Multiple sequence alignment - TraesCS1A01G073100

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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 TraesCS1A01G073100 chr1A 100.000 3593 0 0 1 3593 57191510 57195102 0.000000e+00 6636.0
1 TraesCS1A01G073100 chr1A 82.026 1402 217 29 1057 2451 57392133 57390760 0.000000e+00 1160.0
2 TraesCS1A01G073100 chr1A 91.711 374 22 3 47 419 57393054 57392689 8.900000e-141 510.0
3 TraesCS1A01G073100 chr1A 84.000 250 28 7 3155 3401 57194147 57194387 2.790000e-56 230.0
4 TraesCS1A01G073100 chr1A 84.000 250 28 7 2638 2878 57194664 57194910 2.790000e-56 230.0
5 TraesCS1A01G073100 chr1D 95.979 2512 58 15 559 3065 58451133 58453606 0.000000e+00 4039.0
6 TraesCS1A01G073100 chr1D 95.165 455 17 5 3089 3540 58453584 58454036 0.000000e+00 713.0
7 TraesCS1A01G073100 chr1D 92.347 392 19 5 47 434 58450698 58451082 6.780000e-152 547.0
8 TraesCS1A01G073100 chr1D 82.609 253 33 6 3137 3389 58453161 58453402 2.810000e-51 213.0
9 TraesCS1A01G073100 chr1B 91.873 2387 98 42 529 2878 94184856 94182529 0.000000e+00 3245.0
10 TraesCS1A01G073100 chr1B 85.753 1488 157 41 827 2304 94200146 94198704 0.000000e+00 1522.0
11 TraesCS1A01G073100 chr1B 89.762 420 35 2 1 419 94201296 94200884 6.830000e-147 531.0
12 TraesCS1A01G073100 chr1B 85.476 420 30 17 48 465 94185253 94184863 3.340000e-110 409.0
13 TraesCS1A01G073100 chr1B 92.958 71 2 3 3525 3593 44016886 44016955 2.280000e-17 100.0
14 TraesCS1A01G073100 chr1B 94.030 67 2 2 3528 3593 84424624 84424689 2.280000e-17 100.0
15 TraesCS1A01G073100 chr6B 96.774 62 2 0 3532 3593 353859717 353859778 1.760000e-18 104.0
16 TraesCS1A01G073100 chr6B 89.873 79 4 2 3515 3593 26457296 26457370 8.210000e-17 99.0
17 TraesCS1A01G073100 chr6B 93.182 44 2 1 478 521 453407605 453407563 2.990000e-06 63.9
18 TraesCS1A01G073100 chr4B 96.774 62 2 0 3532 3593 20751027 20751088 1.760000e-18 104.0
19 TraesCS1A01G073100 chr4B 91.667 72 3 3 3523 3593 574589738 574589807 2.950000e-16 97.1
20 TraesCS1A01G073100 chr7B 96.721 61 2 0 3533 3593 578116385 578116445 6.350000e-18 102.0
21 TraesCS1A01G073100 chr5A 96.721 61 2 0 3533 3593 645489994 645489934 6.350000e-18 102.0
22 TraesCS1A01G073100 chr5B 91.667 72 1 2 3522 3593 448806166 448806100 1.060000e-15 95.3
23 TraesCS1A01G073100 chr5B 97.436 39 1 0 490 528 707411604 707411566 2.320000e-07 67.6
24 TraesCS1A01G073100 chr5B 97.297 37 1 0 485 521 136053307 136053343 2.990000e-06 63.9
25 TraesCS1A01G073100 chr5D 95.556 45 2 0 484 528 123089579 123089623 4.980000e-09 73.1
26 TraesCS1A01G073100 chr4A 97.436 39 1 0 490 528 585459854 585459892 2.320000e-07 67.6
27 TraesCS1A01G073100 chr3D 97.436 39 1 0 490 528 143250804 143250766 2.320000e-07 67.6
28 TraesCS1A01G073100 chr2A 97.436 39 1 0 488 526 139434843 139434881 2.320000e-07 67.6
29 TraesCS1A01G073100 chr2A 97.436 39 1 0 490 528 756876990 756876952 2.320000e-07 67.6
30 TraesCS1A01G073100 chr2D 97.368 38 0 1 489 526 472231210 472231174 2.990000e-06 63.9


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 TraesCS1A01G073100 chr1A 57191510 57195102 3592 False 2365.333333 6636 89.333333 1 3593 3 chr1A.!!$F1 3592
