Multiple sequence alignment - TraesCS4A01G292800

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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 TraesCS4A01G292800 chr4A 100.000 4391 0 0 1 4391 595297747 595293357 0.000000e+00 8109.0
1 TraesCS4A01G292800 chr4A 94.643 112 5 1 1506 1617 595283560 595283450 5.840000e-39 172.0
2 TraesCS4A01G292800 chr4D 87.534 1829 97 47 444 2209 8151992 8150232 0.000000e+00 1993.0
3 TraesCS4A01G292800 chr4D 90.852 1432 85 18 717 2125 7992152 7993560 0.000000e+00 1877.0
4 TraesCS4A01G292800 chr4D 90.981 887 48 14 3124 4001 8149316 8148453 0.000000e+00 1166.0
5 TraesCS4A01G292800 chr4D 87.139 832 76 17 2214 3027 8150171 8149353 0.000000e+00 915.0
6 TraesCS4A01G292800 chr4D 88.348 678 43 6 17 663 7991471 7992143 0.000000e+00 782.0
7 TraesCS4A01G292800 chr4D 90.141 284 24 4 90 371 8153028 8152747 2.500000e-97 366.0
8 TraesCS4A01G292800 chr4D 80.590 407 42 18 3164 3541 7995025 7995423 3.340000e-71 279.0
9 TraesCS4A01G292800 chr4D 87.898 157 15 4 2776 2930 7994849 7995003 9.700000e-42 182.0
10 TraesCS4A01G292800 chr4D 76.970 330 55 17 1506 1823 8136961 8136641 7.550000e-38 169.0
11 TraesCS4A01G292800 chr4B 88.204 1704 103 38 444 2125 15432139 15430512 0.000000e+00 1943.0
12 TraesCS4A01G292800 chr4B 89.422 1229 111 12 3102 4328 15260332 15259121 0.000000e+00 1531.0
13 TraesCS4A01G292800 chr4B 84.553 1599 116 55 667 2211 14842891 14841370 0.000000e+00 1463.0
14 TraesCS4A01G292800 chr4B 89.226 1188 62 28 955 2125 15262732 15261594 0.000000e+00 1424.0
15 TraesCS4A01G292800 chr4B 87.372 1267 81 36 941 2173 15150705 15149484 0.000000e+00 1380.0
16 TraesCS4A01G292800 chr4B 87.218 1064 107 16 2402 3451 15199236 15198188 0.000000e+00 1184.0
17 TraesCS4A01G292800 chr4B 87.030 1064 103 15 2402 3452 15147219 15146178 0.000000e+00 1168.0
18 TraesCS4A01G292800 chr4B 86.748 1064 112 18 2402 3451 15183360 15182312 0.000000e+00 1157.0
19 TraesCS4A01G292800 chr4B 87.868 882 85 13 3450 4328 15198026 15197164 0.000000e+00 1016.0
20 TraesCS4A01G292800 chr4B 87.246 886 99 10 3444 4328 15130611 15129739 0.000000e+00 998.0
21 TraesCS4A01G292800 chr4B 88.550 786 60 12 2253 3017 15261561 15260785 0.000000e+00 926.0
22 TraesCS4A01G292800 chr4B 86.774 809 90 13 3522 4328 15177540 15176747 0.000000e+00 885.0
23 TraesCS4A01G292800 chr4B 86.128 829 63 26 115 911 15263554 15262746 0.000000e+00 846.0
24 TraesCS4A01G292800 chr4B 91.598 607 41 5 3096 3700 15427629 15427031 0.000000e+00 830.0
25 TraesCS4A01G292800 chr4B 84.406 917 64 34 1445 2338 15184221 15183361 0.000000e+00 828.0
26 TraesCS4A01G292800 chr4B 87.054 757 50 25 80 802 14844237 14843495 0.000000e+00 811.0
27 TraesCS4A01G292800 chr4B 87.822 698 66 9 2251 2933 14841288 14840595 0.000000e+00 800.0
28 TraesCS4A01G292800 chr4B 86.014 715 71 13 2216 2911 15429069 15428365 0.000000e+00 739.0
29 TraesCS4A01G292800 chr4B 91.241 548 39 6 3103 3648 14840238 14839698 0.000000e+00 737.0
30 TraesCS4A01G292800 chr4B 85.714 742 56 18 85 802 15186193 15185478 0.000000e+00 737.0
31 TraesCS4A01G292800 chr4B 85.542 747 58 18 80 802 15201362 15200642 0.000000e+00 736.0
32 TraesCS4A01G292800 chr4B 86.545 550 63 9 3643 4188 14837908 14837366 2.920000e-166 595.0
33 TraesCS4A01G292800 chr4B 86.250 480 47 6 2549 3027 15428091 15427630 1.820000e-138 503.0
34 TraesCS4A01G292800 chr4B 85.682 447 26 16 960 1381 15184670 15184237 1.880000e-118 436.0
