 0.00 0.00 3.68
304 311 4.339814 TCCGGAAGTAAACACATTTTTGCT 59.660 37.500 0.00 0.00 33.35 3.91
305 312 4.679654 CCGGAAGTAAACACATTTTTGCTC 59.320 41.667 0.00 0.00 31.01 4.26
306 313 4.378616 CGGAAGTAAACACATTTTTGCTCG 59.621 41.667 0.00 0.00 31.01 5.03
307 314 5.278604 GGAAGTAAACACATTTTTGCTCGT 58.721 37.500 0.00 0.00 31.01 4.18
308 315 5.173131 GGAAGTAAACACATTTTTGCTCGTG 59.827 40.000 0.00 0.00 31.01 4.35
309 316 5.243426 AGTAAACACATTTTTGCTCGTGT 57.757 34.783 0.00 0.00 44.17 4.49
310 317 5.270853 AGTAAACACATTTTTGCTCGTGTC 58.729 37.500 0.00 0.00 41.56 3.67
311 318 3.773860 AACACATTTTTGCTCGTGTCA 57.226 38.095 0.00 0.00 41.56 3.58
312 319 3.065019 ACACATTTTTGCTCGTGTCAC 57.935 42.857 0.00 0.00 38.13 3.67
313 320 2.036217 CACATTTTTGCTCGTGTCACG 58.964 47.619 19.38 19.38 44.19 4.35
314 321 1.002900 ACATTTTTGCTCGTGTCACGG 60.003 47.619 24.33 15.88 42.81 4.94
315 322 1.262950 CATTTTTGCTCGTGTCACGGA 59.737 47.619 24.33 10.80 42.81 4.69
316 323 1.588674 TTTTTGCTCGTGTCACGGAT 58.411 45.000 24.33 0.00 42.81 4.18
317 324 0.865111 TTTTGCTCGTGTCACGGATG 59.135 50.000 24.33 15.49 42.81 3.51
318 325 0.032815 TTTGCTCGTGTCACGGATGA 59.967 50.000 24.33 4.95 42.81 2.92
319 326 0.032815 TTGCTCGTGTCACGGATGAA 59.967 50.000 24.33 10.07 42.81 2.57
320 327 0.666274 TGCTCGTGTCACGGATGAAC 60.666 55.000 24.33 8.90 42.81 3.18
321 328 0.388649 GCTCGTGTCACGGATGAACT 60.389 55.000 24.33 0.00 42.81 3.01
322 329 1.618861 CTCGTGTCACGGATGAACTC 58.381 55.000 24.33 0.00 42.81 3.01
323 330 0.109919 TCGTGTCACGGATGAACTCG 60.110 55.000 24.33 0.00 42.81 4.18
324 331 0.109919 CGTGTCACGGATGAACTCGA 60.110 55.000 17.75 0.00 38.08 4.04
325 332 1.467543 CGTGTCACGGATGAACTCGAT 60.468 52.381 17.75 0.00 38.08 3.59
326 333 1.920574 GTGTCACGGATGAACTCGATG 59.079 52.381 0.00 0.00 36.31 3.84
327 334 1.544246 TGTCACGGATGAACTCGATGT 59.456 47.619 0.00 0.00 36.31 3.06
328 335 2.750712 TGTCACGGATGAACTCGATGTA 59.249 45.455 0.00 0.00 36.31 2.29
329 336 3.380320 TGTCACGGATGAACTCGATGTAT 59.620 43.478 0.00 0.00 36.31 2.29
330 337 3.731216 GTCACGGATGAACTCGATGTATG 59.269 47.826 0.00 0.00 36.31 2.39
331 338 2.472861 CACGGATGAACTCGATGTATGC 59.527 50.000 0.00 0.00 0.00 3.14
332 339 2.061773 CGGATGAACTCGATGTATGCC 58.938 52.381 0.00 0.00 0.00 4.40
353 360 4.335037 GCCACAACCAATTTCATGTTTTGT 59.665 37.500 0.00 0.00 0.00 2.83
391 398 3.691049 ATTATGCATCGAAAACCACCG 57.309 42.857 0.19 0.00 0.00 4.94
456 463 8.150945 GGCATATATGATATCAAAGTATCCGGT 58.849 37.037 17.10 0.00 31.47 5.28
465 472 5.468540 TCAAAGTATCCGGTATCCATGAG 57.531 43.478 0.00 0.00 0.00 2.90
