Multiple sequence alignment - TraesCS6B01G228400

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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 TraesCS6B01G228400 chr6B 100.000 8086 0 0 1 8086 361275583 361267498 0.000000e+00 14933
1 TraesCS6B01G228400 chr6B 95.522 5829 213 18 2269 8086 570078237 570084028 0.000000e+00 9274
2 TraesCS6B01G228400 chr6B 95.653 4946 196 9 2073 7013 308975586 308980517 0.000000e+00 7925
3 TraesCS6B01G228400 chr6B 89.323 946 79 11 1 928 454864788 454863847 0.000000e+00 1168
4 TraesCS6B01G228400 chr6B 90.476 777 64 9 7316 8085 420703391 420702618 0.000000e+00 1016
5 TraesCS6B01G228400 chr6B 93.924 576 30 5 1509 2082 308974344 308974916 0.000000e+00 865
6 TraesCS6B01G228400 chr6B 90.283 247 20 4 1090 1333 644656033 644655788 3.640000e-83 320
7 TraesCS6B01G228400 chr6B 87.330 221 27 1 1282 1502 269791061 269790842 1.350000e-62 252
8 TraesCS6B01G228400 chr5B 95.866 4935 177 16 3163 8086 176794240 176789322 0.000000e+00 7958
9 TraesCS6B01G228400 chr5B 95.095 4934 215 20 3163 8086 204616338 204611422 0.000000e+00 7745
10 TraesCS6B01G228400 chr5B 89.460 778 70 10 7316 8085 363794495 363795268 0.000000e+00 972
11 TraesCS6B01G228400 chr5B 90.135 223 20 1 1282 1502 159180175 159180397 1.030000e-73 289
12 TraesCS6B01G228400 chr1B 95.319 4935 200 17 3163 8086 177158128 177163042 0.000000e+00 7805
13 TraesCS6B01G228400 chr1B 95.175 4933 209 16 3163 8086 192673423 192678335 0.000000e+00 7764
14 TraesCS6B01G228400 chr1B 95.207 1210 49 3 2656 3865 411019498 411018298 0.000000e+00 1905
15 TraesCS6B01G228400 chr1B 90.488 778 63 10 7316 8086 180009123 180009896 0.000000e+00 1016
16 TraesCS6B01G228400 chr1B 91.652 551 41 5 953 1501 555875580 555875033 0.000000e+00 758
17 TraesCS6B01G228400 chr1B 90.649 385 31 4 1013 1395 292053021 292052640 2.600000e-139 507
18 TraesCS6B01G228400 chr1B 82.600 500 59 17 196 675 105398741 105399232 4.510000e-112 416
19 TraesCS6B01G228400 chr2D 93.494 2813 156 11 3700 6501 244754336 244757132 0.000000e+00 4156
20 TraesCS6B01G228400 chr2D 87.093 860 72 19 6447 7270 300875309 300876165 0.000000e+00 937
21 TraesCS6B01G228400 chr2D 90.451 377 30 6 962 1333 455245958 455245583 7.290000e-135 492
22 TraesCS6B01G228400 chr2B 95.709 2540 92 8 2073 4610 407885026 407887550 0.000000e+00 4071
23 TraesCS6B01G228400 chr2B 96.379 1795 54 5 2073 3865 371367990 371366205 0.000000e+00 2944
24 TraesCS6B01G228400 chr2B 94.354 1789 81 17 6309 8085 51455682 51453902 0.000000e+00 2726
25 TraesCS6B01G228400 chr2B 93.563 1771 53 16 5630 7389 407887555 407889275 0.000000e+00 2582
26 TraesCS6B01G228400 chr2B 88.384 594 46 7 1510 2082 707737700 707738291 0.000000e+00 693
27 TraesCS6B01G228400 chr2B 90.946 497 39 5 436 928 312397391 312397885 0.000000e+00 664
28 TraesCS6B01G228400 chr2B 90.562 498 39 7 436 928 312391123 312391617 0.000000e+00 652
29 TraesCS6B01G228400 chr2B 90.631 491 39 6 442 928 382674413 382673926 0.000000e+00 645
30 TraesCS6B01G228400 chr2B 83.036 448 59 13 119 556 304262133 304262573 2.740000e-104 390
31 TraesCS6B01G228400 chr6D 92.220 2815 184 13 3700 6504 77327965 77330754 0.000000e+00 3952
32 TraesCS6B01G228400 chr6D 91.034 1450 83 15 2076 3521 225587444 225586038 0.000000e+00 1914
33 TraesCS6B01G228400 chr6D 91.221 467 40 1 4625 5090 387786119 387786585 1.140000e-177 634
34 TraesCS6B01G228400 chr6D 83.813 556 68 11 5085 5621 10401596 10402148 7.240000e-140 508
35 TraesCS6B01G228400 chr7B 96.158 1666 49 11 5744 7401 131515161 131513503 0.000000e+00 2708
36 TraesCS6B01G228400 chr7B 94.444 864 37 5 2901 3763 131516019 131515166 0.000000e+00 1319
