Multiple sequence alignment - TraesCS6B01G375700

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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 TraesCS6B01G375700 chr6B 100.000 3164 0 0 1 3164 650598525 650595362 0.000000e+00 5843.0
1 TraesCS6B01G375700 chr6D 93.191 1307 45 16 1431 2722 431153846 431152569 0.000000e+00 1881.0
2 TraesCS6B01G375700 chr6D 96.429 756 21 3 1 751 431160655 431159901 0.000000e+00 1242.0
3 TraesCS6B01G375700 chr6D 95.975 472 19 0 747 1218 431154678 431154207 0.000000e+00 767.0
4 TraesCS6B01G375700 chr6D 93.128 422 21 3 2740 3155 431152588 431152169 2.090000e-171 612.0
5 TraesCS6B01G375700 chr6D 88.391 379 44 0 679 1057 431078788 431078410 1.030000e-124 457.0
6 TraesCS6B01G375700 chr6D 93.296 179 11 1 1213 1390 431154023 431153845 2.420000e-66 263.0
7 TraesCS6B01G375700 chr6D 88.776 98 11 0 1479 1576 431073067 431072970 1.540000e-23 121.0
8 TraesCS6B01G375700 chr3A 78.515 754 96 24 1 697 566332242 566332986 4.850000e-118 435.0
9 TraesCS6B01G375700 chr3D 78.220 753 91 35 1 697 422552560 422551825 6.310000e-112 414.0
10 TraesCS6B01G375700 chr4B 80.756 291 37 11 14 287 625349538 625349826 3.200000e-50 209.0
11 TraesCS6B01G375700 chr6A 89.796 49 2 3 2334 2380 577847079 577847032 3.410000e-05 60.2


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 TraesCS6B01G375700 chr6B 650595362 650598525 3163 True 5843.00 5843 100.0000 1 3164 1 chr6B.!!$R1 3163
1 TraesCS6B01G375700 chr6D 431159901 431160655 754 True 1242.00 1242 96.4290 1 751 1 chr6D.!!$R3 750
2 TraesCS6B01G375700 chr6D 431152169 431154678 2509 True 880.75 1881 93.8975 747 3155 4 chr6D.!!$R4 2408
3 TraesCS6B01G375700 chr3A 566332242 566332986 744 False 435.00 435 78.5150 1 697 1 chr3A.!!$F1 696
4 TraesCS6B01G375700 chr3D 422551825 422552560 735 True 414.00 414 78.2200 1 697 1 chr3D.!!$R1 696

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
721 782 1.133025 CCAAACGATTCCATGTCAGGC 59.867 52.381 0.0 0.0 0.00 4.85 F
1024 1085 0.392706 TCGCAAGAGGAAGAGCACAA 59.607 50.000 0.0 0.0 45.01 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2121 2379 0.456824 TGCTCTCGCTCTTGCTAACG 60.457 55.000 0.00 0.0 36.97 3.18 R
2951 3220 1.002792 AAGGGCCTGAGAGGAGGAG 59.997 63.158 6.92 0.0 37.67 3.69 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
227 244 5.477984 TGAAGAACTACGTTAAGAGCCCTTA 59.522 40.000 0.00 0.00 33.94 2.69
262 280 1.897802 TCCCGGTTGTCTCTCCTTTAC 59.102 52.381 0.00 0.00 0.00 2.01
346 391 9.140286 GGTATTTCAAGAGAACAAAAATTAGCC 57.860 33.333 0.00 0.00 32.39 3.93
492 541 6.587273 TCGGATTAACATACCATCATGTTGA 58.413 36.000 10.85 4.23 46.13 3.18
493 542 6.481976 TCGGATTAACATACCATCATGTTGAC 59.518 38.462 10.85 3.66 46.13 3.18
573 626 4.649674 TCAGTATCACCCTCAACATAGACC 59.350 45.833 0.00 0.00 0.00 3.85
671 732 5.634118 TCTCAAGGTGGAAAACTGAATCAT 58.366 37.500 0.00 0.00 0.00 2.45
721 782 1.133025 CCAAACGATTCCATGTCAGGC 59.867 52.381 0.00 0.00 0.00 4.85
730 791 5.504665 CGATTCCATGTCAGGCAGAATTTAC 60.505 44.000 0.00 0.00 0.00 2.01
923 984 6.430925 CCACTCCTATTGTGTTCTTGATTTCA 59.569 38.462 0.00 0.00 33.92 2.69
