Multiple sequence alignment - TraesCS3B01G425500

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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 TraesCS3B01G425500 chr3B 100.000 7645 0 0 1 7645 663183191 663190835 0.000000e+00 14118.0
1 TraesCS3B01G425500 chr3B 92.857 42 3 0 380 421 778332143 778332102 2.300000e-05 62.1
2 TraesCS3B01G425500 chr3A 94.984 6698 257 41 431 7092 641403292 641409946 0.000000e+00 10434.0
3 TraesCS3B01G425500 chr3A 78.755 273 38 14 122 383 641403038 641403301 1.710000e-36 165.0
4 TraesCS3B01G425500 chr3A 85.816 141 17 3 1 140 641402886 641403024 6.180000e-31 147.0
5 TraesCS3B01G425500 chr3D 94.439 4010 158 23 3569 7566 502052321 502056277 0.000000e+00 6109.0
6 TraesCS3B01G425500 chr3D 95.361 2910 103 16 676 3564 502049361 502052259 0.000000e+00 4597.0
7 TraesCS3B01G425500 chr3D 84.652 417 24 10 1 383 502048654 502049064 5.600000e-101 379.0
8 TraesCS3B01G425500 chr3D 94.323 229 6 3 435 663 502049061 502049282 2.040000e-90 344.0
9 TraesCS3B01G425500 chr3D 93.684 95 6 0 7551 7645 502062221 502062315 8.000000e-30 143.0
10 TraesCS3B01G425500 chr6D 95.652 46 2 0 380 425 1488614 1488659 2.960000e-09 75.0
11 TraesCS3B01G425500 chr6D 91.304 46 4 0 380 425 453351501 453351456 6.400000e-06 63.9
12 TraesCS3B01G425500 chr4A 95.652 46 2 0 380 425 710717443 710717488 2.960000e-09 75.0
13 TraesCS3B01G425500 chr2D 95.652 46 2 0 380 425 81298282 81298237 2.960000e-09 75.0
14 TraesCS3B01G425500 chr1B 97.619 42 1 0 214 255 645348131 645348172 1.060000e-08 73.1
15 TraesCS3B01G425500 chr1B 89.362 47 1 3 212 256 26131686 26131642 1.000000e-03 56.5
16 TraesCS3B01G425500 chr7B 97.500 40 1 0 386 425 255523732 255523771 1.380000e-07 69.4
17 TraesCS3B01G425500 chr5A 93.478 46 3 0 380 425 661052157 661052112 1.380000e-07 69.4
18 TraesCS3B01G425500 chr5A 91.111 45 4 0 212 256 632274690 632274646 2.300000e-05 62.1
19 TraesCS3B01G425500 chr6B 91.304 46 4 0 380 425 421540493 421540538 6.400000e-06 63.9
20 TraesCS3B01G425500 chr1D 91.304 46 4 0 380 425 377806785 377806740 6.400000e-06 63.9
21 TraesCS3B01G425500 chr5D 94.595 37 2 0 216 252 199080930 199080894 2.980000e-04 58.4


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 TraesCS3B01G425500 chr3B 663183191 663190835 7644 False 14118.00 14118 100.000000 1 7645 1 chr3B.!!$F1 7644
1 TraesCS3B01G425500 chr3A 641402886 641409946 7060 False 3582.00 10434 86.518333 1 7092 3 chr3A.!!$F1 7091
2 TraesCS3B01G425500 chr3D 502048654 502056277 7623 False 2857.25 6109 92.193750 1 7566 4 chr3D.!!$F2 7565

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
296 393 0.594110 GAGGCTCGACTTATCTCCGG 59.406 60.000 0.00 0.00 0.00 5.14 F
1400 1581 0.106419 TGGCCTCCGGTTCTTGTTTT 60.106 50.000 3.32 0.00 0.00 2.43 F
1587 1768 0.321671 TGAACCAGCCACTACTGCTC 59.678 55.000 0.00 0.00 36.81 4.26 F
1668 1849 0.327924 TCACATTCCGGTGGCTGAAT 59.672 50.000 0.00 0.00 39.27 2.57 F
2885 3073 0.459489 GGCAATGGCTGGCGAAATAA 59.541 50.000 0.00 0.00 41.35 1.40 F
3109 3297 0.550914 GGTCAAGGGCATATGTCCCA 59.449 55.000 26.96 10.96 46.36 4.37 F
3118 3306 1.134280 GCATATGTCCCACAGAGTGCT 60.134 52.381 4.29 0.00 33.65 4.40 F
4553 4799 1.235724 GGTGAGCCAACAACTGTACC 58.764 55.000 0.00 0.00 34.09 3.34 F
5879 6126 2.134201 GCAAAAGGCGCTTTAGTGTT 57.866 45.000 4.75 0.00 31.99 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2206 0.108585 TGGCCCTTGTCAGTGTTCTC 59.891 55.000 0.00 0.00 0.00 2.87 R
2856 3044 0.112995 AGCCATTGCCAAGTCCTTCA 59.887 50.000 0.00 0.00 38.69 3.02 R
3352 3540 0.325933 CATCCACAGCACTGAAGGGA 59.674 55.000 4.31 8.52 35.01 4.20 R
3494 3683 4.328536 TGGTTATGTTTCACGCCTTATGT 58.671 39.130 0.00 0.00 0.00 2.29 R
4138 4384 0.686789 TCCCTATGACATGGCCATCG 59.313 55.000 17.61 14.17 0.00 3.84 R
4216 4462 1.878522 GCCGTATGCAGAGGTGACG 60.879 63.158 0.00 0.00 40.77 4.35 R
5085 5331 4.283722 AGGTTGAAGAGGAAGTTGATACGT 59.716 41.667 0.00 0.00 0.00 3.57 R
6349 6597 0.695924 TGTCAATCACGGTGGGGATT 59.304 50.000 8.50 0.00 34.19 3.01 R
7535 7795 0.030235 GTGTTGCCCGTTTCCACTTC 59.970 55.000 0.00 0.00 0.00 3.01 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
95 96 1.031571 GCCGTGCCCAGATTTGATCA 61.032 55.000 0.00 0.00 0.00 2.92
98 99 1.262417 CGTGCCCAGATTTGATCATCG 59.738 52.381 0.00 0.00 0.00 3.84
193 238 7.706281 TCGATATTTGCTTCTTCATCTTCTC 57.294 36.000 0.00 0.00 0.00 2.87
