Multiple sequence alignment - TraesCS2B01G437900

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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 TraesCS2B01G437900 chr2B 100.000 5006 0 0 1 5006 629810497 629815502 0.000000e+00 9245.0
1 TraesCS2B01G437900 chr2B 92.373 118 9 0 4685 4802 150891052 150891169 8.620000e-38 169.0
2 TraesCS2B01G437900 chr2B 83.077 130 13 7 139 263 154490688 154490563 5.300000e-20 110.0
3 TraesCS2B01G437900 chr2B 85.870 92 7 5 139 227 154500174 154500086 5.340000e-15 93.5
4 TraesCS2B01G437900 chr2B 78.947 133 22 6 139 267 710986218 710986088 8.930000e-13 86.1
5 TraesCS2B01G437900 chr2B 79.104 134 18 9 139 267 711307361 711307233 3.210000e-12 84.2
6 TraesCS2B01G437900 chr2A 93.632 3439 143 43 831 4241 674529060 674532450 0.000000e+00 5068.0
7 TraesCS2B01G437900 chr2A 94.282 752 34 5 4264 5006 674532510 674533261 0.000000e+00 1142.0
8 TraesCS2B01G437900 chr2A 88.147 464 33 11 139 590 674510353 674510806 2.650000e-147 532.0
9 TraesCS2B01G437900 chr2A 83.851 322 48 4 4664 4983 679964625 679964944 2.260000e-78 303.0
10 TraesCS2B01G437900 chr2A 81.290 310 56 2 4667 4975 679977365 679977057 2.990000e-62 250.0
11 TraesCS2B01G437900 chr2A 91.057 123 8 3 592 714 674528939 674529058 4.010000e-36 163.0
12 TraesCS2B01G437900 chr2A 88.119 101 8 3 28 128 674509896 674509992 3.170000e-22 117.0
13 TraesCS2B01G437900 chr2A 80.741 135 17 8 139 268 722749616 722749486 4.130000e-16 97.1
14 TraesCS2B01G437900 chr2D 92.365 2842 154 36 878 3688 529680476 529683285 0.000000e+00 3988.0
15 TraesCS2B01G437900 chr2D 92.869 1206 68 11 3806 5004 529683286 529684480 0.000000e+00 1735.0
16 TraesCS2B01G437900 chr2D 96.078 204 7 1 139 342 529675304 529675506 1.040000e-86 331.0
17 TraesCS2B01G437900 chr2D 84.161 322 47 4 4664 4983 537338598 537338917 4.870000e-80 309.0
18 TraesCS2B01G437900 chr2D 85.714 245 35 0 4741 4985 537438568 537438324 4.970000e-65 259.0
19 TraesCS2B01G437900 chr2D 94.017 117 7 0 716 832 418057634 418057518 1.430000e-40 178.0
20 TraesCS2B01G437900 chr2D 90.476 126 8 2 3 128 529673385 529673506 4.010000e-36 163.0
21 TraesCS2B01G437900 chr2D 78.295 129 20 8 139 263 102944129 102944005 5.370000e-10 76.8
22 TraesCS2B01G437900 chr3B 94.068 118 7 0 716 833 819521303 819521186 3.980000e-41 180.0
23 TraesCS2B01G437900 chr3B 94.017 117 7 0 716 832 457968682 457968798 1.430000e-40 178.0
24 TraesCS2B01G437900 chr4B 90.441 136 11 2 702 836 636915218 636915352 1.430000e-40 178.0
25 TraesCS2B01G437900 chr6B 93.277 119 8 0 714 832 653709200 653709318 5.150000e-40 176.0
26 TraesCS2B01G437900 chr5B 93.277 119 8 0 714 832 706349461 706349343 5.150000e-40 176.0
27 TraesCS2B01G437900 chr4A 92.683 123 8 1 711 832 660714411 660714289 5.150000e-40 176.0
28 TraesCS2B01G437900 chr7B 93.220 118 8 0 716 833 115517861 115517978 1.850000e-39 174.0
29 TraesCS2B01G437900 chr1B 91.339 127 10 1 714 840 507765942 507766067 6.660000e-39 172.0
30 TraesCS2B01G437900 chr1B 79.070 129 20 7 139 263 17392013 17392138 1.160000e-11 82.4


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 TraesCS2B01G437900 chr2B 629810497 629815502 5005 False 9245.000000 9245 100.000000 1 5006 1 chr2B.!!$F2 5005
1 TraesCS2B01G437900 chr2A 674528939 674533261 4322 False 2124.333333 5068 92.990333 592 5006 3 chr2A.!!$F3 4414
2 TraesCS2B01G437900 chr2A 674509896 674510806 910 False 324.500000 532 88.133000 28 590 2 chr2A.!!$F2 562
3 TraesCS2B01G437900 chr2D 529680476 529684480 4004 False 2861.500000 3988 92.617000 878 5004 2 chr2D.!!$F3 4126
4 TraesCS2B01G437900 chr2D 529673385 529675506 2121 False 247.000000 331 93.277000 3 342 2 chr2D.!!$F2 339

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
358 2170 0.106719 ACAATTATGGACCAGGCCCG 60.107 55.000 0.00 0.00 0.00 6.13 F
359 2171 0.106719 CAATTATGGACCAGGCCCGT 60.107 55.000 0.00 0.00 0.00 5.28 F
360 2172 0.106719 AATTATGGACCAGGCCCGTG 60.107 55.000 0.00 0.00 0.00 4.94 F
875 2698 0.600057 GGAAGCCAAGACAAAGCAGG 59.400 55.000 0.00 0.00 0.00 4.85 F
891 2714 0.673437 CAGGCATGGAAACCGTGTTT 59.327 50.000 10.96 2.23 42.15 2.83 F
1883 3712 1.072806 TGCTGACTGCTCTTCCACAAT 59.927 47.619 5.87 0.00 43.37 2.71 F
2560 4406 1.404035 GTTTCGGTTGTGCTGGTCTTT 59.596 47.619 0.00 0.00 0.00 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1457 3282 0.110056 CTGCAATCAAGCACGACCAC 60.110 55.000 0.00 0.00 40.11 4.16 R
2245 4078 0.316204 CCGACAGTAAAGTCACGGGT 59.684 55.000 0.00 0.00 38.43 5.28 R
2246 4079 0.316204 ACCGACAGTAAAGTCACGGG 59.684 55.000 0.00 0.00 43.76 5.28 R
