Multiple sequence alignment - TraesCS4D01G238300

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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 TraesCS4D01G238300 chr4D 100.000 3896 0 0 1 3896 400650375 400646480 0.000000e+00 7195.0
1 TraesCS4D01G238300 chr4D 94.318 88 3 1 57 142 400650233 400650146 2.440000e-27 134.0
2 TraesCS4D01G238300 chr4D 94.318 88 3 1 143 230 400650319 400650234 2.440000e-27 134.0
3 TraesCS4D01G238300 chr4B 96.319 2309 73 5 706 3009 495016671 495014370 0.000000e+00 3783.0
4 TraesCS4D01G238300 chr4B 92.941 850 42 5 3062 3896 495013987 495013141 0.000000e+00 1221.0
5 TraesCS4D01G238300 chr4B 82.477 428 44 17 279 696 495017131 495016725 2.880000e-91 346.0
6 TraesCS4D01G238300 chr4B 95.918 98 4 0 2963 3060 495014337 495014240 4.030000e-35 159.0
7 TraesCS4D01G238300 chr4B 92.857 70 3 2 78 145 495017280 495017211 2.480000e-17 100.0
8 TraesCS4D01G238300 chr4A 95.145 2245 83 14 758 2989 58515267 58513036 0.000000e+00 3518.0
9 TraesCS4D01G238300 chr4A 91.566 249 17 4 3613 3861 58507124 58506880 1.340000e-89 340.0
10 TraesCS4D01G238300 chr4A 77.872 592 50 29 143 696 58518057 58517509 3.810000e-75 292.0
11 TraesCS4D01G238300 chr4A 95.385 130 6 0 1 130 58518113 58517984 1.420000e-49 207.0
12 TraesCS4D01G238300 chr4A 82.126 207 15 6 2986 3187 58507669 58507480 1.450000e-34 158.0
13 TraesCS4D01G238300 chr3D 83.333 234 34 5 3359 3589 418717185 418716954 1.100000e-50 211.0
14 TraesCS4D01G238300 chr3D 83.117 231 36 3 3359 3587 571552626 571552855 1.420000e-49 207.0
15 TraesCS4D01G238300 chr3D 100.000 31 0 0 3062 3092 315484807 315484837 1.510000e-04 58.4
16 TraesCS4D01G238300 chr2A 83.262 233 33 6 3359 3588 6106653 6106424 3.940000e-50 209.0
17 TraesCS4D01G238300 chr2A 82.833 233 34 6 3359 3588 6158368 6158139 1.840000e-48 204.0
18 TraesCS4D01G238300 chr2A 97.059 34 0 1 3059 3092 10742566 10742598 5.440000e-04 56.5
19 TraesCS4D01G238300 chr7D 82.833 233 37 3 3359 3589 146089341 146089572 5.100000e-49 206.0
20 TraesCS4D01G238300 chr7D 97.059 34 1 0 3321 3354 36456016 36456049 1.510000e-04 58.4
21 TraesCS4D01G238300 chr2B 82.609 230 39 1 3359 3587 734215253 734215024 6.600000e-48 202.0
22 TraesCS4D01G238300 chr7B 82.328 232 38 3 3359 3588 726491915 726491685 8.540000e-47 198.0
23 TraesCS4D01G238300 chr7B 100.000 28 0 0 3062 3089 736631541 736631514 7.000000e-03 52.8
24 TraesCS4D01G238300 chr2D 82.251 231 38 3 3359 3587 547037001 547036772 3.070000e-46 196.0
25 TraesCS4D01G238300 chrUn 97.059 34 1 0 3321 3354 108603454 108603487 1.510000e-04 58.4
26 TraesCS4D01G238300 chr7A 100.000 29 0 0 3060 3088 589837565 589837537 2.000000e-03 54.7


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 TraesCS4D01G238300 chr4D 400646480 400650375 3895 True 2487.666667 7195 96.212000 1 3896 3 chr4D.!!$R1 3895
1 TraesCS4D01G238300 chr4B 495013141 495017280 4139 True 1121.800000 3783 92.102400 78 3896 5 chr4B.!!$R1 3818
2 TraesCS4D01G238300 chr4A 58513036 58518113 5077 True 1339.000000 3518 89.467333 1 2989 3 chr4A.!!$R2 2988
3 TraesCS4D01G238300 chr4A 58506880 58507669 789 True 249.000000 340 86.846000 2986 3861 2 chr4A.!!$R1 875