205 250 3.555966 TCATCTTCTCCGCTGATACTCA 58.444 45.455 0.00 0.00 0.00 3.41
210 255 2.566913 TCTCCGCTGATACTCACTCTC 58.433 52.381 0.00 0.00 0.00 3.20
212 257 2.017782 TCCGCTGATACTCACTCTCAC 58.982 52.381 0.00 0.00 0.00 3.51
257 353 4.399483 TTCCTTACAGAGGGAGTACAGT 57.601 45.455 0.00 0.00 46.31 3.55
262 358 5.357596 CCTTACAGAGGGAGTACAGTAGTTC 59.642 48.000 0.00 0.00 42.26 3.01
296 393 0.594110 GAGGCTCGACTTATCTCCGG 59.406 60.000 0.00 0.00 0.00 5.14
298 395 1.734137 GCTCGACTTATCTCCGGCA 59.266 57.895 0.00 0.00 0.00 5.69
335 432 8.328758 TGTTTATTATATAGGGCCATCTTCCTG 58.671 37.037 6.18 0.00 34.75 3.86
336 433 4.844349 TTATATAGGGCCATCTTCCTGC 57.156 45.455 6.18 0.00 34.75 4.85
337 434 2.116869 TATAGGGCCATCTTCCTGCA 57.883 50.000 6.18 0.00 34.75 4.41
338 435 1.453633 ATAGGGCCATCTTCCTGCAT 58.546 50.000 6.18 0.00 34.75 3.96
363 460 2.335316 AACACAAAGGGCACGTTAGA 57.665 45.000 0.00 0.00 34.32 2.10
395 492 6.925211 CAGGATGTTACTCACTCTGTAAAGA 58.075 40.000 0.00 0.00 32.58 2.52
396 493 7.378966 CAGGATGTTACTCACTCTGTAAAGAA 58.621 38.462 0.00 0.00 32.58 2.52
397 494 7.872993 CAGGATGTTACTCACTCTGTAAAGAAA 59.127 37.037 0.00 0.00 32.58 2.52
398 495 8.598041 AGGATGTTACTCACTCTGTAAAGAAAT 58.402 33.333 0.00 0.00 32.58 2.17
399 496 9.871238 GGATGTTACTCACTCTGTAAAGAAATA 57.129 33.333 0.00 0.00 32.58 1.40
430 527 8.478877 AGTGTTTAGATCACTACTTTATGGAGG 58.521 37.037 0.00 0.00 43.17 4.30
431 528 7.711339 GTGTTTAGATCACTACTTTATGGAGGG 59.289 40.741 0.00 0.00 33.59 4.30
432 529 7.622081 TGTTTAGATCACTACTTTATGGAGGGA 59.378 37.037 0.00 0.00 0.00 4.20
433 530 7.841282 TTAGATCACTACTTTATGGAGGGAG 57.159 40.000 0.00 0.00 0.00 4.30
434 531 5.782925 AGATCACTACTTTATGGAGGGAGT 58.217 41.667 0.00 0.00 0.00 3.85
514 611 2.039818 AGATTAGCTGAGACCGACGA 57.960 50.000 0.00 0.00 0.00 4.20
515 612 1.671845 AGATTAGCTGAGACCGACGAC 59.328 52.381 0.00 0.00 0.00 4.34
528 625 1.472552 CCGACGACCATATGCTTTGGA 60.473 52.381 0.00 0.00 37.69 3.53
592 689 1.202313 CGACCAGCTCTAGTTGCCTAC 60.202 57.143 6.82 0.00 0.00 3.18
610 707 3.502211 CCTACTTGGTGCATCTTTCGTTT 59.498 43.478 0.00 0.00 0.00 3.60
611 708 4.693566 CCTACTTGGTGCATCTTTCGTTTA 59.306 41.667 0.00 0.00 0.00 2.01
612 709 5.354234 CCTACTTGGTGCATCTTTCGTTTAT 59.646 40.000 0.00 0.00 0.00 1.40
614 711 4.156008 ACTTGGTGCATCTTTCGTTTATCC 59.844 41.667 0.00 0.00 0.00 2.59
615 712 2.675844 TGGTGCATCTTTCGTTTATCCG 59.324 45.455 0.00 0.00 0.00 4.18
616 713 2.031683 GGTGCATCTTTCGTTTATCCGG 59.968 50.000 0.00 0.00 0.00 5.14
617 714 2.933906 GTGCATCTTTCGTTTATCCGGA 59.066 45.455 6.61 6.61 0.00 5.14
618 715 2.933906 TGCATCTTTCGTTTATCCGGAC 59.066 45.455 6.12 0.00 0.00 4.79
619 716 2.933906 GCATCTTTCGTTTATCCGGACA 59.066 45.455 6.12 0.00 0.00 4.02
637 734 3.589988 GACAGACACTGATACCAACCTG 58.410 50.000 5.76 0.00 35.18 4.00
663 762 2.094675 TCCTGCTTATGCCAAAAGAGC 58.905 47.619 0.00 0.00 38.71 4.09
705 870 2.354422 CACGCATGCCGCAAAACA 60.354 55.556 13.15 0.00 42.60 2.83
779 949 1.588404 CAGTAAACACTAGCATCGCCG 59.412 52.381 0.00 0.00 0.00 6.46
790 960 1.072666 GCATCGCCGCTTGAAAAAGG 61.073 55.000 0.00 0.00 0.00 3.11
823 997 1.529010 GATGCCATTGCCGATCCCA 60.529 57.895 0.00 0.00 36.33 4.37
828 1002 1.819305 GCCATTGCCGATCCCAAGTAT 60.819 52.381 0.00 0.00 0.00 2.12
908 1082 2.363361 CCGTCCCCTCCCACTACT 59.637 66.667 0.00 0.00 0.00 2.57
976 1152 2.752354 TCAATGTAACAGGCCAATTCGG 59.248 45.455 5.01 0.00 38.11 4.30
989 1165 1.545582 CAATTCGGTGCCATCTTGGTT 59.454 47.619 0.00 0.00 40.46 3.67
990 1166 1.463674 ATTCGGTGCCATCTTGGTTC 58.536 50.000 0.00 0.00 40.46 3.62
1019 1197 3.028850 CCATGCCACCTTCTCATGATTT 58.971 45.455 0.00 0.00 39.80 2.17
1026 1204 3.128242 CACCTTCTCATGATTTCCAGCAC 59.872 47.826 0.00 0.00 0.00 4.40
1036 1214 2.786512 TTTCCAGCACCCCATGGAGC 62.787 60.000 15.22 14.33 46.01 4.70
1107 1285 0.250901 TTTGGACCCTTGCAGAGCTC 60.251 55.000 5.27 5.27 0.00 4.09
1232 1413 1.129251 CAATGCTTCGATCACGCTGTT 59.871 47.619 0.00 0.00 39.58 3.16
1233 1414 0.723414 ATGCTTCGATCACGCTGTTG 59.277 50.000 0.00 0.00 39.58 3.33
1239 1420 3.363341 TCGATCACGCTGTTGCATATA 57.637 42.857 0.00 0.00 39.64 0.86
1243 1424 0.588252 CACGCTGTTGCATATAGGGC 59.412 55.000 8.64 0.00 39.64 5.19
1258 1439 2.593956 GGGCTCTCGGTTCTTGGGT 61.594 63.158 0.00 0.00 0.00 4.51
1259 1440 1.376037 GGCTCTCGGTTCTTGGGTG 60.376 63.158 0.00 0.00 0.00 4.61
