Multiple sequence alignment - TraesCS2B01G080800

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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 TraesCS2B01G080800 chr2B 100.000 2585 0 0 1 2585 45135076 45132492 0.000000e+00 4774.0
1 TraesCS2B01G080800 chr2B 91.469 1981 87 23 1 1967 45031388 45029476 0.000000e+00 2647.0
2 TraesCS2B01G080800 chr2B 88.321 2132 186 31 1 2076 44752994 44750870 0.000000e+00 2499.0
3 TraesCS2B01G080800 chr2B 93.402 1455 90 4 36 1488 45667932 45669382 0.000000e+00 2150.0
4 TraesCS2B01G080800 chr2B 92.559 981 69 3 1 979 45544117 45545095 0.000000e+00 1404.0
5 TraesCS2B01G080800 chr2B 82.920 1370 207 12 240 1605 44926463 44927809 0.000000e+00 1208.0
6 TraesCS2B01G080800 chr2B 82.580 1372 208 14 240 1605 45625117 45626463 0.000000e+00 1181.0
7 TraesCS2B01G080800 chr2B 91.391 453 30 7 1961 2412 44974323 44973879 1.700000e-171 612.0
8 TraesCS2B01G080800 chr2B 76.708 644 85 27 1481 2069 45669718 45670351 5.410000e-77 298.0
9 TraesCS2B01G080800 chr2B 96.023 176 7 0 2410 2585 44969806 44969631 1.170000e-73 287.0
10 TraesCS2B01G080800 chr2D 95.886 1653 65 2 1 1651 27958543 27960194 0.000000e+00 2673.0
11 TraesCS2B01G080800 chr2D 89.328 2127 165 31 1 2069 28000022 27997900 0.000000e+00 2614.0
12 TraesCS2B01G080800 chr2D 82.213 1844 261 37 1 1814 28416845 28415039 0.000000e+00 1526.0
13 TraesCS2B01G080800 chr2D 97.248 872 20 2 1 872 27977331 27976464 0.000000e+00 1474.0
14 TraesCS2B01G080800 chr2D 92.249 787 42 7 1416 2188 27976408 27975627 0.000000e+00 1098.0
15 TraesCS2B01G080800 chr2D 88.259 758 42 18 1684 2405 27960416 27961162 0.000000e+00 863.0
16 TraesCS2B01G080800 chr2A 90.072 2095 136 30 1 2036 30163174 30161093 0.000000e+00 2651.0
17 TraesCS2B01G080800 chr2A 84.477 1617 218 14 1 1606 30302708 30304302 0.000000e+00 1565.0
18 TraesCS2B01G080800 chr2A 94.444 36 2 0 2490 2525 440925142 440925107 3.590000e-04 56.5
19 TraesCS2B01G080800 chr6D 90.000 50 5 0 2490 2539 391562153 391562104 5.970000e-07 65.8
20 TraesCS2B01G080800 chr6A 89.130 46 5 0 2489 2534 46613886 46613841 9.990000e-05 58.4
21 TraesCS2B01G080800 chr6A 100.000 29 0 0 2488 2516 532633931 532633903 1.000000e-03 54.7
22 TraesCS2B01G080800 chrUn 88.889 45 5 0 2489 2533 27577673 27577629 3.590000e-04 56.5
23 TraesCS2B01G080800 chr7B 84.211 57 9 0 2497 2553 439671909 439671853 3.590000e-04 56.5
24 TraesCS2B01G080800 chr5A 100.000 30 0 0 2489 2518 485590400 485590429 3.590000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G080800 chr2B 45132492 45135076 2584 True 4774 4774 100.0000 1 2585 1 chr2B.!!$R5 2584
1 TraesCS2B01G080800 chr2B 45029476 45031388 1912 True 2647 2647 91.4690 1 1967 1 chr2B.!!$R4 1966
2 TraesCS2B01G080800 chr2B 44750870 44752994 2124 True 2499 2499 88.3210 1 2076 1 chr2B.!!$R1 2075
3 TraesCS2B01G080800 chr2B 45544117 45545095 978 False 1404 1404 92.5590 1 979 1 chr2B.!!$F2 978
4 TraesCS2B01G080800 chr2B 45667932 45670351 2419 False 1224 2150 85.0550 36 2069 2 chr2B.!!$F4 2033
5 TraesCS2B01G080800 chr2B 44926463 44927809 1346 False 1208 1208 82.9200 240 1605 1 chr2B.!!$F1 1365
6 TraesCS2B01G080800 chr2B 45625117 45626463 1346 False 1181 1181 82.5800 240 1605 1 chr2B.!!$F3 1365
7 TraesCS2B01G080800 chr2D 27997900 28000022 2122 True 2614 2614 89.3280 1 2069 1 chr2D.!!$R1 2068
8 TraesCS2B01G080800 chr2D 27958543 27961162 2619 False 1768 2673 92.0725 1 2405 2 chr2D.!!$F1 2404
9 TraesCS2B01G080800 chr2D 28415039 28416845 1806 True 1526 1526 82.2130 1 1814 1 chr2D.!!$R2 1813
