Multiple sequence alignment - TraesCS4B01G137500

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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 TraesCS4B01G137500 chr4B 100.000 3776 0 0 1 3776 181428407 181432182 0.000000e+00 6974.0
1 TraesCS4B01G137500 chr4B 100.000 32 0 0 2254 2285 629745076 629745107 4.070000e-05 60.2
2 TraesCS4B01G137500 chr4D 95.148 1319 49 9 559 1866 119224887 119226201 0.000000e+00 2067.0
3 TraesCS4B01G137500 chr4D 91.205 1137 38 21 1865 2954 119226283 119227404 0.000000e+00 1489.0
4 TraesCS4B01G137500 chr4D 90.323 341 15 5 3439 3772 119228391 119228720 7.490000e-117 431.0
5 TraesCS4B01G137500 chr4D 82.960 446 42 12 2951 3378 119227482 119227911 4.610000e-99 372.0
6 TraesCS4B01G137500 chr4A 92.213 1387 43 21 509 1858 454589818 454591176 0.000000e+00 1903.0
7 TraesCS4B01G137500 chr4A 91.460 1007 34 9 1985 2954 454591183 454592174 0.000000e+00 1336.0
8 TraesCS4B01G137500 chr4A 82.890 526 72 13 3 518 130450251 130450768 1.240000e-124 457.0
9 TraesCS4B01G137500 chr4A 92.361 288 9 5 3487 3772 454592745 454593021 7.600000e-107 398.0
10 TraesCS4B01G137500 chr7A 86.832 524 58 9 3 521 708468373 708467856 3.270000e-160 575.0
11 TraesCS4B01G137500 chr7A 97.059 34 1 0 2254 2287 627163451 627163418 1.470000e-04 58.4
12 TraesCS4B01G137500 chr7B 86.692 526 52 15 3 521 708673067 708672553 5.470000e-158 568.0
13 TraesCS4B01G137500 chr7B 88.976 127 12 2 3 128 549595840 549595965 5.050000e-34 156.0
14 TraesCS4B01G137500 chr2D 86.502 526 56 13 3 521 290733689 290734206 7.080000e-157 564.0
15 TraesCS4B01G137500 chr2D 94.737 38 2 0 2254 2291 14271740 14271703 4.070000e-05 60.2
16 TraesCS4B01G137500 chr5B 85.822 529 63 11 3 525 657135714 657136236 5.510000e-153 551.0
17 TraesCS4B01G137500 chr5B 82.409 523 77 13 9 524 706944783 706944269 3.460000e-120 442.0
18 TraesCS4B01G137500 chr5D 83.236 513 70 13 3 505 216158764 216159270 1.240000e-124 457.0
19 TraesCS4B01G137500 chr5A 84.914 464 55 10 80 532 491235797 491235338 4.450000e-124 455.0
20 TraesCS4B01G137500 chr2B 84.527 433 59 7 3 429 445501472 445501042 4.510000e-114 422.0
21 TraesCS4B01G137500 chr2B 80.851 141 16 4 397 526 601211698 601211838 2.400000e-17 100.0
22 TraesCS4B01G137500 chr7D 94.444 36 2 0 2255 2290 21701634 21701599 5.270000e-04 56.5
23 TraesCS4B01G137500 chr7D 100.000 30 0 0 2254 2283 439236294 439236265 5.270000e-04 56.5
24 TraesCS4B01G137500 chr6B 100.000 30 0 0 2254 2283 568865855 568865884 5.270000e-04 56.5
25 TraesCS4B01G137500 chr1B 100.000 30 0 0 2255 2284 399203469 399203440 5.270000e-04 56.5


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 TraesCS4B01G137500 chr4B 181428407 181432182 3775 False 6974.000000 6974 100.000000 1 3776 1 chr4B.!!$F1 3775
1 TraesCS4B01G137500 chr4D 119224887 119228720 3833 False 1089.750000 2067 89.909000 559 3772 4 chr4D.!!$F1 3213
2 TraesCS4B01G137500 chr4A 454589818 454593021 3203 False 1212.333333 1903 92.011333 509 3772 3 chr4A.!!$F2 3263
3 TraesCS4B01G137500 chr4A 130450251 130450768 517 False 457.000000 457 82.890000 3 518 1 chr4A.!!$F1 515
4 TraesCS4B01G137500 chr7A 708467856 708468373 517 True 575.000000 575 86.832000 3 521 1 chr7A.!!$R2 518
5 TraesCS4B01G137500 chr7B 708672553 708673067 514 True 568.000000 568 86.692000 3 521 1 chr7B.!!$R1 518