35 TraesCS4A01G292800 chr4B 86.930 329 21 9 998 1319 15199796 15199483 2.510000e-92 350.0
36 TraesCS4A01G292800 chr4B 89.011 273 22 7 104 372 15433192 15432924 9.100000e-87 331.0
37 TraesCS4A01G292800 chr4B 95.055 182 7 1 426 605 15151118 15150937 7.190000e-73 285.0
38 TraesCS4A01G292800 chr4B 95.055 182 7 1 426 605 15185112 15184931 7.190000e-73 285.0
39 TraesCS4A01G292800 chr4B 87.805 123 13 2 2926 3047 14840356 14840235 4.580000e-30 143.0
40 TraesCS4A01G292800 chr4B 96.429 56 2 0 4336 4391 15128350 15128295 4.680000e-15 93.5
41 TraesCS4A01G292800 chr5A 84.328 134 19 2 2229 2361 695696658 695696526 3.560000e-26 130.0
42 TraesCS4A01G292800 chr5A 84.328 134 20 1 2229 2361 695739590 695739457 3.560000e-26 130.0
43 TraesCS4A01G292800 chr5A 97.059 34 1 0 4110 4143 338559822 338559855 1.710000e-04 58.4
44 TraesCS4A01G292800 chr6B 83.333 138 16 6 2230 2361 298824778 298824914 2.140000e-23 121.0
45 TraesCS4A01G292800 chr5B 82.946 129 16 2 2239 2361 322866479 322866351 1.290000e-20 111.0
46 TraesCS4A01G292800 chr7D 82.031 128 18 3 2239 2362 464028058 464027932 2.160000e-18 104.0


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 TraesCS4A01G292800 chr4A 595293357 595297747 4390 True 8109.000000 8109 100.000000 1 4391 1 chr4A.!!$R2 4390
1 TraesCS4A01G292800 chr4D 8148453 8153028 4575 True 1110.000000 1993 88.948750 90 4001 4 chr4D.!!$R2 3911
2 TraesCS4A01G292800 chr4D 7991471 7995423 3952 False 780.000000 1877 86.922000 17 3541 4 chr4D.!!$F1 3524
3 TraesCS4A01G292800 chr4B 15259121 15263554 4433 True 1181.750000 1531 88.331500 115 4328 4 chr4B.!!$R7 4213
4 TraesCS4A01G292800 chr4B 15146178 15151118 4940 True 944.333333 1380 89.819000 426 3452 3 chr4B.!!$R4 3026
5 TraesCS4A01G292800 chr4B 15176747 15177540 793 True 885.000000 885 86.774000 3522 4328 1 chr4B.!!$R1 806
6 TraesCS4A01G292800 chr4B 15427031 15433192 6161 True 869.200000 1943 88.215400 104 3700 5 chr4B.!!$R8 3596
7 TraesCS4A01G292800 chr4B 15197164 15201362 4198 True 821.500000 1184 86.889500 80 4328 4 chr4B.!!$R6 4248
8 TraesCS4A01G292800 chr4B 14837366 14844237 6871 True 758.166667 1463 87.503333 80 4188 6 chr4B.!!$R2 4108
9 TraesCS4A01G292800 chr4B 15182312 15186193 3881 True 688.600000 1157 87.521000 85 3451 5 chr4B.!!$R5 3366
10 TraesCS4A01G292800 chr4B 15128295 15130611 2316 True 545.750000 998 91.837500 3444 4391 2 chr4B.!!$R3 947

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
680 1455 0.393077 GCGGTGTCACTGCCCTATAT 59.607 55.0 23.92 0.00 44.50 0.86 F
1354 3050 0.371645 GACGAGCTGGAATTTCTGCG 59.628 55.0 9.71 0.17 36.82 5.18 F
1868 3629 0.756294 TTCAGACCAGAACGGCTTGA 59.244 50.0 0.00 0.00 39.03 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2156 4024 1.261619 GTTCCGCGGAGATATTTGCTG 59.738 52.381 29.20 0.0 0.0 4.41 R
3049 8962 0.327770 TTAAATACCCCCTCCGCCCT 60.328 55.000 0.00 0.0 0.0 5.19 R
3535 10044 0.944386 GTGTCGTTGCACCAACAGAT 59.056 50.000 8.59 0.0 43.7 2.90 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
51 52 0.456995 TATCATGTTGCGACGCACGA 60.457 50.000 24.42 16.57 45.77 4.35
56 57 2.126267 TTGCGACGCACGAGCATA 60.126 55.556 24.42 2.41 45.77 3.14
59 60 2.568912 GCGACGCACGAGCATAGTC 61.569 63.158 16.42 3.59 45.77 2.59
106 109 5.579511 AGTTATGTTTCCATCCGTTCTAACG 59.420 40.000 8.24 8.24 40.94 3.18
