Multiple sequence alignment - TraesCS1B01G146700

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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 TraesCS1B01G146700 chr1B 100.000 6133 0 0 1 6133 206425854 206431986 0.000000e+00 11326.0
1 TraesCS1B01G146700 chr1D 95.682 2478 81 8 3322 5775 131289262 131291737 0.000000e+00 3960.0
2 TraesCS1B01G146700 chr1D 96.922 2274 37 14 1058 3322 131286686 131288935 0.000000e+00 3781.0
3 TraesCS1B01G146700 chr1D 94.937 158 5 2 5851 6006 131304623 131304779 1.710000e-60 244.0
4 TraesCS1B01G146700 chr1A 97.351 2001 46 4 1734 3727 157315662 157313662 0.000000e+00 3395.0
5 TraesCS1B01G146700 chr1A 94.353 1877 67 10 3725 5580 157313564 157311706 0.000000e+00 2843.0
6 TraesCS1B01G146700 chr1A 96.880 609 15 2 1058 1665 157316837 157316232 0.000000e+00 1016.0
7 TraesCS1B01G146700 chr1A 90.789 532 32 2 5617 6131 157311714 157311183 0.000000e+00 695.0
8 TraesCS1B01G146700 chr6A 88.130 893 93 8 26 915 508354727 508355609 0.000000e+00 1050.0
9 TraesCS1B01G146700 chr6A 86.130 894 105 11 30 919 474747250 474746372 0.000000e+00 946.0
10 TraesCS1B01G146700 chr6A 88.540 637 59 11 280 913 474746363 474745738 0.000000e+00 760.0
11 TraesCS1B01G146700 chr3D 90.947 486 38 4 439 918 518746217 518745732 0.000000e+00 649.0
12 TraesCS1B01G146700 chr7B 81.696 519 75 12 402 918 581398364 581397864 1.230000e-111 414.0
13 TraesCS1B01G146700 chr5A 81.359 515 76 12 402 914 400508976 400509472 9.580000e-108 401.0
14 TraesCS1B01G146700 chr7A 81.303 476 69 12 439 912 588275753 588275296 9.710000e-98 368.0
15 TraesCS1B01G146700 chr7A 81.250 480 64 13 457 934 588268071 588267616 1.260000e-96 364.0
16 TraesCS1B01G146700 chr7A 80.204 490 76 13 402 889 588281733 588281263 1.270000e-91 348.0
17 TraesCS1B01G146700 chr7A 77.451 102 18 4 820 918 677975840 677975939 8.590000e-04 56.5
18 TraesCS1B01G146700 chr5B 84.320 338 44 6 571 905 185183953 185184284 7.670000e-84 322.0
19 TraesCS1B01G146700 chr2D 86.307 241 30 2 681 918 630470979 630471219 6.100000e-65 259.0
20 TraesCS1B01G146700 chr2D 85.393 89 10 2 928 1013 383544420 383544332 8.470000e-14 89.8
21 TraesCS1B01G146700 chr2D 85.135 74 10 1 926 999 625443501 625443429 2.370000e-09 75.0
22 TraesCS1B01G146700 chr4D 86.667 90 9 2 926 1013 28426814 28426726 5.060000e-16 97.1
23 TraesCS1B01G146700 chr2B 90.909 44 2 1 887 930 140779231 140779190 2.390000e-04 58.4


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 TraesCS1B01G146700 chr1B 206425854 206431986 6132 False 11326.00 11326 100.00000 1 6133 1 chr1B.!!$F1 6132
1 TraesCS1B01G146700 chr1D 131286686 131291737 5051 False 3870.50 3960 96.30200 1058 5775 2 chr1D.!!$F2 4717
2 TraesCS1B01G146700 chr1A 157311183 157316837 5654 True 1987.25 3395 94.84325 1058 6131 4 chr1A.!!$R1 5073
3 TraesCS1B01G146700 chr6A 508354727 508355609 882 False 1050.00 1050 88.13000 26 915 1 chr6A.!!$F1 889
4 TraesCS1B01G146700 chr6A 474745738 474747250 1512 True 853.00 946 87.33500 30 919 2 chr6A.!!$R1 889
5 TraesCS1B01G146700 chr7B 581397864 581398364 500 True 414.00 414 81.69600 402 918 1 chr7B.!!$R1 516

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
328 966 0.027194 CGCTCGCATCAAACTCATGG 59.973 55.0 0.00 0.00 0.00 3.66 F
1029 1671 0.036765 TTACTTACCGTGGCTGCCTG 60.037 55.0 21.03 12.17 0.00 4.85 F
1850 2994 0.606401 CGCCGGGGCAATATGATTCT 60.606 55.0 5.22 0.00 42.06 2.40 F
3526 5010 1.681229 TTTTATGGAGGGTGGGCTCT 58.319 50.0 0.00 0.00 0.00 4.09 F
