Multiple sequence alignment - TraesCS4D01G344000

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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 TraesCS4D01G344000 chr4D 100.000 3914 0 0 1 3914 499505572 499501659 0.000000e+00 7228.0
1 TraesCS4D01G344000 chr4D 90.116 172 16 1 514 684 489488177 489488348 5.090000e-54 222.0
2 TraesCS4D01G344000 chr4D 89.881 168 16 1 517 683 454926476 454926309 8.520000e-52 215.0
3 TraesCS4D01G344000 chr4D 89.349 169 17 1 517 684 25278367 25278199 1.100000e-50 211.0
4 TraesCS4D01G344000 chr4D 88.757 169 16 3 517 683 359302799 359302632 1.840000e-48 204.0
5 TraesCS4D01G344000 chr4D 88.166 169 19 1 517 684 326309172 326309340 2.390000e-47 200.0
6 TraesCS4D01G344000 chr4D 88.095 168 19 1 517 683 222696021 222695854 8.580000e-47 198.0
7 TraesCS4D01G344000 chr4B 91.722 2718 119 46 1275 3914 642458393 642455704 0.000000e+00 3675.0
8 TraesCS4D01G344000 chr4B 91.767 583 22 3 689 1271 642459004 642458448 0.000000e+00 787.0
9 TraesCS4D01G344000 chr4B 81.350 311 49 4 1964 2271 642774239 642773935 1.090000e-60 244.0
10 TraesCS4D01G344000 chr4B 83.333 258 31 9 993 1240 642958618 642958873 1.090000e-55 228.0
11 TraesCS4D01G344000 chr4B 79.775 267 47 6 999 1260 642746619 642746883 1.860000e-43 187.0
12 TraesCS4D01G344000 chr5A 91.009 1635 134 11 1268 2896 680504392 680502765 0.000000e+00 2193.0
13 TraesCS4D01G344000 chr5A 91.952 584 29 10 689 1271 680504998 680504432 0.000000e+00 802.0
14 TraesCS4D01G344000 chr5A 97.409 193 5 0 3720 3912 680502457 680502265 2.920000e-86 329.0
15 TraesCS4D01G344000 chr5A 85.375 253 27 6 996 1240 627014970 627015220 1.810000e-63 254.0
16 TraesCS4D01G344000 chr5A 85.837 233 28 4 1009 1240 624967427 624967199 3.910000e-60 243.0
17 TraesCS4D01G344000 chr5A 83.333 264 30 7 993 1243 680720076 680720338 8.460000e-57 231.0
18 TraesCS4D01G344000 chr7D 93.056 504 26 3 22 520 611455653 611456152 0.000000e+00 728.0
19 TraesCS4D01G344000 chr7D 88.000 500 51 8 22 516 624812868 624812373 2.030000e-162 582.0
20 TraesCS4D01G344000 chr7D 88.235 170 16 3 517 683 399132650 399132818 2.390000e-47 200.0
21 TraesCS4D01G344000 chr1D 89.866 523 31 12 1 516 271816052 271816559 0.000000e+00 652.0
22 TraesCS4D01G344000 chr1D 80.332 844 141 11 1826 2655 368318945 368319777 2.000000e-172 616.0
23 TraesCS4D01G344000 chr1D 87.873 503 45 10 22 517 35752856 35753349 9.430000e-161 577.0
24 TraesCS4D01G344000 chr1D 89.941 169 15 2 517 684 60915328 60915161 2.370000e-52 217.0
25 TraesCS4D01G344000 chr5D 89.168 517 36 10 1 516 422050091 422050588 9.230000e-176 627.0
26 TraesCS4D01G344000 chr5D 85.632 522 58 8 1 516 523051147 523051657 2.070000e-147 532.0
27 TraesCS4D01G344000 chr5D 85.214 257 27 7 992 1240 500646683 500646936 1.810000e-63 254.0
28 TraesCS4D01G344000 chr5D 85.366 246 31 4 996 1240 500681071 500681312 2.330000e-62 250.0
29 TraesCS4D01G344000 chr5D 89.286 168 17 1 517 683 324319918 324319751 3.960000e-50 209.0
30 TraesCS4D01G344000 chr5D 89.286 168 17 1 517 683 442196389 442196556 3.960000e-50 209.0
31 TraesCS4D01G344000 chr1B 80.496 846 139 11 1826 2655 492334749 492335584 3.320000e-175 625.0
32 TraesCS4D01G344000 chr1B 82.379 454 52 14 808 1260 492333492 492333918 1.720000e-98 370.0
33 TraesCS4D01G344000 chr3D 88.996 518 38 10 1 516 571098310 571097810 1.190000e-174 623.0
34 TraesCS4D01G344000 chr1A 80.213 844 142 10 1826 2655 467256718 467257550 9.300000e-171 610.0
35 TraesCS4D01G344000 chr5B 86.720 497 48 13 22 516 545967195 545967675 1.600000e-148 536.0
36 TraesCS4D01G344000 chr5B 84.553 246 33 4 996 1240 622073435 622073676 5.050000e-59 239.0
37 TraesCS4D01G344000 chr6A 86.410 493 55 7 22 512 592933382 592933864 2.680000e-146 529.0
38 TraesCS4D01G344000 chr6D 88.889 162 17 1 523 683 343004377 343004216 8.580000e-47 198.0
39 TraesCS4D01G344000 chr6D 88.095 168 19 1 517 683 418472511 418472678 8.580000e-47 198.0
40 TraesCS4D01G344000 chr6D 82.635 167 27 2 517 682 58570808 58570973 3.150000e-31 147.0
41 TraesCS4D01G344000 chr2B 100.000 31 0 0 1718 1748 249201427 249201457 1.520000e-04 58.4
42 TraesCS4D01G344000 chr2A 100.000 30 0 0 1720 1749 206839362 206839391 5.460000e-04 56.5
43 TraesCS4D01G344000 chr3B 100.000 28 0 0 1722 1749 459253005 459253032 7.000000e-03 52.8
44 TraesCS4D01G344000 chr3A 100.000 28 0 0 1722 1749 477142906 477142933 7.000000e-03 52.8


