Multiple sequence alignment - TraesCS2B01G391100

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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 TraesCS2B01G391100 chr2B 100.000 4354 0 0 1 4354 555778292 555782645 0.000000e+00 8041
1 TraesCS2B01G391100 chr2B 96.591 88 1 2 3813 3900 539338967 539339052 1.260000e-30 145
2 TraesCS2B01G391100 chr2B 80.519 154 27 2 2545 2695 555780515 555780668 9.890000e-22 115
3 TraesCS2B01G391100 chr2B 80.519 154 27 2 2224 2377 555780836 555780986 9.890000e-22 115
4 TraesCS2B01G391100 chr2D 92.536 3443 153 43 84 3487 474675567 474678944 0.000000e+00 4839
5 TraesCS2B01G391100 chr2D 84.507 639 70 17 3556 4180 474678953 474679576 4.820000e-169 604
6 TraesCS2B01G391100 chr2D 88.863 422 38 6 3934 4354 474680374 474680787 1.080000e-140 510
7 TraesCS2B01G391100 chr2D 81.818 154 25 2 2224 2377 474678011 474678161 4.570000e-25 126
8 TraesCS2B01G391100 chr2D 79.870 154 28 2 2545 2695 474677681 474677834 4.600000e-20 110
9 TraesCS2B01G391100 chr2A 91.727 3445 172 46 84 3485 617104363 617107737 0.000000e+00 4678
10 TraesCS2B01G391100 chr2A 92.723 426 27 4 3810 4234 617108498 617108920 2.880000e-171 612
11 TraesCS2B01G391100 chr2A 83.095 698 64 34 3556 4232 617107748 617108412 1.740000e-163 586
12 TraesCS2B01G391100 chr2A 91.826 367 25 4 3870 4234 617108991 617109354 1.400000e-139 507
13 TraesCS2B01G391100 chr2A 93.878 98 2 4 3813 3910 601729429 601729522 1.260000e-30 145
14 TraesCS2B01G391100 chr2A 82.468 154 24 2 2224 2377 617106801 617106951 9.830000e-27 132
15 TraesCS2B01G391100 chr2A 80.519 154 27 2 2545 2695 617106471 617106624 9.890000e-22 115
16 TraesCS2B01G391100 chr4B 90.305 361 35 0 2663 3023 653738039 653737679 1.420000e-129 473
17 TraesCS2B01G391100 chr3B 95.652 92 2 2 3812 3903 24517711 24517622 3.510000e-31 147
18 TraesCS2B01G391100 chr5B 96.552 87 3 0 3813 3899 588883777 588883863 1.260000e-30 145
19 TraesCS2B01G391100 chr3D 96.591 88 1 2 3809 3895 17114904 17114818 1.260000e-30 145
20 TraesCS2B01G391100 chr3A 96.591 88 2 1 3809 3895 19771248 19771335 1.260000e-30 145
21 TraesCS2B01G391100 chr6D 92.683 82 6 0 1332 1413 307113080 307112999 7.650000e-23 119
22 TraesCS2B01G391100 chr6B 92.683 82 6 0 1332 1413 474429705 474429624 7.650000e-23 119
23 TraesCS2B01G391100 chr6A 90.244 82 8 0 1332 1413 443416868 443416787 1.660000e-19 108


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 TraesCS2B01G391100 chr2B 555778292 555782645 4353 False 2757.0 8041 87.012667 1 4354 3 chr2B.!!$F2 4353
1 TraesCS2B01G391100 chr2D 474675567 474680787 5220 False 1237.8 4839 85.518800 84 4354 5 chr2D.!!$F1 4270
2 TraesCS2B01G391100 chr2A 617104363 617109354 4991 False 1105.0 4678 87.059667 84 4234 6 chr2A.!!$F2 4150

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
79 80 0.028902 GCCTTTTGTTCGTTCGCTGT 59.971 50.0 0.00 0.00 0.00 4.40 F
1499 1551 0.035247 AGGAGCTACGACTTCGACCT 60.035 55.0 5.47 3.52 43.02 3.85 F
2208 2263 0.318441 CCAGACTGCGAAGGACAAGA 59.682 55.0 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1807 1859 1.303888 ACGCGTACCTCTTCCCAGA 60.304 57.895 11.67 0.0 0.00 3.86 R
3200 3264 0.601046 TGCTCTGCCAAGACTGTTCG 60.601 55.000 0.00 0.0 0.00 3.95 R
3800 3884 0.311790 ATGAAAGCACTGCGGTTGTG 59.688 50.000 0.00 0.0 34.92 3.33 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
17 18 3.930504 GAGATGCAAAGGGCTGGG 58.069 61.111 0.00 0.00 45.15 4.45
18 19 1.304282 GAGATGCAAAGGGCTGGGA 59.696 57.895 0.00 0.00 45.15 4.37
19 20 1.000396 AGATGCAAAGGGCTGGGAC 60.000 57.895 0.00 0.00 45.15 4.46
20 21 1.304381 GATGCAAAGGGCTGGGACA 60.304 57.895 0.00 0.00 45.15 4.02
21 22 1.598701 GATGCAAAGGGCTGGGACAC 61.599 60.000 0.00 0.00 45.15 3.67
22 23 3.365265 GCAAAGGGCTGGGACACG 61.365 66.667 0.00 0.00 40.25 4.49
23 24 2.429930 CAAAGGGCTGGGACACGA 59.570 61.111 0.00 0.00 0.00 4.35
24 25 1.672356 CAAAGGGCTGGGACACGAG 60.672 63.158 0.00 0.00 0.00 4.18
25 26 1.841556 AAAGGGCTGGGACACGAGA 60.842 57.895 0.00 0.00 0.00 4.04
26 27 2.113243 AAAGGGCTGGGACACGAGAC 62.113 60.000 0.00 0.00 0.00 3.36
27 28 3.311110 GGGCTGGGACACGAGACA 61.311 66.667 0.00 0.00 30.97 3.41
28 29 2.262915 GGCTGGGACACGAGACAG 59.737 66.667 0.00 0.00 29.60 3.51
30 31 3.371021 CTGGGACACGAGACAGCT 58.629 61.111 0.00 0.00 0.00 4.24
31 32 1.214062 CTGGGACACGAGACAGCTC 59.786 63.158 0.00 0.00 37.81 4.09
32 33 2.219325 CTGGGACACGAGACAGCTCC 62.219 65.000 0.00 0.00 37.91 4.70
33 34 2.574399 GGACACGAGACAGCTCCC 59.426 66.667 0.00 0.00 37.91 4.30
34 35 1.979693 GGACACGAGACAGCTCCCT 60.980 63.158 0.00 0.00 37.91 4.20
35 36 1.536943 GGACACGAGACAGCTCCCTT 61.537 60.000 0.00 0.00 37.91 3.95
36 37 0.318762 GACACGAGACAGCTCCCTTT 59.681 55.000 0.00 0.00 37.91 3.11
