Multiple sequence alignment - TraesCS1A01G433200

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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 TraesCS1A01G433200 chr1A 100.000 2261 0 0 1 2261 584537184 584539444 0.000000e+00 4176.0
1 TraesCS1A01G433200 chr1A 100.000 461 0 0 2623 3083 584539806 584540266 0.000000e+00 852.0
2 TraesCS1A01G433200 chr1A 87.043 301 38 1 20 320 148258046 148258345 3.810000e-89 339.0
3 TraesCS1A01G433200 chr1A 93.478 92 4 2 2771 2861 584540044 584539954 5.360000e-28 135.0
4 TraesCS1A01G433200 chr1A 100.000 41 0 0 1076 1116 584538197 584538237 3.300000e-10 76.8
5 TraesCS1A01G433200 chr1A 100.000 41 0 0 1014 1054 584538259 584538299 3.300000e-10 76.8
6 TraesCS1A01G433200 chr1B 95.863 1136 40 5 1126 2261 678218703 678219831 0.000000e+00 1831.0
7 TraesCS1A01G433200 chr1B 95.058 344 14 2 741 1081 678218177 678218520 3.500000e-149 538.0
8 TraesCS1A01G433200 chr1B 96.250 320 11 1 1 320 678215603 678215921 9.800000e-145 523.0
9 TraesCS1A01G433200 chr1B 90.040 251 24 1 325 574 678217703 678217953 1.070000e-84 324.0
10 TraesCS1A01G433200 chr1B 96.277 188 7 0 2819 3006 678220264 678220451 2.990000e-80 309.0
11 TraesCS1A01G433200 chr1B 94.702 151 8 0 575 725 218280727 218280877 5.140000e-58 235.0
12 TraesCS1A01G433200 chr1B 95.890 73 1 1 2666 2736 678220178 678220250 1.940000e-22 117.0
13 TraesCS1A01G433200 chr1B 81.061 132 23 2 325 455 280153205 280153335 1.510000e-18 104.0
14 TraesCS1A01G433200 chr1B 79.699 133 23 4 325 455 491037918 491038048 3.270000e-15 93.5
15 TraesCS1A01G433200 chr1B 97.561 41 1 0 1076 1116 678218453 678218493 1.530000e-08 71.3
16 TraesCS1A01G433200 chr1D 95.423 1136 45 5 1126 2261 487042175 487043303 0.000000e+00 1803.0
17 TraesCS1A01G433200 chr1D 95.312 320 14 1 1 320 487032731 487033049 9.860000e-140 507.0
18 TraesCS1A01G433200 chr1D 92.883 281 13 2 802 1081 487041718 487041992 4.790000e-108 401.0
19 TraesCS1A01G433200 chr1D 87.043 301 38 1 20 320 491532241 491532540 3.810000e-89 339.0
20 TraesCS1A01G433200 chr1D 95.812 191 8 0 2816 3006 487043833 487044023 2.990000e-80 309.0
21 TraesCS1A01G433200 chr1D 80.000 110 19 2 342 450 404676946 404676839 9.170000e-11 78.7
22 TraesCS1A01G433200 chr5D 89.037 301 32 1 20 320 231753679 231753380 3.750000e-99 372.0
23 TraesCS1A01G433200 chr2A 88.040 301 35 1 20 320 624481973 624481674 3.780000e-94 355.0
24 TraesCS1A01G433200 chr2A 79.070 129 21 5 328 455 27321592 27321715 1.970000e-12 84.2
25 TraesCS1A01G433200 chr2A 100.000 30 0 0 3054 3083 726978777 726978806 4.290000e-04 56.5
26 TraesCS1A01G433200 chr7D 87.375 301 37 1 20 320 164676051 164676350 8.180000e-91 344.0
27 TraesCS1A01G433200 chr3B 87.797 295 30 6 26 318 464732401 464732111 1.060000e-89 340.0
28 TraesCS1A01G433200 chr3B 97.222 144 4 0 578 721 111256556 111256699 8.540000e-61 244.0
29 TraesCS1A01G433200 chr3B 80.153 131 23 3 327 455 492210914 492211043 9.100000e-16 95.3
30 TraesCS1A01G433200 chr4B 87.086 302 35 4 20 320 207353509 207353211 3.810000e-89 339.0
31 TraesCS1A01G433200 chr4B 97.163 141 4 0 582 722 519351195 519351055 3.970000e-59 239.0
32 TraesCS1A01G433200 chr7A 100.000 141 0 0 581 721 706263777 706263917 8.480000e-66 261.0
33 TraesCS1A01G433200 chr5A 98.621 145 1 1 582 726 552678403 552678546 3.950000e-64 255.0
34 TraesCS1A01G433200 chr5A 86.000 50 7 0 3034 3083 370065557 370065606 2.000000e-03 54.7
35 TraesCS1A01G433200 chr3D 96.178 157 4 2 579 733 61800310 61800154 3.950000e-64 255.0
36 TraesCS1A01G433200 chrUn 97.260 146 4 0 578 723 11029433 11029578 6.600000e-62 248.0
37 TraesCS1A01G433200 chrUn 97.222 144 4 0 581 724 395822669 395822526 8.540000e-61 244.0
38 TraesCS1A01G433200 chrUn 78.947 114 23 1 342 455 45538191 45538303 3.300000e-10 76.8
39 TraesCS1A01G433200 chrUn 80.000 80 14 2 3005 3083 78173126 78173204 1.190000e-04 58.4
40 TraesCS1A01G433200 chr2D 97.163 141 4 0 581 721 204140346 204140206 3.970000e-59 239.0
41 TraesCS1A01G433200 chr7B 82.456 114 18 2 342 455 690260519 690260408 7.040000e-17 99.0
42 TraesCS1A01G433200 chr2B 78.626 131 26 2 325 455 232248335 232248463 5.480000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS1A01G433200 chr1A 584537184 584540266 3082 False 1295.400000 4176 100.000 1 3083 4 chr1A.!!$F2 3082
1 TraesCS1A01G433200 chr1B 678215603 678220451 4848 False 530.471429 1831 95.277 1 3006 7 chr1B.!!$F4 3005
2 TraesCS1A01G433200 chr1D 487041718 487044023 2305 False 837.666667 1803 94.706 802 3006 3 chr1D.!!$F3 2204

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
651 2430 0.026803 GGTGCTAGCTCATTTTCGCG 59.973 55.0 17.23 0.0 0.0 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2204 4190 0.101759 GCCGATACTACCACGCAAGA 59.898 55.0 0.0 0.0 43.62 3.02 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
24 25 2.060980 GGAGGAGGATGACTGCCGT 61.061 63.158 0.00 0.00 38.49 5.68
103 104 6.413818 GTGTTTCAAGTTGATTAACCGAACTG 59.586 38.462 14.83 0.00 37.52 3.16
115 116 4.749245 AACCGAACTGATCATGTTGTTC 57.251 40.909 13.06 13.06 36.44 3.18
132 133 6.035217 TGTTGTTCATCGGCATATGAATTTG 58.965 36.000 6.97 0.00 45.13 2.32
