Multiple sequence alignment - TraesCS1B01G277700

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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 TraesCS1B01G277700 chr1B 100.000 2495 0 0 1 2495 486157167 486159661 0.000000e+00 4608.0
1 TraesCS1B01G277700 chr1D 90.689 1815 117 20 657 2445 362920375 362922163 0.000000e+00 2368.0
2 TraesCS1B01G277700 chr1D 91.225 547 34 8 81 617 362918666 362919208 0.000000e+00 732.0
3 TraesCS1B01G277700 chr1A 88.352 1966 128 46 48 1948 462135955 462137884 0.000000e+00 2268.0
4 TraesCS1B01G277700 chr1A 85.676 377 45 4 2077 2445 286122777 286122402 3.010000e-104 388.0
5 TraesCS1B01G277700 chr1A 100.000 47 0 0 2449 2495 451671349 451671395 1.230000e-13 87.9
6 TraesCS1B01G277700 chr1A 100.000 46 0 0 2450 2495 167330857 167330902 4.420000e-13 86.1
7 TraesCS1B01G277700 chr2D 88.482 382 35 6 2073 2445 167421647 167421266 1.050000e-123 453.0
8 TraesCS1B01G277700 chr2D 84.293 382 49 9 2074 2445 218389397 218389777 1.820000e-96 363.0
9 TraesCS1B01G277700 chr2D 84.252 381 50 7 2072 2443 301346048 301346427 1.820000e-96 363.0
10 TraesCS1B01G277700 chr3D 85.117 383 47 8 2073 2445 226730961 226730579 1.400000e-102 383.0
11 TraesCS1B01G277700 chr3D 94.286 35 2 0 1227 1261 497369174 497369140 1.000000e-03 54.7
12 TraesCS1B01G277700 chr4D 85.079 382 48 7 2072 2444 336115865 336115484 5.040000e-102 381.0
13 TraesCS1B01G277700 chr4D 76.037 434 69 21 2075 2495 164870189 164870600 2.530000e-45 193.0
14 TraesCS1B01G277700 chr2B 84.817 382 49 7 2073 2445 256993550 256993931 2.340000e-100 375.0
15 TraesCS1B01G277700 chr2B 84.211 380 51 7 2075 2445 257069900 257070279 6.560000e-96 361.0
16 TraesCS1B01G277700 chrUn 77.705 305 36 20 2202 2495 11255150 11255433 9.240000e-35 158.0
17 TraesCS1B01G277700 chr4A 100.000 47 0 0 2449 2495 255201954 255202000 1.230000e-13 87.9
18 TraesCS1B01G277700 chr4A 100.000 47 0 0 2449 2495 277218535 277218489 1.230000e-13 87.9
19 TraesCS1B01G277700 chr4A 100.000 47 0 0 2449 2495 709811227 709811273 1.230000e-13 87.9
20 TraesCS1B01G277700 chr3A 100.000 47 0 0 2449 2495 681147815 681147861 1.230000e-13 87.9
21 TraesCS1B01G277700 chr5D 100.000 46 0 0 2450 2495 7820159 7820114 4.420000e-13 86.1


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 TraesCS1B01G277700 chr1B 486157167 486159661 2494 False 4608 4608 100.000 1 2495 1 chr1B.!!$F1 2494
1 TraesCS1B01G277700 chr1D 362918666 362922163 3497 False 1550 2368 90.957 81 2445 2 chr1D.!!$F1 2364
2 TraesCS1B01G277700 chr1A 462135955 462137884 1929 False 2268 2268 88.352 48 1948 1 chr1A.!!$F3 1900

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
493 504 0.172803 CTCGTGACCCCCGACTTAAG 59.827 60.0 0.0 0.0 0.0 1.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1801 3030 0.036306 GGGTGTCCATTTGTCTCCGT 59.964 55.0 0.0 0.0 0.0 4.69 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
23 24 5.906073 GCCCACATCAGCATTTATTAAACT 58.094 37.500 0.00 0.00 0.00 2.66
24 25 5.750067 GCCCACATCAGCATTTATTAAACTG 59.250 40.000 0.00 0.00 0.00 3.16
25 26 5.750067 CCCACATCAGCATTTATTAAACTGC 59.250 40.000 12.05 12.05 34.85 4.40
26 27 6.406177 CCCACATCAGCATTTATTAAACTGCT 60.406 38.462 14.79 14.79 45.41 4.24
27 28 7.037438 CCACATCAGCATTTATTAAACTGCTT 58.963 34.615 16.58 7.24 42.79 3.91
28 29 8.190122 CCACATCAGCATTTATTAAACTGCTTA 58.810 33.333 16.58 12.50 42.79 3.09
29 30 9.013490 CACATCAGCATTTATTAAACTGCTTAC 57.987 33.333 16.58 0.00 42.79 2.34