943 1004 3.152341 CAGCCAGTGTTTCTCTTGGATT 58.848 45.455 0.00 0.00 0.00 3.01
964 1025 4.537135 TGGTTAACCATCTCTCTCACAC 57.463 45.455 23.69 0.00 42.01 3.82
1024 1085 0.392706 TCGCAAGAGGAAGAGCACAA 59.607 50.000 0.00 0.00 45.01 3.33
1026 1087 1.129998 CGCAAGAGGAAGAGCACAATG 59.870 52.381 0.00 0.00 43.02 2.82
1079 1140 4.988598 CTGCAAGTCGGTGGCGGT 62.989 66.667 0.00 0.00 0.00 5.68
1094 1155 1.741770 CGGTGCCCAGTCTAGTTGC 60.742 63.158 0.00 0.00 0.00 4.17
1176 1237 1.276622 GAGGACCAGGGCTACTCAAA 58.723 55.000 0.00 0.00 0.00 2.69
1177 1238 0.984995 AGGACCAGGGCTACTCAAAC 59.015 55.000 0.00 0.00 0.00 2.93
1224 1474 1.852067 CGGCGAAGGAAAAGGTGGTG 61.852 60.000 0.00 0.00 0.00 4.17
1236 1486 1.629043 AGGTGGTGAAGCTCGACTTA 58.371 50.000 0.00 0.00 39.29 2.24
1273 1523 1.557443 GCTAAACTGCGACGTGTGCT 61.557 55.000 10.37 0.00 0.00 4.40
1284 1534 1.522355 CGTGTGCTATGGCCTCCTG 60.522 63.158 3.32 0.00 37.74 3.86
1322 1572 3.860536 CAGGTAAACAAACAAACCAACCG 59.139 43.478 0.00 0.00 34.29 4.44
1357 1607 3.791887 CGTACAGTCCACGAGATTGATTC 59.208 47.826 9.05 0.88 41.91 2.52
1394 1645 6.519353 TTGTAATCTTTATGTATGGCGTCG 57.481 37.500 0.00 0.00 0.00 5.12
1395 1646 5.834169 TGTAATCTTTATGTATGGCGTCGA 58.166 37.500 0.00 0.00 0.00 4.20
1396 1647 6.452242 TGTAATCTTTATGTATGGCGTCGAT 58.548 36.000 0.00 0.00 0.00 3.59
1397 1648 6.584942 TGTAATCTTTATGTATGGCGTCGATC 59.415 38.462 0.00 0.00 0.00 3.69
1398 1649 3.561503 TCTTTATGTATGGCGTCGATCG 58.438 45.455 9.36 9.36 43.12 3.69
1407 1658 2.951745 CGTCGATCGCAGTGCTCC 60.952 66.667 14.33 0.87 0.00 4.70
1408 1659 2.583593 GTCGATCGCAGTGCTCCC 60.584 66.667 14.33 0.50 0.00 4.30
1409 1660 2.755876 TCGATCGCAGTGCTCCCT 60.756 61.111 14.33 0.00 0.00 4.20
1410 1661 2.185350 CGATCGCAGTGCTCCCTT 59.815 61.111 14.33 0.00 0.00 3.95
1411 1662 1.880340 CGATCGCAGTGCTCCCTTC 60.880 63.158 14.33 1.94 0.00 3.46
1412 1663 1.519719 GATCGCAGTGCTCCCTTCT 59.480 57.895 14.33 0.00 0.00 2.85
1413 1664 0.809241 GATCGCAGTGCTCCCTTCTG 60.809 60.000 14.33 0.00 0.00 3.02
1415 1666 3.123620 GCAGTGCTCCCTTCTGCG 61.124 66.667 8.18 0.00 43.49 5.18
1416 1667 2.435586 CAGTGCTCCCTTCTGCGG 60.436 66.667 0.00 0.00 0.00 5.69
1417 1668 4.400961 AGTGCTCCCTTCTGCGGC 62.401 66.667 0.00 0.00 0.00 6.53
1418 1669 4.704833 GTGCTCCCTTCTGCGGCA 62.705 66.667 1.29 1.29 0.00 5.69
1419 1670 4.704833 TGCTCCCTTCTGCGGCAC 62.705 66.667 0.00 0.00 0.00 5.01
1471 1722 2.639286 GCAAGTGCCGTCCTTGTG 59.361 61.111 0.00 0.00 41.08 3.33
1497 1748 4.874977 GCCGCCTCCGCTGTCTAC 62.875 72.222 0.00 0.00 0.00 2.59
1498 1749 4.554363 CCGCCTCCGCTGTCTACG 62.554 72.222 0.00 0.00 0.00 3.51
1499 1750 3.812019 CGCCTCCGCTGTCTACGT 61.812 66.667 0.00 0.00 0.00 3.57
1500 1751 2.102553 GCCTCCGCTGTCTACGTC 59.897 66.667 0.00 0.00 0.00 4.34
1501 1752 2.799371 CCTCCGCTGTCTACGTCC 59.201 66.667 0.00 0.00 0.00 4.79
1502 1753 2.044555 CCTCCGCTGTCTACGTCCA 61.045 63.158 0.00 0.00 0.00 4.02
1551 1802 3.801997 ATCAAGGAGGCCTGCCCG 61.802 66.667 22.24 12.58 39.21 6.13
1726 1977 0.889186 GTCCGCCCACAAGTTCACAT 60.889 55.000 0.00 0.00 0.00 3.21
1964 2222 1.471684 GGTGTACACCTACTCGGTCAG 59.528 57.143 33.47 0.00 44.93 3.51