1260 1441 1.371558 GCTCTCGGTTCTTGGGTGT 59.628 57.895 0.00 0.00 0.00 4.16
1273 1454 2.494530 GGGTGTTGGAAGCGGCAAA 61.495 57.895 1.45 0.00 0.00 3.68
1276 1457 1.754621 TGTTGGAAGCGGCAAACCA 60.755 52.632 1.45 5.73 34.57 3.67
1329 1510 2.027653 GTGGCTTCTGGCTACTCTCTTT 60.028 50.000 0.00 0.00 46.77 2.52
1344 1525 3.919216 TCTCTTTCTGCTCTACTGCAAC 58.081 45.455 0.00 0.00 42.83 4.17
1351 1532 3.076621 CTGCTCTACTGCAACCATGAAA 58.923 45.455 0.00 0.00 42.83 2.69
1374 1555 1.269998 GCTGCAGGGGTAGTAGTATCG 59.730 57.143 17.12 0.00 0.00 2.92
1400 1581 0.106419 TGGCCTCCGGTTCTTGTTTT 60.106 50.000 3.32 0.00 0.00 2.43
1437 1618 3.800604 GCTTCTTATCGGAATCGCTCCTT 60.801 47.826 2.40 0.00 42.85 3.36
1570 1751 2.645838 AGCAAACCAGAAAGAGCTGA 57.354 45.000 0.00 0.00 38.14 4.26
1587 1768 0.321671 TGAACCAGCCACTACTGCTC 59.678 55.000 0.00 0.00 36.81 4.26
1623 1804 1.127567 ACAGCAGCAGGGACAGGTTA 61.128 55.000 0.00 0.00 0.00 2.85
1668 1849 0.327924 TCACATTCCGGTGGCTGAAT 59.672 50.000 0.00 0.00 39.27 2.57
1931 2119 6.992123 TGTCCTGGCAATCTATTAATACAGTG 59.008 38.462 7.40 2.08 0.00 3.66
2018 2206 0.736053 GGTGGAGCTACTCTCTGACG 59.264 60.000 0.00 0.00 41.60 4.35
2113 2301 1.219124 CTCACAGCGGCAGTGGTAT 59.781 57.895 22.77 0.00 37.58 2.73
2200 2388 0.976641 TGCTGATGAAGAACTCGGGT 59.023 50.000 0.00 0.00 0.00 5.28
2422 2610 1.730446 GCAAATTCGCAGCAGAACCTC 60.730 52.381 0.00 0.00 32.39 3.85
2559 2747 2.290514 TGAAGCTCAGGGATGTGGAAAG 60.291 50.000 0.00 0.00 0.00 2.62
2569 2757 1.739608 ATGTGGAAAGGGGGTGGCTT 61.740 55.000 0.00 0.00 0.00 4.35
2647 2835 2.613595 GTTGGTTTCGGTCGTTACCTTT 59.386 45.455 13.99 0.00 44.35 3.11
2827 3015 5.576563 TCAAAGAAGATCACCAGGGTAAA 57.423 39.130 0.00 0.00 0.00 2.01
2885 3073 0.459489 GGCAATGGCTGGCGAAATAA 59.541 50.000 0.00 0.00 41.35 1.40
2995 3183 0.955919 GGAAGGGTCTCAAGGTTGCG 60.956 60.000 0.00 0.00 0.00 4.85
3091 3279 0.944386 CAGAACCAACAGTTGTCGGG 59.056 55.000 12.42 0.00 39.40 5.14
3109 3297 0.550914 GGTCAAGGGCATATGTCCCA 59.449 55.000 26.96 10.96 46.36 4.37
3118 3306 1.134280 GCATATGTCCCACAGAGTGCT 60.134 52.381 4.29 0.00 33.65 4.40
3325 3513 4.743018 GCCAGGGCATTGTACAGT 57.257 55.556 5.20 0.00 41.49 3.55
3352 3540 9.118300 GATTCTGATGTTTACTTCTTGGATGAT 57.882 33.333 0.00 0.00 0.00 2.45
3413 3602 6.015688 TCTCTTCAAGGTACGTAAACATGAGT 60.016 38.462 0.00 0.00 0.00 3.41
3414 3603 5.924254 TCTTCAAGGTACGTAAACATGAGTG 59.076 40.000 0.00 0.82 0.00 3.51
3470 3659 2.358267 GCTTCATGAGATTCAAGGGCAG 59.642 50.000 0.00 0.00 0.00 4.85
3494 3683 6.432783 AGTTACTGCAATTTACATGCCTACAA 59.567 34.615 0.00 0.00 43.16 2.41
3526 3715 6.639279 GCGTGAAACATAACCAAACAAGTAAT 59.361 34.615 0.00 0.00 35.74 1.89
3527 3716 7.804129 GCGTGAAACATAACCAAACAAGTAATA 59.196 33.333 0.00 0.00 35.74 0.98
3528 3717 9.666626 CGTGAAACATAACCAAACAAGTAATAA 57.333 29.630 0.00 0.00 35.74 1.40
3535 3724 9.959749 CATAACCAAACAAGTAATAAACACACT 57.040 29.630 0.00 0.00 0.00 3.55
3597 3843 6.412362 AGCAAGAGTATTTCCATCGAGTAT 57.588 37.500 0.00 0.00 0.00 2.12
3648 3894 8.777865 ACTTCGAGAAAATGAATCAACTGATA 57.222 30.769 0.00 0.00 33.73 2.15
3732 3978 2.200067 CATCAGCTAGAGTTCTTGCGG 58.800 52.381 9.33 9.05 46.62 5.69
3790 4036 8.842280 CCAGTTTCCACACATAACTAGTTTTTA 58.158 33.333 14.49 0.00 31.30 1.52
3829 4075 6.613755 TTTTGTGCAGTTTAGACTAGGTTC 57.386 37.500 0.00 0.00 33.90 3.62
3839 4085 8.242053 CAGTTTAGACTAGGTTCGAACAGAATA 58.758 37.037 28.24 14.22 36.47 1.75
4138 4384 4.429854 AGAGGCCACAGAAATAGAATCC 57.570 45.455 5.01 0.00 0.00 3.01
4216 4462 2.156098 TGGGATGTTTACCGCAAGTTC 58.844 47.619 0.00 0.00 0.00 3.01
4271 4517 3.010420 GTGGTTCTTCTATGCCAAGTCC 58.990 50.000 0.00 0.00 32.26 3.85
4553 4799 1.235724 GGTGAGCCAACAACTGTACC 58.764 55.000 0.00 0.00 34.09 3.34
4588 4834 6.596497 GGGAAATTGTACAAAATACTCTCCGA 59.404 38.462 13.23 0.00 0.00 4.55
4649 4895 2.294233 GCTTCAACAGATCAAGCCACAA 59.706 45.455 3.87 0.00 37.20 3.33
4856 5102 8.752766 TCAAAATGCACACTAGTAAGTAGTAC 57.247 34.615 0.00 0.00 40.27 2.73
4860 5106 8.585471 AATGCACACTAGTAAGTAGTACCTTA 57.415 34.615 0.00 0.00 40.27 2.69
4999 5245 7.623999 ATTAGATGCTTTAATCAGGGAGAGA 57.376 36.000 0.00 0.00 0.00 3.10
5049 5295 4.530710 TGATGACTATACCCGCATTACC 57.469 45.455 0.00 0.00 0.00 2.85
5085 5331 3.809279 CGACAGTTGAATGGCTATGCATA 59.191 43.478 6.20 6.20 0.00 3.14
5136 5382 6.310467 TGTTTTTCGTGATGCTAGTCATACTC 59.690 38.462 0.00 0.00 35.05 2.59
