Multiple sequence alignment - TraesCS7B01G430000

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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 TraesCS7B01G430000 chr7B 100.000 2797 0 0 1 2797 698858808 698856012 0.000000e+00 5166.0
1 TraesCS7B01G430000 chr7B 82.968 593 54 26 520 1093 693793548 693792984 2.500000e-135 492.0
2 TraesCS7B01G430000 chr7B 76.478 846 109 48 1237 2031 696595141 696594335 7.310000e-101 377.0
3 TraesCS7B01G430000 chr7B 80.769 468 65 21 1258 1716 696382870 696382419 2.670000e-90 342.0
4 TraesCS7B01G430000 chr7B 87.778 270 17 4 2528 2797 424620623 424620370 4.530000e-78 302.0
5 TraesCS7B01G430000 chr7B 84.494 316 30 8 829 1139 693198438 693198137 7.580000e-76 294.0
6 TraesCS7B01G430000 chr7B 78.925 465 52 31 1032 1474 696283632 696283192 9.870000e-70 274.0
7 TraesCS7B01G430000 chr7B 83.920 199 14 8 545 732 693198674 693198483 1.030000e-39 174.0
8 TraesCS7B01G430000 chr7B 91.935 124 6 1 807 930 694767019 694766900 1.330000e-38 171.0
9 TraesCS7B01G430000 chr7B 79.646 226 32 10 1827 2046 694798099 694797882 1.740000e-32 150.0
10 TraesCS7B01G430000 chr7B 88.889 126 6 6 586 706 694767292 694767170 6.240000e-32 148.0
11 TraesCS7B01G430000 chr7B 80.402 199 31 7 1846 2043 693199743 693199552 8.070000e-31 145.0
12 TraesCS7B01G430000 chr7B 84.286 140 10 3 597 734 696286719 696286590 2.920000e-25 126.0
13 TraesCS7B01G430000 chr7B 93.333 60 4 0 1626 1685 693197740 693197681 3.840000e-14 89.8
14 TraesCS7B01G430000 chr7B 94.643 56 3 0 1626 1681 694766430 694766375 1.380000e-13 87.9
15 TraesCS7B01G430000 chr7B 92.453 53 3 1 1913 1964 696362393 696362341 1.070000e-09 75.0
16 TraesCS7B01G430000 chr7B 91.667 48 1 3 1072 1118 696363204 696363159 2.330000e-06 63.9
17 TraesCS7B01G430000 chr7B 96.970 33 1 0 1839 1871 694764966 694764934 3.890000e-04 56.5
18 TraesCS7B01G430000 chr4A 88.407 1199 65 26 807 1964 661973288 661974453 0.000000e+00 1376.0
19 TraesCS7B01G430000 chr4A 91.787 414 29 3 1 411 661972441 661972852 3.130000e-159 571.0
20 TraesCS7B01G430000 chr4A 95.912 318 11 2 2480 2797 661975133 661975448 5.340000e-142 514.0
21 TraesCS7B01G430000 chr4A 90.415 386 18 11 1960 2327 661974532 661974916 9.000000e-135 490.0
22 TraesCS7B01G430000 chr4A 87.126 334 25 10 1141 1474 661976339 661976654 2.050000e-96 363.0
23 TraesCS7B01G430000 chr4A 84.131 397 29 19 413 809 661972892 661973254 1.230000e-93 353.0
24 TraesCS7B01G430000 chr4A 76.596 705 111 44 985 1673 661969278 661969944 3.450000e-89 339.0
25 TraesCS7B01G430000 chr4A 86.869 198 24 2 115 312 718475900 718475705 1.300000e-53 220.0
26 TraesCS7B01G430000 chr4A 87.143 70 8 1 2082 2151 661977667 661977735 8.310000e-11 78.7
27 TraesCS7B01G430000 chr4A 83.562 73 11 1 120 191 29078523 29078595 1.800000e-07 67.6
28 TraesCS7B01G430000 chr7D 83.984 1024 77 37 895 1877 610240232 610241209 0.000000e+00 902.0
29 TraesCS7B01G430000 chr7D 83.908 783 59 29 829 1597 607547015 607546286 0.000000e+00 686.0
30 TraesCS7B01G430000 chr7D 85.246 366 37 14 1237 1596 608488101 608487747 7.370000e-96 361.0
31 TraesCS7B01G430000 chr7D 80.318 503 64 22 1246 1729 607562198 607561712 5.730000e-92 348.0
32 TraesCS7B01G430000 chr7D 88.276 290 24 6 1186 1474 608450508 608450228 3.450000e-89 339.0
33 TraesCS7B01G430000 chr7D 86.222 225 23 4 2529 2750 267138767 267138986 1.290000e-58 237.0
34 TraesCS7B01G430000 chr7D 87.442 215 13 5 523 734 610239947 610240150 4.660000e-58 235.0
35 TraesCS7B01G430000 chr7D 86.239 218 13 6 523 734 607547271 607547065 1.300000e-53 220.0
36 TraesCS7B01G430000 chr7D 81.752 274 37 7 2528 2797 329730630 329730894 1.690000e-52 217.0
