Multiple sequence alignment - TraesCS7D01G401800

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 TraesCS7D01G401800 chr7D 100.000 4899 0 0 1 4899 518784110 518779212 0.000000e+00 9047.0
1 TraesCS7D01G401800 chr7D 86.334 461 57 4 1787 2242 518664226 518663767 9.470000e-137 497.0
2 TraesCS7D01G401800 chr7D 96.181 288 11 0 4612 4899 545656612 545656325 5.740000e-129 472.0
3 TraesCS7D01G401800 chr7D 88.325 394 37 4 2503 2895 518663590 518663205 9.600000e-127 464.0
4 TraesCS7D01G401800 chr7D 94.425 287 16 0 4612 4898 545661895 545661609 4.500000e-120 442.0
5 TraesCS7D01G401800 chr7D 92.440 291 22 0 4609 4899 546128067 546128357 2.730000e-112 416.0
6 TraesCS7D01G401800 chr7D 78.140 430 55 16 1215 1626 518682490 518682082 2.280000e-58 237.0
7 TraesCS7D01G401800 chr7D 100.000 39 0 0 4340 4378 518779734 518779696 6.800000e-09 73.1
8 TraesCS7D01G401800 chr7D 100.000 39 0 0 4377 4415 518779771 518779733 6.800000e-09 73.1
9 TraesCS7D01G401800 chr7A 93.661 3707 143 23 715 4346 594462527 594458838 0.000000e+00 5459.0
10 TraesCS7D01G401800 chr7A 97.701 522 6 3 4379 4899 594454598 594454082 0.000000e+00 893.0
11 TraesCS7D01G401800 chr7A 82.402 716 92 15 2503 3214 593680716 593680031 1.170000e-165 593.0
12 TraesCS7D01G401800 chr7A 88.034 468 53 3 1787 2252 593681349 593680883 7.170000e-153 551.0
13 TraesCS7D01G401800 chr7A 98.611 288 4 0 4612 4899 628655027 628654740 1.220000e-140 510.0
14 TraesCS7D01G401800 chr7A 90.938 320 20 5 1 320 594465118 594464808 5.860000e-114 422.0
15 TraesCS7D01G401800 chr7A 92.440 291 22 0 4609 4899 628865396 628865686 2.730000e-112 416.0
16 TraesCS7D01G401800 chr7A 89.310 290 31 0 4609 4898 169951106 169951395 1.000000e-96 364.0
17 TraesCS7D01G401800 chr7A 95.694 209 6 1 492 697 594462875 594462667 2.830000e-87 333.0
18 TraesCS7D01G401800 chr7A 97.740 177 4 0 316 492 594463207 594463031 6.160000e-79 305.0
19 TraesCS7D01G401800 chr7A 86.620 142 17 1 1204 1345 593694066 593693927 6.570000e-34 156.0
20 TraesCS7D01G401800 chr7A 97.778 45 1 0 4333 4377 594454607 594454563 1.460000e-10 78.7
21 TraesCS7D01G401800 chr7B 94.917 3187 125 19 1219 4377 552118658 552115481 0.000000e+00 4953.0
22 TraesCS7D01G401800 chr7B 86.555 714 82 7 2503 3211 552010841 552010137 0.000000e+00 774.0
23 TraesCS7D01G401800 chr7B 85.370 622 82 5 1633 2252 552011624 552011010 1.920000e-178 636.0
24 TraesCS7D01G401800 chr7B 91.925 322 13 7 1 320 552122800 552122490 5.820000e-119 438.0
25 TraesCS7D01G401800 chr7B 87.121 396 32 7 715 1095 552119576 552119185 9.740000e-117 431.0
26 TraesCS7D01G401800 chr7B 90.572 297 28 0 4603 4899 590105675 590105971 1.280000e-105 394.0
27 TraesCS7D01G401800 chr7B 89.474 285 30 0 4612 4896 589901014 589900730 1.300000e-95 361.0
28 TraesCS7D01G401800 chr7B 94.949 198 10 0 492 689 552120047 552119850 1.320000e-80 311.0
29 TraesCS7D01G401800 chr7B 80.505 436 47 19 1194 1611 552018400 552017985 2.870000e-77 300.0
30 TraesCS7D01G401800 chr7B 80.230 435 43 18 1195 1611 552013165 552012756 2.230000e-73 287.0
31 TraesCS7D01G401800 chr7B 96.045 177 5 1 316 492 552120374 552120200 2.230000e-73 287.0
32 TraesCS7D01G401800 chr7B 89.121 239 12 7 4377 4605 552115518 552115284 8.030000e-73 285.0
33 TraesCS7D01G401800 chr7B 78.222 225 34 10 932 1150 552014916 552015131 3.980000e-26 130.0
34 TraesCS7D01G401800 chr7B 84.091 132 20 1 3736 3867 552009837 552009707 5.150000e-25 126.0
35 TraesCS7D01G401800 chr7B 83.621 116 13 1 138 253 184982517 184982626 2.410000e-18 104.0
36 TraesCS7D01G401800 chr1B 75.889 253 27 12 1 253 15889644 15889862 1.120000e-16 99.0