37 TraesCS6B01G228400 chr7B 83.596 445 61 11 119 556 162028206 162027767 2.720000e-109 407
38 TraesCS6B01G228400 chr7A 90.795 1597 122 10 2073 3667 587285674 587284101 0.000000e+00 2111
39 TraesCS6B01G228400 chr7A 92.330 339 22 4 1746 2082 587286705 587286369 5.680000e-131 479
40 TraesCS6B01G228400 chr7A 86.717 399 41 11 985 1379 370801477 370801867 4.480000e-117 433
41 TraesCS6B01G228400 chr7A 88.321 137 15 1 1368 1504 370813395 370813530 6.490000e-36 163
42 TraesCS6B01G228400 chr3A 93.575 1323 69 8 2073 3392 87731115 87732424 0.000000e+00 1958
43 TraesCS6B01G228400 chr3A 89.785 558 35 12 1547 2082 87729863 87730420 0.000000e+00 695
44 TraesCS6B01G228400 chr3A 88.067 595 45 7 1510 2082 679990073 679990663 0.000000e+00 682
45 TraesCS6B01G228400 chr3A 88.551 559 40 12 1547 2082 476157358 476156801 0.000000e+00 656
46 TraesCS6B01G228400 chr3A 90.707 495 40 4 436 926 520863911 520864403 0.000000e+00 654
47 TraesCS6B01G228400 chr3A 90.121 496 44 4 436 928 59682159 59681666 2.460000e-179 640
48 TraesCS6B01G228400 chr4D 91.379 1450 82 13 2076 3521 255552141 255553551 0.000000e+00 1945
49 TraesCS6B01G228400 chr4D 90.282 710 48 8 1 690 235439446 235440154 0.000000e+00 909
50 TraesCS6B01G228400 chr4D 92.126 508 38 2 929 1434 441536020 441536527 0.000000e+00 715
51 TraesCS6B01G228400 chr4D 92.308 221 17 0 1282 1502 332621252 332621472 1.690000e-81 315
52 TraesCS6B01G228400 chr4D 95.946 74 2 1 1432 1504 441562751 441562824 1.430000e-22 119
53 TraesCS6B01G228400 chr4B 89.779 949 72 13 1 928 470626530 470625586 0.000000e+00 1192
54 TraesCS6B01G228400 chr4B 90.991 777 61 9 7316 8085 509282515 509283289 0.000000e+00 1038
55 TraesCS6B01G228400 chr4B 90.338 207 19 1 1510 1716 370704765 370704970 3.720000e-68 270
56 TraesCS6B01G228400 chr3D 89.218 946 71 12 1 928 208623311 208624243 0.000000e+00 1153
57 TraesCS6B01G228400 chr3B 94.306 720 38 3 2073 2789 522281288 522280569 0.000000e+00 1099
58 TraesCS6B01G228400 chr3B 90.144 416 36 5 983 1395 341337764 341338177 3.320000e-148 536
59 TraesCS6B01G228400 chr1A 89.697 825 60 16 2708 3521 371319698 371320508 0.000000e+00 1029
60 TraesCS6B01G228400 chr1A 90.744 497 40 5 436 928 282827991 282828485 0.000000e+00 658
61 TraesCS6B01G228400 chr1A 93.030 330 21 2 1755 2082 371318917 371319246 1.580000e-131 481
62 TraesCS6B01G228400 chr1A 84.270 445 58 11 119 556 186755545 186755106 2.700000e-114 424
63 TraesCS6B01G228400 chr1A 92.344 209 15 1 950 1157 7987720 7987512 6.140000e-76 296
64 TraesCS6B01G228400 chr5A 92.280 557 37 4 953 1504 12670905 12671460 0.000000e+00 785
65 TraesCS6B01G228400 chr5A 90.859 547 46 4 960 1504 139791201 139791745 0.000000e+00 730
66 TraesCS6B01G228400 chr5A 88.758 596 41 7 1510 2082 564441949 564441357 0.000000e+00 706
67 TraesCS6B01G228400 chr5A 90.524 496 42 5 436 928 15472330 15471837 0.000000e+00 651
68 TraesCS6B01G228400 chr6A 89.580 595 37 11 1510 2082 29435915 29436506 0.000000e+00 732
69 TraesCS6B01G228400 chr6A 80.814 172 17 12 1341 1500 409736480 409736647 3.960000e-23 121
70 TraesCS6B01G228400 chr2A 88.403 595 44 6 1510 2082 30689481 30690072 0.000000e+00 693
71 TraesCS6B01G228400 chr2A 91.147 497 38 5 436 928 625766529 625767023 0.000000e+00 669
72 TraesCS6B01G228400 chr4A 91.532 496 37 4 436 928 576361902 576362395 0.000000e+00 678
73 TraesCS6B01G228400 chrUn 82.921 445 64 11 119 556 51027921 51028360 2.740000e-104 390


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 TraesCS6B01G228400 chr6B 361267498 361275583 8085 True 14933.0 14933 100.0000 1 8086 1 chr6B.!!$R2 8085
1 TraesCS6B01G228400 chr6B 570078237 570084028 5791 False 9274.0 9274 95.5220 2269 8086 1 chr6B.!!$F1 5817
