Multiple sequence alignment - TraesCS3D01G370700

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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 TraesCS3D01G370700 chr3D 100.000 4205 0 0 1 4205 484344587 484348791 0.000000e+00 7766.0
1 TraesCS3D01G370700 chr3D 88.335 1003 70 18 2504 3496 484452428 484453393 0.000000e+00 1160.0
2 TraesCS3D01G370700 chr3D 88.202 178 21 0 4028 4205 58372129 58372306 3.290000e-51 213.0
3 TraesCS3D01G370700 chr3A 86.421 3115 229 90 1 3042 627274632 627277625 0.000000e+00 3230.0
4 TraesCS3D01G370700 chr3A 93.521 1173 56 10 3039 4205 627277657 627278815 0.000000e+00 1727.0
5 TraesCS3D01G370700 chr3A 86.536 869 98 10 2506 3372 627676890 627677741 0.000000e+00 939.0
6 TraesCS3D01G370700 chr3A 78.245 809 111 33 999 1783 107618000 107617233 3.830000e-125 459.0
7 TraesCS3D01G370700 chr3A 90.000 80 8 0 4124 4203 67350699 67350778 2.070000e-18 104.0
8 TraesCS3D01G370700 chr3B 87.937 2089 134 52 1430 3479 647178381 647180390 0.000000e+00 2353.0
9 TraesCS3D01G370700 chr3B 86.074 1192 74 42 287 1431 647177200 647178346 0.000000e+00 1197.0
10 TraesCS3D01G370700 chr3B 81.152 191 17 7 46 228 647177022 647177201 7.330000e-28 135.0
11 TraesCS3D01G370700 chr7D 79.505 727 116 16 3502 4203 153947449 153946731 1.760000e-133 486.0
12 TraesCS3D01G370700 chr7D 79.184 735 104 25 3497 4203 572730393 572729680 8.230000e-127 464.0
13 TraesCS3D01G370700 chr7D 78.378 777 105 31 999 1750 2873014 2872276 2.980000e-121 446.0
14 TraesCS3D01G370700 chr7D 100.000 29 0 0 3635 3663 63458073 63458101 2.000000e-03 54.7
15 TraesCS3D01G370700 chr5D 79.070 774 105 26 999 1750 10495640 10494902 2.940000e-131 479.0
16 TraesCS3D01G370700 chr5D 77.503 809 109 43 999 1778 511490989 511490225 6.500000e-113 418.0
17 TraesCS3D01G370700 chr5D 77.778 549 83 15 3625 4153 505177544 505177015 6.830000e-78 302.0
18 TraesCS3D01G370700 chr7B 79.098 732 105 22 3497 4203 630155402 630154694 1.070000e-125 460.0
19 TraesCS3D01G370700 chr7B 80.337 178 29 6 3490 3663 573102797 573102972 3.410000e-26 130.0
20 TraesCS3D01G370700 chr2D 78.737 776 101 30 999 1750 33338451 33337716 1.070000e-125 460.0
21 TraesCS3D01G370700 chr5B 77.393 867 135 38 939 1783 76158224 76159051 3.830000e-125 459.0
22 TraesCS3D01G370700 chr5B 76.349 723 134 21 3500 4203 130735160 130734456 1.860000e-93 353.0
23 TraesCS3D01G370700 chr2B 80.000 530 84 16 3502 4024 6272728 6272214 5.130000e-99 372.0
24 TraesCS3D01G370700 chr2B 76.808 733 117 32 3506 4203 202903797 202903083 3.090000e-96 363.0
25 TraesCS3D01G370700 chr2B 75.886 734 118 18 3500 4203 233743759 233744463 1.890000e-83 320.0
26 TraesCS3D01G370700 chr2B 78.443 167 34 2 4029 4194 247625666 247625501 1.600000e-19 108.0
27 TraesCS3D01G370700 chr2B 100.000 28 0 0 3635 3662 551477152 551477125 8.000000e-03 52.8
28 TraesCS3D01G370700 chr1D 92.694 219 16 0 995 1213 368322525 368322307 2.440000e-82 316.0
29 TraesCS3D01G370700 chr1D 92.694 219 16 0 995 1213 369903971 369903753 2.440000e-82 316.0
30 TraesCS3D01G370700 chr1D 77.316 529 87 20 3701 4203 182082133 182081612 8.900000e-72 281.0
31 TraesCS3D01G370700 chr1D 90.426 94 7 2 1320 1411 368322216 368322123 5.710000e-24 122.0
32 TraesCS3D01G370700 chr1D 89.333 75 8 0 1663 1737 369903428 369903354 1.240000e-15 95.3
33 TraesCS3D01G370700 chr1D 90.698 43 4 0 4143 4185 434066839 434066881 1.630000e-04 58.4
34 TraesCS3D01G370700 chr1B 92.694 219 16 0 995 1213 492358038 492357820 2.440000e-82 316.0
35 TraesCS3D01G370700 chr1B 93.827 81 5 0 1320 1400 492357733 492357653 5.710000e-24 122.0