37 TraesCS7D01G401800 chr3B 86.420 81 11 0 1 81 770762089 770762169 6.750000e-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 TraesCS7D01G401800 chr7D 518779212 518784110 4898 True 9047.00 9047 100.000000 1 4899 1 chr7D.!!$R2 4898
1 TraesCS7D01G401800 chr7D 518663205 518664226 1021 True 480.50 497 87.329500 1787 2895 2 chr7D.!!$R5 1108
2 TraesCS7D01G401800 chr7A 594458838 594465118 6280 True 1629.75 5459 94.508250 1 4346 4 chr7A.!!$R5 4345
3 TraesCS7D01G401800 chr7A 593680031 593681349 1318 True 572.00 593 85.218000 1787 3214 2 chr7A.!!$R3 1427
4 TraesCS7D01G401800 chr7A 594454082 594454607 525 True 485.85 893 97.739500 4333 4899 2 chr7A.!!$R4 566
5 TraesCS7D01G401800 chr7B 552115284 552122800 7516 True 1117.50 4953 92.346333 1 4605 6 chr7B.!!$R4 4604
6 TraesCS7D01G401800 chr7B 552009707 552013165 3458 True 455.75 774 84.061500 1195 3867 4 chr7B.!!$R3 2672

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
104 105 0.107508 CCCTTGACTGCATCATCCGT 60.108 55.0 0.0 0.0 37.11 4.69 F
964 3514 0.247460 CATCTCCTTCTGCGACACCA 59.753 55.0 0.0 0.0 0.00 4.17 F
1763 5854 0.255890 ACAACTGCACCTTCAGTGGT 59.744 50.0 0.0 0.0 45.77 4.16 F
2389 6504 0.179234 TTGAACCCTCAACTGCGACA 59.821 50.0 0.0 0.0 36.62 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 3678 0.659123 AATCAAACGAAACGCACGCC 60.659 50.000 0.00 0.0 0.00 5.68 R
1901 5995 0.665068 CAGCGCACACAAATGCACAT 60.665 50.000 11.47 0.0 46.47 3.21 R
2875 7016 1.072648 TGTATTAGCATTACCCCGCCC 59.927 52.381 0.00 0.0 0.00 6.13 R
4276 8442 2.161855 CGAGATCTGCTCTATGAGGCT 58.838 52.381 0.00 0.0 41.66 4.58 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
44 45 9.191995 GGGACTATTGTTTATTTTTGTGACTTG 57.808 33.333 0.00 0.00 0.00 3.16
81 82 4.038642 GGAATGTGAGTCTAGATCAGGGAC 59.961 50.000 0.00 0.03 0.00 4.46
95 96 2.360475 GGACTGCCCCTTGACTGC 60.360 66.667 0.00 0.00 0.00 4.40
96 97 2.431683 GACTGCCCCTTGACTGCA 59.568 61.111 0.00 0.00 0.00 4.41
97 98 1.001641 GACTGCCCCTTGACTGCAT 60.002 57.895 0.00 0.00 33.97 3.96
99 100 1.001764 CTGCCCCTTGACTGCATCA 60.002 57.895 0.00 0.00 33.97 3.07
100 101 0.395311 CTGCCCCTTGACTGCATCAT 60.395 55.000 0.00 0.00 37.11 2.45
101 102 0.394762 TGCCCCTTGACTGCATCATC 60.395 55.000 0.00 0.00 37.11 2.92
102 103 1.105759 GCCCCTTGACTGCATCATCC 61.106 60.000 0.00 0.00 37.11 3.51
103 104 0.816825 CCCCTTGACTGCATCATCCG 60.817 60.000 0.00 0.00 37.11 4.18
104 105 0.107508 CCCTTGACTGCATCATCCGT 60.108 55.000 0.00 0.00 37.11 4.69
105 106 1.138859 CCCTTGACTGCATCATCCGTA 59.861 52.381 0.00 0.00 37.11 4.02
106 107 2.419990 CCCTTGACTGCATCATCCGTAA 60.420 50.000 0.00 0.00 37.11 3.18
107 108 2.868583 CCTTGACTGCATCATCCGTAAG 59.131 50.000 0.00 0.00 37.11 2.34
197 198 1.605457 GCCGACATGTCAGAGTTCACA 60.605 52.381 24.93 0.00 0.00 3.58
209 210 0.250467 AGTTCACAGCGCAGTTGGAT 60.250 50.000 11.47 0.00 45.20 3.41
230 231 7.060421 TGGATTCCATTGGGTTTAAGATAGTC 58.940 38.462 0.00 0.00 34.93 2.59
348 2476 8.100164 TCACTGTAACCATTACATGATTCAAGA 58.900 33.333 0.00 0.00 44.46 3.02
447 2575 5.847111 ACTTTTAGTGTTTTGGAAGACCC 57.153 39.130 0.00 0.00 34.81 4.46
574 2861 6.713731 TGGAAACCCTAAGGAAAAGTCTAT 57.286 37.500 0.00 0.00 36.73 1.98
644 2931 4.406456 TCCAAAACCATCTAATGTGCACT 58.594 39.130 19.41 0.28 0.00 4.40
697 2984 3.091545 AGGGAAGTATTTGTGCATGGTG 58.908 45.455 0.00 0.00 0.00 4.17
698 2985 2.166254 GGGAAGTATTTGTGCATGGTGG 59.834 50.000 0.00 0.00 0.00 4.61
699 2986 3.088532 GGAAGTATTTGTGCATGGTGGA 58.911 45.455 0.00 0.00 0.00 4.02
700 2987 3.129287 GGAAGTATTTGTGCATGGTGGAG 59.871 47.826 0.00 0.00 0.00 3.86
701 2988 3.719268 AGTATTTGTGCATGGTGGAGA 57.281 42.857 0.00 0.00 0.00 3.71