1965 2223 1.471684 GTGTACACCTACTCGGTCAGG 59.528 57.143 15.42 0.00 44.93 3.86
1966 2224 1.101331 GTACACCTACTCGGTCAGGG 58.899 60.000 0.00 0.00 44.93 4.45
1967 2225 0.682209 TACACCTACTCGGTCAGGGC 60.682 60.000 0.00 0.00 44.93 5.19
1968 2226 2.754658 ACCTACTCGGTCAGGGCG 60.755 66.667 0.00 0.00 44.93 6.13
1969 2227 3.528370 CCTACTCGGTCAGGGCGG 61.528 72.222 0.00 0.00 0.00 6.13
1970 2228 2.439701 CTACTCGGTCAGGGCGGA 60.440 66.667 0.00 0.00 0.00 5.54
1971 2229 1.828660 CTACTCGGTCAGGGCGGAT 60.829 63.158 0.00 0.00 0.00 4.18
1972 2230 2.076622 CTACTCGGTCAGGGCGGATG 62.077 65.000 0.00 0.00 0.00 3.51
1973 2231 4.899239 CTCGGTCAGGGCGGATGC 62.899 72.222 0.00 0.00 41.71 3.91
1984 2242 4.247380 CGGATGCCCCTCCTGCTC 62.247 72.222 0.00 0.00 32.77 4.26
2052 2310 1.142748 CTGGAGGATGGAGCGTGAC 59.857 63.158 0.00 0.00 0.00 3.67
2089 2347 1.377202 GGGATGCTGCGTGAGGAAA 60.377 57.895 0.00 0.00 0.00 3.13
2112 2370 1.233019 CCAGCAAGAGTGTCCTTGTG 58.767 55.000 0.00 0.00 43.96 3.33
2121 2379 2.327343 TGTCCTTGTGCGCATCTGC 61.327 57.895 15.91 0.00 37.78 4.26
2171 2429 1.289160 TGCTCAAGTTAGAGGGGCAT 58.711 50.000 0.00 0.00 36.15 4.40
2198 2456 4.970662 ATGCAGTTATCTTTGCGTGAAT 57.029 36.364 0.00 0.00 43.13 2.57
2201 2459 3.785505 GCAGTTATCTTTGCGTGAATCCG 60.786 47.826 0.00 0.00 0.00 4.18
2209 2467 2.672961 TGCGTGAATCCGAGAAGAAT 57.327 45.000 0.00 0.00 0.00 2.40
2229 2490 9.271738 GAAGAATGTGTAGTTTCGTAGTACTAC 57.728 37.037 21.06 21.06 42.43 2.73
2231 2492 9.658799 AGAATGTGTAGTTTCGTAGTACTACTA 57.341 33.333 26.36 15.99 42.50 1.82
2232 2493 9.913451 GAATGTGTAGTTTCGTAGTACTACTAG 57.087 37.037 26.36 14.66 42.50 2.57
2284 2548 9.897744 GTGTCTTTTTGTATTCTTGATTGATGA 57.102 29.630 0.00 0.00 0.00 2.92
2351 2615 2.496899 AATGTGTAAGAGTGGCAGGG 57.503 50.000 0.00 0.00 0.00 4.45
2357 2621 1.071699 GTAAGAGTGGCAGGGTGTTGA 59.928 52.381 0.00 0.00 0.00 3.18
2432 2696 5.036737 CGATGCTTGTTTCCATCATAAACC 58.963 41.667 0.00 0.00 38.14 3.27
2445 2709 5.182570 CCATCATAAACCGATGATTGATGCT 59.817 40.000 1.78 0.00 42.69 3.79
2494 2758 3.632145 CGGCTATACCCAAATCTTGCTTT 59.368 43.478 0.00 0.00 33.26 3.51
2496 2760 5.351458 GGCTATACCCAAATCTTGCTTTTG 58.649 41.667 0.00 0.00 34.55 2.44
2497 2761 5.105351 GGCTATACCCAAATCTTGCTTTTGT 60.105 40.000 0.00 0.00 33.23 2.83
2498 2762 6.398095 GCTATACCCAAATCTTGCTTTTGTT 58.602 36.000 0.00 0.00 33.23 2.83
2499 2763 6.531594 GCTATACCCAAATCTTGCTTTTGTTC 59.468 38.462 0.00 0.00 33.23 3.18
2500 2764 3.716601 ACCCAAATCTTGCTTTTGTTCG 58.283 40.909 0.00 0.00 33.23 3.95
2501 2765 3.059166 CCCAAATCTTGCTTTTGTTCGG 58.941 45.455 0.00 0.00 33.23 4.30
2502 2766 2.476241 CCAAATCTTGCTTTTGTTCGGC 59.524 45.455 0.00 0.00 33.23 5.54
2503 2767 3.383761 CAAATCTTGCTTTTGTTCGGCT 58.616 40.909 0.00 0.00 31.05 5.52
2504 2768 4.545610 CAAATCTTGCTTTTGTTCGGCTA 58.454 39.130 0.00 0.00 31.05 3.93
2553 2817 3.256631 ACCCAAATCTTGCTTGTGATGTC 59.743 43.478 0.00 0.00 0.00 3.06
2556 2820 4.153986 CAAATCTTGCTTGTGATGTCGAC 58.846 43.478 9.11 9.11 0.00 4.20
2586 2850 8.638873 AGGTGGCCTAATATTACTTTTTATTGC 58.361 33.333 3.32 0.00 28.47 3.56
2589 2853 9.073475 TGGCCTAATATTACTTTTTATTGCGAT 57.927 29.630 3.32 0.00 0.00 4.58