36 TraesCS3D01G370700 chr1B 83.065 124 20 1 3554 3676 448144021 448144144 1.240000e-20 111.0
37 TraesCS3D01G370700 chr1A 92.308 221 16 1 993 1213 467259934 467259715 3.160000e-81 313.0
38 TraesCS3D01G370700 chr1A 92.473 93 7 0 2710 2802 467258493 467258401 2.640000e-27 134.0
39 TraesCS3D01G370700 chr1A 93.827 81 5 0 1320 1400 467259638 467259558 5.710000e-24 122.0
40 TraesCS3D01G370700 chrUn 84.167 240 29 7 2065 2296 87129871 87129633 1.520000e-54 224.0
41 TraesCS3D01G370700 chr7A 77.976 336 48 8 1020 1352 317691539 317691851 2.000000e-43 187.0
42 TraesCS3D01G370700 chr6D 80.000 175 35 0 4029 4203 462195344 462195170 3.410000e-26 130.0
43 TraesCS3D01G370700 chr6B 79.231 130 25 2 4073 4201 93981649 93981777 5.790000e-14 89.8


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 TraesCS3D01G370700 chr3D 484344587 484348791 4204 False 7766.000000 7766 100.000000 1 4205 1 chr3D.!!$F2 4204
1 TraesCS3D01G370700 chr3D 484452428 484453393 965 False 1160.000000 1160 88.335000 2504 3496 1 chr3D.!!$F3 992
2 TraesCS3D01G370700 chr3A 627274632 627278815 4183 False 2478.500000 3230 89.971000 1 4205 2 chr3A.!!$F3 4204
3 TraesCS3D01G370700 chr3A 627676890 627677741 851 False 939.000000 939 86.536000 2506 3372 1 chr3A.!!$F2 866
4 TraesCS3D01G370700 chr3A 107617233 107618000 767 True 459.000000 459 78.245000 999 1783 1 chr3A.!!$R1 784
5 TraesCS3D01G370700 chr3B 647177022 647180390 3368 False 1228.333333 2353 85.054333 46 3479 3 chr3B.!!$F1 3433
6 TraesCS3D01G370700 chr7D 153946731 153947449 718 True 486.000000 486 79.505000 3502 4203 1 chr7D.!!$R2 701
7 TraesCS3D01G370700 chr7D 572729680 572730393 713 True 464.000000 464 79.184000 3497 4203 1 chr7D.!!$R3 706
8 TraesCS3D01G370700 chr7D 2872276 2873014 738 True 446.000000 446 78.378000 999 1750 1 chr7D.!!$R1 751
9 TraesCS3D01G370700 chr5D 10494902 10495640 738 True 479.000000 479 79.070000 999 1750 1 chr5D.!!$R1 751
10 TraesCS3D01G370700 chr5D 511490225 511490989 764 True 418.000000 418 77.503000 999 1778 1 chr5D.!!$R3 779
11 TraesCS3D01G370700 chr5D 505177015 505177544 529 True 302.000000 302 77.778000 3625 4153 1 chr5D.!!$R2 528
12 TraesCS3D01G370700 chr7B 630154694 630155402 708 True 460.000000 460 79.098000 3497 4203 1 chr7B.!!$R1 706
13 TraesCS3D01G370700 chr2D 33337716 33338451 735 True 460.000000 460 78.737000 999 1750 1 chr2D.!!$R1 751
14 TraesCS3D01G370700 chr5B 76158224 76159051 827 False 459.000000 459 77.393000 939 1783 1 chr5B.!!$F1 844
15 TraesCS3D01G370700 chr5B 130734456 130735160 704 True 353.000000 353 76.349000 3500 4203 1 chr5B.!!$R1 703
16 TraesCS3D01G370700 chr2B 6272214 6272728 514 True 372.000000 372 80.000000 3502 4024 1 chr2B.!!$R1 522
17 TraesCS3D01G370700 chr2B 202903083 202903797 714 True 363.000000 363 76.808000 3506 4203 1 chr2B.!!$R2 697
18 TraesCS3D01G370700 chr2B 233743759 233744463 704 False 320.000000 320 75.886000 3500 4203 1 chr2B.!!$F1 703
19 TraesCS3D01G370700 chr1D 182081612 182082133 521 True 281.000000 281 77.316000 3701 4203 1 chr1D.!!$R1 502
20 TraesCS3D01G370700 chr1D 369903354 369903971 617 True 205.650000 316 91.013500 995 1737 2 chr1D.!!$R3 742

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
576 621 0.037882 CATCGTCACTGTCCTGCTGT 60.038 55.0 0.00 0.00 0.00 4.40 F
1461 1640 0.316442 CTGCTTTGTGACACACTGCG 60.316 55.0 20.23 14.01 35.11 5.18 F
2059 2281 0.252197 GGGAGTTCCTGCACGGTAAT 59.748 55.0 0.00 0.00 35.95 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1930 2152 0.034767 CCCAAAGATCTGCAGAGCCA 60.035 55.000 27.52 1.13 0.0 4.75 R
2321 2560 0.459585 TTCGGCGGTATCTGAAGCAC 60.460 55.000 7.21 0.00 0.0 4.40 R
