Multiple sequence alignment - TraesCS3D01G287500

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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 TraesCS3D01G287500 chr3D 100.000 4022 0 0 1 4022 396210529 396214550 0.000000e+00 7428.0
1 TraesCS3D01G287500 chr3D 82.102 352 42 11 973 1322 396211464 396211796 8.510000e-72 281.0
2 TraesCS3D01G287500 chr3D 82.102 352 42 10 936 1268 396211501 396211850 8.510000e-72 281.0
3 TraesCS3D01G287500 chr3D 84.651 215 22 8 1010 1214 396211637 396211850 1.900000e-48 204.0
4 TraesCS3D01G287500 chr3D 80.588 170 30 3 1266 1433 294350399 294350231 1.170000e-25 128.0
5 TraesCS3D01G287500 chr3D 96.721 61 2 0 3382 3442 598874338 598874398 7.110000e-18 102.0
6 TraesCS3D01G287500 chr3A 94.918 2243 53 26 494 2702 515912825 515915040 0.000000e+00 3454.0
7 TraesCS3D01G287500 chr3A 96.516 488 17 0 10 497 515889632 515890119 0.000000e+00 808.0
8 TraesCS3D01G287500 chr3A 94.195 534 18 7 2754 3276 515915212 515915743 0.000000e+00 802.0
9 TraesCS3D01G287500 chr3A 91.103 281 14 5 3544 3820 515950112 515950385 1.770000e-98 370.0
10 TraesCS3D01G287500 chr3A 96.020 201 8 0 3820 4020 515950425 515950625 1.080000e-85 327.0
11 TraesCS3D01G287500 chr3A 82.336 351 43 10 973 1322 515913277 515913609 1.830000e-73 287.0
12 TraesCS3D01G287500 chr3A 82.336 351 43 8 936 1268 515913314 515913663 1.830000e-73 287.0
13 TraesCS3D01G287500 chr3A 97.917 96 2 0 407 502 515890118 515890213 2.490000e-37 167.0
14 TraesCS3D01G287500 chr3A 96.040 101 4 0 3452 3552 515915874 515915974 8.940000e-37 165.0
15 TraesCS3D01G287500 chr3A 80.588 170 30 3 1266 1433 389129625 389129457 1.170000e-25 128.0
16 TraesCS3D01G287500 chr3A 96.429 56 2 0 3315 3370 515915747 515915802 4.280000e-15 93.5
17 TraesCS3D01G287500 chr3A 97.222 36 1 0 494 529 515905864 515905899 1.210000e-05 62.1
18 TraesCS3D01G287500 chr3A 97.222 36 1 0 494 529 515908182 515908217 1.210000e-05 62.1
19 TraesCS3D01G287500 chr3A 97.222 36 1 0 494 529 515908988 515909023 1.210000e-05 62.1
20 TraesCS3D01G287500 chr3B 83.421 1327 136 44 1 1268 521698678 521699979 0.000000e+00 1155.0
21 TraesCS3D01G287500 chr3B 86.654 1094 85 30 970 2045 521699626 521700676 0.000000e+00 1155.0
22 TraesCS3D01G287500 chr3B 85.489 696 53 14 2433 3111 521701721 521702385 0.000000e+00 682.0
23 TraesCS3D01G287500 chr3B 93.500 200 13 0 1123 1322 521699726 521699925 8.450000e-77 298.0
24 TraesCS3D01G287500 chr3B 91.781 146 12 0 1177 1322 521699726 521699871 1.900000e-48 204.0
25 TraesCS3D01G287500 chr3B 84.694 196 19 4 3185 3369 521702396 521702591 6.860000e-43 185.0
26 TraesCS3D01G287500 chr3B 80.588 170 30 3 1266 1433 388106430 388106262 1.170000e-25 128.0
27 TraesCS3D01G287500 chr3B 94.595 37 1 1 498 533 782646584 782646548 5.620000e-04 56.5
28 TraesCS3D01G287500 chr1B 87.395 238 30 0 26 263 599223363 599223600 1.420000e-69 274.0
29 TraesCS3D01G287500 chr1B 86.975 238 31 0 26 263 599227531 599227768 6.630000e-68 268.0