30 31 8.190784 ACATCAGCATTTATTAAACTGCTTACC 58.809 33.333 16.58 0.00 42.79 2.85
31 32 7.938140 TCAGCATTTATTAAACTGCTTACCT 57.062 32.000 16.58 2.42 42.79 3.08
32 33 9.627123 ATCAGCATTTATTAAACTGCTTACCTA 57.373 29.630 16.58 7.14 42.79 3.08
33 34 9.456147 TCAGCATTTATTAAACTGCTTACCTAA 57.544 29.630 16.58 4.26 42.79 2.69
34 35 9.722056 CAGCATTTATTAAACTGCTTACCTAAG 57.278 33.333 16.58 6.77 42.79 2.18
54 55 4.247267 AGCAGTGTGAAATGGTCAAATG 57.753 40.909 0.00 0.00 38.23 2.32
56 57 3.243839 GCAGTGTGAAATGGTCAAATGGT 60.244 43.478 0.00 0.00 38.23 3.55
84 92 2.319032 CGCTTCTTCATCTGCGCG 59.681 61.111 0.00 0.00 41.85 6.86
121 129 0.733729 GCGAGTCGAGAGCCTCTTTA 59.266 55.000 18.61 0.00 0.00 1.85
134 142 2.175811 CTTTACGTTGGCGGCTGC 59.824 61.111 9.72 9.72 43.45 5.25
145 153 4.680237 CGGCTGCCCTGAACGTCA 62.680 66.667 14.12 0.00 0.00 4.35
152 160 1.444119 GCCCTGAACGTCAACAAGCA 61.444 55.000 0.00 0.00 0.00 3.91
163 171 0.936297 CAACAAGCAGCACGCCTTTC 60.936 55.000 0.00 0.00 44.04 2.62
182 190 2.665165 TCCCAACTGCACAAAAGTGAT 58.335 42.857 0.00 0.00 0.00 3.06
187 195 4.501915 CCAACTGCACAAAAGTGATGGATT 60.502 41.667 0.00 0.00 0.00 3.01
249 257 5.800438 GGTTAATCAACGCCATTCTTTTCTC 59.200 40.000 0.00 0.00 35.34 2.87
252 260 4.749245 TCAACGCCATTCTTTTCTCTTC 57.251 40.909 0.00 0.00 0.00 2.87
317 325 4.124851 ACACGAAGTCTTGTCAAACTCT 57.875 40.909 0.00 0.00 41.61 3.24
336 347 2.366266 TCTGTGGTAAAGCTGGTACGTT 59.634 45.455 0.00 0.00 0.00 3.99
363 374 1.274703 ATCTGCCCGACAAGGTCCAT 61.275 55.000 0.00 0.00 38.74 3.41
391 402 1.006102 CGACTTCCACTCCGCAGTT 60.006 57.895 0.00 0.00 0.00 3.16
417 428 2.676750 CGATTTGACCCGATGTCTTCCA 60.677 50.000 6.61 0.00 44.75 3.53
418 429 2.472695 TTTGACCCGATGTCTTCCAG 57.527 50.000 6.61 0.00 44.75 3.86
419 430 0.613260 TTGACCCGATGTCTTCCAGG 59.387 55.000 6.61 0.00 44.75 4.45
420 431 1.264749 TGACCCGATGTCTTCCAGGG 61.265 60.000 6.61 0.00 44.75 4.45
421 432 1.972660 GACCCGATGTCTTCCAGGGG 61.973 65.000 3.73 0.00 46.10 4.79
447 458 6.293190 CCGTGAGCACTGTAGTAATTTTCAAA 60.293 38.462 0.00 0.00 0.00 2.69
485 496 4.222847 GATCCGCTCGTGACCCCC 62.223 72.222 0.00 0.00 0.00 5.40
493 504 0.172803 CTCGTGACCCCCGACTTAAG 59.827 60.000 0.00 0.00 0.00 1.85
507 523 0.727398 CTTAAGCACACCGCCTAAGC 59.273 55.000 0.00 0.00 44.04 3.09
542 558 2.438411 AGACACTAGGAACAGAGACCG 58.562 52.381 0.00 0.00 0.00 4.79
632 659 3.935203 CCGTGCTAAAATCAGTGATCTGT 59.065 43.478 5.98 0.00 41.91 3.41
636 663 6.017933 GTGCTAAAATCAGTGATCTGTTTCG 58.982 40.000 5.98 1.50 41.91 3.46
779 1950 4.024302 GCTGAAAAACTAACCGTGCTAGTT 60.024 41.667 0.00 0.00 40.52 2.24
848 2039 7.659390 CAGGAGACAGGAGGTGAATATAAATTC 59.341 40.741 0.00 0.00 41.69 2.17
877 2068 1.817099 CTTGGATGCTCTCACGGGC 60.817 63.158 0.00 0.00 0.00 6.13
921 2112 3.603532 TGATCTTGTCCTTGTGCTGATC 58.396 45.455 0.00 0.00 0.00 2.92
990 2181 4.445699 GCAAGGAGCCTACATCCG 57.554 61.111 0.00 0.00 42.02 4.18
992 2183 0.530870 GCAAGGAGCCTACATCCGTC 60.531 60.000 0.00 0.00 42.02 4.79
994 2185 0.683504 AAGGAGCCTACATCCGTCGT 60.684 55.000 0.00 0.00 42.02 4.34
1125 2325 4.699522 AACGCGTGGGAAGGGCTC 62.700 66.667 14.98 0.00 0.00 4.70
1343 2543 2.736995 CGACGACCACAATGCGGT 60.737 61.111 0.00 0.00 40.30 5.68
1419 2619 1.885163 GAGAGGAAGGTCGGCCGAAA 61.885 60.000 32.93 5.72 40.50 3.46
1461 2661 2.664402 AGAGAGGCAACCACAACATT 57.336 45.000 0.00 0.00 37.17 2.71
1542 2755 3.502920 CGACGAAATGTACTTGCTCTCT 58.497 45.455 0.00 0.00 0.00 3.10