135 136 5.356470 TGTTCATCGGCATATGAATTTGTGA 59.644 36.000 6.97 0.00 45.13 3.58
281 282 2.897969 AGGGCTAGTCGGTACATTATGG 59.102 50.000 0.00 0.00 0.00 2.74
290 291 7.120923 AGTCGGTACATTATGGTCATTAAGT 57.879 36.000 0.00 0.00 0.00 2.24
323 324 7.775397 AACAACATATGAATTATTTGCTGGC 57.225 32.000 10.38 0.00 0.00 4.85
324 325 7.116075 ACAACATATGAATTATTTGCTGGCT 57.884 32.000 10.38 0.00 0.00 4.75
325 326 7.558604 ACAACATATGAATTATTTGCTGGCTT 58.441 30.769 10.38 0.00 0.00 4.35
326 327 8.042515 ACAACATATGAATTATTTGCTGGCTTT 58.957 29.630 10.38 0.00 0.00 3.51
328 329 9.452287 AACATATGAATTATTTGCTGGCTTTTT 57.548 25.926 10.38 0.00 0.00 1.94
355 2133 5.118971 GTGTGCATATTTGATGTTGGTTGTG 59.881 40.000 0.00 0.00 0.00 3.33
382 2160 7.180322 CATCCTACCTATGCAGATGTTAGAT 57.820 40.000 0.00 0.00 31.71 1.98
391 2169 9.363763 CCTATGCAGATGTTAGATATGTACTTG 57.636 37.037 0.00 0.00 0.00 3.16
455 2233 6.656314 AAAATTCACCCTTTGTCGAAAAAC 57.344 33.333 0.00 0.00 0.00 2.43
458 2236 1.751924 CACCCTTTGTCGAAAAACCCA 59.248 47.619 0.00 0.00 0.00 4.51
464 2242 4.429108 CTTTGTCGAAAAACCCACATGTT 58.571 39.130 0.00 0.00 0.00 2.71
478 2256 5.163195 ACCCACATGTTCTTTACTTCTCACT 60.163 40.000 0.00 0.00 0.00 3.41
483 2261 4.617959 TGTTCTTTACTTCTCACTGTCGG 58.382 43.478 0.00 0.00 0.00 4.79
492 2270 2.887790 TCACTGTCGGAGGGAGATG 58.112 57.895 0.00 0.00 27.62 2.90
526 2304 0.907486 CTTGAGAGGCAGGTGGATCA 59.093 55.000 0.00 0.00 0.00 2.92
549 2328 4.527038 AGTCGATACAGGAGGAAGAAAACA 59.473 41.667 0.00 0.00 0.00 2.83
569 2348 0.589708 TTTGAACGAGTCGCGAGAGA 59.410 50.000 10.24 0.00 44.57 3.10
574 2353 0.390866 ACGAGTCGCGAGAGAAGGTA 60.391 55.000 10.24 0.00 44.57 3.08
575 2354 0.938713 CGAGTCGCGAGAGAAGGTAT 59.061 55.000 10.24 0.00 44.57 2.73
576 2355 2.133553 CGAGTCGCGAGAGAAGGTATA 58.866 52.381 10.24 0.00 44.57 1.47
577 2356 2.096811 CGAGTCGCGAGAGAAGGTATAC 60.097 54.545 10.24 0.00 44.57 1.47
578 2357 3.132925 GAGTCGCGAGAGAAGGTATACT 58.867 50.000 10.24 0.00 43.49 2.12
579 2358 3.543665 AGTCGCGAGAGAAGGTATACTT 58.456 45.455 10.24 0.00 43.49 2.24
580 2359 4.701765 AGTCGCGAGAGAAGGTATACTTA 58.298 43.478 10.24 0.00 43.49 2.24
581 2360 4.751098 AGTCGCGAGAGAAGGTATACTTAG 59.249 45.833 10.24 0.00 43.49 2.18
582 2361 4.063689 TCGCGAGAGAAGGTATACTTAGG 58.936 47.826 3.71 0.00 35.40 2.69
583 2362 3.365164 CGCGAGAGAAGGTATACTTAGGC 60.365 52.174 0.00 0.00 40.21 3.93
584 2363 3.057386 GCGAGAGAAGGTATACTTAGGCC 60.057 52.174 2.25 0.00 40.21 5.19
585 2364 3.188873 CGAGAGAAGGTATACTTAGGCCG 59.811 52.174 2.25 0.00 40.21 6.13
586 2365 2.892215 AGAGAAGGTATACTTAGGCCGC 59.108 50.000 2.25 0.00 40.21 6.53
587 2366 1.612463 AGAAGGTATACTTAGGCCGCG 59.388 52.381 0.00 0.00 40.21 6.46
588 2367 1.339291 GAAGGTATACTTAGGCCGCGT 59.661 52.381 4.92 0.00 40.21 6.01
589 2368 1.406903 AGGTATACTTAGGCCGCGTT 58.593 50.000 4.92 0.00 0.00 4.84
590 2369 1.339291 AGGTATACTTAGGCCGCGTTC 59.661 52.381 4.92 0.00 0.00 3.95
591 2370 1.402511 GTATACTTAGGCCGCGTTCG 58.597 55.000 4.92 0.00 0.00 3.95
601 2380 4.856607 CGCGTTCGGCTCCTCTCC 62.857 72.222 0.00 0.00 40.44 3.71
603 2382 4.856607 CGTTCGGCTCCTCTCCGC 62.857 72.222 0.00 0.00 46.05 5.54
604 2383 3.453679 GTTCGGCTCCTCTCCGCT 61.454 66.667 0.00 0.00 46.05 5.52
605 2384 3.141488 TTCGGCTCCTCTCCGCTC 61.141 66.667 0.00 0.00 46.05 5.03
608 2387 4.851214 GGCTCCTCTCCGCTCCCT 62.851 72.222 0.00 0.00 0.00 4.20
609 2388 3.223589 GCTCCTCTCCGCTCCCTC 61.224 72.222 0.00 0.00 0.00 4.30
610 2389 2.520741 CTCCTCTCCGCTCCCTCC 60.521 72.222 0.00 0.00 0.00 4.30
611 2390 3.347590 TCCTCTCCGCTCCCTCCA 61.348 66.667 0.00 0.00 0.00 3.86
612 2391 3.151022 CCTCTCCGCTCCCTCCAC 61.151 72.222 0.00 0.00 0.00 4.02
613 2392 2.043450 CTCTCCGCTCCCTCCACT 60.043 66.667 0.00 0.00 0.00 4.00
614 2393 2.043852 TCTCCGCTCCCTCCACTC 60.044 66.667 0.00 0.00 0.00 3.51
615 2394 3.151022 CTCCGCTCCCTCCACTCC 61.151 72.222 0.00 0.00 0.00 3.85
619 2398 3.844090 GCTCCCTCCACTCCGCTC 61.844 72.222 0.00 0.00 0.00 5.03
620 2399 3.151022 CTCCCTCCACTCCGCTCC 61.151 72.222 0.00 0.00 0.00 4.70
638 2417 3.075005 GGAGCGGACCAGGTGCTA 61.075 66.667 9.78 0.00 39.49 3.49
639 2418 2.496817 GAGCGGACCAGGTGCTAG 59.503 66.667 9.78 0.00 39.49 3.42
640 2419 3.724914 GAGCGGACCAGGTGCTAGC 62.725 68.421 8.10 8.10 39.49 3.42
641 2420 3.775654 GCGGACCAGGTGCTAGCT 61.776 66.667 17.23 0.00 0.00 3.32
642 2421 2.496817 CGGACCAGGTGCTAGCTC 59.503 66.667 17.23 12.62 0.00 4.09
643 2422 2.351244 CGGACCAGGTGCTAGCTCA 61.351 63.158 17.23 0.00 0.00 4.26
644 2423 1.680522 CGGACCAGGTGCTAGCTCAT 61.681 60.000 17.23 7.28 0.00 2.90
645 2424 0.543749 GGACCAGGTGCTAGCTCATT 59.456 55.000 17.23 1.71 0.00 2.57
646 2425 1.065126 GGACCAGGTGCTAGCTCATTT 60.065 52.381 17.23 0.00 0.00 2.32
647 2426 2.619074 GGACCAGGTGCTAGCTCATTTT 60.619 50.000 17.23 0.00 0.00 1.82
648 2427 2.680339 GACCAGGTGCTAGCTCATTTTC 59.320 50.000 17.23 4.92 0.00 2.29
649 2428 1.667724 CCAGGTGCTAGCTCATTTTCG 59.332 52.381 17.23 0.00 0.00 3.46
650 2429 1.063174 CAGGTGCTAGCTCATTTTCGC 59.937 52.381 17.23 0.00 0.00 4.70
651 2430 0.026803 GGTGCTAGCTCATTTTCGCG 59.973 55.000 17.23 0.00 0.00 5.87
652 2431 0.026803 GTGCTAGCTCATTTTCGCGG 59.973 55.000 17.23 0.00 0.00 6.46