2635 2899 9.393249 TGCTGATAGTTTCTTAAAATGAAAACG 57.607 29.630 0.00 0.00 35.54 3.60
2636 2900 9.394477 GCTGATAGTTTCTTAAAATGAAAACGT 57.606 29.630 0.00 0.00 35.54 3.99
2645 2909 6.708949 TCTTAAAATGAAAACGTAGTCCTGCT 59.291 34.615 0.00 0.00 45.00 4.24
2663 2927 7.867909 AGTCCTGCTAAAAGAAACATTTTAAGC 59.132 33.333 0.00 0.00 34.97 3.09
2672 2936 4.898861 AGAAACATTTTAAGCAACCCTCCA 59.101 37.500 0.00 0.00 0.00 3.86
2673 2937 5.365314 AGAAACATTTTAAGCAACCCTCCAA 59.635 36.000 0.00 0.00 0.00 3.53
2674 2938 4.600692 ACATTTTAAGCAACCCTCCAAC 57.399 40.909 0.00 0.00 0.00 3.77
2675 2939 3.964031 ACATTTTAAGCAACCCTCCAACA 59.036 39.130 0.00 0.00 0.00 3.33
2676 2940 4.592778 ACATTTTAAGCAACCCTCCAACAT 59.407 37.500 0.00 0.00 0.00 2.71
2694 2959 6.156083 TCCAACATGTCTCTGTATTGGACATA 59.844 38.462 7.41 0.00 45.30 2.29
2697 2962 8.554528 CAACATGTCTCTGTATTGGACATAATC 58.445 37.037 0.00 0.00 45.30 1.75
2701 2966 5.403766 GTCTCTGTATTGGACATAATCGCAG 59.596 44.000 0.00 0.00 37.45 5.18
2702 2967 5.301805 TCTCTGTATTGGACATAATCGCAGA 59.698 40.000 0.00 0.00 38.25 4.26
2703 2968 5.532557 TCTGTATTGGACATAATCGCAGAG 58.467 41.667 0.00 0.00 37.43 3.35
2704 2969 5.069119 TCTGTATTGGACATAATCGCAGAGT 59.931 40.000 0.00 0.00 37.43 3.24
2705 2970 5.670485 TGTATTGGACATAATCGCAGAGTT 58.330 37.500 0.00 0.00 33.56 3.01
2706 2971 6.811954 TGTATTGGACATAATCGCAGAGTTA 58.188 36.000 0.00 0.00 33.56 2.24
2707 2972 6.700081 TGTATTGGACATAATCGCAGAGTTAC 59.300 38.462 0.00 0.00 33.56 2.50
2708 2973 4.729227 TGGACATAATCGCAGAGTTACA 57.271 40.909 0.00 0.00 43.63 2.41
2709 2974 4.430007 TGGACATAATCGCAGAGTTACAC 58.570 43.478 0.00 0.00 43.63 2.90
2710 2975 4.159693 TGGACATAATCGCAGAGTTACACT 59.840 41.667 0.00 0.00 43.63 3.55
2711 2976 4.504461 GGACATAATCGCAGAGTTACACTG 59.496 45.833 5.45 5.45 43.63 3.66
2712 2977 5.324784 ACATAATCGCAGAGTTACACTGA 57.675 39.130 13.66 0.00 43.63 3.41
2713 2978 5.103000 ACATAATCGCAGAGTTACACTGAC 58.897 41.667 13.66 4.46 43.63 3.51
2714 2979 3.660501 AATCGCAGAGTTACACTGACA 57.339 42.857 13.66 0.00 43.63 3.58
2715 2980 2.706555 TCGCAGAGTTACACTGACAG 57.293 50.000 13.66 0.00 37.54 3.51
2716 2981 2.227194 TCGCAGAGTTACACTGACAGA 58.773 47.619 13.66 6.50 37.54 3.41
2717 2982 2.031069 TCGCAGAGTTACACTGACAGAC 60.031 50.000 13.66 0.00 37.54 3.51
2718 2983 2.678324 GCAGAGTTACACTGACAGACC 58.322 52.381 13.66 0.00 37.54 3.85
2719 2984 2.610727 GCAGAGTTACACTGACAGACCC 60.611 54.545 13.66 0.00 37.54 4.46
2720 2985 2.894126 CAGAGTTACACTGACAGACCCT 59.106 50.000 10.08 0.00 37.54 4.34
2721 2986 2.894126 AGAGTTACACTGACAGACCCTG 59.106 50.000 10.08 0.00 37.52 4.45
2722 2987 1.971357 AGTTACACTGACAGACCCTGG 59.029 52.381 10.08 0.00 35.51 4.45
2723 2988 1.692519 GTTACACTGACAGACCCTGGT 59.307 52.381 10.08 0.00 35.51 4.00
2724 2989 2.097110 TACACTGACAGACCCTGGTT 57.903 50.000 10.08 0.00 35.51 3.67
2725 2990 2.097110 ACACTGACAGACCCTGGTTA 57.903 50.000 10.08 0.00 35.51 2.85
2726 2991 2.404559 ACACTGACAGACCCTGGTTAA 58.595 47.619 10.08 0.00 35.51 2.01
2727 2992 2.979678 ACACTGACAGACCCTGGTTAAT 59.020 45.455 10.08 0.00 35.51 1.40
2728 2993 3.394606 ACACTGACAGACCCTGGTTAATT 59.605 43.478 10.08 0.00 35.51 1.40