2 TraesCS6B01G228400 chr6B 308974344 308980517 6173 False 4395.0 7925 94.7885 1509 7013 2 chr6B.!!$F2 5504
3 TraesCS6B01G228400 chr6B 454863847 454864788 941 True 1168.0 1168 89.3230 1 928 1 chr6B.!!$R4 927
4 TraesCS6B01G228400 chr6B 420702618 420703391 773 True 1016.0 1016 90.4760 7316 8085 1 chr6B.!!$R3 769
5 TraesCS6B01G228400 chr5B 176789322 176794240 4918 True 7958.0 7958 95.8660 3163 8086 1 chr5B.!!$R1 4923
6 TraesCS6B01G228400 chr5B 204611422 204616338 4916 True 7745.0 7745 95.0950 3163 8086 1 chr5B.!!$R2 4923
7 TraesCS6B01G228400 chr5B 363794495 363795268 773 False 972.0 972 89.4600 7316 8085 1 chr5B.!!$F2 769
8 TraesCS6B01G228400 chr1B 177158128 177163042 4914 False 7805.0 7805 95.3190 3163 8086 1 chr1B.!!$F2 4923
9 TraesCS6B01G228400 chr1B 192673423 192678335 4912 False 7764.0 7764 95.1750 3163 8086 1 chr1B.!!$F4 4923
10 TraesCS6B01G228400 chr1B 411018298 411019498 1200 True 1905.0 1905 95.2070 2656 3865 1 chr1B.!!$R2 1209
11 TraesCS6B01G228400 chr1B 180009123 180009896 773 False 1016.0 1016 90.4880 7316 8086 1 chr1B.!!$F3 770
12 TraesCS6B01G228400 chr1B 555875033 555875580 547 True 758.0 758 91.6520 953 1501 1 chr1B.!!$R3 548
13 TraesCS6B01G228400 chr2D 244754336 244757132 2796 False 4156.0 4156 93.4940 3700 6501 1 chr2D.!!$F1 2801
14 TraesCS6B01G228400 chr2D 300875309 300876165 856 False 937.0 937 87.0930 6447 7270 1 chr2D.!!$F2 823
15 TraesCS6B01G228400 chr2B 407885026 407889275 4249 False 3326.5 4071 94.6360 2073 7389 2 chr2B.!!$F5 5316
16 TraesCS6B01G228400 chr2B 371366205 371367990 1785 True 2944.0 2944 96.3790 2073 3865 1 chr2B.!!$R2 1792
17 TraesCS6B01G228400 chr2B 51453902 51455682 1780 True 2726.0 2726 94.3540 6309 8085 1 chr2B.!!$R1 1776
18 TraesCS6B01G228400 chr2B 707737700 707738291 591 False 693.0 693 88.3840 1510 2082 1 chr2B.!!$F4 572
19 TraesCS6B01G228400 chr6D 77327965 77330754 2789 False 3952.0 3952 92.2200 3700 6504 1 chr6D.!!$F2 2804
20 TraesCS6B01G228400 chr6D 225586038 225587444 1406 True 1914.0 1914 91.0340 2076 3521 1 chr6D.!!$R1 1445
21 TraesCS6B01G228400 chr6D 10401596 10402148 552 False 508.0 508 83.8130 5085 5621 1 chr6D.!!$F1 536
22 TraesCS6B01G228400 chr7B 131513503 131516019 2516 True 2013.5 2708 95.3010 2901 7401 2 chr7B.!!$R2 4500
23 TraesCS6B01G228400 chr7A 587284101 587286705 2604 True 1295.0 2111 91.5625 1746 3667 2 chr7A.!!$R1 1921
24 TraesCS6B01G228400 chr3A 87729863 87732424 2561 False 1326.5 1958 91.6800 1547 3392 2 chr3A.!!$F3 1845
25 TraesCS6B01G228400 chr3A 679990073 679990663 590 False 682.0 682 88.0670 1510 2082 1 chr3A.!!$F2 572
26 TraesCS6B01G228400 chr3A 476156801 476157358 557 True 656.0 656 88.5510 1547 2082 1 chr3A.!!$R2 535
27 TraesCS6B01G228400 chr4D 255552141 255553551 1410 False 1945.0 1945 91.3790 2076 3521 1 chr4D.!!$F2 1445
28 TraesCS6B01G228400 chr4D 235439446 235440154 708 False 909.0 909 90.2820 1 690 1 chr4D.!!$F1 689
29 TraesCS6B01G228400 chr4D 441536020 441536527 507 False 715.0 715 92.1260 929 1434 1 chr4D.!!$F4 505
30 TraesCS6B01G228400 chr4B 470625586 470626530 944 True 1192.0 1192 89.7790 1 928 1 chr4B.!!$R1 927
31 TraesCS6B01G228400 chr4B 509282515 509283289 774 False 1038.0 1038 90.9910 7316 8085 1 chr4B.!!$F2 769
32 TraesCS6B01G228400 chr3D 208623311 208624243 932 False 1153.0 1153 89.2180 1 928 1 chr3D.!!$F1 927
33 TraesCS6B01G228400 chr3B 522280569 522281288 719 True 1099.0 1099 94.3060 2073 2789 1 chr3B.!!$R1 716
34 TraesCS6B01G228400 chr1A 371318917 371320508 1591 False 755.0 1029 91.3635 1755 3521 2 chr1A.!!$F2 1766
35 TraesCS6B01G228400 chr5A 12670905 12671460 555 False 785.0 785 92.2800 953 1504 1 chr5A.!!$F1 551