2644 4490 1.146263 GGAATTCGAGCGGTCCCAT 59.854 57.895 9.39 0.00 0.00 4.00 R
2751 4600 8.503486 CTTGAAACTTCATCTGTCAATTCAAG 57.497 34.615 9.63 9.63 43.17 3.02 R
3168 5019 0.905357 ATCCACTGTGTAGGACCTGC 59.095 55.000 3.53 2.72 36.60 4.85 R
4192 6056 0.103572 ACGGTTCGTAATATGCGGCT 59.896 50.000 0.00 0.00 38.73 5.52 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
71 72 9.788960 GACTAAAATCATCCATACCAAAACTTC 57.211 33.333 0.00 0.00 0.00 3.01
76 77 5.579047 TCATCCATACCAAAACTTCCATGT 58.421 37.500 0.00 0.00 0.00 3.21
83 84 3.573967 ACCAAAACTTCCATGTCATGACC 59.426 43.478 22.85 5.91 0.00 4.02
90 91 1.066215 TCCATGTCATGACCAGAACCG 60.066 52.381 22.85 3.96 0.00 4.44
94 95 0.320771 GTCATGACCAGAACCGCACT 60.321 55.000 15.31 0.00 0.00 4.40
136 137 6.038603 GCCATCAGCAGTGATACTTTTATGAA 59.961 38.462 0.00 0.00 41.85 2.57
170 1982 2.526304 TAGTTCGCTTTGTGCTCACT 57.474 45.000 1.47 0.00 40.11 3.41
219 2031 2.093235 CCCTGCTGCTCCTTATATAGCC 60.093 54.545 0.00 0.00 37.97 3.93
279 2091 1.686325 TAATCTCCACTGCGCCCTCC 61.686 60.000 4.18 0.00 0.00 4.30
343 2155 1.003355 CCCGTGACAGCTCCACAAT 60.003 57.895 14.10 0.00 34.36 2.71
352 2164 2.308570 ACAGCTCCACAATTATGGACCA 59.691 45.455 0.00 0.00 44.14 4.02
354 2166 2.092212 AGCTCCACAATTATGGACCAGG 60.092 50.000 0.00 0.00 44.14 4.45
356 2168 1.064017 TCCACAATTATGGACCAGGCC 60.064 52.381 0.00 0.00 44.14 5.19
357 2169 1.402787 CACAATTATGGACCAGGCCC 58.597 55.000 0.00 0.00 0.00 5.80
358 2170 0.106719 ACAATTATGGACCAGGCCCG 60.107 55.000 0.00 0.00 0.00 6.13
359 2171 0.106719 CAATTATGGACCAGGCCCGT 60.107 55.000 0.00 0.00 0.00 5.28
360 2172 0.106719 AATTATGGACCAGGCCCGTG 60.107 55.000 0.00 0.00 0.00 4.94
361 2173 1.994885 ATTATGGACCAGGCCCGTGG 61.995 60.000 9.48 9.48 44.01 4.94
389 2210 3.382015 GCTTCTTCGCTAAAGCAGAAG 57.618 47.619 19.97 19.97 45.92 2.85
403 2224 1.195115 CAGAAGTAGCCCAGTGCCTA 58.805 55.000 0.00 0.00 42.71 3.93
418 2241 0.817654 GCCTATGTGCCCACCTTTTC 59.182 55.000 0.00 0.00 0.00 2.29
421 2244 3.165071 CCTATGTGCCCACCTTTTCTTT 58.835 45.455 0.00 0.00 0.00 2.52
458 2281 3.459232 ACTGCCTCCTTTTCTTTTTGC 57.541 42.857 0.00 0.00 0.00 3.68
459 2282 2.223805 ACTGCCTCCTTTTCTTTTTGCG 60.224 45.455 0.00 0.00 0.00 4.85
492 2315 6.013725 ACTTCCTATTTTTAGGGGCTTTTTGG 60.014 38.462 0.00 0.00 37.81 3.28
519 2342 1.536766 CTGCTTGCCAACAATCGAAGA 59.463 47.619 0.00 0.00 45.75 2.87
521 2344 2.030893 TGCTTGCCAACAATCGAAGAAG 60.031 45.455 0.00 0.00 43.58 2.85
531 2354 2.832672 ATCGAAGAAGATTTTGCGCC 57.167 45.000 4.18 0.00 43.58 6.53
532 2355 1.518325 TCGAAGAAGATTTTGCGCCA 58.482 45.000 4.18 0.00 0.00 5.69
533 2356 2.083774 TCGAAGAAGATTTTGCGCCAT 58.916 42.857 4.18 0.00 0.00 4.40
534 2357 2.159531 TCGAAGAAGATTTTGCGCCATG 60.160 45.455 4.18 0.00 0.00 3.66
535 2358 1.922545 GAAGAAGATTTTGCGCCATGC 59.077 47.619 4.18 0.00 46.70 4.06
544 2367 2.570181 GCGCCATGCAAGAGCTTT 59.430 55.556 0.00 0.00 45.45 3.51
546 2369 1.878070 CGCCATGCAAGAGCTTTCA 59.122 52.632 0.00 0.00 42.74 2.69
561 2384 3.582208 AGCTTTCAAAATACCAATGGCCA 59.418 39.130 8.56 8.56 0.00 5.36
562 2385 4.225717 AGCTTTCAAAATACCAATGGCCAT 59.774 37.500 14.09 14.09 0.00 4.40
563 2386 4.571984 GCTTTCAAAATACCAATGGCCATC 59.428 41.667 21.08 0.00 0.00 3.51
564 2387 5.732633 CTTTCAAAATACCAATGGCCATCA 58.267 37.500 21.08 5.17 0.00 3.07
565 2388 5.752036 TTCAAAATACCAATGGCCATCAA 57.248 34.783 21.08 5.16 0.00 2.57
566 2389 5.954153 TCAAAATACCAATGGCCATCAAT 57.046 34.783 21.08 9.76 0.00 2.57
567 2390 5.916318 TCAAAATACCAATGGCCATCAATC 58.084 37.500 21.08 0.00 0.00 2.67
568 2391 5.424573 TCAAAATACCAATGGCCATCAATCA 59.575 36.000 21.08 3.99 0.00 2.57
569 2392 4.942761 AATACCAATGGCCATCAATCAC 57.057 40.909 21.08 0.00 0.00 3.06
570 2393 2.234896 ACCAATGGCCATCAATCACA 57.765 45.000 21.08 0.00 0.00 3.58
571 2394 2.754465 ACCAATGGCCATCAATCACAT 58.246 42.857 21.08 0.00 0.00 3.21
572 2395 2.696707 ACCAATGGCCATCAATCACATC 59.303 45.455 21.08 0.00 0.00 3.06
573 2396 2.696187 CCAATGGCCATCAATCACATCA 59.304 45.455 21.08 0.00 0.00 3.07
574 2397 3.133183 CCAATGGCCATCAATCACATCAA 59.867 43.478 21.08 0.00 0.00 2.57
575 2398 4.383226 CCAATGGCCATCAATCACATCAAA 60.383 41.667 21.08 0.00 0.00 2.69
576 2399 5.364778 CAATGGCCATCAATCACATCAAAT 58.635 37.500 21.08 0.00 0.00 2.32
577 2400 4.659111 TGGCCATCAATCACATCAAATC 57.341 40.909 0.00 0.00 0.00 2.17
578 2401 4.024670 TGGCCATCAATCACATCAAATCA 58.975 39.130 0.00 0.00 0.00 2.57
579 2402 4.466726 TGGCCATCAATCACATCAAATCAA 59.533 37.500 0.00 0.00 0.00 2.57
580 2403 5.046520 TGGCCATCAATCACATCAAATCAAA 60.047 36.000 0.00 0.00 0.00 2.69