517 1051 2.036098 TAGGAGGCGTTCGGGACA 59.964 61.111 0.00 0.00 0.00 4.02
525 1059 1.301401 CGTTCGGGACAAGGAGCAA 60.301 57.895 0.00 0.00 0.00 3.91
531 1065 1.001378 CGGGACAAGGAGCAAAAACAG 60.001 52.381 0.00 0.00 0.00 3.16
536 1070 0.752658 AAGGAGCAAAAACAGGGCAC 59.247 50.000 0.00 0.00 0.00 5.01
540 1074 0.102300 AGCAAAAACAGGGCACGTTC 59.898 50.000 0.00 0.00 0.00 3.95
551 1085 1.537562 GGGCACGTTCGGGAGTTATAG 60.538 57.143 0.00 0.00 0.00 1.31
556 1090 4.735578 GCACGTTCGGGAGTTATAGAATCA 60.736 45.833 0.00 0.00 0.00 2.57
563 1097 9.790389 GTTCGGGAGTTATAGAATCAGTATATG 57.210 37.037 0.00 0.00 0.00 1.78
580 1114 9.734984 TCAGTATATGAAAGTATCGAGTATCCA 57.265 33.333 0.00 0.00 34.02 3.41
622 1156 0.240945 ATTGGCAAGCGAACTTTCCG 59.759 50.000 5.96 0.00 41.64 4.30
624 1158 0.249953 TGGCAAGCGAACTTTCCGTA 60.250 50.000 0.00 0.00 41.64 4.02
626 1160 1.467342 GGCAAGCGAACTTTCCGTAAT 59.533 47.619 0.00 0.00 32.29 1.89
628 1162 3.561503 GCAAGCGAACTTTCCGTAATTT 58.438 40.909 0.00 0.00 32.29 1.82
629 1163 3.360758 GCAAGCGAACTTTCCGTAATTTG 59.639 43.478 0.00 0.00 32.29 2.32
630 1164 4.778904 CAAGCGAACTTTCCGTAATTTGA 58.221 39.130 0.00 0.00 32.29 2.69
631 1165 5.390613 CAAGCGAACTTTCCGTAATTTGAT 58.609 37.500 0.00 0.00 32.29 2.57
651 1188 5.192927 TGATATGACCCCTTTTTGCTACAG 58.807 41.667 0.00 0.00 0.00 2.74
654 1193 2.441750 TGACCCCTTTTTGCTACAGACT 59.558 45.455 0.00 0.00 0.00 3.24
657 1196 1.197721 CCCTTTTTGCTACAGACTGCG 59.802 52.381 1.25 0.00 0.00 5.18
661 1200 2.472695 TTTGCTACAGACTGCGGAAT 57.527 45.000 0.00 0.00 0.00 3.01
663 1202 2.010145 TGCTACAGACTGCGGAATTC 57.990 50.000 0.00 0.00 0.00 2.17
665 1204 2.028112 TGCTACAGACTGCGGAATTCTT 60.028 45.455 5.23 0.00 0.00 2.52
677 1216 5.401550 TGCGGAATTCTTTTGTGATGATTC 58.598 37.500 5.23 0.00 0.00 2.52
688 1227 5.725325 TTGTGATGATTCAAGATGCCAAA 57.275 34.783 0.00 0.00 32.48 3.28
689 1228 5.725325 TGTGATGATTCAAGATGCCAAAA 57.275 34.783 0.00 0.00 32.48 2.44
690 1229 6.099159 TGTGATGATTCAAGATGCCAAAAA 57.901 33.333 0.00 0.00 32.48 1.94
733 1272 4.640771 AGATTGTACCACAGTTGTCCAT 57.359 40.909 0.00 0.00 0.00 3.41
746 1285 1.144057 GTCCATCGACGATTGCCCT 59.856 57.895 7.83 0.00 0.00 5.19
747 1286 0.387929 GTCCATCGACGATTGCCCTA 59.612 55.000 7.83 0.00 0.00 3.53
751 1290 0.249489 ATCGACGATTGCCCTAGTGC 60.249 55.000 4.05 0.00 0.00 4.40
818 1358 6.767524 TTTTGAAGCTTTTACCTTCTGACA 57.232 33.333 0.00 0.00 39.47 3.58
870 1446 3.254654 CATGCTCGCACGGTACCG 61.255 66.667 32.22 32.22 46.03 4.02
874 1450 2.879462 CTCGCACGGTACCGCTTC 60.879 66.667 33.62 20.53 44.19 3.86
