Multiple sequence alignment - TraesCS6D01G086600

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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 TraesCS6D01G086600 chr6D 100.000 6640 0 0 988 7627 52285210 52291849 0.000000e+00 12262
1 TraesCS6D01G086600 chr6D 100.000 637 0 0 1 637 52284223 52284859 0.000000e+00 1177
2 TraesCS6D01G086600 chr6D 93.496 123 6 2 6859 6980 128989374 128989253 1.690000e-41 182
3 TraesCS6D01G086600 chr6D 93.496 123 6 2 6859 6980 276068414 276068293 1.690000e-41 182
4 TraesCS6D01G086600 chr6D 88.028 142 14 2 7487 7627 83429692 83429831 1.700000e-36 165
5 TraesCS6D01G086600 chr6D 89.062 128 13 1 7501 7627 83399546 83399419 2.850000e-34 158
6 TraesCS6D01G086600 chr6A 95.383 5913 181 32 988 6848 63099729 63105601 0.000000e+00 9323
7 TraesCS6D01G086600 chr6A 95.103 1552 55 5 5315 6848 49776390 49777938 0.000000e+00 2425
8 TraesCS6D01G086600 chr6A 93.452 336 15 5 6965 7294 63105609 63105943 6.880000e-135 492
9 TraesCS6D01G086600 chr6A 84.948 485 71 2 1 484 63098867 63099350 2.470000e-134 490
10 TraesCS6D01G086600 chr6A 92.192 333 22 3 6965 7294 49777946 49778277 1.160000e-127 468
11 TraesCS6D01G086600 chr6A 87.251 251 17 6 7392 7627 63106158 63106408 9.750000e-69 272
12 TraesCS6D01G086600 chr6A 90.076 131 12 1 7498 7627 100664462 100664592 1.320000e-37 169
13 TraesCS6D01G086600 chr6A 85.926 135 15 4 7496 7627 100644381 100644248 2.870000e-29 141
14 TraesCS6D01G086600 chr6A 86.486 111 15 0 7512 7622 94214793 94214903 1.040000e-23 122
15 TraesCS6D01G086600 chr6A 88.636 88 7 3 544 630 63099573 63099658 3.760000e-18 104
16 TraesCS6D01G086600 chr6B 98.100 5158 81 8 988 6134 118954960 118960111 0.000000e+00 8966
17 TraesCS6D01G086600 chr6B 94.660 749 21 3 6118 6848 118967032 118967779 0.000000e+00 1144
18 TraesCS6D01G086600 chr6B 83.299 485 76 5 1 484 118954133 118954613 7.020000e-120 442
19 TraesCS6D01G086600 chr6B 85.360 444 21 17 6965 7380 118967787 118968214 3.290000e-113 420
20 TraesCS6D01G086600 chr6B 81.391 489 86 4 34 519 183302722 183302236 1.990000e-105 394
21 TraesCS6D01G086600 chr6B 90.104 192 16 2 7437 7627 118968338 118968527 5.910000e-61 246
22 TraesCS6D01G086600 chr6B 87.324 142 15 2 7487 7627 159137905 159138044 7.920000e-35 159
23 TraesCS6D01G086600 chr2A 85.010 1948 216 53 4004 5932 516706610 516708500 0.000000e+00 1910
24 TraesCS6D01G086600 chr2A 82.696 1439 187 39 1868 3275 516703840 516705247 0.000000e+00 1221
25 TraesCS6D01G086600 chr2A 83.814 624 71 18 3300 3910 516705957 516706563 3.990000e-157 566
26 TraesCS6D01G086600 chr2A 85.680 419 47 9 1214 1622 26016839 26017254 5.470000e-116 429
27 TraesCS6D01G086600 chr2A 83.812 383 56 6 138 518 57719851 57720229 7.280000e-95 359
28 TraesCS6D01G086600 chr2A 78.889 270 28 15 1618 1885 26025931 26026173 1.020000e-33 156
29 TraesCS6D01G086600 chr2A 86.713 143 16 2 6202 6344 516708744 516708883 1.020000e-33 156
30 TraesCS6D01G086600 chr2D 83.253 1451 190 35 1881 3296 382337478 382338910 0.000000e+00 1284
31 TraesCS6D01G086600 chr2D 80.300 1066 138 50 4275 5325 382352970 382353978 0.000000e+00 739
32 TraesCS6D01G086600 chr2D 82.484 628 80 15 3300 3913 382338952 382339563 2.440000e-144 523
33 TraesCS6D01G086600 chr2D 82.937 504 81 4 19 519 222599965 222599464 4.200000e-122 449
34 TraesCS6D01G086600 chr2D 93.373 166 11 0 4004 4169 382339607 382339772 5.910000e-61 246
35 TraesCS6D01G086600 chr4D 86.859 624 57 13 3146 3760 489725214 489725821 0.000000e+00 675
36 TraesCS6D01G086600 chr4D 93.496 123 6 2 6859 6980 29093476 29093355 1.690000e-41 182
37 TraesCS6D01G086600 chr4D 93.496 123 6 2 6859 6980 333227490 333227611 1.690000e-41 182
38 TraesCS6D01G086600 chr5A 86.256 633 53 10 3146 3760 671167902 671168518 0.000000e+00 656
39 TraesCS6D01G086600 chr5A 83.772 684 64 29 1214 1885 523021675 523022323 8.470000e-169 604
40 TraesCS6D01G086600 chr5A 81.548 504 85 7 19 517 10829201 10829701 7.120000e-110 409
41 TraesCS6D01G086600 chr1D 83.433 501 75 5 19 514 10334353 10334850 6.970000e-125 459
42 TraesCS6D01G086600 chr1D 93.496 123 6 2 6859 6980 129479265 129479386 1.690000e-41 182
43 TraesCS6D01G086600 chr1B 82.556 493 76 8 34 519 286952689 286952200 7.070000e-115 425
44 TraesCS6D01G086600 chr5B 81.563 499 84 8 21 515 517407994 517408488 9.220000e-109 405
45 TraesCS6D01G086600 chr4B 85.676 377 35 10 3146 3507 628065036 628065408 5.590000e-101 379
46 TraesCS6D01G086600 chr4B 93.307 254 17 0 3507 3760 628065570 628065823 7.230000e-100 375
47 TraesCS6D01G086600 chrUn 91.241 137 7 5 6851 6983 92940913 92940778 1.690000e-41 182
48 TraesCS6D01G086600 chr7D 93.496 123 6 2 6859 6980 183409772 183409651 1.690000e-41 182
49 TraesCS6D01G086600 chr7D 93.496 123 6 2 6859 6980 498734670 498734549 1.690000e-41 182
50 TraesCS6D01G086600 chr1A 93.496 123 6 2 6859 6980 451750749 451750628 1.690000e-41 182
51 TraesCS6D01G086600 chr3B 91.150 113 8 2 7516 7627 174677597 174677708 1.330000e-32 152