5224 5470 4.250464 CACGAACTGTATTTTCTAGGGCA 58.750 43.478 0.00 0.00 0.00 5.36
5225 5471 4.876107 CACGAACTGTATTTTCTAGGGCAT 59.124 41.667 0.00 0.00 0.00 4.40
5240 5486 8.650143 TTCTAGGGCATTTTTAGAGTCAAAAT 57.350 30.769 0.00 0.00 34.75 1.82
5313 5560 9.101655 ACAACAAATCATTTTTCTTTCTCCTTG 57.898 29.630 0.00 0.00 0.00 3.61
5458 5705 5.400066 TCTCAAACATACCGAGTGAATCA 57.600 39.130 0.00 0.00 0.00 2.57
5698 5945 4.218635 TCTGCAGGACGGATATTCATAGAC 59.781 45.833 15.13 0.00 0.00 2.59
5743 5990 3.924238 GCATGATTTGCGGTGTAGG 57.076 52.632 0.00 0.00 42.54 3.18
5879 6126 2.134201 GCAAAAGGCGCTTTAGTGTT 57.866 45.000 4.75 0.00 31.99 3.32
5948 6195 3.430042 ACCTGTTCATGAATCAGCAGT 57.570 42.857 22.35 16.42 0.00 4.40
6149 6397 6.404293 GCCCTGTTACATGGTTGTAGTTTATG 60.404 42.308 8.38 0.00 39.43 1.90
6277 6525 5.212494 GCTACAGCATCAGTTGATACTGCA 61.212 45.833 18.03 8.19 45.43 4.41
6349 6597 6.667370 CACAGTTATTACAATTGCACACAGA 58.333 36.000 5.05 0.00 0.00 3.41
6390 6638 2.606308 GCGACCTTGTTCTTGTACTCGA 60.606 50.000 0.00 0.00 0.00 4.04
6413 6662 6.541111 AAGAAGGTAAAGAACACTAAAGCG 57.459 37.500 0.00 0.00 0.00 4.68
6427 6676 4.321745 CACTAAAGCGCTTGCAGTATTTTG 59.678 41.667 27.72 16.51 42.66 2.44
6428 6677 2.352503 AAGCGCTTGCAGTATTTTGG 57.647 45.000 24.40 0.00 42.66 3.28
6439 6688 7.519649 GCTTGCAGTATTTTGGTTTTTGCATAA 60.520 33.333 0.00 0.00 39.49 1.90
6632 6881 2.124695 GAGGGCCGACATCAACCC 60.125 66.667 0.00 0.00 43.17 4.11
6711 6960 5.358725 TGTGTACATATAAGCTCTGACGGAA 59.641 40.000 0.00 0.00 0.00 4.30
6729 6978 7.450074 TGACGGAATATAAGGAAATACAGCAT 58.550 34.615 0.00 0.00 0.00 3.79
6730 6979 7.387673 TGACGGAATATAAGGAAATACAGCATG 59.612 37.037 0.00 0.00 46.00 4.06
6808 7057 6.986817 GCATATGGACACTTGAACTACTGTAT 59.013 38.462 4.56 0.00 0.00 2.29
6904 7154 7.545362 AAGTGATGTTAGATGTATGCAACTC 57.455 36.000 0.00 0.00 0.00 3.01
6913 7163 8.604890 GTTAGATGTATGCAACTCCTTTTCTAC 58.395 37.037 0.00 0.00 0.00 2.59
6925 7175 6.133356 ACTCCTTTTCTACCAACCATTGAAA 58.867 36.000 0.00 0.00 0.00 2.69
6933 7183 9.581289 TTTCTACCAACCATTGAAAAGAGAATA 57.419 29.630 0.00 0.00 0.00 1.75
7019 7269 5.124138 ACATTTCGAGAGAGACATTCTACGT 59.876 40.000 0.00 0.00 43.69 3.57
7166 7416 1.658596 GCATGCAATCGACAGAACGTA 59.341 47.619 14.21 0.00 34.70 3.57
7535 7795 4.762809 CTGTTTTCGTTTCTTTCTCTCCG 58.237 43.478 0.00 0.00 0.00 4.63
7559 7819 0.874175 GGAAACGGGCAACACAAAGC 60.874 55.000 0.00 0.00 39.74 3.51
7566 7826 2.412525 CAACACAAAGCTGCGGCA 59.587 55.556 21.93 1.29 41.70 5.69
7567 7827 1.659335 CAACACAAAGCTGCGGCAG 60.659 57.895 25.21 25.21 41.70 4.85
7568 7828 1.823470 AACACAAAGCTGCGGCAGA 60.823 52.632 32.72 0.00 41.70 4.26
7569 7829 1.789078 AACACAAAGCTGCGGCAGAG 61.789 55.000 32.72 19.61 41.70 3.35
7570 7830 3.360340 ACAAAGCTGCGGCAGAGC 61.360 61.111 32.72 19.50 41.70 4.09
7571 7831 3.359523 CAAAGCTGCGGCAGAGCA 61.360 61.111 32.72 1.53 45.96 4.26
7572 7832 3.360340 AAAGCTGCGGCAGAGCAC 61.360 61.111 32.72 15.12 42.92 4.40
7573 7833 4.631247 AAGCTGCGGCAGAGCACA 62.631 61.111 32.72 0.00 42.92 4.57
7574 7834 4.631247 AGCTGCGGCAGAGCACAA 62.631 61.111 32.72 0.00 42.92 3.33
7575 7835 3.663176 GCTGCGGCAGAGCACAAA 61.663 61.111 32.72 0.00 42.92 2.83
7576 7836 2.559840 CTGCGGCAGAGCACAAAG 59.440 61.111 25.33 0.00 42.92 2.77
7577 7837 2.203195 TGCGGCAGAGCACAAAGT 60.203 55.556 0.00 0.00 42.92 2.66
7578 7838 1.789078 CTGCGGCAGAGCACAAAGTT 61.789 55.000 25.33 0.00 42.92 2.66
7579 7839 1.360192 GCGGCAGAGCACAAAGTTT 59.640 52.632 0.00 0.00 37.05 2.66
7580 7840 0.936297 GCGGCAGAGCACAAAGTTTG 60.936 55.000 14.13 14.13 37.05 2.93
7581 7841 0.381801 CGGCAGAGCACAAAGTTTGT 59.618 50.000 15.58 15.58 46.75 2.83
7582 7842 1.202290 CGGCAGAGCACAAAGTTTGTT 60.202 47.619 18.59 5.55 43.23 2.83
7583 7843 2.735126 CGGCAGAGCACAAAGTTTGTTT 60.735 45.455 18.59 10.06 43.23 2.83
7584 7844 3.261580 GGCAGAGCACAAAGTTTGTTTT 58.738 40.909 18.59 9.71 43.23 2.43
7585 7845 4.429108 GGCAGAGCACAAAGTTTGTTTTA 58.571 39.130 18.59 0.00 43.23 1.52
7586 7846 4.504097 GGCAGAGCACAAAGTTTGTTTTAG 59.496 41.667 18.59 8.77 43.23 1.85
7587 7847 5.339990 GCAGAGCACAAAGTTTGTTTTAGA 58.660 37.500 18.59 0.00 43.23 2.10
7588 7848 5.804979 GCAGAGCACAAAGTTTGTTTTAGAA 59.195 36.000 18.59 0.00 43.23 2.10
7589 7849 6.310224 GCAGAGCACAAAGTTTGTTTTAGAAA 59.690 34.615 18.59 0.00 43.23 2.52