234 245 9.434420 AGATGAAGATAAAATACTCAGCATAGC 57.566 33.333 0.00 0.00 0.00 2.97
336 349 6.118852 GCATCCAAAGATCTTTCCTACTTCT 58.881 40.000 17.91 0.00 0.00 2.85
343 356 9.061435 CAAAGATCTTTCCTACTTCTTTGTCTT 57.939 33.333 17.91 0.00 43.98 3.01
372 386 2.423926 TCGAAGTGTCACTCTGAAGC 57.576 50.000 5.82 0.00 0.00 3.86
402 473 3.438087 CCCGGCATGAGATTGTGATATTC 59.562 47.826 0.00 0.00 0.00 1.75
424 499 1.560923 CAGGGACGAATTAGCACGAG 58.439 55.000 0.00 0.00 0.00 4.18
433 511 6.018994 GGACGAATTAGCACGAGAAATATTGT 60.019 38.462 0.00 0.00 0.00 2.71
542 1288 5.777526 AGGGGGTGCAAAATATCATTTTT 57.222 34.783 0.00 0.00 0.00 1.94
609 1360 1.891150 CTCCCATGCATTATTGGCCTC 59.109 52.381 3.32 0.00 0.00 4.70
678 1453 2.584608 GCGGTGTCACTGCCCTAT 59.415 61.111 23.92 0.00 44.50 2.57
679 1454 1.820581 GCGGTGTCACTGCCCTATA 59.179 57.895 23.92 0.00 44.50 1.31
680 1455 0.393077 GCGGTGTCACTGCCCTATAT 59.607 55.000 23.92 0.00 44.50 0.86
681 1456 1.605712 GCGGTGTCACTGCCCTATATC 60.606 57.143 23.92 0.00 44.50 1.63
682 1457 1.964223 CGGTGTCACTGCCCTATATCT 59.036 52.381 2.35 0.00 0.00 1.98
683 1458 3.154710 CGGTGTCACTGCCCTATATCTA 58.845 50.000 2.35 0.00 0.00 1.98
684 1459 3.764434 CGGTGTCACTGCCCTATATCTAT 59.236 47.826 2.35 0.00 0.00 1.98
685 1460 4.948004 CGGTGTCACTGCCCTATATCTATA 59.052 45.833 2.35 0.00 0.00 1.31
686 1461 5.594725 CGGTGTCACTGCCCTATATCTATAT 59.405 44.000 2.35 0.00 0.00 0.86
687 1462 6.771267 CGGTGTCACTGCCCTATATCTATATA 59.229 42.308 2.35 0.00 0.00 0.86
688 1463 7.284716 CGGTGTCACTGCCCTATATCTATATAA 59.715 40.741 2.35 0.00 0.00 0.98
689 1464 8.634444 GGTGTCACTGCCCTATATCTATATAAG 58.366 40.741 2.35 0.00 0.00 1.73
690 1465 8.634444 GTGTCACTGCCCTATATCTATATAAGG 58.366 40.741 0.00 1.64 32.39 2.69
691 1466 7.287927 TGTCACTGCCCTATATCTATATAAGGC 59.712 40.741 17.41 17.41 46.17 4.35
698 1473 9.907229 GCCCTATATCTATATAAGGCAAAACTT 57.093 33.333 18.62 0.00 45.67 2.66
704 1479 8.747538 ATCTATATAAGGCAAAACTTTCCGTT 57.252 30.769 0.00 0.00 37.47 4.44
705 1480 7.981142 TCTATATAAGGCAAAACTTTCCGTTG 58.019 34.615 0.00 0.00 35.61 4.10
706 1481 1.934589 AAGGCAAAACTTTCCGTTGC 58.065 45.000 0.00 0.00 45.48 4.17
707 1482 1.111277 AGGCAAAACTTTCCGTTGCT 58.889 45.000 7.46 0.00 45.50 3.91
708 1483 1.480545 AGGCAAAACTTTCCGTTGCTT 59.519 42.857 7.46 0.00 45.50 3.91
709 1484 1.858458 GGCAAAACTTTCCGTTGCTTC 59.142 47.619 7.46 0.00 45.50 3.86
710 1485 2.481276 GGCAAAACTTTCCGTTGCTTCT 60.481 45.455 7.46 0.00 45.50 2.85
711 1486 3.186909 GCAAAACTTTCCGTTGCTTCTT 58.813 40.909 0.53 0.00 43.40 2.52
712 1487 3.616821 GCAAAACTTTCCGTTGCTTCTTT 59.383 39.130 0.53 0.00 43.40 2.52
713 1488 4.492409 GCAAAACTTTCCGTTGCTTCTTTG 60.492 41.667 0.53 0.00 43.40 2.77
714 1489 3.436700 AACTTTCCGTTGCTTCTTTGG 57.563 42.857 0.00 0.00 33.72 3.28
715 1490 1.681264 ACTTTCCGTTGCTTCTTTGGG 59.319 47.619 0.00 0.00 0.00 4.12
764 1585 4.044308 TGGAGGGGACTTGCTAATCATAA 58.956 43.478 0.00 0.00 44.43 1.90
818 1660 6.015603 AGGTAAGTAGTGTACTGAGTTTGGAC 60.016 42.308 0.00 0.00 39.39 4.02
900 2548 4.213482 CAGTTTGGTTTAGAAGGTTCTCGG 59.787 45.833 0.00 0.00 38.70 4.63
911 2559 5.190677 AGAAGGTTCTCGGAAACTTTTCAA 58.809 37.500 15.23 0.00 33.97 2.69
1065 2732 4.087892 CAGGAGCACCCAGACCCG 62.088 72.222 0.00 0.00 37.41 5.28
1221 2888 1.303888 AGACGGTAGCGGAGGTTCA 60.304 57.895 19.72 0.00 40.68 3.18
1350 3046 0.721718 CCGTGACGAGCTGGAATTTC 59.278 55.000 6.54 0.00 0.00 2.17
