Multiple sequence alignment - TraesCS1B01G241300

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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 TraesCS1B01G241300 chr1B 100.000 5938 0 0 1 5938 428814264 428808327 0.000000e+00 10966.0
1 TraesCS1B01G241300 chr1B 93.601 547 35 0 3 549 440657131 440657677 0.000000e+00 817.0
2 TraesCS1B01G241300 chr1B 88.406 69 4 4 2410 2475 4638285 4638218 4.930000e-11 80.5
3 TraesCS1B01G241300 chr1D 93.875 2857 115 24 551 3395 316685937 316683129 0.000000e+00 4252.0
4 TraesCS1B01G241300 chr1D 94.585 1939 68 15 3569 5498 316682793 316680883 0.000000e+00 2964.0
5 TraesCS1B01G241300 chr1D 95.308 341 14 2 3072 3412 316683127 316682789 1.880000e-149 540.0
6 TraesCS1B01G241300 chr1D 91.506 259 16 4 5684 5937 316680703 316680446 9.470000e-93 351.0
7 TraesCS1B01G241300 chr1D 94.149 188 10 1 5533 5720 316680893 316680707 9.740000e-73 285.0
8 TraesCS1B01G241300 chr1A 93.011 2418 124 19 3540 5938 397773793 397771402 0.000000e+00 3487.0
9 TraesCS1B01G241300 chr1A 89.313 1806 88 30 630 2424 397776454 397774743 0.000000e+00 2169.0
10 TraesCS1B01G241300 chr1A 89.378 932 60 11 2500 3423 397774698 397773798 0.000000e+00 1136.0
11 TraesCS1B01G241300 chr1A 93.625 549 34 1 1 549 361207796 361207249 0.000000e+00 819.0
12 TraesCS1B01G241300 chr5A 94.718 549 29 0 1 549 269326314 269325766 0.000000e+00 854.0
13 TraesCS1B01G241300 chr5A 93.293 164 10 1 3407 3570 320214406 320214244 2.140000e-59 241.0
14 TraesCS1B01G241300 chr5A 92.262 168 11 2 3408 3575 558675497 558675662 2.770000e-58 237.0
15 TraesCS1B01G241300 chr3A 94.353 549 31 0 1 549 452935966 452936514 0.000000e+00 843.0
16 TraesCS1B01G241300 chr3A 92.216 167 12 1 3408 3574 600920855 600921020 9.950000e-58 235.0
17 TraesCS1B01G241300 chr4A 93.443 549 35 1 1 549 97383822 97383275 0.000000e+00 813.0
18 TraesCS1B01G241300 chrUn 93.236 547 37 0 3 549 17028618 17028072 0.000000e+00 806.0
19 TraesCS1B01G241300 chrUn 96.000 50 2 0 2426 2475 48357248 48357297 1.370000e-11 82.4
20 TraesCS1B01G241300 chrUn 96.000 50 2 0 2426 2475 282070173 282070222 1.370000e-11 82.4
21 TraesCS1B01G241300 chrUn 96.000 50 2 0 2426 2475 293225865 293225914 1.370000e-11 82.4
22 TraesCS1B01G241300 chr3B 92.687 547 40 0 3 549 798510468 798511014 0.000000e+00 789.0
23 TraesCS1B01G241300 chr2B 91.075 549 49 0 1 549 198375150 198374602 0.000000e+00 743.0
24 TraesCS1B01G241300 chr2B 98.039 51 1 0 2425 2475 712620351 712620301 8.200000e-14 89.8
25 TraesCS1B01G241300 chr7A 89.617 549 57 0 1 549 291521313 291521861 0.000000e+00 699.0
26 TraesCS1B01G241300 chr7A 93.103 58 3 1 2419 2475 610447516 610447573 3.810000e-12 84.2
27 TraesCS1B01G241300 chr4D 92.308 169 11 2 3403 3571 64390467 64390633 7.690000e-59 239.0
28 TraesCS1B01G241300 chr2A 93.252 163 10 1 3408 3570 419206816 419206977 7.690000e-59 239.0
29 TraesCS1B01G241300 chr2A 90.503 179 14 3 3400 3577 184561146 184561322 3.580000e-57 233.0
30 TraesCS1B01G241300 chr5B 92.308 169 10 3 3407 3574 607838553 607838387 2.770000e-58 237.0
31 TraesCS1B01G241300 chr6A 91.716 169 12 1 3408 3574 531524780 531524948 3.580000e-57 233.0
32 TraesCS1B01G241300 chr2D 91.279 172 13 2 3408 3579 169037569 169037738 3.580000e-57 233.0
33 TraesCS1B01G241300 chr2D 96.154 52 0 2 2425 2475 251999142 251999192 3.810000e-12 84.2
34 TraesCS1B01G241300 chr7B 98.039 51 1 0 2425 2475 705539954 705539904 8.200000e-14 89.8


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 TraesCS1B01G241300 chr1B 428808327 428814264 5937 True 10966.0 10966 100.000000 1 5938 1 chr1B.!!$R2 5937
1 TraesCS1B01G241300 chr1B 440657131 440657677 546 False 817.0 817 93.601000 3 549 1 chr1B.!!$F1 546
2 TraesCS1B01G241300 chr1D 316680446 316685937 5491 True 1678.4 4252 93.884600 551 5937 5 chr1D.!!$R1 5386
3 TraesCS1B01G241300 chr1A 397771402 397776454 5052 True 2264.0 3487 90.567333 630 5938 3 chr1A.!!$R2 5308
4 TraesCS1B01G241300 chr1A 361207249 361207796 547 True 819.0 819 93.625000 1 549 1 chr1A.!!$R1 548
5 TraesCS1B01G241300 chr5A 269325766 269326314 548 True 854.0 854 94.718000 1 549 1 chr5A.!!$R1 548
6 TraesCS1B01G241300 chr3A 452935966 452936514 548 False 843.0 843 94.353000 1 549 1 chr3A.!!$F1 548
7 TraesCS1B01G241300 chr4A 97383275 97383822 547 True 813.0 813 93.443000 1 549 1 chr4A.!!$R1 548
8 TraesCS1B01G241300 chrUn 17028072 17028618 546 True 806.0 806 93.236000 3 549 1 chrUn.!!$R1 546
9 TraesCS1B01G241300 chr3B 798510468 798511014 546 False 789.0 789 92.687000 3 549 1 chr3B.!!$F1 546
10 TraesCS1B01G241300 chr2B 198374602 198375150 548 True 743.0 743 91.075000 1 549 1 chr2B.!!$R1 548
11 TraesCS1B01G241300 chr7A 291521313 291521861 548 False 699.0 699 89.617000 1 549 1 chr7A.!!$F1 548

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
175 176 0.108804 CAGGTACGCCATTGACGAGT 60.109 55.0 0.00 0.00 37.19 4.18 F
676 678 0.877071 CAGCACCAACCATCAGTCAC 59.123 55.0 0.00 0.00 0.00 3.67 F
1372 1385 0.305922 CGCCCTTTCTGATGATTCGC 59.694 55.0 0.00 0.00 0.00 4.70 F
1982 1998 0.110295 ATTGGCTGTACACAGTGGCA 59.890 50.0 10.87 5.15 45.45 4.92 F
