Multiple sequence alignment - TraesCS1B01G104000

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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 TraesCS1B01G104000 chr1B 100.000 3244 0 0 1 3244 113818598 113815355 0.000000e+00 5991.0
1 TraesCS1B01G104000 chr1B 86.383 705 74 11 1878 2572 113566654 113565962 0.000000e+00 750.0
2 TraesCS1B01G104000 chr1B 90.231 389 26 8 368 744 113567994 113567606 6.250000e-137 497.0
3 TraesCS1B01G104000 chr1B 85.897 312 31 7 34 336 113568237 113567930 1.450000e-83 320.0
4 TraesCS1B01G104000 chr1B 79.077 325 34 11 2465 2756 113391154 113390831 3.300000e-45 193.0
5 TraesCS1B01G104000 chr1B 89.333 150 15 1 586 734 50992402 50992551 1.540000e-43 187.0
6 TraesCS1B01G104000 chr1B 78.769 325 35 11 2465 2756 113485297 113484974 1.540000e-43 187.0
7 TraesCS1B01G104000 chr1B 84.000 200 22 3 2566 2756 113196573 113196375 1.990000e-42 183.0
8 TraesCS1B01G104000 chr1B 78.154 325 37 11 2465 2756 113298113 113297790 3.330000e-40 176.0
9 TraesCS1B01G104000 chr1A 92.067 1248 85 3 480 1722 71790134 71788896 0.000000e+00 1744.0
10 TraesCS1B01G104000 chr1A 86.161 1568 127 39 1732 3244 71787301 71785769 0.000000e+00 1611.0
11 TraesCS1B01G104000 chr1A 85.000 420 31 13 32 423 71790516 71790101 6.520000e-107 398.0
12 TraesCS1B01G104000 chr1A 84.979 233 32 1 502 734 32190979 32191208 1.950000e-57 233.0
13 TraesCS1B01G104000 chr1A 82.128 235 36 4 506 734 71725065 71724831 2.550000e-46 196.0
14 TraesCS1B01G104000 chr1D 87.619 525 51 6 1911 2429 72500726 72500210 5.990000e-167 597.0
15 TraesCS1B01G104000 chr1D 93.208 265 9 1 480 744 72501964 72501709 6.570000e-102 381.0
16 TraesCS1B01G104000 chr1D 83.575 414 39 13 32 423 72502337 72501931 8.560000e-96 361.0
17 TraesCS1B01G104000 chr1D 83.690 374 42 5 2569 2925 72499621 72499250 5.190000e-88 335.0
18 TraesCS1B01G104000 chr1D 82.203 236 34 6 506 734 71639827 71639593 2.550000e-46 196.0
19 TraesCS1B01G104000 chr6D 81.905 210 34 3 523 730 71053272 71053065 1.200000e-39 174.0
20 TraesCS1B01G104000 chr6B 81.429 210 35 4 523 730 145576198 145575991 5.570000e-38 169.0
21 TraesCS1B01G104000 chr6B 90.566 53 5 0 1346 1398 63767986 63767934 1.610000e-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 TraesCS1B01G104000 chr1B 113815355 113818598 3243 True 5991.000000 5991 100.000000 1 3244 1 chr1B.!!$R5 3243
1 TraesCS1B01G104000 chr1B 113565962 113568237 2275 True 522.333333 750 87.503667 34 2572 3 chr1B.!!$R6 2538
2 TraesCS1B01G104000 chr1A 71785769 71790516 4747 True 1251.000000 1744 87.742667 32 3244 3 chr1A.!!$R2 3212
3 TraesCS1B01G104000 chr1D 72499250 72502337 3087 True 418.500000 597 87.023000 32 2925 4 chr1D.!!$R2 2893

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
416 455 0.243095 GGCCAAGAAGAAAGCAGCAG 59.757 55.0 0.0 0.0 0.00 4.24 F
417 456 0.388263 GCCAAGAAGAAAGCAGCAGC 60.388 55.0 0.0 0.0 42.56 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1849 3526 0.850391 CGTCGCCGATGTTAAAACGC 60.850 55.000 0.00 0.00 35.63 4.84 R
2270 3950 1.065854 CAAGGTCCGGAGAAGCTTCAT 60.066 52.381 27.57 13.09 0.00 2.57 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
25 26 6.913170 TGAATTCAAGACTAATTTGAGCACC 58.087 36.000 5.45 0.00 36.07 5.01
26 27 6.489700 TGAATTCAAGACTAATTTGAGCACCA 59.510 34.615 5.45 0.00 36.07 4.17
27 28 5.689383 TTCAAGACTAATTTGAGCACCAC 57.311 39.130 0.00 0.00 36.07 4.16