10 TraesCS2B01G080800 chr2D 27975627 27977331 1704 True 1286 1474 94.7485 1 2188 2 chr2D.!!$R3 2187
11 TraesCS2B01G080800 chr2A 30161093 30163174 2081 True 2651 2651 90.0720 1 2036 1 chr2A.!!$R1 2035
12 TraesCS2B01G080800 chr2A 30302708 30304302 1594 False 1565 1565 84.4770 1 1606 1 chr2A.!!$F1 1605

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
927 936 0.806102 TGGCTTCTGCGCTCGATTAC 60.806 55.0 9.73 0.0 40.82 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2534 3153 0.108281 GGTCTCCTCCCACTAAACGC 60.108 60.0 0.0 0.0 0.0 4.84 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
123 127 3.120060 CCTGAATTCTTTGAGCACCTTCG 60.120 47.826 7.05 0.00 0.00 3.79
453 457 4.035091 TGTTGTGTCCAAGAAGATGTTTCG 59.965 41.667 0.00 0.00 0.00 3.46
884 891 2.158608 AGGCAGAGTGCTAAACTTTGGT 60.159 45.455 0.00 0.00 44.28 3.67
887 894 4.277423 GGCAGAGTGCTAAACTTTGGTAAA 59.723 41.667 0.00 0.00 44.28 2.01
921 930 1.449246 AGATGTGGCTTCTGCGCTC 60.449 57.895 9.73 0.00 40.82 5.03
927 936 0.806102 TGGCTTCTGCGCTCGATTAC 60.806 55.000 9.73 0.00 40.82 1.89
1125 1135 4.765273 CACCTGGTAAGTTTTGCCTTTTT 58.235 39.130 0.00 0.00 36.27 1.94
1174 1184 7.813148 GTCCTGTACGTATGTGCATTATTCTAT 59.187 37.037 6.31 0.00 40.06 1.98
1297 1307 3.118920 ACGACCAACCGATGATATGTTCA 60.119 43.478 0.00 0.00 39.12 3.18
1430 1442 6.887886 ATGGATGCAGAGATATATTGTCCT 57.112 37.500 0.00 0.00 0.00 3.85
1464 1476 0.109873 GACTGTCGTGTACCGTGGAG 60.110 60.000 0.00 2.47 37.94 3.86
1567 1923 7.318909 GTGATGACATTGACGAATATTTTAGCG 59.681 37.037 0.00 0.00 0.00 4.26
1577 1938 5.462398 ACGAATATTTTAGCGCTGTTAGAGG 59.538 40.000 22.90 4.16 0.00 3.69
1593 1954 7.361031 GCTGTTAGAGGATGCTGATTCATTATG 60.361 40.741 0.00 0.00 0.00 1.90
1627 2005 7.455058 TGTAGTAACATGTTCATTGTACCCTT 58.545 34.615 15.85 0.00 0.00 3.95
1631 2009 5.964958 ACATGTTCATTGTACCCTTTCAG 57.035 39.130 0.00 0.00 0.00 3.02
1820 2408 7.996644 TGTATATATGAAGGTGTTTTTCTCCCC 59.003 37.037 0.00 0.00 0.00 4.81
1904 2513 7.447374 TGACACTATAACATTCAAAACCAGG 57.553 36.000 0.00 0.00 0.00 4.45
1928 2537 4.881157 AATTTGGCCCCTTGTCTATACT 57.119 40.909 0.00 0.00 0.00 2.12
1963 2572 8.043113 AGATGTTTGATTGATGAAGTGCTACTA 58.957 33.333 0.00 0.00 0.00 1.82
2231 2849 7.504924 TTTGTGAAGTTCCGAACATAGAATT 57.495 32.000 13.69 0.00 0.00 2.17
2260 2879 5.393896 CCTCTTCTTTTCCATGCTCCAAATC 60.394 44.000 0.00 0.00 0.00 2.17
2265 2884 0.464373 TCCATGCTCCAAATCGCCTC 60.464 55.000 0.00 0.00 0.00 4.70
2348 2967 6.152831 GGCAACAATAACTGTAGAAATTCCCT 59.847 38.462 0.00 0.00 37.23 4.20
2349 2968 7.029563 GCAACAATAACTGTAGAAATTCCCTG 58.970 38.462 0.00 0.00 37.23 4.45
2350 2969 6.759497 ACAATAACTGTAGAAATTCCCTGC 57.241 37.500 0.00 0.00 36.10 4.85
2352 2971 6.719370 ACAATAACTGTAGAAATTCCCTGCAA 59.281 34.615 0.00 0.00 36.10 4.08
2410 3029 8.706492 ATGATGGCATTTTACTTGTTGTAATG 57.294 30.769 0.00 0.00 40.41 1.90
2411 3030 7.890515 TGATGGCATTTTACTTGTTGTAATGA 58.109 30.769 0.00 0.00 40.41 2.57
2412 3031 8.363390 TGATGGCATTTTACTTGTTGTAATGAA 58.637 29.630 0.00 0.00 40.41 2.57
2413 3032 9.369904 GATGGCATTTTACTTGTTGTAATGAAT 57.630 29.630 0.00 0.00 40.41 2.57
2424 3043 9.912634 ACTTGTTGTAATGAATAAGGATTTGTG 57.087 29.630 0.00 0.00 30.51 3.33
2431 3050 9.455847 GTAATGAATAAGGATTTGTGAATCAGC 57.544 33.333 2.05 0.00 42.82 4.26
2432 3051 6.455360 TGAATAAGGATTTGTGAATCAGCC 57.545 37.500 2.05 0.00 42.82 4.85
2433 3052 6.189859 TGAATAAGGATTTGTGAATCAGCCT 58.810 36.000 2.05 0.00 42.82 4.58
2434 3053 6.095860 TGAATAAGGATTTGTGAATCAGCCTG 59.904 38.462 2.05 0.00 42.82 4.85