4084 5670 0.536006 GGTTGCTTGAGACTGCAGGT 60.536 55.0 19.93 4.31 40.46 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1487 2130 0.465642 GGATCCCCGTCACAAATCCC 60.466 60.000 0.00 0.0 31.56 3.85 R
2946 4096 3.685058 GCTATCCGACAAACAAAGATGC 58.315 45.455 0.00 0.0 0.00 3.91 R
3683 5167 5.163343 ACTGTTAGCACAAGTTCTCTTACCA 60.163 40.000 0.00 0.0 30.36 3.25 R
5058 6662 1.981495 CAGAGAAGGTTCCAGAAGGGT 59.019 52.381 0.00 0.0 38.11 4.34 R
6072 7694 0.313987 GGTTGAGGAAAGTTTGCGGG 59.686 55.000 1.08 0.0 0.00 6.13 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
24 25 2.754658 CGGAGTCTACCACCGCCT 60.755 66.667 0.00 0.00 40.19 5.52
110 111 7.325660 AGTATTCGATCATTGTGCTGATTTT 57.674 32.000 0.00 0.00 36.01 1.82
113 114 5.475273 TCGATCATTGTGCTGATTTTCTC 57.525 39.130 0.00 0.00 36.01 2.87
114 115 4.937015 TCGATCATTGTGCTGATTTTCTCA 59.063 37.500 0.00 0.00 36.01 3.27
120 121 3.059884 TGTGCTGATTTTCTCACTCGTC 58.940 45.455 0.00 0.00 0.00 4.20
165 166 4.051932 GGATGTCCCCGAGAACCT 57.948 61.111 0.00 0.00 0.00 3.50
188 189 1.052124 TGTTTCCTCTCACACCGGGT 61.052 55.000 6.32 0.00 0.00 5.28
265 266 6.126863 TCACCCAAGAGAAACATGAGTAAT 57.873 37.500 0.00 0.00 0.00 1.89
267 268 5.124457 CACCCAAGAGAAACATGAGTAATGG 59.876 44.000 0.00 0.00 40.94 3.16
272 910 7.121759 CCAAGAGAAACATGAGTAATGGTCAAT 59.878 37.037 0.00 0.00 40.94 2.57
273 911 8.517878 CAAGAGAAACATGAGTAATGGTCAATT 58.482 33.333 0.00 0.00 40.94 2.32
276 914 9.167311 GAGAAACATGAGTAATGGTCAATTAGT 57.833 33.333 0.00 0.00 40.94 2.24
320 958 0.037326 AGGAAACTCGCTCGCATCAA 60.037 50.000 0.00 0.00 32.90 2.57
328 966 0.027194 CGCTCGCATCAAACTCATGG 59.973 55.000 0.00 0.00 0.00 3.66
370 1009 8.994429 AATCTGATCTTAGCCAATTATACTCG 57.006 34.615 0.00 0.00 0.00 4.18
432 1071 5.008415 GTGAGAAAGATAGATTCGACGGGTA 59.992 44.000 0.00 0.00 32.04 3.69
434 1073 4.519730 AGAAAGATAGATTCGACGGGTAGG 59.480 45.833 0.00 0.00 32.04 3.18
435 1074 2.161030 AGATAGATTCGACGGGTAGGC 58.839 52.381 0.00 0.00 0.00 3.93
453 1092 2.393768 CGCATGTGTGGCTCACCTC 61.394 63.158 16.29 5.32 45.61 3.85
459 1098 0.106708 GTGTGGCTCACCTCTGTTGA 59.893 55.000 8.47 0.00 40.84 3.18
503 1142 0.657368 GTGCTTGTTGTTTCGGCTCG 60.657 55.000 0.00 0.00 0.00 5.03
558 1197 3.051210 CCGATCTAGGCGGCATCA 58.949 61.111 13.08 0.00 42.55 3.07
564 1203 3.071837 TAGGCGGCATCACGTGGA 61.072 61.111 17.00 2.69 35.98 4.02
614 1254 1.200716 GTTGGTGATGACTCCGTACGA 59.799 52.381 18.76 1.79 32.93 3.43
637 1277 3.569210 TGTGTGCCTCCTGTGGGG 61.569 66.667 0.00 0.00 0.00 4.96
652 1292 4.162690 GGGCGCTGGTGGTAGGAG 62.163 72.222 7.64 0.00 0.00 3.69
663 1304 2.908351 GGTGGTAGGAGTTTTGGTAGGA 59.092 50.000 0.00 0.00 0.00 2.94
673 1314 5.416013 GGAGTTTTGGTAGGAGAGAAATTGG 59.584 44.000 0.00 0.00 0.00 3.16
696 1337 0.947244 GCAGGGATTAGCGTGATTGG 59.053 55.000 0.00 0.00 0.00 3.16
729 1370 2.047443 GCCGGCCCGTGGAATTTTA 61.047 57.895 18.11 0.00 0.00 1.52
825 1467 4.021981 GCCATTAGATTTTATCCAGTGGGC 60.022 45.833 9.92 0.00 0.00 5.36
845 1487 4.065789 GGCTTAATCTAGCGGTGCTAATT 58.934 43.478 0.00 5.94 40.82 1.40
865 1507 6.699575 AATTAATCTGGGTACATCTGTTGC 57.300 37.500 0.00 0.00 0.00 4.17
870 1512 0.321298 GGGTACATCTGTTGCGTGGT 60.321 55.000 0.00 0.00 0.00 4.16
871 1513 1.076332 GGTACATCTGTTGCGTGGTC 58.924 55.000 0.00 0.00 0.00 4.02
975 1617 9.955208 TGTTATAATGTCGATATTTACGTGACT 57.045 29.630 12.87 0.00 0.00 3.41
978 1620 8.867112 ATAATGTCGATATTTACGTGACTTGT 57.133 30.769 12.87 0.00 0.00 3.16
979 1621 9.955208 ATAATGTCGATATTTACGTGACTTGTA 57.045 29.630 12.87 0.00 0.00 2.41
