Multiple sequence alignment - TraesCS7B01G481200

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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 TraesCS7B01G481200 chr7B 100.000 4500 0 0 1 4500 734683005 734687504 0.000000e+00 8311
1 TraesCS7B01G481200 chr7D 94.753 2954 100 29 586 3502 638259462 638262397 0.000000e+00 4545
2 TraesCS7B01G481200 chr7D 92.265 362 16 4 3499 3849 638262480 638262840 1.870000e-138 503
3 TraesCS7B01G481200 chr7D 85.309 388 53 4 1 386 638258738 638259123 9.070000e-107 398
4 TraesCS7B01G481200 chr7D 93.525 139 8 1 384 521 638259204 638259342 5.900000e-49 206
5 TraesCS7B01G481200 chr7A 95.206 2837 97 18 682 3486 727851108 727848279 0.000000e+00 4449
6 TraesCS7B01G481200 chr7A 96.698 636 21 0 1542 2177 727838860 727838225 0.000000e+00 1059
7 TraesCS7B01G481200 chr7A 90.746 335 20 7 3499 3827 727848170 727847841 1.920000e-118 436
8 TraesCS7B01G481200 chr7A 85.385 390 55 2 1 389 727852084 727851696 1.950000e-108 403
9 TraesCS7B01G481200 chr7A 94.500 200 11 0 3849 4048 691673853 691674052 4.370000e-80 309
10 TraesCS7B01G481200 chr7A 94.118 136 7 1 387 521 727851615 727851480 5.900000e-49 206
11 TraesCS7B01G481200 chr2A 94.181 653 36 2 3849 4500 746628315 746627664 0.000000e+00 994
12 TraesCS7B01G481200 chr4A 91.590 654 52 3 3849 4500 728109182 728109834 0.000000e+00 900
13 TraesCS7B01G481200 chr6B 79.063 726 146 6 1113 1835 717537685 717538407 1.120000e-135 494
14 TraesCS7B01G481200 chr6B 79.294 623 127 2 2841 3462 717539230 717539851 6.910000e-118 435
15 TraesCS7B01G481200 chr6D 79.421 622 128 0 2841 3462 472526658 472527279 1.490000e-119 440
16 TraesCS7B01G481200 chr6A 77.686 726 156 6 1113 1835 617184251 617183529 5.340000e-119 438
17 TraesCS7B01G481200 chr6A 78.837 619 131 0 2844 3462 617182709 617182091 6.960000e-113 418


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 TraesCS7B01G481200 chr7B 734683005 734687504 4499 False 8311.0 8311 100.00000 1 4500 1 chr7B.!!$F1 4499
1 TraesCS7B01G481200 chr7D 638258738 638262840 4102 False 1413.0 4545 91.46300 1 3849 4 chr7D.!!$F1 3848
2 TraesCS7B01G481200 chr7A 727847841 727852084 4243 True 1373.5 4449 91.36375 1 3827 4 chr7A.!!$R2 3826
3 TraesCS7B01G481200 chr7A 727838225 727838860 635 True 1059.0 1059 96.69800 1542 2177 1 chr7A.!!$R1 635
4 TraesCS7B01G481200 chr2A 746627664 746628315 651 True 994.0 994 94.18100 3849 4500 1 chr2A.!!$R1 651
5 TraesCS7B01G481200 chr4A 728109182 728109834 652 False 900.0 900 91.59000 3849 4500 1 chr4A.!!$F1 651
6 TraesCS7B01G481200 chr6B 717537685 717539851 2166 False 464.5 494 79.17850 1113 3462 2 chr6B.!!$F1 2349
7 TraesCS7B01G481200 chr6D 472526658 472527279 621 False 440.0 440 79.42100 2841 3462 1 chr6D.!!$F1 621
8 TraesCS7B01G481200 chr6A 617182091 617184251 2160 True 428.0 438 78.26150 1113 3462 2 chr6A.!!$R1 2349

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
200 201 0.106769 TTGGCTGCTGGACTTCAACA 60.107 50.0 0.00 0.00 0.00 3.33 F
310 311 0.382158 TCGGTCGCAGCTATTCTCAG 59.618 55.0 0.00 0.00 0.00 3.35 F
706 1013 0.535335 AATATCTGTGCACGACGGGT 59.465 50.0 13.13 1.23 0.00 5.28 F
1055 1414 0.627469 AGGCCCTCCTCTCTCTCTCT 60.627 60.0 0.00 0.00 38.72 3.10 F
2312 2738 0.971386 GGTGGAGGGTAAGACGAACA 59.029 55.0 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1396 1760 0.170339 CGATGAGGAGCACGTACACA 59.830 55.0 0.00 0.00 0.00 3.72 R