1 TraesCS1A01G073100 chr1A 57390760 57393054 2294 True 835.000000 1160 86.868500 47 2451 2 chr1A.!!$R1 2404
2 TraesCS1A01G073100 chr1D 58450698 58454036 3338 False 1378.000000 4039 91.525000 47 3540 4 chr1D.!!$F1 3493
3 TraesCS1A01G073100 chr1B 94182529 94185253 2724 True 1827.000000 3245 88.674500 48 2878 2 chr1B.!!$R1 2830
4 TraesCS1A01G073100 chr1B 94198704 94201296 2592 True 1026.500000 1522 87.757500 1 2304 2 chr1B.!!$R2 2303

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
998 1464 0.602638 TGCACTGTTCCATCGTCCAC 60.603 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2604 3070 0.719465 GTATTTGACACTCCGGTGCG 59.281 55.0 0.0 0.0 46.57 5.34 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 6.819146 GCCTAAAAGAGTAGCTTATTGAGTGT 59.181 38.462 0.00 0.00 35.24 3.55
31 32 7.897575 AGAGTAGCTTATTGAGTGTCTTTTG 57.102 36.000 0.00 0.00 0.00 2.44
40 41 9.736023 CTTATTGAGTGTCTTTTGCTAAAAACT 57.264 29.630 0.00 1.82 31.94 2.66
42 43 6.509418 TGAGTGTCTTTTGCTAAAAACTGT 57.491 33.333 7.62 0.00 31.94 3.55
44 45 6.806249 TGAGTGTCTTTTGCTAAAAACTGTTG 59.194 34.615 7.62 0.00 31.94 3.33
132 133 3.643792 AGACTATAGCTGCCAGGTAAAGG 59.356 47.826 7.83 4.04 31.35 3.11
133 134 3.641906 GACTATAGCTGCCAGGTAAAGGA 59.358 47.826 7.83 0.00 31.35 3.36
134 135 4.037927 ACTATAGCTGCCAGGTAAAGGAA 58.962 43.478 7.83 0.00 31.35 3.36
135 136 4.473559 ACTATAGCTGCCAGGTAAAGGAAA 59.526 41.667 7.83 0.00 31.35 3.13
136 137 2.907458 AGCTGCCAGGTAAAGGAAAT 57.093 45.000 0.00 0.00 0.00 2.17
137 138 3.175438 AGCTGCCAGGTAAAGGAAATT 57.825 42.857 0.00 0.00 0.00 1.82
138 139 3.092301 AGCTGCCAGGTAAAGGAAATTC 58.908 45.455 0.00 0.00 0.00 2.17
141 142 3.430453 TGCCAGGTAAAGGAAATTCAGG 58.570 45.455 0.00 0.00 0.00 3.86
143 144 4.086457 GCCAGGTAAAGGAAATTCAGGAA 58.914 43.478 0.00 0.00 0.00 3.36
213 218 8.200120 AGCTATGCTCATTTTTATCCCTTTTTC 58.800 33.333 0.00 0.00 30.62 2.29
228 233 3.433456 CCTTTTTCCAACCAAATGCCACT 60.433 43.478 0.00 0.00 0.00 4.00
238 243 2.352421 CCAAATGCCACTGAAGAAGCAG 60.352 50.000 0.00 0.00 38.89 4.24
347 353 1.819928 TGGACATATGCACAAACGCT 58.180 45.000 1.58 0.00 0.00 5.07
439 445 4.574892 TCTGAAAGGACGCACATGATAAA 58.425 39.130 0.00 0.00 0.00 1.40
440 446 5.185454 TCTGAAAGGACGCACATGATAAAT 58.815 37.500 0.00 0.00 0.00 1.40
441 447 6.345298 TCTGAAAGGACGCACATGATAAATA 58.655 36.000 0.00 0.00 0.00 1.40
442 448 6.257849 TCTGAAAGGACGCACATGATAAATAC 59.742 38.462 0.00 0.00 0.00 1.89
493 501 9.971922 TTTTTAGGGCTAAGTACGAATATACTC 57.028 33.333 0.00 0.00 34.18 2.59
494 502 7.693969 TTAGGGCTAAGTACGAATATACTCC 57.306 40.000 0.00 0.00 34.18 3.85
495 503 5.015515 AGGGCTAAGTACGAATATACTCCC 58.984 45.833 0.00 0.00 37.15 4.30
496 504 5.015515 GGGCTAAGTACGAATATACTCCCT 58.984 45.833 0.00 0.00 35.35 4.20
498 506 5.945191 GGCTAAGTACGAATATACTCCCTCT 59.055 44.000 0.00 0.00 34.18 3.69
502 510 5.315348 AGTACGAATATACTCCCTCTGTCC 58.685 45.833 0.00 0.00 28.86 4.02
503 511 3.498334 ACGAATATACTCCCTCTGTCCC 58.502 50.000 0.00 0.00 0.00 4.46
507 515 2.642171 ATACTCCCTCTGTCCCACAA 57.358 50.000 0.00 0.00 0.00 3.33
513 521 4.656112 ACTCCCTCTGTCCCACAATATAAG 59.344 45.833 0.00 0.00 0.00 1.73