1553 2777 2.298729 ACTTGCTCTCTGTCTCTTGGTC 59.701 50.000 0.00 0.00 0.00 4.02
1554 2778 2.001076 TGCTCTCTGTCTCTTGGTCA 57.999 50.000 0.00 0.00 0.00 4.02
1565 2789 2.176798 TCTCTTGGTCAATTGTTGGGGT 59.823 45.455 5.13 0.00 0.00 4.95
1566 2790 2.297033 CTCTTGGTCAATTGTTGGGGTG 59.703 50.000 5.13 0.00 0.00 4.61
1567 2791 2.038659 CTTGGTCAATTGTTGGGGTGT 58.961 47.619 5.13 0.00 0.00 4.16
1568 2792 2.166907 TGGTCAATTGTTGGGGTGTT 57.833 45.000 5.13 0.00 0.00 3.32
1569 2793 2.472029 TGGTCAATTGTTGGGGTGTTT 58.528 42.857 5.13 0.00 0.00 2.83
1570 2794 2.840651 TGGTCAATTGTTGGGGTGTTTT 59.159 40.909 5.13 0.00 0.00 2.43
1571 2795 3.264450 TGGTCAATTGTTGGGGTGTTTTT 59.736 39.130 5.13 0.00 0.00 1.94
1606 2830 1.698506 TTGTTGGGGGTGTTCATGTC 58.301 50.000 0.00 0.00 0.00 3.06
1625 2849 2.396185 GTCGCATTTGTTTCGTTCGTTC 59.604 45.455 0.00 0.00 0.00 3.95
1637 2861 1.334779 CGTTCGTTCTCGTTGAGGAGT 60.335 52.381 1.19 0.00 38.33 3.85
1724 2953 4.177026 TGAGTGCGAGCTTTTTAGATCTC 58.823 43.478 0.00 0.00 0.00 2.75
1787 3016 1.841302 TTTGCTGGTCTCCGATGCCT 61.841 55.000 0.00 0.00 0.00 4.75
1837 3073 2.243957 CCAGAGTTCGTGCGCAACA 61.244 57.895 14.00 0.00 0.00 3.33
1929 3168 5.507315 CCGAAATAGCCCAAATACAATCACC 60.507 44.000 0.00 0.00 0.00 4.02
1948 3187 3.056080 ACCACTACCCCATGCATAAGAT 58.944 45.455 0.00 0.00 0.00 2.40
1956 3195 5.380043 ACCCCATGCATAAGATAGTCTTTG 58.620 41.667 0.00 0.00 37.89 2.77
1988 3227 1.199558 GCATCTATAGTCGGACGTCCC 59.800 57.143 28.52 15.65 0.00 4.46
1993 3232 1.553706 ATAGTCGGACGTCCCAAACT 58.446 50.000 28.52 27.03 35.48 2.66
1999 3238 0.108019 GGACGTCCCAAACTCACCTT 59.892 55.000 24.75 0.00 34.14 3.50
2006 3245 4.204799 GTCCCAAACTCACCTTAAACACT 58.795 43.478 0.00 0.00 0.00 3.55
2011 3250 4.618920 AACTCACCTTAAACACTCGGAT 57.381 40.909 0.00 0.00 0.00 4.18
2012 3251 5.733620 AACTCACCTTAAACACTCGGATA 57.266 39.130 0.00 0.00 0.00 2.59
2017 3256 4.012374 ACCTTAAACACTCGGATAGACGA 58.988 43.478 0.00 0.00 41.13 4.20
2037 3276 1.153823 CCGATCACTGACCGGTCAC 60.154 63.158 33.23 21.22 38.55 3.67
2039 3278 0.456824 CGATCACTGACCGGTCACAG 60.457 60.000 33.23 25.59 39.65 3.66
2040 3279 0.888619 GATCACTGACCGGTCACAGA 59.111 55.000 33.23 29.70 37.54 3.41
2043 3282 2.521126 TCACTGACCGGTCACAGATAA 58.479 47.619 33.23 10.87 37.54 1.75
2044 3283 3.096852 TCACTGACCGGTCACAGATAAT 58.903 45.455 33.23 9.79 37.54 1.28
2045 3284 3.130516 TCACTGACCGGTCACAGATAATC 59.869 47.826 33.23 4.24 37.54 1.75
2047 3286 1.407618 TGACCGGTCACAGATAATCGG 59.592 52.381 33.23 0.00 42.69 4.18
2049 3288 0.600255 CCGGTCACAGATAATCGGCC 60.600 60.000 0.00 0.00 0.00 6.13
2050 3289 0.939577 CGGTCACAGATAATCGGCCG 60.940 60.000 22.12 22.12 0.00 6.13
2051 3290 0.387929 GGTCACAGATAATCGGCCGA 59.612 55.000 33.12 33.12 0.00 5.54
2053 3292 1.337071 GTCACAGATAATCGGCCGAGA 59.663 52.381 33.87 23.73 0.00 4.04
2094 3333 1.553248 TGACGGTGTTCTGGATAAGGG 59.447 52.381 0.00 0.00 0.00 3.95
2102 3342 5.163332 GGTGTTCTGGATAAGGGGTACTAAG 60.163 48.000 0.00 0.00 0.00 2.18
2103 3343 5.659971 GTGTTCTGGATAAGGGGTACTAAGA 59.340 44.000 0.00 0.00 0.00 2.10
2104 3344 5.897824 TGTTCTGGATAAGGGGTACTAAGAG 59.102 44.000 0.00 0.00 0.00 2.85
2119 3359 1.280457 AAGAGAGTCGGCCCATTCTT 58.720 50.000 0.00 0.00 0.00 2.52
2120 3360 0.539051 AGAGAGTCGGCCCATTCTTG 59.461 55.000 0.00 0.00 0.00 3.02
2123 3363 0.036388 GAGTCGGCCCATTCTTGTCA 60.036 55.000 0.00 0.00 0.00 3.58
2126 3366 1.750399 CGGCCCATTCTTGTCAGGG 60.750 63.158 0.00 0.00 44.37 4.45