653 2432 0.108377 TGCTAGCTCATTTTCGCGGA 60.108 50.000 17.23 0.00 0.00 5.54
654 2433 0.579156 GCTAGCTCATTTTCGCGGAG 59.421 55.000 7.70 5.51 0.00 4.63
668 2447 3.761481 CGGAGCTGCAAAAACTGAG 57.239 52.632 5.91 0.00 0.00 3.35
669 2448 0.386478 CGGAGCTGCAAAAACTGAGC 60.386 55.000 5.91 0.00 0.00 4.26
670 2449 0.957362 GGAGCTGCAAAAACTGAGCT 59.043 50.000 0.00 0.00 39.64 4.09
671 2450 1.068679 GGAGCTGCAAAAACTGAGCTC 60.069 52.381 6.82 6.82 45.24 4.09
672 2451 0.957362 AGCTGCAAAAACTGAGCTCC 59.043 50.000 12.15 0.00 35.10 4.70
673 2452 0.670162 GCTGCAAAAACTGAGCTCCA 59.330 50.000 12.15 0.00 0.00 3.86
674 2453 1.601412 GCTGCAAAAACTGAGCTCCAC 60.601 52.381 12.15 0.00 0.00 4.02
675 2454 0.662619 TGCAAAAACTGAGCTCCACG 59.337 50.000 12.15 2.07 0.00 4.94
676 2455 0.944386 GCAAAAACTGAGCTCCACGA 59.056 50.000 12.15 0.00 0.00 4.35
677 2456 1.334149 GCAAAAACTGAGCTCCACGAC 60.334 52.381 12.15 0.00 0.00 4.34
678 2457 2.213499 CAAAAACTGAGCTCCACGACT 58.787 47.619 12.15 0.00 0.00 4.18
679 2458 2.156343 AAAACTGAGCTCCACGACTC 57.844 50.000 12.15 0.00 0.00 3.36
680 2459 0.318762 AAACTGAGCTCCACGACTCC 59.681 55.000 12.15 0.00 31.65 3.85
681 2460 0.827925 AACTGAGCTCCACGACTCCA 60.828 55.000 12.15 0.00 31.65 3.86
682 2461 1.214062 CTGAGCTCCACGACTCCAC 59.786 63.158 12.15 0.00 31.65 4.02
683 2462 2.179517 GAGCTCCACGACTCCACG 59.820 66.667 0.87 0.00 39.31 4.94
684 2463 3.343788 GAGCTCCACGACTCCACGG 62.344 68.421 0.87 0.00 37.61 4.94
685 2464 3.371063 GCTCCACGACTCCACGGA 61.371 66.667 0.00 0.00 37.61 4.69
686 2465 2.878429 CTCCACGACTCCACGGAG 59.122 66.667 11.67 11.67 46.91 4.63
694 2473 4.180946 CTCCACGGAGTCGGAGCG 62.181 72.222 4.83 0.00 44.23 5.03
707 2552 2.503382 GGAGCGGTGAGGAGGGATC 61.503 68.421 0.00 0.00 0.00 3.36
710 2555 3.227276 CGGTGAGGAGGGATCCCG 61.227 72.222 25.48 6.76 41.95 5.14
714 2559 0.976073 GTGAGGAGGGATCCCGAACA 60.976 60.000 25.48 19.50 41.95 3.18
715 2560 0.687757 TGAGGAGGGATCCCGAACAG 60.688 60.000 25.48 0.00 41.95 3.16
716 2561 0.397254 GAGGAGGGATCCCGAACAGA 60.397 60.000 25.48 0.00 41.95 3.41
717 2562 0.397816 AGGAGGGATCCCGAACAGAG 60.398 60.000 25.48 0.00 41.95 3.35
718 2563 1.443828 GAGGGATCCCGAACAGAGC 59.556 63.158 25.48 4.85 41.95 4.09
719 2564 2.034048 GAGGGATCCCGAACAGAGCC 62.034 65.000 25.48 3.65 41.95 4.70
721 2566 1.627297 GGGATCCCGAACAGAGCCTT 61.627 60.000 17.02 0.00 39.80 4.35
723 2568 1.069358 GGATCCCGAACAGAGCCTTAG 59.931 57.143 0.00 0.00 36.84 2.18
724 2569 2.032620 GATCCCGAACAGAGCCTTAGA 58.967 52.381 0.00 0.00 0.00 2.10
725 2570 2.160721 TCCCGAACAGAGCCTTAGAT 57.839 50.000 0.00 0.00 0.00 1.98
726 2571 1.757118 TCCCGAACAGAGCCTTAGATG 59.243 52.381 0.00 0.00 0.00 2.90
727 2572 1.757118 CCCGAACAGAGCCTTAGATGA 59.243 52.381 0.00 0.00 0.00 2.92
729 2574 3.388308 CCGAACAGAGCCTTAGATGATG 58.612 50.000 0.00 0.00 0.00 3.07
730 2575 2.799412 CGAACAGAGCCTTAGATGATGC 59.201 50.000 0.00 0.00 0.00 3.91
731 2576 3.492309 CGAACAGAGCCTTAGATGATGCT 60.492 47.826 0.00 0.00 36.62 3.79
734 2579 2.077413 GAGCCTTAGATGATGCTCGG 57.923 55.000 0.00 0.00 40.61 4.63
735 2580 0.683973 AGCCTTAGATGATGCTCGGG 59.316 55.000 0.00 0.00 0.00 5.14
737 2582 0.321122 CCTTAGATGATGCTCGGGGC 60.321 60.000 0.00 0.00 42.22 5.80
738 2583 0.321122 CTTAGATGATGCTCGGGGCC 60.321 60.000 0.00 0.00 40.92 5.80
739 2584 1.768684 TTAGATGATGCTCGGGGCCC 61.769 60.000 15.76 15.76 40.92 5.80
740 2585 2.963391 TAGATGATGCTCGGGGCCCA 62.963 60.000 26.86 9.05 40.92 5.36
741 2586 3.180799 ATGATGCTCGGGGCCCAT 61.181 61.111 26.86 7.90 40.92 4.00
742 2587 1.841302 GATGATGCTCGGGGCCCATA 61.841 60.000 26.86 9.98 40.92 2.74
743 2588 1.210204 ATGATGCTCGGGGCCCATAT 61.210 55.000 26.86 10.50 40.92 1.78
744 2589 0.546507 TGATGCTCGGGGCCCATATA 60.547 55.000 26.86 6.17 40.92 0.86
748 2593 2.487775 TGCTCGGGGCCCATATATAAT 58.512 47.619 26.86 0.00 40.92 1.28
786 2631 2.040412 GGGGCCCATAATTAGTCTCCTG 59.960 54.545 26.86 0.00 0.00 3.86
823 2669 4.022603 CCCACCACAATCCACATATGAAA 58.977 43.478 10.38 0.00 0.00 2.69
843 2691 4.329462 AAGTAATCAGCAGGCTAGCTAC 57.671 45.455 15.72 6.54 44.54 3.58
919 2767 9.103048 CGCGAAACAATCAAGATTAAATATACC 57.897 33.333 0.00 0.00 0.00 2.73
1045 2893 1.700186 ACCTTGTCCTTGAGGTTCTCC 59.300 52.381 0.00 0.00 43.64 3.71
1081 2929 4.785453 CCACCCTCTTCCGCTGCC 62.785 72.222 0.00 0.00 0.00 4.85
1093 2941 4.681978 GCTGCCGGACGACCTTGT 62.682 66.667 5.05 0.00 0.00 3.16
1094 2942 2.432628 CTGCCGGACGACCTTGTC 60.433 66.667 5.05 0.00 38.17 3.18
1103 2951 1.070289 GACGACCTTGTCCTTGAGGTT 59.930 52.381 0.00 0.00 46.01 3.50
1105 2953 1.344763 CGACCTTGTCCTTGAGGTTCT 59.655 52.381 0.00 0.00 46.01 3.01
1106 2954 2.610727 CGACCTTGTCCTTGAGGTTCTC 60.611 54.545 0.00 0.00 46.01 2.87
1108 2956 1.699634 CCTTGTCCTTGAGGTTCTCCA 59.300 52.381 0.00 0.00 36.34 3.86
1109 2957 2.106511 CCTTGTCCTTGAGGTTCTCCAA 59.893 50.000 0.00 0.00 36.34 3.53
1110 2958 2.930826 TGTCCTTGAGGTTCTCCAAC 57.069 50.000 0.00 0.00 36.34 3.77
1113 2961 1.070134 TCCTTGAGGTTCTCCAACGTG 59.930 52.381 0.00 0.00 36.34 4.49
1114 2962 1.202651 CCTTGAGGTTCTCCAACGTGT 60.203 52.381 0.00 0.00 35.89 4.49
1115 2963 2.135933 CTTGAGGTTCTCCAACGTGTC 58.864 52.381 0.00 0.00 35.89 3.67
