Multiple sequence alignment - TraesCS7D01G477900

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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 TraesCS7D01G477900 chr7D 100.000 3582 0 0 1 3582 588695830 588699411 0.000000e+00 6615
1 TraesCS7D01G477900 chr7D 87.234 188 19 4 1081 1268 588555919 588555737 3.620000e-50 209
2 TraesCS7D01G477900 chr7A 93.265 2242 92 23 777 3001 680398831 680396632 0.000000e+00 3249
3 TraesCS7D01G477900 chr7A 90.646 759 60 8 1 755 680399577 680398826 0.000000e+00 998
4 TraesCS7D01G477900 chr7A 94.231 260 14 1 3012 3271 680396330 680396072 2.590000e-106 396
5 TraesCS7D01G477900 chr7A 91.667 156 13 0 1113 1268 680343200 680343045 2.170000e-52 217
6 TraesCS7D01G477900 chr7B 88.689 1167 63 27 2120 3266 662983525 662982408 0.000000e+00 1360
7 TraesCS7D01G477900 chr7B 92.518 695 31 13 851 1528 662984816 662984126 0.000000e+00 976
8 TraesCS7D01G477900 chr7B 90.595 723 56 9 27 745 662985536 662984822 0.000000e+00 948
9 TraesCS7D01G477900 chr7B 94.281 612 25 3 1492 2096 662984126 662983518 0.000000e+00 928
10 TraesCS7D01G477900 chr7B 90.909 154 14 0 1115 1268 662676249 662676096 1.300000e-49 207


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 TraesCS7D01G477900 chr7D 588695830 588699411 3581 False 6615.000000 6615 100.00000 1 3582 1 chr7D.!!$F1 3581
1 TraesCS7D01G477900 chr7A 680396072 680399577 3505 True 1547.666667 3249 92.71400 1 3271 3 chr7A.!!$R2 3270
2 TraesCS7D01G477900 chr7B 662982408 662985536 3128 True 1053.000000 1360 91.52075 27 3266 4 chr7B.!!$R2 3239

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
372 376 0.253044 TATTCCCTGTGGTGCTCAGC 59.747 55.000 0.0 0.0 0.00 4.26 F
597 605 1.070914 TCACGTGGTGCCATTAAGTCA 59.929 47.619 17.0 0.0 32.98 3.41 F
2208 2290 0.666374 GCCACTGCTACCGTTTTTGT 59.334 50.000 0.0 0.0 33.53 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1923 1996 0.182061 CAGCCACATCCTATGCAGGT 59.818 55.0 0.0 0.0 43.18 4.00 R
2215 2297 0.966920 TTCGGTGAGAAGTCTGGTCC 59.033 55.0 0.0 0.0 34.26 4.46 R
3386 3766 0.108585 TCTCTTGCTTTGGGCTTCGT 59.891 50.0 0.0 0.0 42.39 3.85 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
31 32 5.521010 TGAGTAAATTCACCCGCGTAAATAG 59.479 40.000 4.92 0.00 0.00 1.73
40 41 1.268692 CCGCGTAAATAGCTCCGTACA 60.269 52.381 4.92 0.00 0.00 2.90
59 60 8.018520 TCCGTACAAAATTGACACAATTATGAC 58.981 33.333 9.58 6.03 0.00 3.06
71 72 7.104043 ACACAATTATGACAGCAGCATAAAT 57.896 32.000 9.10 0.81 40.43 1.40
108 109 3.572539 ACGTGCAGCACCGTTGTG 61.573 61.111 20.16 7.12 45.65 3.33
183 185 4.818546 AGCAGCATTAAGTTACTGGCATAG 59.181 41.667 0.00 0.00 0.00 2.23
186 188 3.607078 GCATTAAGTTACTGGCATAGCGC 60.607 47.826 0.00 0.00 41.28 5.92
242 246 5.163953 GCTTACTTGCATATATACGGTGCTG 60.164 44.000 8.00 4.47 39.52 4.41
244 248 3.323691 ACTTGCATATATACGGTGCTGGA 59.676 43.478 8.00 0.00 39.52 3.86
294 298 8.543774 CGTAGTTGGAATCATTAAGAACTGATC 58.456 37.037 0.00 0.00 30.98 2.92
301 305 2.624316 TTAAGAACTGATCGTCGCGT 57.376 45.000 5.77 0.00 0.00 6.01
316 320 2.258013 GCGTGGTTGGCTAACAGCA 61.258 57.895 15.34 1.48 44.75 4.41
321 325 0.453390 GGTTGGCTAACAGCATCTGC 59.547 55.000 15.34 0.00 44.75 4.26
325 329 1.372087 GGCTAACAGCATCTGCGCTT 61.372 55.000 9.73 0.00 44.75 4.68
355 359 1.445942 CCGGGTTCGAGGCATGTAT 59.554 57.895 0.00 0.00 39.00 2.29
360 364 1.141053 GGTTCGAGGCATGTATTCCCT 59.859 52.381 0.00 0.00 0.00 4.20
372 376 0.253044 TATTCCCTGTGGTGCTCAGC 59.747 55.000 0.00 0.00 0.00 4.26
482 488 4.711399 TCAAATGGCATGATAGTCAGAGG 58.289 43.478 0.00 0.00 0.00 3.69
483 489 4.409901 TCAAATGGCATGATAGTCAGAGGA 59.590 41.667 0.00 0.00 0.00 3.71
509 515 2.301346 AGTAGGCTGCATAAATGGCAC 58.699 47.619 5.14 0.00 36.11 5.01
516 522 3.797865 GCTGCATAAATGGCACCTTCATC 60.798 47.826 0.00 0.00 36.11 2.92
523 529 2.380084 TGGCACCTTCATCGACTAAC 57.620 50.000 0.00 0.00 0.00 2.34
580 588 6.402983 GCTTGCAGGCATTAGTCATATATCAC 60.403 42.308 16.98 0.00 0.00 3.06
587 595 5.163953 GCATTAGTCATATATCACGTGGTGC 60.164 44.000 17.00 0.00 32.98 5.01
597 605 1.070914 TCACGTGGTGCCATTAAGTCA 59.929 47.619 17.00 0.00 32.98 3.41
620 628 6.914215 TCATTACTTATAGCGGTTGTTCGTAG 59.086 38.462 0.00 0.00 0.00 3.51
634 642 6.238266 GGTTGTTCGTAGTCTGAATGTTTGAA 60.238 38.462 0.00 0.00 0.00 2.69
683 691 8.726988 ACATCCACACAACAATAATTGTAGTAC 58.273 33.333 0.00 0.00 44.59 2.73
745 753 3.429085 GCCATTACGAAAGCAGAACATG 58.571 45.455 0.00 0.00 0.00 3.21
779 787 2.595095 CCCCCACACACACACACT 59.405 61.111 0.00 0.00 0.00 3.55
952 962 7.094118 GGCTTTGTTGTCATTAAAGGGTACATA 60.094 37.037 0.00 0.00 33.25 2.29
1017 1032 2.301346 GTTATGGCTTCCATGGTGAGG 58.699 52.381 12.58 0.00 44.84 3.86
1022 1037 2.785269 TGGCTTCCATGGTGAGGATAAT 59.215 45.455 12.58 0.00 34.56 1.28
1023 1038 3.205056 TGGCTTCCATGGTGAGGATAATT 59.795 43.478 12.58 0.00 34.56 1.40
1082 1097 6.599638 GTGGGAAAGAGTTATATGCTGTCTTT 59.400 38.462 0.00 0.00 39.57 2.52
1158 1173 2.821378 CCAACTGTCATCAGGCAATTGA 59.179 45.455 10.34 0.00 45.14 2.57
1363 1378 3.932459 GCTACTTGCATGATGGTGC 57.068 52.632 6.60 0.00 45.25 5.01
1387 1402 6.010219 CCCCTTTTCTATTCTTGTCTTTCCA 58.990 40.000 0.00 0.00 0.00 3.53
1395 1411 8.498054 TCTATTCTTGTCTTTCCATCACATTC 57.502 34.615 0.00 0.00 0.00 2.67