37 38 0.034059 ACACGAGACAGCTCCCTTTG 59.966 55.000 0.00 0.00 37.91 2.77
38 39 0.671781 CACGAGACAGCTCCCTTTGG 60.672 60.000 0.00 0.00 37.91 3.28
39 40 1.743252 CGAGACAGCTCCCTTTGGC 60.743 63.158 0.00 0.00 37.91 4.52
40 41 1.682257 GAGACAGCTCCCTTTGGCT 59.318 57.895 0.00 0.00 39.60 4.75
41 42 0.392327 GAGACAGCTCCCTTTGGCTC 60.392 60.000 0.00 0.00 41.84 4.70
42 43 1.377856 GACAGCTCCCTTTGGCTCC 60.378 63.158 0.00 0.00 36.59 4.70
43 44 1.846712 GACAGCTCCCTTTGGCTCCT 61.847 60.000 0.00 0.00 36.59 3.69
44 45 1.378250 CAGCTCCCTTTGGCTCCTG 60.378 63.158 0.00 0.00 36.59 3.86
45 46 1.849823 AGCTCCCTTTGGCTCCTGT 60.850 57.895 0.00 0.00 32.98 4.00
46 47 1.676967 GCTCCCTTTGGCTCCTGTG 60.677 63.158 0.00 0.00 0.00 3.66
47 48 1.676967 CTCCCTTTGGCTCCTGTGC 60.677 63.158 0.00 0.00 0.00 4.57
55 56 4.385405 GCTCCTGTGCCGACTGCT 62.385 66.667 0.00 0.00 42.00 4.24
56 57 2.433838 CTCCTGTGCCGACTGCTG 60.434 66.667 0.00 0.00 42.00 4.41
57 58 2.917227 TCCTGTGCCGACTGCTGA 60.917 61.111 0.00 0.00 42.00 4.26
58 59 2.433838 CCTGTGCCGACTGCTGAG 60.434 66.667 0.00 0.00 42.00 3.35
59 60 2.433838 CTGTGCCGACTGCTGAGG 60.434 66.667 0.00 1.57 42.00 3.86
60 61 3.947132 CTGTGCCGACTGCTGAGGG 62.947 68.421 0.00 0.00 42.00 4.30
64 65 3.710722 CCGACTGCTGAGGGCCTT 61.711 66.667 7.89 0.00 40.92 4.35
65 66 2.348998 CGACTGCTGAGGGCCTTT 59.651 61.111 7.89 0.00 40.92 3.11
66 67 1.302832 CGACTGCTGAGGGCCTTTT 60.303 57.895 7.89 0.00 40.92 2.27
67 68 1.580845 CGACTGCTGAGGGCCTTTTG 61.581 60.000 7.89 1.87 40.92 2.44
68 69 0.538287 GACTGCTGAGGGCCTTTTGT 60.538 55.000 7.89 2.71 40.92 2.83
69 70 0.106015 ACTGCTGAGGGCCTTTTGTT 60.106 50.000 7.89 0.00 40.92 2.83
70 71 0.600057 CTGCTGAGGGCCTTTTGTTC 59.400 55.000 7.89 0.00 40.92 3.18
71 72 1.172180 TGCTGAGGGCCTTTTGTTCG 61.172 55.000 7.89 0.00 40.92 3.95
72 73 1.172812 GCTGAGGGCCTTTTGTTCGT 61.173 55.000 7.89 0.00 34.27 3.85
73 74 1.318576 CTGAGGGCCTTTTGTTCGTT 58.681 50.000 7.89 0.00 0.00 3.85
74 75 1.266989 CTGAGGGCCTTTTGTTCGTTC 59.733 52.381 7.89 0.00 0.00 3.95
75 76 0.237498 GAGGGCCTTTTGTTCGTTCG 59.763 55.000 7.89 0.00 0.00 3.95
76 77 1.371267 GGGCCTTTTGTTCGTTCGC 60.371 57.895 0.84 0.00 0.00 4.70
77 78 1.652563 GGCCTTTTGTTCGTTCGCT 59.347 52.632 0.00 0.00 0.00 4.93
78 79 0.660300 GGCCTTTTGTTCGTTCGCTG 60.660 55.000 0.00 0.00 0.00 5.18
79 80 0.028902 GCCTTTTGTTCGTTCGCTGT 59.971 50.000 0.00 0.00 0.00 4.40
80 81 1.533129 GCCTTTTGTTCGTTCGCTGTT 60.533 47.619 0.00 0.00 0.00 3.16
81 82 2.286536 GCCTTTTGTTCGTTCGCTGTTA 60.287 45.455 0.00 0.00 0.00 2.41
82 83 3.285745 CCTTTTGTTCGTTCGCTGTTAC 58.714 45.455 0.00 0.00 0.00 2.50
158 163 2.029244 GTCGCACTGATCAAATACCACG 59.971 50.000 0.00 0.00 0.00 4.94
170 175 7.442969 TGATCAAATACCACGTACTTTTGTCTT 59.557 33.333 0.00 0.00 0.00 3.01
199 204 1.131315 GCTCTGAACTTTGGATTCCGC 59.869 52.381 0.00 0.00 0.00 5.54
213 218 1.729284 TTCCGCTGGTCGAAAATACC 58.271 50.000 0.00 0.00 41.67 2.73
321 336 2.179018 GCATGCGCGGTCAAATGT 59.821 55.556 8.83 0.00 0.00 2.71
355 370 1.884075 CGGATCAAGGGTGACGGACA 61.884 60.000 0.00 0.00 36.31 4.02
379 394 1.270305 ACGCATGGTCCATTCTATCCG 60.270 52.381 0.00 1.47 0.00 4.18
383 398 3.197766 GCATGGTCCATTCTATCCGGATA 59.802 47.826 22.71 22.71 0.00 2.59
395 410 8.935844 CATTCTATCCGGATATGATTCGAAAAA 58.064 33.333 24.22 7.21 0.00 1.94
399 414 7.801716 ATCCGGATATGATTCGAAAAAGAAA 57.198 32.000 17.43 0.00 33.43 2.52
400 415 7.011828 TCCGGATATGATTCGAAAAAGAAAC 57.988 36.000 0.00 0.00 33.43 2.78
402 417 7.282224 TCCGGATATGATTCGAAAAAGAAACAT 59.718 33.333 0.00 7.43 43.12 2.71
403 418 7.587757 CCGGATATGATTCGAAAAAGAAACATC 59.412 37.037 0.00 0.00 40.93 3.06
404 419 7.318909 CGGATATGATTCGAAAAAGAAACATCG 59.681 37.037 0.00 2.04 40.93 3.84
405 420 8.122952 GGATATGATTCGAAAAAGAAACATCGT 58.877 33.333 0.00 0.00 40.93 3.73
406 421 8.826546 ATATGATTCGAAAAAGAAACATCGTG 57.173 30.769 0.00 0.00 40.93 4.35
495 520 0.737715 GGAAGAATGACGACGCTGCT 60.738 55.000 0.00 0.00 0.00 4.24
496 521 1.469251 GGAAGAATGACGACGCTGCTA 60.469 52.381 0.00 0.00 0.00 3.49
523 548 1.741706 CTGCAGCCAAACTCGAATCAT 59.258 47.619 0.00 0.00 0.00 2.45
613 641 8.128582 ACACACATATACAAATAGAAAATGCCG 58.871 33.333 0.00 0.00 0.00 5.69
632 660 2.351726 CCGGGTCTCAATTTGAATCGAC 59.648 50.000 0.00 4.89 0.00 4.20
633 661 2.351726 CGGGTCTCAATTTGAATCGACC 59.648 50.000 20.30 20.30 40.04 4.79
636 664 2.351726 GTCTCAATTTGAATCGACCCGG 59.648 50.000 0.00 0.00 0.00 5.73
639 667 2.093394 TCAATTTGAATCGACCCGGCTA 60.093 45.455 0.00 0.00 0.00 3.93
640 668 1.949465 ATTTGAATCGACCCGGCTAC 58.051 50.000 0.00 0.00 0.00 3.58
641 669 0.609151 TTTGAATCGACCCGGCTACA 59.391 50.000 0.00 0.00 0.00 2.74
642 670 0.609151 TTGAATCGACCCGGCTACAA 59.391 50.000 0.00 0.00 0.00 2.41
651 679 0.250553 CCCGGCTACAAACAACCAGA 60.251 55.000 0.00 0.00 0.00 3.86