3266 3561 1.457303 GCCTGACATACGAATCGCATC 59.543 52.381 1.15 0.00 0.0 3.91 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
129 157 5.523916 GGCACGTTATCTCTGTTGACATTAT 59.476 40.000 0.00 0.00 0.00 1.28
131 159 6.901887 GCACGTTATCTCTGTTGACATTATTG 59.098 38.462 0.00 0.00 0.00 1.90
133 161 7.064609 CACGTTATCTCTGTTGACATTATTGGT 59.935 37.037 0.00 0.00 0.00 3.67
135 163 7.277760 CGTTATCTCTGTTGACATTATTGGTCA 59.722 37.037 0.00 0.00 43.12 4.02
171 199 0.166814 CAAGTTTGCGCTAGTGGCTC 59.833 55.000 9.73 0.00 39.13 4.70
174 202 0.108329 GTTTGCGCTAGTGGCTCCTA 60.108 55.000 9.73 0.00 39.13 2.94
188 216 2.342179 GCTCCTACAAGTCTTGACTGC 58.658 52.381 19.53 11.12 0.00 4.40
252 280 2.149973 AAAAGCAGCTATTCCCCTGG 57.850 50.000 0.00 0.00 0.00 4.45
312 340 1.657804 GGCTGGGCCTGGTATATACT 58.342 55.000 12.70 0.00 46.69 2.12
313 341 1.555533 GGCTGGGCCTGGTATATACTC 59.444 57.143 12.70 3.99 46.69 2.59
314 342 1.555533 GCTGGGCCTGGTATATACTCC 59.444 57.143 12.70 8.60 0.00 3.85
353 386 6.893020 AAAGGTACTCCAGGATATTCACTT 57.107 37.500 0.00 0.00 38.49 3.16
430 466 2.422832 CCATCAAGCAAAGCTCCTCTTC 59.577 50.000 0.00 0.00 38.25 2.87
432 468 3.430042 TCAAGCAAAGCTCCTCTTCAT 57.570 42.857 0.00 0.00 38.25 2.57
434 470 3.755378 TCAAGCAAAGCTCCTCTTCATTC 59.245 43.478 0.00 0.00 38.25 2.67
435 471 3.717452 AGCAAAGCTCCTCTTCATTCT 57.283 42.857 0.00 0.00 30.62 2.40
438 474 4.458642 AGCAAAGCTCCTCTTCATTCTTTC 59.541 41.667 0.00 0.00 30.62 2.62
457 494 6.985117 TCTTTCTGAATGCAATAACAGCTTT 58.015 32.000 0.00 0.00 33.14 3.51
458 495 8.109705 TCTTTCTGAATGCAATAACAGCTTTA 57.890 30.769 0.00 0.00 33.14 1.85
459 496 8.023128 TCTTTCTGAATGCAATAACAGCTTTAC 58.977 33.333 0.00 0.00 33.14 2.01
460 497 6.816134 TCTGAATGCAATAACAGCTTTACA 57.184 33.333 0.00 0.00 33.14 2.41
461 498 7.213216 TCTGAATGCAATAACAGCTTTACAA 57.787 32.000 0.00 0.00 33.14 2.41
462 499 7.307694 TCTGAATGCAATAACAGCTTTACAAG 58.692 34.615 0.00 0.00 33.14 3.16
463 500 7.174772 TCTGAATGCAATAACAGCTTTACAAGA 59.825 33.333 0.00 0.00 33.14 3.02
464 501 7.656412 TGAATGCAATAACAGCTTTACAAGAA 58.344 30.769 0.00 0.00 30.66 2.52
474 511 2.287368 GCTTTACAAGAACAACACCCCG 60.287 50.000 0.00 0.00 0.00 5.73
571 616 2.563179 AGCTAAACATCGTCACTGTCCT 59.437 45.455 0.00 0.00 0.00 3.85
576 621 0.037882 CATCGTCACTGTCCTGCTGT 60.038 55.000 0.00 0.00 0.00 4.40
885 937 2.202837 GCCGTACTACTTGGGCGG 60.203 66.667 0.00 0.00 44.60 6.13
886 938 2.202837 CCGTACTACTTGGGCGGC 60.203 66.667 0.00 0.00 35.90 6.53
887 939 2.574929 CGTACTACTTGGGCGGCA 59.425 61.111 12.47 0.00 0.00 5.69
888 940 1.143183 CGTACTACTTGGGCGGCAT 59.857 57.895 12.47 0.00 0.00 4.40
889 941 0.386476 CGTACTACTTGGGCGGCATA 59.614 55.000 12.47 0.00 0.00 3.14
890 942 1.602165 CGTACTACTTGGGCGGCATAG 60.602 57.143 12.47 9.73 0.00 2.23
897 949 2.234908 ACTTGGGCGGCATAGATAGATC 59.765 50.000 12.47 0.00 0.00 2.75
899 951 0.528684 GGGCGGCATAGATAGATCGC 60.529 60.000 12.47 0.00 42.02 4.58
912 964 1.139734 GATCGCTCGCTCACTTCCA 59.860 57.895 0.00 0.00 0.00 3.53
1228 1296 2.744768 AAGCTGCTGCGCTCTTCCTT 62.745 55.000 16.73 3.08 45.42 3.36
1229 1297 2.748843 GCTGCTGCGCTCTTCCTTC 61.749 63.158 9.73 0.00 0.00 3.46
1230 1298 2.046892 TGCTGCGCTCTTCCTTCC 60.047 61.111 9.73 0.00 0.00 3.46
1234 1302 1.610673 TGCGCTCTTCCTTCCTCCT 60.611 57.895 9.73 0.00 0.00 3.69
1235 1303 1.153469 GCGCTCTTCCTTCCTCCTG 60.153 63.158 0.00 0.00 0.00 3.86
1236 1304 1.153469 CGCTCTTCCTTCCTCCTGC 60.153 63.158 0.00 0.00 0.00 4.85
1238 1306 0.617935 GCTCTTCCTTCCTCCTGCTT 59.382 55.000 0.00 0.00 0.00 3.91
1239 1307 1.406751 GCTCTTCCTTCCTCCTGCTTC 60.407 57.143 0.00 0.00 0.00 3.86
1272 1362 3.390135 TCATCACAGTTGTTCTTCCGTC 58.610 45.455 0.00 0.00 0.00 4.79