2435 3054 2.097825 AGGATTTGTGAATCAGCCTGC 58.902 47.619 2.05 0.00 42.82 4.85
2436 3055 1.202222 GGATTTGTGAATCAGCCTGCG 60.202 52.381 2.05 0.00 42.82 5.18
2437 3056 0.813184 ATTTGTGAATCAGCCTGCGG 59.187 50.000 0.00 0.00 0.00 5.69
2438 3057 0.537143 TTTGTGAATCAGCCTGCGGT 60.537 50.000 0.00 0.00 0.00 5.68
2439 3058 0.537143 TTGTGAATCAGCCTGCGGTT 60.537 50.000 0.00 0.00 0.00 4.44
2440 3059 1.236616 TGTGAATCAGCCTGCGGTTG 61.237 55.000 5.34 5.34 35.19 3.77
2441 3060 1.675310 TGAATCAGCCTGCGGTTGG 60.675 57.895 10.47 0.00 34.63 3.77
2442 3061 1.377202 GAATCAGCCTGCGGTTGGA 60.377 57.895 10.47 0.00 34.63 3.53
2443 3062 0.749454 GAATCAGCCTGCGGTTGGAT 60.749 55.000 10.47 0.00 34.63 3.41
2444 3063 1.033746 AATCAGCCTGCGGTTGGATG 61.034 55.000 10.47 4.61 41.85 3.51
2445 3064 2.898920 ATCAGCCTGCGGTTGGATGG 62.899 60.000 10.47 0.00 40.95 3.51
2446 3065 3.650950 AGCCTGCGGTTGGATGGT 61.651 61.111 0.00 0.00 0.00 3.55
2447 3066 2.676471 GCCTGCGGTTGGATGGTT 60.676 61.111 0.00 0.00 0.00 3.67
2448 3067 1.377987 GCCTGCGGTTGGATGGTTA 60.378 57.895 0.00 0.00 0.00 2.85
2449 3068 0.751643 GCCTGCGGTTGGATGGTTAT 60.752 55.000 0.00 0.00 0.00 1.89
2450 3069 1.024271 CCTGCGGTTGGATGGTTATG 58.976 55.000 0.00 0.00 0.00 1.90
2451 3070 1.408127 CCTGCGGTTGGATGGTTATGA 60.408 52.381 0.00 0.00 0.00 2.15
2452 3071 1.942657 CTGCGGTTGGATGGTTATGAG 59.057 52.381 0.00 0.00 0.00 2.90
2453 3072 1.308998 GCGGTTGGATGGTTATGAGG 58.691 55.000 0.00 0.00 0.00 3.86
2454 3073 1.134220 GCGGTTGGATGGTTATGAGGA 60.134 52.381 0.00 0.00 0.00 3.71
2455 3074 2.561569 CGGTTGGATGGTTATGAGGAC 58.438 52.381 0.00 0.00 0.00 3.85
2456 3075 2.093181 CGGTTGGATGGTTATGAGGACA 60.093 50.000 0.00 0.00 0.00 4.02
2457 3076 3.433598 CGGTTGGATGGTTATGAGGACAT 60.434 47.826 0.00 0.00 40.16 3.06
2458 3077 4.536765 GGTTGGATGGTTATGAGGACATT 58.463 43.478 0.00 0.00 37.87 2.71
2459 3078 4.339247 GGTTGGATGGTTATGAGGACATTG 59.661 45.833 0.00 0.00 37.87 2.82
2460 3079 5.192927 GTTGGATGGTTATGAGGACATTGA 58.807 41.667 0.00 0.00 37.87 2.57
2461 3080 5.651612 TGGATGGTTATGAGGACATTGAT 57.348 39.130 0.00 0.00 37.87 2.57
2462 3081 6.762077 TGGATGGTTATGAGGACATTGATA 57.238 37.500 0.00 0.00 37.87 2.15
2463 3082 6.533730 TGGATGGTTATGAGGACATTGATAC 58.466 40.000 0.00 0.00 37.87 2.24
2464 3083 5.940470 GGATGGTTATGAGGACATTGATACC 59.060 44.000 0.00 0.00 37.87 2.73
2465 3084 5.304686 TGGTTATGAGGACATTGATACCC 57.695 43.478 0.00 0.00 37.87 3.69
2466 3085 4.104102 TGGTTATGAGGACATTGATACCCC 59.896 45.833 0.00 0.00 37.87 4.95
2467 3086 4.104102 GGTTATGAGGACATTGATACCCCA 59.896 45.833 0.00 0.00 37.87 4.96
2468 3087 5.308825 GTTATGAGGACATTGATACCCCAG 58.691 45.833 0.00 0.00 37.87 4.45
2469 3088 1.490490 TGAGGACATTGATACCCCAGC 59.510 52.381 0.00 0.00 0.00 4.85
2470 3089 0.846693 AGGACATTGATACCCCAGCC 59.153 55.000 0.00 0.00 0.00 4.85
2471 3090 0.178990 GGACATTGATACCCCAGCCC 60.179 60.000 0.00 0.00 0.00 5.19
2472 3091 0.550914 GACATTGATACCCCAGCCCA 59.449 55.000 0.00 0.00 0.00 5.36
2473 3092 0.258774 ACATTGATACCCCAGCCCAC 59.741 55.000 0.00 0.00 0.00 4.61
2474 3093 0.468029 CATTGATACCCCAGCCCACC 60.468 60.000 0.00 0.00 0.00 4.61
2475 3094 0.923729 ATTGATACCCCAGCCCACCA 60.924 55.000 0.00 0.00 0.00 4.17
2476 3095 1.143329 TTGATACCCCAGCCCACCAA 61.143 55.000 0.00 0.00 0.00 3.67
2477 3096 0.923729 TGATACCCCAGCCCACCAAT 60.924 55.000 0.00 0.00 0.00 3.16
2478 3097 0.468029 GATACCCCAGCCCACCAATG 60.468 60.000 0.00 0.00 0.00 2.82
2479 3098 1.221213 ATACCCCAGCCCACCAATGT 61.221 55.000 0.00 0.00 0.00 2.71
