Multiple sequence alignment - TraesCS3B01G463600

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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 TraesCS3B01G463600 chr3B 100.000 3783 0 0 1 3783 706530081 706526299 0.000000e+00 6986.0
1 TraesCS3B01G463600 chr3B 89.035 1213 126 5 1664 2873 707572345 707573553 0.000000e+00 1496.0
2 TraesCS3B01G463600 chr3B 84.246 1352 186 19 1516 2848 511631011 511632354 0.000000e+00 1291.0
3 TraesCS3B01G463600 chr3B 87.476 1038 123 5 1662 2697 682121838 682120806 0.000000e+00 1190.0
4 TraesCS3B01G463600 chr3B 84.121 1228 179 13 1664 2880 707449711 707450933 0.000000e+00 1173.0
5 TraesCS3B01G463600 chr3B 84.490 980 83 28 685 1641 682122838 682121905 0.000000e+00 904.0
6 TraesCS3B01G463600 chr3B 81.508 703 50 28 718 1388 511630226 511630880 4.360000e-139 505.0
7 TraesCS3B01G463600 chr3B 93.243 148 9 1 3368 3515 52744108 52743962 2.290000e-52 217.0
8 TraesCS3B01G463600 chr3B 97.826 46 1 0 1122 1167 706528654 706528609 3.130000e-11 80.5
9 TraesCS3B01G463600 chr3B 97.826 46 1 0 1428 1473 706528960 706528915 3.130000e-11 80.5
10 TraesCS3B01G463600 chr3D 97.697 2432 41 5 949 3372 534670526 534668102 0.000000e+00 4167.0
11 TraesCS3B01G463600 chr3D 84.103 1170 174 10 1663 2825 535868666 535869830 0.000000e+00 1120.0
12 TraesCS3B01G463600 chr3D 96.038 530 14 6 1 529 534676317 534675794 0.000000e+00 856.0
13 TraesCS3B01G463600 chr3D 93.434 396 8 9 536 927 534674654 534674273 4.240000e-159 571.0
14 TraesCS3B01G463600 chr3D 94.909 275 13 1 3509 3783 534668092 534667819 2.700000e-116 429.0
15 TraesCS3B01G463600 chr3D 93.289 149 10 0 3367 3515 84509688 84509540 1.770000e-53 220.0
16 TraesCS3B01G463600 chr3D 97.826 46 1 0 1122 1167 534670047 534670002 3.130000e-11 80.5
17 TraesCS3B01G463600 chr3D 97.826 46 1 0 1428 1473 534670353 534670308 3.130000e-11 80.5
18 TraesCS3B01G463600 chr3A 95.710 2191 59 13 1253 3430 669969440 669971608 0.000000e+00 3493.0
19 TraesCS3B01G463600 chr3A 95.162 2191 56 14 1253 3430 669986814 669984661 0.000000e+00 3413.0
20 TraesCS3B01G463600 chr3A 83.713 1228 187 9 1664 2881 671273534 671274758 0.000000e+00 1147.0
21 TraesCS3B01G463600 chr3A 91.722 749 20 11 562 1307 669987523 669986814 0.000000e+00 1002.0
22 TraesCS3B01G463600 chr3A 91.455 749 22 11 562 1307 669968731 669969440 0.000000e+00 990.0
23 TraesCS3B01G463600 chr3A 92.278 518 32 8 1 517 669967098 669967608 0.000000e+00 728.0
24 TraesCS3B01G463600 chr3A 92.278 518 32 8 1 517 669989156 669988646 0.000000e+00 728.0
25 TraesCS3B01G463600 chr3A 91.429 280 14 4 3509 3783 669971722 669971996 3.570000e-100 375.0
26 TraesCS3B01G463600 chr3A 91.429 280 14 4 3509 3783 669984547 669984273 3.570000e-100 375.0
27 TraesCS3B01G463600 chr3A 88.571 70 8 0 1249 1318 669986739 669986670 6.730000e-13 86.1
28 TraesCS3B01G463600 chr3A 96.078 51 1 1 1428 1478 669969261 669969310 8.710000e-12 82.4
29 TraesCS3B01G463600 chr3A 96.078 51 1 1 1428 1478 669986993 669986944 8.710000e-12 82.4