1274 1364 3.469008 TCACAGTTGTTCTTCCGTCAT 57.531 42.857 0.00 0.00 0.00 3.06
1282 1372 5.530915 AGTTGTTCTTCCGTCATGATGAAAA 59.469 36.000 16.77 9.10 32.31 2.29
1288 1401 7.482654 TCTTCCGTCATGATGAAAATATGAC 57.517 36.000 16.77 0.00 44.39 3.06
1297 1410 6.375945 TGATGAAAATATGACGATGGTTGG 57.624 37.500 0.00 0.00 0.00 3.77
1298 1411 6.118852 TGATGAAAATATGACGATGGTTGGA 58.881 36.000 0.00 0.00 0.00 3.53
1299 1412 6.601217 TGATGAAAATATGACGATGGTTGGAA 59.399 34.615 0.00 0.00 0.00 3.53
1303 1416 7.758980 TGAAAATATGACGATGGTTGGAAATTG 59.241 33.333 0.00 0.00 0.00 2.32
1306 1419 2.556189 TGACGATGGTTGGAAATTGGTG 59.444 45.455 0.00 0.00 0.00 4.17
1307 1420 1.892474 ACGATGGTTGGAAATTGGTGG 59.108 47.619 0.00 0.00 0.00 4.61
1308 1421 1.892474 CGATGGTTGGAAATTGGTGGT 59.108 47.619 0.00 0.00 0.00 4.16
1351 1474 0.320247 AGAAGAAGCTGGACGTGCTG 60.320 55.000 8.99 9.33 41.03 4.41
1414 1556 3.001330 GCACCGTATGAATTTTCTCTCGG 59.999 47.826 14.05 14.05 38.71 4.63
1456 1635 2.017138 TCGTTCTGCTTTGTGACACA 57.983 45.000 3.56 3.56 0.00 3.72
1457 1636 1.663643 TCGTTCTGCTTTGTGACACAC 59.336 47.619 8.05 0.00 34.56 3.82
1461 1640 0.316442 CTGCTTTGTGACACACTGCG 60.316 55.000 20.23 14.01 35.11 5.18
1558 1738 3.252458 GCTCCGTGGAAAGTGTGTAAAAT 59.748 43.478 0.00 0.00 0.00 1.82
1568 1749 6.293790 GGAAAGTGTGTAAAATACTTCGGCTT 60.294 38.462 0.00 0.00 39.12 4.35
1576 1758 3.914426 AATACTTCGGCTTCTCCATGT 57.086 42.857 0.00 0.00 34.01 3.21
1580 1762 2.832129 ACTTCGGCTTCTCCATGTTCTA 59.168 45.455 0.00 0.00 34.01 2.10
1591 1774 5.269189 TCTCCATGTTCTACTCACATACCA 58.731 41.667 0.00 0.00 32.88 3.25
1610 1797 3.144506 CCATGATATGGTTGAGGAGCAC 58.855 50.000 0.00 0.00 45.54 4.40
1787 1991 1.816224 GGAACACGCACAATTATGGGT 59.184 47.619 0.00 0.00 45.82 4.51
1793 1997 3.876914 CACGCACAATTATGGGTAGTCAT 59.123 43.478 6.07 0.00 43.31 3.06
1795 1999 5.525745 CACGCACAATTATGGGTAGTCATAA 59.474 40.000 6.07 0.00 43.31 1.90
1814 2030 7.869429 AGTCATAATTTGCCTTTTCAAAGTCTG 59.131 33.333 0.00 0.00 39.06 3.51
1817 2033 4.654091 TTTGCCTTTTCAAAGTCTGAGG 57.346 40.909 0.00 0.00 34.81 3.86
1818 2034 2.586425 TGCCTTTTCAAAGTCTGAGGG 58.414 47.619 0.00 0.00 34.81 4.30
1819 2035 2.174639 TGCCTTTTCAAAGTCTGAGGGA 59.825 45.455 0.00 0.00 34.81 4.20
1820 2036 3.222603 GCCTTTTCAAAGTCTGAGGGAA 58.777 45.455 0.00 0.00 34.81 3.97
1821 2037 3.829026 GCCTTTTCAAAGTCTGAGGGAAT 59.171 43.478 0.00 0.00 34.81 3.01
1822 2038 5.010282 GCCTTTTCAAAGTCTGAGGGAATA 58.990 41.667 0.00 0.00 34.81 1.75
1823 2039 5.654209 GCCTTTTCAAAGTCTGAGGGAATAT 59.346 40.000 0.00 0.00 34.81 1.28
1824 2040 6.828785 GCCTTTTCAAAGTCTGAGGGAATATA 59.171 38.462 0.00 0.00 34.81 0.86
1825 2041 7.503902 GCCTTTTCAAAGTCTGAGGGAATATAT 59.496 37.037 0.00 0.00 34.81 0.86
1826 2042 9.061435 CCTTTTCAAAGTCTGAGGGAATATATC 57.939 37.037 0.00 0.00 34.81 1.63
1827 2043 9.844257 CTTTTCAAAGTCTGAGGGAATATATCT 57.156 33.333 0.00 0.00 34.81 1.98
1830 2046 9.838339 TTCAAAGTCTGAGGGAATATATCTTTC 57.162 33.333 0.00 0.00 34.81 2.62
1831 2047 8.432805 TCAAAGTCTGAGGGAATATATCTTTCC 58.567 37.037 8.29 8.29 41.64 3.13
1832 2048 7.937700 AAGTCTGAGGGAATATATCTTTCCA 57.062 36.000 15.62 0.14 43.72 3.53
1833 2049 7.937700 AGTCTGAGGGAATATATCTTTCCAA 57.062 36.000 15.62 4.23 43.72 3.53
1834 2050 8.337118 AGTCTGAGGGAATATATCTTTCCAAA 57.663 34.615 15.62 3.98 43.72 3.28
1835 2051 8.781951 AGTCTGAGGGAATATATCTTTCCAAAA 58.218 33.333 15.62 3.72 43.72 2.44
1836 2052 9.408648 GTCTGAGGGAATATATCTTTCCAAAAA 57.591 33.333 15.62 2.46 43.72 1.94
1861 2077 5.736951 AGTCTCAGGGAATATGCTCATAC 57.263 43.478 0.00 0.00 0.00 2.39
1866 2082 7.446625 GTCTCAGGGAATATGCTCATACAAAAT 59.553 37.037 0.00 0.00 0.00 1.82