1429 1453 2.109126 CAAGTAGGAGCTTGCGGCC 61.109 63.158 0.00 0.00 43.05 6.13
1456 1482 9.474920 TCTGGCTTTTGTAAATTAAAGAACATG 57.525 29.630 3.16 0.00 0.00 3.21
1640 1710 6.469782 ACATTTTGTCAGACTTCCATTGTT 57.530 33.333 1.31 0.00 0.00 2.83
1702 1772 4.274147 TGAAAGTCTGTTGGCCTTGTTTA 58.726 39.130 3.32 0.00 0.00 2.01
1703 1773 4.707448 TGAAAGTCTGTTGGCCTTGTTTAA 59.293 37.500 3.32 0.00 0.00 1.52
1704 1774 5.362430 TGAAAGTCTGTTGGCCTTGTTTAAT 59.638 36.000 3.32 0.00 0.00 1.40
1739 1809 5.539582 TCACGACTAAAATTTTCCATCCG 57.460 39.130 6.72 7.89 0.00 4.18
1858 1928 2.425312 TCAACACACAACAACCCATGTC 59.575 45.455 0.00 0.00 42.99 3.06
1923 1996 8.754991 TTTGGTTATGGAAGAAGTTTGAACTA 57.245 30.769 0.00 0.00 38.57 2.24
1947 2020 2.216898 GCATAGGATGTGGCTGACTTC 58.783 52.381 0.00 0.00 0.00 3.01
1951 2024 2.611225 GGATGTGGCTGACTTCCTAG 57.389 55.000 11.64 0.00 42.98 3.02
2096 2169 8.103948 AGGTCAGTAATCTTCAACTTCATTTG 57.896 34.615 0.00 0.00 0.00 2.32
2098 2171 6.803807 GTCAGTAATCTTCAACTTCATTTGGC 59.196 38.462 0.00 0.00 0.00 4.52
2124 2197 1.202915 TGGTGTCATGTGGTGCTTCAT 60.203 47.619 0.00 0.00 0.00 2.57
2127 2200 2.294233 GTGTCATGTGGTGCTTCATGTT 59.706 45.455 0.00 0.00 41.22 2.71
2129 2202 3.243468 TGTCATGTGGTGCTTCATGTTTG 60.243 43.478 0.00 0.00 41.22 2.93
2153 2230 7.199766 TGTTCTTATTGGTTAAAGTTGCACTG 58.800 34.615 0.00 0.00 0.00 3.66
2158 2235 2.890311 TGGTTAAAGTTGCACTGGGATG 59.110 45.455 0.00 0.00 0.00 3.51
2201 2279 1.539065 CCTAGAATGCCACTGCTACCG 60.539 57.143 0.00 0.00 38.71 4.02
2205 2287 1.539827 GAATGCCACTGCTACCGTTTT 59.460 47.619 0.00 0.00 38.71 2.43
2208 2290 0.666374 GCCACTGCTACCGTTTTTGT 59.334 50.000 0.00 0.00 33.53 2.83
2215 2297 4.022464 TGCTACCGTTTTTGTCAAGTTG 57.978 40.909 0.00 0.00 0.00 3.16
2224 2306 3.644966 TTTGTCAAGTTGGACCAGACT 57.355 42.857 11.63 7.95 36.97 3.24
2325 2407 1.134461 CCATGCTCTCAGACCCAAGAG 60.134 57.143 0.00 0.00 41.62 2.85
2449 2531 1.531739 TTGGCCCAAATTCGCAGGAC 61.532 55.000 0.00 0.00 0.00 3.85
2515 2597 2.529389 AGGAAGGACGGGCCACTT 60.529 61.111 4.39 4.38 40.02 3.16
2640 2722 7.730364 ATTTGTTCTGTACTTAGTTGTCTGG 57.270 36.000 0.00 0.00 0.00 3.86
2675 2757 5.932883 GTCCCAGAAATAACGAGAAGAAACT 59.067 40.000 0.00 0.00 0.00 2.66
2676 2758 5.932303 TCCCAGAAATAACGAGAAGAAACTG 59.068 40.000 0.00 0.00 0.00 3.16
2677 2759 5.122396 CCCAGAAATAACGAGAAGAAACTGG 59.878 44.000 0.00 0.00 40.23 4.00
2678 2760 5.701290 CCAGAAATAACGAGAAGAAACTGGT 59.299 40.000 0.00 0.00 37.14 4.00
2679 2761 6.204882 CCAGAAATAACGAGAAGAAACTGGTT 59.795 38.462 0.00 0.00 40.65 3.67
2680 2762 7.386848 CCAGAAATAACGAGAAGAAACTGGTTA 59.613 37.037 0.00 0.00 42.10 2.85
2688 2770 5.107065 CGAGAAGAAACTGGTTATGGTTGTC 60.107 44.000 0.00 0.00 0.00 3.18
2720 2802 3.007398 AGGATTGCTTCTCTTCTGTTCGT 59.993 43.478 0.00 0.00 0.00 3.85
2747 2829 0.251916 TATTGGACCCTGTTGAGCCG 59.748 55.000 0.00 0.00 0.00 5.52
2823 2906 2.363788 TTACTAGTGCTGCTGTTCCG 57.636 50.000 5.39 0.00 0.00 4.30
2845 2930 4.165779 GGCGTCTGTTTGTGATTTAATGG 58.834 43.478 0.00 0.00 0.00 3.16
2848 2933 5.342259 GCGTCTGTTTGTGATTTAATGGTTC 59.658 40.000 0.00 0.00 0.00 3.62
2866 2951 3.829886 TTCGATGTGAACTTGAATGGC 57.170 42.857 0.00 0.00 0.00 4.40
2871 2956 1.071542 TGTGAACTTGAATGGCGGAGA 59.928 47.619 0.00 0.00 0.00 3.71
3024 3404 3.610040 ATCTGGCGTGATGTTGAACTA 57.390 42.857 0.00 0.00 0.00 2.24
3156 3536 1.160137 GGAATCATGTAGGCGGCATC 58.840 55.000 13.08 3.91 0.00 3.91
3211 3591 7.120873 GGATGATGATGCTGAAGTATATTGCTT 59.879 37.037 0.00 0.00 0.00 3.91
3255 3635 1.902508 TGGAGGACTAGCAAACTGAGG 59.097 52.381 0.00 0.00 0.00 3.86
3271 3651 1.528292 GAGGTCGTCCTGCACTGACT 61.528 60.000 5.76 0.00 45.24 3.41
3272 3652 1.373497 GGTCGTCCTGCACTGACTG 60.373 63.158 9.32 4.42 32.42 3.51
3273 3653 1.660355 GTCGTCCTGCACTGACTGA 59.340 57.895 9.32 6.22 0.00 3.41
3274 3654 0.664767 GTCGTCCTGCACTGACTGAC 60.665 60.000 14.62 14.62 33.05 3.51
3275 3655 1.106944 TCGTCCTGCACTGACTGACA 61.107 55.000 9.32 0.00 0.00 3.58
3276 3656 0.941463 CGTCCTGCACTGACTGACAC 60.941 60.000 9.32 0.00 0.00 3.67
3277 3657 0.390860 GTCCTGCACTGACTGACACT 59.609 55.000 4.70 0.00 0.00 3.55
3278 3658 1.123077 TCCTGCACTGACTGACACTT 58.877 50.000 0.00 0.00 0.00 3.16
3279 3659 2.035961 GTCCTGCACTGACTGACACTTA 59.964 50.000 4.70 0.00 0.00 2.24
3280 3660 2.297315 TCCTGCACTGACTGACACTTAG 59.703 50.000 0.00 0.00 0.00 2.18
3281 3661 2.297315 CCTGCACTGACTGACACTTAGA 59.703 50.000 0.00 0.00 0.00 2.10
3282 3662 3.056250 CCTGCACTGACTGACACTTAGAT 60.056 47.826 0.00 0.00 0.00 1.98
3283 3663 3.917988 TGCACTGACTGACACTTAGATG 58.082 45.455 0.00 0.00 0.00 2.90
3284 3664 3.321968 TGCACTGACTGACACTTAGATGT 59.678 43.478 0.00 0.00 34.78 3.06
3285 3665 4.522789 TGCACTGACTGACACTTAGATGTA 59.477 41.667 0.00 0.00 31.24 2.29
3286 3666 5.010617 TGCACTGACTGACACTTAGATGTAA 59.989 40.000 0.00 0.00 31.24 2.41
3287 3667 5.574830 GCACTGACTGACACTTAGATGTAAG 59.425 44.000 8.04 8.04 41.45 2.34
3303 3683 9.967346 TTAGATGTAAGTCTATTATCTGCACAC 57.033 33.333 0.00 0.00 31.19 3.82
3304 3684 8.011844 AGATGTAAGTCTATTATCTGCACACA 57.988 34.615 0.00 0.00 0.00 3.72
3305 3685 8.646004 AGATGTAAGTCTATTATCTGCACACAT 58.354 33.333 0.00 0.00 0.00 3.21
3306 3686 8.599055 ATGTAAGTCTATTATCTGCACACATG 57.401 34.615 0.00 0.00 0.00 3.21
3307 3687 7.555965 TGTAAGTCTATTATCTGCACACATGT 58.444 34.615 0.00 0.00 0.00 3.21