2167 3407 1.152419 TGGTCAAGGTGGACTCCGA 60.152 57.895 0.00 0.00 37.91 4.55
2198 3438 1.336440 CAGGAGGCGTGATCTAGACTG 59.664 57.143 0.00 0.00 0.00 3.51
2229 3469 3.644884 AGACTTGACGTGTACTCCAAG 57.355 47.619 10.01 10.01 41.12 3.61
2234 3474 4.281182 ACTTGACGTGTACTCCAAGATCTT 59.719 41.667 16.57 0.88 39.28 2.40
2299 3541 1.518774 CCCCGGCGTGTATACAAGT 59.481 57.895 18.20 0.00 0.00 3.16
2305 3553 4.365723 CCGGCGTGTATACAAGTCTTTAT 58.634 43.478 18.96 0.00 0.00 1.40
2309 3557 5.452917 GGCGTGTATACAAGTCTTTATCCCT 60.453 44.000 18.20 0.00 0.00 4.20
2340 3588 3.913763 ACATCAACACAAAATCATTCGCG 59.086 39.130 0.00 0.00 0.00 5.87
2342 3590 4.733972 TCAACACAAAATCATTCGCGTA 57.266 36.364 5.77 0.00 0.00 4.42
2362 3610 4.762765 CGTAGCCCTAGAGTTAGATCACAT 59.237 45.833 0.00 0.00 0.00 3.21
2363 3611 5.335269 CGTAGCCCTAGAGTTAGATCACATG 60.335 48.000 0.00 0.00 0.00 3.21
2368 3616 6.183360 GCCCTAGAGTTAGATCACATGTTACA 60.183 42.308 0.00 0.00 0.00 2.41
2377 3625 5.595885 AGATCACATGTTACAATCTCGAGG 58.404 41.667 13.56 0.00 0.00 4.63
2380 3628 5.891451 TCACATGTTACAATCTCGAGGTAG 58.109 41.667 13.56 5.00 0.00 3.18
2388 3636 5.508200 ACAATCTCGAGGTAGATCAACTC 57.492 43.478 13.56 0.00 35.10 3.01
2413 3661 9.538508 TCTGTACTTGATACATCTTCATCAATG 57.461 33.333 0.00 0.00 43.01 2.82
2426 3675 9.880064 CATCTTCATCAATGTAAATAAGAGCAG 57.120 33.333 0.00 0.00 0.00 4.24
2445 3694 2.830321 CAGGACGTAGGGTTTTACCTCT 59.170 50.000 0.00 0.00 42.09 3.69
2446 3695 3.260128 CAGGACGTAGGGTTTTACCTCTT 59.740 47.826 0.00 0.00 42.09 2.85
2447 3696 3.260128 AGGACGTAGGGTTTTACCTCTTG 59.740 47.826 0.00 0.00 42.09 3.02
2448 3697 3.259123 GGACGTAGGGTTTTACCTCTTGA 59.741 47.826 0.00 0.00 42.09 3.02
2449 3698 4.081254 GGACGTAGGGTTTTACCTCTTGAT 60.081 45.833 0.00 0.00 42.09 2.57
2450 3699 5.127682 GGACGTAGGGTTTTACCTCTTGATA 59.872 44.000 0.00 0.00 42.09 2.15
2451 3700 6.218108 ACGTAGGGTTTTACCTCTTGATAG 57.782 41.667 0.00 0.00 42.09 2.08
2452 3701 5.128335 ACGTAGGGTTTTACCTCTTGATAGG 59.872 44.000 0.00 0.00 42.09 2.57
2453 3702 5.452917 CGTAGGGTTTTACCTCTTGATAGGG 60.453 48.000 0.00 0.00 42.09 3.53
2454 3703 4.445564 AGGGTTTTACCTCTTGATAGGGT 58.554 43.478 0.00 0.00 41.32 4.34
2455 3704 4.856182 AGGGTTTTACCTCTTGATAGGGTT 59.144 41.667 0.00 0.00 41.32 4.11
2456 3705 5.315109 AGGGTTTTACCTCTTGATAGGGTTT 59.685 40.000 0.00 0.00 41.32 3.27
2457 3706 6.014647 GGGTTTTACCTCTTGATAGGGTTTT 58.985 40.000 0.00 0.00 41.32 2.43
2458 3707 7.018851 AGGGTTTTACCTCTTGATAGGGTTTTA 59.981 37.037 0.00 0.00 41.32 1.52
2459 3708 7.121759 GGGTTTTACCTCTTGATAGGGTTTTAC 59.878 40.741 0.00 0.00 41.32 2.01
2460 3709 7.121759 GGTTTTACCTCTTGATAGGGTTTTACC 59.878 40.741 0.00 0.00 41.32 2.85
2461 3710 7.578458 TTTACCTCTTGATAGGGTTTTACCT 57.422 36.000 0.00 0.00 44.75 3.08
2462 3711 5.695424 ACCTCTTGATAGGGTTTTACCTC 57.305 43.478 0.00 0.00 42.09 3.85
2463 3712 4.473922 ACCTCTTGATAGGGTTTTACCTCC 59.526 45.833 0.00 0.00 42.09 4.30
2464 3713 4.473559 CCTCTTGATAGGGTTTTACCTCCA 59.526 45.833 0.00 0.00 42.09 3.86
2465 3714 5.132816 CCTCTTGATAGGGTTTTACCTCCAT 59.867 44.000 0.00 0.00 42.09 3.41
2466 3715 6.248569 TCTTGATAGGGTTTTACCTCCATC 57.751 41.667 0.00 0.00 42.09 3.51
2467 3716 5.729229 TCTTGATAGGGTTTTACCTCCATCA 59.271 40.000 0.00 0.00 42.09 3.07
2468 3717 6.216662 TCTTGATAGGGTTTTACCTCCATCAA 59.783 38.462 9.06 9.06 42.09 2.57
2469 3718 6.001449 TGATAGGGTTTTACCTCCATCAAG 57.999 41.667 0.00 0.00 42.09 3.02
2470 3719 5.729229 TGATAGGGTTTTACCTCCATCAAGA 59.271 40.000 0.00 0.00 42.09 3.02