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 TraesCS6D01G086600 chr6D 52284223 52291849 7626 False 6719.500000 12262 100.000000 1 7627 2 chr6D.!!$F2 7626
1 TraesCS6D01G086600 chr6A 63098867 63106408 7541 False 2136.200000 9323 89.934000 1 7627 5 chr6A.!!$F4 7626
2 TraesCS6D01G086600 chr6A 49776390 49778277 1887 False 1446.500000 2425 93.647500 5315 7294 2 chr6A.!!$F3 1979
3 TraesCS6D01G086600 chr6B 118954133 118960111 5978 False 4704.000000 8966 90.699500 1 6134 2 chr6B.!!$F2 6133
4 TraesCS6D01G086600 chr6B 118967032 118968527 1495 False 603.333333 1144 90.041333 6118 7627 3 chr6B.!!$F3 1509
5 TraesCS6D01G086600 chr2A 516703840 516708883 5043 False 963.250000 1910 84.558250 1868 6344 4 chr2A.!!$F4 4476
6 TraesCS6D01G086600 chr2D 382352970 382353978 1008 False 739.000000 739 80.300000 4275 5325 1 chr2D.!!$F1 1050
7 TraesCS6D01G086600 chr2D 382337478 382339772 2294 False 684.333333 1284 86.370000 1881 4169 3 chr2D.!!$F2 2288
8 TraesCS6D01G086600 chr2D 222599464 222599965 501 True 449.000000 449 82.937000 19 519 1 chr2D.!!$R1 500
9 TraesCS6D01G086600 chr4D 489725214 489725821 607 False 675.000000 675 86.859000 3146 3760 1 chr4D.!!$F2 614
10 TraesCS6D01G086600 chr5A 671167902 671168518 616 False 656.000000 656 86.256000 3146 3760 1 chr5A.!!$F3 614
11 TraesCS6D01G086600 chr5A 523021675 523022323 648 False 604.000000 604 83.772000 1214 1885 1 chr5A.!!$F2 671
12 TraesCS6D01G086600 chr5A 10829201 10829701 500 False 409.000000 409 81.548000 19 517 1 chr5A.!!$F1 498
13 TraesCS6D01G086600 chr4B 628065036 628065823 787 False 377.000000 379 89.491500 3146 3760 2 chr4B.!!$F1 614

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
533 729 0.253044 TGATGAGGCCTTACCACTGC 59.747 55.000 6.77 0.00 43.14 4.40 F
570 767 0.652592 CCGAGAACGCTGCAATAAGG 59.347 55.000 0.00 0.00 38.29 2.69 F
1107 1307 0.898326 TCGTGCTCAGCTGGGACTAA 60.898 55.000 20.53 6.28 0.00 2.24 F
1395 1599 1.295423 GTGGGCTTCGCTCCACTTA 59.705 57.895 14.92 0.00 42.40 2.24 F
2720 2967 3.084039 TCTGTGGACATTGCATTCCTTC 58.916 45.455 10.09 5.28 32.55 3.46 F
3455 4434 3.006112 TGTGCTGTGTGGGAACTTTTA 57.994 42.857 0.00 0.00 0.00 1.52 F
4190 5355 6.818644 ACTTGTGTCAATTATAGCGAGTTCAT 59.181 34.615 0.00 0.00 0.00 2.57 F
4714 5900 5.009854 ACCTTTTCCTTGTCAATGTGTTG 57.990 39.130 0.00 0.00 36.65 3.33 F
6425 7722 0.821301 TGACAAAGCCATTCACCGCA 60.821 50.000 0.00 0.00 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1395 1599 1.531149 CGAGAAATTCACACAAGCGGT 59.469 47.619 0.00 0.00 0.00 5.68 R
1932 2154 2.028748 CCCTCCTCAAACTGCAAAATGG 60.029 50.000 0.00 0.00 0.00 3.16 R
2720 2967 2.485426 ACAGTCAATGGTTCATGCTTCG 59.515 45.455 0.00 0.00 0.00 3.79 R
3176 3453 1.198637 CTTTCCTTCAGCGCTCCAAAG 59.801 52.381 7.13 11.82 0.00 2.77 R
4358 5530 5.941948 AACACCTACGAATTTTCCTTGAG 57.058 39.130 0.00 0.00 0.00 3.02 R
4687 5873 5.983118 CACATTGACAAGGAAAAGGTAAACC 59.017 40.000 6.88 0.00 0.00 3.27 R
6085 7332 3.545633 GCACAGCTTGTTCGTCTAAAAG 58.454 45.455 0.00 0.00 0.00 2.27 R
6473 7770 0.037790 GTGATATCCTCGCCTCTGGC 60.038 60.000 0.00 0.00 46.75 4.85 R
7257 8577 2.300956 TAATGCCAGGTGCCTCAAAA 57.699 45.000 0.00 0.00 40.16 2.44 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
23 24 1.607148 GAACCAAACCAAAGGAGACCG 59.393 52.381 0.00 0.00 0.00 4.79
30 31 2.097038 CAAAGGAGACCGAGCAGCG 61.097 63.158 0.00 0.00 40.47 5.18
32 33 1.608717 AAAGGAGACCGAGCAGCGAT 61.609 55.000 0.21 0.00 44.57 4.58
48 49 4.201812 GCAGCGATTATGTGAAGCTAAACA 60.202 41.667 4.04 4.04 36.28 2.83
56 57 2.754552 TGTGAAGCTAAACATGGATGGC 59.245 45.455 0.00 0.00 0.00 4.40
57 58 3.019564 GTGAAGCTAAACATGGATGGCT 58.980 45.455 5.25 5.25 0.00 4.75
80 81 7.417003 GGCTCTTTTGACCCAAACTTACTAAAA 60.417 37.037 0.00 0.00 32.79 1.52
83 86 5.777850 TTGACCCAAACTTACTAAAAGCC 57.222 39.130 0.00 0.00 0.00 4.35
114 117 4.823989 TGCTATCATCAGAGACTCGAATGA 59.176 41.667 18.96 18.96 30.69 2.57
131 134 3.060020 GACAGATTCGCCCCGTCGA 62.060 63.158 0.00 0.00 36.60 4.20
136 140 3.332366 TTCGCCCCGTCGAAAAAC 58.668 55.556 0.00 0.00 44.30 2.43
173 177 1.153168 AAGATGCGCTTATGGCCGT 60.153 52.632 9.73 1.35 34.31 5.68
193 197 3.162448 GCACTGGCCATACGGTTTA 57.838 52.632 5.51 0.00 33.28 2.01
217 221 6.711277 AGTCTCAATTTGGCAACTATAGTCA 58.289 36.000 5.70 0.00 37.61 3.41
218 222 7.341805 AGTCTCAATTTGGCAACTATAGTCAT 58.658 34.615 5.70 0.00 37.61 3.06
219 223 8.486210 AGTCTCAATTTGGCAACTATAGTCATA 58.514 33.333 5.70 0.00 37.61 2.15
240 244 9.358872 GTCATATGTAATCGCATAGAGATGAAA 57.641 33.333 1.90 0.00 35.16 2.69
268 272 2.032620 ACATCGGGGTGATAGAGACAC 58.967 52.381 0.00 0.00 34.83 3.67
290 294 3.679389 TGAAGAATGGAGGTTGCTCTTC 58.321 45.455 3.70 3.70 41.47 2.87
325 329 8.443160 CGGCGACAGTTTTTGATGATATATATT 58.557 33.333 0.00 0.00 0.00 1.28
394 398 5.089970 AGAGACTAATTGTGCTGCACATA 57.910 39.130 33.25 22.61 44.16 2.29
426 430 5.402997 AACTAGTTAGAAGTAGGGTGTGC 57.597 43.478 6.26 0.00 36.47 4.57
427 431 4.413760 ACTAGTTAGAAGTAGGGTGTGCA 58.586 43.478 8.60 0.00 36.47 4.57
445 449 1.955208 GCACGGGGTGGATGAAAGATT 60.955 52.381 0.00 0.00 33.64 2.40