30 TraesCS3B01G463600 chr3A 95.652 46 2 0 1122 1167 669969616 669969661 1.460000e-09 75.0
31 TraesCS3B01G463600 chrUn 84.114 598 37 17 721 1308 119082297 119081748 3.350000e-145 525.0
32 TraesCS3B01G463600 chrUn 92.625 339 15 3 1327 1658 119081687 119081352 2.640000e-131 479.0
33 TraesCS3B01G463600 chr6D 95.775 142 6 0 3368 3509 366480274 366480415 2.940000e-56 230.0
34 TraesCS3B01G463600 chr5D 95.775 142 6 0 3368 3509 72087033 72086892 2.940000e-56 230.0
35 TraesCS3B01G463600 chr2D 95.105 143 7 0 3367 3509 593801763 593801621 3.800000e-55 226.0
36 TraesCS3B01G463600 chr7A 94.483 145 8 0 3365 3509 643186885 643187029 1.370000e-54 224.0
37 TraesCS3B01G463600 chr4B 93.333 150 10 0 3366 3515 512755416 512755267 4.920000e-54 222.0
38 TraesCS3B01G463600 chr4A 93.960 149 6 3 3360 3508 274744888 274745033 4.920000e-54 222.0
39 TraesCS3B01G463600 chr4A 77.899 276 52 6 3511 3782 576586159 576585889 3.020000e-36 163.0
40 TraesCS3B01G463600 chr4A 77.323 269 48 10 3509 3776 537185263 537185007 3.050000e-31 147.0
41 TraesCS3B01G463600 chr1A 93.919 148 7 2 3363 3509 90767543 90767689 4.920000e-54 222.0
42 TraesCS3B01G463600 chr1A 100.000 38 0 0 3149 3186 298603676 298603639 1.890000e-08 71.3
43 TraesCS3B01G463600 chr5A 78.261 276 51 6 3511 3782 665769569 665769299 6.500000e-38 169.0
44 TraesCS3B01G463600 chr1B 85.345 116 13 4 65 179 539144639 539144527 2.390000e-22 117.0
45 TraesCS3B01G463600 chr1B 93.617 47 2 1 112 158 584490964 584490919 6.780000e-08 69.4
46 TraesCS3B01G463600 chr1D 90.741 54 5 0 3133 3186 484242374 484242427 5.240000e-09 73.1
47 TraesCS3B01G463600 chr1D 92.000 50 4 0 3137 3186 249030320 249030369 1.890000e-08 71.3
48 TraesCS3B01G463600 chr1D 90.000 50 5 0 3137 3186 372835755 372835804 8.770000e-07 65.8
49 TraesCS3B01G463600 chr7D 100.000 38 0 0 3149 3186 4027549 4027586 1.890000e-08 71.3
50 TraesCS3B01G463600 chr7D 95.455 44 1 1 111 153 242632993 242633036 6.780000e-08 69.4
51 TraesCS3B01G463600 chr2A 87.097 62 4 4 118 179 164605130 164605187 2.440000e-07 67.6
52 TraesCS3B01G463600 chr2B 97.222 36 1 0 3149 3184 660157827 660157792 1.130000e-05 62.1


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 TraesCS3B01G463600 chr3B 706526299 706530081 3782 True 2382.333333 6986 98.550667 1 3783 3 chr3B.!!$R3 3782
1 TraesCS3B01G463600 chr3B 707572345 707573553 1208 False 1496.000000 1496 89.035000 1664 2873 1 chr3B.!!$F2 1209
2 TraesCS3B01G463600 chr3B 707449711 707450933 1222 False 1173.000000 1173 84.121000 1664 2880 1 chr3B.!!$F1 1216
3 TraesCS3B01G463600 chr3B 682120806 682122838 2032 True 1047.000000 1190 85.983000 685 2697 2 chr3B.!!$R2 2012
4 TraesCS3B01G463600 chr3B 511630226 511632354 2128 False 898.000000 1291 82.877000 718 2848 2 chr3B.!!$F3 2130
5 TraesCS3B01G463600 chr3D 535868666 535869830 1164 False 1120.000000 1120 84.103000 1663 2825 1 chr3D.!!$F1 1162
6 TraesCS3B01G463600 chr3D 534667819 534676317 8498 True 1030.666667 4167 96.288333 1 3783 6 chr3D.!!$R2 3782