28 29 4.973168 TCAAGACTAATTTGAGCACCACT 58.027 39.130 0.00 0.00 31.35 4.00
29 30 4.997395 TCAAGACTAATTTGAGCACCACTC 59.003 41.667 0.00 0.00 46.45 3.51
44 45 4.324402 GCACCACTCGCATTTTATTCAAAG 59.676 41.667 0.00 0.00 0.00 2.77
53 54 4.423732 CATTTTATTCAAAGCTGGTCGGG 58.576 43.478 0.00 0.00 0.00 5.14
65 66 0.534203 TGGTCGGGCTTGAGTGAAAC 60.534 55.000 0.00 0.00 0.00 2.78
98 104 1.346479 TTGGAGAAACACCCGGGACA 61.346 55.000 32.02 9.51 0.00 4.02
119 125 2.072487 GCCTCTACATCCCAGCCCA 61.072 63.158 0.00 0.00 0.00 5.36
161 183 3.239627 TTCCGGCTCCCCACTCTCT 62.240 63.158 0.00 0.00 0.00 3.10
162 184 3.151022 CCGGCTCCCCACTCTCTC 61.151 72.222 0.00 0.00 0.00 3.20
175 205 0.612174 CTCTCTCCGGTCCCAGTTCA 60.612 60.000 0.00 0.00 0.00 3.18
204 234 4.430423 CTGCACTCGAAACGGCGC 62.430 66.667 6.90 0.00 0.00 6.53
275 305 3.276857 CAATCTCCACACATGAGGAAGG 58.723 50.000 0.00 0.00 34.44 3.46
276 306 0.615331 TCTCCACACATGAGGAAGGC 59.385 55.000 0.00 0.00 34.44 4.35
278 308 1.746615 CCACACATGAGGAAGGCGG 60.747 63.158 0.00 0.00 0.00 6.13
279 309 2.045926 ACACATGAGGAAGGCGGC 60.046 61.111 0.00 0.00 0.00 6.53
408 447 2.585341 TACCCGCGGCCAAGAAGAA 61.585 57.895 22.85 0.00 0.00 2.52
409 448 2.114488 TACCCGCGGCCAAGAAGAAA 62.114 55.000 22.85 0.00 0.00 2.52
410 449 2.690778 CCCGCGGCCAAGAAGAAAG 61.691 63.158 22.85 0.00 0.00 2.62
411 450 2.176792 CGCGGCCAAGAAGAAAGC 59.823 61.111 2.24 0.00 0.00 3.51
412 451 2.616330 CGCGGCCAAGAAGAAAGCA 61.616 57.895 2.24 0.00 0.00 3.91
413 452 1.211190 GCGGCCAAGAAGAAAGCAG 59.789 57.895 2.24 0.00 0.00 4.24
414 453 1.211190 CGGCCAAGAAGAAAGCAGC 59.789 57.895 2.24 0.00 0.00 5.25
415 454 1.518056 CGGCCAAGAAGAAAGCAGCA 61.518 55.000 2.24 0.00 0.00 4.41
416 455 0.243095 GGCCAAGAAGAAAGCAGCAG 59.757 55.000 0.00 0.00 0.00 4.24
417 456 0.388263 GCCAAGAAGAAAGCAGCAGC 60.388 55.000 0.00 0.00 42.56 5.25
437 476 4.124351 CGGTACCTGCGGCGAAGA 62.124 66.667 18.55 0.00 0.00 2.87
438 477 2.263540 GGTACCTGCGGCGAAGAA 59.736 61.111 18.55 0.25 0.00 2.52
439 478 1.810030 GGTACCTGCGGCGAAGAAG 60.810 63.158 18.55 2.49 0.00 2.85
440 479 1.214589 GTACCTGCGGCGAAGAAGA 59.785 57.895 18.55 0.00 0.00 2.87
451 490 4.329545 AAGAAGAAGGCGGCGGCA 62.330 61.111 34.87 0.00 42.47 5.69
481 520 2.631062 TGCCAAGAAGAAGAAGACGGTA 59.369 45.455 0.00 0.00 0.00 4.02
500 539 2.042831 CCCGCAGCCAAGAAGAAGG 61.043 63.158 0.00 0.00 0.00 3.46
506 545 3.127533 CCAAGAAGAAGGCGGCGG 61.128 66.667 9.78 0.00 0.00 6.13
734 818 2.202492 CTCTCAACCTCGACGCCG 60.202 66.667 0.00 0.00 37.07 6.46
744 828 2.257371 CGACGCCGAGAACCTCAA 59.743 61.111 0.00 0.00 38.22 3.02
823 907 2.284754 TCATCTCCAGGATCCTCTCG 57.715 55.000 12.69 0.05 31.27 4.04
873 957 4.192317 GACTTCCGATTAACCTGCATCTT 58.808 43.478 0.00 0.00 0.00 2.40
914 999 2.611473 CCAAGAGTGTTGCTCAGATCGT 60.611 50.000 0.00 0.00 46.47 3.73
925 1010 3.510388 CTCAGATCGTGAGCTGGTTAA 57.490 47.619 14.48 0.00 46.41 2.01
966 1051 4.820775 ACCTTGAGGAGCTCCATATCTTA 58.179 43.478 33.90 13.84 38.89 2.10
1006 1091 3.083349 CTCCGACCCCCATGCTCA 61.083 66.667 0.00 0.00 0.00 4.26
1007 1092 3.083349 TCCGACCCCCATGCTCAG 61.083 66.667 0.00 0.00 0.00 3.35
1060 1145 2.519063 CCACTGTTGGCCACTGCA 60.519 61.111 3.88 4.03 40.13 4.41
1063 1148 0.390124 CACTGTTGGCCACTGCAATT 59.610 50.000 3.88 0.00 40.13 2.32
1065 1150 1.485895 ACTGTTGGCCACTGCAATTTT 59.514 42.857 3.88 0.00 40.13 1.82
