Multiple sequence alignment - TraesCS2B01G498600

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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 TraesCS2B01G498600 chr2B 100.000 4710 0 0 1 4710 695105864 695110573 0.000000e+00 8698.0
1 TraesCS2B01G498600 chr2B 86.905 1512 145 28 988 2482 695379990 695378515 0.000000e+00 1646.0
2 TraesCS2B01G498600 chr2B 84.211 1615 194 34 3086 4665 695170414 695168826 0.000000e+00 1513.0
3 TraesCS2B01G498600 chr2B 84.343 1354 156 24 996 2317 695172117 695170788 0.000000e+00 1275.0
4 TraesCS2B01G498600 chr2B 81.420 1394 199 29 996 2341 695508139 695509520 0.000000e+00 1085.0
5 TraesCS2B01G498600 chr2B 80.000 1440 215 41 988 2378 695439916 695438501 0.000000e+00 996.0
6 TraesCS2B01G498600 chr2B 88.762 614 45 10 2579 3170 695378393 695377782 0.000000e+00 730.0
7 TraesCS2B01G498600 chr2B 81.156 865 139 13 988 1833 695414334 695413475 0.000000e+00 673.0
8 TraesCS2B01G498600 chr2B 80.714 700 77 27 3073 3728 695410486 695409801 4.230000e-135 492.0
9 TraesCS2B01G498600 chr2B 86.375 389 35 4 3174 3550 695377747 695377365 4.390000e-110 409.0
10 TraesCS2B01G498600 chr2B 83.333 150 14 5 2579 2721 695411640 695411495 1.380000e-25 128.0
11 TraesCS2B01G498600 chr2B 91.566 83 5 2 2501 2583 695378524 695378444 3.850000e-21 113.0
12 TraesCS2B01G498600 chr2D 92.854 2421 112 24 12 2414 577582880 577580503 0.000000e+00 3456.0
13 TraesCS2B01G498600 chr2D 89.805 2668 177 53 1150 3785 577440816 577443420 0.000000e+00 3332.0
14 TraesCS2B01G498600 chr2D 91.139 2178 116 30 2526 4664 577580507 577578368 0.000000e+00 2881.0
15 TraesCS2B01G498600 chr2D 84.693 1581 181 31 3118 4665 577537952 577539504 0.000000e+00 1522.0
16 TraesCS2B01G498600 chr2D 86.169 1381 133 31 988 2337 577802853 577801500 0.000000e+00 1439.0
17 TraesCS2B01G498600 chr2D 85.417 1344 148 19 996 2314 577536221 577537541 0.000000e+00 1352.0
18 TraesCS2B01G498600 chr2D 84.846 1267 109 34 2486 3705 577801390 577800160 0.000000e+00 1199.0
19 TraesCS2B01G498600 chr2D 78.014 705 89 31 3118 3791 578325205 578325874 2.660000e-102 383.0
20 TraesCS2B01G498600 chr2D 81.186 489 51 14 3290 3747 577827648 577827170 5.800000e-94 355.0
21 TraesCS2B01G498600 chr2D 81.443 291 36 12 2439 2724 578308833 578309110 6.130000e-54 222.0
22 TraesCS2B01G498600 chr2D 85.922 206 10 10 943 1134 577440655 577440855 7.990000e-48 202.0
23 TraesCS2B01G498600 chr2A 85.154 3085 251 92 781 3785 715951423 715948466 0.000000e+00 2968.0
24 TraesCS2B01G498600 chr2A 92.380 2021 121 10 1 2015 715879657 715881650 0.000000e+00 2848.0
25 TraesCS2B01G498600 chr2A 88.962 1667 123 24 3017 4664 715890391 715892015 0.000000e+00 2002.0
26 TraesCS2B01G498600 chr2A 96.373 965 29 3 2056 3019 715887434 715888393 0.000000e+00 1583.0
27 TraesCS2B01G498600 chr2A 84.383 1620 185 38 3086 4664 715916302 715914710 0.000000e+00 1528.0
28 TraesCS2B01G498600 chr2A 85.210 1359 139 25 996 2317 715917977 715916644 0.000000e+00 1339.0
29 TraesCS2B01G498600 chr2A 96.029 680 19 3 2056 2735 715881656 715882327 0.000000e+00 1099.0
30 TraesCS2B01G498600 chrUn 83.333 150 14 5 2579 2721 476501721 476501866 1.380000e-25 128.0
31 TraesCS2B01G498600 chrUn 94.000 50 2 1 2392 2441 26664185 26664137 1.820000e-09 75.0
32 TraesCS2B01G498600 chr3D 97.727 44 1 0 2397 2440 542823564 542823521 5.050000e-10 76.8
33 TraesCS2B01G498600 chr1D 97.674 43 1 0 2397 2439 435345183 435345141 1.820000e-09 75.0
34 TraesCS2B01G498600 chr6A 90.741 54 4 1 2388 2441 539230010 539229958 2.350000e-08 71.3