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
270 271 0.033796 TGGGATCGTACGGTCTTCCT 60.034 55.0 26.44 0.0 0.00 3.36 F
310 345 0.108186 CTATCAACTCGGCTGGCACA 60.108 55.0 1.08 0.0 0.00 4.57 F
666 739 0.322975 CAGAATATAGCAGCCCGCCT 59.677 55.0 0.00 0.0 44.04 5.52 F
1993 4255 0.445436 GCAGTTCATCGACAAGCCTG 59.555 55.0 0.00 0.0 0.00 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2199 4461 0.464452 GGAAGGTGTAGTCCCCATCG 59.536 60.0 0.00 0.00 0.00 3.84 R
2535 4797 1.027255 CGGAGAGAAGCTCGAGGACA 61.027 60.0 15.58 0.00 44.91 4.02 R
2778 5040 1.086634 GCATCGAGAGGCTGAACACC 61.087 60.0 2.22 0.00 34.92 4.16 R
3095 5690 0.318699 CAAAGGACTGTCGCGTCTCA 60.319 55.0 5.77 3.57 34.38 3.27 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
34 35 9.030452 TGGAGAATAGATAAAGAAGATAGAGCC 57.970 37.037 0.00 0.00 0.00 4.70
70 71 1.269723 GAAAGGGCTGGTTTCTTTCCG 59.730 52.381 0.00 0.00 39.98 4.30
71 72 0.539669 AAGGGCTGGTTTCTTTCCGG 60.540 55.000 0.00 0.00 34.70 5.14
72 73 1.228459 GGGCTGGTTTCTTTCCGGT 60.228 57.895 0.00 0.00 34.14 5.28
73 74 0.826256 GGGCTGGTTTCTTTCCGGTT 60.826 55.000 0.00 0.00 34.14 4.44
74 75 1.037493 GGCTGGTTTCTTTCCGGTTT 58.963 50.000 0.00 0.00 34.14 3.27
75 76 2.232399 GGCTGGTTTCTTTCCGGTTTA 58.768 47.619 0.00 0.00 34.14 2.01
76 77 2.624364 GGCTGGTTTCTTTCCGGTTTAA 59.376 45.455 0.00 0.00 34.14 1.52
112 113 4.124970 ACTCGAGTGAAAACAAGGGTAAC 58.875 43.478 19.30 0.00 0.00 2.50
127 128 1.737793 GGTAACCTGAATCACTTGCGG 59.262 52.381 0.00 0.00 0.00 5.69
128 129 1.130561 GTAACCTGAATCACTTGCGGC 59.869 52.381 0.00 0.00 0.00 6.53
129 130 1.577328 AACCTGAATCACTTGCGGCG 61.577 55.000 0.51 0.51 0.00 6.46
130 131 2.034879 CCTGAATCACTTGCGGCGT 61.035 57.895 9.37 0.00 0.00 5.68
131 132 1.577328 CCTGAATCACTTGCGGCGTT 61.577 55.000 9.37 0.00 0.00 4.84
132 133 0.179215 CTGAATCACTTGCGGCGTTC 60.179 55.000 9.37 2.76 0.00 3.95
133 134 1.134694 GAATCACTTGCGGCGTTCC 59.865 57.895 9.37 0.00 0.00 3.62
134 135 1.298859 GAATCACTTGCGGCGTTCCT 61.299 55.000 9.37 0.00 0.00 3.36
135 136 1.298859 AATCACTTGCGGCGTTCCTC 61.299 55.000 9.37 0.00 0.00 3.71
136 137 3.777925 CACTTGCGGCGTTCCTCG 61.778 66.667 9.37 0.00 43.12 4.63
137 138 4.295119 ACTTGCGGCGTTCCTCGT 62.295 61.111 9.37 0.00 42.13 4.18
138 139 3.041940 CTTGCGGCGTTCCTCGTT 61.042 61.111 9.37 0.00 42.13 3.85
139 140 2.589442 TTGCGGCGTTCCTCGTTT 60.589 55.556 9.37 0.00 42.13 3.60
140 141 1.286354 CTTGCGGCGTTCCTCGTTTA 61.286 55.000 9.37 0.00 42.13 2.01
141 142 0.671163 TTGCGGCGTTCCTCGTTTAT 60.671 50.000 9.37 0.00 42.13 1.40
142 143 1.347221 GCGGCGTTCCTCGTTTATG 59.653 57.895 9.37 0.00 42.13 1.90
143 144 1.347221 CGGCGTTCCTCGTTTATGC 59.653 57.895 0.00 0.00 42.13 3.14
144 145 1.082117 CGGCGTTCCTCGTTTATGCT 61.082 55.000 0.00 0.00 42.13 3.79
145 146 0.373716 GGCGTTCCTCGTTTATGCTG 59.626 55.000 0.00 0.00 42.13 4.41
146 147 0.373716 GCGTTCCTCGTTTATGCTGG 59.626 55.000 0.00 0.00 42.13 4.85
147 148 2.004583 CGTTCCTCGTTTATGCTGGA 57.995 50.000 0.00 0.00 34.52 3.86
148 149 2.550978 CGTTCCTCGTTTATGCTGGAT 58.449 47.619 0.00 0.00 34.52 3.41
149 150 2.936498 CGTTCCTCGTTTATGCTGGATT 59.064 45.455 0.00 0.00 34.52 3.01
