Multiple sequence alignment - TraesCS4D01G097100

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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 TraesCS4D01G097100 chr4D 100.000 4406 0 0 1 4406 73998996 73994591 0.000000e+00 8137.0
1 TraesCS4D01G097100 chr4A 91.759 2160 114 16 846 2980 514341358 514343478 0.000000e+00 2944.0
2 TraesCS4D01G097100 chr4A 92.615 1327 63 16 2964 4261 514343658 514344978 0.000000e+00 1875.0
3 TraesCS4D01G097100 chr4A 84.322 236 36 1 33 268 514340285 514340519 3.430000e-56 230.0
4 TraesCS4D01G097100 chr4A 96.970 33 1 0 3127 3159 514343633 514343601 6.160000e-04 56.5
5 TraesCS4D01G097100 chr4B 89.241 2147 130 42 2303 4406 106058853 106056765 0.000000e+00 2591.0
6 TraesCS4D01G097100 chr4B 95.430 1488 60 2 818 2305 106060492 106059013 0.000000e+00 2364.0
7 TraesCS4D01G097100 chr5A 81.934 1644 235 41 916 2533 657549951 657551558 0.000000e+00 1334.0
8 TraesCS4D01G097100 chr5A 81.879 447 54 13 2152 2579 657552227 657552665 7.010000e-93 351.0
9 TraesCS4D01G097100 chr5A 78.402 338 46 11 2695 3013 657553147 657553476 1.250000e-45 195.0
10 TraesCS4D01G097100 chr6B 82.640 1538 219 30 1023 2534 50068185 50066670 0.000000e+00 1317.0
11 TraesCS4D01G097100 chr6B 75.331 1208 233 46 1033 2197 62001313 62002498 1.820000e-143 520.0
12 TraesCS4D01G097100 chr6B 79.469 414 52 19 3199 3586 50066462 50066056 3.380000e-66 263.0
13 TraesCS4D01G097100 chr6B 79.464 112 17 5 867 975 50068302 50068194 1.700000e-09 75.0
14 TraesCS4D01G097100 chrUn 82.784 1365 197 18 1023 2374 137770604 137771943 0.000000e+00 1184.0
15 TraesCS4D01G097100 chrUn 80.586 989 150 20 1573 2533 137663129 137664103 0.000000e+00 725.0
16 TraesCS4D01G097100 chrUn 81.857 463 53 20 2095 2537 178720282 178720733 1.160000e-95 361.0
17 TraesCS4D01G097100 chrUn 80.915 503 55 22 3119 3586 137772558 137773054 4.190000e-95 359.0
18 TraesCS4D01G097100 chrUn 82.080 452 51 18 2095 2526 196161577 196161136 4.190000e-95 359.0
19 TraesCS4D01G097100 chrUn 82.080 452 51 18 2095 2526 366700801 366701242 4.190000e-95 359.0
20 TraesCS4D01G097100 chrUn 80.561 499 63 19 3119 3588 137664663 137665156 1.950000e-93 353.0
21 TraesCS4D01G097100 chrUn 81.858 452 52 19 2095 2526 315743810 315744251 1.950000e-93 353.0
22 TraesCS4D01G097100 chrUn 81.858 452 52 19 2095 2526 333538054 333537613 1.950000e-93 353.0
23 TraesCS4D01G097100 chr6A 84.197 1177 163 12 1023 2189 30905843 30904680 0.000000e+00 1122.0
24 TraesCS4D01G097100 chr6A 77.718 1122 220 19 1034 2134 52039014 52037902 0.000000e+00 660.0
25 TraesCS4D01G097100 chr6A 79.719 498 61 20 3119 3586 30903004 30902517 1.530000e-84 324.0
26 TraesCS4D01G097100 chr6A 83.386 319 51 2 1818 2135 5037147 5037464 1.200000e-75 294.0
27 TraesCS4D01G097100 chr6A 77.222 180 23 9 3494 3666 30902492 30902324 6.070000e-14 89.8
28 TraesCS4D01G097100 chr6A 88.525 61 4 1 915 975 30905909 30905852 2.200000e-08 71.3
29 TraesCS4D01G097100 chr6D 79.135 1203 211 32 1027 2204 404607537 404608724 0.000000e+00 795.0
30 TraesCS4D01G097100 chr6D 77.768 1129 219 18 1028 2134 41545294 41544176 0.000000e+00 665.0
31 TraesCS4D01G097100 chr6D 76.421 1073 206 33 1028 2069 41596445 41595389 1.800000e-148 536.0
32 TraesCS4D01G097100 chr2A 94.737 38 2 0 935 972 721504410 721504447 4.760000e-05 60.2
33 TraesCS4D01G097100 chr1A 92.683 41 3 0 935 975 362018166 362018126 4.760000e-05 60.2
34 TraesCS4D01G097100 chr2B 89.583 48 2 2 927 972 708183391 708183437 1.710000e-04 58.4
35 TraesCS4D01G097100 chr2B 89.130 46 2 2 927 970 708166972 708167016 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 TraesCS4D01G097100 chr4D 73994591 73998996 4405 True 8137.000000 8137 100.000000 1 4406 1 chr4D.!!$R1 4405
1 TraesCS4D01G097100 chr4A 514340285 514344978 4693 False 1683.000000 2944 89.565333 33 4261 3 chr4A.!!$F1 4228
2 TraesCS4D01G097100 chr4B 106056765 106060492 3727 True 2477.500000 2591 92.335500 818 4406 2 chr4B.!!$R1 3588
3 TraesCS4D01G097100 chr5A 657549951 657553476 3525 False 626.666667 1334 80.738333 916 3013 3 chr5A.!!$F1 2097