3308 3688 8.691797 TGTAAGTCTATTATCTGCACACATGTA 58.308 33.333 0.00 0.00 0.00 2.29
3309 3689 9.186323 GTAAGTCTATTATCTGCACACATGTAG 57.814 37.037 0.00 0.00 39.75 2.74
3310 3690 7.353414 AGTCTATTATCTGCACACATGTAGT 57.647 36.000 0.00 0.00 39.42 2.73
3311 3691 7.786030 AGTCTATTATCTGCACACATGTAGTT 58.214 34.615 0.00 0.00 39.42 2.24
3312 3692 8.260818 AGTCTATTATCTGCACACATGTAGTTT 58.739 33.333 0.00 0.00 39.42 2.66
3313 3693 8.883731 GTCTATTATCTGCACACATGTAGTTTT 58.116 33.333 0.00 0.00 39.42 2.43
3318 3698 7.686438 ATCTGCACACATGTAGTTTTATTCA 57.314 32.000 0.00 0.00 39.42 2.57
3319 3699 7.132694 TCTGCACACATGTAGTTTTATTCAG 57.867 36.000 0.00 0.00 39.42 3.02
3320 3700 5.698832 TGCACACATGTAGTTTTATTCAGC 58.301 37.500 0.00 0.00 0.00 4.26
3321 3701 5.473162 TGCACACATGTAGTTTTATTCAGCT 59.527 36.000 0.00 0.00 0.00 4.24
3322 3702 6.652900 TGCACACATGTAGTTTTATTCAGCTA 59.347 34.615 0.00 0.00 0.00 3.32
3323 3703 6.961554 GCACACATGTAGTTTTATTCAGCTAC 59.038 38.462 0.00 0.00 35.62 3.58
3324 3704 7.173419 CACACATGTAGTTTTATTCAGCTACG 58.827 38.462 0.00 0.00 37.28 3.51
3325 3705 6.872020 ACACATGTAGTTTTATTCAGCTACGT 59.128 34.615 0.00 0.00 37.28 3.57
3326 3706 8.030692 ACACATGTAGTTTTATTCAGCTACGTA 58.969 33.333 0.00 0.00 37.28 3.57
3327 3707 8.318876 CACATGTAGTTTTATTCAGCTACGTAC 58.681 37.037 0.00 0.00 37.28 3.67
3328 3708 8.030692 ACATGTAGTTTTATTCAGCTACGTACA 58.969 33.333 0.00 0.00 37.28 2.90
3329 3709 8.532341 CATGTAGTTTTATTCAGCTACGTACAG 58.468 37.037 0.00 0.00 37.28 2.74
3330 3710 6.529125 TGTAGTTTTATTCAGCTACGTACAGC 59.471 38.462 1.93 1.93 42.12 4.40
3336 3716 4.403976 GCTACGTACAGCTCAGCC 57.596 61.111 3.01 0.00 38.57 4.85
3337 3717 1.586564 GCTACGTACAGCTCAGCCG 60.587 63.158 3.01 0.00 38.57 5.52
3338 3718 1.801332 CTACGTACAGCTCAGCCGT 59.199 57.895 4.10 4.10 35.68 5.68
3339 3719 0.523546 CTACGTACAGCTCAGCCGTG 60.524 60.000 8.72 0.00 33.32 4.94
3340 3720 1.929806 TACGTACAGCTCAGCCGTGG 61.930 60.000 8.72 0.00 33.32 4.94
3341 3721 2.970639 GTACAGCTCAGCCGTGGA 59.029 61.111 0.00 0.00 0.00 4.02
3342 3722 1.153745 GTACAGCTCAGCCGTGGAG 60.154 63.158 0.00 0.00 35.47 3.86
3343 3723 2.351244 TACAGCTCAGCCGTGGAGG 61.351 63.158 0.00 0.00 44.97 4.30
3352 3732 4.832608 CCGTGGAGGCCGGTAAGC 62.833 72.222 1.90 0.00 40.59 3.09
3353 3733 4.077184 CGTGGAGGCCGGTAAGCA 62.077 66.667 1.90 0.00 0.00 3.91
3354 3734 2.436115 GTGGAGGCCGGTAAGCAC 60.436 66.667 1.90 0.00 0.00 4.40
3355 3735 4.077184 TGGAGGCCGGTAAGCACG 62.077 66.667 1.90 0.00 0.00 5.34
3357 3737 4.752879 GAGGCCGGTAAGCACGCA 62.753 66.667 1.90 0.00 0.00 5.24
3358 3738 4.760047 AGGCCGGTAAGCACGCAG 62.760 66.667 1.90 0.00 0.00 5.18
3360 3740 2.125832 GCCGGTAAGCACGCAGTA 60.126 61.111 1.90 0.00 41.61 2.74
3361 3741 1.738830 GCCGGTAAGCACGCAGTAA 60.739 57.895 1.90 0.00 41.61 2.24
3362 3742 1.963190 GCCGGTAAGCACGCAGTAAC 61.963 60.000 1.90 0.00 41.61 2.50
3363 3743 1.680105 CCGGTAAGCACGCAGTAACG 61.680 60.000 0.00 3.89 41.61 3.18
3364 3744 1.680105 CGGTAAGCACGCAGTAACGG 61.680 60.000 3.12 0.00 41.61 4.44
3365 3745 1.418755 GTAAGCACGCAGTAACGGC 59.581 57.895 0.00 0.00 41.61 5.68
3372 3752 2.736995 GCAGTAACGGCGCTGACA 60.737 61.111 25.98 6.85 34.87 3.58
3373 3753 3.011760 GCAGTAACGGCGCTGACAC 62.012 63.158 25.98 19.03 34.87 3.67
3374 3754 1.372997 CAGTAACGGCGCTGACACT 60.373 57.895 25.98 20.98 34.87 3.55
3375 3755 1.372997 AGTAACGGCGCTGACACTG 60.373 57.895 25.98 0.00 0.00 3.66
3376 3756 1.372499 GTAACGGCGCTGACACTGA 60.372 57.895 25.98 0.00 0.00 3.41
3377 3757 0.942410 GTAACGGCGCTGACACTGAA 60.942 55.000 25.98 0.00 0.00 3.02
3378 3758 0.942410 TAACGGCGCTGACACTGAAC 60.942 55.000 25.98 0.00 0.00 3.18
3379 3759 2.661537 CGGCGCTGACACTGAACA 60.662 61.111 11.90 0.00 0.00 3.18
3380 3760 2.939022 GGCGCTGACACTGAACAC 59.061 61.111 7.64 0.00 0.00 3.32
3381 3761 1.595382 GGCGCTGACACTGAACACT 60.595 57.895 7.64 0.00 0.00 3.55
3382 3762 1.560860 GGCGCTGACACTGAACACTC 61.561 60.000 7.64 0.00 0.00 3.51
3383 3763 0.598680 GCGCTGACACTGAACACTCT 60.599 55.000 0.00 0.00 0.00 3.24
3384 3764 1.135046 CGCTGACACTGAACACTCTG 58.865 55.000 0.00 0.00 0.00 3.35
3385 3765 1.269257 CGCTGACACTGAACACTCTGA 60.269 52.381 0.00 0.00 0.00 3.27
3386 3766 2.799562 CGCTGACACTGAACACTCTGAA 60.800 50.000 0.00 0.00 0.00 3.02
3387 3767 2.541762 GCTGACACTGAACACTCTGAAC 59.458 50.000 0.00 0.00 0.00 3.18
3388 3768 2.791560 CTGACACTGAACACTCTGAACG 59.208 50.000 0.00 0.00 0.00 3.95
3389 3769 2.425668 TGACACTGAACACTCTGAACGA 59.574 45.455 0.00 0.00 0.00 3.85
3390 3770 3.119280 TGACACTGAACACTCTGAACGAA 60.119 43.478 0.00 0.00 0.00 3.85
3391 3771 3.448686 ACACTGAACACTCTGAACGAAG 58.551 45.455 0.00 0.00 0.00 3.79
3392 3772 2.219674 CACTGAACACTCTGAACGAAGC 59.780 50.000 0.00 0.00 0.00 3.86
3393 3773 1.795286 CTGAACACTCTGAACGAAGCC 59.205 52.381 0.00 0.00 0.00 4.35
3394 3774 1.149148 GAACACTCTGAACGAAGCCC 58.851 55.000 0.00 0.00 0.00 5.19
3395 3775 0.468226 AACACTCTGAACGAAGCCCA 59.532 50.000 0.00 0.00 0.00 5.36
3396 3776 0.468226 ACACTCTGAACGAAGCCCAA 59.532 50.000 0.00 0.00 0.00 4.12
3397 3777 1.134220 ACACTCTGAACGAAGCCCAAA 60.134 47.619 0.00 0.00 0.00 3.28
3398 3778 1.532868 CACTCTGAACGAAGCCCAAAG 59.467 52.381 0.00 0.00 0.00 2.77
3399 3779 0.519077 CTCTGAACGAAGCCCAAAGC 59.481 55.000 0.00 0.00 44.25 3.51
