Multiple sequence alignment - TraesCS4B01G040700

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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 TraesCS4B01G040700 chr4B 100.000 4145 0 0 1 4145 28320984 28316840 0.000000e+00 7655
1 TraesCS4B01G040700 chr4A 91.857 3328 210 31 1 3283 584039445 584042756 0.000000e+00 4588
2 TraesCS4B01G040700 chr4A 87.931 406 26 5 3760 4145 584043439 584043841 1.360000e-124 457
3 TraesCS4B01G040700 chr4A 82.510 526 68 15 38 551 584032415 584032928 1.370000e-119 440
4 TraesCS4B01G040700 chr4D 93.622 3026 161 19 271 3286 16450062 16447059 0.000000e+00 4490
5 TraesCS4B01G040700 chr4D 92.388 1524 102 6 1711 3232 16375605 16374094 0.000000e+00 2159
6 TraesCS4B01G040700 chr4D 88.222 917 53 18 1 898 16404416 16403536 0.000000e+00 1044
7 TraesCS4B01G040700 chr4D 90.600 500 45 2 900 1399 16403450 16402953 0.000000e+00 662
8 TraesCS4B01G040700 chr4D 89.904 416 20 7 3280 3687 16447023 16446622 2.210000e-142 516
9 TraesCS4B01G040700 chr4D 96.943 229 7 0 3 231 16450562 16450334 6.500000e-103 385
10 TraesCS4B01G040700 chr4D 88.415 328 17 10 3818 4145 16446620 16446314 3.910000e-100 375
11 TraesCS4B01G040700 chr6B 78.175 2126 424 33 1024 3120 160716911 160714797 0.000000e+00 1319
12 TraesCS4B01G040700 chr6B 77.674 2150 436 33 1040 3155 160683066 160680927 0.000000e+00 1271
13 TraesCS4B01G040700 chr6B 75.930 2177 456 49 1040 3167 160912079 160909922 0.000000e+00 1055
14 TraesCS4B01G040700 chr6B 79.462 1227 232 17 1028 2243 160908188 160906971 0.000000e+00 852
15 TraesCS4B01G040700 chr6B 71.744 1950 500 41 1035 2960 157900391 157902313 6.190000e-138 501
16 TraesCS4B01G040700 chr6A 77.184 2152 443 37 1024 3148 101865329 101863199 0.000000e+00 1210
17 TraesCS4B01G040700 chr6A 76.637 2123 445 48 1030 3116 101554711 101552604 0.000000e+00 1125
18 TraesCS4B01G040700 chr6A 78.947 418 82 4 2753 3169 101843196 101842784 3.160000e-71 279
19 TraesCS4B01G040700 chr6D 76.766 2109 444 41 1041 3116 84224354 84222259 0.000000e+00 1138
20 TraesCS4B01G040700 chr6D 76.008 2059 438 47 1126 3148 84653751 84651713 0.000000e+00 1014


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 TraesCS4B01G040700 chr4B 28316840 28320984 4144 True 7655.0 7655 100.000 1 4145 1 chr4B.!!$R1 4144
1 TraesCS4B01G040700 chr4A 584039445 584043841 4396 False 2522.5 4588 89.894 1 4145 2 chr4A.!!$F2 4144
2 TraesCS4B01G040700 chr4A 584032415 584032928 513 False 440.0 440 82.510 38 551 1 chr4A.!!$F1 513
3 TraesCS4B01G040700 chr4D 16374094 16375605 1511 True 2159.0 2159 92.388 1711 3232 1 chr4D.!!$R1 1521
4 TraesCS4B01G040700 chr4D 16446314 16450562 4248 True 1441.5 4490 92.221 3 4145 4 chr4D.!!$R3 4142
5 TraesCS4B01G040700 chr4D 16402953 16404416 1463 True 853.0 1044 89.411 1 1399 2 chr4D.!!$R2 1398
6 TraesCS4B01G040700 chr6B 160714797 160716911 2114 True 1319.0 1319 78.175 1024 3120 1 chr6B.!!$R2 2096
7 TraesCS4B01G040700 chr6B 160680927 160683066 2139 True 1271.0 1271 77.674 1040 3155 1 chr6B.!!$R1 2115
8 TraesCS4B01G040700 chr6B 160906971 160912079 5108 True 953.5 1055 77.696 1028 3167 2 chr6B.!!$R3 2139
9 TraesCS4B01G040700 chr6B 157900391 157902313 1922 False 501.0 501 71.744 1035 2960 1 chr6B.!!$F1 1925
10 TraesCS4B01G040700 chr6A 101863199 101865329 2130 True 1210.0 1210 77.184 1024 3148 1 chr6A.!!$R3 2124
11 TraesCS4B01G040700 chr6A 101552604 101554711 2107 True 1125.0 1125 76.637 1030 3116 1 chr6A.!!$R1 2086
12 TraesCS4B01G040700 chr6D 84222259 84224354 2095 True 1138.0 1138 76.766 1041 3116 1 chr6D.!!$R1 2075
13 TraesCS4B01G040700 chr6D 84651713 84653751 2038 True 1014.0 1014 76.008 1126 3148 1 chr6D.!!$R2 2022

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
630 907 0.187361 TATGGGGTAATGGGCAAGCC 59.813 55.0 1.52 1.52 0.00 4.35 F
1021 1403 0.107508 GCATTCTGCAGCCCTAGTCA 60.108 55.0 9.47 0.00 44.26 3.41 F
2298 2698 0.325933 TGCCACAAGATGAGACCCTG 59.674 55.0 0.00 0.00 0.00 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1523 1914 1.024271 GGTGAAGCTGTTGTTGCTGA 58.976 50.000 0.00 0.0 41.03 4.26 R
2970 3393 3.222603 TGCTCTGACTGAACTACACTGA 58.777 45.455 0.00 0.0 0.00 3.41 R
3739 4552 0.108774 GGACTATAGGGTGGCAAGGC 59.891 60.000 4.43 0.0 0.00 4.35 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
