Multiple sequence alignment - TraesCS7A01G416800

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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 TraesCS7A01G416800 chr7A 100.000 5189 0 0 1 5189 608678343 608673155 0.000000e+00 9583.0
1 TraesCS7A01G416800 chr7A 97.867 844 16 1 4348 5189 536712827 536711984 0.000000e+00 1458.0
2 TraesCS7A01G416800 chr7A 87.271 1092 90 20 3227 4297 314418962 314420025 0.000000e+00 1201.0
3 TraesCS7A01G416800 chr7A 90.672 729 62 4 1814 2542 314412010 314412732 0.000000e+00 965.0
4 TraesCS7A01G416800 chr7A 92.058 617 46 3 4575 5189 480988953 480988338 0.000000e+00 865.0
5 TraesCS7A01G416800 chr7A 95.181 498 13 1 4348 4845 649156023 649156509 0.000000e+00 776.0
6 TraesCS7A01G416800 chr7A 90.631 555 46 6 2612 3163 314418386 314418937 0.000000e+00 732.0
7 TraesCS7A01G416800 chr7A 83.947 380 46 10 950 1326 314410608 314410975 2.970000e-92 350.0
8 TraesCS7A01G416800 chr7B 94.182 3025 118 23 1355 4342 566482632 566479629 0.000000e+00 4558.0
9 TraesCS7A01G416800 chr7B 89.435 1221 104 15 113 1330 566483818 566482620 0.000000e+00 1517.0
10 TraesCS7A01G416800 chr7B 85.915 1136 104 18 3227 4338 252684729 252685832 0.000000e+00 1160.0
11 TraesCS7A01G416800 chr7B 91.221 729 56 5 1814 2542 252681353 252682073 0.000000e+00 985.0
12 TraesCS7A01G416800 chr7B 91.171 555 44 5 2612 3163 252684152 252684704 0.000000e+00 749.0
13 TraesCS7A01G416800 chr7B 95.339 236 10 1 4338 4573 10150388 10150154 1.760000e-99 374.0
14 TraesCS7A01G416800 chr7B 85.714 343 36 8 985 1326 252679936 252680266 2.970000e-92 350.0
15 TraesCS7A01G416800 chr7D 90.984 1331 85 18 1 1329 528908261 528906964 0.000000e+00 1760.0
16 TraesCS7A01G416800 chr7D 93.773 1076 43 7 1496 2565 528906834 528905777 0.000000e+00 1594.0
17 TraesCS7A01G416800 chr7D 90.909 1199 71 12 3168 4342 528904256 528903072 0.000000e+00 1576.0
18 TraesCS7A01G416800 chr7D 91.610 739 54 6 1814 2550 282877431 282876699 0.000000e+00 1014.0
19 TraesCS7A01G416800 chr7D 88.985 808 53 10 3227 4011 282870742 282869948 0.000000e+00 966.0
20 TraesCS7A01G416800 chr7D 95.122 533 26 0 2615 3147 528905777 528905245 0.000000e+00 841.0
21 TraesCS7A01G416800 chr7D 90.991 555 45 5 2612 3163 282871319 282870767 0.000000e+00 743.0
22 TraesCS7A01G416800 chr7D 82.677 381 41 14 950 1326 282879121 282878762 1.080000e-81 315.0
23 TraesCS7A01G416800 chr1A 98.100 842 16 0 4348 5189 576628898 576629739 0.000000e+00 1467.0
24 TraesCS7A01G416800 chr1A 92.157 51 3 1 2563 2613 557887584 557887633 2.590000e-08 71.3
25 TraesCS7A01G416800 chr4A 95.848 843 27 3 4348 5189 725277935 725277100 0.000000e+00 1356.0
26 TraesCS7A01G416800 chr3A 97.923 674 14 0 4348 5021 594625039 594624366 0.000000e+00 1168.0
27 TraesCS7A01G416800 chr3A 97.095 241 6 1 4348 4588 369078703 369078464 6.260000e-109 405.0
28 TraesCS7A01G416800 chr4D 94.489 617 32 2 4575 5189 3304383 3303767 0.000000e+00 950.0
29 TraesCS7A01G416800 chr3D 94.327 617 33 2 4575 5189 548541832 548542448 0.000000e+00 944.0
30 TraesCS7A01G416800 chr6A 93.559 621 36 4 4570 5189 8397641 8397024 0.000000e+00 922.0
31 TraesCS7A01G416800 chr6A 88.525 61 3 3 2558 2615 604571380 604571321 2.590000e-08 71.3
32 TraesCS7A01G416800 chr5A 93.262 282 10 6 4348 4627 645390805 645390531 1.740000e-109 407.0
33 TraesCS7A01G416800 chr5A 80.549 401 58 11 4734 5133 537995255 537994874 1.830000e-74 291.0
34 TraesCS7A01G416800 chr5A 94.737 38 1 1 790 827 311944241 311944277 2.020000e-04 58.4
35 TraesCS7A01G416800 chr3B 92.143 280 11 7 4348 4624 29393986 29394257 8.150000e-103 385.0