3410 3790 1.831580 GCCCAAAGCAAGAGATGACT 58.168 50.000 0.00 0.00 42.97 3.41
3411 3791 1.742268 GCCCAAAGCAAGAGATGACTC 59.258 52.381 0.00 0.00 42.97 3.36
3412 3792 2.005451 CCCAAAGCAAGAGATGACTCG 58.995 52.381 0.00 0.00 46.64 4.18
3413 3793 2.354103 CCCAAAGCAAGAGATGACTCGA 60.354 50.000 0.00 0.00 46.64 4.04
3414 3794 3.529533 CCAAAGCAAGAGATGACTCGAT 58.470 45.455 0.00 0.00 46.64 3.59
3415 3795 3.937706 CCAAAGCAAGAGATGACTCGATT 59.062 43.478 0.00 0.00 46.64 3.34
3416 3796 4.394300 CCAAAGCAAGAGATGACTCGATTT 59.606 41.667 0.00 0.00 46.64 2.17
3417 3797 5.322310 CAAAGCAAGAGATGACTCGATTTG 58.678 41.667 0.00 0.00 46.64 2.32
3418 3798 2.935201 AGCAAGAGATGACTCGATTTGC 59.065 45.455 11.80 11.80 44.62 3.68
3419 3799 2.031437 GCAAGAGATGACTCGATTTGCC 59.969 50.000 0.00 0.00 46.64 4.52
3420 3800 3.264947 CAAGAGATGACTCGATTTGCCA 58.735 45.455 0.00 0.00 46.64 4.92
3421 3801 3.834489 AGAGATGACTCGATTTGCCAT 57.166 42.857 0.00 0.00 46.64 4.40
3422 3802 3.464907 AGAGATGACTCGATTTGCCATG 58.535 45.455 0.00 0.00 46.64 3.66
3423 3803 1.945394 AGATGACTCGATTTGCCATGC 59.055 47.619 0.00 0.00 0.00 4.06
3424 3804 0.659427 ATGACTCGATTTGCCATGCG 59.341 50.000 0.00 0.00 0.00 4.73
3425 3805 0.673333 TGACTCGATTTGCCATGCGT 60.673 50.000 0.00 0.00 0.00 5.24
3426 3806 0.247814 GACTCGATTTGCCATGCGTG 60.248 55.000 0.00 0.00 0.00 5.34
3427 3807 0.955428 ACTCGATTTGCCATGCGTGT 60.955 50.000 4.96 0.00 0.00 4.49
3428 3808 0.168788 CTCGATTTGCCATGCGTGTT 59.831 50.000 4.96 0.00 0.00 3.32
3429 3809 0.595588 TCGATTTGCCATGCGTGTTT 59.404 45.000 4.96 0.00 0.00 2.83
3430 3810 0.984109 CGATTTGCCATGCGTGTTTC 59.016 50.000 4.96 0.00 0.00 2.78
3431 3811 1.665448 CGATTTGCCATGCGTGTTTCA 60.665 47.619 4.96 0.00 0.00 2.69
3432 3812 1.987770 GATTTGCCATGCGTGTTTCAG 59.012 47.619 4.96 0.00 0.00 3.02
3433 3813 0.743688 TTTGCCATGCGTGTTTCAGT 59.256 45.000 4.96 0.00 0.00 3.41
3434 3814 0.310543 TTGCCATGCGTGTTTCAGTC 59.689 50.000 4.96 0.00 0.00 3.51
3435 3815 1.154413 GCCATGCGTGTTTCAGTCG 60.154 57.895 4.96 0.00 0.00 4.18
3436 3816 1.565156 GCCATGCGTGTTTCAGTCGA 61.565 55.000 4.96 0.00 0.00 4.20
3437 3817 0.439985 CCATGCGTGTTTCAGTCGAG 59.560 55.000 4.96 0.00 0.00 4.04
3438 3818 1.418373 CATGCGTGTTTCAGTCGAGA 58.582 50.000 0.00 0.00 0.00 4.04
3439 3819 1.995484 CATGCGTGTTTCAGTCGAGAT 59.005 47.619 0.00 0.00 0.00 2.75
3440 3820 1.698165 TGCGTGTTTCAGTCGAGATC 58.302 50.000 0.00 0.00 0.00 2.75
3441 3821 0.992802 GCGTGTTTCAGTCGAGATCC 59.007 55.000 0.00 0.00 0.00 3.36
3442 3822 1.260206 CGTGTTTCAGTCGAGATCCG 58.740 55.000 0.00 0.00 40.25 4.18
3443 3823 1.135774 CGTGTTTCAGTCGAGATCCGA 60.136 52.381 2.65 2.65 46.35 4.55
3450 3830 3.920031 TCGAGATCCGACCAGGTG 58.080 61.111 0.00 0.00 43.23 4.00
3451 3831 1.301954 TCGAGATCCGACCAGGTGA 59.698 57.895 0.00 0.00 43.23 4.02
3452 3832 1.030488 TCGAGATCCGACCAGGTGAC 61.030 60.000 0.00 0.00 43.23 3.67
3453 3833 1.433879 GAGATCCGACCAGGTGACG 59.566 63.158 0.00 0.00 41.99 4.35
3454 3834 2.005960 GAGATCCGACCAGGTGACGG 62.006 65.000 12.69 12.69 46.71 4.79
3455 3835 3.718210 GATCCGACCAGGTGACGGC 62.718 68.421 13.86 0.00 45.25 5.68
3490 3870 2.993264 GGTCGACCCCGTTCCAGA 60.993 66.667 24.75 0.00 37.05 3.86
3491 3871 2.572284 GTCGACCCCGTTCCAGAG 59.428 66.667 3.51 0.00 37.05 3.35
3492 3872 2.116772 TCGACCCCGTTCCAGAGT 59.883 61.111 0.00 0.00 37.05 3.24
3493 3873 2.261671 CGACCCCGTTCCAGAGTG 59.738 66.667 0.00 0.00 0.00 3.51
3494 3874 2.047179 GACCCCGTTCCAGAGTGC 60.047 66.667 0.00 0.00 0.00 4.40
3495 3875 3.607370 GACCCCGTTCCAGAGTGCC 62.607 68.421 0.00 0.00 0.00 5.01
3496 3876 3.322466 CCCCGTTCCAGAGTGCCT 61.322 66.667 0.00 0.00 0.00 4.75
3497 3877 2.750350 CCCGTTCCAGAGTGCCTT 59.250 61.111 0.00 0.00 0.00 4.35
3498 3878 1.376037 CCCGTTCCAGAGTGCCTTC 60.376 63.158 0.00 0.00 0.00 3.46
3499 3879 1.376037 CCGTTCCAGAGTGCCTTCC 60.376 63.158 0.00 0.00 0.00 3.46
3500 3880 1.371183 CGTTCCAGAGTGCCTTCCA 59.629 57.895 0.00 0.00 0.00 3.53
3501 3881 0.951040 CGTTCCAGAGTGCCTTCCAC 60.951 60.000 0.00 0.00 45.01 4.02
3530 3910 2.807045 CGTGCTGAGCTCGGTGTC 60.807 66.667 23.36 12.72 40.98 3.67
3531 3911 2.807045 GTGCTGAGCTCGGTGTCG 60.807 66.667 23.36 1.92 37.82 4.35
3532 3912 4.724602 TGCTGAGCTCGGTGTCGC 62.725 66.667 23.36 11.70 36.13 5.19
3552 3932 3.121030 CAGCCCTTGCCGAAGTCG 61.121 66.667 0.00 0.00 38.69 4.18
3555 3935 3.423154 CCCTTGCCGAAGTCGCAC 61.423 66.667 0.00 0.00 38.18 5.34
3556 3936 2.357517 CCTTGCCGAAGTCGCACT 60.358 61.111 0.00 0.00 38.18 4.40
3557 3937 2.383527 CCTTGCCGAAGTCGCACTC 61.384 63.158 0.00 0.00 38.18 3.51
3558 3938 2.720758 CTTGCCGAAGTCGCACTCG 61.721 63.158 0.00 0.00 38.18 4.18
3559 3939 3.493830 TTGCCGAAGTCGCACTCGT 62.494 57.895 0.00 0.00 38.18 4.18
3560 3940 3.173240 GCCGAAGTCGCACTCGTC 61.173 66.667 0.00 0.00 38.18 4.20
3561 3941 2.870161 CCGAAGTCGCACTCGTCG 60.870 66.667 0.00 0.00 38.18 5.12
3562 3942 2.172659 CGAAGTCGCACTCGTCGA 59.827 61.111 0.00 0.00 34.87 4.20
3566 3946 2.864248 GTCGCACTCGTCGACGAC 60.864 66.667 34.97 24.12 45.19 4.34
3567 3947 4.081030 TCGCACTCGTCGACGACC 62.081 66.667 34.97 23.42 44.22 4.79
3568 3948 4.379143 CGCACTCGTCGACGACCA 62.379 66.667 34.97 16.80 44.22 4.02
3569 3949 2.178521 GCACTCGTCGACGACCAT 59.821 61.111 34.97 20.78 44.22 3.55