671 699 0.746923 GGTAGTGGGCGGAACCATTC 60.747 60.000 0.00 0.00 43.59 2.67
673 701 2.246761 TAGTGGGCGGAACCATTCGG 62.247 60.000 0.00 0.00 43.59 4.30
778 806 0.541863 TTGAAATCCCCTCGAGCTCC 59.458 55.000 6.99 0.00 0.00 4.70
789 817 2.542907 CGAGCTCCCTCTCTCGCTC 61.543 68.421 8.47 0.00 44.30 5.03
790 818 1.453015 GAGCTCCCTCTCTCGCTCA 60.453 63.158 0.87 0.00 46.06 4.26
792 820 2.781158 GCTCCCTCTCTCGCTCACC 61.781 68.421 0.00 0.00 0.00 4.02
793 821 1.379176 CTCCCTCTCTCGCTCACCA 60.379 63.158 0.00 0.00 0.00 4.17
794 822 1.379176 TCCCTCTCTCGCTCACCAG 60.379 63.158 0.00 0.00 0.00 4.00
795 823 1.379176 CCCTCTCTCGCTCACCAGA 60.379 63.158 0.00 0.00 0.00 3.86
796 824 1.662438 CCCTCTCTCGCTCACCAGAC 61.662 65.000 0.00 0.00 0.00 3.51
799 827 2.680352 TCTCGCTCACCAGACCCC 60.680 66.667 0.00 0.00 0.00 4.95
800 828 2.997315 CTCGCTCACCAGACCCCA 60.997 66.667 0.00 0.00 0.00 4.96
801 829 3.302347 CTCGCTCACCAGACCCCAC 62.302 68.421 0.00 0.00 0.00 4.61
802 830 3.314331 CGCTCACCAGACCCCACT 61.314 66.667 0.00 0.00 0.00 4.00
807 835 2.532715 ACCAGACCCCACTGCCAT 60.533 61.111 0.00 0.00 36.67 4.40
823 851 1.660560 CCATTGCCAGCAGCCACTAC 61.661 60.000 0.00 0.00 42.71 2.73
949 980 3.966543 CACCCCCACCCTCACCAC 61.967 72.222 0.00 0.00 0.00 4.16
1212 1264 2.664851 TTCGTGGTCAAGGCTGCG 60.665 61.111 0.00 0.00 0.00 5.18
1499 1551 0.035247 AGGAGCTACGACTTCGACCT 60.035 55.000 5.47 3.52 43.02 3.85
1821 1873 1.516423 GCCGTCTGGGAAGAGGTAC 59.484 63.158 0.00 0.00 38.47 3.34
2034 2086 1.370810 CAACGGCAAGCCCCAAAAT 59.629 52.632 5.34 0.00 0.00 1.82
2106 2158 6.418057 TTTTAGCCATCATTTTTGTCCACT 57.582 33.333 0.00 0.00 0.00 4.00
2208 2263 0.318441 CCAGACTGCGAAGGACAAGA 59.682 55.000 0.00 0.00 0.00 3.02
2314 2369 1.419374 GAGAGCGTCGTCAACAACAT 58.581 50.000 0.00 0.00 0.00 2.71
2391 2446 1.497722 GGCAGTTCTTTCGCCTTCG 59.502 57.895 0.00 0.00 42.78 3.79
2400 2455 0.323629 TTTCGCCTTCGTGGAGGATT 59.676 50.000 0.00 0.00 39.25 3.01
2636 2700 2.203337 AGCGTTGCCAGCCAGAAA 60.203 55.556 0.00 0.00 34.64 2.52
2684 2748 1.065928 GTCATCCCGCGACTTCGAT 59.934 57.895 8.23 0.00 43.02 3.59
2735 2799 2.890311 CCTCGAAGACATCCAGAGCTAT 59.110 50.000 0.00 0.00 0.00 2.97
2849 2913 2.182030 GACCTCAACTCCTCGCCG 59.818 66.667 0.00 0.00 0.00 6.46
3256 3320 3.555324 TGCGTGGTTGGGCTCTGA 61.555 61.111 0.00 0.00 0.00 3.27
3323 3393 2.954868 GCGCGATCCGATGTTCGT 60.955 61.111 12.10 0.00 38.40 3.85
3329 3399 1.533129 CGATCCGATGTTCGTACTGCA 60.533 52.381 0.00 0.00 38.40 4.41
3332 3402 1.474879 TCCGATGTTCGTACTGCATCA 59.525 47.619 16.06 0.84 38.40 3.07
3375 3445 5.732633 AGCAAATGCCAAATAACAATGCTA 58.267 33.333 0.94 0.00 39.66 3.49
3386 3456 9.853555 CCAAATAACAATGCTACTGTCATTTTA 57.146 29.630 0.00 0.00 32.30 1.52
3389 3459 5.567138 ACAATGCTACTGTCATTTTAGGC 57.433 39.130 0.00 0.00 32.30 3.93
3391 3461 4.510167 ATGCTACTGTCATTTTAGGCCT 57.490 40.909 11.78 11.78 0.00 5.19
3393 3463 4.261801 TGCTACTGTCATTTTAGGCCTTC 58.738 43.478 12.58 0.00 0.00 3.46
3394 3464 4.019321 TGCTACTGTCATTTTAGGCCTTCT 60.019 41.667 12.58 0.00 0.00 2.85
3397 3467 4.985538 ACTGTCATTTTAGGCCTTCTTGA 58.014 39.130 12.58 6.94 0.00 3.02
3399 3469 6.721318 ACTGTCATTTTAGGCCTTCTTGATA 58.279 36.000 12.58 7.23 0.00 2.15
3400 3470 7.175104 ACTGTCATTTTAGGCCTTCTTGATAA 58.825 34.615 12.58 0.00 0.00 1.75
3401 3471 7.337942 ACTGTCATTTTAGGCCTTCTTGATAAG 59.662 37.037 12.58 13.00 0.00 1.73
3404 3474 8.523658 GTCATTTTAGGCCTTCTTGATAAGTTT 58.476 33.333 12.58 0.00 0.00 2.66
3468 3538 7.995289 TCATTTGATAATACCTTTGCGATGTT 58.005 30.769 0.00 0.00 0.00 2.71
3487 3557 7.116519 GCGATGTTCTTATCCTTGGTAATCTAC 59.883 40.741 0.00 0.00 0.00 2.59
3491 3561 9.213777 TGTTCTTATCCTTGGTAATCTACTGAT 57.786 33.333 0.00 0.00 33.70 2.90
3494 3564 9.607333 TCTTATCCTTGGTAATCTACTGATGAT 57.393 33.333 0.00 0.00 32.44 2.45
3498 3568 7.615403 TCCTTGGTAATCTACTGATGATATGC 58.385 38.462 0.00 0.00 32.44 3.14
3499 3569 6.820656 CCTTGGTAATCTACTGATGATATGCC 59.179 42.308 0.00 0.00 32.44 4.40
3500 3570 5.965922 TGGTAATCTACTGATGATATGCCG 58.034 41.667 0.00 0.00 32.44 5.69
3501 3571 5.714806 TGGTAATCTACTGATGATATGCCGA 59.285 40.000 0.00 0.00 32.44 5.54
3502 3572 6.127619 TGGTAATCTACTGATGATATGCCGAG 60.128 42.308 0.00 0.00 32.44 4.63
3503 3573 6.095580 GGTAATCTACTGATGATATGCCGAGA 59.904 42.308 0.00 0.00 32.44 4.04
3504 3574 5.833406 ATCTACTGATGATATGCCGAGAG 57.167 43.478 0.00 0.00 0.00 3.20
3505 3575 2.739885 ACTGATGATATGCCGAGAGC 57.260 50.000 0.00 0.00 44.14 4.09
3506 3576 2.246469 ACTGATGATATGCCGAGAGCT 58.754 47.619 0.00 0.00 44.23 4.09
3507 3577 2.632028 ACTGATGATATGCCGAGAGCTT 59.368 45.455 0.00 0.00 44.23 3.74
3508 3578 3.070734 ACTGATGATATGCCGAGAGCTTT 59.929 43.478 0.00 0.00 44.23 3.51
3509 3579 4.281941 ACTGATGATATGCCGAGAGCTTTA 59.718 41.667 0.00 0.00 44.23 1.85
