Multiple sequence alignment - TraesCS4B01G110400

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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 TraesCS4B01G110400 chr4B 100.000 4088 0 0 1 4088 123919597 123923684 0.000000e+00 7550.0
1 TraesCS4B01G110400 chr4B 84.763 1306 174 13 1125 2417 9462730 9464023 0.000000e+00 1286.0
2 TraesCS4B01G110400 chr4B 91.848 184 14 1 642 825 123919447 123919265 5.240000e-64 255.0
3 TraesCS4B01G110400 chr4B 80.070 286 33 7 2491 2774 9464241 9464504 1.500000e-44 191.0
4 TraesCS4B01G110400 chr4A 98.951 3147 30 3 826 3969 509225016 509221870 0.000000e+00 5626.0
5 TraesCS4B01G110400 chr4A 97.028 2961 77 5 1131 4088 508838837 508835885 0.000000e+00 4970.0
6 TraesCS4B01G110400 chr4A 99.451 728 0 1 100 827 729826952 729826229 0.000000e+00 1319.0
7 TraesCS4B01G110400 chr4A 84.100 1283 172 20 1119 2390 598453289 598454550 0.000000e+00 1210.0
8 TraesCS4B01G110400 chr4A 98.387 310 5 0 826 1135 508847820 508847511 2.780000e-151 545.0
9 TraesCS4B01G110400 chr4A 91.848 184 14 1 642 825 729827141 729827323 5.240000e-64 255.0
10 TraesCS4B01G110400 chr4A 80.734 327 40 15 2465 2774 598454689 598455009 2.460000e-57 233.0
11 TraesCS4B01G110400 chr4A 95.833 120 5 0 3969 4088 509207225 509207106 1.160000e-45 195.0
12 TraesCS4B01G110400 chr4A 100.000 42 0 0 1 42 729826991 729826950 1.220000e-10 78.7
13 TraesCS4B01G110400 chr4D 97.716 3284 35 9 826 4088 86531789 86535053 0.000000e+00 5613.0
14 TraesCS4B01G110400 chr4D 98.500 1133 14 3 2697 3829 86058241 86059370 0.000000e+00 1995.0
15 TraesCS4B01G110400 chr4D 99.098 998 9 0 826 1823 86312953 86313950 0.000000e+00 1794.0
16 TraesCS4B01G110400 chr4D 99.095 884 7 1 2045 2927 86313948 86314831 0.000000e+00 1587.0
17 TraesCS4B01G110400 chr4D 98.031 914 11 4 2922 3829 86320404 86321316 0.000000e+00 1581.0
18 TraesCS4B01G110400 chr4D 98.106 264 5 0 3825 4088 86059414 86059677 1.040000e-125 460.0
19 TraesCS4B01G110400 chr4D 96.970 264 7 1 3825 4088 86321352 86321614 3.750000e-120 442.0
20 TraesCS4B01G110400 chr3B 86.946 1624 168 20 855 2454 793104034 793102431 0.000000e+00 1784.0
21 TraesCS4B01G110400 chr3B 87.153 288 31 4 2492 2774 793100221 793099935 5.100000e-84 322.0
22 TraesCS4B01G110400 chr3B 79.521 459 53 28 2831 3281 793099936 793099511 5.170000e-74 289.0
23 TraesCS4B01G110400 chr2B 85.723 1562 189 18 826 2379 188023600 188022065 0.000000e+00 1618.0
24 TraesCS4B01G110400 chr2B 89.306 720 73 4 826 1544 188151729 188151013 0.000000e+00 900.0
25 TraesCS4B01G110400 chr2B 89.167 720 75 3 826 1544 188262336 188261619 0.000000e+00 894.0
26 TraesCS4B01G110400 chr2B 83.245 758 99 13 1629 2379 188150995 188150259 0.000000e+00 671.0
27 TraesCS4B01G110400 chr2B 88.235 340 38 2 2465 2803 188256201 188255863 4.920000e-109 405.0
28 TraesCS4B01G110400 chr2B 87.941 340 37 3 2465 2803 188149927 188149591 8.230000e-107 398.0
29 TraesCS4B01G110400 chr2B 87.383 214 21 6 2810 3019 188021233 188021022 1.470000e-59 241.0
30 TraesCS4B01G110400 chr5B 99.879 826 1 0 1 826 214106646 214107471 0.000000e+00 1520.0
31 TraesCS4B01G110400 chr5B 99.699 664 2 0 162 825 366004826 366004163 0.000000e+00 1216.0
32 TraesCS4B01G110400 chr5B 99.329 149 1 0 1 149 366004956 366004808 1.870000e-68 270.0
33 TraesCS4B01G110400 chr5B 91.848 184 14 1 642 825 214106496 214106314 5.240000e-64 255.0
34 TraesCS4B01G110400 chr3A 99.737 760 1 1 1 760 19966441 19965683 0.000000e+00 1391.0
35 TraesCS4B01G110400 chr3A 99.804 509 1 0 317 825 19965582 19965074 0.000000e+00 935.0
36 TraesCS4B01G110400 chr3A 100.000 298 0 0 1 298 19967045 19966748 5.970000e-153 551.0
37 TraesCS4B01G110400 chr3A 99.320 147 1 0 1 147 19967535 19967389 2.420000e-67 267.0
38 TraesCS4B01G110400 chr3A 91.848 184 14 1 642 825 19967195 19967377 5.240000e-64 255.0
39 TraesCS4B01G110400 chr3A 92.517 147 9 1 2831 2977 721597596 721597740 4.140000e-50 209.0
40 TraesCS4B01G110400 chr3D 87.727 880 95 5 1436 2308 591343467 591344340 0.000000e+00 1014.0
41 TraesCS4B01G110400 chr3D 85.493 517 56 11 855 1360 591342956 591343464 4.680000e-144 521.0
42 TraesCS4B01G110400 chr3D 88.365 318 29 5 2465 2776 591344641 591344956 3.860000e-100 375.0
43 TraesCS4B01G110400 chr3D 84.821 112 15 2 3978 4088 613606106 613606216 1.200000e-20 111.0
44 TraesCS4B01G110400 chr3D 100.000 28 0 0 2809 2836 391258079 391258106 7.000000e-03 52.8
45 TraesCS4B01G110400 chrUn 100.000 388 0 0 1436 1823 480261513 480261900 0.000000e+00 717.0
46 TraesCS4B01G110400 chr5D 81.600 125 21 2 3963 4087 399968645 399968767 7.230000e-18 102.0
47 TraesCS4B01G110400 chr1A 83.333 108 18 0 3980 4087 471888960 471888853 2.600000e-17 100.0
48 TraesCS4B01G110400 chr2D 87.952 83 5 1 1 78 26507230 26507312 4.350000e-15 93.5
49 TraesCS4B01G110400 chr2D 97.059 34 0 1 2806 2838 637449574 637449607 5.710000e-04 56.5
50 TraesCS4B01G110400 chr7A 100.000 31 0 0 2774 2804 316267236 316267206 1.590000e-04 58.4
51 TraesCS4B01G110400 chr6B 100.000 28 0 0 2809 2836 588833449 588833422 7.000000e-03 52.8


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 TraesCS4B01G110400 chr4B 123919597 123923684 4087 False 7550.000000 7550 100.000000 1 4088 1 chr4B.!!$F1 4087
1 TraesCS4B01G110400 chr4B 9462730 9464504 1774 False 738.500000 1286 82.416500 1125 2774 2 chr4B.!!$F2 1649