150 151 3.001330 CGTTCCTCGTTTATGCTGGATTC 59.999 47.826 0.00 0.00 34.52 2.52
151 152 4.192317 GTTCCTCGTTTATGCTGGATTCT 58.808 43.478 0.00 0.00 0.00 2.40
152 153 4.487714 TCCTCGTTTATGCTGGATTCTT 57.512 40.909 0.00 0.00 0.00 2.52
153 154 4.843728 TCCTCGTTTATGCTGGATTCTTT 58.156 39.130 0.00 0.00 0.00 2.52
154 155 4.876107 TCCTCGTTTATGCTGGATTCTTTC 59.124 41.667 0.00 0.00 0.00 2.62
155 156 4.035675 CCTCGTTTATGCTGGATTCTTTCC 59.964 45.833 0.00 0.00 45.69 3.13
167 168 6.486993 GCTGGATTCTTTCCCGTTTAATAGAT 59.513 38.462 0.00 0.00 44.77 1.98
197 198 4.165372 AGACTCCAGTGAAAACAAGGGTAA 59.835 41.667 0.00 0.00 0.00 2.85
198 199 4.204799 ACTCCAGTGAAAACAAGGGTAAC 58.795 43.478 0.00 0.00 0.00 2.50
218 219 2.034879 CCTGAATCACTTGCGGCGT 61.035 57.895 9.37 0.00 0.00 5.68
223 224 1.298859 AATCACTTGCGGCGTTCCTC 61.299 55.000 9.37 0.00 0.00 3.71
228 229 1.286354 CTTGCGGCGTTCCTCGTTTA 61.286 55.000 9.37 0.00 42.13 2.01
229 230 0.671163 TTGCGGCGTTCCTCGTTTAT 60.671 50.000 9.37 0.00 42.13 1.40
243 244 6.119536 TCCTCGTTTATTATGCTTTGGACAT 58.880 36.000 0.00 0.00 0.00 3.06
250 251 2.530460 ATGCTTTGGACATAGCCCAA 57.470 45.000 11.31 0.00 41.53 4.12
270 271 0.033796 TGGGATCGTACGGTCTTCCT 60.034 55.000 26.44 0.00 0.00 3.36
287 288 3.792053 CTGCGGCGATACCAGGACC 62.792 68.421 12.98 0.00 39.03 4.46
291 292 0.600255 CGGCGATACCAGGACCAATC 60.600 60.000 0.00 0.00 39.03 2.67
297 298 4.262463 GCGATACCAGGACCAATCTATCAA 60.262 45.833 0.00 0.00 0.00 2.57
298 299 5.230942 CGATACCAGGACCAATCTATCAAC 58.769 45.833 0.00 0.00 0.00 3.18
301 302 3.133003 ACCAGGACCAATCTATCAACTCG 59.867 47.826 0.00 0.00 0.00 4.18
302 303 3.493350 CCAGGACCAATCTATCAACTCGG 60.493 52.174 0.00 0.00 0.00 4.63
304 305 2.103263 GGACCAATCTATCAACTCGGCT 59.897 50.000 0.00 0.00 0.00 5.52
310 345 0.108186 CTATCAACTCGGCTGGCACA 60.108 55.000 1.08 0.00 0.00 4.57
416 455 5.851047 ATAACTTGTTGGTTAGCGTGTAC 57.149 39.130 0.00 0.00 35.52 2.90
463 536 2.953466 TCCTCTGAAAACGATACCGG 57.047 50.000 0.00 0.00 40.78 5.28
464 537 2.173519 TCCTCTGAAAACGATACCGGT 58.826 47.619 13.98 13.98 40.78 5.28
465 538 3.355378 TCCTCTGAAAACGATACCGGTA 58.645 45.455 18.46 18.46 40.78 4.02
467 540 3.129988 CCTCTGAAAACGATACCGGTAGT 59.870 47.826 20.91 10.61 40.78 2.73
468 541 4.336433 CCTCTGAAAACGATACCGGTAGTA 59.664 45.833 20.91 0.00 40.78 1.82
469 542 5.235305 TCTGAAAACGATACCGGTAGTAC 57.765 43.478 20.91 12.49 40.78 2.73
470 543 4.943705 TCTGAAAACGATACCGGTAGTACT 59.056 41.667 20.91 2.26 40.78 2.73
471 544 5.065218 TCTGAAAACGATACCGGTAGTACTC 59.935 44.000 20.91 11.45 40.78 2.59
472 545 4.096382 TGAAAACGATACCGGTAGTACTCC 59.904 45.833 20.91 6.99 40.78 3.85
473 546 2.262423 ACGATACCGGTAGTACTCCC 57.738 55.000 20.91 0.00 40.78 4.30
474 547 1.771255 ACGATACCGGTAGTACTCCCT 59.229 52.381 20.91 0.00 40.78 4.20
475 548 2.173569 ACGATACCGGTAGTACTCCCTT 59.826 50.000 20.91 0.00 40.78 3.95
476 549 3.217626 CGATACCGGTAGTACTCCCTTT 58.782 50.000 20.91 0.00 32.46 3.11
477 550 4.141482 ACGATACCGGTAGTACTCCCTTTA 60.141 45.833 20.91 0.00 40.78 1.85
478 551 4.821805 CGATACCGGTAGTACTCCCTTTAA 59.178 45.833 20.91 0.00 32.46 1.52
479 552 5.299279 CGATACCGGTAGTACTCCCTTTAAA 59.701 44.000 20.91 0.00 32.46 1.52
