Multiple sequence alignment - TraesCS1A01G208700

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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 TraesCS1A01G208700 chr1A 100.000 3701 0 0 1 3701 370111524 370107824 0.000000e+00 6835.0
1 TraesCS1A01G208700 chr1A 92.174 115 9 0 1295 1409 478567443 478567557 2.960000e-36 163.0
2 TraesCS1A01G208700 chr1D 93.015 2992 102 48 148 3063 297539787 297536827 0.000000e+00 4268.0
3 TraesCS1A01G208700 chr1D 92.157 408 20 7 3298 3701 297536630 297536231 1.930000e-157 566.0
4 TraesCS1A01G208700 chr1D 95.192 104 5 0 3 106 297540198 297540095 8.220000e-37 165.0
5 TraesCS1A01G208700 chr1D 91.304 115 10 0 1295 1409 377973957 377974071 1.380000e-34 158.0
6 TraesCS1A01G208700 chr1B 94.250 2348 87 28 195 2501 400315063 400312723 0.000000e+00 3544.0
7 TraesCS1A01G208700 chr1B 85.873 1168 92 39 2581 3701 400312711 400311570 0.000000e+00 1175.0
8 TraesCS1A01G208700 chr1B 94.608 204 11 0 3 206 400315505 400315302 2.150000e-82 316.0
9 TraesCS1A01G208700 chr1B 91.304 115 10 0 1295 1409 505626346 505626460 1.380000e-34 158.0
10 TraesCS1A01G208700 chr2B 76.630 368 52 18 2065 2430 612688630 612688295 4.910000e-39 172.0
11 TraesCS1A01G208700 chr2D 76.454 361 51 17 2065 2423 520525976 520525648 8.220000e-37 165.0
12 TraesCS1A01G208700 chr2D 94.175 103 6 0 1310 1412 520526995 520526893 1.380000e-34 158.0
13 TraesCS1A01G208700 chr5A 86.957 138 17 1 1285 1421 547332381 547332244 1.780000e-33 154.0
14 TraesCS1A01G208700 chr6B 89.831 118 12 0 1295 1412 708668023 708667906 6.400000e-33 152.0
15 TraesCS1A01G208700 chr5D 93.204 103 7 0 1310 1412 432514628 432514526 6.400000e-33 152.0
16 TraesCS1A01G208700 chr2A 83.041 171 25 3 3342 3511 62608952 62609119 6.400000e-33 152.0
17 TraesCS1A01G208700 chr2A 84.252 127 19 1 2305 2430 665710108 665709982 5.020000e-24 122.0
18 TraesCS1A01G208700 chr7A 100.000 29 0 0 3277 3305 63471318 63471346 2.000000e-03 54.7


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 TraesCS1A01G208700 chr1A 370107824 370111524 3700 True 6835.000000 6835 100.000000 1 3701 1 chr1A.!!$R1 3700
1 TraesCS1A01G208700 chr1D 297536231 297540198 3967 True 1666.333333 4268 93.454667 3 3701 3 chr1D.!!$R1 3698
2 TraesCS1A01G208700 chr1B 400311570 400315505 3935 True 1678.333333 3544 91.577000 3 3701 3 chr1B.!!$R1 3698

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
908 1455 0.096281 TTTCGATGGATTTGTCGCGC 59.904 50.0 0.0 0.0 37.74 6.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2747 3356 1.055476 GTAAGAGCGTTCGTTCGTTCG 59.945 52.381 3.16 7.17 43.61 3.95 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.414436 CAAGGTATTTTCGTTCACTTTTCTCA 58.586 34.615 0.00 0.00 0.00 3.27
83 84 6.534436 TGTCATTTAAACATGCATTGTATGGC 59.466 34.615 17.41 2.48 37.68 4.40
115 116 9.065871 GCTTAAAATGTGTAACTAGAAAGCATG 57.934 33.333 0.00 0.00 36.26 4.06
168 435 8.167392 TGTGTCATTTTCCCCTCTTCTTTTATA 58.833 33.333 0.00 0.00 0.00 0.98
337 858 9.378551 GACCAATAAAATAAGGGAAACAAATCC 57.621 33.333 0.00 0.00 38.86 3.01
393 916 4.202620 TGACCAAGGAAAACATACCATCCA 60.203 41.667 0.00 0.00 34.30 3.41