3510 3580 4.560128 TGATGATATGCCGAGAGCTTTAC 58.440 43.478 0.00 0.00 44.23 2.01
3511 3581 4.281941 TGATGATATGCCGAGAGCTTTACT 59.718 41.667 0.00 0.00 44.23 2.24
3512 3582 3.982475 TGATATGCCGAGAGCTTTACTG 58.018 45.455 0.00 0.00 44.23 2.74
3513 3583 2.890808 TATGCCGAGAGCTTTACTGG 57.109 50.000 0.00 0.00 44.23 4.00
3514 3584 1.195115 ATGCCGAGAGCTTTACTGGA 58.805 50.000 0.00 0.00 44.23 3.86
3515 3585 0.973632 TGCCGAGAGCTTTACTGGAA 59.026 50.000 0.00 0.00 44.23 3.53
3516 3586 1.066858 TGCCGAGAGCTTTACTGGAAG 60.067 52.381 0.00 0.00 44.23 3.46
3517 3587 1.066787 GCCGAGAGCTTTACTGGAAGT 60.067 52.381 0.00 0.00 45.56 3.01
3518 3588 2.991597 GCCGAGAGCTTTACTGGAAGTC 60.992 54.545 0.00 0.00 43.24 3.01
3519 3589 5.235623 GCCGAGAGCTTTACTGGAAGTCT 62.236 52.174 0.00 0.00 43.24 3.24
3520 3590 6.649663 GCCGAGAGCTTTACTGGAAGTCTT 62.650 50.000 0.00 0.00 43.24 3.01
3535 3605 8.494236 CTGGAAGTCTTTTTAGTCAAAAATCG 57.506 34.615 0.00 0.00 41.54 3.34
3536 3606 6.915843 TGGAAGTCTTTTTAGTCAAAAATCGC 59.084 34.615 0.00 0.00 41.54 4.58
3537 3607 7.139392 GGAAGTCTTTTTAGTCAAAAATCGCT 58.861 34.615 0.00 0.00 41.54 4.93
3538 3608 7.323895 GGAAGTCTTTTTAGTCAAAAATCGCTC 59.676 37.037 0.00 0.00 41.54 5.03
3539 3609 7.259290 AGTCTTTTTAGTCAAAAATCGCTCA 57.741 32.000 0.00 0.00 41.54 4.26
3540 3610 7.132863 AGTCTTTTTAGTCAAAAATCGCTCAC 58.867 34.615 0.00 0.00 41.54 3.51
3541 3611 6.085068 GTCTTTTTAGTCAAAAATCGCTCACG 59.915 38.462 0.00 0.00 41.54 4.35
3542 3612 3.449322 TTAGTCAAAAATCGCTCACGC 57.551 42.857 0.00 0.00 39.84 5.34
3543 3613 1.225855 AGTCAAAAATCGCTCACGCA 58.774 45.000 0.00 0.00 39.84 5.24
3544 3614 1.601903 AGTCAAAAATCGCTCACGCAA 59.398 42.857 0.00 0.00 39.84 4.85
3545 3615 2.032799 AGTCAAAAATCGCTCACGCAAA 59.967 40.909 0.00 0.00 39.84 3.68
3546 3616 2.151172 GTCAAAAATCGCTCACGCAAAC 59.849 45.455 0.00 0.00 39.84 2.93
3547 3617 2.115595 CAAAAATCGCTCACGCAAACA 58.884 42.857 0.00 0.00 39.84 2.83
3548 3618 1.753956 AAAATCGCTCACGCAAACAC 58.246 45.000 0.00 0.00 39.84 3.32
3549 3619 0.384230 AAATCGCTCACGCAAACACG 60.384 50.000 0.00 0.00 39.84 4.49
3550 3620 2.764251 AATCGCTCACGCAAACACGC 62.764 55.000 0.00 0.00 39.84 5.34
3551 3621 4.292208 CGCTCACGCAAACACGCA 62.292 61.111 0.00 0.00 36.19 5.24
3552 3622 2.425773 GCTCACGCAAACACGCAG 60.426 61.111 0.00 0.00 36.19 5.18
3553 3623 3.168237 GCTCACGCAAACACGCAGT 62.168 57.895 0.00 0.00 37.38 4.40
3554 3624 1.351707 CTCACGCAAACACGCAGTT 59.648 52.632 0.00 0.00 41.61 3.16
3592 3664 7.061441 CGAACATGAAACTTCTGAAATGGATTG 59.939 37.037 0.00 0.00 0.00 2.67
3604 3676 1.098050 ATGGATTGCGCACCTTCTTC 58.902 50.000 11.12 0.00 0.00 2.87
3610 3682 0.179032 TGCGCACCTTCTTCTTTCCA 60.179 50.000 5.66 0.00 0.00 3.53
3611 3683 1.168714 GCGCACCTTCTTCTTTCCAT 58.831 50.000 0.30 0.00 0.00 3.41
3613 3685 2.426522 CGCACCTTCTTCTTTCCATGA 58.573 47.619 0.00 0.00 0.00 3.07
3615 3687 3.253188 CGCACCTTCTTCTTTCCATGAAA 59.747 43.478 0.00 0.00 0.00 2.69
3617 3689 5.600696 GCACCTTCTTCTTTCCATGAAAAA 58.399 37.500 0.00 0.00 30.84 1.94
3618 3690 5.693555 GCACCTTCTTCTTTCCATGAAAAAG 59.306 40.000 12.01 12.01 35.49 2.27
3620 3702 7.267857 CACCTTCTTCTTTCCATGAAAAAGTT 58.732 34.615 15.73 0.00 35.64 2.66
3622 3704 7.093333 ACCTTCTTCTTTCCATGAAAAAGTTGT 60.093 33.333 15.73 6.83 35.64 3.32
3654 3736 9.999009 CCTATGTTCAATTCATATATCATGTGC 57.001 33.333 0.00 0.00 0.00 4.57
3657 3739 7.799784 TGTTCAATTCATATATCATGTGCTCG 58.200 34.615 0.00 0.00 0.00 5.03
3658 3740 7.442062 TGTTCAATTCATATATCATGTGCTCGT 59.558 33.333 0.00 0.00 0.00 4.18
3659 3741 7.967890 TCAATTCATATATCATGTGCTCGTT 57.032 32.000 0.00 0.00 0.00 3.85
3665 3749 7.378181 TCATATATCATGTGCTCGTTATGTGT 58.622 34.615 0.00 0.00 0.00 3.72
3698 3782 8.718734 ACCTCTAATTTGTTGAAACGAGTTATC 58.281 33.333 0.00 0.00 0.00 1.75
3709 3793 5.104941 TGAAACGAGTTATCAGACCCATCAT 60.105 40.000 0.00 0.00 0.00 2.45
3733 3817 5.762825 TTTAGATAGAGCGACCATTACGT 57.237 39.130 0.00 0.00 0.00 3.57
3742 3826 2.413796 GCGACCATTACGTGATGAAACA 59.586 45.455 20.86 0.00 0.00 2.83
3743 3827 3.120477 GCGACCATTACGTGATGAAACAA 60.120 43.478 20.86 0.00 0.00 2.83
3746 3830 5.559225 CGACCATTACGTGATGAAACAACAA 60.559 40.000 20.86 0.00 0.00 2.83
3747 3831 5.516090 ACCATTACGTGATGAAACAACAAC 58.484 37.500 20.86 0.00 0.00 3.32
3748 3832 5.066634 ACCATTACGTGATGAAACAACAACA 59.933 36.000 20.86 0.00 0.00 3.33
3750 3834 6.640499 CCATTACGTGATGAAACAACAACAAT 59.360 34.615 20.86 0.00 0.00 2.71
3757 3841 6.418819 GTGATGAAACAACAACAATCCAAGAG 59.581 38.462 0.00 0.00 0.00 2.85
3767 3851 6.681777 ACAACAATCCAAGAGCAATTAGTTC 58.318 36.000 0.00 0.00 0.00 3.01
3769 3853 6.259550 ACAATCCAAGAGCAATTAGTTCAC 57.740 37.500 0.00 0.00 0.00 3.18
3787 3871 7.916077 AGTTCACCCAGTAACTAATATAGCT 57.084 36.000 0.00 0.00 34.23 3.32
3788 3872 8.320338 AGTTCACCCAGTAACTAATATAGCTT 57.680 34.615 0.00 0.00 34.23 3.74