876 1452 2.508439 CGCACGGTACCGCTTCAT 60.508 61.111 33.62 11.69 44.19 2.57
877 1453 2.098233 CGCACGGTACCGCTTCATT 61.098 57.895 33.62 10.87 44.19 2.57
932 1517 6.071896 AGGAAAGAAATTGAAACGGAAGATCC 60.072 38.462 0.00 0.00 0.00 3.36
1039 1624 1.002544 CCACTCACACCTTTCTCCTCC 59.997 57.143 0.00 0.00 0.00 4.30
1044 1629 0.115745 ACACCTTTCTCCTCCCCGTA 59.884 55.000 0.00 0.00 0.00 4.02
1053 1638 1.455959 CCTCCCCGTACTCCTCCTG 60.456 68.421 0.00 0.00 0.00 3.86
1822 2407 1.599797 TCGGAGATAGGCGCGATGA 60.600 57.895 12.10 0.00 0.00 2.92
2353 2938 0.178950 ATCGATAGGGGAGCTGAGCA 60.179 55.000 7.39 0.00 0.00 4.26
2712 3297 1.516603 GAGCCTAACAGCCGTCGAC 60.517 63.158 5.18 5.18 0.00 4.20
3607 6418 5.682862 CCTCTGTTTTCATTCTTCACAAACG 59.317 40.000 0.00 0.00 31.24 3.60
3661 6508 6.128742 GCTTTGGTATGCTCTGATTGTTTTTG 60.129 38.462 0.00 0.00 0.00 2.44
3786 6634 1.460504 ATGTGGCTGCATTCTCTGTG 58.539 50.000 0.50 0.00 0.00 3.66
3789 6637 1.610522 GTGGCTGCATTCTCTGTGTTT 59.389 47.619 0.50 0.00 0.00 2.83
3828 6677 0.108138 ATGCCTACACGCTGAAGGTC 60.108 55.000 0.00 0.00 32.67 3.85
4200 7049 4.394712 CAGGACGGGCCACAGGAC 62.395 72.222 4.39 0.00 40.02 3.85
4331 7196 3.136763 CAGGCATGTGCTAGATTAGTGG 58.863 50.000 4.84 0.00 41.70 4.00
4374 7239 7.289317 TGGATTAATTAGACCGGTGTAATCTCT 59.711 37.037 30.71 20.47 30.02 3.10
4375 7240 7.599245 GGATTAATTAGACCGGTGTAATCTCTG 59.401 40.741 30.71 0.00 30.02 3.35
4376 7241 5.934402 AATTAGACCGGTGTAATCTCTGT 57.066 39.130 30.71 16.30 30.02 3.41
4380 7245 4.084287 AGACCGGTGTAATCTCTGTTGTA 58.916 43.478 14.63 0.00 0.00 2.41
4386 7254 4.929808 GGTGTAATCTCTGTTGTAGTGGTG 59.070 45.833 0.00 0.00 0.00 4.17
4393 7261 2.631062 TCTGTTGTAGTGGTGGTACTGG 59.369 50.000 0.00 0.00 32.19 4.00
4406 7274 1.463444 GGTACTGGCTTGTACAAAGCG 59.537 52.381 10.03 6.58 43.17 4.68
4441 7309 3.000724 CGTCTCTCCAATTGAATCGAAGC 59.999 47.826 7.12 0.00 0.00 3.86
4464 7333 5.439828 CGATTTGTTTCTGAAATCACACGA 58.560 37.500 6.06 0.00 39.01 4.35
4477 7346 0.955919 CACACGAAAAGAGGAGGCCC 60.956 60.000 0.00 0.00 0.00 5.80
4552 7429 4.470170 ACATGCATGCACAGCGCG 62.470 61.111 25.37 0.00 46.97 6.86
4659 7541 4.020617 TGCTCACCTTCCCCAGCG 62.021 66.667 0.00 0.00 34.39 5.18
4732 7746 2.042297 TCTCATCTCCTCTCCACAGTGT 59.958 50.000 0.00 0.00 0.00 3.55
4844 7867 4.062293 TGTGTCGGGTTAGAAAGATGTTG 58.938 43.478 0.00 0.00 0.00 3.33
4847 7870 1.743394 CGGGTTAGAAAGATGTTGGCC 59.257 52.381 0.00 0.00 0.00 5.36
4964 8029 3.207778 CACTGTAAAAACTGTCGGGGAA 58.792 45.455 0.00 0.00 0.00 3.97