4 TraesCS4D01G097100 chr6B 50066056 50068302 2246 True 551.666667 1317 80.524333 867 3586 3 chr6B.!!$R1 2719
5 TraesCS4D01G097100 chr6B 62001313 62002498 1185 False 520.000000 520 75.331000 1033 2197 1 chr6B.!!$F1 1164
6 TraesCS4D01G097100 chrUn 137770604 137773054 2450 False 771.500000 1184 81.849500 1023 3586 2 chrUn.!!$F5 2563
7 TraesCS4D01G097100 chrUn 137663129 137665156 2027 False 539.000000 725 80.573500 1573 3588 2 chrUn.!!$F4 2015
8 TraesCS4D01G097100 chr6A 52037902 52039014 1112 True 660.000000 660 77.718000 1034 2134 1 chr6A.!!$R1 1100
9 TraesCS4D01G097100 chr6A 30902324 30905909 3585 True 401.775000 1122 82.415750 915 3666 4 chr6A.!!$R2 2751
10 TraesCS4D01G097100 chr6D 404607537 404608724 1187 False 795.000000 795 79.135000 1027 2204 1 chr6D.!!$F1 1177
11 TraesCS4D01G097100 chr6D 41544176 41545294 1118 True 665.000000 665 77.768000 1028 2134 1 chr6D.!!$R1 1106
12 TraesCS4D01G097100 chr6D 41595389 41596445 1056 True 536.000000 536 76.421000 1028 2069 1 chr6D.!!$R2 1041

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
140 141 0.179124 CTAGCTCAGTTGGTCCTCGC 60.179 60.0 0.0 0.0 0.00 5.03 F
539 606 0.318120 GCCCCAGTTTGATGGTTGTG 59.682 55.0 0.0 0.0 38.81 3.33 F
1729 2105 0.909623 AGTTCGGTGGGGTAATCCAG 59.090 55.0 0.0 0.0 37.50 3.86 F
2783 4195 0.609131 TAGTGCTTGGCTTGGCTTCC 60.609 55.0 0.0 0.0 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 2133 3.181455 CGGTGGGTCAATCATGGATAAGA 60.181 47.826 0.00 0.0 0.00 2.10 R
2197 2616 1.679032 GGAAGAACCAGCGCCAACTAT 60.679 52.381 2.29 0.0 38.79 2.12 R
3390 5540 1.134670 GGCGATCAGTTAGTCCTTGCT 60.135 52.381 0.00 0.0 0.00 3.91 R
4180 6907 0.242017 GCCACACATGCTCAAACCTC 59.758 55.000 0.00 0.0 0.00 3.85 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
25 26 7.781324 ACAATTCAACCTAAATCCACAATCT 57.219 32.000 0.00 0.00 0.00 2.40
26 27 8.877864 ACAATTCAACCTAAATCCACAATCTA 57.122 30.769 0.00 0.00 0.00 1.98
27 28 9.479549 ACAATTCAACCTAAATCCACAATCTAT 57.520 29.630 0.00 0.00 0.00 1.98
30 31 9.799106 ATTCAACCTAAATCCACAATCTATAGG 57.201 33.333 0.00 0.00 35.62 2.57
31 32 8.331931 TCAACCTAAATCCACAATCTATAGGT 57.668 34.615 0.00 0.00 42.49 3.08
33 34 9.408648 CAACCTAAATCCACAATCTATAGGTTT 57.591 33.333 10.69 0.00 45.30 3.27
34 35 9.628500 AACCTAAATCCACAATCTATAGGTTTC 57.372 33.333 8.17 0.00 45.30 2.78
66 67 3.818773 CGACAAACCCTAGAACAACCATT 59.181 43.478 0.00 0.00 0.00 3.16
74 75 4.591072 CCCTAGAACAACCATTCCCAAAAA 59.409 41.667 0.00 0.00 0.00 1.94
107 108 2.394930 GAAGGAGAGAACTTCCCTGC 57.605 55.000 0.00 0.00 38.67 4.85
108 109 1.905894 GAAGGAGAGAACTTCCCTGCT 59.094 52.381 0.00 0.00 38.67 4.24
115 116 2.037772 GAGAACTTCCCTGCTGTCAGAA 59.962 50.000 3.32 0.00 42.95 3.02
118 119 2.576615 ACTTCCCTGCTGTCAGAAAAC 58.423 47.619 3.32 0.00 42.95 2.43
121 122 3.402628 TCCCTGCTGTCAGAAAACTAC 57.597 47.619 3.32 0.00 42.95 2.73
123 124 4.157246 TCCCTGCTGTCAGAAAACTACTA 58.843 43.478 3.32 0.00 42.95 1.82
129 130 4.862018 GCTGTCAGAAAACTACTAGCTCAG 59.138 45.833 3.32 0.00 0.00 3.35
130 131 5.565834 GCTGTCAGAAAACTACTAGCTCAGT 60.566 44.000 3.32 0.00 41.62 3.41
140 141 0.179124 CTAGCTCAGTTGGTCCTCGC 60.179 60.000 0.00 0.00 0.00 5.03
141 142 1.605058 TAGCTCAGTTGGTCCTCGCC 61.605 60.000 0.00 0.00 0.00 5.54
146 147 3.379445 GTTGGTCCTCGCCGGAGA 61.379 66.667 5.05 6.70 44.20 3.71
154 155 1.519455 CTCGCCGGAGATGTTGGTC 60.519 63.158 8.83 0.00 43.27 4.02
157 158 2.264480 CCGGAGATGTTGGTCGCA 59.736 61.111 0.00 0.00 0.00 5.10
158 159 1.811266 CCGGAGATGTTGGTCGCAG 60.811 63.158 0.00 0.00 0.00 5.18
161 162 1.078759 GGAGATGTTGGTCGCAGTCG 61.079 60.000 0.00 0.00 0.00 4.18
180 181 1.726865 CGCAAACCTTGTGCACTCA 59.273 52.632 19.41 3.62 42.33 3.41
200 201 1.202976 AGCAAAGTGAGGCAGGTGATT 60.203 47.619 0.00 0.00 0.00 2.57
202 203 1.815003 CAAAGTGAGGCAGGTGATTCC 59.185 52.381 0.00 0.00 0.00 3.01
203 204 1.067295 AAGTGAGGCAGGTGATTCCA 58.933 50.000 0.00 0.00 39.02 3.53
213 214 3.777478 CAGGTGATTCCAACAATGATGC 58.223 45.455 0.00 0.00 39.02 3.91
219 220 1.175654 TCCAACAATGATGCGTGCAT 58.824 45.000 7.12 7.12 39.69 3.96
223 224 1.942223 CAATGATGCGTGCATGCCG 60.942 57.895 27.43 18.68 36.70 5.69