3789 3873 9.430399 AGTTCACCCAGTAACTAATATAGCTTA 57.570 33.333 0.00 0.00 34.23 3.09
3811 3897 7.327518 GCTTATTTTAAAATACACAACCGCAGT 59.672 33.333 18.16 0.00 31.03 4.40
3886 3972 5.237996 TGAGTTCAACTCTCAATGAAAGCAG 59.762 40.000 18.49 0.00 45.27 4.24
3896 3982 5.291614 TCTCAATGAAAGCAGTTTTGTTTGC 59.708 36.000 0.00 0.00 40.57 3.68
3916 4002 9.462174 TGTTTGCTTCATATGTTTTTGACTAAG 57.538 29.630 1.90 0.00 0.00 2.18
3917 4003 9.463443 GTTTGCTTCATATGTTTTTGACTAAGT 57.537 29.630 1.90 0.00 0.00 2.24
3961 4050 6.978659 CCTAGACGTACTCAGCAATATTTTCA 59.021 38.462 0.00 0.00 0.00 2.69
4052 4142 4.932200 GGTCTCTTTTGATTCACGTGATCT 59.068 41.667 20.80 10.10 0.00 2.75
4054 4144 5.406780 GTCTCTTTTGATTCACGTGATCTGT 59.593 40.000 20.80 6.02 0.00 3.41
4100 5430 4.406972 CCAAGATTAGAGTGTCATCTCCCA 59.593 45.833 0.00 0.00 35.28 4.37
4126 5456 5.688621 CGAATCCTACATGAATTTGCATTGG 59.311 40.000 0.00 0.00 0.00 3.16
4135 5465 5.125100 TGAATTTGCATTGGAGAGTGTTC 57.875 39.130 0.00 0.00 0.00 3.18
4155 5485 8.567948 AGTGTTCAATATCACGAGAAAAACAAT 58.432 29.630 0.00 0.00 39.25 2.71
4190 5520 6.070021 ACAAGATGTCTGAGTGGATGGAAATA 60.070 38.462 0.00 0.00 0.00 1.40
4297 5789 7.120873 AGACAATGTCTCTCATCTTTTTCATGG 59.879 37.037 10.56 0.00 38.71 3.66
4300 5792 6.119240 TGTCTCTCATCTTTTTCATGGACT 57.881 37.500 0.00 0.00 0.00 3.85
4318 5810 3.282885 GACTTCCATGGTCCCTTTGATC 58.717 50.000 12.58 0.00 0.00 2.92
4345 5837 3.141398 GACCTGCAGAACACATGAAGAA 58.859 45.455 17.39 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.034292 GTCCCAGCCCTTTGCATCTC 61.034 60.000 0.00 0.00 44.83 2.75
1 2 1.000396 GTCCCAGCCCTTTGCATCT 60.000 57.895 0.00 0.00 44.83 2.90
2 3 1.304381 TGTCCCAGCCCTTTGCATC 60.304 57.895 0.00 0.00 44.83 3.91
3 4 1.607467 GTGTCCCAGCCCTTTGCAT 60.607 57.895 0.00 0.00 44.83 3.96
4 5 2.203480 GTGTCCCAGCCCTTTGCA 60.203 61.111 0.00 0.00 44.83 4.08
5 6 3.365265 CGTGTCCCAGCCCTTTGC 61.365 66.667 0.00 0.00 41.71 3.68
6 7 1.672356 CTCGTGTCCCAGCCCTTTG 60.672 63.158 0.00 0.00 0.00 2.77
7 8 1.841556 TCTCGTGTCCCAGCCCTTT 60.842 57.895 0.00 0.00 0.00 3.11
8 9 2.203788 TCTCGTGTCCCAGCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
9 10 2.997897 GTCTCGTGTCCCAGCCCT 60.998 66.667 0.00 0.00 0.00 5.19
10 11 3.302347 CTGTCTCGTGTCCCAGCCC 62.302 68.421 0.00 0.00 0.00 5.19
11 12 2.262915 CTGTCTCGTGTCCCAGCC 59.737 66.667 0.00 0.00 0.00 4.85
12 13 2.433318 GCTGTCTCGTGTCCCAGC 60.433 66.667 9.47 9.47 42.94 4.85
13 14 1.214062 GAGCTGTCTCGTGTCCCAG 59.786 63.158 0.00 0.00 0.00 4.45
14 15 2.276116 GGAGCTGTCTCGTGTCCCA 61.276 63.158 0.00 0.00 40.26 4.37
15 16 2.574399 GGAGCTGTCTCGTGTCCC 59.426 66.667 0.00 0.00 40.26 4.46
16 17 1.536943 AAGGGAGCTGTCTCGTGTCC 61.537 60.000 0.00 0.00 40.26 4.02
17 18 0.318762 AAAGGGAGCTGTCTCGTGTC 59.681 55.000 0.00 0.00 40.26 3.67
18 19 0.034059 CAAAGGGAGCTGTCTCGTGT 59.966 55.000 0.00 0.00 40.26 4.49
19 20 0.671781 CCAAAGGGAGCTGTCTCGTG 60.672 60.000 0.00 0.00 40.26 4.35
20 21 1.674057 CCAAAGGGAGCTGTCTCGT 59.326 57.895 0.00 0.00 40.26 4.18
21 22 1.743252 GCCAAAGGGAGCTGTCTCG 60.743 63.158 0.00 0.00 40.26 4.04
22 23 0.392327 GAGCCAAAGGGAGCTGTCTC 60.392 60.000 0.00 0.00 40.11 3.36
23 24 1.682257 GAGCCAAAGGGAGCTGTCT 59.318 57.895 0.00 0.00 40.11 3.41
24 25 1.377856 GGAGCCAAAGGGAGCTGTC 60.378 63.158 0.00 0.00 40.11 3.51
25 26 1.849823 AGGAGCCAAAGGGAGCTGT 60.850 57.895 0.00 0.00 40.11 4.40
26 27 1.378250 CAGGAGCCAAAGGGAGCTG 60.378 63.158 0.00 0.00 40.11 4.24
27 28 1.849823 ACAGGAGCCAAAGGGAGCT 60.850 57.895 0.00 0.00 43.55 4.09
28 29 1.676967 CACAGGAGCCAAAGGGAGC 60.677 63.158 0.00 0.00 35.59 4.70
29 30 1.676967 GCACAGGAGCCAAAGGGAG 60.677 63.158 0.00 0.00 35.59 4.30
30 31 2.436109 GCACAGGAGCCAAAGGGA 59.564 61.111 0.00 0.00 35.59 4.20
47 48 2.754664 AAAAGGCCCTCAGCAGTCGG 62.755 60.000 0.00 0.00 46.50 4.79
48 49 1.302832 AAAAGGCCCTCAGCAGTCG 60.303 57.895 0.00 0.00 46.50 4.18
49 50 0.538287 ACAAAAGGCCCTCAGCAGTC 60.538 55.000 0.00 0.00 46.50 3.51
50 51 0.106015 AACAAAAGGCCCTCAGCAGT 60.106 50.000 0.00 0.00 46.50 4.40
51 52 0.600057 GAACAAAAGGCCCTCAGCAG 59.400 55.000 0.00 0.00 46.50 4.24
52 53 1.172180 CGAACAAAAGGCCCTCAGCA 61.172 55.000 0.00 0.00 46.50 4.41
53 54 1.172812 ACGAACAAAAGGCCCTCAGC 61.173 55.000 0.00 0.00 42.60 4.26
54 55 1.266989 GAACGAACAAAAGGCCCTCAG 59.733 52.381 0.00 0.00 0.00 3.35
55 56 1.314730 GAACGAACAAAAGGCCCTCA 58.685 50.000 0.00 0.00 0.00 3.86
56 57 0.237498 CGAACGAACAAAAGGCCCTC 59.763 55.000 0.00 0.00 0.00 4.30
57 58 1.792118 GCGAACGAACAAAAGGCCCT 61.792 55.000 0.00 0.00 0.00 5.19
58 59 1.371267 GCGAACGAACAAAAGGCCC 60.371 57.895 0.00 0.00 0.00 5.80
59 60 0.660300 CAGCGAACGAACAAAAGGCC 60.660 55.000 0.00 0.00 0.00 5.19
60 61 0.028902 ACAGCGAACGAACAAAAGGC 59.971 50.000 0.00 0.00 0.00 4.35