1540 1904 0.748005 AGTACGCCATGAACATGCCC 60.748 55.0 9.03 2.44 37.49 5.36 R
2299 2725 1.142474 CGTTGGTGTTCGTCTTACCC 58.858 55.0 0.00 0.00 33.51 3.69 R
2829 3309 1.438651 GGAGAACTGCATGCGTGTTA 58.561 50.0 22.88 1.99 0.00 2.41 R
4078 4674 0.034896 TGAAGCCCTCCGACAAGAAC 59.965 55.0 0.00 0.00 0.00 3.01 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.998315 CTGGATCAAGTGAACTCGCTG 59.002 52.381 0.00 0.00 36.72 5.18
33 34 2.417379 GGATCAAGTGAACTCGCTGCTA 60.417 50.000 0.00 0.00 36.72 3.49
40 41 1.001974 TGAACTCGCTGCTACACCAAT 59.998 47.619 0.00 0.00 0.00 3.16
45 46 1.164411 CGCTGCTACACCAATGGAAA 58.836 50.000 6.16 0.00 0.00 3.13
56 57 2.821969 ACCAATGGAAAGTGATCTGTGC 59.178 45.455 6.16 0.00 0.00 4.57
58 59 2.821378 CAATGGAAAGTGATCTGTGCCA 59.179 45.455 0.00 0.00 0.00 4.92
66 67 1.814394 GTGATCTGTGCCAATGCTCAA 59.186 47.619 0.00 0.00 40.20 3.02
69 70 0.609957 TCTGTGCCAATGCTCAAGGG 60.610 55.000 0.00 0.00 40.20 3.95
73 74 2.037687 CCAATGCTCAAGGGGCCA 59.962 61.111 4.39 0.00 0.00 5.36
78 79 0.396695 ATGCTCAAGGGGCCATTCTG 60.397 55.000 4.39 0.01 0.00 3.02
83 84 0.324091 CAAGGGGCCATTCTGCTTCT 60.324 55.000 4.39 0.00 0.00 2.85
87 88 0.108472 GGGCCATTCTGCTTCTTTGC 60.108 55.000 4.39 0.00 0.00 3.68
174 175 1.174783 GGTAACCAGCGAGTGAGAGA 58.825 55.000 0.00 0.00 0.00 3.10
175 176 1.135344 GGTAACCAGCGAGTGAGAGAC 60.135 57.143 0.00 0.00 0.00 3.36
176 177 0.803117 TAACCAGCGAGTGAGAGACG 59.197 55.000 0.00 0.00 0.00 4.18
177 178 0.889638 AACCAGCGAGTGAGAGACGA 60.890 55.000 0.00 0.00 0.00 4.20
178 179 1.135731 CCAGCGAGTGAGAGACGAC 59.864 63.158 0.00 0.00 0.00 4.34
180 181 0.238553 CAGCGAGTGAGAGACGACAA 59.761 55.000 0.00 0.00 0.00 3.18
189 190 0.322975 AGAGACGACAATTGGCTGCT 59.677 50.000 10.18 6.09 0.00 4.24
199 200 1.251251 ATTGGCTGCTGGACTTCAAC 58.749 50.000 0.00 0.00 0.00 3.18
200 201 0.106769 TTGGCTGCTGGACTTCAACA 60.107 50.000 0.00 0.00 0.00 3.33
210 211 3.221771 TGGACTTCAACAGGTTTCATGG 58.778 45.455 0.00 0.00 0.00 3.66
220 221 6.208599 TCAACAGGTTTCATGGGAAATAAGTC 59.791 38.462 0.00 0.00 44.32 3.01
223 224 5.711976 CAGGTTTCATGGGAAATAAGTCTGT 59.288 40.000 0.00 0.00 44.32 3.41
224 225 5.946377 AGGTTTCATGGGAAATAAGTCTGTC 59.054 40.000 0.00 0.00 44.32 3.51
226 227 6.434340 GGTTTCATGGGAAATAAGTCTGTCTT 59.566 38.462 0.00 0.00 44.32 3.01
237 238 7.801716 AATAAGTCTGTCTTGTGTTTTGCTA 57.198 32.000 0.00 0.00 37.56 3.49
254 255 6.801539 TTTGCTATTGTGTAGTTTCCTCTG 57.198 37.500 0.00 0.00 0.00 3.35
257 258 5.186992 TGCTATTGTGTAGTTTCCTCTGCTA 59.813 40.000 0.00 0.00 0.00 3.49
262 263 7.476540 TTGTGTAGTTTCCTCTGCTAATCTA 57.523 36.000 0.00 0.00 0.00 1.98
267 268 5.281314 AGTTTCCTCTGCTAATCTAGGGAA 58.719 41.667 0.00 0.00 0.00 3.97
293 294 7.081349 TGTGAACTTGGCTGTAATAAAATTCG 58.919 34.615 0.00 0.00 0.00 3.34
304 305 5.756347 TGTAATAAAATTCGGTCGCAGCTAT 59.244 36.000 0.00 0.00 0.00 2.97
310 311 0.382158 TCGGTCGCAGCTATTCTCAG 59.618 55.000 0.00 0.00 0.00 3.35
317 318 2.704572 GCAGCTATTCTCAGGTTGTGT 58.295 47.619 0.00 0.00 0.00 3.72
318 319 2.675348 GCAGCTATTCTCAGGTTGTGTC 59.325 50.000 0.00 0.00 0.00 3.67
325 326 3.414700 CAGGTTGTGTCCGAGCGC 61.415 66.667 0.00 0.00 0.00 5.92
354 355 2.412325 CGATGTTTGACGGTAGTTTGCC 60.412 50.000 0.00 0.00 0.00 4.52
358 359 2.876550 GTTTGACGGTAGTTTGCCTCTT 59.123 45.455 0.00 0.00 0.00 2.85
