Multiple sequence alignment - TraesCS2D01G104000

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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 TraesCS2D01G104000 chr2D 100.000 2929 0 0 1 2929 56112738 56115666 0.000000e+00 5409.0
1 TraesCS2D01G104000 chr2D 81.462 383 69 2 1 383 576579289 576579669 2.190000e-81 313.0
2 TraesCS2D01G104000 chr2B 90.454 1718 107 31 1 1678 88849219 88850919 0.000000e+00 2211.0
3 TraesCS2D01G104000 chr2B 94.872 702 31 2 1676 2372 88851105 88851806 0.000000e+00 1092.0
4 TraesCS2D01G104000 chr2B 94.444 702 34 2 1676 2372 88906152 88906853 0.000000e+00 1075.0
5 TraesCS2D01G104000 chr2B 91.436 362 31 0 2566 2927 88851828 88852189 5.640000e-137 497.0
6 TraesCS2D01G104000 chr2B 91.160 362 32 0 2566 2927 88906875 88907236 2.620000e-135 492.0
7 TraesCS2D01G104000 chr2B 90.237 379 14 14 1321 1678 88905592 88905968 9.500000e-130 473.0
8 TraesCS2D01G104000 chr2B 83.537 328 47 6 2566 2891 767024232 767023910 1.710000e-77 300.0
9 TraesCS2D01G104000 chr2B 86.598 97 12 1 2829 2925 92496624 92496529 3.990000e-19 106.0
10 TraesCS2D01G104000 chr2B 74.790 238 43 14 554 782 521926836 521927065 1.120000e-14 91.6
11 TraesCS2D01G104000 chr2A 91.710 1146 82 8 1 1142 57701074 57702210 0.000000e+00 1578.0
12 TraesCS2D01G104000 chr2A 82.677 381 63 3 1 380 714526401 714526779 4.680000e-88 335.0
13 TraesCS2D01G104000 chr2A 86.301 219 10 7 1147 1362 57708403 57708604 1.370000e-53 220.0
14 TraesCS2D01G104000 chr5D 89.135 451 47 2 2111 2560 542563196 542562747 7.090000e-156 560.0
15 TraesCS2D01G104000 chr5D 87.939 456 53 2 2109 2562 514129309 514128854 1.190000e-148 536.0
16 TraesCS2D01G104000 chr5D 87.555 458 54 3 2107 2562 329620231 329620687 7.190000e-146 527.0
17 TraesCS2D01G104000 chr5D 85.399 363 49 2 2566 2927 514128987 514128628 9.910000e-100 374.0
18 TraesCS2D01G104000 chr6D 87.965 457 52 2 2107 2563 400554411 400553958 1.190000e-148 536.0
19 TraesCS2D01G104000 chr6D 87.391 460 50 5 2106 2562 433646910 433647364 3.350000e-144 521.0
20 TraesCS2D01G104000 chr1B 87.281 456 56 2 2109 2562 536777830 536778285 1.200000e-143 520.0
21 TraesCS2D01G104000 chr1B 82.228 377 65 2 1 377 421545103 421545477 1.010000e-84 324.0
22 TraesCS2D01G104000 chr1B 82.428 313 47 6 2566 2875 130932576 130932883 1.730000e-67 267.0
23 TraesCS2D01G104000 chr1B 73.507 268 55 13 519 776 46015754 46016015 1.450000e-13 87.9
24 TraesCS2D01G104000 chr1B 73.507 268 55 13 519 776 46085767 46086028 1.450000e-13 87.9
25 TraesCS2D01G104000 chr1B 100.000 31 0 0 1129 1159 682003559 682003589 1.130000e-04 58.4
26 TraesCS2D01G104000 chr1B 100.000 31 0 0 1129 1159 682025879 682025849 1.130000e-04 58.4
27 TraesCS2D01G104000 chr1B 94.444 36 1 1 1125 1159 681834610 681834645 1.000000e-03 54.7
28 TraesCS2D01G104000 chr5B 86.354 469 50 10 2107 2562 428133885 428134352 1.570000e-137 499.0
29 TraesCS2D01G104000 chr5B 85.519 366 42 9 2566 2927 684224316 684223958 3.560000e-99 372.0
30 TraesCS2D01G104000 chr5B 85.434 357 45 6 2566 2920 428134220 428134571 5.970000e-97 364.0
31 TraesCS2D01G104000 chr6B 83.196 363 57 3 2566 2927 683825072 683825431 2.180000e-86 329.0
32 TraesCS2D01G104000 chr4B 80.861 418 71 7 1 412 90464392 90463978 1.310000e-83 320.0
33 TraesCS2D01G104000 chr4B 79.808 416 79 5 1 412 24732119 24732533 6.140000e-77 298.0
34 TraesCS2D01G104000 chr4D 81.039 385 67 5 1 383 95285512 95285892 4.740000e-78 302.0
35 TraesCS2D01G104000 chr1A 80.000 415 75 6 3 411 543461406 543461818 1.710000e-77 300.0
36 TraesCS2D01G104000 chr1D 83.860 285 42 2 2566 2849 81064274 81063993 4.810000e-68 268.0
37 TraesCS2D01G104000 chr1D 100.000 30 0 0 1129 1158 489300933 489300904 4.080000e-04 56.5
38 TraesCS2D01G104000 chr1D 100.000 30 0 0 1129 1158 489326054 489326025 4.080000e-04 56.5
39 TraesCS2D01G104000 chr1D 100.000 30 0 0 1129 1158 489433821 489433792 4.080000e-04 56.5
40 TraesCS2D01G104000 chr3B 75.688 218 42 11 561 773 61700626 61700415 6.680000e-17 99.0
41 TraesCS2D01G104000 chr6A 74.330 261 51 14 519 769 40297483 40297737 2.400000e-16 97.1
42 TraesCS2D01G104000 chr6A 74.231 260 53 11 519 769 93079041 93079295 2.400000e-16 97.1
43 TraesCS2D01G104000 chrUn 73.725 255 52 12 528 772 79329756 79329507 5.200000e-13 86.1


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 TraesCS2D01G104000 chr2D 56112738 56115666 2928 False 5409.000000 5409 100.000 1 2929 1 chr2D.!!$F1 2928
1 TraesCS2D01G104000 chr2B 88849219 88852189 2970 False 1266.666667 2211 92.254 1 2927 3 chr2B.!!$F2 2926
2 TraesCS2D01G104000 chr2B 88905592 88907236 1644 False 680.000000 1075 91.947 1321 2927 3 chr2B.!!$F3 1606