61 62 2.468532 AACAGCGAACGAACAAAAGG 57.531 45.000 0.00 0.00 0.00 3.11
62 63 4.191662 AGTAACAGCGAACGAACAAAAG 57.808 40.909 0.00 0.00 0.00 2.27
63 64 3.001533 GGAGTAACAGCGAACGAACAAAA 59.998 43.478 0.00 0.00 0.00 2.44
64 65 2.540931 GGAGTAACAGCGAACGAACAAA 59.459 45.455 0.00 0.00 0.00 2.83
65 66 2.129607 GGAGTAACAGCGAACGAACAA 58.870 47.619 0.00 0.00 0.00 2.83
66 67 1.067364 TGGAGTAACAGCGAACGAACA 59.933 47.619 0.00 0.00 0.00 3.18
67 68 1.719780 CTGGAGTAACAGCGAACGAAC 59.280 52.381 0.00 0.00 0.00 3.95
68 69 2.060326 CTGGAGTAACAGCGAACGAA 57.940 50.000 0.00 0.00 0.00 3.85
69 70 3.786809 CTGGAGTAACAGCGAACGA 57.213 52.632 0.00 0.00 0.00 3.85
76 77 2.079925 GCTGGAAAGCTGGAGTAACAG 58.920 52.381 0.00 0.00 41.41 3.16
77 78 1.699634 AGCTGGAAAGCTGGAGTAACA 59.300 47.619 0.00 0.00 44.44 2.41
78 79 2.481289 AGCTGGAAAGCTGGAGTAAC 57.519 50.000 0.00 0.00 44.44 2.50
79 80 3.149196 CAAAGCTGGAAAGCTGGAGTAA 58.851 45.455 0.12 0.00 45.54 2.24
80 81 2.553028 CCAAAGCTGGAAAGCTGGAGTA 60.553 50.000 0.12 0.00 46.92 2.59
81 82 1.613836 CAAAGCTGGAAAGCTGGAGT 58.386 50.000 0.12 0.00 45.54 3.85
82 83 0.886563 CCAAAGCTGGAAAGCTGGAG 59.113 55.000 0.12 0.00 46.92 3.86
138 140 2.267426 CGTGGTATTTGATCAGTGCGA 58.733 47.619 0.00 0.00 0.00 5.10
139 141 1.999735 ACGTGGTATTTGATCAGTGCG 59.000 47.619 0.00 0.00 0.00 5.34
158 163 3.035942 CACGCAGCAAAGACAAAAGTAC 58.964 45.455 0.00 0.00 0.00 2.73
199 204 1.912001 TACGCGGTATTTTCGACCAG 58.088 50.000 12.47 0.00 36.72 4.00
213 218 3.778718 CGGTTTGAGATTCAAAATACGCG 59.221 43.478 3.53 3.53 46.53 6.01
250 255 2.396157 CCCAACGGTAAAGCCTCGC 61.396 63.158 0.00 0.00 34.25 5.03
254 265 2.459245 CGTACCCAACGGTAAAGCC 58.541 57.895 0.00 0.00 46.44 4.35
321 336 1.488705 ATCCGTTGACCCTGGCTCAA 61.489 55.000 0.23 0.23 0.00 3.02
361 376 1.347707 TCCGGATAGAATGGACCATGC 59.652 52.381 8.02 5.93 0.00 4.06
372 387 7.892609 TCTTTTTCGAATCATATCCGGATAGA 58.107 34.615 27.31 22.81 0.00 1.98
379 394 8.122952 ACGATGTTTCTTTTTCGAATCATATCC 58.877 33.333 0.00 0.00 34.92 2.59
383 398 5.569059 GCACGATGTTTCTTTTTCGAATCAT 59.431 36.000 0.00 0.00 36.53 2.45
395 410 2.325761 GTGAGTACGCACGATGTTTCT 58.674 47.619 14.10 0.00 0.00 2.52
399 414 0.109272 CTGGTGAGTACGCACGATGT 60.109 55.000 21.23 0.00 39.66 3.06
400 415 1.413767 GCTGGTGAGTACGCACGATG 61.414 60.000 21.23 14.76 39.66 3.84
402 417 2.257371 GCTGGTGAGTACGCACGA 59.743 61.111 21.23 17.32 39.66 4.35
403 418 2.088763 CAGCTGGTGAGTACGCACG 61.089 63.158 21.23 11.16 39.66 5.34
404 419 2.383527 GCAGCTGGTGAGTACGCAC 61.384 63.158 20.14 20.14 38.05 5.34
405 420 2.048222 GCAGCTGGTGAGTACGCA 60.048 61.111 17.12 0.00 0.00 5.24
406 421 2.048222 TGCAGCTGGTGAGTACGC 60.048 61.111 17.12 0.00 0.00 4.42
523 548 3.261580 CGTCCAAAGCTATGTGTCATGA 58.738 45.455 0.00 0.00 0.00 3.07
587 612 8.128582 CGGCATTTTCTATTTGTATATGTGTGT 58.871 33.333 0.00 0.00 0.00 3.72
589 614 7.255451 CCCGGCATTTTCTATTTGTATATGTGT 60.255 37.037 0.00 0.00 0.00 3.72
611 639 2.351726 GTCGATTCAAATTGAGACCCGG 59.648 50.000 0.00 0.00 29.63 5.73
632 660 0.250553 TCTGGTTGTTTGTAGCCGGG 60.251 55.000 2.18 0.00 0.00 5.73
633 661 1.156736 CTCTGGTTGTTTGTAGCCGG 58.843 55.000 0.00 0.00 0.00 6.13
636 664 3.746492 CACTACCTCTGGTTGTTTGTAGC 59.254 47.826 1.37 0.00 39.41 3.58
639 667 2.158667 CCCACTACCTCTGGTTGTTTGT 60.159 50.000 1.37 0.00 39.41 2.83
640 668 2.504367 CCCACTACCTCTGGTTGTTTG 58.496 52.381 1.37 0.00 39.41 2.93
641 669 1.202891 GCCCACTACCTCTGGTTGTTT 60.203 52.381 1.37 0.00 39.41 2.83
642 670 0.400594 GCCCACTACCTCTGGTTGTT 59.599 55.000 1.37 0.00 39.41 2.83
651 679 1.205460 AATGGTTCCGCCCACTACCT 61.205 55.000 0.00 0.00 37.31 3.08
740 768 1.710816 AAATTTTGGGGCTGTTCCGA 58.289 45.000 0.00 0.00 34.94 4.55
747 775 3.245229 GGGGATTTCAAAATTTTGGGGCT 60.245 43.478 26.45 11.98 38.66 5.19
778 806 1.662438 GGTCTGGTGAGCGAGAGAGG 61.662 65.000 0.00 0.00 30.08 3.69
786 814 2.348998 CAGTGGGGTCTGGTGAGC 59.651 66.667 0.00 0.00 39.76 4.26
789 817 2.430704 AATGGCAGTGGGGTCTGGTG 62.431 60.000 0.00 0.00 36.12 4.17
790 818 2.162906 AATGGCAGTGGGGTCTGGT 61.163 57.895 0.00 0.00 36.12 4.00
792 820 2.345760 GCAATGGCAGTGGGGTCTG 61.346 63.158 17.41 0.00 40.72 3.51
793 821 2.036256 GCAATGGCAGTGGGGTCT 59.964 61.111 17.41 0.00 40.72 3.85
794 822 3.070576 GGCAATGGCAGTGGGGTC 61.071 66.667 17.41 0.00 43.71 4.46
795 823 3.913445 TGGCAATGGCAGTGGGGT 61.913 61.111 17.41 0.00 43.71 4.95
802 830 4.998798 TGGCTGCTGGCAATGGCA 62.999 61.111 17.61 9.67 46.03 4.92
823 851 5.117355 TCGGAGAGTGTGTTTTGTACTAG 57.883 43.478 0.00 0.00 0.00 2.57
954 985 4.785453 GCTTGAGGGTGGAGCGGG 62.785 72.222 0.00 0.00 0.00 6.13
1096 1148 2.756283 CGCCCTCTTCTCCTCCGT 60.756 66.667 0.00 0.00 0.00 4.69
1320 1372 4.388499 ACCGGCACCCTGCTAACG 62.388 66.667 0.00 0.00 44.28 3.18