2480 3099 1.439524 TACCCCAGCCCACCAATGTT 61.440 55.000 0.00 0.00 0.00 2.71
2481 3100 1.984026 CCCCAGCCCACCAATGTTC 60.984 63.158 0.00 0.00 0.00 3.18
2482 3101 1.228831 CCCAGCCCACCAATGTTCA 60.229 57.895 0.00 0.00 0.00 3.18
2483 3102 0.831288 CCCAGCCCACCAATGTTCAA 60.831 55.000 0.00 0.00 0.00 2.69
2484 3103 0.604578 CCAGCCCACCAATGTTCAAG 59.395 55.000 0.00 0.00 0.00 3.02
2485 3104 1.331214 CAGCCCACCAATGTTCAAGT 58.669 50.000 0.00 0.00 0.00 3.16
2486 3105 1.688197 CAGCCCACCAATGTTCAAGTT 59.312 47.619 0.00 0.00 0.00 2.66
2487 3106 1.963515 AGCCCACCAATGTTCAAGTTC 59.036 47.619 0.00 0.00 0.00 3.01
2488 3107 1.963515 GCCCACCAATGTTCAAGTTCT 59.036 47.619 0.00 0.00 0.00 3.01
2489 3108 2.288395 GCCCACCAATGTTCAAGTTCTG 60.288 50.000 0.00 0.00 0.00 3.02
2490 3109 3.221771 CCCACCAATGTTCAAGTTCTGA 58.778 45.455 0.00 0.00 0.00 3.27
2491 3110 3.828451 CCCACCAATGTTCAAGTTCTGAT 59.172 43.478 0.00 0.00 32.78 2.90
2492 3111 4.321452 CCCACCAATGTTCAAGTTCTGATG 60.321 45.833 0.00 0.00 32.78 3.07
2493 3112 4.232221 CACCAATGTTCAAGTTCTGATGC 58.768 43.478 0.00 0.00 32.78 3.91
2494 3113 4.022589 CACCAATGTTCAAGTTCTGATGCT 60.023 41.667 0.00 0.00 32.78 3.79
2495 3114 4.586001 ACCAATGTTCAAGTTCTGATGCTT 59.414 37.500 0.00 0.00 32.78 3.91
2496 3115 4.921515 CCAATGTTCAAGTTCTGATGCTTG 59.078 41.667 13.11 13.11 42.32 4.01
2497 3116 3.631145 TGTTCAAGTTCTGATGCTTGC 57.369 42.857 13.99 5.81 41.15 4.01
2498 3117 2.950975 TGTTCAAGTTCTGATGCTTGCA 59.049 40.909 13.99 0.00 41.15 4.08
2499 3118 3.570975 TGTTCAAGTTCTGATGCTTGCAT 59.429 39.130 7.91 7.91 41.15 3.96
2500 3119 4.038282 TGTTCAAGTTCTGATGCTTGCATT 59.962 37.500 9.59 0.00 41.15 3.56
2501 3120 4.859304 TCAAGTTCTGATGCTTGCATTT 57.141 36.364 9.59 0.00 41.15 2.32
2502 3121 5.204409 TCAAGTTCTGATGCTTGCATTTT 57.796 34.783 9.59 0.00 41.15 1.82
2503 3122 5.603596 TCAAGTTCTGATGCTTGCATTTTT 58.396 33.333 9.59 0.00 41.15 1.94
2504 3123 5.693104 TCAAGTTCTGATGCTTGCATTTTTC 59.307 36.000 9.59 0.00 41.15 2.29
2505 3124 5.464030 AGTTCTGATGCTTGCATTTTTCT 57.536 34.783 9.59 3.29 0.00 2.52
2506 3125 6.579666 AGTTCTGATGCTTGCATTTTTCTA 57.420 33.333 9.59 0.00 0.00 2.10
2507 3126 6.618811 AGTTCTGATGCTTGCATTTTTCTAG 58.381 36.000 9.59 3.07 0.00 2.43
2508 3127 6.432162 AGTTCTGATGCTTGCATTTTTCTAGA 59.568 34.615 9.59 0.00 0.00 2.43
2509 3128 7.122353 AGTTCTGATGCTTGCATTTTTCTAGAT 59.878 33.333 9.59 0.00 0.00 1.98
2510 3129 7.400599 TCTGATGCTTGCATTTTTCTAGATT 57.599 32.000 9.59 0.00 0.00 2.40
2511 3130 7.833786 TCTGATGCTTGCATTTTTCTAGATTT 58.166 30.769 9.59 0.00 0.00 2.17
2512 3131 8.959548 TCTGATGCTTGCATTTTTCTAGATTTA 58.040 29.630 9.59 0.00 0.00 1.40
2513 3132 9.745880 CTGATGCTTGCATTTTTCTAGATTTAT 57.254 29.630 9.59 0.00 0.00 1.40
2517 3136 9.926158 TGCTTGCATTTTTCTAGATTTATTTCA 57.074 25.926 0.00 0.00 0.00 2.69
2534 3153 7.962934 TTATTTCAAGATTTTTACCGATGCG 57.037 32.000 0.00 0.00 0.00 4.73
2535 3154 3.398954 TCAAGATTTTTACCGATGCGC 57.601 42.857 0.00 0.00 0.00 6.09
2536 3155 2.101125 CAAGATTTTTACCGATGCGCG 58.899 47.619 0.00 0.00 40.47 6.86
2537 3156 1.365699 AGATTTTTACCGATGCGCGT 58.634 45.000 8.43 0.00 38.67 6.01
2538 3157 1.735571 AGATTTTTACCGATGCGCGTT 59.264 42.857 8.43 0.00 38.67 4.84
2539 3158 2.160813 AGATTTTTACCGATGCGCGTTT 59.839 40.909 8.43 0.00 38.67 3.60
2540 3159 3.371591 AGATTTTTACCGATGCGCGTTTA 59.628 39.130 8.43 0.00 38.67 2.01
2541 3160 2.791417 TTTTACCGATGCGCGTTTAG 57.209 45.000 8.43 0.00 38.67 1.85
2542 3161 1.712401 TTTACCGATGCGCGTTTAGT 58.288 45.000 8.43 4.41 38.67 2.24
2543 3162 0.993532 TTACCGATGCGCGTTTAGTG 59.006 50.000 8.43 0.00 38.67 2.74