1351 3047 1.673033 CCGTGACGAGCTGGAATTTCT 60.673 52.381 6.54 0.00 0.00 2.52
1352 3048 1.391485 CGTGACGAGCTGGAATTTCTG 59.609 52.381 0.00 0.00 0.00 3.02
1353 3049 1.129437 GTGACGAGCTGGAATTTCTGC 59.871 52.381 7.50 7.50 0.00 4.26
1354 3050 0.371645 GACGAGCTGGAATTTCTGCG 59.628 55.000 9.71 0.17 36.82 5.18
1355 3051 1.061570 CGAGCTGGAATTTCTGCGC 59.938 57.895 9.71 9.32 36.82 6.09
1356 3052 1.431036 GAGCTGGAATTTCTGCGCC 59.569 57.895 4.18 3.20 36.82 6.53
1357 3053 2.100991 GCTGGAATTTCTGCGCCG 59.899 61.111 4.18 0.00 0.00 6.46
1358 3054 2.100991 CTGGAATTTCTGCGCCGC 59.899 61.111 4.18 0.00 0.00 6.53
1647 3382 4.141711 ACACCTGCACTTAGTTCTTCTTCA 60.142 41.667 0.00 0.00 0.00 3.02
1866 3627 1.543429 CCTTTCAGACCAGAACGGCTT 60.543 52.381 0.00 0.00 39.03 4.35
1868 3629 0.756294 TTCAGACCAGAACGGCTTGA 59.244 50.000 0.00 0.00 39.03 3.02
1882 3643 3.263503 CTTGACCTCGTCGGCGTCA 62.264 63.158 10.18 2.55 39.49 4.35
2104 3865 1.007387 CACGGCCAAGGCAAGTTTC 60.007 57.895 13.87 0.00 44.11 2.78
2105 3866 1.454847 ACGGCCAAGGCAAGTTTCA 60.455 52.632 13.87 0.00 44.11 2.69
2127 3892 7.300556 TCATTCCTTGATTTCACATTTCCAA 57.699 32.000 0.00 0.00 0.00 3.53
2237 6662 8.631797 TGTTTCATCAACCCAACATATATGATG 58.368 33.333 19.63 16.77 43.31 3.07
2487 7503 1.664873 GGGCACGGAATTTCTAGACC 58.335 55.000 0.00 0.00 0.00 3.85
2521 7537 5.803552 TGTATCTCAACATGTGGACATCAA 58.196 37.500 0.00 0.00 33.61 2.57
2542 7560 3.454371 ACGGCTTAATTAGAGCATCGT 57.546 42.857 16.35 14.56 42.67 3.73
2564 7585 8.554835 TCGTCTTAGATATAGGACAATCTCAG 57.445 38.462 9.88 0.00 34.36 3.35
2625 7649 5.867903 TGGACCAAAAAGACATTCATGTT 57.132 34.783 0.00 0.00 41.95 2.71
2643 7667 6.602179 TCATGTTTCGAAGACAATGTGATTC 58.398 36.000 14.24 0.00 34.32 2.52
2651 7675 4.978083 AGACAATGTGATTCCAATGCTC 57.022 40.909 0.00 0.00 0.00 4.26
2723 8375 9.055248 CATTGTTTTAAGCTGAATAGTTCGAAG 57.945 33.333 0.00 0.00 0.00 3.79
2774 8430 7.253950 CCGGCAAAACTTAAAAATTGGATATCG 60.254 37.037 0.00 0.00 0.00 2.92
2775 8431 7.486551 CGGCAAAACTTAAAAATTGGATATCGA 59.513 33.333 0.00 0.00 0.00 3.59
2776 8432 9.313118 GGCAAAACTTAAAAATTGGATATCGAT 57.687 29.630 2.16 2.16 0.00 3.59
2794 8450 5.509716 TCGATCATACCGTCATAGTTGTT 57.490 39.130 0.00 0.00 0.00 2.83
2798 8454 6.577800 CGATCATACCGTCATAGTTGTTCTAC 59.422 42.308 0.00 0.00 0.00 2.59
2819 8475 5.099042 ACGATGGCCTTAACTAATGTTCT 57.901 39.130 3.32 0.00 37.59 3.01
2873 8529 5.047802 TGAGGAAGCTTCTTAATTTGCAAGG 60.048 40.000 25.05 0.00 0.00 3.61
2996 8909 2.548904 ACTGTACGGACGAGCTGATATC 59.451 50.000 9.17 0.00 0.00 1.63
3049 8962 2.556559 GGCCCTAACCCAGTGAAATTCA 60.557 50.000 0.00 0.00 0.00 2.57
3054 8967 0.609131 ACCCAGTGAAATTCAGGGCG 60.609 55.000 17.31 9.28 35.80 6.13
3056 8969 0.322456 CCAGTGAAATTCAGGGCGGA 60.322 55.000 0.00 0.00 0.00 5.54
3059 8972 1.032114 GTGAAATTCAGGGCGGAGGG 61.032 60.000 0.00 0.00 0.00 4.30
3085 9001 9.197306 GGGTATTTAATATTGAGTTTGGAAGGT 57.803 33.333 0.00 0.00 0.00 3.50
3109 9413 6.489127 TCCGTAGAATGTTTGTAAATGGTG 57.511 37.500 0.00 0.00 0.00 4.17
3119 9423 6.500041 TGTTTGTAAATGGTGTAGCACTTTC 58.500 36.000 0.00 0.00 34.40 2.62
3122 9434 3.896648 AAATGGTGTAGCACTTTCGTG 57.103 42.857 0.00 0.00 44.07 4.35
3135 9447 4.083537 GCACTTTCGTGTGATGACCATTAA 60.084 41.667 9.37 0.00 43.16 1.40
3136 9448 5.391950 GCACTTTCGTGTGATGACCATTAAT 60.392 40.000 9.37 0.00 43.16 1.40
3193 9507 3.020647 ATGCATGTTCCCCCGGGA 61.021 61.111 26.32 0.00 43.52 5.14