36 TraesCS7A01G416800 chrUn 82.323 396 50 7 4734 5128 75400035 75400411 5.010000e-85 326.0
37 TraesCS7A01G416800 chrUn 90.741 54 4 1 2561 2613 376482433 376482486 2.590000e-08 71.3
38 TraesCS7A01G416800 chr6B 89.655 58 4 2 2556 2613 48538466 48538411 7.210000e-09 73.1
39 TraesCS7A01G416800 chr5B 90.566 53 4 1 2575 2626 623210563 623210511 9.320000e-08 69.4
40 TraesCS7A01G416800 chr5B 90.566 53 4 1 2575 2626 626871959 626871907 9.320000e-08 69.4
41 TraesCS7A01G416800 chr5B 91.667 48 4 0 2577 2624 509175599 509175552 3.350000e-07 67.6
42 TraesCS7A01G416800 chr1B 91.667 48 3 1 2577 2623 17017378 17017425 1.210000e-06 65.8


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 TraesCS7A01G416800 chr7A 608673155 608678343 5188 True 9583.00 9583 100.00000 1 5189 1 chr7A.!!$R3 5188
1 TraesCS7A01G416800 chr7A 536711984 536712827 843 True 1458.00 1458 97.86700 4348 5189 1 chr7A.!!$R2 841
2 TraesCS7A01G416800 chr7A 314418386 314420025 1639 False 966.50 1201 88.95100 2612 4297 2 chr7A.!!$F3 1685
3 TraesCS7A01G416800 chr7A 480988338 480988953 615 True 865.00 865 92.05800 4575 5189 1 chr7A.!!$R1 614
4 TraesCS7A01G416800 chr7A 314410608 314412732 2124 False 657.50 965 87.30950 950 2542 2 chr7A.!!$F2 1592
5 TraesCS7A01G416800 chr7B 566479629 566483818 4189 True 3037.50 4558 91.80850 113 4342 2 chr7B.!!$R2 4229
6 TraesCS7A01G416800 chr7B 252679936 252685832 5896 False 811.00 1160 88.50525 985 4338 4 chr7B.!!$F1 3353
7 TraesCS7A01G416800 chr7D 528903072 528908261 5189 True 1442.75 1760 92.69700 1 4342 4 chr7D.!!$R3 4341
8 TraesCS7A01G416800 chr7D 282869948 282871319 1371 True 854.50 966 89.98800 2612 4011 2 chr7D.!!$R1 1399
9 TraesCS7A01G416800 chr7D 282876699 282879121 2422 True 664.50 1014 87.14350 950 2550 2 chr7D.!!$R2 1600
10 TraesCS7A01G416800 chr1A 576628898 576629739 841 False 1467.00 1467 98.10000 4348 5189 1 chr1A.!!$F2 841
11 TraesCS7A01G416800 chr4A 725277100 725277935 835 True 1356.00 1356 95.84800 4348 5189 1 chr4A.!!$R1 841
12 TraesCS7A01G416800 chr3A 594624366 594625039 673 True 1168.00 1168 97.92300 4348 5021 1 chr3A.!!$R2 673
13 TraesCS7A01G416800 chr4D 3303767 3304383 616 True 950.00 950 94.48900 4575 5189 1 chr4D.!!$R1 614
14 TraesCS7A01G416800 chr3D 548541832 548542448 616 False 944.00 944 94.32700 4575 5189 1 chr3D.!!$F1 614
15 TraesCS7A01G416800 chr6A 8397024 8397641 617 True 922.00 922 93.55900 4570 5189 1 chr6A.!!$R1 619

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
419 420 0.185901 AGGTGAACTGTGCCATGGTT 59.814 50.0 14.67 0.0 0.00 3.67 F
1726 2461 0.036010 TGCTAAGCACCTCTTCAGGC 60.036 55.0 0.00 0.0 45.05 4.85 F
1747 2482 0.586319 CCTGCGTTTATACATGCCCG 59.414 55.0 0.73 0.0 0.00 6.13 F
1767 2502 0.897621 AATAGCACTTTGCCCTTGCC 59.102 50.0 0.00 0.0 46.52 4.52 F
2329 3409 1.620822 AACCAAGATTGAGGGTGCAC 58.379 50.0 8.80 8.8 34.51 4.57 F
3974 8061 0.819259 TGAGTGTGGGCTTGCTGTTC 60.819 55.0 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 2511 0.328258 GAAGCAGTAAGGGGAGGCAA 59.672 55.000 0.00 0.00 0.00 4.52 R
3686 7767 3.341823 CCCAATGAGAGTTGAGACAAGG 58.658 50.000 0.00 0.00 0.00 3.61 R
3796 7878 0.100682 GCATGTTCATGAGCAGGCAG 59.899 55.000 34.43 17.97 46.07 4.85 R
3974 8061 1.374947 CTACACTGGGTGGTGGGTG 59.625 63.158 0.00 0.00 41.09 4.61 R
3977 8064 0.908910 TATGCTACACTGGGTGGTGG 59.091 55.000 0.00 0.00 41.09 4.61 R
4878 8974 3.928727 AGTTGCACAATCAACATCAGG 57.071 42.857 8.98 0.00 46.44 3.86 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