980 1622 8.692110 AATGTCGATATTTACGTGACTTGTAA 57.308 30.769 0.97 0.00 0.00 2.41
981 1623 7.496704 TGTCGATATTTACGTGACTTGTAAC 57.503 36.000 0.00 0.00 31.88 2.50
982 1624 7.307694 TGTCGATATTTACGTGACTTGTAACT 58.692 34.615 0.00 0.00 31.88 2.24
983 1625 8.450180 TGTCGATATTTACGTGACTTGTAACTA 58.550 33.333 0.00 0.00 31.88 2.24
984 1626 9.277565 GTCGATATTTACGTGACTTGTAACTAA 57.722 33.333 0.00 0.00 31.88 2.24
985 1627 9.838975 TCGATATTTACGTGACTTGTAACTAAA 57.161 29.630 0.00 0.00 31.88 1.85
994 1636 9.924650 ACGTGACTTGTAACTAAATCTTTATCT 57.075 29.630 0.00 0.00 0.00 1.98
1021 1663 8.792831 ATTAATGAGACGTATTACTTACCGTG 57.207 34.615 0.00 0.00 0.00 4.94
1022 1664 4.621068 TGAGACGTATTACTTACCGTGG 57.379 45.455 0.00 0.00 0.00 4.94
1023 1665 3.181497 TGAGACGTATTACTTACCGTGGC 60.181 47.826 0.00 0.00 0.00 5.01
1024 1666 3.019564 AGACGTATTACTTACCGTGGCT 58.980 45.455 0.00 0.00 0.00 4.75
1025 1667 3.111098 GACGTATTACTTACCGTGGCTG 58.889 50.000 0.00 0.00 0.00 4.85
1026 1668 1.856597 CGTATTACTTACCGTGGCTGC 59.143 52.381 0.00 0.00 0.00 5.25
1027 1669 2.207590 GTATTACTTACCGTGGCTGCC 58.792 52.381 12.87 12.87 0.00 4.85
1028 1670 0.909623 ATTACTTACCGTGGCTGCCT 59.090 50.000 21.03 1.26 0.00 4.75
1029 1671 0.036765 TTACTTACCGTGGCTGCCTG 60.037 55.000 21.03 12.17 0.00 4.85
1030 1672 2.515996 TACTTACCGTGGCTGCCTGC 62.516 60.000 21.03 11.67 41.94 4.85
1051 1693 1.495951 GGTAACTTGTTGCGGCTCG 59.504 57.895 0.00 0.00 0.00 5.03
1052 1694 1.495951 GTAACTTGTTGCGGCTCGG 59.504 57.895 0.00 0.00 0.00 4.63
1053 1695 1.669760 TAACTTGTTGCGGCTCGGG 60.670 57.895 0.00 0.00 0.00 5.14
1085 1727 0.869880 TCTACCGCGAATGCATCACG 60.870 55.000 8.23 17.79 42.97 4.35
1409 2052 2.434702 CCAGCCTCTTAATTACCCGTCT 59.565 50.000 0.00 0.00 0.00 4.18
1561 2204 3.384532 GGGCCGACCGACTAACCA 61.385 66.667 0.00 0.00 36.48 3.67
1633 2276 3.165875 TGTTGTTGTTCTTTGGTTGGGA 58.834 40.909 0.00 0.00 0.00 4.37
1649 2292 1.786441 TGGGACTCCTTGAAATGGGTT 59.214 47.619 0.00 0.00 0.00 4.11
1850 2994 0.606401 CGCCGGGGCAATATGATTCT 60.606 55.000 5.22 0.00 42.06 2.40
2009 3155 8.849543 ATCACCCCTTCAATAAGTAGTACTAA 57.150 34.615 3.61 0.00 0.00 2.24
2070 3217 3.126831 CGGCCAGCTTTCTTATCTGTAG 58.873 50.000 2.24 0.00 0.00 2.74
2111 3259 6.768861 TGTTTAGTACTTAGTGCATGTTGGTT 59.231 34.615 0.00 0.00 0.00 3.67
2118 3266 7.938140 ACTTAGTGCATGTTGGTTTGTATAT 57.062 32.000 0.00 0.00 0.00 0.86
2169 3317 8.615211 GCAATTAACTGTGATCATCATTCTGTA 58.385 33.333 0.00 0.00 0.00 2.74
2358 3506 2.231721 AGAGTGCCCTCGAAGTAAGTTC 59.768 50.000 0.00 0.00 42.86 3.01
2439 3587 6.017440 GTCAATGCTACCTTTCACAGTTAACA 60.017 38.462 8.61 0.00 0.00 2.41
2485 3633 7.963465 GCTTTTGTATAGAAACCTAGAAACTGC 59.037 37.037 0.00 0.00 0.00 4.40
2874 4024 8.954950 TTCAATGCTCCATTTTACAAAAGAAA 57.045 26.923 0.00 0.00 31.05 2.52
3102 4255 2.025767 TTGGCCAACTTTGCGTGCAT 62.026 50.000 16.05 0.00 0.00 3.96
3275 4428 9.643693 AATAAAATGTTGCGAGAAAATCAAGAT 57.356 25.926 0.00 0.00 0.00 2.40
3352 4832 9.787435 TGGACAAAACTAACTATGTTTATGACT 57.213 29.630 0.00 0.00 36.72 3.41
3526 5010 1.681229 TTTTATGGAGGGTGGGCTCT 58.319 50.000 0.00 0.00 0.00 4.09
3683 5167 5.867330 TGGGAATTTTGAATTGTGCTCATT 58.133 33.333 0.00 0.00 0.00 2.57
3868 5452 5.530171 GCTATGTCAATGATCAGTCCATGTT 59.470 40.000 12.68 0.00 0.00 2.71
3935 5519 0.890542 TTCATTGCTCTGCAGCCGTT 60.891 50.000 9.47 0.00 46.26 4.44
3993 5577 6.350110 CCATCCGTGTCCTGTTTATTTCATTT 60.350 38.462 0.00 0.00 0.00 2.32
4031 5615 2.029844 GCTGTCTGTCAACCGCCTC 61.030 63.158 0.00 0.00 0.00 4.70
