Multiple sequence alignment - TraesCS7B01G006500

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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 TraesCS7B01G006500 chr7B 100.000 3406 0 0 1 3406 3697459 3694054 0.000000e+00 6290.0
1 TraesCS7B01G006500 chr7B 95.461 749 31 2 237 985 619128101 619127356 0.000000e+00 1192.0
2 TraesCS7B01G006500 chr7B 97.674 129 2 1 2430 2558 3689697 3689570 1.590000e-53 220.0
3 TraesCS7B01G006500 chr7B 83.537 164 24 2 2305 2467 30519127 30519288 2.120000e-32 150.0
4 TraesCS7B01G006500 chr7A 92.849 1720 86 11 983 2698 66167400 66165714 0.000000e+00 2460.0
5 TraesCS7B01G006500 chr7A 88.710 186 10 4 1 176 66167569 66167385 2.060000e-52 217.0
6 TraesCS7B01G006500 chr7D 93.506 924 57 3 2484 3406 63376983 63376062 0.000000e+00 1371.0
7 TraesCS7B01G006500 chr7D 93.800 871 41 4 1592 2462 63377832 63376975 0.000000e+00 1297.0
8 TraesCS7B01G006500 chr7D 95.462 573 20 3 983 1554 63378404 63377837 0.000000e+00 909.0
9 TraesCS7B01G006500 chr7D 78.426 788 141 22 2622 3404 585909264 585908501 1.420000e-133 486.0
10 TraesCS7B01G006500 chr7D 92.179 179 10 3 1 176 63378565 63378388 2.030000e-62 250.0
11 TraesCS7B01G006500 chr6A 95.588 748 31 2 240 986 64561947 64561201 0.000000e+00 1197.0
12 TraesCS7B01G006500 chr6A 95.321 748 30 3 240 987 562522349 562521607 0.000000e+00 1182.0
13 TraesCS7B01G006500 chr6A 84.030 789 111 9 2621 3406 143701797 143701021 0.000000e+00 745.0
14 TraesCS7B01G006500 chr6A 78.698 845 152 18 1568 2390 24054834 24053996 3.870000e-149 538.0
15 TraesCS7B01G006500 chr1B 95.370 756 30 4 235 987 385301601 385302354 0.000000e+00 1197.0
16 TraesCS7B01G006500 chr3B 95.461 749 33 1 242 990 551503309 551504056 0.000000e+00 1194.0
17 TraesCS7B01G006500 chr3B 72.083 720 150 41 1700 2393 70981205 70980511 5.850000e-38 169.0
18 TraesCS7B01G006500 chr3B 100.000 35 0 0 179 213 236038822 236038788 7.890000e-07 65.8
19 TraesCS7B01G006500 chr5B 95.448 747 31 3 240 986 511706068 511705325 0.000000e+00 1188.0
20 TraesCS7B01G006500 chr5B 75.862 174 32 8 1715 1883 489821498 489821666 2.820000e-11 80.5
21 TraesCS7B01G006500 chr2A 95.225 754 30 4 235 986 72964670 72965419 0.000000e+00 1188.0
22 TraesCS7B01G006500 chr2A 79.731 819 151 10 1599 2406 143372733 143373547 2.280000e-161 579.0
23 TraesCS7B01G006500 chr2A 86.765 136 12 5 1068 1200 143289073 143289205 2.740000e-31 147.0
24 TraesCS7B01G006500 chr6B 95.442 746 31 2 240 985 633043121 633042379 0.000000e+00 1186.0
25 TraesCS7B01G006500 chr6B 86.701 391 48 4 1071 1459 42406554 42406166 6.750000e-117 431.0
26 TraesCS7B01G006500 chr6B 79.419 413 71 8 2004 2406 42404555 42404147 2.590000e-71 279.0
27 TraesCS7B01G006500 chr3A 94.960 754 34 3 235 986 718866712 718867463 0.000000e+00 1179.0
28 TraesCS7B01G006500 chr3A 85.533 788 109 5 2622 3405 731994301 731993515 0.000000e+00 819.0
29 TraesCS7B01G006500 chr3D 85.171 789 109 6 2622 3406 602654580 602655364 0.000000e+00 802.0
30 TraesCS7B01G006500 chr3D 77.806 775 137 26 2622 3388 450291336 450290589 2.410000e-121 446.0
