Multiple sequence alignment - TraesCS6A01G382100

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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 TraesCS6A01G382100 chr6A 100.000 2743 0 0 1 2743 601257999 601255257 0.000000e+00 5066.0
1 TraesCS6A01G382100 chr6A 86.521 1328 94 34 648 1957 601241996 601240736 0.000000e+00 1382.0
2 TraesCS6A01G382100 chr6A 81.936 1157 161 30 846 1980 601264807 601263677 0.000000e+00 935.0
3 TraesCS6A01G382100 chr6A 79.755 1225 199 40 780 1964 602075402 602076617 0.000000e+00 843.0
4 TraesCS6A01G382100 chr6A 91.343 335 22 3 3 331 601242731 601242398 4.170000e-123 451.0
5 TraesCS6A01G382100 chr6A 89.097 321 26 6 317 632 601242377 601242061 9.210000e-105 390.0
6 TraesCS6A01G382100 chr6D 88.524 1551 130 18 436 1964 454968566 454967042 0.000000e+00 1834.0
7 TraesCS6A01G382100 chr6D 88.126 1078 108 9 892 1964 454962837 454961775 0.000000e+00 1264.0
8 TraesCS6A01G382100 chr6D 83.608 1153 158 20 846 1980 454996670 454995531 0.000000e+00 1053.0
9 TraesCS6A01G382100 chr6D 88.450 329 38 0 3 331 454969497 454969169 5.500000e-107 398.0
10 TraesCS6A01G382100 chr6D 90.110 91 4 2 317 407 454968648 454968563 2.230000e-21 113.0
11 TraesCS6A01G382100 chr6D 80.597 134 16 5 677 807 454982666 454982540 8.090000e-16 95.3
12 TraesCS6A01G382100 chr6B 86.862 1568 139 37 425 1964 692045261 692043733 0.000000e+00 1692.0
13 TraesCS6A01G382100 chr6B 86.147 1617 157 39 374 1964 691975596 691977171 0.000000e+00 1683.0
14 TraesCS6A01G382100 chr6B 81.762 1124 162 27 846 1947 691944768 691945870 0.000000e+00 900.0
15 TraesCS6A01G382100 chr6B 87.843 255 30 1 78 331 691974802 691975056 5.740000e-77 298.0
16 TraesCS6A01G382100 chr6B 86.275 255 34 1 78 331 692046929 692046675 2.690000e-70 276.0
17 TraesCS6A01G382100 chr6B 86.093 151 20 1 78 227 692051829 692051679 7.860000e-36 161.0
18 TraesCS6A01G382100 chr2B 93.139 685 44 2 2059 2741 415991805 415992488 0.000000e+00 1002.0
19 TraesCS6A01G382100 chr2B 91.959 684 53 2 2058 2741 53404406 53405087 0.000000e+00 957.0
20 TraesCS6A01G382100 chr5B 92.285 674 52 0 2070 2743 37977624 37976951 0.000000e+00 957.0
21 TraesCS6A01G382100 chr7A 90.816 686 61 2 2058 2743 733263024 733262341 0.000000e+00 917.0
22 TraesCS6A01G382100 chrUn 92.587 634 40 6 3 633 79445759 79445130 0.000000e+00 904.0
23 TraesCS6A01G382100 chrUn 87.577 652 54 18 638 1284 79445060 79444431 0.000000e+00 730.0
24 TraesCS6A01G382100 chrUn 84.986 706 91 10 1286 1980 79450182 79449481 0.000000e+00 702.0
25 TraesCS6A01G382100 chr2D 87.591 685 67 11 2059 2743 646079254 646079920 0.000000e+00 778.0
26 TraesCS6A01G382100 chr2A 87.187 679 70 10 2066 2743 773308991 773308329 0.000000e+00 756.0
27 TraesCS6A01G382100 chr2A 83.460 526 75 10 2066 2587 604989236 604988719 1.910000e-131 479.0
28 TraesCS6A01G382100 chr2A 94.253 87 5 0 2059 2145 420141262 420141176 1.710000e-27 134.0
29 TraesCS6A01G382100 chr5A 92.105 342 27 0 2272 2613 686500865 686501206 1.480000e-132 483.0
30 TraesCS6A01G382100 chr7B 90.179 112 10 1 2055 2166 749675073 749675183 7.920000e-31 145.0


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 TraesCS6A01G382100 chr6A 601255257 601257999 2742 True 5066.000000 5066 100.000000 1 2743 1 chr6A.!!$R1 2742