2544 3163 0.802994 TACCGATGCGCGTTTAGTGG 60.803 55.000 8.43 5.31 38.67 4.00
2545 3164 2.701006 CGATGCGCGTTTAGTGGG 59.299 61.111 8.43 0.00 34.64 4.61
2546 3165 1.807981 CGATGCGCGTTTAGTGGGA 60.808 57.895 8.43 0.00 34.64 4.37
2547 3166 1.752501 CGATGCGCGTTTAGTGGGAG 61.753 60.000 8.43 0.00 34.64 4.30
2548 3167 1.429148 GATGCGCGTTTAGTGGGAGG 61.429 60.000 8.43 0.00 0.00 4.30
2549 3168 1.895020 ATGCGCGTTTAGTGGGAGGA 61.895 55.000 8.43 0.00 0.00 3.71
2550 3169 1.810030 GCGCGTTTAGTGGGAGGAG 60.810 63.158 8.43 0.00 0.00 3.69
2551 3170 1.888018 CGCGTTTAGTGGGAGGAGA 59.112 57.895 0.00 0.00 0.00 3.71
2552 3171 0.458025 CGCGTTTAGTGGGAGGAGAC 60.458 60.000 0.00 0.00 0.00 3.36
2553 3172 0.108281 GCGTTTAGTGGGAGGAGACC 60.108 60.000 0.00 0.00 0.00 3.85
2554 3173 0.172803 CGTTTAGTGGGAGGAGACCG 59.827 60.000 0.00 0.00 0.00 4.79
2555 3174 1.553706 GTTTAGTGGGAGGAGACCGA 58.446 55.000 0.00 0.00 0.00 4.69
2556 3175 1.477295 GTTTAGTGGGAGGAGACCGAG 59.523 57.143 0.00 0.00 0.00 4.63
2557 3176 0.702902 TTAGTGGGAGGAGACCGAGT 59.297 55.000 0.00 0.00 0.00 4.18
2558 3177 0.255318 TAGTGGGAGGAGACCGAGTC 59.745 60.000 0.00 0.00 0.00 3.36
2559 3178 1.000646 GTGGGAGGAGACCGAGTCT 60.001 63.158 6.29 6.29 46.42 3.24
2568 3187 2.871096 AGACCGAGTCTCTGAGAAGT 57.129 50.000 9.31 4.89 38.71 3.01
2569 3188 2.432444 AGACCGAGTCTCTGAGAAGTG 58.568 52.381 9.31 1.86 38.71 3.16
2570 3189 0.885196 ACCGAGTCTCTGAGAAGTGC 59.115 55.000 9.31 0.00 0.00 4.40
2571 3190 1.173043 CCGAGTCTCTGAGAAGTGCT 58.827 55.000 9.31 1.91 0.00 4.40
2572 3191 1.132262 CCGAGTCTCTGAGAAGTGCTC 59.868 57.143 9.31 10.45 44.21 4.26
2580 3199 3.337398 GAGAAGTGCTCGTAGGCAG 57.663 57.895 1.37 0.00 43.25 4.85
2581 3200 0.528470 GAGAAGTGCTCGTAGGCAGT 59.472 55.000 1.37 2.35 46.37 4.40
2582 3201 0.244994 AGAAGTGCTCGTAGGCAGTG 59.755 55.000 8.33 0.00 44.02 3.66
2583 3202 0.737715 GAAGTGCTCGTAGGCAGTGG 60.738 60.000 8.33 0.00 44.02 4.00
2584 3203 2.788191 AAGTGCTCGTAGGCAGTGGC 62.788 60.000 9.02 9.02 44.02 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
160 164 1.630878 CTTGTAGGAACAGCCCCTTCT 59.369 52.381 0.00 0.00 36.83 2.85
467 471 6.111382 TGTATGCATTTCTCTTCTCTTCTGG 58.889 40.000 3.54 0.00 0.00 3.86
884 891 2.158827 TCTGCCGCTATGCATCCTTTTA 60.159 45.455 0.19 0.00 41.16 1.52
887 894 0.399454 ATCTGCCGCTATGCATCCTT 59.601 50.000 0.19 0.00 41.16 3.36
921 930 2.409975 AGTTGGTTGTGGACGTAATCG 58.590 47.619 0.00 0.00 43.34 3.34
927 936 0.233848 GCGTTAGTTGGTTGTGGACG 59.766 55.000 0.00 0.00 0.00 4.79
1014 1023 4.144297 ACTTTGCTGAGCCAAAATCACTA 58.856 39.130 0.23 0.00 34.59 2.74
1145 1155 3.603158 TGCACATACGTACAGGACAAT 57.397 42.857 0.00 0.00 0.00 2.71
1464 1476 4.475135 GGCCTGTCCTTCGGAGCC 62.475 72.222 0.00 0.00 33.83 4.70
1567 1923 3.801698 TGAATCAGCATCCTCTAACAGC 58.198 45.455 0.00 0.00 0.00 4.40
1577 1938 9.622004 CATTCTTAACCATAATGAATCAGCATC 57.378 33.333 0.00 0.00 33.38 3.91
1697 2264 7.661536 AGGATAGTTGATACTTTCTGTAGCA 57.338 36.000 0.00 0.00 44.61 3.49
1736 2316 8.995027 TTTGCCATACATAGACCTCAAAATAT 57.005 30.769 0.00 0.00 0.00 1.28
1820 2408 5.048504 TGCTAAGCTGGACAAAAGATTTCAG 60.049 40.000 0.00 0.00 0.00 3.02
1904 2513 6.127101 AGTATAGACAAGGGGCCAAATTTAC 58.873 40.000 4.39 0.00 0.00 2.01
1963 2572 6.710597 TGCTTTCGTCTCCACTACTAATAT 57.289 37.500 0.00 0.00 0.00 1.28
2020 2635 7.181569 TCTTCCTTTTCAAAACACATTTCCT 57.818 32.000 0.00 0.00 0.00 3.36
2154 2772 9.417561 ACATCATGTTTCCTGATTCTTCATAAT 57.582 29.630 0.00 0.00 31.00 1.28
2190 2808 9.846248 ACTTCACAAATCTTTATTTATGAGCAC 57.154 29.630 0.00 0.00 39.14 4.40