3570 3950 2.152699 GCACTCGTCGACGACCATG 61.153 63.158 34.97 29.72 44.22 3.66
3571 3951 1.514228 CACTCGTCGACGACCATGG 60.514 63.158 34.97 26.14 44.22 3.66
3572 3952 2.579787 CTCGTCGACGACCATGGC 60.580 66.667 34.97 3.65 44.22 4.40
3573 3953 4.124351 TCGTCGACGACCATGGCC 62.124 66.667 34.97 0.00 44.22 5.36
3574 3954 4.129737 CGTCGACGACCATGGCCT 62.130 66.667 33.35 0.00 43.02 5.19
3575 3955 2.202756 GTCGACGACCATGGCCTC 60.203 66.667 17.25 1.29 0.00 4.70
3576 3956 3.458163 TCGACGACCATGGCCTCC 61.458 66.667 13.04 0.00 0.00 4.30
3577 3957 3.770040 CGACGACCATGGCCTCCA 61.770 66.667 13.04 0.00 38.19 3.86
3578 3958 2.125106 GACGACCATGGCCTCCAC 60.125 66.667 13.04 0.00 35.80 4.02
3579 3959 2.927856 ACGACCATGGCCTCCACA 60.928 61.111 13.04 0.00 35.80 4.17
3580 3960 2.124983 CGACCATGGCCTCCACAG 60.125 66.667 13.04 0.00 35.80 3.66
3581 3961 2.439156 GACCATGGCCTCCACAGC 60.439 66.667 13.04 0.00 35.80 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.271776 AGCTATTTACGCGGGTGAATTTAC 59.728 41.667 24.09 15.06 34.56 2.01
16 17 0.103572 GGAGCTATTTACGCGGGTGA 59.896 55.000 16.34 3.70 0.00 4.02
31 32 3.889196 TGTGTCAATTTTGTACGGAGC 57.111 42.857 0.00 0.00 0.00 4.70
40 41 6.366877 GCTGCTGTCATAATTGTGTCAATTTT 59.633 34.615 11.93 3.40 0.00 1.82
59 60 5.173774 ACATCGGTAAATTTATGCTGCTG 57.826 39.130 0.31 0.00 0.00 4.41
71 72 5.289917 CACGTGTGAATGATACATCGGTAAA 59.710 40.000 7.58 0.00 32.19 2.01
108 109 6.910536 ACATCAGTAACTTAATGCTGCTAC 57.089 37.500 0.00 0.00 33.60 3.58
213 215 5.164090 CCGTATATATGCAAGTAAGCGTGTG 60.164 44.000 0.00 0.00 37.31 3.82
214 216 4.921515 CCGTATATATGCAAGTAAGCGTGT 59.078 41.667 0.00 0.00 37.31 4.49
268 272 7.827819 TCAGTTCTTAATGATTCCAACTACG 57.172 36.000 0.00 0.00 0.00 3.51
294 298 2.735478 TTAGCCAACCACGCGACG 60.735 61.111 15.93 3.98 0.00 5.12
301 305 1.825090 CAGATGCTGTTAGCCAACCA 58.175 50.000 0.00 0.00 41.51 3.67
355 359 2.149383 AGCTGAGCACCACAGGGAA 61.149 57.895 7.39 0.00 38.05 3.97
360 364 1.117749 AGAGACAGCTGAGCACCACA 61.118 55.000 23.35 0.00 0.00 4.17
465 470 3.319031 TCTCCTCTGACTATCATGCCA 57.681 47.619 0.00 0.00 0.00 4.92
482 488 6.348868 GCCATTTATGCAGCCTACTTTATCTC 60.349 42.308 0.00 0.00 0.00 2.75
483 489 5.474876 GCCATTTATGCAGCCTACTTTATCT 59.525 40.000 0.00 0.00 0.00 1.98
509 515 4.106197 GCAGTACTGTTAGTCGATGAAGG 58.894 47.826 23.44 0.00 0.00 3.46
516 522 6.183360 CCAAGTTATTGCAGTACTGTTAGTCG 60.183 42.308 23.44 5.27 34.91 4.18
523 529 2.423538 GCCCCAAGTTATTGCAGTACTG 59.576 50.000 18.93 18.93 34.91 2.74
580 588 3.938963 AGTAATGACTTAATGGCACCACG 59.061 43.478 0.00 0.00 35.90 4.94
597 605 6.799512 ACTACGAACAACCGCTATAAGTAAT 58.200 36.000 0.00 0.00 0.00 1.89
620 628 9.260002 ACCAAACATAATTTCAAACATTCAGAC 57.740 29.630 0.00 0.00 0.00 3.51
683 691 5.078411 AGAGCACCTTACATGAAGTGTAG 57.922 43.478 0.00 0.00 43.79 2.74
723 731 1.463056 TGTTCTGCTTTCGTAATGGCG 59.537 47.619 0.00 0.00 0.00 5.69
762 770 1.525995 GAGTGTGTGTGTGTGGGGG 60.526 63.158 0.00 0.00 0.00 5.40
763 771 1.525995 GGAGTGTGTGTGTGTGGGG 60.526 63.158 0.00 0.00 0.00 4.96
764 772 0.532862 GAGGAGTGTGTGTGTGTGGG 60.533 60.000 0.00 0.00 0.00 4.61
765 773 0.465705 AGAGGAGTGTGTGTGTGTGG 59.534 55.000 0.00 0.00 0.00 4.17
766 774 1.136891 TGAGAGGAGTGTGTGTGTGTG 59.863 52.381 0.00 0.00 0.00 3.82
767 775 1.485124 TGAGAGGAGTGTGTGTGTGT 58.515 50.000 0.00 0.00 0.00 3.72
768 776 2.410939 CATGAGAGGAGTGTGTGTGTG 58.589 52.381 0.00 0.00 0.00 3.82
769 777 1.345741 CCATGAGAGGAGTGTGTGTGT 59.654 52.381 0.00 0.00 0.00 3.72
770 778 1.345741 ACCATGAGAGGAGTGTGTGTG 59.654 52.381 0.00 0.00 0.00 3.82
771 779 1.722034 ACCATGAGAGGAGTGTGTGT 58.278 50.000 0.00 0.00 0.00 3.72
772 780 3.448660 TGATACCATGAGAGGAGTGTGTG 59.551 47.826 0.00 0.00 0.00 3.82
773 781 3.703556 CTGATACCATGAGAGGAGTGTGT 59.296 47.826 0.00 0.00 0.00 3.72
774 782 3.956848 TCTGATACCATGAGAGGAGTGTG 59.043 47.826 0.00 0.00 0.00 3.82
775 783 4.256983 TCTGATACCATGAGAGGAGTGT 57.743 45.455 0.00 0.00 0.00 3.55
776 784 5.303845 TCAATCTGATACCATGAGAGGAGTG 59.696 44.000 0.00 0.00 0.00 3.51
777 785 5.462240 TCAATCTGATACCATGAGAGGAGT 58.538 41.667 0.00 0.00 0.00 3.85
778 786 6.416631 TTCAATCTGATACCATGAGAGGAG 57.583 41.667 0.00 0.00 0.00 3.69
779 787 7.384524 AATTCAATCTGATACCATGAGAGGA 57.615 36.000 0.00 0.00 0.00 3.71
952 962 4.142816 CGCTAGCTGCTGACTTATTTTTGT 60.143 41.667 13.43 0.00 40.11 2.83
1057 1072 5.675538 AGACAGCATATAACTCTTTCCCAC 58.324 41.667 0.00 0.00 0.00 4.61
1060 1075 7.849804 TGAAAGACAGCATATAACTCTTTCC 57.150 36.000 13.28 0.91 43.10 3.13
1082 1097 7.726216 ACGTGAATAGACCATTAGAATCATGA 58.274 34.615 0.00 0.00 0.00 3.07
1158 1173 7.442666 GTCATCAAGGTTCTTCAGTTCTTTAGT 59.557 37.037 0.00 0.00 0.00 2.24
1363 1378 6.010219 TGGAAAGACAAGAATAGAAAAGGGG 58.990 40.000 0.00 0.00 0.00 4.79
1395 1411 7.865385 GCTCCTACTTGACTAGTGATGAATAAG 59.135 40.741 0.00 0.00 37.73 1.73
1429 1453 9.696917 ATGTTCTTTAATTTACAAAAGCCAGAG 57.303 29.630 0.00 0.00 33.61 3.35
1456 1482 4.733972 AGAAACGCTGCTTTAAGACTTC 57.266 40.909 0.00 0.00 0.00 3.01
1462 1488 6.569179 AATAGGAAAGAAACGCTGCTTTAA 57.431 33.333 0.00 0.00 34.69 1.52
1640 1710 8.197592 TCAGGAACTAAACTAAAGTATGGACA 57.802 34.615 0.00 0.00 36.02 4.02
1703 1773 3.679389 AGTCGTGAAAAATCCTGCAGAT 58.321 40.909 17.39 3.92 36.48 2.90
1704 1774 3.126001 AGTCGTGAAAAATCCTGCAGA 57.874 42.857 17.39 1.21 0.00 4.26