480 553 4.808414 ACCGGTAGTACTCCCTTTAAAC 57.192 45.455 4.49 0.00 0.00 2.01
481 554 4.420206 ACCGGTAGTACTCCCTTTAAACT 58.580 43.478 4.49 0.00 0.00 2.66
482 555 4.221482 ACCGGTAGTACTCCCTTTAAACTG 59.779 45.833 4.49 0.00 0.00 3.16
483 556 4.463891 CCGGTAGTACTCCCTTTAAACTGA 59.536 45.833 0.00 0.00 0.00 3.41
484 557 5.393896 CCGGTAGTACTCCCTTTAAACTGAG 60.394 48.000 0.00 7.40 0.00 3.35
485 558 5.416952 CGGTAGTACTCCCTTTAAACTGAGA 59.583 44.000 0.00 0.00 0.00 3.27
486 559 6.404513 CGGTAGTACTCCCTTTAAACTGAGAG 60.405 46.154 0.00 6.79 0.00 3.20
487 560 6.662663 GGTAGTACTCCCTTTAAACTGAGAGA 59.337 42.308 0.00 2.26 0.00 3.10
488 561 6.844097 AGTACTCCCTTTAAACTGAGAGAG 57.156 41.667 13.54 0.38 0.00 3.20
489 562 6.553857 AGTACTCCCTTTAAACTGAGAGAGA 58.446 40.000 13.54 0.00 0.00 3.10
490 563 5.993748 ACTCCCTTTAAACTGAGAGAGAG 57.006 43.478 13.54 0.00 0.00 3.20
491 564 4.775253 ACTCCCTTTAAACTGAGAGAGAGG 59.225 45.833 13.54 0.00 0.00 3.69
492 565 4.097418 TCCCTTTAAACTGAGAGAGAGGG 58.903 47.826 0.00 0.00 43.15 4.30
606 679 3.100671 AGCTACCTCCTCCAGTTAACAG 58.899 50.000 8.61 0.00 0.00 3.16
619 692 9.624373 CCTCCAGTTAACAGAGTATACTACTAA 57.376 37.037 18.84 0.00 39.59 2.24
666 739 0.322975 CAGAATATAGCAGCCCGCCT 59.677 55.000 0.00 0.00 44.04 5.52
696 769 0.528017 CTGAAGACGCTACCTGCAGA 59.472 55.000 17.39 0.00 39.21 4.26
697 770 0.528017 TGAAGACGCTACCTGCAGAG 59.472 55.000 17.39 6.68 43.06 3.35
698 771 0.804156 GAAGACGCTACCTGCAGAGC 60.804 60.000 17.39 16.34 43.06 4.09
703 776 2.973899 CTACCTGCAGAGCGGTGT 59.026 61.111 17.39 5.73 36.50 4.16
712 839 1.071605 CAGAGCGGTGTTTACTCAGC 58.928 55.000 0.00 0.00 32.71 4.26
761 3015 1.152881 GGGTCTAATGCAGGCAGGG 60.153 63.158 0.00 0.00 0.00 4.45
800 3054 1.078143 GCTCAGCGGGAATTGGAGT 60.078 57.895 0.00 0.00 0.00 3.85
803 3057 2.436646 AGCGGGAATTGGAGTGCG 60.437 61.111 0.00 0.00 0.00 5.34
815 3069 2.582052 TGGAGTGCGGAATCAAAAACT 58.418 42.857 6.72 0.00 0.00 2.66
863 3117 2.885894 GGTTTATTGACCCGAACAACCA 59.114 45.455 0.00 0.00 33.41 3.67
864 3118 3.304861 GGTTTATTGACCCGAACAACCAC 60.305 47.826 0.00 0.00 33.41 4.16
865 3119 2.188062 TATTGACCCGAACAACCACC 57.812 50.000 0.00 0.00 0.00 4.61
866 3120 0.887387 ATTGACCCGAACAACCACCG 60.887 55.000 0.00 0.00 0.00 4.94
901 3155 2.181021 GCACGCCACTAGCTACGT 59.819 61.111 1.61 1.61 40.39 3.57
1584 3846 2.614987 GGTGAGCAAGCTGATGAACTCT 60.615 50.000 0.00 0.00 0.00 3.24
1738 4000 0.876342 CGATCCCGGAGTTAGCAAGC 60.876 60.000 0.73 0.00 0.00 4.01
1783 4045 3.838271 GCATCGCCGGGTCTCTCA 61.838 66.667 2.18 0.00 0.00 3.27
1887 4149 2.668550 GCGAGCCCGAGGTTTTGT 60.669 61.111 0.00 0.00 38.22 2.83
1932 4194 2.806856 GAGCAGCAGTTCCATCGCG 61.807 63.158 0.00 0.00 0.00 5.87
1993 4255 0.445436 GCAGTTCATCGACAAGCCTG 59.555 55.000 0.00 0.00 0.00 4.85
2022 4284 0.462581 GCACAGCGGAGATCATGGAA 60.463 55.000 0.00 0.00 0.00 3.53
2199 4461 3.127533 GGCATATCCATCGGCGCC 61.128 66.667 19.07 19.07 34.01 6.53
2304 4566 2.791927 CCGTCGTCGAGCTCATCA 59.208 61.111 15.40 0.00 39.71 3.07
2601 4863 2.340078 GCGGAGATCGGCATGCTA 59.660 61.111 18.92 6.70 41.19 3.49
2778 5040 2.885644 CCGAAGATGGCCGACGTG 60.886 66.667 0.00 0.00 0.00 4.49
2790 5052 2.022129 CGACGTGGTGTTCAGCCTC 61.022 63.158 0.00 0.00 0.00 4.70