1458 1510 5.311121 CCTCTTAGATCCAGAGTACCTCCTA 59.689 48.000 15.30 0.00 36.75 2.94
1459 1511 4.105697 CCTCTTAGATCCAGAGTACCTCCT 59.894 50.000 15.30 0.00 36.75 3.69
1499 1551 4.421554 CCCCAGCCCTCCTCTCCA 62.422 72.222 0.00 0.00 0.00 3.86
1614 1666 2.507992 CTTCGGCTCTCGTGGCTG 60.508 66.667 0.00 0.00 40.32 4.85
1807 1859 1.303888 ACGCGTACCTCTTCCCAGA 60.304 57.895 11.67 0.00 0.00 3.86
1862 1914 3.289704 TTCTCATTCGCGACGGCCA 62.290 57.895 9.15 0.00 35.02 5.36
2095 2147 7.440856 GGATTTGAGCAATTTAGTGGACAAAAA 59.559 33.333 0.00 0.00 31.61 1.94
2106 2158 9.316730 GCATAATTGAAGGATTTGAGCAATTTA 57.683 29.630 0.00 0.00 39.22 1.40
2194 2249 0.734253 CTCCGTCTTGTCCTTCGCAG 60.734 60.000 0.00 0.00 0.00 5.18
2195 2250 1.176619 TCTCCGTCTTGTCCTTCGCA 61.177 55.000 0.00 0.00 0.00 5.10
2196 2251 0.173708 ATCTCCGTCTTGTCCTTCGC 59.826 55.000 0.00 0.00 0.00 4.70
2208 2263 1.454111 CCTCCTCCGTGATCTCCGT 60.454 63.158 0.00 0.00 0.00 4.69
2391 2446 2.750888 GCGCAACGGAATCCTCCAC 61.751 63.158 0.30 0.00 42.58 4.02
2400 2455 4.980805 GGTGTCTGGCGCAACGGA 62.981 66.667 10.83 0.00 0.00 4.69
2684 2748 1.943968 GCATAGGAGTTGCCGTTGTGA 60.944 52.381 0.00 0.00 43.43 3.58
2735 2799 2.031012 CTGGCGTTCTGCTGGTGA 59.969 61.111 0.00 0.00 45.43 4.02
2849 2913 1.000955 TCAAAGCTCCTGTTCTCCGAC 59.999 52.381 0.00 0.00 0.00 4.79
3200 3264 0.601046 TGCTCTGCCAAGACTGTTCG 60.601 55.000 0.00 0.00 0.00 3.95
3240 3304 3.050275 GTCAGAGCCCAACCACGC 61.050 66.667 0.00 0.00 0.00 5.34
3243 3307 4.329545 GCCGTCAGAGCCCAACCA 62.330 66.667 0.00 0.00 0.00 3.67
3256 3320 4.731612 CGAGCTGAGCACTGCCGT 62.732 66.667 7.39 0.00 40.92 5.68
3319 3389 1.067846 AGTTCGCTGATGCAGTACGAA 60.068 47.619 11.18 11.18 39.64 3.85
3323 3393 2.493675 AGAAGAGTTCGCTGATGCAGTA 59.506 45.455 0.00 0.00 39.64 2.74
3329 3399 1.535015 GCGCTAGAAGAGTTCGCTGAT 60.535 52.381 0.00 0.00 42.19 2.90
3332 3402 4.796225 GCGCTAGAAGAGTTCGCT 57.204 55.556 0.00 0.00 42.19 4.93
3358 3428 4.764308 TGACAGTAGCATTGTTATTTGGCA 59.236 37.500 0.00 0.00 0.00 4.92
3359 3429 5.309323 TGACAGTAGCATTGTTATTTGGC 57.691 39.130 0.00 0.00 0.00 4.52
3360 3430 8.761575 AAAATGACAGTAGCATTGTTATTTGG 57.238 30.769 14.27 0.00 41.18 3.28
3375 3445 4.985538 TCAAGAAGGCCTAAAATGACAGT 58.014 39.130 5.16 0.00 0.00 3.55
3400 3470 6.915843 CGTCTTGCCATTACAAGTTTAAAACT 59.084 34.615 4.37 0.00 45.86 2.66
3401 3471 6.143278 CCGTCTTGCCATTACAAGTTTAAAAC 59.857 38.462 4.37 0.00 45.86 2.43
3404 3474 4.216687 CCCGTCTTGCCATTACAAGTTTAA 59.783 41.667 4.37 0.00 45.86 1.52
3456 3526 4.201950 CCAAGGATAAGAACATCGCAAAGG 60.202 45.833 0.00 0.00 0.00 3.11
3460 3530 3.627395 ACCAAGGATAAGAACATCGCA 57.373 42.857 0.00 0.00 0.00 5.10
3468 3538 9.607333 ATCATCAGTAGATTACCAAGGATAAGA 57.393 33.333 0.00 0.00 30.20 2.10
3487 3557 3.316071 AAGCTCTCGGCATATCATCAG 57.684 47.619 0.00 0.00 44.79 2.90
3491 3561 3.243873 CCAGTAAAGCTCTCGGCATATCA 60.244 47.826 0.00 0.00 44.79 2.15
3494 3564 2.384828 TCCAGTAAAGCTCTCGGCATA 58.615 47.619 0.00 0.00 44.79 3.14
3495 3565 1.195115 TCCAGTAAAGCTCTCGGCAT 58.805 50.000 0.00 0.00 44.79 4.40
3496 3566 0.973632 TTCCAGTAAAGCTCTCGGCA 59.026 50.000 0.00 0.00 44.79 5.69
3497 3567 1.066787 ACTTCCAGTAAAGCTCTCGGC 60.067 52.381 0.00 0.00 42.19 5.54
3498 3568 2.494073 AGACTTCCAGTAAAGCTCTCGG 59.506 50.000 0.00 0.00 0.00 4.63
3499 3569 3.859411 AGACTTCCAGTAAAGCTCTCG 57.141 47.619 0.00 0.00 0.00 4.04
3500 3570 6.869315 AAAAAGACTTCCAGTAAAGCTCTC 57.131 37.500 0.00 0.00 0.00 3.20
3501 3571 7.510407 ACTAAAAAGACTTCCAGTAAAGCTCT 58.490 34.615 0.00 0.00 0.00 4.09
3502 3572 7.441458 TGACTAAAAAGACTTCCAGTAAAGCTC 59.559 37.037 0.00 0.00 0.00 4.09
3503 3573 7.280356 TGACTAAAAAGACTTCCAGTAAAGCT 58.720 34.615 0.00 0.00 0.00 3.74
3504 3574 7.492352 TGACTAAAAAGACTTCCAGTAAAGC 57.508 36.000 0.00 0.00 0.00 3.51
3509 3579 8.129211 CGATTTTTGACTAAAAAGACTTCCAGT 58.871 33.333 0.00 0.00 45.80 4.00
3510 3580 7.113544 GCGATTTTTGACTAAAAAGACTTCCAG 59.886 37.037 0.00 0.00 45.80 3.86
3511 3581 6.915843 GCGATTTTTGACTAAAAAGACTTCCA 59.084 34.615 0.00 0.00 45.80 3.53
3512 3582 7.139392 AGCGATTTTTGACTAAAAAGACTTCC 58.861 34.615 0.00 0.00 45.80 3.46
3513 3583 7.855904 TGAGCGATTTTTGACTAAAAAGACTTC 59.144 33.333 0.00 0.00 45.80 3.01
3514 3584 7.644157 GTGAGCGATTTTTGACTAAAAAGACTT 59.356 33.333 0.00 0.00 45.80 3.01
3515 3585 7.132863 GTGAGCGATTTTTGACTAAAAAGACT 58.867 34.615 0.00 0.00 45.80 3.24
3516 3586 6.085068 CGTGAGCGATTTTTGACTAAAAAGAC 59.915 38.462 0.00 0.00 45.80 3.01
3517 3587 6.133392 CGTGAGCGATTTTTGACTAAAAAGA 58.867 36.000 0.00 0.00 45.80 2.52
3518 3588 6.349347 CGTGAGCGATTTTTGACTAAAAAG 57.651 37.500 0.00 0.00 45.80 2.27
3536 3606 0.654472 GAACTGCGTGTTTGCGTGAG 60.654 55.000 0.00 0.00 39.30 3.51
3537 3607 1.350319 GAACTGCGTGTTTGCGTGA 59.650 52.632 0.00 0.00 39.30 4.35