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 TraesCS4D01G344000 chr4D 499501659 499505572 3913 True 7228.0 7228 100.000000 1 3914 1 chr4D.!!$R5 3913
1 TraesCS4D01G344000 chr4B 642455704 642459004 3300 True 2231.0 3675 91.744500 689 3914 2 chr4B.!!$R2 3225
2 TraesCS4D01G344000 chr5A 680502265 680504998 2733 True 1108.0 2193 93.456667 689 3912 3 chr5A.!!$R2 3223
3 TraesCS4D01G344000 chr1D 271816052 271816559 507 False 652.0 652 89.866000 1 516 1 chr1D.!!$F2 515
4 TraesCS4D01G344000 chr1D 368318945 368319777 832 False 616.0 616 80.332000 1826 2655 1 chr1D.!!$F3 829
5 TraesCS4D01G344000 chr5D 523051147 523051657 510 False 532.0 532 85.632000 1 516 1 chr5D.!!$F5 515
6 TraesCS4D01G344000 chr1B 492333492 492335584 2092 False 497.5 625 81.437500 808 2655 2 chr1B.!!$F1 1847
7 TraesCS4D01G344000 chr3D 571097810 571098310 500 True 623.0 623 88.996000 1 516 1 chr3D.!!$R1 515
8 TraesCS4D01G344000 chr1A 467256718 467257550 832 False 610.0 610 80.213000 1826 2655 1 chr1A.!!$F1 829

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
19 20 0.172803 GGACGTGACAGACCGCTAAT 59.827 55.0 0.00 0.0 0.00 1.73 F
608 617 0.174845 TTTATCCTGCACGCGCTACT 59.825 50.0 5.73 0.0 39.64 2.57 F
1923 2369 0.182061 TGATCAGGATGCTCTTGCCC 59.818 55.0 0.00 0.0 38.71 5.36 F
2273 2720 0.394352 CCCTTAGCCCATTCAGCGTT 60.394 55.0 0.00 0.0 34.64 4.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1203 1218 0.034186 CATGGCAGGCCTCAACCTTA 60.034 55.0 0.00 0.00 38.26 2.69 R
2264 2711 0.249398 ACTTAGGGCGAACGCTGAAT 59.751 50.0 18.14 5.44 39.80 2.57 R
2899 3361 0.034896 CACGACTACCAAAGGCCAGT 59.965 55.0 5.01 0.00 0.00 4.00 R
3332 3824 0.106268 TTGCCTGAGCCCAGTTTCAA 60.106 50.0 0.00 0.00 38.74 2.69 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
19 20 0.172803 GGACGTGACAGACCGCTAAT 59.827 55.000 0.00 0.00 0.00 1.73
20 21 1.402968 GGACGTGACAGACCGCTAATA 59.597 52.381 0.00 0.00 0.00 0.98
21 22 2.034305 GGACGTGACAGACCGCTAATAT 59.966 50.000 0.00 0.00 0.00 1.28
22 23 3.251729 GGACGTGACAGACCGCTAATATA 59.748 47.826 0.00 0.00 0.00 0.86
23 24 4.261322 GGACGTGACAGACCGCTAATATAA 60.261 45.833 0.00 0.00 0.00 0.98
55 56 1.628340 TCTCGGGAAAAATGGAGCTCA 59.372 47.619 17.19 1.87 0.00 4.26
61 62 3.425659 GGAAAAATGGAGCTCAGAGGTT 58.574 45.455 17.19 3.41 0.00 3.50
150 151 0.543749 GGTGAGCTAGAGCACCCAAT 59.456 55.000 18.65 0.00 46.91 3.16
151 152 1.661341 GTGAGCTAGAGCACCCAATG 58.339 55.000 4.01 0.00 45.16 2.82
203 205 2.345244 CCGTGGAGTGCTCTGCTT 59.655 61.111 8.78 0.00 33.13 3.91
225 227 2.565834 GCCGGCGATGGGGTATATATAT 59.434 50.000 12.58 0.00 0.00 0.86
226 228 3.765511 GCCGGCGATGGGGTATATATATA 59.234 47.826 12.58 0.00 0.00 0.86
227 229 4.404715 GCCGGCGATGGGGTATATATATAT 59.595 45.833 12.58 10.10 0.00 0.86
228 230 5.595542 GCCGGCGATGGGGTATATATATATA 59.404 44.000 12.58 8.16 0.00 0.86
255 257 0.604243 CATTTGTCCCGGTTCGTGGA 60.604 55.000 0.00 0.00 0.00 4.02
277 279 1.540617 AACCGGGACTAAAGGCCCT 60.541 57.895 18.97 0.00 42.40 5.19
305 312 2.349755 CGAACCGGGACCAATGGT 59.650 61.111 3.74 3.74 39.44 3.55
430 438 3.379445 GGCTCTCGAACCGGGACA 61.379 66.667 6.32 0.00 31.17 4.02
437 446 1.674322 CGAACCGGGACAAATGCCT 60.674 57.895 6.32 0.00 33.05 4.75
442 451 0.684153 CCGGGACAAATGCCTCCATT 60.684 55.000 0.00 0.00 43.32 3.16
485 494 1.635817 GGACTAATGGGCTGGCCAGA 61.636 60.000 37.21 16.68 37.98 3.86
502 511 3.246880 ACCCGAACGAAAGCCCCT 61.247 61.111 0.00 0.00 0.00 4.79
516 525 4.995624 AAGCCCCTTTTTCTACTAGTGT 57.004 40.909 5.39 0.00 0.00 3.55
517 526 4.995624 AGCCCCTTTTTCTACTAGTGTT 57.004 40.909 5.39 0.00 0.00 3.32
518 527 6.443995 AAGCCCCTTTTTCTACTAGTGTTA 57.556 37.500 5.39 0.00 0.00 2.41
519 528 6.051179 AGCCCCTTTTTCTACTAGTGTTAG 57.949 41.667 5.39 0.00 0.00 2.34
520 529 5.546887 AGCCCCTTTTTCTACTAGTGTTAGT 59.453 40.000 5.39 0.00 42.66 2.24
521 530 6.727697 AGCCCCTTTTTCTACTAGTGTTAGTA 59.272 38.462 5.39 0.00 40.55 1.82
545 554 9.250624 GTAGTGAGAATTTTAGTAGTAGCATGG 57.749 37.037 0.00 0.00 0.00 3.66
546 555 7.852263 AGTGAGAATTTTAGTAGTAGCATGGT 58.148 34.615 1.62 1.62 0.00 3.55
547 556 8.322091 AGTGAGAATTTTAGTAGTAGCATGGTT 58.678 33.333 1.12 0.00 0.00 3.67
548 557 9.595823 GTGAGAATTTTAGTAGTAGCATGGTTA 57.404 33.333 1.12 0.00 0.00 2.85
553 562 8.747538 ATTTTAGTAGTAGCATGGTTAAAGGG 57.252 34.615 1.12 0.00 0.00 3.95
554 563 7.499200 TTTAGTAGTAGCATGGTTAAAGGGA 57.501 36.000 1.12 0.00 0.00 4.20