1867 2083 8.659527 TCTCAGGGAATATGCTCATACAAAATA 58.340 33.333 0.00 0.00 0.00 1.40
1868 2084 8.853077 TCAGGGAATATGCTCATACAAAATAG 57.147 34.615 0.00 0.00 0.00 1.73
1869 2085 8.659527 TCAGGGAATATGCTCATACAAAATAGA 58.340 33.333 0.00 0.00 0.00 1.98
1913 2135 9.802039 TTCCTTATTCTTACTACATGGTTTTGT 57.198 29.630 0.00 0.00 0.00 2.83
1914 2136 9.226606 TCCTTATTCTTACTACATGGTTTTGTG 57.773 33.333 0.00 0.00 0.00 3.33
1918 2140 8.691661 ATTCTTACTACATGGTTTTGTGTTCT 57.308 30.769 0.00 0.00 0.00 3.01
1919 2141 8.514330 TTCTTACTACATGGTTTTGTGTTCTT 57.486 30.769 0.00 0.00 0.00 2.52
1920 2142 9.616156 TTCTTACTACATGGTTTTGTGTTCTTA 57.384 29.630 0.00 0.00 0.00 2.10
1921 2143 9.048446 TCTTACTACATGGTTTTGTGTTCTTAC 57.952 33.333 0.00 0.00 0.00 2.34
1922 2144 8.734218 TTACTACATGGTTTTGTGTTCTTACA 57.266 30.769 0.00 0.00 0.00 2.41
1923 2145 7.259290 ACTACATGGTTTTGTGTTCTTACAG 57.741 36.000 0.00 0.00 34.24 2.74
1924 2146 6.826741 ACTACATGGTTTTGTGTTCTTACAGT 59.173 34.615 0.00 0.00 34.24 3.55
1925 2147 6.524101 ACATGGTTTTGTGTTCTTACAGTT 57.476 33.333 0.00 0.00 34.24 3.16
1926 2148 6.930731 ACATGGTTTTGTGTTCTTACAGTTT 58.069 32.000 0.00 0.00 34.24 2.66
1927 2149 7.382898 ACATGGTTTTGTGTTCTTACAGTTTT 58.617 30.769 0.00 0.00 34.24 2.43
1928 2150 7.875554 ACATGGTTTTGTGTTCTTACAGTTTTT 59.124 29.630 0.00 0.00 34.24 1.94
2059 2281 0.252197 GGGAGTTCCTGCACGGTAAT 59.748 55.000 0.00 0.00 35.95 1.89
2073 2295 7.855904 CCTGCACGGTAATTAATTAATCAAGTC 59.144 37.037 11.08 0.00 0.00 3.01
2074 2296 8.500753 TGCACGGTAATTAATTAATCAAGTCT 57.499 30.769 11.08 0.00 0.00 3.24
2078 2300 9.543783 ACGGTAATTAATTAATCAAGTCTCCTC 57.456 33.333 11.08 0.00 0.00 3.71
2089 2311 3.053455 CAAGTCTCCTCAACTCGTGTTC 58.947 50.000 0.00 0.00 33.52 3.18
2126 2358 4.577834 TCGTGTGTGACTGTATCTGAAA 57.422 40.909 0.00 0.00 0.00 2.69
2131 2363 4.256920 GTGTGACTGTATCTGAAATGGCT 58.743 43.478 0.00 0.00 0.00 4.75
2140 2372 6.413892 TGTATCTGAAATGGCTTGTGTATGA 58.586 36.000 0.00 0.00 0.00 2.15
2141 2373 6.883756 TGTATCTGAAATGGCTTGTGTATGAA 59.116 34.615 0.00 0.00 0.00 2.57
2143 2375 6.839124 TCTGAAATGGCTTGTGTATGAAAT 57.161 33.333 0.00 0.00 0.00 2.17
2146 2378 8.149647 TCTGAAATGGCTTGTGTATGAAATTTT 58.850 29.630 0.00 0.00 0.00 1.82
2253 2487 0.819259 TCAAGGTGTGCTGGCAGAAC 60.819 55.000 19.18 19.18 0.00 3.01
2321 2560 7.377928 GCATACTAGTAAAATCTGCATGCTTTG 59.622 37.037 20.33 9.28 34.78 2.77
2414 2657 5.236047 CCTACTGCAAAGTATGAGATCTTGC 59.764 44.000 0.00 1.04 0.00 4.01
2442 2685 5.135508 TCAGAGTAGTGTTACTTCCTTGC 57.864 43.478 0.00 0.00 40.21 4.01
2445 2688 4.280174 AGAGTAGTGTTACTTCCTTGCGAA 59.720 41.667 0.00 0.00 40.21 4.70
2446 2689 5.047235 AGAGTAGTGTTACTTCCTTGCGAAT 60.047 40.000 0.00 0.00 40.21 3.34
2447 2690 6.152323 AGAGTAGTGTTACTTCCTTGCGAATA 59.848 38.462 0.00 0.00 40.21 1.75
2459 2709 7.715249 ACTTCCTTGCGAATATCAGCTAAAATA 59.285 33.333 0.00 0.00 0.00 1.40
2526 2783 3.364549 GGATGGTTCATCACCCAAATCA 58.635 45.455 9.68 0.00 46.68 2.57
2577 2834 0.037232 AGCCTGCTTACCTGACGAAC 60.037 55.000 0.00 0.00 0.00 3.95
2583 2840 3.311106 TGCTTACCTGACGAACTAAACG 58.689 45.455 0.00 0.00 0.00 3.60
2602 2860 7.914346 ACTAAACGATTTACCTCTCATACTTCG 59.086 37.037 0.00 0.00 0.00 3.79
2621 2879 1.270839 CGGAAGCTTCTCCCTGACAAA 60.271 52.381 25.05 0.00 31.03 2.83
2642 2900 7.563270 ACAAATGCAAATTTTACACGATCAAC 58.437 30.769 0.00 0.00 0.00 3.18
2978 3236 4.060205 GACGGGTATGTGTTGTTGTAACT 58.940 43.478 0.00 0.00 0.00 2.24
3072 3365 2.941891 TTTCTGCGTTGTGAATCGAC 57.058 45.000 0.00 0.00 0.00 4.20
3266 3561 4.680237 TCGTGGGCCTTGCTGACG 62.680 66.667 4.53 5.13 35.59 4.35