21 22 0.327924 ATGATCACCGCAAACCCTCA 59.672 50.000 0.00 0.00 0.00 3.86
66 67 1.133976 CACCCTAAGCCAATCTCCCAG 60.134 57.143 0.00 0.00 0.00 4.45
68 69 1.216990 CCTAAGCCAATCTCCCAGGT 58.783 55.000 0.00 0.00 0.00 4.00
95 96 4.990526 ACACTGGATCATGAAAAGGTTCT 58.009 39.130 0.00 0.00 34.60 3.01
100 101 4.203226 GGATCATGAAAAGGTTCTCCTCC 58.797 47.826 0.00 0.00 44.35 4.30
102 103 4.934797 TCATGAAAAGGTTCTCCTCCAT 57.065 40.909 0.00 0.00 44.35 3.41
105 106 2.637872 TGAAAAGGTTCTCCTCCATCGT 59.362 45.455 0.00 0.00 44.35 3.73
153 154 4.124238 CCCCACGACGTTCACATATATTT 58.876 43.478 0.00 0.00 0.00 1.40
229 230 3.795623 TGCTACGTCCTACATTTCCTC 57.204 47.619 0.00 0.00 0.00 3.71
245 246 3.251479 TCCTCAAAGACCACATCATCG 57.749 47.619 0.00 0.00 0.00 3.84
250 251 5.163550 CCTCAAAGACCACATCATCGTACTA 60.164 44.000 0.00 0.00 0.00 1.82
270 271 2.285275 TCCCTCTTCAATCCCCATCA 57.715 50.000 0.00 0.00 0.00 3.07
387 388 0.769247 ACCCCTAGCAAAAACCGACT 59.231 50.000 0.00 0.00 0.00 4.18
415 416 2.624838 CAAGAAAGGTGAACTGTGCCAT 59.375 45.455 0.00 0.00 0.00 4.40
419 420 0.185901 AGGTGAACTGTGCCATGGTT 59.814 50.000 14.67 0.00 0.00 3.67
454 455 0.676782 GTGTCCCCTTGATCAACCCG 60.677 60.000 3.38 0.00 0.00 5.28
509 510 1.278413 GTTGTTCTGAGGGGGTAGACC 59.722 57.143 0.00 0.00 39.11 3.85
562 563 1.589196 GCTAGTCGCCAGGCTTACG 60.589 63.158 10.54 0.00 32.57 3.18
563 564 1.589196 CTAGTCGCCAGGCTTACGC 60.589 63.158 10.54 0.00 32.57 4.42
581 582 1.787012 GCGGAAAAAGTGTCGTCCTA 58.213 50.000 0.00 0.00 0.00 2.94
586 587 3.493503 GGAAAAAGTGTCGTCCTACTGTG 59.506 47.826 0.00 0.00 0.00 3.66
587 588 3.814005 AAAAGTGTCGTCCTACTGTGT 57.186 42.857 0.00 0.00 0.00 3.72
588 589 3.366440 AAAGTGTCGTCCTACTGTGTC 57.634 47.619 0.00 0.00 0.00 3.67
606 607 1.452108 CCTCCACCTCCAAATCGGC 60.452 63.158 0.00 0.00 33.14 5.54
666 669 9.832445 ATACAATCCTCTCGTAAACAAATACAT 57.168 29.630 0.00 0.00 0.00 2.29
720 724 2.507484 CATCACCTCAACTTTGGAGCA 58.493 47.619 0.00 0.00 0.00 4.26
830 834 1.544246 GGCCTCAACCAAACACATACC 59.456 52.381 0.00 0.00 0.00 2.73
837 841 2.815158 ACCAAACACATACCCCATTCC 58.185 47.619 0.00 0.00 0.00 3.01
840 844 3.774216 CCAAACACATACCCCATTCCAAT 59.226 43.478 0.00 0.00 0.00 3.16
880 884 1.270625 GGAGTGTTCCACGTGGATTGA 60.271 52.381 36.52 20.56 44.98 2.57
904 908 3.826926 GATCCCGGCCGGAATCACC 62.827 68.421 45.44 22.33 46.47 4.02
918 922 4.149598 GGAATCACCCTAACCAAACAAGT 58.850 43.478 0.00 0.00 0.00 3.16
929 933 1.269726 CCAAACAAGTCCTTGCGCAAT 60.270 47.619 25.26 5.57 44.03 3.56
938 942 1.686052 TCCTTGCGCAATTTGTTTCCT 59.314 42.857 25.26 0.00 0.00 3.36
941 945 2.879002 TGCGCAATTTGTTTCCTCAA 57.121 40.000 8.16 0.00 0.00 3.02
942 946 3.383620 TGCGCAATTTGTTTCCTCAAT 57.616 38.095 8.16 0.00 0.00 2.57
943 947 3.316283 TGCGCAATTTGTTTCCTCAATC 58.684 40.909 8.16 0.00 0.00 2.67
944 948 2.342354 GCGCAATTTGTTTCCTCAATCG 59.658 45.455 0.30 0.00 0.00 3.34
945 949 2.916716 CGCAATTTGTTTCCTCAATCGG 59.083 45.455 0.00 0.00 0.00 4.18
946 950 3.365868 CGCAATTTGTTTCCTCAATCGGA 60.366 43.478 0.00 0.00 0.00 4.55
947 951 3.920412 GCAATTTGTTTCCTCAATCGGAC 59.080 43.478 0.00 0.00 31.44 4.79
948 952 4.558496 GCAATTTGTTTCCTCAATCGGACA 60.558 41.667 0.00 0.00 31.44 4.02
968 973 7.778853 TCGGACAATCTATTTTCTAGAGGTAGT 59.221 37.037 0.00 0.00 0.00 2.73
1060 1067 4.778415 CTCGCCGTCACCACCTCG 62.778 72.222 0.00 0.00 0.00 4.63
1137 1144 0.553819 TACCCAGCTCTCCCTCTCTC 59.446 60.000 0.00 0.00 0.00 3.20
1157 1164 4.343526 TCTCAGCAATCCCTTATCTCTGTC 59.656 45.833 0.00 0.00 0.00 3.51
1209 1225 0.465097 GCCACAGGGACATGGAGATG 60.465 60.000 0.00 0.00 38.93 2.90