398 921 3.706086 AGGAAAACATACCATCCATTGCC 59.294 43.478 0.00 0.00 34.30 4.52
424 947 1.984570 CCGCTTCTCCCCTCTGTGA 60.985 63.158 0.00 0.00 0.00 3.58
436 959 2.286872 CCTCTGTGATCTGCCATTGTC 58.713 52.381 0.00 0.00 0.00 3.18
454 978 3.085533 TGTCGAGAGAGAGAAAAGGGAG 58.914 50.000 0.00 0.00 43.49 4.30
495 1020 4.406003 GGAAGCTGATAGAGGGAACACTTA 59.594 45.833 0.00 0.00 31.93 2.24
520 1045 4.819088 AGAGAACACAAGAGCTTTTCTTCC 59.181 41.667 0.00 0.00 44.34 3.46
545 1070 3.953201 GCATATGGCAAGGACAAGC 57.047 52.632 4.56 0.00 43.97 4.01
632 1157 5.333299 TGATTCCTTTGATTTGCATCCAG 57.667 39.130 0.00 0.00 0.00 3.86
660 1185 5.476599 CCAAGAAGAATGTGTGGTGGAATTA 59.523 40.000 0.00 0.00 0.00 1.40
662 1187 4.695455 AGAAGAATGTGTGGTGGAATTACG 59.305 41.667 0.00 0.00 0.00 3.18
668 1193 3.003897 TGTGTGGTGGAATTACGAAAAGC 59.996 43.478 0.00 0.00 0.00 3.51
765 1290 2.298610 CATGGCATGCTCATCAGAAGT 58.701 47.619 18.92 0.00 0.00 3.01
766 1291 3.473625 CATGGCATGCTCATCAGAAGTA 58.526 45.455 18.92 0.00 0.00 2.24
799 1345 8.023128 GTCTAAAAAGCAGCAAATCAAGATGTA 58.977 33.333 0.00 0.00 0.00 2.29
850 1396 4.434067 CGGGAAATGCGCTTAAATTTTGTG 60.434 41.667 9.73 0.00 0.00 3.33
872 1419 4.024387 TGTTAACGCACAGGAGTTCAAATC 60.024 41.667 0.26 0.00 38.11 2.17
879 1426 4.392940 CACAGGAGTTCAAATCTTGTCCT 58.607 43.478 0.00 0.00 35.07 3.85
903 1450 2.689983 GCTCCCATTTCGATGGATTTGT 59.310 45.455 6.63 0.00 44.39 2.83
904 1451 3.243201 GCTCCCATTTCGATGGATTTGTC 60.243 47.826 6.63 0.00 44.39 3.18
905 1452 2.942376 TCCCATTTCGATGGATTTGTCG 59.058 45.455 6.63 0.00 44.39 4.35
906 1453 2.541588 CCCATTTCGATGGATTTGTCGC 60.542 50.000 6.63 0.00 44.39 5.19
907 1454 2.365948 CATTTCGATGGATTTGTCGCG 58.634 47.619 0.00 0.00 37.74 5.87
908 1455 0.096281 TTTCGATGGATTTGTCGCGC 59.904 50.000 0.00 0.00 37.74 6.86
909 1456 1.701545 TTCGATGGATTTGTCGCGCC 61.702 55.000 0.00 0.00 37.74 6.53
910 1457 2.460275 CGATGGATTTGTCGCGCCA 61.460 57.895 0.00 1.32 34.45 5.69
911 1458 1.775039 CGATGGATTTGTCGCGCCAT 61.775 55.000 12.62 12.62 43.46 4.40
951 1507 4.325109 GGACCCTTTCCTTATAAAGCAGGT 60.325 45.833 0.00 0.00 41.95 4.00
952 1508 4.600062 ACCCTTTCCTTATAAAGCAGGTG 58.400 43.478 0.00 0.00 32.84 4.00
956 1512 6.415573 CCTTTCCTTATAAAGCAGGTGTAGT 58.584 40.000 0.00 0.00 35.53 2.73
957 1513 7.365295 CCCTTTCCTTATAAAGCAGGTGTAGTA 60.365 40.741 0.00 0.00 35.53 1.82
958 1514 7.494952 CCTTTCCTTATAAAGCAGGTGTAGTAC 59.505 40.741 0.00 0.00 35.53 2.73
985 1559 2.441410 GAAGGAAGGAAGGAAGCCAAG 58.559 52.381 0.00 0.00 0.00 3.61
988 1562 2.163509 GGAAGGAAGGAAGCCAAGAAC 58.836 52.381 0.00 0.00 0.00 3.01
989 1563 2.163509 GAAGGAAGGAAGCCAAGAACC 58.836 52.381 0.00 0.00 0.00 3.62
991 1565 1.499007 AGGAAGGAAGCCAAGAACCAA 59.501 47.619 0.00 0.00 0.00 3.67
993 1567 1.613925 GAAGGAAGCCAAGAACCAACC 59.386 52.381 0.00 0.00 0.00 3.77
994 1568 0.537371 AGGAAGCCAAGAACCAACCG 60.537 55.000 0.00 0.00 0.00 4.44
995 1569 1.285950 GAAGCCAAGAACCAACCGC 59.714 57.895 0.00 0.00 0.00 5.68
996 1570 1.152756 AAGCCAAGAACCAACCGCT 60.153 52.632 0.00 0.00 0.00 5.52
997 1571 1.455383 AAGCCAAGAACCAACCGCTG 61.455 55.000 0.00 0.00 0.00 5.18
998 1572 2.644992 CCAAGAACCAACCGCTGC 59.355 61.111 0.00 0.00 0.00 5.25