2 TraesCS4B01G110400 chr4A 509221870 509225016 3146 True 5626.000000 5626 98.951000 826 3969 1 chr4A.!!$R4 3143
3 TraesCS4B01G110400 chr4A 508835885 508838837 2952 True 4970.000000 4970 97.028000 1131 4088 1 chr4A.!!$R1 2957
4 TraesCS4B01G110400 chr4A 598453289 598455009 1720 False 721.500000 1210 82.417000 1119 2774 2 chr4A.!!$F2 1655
5 TraesCS4B01G110400 chr4A 729826229 729826991 762 True 698.850000 1319 99.725500 1 827 2 chr4A.!!$R5 826
6 TraesCS4B01G110400 chr4D 86531789 86535053 3264 False 5613.000000 5613 97.716000 826 4088 1 chr4D.!!$F1 3262
7 TraesCS4B01G110400 chr4D 86312953 86314831 1878 False 1690.500000 1794 99.096500 826 2927 2 chr4D.!!$F3 2101
8 TraesCS4B01G110400 chr4D 86058241 86059677 1436 False 1227.500000 1995 98.303000 2697 4088 2 chr4D.!!$F2 1391
9 TraesCS4B01G110400 chr4D 86320404 86321614 1210 False 1011.500000 1581 97.500500 2922 4088 2 chr4D.!!$F4 1166
10 TraesCS4B01G110400 chr3B 793099511 793104034 4523 True 798.333333 1784 84.540000 855 3281 3 chr3B.!!$R1 2426
11 TraesCS4B01G110400 chr2B 188021022 188023600 2578 True 929.500000 1618 86.553000 826 3019 2 chr2B.!!$R3 2193
12 TraesCS4B01G110400 chr2B 188261619 188262336 717 True 894.000000 894 89.167000 826 1544 1 chr2B.!!$R2 718
13 TraesCS4B01G110400 chr2B 188149591 188151729 2138 True 656.333333 900 86.830667 826 2803 3 chr2B.!!$R4 1977
14 TraesCS4B01G110400 chr5B 214106646 214107471 825 False 1520.000000 1520 99.879000 1 826 1 chr5B.!!$F1 825
15 TraesCS4B01G110400 chr5B 366004163 366004956 793 True 743.000000 1216 99.514000 1 825 2 chr5B.!!$R2 824
16 TraesCS4B01G110400 chr3A 19965074 19967535 2461 True 786.000000 1391 99.715250 1 825 4 chr3A.!!$R1 824
17 TraesCS4B01G110400 chr3D 591342956 591344956 2000 False 636.666667 1014 87.195000 855 2776 3 chr3D.!!$F3 1921

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
585 1076 0.033090 GGTTCCGTCGTTCCTCTGTT 59.967 55.0 0.00 0.00 0.00 3.16 F
628 1119 0.179132 TCGTCTCGTCTCCTCTCTCG 60.179 60.0 0.00 0.00 0.00 4.04 F
629 1120 0.179132 CGTCTCGTCTCCTCTCTCGA 60.179 60.0 0.00 0.00 0.00 4.04 F
688 1179 0.313043 AACGTGTAGGTCCTGACGTG 59.687 55.0 24.02 8.89 43.88 4.49 F
807 1298 1.045407 TGTACGAGGAAAGGTGTGCT 58.955 50.0 0.00 0.00 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2367 3835 5.651576 TCTGGTAATGTAATTCAGCATGCAA 59.348 36.000 21.98 6.7 37.87 4.08 R
3005 7132 2.841881 TCCCTATTCACGCCTTTACCTT 59.158 45.455 0.00 0.0 0.00 3.50 R
3023 7150 1.410224 GGGGATCACAGGTCATTTCCC 60.410 57.143 0.00 0.0 41.77 3.97 R
3056 7185 1.760086 CTCTCCGGTCCCAGCTCAT 60.760 63.158 0.00 0.0 0.00 2.90 R
3344 7483 4.033709 AGTCAATACAGAGGGCAGTACAT 58.966 43.478 0.00 0.0 0.00 2.29 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
434 925 4.335647 CGTGCTGCAGGGGGACTT 62.336 66.667 17.12 0.00 0.00 3.01
435 926 2.360475 GTGCTGCAGGGGGACTTC 60.360 66.667 17.12 0.00 0.00 3.01
436 927 2.853542 TGCTGCAGGGGGACTTCA 60.854 61.111 17.12 0.00 0.00 3.02
437 928 2.436109 GCTGCAGGGGGACTTCAA 59.564 61.111 17.12 0.00 0.00 2.69
438 929 1.676967 GCTGCAGGGGGACTTCAAG 60.677 63.158 17.12 0.00 0.00 3.02
439 930 1.763770 CTGCAGGGGGACTTCAAGT 59.236 57.895 5.57 0.00 0.00 3.16
440 931 0.607489 CTGCAGGGGGACTTCAAGTG 60.607 60.000 5.57 0.00 0.00 3.16
441 932 1.303643 GCAGGGGGACTTCAAGTGG 60.304 63.158 0.00 0.00 0.00 4.00
442 933 1.303643 CAGGGGGACTTCAAGTGGC 60.304 63.158 0.00 0.00 0.00 5.01
443 934 2.359975 GGGGGACTTCAAGTGGCG 60.360 66.667 0.00 0.00 0.00 5.69
444 935 2.359975 GGGGACTTCAAGTGGCGG 60.360 66.667 0.00 0.00 0.00 6.13
445 936 3.056328 GGGACTTCAAGTGGCGGC 61.056 66.667 0.00 0.00 0.00 6.53
446 937 3.423154 GGACTTCAAGTGGCGGCG 61.423 66.667 0.51 0.51 0.00 6.46
447 938 4.090057 GACTTCAAGTGGCGGCGC 62.090 66.667 26.17 26.17 0.00 6.53
459 950 4.840005 CGGCGCCCTTCTTCTCCC 62.840 72.222 23.46 0.00 0.00 4.30
460 951 4.840005 GGCGCCCTTCTTCTCCCG 62.840 72.222 18.11 0.00 0.00 5.14
462 953 4.082523 CGCCCTTCTTCTCCCGCA 62.083 66.667 0.00 0.00 0.00 5.69
463 954 2.592308 GCCCTTCTTCTCCCGCAT 59.408 61.111 0.00 0.00 0.00 4.73
464 955 1.077429 GCCCTTCTTCTCCCGCATT 60.077 57.895 0.00 0.00 0.00 3.56
465 956 1.379642 GCCCTTCTTCTCCCGCATTG 61.380 60.000 0.00 0.00 0.00 2.82
466 957 1.379642 CCCTTCTTCTCCCGCATTGC 61.380 60.000 0.00 0.00 0.00 3.56
482 973 4.233635 GCGATGAAGCAGCCGCAG 62.234 66.667 7.96 0.00 46.04 5.18
483 974 4.233635 CGATGAAGCAGCCGCAGC 62.234 66.667 0.00 0.00 42.27 5.25
484 975 3.885521 GATGAAGCAGCCGCAGCC 61.886 66.667 3.83 0.00 42.27 4.85
528 1019 4.382320 GCGGTAAGGTGGCGGACA 62.382 66.667 0.00 0.00 0.00 4.02
529 1020 2.125673 CGGTAAGGTGGCGGACAG 60.126 66.667 0.00 0.00 0.00 3.51
530 1021 2.267961 GGTAAGGTGGCGGACAGG 59.732 66.667 0.00 0.00 0.00 4.00
531 1022 2.267961 GTAAGGTGGCGGACAGGG 59.732 66.667 0.00 0.00 0.00 4.45
532 1023 3.712907 TAAGGTGGCGGACAGGGC 61.713 66.667 0.00 0.00 0.00 5.19
560 1051 3.515687 CGAATCACGGCGAGATCG 58.484 61.111 19.67 18.70 43.27 3.69
561 1052 1.298413 CGAATCACGGCGAGATCGT 60.298 57.895 19.67 5.76 42.22 3.73
566 1057 2.413351 ACGGCGAGATCGTGGATG 59.587 61.111 16.62 0.00 42.22 3.51
567 1058 2.355126 CGGCGAGATCGTGGATGG 60.355 66.667 0.00 0.00 42.22 3.51
568 1059 2.815308 GGCGAGATCGTGGATGGT 59.185 61.111 3.94 0.00 42.22 3.55
569 1060 1.144057 GGCGAGATCGTGGATGGTT 59.856 57.895 3.94 0.00 42.22 3.67
570 1061 0.876342 GGCGAGATCGTGGATGGTTC 60.876 60.000 3.94 0.00 42.22 3.62
571 1062 0.876342 GCGAGATCGTGGATGGTTCC 60.876 60.000 3.94 0.00 42.22 3.62