4084 5670 0.536006 GGTTGCTTGAGACTGCAGGT 60.536 55.000 19.93 4.31 40.46 4.00
4115 5701 5.047377 TGCCTGCGTCATGTTATGATATCTA 60.047 40.000 3.98 0.00 42.04 1.98
4147 5733 6.209986 TCATTTTCTTCTTCCATGCTGAACAT 59.790 34.615 0.00 0.00 40.66 2.71
4151 5737 7.707624 TTCTTCTTCCATGCTGAACATATTT 57.292 32.000 0.00 0.00 36.64 1.40
4216 5802 2.271944 AGGGTGGACTTGTGCTTTAC 57.728 50.000 0.00 0.00 0.00 2.01
4218 5804 0.872388 GGTGGACTTGTGCTTTACGG 59.128 55.000 0.00 0.00 0.00 4.02
4623 6227 2.028130 ACAACATGAAAGTGCCGGAAA 58.972 42.857 5.05 0.00 0.00 3.13
4624 6228 2.627699 ACAACATGAAAGTGCCGGAAAT 59.372 40.909 5.05 0.00 0.00 2.17
4625 6229 3.244976 CAACATGAAAGTGCCGGAAATC 58.755 45.455 5.05 0.00 0.00 2.17
4626 6230 2.513753 ACATGAAAGTGCCGGAAATCA 58.486 42.857 5.05 0.00 0.00 2.57
4627 6231 3.091545 ACATGAAAGTGCCGGAAATCAT 58.908 40.909 5.05 2.80 0.00 2.45
4629 6233 4.704540 ACATGAAAGTGCCGGAAATCATAA 59.295 37.500 5.05 0.00 0.00 1.90
4630 6234 4.963276 TGAAAGTGCCGGAAATCATAAG 57.037 40.909 5.05 0.00 0.00 1.73
4650 6254 9.787435 TCATAAGTTGTGTAACTCTAACCAAAT 57.213 29.630 0.00 0.00 46.14 2.32
4738 6342 5.106987 CCAAAAATTGTCAGGCTTAACATGC 60.107 40.000 0.00 0.00 0.00 4.06
4859 6463 3.736252 CGGTGTATGCTCGAGAAAATAGG 59.264 47.826 18.75 0.00 0.00 2.57
4964 6568 5.251468 TGAGGTGTACCCTACTCAAGTACTA 59.749 44.000 0.00 0.00 46.51 1.82
4970 6574 3.857420 ACCCTACTCAAGTACTACCTCCT 59.143 47.826 0.00 0.00 0.00 3.69
4972 6576 4.325187 CCCTACTCAAGTACTACCTCCTGT 60.325 50.000 0.00 0.00 0.00 4.00
4989 6593 4.687215 TGTCTGCTCGCACTGGGC 62.687 66.667 0.00 0.00 39.90 5.36
5044 6648 7.220030 ACACTCAAACATGTTAACTCATCTCT 58.780 34.615 12.39 0.00 0.00 3.10
5058 6662 0.326904 ATCTCTGGCCTCCACATCCA 60.327 55.000 3.32 0.00 0.00 3.41
5065 6669 1.566298 GCCTCCACATCCACCCTTCT 61.566 60.000 0.00 0.00 0.00 2.85
5074 6678 1.064825 TCCACCCTTCTGGAACCTTC 58.935 55.000 0.00 0.00 37.39 3.46
5096 6700 0.257328 TGGTTGTGCCAGTTTCTCCA 59.743 50.000 0.00 0.00 43.61 3.86
5109 6713 4.750098 CAGTTTCTCCAAAGACGCTTTCTA 59.250 41.667 2.45 0.00 32.51 2.10
5135 6739 6.674694 GCTTCATCTCAAAGCAAATAGAGA 57.325 37.500 3.12 0.00 46.63 3.10
5397 7001 2.479566 TCAGTTGAGGACTTGATGCC 57.520 50.000 0.00 0.00 36.10 4.40
5403 7007 1.965754 GAGGACTTGATGCCGAGGCT 61.966 60.000 15.75 0.69 42.51 4.58
5485 7089 6.313411 TGCAAGCCTTCATTTGTTAATAATGC 59.687 34.615 7.88 0.00 33.91 3.56
5516 7120 4.794278 ATGTTCATCAAGCAAGCAATGA 57.206 36.364 3.59 3.59 0.00 2.57
5537 7141 3.356529 AATCTCCGAGTGCCTGAAAAT 57.643 42.857 0.00 0.00 0.00 1.82
5590 7194 4.739195 AGTAGAATCAAGACGAACTCTGC 58.261 43.478 0.00 0.00 0.00 4.26
5613 7217 4.880886 TGTAATGCACCATCGAAATCAG 57.119 40.909 0.00 0.00 0.00 2.90
5650 7254 1.341531 ACCACTGTTCAGAAGGACGAG 59.658 52.381 17.40 0.00 0.00 4.18
5696 7300 7.166473 GGATTCAGATTTCAACATTACATTCGC 59.834 37.037 0.00 0.00 0.00 4.70
5733 7337 1.150536 ATCCAACCGGTGCACAACT 59.849 52.632 20.43 0.00 0.00 3.16
5748 7353 3.769536 CACAACTTTTTCCAGCTCGTTT 58.230 40.909 0.00 0.00 0.00 3.60
5749 7354 4.173256 CACAACTTTTTCCAGCTCGTTTT 58.827 39.130 0.00 0.00 0.00 2.43
5795 7400 1.733912 GATTGAGTCTTGTGCATGCGA 59.266 47.619 14.09 0.40 0.00 5.10
5832 7437 3.618594 GCAGATCAGTTCTTCGCATACAA 59.381 43.478 0.00 0.00 29.93 2.41
5852 7457 3.961480 AGAATGAGTGTCGTGGATCAA 57.039 42.857 0.00 0.00 0.00 2.57
5910 7515 3.900941 AGTTTGGCTTGCGTAAATCTTG 58.099 40.909 0.00 0.00 0.00 3.02
5978 7585 2.892373 TTTCTTGAACGGCAATAGCG 57.108 45.000 0.00 0.00 43.41 4.26
