Multiple sequence alignment - TraesCS2A01G168300

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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 TraesCS2A01G168300 chr2A 100.000 3978 0 0 1 3978 121214739 121218716 0.000000e+00 7347.0
1 TraesCS2A01G168300 chr2A 87.705 122 15 0 1025 1146 231290872 231290993 4.140000e-30 143.0
2 TraesCS2A01G168300 chr2D 93.484 2916 137 26 468 3343 119262631 119265533 0.000000e+00 4283.0
3 TraesCS2A01G168300 chr2D 94.703 472 20 4 1 470 119253053 119253521 0.000000e+00 728.0
4 TraesCS2A01G168300 chr2D 79.024 553 79 23 1 539 119252052 119252581 1.060000e-90 344.0
5 TraesCS2A01G168300 chr2D 88.312 154 14 3 3038 3190 162717318 162717468 8.780000e-42 182.0
6 TraesCS2A01G168300 chr2D 87.586 145 12 4 3010 3150 82317265 82317407 3.180000e-36 163.0
7 TraesCS2A01G168300 chr2B 92.326 2958 143 41 682 3579 171452925 171455858 0.000000e+00 4128.0
8 TraesCS2A01G168300 chr2B 90.253 554 43 10 1 550 171452152 171452698 0.000000e+00 713.0
9 TraesCS2A01G168300 chr2B 82.759 232 19 10 3749 3978 171456127 171456339 1.890000e-43 187.0
10 TraesCS2A01G168300 chr2B 97.222 72 1 1 3209 3279 535562801 535562730 1.940000e-23 121.0
11 TraesCS2A01G168300 chr4D 77.408 571 104 19 1687 2234 467437536 467436968 2.310000e-82 316.0
12 TraesCS2A01G168300 chr4D 94.262 122 7 0 1025 1146 467437932 467437811 1.890000e-43 187.0
13 TraesCS2A01G168300 chr4D 82.857 105 13 3 2318 2422 467436879 467436780 5.480000e-14 89.8
14 TraesCS2A01G168300 chr7B 86.294 197 23 3 3038 3233 52156898 52156705 1.120000e-50 211.0
15 TraesCS2A01G168300 chr4B 85.222 203 30 0 2032 2234 585464368 585464166 4.030000e-50 209.0
16 TraesCS2A01G168300 chr4B 94.262 122 7 0 1025 1146 585465108 585464987 1.890000e-43 187.0
17 TraesCS2A01G168300 chr4B 87.500 128 9 4 3010 3132 199808083 199807958 1.490000e-29 141.0
18 TraesCS2A01G168300 chr4B 98.611 72 0 1 3209 3279 195134377 195134306 4.170000e-25 126.0
19 TraesCS2A01G168300 chr4B 82.857 105 13 3 2318 2422 585464077 585463978 5.480000e-14 89.8
20 TraesCS2A01G168300 chr4A 84.236 203 32 0 2032 2234 3446953 3447155 8.720000e-47 198.0
21 TraesCS2A01G168300 chr4A 94.262 122 7 0 1025 1146 3446199 3446320 1.890000e-43 187.0
22 TraesCS2A01G168300 chr6D 85.366 164 22 2 2032 2194 450750006 450750168 6.840000e-38 169.0
23 TraesCS2A01G168300 chr7A 90.164 122 12 0 1025 1146 641827441 641827320 4.110000e-35 159.0
24 TraesCS2A01G168300 chr7A 86.207 145 14 4 3010 3150 44775247 44775105 6.890000e-33 152.0
25 TraesCS2A01G168300 chr7A 83.333 162 25 2 2038 2198 641826698 641826538 8.910000e-32 148.0
26 TraesCS2A01G168300 chr7A 91.765 85 6 1 3194 3277 369892022 369892106 2.510000e-22 117.0
27 TraesCS2A01G168300 chr1B 88.000 125 9 3 3015 3134 86444576 86444453 4.140000e-30 143.0
28 TraesCS2A01G168300 chr1B 93.103 87 5 1 3194 3279 399625324 399625410 4.170000e-25 126.0
29 TraesCS2A01G168300 chr6B 86.719 128 10 4 3010 3132 623517092 623517217 6.930000e-28 135.0
30 TraesCS2A01G168300 chr3B 92.941 85 5 1 3194 3277 511909178 511909262 5.400000e-24 122.0
31 TraesCS2A01G168300 chr5A 89.535 86 7 1 3194 3277 109630018 109630103 1.510000e-19 108.0
32 TraesCS2A01G168300 chr1D 95.745 47 2 0 2331 2377 442083503 442083457 4.260000e-10 76.8
33 TraesCS2A01G168300 chr1A 97.727 44 1 0 2331 2374 536444595 536444638 4.260000e-10 76.8


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 TraesCS2A01G168300 chr2A 121214739 121218716 3977 False 7347 7347 100.0000 1 3978 1 chr2A.!!$F1 3977
1 TraesCS2A01G168300 chr2D 119262631 119265533 2902 False 4283 4283 93.4840 468 3343 1 chr2D.!!$F2 2875
2 TraesCS2A01G168300 chr2D 119252052 119253521 1469 False 536 728 86.8635 1 539 2 chr2D.!!$F4 538
3 TraesCS2A01G168300 chr2B 171452152 171456339 4187 False 1676 4128 88.4460 1 3978 3 chr2B.!!$F1 3977

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
643 1691 0.039527 GCATCCAAACAACCACGTCC 60.040 55.0 0.0 0.0 0.00 4.79 F
1280 2393 0.104855 GATCTAGGCATGTGCGGTCA 59.895 55.0 0.0 0.0 43.26 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1764 2898 1.629861 TGCACAATGATGTCCTGAGGA 59.37 47.619 0.00 0.00 37.82 3.71 R
3160 4301 1.639635 ATAACTCCCAGCCCCTGCAG 61.64 60.000 6.78 6.78 41.13 4.41 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
56 1058 9.626045 CTACCTTTGAAAATTGTACAAGAATCC 57.374 33.333 14.65 3.10 0.00 3.01