572 1063 0.595053 CGAGATCGTGGATGGTTCCG 60.595 60.000 0.00 0.00 45.89 4.30
573 1064 0.460311 GAGATCGTGGATGGTTCCGT 59.540 55.000 0.00 0.00 45.89 4.69
574 1065 0.460311 AGATCGTGGATGGTTCCGTC 59.540 55.000 2.69 2.69 45.89 4.79
575 1066 0.870307 GATCGTGGATGGTTCCGTCG 60.870 60.000 5.17 0.00 45.89 5.12
576 1067 1.601419 ATCGTGGATGGTTCCGTCGT 61.601 55.000 5.17 0.00 45.89 4.34
577 1068 1.373748 CGTGGATGGTTCCGTCGTT 60.374 57.895 5.17 0.00 45.89 3.85
578 1069 1.349259 CGTGGATGGTTCCGTCGTTC 61.349 60.000 5.17 0.00 45.89 3.95
579 1070 1.017701 GTGGATGGTTCCGTCGTTCC 61.018 60.000 5.17 0.00 45.89 3.62
580 1071 1.189524 TGGATGGTTCCGTCGTTCCT 61.190 55.000 5.17 0.00 45.89 3.36
581 1072 0.459759 GGATGGTTCCGTCGTTCCTC 60.460 60.000 5.17 0.00 30.72 3.71
582 1073 0.531200 GATGGTTCCGTCGTTCCTCT 59.469 55.000 0.00 0.00 0.00 3.69
583 1074 0.246635 ATGGTTCCGTCGTTCCTCTG 59.753 55.000 0.00 0.00 0.00 3.35
584 1075 1.111116 TGGTTCCGTCGTTCCTCTGT 61.111 55.000 0.00 0.00 0.00 3.41
585 1076 0.033090 GGTTCCGTCGTTCCTCTGTT 59.967 55.000 0.00 0.00 0.00 3.16
586 1077 1.416373 GTTCCGTCGTTCCTCTGTTC 58.584 55.000 0.00 0.00 0.00 3.18
587 1078 0.316204 TTCCGTCGTTCCTCTGTTCC 59.684 55.000 0.00 0.00 0.00 3.62
588 1079 1.443872 CCGTCGTTCCTCTGTTCCG 60.444 63.158 0.00 0.00 0.00 4.30
589 1080 1.443872 CGTCGTTCCTCTGTTCCGG 60.444 63.158 0.00 0.00 0.00 5.14
590 1081 1.664306 GTCGTTCCTCTGTTCCGGT 59.336 57.895 0.00 0.00 0.00 5.28
591 1082 0.666577 GTCGTTCCTCTGTTCCGGTG 60.667 60.000 0.00 0.00 0.00 4.94
592 1083 1.111116 TCGTTCCTCTGTTCCGGTGT 61.111 55.000 0.00 0.00 0.00 4.16
593 1084 0.249741 CGTTCCTCTGTTCCGGTGTT 60.250 55.000 0.00 0.00 0.00 3.32
594 1085 1.509703 GTTCCTCTGTTCCGGTGTTC 58.490 55.000 0.00 0.00 0.00 3.18
595 1086 1.070289 GTTCCTCTGTTCCGGTGTTCT 59.930 52.381 0.00 0.00 0.00 3.01
596 1087 0.966920 TCCTCTGTTCCGGTGTTCTC 59.033 55.000 0.00 0.00 0.00 2.87
597 1088 0.969894 CCTCTGTTCCGGTGTTCTCT 59.030 55.000 0.00 0.00 0.00 3.10
598 1089 1.067495 CCTCTGTTCCGGTGTTCTCTC 60.067 57.143 0.00 0.00 0.00 3.20
599 1090 1.613925 CTCTGTTCCGGTGTTCTCTCA 59.386 52.381 0.00 0.00 0.00 3.27
600 1091 2.232452 CTCTGTTCCGGTGTTCTCTCAT 59.768 50.000 0.00 0.00 0.00 2.90
601 1092 2.231478 TCTGTTCCGGTGTTCTCTCATC 59.769 50.000 0.00 0.00 0.00 2.92
602 1093 1.275291 TGTTCCGGTGTTCTCTCATCC 59.725 52.381 0.00 0.00 0.00 3.51
603 1094 1.550976 GTTCCGGTGTTCTCTCATCCT 59.449 52.381 0.00 0.00 0.00 3.24
604 1095 1.475403 TCCGGTGTTCTCTCATCCTC 58.525 55.000 0.00 0.00 0.00 3.71
605 1096 1.006043 TCCGGTGTTCTCTCATCCTCT 59.994 52.381 0.00 0.00 0.00 3.69
606 1097 1.135915 CCGGTGTTCTCTCATCCTCTG 59.864 57.143 0.00 0.00 0.00 3.35
607 1098 1.135915 CGGTGTTCTCTCATCCTCTGG 59.864 57.143 0.00 0.00 0.00 3.86
608 1099 2.461695 GGTGTTCTCTCATCCTCTGGA 58.538 52.381 0.00 0.00 35.55 3.86
609 1100 3.037549 GGTGTTCTCTCATCCTCTGGAT 58.962 50.000 0.00 0.00 44.21 3.41
610 1101 3.069443 GGTGTTCTCTCATCCTCTGGATC 59.931 52.174 0.00 0.00 40.98 3.36
611 1102 2.954989 TGTTCTCTCATCCTCTGGATCG 59.045 50.000 0.00 0.00 40.98 3.69
612 1103 2.955660 GTTCTCTCATCCTCTGGATCGT 59.044 50.000 0.00 0.00 40.98 3.73
613 1104 2.857483 TCTCTCATCCTCTGGATCGTC 58.143 52.381 0.00 0.00 40.98 4.20
614 1105 2.441375 TCTCTCATCCTCTGGATCGTCT 59.559 50.000 0.00 0.00 40.98 4.18
615 1106 2.813754 CTCTCATCCTCTGGATCGTCTC 59.186 54.545 0.00 0.00 40.98 3.36
616 1107 1.535028 CTCATCCTCTGGATCGTCTCG 59.465 57.143 0.00 0.00 40.98 4.04
617 1108 1.134068 TCATCCTCTGGATCGTCTCGT 60.134 52.381 0.00 0.00 40.98 4.18
618 1109 1.265635 CATCCTCTGGATCGTCTCGTC 59.734 57.143 0.00 0.00 40.98 4.20
619 1110 0.542333 TCCTCTGGATCGTCTCGTCT 59.458 55.000 0.00 0.00 0.00 4.18
620 1111 0.941542 CCTCTGGATCGTCTCGTCTC 59.058 60.000 0.00 0.00 0.00 3.36
621 1112 0.941542 CTCTGGATCGTCTCGTCTCC 59.058 60.000 0.00 0.00 33.17 3.71
622 1113 0.542333 TCTGGATCGTCTCGTCTCCT 59.458 55.000 11.89 0.00 33.50 3.69
623 1114 0.941542 CTGGATCGTCTCGTCTCCTC 59.058 60.000 11.89 0.00 33.50 3.71
624 1115 0.542333 TGGATCGTCTCGTCTCCTCT 59.458 55.000 11.89 0.00 33.50 3.69
625 1116 1.223187 GGATCGTCTCGTCTCCTCTC 58.777 60.000 0.00 0.00 31.19 3.20
626 1117 1.202604 GGATCGTCTCGTCTCCTCTCT 60.203 57.143 0.00 0.00 31.19 3.10
627 1118 2.132762 GATCGTCTCGTCTCCTCTCTC 58.867 57.143 0.00 0.00 0.00 3.20
628 1119 0.179132 TCGTCTCGTCTCCTCTCTCG 60.179 60.000 0.00 0.00 0.00 4.04
629 1120 0.179132 CGTCTCGTCTCCTCTCTCGA 60.179 60.000 0.00 0.00 0.00 4.04
630 1121 1.537348 CGTCTCGTCTCCTCTCTCGAT 60.537 57.143 0.00 0.00 0.00 3.59
631 1122 2.132762 GTCTCGTCTCCTCTCTCGATC 58.867 57.143 0.00 0.00 0.00 3.69
632 1123 1.136690 CTCGTCTCCTCTCTCGATCG 58.863 60.000 9.36 9.36 0.00 3.69
633 1124 0.745468 TCGTCTCCTCTCTCGATCGA 59.255 55.000 18.32 18.32 0.00 3.59
634 1125 1.136500 TCGTCTCCTCTCTCGATCGAA 59.864 52.381 19.92 9.28 0.00 3.71
635 1126 1.259507 CGTCTCCTCTCTCGATCGAAC 59.740 57.143 19.92 10.50 0.00 3.95
636 1127 1.600485 GTCTCCTCTCTCGATCGAACC 59.400 57.143 19.92 0.00 0.00 3.62
637 1128 1.209747 TCTCCTCTCTCGATCGAACCA 59.790 52.381 19.92 5.13 0.00 3.67
638 1129 1.601903 CTCCTCTCTCGATCGAACCAG 59.398 57.143 19.92 14.54 0.00 4.00
639 1130 1.065345 TCCTCTCTCGATCGAACCAGT 60.065 52.381 19.92 0.00 0.00 4.00
640 1131 1.332375 CCTCTCTCGATCGAACCAGTC 59.668 57.143 19.92 0.00 0.00 3.51
641 1132 1.332375 CTCTCTCGATCGAACCAGTCC 59.668 57.143 19.92 0.00 0.00 3.85