31 TraesCS7B01G006500 chr1A 83.544 790 118 10 2622 3404 464085620 464084836 0.000000e+00 728.0
32 TraesCS7B01G006500 chr6D 83.418 790 107 14 2621 3406 115318464 115317695 0.000000e+00 712.0
33 TraesCS7B01G006500 chr4B 83.038 790 123 9 2622 3404 211499416 211500201 0.000000e+00 706.0
34 TraesCS7B01G006500 chr4B 75.850 824 164 26 1594 2394 600605589 600604778 1.480000e-103 387.0
35 TraesCS7B01G006500 chr4B 75.518 821 169 24 1594 2393 600517191 600516382 1.150000e-99 374.0
36 TraesCS7B01G006500 chr4D 75.309 810 181 17 1594 2393 476229109 476228309 1.490000e-98 370.0
37 TraesCS7B01G006500 chr2B 73.902 820 177 30 1597 2393 24906163 24906968 9.240000e-76 294.0
38 TraesCS7B01G006500 chr2B 73.326 881 182 42 1568 2402 24889688 24890561 3.350000e-70 276.0
39 TraesCS7B01G006500 chr2B 73.526 831 175 34 1600 2393 24883252 24884074 1.200000e-69 274.0
40 TraesCS7B01G006500 chr2D 88.095 84 8 2 1065 1147 135511081 135511163 7.780000e-17 99.0
41 TraesCS7B01G006500 chr5A 76.879 173 32 6 1715 1883 514160645 514160813 1.300000e-14 91.6
42 TraesCS7B01G006500 chr5D 79.688 128 19 7 1708 1832 480556023 480556146 6.060000e-13 86.1


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 TraesCS7B01G006500 chr7B 3694054 3697459 3405 True 6290.00 6290 100.00000 1 3406 1 chr7B.!!$R2 3405
1 TraesCS7B01G006500 chr7B 619127356 619128101 745 True 1192.00 1192 95.46100 237 985 1 chr7B.!!$R3 748
2 TraesCS7B01G006500 chr7A 66165714 66167569 1855 True 1338.50 2460 90.77950 1 2698 2 chr7A.!!$R1 2697
3 TraesCS7B01G006500 chr7D 63376062 63378565 2503 True 956.75 1371 93.73675 1 3406 4 chr7D.!!$R2 3405
4 TraesCS7B01G006500 chr7D 585908501 585909264 763 True 486.00 486 78.42600 2622 3404 1 chr7D.!!$R1 782
5 TraesCS7B01G006500 chr6A 64561201 64561947 746 True 1197.00 1197 95.58800 240 986 1 chr6A.!!$R2 746
6 TraesCS7B01G006500 chr6A 562521607 562522349 742 True 1182.00 1182 95.32100 240 987 1 chr6A.!!$R4 747
7 TraesCS7B01G006500 chr6A 143701021 143701797 776 True 745.00 745 84.03000 2621 3406 1 chr6A.!!$R3 785
8 TraesCS7B01G006500 chr6A 24053996 24054834 838 True 538.00 538 78.69800 1568 2390 1 chr6A.!!$R1 822
9 TraesCS7B01G006500 chr1B 385301601 385302354 753 False 1197.00 1197 95.37000 235 987 1 chr1B.!!$F1 752
10 TraesCS7B01G006500 chr3B 551503309 551504056 747 False 1194.00 1194 95.46100 242 990 1 chr3B.!!$F1 748
11 TraesCS7B01G006500 chr5B 511705325 511706068 743 True 1188.00 1188 95.44800 240 986 1 chr5B.!!$R1 746
12 TraesCS7B01G006500 chr2A 72964670 72965419 749 False 1188.00 1188 95.22500 235 986 1 chr2A.!!$F1 751
13 TraesCS7B01G006500 chr2A 143372733 143373547 814 False 579.00 579 79.73100 1599 2406 1 chr2A.!!$F3 807
14 TraesCS7B01G006500 chr6B 633042379 633043121 742 True 1186.00 1186 95.44200 240 985 1 chr6B.!!$R1 745
15 TraesCS7B01G006500 chr6B 42404147 42406554 2407 True 355.00 431 83.06000 1071 2406 2 chr6B.!!$R2 1335
16 TraesCS7B01G006500 chr3A 718866712 718867463 751 False 1179.00 1179 94.96000 235 986 1 chr3A.!!$F1 751