1123 1208 1.078848 AAGCATCTCACCCTGCGTC 60.079 57.895 0.00 0.00 43.17 5.19
1196 1281 2.026262 TGTTGGAGACCCTATTTCTGCC 60.026 50.000 0.00 0.00 30.68 4.85
1199 1284 2.119495 GGAGACCCTATTTCTGCCTGA 58.881 52.381 0.00 0.00 0.00 3.86
1209 1294 7.035612 CCCTATTTCTGCCTGAAAATGTTTAC 58.964 38.462 0.70 0.00 46.32 2.01
1227 1312 1.595311 ACAATGGCTCCCTCCACATA 58.405 50.000 0.00 0.00 39.25 2.29
1233 1318 0.833287 GCTCCCTCCACATAAGCTCA 59.167 55.000 0.00 0.00 0.00 4.26
1238 1323 2.354704 CCCTCCACATAAGCTCACGAAA 60.355 50.000 0.00 0.00 0.00 3.46
1268 1353 4.170292 GCATCTGCTTCAGTGATTGTTT 57.830 40.909 0.00 0.00 38.21 2.83
1277 1362 4.782019 TCAGTGATTGTTTTATGGGCAC 57.218 40.909 0.00 0.00 0.00 5.01
1389 1477 1.607225 AACTGGAGATATTGGGCCCA 58.393 50.000 24.45 24.45 0.00 5.36
1398 1486 0.395036 TATTGGGCCCATTGTCACCG 60.395 55.000 29.23 0.00 0.00 4.94
1411 1499 1.815003 TCACCGCGCATCTCCAATG 60.815 57.895 8.75 0.00 0.00 2.82
1453 1541 3.914426 TTCAGGTAGAAGCATCCTTCC 57.086 47.619 0.00 0.00 46.97 3.46
1687 1779 7.410800 TGCTTGCTTTAAATGTCAAAATGAG 57.589 32.000 0.00 0.00 0.00 2.90
1722 1814 6.943981 TGAAAAAGAACTGATTGACACGTAG 58.056 36.000 0.00 0.00 0.00 3.51
1724 1816 6.526566 AAAAGAACTGATTGACACGTAGTC 57.473 37.500 10.12 10.12 41.61 2.59
1742 3419 8.584600 CACGTAGTCTAGTTAGCAATTACTTTG 58.415 37.037 0.00 0.00 41.61 2.77
1781 3458 6.542735 AGTCTTCTTTCCTTTTACAGTGGAAC 59.457 38.462 0.00 0.00 39.29 3.62
1797 3474 6.015688 ACAGTGGAACGAATACTTAGAGACAA 60.016 38.462 0.00 0.00 45.86 3.18
1849 3526 2.333926 TGAAACATACTCGGCGAACAG 58.666 47.619 12.13 1.35 0.00 3.16
1896 3573 2.914379 AGTGTTACACTCGGCTTGC 58.086 52.632 12.76 0.00 41.21 4.01
2056 3736 7.206981 ACTTAAACACAGAGATGAACAATGG 57.793 36.000 0.00 0.00 0.00 3.16
2195 3875 4.158394 TCTGAATGGGAAAGTGCTAAATGC 59.842 41.667 0.00 0.00 43.25 3.56
2213 3893 1.259316 GCGATCAAATTTGGCGTGAC 58.741 50.000 24.58 12.22 0.00 3.67
2216 3896 2.095768 CGATCAAATTTGGCGTGACTGT 60.096 45.455 17.90 0.00 0.00 3.55
2270 3950 1.003580 CAGGCTGCTAGGAGTGGAAAA 59.996 52.381 13.28 0.00 0.00 2.29
2283 3963 3.077359 AGTGGAAAATGAAGCTTCTCCG 58.923 45.455 26.09 0.00 0.00 4.63
2352 4032 6.262496 CAGATATCCATGACTTGTCAATTGCT 59.738 38.462 7.57 0.00 0.00 3.91
2409 4095 2.157738 GCCCTTCCAGTGATATCATGC 58.842 52.381 9.02 0.00 0.00 4.06
2450 4492 4.641989 GGATAGTACCTGAAGACCGTGTTA 59.358 45.833 0.00 0.00 0.00 2.41
2455 4497 3.926616 ACCTGAAGACCGTGTTATCTTG 58.073 45.455 0.00 0.00 35.29 3.02
2456 4498 2.673368 CCTGAAGACCGTGTTATCTTGC 59.327 50.000 0.00 0.00 35.29 4.01
2463 4505 1.464023 CCGTGTTATCTTGCGCTTGTG 60.464 52.381 9.73 0.00 0.00 3.33
2482 4524 0.663153 GTTTATGGTGCCGATGCCTC 59.337 55.000 0.00 0.00 36.33 4.70
2483 4525 0.813610 TTTATGGTGCCGATGCCTCG 60.814 55.000 4.21 4.21 44.62 4.63
2497 4539 0.815213 GCCTCGATATTGTGCTGCCA 60.815 55.000 0.00 0.00 0.00 4.92
2524 4566 6.197842 CAGTTCAATGCTTGTTTCTCTGTTTC 59.802 38.462 0.00 0.00 0.00 2.78
2633 4768 4.708177 TGTCTTTTGTCTGAGAAAGGAGG 58.292 43.478 11.51 0.58 34.45 4.30
2673 4816 4.669318 CAATGCATTCTTGGTGATCAGAC 58.331 43.478 9.53 0.00 0.00 3.51
2697 4840 3.411446 TGCACCAGTCGAAATCAGAAAT 58.589 40.909 0.00 0.00 0.00 2.17
2701 4844 5.385617 CACCAGTCGAAATCAGAAATTCAC 58.614 41.667 0.00 0.00 0.00 3.18
2741 4884 5.181056 CCCTTTTTCACACAAGCAAAAGTTT 59.819 36.000 0.00 0.00 35.37 2.66
