Multiple sequence alignment - TraesCS2A01G148200

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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 TraesCS2A01G148200 chr2A 100.000 3652 0 0 1 3652 94289344 94292995 0.000000e+00 6745.0
1 TraesCS2A01G148200 chr2A 80.663 362 65 4 1974 2334 95259856 95260213 3.590000e-70 276.0
2 TraesCS2A01G148200 chr2A 94.737 57 3 0 1751 1807 90030228 90030172 5.020000e-14 89.8
3 TraesCS2A01G148200 chr2D 90.531 3559 223 53 140 3649 95771181 95774674 0.000000e+00 4601.0
4 TraesCS2A01G148200 chr2D 79.501 361 71 2 1974 2334 96775488 96775845 1.680000e-63 254.0
5 TraesCS2A01G148200 chr2D 98.837 86 1 0 1 86 95771077 95771162 1.760000e-33 154.0
6 TraesCS2A01G148200 chr2B 88.964 2809 177 71 102 2861 147489988 147492712 0.000000e+00 3347.0
7 TraesCS2A01G148200 chr2B 88.616 773 67 16 2871 3630 147492867 147493631 0.000000e+00 920.0
8 TraesCS2A01G148200 chrUn 79.063 363 69 5 1974 2334 17365208 17365565 3.640000e-60 243.0
9 TraesCS2A01G148200 chr3D 74.161 596 118 33 1716 2295 418875925 418876500 7.940000e-52 215.0
10 TraesCS2A01G148200 chr3D 74.161 596 118 33 1716 2295 418891224 418891799 7.940000e-52 215.0
11 TraesCS2A01G148200 chr3A 72.471 603 128 31 1715 2304 531702356 531701779 3.770000e-35 159.0
12 TraesCS2A01G148200 chr3A 97.778 45 1 0 1763 1807 531944557 531944513 1.090000e-10 78.7
13 TraesCS2A01G148200 chr3B 81.818 121 16 2 1693 1807 545384297 545384417 3.000000e-16 97.1
14 TraesCS2A01G148200 chr4A 94.444 54 3 0 1754 1807 544381229 544381282 2.340000e-12 84.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G148200 chr2A 94289344 94292995 3651 False 6745.0 6745 100.000 1 3652 1 chr2A.!!$F1 3651
1 TraesCS2A01G148200 chr2D 95771077 95774674 3597 False 2377.5 4601 94.684 1 3649 2 chr2D.!!$F2 3648
2 TraesCS2A01G148200 chr2B 147489988 147493631 3643 False 2133.5 3347 88.790 102 3630 2 chr2B.!!$F1 3528
3 TraesCS2A01G148200 chr3D 418875925 418876500 575 False 215.0 215 74.161 1716 2295 1 chr3D.!!$F1 579
4 TraesCS2A01G148200 chr3D 418891224 418891799 575 False 215.0 215 74.161 1716 2295 1 chr3D.!!$F2 579

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
363 364 0.107017 AAGCAACTGGCCGCTGATAT 60.107 50.0 3.43 0.0 46.50 1.63 F
1360 1405 0.108615 CCCTAGTCCAAGCGTGTCTG 60.109 60.0 0.00 0.0 0.00 3.51 F
1449 1494 0.176680 CATTGAGCCCGAGCACTACT 59.823 55.0 0.00 0.0 43.56 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1631 1676 0.393132 GCTTGGGCTGGGAGAGTTAC 60.393 60.000 0.00 0.0 35.22 2.50 R
2607 2668 0.895530 TTCTTCCTGATCTCGCCGTT 59.104 50.000 0.00 0.0 0.00 4.44 R
3236 3463 1.132453 CTGACCATTCTACTCGCGTGA 59.868 52.381 16.04 0.0 0.00 4.35 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 7.655236 CAAATTCATTTAAGGTCACATTGCA 57.345 32.000 0.00 0.00 0.00 4.08
86 87 0.324943 ACGACAAAGTGGATCCCTGG 59.675 55.000 9.90 5.17 0.00 4.45
88 89 1.002134 ACAAAGTGGATCCCTGGCG 60.002 57.895 9.90 0.00 0.00 5.69
89 90 1.299648 CAAAGTGGATCCCTGGCGA 59.700 57.895 9.90 0.00 0.00 5.54
90 91 0.322456 CAAAGTGGATCCCTGGCGAA 60.322 55.000 9.90 0.00 0.00 4.70
91 92 0.625849 AAAGTGGATCCCTGGCGAAT 59.374 50.000 9.90 0.00 0.00 3.34