1117 2965 0.680061 GAGGTTCTCCAACGTGTCCT 59.320 55.000 0.00 0.00 35.89 3.85
1118 2966 1.070289 GAGGTTCTCCAACGTGTCCTT 59.930 52.381 0.00 0.00 35.89 3.36
1119 2967 1.202651 AGGTTCTCCAACGTGTCCTTG 60.203 52.381 0.00 0.00 35.89 3.61
1121 2969 2.135933 GTTCTCCAACGTGTCCTTGAG 58.864 52.381 0.00 0.00 0.00 3.02
1122 2970 0.679505 TCTCCAACGTGTCCTTGAGG 59.320 55.000 0.00 0.00 0.00 3.86
1123 2971 0.393077 CTCCAACGTGTCCTTGAGGT 59.607 55.000 0.00 0.00 36.34 3.85
1124 2972 0.834612 TCCAACGTGTCCTTGAGGTT 59.165 50.000 0.00 0.00 36.34 3.50
1258 3244 3.499737 GCAACCTGATCACCGGCG 61.500 66.667 0.00 0.00 0.00 6.46
1304 3290 2.159043 AGCATACATGGAGTTCCGACAG 60.159 50.000 0.00 0.00 39.43 3.51
1356 3342 1.740585 GCTAGAGACTGTTCGAGCTCA 59.259 52.381 15.40 0.00 41.05 4.26
1362 3348 1.205893 GACTGTTCGAGCTCAAGGGAT 59.794 52.381 15.40 0.00 0.00 3.85
1380 3366 4.020617 CACCCCGAGGAGCAGCAA 62.021 66.667 0.00 0.00 36.73 3.91
1463 3449 2.298411 ACAATTTCATCGGCCAATGC 57.702 45.000 2.24 0.00 0.00 3.56
1464 3450 1.549620 ACAATTTCATCGGCCAATGCA 59.450 42.857 2.24 0.00 40.13 3.96
1727 3713 1.758592 CTGTCAACGGGAAGGGGAA 59.241 57.895 0.00 0.00 0.00 3.97
1846 3832 4.365899 AAACAACCGAACCAGAAGAAAC 57.634 40.909 0.00 0.00 0.00 2.78
1867 3853 5.404466 ACATGAGAAGAAGACTCAAGGAG 57.596 43.478 0.00 0.00 45.44 3.69
1899 3885 3.073650 ACACTTGCTTGGGAGAGAAGAAT 59.926 43.478 0.00 0.00 0.00 2.40
1953 3939 7.652300 TGATGCCTACGTTATTGATATCAAC 57.348 36.000 20.19 8.04 38.86 3.18
1998 3984 2.416244 ATTCACCGCACACTCGTCGT 62.416 55.000 0.00 0.00 0.00 4.34
2057 4043 0.517316 CCGGCCTTCTTTGTTTCTCG 59.483 55.000 0.00 0.00 0.00 4.04
2071 4057 0.613260 TTCTCGGCTTGCTGTGGTAT 59.387 50.000 1.11 0.00 0.00 2.73
2092 4078 7.734865 TGGTATCTACATGGTAGGATTCATCTT 59.265 37.037 0.00 0.00 0.00 2.40
2204 4190 2.553086 CACATGGTTGCACAAGCTTTT 58.447 42.857 13.18 0.00 42.74 2.27
2205 4191 2.540931 CACATGGTTGCACAAGCTTTTC 59.459 45.455 13.18 0.00 42.74 2.29
2207 4193 3.118665 ACATGGTTGCACAAGCTTTTCTT 60.119 39.130 13.18 0.00 42.74 2.52
2246 4232 7.804129 CGGCTTCACTGACTTCTAGTTATATAC 59.196 40.741 0.00 0.00 0.00 1.47
2247 4233 8.852135 GGCTTCACTGACTTCTAGTTATATACT 58.148 37.037 0.00 0.00 41.04 2.12
2659 4687 7.721286 AAATTAAGGATCTCAGCGTAGATTG 57.279 36.000 5.47 0.00 36.33 2.67
2779 4807 7.401484 TTTTGTAATCAAAAAGCACGAATCC 57.599 32.000 4.05 0.00 46.30 3.01
2780 4808 5.957842 TGTAATCAAAAAGCACGAATCCT 57.042 34.783 0.00 0.00 0.00 3.24
2781 4809 7.441890 TTGTAATCAAAAAGCACGAATCCTA 57.558 32.000 0.00 0.00 0.00 2.94
2782 4810 7.441890 TGTAATCAAAAAGCACGAATCCTAA 57.558 32.000 0.00 0.00 0.00 2.69
2783 4811 7.877003 TGTAATCAAAAAGCACGAATCCTAAA 58.123 30.769 0.00 0.00 0.00 1.85
2784 4812 8.020819 TGTAATCAAAAAGCACGAATCCTAAAG 58.979 33.333 0.00 0.00 0.00 1.85
2785 4813 6.575162 ATCAAAAAGCACGAATCCTAAAGT 57.425 33.333 0.00 0.00 0.00 2.66
2786 4814 6.385649 TCAAAAAGCACGAATCCTAAAGTT 57.614 33.333 0.00 0.00 0.00 2.66
2787 4815 7.499321 TCAAAAAGCACGAATCCTAAAGTTA 57.501 32.000 0.00 0.00 0.00 2.24
2788 4816 8.106247 TCAAAAAGCACGAATCCTAAAGTTAT 57.894 30.769 0.00 0.00 0.00 1.89
2789 4817 8.573035 TCAAAAAGCACGAATCCTAAAGTTATT 58.427 29.630 0.00 0.00 0.00 1.40
2790 4818 9.191995 CAAAAAGCACGAATCCTAAAGTTATTT 57.808 29.630 0.00 0.00 0.00 1.40
2893 4921 1.001633 GGAGGTGTACCGAAGCAAGAA 59.998 52.381 0.00 0.00 42.08 2.52
3006 5034 4.521146 ACATGCATCTCCTCCAAGTTTAG 58.479 43.478 0.00 0.00 0.00 1.85
3007 5035 3.634397 TGCATCTCCTCCAAGTTTAGG 57.366 47.619 0.00 0.00 0.00 2.69
3008 5036 2.293170 GCATCTCCTCCAAGTTTAGGC 58.707 52.381 0.00 0.00 32.55 3.93
3009 5037 2.092699 GCATCTCCTCCAAGTTTAGGCT 60.093 50.000 0.00 0.00 32.55 4.58
3010 5038 3.539604 CATCTCCTCCAAGTTTAGGCTG 58.460 50.000 0.00 0.00 32.55 4.85
3011 5039 1.909302 TCTCCTCCAAGTTTAGGCTGG 59.091 52.381 0.00 0.00 32.55 4.85
3012 5040 1.909302 CTCCTCCAAGTTTAGGCTGGA 59.091 52.381 0.00 0.00 32.55 3.86
3013 5041 1.628846 TCCTCCAAGTTTAGGCTGGAC 59.371 52.381 0.00 0.00 32.55 4.02
3014 5042 1.351017 CCTCCAAGTTTAGGCTGGACA 59.649 52.381 0.00 0.00 0.00 4.02
3015 5043 2.427506 CTCCAAGTTTAGGCTGGACAC 58.572 52.381 0.00 0.00 0.00 3.67
3016 5044 1.771854 TCCAAGTTTAGGCTGGACACA 59.228 47.619 0.00 0.00 0.00 3.72
3017 5045 2.173782 TCCAAGTTTAGGCTGGACACAA 59.826 45.455 0.00 0.00 0.00 3.33
3018 5046 3.157087 CCAAGTTTAGGCTGGACACAAT 58.843 45.455 0.00 0.00 0.00 2.71
3019 5047 3.057315 CCAAGTTTAGGCTGGACACAATG 60.057 47.826 0.00 0.00 0.00 2.82
3020 5048 3.788227 AGTTTAGGCTGGACACAATGA 57.212 42.857 0.00 0.00 0.00 2.57
3021 5049 3.679389 AGTTTAGGCTGGACACAATGAG 58.321 45.455 0.00 0.00 0.00 2.90
3022 5050 3.327757 AGTTTAGGCTGGACACAATGAGA 59.672 43.478 0.00 0.00 0.00 3.27
3023 5051 3.616956 TTAGGCTGGACACAATGAGAG 57.383 47.619 0.00 0.00 0.00 3.20
3024 5052 1.356124 AGGCTGGACACAATGAGAGT 58.644 50.000 0.00 0.00 0.00 3.24
3025 5053 2.540383 AGGCTGGACACAATGAGAGTA 58.460 47.619 0.00 0.00 0.00 2.59
3026 5054 2.906389 AGGCTGGACACAATGAGAGTAA 59.094 45.455 0.00 0.00 0.00 2.24
3027 5055 3.003480 GGCTGGACACAATGAGAGTAAC 58.997 50.000 0.00 0.00 0.00 2.50
3028 5056 3.557054 GGCTGGACACAATGAGAGTAACA 60.557 47.826 0.00 0.00 0.00 2.41