2214 2832 7.070074 AGAGGTGATAATTCTATGTTCGGAACT 59.930 37.037 20.53 9.60 0.00 3.01
2215 2833 7.210873 AGAGGTGATAATTCTATGTTCGGAAC 58.789 38.462 13.86 13.86 0.00 3.62
2231 2849 5.431765 GAGCATGGAAAAGAAGAGGTGATA 58.568 41.667 0.00 0.00 0.00 2.15
2260 2879 6.078202 TGTTAGAAGAGAGATTATGAGGCG 57.922 41.667 0.00 0.00 0.00 5.52
2265 2884 8.498054 TTTGCCTTGTTAGAAGAGAGATTATG 57.502 34.615 0.00 0.00 0.00 1.90
2303 2922 7.375053 GTTGCCATCAACCTTCTTGTAAATAA 58.625 34.615 0.00 0.00 45.15 1.40
2405 3024 9.455847 GCTGATTCACAAATCCTTATTCATTAC 57.544 33.333 0.00 0.00 40.57 1.89
2406 3025 8.632679 GGCTGATTCACAAATCCTTATTCATTA 58.367 33.333 0.00 0.00 40.57 1.90
2407 3026 7.343833 AGGCTGATTCACAAATCCTTATTCATT 59.656 33.333 0.00 0.00 40.57 2.57
2408 3027 6.837568 AGGCTGATTCACAAATCCTTATTCAT 59.162 34.615 0.00 0.00 40.57 2.57
2409 3028 6.095860 CAGGCTGATTCACAAATCCTTATTCA 59.904 38.462 9.42 0.00 40.57 2.57
2410 3029 6.501781 CAGGCTGATTCACAAATCCTTATTC 58.498 40.000 9.42 0.00 40.57 1.75
2411 3030 5.163478 GCAGGCTGATTCACAAATCCTTATT 60.163 40.000 20.86 0.00 40.57 1.40
2412 3031 4.340381 GCAGGCTGATTCACAAATCCTTAT 59.660 41.667 20.86 0.00 40.57 1.73
2413 3032 3.696051 GCAGGCTGATTCACAAATCCTTA 59.304 43.478 20.86 0.00 40.57 2.69
2414 3033 2.494870 GCAGGCTGATTCACAAATCCTT 59.505 45.455 20.86 0.00 40.57 3.36
2415 3034 2.097825 GCAGGCTGATTCACAAATCCT 58.902 47.619 20.86 0.00 40.57 3.24
2416 3035 1.202222 CGCAGGCTGATTCACAAATCC 60.202 52.381 20.86 0.00 40.57 3.01
2417 3036 1.202222 CCGCAGGCTGATTCACAAATC 60.202 52.381 20.86 0.00 46.14 2.17
2418 3037 0.813184 CCGCAGGCTGATTCACAAAT 59.187 50.000 20.86 0.00 46.14 2.32
2419 3038 2.256391 CCGCAGGCTGATTCACAAA 58.744 52.632 20.86 0.00 46.14 2.83
2420 3039 3.985877 CCGCAGGCTGATTCACAA 58.014 55.556 20.86 0.00 46.14 3.33
2432 3051 1.942657 CTCATAACCATCCAACCGCAG 59.057 52.381 0.00 0.00 0.00 5.18
2433 3052 1.408127 CCTCATAACCATCCAACCGCA 60.408 52.381 0.00 0.00 0.00 5.69
2434 3053 1.134220 TCCTCATAACCATCCAACCGC 60.134 52.381 0.00 0.00 0.00 5.68
2435 3054 2.093181 TGTCCTCATAACCATCCAACCG 60.093 50.000 0.00 0.00 0.00 4.44
2436 3055 3.644966 TGTCCTCATAACCATCCAACC 57.355 47.619 0.00 0.00 0.00 3.77
2437 3056 5.192927 TCAATGTCCTCATAACCATCCAAC 58.807 41.667 0.00 0.00 33.49 3.77
2438 3057 5.449297 TCAATGTCCTCATAACCATCCAA 57.551 39.130 0.00 0.00 33.49 3.53
2439 3058 5.651612 ATCAATGTCCTCATAACCATCCA 57.348 39.130 0.00 0.00 33.49 3.41
2440 3059 5.940470 GGTATCAATGTCCTCATAACCATCC 59.060 44.000 0.00 0.00 33.49 3.51
2441 3060 5.940470 GGGTATCAATGTCCTCATAACCATC 59.060 44.000 0.00 0.00 33.49 3.51
2442 3061 5.222130 GGGGTATCAATGTCCTCATAACCAT 60.222 44.000 0.00 0.00 33.49 3.55
2443 3062 4.104102 GGGGTATCAATGTCCTCATAACCA 59.896 45.833 0.00 0.00 33.49 3.67
2444 3063 4.104102 TGGGGTATCAATGTCCTCATAACC 59.896 45.833 0.00 0.00 33.49 2.85
2445 3064 5.304686 TGGGGTATCAATGTCCTCATAAC 57.695 43.478 0.00 0.00 33.49 1.89
2446 3065 4.202461 GCTGGGGTATCAATGTCCTCATAA 60.202 45.833 0.00 0.00 30.87 1.90
2447 3066 3.327757 GCTGGGGTATCAATGTCCTCATA 59.672 47.826 0.00 0.00 30.87 2.15
2448 3067 2.107204 GCTGGGGTATCAATGTCCTCAT 59.893 50.000 0.00 0.00 30.87 2.90
2449 3068 1.490490 GCTGGGGTATCAATGTCCTCA 59.510 52.381 0.00 0.00 0.00 3.86
2450 3069 1.202818 GGCTGGGGTATCAATGTCCTC 60.203 57.143 0.00 0.00 0.00 3.71
2451 3070 0.846693 GGCTGGGGTATCAATGTCCT 59.153 55.000 0.00 0.00 0.00 3.85
2452 3071 0.178990 GGGCTGGGGTATCAATGTCC 60.179 60.000 0.00 0.00 0.00 4.02
2453 3072 0.550914 TGGGCTGGGGTATCAATGTC 59.449 55.000 0.00 0.00 0.00 3.06