1210 1226 0.465097 CCACAGGGACATGGAGATGC 60.465 60.000 0.00 0.00 38.93 3.91
1211 1227 0.465097 CACAGGGACATGGAGATGCC 60.465 60.000 0.00 0.00 32.14 4.40
1293 1309 3.576232 GGCCACCGATTATCCCCT 58.424 61.111 0.00 0.00 0.00 4.79
1297 1313 0.977395 CCACCGATTATCCCCTCTCC 59.023 60.000 0.00 0.00 0.00 3.71
1300 1316 1.203199 ACCGATTATCCCCTCTCCCTC 60.203 57.143 0.00 0.00 0.00 4.30
1329 1345 1.898574 CCAACCCGTTGCTGCTTCT 60.899 57.895 0.00 0.00 39.16 2.85
1331 1347 0.040067 CAACCCGTTGCTGCTTCTTC 60.040 55.000 0.00 0.00 33.45 2.87
1334 1350 2.335712 CCGTTGCTGCTTCTTCCCC 61.336 63.158 0.00 0.00 0.00 4.81
1335 1351 2.680913 CGTTGCTGCTTCTTCCCCG 61.681 63.158 0.00 0.00 0.00 5.73
1336 1352 2.672996 TTGCTGCTTCTTCCCCGC 60.673 61.111 0.00 0.00 0.00 6.13
1337 1353 3.490031 TTGCTGCTTCTTCCCCGCA 62.490 57.895 0.00 0.00 0.00 5.69
1338 1354 2.672996 GCTGCTTCTTCCCCGCAA 60.673 61.111 0.00 0.00 32.66 4.85
1339 1355 2.268076 GCTGCTTCTTCCCCGCAAA 61.268 57.895 0.00 0.00 32.66 3.68
1340 1356 1.805428 GCTGCTTCTTCCCCGCAAAA 61.805 55.000 0.00 0.00 32.66 2.44
1341 1357 0.673437 CTGCTTCTTCCCCGCAAAAA 59.327 50.000 0.00 0.00 32.66 1.94
1365 1381 3.659850 AAAAACCCGTTGCTGCTTC 57.340 47.368 0.00 0.00 0.00 3.86
1444 1565 5.589855 TCGTAGGTTATGAACGAATACCAGA 59.410 40.000 0.00 0.00 42.18 3.86
1445 1566 5.684626 CGTAGGTTATGAACGAATACCAGAC 59.315 44.000 0.00 0.00 38.89 3.51
1449 1570 5.293569 GGTTATGAACGAATACCAGACAAGG 59.706 44.000 0.00 0.00 0.00 3.61
1474 1595 9.218440 GGATTCAATTCAAAACACAAATACCAT 57.782 29.630 0.00 0.00 0.00 3.55
1582 1803 6.954684 CACCTATACTCTCCATGGGTACTTAT 59.045 42.308 13.02 5.59 35.26 1.73
1715 2450 6.648725 AGTTCTTTTGTTTTGTTTGCTAAGCA 59.351 30.769 0.00 0.00 36.47 3.91
1716 2451 6.401955 TCTTTTGTTTTGTTTGCTAAGCAC 57.598 33.333 0.00 0.00 38.71 4.40
1717 2452 5.350091 TCTTTTGTTTTGTTTGCTAAGCACC 59.650 36.000 0.00 0.00 38.71 5.01
1718 2453 4.464069 TTGTTTTGTTTGCTAAGCACCT 57.536 36.364 0.00 0.00 38.71 4.00
1719 2454 4.040445 TGTTTTGTTTGCTAAGCACCTC 57.960 40.909 0.00 0.00 38.71 3.85
1720 2455 3.699038 TGTTTTGTTTGCTAAGCACCTCT 59.301 39.130 0.00 0.00 38.71 3.69
1721 2456 4.159506 TGTTTTGTTTGCTAAGCACCTCTT 59.840 37.500 0.00 0.00 38.71 2.85
1722 2457 4.568152 TTTGTTTGCTAAGCACCTCTTC 57.432 40.909 0.00 0.00 38.71 2.87
1723 2458 3.207265 TGTTTGCTAAGCACCTCTTCA 57.793 42.857 0.00 0.00 38.71 3.02
1724 2459 3.141398 TGTTTGCTAAGCACCTCTTCAG 58.859 45.455 0.00 0.00 38.71 3.02
1725 2460 2.479566 TTGCTAAGCACCTCTTCAGG 57.520 50.000 0.00 0.00 46.87 3.86
1726 2461 0.036010 TGCTAAGCACCTCTTCAGGC 60.036 55.000 0.00 0.00 45.05 4.85
1747 2482 0.586319 CCTGCGTTTATACATGCCCG 59.414 55.000 0.73 0.00 0.00 6.13
1759 2494 1.745087 ACATGCCCGAATAGCACTTTG 59.255 47.619 0.00 0.00 44.40 2.77
1767 2502 0.897621 AATAGCACTTTGCCCTTGCC 59.102 50.000 0.00 0.00 46.52 4.52
1776 2511 2.603075 TTGCCCTTGCCTTGACTAAT 57.397 45.000 0.00 0.00 36.33 1.73
1839 2919 3.878778 ACCATGACAGATCAACCTTAGC 58.121 45.455 0.00 0.00 38.69 3.09
1867 2947 6.374894 TCGTTTTTATTTCATTCGTACCCCAT 59.625 34.615 0.00 0.00 0.00 4.00
1870 2950 2.498644 TTTCATTCGTACCCCATGCA 57.501 45.000 0.00 0.00 0.00 3.96
1871 2951 2.727123 TTCATTCGTACCCCATGCAT 57.273 45.000 0.00 0.00 0.00 3.96
1872 2952 1.965935 TCATTCGTACCCCATGCATG 58.034 50.000 20.19 20.19 0.00 4.06
1958 3038 2.358898 TGAAGTTTCTGCAGCTGTTTCC 59.641 45.455 16.64 0.00 0.00 3.13
2329 3409 1.620822 AACCAAGATTGAGGGTGCAC 58.379 50.000 8.80 8.80 34.51 4.57
2487 3567 6.470235 GGATGAATTGATTGTCATTCGTTCAC 59.530 38.462 13.22 9.57 34.61 3.18