2793 5055 1.734477 CGTGGTGTTCAGCCTCTCG 60.734 63.158 0.00 0.00 0.00 4.04
2899 5161 2.855209 AGTGGCAGCCAGATGATATC 57.145 50.000 16.83 0.00 32.34 1.63
2903 5165 1.405256 GGCAGCCAGATGATATCGGAG 60.405 57.143 6.55 0.00 0.00 4.63
2906 5168 2.093606 CAGCCAGATGATATCGGAGCAT 60.094 50.000 0.00 0.00 36.69 3.79
2931 5193 6.701145 ACTGAATTTAGCGACTGATCTAGA 57.299 37.500 0.00 0.00 0.00 2.43
3037 5382 6.091986 GCTTTACTCTGAAGACCAAAGATCAG 59.908 42.308 10.82 0.00 40.46 2.90
3071 5666 6.723282 CAGTTTCCAGCTGCTCTTATATTTC 58.277 40.000 8.66 0.00 0.00 2.17
3078 5673 8.046708 TCCAGCTGCTCTTATATTTCTTTTACA 58.953 33.333 8.66 0.00 0.00 2.41
3095 5690 6.668283 TCTTTTACAGAGGGAGTACTAGCATT 59.332 38.462 0.00 0.00 0.00 3.56
3174 5774 9.436957 CTTAAGCCTAAAACTCAATAGACTGAA 57.563 33.333 0.00 0.00 0.00 3.02
3197 5797 8.282592 TGAAATTTAATCAAGTTCAGTCGACTG 58.717 33.333 34.76 34.76 43.00 3.51
3279 5879 1.408422 GGCATTTTGTCGCACTGTTC 58.592 50.000 0.00 0.00 0.00 3.18
3286 5886 1.367665 GTCGCACTGTTCGCAACAC 60.368 57.895 0.00 0.00 36.25 3.32
3289 5889 1.813212 CGCACTGTTCGCAACACGTA 61.813 55.000 0.00 0.00 44.19 3.57
3301 5901 3.301579 CGCAACACGTATTTCTATCGGTG 60.302 47.826 0.00 0.00 36.87 4.94
3361 5961 1.337167 CGGTCACAACATCTGCTCTCA 60.337 52.381 0.00 0.00 0.00 3.27
3375 5975 1.202200 GCTCTCATCGTTCGTAGCACT 60.202 52.381 0.00 0.00 0.00 4.40
3383 5983 1.248721 GTTCGTAGCACTTCGTCTCG 58.751 55.000 0.00 0.00 0.00 4.04
3407 6007 1.665679 GTCGCAACATCCGTCATTGAT 59.334 47.619 0.00 0.00 0.00 2.57
3584 6184 3.499157 AGTCGACTGAGTTCTAGACACAC 59.501 47.826 19.30 0.00 0.00 3.82
3647 6257 1.901591 AGGATTGCACCACTTGTCTG 58.098 50.000 0.00 0.00 0.00 3.51
3814 6424 8.197592 TGGACCTCAAAAGTTAACTATGACTA 57.802 34.615 8.92 1.39 0.00 2.59
3874 6484 8.814038 AATAAAATACCAGCATCCTATCCATC 57.186 34.615 0.00 0.00 0.00 3.51
3880 6490 4.532126 ACCAGCATCCTATCCATCGAATTA 59.468 41.667 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 5.010415 AGCCCTTTCACAAAGAGAAGAAATG 59.990 40.000 0.00 0.00 41.02 2.32
70 71 8.922058 TCGAGTCTACAAACATCTATTAAACC 57.078 34.615 0.00 0.00 0.00 3.27
71 72 9.570488 ACTCGAGTCTACAAACATCTATTAAAC 57.430 33.333 13.58 0.00 0.00 2.01
72 73 9.569167 CACTCGAGTCTACAAACATCTATTAAA 57.431 33.333 16.96 0.00 0.00 1.52
73 74 8.953313 TCACTCGAGTCTACAAACATCTATTAA 58.047 33.333 16.96 0.00 0.00 1.40
74 75 8.502105 TCACTCGAGTCTACAAACATCTATTA 57.498 34.615 16.96 0.00 0.00 0.98
75 76 7.392494 TCACTCGAGTCTACAAACATCTATT 57.608 36.000 16.96 0.00 0.00 1.73
76 77 7.392494 TTCACTCGAGTCTACAAACATCTAT 57.608 36.000 16.96 0.00 0.00 1.98
112 113 1.577328 AACGCCGCAAGTGATTCAGG 61.577 55.000 0.00 0.00 0.00 3.86
113 114 0.179215 GAACGCCGCAAGTGATTCAG 60.179 55.000 0.00 0.00 0.00 3.02
114 115 1.573829 GGAACGCCGCAAGTGATTCA 61.574 55.000 0.00 0.00 0.00 2.57
115 116 1.134694 GGAACGCCGCAAGTGATTC 59.865 57.895 0.00 0.00 0.00 2.52
116 117 1.298859 GAGGAACGCCGCAAGTGATT 61.299 55.000 0.00 0.00 39.96 2.57
117 118 1.741770 GAGGAACGCCGCAAGTGAT 60.742 57.895 0.00 0.00 39.96 3.06
118 119 2.357034 GAGGAACGCCGCAAGTGA 60.357 61.111 0.00 0.00 39.96 3.41
119 120 3.777925 CGAGGAACGCCGCAAGTG 61.778 66.667 0.00 0.00 39.96 3.16
