Multiple sequence alignment - TraesCS3D01G107700

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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 TraesCS3D01G107700 chr3D 100.000 4179 0 0 1 4179 61310555 61314733 0.000000e+00 7718.0
1 TraesCS3D01G107700 chr3D 85.276 326 19 11 3857 4179 168085939 168086238 4.060000e-80 309.0
2 TraesCS3D01G107700 chr3B 89.958 3565 174 80 689 4179 97076050 97079504 0.000000e+00 4431.0
3 TraesCS3D01G107700 chr3B 88.854 628 28 25 92 693 97075106 97075717 0.000000e+00 734.0
4 TraesCS3D01G107700 chr3B 92.982 228 16 0 3807 4034 378751249 378751476 2.410000e-87 333.0
5 TraesCS3D01G107700 chr3A 91.146 2451 142 35 1147 3550 69506642 69504220 0.000000e+00 3254.0
6 TraesCS3D01G107700 chr3A 80.737 706 47 38 4 675 69507709 69507059 6.330000e-128 468.0
7 TraesCS3D01G107700 chr3A 82.353 493 51 16 3693 4179 69503972 69503510 3.030000e-106 396.0
8 TraesCS3D01G107700 chr3A 84.773 440 17 21 702 1110 69507061 69506641 3.030000e-106 396.0
9 TraesCS3D01G107700 chr2B 85.977 599 54 20 3268 3849 725139475 725140060 7.680000e-172 614.0
10 TraesCS3D01G107700 chr2B 92.544 228 17 0 3807 4034 690338648 690338421 1.120000e-85 327.0
11 TraesCS3D01G107700 chr7A 85.797 521 46 22 3359 3858 675267848 675267335 1.030000e-145 527.0
12 TraesCS3D01G107700 chr1B 85.659 516 47 21 3355 3850 26969563 26969055 6.190000e-143 518.0
13 TraesCS3D01G107700 chr1B 79.699 133 25 2 2011 2142 612863788 612863919 1.240000e-15 95.3
14 TraesCS3D01G107700 chr5D 85.472 413 39 15 3262 3662 431724216 431724619 1.080000e-110 411.0
15 TraesCS3D01G107700 chr5D 84.356 326 22 9 3857 4179 425183304 425183603 4.090000e-75 292.0
16 TraesCS3D01G107700 chr5D 92.547 161 5 2 4019 4179 43950082 43949929 1.510000e-54 224.0
17 TraesCS3D01G107700 chr5D 93.204 103 6 1 3760 3862 431724669 431724770 2.600000e-32 150.0
18 TraesCS3D01G107700 chr7B 94.737 228 12 0 3807 4034 616473171 616473398 5.140000e-94 355.0
19 TraesCS3D01G107700 chr2D 88.839 224 16 3 3956 4179 233308713 233308927 2.480000e-67 267.0
20 TraesCS3D01G107700 chr6B 91.061 179 14 2 3685 3862 712387613 712387436 1.500000e-59 241.0
21 TraesCS3D01G107700 chr6B 90.854 164 15 0 3871 4034 31047554 31047391 1.960000e-53 220.0
22 TraesCS3D01G107700 chr5A 89.431 123 6 2 4057 4179 416302186 416302301 9.360000e-32 148.0


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 TraesCS3D01G107700 chr3D 61310555 61314733 4178 False 7718.0 7718 100.00000 1 4179 1 chr3D.!!$F1 4178
1 TraesCS3D01G107700 chr3B 97075106 97079504 4398 False 2582.5 4431 89.40600 92 4179 2 chr3B.!!$F2 4087
2 TraesCS3D01G107700 chr3A 69503510 69507709 4199 True 1128.5 3254 84.75225 4 4179 4 chr3A.!!$R1 4175
3 TraesCS3D01G107700 chr2B 725139475 725140060 585 False 614.0 614 85.97700 3268 3849 1 chr2B.!!$F1 581
4 TraesCS3D01G107700 chr7A 675267335 675267848 513 True 527.0 527 85.79700 3359 3858 1 chr7A.!!$R1 499
5 TraesCS3D01G107700 chr1B 26969055 26969563 508 True 518.0 518 85.65900 3355 3850 1 chr1B.!!$R1 495
6 TraesCS3D01G107700 chr5D 431724216 431724770 554 False 280.5 411 89.33800 3262 3862 2 chr5D.!!$F2 600

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
888 1337 0.039180 TCTGTTCTGCCCCTCGACTA 59.961 55.0 0.0 0.0 0.0 2.59 F
2270 2826 0.252881 TTGCCTCTCCTCCTCCATGT 60.253 55.0 0.0 0.0 0.0 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 3063 0.378257 CATTGCATTTCGCTACGCCT 59.622 50.0 0.0 0.0 43.06 5.52 R