642 1133 1.095600 CTCTCGATCGAACCAGTCCA 58.904 55.000 19.92 0.00 0.00 4.02
643 1134 1.472878 CTCTCGATCGAACCAGTCCAA 59.527 52.381 19.92 0.00 0.00 3.53
644 1135 1.890489 TCTCGATCGAACCAGTCCAAA 59.110 47.619 19.92 0.00 0.00 3.28
645 1136 2.094700 TCTCGATCGAACCAGTCCAAAG 60.095 50.000 19.92 2.76 0.00 2.77
646 1137 1.616865 TCGATCGAACCAGTCCAAAGT 59.383 47.619 16.99 0.00 0.00 2.66
647 1138 1.726791 CGATCGAACCAGTCCAAAGTG 59.273 52.381 10.26 0.00 0.00 3.16
648 1139 2.767505 GATCGAACCAGTCCAAAGTGT 58.232 47.619 0.00 0.00 0.00 3.55
649 1140 3.613193 CGATCGAACCAGTCCAAAGTGTA 60.613 47.826 10.26 0.00 0.00 2.90
650 1141 3.823281 TCGAACCAGTCCAAAGTGTAA 57.177 42.857 0.00 0.00 0.00 2.41
651 1142 4.139859 TCGAACCAGTCCAAAGTGTAAA 57.860 40.909 0.00 0.00 0.00 2.01
652 1143 4.515361 TCGAACCAGTCCAAAGTGTAAAA 58.485 39.130 0.00 0.00 0.00 1.52
653 1144 5.127491 TCGAACCAGTCCAAAGTGTAAAAT 58.873 37.500 0.00 0.00 0.00 1.82
654 1145 5.237779 TCGAACCAGTCCAAAGTGTAAAATC 59.762 40.000 0.00 0.00 0.00 2.17
655 1146 5.432885 AACCAGTCCAAAGTGTAAAATCG 57.567 39.130 0.00 0.00 0.00 3.34
656 1147 4.457466 ACCAGTCCAAAGTGTAAAATCGT 58.543 39.130 0.00 0.00 0.00 3.73
657 1148 4.514066 ACCAGTCCAAAGTGTAAAATCGTC 59.486 41.667 0.00 0.00 0.00 4.20
658 1149 4.083484 CCAGTCCAAAGTGTAAAATCGTCC 60.083 45.833 0.00 0.00 0.00 4.79
659 1150 4.513692 CAGTCCAAAGTGTAAAATCGTCCA 59.486 41.667 0.00 0.00 0.00 4.02
660 1151 5.008217 CAGTCCAAAGTGTAAAATCGTCCAA 59.992 40.000 0.00 0.00 0.00 3.53
661 1152 5.591067 AGTCCAAAGTGTAAAATCGTCCAAA 59.409 36.000 0.00 0.00 0.00 3.28
662 1153 6.095720 AGTCCAAAGTGTAAAATCGTCCAAAA 59.904 34.615 0.00 0.00 0.00 2.44
663 1154 6.921307 GTCCAAAGTGTAAAATCGTCCAAAAT 59.079 34.615 0.00 0.00 0.00 1.82
664 1155 8.077386 GTCCAAAGTGTAAAATCGTCCAAAATA 58.923 33.333 0.00 0.00 0.00 1.40
665 1156 8.630917 TCCAAAGTGTAAAATCGTCCAAAATAA 58.369 29.630 0.00 0.00 0.00 1.40
666 1157 9.418045 CCAAAGTGTAAAATCGTCCAAAATAAT 57.582 29.630 0.00 0.00 0.00 1.28
678 1169 8.578308 TCGTCCAAAATAATATAACGTGTAGG 57.422 34.615 0.00 0.00 0.00 3.18
679 1170 8.196771 TCGTCCAAAATAATATAACGTGTAGGT 58.803 33.333 0.00 0.00 0.00 3.08
680 1171 8.482429 CGTCCAAAATAATATAACGTGTAGGTC 58.518 37.037 0.00 0.00 0.00 3.85
681 1172 8.768019 GTCCAAAATAATATAACGTGTAGGTCC 58.232 37.037 0.00 0.00 0.00 4.46
682 1173 8.707449 TCCAAAATAATATAACGTGTAGGTCCT 58.293 33.333 0.00 0.00 0.00 3.85
683 1174 8.770828 CCAAAATAATATAACGTGTAGGTCCTG 58.229 37.037 0.00 0.00 0.00 3.86
684 1175 9.537192 CAAAATAATATAACGTGTAGGTCCTGA 57.463 33.333 0.00 0.00 0.00 3.86
685 1176 9.538508 AAAATAATATAACGTGTAGGTCCTGAC 57.461 33.333 0.00 0.00 0.00 3.51
686 1177 4.825546 ATATAACGTGTAGGTCCTGACG 57.174 45.455 18.85 18.85 37.82 4.35
687 1178 1.896220 TAACGTGTAGGTCCTGACGT 58.104 50.000 19.90 19.90 46.46 4.34
688 1179 0.313043 AACGTGTAGGTCCTGACGTG 59.687 55.000 24.02 8.89 43.88 4.49
689 1180 1.211969 CGTGTAGGTCCTGACGTGG 59.788 63.158 14.30 0.00 0.00 4.94
693 1184 2.028385 GTGTAGGTCCTGACGTGGAAAT 60.028 50.000 0.00 0.00 37.93 2.17
696 1187 1.420138 AGGTCCTGACGTGGAAATTGT 59.580 47.619 0.00 0.00 37.93 2.71
697 1188 1.535462 GGTCCTGACGTGGAAATTGTG 59.465 52.381 0.00 0.00 37.93 3.33
699 1190 2.875933 GTCCTGACGTGGAAATTGTGAA 59.124 45.455 0.00 0.00 37.93 3.18
725 1216 7.713764 AAAAGTCAGTTTGTGCCATTTTATC 57.286 32.000 0.00 0.00 0.00 1.75
726 1217 6.655078 AAGTCAGTTTGTGCCATTTTATCT 57.345 33.333 0.00 0.00 0.00 1.98
727 1218 7.759489 AAGTCAGTTTGTGCCATTTTATCTA 57.241 32.000 0.00 0.00 0.00 1.98
728 1219 7.759489 AGTCAGTTTGTGCCATTTTATCTAA 57.241 32.000 0.00 0.00 0.00 2.10
729 1220 7.593825 AGTCAGTTTGTGCCATTTTATCTAAC 58.406 34.615 0.00 0.00 0.00 2.34
730 1221 6.806739 GTCAGTTTGTGCCATTTTATCTAACC 59.193 38.462 0.00 0.00 0.00 2.85
731 1222 6.071616 TCAGTTTGTGCCATTTTATCTAACCC 60.072 38.462 0.00 0.00 0.00 4.11
732 1223 6.016555 AGTTTGTGCCATTTTATCTAACCCT 58.983 36.000 0.00 0.00 0.00 4.34
733 1224 5.913137 TTGTGCCATTTTATCTAACCCTG 57.087 39.130 0.00 0.00 0.00 4.45
734 1225 5.186256 TGTGCCATTTTATCTAACCCTGA 57.814 39.130 0.00 0.00 0.00 3.86
735 1226 5.575157 TGTGCCATTTTATCTAACCCTGAA 58.425 37.500 0.00 0.00 0.00 3.02
736 1227 5.652014 TGTGCCATTTTATCTAACCCTGAAG 59.348 40.000 0.00 0.00 0.00 3.02
737 1228 5.067805 GTGCCATTTTATCTAACCCTGAAGG 59.932 44.000 0.00 0.00 43.78 3.46
739 1230 5.891551 GCCATTTTATCTAACCCTGAAGGAA 59.108 40.000 0.00 0.00 39.89 3.36
740 1231 6.379988 GCCATTTTATCTAACCCTGAAGGAAA 59.620 38.462 0.00 0.00 39.89 3.13
741 1232 7.093509 GCCATTTTATCTAACCCTGAAGGAAAA 60.094 37.037 0.00 0.00 39.89 2.29
742 1233 8.470002 CCATTTTATCTAACCCTGAAGGAAAAG 58.530 37.037 0.00 0.00 39.89 2.27
743 1234 9.025041 CATTTTATCTAACCCTGAAGGAAAAGT 57.975 33.333 0.00 0.00 39.89 2.66
744 1235 7.996098 TTTATCTAACCCTGAAGGAAAAGTG 57.004 36.000 0.00 0.00 39.89 3.16
745 1236 5.584551 ATCTAACCCTGAAGGAAAAGTGT 57.415 39.130 0.00 0.00 39.89 3.55
746 1237 4.714632 TCTAACCCTGAAGGAAAAGTGTG 58.285 43.478 0.00 0.00 39.89 3.82
748 1239 2.932261 ACCCTGAAGGAAAAGTGTGTC 58.068 47.619 0.00 0.00 39.89 3.67
749 1240 2.241176 ACCCTGAAGGAAAAGTGTGTCA 59.759 45.455 0.00 0.00 39.89 3.58
753 1244 5.534654 CCCTGAAGGAAAAGTGTGTCATTTA 59.465 40.000 0.00 0.00 38.24 1.40
754 1245 6.040391 CCCTGAAGGAAAAGTGTGTCATTTAA 59.960 38.462 0.00 0.00 38.24 1.52
755 1246 7.255942 CCCTGAAGGAAAAGTGTGTCATTTAAT 60.256 37.037 0.00 0.00 38.24 1.40
757 1248 8.463930 TGAAGGAAAAGTGTGTCATTTAATCT 57.536 30.769 0.00 0.00 0.00 2.40