3315 9651 0.108329 ATGAGGGCTTCACCGTTACG 60.108 55.000 0.00 0.00 38.99 3.18
3352 9688 1.797635 GAAGACTCAACTCTGTGCTGC 59.202 52.381 0.00 0.00 0.00 5.25
3381 9717 0.460987 GCAGCTGCACTTCTACCGAT 60.461 55.000 33.36 0.00 41.59 4.18
3431 9775 8.080417 ACATGTCATATGTATAGTACGGAACAC 58.920 37.037 1.90 0.00 0.00 3.32
3472 9979 0.545309 TGGAAGTGGTGAGAGGGAGG 60.545 60.000 0.00 0.00 0.00 4.30
3473 9980 1.268283 GGAAGTGGTGAGAGGGAGGG 61.268 65.000 0.00 0.00 0.00 4.30
3474 9981 1.904990 GAAGTGGTGAGAGGGAGGGC 61.905 65.000 0.00 0.00 0.00 5.19
3475 9982 2.607750 GTGGTGAGAGGGAGGGCA 60.608 66.667 0.00 0.00 0.00 5.36
3480 9987 2.372890 TGAGAGGGAGGGCATGCAG 61.373 63.158 21.36 0.00 0.00 4.41
3641 10150 1.073177 GCTGCATGCAAATTGTGGAC 58.927 50.000 22.88 1.17 42.31 4.02
3728 12032 4.741928 ACCACAGGGAATCCTAGTTTTT 57.258 40.909 0.00 0.00 42.67 1.94
3776 12080 4.109050 GACGAAAAATTCAGCCAACACAA 58.891 39.130 0.00 0.00 0.00 3.33
3845 12156 8.214721 ACTCAAAGAGTTCTTTCTTTAGGTTG 57.785 34.615 4.20 0.00 43.62 3.77
3866 12177 3.130340 TGGCTTGAAGAAACCAACTCAAC 59.870 43.478 0.00 0.00 0.00 3.18
3951 12263 1.476471 CCATGCCCAAAAAGCCAAACA 60.476 47.619 0.00 0.00 0.00 2.83
3966 12278 3.944650 GCCAAACAACAAGGAAACCAATT 59.055 39.130 0.00 0.00 0.00 2.32
4021 12333 2.874245 TCCCCTCCTGTCTCCCCA 60.874 66.667 0.00 0.00 0.00 4.96
4040 12352 2.030562 CGACACAAACGAGCCCCT 59.969 61.111 0.00 0.00 0.00 4.79
4045 12357 2.594303 CAAACGAGCCCCTGTGCA 60.594 61.111 0.00 0.00 0.00 4.57
4048 12360 2.129555 AAACGAGCCCCTGTGCATCT 62.130 55.000 0.00 0.00 0.00 2.90
4071 12383 3.089217 TGCGATCCCATGCCTCCA 61.089 61.111 0.00 0.00 0.00 3.86
4074 12386 2.111878 GATCCCATGCCTCCACCG 59.888 66.667 0.00 0.00 0.00 4.94
4077 12389 0.986019 ATCCCATGCCTCCACCGTTA 60.986 55.000 0.00 0.00 0.00 3.18
4078 12390 1.202099 TCCCATGCCTCCACCGTTAA 61.202 55.000 0.00 0.00 0.00 2.01
4079 12391 0.322997 CCCATGCCTCCACCGTTAAA 60.323 55.000 0.00 0.00 0.00 1.52
4091 12403 4.409574 TCCACCGTTAAAAGCCTCCATATA 59.590 41.667 0.00 0.00 0.00 0.86
4098 12410 9.063615 CCGTTAAAAGCCTCCATATAAAGTAAT 57.936 33.333 0.00 0.00 0.00 1.89
4121 12433 0.603065 GGCCCTCCAACAACACAATC 59.397 55.000 0.00 0.00 0.00 2.67
4144 12456 8.954950 ATCTCAAGAATTATTCAAGACATCGT 57.045 30.769 7.74 0.00 0.00 3.73
4217 12529 0.899720 CCAAAATGCCATGCTGGAGT 59.100 50.000 6.40 0.00 40.96 3.85
4219 12531 0.899720 AAAATGCCATGCTGGAGTGG 59.100 50.000 6.40 0.00 40.96 4.00
4253 12565 2.491693 ACCAAGGCATTAACATCAACCG 59.508 45.455 0.00 0.00 0.00 4.44
4257 12569 0.450184 GCATTAACATCAACCGCCGT 59.550 50.000 0.00 0.00 0.00 5.68
4271 12583 3.047877 CCGTCCTTGACAACGCCC 61.048 66.667 0.00 0.00 37.56 6.13
4287 12599 1.127951 CGCCCAACTACGACAAATGTC 59.872 52.381 3.43 3.43 41.47 3.06
4306 12618 3.322541 TGTCATCCGACCACTTAAGTTCA 59.677 43.478 5.07 0.00 41.85 3.18
4313 12625 4.994852 CCGACCACTTAAGTTCAGATGAAA 59.005 41.667 5.07 0.00 35.58 2.69
4320 12632 9.617975 CCACTTAAGTTCAGATGAAAGATTTTC 57.382 33.333 5.07 0.00 35.58 2.29
4328 12640 7.149569 TCAGATGAAAGATTTTCACCATGAC 57.850 36.000 6.40 0.00 0.00 3.06
4331 14024 6.878923 AGATGAAAGATTTTCACCATGACGTA 59.121 34.615 6.40 0.00 0.00 3.57
4334 14027 4.207891 AGATTTTCACCATGACGTAGCT 57.792 40.909 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.878769 TGCGTCGCAACATGATATAAATATTAT 58.121 29.630 19.38 0.00 34.76 1.28
23 24 8.166066 GTGCGTCGCAACATGATATAAATATTA 58.834 33.333 23.58 0.00 41.47 0.98