129 1131 4.671377 GTTTTCACATCTTGAAGTGCACA 58.329 39.130 21.04 0.00 45.22 4.57
149 1151 7.012704 GTGCACATCTTAACAATCCATATGACT 59.987 37.037 13.17 0.00 0.00 3.41
161 1163 9.042008 ACAATCCATATGACTACGTAATGTTTC 57.958 33.333 3.65 0.00 0.00 2.78
162 1164 9.261180 CAATCCATATGACTACGTAATGTTTCT 57.739 33.333 3.65 0.00 0.00 2.52
163 1165 9.832445 AATCCATATGACTACGTAATGTTTCTT 57.168 29.630 3.65 0.00 0.00 2.52
216 1218 7.396339 TGCTATCTTATGGAATAGTACCACGAT 59.604 37.037 0.00 0.00 40.36 3.73
259 1261 6.940714 GCATTCATTTTCTGCCAATATCAAC 58.059 36.000 0.00 0.00 0.00 3.18
319 1322 8.548721 GGTTGACGATAATAATGTTTCCTACAG 58.451 37.037 0.00 0.00 40.83 2.74
470 1476 2.247372 TCCTATGACATCCTCTGGGTCA 59.753 50.000 0.00 0.00 44.73 4.02
480 1486 1.198713 CTCTGGGTCATAGTGCCACT 58.801 55.000 1.54 1.54 0.00 4.00
554 1560 5.921976 TCTAAACATCGCTCGAACTTACAAA 59.078 36.000 0.00 0.00 0.00 2.83
560 1566 4.052608 TCGCTCGAACTTACAAAACATGA 58.947 39.130 0.00 0.00 0.00 3.07
584 1626 7.233553 TGACATTTGTTTCTCCTCTTCTCTCTA 59.766 37.037 0.00 0.00 0.00 2.43
585 1627 7.967908 ACATTTGTTTCTCCTCTTCTCTCTAA 58.032 34.615 0.00 0.00 0.00 2.10
586 1628 8.432805 ACATTTGTTTCTCCTCTTCTCTCTAAA 58.567 33.333 0.00 0.00 0.00 1.85
589 1637 8.894768 TTGTTTCTCCTCTTCTCTCTAAAAAG 57.105 34.615 0.00 0.00 0.00 2.27
591 1639 8.875168 TGTTTCTCCTCTTCTCTCTAAAAAGAT 58.125 33.333 0.00 0.00 0.00 2.40
642 1690 0.951558 AGCATCCAAACAACCACGTC 59.048 50.000 0.00 0.00 0.00 4.34
643 1691 0.039527 GCATCCAAACAACCACGTCC 60.040 55.000 0.00 0.00 0.00 4.79
653 1701 1.663643 CAACCACGTCCATACCATTCG 59.336 52.381 0.00 0.00 0.00 3.34
666 1714 5.446709 CATACCATTCGTGCATTTCAGATC 58.553 41.667 0.00 0.00 0.00 2.75
705 1812 5.069516 ACATGGCATCAAATTCCTACAATCC 59.930 40.000 0.00 0.00 0.00 3.01
710 1817 5.733373 GCATCAAATTCCTACAATCCGTTCC 60.733 44.000 0.00 0.00 0.00 3.62
719 1826 5.424252 TCCTACAATCCGTTCCATTTCTACT 59.576 40.000 0.00 0.00 0.00 2.57
720 1827 6.070424 TCCTACAATCCGTTCCATTTCTACTT 60.070 38.462 0.00 0.00 0.00 2.24
729 1836 7.067737 TCCGTTCCATTTCTACTTTTTGTTTCT 59.932 33.333 0.00 0.00 0.00 2.52
746 1853 7.810766 TTGTTTCTTGTCTTGTGTTTCAATC 57.189 32.000 0.00 0.00 35.35 2.67
764 1871 3.584733 ATCTTCAAATAGTCCTGGGCC 57.415 47.619 0.00 0.00 0.00 5.80
788 1895 3.363178 CAGAAACCTCAGAAACGCAAAC 58.637 45.455 0.00 0.00 0.00 2.93
1167 2274 2.690778 GCGAATCCCTTTGCGCTGT 61.691 57.895 9.73 0.00 45.41 4.40
1169 2276 0.240945 CGAATCCCTTTGCGCTGTTT 59.759 50.000 9.73 0.00 0.00 2.83
1203 2310 4.212847 TCTTAGAAATCGTAGATCCGTCCG 59.787 45.833 0.00 0.00 45.12 4.79
1205 2312 2.033049 AGAAATCGTAGATCCGTCCGTG 59.967 50.000 0.00 0.00 45.12 4.94
1207 2314 1.793134 ATCGTAGATCCGTCCGTGCC 61.793 60.000 0.00 0.00 45.12 5.01
1208 2315 2.767445 CGTAGATCCGTCCGTGCCA 61.767 63.158 0.00 0.00 0.00 4.92
1216 2323 0.956410 CCGTCCGTGCCATTGGTTTA 60.956 55.000 4.26 0.00 0.00 2.01
1217 2324 1.091537 CGTCCGTGCCATTGGTTTAT 58.908 50.000 4.26 0.00 0.00 1.40
1251 2358 5.562696 CGAGAAAGCTGCTGTTAAATCCAAA 60.563 40.000 1.35 0.00 0.00 3.28
1252 2359 5.776744 AGAAAGCTGCTGTTAAATCCAAAG 58.223 37.500 1.35 0.00 0.00 2.77
1257 2364 7.321745 AGCTGCTGTTAAATCCAAAGTATAC 57.678 36.000 0.00 0.00 0.00 1.47
1279 2392 0.601311 GGATCTAGGCATGTGCGGTC 60.601 60.000 0.00 0.00 43.26 4.79
1280 2393 0.104855 GATCTAGGCATGTGCGGTCA 59.895 55.000 0.00 0.00 43.26 4.02
1281 2394 0.541392 ATCTAGGCATGTGCGGTCAA 59.459 50.000 0.00 0.00 43.26 3.18
1292 2405 0.398696 TGCGGTCAATAGGTTGTGGT 59.601 50.000 0.00 0.00 36.69 4.16
1294 2407 1.880646 GCGGTCAATAGGTTGTGGTGT 60.881 52.381 0.00 0.00 36.69 4.16
1317 2431 8.395633 GTGTAGTGCTTACTTGTTAATTATGGG 58.604 37.037 0.00 0.00 33.23 4.00
1322 2436 2.361789 ACTTGTTAATTATGGGCGCGT 58.638 42.857 8.43 0.00 0.00 6.01
1335 2449 2.321060 CGCGTGCGATGGAATGAC 59.679 61.111 8.89 0.00 42.83 3.06
1376 2490 5.743398 GCATGCTGTGCGAAAATATTTCTTA 59.257 36.000 11.37 0.00 45.23 2.10
1463 2578 5.824904 ATGTAACTTGATGATTCAGTGGC 57.175 39.130 0.00 0.00 32.27 5.01
1545 2671 7.102346 AGAGTCTGGAATCACTGTATTTTCAG 58.898 38.462 0.00 4.56 40.80 3.02
1565 2691 8.628630 TTTCAGATGGTGTCATTTAACATGTA 57.371 30.769 0.00 0.00 32.98 2.29
1566 2692 8.628630 TTCAGATGGTGTCATTTAACATGTAA 57.371 30.769 0.00 0.00 32.98 2.41
1567 2693 8.806429 TCAGATGGTGTCATTTAACATGTAAT 57.194 30.769 0.00 0.00 32.98 1.89