120 121 3.802418 AACGAGGAACGCCGCAAGT 62.802 57.895 0.00 0.00 46.94 3.16
121 122 1.286354 TAAACGAGGAACGCCGCAAG 61.286 55.000 0.00 0.00 46.94 4.01
122 123 0.671163 ATAAACGAGGAACGCCGCAA 60.671 50.000 0.00 0.00 46.94 4.85
123 124 1.079681 ATAAACGAGGAACGCCGCA 60.080 52.632 0.00 0.00 46.94 5.69
124 125 1.347221 CATAAACGAGGAACGCCGC 59.653 57.895 0.00 0.00 46.94 6.53
125 126 1.082117 AGCATAAACGAGGAACGCCG 61.082 55.000 0.00 0.00 46.94 6.46
126 127 0.373716 CAGCATAAACGAGGAACGCC 59.626 55.000 0.00 0.00 46.94 5.68
127 128 0.373716 CCAGCATAAACGAGGAACGC 59.626 55.000 0.00 0.00 46.94 4.84
129 130 4.192317 AGAATCCAGCATAAACGAGGAAC 58.808 43.478 0.00 0.00 31.17 3.62
130 131 4.487714 AGAATCCAGCATAAACGAGGAA 57.512 40.909 0.00 0.00 31.17 3.36
131 132 4.487714 AAGAATCCAGCATAAACGAGGA 57.512 40.909 0.00 0.00 0.00 3.71
132 133 5.162000 GAAAGAATCCAGCATAAACGAGG 57.838 43.478 0.00 0.00 0.00 4.63
146 147 9.503427 CAAACATCTATTAAACGGGAAAGAATC 57.497 33.333 0.00 0.00 0.00 2.52
147 148 9.020731 ACAAACATCTATTAAACGGGAAAGAAT 57.979 29.630 0.00 0.00 0.00 2.40
148 149 8.398878 ACAAACATCTATTAAACGGGAAAGAA 57.601 30.769 0.00 0.00 0.00 2.52
149 150 7.989416 ACAAACATCTATTAAACGGGAAAGA 57.011 32.000 0.00 0.00 0.00 2.52
150 151 9.158233 TCTACAAACATCTATTAAACGGGAAAG 57.842 33.333 0.00 0.00 0.00 2.62
151 152 8.938906 GTCTACAAACATCTATTAAACGGGAAA 58.061 33.333 0.00 0.00 0.00 3.13
152 153 8.316214 AGTCTACAAACATCTATTAAACGGGAA 58.684 33.333 0.00 0.00 0.00 3.97
153 154 7.844009 AGTCTACAAACATCTATTAAACGGGA 58.156 34.615 0.00 0.00 0.00 5.14
154 155 7.224167 GGAGTCTACAAACATCTATTAAACGGG 59.776 40.741 0.00 0.00 0.00 5.28
155 156 7.762615 TGGAGTCTACAAACATCTATTAAACGG 59.237 37.037 0.00 0.00 0.00 4.44
167 168 5.492895 TGTTTTCACTGGAGTCTACAAACA 58.507 37.500 0.00 0.00 32.02 2.83
197 198 1.237285 GCCGCAAGTGATTCAGGTGT 61.237 55.000 0.00 0.00 0.00 4.16
198 199 1.503542 GCCGCAAGTGATTCAGGTG 59.496 57.895 0.00 0.00 0.00 4.00
218 219 5.941058 TGTCCAAAGCATAATAAACGAGGAA 59.059 36.000 0.00 0.00 0.00 3.36
223 224 6.142817 GGCTATGTCCAAAGCATAATAAACG 58.857 40.000 0.00 0.00 40.61 3.60
228 229 4.183223 TGGGCTATGTCCAAAGCATAAT 57.817 40.909 0.00 0.00 40.61 1.28
229 230 3.660970 TGGGCTATGTCCAAAGCATAA 57.339 42.857 0.00 0.00 40.61 1.90
243 244 0.677288 CGTACGATCCCATTGGGCTA 59.323 55.000 17.60 0.57 43.94 3.93
250 251 1.038280 GGAAGACCGTACGATCCCAT 58.962 55.000 18.76 0.00 0.00 4.00
270 271 3.845259 GGTCCTGGTATCGCCGCA 61.845 66.667 0.00 0.00 41.21 5.69
287 288 1.869767 GCCAGCCGAGTTGATAGATTG 59.130 52.381 0.00 0.00 0.00 2.67
291 292 0.108186 TGTGCCAGCCGAGTTGATAG 60.108 55.000 0.00 0.00 0.00 2.08
297 298 1.257750 TATCTGTGTGCCAGCCGAGT 61.258 55.000 0.00 0.00 41.25 4.18
298 299 0.105593 ATATCTGTGTGCCAGCCGAG 59.894 55.000 0.00 0.00 41.25 4.63
301 302 2.103094 TGTAGATATCTGTGTGCCAGCC 59.897 50.000 15.79 0.00 41.25 4.85
302 303 3.126831 GTGTAGATATCTGTGTGCCAGC 58.873 50.000 15.79 0.00 41.25 4.85
304 305 2.481276 GCGTGTAGATATCTGTGTGCCA 60.481 50.000 15.79 0.07 0.00 4.92
310 345 5.765677 ACAGATACAGCGTGTAGATATCTGT 59.234 40.000 15.79 15.92 43.02 3.41
463 536 7.611079 TCTCTCTCAGTTTAAAGGGAGTACTAC 59.389 40.741 13.08 0.00 40.40 2.73