581 2404 6.053005 GGCCATCAATCACATCAAATCAAAT 58.947 36.000 0.00 0.00 0.00 2.32
582 2405 6.202188 GGCCATCAATCACATCAAATCAAATC 59.798 38.462 0.00 0.00 0.00 2.17
583 2406 6.759356 GCCATCAATCACATCAAATCAAATCA 59.241 34.615 0.00 0.00 0.00 2.57
584 2407 7.441157 GCCATCAATCACATCAAATCAAATCAT 59.559 33.333 0.00 0.00 0.00 2.45
585 2408 9.974980 CCATCAATCACATCAAATCAAATCATA 57.025 29.630 0.00 0.00 0.00 2.15
589 2412 9.797556 CAATCACATCAAATCAAATCATACAGT 57.202 29.630 0.00 0.00 0.00 3.55
627 2450 1.816074 TTTATCTTGTGGGTGCGACC 58.184 50.000 0.00 0.00 37.60 4.79
629 2452 2.845752 TATCTTGTGGGTGCGACCGC 62.846 60.000 7.53 7.53 39.83 5.68
643 2466 1.737696 CGACCGCAAGTATGGCACTAA 60.738 52.381 0.00 0.00 30.95 2.24
644 2467 2.561569 GACCGCAAGTATGGCACTAAT 58.438 47.619 0.00 0.00 30.95 1.73
663 2486 8.349983 GCACTAATAGAAGACCAAAAAGACAAA 58.650 33.333 0.00 0.00 0.00 2.83
720 2543 9.257651 AGTAGCGTGAATACAAAATTATACTCC 57.742 33.333 0.00 0.00 0.00 3.85
721 2544 7.492352 AGCGTGAATACAAAATTATACTCCC 57.508 36.000 0.00 0.00 0.00 4.30
722 2545 7.280356 AGCGTGAATACAAAATTATACTCCCT 58.720 34.615 0.00 0.00 0.00 4.20
723 2546 7.441458 AGCGTGAATACAAAATTATACTCCCTC 59.559 37.037 0.00 0.00 0.00 4.30
724 2547 7.307811 GCGTGAATACAAAATTATACTCCCTCC 60.308 40.741 0.00 0.00 0.00 4.30
725 2548 7.095774 CGTGAATACAAAATTATACTCCCTCCG 60.096 40.741 0.00 0.00 0.00 4.63
726 2549 7.713942 GTGAATACAAAATTATACTCCCTCCGT 59.286 37.037 0.00 0.00 0.00 4.69
727 2550 8.269317 TGAATACAAAATTATACTCCCTCCGTT 58.731 33.333 0.00 0.00 0.00 4.44
728 2551 9.117183 GAATACAAAATTATACTCCCTCCGTTT 57.883 33.333 0.00 0.00 0.00 3.60
729 2552 6.753107 ACAAAATTATACTCCCTCCGTTTG 57.247 37.500 0.00 0.00 0.00 2.93
730 2553 6.478129 ACAAAATTATACTCCCTCCGTTTGA 58.522 36.000 0.00 0.00 0.00 2.69
731 2554 6.943718 ACAAAATTATACTCCCTCCGTTTGAA 59.056 34.615 0.00 0.00 0.00 2.69
732 2555 7.449086 ACAAAATTATACTCCCTCCGTTTGAAA 59.551 33.333 0.00 0.00 0.00 2.69
733 2556 8.466798 CAAAATTATACTCCCTCCGTTTGAAAT 58.533 33.333 0.00 0.00 0.00 2.17
734 2557 8.589701 AAATTATACTCCCTCCGTTTGAAATT 57.410 30.769 0.00 0.00 0.00 1.82
735 2558 9.689501 AAATTATACTCCCTCCGTTTGAAATTA 57.310 29.630 0.00 0.00 0.00 1.40
736 2559 8.672823 ATTATACTCCCTCCGTTTGAAATTAC 57.327 34.615 0.00 0.00 0.00 1.89
737 2560 4.635699 ACTCCCTCCGTTTGAAATTACT 57.364 40.909 0.00 0.00 0.00 2.24
738 2561 4.981812 ACTCCCTCCGTTTGAAATTACTT 58.018 39.130 0.00 0.00 0.00 2.24
739 2562 4.760204 ACTCCCTCCGTTTGAAATTACTTG 59.240 41.667 0.00 0.00 0.00 3.16
740 2563 4.721132 TCCCTCCGTTTGAAATTACTTGT 58.279 39.130 0.00 0.00 0.00 3.16
741 2564 5.134661 TCCCTCCGTTTGAAATTACTTGTT 58.865 37.500 0.00 0.00 0.00 2.83
742 2565 6.297582 TCCCTCCGTTTGAAATTACTTGTTA 58.702 36.000 0.00 0.00 0.00 2.41
743 2566 6.205270 TCCCTCCGTTTGAAATTACTTGTTAC 59.795 38.462 0.00 0.00 0.00 2.50
744 2567 6.016943 CCCTCCGTTTGAAATTACTTGTTACA 60.017 38.462 0.00 0.00 0.00 2.41
745 2568 7.419204 CCTCCGTTTGAAATTACTTGTTACAA 58.581 34.615 0.00 0.00 0.00 2.41
746 2569 7.916450 CCTCCGTTTGAAATTACTTGTTACAAA 59.084 33.333 0.00 0.00 0.00 2.83
747 2570 9.291664 CTCCGTTTGAAATTACTTGTTACAAAA 57.708 29.630 0.00 0.00 0.00 2.44
748 2571 9.635520 TCCGTTTGAAATTACTTGTTACAAAAA 57.364 25.926 0.00 0.00 0.00 1.94
820 2643 9.884636 TTCATTTCTTAGATGAGTAATTCCGAA 57.115 29.630 0.00 0.00 35.17 4.30
821 2644 9.314321 TCATTTCTTAGATGAGTAATTCCGAAC 57.686 33.333 0.00 0.00 0.00 3.95
822 2645 7.751047 TTTCTTAGATGAGTAATTCCGAACG 57.249 36.000 0.00 0.00 0.00 3.95
823 2646 5.828747 TCTTAGATGAGTAATTCCGAACGG 58.171 41.667 6.94 6.94 0.00 4.44
824 2647 5.591472 TCTTAGATGAGTAATTCCGAACGGA 59.409 40.000 12.04 12.04 43.52 4.69
825 2648 4.308899 AGATGAGTAATTCCGAACGGAG 57.691 45.455 15.34 0.00 46.06 4.63
826 2649 2.953466 TGAGTAATTCCGAACGGAGG 57.047 50.000 15.34 0.00 46.06 4.30
827 2650 1.479323 TGAGTAATTCCGAACGGAGGG 59.521 52.381 15.34 0.00 46.06 4.30
828 2651 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
829 2652 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
830 2653 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
831 2654 1.856629 AATTCCGAACGGAGGGAGTA 58.143 50.000 15.34 1.05 46.06 2.59
832 2655 1.400737 ATTCCGAACGGAGGGAGTAG 58.599 55.000 15.34 0.00 46.06 2.57
833 2656 0.682209 TTCCGAACGGAGGGAGTAGG 60.682 60.000 15.34 0.00 46.06 3.18
834 2657 1.379576 CCGAACGGAGGGAGTAGGT 60.380 63.158 7.53 0.00 37.50 3.08
845 2668 4.141459 GGAGGGAGTAGGTAGAAAAATGGG 60.141 50.000 0.00 0.00 0.00 4.00
874 2697 1.613836 AGGAAGCCAAGACAAAGCAG 58.386 50.000 0.00 0.00 0.00 4.24
875 2698 0.600057 GGAAGCCAAGACAAAGCAGG 59.400 55.000 0.00 0.00 0.00 4.85