1739 1809 4.065088 TCTCACCACTAGTTGCAATGTTC 58.935 43.478 0.59 0.00 0.00 3.18
1858 1928 5.458452 ACAAAACAAATCATGCACTACAACG 59.542 36.000 0.00 0.00 0.00 4.10
1923 1996 0.182061 CAGCCACATCCTATGCAGGT 59.818 55.000 0.00 0.00 43.18 4.00
1940 2013 4.699257 AGCAAGCAATTTCTAGGAAGTCAG 59.301 41.667 0.00 0.00 0.00 3.51
1941 2014 4.456911 CAGCAAGCAATTTCTAGGAAGTCA 59.543 41.667 0.00 0.00 0.00 3.41
1947 2020 3.128242 CCTGTCAGCAAGCAATTTCTAGG 59.872 47.826 0.00 0.00 0.00 3.02
1951 2024 3.503748 ACTACCTGTCAGCAAGCAATTTC 59.496 43.478 0.00 0.00 0.00 2.17
2096 2169 3.203442 CATGACACCATGCTGGCC 58.797 61.111 0.00 0.00 42.67 5.36
2110 2183 3.374220 ACAAACATGAAGCACCACATG 57.626 42.857 0.00 0.00 46.11 3.21
2114 2187 6.215121 CAATAAGAACAAACATGAAGCACCA 58.785 36.000 0.00 0.00 0.00 4.17
2124 2197 8.035394 TGCAACTTTAACCAATAAGAACAAACA 58.965 29.630 0.00 0.00 0.00 2.83
2127 2200 7.995463 GTGCAACTTTAACCAATAAGAACAA 57.005 32.000 0.00 0.00 0.00 2.83
2145 2222 2.128771 ATACACCATCCCAGTGCAAC 57.871 50.000 0.00 0.00 38.87 4.17
2153 2230 4.432712 GCATTGTTTGAATACACCATCCC 58.567 43.478 0.00 0.00 0.00 3.85
2158 2235 4.381566 GTGTTCGCATTGTTTGAATACACC 59.618 41.667 0.00 0.00 34.90 4.16
2201 2279 4.157840 AGTCTGGTCCAACTTGACAAAAAC 59.842 41.667 10.66 0.00 36.97 2.43
2205 2287 3.199946 AGAAGTCTGGTCCAACTTGACAA 59.800 43.478 18.44 0.00 35.90 3.18
2208 2290 3.038280 TGAGAAGTCTGGTCCAACTTGA 58.962 45.455 18.44 0.20 35.90 3.02
2215 2297 0.966920 TTCGGTGAGAAGTCTGGTCC 59.033 55.000 0.00 0.00 34.26 4.46
2224 2306 2.766313 CACCAGATGTTTCGGTGAGAA 58.234 47.619 1.50 0.00 43.33 2.87
2449 2531 2.815647 GAAGGAGCAGCGTTCCGG 60.816 66.667 0.00 0.00 39.77 5.14
2461 2543 0.972134 CACCTGAGACAGCAGAAGGA 59.028 55.000 0.00 0.00 38.14 3.36
2515 2597 3.524648 GACGGGGACTTTCACGGCA 62.525 63.158 0.00 0.00 33.82 5.69
2586 2668 4.099266 AGCATTGACAGTTTGGTTTGCTTA 59.901 37.500 0.00 0.00 35.81 3.09
2587 2669 3.118665 AGCATTGACAGTTTGGTTTGCTT 60.119 39.130 0.00 0.00 35.81 3.91
2640 2722 4.767255 CTGGGACTCTGGCACCGC 62.767 72.222 0.00 0.00 0.00 5.68
2675 2757 1.338674 CCTCGCAGACAACCATAACCA 60.339 52.381 0.00 0.00 0.00 3.67
2676 2758 1.369625 CCTCGCAGACAACCATAACC 58.630 55.000 0.00 0.00 0.00 2.85
2677 2759 1.066430 TCCCTCGCAGACAACCATAAC 60.066 52.381 0.00 0.00 0.00 1.89
2678 2760 1.271856 TCCCTCGCAGACAACCATAA 58.728 50.000 0.00 0.00 0.00 1.90
2679 2761 1.207089 CTTCCCTCGCAGACAACCATA 59.793 52.381 0.00 0.00 0.00 2.74
2680 2762 0.036010 CTTCCCTCGCAGACAACCAT 60.036 55.000 0.00 0.00 0.00 3.55
2688 2770 0.393537 AAGCAATCCTTCCCTCGCAG 60.394 55.000 0.00 0.00 0.00 5.18
2734 2816 0.535102 CAGTTTCGGCTCAACAGGGT 60.535 55.000 0.00 0.00 0.00 4.34
2737 2819 0.588252 CCACAGTTTCGGCTCAACAG 59.412 55.000 0.00 0.00 0.00 3.16
2747 2829 5.904362 AATTATTCTGCCTCCACAGTTTC 57.096 39.130 0.00 0.00 38.84 2.78
2760 2842 3.365666 CCCAGCAGCGCATAATTATTCTG 60.366 47.826 11.47 11.81 0.00 3.02
2823 2906 4.165779 CCATTAAATCACAAACAGACGCC 58.834 43.478 0.00 0.00 0.00 5.68
2848 2933 1.202065 CCGCCATTCAAGTTCACATCG 60.202 52.381 0.00 0.00 0.00 3.84
2866 2951 4.846779 TTGGGAAGAAAATGTTTCTCCG 57.153 40.909 3.82 0.00 0.00 4.63
2871 2956 6.358974 CCACCTATTGGGAAGAAAATGTTT 57.641 37.500 0.00 0.00 42.54 2.83
2930 3015 3.698539 TCACCAAGTTTGATGACTTTGCA 59.301 39.130 0.00 0.00 37.76 4.08
3001 3090 2.309528 TCAACATCACGCCAGATACC 57.690 50.000 0.00 0.00 0.00 2.73
3024 3404 9.234384 CTCATAATATGACTCGTTAACGAAACT 57.766 33.333 28.82 15.60 40.40 2.66
3136 3516 0.250901 ATGCCGCCTACATGATTCCC 60.251 55.000 0.00 0.00 0.00 3.97
3168 3548 7.535139 TCATCATCCCGTAAAATTTTGACTTC 58.465 34.615 13.76 0.00 0.00 3.01
3178 3558 4.149511 TCAGCATCATCATCCCGTAAAA 57.850 40.909 0.00 0.00 0.00 1.52
3183 3563 2.251409 ACTTCAGCATCATCATCCCG 57.749 50.000 0.00 0.00 0.00 5.14
3211 3591 2.092267 AGACCATGAGCAATGCATACCA 60.092 45.455 8.35 0.00 34.67 3.25
3255 3635 0.664767 GTCAGTCAGTGCAGGACGAC 60.665 60.000 18.28 18.28 40.20 4.34
3277 3657 9.967346 GTGTGCAGATAATAGACTTACATCTAA 57.033 33.333 0.00 0.00 34.86 2.10
3278 3658 9.131791 TGTGTGCAGATAATAGACTTACATCTA 57.868 33.333 0.00 0.00 35.67 1.98
3279 3659 8.011844 TGTGTGCAGATAATAGACTTACATCT 57.988 34.615 0.00 0.00 0.00 2.90
3280 3660 8.706936 CATGTGTGCAGATAATAGACTTACATC 58.293 37.037 0.00 0.00 0.00 3.06
3281 3661 8.206867 ACATGTGTGCAGATAATAGACTTACAT 58.793 33.333 0.00 0.00 0.00 2.29
3282 3662 7.555965 ACATGTGTGCAGATAATAGACTTACA 58.444 34.615 0.00 0.00 0.00 2.41
3283 3663 9.186323 CTACATGTGTGCAGATAATAGACTTAC 57.814 37.037 9.11 0.00 0.00 2.34
3284 3664 8.914011 ACTACATGTGTGCAGATAATAGACTTA 58.086 33.333 9.11 0.00 0.00 2.24
3285 3665 7.786030 ACTACATGTGTGCAGATAATAGACTT 58.214 34.615 9.11 0.00 0.00 3.01
3286 3666 7.353414 ACTACATGTGTGCAGATAATAGACT 57.647 36.000 9.11 0.00 0.00 3.24
3287 3667 8.425577 AAACTACATGTGTGCAGATAATAGAC 57.574 34.615 9.11 0.00 0.00 2.59
3292 3672 9.225436 TGAATAAAACTACATGTGTGCAGATAA 57.775 29.630 9.11 0.00 0.00 1.75
3293 3673 8.785329 TGAATAAAACTACATGTGTGCAGATA 57.215 30.769 9.11 0.00 0.00 1.98
3294 3674 7.627088 GCTGAATAAAACTACATGTGTGCAGAT 60.627 37.037 9.11 0.00 0.00 2.90
3295 3675 6.348458 GCTGAATAAAACTACATGTGTGCAGA 60.348 38.462 9.11 0.00 0.00 4.26
3296 3676 5.796935 GCTGAATAAAACTACATGTGTGCAG 59.203 40.000 9.11 0.00 0.00 4.41