2454 3073 0.258774 GTGGGCTGGGGTATCAATGT 59.741 55.000 0.00 0.00 0.00 2.71
2455 3074 0.468029 GGTGGGCTGGGGTATCAATG 60.468 60.000 0.00 0.00 0.00 2.82
2456 3075 0.923729 TGGTGGGCTGGGGTATCAAT 60.924 55.000 0.00 0.00 0.00 2.57
2457 3076 1.143329 TTGGTGGGCTGGGGTATCAA 61.143 55.000 0.00 0.00 0.00 2.57
2458 3077 0.923729 ATTGGTGGGCTGGGGTATCA 60.924 55.000 0.00 0.00 0.00 2.15
2459 3078 0.468029 CATTGGTGGGCTGGGGTATC 60.468 60.000 0.00 0.00 0.00 2.24
2460 3079 1.221213 ACATTGGTGGGCTGGGGTAT 61.221 55.000 0.00 0.00 0.00 2.73
2461 3080 1.439524 AACATTGGTGGGCTGGGGTA 61.440 55.000 0.00 0.00 0.00 3.69
2462 3081 2.730129 GAACATTGGTGGGCTGGGGT 62.730 60.000 0.00 0.00 0.00 4.95
2463 3082 1.984026 GAACATTGGTGGGCTGGGG 60.984 63.158 0.00 0.00 0.00 4.96
2464 3083 0.831288 TTGAACATTGGTGGGCTGGG 60.831 55.000 0.00 0.00 0.00 4.45
2465 3084 0.604578 CTTGAACATTGGTGGGCTGG 59.395 55.000 0.00 0.00 0.00 4.85
2466 3085 1.331214 ACTTGAACATTGGTGGGCTG 58.669 50.000 0.00 0.00 0.00 4.85
2467 3086 1.963515 GAACTTGAACATTGGTGGGCT 59.036 47.619 0.00 0.00 0.00 5.19
2468 3087 1.963515 AGAACTTGAACATTGGTGGGC 59.036 47.619 0.00 0.00 0.00 5.36
2469 3088 3.221771 TCAGAACTTGAACATTGGTGGG 58.778 45.455 0.00 0.00 31.34 4.61
2470 3089 4.801891 CATCAGAACTTGAACATTGGTGG 58.198 43.478 0.00 0.00 39.77 4.61
2471 3090 4.022589 AGCATCAGAACTTGAACATTGGTG 60.023 41.667 0.00 0.00 39.77 4.17
2472 3091 4.147321 AGCATCAGAACTTGAACATTGGT 58.853 39.130 0.00 0.00 39.77 3.67
2473 3092 4.778534 AGCATCAGAACTTGAACATTGG 57.221 40.909 0.00 0.00 39.77 3.16
2474 3093 4.384846 GCAAGCATCAGAACTTGAACATTG 59.615 41.667 16.97 1.88 44.89 2.82
2475 3094 4.038282 TGCAAGCATCAGAACTTGAACATT 59.962 37.500 16.97 0.00 44.89 2.71
2476 3095 3.570975 TGCAAGCATCAGAACTTGAACAT 59.429 39.130 16.97 0.00 44.89 2.71
2477 3096 2.950975 TGCAAGCATCAGAACTTGAACA 59.049 40.909 16.97 6.71 44.89 3.18
2478 3097 3.631145 TGCAAGCATCAGAACTTGAAC 57.369 42.857 16.97 4.72 44.89 3.18
2479 3098 4.859304 AATGCAAGCATCAGAACTTGAA 57.141 36.364 16.97 9.45 44.89 2.69
2480 3099 4.859304 AAATGCAAGCATCAGAACTTGA 57.141 36.364 16.97 6.15 44.89 3.02
2481 3100 5.694910 AGAAAAATGCAAGCATCAGAACTTG 59.305 36.000 8.14 10.80 44.88 3.16
2482 3101 5.850614 AGAAAAATGCAAGCATCAGAACTT 58.149 33.333 8.14 0.00 35.31 2.66
2483 3102 5.464030 AGAAAAATGCAAGCATCAGAACT 57.536 34.783 8.14 2.63 35.31 3.01
2484 3103 6.615088 TCTAGAAAAATGCAAGCATCAGAAC 58.385 36.000 8.14 0.47 35.31 3.01
2485 3104 6.822667 TCTAGAAAAATGCAAGCATCAGAA 57.177 33.333 8.14 0.00 35.31 3.02
2486 3105 7.400599 AATCTAGAAAAATGCAAGCATCAGA 57.599 32.000 8.14 5.27 35.31 3.27
2487 3106 9.745880 ATAAATCTAGAAAAATGCAAGCATCAG 57.254 29.630 8.14 0.37 35.31 2.90
2491 3110 9.926158 TGAAATAAATCTAGAAAAATGCAAGCA 57.074 25.926 0.00 0.00 0.00 3.91
2508 3127 9.019764 CGCATCGGTAAAAATCTTGAAATAAAT 57.980 29.630 0.00 0.00 0.00 1.40
2509 3128 7.008810 GCGCATCGGTAAAAATCTTGAAATAAA 59.991 33.333 0.30 0.00 0.00 1.40
2510 3129 6.470877 GCGCATCGGTAAAAATCTTGAAATAA 59.529 34.615 0.30 0.00 0.00 1.40
2511 3130 5.968848 GCGCATCGGTAAAAATCTTGAAATA 59.031 36.000 0.30 0.00 0.00 1.40
2512 3131 4.798387 GCGCATCGGTAAAAATCTTGAAAT 59.202 37.500 0.30 0.00 0.00 2.17
2513 3132 4.162812 GCGCATCGGTAAAAATCTTGAAA 58.837 39.130 0.30 0.00 0.00 2.69
2514 3133 3.726486 CGCGCATCGGTAAAAATCTTGAA 60.726 43.478 8.75 0.00 33.78 2.69
2515 3134 2.222931 CGCGCATCGGTAAAAATCTTGA 60.223 45.455 8.75 0.00 33.78 3.02
2516 3135 2.101125 CGCGCATCGGTAAAAATCTTG 58.899 47.619 8.75 0.00 33.78 3.02