456 460 4.766375 GGATGAAAGATTCACCCGTAGAA 58.234 43.478 0.00 0.00 43.48 2.10
519 715 6.152661 CCTTGCAATAAAGGGTACTTTGATGA 59.847 38.462 0.00 0.00 46.03 2.92
520 716 6.757897 TGCAATAAAGGGTACTTTGATGAG 57.242 37.500 3.16 0.00 46.03 2.90
521 717 5.652014 TGCAATAAAGGGTACTTTGATGAGG 59.348 40.000 3.16 0.00 46.03 3.86
522 718 5.450550 GCAATAAAGGGTACTTTGATGAGGC 60.451 44.000 3.16 0.00 46.03 4.70
523 719 2.808906 AAGGGTACTTTGATGAGGCC 57.191 50.000 0.00 0.00 31.39 5.19
524 720 1.972588 AGGGTACTTTGATGAGGCCT 58.027 50.000 3.86 3.86 0.00 5.19
525 721 2.279173 AGGGTACTTTGATGAGGCCTT 58.721 47.619 6.77 0.00 0.00 4.35
526 722 3.460825 AGGGTACTTTGATGAGGCCTTA 58.539 45.455 6.77 1.66 0.00 2.69
527 723 3.200165 AGGGTACTTTGATGAGGCCTTAC 59.800 47.826 6.77 2.06 0.00 2.34
528 724 3.542648 GGTACTTTGATGAGGCCTTACC 58.457 50.000 6.77 8.63 39.61 2.85
529 725 3.054655 GGTACTTTGATGAGGCCTTACCA 60.055 47.826 17.51 4.24 43.14 3.25
530 726 3.073274 ACTTTGATGAGGCCTTACCAC 57.927 47.619 6.77 0.00 43.14 4.16
531 727 2.644798 ACTTTGATGAGGCCTTACCACT 59.355 45.455 6.77 0.00 43.14 4.00
532 728 2.787473 TTGATGAGGCCTTACCACTG 57.213 50.000 6.77 0.00 43.14 3.66
533 729 0.253044 TGATGAGGCCTTACCACTGC 59.747 55.000 6.77 0.00 43.14 4.40
534 730 0.811616 GATGAGGCCTTACCACTGCG 60.812 60.000 6.77 0.00 43.14 5.18
535 731 2.125106 GAGGCCTTACCACTGCGG 60.125 66.667 6.77 0.00 43.14 5.69
560 756 1.022451 TAACATTGGGCCGAGAACGC 61.022 55.000 0.00 0.00 38.29 4.84
570 767 0.652592 CCGAGAACGCTGCAATAAGG 59.347 55.000 0.00 0.00 38.29 2.69
601 798 1.954651 GAGCCCGCGCCAGTATTAC 60.955 63.158 0.00 0.00 34.57 1.89
602 799 2.970868 GCCCGCGCCAGTATTACC 60.971 66.667 0.00 0.00 0.00 2.85
603 800 2.660552 CCCGCGCCAGTATTACCG 60.661 66.667 0.00 0.00 0.00 4.02
604 801 2.414179 CCGCGCCAGTATTACCGA 59.586 61.111 0.00 0.00 0.00 4.69
624 821 4.039730 CCGAATCTCTCTCTCTCTCTCTCT 59.960 50.000 0.00 0.00 0.00 3.10
625 822 5.226396 CGAATCTCTCTCTCTCTCTCTCTC 58.774 50.000 0.00 0.00 0.00 3.20
626 823 5.010516 CGAATCTCTCTCTCTCTCTCTCTCT 59.989 48.000 0.00 0.00 0.00 3.10
627 824 6.418057 AATCTCTCTCTCTCTCTCTCTCTC 57.582 45.833 0.00 0.00 0.00 3.20
628 825 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
630 827 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
631 828 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
632 829 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
636 833 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
1107 1307 0.898326 TCGTGCTCAGCTGGGACTAA 60.898 55.000 20.53 6.28 0.00 2.24
1216 1416 2.240667 CCTTCACCATCTCCTGATTGGT 59.759 50.000 0.00 0.00 35.78 3.67
1365 1568 4.148825 CCGCAACGAGGAGGAGGG 62.149 72.222 0.00 0.00 0.00 4.30
1372 1575 2.784654 CGAGGAGGAGGGGGAGGAT 61.785 68.421 0.00 0.00 0.00 3.24
1395 1599 1.295423 GTGGGCTTCGCTCCACTTA 59.705 57.895 14.92 0.00 42.40 2.24
1452 1656 9.573133 CTTGGTTTATTATTAAGCAGTTCTTGG 57.427 33.333 0.00 0.00 36.25 3.61
1453 1657 8.644374 TGGTTTATTATTAAGCAGTTCTTGGT 57.356 30.769 0.00 0.00 39.75 3.67
1455 1659 9.923143 GGTTTATTATTAAGCAGTTCTTGGTTT 57.077 29.630 0.00 0.00 44.75 3.27
1754 1975 7.396540 AAACAATGAATATCTGAGACCAACC 57.603 36.000 0.00 0.00 0.00 3.77
1809 2031 9.793252 CGATGAATGTTTTCAGATAATTTCCTT 57.207 29.630 0.00 0.00 44.75 3.36
1932 2154 6.705302 TGAATGATGAGTTAGGATATGCCTC 58.295 40.000 0.00 0.00 46.97 4.70
2270 2495 4.202192 CCTCAGATGTGCAGCTTATCTACA 60.202 45.833 10.46 0.00 30.43 2.74
2632 2863 4.382291 TGCAGTGTATTGTCGTTTACCTT 58.618 39.130 0.00 0.00 0.00 3.50
2633 2864 4.212425 TGCAGTGTATTGTCGTTTACCTTG 59.788 41.667 0.00 0.00 0.00 3.61
2634 2865 4.212636 GCAGTGTATTGTCGTTTACCTTGT 59.787 41.667 0.00 0.00 0.00 3.16
2635 2866 5.614013 GCAGTGTATTGTCGTTTACCTTGTC 60.614 44.000 0.00 0.00 0.00 3.18
2636 2867 5.464057 CAGTGTATTGTCGTTTACCTTGTCA 59.536 40.000 0.00 0.00 0.00 3.58
2637 2868 6.018588 CAGTGTATTGTCGTTTACCTTGTCAA 60.019 38.462 0.00 0.00 0.00 3.18
2638 2869 6.202188 AGTGTATTGTCGTTTACCTTGTCAAG 59.798 38.462 5.53 5.53 0.00 3.02
2639 2870 6.201425 GTGTATTGTCGTTTACCTTGTCAAGA 59.799 38.462 14.42 0.00 0.00 3.02
2640 2871 6.762187 TGTATTGTCGTTTACCTTGTCAAGAA 59.238 34.615 14.42 0.00 0.00 2.52
2641 2872 6.687081 ATTGTCGTTTACCTTGTCAAGAAA 57.313 33.333 14.42 4.88 0.00 2.52
2642 2873 6.497785 TTGTCGTTTACCTTGTCAAGAAAA 57.502 33.333 14.42 10.75 0.00 2.29
2643 2874 6.497785 TGTCGTTTACCTTGTCAAGAAAAA 57.502 33.333 14.42 10.42 0.00 1.94
2720 2967 3.084039 TCTGTGGACATTGCATTCCTTC 58.916 45.455 10.09 5.28 32.55 3.46
3040 3310 8.786826 TTGTCGTAATGTTTCTTCCAGATAAT 57.213 30.769 0.00 0.00 0.00 1.28
3176 3453 6.319141 AGTTAGTTTCTGACATTCTTTGGC 57.681 37.500 0.00 0.00 0.00 4.52
3455 4434 3.006112 TGTGCTGTGTGGGAACTTTTA 57.994 42.857 0.00 0.00 0.00 1.52
3683 4846 9.084533 GGAATGATCTGGTACTCTTCTATACTT 57.915 37.037 0.00 0.00 0.00 2.24
4190 5355 6.818644 ACTTGTGTCAATTATAGCGAGTTCAT 59.181 34.615 0.00 0.00 0.00 2.57
4687 5873 7.525688 TTTTACACATCTCTTCTATTCAGCG 57.474 36.000 0.00 0.00 0.00 5.18
4714 5900 5.009854 ACCTTTTCCTTGTCAATGTGTTG 57.990 39.130 0.00 0.00 36.65 3.33