2749 4892 4.629634 ACACAAGCAAAAGTTTAACTTGCC 59.370 37.500 21.63 6.41 45.23 4.52
2756 4899 5.121611 GCAAAAGTTTAACTTGCCACTGTTT 59.878 36.000 11.35 0.00 38.66 2.83
2759 4902 8.878769 CAAAAGTTTAACTTGCCACTGTTTATT 58.121 29.630 11.35 0.00 38.66 1.40
2779 4922 9.772973 GTTTATTACTTTTTGGTTCCCTTTGAT 57.227 29.630 0.00 0.00 0.00 2.57
2790 4950 5.418840 TGGTTCCCTTTGATGAGAATAAAGC 59.581 40.000 0.00 0.00 0.00 3.51
2795 4955 5.105756 CCCTTTGATGAGAATAAAGCCGTTT 60.106 40.000 0.00 0.00 0.00 3.60
2799 4959 4.635765 TGATGAGAATAAAGCCGTTTCAGG 59.364 41.667 0.00 0.00 0.00 3.86
2818 4978 6.012337 TCAGGGATGCATATTTAGTTCCAA 57.988 37.500 0.00 0.00 0.00 3.53
2821 4981 6.322201 CAGGGATGCATATTTAGTTCCAAACT 59.678 38.462 0.00 0.00 45.40 2.66
2822 4982 7.502226 CAGGGATGCATATTTAGTTCCAAACTA 59.498 37.037 0.00 0.00 42.81 2.24
2824 4984 9.515226 GGGATGCATATTTAGTTCCAAACTATA 57.485 33.333 0.00 0.00 43.09 1.31
2858 5022 4.095483 GTGTCAAGATTCATGGTCCATGTC 59.905 45.833 27.50 19.72 41.98 3.06
2890 5055 9.635404 TTTTCCTCTTCATTCACTAAGGTTTAA 57.365 29.630 0.00 0.00 0.00 1.52
2913 5078 5.862845 AGGTGAATAATATGCAGAGTCCTG 58.137 41.667 0.00 0.00 43.22 3.86
2916 5081 6.370994 GGTGAATAATATGCAGAGTCCTGATG 59.629 42.308 0.00 0.00 43.02 3.07
2921 5086 1.351076 TGCAGAGTCCTGATGTCCAA 58.649 50.000 0.00 0.00 43.02 3.53
2948 5113 5.690409 ACTGGAATTATTCGTACACATAGCG 59.310 40.000 0.00 0.00 0.00 4.26
2949 5114 4.986034 TGGAATTATTCGTACACATAGCGG 59.014 41.667 0.00 0.00 0.00 5.52
2953 5118 5.705813 TTATTCGTACACATAGCGGTTTG 57.294 39.130 3.41 3.41 0.00 2.93
2982 5147 0.826062 GGCTGCATATTTGGTTGCCT 59.174 50.000 0.50 0.00 38.08 4.75
2989 5154 4.769488 TGCATATTTGGTTGCCTAACTTCA 59.231 37.500 0.00 0.00 38.08 3.02
3003 5168 5.589050 GCCTAACTTCAACAGGTAATAAGGG 59.411 44.000 0.00 0.00 0.00 3.95
3011 5183 6.252995 TCAACAGGTAATAAGGGCAAGATTT 58.747 36.000 0.00 0.00 0.00 2.17
3024 5196 3.701040 GGCAAGATTTATGGTCCATGTGT 59.299 43.478 15.10 0.00 0.00 3.72
3027 5199 6.127479 GGCAAGATTTATGGTCCATGTGTAAA 60.127 38.462 15.10 7.27 0.00 2.01
3029 5201 7.816995 GCAAGATTTATGGTCCATGTGTAAAAA 59.183 33.333 15.10 6.18 0.00 1.94
3036 5208 6.739331 TGGTCCATGTGTAAAAATTTCCTT 57.261 33.333 0.00 0.00 0.00 3.36
3076 5248 8.682936 AAGTTTAGGGTGAATAATATGCAGAG 57.317 34.615 0.00 0.00 0.00 3.35
3077 5249 7.806180 AGTTTAGGGTGAATAATATGCAGAGT 58.194 34.615 0.00 0.00 0.00 3.24
3078 5250 7.934120 AGTTTAGGGTGAATAATATGCAGAGTC 59.066 37.037 0.00 0.00 0.00 3.36
3079 5251 5.234466 AGGGTGAATAATATGCAGAGTCC 57.766 43.478 0.00 0.00 0.00 3.85
3080 5252 4.910304 AGGGTGAATAATATGCAGAGTCCT 59.090 41.667 0.00 0.00 0.00 3.85
3081 5253 5.012561 AGGGTGAATAATATGCAGAGTCCTC 59.987 44.000 0.00 0.00 0.00 3.71
3082 5254 4.926238 GGTGAATAATATGCAGAGTCCTCG 59.074 45.833 0.00 0.00 34.09 4.63
3103 5275 5.836347 TCGTCTCCAGATACTGAAATCATG 58.164 41.667 0.00 0.00 32.44 3.07
3105 5277 5.221322 CGTCTCCAGATACTGAAATCATGGA 60.221 44.000 0.00 3.42 34.66 3.41
3107 5279 7.309438 CGTCTCCAGATACTGAAATCATGGATA 60.309 40.741 3.79 0.00 35.01 2.59
3109 5281 9.774071 TCTCCAGATACTGAAATCATGGATATA 57.226 33.333 3.79 0.00 35.01 0.86
3110 5282 9.814899 CTCCAGATACTGAAATCATGGATATAC 57.185 37.037 3.79 0.00 35.01 1.47
3118 5290 8.819845 ACTGAAATCATGGATATACATAGCTCA 58.180 33.333 0.00 1.24 0.00 4.26
3119 5291 9.096160 CTGAAATCATGGATATACATAGCTCAC 57.904 37.037 0.00 0.00 0.00 3.51