1 TraesCS6A01G382100 chr6A 601263677 601264807 1130 True 935.000000 935 81.936000 846 1980 1 chr6A.!!$R2 1134
2 TraesCS6A01G382100 chr6A 602075402 602076617 1215 False 843.000000 843 79.755000 780 1964 1 chr6A.!!$F1 1184
3 TraesCS6A01G382100 chr6A 601240736 601242731 1995 True 741.000000 1382 88.987000 3 1957 3 chr6A.!!$R3 1954
4 TraesCS6A01G382100 chr6D 454961775 454962837 1062 True 1264.000000 1264 88.126000 892 1964 1 chr6D.!!$R1 1072
5 TraesCS6A01G382100 chr6D 454995531 454996670 1139 True 1053.000000 1053 83.608000 846 1980 1 chr6D.!!$R3 1134
6 TraesCS6A01G382100 chr6D 454967042 454969497 2455 True 781.666667 1834 89.028000 3 1964 3 chr6D.!!$R4 1961
7 TraesCS6A01G382100 chr6B 691974802 691977171 2369 False 990.500000 1683 86.995000 78 1964 2 chr6B.!!$F2 1886
8 TraesCS6A01G382100 chr6B 692043733 692046929 3196 True 984.000000 1692 86.568500 78 1964 2 chr6B.!!$R2 1886
9 TraesCS6A01G382100 chr6B 691944768 691945870 1102 False 900.000000 900 81.762000 846 1947 1 chr6B.!!$F1 1101
10 TraesCS6A01G382100 chr2B 415991805 415992488 683 False 1002.000000 1002 93.139000 2059 2741 1 chr2B.!!$F2 682
11 TraesCS6A01G382100 chr2B 53404406 53405087 681 False 957.000000 957 91.959000 2058 2741 1 chr2B.!!$F1 683
12 TraesCS6A01G382100 chr5B 37976951 37977624 673 True 957.000000 957 92.285000 2070 2743 1 chr5B.!!$R1 673
13 TraesCS6A01G382100 chr7A 733262341 733263024 683 True 917.000000 917 90.816000 2058 2743 1 chr7A.!!$R1 685
14 TraesCS6A01G382100 chrUn 79444431 79450182 5751 True 778.666667 904 88.383333 3 1980 3 chrUn.!!$R1 1977
15 TraesCS6A01G382100 chr2D 646079254 646079920 666 False 778.000000 778 87.591000 2059 2743 1 chr2D.!!$F1 684
16 TraesCS6A01G382100 chr2A 773308329 773308991 662 True 756.000000 756 87.187000 2066 2743 1 chr2A.!!$R3 677
17 TraesCS6A01G382100 chr2A 604988719 604989236 517 True 479.000000 479 83.460000 2066 2587 1 chr2A.!!$R2 521

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
596 6845 0.249911 AGTGAACAGCTTCGTCCCAC 60.25 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 8802 0.535102 CCCTGTTGAAGGTGTCGCTT 60.535 55.0 0.0 0.0 45.78 4.68 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
31 4453 4.479993 GGAGCAGCAGACCCGCAT 62.480 66.667 0.00 0.00 0.00 4.73
32 4454 2.437359 GAGCAGCAGACCCGCATT 60.437 61.111 0.00 0.00 0.00 3.56
43 4465 1.675310 CCCGCATTCCTGCTCAACA 60.675 57.895 0.00 0.00 46.65 3.33
169 4598 1.068472 CAGTTAGACGACGGTGAGCTT 60.068 52.381 0.00 0.00 0.00 3.74
186 4616 0.519077 CTTTTCGGACAAGGCAGAGC 59.481 55.000 0.00 0.00 0.00 4.09
258 4688 1.679139 CCGGCCAGCTATTGATTTGA 58.321 50.000 2.24 0.00 0.00 2.69
420 6571 2.094700 GGTCTCAGTCTCATAACACGCA 60.095 50.000 0.00 0.00 0.00 5.24
422 6573 2.094700 TCTCAGTCTCATAACACGCACC 60.095 50.000 0.00 0.00 0.00 5.01
449 6684 3.515901 GGACTAGGTCAGACAATTCCACT 59.484 47.826 2.17 0.00 33.68 4.00
457 6695 5.063880 GTCAGACAATTCCACTACTGGTTT 58.936 41.667 0.00 0.00 38.90 3.27
470 6708 6.595716 CCACTACTGGTTTTATTCTTCTCTGG 59.404 42.308 0.00 0.00 32.03 3.86
589 6837 3.668447 TCTGATCCAAGTGAACAGCTTC 58.332 45.455 0.00 0.00 42.10 3.86
590 6838 2.414481 CTGATCCAAGTGAACAGCTTCG 59.586 50.000 0.00 0.00 37.11 3.79
591 6839 2.224281 TGATCCAAGTGAACAGCTTCGT 60.224 45.455 0.00 0.00 0.00 3.85
595 6844 0.468226 AAGTGAACAGCTTCGTCCCA 59.532 50.000 0.00 0.00 0.00 4.37