7 TraesCS3B01G463600 chr3A 671273534 671274758 1224 False 1147.000000 1147 83.713000 1664 2881 1 chr3A.!!$F1 1217
8 TraesCS3B01G463600 chr3A 669967098 669971996 4898 False 957.233333 3493 93.767000 1 3783 6 chr3A.!!$F2 3782
9 TraesCS3B01G463600 chr3A 669984273 669989156 4883 True 947.750000 3413 92.540000 1 3783 6 chr3A.!!$R1 3782
10 TraesCS3B01G463600 chrUn 119081352 119082297 945 True 502.000000 525 88.369500 721 1658 2 chrUn.!!$R1 937

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
453 456 2.092699 GGCTTAAGAGAGTCCAATGGCT 60.093 50.0 6.67 0.00 0.0 4.75 F
1736 7303 0.781787 CGTTCTCGCATTTGACGTCA 59.218 50.0 15.76 15.76 0.0 4.35 F
2454 8025 0.033504 ACTGTTCCATTGACGTCGCT 59.966 50.0 11.62 0.00 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1982 7550 0.181587 ACGTGGTTGTGGTCATGGAA 59.818 50.0 0.0 0.0 0.00 3.53 R
2701 8287 0.904649 ACAAGCCAGATGGTCGATCA 59.095 50.0 0.0 0.0 37.57 2.92 R
3753 9514 0.320374 GGGATCTGTCGTGACAACCA 59.680 55.0 16.5 2.2 41.33 3.67 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
410 413 2.606961 TTGGCGCTGCTTTGAGTCG 61.607 57.895 7.64 0.00 0.00 4.18
453 456 2.092699 GGCTTAAGAGAGTCCAATGGCT 60.093 50.000 6.67 0.00 0.00 4.75
529 532 4.021925 GTGGGCCGGAGCTTCAGT 62.022 66.667 5.05 0.00 39.73 3.41
530 533 3.249189 TGGGCCGGAGCTTCAGTT 61.249 61.111 5.05 0.00 39.73 3.16
531 534 2.747855 GGGCCGGAGCTTCAGTTG 60.748 66.667 5.05 0.00 39.73 3.16
575 2177 3.253230 GCGGGTTCATCCTTGATTTTTG 58.747 45.455 0.00 0.00 36.25 2.44
723 2325 4.481368 TTATTAGATTCTGCCACCACGT 57.519 40.909 0.00 0.00 0.00 4.49
901 2517 3.561744 CCGTCCCACCAATTTAACCCTAA 60.562 47.826 0.00 0.00 0.00 2.69
1255 6634 5.224888 CAACCAAGATTTGTCATCAACCTG 58.775 41.667 0.00 0.00 32.93 4.00
1256 6635 4.473444 ACCAAGATTTGTCATCAACCTGT 58.527 39.130 0.00 0.00 32.93 4.00
1262 6725 2.865119 TGTCATCAACCTGTGCTCAT 57.135 45.000 0.00 0.00 0.00 2.90
1334 6839 1.231963 AACTTTCCCCCTCAACCTGT 58.768 50.000 0.00 0.00 0.00 4.00
1736 7303 0.781787 CGTTCTCGCATTTGACGTCA 59.218 50.000 15.76 15.76 0.00 4.35
1982 7550 1.920835 GAGGGCCTCCTTGTCCTGT 60.921 63.158 23.49 0.00 45.05 4.00
1987 7555 0.329596 GCCTCCTTGTCCTGTTCCAT 59.670 55.000 0.00 0.00 0.00 3.41
2017 7585 4.329545 GTCCGCCTGCTCAACCCA 62.330 66.667 0.00 0.00 0.00 4.51
2072 7640 1.464997 CCACGCTGCTTCCTTCTAAAC 59.535 52.381 0.00 0.00 0.00 2.01
2320 7888 2.042831 GGCGCTGCAAATCTGTCCT 61.043 57.895 7.64 0.00 0.00 3.85
2436 8004 0.176680 ATGCTGATCCACCGTCAGAC 59.823 55.000 7.28 0.00 44.57 3.51
2454 8025 0.033504 ACTGTTCCATTGACGTCGCT 59.966 50.000 11.62 0.00 0.00 4.93
2701 8287 3.572632 CATCTCCTGGATGGACACATT 57.427 47.619 0.00 0.00 45.85 2.71
2704 8290 3.117745 TCTCCTGGATGGACACATTGAT 58.882 45.455 0.00 0.00 40.56 2.57
2770 8356 6.045072 TGTCTATCTTTGTCCAATACGGTT 57.955 37.500 0.00 0.00 35.57 4.44
2800 8391 3.712218 AGTAGTCTAGCCCCATTTCCTTC 59.288 47.826 0.00 0.00 0.00 3.46
3046 8644 1.132721 TCCACCTGGGCTGCTATCTAT 60.133 52.381 0.00 0.00 36.21 1.98
3372 9128 8.854614 ATCAATGAGCTTCAAAGTTAACTACT 57.145 30.769 8.92 0.00 39.32 2.57