30 TraesCS3D01G287500 chr1B 84.795 171 25 1 1266 1435 599332806 599332976 1.920000e-38 171.0
31 TraesCS3D01G287500 chr1B 96.721 61 2 0 3382 3442 516682067 516682127 7.110000e-18 102.0
32 TraesCS3D01G287500 chr1A 87.395 238 30 0 26 263 536882723 536882486 1.420000e-69 274.0
33 TraesCS3D01G287500 chr1A 84.795 171 25 1 1266 1435 536667006 536666836 1.920000e-38 171.0
34 TraesCS3D01G287500 chr1D 80.186 323 53 10 1737 2058 239334280 239333968 8.690000e-57 231.0
35 TraesCS3D01G287500 chr1D 83.041 171 28 1 1266 1435 441296965 441297135 1.940000e-33 154.0
36 TraesCS3D01G287500 chr1D 96.721 61 2 0 3382 3442 487312607 487312547 7.110000e-18 102.0
37 TraesCS3D01G287500 chrUn 96.721 61 2 0 3382 3442 458726381 458726441 7.110000e-18 102.0
38 TraesCS3D01G287500 chr6A 96.721 61 2 0 3382 3442 215594413 215594473 7.110000e-18 102.0
39 TraesCS3D01G287500 chr5D 96.721 61 2 0 3382 3442 6185408 6185348 7.110000e-18 102.0
40 TraesCS3D01G287500 chr5D 96.721 61 2 0 3382 3442 483808054 483807994 7.110000e-18 102.0
41 TraesCS3D01G287500 chr5D 96.721 61 2 0 3382 3442 503282832 503282892 7.110000e-18 102.0
42 TraesCS3D01G287500 chr4D 96.721 61 2 0 3382 3442 329762206 329762146 7.110000e-18 102.0
43 TraesCS3D01G287500 chr6D 100.000 30 0 0 3199 3228 202662888 202662917 5.620000e-04 56.5
44 TraesCS3D01G287500 chr2B 100.000 30 0 0 498 527 375135997 375136026 5.620000e-04 56.5
45 TraesCS3D01G287500 chr2A 100.000 30 0 0 498 527 218126086 218126115 5.620000e-04 56.5


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 TraesCS3D01G287500 chr3D 396210529 396214550 4021 False 2048.500000 7428 87.213750 1 4022 4 chr3D.!!$F2 4021
1 TraesCS3D01G287500 chr3A 515905864 515915974 10110 False 586.088889 3454 93.102222 494 3552 9 chr3A.!!$F2 3058
2 TraesCS3D01G287500 chr3A 515889632 515890213 581 False 487.500000 808 97.216500 10 502 2 chr3A.!!$F1 492
3 TraesCS3D01G287500 chr3A 515950112 515950625 513 False 348.500000 370 93.561500 3544 4020 2 chr3A.!!$F3 476
4 TraesCS3D01G287500 chr3B 521698678 521702591 3913 False 613.166667 1155 87.589833 1 3369 6 chr3B.!!$F1 3368
5 TraesCS3D01G287500 chr1B 599223363 599227768 4405 False 271.000000 274 87.185000 26 263 2 chr1B.!!$F3 237

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
123 124 0.038159 ACTCCTACTCTGTTGTGCGC 60.038 55.0 0.0 0.0 0.00 6.09 F
379 391 0.330941 TGCCTGGTTGGATGTATGCA 59.669 50.0 0.0 0.0 38.35 3.96 F
1458 8546 0.471401 GATCCCTAGCCCCTACCGTT 60.471 60.0 0.0 0.0 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1331 8418 0.179097 GTTCCTCTCCATGAGCGTCC 60.179 60.0 0.0 0.0 41.35 4.79 R
1718 8902 0.543646 AGCCAGAGCCCTTTTGCATT 60.544 50.0 0.0 0.0 41.25 3.56 R
3377 12234 0.173708 CCCGCTACTCTCCTCAACAC 59.826 60.0 0.0 0.0 0.00 3.32 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
36 37 6.183360 GCAACTTTATCTGCAGGGTTTATGAT 60.183 38.462 15.13 0.00 38.48 2.45