369 370 8.175716 CGGTAGTTTGCCTCTTCTTTAATAAAG 58.824 37.037 6.42 6.42 39.88 1.85
419 503 5.747342 ACGGCTAGGGTTTGTATTCAATTA 58.253 37.500 0.00 0.00 33.32 1.40
433 517 7.598278 TGTATTCAATTAGGAATTTGCACGTT 58.402 30.769 0.00 0.00 38.41 3.99
440 524 4.320608 AGGAATTTGCACGTTCAAACAT 57.679 36.364 15.48 7.89 38.58 2.71
441 525 4.692228 AGGAATTTGCACGTTCAAACATT 58.308 34.783 15.48 7.31 38.58 2.71
525 642 8.382030 TGCGGAATGAAAGGCATATATATATG 57.618 34.615 23.19 23.19 42.30 1.78
559 676 7.123355 TCATGGAGATGAAAACTTTTTGGTT 57.877 32.000 0.00 0.00 35.55 3.67
560 677 7.209475 TCATGGAGATGAAAACTTTTTGGTTC 58.791 34.615 0.00 0.00 35.55 3.62
590 707 2.919228 CCAGCCAACACTAGGGATAAC 58.081 52.381 0.00 0.00 0.00 1.89
594 711 3.587506 AGCCAACACTAGGGATAACAAGT 59.412 43.478 0.00 0.00 0.00 3.16
597 714 5.556915 CCAACACTAGGGATAACAAGTTCA 58.443 41.667 0.00 0.00 0.00 3.18
598 715 6.180472 CCAACACTAGGGATAACAAGTTCAT 58.820 40.000 0.00 0.00 0.00 2.57
600 717 7.280205 CCAACACTAGGGATAACAAGTTCATAC 59.720 40.741 0.00 0.00 0.00 2.39
602 719 8.834004 ACACTAGGGATAACAAGTTCATACTA 57.166 34.615 0.00 0.00 33.17 1.82
603 720 8.915036 ACACTAGGGATAACAAGTTCATACTAG 58.085 37.037 0.00 0.00 33.17 2.57
604 721 8.915036 CACTAGGGATAACAAGTTCATACTAGT 58.085 37.037 0.00 0.00 38.24 2.57
671 978 5.009610 TCTGCGTAATGTATACTCTGCATGA 59.990 40.000 4.17 4.94 29.77 3.07
673 980 6.919721 TGCGTAATGTATACTCTGCATGATA 58.080 36.000 4.17 0.00 29.77 2.15
706 1013 0.535335 AATATCTGTGCACGACGGGT 59.465 50.000 13.13 1.23 0.00 5.28
709 1016 4.012895 CTGTGCACGACGGGTTGC 62.013 66.667 13.13 0.00 0.00 4.17
710 1017 4.840005 TGTGCACGACGGGTTGCA 62.840 61.111 13.13 7.45 32.68 4.08
727 1034 2.608467 GCAGTAGCAAAACAGAGCAG 57.392 50.000 0.00 0.00 41.58 4.24
753 1060 2.798847 ACGTAGTTGCGGAAAAAGAGAC 59.201 45.455 0.00 0.00 37.78 3.36
766 1073 6.342111 GGAAAAAGAGACGAGGATAAGTGAT 58.658 40.000 0.00 0.00 0.00 3.06
767 1074 7.490000 GGAAAAAGAGACGAGGATAAGTGATA 58.510 38.462 0.00 0.00 0.00 2.15
769 1076 6.394025 AAAGAGACGAGGATAAGTGATACC 57.606 41.667 0.00 0.00 0.00 2.73
771 1078 4.105057 AGAGACGAGGATAAGTGATACCCT 59.895 45.833 0.00 0.00 0.00 4.34
774 1081 3.637229 ACGAGGATAAGTGATACCCTGTG 59.363 47.826 0.00 0.00 0.00 3.66
775 1082 3.005897 CGAGGATAAGTGATACCCTGTGG 59.994 52.174 0.00 0.00 37.80 4.17
785 1092 0.688487 TACCCTGTGGTAACTGTGGC 59.312 55.000 0.00 0.00 45.45 5.01
786 1093 1.349542 ACCCTGTGGTAACTGTGGCA 61.350 55.000 0.00 0.00 45.45 4.92
787 1094 0.889186 CCCTGTGGTAACTGTGGCAC 60.889 60.000 11.55 11.55 37.61 5.01
788 1095 1.227999 CCTGTGGTAACTGTGGCACG 61.228 60.000 13.77 10.33 37.61 5.34
789 1096 1.227704 TGTGGTAACTGTGGCACGG 60.228 57.895 24.47 24.47 37.61 4.94
790 1097 1.227734 GTGGTAACTGTGGCACGGT 60.228 57.895 25.95 25.95 39.91 4.83
791 1098 1.227704 TGGTAACTGTGGCACGGTG 60.228 57.895 31.24 16.88 37.84 4.94
827 1181 2.866762 CGTGTATAGCAGAAAAGAGGCC 59.133 50.000 0.00 0.00 0.00 5.19
828 1182 3.206964 GTGTATAGCAGAAAAGAGGCCC 58.793 50.000 0.00 0.00 0.00 5.80
852 1206 2.073037 GACCGACCGAGGCTGGATAC 62.073 65.000 9.53 1.60 33.69 2.24
944 1302 0.744771 CGGCCCAAGTTTAGCTCCTC 60.745 60.000 0.00 0.00 0.00 3.71
945 1303 0.744771 GGCCCAAGTTTAGCTCCTCG 60.745 60.000 0.00 0.00 0.00 4.63
969 1327 2.051518 TGGATCCATTGCCAACCGC 61.052 57.895 11.44 0.00 38.31 5.68