142 144 6.631971 TTTATCATTGTCACTTGTCTTGCA 57.368 33.333 0.00 0.00 0.00 4.08
253 370 6.429078 ACTTGTTATGATAATGATGCGATGCT 59.571 34.615 0.00 0.00 0.00 3.79
334 601 8.969121 CACTTGTTGTGCAATTATTCTATTGA 57.031 30.769 0.00 0.00 40.06 2.57
335 602 9.409312 CACTTGTTGTGCAATTATTCTATTGAA 57.591 29.630 0.00 0.00 40.06 2.69
396 663 6.375174 ACTTGTGCTGTGCAATTATTCTATCA 59.625 34.615 0.00 0.00 41.47 2.15
555 831 0.835276 GAAAGGGCGGGTATACCTGT 59.165 55.000 27.83 11.08 44.34 4.00
559 835 2.110420 GCGGGTATACCTGTGGGC 59.890 66.667 27.83 16.42 44.34 5.36
630 907 0.187361 TATGGGGTAATGGGCAAGCC 59.813 55.000 1.52 1.52 0.00 4.35
653 933 1.000385 TGCTTTCACGGGCATGAAAAG 60.000 47.619 14.65 10.80 45.52 2.27
659 939 2.038426 TCACGGGCATGAAAAGAAGAGA 59.962 45.455 0.00 0.00 0.00 3.10
660 940 2.417933 CACGGGCATGAAAAGAAGAGAG 59.582 50.000 0.00 0.00 0.00 3.20
661 941 2.012673 CGGGCATGAAAAGAAGAGAGG 58.987 52.381 0.00 0.00 0.00 3.69
662 942 1.747924 GGGCATGAAAAGAAGAGAGGC 59.252 52.381 0.00 0.00 0.00 4.70
663 943 2.620108 GGGCATGAAAAGAAGAGAGGCT 60.620 50.000 0.00 0.00 0.00 4.58
664 944 3.087781 GGCATGAAAAGAAGAGAGGCTT 58.912 45.455 0.00 0.00 40.25 4.35
665 945 3.509184 GGCATGAAAAGAAGAGAGGCTTT 59.491 43.478 0.00 0.00 36.83 3.51
666 946 4.702131 GGCATGAAAAGAAGAGAGGCTTTA 59.298 41.667 0.00 0.00 36.83 1.85
667 947 5.163673 GGCATGAAAAGAAGAGAGGCTTTAG 60.164 44.000 0.00 0.00 36.83 1.85
668 948 5.414144 GCATGAAAAGAAGAGAGGCTTTAGT 59.586 40.000 0.00 0.00 36.83 2.24
677 957 3.055021 AGAGAGGCTTTAGTGCTTTACCC 60.055 47.826 0.00 0.00 0.00 3.69
708 988 2.057137 TACCCATTGCCATCTTGAGC 57.943 50.000 0.00 0.00 0.00 4.26
740 1020 3.442977 GCATGCTCAGAAAGAACCAGATT 59.557 43.478 11.37 0.00 0.00 2.40
742 1022 4.356405 TGCTCAGAAAGAACCAGATTGA 57.644 40.909 0.00 0.00 0.00 2.57
744 1024 3.438434 GCTCAGAAAGAACCAGATTGACC 59.562 47.826 0.00 0.00 0.00 4.02
745 1025 4.645535 CTCAGAAAGAACCAGATTGACCA 58.354 43.478 0.00 0.00 0.00 4.02
746 1026 5.246981 TCAGAAAGAACCAGATTGACCAT 57.753 39.130 0.00 0.00 0.00 3.55
747 1027 5.005740 TCAGAAAGAACCAGATTGACCATG 58.994 41.667 0.00 0.00 0.00 3.66
748 1028 4.763793 CAGAAAGAACCAGATTGACCATGT 59.236 41.667 0.00 0.00 0.00 3.21
749 1029 4.763793 AGAAAGAACCAGATTGACCATGTG 59.236 41.667 0.00 0.00 0.00 3.21
750 1030 2.440409 AGAACCAGATTGACCATGTGC 58.560 47.619 0.00 0.00 0.00 4.57
793 1073 0.606673 GTGGACCTCAAGAGCCAACC 60.607 60.000 0.00 0.00 31.18 3.77
862 1148 3.687125 TCGTACCTCAGTGACAGAAGAT 58.313 45.455 0.00 0.00 0.00 2.40
921 1291 5.579511 AGTTATAACGATACCACTGCAACAC 59.420 40.000 9.91 0.00 0.00 3.32
979 1353 3.253188 TGCACAAACAGGTTAAGATGAGC 59.747 43.478 0.00 0.00 0.00 4.26
981 1355 4.261572 GCACAAACAGGTTAAGATGAGCAA 60.262 41.667 0.00 0.00 0.00 3.91
983 1357 5.009010 CACAAACAGGTTAAGATGAGCAAGT 59.991 40.000 0.00 0.00 0.00 3.16
1009 1391 1.066605 GCTTACCAGCCATGCATTCTG 59.933 52.381 15.44 15.44 40.61 3.02
1021 1403 0.107508 GCATTCTGCAGCCCTAGTCA 60.108 55.000 9.47 0.00 44.26 3.41
1022 1404 1.661341 CATTCTGCAGCCCTAGTCAC 58.339 55.000 9.47 0.00 0.00 3.67
1026 1408 1.667154 CTGCAGCCCTAGTCACGCTA 61.667 60.000 0.00 0.00 0.00 4.26
1104 1490 1.613630 GGAGCACTCCCTCCTCCAA 60.614 63.158 5.30 0.00 46.39 3.53
1122 1508 2.572290 CAATTCCTCACCGGGTTATCC 58.428 52.381 6.32 0.00 0.00 2.59
1138 1524 4.113815 CCCAAGATGGCGGCCTCA 62.114 66.667 21.46 0.00 35.79 3.86
1393 1784 1.847968 AGCAGGCTTAGTGGGGTGT 60.848 57.895 0.00 0.00 0.00 4.16
1420 1811 1.520666 CCGCCATCTTCGGTTACCT 59.479 57.895 0.00 0.00 41.85 3.08
1421 1812 0.748450 CCGCCATCTTCGGTTACCTA 59.252 55.000 0.00 0.00 41.85 3.08
1497 1888 2.086869 CCATCACACACATGGAAGGTC 58.913 52.381 0.00 0.00 43.32 3.85
1518 1909 1.317613 TGCAGAATTTGGTCGTGCTT 58.682 45.000 0.00 0.00 35.11 3.91
1556 1947 1.485294 TTCACCGGGCACATACCACT 61.485 55.000 6.32 0.00 0.00 4.00
1873 2270 4.442192 CCATAGGTCAGTTGAAGAGGCTAC 60.442 50.000 0.00 0.00 0.00 3.58
2007 2404 0.398318 GCAGGGTCAACTTCTCCACT 59.602 55.000 0.00 0.00 0.00 4.00
2298 2698 0.325933 TGCCACAAGATGAGACCCTG 59.674 55.000 0.00 0.00 0.00 4.45
2865 3288 4.797471 TCCTTTCTGCATTCAACATTTCG 58.203 39.130 0.00 0.00 0.00 3.46
2960 3383 0.593128 CCAAAGCTGTGTGGCACTAC 59.407 55.000 19.83 15.05 35.11 2.73
