Multiple sequence alignment - TraesCS7B01G131800

Loading Multiple Alignment...

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 TraesCS7B01G131800 chr7B 100.000 4387 0 0 1 4387 159504661 159509047 0.000000e+00 8102.0
1 TraesCS7B01G131800 chr7D 95.320 2778 99 15 1620 4387 195619540 195622296 0.000000e+00 4381.0
2 TraesCS7B01G131800 chr7D 88.016 1285 98 29 1 1257 195614567 195615823 0.000000e+00 1469.0
3 TraesCS7B01G131800 chr7D 95.833 216 7 1 1285 1498 195619164 195619379 9.030000e-92 348.0
4 TraesCS7B01G131800 chr7D 97.143 35 1 0 1541 1575 195619508 195619542 4.740000e-05 60.2
5 TraesCS7B01G131800 chr7A 94.268 2774 105 14 1620 4387 205455592 205458317 0.000000e+00 4193.0
6 TraesCS7B01G131800 chr7A 94.109 679 37 3 823 1498 205454724 205455402 0.000000e+00 1029.0
7 TraesCS7B01G131800 chr7A 97.531 81 0 1 1497 1575 205455514 205455594 2.130000e-28 137.0
8 TraesCS7B01G131800 chr6B 81.829 809 130 15 1 798 14409266 14410068 0.000000e+00 664.0
9 TraesCS7B01G131800 chr6B 77.669 712 129 20 117 807 692491508 692492210 1.470000e-109 407.0
10 TraesCS7B01G131800 chr5D 80.125 800 145 10 1 792 322394112 322394905 6.320000e-163 584.0
11 TraesCS7B01G131800 chr4B 75.287 785 168 23 25 798 179841162 179841931 6.980000e-93 351.0
12 TraesCS7B01G131800 chr3D 74.129 804 184 21 14 807 187853877 187853088 1.180000e-80 311.0
13 TraesCS7B01G131800 chr5B 73.138 819 189 29 3 807 526115564 526116365 9.360000e-67 265.0
14 TraesCS7B01G131800 chr1B 100.000 49 0 0 1576 1624 286034964 286035012 1.680000e-14 91.6
15 TraesCS7B01G131800 chrUn 100.000 48 0 0 1576 1623 209401457 209401504 6.040000e-14 89.8
16 TraesCS7B01G131800 chrUn 100.000 48 0 0 1576 1623 267896851 267896804 6.040000e-14 89.8
17 TraesCS7B01G131800 chrUn 100.000 48 0 0 1576 1623 298936072 298936119 6.040000e-14 89.8
18 TraesCS7B01G131800 chrUn 100.000 48 0 0 1576 1623 359774467 359774420 6.040000e-14 89.8
19 TraesCS7B01G131800 chr4D 100.000 48 0 0 1576 1623 374918354 374918401 6.040000e-14 89.8
20 TraesCS7B01G131800 chr4D 100.000 48 0 0 1576 1623 427945229 427945182 6.040000e-14 89.8
21 TraesCS7B01G131800 chr1D 100.000 48 0 0 1576 1623 254467302 254467255 6.040000e-14 89.8
22 TraesCS7B01G131800 chr1D 100.000 48 0 0 1576 1623 351089408 351089455 6.040000e-14 89.8


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G131800 chr7B 159504661 159509047 4386 False 8102.000000 8102 100.000000 1 4387 1 chr7B.!!$F1 4386
1 TraesCS7B01G131800 chr7D 195614567 195622296 7729 False 1564.550000 4381 94.078000 1 4387 4 chr7D.!!$F1 4386
2 TraesCS7B01G131800 chr7A 205454724 205458317 3593 False 1786.333333 4193 95.302667 823 4387 3 chr7A.!!$F1 3564
3 TraesCS7B01G131800 chr6B 14409266 14410068 802 False 664.000000 664 81.829000 1 798 1 chr6B.!!$F1 797
4 TraesCS7B01G131800 chr6B 692491508 692492210 702 False 407.000000 407 77.669000 117 807 1 chr6B.!!$F2 690
5 TraesCS7B01G131800 chr5D 322394112 322394905 793 False 584.000000 584 80.125000 1 792 1 chr5D.!!$F1 791
6 TraesCS7B01G131800 chr4B 179841162 179841931 769 False 351.000000 351 75.287000 25 798 1 chr4B.!!$F1 773