1568 2694 9.241919 TCAGATGGTGTCATTTAACATGTAATT 57.758 29.630 0.00 0.00 32.98 1.40
1569 2695 9.507280 CAGATGGTGTCATTTAACATGTAATTC 57.493 33.333 0.00 0.00 32.98 2.17
1570 2696 9.241919 AGATGGTGTCATTTAACATGTAATTCA 57.758 29.630 0.00 0.00 32.98 2.57
1623 2757 7.652507 ACTGCTTTAGTGTAGAGTAAACAGTTC 59.347 37.037 18.79 3.06 36.80 3.01
1630 2764 7.210873 AGTGTAGAGTAAACAGTTCCTTTCAG 58.789 38.462 0.00 0.00 0.00 3.02
1642 2776 6.775629 ACAGTTCCTTTCAGCAATTTACCTTA 59.224 34.615 0.00 0.00 0.00 2.69
1764 2898 4.021192 AGGGTCATTGTTGCGATTGAAAAT 60.021 37.500 0.00 0.00 0.00 1.82
1966 3101 5.916661 TCACCAGGTACACTTCTATTCTC 57.083 43.478 0.00 0.00 0.00 2.87
2081 3216 1.077265 CCCCACCATTGCCTTCTGT 59.923 57.895 0.00 0.00 0.00 3.41
2247 3382 7.014615 GGGAAATCATGGTTAGCTTTCACATAT 59.985 37.037 0.00 0.00 31.21 1.78
2277 3412 5.536161 AGTCTGCTTGTCATTGTTTGGTTAT 59.464 36.000 0.00 0.00 0.00 1.89
2547 3682 0.890683 GGTGCTCCAGGTTTGAATGG 59.109 55.000 0.00 0.00 37.97 3.16
2624 3759 3.319122 GTCTCAGTTTCAGCCCACATTTT 59.681 43.478 0.00 0.00 0.00 1.82
2637 3772 4.019174 CCCACATTTTAGATCAACCTGCT 58.981 43.478 0.00 0.00 0.00 4.24
2650 3785 4.832248 TCAACCTGCTGTCCTAGTTTATG 58.168 43.478 0.00 0.00 0.00 1.90
2651 3786 4.286032 TCAACCTGCTGTCCTAGTTTATGT 59.714 41.667 0.00 0.00 0.00 2.29
2694 3829 1.704628 TGGTCTTTGCTTGATCTGGGA 59.295 47.619 0.00 0.00 0.00 4.37
2732 3871 7.123547 TCAAGTTCACATTTAATTCATACCCCC 59.876 37.037 0.00 0.00 0.00 5.40
2738 3877 9.548631 TCACATTTAATTCATACCCCCTTTTTA 57.451 29.630 0.00 0.00 0.00 1.52
2751 3891 4.495565 CCCCTTTTTAACCCTACCCTTTT 58.504 43.478 0.00 0.00 0.00 2.27
2752 3892 5.460869 CCCCCTTTTTAACCCTACCCTTTTA 60.461 44.000 0.00 0.00 0.00 1.52
2772 3913 7.650903 CCTTTTAAGATGCCATTTGCTATTCTC 59.349 37.037 0.00 0.00 42.00 2.87
2835 3976 6.169094 TGTTTGAAGCCTGAAATGTTCAAAA 58.831 32.000 9.90 0.97 45.59 2.44
3041 4182 1.293963 GGAGTTCGGCCGTGGTTTAC 61.294 60.000 27.15 14.00 0.00 2.01
3160 4301 4.749245 TCGATTTTTGTCTTCTTGGCTC 57.251 40.909 0.00 0.00 0.00 4.70
3169 4310 3.574074 TTCTTGGCTCTGCAGGGGC 62.574 63.158 32.16 32.16 41.68 5.80
3195 4336 0.255890 TTATCACCCCAGCCTTCTGC 59.744 55.000 0.00 0.00 39.00 4.26
3294 4435 1.722034 AGCCCGGATCATGTGATACT 58.278 50.000 0.73 0.00 33.17 2.12
3344 4488 2.617250 TTGCTCATAACTTGCAAGCG 57.383 45.000 26.27 12.31 41.06 4.68
3348 4511 2.350522 CTCATAACTTGCAAGCGGTCT 58.649 47.619 26.27 3.26 0.00 3.85
3352 4515 5.666462 TCATAACTTGCAAGCGGTCTTATA 58.334 37.500 26.27 7.21 0.00 0.98
3366 4529 5.503357 GCGGTCTTATAATCGTTGCATTTCA 60.503 40.000 0.00 0.00 0.00 2.69
3377 4540 0.318869 TGCATTTCAAAGGCAGCACG 60.319 50.000 5.11 0.00 32.95 5.34
3389 4552 1.154225 CAGCACGAAATTGGTCGGC 60.154 57.895 4.68 5.10 45.40 5.54
3400 4563 4.719369 GGTCGGCGCGTCTCTGTT 62.719 66.667 9.90 0.00 0.00 3.16
3409 4572 0.603975 GCGTCTCTGTTCCTGGCTTT 60.604 55.000 0.00 0.00 0.00 3.51
3410 4573 1.151668 CGTCTCTGTTCCTGGCTTTG 58.848 55.000 0.00 0.00 0.00 2.77
3411 4574 1.528129 GTCTCTGTTCCTGGCTTTGG 58.472 55.000 0.00 0.00 0.00 3.28
3412 4575 1.140312 TCTCTGTTCCTGGCTTTGGT 58.860 50.000 0.00 0.00 0.00 3.67
3413 4576 1.494721 TCTCTGTTCCTGGCTTTGGTT 59.505 47.619 0.00 0.00 0.00 3.67
3414 4577 1.882623 CTCTGTTCCTGGCTTTGGTTC 59.117 52.381 0.00 0.00 0.00 3.62
3415 4578 1.494721 TCTGTTCCTGGCTTTGGTTCT 59.505 47.619 0.00 0.00 0.00 3.01
3416 4579 2.091885 TCTGTTCCTGGCTTTGGTTCTT 60.092 45.455 0.00 0.00 0.00 2.52
3417 4580 2.695147 CTGTTCCTGGCTTTGGTTCTTT 59.305 45.455 0.00 0.00 0.00 2.52
3418 4581 2.430332 TGTTCCTGGCTTTGGTTCTTTG 59.570 45.455 0.00 0.00 0.00 2.77
3419 4582 1.039856 TCCTGGCTTTGGTTCTTTGC 58.960 50.000 0.00 0.00 0.00 3.68
3420 4583 0.752054 CCTGGCTTTGGTTCTTTGCA 59.248 50.000 0.00 0.00 0.00 4.08
3421 4584 1.345415 CCTGGCTTTGGTTCTTTGCAT 59.655 47.619 0.00 0.00 0.00 3.96
3422 4585 2.224354 CCTGGCTTTGGTTCTTTGCATT 60.224 45.455 0.00 0.00 0.00 3.56
3429 4592 1.336440 TGGTTCTTTGCATTGGACACG 59.664 47.619 0.00 0.00 0.00 4.49
3435 4598 3.129462 TCTTTGCATTGGACACGAACAAA 59.871 39.130 0.00 0.00 0.00 2.83
3446 4609 6.721321 TGGACACGAACAAACTCTAATTTTC 58.279 36.000 0.00 0.00 0.00 2.29
3451 4614 7.065324 ACACGAACAAACTCTAATTTTCAGTGA 59.935 33.333 0.00 0.00 0.00 3.41
3491 4664 0.743688 AATTGTGAACGTGCTGGCAA 59.256 45.000 0.00 0.00 0.00 4.52
3516 4689 4.097892 ACGAATGCTTCCAACCCATAAATC 59.902 41.667 0.00 0.00 0.00 2.17