997 1355 2.103934 CTCCTCGCTGCTCCTTCG 59.896 66.667 0.00 0.00 0.00 3.79
998 1356 3.423162 CTCCTCGCTGCTCCTTCGG 62.423 68.421 0.00 0.00 0.00 4.30
1001 1359 4.742201 TCGCTGCTCCTTCGGCAC 62.742 66.667 0.00 0.00 38.22 5.01
1020 1378 3.896888 GCACCCATATGATCCATTTTCCA 59.103 43.478 3.65 0.00 0.00 3.53
1025 1383 5.105635 CCCATATGATCCATTTTCCAATCCG 60.106 44.000 3.65 0.00 0.00 4.18
1030 1389 3.162147 TCCATTTTCCAATCCGACCAA 57.838 42.857 0.00 0.00 0.00 3.67
1054 1413 1.930520 AGGCCCTCCTCTCTCTCTC 59.069 63.158 0.00 0.00 38.72 3.20
1055 1414 0.627469 AGGCCCTCCTCTCTCTCTCT 60.627 60.000 0.00 0.00 38.72 3.10
1079 1442 3.596046 TCTTCTCTCTTCTCCCTCCTCTT 59.404 47.826 0.00 0.00 0.00 2.85
1082 1445 3.596046 TCTCTCTTCTCCCTCCTCTTCTT 59.404 47.826 0.00 0.00 0.00 2.52
1366 1730 1.285373 TCCTCGCTCCTCTACTTCCTT 59.715 52.381 0.00 0.00 0.00 3.36
1384 1748 4.221422 GGCGGGCTCGTCATGCTA 62.221 66.667 5.26 0.00 41.24 3.49
1396 1760 1.145738 GTCATGCTATGGTCCCCCAAT 59.854 52.381 0.00 0.00 46.04 3.16
1522 1886 1.166531 GCCTGCTCAACACGTTTCCT 61.167 55.000 0.00 0.00 0.00 3.36
1540 1904 2.885644 CAGTTCACGGGATCGGCG 60.886 66.667 0.00 0.00 41.39 6.46
1555 1919 4.557605 GCGGGCATGTTCATGGCG 62.558 66.667 25.15 21.45 46.64 5.69
2299 2725 2.575993 CAGAGCACGGAGGTGGAG 59.424 66.667 0.00 0.00 44.54 3.86
2312 2738 0.971386 GGTGGAGGGTAAGACGAACA 59.029 55.000 0.00 0.00 0.00 3.18
2320 2746 1.788886 GGTAAGACGAACACCAACGAC 59.211 52.381 0.00 0.00 32.32 4.34
2770 3250 5.758296 CCAGCAGGTACGTGTTCAATATATT 59.242 40.000 16.36 0.00 0.00 1.28
2829 3309 0.107456 GACATGGATCCCACGATGCT 59.893 55.000 9.90 0.00 37.70 3.79
3067 3551 0.816825 CCATCCCGGTGCTCATCTTG 60.817 60.000 0.00 0.00 0.00 3.02
3108 3592 3.430862 CAACGTCGTGCCCATGGG 61.431 66.667 27.87 27.87 38.57 4.00
3471 3955 2.953284 ATCCCAGAGCAGATGGATTG 57.047 50.000 3.61 0.00 40.51 2.67
3476 3960 4.600547 TCCCAGAGCAGATGGATTGATTAT 59.399 41.667 3.61 0.00 40.51 1.28
3477 3961 5.786975 TCCCAGAGCAGATGGATTGATTATA 59.213 40.000 3.61 0.00 40.51 0.98
3478 3962 6.273026 TCCCAGAGCAGATGGATTGATTATAA 59.727 38.462 3.61 0.00 40.51 0.98
3479 3963 7.037080 TCCCAGAGCAGATGGATTGATTATAAT 60.037 37.037 0.00 0.00 40.51 1.28
3480 3964 7.614583 CCCAGAGCAGATGGATTGATTATAATT 59.385 37.037 0.00 0.00 40.51 1.40
3481 3965 9.676861 CCAGAGCAGATGGATTGATTATAATTA 57.323 33.333 0.00 0.00 40.51 1.40
3515 4098 0.694771 TTGGTCTCTTGCTCCATGCT 59.305 50.000 0.00 0.00 43.37 3.79
3555 4139 4.301072 TGTTAGGCTAAAGCAGACCAAT 57.699 40.909 8.86 0.00 44.36 3.16
3556 4140 4.009675 TGTTAGGCTAAAGCAGACCAATG 58.990 43.478 8.86 0.00 44.36 2.82
3557 4141 4.261801 GTTAGGCTAAAGCAGACCAATGA 58.738 43.478 8.86 0.00 44.36 2.57
3558 4142 3.659183 AGGCTAAAGCAGACCAATGAT 57.341 42.857 4.07 0.00 44.36 2.45
3559 4143 3.285484 AGGCTAAAGCAGACCAATGATG 58.715 45.455 4.07 0.00 44.36 3.07
3560 4144 3.705043 GCTAAAGCAGACCAATGATGG 57.295 47.619 0.00 0.00 46.19 3.51
3599 4192 7.716123 TCAGTTTTACTTCCTTCATTCGGTTTA 59.284 33.333 0.00 0.00 0.00 2.01
3762 4357 8.505625 TGAATTTCGGTTTATTGTAGTACCAAC 58.494 33.333 0.00 0.00 0.00 3.77
3779 4374 3.067601 ACCAACTGATGCATGCATGTATG 59.932 43.478 36.73 25.67 36.70 2.39
3792 4387 7.066766 TGCATGCATGTATGAAGTGTTGTATAA 59.933 33.333 25.73 0.00 0.00 0.98
3820 4415 9.612620 ACTTTGATTTTGAACGATGAATTCTAC 57.387 29.630 7.05 0.00 0.00 2.59
3840 4435 7.468141 TCTACATATTCACTCACAAGTCACT 57.532 36.000 0.00 0.00 31.71 3.41