5988 7595 1.132588 GGCAATAGCGATCTGACGTC 58.867 55.000 9.11 9.11 43.41 4.34
6046 7668 3.032265 ACCCCTCCAAATCCTATTTGC 57.968 47.619 6.82 0.00 0.00 3.68
6056 7678 1.209621 TCCTATTTGCGCCCTTAGGT 58.790 50.000 19.85 0.00 34.18 3.08
6062 7684 0.178068 TTGCGCCCTTAGGTCATCTC 59.822 55.000 4.18 0.00 34.57 2.75
6063 7685 1.069935 GCGCCCTTAGGTCATCTCC 59.930 63.158 0.00 0.00 34.57 3.71
6066 7688 0.389757 GCCCTTAGGTCATCTCCGAC 59.610 60.000 0.00 0.00 34.57 4.79
6072 7694 2.278013 GTCATCTCCGACGCCGAC 60.278 66.667 0.00 0.00 38.22 4.79
6083 7705 3.656045 CGCCGACCCGCAAACTTT 61.656 61.111 0.00 0.00 0.00 2.66
6084 7706 2.254350 GCCGACCCGCAAACTTTC 59.746 61.111 0.00 0.00 0.00 2.62
6086 7708 1.599797 CCGACCCGCAAACTTTCCT 60.600 57.895 0.00 0.00 0.00 3.36
6100 7722 0.754472 TTTCCTCAACCGTTCGGACT 59.246 50.000 18.28 1.72 0.00 3.85
6101 7723 1.619654 TTCCTCAACCGTTCGGACTA 58.380 50.000 18.28 1.71 0.00 2.59
6123 7745 1.913317 GAAGCCATCCAACGCAATTC 58.087 50.000 0.00 0.00 0.00 2.17
6131 7753 1.663643 TCCAACGCAATTCTGTATCGC 59.336 47.619 0.00 0.00 0.00 4.58
6132 7754 1.665679 CCAACGCAATTCTGTATCGCT 59.334 47.619 0.00 0.00 0.00 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.004560 TGGTAGACTCCGTCGTCGT 60.005 57.895 0.71 0.00 38.90 4.34
1 2 1.423056 GTGGTAGACTCCGTCGTCG 59.577 63.158 0.00 0.00 38.90 5.12
2 3 1.799383 GGTGGTAGACTCCGTCGTC 59.201 63.158 0.00 0.00 37.67 4.20
3 4 3.993535 GGTGGTAGACTCCGTCGT 58.006 61.111 0.00 0.00 37.67 4.34
8 9 3.208335 GAGGCGGTGGTAGACTCC 58.792 66.667 0.00 0.00 37.79 3.85
9 10 2.424733 GGGAGGCGGTGGTAGACTC 61.425 68.421 0.00 0.00 42.88 3.36
10 11 2.363925 GGGAGGCGGTGGTAGACT 60.364 66.667 0.00 0.00 0.00 3.24
11 12 3.834799 CGGGAGGCGGTGGTAGAC 61.835 72.222 0.00 0.00 0.00 2.59
73 74 1.918595 GAATACTCGACCGGTTCCAC 58.081 55.000 9.42 0.00 0.00 4.02
86 87 6.932356 AAATCAGCACAATGATCGAATACT 57.068 33.333 0.00 0.00 39.00 2.12
134 135 2.503375 ATCCGCAACGTCGTCGAC 60.503 61.111 15.51 15.51 40.62 4.20
136 137 2.774951 GACATCCGCAACGTCGTCG 61.775 63.158 0.00 0.00 43.34 5.12
150 151 2.670148 GGCAGGTTCTCGGGGACAT 61.670 63.158 0.00 0.00 0.00 3.06
165 166 0.108585 GGTGTGAGAGGAAACAGGCA 59.891 55.000 0.00 0.00 0.00 4.75
214 215 2.809174 CCGCATGAACGACAGCGA 60.809 61.111 20.70 0.00 43.30 4.93
216 217 3.422303 TGCCGCATGAACGACAGC 61.422 61.111 0.00 0.00 34.06 4.40
220 221 2.723586 TTCAGGTGCCGCATGAACGA 62.724 55.000 0.55 0.00 42.13 3.85
265 266 6.801539 GTCAATCAAGTGACTAATTGACCA 57.198 37.500 26.95 8.47 46.24 4.02
272 910 3.723260 TGTGCGTCAATCAAGTGACTAA 58.277 40.909 8.71 0.00 44.79 2.24
273 911 3.005367 TCTGTGCGTCAATCAAGTGACTA 59.995 43.478 8.71 0.00 44.79 2.59
276 914 2.135139 GTCTGTGCGTCAATCAAGTGA 58.865 47.619 0.00 0.00 0.00 3.41
278 916 1.512926 GGTCTGTGCGTCAATCAAGT 58.487 50.000 0.00 0.00 0.00 3.16
293 931 2.657237 CGAGTTTCCTGCCGGTCT 59.343 61.111 1.90 0.00 0.00 3.85
320 958 8.877864 TTTATCTATGTTTCCAACCATGAGTT 57.122 30.769 0.00 0.00 40.16 3.01
378 1017 5.629849 CGTTGGGTTTATCTCTCGATATGTC 59.370 44.000 0.00 0.00 32.42 3.06
380 1019 4.923871 CCGTTGGGTTTATCTCTCGATATG 59.076 45.833 0.00 0.00 32.42 1.78
382 1021 3.243636 GCCGTTGGGTTTATCTCTCGATA 60.244 47.826 0.00 0.00 34.97 2.92
392 1031 4.622650 ACCGCGCCGTTGGGTTTA 62.623 61.111 0.00 0.00 34.97 2.01
432 1071 4.334118 TGAGCCACACATGCGCCT 62.334 61.111 4.18 0.00 0.00 5.52
503 1142 1.635663 CTCCGCCATGTTCCGTTCAC 61.636 60.000 0.00 0.00 0.00 3.18
533 1172 1.248486 CGCCTAGATCGGAGGAATCA 58.752 55.000 18.11 0.00 35.99 2.57