36 TraesCS6B01G228400 chr5A 139791201 139791745 544 False 730.0 730 90.8590 960 1504 1 chr5A.!!$F2 544
37 TraesCS6B01G228400 chr5A 564441357 564441949 592 True 706.0 706 88.7580 1510 2082 1 chr5A.!!$R2 572
38 TraesCS6B01G228400 chr6A 29435915 29436506 591 False 732.0 732 89.5800 1510 2082 1 chr6A.!!$F1 572
39 TraesCS6B01G228400 chr2A 30689481 30690072 591 False 693.0 693 88.4030 1510 2082 1 chr2A.!!$F1 572

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
129 130 0.108138 GTAGCACTCAGGCCGTTCAT 60.108 55.000 0.00 0.0 0.00 2.57 F
1206 1257 0.041386 ACCGACTCCCTTTCCTAGCT 59.959 55.000 0.00 0.0 0.00 3.32 F
1550 1605 0.804364 GCGCAACATTGAGGTCATGA 59.196 50.000 0.30 0.0 0.00 3.07 F
3245 4049 1.070134 TCTTGTTTCACTACAGCGGCT 59.930 47.619 0.00 0.0 0.00 5.52 F
4676 5497 0.105039 GCAGCTACTAGGCCGATTGT 59.895 55.000 0.00 0.0 0.00 2.71 F
4845 5667 1.002366 GCAGTACATCTCCTTGTGCG 58.998 55.000 0.00 0.0 37.31 5.34 F
6106 6957 2.604914 GTCACATATGAGTTGGTGCTCG 59.395 50.000 10.38 0.0 38.28 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1318 1370 0.698238 CTCCCTTGGATTCCACCACA 59.302 55.0 4.45 0.0 39.85 4.17 R
3113 3917 0.391228 TTCAGTAGCCGCTCAACACA 59.609 50.0 0.00 0.0 0.00 3.72 R
3434 4242 0.036022 GGCATGATGCTCCTACTCCC 59.964 60.0 17.84 0.0 44.28 4.30 R
4757 5579 0.107410 AACTGCTTCGGGTTGTGTCA 60.107 50.0 0.00 0.0 0.00 3.58 R
6009 6860 0.313043 CAAGGAACAACAGCAGCAGG 59.687 55.0 0.00 0.0 0.00 4.85 R
6417 7269 0.980423 GGAGCTGGGATGGATAGGAC 59.020 60.0 0.00 0.0 0.00 3.85 R
7666 8574 0.598158 TTATTGTATCGTCGCGCCCC 60.598 55.0 0.00 0.0 0.00 5.80 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
29 30 1.050988 CGGTGACATCCCTCCATCCT 61.051 60.000 0.00 0.00 0.00 3.24
54 55 4.431131 CGCCTCCCCACCTTGCAT 62.431 66.667 0.00 0.00 0.00 3.96
79 80 1.982938 GCCACCGTCCTACACTCCT 60.983 63.158 0.00 0.00 0.00 3.69
82 83 0.966920 CACCGTCCTACACTCCTTGT 59.033 55.000 0.00 0.00 42.84 3.16
90 91 4.466726 GTCCTACACTCCTTGTTATGTCCT 59.533 45.833 0.00 0.00 39.91 3.85
129 130 0.108138 GTAGCACTCAGGCCGTTCAT 60.108 55.000 0.00 0.00 0.00 2.57
131 132 2.109126 GCACTCAGGCCGTTCATCC 61.109 63.158 0.00 0.00 0.00 3.51
255 257 7.877612 TGCAAAAATATCAGACACTCTCAACTA 59.122 33.333 0.00 0.00 0.00 2.24
261 263 5.152623 TCAGACACTCTCAACTAAATGGG 57.847 43.478 0.00 0.00 0.00 4.00
302 305 4.184629 CAGTATAACCACTGCAGGAGTTC 58.815 47.826 22.33 11.73 39.54 3.01
320 323 7.959651 CAGGAGTTCGAAAATCTCAACAAATAG 59.040 37.037 14.15 0.00 0.00 1.73
394 397 4.882427 TGGTTAATTCGTTGTTCTGGACAA 59.118 37.500 0.00 0.00 45.70 3.18
503 509 3.851458 AAACCCGGAACACTCTAGTTT 57.149 42.857 0.73 0.00 0.00 2.66
512 521 6.395629 CGGAACACTCTAGTTTTGGAATCTA 58.604 40.000 0.00 0.00 0.00 1.98
513 522 6.872020 CGGAACACTCTAGTTTTGGAATCTAA 59.128 38.462 0.00 0.00 0.00 2.10
551 562 3.712016 TCCAAAATGAACATCGGGAGA 57.288 42.857 0.00 0.00 46.90 3.71
572 583 8.522830 GGGAGAGTTTGAAAAATACATCATGAA 58.477 33.333 0.00 0.00 0.00 2.57
654 680 7.767261 ACTTATTCATCCTATCACTCGATAGC 58.233 38.462 4.30 0.00 46.77 2.97
680 706 4.019792 TGGCTGTTATGATGTGACTTGT 57.980 40.909 0.00 0.00 0.00 3.16
685 711 5.122869 GCTGTTATGATGTGACTTGTCATGT 59.877 40.000 6.74 0.00 34.62 3.21
698 724 5.869579 ACTTGTCATGTAATCACTCTTGGT 58.130 37.500 0.00 0.00 0.00 3.67
702 728 6.764379 TGTCATGTAATCACTCTTGGTGTTA 58.236 36.000 0.00 0.00 45.50 2.41
708 734 6.653320 TGTAATCACTCTTGGTGTTATTCCAC 59.347 38.462 0.00 0.00 45.50 4.02
712 738 6.068010 TCACTCTTGGTGTTATTCCACAAAT 58.932 36.000 0.00 0.00 45.50 2.32
789 815 4.427312 CTCATTAGGACAGGCAAAAATGC 58.573 43.478 0.00 0.00 0.00 3.56
790 816 3.831333 TCATTAGGACAGGCAAAAATGCA 59.169 39.130 2.97 0.00 36.33 3.96