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 TraesCS2B01G498600 chr2B 695105864 695110573 4709 False 8698.0 8698 100.000000 1 4710 1 chr2B.!!$F1 4709
1 TraesCS2B01G498600 chr2B 695168826 695172117 3291 True 1394.0 1513 84.277000 996 4665 2 chr2B.!!$R2 3669
2 TraesCS2B01G498600 chr2B 695508139 695509520 1381 False 1085.0 1085 81.420000 996 2341 1 chr2B.!!$F2 1345
3 TraesCS2B01G498600 chr2B 695438501 695439916 1415 True 996.0 996 80.000000 988 2378 1 chr2B.!!$R1 1390
4 TraesCS2B01G498600 chr2B 695377365 695379990 2625 True 724.5 1646 88.402000 988 3550 4 chr2B.!!$R3 2562
5 TraesCS2B01G498600 chr2B 695409801 695414334 4533 True 431.0 673 81.734333 988 3728 3 chr2B.!!$R4 2740
6 TraesCS2B01G498600 chr2D 577578368 577582880 4512 True 3168.5 3456 91.996500 12 4664 2 chr2D.!!$R2 4652
7 TraesCS2B01G498600 chr2D 577440655 577443420 2765 False 1767.0 3332 87.863500 943 3785 2 chr2D.!!$F3 2842
8 TraesCS2B01G498600 chr2D 577536221 577539504 3283 False 1437.0 1522 85.055000 996 4665 2 chr2D.!!$F4 3669
9 TraesCS2B01G498600 chr2D 577800160 577802853 2693 True 1319.0 1439 85.507500 988 3705 2 chr2D.!!$R3 2717
10 TraesCS2B01G498600 chr2D 578325205 578325874 669 False 383.0 383 78.014000 3118 3791 1 chr2D.!!$F2 673
11 TraesCS2B01G498600 chr2A 715948466 715951423 2957 True 2968.0 2968 85.154000 781 3785 1 chr2A.!!$R1 3004
12 TraesCS2B01G498600 chr2A 715879657 715882327 2670 False 1973.5 2848 94.204500 1 2735 2 chr2A.!!$F1 2734
13 TraesCS2B01G498600 chr2A 715887434 715892015 4581 False 1792.5 2002 92.667500 2056 4664 2 chr2A.!!$F2 2608
14 TraesCS2B01G498600 chr2A 715914710 715917977 3267 True 1433.5 1528 84.796500 996 4664 2 chr2A.!!$R2 3668


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
260 261 0.107017 CATCTTGTCGGGCCTCCATT 60.107 55.000 0.84 0.0 0.00 3.16 F
962 1014 0.108424 CCTCACTCCTCTTCCAAGCG 60.108 60.000 0.00 0.0 0.00 4.68 F
964 1016 0.318441 TCACTCCTCTTCCAAGCGTG 59.682 55.000 0.00 0.0 0.00 5.34 F
1408 1535 1.079612 GGAGTTCGGTACAACCCCG 60.080 63.158 0.00 0.0 46.83 5.73 F
1690 1817 1.523154 TTGGCAAACCGAGTCCATGC 61.523 55.000 0.00 0.0 39.70 4.06 F
2445 3774 2.889678 GGGACCGAGGTTGTATAGTAGG 59.110 54.545 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2053 3318 0.328258 CCACTCCGGGGATTTGAAGT 59.672 55.000 9.33 0.0 0.00 3.01 R
2445 3774 2.863401 AAACGGAAAGTTGAGGTTGC 57.137 45.000 0.00 0.0 43.37 4.17 R
2923 4597 3.890756 GTGCCATTGGGATAATCATGTGA 59.109 43.478 4.53 0.0 35.59 3.58 R
3186 7132 2.218603 ACACCACTGCCTTCTAAAACG 58.781 47.619 0.00 0.0 0.00 3.60 R
3361 7314 3.408634 ACCAACATTTCCAGTAACCTCG 58.591 45.455 0.00 0.0 0.00 4.63 R
4099 8135 0.399454 AGATGGCCGAAGCATAGCAT 59.601 50.000 0.00 0.0 42.56 3.79 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
30 31 1.675310 CACCCAGAAGCGGCATTCA 60.675 57.895 1.45 0.00 0.00 2.57
92 93 1.843206 ACAACAAAGGGCCACCAAATT 59.157 42.857 6.18 0.00 40.13 1.82
128 129 1.300620 CGGCGAACACCTCTCACAA 60.301 57.895 0.00 0.00 0.00 3.33
141 142 1.021202 CTCACAACGGAAACCTGCAA 58.979 50.000 0.00 0.00 0.00 4.08
143 144 0.453793 CACAACGGAAACCTGCAACA 59.546 50.000 0.00 0.00 0.00 3.33
214 215 3.593328 TGGATCAAGAAAGGGGAACTCAT 59.407 43.478 0.00 0.00 0.00 2.90
217 218 5.131142 GGATCAAGAAAGGGGAACTCATCTA 59.869 44.000 0.00 0.00 0.00 1.98
228 229 5.010933 GGGAACTCATCTATCGACTGGATA 58.989 45.833 0.00 0.00 36.55 2.59
256 257 1.153349 GTCCATCTTGTCGGGCCTC 60.153 63.158 0.84 0.00 0.00 4.70
260 261 0.107017 CATCTTGTCGGGCCTCCATT 60.107 55.000 0.84 0.00 0.00 3.16
266 267 3.781307 CGGGCCTCCATTCCGTCA 61.781 66.667 0.84 0.00 39.04 4.35