514 522 4.890988 TCCCTCTGTCCCACAATATAAGA 58.109 43.478 0.00 0.00 0.00 2.10
523 531 6.148150 TGTCCCACAATATAAGAACGTTTGTC 59.852 38.462 0.46 0.00 0.00 3.18
557 770 4.666253 TGCCCCTGCTTCACCTGC 62.666 66.667 0.00 0.00 38.71 4.85
577 804 4.769688 TGCGACTGAAGATGGATTTGTAT 58.230 39.130 0.00 0.00 0.00 2.29
579 824 4.572389 GCGACTGAAGATGGATTTGTATGT 59.428 41.667 0.00 0.00 0.00 2.29
613 858 2.506472 GCCGGCTTCTTCCCTAGG 59.494 66.667 22.15 0.06 0.00 3.02
806 1202 5.349817 GCTGACGGAAGCTACGTATATACTA 59.650 44.000 15.23 2.47 45.68 1.82
817 1213 7.601886 AGCTACGTATATACTACCTGTGTGTAG 59.398 40.741 11.05 11.26 43.13 2.74
840 1301 3.657634 CGTACATCATTGAGGGATCCTG 58.342 50.000 12.58 1.15 31.76 3.86
841 1302 3.070159 CGTACATCATTGAGGGATCCTGT 59.930 47.826 12.58 7.94 31.76 4.00
842 1303 3.853355 ACATCATTGAGGGATCCTGTC 57.147 47.619 12.58 9.59 31.76 3.51
889 1352 3.368220 CCATCTCATCATCATCGTCTCCC 60.368 52.174 0.00 0.00 0.00 4.30
890 1353 3.235750 TCTCATCATCATCGTCTCCCT 57.764 47.619 0.00 0.00 0.00 4.20
891 1354 3.153130 TCTCATCATCATCGTCTCCCTC 58.847 50.000 0.00 0.00 0.00 4.30
892 1355 2.889678 CTCATCATCATCGTCTCCCTCA 59.110 50.000 0.00 0.00 0.00 3.86
893 1356 2.889678 TCATCATCATCGTCTCCCTCAG 59.110 50.000 0.00 0.00 0.00 3.35
905 1371 0.619832 TCCCTCAGAGCTGGCATTCT 60.620 55.000 0.00 0.00 0.00 2.40
995 1461 0.944311 ACGTGCACTGTTCCATCGTC 60.944 55.000 16.19 0.00 0.00 4.20
998 1464 0.602638 TGCACTGTTCCATCGTCCAC 60.603 55.000 0.00 0.00 0.00 4.02
1020 1486 1.227409 GCCTAGAGAGCGGCCTTTC 60.227 63.158 0.00 0.00 40.43 2.62
1656 2122 4.452733 GAGTTCGAGGCCACCGGG 62.453 72.222 15.95 0.00 37.18 5.73
2415 2881 1.139947 GCTGGTGACGAGCTACCTC 59.860 63.158 12.50 0.00 37.84 3.85
2603 3069 2.202388 CAGCTGAAATGCACCGCG 60.202 61.111 8.42 0.00 34.99 6.46
2604 3070 4.107051 AGCTGAAATGCACCGCGC 62.107 61.111 0.00 0.00 42.89 6.86
2620 3086 2.970324 GCGCACCGGAGTGTCAAA 60.970 61.111 9.46 0.00 46.35 2.69
2621 3087 2.325082 GCGCACCGGAGTGTCAAAT 61.325 57.895 9.46 0.00 46.35 2.32
2626 3092 2.073816 CACCGGAGTGTCAAATACCAC 58.926 52.381 9.46 0.00 39.30 4.16
2629 3095 2.482721 CCGGAGTGTCAAATACCACAAC 59.517 50.000 0.00 0.00 33.99 3.32
2635 3101 3.312973 GTGTCAAATACCACAACGTCCAA 59.687 43.478 0.00 0.00 0.00 3.53
2807 3302 8.579682 ACTTGAGCTTGATGAATGTTTAAAAC 57.420 30.769 0.00 0.00 0.00 2.43
2907 3402 6.591062 ACACATGCTTTAATATGCCACAAAAG 59.409 34.615 0.00 0.00 0.00 2.27
2975 3470 5.450412 CCAGGAACCGTTAATCAATGAATGG 60.450 44.000 0.00 0.00 37.67 3.16
3065 3565 2.115427 CTCCTTCTTCCTTCCCTCTCC 58.885 57.143 0.00 0.00 0.00 3.71
3066 3566 0.827368 CCTTCTTCCTTCCCTCTCCG 59.173 60.000 0.00 0.00 0.00 4.63
3067 3567 0.827368 CTTCTTCCTTCCCTCTCCGG 59.173 60.000 0.00 0.00 0.00 5.14
3068 3568 0.116541 TTCTTCCTTCCCTCTCCGGT 59.883 55.000 0.00 0.00 0.00 5.28
3069 3569 0.324460 TCTTCCTTCCCTCTCCGGTC 60.324 60.000 0.00 0.00 0.00 4.79
3070 3570 1.305887 TTCCTTCCCTCTCCGGTCC 60.306 63.158 0.00 0.00 0.00 4.46
3071 3571 2.764547 CCTTCCCTCTCCGGTCCC 60.765 72.222 0.00 0.00 0.00 4.46
3072 3572 2.764547 CTTCCCTCTCCGGTCCCC 60.765 72.222 0.00 0.00 0.00 4.81
3073 3573 3.281787 TTCCCTCTCCGGTCCCCT 61.282 66.667 0.00 0.00 0.00 4.79