789 1280 9.643693 AAAGAAAGGTGTGCTATTTTATCAATG 57.356 29.630 0.00 0.00 0.00 2.82
790 1281 8.353423 AGAAAGGTGTGCTATTTTATCAATGT 57.647 30.769 0.00 0.00 0.00 2.71
791 1282 9.461312 AGAAAGGTGTGCTATTTTATCAATGTA 57.539 29.630 0.00 0.00 0.00 2.29
792 1283 9.503427 GAAAGGTGTGCTATTTTATCAATGTAC 57.497 33.333 0.00 0.00 0.00 2.90
793 1284 7.246674 AGGTGTGCTATTTTATCAATGTACG 57.753 36.000 0.00 0.00 0.00 3.67
794 1285 7.045416 AGGTGTGCTATTTTATCAATGTACGA 58.955 34.615 0.00 0.00 0.00 3.43
795 1286 7.224753 AGGTGTGCTATTTTATCAATGTACGAG 59.775 37.037 0.00 0.00 0.00 4.18
796 1287 7.345192 GTGTGCTATTTTATCAATGTACGAGG 58.655 38.462 0.00 0.00 0.00 4.63
797 1288 7.223971 GTGTGCTATTTTATCAATGTACGAGGA 59.776 37.037 0.00 0.00 0.00 3.71
798 1289 7.766738 TGTGCTATTTTATCAATGTACGAGGAA 59.233 33.333 0.00 0.00 0.00 3.36
799 1290 8.609176 GTGCTATTTTATCAATGTACGAGGAAA 58.391 33.333 0.00 0.00 0.00 3.13
800 1291 8.826710 TGCTATTTTATCAATGTACGAGGAAAG 58.173 33.333 0.00 0.00 0.00 2.62
801 1292 8.283291 GCTATTTTATCAATGTACGAGGAAAGG 58.717 37.037 0.00 0.00 0.00 3.11
802 1293 9.326413 CTATTTTATCAATGTACGAGGAAAGGT 57.674 33.333 0.00 0.00 0.00 3.50
803 1294 6.978343 TTTATCAATGTACGAGGAAAGGTG 57.022 37.500 0.00 0.00 0.00 4.00
804 1295 4.553330 ATCAATGTACGAGGAAAGGTGT 57.447 40.909 0.00 0.00 0.00 4.16
805 1296 3.659786 TCAATGTACGAGGAAAGGTGTG 58.340 45.455 0.00 0.00 0.00 3.82
806 1297 2.094762 ATGTACGAGGAAAGGTGTGC 57.905 50.000 0.00 0.00 0.00 4.57
807 1298 1.045407 TGTACGAGGAAAGGTGTGCT 58.955 50.000 0.00 0.00 0.00 4.40
808 1299 2.241160 TGTACGAGGAAAGGTGTGCTA 58.759 47.619 0.00 0.00 0.00 3.49
809 1300 2.829720 TGTACGAGGAAAGGTGTGCTAT 59.170 45.455 0.00 0.00 0.00 2.97
810 1301 3.259876 TGTACGAGGAAAGGTGTGCTATT 59.740 43.478 0.00 0.00 0.00 1.73
811 1302 3.418684 ACGAGGAAAGGTGTGCTATTT 57.581 42.857 0.00 0.00 0.00 1.40
812 1303 3.751518 ACGAGGAAAGGTGTGCTATTTT 58.248 40.909 0.00 0.00 0.00 1.82
813 1304 4.901868 ACGAGGAAAGGTGTGCTATTTTA 58.098 39.130 0.00 0.00 0.00 1.52
814 1305 5.497474 ACGAGGAAAGGTGTGCTATTTTAT 58.503 37.500 0.00 0.00 0.00 1.40
815 1306 5.585047 ACGAGGAAAGGTGTGCTATTTTATC 59.415 40.000 0.00 0.00 0.00 1.75
816 1307 5.584649 CGAGGAAAGGTGTGCTATTTTATCA 59.415 40.000 0.00 0.00 0.00 2.15
817 1308 6.093495 CGAGGAAAGGTGTGCTATTTTATCAA 59.907 38.462 0.00 0.00 0.00 2.57
818 1309 7.361713 CGAGGAAAGGTGTGCTATTTTATCAAA 60.362 37.037 0.00 0.00 0.00 2.69
819 1310 8.366359 AGGAAAGGTGTGCTATTTTATCAAAT 57.634 30.769 0.00 0.00 36.52 2.32
820 1311 8.815912 AGGAAAGGTGTGCTATTTTATCAAATT 58.184 29.630 0.00 0.00 34.29 1.82
821 1312 8.872845 GGAAAGGTGTGCTATTTTATCAAATTG 58.127 33.333 0.00 0.00 34.29 2.32
822 1313 7.832503 AAGGTGTGCTATTTTATCAAATTGC 57.167 32.000 10.61 10.61 45.80 3.56
823 1314 7.174107 AGGTGTGCTATTTTATCAAATTGCT 57.826 32.000 16.18 0.00 45.80 3.91
824 1315 7.260603 AGGTGTGCTATTTTATCAAATTGCTC 58.739 34.615 16.18 13.73 45.80 4.26
1428 2843 1.602311 GCCTCGTCCTTCTATCCGTA 58.398 55.000 0.00 0.00 0.00 4.02
1434 2856 4.375272 TCGTCCTTCTATCCGTAGTAGTG 58.625 47.826 0.00 0.00 0.00 2.74
2367 3835 2.092212 CCTTACCATCTGCCACTTCCAT 60.092 50.000 0.00 0.00 0.00 3.41
2557 6435 4.628715 GCTATGGATTTGGGAAGAACCTGA 60.629 45.833 0.00 0.00 38.98 3.86
3023 7150 3.869065 TGGAAGGTAAAGGCGTGAATAG 58.131 45.455 0.00 0.00 0.00 1.73
3558 7697 7.573968 ATTTCTTCCTGTAATAATGTCTGCC 57.426 36.000 0.00 0.00 0.00 4.85
3851 8042 1.540267 TGGCCATTACTTTTGTCCCG 58.460 50.000 0.00 0.00 0.00 5.14
3857 8048 4.007659 CCATTACTTTTGTCCCGCTACTT 58.992 43.478 0.00 0.00 0.00 2.24
3976 8167 7.684670 AGACGTTGTTACATGTTATATTGCTG 58.315 34.615 2.30 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
417 908 4.335647 AAGTCCCCCTGCAGCACG 62.336 66.667 8.66 0.00 0.00 5.34
418 909 2.360475 GAAGTCCCCCTGCAGCAC 60.360 66.667 8.66 1.61 0.00 4.40
419 910 2.416107 CTTGAAGTCCCCCTGCAGCA 62.416 60.000 8.66 0.00 27.50 4.41
420 911 1.676967 CTTGAAGTCCCCCTGCAGC 60.677 63.158 8.66 0.00 27.50 5.25
421 912 0.607489 CACTTGAAGTCCCCCTGCAG 60.607 60.000 6.78 6.78 27.50 4.41
422 913 1.455849 CACTTGAAGTCCCCCTGCA 59.544 57.895 0.00 0.00 0.00 4.41
423 914 1.303643 CCACTTGAAGTCCCCCTGC 60.304 63.158 0.00 0.00 0.00 4.85
424 915 1.303643 GCCACTTGAAGTCCCCCTG 60.304 63.158 0.00 0.00 0.00 4.45
425 916 2.895424 CGCCACTTGAAGTCCCCCT 61.895 63.158 0.00 0.00 0.00 4.79
426 917 2.359975 CGCCACTTGAAGTCCCCC 60.360 66.667 0.00 0.00 0.00 5.40
427 918 2.359975 CCGCCACTTGAAGTCCCC 60.360 66.667 0.00 0.00 0.00 4.81
428 919 3.056328 GCCGCCACTTGAAGTCCC 61.056 66.667 0.00 0.00 0.00 4.46
429 920 3.423154 CGCCGCCACTTGAAGTCC 61.423 66.667 0.00 0.00 0.00 3.85
430 921 4.090057 GCGCCGCCACTTGAAGTC 62.090 66.667 0.00 0.00 0.00 3.01
442 933 4.840005 GGGAGAAGAAGGGCGCCG 62.840 72.222 22.54 0.00 0.00 6.46
443 934 4.840005 CGGGAGAAGAAGGGCGCC 62.840 72.222 21.18 21.18 0.00 6.53
445 936 2.876368 AATGCGGGAGAAGAAGGGCG 62.876 60.000 0.00 0.00 0.00 6.13
446 937 1.077429 AATGCGGGAGAAGAAGGGC 60.077 57.895 0.00 0.00 0.00 5.19
447 938 1.379642 GCAATGCGGGAGAAGAAGGG 61.380 60.000 0.00 0.00 0.00 3.95
448 939 2.101700 GCAATGCGGGAGAAGAAGG 58.898 57.895 0.00 0.00 0.00 3.46
460 951 1.588139 GGCTGCTTCATCGCAATGC 60.588 57.895 0.00 0.00 39.80 3.56
461 952 1.298116 CGGCTGCTTCATCGCAATG 60.298 57.895 0.00 0.00 39.80 2.82
462 953 3.104766 CGGCTGCTTCATCGCAAT 58.895 55.556 0.00 0.00 39.80 3.56
463 954 3.803082 GCGGCTGCTTCATCGCAA 61.803 61.111 11.21 0.00 46.33 4.85