3520 4693 4.272489 TGCTTCCAACCCATAAATCTCTG 58.728 43.478 0.00 0.00 0.00 3.35
3522 4695 4.336713 GCTTCCAACCCATAAATCTCTGAC 59.663 45.833 0.00 0.00 0.00 3.51
3556 4729 3.443045 CCATGCACCCCAGCGAAC 61.443 66.667 0.00 0.00 37.31 3.95
3569 4742 1.959042 AGCGAACATGGGCTGAATAG 58.041 50.000 7.29 0.00 38.27 1.73
3584 4757 5.649782 CTGAATAGCATCACCCTGTTTTT 57.350 39.130 0.00 0.00 0.00 1.94
3633 4806 9.371136 TGTTTATAGAGATACAAAACAGAGCTG 57.629 33.333 0.00 0.00 35.69 4.24
3634 4807 8.821894 GTTTATAGAGATACAAAACAGAGCTGG 58.178 37.037 0.00 0.00 31.85 4.85
3635 4808 6.798427 ATAGAGATACAAAACAGAGCTGGA 57.202 37.500 0.00 0.00 34.19 3.86
3636 4809 5.083533 AGAGATACAAAACAGAGCTGGAG 57.916 43.478 0.00 0.00 34.19 3.86
3637 4810 4.081198 AGAGATACAAAACAGAGCTGGAGG 60.081 45.833 0.00 0.00 34.19 4.30
3638 4811 3.840666 AGATACAAAACAGAGCTGGAGGA 59.159 43.478 0.00 0.00 34.19 3.71
3639 4812 4.287067 AGATACAAAACAGAGCTGGAGGAA 59.713 41.667 0.00 0.00 34.19 3.36
3641 4814 3.416156 ACAAAACAGAGCTGGAGGAATC 58.584 45.455 0.00 0.00 34.19 2.52
3643 4816 0.915364 AACAGAGCTGGAGGAATCCC 59.085 55.000 0.00 0.00 34.19 3.85
3655 4828 2.243810 AGGAATCCCTCGTCATCTAGC 58.756 52.381 0.00 0.00 38.86 3.42
3656 4829 1.964223 GGAATCCCTCGTCATCTAGCA 59.036 52.381 0.00 0.00 0.00 3.49
3657 4830 2.365617 GGAATCCCTCGTCATCTAGCAA 59.634 50.000 0.00 0.00 0.00 3.91
3658 4831 3.553922 GGAATCCCTCGTCATCTAGCAAG 60.554 52.174 0.00 0.00 0.00 4.01
3659 4832 2.145397 TCCCTCGTCATCTAGCAAGT 57.855 50.000 0.00 0.00 0.00 3.16
3660 4833 1.751351 TCCCTCGTCATCTAGCAAGTG 59.249 52.381 0.00 0.00 0.00 3.16
3661 4834 1.565305 CCTCGTCATCTAGCAAGTGC 58.435 55.000 0.00 0.00 42.49 4.40
3662 4835 1.565305 CTCGTCATCTAGCAAGTGCC 58.435 55.000 0.00 0.00 43.38 5.01
3663 4836 0.894835 TCGTCATCTAGCAAGTGCCA 59.105 50.000 0.00 0.00 43.38 4.92
3664 4837 1.275010 TCGTCATCTAGCAAGTGCCAA 59.725 47.619 0.00 0.00 43.38 4.52
3665 4838 2.076100 CGTCATCTAGCAAGTGCCAAA 58.924 47.619 0.00 0.00 43.38 3.28
3666 4839 2.159653 CGTCATCTAGCAAGTGCCAAAC 60.160 50.000 0.00 0.00 43.38 2.93
3667 4840 3.077359 GTCATCTAGCAAGTGCCAAACT 58.923 45.455 0.00 0.00 43.38 2.66
3668 4841 4.253685 GTCATCTAGCAAGTGCCAAACTA 58.746 43.478 0.00 0.00 43.38 2.24
3669 4842 4.878397 GTCATCTAGCAAGTGCCAAACTAT 59.122 41.667 0.00 0.00 43.38 2.12
3670 4843 6.049149 GTCATCTAGCAAGTGCCAAACTATA 58.951 40.000 0.00 0.00 43.38 1.31
3671 4844 6.018669 GTCATCTAGCAAGTGCCAAACTATAC 60.019 42.308 0.00 0.00 43.38 1.47
3677 4850 3.328382 AGTGCCAAACTATACGCTTGA 57.672 42.857 0.00 0.00 37.36 3.02
3685 4858 6.607689 CCAAACTATACGCTTGAAAATGACA 58.392 36.000 0.00 0.00 0.00 3.58
3686 4859 7.081349 CCAAACTATACGCTTGAAAATGACAA 58.919 34.615 0.00 0.00 0.00 3.18
3687 4860 7.271223 CCAAACTATACGCTTGAAAATGACAAG 59.729 37.037 0.00 0.00 44.92 3.16
3688 4861 7.435068 AACTATACGCTTGAAAATGACAAGT 57.565 32.000 0.00 0.00 44.25 3.16
3689 4862 7.435068 ACTATACGCTTGAAAATGACAAGTT 57.565 32.000 0.00 0.00 44.25 2.66
3691 4864 8.015658 ACTATACGCTTGAAAATGACAAGTTTC 58.984 33.333 0.00 7.65 44.25 2.78
3697 4872 5.886715 TGAAAATGACAAGTTTCGCAATG 57.113 34.783 9.28 0.00 42.03 2.82
3707 4882 2.821969 AGTTTCGCAATGCAAAGATCCT 59.178 40.909 5.91 0.00 0.00 3.24
3708 4883 3.256631 AGTTTCGCAATGCAAAGATCCTT 59.743 39.130 5.91 0.00 0.00 3.36
3709 4884 2.925578 TCGCAATGCAAAGATCCTTG 57.074 45.000 5.91 0.00 0.00 3.61
3712 4887 1.917273 CAATGCAAAGATCCTTGGCG 58.083 50.000 6.20 0.00 0.00 5.69
3714 4889 1.386533 ATGCAAAGATCCTTGGCGAG 58.613 50.000 6.20 0.00 0.00 5.03
3718 4893 2.704572 CAAAGATCCTTGGCGAGAACT 58.295 47.619 2.43 0.00 0.00 3.01
3719 4894 3.861840 CAAAGATCCTTGGCGAGAACTA 58.138 45.455 2.43 0.00 0.00 2.24
3720 4895 3.528597 AAGATCCTTGGCGAGAACTAC 57.471 47.619 2.43 0.00 0.00 2.73
3732 4907 1.819903 GAGAACTACCGCCTCTCACTT 59.180 52.381 0.00 0.00 36.43 3.16
3733 4908 2.231721 GAGAACTACCGCCTCTCACTTT 59.768 50.000 0.00 0.00 36.43 2.66
3745 4920 3.136763 CTCTCACTTTCTGCAAGCTTCA 58.863 45.455 0.00 0.00 35.65 3.02
3746 4921 3.544684 TCTCACTTTCTGCAAGCTTCAA 58.455 40.909 0.00 0.00 35.65 2.69
3750 5065 4.098349 TCACTTTCTGCAAGCTTCAAATGT 59.902 37.500 0.00 0.00 35.65 2.71
3760 5075 4.691860 AGCTTCAAATGTTTCTGGATCG 57.308 40.909 0.00 0.00 0.00 3.69
3772 5087 2.184020 CTGGATCGTTGGTGCCCTCA 62.184 60.000 0.00 0.00 0.00 3.86
3792 5107 1.444119 AAACACAACTGCCGATGCGT 61.444 50.000 0.00 0.00 41.78 5.24
