Multiple sequence alignment - TraesCS7A01G331500

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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 TraesCS7A01G331500 chr7A 100.000 5223 0 0 1 5223 484592774 484597996 0.000000e+00 9646.0
1 TraesCS7A01G331500 chr7B 95.974 2881 79 24 1530 4384 451352766 451355635 0.000000e+00 4643.0
2 TraesCS7A01G331500 chr7B 94.718 852 39 4 628 1474 451351918 451352768 0.000000e+00 1319.0
3 TraesCS7A01G331500 chr7B 91.837 147 11 1 4650 4795 451359762 451359908 2.470000e-48 204.0
4 TraesCS7A01G331500 chr7B 91.156 147 13 0 5074 5220 451359939 451360085 3.190000e-47 200.0
5 TraesCS7A01G331500 chr7B 89.873 158 9 1 4495 4652 451359183 451359333 4.130000e-46 196.0
6 TraesCS7A01G331500 chr7D 95.787 2872 91 19 1530 4391 434147210 434150061 0.000000e+00 4606.0
7 TraesCS7A01G331500 chr7D 95.416 829 35 1 649 1474 434146384 434147212 0.000000e+00 1317.0
8 TraesCS7A01G331500 chr7D 78.771 1107 204 29 3118 4210 14881516 14880427 0.000000e+00 713.0
9 TraesCS7A01G331500 chr7D 89.619 472 42 4 129 597 163500902 163500435 1.250000e-165 593.0
10 TraesCS7A01G331500 chr7D 82.886 596 62 24 4650 5220 434150905 434151485 2.810000e-137 499.0
11 TraesCS7A01G331500 chr7D 89.767 215 15 1 4438 4652 434150183 434150390 8.620000e-68 268.0
12 TraesCS7A01G331500 chr5B 79.267 1119 196 32 3089 4186 127504495 127505598 0.000000e+00 749.0
13 TraesCS7A01G331500 chr5B 82.599 431 73 2 2567 2996 127503925 127504354 3.820000e-101 379.0
14 TraesCS7A01G331500 chr5A 79.159 1118 199 32 3089 4186 122956599 122957702 0.000000e+00 743.0
15 TraesCS7A01G331500 chr5A 82.558 430 73 2 2567 2995 122956029 122956457 1.370000e-100 377.0
16 TraesCS7A01G331500 chr5D 80.333 1022 165 33 3186 4186 115950588 115951594 0.000000e+00 741.0
17 TraesCS7A01G331500 chr5D 82.850 414 69 2 2583 2995 115949937 115950349 2.300000e-98 370.0
18 TraesCS7A01G331500 chr3D 89.194 583 55 5 1 579 131640761 131641339 0.000000e+00 721.0
19 TraesCS7A01G331500 chr2B 89.706 408 38 4 2583 2988 110854160 110854565 7.750000e-143 518.0
20 TraesCS7A01G331500 chr2B 78.278 755 143 14 1671 2410 110853234 110853982 2.850000e-127 466.0
21 TraesCS7A01G331500 chr2B 76.331 169 39 1 1835 2003 236527944 236527777 7.200000e-14 89.8
22 TraesCS7A01G331500 chr2A 88.194 432 48 3 2556 2986 72693412 72693841 3.610000e-141 512.0
23 TraesCS7A01G331500 chr2A 78.117 754 146 12 1671 2410 72692513 72693261 1.330000e-125 460.0
24 TraesCS7A01G331500 chr2A 73.896 249 58 7 1835 2080 194130693 194130449 5.570000e-15 93.5
25 TraesCS7A01G331500 chr2D 89.567 393 38 3 2595 2986 73323867 73323477 3.630000e-136 496.0
26 TraesCS7A01G331500 chr2D 77.086 755 152 14 1671 2410 73324861 73324113 2.910000e-112 416.0
27 TraesCS7A01G331500 chr2D 74.153 236 56 5 1835 2068 179692826 179692594 5.570000e-15 93.5
28 TraesCS7A01G331500 chrUn 80.693 404 71 7 2553 2951 5436087 5435686 1.830000e-79 307.0
29 TraesCS7A01G331500 chr6D 87.234 235 25 5 368 601 68849661 68849431 4.010000e-66 263.0
30 TraesCS7A01G331500 chr4D 75.085 590 128 17 1 578 110215955 110215373 1.870000e-64 257.0
31 TraesCS7A01G331500 chr4D 88.571 70 8 0 4983 5052 209100991 209101060 9.320000e-13 86.1
32 TraesCS7A01G331500 chr4B 90.000 70 7 0 4983 5052 310983231 310983300 2.000000e-14 91.6


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 TraesCS7A01G331500 chr7A 484592774 484597996 5222 False 9646.0 9646 100.0000 1 5223 1 chr7A.!!$F1 5222
1 TraesCS7A01G331500 chr7B 451351918 451360085 8167 False 1312.4 4643 92.7116 628 5220 5 chr7B.!!$F1 4592
2 TraesCS7A01G331500 chr7D 434146384 434151485 5101 False 1672.5 4606 90.9640 649 5220 4 chr7D.!!$F1 4571
3 TraesCS7A01G331500 chr7D 14880427 14881516 1089 True 713.0 713 78.7710 3118 4210 1 chr7D.!!$R1 1092