2586 4021 5.741962 ACTCCCTCCTAGTGAACTAAAAC 57.258 43.478 0.00 0.00 0.00 2.43
2594 4029 4.446719 CCTAGTGAACTAAAACCACGACAC 59.553 45.833 0.00 0.00 36.06 3.67
2607 4042 4.906618 ACCACGACACTTATTTTGGATCT 58.093 39.130 0.00 0.00 0.00 2.75
2608 4043 4.695455 ACCACGACACTTATTTTGGATCTG 59.305 41.667 0.00 0.00 0.00 2.90
2610 4045 5.063944 CCACGACACTTATTTTGGATCTGAG 59.936 44.000 0.00 0.00 0.00 3.35
2611 4046 5.063944 CACGACACTTATTTTGGATCTGAGG 59.936 44.000 0.00 0.00 0.00 3.86
2612 4047 4.572389 CGACACTTATTTTGGATCTGAGGG 59.428 45.833 0.00 0.00 0.00 4.30
2613 4048 4.860022 ACACTTATTTTGGATCTGAGGGG 58.140 43.478 0.00 0.00 0.00 4.79
2620 5710 4.778213 TTTGGATCTGAGGGGATACAAG 57.222 45.455 2.96 0.00 44.34 3.16
3394 7466 7.015877 AGGGAGCATATAACGGTAAGTTGATTA 59.984 37.037 0.00 0.00 44.01 1.75
3426 7498 6.431543 TGAAGCATAACCTTTTCAATCGGTAA 59.568 34.615 0.00 0.00 0.00 2.85
3686 7767 4.841422 CATGGATTACAGGGATCATCCTC 58.159 47.826 2.93 0.00 36.83 3.71
3796 7878 3.875727 ACTATGTGCTGATTGTGCAGATC 59.124 43.478 1.76 0.00 42.23 2.75
3905 7991 3.511146 ACGATGGCATGGAAGTTTTCAAT 59.489 39.130 16.77 0.00 0.00 2.57
3974 8061 0.819259 TGAGTGTGGGCTTGCTGTTC 60.819 55.000 0.00 0.00 0.00 3.18
3975 8062 0.819259 GAGTGTGGGCTTGCTGTTCA 60.819 55.000 0.00 0.00 0.00 3.18
3976 8063 1.103398 AGTGTGGGCTTGCTGTTCAC 61.103 55.000 0.00 0.00 0.00 3.18
3977 8064 1.827789 TGTGGGCTTGCTGTTCACC 60.828 57.895 0.00 0.00 0.00 4.02
3978 8065 2.203480 TGGGCTTGCTGTTCACCC 60.203 61.111 0.00 0.00 41.24 4.61
3979 8066 2.203480 GGGCTTGCTGTTCACCCA 60.203 61.111 0.00 0.00 40.52 4.51
3980 8067 2.564721 GGGCTTGCTGTTCACCCAC 61.565 63.158 0.00 0.00 40.52 4.61
4016 8105 8.279970 AGCATAAAAATACTGTTGCTATGTGA 57.720 30.769 0.00 0.00 38.57 3.58
4020 8109 5.545658 AAATACTGTTGCTATGTGAACCG 57.454 39.130 0.00 0.00 0.00 4.44
4026 8115 3.435327 TGTTGCTATGTGAACCGTTCATC 59.565 43.478 16.80 11.00 42.47 2.92
4043 8133 5.755375 CGTTCATCTAGAATTGTACTGCCAT 59.245 40.000 0.00 0.00 38.76 4.40
4064 8154 1.605992 CCTGCATGGGCTTCTCTCA 59.394 57.895 0.00 0.00 41.91 3.27
4133 8223 8.575565 TGTTAATATCAGCGAAGATTGTACTC 57.424 34.615 0.00 0.00 0.00 2.59
4273 8365 6.684686 ACATTTATTGATCATATGTGCTGCC 58.315 36.000 1.90 0.00 0.00 4.85
4297 8389 2.638480 TAGGGAACATACTGCCATGC 57.362 50.000 0.00 0.00 0.00 4.06
4315 8407 1.492720 GCGTCGGCAAAAATCCAAAA 58.507 45.000 0.00 0.00 39.62 2.44
4327 8419 8.839947 GCAAAAATCCAAAACATAATATTGCC 57.160 30.769 0.00 0.00 33.94 4.52
4328 8420 8.457261 GCAAAAATCCAAAACATAATATTGCCA 58.543 29.630 0.00 0.00 33.94 4.92
4342 8434 2.453983 TTGCCATGATCGATGCGATA 57.546 45.000 0.54 0.00 47.00 2.92
4343 8435 1.713597 TGCCATGATCGATGCGATAC 58.286 50.000 0.54 0.00 47.00 2.24
4344 8436 1.000731 TGCCATGATCGATGCGATACA 59.999 47.619 0.54 0.00 47.00 2.29
4345 8437 2.274437 GCCATGATCGATGCGATACAT 58.726 47.619 0.54 0.00 47.00 2.29
4346 8438 2.030091 GCCATGATCGATGCGATACATG 59.970 50.000 21.48 21.48 47.00 3.21
4514 8608 8.028938 GCAACTAAATTTTTCATAGGAGCAAGA 58.971 33.333 0.00 0.00 0.00 3.02
4616 8711 4.102524 AGTCTCTAACATGAACAACCACCA 59.897 41.667 0.00 0.00 0.00 4.17
4646 8741 8.763356 CAGCAACAATACAACACAAAATAACAT 58.237 29.630 0.00 0.00 0.00 2.71
4759 8855 4.579454 AATGCATTTCATCATCTTCCGG 57.421 40.909 5.99 0.00 33.40 5.14
4846 8942 4.171878 TCCTAGGACGAGATTGAGACAT 57.828 45.455 7.62 0.00 0.00 3.06
5099 9195 5.645067 TCTCATTTTGTCATGAAGTAGCCTG 59.355 40.000 0.00 0.00 32.63 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 1.576421 GCACTTCTGAGGGTTTGCG 59.424 57.895 0.00 0.00 0.00 4.85
21 22 1.980772 GCAAGGCCATGGCACTTCT 60.981 57.895 36.56 22.05 44.11 2.85