2970 3393 2.936498 GTGTGGCACTACGCTTATTCAT 59.064 45.455 19.83 0.00 41.91 2.57
3253 3692 9.845740 TCTTATTTTATATTAGTTGAGCCTGCA 57.154 29.630 0.00 0.00 0.00 4.41
3369 3860 9.016438 GGAAGTGTTCAGGGTAATGTAATTTTA 57.984 33.333 0.00 0.00 37.87 1.52
3398 3889 1.277273 AGGGTTGGACCTAGCGTAAAC 59.723 52.381 0.00 0.00 39.65 2.01
3439 4033 6.260271 AGTTGACCAGACAGCTAAAACTTTAC 59.740 38.462 0.00 0.00 30.14 2.01
3540 4136 8.184192 ACTACTTCATGCAAATATGTTAGCAAC 58.816 33.333 0.00 0.00 40.76 4.17
3566 4162 3.616956 TGCGGAAACATCTTCAGAGAT 57.383 42.857 0.00 0.00 43.43 2.75
3658 4293 6.174720 GGTCAGATCACCCTACATTTCATA 57.825 41.667 0.00 0.00 0.00 2.15
3687 4500 5.782047 CTCAATCTACAGATCCAGATCACC 58.218 45.833 10.17 0.00 40.22 4.02
3688 4501 5.211201 TCAATCTACAGATCCAGATCACCA 58.789 41.667 10.17 0.00 40.22 4.17
3689 4502 5.842874 TCAATCTACAGATCCAGATCACCAT 59.157 40.000 10.17 0.00 40.22 3.55
3690 4503 7.012607 TCAATCTACAGATCCAGATCACCATA 58.987 38.462 10.17 0.00 40.22 2.74
3691 4504 7.178097 TCAATCTACAGATCCAGATCACCATAG 59.822 40.741 10.17 5.99 40.22 2.23
3692 4505 6.206180 TCTACAGATCCAGATCACCATAGA 57.794 41.667 10.17 7.83 40.22 1.98
3693 4506 6.007076 TCTACAGATCCAGATCACCATAGAC 58.993 44.000 10.17 0.00 40.22 2.59
3694 4507 4.550669 ACAGATCCAGATCACCATAGACA 58.449 43.478 10.17 0.00 40.22 3.41
3695 4508 4.588106 ACAGATCCAGATCACCATAGACAG 59.412 45.833 10.17 0.00 40.22 3.51
3696 4509 3.577848 AGATCCAGATCACCATAGACAGC 59.422 47.826 10.17 0.00 40.22 4.40
3697 4510 2.750814 TCCAGATCACCATAGACAGCA 58.249 47.619 0.00 0.00 0.00 4.41
3698 4511 2.697229 TCCAGATCACCATAGACAGCAG 59.303 50.000 0.00 0.00 0.00 4.24
3699 4512 2.433604 CCAGATCACCATAGACAGCAGT 59.566 50.000 0.00 0.00 0.00 4.40
3700 4513 3.638627 CCAGATCACCATAGACAGCAGTA 59.361 47.826 0.00 0.00 0.00 2.74
3701 4514 4.100035 CCAGATCACCATAGACAGCAGTAA 59.900 45.833 0.00 0.00 0.00 2.24
3702 4515 5.046529 CAGATCACCATAGACAGCAGTAAC 58.953 45.833 0.00 0.00 0.00 2.50
3703 4516 4.711846 AGATCACCATAGACAGCAGTAACA 59.288 41.667 0.00 0.00 0.00 2.41
3704 4517 4.882842 TCACCATAGACAGCAGTAACAA 57.117 40.909 0.00 0.00 0.00 2.83
3705 4518 4.820897 TCACCATAGACAGCAGTAACAAG 58.179 43.478 0.00 0.00 0.00 3.16
3706 4519 4.283467 TCACCATAGACAGCAGTAACAAGT 59.717 41.667 0.00 0.00 0.00 3.16
3707 4520 5.479027 TCACCATAGACAGCAGTAACAAGTA 59.521 40.000 0.00 0.00 0.00 2.24
3708 4521 6.014925 TCACCATAGACAGCAGTAACAAGTAA 60.015 38.462 0.00 0.00 0.00 2.24
3709 4522 6.818644 CACCATAGACAGCAGTAACAAGTAAT 59.181 38.462 0.00 0.00 0.00 1.89
3710 4523 7.010552 CACCATAGACAGCAGTAACAAGTAATC 59.989 40.741 0.00 0.00 0.00 1.75
3711 4524 7.041721 CCATAGACAGCAGTAACAAGTAATCA 58.958 38.462 0.00 0.00 0.00 2.57
3712 4525 7.549134 CCATAGACAGCAGTAACAAGTAATCAA 59.451 37.037 0.00 0.00 0.00 2.57
3713 4526 6.787085 AGACAGCAGTAACAAGTAATCAAC 57.213 37.500 0.00 0.00 0.00 3.18
3714 4527 5.405571 AGACAGCAGTAACAAGTAATCAACG 59.594 40.000 0.00 0.00 0.00 4.10
3715 4528 5.294356 ACAGCAGTAACAAGTAATCAACGA 58.706 37.500 0.00 0.00 0.00 3.85
3716 4529 5.756347 ACAGCAGTAACAAGTAATCAACGAA 59.244 36.000 0.00 0.00 0.00 3.85
3717 4530 6.071463 CAGCAGTAACAAGTAATCAACGAAC 58.929 40.000 0.00 0.00 0.00 3.95
3718 4531 5.070862 GCAGTAACAAGTAATCAACGAACG 58.929 41.667 0.00 0.00 0.00 3.95
3719 4532 5.605327 CAGTAACAAGTAATCAACGAACGG 58.395 41.667 0.00 0.00 0.00 4.44
3720 4533 3.531262 AACAAGTAATCAACGAACGGC 57.469 42.857 0.00 0.00 0.00 5.68
3721 4534 2.485903 ACAAGTAATCAACGAACGGCA 58.514 42.857 0.00 0.00 0.00 5.69
3722 4535 2.222445 ACAAGTAATCAACGAACGGCAC 59.778 45.455 0.00 0.00 0.00 5.01
3723 4536 2.157834 AGTAATCAACGAACGGCACA 57.842 45.000 0.00 0.00 0.00 4.57
3724 4537 2.695359 AGTAATCAACGAACGGCACAT 58.305 42.857 0.00 0.00 0.00 3.21
3725 4538 2.671396 AGTAATCAACGAACGGCACATC 59.329 45.455 0.00 0.00 0.00 3.06
3726 4539 1.518325 AATCAACGAACGGCACATCA 58.482 45.000 0.00 0.00 0.00 3.07
3727 4540 1.518325 ATCAACGAACGGCACATCAA 58.482 45.000 0.00 0.00 0.00 2.57
3728 4541 1.518325 TCAACGAACGGCACATCAAT 58.482 45.000 0.00 0.00 0.00 2.57
3729 4542 1.876799 TCAACGAACGGCACATCAATT 59.123 42.857 0.00 0.00 0.00 2.32
3730 4543 3.067833 TCAACGAACGGCACATCAATTA 58.932 40.909 0.00 0.00 0.00 1.40
3731 4544 3.120477 TCAACGAACGGCACATCAATTAC 60.120 43.478 0.00 0.00 0.00 1.89