3074 3574 3.312989 TTCCCTCTCCGGTCCCCTC 62.313 68.421 0.00 0.00 0.00 4.30
3076 3576 4.444081 CCTCTCCGGTCCCCTCGT 62.444 72.222 0.00 0.00 0.00 4.18
3077 3577 3.141488 CTCTCCGGTCCCCTCGTG 61.141 72.222 0.00 0.00 0.00 4.35
3082 3582 4.452733 CGGTCCCCTCGTGCCTTC 62.453 72.222 0.00 0.00 0.00 3.46
3083 3583 4.452733 GGTCCCCTCGTGCCTTCG 62.453 72.222 0.00 0.00 0.00 3.79
3084 3584 3.692406 GTCCCCTCGTGCCTTCGT 61.692 66.667 0.00 0.00 0.00 3.85
3085 3585 3.379445 TCCCCTCGTGCCTTCGTC 61.379 66.667 0.00 0.00 0.00 4.20
3086 3586 4.452733 CCCCTCGTGCCTTCGTCC 62.453 72.222 0.00 0.00 0.00 4.79
3087 3587 3.382832 CCCTCGTGCCTTCGTCCT 61.383 66.667 0.00 0.00 0.00 3.85
3088 3588 2.182030 CCTCGTGCCTTCGTCCTC 59.818 66.667 0.00 0.00 0.00 3.71
3089 3589 2.182030 CTCGTGCCTTCGTCCTCC 59.818 66.667 0.00 0.00 0.00 4.30
3090 3590 3.358076 CTCGTGCCTTCGTCCTCCC 62.358 68.421 0.00 0.00 0.00 4.30
3091 3591 4.452733 CGTGCCTTCGTCCTCCCC 62.453 72.222 0.00 0.00 0.00 4.81
3092 3592 3.003763 GTGCCTTCGTCCTCCCCT 61.004 66.667 0.00 0.00 0.00 4.79
3093 3593 2.683933 TGCCTTCGTCCTCCCCTC 60.684 66.667 0.00 0.00 0.00 4.30
3094 3594 3.471806 GCCTTCGTCCTCCCCTCC 61.472 72.222 0.00 0.00 0.00 4.30
3095 3595 2.364961 CCTTCGTCCTCCCCTCCT 59.635 66.667 0.00 0.00 0.00 3.69
3096 3596 1.758906 CCTTCGTCCTCCCCTCCTC 60.759 68.421 0.00 0.00 0.00 3.71
3097 3597 1.308326 CTTCGTCCTCCCCTCCTCT 59.692 63.158 0.00 0.00 0.00 3.69
3098 3598 0.753848 CTTCGTCCTCCCCTCCTCTC 60.754 65.000 0.00 0.00 0.00 3.20
3099 3599 2.123640 CGTCCTCCCCTCCTCTCC 60.124 72.222 0.00 0.00 0.00 3.71
3100 3600 2.695970 CGTCCTCCCCTCCTCTCCT 61.696 68.421 0.00 0.00 0.00 3.69
3101 3601 1.231928 GTCCTCCCCTCCTCTCCTC 59.768 68.421 0.00 0.00 0.00 3.71
3102 3602 2.015726 TCCTCCCCTCCTCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
3103 3603 2.018086 CCTCCCCTCCTCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
3104 3604 1.541672 CTCCCCTCCTCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
3105 3605 2.015726 TCCCCTCCTCTCCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
3106 3606 2.018086 CCCCTCCTCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
3107 3607 1.598856 CCCCTCCTCTCCTCCTCCTT 61.599 65.000 0.00 0.00 0.00 3.36
3108 3608 0.105709 CCCTCCTCTCCTCCTCCTTC 60.106 65.000 0.00 0.00 0.00 3.46
3116 3616 0.178891 TCCTCCTCCTTCTGCCTTGT 60.179 55.000 0.00 0.00 0.00 3.16
3121 3621 0.034059 CTCCTTCTGCCTTGTCGTGT 59.966 55.000 0.00 0.00 0.00 4.49
3160 3660 7.674240 GCGTCAAGTACCAGAACATTATCTTTC 60.674 40.741 0.00 0.00 0.00 2.62
3163 3663 4.804139 AGTACCAGAACATTATCTTTCGCG 59.196 41.667 0.00 0.00 0.00 5.87
3218 3718 1.921346 TAGTCCACGGGCCCATGTT 60.921 57.895 24.92 7.32 0.00 2.71
3251 3751 9.098355 GTGTGCATATACAAGAGAAGTGATTTA 57.902 33.333 0.00 0.00 31.36 1.40
3317 3817 6.645790 AGAAACTTGAGCTTGATGAATGTT 57.354 33.333 0.00 0.00 0.00 2.71
3540 4040 4.481368 TCACCTCCCATGTTACATACAC 57.519 45.455 0.00 0.00 40.19 2.90
3541 4041 4.101114 TCACCTCCCATGTTACATACACT 58.899 43.478 0.00 0.00 40.19 3.55
3542 4042 5.274015 TCACCTCCCATGTTACATACACTA 58.726 41.667 0.00 0.00 40.19 2.74
3543 4043 5.722441 TCACCTCCCATGTTACATACACTAA 59.278 40.000 0.00 0.00 40.19 2.24