17 TraesCS7B01G006500 chr3A 731993515 731994301 786 True 819.00 819 85.53300 2622 3405 1 chr3A.!!$R1 783
18 TraesCS7B01G006500 chr3D 602654580 602655364 784 False 802.00 802 85.17100 2622 3406 1 chr3D.!!$F1 784
19 TraesCS7B01G006500 chr3D 450290589 450291336 747 True 446.00 446 77.80600 2622 3388 1 chr3D.!!$R1 766
20 TraesCS7B01G006500 chr1A 464084836 464085620 784 True 728.00 728 83.54400 2622 3404 1 chr1A.!!$R1 782
21 TraesCS7B01G006500 chr6D 115317695 115318464 769 True 712.00 712 83.41800 2621 3406 1 chr6D.!!$R1 785
22 TraesCS7B01G006500 chr4B 211499416 211500201 785 False 706.00 706 83.03800 2622 3404 1 chr4B.!!$F1 782
23 TraesCS7B01G006500 chr4B 600604778 600605589 811 True 387.00 387 75.85000 1594 2394 1 chr4B.!!$R2 800
24 TraesCS7B01G006500 chr4B 600516382 600517191 809 True 374.00 374 75.51800 1594 2393 1 chr4B.!!$R1 799
25 TraesCS7B01G006500 chr4D 476228309 476229109 800 True 370.00 370 75.30900 1594 2393 1 chr4D.!!$R1 799
26 TraesCS7B01G006500 chr2B 24906163 24906968 805 False 294.00 294 73.90200 1597 2393 1 chr2B.!!$F3 796
27 TraesCS7B01G006500 chr2B 24889688 24890561 873 False 276.00 276 73.32600 1568 2402 1 chr2B.!!$F2 834
28 TraesCS7B01G006500 chr2B 24883252 24884074 822 False 274.00 274 73.52600 1600 2393 1 chr2B.!!$F1 793

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
189 200 0.255890 GAGGCAGGCCAGTCCAATTA 59.744 55.0 13.63 0.0 38.92 1.4 F
1178 1190 0.389817 TTCTCGCCGTTGTCCATCTG 60.390 55.0 0.00 0.0 0.00 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1535 1.136336 CGATCGATCTGTGCATGCATG 60.136 52.381 25.64 22.7 0.0 4.06 R
2690 3890 0.039618 AATCCTGCCGGTTTGATGGT 59.960 50.000 1.90 0.0 0.0 3.55 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
59 60 9.255304 CCAACGAAGGAAAAATAAATCAGAAAA 57.745 29.630 0.00 0.00 0.00 2.29
174 185 4.056125 GCCAAAACCCTGCGAGGC 62.056 66.667 0.00 0.00 32.73 4.70
175 186 2.597217 CCAAAACCCTGCGAGGCA 60.597 61.111 0.00 0.00 36.92 4.75
186 197 4.020617 CGAGGCAGGCCAGTCCAA 62.021 66.667 13.63 0.00 38.92 3.53
187 198 2.679716 GAGGCAGGCCAGTCCAAT 59.320 61.111 13.63 0.00 38.92 3.16
188 199 1.000396 GAGGCAGGCCAGTCCAATT 60.000 57.895 13.63 0.00 38.92 2.32
189 200 0.255890 GAGGCAGGCCAGTCCAATTA 59.744 55.000 13.63 0.00 38.92 1.40
190 201 0.704076 AGGCAGGCCAGTCCAATTAA 59.296 50.000 13.63 0.00 38.92 1.40
191 202 0.817654 GGCAGGCCAGTCCAATTAAC 59.182 55.000 5.01 0.00 37.29 2.01
192 203 0.451783 GCAGGCCAGTCCAATTAACG 59.548 55.000 5.01 0.00 37.29 3.18
193 204 0.451783 CAGGCCAGTCCAATTAACGC 59.548 55.000 5.01 0.00 37.29 4.84
194 205 0.679960 AGGCCAGTCCAATTAACGCC 60.680 55.000 5.01 0.00 37.29 5.68
195 206 0.679960 GGCCAGTCCAATTAACGCCT 60.680 55.000 0.00 0.00 34.01 5.52
196 207 1.407712 GGCCAGTCCAATTAACGCCTA 60.408 52.381 0.00 0.00 34.01 3.93
197 208 1.940613 GCCAGTCCAATTAACGCCTAG 59.059 52.381 0.00 0.00 0.00 3.02
198 209 2.679930 GCCAGTCCAATTAACGCCTAGT 60.680 50.000 0.00 0.00 0.00 2.57
199 210 2.936498 CCAGTCCAATTAACGCCTAGTG 59.064 50.000 0.00 0.00 0.00 2.74
200 211 3.369052 CCAGTCCAATTAACGCCTAGTGA 60.369 47.826 0.00 0.00 0.00 3.41