702 2989 4.032960 AGTATTTGTGCATGGTGGAGAA 57.967 40.909 0.00 0.00 0.00 2.87
703 2990 4.406456 AGTATTTGTGCATGGTGGAGAAA 58.594 39.130 0.00 0.00 35.64 2.52
705 2992 2.655090 TTGTGCATGGTGGAGAAAGA 57.345 45.000 0.00 0.00 0.00 2.52
706 2993 2.655090 TGTGCATGGTGGAGAAAGAA 57.345 45.000 0.00 0.00 0.00 2.52
707 2994 3.159213 TGTGCATGGTGGAGAAAGAAT 57.841 42.857 0.00 0.00 0.00 2.40
708 2995 4.299586 TGTGCATGGTGGAGAAAGAATA 57.700 40.909 0.00 0.00 0.00 1.75
709 2996 4.858850 TGTGCATGGTGGAGAAAGAATAT 58.141 39.130 0.00 0.00 0.00 1.28
710 2997 5.263599 TGTGCATGGTGGAGAAAGAATATT 58.736 37.500 0.00 0.00 0.00 1.28
711 2998 5.716228 TGTGCATGGTGGAGAAAGAATATTT 59.284 36.000 0.00 0.00 0.00 1.40
712 2999 6.038356 GTGCATGGTGGAGAAAGAATATTTG 58.962 40.000 0.00 0.00 0.00 2.32
713 3000 5.045872 GCATGGTGGAGAAAGAATATTTGC 58.954 41.667 0.00 0.00 0.00 3.68
714 3001 5.594926 CATGGTGGAGAAAGAATATTTGCC 58.405 41.667 0.00 0.00 0.00 4.52
715 3002 4.671831 TGGTGGAGAAAGAATATTTGCCA 58.328 39.130 0.00 0.00 0.00 4.92
716 3003 4.706476 TGGTGGAGAAAGAATATTTGCCAG 59.294 41.667 0.00 0.00 0.00 4.85
717 3004 4.949856 GGTGGAGAAAGAATATTTGCCAGA 59.050 41.667 0.00 0.00 0.00 3.86
719 3006 5.067023 GTGGAGAAAGAATATTTGCCAGAGG 59.933 44.000 0.00 0.00 0.00 3.69
720 3007 5.196695 GGAGAAAGAATATTTGCCAGAGGT 58.803 41.667 0.00 0.00 0.00 3.85
753 3301 4.536765 CCCCAATATCTAATATGTGGGGC 58.463 47.826 20.90 0.00 45.68 5.80
775 3323 3.259374 CCTACTGCTCAGTGGAGAAAGAA 59.741 47.826 13.88 0.00 44.26 2.52
777 3325 5.127845 CCTACTGCTCAGTGGAGAAAGAATA 59.872 44.000 13.88 0.00 44.26 1.75
787 3335 4.400567 GTGGAGAAAGAATATTTGCCAGCT 59.599 41.667 0.00 0.00 0.00 4.24
806 3354 2.386249 CTATCTCGCCAAGTAACGCTC 58.614 52.381 0.00 0.00 0.00 5.03
862 3410 2.614829 AAGGCGACAAACTAGTGTGT 57.385 45.000 18.89 18.89 0.00 3.72
869 3417 4.977963 GCGACAAACTAGTGTGTACTGTAA 59.022 41.667 18.84 0.00 37.78 2.41
875 3423 8.145767 ACAAACTAGTGTGTACTGTAAGCAATA 58.854 33.333 17.41 0.00 37.60 1.90
877 3425 9.550406 AAACTAGTGTGTACTGTAAGCAATAAA 57.450 29.630 0.00 0.00 37.60 1.40
957 3507 2.170187 AGTCACATCCATCTCCTTCTGC 59.830 50.000 0.00 0.00 0.00 4.26
964 3514 0.247460 CATCTCCTTCTGCGACACCA 59.753 55.000 0.00 0.00 0.00 4.17
995 3545 3.525800 AAGCCATACTTCAAACCTGGT 57.474 42.857 0.00 0.00 30.77 4.00
996 3546 3.073274 AGCCATACTTCAAACCTGGTC 57.927 47.619 0.00 0.00 0.00 4.02
1006 3564 1.149101 AAACCTGGTCACCATGGAGT 58.851 50.000 21.47 0.00 30.82 3.85
1103 3664 2.554462 GTGTCTCAGTACTGTGAGCAGA 59.446 50.000 24.17 15.63 45.28 4.26
1148 3710 6.020995 CGTTTCGTTTGATTTGCTAGTTGTTT 60.021 34.615 0.00 0.00 0.00 2.83
1200 4039 1.203038 TGTGGATGTGATGGGTTGCTT 60.203 47.619 0.00 0.00 0.00 3.91
1202 4041 3.290710 GTGGATGTGATGGGTTGCTTAT 58.709 45.455 0.00 0.00 0.00 1.73
1397 4377 5.065704 TGTTGCTGTCAGATTAGAGAGTC 57.934 43.478 3.32 0.00 31.96 3.36
1399 4379 5.946377 TGTTGCTGTCAGATTAGAGAGTCTA 59.054 40.000 3.32 0.00 31.96 2.59
1407 4387 8.191446 TGTCAGATTAGAGAGTCTAATTTTCGG 58.809 37.037 9.92 1.67 46.46 4.30
1441 4421 5.542779 AGCGAGGTATATTCCATTTCTGTC 58.457 41.667 0.78 0.00 0.00 3.51
1489 4469 8.701908 ATCTTGATATGCTGATTGGTATGTTT 57.298 30.769 0.00 0.00 0.00 2.83
1512 4492 1.996191 GCTTAGAACAGGAGTGCTTCG 59.004 52.381 0.00 0.00 34.64 3.79
1527 4507 3.058085 GTGCTTCGGGCTACTAGTCTATC 60.058 52.174 0.00 0.00 42.39 2.08
1528 4508 2.160022 GCTTCGGGCTACTAGTCTATCG 59.840 54.545 0.00 0.26 38.06 2.92
1543 4523 4.095782 AGTCTATCGAAGTCTCAAGCTCAC 59.904 45.833 0.00 0.00 0.00 3.51
1717 5808 2.976185 TGAGGGACACCACACTTGATTA 59.024 45.455 0.00 0.00 40.13 1.75
1762 5853 1.334869 GAACAACTGCACCTTCAGTGG 59.665 52.381 0.00 0.00 45.77 4.00