999 1573 2.644992 CAAGAACCAACCGCTGCC 59.355 61.111 0.00 0.00 0.00 4.85
1028 1602 3.414700 CAGCAACAGCCCGTCGAC 61.415 66.667 5.18 5.18 0.00 4.20
1696 2272 5.641209 CGAGGTGATGATCTTTCTTTGTTCT 59.359 40.000 0.00 0.00 0.00 3.01
1706 2282 8.562892 TGATCTTTCTTTGTTCTGAATTCTGAC 58.437 33.333 13.97 10.15 0.00 3.51
1717 2293 1.197721 GAATTCTGACCAGTGCCAACG 59.802 52.381 0.00 0.00 0.00 4.10
1866 2445 3.434319 TCTACGACGACGGCCCAC 61.434 66.667 12.58 0.00 44.46 4.61
2130 2709 1.031029 AGTTCTCGCCGGACTACCTC 61.031 60.000 5.05 0.00 0.00 3.85
2525 3134 5.367302 TCATCAGTTCATCACACACTTGAA 58.633 37.500 0.00 0.00 0.00 2.69
2534 3143 6.232692 TCATCACACACTTGAATCTTGATGA 58.767 36.000 7.17 7.17 43.37 2.92
2540 3149 6.150641 ACACACTTGAATCTTGATGAAGATGG 59.849 38.462 8.26 2.81 46.45 3.51
2557 3166 5.578005 AGATGGAATGCTGTTTTCTGATG 57.422 39.130 0.00 0.00 0.00 3.07
2561 3170 2.610438 ATGCTGTTTTCTGATGGGGT 57.390 45.000 0.00 0.00 0.00 4.95
2572 3181 1.773052 CTGATGGGGTGAGATGGATGT 59.227 52.381 0.00 0.00 0.00 3.06
2574 3183 3.392285 CTGATGGGGTGAGATGGATGTTA 59.608 47.826 0.00 0.00 0.00 2.41
2577 3186 4.879295 TGGGGTGAGATGGATGTTATTT 57.121 40.909 0.00 0.00 0.00 1.40
2578 3187 4.792068 TGGGGTGAGATGGATGTTATTTC 58.208 43.478 0.00 0.00 0.00 2.17
2652 3261 1.497278 CCTGGCGTTCAACATCGTG 59.503 57.895 0.00 0.00 0.00 4.35
2755 3364 0.966407 CGTCGAGAGAACGAACGAAC 59.034 55.000 0.14 0.00 45.01 3.95
2759 3368 1.378155 CGAGAGAACGAACGAACGAAC 59.622 52.381 11.97 6.21 37.03 3.95
2767 3376 1.055476 CGAACGAACGAACGCTCTTAC 59.945 52.381 0.14 0.00 36.70 2.34
2768 3377 2.046313 GAACGAACGAACGCTCTTACA 58.954 47.619 0.14 0.00 36.70 2.41
2849 3461 4.381079 GGCGTAGGTTAGGATGATGATCTC 60.381 50.000 0.00 0.00 0.00 2.75
2908 3520 3.502211 CGTAGTCAAGGATTTGCAAGGTT 59.498 43.478 0.00 0.00 34.21 3.50
2956 3568 3.055094 AGAGTTTGTCTGACCAACAGTGT 60.055 43.478 22.05 5.90 45.86 3.55
2957 3569 3.009723 AGTTTGTCTGACCAACAGTGTG 58.990 45.455 22.05 0.00 45.86 3.82
2958 3570 2.747446 GTTTGTCTGACCAACAGTGTGT 59.253 45.455 17.06 0.00 45.86 3.72
3006 3626 4.771590 TCATCTGATTTTCAGGTTGTGC 57.228 40.909 4.78 0.00 44.39 4.57
3016 3636 4.251246 GGTTGTGCCTGACCAACA 57.749 55.556 0.00 0.00 42.09 3.33
3017 3637 2.499214 GGTTGTGCCTGACCAACAA 58.501 52.632 0.00 0.00 42.09 2.83
3028 3648 3.500982 CTGACCAACAAAACAGTGTGTG 58.499 45.455 0.00 0.59 0.00 3.82
3031 3651 2.625790 ACCAACAAAACAGTGTGTGTGT 59.374 40.909 12.33 7.15 40.26 3.72
3062 3684 4.736126 TTCTTGCTCATCGATCTTGGTA 57.264 40.909 0.00 0.00 0.00 3.25
3066 3688 4.471904 TGCTCATCGATCTTGGTAAAGT 57.528 40.909 0.00 0.00 34.78 2.66
3080 3702 4.139038 TGGTAAAGTTAAGGACCAAGTGC 58.861 43.478 0.00 0.00 39.01 4.40
3086 3715 0.392461 TAAGGACCAAGTGCGATGCC 60.392 55.000 0.00 0.00 0.00 4.40
3092 3721 1.091771 CCAAGTGCGATGCCTGGTAG 61.092 60.000 0.00 0.00 0.00 3.18
3096 3725 0.598680 GTGCGATGCCTGGTAGCTAG 60.599 60.000 0.00 0.00 0.00 3.42
3099 3728 1.040646 CGATGCCTGGTAGCTAGGAA 58.959 55.000 5.13 0.00 37.52 3.36
3137 3766 8.651589 TGTTATATATCAGAGTTAGGACTGGG 57.348 38.462 0.00 0.00 35.88 4.45
3147 3776 2.572104 GTTAGGACTGGGACATCCAACT 59.428 50.000 0.00 0.00 46.51 3.16
3151 3780 3.009143 AGGACTGGGACATCCAACTTAAC 59.991 47.826 0.00 0.00 46.51 2.01
