Multiple sequence alignment - TraesCS7B01G102800

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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 TraesCS7B01G102800 chr7B 100.000 6831 0 0 1 6831 117620954 117627784 0.000000e+00 12615.0
1 TraesCS7B01G102800 chr7B 84.862 1123 128 24 675 1793 117614159 117615243 0.000000e+00 1094.0
2 TraesCS7B01G102800 chr7B 95.858 676 26 2 1 674 706193713 706194388 0.000000e+00 1092.0
3 TraesCS7B01G102800 chr7B 95.259 675 31 1 1 674 667422058 667421384 0.000000e+00 1068.0
4 TraesCS7B01G102800 chr7B 84.673 672 80 8 2058 2711 117622766 117623432 0.000000e+00 649.0
5 TraesCS7B01G102800 chr7B 84.673 672 80 8 1813 2479 117623011 117623664 0.000000e+00 649.0
6 TraesCS7B01G102800 chr7B 80.000 490 70 13 2241 2711 117622719 117623199 3.050000e-88 337.0
7 TraesCS7B01G102800 chr7B 80.000 490 70 13 1766 2246 117623194 117623664 3.050000e-88 337.0
8 TraesCS7B01G102800 chr7D 96.767 5290 114 20 680 5937 155690494 155695758 0.000000e+00 8769.0
9 TraesCS7B01G102800 chr7D 86.348 1128 109 27 675 1793 155679563 155680654 0.000000e+00 1188.0
10 TraesCS7B01G102800 chr7D 95.652 736 25 5 6097 6826 155695751 155696485 0.000000e+00 1175.0
11 TraesCS7B01G102800 chr7D 87.634 655 75 4 2058 2711 155691641 155692290 0.000000e+00 756.0
12 TraesCS7B01G102800 chr7D 84.979 719 83 9 1766 2479 155691824 155692522 0.000000e+00 706.0
13 TraesCS7B01G102800 chr7D 86.864 472 49 6 678 1137 158710753 158710283 3.650000e-142 516.0
14 TraesCS7B01G102800 chr7D 83.932 473 65 7 2241 2711 155691594 155692057 6.290000e-120 442.0
15 TraesCS7B01G102800 chr7A 96.498 5283 130 23 679 5937 157398199 157403450 0.000000e+00 8680.0
16 TraesCS7B01G102800 chr7A 95.000 740 31 5 6097 6831 157403443 157404181 0.000000e+00 1157.0
17 TraesCS7B01G102800 chr7A 85.372 1128 119 29 675 1793 157393021 157394111 0.000000e+00 1127.0
18 TraesCS7B01G102800 chr7A 86.890 656 78 6 2058 2711 157399335 157399984 0.000000e+00 728.0
19 TraesCS7B01G102800 chr7A 84.979 719 83 9 1766 2479 157399518 157400216 0.000000e+00 706.0
20 TraesCS7B01G102800 chr7A 79.796 490 71 13 1766 2246 157399746 157400216 1.420000e-86 331.0
21 TraesCS7B01G102800 chr3A 81.792 1373 182 46 3777 5098 52350159 52348804 0.000000e+00 1088.0
22 TraesCS7B01G102800 chr3A 77.574 981 139 51 1056 2001 52351338 52350404 1.020000e-142 518.0
23 TraesCS7B01G102800 chr3A 79.508 244 27 6 2476 2714 52350626 52350401 1.190000e-32 152.0
24 TraesCS7B01G102800 chr3D 81.680 1381 179 40 3777 5098 40254436 40253071 0.000000e+00 1081.0
25 TraesCS7B01G102800 chr3D 81.191 638 88 15 5113 5733 40253029 40252407 1.030000e-132 484.0
26 TraesCS7B01G102800 chr3D 78.866 582 102 16 1431 2001 40255255 40254684 2.330000e-99 374.0
27 TraesCS7B01G102800 chr2B 95.562 676 28 2 1 674 747670298 747669623 0.000000e+00 1081.0
28 TraesCS7B01G102800 chr5B 95.421 677 29 2 3 677 55361716 55362392 0.000000e+00 1077.0
29 TraesCS7B01G102800 chr5B 95.620 137 6 0 5937 6073 19531103 19530967 3.210000e-53 220.0
30 TraesCS7B01G102800 chrUn 95.414 676 29 2 1 674 79252267 79251592 0.000000e+00 1075.0
31 TraesCS7B01G102800 chrUn 95.266 676 30 2 1 674 372782953 372782278 0.000000e+00 1070.0
32 TraesCS7B01G102800 chr4A 95.133 678 31 2 1 677 688887061 688887737 0.000000e+00 1068.0
33 TraesCS7B01G102800 chr4A 95.000 680 32 2 1 678 733553698 733554377 0.000000e+00 1066.0
34 TraesCS7B01G102800 chr6B 95.133 678 30 3 1 676 514671037 514671713 0.000000e+00 1066.0
35 TraesCS7B01G102800 chr6B 79.487 468 70 18 1431 1878 68102925 68103386 6.650000e-80 309.0