466 957 4.233635 GCTGCGGCTGCTTCATCG 62.234 66.667 22.46 1.38 43.34 3.84
467 958 3.885521 GGCTGCGGCTGCTTCATC 61.886 66.667 27.14 9.99 43.34 2.92
511 1002 4.382320 TGTCCGCCACCTTACCGC 62.382 66.667 0.00 0.00 0.00 5.68
512 1003 2.125673 CTGTCCGCCACCTTACCG 60.126 66.667 0.00 0.00 0.00 4.02
513 1004 2.267961 CCTGTCCGCCACCTTACC 59.732 66.667 0.00 0.00 0.00 2.85
514 1005 2.267961 CCCTGTCCGCCACCTTAC 59.732 66.667 0.00 0.00 0.00 2.34
515 1006 3.712907 GCCCTGTCCGCCACCTTA 61.713 66.667 0.00 0.00 0.00 2.69
532 1023 3.833645 TGATTCGTCCCCGAGCCG 61.834 66.667 0.00 0.00 45.24 5.52
533 1024 2.202892 GTGATTCGTCCCCGAGCC 60.203 66.667 0.00 0.00 45.24 4.70
534 1025 2.582498 CGTGATTCGTCCCCGAGC 60.582 66.667 0.00 0.00 45.24 5.03
535 1026 2.104331 CCGTGATTCGTCCCCGAG 59.896 66.667 0.00 0.00 45.24 4.63
536 1027 4.137872 GCCGTGATTCGTCCCCGA 62.138 66.667 0.00 0.00 42.41 5.14
538 1029 4.137872 TCGCCGTGATTCGTCCCC 62.138 66.667 0.00 0.00 37.94 4.81
539 1030 2.351336 ATCTCGCCGTGATTCGTCCC 62.351 60.000 0.00 0.00 37.94 4.46
540 1031 0.935366 GATCTCGCCGTGATTCGTCC 60.935 60.000 2.92 0.00 37.94 4.79
541 1032 1.262824 CGATCTCGCCGTGATTCGTC 61.263 60.000 2.92 0.00 37.94 4.20
542 1033 1.298413 CGATCTCGCCGTGATTCGT 60.298 57.895 2.92 0.00 37.94 3.85
543 1034 1.298413 ACGATCTCGCCGTGATTCG 60.298 57.895 2.92 10.27 44.43 3.34
544 1035 4.711980 ACGATCTCGCCGTGATTC 57.288 55.556 2.92 0.00 44.43 2.52
549 1040 2.413351 CATCCACGATCTCGCCGT 59.587 61.111 0.00 0.00 44.43 5.68
550 1041 2.355126 CCATCCACGATCTCGCCG 60.355 66.667 0.00 0.00 44.43 6.46
551 1042 0.876342 GAACCATCCACGATCTCGCC 60.876 60.000 0.00 0.00 44.43 5.54
552 1043 0.876342 GGAACCATCCACGATCTCGC 60.876 60.000 0.00 0.00 45.79 5.03
553 1044 0.595053 CGGAACCATCCACGATCTCG 60.595 60.000 0.00 0.00 46.97 4.04
554 1045 0.460311 ACGGAACCATCCACGATCTC 59.540 55.000 0.00 0.00 46.97 2.75
555 1046 0.460311 GACGGAACCATCCACGATCT 59.540 55.000 0.00 0.00 46.97 2.75
556 1047 0.870307 CGACGGAACCATCCACGATC 60.870 60.000 0.00 0.00 46.97 3.69
557 1048 1.141019 CGACGGAACCATCCACGAT 59.859 57.895 0.00 0.00 46.97 3.73
558 1049 1.808531 AACGACGGAACCATCCACGA 61.809 55.000 14.86 0.00 46.97 4.35
559 1050 1.349259 GAACGACGGAACCATCCACG 61.349 60.000 0.00 8.96 46.97 4.94
560 1051 1.017701 GGAACGACGGAACCATCCAC 61.018 60.000 0.00 0.00 46.97 4.02
561 1052 1.189524 AGGAACGACGGAACCATCCA 61.190 55.000 0.00 0.00 46.97 3.41
562 1053 0.459759 GAGGAACGACGGAACCATCC 60.460 60.000 0.00 0.00 42.80 3.51
563 1054 0.531200 AGAGGAACGACGGAACCATC 59.469 55.000 0.00 0.41 0.00 3.51
564 1055 0.246635 CAGAGGAACGACGGAACCAT 59.753 55.000 0.00 0.00 0.00 3.55
565 1056 1.111116 ACAGAGGAACGACGGAACCA 61.111 55.000 0.00 0.00 0.00 3.67
566 1057 0.033090 AACAGAGGAACGACGGAACC 59.967 55.000 0.00 0.00 0.00 3.62
567 1058 1.416373 GAACAGAGGAACGACGGAAC 58.584 55.000 0.00 0.00 0.00 3.62
568 1059 0.316204 GGAACAGAGGAACGACGGAA 59.684 55.000 0.00 0.00 0.00 4.30
569 1060 1.859427 CGGAACAGAGGAACGACGGA 61.859 60.000 0.00 0.00 0.00 4.69
570 1061 1.443872 CGGAACAGAGGAACGACGG 60.444 63.158 0.00 0.00 0.00 4.79
571 1062 1.443872 CCGGAACAGAGGAACGACG 60.444 63.158 0.00 0.00 0.00 5.12
572 1063 0.666577 CACCGGAACAGAGGAACGAC 60.667 60.000 9.46 0.00 0.00 4.34
573 1064 1.111116 ACACCGGAACAGAGGAACGA 61.111 55.000 9.46 0.00 0.00 3.85
574 1065 0.249741 AACACCGGAACAGAGGAACG 60.250 55.000 9.46 0.00 0.00 3.95
575 1066 1.070289 AGAACACCGGAACAGAGGAAC 59.930 52.381 9.46 0.00 0.00 3.62
576 1067 1.343465 GAGAACACCGGAACAGAGGAA 59.657 52.381 9.46 0.00 0.00 3.36
577 1068 0.966920 GAGAACACCGGAACAGAGGA 59.033 55.000 9.46 0.00 0.00 3.71
578 1069 0.969894 AGAGAACACCGGAACAGAGG 59.030 55.000 9.46 0.00 0.00 3.69
579 1070 1.613925 TGAGAGAACACCGGAACAGAG 59.386 52.381 9.46 0.00 0.00 3.35
580 1071 1.699730 TGAGAGAACACCGGAACAGA 58.300 50.000 9.46 0.00 0.00 3.41
581 1072 2.611518 GATGAGAGAACACCGGAACAG 58.388 52.381 9.46 0.00 0.00 3.16
582 1073 1.275291 GGATGAGAGAACACCGGAACA 59.725 52.381 9.46 0.00 0.00 3.18
583 1074 1.550976 AGGATGAGAGAACACCGGAAC 59.449 52.381 9.46 0.00 0.00 3.62
584 1075 1.825474 GAGGATGAGAGAACACCGGAA 59.175 52.381 9.46 0.00 0.00 4.30
585 1076 1.006043 AGAGGATGAGAGAACACCGGA 59.994 52.381 9.46 0.00 0.00 5.14
586 1077 1.135915 CAGAGGATGAGAGAACACCGG 59.864 57.143 0.00 0.00 0.00 5.28
587 1078 1.135915 CCAGAGGATGAGAGAACACCG 59.864 57.143 0.00 0.00 0.00 4.94
588 1079 2.461695 TCCAGAGGATGAGAGAACACC 58.538 52.381 0.00 0.00 0.00 4.16
589 1080 3.243367 CGATCCAGAGGATGAGAGAACAC 60.243 52.174 2.74 0.00 43.27 3.32
590 1081 2.954989 CGATCCAGAGGATGAGAGAACA 59.045 50.000 2.74 0.00 43.27 3.18
591 1082 2.955660 ACGATCCAGAGGATGAGAGAAC 59.044 50.000 2.74 0.00 43.27 3.01
592 1083 3.117701 AGACGATCCAGAGGATGAGAGAA 60.118 47.826 2.74 0.00 43.27 2.87
593 1084 2.441375 AGACGATCCAGAGGATGAGAGA 59.559 50.000 2.74 0.00 43.27 3.10
594 1085 2.813754 GAGACGATCCAGAGGATGAGAG 59.186 54.545 2.74 0.00 43.27 3.20
595 1086 2.808567 CGAGACGATCCAGAGGATGAGA 60.809 54.545 2.74 0.00 43.27 3.27
596 1087 1.535028 CGAGACGATCCAGAGGATGAG 59.465 57.143 2.74 0.36 43.27 2.90
597 1088 1.134068 ACGAGACGATCCAGAGGATGA 60.134 52.381 2.74 0.00 43.27 2.92
598 1089 1.265635 GACGAGACGATCCAGAGGATG 59.734 57.143 2.74 0.00 43.27 3.51
599 1090 1.142060 AGACGAGACGATCCAGAGGAT 59.858 52.381 0.00 0.00 46.28 3.24
600 1091 0.542333 AGACGAGACGATCCAGAGGA 59.458 55.000 0.00 0.00 35.55 3.71