3732 4545 1.735571 ACGAACGGCACATCAATTACC 59.264 47.619 0.00 0.00 0.00 2.85
3733 4546 1.735018 CGAACGGCACATCAATTACCA 59.265 47.619 0.00 0.00 0.00 3.25
3734 4547 2.160615 CGAACGGCACATCAATTACCAA 59.839 45.455 0.00 0.00 0.00 3.67
3735 4548 3.181501 CGAACGGCACATCAATTACCAAT 60.182 43.478 0.00 0.00 0.00 3.16
3736 4549 4.674101 CGAACGGCACATCAATTACCAATT 60.674 41.667 0.00 0.00 0.00 2.32
3738 4551 2.859538 CGGCACATCAATTACCAATTGC 59.140 45.455 0.00 0.00 46.09 3.56
3739 4552 2.859538 GGCACATCAATTACCAATTGCG 59.140 45.455 0.00 0.00 46.09 4.85
3740 4553 2.282290 GCACATCAATTACCAATTGCGC 59.718 45.455 0.00 0.00 46.09 6.09
3741 4554 2.859538 CACATCAATTACCAATTGCGCC 59.140 45.455 4.18 0.00 46.09 6.53
3742 4555 2.760092 ACATCAATTACCAATTGCGCCT 59.240 40.909 4.18 0.00 46.09 5.52
3743 4556 3.195396 ACATCAATTACCAATTGCGCCTT 59.805 39.130 4.18 0.00 46.09 4.35
3744 4557 3.229276 TCAATTACCAATTGCGCCTTG 57.771 42.857 4.18 8.98 46.09 3.61
3745 4558 1.660104 CAATTACCAATTGCGCCTTGC 59.340 47.619 4.18 0.00 41.48 4.01
3746 4559 0.175531 ATTACCAATTGCGCCTTGCC 59.824 50.000 4.18 0.00 45.60 4.52
3747 4560 1.181741 TTACCAATTGCGCCTTGCCA 61.182 50.000 4.18 0.00 45.60 4.92
3748 4561 1.872197 TACCAATTGCGCCTTGCCAC 61.872 55.000 4.18 0.00 45.60 5.01
3749 4562 2.432972 CAATTGCGCCTTGCCACC 60.433 61.111 4.18 0.00 45.60 4.61
3750 4563 3.694538 AATTGCGCCTTGCCACCC 61.695 61.111 4.18 0.00 45.60 4.61
3751 4564 4.684134 ATTGCGCCTTGCCACCCT 62.684 61.111 4.18 0.00 45.60 4.34
3752 4565 2.779742 AATTGCGCCTTGCCACCCTA 62.780 55.000 4.18 0.00 45.60 3.53
3753 4566 2.572333 ATTGCGCCTTGCCACCCTAT 62.572 55.000 4.18 0.00 45.60 2.57
3754 4567 1.916206 TTGCGCCTTGCCACCCTATA 61.916 55.000 4.18 0.00 45.60 1.31
3755 4568 1.598130 GCGCCTTGCCACCCTATAG 60.598 63.158 0.00 0.00 37.76 1.31
3756 4569 1.830145 CGCCTTGCCACCCTATAGT 59.170 57.895 0.00 0.00 0.00 2.12
3757 4570 0.249911 CGCCTTGCCACCCTATAGTC 60.250 60.000 0.00 0.00 0.00 2.59
3758 4571 0.108774 GCCTTGCCACCCTATAGTCC 59.891 60.000 0.00 0.00 0.00 3.85
3759 4572 1.807814 CCTTGCCACCCTATAGTCCT 58.192 55.000 0.00 0.00 0.00 3.85
3760 4573 2.972348 CCTTGCCACCCTATAGTCCTA 58.028 52.381 0.00 0.00 0.00 2.94
3761 4574 3.521727 CCTTGCCACCCTATAGTCCTAT 58.478 50.000 0.00 0.00 0.00 2.57
3762 4575 4.684724 CCTTGCCACCCTATAGTCCTATA 58.315 47.826 0.00 0.00 0.00 1.31
3763 4576 4.466726 CCTTGCCACCCTATAGTCCTATAC 59.533 50.000 0.00 0.00 0.00 1.47
3764 4577 5.334421 CTTGCCACCCTATAGTCCTATACT 58.666 45.833 0.00 0.00 42.62 2.12
3765 4578 4.673968 TGCCACCCTATAGTCCTATACTG 58.326 47.826 0.00 0.00 39.39 2.74
3766 4579 4.355889 TGCCACCCTATAGTCCTATACTGA 59.644 45.833 0.00 0.00 39.39 3.41
3767 4580 4.705991 GCCACCCTATAGTCCTATACTGAC 59.294 50.000 0.00 0.00 39.39 3.51
3768 4581 5.751128 GCCACCCTATAGTCCTATACTGACA 60.751 48.000 0.00 0.00 39.39 3.58
3769 4582 5.946972 CCACCCTATAGTCCTATACTGACAG 59.053 48.000 0.00 0.00 39.39 3.51
3770 4583 6.240205 CCACCCTATAGTCCTATACTGACAGA 60.240 46.154 10.08 0.00 39.39 3.41
3771 4584 7.232188 CACCCTATAGTCCTATACTGACAGAA 58.768 42.308 10.08 0.00 39.39 3.02
3772 4585 7.891183 CACCCTATAGTCCTATACTGACAGAAT 59.109 40.741 10.08 0.00 39.39 2.40
3773 4586 9.125255 ACCCTATAGTCCTATACTGACAGAATA 57.875 37.037 10.08 0.00 39.39 1.75
3774 4587 9.398538 CCCTATAGTCCTATACTGACAGAATAC 57.601 40.741 10.08 0.00 39.39 1.89
3775 4588 9.961264 CCTATAGTCCTATACTGACAGAATACA 57.039 37.037 10.08 0.00 39.39 2.29
3778 4591 7.045126 AGTCCTATACTGACAGAATACAAGC 57.955 40.000 10.08 0.00 36.93 4.01
3779 4592 5.915758 GTCCTATACTGACAGAATACAAGCG 59.084 44.000 10.08 0.00 32.91 4.68
3780 4593 5.826208 TCCTATACTGACAGAATACAAGCGA 59.174 40.000 10.08 0.00 0.00 4.93
3781 4594 5.915758 CCTATACTGACAGAATACAAGCGAC 59.084 44.000 10.08 0.00 0.00 5.19
3782 4595 3.944055 ACTGACAGAATACAAGCGACT 57.056 42.857 10.08 0.00 0.00 4.18
3783 4596 3.579709 ACTGACAGAATACAAGCGACTG 58.420 45.455 10.08 0.00 35.14 3.51
3784 4597 2.337583 TGACAGAATACAAGCGACTGC 58.662 47.619 0.00 0.00 43.24 4.40
3794 4607 4.110493 GCGACTGCTACATCCACC 57.890 61.111 0.00 0.00 38.39 4.61
3795 4608 1.878522 GCGACTGCTACATCCACCG 60.879 63.158 0.00 0.00 38.39 4.94
3796 4609 1.807226 CGACTGCTACATCCACCGA 59.193 57.895 0.00 0.00 0.00 4.69
3797 4610 0.172578 CGACTGCTACATCCACCGAA 59.827 55.000 0.00 0.00 0.00 4.30