555 564 5.615925 AGTAGTAGCATGGTTAAAGGGAG 57.384 43.478 1.12 0.00 0.00 4.30
556 565 3.933861 AGTAGCATGGTTAAAGGGAGG 57.066 47.619 1.12 0.00 0.00 4.30
557 566 2.092375 AGTAGCATGGTTAAAGGGAGGC 60.092 50.000 1.12 0.00 0.00 4.70
558 567 0.394352 AGCATGGTTAAAGGGAGGCG 60.394 55.000 0.00 0.00 0.00 5.52
559 568 2.004808 GCATGGTTAAAGGGAGGCGC 62.005 60.000 0.00 0.00 0.00 6.53
560 569 1.451387 ATGGTTAAAGGGAGGCGCG 60.451 57.895 0.00 0.00 0.00 6.86
561 570 3.506096 GGTTAAAGGGAGGCGCGC 61.506 66.667 25.94 25.94 0.00 6.86
562 571 2.436115 GTTAAAGGGAGGCGCGCT 60.436 61.111 32.29 17.27 42.29 5.92
563 572 1.153509 GTTAAAGGGAGGCGCGCTA 60.154 57.895 32.29 10.75 39.11 4.26
564 573 1.153509 TTAAAGGGAGGCGCGCTAC 60.154 57.895 32.29 23.36 39.11 3.58
565 574 1.610554 TTAAAGGGAGGCGCGCTACT 61.611 55.000 32.29 20.98 39.11 2.57
566 575 2.292794 TAAAGGGAGGCGCGCTACTG 62.293 60.000 32.29 0.00 39.11 2.74
569 578 3.900892 GGAGGCGCGCTACTGCTA 61.901 66.667 32.29 0.00 36.97 3.49
570 579 2.336809 GAGGCGCGCTACTGCTAT 59.663 61.111 32.29 6.68 36.97 2.97
571 580 2.018866 GAGGCGCGCTACTGCTATG 61.019 63.158 32.29 0.00 36.97 2.23
572 581 2.279517 GGCGCGCTACTGCTATGT 60.280 61.111 32.29 0.00 36.97 2.29
573 582 1.883084 GGCGCGCTACTGCTATGTT 60.883 57.895 32.29 0.00 36.97 2.71
574 583 1.429148 GGCGCGCTACTGCTATGTTT 61.429 55.000 32.29 0.00 36.97 2.83
575 584 0.315382 GCGCGCTACTGCTATGTTTG 60.315 55.000 26.67 0.00 36.97 2.93
576 585 0.999406 CGCGCTACTGCTATGTTTGT 59.001 50.000 5.56 0.00 36.97 2.83
577 586 2.190161 CGCGCTACTGCTATGTTTGTA 58.810 47.619 5.56 0.00 36.97 2.41
578 587 2.794910 CGCGCTACTGCTATGTTTGTAT 59.205 45.455 5.56 0.00 36.97 2.29
579 588 3.121328 CGCGCTACTGCTATGTTTGTATC 60.121 47.826 5.56 0.00 36.97 2.24
580 589 4.051922 GCGCTACTGCTATGTTTGTATCT 58.948 43.478 0.00 0.00 36.97 1.98
581 590 4.084849 GCGCTACTGCTATGTTTGTATCTG 60.085 45.833 0.00 0.00 36.97 2.90
582 591 5.043903 CGCTACTGCTATGTTTGTATCTGT 58.956 41.667 0.00 0.00 36.97 3.41
583 592 6.206498 CGCTACTGCTATGTTTGTATCTGTA 58.794 40.000 0.00 0.00 36.97 2.74
584 593 6.695713 CGCTACTGCTATGTTTGTATCTGTAA 59.304 38.462 0.00 0.00 36.97 2.41
585 594 7.306051 CGCTACTGCTATGTTTGTATCTGTAAC 60.306 40.741 0.00 0.00 36.97 2.50
586 595 6.887376 ACTGCTATGTTTGTATCTGTAACG 57.113 37.500 0.00 0.00 0.00 3.18
587 596 5.291128 ACTGCTATGTTTGTATCTGTAACGC 59.709 40.000 0.00 0.00 0.00 4.84
588 597 4.266739 TGCTATGTTTGTATCTGTAACGCG 59.733 41.667 3.53 3.53 0.00 6.01
589 598 4.266976 GCTATGTTTGTATCTGTAACGCGT 59.733 41.667 5.58 5.58 0.00 6.01
590 599 5.220340 GCTATGTTTGTATCTGTAACGCGTT 60.220 40.000 29.27 29.27 0.00 4.84
591 600 5.600908 ATGTTTGTATCTGTAACGCGTTT 57.399 34.783 31.50 14.35 0.00 3.60
592 601 6.709145 ATGTTTGTATCTGTAACGCGTTTA 57.291 33.333 31.50 18.21 0.00 2.01
593 602 6.709145 TGTTTGTATCTGTAACGCGTTTAT 57.291 33.333 31.50 19.38 0.00 1.40
594 603 6.754206 TGTTTGTATCTGTAACGCGTTTATC 58.246 36.000 31.50 19.96 0.00 1.75
595 604 5.954434 TTGTATCTGTAACGCGTTTATCC 57.046 39.130 31.50 15.67 0.00 2.59
596 605 5.252969 TGTATCTGTAACGCGTTTATCCT 57.747 39.130 31.50 14.66 0.00 3.24
597 606 5.038683 TGTATCTGTAACGCGTTTATCCTG 58.961 41.667 31.50 17.78 0.00 3.86
598 607 2.264813 TCTGTAACGCGTTTATCCTGC 58.735 47.619 31.50 8.79 0.00 4.85
599 608 1.996898 CTGTAACGCGTTTATCCTGCA 59.003 47.619 31.50 13.37 0.00 4.41
600 609 1.727880 TGTAACGCGTTTATCCTGCAC 59.272 47.619 31.50 19.13 0.00 4.57
601 610 0.993532 TAACGCGTTTATCCTGCACG 59.006 50.000 31.50 0.00 36.98 5.34
604 613 2.021380 CGTTTATCCTGCACGCGC 59.979 61.111 5.73 0.00 39.24 6.86
605 614 2.452813 CGTTTATCCTGCACGCGCT 61.453 57.895 5.73 0.00 39.64 5.92
606 615 1.143373 CGTTTATCCTGCACGCGCTA 61.143 55.000 5.73 0.00 39.64 4.26
607 616 0.300789 GTTTATCCTGCACGCGCTAC 59.699 55.000 5.73 0.00 39.64 3.58
608 617 0.174845 TTTATCCTGCACGCGCTACT 59.825 50.000 5.73 0.00 39.64 2.57
609 618 0.527600 TTATCCTGCACGCGCTACTG 60.528 55.000 5.73 0.00 39.64 2.74
610 619 2.954020 TATCCTGCACGCGCTACTGC 62.954 60.000 5.73 9.63 39.64 4.40
612 621 2.202610 CTGCACGCGCTACTGCTA 60.203 61.111 18.50 6.27 39.64 3.49
613 622 2.506217 TGCACGCGCTACTGCTAC 60.506 61.111 18.50 0.00 39.64 3.58
614 623 2.202623 GCACGCGCTACTGCTACT 60.203 61.111 5.73 0.00 36.97 2.57
615 624 1.805945 GCACGCGCTACTGCTACTT 60.806 57.895 5.73 0.00 36.97 2.24
616 625 0.524816 GCACGCGCTACTGCTACTTA 60.525 55.000 5.73 0.00 36.97 2.24