3 TraesCS2D01G104000 chr2A 57701074 57702210 1136 False 1578.000000 1578 91.710 1 1142 1 chr2A.!!$F1 1141
4 TraesCS2D01G104000 chr5D 514128628 514129309 681 True 455.000000 536 86.669 2109 2927 2 chr5D.!!$R2 818
5 TraesCS2D01G104000 chr5B 428133885 428134571 686 False 431.500000 499 85.894 2107 2920 2 chr5B.!!$F1 813

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
440 441 0.320858 TCAATGTTGTTCGGCCGCTA 60.321 50.0 23.51 8.19 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 2666 0.10741 GGAGCGAGAGAGGAGAGTGA 60.107 60.0 0.0 0.0 0.0 3.41 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
60 61 3.918220 CGAAGATGCTGCGACGGC 61.918 66.667 0.00 4.02 33.75 5.68
82 83 2.792947 GGGAAGCGAGGCGGTATGA 61.793 63.158 0.00 0.00 36.27 2.15
88 89 1.432251 CGAGGCGGTATGAGACGTT 59.568 57.895 0.00 0.00 0.00 3.99
128 129 6.384015 TCTTCTTCAAAGGTATCCAGCTATCA 59.616 38.462 0.00 0.00 0.00 2.15
143 144 1.674441 CTATCAAGACGTCGGTAGCCA 59.326 52.381 10.46 0.00 0.00 4.75
152 153 0.389948 GTCGGTAGCCAGACAAGTGG 60.390 60.000 0.00 0.00 41.01 4.00
184 185 2.523015 GCGGCTTCAATGATGAGTTTG 58.477 47.619 0.00 0.00 36.78 2.93
220 221 6.013379 TGGAAACACAAGATCTCTGATTAGGT 60.013 38.462 0.00 0.00 33.40 3.08
267 268 3.593442 TCTTGATGAAGGTGGTGGTTT 57.407 42.857 0.00 0.00 0.00 3.27
331 332 1.437573 GGACTCGTCATCATCGGCA 59.562 57.895 0.00 0.00 0.00 5.69
335 336 0.458370 CTCGTCATCATCGGCACACA 60.458 55.000 0.00 0.00 0.00 3.72
359 360 1.895131 GGCAATTCCTTCTTGAAGGCA 59.105 47.619 21.16 13.33 39.80 4.75
361 362 3.429960 GGCAATTCCTTCTTGAAGGCATC 60.430 47.826 21.16 7.96 39.80 3.91
383 384 6.236017 TCGCCTAGAAGTTGTGTATTTTTG 57.764 37.500 0.00 0.00 0.00 2.44
440 441 0.320858 TCAATGTTGTTCGGCCGCTA 60.321 50.000 23.51 8.19 0.00 4.26
493 495 2.573941 CATCACTCGATGCAGAGACA 57.426 50.000 9.77 0.00 42.54 3.41
535 538 1.463674 AAATCATTGACCCCGCAGAC 58.536 50.000 0.00 0.00 0.00 3.51
540 543 0.389391 ATTGACCCCGCAGACTATCG 59.611 55.000 0.00 0.00 0.00 2.92
548 551 1.067985 CCGCAGACTATCGAGCATCAT 60.068 52.381 0.00 0.00 33.17 2.45
568 571 0.737715 GAGCCGTGGTGACTGATGAC 60.738 60.000 0.00 0.00 0.00 3.06
571 574 1.016130 CCGTGGTGACTGATGACTGC 61.016 60.000 0.00 0.00 0.00 4.40
573 576 1.016130 GTGGTGACTGATGACTGCCG 61.016 60.000 0.00 0.00 0.00 5.69
575 578 1.448540 GTGACTGATGACTGCCGGG 60.449 63.158 2.18 0.00 0.00 5.73
612 615 3.497332 TCAGCAGGGCGATTATAGTACT 58.503 45.455 0.00 0.00 0.00 2.73
625 628 2.627515 TAGTACTCTACGCACGGGAT 57.372 50.000 0.00 0.00 0.00 3.85
633 636 0.878523 TACGCACGGGATAGCAATGC 60.879 55.000 0.00 0.00 0.00 3.56
635 638 1.650912 GCACGGGATAGCAATGCTG 59.349 57.895 19.25 2.68 40.10 4.41
712 715 3.369451 GCGAACATCCTTCTGACTTTCTC 59.631 47.826 0.00 0.00 0.00 2.87
809 812 1.152355 CCCACCCCTTCTTTTGGCA 60.152 57.895 0.00 0.00 0.00 4.92
839 842 0.613777 CGAACAAGGAACCCTAGCCT 59.386 55.000 0.00 0.00 35.61 4.58
929 940 0.464554 GTGAAGGCATGTAGGGGAGC 60.465 60.000 0.00 0.00 0.00 4.70
936 947 2.750657 ATGTAGGGGAGCAGCAGCC 61.751 63.158 0.00 0.00 43.56 4.85
1182 1193 1.474478 TCCTTTTCGCAGTGCAAAACA 59.526 42.857 16.83 1.02 0.00 2.83
1205 1216 0.247460 TCTCACCACATCAAGGAGCG 59.753 55.000 0.00 0.00 0.00 5.03
1214 1225 4.051237 CACATCAAGGAGCGATAATCGAA 58.949 43.478 0.00 0.00 43.74 3.71
1238 1257 1.882912 TTGCAATCGAGACAGCAACT 58.117 45.000 11.08 0.00 41.55 3.16
1258 1277 1.244697 TGTGCTCGACTGGGTCTCTC 61.245 60.000 0.00 0.00 0.00 3.20
1261 1280 0.454196 GCTCGACTGGGTCTCTCTTC 59.546 60.000 0.00 0.00 0.00 2.87
1264 1283 2.422127 CTCGACTGGGTCTCTCTTCTTC 59.578 54.545 0.00 0.00 0.00 2.87
1265 1284 2.040545 TCGACTGGGTCTCTCTTCTTCT 59.959 50.000 0.00 0.00 0.00 2.85
1266 1285 2.422127 CGACTGGGTCTCTCTTCTTCTC 59.578 54.545 0.00 0.00 0.00 2.87
1267 1286 3.697166 GACTGGGTCTCTCTTCTTCTCT 58.303 50.000 0.00 0.00 0.00 3.10
1268 1287 4.086457 GACTGGGTCTCTCTTCTTCTCTT 58.914 47.826 0.00 0.00 0.00 2.85
1269 1288 4.086457 ACTGGGTCTCTCTTCTTCTCTTC 58.914 47.826 0.00 0.00 0.00 2.87
1270 1289 4.202673 ACTGGGTCTCTCTTCTTCTCTTCT 60.203 45.833 0.00 0.00 0.00 2.85
1271 1290 5.014755 ACTGGGTCTCTCTTCTTCTCTTCTA 59.985 44.000 0.00 0.00 0.00 2.10
1272 1291 6.086011 TGGGTCTCTCTTCTTCTCTTCTAT 57.914 41.667 0.00 0.00 0.00 1.98
1273 1292 6.498538 TGGGTCTCTCTTCTTCTCTTCTATT 58.501 40.000 0.00 0.00 0.00 1.73
1274 1293 7.644062 TGGGTCTCTCTTCTTCTCTTCTATTA 58.356 38.462 0.00 0.00 0.00 0.98
1275 1294 7.777910 TGGGTCTCTCTTCTTCTCTTCTATTAG 59.222 40.741 0.00 0.00 0.00 1.73
1276 1295 7.996644 GGGTCTCTCTTCTTCTCTTCTATTAGA 59.003 40.741 0.00 0.00 0.00 2.10
1277 1296 9.403583 GGTCTCTCTTCTTCTCTTCTATTAGAA 57.596 37.037 6.01 6.01 32.50 2.10