2471 3720 4.576330 AGGGTTTTACCTCCATCAAGAG 57.424 45.455 0.00 0.00 38.64 2.85
2478 3727 2.612760 CTCCATCAAGAGGGCCTGA 58.387 57.895 12.95 2.79 31.15 3.86
2479 3728 0.914644 CTCCATCAAGAGGGCCTGAA 59.085 55.000 12.95 0.00 31.15 3.02
2480 3729 0.620556 TCCATCAAGAGGGCCTGAAC 59.379 55.000 12.95 0.00 31.15 3.18
2481 3730 0.394899 CCATCAAGAGGGCCTGAACC 60.395 60.000 12.95 0.00 0.00 3.62
2482 3731 0.622665 CATCAAGAGGGCCTGAACCT 59.377 55.000 12.95 0.00 42.18 3.50
2483 3732 0.622665 ATCAAGAGGGCCTGAACCTG 59.377 55.000 12.95 0.00 38.79 4.00
2484 3733 1.001641 CAAGAGGGCCTGAACCTGG 60.002 63.158 12.95 0.00 38.79 4.45
2485 3734 2.234296 AAGAGGGCCTGAACCTGGG 61.234 63.158 12.95 0.00 38.79 4.45
2486 3735 2.936032 GAGGGCCTGAACCTGGGT 60.936 66.667 12.95 0.00 38.79 4.51
2487 3736 1.615424 GAGGGCCTGAACCTGGGTA 60.615 63.158 12.95 0.00 38.79 3.69
2488 3737 1.151677 AGGGCCTGAACCTGGGTAA 60.152 57.895 4.50 0.00 36.85 2.85
2489 3738 0.774491 AGGGCCTGAACCTGGGTAAA 60.774 55.000 4.50 0.00 36.85 2.01
2490 3739 0.611062 GGGCCTGAACCTGGGTAAAC 60.611 60.000 0.84 0.00 0.00 2.01
2491 3740 0.111639 GGCCTGAACCTGGGTAAACA 59.888 55.000 0.00 0.00 0.00 2.83
2492 3741 1.272480 GGCCTGAACCTGGGTAAACAT 60.272 52.381 0.00 0.00 0.00 2.71
2493 3742 2.092323 GCCTGAACCTGGGTAAACATC 58.908 52.381 0.00 0.00 0.00 3.06
2494 3743 2.356135 CCTGAACCTGGGTAAACATCG 58.644 52.381 0.00 0.00 0.00 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.750067 CAGTTTAATAAATGCTGATGTGGGC 59.250 40.000 0.00 0.00 0.00 5.36
25 26 5.003804 ACCATTTCACACTGCTTAGGTAAG 58.996 41.667 0.00 0.00 36.40 2.34
26 27 4.980573 ACCATTTCACACTGCTTAGGTAA 58.019 39.130 0.00 0.00 0.00 2.85
27 28 4.041075 TGACCATTTCACACTGCTTAGGTA 59.959 41.667 0.00 0.00 0.00 3.08
28 29 3.181445 TGACCATTTCACACTGCTTAGGT 60.181 43.478 0.00 0.00 0.00 3.08
29 30 3.411446 TGACCATTTCACACTGCTTAGG 58.589 45.455 0.00 0.00 0.00 2.69
30 31 5.437289 TTTGACCATTTCACACTGCTTAG 57.563 39.130 0.00 0.00 32.26 2.18
31 32 5.278907 CCATTTGACCATTTCACACTGCTTA 60.279 40.000 0.00 0.00 32.26 3.09
32 33 4.501915 CCATTTGACCATTTCACACTGCTT 60.502 41.667 0.00 0.00 32.26 3.91
33 34 3.006110 CCATTTGACCATTTCACACTGCT 59.994 43.478 0.00 0.00 32.26 4.24
34 35 3.243839 ACCATTTGACCATTTCACACTGC 60.244 43.478 0.00 0.00 32.26 4.40
35 36 4.589216 ACCATTTGACCATTTCACACTG 57.411 40.909 0.00 0.00 32.26 3.66
36 37 5.833131 ACTTACCATTTGACCATTTCACACT 59.167 36.000 0.00 0.00 32.26 3.55
37 38 6.084326 ACTTACCATTTGACCATTTCACAC 57.916 37.500 0.00 0.00 32.26 3.82
38 39 6.514212 CGAACTTACCATTTGACCATTTCACA 60.514 38.462 0.00 0.00 32.26 3.58
39 40 5.856455 CGAACTTACCATTTGACCATTTCAC 59.144 40.000 0.00 0.00 32.26 3.18
40 41 5.533154 ACGAACTTACCATTTGACCATTTCA 59.467 36.000 0.00 0.00 0.00 2.69
41 42 6.009115 ACGAACTTACCATTTGACCATTTC 57.991 37.500 0.00 0.00 0.00 2.17
42 43 5.334569 CGACGAACTTACCATTTGACCATTT 60.335 40.000 0.00 0.00 0.00 2.32
43 44 4.153475 CGACGAACTTACCATTTGACCATT 59.847 41.667 0.00 0.00 0.00 3.16
44 45 3.682858 CGACGAACTTACCATTTGACCAT 59.317 43.478 0.00 0.00 0.00 3.55
45 46 3.061322 CGACGAACTTACCATTTGACCA 58.939 45.455 0.00 0.00 0.00 4.02
46 47 2.159747 GCGACGAACTTACCATTTGACC 60.160 50.000 0.00 0.00 0.00 4.02
54 55 0.731855 AGAAGCGCGACGAACTTACC 60.732 55.000 12.10 0.00 0.00 2.85
56 57 1.334054 GAAGAAGCGCGACGAACTTA 58.666 50.000 12.10 0.00 0.00 2.24
84 92 3.782244 CGGCGACACAAGCAGAGC 61.782 66.667 0.00 0.00 36.08 4.09
134 142 0.588252 CTGCTTGTTGACGTTCAGGG 59.412 55.000 0.00 0.00 0.00 4.45