596 6845 0.249911 AGTGAACAGCTTCGTCCCAC 60.250 55.000 0.00 0.00 0.00 4.61
620 6883 4.218417 GCCCAAGAAATAAGCTCAACTTGA 59.782 41.667 15.47 0.00 39.58 3.02
622 6885 6.095440 GCCCAAGAAATAAGCTCAACTTGATA 59.905 38.462 15.47 0.00 39.58 2.15
623 6886 7.362920 GCCCAAGAAATAAGCTCAACTTGATAA 60.363 37.037 15.47 0.00 39.58 1.75
624 6887 7.970614 CCCAAGAAATAAGCTCAACTTGATAAC 59.029 37.037 15.47 0.00 39.58 1.89
625 6888 7.970614 CCAAGAAATAAGCTCAACTTGATAACC 59.029 37.037 15.47 0.00 39.58 2.85
627 6890 5.485662 AATAAGCTCAACTTGATAACCGC 57.514 39.130 0.00 0.00 39.58 5.68
628 6891 2.770164 AGCTCAACTTGATAACCGCT 57.230 45.000 0.00 0.00 0.00 5.52
728 7083 2.595463 AACGCATGTGCAGCAGGT 60.595 55.556 6.08 0.00 42.21 4.00
729 7084 1.298157 GAACGCATGTGCAGCAGGTA 61.298 55.000 6.08 0.00 42.21 3.08
730 7085 1.577328 AACGCATGTGCAGCAGGTAC 61.577 55.000 6.08 0.00 42.21 3.34
731 7086 2.787249 GCATGTGCAGCAGGTACG 59.213 61.111 0.00 0.00 41.59 3.67
732 7087 2.034879 GCATGTGCAGCAGGTACGT 61.035 57.895 0.00 0.00 41.59 3.57
860 7244 1.642037 CTACGACCTTGAGACGGCGA 61.642 60.000 16.62 0.00 0.00 5.54
861 7245 1.028330 TACGACCTTGAGACGGCGAT 61.028 55.000 16.62 0.11 0.00 4.58
862 7246 1.874019 CGACCTTGAGACGGCGATG 60.874 63.158 16.62 0.00 0.00 3.84
863 7247 2.125512 ACCTTGAGACGGCGATGC 60.126 61.111 16.62 1.94 0.00 3.91
867 7251 1.769098 CTTGAGACGGCGATGCATGG 61.769 60.000 16.62 3.37 0.00 3.66
885 7277 4.870426 GCATGGTATCCATAGTTCCATACG 59.130 45.833 0.74 0.00 43.15 3.06
936 7329 3.754323 CCTACCGTTGCTAATTTCCACAA 59.246 43.478 0.00 0.00 0.00 3.33
951 7344 1.605710 CCACAACCAAGAAGCACTCTG 59.394 52.381 0.00 0.00 33.37 3.35
952 7345 1.605710 CACAACCAAGAAGCACTCTGG 59.394 52.381 0.00 0.00 33.37 3.86
994 7408 0.668401 GCAAGACAGCATTGGCCAAC 60.668 55.000 23.27 9.46 42.56 3.77
1056 7482 3.134792 GTCCTCCTCTCGCTCGCA 61.135 66.667 0.00 0.00 0.00 5.10
1123 7549 2.897207 CCGACTTGGCATCCCGTA 59.103 61.111 0.00 0.00 0.00 4.02
1139 7616 5.925506 TCCCGTAAGTCATCATCTTTGTA 57.074 39.130 0.00 0.00 0.00 2.41
1145 7622 8.504005 CCGTAAGTCATCATCTTTGTAAAGTTT 58.496 33.333 4.45 0.00 37.31 2.66
1168 7655 0.508213 GTTGCATTTTTCGTGCTGGC 59.492 50.000 0.00 0.00 42.92 4.85
1169 7656 0.388659 TTGCATTTTTCGTGCTGGCT 59.611 45.000 0.00 0.00 42.92 4.75
1170 7657 0.039256 TGCATTTTTCGTGCTGGCTC 60.039 50.000 0.00 0.00 42.92 4.70
1177 7664 0.179059 TTCGTGCTGGCTCTTGTTGA 60.179 50.000 0.00 0.00 0.00 3.18
1214 7701 2.734606 CTCAAAACGAATGTCGGTAGCA 59.265 45.455 2.38 0.00 39.92 3.49
1243 7730 4.636435 CGGGTTCCCGTGCAAGGT 62.636 66.667 20.65 0.00 43.86 3.50
1280 7767 0.038159 ACTTCTTCTTCGCCGGTCTG 60.038 55.000 1.90 0.00 0.00 3.51
1385 7872 3.277133 GTGTCCATGGCACGCATT 58.723 55.556 19.12 0.00 0.00 3.56
1520 8007 3.635373 TCTTCACTAAGACCGTCACTGTT 59.365 43.478 0.40 0.00 36.80 3.16
1534 8021 0.874607 ACTGTTGGAGACGTGTTCGC 60.875 55.000 0.00 0.00 41.18 4.70
1574 8061 1.561542 CACTTCCAGCAGAATAGGGGT 59.438 52.381 0.00 0.00 32.82 4.95
1604 8091 4.077184 TCCGTGATCGCCGGCTTT 62.077 61.111 26.68 11.81 45.09 3.51
1746 8233 2.557869 AGGCCAAGTTCATGTAGGGTA 58.442 47.619 5.01 0.00 0.00 3.69
1772 8266 0.456221 CCGTCCGCAACTCTGTATCT 59.544 55.000 0.00 0.00 0.00 1.98
1776 8270 3.427098 CGTCCGCAACTCTGTATCTGTTA 60.427 47.826 0.00 0.00 0.00 2.41
1777 8271 4.491676 GTCCGCAACTCTGTATCTGTTAA 58.508 43.478 0.00 0.00 0.00 2.01