617 626 1.467875 CACGCGCTACTGCTACTTAG 58.532 55.000 5.73 0.00 36.97 2.18
653 662 7.901874 TTTTTAACAAGCGCTACTGTTAAAG 57.098 32.000 35.20 15.18 39.79 1.85
654 663 6.607735 TTTAACAAGCGCTACTGTTAAAGT 57.392 33.333 34.68 17.44 43.40 2.66
655 664 6.607735 TTAACAAGCGCTACTGTTAAAGTT 57.392 33.333 30.92 18.19 40.56 2.66
656 665 5.494632 AACAAGCGCTACTGTTAAAGTTT 57.505 34.783 22.58 0.64 40.56 2.66
657 666 5.494632 ACAAGCGCTACTGTTAAAGTTTT 57.505 34.783 12.05 0.00 40.56 2.43
658 667 5.270853 ACAAGCGCTACTGTTAAAGTTTTG 58.729 37.500 12.05 1.74 40.56 2.44
659 668 5.163693 ACAAGCGCTACTGTTAAAGTTTTGT 60.164 36.000 12.05 2.51 40.56 2.83
660 669 4.844267 AGCGCTACTGTTAAAGTTTTGTG 58.156 39.130 8.99 0.00 40.56 3.33
661 670 4.334481 AGCGCTACTGTTAAAGTTTTGTGT 59.666 37.500 8.99 0.00 40.56 3.72
662 671 5.524646 AGCGCTACTGTTAAAGTTTTGTGTA 59.475 36.000 8.99 0.00 40.56 2.90
663 672 6.204108 AGCGCTACTGTTAAAGTTTTGTGTAT 59.796 34.615 8.99 0.00 40.56 2.29
664 673 7.385752 AGCGCTACTGTTAAAGTTTTGTGTATA 59.614 33.333 8.99 0.00 40.56 1.47
665 674 8.011106 GCGCTACTGTTAAAGTTTTGTGTATAA 58.989 33.333 0.00 0.00 40.56 0.98
666 675 9.525007 CGCTACTGTTAAAGTTTTGTGTATAAG 57.475 33.333 0.00 0.00 40.56 1.73
667 676 9.821662 GCTACTGTTAAAGTTTTGTGTATAAGG 57.178 33.333 0.00 0.00 40.56 2.69
1093 1108 1.004080 TTCGTCGACGTCCTCCTCT 60.004 57.895 34.40 0.00 40.80 3.69
1094 1109 1.018226 TTCGTCGACGTCCTCCTCTC 61.018 60.000 34.40 0.00 40.80 3.20
1138 1153 2.449031 AATCCAGTTCTGTGCGGCGA 62.449 55.000 12.98 0.00 0.00 5.54
1157 1172 1.528824 CATCACCGGGATGCCTCTT 59.471 57.895 16.71 0.00 46.35 2.85
1203 1218 2.284699 ACGGGAGGTAGGCTGCTT 60.285 61.111 1.79 0.00 0.00 3.91
1223 1238 1.792757 AAGGTTGAGGCCTGCCATGA 61.793 55.000 12.00 0.00 39.17 3.07
1371 1456 0.979665 TCCTCAGGAGCAGTTTCTGG 59.020 55.000 0.00 0.00 31.21 3.86
1493 1584 1.071385 CAAAGTGAGCTCTGGGTCTGT 59.929 52.381 16.19 0.00 40.29 3.41
1574 1665 1.075482 CCACCAGGACCATGCAGTT 59.925 57.895 0.00 0.00 36.89 3.16
1609 1700 4.554036 GCCCTGGTGCGATCCTCC 62.554 72.222 0.00 0.00 0.00 4.30
1629 1726 1.066286 CCTGACTTTGAGGAGCTGGAG 60.066 57.143 0.00 0.00 31.48 3.86
1765 1863 2.432874 CGGGGGTGAAACTTTCCTTTTT 59.567 45.455 0.00 0.00 36.74 1.94
1766 1864 3.739830 CGGGGGTGAAACTTTCCTTTTTG 60.740 47.826 0.00 0.00 36.74 2.44
1771 1869 6.093495 GGGGTGAAACTTTCCTTTTTGAAAAG 59.907 38.462 8.83 8.83 40.26 2.27
1802 1901 4.394795 CCGTTCACTCATCAATTCGTTTC 58.605 43.478 0.00 0.00 0.00 2.78
1807 1906 3.062639 CACTCATCAATTCGTTTCCTCCG 59.937 47.826 0.00 0.00 0.00 4.63
1899 2345 3.828451 CGATATTTTTCTGCCCATGGGAT 59.172 43.478 36.00 18.83 37.50 3.85
1901 2347 2.925966 TTTTTCTGCCCATGGGATCT 57.074 45.000 36.00 0.00 37.50 2.75
1923 2369 0.182061 TGATCAGGATGCTCTTGCCC 59.818 55.000 0.00 0.00 38.71 5.36
1950 2396 3.904136 AACCGAGCATCAACAAGAAAG 57.096 42.857 0.00 0.00 33.17 2.62
1997 2443 1.686052 GGACCTCATGCTCCACTAGAG 59.314 57.143 0.00 0.00 46.29 2.43
2124 2570 2.415090 GGCTGTGTGATCAAGAACATGC 60.415 50.000 0.00 8.25 0.00 4.06
2125 2571 2.726989 GCTGTGTGATCAAGAACATGCG 60.727 50.000 0.00 0.00 0.00 4.73
2182 2628 3.064207 GTGGCTTCGACAATCTGTACAA 58.936 45.455 0.00 0.00 0.00 2.41
2194 2640 1.334992 CTGTACAACAGCGTCGTCGG 61.335 60.000 3.90 0.00 39.62 4.79
2225 2672 1.098050 CAGGCTTCATAACAGGTGGC 58.902 55.000 0.00 0.00 0.00 5.01
2229 2676 2.162681 GCTTCATAACAGGTGGCAAGT 58.837 47.619 0.00 0.00 0.00 3.16
2241 2688 2.029844 GGCAAGTCCACTGAGACGC 61.030 63.158 0.00 0.00 41.83 5.19
2264 2711 0.551377 TGAATCCACCCCTTAGCCCA 60.551 55.000 0.00 0.00 0.00 5.36
2273 2720 0.394352 CCCTTAGCCCATTCAGCGTT 60.394 55.000 0.00 0.00 34.64 4.84
2308 2755 2.422803 CCACTCCCAAAGAACACCAAGA 60.423 50.000 0.00 0.00 0.00 3.02
2326 2773 4.131596 CAAGAGGAACCGGAAAACTACAA 58.868 43.478 9.46 0.00 0.00 2.41
2327 2774 3.736720 AGAGGAACCGGAAAACTACAAC 58.263 45.455 9.46 0.00 0.00 3.32
2360 2807 3.783020 TATAGCTGGTGTGCTGGCTGC 62.783 57.143 9.67 9.67 43.87 5.25
2365 2812 2.281345 GTGTGCTGGCTGCTGTCT 60.281 61.111 17.45 0.00 43.37 3.41
2752 3214 2.268076 ACCATTGCCACCGTCAAGC 61.268 57.895 0.00 0.00 0.00 4.01
2763 3225 1.421485 CGTCAAGCGCAGGATCAAC 59.579 57.895 11.47 0.00 0.00 3.18
2844 3306 3.121030 GATTCGTGCACCGCTGCT 61.121 61.111 12.15 0.00 44.57 4.24
2896 3358 5.424757 TCACCCTCGAATTTCGTCAATTAT 58.575 37.500 17.61 0.00 41.35 1.28
2897 3359 5.522460 TCACCCTCGAATTTCGTCAATTATC 59.478 40.000 17.61 0.00 41.35 1.75