1763 5854 0.255890 ACAACTGCACCTTCAGTGGT 59.744 50.000 0.00 0.00 45.77 4.16
1764 5855 1.340991 ACAACTGCACCTTCAGTGGTT 60.341 47.619 0.00 0.00 46.20 3.67
1805 5899 2.352715 CCAGTGCAGACTATCAACGACA 60.353 50.000 0.00 0.00 0.00 4.35
1810 5904 2.030946 GCAGACTATCAACGACAATGCC 59.969 50.000 0.00 0.00 0.00 4.40
1901 5995 0.744281 TGCTTGGACGAGCGATCATA 59.256 50.000 0.00 0.00 45.64 2.15
2086 6183 6.677781 TTTAGTATGTTTGCTGCATACCTC 57.322 37.500 18.32 9.89 45.79 3.85
2100 6197 4.202080 TGCATACCTCGTGAATACTGGTAC 60.202 45.833 0.00 0.00 36.83 3.34
2160 6258 6.976934 AATGTTCTTTTCCCTTGAGCTTTA 57.023 33.333 0.00 0.00 0.00 1.85
2265 6363 5.220710 ACGAGATTGGATCATTTAGAGGG 57.779 43.478 0.00 0.00 0.00 4.30
2287 6400 9.842775 GAGGGCATATCATCAGATAATCATTTA 57.157 33.333 0.00 0.00 39.99 1.40
2389 6504 0.179234 TTGAACCCTCAACTGCGACA 59.821 50.000 0.00 0.00 36.62 4.35
2452 6567 0.977395 AGGTACAGAGCAACCTCCAC 59.023 55.000 0.00 0.00 42.60 4.02
2473 6588 1.838077 AGGGTGCTATCTGGTGGTAAC 59.162 52.381 0.00 0.00 0.00 2.50
2509 6624 4.021981 GGTATGCCCCTTCATGATTTTAGC 60.022 45.833 0.00 0.00 0.00 3.09
2775 6916 3.758755 AGCATGCTATTCCGAAGATCA 57.241 42.857 21.21 0.00 0.00 2.92
2875 7016 6.239908 AGTTTGCAAAAAGTTTGTTTGAGG 57.760 33.333 14.67 0.00 38.05 3.86
3127 7271 2.816958 AGCTCAGCCGTGAATGCG 60.817 61.111 0.00 0.00 30.84 4.73
3289 7433 0.994995 CTTCAAGGACACTCGATGCG 59.005 55.000 0.00 0.00 0.00 4.73
3396 7543 2.501723 ACCAGTGAGACATGTATGGGTC 59.498 50.000 0.00 0.00 31.95 4.46
3477 7624 4.158384 GTTTGACATATGTGAAGGTTGCG 58.842 43.478 14.43 0.00 0.00 4.85
3583 7731 2.106566 CTCCTCTAGCTTGCTTCCTCA 58.893 52.381 0.00 0.00 0.00 3.86
3698 7846 7.775561 AGACAGGAATTCCTATTAACATGTTCC 59.224 37.037 26.61 6.05 46.65 3.62
3732 7880 6.892310 AAAATTTCAGTTTGACTGTGAAGC 57.108 33.333 7.85 0.00 46.03 3.86
3768 7916 4.343239 GCTTCAAATGGCTGAGGGAATATT 59.657 41.667 0.00 0.00 0.00 1.28
3905 8053 4.520179 TGTCAAGACGTACTAGGATGCTA 58.480 43.478 0.00 0.00 0.00 3.49
4070 8218 1.541588 GGGAAACTTGCTTGCTACCAG 59.458 52.381 0.00 0.00 0.00 4.00
4078 8226 6.049955 ACTTGCTTGCTACCAGTTATCTAA 57.950 37.500 0.00 0.00 0.00 2.10
4085 8233 7.281100 GCTTGCTACCAGTTATCTAAGTTGATT 59.719 37.037 0.00 0.00 0.00 2.57
4276 8442 2.418777 CGCCATGATCGCCTCTCA 59.581 61.111 0.00 0.00 0.00 3.27
4377 8543 0.718343 GAATCTGAGTGCACTGACGC 59.282 55.000 27.27 10.48 0.00 5.19
4378 8544 0.033920 AATCTGAGTGCACTGACGCA 59.966 50.000 27.27 14.98 40.32 5.24
4379 8545 0.248565 ATCTGAGTGCACTGACGCAT 59.751 50.000 27.27 5.82 45.26 4.73
4380 8546 0.668401 TCTGAGTGCACTGACGCATG 60.668 55.000 27.27 3.26 45.26 4.06
4381 8547 0.947660 CTGAGTGCACTGACGCATGT 60.948 55.000 27.27 0.00 45.26 3.21
4382 8548 0.532640 TGAGTGCACTGACGCATGTT 60.533 50.000 27.27 0.00 45.26 2.71
4383 8549 0.110509 GAGTGCACTGACGCATGTTG 60.111 55.000 27.27 0.00 45.26 3.33
4384 8550 1.727022 GTGCACTGACGCATGTTGC 60.727 57.895 10.32 0.00 45.26 4.17
4385 8551 2.126734 GCACTGACGCATGTTGCC 60.127 61.111 0.00 0.00 41.12 4.52
4386 8552 2.906939 GCACTGACGCATGTTGCCA 61.907 57.895 0.00 0.00 41.12 4.92
4387 8553 1.208358 CACTGACGCATGTTGCCAG 59.792 57.895 0.00 0.00 41.12 4.85
4388 8554 1.227943 ACTGACGCATGTTGCCAGT 60.228 52.632 3.82 3.82 41.12 4.00
4389 8555 0.034756 ACTGACGCATGTTGCCAGTA 59.965 50.000 7.14 0.00 41.69 2.74
4390 8556 1.339055 ACTGACGCATGTTGCCAGTAT 60.339 47.619 7.14 0.00 41.69 2.12
4391 8557 1.328680 CTGACGCATGTTGCCAGTATC 59.671 52.381 0.00 0.00 41.12 2.24
4392 8558 1.066215 TGACGCATGTTGCCAGTATCT 60.066 47.619 0.00 0.00 41.12 1.98
4393 8559 2.009774 GACGCATGTTGCCAGTATCTT 58.990 47.619 0.00 0.00 41.12 2.40