791 817 3.940209 TTAGGACAGGCAAAAATGCAG 57.060 42.857 2.97 0.00 36.33 4.41
792 818 1.999648 AGGACAGGCAAAAATGCAGA 58.000 45.000 2.97 0.00 36.33 4.26
873 899 7.365742 TACATGCTCTGTACTAGAACTCTAGGT 60.366 40.741 16.29 6.45 43.05 3.08
928 954 0.445436 GATTGCAGCAGAGTTGGACG 59.555 55.000 0.00 0.00 0.00 4.79
929 955 1.580845 ATTGCAGCAGAGTTGGACGC 61.581 55.000 0.00 0.00 0.00 5.19
930 956 3.782244 GCAGCAGAGTTGGACGCG 61.782 66.667 3.53 3.53 0.00 6.01
931 957 3.782244 CAGCAGAGTTGGACGCGC 61.782 66.667 5.73 0.00 0.00 6.86
946 972 4.722700 CGCCACCCCCACCTTCTG 62.723 72.222 0.00 0.00 0.00 3.02
947 973 4.366684 GCCACCCCCACCTTCTGG 62.367 72.222 0.00 0.00 40.26 3.86
1021 1072 3.400054 GCCCCACGCCTCCTAACT 61.400 66.667 0.00 0.00 0.00 2.24
1206 1257 0.041386 ACCGACTCCCTTTCCTAGCT 59.959 55.000 0.00 0.00 0.00 3.32
1209 1261 1.199615 GACTCCCTTTCCTAGCTGCT 58.800 55.000 7.57 7.57 0.00 4.24
1215 1267 2.866085 CTTTCCTAGCTGCTGCCGCT 62.866 60.000 21.84 21.84 40.80 5.52
1219 1271 3.368190 CTAGCTGCTGCCGCTGACT 62.368 63.158 25.77 4.91 40.80 3.41
1318 1370 1.216990 CCATCTTCCCCTAGTGCCTT 58.783 55.000 0.00 0.00 0.00 4.35
1361 1413 3.272334 GCCGTTCATAGCCGCCAG 61.272 66.667 0.00 0.00 0.00 4.85
1447 1499 3.430556 GTCAGAAGCTTTCCTCTCGTTTC 59.569 47.826 0.00 0.00 0.00 2.78
1550 1605 0.804364 GCGCAACATTGAGGTCATGA 59.196 50.000 0.30 0.00 0.00 3.07
1655 1710 1.178276 AGCAACTCTACTAGCACGCT 58.822 50.000 0.00 0.00 0.00 5.07
1659 1714 3.575630 CAACTCTACTAGCACGCTTGAA 58.424 45.455 7.48 0.00 0.00 2.69
1667 1722 1.968540 GCACGCTTGAAGCTCCCTT 60.969 57.895 15.92 0.00 39.60 3.95
1781 1857 5.000012 TGCGGTTCAACAAAAATAACAGT 58.000 34.783 0.00 0.00 0.00 3.55
1786 1862 6.861055 CGGTTCAACAAAAATAACAGTAGCAT 59.139 34.615 0.00 0.00 0.00 3.79
1858 1935 2.048222 TGTACTGCAGCACGAGGC 60.048 61.111 15.27 0.00 45.30 4.70
2448 3242 8.914011 AGCTTACTTTCAAAAACTGAACCTTAT 58.086 29.630 0.00 0.00 43.90 1.73
2778 3574 2.371841 TGTTGTTCTGGGCAGTACAGAT 59.628 45.455 0.00 0.00 43.82 2.90
2933 3736 7.932335 ACATTTCATTGTTGCAAAAATGTGAT 58.068 26.923 31.85 24.77 44.51 3.06
2934 3737 9.053840 ACATTTCATTGTTGCAAAAATGTGATA 57.946 25.926 31.85 19.82 44.51 2.15
2939 3742 9.872721 TCATTGTTGCAAAAATGTGATATATGT 57.127 25.926 31.85 0.63 35.66 2.29
3161 3965 1.152694 TGCTGCTTTTGGACTGCCT 60.153 52.632 0.00 0.00 34.31 4.75
3234 4038 6.567687 TGTTTGTTCTGACTTCTTGTTTCA 57.432 33.333 0.00 0.00 0.00 2.69
3245 4049 1.070134 TCTTGTTTCACTACAGCGGCT 59.930 47.619 0.00 0.00 0.00 5.52
3482 4291 7.257722 CAACAAACAAGAACAGAAGGTATGTT 58.742 34.615 0.00 0.00 43.38 2.71
3954 4772 5.219343 TGCAGATACATGACTTATGAGGG 57.781 43.478 0.00 0.00 39.21 4.30
4064 4882 3.954904 TCGGCTACTTCAGAGAGCTATTT 59.045 43.478 0.00 0.00 36.43 1.40
4076 4894 6.609212 TCAGAGAGCTATTTCTATTCTGTGGT 59.391 38.462 0.00 0.00 33.32 4.16
4220 5038 6.570692 TCATAACTTCTCTTATTGTCGGTCC 58.429 40.000 0.00 0.00 0.00 4.46
4275 5093 7.832769 TGGCAAATGTTAAGGACCTTTATTAC 58.167 34.615 13.11 6.77 0.00 1.89
4333 5151 1.849097 CCGCTGTAGTATTTCGGTCC 58.151 55.000 0.00 0.00 35.75 4.46
4429 5248 0.182775 AGTAAATGGGATCGTGGGCC 59.817 55.000 0.00 0.00 0.00 5.80
4499 5319 2.925966 TCAAATGGCTTCTTCCCCAT 57.074 45.000 0.00 0.00 43.47 4.00
4510 5330 0.758734 CTTCCCCATACCATGCTCGA 59.241 55.000 0.00 0.00 0.00 4.04
4524 5344 2.384828 TGCTCGACTTTATGCCTAGGA 58.615 47.619 14.75 0.00 0.00 2.94
4572 5392 4.062293 CAACCACGACATCCTTTTCAGTA 58.938 43.478 0.00 0.00 0.00 2.74
4611 5431 3.686016 ACGGTCCAAGTTCAGCAAATAT 58.314 40.909 0.00 0.00 0.00 1.28
4676 5497 0.105039 GCAGCTACTAGGCCGATTGT 59.895 55.000 0.00 0.00 0.00 2.71
4693 5515 2.917227 TGTCGAGCCTCTGCCACA 60.917 61.111 0.00 0.00 38.69 4.17