36 TraesCS7B01G102800 chr3B 85.625 960 128 8 3777 4732 63470979 63470026 0.000000e+00 1000.0
37 TraesCS7B01G102800 chr3B 80.277 578 79 18 1431 2001 63471772 63471223 2.970000e-108 403.0
38 TraesCS7B01G102800 chr3B 84.755 387 47 6 5113 5490 63469498 63469115 1.800000e-100 377.0
39 TraesCS7B01G102800 chr3B 87.578 161 19 1 5937 6097 70852650 70852809 1.170000e-42 185.0
40 TraesCS7B01G102800 chr1B 96.528 144 3 2 5938 6081 490725396 490725255 3.180000e-58 237.0
41 TraesCS7B01G102800 chr1B 94.815 135 7 0 5939 6073 608959618 608959752 1.930000e-50 211.0
42 TraesCS7B01G102800 chr1B 88.356 146 16 1 5929 6074 647595052 647595196 2.530000e-39 174.0
43 TraesCS7B01G102800 chr1B 86.164 159 17 4 5938 6095 66313208 66313362 4.240000e-37 167.0
44 TraesCS7B01G102800 chr5D 97.059 136 4 0 5938 6073 57853479 57853344 5.330000e-56 230.0
45 TraesCS7B01G102800 chr5A 96.350 137 4 1 5937 6073 595688940 595688805 2.480000e-54 224.0
46 TraesCS7B01G102800 chr2D 96.324 136 4 1 5938 6073 82652151 82652285 8.920000e-54 222.0
47 TraesCS7B01G102800 chr6D 92.453 53 4 0 3597 3649 442170383 442170435 7.350000e-10 76.8


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 TraesCS7B01G102800 chr7B 117620954 117627784 6830 False 12615.000000 12615 100.000000 1 6831 1 chr7B.!!$F2 6830
1 TraesCS7B01G102800 chr7B 117614159 117615243 1084 False 1094.000000 1094 84.862000 675 1793 1 chr7B.!!$F1 1118
2 TraesCS7B01G102800 chr7B 706193713 706194388 675 False 1092.000000 1092 95.858000 1 674 1 chr7B.!!$F3 673
3 TraesCS7B01G102800 chr7B 667421384 667422058 674 True 1068.000000 1068 95.259000 1 674 1 chr7B.!!$R1 673
4 TraesCS7B01G102800 chr7B 117622719 117623664 945 False 493.000000 649 82.336500 1766 2711 4 chr7B.!!$F4 945
5 TraesCS7B01G102800 chr7D 155690494 155695758 5264 False 8769.000000 8769 96.767000 680 5937 1 chr7D.!!$F2 5257
6 TraesCS7B01G102800 chr7D 155679563 155680654 1091 False 1188.000000 1188 86.348000 675 1793 1 chr7D.!!$F1 1118
7 TraesCS7B01G102800 chr7D 155691594 155696485 4891 False 769.750000 1175 88.049250 1766 6826 4 chr7D.!!$F3 5060
8 TraesCS7B01G102800 chr7A 157398199 157403450 5251 False 8680.000000 8680 96.498000 679 5937 1 chr7A.!!$F2 5258
9 TraesCS7B01G102800 chr7A 157393021 157394111 1090 False 1127.000000 1127 85.372000 675 1793 1 chr7A.!!$F1 1118
10 TraesCS7B01G102800 chr7A 157399335 157404181 4846 False 730.500000 1157 86.666250 1766 6831 4 chr7A.!!$F3 5065
11 TraesCS7B01G102800 chr3A 52348804 52351338 2534 True 586.000000 1088 79.624667 1056 5098 3 chr3A.!!$R1 4042
12 TraesCS7B01G102800 chr3D 40252407 40255255 2848 True 646.333333 1081 80.579000 1431 5733 3 chr3D.!!$R1 4302
13 TraesCS7B01G102800 chr2B 747669623 747670298 675 True 1081.000000 1081 95.562000 1 674 1 chr2B.!!$R1 673
14 TraesCS7B01G102800 chr5B 55361716 55362392 676 False 1077.000000 1077 95.421000 3 677 1 chr5B.!!$F1 674
15 TraesCS7B01G102800 chrUn 79251592 79252267 675 True 1075.000000 1075 95.414000 1 674 1 chrUn.!!$R1 673
16 TraesCS7B01G102800 chrUn 372782278 372782953 675 True 1070.000000 1070 95.266000 1 674 1 chrUn.!!$R2 673
17 TraesCS7B01G102800 chr4A 688887061 688887737 676 False 1068.000000 1068 95.133000 1 677 1 chr4A.!!$F1 676
18 TraesCS7B01G102800 chr4A 733553698 733554377 679 False 1066.000000 1066 95.000000 1 678 1 chr4A.!!$F2 677
19 TraesCS7B01G102800 chr6B 514671037 514671713 676 False 1066.000000 1066 95.133000 1 676 1 chr6B.!!$F2 675
20 TraesCS7B01G102800 chr3B 63469115 63471772 2657 True 593.333333 1000 83.552333 1431 5490 3 chr3B.!!$R1 4059

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