3844 4439 4.955811 ATTCACTCACAAGTCACTACCA 57.044 40.909 0.00 0.00 31.71 3.25
3858 4453 1.678627 ACTACCAGTATGAGCAGCTCG 59.321 52.381 17.81 4.62 39.69 5.03
3880 4475 1.438469 CATAGGCCTGAATCCCTGGA 58.562 55.000 17.99 0.00 36.07 3.86
3888 4483 4.390264 GCCTGAATCCCTGGAAAGTATAC 58.610 47.826 0.00 0.00 36.07 1.47
3900 4495 6.201044 CCTGGAAAGTATACAACGCTTCATAG 59.799 42.308 5.50 3.20 30.53 2.23
3921 4516 1.915141 AACCTTGGACTTCTGCATGG 58.085 50.000 0.00 0.00 38.58 3.66
4020 4615 3.391506 GCCTGGGCATGAAAATATTCC 57.608 47.619 6.75 0.00 41.49 3.01
4078 4674 4.497006 GGATCTTTGACGCATCCAGATTTG 60.497 45.833 0.00 0.00 36.78 2.32
4098 4694 0.984230 TTCTTGTCGGAGGGCTTCAT 59.016 50.000 0.00 0.00 0.00 2.57
4235 4831 1.228675 CTTGGCTCCCCAACTTGCT 60.229 57.895 0.00 0.00 46.01 3.91
4258 4854 5.051891 AGTTTCTGCTGCATATTGTTGAC 57.948 39.130 1.31 0.00 0.00 3.18
4287 4883 2.283388 CACCAGCCAACCCATGCT 60.283 61.111 0.00 0.00 38.67 3.79
4288 4884 1.001020 CACCAGCCAACCCATGCTA 60.001 57.895 0.00 0.00 35.69 3.49
4335 4931 5.009710 TGAAGTACTAGCTGGTCATAATCGG 59.990 44.000 5.78 0.00 0.00 4.18
4405 5001 6.402766 CGTGTTCTTGTTCCTGACAAACTTTA 60.403 38.462 0.00 0.00 46.99 1.85
4434 5030 6.322456 TGGATCAACCAGTACAAAACAATGAA 59.678 34.615 0.00 0.00 44.64 2.57
4472 5068 4.666655 GCAATATGTCGAACATGCGTATCC 60.667 45.833 9.77 0.00 39.53 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 1.605712 GGTGTAGCAGCGAGTTCACTT 60.606 52.381 0.00 0.00 0.00 3.16
30 31 4.095483 CAGATCACTTTCCATTGGTGTAGC 59.905 45.833 1.86 0.00 33.30 3.58
33 34 3.822735 CACAGATCACTTTCCATTGGTGT 59.177 43.478 1.86 0.00 33.30 4.16
40 41 2.655090 TTGGCACAGATCACTTTCCA 57.345 45.000 0.00 0.00 42.39 3.53
45 46 1.003928 TGAGCATTGGCACAGATCACT 59.996 47.619 2.57 0.00 44.61 3.41
56 57 0.979187 AATGGCCCCTTGAGCATTGG 60.979 55.000 0.00 0.00 0.00 3.16
58 59 0.337428 AGAATGGCCCCTTGAGCATT 59.663 50.000 0.00 0.00 0.00 3.56
66 67 0.411058 AAAGAAGCAGAATGGCCCCT 59.589 50.000 0.00 0.00 35.86 4.79
69 70 0.108472 GGCAAAGAAGCAGAATGGCC 60.108 55.000 0.00 0.00 35.86 5.36
73 74 1.544691 CAGCAGGCAAAGAAGCAGAAT 59.455 47.619 0.00 0.00 35.83 2.40
87 88 1.134189 TGATGATCAAGGAGCAGCAGG 60.134 52.381 0.00 0.00 39.39 4.85
121 122 2.123589 TCAGTTCCTGGTTGTCCTCAA 58.876 47.619 0.00 0.00 31.51 3.02
130 131 1.694696 GAGAAGTGGTCAGTTCCTGGT 59.305 52.381 13.18 0.00 40.69 4.00
133 134 1.889829 CTCGAGAAGTGGTCAGTTCCT 59.110 52.381 6.58 3.53 40.69 3.36
148 149 2.579787 CGCTGGTTACCGCTCGAG 60.580 66.667 8.45 8.45 0.00 4.04
150 151 2.579787 CTCGCTGGTTACCGCTCG 60.580 66.667 14.06 9.29 0.00 5.03
165 166 1.996191 GCCAATTGTCGTCTCTCACTC 59.004 52.381 4.43 0.00 0.00 3.51
167 168 1.728971 CAGCCAATTGTCGTCTCTCAC 59.271 52.381 4.43 0.00 0.00 3.51
168 169 1.941209 GCAGCCAATTGTCGTCTCTCA 60.941 52.381 4.43 0.00 0.00 3.27
170 171 0.322975 AGCAGCCAATTGTCGTCTCT 59.677 50.000 4.43 0.00 0.00 3.10
171 172 0.445436 CAGCAGCCAATTGTCGTCTC 59.555 55.000 4.43 0.00 0.00 3.36
172 173 0.957395 CCAGCAGCCAATTGTCGTCT 60.957 55.000 4.43 0.00 0.00 4.18
174 175 1.073025 TCCAGCAGCCAATTGTCGT 59.927 52.632 4.43 0.00 0.00 4.34
175 176 0.957395 AGTCCAGCAGCCAATTGTCG 60.957 55.000 4.43 0.00 0.00 4.35
176 177 1.200948 GAAGTCCAGCAGCCAATTGTC 59.799 52.381 4.43 0.00 0.00 3.18
177 178 1.251251 GAAGTCCAGCAGCCAATTGT 58.749 50.000 4.43 0.00 0.00 2.71