1778 8272 4.326548 GTCCGCAACTCTGTATCTGTTAAC 59.673 45.833 0.00 0.00 0.00 2.01
1779 8273 4.021807 TCCGCAACTCTGTATCTGTTAACA 60.022 41.667 8.28 8.28 0.00 2.41
1796 8294 8.545420 TCTGTTAACAAGAAAAATCGTCTGTAC 58.455 33.333 10.03 0.00 0.00 2.90
1832 8338 1.473278 GGTACTCAAGCGAGCTGTAGT 59.527 52.381 14.33 14.33 43.66 2.73
1844 8350 4.099120 CGAGCTGTAGTGTGTAGTTGATC 58.901 47.826 0.00 0.00 0.00 2.92
1860 8366 6.974932 AGTTGATCTGTTGATGTGTATGTC 57.025 37.500 0.00 0.00 32.19 3.06
1862 8371 5.072040 TGATCTGTTGATGTGTATGTCGT 57.928 39.130 0.00 0.00 32.19 4.34
1909 8418 6.670233 ACAAAACTGTTTCTGTTTCACGTAA 58.330 32.000 6.20 0.00 35.16 3.18
1936 8451 9.131416 TGTATGTTACATTTTACTAGTGTGTCG 57.869 33.333 5.39 0.00 32.89 4.35
1957 8472 9.901724 GTGTCGTTGATTTCTTTATGTGTATAG 57.098 33.333 0.00 0.00 0.00 1.31
1982 8497 8.879759 AGTACATTTGATACATTCCTTTACGTG 58.120 33.333 0.00 0.00 0.00 4.49
1983 8498 7.681939 ACATTTGATACATTCCTTTACGTGT 57.318 32.000 0.00 0.00 0.00 4.49
1984 8499 8.780846 ACATTTGATACATTCCTTTACGTGTA 57.219 30.769 0.00 0.00 0.00 2.90
1985 8500 9.391006 ACATTTGATACATTCCTTTACGTGTAT 57.609 29.630 0.00 0.00 39.68 2.29
1986 8501 9.650371 CATTTGATACATTCCTTTACGTGTATG 57.350 33.333 0.00 0.00 37.76 2.39
1987 8502 8.780846 TTTGATACATTCCTTTACGTGTATGT 57.219 30.769 0.00 0.00 37.76 2.29
1988 8503 8.780846 TTGATACATTCCTTTACGTGTATGTT 57.219 30.769 0.00 0.00 37.76 2.71
1989 8504 9.872721 TTGATACATTCCTTTACGTGTATGTTA 57.127 29.630 0.00 0.00 37.76 2.41
1990 8505 9.304731 TGATACATTCCTTTACGTGTATGTTAC 57.695 33.333 0.00 0.00 37.76 2.50
1991 8506 9.304731 GATACATTCCTTTACGTGTATGTTACA 57.695 33.333 0.00 0.00 37.76 2.41
1992 8507 9.826574 ATACATTCCTTTACGTGTATGTTACAT 57.173 29.630 2.58 2.58 41.34 2.29
1993 8508 8.556213 ACATTCCTTTACGTGTATGTTACATT 57.444 30.769 2.23 0.00 41.34 2.71
1994 8509 9.005777 ACATTCCTTTACGTGTATGTTACATTT 57.994 29.630 2.23 0.00 41.34 2.32
1995 8510 9.834628 CATTCCTTTACGTGTATGTTACATTTT 57.165 29.630 2.23 0.00 41.34 1.82
2028 8543 7.061752 ACTTGTCGACAAATCTATAACTTGC 57.938 36.000 29.32 0.00 35.15 4.01
2029 8544 6.874134 ACTTGTCGACAAATCTATAACTTGCT 59.126 34.615 29.32 4.34 35.15 3.91
2030 8545 8.033038 ACTTGTCGACAAATCTATAACTTGCTA 58.967 33.333 29.32 3.59 35.15 3.49
2031 8546 7.987268 TGTCGACAAATCTATAACTTGCTAG 57.013 36.000 17.62 0.00 0.00 3.42
2032 8547 7.768240 TGTCGACAAATCTATAACTTGCTAGA 58.232 34.615 17.62 0.00 0.00 2.43
2033 8548 8.414003 TGTCGACAAATCTATAACTTGCTAGAT 58.586 33.333 17.62 0.00 36.49 1.98
2034 8549 9.250624 GTCGACAAATCTATAACTTGCTAGATT 57.749 33.333 11.55 0.00 43.28 2.40
2038 8553 9.343539 ACAAATCTATAACTTGCTAGATTTCCC 57.656 33.333 11.44 0.00 45.11 3.97
2039 8554 9.342308 CAAATCTATAACTTGCTAGATTTCCCA 57.658 33.333 11.44 0.00 45.11 4.37
2040 8555 9.920946 AAATCTATAACTTGCTAGATTTCCCAA 57.079 29.630 1.04 0.00 45.11 4.12
2041 8556 9.566432 AATCTATAACTTGCTAGATTTCCCAAG 57.434 33.333 1.04 0.00 40.21 3.61
2042 8557 8.319057 TCTATAACTTGCTAGATTTCCCAAGA 57.681 34.615 11.14 0.00 38.37 3.02
2043 8558 8.938883 TCTATAACTTGCTAGATTTCCCAAGAT 58.061 33.333 11.14 3.88 38.37 2.40
2044 8559 9.566432 CTATAACTTGCTAGATTTCCCAAGATT 57.434 33.333 11.14 5.92 38.37 2.40
2045 8560 8.829373 ATAACTTGCTAGATTTCCCAAGATTT 57.171 30.769 11.14 1.53 38.37 2.17
2046 8561 6.521151 ACTTGCTAGATTTCCCAAGATTTG 57.479 37.500 11.14 0.00 38.37 2.32