2729 2994 4.141251 ACACTGACAGACCCTGGTTAATTT 60.141 41.667 10.08 0.00 35.51 1.82
2730 2995 5.072600 ACACTGACAGACCCTGGTTAATTTA 59.927 40.000 10.08 0.00 35.51 1.40
2731 2996 5.411669 CACTGACAGACCCTGGTTAATTTAC 59.588 44.000 10.08 0.00 35.51 2.01
2732 2997 5.309806 ACTGACAGACCCTGGTTAATTTACT 59.690 40.000 10.08 0.00 35.51 2.24
2733 2998 5.556915 TGACAGACCCTGGTTAATTTACTG 58.443 41.667 0.00 0.00 35.51 2.74
2734 2999 5.072600 TGACAGACCCTGGTTAATTTACTGT 59.927 40.000 0.00 0.00 38.48 3.55
2735 3000 5.948842 ACAGACCCTGGTTAATTTACTGTT 58.051 37.500 0.00 0.00 35.51 3.16
2736 3001 7.081857 ACAGACCCTGGTTAATTTACTGTTA 57.918 36.000 0.00 0.00 35.51 2.41
2737 3002 7.166167 ACAGACCCTGGTTAATTTACTGTTAG 58.834 38.462 0.00 0.00 35.51 2.34
2738 3003 7.166167 CAGACCCTGGTTAATTTACTGTTAGT 58.834 38.462 0.00 0.00 0.00 2.24
2843 3112 1.477553 TGGCAATTGCTCCTTCATCC 58.522 50.000 28.42 10.14 41.70 3.51
2876 3145 2.599082 CGAGGAGACACTGATAAAACGC 59.401 50.000 0.00 0.00 0.00 4.84
2881 3150 3.326747 AGACACTGATAAAACGCCTCAC 58.673 45.455 0.00 0.00 0.00 3.51
2884 3153 3.244078 ACACTGATAAAACGCCTCACAGA 60.244 43.478 0.00 0.00 0.00 3.41
2888 3157 0.320073 TAAAACGCCTCACAGACCCG 60.320 55.000 0.00 0.00 0.00 5.28
2911 3180 3.830192 CTCCGCATGGGGCAAAGC 61.830 66.667 23.55 0.00 45.17 3.51
2915 3184 3.381136 GCATGGGGCAAAGCGGAA 61.381 61.111 0.00 0.00 43.97 4.30
3026 3295 0.824109 GATGGGACGGATGTGTGAGA 59.176 55.000 0.00 0.00 0.00 3.27
3043 3312 3.044059 GACATGCTTGGAGTGCGGC 62.044 63.158 4.44 0.00 0.00 6.53
3114 3383 1.749033 GCTTCGGATCCGGGAGATT 59.251 57.895 32.79 0.00 40.25 2.40
3115 3384 0.106894 GCTTCGGATCCGGGAGATTT 59.893 55.000 32.79 0.00 40.25 2.17
3134 3405 4.659111 TTTAGAGGTGTTTCTGTCGTGA 57.341 40.909 0.00 0.00 0.00 4.35
3136 3407 2.307768 AGAGGTGTTTCTGTCGTGAGA 58.692 47.619 0.00 0.00 38.16 3.27
3144 3415 0.037326 TCTGTCGTGAGATTGTGCCC 60.037 55.000 0.00 0.00 45.19 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 244 1.073897 GGGAGCTGCTTGTGGAGTT 59.926 57.895 2.53 0.00 33.91 3.01
262 280 2.289945 ACTAGCTCCTGTGGCTTTTCTG 60.290 50.000 0.00 0.00 40.74 3.02
385 430 8.702163 AATTTACTAATGCAAATGTGTTAGCC 57.298 30.769 0.00 0.00 0.00 3.93
470 519 6.545666 TGGTCAACATGATGGTATGTTAATCC 59.454 38.462 0.00 7.50 46.49 3.01
492 541 3.582647 TGAACATACCTGAGATGTGTGGT 59.417 43.478 0.00 0.00 37.59 4.16
493 542 4.186926 CTGAACATACCTGAGATGTGTGG 58.813 47.826 0.00 0.00 37.59 4.17
573 626 6.632834 GTGGTTATTATTATGTCTTTGCTGCG 59.367 38.462 0.00 0.00 0.00 5.18
671 732 5.414789 TGTGCTTTGTACTCTATGGCTTA 57.585 39.130 0.00 0.00 0.00 3.09
721 782 4.062293 TCAACCACACCGAGTAAATTCTG 58.938 43.478 0.00 0.00 0.00 3.02
730 791 3.027170 GCGCATCAACCACACCGAG 62.027 63.158 0.30 0.00 0.00 4.63
858 919 1.845809 GAGCACAAGAACACGGCTGG 61.846 60.000 0.00 0.00 34.44 4.85
863 924 3.029074 CGAAAAAGAGCACAAGAACACG 58.971 45.455 0.00 0.00 0.00 4.49
923 984 3.152341 CAATCCAAGAGAAACACTGGCT 58.848 45.455 0.00 0.00 0.00 4.75
964 1025 4.013267 AGGATGAGAGGGCATATTTTCG 57.987 45.455 0.00 0.00 0.00 3.46
1079 1140 0.901114 TACGGCAACTAGACTGGGCA 60.901 55.000 0.00 0.00 0.00 5.36