3154 3785 4.398319 ACTGGGACATCCAACTTAACAAG 58.602 43.478 0.00 0.00 46.51 3.16
3158 3789 6.074648 TGGGACATCCAACTTAACAAGAAAT 58.925 36.000 0.00 0.00 43.84 2.17
3161 3792 8.581578 GGGACATCCAACTTAACAAGAAATAAA 58.418 33.333 0.00 0.00 37.91 1.40
3185 3816 5.490139 AATCACATTCATTCATGACCGTC 57.510 39.130 0.00 0.00 36.36 4.79
3186 3817 4.206477 TCACATTCATTCATGACCGTCT 57.794 40.909 0.00 0.00 36.36 4.18
3188 3819 5.917462 TCACATTCATTCATGACCGTCTAT 58.083 37.500 0.00 0.00 36.36 1.98
3189 3820 7.049799 TCACATTCATTCATGACCGTCTATA 57.950 36.000 0.00 0.00 36.36 1.31
3190 3821 7.496747 TCACATTCATTCATGACCGTCTATAA 58.503 34.615 0.00 0.00 36.36 0.98
3191 3822 7.653311 TCACATTCATTCATGACCGTCTATAAG 59.347 37.037 0.00 0.00 36.36 1.73
3192 3823 6.425114 ACATTCATTCATGACCGTCTATAAGC 59.575 38.462 0.00 0.00 36.36 3.09
3193 3824 4.883083 TCATTCATGACCGTCTATAAGCC 58.117 43.478 0.00 0.00 0.00 4.35
3194 3825 4.588951 TCATTCATGACCGTCTATAAGCCT 59.411 41.667 0.00 0.00 0.00 4.58
3196 3827 6.266786 TCATTCATGACCGTCTATAAGCCTTA 59.733 38.462 0.00 0.00 0.00 2.69
3198 3829 5.382616 TCATGACCGTCTATAAGCCTTAGA 58.617 41.667 0.00 0.00 0.00 2.10
3199 3830 5.473846 TCATGACCGTCTATAAGCCTTAGAG 59.526 44.000 0.00 0.00 0.00 2.43
3200 3831 5.045012 TGACCGTCTATAAGCCTTAGAGA 57.955 43.478 4.73 4.73 31.52 3.10
3219 3863 6.229561 AGAGAAAGTTGAATTTACTGCGAC 57.770 37.500 0.00 0.00 0.00 5.19
3222 3866 6.970484 AGAAAGTTGAATTTACTGCGACAAT 58.030 32.000 0.00 0.00 0.00 2.71
3224 3868 8.564574 AGAAAGTTGAATTTACTGCGACAATAA 58.435 29.630 0.00 0.00 0.00 1.40
3225 3869 8.502161 AAAGTTGAATTTACTGCGACAATAAC 57.498 30.769 0.00 0.00 0.00 1.89
3227 3871 7.816640 AGTTGAATTTACTGCGACAATAACAT 58.183 30.769 0.00 0.00 0.00 2.71
3228 3872 8.296713 AGTTGAATTTACTGCGACAATAACATT 58.703 29.630 0.00 0.00 0.00 2.71
3229 3873 8.911662 GTTGAATTTACTGCGACAATAACATTT 58.088 29.630 0.00 0.00 0.00 2.32
3230 3874 8.446489 TGAATTTACTGCGACAATAACATTTG 57.554 30.769 0.00 0.00 0.00 2.32
3233 3877 9.469807 AATTTACTGCGACAATAACATTTGAAA 57.530 25.926 0.00 0.00 0.00 2.69
3238 3882 5.689514 TGCGACAATAACATTTGAAAGTTGG 59.310 36.000 0.00 0.00 0.00 3.77
3270 3914 2.096762 CACTGCACTTCATACACACACG 60.097 50.000 0.00 0.00 0.00 4.49
3271 3915 2.223947 ACTGCACTTCATACACACACGA 60.224 45.455 0.00 0.00 0.00 4.35
3272 3916 2.131972 TGCACTTCATACACACACGAC 58.868 47.619 0.00 0.00 0.00 4.34
3273 3917 1.124297 GCACTTCATACACACACGACG 59.876 52.381 0.00 0.00 0.00 5.12
3274 3918 2.390938 CACTTCATACACACACGACGT 58.609 47.619 0.00 0.00 0.00 4.34
3276 3920 2.292569 ACTTCATACACACACGACGTCT 59.707 45.455 14.70 0.00 0.00 4.18
3277 3921 3.243301 ACTTCATACACACACGACGTCTT 60.243 43.478 14.70 0.03 0.00 3.01
3279 3923 4.690184 TCATACACACACGACGTCTTAT 57.310 40.909 14.70 0.00 0.00 1.73
3281 3925 6.367686 TCATACACACACGACGTCTTATAT 57.632 37.500 14.70 0.00 0.00 0.86
3282 3926 6.788243 TCATACACACACGACGTCTTATATT 58.212 36.000 14.70 0.00 0.00 1.28
3283 3927 7.252708 TCATACACACACGACGTCTTATATTT 58.747 34.615 14.70 0.00 0.00 1.40
3284 3928 7.756272 TCATACACACACGACGTCTTATATTTT 59.244 33.333 14.70 0.00 0.00 1.82
3285 3929 6.148270 ACACACACGACGTCTTATATTTTG 57.852 37.500 14.70 3.21 0.00 2.44