3794 5109 2.030412 ACAACTGCCGATGCGTCA 59.970 55.556 6.75 0.00 41.78 4.35
3823 5138 6.278363 ACTATACGTTGACAACACTTCTGTT 58.722 36.000 18.09 1.94 41.61 3.16
3824 5139 5.652744 ATACGTTGACAACACTTCTGTTC 57.347 39.130 18.09 0.00 38.66 3.18
3825 5140 2.347452 ACGTTGACAACACTTCTGTTCG 59.653 45.455 18.09 2.90 38.66 3.95
3826 5141 2.347452 CGTTGACAACACTTCTGTTCGT 59.653 45.455 18.09 0.00 38.66 3.85
3827 5142 3.548668 CGTTGACAACACTTCTGTTCGTA 59.451 43.478 18.09 0.00 38.66 3.43
3828 5143 4.317139 CGTTGACAACACTTCTGTTCGTAG 60.317 45.833 18.09 0.00 38.66 3.51
3829 5144 3.120792 TGACAACACTTCTGTTCGTAGC 58.879 45.455 0.00 0.00 38.66 3.58
3830 5145 3.181479 TGACAACACTTCTGTTCGTAGCT 60.181 43.478 0.00 0.00 38.66 3.32
3831 5146 3.793559 ACAACACTTCTGTTCGTAGCTT 58.206 40.909 0.00 0.00 38.66 3.74
3832 5147 4.189231 ACAACACTTCTGTTCGTAGCTTT 58.811 39.130 0.00 0.00 38.66 3.51
3833 5148 4.034048 ACAACACTTCTGTTCGTAGCTTTG 59.966 41.667 0.00 0.00 38.66 2.77
3834 5149 3.131396 ACACTTCTGTTCGTAGCTTTGG 58.869 45.455 0.00 0.00 0.00 3.28
3835 5150 2.096218 CACTTCTGTTCGTAGCTTTGGC 60.096 50.000 0.00 0.00 39.06 4.52
3836 5151 2.143122 CTTCTGTTCGTAGCTTTGGCA 58.857 47.619 0.00 0.00 41.70 4.92
3837 5152 2.248280 TCTGTTCGTAGCTTTGGCAA 57.752 45.000 0.00 0.00 41.70 4.52
3838 5153 1.871039 TCTGTTCGTAGCTTTGGCAAC 59.129 47.619 0.00 0.00 41.70 4.17
3859 5174 3.868985 ACCGACCACGCCCAACTT 61.869 61.111 0.00 0.00 38.29 2.66
3860 5175 3.353836 CCGACCACGCCCAACTTG 61.354 66.667 0.00 0.00 38.29 3.16
3883 5199 0.039618 TGCCCACCAAAGGAGGAATC 59.960 55.000 0.76 0.00 35.40 2.52
3893 5209 0.398664 AGGAGGAATCCACTACCGGG 60.399 60.000 6.32 0.00 0.00 5.73
3908 5224 1.743252 CGGGCTTCTTGCAGGTCTC 60.743 63.158 0.00 0.00 45.15 3.36
3909 5225 1.376466 GGGCTTCTTGCAGGTCTCA 59.624 57.895 0.00 0.00 45.15 3.27
3910 5226 0.034670 GGGCTTCTTGCAGGTCTCAT 60.035 55.000 0.00 0.00 45.15 2.90
3913 5230 2.355108 GGCTTCTTGCAGGTCTCATGTA 60.355 50.000 0.00 0.00 45.15 2.29
3919 5236 4.406649 TCTTGCAGGTCTCATGTATGATCA 59.593 41.667 0.00 0.00 36.02 2.92
3920 5237 4.063998 TGCAGGTCTCATGTATGATCAC 57.936 45.455 0.00 0.00 36.02 3.06
3930 5247 6.836007 TCTCATGTATGATCACAGAGGTACTT 59.164 38.462 0.00 0.00 35.48 2.24
3933 5250 5.965922 TGTATGATCACAGAGGTACTTGTG 58.034 41.667 15.10 15.10 41.55 3.33
3967 5284 2.476873 TCGATAGCGAGCTCTGAAAC 57.523 50.000 12.85 0.00 42.51 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.956377 CCCAGAGGGCGTCATAGT 58.044 61.111 10.15 0.00 35.35 2.12
56 1058 3.255642 TCCAAAATGCGAAGGAAAGGAAG 59.744 43.478 0.00 0.00 0.00 3.46
216 1218 2.029739 TGCCTCGTCATCGTAGTTGAAA 60.030 45.455 0.00 0.00 38.33 2.69
259 1261 2.034254 CGAGTCACATTTATGCAGAGCG 60.034 50.000 0.00 0.00 0.00 5.03
319 1322 0.038166 TCTGCAATTCCAGGGGTGAC 59.962 55.000 0.00 0.00 33.64 3.67
470 1476 8.584157 TGTATGATTTTTCAAAAGTGGCACTAT 58.416 29.630 22.37 10.42 0.00 2.12
524 1530 5.517054 AGTTCGAGCGATGTTTAGATTCTTC 59.483 40.000 0.00 0.00 0.00 2.87
529 1535 5.647589 TGTAAGTTCGAGCGATGTTTAGAT 58.352 37.500 0.00 0.00 0.00 1.98
554 1560 6.774656 AGAAGAGGAGAAACAAATGTCATGTT 59.225 34.615 0.00 0.00 42.56 2.71
560 1566 6.432403 AGAGAGAAGAGGAGAAACAAATGT 57.568 37.500 0.00 0.00 0.00 2.71
589 1637 8.842358 TCCACGGGAATTTTATAGATTGTATC 57.158 34.615 0.00 0.00 0.00 2.24
591 1639 7.881232 GGATCCACGGGAATTTTATAGATTGTA 59.119 37.037 6.95 0.00 34.34 2.41
639 1687 1.581934 ATGCACGAATGGTATGGACG 58.418 50.000 0.00 0.00 0.00 4.79
642 1690 3.627123 TCTGAAATGCACGAATGGTATGG 59.373 43.478 0.00 0.00 0.00 2.74
643 1691 4.880886 TCTGAAATGCACGAATGGTATG 57.119 40.909 0.00 0.00 0.00 2.39
653 1701 7.977853 ACATTCCTAAAATGATCTGAAATGCAC 59.022 33.333 4.86 0.00 0.00 4.57
666 1714 7.490840 TGATGCCATGTTACATTCCTAAAATG 58.509 34.615 0.00 0.00 0.00 2.32
705 1812 8.531530 CAAGAAACAAAAAGTAGAAATGGAACG 58.468 33.333 0.00 0.00 0.00 3.95
719 1826 8.425577 TTGAAACACAAGACAAGAAACAAAAA 57.574 26.923 0.00 0.00 34.20 1.94
720 1827 8.600449 ATTGAAACACAAGACAAGAAACAAAA 57.400 26.923 0.00 0.00 42.02 2.44
729 1836 9.734620 CTATTTGAAGATTGAAACACAAGACAA 57.265 29.630 0.00 0.00 42.02 3.18
746 1853 2.422093 GGAGGCCCAGGACTATTTGAAG 60.422 54.545 0.00 0.00 30.74 3.02
764 1871 1.801178 GCGTTTCTGAGGTTTCTGGAG 59.199 52.381 0.00 0.00 0.00 3.86
788 1895 0.771127 TCTGTGGGGAAAAGGACCTG 59.229 55.000 0.00 0.00 0.00 4.00