227 228 4.783621 ATGCGTGCATGCCGTCCT 62.784 61.111 27.43 4.94 35.03 3.85
230 231 4.758251 CGTGCATGCCGTCCTCCA 62.758 66.667 16.68 0.00 0.00 3.86
233 234 1.001020 TGCATGCCGTCCTCCAAAT 60.001 52.632 16.68 0.00 0.00 2.32
239 240 0.322546 GCCGTCCTCCAAATCCACTT 60.323 55.000 0.00 0.00 0.00 3.16
260 261 2.122413 ATCCAGCATAGGGCCCGA 60.122 61.111 18.44 13.02 46.50 5.14
296 363 1.266178 TCGTCTCTTGCATGGGAGAA 58.734 50.000 1.68 0.00 39.81 2.87
308 375 3.625716 GCATGGGAGAAAATGAGAGGGAA 60.626 47.826 0.00 0.00 0.00 3.97
309 376 4.801164 CATGGGAGAAAATGAGAGGGAAT 58.199 43.478 0.00 0.00 0.00 3.01
320 387 1.380380 GAGGGAATGGGTTGGCTGG 60.380 63.158 0.00 0.00 0.00 4.85
321 388 2.364186 GGGAATGGGTTGGCTGGG 60.364 66.667 0.00 0.00 0.00 4.45
322 389 2.364186 GGAATGGGTTGGCTGGGG 60.364 66.667 0.00 0.00 0.00 4.96
323 390 2.445155 GAATGGGTTGGCTGGGGT 59.555 61.111 0.00 0.00 0.00 4.95
324 391 1.984026 GAATGGGTTGGCTGGGGTG 60.984 63.158 0.00 0.00 0.00 4.61
325 392 3.544503 AATGGGTTGGCTGGGGTGG 62.545 63.158 0.00 0.00 0.00 4.61
351 418 2.081462 GTGGGGGTGATAAGTGAAACG 58.919 52.381 0.00 0.00 45.86 3.60
352 419 1.003812 TGGGGGTGATAAGTGAAACGG 59.996 52.381 0.00 0.00 45.86 4.44
360 427 0.945813 TAAGTGAAACGGCCAAACGG 59.054 50.000 2.24 0.00 45.86 4.44
372 439 1.304052 CAAACGGCCATCTTCCCCA 60.304 57.895 2.24 0.00 0.00 4.96
385 452 2.571653 TCTTCCCCACACTGTCTATTGG 59.428 50.000 0.00 0.00 0.00 3.16
392 459 1.078709 CACTGTCTATTGGTGCCACG 58.921 55.000 0.00 0.00 0.00 4.94
404 471 2.201708 TGCCACGTAGACCCGACAA 61.202 57.895 0.00 0.00 0.00 3.18
418 485 4.335647 ACAAGTGGGCCCGAGCAG 62.336 66.667 19.37 8.47 42.56 4.24
420 487 4.335647 AAGTGGGCCCGAGCAGTG 62.336 66.667 19.37 0.00 42.56 3.66
424 491 4.154347 GGGCCCGAGCAGTGAGAG 62.154 72.222 5.69 0.00 42.56 3.20
448 515 9.745323 GAGAACATGTTAAAATAAGCAAATTGC 57.255 29.630 11.95 10.41 45.46 3.56
468 535 7.701539 ATTGCATAGTCAGTCCAATTTGTTA 57.298 32.000 0.00 0.00 0.00 2.41
478 545 1.533731 CCAATTTGTTACGCACCGACT 59.466 47.619 0.00 0.00 0.00 4.18
479 546 2.031508 CCAATTTGTTACGCACCGACTT 60.032 45.455 0.00 0.00 0.00 3.01
480 547 3.549221 CCAATTTGTTACGCACCGACTTT 60.549 43.478 0.00 0.00 0.00 2.66
482 549 5.206299 CAATTTGTTACGCACCGACTTTAA 58.794 37.500 0.00 0.00 0.00 1.52
483 550 5.616488 ATTTGTTACGCACCGACTTTAAT 57.384 34.783 0.00 0.00 0.00 1.40
484 551 6.724694 ATTTGTTACGCACCGACTTTAATA 57.275 33.333 0.00 0.00 0.00 0.98
485 552 6.536731 TTTGTTACGCACCGACTTTAATAA 57.463 33.333 0.00 0.00 0.00 1.40
486 553 6.536731 TTGTTACGCACCGACTTTAATAAA 57.463 33.333 0.00 0.00 0.00 1.40
487 554 6.536731 TGTTACGCACCGACTTTAATAAAA 57.463 33.333 0.00 0.00 0.00 1.52
488 555 6.952743 TGTTACGCACCGACTTTAATAAAAA 58.047 32.000 0.00 0.00 0.00 1.94
489 556 7.070798 TGTTACGCACCGACTTTAATAAAAAG 58.929 34.615 0.00 0.00 0.00 2.27
490 557 5.678132 ACGCACCGACTTTAATAAAAAGT 57.322 34.783 2.92 2.92 42.62 2.66
491 558 6.063640 ACGCACCGACTTTAATAAAAAGTT 57.936 33.333 4.75 0.00 40.27 2.66
528 595 1.566231 CTTGAATCCCTAGCCCCAGTT 59.434 52.381 0.00 0.00 0.00 3.16
531 598 1.564348 GAATCCCTAGCCCCAGTTTGA 59.436 52.381 0.00 0.00 0.00 2.69
539 606 0.318120 GCCCCAGTTTGATGGTTGTG 59.682 55.000 0.00 0.00 38.81 3.33
542 609 1.340889 CCCAGTTTGATGGTTGTGTGG 59.659 52.381 0.00 0.00 38.81 4.17
562 629 4.079253 TGGAATTTACTCCAACTCCAAGC 58.921 43.478 0.00 0.00 42.69 4.01
569 636 1.272490 CTCCAACTCCAAGCTGTACGA 59.728 52.381 0.00 0.00 0.00 3.43
580 647 5.637810 TCCAAGCTGTACGAAAGAAACATAG 59.362 40.000 0.00 0.00 32.09 2.23
583 650 6.707599 AGCTGTACGAAAGAAACATAGAAC 57.292 37.500 0.00 0.00 32.09 3.01
588 655 8.511465 TGTACGAAAGAAACATAGAACAGTAC 57.489 34.615 0.00 0.00 0.00 2.73
594 661 8.967552 AAAGAAACATAGAACAGTACTACTCG 57.032 34.615 0.00 0.00 0.00 4.18
606 673 1.139095 CTACTCGCTCCGGTCAACC 59.861 63.158 0.00 0.00 0.00 3.77
623 690 5.352569 GGTCAACCTCACATAGTCTTTGATG 59.647 44.000 0.00 0.00 0.00 3.07
631 698 7.331440 CCTCACATAGTCTTTGATGCATATCTC 59.669 40.741 0.00 0.00 34.31 2.75
634 701 6.649973 ACATAGTCTTTGATGCATATCTCTGC 59.350 38.462 0.00 0.00 42.62 4.26
638 705 5.701750 GTCTTTGATGCATATCTCTGCTCAT 59.298 40.000 0.00 0.00 42.75 2.90