4757 5579 2.279741 CACCACATCGGATCGTTCAAT 58.720 47.619 0.00 0.00 38.63 2.57
4820 5642 3.878667 CTTCGCCCCTCCATCCCC 61.879 72.222 0.00 0.00 0.00 4.81
4845 5667 1.002366 GCAGTACATCTCCTTGTGCG 58.998 55.000 0.00 0.00 37.31 5.34
5205 6031 7.920738 ACTGAAGAACAATGTACTGAGTTTTC 58.079 34.615 0.00 4.44 0.00 2.29
5839 6688 4.823442 TCTGTAATTGCATCAGGCCATTAG 59.177 41.667 5.01 0.00 39.83 1.73
5987 6836 4.278919 GCTATAGGGTAAGGTGAGTGAGAC 59.721 50.000 1.04 0.00 0.00 3.36
5998 6847 5.329399 AGGTGAGTGAGACAGAGATTACTT 58.671 41.667 0.00 0.00 0.00 2.24
6009 6860 8.245195 AGACAGAGATTACTTAGAGGGATTTC 57.755 38.462 0.00 0.00 0.00 2.17
6106 6957 2.604914 GTCACATATGAGTTGGTGCTCG 59.395 50.000 10.38 0.00 38.28 5.03
6417 7269 2.022195 AGCTCTGCTGGTAATGCAATG 58.978 47.619 0.00 0.00 40.13 2.82
6506 7359 5.458779 GTGTTTGTTGCATAAGTTCTGAACC 59.541 40.000 16.48 2.19 0.00 3.62
6539 7392 2.017138 TGCACAAGTTCGAGTTGTCA 57.983 45.000 11.24 9.96 39.57 3.58
6553 7426 2.820787 AGTTGTCACTACTCGGAGAAGG 59.179 50.000 12.86 3.79 34.09 3.46
6746 7627 2.937519 TGGGCAGTACAAACACATCAA 58.062 42.857 0.00 0.00 0.00 2.57
7060 7946 6.877611 AAAACCAATTATCAGTTCGAGTGT 57.122 33.333 0.00 0.00 0.00 3.55
7061 7947 6.481954 AAACCAATTATCAGTTCGAGTGTC 57.518 37.500 0.00 0.00 0.00 3.67
7062 7948 5.407407 ACCAATTATCAGTTCGAGTGTCT 57.593 39.130 0.00 0.00 0.00 3.41
7093 7984 6.903516 TCCTATTTGATGTCCATGAACAGAT 58.096 36.000 0.00 0.00 31.50 2.90
7309 8203 6.227522 TGGTTCGATGATGAAAGTTTGACTA 58.772 36.000 0.00 0.00 0.00 2.59
7358 8253 5.171337 GTGAAAACACGCTCAGTACAAAATG 59.829 40.000 0.00 0.00 0.00 2.32
7389 8284 7.548196 ACATTCGTTCAAGTACTCTTTTTCA 57.452 32.000 0.00 0.00 0.00 2.69
7391 8286 7.280205 ACATTCGTTCAAGTACTCTTTTTCACT 59.720 33.333 0.00 0.00 0.00 3.41
7666 8574 5.460748 TGACGATATAAACCATGCAAGTACG 59.539 40.000 0.00 0.00 0.00 3.67
7670 8578 1.248101 AAACCATGCAAGTACGGGGC 61.248 55.000 0.00 0.32 0.00 5.80
7692 8600 5.343058 GGCGCGACGATACAATAAACTATTA 59.657 40.000 12.10 0.00 0.00 0.98
7772 8682 2.479049 CCATGCAAGCATCAGTACAAGC 60.479 50.000 4.24 0.00 33.90 4.01
7878 8788 6.677781 TTTTTCAGACGAGAAAACATCAGT 57.322 33.333 12.26 0.00 44.55 3.41
7954 8864 4.807304 ACGTTCAACATGACTAAGTTTCGT 59.193 37.500 0.00 0.00 0.00 3.85
8009 8920 6.761731 TGCCATATTTCGACAAACTTTTTG 57.238 33.333 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.048724 GGATGGAGGGATGTCACCGA 61.049 60.000 0.00 0.00 0.00 4.69
13 14 0.621280 TGCAGGATGGAGGGATGTCA 60.621 55.000 0.00 0.00 35.86 3.58
15 16 0.622738 AGTGCAGGATGGAGGGATGT 60.623 55.000 0.00 0.00 36.81 3.06
54 55 0.609662 GTAGGACGGTGGCAAGGTTA 59.390 55.000 0.00 0.00 0.00 2.85
79 80 1.549037 GGGTGGCCAAGGACATAACAA 60.549 52.381 7.24 0.00 34.62 2.83
82 83 0.623723 GAGGGTGGCCAAGGACATAA 59.376 55.000 7.24 0.00 34.62 1.90
115 116 2.670148 GGGGATGAACGGCCTGAGT 61.670 63.158 0.00 0.00 0.00 3.41
129 130 3.315949 GTACTGTGGTGCCGGGGA 61.316 66.667 2.18 0.00 0.00 4.81
131 132 3.524648 AACGTACTGTGGTGCCGGG 62.525 63.158 2.18 0.00 0.00 5.73
156 157 1.393487 TTGAACGACCTCGGGTGTCA 61.393 55.000 0.00 0.00 44.95 3.58
245 247 5.163195 ACACACTTCCCATTTAGTTGAGAGT 60.163 40.000 0.00 0.00 0.00 3.24
302 305 7.065216 TGAGCTCTATTTGTTGAGATTTTCG 57.935 36.000 16.19 0.00 32.44 3.46
320 323 4.836125 TCTTGAACATTGGTTTGAGCTC 57.164 40.909 6.82 6.82 37.36 4.09
488 493 5.238583 AGATTCCAAAACTAGAGTGTTCCG 58.761 41.667 0.00 0.00 0.00 4.30
490 495 9.145865 CTCTTAGATTCCAAAACTAGAGTGTTC 57.854 37.037 0.00 0.00 0.00 3.18
492 497 8.196378 ACTCTTAGATTCCAAAACTAGAGTGT 57.804 34.615 0.00 0.00 32.56 3.55
493 498 9.145865 GAACTCTTAGATTCCAAAACTAGAGTG 57.854 37.037 0.00 0.00 33.84 3.51