319 320 2.580867 CTTCTTCGCCTCGCCTCG 60.581 66.667 0.00 0.00 0.00 4.63
320 321 3.343788 CTTCTTCGCCTCGCCTCGT 62.344 63.158 0.00 0.00 0.00 4.18
363 364 2.742372 GACGCACGAAGCCCACAT 60.742 61.111 0.00 0.00 41.38 3.21
388 389 1.802337 CGAGACGTCCTGGTCCACAA 61.802 60.000 13.01 0.00 37.66 3.33
401 402 3.006752 TGGTCCACAATTCAGGAAAATGC 59.993 43.478 0.00 0.00 35.29 3.56
406 407 2.264813 CAATTCAGGAAAATGCTGCGG 58.735 47.619 0.00 0.00 35.65 5.69
420 421 1.985447 CTGCGGCGACCTACTAACGA 61.985 60.000 12.98 0.00 0.00 3.85
452 454 1.745087 CGCATATGAATATGGCCCACC 59.255 52.381 6.97 0.00 40.31 4.61
493 497 1.933853 GGTCATGGACGCACTGTATTC 59.066 52.381 0.00 0.00 32.65 1.75
497 501 3.195610 TCATGGACGCACTGTATTCTCTT 59.804 43.478 0.00 0.00 0.00 2.85
537 541 0.529992 TATCGAGCTCTGACGCGAGA 60.530 55.000 15.93 4.96 44.87 4.04
538 542 1.771073 ATCGAGCTCTGACGCGAGAG 61.771 60.000 15.93 17.19 44.87 3.20
539 543 2.745785 CGAGCTCTGACGCGAGAGT 61.746 63.158 21.63 11.45 41.50 3.24
543 547 1.719117 CTCTGACGCGAGAGTCCTC 59.281 63.158 15.93 0.00 40.26 3.71
546 550 0.523966 CTGACGCGAGAGTCCTCTTT 59.476 55.000 15.93 0.00 40.61 2.52
547 551 0.959553 TGACGCGAGAGTCCTCTTTT 59.040 50.000 15.93 0.00 40.61 2.27
548 552 1.068472 TGACGCGAGAGTCCTCTTTTC 60.068 52.381 15.93 0.00 40.61 2.29
549 553 1.200484 GACGCGAGAGTCCTCTTTTCT 59.800 52.381 15.93 0.00 40.61 2.52
577 581 2.070783 CAAAGCAACAATGGATGCACC 58.929 47.619 14.09 0.00 44.50 5.01
596 600 2.455674 CGGATTTCGGGCTCATATCA 57.544 50.000 0.00 0.00 34.75 2.15
732 742 6.985117 AGCAATCAGATTTGAACAAGCTTAA 58.015 32.000 0.00 0.00 36.78 1.85
955 1007 1.713647 TCCTCAGTCCTCACTCCTCTT 59.286 52.381 0.00 0.00 0.00 2.85
956 1008 2.099405 CCTCAGTCCTCACTCCTCTTC 58.901 57.143 0.00 0.00 0.00 2.87
957 1009 2.099405 CTCAGTCCTCACTCCTCTTCC 58.901 57.143 0.00 0.00 0.00 3.46
958 1010 1.429299 TCAGTCCTCACTCCTCTTCCA 59.571 52.381 0.00 0.00 0.00 3.53
959 1011 2.158310 TCAGTCCTCACTCCTCTTCCAA 60.158 50.000 0.00 0.00 0.00 3.53
960 1012 2.233431 CAGTCCTCACTCCTCTTCCAAG 59.767 54.545 0.00 0.00 0.00 3.61
961 1013 1.066502 GTCCTCACTCCTCTTCCAAGC 60.067 57.143 0.00 0.00 0.00 4.01
962 1014 0.108424 CCTCACTCCTCTTCCAAGCG 60.108 60.000 0.00 0.00 0.00 4.68
963 1015 0.605589 CTCACTCCTCTTCCAAGCGT 59.394 55.000 0.00 0.00 0.00 5.07
964 1016 0.318441 TCACTCCTCTTCCAAGCGTG 59.682 55.000 0.00 0.00 0.00 5.34
966 1018 1.743252 CTCCTCTTCCAAGCGTGGC 60.743 63.158 14.54 0.00 45.54 5.01
967 1019 2.747855 CCTCTTCCAAGCGTGGCC 60.748 66.667 14.54 0.00 45.54 5.36
968 1020 2.032528 CTCTTCCAAGCGTGGCCA 59.967 61.111 14.54 0.00 45.54 5.36
969 1021 2.032528 TCTTCCAAGCGTGGCCAG 59.967 61.111 14.54 12.04 45.54 4.85
970 1022 3.058160 CTTCCAAGCGTGGCCAGG 61.058 66.667 21.22 21.22 45.54 4.45
971 1023 3.850098 CTTCCAAGCGTGGCCAGGT 62.850 63.158 25.40 13.46 45.54 4.00
972 1024 3.842925 TTCCAAGCGTGGCCAGGTC 62.843 63.158 25.40 17.47 45.54 3.85
973 1025 4.335647 CCAAGCGTGGCCAGGTCT 62.336 66.667 25.40 19.28 38.35 3.85
974 1026 2.743928 CAAGCGTGGCCAGGTCTC 60.744 66.667 25.40 10.11 0.00 3.36
975 1027 2.925170 AAGCGTGGCCAGGTCTCT 60.925 61.111 25.40 12.24 0.00 3.10
1339 1454 2.425578 GGTCGATTTCTCCGATCCTC 57.574 55.000 0.00 0.00 38.38 3.71
1408 1535 1.079612 GGAGTTCGGTACAACCCCG 60.080 63.158 0.00 0.00 46.83 5.73
1670 1797 3.199071 ACCGTGCTGGATTGGTTTATCTA 59.801 43.478 2.38 0.00 42.00 1.98
1690 1817 1.523154 TTGGCAAACCGAGTCCATGC 61.523 55.000 0.00 0.00 39.70 4.06
1731 1858 4.855531 AGTACATTTTCGTGCTCAAAACC 58.144 39.130 0.00 0.00 0.00 3.27