4971 8036 3.329929 AAACTGTCGGGGAATCAGTAC 57.670 47.619 0.00 0.00 40.81 2.73
4975 8040 3.021695 CTGTCGGGGAATCAGTACACTA 58.978 50.000 0.00 0.00 0.00 2.74
4976 8041 2.756760 TGTCGGGGAATCAGTACACTAC 59.243 50.000 0.00 0.00 0.00 2.73
4977 8042 2.019249 TCGGGGAATCAGTACACTACG 58.981 52.381 0.00 0.00 0.00 3.51
5011 8076 0.876342 GGGCTGAATCGACGGTGATC 60.876 60.000 0.00 0.00 0.00 2.92
5059 8124 2.950172 GCCGTGCGTGTTAGTGGTG 61.950 63.158 0.00 0.00 0.00 4.17
5060 8125 2.314647 CCGTGCGTGTTAGTGGTGG 61.315 63.158 0.00 0.00 0.00 4.61
5061 8126 1.593209 CGTGCGTGTTAGTGGTGGT 60.593 57.895 0.00 0.00 0.00 4.16
5118 8191 1.136984 GACTGAGCACGTAGTCGGG 59.863 63.158 9.37 0.00 41.61 5.14
5126 8199 2.027169 CGTAGTCGGGCGGAATCC 59.973 66.667 0.00 0.00 0.00 3.01
5219 8304 4.521559 TCCTGCGAGGAGTTCAGT 57.478 55.556 1.25 0.00 40.06 3.41
5220 8305 3.664240 TCCTGCGAGGAGTTCAGTA 57.336 52.632 1.25 0.00 40.06 2.74
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 7.468141 TGTTATGATGGGAGCTACACTATAG 57.532 40.000 0.00 0.00 0.00 1.31
79 80 6.270927 ACATGTTATGATGGGAGCTACACTAT 59.729 38.462 0.00 0.00 0.00 2.12
83 84 6.686484 ATACATGTTATGATGGGAGCTACA 57.314 37.500 2.30 0.00 0.00 2.74
84 85 9.672673 AATTATACATGTTATGATGGGAGCTAC 57.327 33.333 2.30 0.00 0.00 3.58
85 86 9.671279 CAATTATACATGTTATGATGGGAGCTA 57.329 33.333 2.30 0.00 0.00 3.32
86 87 8.166061 ACAATTATACATGTTATGATGGGAGCT 58.834 33.333 2.30 0.00 0.00 4.09
87 88 8.340618 ACAATTATACATGTTATGATGGGAGC 57.659 34.615 2.30 0.00 0.00 4.70
88 89 9.730705 AGACAATTATACATGTTATGATGGGAG 57.269 33.333 2.30 0.00 0.00 4.30
105 106 9.646522 ATGGGAGCTACATAAAAAGACAATTAT 57.353 29.630 0.00 0.00 0.00 1.28
106 107 9.120538 GATGGGAGCTACATAAAAAGACAATTA 57.879 33.333 0.00 0.00 0.00 1.40
107 108 7.615365 TGATGGGAGCTACATAAAAAGACAATT 59.385 33.333 0.00 0.00 0.00 2.32
108 109 7.118723 TGATGGGAGCTACATAAAAAGACAAT 58.881 34.615 0.00 0.00 0.00 2.71
109 110 6.480763 TGATGGGAGCTACATAAAAAGACAA 58.519 36.000 0.00 0.00 0.00 3.18
110 111 6.061022 TGATGGGAGCTACATAAAAAGACA 57.939 37.500 0.00 0.00 0.00 3.41
111 112 8.560374 GTTATGATGGGAGCTACATAAAAAGAC 58.440 37.037 0.00 0.00 37.10 3.01
112 113 7.441157 CGTTATGATGGGAGCTACATAAAAAGA 59.559 37.037 0.00 0.00 37.10 2.52
113 114 7.226720 ACGTTATGATGGGAGCTACATAAAAAG 59.773 37.037 0.00 2.02 37.10 2.27
114 115 7.051623 ACGTTATGATGGGAGCTACATAAAAA 58.948 34.615 0.00 0.00 37.10 1.94
115 116 6.588204 ACGTTATGATGGGAGCTACATAAAA 58.412 36.000 0.00 0.00 37.10 1.52
116 117 6.169557 ACGTTATGATGGGAGCTACATAAA 57.830 37.500 0.00 0.00 37.10 1.40