3251 3834 0.533755 GCAGCACCAAGACACTGACT 60.534 55.0 0.0 0.0 31.67 3.41 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
30 31 4.555709 AAACGTGACCCCGCTGCA 62.556 61.111 0.00 0.00 0.00 4.41
39 40 2.594303 CCCGCTGCACAAGACCAA 60.594 61.111 0.00 0.00 0.00 3.67
40 41 2.620112 CCCGCTGCACAAGACCAAG 61.620 63.158 0.00 0.00 0.00 3.61
41 42 1.597854 CCGCTGCACAAGACCAAGA 60.598 57.895 0.00 0.00 0.00 3.02
42 43 1.571460 CGCTGCACAAGACCAAGAC 59.429 57.895 0.00 0.00 0.00 3.01
43 44 1.845809 CGCTGCACAAGACCAAGACC 61.846 60.000 0.00 0.00 0.00 3.85
44 45 0.819259 GCTGCACAAGACCAAGACCA 60.819 55.000 0.00 0.00 0.00 4.02
45 46 0.947244 CTGCACAAGACCAAGACCAC 59.053 55.000 0.00 0.00 0.00 4.16
46 47 0.546122 TGCACAAGACCAAGACCACT 59.454 50.000 0.00 0.00 0.00 4.00
47 48 0.947244 GCACAAGACCAAGACCACTG 59.053 55.000 0.00 0.00 0.00 3.66
48 49 1.747206 GCACAAGACCAAGACCACTGT 60.747 52.381 0.00 0.00 0.00 3.55
49 50 2.484770 GCACAAGACCAAGACCACTGTA 60.485 50.000 0.00 0.00 0.00 2.74
50 51 3.393800 CACAAGACCAAGACCACTGTAG 58.606 50.000 0.00 0.00 0.00 2.74
51 52 3.039011 ACAAGACCAAGACCACTGTAGT 58.961 45.455 0.00 0.00 0.00 2.73
52 53 3.069729 ACAAGACCAAGACCACTGTAGTC 59.930 47.826 0.00 0.00 34.31 2.59
205 229 2.760385 CACTCTCCGACCCTCCCC 60.760 72.222 0.00 0.00 0.00 4.81
206 230 4.444081 ACTCTCCGACCCTCCCCG 62.444 72.222 0.00 0.00 0.00 5.73
428 455 3.776340 ACAACAGCAACGGGTTAAAAAG 58.224 40.909 0.00 0.00 0.00 2.27
444 478 1.705997 AAAGACGGCCCCAGTGAAGT 61.706 55.000 0.00 0.00 0.00 3.01
449 483 2.529744 GGCCCCAGTGAAGTGAGGT 61.530 63.158 0.00 0.00 0.00 3.85
514 561 7.147897 GGATGGACGGGAGAAAATCTTTTATTT 60.148 37.037 0.00 0.00 0.00 1.40
558 605 3.589654 TTCTCGTGCTTCCCAGCCG 62.590 63.158 0.00 0.00 46.74 5.52
600 647 5.913137 TTCTTTGCTTCTCCTTTTTGTCA 57.087 34.783 0.00 0.00 0.00 3.58
605 661 6.377327 TTGCTTCTCCTTTTTGTCAAGTAG 57.623 37.500 0.00 0.00 0.00 2.57
633 689 5.765182 CAGTTTCTTTCCTGGTGATTAGTGT 59.235 40.000 0.00 0.00 0.00 3.55
634 690 5.998363 AGTTTCTTTCCTGGTGATTAGTGTC 59.002 40.000 0.00 0.00 0.00 3.67
635 691 4.553330 TCTTTCCTGGTGATTAGTGTCC 57.447 45.455 0.00 0.00 0.00 4.02
636 692 3.907474 TCTTTCCTGGTGATTAGTGTCCA 59.093 43.478 0.00 0.00 0.00 4.02
638 694 2.902608 TCCTGGTGATTAGTGTCCAGT 58.097 47.619 8.83 0.00 43.96 4.00
640 696 2.567169 CCTGGTGATTAGTGTCCAGTGA 59.433 50.000 8.83 0.00 43.96 3.41
641 697 3.007940 CCTGGTGATTAGTGTCCAGTGAA 59.992 47.826 8.83 0.00 43.96 3.18
644 701 4.836175 TGGTGATTAGTGTCCAGTGAAGTA 59.164 41.667 0.00 0.00 0.00 2.24
691 1114 4.056125 CGACGAGCTGCCCACTGA 62.056 66.667 0.00 0.00 0.00 3.41
692 1115 2.125753 GACGAGCTGCCCACTGAG 60.126 66.667 0.00 0.00 0.00 3.35
693 1116 4.385405 ACGAGCTGCCCACTGAGC 62.385 66.667 0.00 0.00 35.28 4.26
696 1119 4.079850 AGCTGCCCACTGAGCTCG 62.080 66.667 9.64 6.63 41.94 5.03
698 1121 4.079850 CTGCCCACTGAGCTCGCT 62.080 66.667 9.64 0.00 0.00 4.93
699 1122 4.074526 TGCCCACTGAGCTCGCTC 62.075 66.667 9.64 11.83 43.01 5.03
700 1123 3.768922 GCCCACTGAGCTCGCTCT 61.769 66.667 18.63 0.00 43.12 4.09
701 1124 2.183811 CCCACTGAGCTCGCTCTG 59.816 66.667 19.90 19.90 43.12 3.35
702 1125 2.183811 CCACTGAGCTCGCTCTGG 59.816 66.667 23.58 17.72 43.41 3.86
703 1126 2.508887 CACTGAGCTCGCTCTGGC 60.509 66.667 23.58 0.45 43.41 4.85