37 TraesCS7B01G430000 chr7D 77.129 411 48 20 749 1148 608450888 608450513 2.200000e-46 196.0
38 TraesCS7B01G430000 chr7D 86.842 152 10 5 586 734 608451011 608450867 8.020000e-36 161.0
39 TraesCS7B01G430000 chr7D 79.646 226 27 11 1816 2031 610236252 610236468 8.070000e-31 145.0
40 TraesCS7B01G430000 chr7D 87.000 100 13 0 1626 1725 607546288 607546189 2.280000e-21 113.0
41 TraesCS7B01G430000 chr7D 83.200 125 15 3 1919 2043 608487375 608487257 2.950000e-20 110.0
42 TraesCS7B01G430000 chr7D 83.077 130 12 2 894 1022 608488401 608488281 2.950000e-20 110.0
43 TraesCS7B01G430000 chr7D 77.711 166 17 10 991 1139 607563926 607563764 1.790000e-12 84.2
44 TraesCS7B01G430000 chr7D 87.838 74 5 2 345 414 608485264 608485191 1.790000e-12 84.2
45 TraesCS7B01G430000 chr7D 88.406 69 4 2 350 414 608451892 608451824 2.310000e-11 80.5
46 TraesCS7B01G430000 chr7D 85.714 70 2 1 1933 2002 608454719 608454658 1.800000e-07 67.6
47 TraesCS7B01G430000 chr7D 82.500 80 4 7 337 407 514995050 514994972 8.370000e-06 62.1
48 TraesCS7B01G430000 chr7A 80.018 1131 137 42 807 1902 700451747 700450671 0.000000e+00 754.0
49 TraesCS7B01G430000 chr7A 74.778 1237 179 88 894 2043 699766805 699765615 1.540000e-117 433.0
50 TraesCS7B01G430000 chr7A 88.793 348 24 7 827 1168 699741119 699740781 2.000000e-111 412.0
51 TraesCS7B01G430000 chr7A 85.099 302 26 12 520 812 700452066 700451775 9.800000e-75 291.0
52 TraesCS7B01G430000 chr7A 86.813 273 18 8 530 802 699741442 699741188 3.520000e-74 289.0
53 TraesCS7B01G430000 chr7A 90.083 121 9 2 2674 2794 202162132 202162249 1.340000e-33 154.0
54 TraesCS7B01G430000 chr7A 97.778 45 1 0 448 492 699741554 699741510 8.310000e-11 78.7
55 TraesCS7B01G430000 chr1B 89.259 270 23 4 2528 2797 550270333 550270070 1.610000e-87 333.0
56 TraesCS7B01G430000 chr1B 88.793 116 13 0 212 327 580216057 580216172 2.900000e-30 143.0
57 TraesCS7B01G430000 chr6A 86.232 276 23 9 2528 2797 486269407 486269673 4.560000e-73 285.0
58 TraesCS7B01G430000 chr6A 81.915 94 11 5 101 191 18438095 18438185 1.070000e-09 75.0
59 TraesCS7B01G430000 chr1D 85.075 268 31 4 2528 2792 298513326 298513065 5.940000e-67 265.0
60 TraesCS7B01G430000 chr5B 84.706 255 21 8 2528 2779 669741079 669741318 3.600000e-59 239.0
61 TraesCS7B01G430000 chr5A 89.005 191 15 3 2528 2715 631792547 631792360 6.030000e-57 231.0
62 TraesCS7B01G430000 chr5A 88.136 59 4 3 137 192 623219650 623219708 1.800000e-07 67.6
63 TraesCS7B01G430000 chr3B 85.581 215 29 2 120 332 779691368 779691582 1.010000e-54 224.0
64 TraesCS7B01G430000 chr3B 88.961 154 15 1 2643 2796 532926158 532926309 3.680000e-44 189.0
65 TraesCS7B01G430000 chr3B 94.215 121 6 1 2674 2794 501652387 501652268 1.710000e-42 183.0
66 TraesCS7B01G430000 chr6B 82.609 230 35 5 107 332 68123200 68122972 6.110000e-47 198.0
67 TraesCS7B01G430000 chr6B 87.755 98 12 0 2429 2526 687066724 687066627 6.330000e-22 115.0
68 TraesCS7B01G430000 chr4B 81.481 216 36 2 115 326 33067652 33067437 1.030000e-39 174.0
69 TraesCS7B01G430000 chr3A 77.928 222 48 1 109 329 24773773 24773994 1.350000e-28 137.0
70 TraesCS7B01G430000 chr1A 89.362 47 5 0 280 326 499193154 499193108 3.010000e-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 TraesCS7B01G430000 chr7B 698856012 698858808 2796 True 5166.000000 5166 100.000000 1 2797 1 chr7B.!!$R6 2796
1 TraesCS7B01G430000 chr7B 693792984 693793548 564 True 492.000000 492 82.968000 520 1093 1 chr7B.!!$R2 573
2 TraesCS7B01G430000 chr7B 696594335 696595141 806 True 377.000000 377 76.478000 1237 2031 1 chr7B.!!$R5 794
3 TraesCS7B01G430000 chr4A 661969278 661977735 8457 False 510.587500 1376 87.689625 1 2797 8 chr4A.!!$F2 2796