645 712 9.074576 TGATGCATATCTCTGCTCATTATTTTT 57.925 29.630 0.00 0.00 42.75 1.94
785 852 3.948473 GGCAGGAGTAATCCTTCTTTTCC 59.052 47.826 9.53 0.77 38.22 3.13
788 855 5.476945 GCAGGAGTAATCCTTCTTTTCCAAA 59.523 40.000 9.53 0.00 38.22 3.28
789 856 6.153510 GCAGGAGTAATCCTTCTTTTCCAAAT 59.846 38.462 9.53 0.00 38.22 2.32
790 857 7.629437 GCAGGAGTAATCCTTCTTTTCCAAATC 60.629 40.741 9.53 0.00 38.22 2.17
791 858 6.892456 AGGAGTAATCCTTCTTTTCCAAATCC 59.108 38.462 5.74 0.00 36.56 3.01
792 859 6.096987 GGAGTAATCCTTCTTTTCCAAATCCC 59.903 42.308 0.88 0.00 0.00 3.85
793 860 5.958380 AGTAATCCTTCTTTTCCAAATCCCC 59.042 40.000 0.00 0.00 0.00 4.81
794 861 3.184382 TCCTTCTTTTCCAAATCCCCC 57.816 47.619 0.00 0.00 0.00 5.40
865 1207 1.801771 CTCATGCGTTCAAACCGGTTA 59.198 47.619 22.60 2.14 0.00 2.85
1687 2063 2.501610 CTAGGCGAGGCACCCTTC 59.498 66.667 0.00 0.00 31.76 3.46
1729 2105 0.909623 AGTTCGGTGGGGTAATCCAG 59.090 55.000 0.00 0.00 37.50 3.86
2197 2616 8.840833 TTCTGTATGTTTGCTTACATAGTTGA 57.159 30.769 10.47 7.48 40.60 3.18
2204 2624 8.039603 TGTTTGCTTACATAGTTGATAGTTGG 57.960 34.615 0.00 0.00 0.00 3.77
2205 2625 6.677781 TTGCTTACATAGTTGATAGTTGGC 57.322 37.500 0.00 0.00 0.00 4.52
2206 2626 4.808895 TGCTTACATAGTTGATAGTTGGCG 59.191 41.667 0.00 0.00 0.00 5.69
2412 3010 8.755941 GCTTCAGATTTTCTTTTTGTAAACTCC 58.244 33.333 0.00 0.00 0.00 3.85
2466 3068 3.067833 GGCTCAGTCTTGTAACCTTCAC 58.932 50.000 0.00 0.00 0.00 3.18
2477 3079 8.709646 GTCTTGTAACCTTCACAATTAGTACTG 58.290 37.037 5.39 0.00 35.46 2.74
2485 3087 6.767902 CCTTCACAATTAGTACTGGCACATAT 59.232 38.462 5.39 0.00 38.20 1.78
2550 3158 7.538575 AGTTTTGTGTATTAACTGATCATGGC 58.461 34.615 0.00 0.00 31.31 4.40
2551 3159 7.176515 AGTTTTGTGTATTAACTGATCATGGCA 59.823 33.333 0.00 0.00 31.31 4.92
2552 3160 6.435430 TTGTGTATTAACTGATCATGGCAC 57.565 37.500 0.00 0.37 0.00 5.01
2602 3385 5.478233 TGGCACATTGTTATCGTTATGAC 57.522 39.130 0.00 0.00 0.00 3.06
2604 3387 5.645929 TGGCACATTGTTATCGTTATGACTT 59.354 36.000 0.00 0.00 0.00 3.01
2607 3390 7.798516 GGCACATTGTTATCGTTATGACTTATG 59.201 37.037 0.00 0.00 0.00 1.90
2711 4118 7.860872 GTGTGTTTCTTTGTCGAAATTATCCTT 59.139 33.333 0.00 0.00 35.56 3.36
2743 4152 8.424731 GTTGAAAAGTTTTTAATATGTCAGGCG 58.575 33.333 8.59 0.00 0.00 5.52
2781 4193 1.467920 GATAGTGCTTGGCTTGGCTT 58.532 50.000 0.00 0.00 0.00 4.35
2783 4195 0.609131 TAGTGCTTGGCTTGGCTTCC 60.609 55.000 0.00 0.00 0.00 3.46
2784 4196 2.985282 TGCTTGGCTTGGCTTCCG 60.985 61.111 0.00 0.00 0.00 4.30
2798 4212 4.862371 TGGCTTCCGGGAACTAAATTTAT 58.138 39.130 5.09 0.00 0.00 1.40
2829 4243 9.482627 AGTCTATGTTGTTTCTCTTTACTTGAG 57.517 33.333 0.00 0.00 0.00 3.02
2904 4318 5.008316 AGACGTTTTGGACTTACAATTGGAC 59.992 40.000 10.83 0.00 0.00 4.02
3035 4645 4.559153 GCTTGTACTGCAAACATTGGAAT 58.441 39.130 2.62 0.00 36.53 3.01
3162 4856 4.396166 TGAACTTGCTGCTAGGCTAAAATC 59.604 41.667 15.18 3.31 0.00 2.17
3174 4868 6.128688 GCTAGGCTAAAATCGAGATTGCTAAG 60.129 42.308 0.00 3.01 0.00 2.18
3194 4890 9.352784 TGCTAAGTAATTGAATAAACATGTTGC 57.647 29.630 12.82 5.70 0.00 4.17
3208 4964 7.643569 AAACATGTTGCATGATATTGTCCTA 57.356 32.000 12.82 0.00 0.00 2.94
3378 5528 2.093306 TGTTTACAGATCGTGGCAGG 57.907 50.000 0.00 0.00 0.00 4.85
3390 5540 0.882927 GTGGCAGGTTGTTGTCGCTA 60.883 55.000 0.00 0.00 30.79 4.26
3479 5641 1.895707 GAGTGTGCTGCTGTTGCCT 60.896 57.895 0.00 0.00 38.71 4.75
3514 5681 5.361285 AGCTACTACTATCAAGTTGGTCTGG 59.639 44.000 2.34 0.00 37.15 3.86
3605 6284 2.160205 CGGTCAGGTCAGAGACTTGTA 58.840 52.381 8.76 0.00 39.97 2.41
3642 6321 2.621338 TGGCTTCTTATCTGTTGAGCG 58.379 47.619 0.00 0.00 0.00 5.03
3658 6337 4.612264 TGAGCGGTTTTAAGTAGGAGTT 57.388 40.909 0.00 0.00 0.00 3.01
3689 6368 7.267128 AGTCATCATGTTCAATTGTGTTTGTT 58.733 30.769 5.13 0.00 0.00 2.83
3827 6545 4.766891 TGTGGGCTTCTAATTTCTGGAAAG 59.233 41.667 2.29 0.00 33.32 2.62
3872 6590 3.181440 TGGTCTCTTGCCTTGAAGAATGT 60.181 43.478 0.00 0.00 31.52 2.71
3936 6654 6.663523 CCCTGTTTTCTCCTGTGGTTTTATAT 59.336 38.462 0.00 0.00 0.00 0.86
3974 6696 3.116096 AGTGGCCTGAACCTAGATGTA 57.884 47.619 3.32 0.00 0.00 2.29
4050 6772 4.805219 AGGTTTATTTGGCACTAAAAGCG 58.195 39.130 9.68 0.00 33.87 4.68