4 TraesCS7A01G331500 chr5B 127503925 127505598 1673 False 564.0 749 80.9330 2567 4186 2 chr5B.!!$F1 1619
5 TraesCS7A01G331500 chr5A 122956029 122957702 1673 False 560.0 743 80.8585 2567 4186 2 chr5A.!!$F1 1619
6 TraesCS7A01G331500 chr5D 115949937 115951594 1657 False 555.5 741 81.5915 2583 4186 2 chr5D.!!$F1 1603
7 TraesCS7A01G331500 chr3D 131640761 131641339 578 False 721.0 721 89.1940 1 579 1 chr3D.!!$F1 578
8 TraesCS7A01G331500 chr2B 110853234 110854565 1331 False 492.0 518 83.9920 1671 2988 2 chr2B.!!$F1 1317
9 TraesCS7A01G331500 chr2A 72692513 72693841 1328 False 486.0 512 83.1555 1671 2986 2 chr2A.!!$F1 1315
10 TraesCS7A01G331500 chr2D 73323477 73324861 1384 True 456.0 496 83.3265 1671 2986 2 chr2D.!!$R2 1315
11 TraesCS7A01G331500 chr4D 110215373 110215955 582 True 257.0 257 75.0850 1 578 1 chr4D.!!$R1 577

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
825 835 0.031857 CAGTTTGCAACAATGGCGGA 59.968 50.0 0.00 0.0 0.00 5.54 F
829 839 0.250684 TTGCAACAATGGCGGAGAGA 60.251 50.0 0.00 0.0 0.00 3.10 F
1562 1575 0.731514 ATGTTACGACACGAGCACGG 60.732 55.0 8.74 0.0 44.46 4.94 F
2414 2449 0.803768 CAGCATCGTCCAGGTCTTCG 60.804 60.0 0.00 0.0 0.00 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2414 2449 0.951558 ACGAAATGGCCAGTGTTGAC 59.048 50.000 13.05 0.0 0.00 3.18 R
2455 2550 2.517650 TCGTAGCATGAACACACACA 57.482 45.000 0.00 0.0 0.00 3.72 R
2456 2551 3.254060 AGATCGTAGCATGAACACACAC 58.746 45.455 0.00 0.0 0.00 3.82 R
4308 4470 0.740868 TGCACTTCGTAGCTGATGGC 60.741 55.000 0.00 0.0 42.19 4.40 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
45 46 2.047274 GCTGGCGGCTCAGTACAA 60.047 61.111 11.99 0.00 37.12 2.41
116 117 5.105310 ACATCTCCTTGTTACTTATGCGAGT 60.105 40.000 0.00 0.00 0.00 4.18
122 123 5.067413 CCTTGTTACTTATGCGAGTAGGAGA 59.933 44.000 0.00 0.00 33.91 3.71
130 131 0.099082 GCGAGTAGGAGAAGGACACG 59.901 60.000 0.00 0.00 0.00 4.49
131 132 1.735386 CGAGTAGGAGAAGGACACGA 58.265 55.000 0.00 0.00 30.13 4.35
172 173 2.186160 TGTGTTCGCCAGGCAAGTG 61.186 57.895 13.30 0.00 0.00 3.16
199 200 2.241176 CCAATGCCTTACTAGGGTTGGA 59.759 50.000 0.00 0.00 42.25 3.53
204 205 3.245875 TGCCTTACTAGGGTTGGACTACT 60.246 47.826 0.00 0.00 42.25 2.57
210 211 1.201429 AGGGTTGGACTACTGCTGGG 61.201 60.000 0.00 0.00 0.00 4.45
237 238 1.069049 GCCAACTGGACAAGCAACAAT 59.931 47.619 0.00 0.00 37.39 2.71
238 239 2.295909 GCCAACTGGACAAGCAACAATA 59.704 45.455 0.00 0.00 37.39 1.90
254 255 5.679638 GCAACAATATGGAAGAATGGTGGAC 60.680 44.000 0.00 0.00 0.00 4.02
258 259 0.037697 TGGAAGAATGGTGGACGACG 60.038 55.000 0.00 0.00 0.00 5.12
279 280 1.580845 CTCGGAAGCTGGTGCCAAAG 61.581 60.000 4.47 0.00 40.80 2.77
348 349 0.821711 TGTGGAAGCAAAGGAACGGG 60.822 55.000 0.00 0.00 0.00 5.28
378 379 6.730960 TTCGGTAGGAATGACAATTGTAAC 57.269 37.500 11.95 0.16 0.00 2.50
420 421 5.932303 GCTCATATTTAGGGAGCGTCATTTA 59.068 40.000 0.00 0.00 43.83 1.40
427 428 1.507141 GGAGCGTCATTTATGGGCGG 61.507 60.000 0.00 0.00 34.41 6.13
465 466 6.017440 GTGGAGTGCTACAATTTTGTGAGTAA 60.017 38.462 6.21 0.00 42.31 2.24
482 483 8.856153 TGTGAGTAATTCCTAGCATGTTTAAA 57.144 30.769 0.00 0.00 0.00 1.52
501 502 2.787567 GGAGGGCTCGAGTGTAGGC 61.788 68.421 15.13 0.00 38.73 3.93
502 503 2.037367 AGGGCTCGAGTGTAGGCA 59.963 61.111 15.13 0.00 41.11 4.75
517 525 3.264897 GCACACCTAGGCGATGCG 61.265 66.667 9.30 0.00 0.00 4.73
573 583 8.370182 TCTTCTTTCCATAAAGTTAAGGTACGT 58.630 33.333 0.00 0.00 42.36 3.57
579 589 7.669427 TCCATAAAGTTAAGGTACGTCTTTGA 58.331 34.615 0.00 0.00 32.01 2.69
580 590 8.316214 TCCATAAAGTTAAGGTACGTCTTTGAT 58.684 33.333 0.00 0.90 32.01 2.57
581 591 8.388103 CCATAAAGTTAAGGTACGTCTTTGATG 58.612 37.037 0.00 9.04 32.01 3.07
582 592 8.932791 CATAAAGTTAAGGTACGTCTTTGATGT 58.067 33.333 0.00 0.00 35.78 3.06