7590 7850 7.463251 GCAGAGCACAAAGTTTGTTTTAGAAAG 60.463 37.037 18.59 6.32 43.23 2.62
7591 7851 7.754924 CAGAGCACAAAGTTTGTTTTAGAAAGA 59.245 33.333 18.59 0.00 43.23 2.52
7592 7852 8.303876 AGAGCACAAAGTTTGTTTTAGAAAGAA 58.696 29.630 18.59 0.00 43.23 2.52
7593 7853 8.466086 AGCACAAAGTTTGTTTTAGAAAGAAG 57.534 30.769 18.59 4.46 43.23 2.85
7594 7854 8.303876 AGCACAAAGTTTGTTTTAGAAAGAAGA 58.696 29.630 18.59 0.00 43.23 2.87
7595 7855 8.921670 GCACAAAGTTTGTTTTAGAAAGAAGAA 58.078 29.630 18.59 0.00 43.23 2.52
7597 7857 9.974980 ACAAAGTTTGTTTTAGAAAGAAGAACA 57.025 25.926 15.58 0.00 42.22 3.18
7612 7872 9.841880 GAAAGAAGAACAGTAAACAAAAAGAGT 57.158 29.630 0.00 0.00 0.00 3.24
7620 7880 9.646427 AACAGTAAACAAAAAGAGTAAAATGCA 57.354 25.926 0.00 0.00 0.00 3.96
7621 7881 9.083080 ACAGTAAACAAAAAGAGTAAAATGCAC 57.917 29.630 0.00 0.00 0.00 4.57
7622 7882 9.301153 CAGTAAACAAAAAGAGTAAAATGCACT 57.699 29.630 0.00 0.00 0.00 4.40
7623 7883 9.301153 AGTAAACAAAAAGAGTAAAATGCACTG 57.699 29.630 0.00 0.00 0.00 3.66
7624 7884 6.588348 AACAAAAAGAGTAAAATGCACTGC 57.412 33.333 0.00 0.00 0.00 4.40
7625 7885 5.906073 ACAAAAAGAGTAAAATGCACTGCT 58.094 33.333 1.98 0.00 0.00 4.24
7626 7886 7.038154 ACAAAAAGAGTAAAATGCACTGCTA 57.962 32.000 1.98 0.00 0.00 3.49
7627 7887 7.141363 ACAAAAAGAGTAAAATGCACTGCTAG 58.859 34.615 1.98 0.00 0.00 3.42
7628 7888 6.884280 AAAAGAGTAAAATGCACTGCTAGT 57.116 33.333 1.98 0.00 0.00 2.57
7629 7889 6.487689 AAAGAGTAAAATGCACTGCTAGTC 57.512 37.500 1.98 0.00 0.00 2.59
7630 7890 4.508662 AGAGTAAAATGCACTGCTAGTCC 58.491 43.478 1.98 0.00 0.00 3.85
7631 7891 3.262420 AGTAAAATGCACTGCTAGTCCG 58.738 45.455 1.98 0.00 0.00 4.79
7632 7892 2.185004 AAAATGCACTGCTAGTCCGT 57.815 45.000 1.98 0.00 0.00 4.69
7633 7893 3.328382 AAAATGCACTGCTAGTCCGTA 57.672 42.857 1.98 0.00 0.00 4.02
7634 7894 3.328382 AAATGCACTGCTAGTCCGTAA 57.672 42.857 1.98 0.00 0.00 3.18
7635 7895 3.328382 AATGCACTGCTAGTCCGTAAA 57.672 42.857 1.98 0.00 0.00 2.01
7636 7896 2.074547 TGCACTGCTAGTCCGTAAAC 57.925 50.000 1.98 0.00 0.00 2.01
7637 7897 1.616865 TGCACTGCTAGTCCGTAAACT 59.383 47.619 1.98 0.00 0.00 2.66
7638 7898 2.260481 GCACTGCTAGTCCGTAAACTC 58.740 52.381 0.00 0.00 0.00 3.01
7639 7899 2.516923 CACTGCTAGTCCGTAAACTCG 58.483 52.381 0.00 0.00 0.00 4.18
7640 7900 2.161012 CACTGCTAGTCCGTAAACTCGA 59.839 50.000 0.00 0.00 0.00 4.04
7641 7901 2.419324 ACTGCTAGTCCGTAAACTCGAG 59.581 50.000 11.84 11.84 0.00 4.04
7642 7902 1.131883 TGCTAGTCCGTAAACTCGAGC 59.868 52.381 13.61 0.00 33.39 5.03
7643 7903 1.131883 GCTAGTCCGTAAACTCGAGCA 59.868 52.381 13.61 0.00 33.13 4.26
7644 7904 2.415090 GCTAGTCCGTAAACTCGAGCAA 60.415 50.000 13.61 0.00 33.13 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 2.746375 GGGCATCTCCATCGGTGGT 61.746 63.158 15.92 0.00 46.16 4.16
98 99 0.243636 CCAAATTGCCCACGGAGAAC 59.756 55.000 0.00 0.00 0.00 3.01
205 250 7.416964 AAGCATTTAGATCACTAGTGAGAGT 57.583 36.000 28.29 17.86 43.61 3.24
239 331 5.944599 TGAACTACTGTACTCCCTCTGTAAG 59.055 44.000 0.00 0.00 0.00 2.34
241 333 5.498393 CTGAACTACTGTACTCCCTCTGTA 58.502 45.833 0.00 0.00 0.00 2.74
243 335 3.129638 GCTGAACTACTGTACTCCCTCTG 59.870 52.174 0.00 0.00 0.00 3.35
244 336 3.010808 AGCTGAACTACTGTACTCCCTCT 59.989 47.826 0.00 0.00 0.00 3.69
247 343 4.538746 AAAGCTGAACTACTGTACTCCC 57.461 45.455 0.00 0.00 0.00 4.30
257 353 3.708890 TCGTGTCGAAAAAGCTGAACTA 58.291 40.909 0.00 0.00 31.06 2.24
262 358 0.110644 GCCTCGTGTCGAAAAAGCTG 60.111 55.000 0.00 0.00 34.74 4.24
307 404 9.178758 GGAAGATGGCCCTATATAATAAACAAG 57.821 37.037 0.00 0.00 0.00 3.16
335 432 1.787012 CCCTTTGTGTTTCTGCATGC 58.213 50.000 11.82 11.82 0.00 4.06
336 433 1.068895 TGCCCTTTGTGTTTCTGCATG 59.931 47.619 0.00 0.00 0.00 4.06
337 434 1.069049 GTGCCCTTTGTGTTTCTGCAT 59.931 47.619 0.00 0.00 0.00 3.96
338 435 0.459489 GTGCCCTTTGTGTTTCTGCA 59.541 50.000 0.00 0.00 0.00 4.41
363 460 2.840038 TGAGTAACATCCTGTGAGCCAT 59.160 45.455 0.00 0.00 0.00 4.40
405 502 7.711339 CCCTCCATAAAGTAGTGATCTAAACAC 59.289 40.741 0.00 0.00 38.38 3.32
406 503 7.622081 TCCCTCCATAAAGTAGTGATCTAAACA 59.378 37.037 0.00 0.00 0.00 2.83
407 504 8.019656 TCCCTCCATAAAGTAGTGATCTAAAC 57.980 38.462 0.00 0.00 0.00 2.01
408 505 7.844779 ACTCCCTCCATAAAGTAGTGATCTAAA 59.155 37.037 0.00 0.00 0.00 1.85
409 506 7.363031 ACTCCCTCCATAAAGTAGTGATCTAA 58.637 38.462 0.00 0.00 0.00 2.10