3297 3677 5.473162 AGCTGAATAAAACTACATGTGTGCA 59.527 36.000 9.11 0.00 0.00 4.57
3298 3678 5.942872 AGCTGAATAAAACTACATGTGTGC 58.057 37.500 9.11 2.46 0.00 4.57
3299 3679 7.148639 ACGTAGCTGAATAAAACTACATGTGTG 60.149 37.037 9.11 3.79 35.76 3.82
3300 3680 6.872020 ACGTAGCTGAATAAAACTACATGTGT 59.128 34.615 9.11 1.62 35.76 3.72
3301 3681 7.290857 ACGTAGCTGAATAAAACTACATGTG 57.709 36.000 9.11 0.93 35.76 3.21
3302 3682 8.030692 TGTACGTAGCTGAATAAAACTACATGT 58.969 33.333 2.69 2.69 35.76 3.21
3303 3683 8.402326 TGTACGTAGCTGAATAAAACTACATG 57.598 34.615 0.00 0.00 35.76 3.21
3304 3684 7.222224 GCTGTACGTAGCTGAATAAAACTACAT 59.778 37.037 3.01 0.00 40.52 2.29
3305 3685 6.529125 GCTGTACGTAGCTGAATAAAACTACA 59.471 38.462 3.01 0.00 40.52 2.74
3306 3686 6.920254 GCTGTACGTAGCTGAATAAAACTAC 58.080 40.000 3.01 0.00 40.52 2.73
3319 3699 1.586564 CGGCTGAGCTGTACGTAGC 60.587 63.158 4.80 1.93 44.01 3.58
3320 3700 4.692129 CGGCTGAGCTGTACGTAG 57.308 61.111 4.80 0.00 0.00 3.51
3336 3716 4.077184 TGCTTACCGGCCTCCACG 62.077 66.667 0.00 0.00 0.00 4.94
3337 3717 2.436115 GTGCTTACCGGCCTCCAC 60.436 66.667 0.00 0.00 0.00 4.02
3338 3718 4.077184 CGTGCTTACCGGCCTCCA 62.077 66.667 0.00 0.00 0.00 3.86
3340 3720 4.752879 TGCGTGCTTACCGGCCTC 62.753 66.667 0.00 0.00 0.00 4.70
3341 3721 4.760047 CTGCGTGCTTACCGGCCT 62.760 66.667 0.00 0.00 0.00 5.19
3342 3722 3.652539 TACTGCGTGCTTACCGGCC 62.653 63.158 0.00 0.00 0.00 6.13
3343 3723 1.738830 TTACTGCGTGCTTACCGGC 60.739 57.895 0.00 0.00 0.00 6.13
3344 3724 1.680105 CGTTACTGCGTGCTTACCGG 61.680 60.000 0.00 0.00 0.00 5.28
3345 3725 1.680105 CCGTTACTGCGTGCTTACCG 61.680 60.000 0.00 0.00 0.00 4.02
3346 3726 1.963190 GCCGTTACTGCGTGCTTACC 61.963 60.000 0.00 0.00 0.00 2.85
3347 3727 1.418755 GCCGTTACTGCGTGCTTAC 59.581 57.895 0.00 0.00 0.00 2.34
3348 3728 2.089936 CGCCGTTACTGCGTGCTTA 61.090 57.895 12.73 0.00 46.59 3.09
3349 3729 3.411351 CGCCGTTACTGCGTGCTT 61.411 61.111 12.73 0.00 46.59 3.91
3355 3735 2.736995 TGTCAGCGCCGTTACTGC 60.737 61.111 2.29 0.00 33.80 4.40
3356 3736 1.372997 AGTGTCAGCGCCGTTACTG 60.373 57.895 2.29 0.00 35.15 2.74
3357 3737 1.372997 CAGTGTCAGCGCCGTTACT 60.373 57.895 2.29 0.77 0.00 2.24
3358 3738 0.942410 TTCAGTGTCAGCGCCGTTAC 60.942 55.000 2.29 0.00 0.00 2.50
3359 3739 0.942410 GTTCAGTGTCAGCGCCGTTA 60.942 55.000 2.29 0.00 0.00 3.18
3360 3740 2.108157 TTCAGTGTCAGCGCCGTT 59.892 55.556 2.29 0.00 0.00 4.44
3361 3741 2.661866 GTTCAGTGTCAGCGCCGT 60.662 61.111 2.29 0.00 0.00 5.68
3362 3742 2.661537 TGTTCAGTGTCAGCGCCG 60.662 61.111 2.29 0.00 0.00 6.46
3363 3743 1.560860 GAGTGTTCAGTGTCAGCGCC 61.561 60.000 2.29 0.00 0.00 6.53
3364 3744 0.598680 AGAGTGTTCAGTGTCAGCGC 60.599 55.000 0.00 0.00 0.00 5.92
3365 3745 1.135046 CAGAGTGTTCAGTGTCAGCG 58.865 55.000 0.00 0.00 0.00 5.18
3366 3746 2.515926 TCAGAGTGTTCAGTGTCAGC 57.484 50.000 0.00 0.00 0.00 4.26
3367 3747 2.791560 CGTTCAGAGTGTTCAGTGTCAG 59.208 50.000 0.00 0.00 0.00 3.51
3368 3748 2.425668 TCGTTCAGAGTGTTCAGTGTCA 59.574 45.455 0.00 0.00 0.00 3.58
3369 3749 3.079960 TCGTTCAGAGTGTTCAGTGTC 57.920 47.619 0.00 0.00 0.00 3.67
3370 3750 3.448686 CTTCGTTCAGAGTGTTCAGTGT 58.551 45.455 0.00 0.00 0.00 3.55
3371 3751 2.219674 GCTTCGTTCAGAGTGTTCAGTG 59.780 50.000 0.00 0.00 0.00 3.66
3372 3752 2.474816 GCTTCGTTCAGAGTGTTCAGT 58.525 47.619 0.00 0.00 0.00 3.41
3373 3753 1.795286 GGCTTCGTTCAGAGTGTTCAG 59.205 52.381 0.00 0.00 0.00 3.02
3374 3754 1.540363 GGGCTTCGTTCAGAGTGTTCA 60.540 52.381 0.00 0.00 0.00 3.18
3375 3755 1.149148 GGGCTTCGTTCAGAGTGTTC 58.851 55.000 0.00 0.00 0.00 3.18
3376 3756 0.468226 TGGGCTTCGTTCAGAGTGTT 59.532 50.000 0.00 0.00 0.00 3.32
3377 3757 0.468226 TTGGGCTTCGTTCAGAGTGT 59.532 50.000 0.00 0.00 0.00 3.55
3378 3758 1.532868 CTTTGGGCTTCGTTCAGAGTG 59.467 52.381 0.00 0.00 0.00 3.51
3379 3759 1.884235 CTTTGGGCTTCGTTCAGAGT 58.116 50.000 0.00 0.00 0.00 3.24
3380 3760 0.519077 GCTTTGGGCTTCGTTCAGAG 59.481 55.000 0.00 0.00 38.06 3.35
3381 3761 0.179032 TGCTTTGGGCTTCGTTCAGA 60.179 50.000 0.00 0.00 42.39 3.27
3382 3762 0.667993 TTGCTTTGGGCTTCGTTCAG 59.332 50.000 0.00 0.00 42.39 3.02
3383 3763 0.667993 CTTGCTTTGGGCTTCGTTCA 59.332 50.000 0.00 0.00 42.39 3.18
3384 3764 0.951558 TCTTGCTTTGGGCTTCGTTC 59.048 50.000 0.00 0.00 42.39 3.95
3385 3765 0.954452 CTCTTGCTTTGGGCTTCGTT 59.046 50.000 0.00 0.00 42.39 3.85
3386 3766 0.108585 TCTCTTGCTTTGGGCTTCGT 59.891 50.000 0.00 0.00 42.39 3.85
3387 3767 1.131883 CATCTCTTGCTTTGGGCTTCG 59.868 52.381 0.00 0.00 42.39 3.79
3388 3768 2.163211 GTCATCTCTTGCTTTGGGCTTC 59.837 50.000 0.00 0.00 42.39 3.86
3389 3769 2.165998 GTCATCTCTTGCTTTGGGCTT 58.834 47.619 0.00 0.00 42.39 4.35
3390 3770 1.353694 AGTCATCTCTTGCTTTGGGCT 59.646 47.619 0.00 0.00 42.39 5.19
3391 3771 1.742268 GAGTCATCTCTTGCTTTGGGC 59.258 52.381 0.00 0.00 37.68 5.36
3392 3772 2.005451 CGAGTCATCTCTTGCTTTGGG 58.995 52.381 0.00 0.00 38.45 4.12
3393 3773 2.964740 TCGAGTCATCTCTTGCTTTGG 58.035 47.619 0.00 0.00 38.45 3.28
3394 3774 5.322310 CAAATCGAGTCATCTCTTGCTTTG 58.678 41.667 0.00 0.00 38.45 2.77
3395 3775 4.142730 GCAAATCGAGTCATCTCTTGCTTT 60.143 41.667 10.97 0.00 41.70 3.51
3396 3776 3.373439 GCAAATCGAGTCATCTCTTGCTT 59.627 43.478 10.97 0.00 41.70 3.91
3397 3777 2.935201 GCAAATCGAGTCATCTCTTGCT 59.065 45.455 10.97 0.00 41.70 3.91