4 TraesCS7B01G430000 chr7D 610236252 610241209 4957 False 427.333333 902 83.690667 523 2031 3 chr7D.!!$F3 1508
5 TraesCS7B01G430000 chr7D 607546189 607547271 1082 True 339.666667 686 85.715667 523 1725 3 chr7D.!!$R2 1202
6 TraesCS7B01G430000 chr7D 607561712 607563926 2214 True 216.100000 348 79.014500 991 1729 2 chr7D.!!$R3 738
7 TraesCS7B01G430000 chr7A 700450671 700452066 1395 True 522.500000 754 82.558500 520 1902 2 chr7A.!!$R3 1382
8 TraesCS7B01G430000 chr7A 699765615 699766805 1190 True 433.000000 433 74.778000 894 2043 1 chr7A.!!$R1 1149
9 TraesCS7B01G430000 chr7A 699740781 699741554 773 True 259.900000 412 91.128000 448 1168 3 chr7A.!!$R2 720

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
541 3776 0.179001 ACGAAACCCTTTGACCCAGG 60.179 55.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2347 7432 0.031043 CCGTGGGCGATGAATACGTA 59.969 55.0 0.0 0.0 41.33 3.57 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
91 3255 5.493809 CCCTATCCTGCTCTAGTAGTACTC 58.506 50.000 5.96 0.00 0.00 2.59
111 3275 8.286800 AGTACTCTACTACTGTACGATACTACG 58.713 40.741 0.00 0.00 40.77 3.51
135 3299 4.650734 TCTCCATTTCACAATGTAGTGCA 58.349 39.130 0.00 0.00 38.58 4.57
244 3410 8.839310 ATCTTTAGATACATCACAAGCCATAC 57.161 34.615 0.00 0.00 32.01 2.39
245 3411 8.023021 TCTTTAGATACATCACAAGCCATACT 57.977 34.615 0.00 0.00 0.00 2.12
337 3503 9.803130 GTATAGTTTGACTTTTTAGAACGGAAC 57.197 33.333 0.00 0.00 0.00 3.62
377 3543 2.388232 GGAACACGCACGGGATGTC 61.388 63.158 0.00 0.00 0.00 3.06
393 3559 0.745128 TGTCCCGTGTTGTGTTGGTC 60.745 55.000 0.00 0.00 0.00 4.02
414 3580 1.795768 CTTCTGCAGGCTACGTTGAA 58.204 50.000 15.13 0.00 0.00 2.69
493 3703 4.994201 TCGCCGTCGCTGTCACAC 62.994 66.667 0.00 0.00 35.26 3.82
501 3711 3.103007 CGTCGCTGTCACACGAATTATA 58.897 45.455 4.38 0.00 40.47 0.98
539 3774 1.682740 GAACGAAACCCTTTGACCCA 58.317 50.000 0.00 0.00 0.00 4.51
541 3776 0.179001 ACGAAACCCTTTGACCCAGG 60.179 55.000 0.00 0.00 0.00 4.45
543 3778 0.469144 GAAACCCTTTGACCCAGGCA 60.469 55.000 0.00 0.00 0.00 4.75
571 3808 2.738521 CATCCTATTCGGCCGGCG 60.739 66.667 27.83 16.23 0.00 6.46
572 3809 3.231736 ATCCTATTCGGCCGGCGT 61.232 61.111 27.83 14.10 0.00 5.68
573 3810 2.803817 ATCCTATTCGGCCGGCGTT 61.804 57.895 27.83 10.26 0.00 4.84
574 3811 2.710724 ATCCTATTCGGCCGGCGTTC 62.711 60.000 27.83 5.60 0.00 3.95
575 3812 2.202824 CTATTCGGCCGGCGTTCA 60.203 61.111 27.83 0.17 0.00 3.18
595 3832 3.119137 TCACTTCACATCCATCGATTCGT 60.119 43.478 5.89 0.00 0.00 3.85
706 3953 4.272991 GAGCATCAGATGTTGATCTCCAAC 59.727 45.833 12.18 0.00 44.76 3.77
707 3954 6.709994 GAGCATCAGATGTTGATCTCCAACC 61.710 48.000 12.18 0.00 44.76 3.77
749 3999 6.268566 CAACTGTTTCTTCTTTGAGGGAAAG 58.731 40.000 0.00 0.00 42.33 2.62
779 4029 4.344102 AGAGTACCAGCTGTTTGACACTTA 59.656 41.667 13.81 0.00 0.00 2.24
1085 4440 1.148498 CGGCCCCTGTTCTTATCCC 59.852 63.158 0.00 0.00 0.00 3.85
1119 4474 0.754472 TTCCTATTTAGTCCCGCCCG 59.246 55.000 0.00 0.00 0.00 6.13
1209 4599 4.832266 CCACATCCATCTCTAGCTTCTACT 59.168 45.833 0.00 0.00 0.00 2.57
1210 4600 6.007076 CCACATCCATCTCTAGCTTCTACTA 58.993 44.000 0.00 0.00 0.00 1.82
1211 4601 6.072175 CCACATCCATCTCTAGCTTCTACTAC 60.072 46.154 0.00 0.00 0.00 2.73
1212 4602 6.007703 ACATCCATCTCTAGCTTCTACTACC 58.992 44.000 0.00 0.00 0.00 3.18
1213 4603 5.648330 TCCATCTCTAGCTTCTACTACCA 57.352 43.478 0.00 0.00 0.00 3.25
1214 4604 5.626142 TCCATCTCTAGCTTCTACTACCAG 58.374 45.833 0.00 0.00 0.00 4.00
1215 4605 4.217550 CCATCTCTAGCTTCTACTACCAGC 59.782 50.000 0.00 0.00 0.00 4.85
1216 4606 3.822940 TCTCTAGCTTCTACTACCAGCC 58.177 50.000 0.00 0.00 33.73 4.85
1217 4607 2.550606 CTCTAGCTTCTACTACCAGCCG 59.449 54.545 0.00 0.00 33.73 5.52