410 507 6.923670 ACTCCCTCCATAAAGTAGTGATCTA 58.076 40.000 0.00 0.00 0.00 1.98
411 508 5.782925 ACTCCCTCCATAAAGTAGTGATCT 58.217 41.667 0.00 0.00 0.00 2.75
412 509 6.778559 AGTACTCCCTCCATAAAGTAGTGATC 59.221 42.308 0.00 0.00 0.00 2.92
413 510 6.684538 AGTACTCCCTCCATAAAGTAGTGAT 58.315 40.000 0.00 0.00 0.00 3.06
414 511 6.088541 AGTACTCCCTCCATAAAGTAGTGA 57.911 41.667 0.00 0.00 0.00 3.41
415 512 6.793505 AAGTACTCCCTCCATAAAGTAGTG 57.206 41.667 0.00 0.00 30.33 2.74
416 513 6.545298 CGTAAGTACTCCCTCCATAAAGTAGT 59.455 42.308 0.00 0.00 30.94 2.73
417 514 6.968250 CGTAAGTACTCCCTCCATAAAGTAG 58.032 44.000 0.00 0.00 0.00 2.57
418 515 6.949352 CGTAAGTACTCCCTCCATAAAGTA 57.051 41.667 0.00 0.00 0.00 2.24
419 516 5.848833 CGTAAGTACTCCCTCCATAAAGT 57.151 43.478 0.00 0.00 0.00 2.66
528 625 5.365021 ACTATTGTTCTTATCAGCCAGCT 57.635 39.130 0.00 0.00 0.00 4.24
592 689 4.662145 GGATAAACGAAAGATGCACCAAG 58.338 43.478 0.00 0.00 0.00 3.61
610 707 3.220110 GGTATCAGTGTCTGTCCGGATA 58.780 50.000 7.81 3.21 32.61 2.59
611 708 2.032620 GGTATCAGTGTCTGTCCGGAT 58.967 52.381 7.81 0.00 32.61 4.18
612 709 1.272258 TGGTATCAGTGTCTGTCCGGA 60.272 52.381 0.00 0.00 32.61 5.14
614 711 2.607187 GTTGGTATCAGTGTCTGTCCG 58.393 52.381 0.00 0.00 32.61 4.79
615 712 2.567615 AGGTTGGTATCAGTGTCTGTCC 59.432 50.000 0.00 0.00 32.61 4.02
616 713 3.589988 CAGGTTGGTATCAGTGTCTGTC 58.410 50.000 0.00 0.00 32.61 3.51
617 714 2.289694 GCAGGTTGGTATCAGTGTCTGT 60.290 50.000 0.00 0.00 32.61 3.41
618 715 2.027745 AGCAGGTTGGTATCAGTGTCTG 60.028 50.000 0.00 0.00 0.00 3.51
619 716 2.260822 AGCAGGTTGGTATCAGTGTCT 58.739 47.619 0.00 0.00 0.00 3.41
637 734 1.755179 TGGCATAAGCAGGAGAAAGC 58.245 50.000 0.00 0.00 44.61 3.51
663 762 1.291906 GATTGGGTTTGTTGGCCGG 59.708 57.895 0.00 0.00 0.00 6.13
742 907 3.202829 ACTGCCGACCTAAAACAAGAA 57.797 42.857 0.00 0.00 0.00 2.52
779 949 2.023771 GCGCTGGCCTTTTTCAAGC 61.024 57.895 3.32 0.74 0.00 4.01
811 985 1.609208 GCATACTTGGGATCGGCAAT 58.391 50.000 0.00 0.00 0.00 3.56
823 997 3.889538 TGAGAGGCTATGTACGCATACTT 59.110 43.478 0.00 0.00 36.58 2.24
828 1002 1.202417 GCTTGAGAGGCTATGTACGCA 60.202 52.381 0.00 0.00 0.00 5.24
908 1082 3.443681 GGGCAAAATAAGCTAAGCAGTGA 59.556 43.478 0.00 0.00 0.00 3.41
976 1152 1.740025 GCTGTAGAACCAAGATGGCAC 59.260 52.381 0.00 0.00 42.67 5.01
989 1165 0.618680 AGGTGGCATGGAGCTGTAGA 60.619 55.000 0.00 0.00 44.79 2.59
990 1166 0.254178 AAGGTGGCATGGAGCTGTAG 59.746 55.000 0.00 0.00 44.79 2.74
1026 1204 1.731433 CTTGCAATCGCTCCATGGGG 61.731 60.000 13.02 10.39 39.64 4.96
1036 1214 2.537529 CGTAGTCCAATGCTTGCAATCG 60.538 50.000 0.00 0.00 0.00 3.34
1037 1215 2.420022 ACGTAGTCCAATGCTTGCAATC 59.580 45.455 0.00 0.00 29.74 2.67
1071 1249 2.748058 AAACCAGCAGGACGGCGAAT 62.748 55.000 16.62 0.00 39.27 3.34
1107 1285 1.566018 GCCTGTTCCTCCGTTTCACG 61.566 60.000 0.00 0.00 42.11 4.35
1162 1343 4.827087 CTGCTGCGCCGAGACCAT 62.827 66.667 4.18 0.00 0.00 3.55
1232 1413 1.618837 GAACCGAGAGCCCTATATGCA 59.381 52.381 0.00 0.00 0.00 3.96
1233 1414 1.896465 AGAACCGAGAGCCCTATATGC 59.104 52.381 0.00 0.00 0.00 3.14
1239 1420 2.294078 CCCAAGAACCGAGAGCCCT 61.294 63.158 0.00 0.00 0.00 5.19
1243 1424 1.512926 CAACACCCAAGAACCGAGAG 58.487 55.000 0.00 0.00 0.00 3.20
1258 1439 1.112315 ATGGTTTGCCGCTTCCAACA 61.112 50.000 6.01 0.00 37.67 3.33
1259 1440 0.388520 GATGGTTTGCCGCTTCCAAC 60.389 55.000 6.01 1.36 37.67 3.77
1260 1441 0.539438 AGATGGTTTGCCGCTTCCAA 60.539 50.000 6.01 0.00 37.67 3.53
1276 1457 2.638025 AATACCAGGCCCGGGGAGAT 62.638 60.000 25.28 0.00 0.00 2.75
1329 1510 1.901833 TCATGGTTGCAGTAGAGCAGA 59.098 47.619 0.00 0.00 46.54 4.26
1344 1525 1.601419 CCCCTGCAGCACTTTCATGG 61.601 60.000 8.66 0.00 0.00 3.66
1351 1532 0.252284 ACTACTACCCCTGCAGCACT 60.252 55.000 8.66 0.00 0.00 4.40
1400 1581 3.297134 AGAAGCTGAAGAACCACCAAA 57.703 42.857 0.00 0.00 0.00 3.28
1570 1751 0.322975 CTGAGCAGTAGTGGCTGGTT 59.677 55.000 0.00 0.00 45.80 3.67
1623 1804 1.762460 CCACCACCCCGAGCTAGAT 60.762 63.158 0.00 0.00 0.00 1.98
1668 1849 1.258445 GCCCCTTCTCGAAGACTGGA 61.258 60.000 8.19 0.00 40.79 3.86
1894 2080 3.873910 TGCCAGGACAAATACTTAGCTC 58.126 45.455 0.00 0.00 0.00 4.09
1895 2081 4.301072 TTGCCAGGACAAATACTTAGCT 57.699 40.909 0.00 0.00 0.00 3.32
1896 2082 4.884164 AGATTGCCAGGACAAATACTTAGC 59.116 41.667 0.00 0.00 32.27 3.09
1897 2083 8.682936 AATAGATTGCCAGGACAAATACTTAG 57.317 34.615 0.00 0.00 32.27 2.18