178 179 1.250328 TGAAGTCCAGCAGCCAATTG 58.750 50.000 0.00 0.00 0.00 2.32
180 181 1.251251 GTTGAAGTCCAGCAGCCAAT 58.749 50.000 0.00 0.00 0.00 3.16
189 190 3.221771 CCATGAAACCTGTTGAAGTCCA 58.778 45.455 0.00 0.00 0.00 4.02
199 200 5.711976 ACAGACTTATTTCCCATGAAACCTG 59.288 40.000 0.00 0.00 42.97 4.00
200 201 5.892348 ACAGACTTATTTCCCATGAAACCT 58.108 37.500 0.00 0.00 42.97 3.50
210 211 6.417930 GCAAAACACAAGACAGACTTATTTCC 59.582 38.462 0.00 0.00 37.03 3.13
220 221 5.581605 ACACAATAGCAAAACACAAGACAG 58.418 37.500 0.00 0.00 0.00 3.51
223 224 6.935741 ACTACACAATAGCAAAACACAAGA 57.064 33.333 0.00 0.00 0.00 3.02
224 225 7.167468 GGAAACTACACAATAGCAAAACACAAG 59.833 37.037 0.00 0.00 0.00 3.16
226 227 6.320164 AGGAAACTACACAATAGCAAAACACA 59.680 34.615 0.00 0.00 40.61 3.72
237 238 6.951971 AGATTAGCAGAGGAAACTACACAAT 58.048 36.000 0.00 0.00 44.43 2.71
254 255 5.529060 CCAAGTTCACATTCCCTAGATTAGC 59.471 44.000 0.00 0.00 0.00 3.09
257 258 4.018050 AGCCAAGTTCACATTCCCTAGATT 60.018 41.667 0.00 0.00 0.00 2.40
262 263 1.145738 ACAGCCAAGTTCACATTCCCT 59.854 47.619 0.00 0.00 0.00 4.20
267 268 7.754924 CGAATTTTATTACAGCCAAGTTCACAT 59.245 33.333 0.00 0.00 0.00 3.21
293 294 0.461961 ACCTGAGAATAGCTGCGACC 59.538 55.000 0.00 0.00 0.00 4.79
304 305 0.033504 GCTCGGACACAACCTGAGAA 59.966 55.000 0.00 0.00 34.82 2.87
317 318 4.764336 CGTTACACGGCGCTCGGA 62.764 66.667 19.73 4.89 44.45 4.55
318 319 4.764336 TCGTTACACGGCGCTCGG 62.764 66.667 19.73 12.20 42.81 4.63
325 326 1.125384 CCGTCAAACATCGTTACACGG 59.875 52.381 12.48 12.48 42.81 4.94
343 344 7.605410 TTATTAAAGAAGAGGCAAACTACCG 57.395 36.000 0.00 0.00 0.00 4.02
354 355 6.152831 CCCACCCAACCTTTATTAAAGAAGAG 59.847 42.308 16.13 3.79 41.02 2.85
358 359 4.511294 CCCCCACCCAACCTTTATTAAAGA 60.511 45.833 16.13 0.00 41.02 2.52
369 370 4.548513 TGTTGCCCCCACCCAACC 62.549 66.667 0.00 0.00 40.34 3.77
419 503 3.791973 TGTTTGAACGTGCAAATTCCT 57.208 38.095 24.12 0.00 39.65 3.36
433 517 1.614996 ATGCCGGTCACAATGTTTGA 58.385 45.000 1.90 0.00 0.00 2.69
493 578 2.682856 GCCTTTCATTCCGCAGTTCATA 59.317 45.455 0.00 0.00 0.00 2.15
501 586 7.094634 CCCATATATATATGCCTTTCATTCCGC 60.095 40.741 22.44 0.00 38.99 5.54
525 642 8.160106 AGTTTTCATCTCCATGATTATAGACCC 58.840 37.037 0.00 0.00 38.89 4.46
532 649 8.869109 ACCAAAAAGTTTTCATCTCCATGATTA 58.131 29.630 0.32 0.00 38.89 1.75
535 652 6.729690 ACCAAAAAGTTTTCATCTCCATGA 57.270 33.333 0.32 0.00 37.24 3.07
578 695 8.915036 ACTAGTATGAACTTGTTATCCCTAGTG 58.085 37.037 0.00 0.00 38.32 2.74
582 699 9.710818 TCTTACTAGTATGAACTTGTTATCCCT 57.289 33.333 14.38 0.00 41.17 4.20
590 707 7.702772 ACGCATCTTCTTACTAGTATGAACTTG 59.297 37.037 21.31 20.27 37.15 3.16
594 711 5.977725 GCACGCATCTTCTTACTAGTATGAA 59.022 40.000 22.84 22.84 0.00 2.57
597 714 5.515797 TGCACGCATCTTCTTACTAGTAT 57.484 39.130 2.79 0.00 0.00 2.12
598 715 4.976224 TGCACGCATCTTCTTACTAGTA 57.024 40.909 0.00 0.00 0.00 1.82
600 717 4.963237 GATGCACGCATCTTCTTACTAG 57.037 45.455 21.88 0.00 46.67 2.57
633 780 7.920738 ACATTACGCAGATCTTTATTCCTTTC 58.079 34.615 0.00 0.00 0.00 2.62
634 781 7.865706 ACATTACGCAGATCTTTATTCCTTT 57.134 32.000 0.00 0.00 0.00 3.11
641 788 7.808381 GCAGAGTATACATTACGCAGATCTTTA 59.192 37.037 5.50 0.00 0.00 1.85
648 795 5.222631 TCATGCAGAGTATACATTACGCAG 58.777 41.667 5.50 2.13 0.00 5.18