2898 3360 5.523916 CACCCTCGAATTTCGTCAATTATCT 59.476 40.000 17.61 0.00 41.35 1.98
2899 3361 6.700081 CACCCTCGAATTTCGTCAATTATCTA 59.300 38.462 17.61 0.00 41.35 1.98
2900 3362 6.700520 ACCCTCGAATTTCGTCAATTATCTAC 59.299 38.462 17.61 0.00 41.35 2.59
2901 3363 6.924060 CCCTCGAATTTCGTCAATTATCTACT 59.076 38.462 17.61 0.00 41.35 2.57
2902 3364 7.096023 CCCTCGAATTTCGTCAATTATCTACTG 60.096 40.741 17.61 0.00 41.35 2.74
2903 3365 7.096023 CCTCGAATTTCGTCAATTATCTACTGG 60.096 40.741 17.61 0.00 41.35 4.00
2904 3366 6.200286 TCGAATTTCGTCAATTATCTACTGGC 59.800 38.462 17.61 0.00 41.35 4.85
2905 3367 6.564125 CGAATTTCGTCAATTATCTACTGGCC 60.564 42.308 10.61 0.00 35.02 5.36
2906 3368 5.353394 TTTCGTCAATTATCTACTGGCCT 57.647 39.130 3.32 0.00 0.00 5.19
2907 3369 5.353394 TTCGTCAATTATCTACTGGCCTT 57.647 39.130 3.32 0.00 0.00 4.35
2908 3370 5.353394 TCGTCAATTATCTACTGGCCTTT 57.647 39.130 3.32 0.00 0.00 3.11
2909 3371 5.116180 TCGTCAATTATCTACTGGCCTTTG 58.884 41.667 3.32 0.00 0.00 2.77
2910 3372 4.273480 CGTCAATTATCTACTGGCCTTTGG 59.727 45.833 3.32 0.00 0.00 3.28
2938 3426 0.777631 CAATCGTTTTGCCGCTGTTG 59.222 50.000 0.00 0.00 0.00 3.33
2962 3450 1.898574 GTTCTGGTGCCTGGTGGTG 60.899 63.158 0.00 0.00 35.27 4.17
3003 3491 4.133820 TGTCCTGTAATTTGACAGTGGTG 58.866 43.478 7.43 0.00 44.54 4.17
3004 3492 3.502211 GTCCTGTAATTTGACAGTGGTGG 59.498 47.826 7.43 0.00 44.54 4.61
3005 3493 3.137544 TCCTGTAATTTGACAGTGGTGGT 59.862 43.478 7.43 0.00 44.54 4.16
3006 3494 3.502211 CCTGTAATTTGACAGTGGTGGTC 59.498 47.826 7.43 0.00 44.54 4.02
3063 3551 5.189928 TGTCCAGTCTGCTTGAAAAACTTA 58.810 37.500 0.00 0.00 0.00 2.24
3065 3553 6.017109 TGTCCAGTCTGCTTGAAAAACTTATC 60.017 38.462 0.00 0.00 0.00 1.75
3131 3621 1.814169 GGATGGAAGACGGAACCGC 60.814 63.158 13.32 6.39 44.19 5.68
3250 3742 8.655092 ACAAAAATTAAACCGCATTATGTCATG 58.345 29.630 0.00 0.00 0.00 3.07
3265 3757 9.315525 CATTATGTCATGTTAATCCAATTTGCA 57.684 29.630 0.00 0.00 0.00 4.08
3276 3768 9.437045 GTTAATCCAATTTGCAAAGACAAAAAG 57.563 29.630 18.19 0.87 42.45 2.27
3414 3910 1.813477 GCCTTTCCCAGCATAGAGAGC 60.813 57.143 0.00 0.00 0.00 4.09
3418 3914 0.031716 TCCCAGCATAGAGAGCCAGT 60.032 55.000 0.00 0.00 0.00 4.00
3510 4037 6.904626 AGAAATCATCTGGCCTATTACAGTT 58.095 36.000 3.32 0.00 36.88 3.16
3511 4038 7.349598 AGAAATCATCTGGCCTATTACAGTTT 58.650 34.615 3.32 0.00 36.88 2.66
3597 4187 4.490319 GCACGTCATTAATCACACACTACG 60.490 45.833 0.00 0.00 0.00 3.51
3703 4293 3.957535 CCGGCATGCCAAGCGATC 61.958 66.667 34.93 6.89 35.37 3.69
3705 4295 4.619140 GGCATGCCAAGCGATCGC 62.619 66.667 32.15 32.15 37.45 4.58
3706 4296 4.619140 GCATGCCAAGCGATCGCC 62.619 66.667 34.89 20.58 43.17 5.54
3707 4297 3.957535 CATGCCAAGCGATCGCCC 61.958 66.667 34.89 20.99 43.17 6.13
3834 4424 2.868566 TTGGCCAGGAACCCCCAT 60.869 61.111 5.11 0.00 37.41 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.664552 TTCCCGAGATTTGTCTAGGTTTATA 57.335 36.000 4.31 0.00 31.67 0.98
20 21 6.555463 TTCCCGAGATTTGTCTAGGTTTAT 57.445 37.500 4.31 0.00 31.67 1.40
21 22 6.363167 TTTCCCGAGATTTGTCTAGGTTTA 57.637 37.500 4.31 0.00 31.67 2.01
22 23 4.903045 TTCCCGAGATTTGTCTAGGTTT 57.097 40.909 4.31 0.00 31.67 3.27
23 24 4.903045 TTTCCCGAGATTTGTCTAGGTT 57.097 40.909 4.31 0.00 31.67 3.50
55 56 1.181786 CCTCTCGAAGCTCAACCTCT 58.818 55.000 0.00 0.00 0.00 3.69
61 62 1.203523 GCTTTCTCCTCTCGAAGCTCA 59.796 52.381 0.00 0.00 0.00 4.26
187 189 2.675056 GCAAGCAGAGCACTCCACG 61.675 63.158 0.00 0.00 0.00 4.94
203 205 0.615261 TATATACCCCATCGCCGGCA 60.615 55.000 28.98 14.46 0.00 5.69
225 227 3.433031 CCGGGACAAATGAGTTGCCTATA 60.433 47.826 0.00 0.00 41.31 1.31
226 228 2.643551 CGGGACAAATGAGTTGCCTAT 58.356 47.619 0.00 0.00 41.31 2.57
227 229 1.339631 CCGGGACAAATGAGTTGCCTA 60.340 52.381 0.00 0.00 41.31 3.93
228 230 0.609131 CCGGGACAAATGAGTTGCCT 60.609 55.000 0.00 0.00 41.31 4.75
255 257 0.255033 GCCTTTAGTCCCGGTTCCAT 59.745 55.000 0.00 0.00 0.00 3.41
277 279 3.691342 CGGTTCGTGGCAGGAGGA 61.691 66.667 10.06 0.00 0.00 3.71
305 312 4.020617 CTCGCTCCTGGCCCACAA 62.021 66.667 0.00 0.00 37.74 3.33
327 334 2.340328 GGCATGAACCGGGACCAAC 61.340 63.158 6.32 0.00 0.00 3.77
418 426 1.673009 GGCATTTGTCCCGGTTCGA 60.673 57.895 0.00 0.00 0.00 3.71
430 438 0.684153 CGGGACCAATGGAGGCATTT 60.684 55.000 6.16 0.00 0.00 2.32
437 446 2.218454 ACGAACCGGGACCAATGGA 61.218 57.895 6.16 0.00 0.00 3.41
485 494 2.347691 AAAGGGGCTTTCGTTCGGGT 62.348 55.000 0.00 0.00 0.00 5.28