201 212 4.442706 CAGTCCAATTAACGCCTAGTGAT 58.557 43.478 0.00 0.00 0.00 3.06
202 213 4.876107 CAGTCCAATTAACGCCTAGTGATT 59.124 41.667 0.00 0.00 0.00 2.57
203 214 6.046593 CAGTCCAATTAACGCCTAGTGATTA 58.953 40.000 0.00 0.00 0.00 1.75
204 215 6.201044 CAGTCCAATTAACGCCTAGTGATTAG 59.799 42.308 0.00 0.00 0.00 1.73
205 216 6.047231 GTCCAATTAACGCCTAGTGATTAGT 58.953 40.000 0.00 0.00 0.00 2.24
206 217 6.537660 GTCCAATTAACGCCTAGTGATTAGTT 59.462 38.462 0.00 0.00 0.00 2.24
207 218 7.707893 GTCCAATTAACGCCTAGTGATTAGTTA 59.292 37.037 0.00 0.00 0.00 2.24
208 219 7.924412 TCCAATTAACGCCTAGTGATTAGTTAG 59.076 37.037 0.00 0.00 0.00 2.34
209 220 7.307219 CCAATTAACGCCTAGTGATTAGTTAGC 60.307 40.741 0.00 0.00 0.00 3.09
210 221 3.729862 ACGCCTAGTGATTAGTTAGCC 57.270 47.619 0.00 0.00 0.00 3.93
211 222 3.028850 ACGCCTAGTGATTAGTTAGCCA 58.971 45.455 0.00 0.00 0.00 4.75
212 223 3.181478 ACGCCTAGTGATTAGTTAGCCAC 60.181 47.826 0.00 0.00 0.00 5.01
213 224 3.381949 GCCTAGTGATTAGTTAGCCACG 58.618 50.000 0.00 0.00 34.93 4.94
214 225 3.381949 CCTAGTGATTAGTTAGCCACGC 58.618 50.000 0.00 0.00 34.93 5.34
215 226 3.181479 CCTAGTGATTAGTTAGCCACGCA 60.181 47.826 0.00 0.00 34.93 5.24
216 227 3.328382 AGTGATTAGTTAGCCACGCAA 57.672 42.857 0.00 0.00 34.93 4.85
218 229 2.351726 GTGATTAGTTAGCCACGCAAGG 59.648 50.000 0.00 0.00 46.39 3.61
219 230 1.940613 GATTAGTTAGCCACGCAAGGG 59.059 52.381 0.00 0.00 46.39 3.95
230 241 1.084289 ACGCAAGGGATAACGAAAGC 58.916 50.000 0.00 0.00 46.39 3.51
231 242 1.083489 CGCAAGGGATAACGAAAGCA 58.917 50.000 0.00 0.00 0.00 3.91
232 243 1.062587 CGCAAGGGATAACGAAAGCAG 59.937 52.381 0.00 0.00 0.00 4.24
233 244 1.202188 GCAAGGGATAACGAAAGCAGC 60.202 52.381 0.00 0.00 0.00 5.25
234 245 2.083774 CAAGGGATAACGAAAGCAGCA 58.916 47.619 0.00 0.00 0.00 4.41
235 246 2.487762 CAAGGGATAACGAAAGCAGCAA 59.512 45.455 0.00 0.00 0.00 3.91
294 305 1.229853 GTCCCCCTCCTCTTTCCCA 60.230 63.158 0.00 0.00 0.00 4.37
352 363 4.338964 ACCCGTCCGTCTTGTTTTATTTTT 59.661 37.500 0.00 0.00 0.00 1.94
375 386 5.177725 TCTTAGGTTTTTGTTTCTTCGGC 57.822 39.130 0.00 0.00 0.00 5.54
433 444 4.403113 GGAATAAAGTCTCTCCGGTCTCTT 59.597 45.833 0.00 0.00 0.00 2.85
444 455 1.477195 CCGGTCTCTTCCTACCTCGAT 60.477 57.143 0.00 0.00 33.34 3.59
526 537 2.376518 TCCCTTCAGATCTTGGCAGTTT 59.623 45.455 0.00 0.00 0.00 2.66
532 543 1.610522 AGATCTTGGCAGTTTGTGTGC 59.389 47.619 0.00 0.00 40.42 4.57
594 605 4.038763 ACCACGACATCTTCTTCTGTGTTA 59.961 41.667 0.00 0.00 0.00 2.41
609 620 5.865085 TCTGTGTTATTCTGTGGCTTAACT 58.135 37.500 0.00 0.00 0.00 2.24
633 644 3.867857 GTTTCTCCAACCCTCTGATCTC 58.132 50.000 0.00 0.00 0.00 2.75
751 762 1.202710 TGCGGTCTTCAAAGCCTTGTA 60.203 47.619 0.00 0.00 33.94 2.41
770 781 2.751436 GGCGAGGGCATTTGCAGA 60.751 61.111 4.74 0.00 44.36 4.26
856 867 7.406916 TCAGAGGAAGAAGAAGACTAGTATGT 58.593 38.462 0.00 0.00 0.00 2.29
913 925 6.182627 TCTACGTCCAGTTGTCTATCCTTTA 58.817 40.000 0.00 0.00 0.00 1.85
917 929 6.183360 ACGTCCAGTTGTCTATCCTTTATACC 60.183 42.308 0.00 0.00 0.00 2.73
919 931 5.895534 TCCAGTTGTCTATCCTTTATACCGT 59.104 40.000 0.00 0.00 0.00 4.83