7 TraesCS7B01G131800 chr3D 187853088 187853877 789 True 311.000000 311 74.129000 14 807 1 chr3D.!!$R1 793
8 TraesCS7B01G131800 chr5B 526115564 526116365 801 False 265.000000 265 73.138000 3 807 1 chr5B.!!$F1 804

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
840 894 0.178990 ATTATGCCGCCTTCCTTCCC 60.179 55.0 0.00 0.00 0.00 3.97 F
1602 5089 0.324275 GGCTCACAAGGGCCCATTTA 60.324 55.0 27.56 3.89 42.30 1.40 F
1621 5108 0.625849 ACAGGACAAGGCCATAAGGG 59.374 55.0 5.01 0.00 40.85 3.95 F
2010 5497 0.821517 ATGTTGTGATCTCGGCCGTA 59.178 50.0 27.15 15.53 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2715 6210 0.109153 TCCATGATCCCAATCTGCGG 59.891 55.000 0.0 0.0 32.75 5.69 R
3327 6823 0.392461 TGCACATCGGGGTAAAGCTC 60.392 55.000 0.0 0.0 0.00 4.09 R
3338 6834 4.926832 TCCACGGTAATATAATGCACATCG 59.073 41.667 0.0 0.0 0.00 3.84 R
3968 7464 2.999331 TGGTAGCTCCTTTGTAATGCC 58.001 47.619 0.0 0.0 37.07 4.40 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 32 3.845259 CGGGCAGCCTTACCGCTA 61.845 66.667 12.43 0.00 41.23 4.26
49 50 2.168521 GCTAGTGTTGCTGGACTATCCA 59.831 50.000 0.00 0.00 45.98 3.41
61 62 3.220110 GGACTATCCAGACACCGTATCA 58.780 50.000 0.00 0.00 36.28 2.15
79 80 2.369633 ATGGCGGCTCTCACCATCA 61.370 57.895 11.43 0.00 40.14 3.07
179 181 1.143889 CCCCTTTGCCCTTAGAGATCC 59.856 57.143 0.00 0.00 0.00 3.36
221 225 3.383505 TCTTAGAAATCGCATCCCTTCGA 59.616 43.478 0.00 0.00 39.17 3.71
325 338 1.096967 TCTTATGTACGGCGGCTCGA 61.097 55.000 13.24 0.00 0.00 4.04
336 349 1.528292 GCGGCTCGAGTCCTATGGAT 61.528 60.000 12.25 0.00 32.73 3.41
355 369 4.657504 TGGATGTTCATCCTGAAGCTCTAT 59.342 41.667 25.77 0.00 37.00 1.98
414 431 0.541863 AGACCAAGGCTATCCAACCG 59.458 55.000 0.00 0.00 33.74 4.44
419 436 3.489513 GGCTATCCAACCGGGGCT 61.490 66.667 6.32 0.00 37.22 5.19
442 468 0.810031 TCGCCGCTTTATTCTGGCTC 60.810 55.000 0.21 0.00 45.36 4.70
497 523 7.094508 ACAATGCGTAATAAAATGGTGATCA 57.905 32.000 0.00 0.00 0.00 2.92
501 527 4.976116 GCGTAATAAAATGGTGATCAAGCC 59.024 41.667 0.00 0.00 0.00 4.35
526 552 2.765250 TTCCGAGGCAAGCGTCTGAC 62.765 60.000 12.23 0.00 0.00 3.51
527 553 2.259818 CGAGGCAAGCGTCTGACT 59.740 61.111 12.23 0.00 37.39 3.41
528 554 1.373497 CGAGGCAAGCGTCTGACTT 60.373 57.895 12.23 0.00 33.64 3.01
531 557 0.394565 AGGCAAGCGTCTGACTTCTT 59.605 50.000 6.21 6.33 26.24 2.52
560 586 1.133823 TCCTTCCTTTTCTGCAGCACA 60.134 47.619 9.47 0.00 0.00 4.57
623 649 2.417586 CTCATGTTTGATGCGCTTCTGA 59.582 45.455 22.11 15.73 0.00 3.27
654 680 1.683385 TCGACTATCGTCCTCGTAGGA 59.317 52.381 0.00 0.11 39.48 2.94
718 752 9.507329 TTTCTCCTATGTTTATTAGGCATGATC 57.493 33.333 0.00 0.00 0.00 2.92
732 766 0.965363 ATGATCGTGTTGTTGCCCCC 60.965 55.000 0.00 0.00 0.00 5.40
734 768 3.185299 ATCGTGTTGTTGCCCCCGA 62.185 57.895 0.00 0.00 0.00 5.14
736 770 3.292159 GTGTTGTTGCCCCCGACC 61.292 66.667 0.00 0.00 0.00 4.79
807 845 7.733773 ATTTATAAAGCAGGGTAAAAGCCTT 57.266 32.000 3.94 0.00 45.25 4.35
809 847 5.661056 ATAAAGCAGGGTAAAAGCCTTTC 57.339 39.130 0.00 0.00 45.25 2.62