92 93 0.181350 AAGTGGATCCCTGGCGAATC 59.819 55.000 9.90 0.00 0.00 2.52
93 94 1.227973 GTGGATCCCTGGCGAATCC 60.228 63.158 9.90 11.84 0.00 3.01
94 95 1.384502 TGGATCCCTGGCGAATCCT 60.385 57.895 9.90 0.00 35.26 3.24
95 96 1.072159 GGATCCCTGGCGAATCCTG 59.928 63.158 0.00 0.00 35.26 3.86
96 97 1.599240 GATCCCTGGCGAATCCTGC 60.599 63.158 0.00 0.00 35.26 4.85
97 98 3.466791 ATCCCTGGCGAATCCTGCG 62.467 63.158 0.00 0.00 35.26 5.18
121 122 4.293648 CGTCTGGTGGGTGCGTCA 62.294 66.667 0.00 0.00 0.00 4.35
122 123 2.110213 GTCTGGTGGGTGCGTCAA 59.890 61.111 0.00 0.00 0.00 3.18
123 124 1.525077 GTCTGGTGGGTGCGTCAAA 60.525 57.895 0.00 0.00 0.00 2.69
124 125 1.525077 TCTGGTGGGTGCGTCAAAC 60.525 57.895 0.00 0.00 0.00 2.93
125 126 2.517402 TGGTGGGTGCGTCAAACC 60.517 61.111 0.00 0.00 36.94 3.27
150 151 4.619973 CACTGCAGCTTGGTTTTATTTCA 58.380 39.130 15.27 0.00 0.00 2.69
153 154 3.640967 TGCAGCTTGGTTTTATTTCACCT 59.359 39.130 0.00 0.00 33.76 4.00
164 165 6.018262 GGTTTTATTTCACCTTTCCTTTGTGC 60.018 38.462 0.00 0.00 0.00 4.57
205 206 4.421058 GCACGACATACACATCTTACTCA 58.579 43.478 0.00 0.00 0.00 3.41
342 343 3.626217 GGCCAAAACTACGCTAAGCTAAT 59.374 43.478 0.00 0.00 0.00 1.73
343 344 4.095932 GGCCAAAACTACGCTAAGCTAATT 59.904 41.667 0.00 0.00 0.00 1.40
344 345 5.295045 GGCCAAAACTACGCTAAGCTAATTA 59.705 40.000 0.00 0.00 0.00 1.40
345 346 6.183360 GGCCAAAACTACGCTAAGCTAATTAA 60.183 38.462 0.00 0.00 0.00 1.40
357 358 2.475200 CTAATTAAGCAACTGGCCGC 57.525 50.000 0.00 0.00 46.50 6.53
359 360 0.527565 AATTAAGCAACTGGCCGCTG 59.472 50.000 3.43 0.00 46.50 5.18
360 361 0.322456 ATTAAGCAACTGGCCGCTGA 60.322 50.000 3.43 0.00 46.50 4.26
361 362 0.322456 TTAAGCAACTGGCCGCTGAT 60.322 50.000 3.43 0.00 46.50 2.90
362 363 0.539518 TAAGCAACTGGCCGCTGATA 59.460 50.000 3.43 0.00 46.50 2.15
363 364 0.107017 AAGCAACTGGCCGCTGATAT 60.107 50.000 3.43 0.00 46.50 1.63
364 365 0.758734 AGCAACTGGCCGCTGATATA 59.241 50.000 1.67 0.00 46.50 0.86
365 366 1.151668 GCAACTGGCCGCTGATATAG 58.848 55.000 0.00 0.00 36.11 1.31
386 387 2.480244 GCTAGCATAGGCAAAAGCCAAC 60.480 50.000 10.63 0.00 44.61 3.77
389 390 1.672737 GCATAGGCAAAAGCCAACACC 60.673 52.381 9.42 0.00 40.72 4.16
404 405 1.549203 ACACCATGACATTTGGAGCC 58.451 50.000 1.99 0.00 37.69 4.70
412 413 2.017049 GACATTTGGAGCCGCTACAAT 58.983 47.619 18.89 4.16 33.96 2.71
416 417 2.192664 TTGGAGCCGCTACAATTCAA 57.807 45.000 14.38 0.00 28.11 2.69
420 421 2.414161 GGAGCCGCTACAATTCAACAAC 60.414 50.000 0.00 0.00 0.00 3.32
529 538 6.716628 ACCGATCAATGCATCCATTTTAGTAT 59.283 34.615 0.00 0.00 39.60 2.12
531 540 7.094677 CCGATCAATGCATCCATTTTAGTATCA 60.095 37.037 0.00 0.00 39.60 2.15
559 568 6.992063 TTCTACTTGAATCAATGAGGAAGC 57.008 37.500 0.00 0.00 0.00 3.86
604 613 0.439600 GTTTTGTACGCGGCGTGTAT 59.560 50.000 35.53 13.37 41.39 2.29
626 635 8.255206 TGTATTACACACTTACAACCATCCTAG 58.745 37.037 0.00 0.00 30.04 3.02
693 702 7.162082 ACGATGATTATTCCCCATCTAGTTTC 58.838 38.462 0.00 0.00 35.71 2.78
717 726 3.798646 CAAATGATTGCGTGCCAGT 57.201 47.368 0.00 0.00 0.00 4.00
849 863 4.129148 AGGCTTCCCCGGATTGCC 62.129 66.667 0.73 11.44 41.28 4.52