3373 9129 8.311650 TCAATGAGCTTCAAAGTTAACTACTC 57.688 34.615 8.92 9.48 35.54 2.59
3374 9130 7.387948 TCAATGAGCTTCAAAGTTAACTACTCC 59.612 37.037 8.92 0.00 35.54 3.85
3375 9131 5.548406 TGAGCTTCAAAGTTAACTACTCCC 58.452 41.667 8.92 0.00 35.54 4.30
3376 9132 5.307196 TGAGCTTCAAAGTTAACTACTCCCT 59.693 40.000 8.92 1.71 35.54 4.20
3377 9133 5.795972 AGCTTCAAAGTTAACTACTCCCTC 58.204 41.667 8.92 0.00 35.54 4.30
3378 9134 4.936411 GCTTCAAAGTTAACTACTCCCTCC 59.064 45.833 8.92 0.00 35.54 4.30
3379 9135 4.796038 TCAAAGTTAACTACTCCCTCCG 57.204 45.455 8.92 0.00 35.54 4.63
3380 9136 4.154942 TCAAAGTTAACTACTCCCTCCGT 58.845 43.478 8.92 0.00 35.54 4.69
3381 9137 4.590222 TCAAAGTTAACTACTCCCTCCGTT 59.410 41.667 8.92 0.00 35.54 4.44
3382 9138 4.797800 AAGTTAACTACTCCCTCCGTTC 57.202 45.455 8.92 0.00 35.54 3.95
3383 9139 3.095332 AGTTAACTACTCCCTCCGTTCC 58.905 50.000 6.26 0.00 28.23 3.62
3384 9140 3.095332 GTTAACTACTCCCTCCGTTCCT 58.905 50.000 0.00 0.00 0.00 3.36
3385 9141 4.018050 AGTTAACTACTCCCTCCGTTCCTA 60.018 45.833 6.26 0.00 28.23 2.94
3386 9142 3.463048 AACTACTCCCTCCGTTCCTAA 57.537 47.619 0.00 0.00 0.00 2.69
3387 9143 3.463048 ACTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
3388 9144 3.991683 ACTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
3389 9145 5.134725 ACTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
3390 9146 5.713807 ACTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
3391 9147 6.856757 ACTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
3392 9148 7.300658 ACTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
3393 9149 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3394 9150 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3395 9151 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3396 9152 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3397 9153 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3398 9154 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3399 9155 7.656542 CCCTCCGTTCCTAAATATAAGTCTTTC 59.343 40.741 0.00 0.00 0.00 2.62
3400 9156 8.422566 CCTCCGTTCCTAAATATAAGTCTTTCT 58.577 37.037 0.00 0.00 0.00 2.52
3415 9171 9.883142 ATAAGTCTTTCTAGAGATTCCAACAAG 57.117 33.333 0.00 0.00 0.00 3.16
3416 9172 7.309770 AGTCTTTCTAGAGATTCCAACAAGT 57.690 36.000 0.00 0.00 0.00 3.16
3417 9173 7.158021 AGTCTTTCTAGAGATTCCAACAAGTG 58.842 38.462 0.00 0.00 0.00 3.16
3418 9174 7.015682 AGTCTTTCTAGAGATTCCAACAAGTGA 59.984 37.037 0.00 0.00 0.00 3.41
3419 9175 7.117092 GTCTTTCTAGAGATTCCAACAAGTGAC 59.883 40.741 0.00 0.00 0.00 3.67
3420 9176 6.672266 TTCTAGAGATTCCAACAAGTGACT 57.328 37.500 0.00 0.00 0.00 3.41
3421 9177 7.776618 TTCTAGAGATTCCAACAAGTGACTA 57.223 36.000 0.00 0.00 0.00 2.59
3422 9178 7.159322 TCTAGAGATTCCAACAAGTGACTAC 57.841 40.000 0.00 0.00 0.00 2.73
3423 9179 5.808366 AGAGATTCCAACAAGTGACTACA 57.192 39.130 0.00 0.00 0.00 2.74
3424 9180 6.365970 AGAGATTCCAACAAGTGACTACAT 57.634 37.500 0.00 0.00 0.00 2.29
3425 9181 7.482169 AGAGATTCCAACAAGTGACTACATA 57.518 36.000 0.00 0.00 0.00 2.29