1222 4612 1.476891 CTTCTACTACCAGCCGAAGCA 59.523 52.381 0.00 0.00 43.56 3.91
1224 4614 0.525668 CTACTACCAGCCGAAGCACG 60.526 60.000 0.00 0.00 43.56 5.34
1225 4615 1.246056 TACTACCAGCCGAAGCACGT 61.246 55.000 3.00 0.00 43.56 4.49
1251 6104 1.565390 TAGCACCAAGGCAGAGGCAT 61.565 55.000 0.00 0.00 43.71 4.40
1256 6109 0.034767 CCAAGGCAGAGGCATTCTCA 60.035 55.000 0.00 0.00 43.08 3.27
1322 6184 2.591429 CACAAGCTGCGGACCACA 60.591 61.111 0.00 0.00 0.00 4.17
1382 6247 3.171348 GGGGAGAGGCCACAAAGT 58.829 61.111 5.01 0.00 41.00 2.66
1553 6421 4.617520 TTCAACTCGCGCCTGCCA 62.618 61.111 0.00 0.00 38.08 4.92
1709 6628 7.140705 TGTATTGACTCTGTGAAAGCATTTTG 58.859 34.615 0.00 0.00 39.27 2.44
1718 6637 0.388006 AAAGCATTTTGTACGGCCGC 60.388 50.000 28.58 11.02 31.62 6.53
1750 6695 6.021390 CGTAGCGATGTAGCATCATTGTATAC 60.021 42.308 9.40 0.00 40.15 1.47
1758 6703 9.788960 ATGTAGCATCATTGTATACTGTATACG 57.211 33.333 25.01 15.33 43.05 3.06
1807 6753 5.453648 CAATTTTAATGTTCCGTCGGTTCA 58.546 37.500 11.88 11.88 0.00 3.18
1819 6788 2.095768 CGTCGGTTCACAATGCAAGATT 60.096 45.455 0.00 0.00 0.00 2.40
1831 6800 7.814107 TCACAATGCAAGATTAAGATTTGGTTC 59.186 33.333 0.00 0.00 0.00 3.62
1833 6802 5.957842 TGCAAGATTAAGATTTGGTTCGT 57.042 34.783 0.00 0.00 0.00 3.85
1866 6846 6.317789 TCTTTTGGATGATGAACTGTGAAC 57.682 37.500 0.00 0.00 0.00 3.18
1908 6891 1.256812 GTGGTGGGTGGAAATGGAAG 58.743 55.000 0.00 0.00 0.00 3.46
1909 6892 1.153539 TGGTGGGTGGAAATGGAAGA 58.846 50.000 0.00 0.00 0.00 2.87
1910 6893 1.075374 TGGTGGGTGGAAATGGAAGAG 59.925 52.381 0.00 0.00 0.00 2.85
1911 6894 1.075536 GGTGGGTGGAAATGGAAGAGT 59.924 52.381 0.00 0.00 0.00 3.24
1988 7055 1.619827 CTGTACGTGGGTGAAAGGGTA 59.380 52.381 0.00 0.00 0.00 3.69
2031 7098 8.665685 AGTAGCGAAAAGTCAAAAATATCGAAT 58.334 29.630 0.00 0.00 0.00 3.34
2033 7100 6.682863 AGCGAAAAGTCAAAAATATCGAATCG 59.317 34.615 0.00 0.00 0.00 3.34
2036 7103 7.898309 CGAAAAGTCAAAAATATCGAATCGACT 59.102 33.333 7.77 0.00 39.18 4.18
2037 7104 8.880768 AAAAGTCAAAAATATCGAATCGACTG 57.119 30.769 7.77 0.00 39.18 3.51
2159 7230 7.040478 TGTCACATACCAAGAAAAATCTTCCTG 60.040 37.037 0.00 0.00 0.00 3.86
2160 7231 6.071952 TCACATACCAAGAAAAATCTTCCTGC 60.072 38.462 0.00 0.00 0.00 4.85
2161 7232 5.774690 ACATACCAAGAAAAATCTTCCTGCA 59.225 36.000 0.00 0.00 0.00 4.41
2162 7233 4.861102 ACCAAGAAAAATCTTCCTGCAG 57.139 40.909 6.78 6.78 0.00 4.41
2169 7254 7.117285 AGAAAAATCTTCCTGCAGTTTCTTT 57.883 32.000 13.81 3.09 31.55 2.52
2170 7255 7.205992 AGAAAAATCTTCCTGCAGTTTCTTTC 58.794 34.615 13.81 11.23 31.55 2.62
2178 7263 6.530019 TCCTGCAGTTTCTTTCTTTCTTTT 57.470 33.333 13.81 0.00 0.00 2.27
2205 7290 6.010219 TCTATTCTTTCAAGGAAAACAGGGG 58.990 40.000 0.00 0.00 30.84 4.79
2206 7291 2.316108 TCTTTCAAGGAAAACAGGGGC 58.684 47.619 0.00 0.00 30.84 5.80
2249 7334 0.397941 GCCCAGGCAGCTACATATGA 59.602 55.000 10.38 0.00 41.49 2.15
2252 7337 2.498167 CCAGGCAGCTACATATGAACC 58.502 52.381 10.38 1.41 0.00 3.62
2303 7388 9.632638 AAAAACAATCTACAGCTACATATGGAT 57.367 29.630 7.80 0.00 0.00 3.41
2304 7389 8.839310 AAACAATCTACAGCTACATATGGATC 57.161 34.615 7.80 0.00 0.00 3.36
2312 7397 7.411486 ACAGCTACATATGGATCCATACTAC 57.589 40.000 32.22 20.46 41.09 2.73
2327 7412 4.395542 CCATACTACTATACGACTGGCCTC 59.604 50.000 3.32 0.00 0.00 4.70
2328 7413 3.860968 ACTACTATACGACTGGCCTCT 57.139 47.619 3.32 0.00 0.00 3.69
2329 7414 3.478509 ACTACTATACGACTGGCCTCTG 58.521 50.000 3.32 0.00 0.00 3.35
2330 7415 1.033574 ACTATACGACTGGCCTCTGC 58.966 55.000 3.32 0.00 0.00 4.26
2344 7429 4.596585 CTGCCCCCACCCACGTTT 62.597 66.667 0.00 0.00 0.00 3.60
2345 7430 4.589675 TGCCCCCACCCACGTTTC 62.590 66.667 0.00 0.00 0.00 2.78
2347 7432 4.259131 CCCCCACCCACGTTTCGT 62.259 66.667 0.00 0.00 42.36 3.85