1303 1322 5.340439 AGCGCAAGATTACTTACTAACCT 57.660 39.130 11.47 0.00 43.02 3.50
1304 1323 6.461110 AGCGCAAGATTACTTACTAACCTA 57.539 37.500 11.47 0.00 43.02 3.08
1305 1324 6.271566 AGCGCAAGATTACTTACTAACCTAC 58.728 40.000 11.47 0.00 43.02 3.18
1317 1336 6.442885 ACTTACTAACCTACCCAAAGTAGCAT 59.557 38.462 0.00 0.00 46.21 3.79
1318 1337 5.354842 ACTAACCTACCCAAAGTAGCATC 57.645 43.478 0.00 0.00 46.21 3.91
1319 1338 4.781087 ACTAACCTACCCAAAGTAGCATCA 59.219 41.667 0.00 0.00 46.21 3.07
1322 1349 5.291905 ACCTACCCAAAGTAGCATCATAC 57.708 43.478 0.00 0.00 46.21 2.39
1340 1367 6.428083 TCATACTTGTTTAACCTGACCTGA 57.572 37.500 0.00 0.00 0.00 3.86
1362 1399 5.250543 TGAACCTATCCTGACCTTTGATTCA 59.749 40.000 0.00 0.00 0.00 2.57
1366 1403 5.587844 CCTATCCTGACCTTTGATTCAGTTG 59.412 44.000 0.00 0.00 38.06 3.16
1383 1420 1.135972 GTTGGCAGTTGCTGTACATCG 60.136 52.381 0.00 0.00 41.70 3.84
1387 1424 1.147473 CAGTTGCTGTACATCGTGCA 58.853 50.000 3.57 3.57 0.00 4.57
1435 1472 5.324409 TGGTAATCTTCTTGTTGGCAATCT 58.676 37.500 1.92 0.00 33.65 2.40
1436 1473 5.774690 TGGTAATCTTCTTGTTGGCAATCTT 59.225 36.000 1.92 0.00 33.65 2.40
1437 1474 6.267471 TGGTAATCTTCTTGTTGGCAATCTTT 59.733 34.615 1.92 0.00 33.65 2.52
1439 1476 8.303876 GGTAATCTTCTTGTTGGCAATCTTTAA 58.696 33.333 1.92 0.00 33.65 1.52
1440 1477 9.860898 GTAATCTTCTTGTTGGCAATCTTTAAT 57.139 29.630 1.92 0.00 33.65 1.40
1441 1478 8.767478 AATCTTCTTGTTGGCAATCTTTAATG 57.233 30.769 1.92 0.00 33.65 1.90
1442 1479 7.523293 TCTTCTTGTTGGCAATCTTTAATGA 57.477 32.000 1.92 0.00 33.65 2.57
1444 1481 9.241919 TCTTCTTGTTGGCAATCTTTAATGATA 57.758 29.630 1.92 0.00 33.65 2.15
1500 1548 1.370051 GGTGAAGACGTTTTGCGCC 60.370 57.895 4.18 0.94 46.11 6.53
1533 1581 6.540189 GCAGAAGAAAAAGGAGCTGTATGATA 59.460 38.462 0.00 0.00 0.00 2.15
1635 1683 0.889994 TCCAATGCCACATGACTTGC 59.110 50.000 0.00 0.00 0.00 4.01
1636 1684 0.604073 CCAATGCCACATGACTTGCA 59.396 50.000 0.00 2.54 38.23 4.08
1662 1710 5.586643 TGGTACAATTAATATCAAGCACGCA 59.413 36.000 0.00 0.00 31.92 5.24
1674 1722 8.955061 ATATCAAGCACGCAATGTAAATTATC 57.045 30.769 0.00 0.00 0.00 1.75
1678 1915 8.282592 TCAAGCACGCAATGTAAATTATCTATC 58.717 33.333 0.00 0.00 0.00 2.08
1715 1952 7.548097 TGTTTGACAGGAGTTGATATAGTCTC 58.452 38.462 0.00 0.00 0.00 3.36
1735 1972 0.250727 GTTTGACCTACCTGCAGGCA 60.251 55.000 33.06 20.12 39.53 4.75
1761 1998 5.512298 GGTTAAGGTTATCCAAAAGGGCTA 58.488 41.667 0.00 0.00 36.21 3.93
1796 2033 9.841295 GTGAAGATAGTTGGGGTTATTACATTA 57.159 33.333 0.00 0.00 0.00 1.90
1820 2057 3.520290 TCTATGGTTGCTACTGGTTCG 57.480 47.619 0.00 0.00 0.00 3.95
1829 2066 5.107337 GGTTGCTACTGGTTCGTTTAGTTAC 60.107 44.000 0.00 0.00 0.00 2.50
1875 2112 3.008485 AGACAGAAAGAAGCTACCCAAGG 59.992 47.826 0.00 0.00 0.00 3.61
1920 2157 1.134965 CACAGGAAGAAGCTAGTCCGG 60.135 57.143 0.00 0.00 36.49 5.14
2014 2255 7.639113 TCAACTTGTTTTCAGTTTATGACCT 57.361 32.000 0.00 0.00 37.77 3.85
2173 2414 0.395686 CAGGCCATCCGATCACTGAT 59.604 55.000 5.01 0.00 37.47 2.90
2196 2437 2.486592 GGTCACAAAATACCGACCCAAG 59.513 50.000 0.00 0.00 41.77 3.61
2214 2455 2.657237 CGGAGCTCTCAAACGGGT 59.343 61.111 14.64 0.00 0.00 5.28
2369 2648 3.933722 CCCATCGGGCTCATCGCT 61.934 66.667 0.00 0.00 35.35 4.93
2370 2649 2.356793 CCATCGGGCTCATCGCTC 60.357 66.667 0.00 0.00 39.13 5.03
2371 2650 2.356793 CATCGGGCTCATCGCTCC 60.357 66.667 0.00 0.00 34.87 4.70
2372 2651 2.839632 ATCGGGCTCATCGCTCCA 60.840 61.111 0.00 0.00 34.87 3.86
2373 2652 2.434843 ATCGGGCTCATCGCTCCAA 61.435 57.895 0.00 0.00 34.87 3.53
2374 2653 1.971505 ATCGGGCTCATCGCTCCAAA 61.972 55.000 0.00 0.00 34.87 3.28
2375 2654 1.745115 CGGGCTCATCGCTCCAAAA 60.745 57.895 0.00 0.00 34.87 2.44
2376 2655 1.803289 GGGCTCATCGCTCCAAAAC 59.197 57.895 0.00 0.00 39.13 2.43
2377 2656 1.657751 GGGCTCATCGCTCCAAAACC 61.658 60.000 0.00 0.00 39.13 3.27
2378 2657 1.657751 GGCTCATCGCTCCAAAACCC 61.658 60.000 0.00 0.00 39.13 4.11
2379 2658 0.678048 GCTCATCGCTCCAAAACCCT 60.678 55.000 0.00 0.00 35.14 4.34
2380 2659 1.406887 GCTCATCGCTCCAAAACCCTA 60.407 52.381 0.00 0.00 35.14 3.53
2381 2660 2.555199 CTCATCGCTCCAAAACCCTAG 58.445 52.381 0.00 0.00 0.00 3.02
2382 2661 1.017387 CATCGCTCCAAAACCCTAGC 58.983 55.000 0.00 0.00 0.00 3.42
2383 2662 0.912486 ATCGCTCCAAAACCCTAGCT 59.088 50.000 0.00 0.00 32.73 3.32
2384 2663 0.249398 TCGCTCCAAAACCCTAGCTC 59.751 55.000 0.00 0.00 32.73 4.09
2385 2664 0.036388 CGCTCCAAAACCCTAGCTCA 60.036 55.000 0.00 0.00 32.73 4.26
2386 2665 1.454201 GCTCCAAAACCCTAGCTCAC 58.546 55.000 0.00 0.00 32.18 3.51
2387 2666 1.003696 GCTCCAAAACCCTAGCTCACT 59.996 52.381 0.00 0.00 32.18 3.41
2388 2667 2.937433 GCTCCAAAACCCTAGCTCACTC 60.937 54.545 0.00 0.00 32.18 3.51