884 896 0.183971 TCCGAGATCTGACCCTCCTC 59.816 60.000 0.00 0.00 0.00 3.71 F
1502 1560 0.833287 CCGAGGACATGACCAAGGAT 59.167 55.000 16.63 0.00 33.02 3.24 F
1600 1676 5.820423 CACGGTCATAATGGGATTTCTTGTA 59.180 40.000 0.00 0.00 0.00 2.41 F
3154 3250 6.035975 GCATTATGTAATTGTTGTTTCAGCCC 59.964 38.462 0.00 0.00 0.00 5.19 F
4281 4388 2.168496 AGCTGCATGTGCTGAATTTCT 58.832 42.857 14.87 0.66 41.71 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2973 3069 0.171007 ATGGCGCTTGTATTGCACAC 59.829 50.000 7.64 0.0 36.69 3.82 R
3378 3474 2.143122 TGGATCGTCTCAAAACAGTGC 58.857 47.619 0.00 0.0 0.00 4.40 R
3651 3749 1.014352 ACGCTCCACACAAACAAGTC 58.986 50.000 0.00 0.0 0.00 3.01 R
4757 4899 1.331756 GCAAGACATCAAGCATACGGG 59.668 52.381 0.00 0.0 0.00 5.28 R
5969 6280 0.040204 ATTTTGAGTGGGGGCTCAGG 59.960 55.000 0.00 0.0 45.03 3.86 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
99 100 1.388768 TCGCTTATGAAGAACAACGCG 59.611 47.619 3.53 3.53 40.75 6.01
255 257 3.376935 ATCCTGAACGAGCTGCCGG 62.377 63.158 13.50 0.00 0.00 6.13
420 422 4.124351 CGACTCCGCCAACGCCTA 62.124 66.667 0.00 0.00 38.22 3.93
494 496 1.712018 CGCCAGACTACGTCCGATCA 61.712 60.000 0.00 0.00 32.18 2.92
506 508 4.102561 CGATCACCGGATTTGCGA 57.897 55.556 9.46 0.00 32.67 5.10
522 524 1.002250 GCGACGTCTTTTGAGAGCGA 61.002 55.000 14.70 0.00 0.00 4.93
586 589 1.395826 GGAGCGTGACTGGGAGCTAT 61.396 60.000 0.00 0.00 40.39 2.97
644 648 1.594293 GCCGCTCTATTTAGGCGCA 60.594 57.895 10.83 0.00 46.29 6.09
648 652 1.536072 CGCTCTATTTAGGCGCACTGA 60.536 52.381 10.83 0.00 42.28 3.41
678 682 1.424638 GGCTGGAGATGCCCTTACTA 58.575 55.000 0.00 0.00 44.32 1.82
735 745 1.079057 GACGAGCTGGGAGGGAAAC 60.079 63.158 0.00 0.00 0.00 2.78
802 814 4.457603 GGAAAATTTCAAAATTTCCGGGGG 59.542 41.667 12.93 0.00 45.16 5.40
831 843 2.821366 GCCATCCGACACCAGCTG 60.821 66.667 6.78 6.78 0.00 4.24
884 896 0.183971 TCCGAGATCTGACCCTCCTC 59.816 60.000 0.00 0.00 0.00 3.71
1063 1077 4.247380 CGCAGATGGAGGAGGCCC 62.247 72.222 0.00 0.00 0.00 5.80
1232 1281 3.161866 GGATTTGGCTGACCCTTTGTTA 58.838 45.455 0.00 0.00 33.59 2.41
1233 1282 3.056821 GGATTTGGCTGACCCTTTGTTAC 60.057 47.826 0.00 0.00 33.59 2.50
1372 1424 5.779806 ACAGGTAAACGATGATTTCTTCG 57.220 39.130 12.61 12.61 45.38 3.79
1502 1560 0.833287 CCGAGGACATGACCAAGGAT 59.167 55.000 16.63 0.00 33.02 3.24
1600 1676 5.820423 CACGGTCATAATGGGATTTCTTGTA 59.180 40.000 0.00 0.00 0.00 2.41
2972 3068 7.391148 TTCAGCTTTACTTTCTTGTTCTGTT 57.609 32.000 0.00 0.00 0.00 3.16
2973 3069 6.785191 TCAGCTTTACTTTCTTGTTCTGTTG 58.215 36.000 0.00 0.00 0.00 3.33
3154 3250 6.035975 GCATTATGTAATTGTTGTTTCAGCCC 59.964 38.462 0.00 0.00 0.00 5.19
3378 3474 7.704899 TGAAATACTGACACGTGATAATGGTAG 59.295 37.037 25.01 9.98 0.00 3.18
3651 3749 8.474025 TGGGAGTTGGTTGCAATATATTTTAAG 58.526 33.333 0.59 0.00 0.00 1.85
3833 3932 3.840437 GCACCTTGTGGCTGTTGA 58.160 55.556 0.00 0.00 36.63 3.18
3869 3973 8.986847 TGTTTTGTAAATGGAATAATGTTGCAG 58.013 29.630 0.00 0.00 0.00 4.41
3873 3977 6.979817 TGTAAATGGAATAATGTTGCAGATGC 59.020 34.615 0.00 0.00 42.50 3.91
3874 3978 5.864418 AATGGAATAATGTTGCAGATGCT 57.136 34.783 6.35 0.00 42.66 3.79
3875 3979 5.864418 ATGGAATAATGTTGCAGATGCTT 57.136 34.783 6.35 0.00 42.66 3.91
4036 4141 6.015856 CCAAGAAGACAGAGAAGAGAAGTACA 60.016 42.308 0.00 0.00 0.00 2.90
4041 4146 7.624360 AGACAGAGAAGAGAAGTACATACAG 57.376 40.000 0.00 0.00 0.00 2.74
4280 4387 2.649331 AGCTGCATGTGCTGAATTTC 57.351 45.000 14.87 0.00 41.71 2.17
4281 4388 2.168496 AGCTGCATGTGCTGAATTTCT 58.832 42.857 14.87 0.66 41.71 2.52
4346 4453 7.931948 ACTGTATTTGCTGTAGTAGTTCACTTT 59.068 33.333 0.00 0.00 38.80 2.66