3029 5057 4.256920 GCTGGACACAATGAGAGTAACAT 58.743 43.478 0.00 0.00 0.00 2.71
3030 5058 4.331168 GCTGGACACAATGAGAGTAACATC 59.669 45.833 0.00 0.00 0.00 3.06
3031 5059 5.482006 CTGGACACAATGAGAGTAACATCA 58.518 41.667 0.00 0.00 0.00 3.07
3032 5060 5.237815 TGGACACAATGAGAGTAACATCAC 58.762 41.667 0.00 0.00 0.00 3.06
3033 5061 5.012046 TGGACACAATGAGAGTAACATCACT 59.988 40.000 0.00 0.00 0.00 3.41
3034 5062 6.210584 TGGACACAATGAGAGTAACATCACTA 59.789 38.462 0.00 0.00 0.00 2.74
3035 5063 6.754209 GGACACAATGAGAGTAACATCACTAG 59.246 42.308 0.00 0.00 0.00 2.57
3036 5064 7.233389 ACACAATGAGAGTAACATCACTAGT 57.767 36.000 0.00 0.00 0.00 2.57
3037 5065 8.349568 ACACAATGAGAGTAACATCACTAGTA 57.650 34.615 0.00 0.00 0.00 1.82
3038 5066 8.803235 ACACAATGAGAGTAACATCACTAGTAA 58.197 33.333 0.00 0.00 0.00 2.24
3039 5067 9.077674 CACAATGAGAGTAACATCACTAGTAAC 57.922 37.037 0.00 0.00 0.00 2.50
3040 5068 7.968956 ACAATGAGAGTAACATCACTAGTAACG 59.031 37.037 0.00 0.00 0.00 3.18
3041 5069 7.627298 ATGAGAGTAACATCACTAGTAACGT 57.373 36.000 0.00 0.00 0.00 3.99
3042 5070 7.069852 TGAGAGTAACATCACTAGTAACGTC 57.930 40.000 0.00 0.00 0.00 4.34
3043 5071 6.652062 TGAGAGTAACATCACTAGTAACGTCA 59.348 38.462 0.00 0.00 0.00 4.35
3044 5072 7.336176 TGAGAGTAACATCACTAGTAACGTCAT 59.664 37.037 0.00 0.00 0.00 3.06
3045 5073 8.728337 AGAGTAACATCACTAGTAACGTCATA 57.272 34.615 0.00 0.00 0.00 2.15
3046 5074 8.610896 AGAGTAACATCACTAGTAACGTCATAC 58.389 37.037 0.00 0.00 0.00 2.39
3047 5075 8.503458 AGTAACATCACTAGTAACGTCATACT 57.497 34.615 5.33 5.33 39.41 2.12
3048 5076 8.954350 AGTAACATCACTAGTAACGTCATACTT 58.046 33.333 5.30 0.00 37.34 2.24
3049 5077 9.565213 GTAACATCACTAGTAACGTCATACTTT 57.435 33.333 5.30 0.00 37.34 2.66
3051 5079 8.684973 ACATCACTAGTAACGTCATACTTTTC 57.315 34.615 5.30 0.00 37.34 2.29
3052 5080 8.301720 ACATCACTAGTAACGTCATACTTTTCA 58.698 33.333 5.30 0.00 37.34 2.69
3053 5081 9.135843 CATCACTAGTAACGTCATACTTTTCAA 57.864 33.333 5.30 0.00 37.34 2.69
3054 5082 9.701098 ATCACTAGTAACGTCATACTTTTCAAA 57.299 29.630 5.30 0.00 37.34 2.69
3055 5083 9.531942 TCACTAGTAACGTCATACTTTTCAAAA 57.468 29.630 5.30 0.00 37.34 2.44
3076 5104 6.645700 AAATAATTTTGCTTATGTGGCACG 57.354 33.333 13.77 0.00 39.55 5.34
3077 5105 3.658757 AATTTTGCTTATGTGGCACGT 57.341 38.095 17.65 17.65 39.55 4.49
3078 5106 4.775058 AATTTTGCTTATGTGGCACGTA 57.225 36.364 15.38 15.38 39.55 3.57
3079 5107 4.981806 ATTTTGCTTATGTGGCACGTAT 57.018 36.364 19.55 7.98 39.55 3.06
3080 5108 4.775058 TTTTGCTTATGTGGCACGTATT 57.225 36.364 19.55 4.10 39.55 1.89
3081 5109 4.775058 TTTGCTTATGTGGCACGTATTT 57.225 36.364 19.55 1.66 39.55 1.40
3082 5110 5.881777 TTTGCTTATGTGGCACGTATTTA 57.118 34.783 19.55 5.10 39.55 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.758514 GGCAGTCATCCTCCTCCGA 60.759 63.158 0.00 0.00 0.00 4.55
6 7 1.617947 AACGGCAGTCATCCTCCTCC 61.618 60.000 0.00 0.00 0.00 4.30
24 25 9.495572 AACAAAGTGTTTCACCTTTTTATTCAA 57.504 25.926 0.00 0.00 37.26 2.69
103 104 3.976793 ATGCCGATGAACAACATGATC 57.023 42.857 0.00 0.00 39.56 2.92
115 116 4.276678 ACCTCACAAATTCATATGCCGATG 59.723 41.667 0.00 0.00 0.00 3.84
185 186 7.168219 ACTTACATGCCTCAACTTCTTATGAA 58.832 34.615 0.00 0.00 0.00 2.57
200 201 5.969435 GCCGATTTAAAGTAACTTACATGCC 59.031 40.000 1.79 0.00 0.00 4.40
268 269 7.114866 TCACTTAATGACCATAATGTACCGA 57.885 36.000 0.00 0.00 29.99 4.69
326 327 6.765036 ACCAACATCAAATATGCACACAAAAA 59.235 30.769 0.00 0.00 0.00 1.94
328 329 5.851720 ACCAACATCAAATATGCACACAAA 58.148 33.333 0.00 0.00 0.00 2.83
329 330 5.465532 ACCAACATCAAATATGCACACAA 57.534 34.783 0.00 0.00 0.00 3.33
330 331 5.221402 ACAACCAACATCAAATATGCACACA 60.221 36.000 0.00 0.00 0.00 3.72
331 332 5.118971 CACAACCAACATCAAATATGCACAC 59.881 40.000 0.00 0.00 0.00 3.82
332 333 5.221402 ACACAACCAACATCAAATATGCACA 60.221 36.000 0.00 0.00 0.00 4.57
333 334 5.118971 CACACAACCAACATCAAATATGCAC 59.881 40.000 0.00 0.00 0.00 4.57
334 335 5.228665 CACACAACCAACATCAAATATGCA 58.771 37.500 0.00 0.00 0.00 3.96
335 336 4.091800 GCACACAACCAACATCAAATATGC 59.908 41.667 0.00 0.00 0.00 3.14
336 337 5.228665 TGCACACAACCAACATCAAATATG 58.771 37.500 0.00 0.00 0.00 1.78
337 338 5.465532 TGCACACAACCAACATCAAATAT 57.534 34.783 0.00 0.00 0.00 1.28
338 339 4.926140 TGCACACAACCAACATCAAATA 57.074 36.364 0.00 0.00 0.00 1.40
339 340 3.815856 TGCACACAACCAACATCAAAT 57.184 38.095 0.00 0.00 0.00 2.32
455 2233 5.180117 CAGTGAGAAGTAAAGAACATGTGGG 59.820 44.000 0.00 0.00 0.00 4.61
458 2236 5.692204 CGACAGTGAGAAGTAAAGAACATGT 59.308 40.000 0.00 0.00 0.00 3.21
464 2242 3.506455 CCTCCGACAGTGAGAAGTAAAGA 59.494 47.826 0.00 0.00 31.26 2.52
478 2256 2.764128 GCCCATCTCCCTCCGACA 60.764 66.667 0.00 0.00 0.00 4.35
483 2261 2.771762 AGCTGGCCCATCTCCCTC 60.772 66.667 0.00 0.00 0.00 4.30
517 2295 2.091830 TCCTGTATCGACTGATCCACCT 60.092 50.000 0.00 0.00 35.99 4.00
526 2304 4.527038 TGTTTTCTTCCTCCTGTATCGACT 59.473 41.667 0.00 0.00 0.00 4.18
549 2328 1.199327 TCTCTCGCGACTCGTTCAAAT 59.801 47.619 3.71 0.00 39.67 2.32
569 2348 1.406903 ACGCGGCCTAAGTATACCTT 58.593 50.000 12.47 0.00 37.17 3.50
574 2353 4.724022 CGAACGCGGCCTAAGTAT 57.276 55.556 12.47 0.00 0.00 2.12