891 2714 0.673437 CAGGCATGGAAACCGTGTTT 59.327 50.000 10.96 2.23 42.15 2.83
893 2716 1.339929 AGGCATGGAAACCGTGTTTTC 59.660 47.619 10.96 2.94 42.15 2.29
894 2717 1.339929 GGCATGGAAACCGTGTTTTCT 59.660 47.619 10.96 0.00 42.15 2.52
895 2718 2.607038 GGCATGGAAACCGTGTTTTCTC 60.607 50.000 10.96 2.47 42.15 2.87
927 2751 3.306225 GCAGCATGGAAAATGAGTTGGAA 60.306 43.478 0.00 0.00 35.86 3.53
1029 2854 3.786048 CGCATCGTTAGAAAATTTCCAGC 59.214 43.478 1.57 0.00 0.00 4.85
1211 3036 3.402681 CTGGCCGTGATCCCCACT 61.403 66.667 0.00 0.00 43.53 4.00
1428 3253 2.353030 GTCGCCCAACACGTTTGC 60.353 61.111 0.00 0.00 0.00 3.68
1429 3254 2.515057 TCGCCCAACACGTTTGCT 60.515 55.556 0.00 0.00 0.00 3.91
1457 3282 5.796935 CGTGAAATTCAGATTTGTGCTTAGG 59.203 40.000 0.00 0.00 35.65 2.69
1458 3283 6.568462 CGTGAAATTCAGATTTGTGCTTAGGT 60.568 38.462 0.00 0.00 35.65 3.08
1459 3284 6.583806 GTGAAATTCAGATTTGTGCTTAGGTG 59.416 38.462 0.00 0.00 35.65 4.00
1567 3393 3.924073 GGTGCGATTTCCCATTTTTGTAC 59.076 43.478 0.00 0.00 0.00 2.90
1589 3415 9.074576 TGTACATATCTTTAAGCTCCGATCTTA 57.925 33.333 0.00 0.00 0.00 2.10
1610 3436 7.922382 TCTTAGTGGGATTTCTCTGATTTCTT 58.078 34.615 0.00 0.00 0.00 2.52
1640 3466 9.213777 AGGATGTTTCATTATTAGAGTGTAGGA 57.786 33.333 0.00 0.00 0.00 2.94
1641 3467 9.482627 GGATGTTTCATTATTAGAGTGTAGGAG 57.517 37.037 0.00 0.00 0.00 3.69
1654 3480 7.956328 AGAGTGTAGGAGTATTTGTATGTGA 57.044 36.000 0.00 0.00 0.00 3.58
1662 3488 6.879458 AGGAGTATTTGTATGTGAAACCTGTC 59.121 38.462 0.00 0.00 34.36 3.51
1684 3510 6.150976 TGTCAATTTTGATTAGAAGCGTGGAT 59.849 34.615 0.00 0.00 39.73 3.41
1704 3531 7.359264 CGTGGATTTTTAGACTTGTAGTGTCTG 60.359 40.741 6.65 0.00 43.66 3.51
1713 3540 7.820578 AGACTTGTAGTGTCTGTTTAGTAGT 57.179 36.000 0.00 0.00 42.46 2.73
1714 3541 8.915057 AGACTTGTAGTGTCTGTTTAGTAGTA 57.085 34.615 0.00 0.00 42.46 1.82
1724 3551 8.355913 GTGTCTGTTTAGTAGTACAAACCTAGT 58.644 37.037 17.87 0.00 34.44 2.57
1733 3560 6.952938 AGTAGTACAAACCTAGTCTAAAGCCT 59.047 38.462 2.52 0.00 0.00 4.58
1748 3575 7.173390 AGTCTAAAGCCTTGTCATGTTAGTTTC 59.827 37.037 0.00 0.00 0.00 2.78
1754 3581 6.040842 AGCCTTGTCATGTTAGTTTCATTTGT 59.959 34.615 0.00 0.00 0.00 2.83
1767 3594 9.959749 TTAGTTTCATTTGTCTGTTTATGGTTC 57.040 29.630 0.00 0.00 0.00 3.62
1794 3621 2.318908 GGCTTCCAATGCCCATGATTA 58.681 47.619 0.00 0.00 44.32 1.75
1807 3635 3.313012 CATGATTATTGGCCATGGCAG 57.687 47.619 36.56 9.80 44.11 4.85
1858 3687 8.036575 TCATGAAATTGGATGGAATTTGTCTTC 58.963 33.333 0.00 0.00 36.00 2.87
1860 3689 6.497954 TGAAATTGGATGGAATTTGTCTTCCT 59.502 34.615 4.63 0.00 44.27 3.36
1862 3691 8.613922 AAATTGGATGGAATTTGTCTTCCTAT 57.386 30.769 4.63 0.00 44.27 2.57
1873 3702 2.568956 TGTCTTCCTATTGCTGACTGCT 59.431 45.455 5.87 0.00 43.37 4.24
1883 3712 1.072806 TGCTGACTGCTCTTCCACAAT 59.927 47.619 5.87 0.00 43.37 2.71
1887 3716 4.500375 GCTGACTGCTCTTCCACAATTTTT 60.500 41.667 0.00 0.00 38.95 1.94
1910 3739 5.339008 TGTGAGTTTTAGTGTCACTCTGT 57.661 39.130 9.26 0.00 41.06 3.41
1916 3745 5.817816 AGTTTTAGTGTCACTCTGTTGGAAG 59.182 40.000 9.26 0.00 0.00 3.46
1950 3782 5.181690 TGTTTGACTTATCAAGGTTGCAC 57.818 39.130 0.00 0.00 45.54 4.57
1955 3787 5.069318 TGACTTATCAAGGTTGCACAATGA 58.931 37.500 0.00 0.00 0.00 2.57
1968 3800 4.439968 TGCACAATGAAAATTTCACAGCA 58.560 34.783 10.91 14.45 43.48 4.41
2219 4052 4.010349 AGCTACTAAACCAGATTTGTGGC 58.990 43.478 3.38 3.38 41.90 5.01
2249 4082 7.064728 TGGTTCAAAAGAATTAAAACAAACCCG 59.935 33.333 0.00 0.00 33.21 5.28
2250 4083 7.064847 GGTTCAAAAGAATTAAAACAAACCCGT 59.935 33.333 0.00 0.00 0.00 5.28
2251 4084 7.527084 TCAAAAGAATTAAAACAAACCCGTG 57.473 32.000 0.00 0.00 0.00 4.94
2252 4085 7.321153 TCAAAAGAATTAAAACAAACCCGTGA 58.679 30.769 0.00 0.00 0.00 4.35
2273 4117 5.464389 GTGACTTTACTGTCGGTTACACAAT 59.536 40.000 0.00 0.00 39.64 2.71
2348 4192 7.433680 GGGAATGCTAATTACCATTAACTTGG 58.566 38.462 6.08 0.00 45.27 3.61
2418 4264 7.520614 GCTTGCTAGTTGACAAATTACTGAAGT 60.521 37.037 0.00 0.00 0.00 3.01
2560 4406 1.404035 GTTTCGGTTGTGCTGGTCTTT 59.596 47.619 0.00 0.00 0.00 2.52
2592 4438 6.503524 ACAAGTAACATTACCTGCAAAACTG 58.496 36.000 1.13 0.00 34.19 3.16
2644 4490 7.928167 AGATCGTGATGTAGATGCAGAAAATAA 59.072 33.333 0.00 0.00 0.00 1.40
2659 4505 2.930826 AATAATGGGACCGCTCGAAT 57.069 45.000 0.00 0.00 0.00 3.34
2696 4542 2.760092 TGCTGCTCAACCTCAAAAGTTT 59.240 40.909 0.00 0.00 0.00 2.66
2741 4590 6.265577 AGTTTGTGTCTTTTCCTTGATTTCG 58.734 36.000 0.00 0.00 0.00 3.46
2871 4720 8.073355 ACTCTTACTGTTGAACAACTAAATCG 57.927 34.615 16.70 5.11 41.67 3.34