794 1221 4.796495 AATCCCAGCCGGCCGTTC 62.796 66.667 26.15 15.59 0.00 3.95
873 1322 1.227263 GTCGCACACACCTGTCTGT 60.227 57.895 0.00 0.00 0.00 3.41
876 1325 0.530650 CGCACACACCTGTCTGTTCT 60.531 55.000 0.00 0.00 0.00 3.01
880 1329 0.886490 CACACCTGTCTGTTCTGCCC 60.886 60.000 0.00 0.00 0.00 5.36
882 1331 1.462238 ACCTGTCTGTTCTGCCCCT 60.462 57.895 0.00 0.00 0.00 4.79
885 1334 1.533033 TGTCTGTTCTGCCCCTCGA 60.533 57.895 0.00 0.00 0.00 4.04
886 1335 1.079750 GTCTGTTCTGCCCCTCGAC 60.080 63.158 0.00 0.00 0.00 4.20
887 1336 1.228894 TCTGTTCTGCCCCTCGACT 60.229 57.895 0.00 0.00 0.00 4.18
888 1337 0.039180 TCTGTTCTGCCCCTCGACTA 59.961 55.000 0.00 0.00 0.00 2.59
890 1339 1.255667 TGTTCTGCCCCTCGACTACC 61.256 60.000 0.00 0.00 0.00 3.18
891 1340 1.077805 TTCTGCCCCTCGACTACCA 59.922 57.895 0.00 0.00 0.00 3.25
892 1341 1.255667 TTCTGCCCCTCGACTACCAC 61.256 60.000 0.00 0.00 0.00 4.16
893 1342 2.682494 TGCCCCTCGACTACCACC 60.682 66.667 0.00 0.00 0.00 4.61
894 1343 2.682494 GCCCCTCGACTACCACCA 60.682 66.667 0.00 0.00 0.00 4.17
895 1344 3.015312 GCCCCTCGACTACCACCAC 62.015 68.421 0.00 0.00 0.00 4.16
896 1345 2.356780 CCCCTCGACTACCACCACC 61.357 68.421 0.00 0.00 0.00 4.61
897 1346 2.707849 CCCTCGACTACCACCACCG 61.708 68.421 0.00 0.00 0.00 4.94
898 1347 2.181021 CTCGACTACCACCACCGC 59.819 66.667 0.00 0.00 0.00 5.68
899 1348 3.352338 CTCGACTACCACCACCGCC 62.352 68.421 0.00 0.00 0.00 6.13
900 1349 3.379445 CGACTACCACCACCGCCT 61.379 66.667 0.00 0.00 0.00 5.52
901 1350 2.264794 GACTACCACCACCGCCTG 59.735 66.667 0.00 0.00 0.00 4.85
916 1365 2.578128 CTGCTGCTTCGCTCTCCT 59.422 61.111 0.00 0.00 0.00 3.69
917 1366 1.519013 CTGCTGCTTCGCTCTCCTC 60.519 63.158 0.00 0.00 0.00 3.71
923 1372 3.132481 CTTCGCTCTCCTCCTCCGC 62.132 68.421 0.00 0.00 0.00 5.54
941 1390 1.674908 GCGAGGCGTTTCTTTTCTTG 58.325 50.000 0.00 0.00 0.00 3.02
942 1391 1.263217 GCGAGGCGTTTCTTTTCTTGA 59.737 47.619 0.00 0.00 0.00 3.02
943 1392 2.663063 GCGAGGCGTTTCTTTTCTTGAG 60.663 50.000 0.00 0.00 0.00 3.02
947 1403 2.812011 GGCGTTTCTTTTCTTGAGCCTA 59.188 45.455 0.00 0.00 40.12 3.93
987 1449 2.100631 CCGTAGCGCTGTTCTTGGG 61.101 63.158 22.90 6.48 0.00 4.12
1108 1589 2.799207 GCTCTTCTTGCTCTCTCCATCG 60.799 54.545 0.00 0.00 0.00 3.84
1109 1590 2.687425 CTCTTCTTGCTCTCTCCATCGA 59.313 50.000 0.00 0.00 0.00 3.59
1110 1591 2.687425 TCTTCTTGCTCTCTCCATCGAG 59.313 50.000 0.00 0.00 37.48 4.04
1111 1592 2.426842 TCTTGCTCTCTCCATCGAGA 57.573 50.000 0.00 0.00 43.08 4.04
1112 1593 2.942804 TCTTGCTCTCTCCATCGAGAT 58.057 47.619 0.00 0.00 44.25 2.75
1113 1594 3.295093 TCTTGCTCTCTCCATCGAGATT 58.705 45.455 0.00 0.00 44.25 2.40
1114 1595 3.067883 TCTTGCTCTCTCCATCGAGATTG 59.932 47.826 0.00 0.00 44.25 2.67
1115 1596 2.659428 TGCTCTCTCCATCGAGATTGA 58.341 47.619 0.00 0.00 44.25 2.57
1116 1597 3.026694 TGCTCTCTCCATCGAGATTGAA 58.973 45.455 0.00 0.00 44.25 2.69
1117 1598 3.448660 TGCTCTCTCCATCGAGATTGAAA 59.551 43.478 0.00 0.00 44.25 2.69
1118 1599 4.081476 TGCTCTCTCCATCGAGATTGAAAA 60.081 41.667 0.00 0.00 44.25 2.29
1119 1600 4.872691 GCTCTCTCCATCGAGATTGAAAAA 59.127 41.667 0.00 0.00 44.25 1.94
1120 1601 5.526846 GCTCTCTCCATCGAGATTGAAAAAT 59.473 40.000 0.00 0.00 44.25 1.82
1121 1602 6.703607 GCTCTCTCCATCGAGATTGAAAAATA 59.296 38.462 0.00 0.00 44.25 1.40
1122 1603 7.225538 GCTCTCTCCATCGAGATTGAAAAATAA 59.774 37.037 0.00 0.00 44.25 1.40