4086 6808 8.146412 GGCATATTTAAAAGCAATGAGGAGAAT 58.854 33.333 11.23 0.00 0.00 2.40
4087 6809 9.538508 GCATATTTAAAAGCAATGAGGAGAATT 57.461 29.630 0.00 0.00 0.00 2.17
4176 6903 3.056328 GCCCAAACTCCTGCCGAC 61.056 66.667 0.00 0.00 0.00 4.79
4180 6907 1.291877 CCAAACTCCTGCCGACTTCG 61.292 60.000 0.00 0.00 39.44 3.79
4340 7068 8.988064 TTGTTTTGACATAGCTTACAAAAACA 57.012 26.923 16.54 16.54 41.54 2.83
4342 7070 9.593134 TGTTTTGACATAGCTTACAAAAACATT 57.407 25.926 16.54 0.00 41.54 2.71
4354 7082 8.067189 GCTTACAAAAACATTTTACATTGTGGG 58.933 33.333 0.00 0.00 0.00 4.61
4364 7092 0.768622 ACATTGTGGGACGAAGGGAA 59.231 50.000 0.00 0.00 0.00 3.97
4380 7108 7.864770 ACGAAGGGAATAGTTTTTATAGGGAA 58.135 34.615 0.00 0.00 0.00 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.193953 AGATTGTGGATTTAGGTTGAATTGTT 57.806 30.769 0.00 0.00 0.00 2.83
1 2 7.781324 AGATTGTGGATTTAGGTTGAATTGT 57.219 32.000 0.00 0.00 0.00 2.71
4 5 9.799106 CCTATAGATTGTGGATTTAGGTTGAAT 57.201 33.333 0.00 0.00 0.00 2.57
5 6 8.778059 ACCTATAGATTGTGGATTTAGGTTGAA 58.222 33.333 0.00 0.00 35.58 2.69
6 7 8.331931 ACCTATAGATTGTGGATTTAGGTTGA 57.668 34.615 0.00 0.00 35.58 3.18
7 8 8.980481 AACCTATAGATTGTGGATTTAGGTTG 57.020 34.615 9.92 0.00 43.42 3.77
8 9 9.628500 GAAACCTATAGATTGTGGATTTAGGTT 57.372 33.333 0.00 5.80 45.68 3.50
9 10 7.931948 CGAAACCTATAGATTGTGGATTTAGGT 59.068 37.037 0.00 0.00 39.61 3.08
10 11 7.387948 CCGAAACCTATAGATTGTGGATTTAGG 59.612 40.741 0.00 0.00 0.00 2.69
11 12 8.148351 TCCGAAACCTATAGATTGTGGATTTAG 58.852 37.037 0.00 0.00 0.00 1.85
12 13 8.025270 TCCGAAACCTATAGATTGTGGATTTA 57.975 34.615 0.00 0.00 0.00 1.40
13 14 6.895782 TCCGAAACCTATAGATTGTGGATTT 58.104 36.000 0.00 0.00 0.00 2.17
14 15 6.494666 TCCGAAACCTATAGATTGTGGATT 57.505 37.500 0.00 0.00 0.00 3.01
15 16 6.326583 TCTTCCGAAACCTATAGATTGTGGAT 59.673 38.462 0.00 0.00 0.00 3.41
16 17 5.659525 TCTTCCGAAACCTATAGATTGTGGA 59.340 40.000 0.00 0.00 0.00 4.02
17 18 5.914033 TCTTCCGAAACCTATAGATTGTGG 58.086 41.667 0.00 0.00 0.00 4.17
18 19 8.438676 AATTCTTCCGAAACCTATAGATTGTG 57.561 34.615 0.00 0.00 31.91 3.33
19 20 7.438459 CGAATTCTTCCGAAACCTATAGATTGT 59.562 37.037 0.00 0.00 31.91 2.71
20 21 7.652105 TCGAATTCTTCCGAAACCTATAGATTG 59.348 37.037 0.00 0.00 31.91 2.67
21 22 7.652507 GTCGAATTCTTCCGAAACCTATAGATT 59.347 37.037 0.00 0.00 36.50 2.40
22 23 7.146648 GTCGAATTCTTCCGAAACCTATAGAT 58.853 38.462 0.00 0.00 36.50 1.98
23 24 6.095860 TGTCGAATTCTTCCGAAACCTATAGA 59.904 38.462 0.00 0.00 36.50 1.98
24 25 6.270815 TGTCGAATTCTTCCGAAACCTATAG 58.729 40.000 3.52 0.00 36.50 1.31
25 26 6.211587 TGTCGAATTCTTCCGAAACCTATA 57.788 37.500 3.52 0.00 36.50 1.31
26 27 5.080969 TGTCGAATTCTTCCGAAACCTAT 57.919 39.130 3.52 0.00 36.50 2.57
27 28 4.524316 TGTCGAATTCTTCCGAAACCTA 57.476 40.909 3.52 0.00 36.50 3.08
28 29 3.396260 TGTCGAATTCTTCCGAAACCT 57.604 42.857 3.52 0.00 36.50 3.50
29 30 4.216731 GTTTGTCGAATTCTTCCGAAACC 58.783 43.478 3.52 0.00 36.50 3.27
30 31 4.216731 GGTTTGTCGAATTCTTCCGAAAC 58.783 43.478 3.52 5.62 36.50 2.78
31 32 3.251487 GGGTTTGTCGAATTCTTCCGAAA 59.749 43.478 3.52 0.00 36.50 3.46
32 33 2.809696 GGGTTTGTCGAATTCTTCCGAA 59.190 45.455 3.52 0.00 36.50 4.30
33 34 2.038033 AGGGTTTGTCGAATTCTTCCGA 59.962 45.455 3.52 0.00 0.00 4.55
34 35 2.423577 AGGGTTTGTCGAATTCTTCCG 58.576 47.619 3.52 0.00 0.00 4.30
42 43 3.118334 TGGTTGTTCTAGGGTTTGTCGAA 60.118 43.478 0.00 0.00 0.00 3.71
45 46 4.217767 GGAATGGTTGTTCTAGGGTTTGTC 59.782 45.833 0.00 0.00 0.00 3.18
47 48 3.509967 GGGAATGGTTGTTCTAGGGTTTG 59.490 47.826 0.00 0.00 0.00 2.93
51 52 3.449746 TTGGGAATGGTTGTTCTAGGG 57.550 47.619 0.00 0.00 0.00 3.53
74 75 2.926329 TCTCCTTCCCAAGCCCTAAATT 59.074 45.455 0.00 0.00 0.00 1.82
75 76 2.511637 CTCTCCTTCCCAAGCCCTAAAT 59.488 50.000 0.00 0.00 0.00 1.40
106 107 4.810790 TGAGCTAGTAGTTTTCTGACAGC 58.189 43.478 0.00 0.00 0.00 4.40
107 108 6.019779 ACTGAGCTAGTAGTTTTCTGACAG 57.980 41.667 0.00 0.00 38.04 3.51
108 109 6.216569 CAACTGAGCTAGTAGTTTTCTGACA 58.783 40.000 7.54 0.00 39.18 3.58
115 116 4.161102 AGGACCAACTGAGCTAGTAGTTT 58.839 43.478 7.54 0.00 39.18 2.66