810 848 2.675658 AGCAGGGTAAAAGCCTTTCA 57.324 45.000 0.00 0.00 45.25 2.69
811 849 3.175438 AGCAGGGTAAAAGCCTTTCAT 57.825 42.857 0.00 0.00 45.25 2.57
812 850 2.827921 AGCAGGGTAAAAGCCTTTCATG 59.172 45.455 0.00 0.00 45.25 3.07
814 852 3.367395 GCAGGGTAAAAGCCTTTCATGAC 60.367 47.826 0.00 0.00 45.25 3.06
815 853 4.082125 CAGGGTAAAAGCCTTTCATGACT 58.918 43.478 0.00 0.00 45.25 3.41
816 854 4.156739 CAGGGTAAAAGCCTTTCATGACTC 59.843 45.833 0.00 0.00 45.25 3.36
818 856 4.156739 GGGTAAAAGCCTTTCATGACTCTG 59.843 45.833 0.00 0.00 31.81 3.35
819 857 4.762251 GGTAAAAGCCTTTCATGACTCTGT 59.238 41.667 0.00 0.00 0.00 3.41
840 894 0.178990 ATTATGCCGCCTTCCTTCCC 60.179 55.000 0.00 0.00 0.00 3.97
1227 1282 1.651138 CGTCGTGCTCTTCTTTGCTAG 59.349 52.381 0.00 0.00 0.00 3.42
1249 1304 5.393866 AGTCTTATCCAGATCCTTCCTCTC 58.606 45.833 0.00 0.00 32.60 3.20
1257 1312 6.893583 TCCAGATCCTTCCTCTCTTTTTATG 58.106 40.000 0.00 0.00 0.00 1.90
1258 1313 6.673978 TCCAGATCCTTCCTCTCTTTTTATGA 59.326 38.462 0.00 0.00 0.00 2.15
1259 1314 7.182749 TCCAGATCCTTCCTCTCTTTTTATGAA 59.817 37.037 0.00 0.00 0.00 2.57
1260 1315 7.498570 CCAGATCCTTCCTCTCTTTTTATGAAG 59.501 40.741 0.00 0.00 0.00 3.02
1282 4651 5.596763 AGGTTGGTGGGTCTAACTTCTATA 58.403 41.667 0.00 0.00 37.60 1.31
1283 4652 6.027482 AGGTTGGTGGGTCTAACTTCTATAA 58.973 40.000 0.00 0.00 37.60 0.98
1288 4657 6.069847 TGGTGGGTCTAACTTCTATAAAAGGG 60.070 42.308 0.00 0.00 0.00 3.95
1467 4839 6.176183 ACAAGACAGAAATGAGAGTAATGGG 58.824 40.000 0.00 0.00 0.00 4.00
1575 5062 6.916360 AAAGATTAGGTGATTTGCTTGGAA 57.084 33.333 0.00 0.00 0.00 3.53
1576 5063 7.486407 AAAGATTAGGTGATTTGCTTGGAAT 57.514 32.000 0.00 0.00 0.00 3.01
1577 5064 7.486407 AAGATTAGGTGATTTGCTTGGAATT 57.514 32.000 0.00 0.00 0.00 2.17
1578 5065 7.486407 AGATTAGGTGATTTGCTTGGAATTT 57.514 32.000 0.00 0.00 0.00 1.82
1579 5066 7.910584 AGATTAGGTGATTTGCTTGGAATTTT 58.089 30.769 0.00 0.00 0.00 1.82
1580 5067 7.820872 AGATTAGGTGATTTGCTTGGAATTTTG 59.179 33.333 0.00 0.00 0.00 2.44
1581 5068 4.644498 AGGTGATTTGCTTGGAATTTTGG 58.356 39.130 0.00 0.00 0.00 3.28
1582 5069 4.347583 AGGTGATTTGCTTGGAATTTTGGA 59.652 37.500 0.00 0.00 0.00 3.53
1583 5070 4.692155 GGTGATTTGCTTGGAATTTTGGAG 59.308 41.667 0.00 0.00 0.00 3.86
1584 5071 4.692155 GTGATTTGCTTGGAATTTTGGAGG 59.308 41.667 0.00 0.00 0.00 4.30
1585 5072 2.837532 TTGCTTGGAATTTTGGAGGC 57.162 45.000 0.00 0.00 0.00 4.70
1586 5073 2.014010 TGCTTGGAATTTTGGAGGCT 57.986 45.000 0.00 0.00 0.00 4.58
1587 5074 1.895131 TGCTTGGAATTTTGGAGGCTC 59.105 47.619 5.78 5.78 0.00 4.70
1588 5075 1.895131 GCTTGGAATTTTGGAGGCTCA 59.105 47.619 17.69 0.00 0.00 4.26
1589 5076 2.353109 GCTTGGAATTTTGGAGGCTCAC 60.353 50.000 17.69 6.44 0.00 3.51
1590 5077 2.673775 TGGAATTTTGGAGGCTCACA 57.326 45.000 17.69 9.16 0.00 3.58
1591 5078 2.956132 TGGAATTTTGGAGGCTCACAA 58.044 42.857 17.69 14.65 0.00 3.33
1592 5079 2.892852 TGGAATTTTGGAGGCTCACAAG 59.107 45.455 17.69 0.00 0.00 3.16
1593 5080 2.232208 GGAATTTTGGAGGCTCACAAGG 59.768 50.000 17.69 0.00 0.00 3.61
1594 5081 1.928868 ATTTTGGAGGCTCACAAGGG 58.071 50.000 17.69 0.00 0.00 3.95