926 940 2.104530 GGTCGTAGCTCTTCGCCC 59.895 66.667 0.00 0.00 40.39 6.13
980 996 2.596904 ACACAGTTACGAACAGCAGT 57.403 45.000 0.00 0.00 0.00 4.40
1009 1027 2.167281 GCAGTAGCTGAGATGGTGAAGA 59.833 50.000 0.00 0.00 37.91 2.87
1041 1059 4.617520 TTGCTCGCGTTGCTGGGA 62.618 61.111 22.18 4.91 0.00 4.37
1071 1089 2.174334 CCAAGGTGACAATGGCTCG 58.826 57.895 0.00 0.00 33.58 5.03
1096 1135 0.527817 GGAGTCACCGGCGTATTCTG 60.528 60.000 6.01 0.00 0.00 3.02
1134 1173 3.462021 GAGCTTGAAGGCGATCAGTTAT 58.538 45.455 0.00 0.00 37.29 1.89
1140 1179 2.088104 AGGCGATCAGTTATCCTCCA 57.912 50.000 0.00 0.00 0.00 3.86
1142 1181 1.001406 GGCGATCAGTTATCCTCCAGG 59.999 57.143 0.00 0.00 0.00 4.45
1146 1185 1.204146 TCAGTTATCCTCCAGGTGCC 58.796 55.000 0.00 0.00 36.34 5.01
1219 1264 0.179015 TCAGCCTCCTAGTCCTAGCG 60.179 60.000 0.00 0.00 31.95 4.26
1295 1340 2.202676 CGCTCTTCCTCCGTCTGC 60.203 66.667 0.00 0.00 0.00 4.26
1360 1405 0.108615 CCCTAGTCCAAGCGTGTCTG 60.109 60.000 0.00 0.00 0.00 3.51
1403 1448 0.905357 CCTGACCCAAGTCCACCTAG 59.095 60.000 0.00 0.00 42.81 3.02
1405 1450 1.550976 CTGACCCAAGTCCACCTAGTC 59.449 57.143 0.00 0.00 42.81 2.59
1410 1455 2.472029 CCAAGTCCACCTAGTCATCCT 58.528 52.381 0.00 0.00 0.00 3.24
1411 1456 2.432510 CCAAGTCCACCTAGTCATCCTC 59.567 54.545 0.00 0.00 0.00 3.71
1413 1458 1.933765 AGTCCACCTAGTCATCCTCCT 59.066 52.381 0.00 0.00 0.00 3.69
1414 1459 3.132056 AGTCCACCTAGTCATCCTCCTA 58.868 50.000 0.00 0.00 0.00 2.94
1415 1460 3.117436 AGTCCACCTAGTCATCCTCCTAC 60.117 52.174 0.00 0.00 0.00 3.18
1416 1461 2.177233 TCCACCTAGTCATCCTCCTACC 59.823 54.545 0.00 0.00 0.00 3.18
1417 1462 2.091278 CCACCTAGTCATCCTCCTACCA 60.091 54.545 0.00 0.00 0.00 3.25
1418 1463 3.438668 CCACCTAGTCATCCTCCTACCAT 60.439 52.174 0.00 0.00 0.00 3.55
1431 1476 1.843851 CCTACCATTAGTCCAAGCCCA 59.156 52.381 0.00 0.00 0.00 5.36
1446 1491 2.270205 CCATTGAGCCCGAGCACT 59.730 61.111 0.00 0.00 43.56 4.40
1447 1492 1.522092 CCATTGAGCCCGAGCACTA 59.478 57.895 0.00 0.00 43.56 2.74
1448 1493 0.811616 CCATTGAGCCCGAGCACTAC 60.812 60.000 0.00 0.00 43.56 2.73
1449 1494 0.176680 CATTGAGCCCGAGCACTACT 59.823 55.000 0.00 0.00 43.56 2.57
1486 1531 2.438434 CAAGCCCTAGCCAACCCG 60.438 66.667 0.00 0.00 41.25 5.28
1493 1538 0.687354 CCTAGCCAACCCGCATATCT 59.313 55.000 0.00 0.00 0.00 1.98
1521 1566 1.027357 CAAGCCCGATCAATCCAAGG 58.973 55.000 0.00 0.00 0.00 3.61
1534 1579 0.251742 TCCAAGGCAACCCAATCCTG 60.252 55.000 0.00 0.00 37.17 3.86
1535 1580 1.593265 CAAGGCAACCCAATCCTGC 59.407 57.895 0.00 0.00 35.28 4.85
1538 1583 3.291611 GCAACCCAATCCTGCCAG 58.708 61.111 0.00 0.00 0.00 4.85
1539 1584 3.010413 GCAACCCAATCCTGCCAGC 62.010 63.158 0.00 0.00 0.00 4.85
1542 1587 3.747579 CCCAATCCTGCCAGCCCT 61.748 66.667 0.00 0.00 0.00 5.19
1549 1594 2.446610 CTGCCAGCCCTAGCCCTA 60.447 66.667 0.00 0.00 41.25 3.53
1558 1603 1.403687 CCCTAGCCCTAGTCCAGCAC 61.404 65.000 1.99 0.00 0.00 4.40
1560 1605 1.739338 CTAGCCCTAGTCCAGCACCG 61.739 65.000 0.00 0.00 0.00 4.94
1567 1612 3.323979 CCCTAGTCCAGCACCGTATATTT 59.676 47.826 0.00 0.00 0.00 1.40
1581 1626 3.244422 CGTATATTTCAAGCCCTAGCCCA 60.244 47.826 0.00 0.00 41.25 5.36