1123 1604 9.102757 CTCTCTCCATCGAGATTGAAAAATAAA 57.897 33.333 0.00 0.00 44.25 1.40
1124 1605 9.448438 TCTCTCCATCGAGATTGAAAAATAAAA 57.552 29.630 0.00 0.00 44.25 1.52
1143 1624 9.783256 AAATAAAAATAGATTCGGGTTTTCTCG 57.217 29.630 0.00 0.00 46.41 4.04
1144 1625 5.813080 AAAATAGATTCGGGTTTTCTCGG 57.187 39.130 0.00 0.00 44.92 4.63
1145 1626 4.748277 AATAGATTCGGGTTTTCTCGGA 57.252 40.909 0.00 0.00 44.92 4.55
1157 1651 5.163713 GGGTTTTCTCGGAGATTCTTGATTG 60.164 44.000 8.81 0.00 33.89 2.67
1227 1722 5.568685 TCATCTAGAGTTTCTTGAGGTCG 57.431 43.478 0.00 0.00 33.20 4.79
1234 1729 4.941873 AGAGTTTCTTGAGGTCGTGTTTTT 59.058 37.500 0.00 0.00 0.00 1.94
1238 1733 2.092861 TCTTGAGGTCGTGTTTTTCCCA 60.093 45.455 0.00 0.00 0.00 4.37
1290 1794 4.666412 TTGGTTTCCTCAATCCCATACA 57.334 40.909 0.00 0.00 0.00 2.29
1304 1808 2.159254 CCCATACAGGCAAAAATCCACG 60.159 50.000 0.00 0.00 35.39 4.94
1350 1854 4.083110 CCACGCAATGTCTCTTTCATTCTT 60.083 41.667 0.00 0.00 33.92 2.52
1377 1881 3.434641 ACATGTCTCTCAAGATGCAAACG 59.565 43.478 0.00 0.00 33.08 3.60
1402 1906 3.165071 ACAGTGCTTTTTATCCCCTTGG 58.835 45.455 0.00 0.00 0.00 3.61
1420 1924 5.011023 CCCTTGGCTTGATTGTACTTTCTTT 59.989 40.000 0.00 0.00 0.00 2.52
1479 1991 5.888161 AGTAGGGTTATCATTGGCTCAAAAG 59.112 40.000 0.00 0.00 0.00 2.27
1500 2013 4.522114 AGAGGCTTCTTTTAATCTCCTGC 58.478 43.478 0.00 0.00 0.00 4.85
1535 2054 3.141398 TCTTCAAAGTTTCTCGCTGCAT 58.859 40.909 0.00 0.00 0.00 3.96
1539 2058 5.431420 TCAAAGTTTCTCGCTGCATTTTA 57.569 34.783 0.00 0.00 0.00 1.52
1554 2073 5.945155 TGCATTTTATTTACCCGAGTGTTC 58.055 37.500 0.00 0.00 0.00 3.18
1607 2127 4.962836 CATGGCCGGCATCCCCTC 62.963 72.222 30.85 9.47 0.00 4.30
1613 2133 2.584608 CGGCATCCCCTCGTTTCT 59.415 61.111 0.00 0.00 0.00 2.52
1649 2175 2.357517 AAGCTGCAAGTCCCGTCG 60.358 61.111 1.02 0.00 35.30 5.12
1655 2181 3.057337 CAAGTCCCGTCGGTCCTT 58.943 61.111 11.06 8.59 0.00 3.36
1924 2456 1.833787 TTCCGTGGCTTCCTGGTACC 61.834 60.000 4.43 4.43 0.00 3.34
1945 2495 3.549150 CGCTCTTCTCGGCTTGCG 61.549 66.667 0.00 0.00 37.57 4.85
2257 2813 0.393132 GAGGTTACCTGCCTTGCCTC 60.393 60.000 9.39 0.00 36.29 4.70
2270 2826 0.252881 TTGCCTCTCCTCCTCCATGT 60.253 55.000 0.00 0.00 0.00 3.21
2312 2877 1.424493 CGATTCCTTCGCACTGAGCC 61.424 60.000 0.00 0.00 41.69 4.70
2313 2878 1.078143 ATTCCTTCGCACTGAGCCC 60.078 57.895 0.00 0.00 41.38 5.19
2355 2928 4.560108 GCCATCTTTGCTGATTTGACTGTT 60.560 41.667 0.00 0.00 0.00 3.16
2490 3063 1.537348 GCCATCGCCTACGTGTATCAA 60.537 52.381 0.00 0.00 41.18 2.57
2525 3098 9.524106 GAAATGCAATGTATGAATCAATTCTCA 57.476 29.630 0.00 2.52 37.67 3.27
2530 3103 7.468220 GCAATGTATGAATCAATTCTCAGCAGA 60.468 37.037 4.50 0.00 37.67 4.26
2734 3314 0.106819 GGCTGATGGAGGAGCACAAT 60.107 55.000 0.00 0.00 36.90 2.71
2737 3317 2.942752 GCTGATGGAGGAGCACAATCAA 60.943 50.000 0.00 0.00 35.15 2.57
2854 3434 2.612212 GAGGAAGAACAACGTGAGCAAA 59.388 45.455 0.00 0.00 0.00 3.68
2953 3533 0.318120 TGCACAACGATGAGAGCTCA 59.682 50.000 17.77 2.23 44.59 4.26
2987 3567 3.963676 TGCTTTGCATCAACACCAC 57.036 47.368 0.00 0.00 31.71 4.16
3032 3615 0.990374 AGAGAAGACCAATGGCAGCT 59.010 50.000 0.00 0.00 0.00 4.24
3052 3635 1.079127 CGTCAGGTCAAGGCCGAAT 60.079 57.895 0.00 0.00 0.00 3.34
3249 3832 5.334421 TCTAGCTCTCTCTAGGGTGTTTTT 58.666 41.667 0.00 0.00 37.30 1.94
3250 3833 4.545208 AGCTCTCTCTAGGGTGTTTTTC 57.455 45.455 0.00 0.00 0.00 2.29