2047 8562 6.012745 ACTTGCTAGATTTCCCAAGATTTGT 58.987 36.000 11.14 0.00 38.37 2.83
2048 8563 6.494835 ACTTGCTAGATTTCCCAAGATTTGTT 59.505 34.615 11.14 0.00 38.37 2.83
2049 8564 6.515272 TGCTAGATTTCCCAAGATTTGTTC 57.485 37.500 0.00 0.00 0.00 3.18
2050 8565 6.248433 TGCTAGATTTCCCAAGATTTGTTCT 58.752 36.000 0.00 0.00 35.70 3.01
2051 8566 6.375455 TGCTAGATTTCCCAAGATTTGTTCTC 59.625 38.462 0.00 0.00 31.78 2.87
2052 8567 6.375455 GCTAGATTTCCCAAGATTTGTTCTCA 59.625 38.462 0.00 0.00 31.78 3.27
2053 8568 7.067981 GCTAGATTTCCCAAGATTTGTTCTCAT 59.932 37.037 0.00 0.00 31.78 2.90
2054 8569 7.166691 AGATTTCCCAAGATTTGTTCTCATG 57.833 36.000 0.00 0.00 31.78 3.07
2055 8570 6.723052 AGATTTCCCAAGATTTGTTCTCATGT 59.277 34.615 0.00 0.00 31.78 3.21
2056 8571 6.729690 TTTCCCAAGATTTGTTCTCATGTT 57.270 33.333 0.00 0.00 31.78 2.71
2057 8572 5.964958 TCCCAAGATTTGTTCTCATGTTC 57.035 39.130 0.00 0.00 31.78 3.18
2058 8573 5.634118 TCCCAAGATTTGTTCTCATGTTCT 58.366 37.500 0.00 0.00 31.78 3.01
2059 8574 6.070656 TCCCAAGATTTGTTCTCATGTTCTT 58.929 36.000 0.00 0.00 31.78 2.52
2060 8575 6.550854 TCCCAAGATTTGTTCTCATGTTCTTT 59.449 34.615 0.00 0.00 31.78 2.52
2061 8576 6.865205 CCCAAGATTTGTTCTCATGTTCTTTC 59.135 38.462 0.00 0.00 31.78 2.62
2062 8577 7.255730 CCCAAGATTTGTTCTCATGTTCTTTCT 60.256 37.037 0.00 0.00 31.78 2.52
2063 8578 8.139989 CCAAGATTTGTTCTCATGTTCTTTCTT 58.860 33.333 0.00 0.00 31.78 2.52
2064 8579 9.178427 CAAGATTTGTTCTCATGTTCTTTCTTC 57.822 33.333 0.00 0.00 31.78 2.87
2097 8612 7.506114 AGGGCATTCTTTATTGACTCGTAATA 58.494 34.615 0.00 0.00 0.00 0.98
2107 8622 5.883328 TTGACTCGTAATATCGCATCAAC 57.117 39.130 0.00 0.00 33.25 3.18
2108 8623 5.183014 TGACTCGTAATATCGCATCAACT 57.817 39.130 0.00 0.00 0.00 3.16
2145 8660 2.203728 TACACACCCGGCCTCTGT 60.204 61.111 0.00 0.00 0.00 3.41
2150 8665 1.416401 CACACCCGGCCTCTGTATAAT 59.584 52.381 0.00 0.00 0.00 1.28
2285 8802 2.624838 ACGACGAGAAGGTTGTCCTAAA 59.375 45.455 0.00 0.00 44.35 1.85
2302 8819 3.058914 CCTAAAAGCGACACCTTCAACAG 60.059 47.826 0.00 0.00 0.00 3.16
2357 8874 5.023533 TCAAACCACATAGGCTAGATCAC 57.976 43.478 0.00 0.00 43.14 3.06
2369 8886 3.585862 GCTAGATCACGAGTTTTCACCA 58.414 45.455 0.00 0.00 0.00 4.17
2559 9078 4.479786 ACTTGCCATAGAAGAAGTCCTC 57.520 45.455 0.00 0.00 0.00 3.71
2590 9109 4.389992 GTCTCGATCAGCACTGAAATTTCA 59.610 41.667 19.45 19.45 43.58 2.69
2591 9110 5.064452 GTCTCGATCAGCACTGAAATTTCAT 59.936 40.000 20.76 8.95 43.58 2.57
2630 9149 4.256110 CACATCAGGCATTTACTGAGACA 58.744 43.478 0.00 0.00 46.98 3.41
2655 9174 2.509052 TCTGAGAACACAGACAACGG 57.491 50.000 0.00 0.00 41.21 4.44
2726 9245 5.748630 CACCGAAGAACGATGAATATCTTCA 59.251 40.000 13.04 0.00 45.05 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 4433 2.125350 CGGGTCTGCTGCTCCTTC 60.125 66.667 0.00 0.00 0.00 3.46
31 4453 6.489700 TGAAACATTATCTTGTTGAGCAGGAA 59.510 34.615 0.00 0.00 39.68 3.36
32 4454 6.003326 TGAAACATTATCTTGTTGAGCAGGA 58.997 36.000 0.00 0.00 39.68 3.86
43 4465 4.085055 CGCGCGAGTATGAAACATTATCTT 60.085 41.667 28.94 0.00 0.00 2.40
128 4550 3.068691 TCCTCTTCCGGTCGCAGG 61.069 66.667 0.00 3.12 0.00 4.85
169 4598 1.667830 CGCTCTGCCTTGTCCGAAA 60.668 57.895 0.00 0.00 0.00 3.46
186 4616 0.679505 TGGACAAGGAAGGAGACACG 59.320 55.000 0.00 0.00 0.00 4.49