3426 9182 7.324178 AGAGATTCCAACAAGTGACTACATAC 58.676 38.462 0.00 0.00 0.00 2.39
3427 9183 6.100004 AGATTCCAACAAGTGACTACATACG 58.900 40.000 0.00 0.00 0.00 3.06
3428 9184 4.182693 TCCAACAAGTGACTACATACGG 57.817 45.455 0.00 0.00 0.00 4.02
3429 9185 3.827876 TCCAACAAGTGACTACATACGGA 59.172 43.478 0.00 0.00 0.00 4.69
3430 9186 4.082408 TCCAACAAGTGACTACATACGGAG 60.082 45.833 0.00 0.00 0.00 4.63
3431 9187 3.505464 ACAAGTGACTACATACGGAGC 57.495 47.619 0.00 0.00 0.00 4.70
3432 9188 2.823747 ACAAGTGACTACATACGGAGCA 59.176 45.455 0.00 0.00 0.00 4.26
3433 9189 3.257375 ACAAGTGACTACATACGGAGCAA 59.743 43.478 0.00 0.00 0.00 3.91
3434 9190 4.242475 CAAGTGACTACATACGGAGCAAA 58.758 43.478 0.00 0.00 0.00 3.68
3435 9191 4.530710 AGTGACTACATACGGAGCAAAA 57.469 40.909 0.00 0.00 0.00 2.44
3436 9192 5.086104 AGTGACTACATACGGAGCAAAAT 57.914 39.130 0.00 0.00 0.00 1.82
3437 9193 4.870426 AGTGACTACATACGGAGCAAAATG 59.130 41.667 0.00 0.00 0.00 2.32
3438 9194 4.868171 GTGACTACATACGGAGCAAAATGA 59.132 41.667 0.00 0.00 0.00 2.57
3439 9195 5.005779 GTGACTACATACGGAGCAAAATGAG 59.994 44.000 0.00 0.00 0.00 2.90
3440 9196 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3441 9197 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3442 9198 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3443 9199 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3444 9200 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3445 9201 5.065218 ACATACGGAGCAAAATGAGTGAATC 59.935 40.000 0.00 0.00 0.00 2.52
3446 9202 3.679389 ACGGAGCAAAATGAGTGAATCT 58.321 40.909 0.00 0.00 0.00 2.40
3447 9203 4.832248 ACGGAGCAAAATGAGTGAATCTA 58.168 39.130 0.00 0.00 0.00 1.98
3448 9204 4.631813 ACGGAGCAAAATGAGTGAATCTAC 59.368 41.667 0.00 0.00 0.00 2.59
3449 9205 4.631377 CGGAGCAAAATGAGTGAATCTACA 59.369 41.667 0.00 0.00 0.00 2.74
3450 9206 5.446473 CGGAGCAAAATGAGTGAATCTACAC 60.446 44.000 0.00 0.00 40.60 2.90
3464 9220 8.976353 AGTGAATCTACACTCTGAAATATGTCT 58.024 33.333 0.00 0.00 46.36 3.41
3465 9221 9.243637 GTGAATCTACACTCTGAAATATGTCTC 57.756 37.037 0.00 0.00 37.73 3.36
3466 9222 8.417106 TGAATCTACACTCTGAAATATGTCTCC 58.583 37.037 0.00 0.00 0.00 3.71
3467 9223 7.904558 ATCTACACTCTGAAATATGTCTCCA 57.095 36.000 0.00 0.00 0.00 3.86
3468 9224 7.904558 TCTACACTCTGAAATATGTCTCCAT 57.095 36.000 0.00 0.00 34.97 3.41
3469 9225 8.996651 TCTACACTCTGAAATATGTCTCCATA 57.003 34.615 0.00 0.00 37.92 2.74
3470 9226 8.851145 TCTACACTCTGAAATATGTCTCCATAC 58.149 37.037 0.00 0.00 36.40 2.39
3471 9227 7.423844 ACACTCTGAAATATGTCTCCATACA 57.576 36.000 0.00 0.00 36.40 2.29
3472 9228 8.027524 ACACTCTGAAATATGTCTCCATACAT 57.972 34.615 0.00 0.00 42.62 2.29
3473 9229 8.147058 ACACTCTGAAATATGTCTCCATACATC 58.853 37.037 0.00 0.00 40.52 3.06
3474 9230 8.366401 CACTCTGAAATATGTCTCCATACATCT 58.634 37.037 0.00 0.00 40.52 2.90
3475 9231 8.366401 ACTCTGAAATATGTCTCCATACATCTG 58.634 37.037 0.00 0.00 40.52 2.90
3476 9232 8.255111 TCTGAAATATGTCTCCATACATCTGT 57.745 34.615 0.00 0.00 40.52 3.41