464 537 7.696981 TCTCTCTCAGTTTAAAGGGAGTACTA 58.303 38.462 13.08 0.00 40.40 1.82
465 538 6.553857 TCTCTCTCAGTTTAAAGGGAGTACT 58.446 40.000 13.08 0.00 40.40 2.73
467 540 5.952947 CCTCTCTCTCAGTTTAAAGGGAGTA 59.047 44.000 13.08 5.44 40.40 2.59
468 541 4.775253 CCTCTCTCTCAGTTTAAAGGGAGT 59.225 45.833 13.08 0.00 40.40 3.85
469 542 4.161377 CCCTCTCTCTCAGTTTAAAGGGAG 59.839 50.000 8.94 8.94 44.14 4.30
470 543 4.097418 CCCTCTCTCTCAGTTTAAAGGGA 58.903 47.826 0.00 0.00 44.14 4.20
471 544 4.097418 TCCCTCTCTCTCAGTTTAAAGGG 58.903 47.826 0.00 0.00 43.01 3.95
472 545 4.775253 ACTCCCTCTCTCTCAGTTTAAAGG 59.225 45.833 0.00 0.00 0.00 3.11
473 546 5.993748 ACTCCCTCTCTCTCAGTTTAAAG 57.006 43.478 0.00 0.00 0.00 1.85
474 547 9.716556 ATAATACTCCCTCTCTCTCAGTTTAAA 57.283 33.333 0.00 0.00 0.00 1.52
475 548 9.357161 GATAATACTCCCTCTCTCTCAGTTTAA 57.643 37.037 0.00 0.00 0.00 1.52
476 549 8.503573 TGATAATACTCCCTCTCTCTCAGTTTA 58.496 37.037 0.00 0.00 0.00 2.01
477 550 7.358263 TGATAATACTCCCTCTCTCTCAGTTT 58.642 38.462 0.00 0.00 0.00 2.66
478 551 6.916909 TGATAATACTCCCTCTCTCTCAGTT 58.083 40.000 0.00 0.00 0.00 3.16
479 552 6.523035 TGATAATACTCCCTCTCTCTCAGT 57.477 41.667 0.00 0.00 0.00 3.41
480 553 7.337689 CAGATGATAATACTCCCTCTCTCTCAG 59.662 44.444 0.00 0.00 0.00 3.35
481 554 7.174413 CAGATGATAATACTCCCTCTCTCTCA 58.826 42.308 0.00 0.00 0.00 3.27
482 555 6.603201 CCAGATGATAATACTCCCTCTCTCTC 59.397 46.154 0.00 0.00 0.00 3.20
483 556 6.493166 CCAGATGATAATACTCCCTCTCTCT 58.507 44.000 0.00 0.00 0.00 3.10
484 557 5.127031 GCCAGATGATAATACTCCCTCTCTC 59.873 48.000 0.00 0.00 0.00 3.20
485 558 5.022787 GCCAGATGATAATACTCCCTCTCT 58.977 45.833 0.00 0.00 0.00 3.10
486 559 4.774726 TGCCAGATGATAATACTCCCTCTC 59.225 45.833 0.00 0.00 0.00 3.20
487 560 4.756564 TGCCAGATGATAATACTCCCTCT 58.243 43.478 0.00 0.00 0.00 3.69
488 561 5.690464 ATGCCAGATGATAATACTCCCTC 57.310 43.478 0.00 0.00 0.00 4.30
489 562 6.025539 TGTATGCCAGATGATAATACTCCCT 58.974 40.000 0.00 0.00 0.00 4.20
490 563 6.070538 AGTGTATGCCAGATGATAATACTCCC 60.071 42.308 0.00 0.00 0.00 4.30
491 564 6.940739 AGTGTATGCCAGATGATAATACTCC 58.059 40.000 0.00 0.00 0.00 3.85
492 565 8.839310 AAAGTGTATGCCAGATGATAATACTC 57.161 34.615 0.00 0.00 0.00 2.59
619 692 5.297776 GCAGCCATGTTTGATTACTCTGTAT 59.702 40.000 0.00 0.00 0.00 2.29
666 739 5.241064 GGTAGCGTCTTCAGGTAATCTATGA 59.759 44.000 0.00 0.00 0.00 2.15
696 769 1.001974 TGATGCTGAGTAAACACCGCT 59.998 47.619 0.00 0.00 0.00 5.52
697 770 1.438651 TGATGCTGAGTAAACACCGC 58.561 50.000 0.00 0.00 0.00 5.68
698 771 4.154015 TGATTTGATGCTGAGTAAACACCG 59.846 41.667 0.00 0.00 0.00 4.94
699 772 5.627499 TGATTTGATGCTGAGTAAACACC 57.373 39.130 0.00 0.00 0.00 4.16
700 773 5.514204 GCATGATTTGATGCTGAGTAAACAC 59.486 40.000 0.00 0.00 44.57 3.32
701 774 5.393352 GGCATGATTTGATGCTGAGTAAACA 60.393 40.000 0.00 0.00 46.74 2.83
703 776 4.951715 AGGCATGATTTGATGCTGAGTAAA 59.048 37.500 0.00 0.00 46.74 2.01
712 839 2.201732 GCAAGCAGGCATGATTTGATG 58.798 47.619 16.78 1.44 31.17 3.07
761 3015 1.144936 CTCAGATGCCGTCCCTTCC 59.855 63.158 0.00 0.00 0.00 3.46
798 3052 2.554032 CTGGAGTTTTTGATTCCGCACT 59.446 45.455 0.00 0.00 36.97 4.40