494 499 8.871125 TGAACTCTTAGATTCCAAAACTAGAGT 58.129 33.333 0.00 0.00 34.84 3.24
503 509 8.796475 CATTTTTCCTGAACTCTTAGATTCCAA 58.204 33.333 0.00 0.00 0.00 3.53
512 521 7.601705 TTTGGATCATTTTTCCTGAACTCTT 57.398 32.000 0.00 0.00 34.17 2.85
513 522 7.601705 TTTTGGATCATTTTTCCTGAACTCT 57.398 32.000 0.00 0.00 34.17 3.24
551 562 9.480053 CCTTGTTCATGATGTATTTTTCAAACT 57.520 29.630 0.00 0.00 0.00 2.66
572 583 9.686683 ACTAGTGAGCATAAAATAAATCCTTGT 57.313 29.630 0.00 0.00 0.00 3.16
623 634 8.735315 CGAGTGATAGGATGAATAAGTACAGAT 58.265 37.037 0.00 0.00 0.00 2.90
642 667 3.443329 CAGCCATAGAGCTATCGAGTGAT 59.557 47.826 0.00 0.00 42.61 3.06
654 680 5.851720 AGTCACATCATAACAGCCATAGAG 58.148 41.667 0.00 0.00 0.00 2.43
698 724 8.657387 TTCCCTTCATTATTTGTGGAATAACA 57.343 30.769 0.00 0.00 41.64 2.41
702 728 6.384886 AGCATTCCCTTCATTATTTGTGGAAT 59.615 34.615 0.00 0.00 38.57 3.01
708 734 8.477256 TCCTTTTAGCATTCCCTTCATTATTTG 58.523 33.333 0.00 0.00 0.00 2.32
712 738 6.129179 CCTCCTTTTAGCATTCCCTTCATTA 58.871 40.000 0.00 0.00 0.00 1.90
765 791 3.806949 TTTTGCCTGTCCTAATGAGGT 57.193 42.857 0.00 0.00 44.19 3.85
790 816 7.780271 AGTTTTCAGGGTCAGAACTTATTTTCT 59.220 33.333 0.00 0.00 36.18 2.52
791 817 7.862873 CAGTTTTCAGGGTCAGAACTTATTTTC 59.137 37.037 0.00 0.00 0.00 2.29
792 818 7.201911 CCAGTTTTCAGGGTCAGAACTTATTTT 60.202 37.037 0.00 0.00 0.00 1.82
870 896 6.064717 AGCTTCAGAAAAATGTAGTCAACCT 58.935 36.000 0.00 0.00 0.00 3.50
873 899 8.150945 ACTAGAGCTTCAGAAAAATGTAGTCAA 58.849 33.333 0.00 0.00 0.00 3.18
877 903 7.064016 GTCCACTAGAGCTTCAGAAAAATGTAG 59.936 40.741 0.00 0.00 0.00 2.74
929 955 4.722700 CAGAAGGTGGGGGTGGCG 62.723 72.222 0.00 0.00 0.00 5.69
930 956 4.366684 CCAGAAGGTGGGGGTGGC 62.367 72.222 0.00 0.00 43.63 5.01
973 999 2.113139 GAGGTGGGGTGGTGTGTG 59.887 66.667 0.00 0.00 0.00 3.82
1215 1267 2.243774 CTAGGGGAGGGAGCCAGTCA 62.244 65.000 0.00 0.00 0.00 3.41
1219 1271 3.028683 CTCTAGGGGAGGGAGCCA 58.971 66.667 0.00 0.00 38.35 4.75
1279 1331 1.741770 GAAGGGCGCAGTCGATTGT 60.742 57.895 10.83 0.00 38.10 2.71
1281 1333 2.125106 GGAAGGGCGCAGTCGATT 60.125 61.111 10.83 0.00 38.10 3.34
1318 1370 0.698238 CTCCCTTGGATTCCACCACA 59.302 55.000 4.45 0.00 39.85 4.17
1361 1413 2.266055 CTGAACGGACTGAGGGGC 59.734 66.667 0.00 0.00 0.00 5.80
1447 1499 4.783764 AAATTGTTAAAGAGGCGGAAGG 57.216 40.909 0.00 0.00 0.00 3.46
1504 1559 2.849096 ATCCGCGGACAGGGTGACTA 62.849 60.000 33.75 2.92 0.00 2.59
1505 1560 4.988716 TCCGCGGACAGGGTGACT 62.989 66.667 27.28 0.00 0.00 3.41
1506 1561 3.718210 GATCCGCGGACAGGGTGAC 62.718 68.421 33.75 10.50 0.00 3.67
1507 1562 3.458163 GATCCGCGGACAGGGTGA 61.458 66.667 33.75 5.46 0.00 4.02
1683 1738 2.363975 GGGGGACTATCGTGTGGCA 61.364 63.158 0.00 0.00 0.00 4.92
1732 1808 8.634335 TTGAATGTCATAATGAAGAGAAACCA 57.366 30.769 0.00 0.00 0.00 3.67
1781 1857 9.973450 GAGAGAAAAGAGATGTATGTAATGCTA 57.027 33.333 0.00 0.00 0.00 3.49
1858 1935 1.227823 TTGCAGTCCGTCCAACCTG 60.228 57.895 0.00 0.00 0.00 4.00
2047 2128 2.396590 ACACTCTTTGAACGTGTGGT 57.603 45.000 8.39 0.00 40.11 4.16
2343 3135 5.534207 TGACACCAAGATTCTGCAAAAAT 57.466 34.783 0.00 0.00 0.00 1.82
2448 3242 6.946340 TGTTTCTATGCTAATCTGGAGACAA 58.054 36.000 0.00 0.00 42.06 3.18
2778 3574 6.373495 ACACATGTACTACACGAGATTCTACA 59.627 38.462 0.00 0.00 0.00 2.74
3038 3842 8.514330 ACTTTTAAAACATGAACTCTGTGGTA 57.486 30.769 0.00 0.00 0.00 3.25
3113 3917 0.391228 TTCAGTAGCCGCTCAACACA 59.609 50.000 0.00 0.00 0.00 3.72
3161 3965 6.043127 TGCCTTCTATAATGATGTGCTTCCTA 59.957 38.462 0.00 0.00 0.00 2.94
3234 4038 0.104304 CGGGATTTAGCCGCTGTAGT 59.896 55.000 2.16 0.00 0.00 2.73
3245 4049 2.799126 ATCAAGTGTGCCGGGATTTA 57.201 45.000 2.18 0.00 0.00 1.40