976 988 6.434340 AGATGTCCTTTTGGTGTCTTTATTCC 59.566 38.462 0.00 0.00 41.38 3.01
1035 1047 4.849329 CGCACCGTCCGCCTCTAC 62.849 72.222 0.00 0.00 0.00 2.59
1178 1190 0.389817 TTCTCGCCGTTGTCCATCTG 60.390 55.000 0.00 0.00 0.00 2.90
1238 1250 3.531207 CCTGGCGGAGATGCTCGA 61.531 66.667 0.00 0.00 34.52 4.04
1469 1481 2.028930 AGAAGGTCGGTGTCAATCTCAC 60.029 50.000 0.00 0.00 35.36 3.51
1499 1511 1.392756 GCCGTACGTACATGATCGAC 58.607 55.000 24.50 0.00 0.00 4.20
1523 1535 2.555325 GTGTAGGGTTTTTAGGGCACAC 59.445 50.000 0.00 0.00 0.00 3.82
1548 1560 3.429881 GCATGCACAGATCGATCGATAAA 59.570 43.478 29.45 12.35 34.60 1.40
1549 1561 4.665142 GCATGCACAGATCGATCGATAAAC 60.665 45.833 29.45 17.59 34.60 2.01
1550 1562 4.040445 TGCACAGATCGATCGATAAACA 57.960 40.909 29.45 19.37 34.60 2.83
1551 1563 4.620982 TGCACAGATCGATCGATAAACAT 58.379 39.130 29.45 8.59 34.60 2.71
1552 1564 4.681483 TGCACAGATCGATCGATAAACATC 59.319 41.667 29.45 17.24 34.60 3.06
1554 1566 5.387855 GCACAGATCGATCGATAAACATCAC 60.388 44.000 29.45 14.78 34.60 3.06
1555 1567 4.912187 ACAGATCGATCGATAAACATCACG 59.088 41.667 29.45 14.36 34.60 4.35
1557 1569 5.625311 CAGATCGATCGATAAACATCACGAA 59.375 40.000 29.45 0.00 38.22 3.85
1558 1570 5.625721 AGATCGATCGATAAACATCACGAAC 59.374 40.000 29.45 12.70 38.22 3.95
1559 1571 4.664188 TCGATCGATAAACATCACGAACA 58.336 39.130 15.15 0.00 38.22 3.18
1560 1572 5.278604 TCGATCGATAAACATCACGAACAT 58.721 37.500 15.15 0.00 38.22 2.71
1561 1573 5.398416 TCGATCGATAAACATCACGAACATC 59.602 40.000 15.15 0.00 38.22 3.06
1562 1574 5.399596 CGATCGATAAACATCACGAACATCT 59.600 40.000 10.26 0.00 38.22 2.90
1563 1575 6.074835 CGATCGATAAACATCACGAACATCTT 60.075 38.462 10.26 0.00 38.22 2.40
1564 1576 6.961359 TCGATAAACATCACGAACATCTTT 57.039 33.333 0.00 0.00 0.00 2.52
1565 1577 7.359262 TCGATAAACATCACGAACATCTTTT 57.641 32.000 0.00 0.00 0.00 2.27
1566 1578 8.468720 TCGATAAACATCACGAACATCTTTTA 57.531 30.769 0.00 0.00 0.00 1.52
1630 1644 0.179051 GAAGCTGGGGAGCAGATCAG 60.179 60.000 0.00 0.00 37.25 2.90
1862 1882 2.877113 CGTATCGCGTGCCACGAA 60.877 61.111 23.33 8.43 46.05 3.85
1991 2042 1.812922 GCAGCTGACCGACAGGATG 60.813 63.158 20.43 0.00 45.82 3.51
2103 3279 2.593436 CCGAGTTGGCCGGTGTTT 60.593 61.111 1.90 0.00 41.91 2.83
2105 3281 1.730451 CCGAGTTGGCCGGTGTTTTT 61.730 55.000 1.90 0.00 41.91 1.94
2108 3284 0.458260 AGTTGGCCGGTGTTTTTCAC 59.542 50.000 1.90 0.00 45.47 3.18
2140 3316 4.060038 GGACGCTTTCGACCCGGA 62.060 66.667 0.73 0.00 43.08 5.14
2437 3637 2.753966 CGAACATGGCCTTCGCAGG 61.754 63.158 12.06 0.00 44.28 4.85
2454 3654 2.392662 CAGGCTCAGGAAGTCAGGATA 58.607 52.381 0.00 0.00 29.30 2.59
2508 3708 4.269123 TCGTAATTAGGTGCGCTACAATTG 59.731 41.667 9.73 3.24 0.00 2.32
2576 3776 3.272574 AGATAGCTTGGTCCACATGTG 57.727 47.619 19.31 19.31 0.00 3.21
2591 3791 3.308323 CACATGTGGGAAAACAAAAACCG 59.692 43.478 18.51 0.00 32.81 4.44
2596 3796 6.461110 TGTGGGAAAACAAAAACCGTTATA 57.539 33.333 0.00 0.00 0.00 0.98
2690 3890 3.816523 AGCCCGACTTTGAATTAACGAAA 59.183 39.130 0.00 0.00 0.00 3.46