3120 5292 8.819845 TGAAATCATGGATATACATAGCTCACT 58.180 33.333 0.00 0.00 0.00 3.41
3124 5296 9.652114 ATCATGGATATACATAGCTCACTATCA 57.348 33.333 0.00 0.00 36.96 2.15
3125 5297 9.652114 TCATGGATATACATAGCTCACTATCAT 57.348 33.333 0.00 0.00 36.96 2.45
3126 5298 9.911138 CATGGATATACATAGCTCACTATCATC 57.089 37.037 0.00 0.00 36.96 2.92
3127 5299 9.880254 ATGGATATACATAGCTCACTATCATCT 57.120 33.333 0.00 0.00 36.96 2.90
3128 5300 9.706529 TGGATATACATAGCTCACTATCATCTT 57.293 33.333 0.00 0.00 36.96 2.40
3166 5338 6.203723 CCTAGTGATGCTAGTAAGATTTTGCC 59.796 42.308 0.00 0.00 44.37 4.52
3169 5341 6.030228 GTGATGCTAGTAAGATTTTGCCAAC 58.970 40.000 0.00 0.00 0.00 3.77
3171 5343 3.119990 TGCTAGTAAGATTTTGCCAACGC 60.120 43.478 0.00 0.00 0.00 4.84
3186 5358 4.202000 TGCCAACGCAGATTATATTTGTGG 60.202 41.667 0.00 0.00 41.12 4.17
3208 5381 5.221823 TGGAATCTGGTGTTGTATGAGTTGA 60.222 40.000 0.00 0.00 0.00 3.18
3209 5382 5.882557 GGAATCTGGTGTTGTATGAGTTGAT 59.117 40.000 0.00 0.00 0.00 2.57
3211 5384 7.552687 GGAATCTGGTGTTGTATGAGTTGATAA 59.447 37.037 0.00 0.00 0.00 1.75
3213 5386 8.862325 ATCTGGTGTTGTATGAGTTGATAAAA 57.138 30.769 0.00 0.00 0.00 1.52
3214 5387 8.094798 TCTGGTGTTGTATGAGTTGATAAAAC 57.905 34.615 0.00 0.00 29.71 2.43
3240 5413 4.193826 TCTAGCAAACACATCCTCTGTC 57.806 45.455 0.00 0.00 35.29 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.025963 GGTGCTCAAATTAGTCTTGAATTCAG 58.974 38.462 8.41 3.62 32.57 3.02
1 2 6.489700 TGGTGCTCAAATTAGTCTTGAATTCA 59.510 34.615 3.38 3.38 32.57 2.57
2 3 6.803807 GTGGTGCTCAAATTAGTCTTGAATTC 59.196 38.462 0.00 0.00 32.57 2.17
3 4 6.491403 AGTGGTGCTCAAATTAGTCTTGAATT 59.509 34.615 0.00 0.00 32.57 2.17
4 5 6.006449 AGTGGTGCTCAAATTAGTCTTGAAT 58.994 36.000 0.00 0.00 32.57 2.57
5 6 5.376625 AGTGGTGCTCAAATTAGTCTTGAA 58.623 37.500 0.00 0.00 32.57 2.69
6 7 4.973168 AGTGGTGCTCAAATTAGTCTTGA 58.027 39.130 0.00 0.00 0.00 3.02
7 8 4.143030 CGAGTGGTGCTCAAATTAGTCTTG 60.143 45.833 0.00 0.00 44.33 3.02
8 9 3.997021 CGAGTGGTGCTCAAATTAGTCTT 59.003 43.478 0.00 0.00 44.33 3.01
9 10 3.589988 CGAGTGGTGCTCAAATTAGTCT 58.410 45.455 0.00 0.00 44.33 3.24
10 11 2.094417 GCGAGTGGTGCTCAAATTAGTC 59.906 50.000 0.00 0.00 44.33 2.59
11 12 2.076863 GCGAGTGGTGCTCAAATTAGT 58.923 47.619 0.00 0.00 44.33 2.24
12 13 2.076100 TGCGAGTGGTGCTCAAATTAG 58.924 47.619 0.00 0.00 44.33 1.73
13 14 2.177394 TGCGAGTGGTGCTCAAATTA 57.823 45.000 0.00 0.00 44.33 1.40
14 15 1.538047 ATGCGAGTGGTGCTCAAATT 58.462 45.000 0.00 0.00 44.33 1.82
15 16 1.538047 AATGCGAGTGGTGCTCAAAT 58.462 45.000 0.00 0.00 44.33 2.32
16 17 1.317613 AAATGCGAGTGGTGCTCAAA 58.682 45.000 0.00 0.00 44.33 2.69
17 18 1.317613 AAAATGCGAGTGGTGCTCAA 58.682 45.000 0.00 0.00 44.33 3.02
18 19 2.177394 TAAAATGCGAGTGGTGCTCA 57.823 45.000 0.00 0.00 44.33 4.26
19 20 3.126858 TGAATAAAATGCGAGTGGTGCTC 59.873 43.478 0.00 0.00 40.77 4.26
20 21 3.081061 TGAATAAAATGCGAGTGGTGCT 58.919 40.909 0.00 0.00 0.00 4.40
21 22 3.485947 TGAATAAAATGCGAGTGGTGC 57.514 42.857 0.00 0.00 0.00 5.01
22 23 4.324402 GCTTTGAATAAAATGCGAGTGGTG 59.676 41.667 0.00 0.00 0.00 4.17
23 24 4.218417 AGCTTTGAATAAAATGCGAGTGGT 59.782 37.500 0.00 0.00 31.31 4.16
24 25 4.560035 CAGCTTTGAATAAAATGCGAGTGG 59.440 41.667 0.00 0.00 31.31 4.00
25 26 4.560035 CCAGCTTTGAATAAAATGCGAGTG 59.440 41.667 0.00 0.00 31.31 3.51
26 27 4.218417 ACCAGCTTTGAATAAAATGCGAGT 59.782 37.500 0.00 0.00 31.31 4.18