2240 2258 0.599204 ATATAAGGCGCACCGGTTCG 60.599 55.0 22.69 22.69 42.76 3.95 F
3663 4015 0.394938 TGCTTACCTTGCGTCCTTGA 59.605 50.0 0.00 0.00 0.00 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1116 1128 0.458260 AAAACCAACGAGGCCAACAC 59.542 50.000 5.01 0.0 43.14 3.32 R
1761 1776 0.534203 GAACGACAGAGGCCAACCAA 60.534 55.000 5.01 0.0 39.06 3.67 R
2677 2696 0.465460 TTCTGGACAAAGCAAGCGGT 60.465 50.000 0.00 0.0 0.00 5.68 R
3339 3690 1.032014 AACCCAGCAACACACACATC 58.968 50.000 0.00 0.0 0.00 3.06 R
3830 4182 1.347378 TCATTGGCAGCAGTACAGTGA 59.653 47.619 0.00 0.0 0.00 3.41 R
5047 5404 0.319405 ACCTCCGGTTGGTCGTTAAG 59.681 55.000 14.47 0.0 36.30 1.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 0.178992 TCAAACCTTGGGTGAGCCAG 60.179 55.000 2.68 0.00 35.34 4.85
175 176 0.108804 CAGGTACGCCATTGACGAGT 60.109 55.000 0.00 0.00 37.19 4.18
278 279 5.044476 TCAAACAGGAAGGGCCAAGATATAA 60.044 40.000 6.18 0.00 40.02 0.98
295 296 5.465724 AGATATAAAATCAAACGCCCTCGAC 59.534 40.000 0.00 0.00 39.41 4.20
524 526 2.604139 GAAAATCCCCAACCAACTCCA 58.396 47.619 0.00 0.00 0.00 3.86
549 551 3.070159 TCGGATTTCTTAGGGATGAGCAG 59.930 47.826 0.00 0.00 0.00 4.24
617 619 6.713731 TCCCACTCTTCTAACCCTTTAATT 57.286 37.500 0.00 0.00 0.00 1.40
672 674 1.236616 TTCGCAGCACCAACCATCAG 61.237 55.000 0.00 0.00 0.00 2.90
673 675 1.968017 CGCAGCACCAACCATCAGT 60.968 57.895 0.00 0.00 0.00 3.41
674 676 1.878775 GCAGCACCAACCATCAGTC 59.121 57.895 0.00 0.00 0.00 3.51
675 677 0.890542 GCAGCACCAACCATCAGTCA 60.891 55.000 0.00 0.00 0.00 3.41
676 678 0.877071 CAGCACCAACCATCAGTCAC 59.123 55.000 0.00 0.00 0.00 3.67
765 767 1.376037 GTAGACCAGGTGCAGGCAC 60.376 63.158 15.78 15.78 45.49 5.01
967 975 3.177228 CAAAGGGGAAAGGAGAGAGAGA 58.823 50.000 0.00 0.00 0.00 3.10
1119 1131 2.125673 CGATTTCGCCCTCGGTGT 60.126 61.111 0.00 0.00 34.40 4.16
1120 1132 1.740296 CGATTTCGCCCTCGGTGTT 60.740 57.895 0.00 0.00 34.40 3.32
1121 1133 1.794222 GATTTCGCCCTCGGTGTTG 59.206 57.895 0.00 0.00 34.40 3.33
1122 1134 1.644786 GATTTCGCCCTCGGTGTTGG 61.645 60.000 0.00 0.00 34.40 3.77
1127 1139 4.760047 CCCTCGGTGTTGGCCTCG 62.760 72.222 3.32 0.25 0.00 4.63
1128 1140 4.003788 CCTCGGTGTTGGCCTCGT 62.004 66.667 3.32 0.00 0.00 4.18
1129 1141 2.030562 CTCGGTGTTGGCCTCGTT 59.969 61.111 3.32 0.00 0.00 3.85
1130 1142 2.280524 TCGGTGTTGGCCTCGTTG 60.281 61.111 3.32 0.00 0.00 4.10
1131 1143 3.353836 CGGTGTTGGCCTCGTTGG 61.354 66.667 3.32 0.00 39.35 3.77
1137 1149 1.134965 TGTTGGCCTCGTTGGTTTTTG 60.135 47.619 3.32 0.00 38.35 2.44
1372 1385 0.305922 CGCCCTTTCTGATGATTCGC 59.694 55.000 0.00 0.00 0.00 4.70
1373 1386 0.305922 GCCCTTTCTGATGATTCGCG 59.694 55.000 0.00 0.00 0.00 5.87
1374 1387 1.656652 CCCTTTCTGATGATTCGCGT 58.343 50.000 5.77 0.00 0.00 6.01
1375 1388 2.009774 CCCTTTCTGATGATTCGCGTT 58.990 47.619 5.77 0.00 0.00 4.84
1376 1389 2.030946 CCCTTTCTGATGATTCGCGTTC 59.969 50.000 5.77 5.37 0.00 3.95
1377 1390 2.932614 CCTTTCTGATGATTCGCGTTCT 59.067 45.455 5.77 0.00 0.00 3.01
1378 1391 3.372206 CCTTTCTGATGATTCGCGTTCTT 59.628 43.478 5.77 2.88 0.00 2.52
1379 1392 3.997319 TTCTGATGATTCGCGTTCTTG 57.003 42.857 5.77 0.00 0.00 3.02
1380 1393 2.959516 TCTGATGATTCGCGTTCTTGT 58.040 42.857 5.77 0.00 0.00 3.16
1381 1394 2.667969 TCTGATGATTCGCGTTCTTGTG 59.332 45.455 5.77 0.00 0.00 3.33
1382 1395 2.667969 CTGATGATTCGCGTTCTTGTGA 59.332 45.455 5.77 0.00 0.00 3.58
1383 1396 2.411748 TGATGATTCGCGTTCTTGTGAC 59.588 45.455 5.77 0.00 0.00 3.67
1384 1397 2.148916 TGATTCGCGTTCTTGTGACT 57.851 45.000 5.77 0.00 0.00 3.41
1385 1398 2.058798 TGATTCGCGTTCTTGTGACTC 58.941 47.619 5.77 0.00 0.00 3.36
1386 1399 1.057847 GATTCGCGTTCTTGTGACTCG 59.942 52.381 5.77 0.00 0.00 4.18
1392 1405 1.372997 TTCTTGTGACTCGCTCGGC 60.373 57.895 0.00 0.00 0.00 5.54
1415 1428 1.314730 GTCCCGTTTGAGCCTTTGAA 58.685 50.000 0.00 0.00 0.00 2.69
1424 1437 7.041440 CCCGTTTGAGCCTTTGAAATAATTTTT 60.041 33.333 0.00 0.00 0.00 1.94
1452 1465 1.883275 TGGGACATTTTACGCCAAGTG 59.117 47.619 0.00 0.00 0.00 3.16
1466 1479 0.370273 CAAGTGTCGTTAGGATGCGC 59.630 55.000 0.00 0.00 0.00 6.09
1502 1515 4.562394 CGGAAATGTTGATAATGGTGCAAC 59.438 41.667 0.00 0.00 41.57 4.17
1508 1521 4.704540 TGTTGATAATGGTGCAACTAAGGG 59.295 41.667 2.04 0.00 41.71 3.95
1512 1525 1.372501 ATGGTGCAACTAAGGGACCT 58.627 50.000 2.04 0.00 45.90 3.85
1648 1661 5.092554 TCTTGTTTGTCTGTGGTAGTTCA 57.907 39.130 0.00 0.00 0.00 3.18
1666 1679 7.229907 GGTAGTTCAGGTTGGAAATGTAGAAAA 59.770 37.037 0.00 0.00 0.00 2.29
1673 1686 8.410141 CAGGTTGGAAATGTAGAAAACAAGTTA 58.590 33.333 0.00 0.00 42.70 2.24
1761 1776 1.185315 CTGGTTGGAATTGCGGGATT 58.815 50.000 0.00 0.00 0.00 3.01
1775 1790 0.251787 GGGATTTGGTTGGCCTCTGT 60.252 55.000 3.32 0.00 35.27 3.41
1906 1922 1.948104 TGTTGGTTCTGGAGTGAACG 58.052 50.000 0.00 0.00 45.11 3.95
1937 1953 6.542005 TGCAACTAGATGAAAGTCTGAAACAA 59.458 34.615 3.85 0.00 0.00 2.83
1967 1983 5.769662 TGTTATAGCTGGCCAATAAGATTGG 59.230 40.000 7.01 12.95 42.37 3.16
1982 1998 0.110295 ATTGGCTGTACACAGTGGCA 59.890 50.000 10.87 5.15 45.45 4.92