3544 4044 6.213802 TCACCTCCCATGTTACATACACTAAA 59.786 38.462 0.00 0.00 40.19 1.85
3545 4045 6.882140 CACCTCCCATGTTACATACACTAAAA 59.118 38.462 0.00 0.00 40.19 1.52
3546 4046 7.065803 CACCTCCCATGTTACATACACTAAAAG 59.934 40.741 0.00 0.00 40.19 2.27
3547 4047 7.037873 ACCTCCCATGTTACATACACTAAAAGA 60.038 37.037 0.00 0.00 40.19 2.52
3548 4048 7.827236 CCTCCCATGTTACATACACTAAAAGAA 59.173 37.037 0.00 0.00 40.19 2.52
3549 4049 8.556213 TCCCATGTTACATACACTAAAAGAAC 57.444 34.615 0.00 0.00 40.19 3.01
3550 4050 7.332430 TCCCATGTTACATACACTAAAAGAACG 59.668 37.037 0.00 0.00 40.19 3.95
3551 4051 6.959311 CCATGTTACATACACTAAAAGAACGC 59.041 38.462 0.00 0.00 40.19 4.84
3552 4052 6.470557 TGTTACATACACTAAAAGAACGCC 57.529 37.500 0.00 0.00 0.00 5.68
3553 4053 5.409214 TGTTACATACACTAAAAGAACGCCC 59.591 40.000 0.00 0.00 0.00 6.13
3554 4054 2.997986 ACATACACTAAAAGAACGCCCG 59.002 45.455 0.00 0.00 0.00 6.13
3555 4055 2.818130 TACACTAAAAGAACGCCCGT 57.182 45.000 0.00 0.00 0.00 5.28
3556 4056 1.223187 ACACTAAAAGAACGCCCGTG 58.777 50.000 0.00 0.00 0.00 4.94
3557 4057 0.110373 CACTAAAAGAACGCCCGTGC 60.110 55.000 0.00 0.00 0.00 5.34
3575 4075 3.302344 GTTGCAACGGGGCCACAT 61.302 61.111 14.90 0.00 30.39 3.21
3576 4076 2.522923 TTGCAACGGGGCCACATT 60.523 55.556 5.46 0.00 0.00 2.71
3577 4077 1.228583 TTGCAACGGGGCCACATTA 60.229 52.632 5.46 0.00 0.00 1.90
3578 4078 0.827925 TTGCAACGGGGCCACATTAA 60.828 50.000 5.46 0.00 0.00 1.40
3579 4079 1.214325 GCAACGGGGCCACATTAAC 59.786 57.895 5.46 0.00 0.00 2.01
3580 4080 1.248101 GCAACGGGGCCACATTAACT 61.248 55.000 5.46 0.00 0.00 2.24
3581 4081 1.253100 CAACGGGGCCACATTAACTT 58.747 50.000 5.46 0.00 0.00 2.66
3582 4082 1.616374 CAACGGGGCCACATTAACTTT 59.384 47.619 5.46 0.00 0.00 2.66
3583 4083 2.820787 CAACGGGGCCACATTAACTTTA 59.179 45.455 5.46 0.00 0.00 1.85
3584 4084 3.157750 ACGGGGCCACATTAACTTTAA 57.842 42.857 5.46 0.00 0.00 1.52
3585 4085 3.086282 ACGGGGCCACATTAACTTTAAG 58.914 45.455 5.46 0.00 0.00 1.85
3586 4086 3.244981 ACGGGGCCACATTAACTTTAAGA 60.245 43.478 5.46 0.00 0.00 2.10
3587 4087 3.377172 CGGGGCCACATTAACTTTAAGAG 59.623 47.826 5.46 0.00 0.00 2.85
3588 4088 4.341487 GGGGCCACATTAACTTTAAGAGT 58.659 43.478 4.39 0.00 41.47 3.24
3590 4090 5.105877 GGGGCCACATTAACTTTAAGAGTTC 60.106 44.000 4.39 0.00 45.40 3.01
3591 4091 5.475564 GGGCCACATTAACTTTAAGAGTTCA 59.524 40.000 4.39 0.00 45.40 3.18
3592 4092 6.015772 GGGCCACATTAACTTTAAGAGTTCAA 60.016 38.462 4.39 2.81 45.40 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.615878 TTTAGCAAAAGACACTCAATAAGCTA 57.384 30.769 0.00 0.00 0.00 3.32
14 15 9.736023 AGTTTTTAGCAAAAGACACTCAATAAG 57.264 29.630 0.00 0.00 33.28 1.73
20 21 6.806739 ACAACAGTTTTTAGCAAAAGACACTC 59.193 34.615 0.00 0.00 33.28 3.51
23 24 6.919721 AGACAACAGTTTTTAGCAAAAGACA 58.080 32.000 0.00 0.00 33.28 3.41
25 26 9.120538 AGATAGACAACAGTTTTTAGCAAAAGA 57.879 29.630 0.00 0.00 32.32 2.52
31 32 8.774586 TCTGAAAGATAGACAACAGTTTTTAGC 58.225 33.333 0.00 0.00 38.67 3.09
132 133 7.344095 ACATGATTCCTGATTCCTGAATTTC 57.656 36.000 0.00 0.00 0.00 2.17
133 134 7.835682 TGTACATGATTCCTGATTCCTGAATTT 59.164 33.333 0.00 0.00 0.00 1.82
134 135 7.348815 TGTACATGATTCCTGATTCCTGAATT 58.651 34.615 0.00 0.00 0.00 2.17