3251 3834 3.904339 AGCTCTCTCTAGGGTGTTTTTCA 59.096 43.478 0.00 0.00 0.00 2.69
3252 3835 4.020662 AGCTCTCTCTAGGGTGTTTTTCAG 60.021 45.833 0.00 0.00 0.00 3.02
3390 3983 6.019762 GCGGTTTTCTTTGTAACATAGTAGC 58.980 40.000 0.00 0.00 0.00 3.58
3432 4029 8.040132 AGAATTGTGTGGATTTTGTTCTTTCAA 58.960 29.630 0.00 0.00 0.00 2.69
3527 4129 2.551459 AGTCAGTGCTTCATGCTGAAAC 59.449 45.455 2.07 0.00 40.40 2.78
3552 4154 6.675413 TCTTAGTACAAGTTTAGGGCTTCA 57.325 37.500 0.00 0.00 0.00 3.02
3557 4159 5.882557 AGTACAAGTTTAGGGCTTCATGATG 59.117 40.000 0.00 0.00 0.00 3.07
3607 4340 6.783708 TTGGGTTACTGACAAGAAAACATT 57.216 33.333 0.00 0.00 0.00 2.71
3608 4341 7.883391 TTGGGTTACTGACAAGAAAACATTA 57.117 32.000 0.00 0.00 0.00 1.90
3609 4342 7.504924 TGGGTTACTGACAAGAAAACATTAG 57.495 36.000 0.00 0.00 0.00 1.73
3631 4364 9.780186 ATTAGTAGTGAATAAGTAGGCAAATCC 57.220 33.333 0.00 0.00 0.00 3.01
4098 4855 2.092538 ACCTCCTCGGACGAAGAAGATA 60.093 50.000 0.00 0.00 36.31 1.98
4100 4857 3.207778 CTCCTCGGACGAAGAAGATAGT 58.792 50.000 0.00 0.00 0.00 2.12
4126 4883 3.334583 TGGAGGACAGACAACATTAGC 57.665 47.619 0.00 0.00 0.00 3.09
4127 4884 2.637382 TGGAGGACAGACAACATTAGCA 59.363 45.455 0.00 0.00 0.00 3.49
4128 4885 3.265791 GGAGGACAGACAACATTAGCAG 58.734 50.000 0.00 0.00 0.00 4.24
4129 4886 3.307059 GGAGGACAGACAACATTAGCAGT 60.307 47.826 0.00 0.00 0.00 4.40
4130 4887 4.081642 GGAGGACAGACAACATTAGCAGTA 60.082 45.833 0.00 0.00 0.00 2.74
4131 4888 5.479306 GAGGACAGACAACATTAGCAGTAA 58.521 41.667 0.00 0.00 0.00 2.24
4132 4889 5.482908 AGGACAGACAACATTAGCAGTAAG 58.517 41.667 0.00 0.00 0.00 2.34
4133 4890 5.012148 AGGACAGACAACATTAGCAGTAAGT 59.988 40.000 0.00 0.00 0.00 2.24
4134 4891 6.210784 AGGACAGACAACATTAGCAGTAAGTA 59.789 38.462 0.00 0.00 0.00 2.24
4135 4892 6.531948 GGACAGACAACATTAGCAGTAAGTAG 59.468 42.308 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.226831 ACGTTTTGGCGTTTGCAGG 60.227 52.632 0.00 0.00 43.04 4.85
1 2 0.524392 TCACGTTTTGGCGTTTGCAG 60.524 50.000 0.00 0.00 43.83 4.41
2 3 0.798771 GTCACGTTTTGGCGTTTGCA 60.799 50.000 0.00 0.00 43.83 4.08
7 8 2.903350 GGGGTCACGTTTTGGCGT 60.903 61.111 0.00 0.00 46.88 5.68
30 31 3.039011 ACTACAGTGGTCTTGGTCTTGT 58.961 45.455 0.00 0.00 0.00 3.16
39 40 4.317530 TGGATACAGACTACAGTGGTCT 57.682 45.455 13.66 13.66 46.17 3.85
428 455 2.358737 CACTTCACTGGGGCCGTC 60.359 66.667 0.00 0.00 0.00 4.79
444 478 2.013563 GCGCATTGGATTCTCACCTCA 61.014 52.381 0.30 0.00 0.00 3.86
449 483 1.089481 GTCGGCGCATTGGATTCTCA 61.089 55.000 10.83 0.00 0.00 3.27
514 561 3.118702 TCCTATGCGAATTTTGGACGGTA 60.119 43.478 0.00 0.00 0.00 4.02
558 605 4.155280 AGAAAAATGCAGAAATGGCAATGC 59.845 37.500 0.00 0.00 45.60 3.56
600 647 5.071923 ACCAGGAAAGAAACTGCTACTACTT 59.928 40.000 0.00 0.00 33.43 2.24
605 661 3.740115 TCACCAGGAAAGAAACTGCTAC 58.260 45.455 0.00 0.00 33.43 3.58
633 689 6.293735 CCGCTTTGTTTAATTACTTCACTGGA 60.294 38.462 0.00 0.00 0.00 3.86
634 690 5.856455 CCGCTTTGTTTAATTACTTCACTGG 59.144 40.000 0.00 0.00 0.00 4.00
635 691 5.342259 GCCGCTTTGTTTAATTACTTCACTG 59.658 40.000 0.00 0.00 0.00 3.66
636 692 5.458015 GCCGCTTTGTTTAATTACTTCACT 58.542 37.500 0.00 0.00 0.00 3.41
638 694 4.468643 CGCCGCTTTGTTTAATTACTTCA 58.531 39.130 0.00 0.00 0.00 3.02
640 696 3.253921 ACCGCCGCTTTGTTTAATTACTT 59.746 39.130 0.00 0.00 0.00 2.24