1990 2006 2.293122 TGTACACAGTGGCAAATTGAGC 59.707 45.455 5.31 0.00 0.00 4.26
2132 2149 6.370166 CAGTGAAATTCTCCACTTCTCCTAAC 59.630 42.308 5.64 0.00 41.26 2.34
2154 2171 5.689819 ACATTCGTAATGAAAGTGTGAAGC 58.310 37.500 12.53 0.00 41.46 3.86
2236 2254 3.185797 GTCTAAAATATAAGGCGCACCGG 59.814 47.826 10.83 0.00 42.76 5.28
2239 2257 1.589803 AATATAAGGCGCACCGGTTC 58.410 50.000 2.97 0.00 42.76 3.62
2240 2258 0.599204 ATATAAGGCGCACCGGTTCG 60.599 55.000 22.69 22.69 42.76 3.95
2336 2354 3.980646 TTCCAACACGAATCCAACAAG 57.019 42.857 0.00 0.00 0.00 3.16
2418 2436 9.053840 AGATAATCTTGAGAAACATGTGCTATG 57.946 33.333 0.00 0.79 0.00 2.23
2431 2449 4.010667 TGTGCTATGTTTTACCTCCGTT 57.989 40.909 0.00 0.00 0.00 4.44
2488 2506 5.821995 GGATGTATCTACGGAGGGAGTATAC 59.178 48.000 0.00 0.00 0.00 1.47
2491 2509 6.236409 TGTATCTACGGAGGGAGTATACTTG 58.764 44.000 6.88 0.00 0.00 3.16
2493 2511 5.121380 TCTACGGAGGGAGTATACTTGTT 57.879 43.478 6.88 0.00 0.00 2.83
2498 2516 6.608922 ACGGAGGGAGTATACTTGTTAGTAT 58.391 40.000 6.88 0.00 46.68 2.12
2554 2572 8.221965 TCAAGAAAATCTCGTATAGCTACAGA 57.778 34.615 0.00 0.00 0.00 3.41
2740 2759 9.702726 CACGTATTAACATAATCTCTTTTGTGG 57.297 33.333 0.00 0.00 0.00 4.17
2759 2783 6.000246 TGTGGTTATCTTCCATGATTGCTA 58.000 37.500 0.00 0.00 37.30 3.49
2881 2906 9.675464 TTTCTCTTTACAAAGTTCTAGTTTCCA 57.325 29.630 1.86 0.00 37.31 3.53
2922 2947 6.352222 CCCTCTTAGGTGACATGTGTTATTCT 60.352 42.308 1.15 0.00 31.93 2.40
2944 2969 2.810852 GCTCTTCAGTTTGAGTCCCAAG 59.189 50.000 0.00 0.00 35.94 3.61
2945 2970 3.745797 GCTCTTCAGTTTGAGTCCCAAGT 60.746 47.826 0.00 0.00 35.94 3.16
2946 2971 4.061596 CTCTTCAGTTTGAGTCCCAAGTC 58.938 47.826 0.00 0.00 35.94 3.01
2947 2972 2.930826 TCAGTTTGAGTCCCAAGTCC 57.069 50.000 0.00 0.00 35.94 3.85
2948 2973 1.420138 TCAGTTTGAGTCCCAAGTCCC 59.580 52.381 0.00 0.00 35.94 4.46
2949 2974 1.142870 CAGTTTGAGTCCCAAGTCCCA 59.857 52.381 0.00 0.00 35.94 4.37
2950 2975 1.850345 AGTTTGAGTCCCAAGTCCCAA 59.150 47.619 0.00 0.00 35.94 4.12
2951 2976 1.954382 GTTTGAGTCCCAAGTCCCAAC 59.046 52.381 0.00 0.00 35.94 3.77
2952 2977 1.518367 TTGAGTCCCAAGTCCCAACT 58.482 50.000 0.00 0.00 37.32 3.16
3048 3074 5.941948 AGTAGGGCGTGCATTATTAATTC 57.058 39.130 0.00 0.00 0.00 2.17
3126 3477 9.099454 GTAGTTAAGAGTTTGGATCTATGGTTG 57.901 37.037 0.00 0.00 0.00 3.77
3140 3491 5.953183 TCTATGGTTGTTGCACATTTCATC 58.047 37.500 0.00 0.00 0.00 2.92
3224 3575 3.986277 TGAAAAGAGTGGTACCGAACTC 58.014 45.455 19.96 19.96 42.61 3.01
3250 3601 1.813753 TTCGCGATTGCTACCTGGC 60.814 57.895 10.88 0.00 39.65 4.85
3253 3604 1.766143 CGCGATTGCTACCTGGCTTC 61.766 60.000 0.00 0.00 39.65 3.86
3371 3722 4.650972 TGCTGGGTTACCTTGAGTTTAT 57.349 40.909 0.00 0.00 37.76 1.40
3416 3768 9.368674 GAGAGTTAACTAAAACATACTTCCTCC 57.631 37.037 8.42 0.00 0.00 4.30
3419 3771 8.152898 AGTTAACTAAAACATACTTCCTCCGTT 58.847 33.333 6.26 0.00 0.00 4.44
3421 3773 5.485620 ACTAAAACATACTTCCTCCGTTCC 58.514 41.667 0.00 0.00 0.00 3.62
3423 3775 5.750352 AAAACATACTTCCTCCGTTCCTA 57.250 39.130 0.00 0.00 0.00 2.94
3426 3778 5.952347 ACATACTTCCTCCGTTCCTAAAT 57.048 39.130 0.00 0.00 0.00 1.40
3427 3779 7.427989 AACATACTTCCTCCGTTCCTAAATA 57.572 36.000 0.00 0.00 0.00 1.40
3428 3780 7.613551 ACATACTTCCTCCGTTCCTAAATAT 57.386 36.000 0.00 0.00 0.00 1.28
3429 3781 8.716674 ACATACTTCCTCCGTTCCTAAATATA 57.283 34.615 0.00 0.00 0.00 0.86
3430 3782 9.151177 ACATACTTCCTCCGTTCCTAAATATAA 57.849 33.333 0.00 0.00 0.00 0.98
3431 3783 9.640963 CATACTTCCTCCGTTCCTAAATATAAG 57.359 37.037 0.00 0.00 0.00 1.73
3432 3784 7.672122 ACTTCCTCCGTTCCTAAATATAAGT 57.328 36.000 0.00 0.00 0.00 2.24
3433 3785 7.724287 ACTTCCTCCGTTCCTAAATATAAGTC 58.276 38.462 0.00 0.00 0.00 3.01
3434 3786 7.564292 ACTTCCTCCGTTCCTAAATATAAGTCT 59.436 37.037 0.00 0.00 0.00 3.24
3435 3787 7.909485 TCCTCCGTTCCTAAATATAAGTCTT 57.091 36.000 0.00 0.00 0.00 3.01
3436 3788 8.315220 TCCTCCGTTCCTAAATATAAGTCTTT 57.685 34.615 0.00 0.00 0.00 2.52
3437 3789 8.765517 TCCTCCGTTCCTAAATATAAGTCTTTT 58.234 33.333 0.00 0.00 0.00 2.27
3438 3790 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
3468 3820 6.280855 TCCAATATGGACTACATACGGATG 57.719 41.667 5.94 5.94 42.67 3.51
3469 3821 5.778241 TCCAATATGGACTACATACGGATGT 59.222 40.000 19.12 19.12 42.67 3.06
3470 3822 6.949463 TCCAATATGGACTACATACGGATGTA 59.051 38.462 19.32 19.32 42.34 2.29
3471 3823 7.618117 TCCAATATGGACTACATACGGATGTAT 59.382 37.037 20.64 9.39 43.13 2.29
3472 3824 8.909923 CCAATATGGACTACATACGGATGTATA 58.090 37.037 20.64 11.30 42.60 1.47
3477 3829 8.728337 TGGACTACATACGGATGTATATAGAC 57.272 38.462 20.64 10.95 45.42 2.59
3478 3830 8.323567 TGGACTACATACGGATGTATATAGACA 58.676 37.037 20.64 12.12 45.42 3.41
3479 3831 9.339850 GGACTACATACGGATGTATATAGACAT 57.660 37.037 20.64 12.70 45.42 3.06
3500 3852 9.553064 AGACATATTTTGGAGTGTAGATTCATC 57.447 33.333 0.00 0.00 0.00 2.92
3501 3853 8.682936 ACATATTTTGGAGTGTAGATTCATCC 57.317 34.615 0.00 0.00 0.00 3.51
3502 3854 7.442364 ACATATTTTGGAGTGTAGATTCATCCG 59.558 37.037 0.00 0.00 32.47 4.18
3503 3855 4.819105 TTTGGAGTGTAGATTCATCCGT 57.181 40.909 0.00 0.00 32.47 4.69