1146 2253 2.321213 GCGCAAAGGGATTCGCTAT 58.679 52.632 0.30 0.00 43.70 2.97
1149 2256 2.100991 CAGCGCAAAGGGATTCGC 59.899 61.111 11.47 0.00 46.95 4.70
1167 2274 2.048970 TAAGACGGCGCTCGCAAA 60.049 55.556 16.36 0.00 44.11 3.68
1169 2276 2.480853 TTTCTAAGACGGCGCTCGCA 62.481 55.000 16.36 0.00 44.11 5.10
1203 2310 1.065551 GCCGAGATAAACCAATGGCAC 59.934 52.381 0.00 0.00 40.66 5.01
1205 2312 0.307760 CGCCGAGATAAACCAATGGC 59.692 55.000 0.00 0.00 37.66 4.40
1207 2314 1.013596 TGCGCCGAGATAAACCAATG 58.986 50.000 4.18 0.00 0.00 2.82
1208 2315 1.014352 GTGCGCCGAGATAAACCAAT 58.986 50.000 4.18 0.00 0.00 3.16
1251 2358 5.279708 GCACATGCCTAGATCCAAGTATACT 60.280 44.000 0.00 0.00 34.31 2.12
1252 2359 4.932200 GCACATGCCTAGATCCAAGTATAC 59.068 45.833 0.00 0.00 34.31 1.47
1257 2364 1.224075 CGCACATGCCTAGATCCAAG 58.776 55.000 0.00 0.00 37.91 3.61
1279 2392 3.674997 AGCACTACACCACAACCTATTG 58.325 45.455 0.00 0.00 41.98 1.90
1280 2393 4.367039 AAGCACTACACCACAACCTATT 57.633 40.909 0.00 0.00 0.00 1.73
1281 2394 4.530946 AGTAAGCACTACACCACAACCTAT 59.469 41.667 0.00 0.00 31.45 2.57
1292 2405 7.066525 GCCCATAATTAACAAGTAAGCACTACA 59.933 37.037 0.00 0.00 33.48 2.74
1294 2407 6.259167 CGCCCATAATTAACAAGTAAGCACTA 59.741 38.462 0.00 0.00 33.48 2.74
1317 2431 3.563088 TCATTCCATCGCACGCGC 61.563 61.111 5.73 0.00 39.59 6.86
1322 2436 2.777094 TCAACAAGTCATTCCATCGCA 58.223 42.857 0.00 0.00 0.00 5.10
1335 2449 5.915196 CAGCATGCTCATATGATTCAACAAG 59.085 40.000 19.68 0.00 0.00 3.16
1367 2481 8.410673 TCGATGAGAGGCTACTTAAGAAATAT 57.589 34.615 10.09 0.00 0.00 1.28
1376 2490 2.363680 CACCATCGATGAGAGGCTACTT 59.636 50.000 26.86 0.00 0.00 2.24
1448 2563 6.544928 TTCTAGTAGCCACTGAATCATCAA 57.455 37.500 0.00 0.00 36.14 2.57
1457 2572 3.131933 ACAGCAGATTCTAGTAGCCACTG 59.868 47.826 0.00 10.67 36.14 3.66
1463 2578 4.884458 TCGACACAGCAGATTCTAGTAG 57.116 45.455 0.00 0.00 0.00 2.57
1518 2633 5.606348 AATACAGTGATTCCAGACTCTCC 57.394 43.478 0.00 0.00 0.00 3.71
1519 2634 7.099764 TGAAAATACAGTGATTCCAGACTCTC 58.900 38.462 0.00 0.00 0.00 3.20
1520 2635 7.009179 TGAAAATACAGTGATTCCAGACTCT 57.991 36.000 0.00 0.00 0.00 3.24
1566 2692 9.479549 ACCAAGTTAACCTCATGAATTATGAAT 57.520 29.630 0.88 0.00 44.84 2.57
1567 2693 8.739039 CACCAAGTTAACCTCATGAATTATGAA 58.261 33.333 0.88 0.00 44.84 2.57
1568 2694 7.148086 GCACCAAGTTAACCTCATGAATTATGA 60.148 37.037 0.88 0.00 43.40 2.15
1569 2695 6.974622 GCACCAAGTTAACCTCATGAATTATG 59.025 38.462 0.88 0.00 38.17 1.90
1570 2696 6.096846 GGCACCAAGTTAACCTCATGAATTAT 59.903 38.462 0.88 0.00 0.00 1.28
1623 2757 8.306761 AGTTCATTAAGGTAAATTGCTGAAAGG 58.693 33.333 0.00 0.00 0.00 3.11
1630 2764 6.868339 ACTTGCAGTTCATTAAGGTAAATTGC 59.132 34.615 3.20 3.20 0.00 3.56
1642 2776 3.859627 GCATTGCTCACTTGCAGTTCATT 60.860 43.478 0.16 0.00 44.27 2.57
1662 2796 3.211564 GAAGCGCAAAAGGGCAGCA 62.212 57.895 11.47 0.00 36.34 4.41
1669 2803 1.788886 GCCTGAAAAGAAGCGCAAAAG 59.211 47.619 11.47 0.00 0.00 2.27
1764 2898 1.629861 TGCACAATGATGTCCTGAGGA 59.370 47.619 0.00 0.00 37.82 3.71
1966 3101 7.441157 TGACTAACAGAACACAATCCAGTAAAG 59.559 37.037 0.00 0.00 0.00 1.85
2081 3216 1.745653 CGCATAGGAGAGTCAGTGTCA 59.254 52.381 0.00 0.00 0.00 3.58
2589 3724 4.875561 AACTGAGACTAGAGGTTGTTCC 57.124 45.455 0.00 0.00 0.00 3.62
2624 3759 3.982516 ACTAGGACAGCAGGTTGATCTA 58.017 45.455 0.00 0.00 0.00 1.98
2666 3801 7.137426 CAGATCAAGCAAAGACCATATAAAGC 58.863 38.462 0.00 0.00 0.00 3.51
2669 3804 6.064060 CCCAGATCAAGCAAAGACCATATAA 58.936 40.000 0.00 0.00 0.00 0.98
2732 3871 8.033038 GCATCTTAAAAGGGTAGGGTTAAAAAG 58.967 37.037 0.00 0.00 0.00 2.27
2738 3877 3.335484 TGGCATCTTAAAAGGGTAGGGTT 59.665 43.478 0.00 0.00 0.00 4.11
2740 3879 3.662759 TGGCATCTTAAAAGGGTAGGG 57.337 47.619 0.00 0.00 0.00 3.53
2772 3913 4.693095 GGCAGAGACAGGAAAAGAAAGTAG 59.307 45.833 0.00 0.00 0.00 2.57
3041 4182 1.821216 AATAACACAGCCTTCACCCG 58.179 50.000 0.00 0.00 0.00 5.28
3117 4258 6.701841 TCGATTTCCATCTAACATAACTCAGC 59.298 38.462 0.00 0.00 0.00 4.26
3160 4301 1.639635 ATAACTCCCAGCCCCTGCAG 61.640 60.000 6.78 6.78 41.13 4.41
3195 4336 3.383620 AAGCTATTCGATGAGAGGCAG 57.616 47.619 0.00 0.00 0.00 4.85
3343 4487 6.043327 TGAAATGCAACGATTATAAGACCG 57.957 37.500 0.00 0.00 0.00 4.79
3344 4488 7.432252 CCTTTGAAATGCAACGATTATAAGACC 59.568 37.037 0.00 0.00 35.91 3.85