51 52 1.413256 ATGATCAGATGCCCGAGCCA 61.413 55.000 0.09 0.00 38.69 4.75
54 55 4.457496 CAGATGCCCGAGCCACGT 62.457 66.667 0.00 0.00 40.78 4.49
123 124 0.038159 ACTCCTACTCTGTTGTGCGC 60.038 55.000 0.00 0.00 0.00 6.09
379 391 0.330941 TGCCTGGTTGGATGTATGCA 59.669 50.000 0.00 0.00 38.35 3.96
617 7681 2.172505 TGCTCCAAACTTCAAGGACTCA 59.827 45.455 0.00 0.00 0.00 3.41
682 7746 6.783892 AAACTTACCAATCGTACGCTTAAA 57.216 33.333 11.24 2.26 0.00 1.52
688 7752 3.247648 CCAATCGTACGCTTAAAGGGATG 59.752 47.826 11.24 0.00 31.91 3.51
699 7772 6.084277 CGCTTAAAGGGATGTACTTGTTTTC 58.916 40.000 0.00 0.00 0.00 2.29
717 7790 1.167781 TCTTTTGCGGGAAACGGGAC 61.168 55.000 0.00 0.00 44.51 4.46
1331 8418 3.296709 AAGGGCGCGAGTACCACAG 62.297 63.158 12.10 0.00 33.55 3.66
1452 8540 2.201771 GGACGATCCCTAGCCCCT 59.798 66.667 0.00 0.00 0.00 4.79
1453 8541 1.463824 GGACGATCCCTAGCCCCTA 59.536 63.158 0.00 0.00 0.00 3.53
1454 8542 0.899253 GGACGATCCCTAGCCCCTAC 60.899 65.000 0.00 0.00 0.00 3.18
1455 8543 0.899253 GACGATCCCTAGCCCCTACC 60.899 65.000 0.00 0.00 0.00 3.18
1456 8544 1.977544 CGATCCCTAGCCCCTACCG 60.978 68.421 0.00 0.00 0.00 4.02
1457 8545 1.155624 GATCCCTAGCCCCTACCGT 59.844 63.158 0.00 0.00 0.00 4.83
1458 8546 0.471401 GATCCCTAGCCCCTACCGTT 60.471 60.000 0.00 0.00 0.00 4.44
1459 8547 0.763223 ATCCCTAGCCCCTACCGTTG 60.763 60.000 0.00 0.00 0.00 4.10
1460 8548 2.504519 CCTAGCCCCTACCGTTGC 59.495 66.667 0.00 0.00 0.00 4.17
1461 8549 2.363975 CCTAGCCCCTACCGTTGCA 61.364 63.158 0.00 0.00 0.00 4.08
1462 8550 1.153429 CTAGCCCCTACCGTTGCAC 60.153 63.158 0.00 0.00 0.00 4.57
1463 8551 1.611261 TAGCCCCTACCGTTGCACT 60.611 57.895 0.00 0.00 0.00 4.40
1464 8552 1.196104 TAGCCCCTACCGTTGCACTT 61.196 55.000 0.00 0.00 0.00 3.16
1465 8553 1.602605 GCCCCTACCGTTGCACTTT 60.603 57.895 0.00 0.00 0.00 2.66
1466 8554 1.862602 GCCCCTACCGTTGCACTTTG 61.863 60.000 0.00 0.00 0.00 2.77
1467 8555 0.536460 CCCCTACCGTTGCACTTTGT 60.536 55.000 0.00 0.00 0.00 2.83
1468 8556 1.314730 CCCTACCGTTGCACTTTGTT 58.685 50.000 0.00 0.00 0.00 2.83
1469 8557 1.265905 CCCTACCGTTGCACTTTGTTC 59.734 52.381 0.00 0.00 0.00 3.18
1470 8558 2.218603 CCTACCGTTGCACTTTGTTCT 58.781 47.619 0.00 0.00 0.00 3.01
1485 8573 6.093219 CACTTTGTTCTTACCATCCATCTCTG 59.907 42.308 0.00 0.00 0.00 3.35
1553 8659 1.409427 GATGTGCCTACTAGCTTCCGT 59.591 52.381 0.00 0.00 0.00 4.69
1557 8663 2.094130 GTGCCTACTAGCTTCCGTTTCT 60.094 50.000 0.00 0.00 0.00 2.52
1576 8682 7.201496 CCGTTTCTGTTGCGATAACTAGTTAAT 60.201 37.037 18.88 8.11 0.00 1.40
1718 8902 2.076184 GTCGGATGGGGGATTGGGA 61.076 63.158 0.00 0.00 0.00 4.37
1734 8918 0.533951 GGGAATGCAAAAGGGCTCTG 59.466 55.000 0.00 0.00 34.04 3.35
1741 8925 1.553706 CAAAAGGGCTCTGGCTGATT 58.446 50.000 0.00 0.00 38.73 2.57
1749 8939 1.542492 CTCTGGCTGATTGTTTGCCT 58.458 50.000 0.00 0.00 46.23 4.75
1882 9123 2.278332 AGGGAGTTTCAGGCTTTGTC 57.722 50.000 0.00 0.00 0.00 3.18