2389 2668 2.303022 CTCCAAAACCCTAGCTCACTCA 59.697 50.000 0.00 0.00 0.00 3.41
2390 2669 2.038557 TCCAAAACCCTAGCTCACTCAC 59.961 50.000 0.00 0.00 0.00 3.51
2391 2670 2.039084 CCAAAACCCTAGCTCACTCACT 59.961 50.000 0.00 0.00 0.00 3.41
2392 2671 3.330267 CAAAACCCTAGCTCACTCACTC 58.670 50.000 0.00 0.00 0.00 3.51
2393 2672 2.614134 AACCCTAGCTCACTCACTCT 57.386 50.000 0.00 0.00 0.00 3.24
2394 2673 2.137810 ACCCTAGCTCACTCACTCTC 57.862 55.000 0.00 0.00 0.00 3.20
2395 2674 1.341581 ACCCTAGCTCACTCACTCTCC 60.342 57.143 0.00 0.00 0.00 3.71
2396 2675 1.064017 CCCTAGCTCACTCACTCTCCT 60.064 57.143 0.00 0.00 0.00 3.69
2397 2676 2.297701 CCTAGCTCACTCACTCTCCTC 58.702 57.143 0.00 0.00 0.00 3.71
2398 2677 2.092429 CCTAGCTCACTCACTCTCCTCT 60.092 54.545 0.00 0.00 0.00 3.69
2399 2678 2.128771 AGCTCACTCACTCTCCTCTC 57.871 55.000 0.00 0.00 0.00 3.20
2400 2679 1.635487 AGCTCACTCACTCTCCTCTCT 59.365 52.381 0.00 0.00 0.00 3.10
2401 2680 2.017049 GCTCACTCACTCTCCTCTCTC 58.983 57.143 0.00 0.00 0.00 3.20
2402 2681 2.279741 CTCACTCACTCTCCTCTCTCG 58.720 57.143 0.00 0.00 0.00 4.04
2403 2682 0.732571 CACTCACTCTCCTCTCTCGC 59.267 60.000 0.00 0.00 0.00 5.03
2526 2852 4.845580 CCGCATCGCCTTGGAGCT 62.846 66.667 0.00 0.00 0.00 4.09
2527 2853 2.106938 CGCATCGCCTTGGAGCTA 59.893 61.111 0.00 0.00 0.00 3.32
2528 2854 1.301244 CGCATCGCCTTGGAGCTAT 60.301 57.895 0.00 0.00 0.00 2.97
2529 2855 1.287730 CGCATCGCCTTGGAGCTATC 61.288 60.000 0.00 0.00 0.00 2.08
2530 2856 0.952984 GCATCGCCTTGGAGCTATCC 60.953 60.000 0.00 0.00 46.87 2.59
2545 2871 4.232905 TCCAAGGTGGAGACCAGG 57.767 61.111 0.00 0.00 42.67 4.45
2546 2872 1.538876 TCCAAGGTGGAGACCAGGG 60.539 63.158 0.00 0.00 42.67 4.45
2547 2873 2.606587 CCAAGGTGGAGACCAGGGG 61.607 68.421 0.00 0.00 45.98 4.79
2548 2874 2.936032 AAGGTGGAGACCAGGGGC 60.936 66.667 0.00 0.00 45.98 5.80
2549 2875 3.810687 AAGGTGGAGACCAGGGGCA 62.811 63.158 0.00 0.00 45.98 5.36
2550 2876 3.721706 GGTGGAGACCAGGGGCAG 61.722 72.222 0.00 0.00 42.59 4.85
2551 2877 4.416738 GTGGAGACCAGGGGCAGC 62.417 72.222 0.00 0.00 32.34 5.25
2552 2878 4.664267 TGGAGACCAGGGGCAGCT 62.664 66.667 0.00 0.00 0.00 4.24
2553 2879 3.791586 GGAGACCAGGGGCAGCTC 61.792 72.222 0.00 0.00 0.00 4.09
2554 2880 2.686835 GAGACCAGGGGCAGCTCT 60.687 66.667 0.00 0.00 0.00 4.09
2555 2881 3.007920 AGACCAGGGGCAGCTCTG 61.008 66.667 0.00 0.61 0.00 3.35
2559 2885 2.509916 CAGGGGCAGCTCTGGATC 59.490 66.667 0.00 0.00 0.00 3.36
2560 2886 2.071262 CAGGGGCAGCTCTGGATCT 61.071 63.158 0.00 0.00 0.00 2.75
2561 2887 2.071262 AGGGGCAGCTCTGGATCTG 61.071 63.158 0.00 0.00 0.00 2.90
2562 2888 2.373707 GGGGCAGCTCTGGATCTGT 61.374 63.158 0.00 0.00 33.09 3.41
2563 2889 1.153208 GGGCAGCTCTGGATCTGTG 60.153 63.158 0.00 0.00 33.09 3.66
2564 2890 1.153208 GGCAGCTCTGGATCTGTGG 60.153 63.158 0.00 0.00 33.09 4.17
2565 2891 1.153208 GCAGCTCTGGATCTGTGGG 60.153 63.158 0.00 0.00 33.09 4.61
2566 2892 1.620739 GCAGCTCTGGATCTGTGGGA 61.621 60.000 0.00 0.00 33.09 4.37
2567 2893 1.129917 CAGCTCTGGATCTGTGGGAT 58.870 55.000 0.00 0.00 37.37 3.85
2568 2894 1.489649 CAGCTCTGGATCTGTGGGATT 59.510 52.381 0.00 0.00 34.33 3.01
2569 2895 1.767681 AGCTCTGGATCTGTGGGATTC 59.232 52.381 0.00 0.00 34.33 2.52
2570 2896 1.202746 GCTCTGGATCTGTGGGATTCC 60.203 57.143 0.00 0.00 34.33 3.01
2571 2897 1.069823 CTCTGGATCTGTGGGATTCCG 59.930 57.143 0.00 0.00 34.33 4.30
2572 2898 1.123077 CTGGATCTGTGGGATTCCGA 58.877 55.000 0.00 0.00 34.33 4.55
2573 2899 1.696336 CTGGATCTGTGGGATTCCGAT 59.304 52.381 0.00 0.00 34.33 4.18
2574 2900 1.694150 TGGATCTGTGGGATTCCGATC 59.306 52.381 8.88 8.88 34.33 3.69
2575 2901 1.337260 GGATCTGTGGGATTCCGATCG 60.337 57.143 8.51 8.51 34.33 3.69
2576 2902 1.613925 GATCTGTGGGATTCCGATCGA 59.386 52.381 18.66 0.00 34.33 3.59
2577 2903 1.480789 TCTGTGGGATTCCGATCGAA 58.519 50.000 18.66 9.52 35.24 3.71
2578 2904 2.039418 TCTGTGGGATTCCGATCGAAT 58.961 47.619 18.66 13.99 44.20 3.34
2583 2909 4.675404 ATTCCGATCGAATCCGGC 57.325 55.556 18.66 0.00 44.96 6.13
2584 2910 1.372997 ATTCCGATCGAATCCGGCG 60.373 57.895 18.66 0.00 44.96 6.46
2585 2911 4.640855 TCCGATCGAATCCGGCGC 62.641 66.667 18.66 0.00 44.96 6.53
2586 2912 4.942481 CCGATCGAATCCGGCGCA 62.942 66.667 18.66 0.00 39.22 6.09
2587 2913 2.959599 CGATCGAATCCGGCGCAA 60.960 61.111 10.26 0.00 36.24 4.85
2588 2914 2.310233 CGATCGAATCCGGCGCAAT 61.310 57.895 10.26 0.00 36.24 3.56
2589 2915 1.205064 GATCGAATCCGGCGCAATG 59.795 57.895 10.83 0.00 36.24 2.82
2590 2916 1.498865 GATCGAATCCGGCGCAATGT 61.499 55.000 10.83 0.00 36.24 2.71
2591 2917 1.095228 ATCGAATCCGGCGCAATGTT 61.095 50.000 10.83 0.00 36.24 2.71