135 136 6.903516 TGTACATGATTCCTGATTCCTGAAT 58.096 36.000 0.00 0.00 0.00 2.57
136 137 6.312141 TGTACATGATTCCTGATTCCTGAA 57.688 37.500 0.00 0.00 0.00 3.02
137 138 5.955961 TGTACATGATTCCTGATTCCTGA 57.044 39.130 0.00 0.00 0.00 3.86
138 139 6.531923 AGATGTACATGATTCCTGATTCCTG 58.468 40.000 14.43 0.00 0.00 3.86
141 142 6.485984 AGCAAGATGTACATGATTCCTGATTC 59.514 38.462 14.43 0.00 0.00 2.52
143 144 5.938279 AGCAAGATGTACATGATTCCTGAT 58.062 37.500 14.43 0.00 0.00 2.90
213 218 1.962807 TCTTCAGTGGCATTTGGTTGG 59.037 47.619 0.00 0.00 0.00 3.77
228 233 5.227569 TGTTATTGGAGACTGCTTCTTCA 57.772 39.130 0.00 0.00 38.18 3.02
238 243 4.154195 ACGAGCAACATTGTTATTGGAGAC 59.846 41.667 0.86 0.00 0.00 3.36
295 301 2.358737 GGGCCTTGTCCGTGTCAG 60.359 66.667 0.84 0.00 0.00 3.51
296 302 2.847234 AGGGCCTTGTCCGTGTCA 60.847 61.111 0.00 0.00 29.39 3.58
470 478 6.660949 GGGAGTATATTCGTACTTAGCCCTAA 59.339 42.308 0.00 0.00 35.16 2.69
471 479 6.012157 AGGGAGTATATTCGTACTTAGCCCTA 60.012 42.308 9.05 0.00 41.36 3.53
473 481 5.015515 AGGGAGTATATTCGTACTTAGCCC 58.984 45.833 0.00 0.00 36.89 5.19
474 482 5.945191 AGAGGGAGTATATTCGTACTTAGCC 59.055 44.000 0.00 0.00 35.14 3.93
475 483 6.430616 ACAGAGGGAGTATATTCGTACTTAGC 59.569 42.308 0.00 0.00 35.14 3.09
476 484 7.119553 GGACAGAGGGAGTATATTCGTACTTAG 59.880 44.444 0.00 0.00 35.14 2.18
477 485 6.939163 GGACAGAGGGAGTATATTCGTACTTA 59.061 42.308 0.00 0.00 35.14 2.24
479 487 5.315348 GGACAGAGGGAGTATATTCGTACT 58.685 45.833 0.00 0.00 37.61 2.73
480 488 4.458642 GGGACAGAGGGAGTATATTCGTAC 59.541 50.000 0.00 0.00 0.00 3.67
482 490 3.117246 TGGGACAGAGGGAGTATATTCGT 60.117 47.826 0.00 0.00 0.00 3.85
483 491 3.256136 GTGGGACAGAGGGAGTATATTCG 59.744 52.174 0.00 0.00 41.80 3.34
484 492 4.223953 TGTGGGACAGAGGGAGTATATTC 58.776 47.826 0.00 0.00 41.80 1.75
485 493 4.280789 TGTGGGACAGAGGGAGTATATT 57.719 45.455 0.00 0.00 41.80 1.28
486 494 3.993658 TGTGGGACAGAGGGAGTATAT 57.006 47.619 0.00 0.00 41.80 0.86
487 495 3.769189 TTGTGGGACAGAGGGAGTATA 57.231 47.619 0.00 0.00 41.80 1.47
488 496 2.642171 TTGTGGGACAGAGGGAGTAT 57.358 50.000 0.00 0.00 41.80 2.12
489 497 2.642171 ATTGTGGGACAGAGGGAGTA 57.358 50.000 0.00 0.00 41.80 2.59
491 499 4.901849 TCTTATATTGTGGGACAGAGGGAG 59.098 45.833 0.00 0.00 41.80 4.30
493 501 5.368989 GTTCTTATATTGTGGGACAGAGGG 58.631 45.833 0.00 0.00 41.80 4.30
494 502 5.050490 CGTTCTTATATTGTGGGACAGAGG 58.950 45.833 0.00 0.00 41.80 3.69
495 503 5.661458 ACGTTCTTATATTGTGGGACAGAG 58.339 41.667 0.00 0.00 41.80 3.35
496 504 5.670792 ACGTTCTTATATTGTGGGACAGA 57.329 39.130 0.00 0.00 41.80 3.41
498 506 5.998981 ACAAACGTTCTTATATTGTGGGACA 59.001 36.000 0.00 0.00 33.29 4.02
502 510 6.523201 GCTTGACAAACGTTCTTATATTGTGG 59.477 38.462 0.00 0.00 34.59 4.17
503 511 6.523201 GGCTTGACAAACGTTCTTATATTGTG 59.477 38.462 0.00 0.00 34.59 3.33
507 515 5.163754 GCTGGCTTGACAAACGTTCTTATAT 60.164 40.000 0.00 0.00 0.00 0.86
513 521 0.380378 TGCTGGCTTGACAAACGTTC 59.620 50.000 0.00 0.00 0.00 3.95
514 522 0.814457 TTGCTGGCTTGACAAACGTT 59.186 45.000 0.00 0.00 0.00 3.99
557 770 5.007039 CCACATACAAATCCATCTTCAGTCG 59.993 44.000 0.00 0.00 0.00 4.18