558 1197 1.079819 CGCTCTCCAATGTCCACGT 60.080 57.895 0.00 0.00 0.00 4.49
564 1203 1.110442 CTCCTCTCGCTCTCCAATGT 58.890 55.000 0.00 0.00 0.00 2.71
566 1205 1.733402 CGCTCCTCTCGCTCTCCAAT 61.733 60.000 0.00 0.00 0.00 3.16
632 1272 4.778143 CTACCACCAGCGCCCCAC 62.778 72.222 2.29 0.00 0.00 4.61
637 1277 0.605589 AAAACTCCTACCACCAGCGC 60.606 55.000 0.00 0.00 0.00 5.92
640 1280 2.951229 ACCAAAACTCCTACCACCAG 57.049 50.000 0.00 0.00 0.00 4.00
642 1282 2.908351 TCCTACCAAAACTCCTACCACC 59.092 50.000 0.00 0.00 0.00 4.61
651 1291 4.767409 GCCAATTTCTCTCCTACCAAAACT 59.233 41.667 0.00 0.00 0.00 2.66
652 1292 4.522789 TGCCAATTTCTCTCCTACCAAAAC 59.477 41.667 0.00 0.00 0.00 2.43
663 1304 1.006281 TCCCTGCATGCCAATTTCTCT 59.994 47.619 16.68 0.00 0.00 3.10
673 1314 0.815213 TCACGCTAATCCCTGCATGC 60.815 55.000 11.82 11.82 0.00 4.06
696 1337 2.111251 GGCTCCCGCTAATCCCAC 59.889 66.667 0.00 0.00 36.09 4.61
717 1358 0.372334 CGCGGAGTAAAATTCCACGG 59.628 55.000 0.00 0.00 36.79 4.94
802 1444 4.021981 GCCCACTGGATAAAATCTAATGGC 60.022 45.833 0.00 0.00 0.00 4.40
817 1459 1.541233 CCGCTAGATTAAGCCCACTGG 60.541 57.143 0.00 0.00 39.43 4.00
825 1467 8.651588 CAGATTAATTAGCACCGCTAGATTAAG 58.348 37.037 17.81 9.18 42.34 1.85
845 1487 3.196901 ACGCAACAGATGTACCCAGATTA 59.803 43.478 0.00 0.00 0.00 1.75
865 1507 7.327761 TCGAACTAATTCTTTCTTAAGACCACG 59.672 37.037 4.18 0.00 40.04 4.94
949 1591 9.955208 AGTCACGTAAATATCGACATTATAACA 57.045 29.630 0.00 0.00 0.00 2.41
952 1594 9.955208 ACAAGTCACGTAAATATCGACATTATA 57.045 29.630 0.00 0.00 0.00 0.98
953 1595 8.867112 ACAAGTCACGTAAATATCGACATTAT 57.133 30.769 0.00 0.00 0.00 1.28
954 1596 9.786105 TTACAAGTCACGTAAATATCGACATTA 57.214 29.630 0.00 0.00 0.00 1.90
955 1597 8.589629 GTTACAAGTCACGTAAATATCGACATT 58.410 33.333 0.00 0.00 30.96 2.71
956 1598 7.972277 AGTTACAAGTCACGTAAATATCGACAT 59.028 33.333 0.00 0.00 30.96 3.06
957 1599 7.307694 AGTTACAAGTCACGTAAATATCGACA 58.692 34.615 0.00 0.00 30.96 4.35
958 1600 7.731556 AGTTACAAGTCACGTAAATATCGAC 57.268 36.000 0.00 0.00 30.96 4.20
959 1601 9.838975 TTTAGTTACAAGTCACGTAAATATCGA 57.161 29.630 0.00 0.00 31.66 3.59
968 1610 9.924650 AGATAAAGATTTAGTTACAAGTCACGT 57.075 29.630 0.00 0.00 0.00 4.49
995 1637 9.882996 CACGGTAAGTAATACGTCTCATTAATA 57.117 33.333 0.00 0.00 35.19 0.98
996 1638 7.864379 CCACGGTAAGTAATACGTCTCATTAAT 59.136 37.037 0.00 0.00 35.19 1.40
997 1639 7.195646 CCACGGTAAGTAATACGTCTCATTAA 58.804 38.462 0.00 0.00 35.19 1.40
998 1640 6.728200 CCACGGTAAGTAATACGTCTCATTA 58.272 40.000 0.00 0.00 35.19 1.90
999 1641 5.585390 CCACGGTAAGTAATACGTCTCATT 58.415 41.667 0.00 0.00 35.19 2.57
1000 1642 4.498682 GCCACGGTAAGTAATACGTCTCAT 60.499 45.833 0.00 0.00 35.19 2.90
1001 1643 3.181497 GCCACGGTAAGTAATACGTCTCA 60.181 47.826 0.00 0.00 35.19 3.27
1002 1644 3.065925 AGCCACGGTAAGTAATACGTCTC 59.934 47.826 0.00 0.00 35.19 3.36
1003 1645 3.019564 AGCCACGGTAAGTAATACGTCT 58.980 45.455 0.00 0.00 35.19 4.18
1004 1646 3.111098 CAGCCACGGTAAGTAATACGTC 58.889 50.000 0.00 0.00 35.19 4.34
1005 1647 2.736400 GCAGCCACGGTAAGTAATACGT 60.736 50.000 0.00 0.00 35.19 3.57
1006 1648 1.856597 GCAGCCACGGTAAGTAATACG 59.143 52.381 0.00 0.00 35.19 3.06
1007 1649 2.159000 AGGCAGCCACGGTAAGTAATAC 60.159 50.000 15.80 0.00 0.00 1.89
1008 1650 2.112998 AGGCAGCCACGGTAAGTAATA 58.887 47.619 15.80 0.00 0.00 0.98
1009 1651 0.909623 AGGCAGCCACGGTAAGTAAT 59.090 50.000 15.80 0.00 0.00 1.89
1010 1652 0.036765 CAGGCAGCCACGGTAAGTAA 60.037 55.000 15.80 0.00 0.00 2.24