3538 3608 1.998257 CGAACTGCGTGTTTGCGTG 60.998 57.895 0.00 0.00 39.30 5.34
3539 3609 2.323105 CGAACTGCGTGTTTGCGT 59.677 55.556 0.00 0.00 39.30 5.24
3553 3623 3.644823 TCATGTTCGTAGTTCAAGCGAA 58.355 40.909 0.00 0.00 41.45 4.70
3554 3624 3.291809 TCATGTTCGTAGTTCAAGCGA 57.708 42.857 0.00 0.00 0.00 4.93
3566 3636 6.000891 TCCATTTCAGAAGTTTCATGTTCG 57.999 37.500 0.00 0.00 0.00 3.95
3570 3640 5.287752 CGCAATCCATTTCAGAAGTTTCATG 59.712 40.000 0.00 0.00 0.00 3.07
3592 3664 1.135575 CATGGAAAGAAGAAGGTGCGC 60.136 52.381 0.00 0.00 0.00 6.09
3604 3676 9.546428 AGGAAAATACAACTTTTTCATGGAAAG 57.454 29.630 16.17 16.17 42.28 2.62
3628 3710 9.999009 GCACATGATATATGAATTGAACATAGG 57.001 33.333 0.00 0.00 34.43 2.57
3639 3721 7.872483 ACACATAACGAGCACATGATATATGAA 59.128 33.333 0.00 0.00 0.00 2.57
3640 3722 7.378181 ACACATAACGAGCACATGATATATGA 58.622 34.615 0.00 0.00 0.00 2.15
3642 3724 8.498358 CAAACACATAACGAGCACATGATATAT 58.502 33.333 0.00 0.00 0.00 0.86
3646 3728 4.694982 TCAAACACATAACGAGCACATGAT 59.305 37.500 0.00 0.00 0.00 2.45
3647 3729 4.061596 TCAAACACATAACGAGCACATGA 58.938 39.130 0.00 0.00 0.00 3.07
3648 3730 4.403015 TCAAACACATAACGAGCACATG 57.597 40.909 0.00 0.00 0.00 3.21
3651 3733 4.203950 TGTTCAAACACATAACGAGCAC 57.796 40.909 0.00 0.00 33.17 4.40
3665 3749 7.486551 CGTTTCAACAAATTAGAGGTGTTCAAA 59.513 33.333 0.00 0.00 33.27 2.69
3674 3758 9.746711 CTGATAACTCGTTTCAACAAATTAGAG 57.253 33.333 0.00 0.00 31.82 2.43
3698 3782 6.977502 CGCTCTATCTAAATATGATGGGTCTG 59.022 42.308 0.00 0.00 0.00 3.51
3709 3793 7.173735 TCACGTAATGGTCGCTCTATCTAAATA 59.826 37.037 0.00 0.00 0.00 1.40
3721 3805 2.413796 TGTTTCATCACGTAATGGTCGC 59.586 45.455 0.00 0.00 0.00 5.19
3733 3817 6.462552 TCTTGGATTGTTGTTGTTTCATCA 57.537 33.333 0.00 0.00 0.00 3.07
3742 3826 6.655078 ACTAATTGCTCTTGGATTGTTGTT 57.345 33.333 0.00 0.00 0.00 2.83
3743 3827 6.265196 TGAACTAATTGCTCTTGGATTGTTGT 59.735 34.615 0.00 0.00 0.00 3.32
3746 3830 5.183904 GGTGAACTAATTGCTCTTGGATTGT 59.816 40.000 0.00 0.00 0.00 2.71
3747 3831 5.393461 GGGTGAACTAATTGCTCTTGGATTG 60.393 44.000 0.00 0.00 0.00 2.67
3748 3832 4.706962 GGGTGAACTAATTGCTCTTGGATT 59.293 41.667 0.00 0.00 0.00 3.01
3750 3834 3.073798 TGGGTGAACTAATTGCTCTTGGA 59.926 43.478 0.00 0.00 0.00 3.53
3785 3869 7.327518 ACTGCGGTTGTGTATTTTAAAATAAGC 59.672 33.333 19.67 14.81 33.05 3.09
3786 3870 8.635124 CACTGCGGTTGTGTATTTTAAAATAAG 58.365 33.333 19.67 13.16 33.05 1.73
3787 3871 7.115095 GCACTGCGGTTGTGTATTTTAAAATAA 59.885 33.333 19.67 6.08 37.70 1.40
3788 3872 6.583050 GCACTGCGGTTGTGTATTTTAAAATA 59.417 34.615 15.19 15.19 37.70 1.40
3789 3873 5.404066 GCACTGCGGTTGTGTATTTTAAAAT 59.596 36.000 17.18 17.18 37.70 1.82
3791 3875 4.036971 AGCACTGCGGTTGTGTATTTTAAA 59.963 37.500 0.00 0.00 37.70 1.52
3794 3878 1.953686 AGCACTGCGGTTGTGTATTTT 59.046 42.857 0.00 0.00 37.70 1.82
3795 3879 1.604604 AGCACTGCGGTTGTGTATTT 58.395 45.000 0.00 0.00 37.70 1.40
3796 3880 1.604604 AAGCACTGCGGTTGTGTATT 58.395 45.000 0.00 0.00 37.70 1.89
3797 3881 1.535462 GAAAGCACTGCGGTTGTGTAT 59.465 47.619 0.00 0.00 37.70 2.29
3798 3882 0.941542 GAAAGCACTGCGGTTGTGTA 59.058 50.000 0.00 0.00 37.70 2.90
3800 3884 0.311790 ATGAAAGCACTGCGGTTGTG 59.688 50.000 0.00 0.00 34.92 3.33
3802 3886 2.532531 CTATGAAAGCACTGCGGTTG 57.467 50.000 0.00 0.00 34.92 3.77
3886 3972 9.209297 GTCAAAAACATATGAAGCAAACAAAAC 57.791 29.630 10.38 0.00 0.00 2.43
3916 4002 5.904362 AGGAAGCCAAAATCTGTGATAAC 57.096 39.130 0.00 0.00 0.00 1.89
3917 4003 6.823689 GTCTAGGAAGCCAAAATCTGTGATAA 59.176 38.462 0.00 0.00 0.00 1.75
3919 4005 5.189180 GTCTAGGAAGCCAAAATCTGTGAT 58.811 41.667 0.00 0.00 0.00 3.06
3961 4050 9.935241 ATAGAAACGATGCTGTGATAGAAATAT 57.065 29.630 0.00 0.00 0.00 1.28
3967 4056 8.293157 TCTAGAATAGAAACGATGCTGTGATAG 58.707 37.037 0.00 0.00 46.47 2.08
4052 4142 5.524281 TGTTTTGCTATTCGTGTGTTCTACA 59.476 36.000 0.00 0.00 36.82 2.74
4054 4144 5.049954 GGTGTTTTGCTATTCGTGTGTTCTA 60.050 40.000 0.00 0.00 0.00 2.10
4100 5430 6.889301 ATGCAAATTCATGTAGGATTCGAT 57.111 33.333 0.00 0.00 0.00 3.59
4126 5456 7.582435 TTTTCTCGTGATATTGAACACTCTC 57.418 36.000 0.00 0.00 35.23 3.20
4155 5485 9.219603 CCACTCAGACATCTTGTTAAAATTCTA 57.780 33.333 0.00 0.00 0.00 2.10
4190 5520 5.484715 CATTGCATTCTGTTTTGGAGGAAT 58.515 37.500 0.00 0.00 0.00 3.01
4297 5789 2.879103 TCAAAGGGACCATGGAAGTC 57.121 50.000 21.47 5.38 0.00 3.01
4300 5792 1.999295 TGGATCAAAGGGACCATGGAA 59.001 47.619 21.47 0.00 0.00 3.53
4305 5797 0.036164 CACGTGGATCAAAGGGACCA 59.964 55.000 7.95 0.00 0.00 4.02
4310 5802 1.442769 CAGGTCACGTGGATCAAAGG 58.557 55.000 17.00 0.00 0.00 3.11
4318 5810 1.227527 TGTTCTGCAGGTCACGTGG 60.228 57.895 17.00 0.00 0.00 4.94


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

AutoCloner maintained by Alex Coulton.