1735 1862 3.701532 TTTTCGTGCTCAAAACCGATT 57.298 38.095 0.00 0.00 0.00 3.34
2007 3245 5.578005 TGACGGTTTTCAATGGTTTTGTA 57.422 34.783 0.00 0.00 0.00 2.41
2047 3312 5.125417 CCATGGAAAAATTACGTGGATCAGT 59.875 40.000 5.56 0.00 42.54 3.41
2048 3313 6.350110 CCATGGAAAAATTACGTGGATCAGTT 60.350 38.462 5.56 0.00 42.54 3.16
2049 3314 6.249035 TGGAAAAATTACGTGGATCAGTTC 57.751 37.500 0.00 0.00 0.00 3.01
2050 3315 5.765677 TGGAAAAATTACGTGGATCAGTTCA 59.234 36.000 0.00 0.00 0.00 3.18
2051 3316 6.263392 TGGAAAAATTACGTGGATCAGTTCAA 59.737 34.615 0.00 0.00 0.00 2.69
2052 3317 7.142680 GGAAAAATTACGTGGATCAGTTCAAA 58.857 34.615 0.00 0.00 0.00 2.69
2053 3318 7.650104 GGAAAAATTACGTGGATCAGTTCAAAA 59.350 33.333 0.00 0.00 0.00 2.44
2054 3319 7.924103 AAAATTACGTGGATCAGTTCAAAAC 57.076 32.000 0.00 0.00 0.00 2.43
2195 3460 7.176865 CCTTCTATGGAATACATCTCGGTAAGA 59.823 40.741 0.00 0.00 41.03 2.10
2445 3774 2.889678 GGGACCGAGGTTGTATAGTAGG 59.110 54.545 0.00 0.00 0.00 3.18
2570 3905 9.499479 AGATATAAAAGCTCCACATACAGAATG 57.501 33.333 0.00 0.00 46.00 2.67
2811 4478 7.293018 ACGTCGGTTTCAAATTTATGTCTTAC 58.707 34.615 0.00 0.00 0.00 2.34
3258 7204 9.047371 GTCTCCCTAAAAGCTAGATAAAATGAC 57.953 37.037 0.00 0.00 0.00 3.06
3361 7314 4.335416 TGTCACAGGAGGATTCAAAATCC 58.665 43.478 10.16 10.16 38.47 3.01
3386 7351 6.195600 AGGTTACTGGAAATGTTGGTCTTA 57.804 37.500 0.00 0.00 0.00 2.10
3400 7365 9.574516 AATGTTGGTCTTAAGAGTACAGAAAAT 57.425 29.630 5.12 0.00 0.00 1.82
3425 7390 8.213518 TGATTCATCAGTCCTTATAAAAGCAC 57.786 34.615 0.00 0.00 32.11 4.40
3511 7476 6.483307 CCTTCTCACTTTGTATTGACACTGAA 59.517 38.462 0.00 0.00 34.48 3.02
3791 7815 4.950434 TGTGTGATGATGTTATGTGCTG 57.050 40.909 0.00 0.00 0.00 4.41
3962 7995 7.359598 GCGAGCGAGTTTGAAGATCATATTAAT 60.360 37.037 0.00 0.00 0.00 1.40
3975 8008 7.224297 AGATCATATTAATTAAGGCGTGTGGT 58.776 34.615 3.94 0.00 0.00 4.16
3978 8011 6.824196 TCATATTAATTAAGGCGTGTGGTCAA 59.176 34.615 3.94 0.00 0.00 3.18
4046 8079 4.458989 TCCTTTCACCATGATGCTTGTAAC 59.541 41.667 0.00 0.00 0.00 2.50
4051 8084 3.374988 CACCATGATGCTTGTAACGTGAT 59.625 43.478 0.00 0.00 0.00 3.06
4053 8086 5.064579 CACCATGATGCTTGTAACGTGATAA 59.935 40.000 0.00 0.00 0.00 1.75
4055 8088 5.501715 CATGATGCTTGTAACGTGATAACC 58.498 41.667 0.00 0.00 0.00 2.85
4056 8089 3.615056 TGATGCTTGTAACGTGATAACCG 59.385 43.478 0.00 0.00 0.00 4.44
4057 8090 1.727880 TGCTTGTAACGTGATAACCGC 59.272 47.619 0.00 0.00 0.00 5.68
4058 8091 1.997606 GCTTGTAACGTGATAACCGCT 59.002 47.619 0.00 0.00 0.00 5.52
4063 8096 0.246635 AACGTGATAACCGCTCTGCT 59.753 50.000 0.00 0.00 0.00 4.24
4099 8135 3.534357 TGACCAAAAGATTAGGGCCAA 57.466 42.857 6.18 0.00 0.00 4.52
4135 8171 4.095483 GCCATCTGATCGTTGACAAAGATT 59.905 41.667 16.25 0.03 0.00 2.40
4141 8177 0.591170 CGTTGACAAAGATTGGCCGT 59.409 50.000 0.00 0.00 38.13 5.68
4158 8194 1.214062 GTGTCGAGAGCCACTGGAG 59.786 63.158 0.00 0.00 34.23 3.86
4174 8210 1.137614 GAGCAGTGTGATCGAGCGA 59.862 57.895 0.00 0.00 0.00 4.93
4180 8218 2.579787 GTGATCGAGCGACCACCG 60.580 66.667 6.10 0.00 32.63 4.94
4198 8236 1.651240 CGGCTAGCTGCTGCAACATT 61.651 55.000 18.42 0.00 41.61 2.71
4207 8245 0.385029 GCTGCAACATTGGTGACACA 59.615 50.000 5.72 0.00 42.67 3.72
4272 8311 0.037447 TCGGTCATGTTGCAATCCCA 59.963 50.000 0.59 0.00 0.00 4.37
4288 8345 3.121030 CAAGCCGAACGAGCAGGG 61.121 66.667 0.00 0.00 0.00 4.45
4289 8346 3.626924 AAGCCGAACGAGCAGGGT 61.627 61.111 0.00 0.00 37.35 4.34
4290 8347 3.883744 AAGCCGAACGAGCAGGGTG 62.884 63.158 0.00 0.00 35.74 4.61
4291 8348 4.681978 GCCGAACGAGCAGGGTGT 62.682 66.667 0.00 0.00 0.00 4.16