3398 3778 2.031437 GGCAAATCGAGTCATCTCTTGC 59.969 50.000 10.22 10.22 42.93 4.01
3399 3779 3.264947 TGGCAAATCGAGTCATCTCTTG 58.735 45.455 0.00 0.00 38.45 3.02
3400 3780 3.616956 TGGCAAATCGAGTCATCTCTT 57.383 42.857 0.00 0.00 38.45 2.85
3401 3781 3.464907 CATGGCAAATCGAGTCATCTCT 58.535 45.455 0.00 0.00 38.45 3.10
3402 3782 2.032204 GCATGGCAAATCGAGTCATCTC 60.032 50.000 0.00 0.00 37.35 2.75
3403 3783 1.945394 GCATGGCAAATCGAGTCATCT 59.055 47.619 0.00 0.00 0.00 2.90
3404 3784 1.333524 CGCATGGCAAATCGAGTCATC 60.334 52.381 0.00 0.00 0.00 2.92
3405 3785 0.659427 CGCATGGCAAATCGAGTCAT 59.341 50.000 0.00 0.00 0.00 3.06
3406 3786 0.673333 ACGCATGGCAAATCGAGTCA 60.673 50.000 12.13 0.00 0.00 3.41
3407 3787 0.247814 CACGCATGGCAAATCGAGTC 60.248 55.000 12.13 0.00 0.00 3.36
3408 3788 0.955428 ACACGCATGGCAAATCGAGT 60.955 50.000 12.13 8.12 0.00 4.18
3409 3789 0.168788 AACACGCATGGCAAATCGAG 59.831 50.000 12.13 7.58 0.00 4.04
3410 3790 0.595588 AAACACGCATGGCAAATCGA 59.404 45.000 12.13 0.00 0.00 3.59
3411 3791 0.984109 GAAACACGCATGGCAAATCG 59.016 50.000 0.00 0.00 0.00 3.34
3412 3792 1.987770 CTGAAACACGCATGGCAAATC 59.012 47.619 0.00 0.00 0.00 2.17
3413 3793 1.340889 ACTGAAACACGCATGGCAAAT 59.659 42.857 0.00 0.00 0.00 2.32
3414 3794 0.743688 ACTGAAACACGCATGGCAAA 59.256 45.000 0.00 0.00 0.00 3.68
3415 3795 0.310543 GACTGAAACACGCATGGCAA 59.689 50.000 0.00 0.00 0.00 4.52
3416 3796 1.840630 CGACTGAAACACGCATGGCA 61.841 55.000 0.00 0.00 0.00 4.92
3417 3797 1.154413 CGACTGAAACACGCATGGC 60.154 57.895 0.00 0.00 0.00 4.40
3418 3798 0.439985 CTCGACTGAAACACGCATGG 59.560 55.000 0.00 0.00 0.00 3.66
3419 3799 1.418373 TCTCGACTGAAACACGCATG 58.582 50.000 0.00 0.00 0.00 4.06
3420 3800 2.263077 GATCTCGACTGAAACACGCAT 58.737 47.619 0.00 0.00 0.00 4.73
3421 3801 1.668919 GGATCTCGACTGAAACACGCA 60.669 52.381 0.00 0.00 0.00 5.24
3422 3802 0.992802 GGATCTCGACTGAAACACGC 59.007 55.000 0.00 0.00 0.00 5.34
3423 3803 1.135774 TCGGATCTCGACTGAAACACG 60.136 52.381 2.65 0.00 43.74 4.49
3424 3804 2.631418 TCGGATCTCGACTGAAACAC 57.369 50.000 2.65 0.00 43.74 3.32
3433 3813 1.030488 GTCACCTGGTCGGATCTCGA 61.030 60.000 0.00 2.65 46.77 4.04
3434 3814 1.433879 GTCACCTGGTCGGATCTCG 59.566 63.158 0.00 0.00 40.90 4.04
3435 3815 1.433879 CGTCACCTGGTCGGATCTC 59.566 63.158 0.00 0.00 36.31 2.75
3436 3816 2.052690 CCGTCACCTGGTCGGATCT 61.053 63.158 19.19 0.00 46.05 2.75
3437 3817 2.494918 CCGTCACCTGGTCGGATC 59.505 66.667 19.19 0.35 46.05 3.36
3438 3818 3.771160 GCCGTCACCTGGTCGGAT 61.771 66.667 25.90 0.00 46.05 4.18
3473 3853 2.993264 TCTGGAACGGGGTCGACC 60.993 66.667 27.04 27.04 40.11 4.79
3474 3854 2.572284 CTCTGGAACGGGGTCGAC 59.428 66.667 7.13 7.13 40.11 4.20
3479 3859 2.804828 GAAGGCACTCTGGAACGGGG 62.805 65.000 0.00 0.00 44.03 5.73
3480 3860 1.376037 GAAGGCACTCTGGAACGGG 60.376 63.158 0.00 0.00 38.49 5.28
3481 3861 1.376037 GGAAGGCACTCTGGAACGG 60.376 63.158 0.00 0.00 38.49 4.44
3482 3862 0.951040 GTGGAAGGCACTCTGGAACG 60.951 60.000 0.00 0.00 38.49 3.95
3483 3863 0.108585 TGTGGAAGGCACTCTGGAAC 59.891 55.000 0.00 0.00 38.49 3.62
3484 3864 0.108585 GTGTGGAAGGCACTCTGGAA 59.891 55.000 0.00 0.00 38.49 3.53
3485 3865 1.754745 GTGTGGAAGGCACTCTGGA 59.245 57.895 0.00 0.00 38.49 3.86
3486 3866 1.669115 CGTGTGGAAGGCACTCTGG 60.669 63.158 0.00 0.00 38.49 3.86
3487 3867 1.669115 CCGTGTGGAAGGCACTCTG 60.669 63.158 0.00 0.00 38.49 3.35
3488 3868 2.743718 CCGTGTGGAAGGCACTCT 59.256 61.111 0.00 0.00 38.49 3.24
3510 3890 4.406173 ACCGAGCTCAGCACGTCG 62.406 66.667 15.60 7.76 40.66 5.12
3511 3891 2.807045 CACCGAGCTCAGCACGTC 60.807 66.667 15.60 0.00 40.66 4.34
3512 3892 3.559657 GACACCGAGCTCAGCACGT 62.560 63.158 15.60 2.68 40.66 4.49
3513 3893 2.807045 GACACCGAGCTCAGCACG 60.807 66.667 15.40 9.82 41.79 5.34
3514 3894 2.807045 CGACACCGAGCTCAGCAC 60.807 66.667 15.40 0.00 38.22 4.40
3515 3895 4.724602 GCGACACCGAGCTCAGCA 62.725 66.667 15.40 0.00 38.22 4.41
3538 3918 3.423154 GTGCGACTTCGGCAAGGG 61.423 66.667 0.02 0.00 40.23 3.95
3539 3919 2.357517 AGTGCGACTTCGGCAAGG 60.358 61.111 0.02 0.00 40.23 3.61
3540 3920 2.720758 CGAGTGCGACTTCGGCAAG 61.721 63.158 0.02 0.00 40.82 4.01
3541 3921 2.733218 CGAGTGCGACTTCGGCAA 60.733 61.111 0.02 0.00 40.82 4.52
3542 3922 3.891586 GACGAGTGCGACTTCGGCA 62.892 63.158 0.02 0.00 41.64 5.69
3543 3923 3.173240 GACGAGTGCGACTTCGGC 61.173 66.667 0.02 1.13 41.64 5.54
3544 3924 2.870161 CGACGAGTGCGACTTCGG 60.870 66.667 0.02 0.00 41.64 4.30
3545 3925 2.172659 TCGACGAGTGCGACTTCG 59.827 61.111 0.00 0.00 41.64 3.79
3557 3937 4.129737 AGGCCATGGTCGTCGACG 62.130 66.667 31.30 31.30 41.45 5.12
3558 3938 2.202756 GAGGCCATGGTCGTCGAC 60.203 66.667 17.16 17.16 0.00 4.20
3559 3939 3.458163 GGAGGCCATGGTCGTCGA 61.458 66.667 14.67 0.00 0.00 4.20
3560 3940 3.770040 TGGAGGCCATGGTCGTCG 61.770 66.667 14.67 0.00 0.00 5.12
3561 3941 2.125106 GTGGAGGCCATGGTCGTC 60.125 66.667 14.67 15.50 35.28 4.20
3562 3942 2.927856 TGTGGAGGCCATGGTCGT 60.928 61.111 14.67 7.34 35.28 4.34
3563 3943 2.124983 CTGTGGAGGCCATGGTCG 60.125 66.667 14.67 0.00 35.28 4.79
3564 3944 2.439156 GCTGTGGAGGCCATGGTC 60.439 66.667 8.79 8.79 35.28 4.02


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

AutoCloner maintained by Alex Coulton.