601 1092 0.941542 GAGACGAGACGATCCAGAGG 59.058 60.000 0.00 0.00 0.00 3.69
602 1093 0.941542 GGAGACGAGACGATCCAGAG 59.058 60.000 12.33 0.00 36.71 3.35
603 1094 0.542333 AGGAGACGAGACGATCCAGA 59.458 55.000 16.81 0.00 38.18 3.86
604 1095 0.941542 GAGGAGACGAGACGATCCAG 59.058 60.000 16.81 0.00 38.18 3.86
605 1096 0.542333 AGAGGAGACGAGACGATCCA 59.458 55.000 16.81 0.00 38.18 3.41
606 1097 1.202604 AGAGAGGAGACGAGACGATCC 60.203 57.143 0.00 0.00 36.86 3.36
607 1098 2.132762 GAGAGAGGAGACGAGACGATC 58.867 57.143 0.00 0.00 0.00 3.69
608 1099 1.537348 CGAGAGAGGAGACGAGACGAT 60.537 57.143 0.00 0.00 0.00 3.73
609 1100 0.179132 CGAGAGAGGAGACGAGACGA 60.179 60.000 0.00 0.00 0.00 4.20
610 1101 0.179132 TCGAGAGAGGAGACGAGACG 60.179 60.000 0.00 0.00 34.84 4.18
611 1102 3.744941 TCGAGAGAGGAGACGAGAC 57.255 57.895 0.00 0.00 34.84 3.36
623 1114 1.095600 TGGACTGGTTCGATCGAGAG 58.904 55.000 18.54 16.69 0.00 3.20
624 1115 1.541379 TTGGACTGGTTCGATCGAGA 58.459 50.000 18.54 6.89 0.00 4.04
625 1116 2.263077 CTTTGGACTGGTTCGATCGAG 58.737 52.381 18.54 9.21 0.00 4.04
626 1117 1.616865 ACTTTGGACTGGTTCGATCGA 59.383 47.619 15.15 15.15 0.00 3.59
627 1118 1.726791 CACTTTGGACTGGTTCGATCG 59.273 52.381 9.36 9.36 0.00 3.69
628 1119 2.767505 ACACTTTGGACTGGTTCGATC 58.232 47.619 0.00 0.00 0.00 3.69
629 1120 2.930826 ACACTTTGGACTGGTTCGAT 57.069 45.000 0.00 0.00 0.00 3.59
630 1121 3.823281 TTACACTTTGGACTGGTTCGA 57.177 42.857 0.00 0.00 0.00 3.71
631 1122 4.886247 TTTTACACTTTGGACTGGTTCG 57.114 40.909 0.00 0.00 0.00 3.95
632 1123 5.008316 ACGATTTTACACTTTGGACTGGTTC 59.992 40.000 0.00 0.00 0.00 3.62
633 1124 4.885325 ACGATTTTACACTTTGGACTGGTT 59.115 37.500 0.00 0.00 0.00 3.67
634 1125 4.457466 ACGATTTTACACTTTGGACTGGT 58.543 39.130 0.00 0.00 0.00 4.00
635 1126 4.083484 GGACGATTTTACACTTTGGACTGG 60.083 45.833 0.00 0.00 0.00 4.00
636 1127 4.513692 TGGACGATTTTACACTTTGGACTG 59.486 41.667 0.00 0.00 0.00 3.51
637 1128 4.710324 TGGACGATTTTACACTTTGGACT 58.290 39.130 0.00 0.00 0.00 3.85
638 1129 5.427036 TTGGACGATTTTACACTTTGGAC 57.573 39.130 0.00 0.00 0.00 4.02
639 1130 6.452494 TTTTGGACGATTTTACACTTTGGA 57.548 33.333 0.00 0.00 0.00 3.53
640 1131 8.804688 TTATTTTGGACGATTTTACACTTTGG 57.195 30.769 0.00 0.00 0.00 3.28
652 1143 9.199982 CCTACACGTTATATTATTTTGGACGAT 57.800 33.333 0.00 0.00 33.67 3.73
653 1144 8.196771 ACCTACACGTTATATTATTTTGGACGA 58.803 33.333 0.00 0.00 33.67 4.20
654 1145 8.356533 ACCTACACGTTATATTATTTTGGACG 57.643 34.615 0.00 0.00 35.39 4.79
655 1146 8.768019 GGACCTACACGTTATATTATTTTGGAC 58.232 37.037 0.00 0.00 0.00 4.02
656 1147 8.707449 AGGACCTACACGTTATATTATTTTGGA 58.293 33.333 0.00 0.00 0.00 3.53
657 1148 8.770828 CAGGACCTACACGTTATATTATTTTGG 58.229 37.037 0.00 0.00 0.00 3.28
658 1149 9.537192 TCAGGACCTACACGTTATATTATTTTG 57.463 33.333 0.00 0.00 0.00 2.44
659 1150 9.538508 GTCAGGACCTACACGTTATATTATTTT 57.461 33.333 0.00 0.00 0.00 1.82
660 1151 7.864379 CGTCAGGACCTACACGTTATATTATTT 59.136 37.037 14.45 0.00 0.00 1.40
661 1152 7.013655 ACGTCAGGACCTACACGTTATATTATT 59.986 37.037 20.20 0.80 42.67 1.40
662 1153 6.488006 ACGTCAGGACCTACACGTTATATTAT 59.512 38.462 20.20 1.38 42.67 1.28
663 1154 5.822519 ACGTCAGGACCTACACGTTATATTA 59.177 40.000 20.20 0.00 42.67 0.98
664 1155 4.641989 ACGTCAGGACCTACACGTTATATT 59.358 41.667 20.20 2.55 42.67 1.28
665 1156 4.036027 CACGTCAGGACCTACACGTTATAT 59.964 45.833 22.37 4.36 42.67 0.86
666 1157 3.374988 CACGTCAGGACCTACACGTTATA 59.625 47.826 22.37 0.00 42.67 0.98
667 1158 2.163010 CACGTCAGGACCTACACGTTAT 59.837 50.000 22.37 4.96 42.67 1.89
668 1159 1.536766 CACGTCAGGACCTACACGTTA 59.463 52.381 22.37 0.00 42.67 3.18
669 1160 0.313043 CACGTCAGGACCTACACGTT 59.687 55.000 22.37 9.90 42.67 3.99
670 1161 1.521450 CCACGTCAGGACCTACACGT 61.521 60.000 20.20 20.20 46.05 4.49
671 1162 1.211969 CCACGTCAGGACCTACACG 59.788 63.158 19.12 19.12 38.24 4.49
672 1163 0.963962 TTCCACGTCAGGACCTACAC 59.036 55.000 0.00 0.00 37.42 2.90
673 1164 1.707106 TTTCCACGTCAGGACCTACA 58.293 50.000 0.00 0.00 37.42 2.74
674 1165 3.000727 CAATTTCCACGTCAGGACCTAC 58.999 50.000 0.00 0.00 37.42 3.18
675 1166 2.635915 ACAATTTCCACGTCAGGACCTA 59.364 45.455 0.00 0.00 37.42 3.08
676 1167 1.420138 ACAATTTCCACGTCAGGACCT 59.580 47.619 0.00 0.00 37.42 3.85
677 1168 1.535462 CACAATTTCCACGTCAGGACC 59.465 52.381 0.00 0.00 37.42 4.46
678 1169 2.489971 TCACAATTTCCACGTCAGGAC 58.510 47.619 0.00 0.00 37.42 3.85
679 1170 2.920724 TCACAATTTCCACGTCAGGA 57.079 45.000 0.00 0.00 35.41 3.86
680 1171 3.980646 TTTCACAATTTCCACGTCAGG 57.019 42.857 0.00 0.00 0.00 3.86
713 1204 5.067805 CCTTCAGGGTTAGATAAAATGGCAC 59.932 44.000 0.00 0.00 0.00 5.01
714 1205 5.044476 TCCTTCAGGGTTAGATAAAATGGCA 60.044 40.000 0.00 0.00 36.25 4.92
715 1206 5.445964 TCCTTCAGGGTTAGATAAAATGGC 58.554 41.667 0.00 0.00 36.25 4.40
717 1208 9.025041 ACTTTTCCTTCAGGGTTAGATAAAATG 57.975 33.333 0.00 0.00 36.25 2.32
723 1214 5.163088 ACACACTTTTCCTTCAGGGTTAGAT 60.163 40.000 0.00 0.00 36.25 1.98
724 1215 4.165372 ACACACTTTTCCTTCAGGGTTAGA 59.835 41.667 0.00 0.00 36.25 2.10
725 1216 4.461198 ACACACTTTTCCTTCAGGGTTAG 58.539 43.478 0.00 0.00 36.25 2.34
726 1217 4.080243 TGACACACTTTTCCTTCAGGGTTA 60.080 41.667 0.00 0.00 36.25 2.85
727 1218 3.288092 GACACACTTTTCCTTCAGGGTT 58.712 45.455 0.00 0.00 36.25 4.11
728 1219 2.241176 TGACACACTTTTCCTTCAGGGT 59.759 45.455 0.00 0.00 36.25 4.34