3270 3565 3.512516 GGGCCTTGCTGACGATGC 61.513 66.667 0.84 0.00 0.00 3.91
3290 3585 2.096713 GCGATTCGTATGTCAGGCATTC 60.097 50.000 8.03 0.00 38.94 2.67
3316 3611 7.328737 CCTTTTCTATATATACGTCTGTGGCAC 59.671 40.741 11.55 11.55 0.00 5.01
3417 3713 6.070824 TCCACTGATGATGGCACGTAATATAT 60.071 38.462 0.00 0.00 37.13 0.86
3484 3783 1.359848 CAGGTTGTGCAGGACGTATC 58.640 55.000 0.00 0.00 0.00 2.24
3533 3832 2.736400 GCATGCATTACCTTCAACCAGC 60.736 50.000 14.21 0.00 0.00 4.85
3602 3904 1.603802 CGCATCGGCATGAACCTTAAT 59.396 47.619 0.00 0.00 41.24 1.40
3832 4155 4.101741 ACAAGCACTTCCTCTGTTCTTAGT 59.898 41.667 0.00 0.00 0.00 2.24
3892 4232 2.745884 CGGAGGCGGCAACATCAA 60.746 61.111 13.08 0.00 0.00 2.57
4007 4348 1.424493 CTCCGAAGCCGCTAAGCAAG 61.424 60.000 0.00 0.00 34.23 4.01
4119 4495 3.876341 ACGGACAAAACTGGTAGTTCAA 58.124 40.909 0.00 0.00 37.47 2.69
4135 4511 8.687242 TGGTAGTTCAAACAACAACATTGATAA 58.313 29.630 0.00 0.00 33.45 1.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.665835 TGTTGACCATTTGACACGGC 59.334 50.000 0.00 0.00 0.00 5.68
61 72 1.097232 TTGCATCCAGGAAATCAGCG 58.903 50.000 0.00 0.00 0.00 5.18
129 157 4.699637 ACACTGTCGATAACTTTGACCAA 58.300 39.130 0.00 0.00 37.88 3.67
131 159 4.304110 TGACACTGTCGATAACTTTGACC 58.696 43.478 4.71 0.00 37.88 4.02
133 161 5.597806 ACTTGACACTGTCGATAACTTTGA 58.402 37.500 4.71 0.00 34.95 2.69
135 163 6.715464 CAAACTTGACACTGTCGATAACTTT 58.285 36.000 4.71 0.00 34.95 2.66
171 199 2.224281 TGGTGCAGTCAAGACTTGTAGG 60.224 50.000 14.75 6.71 40.20 3.18
174 202 1.668419 GTGGTGCAGTCAAGACTTGT 58.332 50.000 14.75 0.00 40.20 3.16
188 216 0.233590 TCGAATGCGTTTTCGTGGTG 59.766 50.000 17.30 0.00 46.50 4.17
252 280 2.512515 CCTCAACGCTAGCCTGGC 60.513 66.667 11.65 11.65 0.00 4.85
298 326 1.907255 GGTGGGAGTATATACCAGGCC 59.093 57.143 9.32 0.00 34.39 5.19
375 408 2.030540 GCGTACGTGGAATATCCTAGCA 60.031 50.000 17.90 0.00 37.46 3.49
403 439 1.969085 CTTTGCTTGATGGCCTGCA 59.031 52.632 3.32 4.02 0.00 4.41
432 468 6.579666 AGCTGTTATTGCATTCAGAAAGAA 57.420 33.333 10.58 0.00 41.28 2.52
434 470 7.809331 TGTAAAGCTGTTATTGCATTCAGAAAG 59.191 33.333 10.58 0.00 0.00 2.62
435 471 7.656412 TGTAAAGCTGTTATTGCATTCAGAAA 58.344 30.769 10.58 0.00 0.00 2.52
438 474 7.307694 TCTTGTAAAGCTGTTATTGCATTCAG 58.692 34.615 0.00 0.00 45.70 3.02
457 494 1.541670 GCTCGGGGTGTTGTTCTTGTA 60.542 52.381 0.00 0.00 0.00 2.41
458 495 0.818040 GCTCGGGGTGTTGTTCTTGT 60.818 55.000 0.00 0.00 0.00 3.16
459 496 0.535102 AGCTCGGGGTGTTGTTCTTG 60.535 55.000 0.00 0.00 0.00 3.02
460 497 0.182775 AAGCTCGGGGTGTTGTTCTT 59.817 50.000 0.00 0.00 0.00 2.52
461 498 0.182775 AAAGCTCGGGGTGTTGTTCT 59.817 50.000 0.00 0.00 0.00 3.01
462 499 0.310854 CAAAGCTCGGGGTGTTGTTC 59.689 55.000 0.00 0.00 0.00 3.18
463 500 1.734388 GCAAAGCTCGGGGTGTTGTT 61.734 55.000 9.88 0.00 0.00 2.83
464 501 2.193536 GCAAAGCTCGGGGTGTTGT 61.194 57.895 9.88 0.00 0.00 3.32
474 511 0.661483 GTTCGCACCAAGCAAAGCTC 60.661 55.000 0.00 0.00 46.13 4.09
509 554 3.343421 GGCGAGACGGTTTTGCGT 61.343 61.111 4.96 0.00 0.00 5.24
541 586 5.404366 GTGACGATGTTTAGCTGTAAACTGA 59.596 40.000 12.20 0.00 45.75 3.41
716 768 1.665916 CTATCCGCGATGGCTGGTG 60.666 63.158 8.23 0.00 37.80 4.17
784 836 1.301293 GGAGAAAGTGAGGCTGGGG 59.699 63.158 0.00 0.00 0.00 4.96
884 936 1.403679 AGCGAGCGATCTATCTATGCC 59.596 52.381 0.00 0.00 0.00 4.40
885 937 2.096657 TGAGCGAGCGATCTATCTATGC 59.903 50.000 9.60 0.00 0.00 3.14
886 938 3.373748 AGTGAGCGAGCGATCTATCTATG 59.626 47.826 9.60 0.00 0.00 2.23
887 939 3.605634 AGTGAGCGAGCGATCTATCTAT 58.394 45.455 9.60 0.00 0.00 1.98
888 940 3.046968 AGTGAGCGAGCGATCTATCTA 57.953 47.619 9.60 0.00 0.00 1.98