6 TraesCS4B01G137500 chr2D 290733689 290734206 517 False 564.000000 564 86.502000 3 521 1 chr2D.!!$F1 518
7 TraesCS4B01G137500 chr5B 657135714 657136236 522 False 551.000000 551 85.822000 3 525 1 chr5B.!!$F1 522
8 TraesCS4B01G137500 chr5B 706944269 706944783 514 True 442.000000 442 82.409000 9 524 1 chr5B.!!$R1 515
9 TraesCS4B01G137500 chr5D 216158764 216159270 506 False 457.000000 457 83.236000 3 505 1 chr5D.!!$F1 502

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
284 300 0.109781 CTCGCGGGGAAAACAACATG 60.110 55.0 6.13 0.0 0.00 3.21 F
773 809 0.174162 AATTTCGCAAGCATCCAGGC 59.826 50.0 0.00 0.0 37.18 4.85 F
1369 1434 0.323302 TCAGACCAATTAGCACCGCA 59.677 50.0 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1795 1.208535 CAGTATCCGGGGTTGCAGTTA 59.791 52.381 0.00 0.00 0.00 2.24 R
1895 2043 1.539388 TGTTTGCATGATCGTGTTCCC 59.461 47.619 16.18 0.38 0.00 3.97 R
3062 3372 0.181587 CTCAGGTCCGCCTCTAGAGA 59.818 60.000 21.76 0.00 44.97 3.10 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
31 32 6.646267 ACATATCTTTTAAGCCGTAACTCCA 58.354 36.000 0.00 0.00 0.00 3.86
177 182 7.362401 GCATGATCTGTTTTTCTTCATACCAGT 60.362 37.037 0.00 0.00 0.00 4.00
209 216 7.605691 TCCAATTGCAAATAAACACCCATTAAG 59.394 33.333 1.71 0.00 0.00 1.85
224 231 5.130145 ACCCATTAAGACCAGATTGAGAGAG 59.870 44.000 0.00 0.00 0.00 3.20
284 300 0.109781 CTCGCGGGGAAAACAACATG 60.110 55.000 6.13 0.00 0.00 3.21
347 371 1.004979 AGAGACGCCTTAGGACTGACT 59.995 52.381 0.69 0.00 0.00 3.41
357 381 5.582665 GCCTTAGGACTGACTACATTCAAAG 59.417 44.000 0.69 0.00 0.00 2.77
394 418 1.087501 GCACTAAGGCTACAGTTGGC 58.912 55.000 0.00 0.00 0.00 4.52
402 426 2.076863 GGCTACAGTTGGCTAACACAG 58.923 52.381 15.86 9.46 39.30 3.66
430 454 5.479724 TGATGCCATGTGAAAATAAAGGACA 59.520 36.000 0.00 0.00 0.00 4.02
470 494 8.956426 GTCTTGAGTCATGATTATTGGGTTAAA 58.044 33.333 11.51 0.00 0.00 1.52
525 550 5.696724 GCACAGACTCTTTTGCTAGTTTCTA 59.303 40.000 3.07 0.00 32.00 2.10
589 623 6.579666 TTGAATTTCAGAGACATCCAAAGG 57.420 37.500 0.00 0.00 0.00 3.11
590 624 4.460382 TGAATTTCAGAGACATCCAAAGGC 59.540 41.667 0.00 0.00 0.00 4.35
715 751 1.407979 CGGTTTCCTAGCGTCTGGTAT 59.592 52.381 0.00 0.00 42.56 2.73
722 758 3.750130 TCCTAGCGTCTGGTATACGATTC 59.250 47.826 0.00 0.00 42.90 2.52
723 759 3.752222 CCTAGCGTCTGGTATACGATTCT 59.248 47.826 0.00 0.00 42.90 2.40
724 760 4.934001 CCTAGCGTCTGGTATACGATTCTA 59.066 45.833 0.00 0.00 42.90 2.10
773 809 0.174162 AATTTCGCAAGCATCCAGGC 59.826 50.000 0.00 0.00 37.18 4.85
787 823 5.014966 AGCATCCAGGCTTTCAATAGGATAT 59.985 40.000 0.48 0.00 42.71 1.63
805 844 4.335874 GGATATCATAGCAGTATCGTCGGT 59.664 45.833 4.83 0.00 0.00 4.69
873 912 1.492599 CCCTCCCTCCAATCTTCTTCC 59.507 57.143 0.00 0.00 0.00 3.46
882 921 5.777223 CCTCCAATCTTCTTCCCTTCTTTTT 59.223 40.000 0.00 0.00 0.00 1.94
883 922 6.071672 CCTCCAATCTTCTTCCCTTCTTTTTC 60.072 42.308 0.00 0.00 0.00 2.29
884 923 6.372931 TCCAATCTTCTTCCCTTCTTTTTCA 58.627 36.000 0.00 0.00 0.00 2.69
927 970 3.206150 CAAGCCAGACCCATACATACAC 58.794 50.000 0.00 0.00 0.00 2.90
930 973 2.123589 CCAGACCCATACATACACCCA 58.876 52.381 0.00 0.00 0.00 4.51
1012 1062 2.821685 CTCGGATGGCGATGGGAA 59.178 61.111 0.00 0.00 0.00 3.97
1328 1378 4.024556 GGTCTGTCACTGATTTCACACTTG 60.025 45.833 0.00 0.00 0.00 3.16
1335 1385 4.818546 CACTGATTTCACACTTGTTCCTCT 59.181 41.667 0.00 0.00 0.00 3.69