584 2363 4.856607 GGAGAGGAGCCGAACGCG 62.857 72.222 3.53 3.53 44.76 6.01
591 2370 4.851214 AGGGAGCGGAGAGGAGCC 62.851 72.222 0.00 0.00 0.00 4.70
592 2371 3.223589 GAGGGAGCGGAGAGGAGC 61.224 72.222 0.00 0.00 0.00 4.70
593 2372 2.520741 GGAGGGAGCGGAGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
594 2373 3.347590 TGGAGGGAGCGGAGAGGA 61.348 66.667 0.00 0.00 0.00 3.71
595 2374 3.151022 GTGGAGGGAGCGGAGAGG 61.151 72.222 0.00 0.00 0.00 3.69
596 2375 2.043450 AGTGGAGGGAGCGGAGAG 60.043 66.667 0.00 0.00 0.00 3.20
597 2376 2.043852 GAGTGGAGGGAGCGGAGA 60.044 66.667 0.00 0.00 0.00 3.71
598 2377 3.151022 GGAGTGGAGGGAGCGGAG 61.151 72.222 0.00 0.00 0.00 4.63
602 2381 3.844090 GAGCGGAGTGGAGGGAGC 61.844 72.222 0.00 0.00 0.00 4.70
603 2382 3.151022 GGAGCGGAGTGGAGGGAG 61.151 72.222 0.00 0.00 0.00 4.30
621 2400 3.075005 TAGCACCTGGTCCGCTCC 61.075 66.667 14.25 0.00 37.20 4.70
622 2401 2.496817 CTAGCACCTGGTCCGCTC 59.503 66.667 14.25 0.00 37.20 5.03
623 2402 3.775654 GCTAGCACCTGGTCCGCT 61.776 66.667 10.63 15.07 39.80 5.52
624 2403 3.724914 GAGCTAGCACCTGGTCCGC 62.725 68.421 18.83 0.00 0.00 5.54
625 2404 1.680522 ATGAGCTAGCACCTGGTCCG 61.681 60.000 18.83 0.00 0.00 4.79
626 2405 0.543749 AATGAGCTAGCACCTGGTCC 59.456 55.000 18.83 0.00 0.00 4.46
627 2406 2.409948 AAATGAGCTAGCACCTGGTC 57.590 50.000 18.83 4.90 0.00 4.02
628 2407 2.716217 GAAAATGAGCTAGCACCTGGT 58.284 47.619 18.83 0.00 0.00 4.00
629 2408 1.667724 CGAAAATGAGCTAGCACCTGG 59.332 52.381 18.83 0.00 0.00 4.45
630 2409 1.063174 GCGAAAATGAGCTAGCACCTG 59.937 52.381 18.83 0.00 0.00 4.00
631 2410 1.373570 GCGAAAATGAGCTAGCACCT 58.626 50.000 18.83 0.00 0.00 4.00
632 2411 0.026803 CGCGAAAATGAGCTAGCACC 59.973 55.000 18.83 8.86 0.00 5.01
633 2412 0.026803 CCGCGAAAATGAGCTAGCAC 59.973 55.000 18.83 11.88 0.00 4.40
634 2413 0.108377 TCCGCGAAAATGAGCTAGCA 60.108 50.000 18.83 0.00 0.00 3.49
635 2414 0.579156 CTCCGCGAAAATGAGCTAGC 59.421 55.000 8.23 6.62 0.00 3.42
636 2415 0.579156 GCTCCGCGAAAATGAGCTAG 59.421 55.000 21.95 0.00 46.19 3.42
637 2416 2.677971 GCTCCGCGAAAATGAGCTA 58.322 52.632 21.95 0.00 46.19 3.32
638 2417 3.490890 GCTCCGCGAAAATGAGCT 58.509 55.556 21.95 0.00 46.19 4.09
640 2419 1.061570 GCAGCTCCGCGAAAATGAG 59.938 57.895 8.23 6.28 0.00 2.90
641 2420 1.233950 TTGCAGCTCCGCGAAAATGA 61.234 50.000 8.23 0.00 33.35 2.57
642 2421 0.387112 TTTGCAGCTCCGCGAAAATG 60.387 50.000 8.23 1.85 32.24 2.32
643 2422 0.313672 TTTTGCAGCTCCGCGAAAAT 59.686 45.000 8.23 0.00 41.28 1.82
644 2423 1.730487 TTTTGCAGCTCCGCGAAAA 59.270 47.368 8.23 0.89 41.28 2.29
645 2424 0.593773 GTTTTTGCAGCTCCGCGAAA 60.594 50.000 8.23 7.23 42.26 3.46
646 2425 1.008995 GTTTTTGCAGCTCCGCGAA 60.009 52.632 8.23 0.00 33.36 4.70
647 2426 1.891919 AGTTTTTGCAGCTCCGCGA 60.892 52.632 8.23 0.00 33.35 5.87
648 2427 1.727022 CAGTTTTTGCAGCTCCGCG 60.727 57.895 0.00 0.00 33.35 6.46
649 2428 0.386478 CTCAGTTTTTGCAGCTCCGC 60.386 55.000 0.00 0.00 0.00 5.54
650 2429 0.386478 GCTCAGTTTTTGCAGCTCCG 60.386 55.000 0.00 0.00 31.43 4.63
651 2430 0.957362 AGCTCAGTTTTTGCAGCTCC 59.043 50.000 0.00 0.00 36.31 4.70
652 2431 1.068679 GGAGCTCAGTTTTTGCAGCTC 60.069 52.381 17.19 10.68 45.81 4.09
653 2432 0.957362 GGAGCTCAGTTTTTGCAGCT 59.043 50.000 17.19 0.00 40.56 4.24
654 2433 0.670162 TGGAGCTCAGTTTTTGCAGC 59.330 50.000 17.19 0.00 33.11 5.25
655 2434 1.334419 CGTGGAGCTCAGTTTTTGCAG 60.334 52.381 17.19 0.00 0.00 4.41
656 2435 0.662619 CGTGGAGCTCAGTTTTTGCA 59.337 50.000 17.19 0.00 0.00 4.08
657 2436 0.944386 TCGTGGAGCTCAGTTTTTGC 59.056 50.000 17.19 0.00 0.00 3.68
658 2437 2.213499 AGTCGTGGAGCTCAGTTTTTG 58.787 47.619 17.19 0.00 0.00 2.44
659 2438 2.484889 GAGTCGTGGAGCTCAGTTTTT 58.515 47.619 17.19 0.00 0.00 1.94
660 2439 1.270358 GGAGTCGTGGAGCTCAGTTTT 60.270 52.381 17.19 0.00 33.66 2.43
661 2440 0.318762 GGAGTCGTGGAGCTCAGTTT 59.681 55.000 17.19 0.00 33.66 2.66
662 2441 0.827925 TGGAGTCGTGGAGCTCAGTT 60.828 55.000 17.19 0.00 33.66 3.16
663 2442 1.228583 TGGAGTCGTGGAGCTCAGT 60.229 57.895 17.19 0.00 33.66 3.41
664 2443 1.214062 GTGGAGTCGTGGAGCTCAG 59.786 63.158 17.19 6.40 33.66 3.35
665 2444 2.626780 CGTGGAGTCGTGGAGCTCA 61.627 63.158 17.19 0.00 33.66 4.26
666 2445 2.179517 CGTGGAGTCGTGGAGCTC 59.820 66.667 4.71 4.71 0.00 4.09
667 2446 3.374402 CCGTGGAGTCGTGGAGCT 61.374 66.667 0.00 0.00 0.00 4.09
668 2447 3.343788 CTCCGTGGAGTCGTGGAGC 62.344 68.421 7.79 0.00 41.36 4.70
669 2448 2.878429 CTCCGTGGAGTCGTGGAG 59.122 66.667 7.79 8.89 41.82 3.86
680 2459 4.778415 CACCGCTCCGACTCCGTG 62.778 72.222 0.00 0.00 0.00 4.94
682 2461 4.180946 CTCACCGCTCCGACTCCG 62.181 72.222 0.00 0.00 0.00 4.63
683 2462 3.827898 CCTCACCGCTCCGACTCC 61.828 72.222 0.00 0.00 0.00 3.85
684 2463 2.750637 TCCTCACCGCTCCGACTC 60.751 66.667 0.00 0.00 0.00 3.36
685 2464 2.752238 CTCCTCACCGCTCCGACT 60.752 66.667 0.00 0.00 0.00 4.18
686 2465 3.827898 CCTCCTCACCGCTCCGAC 61.828 72.222 0.00 0.00 0.00 4.79
689 2468 2.444895 ATCCCTCCTCACCGCTCC 60.445 66.667 0.00 0.00 0.00 4.70
690 2469 2.503382 GGATCCCTCCTCACCGCTC 61.503 68.421 0.00 0.00 38.65 5.03
691 2470 2.444895 GGATCCCTCCTCACCGCT 60.445 66.667 0.00 0.00 38.65 5.52