889 941 1.890876 AGTGAGCGAGCGATCTATCT 58.109 50.000 9.60 3.14 0.00 1.98
890 942 2.580589 GAAGTGAGCGAGCGATCTATC 58.419 52.381 9.60 0.00 0.00 2.08
897 949 2.507992 CCTGGAAGTGAGCGAGCG 60.508 66.667 0.00 0.00 0.00 5.03
899 951 2.125350 GCCCTGGAAGTGAGCGAG 60.125 66.667 0.00 0.00 0.00 5.03
990 1058 0.598680 CGTGATCCATCTTCTCCGGC 60.599 60.000 0.00 0.00 0.00 6.13
991 1059 0.598680 GCGTGATCCATCTTCTCCGG 60.599 60.000 0.00 0.00 0.00 5.14
1228 1296 3.096092 GAGAAGAGAAGAAGCAGGAGGA 58.904 50.000 0.00 0.00 0.00 3.71
1229 1297 3.099141 AGAGAAGAGAAGAAGCAGGAGG 58.901 50.000 0.00 0.00 0.00 4.30
1230 1298 4.220382 TGAAGAGAAGAGAAGAAGCAGGAG 59.780 45.833 0.00 0.00 0.00 3.69
1234 1302 5.011431 TGTGATGAAGAGAAGAGAAGAAGCA 59.989 40.000 0.00 0.00 0.00 3.91
1235 1303 5.477510 TGTGATGAAGAGAAGAGAAGAAGC 58.522 41.667 0.00 0.00 0.00 3.86
1236 1304 6.690530 ACTGTGATGAAGAGAAGAGAAGAAG 58.309 40.000 0.00 0.00 0.00 2.85
1238 1306 6.041409 ACAACTGTGATGAAGAGAAGAGAAGA 59.959 38.462 0.00 0.00 0.00 2.87
1239 1307 6.222389 ACAACTGTGATGAAGAGAAGAGAAG 58.778 40.000 0.00 0.00 0.00 2.85
1272 1362 6.859508 CCAACCATCGTCATATTTTCATCATG 59.140 38.462 0.00 0.00 0.00 3.07
1274 1364 6.118852 TCCAACCATCGTCATATTTTCATCA 58.881 36.000 0.00 0.00 0.00 3.07
1282 1372 5.067674 CACCAATTTCCAACCATCGTCATAT 59.932 40.000 0.00 0.00 0.00 1.78
1288 1401 1.892474 ACCACCAATTTCCAACCATCG 59.108 47.619 0.00 0.00 0.00 3.84
1297 1410 1.343142 GGAACCCACACCACCAATTTC 59.657 52.381 0.00 0.00 0.00 2.17
1298 1411 1.062505 AGGAACCCACACCACCAATTT 60.063 47.619 0.00 0.00 0.00 1.82
1299 1412 0.560688 AGGAACCCACACCACCAATT 59.439 50.000 0.00 0.00 0.00 2.32
1303 1416 1.073199 CTGAGGAACCCACACCACC 59.927 63.158 0.00 0.00 0.00 4.61
1306 1419 2.757077 CCCTGAGGAACCCACACC 59.243 66.667 0.00 0.00 33.47 4.16
1307 1420 2.757077 CCCCTGAGGAACCCACAC 59.243 66.667 0.00 0.00 38.24 3.82
1308 1421 2.531685 CCCCCTGAGGAACCCACA 60.532 66.667 0.00 0.00 38.24 4.17
1414 1556 6.237915 CGAATCAGCAAATAAAAGAAATGGGC 60.238 38.462 0.00 0.00 0.00 5.36
1461 1640 3.186047 CATCCGGTCGTTCGCACC 61.186 66.667 0.00 4.60 0.00 5.01
1558 1738 2.832129 AGAACATGGAGAAGCCGAAGTA 59.168 45.455 0.00 0.00 40.66 2.24
1568 1749 5.269189 TGGTATGTGAGTAGAACATGGAGA 58.731 41.667 0.00 0.00 38.67 3.71
1591 1774 4.785346 AAGTGCTCCTCAACCATATCAT 57.215 40.909 0.00 0.00 0.00 2.45
1601 1784 3.631250 ACAAAGGAAAAAGTGCTCCTCA 58.369 40.909 0.00 0.00 41.40 3.86
1602 1785 4.142160 ACAACAAAGGAAAAAGTGCTCCTC 60.142 41.667 0.00 0.00 41.40 3.71
1610 1797 8.477984 TTCATCAGAAACAACAAAGGAAAAAG 57.522 30.769 0.00 0.00 0.00 2.27
1638 1829 4.209538 TGATGGAAAATGAAGATCCGCAT 58.790 39.130 0.00 0.00 35.96 4.73
1739 1940 9.891828 AACAACTTTTTGGTTTTGAAATTTCTC 57.108 25.926 18.64 7.10 37.00 2.87
1793 1997 6.239289 CCCTCAGACTTTGAAAAGGCAAATTA 60.239 38.462 11.13 0.00 46.69 1.40
1795 1999 4.039609 CCCTCAGACTTTGAAAAGGCAAAT 59.960 41.667 11.13 0.00 46.69 2.32
1835 2051 5.819991 TGAGCATATTCCCTGAGACTTTTT 58.180 37.500 0.00 0.00 0.00 1.94
1836 2052 5.441718 TGAGCATATTCCCTGAGACTTTT 57.558 39.130 0.00 0.00 0.00 2.27
1837 2053 5.643421 ATGAGCATATTCCCTGAGACTTT 57.357 39.130 0.00 0.00 0.00 2.66
1838 2054 5.604231 TGTATGAGCATATTCCCTGAGACTT 59.396 40.000 0.00 0.00 0.00 3.01
1839 2055 5.150715 TGTATGAGCATATTCCCTGAGACT 58.849 41.667 0.00 0.00 0.00 3.24
1840 2056 5.474578 TGTATGAGCATATTCCCTGAGAC 57.525 43.478 0.00 0.00 0.00 3.36
1843 2059 8.659527 TCTATTTTGTATGAGCATATTCCCTGA 58.340 33.333 0.00 0.00 0.00 3.86
1861 2077 7.894376 AAACTGTCCATGCAATTCTATTTTG 57.106 32.000 0.00 0.00 0.00 2.44
1866 2082 7.118723 AGGAATAAACTGTCCATGCAATTCTA 58.881 34.615 0.00 0.00 36.28 2.10