4394 8560 1.739466 ACGCATGTTGCCAGTATCTTG 59.261 47.619 0.00 0.00 41.12 3.02
4395 8561 1.064505 CGCATGTTGCCAGTATCTTGG 59.935 52.381 0.00 0.00 41.12 3.61
4396 8562 2.368439 GCATGTTGCCAGTATCTTGGA 58.632 47.619 0.00 0.00 40.87 3.53
4397 8563 2.754552 GCATGTTGCCAGTATCTTGGAA 59.245 45.455 0.00 0.00 40.87 3.53
4398 8564 3.382546 GCATGTTGCCAGTATCTTGGAAT 59.617 43.478 0.00 0.00 40.87 3.01
4399 8565 4.498682 GCATGTTGCCAGTATCTTGGAATC 60.499 45.833 0.00 0.00 40.87 2.52
4400 8566 4.574674 TGTTGCCAGTATCTTGGAATCT 57.425 40.909 0.00 0.00 40.87 2.40
4401 8567 4.264253 TGTTGCCAGTATCTTGGAATCTG 58.736 43.478 0.00 0.00 40.87 2.90
4402 8568 4.019411 TGTTGCCAGTATCTTGGAATCTGA 60.019 41.667 0.00 0.00 40.87 3.27
4403 8569 4.412796 TGCCAGTATCTTGGAATCTGAG 57.587 45.455 0.00 0.00 40.87 3.35
4404 8570 3.776969 TGCCAGTATCTTGGAATCTGAGT 59.223 43.478 0.00 0.00 40.87 3.41
4405 8571 4.125703 GCCAGTATCTTGGAATCTGAGTG 58.874 47.826 0.00 0.00 40.87 3.51
4406 8572 4.125703 CCAGTATCTTGGAATCTGAGTGC 58.874 47.826 0.00 0.00 40.87 4.40
4407 8573 4.383444 CCAGTATCTTGGAATCTGAGTGCA 60.383 45.833 0.00 0.00 40.87 4.57
4408 8574 4.569966 CAGTATCTTGGAATCTGAGTGCAC 59.430 45.833 9.40 9.40 0.00 4.57
4409 8575 3.996921 ATCTTGGAATCTGAGTGCACT 57.003 42.857 21.88 21.88 0.00 4.40
4410 8576 3.049708 TCTTGGAATCTGAGTGCACTG 57.950 47.619 27.27 11.39 0.00 3.66
4411 8577 2.634453 TCTTGGAATCTGAGTGCACTGA 59.366 45.455 27.27 16.42 0.00 3.41
4412 8578 2.462456 TGGAATCTGAGTGCACTGAC 57.538 50.000 27.27 11.73 0.00 3.51
4464 8639 4.380867 GGGACATGATTTTGCTACAAGGTG 60.381 45.833 0.00 0.00 0.00 4.00
4585 8760 9.087424 GACAAAGAAGTTTAAAATGCAGTTTCT 57.913 29.630 16.40 4.42 0.00 2.52
4814 8989 2.281276 GGGAAAAGCACCGACCGT 60.281 61.111 0.00 0.00 0.00 4.83
4815 8990 2.322830 GGGAAAAGCACCGACCGTC 61.323 63.158 0.00 0.00 0.00 4.79
4816 8991 2.322830 GGAAAAGCACCGACCGTCC 61.323 63.158 0.00 0.00 0.00 4.79
4817 8992 2.663852 AAAAGCACCGACCGTCCG 60.664 61.111 0.00 0.00 0.00 4.79
4833 9008 0.179094 TCCGGTATTGACGTGATGGC 60.179 55.000 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.747898 ATAAACAATAGTCCCACAATTTACAGA 57.252 29.630 0.00 0.00 0.00 3.41
44 45 8.204836 AGACTCACATTCCAATTGTATACTACC 58.795 37.037 4.43 0.00 0.00 3.18
81 82 0.395311 ATGATGCAGTCAAGGGGCAG 60.395 55.000 0.00 0.00 41.40 4.85
83 84 1.105759 GGATGATGCAGTCAAGGGGC 61.106 60.000 0.00 0.00 40.97 5.80
84 85 0.816825 CGGATGATGCAGTCAAGGGG 60.817 60.000 0.00 0.00 40.97 4.79
87 88 2.868583 CCTTACGGATGATGCAGTCAAG 59.131 50.000 0.00 0.00 40.97 3.02
88 89 2.905075 CCTTACGGATGATGCAGTCAA 58.095 47.619 0.00 0.00 40.97 3.18
89 90 1.473257 GCCTTACGGATGATGCAGTCA 60.473 52.381 0.00 0.00 42.06 3.41
90 91 1.221414 GCCTTACGGATGATGCAGTC 58.779 55.000 0.00 0.00 0.00 3.51
91 92 0.179045 GGCCTTACGGATGATGCAGT 60.179 55.000 0.00 0.00 0.00 4.40
92 93 1.224069 CGGCCTTACGGATGATGCAG 61.224 60.000 0.00 0.00 0.00 4.41
93 94 1.227527 CGGCCTTACGGATGATGCA 60.228 57.895 0.00 0.00 0.00 3.96
94 95 3.642755 CGGCCTTACGGATGATGC 58.357 61.111 0.00 0.00 0.00 3.91
102 103 1.136305 TCTGAATTCTCCGGCCTTACG 59.864 52.381 7.05 0.00 0.00 3.18
103 104 2.168728 AGTCTGAATTCTCCGGCCTTAC 59.831 50.000 7.05 0.00 0.00 2.34
104 105 2.168521 CAGTCTGAATTCTCCGGCCTTA 59.831 50.000 7.05 0.00 0.00 2.69
105 106 1.065854 CAGTCTGAATTCTCCGGCCTT 60.066 52.381 7.05 0.00 0.00 4.35
106 107 0.539051 CAGTCTGAATTCTCCGGCCT 59.461 55.000 7.05 0.00 0.00 5.19
107 108 1.092345 GCAGTCTGAATTCTCCGGCC 61.092 60.000 3.32 0.00 0.00 6.13
108 109 1.092345 GGCAGTCTGAATTCTCCGGC 61.092 60.000 3.32 6.59 0.00 6.13