1595 5082 0.827507 TTTTGGAGGCTCACAAGGGC 60.828 55.000 17.69 0.00 0.00 5.19
1600 5087 2.037847 GGCTCACAAGGGCCCATT 59.962 61.111 27.56 12.87 42.30 3.16
1601 5088 1.610379 GGCTCACAAGGGCCCATTT 60.610 57.895 27.56 7.69 42.30 2.32
1602 5089 0.324275 GGCTCACAAGGGCCCATTTA 60.324 55.000 27.56 3.89 42.30 1.40
1603 5090 0.817654 GCTCACAAGGGCCCATTTAC 59.182 55.000 27.56 2.63 0.00 2.01
1604 5091 1.890573 GCTCACAAGGGCCCATTTACA 60.891 52.381 27.56 1.32 0.00 2.41
1605 5092 2.094675 CTCACAAGGGCCCATTTACAG 58.905 52.381 27.56 8.48 0.00 2.74
1606 5093 1.185315 CACAAGGGCCCATTTACAGG 58.815 55.000 27.56 0.48 0.00 4.00
1607 5094 1.080638 ACAAGGGCCCATTTACAGGA 58.919 50.000 27.56 0.00 0.00 3.86
1608 5095 1.272480 ACAAGGGCCCATTTACAGGAC 60.272 52.381 27.56 0.00 0.00 3.85
1609 5096 1.080638 AAGGGCCCATTTACAGGACA 58.919 50.000 27.56 0.00 30.00 4.02
1610 5097 1.080638 AGGGCCCATTTACAGGACAA 58.919 50.000 27.56 0.00 30.00 3.18
1611 5098 1.005924 AGGGCCCATTTACAGGACAAG 59.994 52.381 27.56 0.00 30.00 3.16
1612 5099 1.474330 GGCCCATTTACAGGACAAGG 58.526 55.000 0.00 0.00 0.00 3.61
1613 5100 0.817654 GCCCATTTACAGGACAAGGC 59.182 55.000 0.00 0.00 0.00 4.35
1614 5101 1.474330 CCCATTTACAGGACAAGGCC 58.526 55.000 0.00 0.00 0.00 5.19
1615 5102 1.272425 CCCATTTACAGGACAAGGCCA 60.272 52.381 5.01 0.00 0.00 5.36
1616 5103 2.624029 CCCATTTACAGGACAAGGCCAT 60.624 50.000 5.01 0.00 0.00 4.40
1617 5104 3.372566 CCCATTTACAGGACAAGGCCATA 60.373 47.826 5.01 0.00 0.00 2.74
1618 5105 4.277476 CCATTTACAGGACAAGGCCATAA 58.723 43.478 5.01 0.00 0.00 1.90
1619 5106 4.339247 CCATTTACAGGACAAGGCCATAAG 59.661 45.833 5.01 0.00 0.00 1.73
1620 5107 3.644966 TTACAGGACAAGGCCATAAGG 57.355 47.619 5.01 0.00 38.23 2.69
1621 5108 0.625849 ACAGGACAAGGCCATAAGGG 59.374 55.000 5.01 0.00 40.85 3.95
1719 5206 6.419791 TGGGGACAAAAGGTATATGTTGTAG 58.580 40.000 0.00 0.00 37.44 2.74
1722 5209 6.546034 GGGACAAAAGGTATATGTTGTAGCAT 59.454 38.462 0.00 0.00 34.44 3.79
1795 5282 1.963515 AGTCAACAACCTTTCATGCCC 59.036 47.619 0.00 0.00 0.00 5.36
1936 5423 8.780249 GTGTAACTGTTACATTACTGTTGGATT 58.220 33.333 29.66 0.00 46.73 3.01
2010 5497 0.821517 ATGTTGTGATCTCGGCCGTA 59.178 50.000 27.15 15.53 0.00 4.02
2140 5627 3.262151 TGTGCACACCTTATGGCTTACTA 59.738 43.478 17.42 0.00 36.63 1.82
2245 5738 3.127425 ACTGTGCACCCTAAACTCTTC 57.873 47.619 15.69 0.00 0.00 2.87
2281 5774 7.846644 ACTTGTGAATTGCATTTTCTTCAAA 57.153 28.000 10.27 0.00 30.06 2.69
2444 5939 2.014010 AACATGTTGAATGTGCCCCT 57.986 45.000 11.07 0.00 31.80 4.79
2481 5976 3.713248 AGACTGATACCATGCATTCCTCA 59.287 43.478 0.00 0.00 0.00 3.86
2491 5986 6.545567 ACCATGCATTCCTCATGTCATTATA 58.454 36.000 0.00 0.00 39.60 0.98
2595 6090 3.055747 TGTGGATCGTAACCATGCAGTTA 60.056 43.478 0.00 0.00 39.69 2.24
2727 6222 1.852157 AAGCCTTCCGCAGATTGGGA 61.852 55.000 0.00 0.00 41.38 4.37
2731 6226 1.202855 CCTTCCGCAGATTGGGATCAT 60.203 52.381 0.00 0.00 34.60 2.45
2789 6284 7.013369 GGTGATGGAAATGTAAAAGGTAGATCC 59.987 40.741 0.00 0.00 0.00 3.36
2821 6316 7.880195 AGATGCCCTTAATATGATTGTACAGTC 59.120 37.037 11.23 11.23 0.00 3.51