1867 2083 5.954150 AGGAATAAACTGTCCATGCAATTCT 59.046 36.000 0.00 0.00 36.28 2.40
1868 2084 6.212888 AGGAATAAACTGTCCATGCAATTC 57.787 37.500 0.00 0.00 36.28 2.17
1869 2085 6.610075 AAGGAATAAACTGTCCATGCAATT 57.390 33.333 0.00 0.00 36.28 2.32
1871 2087 7.615365 AGAATAAGGAATAAACTGTCCATGCAA 59.385 33.333 0.00 0.00 36.28 4.08
1901 2123 7.633193 AACTGTAAGAACACAAAACCATGTA 57.367 32.000 0.00 0.00 37.43 2.29
1902 2124 6.524101 AACTGTAAGAACACAAAACCATGT 57.476 33.333 0.00 0.00 37.43 3.21
1903 2125 7.826260 AAAACTGTAAGAACACAAAACCATG 57.174 32.000 0.00 0.00 37.43 3.66
1926 2148 3.006110 CCAAAGATCTGCAGAGCCAAAAA 59.994 43.478 27.52 0.00 0.00 1.94
1927 2149 2.559668 CCAAAGATCTGCAGAGCCAAAA 59.440 45.455 27.52 0.00 0.00 2.44
1928 2150 2.165167 CCAAAGATCTGCAGAGCCAAA 58.835 47.619 27.52 0.00 0.00 3.28
1929 2151 1.615116 CCCAAAGATCTGCAGAGCCAA 60.615 52.381 27.52 0.69 0.00 4.52
1930 2152 0.034767 CCCAAAGATCTGCAGAGCCA 60.035 55.000 27.52 1.13 0.00 4.75
1931 2153 0.254178 TCCCAAAGATCTGCAGAGCC 59.746 55.000 27.52 18.12 0.00 4.70
1932 2154 2.220313 GATCCCAAAGATCTGCAGAGC 58.780 52.381 24.27 24.27 46.85 4.09
2059 2281 8.311836 ACGAGTTGAGGAGACTTGATTAATTAA 58.688 33.333 0.00 0.00 44.43 1.40
2089 2311 4.083324 ACACACGATTTATCTTGCTTGTGG 60.083 41.667 0.00 0.00 37.91 4.17
2126 2358 5.996513 TGCAAAAATTTCATACACAAGCCAT 59.003 32.000 0.00 0.00 0.00 4.40
2131 2363 6.538021 ACAAGCTGCAAAAATTTCATACACAA 59.462 30.769 1.02 0.00 0.00 3.33
2140 2372 4.374399 CTCAGGACAAGCTGCAAAAATTT 58.626 39.130 1.02 0.00 0.00 1.82
2141 2373 3.801293 GCTCAGGACAAGCTGCAAAAATT 60.801 43.478 1.02 0.00 36.80 1.82
2143 2375 1.067516 GCTCAGGACAAGCTGCAAAAA 59.932 47.619 1.02 0.00 36.80 1.94
2146 2378 1.148949 TGCTCAGGACAAGCTGCAA 59.851 52.632 1.02 0.00 40.50 4.08
2292 2531 7.933577 AGCATGCAGATTTTACTAGTATGCTTA 59.066 33.333 21.98 7.23 44.25 3.09
2294 2533 6.294473 AGCATGCAGATTTTACTAGTATGCT 58.706 36.000 21.98 17.88 42.54 3.79
2303 2542 4.572950 GCACAAAGCATGCAGATTTTAC 57.427 40.909 21.98 1.44 44.79 2.01
2321 2560 0.459585 TTCGGCGGTATCTGAAGCAC 60.460 55.000 7.21 0.00 0.00 4.40
2414 2657 7.210873 AGGAAGTAACACTACTCTGAAAACAG 58.789 38.462 0.00 0.00 37.39 3.16
2459 2709 8.308931 CCACGTACCTGTTATATATGTGGTAAT 58.691 37.037 11.94 1.61 45.23 1.89
2526 2783 5.018809 ACAAACCTGCCAATGTATCTCAAT 58.981 37.500 0.00 0.00 0.00 2.57
2577 2834 7.378995 CCGAAGTATGAGAGGTAAATCGTTTAG 59.621 40.741 0.00 0.00 0.00 1.85
2583 2840 5.692654 GCTTCCGAAGTATGAGAGGTAAATC 59.307 44.000 9.87 0.00 0.00 2.17
2602 2860 2.568623 TTTGTCAGGGAGAAGCTTCC 57.431 50.000 22.81 13.78 36.46 3.46
2621 2879 5.694816 TCGTTGATCGTGTAAAATTTGCAT 58.305 33.333 0.00 0.00 40.80 3.96
2642 2900 6.614162 GCATTTTACAAGTTTGCTGACATTCG 60.614 38.462 0.00 0.00 0.00 3.34
3075 3368 1.875813 CAGGTCGAGCGACTGCATC 60.876 63.158 20.62 5.69 46.23 3.91
3266 3561 1.457303 GCCTGACATACGAATCGCATC 59.543 52.381 1.15 0.00 0.00 3.91
3270 3565 2.476619 GGAATGCCTGACATACGAATCG 59.523 50.000 0.00 0.00 38.34 3.34
3290 3585 7.328737 GTGCCACAGACGTATATATAGAAAAGG 59.671 40.741 0.00 0.00 0.00 3.11
3316 3611 5.183014 TCCACACGCTATATTACACTGAG 57.817 43.478 0.00 0.00 0.00 3.35
3484 3783 3.897325 ACACGTCCTACATGTATATGCG 58.103 45.455 5.91 11.00 37.85 4.73
3602 3904 4.405671 GCCAGGCTCTGAGCTGCA 62.406 66.667 27.09 0.00 41.99 4.41
3832 4155 1.662629 GAGTCATCTTCGTCGTCGGTA 59.337 52.381 1.55 0.00 37.69 4.02
4119 4495 6.463995 ACCACAGTTATCAATGTTGTTGTT 57.536 33.333 0.00 0.00 0.00 2.83
4135 4511 0.767375 AGGCATGTCTGAACCACAGT 59.233 50.000 0.00 0.00 45.86 3.55


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

AutoCloner maintained by Alex Coulton.