1011 1653 1.594833 CAGGCAGCCACGGTAAGTA 59.405 57.895 15.80 0.00 0.00 2.24
1012 1654 2.347490 CAGGCAGCCACGGTAAGT 59.653 61.111 15.80 0.00 0.00 2.24
1013 1655 3.127533 GCAGGCAGCCACGGTAAG 61.128 66.667 15.80 0.00 37.23 2.34
1022 1664 1.303643 AAGTTACCTGGCAGGCAGC 60.304 57.895 33.04 22.64 39.63 5.25
1023 1665 0.250901 ACAAGTTACCTGGCAGGCAG 60.251 55.000 33.04 17.24 39.63 4.85
1024 1666 0.184933 AACAAGTTACCTGGCAGGCA 59.815 50.000 33.04 19.18 39.63 4.75
1025 1667 0.598065 CAACAAGTTACCTGGCAGGC 59.402 55.000 33.04 17.17 39.63 4.85
1026 1668 0.598065 GCAACAAGTTACCTGGCAGG 59.402 55.000 31.62 31.62 42.49 4.85
1027 1669 0.238289 CGCAACAAGTTACCTGGCAG 59.762 55.000 7.75 7.75 0.00 4.85
1028 1670 1.169661 CCGCAACAAGTTACCTGGCA 61.170 55.000 0.00 0.00 0.00 4.92
1029 1671 1.579429 CCGCAACAAGTTACCTGGC 59.421 57.895 0.00 0.00 0.00 4.85
1030 1672 0.889186 AGCCGCAACAAGTTACCTGG 60.889 55.000 0.00 0.00 0.00 4.45
1031 1673 0.517316 GAGCCGCAACAAGTTACCTG 59.483 55.000 0.00 0.00 0.00 4.00
1032 1674 0.949105 CGAGCCGCAACAAGTTACCT 60.949 55.000 0.00 0.00 0.00 3.08
1033 1675 1.495951 CGAGCCGCAACAAGTTACC 59.504 57.895 0.00 0.00 0.00 2.85
1034 1676 1.495951 CCGAGCCGCAACAAGTTAC 59.504 57.895 0.00 0.00 0.00 2.50
1035 1677 1.669760 CCCGAGCCGCAACAAGTTA 60.670 57.895 0.00 0.00 0.00 2.24
1036 1678 2.978010 CCCGAGCCGCAACAAGTT 60.978 61.111 0.00 0.00 0.00 2.66
1052 1694 2.757099 TAGACCGGGACTTCGCCC 60.757 66.667 6.32 0.00 45.10 6.13
1053 1695 2.493501 GTAGACCGGGACTTCGCC 59.506 66.667 6.32 0.00 0.00 5.54
1054 1696 2.493501 GGTAGACCGGGACTTCGC 59.506 66.667 6.32 0.00 0.00 4.70
1487 2130 0.465642 GGATCCCCGTCACAAATCCC 60.466 60.000 0.00 0.00 31.56 3.85
1561 2204 2.887152 GCCCATCCAGCTCGAATAAAAT 59.113 45.455 0.00 0.00 0.00 1.82
1633 2276 4.724279 AGTACAACCCATTTCAAGGAGT 57.276 40.909 0.00 0.00 0.00 3.85
1649 2292 7.118101 CGGGTAAAACACTAAGCAATAAGTACA 59.882 37.037 0.00 0.00 0.00 2.90
1713 2356 3.706373 GGAAGAGTCCTGCGCCCA 61.706 66.667 4.18 0.00 41.24 5.36
1850 2994 3.749064 GGCTGCTGTCTCGTCGGA 61.749 66.667 0.00 0.00 0.00 4.55
2009 3155 5.698545 GCAGAAGTCAAAGTTCAGACTGTAT 59.301 40.000 10.62 0.00 43.88 2.29
2118 3266 7.340999 GCACAAGGTTAAAAGGGAGGATTATAA 59.659 37.037 0.00 0.00 0.00 0.98
2485 3633 6.737254 ATACTGACAGGTTAAAATGGTTCG 57.263 37.500 7.51 0.00 0.00 3.95
2841 3991 9.368674 TGTAAAATGGAGCATTGAAACAATATG 57.631 29.630 0.00 0.00 34.04 1.78
2874 4024 4.942761 ACACAATTGCAGAACTTCCAAT 57.057 36.364 5.05 0.00 0.00 3.16
2946 4096 3.685058 GCTATCCGACAAACAAAGATGC 58.315 45.455 0.00 0.00 0.00 3.91
3102 4255 8.985315 AGATGGAGCAATTAATAATTCACTCA 57.015 30.769 18.97 10.72 34.82 3.41
3275 4428 6.823286 TCATCTTCTGGGTTATCACCATTA 57.177 37.500 0.00 0.00 46.43 1.90
3352 4832 8.421249 AATCAAAATCAAAAGGATGGACTACA 57.579 30.769 0.00 0.00 36.02 2.74
3526 5010 6.038936 TCAATTCGGTAGTGATTCGTCATCTA 59.961 38.462 0.00 0.00 32.34 1.98
3645 5129 7.723616 TCAAAATTCCCAACTAATGAGAGAACA 59.276 33.333 0.00 0.00 0.00 3.18
3683 5167 5.163343 ACTGTTAGCACAAGTTCTCTTACCA 60.163 40.000 0.00 0.00 30.36 3.25
3868 5452 3.704566 AGGGCAGTCGATTTGTGTCTATA 59.295 43.478 0.00 0.00 0.00 1.31
3935 5519 1.652947 GGTCCCAAACCCTCTAGTGA 58.347 55.000 0.00 0.00 42.85 3.41
3993 5577 2.925706 TTACCAGCGCACCAGGGA 60.926 61.111 11.47 0.00 0.00 4.20
4084 5670 1.071299 ATGACGCAGGCACAGACAA 59.929 52.632 0.00 0.00 0.00 3.18
4115 5701 6.678900 GCATGGAAGAAGAAAATGAAGCGTAT 60.679 38.462 0.00 0.00 0.00 3.06
4147 5733 9.434420 CCATGGAATGCTTTTTCTGTTTAAATA 57.566 29.630 5.56 0.00 44.97 1.40