1899 2085 9.646522 ATTAATAGATTGCCAGGACAAATACTT 57.353 29.630 0.00 0.00 32.27 2.24
1931 2119 2.369394 CCCTGGTAATGAAAGCCAGTC 58.631 52.381 8.71 0.00 46.09 3.51
2018 2206 0.108585 TGGCCCTTGTCAGTGTTCTC 59.891 55.000 0.00 0.00 0.00 2.87
2113 2301 2.569354 AATTCTGCGGGCGCCAAAA 61.569 52.632 30.85 14.35 41.09 2.44
2200 2388 1.064017 ACAACTTTCCCTGCAACTGGA 60.064 47.619 0.00 0.00 0.00 3.86
2422 2610 6.093219 CCTTCGCCTCCATTATCTTCATATTG 59.907 42.308 0.00 0.00 0.00 1.90
2452 2640 4.462394 GCCATAGCCTTGATGCGA 57.538 55.556 0.00 0.00 36.02 5.10
2559 2747 1.420514 GATACTTCCTAAGCCACCCCC 59.579 57.143 0.00 0.00 0.00 5.40
2569 2757 4.778579 AGCACGTGTAGAGATACTTCCTA 58.221 43.478 18.38 0.00 0.00 2.94
2602 2790 0.322008 GTGAGGCCCAGAACAGGAAG 60.322 60.000 0.00 0.00 0.00 3.46
2647 2835 1.142667 TCCACAAGAATGCAGACACCA 59.857 47.619 0.00 0.00 0.00 4.17
2815 3003 2.938838 CAACTTGGTTTACCCTGGTGA 58.061 47.619 0.00 0.00 34.29 4.02
2856 3044 0.112995 AGCCATTGCCAAGTCCTTCA 59.887 50.000 0.00 0.00 38.69 3.02
2878 3066 8.438676 ACTCTCCTGGTTCAATTATTATTTCG 57.561 34.615 0.00 0.00 0.00 3.46
2885 3073 6.875972 ACTGTACTCTCCTGGTTCAATTAT 57.124 37.500 0.00 0.00 0.00 1.28
2975 3163 0.402121 GCAACCTTGAGACCCTTCCT 59.598 55.000 0.00 0.00 0.00 3.36
3082 3270 1.779061 ATGCCCTTGACCCGACAACT 61.779 55.000 0.00 0.00 0.00 3.16
3091 3279 1.064758 TGTGGGACATATGCCCTTGAC 60.065 52.381 25.93 19.26 46.19 3.18
3109 3297 3.567164 CAGTTTGAATCCAAGCACTCTGT 59.433 43.478 0.00 0.00 36.17 3.41
3118 3306 4.898265 TGAATTGTCCCAGTTTGAATCCAA 59.102 37.500 0.00 0.00 0.00 3.53
3325 3513 8.102676 TCATCCAAGAAGTAAACATCAGAATCA 58.897 33.333 0.00 0.00 0.00 2.57
3352 3540 0.325933 CATCCACAGCACTGAAGGGA 59.674 55.000 4.31 8.52 35.01 4.20
3470 3659 6.189677 TGTAGGCATGTAAATTGCAGTAAC 57.810 37.500 0.00 0.00 41.95 2.50
3494 3683 4.328536 TGGTTATGTTTCACGCCTTATGT 58.671 39.130 0.00 0.00 0.00 2.29
3565 3754 9.771534 GATGGAAATACTCTTGCTTAGACTATT 57.228 33.333 0.00 0.00 0.00 1.73
3566 3755 8.085296 CGATGGAAATACTCTTGCTTAGACTAT 58.915 37.037 0.00 0.00 0.00 2.12
3567 3756 7.284716 TCGATGGAAATACTCTTGCTTAGACTA 59.715 37.037 0.00 0.00 0.00 2.59
3571 3817 6.276847 ACTCGATGGAAATACTCTTGCTTAG 58.723 40.000 0.00 0.00 0.00 2.18
3766 4012 8.843262 GGTAAAAACTAGTTATGTGTGGAAACT 58.157 33.333 8.92 0.00 37.27 2.66
3790 4036 6.872920 TGCACAAAATTTCTTTAACTCAGGT 58.127 32.000 0.00 0.00 0.00 4.00
3806 4052 5.235616 CGAACCTAGTCTAAACTGCACAAAA 59.764 40.000 0.00 0.00 36.92 2.44
3914 4160 6.761242 CCATTCACGACCATCTGTTAGAATTA 59.239 38.462 0.00 0.00 0.00 1.40
4138 4384 0.686789 TCCCTATGACATGGCCATCG 59.313 55.000 17.61 14.17 0.00 3.84
4216 4462 1.878522 GCCGTATGCAGAGGTGACG 60.879 63.158 0.00 0.00 40.77 4.35
4271 4517 4.891756 ACATATCTGCAATCCCTGGAAAAG 59.108 41.667 0.00 0.00 0.00 2.27
4553 4799 7.938140 TTTGTACAATTTCCCTAATGGAGAG 57.062 36.000 9.56 0.00 46.24 3.20
4649 4895 5.455326 GCCTGTAGGGAATATCTGTGTCAAT 60.455 44.000 0.00 0.00 37.23 2.57
4856 5102 9.929180 TGTAATAGCTCTGCATTAAGTATAAGG 57.071 33.333 0.00 0.00 0.00 2.69
4860 5106 9.650539 CTGATGTAATAGCTCTGCATTAAGTAT 57.349 33.333 0.00 0.00 0.00 2.12
4874 5120 5.048643 TCTCTAGCCGAACTGATGTAATAGC 60.049 44.000 0.00 0.00 0.00 2.97
5049 5295 4.631377 TCAACTGTCGCTGAATTATGGAAG 59.369 41.667 0.00 0.00 0.00 3.46
5085 5331 4.283722 AGGTTGAAGAGGAAGTTGATACGT 59.716 41.667 0.00 0.00 0.00 3.57
5136 5382 1.672854 TATCCCGTGGCAAGGAGACG 61.673 60.000 21.59 3.26 35.08 4.18
5198 5444 6.183360 GCCCTAGAAAATACAGTTCGTGTAAC 60.183 42.308 0.00 0.00 45.00 2.50
5313 5560 1.541588 CAAGCCCTGCAAGACCTAAAC 59.458 52.381 0.00 0.00 34.07 2.01
5458 5705 7.093684 GGTCTAGAGTTCTCAATCACTAAAGGT 60.094 40.741 0.00 0.00 0.00 3.50
5698 5945 2.225068 AAAGCGATATGTCCACTCCG 57.775 50.000 0.00 0.00 0.00 4.63
5743 5990 8.448615 GTTGGTTCTTGTGGTATAATACTCAAC 58.551 37.037 0.00 0.00 0.00 3.18
5994 6241 2.898729 ACGCAGAACCTGATAGATGG 57.101 50.000 0.00 0.00 32.44 3.51
6149 6397 3.617263 CCGCCATCTTCAACTACTGTTAC 59.383 47.826 0.00 0.00 34.60 2.50
6349 6597 0.695924 TGTCAATCACGGTGGGGATT 59.304 50.000 8.50 0.00 34.19 3.01
6390 6638 5.049612 GCGCTTTAGTGTTCTTTACCTTCTT 60.050 40.000 0.00 0.00 0.00 2.52
6413 6662 4.034975 TGCAAAAACCAAAATACTGCAAGC 59.965 37.500 0.00 0.00 37.60 4.01
6427 6676 5.300539 ACACCCCAAAATTTATGCAAAAACC 59.699 36.000 0.00 0.00 0.00 3.27