4292 8349 2.030562 CCGAACGAGCAGGGTGTT 59.969 61.111 0.00 0.00 0.00 3.32
4293 8350 1.290955 CCGAACGAGCAGGGTGTTA 59.709 57.895 0.00 0.00 0.00 2.41
4294 8351 0.736325 CCGAACGAGCAGGGTGTTAG 60.736 60.000 0.00 0.00 0.00 2.34
4295 8352 1.352156 CGAACGAGCAGGGTGTTAGC 61.352 60.000 0.00 0.00 0.00 3.09
4296 8353 1.003718 AACGAGCAGGGTGTTAGCC 60.004 57.895 0.00 0.00 35.59 3.93
4297 8354 2.509336 CGAGCAGGGTGTTAGCCG 60.509 66.667 0.00 0.00 41.56 5.52
4298 8355 2.820037 GAGCAGGGTGTTAGCCGC 60.820 66.667 0.00 0.00 41.56 6.53
4299 8356 4.760047 AGCAGGGTGTTAGCCGCG 62.760 66.667 0.00 0.00 41.56 6.46
4300 8357 4.752879 GCAGGGTGTTAGCCGCGA 62.753 66.667 8.23 0.00 41.56 5.87
4301 8358 2.509336 CAGGGTGTTAGCCGCGAG 60.509 66.667 8.23 0.00 41.56 5.03
4302 8359 4.452733 AGGGTGTTAGCCGCGAGC 62.453 66.667 8.23 9.98 41.56 5.03
4514 8580 4.319911 GCAACATTGAGTAGTTTGCGGTAA 60.320 41.667 0.00 0.00 0.00 2.85
4575 8641 1.069227 GCTGGGTGCTTTGTAGAAACG 60.069 52.381 0.00 0.00 38.95 3.60
4576 8642 0.948678 TGGGTGCTTTGTAGAAACGC 59.051 50.000 0.00 1.54 0.00 4.84
4582 8648 4.403453 GTGCTTTGTAGAAACGCAATAGG 58.597 43.478 9.79 0.00 31.42 2.57
4598 8667 3.611766 ATAGGCATACGATGTTAGGGC 57.388 47.619 0.00 0.00 0.00 5.19
4600 8669 1.699634 AGGCATACGATGTTAGGGCAT 59.300 47.619 0.00 0.00 0.00 4.40
4601 8670 2.076863 GGCATACGATGTTAGGGCATC 58.923 52.381 0.00 0.00 41.21 3.91
4605 8674 4.994852 GCATACGATGTTAGGGCATCTTTA 59.005 41.667 0.00 0.00 42.14 1.85
4606 8675 5.120830 GCATACGATGTTAGGGCATCTTTAG 59.879 44.000 0.00 0.00 42.14 1.85
4665 8744 9.468532 TGAGAGATATATTGAATCGAGTTGTTG 57.531 33.333 0.00 0.00 0.00 3.33
4666 8745 9.684448 GAGAGATATATTGAATCGAGTTGTTGA 57.316 33.333 0.00 0.00 0.00 3.18
4672 8751 6.668541 ATTGAATCGAGTTGTTGATAGGTG 57.331 37.500 0.00 0.00 0.00 4.00
4673 8752 4.503910 TGAATCGAGTTGTTGATAGGTGG 58.496 43.478 0.00 0.00 0.00 4.61
4674 8753 4.221924 TGAATCGAGTTGTTGATAGGTGGA 59.778 41.667 0.00 0.00 0.00 4.02
4675 8754 3.868757 TCGAGTTGTTGATAGGTGGAG 57.131 47.619 0.00 0.00 0.00 3.86
4676 8755 3.427573 TCGAGTTGTTGATAGGTGGAGA 58.572 45.455 0.00 0.00 0.00 3.71
4677 8756 3.192844 TCGAGTTGTTGATAGGTGGAGAC 59.807 47.826 0.00 0.00 0.00 3.36
4678 8757 3.676324 CGAGTTGTTGATAGGTGGAGACC 60.676 52.174 0.00 0.00 43.52 3.85
4679 8758 2.572104 AGTTGTTGATAGGTGGAGACCC 59.428 50.000 0.00 0.00 44.40 4.46
4680 8759 2.304761 GTTGTTGATAGGTGGAGACCCA 59.695 50.000 0.00 0.00 44.40 4.51
4681 8760 2.845659 TGTTGATAGGTGGAGACCCAT 58.154 47.619 0.00 0.00 45.68 4.00
4682 8761 4.002256 TGTTGATAGGTGGAGACCCATA 57.998 45.455 0.00 0.00 45.68 2.74
4683 8762 3.967326 TGTTGATAGGTGGAGACCCATAG 59.033 47.826 0.00 0.00 45.68 2.23
4684 8763 4.223953 GTTGATAGGTGGAGACCCATAGA 58.776 47.826 0.00 0.00 45.68 1.98
4685 8764 4.552883 TGATAGGTGGAGACCCATAGAA 57.447 45.455 0.00 0.00 45.68 2.10
4686 8765 4.223953 TGATAGGTGGAGACCCATAGAAC 58.776 47.826 0.00 0.00 45.68 3.01
4687 8766 1.486211 AGGTGGAGACCCATAGAACG 58.514 55.000 0.00 0.00 45.68 3.95
4688 8767 1.006758 AGGTGGAGACCCATAGAACGA 59.993 52.381 0.00 0.00 45.68 3.85
4689 8768 1.409427 GGTGGAGACCCATAGAACGAG 59.591 57.143 0.00 0.00 45.68 4.18
4690 8769 2.100989 GTGGAGACCCATAGAACGAGT 58.899 52.381 0.00 0.00 45.68 4.18
4691 8770 2.496470 GTGGAGACCCATAGAACGAGTT 59.504 50.000 0.00 0.00 45.68 3.01
4692 8771 2.758979 TGGAGACCCATAGAACGAGTTC 59.241 50.000 7.83 7.83 37.58 3.01
4693 8772 2.758979 GGAGACCCATAGAACGAGTTCA 59.241 50.000 17.00 5.00 41.84 3.18
4694 8773 3.429135 GGAGACCCATAGAACGAGTTCAC 60.429 52.174 17.00 0.00 41.84 3.18
4695 8774 2.163815 AGACCCATAGAACGAGTTCACG 59.836 50.000 17.00 5.74 41.84 4.35