117 118 5.801531 ACGTTATGATGGGAGCTACATAA 57.198 39.130 0.00 2.45 34.34 1.90
118 119 5.801531 AACGTTATGATGGGAGCTACATA 57.198 39.130 0.00 0.00 0.00 2.29
119 120 4.689612 AACGTTATGATGGGAGCTACAT 57.310 40.909 0.00 0.00 0.00 2.29
140 141 9.986833 CATGTGTGTAAAATTTCGAGATGATAA 57.013 29.630 0.00 0.00 0.00 1.75
258 265 2.893637 TGCTAAATTGAGGACGAGCTC 58.106 47.619 2.73 2.73 0.00 4.09
282 289 4.616953 AGCAAAAATGTGTTTACTTCCGG 58.383 39.130 0.00 0.00 0.00 5.14
286 293 5.646606 ACACGAGCAAAAATGTGTTTACTT 58.353 33.333 0.00 0.00 42.53 2.24
287 294 5.163703 TGACACGAGCAAAAATGTGTTTACT 60.164 36.000 0.00 0.00 44.93 2.24
288 295 5.031578 TGACACGAGCAAAAATGTGTTTAC 58.968 37.500 0.00 0.00 44.93 2.01
290 297 3.857093 GTGACACGAGCAAAAATGTGTTT 59.143 39.130 0.00 0.00 44.93 2.83
291 298 3.434637 GTGACACGAGCAAAAATGTGTT 58.565 40.909 0.00 0.00 44.93 3.32
292 299 2.538737 CGTGACACGAGCAAAAATGTGT 60.539 45.455 23.39 0.00 46.05 3.72
293 300 2.036217 CGTGACACGAGCAAAAATGTG 58.964 47.619 23.39 0.00 46.05 3.21
294 301 1.002900 CCGTGACACGAGCAAAAATGT 60.003 47.619 28.83 0.00 46.05 2.71
295 302 1.262950 TCCGTGACACGAGCAAAAATG 59.737 47.619 28.83 9.00 46.05 2.32
296 303 1.588674 TCCGTGACACGAGCAAAAAT 58.411 45.000 28.83 0.00 46.05 1.82
297 304 1.262950 CATCCGTGACACGAGCAAAAA 59.737 47.619 28.83 5.80 46.05 1.94
298 305 0.865111 CATCCGTGACACGAGCAAAA 59.135 50.000 28.83 7.46 46.05 2.44
299 306 0.032815 TCATCCGTGACACGAGCAAA 59.967 50.000 28.83 9.16 46.05 3.68
300 307 0.032815 TTCATCCGTGACACGAGCAA 59.967 50.000 28.83 12.56 46.05 3.91
301 308 0.666274 GTTCATCCGTGACACGAGCA 60.666 55.000 28.83 12.60 46.05 4.26
302 309 0.388649 AGTTCATCCGTGACACGAGC 60.389 55.000 28.83 11.03 46.05 5.03
303 310 1.618861 GAGTTCATCCGTGACACGAG 58.381 55.000 28.83 18.11 46.05 4.18
304 311 0.109919 CGAGTTCATCCGTGACACGA 60.110 55.000 28.83 15.08 46.05 4.35
305 312 0.109919 TCGAGTTCATCCGTGACACG 60.110 55.000 21.02 21.02 42.11 4.49
306 313 1.920574 CATCGAGTTCATCCGTGACAC 59.079 52.381 0.00 0.00 33.11 3.67
307 314 1.544246 ACATCGAGTTCATCCGTGACA 59.456 47.619 0.00 0.00 33.11 3.58
308 315 2.279582 ACATCGAGTTCATCCGTGAC 57.720 50.000 0.00 0.00 33.11 3.67
309 316 3.795488 GCATACATCGAGTTCATCCGTGA 60.795 47.826 0.00 0.00 0.00 4.35
310 317 2.472861 GCATACATCGAGTTCATCCGTG 59.527 50.000 0.00 0.00 0.00 4.94
311 318 2.545952 GGCATACATCGAGTTCATCCGT 60.546 50.000 0.00 0.00 0.00 4.69
312 319 2.061773 GGCATACATCGAGTTCATCCG 58.938 52.381 0.00 0.00 0.00 4.18
313 320 2.802816 GTGGCATACATCGAGTTCATCC 59.197 50.000 0.00 0.00 0.00 3.51