6428 6677 6.384258 ACACCCCAAAATTTATGCAAAAAC 57.616 33.333 0.00 0.00 0.00 2.43
6439 6688 5.308237 TGCCAACTTATAACACCCCAAAATT 59.692 36.000 0.00 0.00 0.00 1.82
6711 6960 6.718593 TCCCCATGCTGTATTTCCTTATAT 57.281 37.500 0.00 0.00 0.00 0.86
6729 6978 3.783082 ACCAAATTTTCCTTGTTTCCCCA 59.217 39.130 0.00 0.00 0.00 4.96
6730 6979 4.431416 ACCAAATTTTCCTTGTTTCCCC 57.569 40.909 0.00 0.00 0.00 4.81
6843 7093 5.174035 CGATATGAACAAACGCTAGGAGAAG 59.826 44.000 0.00 0.00 0.00 2.85
6925 7175 6.567602 AGCAGGGTGACTATTTATTCTCTT 57.432 37.500 0.00 0.00 0.00 2.85
6928 7178 9.343539 GAAAATAGCAGGGTGACTATTTATTCT 57.656 33.333 8.07 0.00 44.39 2.40
6933 7183 7.232534 TGTTTGAAAATAGCAGGGTGACTATTT 59.767 33.333 0.00 0.00 46.13 1.40
7019 7269 3.957497 TCTGTTGGCCTGAAAAAGCTAAA 59.043 39.130 3.32 0.00 30.85 1.85
7166 7416 7.169813 GCATGCTTTTACTCTTTTTAGCAACTT 59.830 33.333 11.37 0.00 41.38 2.66
7173 7423 5.010516 TGCTGGCATGCTTTTACTCTTTTTA 59.989 36.000 18.92 0.00 0.00 1.52
7242 7492 0.647410 CTCAGCAACTGCGGATTACG 59.353 55.000 0.00 0.00 43.76 3.18
7245 7495 0.392193 CCTCTCAGCAACTGCGGATT 60.392 55.000 0.00 0.00 43.76 3.01
7350 7600 2.202440 AGTCGTTCGATCGCCGTG 60.202 61.111 20.93 8.11 39.75 4.94
7535 7795 0.030235 GTGTTGCCCGTTTCCACTTC 59.970 55.000 0.00 0.00 0.00 3.01
7559 7819 1.789078 AACTTTGTGCTCTGCCGCAG 61.789 55.000 14.62 14.62 41.21 5.18
7566 7826 7.826690 TCTTTCTAAAACAAACTTTGTGCTCT 58.173 30.769 7.93 0.00 44.59 4.09
7567 7827 8.460831 TTCTTTCTAAAACAAACTTTGTGCTC 57.539 30.769 7.93 0.00 44.59 4.26
7568 7828 8.303876 TCTTCTTTCTAAAACAAACTTTGTGCT 58.696 29.630 7.93 1.65 44.59 4.40
7569 7829 8.460831 TCTTCTTTCTAAAACAAACTTTGTGC 57.539 30.769 7.93 0.00 44.59 4.57
7586 7846 9.841880 ACTCTTTTTGTTTACTGTTCTTCTTTC 57.158 29.630 0.00 0.00 0.00 2.62
7594 7854 9.646427 TGCATTTTACTCTTTTTGTTTACTGTT 57.354 25.926 0.00 0.00 0.00 3.16
7595 7855 9.083080 GTGCATTTTACTCTTTTTGTTTACTGT 57.917 29.630 0.00 0.00 0.00 3.55
7596 7856 9.301153 AGTGCATTTTACTCTTTTTGTTTACTG 57.699 29.630 0.00 0.00 0.00 2.74
7597 7857 9.301153 CAGTGCATTTTACTCTTTTTGTTTACT 57.699 29.630 0.00 0.00 0.00 2.24
7598 7858 8.055986 GCAGTGCATTTTACTCTTTTTGTTTAC 58.944 33.333 11.09 0.00 0.00 2.01
7599 7859 7.978975 AGCAGTGCATTTTACTCTTTTTGTTTA 59.021 29.630 19.20 0.00 0.00 2.01
7600 7860 6.818142 AGCAGTGCATTTTACTCTTTTTGTTT 59.182 30.769 19.20 0.00 0.00 2.83
7601 7861 6.340522 AGCAGTGCATTTTACTCTTTTTGTT 58.659 32.000 19.20 0.00 0.00 2.83
7602 7862 5.906073 AGCAGTGCATTTTACTCTTTTTGT 58.094 33.333 19.20 0.00 0.00 2.83
7603 7863 7.141363 ACTAGCAGTGCATTTTACTCTTTTTG 58.859 34.615 19.20 0.00 0.00 2.44
7604 7864 7.277174 ACTAGCAGTGCATTTTACTCTTTTT 57.723 32.000 19.20 0.00 0.00 1.94
7605 7865 6.072452 GGACTAGCAGTGCATTTTACTCTTTT 60.072 38.462 19.20 0.00 36.49 2.27
7606 7866 5.412904 GGACTAGCAGTGCATTTTACTCTTT 59.587 40.000 19.20 0.00 36.49 2.52
7607 7867 4.938226 GGACTAGCAGTGCATTTTACTCTT 59.062 41.667 19.20 0.00 36.49 2.85
7608 7868 4.508662 GGACTAGCAGTGCATTTTACTCT 58.491 43.478 19.20 0.00 36.49 3.24
7609 7869 3.307242 CGGACTAGCAGTGCATTTTACTC 59.693 47.826 19.20 1.45 36.23 2.59
7610 7870 3.262420 CGGACTAGCAGTGCATTTTACT 58.738 45.455 19.20 0.00 36.23 2.24
7611 7871 3.000727 ACGGACTAGCAGTGCATTTTAC 58.999 45.455 19.20 3.35 36.23 2.01
7612 7872 3.328382 ACGGACTAGCAGTGCATTTTA 57.672 42.857 19.20 0.00 36.23 1.52
7613 7873 2.185004 ACGGACTAGCAGTGCATTTT 57.815 45.000 19.20 0.00 36.23 1.82
7614 7874 3.328382 TTACGGACTAGCAGTGCATTT 57.672 42.857 19.20 0.00 36.23 2.32
7615 7875 3.000727 GTTTACGGACTAGCAGTGCATT 58.999 45.455 19.20 0.00 36.23 3.56
7616 7876 2.233922 AGTTTACGGACTAGCAGTGCAT 59.766 45.455 19.20 1.47 36.23 3.96
7617 7877 1.616865 AGTTTACGGACTAGCAGTGCA 59.383 47.619 19.20 2.32 36.23 4.57
7618 7878 2.260481 GAGTTTACGGACTAGCAGTGC 58.740 52.381 7.13 7.13 32.81 4.40
7619 7879 2.161012 TCGAGTTTACGGACTAGCAGTG 59.839 50.000 0.00 0.00 0.00 3.66
7620 7880 2.419324 CTCGAGTTTACGGACTAGCAGT 59.581 50.000 3.62 0.00 0.00 4.40
7621 7881 2.791849 GCTCGAGTTTACGGACTAGCAG 60.792 54.545 15.13 0.00 33.47 4.24
7622 7882 1.131883 GCTCGAGTTTACGGACTAGCA 59.868 52.381 15.13 0.00 33.47 3.49
7623 7883 1.131883 TGCTCGAGTTTACGGACTAGC 59.868 52.381 15.13 0.00 33.73 3.42
7624 7884 3.482722 TTGCTCGAGTTTACGGACTAG 57.517 47.619 15.13 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.