135 136 5.745312 TTCTTCACCTGCAGATAAGAAGA 57.255 39.130 23.69 23.69 39.53 2.87
137 138 5.482908 GACTTCTTCACCTGCAGATAAGAA 58.517 41.667 24.25 24.25 35.49 2.52
138 139 4.081420 GGACTTCTTCACCTGCAGATAAGA 60.081 45.833 17.39 16.86 0.00 2.10
197 198 0.813184 CAATGGAATCCAACTGCGCT 59.187 50.000 5.89 0.00 36.95 5.92
209 210 6.302535 TCGACTATCTTAAACCCAATGGAA 57.697 37.500 0.00 0.00 34.81 3.53
230 231 1.448540 GCCATCCACAGTGACCTCG 60.449 63.158 0.62 0.00 0.00 4.63
309 310 6.296026 TGGTTACAGTGAAACAAAGATAGCT 58.704 36.000 0.00 0.00 41.43 3.32
445 2573 1.549170 ACTTGCTACGACCACTTAGGG 59.451 52.381 0.00 0.00 43.89 3.53
447 2575 3.570926 TGACTTGCTACGACCACTTAG 57.429 47.619 0.00 0.00 0.00 2.18
520 2804 7.663043 AATTTGAAGGTTAAACCCTACAACA 57.337 32.000 0.00 0.00 39.75 3.33
574 2861 6.719370 AGACAATAATAGTTGAGGCACCAAAA 59.281 34.615 0.00 0.00 33.37 2.44
644 2931 7.443302 AATCAGAAAGGGTTCATATCTGAGA 57.557 36.000 9.34 0.00 46.74 3.27
674 2961 3.245229 ACCATGCACAAATACTTCCCTGA 60.245 43.478 0.00 0.00 0.00 3.86
697 2984 5.196695 ACCTCTGGCAAATATTCTTTCTCC 58.803 41.667 0.00 0.00 0.00 3.71
698 2985 6.765915 AACCTCTGGCAAATATTCTTTCTC 57.234 37.500 0.00 0.00 0.00 2.87
699 2986 6.153510 GGAAACCTCTGGCAAATATTCTTTCT 59.846 38.462 0.00 0.00 0.00 2.52
700 2987 6.071391 TGGAAACCTCTGGCAAATATTCTTTC 60.071 38.462 0.00 0.00 0.00 2.62
701 2988 5.779771 TGGAAACCTCTGGCAAATATTCTTT 59.220 36.000 0.00 0.00 0.00 2.52
702 2989 5.332743 TGGAAACCTCTGGCAAATATTCTT 58.667 37.500 0.00 0.00 0.00 2.52
703 2990 4.934356 TGGAAACCTCTGGCAAATATTCT 58.066 39.130 0.00 0.00 0.00 2.40
705 2992 6.625532 AAATGGAAACCTCTGGCAAATATT 57.374 33.333 0.00 0.00 0.00 1.28
706 2993 6.352137 GGAAAATGGAAACCTCTGGCAAATAT 60.352 38.462 0.00 0.00 0.00 1.28
707 2994 5.046663 GGAAAATGGAAACCTCTGGCAAATA 60.047 40.000 0.00 0.00 0.00 1.40
708 2995 4.263025 GGAAAATGGAAACCTCTGGCAAAT 60.263 41.667 0.00 0.00 0.00 2.32
709 2996 3.070878 GGAAAATGGAAACCTCTGGCAAA 59.929 43.478 0.00 0.00 0.00 3.68
710 2997 2.632512 GGAAAATGGAAACCTCTGGCAA 59.367 45.455 0.00 0.00 0.00 4.52
711 2998 2.247358 GGAAAATGGAAACCTCTGGCA 58.753 47.619 0.00 0.00 0.00 4.92
712 2999 1.550524 GGGAAAATGGAAACCTCTGGC 59.449 52.381 0.00 0.00 0.00 4.85
713 3000 2.179427 GGGGAAAATGGAAACCTCTGG 58.821 52.381 0.00 0.00 0.00 3.86
714 3001 2.179427 GGGGGAAAATGGAAACCTCTG 58.821 52.381 0.00 0.00 0.00 3.35
715 3002 1.792651 TGGGGGAAAATGGAAACCTCT 59.207 47.619 0.00 0.00 0.00 3.69
716 3003 2.319025 TGGGGGAAAATGGAAACCTC 57.681 50.000 0.00 0.00 0.00 3.85
717 3004 2.805290 TTGGGGGAAAATGGAAACCT 57.195 45.000 0.00 0.00 0.00 3.50
719 3006 7.669089 TTAGATATTGGGGGAAAATGGAAAC 57.331 36.000 0.00 0.00 0.00 2.78
753 3301 2.828520 TCTTTCTCCACTGAGCAGTAGG 59.171 50.000 2.36 7.61 40.20 3.18
775 3323 2.038952 TGGCGAGATAGCTGGCAAATAT 59.961 45.455 16.94 0.00 46.36 1.28
777 3325 0.181114 TGGCGAGATAGCTGGCAAAT 59.819 50.000 16.94 0.00 46.36 2.32
787 3335 1.268386 CGAGCGTTACTTGGCGAGATA 60.268 52.381 9.20 0.00 0.00 1.98
835 3383 4.995487 ACTAGTTTGTCGCCTTTTCCTTAG 59.005 41.667 0.00 0.00 0.00 2.18
869 3417 6.423604 AGCGCAAAATTACAAAGTTTATTGCT 59.576 30.769 11.47 0.00 39.65 3.91
875 3423 4.209080 GCTCAGCGCAAAATTACAAAGTTT 59.791 37.500 11.47 0.00 38.92 2.66
877 3425 3.308530 GCTCAGCGCAAAATTACAAAGT 58.691 40.909 11.47 0.00 38.92 2.66
904 3452 2.577700 AGGTTGTAACGCCAATGACAA 58.422 42.857 0.00 0.00 0.00 3.18
910 3458 2.257691 TAGCAAGGTTGTAACGCCAA 57.742 45.000 0.00 0.00 0.00 4.52
954 3504 3.220999 TTCCGGACTGGTGTCGCAG 62.221 63.158 1.83 0.00 43.79 5.18
957 3507 1.812686 TTCCTTCCGGACTGGTGTCG 61.813 60.000 18.89 0.00 43.79 4.35
964 3514 0.831307 GTATGGCTTCCTTCCGGACT 59.169 55.000 1.83 0.00 39.60 3.85