314 321 3.457234 TGTGGCATACATCGAGTTCATC 58.543 45.455 0.00 0.00 33.42 2.92
315 322 3.541996 TGTGGCATACATCGAGTTCAT 57.458 42.857 0.00 0.00 33.42 2.57
316 323 3.000041 GTTGTGGCATACATCGAGTTCA 59.000 45.455 0.00 0.00 39.48 3.18
317 324 2.351726 GGTTGTGGCATACATCGAGTTC 59.648 50.000 0.00 0.00 39.48 3.01
318 325 2.290008 TGGTTGTGGCATACATCGAGTT 60.290 45.455 0.00 0.00 39.48 3.01
319 326 1.277842 TGGTTGTGGCATACATCGAGT 59.722 47.619 0.00 0.00 39.48 4.18
320 327 2.022764 TGGTTGTGGCATACATCGAG 57.977 50.000 0.00 0.00 39.48 4.04
321 328 2.481289 TTGGTTGTGGCATACATCGA 57.519 45.000 0.00 0.00 39.48 3.59
322 329 3.781079 AATTGGTTGTGGCATACATCG 57.219 42.857 0.00 0.00 39.48 3.84
323 330 5.070770 TGAAATTGGTTGTGGCATACATC 57.929 39.130 0.00 0.00 39.48 3.06
324 331 5.046448 ACATGAAATTGGTTGTGGCATACAT 60.046 36.000 0.00 0.00 39.48 2.29
325 332 4.282957 ACATGAAATTGGTTGTGGCATACA 59.717 37.500 0.00 0.00 37.56 2.29
326 333 4.819769 ACATGAAATTGGTTGTGGCATAC 58.180 39.130 0.00 0.00 0.00 2.39
327 334 5.480642 AACATGAAATTGGTTGTGGCATA 57.519 34.783 0.00 0.00 0.00 3.14
328 335 4.354893 AACATGAAATTGGTTGTGGCAT 57.645 36.364 0.00 0.00 0.00 4.40
329 336 3.834489 AACATGAAATTGGTTGTGGCA 57.166 38.095 0.00 0.00 0.00 4.92
330 337 4.335037 ACAAAACATGAAATTGGTTGTGGC 59.665 37.500 0.00 0.00 34.73 5.01
331 338 7.493971 TCTTACAAAACATGAAATTGGTTGTGG 59.506 33.333 0.00 0.00 34.73 4.17
332 339 8.417780 TCTTACAAAACATGAAATTGGTTGTG 57.582 30.769 0.00 0.00 36.16 3.33
373 380 0.730265 GCGGTGGTTTTCGATGCATA 59.270 50.000 0.00 0.00 0.00 3.14
376 383 0.729140 CTTGCGGTGGTTTTCGATGC 60.729 55.000 0.00 0.00 0.00 3.91
380 387 2.050691 CATTTCTTGCGGTGGTTTTCG 58.949 47.619 0.00 0.00 0.00 3.46
391 398 7.380602 GCACATATCAGATTAACCATTTCTTGC 59.619 37.037 0.00 0.00 0.00 4.01
495 1029 2.202570 CGAACGCCTCCTACACCG 60.203 66.667 0.00 0.00 0.00 4.94
499 1033 1.880819 TTGTCCCGAACGCCTCCTAC 61.881 60.000 0.00 0.00 0.00 3.18
517 1051 0.752658 GTGCCCTGTTTTTGCTCCTT 59.247 50.000 0.00 0.00 0.00 3.36
525 1059 2.190841 CCCGAACGTGCCCTGTTTT 61.191 57.895 0.00 0.00 0.00 2.43
531 1065 0.461135 TATAACTCCCGAACGTGCCC 59.539 55.000 0.00 0.00 0.00 5.36
536 1070 5.184340 ACTGATTCTATAACTCCCGAACG 57.816 43.478 0.00 0.00 0.00 3.95
595 1129 4.270008 AGTTCGCTTGCCAATATTACCTT 58.730 39.130 0.00 0.00 0.00 3.50
597 1131 4.632538 AAGTTCGCTTGCCAATATTACC 57.367 40.909 0.00 0.00 35.84 2.85
622 1156 7.555965 AGCAAAAAGGGGTCATATCAAATTAC 58.444 34.615 0.00 0.00 0.00 1.89
624 1158 6.625532 AGCAAAAAGGGGTCATATCAAATT 57.374 33.333 0.00 0.00 0.00 1.82