2904 6399 4.453819 GGATTATGGCTGCACTCTTATGTC 59.546 45.833 0.50 0.00 0.00 3.06
2998 6493 3.922375 TCCAAGGACCCTGAACAAAATT 58.078 40.909 0.00 0.00 0.00 1.82
3010 6505 6.881065 CCCTGAACAAAATTCTGTATCTGAGA 59.119 38.462 0.00 0.00 0.00 3.27
3015 6510 5.639506 ACAAAATTCTGTATCTGAGACCACG 59.360 40.000 0.00 0.00 0.00 4.94
3128 6623 7.093465 ACGAACTCCTGAATAAGATTCAAGGTA 60.093 37.037 3.66 0.00 0.00 3.08
3130 6625 9.449719 GAACTCCTGAATAAGATTCAAGGTAAA 57.550 33.333 3.66 0.00 0.00 2.01
3132 6627 9.807921 ACTCCTGAATAAGATTCAAGGTAAAAA 57.192 29.630 3.66 0.00 0.00 1.94
3338 6834 3.652581 AGCAACTGAGCTTTACCCC 57.347 52.632 0.00 0.00 43.70 4.95
3346 6842 0.392461 GAGCTTTACCCCGATGTGCA 60.392 55.000 0.00 0.00 0.00 4.57
3350 6846 2.884639 GCTTTACCCCGATGTGCATTAT 59.115 45.455 0.00 0.00 0.00 1.28
3617 7113 0.256752 GTAACAGCCCGGGGGTTTAT 59.743 55.000 25.28 7.23 37.65 1.40
3737 7233 5.878332 AAATGATGAATAAGTGTCGCACA 57.122 34.783 11.58 0.00 36.74 4.57
3750 7246 2.290367 TGTCGCACACCAAAAATCTGAG 59.710 45.455 0.00 0.00 0.00 3.35
3785 7281 5.455056 TTACTCTGTTCTGTCTTCTGTCC 57.545 43.478 0.00 0.00 0.00 4.02
3803 7299 5.951747 TCTGTCCTTTTTGGGATCTATTTGG 59.048 40.000 0.00 0.00 37.73 3.28
3807 7303 6.437477 GTCCTTTTTGGGATCTATTTGGAACT 59.563 38.462 0.00 0.00 37.73 3.01
4217 7715 5.633182 CCAATGTTGATCTTTGGTAAAACCG 59.367 40.000 0.00 0.00 42.58 4.44
4219 7717 7.364200 CAATGTTGATCTTTGGTAAAACCGTA 58.636 34.615 0.00 0.00 42.58 4.02
4220 7718 6.939132 TGTTGATCTTTGGTAAAACCGTAA 57.061 33.333 0.00 0.00 42.58 3.18
4221 7719 7.330900 TGTTGATCTTTGGTAAAACCGTAAA 57.669 32.000 0.00 0.00 42.58 2.01
4222 7720 7.769220 TGTTGATCTTTGGTAAAACCGTAAAA 58.231 30.769 0.00 0.00 42.58 1.52
4223 7721 7.916450 TGTTGATCTTTGGTAAAACCGTAAAAG 59.084 33.333 0.00 2.52 42.58 2.27
4224 7722 7.571080 TGATCTTTGGTAAAACCGTAAAAGT 57.429 32.000 0.00 0.00 42.58 2.66
4225 7723 7.419204 TGATCTTTGGTAAAACCGTAAAAGTG 58.581 34.615 0.00 0.00 42.58 3.16
4226 7724 6.756299 TCTTTGGTAAAACCGTAAAAGTGT 57.244 33.333 7.07 0.00 42.58 3.55
4227 7725 6.553524 TCTTTGGTAAAACCGTAAAAGTGTG 58.446 36.000 7.07 0.00 42.58 3.82
4248 7746 4.472833 GTGAGCCCCAAGATCATCCTATAT 59.527 45.833 0.00 0.00 0.00 0.86
4277 7775 6.183360 GCCCTTCCTTTATAACCTTCCAAATC 60.183 42.308 0.00 0.00 0.00 2.17
4278 7776 6.039382 CCCTTCCTTTATAACCTTCCAAATCG 59.961 42.308 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 1.441729 CCGCCATGATACGGTGTCT 59.558 57.895 12.07 0.00 44.46 3.41
79 80 1.614413 GAGTTGACGGAGAACTCACCT 59.386 52.381 14.91 0.00 45.84 4.00
173 175 5.138125 TGCCAAACAAAAATCTGGATCTC 57.862 39.130 0.00 0.00 0.00 2.75
179 181 6.667007 AAGAAGTTGCCAAACAAAAATCTG 57.333 33.333 0.00 0.00 40.82 2.90
221 225 0.460284 CGCTTAAGCACATCGGTCCT 60.460 55.000 26.29 0.00 42.21 3.85
267 272 1.002366 CTCAGACACCGTGCATAAGC 58.998 55.000 0.00 0.00 42.57 3.09
401 416 2.615191 TAGCCCCGGTTGGATAGCCT 62.615 60.000 0.00 0.00 37.49 4.58
419 436 2.479837 CCAGAATAAAGCGGCGATGTA 58.520 47.619 12.98 3.39 0.00 2.29
430 447 3.378112 CCGCAAAGATGAGCCAGAATAAA 59.622 43.478 0.00 0.00 0.00 1.40