34 35 2.355244 TCGTGCGTCGCAACATGA 60.355 55.556 23.58 14.42 41.47 3.07
35 36 2.094539 CTCGTGCGTCGCAACATG 59.905 61.111 23.58 12.25 41.47 3.21
36 37 3.777925 GCTCGTGCGTCGCAACAT 61.778 61.111 23.58 0.00 41.47 2.71
43 44 0.661552 TAGGACTATGCTCGTGCGTC 59.338 55.000 7.57 7.38 43.34 5.19
106 109 3.436700 AAGCACTTGCAACCTTTACAC 57.563 42.857 3.62 0.00 45.16 2.90
234 245 4.044426 TCGATGCTGATGTCTTATTCGTG 58.956 43.478 0.00 0.00 0.00 4.35
336 349 6.990349 ACACTTCGATAAAAGGAGAAGACAAA 59.010 34.615 10.50 0.00 41.73 2.83
343 356 5.477291 AGAGTGACACTTCGATAAAAGGAGA 59.523 40.000 10.01 0.00 0.00 3.71
402 473 1.369625 GTGCTAATTCGTCCCTGGTG 58.630 55.000 0.00 0.00 0.00 4.17
404 475 0.174845 TCGTGCTAATTCGTCCCTGG 59.825 55.000 0.00 0.00 0.00 4.45
582 1330 5.353938 CCAATAATGCATGGGAGAAAACAG 58.646 41.667 0.00 0.00 32.87 3.16
609 1360 0.627986 AATGGCTCCTCCCTTTCCAG 59.372 55.000 0.00 0.00 0.00 3.86
678 1453 9.841295 AACGGAAAGTTTTGCCTTATATAGATA 57.159 29.630 0.00 0.00 40.88 1.98
679 1454 8.621286 CAACGGAAAGTTTTGCCTTATATAGAT 58.379 33.333 0.00 0.00 42.02 1.98
680 1455 7.414762 GCAACGGAAAGTTTTGCCTTATATAGA 60.415 37.037 0.00 0.00 42.02 1.98
681 1456 6.691388 GCAACGGAAAGTTTTGCCTTATATAG 59.309 38.462 0.00 0.00 42.02 1.31
682 1457 6.376018 AGCAACGGAAAGTTTTGCCTTATATA 59.624 34.615 6.42 0.00 45.58 0.86
683 1458 5.185056 AGCAACGGAAAGTTTTGCCTTATAT 59.815 36.000 6.42 0.00 45.58 0.86
684 1459 4.521256 AGCAACGGAAAGTTTTGCCTTATA 59.479 37.500 6.42 0.00 45.58 0.98
685 1460 3.320826 AGCAACGGAAAGTTTTGCCTTAT 59.679 39.130 6.42 0.00 45.58 1.73
686 1461 2.691011 AGCAACGGAAAGTTTTGCCTTA 59.309 40.909 6.42 0.00 45.58 2.69
687 1462 1.480545 AGCAACGGAAAGTTTTGCCTT 59.519 42.857 6.42 0.00 45.58 4.35
688 1463 1.111277 AGCAACGGAAAGTTTTGCCT 58.889 45.000 6.42 0.00 45.58 4.75
689 1464 1.858458 GAAGCAACGGAAAGTTTTGCC 59.142 47.619 6.42 0.00 45.58 4.52
690 1465 2.809446 AGAAGCAACGGAAAGTTTTGC 58.191 42.857 2.39 2.39 44.93 3.68
691 1466 4.032786 CCAAAGAAGCAACGGAAAGTTTTG 59.967 41.667 0.00 0.00 42.02 2.44
692 1467 4.180817 CCAAAGAAGCAACGGAAAGTTTT 58.819 39.130 0.00 0.00 42.02 2.43
693 1468 3.430236 CCCAAAGAAGCAACGGAAAGTTT 60.430 43.478 0.00 0.00 42.02 2.66
694 1469 2.100749 CCCAAAGAAGCAACGGAAAGTT 59.899 45.455 0.00 0.00 45.45 2.66
695 1470 1.681264 CCCAAAGAAGCAACGGAAAGT 59.319 47.619 0.00 0.00 0.00 2.66
696 1471 1.681264 ACCCAAAGAAGCAACGGAAAG 59.319 47.619 0.00 0.00 0.00 2.62
697 1472 1.770294 ACCCAAAGAAGCAACGGAAA 58.230 45.000 0.00 0.00 0.00 3.13
698 1473 2.500229 CTACCCAAAGAAGCAACGGAA 58.500 47.619 0.00 0.00 0.00 4.30
699 1474 1.880646 GCTACCCAAAGAAGCAACGGA 60.881 52.381 0.00 0.00 36.26 4.69
700 1475 0.521735 GCTACCCAAAGAAGCAACGG 59.478 55.000 0.00 0.00 36.26 4.44
701 1476 0.165944 CGCTACCCAAAGAAGCAACG 59.834 55.000 0.00 0.00 35.98 4.10
702 1477 0.109735 GCGCTACCCAAAGAAGCAAC 60.110 55.000 0.00 0.00 35.98 4.17
703 1478 0.250727 AGCGCTACCCAAAGAAGCAA 60.251 50.000 8.99 0.00 35.98 3.91
704 1479 0.955428 CAGCGCTACCCAAAGAAGCA 60.955 55.000 10.99 0.00 35.98 3.91
705 1480 1.796796 CAGCGCTACCCAAAGAAGC 59.203 57.895 10.99 0.00 0.00 3.86
706 1481 0.955428 TGCAGCGCTACCCAAAGAAG 60.955 55.000 10.99 0.00 0.00 2.85
707 1482 0.322456 ATGCAGCGCTACCCAAAGAA 60.322 50.000 10.99 0.00 0.00 2.52
708 1483 1.026182 CATGCAGCGCTACCCAAAGA 61.026 55.000 10.99 0.00 0.00 2.52
709 1484 1.430632 CATGCAGCGCTACCCAAAG 59.569 57.895 10.99 0.00 0.00 2.77