4696 8775 1.278238 CCCATAGAACGAGTTCACGC 58.722 55.000 17.00 0.00 41.84 5.34
4697 8776 1.278238 CCATAGAACGAGTTCACGCC 58.722 55.000 17.00 0.00 41.84 5.68
4698 8777 1.135083 CCATAGAACGAGTTCACGCCT 60.135 52.381 17.00 0.16 41.84 5.52
4699 8778 1.920574 CATAGAACGAGTTCACGCCTG 59.079 52.381 17.00 4.46 41.84 4.85
4700 8779 1.241165 TAGAACGAGTTCACGCCTGA 58.759 50.000 17.00 0.00 41.84 3.86
4701 8780 0.039074 AGAACGAGTTCACGCCTGAG 60.039 55.000 17.00 0.00 41.84 3.35
4702 8781 1.006102 AACGAGTTCACGCCTGAGG 60.006 57.895 0.00 0.00 36.70 3.86
4703 8782 2.125912 CGAGTTCACGCCTGAGGG 60.126 66.667 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.866379 AATGCCGCTTCTGGGTGCA 62.866 57.895 0.00 0.00 37.00 4.57
30 31 0.179124 GCAGAAGCGATCGAGGAGTT 60.179 55.000 21.57 2.98 0.00 3.01
74 75 2.507471 TCAAATTTGGTGGCCCTTTGTT 59.493 40.909 17.90 0.00 0.00 2.83
92 93 2.477972 CGACAGCCTCGAGCACTCAA 62.478 60.000 6.99 0.00 46.14 3.02
128 129 2.224426 TGAGTATGTTGCAGGTTTCCGT 60.224 45.455 0.00 0.00 0.00 4.69
217 218 5.184864 GGACATCTTGATCTATCCAGTCGAT 59.815 44.000 0.00 0.00 34.73 3.59
246 247 3.781307 CGGAATGGAGGCCCGACA 61.781 66.667 0.00 0.00 45.58 4.35
248 249 3.467226 GACGGAATGGAGGCCCGA 61.467 66.667 0.00 0.00 45.58 5.14
251 252 2.514824 GCTGACGGAATGGAGGCC 60.515 66.667 0.00 0.00 0.00 5.19
256 257 1.503542 GCAACTGCTGACGGAATGG 59.496 57.895 0.00 0.00 38.21 3.16
277 278 0.099791 CGGCAACAGGTTTGTCGTTT 59.900 50.000 2.92 0.00 41.95 3.60
278 279 1.725066 CGGCAACAGGTTTGTCGTT 59.275 52.632 2.92 0.00 41.95 3.85
319 320 3.279875 GAATGGGGCGGCGATGAC 61.280 66.667 12.98 0.00 0.00 3.06
320 321 3.791586 TGAATGGGGCGGCGATGA 61.792 61.111 12.98 0.00 0.00 2.92
363 364 2.335011 CAGGACGTCTCGTGTGCA 59.665 61.111 16.46 0.00 41.37 4.57
388 389 0.174162 GCCGCAGCATTTTCCTGAAT 59.826 50.000 0.00 0.00 39.53 2.57
401 402 1.585521 CGTTAGTAGGTCGCCGCAG 60.586 63.158 0.00 0.00 0.00 5.18
406 407 0.585029 CGTCGTCGTTAGTAGGTCGC 60.585 60.000 0.00 0.00 0.00 5.19
477 481 3.895232 AAGAGAATACAGTGCGTCCAT 57.105 42.857 0.00 0.00 0.00 3.41
493 497 7.206687 AGCGAGAAGAATAAGGATACAAAGAG 58.793 38.462 0.00 0.00 41.41 2.85
497 501 7.174426 TCGATAGCGAGAAGAATAAGGATACAA 59.826 37.037 0.00 0.00 42.51 2.41
537 541 7.057264 GCTTTGGGATATTAGAAAAGAGGACT 58.943 38.462 0.00 0.00 31.01 3.85
538 542 6.828785 TGCTTTGGGATATTAGAAAAGAGGAC 59.171 38.462 0.00 0.00 31.01 3.85
539 543 6.969043 TGCTTTGGGATATTAGAAAAGAGGA 58.031 36.000 0.00 0.00 31.01 3.71
543 547 9.090692 CATTGTTGCTTTGGGATATTAGAAAAG 57.909 33.333 0.00 0.00 0.00 2.27
546 550 6.894654 TCCATTGTTGCTTTGGGATATTAGAA 59.105 34.615 0.00 0.00 0.00 2.10
547 551 6.430864 TCCATTGTTGCTTTGGGATATTAGA 58.569 36.000 0.00 0.00 0.00 2.10
548 552 6.713762 TCCATTGTTGCTTTGGGATATTAG 57.286 37.500 0.00 0.00 0.00 1.73
549 553 6.462768 GCATCCATTGTTGCTTTGGGATATTA 60.463 38.462 0.00 0.00 34.91 0.98
577 581 2.029020 TCTGATATGAGCCCGAAATCCG 60.029 50.000 0.00 0.00 38.18 4.18
631 635 2.358322 AAGGGCTTGAAGAACCGAAA 57.642 45.000 0.00 0.00 0.00 3.46
764 776 8.983724 GCAGTGCCAATTTTACATTTTTACTAA 58.016 29.630 2.85 0.00 0.00 2.24
827 844 4.141041 TCCTCCTCTTCTCTAGGGATGAAG 60.141 50.000 9.34 4.03 38.69 3.02
957 1009 2.743928 GAGACCTGGCCACGCTTG 60.744 66.667 0.00 0.00 0.00 4.01
958 1010 2.925170 AGAGACCTGGCCACGCTT 60.925 61.111 0.00 0.00 0.00 4.68
959 1011 3.699894 CAGAGACCTGGCCACGCT 61.700 66.667 0.00 0.00 36.77 5.07
960 1012 3.537206 AACAGAGACCTGGCCACGC 62.537 63.158 0.00 0.00 44.60 5.34
961 1013 0.535102 AAAACAGAGACCTGGCCACG 60.535 55.000 0.00 0.00 44.60 4.94