3798 4611 1.403647 CGACTGCTACATCCACCGAAA 60.404 52.381 0.00 0.00 0.00 3.46
3799 4612 2.695359 GACTGCTACATCCACCGAAAA 58.305 47.619 0.00 0.00 0.00 2.29
3800 4613 2.415512 GACTGCTACATCCACCGAAAAC 59.584 50.000 0.00 0.00 0.00 2.43
3801 4614 1.737793 CTGCTACATCCACCGAAAACC 59.262 52.381 0.00 0.00 0.00 3.27
3802 4615 1.349688 TGCTACATCCACCGAAAACCT 59.650 47.619 0.00 0.00 0.00 3.50
3803 4616 1.737793 GCTACATCCACCGAAAACCTG 59.262 52.381 0.00 0.00 0.00 4.00
3804 4617 2.874457 GCTACATCCACCGAAAACCTGT 60.874 50.000 0.00 0.00 0.00 4.00
3805 4618 3.618019 GCTACATCCACCGAAAACCTGTA 60.618 47.826 0.00 0.00 0.00 2.74
3806 4619 3.495434 ACATCCACCGAAAACCTGTAA 57.505 42.857 0.00 0.00 0.00 2.41
3807 4620 3.408634 ACATCCACCGAAAACCTGTAAG 58.591 45.455 0.00 0.00 0.00 2.34
3808 4621 1.886886 TCCACCGAAAACCTGTAAGC 58.113 50.000 0.00 0.00 0.00 3.09
3809 4622 1.141254 TCCACCGAAAACCTGTAAGCA 59.859 47.619 0.00 0.00 0.00 3.91
3810 4623 1.950909 CCACCGAAAACCTGTAAGCAA 59.049 47.619 0.00 0.00 0.00 3.91
3811 4624 2.031157 CCACCGAAAACCTGTAAGCAAG 60.031 50.000 0.00 0.00 0.00 4.01
3812 4625 2.875933 CACCGAAAACCTGTAAGCAAGA 59.124 45.455 0.00 0.00 0.00 3.02
3813 4626 3.314080 CACCGAAAACCTGTAAGCAAGAA 59.686 43.478 0.00 0.00 0.00 2.52
3814 4627 3.949113 ACCGAAAACCTGTAAGCAAGAAA 59.051 39.130 0.00 0.00 0.00 2.52
3815 4628 4.201980 ACCGAAAACCTGTAAGCAAGAAAC 60.202 41.667 0.00 0.00 0.00 2.78
3816 4629 4.201970 CCGAAAACCTGTAAGCAAGAAACA 60.202 41.667 0.00 0.00 0.00 2.83
3857 4670 2.880890 GCATACCACCAGATCATTCACC 59.119 50.000 0.00 0.00 0.00 4.02
4017 5857 1.738700 CGGGCTCTCTCTCTCTTTTGC 60.739 57.143 0.00 0.00 0.00 3.68
4035 5875 3.503363 GTGCTCTGGATGTGCGCC 61.503 66.667 4.18 0.00 39.07 6.53
4139 5979 0.037605 GACCAACCGGAATCTGTCGT 60.038 55.000 9.46 0.00 35.59 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.196911 CCGTGGGTAACAGGTATGGA 58.803 55.000 0.00 0.00 39.74 3.41
79 80 0.762418 AGACGGGGTTCACATGTCAA 59.238 50.000 0.00 0.00 32.08 3.18
142 144 9.717942 GAGTAATTCTAGATGGCATAGTTCATT 57.282 33.333 0.00 0.00 0.00 2.57
183 185 7.619050 AGTATCAAAACTCTCACATCTCACAT 58.381 34.615 0.00 0.00 0.00 3.21
338 605 9.645059 CATCAGATCGTAACACTATTATCCATT 57.355 33.333 0.00 0.00 0.00 3.16
339 606 8.253810 CCATCAGATCGTAACACTATTATCCAT 58.746 37.037 0.00 0.00 0.00 3.41
340 607 7.232737 ACCATCAGATCGTAACACTATTATCCA 59.767 37.037 0.00 0.00 0.00 3.41
341 608 7.603651 ACCATCAGATCGTAACACTATTATCC 58.396 38.462 0.00 0.00 0.00 2.59
345 612 9.074576 TGTATACCATCAGATCGTAACACTATT 57.925 33.333 0.00 0.00 0.00 1.73
346 613 8.512956 GTGTATACCATCAGATCGTAACACTAT 58.487 37.037 16.93 0.00 32.75 2.12
347 614 7.718314 AGTGTATACCATCAGATCGTAACACTA 59.282 37.037 21.06 0.89 41.30 2.74
348 615 6.546403 AGTGTATACCATCAGATCGTAACACT 59.454 38.462 19.00 19.00 39.07 3.55
349 616 6.736123 AGTGTATACCATCAGATCGTAACAC 58.264 40.000 16.71 16.71 35.04 3.32
350 617 6.954487 AGTGTATACCATCAGATCGTAACA 57.046 37.500 0.00 0.00 0.00 2.41
351 618 7.167635 CACAAGTGTATACCATCAGATCGTAAC 59.832 40.741 0.00 0.00 0.00 2.50
352 619 7.200455 CACAAGTGTATACCATCAGATCGTAA 58.800 38.462 0.00 0.00 0.00 3.18
353 620 6.734871 GCACAAGTGTATACCATCAGATCGTA 60.735 42.308 0.00 0.00 0.00 3.43
354 621 5.592054 CACAAGTGTATACCATCAGATCGT 58.408 41.667 0.00 0.00 0.00 3.73
355 622 4.445718 GCACAAGTGTATACCATCAGATCG 59.554 45.833 0.00 0.00 0.00 3.69
356 623 5.464722 CAGCACAAGTGTATACCATCAGATC 59.535 44.000 0.00 0.00 0.00 2.75
359 626 4.330894 CACAGCACAAGTGTATACCATCAG 59.669 45.833 0.00 0.00 32.44 2.90
369 636 4.279169 AGAATAATTGCACAGCACAAGTGT 59.721 37.500 1.79 0.00 38.71 3.55
410 677 6.121590 TGCATACCATCACATCATAACACTT 58.878 36.000 0.00 0.00 0.00 3.16
555 831 2.917933 CCGACAGATAATTCTTGCCCA 58.082 47.619 0.00 0.00 0.00 5.36
559 835 2.216488 CGTCGCCGACAGATAATTCTTG 59.784 50.000 18.40 0.00 35.63 3.02
587 864 0.676782 CCGCGGGGAAGAATTTCACT 60.677 55.000 20.10 0.00 36.91 3.41
630 907 1.210931 CATGCCCGTGAAAGCACAG 59.789 57.895 0.00 0.00 45.41 3.66
653 933 4.632251 GGTAAAGCACTAAAGCCTCTCTTC 59.368 45.833 0.00 0.00 32.88 2.87
659 939 1.339727 CCGGGTAAAGCACTAAAGCCT 60.340 52.381 0.00 0.00 34.23 4.58
660 940 1.092348 CCGGGTAAAGCACTAAAGCC 58.908 55.000 0.00 0.00 34.23 4.35