3504 3856 4.819105 TTGGAGTGTAGATTCATCCGTT 57.181 40.909 0.00 0.00 32.47 4.44
3505 3857 4.819105 TGGAGTGTAGATTCATCCGTTT 57.181 40.909 0.00 0.00 32.47 3.60
3506 3858 5.160607 TGGAGTGTAGATTCATCCGTTTT 57.839 39.130 0.00 0.00 32.47 2.43
3507 3859 5.556915 TGGAGTGTAGATTCATCCGTTTTT 58.443 37.500 0.00 0.00 32.47 1.94
3508 3860 5.411361 TGGAGTGTAGATTCATCCGTTTTTG 59.589 40.000 0.00 0.00 32.47 2.44
3509 3861 5.296813 AGTGTAGATTCATCCGTTTTTGC 57.703 39.130 0.00 0.00 0.00 3.68
3510 3862 5.003804 AGTGTAGATTCATCCGTTTTTGCT 58.996 37.500 0.00 0.00 0.00 3.91
3511 3863 5.122396 AGTGTAGATTCATCCGTTTTTGCTC 59.878 40.000 0.00 0.00 0.00 4.26
3512 3864 4.394920 TGTAGATTCATCCGTTTTTGCTCC 59.605 41.667 0.00 0.00 0.00 4.70
3513 3865 2.420022 AGATTCATCCGTTTTTGCTCCG 59.580 45.455 0.00 0.00 0.00 4.63
3514 3866 1.600023 TTCATCCGTTTTTGCTCCGT 58.400 45.000 0.00 0.00 0.00 4.69
3515 3867 2.459060 TCATCCGTTTTTGCTCCGTA 57.541 45.000 0.00 0.00 0.00 4.02
3516 3868 2.980568 TCATCCGTTTTTGCTCCGTAT 58.019 42.857 0.00 0.00 0.00 3.06
3517 3869 2.675844 TCATCCGTTTTTGCTCCGTATG 59.324 45.455 0.00 0.00 0.00 2.39
3518 3870 2.172851 TCCGTTTTTGCTCCGTATGT 57.827 45.000 0.00 0.00 0.00 2.29
3519 3871 3.316071 TCCGTTTTTGCTCCGTATGTA 57.684 42.857 0.00 0.00 0.00 2.29
3520 3872 3.255725 TCCGTTTTTGCTCCGTATGTAG 58.744 45.455 0.00 0.00 0.00 2.74
3521 3873 2.997986 CCGTTTTTGCTCCGTATGTAGT 59.002 45.455 0.00 0.00 0.00 2.73
3522 3874 3.434299 CCGTTTTTGCTCCGTATGTAGTT 59.566 43.478 0.00 0.00 0.00 2.24
3523 3875 4.435121 CCGTTTTTGCTCCGTATGTAGTTC 60.435 45.833 0.00 0.00 0.00 3.01
3524 3876 4.150980 CGTTTTTGCTCCGTATGTAGTTCA 59.849 41.667 0.00 0.00 0.00 3.18
3525 3877 5.163893 CGTTTTTGCTCCGTATGTAGTTCAT 60.164 40.000 0.00 0.00 40.25 2.57
3526 3878 6.035220 CGTTTTTGCTCCGTATGTAGTTCATA 59.965 38.462 0.00 0.00 37.91 2.15
3527 3879 7.254319 CGTTTTTGCTCCGTATGTAGTTCATAT 60.254 37.037 0.00 0.00 40.54 1.78
3528 3880 8.395633 GTTTTTGCTCCGTATGTAGTTCATATT 58.604 33.333 0.00 0.00 40.54 1.28
3529 3881 7.477144 TTTGCTCCGTATGTAGTTCATATTG 57.523 36.000 0.00 0.00 40.54 1.90
3530 3882 5.538118 TGCTCCGTATGTAGTTCATATTGG 58.462 41.667 5.26 5.26 40.54 3.16
3531 3883 5.303333 TGCTCCGTATGTAGTTCATATTGGA 59.697 40.000 10.96 10.96 40.63 3.53
3532 3884 6.183360 TGCTCCGTATGTAGTTCATATTGGAA 60.183 38.462 11.96 1.11 41.44 3.53
3533 3885 6.874134 GCTCCGTATGTAGTTCATATTGGAAT 59.126 38.462 11.96 0.00 41.44 3.01
3534 3886 7.063544 GCTCCGTATGTAGTTCATATTGGAATC 59.936 40.741 11.96 6.35 41.44 2.52
3535 3887 8.190326 TCCGTATGTAGTTCATATTGGAATCT 57.810 34.615 9.72 0.00 40.31 2.40
3536 3888 8.304596 TCCGTATGTAGTTCATATTGGAATCTC 58.695 37.037 9.72 0.00 40.31 2.75
3537 3889 8.307483 CCGTATGTAGTTCATATTGGAATCTCT 58.693 37.037 5.56 0.00 40.54 3.10
3538 3890 9.698309 CGTATGTAGTTCATATTGGAATCTCTT 57.302 33.333 0.00 0.00 40.54 2.85
3607 3959 7.238486 TGTATTGGACATAATTGGCAGTTTT 57.762 32.000 0.00 0.00 31.20 2.43
3663 4015 0.394938 TGCTTACCTTGCGTCCTTGA 59.605 50.000 0.00 0.00 0.00 3.02
3765 4117 0.400213 CTGTGCTACAAGGGTTGGGA 59.600 55.000 0.00 0.00 34.12 4.37
3773 4125 0.688487 CAAGGGTTGGGACGGACTTA 59.312 55.000 0.00 0.00 0.00 2.24
3854 4207 1.347378 TGTACTGCTGCCAATGAGTGA 59.653 47.619 0.00 0.00 0.00 3.41
3905 4258 6.314896 GTCCTCTTCAGAATACATGGTTTCTG 59.685 42.308 23.65 23.65 46.57 3.02
4357 4710 2.352960 GTGCATAGCCAGTACAGCTTTC 59.647 50.000 14.70 6.35 41.83 2.62
4371 4724 3.777522 ACAGCTTTCTATGCCCTCTAAGT 59.222 43.478 0.00 0.00 0.00 2.24
4421 4774 8.359060 TGCCAATTAAGTTTTGTCATTGTTAC 57.641 30.769 0.00 0.00 0.00 2.50
4465 4818 8.042515 GTCTGTTATGGTTATGTGGTTACCTTA 58.957 37.037 2.07 0.00 33.05 2.69
4476 4829 6.971527 TGTGGTTACCTTATTGACGTATTG 57.028 37.500 2.07 0.00 0.00 1.90
4489 4842 6.746745 TTGACGTATTGGTTATCCCTTTTC 57.253 37.500 0.00 0.00 0.00 2.29
4539 4892 7.325660 TCCTTAATCTGCTTGACATCATTTC 57.674 36.000 0.00 0.00 0.00 2.17
4547 4900 5.472148 TGCTTGACATCATTTCATTTGGAC 58.528 37.500 0.00 0.00 0.00 4.02
4566 4919 7.938140 TTGGACGATATTTCTCCAAGAAAAT 57.062 32.000 6.25 2.66 46.08 1.82
4599 4952 3.981416 ACTTACGCATGTGCTGTATATCG 59.019 43.478 6.08 0.00 39.32 2.92
4616 4969 8.143673 TGTATATCGTAGTAGTCTACCCATCT 57.856 38.462 6.38 0.00 42.36 2.90
4668 5021 3.118775 GGGCCTTATGGTTTTTGATGACC 60.119 47.826 0.84 0.00 36.45 4.02
4684 5037 1.211703 TGACCTGTTGCTCACCAGAAA 59.788 47.619 0.00 0.00 0.00 2.52
4795 5149 9.944663 TTTTGCTGTAGTTTAATAGTTCTTGTG 57.055 29.630 0.00 0.00 0.00 3.33
4886 5242 3.121030 CGGGCTCAAAGGAGTGCG 61.121 66.667 0.00 0.00 43.37 5.34
5491 5905 2.026915 TCACATGTTGGGTCTCCATCTG 60.027 50.000 0.00 0.00 43.63 2.90
5492 5906 2.026915 CACATGTTGGGTCTCCATCTGA 60.027 50.000 0.00 0.00 43.63 3.27
5493 5907 2.848694 ACATGTTGGGTCTCCATCTGAT 59.151 45.455 0.00 0.00 43.63 2.90
5494 5908 4.040047 ACATGTTGGGTCTCCATCTGATA 58.960 43.478 0.00 0.00 43.63 2.15
5495 5909 4.102210 ACATGTTGGGTCTCCATCTGATAG 59.898 45.833 0.00 0.00 43.63 2.08
5496 5910 2.435805 TGTTGGGTCTCCATCTGATAGC 59.564 50.000 0.00 0.00 43.63 2.97
5497 5911 2.435805 GTTGGGTCTCCATCTGATAGCA 59.564 50.000 0.00 0.00 43.63 3.49