3348 4511 6.625362 TGCCTTTGAAATGCAACGATTATAA 58.375 32.000 5.40 0.00 35.91 0.98
3352 4515 3.319755 CTGCCTTTGAAATGCAACGATT 58.680 40.909 9.08 0.00 35.91 3.34
3366 4529 1.000274 GACCAATTTCGTGCTGCCTTT 60.000 47.619 0.00 0.00 0.00 3.11
3377 4540 2.097728 GACGCGCCGACCAATTTC 59.902 61.111 5.73 0.00 0.00 2.17
3389 4552 2.771763 AAGCCAGGAACAGAGACGCG 62.772 60.000 3.53 3.53 0.00 6.01
3400 4563 1.039856 GCAAAGAACCAAAGCCAGGA 58.960 50.000 0.00 0.00 0.00 3.86
3409 4572 1.336440 CGTGTCCAATGCAAAGAACCA 59.664 47.619 0.00 0.00 0.00 3.67
3410 4573 1.606668 TCGTGTCCAATGCAAAGAACC 59.393 47.619 0.00 0.00 0.00 3.62
3411 4574 3.042887 GTTCGTGTCCAATGCAAAGAAC 58.957 45.455 0.00 0.00 32.77 3.01
3412 4575 2.685388 TGTTCGTGTCCAATGCAAAGAA 59.315 40.909 0.00 0.00 0.00 2.52
3413 4576 2.293170 TGTTCGTGTCCAATGCAAAGA 58.707 42.857 0.00 0.00 0.00 2.52
3414 4577 2.772568 TGTTCGTGTCCAATGCAAAG 57.227 45.000 0.00 0.00 0.00 2.77
3415 4578 3.119316 AGTTTGTTCGTGTCCAATGCAAA 60.119 39.130 0.00 0.00 0.00 3.68
3416 4579 2.425312 AGTTTGTTCGTGTCCAATGCAA 59.575 40.909 0.00 0.00 0.00 4.08
3417 4580 2.020720 AGTTTGTTCGTGTCCAATGCA 58.979 42.857 0.00 0.00 0.00 3.96
3418 4581 2.290641 AGAGTTTGTTCGTGTCCAATGC 59.709 45.455 0.00 0.00 0.00 3.56
3419 4582 5.666969 TTAGAGTTTGTTCGTGTCCAATG 57.333 39.130 0.00 0.00 0.00 2.82
3420 4583 6.877611 AATTAGAGTTTGTTCGTGTCCAAT 57.122 33.333 0.00 0.00 0.00 3.16
3421 4584 6.687081 AAATTAGAGTTTGTTCGTGTCCAA 57.313 33.333 0.00 0.00 0.00 3.53
3422 4585 6.316640 TGAAAATTAGAGTTTGTTCGTGTCCA 59.683 34.615 0.00 0.00 0.00 4.02
3429 4592 9.736023 ACATTCACTGAAAATTAGAGTTTGTTC 57.264 29.630 0.00 0.00 0.00 3.18
3435 4598 7.864379 CAGCAAACATTCACTGAAAATTAGAGT 59.136 33.333 0.00 0.00 31.67 3.24
3446 4609 1.955778 TCCCACAGCAAACATTCACTG 59.044 47.619 0.00 0.00 36.22 3.66
3451 4614 3.495331 TGTATGTCCCACAGCAAACATT 58.505 40.909 0.00 0.00 34.39 2.71
3457 4620 2.819019 CACAATTGTATGTCCCACAGCA 59.181 45.455 11.53 0.00 0.00 4.41
3516 4689 1.871080 AACCAGCGTTTCTGTCAGAG 58.129 50.000 2.12 0.00 41.25 3.35
3520 4693 1.477105 GCAAAACCAGCGTTTCTGTC 58.523 50.000 0.00 0.00 41.42 3.51
3522 4695 0.102120 TGGCAAAACCAGCGTTTCTG 59.898 50.000 0.00 0.00 46.36 3.02
3562 4735 5.649782 AAAAACAGGGTGATGCTATTCAG 57.350 39.130 0.00 0.00 0.00 3.02
3619 4792 4.565652 GGATTCCTCCAGCTCTGTTTTGTA 60.566 45.833 0.00 0.00 41.64 2.41
3636 4809 1.964223 TGCTAGATGACGAGGGATTCC 59.036 52.381 0.00 0.00 0.00 3.01
3637 4810 3.068873 ACTTGCTAGATGACGAGGGATTC 59.931 47.826 1.04 0.00 0.00 2.52
3638 4811 3.034635 ACTTGCTAGATGACGAGGGATT 58.965 45.455 1.04 0.00 0.00 3.01
3639 4812 2.363680 CACTTGCTAGATGACGAGGGAT 59.636 50.000 1.04 0.00 0.00 3.85
3641 4814 1.804372 GCACTTGCTAGATGACGAGGG 60.804 57.143 1.04 0.00 38.21 4.30
3643 4816 1.134995 TGGCACTTGCTAGATGACGAG 60.135 52.381 1.04 0.00 41.70 4.18
3644 4817 0.894835 TGGCACTTGCTAGATGACGA 59.105 50.000 1.04 0.00 41.70 4.20
3645 4818 1.725641 TTGGCACTTGCTAGATGACG 58.274 50.000 1.04 0.00 41.70 4.35
3648 4821 5.050769 CGTATAGTTTGGCACTTGCTAGATG 60.051 44.000 1.04 0.00 41.70 2.90
3649 4822 5.050490 CGTATAGTTTGGCACTTGCTAGAT 58.950 41.667 1.04 0.00 41.70 1.98
3651 4824 3.001330 GCGTATAGTTTGGCACTTGCTAG 59.999 47.826 0.38 0.00 41.70 3.42
3652 4825 2.933906 GCGTATAGTTTGGCACTTGCTA 59.066 45.455 0.38 0.00 41.70 3.49
3654 4827 1.737793 AGCGTATAGTTTGGCACTTGC 59.262 47.619 0.00 0.00 36.88 4.01
3655 4828 3.435327 TCAAGCGTATAGTTTGGCACTTG 59.565 43.478 0.00 0.00 40.79 3.16
3656 4829 3.670625 TCAAGCGTATAGTTTGGCACTT 58.329 40.909 0.00 0.00 40.79 3.16
3657 4830 3.328382 TCAAGCGTATAGTTTGGCACT 57.672 42.857 0.00 0.00 40.79 4.40
3658 4831 4.413495 TTTCAAGCGTATAGTTTGGCAC 57.587 40.909 0.00 0.00 40.79 5.01
3659 4832 5.182190 TCATTTTCAAGCGTATAGTTTGGCA 59.818 36.000 0.00 0.00 40.79 4.92
3660 4833 5.511729 GTCATTTTCAAGCGTATAGTTTGGC 59.488 40.000 0.00 0.00 40.79 4.52
3661 4834 6.607689 TGTCATTTTCAAGCGTATAGTTTGG 58.392 36.000 0.00 0.00 40.79 3.28
3662 4835 7.803189 ACTTGTCATTTTCAAGCGTATAGTTTG 59.197 33.333 5.72 0.00 43.97 2.93
3663 4836 7.871853 ACTTGTCATTTTCAAGCGTATAGTTT 58.128 30.769 5.72 0.00 43.97 2.66
3664 4837 7.435068 ACTTGTCATTTTCAAGCGTATAGTT 57.565 32.000 5.72 0.00 43.97 2.24
3665 4838 7.435068 AACTTGTCATTTTCAAGCGTATAGT 57.565 32.000 5.72 0.00 43.97 2.12
3666 4839 7.214449 CGAAACTTGTCATTTTCAAGCGTATAG 59.786 37.037 5.72 0.00 43.97 1.31