600 845 1.405661 CCGTTCACCTAGGGAAGAAGC 60.406 57.143 14.81 8.11 0.00 3.86
613 858 4.715520 CACATCATGCTATACCGTTCAC 57.284 45.455 0.00 0.00 0.00 3.18
657 902 2.430332 ACATCCCAATTAAACCCATGCG 59.570 45.455 0.00 0.00 0.00 4.73
806 1202 1.203994 GATGTACGCCTACACACAGGT 59.796 52.381 0.00 0.00 35.63 4.00
817 1213 2.417719 GATCCCTCAATGATGTACGCC 58.582 52.381 0.00 0.00 0.00 5.68
840 1301 4.458708 GCAAGAACAAATCTGAGAACGAC 58.541 43.478 0.00 0.00 38.79 4.34
841 1302 3.184379 CGCAAGAACAAATCTGAGAACGA 59.816 43.478 0.00 0.00 38.79 3.85
842 1303 3.059597 ACGCAAGAACAAATCTGAGAACG 60.060 43.478 0.00 0.00 38.79 3.95
892 1355 1.913722 CCCAGAGAATGCCAGCTCT 59.086 57.895 0.00 0.00 41.95 4.09
893 1356 1.823041 GCCCAGAGAATGCCAGCTC 60.823 63.158 0.00 0.00 0.00 4.09
995 1461 1.007964 CGCTCTCTAGGCATCGTGG 60.008 63.158 0.00 0.00 0.00 4.94
1995 2461 1.608055 TCTTGAACTGCACACCCATG 58.392 50.000 0.00 0.00 0.00 3.66
2166 2632 1.153765 CTGCTCGAACGCCATCAGA 60.154 57.895 0.00 0.00 0.00 3.27
2415 2881 2.357881 TTCTCCAGCAGCACGCAG 60.358 61.111 0.00 0.00 46.13 5.18
2603 3069 1.017177 TATTTGACACTCCGGTGCGC 61.017 55.000 0.00 0.00 46.57 6.09
2604 3070 0.719465 GTATTTGACACTCCGGTGCG 59.281 55.000 0.00 0.00 46.57 5.34
2607 3073 1.695242 TGTGGTATTTGACACTCCGGT 59.305 47.619 0.00 0.00 38.39 5.28
2609 3075 2.156891 CGTTGTGGTATTTGACACTCCG 59.843 50.000 0.00 0.00 38.39 4.63
2610 3076 3.135994 ACGTTGTGGTATTTGACACTCC 58.864 45.455 0.00 0.00 38.39 3.85
2620 3086 5.278758 CCAAAGATTTTGGACGTTGTGGTAT 60.279 40.000 13.95 0.00 42.06 2.73
2621 3087 4.036971 CCAAAGATTTTGGACGTTGTGGTA 59.963 41.667 13.95 0.00 42.06 3.25
2626 3092 3.090952 TGCCAAAGATTTTGGACGTTG 57.909 42.857 21.42 0.00 42.06 4.10
2629 3095 3.490526 CAGTTTGCCAAAGATTTTGGACG 59.509 43.478 21.42 6.57 42.06 4.79
2635 3101 4.646492 AGACAGTCAGTTTGCCAAAGATTT 59.354 37.500 2.66 0.00 0.00 2.17
2907 3402 2.553602 TCCGGCAACATAATGATCATGC 59.446 45.455 9.46 8.60 0.00 4.06
2908 3403 5.381174 AATCCGGCAACATAATGATCATG 57.619 39.130 9.46 0.50 0.00 3.07
2975 3470 3.169908 AGAGAGGAGAGGAGAAAACCAC 58.830 50.000 0.00 0.00 0.00 4.16
3037 3537 2.188207 GAAGAAGGAGGGGCGAGC 59.812 66.667 0.00 0.00 0.00 5.03
3067 3567 3.644399 GACGAAGGCACGAGGGGAC 62.644 68.421 10.66 0.00 37.03 4.46
3068 3568 3.379445 GACGAAGGCACGAGGGGA 61.379 66.667 10.66 0.00 37.03 4.81
3069 3569 4.452733 GGACGAAGGCACGAGGGG 62.453 72.222 10.66 0.00 37.03 4.79
3070 3570 3.358076 GAGGACGAAGGCACGAGGG 62.358 68.421 10.66 0.00 37.03 4.30
3071 3571 2.182030 GAGGACGAAGGCACGAGG 59.818 66.667 10.66 0.00 37.03 4.63
3072 3572 2.182030 GGAGGACGAAGGCACGAG 59.818 66.667 10.66 0.00 37.03 4.18
3073 3573 3.379445 GGGAGGACGAAGGCACGA 61.379 66.667 10.66 0.00 37.03 4.35
3074 3574 4.452733 GGGGAGGACGAAGGCACG 62.453 72.222 0.00 2.85 39.31 5.34
3075 3575 3.003763 AGGGGAGGACGAAGGCAC 61.004 66.667 0.00 0.00 0.00 5.01
3076 3576 2.683933 GAGGGGAGGACGAAGGCA 60.684 66.667 0.00 0.00 0.00 4.75
3077 3577 3.471806 GGAGGGGAGGACGAAGGC 61.472 72.222 0.00 0.00 0.00 4.35
3078 3578 1.758906 GAGGAGGGGAGGACGAAGG 60.759 68.421 0.00 0.00 0.00 3.46
3079 3579 0.753848 GAGAGGAGGGGAGGACGAAG 60.754 65.000 0.00 0.00 0.00 3.79
3080 3580 1.306970 GAGAGGAGGGGAGGACGAA 59.693 63.158 0.00 0.00 0.00 3.85