44 45 1.777272 GGGAGATTGGCTTAGGGTGAT 59.223 52.381 0.00 0.00 0.00 3.06
66 67 6.127897 CCTTTTCATGATCCAGTGTTCTTACC 60.128 42.308 0.00 0.00 0.00 2.85
68 69 6.542821 ACCTTTTCATGATCCAGTGTTCTTA 58.457 36.000 0.00 0.00 0.00 2.10
95 96 1.938585 AAGTTCAGGACGATGGAGGA 58.061 50.000 0.00 0.00 0.00 3.71
100 101 3.997021 AGCAAGTTAAGTTCAGGACGATG 59.003 43.478 0.00 0.00 0.00 3.84
102 103 3.069016 TGAGCAAGTTAAGTTCAGGACGA 59.931 43.478 0.00 0.00 0.00 4.20
105 106 4.632153 GACTGAGCAAGTTAAGTTCAGGA 58.368 43.478 12.82 0.00 45.18 3.86
138 139 9.444600 ACCTTTTACTCAAATATATGTGAACGT 57.555 29.630 7.03 5.28 0.00 3.99
153 154 5.576563 TTGATCCTCCAACCTTTTACTCA 57.423 39.130 0.00 0.00 0.00 3.41
172 173 4.152759 GGTTCATACCACGAACGAATTTGA 59.847 41.667 0.00 0.00 44.36 2.69
229 230 5.692204 GGATAGTACGATGATGTGGTCTTTG 59.308 44.000 0.00 0.00 0.00 2.77
245 246 4.232091 TGGGGATTGAAGAGGGATAGTAC 58.768 47.826 0.00 0.00 0.00 2.73
250 251 2.793017 TGATGGGGATTGAAGAGGGAT 58.207 47.619 0.00 0.00 0.00 3.85
270 271 4.411212 TGATCTTGGTGAGATGATGTGGAT 59.589 41.667 0.00 0.00 45.17 3.41
387 388 4.199310 CAGTTCACCTTTCTTGGAGTCAA 58.801 43.478 0.00 0.00 0.00 3.18
415 416 0.764890 CTGGACTGTCTTCCCAACCA 59.235 55.000 7.85 0.00 34.33 3.67
419 420 0.399949 ACACCTGGACTGTCTTCCCA 60.400 55.000 7.85 0.00 34.33 4.37
454 455 4.036852 CCTCCACTTTGTTTTCTCCTGTTC 59.963 45.833 0.00 0.00 0.00 3.18
562 563 1.458445 GTAGGACGACACTTTTTCCGC 59.542 52.381 0.00 0.00 32.97 5.54
563 564 2.729882 CAGTAGGACGACACTTTTTCCG 59.270 50.000 0.00 0.00 32.97 4.30
564 565 3.493503 CACAGTAGGACGACACTTTTTCC 59.506 47.826 0.00 0.00 0.00 3.13
586 587 0.107654 CCGATTTGGAGGTGGAGGAC 60.108 60.000 0.00 0.00 42.00 3.85
587 588 1.910580 GCCGATTTGGAGGTGGAGGA 61.911 60.000 0.00 0.00 42.00 3.71
588 589 1.452108 GCCGATTTGGAGGTGGAGG 60.452 63.158 0.00 0.00 42.00 4.30
606 607 2.996631 ACATGGCCTAAAGAAGAGCAG 58.003 47.619 3.32 0.00 0.00 4.24
649 650 5.188163 TCCCTGGATGTATTTGTTTACGAGA 59.812 40.000 0.00 0.00 0.00 4.04
652 653 6.494842 CAATCCCTGGATGTATTTGTTTACG 58.505 40.000 0.00 0.00 34.70 3.18
686 689 2.834549 AGGTGATGGGTGTCAAGTAGAG 59.165 50.000 0.00 0.00 0.00 2.43
904 908 2.031157 CGCAAGGACTTGTTTGGTTAGG 60.031 50.000 13.08 0.00 42.31 2.69
918 922 1.686052 AGGAAACAAATTGCGCAAGGA 59.314 42.857 28.62 5.72 34.01 3.36
929 933 5.070001 AGATTGTCCGATTGAGGAAACAAA 58.930 37.500 0.00 0.00 42.77 2.83
938 942 8.144478 CCTCTAGAAAATAGATTGTCCGATTGA 58.856 37.037 0.00 0.00 0.00 2.57
941 945 7.604657 ACCTCTAGAAAATAGATTGTCCGAT 57.395 36.000 0.00 0.00 0.00 4.18
942 946 7.778853 ACTACCTCTAGAAAATAGATTGTCCGA 59.221 37.037 10.20 0.00 0.00 4.55
943 947 7.942990 ACTACCTCTAGAAAATAGATTGTCCG 58.057 38.462 10.20 0.00 0.00 4.79
944 948 8.915036 TGACTACCTCTAGAAAATAGATTGTCC 58.085 37.037 10.20 0.00 0.00 4.02
945 949 9.959749 CTGACTACCTCTAGAAAATAGATTGTC 57.040 37.037 10.20 0.00 0.00 3.18
946 950 9.702253 TCTGACTACCTCTAGAAAATAGATTGT 57.298 33.333 10.20 0.00 0.00 2.71
948 952 9.362151 CCTCTGACTACCTCTAGAAAATAGATT 57.638 37.037 10.20 0.00 0.00 2.40
990 997 4.436242 TCGAGTCGCTACAGAAGATTTT 57.564 40.909 7.92 0.00 0.00 1.82
1060 1067 1.454295 GGAGAGGGAGGAGGACGAC 60.454 68.421 0.00 0.00 0.00 4.34
1063 1070 1.152839 CGAGGAGAGGGAGGAGGAC 60.153 68.421 0.00 0.00 0.00 3.85
1137 1144 3.388308 CGACAGAGATAAGGGATTGCTG 58.612 50.000 0.00 0.00 0.00 4.41
1292 1308 1.202722 GGTCCGTAGAGAGAGGGAGAG 60.203 61.905 0.00 0.00 34.12 3.20
1293 1309 0.838608 GGTCCGTAGAGAGAGGGAGA 59.161 60.000 0.00 0.00 34.12 3.71