641 697 2.815503 ACCGCCGCTTTGTTTAATTACT 59.184 40.909 0.00 0.00 0.00 2.24
644 701 1.400500 CGACCGCCGCTTTGTTTAATT 60.400 47.619 0.00 0.00 0.00 1.40
675 1098 2.125753 CTCAGTGGGCAGCTCGTC 60.126 66.667 0.00 0.00 0.00 4.20
676 1099 4.385405 GCTCAGTGGGCAGCTCGT 62.385 66.667 11.01 0.00 32.48 4.18
677 1100 4.079850 AGCTCAGTGGGCAGCTCG 62.080 66.667 19.27 0.00 42.60 5.03
681 1104 4.079850 AGCGAGCTCAGTGGGCAG 62.080 66.667 19.27 12.00 0.00 4.85
682 1105 4.074526 GAGCGAGCTCAGTGGGCA 62.075 66.667 19.27 0.00 42.31 5.36
683 1106 3.768922 AGAGCGAGCTCAGTGGGC 61.769 66.667 24.70 6.98 44.99 5.36
684 1107 2.183811 CAGAGCGAGCTCAGTGGG 59.816 66.667 24.70 7.01 44.99 4.61
685 1108 2.183811 CCAGAGCGAGCTCAGTGG 59.816 66.667 24.70 19.93 44.99 4.00
686 1109 2.504163 AAGCCAGAGCGAGCTCAGTG 62.504 60.000 24.70 15.57 46.67 3.66
687 1110 1.825281 AAAGCCAGAGCGAGCTCAGT 61.825 55.000 24.70 4.54 46.67 3.41
688 1111 0.673022 AAAAGCCAGAGCGAGCTCAG 60.673 55.000 24.70 17.51 46.67 3.35
689 1112 0.250467 AAAAAGCCAGAGCGAGCTCA 60.250 50.000 24.70 0.00 46.67 4.26
690 1113 0.167689 CAAAAAGCCAGAGCGAGCTC 59.832 55.000 16.63 16.63 46.67 4.09
691 1114 0.536006 ACAAAAAGCCAGAGCGAGCT 60.536 50.000 0.00 0.00 46.67 4.09
692 1115 0.312102 AACAAAAAGCCAGAGCGAGC 59.688 50.000 0.00 0.00 46.67 5.03
693 1116 1.927710 GCAACAAAAAGCCAGAGCGAG 60.928 52.381 0.00 0.00 46.67 5.03
694 1117 0.030638 GCAACAAAAAGCCAGAGCGA 59.969 50.000 0.00 0.00 46.67 4.93
695 1118 0.248990 TGCAACAAAAAGCCAGAGCG 60.249 50.000 0.00 0.00 46.67 5.03
696 1119 1.796459 CATGCAACAAAAAGCCAGAGC 59.204 47.619 0.00 0.00 40.32 4.09
697 1120 1.796459 GCATGCAACAAAAAGCCAGAG 59.204 47.619 14.21 0.00 0.00 3.35
698 1121 1.138464 TGCATGCAACAAAAAGCCAGA 59.862 42.857 20.30 0.00 0.00 3.86
699 1122 1.584175 TGCATGCAACAAAAAGCCAG 58.416 45.000 20.30 0.00 0.00 4.85
700 1123 2.034104 TTGCATGCAACAAAAAGCCA 57.966 40.000 28.80 2.84 0.00 4.75
701 1124 2.923643 CATTGCATGCAACAAAAAGCC 58.076 42.857 34.10 0.00 38.88 4.35
747 1174 3.449737 CGAAATGGAGGGAACTGGTAGTA 59.550 47.826 0.00 0.00 44.43 1.82
748 1175 2.236395 CGAAATGGAGGGAACTGGTAGT 59.764 50.000 0.00 0.00 44.43 2.73
749 1176 2.500098 TCGAAATGGAGGGAACTGGTAG 59.500 50.000 0.00 0.00 44.43 3.18
873 1322 1.077805 TGGTAGTCGAGGGGCAGAA 59.922 57.895 0.00 0.00 0.00 3.02
876 1325 2.682494 GGTGGTAGTCGAGGGGCA 60.682 66.667 0.00 0.00 0.00 5.36
880 1329 2.882876 CGGTGGTGGTAGTCGAGG 59.117 66.667 0.00 0.00 0.00 4.63
882 1331 3.376078 GGCGGTGGTGGTAGTCGA 61.376 66.667 0.00 0.00 0.00 4.20
885 1334 4.016706 GCAGGCGGTGGTGGTAGT 62.017 66.667 0.00 0.00 0.00 2.73
886 1335 3.706373 AGCAGGCGGTGGTGGTAG 61.706 66.667 0.00 0.00 34.82 3.18
923 1372 2.663063 GCTCAAGAAAAGAAACGCCTCG 60.663 50.000 0.00 0.00 0.00 4.63
925 1374 1.609072 GGCTCAAGAAAAGAAACGCCT 59.391 47.619 0.00 0.00 33.68 5.52
937 1386 1.063567 GGAGAGGAGGTAGGCTCAAGA 60.064 57.143 0.00 0.00 0.00 3.02
938 1387 1.408969 GGAGAGGAGGTAGGCTCAAG 58.591 60.000 0.00 0.00 0.00 3.02
941 1390 1.529713 CCGGAGAGGAGGTAGGCTC 60.530 68.421 0.00 0.00 45.00 4.70
942 1391 2.604152 CCGGAGAGGAGGTAGGCT 59.396 66.667 0.00 0.00 45.00 4.58
943 1392 3.228017 GCCGGAGAGGAGGTAGGC 61.228 72.222 5.05 0.00 45.00 3.93
970 1426 2.100631 CCCCAAGAACAGCGCTACG 61.101 63.158 10.99 0.00 0.00 3.51
987 1449 2.774351 CCCATCCCCTCCTCCACC 60.774 72.222 0.00 0.00 0.00 4.61
1117 1598 9.783256 CGAGAAAACCCGAATCTATTTTTATTT 57.217 29.630 0.00 0.00 0.00 1.40