1360 1414 4.764823 TCGCCAAACTAAATCAGACCAATT 59.235 37.500 0.00 0.00 0.00 2.32
1369 1434 0.323302 TCAGACCAATTAGCACCGCA 59.677 50.000 0.00 0.00 0.00 5.69
1597 1662 0.890683 TCAAGACAGCGATGCTCTCA 59.109 50.000 0.00 0.00 36.40 3.27
1673 1738 1.214589 CCTGCCAACGTACGCTACT 59.785 57.895 16.72 0.00 0.00 2.57
1730 1795 4.508551 TGACTGCCAATCTTATCCATGT 57.491 40.909 0.00 0.00 0.00 3.21
1774 1839 1.339920 TGAGCTCAATTCGAATGGCCA 60.340 47.619 15.67 8.56 0.00 5.36
1775 1840 1.332997 GAGCTCAATTCGAATGGCCAG 59.667 52.381 13.05 4.15 0.00 4.85
1784 1849 0.819582 CGAATGGCCAGGCTGATTTT 59.180 50.000 17.94 0.00 0.00 1.82
1828 1893 4.022589 CGGACTACTGACTGGTTTAGTGAA 60.023 45.833 0.00 0.00 40.53 3.18
1879 2027 9.639601 CAAATCCTATATAGTTCTGAACGCATA 57.360 33.333 14.35 15.02 36.23 3.14
1895 2043 9.110617 CTGAACGCATAATTATTCTGCTTATTG 57.889 33.333 12.29 1.11 33.75 1.90
1916 2064 2.414559 GGGAACACGATCATGCAAACAG 60.415 50.000 0.00 0.00 0.00 3.16
1954 2102 3.157087 ACCAACTTGGATGCTTTGTAGG 58.843 45.455 15.14 0.00 40.96 3.18
1955 2103 2.094545 CCAACTTGGATGCTTTGTAGGC 60.095 50.000 0.92 0.00 40.96 3.93
2146 2299 8.786826 TTGTAGACCTAAAACGATCAATGAAT 57.213 30.769 0.00 0.00 0.00 2.57
2147 2300 8.786826 TGTAGACCTAAAACGATCAATGAATT 57.213 30.769 0.00 0.00 0.00 2.17
2148 2301 9.226606 TGTAGACCTAAAACGATCAATGAATTT 57.773 29.630 0.00 0.00 0.00 1.82
2223 2379 6.925211 AGTGATATTCTTGAGACTCGTTTGA 58.075 36.000 0.00 0.00 0.00 2.69
2262 2424 4.523173 CCATGTTACTCCCTCGCTCTTATA 59.477 45.833 0.00 0.00 0.00 0.98
2263 2425 5.186021 CCATGTTACTCCCTCGCTCTTATAT 59.814 44.000 0.00 0.00 0.00 0.86
2272 2434 4.141914 CCCTCGCTCTTATATTATGGGACC 60.142 50.000 0.00 0.00 34.34 4.46
2454 2626 4.223700 TGGCAGATGTCAGATCTTAACAGT 59.776 41.667 12.07 1.87 0.00 3.55
2455 2627 4.569966 GGCAGATGTCAGATCTTAACAGTG 59.430 45.833 12.07 12.04 0.00 3.66
2456 2628 4.569966 GCAGATGTCAGATCTTAACAGTGG 59.430 45.833 12.07 6.21 0.00 4.00
2457 2629 5.625426 GCAGATGTCAGATCTTAACAGTGGA 60.625 44.000 12.07 0.00 0.00 4.02
2458 2630 5.809562 CAGATGTCAGATCTTAACAGTGGAC 59.190 44.000 12.07 6.31 0.00 4.02
2517 2690 5.645067 TGCTATATGCCATTGCTCATCTAAC 59.355 40.000 4.11 0.00 42.00 2.34
2523 2701 4.162131 TGCCATTGCTCATCTAACAGACTA 59.838 41.667 0.00 0.00 38.71 2.59
2524 2702 5.118990 GCCATTGCTCATCTAACAGACTAA 58.881 41.667 0.00 0.00 33.53 2.24
2525 2703 5.762218 GCCATTGCTCATCTAACAGACTAAT 59.238 40.000 0.00 0.00 33.53 1.73
2526 2704 6.931281 GCCATTGCTCATCTAACAGACTAATA 59.069 38.462 0.00 0.00 33.53 0.98
2527 2705 7.605691 GCCATTGCTCATCTAACAGACTAATAT 59.394 37.037 0.00 0.00 33.53 1.28
2852 3080 5.930837 TGGTTTGCTAGGGAATAATTTGG 57.069 39.130 0.00 0.00 0.00 3.28
2855 3083 6.154363 TGGTTTGCTAGGGAATAATTTGGAAG 59.846 38.462 0.00 0.00 0.00 3.46
2856 3084 6.406961 GGTTTGCTAGGGAATAATTTGGAAGG 60.407 42.308 0.00 0.00 0.00 3.46
2857 3085 4.215109 TGCTAGGGAATAATTTGGAAGGC 58.785 43.478 0.00 0.00 0.00 4.35
2870 3098 6.731292 ATTTGGAAGGCCTGTATTTAATCC 57.269 37.500 5.69 7.58 34.31 3.01
2877 3105 3.889538 GGCCTGTATTTAATCCCCTCAAC 59.110 47.826 0.00 0.00 0.00 3.18
2878 3106 4.532834 GCCTGTATTTAATCCCCTCAACA 58.467 43.478 0.00 0.00 0.00 3.33
2884 3112 9.354673 CTGTATTTAATCCCCTCAACATTACAT 57.645 33.333 0.00 0.00 0.00 2.29
3008 3318 8.524487 AGCGGTTATTAGATAAAGAGGTGATAG 58.476 37.037 0.00 0.00 0.00 2.08