3168 5019 1.135315 CCTCAACGCCGCTCATTTG 59.865 57.895 0.00 0.00 0.00 2.32
3200 5051 2.242043 CAGTGGATTATCAATGGGGGC 58.758 52.381 0.00 0.00 0.00 5.80
3214 5065 1.635487 TGGGGGCCTGCTATATTCATC 59.365 52.381 0.84 0.00 0.00 2.92
3487 5342 8.044908 GGTTCACCAGTATTTATAACCTCTCAA 58.955 37.037 0.00 0.00 33.67 3.02
3600 5461 2.945008 TGGAACAGAGCACAAAGACTTG 59.055 45.455 0.00 0.00 38.61 3.16
3698 5559 3.074412 CAAGCTGGTTTAGTTCATCGGT 58.926 45.455 0.00 0.00 0.00 4.69
3709 5570 4.294416 AGTTCATCGGTATGTCTCTTCG 57.706 45.455 0.00 0.00 34.50 3.79
3758 5619 4.017126 GGGTAATAATTCCTATGCCAGGC 58.983 47.826 3.66 3.66 45.10 4.85
3767 5628 1.410648 CCTATGCCAGGCCATCTGTTT 60.411 52.381 9.64 0.00 41.83 2.83
3798 5659 2.413765 CGTGTATCGTTGGAGTTCTCGT 60.414 50.000 0.00 0.00 34.52 4.18
3854 5715 2.957474 AGGCCATTGTAGTTTTGGTGT 58.043 42.857 5.01 0.00 32.90 4.16
4008 5871 1.662517 TGAAGCTCGTTTTCAGCACA 58.337 45.000 0.00 0.00 39.56 4.57
4013 5876 2.028112 AGCTCGTTTTCAGCACATCCTA 60.028 45.455 0.00 0.00 39.56 2.94
4058 5922 1.665679 CAGATTCGTTAAGGCGTGCAT 59.334 47.619 0.00 0.00 0.00 3.96
4173 6037 8.660968 GAAAAAGTCGAAATGTTTCCTCTATG 57.339 34.615 4.01 0.00 33.68 2.23
4174 6038 6.743575 AAAGTCGAAATGTTTCCTCTATGG 57.256 37.500 0.00 0.00 33.68 2.74
4175 6039 4.192317 AGTCGAAATGTTTCCTCTATGGC 58.808 43.478 0.00 0.00 33.68 4.40
4176 6040 4.080863 AGTCGAAATGTTTCCTCTATGGCT 60.081 41.667 0.00 0.00 33.68 4.75
4177 6041 4.271291 GTCGAAATGTTTCCTCTATGGCTC 59.729 45.833 0.00 0.00 33.68 4.70
4178 6042 4.162320 TCGAAATGTTTCCTCTATGGCTCT 59.838 41.667 0.25 0.00 33.68 4.09
4179 6043 5.362717 TCGAAATGTTTCCTCTATGGCTCTA 59.637 40.000 0.25 0.00 33.68 2.43
4192 6056 8.043113 CCTCTATGGCTCTATACATTATGCAAA 58.957 37.037 0.00 0.00 0.00 3.68
4193 6057 9.096160 CTCTATGGCTCTATACATTATGCAAAG 57.904 37.037 0.00 0.00 0.00 2.77
4207 6071 2.010497 TGCAAAGCCGCATATTACGAA 58.990 42.857 0.00 0.00 36.86 3.85
4210 6074 1.214367 AAGCCGCATATTACGAACCG 58.786 50.000 0.00 0.00 0.00 4.44
4214 6078 1.784856 CCGCATATTACGAACCGTGAG 59.215 52.381 1.93 0.00 41.39 3.51
4354 6266 8.789825 TTGTGTTTGTTAGTTTCCAGTAGTTA 57.210 30.769 0.00 0.00 0.00 2.24
4408 6320 3.083349 TATCAGCTGGCCGTGGCT 61.083 61.111 15.13 11.17 41.60 4.75
4424 6336 1.213296 GGCTGATTACTGGAAGGGGA 58.787 55.000 0.00 0.00 39.30 4.81
4465 6377 0.749454 CAGCTACTGCATGGGTTCCC 60.749 60.000 0.12 0.12 42.74 3.97
4638 6553 2.738521 GTTCGAGGAAGCAGCGCA 60.739 61.111 11.47 0.00 0.00 6.09
4831 6746 2.266055 CACTTCGTCAGGGCCTCC 59.734 66.667 0.95 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.356426 TCATAATATCCGGGTATCAATGCG 58.644 41.667 18.75 3.70 0.00 4.73
1 2 7.807977 ATTCATAATATCCGGGTATCAATGC 57.192 36.000 18.75 0.00 0.00 3.56
57 58 5.418524 TCATGACATGGAAGTTTTGGTATGG 59.581 40.000 15.37 0.00 0.00 2.74
71 72 1.372582 CGGTTCTGGTCATGACATGG 58.627 55.000 26.47 15.20 0.00 3.66
76 77 0.396435 AAGTGCGGTTCTGGTCATGA 59.604 50.000 0.00 0.00 0.00 3.07
133 134 7.000575 CGAACTATTCTTTCGCCTTTATTCA 57.999 36.000 0.00 0.00 39.43 2.57
203 2015 3.704061 GAGGGAGGCTATATAAGGAGCAG 59.296 52.174 6.89 0.00 40.64 4.24
257 2069 0.750850 GGGCGCAGTGGAGATTAGTA 59.249 55.000 10.83 0.00 0.00 1.82
343 2155 2.675242 CCACGGGCCTGGTCCATAA 61.675 63.158 19.08 0.00 0.00 1.90
359 2171 7.397238 CTTTAGCGAAGAAGCTCTCTAGCCA 62.397 48.000 15.57 6.54 45.67 4.75
360 2172 5.026947 CTTTAGCGAAGAAGCTCTCTAGCC 61.027 50.000 15.57 4.29 45.67 3.93
361 2173 3.701532 TTAGCGAAGAAGCTCTCTAGC 57.298 47.619 13.30 13.30 45.67 3.42
372 2193 3.512680 GCTACTTCTGCTTTAGCGAAGA 58.487 45.455 27.07 12.87 45.39 2.87
403 2224 3.070015 CAGAAAAGAAAAGGTGGGCACAT 59.930 43.478 0.00 0.00 0.00 3.21
433 2256 3.372440 AAGAAAAGGAGGCAGTATGGG 57.628 47.619 0.00 0.00 35.86 4.00
434 2257 5.473039 CAAAAAGAAAAGGAGGCAGTATGG 58.527 41.667 0.00 0.00 35.86 2.74
435 2258 4.925646 GCAAAAAGAAAAGGAGGCAGTATG 59.074 41.667 0.00 0.00 40.87 2.39
474 2297 4.656100 ATGCCAAAAAGCCCCTAAAAAT 57.344 36.364 0.00 0.00 0.00 1.82
506 2329 4.321745 CGCAAAATCTTCTTCGATTGTTGG 59.678 41.667 0.00 0.00 34.07 3.77
531 2354 5.472148 TGGTATTTTGAAAGCTCTTGCATG 58.528 37.500 0.00 0.00 42.74 4.06
532 2355 5.726980 TGGTATTTTGAAAGCTCTTGCAT 57.273 34.783 0.00 0.00 42.74 3.96
533 2356 5.528043 TTGGTATTTTGAAAGCTCTTGCA 57.472 34.783 0.00 0.00 42.74 4.08
534 2357 5.349543 CCATTGGTATTTTGAAAGCTCTTGC 59.650 40.000 0.00 0.00 40.05 4.01
535 2358 5.349543 GCCATTGGTATTTTGAAAGCTCTTG 59.650 40.000 4.26 0.00 0.00 3.02
544 2367 5.424573 TGATTGATGGCCATTGGTATTTTGA 59.575 36.000 21.84 0.00 0.00 2.69
546 2369 5.189342 TGTGATTGATGGCCATTGGTATTTT 59.811 36.000 21.84 0.00 0.00 1.82