729 1220 2.930950 TGACACACTTTTCCTTCAGGG 58.069 47.619 0.00 0.00 35.41 4.45
730 1221 5.520376 AAATGACACACTTTTCCTTCAGG 57.480 39.130 0.00 0.00 0.00 3.86
731 1222 8.571336 AGATTAAATGACACACTTTTCCTTCAG 58.429 33.333 0.00 0.00 0.00 3.02
732 1223 8.463930 AGATTAAATGACACACTTTTCCTTCA 57.536 30.769 0.00 0.00 0.00 3.02
763 1254 9.643693 CATTGATAAAATAGCACACCTTTCTTT 57.356 29.630 0.00 0.00 0.00 2.52
764 1255 8.806146 ACATTGATAAAATAGCACACCTTTCTT 58.194 29.630 0.00 0.00 0.00 2.52
765 1256 8.353423 ACATTGATAAAATAGCACACCTTTCT 57.647 30.769 0.00 0.00 0.00 2.52
766 1257 9.503427 GTACATTGATAAAATAGCACACCTTTC 57.497 33.333 0.00 0.00 0.00 2.62
767 1258 8.181573 CGTACATTGATAAAATAGCACACCTTT 58.818 33.333 0.00 0.00 0.00 3.11
768 1259 7.551262 TCGTACATTGATAAAATAGCACACCTT 59.449 33.333 0.00 0.00 0.00 3.50
769 1260 7.045416 TCGTACATTGATAAAATAGCACACCT 58.955 34.615 0.00 0.00 0.00 4.00
771 1262 7.223971 TCCTCGTACATTGATAAAATAGCACAC 59.776 37.037 0.00 0.00 0.00 3.82
773 1264 7.709269 TCCTCGTACATTGATAAAATAGCAC 57.291 36.000 0.00 0.00 0.00 4.40
776 1267 9.326413 ACCTTTCCTCGTACATTGATAAAATAG 57.674 33.333 0.00 0.00 0.00 1.73
778 1269 7.610305 ACACCTTTCCTCGTACATTGATAAAAT 59.390 33.333 0.00 0.00 0.00 1.82
780 1271 6.370442 CACACCTTTCCTCGTACATTGATAAA 59.630 38.462 0.00 0.00 0.00 1.40
781 1272 5.872617 CACACCTTTCCTCGTACATTGATAA 59.127 40.000 0.00 0.00 0.00 1.75
782 1273 5.416083 CACACCTTTCCTCGTACATTGATA 58.584 41.667 0.00 0.00 0.00 2.15
783 1274 4.253685 CACACCTTTCCTCGTACATTGAT 58.746 43.478 0.00 0.00 0.00 2.57
784 1275 3.659786 CACACCTTTCCTCGTACATTGA 58.340 45.455 0.00 0.00 0.00 2.57
785 1276 2.159627 GCACACCTTTCCTCGTACATTG 59.840 50.000 0.00 0.00 0.00 2.82
786 1277 2.038557 AGCACACCTTTCCTCGTACATT 59.961 45.455 0.00 0.00 0.00 2.71
788 1279 1.045407 AGCACACCTTTCCTCGTACA 58.955 50.000 0.00 0.00 0.00 2.90
789 1280 3.521947 ATAGCACACCTTTCCTCGTAC 57.478 47.619 0.00 0.00 0.00 3.67
790 1281 4.546829 AAATAGCACACCTTTCCTCGTA 57.453 40.909 0.00 0.00 0.00 3.43
791 1282 3.418684 AAATAGCACACCTTTCCTCGT 57.581 42.857 0.00 0.00 0.00 4.18
792 1283 5.584649 TGATAAAATAGCACACCTTTCCTCG 59.415 40.000 0.00 0.00 0.00 4.63
793 1284 7.391148 TTGATAAAATAGCACACCTTTCCTC 57.609 36.000 0.00 0.00 0.00 3.71
794 1285 7.775053 TTTGATAAAATAGCACACCTTTCCT 57.225 32.000 0.00 0.00 0.00 3.36
795 1286 8.872845 CAATTTGATAAAATAGCACACCTTTCC 58.127 33.333 0.00 0.00 0.00 3.13
796 1287 8.382875 GCAATTTGATAAAATAGCACACCTTTC 58.617 33.333 0.00 0.00 0.00 2.62
797 1288 8.096414 AGCAATTTGATAAAATAGCACACCTTT 58.904 29.630 0.00 0.00 0.00 3.11
798 1289 7.614494 AGCAATTTGATAAAATAGCACACCTT 58.386 30.769 0.00 0.00 0.00 3.50
799 1290 7.174107 AGCAATTTGATAAAATAGCACACCT 57.826 32.000 0.00 0.00 0.00 4.00
800 1291 6.476706 GGAGCAATTTGATAAAATAGCACACC 59.523 38.462 0.00 0.00 0.00 4.16
801 1292 7.260603 AGGAGCAATTTGATAAAATAGCACAC 58.739 34.615 0.00 0.00 0.00 3.82
802 1293 7.408756 AGGAGCAATTTGATAAAATAGCACA 57.591 32.000 0.00 0.00 0.00 4.57
803 1294 6.920210 GGAGGAGCAATTTGATAAAATAGCAC 59.080 38.462 0.00 0.00 0.00 4.40
804 1295 6.040842 GGGAGGAGCAATTTGATAAAATAGCA 59.959 38.462 0.00 0.00 0.00 3.49
805 1296 6.450545 GGGAGGAGCAATTTGATAAAATAGC 58.549 40.000 0.00 0.00 0.00 2.97
806 1297 6.779539 AGGGGAGGAGCAATTTGATAAAATAG 59.220 38.462 0.00 0.00 0.00 1.73
807 1298 6.682537 AGGGGAGGAGCAATTTGATAAAATA 58.317 36.000 0.00 0.00 0.00 1.40
808 1299 5.532155 AGGGGAGGAGCAATTTGATAAAAT 58.468 37.500 0.00 0.00 0.00 1.82
809 1300 4.946646 AGGGGAGGAGCAATTTGATAAAA 58.053 39.130 0.00 0.00 0.00 1.52
810 1301 4.608170 AGGGGAGGAGCAATTTGATAAA 57.392 40.909 0.00 0.00 0.00 1.40
811 1302 4.608170 AAGGGGAGGAGCAATTTGATAA 57.392 40.909 0.00 0.00 0.00 1.75
812 1303 4.608170 AAAGGGGAGGAGCAATTTGATA 57.392 40.909 0.00 0.00 0.00 2.15
813 1304 3.479866 AAAGGGGAGGAGCAATTTGAT 57.520 42.857 0.00 0.00 0.00 2.57
814 1305 2.899256 CAAAAGGGGAGGAGCAATTTGA 59.101 45.455 0.00 0.00 0.00 2.69
815 1306 2.613725 GCAAAAGGGGAGGAGCAATTTG 60.614 50.000 0.00 0.00 0.00 2.32
816 1307 1.625315 GCAAAAGGGGAGGAGCAATTT 59.375 47.619 0.00 0.00 0.00 1.82
817 1308 1.203225 AGCAAAAGGGGAGGAGCAATT 60.203 47.619 0.00 0.00 0.00 2.32
818 1309 0.411058 AGCAAAAGGGGAGGAGCAAT 59.589 50.000 0.00 0.00 0.00 3.56
819 1310 0.251341 GAGCAAAAGGGGAGGAGCAA 60.251 55.000 0.00 0.00 0.00 3.91
820 1311 1.380302 GAGCAAAAGGGGAGGAGCA 59.620 57.895 0.00 0.00 0.00 4.26
821 1312 1.379176 GGAGCAAAAGGGGAGGAGC 60.379 63.158 0.00 0.00 0.00 4.70
822 1313 1.078143 CGGAGCAAAAGGGGAGGAG 60.078 63.158 0.00 0.00 0.00 3.69
823 1314 2.602676 CCGGAGCAAAAGGGGAGGA 61.603 63.158 0.00 0.00 0.00 3.71
824 1315 2.044946 CCGGAGCAAAAGGGGAGG 60.045 66.667 0.00 0.00 0.00 4.30
2367 3835 5.651576 TCTGGTAATGTAATTCAGCATGCAA 59.348 36.000 21.98 6.70 37.87 4.08
3005 7132 2.841881 TCCCTATTCACGCCTTTACCTT 59.158 45.455 0.00 0.00 0.00 3.50
3023 7150 1.410224 GGGGATCACAGGTCATTTCCC 60.410 57.143 0.00 0.00 41.77 3.97
3056 7185 1.760086 CTCTCCGGTCCCAGCTCAT 60.760 63.158 0.00 0.00 0.00 2.90
3344 7483 4.033709 AGTCAATACAGAGGGCAGTACAT 58.966 43.478 0.00 0.00 0.00 2.29
3639 7778 4.615912 GCAGCAAATGTCTAACGGAAATGT 60.616 41.667 0.00 0.00 0.00 2.71
3851 8042 5.385509 TTCCAATGGCAAAACTAAGTAGC 57.614 39.130 0.00 0.00 0.00 3.58
3857 8048 4.402829 TGTAGCTTCCAATGGCAAAACTA 58.597 39.130 0.00 0.00 0.00 2.24
3976 8167 8.062065 TGACATGTTGAATTAGGGGTATTTTC 57.938 34.615 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.