118 119 2.356382 CGAGGACCAACTGAGCTAGTAG 59.644 54.545 0.00 0.00 39.18 2.57
121 122 0.179124 GCGAGGACCAACTGAGCTAG 60.179 60.000 0.00 0.00 0.00 3.42
123 124 2.659610 GCGAGGACCAACTGAGCT 59.340 61.111 0.00 0.00 0.00 4.09
129 130 2.722201 ATCTCCGGCGAGGACCAAC 61.722 63.158 9.30 0.00 45.98 3.77
130 131 2.363795 ATCTCCGGCGAGGACCAA 60.364 61.111 9.30 0.00 45.98 3.67
140 141 1.811266 CTGCGACCAACATCTCCGG 60.811 63.158 0.00 0.00 0.00 5.14
141 142 1.078759 GACTGCGACCAACATCTCCG 61.079 60.000 0.00 0.00 0.00 4.63
157 158 3.022287 CACAAGGTTTGCGCGACT 58.978 55.556 12.10 0.00 0.00 4.18
158 159 2.725815 GCACAAGGTTTGCGCGAC 60.726 61.111 12.10 3.71 0.00 5.19
180 181 0.403271 ATCACCTGCCTCACTTTGCT 59.597 50.000 0.00 0.00 0.00 3.91
185 186 1.067295 TTGGAATCACCTGCCTCACT 58.933 50.000 0.00 0.00 39.86 3.41
200 201 1.135344 CATGCACGCATCATTGTTGGA 60.135 47.619 0.44 0.00 33.90 3.53
202 203 0.643310 GCATGCACGCATCATTGTTG 59.357 50.000 14.21 0.00 33.90 3.33
203 204 0.458889 GGCATGCACGCATCATTGTT 60.459 50.000 21.36 0.00 33.90 2.83
213 214 4.758251 TGGAGGACGGCATGCACG 62.758 66.667 21.36 21.64 37.36 5.34
219 220 1.002624 GTGGATTTGGAGGACGGCA 60.003 57.895 0.00 0.00 0.00 5.69
268 269 1.806542 TGCAAGAGACGAAGCCATTTC 59.193 47.619 0.00 0.00 0.00 2.17
269 270 1.896220 TGCAAGAGACGAAGCCATTT 58.104 45.000 0.00 0.00 0.00 2.32
270 271 1.741706 CATGCAAGAGACGAAGCCATT 59.258 47.619 0.00 0.00 0.00 3.16
272 273 0.674581 CCATGCAAGAGACGAAGCCA 60.675 55.000 0.00 0.00 0.00 4.75
273 274 1.372087 CCCATGCAAGAGACGAAGCC 61.372 60.000 0.00 0.00 0.00 4.35
274 275 0.391661 TCCCATGCAAGAGACGAAGC 60.392 55.000 0.00 0.00 0.00 3.86
275 276 1.205655 TCTCCCATGCAAGAGACGAAG 59.794 52.381 9.66 0.00 34.23 3.79
276 277 1.266178 TCTCCCATGCAAGAGACGAA 58.734 50.000 9.66 0.00 34.23 3.85
277 278 1.266178 TTCTCCCATGCAAGAGACGA 58.734 50.000 12.51 0.00 38.83 4.20
296 363 2.889756 GCCAACCCATTCCCTCTCATTT 60.890 50.000 0.00 0.00 0.00 2.32
308 375 3.996621 CCACCCCAGCCAACCCAT 61.997 66.667 0.00 0.00 0.00 4.00
324 391 3.974296 TATCACCCCCACCCACCCC 62.974 68.421 0.00 0.00 0.00 4.95
325 392 1.931705 TTATCACCCCCACCCACCC 60.932 63.158 0.00 0.00 0.00 4.61
326 393 1.212250 ACTTATCACCCCCACCCACC 61.212 60.000 0.00 0.00 0.00 4.61
327 394 0.034477 CACTTATCACCCCCACCCAC 60.034 60.000 0.00 0.00 0.00 4.61
328 395 0.178858 TCACTTATCACCCCCACCCA 60.179 55.000 0.00 0.00 0.00 4.51
360 427 0.678048 GACAGTGTGGGGAAGATGGC 60.678 60.000 0.00 0.00 0.00 4.40
361 428 0.987294 AGACAGTGTGGGGAAGATGG 59.013 55.000 0.00 0.00 0.00 3.51
363 430 3.200825 CCAATAGACAGTGTGGGGAAGAT 59.799 47.826 0.00 0.00 0.00 2.40
372 439 1.608025 CGTGGCACCAATAGACAGTGT 60.608 52.381 12.86 0.00 33.96 3.55
385 452 2.126189 GTCGGGTCTACGTGGCAC 60.126 66.667 7.79 7.79 34.94 5.01
392 459 1.079336 GCCCACTTGTCGGGTCTAC 60.079 63.158 0.00 0.00 46.40 2.59
411 478 1.067283 ACATGTTCTCTCACTGCTCGG 60.067 52.381 0.00 0.00 0.00 4.63
418 485 9.677567 TTTGCTTATTTTAACATGTTCTCTCAC 57.322 29.630 15.85 0.20 0.00 3.51
423 490 9.270640 TGCAATTTGCTTATTTTAACATGTTCT 57.729 25.926 21.19 1.37 45.31 3.01
447 514 5.560148 CGTAACAAATTGGACTGACTATGC 58.440 41.667 0.00 0.00 0.00 3.14
448 515 5.121611 TGCGTAACAAATTGGACTGACTATG 59.878 40.000 0.00 0.00 0.00 2.23
450 517 4.449743 GTGCGTAACAAATTGGACTGACTA 59.550 41.667 0.00 0.00 0.00 2.59
451 518 3.250040 GTGCGTAACAAATTGGACTGACT 59.750 43.478 0.00 0.00 0.00 3.41
456 523 1.532007 TCGGTGCGTAACAAATTGGAC 59.468 47.619 0.00 0.00 0.00 4.02
458 525 1.533731 AGTCGGTGCGTAACAAATTGG 59.466 47.619 0.00 0.00 0.00 3.16
465 532 7.071414 ACTTTTTATTAAAGTCGGTGCGTAAC 58.929 34.615 0.00 0.00 35.76 2.50
468 535 5.678132 ACTTTTTATTAAAGTCGGTGCGT 57.322 34.783 0.00 0.00 35.76 5.24
486 553 9.416284 TCAAGGAACTACCATCTTTTTAACTTT 57.584 29.630 0.00 0.00 38.49 2.66
487 554 8.990163 TCAAGGAACTACCATCTTTTTAACTT 57.010 30.769 0.00 0.00 38.49 2.66
488 555 8.990163 TTCAAGGAACTACCATCTTTTTAACT 57.010 30.769 0.00 0.00 38.49 2.24
489 556 9.841880 GATTCAAGGAACTACCATCTTTTTAAC 57.158 33.333 0.00 0.00 38.49 2.01
490 557 9.020731 GGATTCAAGGAACTACCATCTTTTTAA 57.979 33.333 0.00 0.00 38.49 1.52