5498 5912 2.763039 TGGGTCTCCATCTGATAGCAA 58.237 47.619 0.00 0.00 38.32 3.91
5499 5913 3.114606 TGGGTCTCCATCTGATAGCAAA 58.885 45.455 0.00 0.00 38.32 3.68
5500 5914 3.118261 TGGGTCTCCATCTGATAGCAAAC 60.118 47.826 0.00 0.00 38.32 2.93
5501 5915 3.135530 GGGTCTCCATCTGATAGCAAACT 59.864 47.826 0.00 0.00 0.00 2.66
5502 5916 4.384647 GGGTCTCCATCTGATAGCAAACTT 60.385 45.833 0.00 0.00 0.00 2.66
5503 5917 4.574013 GGTCTCCATCTGATAGCAAACTTG 59.426 45.833 0.00 0.00 0.00 3.16
5504 5918 5.423015 GTCTCCATCTGATAGCAAACTTGA 58.577 41.667 0.00 0.00 0.00 3.02
5505 5919 6.054295 GTCTCCATCTGATAGCAAACTTGAT 58.946 40.000 0.00 0.00 0.00 2.57
5506 5920 7.212976 GTCTCCATCTGATAGCAAACTTGATA 58.787 38.462 0.00 0.00 33.15 2.15
5507 5921 7.384660 GTCTCCATCTGATAGCAAACTTGATAG 59.615 40.741 0.00 0.00 32.01 2.08
5508 5922 7.288621 TCTCCATCTGATAGCAAACTTGATAGA 59.711 37.037 0.00 0.00 32.01 1.98
5509 5923 7.971201 TCCATCTGATAGCAAACTTGATAGAT 58.029 34.615 0.00 0.00 32.01 1.98
5510 5924 9.093458 TCCATCTGATAGCAAACTTGATAGATA 57.907 33.333 0.00 0.00 32.01 1.98
5511 5925 9.368674 CCATCTGATAGCAAACTTGATAGATAG 57.631 37.037 0.00 0.00 32.01 2.08
5512 5926 8.871862 CATCTGATAGCAAACTTGATAGATAGC 58.128 37.037 0.00 0.00 32.01 2.97
5513 5927 7.955918 TCTGATAGCAAACTTGATAGATAGCA 58.044 34.615 0.00 0.00 32.01 3.49
5514 5928 8.591940 TCTGATAGCAAACTTGATAGATAGCAT 58.408 33.333 0.00 0.00 32.01 3.79
5515 5929 8.543862 TGATAGCAAACTTGATAGATAGCATG 57.456 34.615 0.00 0.00 32.01 4.06
5516 5930 5.686159 AGCAAACTTGATAGATAGCATGC 57.314 39.130 10.51 10.51 0.00 4.06
5517 5931 4.518211 AGCAAACTTGATAGATAGCATGCC 59.482 41.667 15.66 0.00 30.76 4.40
5518 5932 4.276678 GCAAACTTGATAGATAGCATGCCA 59.723 41.667 15.66 0.00 0.00 4.92
5519 5933 5.221106 GCAAACTTGATAGATAGCATGCCAA 60.221 40.000 15.66 8.54 0.00 4.52
5520 5934 6.516194 GCAAACTTGATAGATAGCATGCCAAT 60.516 38.462 15.66 8.62 0.00 3.16
5521 5935 6.814506 AACTTGATAGATAGCATGCCAATC 57.185 37.500 15.66 17.41 0.00 2.67
5522 5936 4.934001 ACTTGATAGATAGCATGCCAATCG 59.066 41.667 15.66 6.72 0.00 3.34
5523 5937 4.806640 TGATAGATAGCATGCCAATCGA 57.193 40.909 15.66 14.24 0.00 3.59
5524 5938 5.151297 TGATAGATAGCATGCCAATCGAA 57.849 39.130 15.66 11.69 0.00 3.71
5525 5939 5.173664 TGATAGATAGCATGCCAATCGAAG 58.826 41.667 15.66 0.00 0.00 3.79
5526 5940 2.149578 AGATAGCATGCCAATCGAAGC 58.850 47.619 15.66 0.00 0.00 3.86
5527 5941 2.149578 GATAGCATGCCAATCGAAGCT 58.850 47.619 15.66 0.00 36.20 3.74
5528 5942 1.302366 TAGCATGCCAATCGAAGCTG 58.698 50.000 15.66 4.53 33.83 4.24
5529 5943 0.679002 AGCATGCCAATCGAAGCTGT 60.679 50.000 15.66 0.00 0.00 4.40
5530 5944 1.016627 GCATGCCAATCGAAGCTGTA 58.983 50.000 6.36 0.00 0.00 2.74
5531 5945 1.605710 GCATGCCAATCGAAGCTGTAT 59.394 47.619 6.36 0.00 0.00 2.29
5532 5946 2.807967 GCATGCCAATCGAAGCTGTATA 59.192 45.455 6.36 0.00 0.00 1.47
5533 5947 3.438087 GCATGCCAATCGAAGCTGTATAT 59.562 43.478 6.36 0.00 0.00 0.86
5534 5948 4.436584 GCATGCCAATCGAAGCTGTATATC 60.437 45.833 6.36 0.00 0.00 1.63
5535 5949 4.607293 TGCCAATCGAAGCTGTATATCT 57.393 40.909 6.95 0.00 0.00 1.98
5551 5965 8.031864 GCTGTATATCTAATTGCAGCTTCTCTA 58.968 37.037 7.04 0.00 43.94 2.43
5590 6004 3.127203 ACGAAATTCAGAGACTCGACGAT 59.873 43.478 0.00 0.00 33.81 3.73
5597 6011 2.609916 CAGAGACTCGACGATGAAGCTA 59.390 50.000 0.00 0.00 0.00 3.32
5632 6046 4.092675 GCAACTTCTCTGCTGTAGATTGAC 59.907 45.833 9.90 0.72 36.84 3.18
5672 6086 7.680730 AGCTGAACCTGAGATTTACTAAAAGA 58.319 34.615 0.00 0.00 0.00 2.52
5678 6092 5.520649 CCTGAGATTTACTAAAAGAGGCGTC 59.479 44.000 0.00 0.00 0.00 5.19
5788 6246 8.612233 TTGAAAATTCAAAATTTTCTTTGGCG 57.388 26.923 26.03 0.00 43.62 5.69
5823 6282 9.726438 AAAATGCTATCCTATTAGGTATGTGAC 57.274 33.333 9.57 0.00 36.53 3.67
5854 6313 3.825143 AATGGCCTGGCAATAATGTTC 57.175 42.857 22.05 0.00 0.00 3.18
5859 6318 2.163412 GCCTGGCAATAATGTTCGTTCA 59.837 45.455 15.17 0.00 0.00 3.18
5879 6338 5.860182 GTTCATTTTGTGATCACCATGAGTG 59.140 40.000 22.85 13.42 39.16 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 1.019805 GCGTACCTGGCAGGAGTTTC 61.020 60.000 38.99 20.54 37.67 2.78
175 176 1.402968 CGCACGGCCTCTACTAAAGTA 59.597 52.381 0.00 0.00 0.00 2.24
278 279 1.468520 CATGTCGAGGGCGTTTGATTT 59.531 47.619 0.00 0.00 38.98 2.17
295 296 4.003648 GGGTGTTCCTGAAGTTAGACATG 58.996 47.826 0.00 0.00 0.00 3.21
472 474 0.035598 TTACCCACAGCGCTGCTAAA 59.964 50.000 36.28 20.05 36.40 1.85
524 526 4.503991 GCTCATCCCTAAGAAATCCGATGT 60.504 45.833 0.00 0.00 0.00 3.06
549 551 9.791820 GTAGTACTTGAGAAGAAGTATTTCCTC 57.208 37.037 0.00 0.00 39.89 3.71
577 579 4.227527 AGTGGGAAATCGGAATTTCTAGGT 59.772 41.667 9.90 0.00 46.65 3.08
672 674 2.288213 TGGTGAGATTCTGTCACGTGAC 60.288 50.000 36.01 36.01 44.52 3.67
673 675 1.960689 TGGTGAGATTCTGTCACGTGA 59.039 47.619 15.76 15.76 44.52 4.35
674 676 2.438868 TGGTGAGATTCTGTCACGTG 57.561 50.000 9.94 9.94 44.52 4.49
675 677 3.469008 TTTGGTGAGATTCTGTCACGT 57.531 42.857 0.00 0.00 44.52 4.49
676 678 4.811555 TTTTTGGTGAGATTCTGTCACG 57.188 40.909 0.00 0.00 44.52 4.35
765 767 1.683441 GAGGGTGGTAGTTGGTGGG 59.317 63.158 0.00 0.00 0.00 4.61