1962 9207 4.216902 GGACTACAACAAATTTTACGGCCT 59.783 41.667 0.00 0.00 0.00 5.19
2385 10379 3.181454 ACAGTTGGTTGTCACCTCCTAAG 60.181 47.826 0.00 0.00 44.61 2.18
2447 10763 3.625764 TCTTTTGTTTCGAACCTGTCCAG 59.374 43.478 0.00 0.00 0.00 3.86
2706 11029 6.217294 ACTGGTTCGAAACAAAAACAAAGAA 58.783 32.000 18.03 0.00 0.00 2.52
2707 11030 6.871492 ACTGGTTCGAAACAAAAACAAAGAAT 59.129 30.769 18.03 0.00 0.00 2.40
2931 11759 0.913451 AGGACCTGAAGGCTGAGCAT 60.913 55.000 6.82 0.00 39.32 3.79
3118 11955 4.345257 AGTCTACATTTGCCATCGGATACT 59.655 41.667 0.00 0.00 0.00 2.12
3170 12009 1.952296 AGTTTGTTCTTGCCTCTGCTG 59.048 47.619 0.00 0.00 38.71 4.41
3171 12010 1.949525 GTTTGTTCTTGCCTCTGCTGA 59.050 47.619 0.00 0.00 38.71 4.26
3174 12013 1.155042 GTTCTTGCCTCTGCTGAGTG 58.845 55.000 18.11 11.18 38.61 3.51
3182 12021 2.775890 CCTCTGCTGAGTGAAATGTGT 58.224 47.619 18.11 0.00 38.61 3.72
3184 12023 3.556633 CCTCTGCTGAGTGAAATGTGTCT 60.557 47.826 18.11 0.00 38.61 3.41
3186 12025 5.213891 TCTGCTGAGTGAAATGTGTCTTA 57.786 39.130 0.00 0.00 0.00 2.10
3187 12026 4.991056 TCTGCTGAGTGAAATGTGTCTTAC 59.009 41.667 0.00 0.00 0.00 2.34
3200 12046 5.755409 TGTGTCTTACTTGTGTGGGATAT 57.245 39.130 0.00 0.00 0.00 1.63
3235 12081 2.821366 CCTGAGATGGCCGTGTGC 60.821 66.667 0.00 0.00 40.16 4.57
3282 12138 4.867599 CGCGGCGTACTCCCTTCC 62.868 72.222 15.36 0.00 0.00 3.46
3310 12167 0.810648 TCATCTGGCGAATTTGGCAC 59.189 50.000 17.59 1.78 39.79 5.01
3367 12224 3.118592 GGAAGCAGGTAGTAGCTGAACAT 60.119 47.826 29.05 13.26 45.98 2.71
3368 12225 4.099573 GGAAGCAGGTAGTAGCTGAACATA 59.900 45.833 29.05 0.00 45.98 2.29
3369 12226 5.221541 GGAAGCAGGTAGTAGCTGAACATAT 60.222 44.000 29.05 10.17 45.98 1.78
3370 12227 5.207110 AGCAGGTAGTAGCTGAACATATG 57.793 43.478 29.05 0.00 45.98 1.78
3371 12228 4.895889 AGCAGGTAGTAGCTGAACATATGA 59.104 41.667 29.05 0.00 45.98 2.15
3372 12229 5.541868 AGCAGGTAGTAGCTGAACATATGAT 59.458 40.000 29.05 0.00 45.98 2.45
3373 12230 6.042552 AGCAGGTAGTAGCTGAACATATGATT 59.957 38.462 29.05 0.00 45.98 2.57
3374 12231 6.367422 GCAGGTAGTAGCTGAACATATGATTC 59.633 42.308 29.05 9.93 45.98 2.52
3375 12232 6.870965 CAGGTAGTAGCTGAACATATGATTCC 59.129 42.308 22.24 0.00 45.98 3.01
3376 12233 6.554982 AGGTAGTAGCTGAACATATGATTCCA 59.445 38.462 10.38 0.82 0.00 3.53
3377 12234 6.870965 GGTAGTAGCTGAACATATGATTCCAG 59.129 42.308 10.38 10.96 0.00 3.86
3378 12235 6.491714 AGTAGCTGAACATATGATTCCAGT 57.508 37.500 10.38 4.85 0.00 4.00
3379 12236 6.286758 AGTAGCTGAACATATGATTCCAGTG 58.713 40.000 10.38 2.65 0.00 3.66
3380 12237 5.108187 AGCTGAACATATGATTCCAGTGT 57.892 39.130 10.38 1.05 0.00 3.55
3381 12238 5.503927 AGCTGAACATATGATTCCAGTGTT 58.496 37.500 10.38 0.00 37.60 3.32
3382 12239 5.356190 AGCTGAACATATGATTCCAGTGTTG 59.644 40.000 10.38 0.00 36.12 3.33
3383 12240 5.355071 GCTGAACATATGATTCCAGTGTTGA 59.645 40.000 10.38 0.00 36.12 3.18
3384 12241 6.457934 GCTGAACATATGATTCCAGTGTTGAG 60.458 42.308 10.38 0.00 38.18 3.02