1629 1674 1.073706 TCCAGCCCCTTATCCTCCC 60.074 63.158 0.00 0.00 0.00 4.30
1631 1676 1.422161 CCAGCCCCTTATCCTCCCAG 61.422 65.000 0.00 0.00 0.00 4.45
1632 1677 0.695803 CAGCCCCTTATCCTCCCAGT 60.696 60.000 0.00 0.00 0.00 4.00
1638 1686 3.375430 CCCCTTATCCTCCCAGTAACTCT 60.375 52.174 0.00 0.00 0.00 3.24
1647 1695 0.909610 CCAGTAACTCTCCCAGCCCA 60.910 60.000 0.00 0.00 0.00 5.36
1648 1696 0.984230 CAGTAACTCTCCCAGCCCAA 59.016 55.000 0.00 0.00 0.00 4.12
1649 1697 1.065854 CAGTAACTCTCCCAGCCCAAG 60.066 57.143 0.00 0.00 0.00 3.61
1650 1698 0.393132 GTAACTCTCCCAGCCCAAGC 60.393 60.000 0.00 0.00 40.32 4.01
1651 1699 0.840288 TAACTCTCCCAGCCCAAGCA 60.840 55.000 0.00 0.00 43.56 3.91
1652 1700 2.045536 CTCTCCCAGCCCAAGCAC 60.046 66.667 0.00 0.00 43.56 4.40
1653 1701 2.530151 TCTCCCAGCCCAAGCACT 60.530 61.111 0.00 0.00 43.56 4.40
1654 1702 2.045536 CTCCCAGCCCAAGCACTC 60.046 66.667 0.00 0.00 43.56 3.51
1655 1703 3.635268 CTCCCAGCCCAAGCACTCC 62.635 68.421 0.00 0.00 43.56 3.85
1656 1704 4.748144 CCCAGCCCAAGCACTCCC 62.748 72.222 0.00 0.00 43.56 4.30
1658 1706 4.335647 CAGCCCAAGCACTCCCGT 62.336 66.667 0.00 0.00 43.56 5.28
1659 1707 3.570212 AGCCCAAGCACTCCCGTT 61.570 61.111 0.00 0.00 43.56 4.44
1660 1708 2.597510 GCCCAAGCACTCCCGTTT 60.598 61.111 0.00 0.00 39.53 3.60
1661 1709 2.626780 GCCCAAGCACTCCCGTTTC 61.627 63.158 0.00 0.00 39.53 2.78
1662 1710 1.228124 CCCAAGCACTCCCGTTTCA 60.228 57.895 0.00 0.00 0.00 2.69
1835 1883 3.129462 CCAGACGCTCACATCTCTTCTAA 59.871 47.826 0.00 0.00 0.00 2.10
2045 2106 2.203788 TGCCCCGGAGTTGTCTCT 60.204 61.111 0.73 0.00 40.29 3.10
2093 2154 1.004918 CGACGCCACCTTCTTCCTT 60.005 57.895 0.00 0.00 0.00 3.36
2214 2275 2.033141 GCCTCCAGCAGCTCAACA 59.967 61.111 0.00 0.00 42.97 3.33
2313 2374 4.351938 CGTCCTTCCACGACCGCA 62.352 66.667 0.00 0.00 42.69 5.69
2316 2377 2.511600 CCTTCCACGACCGCATCC 60.512 66.667 0.00 0.00 0.00 3.51
2528 2589 0.249489 GGATGGTGCTCGATAACGCT 60.249 55.000 0.00 0.00 39.58 5.07
2637 2698 2.910199 TCAGGAAGAAATGCTGGATCG 58.090 47.619 0.00 0.00 46.68 3.69
2724 2785 1.153978 CCACATTCGGCACATGCAC 60.154 57.895 6.15 0.00 44.36 4.57
2781 2850 5.885230 TTCAGACTAGGACATGCAAAATG 57.115 39.130 0.00 0.00 0.00 2.32
2788 2859 6.707290 ACTAGGACATGCAAAATGTAGTACA 58.293 36.000 5.24 5.24 31.52 2.90
2846 2917 8.837389 AGTGAGAAACTTGGAACTACAAAATAC 58.163 33.333 0.00 0.00 34.57 1.89
2847 2918 8.617809 GTGAGAAACTTGGAACTACAAAATACA 58.382 33.333 0.00 0.00 0.00 2.29
2855 2926 9.620660 CTTGGAACTACAAAATACATTTACACC 57.379 33.333 0.00 0.00 0.00 4.16
2892 3108 0.955428 TGGTTCTAGCGGCAAAGCAG 60.955 55.000 1.45 0.00 40.15 4.24
2929 3145 6.475402 CCAACCTTGTTTGTCTTTGTGAATAC 59.525 38.462 0.00 0.00 0.00 1.89
2980 3197 0.511653 GAAACTTGGACGCGGACTTC 59.488 55.000 12.47 0.00 0.00 3.01
2983 3200 1.289066 CTTGGACGCGGACTTCTGA 59.711 57.895 12.47 0.00 0.00 3.27
2995 3212 3.058224 CGGACTTCTGAAACATGGTTTCC 60.058 47.826 16.61 0.00 0.00 3.13
2996 3213 4.145052 GGACTTCTGAAACATGGTTTCCT 58.855 43.478 16.61 0.00 0.00 3.36
2997 3214 4.022849 GGACTTCTGAAACATGGTTTCCTG 60.023 45.833 16.61 10.84 0.00 3.86
3001 3218 4.144297 TCTGAAACATGGTTTCCTGGAAG 58.856 43.478 16.61 8.82 0.00 3.46