3013 3323 2.900546 AGATAAAGAGGTGATAGGCGGG 59.099 50.000 0.00 0.00 0.00 6.13
3027 3337 2.665165 AGGCGGGAAATAATTCATGCA 58.335 42.857 8.06 0.00 38.34 3.96
3033 3343 5.051816 CGGGAAATAATTCATGCAAATGCT 58.948 37.500 6.97 0.00 38.44 3.79
3034 3344 5.050634 CGGGAAATAATTCATGCAAATGCTG 60.051 40.000 6.97 3.14 38.44 4.41
3040 3350 2.647529 TCATGCAAATGCTGAGCTTG 57.352 45.000 5.83 3.85 42.66 4.01
3093 3403 2.103771 CGGACCTGAGTTGGATCATGAT 59.896 50.000 8.25 8.25 0.00 2.45
3094 3404 3.432749 CGGACCTGAGTTGGATCATGATT 60.433 47.826 10.14 0.00 0.00 2.57
3095 3405 4.133078 GGACCTGAGTTGGATCATGATTC 58.867 47.826 10.14 8.56 0.00 2.52
3096 3406 4.384537 GGACCTGAGTTGGATCATGATTCA 60.385 45.833 12.97 12.97 0.00 2.57
3097 3407 5.374921 GACCTGAGTTGGATCATGATTCAT 58.625 41.667 17.58 3.52 0.00 2.57
3098 3408 5.131067 ACCTGAGTTGGATCATGATTCATG 58.869 41.667 17.58 18.71 42.60 3.07
3124 3579 0.610232 AAGTGAACCTGCCATGCCTC 60.610 55.000 0.00 0.00 0.00 4.70
3134 3589 0.449388 GCCATGCCTCTCAAAACTCG 59.551 55.000 0.00 0.00 0.00 4.18
3138 3593 3.120060 CCATGCCTCTCAAAACTCGAAAG 60.120 47.826 0.00 0.00 0.00 2.62
3140 3595 1.136224 GCCTCTCAAAACTCGAAAGCG 60.136 52.381 0.00 0.00 39.35 4.68
3146 3601 2.798283 TCAAAACTCGAAAGCGATCGTT 59.202 40.909 17.81 8.05 46.80 3.85
3163 3618 3.277715 TCGTTGCTGATGATTTGGCATA 58.722 40.909 0.00 0.00 34.59 3.14
3168 3623 5.294734 TGCTGATGATTTGGCATACTCTA 57.705 39.130 0.00 0.00 0.00 2.43
3202 3668 7.565450 AAGACAATTTTTGCTTTTGTTTTGC 57.435 28.000 0.00 0.00 33.92 3.68
3221 3687 0.095935 CTGTCAAATTGAGCTCCGCG 59.904 55.000 12.15 0.00 0.00 6.46
3241 3707 4.201773 CGCGTATCCTGATTTGCTTTACAA 60.202 41.667 0.00 0.00 36.13 2.41
3247 3713 9.076596 GTATCCTGATTTGCTTTACAATTCAAC 57.923 33.333 5.00 0.00 44.06 3.18
3263 3729 8.006298 ACAATTCAACTTTATTGTTCTGGTCA 57.994 30.769 0.00 0.00 40.97 4.02
3267 3733 2.812011 ACTTTATTGTTCTGGTCACCGC 59.188 45.455 0.00 0.00 0.00 5.68
3268 3734 2.552599 TTATTGTTCTGGTCACCGCA 57.447 45.000 0.00 0.00 0.00 5.69
3269 3735 2.552599 TATTGTTCTGGTCACCGCAA 57.447 45.000 0.00 0.00 0.00 4.85
3270 3736 1.686355 ATTGTTCTGGTCACCGCAAA 58.314 45.000 0.00 0.00 0.00 3.68
3271 3737 1.464734 TTGTTCTGGTCACCGCAAAA 58.535 45.000 0.00 0.00 0.00 2.44
3272 3738 1.021202 TGTTCTGGTCACCGCAAAAG 58.979 50.000 0.00 0.00 0.00 2.27
3273 3739 1.305201 GTTCTGGTCACCGCAAAAGA 58.695 50.000 0.00 0.00 0.00 2.52
3277 3743 2.357637 TCTGGTCACCGCAAAAGAAAAG 59.642 45.455 0.00 0.00 0.00 2.27
3282 3748 4.627900 GGTCACCGCAAAAGAAAAGAAAAA 59.372 37.500 0.00 0.00 0.00 1.94
3316 3782 2.290960 GGGTCCAAGGTGTAGAAGCATT 60.291 50.000 0.00 0.00 0.00 3.56
3319 3785 4.265073 GTCCAAGGTGTAGAAGCATTGAT 58.735 43.478 0.00 0.00 0.00 2.57
3328 3798 6.071952 GGTGTAGAAGCATTGATGGAAAAGAA 60.072 38.462 0.00 0.00 0.00 2.52
3342 3812 4.098654 TGGAAAAGAAGGCGAAAAACATCA 59.901 37.500 0.00 0.00 0.00 3.07
3345 3815 6.202762 GGAAAAGAAGGCGAAAAACATCAAAT 59.797 34.615 0.00 0.00 0.00 2.32
3348 3818 6.529463 AGAAGGCGAAAAACATCAAATTTG 57.471 33.333 12.15 12.15 0.00 2.32
3349 3819 6.279882 AGAAGGCGAAAAACATCAAATTTGA 58.720 32.000 22.52 22.52 42.14 2.69
3351 3821 8.087750 AGAAGGCGAAAAACATCAAATTTGATA 58.912 29.630 28.61 7.64 45.62 2.15
3352 3822 8.600449 AAGGCGAAAAACATCAAATTTGATAA 57.400 26.923 28.61 6.92 45.62 1.75
3353 3823 8.776376 AGGCGAAAAACATCAAATTTGATAAT 57.224 26.923 28.61 18.86 45.62 1.28