493 502 5.314529 ACACTAGTAGAAAAAGGGGCTTTC 58.685 41.667 3.59 0.00 31.99 2.62
519 528 9.250624 CCATGCTACTACTAAAATTCTCACTAC 57.749 37.037 0.00 0.00 0.00 2.73
520 529 8.978472 ACCATGCTACTACTAAAATTCTCACTA 58.022 33.333 0.00 0.00 0.00 2.74
521 530 7.852263 ACCATGCTACTACTAAAATTCTCACT 58.148 34.615 0.00 0.00 0.00 3.41
522 531 8.494016 AACCATGCTACTACTAAAATTCTCAC 57.506 34.615 0.00 0.00 0.00 3.51
527 536 9.185680 CCCTTTAACCATGCTACTACTAAAATT 57.814 33.333 0.00 0.00 0.00 1.82
528 537 8.554011 TCCCTTTAACCATGCTACTACTAAAAT 58.446 33.333 0.00 0.00 0.00 1.82
529 538 7.920227 TCCCTTTAACCATGCTACTACTAAAA 58.080 34.615 0.00 0.00 0.00 1.52
530 539 7.365295 CCTCCCTTTAACCATGCTACTACTAAA 60.365 40.741 0.00 0.00 0.00 1.85
531 540 6.099269 CCTCCCTTTAACCATGCTACTACTAA 59.901 42.308 0.00 0.00 0.00 2.24
532 541 5.601313 CCTCCCTTTAACCATGCTACTACTA 59.399 44.000 0.00 0.00 0.00 1.82
533 542 4.409247 CCTCCCTTTAACCATGCTACTACT 59.591 45.833 0.00 0.00 0.00 2.57
534 543 4.704965 CCTCCCTTTAACCATGCTACTAC 58.295 47.826 0.00 0.00 0.00 2.73
535 544 3.135895 GCCTCCCTTTAACCATGCTACTA 59.864 47.826 0.00 0.00 0.00 1.82
536 545 2.092375 GCCTCCCTTTAACCATGCTACT 60.092 50.000 0.00 0.00 0.00 2.57
537 546 2.298610 GCCTCCCTTTAACCATGCTAC 58.701 52.381 0.00 0.00 0.00 3.58
538 547 1.134220 CGCCTCCCTTTAACCATGCTA 60.134 52.381 0.00 0.00 0.00 3.49
539 548 0.394352 CGCCTCCCTTTAACCATGCT 60.394 55.000 0.00 0.00 0.00 3.79
540 549 2.004808 GCGCCTCCCTTTAACCATGC 62.005 60.000 0.00 0.00 0.00 4.06
541 550 1.714899 CGCGCCTCCCTTTAACCATG 61.715 60.000 0.00 0.00 0.00 3.66
542 551 1.451387 CGCGCCTCCCTTTAACCAT 60.451 57.895 0.00 0.00 0.00 3.55
543 552 2.046700 CGCGCCTCCCTTTAACCA 60.047 61.111 0.00 0.00 0.00 3.67
544 553 2.582734 TAGCGCGCCTCCCTTTAACC 62.583 60.000 30.33 0.00 0.00 2.85
545 554 1.153509 TAGCGCGCCTCCCTTTAAC 60.154 57.895 30.33 0.00 0.00 2.01
546 555 1.153509 GTAGCGCGCCTCCCTTTAA 60.154 57.895 30.33 0.00 0.00 1.52
547 556 2.056223 AGTAGCGCGCCTCCCTTTA 61.056 57.895 30.33 8.92 0.00 1.85
548 557 3.391382 AGTAGCGCGCCTCCCTTT 61.391 61.111 30.33 10.14 0.00 3.11
549 558 4.148825 CAGTAGCGCGCCTCCCTT 62.149 66.667 30.33 11.01 0.00 3.95
560 569 7.306051 CGTTACAGATACAAACATAGCAGTAGC 60.306 40.741 0.00 0.00 42.56 3.58
561 570 7.306051 GCGTTACAGATACAAACATAGCAGTAG 60.306 40.741 0.00 0.00 0.00 2.57
562 571 6.474427 GCGTTACAGATACAAACATAGCAGTA 59.526 38.462 0.00 0.00 0.00 2.74
563 572 5.291128 GCGTTACAGATACAAACATAGCAGT 59.709 40.000 0.00 0.00 0.00 4.40
564 573 5.554510 CGCGTTACAGATACAAACATAGCAG 60.555 44.000 0.00 0.00 0.00 4.24
565 574 4.266739 CGCGTTACAGATACAAACATAGCA 59.733 41.667 0.00 0.00 0.00 3.49
566 575 4.266976 ACGCGTTACAGATACAAACATAGC 59.733 41.667 5.58 0.00 0.00 2.97
567 576 5.944049 ACGCGTTACAGATACAAACATAG 57.056 39.130 5.58 0.00 0.00 2.23
568 577 6.709145 AAACGCGTTACAGATACAAACATA 57.291 33.333 26.87 0.00 0.00 2.29
569 578 5.600908 AAACGCGTTACAGATACAAACAT 57.399 34.783 26.87 0.35 0.00 2.71
570 579 6.183360 GGATAAACGCGTTACAGATACAAACA 60.183 38.462 26.87 0.00 0.00 2.83
571 580 6.035327 AGGATAAACGCGTTACAGATACAAAC 59.965 38.462 26.87 6.09 0.00 2.93
572 581 6.035220 CAGGATAAACGCGTTACAGATACAAA 59.965 38.462 26.87 1.32 0.00 2.83
573 582 5.517411 CAGGATAAACGCGTTACAGATACAA 59.483 40.000 26.87 2.89 0.00 2.41
574 583 5.038683 CAGGATAAACGCGTTACAGATACA 58.961 41.667 26.87 3.60 0.00 2.29
575 584 4.085210 GCAGGATAAACGCGTTACAGATAC 60.085 45.833 26.87 16.21 0.00 2.24
576 585 4.046462 GCAGGATAAACGCGTTACAGATA 58.954 43.478 26.87 13.92 0.00 1.98
577 586 2.864343 GCAGGATAAACGCGTTACAGAT 59.136 45.455 26.87 15.79 0.00 2.90
578 587 2.264813 GCAGGATAAACGCGTTACAGA 58.735 47.619 26.87 11.47 0.00 3.41
579 588 1.996898 TGCAGGATAAACGCGTTACAG 59.003 47.619 26.87 13.41 0.00 2.74
580 589 1.727880 GTGCAGGATAAACGCGTTACA 59.272 47.619 26.87 16.68 0.00 2.41
581 590 1.266696 CGTGCAGGATAAACGCGTTAC 60.267 52.381 26.87 18.46 32.93 2.50
582 591 0.993532 CGTGCAGGATAAACGCGTTA 59.006 50.000 26.87 13.85 32.93 3.18
583 592 1.785321 CGTGCAGGATAAACGCGTT 59.215 52.632 20.79 20.79 32.93 4.84
584 593 3.470267 CGTGCAGGATAAACGCGT 58.530 55.556 5.58 5.58 32.93 6.01
587 596 1.143373 TAGCGCGTGCAGGATAAACG 61.143 55.000 24.79 4.79 46.23 3.60
588 597 0.300789 GTAGCGCGTGCAGGATAAAC 59.699 55.000 24.79 5.47 46.23 2.01
589 598 0.174845 AGTAGCGCGTGCAGGATAAA 59.825 50.000 24.79 0.00 46.23 1.40