27 28 4.737054 ACCAGCTTTGAATAAAATGCGAG 58.263 39.130 0.00 0.00 31.31 5.03
28 29 4.671508 CGACCAGCTTTGAATAAAATGCGA 60.672 41.667 0.00 0.00 31.31 5.10
29 30 3.543494 CGACCAGCTTTGAATAAAATGCG 59.457 43.478 0.00 0.00 31.31 4.73
30 31 3.859386 CCGACCAGCTTTGAATAAAATGC 59.141 43.478 0.00 0.00 0.00 3.56
44 45 2.731691 TTCACTCAAGCCCGACCAGC 62.732 60.000 0.00 0.00 0.00 4.85
53 54 3.068024 TGACATTTGGGTTTCACTCAAGC 59.932 43.478 0.00 0.00 40.10 4.01
98 104 1.341156 GGCTGGGATGTAGAGGCTGT 61.341 60.000 0.00 0.00 0.00 4.40
161 183 1.559065 GGGATTGAACTGGGACCGGA 61.559 60.000 9.46 0.00 0.00 5.14
162 184 1.077716 GGGATTGAACTGGGACCGG 60.078 63.158 0.00 0.00 0.00 5.28
175 205 0.106819 GAGTGCAGCTGATGGGGATT 60.107 55.000 20.43 0.00 0.00 3.01
204 234 0.617535 GGGGAATTTGGGGGTTCTGG 60.618 60.000 0.00 0.00 0.00 3.86
214 244 1.690352 GCATCTGGGATGGGGAATTTG 59.310 52.381 9.18 0.00 0.00 2.32
426 465 2.744768 GCCTTCTTCTTCGCCGCAG 61.745 63.158 0.00 0.00 0.00 5.18
427 466 2.742372 GCCTTCTTCTTCGCCGCA 60.742 61.111 0.00 0.00 0.00 5.69
428 467 3.854459 CGCCTTCTTCTTCGCCGC 61.854 66.667 0.00 0.00 0.00 6.53
429 468 3.188786 CCGCCTTCTTCTTCGCCG 61.189 66.667 0.00 0.00 0.00 6.46
430 469 3.500642 GCCGCCTTCTTCTTCGCC 61.501 66.667 0.00 0.00 0.00 5.54
431 470 3.854459 CGCCGCCTTCTTCTTCGC 61.854 66.667 0.00 0.00 0.00 4.70
432 471 3.188786 CCGCCGCCTTCTTCTTCG 61.189 66.667 0.00 0.00 0.00 3.79
433 472 3.500642 GCCGCCGCCTTCTTCTTC 61.501 66.667 0.00 0.00 0.00 2.87
434 473 4.329545 TGCCGCCGCCTTCTTCTT 62.330 61.111 0.00 0.00 0.00 2.52
435 474 4.767255 CTGCCGCCGCCTTCTTCT 62.767 66.667 0.00 0.00 0.00 2.85
481 520 1.302832 CTTCTTCTTGGCTGCGGGT 60.303 57.895 0.00 0.00 0.00 5.28
521 560 3.127533 GGATGCGCGCTTCTTGGT 61.128 61.111 35.91 14.41 0.00 3.67
628 667 0.769873 GGAGGGAGATGATGGTGCAT 59.230 55.000 0.00 0.00 0.00 3.96
734 818 5.241506 TGAAATCATTGGTGTTGAGGTTCTC 59.758 40.000 0.00 0.00 0.00 2.87
744 828 2.028748 GGCTGCTTGAAATCATTGGTGT 60.029 45.455 0.00 0.00 0.00 4.16
873 957 1.956477 GCTGCTCTCTTTTTGTTGGGA 59.044 47.619 0.00 0.00 0.00 4.37
914 999 2.231478 CTCCGAGAGTTTAACCAGCTCA 59.769 50.000 9.63 0.00 0.00 4.26
924 1009 0.894184 TGTCGAGGCTCCGAGAGTTT 60.894 55.000 9.32 0.00 39.43 2.66
925 1010 0.894184 TTGTCGAGGCTCCGAGAGTT 60.894 55.000 9.32 0.00 39.43 3.01
966 1051 1.471676 GCTCGACACAAGATCGGGAAT 60.472 52.381 0.00 0.00 42.92 3.01
995 1080 2.429058 CGGATCTGAGCATGGGGG 59.571 66.667 0.00 0.00 0.00 5.40
1000 1085 1.445095 GGAGCACGGATCTGAGCAT 59.555 57.895 23.46 10.40 0.00 3.79
1060 1145 4.133078 GGAGCGATCTCATCTGGAAAATT 58.867 43.478 0.00 0.00 41.13 1.82
1063 1148 2.392662 AGGAGCGATCTCATCTGGAAA 58.607 47.619 0.00 0.00 41.13 3.13
1065 1150 1.959985 GAAGGAGCGATCTCATCTGGA 59.040 52.381 0.00 0.00 41.13 3.86
1190 1275 6.222389 CCATTGTAAACATTTTCAGGCAGAA 58.778 36.000 0.00 0.00 0.00 3.02
1196 1281 5.047092 AGGGAGCCATTGTAAACATTTTCAG 60.047 40.000 0.00 0.00 0.00 3.02
1199 1284 4.222810 GGAGGGAGCCATTGTAAACATTTT 59.777 41.667 0.00 0.00 0.00 1.82
1209 1294 2.579873 CTTATGTGGAGGGAGCCATTG 58.420 52.381 0.00 0.00 40.68 2.82
1227 1312 3.055819 TGCTCCTAAGATTTCGTGAGCTT 60.056 43.478 10.26 0.00 44.16 3.74
1233 1318 3.462021 GCAGATGCTCCTAAGATTTCGT 58.538 45.455 0.00 0.00 38.21 3.85
1261 1346 4.551388 TCGTTTGTGCCCATAAAACAATC 58.449 39.130 0.00 0.00 34.04 2.67
1268 1353 2.894126 ACCAATTCGTTTGTGCCCATAA 59.106 40.909 1.37 0.00 33.15 1.90