3385 12242 5.882000 TGAACATATGATTCCAGTGTTGAGG 59.118 40.000 10.38 0.00 36.12 3.86
3386 12243 5.698741 ACATATGATTCCAGTGTTGAGGA 57.301 39.130 10.38 0.00 0.00 3.71
3387 12244 5.678583 ACATATGATTCCAGTGTTGAGGAG 58.321 41.667 10.38 0.00 34.91 3.69
3388 12245 5.426509 ACATATGATTCCAGTGTTGAGGAGA 59.573 40.000 10.38 0.00 34.91 3.71
3389 12246 3.969287 TGATTCCAGTGTTGAGGAGAG 57.031 47.619 0.00 0.00 34.91 3.20
3390 12247 3.242867 TGATTCCAGTGTTGAGGAGAGT 58.757 45.455 0.00 0.00 34.91 3.24
3391 12248 4.416516 TGATTCCAGTGTTGAGGAGAGTA 58.583 43.478 0.00 0.00 34.91 2.59
3392 12249 4.464244 TGATTCCAGTGTTGAGGAGAGTAG 59.536 45.833 0.00 0.00 34.91 2.57
3393 12250 2.171840 TCCAGTGTTGAGGAGAGTAGC 58.828 52.381 0.00 0.00 0.00 3.58
3394 12251 1.135257 CCAGTGTTGAGGAGAGTAGCG 60.135 57.143 0.00 0.00 0.00 4.26
3395 12252 1.135257 CAGTGTTGAGGAGAGTAGCGG 60.135 57.143 0.00 0.00 0.00 5.52
3396 12253 0.173708 GTGTTGAGGAGAGTAGCGGG 59.826 60.000 0.00 0.00 0.00 6.13
3397 12254 0.970937 TGTTGAGGAGAGTAGCGGGG 60.971 60.000 0.00 0.00 0.00 5.73
3398 12255 0.683504 GTTGAGGAGAGTAGCGGGGA 60.684 60.000 0.00 0.00 0.00 4.81
3399 12256 0.683504 TTGAGGAGAGTAGCGGGGAC 60.684 60.000 0.00 0.00 0.00 4.46
3400 12257 1.227946 GAGGAGAGTAGCGGGGACT 59.772 63.158 0.00 0.00 0.00 3.85
3401 12258 0.473326 GAGGAGAGTAGCGGGGACTA 59.527 60.000 0.00 0.00 0.00 2.59
3402 12259 1.074244 GAGGAGAGTAGCGGGGACTAT 59.926 57.143 0.00 0.00 0.00 2.12
3403 12260 1.202952 AGGAGAGTAGCGGGGACTATG 60.203 57.143 0.00 0.00 0.00 2.23
3404 12261 1.249407 GAGAGTAGCGGGGACTATGG 58.751 60.000 0.00 0.00 0.00 2.74
3460 12317 2.359975 GACAAGCCAACTCCCGGG 60.360 66.667 16.85 16.85 0.00 5.73
3494 12379 0.798776 GTCGATGGTTGGCTTCAGTG 59.201 55.000 0.00 0.00 0.00 3.66
3528 12413 2.756760 AGCAACTTGCCAGTTATCATGG 59.243 45.455 10.25 0.00 46.52 3.66
3554 12439 7.624360 AACGGAGTGCTCATATTTTCAAATA 57.376 32.000 1.41 0.00 45.00 1.40
3606 12491 3.329889 CCTGGCTGGCCACCACTA 61.330 66.667 19.44 2.74 41.89 2.74
3607 12492 2.045926 CTGGCTGGCCACCACTAC 60.046 66.667 19.44 0.73 41.89 2.73
3614 12503 0.616679 TGGCCACCACTACTACTCCC 60.617 60.000 0.00 0.00 0.00 4.30
3669 12632 3.455619 TTCTTTTCGCGCATTCTCTTC 57.544 42.857 8.75 0.00 0.00 2.87
3674 12637 2.272146 GCGCATTCTCTTCCCCCA 59.728 61.111 0.30 0.00 0.00 4.96
3699 12827 1.997928 GCCTTGCTCCGAATTGAGGC 61.998 60.000 0.00 0.00 42.35 4.70
3720 12848 1.227556 AAGGACTGCACACGTCACC 60.228 57.895 6.88 0.00 33.11 4.02
3722 12850 1.956170 GGACTGCACACGTCACCTG 60.956 63.158 6.88 0.00 33.11 4.00
3723 12851 1.067416 GACTGCACACGTCACCTGA 59.933 57.895 0.00 0.00 0.00 3.86
3724 12852 0.319900 GACTGCACACGTCACCTGAT 60.320 55.000 0.00 0.00 0.00 2.90
3800 12932 2.092968 ACATATTCTTCGAGCAAGGCCA 60.093 45.455 5.01 0.00 32.22 5.36
3801 12933 2.315925 TATTCTTCGAGCAAGGCCAG 57.684 50.000 5.01 0.00 32.22 4.85
3816 12948 0.610232 GCCAGCACACCCAAATCTCT 60.610 55.000 0.00 0.00 0.00 3.10
3851 13023 2.583593 GCCGACGCTGGAGATGAC 60.584 66.667 0.00 0.00 0.00 3.06