1118 1599 8.403236 CCGAGAAAACCCGAATCTATTTTTATT 58.597 33.333 0.00 0.00 0.00 1.40
1119 1600 7.771826 TCCGAGAAAACCCGAATCTATTTTTAT 59.228 33.333 0.00 0.00 0.00 1.40
1120 1601 7.104939 TCCGAGAAAACCCGAATCTATTTTTA 58.895 34.615 0.00 0.00 0.00 1.52
1121 1602 5.941647 TCCGAGAAAACCCGAATCTATTTTT 59.058 36.000 0.00 0.00 0.00 1.94
1122 1603 5.493809 TCCGAGAAAACCCGAATCTATTTT 58.506 37.500 0.00 0.00 0.00 1.82
1123 1604 5.093849 TCCGAGAAAACCCGAATCTATTT 57.906 39.130 0.00 0.00 0.00 1.40
1124 1605 4.404715 TCTCCGAGAAAACCCGAATCTATT 59.595 41.667 0.00 0.00 0.00 1.73
1125 1606 3.958798 TCTCCGAGAAAACCCGAATCTAT 59.041 43.478 0.00 0.00 0.00 1.98
1126 1607 3.359033 TCTCCGAGAAAACCCGAATCTA 58.641 45.455 0.00 0.00 0.00 1.98
1127 1608 2.176889 TCTCCGAGAAAACCCGAATCT 58.823 47.619 0.00 0.00 0.00 2.40
1128 1609 2.667473 TCTCCGAGAAAACCCGAATC 57.333 50.000 0.00 0.00 0.00 2.52
1129 1610 3.197983 AGAATCTCCGAGAAAACCCGAAT 59.802 43.478 1.27 0.00 0.00 3.34
1130 1611 2.565834 AGAATCTCCGAGAAAACCCGAA 59.434 45.455 1.27 0.00 0.00 4.30
1131 1612 2.176889 AGAATCTCCGAGAAAACCCGA 58.823 47.619 1.27 0.00 0.00 5.14
1132 1613 2.673368 CAAGAATCTCCGAGAAAACCCG 59.327 50.000 1.27 0.00 0.00 5.28
1133 1614 3.939066 TCAAGAATCTCCGAGAAAACCC 58.061 45.455 1.27 0.00 0.00 4.11
1134 1615 5.163713 CCAATCAAGAATCTCCGAGAAAACC 60.164 44.000 1.27 0.00 0.00 3.27
1135 1616 5.643777 TCCAATCAAGAATCTCCGAGAAAAC 59.356 40.000 1.27 0.00 0.00 2.43
1136 1617 5.804639 TCCAATCAAGAATCTCCGAGAAAA 58.195 37.500 1.27 0.00 0.00 2.29
1137 1618 5.420725 TCCAATCAAGAATCTCCGAGAAA 57.579 39.130 1.27 0.00 0.00 2.52
1138 1619 5.104776 ACATCCAATCAAGAATCTCCGAGAA 60.105 40.000 1.27 0.00 0.00 2.87
1139 1620 4.406972 ACATCCAATCAAGAATCTCCGAGA 59.593 41.667 0.00 0.00 0.00 4.04
1140 1621 4.510711 CACATCCAATCAAGAATCTCCGAG 59.489 45.833 0.00 0.00 0.00 4.63
1141 1622 4.445453 CACATCCAATCAAGAATCTCCGA 58.555 43.478 0.00 0.00 0.00 4.55
1142 1623 3.003068 GCACATCCAATCAAGAATCTCCG 59.997 47.826 0.00 0.00 0.00 4.63
1143 1624 3.949754 TGCACATCCAATCAAGAATCTCC 59.050 43.478 0.00 0.00 0.00 3.71
1144 1625 4.880120 TCTGCACATCCAATCAAGAATCTC 59.120 41.667 0.00 0.00 0.00 2.75
1145 1626 4.851843 TCTGCACATCCAATCAAGAATCT 58.148 39.130 0.00 0.00 0.00 2.40
1157 1651 1.812571 ACGGAATGTTTCTGCACATCC 59.187 47.619 0.00 0.00 39.72 3.51
1183 1677 9.358872 GATGAATCTAAACCAAGAAAATCAACC 57.641 33.333 0.00 0.00 0.00 3.77
1227 1722 9.249457 CTCTTTCTTCTATTTTGGGAAAAACAC 57.751 33.333 0.00 0.00 33.47 3.32
1234 1729 8.150827 TCATCTCTCTTTCTTCTATTTTGGGA 57.849 34.615 0.00 0.00 0.00 4.37
1265 1769 4.402616 TGGGATTGAGGAAACCAATCTT 57.597 40.909 13.40 0.00 45.49 2.40
1282 1786 3.096092 GTGGATTTTTGCCTGTATGGGA 58.904 45.455 0.00 0.00 36.00 4.37
1290 1794 0.539438 TCAGCCGTGGATTTTTGCCT 60.539 50.000 0.00 0.00 0.00 4.75
1304 1808 4.339530 GTCATTAGAGGGGAATTTTCAGCC 59.660 45.833 0.00 0.00 0.00 4.85
1350 1854 0.318120 TCTTGAGAGACATGTGCGCA 59.682 50.000 5.66 5.66 0.00 6.09
1377 1881 3.826729 AGGGGATAAAAAGCACTGTTGTC 59.173 43.478 0.00 0.00 0.00 3.18
1402 1906 4.383948 GCAGCAAAGAAAGTACAATCAAGC 59.616 41.667 0.00 0.00 0.00 4.01
1479 1991 3.311048 CGCAGGAGATTAAAAGAAGCCTC 59.689 47.826 0.00 0.00 0.00 4.70
1500 2013 6.727824 ACTTTGAAGATGAGATTAACCACG 57.272 37.500 0.00 0.00 0.00 4.94
1535 2054 7.989416 ATGAAGAACACTCGGGTAAATAAAA 57.011 32.000 0.00 0.00 0.00 1.52