585 595 9.498176 AAAGTTAAGGTACGTCTTTGATGTATT 57.502 29.630 0.00 0.00 36.59 1.89
586 596 8.699283 AGTTAAGGTACGTCTTTGATGTATTC 57.301 34.615 0.00 0.97 36.59 1.75
587 597 8.529476 AGTTAAGGTACGTCTTTGATGTATTCT 58.471 33.333 0.00 2.82 36.59 2.40
588 598 9.148104 GTTAAGGTACGTCTTTGATGTATTCTT 57.852 33.333 0.00 15.45 36.59 2.52
589 599 7.596749 AAGGTACGTCTTTGATGTATTCTTG 57.403 36.000 0.00 0.00 36.59 3.02
590 600 6.931838 AGGTACGTCTTTGATGTATTCTTGA 58.068 36.000 0.00 0.00 36.59 3.02
591 601 7.383687 AGGTACGTCTTTGATGTATTCTTGAA 58.616 34.615 0.00 0.00 36.59 2.69
592 602 7.545965 AGGTACGTCTTTGATGTATTCTTGAAG 59.454 37.037 0.00 0.00 36.59 3.02
593 603 7.544566 GGTACGTCTTTGATGTATTCTTGAAGA 59.455 37.037 0.00 0.00 36.59 2.87
594 604 7.962964 ACGTCTTTGATGTATTCTTGAAGAA 57.037 32.000 10.39 10.39 38.78 2.52
595 605 8.378172 ACGTCTTTGATGTATTCTTGAAGAAA 57.622 30.769 12.10 0.00 37.82 2.52
596 606 8.836413 ACGTCTTTGATGTATTCTTGAAGAAAA 58.164 29.630 12.10 1.48 37.82 2.29
597 607 9.663904 CGTCTTTGATGTATTCTTGAAGAAAAA 57.336 29.630 12.10 5.97 37.82 1.94
618 628 4.820894 AAAAGACCCTTGCGTCTATACT 57.179 40.909 0.00 0.00 42.35 2.12
619 629 4.388378 AAAGACCCTTGCGTCTATACTC 57.612 45.455 0.00 0.00 42.35 2.59
620 630 3.300239 AGACCCTTGCGTCTATACTCT 57.700 47.619 0.00 0.00 41.37 3.24
621 631 2.952978 AGACCCTTGCGTCTATACTCTG 59.047 50.000 0.00 0.00 41.37 3.35
622 632 2.688958 GACCCTTGCGTCTATACTCTGT 59.311 50.000 0.00 0.00 0.00 3.41
623 633 3.097614 ACCCTTGCGTCTATACTCTGTT 58.902 45.455 0.00 0.00 0.00 3.16
624 634 3.514309 ACCCTTGCGTCTATACTCTGTTT 59.486 43.478 0.00 0.00 0.00 2.83
625 635 4.708421 ACCCTTGCGTCTATACTCTGTTTA 59.292 41.667 0.00 0.00 0.00 2.01
626 636 5.186409 ACCCTTGCGTCTATACTCTGTTTAA 59.814 40.000 0.00 0.00 0.00 1.52
627 637 6.103997 CCCTTGCGTCTATACTCTGTTTAAA 58.896 40.000 0.00 0.00 0.00 1.52
628 638 6.592607 CCCTTGCGTCTATACTCTGTTTAAAA 59.407 38.462 0.00 0.00 0.00 1.52
629 639 7.118680 CCCTTGCGTCTATACTCTGTTTAAAAA 59.881 37.037 0.00 0.00 0.00 1.94
744 754 2.202797 CGCCACTCCACATCTCGG 60.203 66.667 0.00 0.00 0.00 4.63
825 835 0.031857 CAGTTTGCAACAATGGCGGA 59.968 50.000 0.00 0.00 0.00 5.54
829 839 0.250684 TTGCAACAATGGCGGAGAGA 60.251 50.000 0.00 0.00 0.00 3.10
909 919 3.316573 GAAGCTACCGGCAGCAGGT 62.317 63.158 28.15 21.76 44.35 4.00
1062 1072 2.034687 CCAGACAACCAGCCAGGG 59.965 66.667 0.00 0.00 43.89 4.45
1124 1134 2.747855 CCTTCCCTTGCCACGCTC 60.748 66.667 0.00 0.00 0.00 5.03
1125 1135 3.121030 CTTCCCTTGCCACGCTCG 61.121 66.667 0.00 0.00 0.00 5.03
1204 1217 3.325201 ATGGACCGTCGGCTTTCCC 62.325 63.158 12.28 5.78 0.00 3.97
1260 1273 4.778143 CGGAGCCAAACCGGGGAG 62.778 72.222 6.32 0.00 45.65 4.30
1458 1471 3.809905 CATTCTAAGCCCCTACAGGTTC 58.190 50.000 0.00 0.00 0.00 3.62
1468 1481 2.817258 CCCTACAGGTTCGCAAAATTCA 59.183 45.455 0.00 0.00 0.00 2.57
1474 1487 4.803613 ACAGGTTCGCAAAATTCAAGAAAC 59.196 37.500 0.00 0.00 0.00 2.78
1475 1488 5.043248 CAGGTTCGCAAAATTCAAGAAACT 58.957 37.500 0.00 0.00 39.18 2.66
1476 1489 5.519927 CAGGTTCGCAAAATTCAAGAAACTT 59.480 36.000 2.12 0.00 36.81 2.66
1477 1490 5.519927 AGGTTCGCAAAATTCAAGAAACTTG 59.480 36.000 5.29 5.29 35.58 3.16
1478 1491 5.290885 GGTTCGCAAAATTCAAGAAACTTGT 59.709 36.000 10.56 0.00 0.00 3.16
1479 1492 6.183360 GGTTCGCAAAATTCAAGAAACTTGTT 60.183 34.615 10.56 0.00 0.00 2.83
1480 1493 6.329838 TCGCAAAATTCAAGAAACTTGTTG 57.670 33.333 10.56 8.92 33.19 3.33
1481 1494 6.096036 TCGCAAAATTCAAGAAACTTGTTGA 58.904 32.000 10.56 0.00 38.49 3.18
1482 1495 6.253298 TCGCAAAATTCAAGAAACTTGTTGAG 59.747 34.615 10.56 9.45 40.81 3.02
1483 1496 6.034898 CGCAAAATTCAAGAAACTTGTTGAGT 59.965 34.615 10.56 0.00 40.81 3.41
1518 1531 9.679661 AAAAATTGAAAAACTTTACATGGGAGT 57.320 25.926 0.00 0.00 0.00 3.85