1277 1362 5.856455 GTGTCCTCAATAACCAATTCGTTTG 59.144 40.000 0.00 0.00 34.93 2.93
1340 1425 4.330250 CCTATTTACCCGGATAGTCTCGA 58.670 47.826 0.73 0.00 0.00 4.04
1389 1477 1.815421 GGAGATGCGCGGTGACAAT 60.815 57.895 8.83 0.00 0.00 2.71
1398 1486 1.372582 TCTGAACATTGGAGATGCGC 58.627 50.000 0.00 0.00 0.00 6.09
1411 1499 5.948992 AAGACTAGGTTTGCAATCTGAAC 57.051 39.130 0.00 0.00 0.00 3.18
1480 1568 8.970691 ACAACAATGAGCATAAAACTAATGTC 57.029 30.769 0.00 0.00 0.00 3.06
1577 1665 1.552226 CGCATTCAAATCAGCGCAAT 58.448 45.000 11.47 0.00 43.80 3.56
1722 1814 9.151471 TGATGTCAAAGTAATTGCTAACTAGAC 57.849 33.333 0.00 2.36 38.98 2.59
1727 1819 9.846248 AAAGATGATGTCAAAGTAATTGCTAAC 57.154 29.630 0.00 0.00 38.98 2.34
1742 3419 9.225436 AGGAAAGAAGACTTAAAAGATGATGTC 57.775 33.333 0.00 0.00 35.05 3.06
1781 3458 9.666626 CCTATAGTGTTTGTCTCTAAGTATTCG 57.333 37.037 0.00 0.00 0.00 3.34
1797 3474 9.343539 GGCTTCATTTATTTCTCCTATAGTGTT 57.656 33.333 0.00 0.00 0.00 3.32
1809 3486 8.181573 TGTTTCATACTCGGCTTCATTTATTTC 58.818 33.333 0.00 0.00 0.00 2.17
1849 3526 0.850391 CGTCGCCGATGTTAAAACGC 60.850 55.000 0.00 0.00 35.63 4.84
1859 3536 2.202703 GGCTTACACGTCGCCGAT 60.203 61.111 0.00 0.00 37.88 4.18
1895 3572 6.127451 AAATACACATTTAAGCCAAGTAGGGC 60.127 38.462 0.00 0.00 42.24 5.19
1896 3573 7.257722 CAAATACACATTTAAGCCAAGTAGGG 58.742 38.462 0.00 0.00 33.55 3.53
2114 3794 4.576873 TCGCCTTTGTAATTCTTCAACACA 59.423 37.500 0.00 0.00 0.00 3.72
2151 3831 4.953579 AGAACAAAGAACTTGGCAAAGGTA 59.046 37.500 5.66 0.00 39.56 3.08
2152 3832 3.769300 AGAACAAAGAACTTGGCAAAGGT 59.231 39.130 5.66 0.00 39.56 3.50
2153 3833 4.114794 CAGAACAAAGAACTTGGCAAAGG 58.885 43.478 5.66 0.00 39.56 3.11
2195 3875 2.095768 ACAGTCACGCCAAATTTGATCG 60.096 45.455 19.86 21.39 0.00 3.69
2213 3893 3.121944 CCATTTCTCGTCGAACTTCACAG 59.878 47.826 0.00 0.00 0.00 3.66
2216 3896 2.036733 ACCCATTTCTCGTCGAACTTCA 59.963 45.455 0.00 0.00 0.00 3.02
2270 3950 1.065854 CAAGGTCCGGAGAAGCTTCAT 60.066 52.381 27.57 13.09 0.00 2.57
2283 3963 5.912955 CGAACAATGTTTAAACTCAAGGTCC 59.087 40.000 18.72 0.00 0.00 4.46
2333 4013 3.753815 TCAGCAATTGACAAGTCATGGA 58.246 40.909 10.34 0.00 39.64 3.41
2352 4032 5.694995 AGAAAAGAGTTGTTGAAGGGATCA 58.305 37.500 0.00 0.00 35.85 2.92
2409 4095 2.163509 TCCTCGTCAGAACTGGAAGAG 58.836 52.381 1.93 8.07 37.43 2.85
2450 4492 2.819608 ACCATAAACACAAGCGCAAGAT 59.180 40.909 11.47 0.00 43.02 2.40
2455 4497 0.732538 GGCACCATAAACACAAGCGC 60.733 55.000 0.00 0.00 0.00 5.92
2456 4498 0.454285 CGGCACCATAAACACAAGCG 60.454 55.000 0.00 0.00 0.00 4.68
2463 4505 0.663153 GAGGCATCGGCACCATAAAC 59.337 55.000 0.00 0.00 43.71 2.01
2544 4586 4.104579 ACATGACATACCATGCTGGGAATA 59.895 41.667 0.00 0.00 45.79 1.75
2567 4609 4.321304 GCTGAGTTCACTAGCTCACAGTTA 60.321 45.833 0.00 0.00 36.89 2.24
2644 4787 2.029649 ACCAAGAATGCATTGCTGACAC 60.030 45.455 18.59 0.00 0.00 3.67
2667 4810 0.667487 CGACTGGTGCAACGTCTGAT 60.667 55.000 19.48 0.00 38.12 2.90
2673 4816 0.865111 TGATTTCGACTGGTGCAACG 59.135 50.000 0.00 0.00 38.12 4.10
2697 4840 2.210116 GCAACTGAGAGGTTTCGTGAA 58.790 47.619 0.00 0.00 0.00 3.18
2701 4844 0.035458 AGGGCAACTGAGAGGTTTCG 59.965 55.000 0.00 0.00 0.00 3.46
2741 4884 9.522804 CAAAAAGTAATAAACAGTGGCAAGTTA 57.477 29.630 6.96 0.00 0.00 2.24
2779 4922 3.008594 TCCCTGAAACGGCTTTATTCTCA 59.991 43.478 0.00 0.00 0.00 3.27