6084 7331 4.443621 GAGGTTATAGTGCCTGAGTTTCC 58.556 47.826 0.00 0.00 34.81 3.13
6085 7332 3.200165 AGGTTATAGTGCCTGAGTTTCCC 59.800 47.826 0.00 0.00 33.13 3.97
6425 7722 0.821301 TGACAAAGCCATTCACCGCA 60.821 50.000 0.00 0.00 0.00 5.69
6452 7749 4.963373 TCACCGAGGATAGTTTCAAAACA 58.037 39.130 8.23 0.00 41.30 2.83
6473 7770 2.638480 TGAAGGTGGAAAGACCTGTG 57.362 50.000 0.00 0.00 46.29 3.66
6479 7776 0.397941 TGGAAAGACCTGTGCCAGAG 59.602 55.000 4.00 0.00 39.86 3.35
6498 7795 0.106708 GGCGAGGATATCACAGGCAA 59.893 55.000 4.83 0.00 0.00 4.52
6506 7803 3.681897 GGATATCACAGGCAATAGAAGCG 59.318 47.826 4.83 0.00 0.00 4.68
6829 8145 3.576004 CAGAACTGCAGCAGCTCC 58.424 61.111 23.05 11.39 42.74 4.70
6848 8164 1.565305 CGGCTTCTGCTGTGTCTATC 58.435 55.000 0.00 0.00 40.53 2.08
6850 8166 2.359214 CGGCTTCTGCTGTGTCTATCTA 59.641 50.000 0.00 0.00 40.53 1.98
6851 8167 3.005261 CGGCTTCTGCTGTGTCTATCTAT 59.995 47.826 0.00 0.00 40.53 1.98
6852 8168 4.216472 CGGCTTCTGCTGTGTCTATCTATA 59.784 45.833 0.00 0.00 40.53 1.31
6854 8170 6.098679 GGCTTCTGCTGTGTCTATCTATATG 58.901 44.000 0.00 0.00 39.59 1.78
6855 8171 5.576384 GCTTCTGCTGTGTCTATCTATATGC 59.424 44.000 0.00 0.00 36.03 3.14
6856 8172 6.572119 GCTTCTGCTGTGTCTATCTATATGCT 60.572 42.308 0.00 0.00 36.03 3.79
6860 8176 9.686683 TCTGCTGTGTCTATCTATATGCTTATA 57.313 33.333 0.00 0.00 0.00 0.98
6861 8177 9.729023 CTGCTGTGTCTATCTATATGCTTATAC 57.271 37.037 0.00 0.00 0.00 1.47
6863 8179 9.944663 GCTGTGTCTATCTATATGCTTATACTC 57.055 37.037 0.00 0.00 0.00 2.59
6865 8181 9.409918 TGTGTCTATCTATATGCTTATACTCCC 57.590 37.037 0.00 0.00 0.00 4.30
6866 8182 9.635404 GTGTCTATCTATATGCTTATACTCCCT 57.365 37.037 0.00 0.00 0.00 4.20
6867 8183 9.854668 TGTCTATCTATATGCTTATACTCCCTC 57.145 37.037 0.00 0.00 0.00 4.30
6868 8184 9.292195 GTCTATCTATATGCTTATACTCCCTCC 57.708 40.741 0.00 0.00 0.00 4.30
6869 8185 8.158132 TCTATCTATATGCTTATACTCCCTCCG 58.842 40.741 0.00 0.00 0.00 4.63
6870 8186 6.075949 TCTATATGCTTATACTCCCTCCGT 57.924 41.667 0.00 0.00 0.00 4.69
6871 8187 6.491383 TCTATATGCTTATACTCCCTCCGTT 58.509 40.000 0.00 0.00 0.00 4.44
6872 8188 5.662674 ATATGCTTATACTCCCTCCGTTC 57.337 43.478 0.00 0.00 0.00 3.95
6873 8189 1.679680 TGCTTATACTCCCTCCGTTCG 59.320 52.381 0.00 0.00 0.00 3.95
6874 8190 1.000496 GCTTATACTCCCTCCGTTCGG 60.000 57.143 4.74 4.74 0.00 4.30
6875 8191 2.579873 CTTATACTCCCTCCGTTCGGA 58.420 52.381 13.34 13.34 0.00 4.55
6876 8192 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
6877 8193 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
6878 8194 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
6879 8195 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
6880 8196 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
6881 8197 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
6882 8198 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
6883 8199 1.535437 CCCTCCGTTCGGAATTACTCG 60.535 57.143 14.79 1.97 33.41 4.18
6884 8200 1.133790 CCTCCGTTCGGAATTACTCGT 59.866 52.381 14.79 0.00 33.41 4.18
6885 8201 2.448219 CTCCGTTCGGAATTACTCGTC 58.552 52.381 14.79 0.00 33.41 4.20
6886 8202 1.133025 TCCGTTCGGAATTACTCGTCC 59.867 52.381 11.66 0.00 0.00 4.79
6887 8203 1.135315 CCGTTCGGAATTACTCGTCCA 60.135 52.381 5.19 0.00 33.10 4.02
6888 8204 2.598589 CGTTCGGAATTACTCGTCCAA 58.401 47.619 0.00 0.00 33.10 3.53
6889 8205 2.597305 CGTTCGGAATTACTCGTCCAAG 59.403 50.000 0.00 0.00 33.10 3.61
6890 8206 3.671433 CGTTCGGAATTACTCGTCCAAGA 60.671 47.826 0.00 0.00 33.10 3.02
6891 8207 4.240096 GTTCGGAATTACTCGTCCAAGAA 58.760 43.478 0.00 0.00 33.10 2.52
6892 8208 4.524316 TCGGAATTACTCGTCCAAGAAA 57.476 40.909 0.00 0.00 33.10 2.52
6893 8209 5.080969 TCGGAATTACTCGTCCAAGAAAT 57.919 39.130 0.00 0.00 33.10 2.17
6894 8210 4.868171 TCGGAATTACTCGTCCAAGAAATG 59.132 41.667 0.00 0.00 33.10 2.32
6895 8211 4.868171 CGGAATTACTCGTCCAAGAAATGA 59.132 41.667 0.00 0.00 33.10 2.57
6896 8212 5.350365 CGGAATTACTCGTCCAAGAAATGAA 59.650 40.000 0.00 0.00 33.10 2.57
6897 8213 6.037172 CGGAATTACTCGTCCAAGAAATGAAT 59.963 38.462 0.00 0.00 33.10 2.57
6898 8214 7.189512 GGAATTACTCGTCCAAGAAATGAATG 58.810 38.462 0.00 0.00 33.79 2.67
6899 8215 7.148239 GGAATTACTCGTCCAAGAAATGAATGT 60.148 37.037 0.00 0.00 33.79 2.71
6900 8216 8.786826 AATTACTCGTCCAAGAAATGAATGTA 57.213 30.769 0.00 0.00 0.00 2.29
6901 8217 8.964476 ATTACTCGTCCAAGAAATGAATGTAT 57.036 30.769 0.00 0.00 0.00 2.29
6902 8218 6.910536 ACTCGTCCAAGAAATGAATGTATC 57.089 37.500 0.00 0.00 0.00 2.24
6903 8219 6.644347 ACTCGTCCAAGAAATGAATGTATCT 58.356 36.000 0.00 0.00 0.00 1.98
6904 8220 7.782049 ACTCGTCCAAGAAATGAATGTATCTA 58.218 34.615 0.00 0.00 0.00 1.98
6905 8221 7.923344 ACTCGTCCAAGAAATGAATGTATCTAG 59.077 37.037 0.00 0.00 0.00 2.43
6906 8222 8.007405 TCGTCCAAGAAATGAATGTATCTAGA 57.993 34.615 0.00 0.00 0.00 2.43
6907 8223 8.642432 TCGTCCAAGAAATGAATGTATCTAGAT 58.358 33.333 10.73 10.73 0.00 1.98
6908 8224 8.706936 CGTCCAAGAAATGAATGTATCTAGATG 58.293 37.037 15.79 0.00 0.00 2.90