962 1014 1.239347 GAAAACAGAGACCTGGCCAC 58.761 55.000 0.00 0.00 44.60 5.01
963 1015 0.250295 CGAAAACAGAGACCTGGCCA 60.250 55.000 4.71 4.71 44.60 5.36
964 1016 1.578206 GCGAAAACAGAGACCTGGCC 61.578 60.000 0.00 0.00 44.60 5.36
965 1017 0.603975 AGCGAAAACAGAGACCTGGC 60.604 55.000 0.00 0.00 44.60 4.85
966 1018 1.532868 CAAGCGAAAACAGAGACCTGG 59.467 52.381 0.00 0.00 44.60 4.45
967 1019 2.478134 CTCAAGCGAAAACAGAGACCTG 59.522 50.000 0.00 0.00 45.76 4.00
968 1020 2.760374 CTCAAGCGAAAACAGAGACCT 58.240 47.619 0.00 0.00 0.00 3.85
969 1021 1.195674 GCTCAAGCGAAAACAGAGACC 59.804 52.381 0.00 0.00 0.00 3.85
970 1022 2.585888 GCTCAAGCGAAAACAGAGAC 57.414 50.000 0.00 0.00 0.00 3.36
1357 1481 1.218854 GGTGTTTGATGGCCATGGC 59.781 57.895 29.47 29.47 41.06 4.40
1408 1535 1.456165 GAGAAACAGAGCCGTCGTTTC 59.544 52.381 6.20 6.20 41.46 2.78
1670 1797 1.176527 CATGGACTCGGTTTGCCAAT 58.823 50.000 0.00 0.00 33.51 3.16
1690 1817 1.200252 CTCGCTGACATATACCCCGAG 59.800 57.143 0.00 0.00 35.46 4.63
1889 3127 2.786777 TGTGCAGCACAAATCTCTCAT 58.213 42.857 26.34 0.00 41.69 2.90
2047 3312 3.567397 TCCGGGGATTTGAAGTTTTGAA 58.433 40.909 0.00 0.00 0.00 2.69
2048 3313 3.153919 CTCCGGGGATTTGAAGTTTTGA 58.846 45.455 0.00 0.00 0.00 2.69
2049 3314 2.890945 ACTCCGGGGATTTGAAGTTTTG 59.109 45.455 9.33 0.00 0.00 2.44
2050 3315 2.890945 CACTCCGGGGATTTGAAGTTTT 59.109 45.455 9.33 0.00 0.00 2.43
2051 3316 2.514803 CACTCCGGGGATTTGAAGTTT 58.485 47.619 9.33 0.00 0.00 2.66
2052 3317 1.271926 CCACTCCGGGGATTTGAAGTT 60.272 52.381 9.33 0.00 0.00 2.66
2053 3318 0.328258 CCACTCCGGGGATTTGAAGT 59.672 55.000 9.33 0.00 0.00 3.01
2054 3319 0.328258 ACCACTCCGGGGATTTGAAG 59.672 55.000 9.33 0.00 40.22 3.02
2195 3460 3.091545 CCTTAGCACCATGGTCACATTT 58.908 45.455 16.53 0.00 34.35 2.32
2445 3774 2.863401 AAACGGAAAGTTGAGGTTGC 57.137 45.000 0.00 0.00 43.37 4.17
2923 4597 3.890756 GTGCCATTGGGATAATCATGTGA 59.109 43.478 4.53 0.00 35.59 3.58
3013 4693 5.065218 CGGACTTAATGGATGGCTAATATGC 59.935 44.000 0.00 0.00 0.00 3.14
3172 7077 8.381387 GCCTTCTAAAACGTTCTAAATCTACTG 58.619 37.037 0.00 0.00 0.00 2.74
3186 7132 2.218603 ACACCACTGCCTTCTAAAACG 58.781 47.619 0.00 0.00 0.00 3.60
3237 7183 8.964476 TCTGGTCATTTTATCTAGCTTTTAGG 57.036 34.615 0.00 0.00 0.00 2.69
3258 7204 6.234177 AGGGAATAGAATTTAGCGATTCTGG 58.766 40.000 17.65 0.00 44.05 3.86
3361 7314 3.408634 ACCAACATTTCCAGTAACCTCG 58.591 45.455 0.00 0.00 0.00 4.63
3386 7351 9.160496 GACTGATGAATCATTTTCTGTACTCTT 57.840 33.333 0.00 0.00 36.02 2.85
3400 7365 8.213518 GTGCTTTTATAAGGACTGATGAATCA 57.786 34.615 9.73 0.00 45.94 2.57
3791 7815 5.622233 GCCATCAGTGTTTATTCAGAAACCC 60.622 44.000 0.00 0.00 38.33 4.11
3901 7929 8.122330 GCACTTCTAAAACAAAAAGGGAAAATG 58.878 33.333 0.00 0.00 0.00 2.32
3962 7995 2.301870 AGAGATTGACCACACGCCTTAA 59.698 45.455 0.00 0.00 0.00 1.85
3975 8008 9.665719 TTACAGTTATTATGCAACAGAGATTGA 57.334 29.630 0.00 0.00 0.00 2.57
4046 8079 1.359848 AAAGCAGAGCGGTTATCACG 58.640 50.000 0.00 0.00 34.08 4.35
4099 8135 0.399454 AGATGGCCGAAGCATAGCAT 59.601 50.000 0.00 0.00 42.56 3.79
4141 8177 2.640302 GCTCCAGTGGCTCTCGACA 61.640 63.158 3.51 0.00 0.00 4.35
4158 8194 2.161486 GGTCGCTCGATCACACTGC 61.161 63.158 0.00 0.00 0.00 4.40
4198 8236 1.543208 GGTCAGATTGCTGTGTCACCA 60.543 52.381 0.00 0.00 42.84 4.17
4207 8245 1.089920 GATGTTGCGGTCAGATTGCT 58.910 50.000 0.00 0.00 0.00 3.91
4236 8274 1.227999 CGACATTGCGGCCGGATTAT 61.228 55.000 29.38 13.32 0.00 1.28
4272 8311 3.626924 ACCCTGCTCGTTCGGCTT 61.627 61.111 7.06 0.00 0.00 4.35