3006 3223 2.037367 GGTTTCCTGGAAGCCCCC 59.963 66.667 26.73 13.92 37.02 5.40
3007 3224 2.851045 GTTTCCTGGAAGCCCCCA 59.149 61.111 11.80 0.00 34.52 4.96
3009 3226 0.252239 GTTTCCTGGAAGCCCCCATT 60.252 55.000 11.80 0.00 35.33 3.16
3087 3309 7.341805 ACCATATATAGTCGACCGGTATACTT 58.658 38.462 22.44 14.19 0.00 2.24
3088 3310 7.281774 ACCATATATAGTCGACCGGTATACTTG 59.718 40.741 22.44 15.16 0.00 3.16
3089 3311 7.255035 CCATATATAGTCGACCGGTATACTTGG 60.255 44.444 22.44 19.03 0.00 3.61
3113 3335 9.308000 TGGGTATGAAGTTTTATGAAGAAATGT 57.692 29.630 0.00 0.00 0.00 2.71
3130 3352 8.459911 AAGAAATGTCATCATGATATTCTGCA 57.540 30.769 8.15 0.90 37.24 4.41
3153 3375 6.683708 GCACAAAAATGACAAAACTGATGTTG 59.316 34.615 0.00 0.00 36.39 3.33
3160 3382 8.721019 AATGACAAAACTGATGTTGAACAAAT 57.279 26.923 0.62 0.00 36.39 2.32
3168 3390 9.086336 AAACTGATGTTGAACAAATACTGTTTG 57.914 29.630 19.75 0.00 40.97 2.93
3225 3452 6.530019 AAATACAATGGGTGTCATTCCTTC 57.470 37.500 0.00 0.00 43.70 3.46
3228 3455 3.765511 ACAATGGGTGTCATTCCTTCATG 59.234 43.478 0.00 0.00 43.70 3.07
3229 3456 3.744940 ATGGGTGTCATTCCTTCATGT 57.255 42.857 0.00 0.00 30.55 3.21
3236 3463 5.940470 GGTGTCATTCCTTCATGTAACTTCT 59.060 40.000 0.00 0.00 0.00 2.85
3241 3468 3.585862 TCCTTCATGTAACTTCTCACGC 58.414 45.455 0.00 0.00 0.00 5.34
3274 3501 3.136626 GTCAGCCTAGTTTGATACCCCAT 59.863 47.826 0.00 0.00 0.00 4.00
3278 3505 6.102615 TCAGCCTAGTTTGATACCCCATAATT 59.897 38.462 0.00 0.00 0.00 1.40
3283 3510 9.367160 CCTAGTTTGATACCCCATAATTCAAAT 57.633 33.333 0.00 0.00 38.24 2.32
3359 3587 6.493115 TGAAACCATGTTCACCTCAATGTATT 59.507 34.615 0.00 0.00 32.56 1.89
3398 3627 9.296400 GTTTTAGTACTTTCAAGTTTGCAATCA 57.704 29.630 0.00 0.00 40.37 2.57
3404 3633 7.704789 ACTTTCAAGTTTGCAATCATTTCTC 57.295 32.000 10.05 0.00 35.21 2.87
3405 3634 6.703165 ACTTTCAAGTTTGCAATCATTTCTCC 59.297 34.615 10.05 0.00 35.21 3.71
3541 3772 1.419012 TCAGATCCAATAGCTGCCCTG 59.581 52.381 0.00 0.00 41.56 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 2.639286 CTGCAGTGCGGGTTTGAC 59.361 61.111 16.66 0.00 0.00 3.18
119 120 3.286751 GCTGCAGTGCGGGTTTGA 61.287 61.111 25.02 0.00 35.15 2.69
120 121 3.289834 AGCTGCAGTGCGGGTTTG 61.290 61.111 22.74 3.54 43.48 2.93
125 126 2.354074 AAAACCAAGCTGCAGTGCGG 62.354 55.000 20.08 20.08 38.13 5.69
126 127 0.310543 TAAAACCAAGCTGCAGTGCG 59.689 50.000 16.64 6.61 38.13 5.34
150 151 1.115326 GCCAGGCACAAAGGAAAGGT 61.115 55.000 6.55 0.00 0.00 3.50
153 154 0.968405 GATGCCAGGCACAAAGGAAA 59.032 50.000 19.10 0.00 43.04 3.13
227 228 1.890489 ACTACCACACTCGTGTATGCA 59.110 47.619 1.90 0.00 42.83 3.96
342 343 0.322456 ATCAGCGGCCAGTTGCTTAA 60.322 50.000 2.24 0.00 40.03 1.85
343 344 0.539518 TATCAGCGGCCAGTTGCTTA 59.460 50.000 2.24 0.00 40.03 3.09
344 345 0.107017 ATATCAGCGGCCAGTTGCTT 60.107 50.000 2.24 0.00 40.03 3.91
345 346 0.758734 TATATCAGCGGCCAGTTGCT 59.241 50.000 2.24 0.00 43.58 3.91
355 356 3.067320 TGCCTATGCTAGCTATATCAGCG 59.933 47.826 17.23 0.95 46.72 5.18
357 358 6.036953 GCTTTTGCCTATGCTAGCTATATCAG 59.963 42.308 17.23 3.87 40.15 2.90
359 360 6.356757 GCTTTTGCCTATGCTAGCTATATC 57.643 41.667 17.23 3.25 40.15 1.63