800 3054 2.813754 CTCTGGAGTTTTTGATTCCGCA 59.186 45.455 0.00 0.00 36.97 5.69
803 3057 2.162408 CGGCTCTGGAGTTTTTGATTCC 59.838 50.000 0.00 0.00 34.83 3.01
815 3069 1.667830 CTTTTGTCGCGGCTCTGGA 60.668 57.895 13.81 0.00 0.00 3.86
901 3155 2.431782 GGTGTGGGCTCGGTTTAGTATA 59.568 50.000 0.00 0.00 0.00 1.47
1596 3858 1.132640 GTTGTTCACCGCAGCGATC 59.867 57.895 18.75 2.12 0.00 3.69
1773 4035 3.471244 GACCGCGATGAGAGACCCG 62.471 68.421 8.23 0.00 0.00 5.28
1887 4149 1.504359 CGTAGGCGTTCTGGTTGAAA 58.496 50.000 0.00 0.00 36.30 2.69
1932 4194 2.537560 CCCTCCGTTGATCATGCGC 61.538 63.158 0.00 0.00 0.00 6.09
1993 4255 2.456119 CCGCTGTGCCGAAGATGAC 61.456 63.158 0.00 0.00 0.00 3.06
2022 4284 0.732880 CGTCCAAGTTCATCGTCGCT 60.733 55.000 0.00 0.00 0.00 4.93
2199 4461 0.464452 GGAAGGTGTAGTCCCCATCG 59.536 60.000 0.00 0.00 0.00 3.84
2535 4797 1.027255 CGGAGAGAAGCTCGAGGACA 61.027 60.000 15.58 0.00 44.91 4.02
2601 4863 3.171388 GCCCGGATGTCCCTCCAT 61.171 66.667 0.73 0.00 34.78 3.41
2778 5040 1.086634 GCATCGAGAGGCTGAACACC 61.087 60.000 2.22 0.00 34.92 4.16
2899 5161 3.802139 TCGCTAAATTCAGTTATGCTCCG 59.198 43.478 0.00 0.00 0.00 4.63
2903 5165 5.718649 TCAGTCGCTAAATTCAGTTATGC 57.281 39.130 0.00 0.00 0.00 3.14
2906 5168 8.221965 TCTAGATCAGTCGCTAAATTCAGTTA 57.778 34.615 0.00 0.00 0.00 2.24
2931 5193 4.439563 CGCAACACCCAAACTAAGAACTTT 60.440 41.667 0.00 0.00 0.00 2.66
3023 5368 5.682212 GCAACAAAACCTGATCTTTGGTCTT 60.682 40.000 9.26 0.00 36.94 3.01
3066 5411 8.693625 GCTAGTACTCCCTCTGTAAAAGAAATA 58.306 37.037 0.00 0.00 33.37 1.40
3067 5412 7.180408 TGCTAGTACTCCCTCTGTAAAAGAAAT 59.820 37.037 0.00 0.00 33.37 2.17
3068 5413 6.495872 TGCTAGTACTCCCTCTGTAAAAGAAA 59.504 38.462 0.00 0.00 33.37 2.52
3071 5666 5.916661 TGCTAGTACTCCCTCTGTAAAAG 57.083 43.478 0.00 0.00 0.00 2.27
3078 5673 4.211920 GTCTCAATGCTAGTACTCCCTCT 58.788 47.826 0.00 0.00 0.00 3.69
3095 5690 0.318699 CAAAGGACTGTCGCGTCTCA 60.319 55.000 5.77 3.57 34.38 3.27
3174 5774 7.730364 ACAGTCGACTGAACTTGATTAAATT 57.270 32.000 43.55 19.11 46.59 1.82
3197 5797 3.061006 CGTGCAAAAATCAACAGCTGAAC 60.061 43.478 23.35 0.00 37.67 3.18
3235 5835 4.464008 GAGGTCCATTGGATGATGCTTAA 58.536 43.478 9.01 0.00 32.73 1.85
3271 5871 0.511221 ATACGTGTTGCGAACAGTGC 59.489 50.000 0.00 0.00 43.10 4.40
3279 5879 2.855963 ACCGATAGAAATACGTGTTGCG 59.144 45.455 0.00 0.00 43.30 4.85
3286 5886 1.792949 GCTGCCACCGATAGAAATACG 59.207 52.381 0.00 0.00 39.76 3.06
3289 5889 2.498167 GATGCTGCCACCGATAGAAAT 58.502 47.619 0.00 0.00 39.76 2.17
3301 5901 2.410469 GCAATGACGGATGCTGCC 59.590 61.111 0.00 0.00 39.46 4.85
3334 5934 1.902508 AGATGTTGTGACCGGTGAGAT 59.097 47.619 14.63 0.00 0.00 2.75
3407 6007 5.335583 GCTGTGCAACTAAATGATACAACCA 60.336 40.000 0.00 0.00 38.04 3.67
3565 6165 2.095161 GGGTGTGTCTAGAACTCAGTCG 60.095 54.545 0.00 0.00 32.30 4.18
3584 6184 2.860009 AGCATGCTGATACATCAAGGG 58.140 47.619 21.98 0.00 36.18 3.95
3647 6257 2.861462 TTGTACAAACAAGCAGTGCC 57.139 45.000 12.58 0.00 40.69 5.01
3752 6362 6.349694 CCTTTGAACCAATCTAGCCTCTTTTC 60.350 42.308 0.00 0.00 0.00 2.29
3861 6471 6.037610 GGTGATTAATTCGATGGATAGGATGC 59.962 42.308 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.