6909 8225 9.553064 GTCCAAGAAATGAATGTATCTAGATGT 57.447 33.333 15.79 0.00 0.00 3.06
6940 8256 8.373048 AGTTGTAGATACGTTCATTTTTGTGA 57.627 30.769 0.00 0.00 0.00 3.58
6941 8257 8.280497 AGTTGTAGATACGTTCATTTTTGTGAC 58.720 33.333 0.00 0.00 0.00 3.67
6942 8258 7.716768 TGTAGATACGTTCATTTTTGTGACA 57.283 32.000 0.00 0.00 0.00 3.58
6943 8259 8.144155 TGTAGATACGTTCATTTTTGTGACAA 57.856 30.769 0.00 0.00 0.00 3.18
6944 8260 8.279800 TGTAGATACGTTCATTTTTGTGACAAG 58.720 33.333 0.00 0.00 0.00 3.16
6945 8261 7.259290 AGATACGTTCATTTTTGTGACAAGT 57.741 32.000 0.00 0.00 0.00 3.16
6946 8262 8.373048 AGATACGTTCATTTTTGTGACAAGTA 57.627 30.769 0.00 0.00 0.00 2.24
6947 8263 8.832521 AGATACGTTCATTTTTGTGACAAGTAA 58.167 29.630 0.00 0.00 0.00 2.24
6948 8264 9.607285 GATACGTTCATTTTTGTGACAAGTAAT 57.393 29.630 0.00 0.32 0.00 1.89
6949 8265 9.959749 ATACGTTCATTTTTGTGACAAGTAATT 57.040 25.926 0.00 0.00 0.00 1.40
6950 8266 8.335256 ACGTTCATTTTTGTGACAAGTAATTC 57.665 30.769 0.00 0.00 0.00 2.17
6951 8267 8.188139 ACGTTCATTTTTGTGACAAGTAATTCT 58.812 29.630 0.00 0.00 0.00 2.40
6952 8268 8.471457 CGTTCATTTTTGTGACAAGTAATTCTG 58.529 33.333 0.00 0.00 0.00 3.02
6953 8269 9.515020 GTTCATTTTTGTGACAAGTAATTCTGA 57.485 29.630 0.00 0.00 0.00 3.27
6957 8273 8.870160 TTTTTGTGACAAGTAATTCTGAATGG 57.130 30.769 3.22 0.00 0.00 3.16
6958 8274 7.815840 TTTGTGACAAGTAATTCTGAATGGA 57.184 32.000 3.22 0.00 0.00 3.41
6959 8275 7.439157 TTGTGACAAGTAATTCTGAATGGAG 57.561 36.000 3.22 0.00 0.00 3.86
6960 8276 5.939883 TGTGACAAGTAATTCTGAATGGAGG 59.060 40.000 3.22 0.00 0.00 4.30
6961 8277 5.355350 GTGACAAGTAATTCTGAATGGAGGG 59.645 44.000 3.22 0.00 0.00 4.30
6962 8278 5.250543 TGACAAGTAATTCTGAATGGAGGGA 59.749 40.000 3.22 0.00 0.00 4.20
6963 8279 5.749462 ACAAGTAATTCTGAATGGAGGGAG 58.251 41.667 3.22 0.00 0.00 4.30
6964 8280 5.251700 ACAAGTAATTCTGAATGGAGGGAGT 59.748 40.000 3.22 0.00 0.00 3.85
6965 8281 6.443849 ACAAGTAATTCTGAATGGAGGGAGTA 59.556 38.462 3.22 0.00 0.00 2.59
6966 8282 7.127955 ACAAGTAATTCTGAATGGAGGGAGTAT 59.872 37.037 3.22 0.00 0.00 2.12
6967 8283 8.651389 CAAGTAATTCTGAATGGAGGGAGTATA 58.349 37.037 3.22 0.00 0.00 1.47
6968 8284 8.980832 AGTAATTCTGAATGGAGGGAGTATAT 57.019 34.615 3.22 0.00 0.00 0.86
6969 8285 9.041354 AGTAATTCTGAATGGAGGGAGTATATC 57.959 37.037 3.22 0.00 0.00 1.63
6970 8286 5.984695 TTCTGAATGGAGGGAGTATATCG 57.015 43.478 0.00 0.00 0.00 2.92
6971 8287 4.999310 TCTGAATGGAGGGAGTATATCGT 58.001 43.478 0.00 0.00 0.00 3.73
6972 8288 6.135819 TCTGAATGGAGGGAGTATATCGTA 57.864 41.667 0.00 0.00 0.00 3.43
7082 8399 2.353958 CCAGAGGCTGGCACATGT 59.646 61.111 3.38 0.00 45.13 3.21
7111 8428 2.216898 CTTGCTGTAGCTCTTATGGCC 58.783 52.381 0.00 0.00 42.66 5.36
7145 8462 3.138304 TGTTCCCATCTCACAAAACTCG 58.862 45.455 0.00 0.00 0.00 4.18
7294 8614 5.010012 GGCATTATATTGTCCAACCCTGAAG 59.990 44.000 0.00 0.00 0.00 3.02
7295 8615 5.827797 GCATTATATTGTCCAACCCTGAAGA 59.172 40.000 0.00 0.00 0.00 2.87
7296 8616 6.321181 GCATTATATTGTCCAACCCTGAAGAA 59.679 38.462 0.00 0.00 0.00 2.52
7297 8617 7.682021 GCATTATATTGTCCAACCCTGAAGAAC 60.682 40.741 0.00 0.00 0.00 3.01
7311 8661 4.999950 CCTGAAGAACTAAGAATGTGCAGT 59.000 41.667 0.00 0.00 0.00 4.40
7315 8665 5.483685 AGAACTAAGAATGTGCAGTGGTA 57.516 39.130 0.00 0.00 0.00 3.25
7325 8675 2.167487 TGTGCAGTGGTATGCTCGATTA 59.833 45.455 0.00 0.00 46.63 1.75
7380 8730 8.009622 TGTATAATCAACCAAATCATGTGCAT 57.990 30.769 0.00 0.00 0.00 3.96
7421 8868 3.508793 CCATCCTTGTTTTCTGATGCACT 59.491 43.478 0.00 0.00 34.61 4.40
7459 8910 9.965902 AAAGAATCTAACAGATTGATGTAACCT 57.034 29.630 6.15 0.00 44.41 3.50
7565 9019 3.127533 GCCCAGGCGACACATGAC 61.128 66.667 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.208431 AGCTTCACATAATCGCTGCTC 58.792 47.619 0.00 0.00 0.00 4.26
30 31 7.365741 CCATCCATGTTTAGCTTCACATAATC 58.634 38.462 9.50 0.00 32.16 1.75
32 33 5.067674 GCCATCCATGTTTAGCTTCACATAA 59.932 40.000 9.50 3.46 32.16 1.90
48 49 1.358787 TGGGTCAAAAGAGCCATCCAT 59.641 47.619 11.97 0.00 46.46 3.41
56 57 7.648112 GCTTTTAGTAAGTTTGGGTCAAAAGAG 59.352 37.037 7.45 0.00 35.03 2.85
57 58 7.417003 GGCTTTTAGTAAGTTTGGGTCAAAAGA 60.417 37.037 7.45 0.00 35.03 2.52
80 81 1.276421 GATGATAGCACCATACGGGCT 59.724 52.381 0.00 0.00 42.05 5.19
83 86 3.507622 TCTCTGATGATAGCACCATACGG 59.492 47.826 0.00 0.00 38.77 4.02
114 117 2.642254 TTCGACGGGGCGAATCTGT 61.642 57.895 5.05 0.00 44.43 3.41
131 134 3.365969 GCACCAATCGATCTTCCGTTTTT 60.366 43.478 0.00 0.00 0.00 1.94
135 139 0.806102 CGCACCAATCGATCTTCCGT 60.806 55.000 0.00 0.00 0.00 4.69
136 140 0.527600 TCGCACCAATCGATCTTCCG 60.528 55.000 0.00 0.00 0.00 4.30
141 145 1.070309 GCATCTTCGCACCAATCGATC 60.070 52.381 0.00 0.00 35.75 3.69
184 188 5.250200 TGCCAAATTGAGACTAAACCGTAT 58.750 37.500 0.00 0.00 0.00 3.06
193 197 6.711277 TGACTATAGTTGCCAAATTGAGACT 58.289 36.000 6.88 0.00 0.00 3.24
218 222 9.578439 CAGATTTCATCTCTATGCGATTACATA 57.422 33.333 0.00 0.00 37.58 2.29
219 223 8.309656 TCAGATTTCATCTCTATGCGATTACAT 58.690 33.333 0.00 0.00 37.58 2.29
240 244 1.793414 TCACCCCGATGTCATCAGAT 58.207 50.000 13.22 0.00 0.00 2.90