3434 4242 0.036022 GGCATGATGCTCCTACTCCC 59.964 60.000 17.84 0.00 44.28 4.30
3693 4502 9.890352 GTACCGGTTTACACATTAATTTTGTAA 57.110 29.630 15.04 12.48 34.63 2.41
3698 4507 7.030768 GCATGTACCGGTTTACACATTAATTT 58.969 34.615 15.04 0.00 34.79 1.82
3954 4772 2.950975 GAGGTGTAGTAGCCTCTGGTAC 59.049 54.545 11.57 0.00 45.78 3.34
3978 4796 4.445452 AAGTTGCAGGCTGTCATTAATG 57.555 40.909 17.16 9.29 0.00 1.90
4064 4882 5.783360 TGAGGACCTTTAACCACAGAATAGA 59.217 40.000 0.00 0.00 0.00 1.98
4076 4894 6.553100 ACCATCAACAAAATGAGGACCTTTAA 59.447 34.615 0.00 0.00 33.08 1.52
4199 5017 5.021458 AGGGACCGACAATAAGAGAAGTTA 58.979 41.667 0.00 0.00 0.00 2.24
4220 5038 5.649395 TGAATTATTCAAGCACCTTCTGAGG 59.351 40.000 5.03 0.00 42.06 3.86
4333 5151 2.939460 GGGTTTGATCCCAATGTTCG 57.061 50.000 0.00 0.00 46.30 3.95
4458 5278 4.360951 TCCCGTTTATCCTGAAAACTGT 57.639 40.909 0.00 0.00 35.20 3.55
4499 5319 2.434336 AGGCATAAAGTCGAGCATGGTA 59.566 45.455 0.00 0.00 0.00 3.25
4510 5330 3.596500 AGGGGTTTTCCTAGGCATAAAGT 59.403 43.478 2.96 0.00 40.46 2.66
4524 5344 4.425772 CTGGGAGGAATAAAAGGGGTTTT 58.574 43.478 0.00 0.00 0.00 2.43
4572 5392 2.066262 CGTAGTCAGCGGTCAATTTGT 58.934 47.619 0.00 0.00 0.00 2.83
4676 5497 2.917227 TGTGGCAGAGGCTCGACA 60.917 61.111 9.22 9.79 40.87 4.35
4714 5536 1.140252 GGTGAACGGTATGGGCAGTAT 59.860 52.381 0.00 0.00 0.00 2.12
4757 5579 0.107410 AACTGCTTCGGGTTGTGTCA 60.107 50.000 0.00 0.00 0.00 3.58
4845 5667 3.793144 CGGCAAAGGACTGCTCGC 61.793 66.667 0.00 0.00 42.25 5.03
5013 5835 1.066430 CGGGAAGGATGAGGAAAACGA 60.066 52.381 0.00 0.00 0.00 3.85
5839 6688 9.771534 ATAATGAACTACTAGAGCCATTTTCTC 57.228 33.333 0.00 0.00 35.01 2.87
5987 6836 7.441017 CAGGAAATCCCTCTAAGTAATCTCTG 58.559 42.308 0.00 0.00 45.60 3.35
5998 6847 1.487976 CAGCAGCAGGAAATCCCTCTA 59.512 52.381 0.00 0.00 45.60 2.43
6009 6860 0.313043 CAAGGAACAACAGCAGCAGG 59.687 55.000 0.00 0.00 0.00 4.85
6106 6957 6.721571 TTGCTAATTAGAACACTACTGCAC 57.278 37.500 16.85 0.00 0.00 4.57
6194 7045 7.754924 CAGTCACACATTGTTTTATGTTATCCC 59.245 37.037 0.00 0.00 36.64 3.85
6350 7201 2.279784 GCGAATGGGAGGAGAGCG 60.280 66.667 0.00 0.00 0.00 5.03
6417 7269 0.980423 GGAGCTGGGATGGATAGGAC 59.020 60.000 0.00 0.00 0.00 3.85
6476 7329 5.941948 ACTTATGCAACAAACACCTACTC 57.058 39.130 0.00 0.00 0.00 2.59
6539 7392 6.745794 ATAGTAGTACCTTCTCCGAGTAGT 57.254 41.667 0.00 0.00 0.00 2.73
6553 7426 5.163332 ACCCCAAAGCTAGCAATAGTAGTAC 60.163 44.000 18.83 0.00 0.00 2.73
6746 7627 2.289694 GCCACATCCTTACTCACTGTGT 60.290 50.000 7.79 0.00 36.37 3.72
7041 7927 6.102663 AGAAGACACTCGAACTGATAATTGG 58.897 40.000 0.00 0.00 0.00 3.16
7060 7946 5.726308 TGGACATCAAATAGGAAGGAGAAGA 59.274 40.000 0.00 0.00 0.00 2.87
7061 7947 5.994250 TGGACATCAAATAGGAAGGAGAAG 58.006 41.667 0.00 0.00 0.00 2.85
7062 7948 6.158520 TCATGGACATCAAATAGGAAGGAGAA 59.841 38.462 0.00 0.00 0.00 2.87
7309 8203 2.080693 TGAGCGTGTTTTGTGTTGAGT 58.919 42.857 0.00 0.00 0.00 3.41
7358 8253 9.517609 AAGAGTACTTGAACGAATGTATGTATC 57.482 33.333 0.00 0.00 34.80 2.24
7645 8553 4.151689 CCCGTACTTGCATGGTTTATATCG 59.848 45.833 4.44 0.00 0.00 2.92
7666 8574 0.598158 TTATTGTATCGTCGCGCCCC 60.598 55.000 0.00 0.00 0.00 5.80
7670 8578 9.622366 TTTTTAATAGTTTATTGTATCGTCGCG 57.378 29.630 0.00 0.00 0.00 5.87
7692 8600 4.627035 GCTCTGTTTTGCTTGTCAGTTTTT 59.373 37.500 0.00 0.00 0.00 1.94
7699 8607 3.774066 ACTTTGCTCTGTTTTGCTTGTC 58.226 40.909 0.00 0.00 0.00 3.18
7702 8610 4.884164 ACTAGACTTTGCTCTGTTTTGCTT 59.116 37.500 0.00 0.00 0.00 3.91
7878 8788 3.737032 TTGAATACGGCATGACGGATA 57.263 42.857 27.41 10.12 36.13 2.59


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

AutoCloner maintained by Alex Coulton.