3287 3931 6.089016 ACACACACGACGTCTTATATTTTGAG 59.911 38.462 14.70 0.00 0.00 3.02
3288 3932 6.307077 CACACACGACGTCTTATATTTTGAGA 59.693 38.462 14.70 0.00 0.00 3.27
3291 3935 6.527023 ACACGACGTCTTATATTTTGAGACAG 59.473 38.462 14.70 0.00 39.74 3.51
3292 3936 6.745907 CACGACGTCTTATATTTTGAGACAGA 59.254 38.462 14.70 0.00 39.74 3.41
3293 3937 6.967767 ACGACGTCTTATATTTTGAGACAGAG 59.032 38.462 14.70 0.00 39.74 3.35
3294 3938 6.415280 CGACGTCTTATATTTTGAGACAGAGG 59.585 42.308 14.70 0.00 39.74 3.69
3295 3939 7.406031 ACGTCTTATATTTTGAGACAGAGGA 57.594 36.000 0.00 0.00 39.74 3.71
3296 3940 7.837863 ACGTCTTATATTTTGAGACAGAGGAA 58.162 34.615 0.00 0.00 39.74 3.36
3309 3960 5.329399 AGACAGAGGAAGTAGTTGACATCT 58.671 41.667 0.00 0.00 0.00 2.90
3340 3991 2.893637 ACAGCAAATACAGGTAGAGCG 58.106 47.619 0.00 0.00 0.00 5.03
3362 4014 4.858692 CGCATGTTTATCCAAGGAAACAAG 59.141 41.667 9.66 7.28 45.78 3.16
3364 4016 5.047377 GCATGTTTATCCAAGGAAACAAGGA 60.047 40.000 9.66 0.00 45.78 3.36
3367 4019 6.133356 TGTTTATCCAAGGAAACAAGGAGTT 58.867 36.000 4.34 0.00 41.37 3.01
3371 4023 3.202151 TCCAAGGAAACAAGGAGTTGTCT 59.798 43.478 0.00 0.00 46.68 3.41
3381 4033 8.803397 AAACAAGGAGTTGTCTAACTTAACTT 57.197 30.769 0.00 0.00 46.68 2.66
3383 4035 9.543783 AACAAGGAGTTGTCTAACTTAACTTAG 57.456 33.333 0.00 0.00 46.68 2.18
3417 4069 5.982890 ATTTCGGAAAATGAAGACCATGT 57.017 34.783 7.33 0.00 33.78 3.21
3508 4163 6.089476 CACATGTACACACAAACACAAAGAA 58.911 36.000 0.00 0.00 38.42 2.52
3509 4164 6.584184 CACATGTACACACAAACACAAAGAAA 59.416 34.615 0.00 0.00 38.42 2.52
3510 4165 7.115520 CACATGTACACACAAACACAAAGAAAA 59.884 33.333 0.00 0.00 38.42 2.29
3511 4166 7.328249 ACATGTACACACAAACACAAAGAAAAG 59.672 33.333 0.00 0.00 38.42 2.27
3512 4167 6.153067 TGTACACACAAACACAAAGAAAAGG 58.847 36.000 0.00 0.00 0.00 3.11
3515 4170 6.284459 ACACACAAACACAAAGAAAAGGAAA 58.716 32.000 0.00 0.00 0.00 3.13
3580 4235 1.970640 AGGAAAATCCGCAAAGCCTTT 59.029 42.857 0.00 0.00 42.75 3.11
3627 4282 1.002868 GAGGCATGGCTGTGACAGT 60.003 57.895 28.55 0.00 33.43 3.55
3628 4283 0.607489 GAGGCATGGCTGTGACAGTT 60.607 55.000 28.55 0.00 33.43 3.16
3629 4284 0.692476 AGGCATGGCTGTGACAGTTA 59.308 50.000 22.69 3.94 33.43 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.278604 AGTGAACGAAAATACCTTGCAAAC 58.721 37.500 0.00 0.00 0.00 2.93
1 2 5.508200 AGTGAACGAAAATACCTTGCAAA 57.492 34.783 0.00 0.00 0.00 3.68
30 31 8.636213 GGAAATATCACAGACAATCCATTGATT 58.364 33.333 6.29 0.00 41.96 2.57
42 43 6.422776 AAATGACACGGAAATATCACAGAC 57.577 37.500 0.00 0.00 0.00 3.51
337 858 2.044793 TGCCATAGGGAGGGATTAGG 57.955 55.000 0.00 0.00 35.59 2.69
393 916 2.229690 GAAGCGGCAATGTGGGCAAT 62.230 55.000 1.45 0.00 0.00 3.56
398 921 2.409870 GGGAGAAGCGGCAATGTGG 61.410 63.158 1.45 0.00 0.00 4.17
424 947 2.361757 CTCTCTCTCGACAATGGCAGAT 59.638 50.000 0.00 0.00 0.00 2.90
436 959 2.425668 GGTCTCCCTTTTCTCTCTCTCG 59.574 54.545 0.00 0.00 0.00 4.04
473 997 4.479786 AAGTGTTCCCTCTATCAGCTTC 57.520 45.455 0.00 0.00 0.00 3.86
495 1020 5.289083 AGAAAAGCTCTTGTGTTCTCTCT 57.711 39.130 0.00 0.00 0.00 3.10
545 1070 4.362470 TGATCCCTAAGCCAATGATCTG 57.638 45.455 0.00 0.00 34.36 2.90