243 247 2.893489 CTCTATCACCCCGATGTCATCA 59.107 50.000 13.22 0.00 35.39 3.07
247 251 2.034812 GTGTCTCTATCACCCCGATGTC 59.965 54.545 0.00 0.00 35.39 3.06
268 272 3.347077 AGAGCAACCTCCATTCTTCAG 57.653 47.619 0.00 0.00 38.96 3.02
342 346 7.225145 GGAGCATGCTCAAAAATAATATGCAAA 59.775 33.333 40.37 0.00 44.40 3.68
343 347 6.702723 GGAGCATGCTCAAAAATAATATGCAA 59.297 34.615 40.37 0.00 44.40 4.08
394 398 9.668497 CCTACTTCTAACTAGTTTGGCTAAATT 57.332 33.333 14.49 0.00 0.00 1.82
426 430 2.017049 GAATCTTTCATCCACCCCGTG 58.983 52.381 0.00 0.00 0.00 4.94
427 431 1.633432 TGAATCTTTCATCCACCCCGT 59.367 47.619 0.00 0.00 34.08 5.28
486 681 3.763360 CCCTTTATTGCAAGGTGATCACA 59.237 43.478 26.47 5.97 41.84 3.58
507 703 3.054655 TGGTAAGGCCTCATCAAAGTACC 60.055 47.826 16.12 16.12 38.35 3.34
527 723 1.243902 ATGTTACCAAACCGCAGTGG 58.756 50.000 0.00 0.00 46.41 4.00
528 724 2.606795 CCAATGTTACCAAACCGCAGTG 60.607 50.000 0.00 0.00 34.49 3.66
529 725 1.611491 CCAATGTTACCAAACCGCAGT 59.389 47.619 0.00 0.00 34.49 4.40
530 726 1.067915 CCCAATGTTACCAAACCGCAG 60.068 52.381 0.00 0.00 34.49 5.18
531 727 0.962489 CCCAATGTTACCAAACCGCA 59.038 50.000 0.00 0.00 34.49 5.69
532 728 0.389296 GCCCAATGTTACCAAACCGC 60.389 55.000 0.00 0.00 34.49 5.68
533 729 0.245266 GGCCCAATGTTACCAAACCG 59.755 55.000 0.00 0.00 34.49 4.44
534 730 0.245266 CGGCCCAATGTTACCAAACC 59.755 55.000 0.00 0.00 34.49 3.27
535 731 1.201414 CTCGGCCCAATGTTACCAAAC 59.799 52.381 0.00 0.00 36.07 2.93
536 732 1.074084 TCTCGGCCCAATGTTACCAAA 59.926 47.619 0.00 0.00 0.00 3.28
537 733 0.693622 TCTCGGCCCAATGTTACCAA 59.306 50.000 0.00 0.00 0.00 3.67
538 734 0.693622 TTCTCGGCCCAATGTTACCA 59.306 50.000 0.00 0.00 0.00 3.25
539 735 1.092348 GTTCTCGGCCCAATGTTACC 58.908 55.000 0.00 0.00 0.00 2.85
540 736 0.725117 CGTTCTCGGCCCAATGTTAC 59.275 55.000 0.00 0.00 0.00 2.50
541 737 1.022451 GCGTTCTCGGCCCAATGTTA 61.022 55.000 0.00 0.00 37.56 2.41
554 750 1.032114 GGCCCTTATTGCAGCGTTCT 61.032 55.000 0.00 0.00 0.00 3.01
560 756 1.410153 GATGTTGGGCCCTTATTGCAG 59.590 52.381 25.70 0.00 0.00 4.41
570 767 2.514824 GGCTCTCGATGTTGGGCC 60.515 66.667 0.00 0.00 0.00 5.80
601 798 4.039730 AGAGAGAGAGAGAGAGAGATTCGG 59.960 50.000 0.00 0.00 0.00 4.30
602 799 5.010516 AGAGAGAGAGAGAGAGAGAGATTCG 59.989 48.000 0.00 0.00 0.00 3.34
603 800 6.267471 AGAGAGAGAGAGAGAGAGAGAGATTC 59.733 46.154 0.00 0.00 0.00 2.52
604 801 6.142498 AGAGAGAGAGAGAGAGAGAGAGATT 58.858 44.000 0.00 0.00 0.00 2.40
991 1188 0.394216 TCCACCGCCATGGATTTCTG 60.394 55.000 18.40 2.11 44.14 3.02
1365 1568 1.649271 AAGCCCACCATCATCCTCCC 61.649 60.000 0.00 0.00 0.00 4.30
1395 1599 1.531149 CGAGAAATTCACACAAGCGGT 59.469 47.619 0.00 0.00 0.00 5.68
1450 1654 2.223803 AGACCACAAACCACAAACCA 57.776 45.000 0.00 0.00 0.00 3.67
1451 1655 4.929819 AATAGACCACAAACCACAAACC 57.070 40.909 0.00 0.00 0.00 3.27
1452 1656 5.897050 TCAAATAGACCACAAACCACAAAC 58.103 37.500 0.00 0.00 0.00 2.93
1453 1657 5.654650 ACTCAAATAGACCACAAACCACAAA 59.345 36.000 0.00 0.00 0.00 2.83
1454 1658 5.197451 ACTCAAATAGACCACAAACCACAA 58.803 37.500 0.00 0.00 0.00 3.33
1455 1659 4.787551 ACTCAAATAGACCACAAACCACA 58.212 39.130 0.00 0.00 0.00 4.17
1456 1660 6.228258 TCTACTCAAATAGACCACAAACCAC 58.772 40.000 0.00 0.00 0.00 4.16
1809 2031 6.247676 TCTGATGGACTGATCAATTTTCCAA 58.752 36.000 15.36 3.96 39.77 3.53
1810 2032 5.818887 TCTGATGGACTGATCAATTTTCCA 58.181 37.500 14.27 14.27 40.61 3.53
1932 2154 2.028748 CCCTCCTCAAACTGCAAAATGG 60.029 50.000 0.00 0.00 0.00 3.16
2079 2302 2.981560 GCAAAGCGCTGCAGCCTTA 61.982 57.895 30.25 0.00 42.17 2.69
2270 2495 3.887352 TCCAGAGTACTCTCGCAGTATT 58.113 45.455 22.76 0.00 44.65 1.89
2632 2863 6.458751 GCTCTCACTTGACATTTTTCTTGACA 60.459 38.462 0.00 0.00 0.00 3.58
2633 2864 5.911838 GCTCTCACTTGACATTTTTCTTGAC 59.088 40.000 0.00 0.00 0.00 3.18
2634 2865 5.589855 TGCTCTCACTTGACATTTTTCTTGA 59.410 36.000 0.00 0.00 0.00 3.02
2635 2866 5.824429 TGCTCTCACTTGACATTTTTCTTG 58.176 37.500 0.00 0.00 0.00 3.02
2636 2867 6.455360 TTGCTCTCACTTGACATTTTTCTT 57.545 33.333 0.00 0.00 0.00 2.52
2637 2868 6.645790 ATTGCTCTCACTTGACATTTTTCT 57.354 33.333 0.00 0.00 0.00 2.52
2638 2869 7.704789 AAATTGCTCTCACTTGACATTTTTC 57.295 32.000 0.00 0.00 0.00 2.29
2639 2870 7.011669 CCAAAATTGCTCTCACTTGACATTTTT 59.988 33.333 0.00 0.00 0.00 1.94
2640 2871 6.480981 CCAAAATTGCTCTCACTTGACATTTT 59.519 34.615 0.00 0.00 0.00 1.82
2641 2872 5.987347 CCAAAATTGCTCTCACTTGACATTT 59.013 36.000 0.00 0.00 0.00 2.32
2642 2873 5.302568 TCCAAAATTGCTCTCACTTGACATT 59.697 36.000 0.00 0.00 0.00 2.71
2643 2874 4.828939 TCCAAAATTGCTCTCACTTGACAT 59.171 37.500 0.00 0.00 0.00 3.06
2720 2967 2.485426 ACAGTCAATGGTTCATGCTTCG 59.515 45.455 0.00 0.00 0.00 3.79
2869 3121 7.756272 TGCATTGCACTTGATATTACAGAAAAG 59.244 33.333 7.38 0.00 31.71 2.27
2870 3122 7.600960 TGCATTGCACTTGATATTACAGAAAA 58.399 30.769 7.38 0.00 31.71 2.29
2871 3123 7.155655 TGCATTGCACTTGATATTACAGAAA 57.844 32.000 7.38 0.00 31.71 2.52
3040 3310 5.976458 TGTGAGATACATGCACACTCATTA 58.024 37.500 12.92 6.01 39.27 1.90