258 4688 0.912486 AAAACCTGGCGGCTAGAGAT 59.088 50.000 15.52 0.00 0.00 2.75
319 4749 9.403110 CAAGTTGATCTCCTTAAATTCACAAAG 57.597 33.333 0.00 0.00 0.00 2.77
356 5328 0.818040 AAGGCCACGTTCCAGTGTTC 60.818 55.000 5.01 0.00 40.33 3.18
422 6573 2.516227 TGTCTGACCTAGTCCTCCAG 57.484 55.000 5.17 0.00 0.00 3.86
449 6684 6.209986 TCGTCCAGAGAAGAATAAAACCAGTA 59.790 38.462 0.00 0.00 0.00 2.74
491 6729 3.031964 CTTTTGCTGCTCGCGAGGG 62.032 63.158 35.10 14.75 43.27 4.30
589 6837 0.391927 TATTTCTTGGGCGTGGGACG 60.392 55.000 0.00 0.00 45.88 4.79
590 6838 1.743394 CTTATTTCTTGGGCGTGGGAC 59.257 52.381 0.00 0.00 0.00 4.46
591 6839 1.953311 GCTTATTTCTTGGGCGTGGGA 60.953 52.381 0.00 0.00 0.00 4.37
595 6844 2.488153 GTTGAGCTTATTTCTTGGGCGT 59.512 45.455 0.00 0.00 0.00 5.68
596 6845 2.749621 AGTTGAGCTTATTTCTTGGGCG 59.250 45.455 0.00 0.00 0.00 6.13
620 6883 7.117812 GCACATGATAGTTTGTATAGCGGTTAT 59.882 37.037 0.00 0.00 0.00 1.89
622 6885 5.236478 GCACATGATAGTTTGTATAGCGGTT 59.764 40.000 0.00 0.00 0.00 4.44
623 6886 4.750098 GCACATGATAGTTTGTATAGCGGT 59.250 41.667 0.00 0.00 0.00 5.68
624 6887 4.749598 TGCACATGATAGTTTGTATAGCGG 59.250 41.667 0.00 0.00 0.00 5.52
625 6888 5.905480 TGCACATGATAGTTTGTATAGCG 57.095 39.130 0.00 0.00 0.00 4.26
627 6890 7.306807 CCGAGTTGCACATGATAGTTTGTATAG 60.307 40.741 0.00 0.00 0.00 1.31
628 6891 6.478673 CCGAGTTGCACATGATAGTTTGTATA 59.521 38.462 0.00 0.00 0.00 1.47
728 7083 2.022195 CTCCTTGCAGGCTAGTACGTA 58.978 52.381 0.00 0.00 34.61 3.57
729 7084 0.818296 CTCCTTGCAGGCTAGTACGT 59.182 55.000 0.00 0.00 34.61 3.57
730 7085 0.818296 ACTCCTTGCAGGCTAGTACG 59.182 55.000 0.95 0.00 34.61 3.67
731 7086 2.301577 CACTCCTTGCAGGCTAGTAC 57.698 55.000 2.42 0.00 34.61 2.73
860 7244 4.999469 TGGAACTATGGATACCATGCAT 57.001 40.909 12.78 0.00 44.84 3.96
861 7245 4.999469 ATGGAACTATGGATACCATGCA 57.001 40.909 12.78 0.00 44.84 3.96
862 7246 4.870426 CGTATGGAACTATGGATACCATGC 59.130 45.833 12.78 0.00 44.84 4.06
863 7247 4.870426 GCGTATGGAACTATGGATACCATG 59.130 45.833 12.78 6.21 44.84 3.66
867 7251 5.178809 GGTTTGCGTATGGAACTATGGATAC 59.821 44.000 0.00 0.00 0.00 2.24
885 7277 3.081804 ACTTATAGGCAGTGTGGTTTGC 58.918 45.455 0.00 0.00 39.56 3.68
936 7329 0.183492 TTGCCAGAGTGCTTCTTGGT 59.817 50.000 0.00 0.00 32.41 3.67
951 7344 0.537371 AGCTTGGTGGTGTAGTTGCC 60.537 55.000 0.00 0.00 0.00 4.52
952 7345 0.593128 CAGCTTGGTGGTGTAGTTGC 59.407 55.000 0.00 0.00 39.17 4.17
994 7408 1.958205 GAAGCCTCGCCATGATCGG 60.958 63.158 0.00 0.00 0.00 4.18
1123 7549 9.520204 CAACAAACTTTACAAAGATGATGACTT 57.480 29.630 8.65 0.00 39.31 3.01
1139 7616 6.076557 CACGAAAAATGCAACAACAAACTTT 58.923 32.000 0.00 0.00 0.00 2.66
1145 7622 2.602211 CAGCACGAAAAATGCAACAACA 59.398 40.909 0.00 0.00 45.92 3.33
1168 7655 2.483876 ACACCACGTCATCAACAAGAG 58.516 47.619 0.00 0.00 0.00 2.85
1169 7656 2.613026 ACACCACGTCATCAACAAGA 57.387 45.000 0.00 0.00 0.00 3.02
1170 7657 3.691049 AAACACCACGTCATCAACAAG 57.309 42.857 0.00 0.00 0.00 3.16
1177 7664 2.631160 TGAGGAAAACACCACGTCAT 57.369 45.000 0.00 0.00 0.00 3.06
1206 7693 2.346803 GTTCAGCTTGATTGCTACCGA 58.653 47.619 0.00 0.00 41.98 4.69
1214 7701 1.534729 GGAACCCGTTCAGCTTGATT 58.465 50.000 9.65 0.00 41.20 2.57
1243 7730 4.429212 CGTCCGCCGTGATGTCCA 62.429 66.667 0.00 0.00 0.00 4.02
1280 7767 1.973812 GGTGTTGCCAGCCCTCTTC 60.974 63.158 0.00 0.00 37.17 2.87