4151 5737 5.306678 ACCCATGGAATGCTTTTTCTGTTTA 59.693 36.000 15.22 0.00 44.97 2.01
4216 5802 3.538591 GGATTTTACTGGGTAGGTTCCG 58.461 50.000 0.00 0.00 0.00 4.30
4218 5804 3.526430 AGGGGATTTTACTGGGTAGGTTC 59.474 47.826 0.00 0.00 0.00 3.62
4555 6159 2.417719 CCTGAGAACTAGCCACACAAC 58.582 52.381 0.00 0.00 0.00 3.32
4623 6227 9.787435 TTTGGTTAGAGTTACACAACTTATGAT 57.213 29.630 0.00 0.00 45.18 2.45
4624 6228 9.787435 ATTTGGTTAGAGTTACACAACTTATGA 57.213 29.630 0.00 0.00 45.18 2.15
4625 6229 9.825972 CATTTGGTTAGAGTTACACAACTTATG 57.174 33.333 0.00 0.00 45.18 1.90
4626 6230 8.512138 GCATTTGGTTAGAGTTACACAACTTAT 58.488 33.333 0.00 0.00 45.18 1.73
4627 6231 7.717875 AGCATTTGGTTAGAGTTACACAACTTA 59.282 33.333 0.00 0.00 45.18 2.24
4629 6233 6.546034 AAGCATTTGGTTAGAGTTACACAACT 59.454 34.615 0.00 0.00 39.71 3.16
4630 6234 6.313744 AGCATTTGGTTAGAGTTACACAAC 57.686 37.500 0.00 0.00 34.67 3.32
4859 6463 7.972277 TGATACTCTACAATTTCACGTAGGAAC 59.028 37.037 0.00 0.00 36.55 3.62
4964 6568 2.936912 GCGAGCAGACACAGGAGGT 61.937 63.158 0.00 0.00 0.00 3.85
4970 6574 2.029518 CCAGTGCGAGCAGACACA 59.970 61.111 0.00 0.00 39.30 3.72
4972 6576 4.687215 GCCCAGTGCGAGCAGACA 62.687 66.667 0.00 0.00 0.00 3.41
5044 6648 3.338250 GGGTGGATGTGGAGGCCA 61.338 66.667 5.01 0.00 0.00 5.36
5058 6662 1.981495 CAGAGAAGGTTCCAGAAGGGT 59.019 52.381 0.00 0.00 38.11 4.34
5081 6685 2.297701 GTCTTTGGAGAAACTGGCACA 58.702 47.619 0.00 0.00 32.66 4.57
5096 6700 2.038557 TGAAGCCCTAGAAAGCGTCTTT 59.961 45.455 13.31 4.80 38.18 2.52
5109 6713 2.592102 TTGCTTTGAGATGAAGCCCT 57.408 45.000 6.40 0.00 46.85 5.19
5154 6758 3.818773 CCATCTTTACCTGTTGAACGGTT 59.181 43.478 14.87 0.00 34.76 4.44
5397 7001 2.083774 TGCACCTTGAATTTAGCCTCG 58.916 47.619 0.00 0.00 0.00 4.63
5403 7007 3.005261 ACACGCAATGCACCTTGAATTTA 59.995 39.130 5.91 0.00 0.00 1.40
5485 7089 7.219535 GCTTGCTTGATGAACATTACATAACTG 59.780 37.037 0.00 0.00 0.00 3.16
5516 7120 2.859165 TTTCAGGCACTCGGAGATTT 57.141 45.000 12.86 0.00 34.60 2.17
5537 7141 1.965930 GCGTCATGTGCCAACAGGA 60.966 57.895 0.00 0.00 44.42 3.86
5590 7194 5.172460 TGATTTCGATGGTGCATTACATG 57.828 39.130 6.28 0.00 0.00 3.21
5613 7217 2.678336 GTGGTACCTGCTTGATACTTGC 59.322 50.000 14.36 0.00 0.00 4.01
5696 7300 4.157656 TGGATGCCAAAAATAGTTCTTCCG 59.842 41.667 0.00 0.00 0.00 4.30
5733 7337 4.295051 GCATACAAAACGAGCTGGAAAAA 58.705 39.130 1.44 0.00 0.00 1.94
5748 7353 1.889829 CCAAAAGAACGGGGCATACAA 59.110 47.619 0.00 0.00 0.00 2.41
5749 7354 1.202952 ACCAAAAGAACGGGGCATACA 60.203 47.619 0.00 0.00 0.00 2.29
5795 7400 5.877012 ACTGATCTGCATTACGTGAAGAAAT 59.123 36.000 0.00 0.00 45.73 2.17
5832 7437 3.368843 CCTTGATCCACGACACTCATTCT 60.369 47.826 0.00 0.00 0.00 2.40
5852 7457 1.675641 GCATCTGCAACCGAACCCT 60.676 57.895 0.00 0.00 41.59 4.34
5910 7515 2.814336 GGTGGAGATGTTTGGAACTCAC 59.186 50.000 0.00 0.00 0.00 3.51
5942 7549 7.938140 TCAAGAAAATTCGTTCCTAATGGAT 57.062 32.000 0.00 0.00 42.81 3.41
6046 7668 1.107538 TCGGAGATGACCTAAGGGCG 61.108 60.000 0.00 0.00 35.63 6.13
6066 7688 3.588891 GAAAGTTTGCGGGTCGGCG 62.589 63.158 0.00 0.00 35.06 6.46
6072 7694 0.313987 GGTTGAGGAAAGTTTGCGGG 59.686 55.000 1.08 0.00 0.00 6.13
6081 7703 0.754472 AGTCCGAACGGTTGAGGAAA 59.246 50.000 14.02 0.00 34.17 3.13
6083 7705 0.883833 GTAGTCCGAACGGTTGAGGA 59.116 55.000 12.93 9.75 36.47 3.71
6084 7706 0.455633 CGTAGTCCGAACGGTTGAGG 60.456 60.000 12.93 1.64 39.56 3.86


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

AutoCloner maintained by Alex Coulton.