2348 7433 2.742403 CCCCACCCACGTTTCGTA 59.258 61.111 0.00 0.00 38.32 3.43
2349 7434 1.668793 CCCCACCCACGTTTCGTAC 60.669 63.158 0.00 0.00 38.32 3.67
2360 7445 3.118715 CGTTTCGTACGTATTCATCGC 57.881 47.619 16.05 0.00 45.14 4.58
2361 7446 2.098211 CGTTTCGTACGTATTCATCGCC 60.098 50.000 16.05 0.00 45.14 5.54
2362 7447 2.124011 TTCGTACGTATTCATCGCCC 57.876 50.000 16.05 0.00 0.00 6.13
2363 7448 1.023502 TCGTACGTATTCATCGCCCA 58.976 50.000 16.05 0.00 0.00 5.36
2364 7449 1.126079 CGTACGTATTCATCGCCCAC 58.874 55.000 7.22 0.00 0.00 4.61
2365 7450 1.126079 GTACGTATTCATCGCCCACG 58.874 55.000 0.00 0.00 42.01 4.94
2366 7451 0.031043 TACGTATTCATCGCCCACGG 59.969 55.000 0.00 0.00 40.63 4.94
2367 7452 1.066752 CGTATTCATCGCCCACGGA 59.933 57.895 0.00 0.00 40.63 4.69
2368 7453 0.528901 CGTATTCATCGCCCACGGAA 60.529 55.000 0.00 0.00 40.63 4.30
2369 7454 1.872237 CGTATTCATCGCCCACGGAAT 60.872 52.381 0.00 0.00 40.63 3.01
2370 7455 2.218603 GTATTCATCGCCCACGGAATT 58.781 47.619 0.00 0.00 40.63 2.17
2371 7456 1.024271 ATTCATCGCCCACGGAATTG 58.976 50.000 0.00 0.00 40.63 2.32
2372 7457 1.653094 TTCATCGCCCACGGAATTGC 61.653 55.000 0.00 0.00 40.63 3.56
2373 7458 2.045438 ATCGCCCACGGAATTGCA 60.045 55.556 0.00 0.00 40.63 4.08
2374 7459 1.453745 ATCGCCCACGGAATTGCAT 60.454 52.632 0.00 0.00 40.63 3.96
2375 7460 1.727511 ATCGCCCACGGAATTGCATG 61.728 55.000 0.00 0.00 40.63 4.06
2376 7461 2.202783 GCCCACGGAATTGCATGC 60.203 61.111 11.82 11.82 0.00 4.06
2377 7462 2.713967 GCCCACGGAATTGCATGCT 61.714 57.895 20.33 0.00 0.00 3.79
2378 7463 1.140161 CCCACGGAATTGCATGCTG 59.860 57.895 20.33 6.56 0.00 4.41
2379 7464 1.597797 CCCACGGAATTGCATGCTGT 61.598 55.000 20.33 4.25 0.00 4.40
2380 7465 1.093972 CCACGGAATTGCATGCTGTA 58.906 50.000 20.33 4.66 0.00 2.74
2381 7466 1.472082 CCACGGAATTGCATGCTGTAA 59.528 47.619 20.33 5.20 0.00 2.41
2382 7467 2.518949 CACGGAATTGCATGCTGTAAC 58.481 47.619 20.33 5.75 0.00 2.50
2383 7468 2.162208 CACGGAATTGCATGCTGTAACT 59.838 45.455 20.33 0.00 0.00 2.24
2384 7469 2.162208 ACGGAATTGCATGCTGTAACTG 59.838 45.455 20.33 13.19 0.00 3.16
2385 7470 2.162208 CGGAATTGCATGCTGTAACTGT 59.838 45.455 20.33 0.00 0.00 3.55
2386 7471 3.728864 CGGAATTGCATGCTGTAACTGTC 60.729 47.826 20.33 4.90 0.00 3.51
2387 7472 3.428045 GGAATTGCATGCTGTAACTGTCC 60.428 47.826 20.33 10.04 0.00 4.02
2388 7473 2.566833 TTGCATGCTGTAACTGTCCT 57.433 45.000 20.33 0.00 0.00 3.85
2389 7474 3.694043 TTGCATGCTGTAACTGTCCTA 57.306 42.857 20.33 0.00 0.00 2.94
2390 7475 3.251479 TGCATGCTGTAACTGTCCTAG 57.749 47.619 20.33 0.00 0.00 3.02
2391 7476 1.936547 GCATGCTGTAACTGTCCTAGC 59.063 52.381 11.37 0.00 35.06 3.42
2392 7477 2.677902 GCATGCTGTAACTGTCCTAGCA 60.678 50.000 11.37 12.88 46.90 3.49
2393 7478 2.743636 TGCTGTAACTGTCCTAGCAC 57.256 50.000 8.21 0.00 39.26 4.40
2394 7479 2.248248 TGCTGTAACTGTCCTAGCACT 58.752 47.619 8.21 0.00 39.26 4.40
2395 7480 3.427573 TGCTGTAACTGTCCTAGCACTA 58.572 45.455 8.21 0.00 39.26 2.74
2396 7481 4.023980 TGCTGTAACTGTCCTAGCACTAT 58.976 43.478 8.21 0.00 39.26 2.12
2397 7482 5.198207 TGCTGTAACTGTCCTAGCACTATA 58.802 41.667 8.21 0.00 39.26 1.31
2398 7483 5.655090 TGCTGTAACTGTCCTAGCACTATAA 59.345 40.000 8.21 0.00 39.26 0.98
2399 7484 6.323996 TGCTGTAACTGTCCTAGCACTATAAT 59.676 38.462 8.21 0.00 39.26 1.28
2400 7485 6.864165 GCTGTAACTGTCCTAGCACTATAATC 59.136 42.308 0.00 0.00 34.64 1.75
2415 7500 8.034804 AGCACTATAATCAATATGCGTGACATA 58.965 33.333 0.00 0.00 45.25 2.29
2427 7512 2.948979 GCGTGACATATTGGGAATTGGA 59.051 45.455 0.00 0.00 0.00 3.53
2431 7516 6.238897 GCGTGACATATTGGGAATTGGATTAA 60.239 38.462 0.00 0.00 0.00 1.40
2440 7525 7.732222 TTGGGAATTGGATTAAAGCAAGTAT 57.268 32.000 0.00 0.00 0.00 2.12