1539 2058 5.983720 CGATATGAAGAACACTCGGGTAAAT 59.016 40.000 0.00 0.00 35.08 1.40
1554 2073 6.841443 ACAGATTTGAAGCTCGATATGAAG 57.159 37.500 0.00 0.00 0.00 3.02
1607 2127 1.074752 GCAGGAGAAGCAGAGAAACG 58.925 55.000 0.00 0.00 0.00 3.60
1608 2128 2.175878 TGCAGGAGAAGCAGAGAAAC 57.824 50.000 0.00 0.00 37.02 2.78
1643 2169 3.771160 CCTCCAAGGACCGACGGG 61.771 72.222 20.00 0.00 37.67 5.28
1649 2175 2.692741 CCTCCCCCTCCAAGGACC 60.693 72.222 0.00 0.00 37.67 4.46
2257 2813 4.760530 TGTTTGATACATGGAGGAGGAG 57.239 45.455 0.00 0.00 0.00 3.69
2270 2826 3.615155 TCCGGCATGACAATGTTTGATA 58.385 40.909 0.00 0.00 36.08 2.15
2312 2877 3.494048 GGCTGAAGATCCTACATGAGTGG 60.494 52.174 0.00 0.00 0.00 4.00
2313 2878 3.133542 TGGCTGAAGATCCTACATGAGTG 59.866 47.826 0.00 0.00 0.00 3.51
2376 2949 3.074390 TGTCACACCATCCTTCCTGAAAT 59.926 43.478 0.00 0.00 0.00 2.17
2490 3063 0.378257 CATTGCATTTCGCTACGCCT 59.622 50.000 0.00 0.00 43.06 5.52
2525 3098 7.228507 CAGATGAGTAGTAGTGTTCTATCTGCT 59.771 40.741 0.00 0.00 0.00 4.24
2530 3103 9.634021 TCATTCAGATGAGTAGTAGTGTTCTAT 57.366 33.333 0.00 0.00 37.37 1.98
2734 3314 2.250939 CGAGCTGGCGTTGGTTTGA 61.251 57.895 0.00 0.00 0.00 2.69
2854 3434 2.512515 GGCTTCGCGCTGATCCTT 60.513 61.111 5.56 0.00 39.13 3.36
2953 3533 2.202311 CATGACGACGACGACGCT 60.202 61.111 18.98 7.03 43.96 5.07
2987 3567 0.034059 AGCAAGGTGGAGAACGACAG 59.966 55.000 0.00 0.00 0.00 3.51
3032 3615 4.680237 CGGCCTTGACCTGACGCA 62.680 66.667 0.00 0.00 0.00 5.24
3052 3635 2.094182 GGACTCCGTCAAGCTCATGTAA 60.094 50.000 0.00 0.00 33.68 2.41
3113 3696 4.430423 CAACTGCTTCGACGCCGC 62.430 66.667 11.76 0.00 35.37 6.53
3207 3790 5.821995 GCTAGAAAATTGGCTCTTCATCTCT 59.178 40.000 0.00 0.00 0.00 3.10
3249 3832 1.123077 AGCACCAAGACACTGACTGA 58.877 50.000 0.00 0.00 0.00 3.41
3250 3833 1.224075 CAGCACCAAGACACTGACTG 58.776 55.000 0.00 0.00 31.67 3.51
3251 3834 0.533755 GCAGCACCAAGACACTGACT 60.534 55.000 0.00 0.00 31.67 3.41
3252 3835 0.815213 TGCAGCACCAAGACACTGAC 60.815 55.000 0.00 0.00 31.67 3.51
3390 3983 6.201806 ACACAATTCTTTTCTCAGTCGAAGAG 59.798 38.462 9.30 9.30 36.95 2.85
3527 4129 7.103641 TGAAGCCCTAAACTTGTACTAAGATG 58.896 38.462 10.71 0.00 0.00 2.90
3552 4154 4.715297 ACCTTAACCGGTCTACTTCATCAT 59.285 41.667 8.04 0.00 29.14 2.45
3567 4298 2.755103 CCCAAAGCATCAGACCTTAACC 59.245 50.000 0.00 0.00 0.00 2.85
3581 4312 4.911514 TTTCTTGTCAGTAACCCAAAGC 57.088 40.909 0.00 0.00 0.00 3.51
3607 4340 7.431249 CGGATTTGCCTACTTATTCACTACTA 58.569 38.462 0.00 0.00 0.00 1.82
3608 4341 6.281405 CGGATTTGCCTACTTATTCACTACT 58.719 40.000 0.00 0.00 0.00 2.57
3609 4342 5.465724 CCGGATTTGCCTACTTATTCACTAC 59.534 44.000 0.00 0.00 0.00 2.73
3631 4364 7.605410 ATCACAGTACAGTAATTTAAACCCG 57.395 36.000 0.00 0.00 0.00 5.28
3733 4471 4.754114 TGTTTAAGCATGTTGGGAAATTGC 59.246 37.500 0.00 0.00 0.00 3.56
3736 4474 6.767456 TCATTGTTTAAGCATGTTGGGAAAT 58.233 32.000 0.00 0.00 0.00 2.17
4123 4880 9.857656 ACCTACATTATGTACTACTTACTGCTA 57.142 33.333 0.29 0.00 0.00 3.49
4132 4889 9.865321 TGTTCTTTGACCTACATTATGTACTAC 57.135 33.333 0.29 0.00 0.00 2.73
4134 4891 9.959721 AATGTTCTTTGACCTACATTATGTACT 57.040 29.630 0.29 0.00 38.91 2.73
4135 4892 9.988350 CAATGTTCTTTGACCTACATTATGTAC 57.012 33.333 0.29 0.00 38.71 2.90


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

AutoCloner maintained by Alex Coulton.