3477 9233 9.367160 TCTGAAATATGTCTCCATACATCTGTA 57.633 33.333 0.00 0.00 40.52 2.74
3491 9247 5.957771 ACATCTGTATGGTGTAGTCCATT 57.042 39.130 3.55 0.00 44.75 3.16
3492 9248 6.313519 ACATCTGTATGGTGTAGTCCATTT 57.686 37.500 3.55 0.00 44.75 2.32
3493 9249 6.115446 ACATCTGTATGGTGTAGTCCATTTG 58.885 40.000 3.55 0.00 44.75 2.32
3494 9250 6.070251 ACATCTGTATGGTGTAGTCCATTTGA 60.070 38.462 3.55 1.77 44.75 2.69
3495 9251 6.367374 TCTGTATGGTGTAGTCCATTTGAA 57.633 37.500 3.55 0.00 44.75 2.69
3496 9252 6.774673 TCTGTATGGTGTAGTCCATTTGAAA 58.225 36.000 3.55 0.00 44.75 2.69
3497 9253 7.402054 TCTGTATGGTGTAGTCCATTTGAAAT 58.598 34.615 3.55 0.00 44.75 2.17
3498 9254 7.336679 TCTGTATGGTGTAGTCCATTTGAAATG 59.663 37.037 10.84 10.84 44.75 2.32
3499 9255 6.945435 TGTATGGTGTAGTCCATTTGAAATGT 59.055 34.615 15.93 1.43 44.75 2.71
3500 9256 5.957842 TGGTGTAGTCCATTTGAAATGTC 57.042 39.130 15.93 9.10 31.96 3.06
3501 9257 5.630121 TGGTGTAGTCCATTTGAAATGTCT 58.370 37.500 15.93 14.81 31.96 3.41
3502 9258 6.774673 TGGTGTAGTCCATTTGAAATGTCTA 58.225 36.000 15.93 13.97 31.96 2.59
3503 9259 6.878923 TGGTGTAGTCCATTTGAAATGTCTAG 59.121 38.462 15.93 1.90 31.96 2.43
3504 9260 7.103641 GGTGTAGTCCATTTGAAATGTCTAGA 58.896 38.462 15.93 12.79 0.00 2.43
3505 9261 7.606456 GGTGTAGTCCATTTGAAATGTCTAGAA 59.394 37.037 15.93 7.49 0.00 2.10
3506 9262 8.999431 GTGTAGTCCATTTGAAATGTCTAGAAA 58.001 33.333 15.93 0.00 0.00 2.52
3507 9263 9.219603 TGTAGTCCATTTGAAATGTCTAGAAAG 57.780 33.333 15.93 0.00 0.00 2.62
3579 9337 0.839946 ATGGCTCCATACACACCCTC 59.160 55.000 0.00 0.00 34.49 4.30
3585 9343 0.615331 CCATACACACCCTCACTGCT 59.385 55.000 0.00 0.00 0.00 4.24
3640 9401 4.143200 TGTGACGATATGACAAAGTTTCGC 60.143 41.667 0.00 0.00 0.00 4.70
3651 9412 3.003689 ACAAAGTTTCGCACCTGAAGATG 59.996 43.478 0.00 0.00 0.00 2.90
3659 9420 1.675641 ACCTGAAGATGTTGCGCCC 60.676 57.895 4.18 0.00 0.00 6.13
3730 9491 6.763715 TGTACCCCATCAATTATTAGAGCT 57.236 37.500 0.00 0.00 0.00 4.09
3753 9514 2.714808 ACTTCCCAGGAAAGTACCCTT 58.285 47.619 0.00 0.00 33.34 3.95
3771 9532 2.069273 CTTGGTTGTCACGACAGATCC 58.931 52.381 0.00 5.77 42.94 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
410 413 0.179056 TAGAGCTACCCAATTGCGGC 60.179 55.000 11.57 0.00 33.82 6.53
453 456 1.124780 TGTCCAGGGTTCGAACTCAA 58.875 50.000 28.97 11.95 0.00 3.02
558 2160 8.437360 AAAGGAAACAAAAATCAAGGATGAAC 57.563 30.769 0.00 0.00 39.49 3.18
705 2307 3.965379 TTACGTGGTGGCAGAATCTAA 57.035 42.857 0.00 0.00 0.00 2.10
706 2308 3.512329 TCTTTACGTGGTGGCAGAATCTA 59.488 43.478 0.00 0.00 0.00 1.98
707 2309 2.301870 TCTTTACGTGGTGGCAGAATCT 59.698 45.455 0.00 0.00 0.00 2.40
901 2517 1.974875 GTTTCCGCCCCGAAATGGT 60.975 57.895 0.00 0.00 34.41 3.55
1255 6634 2.235898 GGGAGGATCTGGATATGAGCAC 59.764 54.545 0.00 0.00 33.73 4.40
1256 6635 2.544721 GGGAGGATCTGGATATGAGCA 58.455 52.381 0.00 0.00 33.73 4.26
1262 6725 0.793617 GGGAGGGGAGGATCTGGATA 59.206 60.000 0.00 0.00 33.73 2.59
1334 6839 1.035923 GGACGATCTGGATCTGAGCA 58.964 55.000 8.65 0.00 35.72 4.26
1736 7303 1.445716 CGGAAGCGGAGATAGTCGGT 61.446 60.000 0.00 0.00 38.82 4.69