2451 7536 9.000486 GGATTAAAGCAAGTATAATAGGGTGAC 58.000 37.037 0.00 0.00 0.00 3.67
2461 7546 8.671987 AGTATAATAGGGTGACATAAGCTGAT 57.328 34.615 0.00 0.00 0.00 2.90
2533 7744 5.594777 AGGAGAGAGAGGAGAACCAATAAA 58.405 41.667 0.00 0.00 38.94 1.40
2573 7784 2.564771 TGATATGCTGCTACACCAAGC 58.435 47.619 0.00 0.00 43.08 4.01
2574 7785 1.876156 GATATGCTGCTACACCAAGCC 59.124 52.381 0.00 0.00 42.05 4.35
2575 7786 0.617935 TATGCTGCTACACCAAGCCA 59.382 50.000 0.00 0.00 42.05 4.75
2587 7798 4.074970 ACACCAAGCCAGAGTTATTCAAG 58.925 43.478 0.00 0.00 0.00 3.02
2713 7924 6.716628 TGACCATCTCTATTCTTGCAAACTTT 59.283 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 3195 1.001378 GGCTTGAGCACGTGAATGTTT 60.001 47.619 22.23 0.00 44.36 2.83
91 3255 6.148948 AGAGCGTAGTATCGTACAGTAGTAG 58.851 44.000 0.00 0.00 0.00 2.57
111 3275 4.437930 GCACTACATTGTGAAATGGAGAGC 60.438 45.833 15.84 15.13 45.59 4.09
314 3480 6.756074 TCGTTCCGTTCTAAAAAGTCAAACTA 59.244 34.615 0.00 0.00 0.00 2.24
327 3493 2.488937 TGCACATACTCGTTCCGTTCTA 59.511 45.455 0.00 0.00 0.00 2.10
337 3503 1.643292 CGCCCAATGCACATACTCG 59.357 57.895 0.00 0.00 41.33 4.18
377 3543 3.018973 CGACCAACACAACACGGG 58.981 61.111 0.00 0.00 0.00 5.28
393 3559 1.738099 AACGTAGCCTGCAGAAGCG 60.738 57.895 17.39 15.73 46.23 4.68
446 3650 3.637714 GAGCGCTCGGTCAAAACA 58.362 55.556 23.61 0.00 41.72 2.83
493 3703 5.064198 TCCACGTCAGCCTTTTTATAATTCG 59.936 40.000 0.00 0.00 0.00 3.34
501 3711 1.156736 CGATCCACGTCAGCCTTTTT 58.843 50.000 0.00 0.00 37.22 1.94
539 3774 1.000396 GATGCCAAACCTCCTGCCT 60.000 57.895 0.00 0.00 0.00 4.75
541 3776 0.255890 TAGGATGCCAAACCTCCTGC 59.744 55.000 0.62 0.00 39.71 4.85
543 3778 2.158755 CGAATAGGATGCCAAACCTCCT 60.159 50.000 0.00 0.00 42.11 3.69
571 3808 4.259970 CGAATCGATGGATGTGAAGTGAAC 60.260 45.833 0.00 0.00 31.83 3.18
572 3809 3.865164 CGAATCGATGGATGTGAAGTGAA 59.135 43.478 0.00 0.00 31.83 3.18
573 3810 3.119137 ACGAATCGATGGATGTGAAGTGA 60.119 43.478 10.55 0.00 31.83 3.41
574 3811 3.190079 ACGAATCGATGGATGTGAAGTG 58.810 45.455 10.55 0.00 31.83 3.16
575 3812 3.448686 GACGAATCGATGGATGTGAAGT 58.551 45.455 10.55 0.00 31.83 3.01
595 3832 5.639757 CATGATAAAAAGCATTGACACGGA 58.360 37.500 0.00 0.00 0.00 4.69
636 3877 2.288013 CGCACTACGTTCGCATCAT 58.712 52.632 0.00 0.00 36.87 2.45
637 3878 3.761995 CGCACTACGTTCGCATCA 58.238 55.556 0.00 0.00 36.87 3.07
706 3953 1.488393 TGGCACTTTTTCCCCTTTTGG 59.512 47.619 0.00 0.00 39.97 3.28
707 3954 2.942376 GTTGGCACTTTTTCCCCTTTTG 59.058 45.455 0.00 0.00 0.00 2.44
708 3955 2.843730 AGTTGGCACTTTTTCCCCTTTT 59.156 40.909 0.00 0.00 0.00 2.27
709 3956 2.170397 CAGTTGGCACTTTTTCCCCTTT 59.830 45.455 0.00 0.00 0.00 3.11
749 3999 7.041372 TGTCAAACAGCTGGTACTCTTATTTTC 60.041 37.037 19.93 2.94 0.00 2.29
779 4029 2.428890 TGATTGGCCGTTGTTGTCTTTT 59.571 40.909 0.00 0.00 0.00 2.27
1131 4486 0.107606 CTCTGCTGCTGCTGGAGAAT 60.108 55.000 25.61 0.00 39.81 2.40
1209 4599 2.048597 CACGTGCTTCGGCTGGTA 60.049 61.111 0.82 0.00 44.69 3.25
1212 4602 4.374702 GTGCACGTGCTTCGGCTG 62.375 66.667 37.59 0.21 44.69 4.85
1216 4606 3.059472 CTAGCGTGCACGTGCTTCG 62.059 63.158 37.59 36.06 42.48 3.79
1217 4607 2.772189 CTAGCGTGCACGTGCTTC 59.228 61.111 37.59 28.04 42.48 3.86
1225 4615 2.358615 CCTTGGTGCTAGCGTGCA 60.359 61.111 10.77 2.63 41.05 4.57
1251 6104 0.684535 TCCACAGCGTCCATTGAGAA 59.315 50.000 0.00 0.00 0.00 2.87
1256 6109 1.296715 GGACTCCACAGCGTCCATT 59.703 57.895 3.72 0.00 46.98 3.16
1364 6226 1.774217 ACTTTGTGGCCTCTCCCCA 60.774 57.895 3.32 0.00 0.00 4.96
1690 6594 5.140177 CGTACAAAATGCTTTCACAGAGTC 58.860 41.667 0.00 0.00 0.00 3.36
1709 6628 4.568876 CGATTTGCGCGGCCGTAC 62.569 66.667 28.70 19.58 36.67 3.67