3355 3825 9.476761 GGCGAAAAACATCAAATTTGATAATTC 57.523 29.630 28.61 24.65 45.62 2.17
3378 3851 4.635765 CCAAATCCTCTAAAATCGTGAGCA 59.364 41.667 0.00 0.00 0.00 4.26
3379 3852 5.123820 CCAAATCCTCTAAAATCGTGAGCAA 59.876 40.000 0.00 0.00 0.00 3.91
3380 3853 6.253746 CAAATCCTCTAAAATCGTGAGCAAG 58.746 40.000 0.00 0.00 0.00 4.01
3385 3858 5.179368 CCTCTAAAATCGTGAGCAAGAACAA 59.821 40.000 0.00 0.00 0.00 2.83
3386 3859 6.293407 CCTCTAAAATCGTGAGCAAGAACAAA 60.293 38.462 0.00 0.00 0.00 2.83
3387 3860 6.427150 TCTAAAATCGTGAGCAAGAACAAAC 58.573 36.000 0.00 0.00 0.00 2.93
3389 3862 4.836125 AATCGTGAGCAAGAACAAACAT 57.164 36.364 0.00 0.00 0.00 2.71
3391 3864 2.290367 TCGTGAGCAAGAACAAACATGG 59.710 45.455 0.00 0.00 0.00 3.66
3392 3865 2.290367 CGTGAGCAAGAACAAACATGGA 59.710 45.455 0.00 0.00 0.00 3.41
3393 3866 3.607775 CGTGAGCAAGAACAAACATGGAG 60.608 47.826 0.00 0.00 0.00 3.86
3395 3868 4.036734 GTGAGCAAGAACAAACATGGAGAA 59.963 41.667 0.00 0.00 0.00 2.87
3396 3869 4.644234 TGAGCAAGAACAAACATGGAGAAA 59.356 37.500 0.00 0.00 0.00 2.52
3399 3872 6.218746 AGCAAGAACAAACATGGAGAAATTC 58.781 36.000 0.00 0.00 0.00 2.17
3400 3873 5.406477 GCAAGAACAAACATGGAGAAATTCC 59.594 40.000 0.00 0.00 46.98 3.01
3418 4189 2.750815 CGTCTGACGGAATGGAACC 58.249 57.895 21.78 0.00 38.08 3.62
3424 4195 3.568007 TCTGACGGAATGGAACCTTTTTG 59.432 43.478 0.00 0.00 0.00 2.44
3425 4196 3.556999 TGACGGAATGGAACCTTTTTGA 58.443 40.909 0.00 0.00 0.00 2.69
3442 4213 8.722480 CCTTTTTGAGGGAATATTTGGAAATC 57.278 34.615 0.00 0.00 42.26 2.17
3443 4214 8.542926 CCTTTTTGAGGGAATATTTGGAAATCT 58.457 33.333 0.00 0.00 42.26 2.40
3492 4385 8.726870 AATTTTGATAATTTCTTCAGCATGGG 57.273 30.769 0.00 0.00 36.16 4.00
3501 4394 6.514012 TTTCTTCAGCATGGGGAATATCTA 57.486 37.500 0.00 0.00 36.16 1.98
3510 4403 6.556116 AGCATGGGGAATATCTAAAAAGCAAT 59.444 34.615 0.00 0.00 0.00 3.56
3717 4612 6.146347 CACTCTTTTCCTTCCTTTACTCTTCG 59.854 42.308 0.00 0.00 0.00 3.79
3746 4647 3.141838 TCCATGGGCTAGAATCTCTCTCT 59.858 47.826 13.02 0.00 35.41 3.10
3747 4648 3.511146 CCATGGGCTAGAATCTCTCTCTC 59.489 52.174 2.85 0.00 35.41 3.20
3748 4649 4.410099 CATGGGCTAGAATCTCTCTCTCT 58.590 47.826 0.00 0.00 35.41 3.10
3749 4650 4.098914 TGGGCTAGAATCTCTCTCTCTC 57.901 50.000 0.00 0.00 35.41 3.20
3750 4651 3.721575 TGGGCTAGAATCTCTCTCTCTCT 59.278 47.826 0.00 0.00 35.41 3.10
3751 4652 4.202461 TGGGCTAGAATCTCTCTCTCTCTC 60.202 50.000 0.00 0.00 35.41 3.20
3768 4669 2.937149 CTCTCTGCCATCATCACACTTG 59.063 50.000 0.00 0.00 0.00 3.16
3772 4673 3.014623 CTGCCATCATCACACTTGACAT 58.985 45.455 0.00 0.00 33.38 3.06
3773 4674 3.423749 TGCCATCATCACACTTGACATT 58.576 40.909 0.00 0.00 33.38 2.71
3774 4675 3.827876 TGCCATCATCACACTTGACATTT 59.172 39.130 0.00 0.00 33.38 2.32
3775 4676 4.281435 TGCCATCATCACACTTGACATTTT 59.719 37.500 0.00 0.00 33.38 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 4.634443 ACATGTTAGAATTGGAGTTACGGC 59.366 41.667 0.00 0.00 0.00 5.68
159 163 3.252215 CGCCACTGGTATGAAGAAAAACA 59.748 43.478 0.00 0.00 0.00 2.83
177 182 4.180057 GTTTATTTGCAATTGGATCGCCA 58.820 39.130 7.72 0.00 44.17 5.69
240 255 1.668793 CAGAGGTGTGCATGCGTGA 60.669 57.895 14.09 0.00 0.00 4.35
284 300 5.352284 TCGCTCAGGATAAAGATGAGAAAC 58.648 41.667 5.65 0.00 42.48 2.78
297 313 2.182791 CGCACACTCGCTCAGGAT 59.817 61.111 0.00 0.00 0.00 3.24
299 315 3.108289 CACGCACACTCGCTCAGG 61.108 66.667 0.00 0.00 0.00 3.86