1982 7550 0.181587 ACGTGGTTGTGGTCATGGAA 59.818 50.000 0.00 0.00 0.00 3.53
1987 7555 2.107343 CGGACGTGGTTGTGGTCA 59.893 61.111 0.00 0.00 32.39 4.02
2072 7640 5.125900 TGAAATAGGAAAGCATGACATGGTG 59.874 40.000 20.24 0.00 41.46 4.17
2246 7814 3.823873 CCTGCAAACATTAAGGGTGTGTA 59.176 43.478 0.00 0.00 0.00 2.90
2454 8025 8.417884 TGTCATACTGATAACACGATTTATCCA 58.582 33.333 14.23 4.90 37.57 3.41
2701 8287 0.904649 ACAAGCCAGATGGTCGATCA 59.095 50.000 0.00 0.00 37.57 2.92
2704 8290 0.955428 GCAACAAGCCAGATGGTCGA 60.955 55.000 0.00 0.00 37.23 4.20
2770 8356 3.117131 TGGGGCTAGACTACTCATCATCA 60.117 47.826 0.00 0.00 0.00 3.07
2800 8391 8.022550 TGCATAACCATTCATGCTAAATTATCG 58.977 33.333 7.92 0.00 46.19 2.92
2959 8557 8.986929 AATAAAAAGGAGTAGCAGCATAGATT 57.013 30.769 0.00 0.00 0.00 2.40
2960 8558 8.986929 AAATAAAAAGGAGTAGCAGCATAGAT 57.013 30.769 0.00 0.00 0.00 1.98
3073 8671 8.131455 AGTAAATTGTAGACAGTATGCAATCG 57.869 34.615 11.36 0.00 42.53 3.34
3196 8794 3.191371 CCTCAAACAAGAACATAGCCCAC 59.809 47.826 0.00 0.00 0.00 4.61
3200 8798 3.686016 TCCCCTCAAACAAGAACATAGC 58.314 45.455 0.00 0.00 0.00 2.97
3372 9128 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3373 9129 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3374 9130 8.422566 AGAAAGACTTATATTTAGGAACGGAGG 58.577 37.037 0.00 0.00 0.00 4.30
3389 9145 9.883142 CTTGTTGGAATCTCTAGAAAGACTTAT 57.117 33.333 0.00 0.00 0.00 1.73
3390 9146 8.871125 ACTTGTTGGAATCTCTAGAAAGACTTA 58.129 33.333 0.00 0.00 0.00 2.24
3391 9147 7.659390 CACTTGTTGGAATCTCTAGAAAGACTT 59.341 37.037 0.00 0.00 0.00 3.01
3392 9148 7.015682 TCACTTGTTGGAATCTCTAGAAAGACT 59.984 37.037 0.00 0.00 0.00 3.24
3393 9149 7.117092 GTCACTTGTTGGAATCTCTAGAAAGAC 59.883 40.741 0.00 0.00 0.00 3.01
3394 9150 7.015682 AGTCACTTGTTGGAATCTCTAGAAAGA 59.984 37.037 0.00 0.00 0.00 2.52
3395 9151 7.158021 AGTCACTTGTTGGAATCTCTAGAAAG 58.842 38.462 0.00 0.00 0.00 2.62
3396 9152 7.067496 AGTCACTTGTTGGAATCTCTAGAAA 57.933 36.000 0.00 0.00 0.00 2.52
3397 9153 6.672266 AGTCACTTGTTGGAATCTCTAGAA 57.328 37.500 0.00 0.00 0.00 2.10
3398 9154 6.719829 TGTAGTCACTTGTTGGAATCTCTAGA 59.280 38.462 0.00 0.00 0.00 2.43
3399 9155 6.925211 TGTAGTCACTTGTTGGAATCTCTAG 58.075 40.000 0.00 0.00 0.00 2.43
3400 9156 6.911250 TGTAGTCACTTGTTGGAATCTCTA 57.089 37.500 0.00 0.00 0.00 2.43
3401 9157 5.808366 TGTAGTCACTTGTTGGAATCTCT 57.192 39.130 0.00 0.00 0.00 3.10
3402 9158 6.253727 CGTATGTAGTCACTTGTTGGAATCTC 59.746 42.308 0.00 0.00 0.00 2.75
3403 9159 6.100004 CGTATGTAGTCACTTGTTGGAATCT 58.900 40.000 0.00 0.00 0.00 2.40
3404 9160 5.291128 CCGTATGTAGTCACTTGTTGGAATC 59.709 44.000 0.00 0.00 0.00 2.52
3405 9161 5.046878 TCCGTATGTAGTCACTTGTTGGAAT 60.047 40.000 0.00 0.00 0.00 3.01
3406 9162 4.281435 TCCGTATGTAGTCACTTGTTGGAA 59.719 41.667 0.00 0.00 0.00 3.53
3407 9163 3.827876 TCCGTATGTAGTCACTTGTTGGA 59.172 43.478 0.00 0.00 0.00 3.53
3408 9164 4.174009 CTCCGTATGTAGTCACTTGTTGG 58.826 47.826 0.00 0.00 0.00 3.77