2790 4950 4.821805 ACTAAATATGCATCCCTGAAACGG 59.178 41.667 0.19 0.00 0.00 4.44
2795 4955 5.645056 TGGAACTAAATATGCATCCCTGA 57.355 39.130 0.19 0.00 0.00 3.86
2824 4984 9.722184 CCATGAATCTTGACACTATCATCTATT 57.278 33.333 0.00 0.00 37.11 1.73
2826 4986 8.255111 ACCATGAATCTTGACACTATCATCTA 57.745 34.615 0.00 0.00 37.11 1.98
2838 5002 4.573021 TGACATGGACCATGAATCTTGA 57.427 40.909 35.91 9.12 43.81 3.02
2868 5032 7.119846 CACCTTAAACCTTAGTGAATGAAGAGG 59.880 40.741 0.00 0.00 0.00 3.69
2882 5046 9.125026 CTCTGCATATTATTCACCTTAAACCTT 57.875 33.333 0.00 0.00 0.00 3.50
2890 5055 5.604231 TCAGGACTCTGCATATTATTCACCT 59.396 40.000 0.00 0.00 40.69 4.00
2921 5086 9.204570 GCTATGTGTACGAATAATTCCAGTATT 57.795 33.333 0.00 0.00 0.00 1.89
2932 5097 3.552699 GCAAACCGCTATGTGTACGAATA 59.447 43.478 0.00 0.00 37.77 1.75
2936 5101 3.869866 GCAAACCGCTATGTGTACG 57.130 52.632 0.00 0.00 37.77 3.67
2962 5127 0.536260 GGCAACCAAATATGCAGCCA 59.464 50.000 3.18 0.00 44.32 4.75
2979 5144 5.589050 CCCTTATTACCTGTTGAAGTTAGGC 59.411 44.000 0.00 0.00 34.93 3.93
2982 5147 6.129414 TGCCCTTATTACCTGTTGAAGTTA 57.871 37.500 0.00 0.00 0.00 2.24
2989 5154 7.287696 CCATAAATCTTGCCCTTATTACCTGTT 59.712 37.037 0.00 0.00 0.00 3.16
3003 5168 4.989279 ACACATGGACCATAAATCTTGC 57.011 40.909 6.67 0.00 0.00 4.01
3011 5183 8.429237 AAGGAAATTTTTACACATGGACCATA 57.571 30.769 6.67 0.00 0.00 2.74
3036 5208 9.667107 CACCCTAAACTTTAGTGAATAAGATGA 57.333 33.333 7.61 0.00 0.00 2.92
3058 5230 5.234466 AGGACTCTGCATATTATTCACCC 57.766 43.478 0.00 0.00 0.00 4.61
3076 5248 2.920524 TCAGTATCTGGAGACGAGGAC 58.079 52.381 0.00 0.00 31.51 3.85
3077 5249 3.646736 TTCAGTATCTGGAGACGAGGA 57.353 47.619 0.00 0.00 31.51 3.71
3078 5250 4.339530 TGATTTCAGTATCTGGAGACGAGG 59.660 45.833 0.00 0.00 31.51 4.63
3079 5251 5.506686 TGATTTCAGTATCTGGAGACGAG 57.493 43.478 0.00 0.00 31.51 4.18
3080 5252 5.221322 CCATGATTTCAGTATCTGGAGACGA 60.221 44.000 0.00 0.00 30.68 4.20
3081 5253 4.987285 CCATGATTTCAGTATCTGGAGACG 59.013 45.833 0.00 0.00 30.68 4.18
3082 5254 6.166984 TCCATGATTTCAGTATCTGGAGAC 57.833 41.667 0.00 0.00 32.14 3.36
3125 5297 9.935241 GCATCACTAGGAATAAGATGAATAAGA 57.065 33.333 0.00 0.00 38.62 2.10
3126 5298 9.941325 AGCATCACTAGGAATAAGATGAATAAG 57.059 33.333 0.00 0.00 38.62 1.73
3143 5315 6.649155 TGGCAAAATCTTACTAGCATCACTA 58.351 36.000 0.00 0.00 0.00 2.74
3144 5316 5.500234 TGGCAAAATCTTACTAGCATCACT 58.500 37.500 0.00 0.00 0.00 3.41
3166 5338 7.588854 CAGATTCCACAAATATAATCTGCGTTG 59.411 37.037 10.07 0.00 44.76 4.10
3183 5355 4.579869 ACTCATACAACACCAGATTCCAC 58.420 43.478 0.00 0.00 0.00 4.02
3184 5356 4.908601 ACTCATACAACACCAGATTCCA 57.091 40.909 0.00 0.00 0.00 3.53
3186 5358 6.992063 ATCAACTCATACAACACCAGATTC 57.008 37.500 0.00 0.00 0.00 2.52
3208 5381 9.423061 GGATGTGTTTGCTAGATTTTGTTTTAT 57.577 29.630 0.00 0.00 0.00 1.40
3209 5382 8.637986 AGGATGTGTTTGCTAGATTTTGTTTTA 58.362 29.630 0.00 0.00 0.00 1.52
3211 5384 7.014615 AGAGGATGTGTTTGCTAGATTTTGTTT 59.985 33.333 0.00 0.00 0.00 2.83
3213 5386 6.006449 AGAGGATGTGTTTGCTAGATTTTGT 58.994 36.000 0.00 0.00 0.00 2.83
3214 5387 6.072286 ACAGAGGATGTGTTTGCTAGATTTTG 60.072 38.462 0.00 0.00 41.24 2.44
3220 5393 3.930336 TGACAGAGGATGTGTTTGCTAG 58.070 45.455 0.00 0.00 45.61 3.42


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

AutoCloner maintained by Alex Coulton.