626 1160 6.013379 TGTAGCAAAAAGGGGTCATATCAAA 58.987 36.000 0.00 0.00 0.00 2.69
628 1162 5.045213 TCTGTAGCAAAAAGGGGTCATATCA 60.045 40.000 0.00 0.00 0.00 2.15
629 1163 5.297029 GTCTGTAGCAAAAAGGGGTCATATC 59.703 44.000 0.00 0.00 0.00 1.63
630 1164 5.044846 AGTCTGTAGCAAAAAGGGGTCATAT 60.045 40.000 0.00 0.00 0.00 1.78
631 1165 4.288626 AGTCTGTAGCAAAAAGGGGTCATA 59.711 41.667 0.00 0.00 0.00 2.15
651 1188 3.896648 TCACAAAAGAATTCCGCAGTC 57.103 42.857 0.65 0.00 0.00 3.51
654 1193 5.048154 TGAATCATCACAAAAGAATTCCGCA 60.048 36.000 0.65 0.00 0.00 5.69
657 1196 9.084164 CATCTTGAATCATCACAAAAGAATTCC 57.916 33.333 0.65 0.00 34.61 3.01
661 1200 6.015265 TGGCATCTTGAATCATCACAAAAGAA 60.015 34.615 0.00 0.00 34.61 2.52
663 1202 5.716094 TGGCATCTTGAATCATCACAAAAG 58.284 37.500 0.00 0.00 34.61 2.27
665 1204 5.725325 TTGGCATCTTGAATCATCACAAA 57.275 34.783 0.00 0.00 34.61 2.83
695 1234 8.680903 GGTACAATCTTTGAATCATCACAAGAT 58.319 33.333 2.91 2.91 40.77 2.40
696 1235 7.665145 TGGTACAATCTTTGAATCATCACAAGA 59.335 33.333 0.00 0.00 37.24 3.02
733 1272 1.141019 GCACTAGGGCAATCGTCGA 59.859 57.895 13.43 0.00 0.00 4.20
746 1285 9.959721 AAAGATTCAAATTTACCTAGAGCACTA 57.040 29.630 0.00 0.00 0.00 2.74
747 1286 8.870075 AAAGATTCAAATTTACCTAGAGCACT 57.130 30.769 0.00 0.00 0.00 4.40
830 1405 5.166398 GCTGATTTCCAATGTTCTCCTTTG 58.834 41.667 0.00 0.00 0.00 2.77
898 1481 7.337718 GTTTCAATTTCTTTCCTTTTCGCTTC 58.662 34.615 0.00 0.00 0.00 3.86
900 1483 5.458779 CGTTTCAATTTCTTTCCTTTTCGCT 59.541 36.000 0.00 0.00 0.00 4.93
901 1484 5.332280 CCGTTTCAATTTCTTTCCTTTTCGC 60.332 40.000 0.00 0.00 0.00 4.70
902 1485 5.974751 TCCGTTTCAATTTCTTTCCTTTTCG 59.025 36.000 0.00 0.00 0.00 3.46
1039 1624 2.128507 GGAGCAGGAGGAGTACGGG 61.129 68.421 0.00 0.00 0.00 5.28
1044 1629 2.686835 GCCAGGAGCAGGAGGAGT 60.687 66.667 0.00 0.00 42.97 3.85
1246 1831 1.820481 CGGAGAGGTCGAGGGAGAC 60.820 68.421 0.00 0.00 40.25 3.36
1386 1971 3.982372 GAGAACGCGGATGTCGGCA 62.982 63.158 12.47 0.00 41.54 5.69
2313 2898 3.735029 GACACCTCGTCGGCGTCT 61.735 66.667 10.18 0.00 40.85 4.18
2332 2917 0.246086 CTCAGCTCCCCTATCGATGC 59.754 60.000 8.54 1.10 0.00 3.91
2353 2938 5.938125 GGCCAGATAATCGGTTGTTATACAT 59.062 40.000 0.00 0.00 0.00 2.29
2400 2985 2.922503 TTCTGCAGCCCCACGAGA 60.923 61.111 9.47 0.00 0.00 4.04
2677 3262 3.282157 CTGCATTCCGGCGATGGG 61.282 66.667 9.30 0.00 36.28 4.00
2712 3297 0.038526 ACAGGCGGTTGTACGAGAAG 60.039 55.000 0.00 0.00 35.47 2.85
3641 6482 4.860907 CAGCAAAAACAATCAGAGCATACC 59.139 41.667 0.00 0.00 0.00 2.73