692 2471 3.551407 GGGATCCCTCCTCACCGC 61.551 72.222 24.69 0.00 41.74 5.68
693 2472 3.227276 CGGGATCCCTCCTCACCG 61.227 72.222 28.42 8.78 41.74 4.94
694 2473 1.382695 TTCGGGATCCCTCCTCACC 60.383 63.158 28.42 0.00 41.74 4.02
695 2474 0.976073 TGTTCGGGATCCCTCCTCAC 60.976 60.000 28.42 16.44 41.74 3.51
696 2475 0.687757 CTGTTCGGGATCCCTCCTCA 60.688 60.000 28.42 18.85 41.74 3.86
704 2549 2.032620 TCTAAGGCTCTGTTCGGGATC 58.967 52.381 0.00 0.00 0.00 3.36
707 2552 1.757118 TCATCTAAGGCTCTGTTCGGG 59.243 52.381 0.00 0.00 0.00 5.14
710 2555 4.057432 GAGCATCATCTAAGGCTCTGTTC 58.943 47.826 5.31 0.00 46.95 3.18
716 2561 0.683973 CCCGAGCATCATCTAAGGCT 59.316 55.000 0.00 0.00 39.75 4.58
717 2562 0.321122 CCCCGAGCATCATCTAAGGC 60.321 60.000 0.00 0.00 33.17 4.35
718 2563 0.321122 GCCCCGAGCATCATCTAAGG 60.321 60.000 0.00 0.00 42.97 2.69
719 2564 0.321122 GGCCCCGAGCATCATCTAAG 60.321 60.000 0.00 0.00 46.50 2.18
721 2566 2.217038 GGGCCCCGAGCATCATCTA 61.217 63.158 12.23 0.00 46.50 1.98
723 2568 1.841302 TATGGGCCCCGAGCATCATC 61.841 60.000 22.27 0.00 46.50 2.92
724 2569 1.210204 ATATGGGCCCCGAGCATCAT 61.210 55.000 22.27 5.67 46.50 2.45
725 2570 0.546507 TATATGGGCCCCGAGCATCA 60.547 55.000 22.27 0.00 46.50 3.07
726 2571 0.839946 ATATATGGGCCCCGAGCATC 59.160 55.000 22.27 0.00 46.50 3.91
727 2572 2.190398 TATATATGGGCCCCGAGCAT 57.810 50.000 22.27 8.24 46.50 3.79
729 2574 4.699925 TTATTATATATGGGCCCCGAGC 57.300 45.455 22.27 0.00 42.60 5.03
760 2605 2.304761 GACTAATTATGGGCCCCGATCA 59.695 50.000 22.27 0.00 0.00 2.92
766 2611 2.711547 ACAGGAGACTAATTATGGGCCC 59.288 50.000 17.59 17.59 40.21 5.80
786 2631 1.203287 GGTGGGTACGTACTCCTCAAC 59.797 57.143 22.54 13.44 0.00 3.18
823 2669 2.630580 GGTAGCTAGCCTGCTGATTACT 59.369 50.000 12.13 0.00 43.87 2.24
919 2767 5.692928 AGCCGGGTATATATAGTAGGAGTG 58.307 45.833 3.10 0.00 0.00 3.51
1089 2937 3.142174 GTTGGAGAACCTCAAGGACAAG 58.858 50.000 2.30 0.00 38.94 3.16
1091 2939 1.070134 CGTTGGAGAACCTCAAGGACA 59.930 52.381 2.30 0.00 38.94 4.02
1092 2940 1.070289 ACGTTGGAGAACCTCAAGGAC 59.930 52.381 2.30 0.00 38.94 3.85
1093 2941 1.070134 CACGTTGGAGAACCTCAAGGA 59.930 52.381 2.30 0.00 38.94 3.36
1094 2942 1.202651 ACACGTTGGAGAACCTCAAGG 60.203 52.381 0.00 0.00 42.17 3.61
1095 2943 2.135933 GACACGTTGGAGAACCTCAAG 58.864 52.381 0.00 0.00 37.04 3.02
1096 2944 1.202604 GGACACGTTGGAGAACCTCAA 60.203 52.381 0.00 0.00 37.04 3.02
1097 2945 0.391597 GGACACGTTGGAGAACCTCA 59.608 55.000 0.00 0.00 37.04 3.86
1098 2946 0.680061 AGGACACGTTGGAGAACCTC 59.320 55.000 0.00 0.00 37.04 3.85
1099 2947 1.129058 AAGGACACGTTGGAGAACCT 58.871 50.000 0.00 0.00 37.04 3.50
1103 2951 0.679505 CCTCAAGGACACGTTGGAGA 59.320 55.000 0.00 0.00 37.39 3.71
1105 2953 0.834612 AACCTCAAGGACACGTTGGA 59.165 50.000 2.30 0.00 38.94 3.53
1106 2954 1.202651 AGAACCTCAAGGACACGTTGG 60.203 52.381 2.30 0.00 38.94 3.77
1108 2956 1.070289 GGAGAACCTCAAGGACACGTT 59.930 52.381 2.30 0.00 38.94 3.99
1109 2957 0.680061 GGAGAACCTCAAGGACACGT 59.320 55.000 2.30 0.00 38.94 4.49
1110 2958 0.037232 GGGAGAACCTCAAGGACACG 60.037 60.000 2.30 0.00 38.94 4.49
1121 2969 1.916777 TTGGGGACGAGGGAGAACC 60.917 63.158 0.00 0.00 40.67 3.62
1122 2970 1.295746 GTTGGGGACGAGGGAGAAC 59.704 63.158 0.00 0.00 0.00 3.01
1123 2971 0.546747 ATGTTGGGGACGAGGGAGAA 60.547 55.000 0.00 0.00 0.00 2.87
1124 2972 0.976073 GATGTTGGGGACGAGGGAGA 60.976 60.000 0.00 0.00 0.00 3.71
1258 3244 3.195698 GGGGAGCACGTCGAATGC 61.196 66.667 13.71 13.71 43.74 3.56
1282 3268 2.205074 GTCGGAACTCCATGTATGCTG 58.795 52.381 0.00 0.00 35.14 4.41
1304 3290 2.843912 ATAGCCAGCCAGGTGGTTGC 62.844 60.000 16.71 3.40 43.95 4.17
1380 3366 3.903090 TCATCACCTTGAAAAAGGGCAAT 59.097 39.130 9.23 0.00 44.27 3.56
1495 3481 2.289320 TGCTCTGGCTCTTGTTCTTCTC 60.289 50.000 0.00 0.00 39.59 2.87
1496 3482 1.696336 TGCTCTGGCTCTTGTTCTTCT 59.304 47.619 0.00 0.00 39.59 2.85
1497 3483 2.175878 TGCTCTGGCTCTTGTTCTTC 57.824 50.000 0.00 0.00 39.59 2.87
1727 3713 4.202357 TGTTCAAGTAGACCAACATGAGCT 60.202 41.667 0.00 0.00 31.94 4.09
1846 3832 5.657826 TCTCCTTGAGTCTTCTTCTCATG 57.342 43.478 0.00 0.00 40.83 3.07
1867 3853 4.578928 TCCCAAGCAAGTGTAAAGAACTTC 59.421 41.667 0.00 0.00 35.70 3.01
1899 3885 3.244387 TGTCCTTGATGATCAACGTTCCA 60.244 43.478 3.29 0.00 32.21 3.53
1953 3939 4.263572 TCTTGCACCACCCCCGTG 62.264 66.667 0.00 0.00 39.91 4.94
1986 3972 0.985549 GATTGAGACGACGAGTGTGC 59.014 55.000 0.00 0.00 0.00 4.57
1998 3984 3.664107 CACAGTCTTTTCCCGATTGAGA 58.336 45.455 0.00 0.00 0.00 3.27
2057 4043 2.691409 TGTAGATACCACAGCAAGCC 57.309 50.000 0.00 0.00 0.00 4.35
2130 4116 6.523201 GTGATCACAATCAACCGAACATTTAC 59.477 38.462 21.07 0.00 43.42 2.01
2204 4190 0.101759 GCCGATACTACCACGCAAGA 59.898 55.000 0.00 0.00 43.62 3.02
2207 4193 0.101759 GAAGCCGATACTACCACGCA 59.898 55.000 0.00 0.00 0.00 5.24
2208 4194 0.101759 TGAAGCCGATACTACCACGC 59.898 55.000 0.00 0.00 0.00 5.34
2209 4195 1.404391 AGTGAAGCCGATACTACCACG 59.596 52.381 0.00 0.00 32.09 4.94
2633 4619 8.616076 CAATCTACGCTGAGATCCTTAATTTTT 58.384 33.333 0.00 0.00 35.01 1.94
2634 4620 7.987458 TCAATCTACGCTGAGATCCTTAATTTT 59.013 33.333 0.00 0.00 35.01 1.82