442 468 0.168788 ACAACATCGCCGCAAAGATG 59.831 50.000 9.77 9.77 46.95 2.90
526 552 8.637099 AGAAAAGGAAGGAATTTGAAGAAGAAG 58.363 33.333 0.00 0.00 0.00 2.85
527 553 8.416329 CAGAAAAGGAAGGAATTTGAAGAAGAA 58.584 33.333 0.00 0.00 0.00 2.52
528 554 7.470563 GCAGAAAAGGAAGGAATTTGAAGAAGA 60.471 37.037 0.00 0.00 0.00 2.87
531 557 5.598005 TGCAGAAAAGGAAGGAATTTGAAGA 59.402 36.000 0.00 0.00 0.00 2.87
560 586 2.990479 CCTAGAAAGCGGGTGCCT 59.010 61.111 0.00 0.00 44.31 4.75
623 649 2.983166 CGATAGTCGACGCATTGTAGT 58.017 47.619 10.46 0.00 43.74 2.73
698 731 7.658179 ACACGATCATGCCTAATAAACATAG 57.342 36.000 0.00 0.00 0.00 2.23
709 743 0.523072 GCAACAACACGATCATGCCT 59.477 50.000 0.00 0.00 0.00 4.75
718 752 3.656045 GTCGGGGGCAACAACACG 61.656 66.667 0.00 0.00 39.74 4.49
732 766 1.332552 CCAAAACAAGAACGACGGTCG 60.333 52.381 27.33 27.33 46.93 4.79
734 768 2.027003 TCCAAAACAAGAACGACGGT 57.973 45.000 0.00 0.00 0.00 4.83
736 770 3.728718 CCAAATCCAAAACAAGAACGACG 59.271 43.478 0.00 0.00 0.00 5.12
798 836 8.635765 AATAACAGAGTCATGAAAGGCTTTTA 57.364 30.769 14.66 10.70 0.00 1.52
799 837 7.530426 AATAACAGAGTCATGAAAGGCTTTT 57.470 32.000 14.66 0.00 0.00 2.27
807 845 4.511454 GCGGCATAATAACAGAGTCATGAA 59.489 41.667 0.00 0.00 0.00 2.57
809 847 3.187227 GGCGGCATAATAACAGAGTCATG 59.813 47.826 3.07 0.00 0.00 3.07
810 848 3.071602 AGGCGGCATAATAACAGAGTCAT 59.928 43.478 13.08 0.00 0.00 3.06
811 849 2.434336 AGGCGGCATAATAACAGAGTCA 59.566 45.455 13.08 0.00 0.00 3.41
812 850 3.113260 AGGCGGCATAATAACAGAGTC 57.887 47.619 13.08 0.00 0.00 3.36
814 852 2.808543 GGAAGGCGGCATAATAACAGAG 59.191 50.000 13.08 0.00 0.00 3.35
815 853 2.438021 AGGAAGGCGGCATAATAACAGA 59.562 45.455 13.08 0.00 0.00 3.41
816 854 2.851195 AGGAAGGCGGCATAATAACAG 58.149 47.619 13.08 0.00 0.00 3.16
818 856 2.552743 GGAAGGAAGGCGGCATAATAAC 59.447 50.000 13.08 0.00 0.00 1.89
819 857 2.488347 GGGAAGGAAGGCGGCATAATAA 60.488 50.000 13.08 0.00 0.00 1.40
856 910 3.397955 ACAGGGGAAAAGGTGTGATTAGT 59.602 43.478 0.00 0.00 0.00 2.24
932 987 4.729868 AGGCAGAATGTAGTGGTTTTCTT 58.270 39.130 0.00 0.00 39.31 2.52
1227 1282 5.393866 AGAGAGGAAGGATCTGGATAAGAC 58.606 45.833 0.00 0.00 37.88 3.01
1249 1304 4.832823 AGACCCACCAACCTTCATAAAAAG 59.167 41.667 0.00 0.00 0.00 2.27
1257 1312 3.072622 AGAAGTTAGACCCACCAACCTTC 59.927 47.826 0.00 0.00 0.00 3.46
1258 1313 3.053826 AGAAGTTAGACCCACCAACCTT 58.946 45.455 0.00 0.00 0.00 3.50
1259 1314 2.702748 AGAAGTTAGACCCACCAACCT 58.297 47.619 0.00 0.00 0.00 3.50
1260 1315 4.838904 ATAGAAGTTAGACCCACCAACC 57.161 45.455 0.00 0.00 0.00 3.77
1282 4651 1.142667 CCAAAATGGCACCACCCTTTT 59.857 47.619 0.00 0.00 44.35 2.27
1283 4652 0.764271 CCAAAATGGCACCACCCTTT 59.236 50.000 0.00 0.00 37.83 3.11
1288 4657 0.755686 TTGACCCAAAATGGCACCAC 59.244 50.000 0.00 0.00 35.79 4.16
1575 5062 1.928868 CCCTTGTGAGCCTCCAAAAT 58.071 50.000 0.00 0.00 0.00 1.82
1576 5063 0.827507 GCCCTTGTGAGCCTCCAAAA 60.828 55.000 0.00 0.00 0.00 2.44
1577 5064 1.228552 GCCCTTGTGAGCCTCCAAA 60.229 57.895 0.00 0.00 0.00 3.28
1578 5065 2.436109 GCCCTTGTGAGCCTCCAA 59.564 61.111 0.00 0.00 0.00 3.53