4757 4899 8.668510 TTATCTTTCTGCATCTCATTAGTTCC 57.331 34.615 0.00 0.00 0.00 3.62
4773 4915 1.940613 GTTCCCCGTATGCTTGATGTC 59.059 52.381 0.00 0.00 0.00 3.06
5000 5265 7.809331 ACAGAACATTAAACATGTATGCACTTG 59.191 33.333 0.00 0.25 36.23 3.16
5022 5287 6.000891 TGCTAAGTTTCTTAGTTGCATGTG 57.999 37.500 15.05 0.00 0.00 3.21
5329 5631 9.474313 TCTGAAGTTATTATGCAATACCCTTTT 57.526 29.630 0.00 0.00 0.00 2.27
5600 5908 4.698575 TGTTGCATGGTGCTATCGTTATA 58.301 39.130 3.41 0.00 45.31 0.98
5709 6018 1.281867 CACATCTAACTTGGGCCCTGA 59.718 52.381 25.70 11.05 0.00 3.86
5822 6131 5.496556 TGAAAACTCAGACTCCTGTTTCAA 58.503 37.500 0.00 0.00 38.67 2.69
5937 6248 0.808125 TTACAATGGCACCGTCATGC 59.192 50.000 0.00 0.00 45.34 4.06
5950 6261 3.479203 CATGCAGGGGCGGACCTA 61.479 66.667 0.00 0.00 45.35 3.08
5951 6262 3.480133 ATGCAGGGGCGGACCTAC 61.480 66.667 0.00 0.00 45.35 3.18
5953 6264 3.480133 GCAGGGGCGGACCTACAT 61.480 66.667 0.00 0.00 39.34 2.29
5954 6265 3.043999 GCAGGGGCGGACCTACATT 62.044 63.158 0.00 0.00 39.34 2.71
5955 6266 1.153168 CAGGGGCGGACCTACATTG 60.153 63.158 0.00 0.00 39.34 2.82
5956 6267 1.306654 AGGGGCGGACCTACATTGA 60.307 57.895 0.00 0.00 39.65 2.57
5957 6268 1.146263 GGGGCGGACCTACATTGAG 59.854 63.158 0.00 0.00 40.03 3.02
5958 6269 1.146263 GGGCGGACCTACATTGAGG 59.854 63.158 0.00 0.00 42.89 3.86
5966 6277 2.698855 CCTACATTGAGGTGAGTGGG 57.301 55.000 0.00 0.00 0.00 4.61
5967 6278 1.210478 CCTACATTGAGGTGAGTGGGG 59.790 57.143 0.00 0.00 0.00 4.96
5968 6279 1.210478 CTACATTGAGGTGAGTGGGGG 59.790 57.143 0.00 0.00 0.00 5.40
5969 6280 1.379044 CATTGAGGTGAGTGGGGGC 60.379 63.158 0.00 0.00 0.00 5.80
5970 6281 2.616458 ATTGAGGTGAGTGGGGGCC 61.616 63.158 0.00 0.00 0.00 5.80
5971 6282 3.810687 TTGAGGTGAGTGGGGGCCT 62.811 63.158 0.84 0.00 0.00 5.19
5972 6283 3.721706 GAGGTGAGTGGGGGCCTG 61.722 72.222 0.84 0.00 0.00 4.85
5973 6284 4.270153 AGGTGAGTGGGGGCCTGA 62.270 66.667 0.84 0.00 0.00 3.86
5974 6285 3.721706 GGTGAGTGGGGGCCTGAG 61.722 72.222 0.84 0.00 0.00 3.35
5975 6286 4.416738 GTGAGTGGGGGCCTGAGC 62.417 72.222 0.84 0.00 38.76 4.26
5985 6296 3.650950 GCCTGAGCCCCCACTCAA 61.651 66.667 0.00 0.00 45.72 3.02
5986 6297 3.170362 CCTGAGCCCCCACTCAAA 58.830 61.111 0.00 0.00 45.72 2.69
5987 6298 1.460255 CCTGAGCCCCCACTCAAAA 59.540 57.895 0.00 0.00 45.72 2.44
5988 6299 0.040204 CCTGAGCCCCCACTCAAAAT 59.960 55.000 0.00 0.00 45.72 1.82
5989 6300 1.550869 CCTGAGCCCCCACTCAAAATT 60.551 52.381 0.00 0.00 45.72 1.82
5990 6301 2.250924 CTGAGCCCCCACTCAAAATTT 58.749 47.619 0.00 0.00 45.72 1.82
5991 6302 1.969923 TGAGCCCCCACTCAAAATTTG 59.030 47.619 0.00 0.00 43.59 2.32
5992 6303 2.247358 GAGCCCCCACTCAAAATTTGA 58.753 47.619 8.25 8.25 36.65 2.69
5993 6304 2.632512 GAGCCCCCACTCAAAATTTGAA 59.367 45.455 9.85 0.00 39.58 2.69
5994 6305 3.044894 AGCCCCCACTCAAAATTTGAAA 58.955 40.909 9.85 0.00 39.58 2.69
5995 6306 3.652387 AGCCCCCACTCAAAATTTGAAAT 59.348 39.130 9.85 0.00 39.58 2.17
5996 6307 4.104579 AGCCCCCACTCAAAATTTGAAATT 59.895 37.500 9.85 0.00 39.58 1.82
5997 6308 4.455533 GCCCCCACTCAAAATTTGAAATTC 59.544 41.667 9.85 0.00 39.58 2.17
5998 6309 5.745770 GCCCCCACTCAAAATTTGAAATTCT 60.746 40.000 9.85 0.00 39.58 2.40
5999 6310 6.519891 GCCCCCACTCAAAATTTGAAATTCTA 60.520 38.462 9.85 0.00 39.58 2.10
6000 6311 6.873605 CCCCCACTCAAAATTTGAAATTCTAC 59.126 38.462 9.85 0.00 39.58 2.59
6001 6312 7.256296 CCCCCACTCAAAATTTGAAATTCTACT 60.256 37.037 9.85 0.00 39.58 2.57
6002 6313 8.802267 CCCCACTCAAAATTTGAAATTCTACTA 58.198 33.333 9.85 0.00 39.58 1.82
6066 6377 9.710900 CTTTGAATTTTTATAGAATATGCCCCC 57.289 33.333 0.00 0.00 0.00 5.40
6067 6378 8.789767 TTGAATTTTTATAGAATATGCCCCCA 57.210 30.769 0.00 0.00 0.00 4.96