145 153 1.360192 GAAAGGCGTGCTGCTTGTT 59.640 52.632 0.00 0.00 45.43 2.83
152 160 1.898574 CAGTTGGGAAAGGCGTGCT 60.899 57.895 0.00 0.00 0.00 4.40
182 190 1.358152 AAGGAGAACCGGTCAATCCA 58.642 50.000 25.97 0.00 41.83 3.41
187 195 2.885616 AGAGTAAAGGAGAACCGGTCA 58.114 47.619 8.04 0.00 41.83 4.02
249 257 3.791973 AGGTGATAGAACGCTCAGAAG 57.208 47.619 0.00 0.00 0.00 2.85
252 260 3.182967 GTGAAGGTGATAGAACGCTCAG 58.817 50.000 0.00 0.00 0.00 3.35
317 325 2.485903 CAACGTACCAGCTTTACCACA 58.514 47.619 0.00 0.00 0.00 4.17
336 347 1.375908 GTCGGGCAGATGTTCAGCA 60.376 57.895 0.00 0.00 29.77 4.41
363 374 3.857038 GGAAGTCGGGGGCGCATA 61.857 66.667 10.83 0.00 0.00 3.14
391 402 3.194861 GACATCGGGTCAAATCGAATCA 58.805 45.455 0.00 0.00 46.19 2.57
418 429 3.665675 CTACAGTGCTCACGGCCCC 62.666 68.421 0.00 0.00 40.92 5.80
419 430 1.601419 TACTACAGTGCTCACGGCCC 61.601 60.000 0.00 0.00 40.92 5.80
420 431 0.245539 TTACTACAGTGCTCACGGCC 59.754 55.000 0.00 0.00 40.92 6.13
421 432 2.295253 ATTACTACAGTGCTCACGGC 57.705 50.000 0.19 0.00 42.22 5.68
447 458 3.128764 TCGATGTGCTAATGTCTCGTTCT 59.871 43.478 0.00 0.00 0.00 3.01
481 492 1.376812 GGTGTGCTTAAGTCGGGGG 60.377 63.158 4.02 0.00 0.00 5.40
485 496 0.108992 TAGGCGGTGTGCTTAAGTCG 60.109 55.000 4.02 2.74 45.43 4.18
542 558 5.791480 CACGTGATTCCAACGGTTTTATAAC 59.209 40.000 10.90 0.00 0.00 1.89
617 633 6.073003 GGAAGACGAAACAGATCACTGATTTT 60.073 38.462 0.00 0.00 46.03 1.82
618 634 5.409826 GGAAGACGAAACAGATCACTGATTT 59.590 40.000 0.00 0.00 46.03 2.17
619 635 4.932200 GGAAGACGAAACAGATCACTGATT 59.068 41.667 0.00 0.00 46.03 2.57
620 636 4.021104 TGGAAGACGAAACAGATCACTGAT 60.021 41.667 0.00 0.00 46.03 2.90
621 637 3.320826 TGGAAGACGAAACAGATCACTGA 59.679 43.478 0.00 0.00 46.03 3.41
623 639 4.058817 GTTGGAAGACGAAACAGATCACT 58.941 43.478 0.00 0.00 0.00 3.41
624 640 3.807622 TGTTGGAAGACGAAACAGATCAC 59.192 43.478 0.00 0.00 30.62 3.06
636 663 2.569404 AGGGAGATGTCTGTTGGAAGAC 59.431 50.000 0.00 0.00 45.70 3.01
682 1853 1.215647 CTACGAGGGTGTGTCAGGC 59.784 63.158 0.00 0.00 0.00 4.85
877 2068 3.134458 GGACAAGTGAGAGTTGGTGAAG 58.866 50.000 0.00 0.00 32.93 3.02
926 2117 0.890996 GAGTCTTTGTGGGCAGGTGG 60.891 60.000 0.00 0.00 0.00 4.61
976 2167 0.683504 AACGACGGATGTAGGCTCCT 60.684 55.000 0.00 0.00 0.00 3.69
982 2173 2.287103 TCATCTCGAACGACGGATGTAG 59.713 50.000 18.57 9.84 43.32 2.74
983 2174 2.282407 TCATCTCGAACGACGGATGTA 58.718 47.619 18.57 8.89 43.32 2.29
984 2175 1.092348 TCATCTCGAACGACGGATGT 58.908 50.000 18.57 0.00 43.32 3.06
985 2176 2.188837 TTCATCTCGAACGACGGATG 57.811 50.000 15.38 15.38 43.72 3.51
986 2177 2.543861 CCATTCATCTCGAACGACGGAT 60.544 50.000 0.00 0.00 42.82 4.18
987 2178 1.202256 CCATTCATCTCGAACGACGGA 60.202 52.381 0.00 0.00 42.82 4.69
989 2180 0.572590 GCCATTCATCTCGAACGACG 59.427 55.000 0.00 0.00 44.09 5.12
990 2181 1.927895 AGCCATTCATCTCGAACGAC 58.072 50.000 0.00 0.00 36.12 4.34
992 2183 3.046390 GAGTAGCCATTCATCTCGAACG 58.954 50.000 0.00 0.00 36.12 3.95
994 2185 3.031013 TGGAGTAGCCATTCATCTCGAA 58.969 45.455 0.00 0.00 43.33 3.71
1069 2269 4.598894 CTCCAGCGATCGCCTGGG 62.599 72.222 36.21 32.40 43.17 4.45
1419 2619 0.251832 TCTTCGTCTTGGCCTCCTCT 60.252 55.000 3.32 0.00 0.00 3.69
1461 2661 1.230635 GCTTCTTGCACGCCTTGAGA 61.231 55.000 0.00 0.00 42.31 3.27
1521 2734 3.301906 CAGAGAGCAAGTACATTTCGTCG 59.698 47.826 0.00 0.00 0.00 5.12
1522 2735 4.238514 ACAGAGAGCAAGTACATTTCGTC 58.761 43.478 0.00 0.00 0.00 4.20