3409 9165 3.612860 GCTCCGTATGTAGTCACTTGTTG 59.387 47.826 0.00 0.00 0.00 3.33
3410 9166 3.257375 TGCTCCGTATGTAGTCACTTGTT 59.743 43.478 0.00 0.00 0.00 2.83
3411 9167 2.823747 TGCTCCGTATGTAGTCACTTGT 59.176 45.455 0.00 0.00 0.00 3.16
3412 9168 3.503827 TGCTCCGTATGTAGTCACTTG 57.496 47.619 0.00 0.00 0.00 3.16
3413 9169 4.530710 TTTGCTCCGTATGTAGTCACTT 57.469 40.909 0.00 0.00 0.00 3.16
3414 9170 4.530710 TTTTGCTCCGTATGTAGTCACT 57.469 40.909 0.00 0.00 0.00 3.41
3415 9171 4.868171 TCATTTTGCTCCGTATGTAGTCAC 59.132 41.667 0.00 0.00 0.00 3.67
3416 9172 5.079689 TCATTTTGCTCCGTATGTAGTCA 57.920 39.130 0.00 0.00 0.00 3.41
3417 9173 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3418 9174 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3419 9175 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3420 9176 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3421 9177 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3422 9178 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3423 9179 5.431765 AGATTCACTCATTTTGCTCCGTAT 58.568 37.500 0.00 0.00 0.00 3.06
3424 9180 4.832248 AGATTCACTCATTTTGCTCCGTA 58.168 39.130 0.00 0.00 0.00 4.02
3425 9181 3.679389 AGATTCACTCATTTTGCTCCGT 58.321 40.909 0.00 0.00 0.00 4.69
3426 9182 4.631377 TGTAGATTCACTCATTTTGCTCCG 59.369 41.667 0.00 0.00 0.00 4.63
3427 9183 5.645497 AGTGTAGATTCACTCATTTTGCTCC 59.355 40.000 0.00 0.00 44.07 4.70
3428 9184 6.734104 AGTGTAGATTCACTCATTTTGCTC 57.266 37.500 0.00 0.00 44.07 4.26
3439 9195 9.243637 GAGACATATTTCAGAGTGTAGATTCAC 57.756 37.037 0.00 0.00 38.46 3.18
3440 9196 8.417106 GGAGACATATTTCAGAGTGTAGATTCA 58.583 37.037 0.00 0.00 0.00 2.57
3441 9197 8.417106 TGGAGACATATTTCAGAGTGTAGATTC 58.583 37.037 0.00 0.00 33.40 2.52
3442 9198 8.311395 TGGAGACATATTTCAGAGTGTAGATT 57.689 34.615 0.00 0.00 33.40 2.40
3443 9199 7.904558 TGGAGACATATTTCAGAGTGTAGAT 57.095 36.000 0.00 0.00 33.40 1.98
3478 9234 5.630121 AGACATTTCAAATGGACTACACCA 58.370 37.500 14.70 0.00 44.41 4.17
3479 9235 7.103641 TCTAGACATTTCAAATGGACTACACC 58.896 38.462 14.70 0.00 0.00 4.16
3480 9236 8.547967 TTCTAGACATTTCAAATGGACTACAC 57.452 34.615 14.70 0.00 0.00 2.90
3481 9237 9.219603 CTTTCTAGACATTTCAAATGGACTACA 57.780 33.333 14.70 3.48 0.00 2.74
3482 9238 9.436957 TCTTTCTAGACATTTCAAATGGACTAC 57.563 33.333 14.70 1.26 0.00 2.73
3484 9240 8.924511 TTCTTTCTAGACATTTCAAATGGACT 57.075 30.769 14.70 14.18 0.00 3.85
3485 9241 9.965824 TTTTCTTTCTAGACATTTCAAATGGAC 57.034 29.630 14.70 8.04 0.00 4.02
3585 9343 8.486210 AGCAAGTTGTCAATAATATACTGAGGA 58.514 33.333 4.48 0.00 0.00 3.71
3640 9401 1.503542 GGCGCAACATCTTCAGGTG 59.496 57.895 10.83 0.00 0.00 4.00
3651 9412 2.895372 CTATCCCACGGGCGCAAC 60.895 66.667 10.83 0.00 34.68 4.17
3659 9420 1.101635 TGTCGAGAGGCTATCCCACG 61.102 60.000 3.12 0.00 36.07 4.94
3730 9491 2.374170 GGGTACTTTCCTGGGAAGTTCA 59.626 50.000 24.84 5.96 35.38 3.18
3753 9514 0.320374 GGGATCTGTCGTGACAACCA 59.680 55.000 16.50 2.20 41.33 3.67


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

AutoCloner maintained by Alex Coulton.