632 1157 1.068055 CCACACATTCTTCTTGGCTGC 60.068 52.381 0.00 0.00 0.00 5.25
668 1193 1.028905 TGGGAAGAAAACAAGCACGG 58.971 50.000 0.00 0.00 0.00 4.94
758 1283 5.654603 TTTTAGACGATGGCTACTTCTGA 57.345 39.130 0.00 0.00 0.00 3.27
760 1285 4.870991 GCTTTTTAGACGATGGCTACTTCT 59.129 41.667 0.00 0.00 0.00 2.85
761 1286 4.630069 TGCTTTTTAGACGATGGCTACTTC 59.370 41.667 0.00 0.00 0.00 3.01
762 1287 4.575885 TGCTTTTTAGACGATGGCTACTT 58.424 39.130 0.00 0.00 0.00 2.24
763 1288 4.184629 CTGCTTTTTAGACGATGGCTACT 58.815 43.478 0.00 0.00 0.00 2.57
764 1289 3.242446 GCTGCTTTTTAGACGATGGCTAC 60.242 47.826 0.00 0.00 0.00 3.58
765 1290 2.936498 GCTGCTTTTTAGACGATGGCTA 59.064 45.455 0.00 0.00 0.00 3.93
766 1291 1.740025 GCTGCTTTTTAGACGATGGCT 59.260 47.619 0.00 0.00 0.00 4.75
850 1396 3.955771 TTTGAACTCCTGTGCGTTAAC 57.044 42.857 0.00 0.00 0.00 2.01
872 1419 1.815003 GAAATGGGAGCACAGGACAAG 59.185 52.381 0.00 0.00 0.00 3.16
907 1454 0.028110 GGTGAATTCTCGCGAATGGC 59.972 55.000 11.33 0.00 39.72 4.40
908 1455 0.301687 CGGTGAATTCTCGCGAATGG 59.698 55.000 11.33 0.00 39.72 3.16
909 1456 0.301687 CCGGTGAATTCTCGCGAATG 59.698 55.000 11.33 0.00 39.72 2.67
910 1457 0.810031 CCCGGTGAATTCTCGCGAAT 60.810 55.000 11.33 0.00 41.53 3.34
911 1458 1.447140 CCCGGTGAATTCTCGCGAA 60.447 57.895 11.33 0.00 32.47 4.70
951 1507 3.508793 CCTTCCTTCCTTCGTGTACTACA 59.491 47.826 0.00 0.00 0.00 2.74
952 1508 3.760684 TCCTTCCTTCCTTCGTGTACTAC 59.239 47.826 0.00 0.00 0.00 2.73
956 1512 2.565834 CCTTCCTTCCTTCCTTCGTGTA 59.434 50.000 0.00 0.00 0.00 2.90
957 1513 1.348036 CCTTCCTTCCTTCCTTCGTGT 59.652 52.381 0.00 0.00 0.00 4.49
958 1514 1.623811 TCCTTCCTTCCTTCCTTCGTG 59.376 52.381 0.00 0.00 0.00 4.35
960 1534 2.937433 GCTTCCTTCCTTCCTTCCTTCG 60.937 54.545 0.00 0.00 0.00 3.79
965 1539 2.040412 TCTTGGCTTCCTTCCTTCCTTC 59.960 50.000 0.00 0.00 0.00 3.46
985 1559 2.568090 CATGGCAGCGGTTGGTTC 59.432 61.111 0.00 0.00 0.00 3.62
994 1568 3.360340 GCTATCCGCCATGGCAGC 61.360 66.667 34.93 29.92 38.85 5.25
995 1569 2.111669 TGCTATCCGCCATGGCAG 59.888 61.111 34.93 25.44 43.68 4.85
996 1570 2.111669 CTGCTATCCGCCATGGCA 59.888 61.111 34.93 18.52 46.19 4.92
997 1571 3.360340 GCTGCTATCCGCCATGGC 61.360 66.667 27.67 27.67 39.46 4.40
998 1572 1.526686 TTGCTGCTATCCGCCATGG 60.527 57.895 7.63 7.63 38.05 3.66
999 1573 1.096967 TGTTGCTGCTATCCGCCATG 61.097 55.000 0.00 0.00 38.05 3.66
1005 1579 2.182842 CGGGCTGTTGCTGCTATCC 61.183 63.158 0.00 0.00 39.59 2.59
1008 1582 2.047274 GACGGGCTGTTGCTGCTA 60.047 61.111 0.00 0.00 39.59 3.49
1033 1607 2.486042 GGAGCTCTCGTCGGACAC 59.514 66.667 14.64 0.00 0.00 3.67
1152 1726 3.716006 CTGTGGTCAACGCTGCGG 61.716 66.667 26.95 9.56 0.00 5.69
1696 2272 2.229792 GTTGGCACTGGTCAGAATTCA 58.770 47.619 8.44 0.00 0.00 2.57
1706 2282 0.667993 ACACATTTCGTTGGCACTGG 59.332 50.000 0.00 0.00 0.00 4.00
1717 2293 2.233355 CGCATGTCAACGACACATTTC 58.767 47.619 0.00 0.00 45.65 2.17
1861 2440 4.754667 GTCCTCGTTCCGGTGGGC 62.755 72.222 0.00 0.00 0.00 5.36
1866 2445 1.374252 CCACTTGTCCTCGTTCCGG 60.374 63.158 0.00 0.00 0.00 5.14
2130 2709 3.991051 ACGTCCACGCAGTCCAGG 61.991 66.667 0.00 0.00 41.61 4.45