590 599 0.527600 CAGTAGCGCGTGCAGGATAA 60.528 55.000 24.79 0.00 46.23 1.75
591 600 1.065764 CAGTAGCGCGTGCAGGATA 59.934 57.895 24.79 3.35 46.23 2.59
592 601 2.202797 CAGTAGCGCGTGCAGGAT 60.203 61.111 24.79 4.49 46.23 3.24
610 619 2.873133 AAGGCGCTAGTGCTAAGTAG 57.127 50.000 26.36 0.00 36.97 2.57
611 620 3.604875 AAAAGGCGCTAGTGCTAAGTA 57.395 42.857 26.36 0.00 36.97 2.24
612 621 2.474410 AAAAGGCGCTAGTGCTAAGT 57.526 45.000 26.36 8.51 36.97 2.24
629 638 7.474190 ACTTTAACAGTAGCGCTTGTTAAAAA 58.526 30.769 35.85 26.74 42.40 1.94
630 639 7.018635 ACTTTAACAGTAGCGCTTGTTAAAA 57.981 32.000 35.85 26.76 42.40 1.52
631 640 6.607735 ACTTTAACAGTAGCGCTTGTTAAA 57.392 33.333 35.13 35.13 41.47 1.52
632 641 6.607735 AACTTTAACAGTAGCGCTTGTTAA 57.392 33.333 30.03 30.03 32.94 2.01
633 642 6.607735 AAACTTTAACAGTAGCGCTTGTTA 57.392 33.333 24.06 24.06 32.94 2.41
634 643 5.494632 AAACTTTAACAGTAGCGCTTGTT 57.505 34.783 25.84 25.84 32.94 2.83
635 644 5.163693 ACAAAACTTTAACAGTAGCGCTTGT 60.164 36.000 18.68 13.01 32.94 3.16
636 645 5.171337 CACAAAACTTTAACAGTAGCGCTTG 59.829 40.000 18.68 12.18 32.94 4.01
637 646 5.163693 ACACAAAACTTTAACAGTAGCGCTT 60.164 36.000 18.68 0.00 32.94 4.68
638 647 4.334481 ACACAAAACTTTAACAGTAGCGCT 59.666 37.500 17.26 17.26 32.94 5.92
639 648 4.594136 ACACAAAACTTTAACAGTAGCGC 58.406 39.130 0.00 0.00 32.94 5.92
640 649 9.525007 CTTATACACAAAACTTTAACAGTAGCG 57.475 33.333 0.00 0.00 32.94 4.26
641 650 9.821662 CCTTATACACAAAACTTTAACAGTAGC 57.178 33.333 0.00 0.00 32.94 3.58
685 694 9.703892 GACAGCTATATCTTCACTTATTCACAT 57.296 33.333 0.00 0.00 0.00 3.21
686 695 7.862873 CGACAGCTATATCTTCACTTATTCACA 59.137 37.037 0.00 0.00 0.00 3.58
687 696 8.076781 TCGACAGCTATATCTTCACTTATTCAC 58.923 37.037 0.00 0.00 0.00 3.18
728 737 7.362662 TGCTTTTCACTATTTTTGCTCTACTG 58.637 34.615 0.00 0.00 0.00 2.74
966 981 3.637998 TCGTACAAGTTCAGAGGACAC 57.362 47.619 0.00 0.00 0.00 3.67
967 982 4.866508 ATTCGTACAAGTTCAGAGGACA 57.133 40.909 0.00 0.00 0.00 4.02
1093 1108 3.068691 CGGGAGCGTGAGGAAGGA 61.069 66.667 0.00 0.00 0.00 3.36
1119 1134 2.034879 CGCCGCACAGAACTGGATT 61.035 57.895 6.76 0.00 34.19 3.01
1157 1172 2.049156 CGCTGTCGCAGAGGTTGA 60.049 61.111 10.46 0.00 36.95 3.18
1196 1211 1.315981 GGCCTCAACCTTAAGCAGCC 61.316 60.000 0.00 0.00 0.00 4.85
1203 1218 0.034186 CATGGCAGGCCTCAACCTTA 60.034 55.000 0.00 0.00 38.26 2.69
1223 1238 1.016130 CGAAGGCGTGAGAAGCATGT 61.016 55.000 0.00 0.00 35.87 3.21
1333 1413 2.159014 GGATGGCACGGTAAGATGTACA 60.159 50.000 0.00 0.00 0.00 2.90
1334 1414 2.102588 AGGATGGCACGGTAAGATGTAC 59.897 50.000 0.00 0.00 0.00 2.90
1371 1456 4.973396 TGACAAACGCATCATGAGAATTC 58.027 39.130 0.09 0.00 0.00 2.17
1427 1518 1.076777 ACTTGCCAACACCTGCAGT 60.077 52.632 13.81 0.00 38.95 4.40
1493 1584 4.594123 TCTTTACACCTCACGAACATCA 57.406 40.909 0.00 0.00 0.00 3.07
1574 1665 3.043713 CGAAGTTGCGAGCCAGCA 61.044 61.111 0.00 0.00 46.54 4.41
1609 1700 0.979665 TCCAGCTCCTCAAAGTCAGG 59.020 55.000 0.00 0.00 0.00 3.86
1686 1783 3.341857 AGCACGCAAAAATTACAACGA 57.658 38.095 0.00 0.00 0.00 3.85
1687 1784 4.027295 TCAAAGCACGCAAAAATTACAACG 60.027 37.500 0.00 0.00 0.00 4.10
1688 1785 5.382573 TCAAAGCACGCAAAAATTACAAC 57.617 34.783 0.00 0.00 0.00 3.32
1765 1863 2.761208 TGAACGGCCCTTTTTCTTTTCA 59.239 40.909 0.00 0.00 0.00 2.69
1766 1864 3.120792 GTGAACGGCCCTTTTTCTTTTC 58.879 45.455 0.00 0.00 0.00 2.29
1771 1869 1.314730 TGAGTGAACGGCCCTTTTTC 58.685 50.000 0.00 0.00 0.00 2.29
1802 1901 1.123928 AGGATCCAAGTTAGCGGAGG 58.876 55.000 15.82 0.00 33.97 4.30
1807 1906 8.406297 CAACCTAAAATAAGGATCCAAGTTAGC 58.594 37.037 15.82 0.00 39.15 3.09
1899 2345 2.169978 CAAGAGCATCCTGATCACCAGA 59.830 50.000 0.00 0.00 45.78 3.86
1901 2347 1.407851 GCAAGAGCATCCTGATCACCA 60.408 52.381 0.00 0.00 41.58 4.17
1923 2369 1.197721 GTTGATGCTCGGTTTCACAGG 59.802 52.381 0.00 0.00 0.00 4.00
1950 2396 3.380637 TCTTCATTGGGAGCTACTACGAC 59.619 47.826 0.00 0.00 0.00 4.34
1997 2443 6.026513 GTCATAGAAAAGCTTGATCTTGCAC 58.973 40.000 17.36 9.60 0.00 4.57
2124 2570 1.202417 AGAGGTGACGCCATTATCACG 60.202 52.381 7.99 0.00 45.13 4.35
2125 2571 2.474816 GAGAGGTGACGCCATTATCAC 58.525 52.381 7.99 0.00 43.75 3.06
2182 2628 4.086178 CGAGTCCGACGACGCTGT 62.086 66.667 0.64 0.00 44.28 4.40
2225 2672 1.287730 GCAGCGTCTCAGTGGACTTG 61.288 60.000 9.24 8.47 34.38 3.16
2229 2676 1.463553 TTCAGCAGCGTCTCAGTGGA 61.464 55.000 0.00 0.00 0.00 4.02