661 941 1.817357 ACCGGGTAAAGCACTAAAGC 58.183 50.000 6.32 0.00 0.00 3.51
662 942 2.486592 CCAACCGGGTAAAGCACTAAAG 59.513 50.000 6.32 0.00 0.00 1.85
663 943 2.506444 CCAACCGGGTAAAGCACTAAA 58.494 47.619 6.32 0.00 0.00 1.85
664 944 2.188062 CCAACCGGGTAAAGCACTAA 57.812 50.000 6.32 0.00 0.00 2.24
665 945 3.940229 CCAACCGGGTAAAGCACTA 57.060 52.632 6.32 0.00 0.00 2.74
666 946 4.813346 CCAACCGGGTAAAGCACT 57.187 55.556 6.32 0.00 0.00 4.40
740 1020 3.081061 GTCCTACATTTGCACATGGTCA 58.919 45.455 16.81 1.52 0.00 4.02
742 1022 3.439857 AGTCCTACATTTGCACATGGT 57.560 42.857 16.81 5.65 0.00 3.55
744 1024 6.071952 ACCTTTTAGTCCTACATTTGCACATG 60.072 38.462 11.29 11.29 0.00 3.21
745 1025 6.010219 ACCTTTTAGTCCTACATTTGCACAT 58.990 36.000 0.00 0.00 0.00 3.21
746 1026 5.240623 CACCTTTTAGTCCTACATTTGCACA 59.759 40.000 0.00 0.00 0.00 4.57
747 1027 5.240844 ACACCTTTTAGTCCTACATTTGCAC 59.759 40.000 0.00 0.00 0.00 4.57
748 1028 5.381757 ACACCTTTTAGTCCTACATTTGCA 58.618 37.500 0.00 0.00 0.00 4.08
749 1029 5.959618 ACACCTTTTAGTCCTACATTTGC 57.040 39.130 0.00 0.00 0.00 3.68
750 1030 8.504005 CACTAACACCTTTTAGTCCTACATTTG 58.496 37.037 0.00 0.00 39.77 2.32
793 1073 3.970842 ACCTACTAGTCCCTGACTCTTG 58.029 50.000 0.00 0.00 42.40 3.02
862 1148 5.393135 GCTACTGTAGTTGCATCAGAGTACA 60.393 44.000 15.71 8.91 44.19 2.90
921 1291 2.024176 CGATAGGTGGTGGTTTCCAG 57.976 55.000 0.00 0.00 38.23 3.86
1009 1391 1.227002 GTAGCGTGACTAGGGCTGC 60.227 63.158 9.29 0.00 37.62 5.25
1122 1508 2.825836 GTGAGGCCGCCATCTTGG 60.826 66.667 13.15 0.00 41.55 3.61
1138 1524 1.299620 CGTTTCTCCACGACACGGT 60.300 57.895 0.00 0.00 43.15 4.83
1215 1606 1.133199 CCTCTAGATGCCAGGGAGACT 60.133 57.143 0.00 0.00 0.00 3.24
1237 1628 0.811616 GGCGAGATGCGACCTTCAAT 60.812 55.000 0.00 0.00 44.13 2.57
1393 1784 3.899981 AAGATGGCGGCTCGTGCAA 62.900 57.895 11.43 0.00 41.91 4.08
1497 1888 1.200716 AGCACGACCAAATTCTGCATG 59.799 47.619 0.00 0.00 0.00 4.06
1518 1909 1.948104 AGCTGTTGTTGCTGACGTTA 58.052 45.000 0.00 0.00 39.56 3.18
1523 1914 1.024271 GGTGAAGCTGTTGTTGCTGA 58.976 50.000 0.00 0.00 41.03 4.26
1640 2034 1.952296 ACACTTTGAGCTTGGAGCAAG 59.048 47.619 2.47 0.00 45.56 4.01
1704 2098 1.034292 GGGAAGTGGCATGGAAGAGC 61.034 60.000 0.00 0.00 0.00 4.09
1873 2270 4.487714 TGTTACCCAAATAGAGCTCCTG 57.512 45.455 10.93 2.92 0.00 3.86
2007 2404 6.911250 TCTAAATGTGTCAGGTTCTGTAGA 57.089 37.500 0.00 0.00 32.61 2.59
2298 2698 7.535139 TGTATTGAAGATTTCGAAAACCATCC 58.465 34.615 15.66 3.41 0.00 3.51
2865 3288 7.065923 GGTACAGACCCTTCTAAATCATTGTTC 59.934 40.741 0.00 0.00 40.23 3.18
2960 3383 5.807520 ACTGAACTACACTGATGAATAAGCG 59.192 40.000 0.00 0.00 0.00 4.68
2970 3393 3.222603 TGCTCTGACTGAACTACACTGA 58.777 45.455 0.00 0.00 0.00 3.41
3163 3592 8.827177 ATTCATGGCTATTTATTGCTTGATTG 57.173 30.769 0.00 0.00 0.00 2.67
3300 3783 5.124457 CCACGACTTCCAATCTGAAAATCAT 59.876 40.000 0.00 0.00 0.00 2.45
3369 3860 3.833559 AGGTCCAACCCTGATTGAAAT 57.166 42.857 0.00 0.00 39.75 2.17
3373 3864 1.743772 CGCTAGGTCCAACCCTGATTG 60.744 57.143 0.00 0.00 39.75 2.67
3504 4100 5.003692 TGCATGAAGTAGTGTTGCAAAAA 57.996 34.783 0.00 0.00 40.11 1.94
3525 4121 5.914635 CGCAATAGGGTTGCTAACATATTTG 59.085 40.000 10.57 0.00 42.87 2.32
3528 4124 4.072131 CCGCAATAGGGTTGCTAACATAT 58.928 43.478 10.57 0.00 42.87 1.78
3540 4136 3.278574 TGAAGATGTTTCCGCAATAGGG 58.721 45.455 0.00 0.00 0.00 3.53
3566 4162 2.883122 TGGCTGGCATGATATATGCA 57.117 45.000 13.18 0.00 46.21 3.96
3567 4163 3.087031 ACTTGGCTGGCATGATATATGC 58.913 45.455 21.26 3.39 43.85 3.14
3647 4282 9.190858 GTAGATTGAGCTCTGTATGAAATGTAG 57.809 37.037 16.19 0.00 0.00 2.74
3648 4283 8.695456 TGTAGATTGAGCTCTGTATGAAATGTA 58.305 33.333 16.19 4.54 0.00 2.29
3658 4293 4.285020 TGGATCTGTAGATTGAGCTCTGT 58.715 43.478 16.19 2.93 34.37 3.41
3687 4500 8.383619 GTTGATTACTTGTTACTGCTGTCTATG 58.616 37.037 0.00 0.00 0.00 2.23
3688 4501 7.275779 CGTTGATTACTTGTTACTGCTGTCTAT 59.724 37.037 0.00 0.00 0.00 1.98
3689 4502 6.584942 CGTTGATTACTTGTTACTGCTGTCTA 59.415 38.462 0.00 0.00 0.00 2.59
3690 4503 5.405571 CGTTGATTACTTGTTACTGCTGTCT 59.594 40.000 0.00 0.00 0.00 3.41
3691 4504 5.404366 TCGTTGATTACTTGTTACTGCTGTC 59.596 40.000 0.00 0.00 0.00 3.51
3692 4505 5.294356 TCGTTGATTACTTGTTACTGCTGT 58.706 37.500 0.66 0.66 0.00 4.40