651 798 8.409371 AGGATATCATGCAGAGTATACATTACG 58.591 37.037 5.50 0.00 0.00 3.18
680 987 6.093404 CCGTCGTGCACAGATATTTAGATAT 58.907 40.000 18.64 0.00 0.00 1.63
681 988 5.458015 CCGTCGTGCACAGATATTTAGATA 58.542 41.667 18.64 0.00 0.00 1.98
682 989 4.299155 CCGTCGTGCACAGATATTTAGAT 58.701 43.478 18.64 0.00 0.00 1.98
683 990 3.490249 CCCGTCGTGCACAGATATTTAGA 60.490 47.826 18.64 0.00 0.00 2.10
692 999 4.012895 GCAACCCGTCGTGCACAG 62.013 66.667 18.64 9.95 0.00 3.66
709 1016 3.059325 GTGTCTGCTCTGTTTTGCTACTG 60.059 47.826 0.00 0.00 0.00 2.74
710 1017 3.134458 GTGTCTGCTCTGTTTTGCTACT 58.866 45.455 0.00 0.00 0.00 2.57
727 1034 1.210870 TTTCCGCAACTACGTGTGTC 58.789 50.000 0.00 0.00 0.00 3.67
753 1060 3.005897 CCACAGGGTATCACTTATCCTCG 59.994 52.174 0.00 0.00 39.61 4.63
769 1076 1.227999 CGTGCCACAGTTACCACAGG 61.228 60.000 0.00 0.00 0.00 4.00
771 1078 1.227704 CCGTGCCACAGTTACCACA 60.228 57.895 0.00 0.00 0.00 4.17
774 1081 1.964373 CCACCGTGCCACAGTTACC 60.964 63.158 0.00 0.00 0.00 2.85
775 1082 1.964373 CCCACCGTGCCACAGTTAC 60.964 63.158 0.00 0.00 0.00 2.50
776 1083 2.107041 CTCCCACCGTGCCACAGTTA 62.107 60.000 0.00 0.00 0.00 2.24
777 1084 3.476031 CTCCCACCGTGCCACAGTT 62.476 63.158 0.00 0.00 0.00 3.16
778 1085 3.941188 CTCCCACCGTGCCACAGT 61.941 66.667 0.00 0.00 0.00 3.55
787 1094 4.758251 TCACATGCGCTCCCACCG 62.758 66.667 9.73 0.00 0.00 4.94
788 1095 3.127533 GTCACATGCGCTCCCACC 61.128 66.667 9.73 0.00 0.00 4.61
789 1096 3.127533 GGTCACATGCGCTCCCAC 61.128 66.667 9.73 0.00 0.00 4.61
790 1097 4.758251 CGGTCACATGCGCTCCCA 62.758 66.667 9.73 0.00 0.00 4.37
791 1098 4.760047 ACGGTCACATGCGCTCCC 62.760 66.667 9.73 0.00 0.00 4.30
896 1254 0.397816 CTTCCTCCTCCTCCATCGGT 60.398 60.000 0.00 0.00 0.00 4.69
901 1259 1.719378 AGAAGTCTTCCTCCTCCTCCA 59.281 52.381 9.04 0.00 0.00 3.86
922 1280 1.087501 GAGCTAAACTTGGGCCGAAG 58.912 55.000 24.44 24.44 0.00 3.79
944 1302 1.271934 TGGCAATGGATCCACAAAACG 59.728 47.619 18.99 3.07 0.00 3.60
945 1303 3.066380 GTTGGCAATGGATCCACAAAAC 58.934 45.455 18.99 13.34 30.97 2.43
969 1327 2.792599 CGAGGAGGAAGACGACCG 59.207 66.667 0.00 0.00 0.00 4.79
997 1355 3.259123 GGAAAATGGATCATATGGGTGCC 59.741 47.826 2.13 0.44 0.00 5.01
998 1356 3.896888 TGGAAAATGGATCATATGGGTGC 59.103 43.478 2.13 0.00 0.00 5.01
1001 1359 5.105635 CGGATTGGAAAATGGATCATATGGG 60.106 44.000 2.13 0.00 0.00 4.00
1020 1378 0.253327 GCCTCTTCCTTGGTCGGATT 59.747 55.000 0.00 0.00 32.02 3.01
1025 1383 1.604915 GAGGGCCTCTTCCTTGGTC 59.395 63.158 26.44 0.00 34.21 4.02
1054 1413 4.352893 AGGAGGGAGAAGAGAGAAGAAAG 58.647 47.826 0.00 0.00 0.00 2.62
1055 1414 4.045334 AGAGGAGGGAGAAGAGAGAAGAAA 59.955 45.833 0.00 0.00 0.00 2.52
1079 1442 2.126071 GTGCGCACTAGCCGAAGA 60.126 61.111 32.55 0.00 37.52 2.87
1082 1445 2.344981 TAAGGTGCGCACTAGCCGA 61.345 57.895 36.84 15.76 37.52 5.54
1396 1760 0.170339 CGATGAGGAGCACGTACACA 59.830 55.000 0.00 0.00 0.00 3.72
1522 1886 2.577059 GCCGATCCCGTGAACTGA 59.423 61.111 0.00 0.00 0.00 3.41
1540 1904 0.748005 AGTACGCCATGAACATGCCC 60.748 55.000 9.03 2.44 37.49 5.36
1555 1919 4.272018 GTCATGGTGAAGATCATGCAGTAC 59.728 45.833 0.00 0.00 40.14 2.73
1626 1990 1.243902 GAGGTAGATCAGAGAGGGCG 58.756 60.000 0.00 0.00 0.00 6.13
2299 2725 1.142474 CGTTGGTGTTCGTCTTACCC 58.858 55.000 0.00 0.00 33.51 3.69
2312 2738 4.309950 GCTCCGTGGGTCGTTGGT 62.310 66.667 0.00 0.00 37.94 3.67