1520 8007 1.006571 GAAGGCGAACACGTCTCCA 60.007 57.895 0.00 0.00 41.16 3.86
1604 8091 1.002134 GCCCTGAAGCTGGCTGTTA 60.002 57.895 5.56 0.00 44.46 2.41
1631 8118 1.078759 CGAAGAGTGTGGTGGCGATC 61.079 60.000 0.00 0.00 0.00 3.69
1758 8250 5.633601 TCTTGTTAACAGATACAGAGTTGCG 59.366 40.000 8.56 0.00 0.00 4.85
1772 8266 7.280428 TGGTACAGACGATTTTTCTTGTTAACA 59.720 33.333 3.59 3.59 0.00 2.41
1832 8338 5.610398 ACACATCAACAGATCAACTACACA 58.390 37.500 0.00 0.00 0.00 3.72
1844 8350 7.060600 ACAAATACGACATACACATCAACAG 57.939 36.000 0.00 0.00 0.00 3.16
1891 8400 7.572759 ACATACATTACGTGAAACAGAAACAG 58.427 34.615 0.00 0.00 35.74 3.16
1926 8435 7.952101 CACATAAAGAAATCAACGACACACTAG 59.048 37.037 0.00 0.00 0.00 2.57
1957 8472 8.662141 ACACGTAAAGGAATGTATCAAATGTAC 58.338 33.333 0.00 0.00 0.00 2.90
2002 8517 8.653338 GCAAGTTATAGATTTGTCGACAAGTTA 58.347 33.333 28.21 21.13 37.15 2.24
2003 8518 7.387948 AGCAAGTTATAGATTTGTCGACAAGTT 59.612 33.333 28.21 20.56 37.15 2.66
2004 8519 6.874134 AGCAAGTTATAGATTTGTCGACAAGT 59.126 34.615 28.21 26.26 37.15 3.16
2005 8520 7.295952 AGCAAGTTATAGATTTGTCGACAAG 57.704 36.000 28.21 14.65 37.15 3.16
2006 8521 8.248253 TCTAGCAAGTTATAGATTTGTCGACAA 58.752 33.333 26.53 26.53 0.00 3.18
2007 8522 7.768240 TCTAGCAAGTTATAGATTTGTCGACA 58.232 34.615 15.76 15.76 0.00 4.35
2008 8523 8.804688 ATCTAGCAAGTTATAGATTTGTCGAC 57.195 34.615 9.11 9.11 35.66 4.20
2015 8530 9.566432 CTTGGGAAATCTAGCAAGTTATAGATT 57.434 33.333 13.19 13.19 45.99 2.40
2016 8531 8.938883 TCTTGGGAAATCTAGCAAGTTATAGAT 58.061 33.333 0.00 4.64 39.81 1.98
2017 8532 8.319057 TCTTGGGAAATCTAGCAAGTTATAGA 57.681 34.615 0.00 0.77 32.79 1.98
2018 8533 9.566432 AATCTTGGGAAATCTAGCAAGTTATAG 57.434 33.333 0.00 0.00 0.00 1.31
2019 8534 9.920946 AAATCTTGGGAAATCTAGCAAGTTATA 57.079 29.630 0.00 0.00 0.00 0.98
2020 8535 8.689972 CAAATCTTGGGAAATCTAGCAAGTTAT 58.310 33.333 0.00 0.00 0.00 1.89
2021 8536 7.669722 ACAAATCTTGGGAAATCTAGCAAGTTA 59.330 33.333 0.00 0.00 34.12 2.24
2022 8537 6.494835 ACAAATCTTGGGAAATCTAGCAAGTT 59.505 34.615 0.00 0.00 34.12 2.66
2023 8538 6.012745 ACAAATCTTGGGAAATCTAGCAAGT 58.987 36.000 0.00 0.00 34.12 3.16
2024 8539 6.521151 ACAAATCTTGGGAAATCTAGCAAG 57.479 37.500 0.00 0.00 34.12 4.01
2025 8540 6.721208 AGAACAAATCTTGGGAAATCTAGCAA 59.279 34.615 0.00 0.00 33.39 3.91
2026 8541 6.248433 AGAACAAATCTTGGGAAATCTAGCA 58.752 36.000 0.00 0.00 33.39 3.49
2027 8542 6.375455 TGAGAACAAATCTTGGGAAATCTAGC 59.625 38.462 0.00 0.00 38.96 3.42
2028 8543 7.928307 TGAGAACAAATCTTGGGAAATCTAG 57.072 36.000 0.00 0.00 38.96 2.43
2029 8544 7.890127 ACATGAGAACAAATCTTGGGAAATCTA 59.110 33.333 0.00 0.00 38.96 1.98
2030 8545 6.723052 ACATGAGAACAAATCTTGGGAAATCT 59.277 34.615 0.00 0.00 38.96 2.40
2031 8546 6.928520 ACATGAGAACAAATCTTGGGAAATC 58.071 36.000 0.00 0.00 38.96 2.17
2032 8547 6.923199 ACATGAGAACAAATCTTGGGAAAT 57.077 33.333 0.00 0.00 38.96 2.17
2033 8548 6.550854 AGAACATGAGAACAAATCTTGGGAAA 59.449 34.615 0.00 0.00 38.96 3.13
2034 8549 6.070656 AGAACATGAGAACAAATCTTGGGAA 58.929 36.000 0.00 0.00 38.96 3.97
2035 8550 5.634118 AGAACATGAGAACAAATCTTGGGA 58.366 37.500 0.00 0.00 38.96 4.37
2036 8551 5.972107 AGAACATGAGAACAAATCTTGGG 57.028 39.130 0.00 0.00 38.96 4.12
2037 8552 7.655490 AGAAAGAACATGAGAACAAATCTTGG 58.345 34.615 0.00 0.00 38.96 3.61