347 371 4.142138 ACAACCAAAACGCCTTTGAATGTA 60.142 37.500 11.16 0.00 46.35 2.29
357 381 0.869880 GCTCACACAACCAAAACGCC 60.870 55.000 0.00 0.00 0.00 5.68
394 418 3.943381 ACATGGCATCACATCTGTGTTAG 59.057 43.478 9.96 3.38 45.76 2.34
402 426 6.477688 CCTTTATTTTCACATGGCATCACATC 59.522 38.462 0.00 0.00 0.00 3.06
430 454 5.964477 TGACTCAAGACCCTAATAGGTTCAT 59.036 40.000 6.64 0.00 41.42 2.57
470 494 7.712204 ACGGGGAAGAAAATAACATACATTT 57.288 32.000 0.00 0.00 0.00 2.32
476 500 3.829601 TGCAACGGGGAAGAAAATAACAT 59.170 39.130 0.00 0.00 0.00 2.71
600 635 6.183360 GGATGTCTCTATCCTCAAAAGCAAAC 60.183 42.308 0.00 0.00 42.73 2.93
626 661 3.242316 GCGGTTGGATTACGATCAACTTC 60.242 47.826 0.00 0.00 33.77 3.01
722 758 9.868277 GGAGATCTTGACATATCCATTTAGTAG 57.132 37.037 0.00 0.00 34.69 2.57
723 759 9.607333 AGGAGATCTTGACATATCCATTTAGTA 57.393 33.333 0.00 0.00 36.72 1.82
724 760 8.503428 AGGAGATCTTGACATATCCATTTAGT 57.497 34.615 0.00 0.00 36.72 2.24
787 823 2.294979 ACACCGACGATACTGCTATGA 58.705 47.619 0.00 0.00 0.00 2.15
800 839 1.433837 AACGCCAACAGAACACCGAC 61.434 55.000 0.00 0.00 0.00 4.79
805 844 0.681564 AACCCAACGCCAACAGAACA 60.682 50.000 0.00 0.00 0.00 3.18
873 912 6.640092 GCACAAGAGAAAGATGAAAAAGAAGG 59.360 38.462 0.00 0.00 0.00 3.46
882 921 3.811497 CACACAGCACAAGAGAAAGATGA 59.189 43.478 0.00 0.00 0.00 2.92
883 922 3.608707 GCACACAGCACAAGAGAAAGATG 60.609 47.826 0.00 0.00 44.79 2.90
884 923 2.551459 GCACACAGCACAAGAGAAAGAT 59.449 45.455 0.00 0.00 44.79 2.40
927 970 1.152139 ATTGGTGGGTTGGGTTGGG 60.152 57.895 0.00 0.00 0.00 4.12
930 973 0.560688 AGTGATTGGTGGGTTGGGTT 59.439 50.000 0.00 0.00 0.00 4.11
1275 1325 2.028190 CGGAGCGCGATGGAGAAT 59.972 61.111 12.10 0.00 0.00 2.40
1328 1378 3.314541 TTAGTTTGGCGAGAGAGGAAC 57.685 47.619 0.00 0.00 0.00 3.62
1335 1385 3.007506 TGGTCTGATTTAGTTTGGCGAGA 59.992 43.478 0.00 0.00 0.00 4.04
1360 1414 2.938451 CAGATTCAGATTTGCGGTGCTA 59.062 45.455 0.00 0.00 0.00 3.49
1369 1434 4.880696 GCCTAGCAAGACAGATTCAGATTT 59.119 41.667 0.00 0.00 0.00 2.17
1597 1662 1.979693 GAGGCTGACGGTGGAGACT 60.980 63.158 0.00 0.00 0.00 3.24
1633 1698 3.087906 ATGGAGGGGCCGGTGTAC 61.088 66.667 1.90 0.00 40.66 2.90
1673 1738 3.845781 AAAAGGAGCAAGTGAGTGAGA 57.154 42.857 0.00 0.00 0.00 3.27
1730 1795 1.208535 CAGTATCCGGGGTTGCAGTTA 59.791 52.381 0.00 0.00 0.00 2.24
1879 2027 6.601613 TCGTGTTCCCAATAAGCAGAATAATT 59.398 34.615 0.00 0.00 0.00 1.40
1895 2043 1.539388 TGTTTGCATGATCGTGTTCCC 59.461 47.619 16.18 0.38 0.00 3.97
1916 2064 1.631898 TGGTTAACTGGAAGGGCCTAC 59.368 52.381 6.41 3.37 39.30 3.18
1954 2102 9.751542 ATGTACAGATTACTAGATTACAGTTGC 57.248 33.333 0.33 0.00 0.00 4.17
2148 2301 9.678260 CCATGAATGGGGTCAAAAATAAATAAA 57.322 29.630 1.01 0.00 44.31 1.40
2156 2310 4.842948 TCATTCCATGAATGGGGTCAAAAA 59.157 37.500 14.84 0.00 46.43 1.94
2223 2379 3.149196 ACATGGAAATGACGACTTGCTT 58.851 40.909 0.00 0.00 0.00 3.91
2262 2424 2.449730 TCTACTCCCTCGGTCCCATAAT 59.550 50.000 0.00 0.00 0.00 1.28
2263 2425 1.854939 TCTACTCCCTCGGTCCCATAA 59.145 52.381 0.00 0.00 0.00 1.90
2272 2434 4.993029 ACATTTCTCTTCTACTCCCTCG 57.007 45.455 0.00 0.00 0.00 4.63
2454 2626 1.899814 ACTAAAGCATCGTCCAGTCCA 59.100 47.619 0.00 0.00 0.00 4.02
2455 2627 2.674796 ACTAAAGCATCGTCCAGTCC 57.325 50.000 0.00 0.00 0.00 3.85