1183 1244 3.295304 ATACCGCGACTGCACTGCA 62.295 57.895 8.23 3.11 42.97 4.41
1208 1269 1.266989 GCTTCACCACCTTTTCCTTCG 59.733 52.381 0.00 0.00 0.00 3.79
1209 1270 2.554462 GAGCTTCACCACCTTTTCCTTC 59.446 50.000 0.00 0.00 0.00 3.46
1224 1474 3.109619 CGGAACATCTAAGTCGAGCTTC 58.890 50.000 3.94 0.00 38.57 3.86
1236 1486 0.179000 GCACCCTCATCGGAACATCT 59.821 55.000 0.00 0.00 33.16 2.90
1284 1534 0.182299 CCTGGAAGATGGGAGCCTTC 59.818 60.000 0.00 0.00 38.37 3.46
1341 1591 4.446371 AGGAATGAATCAATCTCGTGGAC 58.554 43.478 0.00 0.00 0.00 4.02
1342 1592 4.760530 AGGAATGAATCAATCTCGTGGA 57.239 40.909 0.00 0.00 0.00 4.02
1373 1623 6.237227 CGATCGACGCCATACATAAAGATTAC 60.237 42.308 10.26 0.00 34.51 1.89
1390 1641 2.951745 GGAGCACTGCGATCGACG 60.952 66.667 21.57 10.97 45.66 5.12
1391 1642 2.564553 AAGGGAGCACTGCGATCGAC 62.565 60.000 21.57 10.98 0.00 4.20
1392 1643 2.284798 GAAGGGAGCACTGCGATCGA 62.285 60.000 21.57 3.01 0.00 3.59
1393 1644 1.880340 GAAGGGAGCACTGCGATCG 60.880 63.158 11.69 11.69 0.00 3.69
1394 1645 0.809241 CAGAAGGGAGCACTGCGATC 60.809 60.000 0.00 0.00 0.00 3.69
1395 1646 1.220206 CAGAAGGGAGCACTGCGAT 59.780 57.895 0.00 0.00 0.00 4.58
1396 1647 2.659016 CAGAAGGGAGCACTGCGA 59.341 61.111 0.00 0.00 0.00 5.10
1397 1648 3.123620 GCAGAAGGGAGCACTGCG 61.124 66.667 0.00 0.00 45.25 5.18
1399 1650 2.435586 CCGCAGAAGGGAGCACTG 60.436 66.667 0.00 0.00 35.14 3.66
1400 1651 4.400961 GCCGCAGAAGGGAGCACT 62.401 66.667 0.00 0.00 0.00 4.40
1401 1652 4.704833 TGCCGCAGAAGGGAGCAC 62.705 66.667 0.00 0.00 32.13 4.40
1402 1653 4.704833 GTGCCGCAGAAGGGAGCA 62.705 66.667 0.00 0.00 33.72 4.26
1404 1655 4.379243 ACGTGCCGCAGAAGGGAG 62.379 66.667 0.00 0.00 30.25 4.30
1405 1656 4.373116 GACGTGCCGCAGAAGGGA 62.373 66.667 0.00 0.00 0.00 4.20
1428 1679 0.321122 GGAACTCACTGCAGGACCTG 60.321 60.000 19.93 17.83 34.12 4.00
1429 1680 0.764369 TGGAACTCACTGCAGGACCT 60.764 55.000 19.93 0.00 0.00 3.85
1440 1691 4.243008 TTGCCGCCGTGGAACTCA 62.243 61.111 0.88 0.00 42.00 3.41
1443 1694 4.025401 CACTTGCCGCCGTGGAAC 62.025 66.667 0.88 0.00 42.00 3.62
1470 1721 4.704833 GAGGCGGCCAAGTCTGCA 62.705 66.667 23.09 0.00 40.04 4.41
1491 1742 0.328592 AGGAGCTCTGGACGTAGACA 59.671 55.000 14.64 0.00 0.00 3.41
1495 1746 0.917533 AGGTAGGAGCTCTGGACGTA 59.082 55.000 14.64 0.00 0.00 3.57
1496 1747 0.681564 CAGGTAGGAGCTCTGGACGT 60.682 60.000 14.64 7.98 0.00 4.34
1497 1748 2.111162 CAGGTAGGAGCTCTGGACG 58.889 63.158 14.64 0.00 0.00 4.79
1551 1802 2.288458 TGTGCAGCCGTACTTTTTGTAC 59.712 45.455 0.00 0.00 45.93 2.90
1585 1836 3.849951 CGCCGCCAGGTCACCTAT 61.850 66.667 0.00 0.00 40.50 2.57
1726 1977 5.360429 TGTTGTATATGTAGTCTTGGCCGTA 59.640 40.000 0.00 0.00 0.00 4.02
1967 2225 4.247380 GAGCAGGAGGGGCATCCG 62.247 72.222 2.68 0.36 44.65 4.18
1968 2226 3.092511 TGAGCAGGAGGGGCATCC 61.093 66.667 0.00 0.00 39.89 3.51
1969 2227 2.042404 CTCTGAGCAGGAGGGGCATC 62.042 65.000 0.00 0.00 0.00 3.91
1970 2228 2.041762 TCTGAGCAGGAGGGGCAT 59.958 61.111 0.00 0.00 0.00 4.40
1971 2229 2.686470 CTCTGAGCAGGAGGGGCA 60.686 66.667 0.00 0.00 0.00 5.36
1972 2230 3.478274 CCTCTGAGCAGGAGGGGC 61.478 72.222 10.55 0.00 44.71 5.80
1976 2234 3.767806 TGCGCCTCTGAGCAGGAG 61.768 66.667 4.18 0.84 42.67 3.69