1542 2755 3.221771 CCCAACAATTGACCAAGAGACA 58.778 45.455 13.59 0.00 0.00 3.41
1581 2805 2.038813 CACCCCCAACAATCCCCC 59.961 66.667 0.00 0.00 0.00 5.40
1582 2806 0.902984 GAACACCCCCAACAATCCCC 60.903 60.000 0.00 0.00 0.00 4.81
1583 2807 0.178947 TGAACACCCCCAACAATCCC 60.179 55.000 0.00 0.00 0.00 3.85
1584 2808 1.550072 CATGAACACCCCCAACAATCC 59.450 52.381 0.00 0.00 0.00 3.01
1585 2809 2.231235 GACATGAACACCCCCAACAATC 59.769 50.000 0.00 0.00 0.00 2.67
1586 2810 2.247358 GACATGAACACCCCCAACAAT 58.753 47.619 0.00 0.00 0.00 2.71
1587 2811 1.698506 GACATGAACACCCCCAACAA 58.301 50.000 0.00 0.00 0.00 2.83
1588 2812 0.536233 CGACATGAACACCCCCAACA 60.536 55.000 0.00 0.00 0.00 3.33
1589 2813 1.862602 GCGACATGAACACCCCCAAC 61.863 60.000 0.00 0.00 0.00 3.77
1590 2814 1.602323 GCGACATGAACACCCCCAA 60.602 57.895 0.00 0.00 0.00 4.12
1591 2815 2.033448 GCGACATGAACACCCCCA 59.967 61.111 0.00 0.00 0.00 4.96
1592 2816 0.965363 AATGCGACATGAACACCCCC 60.965 55.000 0.00 0.00 0.00 5.40
1593 2817 0.887933 AAATGCGACATGAACACCCC 59.112 50.000 0.00 0.00 0.00 4.95
1594 2818 1.269448 ACAAATGCGACATGAACACCC 59.731 47.619 0.00 0.00 0.00 4.61
1595 2819 2.704725 ACAAATGCGACATGAACACC 57.295 45.000 0.00 0.00 0.00 4.16
1596 2820 3.117832 CGAAACAAATGCGACATGAACAC 59.882 43.478 0.00 0.00 0.00 3.32
1606 2830 2.635444 AGAACGAACGAAACAAATGCG 58.365 42.857 0.14 0.00 0.00 4.73
1625 2849 3.746492 CCTGGTTTTTACTCCTCAACGAG 59.254 47.826 0.00 0.00 35.88 4.18
1637 2861 1.271163 CCGAGCTCACCCTGGTTTTTA 60.271 52.381 15.40 0.00 0.00 1.52
1716 2945 4.141367 ACTCCCAGTCTCATCGAGATCTAA 60.141 45.833 0.00 0.00 40.98 2.10
1717 2946 3.392947 ACTCCCAGTCTCATCGAGATCTA 59.607 47.826 0.00 0.00 40.98 1.98
1724 2953 0.174389 CCACACTCCCAGTCTCATCG 59.826 60.000 0.00 0.00 0.00 3.84
1787 3016 4.973055 CCGTTGGTCGCCCGTGAA 62.973 66.667 0.00 0.00 38.35 3.18
1801 3030 0.036306 GGGTGTCCATTTGTCTCCGT 59.964 55.000 0.00 0.00 0.00 4.69
1807 3043 2.810400 CGAACTCTGGGTGTCCATTTGT 60.810 50.000 0.00 0.00 43.11 2.83
1821 3057 0.319900 AGATGTTGCGCACGAACTCT 60.320 50.000 11.12 8.11 0.00 3.24
1837 3073 2.036731 TCCCACCCGACGACAGAT 59.963 61.111 0.00 0.00 0.00 2.90
1876 3112 1.872234 CGCATACCACACCGAGTCG 60.872 63.158 5.29 5.29 0.00 4.18
1912 3149 3.456380 AGTGGTGATTGTATTTGGGCT 57.544 42.857 0.00 0.00 0.00 5.19
1929 3168 5.247110 AGACTATCTTATGCATGGGGTAGTG 59.753 44.000 22.60 6.26 0.00 2.74
1978 3217 1.364901 GTGAGTTTGGGACGTCCGA 59.635 57.895 27.68 22.29 38.76 4.55
1980 3219 0.108019 AAGGTGAGTTTGGGACGTCC 59.892 55.000 27.04 27.04 0.00 4.79
1982 3221 3.208594 GTTTAAGGTGAGTTTGGGACGT 58.791 45.455 0.00 0.00 0.00 4.34
1988 3227 4.124238 TCCGAGTGTTTAAGGTGAGTTTG 58.876 43.478 0.00 0.00 0.00 2.93
1993 3232 4.142534 CGTCTATCCGAGTGTTTAAGGTGA 60.143 45.833 0.00 0.00 0.00 4.02
1999 3238 2.684881 GGGTCGTCTATCCGAGTGTTTA 59.315 50.000 0.00 0.00 37.56 2.01
2011 3250 1.376543 GTCAGTGATCGGGTCGTCTA 58.623 55.000 0.00 0.00 0.00 2.59
2012 3251 1.313812 GGTCAGTGATCGGGTCGTCT 61.314 60.000 0.00 0.00 0.00 4.18
2037 3276 0.591659 TCGTCTCGGCCGATTATCTG 59.408 55.000 31.19 16.35 0.00 2.90
2039 3278 0.729816 GCTCGTCTCGGCCGATTATC 60.730 60.000 31.19 17.30 33.27 1.75
2040 3279 1.286260 GCTCGTCTCGGCCGATTAT 59.714 57.895 31.19 0.00 33.27 1.28
2060 3299 3.371063 GTCACCGGGCGTCTGAGA 61.371 66.667 6.32 0.00 0.00 3.27
2094 3333 1.031235 GGGCCGACTCTCTTAGTACC 58.969 60.000 0.00 0.00 39.07 3.34
2102 3342 0.250513 ACAAGAATGGGCCGACTCTC 59.749 55.000 0.00 0.00 0.00 3.20