1579 5066 3.650950 GGCCCTTGTGAGCCTCCA 61.651 66.667 0.00 0.00 46.14 3.86
1584 5071 0.817654 GTAAATGGGCCCTTGTGAGC 59.182 55.000 25.70 3.31 0.00 4.26
1585 5072 2.094675 CTGTAAATGGGCCCTTGTGAG 58.905 52.381 25.70 8.72 0.00 3.51
1586 5073 1.272425 CCTGTAAATGGGCCCTTGTGA 60.272 52.381 25.70 1.02 0.00 3.58
1587 5074 1.185315 CCTGTAAATGGGCCCTTGTG 58.815 55.000 25.70 6.52 0.00 3.33
1588 5075 1.080638 TCCTGTAAATGGGCCCTTGT 58.919 50.000 25.70 15.27 0.00 3.16
1589 5076 1.272425 TGTCCTGTAAATGGGCCCTTG 60.272 52.381 25.70 4.00 0.00 3.61
1590 5077 1.080638 TGTCCTGTAAATGGGCCCTT 58.919 50.000 25.70 15.22 0.00 3.95
1591 5078 1.005924 CTTGTCCTGTAAATGGGCCCT 59.994 52.381 25.70 5.02 0.00 5.19
1592 5079 1.474330 CTTGTCCTGTAAATGGGCCC 58.526 55.000 17.59 17.59 0.00 5.80
1593 5080 1.474330 CCTTGTCCTGTAAATGGGCC 58.526 55.000 0.00 0.00 0.00 5.80
1594 5081 0.817654 GCCTTGTCCTGTAAATGGGC 59.182 55.000 0.00 0.00 0.00 5.36
1595 5082 1.272425 TGGCCTTGTCCTGTAAATGGG 60.272 52.381 3.32 0.00 0.00 4.00
1596 5083 2.214376 TGGCCTTGTCCTGTAAATGG 57.786 50.000 3.32 0.00 0.00 3.16
1597 5084 4.339247 CCTTATGGCCTTGTCCTGTAAATG 59.661 45.833 3.32 0.00 0.00 2.32
1598 5085 4.536765 CCTTATGGCCTTGTCCTGTAAAT 58.463 43.478 3.32 0.00 0.00 1.40
1599 5086 3.308832 CCCTTATGGCCTTGTCCTGTAAA 60.309 47.826 3.32 0.00 0.00 2.01
1600 5087 2.241176 CCCTTATGGCCTTGTCCTGTAA 59.759 50.000 3.32 0.00 0.00 2.41
1601 5088 1.843851 CCCTTATGGCCTTGTCCTGTA 59.156 52.381 3.32 0.00 0.00 2.74
1602 5089 0.625849 CCCTTATGGCCTTGTCCTGT 59.374 55.000 3.32 0.00 0.00 4.00
1603 5090 0.625849 ACCCTTATGGCCTTGTCCTG 59.374 55.000 3.32 0.00 37.83 3.86
1604 5091 1.382914 AACCCTTATGGCCTTGTCCT 58.617 50.000 3.32 0.00 37.83 3.85
1605 5092 3.222603 CATAACCCTTATGGCCTTGTCC 58.777 50.000 3.32 0.00 39.42 4.02
1606 5093 3.898482 ACATAACCCTTATGGCCTTGTC 58.102 45.455 3.32 0.00 45.67 3.18
1607 5094 4.228666 TGTACATAACCCTTATGGCCTTGT 59.771 41.667 3.32 0.00 45.67 3.16
1608 5095 4.787551 TGTACATAACCCTTATGGCCTTG 58.212 43.478 3.32 0.00 45.67 3.61
1609 5096 4.724798 TCTGTACATAACCCTTATGGCCTT 59.275 41.667 3.32 0.00 45.67 4.35
1610 5097 4.303794 TCTGTACATAACCCTTATGGCCT 58.696 43.478 3.32 0.00 45.67 5.19
1611 5098 4.699925 TCTGTACATAACCCTTATGGCC 57.300 45.455 0.00 0.00 45.67 5.36
1612 5099 7.582667 AAATTCTGTACATAACCCTTATGGC 57.417 36.000 0.00 1.26 45.67 4.40
1719 5206 4.725556 TCAAACAGAACAACGACTATGC 57.274 40.909 0.00 0.00 0.00 3.14
1757 5244 1.526575 CTTGCCGCCACCTTGTGAAT 61.527 55.000 0.00 0.00 35.23 2.57
1767 5254 2.485795 GGTTGTTGACTTGCCGCCA 61.486 57.895 0.00 0.00 0.00 5.69
1795 5282 8.946085 TGCCAACATTATAGTTTAGTCTTGAAG 58.054 33.333 0.00 0.00 0.00 3.02
2010 5497 2.463752 TCCGGTAGCTGTTGATAACCT 58.536 47.619 0.00 0.00 0.00 3.50
2172 5659 8.984891 TTGCATAACCATCAATAACAAAGAAG 57.015 30.769 0.00 0.00 0.00 2.85
2245 5738 6.696583 TGCAATTCACAAGTTGTTTCACATAG 59.303 34.615 5.57 0.00 0.00 2.23
2258 5751 9.724839 AATTTTGAAGAAAATGCAATTCACAAG 57.275 25.926 15.48 0.00 40.27 3.16
2281 5774 7.023575 GTGTTCTCATCAGCAAAATACGAATT 58.976 34.615 0.00 0.00 0.00 2.17