6068 6379 8.421249 TGAATTTTTATAGAATATGCCCCCAG 57.579 34.615 0.00 0.00 0.00 4.45
6069 6380 8.010105 TGAATTTTTATAGAATATGCCCCCAGT 58.990 33.333 0.00 0.00 0.00 4.00
6070 6381 8.422577 AATTTTTATAGAATATGCCCCCAGTC 57.577 34.615 0.00 0.00 0.00 3.51
6071 6382 6.523035 TTTTATAGAATATGCCCCCAGTCA 57.477 37.500 0.00 0.00 0.00 3.41
6072 6383 6.523035 TTTATAGAATATGCCCCCAGTCAA 57.477 37.500 0.00 0.00 0.00 3.18
6073 6384 6.523035 TTATAGAATATGCCCCCAGTCAAA 57.477 37.500 0.00 0.00 0.00 2.69
6074 6385 3.756082 AGAATATGCCCCCAGTCAAAA 57.244 42.857 0.00 0.00 0.00 2.44
6075 6386 4.270317 AGAATATGCCCCCAGTCAAAAT 57.730 40.909 0.00 0.00 0.00 1.82
6076 6387 5.402054 AGAATATGCCCCCAGTCAAAATA 57.598 39.130 0.00 0.00 0.00 1.40
6077 6388 5.969086 AGAATATGCCCCCAGTCAAAATAT 58.031 37.500 0.00 0.00 0.00 1.28
6078 6389 5.776716 AGAATATGCCCCCAGTCAAAATATG 59.223 40.000 0.00 0.00 0.00 1.78
6079 6390 2.917713 TGCCCCCAGTCAAAATATGT 57.082 45.000 0.00 0.00 0.00 2.29
6080 6391 3.182887 TGCCCCCAGTCAAAATATGTT 57.817 42.857 0.00 0.00 0.00 2.71
6081 6392 3.096092 TGCCCCCAGTCAAAATATGTTC 58.904 45.455 0.00 0.00 0.00 3.18
6082 6393 3.245586 TGCCCCCAGTCAAAATATGTTCT 60.246 43.478 0.00 0.00 0.00 3.01
6083 6394 4.017958 TGCCCCCAGTCAAAATATGTTCTA 60.018 41.667 0.00 0.00 0.00 2.10
6084 6395 4.580580 GCCCCCAGTCAAAATATGTTCTAG 59.419 45.833 0.00 0.00 0.00 2.43
6085 6396 5.133221 CCCCCAGTCAAAATATGTTCTAGG 58.867 45.833 0.00 0.00 0.00 3.02
6086 6397 5.340027 CCCCCAGTCAAAATATGTTCTAGGT 60.340 44.000 0.00 0.00 0.00 3.08
6087 6398 5.823045 CCCCAGTCAAAATATGTTCTAGGTC 59.177 44.000 0.00 0.00 0.00 3.85
6088 6399 5.823045 CCCAGTCAAAATATGTTCTAGGTCC 59.177 44.000 0.00 0.00 0.00 4.46
6089 6400 5.523916 CCAGTCAAAATATGTTCTAGGTCCG 59.476 44.000 0.00 0.00 0.00 4.79
6090 6401 5.006746 CAGTCAAAATATGTTCTAGGTCCGC 59.993 44.000 0.00 0.00 0.00 5.54
6091 6402 4.272748 GTCAAAATATGTTCTAGGTCCGCC 59.727 45.833 0.00 0.00 0.00 6.13
6092 6403 4.080807 TCAAAATATGTTCTAGGTCCGCCA 60.081 41.667 0.00 0.00 37.19 5.69
6093 6404 3.470645 AATATGTTCTAGGTCCGCCAC 57.529 47.619 0.00 0.00 37.19 5.01
6094 6405 2.154567 TATGTTCTAGGTCCGCCACT 57.845 50.000 0.00 0.00 37.19 4.00
6095 6406 0.537188 ATGTTCTAGGTCCGCCACTG 59.463 55.000 0.00 0.00 37.19 3.66
6096 6407 1.448013 GTTCTAGGTCCGCCACTGC 60.448 63.158 0.00 0.00 37.19 4.40
6097 6408 2.656069 TTCTAGGTCCGCCACTGCC 61.656 63.158 0.00 0.00 37.19 4.85
6098 6409 4.514577 CTAGGTCCGCCACTGCCG 62.515 72.222 0.00 0.00 37.19 5.69
6102 6413 4.760047 GTCCGCCACTGCCGTCAT 62.760 66.667 0.00 0.00 0.00 3.06
6103 6414 4.758251 TCCGCCACTGCCGTCATG 62.758 66.667 0.00 0.00 0.00 3.07
6116 6427 1.933181 CCGTCATGAGAGCGCATTTTA 59.067 47.619 11.47 0.00 0.00 1.52
6277 6591 2.487762 ACATGCATGGGTTTCGTTGTAG 59.512 45.455 29.41 0.42 0.00 2.74
6281 6595 3.003897 TGCATGGGTTTCGTTGTAGTTTC 59.996 43.478 0.00 0.00 0.00 2.78
6371 6685 4.583871 TGAATGTTTTGTTTTGGCAGGTT 58.416 34.783 0.00 0.00 0.00 3.50
6414 6728 2.280457 GGGCGCTGCAGAGGATAC 60.280 66.667 20.43 0.44 0.00 2.24
6450 6764 4.110506 TTGCTGTAGGGAAGTTACGCAAG 61.111 47.826 0.00 0.00 36.55 4.01
6463 6777 2.866028 GCAAGTGCAGAAGAGCCG 59.134 61.111 0.00 0.00 41.59 5.52
6484 6800 3.667726 CGACATATCTGAAGATGCAGTCG 59.332 47.826 19.67 19.67 42.12 4.18
6512 6828 0.550914 TATTCCCTGGGTCATGCCAC 59.449 55.000 13.56 0.00 39.65 5.01
6674 6991 8.638873 TCACTATGGTTGTATAATCAATCGTCT 58.361 33.333 0.00 0.00 31.79 4.18
6680 6997 7.709182 TGGTTGTATAATCAATCGTCTTGTAGG 59.291 37.037 0.00 0.00 31.79 3.18
6718 7035 8.677148 ACAAATTGACTTCACTGTACTGTATT 57.323 30.769 4.96 0.00 0.00 1.89