2592 2918 1.583451 CGAATCCGGCGCAATGTTG 60.583 57.895 10.83 0.00 0.00 3.33
2593 2919 1.800032 GAATCCGGCGCAATGTTGA 59.200 52.632 10.83 0.00 0.00 3.18
2594 2920 0.248215 GAATCCGGCGCAATGTTGAG 60.248 55.000 10.83 0.00 0.00 3.02
2600 2926 2.787249 CGCAATGTTGAGCTCCGG 59.213 61.111 12.15 0.00 0.00 5.14
2601 2927 2.486966 GCAATGTTGAGCTCCGGC 59.513 61.111 12.15 1.66 39.06 6.13
2602 2928 2.334946 GCAATGTTGAGCTCCGGCA 61.335 57.895 12.15 7.82 41.70 5.69
2603 2929 1.798735 CAATGTTGAGCTCCGGCAG 59.201 57.895 12.15 0.00 41.70 4.85
2630 2956 3.209812 CGACGAGCAGGATCCGGA 61.210 66.667 16.86 6.61 0.00 5.14
2631 2957 2.725008 GACGAGCAGGATCCGGAG 59.275 66.667 16.86 8.33 0.00 4.63
2632 2958 2.043852 ACGAGCAGGATCCGGAGT 60.044 61.111 16.86 8.96 0.00 3.85
2633 2959 0.818445 GACGAGCAGGATCCGGAGTA 60.818 60.000 16.86 0.00 0.00 2.59
2634 2960 0.178987 ACGAGCAGGATCCGGAGTAT 60.179 55.000 16.86 0.00 0.00 2.12
2635 2961 0.242286 CGAGCAGGATCCGGAGTATG 59.758 60.000 16.86 9.27 0.00 2.39
2636 2962 1.621992 GAGCAGGATCCGGAGTATGA 58.378 55.000 16.86 0.00 0.00 2.15
2637 2963 1.543802 GAGCAGGATCCGGAGTATGAG 59.456 57.143 16.86 0.00 0.00 2.90
2638 2964 0.037790 GCAGGATCCGGAGTATGAGC 60.038 60.000 16.86 5.44 0.00 4.26
2639 2965 1.626686 CAGGATCCGGAGTATGAGCT 58.373 55.000 11.34 0.00 0.00 4.09
2640 2966 1.967066 CAGGATCCGGAGTATGAGCTT 59.033 52.381 11.34 0.00 0.00 3.74
2641 2967 1.967066 AGGATCCGGAGTATGAGCTTG 59.033 52.381 11.34 0.00 0.00 4.01
2642 2968 1.689273 GGATCCGGAGTATGAGCTTGT 59.311 52.381 11.34 0.00 0.00 3.16
2643 2969 2.288518 GGATCCGGAGTATGAGCTTGTC 60.289 54.545 11.34 0.00 0.00 3.18
2644 2970 1.112113 TCCGGAGTATGAGCTTGTCC 58.888 55.000 0.00 0.00 0.00 4.02
2645 2971 1.115467 CCGGAGTATGAGCTTGTCCT 58.885 55.000 0.00 0.00 0.00 3.85
2646 2972 1.067821 CCGGAGTATGAGCTTGTCCTC 59.932 57.143 0.00 0.00 0.00 3.71
2647 2973 1.067821 CGGAGTATGAGCTTGTCCTCC 59.932 57.143 11.42 11.42 36.07 4.30
2648 2974 1.067821 GGAGTATGAGCTTGTCCTCCG 59.932 57.143 7.44 0.00 30.16 4.63
2649 2975 0.461961 AGTATGAGCTTGTCCTCCGC 59.538 55.000 0.00 0.00 0.00 5.54
2650 2976 0.175760 GTATGAGCTTGTCCTCCGCA 59.824 55.000 0.00 0.00 0.00 5.69
2651 2977 1.123077 TATGAGCTTGTCCTCCGCAT 58.877 50.000 0.00 0.00 0.00 4.73
2652 2978 0.179062 ATGAGCTTGTCCTCCGCATC 60.179 55.000 0.00 0.00 0.00 3.91
2653 2979 1.880340 GAGCTTGTCCTCCGCATCG 60.880 63.158 0.00 0.00 0.00 3.84
2654 2980 3.567797 GCTTGTCCTCCGCATCGC 61.568 66.667 0.00 0.00 0.00 4.58
2655 2981 2.892425 CTTGTCCTCCGCATCGCC 60.892 66.667 0.00 0.00 0.00 5.54
2656 2982 3.376935 CTTGTCCTCCGCATCGCCT 62.377 63.158 0.00 0.00 0.00 5.52
2657 2983 2.859273 CTTGTCCTCCGCATCGCCTT 62.859 60.000 0.00 0.00 0.00 4.35
2658 2984 2.892425 GTCCTCCGCATCGCCTTG 60.892 66.667 0.00 0.00 0.00 3.61
2659 2985 4.161295 TCCTCCGCATCGCCTTGG 62.161 66.667 0.00 0.00 0.00 3.61
2660 2986 4.161295 CCTCCGCATCGCCTTGGA 62.161 66.667 0.00 0.00 0.00 3.53
2661 2987 2.587194 CTCCGCATCGCCTTGGAG 60.587 66.667 0.00 0.00 41.82 3.86
2662 2988 4.838152 TCCGCATCGCCTTGGAGC 62.838 66.667 0.00 0.00 0.00 4.70
2663 2989 4.845580 CCGCATCGCCTTGGAGCT 62.846 66.667 0.00 0.00 0.00 4.09
2752 3078 4.819761 GCAGCTCGGACGATGGCA 62.820 66.667 8.34 0.00 0.00 4.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 5.132502 TGAAGAAGATGCCAGAAGACAAAA 58.867 37.500 0.00 0.00 0.00 2.44
128 129 0.892358 TGTCTGGCTACCGACGTCTT 60.892 55.000 14.70 2.72 32.65 3.01
143 144 2.834549 CCTCTACCATCACCACTTGTCT 59.165 50.000 0.00 0.00 0.00 3.41
152 153 0.530870 GAAGCCGCCTCTACCATCAC 60.531 60.000 0.00 0.00 0.00 3.06
184 185 2.143122 TGTGTTTCCATTCGAGAGCAC 58.857 47.619 0.00 0.00 0.00 4.40
331 332 0.527565 GAAGGAATTGCCGCATGTGT 59.472 50.000 5.38 0.00 43.43 3.72
335 336 1.838112 TCAAGAAGGAATTGCCGCAT 58.162 45.000 0.00 0.00 43.43 4.73
359 360 6.653320 TCAAAAATACACAACTTCTAGGCGAT 59.347 34.615 0.00 0.00 0.00 4.58
361 362 6.147164 TCTCAAAAATACACAACTTCTAGGCG 59.853 38.462 0.00 0.00 0.00 5.52
383 384 7.939588 ACTAACCCTATGATAAAAGGCAATCTC 59.060 37.037 0.00 0.00 0.00 2.75
493 495 7.954666 TTTTTCGAAAAGGATGATAATCCCT 57.045 32.000 21.53 0.00 41.65 4.20
535 538 1.067985 ACGGCTCATGATGCTCGATAG 60.068 52.381 21.88 3.00 0.00 2.08
540 543 1.153289 ACCACGGCTCATGATGCTC 60.153 57.895 14.20 6.42 0.00 4.26
548 551 1.184970 TCATCAGTCACCACGGCTCA 61.185 55.000 0.00 0.00 0.00 4.26
568 571 0.683973 AGCTCATAATCTCCCGGCAG 59.316 55.000 0.00 0.00 0.00 4.85
571 574 3.070159 TGAAAGAGCTCATAATCTCCCGG 59.930 47.826 17.77 0.00 0.00 5.73
573 576 4.064388 GCTGAAAGAGCTCATAATCTCCC 58.936 47.826 17.77 0.00 45.21 4.30
612 615 1.037493 ATTGCTATCCCGTGCGTAGA 58.963 50.000 0.00 0.00 0.00 2.59