1718 6637 1.136884 GCTACATCGCTACGATTTGCG 60.137 52.381 0.00 0.00 44.59 4.85
1727 6646 7.029563 CAGTATACAATGATGCTACATCGCTA 58.970 38.462 5.50 0.00 0.00 4.26
1807 6753 6.808212 CGAACCAAATCTTAATCTTGCATTGT 59.192 34.615 0.00 0.00 0.00 2.71
1819 6788 2.078392 GCCCGAACGAACCAAATCTTA 58.922 47.619 0.00 0.00 0.00 2.10
1831 6800 1.335496 TCCAAAAGAAAAGCCCGAACG 59.665 47.619 0.00 0.00 0.00 3.95
1833 6802 3.226777 TCATCCAAAAGAAAAGCCCGAA 58.773 40.909 0.00 0.00 0.00 4.30
1866 6846 1.303091 CCCGGCCAAGGTTAACTTCG 61.303 60.000 2.24 0.00 37.29 3.79
1908 6891 2.167861 GGCGACGGCAGATGAACTC 61.168 63.158 17.49 0.00 42.47 3.01
1909 6892 2.125512 GGCGACGGCAGATGAACT 60.126 61.111 17.49 0.00 42.47 3.01
1910 6893 1.766143 GATGGCGACGGCAGATGAAC 61.766 60.000 28.34 11.78 42.43 3.18
1911 6894 1.521457 GATGGCGACGGCAGATGAA 60.521 57.895 28.34 4.70 42.43 2.57
2014 7081 6.092122 TGCAGTCGATTCGATATTTTTGACTT 59.908 34.615 12.54 0.00 38.42 3.01
2033 7100 3.414700 CTTCCCGCGTGTGCAGTC 61.415 66.667 4.92 0.00 42.97 3.51
2036 7103 1.377366 TTTTTCTTCCCGCGTGTGCA 61.377 50.000 4.92 0.00 42.97 4.57
2037 7104 0.039527 ATTTTTCTTCCCGCGTGTGC 60.040 50.000 4.92 0.00 37.91 4.57
2099 7170 0.178950 TCCACTGGTGAGAGCTGACT 60.179 55.000 0.00 0.00 0.00 3.41
2178 7263 8.421002 CCCTGTTTTCCTTGAAAGAATAGAAAA 58.579 33.333 0.00 0.00 32.93 2.29
2189 7274 0.825840 CCGCCCCTGTTTTCCTTGAA 60.826 55.000 0.00 0.00 0.00 2.69
2193 7278 4.678743 GCCCGCCCCTGTTTTCCT 62.679 66.667 0.00 0.00 0.00 3.36
2195 7280 4.678743 AGGCCCGCCCCTGTTTTC 62.679 66.667 0.00 0.00 36.58 2.29
2206 7291 4.760047 CAGTGGAACCGAGGCCCG 62.760 72.222 0.00 2.20 37.80 6.13
2249 7334 2.871096 TAAAGTGGATCCAAGCGGTT 57.129 45.000 18.20 8.75 0.00 4.44
2252 7337 3.941483 AGAACATAAAGTGGATCCAAGCG 59.059 43.478 18.20 4.70 0.00 4.68
2287 7372 8.336987 AGTAGTATGGATCCATATGTAGCTGTA 58.663 37.037 32.15 9.79 40.49 2.74
2303 7388 4.042560 AGGCCAGTCGTATAGTAGTATGGA 59.957 45.833 5.01 0.00 0.00 3.41
2304 7389 4.333690 AGGCCAGTCGTATAGTAGTATGG 58.666 47.826 5.01 0.00 0.00 2.74
2312 7397 3.875838 GCAGAGGCCAGTCGTATAG 57.124 57.895 5.01 0.00 0.00 1.31
2327 7412 4.596585 AAACGTGGGTGGGGGCAG 62.597 66.667 0.00 0.00 0.00 4.85
2328 7413 4.589675 GAAACGTGGGTGGGGGCA 62.590 66.667 0.00 0.00 0.00 5.36
2330 7415 2.881528 TACGAAACGTGGGTGGGGG 61.882 63.158 7.05 0.00 41.39 5.40
2332 7417 2.023223 CGTACGAAACGTGGGTGGG 61.023 63.158 10.44 0.00 46.72 4.61
2333 7418 3.541191 CGTACGAAACGTGGGTGG 58.459 61.111 10.44 0.00 46.72 4.61
2341 7426 2.217167 GGGCGATGAATACGTACGAAAC 59.783 50.000 24.41 10.49 0.00 2.78
2342 7427 2.159268 TGGGCGATGAATACGTACGAAA 60.159 45.455 24.41 10.02 0.00 3.46
2343 7428 1.404748 TGGGCGATGAATACGTACGAA 59.595 47.619 24.41 2.01 0.00 3.85
2344 7429 1.023502 TGGGCGATGAATACGTACGA 58.976 50.000 24.41 6.04 0.00 3.43
2345 7430 1.126079 GTGGGCGATGAATACGTACG 58.874 55.000 15.01 15.01 0.00 3.67
2346 7431 1.126079 CGTGGGCGATGAATACGTAC 58.874 55.000 0.00 0.00 41.33 3.67
2347 7432 0.031043 CCGTGGGCGATGAATACGTA 59.969 55.000 0.00 0.00 41.33 3.57
2348 7433 1.227147 CCGTGGGCGATGAATACGT 60.227 57.895 0.00 0.00 41.33 3.57
2349 7434 0.528901 TTCCGTGGGCGATGAATACG 60.529 55.000 0.00 0.00 41.33 3.06
2350 7435 1.878953 ATTCCGTGGGCGATGAATAC 58.121 50.000 0.00 0.00 41.33 1.89
2351 7436 2.217750 CAATTCCGTGGGCGATGAATA 58.782 47.619 0.00 0.00 41.33 1.75
2352 7437 1.024271 CAATTCCGTGGGCGATGAAT 58.976 50.000 0.00 0.00 41.33 2.57
2353 7438 1.653094 GCAATTCCGTGGGCGATGAA 61.653 55.000 0.00 0.00 41.33 2.57
2354 7439 2.112198 GCAATTCCGTGGGCGATGA 61.112 57.895 0.00 0.00 41.33 2.92
2355 7440 1.727511 ATGCAATTCCGTGGGCGATG 61.728 55.000 0.00 0.00 41.33 3.84
2356 7441 1.453745 ATGCAATTCCGTGGGCGAT 60.454 52.632 0.00 0.00 41.33 4.58