376 377 2.886862 TGTCATGGTGTTGGCTTTTG 57.113 45.000 0.00 0.00 0.00 2.44
386 387 0.452987 CGGCTCCAAATGTCATGGTG 59.547 55.000 0.00 0.00 39.09 4.17
389 390 1.331756 GTAGCGGCTCCAAATGTCATG 59.668 52.381 5.39 0.00 0.00 3.07
404 405 4.379082 GGGTAAGGTTGTTGAATTGTAGCG 60.379 45.833 0.00 0.00 0.00 4.26
473 476 2.307049 GTGTGTAAACAAGTGCATCGC 58.693 47.619 0.00 0.00 0.00 4.58
475 478 2.546368 TCGGTGTGTAAACAAGTGCATC 59.454 45.455 0.00 0.00 0.00 3.91
585 594 0.439600 ATACACGCCGCGTACAAAAC 59.560 50.000 19.71 0.00 38.32 2.43
604 613 6.675413 ACTAGGATGGTTGTAAGTGTGTAA 57.325 37.500 0.00 0.00 0.00 2.41
666 675 6.702329 ACTAGATGGGGAATAATCATCGTTC 58.298 40.000 0.00 0.00 41.35 3.95
667 676 6.688073 ACTAGATGGGGAATAATCATCGTT 57.312 37.500 0.00 0.00 41.35 3.85
668 677 6.688073 AACTAGATGGGGAATAATCATCGT 57.312 37.500 0.00 0.00 41.35 3.73
717 726 0.391228 TAATTGCTCCGCTATGCCGA 59.609 50.000 0.00 0.00 0.00 5.54
721 730 1.882912 TGCCTAATTGCTCCGCTATG 58.117 50.000 0.00 0.00 0.00 2.23
902 916 1.330213 GAAGAGCTACGACCGTCCTAC 59.670 57.143 0.00 0.00 0.00 3.18
926 940 2.549754 CAACTTGTGTGGCTGGACTAAG 59.450 50.000 0.00 0.00 0.00 2.18
962 978 3.897325 TCTACTGCTGTTCGTAACTGTG 58.103 45.455 0.09 0.00 33.43 3.66
996 1012 0.103026 CGGCGATCTTCACCATCTCA 59.897 55.000 0.00 0.00 0.00 3.27
1123 1162 1.689273 ACCTGGAGGATAACTGATCGC 59.311 52.381 0.00 0.00 38.94 4.58
1125 1164 2.224402 GGCACCTGGAGGATAACTGATC 60.224 54.545 0.00 0.00 38.94 2.92
1146 1185 4.387343 ATGGGTTGGCTGGGGCTG 62.387 66.667 0.00 0.00 38.73 4.85
1219 1264 4.849329 CGGTGCGCCTAGGTCGAC 62.849 72.222 23.94 7.13 0.00 4.20
1241 1286 1.079336 GGATATACCGGCGGGCTTC 60.079 63.158 31.78 19.65 36.48 3.86
1269 1314 2.747855 GGAAGAGCGGGTTGGCTG 60.748 66.667 0.00 0.00 44.93 4.85
1295 1340 1.078848 CTCGGGGCACTGGAAGAAG 60.079 63.158 0.00 0.00 37.43 2.85
1360 1405 0.406361 TATGTGGGTGGGGTTTGACC 59.594 55.000 0.00 0.00 37.60 4.02
1403 1448 4.223953 TGGACTAATGGTAGGAGGATGAC 58.776 47.826 0.00 0.00 0.00 3.06
1405 1450 4.503991 GCTTGGACTAATGGTAGGAGGATG 60.504 50.000 0.00 0.00 0.00 3.51
1410 1455 2.124411 GGGCTTGGACTAATGGTAGGA 58.876 52.381 0.00 0.00 0.00 2.94
1411 1456 1.843851 TGGGCTTGGACTAATGGTAGG 59.156 52.381 0.00 0.00 0.00 3.18
1413 1458 3.525609 TCAATGGGCTTGGACTAATGGTA 59.474 43.478 0.00 0.00 35.43 3.25
1414 1459 2.311542 TCAATGGGCTTGGACTAATGGT 59.688 45.455 0.00 0.00 35.43 3.55
1415 1460 2.954318 CTCAATGGGCTTGGACTAATGG 59.046 50.000 0.00 0.00 35.43 3.16
1416 1461 2.360165 GCTCAATGGGCTTGGACTAATG 59.640 50.000 0.00 0.00 35.43 1.90
1417 1462 2.659428 GCTCAATGGGCTTGGACTAAT 58.341 47.619 0.00 0.00 35.43 1.73
1418 1463 1.340991 GGCTCAATGGGCTTGGACTAA 60.341 52.381 4.63 0.00 35.43 2.24
1431 1476 1.776662 TAGTAGTGCTCGGGCTCAAT 58.223 50.000 9.62 0.00 39.59 2.57
1446 1491 3.006537 GGCTCGGTGGATAAGCAATAGTA 59.993 47.826 0.00 0.00 37.78 1.82
1447 1492 2.224305 GGCTCGGTGGATAAGCAATAGT 60.224 50.000 0.00 0.00 37.78 2.12
1448 1493 2.417719 GGCTCGGTGGATAAGCAATAG 58.582 52.381 0.00 0.00 37.78 1.73
1449 1494 1.071699 GGGCTCGGTGGATAAGCAATA 59.928 52.381 0.00 0.00 37.78 1.90