967 975 1.306226 AAACCCTAGCCTCGCCTCT 60.306 57.895 0.00 0.00 0.00 3.69
1102 1114 1.740296 AACACCGAGGGCGAAATCG 60.740 57.895 0.00 0.00 40.82 3.34
1103 1115 1.644786 CCAACACCGAGGGCGAAATC 61.645 60.000 0.00 0.00 40.82 2.17
1104 1116 1.674322 CCAACACCGAGGGCGAAAT 60.674 57.895 0.00 0.00 40.82 2.17
1111 1123 3.530910 AACGAGGCCAACACCGAGG 62.531 63.158 5.01 0.00 33.69 4.63
1112 1124 2.030562 AACGAGGCCAACACCGAG 59.969 61.111 5.01 0.00 33.69 4.63
1113 1125 2.280524 CAACGAGGCCAACACCGA 60.281 61.111 5.01 0.00 33.69 4.69
1114 1126 3.353836 CCAACGAGGCCAACACCG 61.354 66.667 5.01 2.51 33.69 4.94
1115 1127 1.388837 AAACCAACGAGGCCAACACC 61.389 55.000 5.01 0.00 43.14 4.16
1116 1128 0.458260 AAAACCAACGAGGCCAACAC 59.542 50.000 5.01 0.00 43.14 3.32
1117 1129 1.134965 CAAAAACCAACGAGGCCAACA 60.135 47.619 5.01 0.00 43.14 3.33
1118 1130 1.135333 TCAAAAACCAACGAGGCCAAC 59.865 47.619 5.01 0.00 43.14 3.77
1119 1131 1.475403 TCAAAAACCAACGAGGCCAA 58.525 45.000 5.01 0.00 43.14 4.52
1120 1132 1.698506 ATCAAAAACCAACGAGGCCA 58.301 45.000 5.01 0.00 43.14 5.36
1121 1133 2.672714 GAATCAAAAACCAACGAGGCC 58.327 47.619 0.00 0.00 43.14 5.19
1122 1134 2.031508 TCGAATCAAAAACCAACGAGGC 60.032 45.455 0.00 0.00 43.14 4.70
1123 1135 3.551551 GTCGAATCAAAAACCAACGAGG 58.448 45.455 0.00 0.00 45.67 4.63
1124 1136 3.215244 CGTCGAATCAAAAACCAACGAG 58.785 45.455 0.00 0.00 0.00 4.18
1125 1137 2.608546 ACGTCGAATCAAAAACCAACGA 59.391 40.909 0.00 0.00 33.44 3.85
1126 1138 2.976729 ACGTCGAATCAAAAACCAACG 58.023 42.857 0.00 0.00 35.20 4.10
1127 1139 3.484285 CCAACGTCGAATCAAAAACCAAC 59.516 43.478 0.00 0.00 0.00 3.77
1128 1140 3.489398 CCCAACGTCGAATCAAAAACCAA 60.489 43.478 0.00 0.00 0.00 3.67
1129 1141 2.033550 CCCAACGTCGAATCAAAAACCA 59.966 45.455 0.00 0.00 0.00 3.67
1130 1142 2.606065 CCCCAACGTCGAATCAAAAACC 60.606 50.000 0.00 0.00 0.00 3.27
1131 1143 2.657184 CCCCAACGTCGAATCAAAAAC 58.343 47.619 0.00 0.00 0.00 2.43
1137 1149 0.462047 ATCAGCCCCAACGTCGAATC 60.462 55.000 0.00 0.00 0.00 2.52
1372 1385 1.337817 CCGAGCGAGTCACAAGAACG 61.338 60.000 0.00 0.00 0.00 3.95
1373 1386 1.618640 GCCGAGCGAGTCACAAGAAC 61.619 60.000 0.00 0.00 0.00 3.01
1374 1387 1.372997 GCCGAGCGAGTCACAAGAA 60.373 57.895 0.00 0.00 0.00 2.52
1375 1388 2.258591 GCCGAGCGAGTCACAAGA 59.741 61.111 0.00 0.00 0.00 3.02
1376 1389 2.811317 GGCCGAGCGAGTCACAAG 60.811 66.667 0.00 0.00 0.00 3.16
1377 1390 4.717629 CGGCCGAGCGAGTCACAA 62.718 66.667 24.07 0.00 0.00 3.33
1410 1423 7.445402 TCCCATTTCGGCAAAAATTATTTCAAA 59.555 29.630 0.00 0.00 0.00 2.69
1415 1428 5.799213 TGTCCCATTTCGGCAAAAATTATT 58.201 33.333 0.00 0.00 0.00 1.40
1424 1437 2.162608 CGTAAAATGTCCCATTTCGGCA 59.837 45.455 2.92 0.00 0.00 5.69
1452 1465 2.514013 CGTGGCGCATCCTAACGAC 61.514 63.158 10.83 0.00 36.63 4.34
1466 1479 0.673644 ATTTCCGTCCTGAAGCGTGG 60.674 55.000 0.00 0.00 0.00 4.94
1474 1487 4.640201 ACCATTATCAACATTTCCGTCCTG 59.360 41.667 0.00 0.00 0.00 3.86
1502 1515 5.166398 CACTAAAACGTACAGGTCCCTTAG 58.834 45.833 0.00 0.00 0.00 2.18
1508 1521 3.426525 CGAACCACTAAAACGTACAGGTC 59.573 47.826 0.00 0.00 0.00 3.85
1512 1525 3.724508 TCCGAACCACTAAAACGTACA 57.275 42.857 0.00 0.00 0.00 2.90
1578 1591 6.817641 AGTCTCATCTTTTCAGCAATCTACAG 59.182 38.462 0.00 0.00 0.00 2.74
1648 1661 7.418337 AACTTGTTTTCTACATTTCCAACCT 57.582 32.000 0.00 0.00 36.44 3.50
1761 1776 0.534203 GAACGACAGAGGCCAACCAA 60.534 55.000 5.01 0.00 39.06 3.67
1775 1790 5.258841 TCATAAAGACTCCTGTAGGAACGA 58.741 41.667 1.74 0.00 44.91 3.85
1906 1922 4.319177 ACTTTCATCTAGTTGCACCAGTC 58.681 43.478 0.00 0.00 0.00 3.51
1921 1937 8.776376 AACACAAAATTGTTTCAGACTTTCAT 57.224 26.923 0.00 0.00 39.91 2.57
1937 1953 5.937975 ATTGGCCAGCTATAACACAAAAT 57.062 34.783 5.11 0.00 0.00 1.82
1982 1998 4.410099 TCCTCCACTTTCATGCTCAATTT 58.590 39.130 0.00 0.00 0.00 1.82
1990 2006 4.711399 TGAGCATATCCTCCACTTTCATG 58.289 43.478 0.00 0.00 0.00 3.07
2119 2135 6.338146 TCATTACGAATGTTAGGAGAAGTGG 58.662 40.000 0.00 0.00 39.87 4.00
2132 2149 4.783036 CGCTTCACACTTTCATTACGAATG 59.217 41.667 0.00 0.00 40.28 2.67
2154 2171 3.623960 TGGTTGTTGTTCAGAAGTTACCG 59.376 43.478 0.00 0.00 0.00 4.02
2207 2224 5.277828 GCGCCTTATATTTTAGACCAAGTGG 60.278 44.000 0.00 0.00 42.17 4.00
2212 2229 4.131596 GGTGCGCCTTATATTTTAGACCA 58.868 43.478 9.68 0.00 0.00 4.02
2336 2354 7.655328 TGTGGATTGTGTGATTTAAAAATGACC 59.345 33.333 3.15 0.00 32.50 4.02
2418 2436 6.564709 ACTAATTTGGAACGGAGGTAAAAC 57.435 37.500 0.00 0.00 0.00 2.43
2431 2449 9.793259 AGACAAATCTAAGACAACTAATTTGGA 57.207 29.630 9.60 0.00 36.32 3.53
2459 2477 3.377485 CCCTCCGTAGATACATCCGTATG 59.623 52.174 0.00 0.00 38.48 2.39
2498 2516 7.823799 AGCAACTTCTTTTCTTTCCAAATTCAA 59.176 29.630 0.00 0.00 0.00 2.69
2603 2621 3.978867 CTCGTCGTCTCGTGTCGCC 62.979 68.421 0.00 0.00 0.00 5.54
2677 2696 0.465460 TTCTGGACAAAGCAAGCGGT 60.465 50.000 0.00 0.00 0.00 5.68
2869 2893 7.659186 TGAGACTAAGAACTGGAAACTAGAAC 58.341 38.462 0.00 0.00 0.00 3.01
2878 2903 2.180276 GGCCTGAGACTAAGAACTGGA 58.820 52.381 0.00 0.00 0.00 3.86
2880 2905 2.167487 GAGGGCCTGAGACTAAGAACTG 59.833 54.545 12.95 0.00 0.00 3.16