1297 1313 1.104630 GGTTGGTCCGTAGAGAGAGG 58.895 60.000 0.00 0.00 0.00 3.69
1300 1316 1.807886 CGGGTTGGTCCGTAGAGAG 59.192 63.158 0.00 0.00 44.60 3.20
1347 1363 1.067060 GAGAAGCAGCAACGGGTTTTT 59.933 47.619 0.00 0.00 0.00 1.94
1348 1364 0.668535 GAGAAGCAGCAACGGGTTTT 59.331 50.000 0.00 0.00 0.00 2.43
1349 1365 0.465460 TGAGAAGCAGCAACGGGTTT 60.465 50.000 0.00 0.00 0.00 3.27
1350 1366 1.148273 TGAGAAGCAGCAACGGGTT 59.852 52.632 0.00 0.00 0.00 4.11
1351 1367 1.598130 GTGAGAAGCAGCAACGGGT 60.598 57.895 0.00 0.00 0.00 5.28
1352 1368 2.671177 CGTGAGAAGCAGCAACGGG 61.671 63.158 0.00 0.00 0.00 5.28
1353 1369 2.856032 CGTGAGAAGCAGCAACGG 59.144 61.111 0.00 0.00 0.00 4.44
1354 1370 2.171940 GCGTGAGAAGCAGCAACG 59.828 61.111 0.00 0.00 34.19 4.10
1355 1371 2.171940 CGCGTGAGAAGCAGCAAC 59.828 61.111 0.00 0.00 34.19 4.17
1356 1372 3.716006 GCGCGTGAGAAGCAGCAA 61.716 61.111 8.43 0.00 36.52 3.91
1357 1373 4.669842 AGCGCGTGAGAAGCAGCA 62.670 61.111 8.43 0.00 38.46 4.41
1358 1374 3.847709 GAGCGCGTGAGAAGCAGC 61.848 66.667 8.43 0.00 38.46 5.25
1359 1375 3.540014 CGAGCGCGTGAGAAGCAG 61.540 66.667 8.43 0.00 38.46 4.24
1360 1376 3.551887 TTCGAGCGCGTGAGAAGCA 62.552 57.895 10.30 0.00 38.46 3.91
1361 1377 2.805353 TTCGAGCGCGTGAGAAGC 60.805 61.111 10.30 0.00 38.98 3.86
1362 1378 2.768920 CGTTCGAGCGCGTGAGAAG 61.769 63.158 9.17 2.08 38.98 2.85
1363 1379 2.799502 CGTTCGAGCGCGTGAGAA 60.800 61.111 9.17 8.08 38.98 2.87
1364 1380 3.719144 TCGTTCGAGCGCGTGAGA 61.719 61.111 17.42 4.83 38.98 3.27
1365 1381 3.524759 GTCGTTCGAGCGCGTGAG 61.525 66.667 17.42 2.35 38.98 3.51
1419 1539 5.824429 TGGTATTCGTTCATAACCTACGAG 58.176 41.667 0.00 0.00 44.03 4.18
1444 1565 8.735692 ATTTGTGTTTTGAATTGAATCCTTGT 57.264 26.923 0.00 0.00 0.00 3.16
1474 1595 5.897250 TCTAGGAGTATTTGGTGCTGTCATA 59.103 40.000 0.00 0.00 0.00 2.15
1715 2450 2.753029 GCAGGTGCCTGAAGAGGT 59.247 61.111 21.34 0.00 46.30 3.85
1716 2451 2.435586 CGCAGGTGCCTGAAGAGG 60.436 66.667 21.34 1.66 46.30 3.69
1717 2452 0.886490 AAACGCAGGTGCCTGAAGAG 60.886 55.000 21.34 11.04 46.30 2.85
1718 2453 0.394938 TAAACGCAGGTGCCTGAAGA 59.605 50.000 21.34 0.00 46.30 2.87
1719 2454 1.453155 ATAAACGCAGGTGCCTGAAG 58.547 50.000 21.34 15.45 46.30 3.02
1720 2455 2.289756 TGTATAAACGCAGGTGCCTGAA 60.290 45.455 21.34 1.98 46.30 3.02
1721 2456 1.276705 TGTATAAACGCAGGTGCCTGA 59.723 47.619 21.34 0.83 46.30 3.86
1722 2457 1.732941 TGTATAAACGCAGGTGCCTG 58.267 50.000 13.59 13.59 46.15 4.85
1723 2458 2.288666 CATGTATAAACGCAGGTGCCT 58.711 47.619 0.00 0.00 37.91 4.75
1724 2459 1.268539 GCATGTATAAACGCAGGTGCC 60.269 52.381 0.00 0.00 37.91 5.01
1725 2460 1.268539 GGCATGTATAAACGCAGGTGC 60.269 52.381 0.00 0.00 37.78 5.01
1726 2461 1.333619 GGGCATGTATAAACGCAGGTG 59.666 52.381 0.00 0.00 0.00 4.00
1747 2482 1.134995 GGCAAGGGCAAAGTGCTATTC 60.135 52.381 0.00 0.00 44.28 1.75
1759 2494 1.134995 GCAATTAGTCAAGGCAAGGGC 60.135 52.381 0.00 0.00 40.13 5.19
1767 2502 3.372440 AAGGGGAGGCAATTAGTCAAG 57.628 47.619 0.00 0.00 0.00 3.02
1776 2511 0.328258 GAAGCAGTAAGGGGAGGCAA 59.672 55.000 0.00 0.00 0.00 4.52
1839 2919 7.271868 GGGGTACGAATGAAATAAAAACGAAAG 59.728 37.037 0.00 0.00 0.00 2.62
1867 2947 3.242011 TGAGATCATACTAGCCCATGCA 58.758 45.455 0.00 0.00 41.13 3.96
1870 2950 9.840690 ATATATCATGAGATCATACTAGCCCAT 57.159 33.333 6.01 0.00 35.67 4.00
1871 2951 9.086758 CATATATCATGAGATCATACTAGCCCA 57.913 37.037 6.01 0.00 35.67 5.36
1872 2952 8.034215 GCATATATCATGAGATCATACTAGCCC 58.966 40.741 6.01 0.00 35.67 5.19
1873 2953 8.034215 GGCATATATCATGAGATCATACTAGCC 58.966 40.741 6.01 7.31 35.67 3.93