2038 8553 9.178427 GAAGAAAGAACATGAGAACAAATCTTG 57.822 33.333 0.00 0.00 38.96 3.02
2039 8554 9.129532 AGAAGAAAGAACATGAGAACAAATCTT 57.870 29.630 0.00 0.00 38.96 2.40
2040 8555 8.688747 AGAAGAAAGAACATGAGAACAAATCT 57.311 30.769 0.00 0.00 42.61 2.40
2041 8556 7.743838 CGAGAAGAAAGAACATGAGAACAAATC 59.256 37.037 0.00 0.00 0.00 2.17
2042 8557 7.442364 TCGAGAAGAAAGAACATGAGAACAAAT 59.558 33.333 0.00 0.00 0.00 2.32
2043 8558 6.761242 TCGAGAAGAAAGAACATGAGAACAAA 59.239 34.615 0.00 0.00 0.00 2.83
2044 8559 6.280643 TCGAGAAGAAAGAACATGAGAACAA 58.719 36.000 0.00 0.00 0.00 2.83
2045 8560 5.842907 TCGAGAAGAAAGAACATGAGAACA 58.157 37.500 0.00 0.00 0.00 3.18
2046 8561 6.959671 ATCGAGAAGAAAGAACATGAGAAC 57.040 37.500 0.00 0.00 0.00 3.01
2047 8562 9.144747 CTTTATCGAGAAGAAAGAACATGAGAA 57.855 33.333 0.00 0.00 32.94 2.87
2048 8563 7.761704 CCTTTATCGAGAAGAAAGAACATGAGA 59.238 37.037 11.68 0.00 32.94 3.27
2049 8564 7.010923 CCCTTTATCGAGAAGAAAGAACATGAG 59.989 40.741 11.68 0.00 32.94 2.90
2050 8565 6.818644 CCCTTTATCGAGAAGAAAGAACATGA 59.181 38.462 11.68 0.00 32.94 3.07
2051 8566 6.457528 GCCCTTTATCGAGAAGAAAGAACATG 60.458 42.308 11.68 0.00 32.94 3.21
2052 8567 5.586643 GCCCTTTATCGAGAAGAAAGAACAT 59.413 40.000 11.68 0.00 32.94 2.71
2053 8568 4.935808 GCCCTTTATCGAGAAGAAAGAACA 59.064 41.667 11.68 0.00 32.94 3.18
2054 8569 4.935808 TGCCCTTTATCGAGAAGAAAGAAC 59.064 41.667 11.68 5.53 32.94 3.01
2055 8570 5.160607 TGCCCTTTATCGAGAAGAAAGAA 57.839 39.130 11.68 0.00 32.94 2.52
2056 8571 4.819105 TGCCCTTTATCGAGAAGAAAGA 57.181 40.909 11.68 0.00 32.94 2.52
2057 8572 5.819901 AGAATGCCCTTTATCGAGAAGAAAG 59.180 40.000 11.68 8.35 0.00 2.62
2058 8573 5.745227 AGAATGCCCTTTATCGAGAAGAAA 58.255 37.500 11.68 0.00 0.00 2.52
2059 8574 5.359194 AGAATGCCCTTTATCGAGAAGAA 57.641 39.130 11.68 0.33 0.00 2.52
2060 8575 5.359194 AAGAATGCCCTTTATCGAGAAGA 57.641 39.130 11.68 0.00 0.00 2.87
2061 8576 7.736447 ATAAAGAATGCCCTTTATCGAGAAG 57.264 36.000 8.94 0.00 42.50 2.85
2062 8577 7.773224 TCAATAAAGAATGCCCTTTATCGAGAA 59.227 33.333 12.97 0.00 44.24 2.87
2063 8578 7.226720 GTCAATAAAGAATGCCCTTTATCGAGA 59.773 37.037 12.97 10.11 44.24 4.04
2064 8579 7.227512 AGTCAATAAAGAATGCCCTTTATCGAG 59.772 37.037 12.97 8.71 44.24 4.04
2097 8612 4.699735 TGTTTTGTATCCAGTTGATGCGAT 59.300 37.500 0.00 0.00 38.78 4.58
2107 8622 5.464057 TGTACTCGTTGTGTTTTGTATCCAG 59.536 40.000 0.00 0.00 0.00 3.86
2108 8623 5.234757 GTGTACTCGTTGTGTTTTGTATCCA 59.765 40.000 0.00 0.00 0.00 3.41
2150 8665 6.214191 TCTTTTTGGTTGTGTGCATCTTAA 57.786 33.333 0.00 0.00 0.00 1.85
2285 8802 0.535102 CCCTGTTGAAGGTGTCGCTT 60.535 55.000 0.00 0.00 45.78 4.68
2302 8819 2.368655 GTGTTCATGCACCATTTCCC 57.631 50.000 0.00 0.00 33.53 3.97
2357 8874 4.260784 CCTTGTCTTCTTGGTGAAAACTCG 60.261 45.833 0.00 0.00 33.79 4.18
2369 8886 1.640917 TAGCCGGTCCTTGTCTTCTT 58.359 50.000 1.90 0.00 0.00 2.52
2559 9078 1.937899 TGCTGATCGAGACATTGCATG 59.062 47.619 0.00 0.00 0.00 4.06
2590 9109 6.003326 TGATGTGTGGTGTTCACTTTGATAT 58.997 36.000 2.98 0.00 46.20 1.63
2591 9110 5.372373 TGATGTGTGGTGTTCACTTTGATA 58.628 37.500 2.98 0.00 46.20 2.15
2630 9149 4.944619 TGTCTGTGTTCTCAGATCTGTT 57.055 40.909 21.92 0.00 44.59 3.16


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

AutoCloner maintained by Alex Coulton.