633 636 1.443194 GCAGGCGAATGCACAACAG 60.443 57.895 7.34 0.00 45.77 3.16
712 715 6.668541 AATCATGTTACACGAGAAGGAATG 57.331 37.500 0.00 0.00 0.00 2.67
809 812 1.203001 TCCTTGTTCGCCTTTCCCAAT 60.203 47.619 0.00 0.00 0.00 3.16
913 924 1.918253 CTGCTCCCCTACATGCCTT 59.082 57.895 0.00 0.00 0.00 4.35
1182 1193 4.712476 GCTCCTTGATGTGGTGAGATATT 58.288 43.478 0.00 0.00 0.00 1.28
1205 1216 6.199154 TCTCGATTGCAAAGAGTTCGATTATC 59.801 38.462 24.99 6.51 38.07 1.75
1214 1225 2.072298 GCTGTCTCGATTGCAAAGAGT 58.928 47.619 24.99 2.88 33.96 3.24
1238 1257 0.827925 AGAGACCCAGTCGAGCACAA 60.828 55.000 0.00 0.00 37.67 3.33
1243 1262 2.122783 AGAAGAGAGACCCAGTCGAG 57.877 55.000 0.00 0.00 37.67 4.04
1246 1265 3.697166 AGAGAAGAAGAGAGACCCAGTC 58.303 50.000 0.00 0.00 0.00 3.51
1250 1269 7.996644 TCTAATAGAAGAGAAGAAGAGAGACCC 59.003 40.741 0.00 0.00 0.00 4.46
1258 1277 8.591312 CGCTTGTTTCTAATAGAAGAGAAGAAG 58.409 37.037 17.47 12.13 35.37 2.85
1261 1280 6.311445 TGCGCTTGTTTCTAATAGAAGAGAAG 59.689 38.462 9.73 9.27 35.37 2.85
1264 1283 6.311445 TCTTGCGCTTGTTTCTAATAGAAGAG 59.689 38.462 9.73 4.74 35.37 2.85
1265 1284 6.163476 TCTTGCGCTTGTTTCTAATAGAAGA 58.837 36.000 9.73 0.48 35.37 2.87
1266 1285 6.408858 TCTTGCGCTTGTTTCTAATAGAAG 57.591 37.500 9.73 0.00 35.37 2.85
1267 1286 6.985188 ATCTTGCGCTTGTTTCTAATAGAA 57.015 33.333 9.73 0.00 31.28 2.10
1268 1287 6.985188 AATCTTGCGCTTGTTTCTAATAGA 57.015 33.333 9.73 0.00 0.00 1.98
1269 1288 7.910304 AGTAATCTTGCGCTTGTTTCTAATAG 58.090 34.615 9.73 0.00 0.00 1.73
1270 1289 7.843490 AGTAATCTTGCGCTTGTTTCTAATA 57.157 32.000 9.73 0.00 0.00 0.98
1271 1290 6.743575 AGTAATCTTGCGCTTGTTTCTAAT 57.256 33.333 9.73 0.00 0.00 1.73
1272 1291 6.554334 AAGTAATCTTGCGCTTGTTTCTAA 57.446 33.333 9.73 0.00 32.09 2.10
1273 1292 6.872020 AGTAAGTAATCTTGCGCTTGTTTCTA 59.128 34.615 9.73 0.00 40.35 2.10
1274 1293 5.701290 AGTAAGTAATCTTGCGCTTGTTTCT 59.299 36.000 9.73 0.00 40.35 2.52
1275 1294 5.928153 AGTAAGTAATCTTGCGCTTGTTTC 58.072 37.500 9.73 0.00 40.35 2.78
1276 1295 5.941948 AGTAAGTAATCTTGCGCTTGTTT 57.058 34.783 9.73 5.43 40.35 2.83
1277 1296 6.128363 GGTTAGTAAGTAATCTTGCGCTTGTT 60.128 38.462 9.73 0.83 40.35 2.83
1278 1297 5.350640 GGTTAGTAAGTAATCTTGCGCTTGT 59.649 40.000 9.73 0.00 40.35 3.16
1298 1317 5.968676 ATGATGCTACTTTGGGTAGGTTA 57.031 39.130 5.19 0.00 45.83 2.85
1299 1318 4.862641 ATGATGCTACTTTGGGTAGGTT 57.137 40.909 5.19 0.00 45.83 3.50
1300 1319 4.969359 AGTATGATGCTACTTTGGGTAGGT 59.031 41.667 5.19 0.00 45.83 3.08
1301 1320 5.552870 AGTATGATGCTACTTTGGGTAGG 57.447 43.478 5.19 0.00 45.83 3.18
1303 1322 6.308015 ACAAGTATGATGCTACTTTGGGTA 57.692 37.500 0.00 0.00 39.37 3.69
1304 1323 5.179452 ACAAGTATGATGCTACTTTGGGT 57.821 39.130 0.00 0.00 39.37 4.51
1305 1324 6.515272 AAACAAGTATGATGCTACTTTGGG 57.485 37.500 0.00 0.00 39.37 4.12
1317 1336 6.428083 TCAGGTCAGGTTAAACAAGTATGA 57.572 37.500 0.00 0.00 0.00 2.15
1318 1337 6.072673 GGTTCAGGTCAGGTTAAACAAGTATG 60.073 42.308 0.00 0.00 0.00 2.39
1319 1338 6.002082 GGTTCAGGTCAGGTTAAACAAGTAT 58.998 40.000 0.00 0.00 0.00 2.12
1322 1349 4.461198 AGGTTCAGGTCAGGTTAAACAAG 58.539 43.478 0.00 0.00 0.00 3.16
1340 1367 5.251700 ACTGAATCAAAGGTCAGGATAGGTT 59.748 40.000 5.72 0.00 44.61 3.50
1362 1399 2.154462 GATGTACAGCAACTGCCAACT 58.846 47.619 6.17 0.00 43.38 3.16
1366 1403 0.443869 CACGATGTACAGCAACTGCC 59.556 55.000 12.28 0.00 43.38 4.85
1383 1420 2.281762 GGTTCGACGATACAGAATGCAC 59.718 50.000 0.00 0.00 42.53 4.57
1387 1424 2.681848 ACGAGGTTCGACGATACAGAAT 59.318 45.455 5.38 0.00 43.74 2.40
1500 1548 4.330250 TCCTTTTTCTTCTGCTGGATCTG 58.670 43.478 0.00 0.00 0.00 2.90
1533 1581 5.871396 TTCTTCTCCGCCTTAAGTATCAT 57.129 39.130 0.97 0.00 0.00 2.45
1635 1683 7.113404 GCGTGCTTGATATTAATTGTACCATTG 59.887 37.037 2.51 0.00 0.00 2.82
1636 1684 7.138736 GCGTGCTTGATATTAATTGTACCATT 58.861 34.615 0.00 0.00 0.00 3.16
1648 1696 9.398170 GATAATTTACATTGCGTGCTTGATATT 57.602 29.630 0.00 0.00 0.00 1.28
1674 1722 6.936279 TGTCAAACAGGTAAGGAAGAGATAG 58.064 40.000 0.00 0.00 0.00 2.08
1711 1948 1.000506 TGCAGGTAGGTCAAACGAGAC 59.999 52.381 0.00 0.00 37.80 3.36
1715 1952 1.298859 GCCTGCAGGTAGGTCAAACG 61.299 60.000 32.81 4.20 40.11 3.60
1735 1972 4.338012 CCTTTTGGATAACCTTAACCGGT 58.662 43.478 0.00 0.00 44.07 5.28
1780 2017 9.581289 CCATAGATGTTAATGTAATAACCCCAA 57.419 33.333 0.00 0.00 35.38 4.12
1796 2033 4.844349 ACCAGTAGCAACCATAGATGTT 57.156 40.909 0.00 0.00 0.00 2.71
1829 2066 7.011763 TCTGCGAGATAATCTTTGAAATCTTGG 59.988 37.037 0.00 0.00 32.61 3.61
1875 2112 4.322009 GCGCTGATTTTTCTTCTTAACAGC 59.678 41.667 0.00 0.00 43.63 4.40
1920 2157 5.934625 TCACTGATCTTTCTTCTTAACAGGC 59.065 40.000 0.00 0.00 0.00 4.85