2241 2820 4.803426 CTCCACTGCGCCGACCTC 62.803 72.222 4.18 0.00 0.00 3.85
2490 3073 7.696872 GTGATGAACTGATGATCATTCAAGTTG 59.303 37.037 25.11 0.00 34.54 3.16
2534 3143 5.105473 CCATCAGAAAACAGCATTCCATCTT 60.105 40.000 0.00 0.00 0.00 2.40
2540 3149 2.827921 ACCCCATCAGAAAACAGCATTC 59.172 45.455 0.00 0.00 0.00 2.67
2557 3166 5.053978 AGAAATAACATCCATCTCACCCC 57.946 43.478 0.00 0.00 0.00 4.95
2561 3170 7.770433 CCTACACAAGAAATAACATCCATCTCA 59.230 37.037 0.00 0.00 0.00 3.27
2572 3181 5.417580 GCCCAACATCCTACACAAGAAATAA 59.582 40.000 0.00 0.00 0.00 1.40
2574 3183 3.763897 GCCCAACATCCTACACAAGAAAT 59.236 43.478 0.00 0.00 0.00 2.17
2577 3186 1.702401 TGCCCAACATCCTACACAAGA 59.298 47.619 0.00 0.00 0.00 3.02
2578 3187 2.086869 CTGCCCAACATCCTACACAAG 58.913 52.381 0.00 0.00 0.00 3.16
2652 3261 2.793010 GAACCTCGTCCGTCCACGAC 62.793 65.000 0.00 0.00 43.79 4.34
2747 3356 1.055476 GTAAGAGCGTTCGTTCGTTCG 59.945 52.381 3.16 7.17 43.61 3.95
2767 3376 9.478019 CGAAAGTAAGTACATTTTGCTCTTATG 57.522 33.333 0.00 0.00 0.00 1.90
2768 3377 9.431887 TCGAAAGTAAGTACATTTTGCTCTTAT 57.568 29.630 0.00 0.00 0.00 1.73
2926 3538 4.937620 TGGTCAGACAAACTCTGCATATTC 59.062 41.667 2.17 0.00 45.64 1.75
3006 3626 2.491693 ACACACTGTTTTGTTGGTCAGG 59.508 45.455 0.00 0.00 32.92 3.86
3014 3634 5.224135 GGTAAAACACACACACTGTTTTGT 58.776 37.500 16.00 0.00 46.44 2.83
3015 3635 4.623595 GGGTAAAACACACACACTGTTTTG 59.376 41.667 16.00 0.00 46.44 2.44
3017 3637 3.193903 GGGGTAAAACACACACACTGTTT 59.806 43.478 0.00 0.00 42.41 2.83
3028 3648 3.634910 TGAGCAAGAAAGGGGTAAAACAC 59.365 43.478 0.00 0.00 0.00 3.32
3031 3651 3.756434 CGATGAGCAAGAAAGGGGTAAAA 59.244 43.478 0.00 0.00 0.00 1.52
3035 3655 0.984230 TCGATGAGCAAGAAAGGGGT 59.016 50.000 0.00 0.00 0.00 4.95
3062 3684 3.202829 TCGCACTTGGTCCTTAACTTT 57.797 42.857 0.00 0.00 0.00 2.66
3066 3688 1.448985 GCATCGCACTTGGTCCTTAA 58.551 50.000 0.00 0.00 0.00 1.85
3080 3702 1.040646 TTCCTAGCTACCAGGCATCG 58.959 55.000 0.00 0.00 32.82 3.84
3123 3752 2.044492 TGGATGTCCCAGTCCTAACTCT 59.956 50.000 0.00 0.00 40.82 3.24
3124 3753 2.467880 TGGATGTCCCAGTCCTAACTC 58.532 52.381 0.00 0.00 40.82 3.01
3125 3754 2.642171 TGGATGTCCCAGTCCTAACT 57.358 50.000 0.00 0.00 40.82 2.24
3134 3763 4.715534 TCTTGTTAAGTTGGATGTCCCA 57.284 40.909 0.00 0.00 44.93 4.37
3135 3764 6.590234 ATTTCTTGTTAAGTTGGATGTCCC 57.410 37.500 0.00 0.00 34.29 4.46
3158 3789 9.119418 ACGGTCATGAATGAATGTGATTATTTA 57.881 29.630 0.00 0.00 38.75 1.40
3161 3792 6.994496 AGACGGTCATGAATGAATGTGATTAT 59.006 34.615 11.27 0.00 38.75 1.28
3164 3795 4.774124 AGACGGTCATGAATGAATGTGAT 58.226 39.130 11.27 0.00 38.75 3.06
3168 3799 6.128445 GGCTTATAGACGGTCATGAATGAATG 60.128 42.308 11.27 0.00 38.75 2.67
3169 3800 5.934625 GGCTTATAGACGGTCATGAATGAAT 59.065 40.000 11.27 0.00 38.75 2.57
3170 3801 5.070446 AGGCTTATAGACGGTCATGAATGAA 59.930 40.000 11.27 0.00 38.75 2.57
3171 3802 4.588951 AGGCTTATAGACGGTCATGAATGA 59.411 41.667 11.27 0.00 0.00 2.57
3183 3814 9.825109 ATTCAACTTTCTCTAAGGCTTATAGAC 57.175 33.333 18.68 0.00 38.23 2.59
3189 3820 8.787852 CAGTAAATTCAACTTTCTCTAAGGCTT 58.212 33.333 4.58 4.58 38.23 4.35
3190 3821 7.094592 GCAGTAAATTCAACTTTCTCTAAGGCT 60.095 37.037 0.00 0.00 38.23 4.58