3789 6637 5.288804 GCATACTCTGAAAAAGGCACAAAA 58.711 37.500 0.00 0.00 0.00 2.44
3796 6644 4.330074 CGTGTAGGCATACTCTGAAAAAGG 59.670 45.833 10.25 0.00 32.75 3.11
3797 6645 4.201724 GCGTGTAGGCATACTCTGAAAAAG 60.202 45.833 10.25 0.00 32.75 2.27
3810 6659 1.292223 GACCTTCAGCGTGTAGGCA 59.708 57.895 9.46 0.00 38.34 4.75
3828 6677 1.859564 CACGTCGCTCTTCTCGTCG 60.860 63.158 0.00 0.00 42.27 5.12
3876 6725 4.980805 GGCTTGCGTCCGGTGACA 62.981 66.667 0.00 0.00 41.85 3.58
4160 7009 1.398692 CTCCTCCTCTTCTCCTTCGG 58.601 60.000 0.00 0.00 0.00 4.30
4374 7239 1.071071 GCCAGTACCACCACTACAACA 59.929 52.381 0.00 0.00 0.00 3.33
4375 7240 1.346722 AGCCAGTACCACCACTACAAC 59.653 52.381 0.00 0.00 0.00 3.32
4376 7241 1.724545 AGCCAGTACCACCACTACAA 58.275 50.000 0.00 0.00 0.00 2.41
4380 7245 1.346722 GTACAAGCCAGTACCACCACT 59.653 52.381 5.26 0.00 38.70 4.00
4386 7254 1.463444 CGCTTTGTACAAGCCAGTACC 59.537 52.381 18.30 0.41 42.84 3.34
4393 7261 2.095919 CCACTAACCGCTTTGTACAAGC 60.096 50.000 8.56 12.98 39.77 4.01
4406 7274 1.744522 GAGAGACGAGACCCACTAACC 59.255 57.143 0.00 0.00 0.00 2.85
4441 7309 5.439828 TCGTGTGATTTCAGAAACAAATCG 58.560 37.500 0.00 2.07 41.38 3.34
4464 7333 2.972819 GCCTCGGGCCTCCTCTTTT 61.973 63.158 0.84 0.00 44.06 2.27
4487 7356 2.797850 TCGAAGCGTGCACGTACG 60.798 61.111 36.80 33.57 46.28 3.67
4488 7357 2.761354 GTCGAAGCGTGCACGTAC 59.239 61.111 36.80 25.90 42.22 3.67
4489 7358 2.797850 CGTCGAAGCGTGCACGTA 60.798 61.111 36.80 16.91 42.22 3.57
4490 7359 4.918129 ACGTCGAAGCGTGCACGT 62.918 61.111 36.80 21.31 43.99 4.49
4584 7461 2.579738 GTCCTCTCCTGCCCGAAC 59.420 66.667 0.00 0.00 0.00 3.95
4641 7523 2.360475 GCTGGGGAAGGTGAGCAC 60.360 66.667 0.00 0.00 0.00 4.40
4732 7746 1.073763 AGTGAAACCAGGCATGCACTA 59.926 47.619 21.36 0.00 37.80 2.74
4971 8036 0.037697 TGCCTGCCTTGTACGTAGTG 60.038 55.000 0.00 0.00 45.73 2.74
4975 8040 1.302511 CCTTGCCTGCCTTGTACGT 60.303 57.895 0.00 0.00 0.00 3.57
4976 8041 2.040544 CCCTTGCCTGCCTTGTACG 61.041 63.158 0.00 0.00 0.00 3.67
4977 8042 2.343426 GCCCTTGCCTGCCTTGTAC 61.343 63.158 0.00 0.00 0.00 2.90
5011 8076 2.283298 AGAATGCTGCATGGTAACTCG 58.717 47.619 17.00 0.00 37.61 4.18
5018 8083 2.286831 CGCTTAAGAGAATGCTGCATGG 60.287 50.000 17.00 1.19 0.00 3.66
5129 8202 4.010414 GCTGCAGCGCCGATCATC 62.010 66.667 25.23 0.00 0.00 2.92
5159 8244 2.433318 GTCACAGTCGCCTGCCTC 60.433 66.667 0.00 0.00 42.81 4.70
5160 8245 4.008933 GGTCACAGTCGCCTGCCT 62.009 66.667 0.00 0.00 42.81 4.75


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

AutoCloner maintained by Alex Coulton.