491 558 7.614192 GGGATTCAAGGAACTACCATCTTTTTA 59.386 37.037 0.00 0.00 38.49 1.52
501 568 3.181453 GGGCTAGGGATTCAAGGAACTAC 60.181 52.174 0.00 0.00 38.49 2.73
528 595 5.242838 GGAGTAAATTCCACACAACCATCAA 59.757 40.000 0.00 0.00 37.20 2.57
531 598 4.735369 TGGAGTAAATTCCACACAACCAT 58.265 39.130 0.00 0.00 42.24 3.55
539 606 4.082733 GCTTGGAGTTGGAGTAAATTCCAC 60.083 45.833 1.13 0.00 46.61 4.02
542 609 4.762251 ACAGCTTGGAGTTGGAGTAAATTC 59.238 41.667 0.00 0.00 30.10 2.17
562 629 7.639162 ACTGTTCTATGTTTCTTTCGTACAG 57.361 36.000 0.00 0.00 0.00 2.74
569 636 7.541437 GCGAGTAGTACTGTTCTATGTTTCTTT 59.459 37.037 7.76 0.00 0.00 2.52
580 647 1.063764 CCGGAGCGAGTAGTACTGTTC 59.936 57.143 7.76 7.63 0.00 3.18
583 650 0.656785 GACCGGAGCGAGTAGTACTG 59.343 60.000 9.46 1.62 0.00 2.74
588 655 1.139095 GGTTGACCGGAGCGAGTAG 59.861 63.158 9.46 0.00 0.00 2.57
594 661 0.535335 TATGTGAGGTTGACCGGAGC 59.465 55.000 9.46 0.00 42.08 4.70
606 673 8.089597 AGAGATATGCATCAAAGACTATGTGAG 58.910 37.037 0.19 0.00 33.21 3.51
677 744 9.706691 TCGAAGAGAAACAAAAACATATACTCT 57.293 29.630 0.00 0.00 34.38 3.24
715 782 8.975439 GCCTCGTTCTCGAAAAAGAATATATAA 58.025 33.333 0.00 0.00 45.61 0.98
719 786 5.063564 GTGCCTCGTTCTCGAAAAAGAATAT 59.936 40.000 0.00 0.00 45.61 1.28
720 787 4.387862 GTGCCTCGTTCTCGAAAAAGAATA 59.612 41.667 0.00 0.00 45.61 1.75
721 788 3.186613 GTGCCTCGTTCTCGAAAAAGAAT 59.813 43.478 0.00 0.00 45.61 2.40
722 789 2.542595 GTGCCTCGTTCTCGAAAAAGAA 59.457 45.455 0.00 0.00 45.61 2.52
723 790 2.132762 GTGCCTCGTTCTCGAAAAAGA 58.867 47.619 0.00 0.00 45.61 2.52
724 791 1.864711 TGTGCCTCGTTCTCGAAAAAG 59.135 47.619 0.00 0.00 45.61 2.27
725 792 1.942677 TGTGCCTCGTTCTCGAAAAA 58.057 45.000 0.00 0.00 45.61 1.94
726 793 1.942677 TTGTGCCTCGTTCTCGAAAA 58.057 45.000 0.00 0.00 45.61 2.29
727 794 1.798223 CATTGTGCCTCGTTCTCGAAA 59.202 47.619 0.00 0.00 45.61 3.46
728 795 1.000394 TCATTGTGCCTCGTTCTCGAA 60.000 47.619 0.00 0.00 45.61 3.71
729 796 0.601057 TCATTGTGCCTCGTTCTCGA 59.399 50.000 0.00 0.00 44.12 4.04
730 797 1.325640 CATCATTGTGCCTCGTTCTCG 59.674 52.381 0.00 0.00 38.55 4.04
731 798 2.621338 TCATCATTGTGCCTCGTTCTC 58.379 47.619 0.00 0.00 0.00 2.87
732 799 2.768253 TCATCATTGTGCCTCGTTCT 57.232 45.000 0.00 0.00 0.00 3.01
733 800 2.679837 ACATCATCATTGTGCCTCGTTC 59.320 45.455 0.00 0.00 0.00 3.95
734 801 2.421073 CACATCATCATTGTGCCTCGTT 59.579 45.455 0.00 0.00 38.18 3.85
735 802 2.011947 CACATCATCATTGTGCCTCGT 58.988 47.619 0.00 0.00 38.18 4.18
736 803 2.011947 ACACATCATCATTGTGCCTCG 58.988 47.619 3.85 0.00 46.65 4.63
737 804 3.766151 CAACACATCATCATTGTGCCTC 58.234 45.455 3.85 0.00 46.65 4.70
738 805 2.094390 GCAACACATCATCATTGTGCCT 60.094 45.455 3.85 0.00 46.65 4.75
739 806 2.264813 GCAACACATCATCATTGTGCC 58.735 47.619 3.85 0.00 46.65 5.01
740 807 2.921121 CTGCAACACATCATCATTGTGC 59.079 45.455 3.85 0.00 46.65 4.57
742 809 3.442625 CCTCTGCAACACATCATCATTGT 59.557 43.478 0.00 0.00 0.00 2.71
743 810 3.733988 GCCTCTGCAACACATCATCATTG 60.734 47.826 0.00 0.00 37.47 2.82
744 811 2.426024 GCCTCTGCAACACATCATCATT 59.574 45.455 0.00 0.00 37.47 2.57
853 1195 2.807392 GTTCGACCATAACCGGTTTGAA 59.193 45.455 27.64 13.46 40.22 2.69
876 1218 2.095161 CAGTCGTCTTTCTACTCGGCTT 60.095 50.000 0.00 0.00 36.11 4.35
1080 1429 4.742201 GCGCGGAAGAGGTGCTCA 62.742 66.667 8.83 0.00 37.89 4.26
1687 2063 4.180057 GTGAAGTAGACTGCATCTCCAAG 58.820 47.826 0.00 0.00 39.04 3.61
1757 2133 3.181455 CGGTGGGTCAATCATGGATAAGA 60.181 47.826 0.00 0.00 0.00 2.10
2197 2616 1.679032 GGAAGAACCAGCGCCAACTAT 60.679 52.381 2.29 0.00 38.79 2.12
2412 3010 5.461737 GCTACAGCTATGCTAGAAAACAGAG 59.538 44.000 0.00 0.00 36.40 3.35
2466 3068 6.425114 GGTGAGATATGTGCCAGTACTAATTG 59.575 42.308 0.00 0.00 0.00 2.32
2477 3079 2.684881 CCACTTTGGTGAGATATGTGCC 59.315 50.000 0.00 0.00 45.61 5.01
2485 3087 2.106338 TCAGCATTCCACTTTGGTGAGA 59.894 45.455 1.06 0.00 43.30 3.27
2537 3145 7.877612 ACGATAATAATGTGCCATGATCAGTTA 59.122 33.333 0.09 0.00 0.00 2.24
2538 3146 6.712095 ACGATAATAATGTGCCATGATCAGTT 59.288 34.615 0.09 0.00 0.00 3.16
2539 3147 6.233434 ACGATAATAATGTGCCATGATCAGT 58.767 36.000 0.09 0.00 0.00 3.41