2456 2628 4.106197 CAGTACTAAAGCATCGTCCAGTC 58.894 47.826 0.00 0.00 0.00 3.51
2457 2629 3.762288 TCAGTACTAAAGCATCGTCCAGT 59.238 43.478 0.00 0.00 0.00 4.00
2458 2630 4.371855 TCAGTACTAAAGCATCGTCCAG 57.628 45.455 0.00 0.00 0.00 3.86
2824 3052 2.507407 TCCCTAGCAAACCATGTTCC 57.493 50.000 0.00 0.00 0.00 3.62
2852 3080 4.141251 TGAGGGGATTAAATACAGGCCTTC 60.141 45.833 0.00 0.00 0.00 3.46
2855 3083 3.876309 TGAGGGGATTAAATACAGGCC 57.124 47.619 0.00 0.00 0.00 5.19
2856 3084 4.532834 TGTTGAGGGGATTAAATACAGGC 58.467 43.478 0.00 0.00 0.00 4.85
2857 3085 7.777910 TGTAATGTTGAGGGGATTAAATACAGG 59.222 37.037 0.00 0.00 0.00 4.00
2870 3098 5.818136 AAACATCGATGTAATGTTGAGGG 57.182 39.130 30.16 0.03 44.44 4.30
2984 3294 7.760340 GCCTATCACCTCTTTATCTAATAACCG 59.240 40.741 0.00 0.00 0.00 4.44
2987 3297 7.093465 CCCGCCTATCACCTCTTTATCTAATAA 60.093 40.741 0.00 0.00 0.00 1.40
2996 3306 1.580059 TTCCCGCCTATCACCTCTTT 58.420 50.000 0.00 0.00 0.00 2.52
3008 3318 3.451141 TTGCATGAATTATTTCCCGCC 57.549 42.857 0.00 0.00 30.74 6.13
3013 3323 6.479001 AGCTCAGCATTTGCATGAATTATTTC 59.521 34.615 0.00 0.00 45.16 2.17
3027 3337 6.523840 TCAAAATAAACCAAGCTCAGCATTT 58.476 32.000 0.00 0.00 0.00 2.32
3033 3343 4.522789 GGTCCTCAAAATAAACCAAGCTCA 59.477 41.667 0.00 0.00 0.00 4.26
3034 3344 4.767409 AGGTCCTCAAAATAAACCAAGCTC 59.233 41.667 0.00 0.00 32.25 4.09
3062 3372 0.181587 CTCAGGTCCGCCTCTAGAGA 59.818 60.000 21.76 0.00 44.97 3.10
3072 3382 1.482182 TCATGATCCAACTCAGGTCCG 59.518 52.381 0.00 0.00 0.00 4.79
3075 3385 4.849813 TGAATCATGATCCAACTCAGGT 57.150 40.909 9.06 0.00 0.00 4.00
3093 3403 4.136796 CAGGTTCACTTCCTTGTCATGAA 58.863 43.478 0.00 0.00 32.37 2.57
3094 3404 3.743521 CAGGTTCACTTCCTTGTCATGA 58.256 45.455 0.00 0.00 32.37 3.07
3095 3405 2.227388 GCAGGTTCACTTCCTTGTCATG 59.773 50.000 0.00 0.00 32.37 3.07
3096 3406 2.508526 GCAGGTTCACTTCCTTGTCAT 58.491 47.619 0.00 0.00 32.37 3.06
3097 3407 1.476833 GGCAGGTTCACTTCCTTGTCA 60.477 52.381 0.00 0.00 32.37 3.58
3098 3408 1.239347 GGCAGGTTCACTTCCTTGTC 58.761 55.000 0.00 0.00 32.37 3.18
3099 3409 0.550914 TGGCAGGTTCACTTCCTTGT 59.449 50.000 0.00 0.00 33.17 3.16
3100 3410 1.542915 CATGGCAGGTTCACTTCCTTG 59.457 52.381 0.00 0.00 33.17 3.61
3134 3589 1.660607 TCATCAGCAACGATCGCTTTC 59.339 47.619 16.60 3.61 37.72 2.62
3138 3593 2.369600 CAAATCATCAGCAACGATCGC 58.630 47.619 16.60 0.00 0.00 4.58
3140 3595 2.097954 TGCCAAATCATCAGCAACGATC 59.902 45.455 0.00 0.00 30.97 3.69
3146 3601 4.160642 AGAGTATGCCAAATCATCAGCA 57.839 40.909 0.00 0.00 40.00 4.41
3168 3623 8.518430 AAGCAAAAATTGTCTTTTGGGTAAAT 57.482 26.923 9.99 0.00 43.49 1.40
3221 3687 9.076596 GTTGAATTGTAAAGCAAATCAGGATAC 57.923 33.333 0.00 0.00 44.77 2.24
3241 3707 6.293955 CGGTGACCAGAACAATAAAGTTGAAT 60.294 38.462 1.11 0.00 0.00 2.57
3247 3713 2.811431 TGCGGTGACCAGAACAATAAAG 59.189 45.455 1.11 0.00 0.00 1.85
3259 3725 3.430333 TTCTTTTCTTTTGCGGTGACC 57.570 42.857 0.00 0.00 0.00 4.02
3282 3748 4.411869 ACCTTGGACCCAAAACAATGAATT 59.588 37.500 2.84 0.00 35.33 2.17
3283 3749 3.973305 ACCTTGGACCCAAAACAATGAAT 59.027 39.130 2.84 0.00 35.33 2.57
3316 3782 4.098654 TGTTTTTCGCCTTCTTTTCCATCA 59.901 37.500 0.00 0.00 0.00 3.07
3319 3785 4.098654 TGATGTTTTTCGCCTTCTTTTCCA 59.901 37.500 0.00 0.00 0.00 3.53
3328 3798 8.776376 ATTATCAAATTTGATGTTTTTCGCCT 57.224 26.923 33.94 13.90 46.68 5.52