563 2386 9.797556 ACTGTATGATTTGATTTGATGTGATTG 57.202 29.630 0.00 0.00 0.00 2.67
565 2388 9.404848 AGACTGTATGATTTGATTTGATGTGAT 57.595 29.630 0.00 0.00 0.00 3.06
566 2389 8.797350 AGACTGTATGATTTGATTTGATGTGA 57.203 30.769 0.00 0.00 0.00 3.58
567 2390 9.850628 AAAGACTGTATGATTTGATTTGATGTG 57.149 29.630 0.00 0.00 0.00 3.21
569 2392 9.512435 GGAAAGACTGTATGATTTGATTTGATG 57.488 33.333 0.00 0.00 0.00 3.07
570 2393 9.471702 AGGAAAGACTGTATGATTTGATTTGAT 57.528 29.630 0.00 0.00 0.00 2.57
571 2394 8.868522 AGGAAAGACTGTATGATTTGATTTGA 57.131 30.769 0.00 0.00 0.00 2.69
572 2395 9.994432 GTAGGAAAGACTGTATGATTTGATTTG 57.006 33.333 0.00 0.00 0.00 2.32
573 2396 9.178758 GGTAGGAAAGACTGTATGATTTGATTT 57.821 33.333 0.00 0.00 0.00 2.17
574 2397 8.328758 TGGTAGGAAAGACTGTATGATTTGATT 58.671 33.333 0.00 0.00 0.00 2.57
575 2398 7.861629 TGGTAGGAAAGACTGTATGATTTGAT 58.138 34.615 0.00 0.00 0.00 2.57
576 2399 7.252612 TGGTAGGAAAGACTGTATGATTTGA 57.747 36.000 0.00 0.00 0.00 2.69
577 2400 7.148239 GGTTGGTAGGAAAGACTGTATGATTTG 60.148 40.741 0.00 0.00 0.00 2.32
578 2401 6.884836 GGTTGGTAGGAAAGACTGTATGATTT 59.115 38.462 0.00 0.00 0.00 2.17
579 2402 6.415573 GGTTGGTAGGAAAGACTGTATGATT 58.584 40.000 0.00 0.00 0.00 2.57
580 2403 5.104485 GGGTTGGTAGGAAAGACTGTATGAT 60.104 44.000 0.00 0.00 0.00 2.45
581 2404 4.224370 GGGTTGGTAGGAAAGACTGTATGA 59.776 45.833 0.00 0.00 0.00 2.15
582 2405 4.225267 AGGGTTGGTAGGAAAGACTGTATG 59.775 45.833 0.00 0.00 0.00 2.39
583 2406 4.436079 AGGGTTGGTAGGAAAGACTGTAT 58.564 43.478 0.00 0.00 0.00 2.29
584 2407 3.865571 AGGGTTGGTAGGAAAGACTGTA 58.134 45.455 0.00 0.00 0.00 2.74
585 2408 2.702748 AGGGTTGGTAGGAAAGACTGT 58.297 47.619 0.00 0.00 0.00 3.55
586 2409 3.790089 AAGGGTTGGTAGGAAAGACTG 57.210 47.619 0.00 0.00 0.00 3.51
587 2410 6.464530 AAATAAGGGTTGGTAGGAAAGACT 57.535 37.500 0.00 0.00 0.00 3.24
588 2411 8.272889 AGATAAATAAGGGTTGGTAGGAAAGAC 58.727 37.037 0.00 0.00 0.00 3.01
589 2412 8.401955 AGATAAATAAGGGTTGGTAGGAAAGA 57.598 34.615 0.00 0.00 0.00 2.52
590 2413 8.903820 CAAGATAAATAAGGGTTGGTAGGAAAG 58.096 37.037 0.00 0.00 0.00 2.62
627 2450 5.175856 GTCTTCTATTAGTGCCATACTTGCG 59.824 44.000 0.00 0.00 40.89 4.85
629 2452 6.582636 TGGTCTTCTATTAGTGCCATACTTG 58.417 40.000 0.00 0.00 40.89 3.16
631 2454 6.808321 TTGGTCTTCTATTAGTGCCATACT 57.192 37.500 0.00 0.00 43.56 2.12
632 2455 7.859325 TTTTGGTCTTCTATTAGTGCCATAC 57.141 36.000 0.00 0.00 0.00 2.39
637 2460 7.435068 TGTCTTTTTGGTCTTCTATTAGTGC 57.565 36.000 0.00 0.00 0.00 4.40
714 2537 6.309389 AGTAATTTCAAACGGAGGGAGTAT 57.691 37.500 0.00 0.00 0.00 2.12
717 2540 4.760204 ACAAGTAATTTCAAACGGAGGGAG 59.240 41.667 0.00 0.00 0.00 4.30
718 2541 4.721132 ACAAGTAATTTCAAACGGAGGGA 58.279 39.130 0.00 0.00 0.00 4.20
719 2542 5.447624 AACAAGTAATTTCAAACGGAGGG 57.552 39.130 0.00 0.00 0.00 4.30
720 2543 6.961576 TGTAACAAGTAATTTCAAACGGAGG 58.038 36.000 0.00 0.00 0.00 4.30
721 2544 8.844441 TTTGTAACAAGTAATTTCAAACGGAG 57.156 30.769 0.00 0.00 0.00 4.63
722 2545 9.635520 TTTTTGTAACAAGTAATTTCAAACGGA 57.364 25.926 0.00 0.00 29.46 4.69
794 2617 9.884636 TTCGGAATTACTCATCTAAGAAATGAA 57.115 29.630 0.00 0.00 32.96 2.57
795 2618 9.314321 GTTCGGAATTACTCATCTAAGAAATGA 57.686 33.333 0.00 0.00 0.00 2.57
796 2619 8.269424 CGTTCGGAATTACTCATCTAAGAAATG 58.731 37.037 0.00 0.00 0.00 2.32
797 2620 7.438459 CCGTTCGGAATTACTCATCTAAGAAAT 59.562 37.037 5.19 0.00 0.00 2.17
798 2621 6.755141 CCGTTCGGAATTACTCATCTAAGAAA 59.245 38.462 5.19 0.00 0.00 2.52
799 2622 6.095860 TCCGTTCGGAATTACTCATCTAAGAA 59.904 38.462 11.66 0.00 0.00 2.52
800 2623 5.591472 TCCGTTCGGAATTACTCATCTAAGA 59.409 40.000 11.66 0.00 0.00 2.10
801 2624 5.828747 TCCGTTCGGAATTACTCATCTAAG 58.171 41.667 11.66 0.00 0.00 2.18
802 2625 5.221185 CCTCCGTTCGGAATTACTCATCTAA 60.221 44.000 14.79 0.00 33.41 2.10
803 2626 4.277672 CCTCCGTTCGGAATTACTCATCTA 59.722 45.833 14.79 0.00 33.41 1.98
804 2627 3.068307 CCTCCGTTCGGAATTACTCATCT 59.932 47.826 14.79 0.00 33.41 2.90
805 2628 3.381949 CCTCCGTTCGGAATTACTCATC 58.618 50.000 14.79 0.00 33.41 2.92
806 2629 2.102588 CCCTCCGTTCGGAATTACTCAT 59.897 50.000 14.79 0.00 33.41 2.90
807 2630 1.479323 CCCTCCGTTCGGAATTACTCA 59.521 52.381 14.79 0.00 33.41 3.41
808 2631 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
809 2632 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
810 2633 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
811 2634 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
812 2635 1.755380 CTACTCCCTCCGTTCGGAATT 59.245 52.381 14.79 0.00 33.41 2.17