4288 8345 2.907897 ATCCTGCTCGCGGCTAACAC 62.908 60.000 18.14 0.00 42.39 3.32
4289 8346 2.721167 ATCCTGCTCGCGGCTAACA 61.721 57.895 18.14 4.58 42.39 2.41
4290 8347 2.107141 ATCCTGCTCGCGGCTAAC 59.893 61.111 18.14 0.25 42.39 2.34
4291 8348 2.106938 CATCCTGCTCGCGGCTAA 59.893 61.111 18.14 6.41 42.39 3.09
4292 8349 3.916544 CCATCCTGCTCGCGGCTA 61.917 66.667 18.14 6.69 42.39 3.93
4296 8353 3.869272 GTTGCCATCCTGCTCGCG 61.869 66.667 0.00 0.00 0.00 5.87
4297 8354 3.512516 GGTTGCCATCCTGCTCGC 61.513 66.667 0.00 0.00 0.00 5.03
4298 8355 3.197790 CGGTTGCCATCCTGCTCG 61.198 66.667 0.00 0.00 0.00 5.03
4299 8356 3.512516 GCGGTTGCCATCCTGCTC 61.513 66.667 2.68 0.00 33.98 4.26
4310 8367 2.025441 CAACACGGTTGGCGGTTG 59.975 61.111 8.40 0.00 35.25 3.77
4311 8368 3.894947 GCAACACGGTTGGCGGTT 61.895 61.111 15.52 0.00 0.00 4.44
4346 8403 1.003839 CAGAAGTACCGCCTTGCCA 60.004 57.895 0.00 0.00 0.00 4.92
4358 8415 3.884774 TGGCCCCGTTGCAGAAGT 61.885 61.111 0.00 0.00 0.00 3.01
4392 8449 2.239341 AATGCCATGTTGTCGTCGCG 62.239 55.000 0.00 0.00 0.00 5.87
4467 8532 1.007734 GACGCTCAAGGACGACACA 60.008 57.895 0.00 0.00 0.00 3.72
4494 8560 3.430895 CGTTACCGCAAACTACTCAATGT 59.569 43.478 0.00 0.00 0.00 2.71
4514 8580 4.656117 TGTCCACGATGCACGCGT 62.656 61.111 5.58 5.58 46.94 6.01
4519 8585 2.743538 GCTGCTGTCCACGATGCA 60.744 61.111 0.00 0.00 0.00 3.96
4575 8641 3.684788 CCCTAACATCGTATGCCTATTGC 59.315 47.826 0.00 0.00 41.77 3.56
4576 8642 3.684788 GCCCTAACATCGTATGCCTATTG 59.315 47.826 0.00 0.00 0.00 1.90
4598 8667 3.560636 AATCGTGTCCCCCTAAAGATG 57.439 47.619 0.00 0.00 0.00 2.90
4600 8669 3.307904 GGAAAATCGTGTCCCCCTAAAGA 60.308 47.826 0.00 0.00 0.00 2.52
4601 8670 3.014623 GGAAAATCGTGTCCCCCTAAAG 58.985 50.000 0.00 0.00 0.00 1.85
4605 8674 1.689412 GGGAAAATCGTGTCCCCCT 59.311 57.895 0.00 0.00 46.96 4.79
4606 8675 4.331622 GGGAAAATCGTGTCCCCC 57.668 61.111 0.00 0.00 46.96 5.40
4650 8729 4.935205 CCACCTATCAACAACTCGATTCAA 59.065 41.667 0.00 0.00 0.00 2.69
4656 8735 3.512680 GTCTCCACCTATCAACAACTCG 58.487 50.000 0.00 0.00 0.00 4.18
4669 8748 6.468115 GAACTCGTTCTATGGGTCTCCACC 62.468 54.167 2.66 0.00 40.01 4.61
4670 8749 3.429135 GAACTCGTTCTATGGGTCTCCAC 60.429 52.174 2.66 0.00 40.01 4.02
4671 8750 2.758979 GAACTCGTTCTATGGGTCTCCA 59.241 50.000 2.66 0.00 40.75 3.86
4672 8751 2.758979 TGAACTCGTTCTATGGGTCTCC 59.241 50.000 10.75 0.00 40.14 3.71
4673 8752 3.731264 CGTGAACTCGTTCTATGGGTCTC 60.731 52.174 10.75 0.00 40.14 3.36
4674 8753 2.163815 CGTGAACTCGTTCTATGGGTCT 59.836 50.000 10.75 0.00 40.14 3.85
4675 8754 2.527100 CGTGAACTCGTTCTATGGGTC 58.473 52.381 10.75 0.00 40.14 4.46
4676 8755 1.403780 GCGTGAACTCGTTCTATGGGT 60.404 52.381 10.75 0.00 40.14 4.51
4677 8756 1.278238 GCGTGAACTCGTTCTATGGG 58.722 55.000 10.75 0.00 40.14 4.00
4678 8757 1.135083 AGGCGTGAACTCGTTCTATGG 60.135 52.381 10.75 0.18 40.14 2.74
4679 8758 1.920574 CAGGCGTGAACTCGTTCTATG 59.079 52.381 0.00 4.80 40.14 2.23
4680 8759 1.816835 TCAGGCGTGAACTCGTTCTAT 59.183 47.619 6.64 0.00 40.14 1.98
4681 8760 1.199327 CTCAGGCGTGAACTCGTTCTA 59.801 52.381 10.76 0.00 40.14 2.10
4682 8761 0.039074 CTCAGGCGTGAACTCGTTCT 60.039 55.000 10.76 0.00 40.14 3.01
4683 8762 1.009389 CCTCAGGCGTGAACTCGTTC 61.009 60.000 10.76 2.92 39.91 3.95
4684 8763 1.006102 CCTCAGGCGTGAACTCGTT 60.006 57.895 10.76 0.00 30.14 3.85
4685 8764 2.651361 CCTCAGGCGTGAACTCGT 59.349 61.111 10.76 0.00 30.14 4.18
4686 8765 2.125912 CCCTCAGGCGTGAACTCG 60.126 66.667 10.76 0.00 30.14 4.18



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

AutoCloner maintained by Alex Coulton.