6809 7126 6.238731 GCTGTGTATGTTATGCCACATATGTT 60.239 38.462 5.37 0.00 40.85 2.71
6827 7144 9.955208 ACATATGTTAAACTTATGCATGTCATG 57.045 29.630 10.16 8.56 38.84 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
188 190 0.032130 TGAGCTTCTCGTCGTTGCTT 59.968 50.000 0.00 0.00 33.83 3.91
255 257 3.749373 CGTCGTCGGTGTTGTCGC 61.749 66.667 0.00 0.00 0.00 5.19
420 422 3.764466 CTCGGCTTGGTCGGCTCT 61.764 66.667 0.00 0.00 0.00 4.09
494 496 0.601841 AAAGACGTCGCAAATCCGGT 60.602 50.000 10.46 0.00 0.00 5.28
506 508 2.395654 GTTCTCGCTCTCAAAAGACGT 58.604 47.619 0.00 0.00 31.92 4.34
522 524 4.037565 GGGAAATTCAAACTTGGTCGTTCT 59.962 41.667 0.00 0.00 0.00 3.01
569 571 0.972983 ACATAGCTCCCAGTCACGCT 60.973 55.000 0.00 0.00 36.56 5.07
623 627 0.601558 CGCCTAAATAGAGCGGCCTA 59.398 55.000 0.00 0.00 45.88 3.93
678 682 1.021968 GGCAACCTTTGTTCGTGAGT 58.978 50.000 0.00 0.00 30.42 3.41
735 745 3.204827 CCCGCCTTTGCTCGATGG 61.205 66.667 0.00 0.00 34.43 3.51
802 814 1.729881 GGATGGCGCCAGTGAATTC 59.270 57.895 35.36 24.76 0.00 2.17
884 896 0.894141 TGATGAATTTTGGTGGCGGG 59.106 50.000 0.00 0.00 0.00 6.13
890 903 5.990996 GGTGTTTGATGTGATGAATTTTGGT 59.009 36.000 0.00 0.00 0.00 3.67
1023 1037 1.734477 CACGACCACGCTCTCCTTG 60.734 63.158 0.00 0.00 43.96 3.61
1024 1038 2.651361 CACGACCACGCTCTCCTT 59.349 61.111 0.00 0.00 43.96 3.36
1063 1077 3.551496 TTCGTGGAGGCCCTTGCTG 62.551 63.158 0.00 0.00 37.74 4.41
1077 1091 3.645975 CACGGGTTGCGCTTTCGT 61.646 61.111 9.73 10.79 38.14 3.85
1179 1193 0.692419 TCCAGAAGGATGGAGGAGGC 60.692 60.000 0.00 0.00 44.56 4.70
1180 1194 3.642977 TCCAGAAGGATGGAGGAGG 57.357 57.895 0.00 0.00 44.56 4.30
1359 1411 3.729526 AACTGTGCGAAGAAATCATCG 57.270 42.857 3.86 3.86 39.71 3.84
1363 1415 3.665871 GCTTGAAACTGTGCGAAGAAATC 59.334 43.478 0.00 0.00 0.00 2.17
1372 1424 2.229543 TGATGATGGCTTGAAACTGTGC 59.770 45.455 0.00 0.00 0.00 4.57
1600 1676 8.870075 AACAAACCAAGCTAAGAGAGAAATAT 57.130 30.769 0.00 0.00 0.00 1.28
1608 1684 5.296780 TCTGTCAAACAAACCAAGCTAAGAG 59.703 40.000 0.00 0.00 0.00 2.85
2972 3068 1.169034 TGGCGCTTGTATTGCACACA 61.169 50.000 7.64 0.00 36.69 3.72
2973 3069 0.171007 ATGGCGCTTGTATTGCACAC 59.829 50.000 7.64 0.00 36.69 3.82
3154 3250 6.623767 GCTTTAGTTCTAACATTGGCCTGAAG 60.624 42.308 3.32 0.00 0.00 3.02
3378 3474 2.143122 TGGATCGTCTCAAAACAGTGC 58.857 47.619 0.00 0.00 0.00 4.40
3651 3749 1.014352 ACGCTCCACACAAACAAGTC 58.986 50.000 0.00 0.00 0.00 3.01
4208 4315 8.053355 CCTAATACCCCTTGACTTAAACAATCT 58.947 37.037 0.00 0.00 0.00 2.40
4280 4387 1.815003 GAAAGGGCCTCATCACACAAG 59.185 52.381 6.46 0.00 0.00 3.16
4281 4388 1.425066 AGAAAGGGCCTCATCACACAA 59.575 47.619 6.46 0.00 0.00 3.33
4501 4608 6.202954 AGCAAGTGACTAGACACACATAAAAC 59.797 38.462 23.90 7.32 42.45 2.43
4757 4899 1.331756 GCAAGACATCAAGCATACGGG 59.668 52.381 0.00 0.00 0.00 5.28
5000 5265 5.393962 CCACATGCAACTAAGAAACTTAGC 58.606 41.667 15.55 6.43 0.00 3.09
5373 5675 7.041712 TGTTGCGTCAAACTCTGATACAAATAA 60.042 33.333 0.00 0.00 35.02 1.40
5585 5893 6.040504 AGACTTGTCATATAACGATAGCACCA 59.959 38.462 3.49 0.00 42.67 4.17
5600 5908 5.157940 ACATTGCTAGTCAGACTTGTCAT 57.842 39.130 8.80 0.68 0.00 3.06
5709 6018 5.613544 TGGGGCCTATATTAACCAGTTACAT 59.386 40.000 0.84 0.00 0.00 2.29
5822 6131 9.533831 AGGATCAAATAAATACCTTCAAACAGT 57.466 29.630 0.00 0.00 0.00 3.55
5891 6200 8.939929 CATAACACATTTCAGTCTCTTGTATGT 58.060 33.333 0.00 0.00 0.00 2.29
5937 6248 1.153168 CAATGTAGGTCCGCCCCTG 60.153 63.158 1.64 0.00 35.97 4.45
5938 6249 1.306654 TCAATGTAGGTCCGCCCCT 60.307 57.895 0.00 0.00 38.70 4.79
5939 6250 1.146263 CTCAATGTAGGTCCGCCCC 59.854 63.158 0.00 0.00 34.57 5.80