1520 1533 9.758651 AAATTGAAAAACTTTACATGGGAGTAC 57.241 29.630 0.00 0.00 0.00 2.73
1521 1534 7.883391 TTGAAAAACTTTACATGGGAGTACA 57.117 32.000 0.00 0.00 0.00 2.90
1522 1535 7.883391 TGAAAAACTTTACATGGGAGTACAA 57.117 32.000 0.00 0.00 0.00 2.41
1523 1536 8.472007 TGAAAAACTTTACATGGGAGTACAAT 57.528 30.769 0.00 0.00 0.00 2.71
1524 1537 8.919145 TGAAAAACTTTACATGGGAGTACAATT 58.081 29.630 0.00 0.00 0.00 2.32
1525 1538 9.758651 GAAAAACTTTACATGGGAGTACAATTT 57.241 29.630 0.00 0.00 0.00 1.82
1529 1542 9.747898 AACTTTACATGGGAGTACAATTTATCA 57.252 29.630 0.00 0.00 0.00 2.15
1530 1543 9.747898 ACTTTACATGGGAGTACAATTTATCAA 57.252 29.630 0.00 0.00 0.00 2.57
1557 1570 5.911421 TCAATCAAAATGTTACGACACGAG 58.089 37.500 0.00 0.00 38.91 4.18
1558 1571 3.781341 TCAAAATGTTACGACACGAGC 57.219 42.857 0.00 0.00 38.91 5.03
1559 1572 3.124560 TCAAAATGTTACGACACGAGCA 58.875 40.909 0.00 0.00 38.91 4.26
1560 1573 3.060138 TCAAAATGTTACGACACGAGCAC 60.060 43.478 0.00 0.00 38.91 4.40
1561 1574 1.057636 AATGTTACGACACGAGCACG 58.942 50.000 0.76 0.76 45.75 5.34
1562 1575 0.731514 ATGTTACGACACGAGCACGG 60.732 55.000 8.74 0.00 44.46 4.94
1579 1602 4.864247 AGCACGGCACATGATTTAAATTTC 59.136 37.500 0.00 0.00 0.00 2.17
2161 2184 4.367023 TTCGTCAAGGACCGGCGG 62.367 66.667 27.06 27.06 0.00 6.13
2414 2449 0.803768 CAGCATCGTCCAGGTCTTCG 60.804 60.000 0.00 0.00 0.00 3.79
2424 2459 1.502231 CAGGTCTTCGTCAACACTGG 58.498 55.000 0.00 0.00 0.00 4.00
2455 2550 0.243365 TTGAATTTTGGCGCGCAGAT 59.757 45.000 34.42 17.03 0.00 2.90
2456 2551 0.456482 TGAATTTTGGCGCGCAGATG 60.456 50.000 34.42 0.00 0.00 2.90
2469 2564 1.726892 CGCAGATGTGTGTGTTCATGC 60.727 52.381 0.00 0.00 0.00 4.06
3508 3664 1.723542 CAAGAACAACGCGCTGCTG 60.724 57.895 9.87 3.35 0.00 4.41
3670 3826 0.032017 ACCCGACCTTCCTCTGCTAT 60.032 55.000 0.00 0.00 0.00 2.97
3745 3901 2.768344 GGGATCGGGCTGGAGGAA 60.768 66.667 0.00 0.00 0.00 3.36
4226 4388 1.142748 GGCATCGAGGTGTGAGGAG 59.857 63.158 0.00 0.00 0.00 3.69
4227 4389 1.520342 GCATCGAGGTGTGAGGAGC 60.520 63.158 0.00 0.00 0.00 4.70
4228 4390 1.893062 CATCGAGGTGTGAGGAGCA 59.107 57.895 0.00 0.00 0.00 4.26
4229 4391 0.179116 CATCGAGGTGTGAGGAGCAG 60.179 60.000 0.00 0.00 0.00 4.24
4230 4392 0.323816 ATCGAGGTGTGAGGAGCAGA 60.324 55.000 0.00 0.00 0.00 4.26
4257 4419 1.658717 AGGAAATCGATCGAGCGCG 60.659 57.895 23.84 2.41 39.35 6.86
4306 4468 4.179579 GCCAAGAACCGCGCCATC 62.180 66.667 0.00 0.00 0.00 3.51
4307 4469 2.745884 CCAAGAACCGCGCCATCA 60.746 61.111 0.00 0.00 0.00 3.07
4308 4470 2.753966 CCAAGAACCGCGCCATCAG 61.754 63.158 0.00 0.00 0.00 2.90
4309 4471 3.127533 AAGAACCGCGCCATCAGC 61.128 61.111 0.00 0.00 38.52 4.26
4328 4490 1.725641 CCATCAGCTACGAAGTGCAA 58.274 50.000 0.00 0.00 45.73 4.08
4329 4491 1.662629 CCATCAGCTACGAAGTGCAAG 59.337 52.381 0.00 0.00 45.73 4.01
4337 4499 3.968724 GCTACGAAGTGCAAGAAAACAAG 59.031 43.478 0.00 0.00 45.73 3.16
4392 4611 7.333423 GGATGCACAAGATTAGTAACACTGTAA 59.667 37.037 0.00 0.00 0.00 2.41
4404 4623 5.701290 AGTAACACTGTAAGCAGGTCAATTC 59.299 40.000 0.00 0.00 46.62 2.17
4413 4632 2.568956 AGCAGGTCAATTCTGTAGCTGA 59.431 45.455 0.00 0.00 40.34 4.26
4438 4668 3.198863 CGTACCTACGCACTGATATCC 57.801 52.381 0.00 0.00 43.14 2.59
4439 4669 2.551032 CGTACCTACGCACTGATATCCA 59.449 50.000 0.00 0.00 43.14 3.41
4440 4670 3.190744 CGTACCTACGCACTGATATCCAT 59.809 47.826 0.00 0.00 43.14 3.41
4441 4671 4.393990 CGTACCTACGCACTGATATCCATA 59.606 45.833 0.00 0.00 43.14 2.74
4443 4673 4.408276 ACCTACGCACTGATATCCATACT 58.592 43.478 0.00 0.00 0.00 2.12
4444 4674 4.459685 ACCTACGCACTGATATCCATACTC 59.540 45.833 0.00 0.00 0.00 2.59
4446 4676 5.126222 CCTACGCACTGATATCCATACTCAT 59.874 44.000 0.00 0.00 0.00 2.90
4530 8173 9.636789 ACATATATGCTCCCGTATTATGTAGTA 57.363 33.333 12.79 0.00 0.00 1.82