2388 5883 3.871594 CACAACTAATTCCCGTCCATCTC 59.128 47.826 0.00 0.00 0.00 2.75
2595 6090 3.502211 CCGAATACTGTCTTTGCAGGTTT 59.498 43.478 0.00 0.00 40.59 3.27
2715 6210 0.109153 TCCATGATCCCAATCTGCGG 59.891 55.000 0.00 0.00 32.75 5.69
2731 6226 0.979665 CTTCTCAGTTGGAGGCTCCA 59.020 55.000 32.01 32.01 46.61 3.86
2789 6284 7.120285 ACAATCATATTAAGGGCATCTTGATCG 59.880 37.037 2.32 0.00 36.93 3.69
2868 6363 4.229582 AGCCATAATCCCAGTCCTTGTTTA 59.770 41.667 0.00 0.00 0.00 2.01
2904 6399 9.708222 CAAAGATTCCTATTGTCGAAAATACAG 57.292 33.333 3.81 0.00 0.00 2.74
2998 6493 2.423892 GCTTCGTGGTCTCAGATACAGA 59.576 50.000 0.00 0.00 0.00 3.41
3010 6505 1.400494 GACAAAGTGTTGCTTCGTGGT 59.600 47.619 0.00 0.00 38.39 4.16
3148 6644 9.609346 AGACGGCAACTACAATATTATAAAAGT 57.391 29.630 0.00 0.00 0.00 2.66
3159 6655 8.179509 AGATAAGTATAGACGGCAACTACAAT 57.820 34.615 0.00 0.00 0.00 2.71
3323 6819 1.628846 ACATCGGGGTAAAGCTCAGTT 59.371 47.619 0.00 0.00 0.00 3.16
3327 6823 0.392461 TGCACATCGGGGTAAAGCTC 60.392 55.000 0.00 0.00 0.00 4.09
3338 6834 4.926832 TCCACGGTAATATAATGCACATCG 59.073 41.667 0.00 0.00 0.00 3.84
3431 6927 9.620660 CTAATAAAAATACACAACCTCCAACAC 57.379 33.333 0.00 0.00 0.00 3.32
3733 7229 4.036734 TCTCAACTCAGATTTTTGGTGTGC 59.963 41.667 0.00 0.00 0.00 4.57
3785 7281 9.025041 AGTAAGTTCCAAATAGATCCCAAAAAG 57.975 33.333 0.00 0.00 0.00 2.27
3803 7299 8.561738 TCTCATACCAAATTCCAAGTAAGTTC 57.438 34.615 0.00 0.00 0.00 3.01
3807 7303 9.527157 TTTCATCTCATACCAAATTCCAAGTAA 57.473 29.630 0.00 0.00 0.00 2.24
3962 7458 3.026694 GCTCCTTTGTAATGCCAGGAAT 58.973 45.455 0.00 0.00 34.93 3.01
3968 7464 2.999331 TGGTAGCTCCTTTGTAATGCC 58.001 47.619 0.00 0.00 37.07 4.40
4098 7594 6.994421 AAAGGGCAGGAAAGAAAAGAATTA 57.006 33.333 0.00 0.00 0.00 1.40
4215 7713 0.250553 TGGGGCTCACACTTTTACGG 60.251 55.000 0.00 0.00 0.00 4.02
4216 7714 1.535462 CTTGGGGCTCACACTTTTACG 59.465 52.381 0.00 0.00 0.00 3.18
4217 7715 2.858745 TCTTGGGGCTCACACTTTTAC 58.141 47.619 0.00 0.00 0.00 2.01
4219 7717 2.158475 TGATCTTGGGGCTCACACTTTT 60.158 45.455 0.00 0.00 0.00 2.27
4220 7718 1.425066 TGATCTTGGGGCTCACACTTT 59.575 47.619 0.00 0.00 0.00 2.66
4221 7719 1.067295 TGATCTTGGGGCTCACACTT 58.933 50.000 0.00 0.00 0.00 3.16
4222 7720 1.211457 GATGATCTTGGGGCTCACACT 59.789 52.381 0.00 0.00 0.00 3.55
4223 7721 1.673168 GATGATCTTGGGGCTCACAC 58.327 55.000 0.00 0.00 0.00 3.82
4224 7722 0.548031 GGATGATCTTGGGGCTCACA 59.452 55.000 0.00 0.00 0.00 3.58
4225 7723 0.842635 AGGATGATCTTGGGGCTCAC 59.157 55.000 0.00 0.00 0.00 3.51
4226 7724 2.494888 TAGGATGATCTTGGGGCTCA 57.505 50.000 0.00 0.00 0.00 4.26
4227 7725 6.814954 TTATATAGGATGATCTTGGGGCTC 57.185 41.667 0.00 0.00 0.00 4.70
4248 7746 6.068735 TGGAAGGTTATAAAGGAAGGGCATTA 60.069 38.462 0.00 0.00 0.00 1.90
4277 7775 2.003196 ACAAAAGTGTGTTTTGGCCG 57.997 45.000 13.28 0.00 42.09 6.13
4278 7776 4.118093 AGTACAAAAGTGTGTTTTGGCC 57.882 40.909 13.28 0.00 42.09 5.36
4318 7816 5.357742 AATTTTATGGGGGTTTGATCTGC 57.642 39.130 0.00 0.00 0.00 4.26


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

AutoCloner maintained by Alex Coulton.