3348 3818 9.884465 CACGATTTTAGAGGATTTGGAATTATC 57.116 33.333 0.00 0.00 0.00 1.75
3349 3819 9.627123 TCACGATTTTAGAGGATTTGGAATTAT 57.373 29.630 0.00 0.00 0.00 1.28
3350 3820 9.109393 CTCACGATTTTAGAGGATTTGGAATTA 57.891 33.333 0.00 0.00 0.00 1.40
3351 3821 7.415653 GCTCACGATTTTAGAGGATTTGGAATT 60.416 37.037 0.00 0.00 0.00 2.17
3352 3822 6.038714 GCTCACGATTTTAGAGGATTTGGAAT 59.961 38.462 0.00 0.00 0.00 3.01
3353 3823 5.354234 GCTCACGATTTTAGAGGATTTGGAA 59.646 40.000 0.00 0.00 0.00 3.53
3355 3825 4.635765 TGCTCACGATTTTAGAGGATTTGG 59.364 41.667 0.00 0.00 0.00 3.28
3370 3843 2.290367 CCATGTTTGTTCTTGCTCACGA 59.710 45.455 0.00 0.00 0.00 4.35
3378 3851 5.301805 ACGGAATTTCTCCATGTTTGTTCTT 59.698 36.000 0.00 0.00 45.74 2.52
3379 3852 4.827284 ACGGAATTTCTCCATGTTTGTTCT 59.173 37.500 0.00 0.00 45.74 3.01
3380 3853 5.048713 AGACGGAATTTCTCCATGTTTGTTC 60.049 40.000 0.00 0.00 45.74 3.18
3385 3858 4.003648 GTCAGACGGAATTTCTCCATGTT 58.996 43.478 0.00 0.00 45.74 2.71
3386 3859 3.600388 GTCAGACGGAATTTCTCCATGT 58.400 45.455 0.00 0.00 45.74 3.21
3387 3860 2.604914 CGTCAGACGGAATTTCTCCATG 59.395 50.000 15.64 0.00 45.74 3.66
3389 3862 2.363788 CGTCAGACGGAATTTCTCCA 57.636 50.000 15.64 0.00 45.74 3.86
3400 3873 0.246635 AGGTTCCATTCCGTCAGACG 59.753 55.000 16.50 16.50 42.11 4.18
3401 3874 2.474410 AAGGTTCCATTCCGTCAGAC 57.526 50.000 0.00 0.00 0.00 3.51
3403 3876 3.568007 TCAAAAAGGTTCCATTCCGTCAG 59.432 43.478 0.00 0.00 0.00 3.51
3404 3877 3.556999 TCAAAAAGGTTCCATTCCGTCA 58.443 40.909 0.00 0.00 0.00 4.35
3405 3878 3.057526 CCTCAAAAAGGTTCCATTCCGTC 60.058 47.826 0.00 0.00 40.67 4.79
3418 4189 9.948964 AAGATTTCCAAATATTCCCTCAAAAAG 57.051 29.630 0.00 0.00 0.00 2.27
3424 4195 5.221521 GCCCAAGATTTCCAAATATTCCCTC 60.222 44.000 0.00 0.00 28.13 4.30
3425 4196 4.655649 GCCCAAGATTTCCAAATATTCCCT 59.344 41.667 0.00 0.00 28.13 4.20
3436 4207 3.633986 CCAAGTCATAGCCCAAGATTTCC 59.366 47.826 0.00 0.00 0.00 3.13
3437 4208 3.067320 GCCAAGTCATAGCCCAAGATTTC 59.933 47.826 0.00 0.00 0.00 2.17
3442 4213 1.838112 TTGCCAAGTCATAGCCCAAG 58.162 50.000 0.00 0.00 0.00 3.61
3443 4214 2.300956 TTTGCCAAGTCATAGCCCAA 57.699 45.000 0.00 0.00 0.00 4.12
3473 4366 6.661304 ATTCCCCATGCTGAAGAAATTATC 57.339 37.500 0.00 0.00 0.00 1.75
3476 4369 6.379579 AGATATTCCCCATGCTGAAGAAATT 58.620 36.000 0.00 0.00 0.00 1.82
3492 4385 7.435192 CCGGTTTCATTGCTTTTTAGATATTCC 59.565 37.037 0.00 0.00 0.00 3.01
3501 4394 4.500716 CCAGTACCGGTTTCATTGCTTTTT 60.501 41.667 15.04 0.00 0.00 1.94
3572 4465 2.832129 ACCTTCGTTCAGAGAGCCAATA 59.168 45.455 0.00 0.00 0.00 1.90
3573 4466 1.625818 ACCTTCGTTCAGAGAGCCAAT 59.374 47.619 0.00 0.00 0.00 3.16
3574 4467 1.000955 GACCTTCGTTCAGAGAGCCAA 59.999 52.381 0.00 0.00 0.00 4.52
3575 4468 0.603569 GACCTTCGTTCAGAGAGCCA 59.396 55.000 0.00 0.00 0.00 4.75
3746 4647 2.464782 AGTGTGATGATGGCAGAGAGA 58.535 47.619 0.00 0.00 0.00 3.10
3747 4648 2.937149 CAAGTGTGATGATGGCAGAGAG 59.063 50.000 0.00 0.00 0.00 3.20
3748 4649 2.568509 TCAAGTGTGATGATGGCAGAGA 59.431 45.455 0.00 0.00 0.00 3.10
3749 4650 2.676839 GTCAAGTGTGATGATGGCAGAG 59.323 50.000 0.00 0.00 35.80 3.35
3750 4651 2.038820 TGTCAAGTGTGATGATGGCAGA 59.961 45.455 0.00 0.00 35.80 4.26
3751 4652 2.429478 TGTCAAGTGTGATGATGGCAG 58.571 47.619 0.00 0.00 35.80 4.85


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

AutoCloner maintained by Alex Coulton.