2881 2906 2.043801 AGAGGGCCTGAGACTAAGAACT 59.956 50.000 12.95 0.00 0.00 3.01
2922 2947 1.768275 TGGGACTCAAACTGAAGAGCA 59.232 47.619 0.00 0.00 35.28 4.26
2944 2969 8.941977 ACAAGAAAAACAATTAAAAGTTGGGAC 58.058 29.630 0.00 0.00 0.00 4.46
2945 2970 9.508642 AACAAGAAAAACAATTAAAAGTTGGGA 57.491 25.926 0.00 0.00 0.00 4.37
3048 3074 6.519761 GCAACTGTATCTCAAACAACATAACG 59.480 38.462 0.00 0.00 0.00 3.18
3067 3093 4.865865 GGCCTAGCCTAGCAACTG 57.134 61.111 0.00 0.00 46.69 3.16
3126 3477 5.120830 ACTTCTACTCGATGAAATGTGCAAC 59.879 40.000 0.00 0.00 37.35 4.17
3140 3491 2.293677 AGTGTGACACCACTTCTACTCG 59.706 50.000 12.81 0.00 42.99 4.18
3224 3575 3.612860 GGTAGCAATCGCGAACCATATAG 59.387 47.826 19.45 3.22 44.22 1.31
3226 3577 2.037251 AGGTAGCAATCGCGAACCATAT 59.963 45.455 24.55 5.66 46.06 1.78
3272 3623 8.241497 TCTCTAGTGTCCTTAAACAGTAAACA 57.759 34.615 0.00 0.00 35.27 2.83
3339 3690 1.032014 AACCCAGCAACACACACATC 58.968 50.000 0.00 0.00 0.00 3.06
3371 3722 4.673968 TCTCTCTAGGCTTACAGTCCAAA 58.326 43.478 0.00 0.00 0.00 3.28
3411 3763 7.909485 AAGACTTATATTTAGGAACGGAGGA 57.091 36.000 0.00 0.00 0.00 3.71
3443 3795 7.038302 ACATCCGTATGTAGTCCATATTGGAAT 60.038 37.037 1.81 1.81 45.76 3.01
3444 3796 6.269077 ACATCCGTATGTAGTCCATATTGGAA 59.731 38.462 0.00 0.00 45.76 3.53
3445 3797 5.778241 ACATCCGTATGTAGTCCATATTGGA 59.222 40.000 0.00 3.26 44.66 3.53
3446 3798 6.037786 ACATCCGTATGTAGTCCATATTGG 57.962 41.667 0.00 0.00 44.66 3.16
3474 3826 9.553064 GATGAATCTACACTCCAAAATATGTCT 57.447 33.333 0.00 0.00 0.00 3.41
3475 3827 8.778358 GGATGAATCTACACTCCAAAATATGTC 58.222 37.037 0.00 0.00 0.00 3.06
3476 3828 7.442364 CGGATGAATCTACACTCCAAAATATGT 59.558 37.037 0.00 0.00 0.00 2.29
3477 3829 7.442364 ACGGATGAATCTACACTCCAAAATATG 59.558 37.037 0.00 0.00 0.00 1.78
3478 3830 7.509546 ACGGATGAATCTACACTCCAAAATAT 58.490 34.615 0.00 0.00 0.00 1.28
3479 3831 6.884832 ACGGATGAATCTACACTCCAAAATA 58.115 36.000 0.00 0.00 0.00 1.40
3480 3832 5.745227 ACGGATGAATCTACACTCCAAAAT 58.255 37.500 0.00 0.00 0.00 1.82
3481 3833 5.160607 ACGGATGAATCTACACTCCAAAA 57.839 39.130 0.00 0.00 0.00 2.44
3482 3834 4.819105 ACGGATGAATCTACACTCCAAA 57.181 40.909 0.00 0.00 0.00 3.28
3483 3835 4.819105 AACGGATGAATCTACACTCCAA 57.181 40.909 0.00 0.00 0.00 3.53
3484 3836 4.819105 AAACGGATGAATCTACACTCCA 57.181 40.909 0.00 0.00 0.00 3.86
3485 3837 5.673818 GCAAAAACGGATGAATCTACACTCC 60.674 44.000 0.00 0.00 0.00 3.85
3486 3838 5.122396 AGCAAAAACGGATGAATCTACACTC 59.878 40.000 0.00 0.00 0.00 3.51
3487 3839 5.003804 AGCAAAAACGGATGAATCTACACT 58.996 37.500 0.00 0.00 0.00 3.55
3488 3840 5.296813 AGCAAAAACGGATGAATCTACAC 57.703 39.130 0.00 0.00 0.00 2.90
3489 3841 4.394920 GGAGCAAAAACGGATGAATCTACA 59.605 41.667 0.00 0.00 0.00 2.74
3490 3842 4.494199 CGGAGCAAAAACGGATGAATCTAC 60.494 45.833 0.00 0.00 0.00 2.59
3491 3843 3.621268 CGGAGCAAAAACGGATGAATCTA 59.379 43.478 0.00 0.00 0.00 1.98
3492 3844 2.420022 CGGAGCAAAAACGGATGAATCT 59.580 45.455 0.00 0.00 0.00 2.40
3493 3845 2.161609 ACGGAGCAAAAACGGATGAATC 59.838 45.455 0.00 0.00 0.00 2.52
3494 3846 2.159382 ACGGAGCAAAAACGGATGAAT 58.841 42.857 0.00 0.00 0.00 2.57
3495 3847 1.600023 ACGGAGCAAAAACGGATGAA 58.400 45.000 0.00 0.00 0.00 2.57
3496 3848 2.459060 TACGGAGCAAAAACGGATGA 57.541 45.000 0.00 0.00 0.00 2.92
3497 3849 3.051606 CATACGGAGCAAAAACGGATG 57.948 47.619 0.00 0.00 41.81 3.51
3498 3850 2.706890 ACATACGGAGCAAAAACGGAT 58.293 42.857 0.00 0.00 0.00 4.18
3499 3851 2.172851 ACATACGGAGCAAAAACGGA 57.827 45.000 0.00 0.00 0.00 4.69
3500 3852 2.997986 ACTACATACGGAGCAAAAACGG 59.002 45.455 0.00 0.00 0.00 4.44
3501 3853 4.150980 TGAACTACATACGGAGCAAAAACG 59.849 41.667 0.00 0.00 0.00 3.60
3502 3854 5.600908 TGAACTACATACGGAGCAAAAAC 57.399 39.130 0.00 0.00 0.00 2.43
3503 3855 8.394877 CAATATGAACTACATACGGAGCAAAAA 58.605 33.333 0.00 0.00 43.12 1.94
3504 3856 7.011950 CCAATATGAACTACATACGGAGCAAAA 59.988 37.037 0.00 0.00 43.12 2.44
3505 3857 6.481976 CCAATATGAACTACATACGGAGCAAA 59.518 38.462 0.00 0.00 43.12 3.68
3506 3858 5.989168 CCAATATGAACTACATACGGAGCAA 59.011 40.000 0.00 0.00 43.12 3.91
3507 3859 5.303333 TCCAATATGAACTACATACGGAGCA 59.697 40.000 0.00 0.00 43.12 4.26
3508 3860 5.779922 TCCAATATGAACTACATACGGAGC 58.220 41.667 0.00 0.00 43.12 4.70
3509 3861 8.307483 AGATTCCAATATGAACTACATACGGAG 58.693 37.037 0.00 0.00 42.33 4.63
3510 3862 8.190326 AGATTCCAATATGAACTACATACGGA 57.810 34.615 0.00 0.00 43.12 4.69
3511 3863 8.307483 AGAGATTCCAATATGAACTACATACGG 58.693 37.037 0.00 0.00 43.12 4.02
3512 3864 9.698309 AAGAGATTCCAATATGAACTACATACG 57.302 33.333 0.00 0.00 43.12 3.06
3542 3894 8.019652 ACTCCCTCCATTCCTAAATATAAGTCT 58.980 37.037 0.00 0.00 0.00 3.24
3544 3896 9.327731 CTACTCCCTCCATTCCTAAATATAAGT 57.672 37.037 0.00 0.00 0.00 2.24
3553 3905 8.401955 AAAATTAACTACTCCCTCCATTCCTA 57.598 34.615 0.00 0.00 0.00 2.94
3554 3906 6.910259 AAATTAACTACTCCCTCCATTCCT 57.090 37.500 0.00 0.00 0.00 3.36
3557 3909 8.621073 AGGTAAAAATTAACTACTCCCTCCATT 58.379 33.333 0.00 0.00 0.00 3.16