2517 3136 1.735571 ACGCGCATCGGTAAAAATCTT 59.264 42.857 5.73 0.00 43.86 2.40
2518 3137 1.365699 ACGCGCATCGGTAAAAATCT 58.634 45.000 5.73 0.00 43.86 2.40
2519 3138 2.168201 AACGCGCATCGGTAAAAATC 57.832 45.000 5.73 0.00 43.86 2.17
2520 3139 2.622546 AAACGCGCATCGGTAAAAAT 57.377 40.000 5.73 0.00 43.86 1.82
2521 3140 2.479656 ACTAAACGCGCATCGGTAAAAA 59.520 40.909 5.73 0.00 43.86 1.94
2522 3141 2.067766 ACTAAACGCGCATCGGTAAAA 58.932 42.857 5.73 0.00 43.86 1.52
2523 3142 1.390803 CACTAAACGCGCATCGGTAAA 59.609 47.619 5.73 0.00 43.86 2.01
2524 3143 0.993532 CACTAAACGCGCATCGGTAA 59.006 50.000 5.73 0.00 43.86 2.85
2525 3144 0.802994 CCACTAAACGCGCATCGGTA 60.803 55.000 5.73 0.00 43.86 4.02
2526 3145 2.098233 CCACTAAACGCGCATCGGT 61.098 57.895 5.73 0.00 43.86 4.69
2527 3146 2.701006 CCACTAAACGCGCATCGG 59.299 61.111 5.73 0.00 43.86 4.18
2528 3147 1.752501 CTCCCACTAAACGCGCATCG 61.753 60.000 5.73 0.00 45.38 3.84
2529 3148 1.429148 CCTCCCACTAAACGCGCATC 61.429 60.000 5.73 0.00 0.00 3.91
2530 3149 1.449601 CCTCCCACTAAACGCGCAT 60.450 57.895 5.73 0.00 0.00 4.73
2531 3150 2.047655 CCTCCCACTAAACGCGCA 60.048 61.111 5.73 0.00 0.00 6.09
2532 3151 1.810030 CTCCTCCCACTAAACGCGC 60.810 63.158 5.73 0.00 0.00 6.86
2533 3152 0.458025 GTCTCCTCCCACTAAACGCG 60.458 60.000 3.53 3.53 0.00 6.01
2534 3153 0.108281 GGTCTCCTCCCACTAAACGC 60.108 60.000 0.00 0.00 0.00 4.84
2535 3154 0.172803 CGGTCTCCTCCCACTAAACG 59.827 60.000 0.00 0.00 0.00 3.60
2536 3155 1.477295 CTCGGTCTCCTCCCACTAAAC 59.523 57.143 0.00 0.00 0.00 2.01
2537 3156 1.076677 ACTCGGTCTCCTCCCACTAAA 59.923 52.381 0.00 0.00 0.00 1.85
2538 3157 0.702902 ACTCGGTCTCCTCCCACTAA 59.297 55.000 0.00 0.00 0.00 2.24
2539 3158 0.255318 GACTCGGTCTCCTCCCACTA 59.745 60.000 0.00 0.00 0.00 2.74
2540 3159 1.000646 GACTCGGTCTCCTCCCACT 60.001 63.158 0.00 0.00 0.00 4.00
2541 3160 1.000646 AGACTCGGTCTCCTCCCAC 60.001 63.158 1.23 0.00 38.71 4.61
2542 3161 3.509290 AGACTCGGTCTCCTCCCA 58.491 61.111 1.23 0.00 38.71 4.37
2549 3168 2.432444 CACTTCTCAGAGACTCGGTCT 58.568 52.381 0.00 6.29 46.42 3.85
2550 3169 1.135517 GCACTTCTCAGAGACTCGGTC 60.136 57.143 0.00 0.00 0.00 4.79
2551 3170 0.885196 GCACTTCTCAGAGACTCGGT 59.115 55.000 0.00 0.00 0.00 4.69
2552 3171 1.132262 GAGCACTTCTCAGAGACTCGG 59.868 57.143 0.00 0.00 41.51 4.63
2553 3172 1.202020 CGAGCACTTCTCAGAGACTCG 60.202 57.143 18.58 18.58 41.98 4.18
2554 3173 1.810151 ACGAGCACTTCTCAGAGACTC 59.190 52.381 0.00 2.75 41.98 3.36
2555 3174 1.904287 ACGAGCACTTCTCAGAGACT 58.096 50.000 0.00 0.00 41.98 3.24
2556 3175 2.096819 CCTACGAGCACTTCTCAGAGAC 59.903 54.545 0.00 0.00 41.98 3.36
2557 3176 2.360844 CCTACGAGCACTTCTCAGAGA 58.639 52.381 0.00 0.00 41.98 3.10
2558 3177 1.202245 GCCTACGAGCACTTCTCAGAG 60.202 57.143 0.00 0.00 41.98 3.35
2559 3178 0.811915 GCCTACGAGCACTTCTCAGA 59.188 55.000 0.00 0.00 41.98 3.27
2560 3179 0.528017 TGCCTACGAGCACTTCTCAG 59.472 55.000 0.00 0.00 41.98 3.35
2561 3180 0.528017 CTGCCTACGAGCACTTCTCA 59.472 55.000 0.00 0.00 41.98 3.27
2562 3181 0.528470 ACTGCCTACGAGCACTTCTC 59.472 55.000 0.00 0.00 38.00 2.87
2563 3182 0.244994 CACTGCCTACGAGCACTTCT 59.755 55.000 0.00 0.00 38.00 2.85
2564 3183 0.737715 CCACTGCCTACGAGCACTTC 60.738 60.000 0.00 0.00 38.00 3.01
2565 3184 1.293498 CCACTGCCTACGAGCACTT 59.707 57.895 0.00 0.00 38.00 3.16
2566 3185 2.973899 CCACTGCCTACGAGCACT 59.026 61.111 0.00 0.00 38.00 4.40
2567 3186 2.815647 GCCACTGCCTACGAGCAC 60.816 66.667 0.00 0.00 38.00 4.40


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

AutoCloner maintained by Alex Coulton.