2698 3898 7.377397 CGACTTTGAATTAACGAAACCATCAAA 59.623 33.333 0.00 0.00 34.99 2.69
2700 3900 7.436970 ACTTTGAATTAACGAAACCATCAAACC 59.563 33.333 0.00 0.00 33.32 3.27
2702 3902 3.900388 TTAACGAAACCATCAAACCGG 57.100 42.857 0.00 0.00 0.00 5.28
3091 4301 1.369625 GAGGAGCATACCCACAAACG 58.630 55.000 0.00 0.00 0.00 3.60
3121 4331 0.108585 ACCAAGCGAACACCATCACT 59.891 50.000 0.00 0.00 0.00 3.41
3246 4456 2.677875 GCAACAGGAAGGCCAGGG 60.678 66.667 5.01 0.00 36.29 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.447238 TCTGATTTATTTTTCCTTCGTTGGTCT 59.553 33.333 0.00 0.00 0.00 3.85
48 49 9.243105 CAAACCCTATCTTCCTTTTCTGATTTA 57.757 33.333 0.00 0.00 0.00 1.40
59 60 2.311841 CCCAACCAAACCCTATCTTCCT 59.688 50.000 0.00 0.00 0.00 3.36
146 151 2.156098 GGGTTTTGGCGATGTCTACAA 58.844 47.619 0.00 0.00 0.00 2.41
170 181 0.255890 TAATTGGACTGGCCTGCCTC 59.744 55.000 18.87 7.85 37.63 4.70
173 184 0.451783 CGTTAATTGGACTGGCCTGC 59.548 55.000 9.95 2.57 37.63 4.85
174 185 0.451783 GCGTTAATTGGACTGGCCTG 59.548 55.000 8.29 8.29 37.63 4.85
175 186 0.679960 GGCGTTAATTGGACTGGCCT 60.680 55.000 3.32 0.00 37.63 5.19
176 187 0.679960 AGGCGTTAATTGGACTGGCC 60.680 55.000 0.00 0.00 39.33 5.36
177 188 1.940613 CTAGGCGTTAATTGGACTGGC 59.059 52.381 0.00 0.00 0.00 4.85
178 189 2.936498 CACTAGGCGTTAATTGGACTGG 59.064 50.000 0.00 0.00 0.00 4.00
179 190 3.857052 TCACTAGGCGTTAATTGGACTG 58.143 45.455 0.00 0.00 0.00 3.51
180 191 4.755266 ATCACTAGGCGTTAATTGGACT 57.245 40.909 0.00 0.00 0.00 3.85
181 192 6.047231 ACTAATCACTAGGCGTTAATTGGAC 58.953 40.000 0.00 0.00 31.14 4.02
182 193 6.229936 ACTAATCACTAGGCGTTAATTGGA 57.770 37.500 0.00 0.00 31.14 3.53
183 194 6.920569 AACTAATCACTAGGCGTTAATTGG 57.079 37.500 0.00 0.00 31.14 3.16
184 195 7.307219 GGCTAACTAATCACTAGGCGTTAATTG 60.307 40.741 0.00 0.00 31.14 2.32
185 196 6.704937 GGCTAACTAATCACTAGGCGTTAATT 59.295 38.462 0.00 0.00 31.14 1.40
186 197 6.183360 TGGCTAACTAATCACTAGGCGTTAAT 60.183 38.462 0.00 0.00 40.21 1.40
187 198 5.127519 TGGCTAACTAATCACTAGGCGTTAA 59.872 40.000 0.00 0.00 40.21 2.01
188 199 4.646040 TGGCTAACTAATCACTAGGCGTTA 59.354 41.667 0.00 0.00 40.21 3.18
189 200 3.449737 TGGCTAACTAATCACTAGGCGTT 59.550 43.478 0.00 0.00 40.21 4.84
190 201 3.028850 TGGCTAACTAATCACTAGGCGT 58.971 45.455 0.00 0.00 40.21 5.68
191 202 3.381949 GTGGCTAACTAATCACTAGGCG 58.618 50.000 0.00 0.00 40.21 5.52
192 203 3.381949 CGTGGCTAACTAATCACTAGGC 58.618 50.000 0.00 0.00 38.39 3.93
193 204 3.181479 TGCGTGGCTAACTAATCACTAGG 60.181 47.826 0.00 0.00 31.14 3.02
194 205 4.041740 TGCGTGGCTAACTAATCACTAG 57.958 45.455 0.00 0.00 0.00 2.57
195 206 4.430007 CTTGCGTGGCTAACTAATCACTA 58.570 43.478 0.00 0.00 0.00 2.74
196 207 3.262420 CTTGCGTGGCTAACTAATCACT 58.738 45.455 0.00 0.00 0.00 3.41
197 208 2.351726 CCTTGCGTGGCTAACTAATCAC 59.648 50.000 0.00 0.00 0.00 3.06
198 209 2.627945 CCTTGCGTGGCTAACTAATCA 58.372 47.619 0.00 0.00 0.00 2.57
199 210 1.940613 CCCTTGCGTGGCTAACTAATC 59.059 52.381 0.00 0.00 0.00 1.75
200 211 1.557832 TCCCTTGCGTGGCTAACTAAT 59.442 47.619 0.00 0.00 0.00 1.73
201 212 0.978151 TCCCTTGCGTGGCTAACTAA 59.022 50.000 0.00 0.00 0.00 2.24