710 1485 2.699768 GCATGCAGCGCTACCCAAA 61.700 57.895 10.99 0.00 0.00 3.28
711 1486 3.133464 GCATGCAGCGCTACCCAA 61.133 61.111 10.99 0.00 0.00 4.12
764 1585 3.988976 TCCTAAGCTTGCAGAAGATGT 57.011 42.857 9.86 0.00 0.00 3.06
818 1660 8.206325 TGTACGTTACTATAAGAGGAGTCTTG 57.794 38.462 0.00 0.00 43.29 3.02
900 2548 8.794335 ACCTAGATAGATGGTTGAAAAGTTTC 57.206 34.615 0.00 0.00 37.69 2.78
911 2559 6.384305 AGCACAGTTTAACCTAGATAGATGGT 59.616 38.462 0.00 0.00 35.29 3.55
1075 2742 3.103911 GGAGTCGCCGTTGACGTG 61.104 66.667 0.00 0.00 43.70 4.49
1184 2851 1.872679 GTAGTTTCGCCGGAGCTCG 60.873 63.158 5.05 0.00 36.60 5.03
1647 3382 6.655003 ACACTGAGATGATTTATTTTCGTGGT 59.345 34.615 0.00 0.00 0.00 4.16
1814 3566 2.109126 GGCGCGGCTTCTTCTTGAT 61.109 57.895 27.05 0.00 0.00 2.57
1866 3627 3.047718 GATGACGCCGACGAGGTCA 62.048 63.158 18.66 18.66 44.00 4.02
1868 3629 4.175489 CGATGACGCCGACGAGGT 62.175 66.667 0.00 0.00 43.93 3.85
2104 3865 6.369615 GGTTGGAAATGTGAAATCAAGGAATG 59.630 38.462 0.00 0.00 0.00 2.67
2105 3866 6.043012 TGGTTGGAAATGTGAAATCAAGGAAT 59.957 34.615 0.00 0.00 0.00 3.01
2127 3892 9.920946 ATCATTTACCTACTGTGAATAATTGGT 57.079 29.630 0.00 0.00 31.89 3.67
2156 4024 1.261619 GTTCCGCGGAGATATTTGCTG 59.738 52.381 29.20 0.00 0.00 4.41
2212 6637 7.596248 GCATCATATATGTTGGGTTGATGAAAC 59.404 37.037 20.31 1.69 41.74 2.78
2237 6662 7.246171 TCTTATAATAGTGAATGGAGGGAGC 57.754 40.000 0.00 0.00 0.00 4.70
2292 6726 8.128582 GTGTGTTTGTTCATTCATTTCAGTCTA 58.871 33.333 0.00 0.00 0.00 2.59
2294 6728 6.974622 AGTGTGTTTGTTCATTCATTTCAGTC 59.025 34.615 0.00 0.00 0.00 3.51
2305 6739 3.502191 AAACGCAGTGTGTTTGTTCAT 57.498 38.095 29.01 8.49 45.00 2.57
2467 7483 1.287425 GTCTAGAAATTCCGTGCCCG 58.713 55.000 0.00 0.00 0.00 6.13
2484 7500 5.854010 TGAGATACATGTAGAAGTGGGTC 57.146 43.478 11.91 1.44 0.00 4.46
2487 7503 7.474398 CATGTTGAGATACATGTAGAAGTGG 57.526 40.000 11.91 0.00 46.53 4.00
2521 7537 3.793559 ACGATGCTCTAATTAAGCCGTT 58.206 40.909 13.55 3.52 35.19 4.44
2564 7585 8.644318 TTCGGTTTAGCTAAATCTAAGTCATC 57.356 34.615 23.56 7.54 31.01 2.92
2625 7649 5.619757 GCATTGGAATCACATTGTCTTCGAA 60.620 40.000 0.00 0.00 0.00 3.71
2643 7667 5.717038 AAAACAAAACTTTCGAGCATTGG 57.283 34.783 0.00 0.00 0.00 3.16
2651 7675 5.579119 AGCCCAGTTTAAAACAAAACTTTCG 59.421 36.000 0.00 0.00 45.20 3.46
2708 8360 4.864916 TGAATGCTTCGAACTATTCAGC 57.135 40.909 20.24 10.90 35.34 4.26
2736 8388 1.280457 TTTGCCGGGGCCAATATTTT 58.720 45.000 4.39 0.00 41.09 1.82
2740 8394 0.543174 AAGTTTTGCCGGGGCCAATA 60.543 50.000 4.39 0.00 41.09 1.90
2757 8411 9.973246 CGGTATGATCGATATCCAATTTTTAAG 57.027 33.333 0.00 0.00 0.00 1.85
2774 8430 6.577800 CGTAGAACAACTATGACGGTATGATC 59.422 42.308 0.00 0.00 39.67 2.92
2775 8431 6.261603 TCGTAGAACAACTATGACGGTATGAT 59.738 38.462 0.00 0.00 40.78 2.45
2776 8432 5.585844 TCGTAGAACAACTATGACGGTATGA 59.414 40.000 0.00 0.00 40.78 2.15
2777 8433 5.813717 TCGTAGAACAACTATGACGGTATG 58.186 41.667 0.00 0.00 40.78 2.39
2794 8450 5.864418 ACATTAGTTAAGGCCATCGTAGA 57.136 39.130 5.01 0.00 45.75 2.59
2798 8454 4.876107 ACAGAACATTAGTTAAGGCCATCG 59.124 41.667 5.01 0.00 38.30 3.84
2819 8475 8.151596 TGCGGGATAGATTATGTATTTTGTACA 58.848 33.333 0.00 0.00 0.00 2.90
2888 8547 8.649841 CGATAGTACGTTTGTGGAATTTTCTAA 58.350 33.333 0.00 0.00 0.00 2.10
2996 8909 6.494893 TTTATTCTCCAACCAAATCTCACG 57.505 37.500 0.00 0.00 0.00 4.35