3693 4506 5.839262 TCGTTGATTACTTGTTACTGCTG 57.161 39.130 0.00 0.00 0.00 4.41
3694 4507 5.107607 CGTTCGTTGATTACTTGTTACTGCT 60.108 40.000 0.00 0.00 0.00 4.24
3695 4508 5.070862 CGTTCGTTGATTACTTGTTACTGC 58.929 41.667 0.00 0.00 0.00 4.40
3696 4509 5.605327 CCGTTCGTTGATTACTTGTTACTG 58.395 41.667 0.00 0.00 0.00 2.74
3697 4510 4.151157 GCCGTTCGTTGATTACTTGTTACT 59.849 41.667 0.00 0.00 0.00 2.24
3698 4511 4.084433 TGCCGTTCGTTGATTACTTGTTAC 60.084 41.667 0.00 0.00 0.00 2.50
3699 4512 4.056740 TGCCGTTCGTTGATTACTTGTTA 58.943 39.130 0.00 0.00 0.00 2.41
3700 4513 2.873472 TGCCGTTCGTTGATTACTTGTT 59.127 40.909 0.00 0.00 0.00 2.83
3701 4514 2.222445 GTGCCGTTCGTTGATTACTTGT 59.778 45.455 0.00 0.00 0.00 3.16
3702 4515 2.222213 TGTGCCGTTCGTTGATTACTTG 59.778 45.455 0.00 0.00 0.00 3.16
3703 4516 2.485903 TGTGCCGTTCGTTGATTACTT 58.514 42.857 0.00 0.00 0.00 2.24
3704 4517 2.157834 TGTGCCGTTCGTTGATTACT 57.842 45.000 0.00 0.00 0.00 2.24
3705 4518 2.413796 TGATGTGCCGTTCGTTGATTAC 59.586 45.455 0.00 0.00 0.00 1.89
3706 4519 2.689646 TGATGTGCCGTTCGTTGATTA 58.310 42.857 0.00 0.00 0.00 1.75
3707 4520 1.518325 TGATGTGCCGTTCGTTGATT 58.482 45.000 0.00 0.00 0.00 2.57
3708 4521 1.518325 TTGATGTGCCGTTCGTTGAT 58.482 45.000 0.00 0.00 0.00 2.57
3709 4522 1.518325 ATTGATGTGCCGTTCGTTGA 58.482 45.000 0.00 0.00 0.00 3.18
3710 4523 2.330231 AATTGATGTGCCGTTCGTTG 57.670 45.000 0.00 0.00 0.00 4.10
3711 4524 2.160813 GGTAATTGATGTGCCGTTCGTT 59.839 45.455 0.00 0.00 0.00 3.85
3712 4525 1.735571 GGTAATTGATGTGCCGTTCGT 59.264 47.619 0.00 0.00 0.00 3.85
3713 4526 1.735018 TGGTAATTGATGTGCCGTTCG 59.265 47.619 0.00 0.00 0.00 3.95
3714 4527 3.840890 TTGGTAATTGATGTGCCGTTC 57.159 42.857 0.00 0.00 0.00 3.95
3715 4528 4.799564 AATTGGTAATTGATGTGCCGTT 57.200 36.364 0.00 0.00 0.00 4.44
3726 4539 1.405391 GGCAAGGCGCAATTGGTAATT 60.405 47.619 21.55 0.00 45.17 1.40
3727 4540 0.175531 GGCAAGGCGCAATTGGTAAT 59.824 50.000 21.55 0.00 45.17 1.89
3728 4541 1.181741 TGGCAAGGCGCAATTGGTAA 61.182 50.000 21.55 0.00 45.17 2.85
3729 4542 1.604879 TGGCAAGGCGCAATTGGTA 60.605 52.632 21.55 0.00 45.17 3.25
3730 4543 2.916703 TGGCAAGGCGCAATTGGT 60.917 55.556 21.55 0.00 45.17 3.67
3731 4544 2.432972 GTGGCAAGGCGCAATTGG 60.433 61.111 21.55 7.78 45.17 3.16
3732 4545 2.432972 GGTGGCAAGGCGCAATTG 60.433 61.111 17.49 17.49 45.17 2.32
3733 4546 2.779742 TAGGGTGGCAAGGCGCAATT 62.780 55.000 10.83 0.00 45.17 2.32
3734 4547 2.572333 ATAGGGTGGCAAGGCGCAAT 62.572 55.000 10.83 0.00 45.17 3.56
3735 4548 1.916206 TATAGGGTGGCAAGGCGCAA 61.916 55.000 10.83 0.00 45.17 4.85
3736 4549 2.324014 CTATAGGGTGGCAAGGCGCA 62.324 60.000 10.83 0.00 45.17 6.09
3737 4550 1.598130 CTATAGGGTGGCAAGGCGC 60.598 63.158 0.00 0.00 41.28 6.53
3738 4551 0.249911 GACTATAGGGTGGCAAGGCG 60.250 60.000 4.43 0.00 0.00 5.52
3739 4552 0.108774 GGACTATAGGGTGGCAAGGC 59.891 60.000 4.43 0.00 0.00 4.35
3740 4553 1.807814 AGGACTATAGGGTGGCAAGG 58.192 55.000 4.43 0.00 0.00 3.61
3741 4554 5.186021 CAGTATAGGACTATAGGGTGGCAAG 59.814 48.000 4.43 0.00 35.64 4.01
3742 4555 5.084519 CAGTATAGGACTATAGGGTGGCAA 58.915 45.833 4.43 0.00 35.64 4.52
3743 4556 4.355889 TCAGTATAGGACTATAGGGTGGCA 59.644 45.833 4.43 0.00 35.64 4.92
3744 4557 4.705991 GTCAGTATAGGACTATAGGGTGGC 59.294 50.000 4.43 0.00 35.64 5.01
3745 4558 5.888901 TGTCAGTATAGGACTATAGGGTGG 58.111 45.833 4.43 0.00 35.64 4.61
3746 4559 6.780901 TCTGTCAGTATAGGACTATAGGGTG 58.219 44.000 4.43 0.00 35.64 4.61
3747 4560 7.403837 TTCTGTCAGTATAGGACTATAGGGT 57.596 40.000 4.43 0.00 35.64 4.34
3748 4561 9.398538 GTATTCTGTCAGTATAGGACTATAGGG 57.601 40.741 4.43 0.00 35.64 3.53
3749 4562 9.961264 TGTATTCTGTCAGTATAGGACTATAGG 57.039 37.037 4.43 0.00 35.64 2.57
3752 4565 8.798402 GCTTGTATTCTGTCAGTATAGGACTAT 58.202 37.037 0.00 0.00 35.64 2.12
3753 4566 7.041303 CGCTTGTATTCTGTCAGTATAGGACTA 60.041 40.741 0.00 0.00 35.64 2.59
3754 4567 6.238786 CGCTTGTATTCTGTCAGTATAGGACT 60.239 42.308 0.00 0.00 39.82 3.85
3755 4568 5.915758 CGCTTGTATTCTGTCAGTATAGGAC 59.084 44.000 0.00 0.00 35.83 3.85
3756 4569 5.826208 TCGCTTGTATTCTGTCAGTATAGGA 59.174 40.000 0.00 0.00 0.00 2.94
3757 4570 5.915758 GTCGCTTGTATTCTGTCAGTATAGG 59.084 44.000 0.00 0.00 0.00 2.57
3758 4571 6.634837 CAGTCGCTTGTATTCTGTCAGTATAG 59.365 42.308 0.00 0.00 0.00 1.31