202 213 1.200519 ATCCCTTGCGTGGCTAACTA 58.799 50.000 0.00 0.00 0.00 2.24
203 214 1.200519 TATCCCTTGCGTGGCTAACT 58.799 50.000 0.00 0.00 0.00 2.24
204 215 1.669265 GTTATCCCTTGCGTGGCTAAC 59.331 52.381 0.00 0.00 0.00 2.34
205 216 1.741055 CGTTATCCCTTGCGTGGCTAA 60.741 52.381 0.00 0.00 0.00 3.09
206 217 0.179094 CGTTATCCCTTGCGTGGCTA 60.179 55.000 0.00 0.00 0.00 3.93
207 218 1.449601 CGTTATCCCTTGCGTGGCT 60.450 57.895 0.00 0.00 0.00 4.75
208 219 1.022451 TTCGTTATCCCTTGCGTGGC 61.022 55.000 0.00 0.00 0.00 5.01
209 220 1.396996 CTTTCGTTATCCCTTGCGTGG 59.603 52.381 0.00 0.00 0.00 4.94
210 221 1.202031 GCTTTCGTTATCCCTTGCGTG 60.202 52.381 0.00 0.00 0.00 5.34
211 222 1.084289 GCTTTCGTTATCCCTTGCGT 58.916 50.000 0.00 0.00 0.00 5.24
212 223 1.062587 CTGCTTTCGTTATCCCTTGCG 59.937 52.381 0.00 0.00 0.00 4.85
213 224 1.202188 GCTGCTTTCGTTATCCCTTGC 60.202 52.381 0.00 0.00 0.00 4.01
214 225 2.083774 TGCTGCTTTCGTTATCCCTTG 58.916 47.619 0.00 0.00 0.00 3.61
215 226 2.488153 GTTGCTGCTTTCGTTATCCCTT 59.512 45.455 0.00 0.00 0.00 3.95
216 227 2.084546 GTTGCTGCTTTCGTTATCCCT 58.915 47.619 0.00 0.00 0.00 4.20
217 228 1.132453 GGTTGCTGCTTTCGTTATCCC 59.868 52.381 0.00 0.00 0.00 3.85
218 229 1.132453 GGGTTGCTGCTTTCGTTATCC 59.868 52.381 0.00 0.00 0.00 2.59
219 230 1.810151 TGGGTTGCTGCTTTCGTTATC 59.190 47.619 0.00 0.00 0.00 1.75
220 231 1.812571 CTGGGTTGCTGCTTTCGTTAT 59.187 47.619 0.00 0.00 0.00 1.89
221 232 1.234821 CTGGGTTGCTGCTTTCGTTA 58.765 50.000 0.00 0.00 0.00 3.18
222 233 2.032981 CTGGGTTGCTGCTTTCGTT 58.967 52.632 0.00 0.00 0.00 3.85
223 234 2.555547 GCTGGGTTGCTGCTTTCGT 61.556 57.895 0.00 0.00 0.00 3.85
224 235 2.256461 GCTGGGTTGCTGCTTTCG 59.744 61.111 0.00 0.00 0.00 3.46
225 236 2.653115 GGCTGGGTTGCTGCTTTC 59.347 61.111 0.00 0.00 0.00 2.62
226 237 3.297620 CGGCTGGGTTGCTGCTTT 61.298 61.111 0.00 0.00 32.21 3.51
260 271 4.363990 ACTGAGGCGGCGACAGTG 62.364 66.667 30.91 16.17 42.18 3.66
275 286 1.083141 GGGAAAGAGGAGGGGGACT 59.917 63.158 0.00 0.00 0.00 3.85
352 363 5.584442 GCCGAAGAAACAAAAACCTAAGAA 58.416 37.500 0.00 0.00 0.00 2.52
375 386 4.129737 ACCACCTCGTCGATGCCG 62.130 66.667 0.00 0.00 37.07 5.69
433 444 0.812811 CGGACGTCATCGAGGTAGGA 60.813 60.000 18.91 0.00 40.62 2.94
475 486 2.338809 TCTGGGGACACAAACTCTCAT 58.661 47.619 0.00 0.00 35.60 2.90
526 537 2.438021 AGTACTCCTTGAAAGGCACACA 59.562 45.455 4.08 0.00 46.06 3.72
594 605 3.418684 AACCGAGTTAAGCCACAGAAT 57.581 42.857 0.00 0.00 0.00 2.40
633 644 1.580942 CTTGCAATCCACCACCACG 59.419 57.895 0.00 0.00 0.00 4.94
751 762 2.362760 TGCAAATGCCCTCGCCAT 60.363 55.556 2.46 0.00 41.18 4.40
770 781 4.943093 ACCAACAGCAAAGAAAAGCAAAAT 59.057 33.333 0.00 0.00 0.00 1.82
990 1002 1.427020 GAACTGCATCTTGCCTCGC 59.573 57.895 0.00 0.00 44.23 5.03
991 1003 0.392193 AGGAACTGCATCTTGCCTCG 60.392 55.000 0.00 0.00 44.23 4.63
992 1004 3.566130 AGGAACTGCATCTTGCCTC 57.434 52.632 0.00 0.00 44.23 4.70
1035 1047 1.817941 CCATCGCCGTAGTTTGGGG 60.818 63.158 0.00 0.00 40.58 4.96
1469 1481 1.804326 CGTACGGCCAAACGAGAGG 60.804 63.158 19.36 0.00 41.55 3.69