4533 8176 8.998277 ATATGCTCCCGTATTATGTAGTAGAT 57.002 34.615 0.00 0.00 0.00 1.98
4534 8177 6.754702 TGCTCCCGTATTATGTAGTAGATC 57.245 41.667 0.00 0.00 0.00 2.75
4535 8178 5.353400 TGCTCCCGTATTATGTAGTAGATCG 59.647 44.000 0.00 0.00 0.00 3.69
4536 8179 5.583854 GCTCCCGTATTATGTAGTAGATCGA 59.416 44.000 0.00 0.00 0.00 3.59
4548 8191 5.753438 TGTAGTAGATCGATGTTGGCAATTC 59.247 40.000 0.54 3.07 0.00 2.17
4607 8250 4.566759 TGATCTCGATTTTCACATTCGTCC 59.433 41.667 0.00 0.00 34.60 4.79
4617 8260 1.325640 CACATTCGTCCGATCAGCTTG 59.674 52.381 0.00 0.00 0.00 4.01
4668 8828 6.649557 ACTTGATTACTAGGAACTGGAAAACG 59.350 38.462 0.00 0.00 40.33 3.60
4690 8850 3.607078 GCAAGGAGCGTGAAAACTAAGTG 60.607 47.826 0.00 0.00 0.00 3.16
4694 8854 5.790593 AGGAGCGTGAAAACTAAGTGATTA 58.209 37.500 0.00 0.00 0.00 1.75
4696 8856 7.553334 AGGAGCGTGAAAACTAAGTGATTATA 58.447 34.615 0.00 0.00 0.00 0.98
4748 8908 4.488126 TCTTTCTTCTTTGTTGCATCCG 57.512 40.909 0.00 0.00 0.00 4.18
4749 8909 3.882888 TCTTTCTTCTTTGTTGCATCCGT 59.117 39.130 0.00 0.00 0.00 4.69
4777 8937 4.333926 GTGAGGCCATAACAGAAAGTCATC 59.666 45.833 5.01 0.00 0.00 2.92
4804 8965 2.473235 GTCTCGAGTCACAGTTTGAAGC 59.527 50.000 13.13 0.00 35.39 3.86
4817 8978 4.821805 CAGTTTGAAGCTCCTCCACTTTAA 59.178 41.667 0.00 0.00 0.00 1.52
4823 8984 7.016153 TGAAGCTCCTCCACTTTAATTCTTA 57.984 36.000 0.00 0.00 0.00 2.10
4826 8987 7.259088 AGCTCCTCCACTTTAATTCTTAAGA 57.741 36.000 0.00 0.00 0.00 2.10
4829 8990 7.016153 TCCTCCACTTTAATTCTTAAGAGCA 57.984 36.000 5.12 0.00 0.00 4.26
4830 8991 7.458397 TCCTCCACTTTAATTCTTAAGAGCAA 58.542 34.615 5.12 0.00 0.00 3.91
4831 8992 7.942341 TCCTCCACTTTAATTCTTAAGAGCAAA 59.058 33.333 5.12 6.65 0.00 3.68
4832 8993 8.023706 CCTCCACTTTAATTCTTAAGAGCAAAC 58.976 37.037 5.12 0.00 0.00 2.93
4833 8994 8.458573 TCCACTTTAATTCTTAAGAGCAAACA 57.541 30.769 5.12 0.00 0.00 2.83
4847 9008 1.522258 GCAAACATTTGGTTGTCTGCG 59.478 47.619 9.87 0.00 44.25 5.18
4850 9011 0.586319 ACATTTGGTTGTCTGCGTCG 59.414 50.000 0.00 0.00 0.00 5.12
4852 9013 1.002900 CATTTGGTTGTCTGCGTCGTT 60.003 47.619 0.00 0.00 0.00 3.85
4853 9014 1.088306 TTTGGTTGTCTGCGTCGTTT 58.912 45.000 0.00 0.00 0.00 3.60
4901 9062 0.108945 GAGCCTGGTTGAGCAAATGC 60.109 55.000 0.00 0.00 42.49 3.56
4903 9064 0.033781 GCCTGGTTGAGCAAATGCAA 59.966 50.000 8.28 0.00 45.16 4.08
4928 9089 4.642445 AAAAATCATCATCTGCGCATCA 57.358 36.364 12.24 0.00 0.00 3.07
4930 9091 4.848562 AAATCATCATCTGCGCATCATT 57.151 36.364 12.24 0.00 0.00 2.57
4931 9092 4.421033 AATCATCATCTGCGCATCATTC 57.579 40.909 12.24 0.00 0.00 2.67
4938 9099 2.255994 CTGCGCATCATTCGGTTGCA 62.256 55.000 12.24 0.00 41.35 4.08
4951 9112 1.394266 GGTTGCATGCATACCCCCAG 61.394 60.000 27.83 0.00 0.00 4.45
4957 9118 4.902645 GCATACCCCCAGCCTGGC 62.903 72.222 11.65 11.65 35.79 4.85
4958 9119 3.419580 CATACCCCCAGCCTGGCA 61.420 66.667 22.65 0.00 35.79 4.92
4968 9129 1.673665 AGCCTGGCAGCGAAGAAAG 60.674 57.895 22.65 0.00 38.01 2.62
4974 9135 1.237285 GGCAGCGAAGAAAGGCAAGA 61.237 55.000 0.00 0.00 0.00 3.02
4976 9137 1.229428 CAGCGAAGAAAGGCAAGACA 58.771 50.000 0.00 0.00 0.00 3.41
4977 9138 1.808945 CAGCGAAGAAAGGCAAGACAT 59.191 47.619 0.00 0.00 0.00 3.06
4991 9152 2.490328 AGACATGTTGTTTGGTTGCG 57.510 45.000 0.00 0.00 0.00 4.85
4993 9154 1.066303 GACATGTTGTTTGGTTGCGGA 59.934 47.619 0.00 0.00 0.00 5.54
5010 9171 2.095718 GCGGACTTGTTTAGGCAGAAAG 60.096 50.000 0.00 0.00 31.29 2.62
5011 9172 2.095718 CGGACTTGTTTAGGCAGAAAGC 60.096 50.000 0.00 0.00 44.65 3.51
5039 9200 4.515191 TCAGACTGTTTGGTTAGATGCAAC 59.485 41.667 1.59 0.00 0.00 4.17
5061 9222 4.699735 ACGCATGTTGTTTGATAATCTCCA 59.300 37.500 0.00 0.00 0.00 3.86
5063 9224 6.127647 ACGCATGTTGTTTGATAATCTCCATT 60.128 34.615 0.00 0.00 0.00 3.16