3667 4840 7.012943 CGAAACTTGTCATTTTCAAGCGTATA 58.987 34.615 5.72 0.00 43.97 1.47
3668 4841 5.851177 CGAAACTTGTCATTTTCAAGCGTAT 59.149 36.000 5.72 0.00 43.97 3.06
3669 4842 5.201910 CGAAACTTGTCATTTTCAAGCGTA 58.798 37.500 5.72 0.00 43.97 4.42
3670 4843 4.035017 CGAAACTTGTCATTTTCAAGCGT 58.965 39.130 5.72 0.00 43.97 5.07
3671 4844 3.121696 GCGAAACTTGTCATTTTCAAGCG 60.122 43.478 5.72 3.61 43.97 4.68
3677 4850 4.118410 TGCATTGCGAAACTTGTCATTTT 58.882 34.783 3.84 0.00 0.00 1.82
3685 4858 3.256631 AGGATCTTTGCATTGCGAAACTT 59.743 39.130 12.28 0.85 31.00 2.66
3686 4859 2.821969 AGGATCTTTGCATTGCGAAACT 59.178 40.909 12.28 6.02 31.00 2.66
3687 4860 3.221964 AGGATCTTTGCATTGCGAAAC 57.778 42.857 12.28 7.05 31.00 2.78
3688 4861 3.577667 CAAGGATCTTTGCATTGCGAAA 58.422 40.909 12.28 8.85 31.00 3.46
3689 4862 2.094597 CCAAGGATCTTTGCATTGCGAA 60.095 45.455 11.91 10.82 0.00 4.70
3691 4864 1.917273 CCAAGGATCTTTGCATTGCG 58.083 50.000 11.91 0.00 0.00 4.85
3697 4872 1.131315 GTTCTCGCCAAGGATCTTTGC 59.869 52.381 11.91 6.93 0.00 3.68
3712 4887 1.465794 AGTGAGAGGCGGTAGTTCTC 58.534 55.000 0.00 0.00 38.23 2.87
3714 4889 2.231721 AGAAAGTGAGAGGCGGTAGTTC 59.768 50.000 0.00 0.00 0.00 3.01
3718 4893 0.246635 GCAGAAAGTGAGAGGCGGTA 59.753 55.000 0.00 0.00 0.00 4.02
3719 4894 1.004440 GCAGAAAGTGAGAGGCGGT 60.004 57.895 0.00 0.00 0.00 5.68
3720 4895 0.603707 TTGCAGAAAGTGAGAGGCGG 60.604 55.000 0.00 0.00 0.00 6.13
3732 4907 5.045215 CAGAAACATTTGAAGCTTGCAGAA 58.955 37.500 2.10 0.00 0.00 3.02
3733 4908 4.500205 CCAGAAACATTTGAAGCTTGCAGA 60.500 41.667 2.10 0.00 0.00 4.26
3745 4920 3.305335 GCACCAACGATCCAGAAACATTT 60.305 43.478 0.00 0.00 0.00 2.32
3746 4921 2.228822 GCACCAACGATCCAGAAACATT 59.771 45.455 0.00 0.00 0.00 2.71
3750 5065 2.941210 GGCACCAACGATCCAGAAA 58.059 52.632 0.00 0.00 0.00 2.52
3772 5087 0.317770 CGCATCGGCAGTTGTGTTTT 60.318 50.000 0.91 0.00 41.24 2.43
3823 5138 1.332375 GTGTTGTTGCCAAAGCTACGA 59.668 47.619 0.00 0.00 46.19 3.43
3824 5139 1.599419 GGTGTTGTTGCCAAAGCTACG 60.599 52.381 0.00 0.00 46.19 3.51
3825 5140 1.599419 CGGTGTTGTTGCCAAAGCTAC 60.599 52.381 0.00 0.00 43.91 3.58
3826 5141 0.665835 CGGTGTTGTTGCCAAAGCTA 59.334 50.000 0.00 0.00 40.80 3.32
3827 5142 1.034838 TCGGTGTTGTTGCCAAAGCT 61.035 50.000 0.00 0.00 40.80 3.74
3828 5143 0.869880 GTCGGTGTTGTTGCCAAAGC 60.870 55.000 0.00 0.00 40.48 3.51
3829 5144 0.248866 GGTCGGTGTTGTTGCCAAAG 60.249 55.000 0.00 0.00 30.94 2.77
3830 5145 0.965866 TGGTCGGTGTTGTTGCCAAA 60.966 50.000 0.00 0.00 30.94 3.28
3831 5146 1.378646 TGGTCGGTGTTGTTGCCAA 60.379 52.632 0.00 0.00 0.00 4.52
3832 5147 2.115911 GTGGTCGGTGTTGTTGCCA 61.116 57.895 0.00 0.00 0.00 4.92
3833 5148 2.719354 GTGGTCGGTGTTGTTGCC 59.281 61.111 0.00 0.00 0.00 4.52
3834 5149 2.326550 CGTGGTCGGTGTTGTTGC 59.673 61.111 0.00 0.00 0.00 4.17
3835 5150 2.326550 GCGTGGTCGGTGTTGTTG 59.673 61.111 0.00 0.00 37.56 3.33
3836 5151 2.898343 GGCGTGGTCGGTGTTGTT 60.898 61.111 0.00 0.00 37.56 2.83
3837 5152 4.922026 GGGCGTGGTCGGTGTTGT 62.922 66.667 0.00 0.00 37.56 3.32
3838 5153 4.920112 TGGGCGTGGTCGGTGTTG 62.920 66.667 0.00 0.00 37.56 3.33
3845 5160 0.818040 AAGTCAAGTTGGGCGTGGTC 60.818 55.000 2.34 0.00 0.00 4.02
3846 5161 1.101049 CAAGTCAAGTTGGGCGTGGT 61.101 55.000 2.34 0.00 0.00 4.16
3859 5174 0.178992 CTCCTTTGGTGGGCAAGTCA 60.179 55.000 0.00 0.00 0.00 3.41
3860 5175 0.895559 CCTCCTTTGGTGGGCAAGTC 60.896 60.000 0.00 0.00 33.14 3.01
3883 5199 1.745489 GCAAGAAGCCCGGTAGTGG 60.745 63.158 0.00 0.00 37.23 4.00
3893 5209 1.818642 ACATGAGACCTGCAAGAAGC 58.181 50.000 0.00 0.00 45.96 3.86
3908 5224 6.478016 CACAAGTACCTCTGTGATCATACATG 59.522 42.308 12.70 2.29 34.50 3.21
3909 5225 6.381133 TCACAAGTACCTCTGTGATCATACAT 59.619 38.462 15.44 0.00 36.51 2.29
3910 5226 5.714806 TCACAAGTACCTCTGTGATCATACA 59.285 40.000 15.44 0.00 36.51 2.29
3913 5230 5.745312 TTCACAAGTACCTCTGTGATCAT 57.255 39.130 18.49 0.00 40.39 2.45
3919 5236 7.228706 CACCTTTTTATTCACAAGTACCTCTGT 59.771 37.037 0.00 0.00 0.00 3.41
3920 5237 7.584987 CACCTTTTTATTCACAAGTACCTCTG 58.415 38.462 0.00 0.00 0.00 3.35
3930 5247 5.895636 ATCGATGCACCTTTTTATTCACA 57.104 34.783 0.00 0.00 0.00 3.58
3933 5250 5.050363 TCGCTATCGATGCACCTTTTTATTC 60.050 40.000 8.54 0.00 40.21 1.75


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

AutoCloner maintained by Alex Coulton.