813 2636 1.400737 CTACTCCCTCCGTTCGGAAT 58.599 55.000 14.79 2.09 33.41 3.01
814 2637 0.682209 CCTACTCCCTCCGTTCGGAA 60.682 60.000 14.79 0.04 33.41 4.30
815 2638 1.077212 CCTACTCCCTCCGTTCGGA 60.077 63.158 13.34 13.34 0.00 4.55
816 2639 0.107017 TACCTACTCCCTCCGTTCGG 60.107 60.000 4.74 4.74 0.00 4.30
817 2640 1.134280 TCTACCTACTCCCTCCGTTCG 60.134 57.143 0.00 0.00 0.00 3.95
818 2641 2.725221 TCTACCTACTCCCTCCGTTC 57.275 55.000 0.00 0.00 0.00 3.95
819 2642 3.463048 TTTCTACCTACTCCCTCCGTT 57.537 47.619 0.00 0.00 0.00 4.44
820 2643 3.463048 TTTTCTACCTACTCCCTCCGT 57.537 47.619 0.00 0.00 0.00 4.69
821 2644 4.443034 CCATTTTTCTACCTACTCCCTCCG 60.443 50.000 0.00 0.00 0.00 4.63
822 2645 4.141459 CCCATTTTTCTACCTACTCCCTCC 60.141 50.000 0.00 0.00 0.00 4.30
823 2646 4.686396 GCCCATTTTTCTACCTACTCCCTC 60.686 50.000 0.00 0.00 0.00 4.30
824 2647 3.202373 GCCCATTTTTCTACCTACTCCCT 59.798 47.826 0.00 0.00 0.00 4.20
825 2648 3.053917 TGCCCATTTTTCTACCTACTCCC 60.054 47.826 0.00 0.00 0.00 4.30
826 2649 4.230745 TGCCCATTTTTCTACCTACTCC 57.769 45.455 0.00 0.00 0.00 3.85
827 2650 6.433093 TCTTTTGCCCATTTTTCTACCTACTC 59.567 38.462 0.00 0.00 0.00 2.59
828 2651 6.311735 TCTTTTGCCCATTTTTCTACCTACT 58.688 36.000 0.00 0.00 0.00 2.57
829 2652 6.584185 TCTTTTGCCCATTTTTCTACCTAC 57.416 37.500 0.00 0.00 0.00 3.18
830 2653 7.604657 TTTCTTTTGCCCATTTTTCTACCTA 57.395 32.000 0.00 0.00 0.00 3.08
831 2654 6.493189 TTTCTTTTGCCCATTTTTCTACCT 57.507 33.333 0.00 0.00 0.00 3.08
832 2655 6.204688 CCTTTTCTTTTGCCCATTTTTCTACC 59.795 38.462 0.00 0.00 0.00 3.18
833 2656 6.989759 TCCTTTTCTTTTGCCCATTTTTCTAC 59.010 34.615 0.00 0.00 0.00 2.59
834 2657 7.130681 TCCTTTTCTTTTGCCCATTTTTCTA 57.869 32.000 0.00 0.00 0.00 2.10
845 2668 3.804325 GTCTTGGCTTCCTTTTCTTTTGC 59.196 43.478 0.00 0.00 0.00 3.68
874 2697 1.339929 AGAAAACACGGTTTCCATGCC 59.660 47.619 3.96 0.00 38.10 4.40
875 2698 2.293399 AGAGAAAACACGGTTTCCATGC 59.707 45.455 3.96 0.00 38.10 4.06
894 2717 3.023939 TCCATGCTGCTCTCTCTAAGA 57.976 47.619 0.00 0.00 0.00 2.10
895 2718 3.815856 TTCCATGCTGCTCTCTCTAAG 57.184 47.619 0.00 0.00 0.00 2.18
927 2751 2.093447 GGCAGCTGTATACTGTTGGAGT 60.093 50.000 22.02 0.00 37.47 3.85
993 2817 2.753452 ACGATGCGTTCTCTCCTTCTAA 59.247 45.455 0.00 0.00 36.35 2.10
995 2819 1.178276 ACGATGCGTTCTCTCCTTCT 58.822 50.000 0.00 0.00 36.35 2.85
1211 3036 2.675423 AGCTGCTCGTACGGGTCA 60.675 61.111 17.95 13.91 0.00 4.02
1238 3063 0.816825 CCATGGAGGTGATCTTGCGG 60.817 60.000 5.56 0.00 0.00 5.69
1417 3242 2.353376 CGGGCAGCAAACGTGTTG 60.353 61.111 0.00 0.00 38.88 3.33
1418 3243 2.826738 ACGGGCAGCAAACGTGTT 60.827 55.556 8.04 0.00 39.64 3.32
1428 3253 3.057315 ACAAATCTGAATTTCACGGGCAG 60.057 43.478 0.00 0.00 32.69 4.85
1429 3254 2.890311 ACAAATCTGAATTTCACGGGCA 59.110 40.909 0.00 0.00 32.69 5.36
1457 3282 0.110056 CTGCAATCAAGCACGACCAC 60.110 55.000 0.00 0.00 40.11 4.16
1458 3283 1.236616 CCTGCAATCAAGCACGACCA 61.237 55.000 0.00 0.00 40.11 4.02
1459 3284 1.503542 CCTGCAATCAAGCACGACC 59.496 57.895 0.00 0.00 40.11 4.79
1567 3393 7.543868 CCACTAAGATCGGAGCTTAAAGATATG 59.456 40.741 15.71 6.04 0.00 1.78
1576 3402 2.160721 TCCCACTAAGATCGGAGCTT 57.839 50.000 13.56 13.56 0.00 3.74
1589 3415 7.264294 AGTAAGAAATCAGAGAAATCCCACT 57.736 36.000 0.00 0.00 0.00 4.00
1638 3464 6.653320 TGACAGGTTTCACATACAAATACTCC 59.347 38.462 0.00 0.00 0.00 3.85
1639 3465 7.667043 TGACAGGTTTCACATACAAATACTC 57.333 36.000 0.00 0.00 0.00 2.59
1640 3466 8.635765 ATTGACAGGTTTCACATACAAATACT 57.364 30.769 0.00 0.00 0.00 2.12
1641 3467 9.691362 AAATTGACAGGTTTCACATACAAATAC 57.309 29.630 0.00 0.00 0.00 1.89
1643 3469 9.044150 CAAAATTGACAGGTTTCACATACAAAT 57.956 29.630 0.00 0.00 0.00 2.32
1649 3475 8.859090 TCTAATCAAAATTGACAGGTTTCACAT 58.141 29.630 0.00 0.00 40.49 3.21
1654 3480 6.863126 CGCTTCTAATCAAAATTGACAGGTTT 59.137 34.615 0.00 0.00 40.49 3.27
1662 3488 7.816945 AAATCCACGCTTCTAATCAAAATTG 57.183 32.000 0.00 0.00 0.00 2.32
1684 3510 9.880157 ACTAAACAGACACTACAAGTCTAAAAA 57.120 29.630 0.00 0.00 44.11 1.94
1712 3539 6.228995 ACAAGGCTTTAGACTAGGTTTGTAC 58.771 40.000 0.00 0.00 29.55 2.90
1713 3540 6.042322 TGACAAGGCTTTAGACTAGGTTTGTA 59.958 38.462 0.00 0.00 29.55 2.41
1714 3541 5.163237 TGACAAGGCTTTAGACTAGGTTTGT 60.163 40.000 0.00 0.00 29.55 2.83
1724 3551 6.995686 TGAAACTAACATGACAAGGCTTTAGA 59.004 34.615 0.00 0.00 0.00 2.10
1733 3560 7.995289 ACAGACAAATGAAACTAACATGACAA 58.005 30.769 0.00 0.00 0.00 3.18
1748 3575 7.539710 CACATCAGAACCATAAACAGACAAATG 59.460 37.037 0.00 0.00 0.00 2.32
1754 3581 4.009675 GCCACATCAGAACCATAAACAGA 58.990 43.478 0.00 0.00 0.00 3.41