3033 8946 2.802719 GCCCTGAATTTCACTGGGTTA 58.197 47.619 19.59 0.00 44.68 2.85
3034 8947 1.632589 GCCCTGAATTTCACTGGGTT 58.367 50.000 19.59 0.00 44.68 4.11
3049 8962 0.327770 TTAAATACCCCCTCCGCCCT 60.328 55.000 0.00 0.00 0.00 5.19
3054 8967 7.232737 CCAAACTCAATATTAAATACCCCCTCC 59.767 40.741 0.00 0.00 0.00 4.30
3056 8969 7.889178 TCCAAACTCAATATTAAATACCCCCT 58.111 34.615 0.00 0.00 0.00 4.79
3059 8972 9.197306 ACCTTCCAAACTCAATATTAAATACCC 57.803 33.333 0.00 0.00 0.00 3.69
3085 9001 6.487331 ACACCATTTACAAACATTCTACGGAA 59.513 34.615 0.00 0.00 35.78 4.30
3098 9014 4.817464 ACGAAAGTGCTACACCATTTACAA 59.183 37.500 0.00 0.00 46.97 2.41
3119 9423 9.566530 TCAATAAAAATTAATGGTCATCACACG 57.433 29.630 0.00 0.00 0.00 4.49
3198 9512 7.005062 ACGTATGAACAAACATGATTAGCTC 57.995 36.000 0.00 0.00 0.00 4.09
3315 9651 1.611491 CTTCCTACGATCTCCTCTGCC 59.389 57.143 0.00 0.00 0.00 4.85
3535 10044 0.944386 GTGTCGTTGCACCAACAGAT 59.056 50.000 8.59 0.00 43.70 2.90
3577 10086 4.404394 TGGAATCGTCTACTTGGCTTGATA 59.596 41.667 0.00 0.00 0.00 2.15
3704 12008 3.778622 ACTAGGATTCCCTGTGGTAGT 57.221 47.619 0.00 0.00 44.15 2.73
3705 12009 5.437191 AAAACTAGGATTCCCTGTGGTAG 57.563 43.478 0.00 0.00 44.15 3.18
3728 12032 2.100197 CCAACTCTATGGACTGACCGA 58.900 52.381 0.00 0.00 43.54 4.69
3799 12110 5.380043 AGTCGGTTTTCCTATAGATCCGTA 58.620 41.667 0.00 0.00 36.05 4.02
3845 12156 3.130340 TGTTGAGTTGGTTTCTTCAAGCC 59.870 43.478 0.00 0.00 33.46 4.35
3951 12263 5.023452 GGGAGGATAATTGGTTTCCTTGTT 58.977 41.667 0.00 0.00 39.98 2.83
3966 12278 4.263771 GGTTTTGGTTTGAGAGGGAGGATA 60.264 45.833 0.00 0.00 0.00 2.59
4021 12333 2.665185 GGGCTCGTTTGTGTCGCT 60.665 61.111 0.00 0.00 0.00 4.93
4045 12357 0.691332 ATGGGATCGCAGATGCAGAT 59.309 50.000 18.10 8.47 45.12 2.90
4048 12360 1.895231 GCATGGGATCGCAGATGCA 60.895 57.895 25.20 0.00 45.12 3.96
4056 12368 2.111878 GGTGGAGGCATGGGATCG 59.888 66.667 0.00 0.00 0.00 3.69
4071 12383 6.420638 ACTTTATATGGAGGCTTTTAACGGT 58.579 36.000 0.00 0.00 0.00 4.83
4078 12390 8.204160 GCCAAAATTACTTTATATGGAGGCTTT 58.796 33.333 0.00 0.00 33.38 3.51
4079 12391 7.202001 GGCCAAAATTACTTTATATGGAGGCTT 60.202 37.037 0.00 0.00 36.25 4.35
4121 12433 9.521503 TCTACGATGTCTTGAATAATTCTTGAG 57.478 33.333 0.00 0.00 0.00 3.02
4169 12481 9.896263 TCATGTACGTTTTTCCCTTAAAATAAC 57.104 29.630 0.00 0.00 36.94 1.89
4187 12499 2.227626 TGGCATTTTGGTGTCATGTACG 59.772 45.455 0.00 0.00 0.00 3.67
4220 12532 1.586028 CCTTGGTTCGTGCCATTGG 59.414 57.895 0.00 0.00 38.48 3.16
4231 12543 3.056891 CGGTTGATGTTAATGCCTTGGTT 60.057 43.478 0.00 0.00 0.00 3.67
4257 12569 0.759959 TAGTTGGGCGTTGTCAAGGA 59.240 50.000 9.42 0.00 0.00 3.36
4287 12599 4.188247 TCTGAACTTAAGTGGTCGGATG 57.812 45.455 9.34 0.00 0.00 3.51
4306 12618 5.707298 ACGTCATGGTGAAAATCTTTCATCT 59.293 36.000 12.32 0.00 31.12 2.90
4313 12625 4.081420 AGAGCTACGTCATGGTGAAAATCT 60.081 41.667 0.00 0.00 0.00 2.40
4320 12632 0.532573 ACCAGAGCTACGTCATGGTG 59.467 55.000 8.67 0.00 42.56 4.17
4328 12640 1.153823 CCGGTTCACCAGAGCTACG 60.154 63.158 0.00 0.00 35.14 3.51
4331 14024 0.250513 GAATCCGGTTCACCAGAGCT 59.749 55.000 0.00 0.00 36.80 4.09
4334 14027 0.245539 GTCGAATCCGGTTCACCAGA 59.754 55.000 0.00 0.00 36.60 3.86
4351 14044 1.856265 CGCTTGGGCTTGTTGGAGTC 61.856 60.000 0.00 0.00 36.09 3.36


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

AutoCloner maintained by Alex Coulton.