3176 3453 1.198637 CTTTCCTTCAGCGCTCCAAAG 59.801 52.381 7.13 11.82 0.00 2.77
3254 3535 5.648178 ACAGATGCAGCAATTATGAACAA 57.352 34.783 4.07 0.00 0.00 2.83
3350 4321 9.770097 CAGCAATCTTATCCTTCTGATAAAGTA 57.230 33.333 0.00 0.00 43.59 2.24
4358 5530 5.941948 AACACCTACGAATTTTCCTTGAG 57.058 39.130 0.00 0.00 0.00 3.02
4482 5654 9.655769 CTGATAATGTAAAGATAACATGCACAC 57.344 33.333 0.00 0.00 37.62 3.82
4687 5873 5.983118 CACATTGACAAGGAAAAGGTAAACC 59.017 40.000 6.88 0.00 0.00 3.27
4714 5900 8.382130 CACGCTAGTAGTATAGTGATTAGCTAC 58.618 40.741 0.00 0.00 36.87 3.58
6084 7331 3.607078 GCACAGCTTGTTCGTCTAAAAGG 60.607 47.826 0.00 0.00 0.00 3.11
6085 7332 3.545633 GCACAGCTTGTTCGTCTAAAAG 58.454 45.455 0.00 0.00 0.00 2.27
6422 7719 2.223829 ACTATCCTCGGTGAAGAATGCG 60.224 50.000 0.00 0.00 0.00 4.73
6425 7722 5.677319 TGAAACTATCCTCGGTGAAGAAT 57.323 39.130 0.00 0.00 0.00 2.40
6452 7749 3.490348 CACAGGTCTTTCCACCTTCATT 58.510 45.455 0.00 0.00 45.24 2.57
6473 7770 0.037790 GTGATATCCTCGCCTCTGGC 60.038 60.000 0.00 0.00 46.75 4.85
6479 7776 0.106708 TTGCCTGTGATATCCTCGCC 59.893 55.000 0.00 0.00 33.18 5.54
6498 7795 6.201806 GCAACTACTTCATTGATCGCTTCTAT 59.798 38.462 0.00 0.00 0.00 1.98
6506 7803 4.156556 TGCCTTGCAACTACTTCATTGATC 59.843 41.667 0.00 0.00 34.76 2.92
6766 8065 2.093921 TGTAGATGATTCGTCGGGCAAA 60.094 45.455 0.28 0.00 0.00 3.68
6829 8145 1.135915 AGATAGACACAGCAGAAGCCG 59.864 52.381 0.00 0.00 43.56 5.52
6848 8164 6.458478 CGAACGGAGGGAGTATAAGCATATAG 60.458 46.154 0.00 0.00 0.00 1.31
6850 8166 4.158025 CGAACGGAGGGAGTATAAGCATAT 59.842 45.833 0.00 0.00 0.00 1.78
6851 8167 3.504906 CGAACGGAGGGAGTATAAGCATA 59.495 47.826 0.00 0.00 0.00 3.14
6852 8168 2.296471 CGAACGGAGGGAGTATAAGCAT 59.704 50.000 0.00 0.00 0.00 3.79
6854 8170 1.000496 CCGAACGGAGGGAGTATAAGC 60.000 57.143 7.53 0.00 37.50 3.09
6855 8171 2.579873 TCCGAACGGAGGGAGTATAAG 58.420 52.381 12.04 0.00 39.76 1.73
6856 8172 2.734755 TCCGAACGGAGGGAGTATAA 57.265 50.000 12.04 0.00 39.76 0.98
6860 8176 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
6861 8177 1.755380 AGTAATTCCGAACGGAGGGAG 59.245 52.381 15.34 0.00 46.06 4.30
6863 8179 1.535437 CGAGTAATTCCGAACGGAGGG 60.535 57.143 15.34 0.00 46.06 4.30
6864 8180 1.133790 ACGAGTAATTCCGAACGGAGG 59.866 52.381 15.34 4.28 46.06 4.30
6865 8181 2.448219 GACGAGTAATTCCGAACGGAG 58.552 52.381 15.34 5.60 46.06 4.63
6866 8182 1.133025 GGACGAGTAATTCCGAACGGA 59.867 52.381 12.04 12.04 43.52 4.69
6867 8183 1.135315 TGGACGAGTAATTCCGAACGG 60.135 52.381 6.94 6.94 0.00 4.44
6868 8184 2.267188 TGGACGAGTAATTCCGAACG 57.733 50.000 0.00 0.00 0.00 3.95
6869 8185 3.841643 TCTTGGACGAGTAATTCCGAAC 58.158 45.455 0.00 0.00 0.00 3.95
6870 8186 4.524316 TTCTTGGACGAGTAATTCCGAA 57.476 40.909 0.00 0.00 0.00 4.30
6871 8187 4.524316 TTTCTTGGACGAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
6872 8188 4.868171 TCATTTCTTGGACGAGTAATTCCG 59.132 41.667 0.00 0.00 0.00 4.30
6873 8189 6.737254 TTCATTTCTTGGACGAGTAATTCC 57.263 37.500 0.00 0.00 0.00 3.01
6874 8190 7.752695 ACATTCATTTCTTGGACGAGTAATTC 58.247 34.615 0.00 0.00 0.00 2.17
6875 8191 7.687941 ACATTCATTTCTTGGACGAGTAATT 57.312 32.000 0.00 0.00 0.00 1.40
6876 8192 8.964476 ATACATTCATTTCTTGGACGAGTAAT 57.036 30.769 0.00 0.00 0.00 1.89
6877 8193 8.258007 AGATACATTCATTTCTTGGACGAGTAA 58.742 33.333 0.00 0.00 0.00 2.24
6878 8194 7.782049 AGATACATTCATTTCTTGGACGAGTA 58.218 34.615 0.00 0.00 0.00 2.59
6879 8195 6.644347 AGATACATTCATTTCTTGGACGAGT 58.356 36.000 0.00 0.00 0.00 4.18
6880 8196 8.138074 TCTAGATACATTCATTTCTTGGACGAG 58.862 37.037 0.00 0.00 0.00 4.18
6881 8197 8.007405 TCTAGATACATTCATTTCTTGGACGA 57.993 34.615 0.00 0.00 0.00 4.20
6882 8198 8.706936 CATCTAGATACATTCATTTCTTGGACG 58.293 37.037 4.54 0.00 0.00 4.79
6883 8199 9.553064 ACATCTAGATACATTCATTTCTTGGAC 57.447 33.333 4.54 0.00 0.00 4.02
6914 8230 9.478768 TCACAAAAATGAACGTATCTACAACTA 57.521 29.630 0.00 0.00 0.00 2.24
6915 8231 8.280497 GTCACAAAAATGAACGTATCTACAACT 58.720 33.333 0.00 0.00 0.00 3.16
6916 8232 8.065407 TGTCACAAAAATGAACGTATCTACAAC 58.935 33.333 0.00 0.00 0.00 3.32
6917 8233 8.144155 TGTCACAAAAATGAACGTATCTACAA 57.856 30.769 0.00 0.00 0.00 2.41
6918 8234 7.716768 TGTCACAAAAATGAACGTATCTACA 57.283 32.000 0.00 0.00 0.00 2.74
6919 8235 8.280497 ACTTGTCACAAAAATGAACGTATCTAC 58.720 33.333 0.00 0.00 0.00 2.59
6920 8236 8.373048 ACTTGTCACAAAAATGAACGTATCTA 57.627 30.769 0.00 0.00 0.00 1.98
6921 8237 7.259290 ACTTGTCACAAAAATGAACGTATCT 57.741 32.000 0.00 0.00 0.00 1.98
6922 8238 8.996988 TTACTTGTCACAAAAATGAACGTATC 57.003 30.769 0.00 0.00 0.00 2.24
6923 8239 9.959749 AATTACTTGTCACAAAAATGAACGTAT 57.040 25.926 0.00 0.00 0.00 3.06
6924 8240 9.440784 GAATTACTTGTCACAAAAATGAACGTA 57.559 29.630 0.00 0.00 0.00 3.57
6925 8241 8.188139 AGAATTACTTGTCACAAAAATGAACGT 58.812 29.630 0.00 0.00 0.00 3.99
6926 8242 8.471457 CAGAATTACTTGTCACAAAAATGAACG 58.529 33.333 0.00 0.00 0.00 3.95
6927 8243 9.515020 TCAGAATTACTTGTCACAAAAATGAAC 57.485 29.630 0.00 0.00 0.00 3.18