2635 4621 7.500992 TCAATCTACGCTGAGATCCTTAATTT 58.499 34.615 0.00 0.00 35.01 1.82
2636 4622 7.055667 TCAATCTACGCTGAGATCCTTAATT 57.944 36.000 0.00 0.00 35.01 1.40
2637 4623 6.656632 TCAATCTACGCTGAGATCCTTAAT 57.343 37.500 0.00 0.00 35.01 1.40
2638 4624 6.461648 CCTTCAATCTACGCTGAGATCCTTAA 60.462 42.308 0.00 0.00 35.01 1.85
2639 4625 5.010112 CCTTCAATCTACGCTGAGATCCTTA 59.990 44.000 0.00 0.00 35.01 2.69
2640 4626 4.202202 CCTTCAATCTACGCTGAGATCCTT 60.202 45.833 0.00 0.00 35.01 3.36
2641 4627 3.320541 CCTTCAATCTACGCTGAGATCCT 59.679 47.826 0.00 0.00 35.01 3.24
2642 4628 3.068873 ACCTTCAATCTACGCTGAGATCC 59.931 47.826 0.00 0.00 35.01 3.36
2643 4629 4.047822 CACCTTCAATCTACGCTGAGATC 58.952 47.826 0.00 0.00 35.01 2.75
2644 4630 3.701542 TCACCTTCAATCTACGCTGAGAT 59.298 43.478 0.00 0.00 37.81 2.75
2645 4631 3.089284 TCACCTTCAATCTACGCTGAGA 58.911 45.455 0.00 0.00 0.00 3.27
2646 4632 3.510388 TCACCTTCAATCTACGCTGAG 57.490 47.619 0.00 0.00 0.00 3.35
2647 4633 3.509967 TCTTCACCTTCAATCTACGCTGA 59.490 43.478 0.00 0.00 0.00 4.26
2648 4634 3.849911 TCTTCACCTTCAATCTACGCTG 58.150 45.455 0.00 0.00 0.00 5.18
2649 4635 4.160439 TGATCTTCACCTTCAATCTACGCT 59.840 41.667 0.00 0.00 0.00 5.07
2650 4636 4.433615 TGATCTTCACCTTCAATCTACGC 58.566 43.478 0.00 0.00 0.00 4.42
2651 4637 5.895928 TCTGATCTTCACCTTCAATCTACG 58.104 41.667 0.00 0.00 0.00 3.51
2652 4638 6.760770 CCTTCTGATCTTCACCTTCAATCTAC 59.239 42.308 0.00 0.00 0.00 2.59
2659 4687 4.760878 GGTACCTTCTGATCTTCACCTTC 58.239 47.826 4.06 0.00 0.00 3.46
2756 4784 6.744112 AGGATTCGTGCTTTTTGATTACAAA 58.256 32.000 0.00 0.00 43.10 2.83
2757 4785 6.325919 AGGATTCGTGCTTTTTGATTACAA 57.674 33.333 0.00 0.00 0.00 2.41
2758 4786 5.957842 AGGATTCGTGCTTTTTGATTACA 57.042 34.783 0.00 0.00 0.00 2.41
2759 4787 8.021396 ACTTTAGGATTCGTGCTTTTTGATTAC 58.979 33.333 0.00 0.00 0.00 1.89
2760 4788 8.106247 ACTTTAGGATTCGTGCTTTTTGATTA 57.894 30.769 0.00 0.00 0.00 1.75
2761 4789 6.981722 ACTTTAGGATTCGTGCTTTTTGATT 58.018 32.000 0.00 0.00 0.00 2.57
2762 4790 6.575162 ACTTTAGGATTCGTGCTTTTTGAT 57.425 33.333 0.00 0.00 0.00 2.57
2763 4791 6.385649 AACTTTAGGATTCGTGCTTTTTGA 57.614 33.333 0.00 0.00 0.00 2.69
2764 4792 8.742554 AATAACTTTAGGATTCGTGCTTTTTG 57.257 30.769 0.00 0.00 0.00 2.44
2851 4879 4.754618 CCCCTTAAAAGTTTGCACAAATCC 59.245 41.667 0.00 0.00 32.36 3.01
2856 4884 2.962421 CCTCCCCTTAAAAGTTTGCACA 59.038 45.455 0.00 0.00 0.00 4.57
3006 5034 3.003480 GTTACTCTCATTGTGTCCAGCC 58.997 50.000 0.00 0.00 0.00 4.85
3007 5035 3.664107 TGTTACTCTCATTGTGTCCAGC 58.336 45.455 0.00 0.00 0.00 4.85
3008 5036 5.349817 GTGATGTTACTCTCATTGTGTCCAG 59.650 44.000 0.00 0.00 0.00 3.86
3009 5037 5.012046 AGTGATGTTACTCTCATTGTGTCCA 59.988 40.000 0.00 0.00 0.00 4.02
3010 5038 5.482908 AGTGATGTTACTCTCATTGTGTCC 58.517 41.667 0.00 0.00 0.00 4.02
3011 5039 7.316640 ACTAGTGATGTTACTCTCATTGTGTC 58.683 38.462 0.00 0.00 32.19 3.67
3012 5040 7.233389 ACTAGTGATGTTACTCTCATTGTGT 57.767 36.000 0.00 0.00 32.19 3.72
3013 5041 9.077674 GTTACTAGTGATGTTACTCTCATTGTG 57.922 37.037 5.39 0.00 32.19 3.33
3014 5042 7.968956 CGTTACTAGTGATGTTACTCTCATTGT 59.031 37.037 5.39 0.00 32.19 2.71
3015 5043 7.968956 ACGTTACTAGTGATGTTACTCTCATTG 59.031 37.037 5.39 0.00 32.19 2.82
3016 5044 8.053026 ACGTTACTAGTGATGTTACTCTCATT 57.947 34.615 5.39 0.00 32.19 2.57
3017 5045 7.336176 TGACGTTACTAGTGATGTTACTCTCAT 59.664 37.037 13.24 0.00 32.19 2.90
3018 5046 6.652062 TGACGTTACTAGTGATGTTACTCTCA 59.348 38.462 13.24 3.86 32.19 3.27
3019 5047 7.069852 TGACGTTACTAGTGATGTTACTCTC 57.930 40.000 13.24 1.48 32.19 3.20
3020 5048 7.627298 ATGACGTTACTAGTGATGTTACTCT 57.373 36.000 13.24 0.00 32.19 3.24
3021 5049 8.610896 AGTATGACGTTACTAGTGATGTTACTC 58.389 37.037 13.24 6.86 30.65 2.59
3022 5050 8.503458 AGTATGACGTTACTAGTGATGTTACT 57.497 34.615 13.24 13.84 30.65 2.24
3023 5051 9.565213 AAAGTATGACGTTACTAGTGATGTTAC 57.435 33.333 13.24 12.12 32.16 2.50
3025 5053 9.136952 GAAAAGTATGACGTTACTAGTGATGTT 57.863 33.333 13.24 2.29 32.16 2.71
3026 5054 8.301720 TGAAAAGTATGACGTTACTAGTGATGT 58.698 33.333 12.00 12.00 32.16 3.06
3027 5055 8.683550 TGAAAAGTATGACGTTACTAGTGATG 57.316 34.615 5.39 5.37 32.16 3.07
3028 5056 9.701098 TTTGAAAAGTATGACGTTACTAGTGAT 57.299 29.630 5.39 0.00 32.16 3.06
3029 5057 9.531942 TTTTGAAAAGTATGACGTTACTAGTGA 57.468 29.630 5.39 0.00 32.16 3.41
3052 5080 6.648725 ACGTGCCACATAAGCAAAATTATTTT 59.351 30.769 0.00 0.00 43.02 1.82
3053 5081 6.162777 ACGTGCCACATAAGCAAAATTATTT 58.837 32.000 0.00 0.00 43.02 1.40
3054 5082 5.719173 ACGTGCCACATAAGCAAAATTATT 58.281 33.333 0.00 0.00 43.02 1.40
3055 5083 5.323371 ACGTGCCACATAAGCAAAATTAT 57.677 34.783 0.00 0.00 43.02 1.28
3056 5084 4.775058 ACGTGCCACATAAGCAAAATTA 57.225 36.364 0.00 0.00 43.02 1.40
3057 5085 3.658757 ACGTGCCACATAAGCAAAATT 57.341 38.095 0.00 0.00 43.02 1.82
3058 5086 4.981806 ATACGTGCCACATAAGCAAAAT 57.018 36.364 0.00 0.00 43.02 1.82
3059 5087 4.775058 AATACGTGCCACATAAGCAAAA 57.225 36.364 0.00 0.00 43.02 2.44
3060 5088 4.775058 AAATACGTGCCACATAAGCAAA 57.225 36.364 0.00 0.00 43.02 3.68


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

AutoCloner maintained by Alex Coulton.