2540 3148 6.732531 ACGATAATAATGTGCCATGATCAG 57.267 37.500 0.09 0.00 0.00 2.90
2542 3150 8.882736 TCATAACGATAATAATGTGCCATGATC 58.117 33.333 0.00 0.00 0.00 2.92
2543 3151 8.791327 TCATAACGATAATAATGTGCCATGAT 57.209 30.769 0.00 0.00 0.00 2.45
2557 3165 8.935844 GCCATGATCAGTTAATCATAACGATAA 58.064 33.333 0.09 0.00 43.01 1.75
2558 3166 8.093927 TGCCATGATCAGTTAATCATAACGATA 58.906 33.333 0.09 0.00 43.01 2.92
2559 3167 6.936335 TGCCATGATCAGTTAATCATAACGAT 59.064 34.615 0.09 0.00 43.01 3.73
2560 3168 6.202762 GTGCCATGATCAGTTAATCATAACGA 59.797 38.462 0.09 0.00 43.01 3.85
2561 3169 6.018016 TGTGCCATGATCAGTTAATCATAACG 60.018 38.462 0.09 0.00 43.01 3.18
2562 3170 7.263100 TGTGCCATGATCAGTTAATCATAAC 57.737 36.000 0.09 0.00 43.01 1.89
2563 3171 8.354426 CAATGTGCCATGATCAGTTAATCATAA 58.646 33.333 0.09 0.00 43.01 1.90
2564 3172 7.503230 ACAATGTGCCATGATCAGTTAATCATA 59.497 33.333 0.09 0.00 43.01 2.15
2565 3173 6.322969 ACAATGTGCCATGATCAGTTAATCAT 59.677 34.615 0.09 0.00 45.17 2.45
2566 3174 5.653330 ACAATGTGCCATGATCAGTTAATCA 59.347 36.000 0.09 0.00 39.85 2.57
2567 3175 6.140303 ACAATGTGCCATGATCAGTTAATC 57.860 37.500 0.09 0.00 0.00 1.75
2568 3176 6.534475 AACAATGTGCCATGATCAGTTAAT 57.466 33.333 0.09 0.00 0.00 1.40
2569 3177 5.981088 AACAATGTGCCATGATCAGTTAA 57.019 34.783 0.09 0.00 0.00 2.01
2570 3178 6.018016 CGATAACAATGTGCCATGATCAGTTA 60.018 38.462 0.09 1.40 0.00 2.24
2571 3179 5.220912 CGATAACAATGTGCCATGATCAGTT 60.221 40.000 0.09 0.00 0.00 3.16
2572 3180 4.274214 CGATAACAATGTGCCATGATCAGT 59.726 41.667 0.09 0.00 0.00 3.41
2573 3181 4.274214 ACGATAACAATGTGCCATGATCAG 59.726 41.667 0.09 0.00 0.00 2.90
2574 3182 4.198530 ACGATAACAATGTGCCATGATCA 58.801 39.130 0.00 0.00 0.00 2.92
2674 4032 5.743398 ACAAAGAAACACACACAATCGATTG 59.257 36.000 31.51 31.51 43.26 2.67
2743 4152 8.552034 GCACTATCCAAACATTAACTGAGATAC 58.448 37.037 0.00 0.00 0.00 2.24
2781 4193 6.949715 ACTACACATAAATTTAGTTCCCGGA 58.050 36.000 0.73 0.00 0.00 5.14
2783 4195 9.760077 ATAGACTACACATAAATTTAGTTCCCG 57.240 33.333 3.94 0.00 0.00 5.14
2798 4212 9.472361 GTAAAGAGAAACAACATAGACTACACA 57.528 33.333 0.00 0.00 0.00 3.72
2829 4243 4.327357 CGAGACCAACACTGAACATCATAC 59.673 45.833 0.00 0.00 0.00 2.39
2904 4318 7.645058 AAATAACAACTTGGATCCCTGTATG 57.355 36.000 9.90 10.81 0.00 2.39
3035 4645 4.974645 ACCTTGAGTCCTTGACAATACA 57.025 40.909 0.00 0.00 34.60 2.29
3194 4890 7.756395 AGCAAGGAAATAGGACAATATCATG 57.244 36.000 0.00 0.00 0.00 3.07
3333 5472 5.221501 ACCAAGCACAAAACTCATAAGCAAT 60.222 36.000 0.00 0.00 0.00 3.56
3378 5528 1.194772 GTCCTTGCTAGCGACAACAAC 59.805 52.381 10.77 0.00 0.00 3.32
3390 5540 1.134670 GGCGATCAGTTAGTCCTTGCT 60.135 52.381 0.00 0.00 0.00 3.91
3514 5681 6.303259 CGTCATGCTTAAACTGCTAAAGAAAC 59.697 38.462 0.00 0.00 0.00 2.78
3605 6284 8.409358 AAGAAGCCAACATACTAAACTGAAAT 57.591 30.769 0.00 0.00 0.00 2.17
3642 6321 5.298527 ACTTGCACAACTCCTACTTAAAACC 59.701 40.000 0.00 0.00 0.00 3.27
3658 6337 5.221283 ACAATTGAACATGATGACTTGCACA 60.221 36.000 13.59 0.00 0.00 4.57
3689 6368 2.289382 TGTAAGCAGGACAATTCGCAGA 60.289 45.455 0.00 0.00 0.00 4.26
3827 6545 5.757850 ACACTGAATGACACTTCCTTTTC 57.242 39.130 0.00 0.00 0.00 2.29
3872 6590 4.588899 CATAACATTCCCACAGGAGACAA 58.411 43.478 0.00 0.00 45.19 3.18
3974 6696 1.690219 CCTTAGCCCTGCATCGTCCT 61.690 60.000 0.00 0.00 0.00 3.85
3981 6703 1.685224 CTCCAACCTTAGCCCTGCA 59.315 57.895 0.00 0.00 0.00 4.41
4021 6743 8.973835 TTTAGTGCCAAATAAACCTATTTTCG 57.026 30.769 0.00 0.00 35.88 3.46
4089 6811 6.713762 ACAGTCATCACAGAAAATGGAAAA 57.286 33.333 0.00 0.00 0.00 2.29
4176 6903 2.096069 CACACATGCTCAAACCTCGAAG 60.096 50.000 0.00 0.00 0.00 3.79
4180 6907 0.242017 GCCACACATGCTCAAACCTC 59.758 55.000 0.00 0.00 0.00 3.85
4340 7068 3.761752 CCCTTCGTCCCACAATGTAAAAT 59.238 43.478 0.00 0.00 0.00 1.82
4342 7070 2.372504 TCCCTTCGTCCCACAATGTAAA 59.627 45.455 0.00 0.00 0.00 2.01
4354 7082 7.503549 TCCCTATAAAAACTATTCCCTTCGTC 58.496 38.462 0.00 0.00 0.00 4.20
4380 7108 3.304829 AGCAACCCCAATAGTTGTTGTT 58.695 40.909 5.62 0.00 45.14 2.83


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

AutoCloner maintained by Alex Coulton.