3191 3822 7.024171 GCAGTAAATTCAACTTTCTCTAAGGC 58.976 38.462 0.00 0.00 38.23 4.35
3192 3823 7.117812 TCGCAGTAAATTCAACTTTCTCTAAGG 59.882 37.037 0.00 0.00 38.23 2.69
3193 3824 7.952637 GTCGCAGTAAATTCAACTTTCTCTAAG 59.047 37.037 0.00 0.00 39.87 2.18
3194 3825 7.439955 TGTCGCAGTAAATTCAACTTTCTCTAA 59.560 33.333 0.00 0.00 0.00 2.10
3196 3827 5.758296 TGTCGCAGTAAATTCAACTTTCTCT 59.242 36.000 0.00 0.00 0.00 3.10
3198 3829 6.371809 TTGTCGCAGTAAATTCAACTTTCT 57.628 33.333 0.00 0.00 0.00 2.52
3199 3830 8.627428 GTTATTGTCGCAGTAAATTCAACTTTC 58.373 33.333 0.00 0.00 0.00 2.62
3200 3831 8.132362 TGTTATTGTCGCAGTAAATTCAACTTT 58.868 29.630 0.00 0.00 0.00 2.66
3219 3863 8.815141 TGATCACCAACTTTCAAATGTTATTG 57.185 30.769 0.00 0.00 0.00 1.90
3227 3871 5.523188 GTGCATTTGATCACCAACTTTCAAA 59.477 36.000 0.00 0.00 40.99 2.69
3228 3872 5.049167 GTGCATTTGATCACCAACTTTCAA 58.951 37.500 0.00 0.00 33.85 2.69
3229 3873 4.341806 AGTGCATTTGATCACCAACTTTCA 59.658 37.500 0.00 0.00 33.85 2.69
3230 3874 4.682860 CAGTGCATTTGATCACCAACTTTC 59.317 41.667 0.00 0.00 33.85 2.62
3233 3877 2.029649 GCAGTGCATTTGATCACCAACT 60.030 45.455 11.09 0.00 33.85 3.16
3238 3882 3.240069 GAAGTGCAGTGCATTTGATCAC 58.760 45.455 28.08 11.25 41.91 3.06
3270 3914 7.481642 TCCTCTGTCTCAAAATATAAGACGTC 58.518 38.462 7.70 7.70 41.84 4.34
3271 3915 7.406031 TCCTCTGTCTCAAAATATAAGACGT 57.594 36.000 0.00 0.00 41.84 4.34
3272 3916 7.976734 ACTTCCTCTGTCTCAAAATATAAGACG 59.023 37.037 0.00 0.00 41.84 4.18
3279 3923 8.088981 GTCAACTACTTCCTCTGTCTCAAAATA 58.911 37.037 0.00 0.00 0.00 1.40
3281 3925 6.127168 TGTCAACTACTTCCTCTGTCTCAAAA 60.127 38.462 0.00 0.00 0.00 2.44
3282 3926 5.362717 TGTCAACTACTTCCTCTGTCTCAAA 59.637 40.000 0.00 0.00 0.00 2.69
3283 3927 4.893524 TGTCAACTACTTCCTCTGTCTCAA 59.106 41.667 0.00 0.00 0.00 3.02
3284 3928 4.470602 TGTCAACTACTTCCTCTGTCTCA 58.529 43.478 0.00 0.00 0.00 3.27
3285 3929 5.417580 AGATGTCAACTACTTCCTCTGTCTC 59.582 44.000 0.00 0.00 33.70 3.36
3287 3931 5.652994 AGATGTCAACTACTTCCTCTGTC 57.347 43.478 0.00 0.00 33.70 3.51
3288 3932 6.249951 AGTAGATGTCAACTACTTCCTCTGT 58.750 40.000 15.14 0.00 45.24 3.41
3315 3966 6.700081 CGCTCTACCTGTATTTGCTGTTAATA 59.300 38.462 0.00 0.00 0.00 0.98
3317 3968 4.868171 CGCTCTACCTGTATTTGCTGTTAA 59.132 41.667 0.00 0.00 0.00 2.01
3337 3988 2.418368 TCCTTGGATAAACATGCGCT 57.582 45.000 9.73 0.00 0.00 5.92
3340 3991 5.047377 TCCTTGTTTCCTTGGATAAACATGC 60.047 40.000 7.49 0.00 43.14 4.06
3386 4038 8.879759 GTCTTCATTTTCCGAAATATCAGTGTA 58.120 33.333 0.00 0.00 33.78 2.90
3391 4043 7.339212 ACATGGTCTTCATTTTCCGAAATATCA 59.661 33.333 0.00 0.00 33.78 2.15
3401 4053 6.985188 TGCTACTACATGGTCTTCATTTTC 57.015 37.500 0.00 0.00 32.92 2.29
3580 4235 2.485426 GCTAAAATGCACAGCAGTCTGA 59.515 45.455 3.32 0.00 43.65 3.27
3627 4282 7.672660 TGTCTAGACTAGATGAAGTTTGGGTAA 59.327 37.037 23.01 0.00 37.13 2.85
3628 4283 7.179966 TGTCTAGACTAGATGAAGTTTGGGTA 58.820 38.462 23.01 0.00 37.13 3.69
3629 4284 6.017192 TGTCTAGACTAGATGAAGTTTGGGT 58.983 40.000 23.01 0.00 37.13 4.51


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

AutoCloner maintained by Alex Coulton.