1486 1531 2.431454 GCTTGGGCTAGGAAGATATGC 58.569 52.381 0.00 0.00 35.22 3.14
1493 1538 1.692749 ATCGGGCTTGGGCTAGGAA 60.693 57.895 0.00 0.00 38.73 3.36
1521 1566 3.010413 GCTGGCAGGATTGGGTTGC 62.010 63.158 17.64 0.00 37.11 4.17
1534 1579 2.446802 ACTAGGGCTAGGGCTGGC 60.447 66.667 0.00 0.00 37.49 4.85
1535 1580 1.839296 GGACTAGGGCTAGGGCTGG 60.839 68.421 0.00 0.00 37.49 4.85
1536 1581 1.075226 TGGACTAGGGCTAGGGCTG 60.075 63.158 0.00 0.00 37.49 4.85
1537 1582 1.234529 CTGGACTAGGGCTAGGGCT 59.765 63.158 0.00 0.00 37.49 5.19
1538 1583 2.512355 GCTGGACTAGGGCTAGGGC 61.512 68.421 0.00 0.00 37.49 5.19
1539 1584 1.075226 TGCTGGACTAGGGCTAGGG 60.075 63.158 0.00 0.00 37.49 3.53
1542 1587 1.756950 CGGTGCTGGACTAGGGCTA 60.757 63.158 0.00 0.00 0.00 3.93
1548 1593 5.597806 CTTGAAATATACGGTGCTGGACTA 58.402 41.667 0.00 0.00 0.00 2.59
1549 1594 4.442706 CTTGAAATATACGGTGCTGGACT 58.557 43.478 0.00 0.00 0.00 3.85
1558 1603 3.335579 GGCTAGGGCTTGAAATATACGG 58.664 50.000 0.00 0.00 38.73 4.02
1560 1605 4.367039 TGGGCTAGGGCTTGAAATATAC 57.633 45.455 0.00 0.00 38.73 1.47
1567 1612 2.677228 GCTTGGGCTAGGGCTTGA 59.323 61.111 0.00 0.00 38.73 3.02
1587 1632 2.919043 CTATCCGGGCTTGGGCTT 59.081 61.111 0.00 0.00 38.73 4.35
1629 1674 0.984230 TTGGGCTGGGAGAGTTACTG 59.016 55.000 0.00 0.00 0.00 2.74
1631 1676 0.393132 GCTTGGGCTGGGAGAGTTAC 60.393 60.000 0.00 0.00 35.22 2.50
1632 1677 0.840288 TGCTTGGGCTGGGAGAGTTA 60.840 55.000 0.00 0.00 39.59 2.24
1638 1686 3.650950 GGAGTGCTTGGGCTGGGA 61.651 66.667 0.00 0.00 39.59 4.37
1647 1695 4.800554 CCTGAAACGGGAGTGCTT 57.199 55.556 0.00 0.00 46.69 3.91
1655 1703 0.951040 GACACTGAGCCCTGAAACGG 60.951 60.000 0.00 0.00 0.00 4.44
1656 1704 1.284982 CGACACTGAGCCCTGAAACG 61.285 60.000 0.00 0.00 0.00 3.60
1657 1705 0.951040 CCGACACTGAGCCCTGAAAC 60.951 60.000 0.00 0.00 0.00 2.78
1658 1706 1.371183 CCGACACTGAGCCCTGAAA 59.629 57.895 0.00 0.00 0.00 2.69
1659 1707 1.816863 GACCGACACTGAGCCCTGAA 61.817 60.000 0.00 0.00 0.00 3.02
1660 1708 2.203640 ACCGACACTGAGCCCTGA 60.204 61.111 0.00 0.00 0.00 3.86
1661 1709 2.262915 GACCGACACTGAGCCCTG 59.737 66.667 0.00 0.00 0.00 4.45
1662 1710 2.203640 TGACCGACACTGAGCCCT 60.204 61.111 0.00 0.00 0.00 5.19
1710 1758 1.746615 CACGGCCTCCCTGACAATG 60.747 63.158 0.00 0.00 0.00 2.82
1739 1787 2.174319 GTGCCGCGATTCTTCTCCC 61.174 63.158 8.23 0.00 0.00 4.30
1851 1899 5.584649 CACGTAAGAATGGAGGAATGCTTAA 59.415 40.000 0.00 0.00 43.62 1.85
1894 1949 1.817099 GAAGCATCGCACCCCTGAG 60.817 63.158 0.00 0.00 0.00 3.35
1943 1998 2.035442 GCCCTTCAACTCTGTCGGC 61.035 63.158 0.00 0.00 0.00 5.54
1946 2004 1.376037 CGGGCCCTTCAACTCTGTC 60.376 63.158 22.43 0.00 0.00 3.51
2036 2097 0.597637 CGTCCGCACAAGAGACAACT 60.598 55.000 0.00 0.00 0.00 3.16
2214 2275 1.302832 CCTTGGCGTGGAAGCTCTT 60.303 57.895 0.00 0.00 37.29 2.85
2364 2425 4.104417 GCTGCTGCTGCACTGCTC 62.104 66.667 23.99 3.91 45.31 4.26
2388 2449 2.166130 TTGAAGTCCTGCATCGCCGA 62.166 55.000 0.00 0.00 0.00 5.54
2591 2652 2.664851 TTGGCGCTGGTCTTGACG 60.665 61.111 7.64 0.00 0.00 4.35
2607 2668 0.895530 TTCTTCCTGATCTCGCCGTT 59.104 50.000 0.00 0.00 0.00 4.44