5940 6251 1.146263 CCTCAATGTAGGTCCGCCC 59.854 63.158 0.00 0.00 34.57 6.13
5941 6252 4.857251 CCTCAATGTAGGTCCGCC 57.143 61.111 0.00 0.00 31.46 6.13
5947 6258 1.210478 CCCCACTCACCTCAATGTAGG 59.790 57.143 0.00 0.00 42.82 3.18
5948 6259 1.210478 CCCCCACTCACCTCAATGTAG 59.790 57.143 0.00 0.00 0.00 2.74
5949 6260 1.285280 CCCCCACTCACCTCAATGTA 58.715 55.000 0.00 0.00 0.00 2.29
5950 6261 2.078452 CCCCCACTCACCTCAATGT 58.922 57.895 0.00 0.00 0.00 2.71
5951 6262 1.379044 GCCCCCACTCACCTCAATG 60.379 63.158 0.00 0.00 0.00 2.82
5952 6263 2.616458 GGCCCCCACTCACCTCAAT 61.616 63.158 0.00 0.00 0.00 2.57
5953 6264 3.256960 GGCCCCCACTCACCTCAA 61.257 66.667 0.00 0.00 0.00 3.02
5954 6265 4.270153 AGGCCCCCACTCACCTCA 62.270 66.667 0.00 0.00 0.00 3.86
5955 6266 3.721706 CAGGCCCCCACTCACCTC 61.722 72.222 0.00 0.00 0.00 3.85
5956 6267 4.270153 TCAGGCCCCCACTCACCT 62.270 66.667 0.00 0.00 0.00 4.00
5957 6268 3.721706 CTCAGGCCCCCACTCACC 61.722 72.222 0.00 0.00 0.00 4.02
5958 6269 4.416738 GCTCAGGCCCCCACTCAC 62.417 72.222 0.00 0.00 0.00 3.51
5968 6279 2.713531 TTTTGAGTGGGGGCTCAGGC 62.714 60.000 0.00 0.00 45.03 4.85
5969 6280 0.040204 ATTTTGAGTGGGGGCTCAGG 59.960 55.000 0.00 0.00 45.03 3.86
5970 6281 1.928868 AATTTTGAGTGGGGGCTCAG 58.071 50.000 0.00 0.00 45.03 3.35
5971 6282 1.969923 CAAATTTTGAGTGGGGGCTCA 59.030 47.619 2.88 0.00 43.03 4.26
5972 6283 2.247358 TCAAATTTTGAGTGGGGGCTC 58.753 47.619 7.74 0.00 34.08 4.70
5973 6284 2.397044 TCAAATTTTGAGTGGGGGCT 57.603 45.000 7.74 0.00 34.08 5.19
5974 6285 3.483808 TTTCAAATTTTGAGTGGGGGC 57.516 42.857 11.41 0.00 41.38 5.80
5975 6286 5.868454 AGAATTTCAAATTTTGAGTGGGGG 58.132 37.500 11.41 0.00 41.38 5.40
5976 6287 7.670364 AGTAGAATTTCAAATTTTGAGTGGGG 58.330 34.615 11.41 0.00 41.38 4.96
6040 6351 9.710900 GGGGGCATATTCTATAAAAATTCAAAG 57.289 33.333 0.00 0.00 0.00 2.77
6041 6352 9.218525 TGGGGGCATATTCTATAAAAATTCAAA 57.781 29.630 0.00 0.00 0.00 2.69
6042 6353 8.789767 TGGGGGCATATTCTATAAAAATTCAA 57.210 30.769 0.00 0.00 0.00 2.69
6043 6354 8.010105 ACTGGGGGCATATTCTATAAAAATTCA 58.990 33.333 0.00 0.00 0.00 2.57
6044 6355 8.422577 ACTGGGGGCATATTCTATAAAAATTC 57.577 34.615 0.00 0.00 0.00 2.17
6045 6356 8.010105 TGACTGGGGGCATATTCTATAAAAATT 58.990 33.333 0.00 0.00 0.00 1.82
6046 6357 7.534852 TGACTGGGGGCATATTCTATAAAAAT 58.465 34.615 0.00 0.00 0.00 1.82
6047 6358 6.916909 TGACTGGGGGCATATTCTATAAAAA 58.083 36.000 0.00 0.00 0.00 1.94
6048 6359 6.523035 TGACTGGGGGCATATTCTATAAAA 57.477 37.500 0.00 0.00 0.00 1.52
6049 6360 6.523035 TTGACTGGGGGCATATTCTATAAA 57.477 37.500 0.00 0.00 0.00 1.40
6050 6361 6.523035 TTTGACTGGGGGCATATTCTATAA 57.477 37.500 0.00 0.00 0.00 0.98
6051 6362 6.523035 TTTTGACTGGGGGCATATTCTATA 57.477 37.500 0.00 0.00 0.00 1.31
6052 6363 5.402054 TTTTGACTGGGGGCATATTCTAT 57.598 39.130 0.00 0.00 0.00 1.98
6053 6364 4.871871 TTTTGACTGGGGGCATATTCTA 57.128 40.909 0.00 0.00 0.00 2.10
6054 6365 3.756082 TTTTGACTGGGGGCATATTCT 57.244 42.857 0.00 0.00 0.00 2.40
6055 6366 5.539955 ACATATTTTGACTGGGGGCATATTC 59.460 40.000 0.00 0.00 0.00 1.75
6056 6367 5.466819 ACATATTTTGACTGGGGGCATATT 58.533 37.500 0.00 0.00 0.00 1.28
6057 6368 5.078683 ACATATTTTGACTGGGGGCATAT 57.921 39.130 0.00 0.00 0.00 1.78
6058 6369 4.534647 ACATATTTTGACTGGGGGCATA 57.465 40.909 0.00 0.00 0.00 3.14
6059 6370 3.403228 ACATATTTTGACTGGGGGCAT 57.597 42.857 0.00 0.00 0.00 4.40
6060 6371 2.917713 ACATATTTTGACTGGGGGCA 57.082 45.000 0.00 0.00 0.00 5.36
6061 6372 3.365472 AGAACATATTTTGACTGGGGGC 58.635 45.455 0.00 0.00 0.00 5.80
6062 6373 5.133221 CCTAGAACATATTTTGACTGGGGG 58.867 45.833 0.00 0.00 33.84 5.40