2357 7442 2.045438 ATGCAATTCCGTGGGCGA 60.045 55.556 0.00 0.00 41.33 5.54
2358 7443 2.102749 CATGCAATTCCGTGGGCG 59.897 61.111 0.00 0.00 37.95 6.13
2359 7444 2.202783 GCATGCAATTCCGTGGGC 60.203 61.111 14.21 0.00 0.00 5.36
2360 7445 1.140161 CAGCATGCAATTCCGTGGG 59.860 57.895 21.98 0.00 0.00 4.61
2361 7446 1.093972 TACAGCATGCAATTCCGTGG 58.906 50.000 21.98 0.00 42.53 4.94
2362 7447 2.162208 AGTTACAGCATGCAATTCCGTG 59.838 45.455 21.98 9.93 42.53 4.94
2363 7448 2.162208 CAGTTACAGCATGCAATTCCGT 59.838 45.455 21.98 9.05 42.53 4.69
2364 7449 2.162208 ACAGTTACAGCATGCAATTCCG 59.838 45.455 21.98 4.94 42.53 4.30
2365 7450 3.428045 GGACAGTTACAGCATGCAATTCC 60.428 47.826 21.98 9.55 42.53 3.01
2366 7451 3.441572 AGGACAGTTACAGCATGCAATTC 59.558 43.478 21.98 6.15 42.53 2.17
2367 7452 3.424703 AGGACAGTTACAGCATGCAATT 58.575 40.909 21.98 5.67 42.53 2.32
2368 7453 3.077484 AGGACAGTTACAGCATGCAAT 57.923 42.857 21.98 9.84 42.53 3.56
2369 7454 2.566833 AGGACAGTTACAGCATGCAA 57.433 45.000 21.98 2.08 42.53 4.08
2370 7455 2.677902 GCTAGGACAGTTACAGCATGCA 60.678 50.000 21.98 0.00 42.53 3.96
2371 7456 1.936547 GCTAGGACAGTTACAGCATGC 59.063 52.381 10.51 10.51 42.53 4.06
2372 7457 2.932614 GTGCTAGGACAGTTACAGCATG 59.067 50.000 9.84 0.00 43.53 4.06
2373 7458 2.834549 AGTGCTAGGACAGTTACAGCAT 59.165 45.455 17.34 0.00 43.53 3.79
2374 7459 2.248248 AGTGCTAGGACAGTTACAGCA 58.752 47.619 17.34 0.00 39.79 4.41
2375 7460 4.657436 ATAGTGCTAGGACAGTTACAGC 57.343 45.455 17.34 0.00 0.00 4.40
2376 7461 7.941919 TGATTATAGTGCTAGGACAGTTACAG 58.058 38.462 17.34 0.00 0.00 2.74
2377 7462 7.891498 TGATTATAGTGCTAGGACAGTTACA 57.109 36.000 17.34 6.62 0.00 2.41
2380 7465 9.935241 CATATTGATTATAGTGCTAGGACAGTT 57.065 33.333 17.34 3.27 0.00 3.16
2381 7466 8.037758 GCATATTGATTATAGTGCTAGGACAGT 58.962 37.037 17.34 6.94 0.00 3.55
2382 7467 7.221645 CGCATATTGATTATAGTGCTAGGACAG 59.778 40.741 17.34 0.00 0.00 3.51
2383 7468 7.035612 CGCATATTGATTATAGTGCTAGGACA 58.964 38.462 17.34 3.16 0.00 4.02
2384 7469 7.009631 CACGCATATTGATTATAGTGCTAGGAC 59.990 40.741 6.22 6.22 0.00 3.85
2385 7470 7.035612 CACGCATATTGATTATAGTGCTAGGA 58.964 38.462 0.00 0.00 0.00 2.94
2386 7471 7.009631 GTCACGCATATTGATTATAGTGCTAGG 59.990 40.741 0.00 0.00 32.50 3.02
2387 7472 7.542130 TGTCACGCATATTGATTATAGTGCTAG 59.458 37.037 0.00 0.00 32.50 3.42
2388 7473 7.375053 TGTCACGCATATTGATTATAGTGCTA 58.625 34.615 0.00 0.00 32.50 3.49
2389 7474 6.223120 TGTCACGCATATTGATTATAGTGCT 58.777 36.000 0.00 0.00 32.50 4.40
2390 7475 6.466308 TGTCACGCATATTGATTATAGTGC 57.534 37.500 0.00 0.00 32.50 4.40
2415 7500 6.625532 ACTTGCTTTAATCCAATTCCCAAT 57.374 33.333 0.00 0.00 0.00 3.16
2417 7502 8.830915 TTATACTTGCTTTAATCCAATTCCCA 57.169 30.769 0.00 0.00 0.00 4.37
2431 7516 7.661847 GCTTATGTCACCCTATTATACTTGCTT 59.338 37.037 0.00 0.00 0.00 3.91
2483 7568 9.765795 CTTCTCTCTCCTTCAACTAAGTAAAAA 57.234 33.333 0.00 0.00 32.89 1.94
2484 7569 9.144298 TCTTCTCTCTCCTTCAACTAAGTAAAA 57.856 33.333 0.00 0.00 32.89 1.52
2485 7570 8.707796 TCTTCTCTCTCCTTCAACTAAGTAAA 57.292 34.615 0.00 0.00 32.89 2.01
2487 7572 6.887545 CCTCTTCTCTCTCCTTCAACTAAGTA 59.112 42.308 0.00 0.00 32.89 2.24
2488 7573 5.714806 CCTCTTCTCTCTCCTTCAACTAAGT 59.285 44.000 0.00 0.00 32.89 2.24
2499 7710 3.181450 CCTCTCTCTCCTCTTCTCTCTCC 60.181 56.522 0.00 0.00 0.00 3.71
2573 7784 6.875726 TCATCAACTGACTTGAATAACTCTGG 59.124 38.462 0.00 0.00 42.37 3.86
2574 7785 7.895975 TCATCAACTGACTTGAATAACTCTG 57.104 36.000 0.00 0.00 42.37 3.35
2606 7817 8.362639 AGACTTCATTGCAGTAAATGTTTGAAT 58.637 29.630 0.00 0.00 38.46 2.57


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

AutoCloner maintained by Alex Coulton.