3881 13168 0.036765 GCTACAACGATGACCCACCA 60.037 55.000 0.00 0.00 0.00 4.17
3939 13660 0.682209 AAGATGGCAGACACCCATGC 60.682 55.000 0.00 0.00 42.94 4.06
3972 13693 0.830648 ACCGTATGCTGGTATGCTGT 59.169 50.000 0.00 0.00 38.15 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 6.470278 CATCTGATCATAAACCCTGCAGATA 58.530 40.000 17.39 3.09 38.99 1.98
19 20 5.314529 CATCTGATCATAAACCCTGCAGAT 58.685 41.667 17.39 0.00 40.96 2.90
36 37 4.147449 CGTGGCTCGGGCATCTGA 62.147 66.667 10.74 0.00 40.92 3.27
51 52 1.448985 CCATCGAAATGACCCAACGT 58.551 50.000 0.00 0.00 34.61 3.99
54 55 0.038890 TGCCCATCGAAATGACCCAA 59.961 50.000 0.00 0.00 34.61 4.12
63 64 2.747460 GCACAGCTGCCCATCGAA 60.747 61.111 15.27 0.00 37.45 3.71
379 391 4.457496 CTCATCCGCACAGCCCGT 62.457 66.667 0.00 0.00 0.00 5.28
409 421 2.541588 GCAGTTACAGCAACACCAAGTG 60.542 50.000 0.00 0.00 39.81 3.16
498 558 8.761575 AAATAGTTTGAATTGCTTACCACATG 57.238 30.769 0.00 0.00 0.00 3.21
682 7746 5.507315 CGCAAAAGAAAACAAGTACATCCCT 60.507 40.000 0.00 0.00 0.00 4.20
688 7752 4.295857 TCCCGCAAAAGAAAACAAGTAC 57.704 40.909 0.00 0.00 0.00 2.73
699 7772 1.284715 GTCCCGTTTCCCGCAAAAG 59.715 57.895 0.00 0.00 34.38 2.27
717 7790 4.847255 GCGCTTTGCACAAGTAGG 57.153 55.556 0.00 3.08 45.45 3.18
1005 8092 2.033141 GCCTTGGACTGCAGCTGA 59.967 61.111 20.43 1.36 0.00 4.26
1158 8245 3.426568 GCCTTGGACTGCAGCGTC 61.427 66.667 15.27 5.48 0.00 5.19
1331 8418 0.179097 GTTCCTCTCCATGAGCGTCC 60.179 60.000 0.00 0.00 41.35 4.79
1452 8540 3.560896 GGTAAGAACAAAGTGCAACGGTA 59.439 43.478 0.00 0.00 45.86 4.02
1453 8541 2.356695 GGTAAGAACAAAGTGCAACGGT 59.643 45.455 0.00 0.00 45.86 4.83
1454 8542 2.356382 TGGTAAGAACAAAGTGCAACGG 59.644 45.455 0.00 0.00 45.86 4.44
1455 8543 3.684103 TGGTAAGAACAAAGTGCAACG 57.316 42.857 0.00 0.00 45.86 4.10
1456 8544 4.037446 TGGATGGTAAGAACAAAGTGCAAC 59.963 41.667 0.00 0.00 0.00 4.17
1457 8545 4.211125 TGGATGGTAAGAACAAAGTGCAA 58.789 39.130 0.00 0.00 0.00 4.08
1458 8546 3.826524 TGGATGGTAAGAACAAAGTGCA 58.173 40.909 0.00 0.00 0.00 4.57
1459 8547 4.702131 AGATGGATGGTAAGAACAAAGTGC 59.298 41.667 0.00 0.00 0.00 4.40
1460 8548 6.093219 CAGAGATGGATGGTAAGAACAAAGTG 59.907 42.308 0.00 0.00 0.00 3.16
1461 8549 6.176183 CAGAGATGGATGGTAAGAACAAAGT 58.824 40.000 0.00 0.00 0.00 2.66
1462 8550 5.065731 GCAGAGATGGATGGTAAGAACAAAG 59.934 44.000 0.00 0.00 0.00 2.77
1463 8551 4.943705 GCAGAGATGGATGGTAAGAACAAA 59.056 41.667 0.00 0.00 0.00 2.83
1464 8552 4.225942 AGCAGAGATGGATGGTAAGAACAA 59.774 41.667 0.00 0.00 0.00 2.83
1465 8553 3.776969 AGCAGAGATGGATGGTAAGAACA 59.223 43.478 0.00 0.00 0.00 3.18
1466 8554 4.125703 CAGCAGAGATGGATGGTAAGAAC 58.874 47.826 0.00 0.00 0.00 3.01
1467 8555 3.776969 ACAGCAGAGATGGATGGTAAGAA 59.223 43.478 0.00 0.00 0.00 2.52
1468 8556 3.133542 CACAGCAGAGATGGATGGTAAGA 59.866 47.826 0.00 0.00 0.00 2.10
1469 8557 3.464907 CACAGCAGAGATGGATGGTAAG 58.535 50.000 0.00 0.00 0.00 2.34