983 3533 1.888512 CCATGGTGACCAGGTTTGAAG 59.111 52.381 15.71 0.00 36.75 3.02
987 3537 1.149101 ACTCCATGGTGACCAGGTTT 58.851 50.000 20.43 3.58 36.75 3.27
990 3540 0.322816 CCAACTCCATGGTGACCAGG 60.323 60.000 20.43 10.45 36.75 4.45
1006 3564 1.195115 CCTCCTCCATCGAAGACCAA 58.805 55.000 0.00 0.00 42.51 3.67
1014 3572 2.503061 CCAGCACCTCCTCCATCG 59.497 66.667 0.00 0.00 0.00 3.84
1069 3630 1.328685 GAGACACGAGACACGCGAAC 61.329 60.000 15.93 3.14 46.94 3.95
1076 3637 2.548480 CACAGTACTGAGACACGAGACA 59.452 50.000 29.30 0.00 0.00 3.41
1084 3645 2.817258 AGTCTGCTCACAGTACTGAGAC 59.183 50.000 29.30 26.17 44.77 3.36
1117 3678 0.659123 AATCAAACGAAACGCACGCC 60.659 50.000 0.00 0.00 0.00 5.68
1118 3679 1.117234 AAATCAAACGAAACGCACGC 58.883 45.000 0.00 0.00 0.00 5.34
1119 3680 1.137287 GCAAATCAAACGAAACGCACG 60.137 47.619 0.00 0.00 0.00 5.34
1120 3681 2.116366 AGCAAATCAAACGAAACGCAC 58.884 42.857 0.00 0.00 0.00 5.34
1121 3682 2.483583 AGCAAATCAAACGAAACGCA 57.516 40.000 0.00 0.00 0.00 5.24
1122 3683 3.551551 ACTAGCAAATCAAACGAAACGC 58.448 40.909 0.00 0.00 0.00 4.84
1124 3685 6.806120 AACAACTAGCAAATCAAACGAAAC 57.194 33.333 0.00 0.00 0.00 2.78
1170 4003 6.044754 ACCCATCACATCCACATACATCTATT 59.955 38.462 0.00 0.00 0.00 1.73
1238 4202 7.201617 GCACTTTCAAGTTAGAACAGTAACACT 60.202 37.037 0.00 0.00 37.08 3.55
1251 4215 4.377021 ACATCTCGTGCACTTTCAAGTTA 58.623 39.130 16.19 0.00 37.08 2.24
1346 4310 0.976641 TCAGTCAATGTCTCGGGCTT 59.023 50.000 0.00 0.00 0.00 4.35
1397 4377 5.051641 CGCTAACAGCTACTCCGAAAATTAG 60.052 44.000 0.00 0.00 39.60 1.73
1399 4379 3.617263 CGCTAACAGCTACTCCGAAAATT 59.383 43.478 0.00 0.00 39.60 1.82
1407 4387 5.883503 ATATACCTCGCTAACAGCTACTC 57.116 43.478 0.00 0.00 39.60 2.59
1489 4469 4.618460 CGAAGCACTCCTGTTCTAAGCTTA 60.618 45.833 5.94 5.94 40.52 3.09
1527 4507 1.707632 CTGGTGAGCTTGAGACTTCG 58.292 55.000 0.00 0.00 0.00 3.79
1528 4508 1.437625 GCTGGTGAGCTTGAGACTTC 58.562 55.000 0.00 0.00 42.52 3.01
1543 4523 4.080469 AGCCCAGATCATATGATAAGCTGG 60.080 45.833 28.98 28.98 40.75 4.85
1626 5717 5.187381 TCACCATTGGTTCGTGGTAGTTATA 59.813 40.000 5.34 0.00 46.62 0.98
1717 5808 7.070946 TCCATTATTGCCACAACCATCAATATT 59.929 33.333 0.00 0.00 33.18 1.28
1762 5853 1.478105 GGATGAATGGCTGGGAACAAC 59.522 52.381 0.00 0.00 42.06 3.32
1763 5854 1.358787 AGGATGAATGGCTGGGAACAA 59.641 47.619 0.00 0.00 42.06 2.83
1764 5855 1.002069 AGGATGAATGGCTGGGAACA 58.998 50.000 0.00 0.00 39.59 3.18
1810 5904 1.451567 CAGTCTGCTCCATGCCTGG 60.452 63.158 0.78 0.78 44.64 4.45
1901 5995 0.665068 CAGCGCACACAAATGCACAT 60.665 50.000 11.47 0.00 46.47 3.21
2002 6096 6.759272 ACTGAAGAATGAGCTGTACTTACAA 58.241 36.000 0.00 0.00 35.50 2.41
2086 6183 6.809689 TGTGAAATACAGTACCAGTATTCACG 59.190 38.462 23.65 0.00 40.30 4.35
2178 6276 6.980397 CACACCAAATCTTTTAGCTTGAAGTT 59.020 34.615 0.00 0.00 0.00 2.66
2230 6328 8.459635 TGATCCAATCTCGTATACAGCTTATAC 58.540 37.037 3.32 12.42 0.00 1.47
2287 6400 6.496144 TGATCATCTGATGAAATGTCCTCT 57.504 37.500 22.91 4.51 43.50 3.69
2389 6504 5.305585 TCACTAAAAATTCCTCGCAGAAGT 58.694 37.500 0.00 0.00 34.09 3.01
2452 6567 1.496060 TACCACCAGATAGCACCCTG 58.504 55.000 0.00 0.00 0.00 4.45
2473 6588 2.610232 GGGCATACCTGTTGCTTTTGTG 60.610 50.000 0.00 0.00 40.03 3.33
2509 6624 4.701651 TGCATTTGAAGGACCTAATGACAG 59.298 41.667 16.52 0.00 31.29 3.51
2775 6916 1.215423 GCTGAAGTCCATAATGGGGGT 59.785 52.381 0.00 0.00 38.32 4.95
2875 7016 1.072648 TGTATTAGCATTACCCCGCCC 59.927 52.381 0.00 0.00 0.00 6.13
3127 7271 5.636543 CCAACTGCAGATTTTCCAAAGATTC 59.363 40.000 23.35 0.00 0.00 2.52