2637 2698 2.534150 CGACACGTCACACTTTGTTGAC 60.534 50.000 0.00 0.00 0.00 3.18
2684 2745 3.624861 GCATCGAACAATTCATGAGACCT 59.375 43.478 0.00 0.00 0.00 3.85
2724 2785 2.346099 AAAAATCATCACCAACGGCG 57.654 45.000 4.80 4.80 0.00 6.46
2781 2850 9.612620 CAAAAGAATTCCAAACAGATGTACTAC 57.387 33.333 0.65 0.00 0.00 2.73
2788 2859 4.039124 ACGCCAAAAGAATTCCAAACAGAT 59.961 37.500 0.65 0.00 0.00 2.90
2864 2935 2.158943 GCCGCTAGAACCAATAGAACCT 60.159 50.000 0.00 0.00 0.00 3.50
2865 2936 2.210961 GCCGCTAGAACCAATAGAACC 58.789 52.381 0.00 0.00 0.00 3.62
2866 2937 2.901249 TGCCGCTAGAACCAATAGAAC 58.099 47.619 0.00 0.00 0.00 3.01
2867 2938 3.620427 TTGCCGCTAGAACCAATAGAA 57.380 42.857 0.00 0.00 0.00 2.10
2868 2939 3.531538 CTTTGCCGCTAGAACCAATAGA 58.468 45.455 0.00 0.00 0.00 1.98
2869 2940 2.032178 GCTTTGCCGCTAGAACCAATAG 59.968 50.000 0.00 0.00 0.00 1.73
2892 3108 7.836842 ACAAACAAGGTTGGAATATTATGGTC 58.163 34.615 2.59 0.00 32.50 4.02
2929 3145 9.627395 CTACCTAAGTATTCAAATGATACTCCG 57.373 37.037 0.00 0.00 31.39 4.63
2945 3162 7.176340 GTCCAAGTTTCAGTCTCTACCTAAGTA 59.824 40.741 0.00 0.00 0.00 2.24
2980 3197 3.305608 GCTTCCAGGAAACCATGTTTCAG 60.306 47.826 18.32 11.37 0.00 3.02
2983 3200 1.970640 GGCTTCCAGGAAACCATGTTT 59.029 47.619 15.91 0.00 29.16 2.83
2995 3212 2.754012 TTCATAATGGGGGCTTCCAG 57.246 50.000 6.32 0.00 40.56 3.86
2996 3213 3.726859 ACTATTCATAATGGGGGCTTCCA 59.273 43.478 2.90 2.90 41.60 3.53
2997 3214 4.388577 ACTATTCATAATGGGGGCTTCC 57.611 45.455 0.00 0.00 0.00 3.46
3001 3218 9.528489 TTAGAATTTACTATTCATAATGGGGGC 57.472 33.333 0.00 0.00 0.00 5.80
3087 3309 9.308000 ACATTTCTTCATAAAACTTCATACCCA 57.692 29.630 0.00 0.00 0.00 4.51
3088 3310 9.788960 GACATTTCTTCATAAAACTTCATACCC 57.211 33.333 0.00 0.00 0.00 3.69
3113 3335 8.688151 TCATTTTTGTGCAGAATATCATGATGA 58.312 29.630 18.72 0.00 0.00 2.92
3130 3352 8.442384 GTTCAACATCAGTTTTGTCATTTTTGT 58.558 29.630 0.00 0.00 35.28 2.83
3225 3452 2.596452 ACTCGCGTGAGAAGTTACATG 58.404 47.619 31.50 2.93 45.57 3.21
3228 3455 3.736530 TCTACTCGCGTGAGAAGTTAC 57.263 47.619 31.50 0.00 45.57 2.50
3229 3456 4.438336 CCATTCTACTCGCGTGAGAAGTTA 60.438 45.833 31.50 12.77 45.57 2.24
3236 3463 1.132453 CTGACCATTCTACTCGCGTGA 59.868 52.381 16.04 0.00 0.00 4.35
3241 3468 2.952978 ACTAGGCTGACCATTCTACTCG 59.047 50.000 0.00 0.00 39.06 4.18
3328 3556 3.387374 AGGTGAACATGGTTTCATTTGCA 59.613 39.130 0.00 0.00 37.80 4.08
3421 3651 2.040278 TGCAGCTCTCCTACATGGTTTT 59.960 45.455 0.00 0.00 37.07 2.43
3422 3652 1.630369 TGCAGCTCTCCTACATGGTTT 59.370 47.619 0.00 0.00 37.07 3.27
3469 3700 6.682746 TGTGTTGCTCTTAAAAACTTTGTCA 58.317 32.000 0.00 0.00 0.00 3.58
3477 3708 7.117092 GGTTCTTTGTTGTGTTGCTCTTAAAAA 59.883 33.333 0.00 0.00 0.00 1.94
3590 3821 4.935352 TTGTCATGCCTTAAAAAGCACT 57.065 36.364 0.00 0.00 42.84 4.40
3591 3822 6.202570 TCAATTTGTCATGCCTTAAAAAGCAC 59.797 34.615 0.00 0.00 42.84 4.40
3592 3823 6.286758 TCAATTTGTCATGCCTTAAAAAGCA 58.713 32.000 0.00 0.00 44.45 3.91
3593 3824 6.619232 GCTCAATTTGTCATGCCTTAAAAAGC 60.619 38.462 0.00 0.00 0.00 3.51
3594 3825 6.400303 CGCTCAATTTGTCATGCCTTAAAAAG 60.400 38.462 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.