1470 8558 2.420547 GCACAGCAGAGATGGATGGTAA 60.421 50.000 0.00 0.00 0.00 2.85
1553 8659 8.542497 ACATTAACTAGTTATCGCAACAGAAA 57.458 30.769 15.92 0.00 0.00 2.52
1557 8663 7.463119 GCGTAACATTAACTAGTTATCGCAACA 60.463 37.037 15.92 0.00 42.76 3.33
1576 8682 2.104451 TGAACCCTACAAAGGCGTAACA 59.896 45.455 0.00 0.00 42.14 2.41
1718 8902 0.543646 AGCCAGAGCCCTTTTGCATT 60.544 50.000 0.00 0.00 41.25 3.56
1842 9083 5.436175 CCTTTTGGGTTTTGGTTCTTGAAT 58.564 37.500 0.00 0.00 35.46 2.57
1882 9123 3.710233 GCGACAATAGGATTTCGCG 57.290 52.632 0.00 0.00 46.37 5.87
1962 9207 3.329520 ACACAAGGGATAACAACTAGGCA 59.670 43.478 0.00 0.00 0.00 4.75
2385 10379 5.105064 TGTTGCCACCTCCTAACTCTAATAC 60.105 44.000 0.00 0.00 0.00 1.89
2554 10870 2.757894 TCCAGGATCCCTACAGTCTC 57.242 55.000 8.55 0.00 29.64 3.36
2739 11062 9.383519 TGTTAAATTGTCCAGTTTTATGCAAAA 57.616 25.926 0.00 0.00 0.00 2.44
2823 11651 1.278637 GCAACAAACGTGTCCTCCG 59.721 57.895 0.00 0.00 36.80 4.63
3053 11890 4.465632 AGACGGCAAATGTATGTAGACA 57.534 40.909 0.00 0.00 0.00 3.41
3170 12009 6.422223 CACACAAGTAAGACACATTTCACTC 58.578 40.000 0.00 0.00 0.00 3.51
3171 12010 5.296780 CCACACAAGTAAGACACATTTCACT 59.703 40.000 0.00 0.00 0.00 3.41
3174 12013 4.819630 TCCCACACAAGTAAGACACATTTC 59.180 41.667 0.00 0.00 0.00 2.17
3182 12021 6.575244 ATTGGATATCCCACACAAGTAAGA 57.425 37.500 19.34 0.00 46.62 2.10
3184 12023 7.684317 TCTATTGGATATCCCACACAAGTAA 57.316 36.000 19.34 3.67 46.62 2.24
3186 12025 6.770286 ATCTATTGGATATCCCACACAAGT 57.230 37.500 19.34 0.00 46.62 3.16
3187 12026 7.444629 CAATCTATTGGATATCCCACACAAG 57.555 40.000 19.34 8.03 46.62 3.16
3235 12081 3.929610 CCTACCAAAGAGCTCGAAAGAAG 59.070 47.826 8.37 3.78 41.32 2.85
3270 12126 1.067821 GAGCATCAGGAAGGGAGTACG 59.932 57.143 0.00 0.00 33.17 3.67
3317 12174 5.221722 TGGTCAGATCTCTGTTTTACTGCTT 60.222 40.000 7.07 0.00 44.12 3.91
3367 12224 5.026121 ACTCTCCTCAACACTGGAATCATA 58.974 41.667 0.00 0.00 31.23 2.15
3368 12225 3.843027 ACTCTCCTCAACACTGGAATCAT 59.157 43.478 0.00 0.00 31.23 2.45
3369 12226 3.242867 ACTCTCCTCAACACTGGAATCA 58.757 45.455 0.00 0.00 31.23 2.57
3370 12227 3.971245 ACTCTCCTCAACACTGGAATC 57.029 47.619 0.00 0.00 31.23 2.52
3371 12228 3.196685 GCTACTCTCCTCAACACTGGAAT 59.803 47.826 0.00 0.00 31.23 3.01
3372 12229 2.563179 GCTACTCTCCTCAACACTGGAA 59.437 50.000 0.00 0.00 31.23 3.53
3373 12230 2.171840 GCTACTCTCCTCAACACTGGA 58.828 52.381 0.00 0.00 0.00 3.86
3374 12231 1.135257 CGCTACTCTCCTCAACACTGG 60.135 57.143 0.00 0.00 0.00 4.00
3375 12232 1.135257 CCGCTACTCTCCTCAACACTG 60.135 57.143 0.00 0.00 0.00 3.66
3376 12233 1.178276 CCGCTACTCTCCTCAACACT 58.822 55.000 0.00 0.00 0.00 3.55
3377 12234 0.173708 CCCGCTACTCTCCTCAACAC 59.826 60.000 0.00 0.00 0.00 3.32
3378 12235 0.970937 CCCCGCTACTCTCCTCAACA 60.971 60.000 0.00 0.00 0.00 3.33
3379 12236 0.683504 TCCCCGCTACTCTCCTCAAC 60.684 60.000 0.00 0.00 0.00 3.18
3380 12237 0.683504 GTCCCCGCTACTCTCCTCAA 60.684 60.000 0.00 0.00 0.00 3.02