3289 7433 4.270008 ACTATGTATTTTGGAGTGCACCC 58.730 43.478 14.63 15.00 0.00 4.61
3477 7624 3.385111 ACCCTGGAGTCATTCTATCGAAC 59.615 47.826 0.00 0.00 30.67 3.95
3648 7796 8.037758 TCTTCAGCTAAGAAAATAGACAAGGAG 58.962 37.037 0.00 0.00 41.35 3.69
4078 8226 6.656270 TGAGCTGTAATGTTCATCAATCAACT 59.344 34.615 0.00 0.00 0.00 3.16
4276 8442 2.161855 CGAGATCTGCTCTATGAGGCT 58.838 52.381 0.00 0.00 41.66 4.58
4312 8478 3.422796 ACGACTGAGGACTCACATTACT 58.577 45.455 0.00 0.00 35.46 2.24
4380 8546 4.517285 TCAGATTCCAAGATACTGGCAAC 58.483 43.478 0.00 0.00 36.32 4.17
4381 8547 4.225942 ACTCAGATTCCAAGATACTGGCAA 59.774 41.667 0.00 0.00 36.32 4.52
4382 8548 3.776969 ACTCAGATTCCAAGATACTGGCA 59.223 43.478 0.00 0.00 36.32 4.92
4383 8549 4.125703 CACTCAGATTCCAAGATACTGGC 58.874 47.826 0.00 0.00 36.32 4.85
4384 8550 4.125703 GCACTCAGATTCCAAGATACTGG 58.874 47.826 0.00 0.00 37.87 4.00
4385 8551 4.569966 GTGCACTCAGATTCCAAGATACTG 59.430 45.833 10.32 0.00 0.00 2.74
4386 8552 4.469227 AGTGCACTCAGATTCCAAGATACT 59.531 41.667 15.25 0.00 0.00 2.12
4387 8553 4.569966 CAGTGCACTCAGATTCCAAGATAC 59.430 45.833 18.64 0.00 0.00 2.24
4388 8554 4.467438 TCAGTGCACTCAGATTCCAAGATA 59.533 41.667 18.64 0.00 0.00 1.98
4389 8555 3.262660 TCAGTGCACTCAGATTCCAAGAT 59.737 43.478 18.64 0.00 0.00 2.40
4390 8556 2.634453 TCAGTGCACTCAGATTCCAAGA 59.366 45.455 18.64 4.08 0.00 3.02
4391 8557 2.740981 GTCAGTGCACTCAGATTCCAAG 59.259 50.000 18.64 1.33 0.00 3.61
4392 8558 2.771089 GTCAGTGCACTCAGATTCCAA 58.229 47.619 18.64 0.00 0.00 3.53
4393 8559 1.337167 CGTCAGTGCACTCAGATTCCA 60.337 52.381 18.64 0.00 0.00 3.53
4394 8560 1.354040 CGTCAGTGCACTCAGATTCC 58.646 55.000 18.64 0.00 0.00 3.01
4395 8561 0.718343 GCGTCAGTGCACTCAGATTC 59.282 55.000 18.64 4.81 34.15 2.52
4396 8562 0.319728 AGCGTCAGTGCACTCAGATT 59.680 50.000 18.64 0.00 37.31 2.40
4397 8563 0.319728 AAGCGTCAGTGCACTCAGAT 59.680 50.000 18.64 7.05 37.31 2.90
4398 8564 0.958822 TAAGCGTCAGTGCACTCAGA 59.041 50.000 18.64 9.86 37.31 3.27
4399 8565 1.657594 CATAAGCGTCAGTGCACTCAG 59.342 52.381 18.64 12.22 37.31 3.35
4400 8566 1.672737 CCATAAGCGTCAGTGCACTCA 60.673 52.381 18.64 0.00 37.31 3.41
4401 8567 1.002366 CCATAAGCGTCAGTGCACTC 58.998 55.000 18.64 5.86 37.31 3.51
4402 8568 0.391661 CCCATAAGCGTCAGTGCACT 60.392 55.000 15.25 15.25 37.31 4.40
4403 8569 1.982073 GCCCATAAGCGTCAGTGCAC 61.982 60.000 9.40 9.40 37.31 4.57
4404 8570 1.745115 GCCCATAAGCGTCAGTGCA 60.745 57.895 0.00 0.00 37.31 4.57
4405 8571 2.472909 GGCCCATAAGCGTCAGTGC 61.473 63.158 0.00 0.00 0.00 4.40
4406 8572 0.392998 AAGGCCCATAAGCGTCAGTG 60.393 55.000 0.00 0.00 0.00 3.66
4407 8573 0.328258 AAAGGCCCATAAGCGTCAGT 59.672 50.000 0.00 0.00 0.00 3.41
4408 8574 0.734889 CAAAGGCCCATAAGCGTCAG 59.265 55.000 0.00 0.00 0.00 3.51
4409 8575 0.679640 CCAAAGGCCCATAAGCGTCA 60.680 55.000 0.00 0.00 0.00 4.35
4410 8576 0.393808 TCCAAAGGCCCATAAGCGTC 60.394 55.000 0.00 0.00 0.00 5.19
4411 8577 0.258774 ATCCAAAGGCCCATAAGCGT 59.741 50.000 0.00 0.00 0.00 5.07
4412 8578 0.670162 CATCCAAAGGCCCATAAGCG 59.330 55.000 0.00 0.00 0.00 4.68
4464 8639 4.881850 AGGTTGTAAATGTTCCATCGGATC 59.118 41.667 0.00 0.00 0.00 3.36
4585 8760 4.028490 CAGCCTGGTAACCCGGCA 62.028 66.667 21.14 0.00 46.45 5.69
4814 8989 0.179094 GCCATCACGTCAATACCGGA 60.179 55.000 9.46 0.00 0.00 5.14
4815 8990 1.487452 CGCCATCACGTCAATACCGG 61.487 60.000 0.00 0.00 0.00 5.28
4816 8991 0.804544 ACGCCATCACGTCAATACCG 60.805 55.000 0.00 0.00 44.43 4.02
4817 8992 3.059603 ACGCCATCACGTCAATACC 57.940 52.632 0.00 0.00 44.43 2.73
4833 9008 2.811431 TGAGTTGCCTGTATTTTGGACG 59.189 45.455 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.