1958 3038 1.199624 GTGCAAAACCAAGCAAGACG 58.800 50.000 0.00 0.00 43.20 4.18
2028 3108 2.349886 CGTGCAAAGACTAGCTGAATCC 59.650 50.000 0.00 0.00 0.00 3.01
2329 3409 1.180029 AGCCCTGTAGCAGCATTTTG 58.820 50.000 0.00 0.00 34.23 2.44
2487 3567 6.993308 AGAACATCTGATCCAGAAGATTCATG 59.007 38.462 6.25 0.00 44.04 3.07
2550 3981 4.045590 AGGAGGGAGTACTAGTTTTCTCCA 59.954 45.833 27.17 0.63 45.65 3.86
2586 4021 4.935205 TCAGATCCAAAATAAGTGTCGTGG 59.065 41.667 0.00 0.00 0.00 4.94
2594 4029 6.841601 TGTATCCCCTCAGATCCAAAATAAG 58.158 40.000 0.00 0.00 0.00 1.73
2607 4042 7.989947 ATAGTTTCTAACTTGTATCCCCTCA 57.010 36.000 0.00 0.00 42.81 3.86
2608 4043 9.984190 CTTATAGTTTCTAACTTGTATCCCCTC 57.016 37.037 0.00 0.00 42.81 4.30
3394 7466 7.288810 TGAAAAGGTTATGCTTCAAGTCAAT 57.711 32.000 0.00 0.00 0.00 2.57
3426 7498 9.284968 AGTAGTGTTCTGCAAATATAACAAGTT 57.715 29.630 0.00 0.00 33.92 2.66
3487 7568 8.428852 GCCCAACAATTTTCCCTATATTAACAT 58.571 33.333 0.00 0.00 0.00 2.71
3569 7650 5.699915 CCGTCTTGAGATATGCAATGAAGAT 59.300 40.000 0.00 0.00 0.00 2.40
3686 7767 3.341823 CCCAATGAGAGTTGAGACAAGG 58.658 50.000 0.00 0.00 0.00 3.61
3796 7878 0.100682 GCATGTTCATGAGCAGGCAG 59.899 55.000 34.43 17.97 46.07 4.85
3974 8061 1.374947 CTACACTGGGTGGTGGGTG 59.625 63.158 0.00 0.00 41.09 4.61
3975 8062 2.526046 GCTACACTGGGTGGTGGGT 61.526 63.158 0.00 0.00 41.09 4.51
3976 8063 1.852157 ATGCTACACTGGGTGGTGGG 61.852 60.000 0.00 0.00 41.09 4.61
3977 8064 0.908910 TATGCTACACTGGGTGGTGG 59.091 55.000 0.00 0.00 41.09 4.61
3978 8065 2.779755 TTATGCTACACTGGGTGGTG 57.220 50.000 0.00 0.00 42.34 4.17
3979 8066 3.799432 TTTTATGCTACACTGGGTGGT 57.201 42.857 0.00 0.00 37.94 4.16
3980 8067 5.885912 AGTATTTTTATGCTACACTGGGTGG 59.114 40.000 0.00 0.00 37.94 4.61
4016 8105 5.581085 GCAGTACAATTCTAGATGAACGGTT 59.419 40.000 0.29 0.00 37.52 4.44
4020 8109 7.412853 CAATGGCAGTACAATTCTAGATGAAC 58.587 38.462 0.29 0.00 37.52 3.18
4026 8115 4.036027 CAGGCAATGGCAGTACAATTCTAG 59.964 45.833 10.05 0.00 43.71 2.43
4133 8223 9.226606 TCAGATACTGGGTTTTTACAACAATAG 57.773 33.333 0.00 0.00 31.51 1.73
4250 8342 6.683715 TGGCAGCACATATGATCAATAAATG 58.316 36.000 10.38 4.45 0.00 2.32
4273 8365 4.422073 TGGCAGTATGTTCCCTATTCTG 57.578 45.455 0.00 0.00 39.31 3.02
4297 8389 2.464865 TGTTTTGGATTTTTGCCGACG 58.535 42.857 0.00 0.00 0.00 5.12
4312 8404 7.543172 GCATCGATCATGGCAATATTATGTTTT 59.457 33.333 0.00 0.00 32.37 2.43
4315 8407 5.220719 CGCATCGATCATGGCAATATTATGT 60.221 40.000 0.00 0.00 32.37 2.29
4327 8419 2.669434 TGCATGTATCGCATCGATCATG 59.331 45.455 22.26 22.26 43.45 3.07
4328 8420 2.963432 TGCATGTATCGCATCGATCAT 58.037 42.857 4.90 6.65 43.45 2.45
4342 8434 4.676471 CGCGCTATTCAAAATATTGCATGT 59.324 37.500 5.56 0.00 36.45 3.21
4343 8435 4.431986 GCGCGCTATTCAAAATATTGCATG 60.432 41.667 26.67 0.00 36.45 4.06
4344 8436 3.670055 GCGCGCTATTCAAAATATTGCAT 59.330 39.130 26.67 0.00 36.45 3.96
4345 8437 3.042189 GCGCGCTATTCAAAATATTGCA 58.958 40.909 26.67 0.00 36.45 4.08
4346 8438 3.300009 AGCGCGCTATTCAAAATATTGC 58.700 40.909 35.79 0.00 36.45 3.56
4514 8608 6.730038 TGGATTTGGCCCTTATGCATATATTT 59.270 34.615 7.36 0.00 0.00 1.40
4616 8711 1.613437 GTGTTGTATTGTTGCTGCCCT 59.387 47.619 0.00 0.00 0.00 5.19
4759 8855 4.250116 TCAGCTGAGTCTTCTTCTGAAC 57.750 45.455 13.74 0.00 33.07 3.18
4846 8942 8.181904 AGTTGCTCCATCAAAAAGAAAGATAA 57.818 30.769 0.00 0.00 0.00 1.75
4878 8974 3.928727 AGTTGCACAATCAACATCAGG 57.071 42.857 8.98 0.00 46.44 3.86
5099 9195 4.204978 CAGATTCACACAAAAAGACGCAAC 59.795 41.667 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.