2241 2688 1.748591 GCTAAGGGGTGGATTCAGCAG 60.749 57.143 5.38 0.00 42.72 4.24
2264 2711 0.249398 ACTTAGGGCGAACGCTGAAT 59.751 50.000 18.14 5.44 39.80 2.57
2308 2755 2.486918 CGTTGTAGTTTTCCGGTTCCT 58.513 47.619 0.00 0.00 0.00 3.36
2326 2773 3.764434 CCAGCTATATGATACCAGACCGT 59.236 47.826 0.00 0.00 0.00 4.83
2327 2774 3.764434 ACCAGCTATATGATACCAGACCG 59.236 47.826 0.00 0.00 0.00 4.79
2360 2807 1.613925 TCTTCGACCAGGTCAAGACAG 59.386 52.381 20.13 7.19 30.82 3.51
2752 3214 0.179100 ACCTGATCGTTGATCCTGCG 60.179 55.000 4.47 0.00 38.20 5.18
2844 3306 7.218228 ACATTTGCTGACAAGATTGTATTCA 57.782 32.000 0.00 0.00 42.43 2.57
2896 3358 1.822990 CGACTACCAAAGGCCAGTAGA 59.177 52.381 21.90 0.00 37.50 2.59
2897 3359 1.549170 ACGACTACCAAAGGCCAGTAG 59.451 52.381 5.01 12.72 39.50 2.57
2898 3360 1.274167 CACGACTACCAAAGGCCAGTA 59.726 52.381 5.01 0.00 0.00 2.74
2899 3361 0.034896 CACGACTACCAAAGGCCAGT 59.965 55.000 5.01 0.00 0.00 4.00
2900 3362 1.298859 GCACGACTACCAAAGGCCAG 61.299 60.000 5.01 0.00 0.00 4.85
2901 3363 1.302192 GCACGACTACCAAAGGCCA 60.302 57.895 5.01 0.00 0.00 5.36
2902 3364 0.887387 TTGCACGACTACCAAAGGCC 60.887 55.000 0.00 0.00 0.00 5.19
2903 3365 1.130561 GATTGCACGACTACCAAAGGC 59.869 52.381 0.00 0.00 0.00 4.35
2904 3366 1.393539 CGATTGCACGACTACCAAAGG 59.606 52.381 0.00 0.00 35.09 3.11
2905 3367 2.066262 ACGATTGCACGACTACCAAAG 58.934 47.619 3.48 0.00 37.03 2.77
2906 3368 2.157834 ACGATTGCACGACTACCAAA 57.842 45.000 3.48 0.00 37.03 3.28
2907 3369 2.157834 AACGATTGCACGACTACCAA 57.842 45.000 3.48 0.00 37.03 3.67
2908 3370 2.157834 AAACGATTGCACGACTACCA 57.842 45.000 3.48 0.00 37.03 3.25
2909 3371 2.834689 CAAAACGATTGCACGACTACC 58.165 47.619 3.48 0.00 37.03 3.18
2910 3372 2.230864 GCAAAACGATTGCACGACTAC 58.769 47.619 20.35 0.00 44.34 2.73
2938 3426 1.348036 ACCAGGCACCAGAACTTACTC 59.652 52.381 0.00 0.00 0.00 2.59
2962 3450 2.224066 ACAGACAGAACACACTGCTACC 60.224 50.000 0.00 0.00 41.06 3.18
3003 3491 3.134127 GCAAGGCACCATCCGACC 61.134 66.667 0.00 0.00 0.00 4.79
3004 3492 2.045926 AGCAAGGCACCATCCGAC 60.046 61.111 0.00 0.00 0.00 4.79
3005 3493 2.244117 GAGAGCAAGGCACCATCCGA 62.244 60.000 0.00 0.00 0.00 4.55
3006 3494 1.817099 GAGAGCAAGGCACCATCCG 60.817 63.158 0.00 0.00 0.00 4.18
3231 3723 8.132362 GGATTAACATGACATAATGCGGTTTAA 58.868 33.333 0.00 0.00 0.00 1.52
3238 3730 8.277713 GCAAATTGGATTAACATGACATAATGC 58.722 33.333 0.00 7.36 32.42 3.56
3250 3742 9.437045 CTTTTTGTCTTTGCAAATTGGATTAAC 57.563 29.630 13.23 2.47 38.05 2.01
3265 3757 4.178956 TGCTAGTCCCCTTTTTGTCTTT 57.821 40.909 0.00 0.00 0.00 2.52
3276 3768 0.328258 TTCTGCCTTTGCTAGTCCCC 59.672 55.000 0.00 0.00 38.71 4.81
3328 3820 2.037641 GCCTGAGCCCAGTTTCAATTTT 59.962 45.455 0.00 0.00 38.74 1.82
3329 3821 1.620323 GCCTGAGCCCAGTTTCAATTT 59.380 47.619 0.00 0.00 38.74 1.82
3330 3822 1.260544 GCCTGAGCCCAGTTTCAATT 58.739 50.000 0.00 0.00 38.74 2.32
3331 3823 0.112995 TGCCTGAGCCCAGTTTCAAT 59.887 50.000 0.00 0.00 38.74 2.57
3332 3824 0.106268 TTGCCTGAGCCCAGTTTCAA 60.106 50.000 0.00 0.00 38.74 2.69
3333 3825 0.106268 TTTGCCTGAGCCCAGTTTCA 60.106 50.000 0.00 0.00 38.74 2.69
3414 3910 2.440539 AGTGTGCTAACTTCGACTGG 57.559 50.000 0.00 0.00 0.00 4.00
3486 4013 6.506538 ACTGTAATAGGCCAGATGATTTCT 57.493 37.500 5.01 0.00 33.90 2.52
3510 4037 7.095355 GCCGCGGATTCTAATAAGAAATAAGAA 60.095 37.037 33.48 0.00 44.75 2.52
3511 4038 6.367969 GCCGCGGATTCTAATAAGAAATAAGA 59.632 38.462 33.48 0.00 44.75 2.10
3665 4255 4.183686 GCGCATGCATCTTGCCGT 62.184 61.111 19.57 0.00 44.23 5.68
3686 4276 3.957535 GATCGCTTGGCATGCCGG 61.958 66.667 30.87 25.31 39.42 6.13
3687 4277 4.303603 CGATCGCTTGGCATGCCG 62.304 66.667 30.87 19.06 39.42 5.69
3688 4278 4.619140 GCGATCGCTTGGCATGCC 62.619 66.667 31.94 30.54 38.26 4.40
3689 4279 4.619140 GGCGATCGCTTGGCATGC 62.619 66.667 36.25 15.82 41.60 4.06
3690 4280 3.957535 GGGCGATCGCTTGGCATG 61.958 66.667 36.25 0.00 41.60 4.06
3712 4302 4.924187 ATCCTCCGCCCTCCTCCG 62.924 72.222 0.00 0.00 0.00 4.63
3713 4303 2.920384 GATCCTCCGCCCTCCTCC 60.920 72.222 0.00 0.00 0.00 4.30
3714 4304 2.123251 TGATCCTCCGCCCTCCTC 60.123 66.667 0.00 0.00 0.00 3.71
3715 4305 2.123077 CTGATCCTCCGCCCTCCT 60.123 66.667 0.00 0.00 0.00 3.69
3716 4306 3.934962 GCTGATCCTCCGCCCTCC 61.935 72.222 0.00 0.00 0.00 4.30
3717 4307 4.292178 CGCTGATCCTCCGCCCTC 62.292 72.222 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.