5064 9225 6.415867 CGCATGTTGTTTGATAATCTCCATTC 59.584 38.462 0.00 0.00 0.00 2.67
5068 9229 6.657117 TGTTGTTTGATAATCTCCATTCGGAA 59.343 34.615 0.00 0.00 42.21 4.30
5071 9232 7.053498 TGTTTGATAATCTCCATTCGGAATGA 58.947 34.615 27.77 14.85 42.21 2.57
5076 9259 3.280197 TCTCCATTCGGAATGATGCAA 57.720 42.857 27.77 9.04 42.21 4.08
5088 9271 6.015095 TCGGAATGATGCAAGACATAGATAGT 60.015 38.462 0.00 0.00 39.84 2.12
5092 9275 6.030548 TGATGCAAGACATAGATAGTAGCC 57.969 41.667 0.00 0.00 39.84 3.93
5124 9307 8.518430 ACATAGTGGCACATAATTCAACATAA 57.482 30.769 21.41 0.00 44.52 1.90
5139 9322 7.861176 TTCAACATAATCTTAAACAAACCGC 57.139 32.000 0.00 0.00 0.00 5.68
5145 9328 3.595709 TCTTAAACAAACCGCTCAACG 57.404 42.857 0.00 0.00 43.15 4.10
5165 9348 2.656422 CGCTAAAATGAAGCAAACCACG 59.344 45.455 0.00 0.00 40.08 4.94
5186 9369 3.362237 CGCAAGAGTGAACTTTCTAGACG 59.638 47.826 0.00 0.00 43.02 4.18
5187 9370 3.122111 GCAAGAGTGAACTTTCTAGACGC 59.878 47.826 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.140623 GCCAGCCACATGAAAATTTTGT 58.859 40.909 8.47 0.00 0.00 2.83
19 20 3.372730 GCCGCCAGCCACATGAAA 61.373 61.111 0.00 0.00 34.35 2.69
45 46 4.678256 TCTCCTGTCTGAAGTCCATAGTT 58.322 43.478 0.00 0.00 0.00 2.24
58 59 1.613630 ATGCCGGGTTCTCCTGTCT 60.614 57.895 2.18 0.00 38.38 3.41
116 117 2.376109 GTCCATCGTGTCCTTCTCCTA 58.624 52.381 0.00 0.00 0.00 2.94
122 123 0.984230 ATGTGGTCCATCGTGTCCTT 59.016 50.000 0.00 0.00 0.00 3.36
131 132 3.507162 TTGTGTCAAGATGTGGTCCAT 57.493 42.857 0.00 0.00 36.13 3.41
148 149 1.795170 GCCTGGCGAACACACATTGT 61.795 55.000 1.35 0.00 41.74 2.71
172 173 3.279434 CCTAGTAAGGCATTGGAACCAC 58.721 50.000 0.00 0.00 35.64 4.16
199 200 0.035056 GCATCAACCCCAGCAGTAGT 60.035 55.000 0.00 0.00 0.00 2.73
204 205 1.907807 GTTGGCATCAACCCCAGCA 60.908 57.895 0.00 0.00 45.50 4.41
237 238 2.159156 CGTCGTCCACCATTCTTCCATA 60.159 50.000 0.00 0.00 0.00 2.74
238 239 1.405526 CGTCGTCCACCATTCTTCCAT 60.406 52.381 0.00 0.00 0.00 3.41
254 255 2.202492 CCAGCTTCCGAGACGTCG 60.202 66.667 10.46 0.00 46.39 5.12
258 259 2.435059 GGCACCAGCTTCCGAGAC 60.435 66.667 0.00 0.00 41.70 3.36
279 280 1.173913 CAAAATCCTTCCGGTGGGTC 58.826 55.000 14.42 0.00 33.83 4.46
304 305 2.627699 ACCAACAAATAAGCACCACCAG 59.372 45.455 0.00 0.00 0.00 4.00
306 307 2.364002 ACACCAACAAATAAGCACCACC 59.636 45.455 0.00 0.00 0.00 4.61
348 349 5.769484 TGTCATTCCTACCGAATACTCTC 57.231 43.478 0.00 0.00 39.28 3.20
378 379 2.046988 TGGACTGTGCCATGCTCG 60.047 61.111 0.00 0.00 31.66 5.03
414 415 1.821759 CGCCACCGCCCATAAATGA 60.822 57.895 0.00 0.00 0.00 2.57
420 421 3.061848 CTTTTCGCCACCGCCCAT 61.062 61.111 0.00 0.00 0.00 4.00
427 428 0.250338 ACTCCACTCCTTTTCGCCAC 60.250 55.000 0.00 0.00 0.00 5.01
465 466 5.449553 CCCTCCTTTAAACATGCTAGGAAT 58.550 41.667 0.00 0.00 34.77 3.01
482 483 1.076632 CCTACACTCGAGCCCTCCT 60.077 63.158 13.61 0.00 0.00 3.69
501 502 2.167219 CACGCATCGCCTAGGTGTG 61.167 63.158 21.61 18.43 46.46 3.82
502 503 2.184322 CACGCATCGCCTAGGTGT 59.816 61.111 21.61 6.89 32.28 4.16
504 505 4.530857 GGCACGCATCGCCTAGGT 62.531 66.667 11.31 0.00 46.56 3.08
517 525 5.600908 TTACAAGAGATTACAAACGGCAC 57.399 39.130 0.00 0.00 0.00 5.01
552 562 8.776470 CAAAGACGTACCTTAACTTTATGGAAA 58.224 33.333 7.70 0.00 33.49 3.13
556 566 8.932791 ACATCAAAGACGTACCTTAACTTTATG 58.067 33.333 0.00 0.00 31.11 1.90
596 606 5.046520 AGAGTATAGACGCAAGGGTCTTTTT 60.047 40.000 22.22 11.85 44.65 1.94
597 607 4.466726 AGAGTATAGACGCAAGGGTCTTTT 59.533 41.667 22.22 13.87 44.65 2.27
598 608 4.024670 AGAGTATAGACGCAAGGGTCTTT 58.975 43.478 22.22 17.26 44.65 2.52
599 609 3.381908 CAGAGTATAGACGCAAGGGTCTT 59.618 47.826 22.22 13.52 44.65 3.01
601 611 2.688958 ACAGAGTATAGACGCAAGGGTC 59.311 50.000 9.01 9.01 46.39 4.46