2320 2746 1.443407 CATAGACTGGCTCCGTGGG 59.557 63.158 0.00 0.00 0.00 4.61
2533 2977 3.066190 TGGACGTACTCGCCAGGG 61.066 66.667 0.00 0.00 41.18 4.45
2770 3250 6.595326 GTCCATGTCAGACACAAGATGATAAA 59.405 38.462 5.05 0.00 38.97 1.40
2829 3309 1.438651 GGAGAACTGCATGCGTGTTA 58.561 50.000 22.88 1.99 0.00 2.41
2929 3413 4.803426 GAGGTGGAGTCGGCGCTG 62.803 72.222 10.86 10.86 0.00 5.18
3067 3551 1.403814 TGATGAGGATGACGAGGGAC 58.596 55.000 0.00 0.00 0.00 4.46
3286 3770 2.044806 GCATGACGGGGAGGCTGTAT 62.045 60.000 0.00 0.00 0.00 2.29
3368 3852 2.155194 CCTTGAGCGCGACGAAGAG 61.155 63.158 12.10 0.00 0.00 2.85
3494 3990 2.923121 GCATGGAGCAAGAGACCAATA 58.077 47.619 0.00 0.00 44.79 1.90
3495 3991 1.760192 GCATGGAGCAAGAGACCAAT 58.240 50.000 0.00 0.00 44.79 3.16
3496 3992 3.254629 GCATGGAGCAAGAGACCAA 57.745 52.632 0.00 0.00 44.79 3.67
3515 4098 1.002576 CATCGCCGCATGAATAGCAAA 60.003 47.619 0.00 0.00 0.00 3.68
3555 4139 6.465439 AACTGACATACTAATCGACCATCA 57.535 37.500 0.00 0.00 0.00 3.07
3556 4140 7.772332 AAAACTGACATACTAATCGACCATC 57.228 36.000 0.00 0.00 0.00 3.51
3557 4141 8.475639 AGTAAAACTGACATACTAATCGACCAT 58.524 33.333 0.00 0.00 0.00 3.55
3558 4142 7.833786 AGTAAAACTGACATACTAATCGACCA 58.166 34.615 0.00 0.00 0.00 4.02
3559 4143 8.699283 AAGTAAAACTGACATACTAATCGACC 57.301 34.615 0.00 0.00 30.03 4.79
3560 4144 8.805688 GGAAGTAAAACTGACATACTAATCGAC 58.194 37.037 0.00 0.00 30.03 4.20
3562 4146 8.928270 AGGAAGTAAAACTGACATACTAATCG 57.072 34.615 0.00 0.00 30.03 3.34
3762 4357 4.036380 ACACTTCATACATGCATGCATCAG 59.964 41.667 30.07 21.61 33.90 2.90
3811 4406 9.371136 GACTTGTGAGTGAATATGTAGAATTCA 57.629 33.333 8.44 0.00 40.21 2.57
3815 4410 7.896811 AGTGACTTGTGAGTGAATATGTAGAA 58.103 34.615 0.00 0.00 35.88 2.10
3820 4415 6.398095 TGGTAGTGACTTGTGAGTGAATATG 58.602 40.000 0.00 0.00 35.88 1.78
3840 4435 1.676529 GACGAGCTGCTCATACTGGTA 59.323 52.381 27.46 0.00 0.00 3.25
3844 4439 1.407936 ATGGACGAGCTGCTCATACT 58.592 50.000 27.46 8.01 0.00 2.12
3858 4453 1.072965 CAGGGATTCAGGCCTATGGAC 59.927 57.143 3.98 0.00 0.00 4.02
3880 4475 7.822822 AGGTTTCTATGAAGCGTTGTATACTTT 59.177 33.333 4.17 0.00 32.52 2.66
3888 4483 3.751175 TCCAAGGTTTCTATGAAGCGTTG 59.249 43.478 16.69 16.69 32.52 4.10
3900 4495 2.229784 CCATGCAGAAGTCCAAGGTTTC 59.770 50.000 0.00 0.00 0.00 2.78
3921 4516 5.911752 ACATGTCAGACTATGGATGAGAAC 58.088 41.667 14.02 0.00 0.00 3.01
4078 4674 0.034896 TGAAGCCCTCCGACAAGAAC 59.965 55.000 0.00 0.00 0.00 3.01
4098 4694 3.305709 CAGTCGGAAAGGAACTGCA 57.694 52.632 0.00 0.00 40.86 4.41
4167 4763 0.593128 AAGCTGCGCACTAAACTTGG 59.407 50.000 5.66 0.00 0.00 3.61
4235 4831 5.704978 TGTCAACAATATGCAGCAGAAACTA 59.295 36.000 0.00 0.00 0.00 2.24
4258 4854 1.582968 GCTGGTGTGGTTGATGCTG 59.417 57.895 0.00 0.00 0.00 4.41
4263 4859 1.454847 GGTTGGCTGGTGTGGTTGA 60.455 57.895 0.00 0.00 0.00 3.18
4287 4883 0.251386 TGGCAAAAAGGTGCGGGATA 60.251 50.000 0.00 0.00 45.91 2.59
4288 4884 0.904394 ATGGCAAAAAGGTGCGGGAT 60.904 50.000 0.00 0.00 45.91 3.85
4335 4931 2.159272 GACGTTTGGCAGACTCACGC 62.159 60.000 6.60 0.00 34.14 5.34
4362 4958 1.523934 ACGAACGGCTAAACAGTTTCG 59.476 47.619 0.48 2.93 36.76 3.46
4405 5001 1.344065 TGTACTGGTTGATCCACGGT 58.656 50.000 0.00 0.00 41.93 4.83
4472 5068 5.163405 CCCTCAGTATATCCATATGTTCCCG 60.163 48.000 1.24 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.