2014 2255 8.389779 TCATAAACTGAAAACAAGCTGATACA 57.610 30.769 0.00 0.00 0.00 2.29
2070 2311 6.600427 TGTCATACAAGATCACAAAGATGCAT 59.400 34.615 0.00 0.00 37.00 3.96
2072 2313 6.426980 TGTCATACAAGATCACAAAGATGC 57.573 37.500 0.00 0.00 37.00 3.91
2073 2314 7.066645 ACCATGTCATACAAGATCACAAAGATG 59.933 37.037 0.00 0.00 37.00 2.90
2196 2437 2.815647 CCCGTTTGAGAGCTCCGC 60.816 66.667 10.93 3.40 0.00 5.54
2240 2481 5.454755 CCTTACATTTGGGACGGATATGAGT 60.455 44.000 0.00 0.00 0.00 3.41
2369 2648 2.038557 GTGAGTGAGCTAGGGTTTTGGA 59.961 50.000 0.00 0.00 0.00 3.53
2370 2649 2.039084 AGTGAGTGAGCTAGGGTTTTGG 59.961 50.000 0.00 0.00 0.00 3.28
2371 2650 3.007398 AGAGTGAGTGAGCTAGGGTTTTG 59.993 47.826 0.00 0.00 0.00 2.44
2372 2651 3.243724 AGAGTGAGTGAGCTAGGGTTTT 58.756 45.455 0.00 0.00 0.00 2.43
2373 2652 2.829120 GAGAGTGAGTGAGCTAGGGTTT 59.171 50.000 0.00 0.00 0.00 3.27
2374 2653 2.452505 GAGAGTGAGTGAGCTAGGGTT 58.547 52.381 0.00 0.00 0.00 4.11
2375 2654 1.341581 GGAGAGTGAGTGAGCTAGGGT 60.342 57.143 0.00 0.00 0.00 4.34
2376 2655 1.064017 AGGAGAGTGAGTGAGCTAGGG 60.064 57.143 0.00 0.00 0.00 3.53
2377 2656 2.092429 AGAGGAGAGTGAGTGAGCTAGG 60.092 54.545 0.00 0.00 0.00 3.02
2378 2657 3.118261 AGAGAGGAGAGTGAGTGAGCTAG 60.118 52.174 0.00 0.00 0.00 3.42
2379 2658 2.843730 AGAGAGGAGAGTGAGTGAGCTA 59.156 50.000 0.00 0.00 0.00 3.32
2380 2659 1.635487 AGAGAGGAGAGTGAGTGAGCT 59.365 52.381 0.00 0.00 0.00 4.09
2381 2660 2.017049 GAGAGAGGAGAGTGAGTGAGC 58.983 57.143 0.00 0.00 0.00 4.26
2382 2661 2.279741 CGAGAGAGGAGAGTGAGTGAG 58.720 57.143 0.00 0.00 0.00 3.51
2383 2662 1.677518 GCGAGAGAGGAGAGTGAGTGA 60.678 57.143 0.00 0.00 0.00 3.41
2384 2663 0.732571 GCGAGAGAGGAGAGTGAGTG 59.267 60.000 0.00 0.00 0.00 3.51
2385 2664 0.618458 AGCGAGAGAGGAGAGTGAGT 59.382 55.000 0.00 0.00 0.00 3.41
2386 2665 1.299541 GAGCGAGAGAGGAGAGTGAG 58.700 60.000 0.00 0.00 0.00 3.51
2387 2666 0.107410 GGAGCGAGAGAGGAGAGTGA 60.107 60.000 0.00 0.00 0.00 3.41
2388 2667 1.436195 CGGAGCGAGAGAGGAGAGTG 61.436 65.000 0.00 0.00 0.00 3.51
2389 2668 1.153249 CGGAGCGAGAGAGGAGAGT 60.153 63.158 0.00 0.00 0.00 3.24
2390 2669 3.731136 CGGAGCGAGAGAGGAGAG 58.269 66.667 0.00 0.00 0.00 3.20
2403 2682 2.520741 GGAGAGGAGAGGGCGGAG 60.521 72.222 0.00 0.00 0.00 4.63
2473 2798 3.838271 GGATCCTGCTCGTCGCCA 61.838 66.667 3.84 0.00 38.05 5.69
2484 2809 1.967066 CAAGCTCATACTCCGGATCCT 59.033 52.381 3.57 0.00 0.00 3.24
2528 2854 1.538876 CCCTGGTCTCCACCTTGGA 60.539 63.158 0.00 0.00 45.98 3.53
2529 2855 2.606587 CCCCTGGTCTCCACCTTGG 61.607 68.421 0.00 0.00 44.17 3.61
2530 2856 3.081554 CCCCTGGTCTCCACCTTG 58.918 66.667 0.00 0.00 44.17 3.61
2531 2857 2.936032 GCCCCTGGTCTCCACCTT 60.936 66.667 0.00 0.00 44.17 3.50
2532 2858 4.270153 TGCCCCTGGTCTCCACCT 62.270 66.667 0.00 0.00 44.17 4.00
2533 2859 3.721706 CTGCCCCTGGTCTCCACC 61.722 72.222 0.00 0.00 44.10 4.61
2534 2860 4.416738 GCTGCCCCTGGTCTCCAC 62.417 72.222 0.00 0.00 0.00 4.02
2535 2861 4.664267 AGCTGCCCCTGGTCTCCA 62.664 66.667 0.00 0.00 0.00 3.86
2536 2862 3.791586 GAGCTGCCCCTGGTCTCC 61.792 72.222 0.00 0.00 0.00 3.71
2537 2863 2.686835 AGAGCTGCCCCTGGTCTC 60.687 66.667 0.00 0.00 35.82 3.36
2538 2864 3.007920 CAGAGCTGCCCCTGGTCT 61.008 66.667 10.65 0.00 39.90 3.85
2539 2865 4.106925 CCAGAGCTGCCCCTGGTC 62.107 72.222 22.96 3.80 43.71 4.02
2542 2868 2.071262 AGATCCAGAGCTGCCCCTG 61.071 63.158 11.33 11.33 0.00 4.45
2543 2869 2.071262 CAGATCCAGAGCTGCCCCT 61.071 63.158 0.00 0.00 38.05 4.79
2544 2870 2.509916 CAGATCCAGAGCTGCCCC 59.490 66.667 0.00 0.00 38.05 5.80
2549 2875 1.767681 GAATCCCACAGATCCAGAGCT 59.232 52.381 0.00 0.00 32.47 4.09
2550 2876 1.202746 GGAATCCCACAGATCCAGAGC 60.203 57.143 0.00 0.00 32.47 4.09
2551 2877 1.069823 CGGAATCCCACAGATCCAGAG 59.930 57.143 0.00 0.00 32.47 3.35
2552 2878 1.123077 CGGAATCCCACAGATCCAGA 58.877 55.000 0.00 0.00 32.47 3.86
2553 2879 1.123077 TCGGAATCCCACAGATCCAG 58.877 55.000 0.00 0.00 32.47 3.86
2554 2880 1.694150 GATCGGAATCCCACAGATCCA 59.306 52.381 0.00 0.00 34.60 3.41
2555 2881 1.337260 CGATCGGAATCCCACAGATCC 60.337 57.143 7.38 0.00 36.27 3.36
2556 2882 1.613925 TCGATCGGAATCCCACAGATC 59.386 52.381 16.41 0.00 36.29 2.75
2557 2883 1.704641 TCGATCGGAATCCCACAGAT 58.295 50.000 16.41 0.00 36.48 2.90
2558 2884 1.480789 TTCGATCGGAATCCCACAGA 58.519 50.000 16.41 0.00 0.00 3.41
2559 2885 2.533266 ATTCGATCGGAATCCCACAG 57.467 50.000 16.41 0.00 41.57 3.66
2570 2896 2.310233 ATTGCGCCGGATTCGATCG 61.310 57.895 5.05 9.36 39.00 3.69
2571 2897 1.205064 CATTGCGCCGGATTCGATC 59.795 57.895 5.05 0.00 39.00 3.69
2572 2898 1.095228 AACATTGCGCCGGATTCGAT 61.095 50.000 5.05 0.00 39.00 3.59