3081 3581 2.691779 GGAGAGGAGGGGAGGACGA 61.692 68.421 0.00 0.00 0.00 4.20
3082 3582 2.123640 GGAGAGGAGGGGAGGACG 60.124 72.222 0.00 0.00 0.00 4.79
3083 3583 1.231928 GAGGAGAGGAGGGGAGGAC 59.768 68.421 0.00 0.00 0.00 3.85
3084 3584 2.015726 GGAGGAGAGGAGGGGAGGA 61.016 68.421 0.00 0.00 0.00 3.71
3085 3585 2.018086 AGGAGGAGAGGAGGGGAGG 61.018 68.421 0.00 0.00 0.00 4.30
3086 3586 1.541672 GAGGAGGAGAGGAGGGGAG 59.458 68.421 0.00 0.00 0.00 4.30
3087 3587 2.015726 GGAGGAGGAGAGGAGGGGA 61.016 68.421 0.00 0.00 0.00 4.81
3088 3588 1.598856 AAGGAGGAGGAGAGGAGGGG 61.599 65.000 0.00 0.00 0.00 4.79
3089 3589 0.105709 GAAGGAGGAGGAGAGGAGGG 60.106 65.000 0.00 0.00 0.00 4.30
3090 3590 0.933700 AGAAGGAGGAGGAGAGGAGG 59.066 60.000 0.00 0.00 0.00 4.30
3091 3591 2.028996 GCAGAAGGAGGAGGAGAGGAG 61.029 61.905 0.00 0.00 0.00 3.69
3092 3592 0.032615 GCAGAAGGAGGAGGAGAGGA 60.033 60.000 0.00 0.00 0.00 3.71
3093 3593 1.048160 GGCAGAAGGAGGAGGAGAGG 61.048 65.000 0.00 0.00 0.00 3.69
3094 3594 0.032217 AGGCAGAAGGAGGAGGAGAG 60.032 60.000 0.00 0.00 0.00 3.20
3095 3595 0.415429 AAGGCAGAAGGAGGAGGAGA 59.585 55.000 0.00 0.00 0.00 3.71
3096 3596 0.540923 CAAGGCAGAAGGAGGAGGAG 59.459 60.000 0.00 0.00 0.00 3.69
3097 3597 0.178891 ACAAGGCAGAAGGAGGAGGA 60.179 55.000 0.00 0.00 0.00 3.71
3098 3598 0.251634 GACAAGGCAGAAGGAGGAGG 59.748 60.000 0.00 0.00 0.00 4.30
3099 3599 0.108424 CGACAAGGCAGAAGGAGGAG 60.108 60.000 0.00 0.00 0.00 3.69
3100 3600 0.832135 ACGACAAGGCAGAAGGAGGA 60.832 55.000 0.00 0.00 0.00 3.71
3101 3601 0.671781 CACGACAAGGCAGAAGGAGG 60.672 60.000 0.00 0.00 0.00 4.30
3102 3602 0.034059 ACACGACAAGGCAGAAGGAG 59.966 55.000 0.00 0.00 0.00 3.69
3103 3603 0.033504 GACACGACAAGGCAGAAGGA 59.966 55.000 0.00 0.00 0.00 3.36
3104 3604 0.951040 GGACACGACAAGGCAGAAGG 60.951 60.000 0.00 0.00 0.00 3.46
3105 3605 1.284982 CGGACACGACAAGGCAGAAG 61.285 60.000 0.00 0.00 44.60 2.85
3106 3606 1.300620 CGGACACGACAAGGCAGAA 60.301 57.895 0.00 0.00 44.60 3.02
3107 3607 2.338620 CGGACACGACAAGGCAGA 59.661 61.111 0.00 0.00 44.60 4.26
3108 3608 2.738521 CCGGACACGACAAGGCAG 60.739 66.667 0.00 0.00 44.60 4.85
3175 3675 2.100631 CGCTAGAACACAAGGCCCG 61.101 63.158 0.00 0.00 0.00 6.13
3366 3866 5.564213 TGACGTACACATTTTACAAGACG 57.436 39.130 0.00 0.00 35.30 4.18
3558 4058 1.528292 TAATGTGGCCCCGTTGCAAC 61.528 55.000 19.89 19.89 35.65 4.17
3559 4059 0.827925 TTAATGTGGCCCCGTTGCAA 60.828 50.000 0.00 0.00 0.00 4.08
3560 4060 1.228583 TTAATGTGGCCCCGTTGCA 60.229 52.632 0.00 0.00 0.00 4.08
3561 4061 1.214325 GTTAATGTGGCCCCGTTGC 59.786 57.895 0.00 0.00 0.00 4.17
3562 4062 1.253100 AAGTTAATGTGGCCCCGTTG 58.747 50.000 0.00 0.00 0.00 4.10
3563 4063 2.003937 AAAGTTAATGTGGCCCCGTT 57.996 45.000 0.00 0.00 0.00 4.44
3564 4064 2.883122 TAAAGTTAATGTGGCCCCGT 57.117 45.000 0.00 0.00 0.00 5.28
3565 4065 3.349022 TCTTAAAGTTAATGTGGCCCCG 58.651 45.455 0.00 0.00 0.00 5.73
3566 4066 4.341487 ACTCTTAAAGTTAATGTGGCCCC 58.659 43.478 0.00 0.00 33.03 5.80
3567 4067 5.977489 AACTCTTAAAGTTAATGTGGCCC 57.023 39.130 0.00 0.00 46.55 5.80


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

AutoCloner maintained by Alex Coulton.