602 612 2.736347 ACAGAGTATAGACGCAAGGGT 58.264 47.619 0.00 0.00 46.39 4.34
603 613 3.802948 AACAGAGTATAGACGCAAGGG 57.197 47.619 0.00 0.00 46.39 3.95
604 614 7.591006 TTTTAAACAGAGTATAGACGCAAGG 57.409 36.000 0.00 0.00 46.39 3.61
626 636 7.654923 GCTCACATTCTTTTTCAGGATCTTTTT 59.345 33.333 0.00 0.00 0.00 1.94
627 637 7.150640 GCTCACATTCTTTTTCAGGATCTTTT 58.849 34.615 0.00 0.00 0.00 2.27
628 638 6.569226 CGCTCACATTCTTTTTCAGGATCTTT 60.569 38.462 0.00 0.00 0.00 2.52
629 639 5.106396 CGCTCACATTCTTTTTCAGGATCTT 60.106 40.000 0.00 0.00 0.00 2.40
630 640 4.394300 CGCTCACATTCTTTTTCAGGATCT 59.606 41.667 0.00 0.00 0.00 2.75
631 641 4.656041 CGCTCACATTCTTTTTCAGGATC 58.344 43.478 0.00 0.00 0.00 3.36
632 642 3.119708 GCGCTCACATTCTTTTTCAGGAT 60.120 43.478 0.00 0.00 0.00 3.24
638 648 3.077359 AGCTAGCGCTCACATTCTTTTT 58.923 40.909 16.34 0.00 45.15 1.94
647 657 2.339728 ATCGAATAGCTAGCGCTCAC 57.660 50.000 16.34 7.48 45.15 3.51
825 835 0.609131 CCGGTTTGGTGCCATTCTCT 60.609 55.000 0.00 0.00 0.00 3.10
829 839 3.310307 GGCCGGTTTGGTGCCATT 61.310 61.111 1.90 0.00 44.70 3.16
994 1004 2.672996 GTCGCTTGCCATGGTGGT 60.673 61.111 14.67 0.00 40.46 4.16
1047 1057 3.971702 GCCCCTGGCTGGTTGTCT 61.972 66.667 9.73 0.00 46.69 3.41
1090 1100 2.561037 GGTTGTCCGGCTTGGTTGG 61.561 63.158 0.00 0.00 39.52 3.77
1092 1102 0.822121 GAAGGTTGTCCGGCTTGGTT 60.822 55.000 0.00 0.00 39.52 3.67
1125 1135 4.070552 ACGAGCTTGGAGCCCGAC 62.071 66.667 10.75 0.00 45.68 4.79
1181 1194 3.195698 GCCGACGGTCCATCTTGC 61.196 66.667 16.73 0.00 0.00 4.01
1260 1273 3.326109 CACCGGTTGTGGTCGAAC 58.674 61.111 2.97 0.00 41.38 3.95
1458 1471 6.034898 ACTCAACAAGTTTCTTGAATTTTGCG 59.965 34.615 15.04 7.44 33.03 4.85
1492 1505 9.679661 ACTCCCATGTAAAGTTTTTCAATTTTT 57.320 25.926 0.00 0.00 0.00 1.94
1494 1507 9.758651 GTACTCCCATGTAAAGTTTTTCAATTT 57.241 29.630 0.00 0.00 0.00 1.82
1495 1508 8.919145 TGTACTCCCATGTAAAGTTTTTCAATT 58.081 29.630 0.00 0.00 0.00 2.32
1496 1509 8.472007 TGTACTCCCATGTAAAGTTTTTCAAT 57.528 30.769 0.00 0.00 0.00 2.57
1497 1510 7.883391 TGTACTCCCATGTAAAGTTTTTCAA 57.117 32.000 0.00 0.00 0.00 2.69
1498 1511 7.883391 TTGTACTCCCATGTAAAGTTTTTCA 57.117 32.000 0.00 0.00 0.00 2.69
1499 1512 9.758651 AAATTGTACTCCCATGTAAAGTTTTTC 57.241 29.630 0.00 0.00 0.00 2.29
1503 1516 9.747898 TGATAAATTGTACTCCCATGTAAAGTT 57.252 29.630 0.00 0.00 0.00 2.66
1504 1517 9.747898 TTGATAAATTGTACTCCCATGTAAAGT 57.252 29.630 0.00 0.00 0.00 2.66
1506 1519 9.747898 ACTTGATAAATTGTACTCCCATGTAAA 57.252 29.630 0.00 0.00 0.00 2.01
1507 1520 9.747898 AACTTGATAAATTGTACTCCCATGTAA 57.252 29.630 0.00 0.00 0.00 2.41
1508 1521 9.747898 AAACTTGATAAATTGTACTCCCATGTA 57.252 29.630 0.00 0.00 0.00 2.29
1509 1522 8.650143 AAACTTGATAAATTGTACTCCCATGT 57.350 30.769 0.00 0.00 0.00 3.21
1510 1523 8.739039 TGAAACTTGATAAATTGTACTCCCATG 58.261 33.333 0.00 0.00 0.00 3.66
1511 1524 8.877864 TGAAACTTGATAAATTGTACTCCCAT 57.122 30.769 0.00 0.00 0.00 4.00
1512 1525 8.698973 TTGAAACTTGATAAATTGTACTCCCA 57.301 30.769 0.00 0.00 0.00 4.37
1513 1526 9.788960 GATTGAAACTTGATAAATTGTACTCCC 57.211 33.333 0.00 0.00 0.00 4.30
1526 1539 9.180678 GTCGTAACATTTTGATTGAAACTTGAT 57.819 29.630 0.00 0.00 0.00 2.57
1527 1540 8.184848 TGTCGTAACATTTTGATTGAAACTTGA 58.815 29.630 0.00 0.00 0.00 3.02
1528 1541 8.259194 GTGTCGTAACATTTTGATTGAAACTTG 58.741 33.333 0.00 0.00 37.81 3.16
1529 1542 7.165154 CGTGTCGTAACATTTTGATTGAAACTT 59.835 33.333 0.00 0.00 37.81 2.66
1530 1543 6.631238 CGTGTCGTAACATTTTGATTGAAACT 59.369 34.615 0.00 0.00 37.81 2.66
1531 1544 6.629649 TCGTGTCGTAACATTTTGATTGAAAC 59.370 34.615 0.00 0.00 37.81 2.78
1557 1570 4.624882 TGAAATTTAAATCATGTGCCGTGC 59.375 37.500 0.10 0.00 0.00 5.34
1558 1571 6.702972 TTGAAATTTAAATCATGTGCCGTG 57.297 33.333 0.10 0.00 0.00 4.94