2103 3343 0.250513 GACAAGAATGGGCCGACTCT 59.749 55.000 0.00 0.00 0.00 3.24
2104 3344 0.036388 TGACAAGAATGGGCCGACTC 60.036 55.000 0.00 0.00 0.00 3.36
2136 3376 0.036388 TTGACCACGAATGAGGGCTC 60.036 55.000 0.00 0.00 34.43 4.70
2139 3379 0.324943 ACCTTGACCACGAATGAGGG 59.675 55.000 0.00 0.00 0.00 4.30
2167 3407 3.771160 CCTCCTGCGTACGGCCTT 61.771 66.667 18.39 0.00 42.61 4.35
2192 3432 2.572556 AGTCTTCGGGAGAGACAGTCTA 59.427 50.000 2.00 0.00 41.75 2.59
2198 3438 1.135632 CGTCAAGTCTTCGGGAGAGAC 60.136 57.143 0.00 0.00 41.75 3.36
2229 3469 2.203015 TAGGCGGCGGCAAAGATC 60.203 61.111 34.87 1.81 42.47 2.75
2284 3526 4.443394 GGATAAAGACTTGTATACACGCCG 59.557 45.833 4.68 0.00 0.00 6.46
2309 3557 4.715534 TTTGTGTTGATGTCCCCTCTAA 57.284 40.909 0.00 0.00 0.00 2.10
2340 3588 5.536916 ACATGTGATCTAACTCTAGGGCTAC 59.463 44.000 0.00 0.00 0.00 3.58
2342 3590 4.551671 ACATGTGATCTAACTCTAGGGCT 58.448 43.478 0.00 0.00 0.00 5.19
2349 3597 7.915923 TCGAGATTGTAACATGTGATCTAACTC 59.084 37.037 0.00 3.37 0.00 3.01
2351 3599 7.168302 CCTCGAGATTGTAACATGTGATCTAAC 59.832 40.741 15.71 0.00 0.00 2.34
2359 3607 6.321435 TGATCTACCTCGAGATTGTAACATGT 59.679 38.462 15.71 0.00 36.27 3.21
2362 3610 6.377429 AGTTGATCTACCTCGAGATTGTAACA 59.623 38.462 15.71 5.88 36.27 2.41
2363 3611 6.797454 AGTTGATCTACCTCGAGATTGTAAC 58.203 40.000 15.71 9.88 36.27 2.50
2368 3616 5.197451 ACAGAGTTGATCTACCTCGAGATT 58.803 41.667 15.71 2.53 36.27 2.40
2388 3636 9.322773 ACATTGATGAAGATGTATCAAGTACAG 57.677 33.333 0.00 0.00 45.94 2.74
2413 3661 4.099113 ACCCTACGTCCTGCTCTTATTTAC 59.901 45.833 0.00 0.00 0.00 2.01
2426 3675 3.259123 TCAAGAGGTAAAACCCTACGTCC 59.741 47.826 0.00 0.00 39.75 4.79
2445 3694 6.216662 TCTTGATGGAGGTAAAACCCTATCAA 59.783 38.462 17.18 17.18 40.44 2.57
2446 3695 5.729229 TCTTGATGGAGGTAAAACCCTATCA 59.271 40.000 8.49 8.49 39.75 2.15
2447 3696 6.248569 TCTTGATGGAGGTAAAACCCTATC 57.751 41.667 0.00 0.00 39.75 2.08
2448 3697 5.132816 CCTCTTGATGGAGGTAAAACCCTAT 59.867 44.000 2.65 0.00 45.65 2.57
2449 3698 4.473559 CCTCTTGATGGAGGTAAAACCCTA 59.526 45.833 2.65 0.00 45.65 3.53
2450 3699 3.267031 CCTCTTGATGGAGGTAAAACCCT 59.733 47.826 2.65 0.00 45.65 4.34
2451 3700 3.621558 CCTCTTGATGGAGGTAAAACCC 58.378 50.000 2.65 0.00 45.65 4.11
2460 3709 0.914644 TTCAGGCCCTCTTGATGGAG 59.085 55.000 0.00 0.00 0.00 3.86
2461 3710 0.620556 GTTCAGGCCCTCTTGATGGA 59.379 55.000 0.00 0.00 0.00 3.41
2462 3711 0.394899 GGTTCAGGCCCTCTTGATGG 60.395 60.000 0.00 0.00 0.00 3.51
2463 3712 0.622665 AGGTTCAGGCCCTCTTGATG 59.377 55.000 0.00 0.00 0.00 3.07
2464 3713 0.622665 CAGGTTCAGGCCCTCTTGAT 59.377 55.000 0.00 0.00 0.00 2.57
2465 3714 1.492133 CCAGGTTCAGGCCCTCTTGA 61.492 60.000 0.00 0.00 0.00 3.02
2466 3715 1.001641 CCAGGTTCAGGCCCTCTTG 60.002 63.158 0.00 0.00 0.00 3.02
2467 3716 2.234296 CCCAGGTTCAGGCCCTCTT 61.234 63.158 0.00 0.00 0.00 2.85
2468 3717 2.119847 TACCCAGGTTCAGGCCCTCT 62.120 60.000 0.00 0.00 0.00 3.69
2469 3718 1.205460 TTACCCAGGTTCAGGCCCTC 61.205 60.000 0.00 0.00 0.00 4.30
2470 3719 0.774491 TTTACCCAGGTTCAGGCCCT 60.774 55.000 0.00 0.00 0.00 5.19
2471 3720 0.611062 GTTTACCCAGGTTCAGGCCC 60.611 60.000 0.00 0.00 0.00 5.80
2472 3721 0.111639 TGTTTACCCAGGTTCAGGCC 59.888 55.000 0.00 0.00 0.00 5.19
2473 3722 2.092323 GATGTTTACCCAGGTTCAGGC 58.908 52.381 0.00 0.00 0.00 4.85
2474 3723 2.356135 CGATGTTTACCCAGGTTCAGG 58.644 52.381 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.