6063 6374 5.755849 ACCTAGAACATATTTTGACTGGGG 58.244 41.667 0.00 0.00 37.79 4.96
6064 6375 5.823045 GGACCTAGAACATATTTTGACTGGG 59.177 44.000 0.00 0.00 38.60 4.45
6065 6376 5.523916 CGGACCTAGAACATATTTTGACTGG 59.476 44.000 0.00 0.00 0.00 4.00
6066 6377 5.006746 GCGGACCTAGAACATATTTTGACTG 59.993 44.000 0.00 0.00 0.00 3.51
6067 6378 5.116882 GCGGACCTAGAACATATTTTGACT 58.883 41.667 0.00 0.00 0.00 3.41
6068 6379 4.272748 GGCGGACCTAGAACATATTTTGAC 59.727 45.833 0.00 0.00 0.00 3.18
6069 6380 4.080807 TGGCGGACCTAGAACATATTTTGA 60.081 41.667 0.00 0.00 36.63 2.69
6070 6381 4.035208 GTGGCGGACCTAGAACATATTTTG 59.965 45.833 0.00 0.00 36.63 2.44
6071 6382 4.080526 AGTGGCGGACCTAGAACATATTTT 60.081 41.667 0.00 0.00 36.63 1.82
6072 6383 3.454812 AGTGGCGGACCTAGAACATATTT 59.545 43.478 0.00 0.00 36.63 1.40
6073 6384 3.039011 AGTGGCGGACCTAGAACATATT 58.961 45.455 0.00 0.00 36.63 1.28
6074 6385 2.365617 CAGTGGCGGACCTAGAACATAT 59.634 50.000 0.00 0.00 36.63 1.78
6075 6386 1.754803 CAGTGGCGGACCTAGAACATA 59.245 52.381 0.00 0.00 36.63 2.29
6076 6387 0.537188 CAGTGGCGGACCTAGAACAT 59.463 55.000 0.00 0.00 36.63 2.71
6077 6388 1.972198 CAGTGGCGGACCTAGAACA 59.028 57.895 0.00 0.00 36.63 3.18
6078 6389 1.448013 GCAGTGGCGGACCTAGAAC 60.448 63.158 0.00 0.00 36.63 3.01
6079 6390 2.656069 GGCAGTGGCGGACCTAGAA 61.656 63.158 0.00 0.00 42.47 2.10
6080 6391 3.075005 GGCAGTGGCGGACCTAGA 61.075 66.667 0.00 0.00 42.47 2.43
6089 6400 1.812922 CTCTCATGACGGCAGTGGC 60.813 63.158 6.62 6.62 40.13 5.01
6090 6401 1.812922 GCTCTCATGACGGCAGTGG 60.813 63.158 0.00 0.00 0.00 4.00
6091 6402 2.163390 CGCTCTCATGACGGCAGTG 61.163 63.158 0.00 0.00 0.00 3.66
6092 6403 2.182791 CGCTCTCATGACGGCAGT 59.817 61.111 0.00 0.00 0.00 4.40
6093 6404 3.260483 GCGCTCTCATGACGGCAG 61.260 66.667 0.00 8.41 0.00 4.85
6094 6405 2.857575 AATGCGCTCTCATGACGGCA 62.858 55.000 9.73 0.00 32.33 5.69
6095 6406 1.709147 AAATGCGCTCTCATGACGGC 61.709 55.000 9.73 5.85 0.00 5.68
6096 6407 0.729116 AAAATGCGCTCTCATGACGG 59.271 50.000 9.73 0.00 0.00 4.79
6097 6408 2.860136 TCTAAAATGCGCTCTCATGACG 59.140 45.455 9.73 0.00 0.00 4.35
6098 6409 4.494855 GGTTCTAAAATGCGCTCTCATGAC 60.495 45.833 9.73 0.00 0.00 3.06
6099 6410 3.623060 GGTTCTAAAATGCGCTCTCATGA 59.377 43.478 9.73 0.00 0.00 3.07
6100 6411 3.624861 AGGTTCTAAAATGCGCTCTCATG 59.375 43.478 9.73 0.00 0.00 3.07
6101 6412 3.624861 CAGGTTCTAAAATGCGCTCTCAT 59.375 43.478 9.73 0.00 0.00 2.90
6102 6413 3.002791 CAGGTTCTAAAATGCGCTCTCA 58.997 45.455 9.73 0.00 0.00 3.27
6103 6414 2.352960 CCAGGTTCTAAAATGCGCTCTC 59.647 50.000 9.73 0.00 0.00 3.20
6116 6427 2.039879 GGTTCACATGTACCCAGGTTCT 59.960 50.000 6.53 0.00 32.25 3.01
6197 6509 0.991920 ACCATCTACTTGTGTGGGGG 59.008 55.000 0.00 0.00 36.05 5.40
6414 6728 0.039437 CAGCAAAGCTCAGCCACTTG 60.039 55.000 6.72 0.00 36.40 3.16
6450 6764 2.131183 GATATGTCGGCTCTTCTGCAC 58.869 52.381 0.00 0.00 34.04 4.57
6463 6777 3.428198 GCGACTGCATCTTCAGATATGTC 59.572 47.826 0.00 0.00 42.15 3.06
6484 6800 1.133668 ACCCAGGGAATAGAATGCTGC 60.134 52.381 14.54 0.00 0.00 5.25
6512 6828 4.568152 AAGTTCCAATCCAGACAAAACG 57.432 40.909 0.00 0.00 0.00 3.60
6549 6865 5.778161 TGTACAGAACAATTGCGATGTAG 57.222 39.130 5.05 0.00 34.29 2.74
6553 6869 5.627499 AACATGTACAGAACAATTGCGAT 57.373 34.783 5.05 0.00 42.70 4.58
6674 6991 4.293662 TGTTGGTACATGCATCCTACAA 57.706 40.909 14.76 8.07 39.30 2.41
6680 6997 5.713025 AGTCAATTTGTTGGTACATGCATC 58.287 37.500 0.00 0.00 39.30 3.91
6718 7035 7.056006 AGCATGAGTAATAACATGATCACCAA 58.944 34.615 0.00 0.00 44.28 3.67


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

AutoCloner maintained by Alex Coulton.