2573 2899 1.743623 AACATTGCGCCGGATTCGA 60.744 52.632 5.05 0.00 39.00 3.71
2574 2900 1.583451 CAACATTGCGCCGGATTCG 60.583 57.895 5.05 0.00 0.00 3.34
2575 2901 0.248215 CTCAACATTGCGCCGGATTC 60.248 55.000 5.05 0.00 0.00 2.52
2576 2902 1.802636 CTCAACATTGCGCCGGATT 59.197 52.632 5.05 0.00 0.00 3.01
2577 2903 2.764314 GCTCAACATTGCGCCGGAT 61.764 57.895 5.05 0.00 33.03 4.18
2578 2904 3.430862 GCTCAACATTGCGCCGGA 61.431 61.111 5.05 0.00 33.03 5.14
2579 2905 3.386867 GAGCTCAACATTGCGCCGG 62.387 63.158 9.40 0.00 39.59 6.13
2580 2906 2.099062 GAGCTCAACATTGCGCCG 59.901 61.111 9.40 0.00 39.59 6.46
2581 2907 2.486966 GGAGCTCAACATTGCGCC 59.513 61.111 17.19 0.00 39.59 6.53
2582 2908 2.099062 CGGAGCTCAACATTGCGC 59.901 61.111 17.19 0.00 39.08 6.09
2583 2909 2.787249 CCGGAGCTCAACATTGCG 59.213 61.111 17.19 7.68 0.00 4.85
2584 2910 2.262471 CTGCCGGAGCTCAACATTGC 62.262 60.000 17.19 8.54 40.80 3.56
2585 2911 1.798735 CTGCCGGAGCTCAACATTG 59.201 57.895 17.19 0.00 40.80 2.82
2586 2912 2.042831 GCTGCCGGAGCTCAACATT 61.043 57.895 17.19 0.00 45.21 2.71
2587 2913 2.437359 GCTGCCGGAGCTCAACAT 60.437 61.111 17.19 0.00 45.21 2.71
2609 2935 4.933064 GATCCTGCTCGTCGCCGG 62.933 72.222 0.00 0.00 43.69 6.13
2610 2936 4.933064 GGATCCTGCTCGTCGCCG 62.933 72.222 3.84 0.00 38.05 6.46
2611 2937 4.933064 CGGATCCTGCTCGTCGCC 62.933 72.222 10.75 0.00 38.05 5.54
2612 2938 4.933064 CCGGATCCTGCTCGTCGC 62.933 72.222 10.75 0.00 39.77 5.19
2613 2939 3.187699 CTCCGGATCCTGCTCGTCG 62.188 68.421 3.57 0.00 0.00 5.12
2614 2940 0.818445 TACTCCGGATCCTGCTCGTC 60.818 60.000 3.57 0.00 0.00 4.20
2615 2941 0.178987 ATACTCCGGATCCTGCTCGT 60.179 55.000 3.57 0.00 0.00 4.18
2616 2942 0.242286 CATACTCCGGATCCTGCTCG 59.758 60.000 3.57 0.00 0.00 5.03
2617 2943 1.543802 CTCATACTCCGGATCCTGCTC 59.456 57.143 3.57 0.00 0.00 4.26
2618 2944 1.626686 CTCATACTCCGGATCCTGCT 58.373 55.000 3.57 0.00 0.00 4.24
2619 2945 0.037790 GCTCATACTCCGGATCCTGC 60.038 60.000 3.57 1.28 0.00 4.85
2620 2946 1.626686 AGCTCATACTCCGGATCCTG 58.373 55.000 3.57 2.93 0.00 3.86
2621 2947 1.967066 CAAGCTCATACTCCGGATCCT 59.033 52.381 3.57 0.00 0.00 3.24
2622 2948 1.689273 ACAAGCTCATACTCCGGATCC 59.311 52.381 3.57 0.00 0.00 3.36
2623 2949 2.288518 GGACAAGCTCATACTCCGGATC 60.289 54.545 3.57 0.00 0.00 3.36
2624 2950 1.689273 GGACAAGCTCATACTCCGGAT 59.311 52.381 3.57 0.00 0.00 4.18
2625 2951 1.112113 GGACAAGCTCATACTCCGGA 58.888 55.000 2.93 2.93 0.00 5.14
2626 2952 1.067821 GAGGACAAGCTCATACTCCGG 59.932 57.143 0.00 0.00 0.00 5.14
2627 2953 1.067821 GGAGGACAAGCTCATACTCCG 59.932 57.143 11.73 0.00 35.65 4.63
2628 2954 1.067821 CGGAGGACAAGCTCATACTCC 59.932 57.143 15.75 15.75 40.76 3.85
2629 2955 1.537135 GCGGAGGACAAGCTCATACTC 60.537 57.143 1.41 1.41 0.00 2.59
2630 2956 0.461961 GCGGAGGACAAGCTCATACT 59.538 55.000 0.00 0.00 0.00 2.12
2631 2957 0.175760 TGCGGAGGACAAGCTCATAC 59.824 55.000 0.00 0.00 0.00 2.39
2632 2958 1.069204 GATGCGGAGGACAAGCTCATA 59.931 52.381 0.00 0.00 0.00 2.15
2633 2959 0.179062 GATGCGGAGGACAAGCTCAT 60.179 55.000 0.00 0.00 0.00 2.90
2634 2960 1.219124 GATGCGGAGGACAAGCTCA 59.781 57.895 0.00 0.00 0.00 4.26
2635 2961 1.880340 CGATGCGGAGGACAAGCTC 60.880 63.158 0.00 0.00 0.00 4.09
2636 2962 2.185350 CGATGCGGAGGACAAGCT 59.815 61.111 0.00 0.00 0.00 3.74
2637 2963 3.567797 GCGATGCGGAGGACAAGC 61.568 66.667 0.00 0.00 0.00 4.01
2638 2964 2.859273 AAGGCGATGCGGAGGACAAG 62.859 60.000 0.00 0.00 0.00 3.16
2639 2965 2.954684 AAGGCGATGCGGAGGACAA 61.955 57.895 0.00 0.00 0.00 3.18
2640 2966 3.390521 AAGGCGATGCGGAGGACA 61.391 61.111 0.00 0.00 0.00 4.02
2641 2967 2.892425 CAAGGCGATGCGGAGGAC 60.892 66.667 0.00 0.00 0.00 3.85
2642 2968 4.161295 CCAAGGCGATGCGGAGGA 62.161 66.667 0.00 0.00 0.00 3.71
2643 2969 4.161295 TCCAAGGCGATGCGGAGG 62.161 66.667 0.00 0.00 0.00 4.30
2644 2970 2.587194 CTCCAAGGCGATGCGGAG 60.587 66.667 0.00 0.00 39.20 4.63
2645 2971 4.838152 GCTCCAAGGCGATGCGGA 62.838 66.667 0.00 0.00 0.00 5.54
2646 2972 2.721971 ATAGCTCCAAGGCGATGCGG 62.722 60.000 0.00 0.00 37.29 5.69
2647 2973 1.287730 GATAGCTCCAAGGCGATGCG 61.288 60.000 0.00 0.00 37.29 4.73
2648 2974 0.952984 GGATAGCTCCAAGGCGATGC 60.953 60.000 0.00 0.00 41.64 3.91
2649 2975 3.223661 GGATAGCTCCAAGGCGATG 57.776 57.895 0.00 0.00 41.64 3.84
2680 3006 4.488911 AGATCCGGAGCTGCCCCT 62.489 66.667 23.99 0.00 0.00 4.79
2712 3038 1.302511 CCGACAGGGAAGTTGTGGG 60.303 63.158 0.00 0.00 37.94 4.61
2856 3183 1.228124 GCACAAGCACCCACCACTA 60.228 57.895 0.00 0.00 41.58 2.74
2859 3186 4.912395 GGGCACAAGCACCCACCA 62.912 66.667 0.00 0.00 46.22 4.17


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

AutoCloner maintained by Alex Coulton.