3759 4572 6.495706 CAGTCGCTTGTATTCTGTCAGTATA 58.504 40.000 0.00 0.00 0.00 1.47
3760 4573 5.344066 CAGTCGCTTGTATTCTGTCAGTAT 58.656 41.667 0.00 0.00 0.00 2.12
3761 4574 4.733850 CAGTCGCTTGTATTCTGTCAGTA 58.266 43.478 0.00 0.00 0.00 2.74
3762 4575 3.579709 CAGTCGCTTGTATTCTGTCAGT 58.420 45.455 0.00 0.00 0.00 3.41
3763 4576 2.346847 GCAGTCGCTTGTATTCTGTCAG 59.653 50.000 0.00 0.00 34.30 3.51
3764 4577 2.337583 GCAGTCGCTTGTATTCTGTCA 58.662 47.619 0.00 0.00 34.30 3.58
3777 4590 1.878522 CGGTGGATGTAGCAGTCGC 60.879 63.158 0.00 0.00 38.99 5.19
3778 4591 0.172578 TTCGGTGGATGTAGCAGTCG 59.827 55.000 0.00 0.00 0.00 4.18
3779 4592 2.380084 TTTCGGTGGATGTAGCAGTC 57.620 50.000 0.00 0.00 0.00 3.51
3780 4593 2.423577 GTTTTCGGTGGATGTAGCAGT 58.576 47.619 0.00 0.00 0.00 4.40
3781 4594 1.737793 GGTTTTCGGTGGATGTAGCAG 59.262 52.381 0.00 0.00 0.00 4.24
3782 4595 1.349688 AGGTTTTCGGTGGATGTAGCA 59.650 47.619 0.00 0.00 0.00 3.49
3783 4596 1.737793 CAGGTTTTCGGTGGATGTAGC 59.262 52.381 0.00 0.00 0.00 3.58
3784 4597 3.053831 ACAGGTTTTCGGTGGATGTAG 57.946 47.619 0.00 0.00 0.00 2.74
3785 4598 4.571919 CTTACAGGTTTTCGGTGGATGTA 58.428 43.478 0.00 0.00 0.00 2.29
3786 4599 3.408634 CTTACAGGTTTTCGGTGGATGT 58.591 45.455 0.00 0.00 0.00 3.06
3787 4600 2.161609 GCTTACAGGTTTTCGGTGGATG 59.838 50.000 0.00 0.00 0.00 3.51
3788 4601 2.224670 TGCTTACAGGTTTTCGGTGGAT 60.225 45.455 0.00 0.00 0.00 3.41
3789 4602 1.141254 TGCTTACAGGTTTTCGGTGGA 59.859 47.619 0.00 0.00 0.00 4.02
3790 4603 1.600023 TGCTTACAGGTTTTCGGTGG 58.400 50.000 0.00 0.00 0.00 4.61
3791 4604 2.875933 TCTTGCTTACAGGTTTTCGGTG 59.124 45.455 0.00 0.00 0.00 4.94
3792 4605 3.202829 TCTTGCTTACAGGTTTTCGGT 57.797 42.857 0.00 0.00 0.00 4.69
3793 4606 4.201970 TGTTTCTTGCTTACAGGTTTTCGG 60.202 41.667 0.00 0.00 0.00 4.30
3794 4607 4.915704 TGTTTCTTGCTTACAGGTTTTCG 58.084 39.130 0.00 0.00 0.00 3.46
3795 4608 5.971792 GTCTGTTTCTTGCTTACAGGTTTTC 59.028 40.000 0.00 0.00 39.71 2.29
3796 4609 5.417580 TGTCTGTTTCTTGCTTACAGGTTTT 59.582 36.000 0.00 0.00 39.71 2.43
3797 4610 4.947388 TGTCTGTTTCTTGCTTACAGGTTT 59.053 37.500 0.00 0.00 39.71 3.27
3798 4611 4.523083 TGTCTGTTTCTTGCTTACAGGTT 58.477 39.130 0.00 0.00 39.71 3.50
3799 4612 4.150897 TGTCTGTTTCTTGCTTACAGGT 57.849 40.909 0.00 0.00 39.71 4.00
3800 4613 5.499139 TTTGTCTGTTTCTTGCTTACAGG 57.501 39.130 0.00 0.00 39.71 4.00
3801 4614 7.591426 GGTATTTTGTCTGTTTCTTGCTTACAG 59.409 37.037 0.00 0.00 40.42 2.74
3802 4615 7.284489 AGGTATTTTGTCTGTTTCTTGCTTACA 59.716 33.333 0.00 0.00 0.00 2.41
3803 4616 7.649057 AGGTATTTTGTCTGTTTCTTGCTTAC 58.351 34.615 0.00 0.00 0.00 2.34
3804 4617 7.040686 GGAGGTATTTTGTCTGTTTCTTGCTTA 60.041 37.037 0.00 0.00 0.00 3.09
3805 4618 6.239036 GGAGGTATTTTGTCTGTTTCTTGCTT 60.239 38.462 0.00 0.00 0.00 3.91
3806 4619 5.241728 GGAGGTATTTTGTCTGTTTCTTGCT 59.758 40.000 0.00 0.00 0.00 3.91
3807 4620 5.009610 TGGAGGTATTTTGTCTGTTTCTTGC 59.990 40.000 0.00 0.00 0.00 4.01
3808 4621 6.486657 TCTGGAGGTATTTTGTCTGTTTCTTG 59.513 38.462 0.00 0.00 0.00 3.02
3809 4622 6.601332 TCTGGAGGTATTTTGTCTGTTTCTT 58.399 36.000 0.00 0.00 0.00 2.52
3810 4623 6.187727 TCTGGAGGTATTTTGTCTGTTTCT 57.812 37.500 0.00 0.00 0.00 2.52
3811 4624 5.412904 CCTCTGGAGGTATTTTGTCTGTTTC 59.587 44.000 8.39 0.00 43.61 2.78
3812 4625 5.316987 CCTCTGGAGGTATTTTGTCTGTTT 58.683 41.667 8.39 0.00 43.61 2.83
3813 4626 4.911390 CCTCTGGAGGTATTTTGTCTGTT 58.089 43.478 8.39 0.00 43.61 3.16
3814 4627 4.559862 CCTCTGGAGGTATTTTGTCTGT 57.440 45.455 8.39 0.00 43.61 3.41
3890 4703 1.064060 GGTGGAATCGAAAATCAGGCG 59.936 52.381 0.00 0.00 0.00 5.52
3893 4706 2.609459 CCTCGGTGGAATCGAAAATCAG 59.391 50.000 0.00 0.00 38.35 2.90
3920 4733 1.372375 GCGAGCCCTAGCGAATCTC 60.372 63.158 0.00 0.00 46.67 2.75
3992 4822 3.910490 GAGAGAGAGCCCGCGCAT 61.910 66.667 8.75 0.00 37.52 4.73
4001 4831 1.991965 GCACGCAAAAGAGAGAGAGAG 59.008 52.381 0.00 0.00 0.00 3.20
4002 4832 1.615883 AGCACGCAAAAGAGAGAGAGA 59.384 47.619 0.00 0.00 0.00 3.10
4017 5857 3.857854 GCGCACATCCAGAGCACG 61.858 66.667 0.30 0.00 32.95 5.34
4035 5875 1.209275 CTCGCCGTTCAAGCTATCGG 61.209 60.000 12.32 12.32 44.86 4.18


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

AutoCloner maintained by Alex Coulton.