6931 8247 9.480053 CCATTCAGAATTACTTGTCACAAAAAT 57.520 29.630 0.00 0.00 0.00 1.82
6932 8248 8.690884 TCCATTCAGAATTACTTGTCACAAAAA 58.309 29.630 0.00 0.00 0.00 1.94
6933 8249 8.231692 TCCATTCAGAATTACTTGTCACAAAA 57.768 30.769 0.00 0.00 0.00 2.44
6934 8250 7.040478 CCTCCATTCAGAATTACTTGTCACAAA 60.040 37.037 0.00 0.00 0.00 2.83
6935 8251 6.430925 CCTCCATTCAGAATTACTTGTCACAA 59.569 38.462 0.00 0.00 0.00 3.33
6936 8252 5.939883 CCTCCATTCAGAATTACTTGTCACA 59.060 40.000 0.00 0.00 0.00 3.58
6937 8253 5.355350 CCCTCCATTCAGAATTACTTGTCAC 59.645 44.000 0.00 0.00 0.00 3.67
6938 8254 5.250543 TCCCTCCATTCAGAATTACTTGTCA 59.749 40.000 0.00 0.00 0.00 3.58
6939 8255 5.745227 TCCCTCCATTCAGAATTACTTGTC 58.255 41.667 0.00 0.00 0.00 3.18
6940 8256 5.251700 ACTCCCTCCATTCAGAATTACTTGT 59.748 40.000 0.00 0.00 0.00 3.16
6941 8257 5.749462 ACTCCCTCCATTCAGAATTACTTG 58.251 41.667 0.00 0.00 0.00 3.16
6942 8258 7.698163 ATACTCCCTCCATTCAGAATTACTT 57.302 36.000 0.00 0.00 0.00 2.24
6943 8259 8.980832 ATATACTCCCTCCATTCAGAATTACT 57.019 34.615 0.00 0.00 0.00 2.24
6944 8260 7.976734 CGATATACTCCCTCCATTCAGAATTAC 59.023 40.741 0.00 0.00 0.00 1.89
6945 8261 7.674348 ACGATATACTCCCTCCATTCAGAATTA 59.326 37.037 0.00 0.00 0.00 1.40
6946 8262 6.498651 ACGATATACTCCCTCCATTCAGAATT 59.501 38.462 0.00 0.00 0.00 2.17
6947 8263 6.019748 ACGATATACTCCCTCCATTCAGAAT 58.980 40.000 0.00 0.00 0.00 2.40
6948 8264 5.394738 ACGATATACTCCCTCCATTCAGAA 58.605 41.667 0.00 0.00 0.00 3.02
6949 8265 4.999310 ACGATATACTCCCTCCATTCAGA 58.001 43.478 0.00 0.00 0.00 3.27
6950 8266 6.378564 ACATACGATATACTCCCTCCATTCAG 59.621 42.308 0.00 0.00 0.00 3.02
6951 8267 6.152831 CACATACGATATACTCCCTCCATTCA 59.847 42.308 0.00 0.00 0.00 2.57
6952 8268 6.153000 ACACATACGATATACTCCCTCCATTC 59.847 42.308 0.00 0.00 0.00 2.67
6953 8269 6.017192 ACACATACGATATACTCCCTCCATT 58.983 40.000 0.00 0.00 0.00 3.16
6954 8270 5.580998 ACACATACGATATACTCCCTCCAT 58.419 41.667 0.00 0.00 0.00 3.41
6955 8271 4.994282 ACACATACGATATACTCCCTCCA 58.006 43.478 0.00 0.00 0.00 3.86
6956 8272 6.602406 ACATACACATACGATATACTCCCTCC 59.398 42.308 0.00 0.00 0.00 4.30
6957 8273 7.627298 ACATACACATACGATATACTCCCTC 57.373 40.000 0.00 0.00 0.00 4.30
6958 8274 7.450634 ACAACATACACATACGATATACTCCCT 59.549 37.037 0.00 0.00 0.00 4.20
6959 8275 7.600065 ACAACATACACATACGATATACTCCC 58.400 38.462 0.00 0.00 0.00 4.30
6960 8276 9.125906 GAACAACATACACATACGATATACTCC 57.874 37.037 0.00 0.00 0.00 3.85
6961 8277 9.673454 TGAACAACATACACATACGATATACTC 57.327 33.333 0.00 0.00 0.00 2.59
6962 8278 9.459640 GTGAACAACATACACATACGATATACT 57.540 33.333 0.00 0.00 35.06 2.12
6963 8279 9.459640 AGTGAACAACATACACATACGATATAC 57.540 33.333 0.00 0.00 37.05 1.47
6965 8281 8.817100 CAAGTGAACAACATACACATACGATAT 58.183 33.333 0.00 0.00 37.05 1.63
6966 8282 8.030106 TCAAGTGAACAACATACACATACGATA 58.970 33.333 0.00 0.00 37.05 2.92
6967 8283 6.871492 TCAAGTGAACAACATACACATACGAT 59.129 34.615 0.00 0.00 37.05 3.73
6968 8284 6.217294 TCAAGTGAACAACATACACATACGA 58.783 36.000 0.00 0.00 37.05 3.43
6969 8285 6.460664 TCAAGTGAACAACATACACATACG 57.539 37.500 0.00 0.00 37.05 3.06
6970 8286 8.289618 ACAATCAAGTGAACAACATACACATAC 58.710 33.333 0.00 0.00 37.05 2.39
6971 8287 8.288913 CACAATCAAGTGAACAACATACACATA 58.711 33.333 0.00 0.00 42.05 2.29
6972 8288 7.140705 CACAATCAAGTGAACAACATACACAT 58.859 34.615 0.00 0.00 42.05 3.21
7082 8399 0.320421 GCTACAGCAAGGTCCACGAA 60.320 55.000 0.00 0.00 41.59 3.85
7111 8428 0.749454 GGGAACATGGCAGCACCTAG 60.749 60.000 0.00 0.00 40.22 3.02
7257 8577 2.300956 TAATGCCAGGTGCCTCAAAA 57.699 45.000 0.00 0.00 40.16 2.44
7259 8579 3.882102 ATATAATGCCAGGTGCCTCAA 57.118 42.857 0.00 0.00 40.16 3.02
7294 8614 5.447818 GCATACCACTGCACATTCTTAGTTC 60.448 44.000 0.00 0.00 41.87 3.01
7295 8615 4.396166 GCATACCACTGCACATTCTTAGTT 59.604 41.667 0.00 0.00 41.87 2.24
7296 8616 3.941483 GCATACCACTGCACATTCTTAGT 59.059 43.478 0.00 0.00 41.87 2.24
7297 8617 4.194640 AGCATACCACTGCACATTCTTAG 58.805 43.478 0.00 0.00 44.77 2.18
7311 8661 6.993786 TTTTGAACATAATCGAGCATACCA 57.006 33.333 0.00 0.00 0.00 3.25
7315 8665 5.068198 AGCCATTTTGAACATAATCGAGCAT 59.932 36.000 0.00 0.00 0.00 3.79
7359 8709 6.527057 TCATGCACATGATTTGGTTGATTA 57.473 33.333 9.23 0.00 42.42 1.75
7380 8730 7.405292 AGGATGGTTCAACTATTCAGATTTCA 58.595 34.615 0.00 0.00 0.00 2.69
7382 8732 7.671398 ACAAGGATGGTTCAACTATTCAGATTT 59.329 33.333 0.00 0.00 0.00 2.17
7383 8733 7.177878 ACAAGGATGGTTCAACTATTCAGATT 58.822 34.615 0.00 0.00 0.00 2.40
7387 8737 7.505585 AGAAAACAAGGATGGTTCAACTATTCA 59.494 33.333 0.00 0.00 34.67 2.57
7388 8738 7.809806 CAGAAAACAAGGATGGTTCAACTATTC 59.190 37.037 0.00 0.00 34.67 1.75
7389 8739 7.505585 TCAGAAAACAAGGATGGTTCAACTATT 59.494 33.333 0.00 0.00 34.67 1.73
7390 8740 7.004086 TCAGAAAACAAGGATGGTTCAACTAT 58.996 34.615 0.00 0.00 34.67 2.12
7421 8868 7.068103 TCTGTTAGATTCTTTTCTTGTTGCCAA 59.932 33.333 0.00 0.00 0.00 4.52
7507 8961 3.046497 GCGCACCCCAACCAATACG 62.046 63.158 0.30 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.