1499 1511 2.224917 TGCCCTAAAAACCCTACACAGG 60.225 50.000 0.00 0.00 42.22 4.00
1523 1535 1.136336 CGATCGATCTGTGCATGCATG 60.136 52.381 25.64 22.70 0.00 4.06
1551 1563 9.605955 CACATTAATTGTAAAAGATGTTCGTGA 57.394 29.630 0.00 0.00 36.57 4.35
1552 1564 9.393249 ACACATTAATTGTAAAAGATGTTCGTG 57.607 29.630 0.00 0.00 36.57 4.35
1554 1566 8.365210 GCACACATTAATTGTAAAAGATGTTCG 58.635 33.333 0.00 0.00 36.57 3.95
1555 1567 8.365210 CGCACACATTAATTGTAAAAGATGTTC 58.635 33.333 0.00 0.00 36.57 3.18
1557 1569 7.367285 ACGCACACATTAATTGTAAAAGATGT 58.633 30.769 0.00 0.00 36.57 3.06
1558 1570 7.795431 ACGCACACATTAATTGTAAAAGATG 57.205 32.000 0.00 0.00 36.57 2.90
1559 1571 8.508062 TGTACGCACACATTAATTGTAAAAGAT 58.492 29.630 0.00 0.00 36.57 2.40
1560 1572 7.862648 TGTACGCACACATTAATTGTAAAAGA 58.137 30.769 0.00 0.00 36.57 2.52
1561 1573 8.574627 CATGTACGCACACATTAATTGTAAAAG 58.425 33.333 0.00 0.00 37.02 2.27
1562 1574 8.290325 TCATGTACGCACACATTAATTGTAAAA 58.710 29.630 0.00 0.00 37.02 1.52
1563 1575 7.807680 TCATGTACGCACACATTAATTGTAAA 58.192 30.769 0.00 0.00 37.02 2.01
1564 1576 7.365840 TCATGTACGCACACATTAATTGTAA 57.634 32.000 0.00 0.00 37.02 2.41
1565 1577 6.969828 TCATGTACGCACACATTAATTGTA 57.030 33.333 0.00 0.00 37.02 2.41
1566 1578 5.871465 TCATGTACGCACACATTAATTGT 57.129 34.783 0.00 0.00 37.02 2.71
1862 1882 1.377994 CTGGAGCACCTTGAAGCCT 59.622 57.895 0.71 0.00 37.04 4.58
1927 1977 3.027412 AGGAAGATGCACATCGAGTAGT 58.973 45.455 5.04 0.00 42.48 2.73
2103 3279 2.833794 CTTGAGTCCCAAGTCGTGAAA 58.166 47.619 0.00 0.00 45.52 2.69
2437 3637 6.902771 TTACTATATCCTGACTTCCTGAGC 57.097 41.667 0.00 0.00 0.00 4.26
2477 3677 5.176958 AGCGCACCTAATTACGAATTCATAC 59.823 40.000 11.47 0.00 32.38 2.39
2486 3686 4.514506 CAATTGTAGCGCACCTAATTACG 58.485 43.478 11.47 0.00 0.00 3.18
2508 3708 6.560711 ACTTTGTATATGGAAACGAAATGGC 58.439 36.000 0.00 0.00 0.00 4.40
2542 3742 6.010650 ACCAAGCTATCTATATAGACCAGGGA 60.011 42.308 14.71 0.00 37.84 4.20
2545 3745 6.892456 TGGACCAAGCTATCTATATAGACCAG 59.108 42.308 14.71 14.75 37.84 4.00
2576 3776 5.530712 TGCTATAACGGTTTTTGTTTTCCC 58.469 37.500 0.00 0.00 0.00 3.97
2647 3847 1.258445 GGTTCCAGCTCTTCTCGGGA 61.258 60.000 0.00 0.00 0.00 5.14
2690 3890 0.039618 AATCCTGCCGGTTTGATGGT 59.960 50.000 1.90 0.00 0.00 3.55
2698 3898 2.375345 CCCCTGTAATCCTGCCGGT 61.375 63.158 1.90 0.00 0.00 5.28
2700 3900 2.203209 GCCCCTGTAATCCTGCCG 60.203 66.667 0.00 0.00 0.00 5.69
2702 3902 1.453928 GGTGCCCCTGTAATCCTGC 60.454 63.158 0.00 0.00 0.00 4.85
2981 4190 2.435693 GGCACCCATCGAGCCTAGT 61.436 63.158 5.43 0.00 44.92 2.57
3091 4301 0.955428 TCGCTTGGTTGGTCATCTGC 60.955 55.000 0.00 0.00 0.00 4.26
3177 4387 1.157585 GCCGTCTTGGGTCTTCTTTC 58.842 55.000 0.00 0.00 38.63 2.62
3246 4456 4.241999 GATGGCGGTGCGTGATGC 62.242 66.667 0.00 0.00 46.70 3.91
3262 4472 1.064758 GTAGGGATGTTGGTGGCATGA 60.065 52.381 0.00 0.00 0.00 3.07
3326 4538 1.228215 TGTCGACGACACCCTGGTA 60.228 57.895 26.04 1.20 37.67 3.25


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

AutoCloner maintained by Alex Coulton.