3559 3911 7.017850 ACAGGTAAAAATTAACTACTCCCTCCA 59.982 37.037 0.00 0.00 0.00 3.86
3560 3912 7.400439 ACAGGTAAAAATTAACTACTCCCTCC 58.600 38.462 0.00 0.00 0.00 4.30
3663 4015 6.207221 TCATCAAACAGTTATGCTCACACAAT 59.793 34.615 0.00 0.00 0.00 2.71
3765 4117 2.835764 TCAAGTGGCCTATTAAGTCCGT 59.164 45.455 3.32 0.00 0.00 4.69
3773 4125 2.756760 CTGCATTGTCAAGTGGCCTATT 59.243 45.455 3.32 0.00 0.00 1.73
3828 4180 2.566833 TTGGCAGCAGTACAGTGAAT 57.433 45.000 0.00 0.00 0.00 2.57
3830 4182 1.347378 TCATTGGCAGCAGTACAGTGA 59.653 47.619 0.00 0.00 0.00 3.41
3854 4207 9.817809 CACACTGTAATATGGTAAAGTCACTAT 57.182 33.333 0.00 0.00 0.00 2.12
3876 4229 4.872691 CCATGTATTCTGAAGAGGACACAC 59.127 45.833 0.00 0.00 0.00 3.82
3928 4281 8.934825 GCTGCATGTATTTTTCATTAAGGAAAA 58.065 29.630 20.75 20.75 43.07 2.29
4371 4724 9.100554 CATCAAGGCTTTGCAATTTTATTCATA 57.899 29.630 0.00 0.00 34.21 2.15
4465 4818 6.037830 CGAAAAGGGATAACCAATACGTCAAT 59.962 38.462 0.00 0.00 43.89 2.57
4476 4829 2.124277 ACAGCCGAAAAGGGATAACC 57.876 50.000 0.00 0.00 41.48 2.85
4489 4842 2.616960 TCAAGCACATACTAACAGCCG 58.383 47.619 0.00 0.00 0.00 5.52
4547 4900 9.765795 ACCTAGTATTTTCTTGGAGAAATATCG 57.234 33.333 4.16 0.00 43.06 2.92
4566 4919 5.165676 CACATGCGTAAGTTCAACCTAGTA 58.834 41.667 0.00 0.00 41.68 1.82
4599 4952 7.820578 AACATACAGATGGGTAGACTACTAC 57.179 40.000 12.31 6.73 40.79 2.73
4717 5071 7.304497 ACCTGCCTATATTTCGAACTTAGAT 57.696 36.000 0.00 0.00 0.00 1.98
4816 5170 3.942829 TCAGCTCTGTAAATTCACCAGG 58.057 45.455 0.00 0.00 0.00 4.45
5047 5404 0.319405 ACCTCCGGTTGGTCGTTAAG 59.681 55.000 14.47 0.00 36.30 1.85
5329 5687 8.303156 CCTCAAATGTCAAATGTACCACAATAA 58.697 33.333 0.00 0.00 0.00 1.40
5330 5688 7.667635 TCCTCAAATGTCAAATGTACCACAATA 59.332 33.333 0.00 0.00 0.00 1.90
5491 5905 7.413877 GGCATGCTATCTATCAAGTTTGCTATC 60.414 40.741 18.92 0.00 0.00 2.08
5492 5906 6.373774 GGCATGCTATCTATCAAGTTTGCTAT 59.626 38.462 18.92 0.00 0.00 2.97
5493 5907 5.702670 GGCATGCTATCTATCAAGTTTGCTA 59.297 40.000 18.92 0.00 0.00 3.49
5494 5908 4.518211 GGCATGCTATCTATCAAGTTTGCT 59.482 41.667 18.92 0.00 0.00 3.91
5495 5909 4.276678 TGGCATGCTATCTATCAAGTTTGC 59.723 41.667 18.92 0.00 0.00 3.68
5496 5910 6.381481 TTGGCATGCTATCTATCAAGTTTG 57.619 37.500 18.92 0.00 0.00 2.93
5497 5911 6.072838 CGATTGGCATGCTATCTATCAAGTTT 60.073 38.462 18.92 0.00 0.00 2.66
5498 5912 5.410746 CGATTGGCATGCTATCTATCAAGTT 59.589 40.000 18.92 0.00 0.00 2.66
5499 5913 4.934001 CGATTGGCATGCTATCTATCAAGT 59.066 41.667 18.92 2.14 0.00 3.16
5500 5914 5.173664 TCGATTGGCATGCTATCTATCAAG 58.826 41.667 18.92 7.32 0.00 3.02
5501 5915 5.151297 TCGATTGGCATGCTATCTATCAA 57.849 39.130 18.92 11.51 0.00 2.57
5502 5916 4.806640 TCGATTGGCATGCTATCTATCA 57.193 40.909 18.92 1.60 0.00 2.15
5503 5917 4.033817 GCTTCGATTGGCATGCTATCTATC 59.966 45.833 18.92 10.68 0.00 2.08
5504 5918 3.937706 GCTTCGATTGGCATGCTATCTAT 59.062 43.478 18.92 1.44 0.00 1.98
5505 5919 3.007290 AGCTTCGATTGGCATGCTATCTA 59.993 43.478 18.92 10.08 0.00 1.98
5506 5920 2.149578 GCTTCGATTGGCATGCTATCT 58.850 47.619 18.92 1.56 0.00 1.98
5507 5921 2.095869 CAGCTTCGATTGGCATGCTATC 60.096 50.000 18.92 18.24 0.00 2.08
5508 5922 1.878088 CAGCTTCGATTGGCATGCTAT 59.122 47.619 18.92 11.50 0.00 2.97
5509 5923 1.302366 CAGCTTCGATTGGCATGCTA 58.698 50.000 18.92 9.16 0.00 3.49
5510 5924 0.679002 ACAGCTTCGATTGGCATGCT 60.679 50.000 18.92 0.00 0.00 3.79
5511 5925 1.016627 TACAGCTTCGATTGGCATGC 58.983 50.000 9.90 9.90 0.00 4.06
5512 5926 4.934001 AGATATACAGCTTCGATTGGCATG 59.066 41.667 7.96 0.00 0.00 4.06
5513 5927 5.157940 AGATATACAGCTTCGATTGGCAT 57.842 39.130 7.96 0.02 0.00 4.40
5514 5928 4.607293 AGATATACAGCTTCGATTGGCA 57.393 40.909 7.96 0.00 0.00 4.92
5515 5929 7.459486 CAATTAGATATACAGCTTCGATTGGC 58.541 38.462 0.00 0.00 0.00 4.52
5516 5930 7.118245 TGCAATTAGATATACAGCTTCGATTGG 59.882 37.037 12.37 0.00 0.00 3.16
5517 5931 8.021955 TGCAATTAGATATACAGCTTCGATTG 57.978 34.615 0.00 0.00 0.00 2.67
5518 5932 7.148507 GCTGCAATTAGATATACAGCTTCGATT 60.149 37.037 5.59 0.00 45.36 3.34
5519 5933 6.312426 GCTGCAATTAGATATACAGCTTCGAT 59.688 38.462 5.59 0.00 45.36 3.59
5520 5934 5.635280 GCTGCAATTAGATATACAGCTTCGA 59.365 40.000 5.59 0.00 45.36 3.71
5521 5935 5.852005 GCTGCAATTAGATATACAGCTTCG 58.148 41.667 5.59 0.00 45.36 3.79
5551 5965 7.389330 TGAATTTCGTTCCGGTGCATATATAAT 59.611 33.333 0.00 0.00 35.91 1.28
5590 6004 8.737168 AAGTTGCAATTAGATGTATAGCTTCA 57.263 30.769 0.59 0.00 0.00 3.02
5597 6011 7.012138 CAGCAGAGAAGTTGCAATTAGATGTAT 59.988 37.037 0.59 0.00 43.92 2.29
5632 6046 4.695928 GGTTCAGCTTTTCTAGGTAAGGTG 59.304 45.833 21.11 21.11 46.11 4.00
5672 6086 1.272769 GACTTGGTAGTGAAGACGCCT 59.727 52.381 0.00 0.00 33.84 5.52
5678 6092 4.184629 GGTGCATAGACTTGGTAGTGAAG 58.815 47.826 0.00 0.00 33.84 3.02
5788 6246 3.033909 AGGATAGCATTTTGAAAGGGCC 58.966 45.455 0.00 0.00 0.00 5.80
5823 6282 1.799994 CCAGGCCATTTTTCTTTTGCG 59.200 47.619 5.01 0.00 0.00 4.85
5854 6313 5.045668 TCATGGTGATCACAAAATGAACG 57.954 39.130 26.47 6.25 41.93 3.95


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

AutoCloner maintained by Alex Coulton.