1794 3621 1.380785 CACCTCTGCCATGGCCAAT 60.381 57.895 33.44 12.05 41.09 3.16
1806 3634 1.249407 GAGTGTTCGACTCCACCTCT 58.751 55.000 5.66 0.00 44.95 3.69
1807 3635 3.796667 GAGTGTTCGACTCCACCTC 57.203 57.895 5.66 0.00 44.95 3.85
1887 3716 5.730550 ACAGAGTGACACTAAAACTCACAA 58.269 37.500 8.41 0.00 42.28 3.33
1910 3739 5.186021 TCAAACAAAAGCTGTAACCTTCCAA 59.814 36.000 0.00 0.00 37.23 3.53
1916 3745 7.422399 TGATAAGTCAAACAAAAGCTGTAACC 58.578 34.615 0.00 0.00 37.23 2.85
1950 3782 8.024146 TGATTGATGCTGTGAAATTTTCATTG 57.976 30.769 14.54 11.23 42.47 2.82
1955 3787 5.790593 AGCTGATTGATGCTGTGAAATTTT 58.209 33.333 0.00 0.00 38.21 1.82
2245 4078 0.316204 CCGACAGTAAAGTCACGGGT 59.684 55.000 0.00 0.00 38.43 5.28
2246 4079 0.316204 ACCGACAGTAAAGTCACGGG 59.684 55.000 0.00 0.00 43.76 5.28
2247 4080 2.144482 AACCGACAGTAAAGTCACGG 57.856 50.000 0.00 0.00 44.77 4.94
2249 4082 4.362279 TGTGTAACCGACAGTAAAGTCAC 58.638 43.478 0.00 0.00 39.29 3.67
2250 4083 4.652421 TGTGTAACCGACAGTAAAGTCA 57.348 40.909 0.00 0.00 39.29 3.41
2251 4084 6.423001 AGAATTGTGTAACCGACAGTAAAGTC 59.577 38.462 0.00 0.00 39.29 3.01
2252 4085 6.202188 CAGAATTGTGTAACCGACAGTAAAGT 59.798 38.462 0.00 0.00 39.29 2.66
2418 4264 5.335740 CCTCTAACTGCGAAGAACAGAAGTA 60.336 44.000 0.00 0.00 38.55 2.24
2423 4269 1.996191 GCCTCTAACTGCGAAGAACAG 59.004 52.381 0.00 0.00 41.08 3.16
2468 4314 8.213518 TCACCAATAAATTATCTTCACTCAGC 57.786 34.615 0.00 0.00 0.00 4.26
2560 4406 6.373216 GCAGGTAATGTTACTTGTCACCAATA 59.627 38.462 14.07 0.00 41.27 1.90
2592 4438 3.047796 CTGTTTCTGACAATTGCTGTGC 58.952 45.455 5.05 0.00 38.84 4.57
2644 4490 1.146263 GGAATTCGAGCGGTCCCAT 59.854 57.895 9.39 0.00 0.00 4.00
2696 4542 9.405587 CAAACTTTGTCTAAACAGAAGTTTTCA 57.594 29.630 18.24 0.00 45.32 2.69
2751 4600 8.503486 CTTGAAACTTCATCTGTCAATTCAAG 57.497 34.615 9.63 9.63 43.17 3.02
2900 4751 6.538742 TGAATACTTCCATAGTAAGCAACTGC 59.461 38.462 2.21 0.00 42.45 4.40
3168 5019 0.905357 ATCCACTGTGTAGGACCTGC 59.095 55.000 3.53 2.72 36.60 4.85
3200 5051 6.805016 ACTATCCCAGATGAATATAGCAGG 57.195 41.667 0.00 0.00 0.00 4.85
3460 5314 7.181305 TGAGAGGTTATAAATACTGGTGAACCA 59.819 37.037 1.48 1.48 45.30 3.67
3529 5390 7.770897 GGTGTCCTGTAGAAATTGATCAAGTAT 59.229 37.037 14.54 6.54 0.00 2.12
3698 5559 4.201753 CGTCGTTTAGACCGAAGAGACATA 60.202 45.833 0.00 0.00 46.92 2.29
3709 5570 2.947448 ATGGTACCGTCGTTTAGACC 57.053 50.000 7.57 0.00 46.92 3.85
3758 5619 2.005451 CGCTCTCTTGGAAACAGATGG 58.995 52.381 0.00 0.00 44.54 3.51
3767 5628 1.460504 ACGATACACGCTCTCTTGGA 58.539 50.000 0.00 0.00 46.94 3.53
3814 5675 4.754114 GCCTATGCACAGATTTCTAAGGAG 59.246 45.833 0.00 0.00 37.47 3.69
3854 5715 3.949586 TCATGTTATTGAGGATGGCCA 57.050 42.857 8.56 8.56 36.29 5.36
4008 5871 4.965532 AGTGTGCAGTAGGAAAGATAGGAT 59.034 41.667 0.00 0.00 0.00 3.24
4013 5876 3.580458 ACTGAGTGTGCAGTAGGAAAGAT 59.420 43.478 0.00 0.00 46.67 2.40
4035 5898 1.463056 CACGCCTTAACGAATCTGCAA 59.537 47.619 0.00 0.00 36.70 4.08
4161 6025 7.618019 AATGTATAGAGCCATAGAGGAAACA 57.382 36.000 0.00 0.00 41.22 2.83
4172 6036 4.761739 GGCTTTGCATAATGTATAGAGCCA 59.238 41.667 5.73 0.00 44.88 4.75
4173 6037 4.142816 CGGCTTTGCATAATGTATAGAGCC 60.143 45.833 0.00 0.00 42.74 4.70
4174 6038 4.670221 GCGGCTTTGCATAATGTATAGAGC 60.670 45.833 0.00 0.00 34.15 4.09
4175 6039 4.452114 TGCGGCTTTGCATAATGTATAGAG 59.548 41.667 0.00 0.00 40.62 2.43
4176 6040 4.384940 TGCGGCTTTGCATAATGTATAGA 58.615 39.130 0.00 0.00 40.62 1.98
4177 6041 4.747540 TGCGGCTTTGCATAATGTATAG 57.252 40.909 0.00 0.00 40.62 1.31
4192 6056 0.103572 ACGGTTCGTAATATGCGGCT 59.896 50.000 0.00 0.00 38.73 5.52
4193 6057 0.231279 CACGGTTCGTAATATGCGGC 59.769 55.000 0.00 0.00 38.32 6.53
4204 6068 0.239347 AACGGTCTACTCACGGTTCG 59.761 55.000 0.00 0.00 35.53 3.95
4207 6071 1.035139 AACAACGGTCTACTCACGGT 58.965 50.000 0.00 0.00 0.00 4.83
4210 6074 2.521105 ACCAACAACGGTCTACTCAC 57.479 50.000 0.00 0.00 32.11 3.51
4354 6266 3.276857 CTGCATGTCAGCAACCTAAGAT 58.723 45.455 4.55 0.00 45.13 2.40
4408 6320 1.213296 GCCTCCCCTTCCAGTAATCA 58.787 55.000 0.00 0.00 0.00 2.57
4475 6387 1.005748 CAGCGACTGTCAGCTCCAA 60.006 57.895 19.18 0.00 42.52 3.53
4481 6393 1.445754 CAGGAGCAGCGACTGTCAG 60.446 63.158 8.73 0.00 33.43 3.51
4638 6553 2.048127 GCTTGTCCTCGAACGCCT 60.048 61.111 0.00 0.00 0.00 5.52
4838 6753 1.716826 GAGTACAGCTCCTCGACGGG 61.717 65.000 0.00 0.00 38.27 5.28
4850 6765 2.202623 GCAGACCGCGGAGTACAG 60.203 66.667 35.90 16.85 0.00 2.74


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

AutoCloner maintained by Alex Coulton.