1984 2242 3.036783 GCTTCAGCTTGCGCCTCTG 62.037 63.158 4.18 9.67 38.21 3.35
2003 2261 1.631388 TCGCCACCTCCTTAATTTCCA 59.369 47.619 0.00 0.00 0.00 3.53
2052 2310 1.237285 CCGGAAGCAGTGGGAAACAG 61.237 60.000 0.00 0.00 0.00 3.16
2089 2347 2.689983 CAAGGACACTCTTGCTGGTTTT 59.310 45.455 0.00 0.00 37.84 2.43
2102 2360 1.499056 CAGATGCGCACAAGGACAC 59.501 57.895 14.90 0.00 0.00 3.67
2121 2379 0.456824 TGCTCTCGCTCTTGCTAACG 60.457 55.000 0.00 0.00 36.97 3.18
2171 2429 4.455533 ACGCAAAGATAACTGCATTTCTGA 59.544 37.500 0.00 0.00 38.52 3.27
2198 2456 4.022589 ACGAAACTACACATTCTTCTCGGA 60.023 41.667 0.00 0.00 0.00 4.55
2201 2459 8.235905 AGTACTACGAAACTACACATTCTTCTC 58.764 37.037 0.00 0.00 0.00 2.87
2209 2467 8.833231 AACTAGTAGTACTACGAAACTACACA 57.167 34.615 23.87 0.00 46.86 3.72
2229 2490 6.147164 TCAATGACTTGAAACGGCTTAACTAG 59.853 38.462 0.00 0.00 38.43 2.57
2231 2492 4.819630 TCAATGACTTGAAACGGCTTAACT 59.180 37.500 0.00 0.00 38.43 2.24
2232 2493 5.049680 TCTCAATGACTTGAAACGGCTTAAC 60.050 40.000 0.00 0.00 40.78 2.01
2284 2548 5.239525 CGAACAGGAGGAAATTCAAGTCTTT 59.760 40.000 0.00 0.00 0.00 2.52
2351 2615 3.270877 AGTCCTGAACACAAGTCAACAC 58.729 45.455 0.00 0.00 0.00 3.32
2357 2621 3.136443 TCCATCAAGTCCTGAACACAAGT 59.864 43.478 0.00 0.00 37.67 3.16
2432 2696 1.871676 CTGGGTCAGCATCAATCATCG 59.128 52.381 0.00 0.00 0.00 3.84
2445 2709 3.321648 ATCAGGTGCGCTGGGTCA 61.322 61.111 9.73 0.00 0.00 4.02
2494 2758 3.621268 GCTCAATGTGTATAGCCGAACAA 59.379 43.478 0.00 0.00 0.00 2.83
2496 2760 3.194861 TGCTCAATGTGTATAGCCGAAC 58.805 45.455 0.00 0.00 33.99 3.95
2497 2761 3.535280 TGCTCAATGTGTATAGCCGAA 57.465 42.857 0.00 0.00 33.99 4.30
2498 2762 3.751479 ATGCTCAATGTGTATAGCCGA 57.249 42.857 0.00 0.00 33.99 5.54
2499 2763 4.530388 CAAATGCTCAATGTGTATAGCCG 58.470 43.478 0.00 0.00 33.99 5.52
2500 2764 4.339247 ACCAAATGCTCAATGTGTATAGCC 59.661 41.667 0.00 0.00 33.99 3.93
2501 2765 5.505173 ACCAAATGCTCAATGTGTATAGC 57.495 39.130 0.00 0.00 35.51 2.97
2502 2766 5.277490 CGGACCAAATGCTCAATGTGTATAG 60.277 44.000 0.00 0.00 0.00 1.31
2503 2767 4.574421 CGGACCAAATGCTCAATGTGTATA 59.426 41.667 0.00 0.00 0.00 1.47
2504 2768 3.378112 CGGACCAAATGCTCAATGTGTAT 59.622 43.478 0.00 0.00 0.00 2.29
2553 2817 1.410004 TATTAGGCCACCTCCTGTCG 58.590 55.000 5.01 0.00 37.01 4.35
2556 2820 5.568620 AAGTAATATTAGGCCACCTCCTG 57.431 43.478 5.01 0.00 37.01 3.86
2586 2850 7.989609 GCAATTCAGAATGCTAACATAAATCG 58.010 34.615 0.00 0.00 39.46 3.34
2626 2890 6.708949 TCTTTTAGCAGGACTACGTTTTCATT 59.291 34.615 0.00 0.00 0.00 2.57
2627 2891 6.228258 TCTTTTAGCAGGACTACGTTTTCAT 58.772 36.000 0.00 0.00 0.00 2.57
2628 2892 5.603596 TCTTTTAGCAGGACTACGTTTTCA 58.396 37.500 0.00 0.00 0.00 2.69
2629 2893 6.535274 TTCTTTTAGCAGGACTACGTTTTC 57.465 37.500 0.00 0.00 0.00 2.29
2632 2896 5.362263 TGTTTCTTTTAGCAGGACTACGTT 58.638 37.500 0.00 0.00 0.00 3.99
2634 2898 6.481954 AATGTTTCTTTTAGCAGGACTACG 57.518 37.500 0.00 0.00 0.00 3.51
2645 2909 7.929245 GGAGGGTTGCTTAAAATGTTTCTTTTA 59.071 33.333 0.00 0.00 31.15 1.52
2663 2927 2.224621 ACAGAGACATGTTGGAGGGTTG 60.225 50.000 0.00 0.00 0.00 3.77