3381 12238 1.076923 GTCCCCGCTACTCTCCTCA 60.077 63.158 0.00 0.00 0.00 3.86
3382 12239 0.473326 TAGTCCCCGCTACTCTCCTC 59.527 60.000 0.00 0.00 0.00 3.71
3383 12240 1.150872 ATAGTCCCCGCTACTCTCCT 58.849 55.000 0.00 0.00 0.00 3.69
3384 12241 1.249407 CATAGTCCCCGCTACTCTCC 58.751 60.000 0.00 0.00 0.00 3.71
3385 12242 1.249407 CCATAGTCCCCGCTACTCTC 58.751 60.000 0.00 0.00 0.00 3.20
3386 12243 0.556747 ACCATAGTCCCCGCTACTCT 59.443 55.000 0.00 0.00 0.00 3.24
3387 12244 2.283145 TACCATAGTCCCCGCTACTC 57.717 55.000 0.00 0.00 0.00 2.59
3388 12245 2.805194 GATACCATAGTCCCCGCTACT 58.195 52.381 0.00 0.00 0.00 2.57
3389 12246 1.471684 CGATACCATAGTCCCCGCTAC 59.528 57.143 0.00 0.00 0.00 3.58
3390 12247 1.074405 ACGATACCATAGTCCCCGCTA 59.926 52.381 0.00 0.00 0.00 4.26
3391 12248 0.178970 ACGATACCATAGTCCCCGCT 60.179 55.000 0.00 0.00 0.00 5.52
3392 12249 1.538047 TACGATACCATAGTCCCCGC 58.462 55.000 0.00 0.00 0.00 6.13
3393 12250 4.796038 AAATACGATACCATAGTCCCCG 57.204 45.455 0.00 0.00 0.00 5.73
3431 12288 4.762251 AGTTGGCTTGTCCTCATTTCTAAC 59.238 41.667 0.00 0.00 35.26 2.34
3435 12292 2.489722 GGAGTTGGCTTGTCCTCATTTC 59.510 50.000 0.00 0.00 35.26 2.17
3460 12317 8.225777 CCAACCATCGACTTTAAGTTTAACTAC 58.774 37.037 0.00 0.00 0.00 2.73
3494 12379 1.523758 AGTTGCTCCATTGGAACGTC 58.476 50.000 6.88 0.12 41.97 4.34
3528 12413 5.545658 TGAAAATATGAGCACTCCGTTTC 57.454 39.130 0.00 1.52 0.00 2.78
3554 12439 0.681733 AGAATATGGGCGCGACTGAT 59.318 50.000 13.91 7.13 0.00 2.90
3592 12477 1.221021 GTAGTAGTGGTGGCCAGCC 59.779 63.158 31.12 22.50 32.34 4.85
3606 12491 1.404843 GAGAAGATGCGGGGAGTAGT 58.595 55.000 0.00 0.00 0.00 2.73
3607 12492 0.676736 GGAGAAGATGCGGGGAGTAG 59.323 60.000 0.00 0.00 0.00 2.57
3614 12503 2.203126 GCCTGGGAGAAGATGCGG 60.203 66.667 0.00 0.00 0.00 5.69
3650 12613 1.732259 GGAAGAGAATGCGCGAAAAGA 59.268 47.619 12.10 0.00 0.00 2.52
3657 12620 2.115291 GTGGGGGAAGAGAATGCGC 61.115 63.158 0.00 0.00 0.00 6.09
3715 12843 1.134699 TGCCGATCTTGATCAGGTGAC 60.135 52.381 4.57 0.00 0.00 3.67
3720 12848 2.728318 CGTGTATGCCGATCTTGATCAG 59.272 50.000 10.69 1.05 0.00 2.90
3722 12850 3.013276 TCGTGTATGCCGATCTTGATC 57.987 47.619 0.78 0.78 0.00 2.92
3723 12851 3.667497 ATCGTGTATGCCGATCTTGAT 57.333 42.857 2.32 0.00 40.85 2.57
3724 12852 3.057526 CCTATCGTGTATGCCGATCTTGA 60.058 47.826 9.64 0.00 43.48 3.02
3800 12932 1.701847 AGACAGAGATTTGGGTGTGCT 59.298 47.619 0.00 0.00 0.00 4.40
3801 12933 2.191128 AGACAGAGATTTGGGTGTGC 57.809 50.000 0.00 0.00 0.00 4.57
3816 12948 1.618837 GGCTCTCACCACTTGTAGACA 59.381 52.381 0.00 0.00 0.00 3.41
3851 13023 0.586319 CGTTGTAGCACAGGTGGTTG 59.414 55.000 9.60 0.00 41.96 3.77
3881 13168 4.021925 GGAGCACGCCAGGTTCCT 62.022 66.667 0.00 0.00 0.00 3.36
3939 13660 3.522568 CGGTTGTCGTCGTCACAG 58.477 61.111 0.00 0.00 0.00 3.66
3987 13708 0.039256 CTCTCGCCATCTCTAGCAGC 60.039 60.000 0.00 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.