2676 2940 5.163457 TGCGATTATGTCCAATACAGAGACA 60.163 40.000 0.00 0.00 42.70 3.41
2703 2968 1.692519 ACCAGGGTCTGTCAGTGTAAC 59.307 52.381 0.00 0.00 0.00 2.50
2704 2969 2.097110 ACCAGGGTCTGTCAGTGTAA 57.903 50.000 0.00 0.00 0.00 2.41
2705 2970 2.097110 AACCAGGGTCTGTCAGTGTA 57.903 50.000 0.00 0.00 0.00 2.90
2706 2971 2.097110 TAACCAGGGTCTGTCAGTGT 57.903 50.000 0.00 0.00 0.00 3.55
2707 2972 3.703001 ATTAACCAGGGTCTGTCAGTG 57.297 47.619 0.00 0.00 0.00 3.66
2708 2973 4.724279 AAATTAACCAGGGTCTGTCAGT 57.276 40.909 0.00 0.00 0.00 3.41
2709 2974 5.643777 CAGTAAATTAACCAGGGTCTGTCAG 59.356 44.000 0.00 0.00 0.00 3.51
2710 2975 5.072600 ACAGTAAATTAACCAGGGTCTGTCA 59.927 40.000 0.00 0.00 0.00 3.58
2711 2976 5.557866 ACAGTAAATTAACCAGGGTCTGTC 58.442 41.667 0.00 0.00 0.00 3.51
2712 2977 5.578157 ACAGTAAATTAACCAGGGTCTGT 57.422 39.130 0.00 0.00 0.00 3.41
2713 2978 7.119262 CACTAACAGTAAATTAACCAGGGTCTG 59.881 40.741 0.00 0.00 0.00 3.51
2714 2979 7.016858 TCACTAACAGTAAATTAACCAGGGTCT 59.983 37.037 0.00 0.00 0.00 3.85
2715 2980 7.163441 TCACTAACAGTAAATTAACCAGGGTC 58.837 38.462 0.00 0.00 0.00 4.46
2716 2981 7.081857 TCACTAACAGTAAATTAACCAGGGT 57.918 36.000 0.00 0.00 0.00 4.34
2717 2982 7.610305 ACATCACTAACAGTAAATTAACCAGGG 59.390 37.037 0.00 0.00 0.00 4.45
2718 2983 8.561738 ACATCACTAACAGTAAATTAACCAGG 57.438 34.615 0.00 0.00 0.00 4.45
2720 2985 9.999660 TGTACATCACTAACAGTAAATTAACCA 57.000 29.630 0.00 0.00 0.00 3.67
2730 2995 8.585881 GGGTCATATATGTACATCACTAACAGT 58.414 37.037 12.68 0.00 0.00 3.55
2731 2996 8.807118 AGGGTCATATATGTACATCACTAACAG 58.193 37.037 12.68 0.00 0.00 3.16
2732 2997 8.585018 CAGGGTCATATATGTACATCACTAACA 58.415 37.037 12.68 0.00 0.00 2.41
2733 2998 8.585881 ACAGGGTCATATATGTACATCACTAAC 58.414 37.037 12.68 6.82 0.00 2.34
2734 2999 8.585018 CACAGGGTCATATATGTACATCACTAA 58.415 37.037 12.68 0.00 0.00 2.24
2735 3000 7.947890 TCACAGGGTCATATATGTACATCACTA 59.052 37.037 12.68 3.54 0.00 2.74
2736 3001 6.782494 TCACAGGGTCATATATGTACATCACT 59.218 38.462 12.68 0.00 0.00 3.41
2737 3002 6.993079 TCACAGGGTCATATATGTACATCAC 58.007 40.000 12.68 0.00 0.00 3.06
2738 3003 6.295292 GCTCACAGGGTCATATATGTACATCA 60.295 42.308 12.68 1.79 0.00 3.07
2843 3112 1.407258 GTCTCCTCGGTCCTCATTCAG 59.593 57.143 0.00 0.00 0.00 3.02
2876 3145 4.778415 CGACGCGGGTCTGTGAGG 62.778 72.222 27.29 9.46 41.16 3.86
2928 3197 1.848652 CTCGGAAGGTTGGGACTAGA 58.151 55.000 0.00 0.00 0.00 2.43
2951 3220 1.002792 AAGGGCCTGAGAGGAGGAG 59.997 63.158 6.92 0.00 37.67 3.69
3026 3295 3.058160 GCCGCACTCCAAGCATGT 61.058 61.111 0.00 0.00 0.00 3.21
3043 3312 1.377202 CACCCAACCCCATGACGAG 60.377 63.158 0.00 0.00 0.00 4.18
3110 3379 5.010719 TCACGACAGAAACACCTCTAAATCT 59.989 40.000 0.00 0.00 0.00 2.40
3114 3383 3.887110 TCTCACGACAGAAACACCTCTAA 59.113 43.478 0.00 0.00 0.00 2.10
3115 3384 3.483421 TCTCACGACAGAAACACCTCTA 58.517 45.455 0.00 0.00 0.00 2.43
3134 3405 4.431131 CGGGGCTGGGCACAATCT 62.431 66.667 0.00 0.00 30.93 2.40
3136 3407 4.299796 AACGGGGCTGGGCACAAT 62.300 61.111 0.00 0.00 30.93 2.71


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

AutoCloner maintained by Alex Coulton.