1559 1572 6.928492 ACTTTGAAATTTAAATCATGTGCCGT 59.072 30.769 0.10 0.00 0.00 5.68
1560 1573 7.116090 TCACTTTGAAATTTAAATCATGTGCCG 59.884 33.333 0.10 0.00 33.90 5.69
1561 1574 8.223100 GTCACTTTGAAATTTAAATCATGTGCC 58.777 33.333 0.10 0.00 33.90 5.01
1562 1575 7.946237 CGTCACTTTGAAATTTAAATCATGTGC 59.054 33.333 0.10 5.85 33.90 4.57
1579 1602 0.109781 CAAATCCCCGCGTCACTTTG 60.110 55.000 4.92 6.23 0.00 2.77
1600 1623 2.032071 AGCAACCTGCCCACGTAC 59.968 61.111 0.00 0.00 46.52 3.67
1602 1625 4.954970 CCAGCAACCTGCCCACGT 62.955 66.667 0.00 0.00 46.52 4.49
1733 1756 2.063378 GGTCCAGGAGCCAGGAGAG 61.063 68.421 7.50 0.00 32.18 3.20
2161 2184 1.472276 CGTACTCGCGCTTGATCCAC 61.472 60.000 5.56 0.00 0.00 4.02
2386 2421 3.649277 GACGATGCTGGCGTGGTCT 62.649 63.158 18.13 0.00 42.77 3.85
2414 2449 0.951558 ACGAAATGGCCAGTGTTGAC 59.048 50.000 13.05 0.00 0.00 3.18
2424 2459 4.674662 GCCAAAATTCAAAAACGAAATGGC 59.325 37.500 10.62 10.62 41.63 4.40
2455 2550 2.517650 TCGTAGCATGAACACACACA 57.482 45.000 0.00 0.00 0.00 3.72
2456 2551 3.254060 AGATCGTAGCATGAACACACAC 58.746 45.455 0.00 0.00 0.00 3.82
2469 2564 6.589830 CCTAATTGGTTGACAAGATCGTAG 57.410 41.667 0.00 0.00 43.48 3.51
3670 3826 1.483827 GTGATGGTGATGAGCAGGAGA 59.516 52.381 0.00 0.00 31.77 3.71
4226 4388 2.079925 GATTTCCTGACCACACTCTGC 58.920 52.381 0.00 0.00 0.00 4.26
4227 4389 2.029020 TCGATTTCCTGACCACACTCTG 60.029 50.000 0.00 0.00 0.00 3.35
4228 4390 2.248248 TCGATTTCCTGACCACACTCT 58.752 47.619 0.00 0.00 0.00 3.24
4229 4391 2.743636 TCGATTTCCTGACCACACTC 57.256 50.000 0.00 0.00 0.00 3.51
4230 4392 2.417379 CGATCGATTTCCTGACCACACT 60.417 50.000 10.26 0.00 0.00 3.55
4263 4425 1.277326 TTTCGCAACTGATCGATCGG 58.723 50.000 28.73 28.73 39.11 4.18
4308 4470 0.740868 TGCACTTCGTAGCTGATGGC 60.741 55.000 0.00 0.00 42.19 4.40
4309 4471 1.662629 CTTGCACTTCGTAGCTGATGG 59.337 52.381 0.00 0.00 0.00 3.51
4310 4472 2.610433 TCTTGCACTTCGTAGCTGATG 58.390 47.619 0.00 0.00 0.00 3.07
4392 4611 2.568956 TCAGCTACAGAATTGACCTGCT 59.431 45.455 0.00 0.00 35.14 4.24
4404 4623 2.093106 AGGTACGTTCCTCAGCTACAG 58.907 52.381 8.09 0.00 31.32 2.74
4438 4668 7.509546 ACAGTTAACCTTCCCATATGAGTATG 58.490 38.462 3.65 0.00 37.93 2.39
4439 4669 7.691993 ACAGTTAACCTTCCCATATGAGTAT 57.308 36.000 3.65 0.00 0.00 2.12
4440 4670 7.620491 TGTACAGTTAACCTTCCCATATGAGTA 59.380 37.037 3.65 0.00 0.00 2.59
4441 4671 6.442564 TGTACAGTTAACCTTCCCATATGAGT 59.557 38.462 3.65 0.00 0.00 3.41
4443 4673 6.670464 TCTGTACAGTTAACCTTCCCATATGA 59.330 38.462 21.99 0.00 0.00 2.15
4444 4674 6.884832 TCTGTACAGTTAACCTTCCCATATG 58.115 40.000 21.99 0.00 0.00 1.78
4446 4676 6.938698 TTCTGTACAGTTAACCTTCCCATA 57.061 37.500 21.99 0.00 0.00 2.74
4460 4731 5.388890 GCAACGAGTCAGAATTTCTGTACAG 60.389 44.000 22.44 17.17 44.58 2.74
4530 8173 6.460123 GGTTTATGAATTGCCAACATCGATCT 60.460 38.462 0.00 0.00 0.00 2.75
4531 8174 5.687285 GGTTTATGAATTGCCAACATCGATC 59.313 40.000 0.00 0.00 0.00 3.69
4532 8175 5.126869 TGGTTTATGAATTGCCAACATCGAT 59.873 36.000 0.00 0.00 0.00 3.59
4533 8176 4.460731 TGGTTTATGAATTGCCAACATCGA 59.539 37.500 0.00 0.00 0.00 3.59
4534 8177 4.742417 TGGTTTATGAATTGCCAACATCG 58.258 39.130 0.00 0.00 0.00 3.84
4548 8191 7.878477 TTTCGAGTAGTAGTGTTGGTTTATG 57.122 36.000 0.00 0.00 0.00 1.90
4583 8226 5.235186 GGACGAATGTGAAAATCGAGATCAT 59.765 40.000 1.03 0.00 39.73 2.45
4591 8234 4.783450 GCTGATCGGACGAATGTGAAAATC 60.783 45.833 5.48 0.00 0.00 2.17
4593 8236 2.415168 GCTGATCGGACGAATGTGAAAA 59.585 45.455 5.48 0.00 0.00 2.29
4597 8240 1.325640 CAAGCTGATCGGACGAATGTG 59.674 52.381 5.48 0.00 0.00 3.21
4617 8260 2.126031 GTTGGTCCTCGAGCGGTC 60.126 66.667 6.99 4.06 32.15 4.79
4668 8828 2.548480 ACTTAGTTTTCACGCTCCTTGC 59.452 45.455 0.00 0.00 38.57 4.01
4694 8854 6.769822 GGACCATGTTCATGTCATTTCTCTAT 59.230 38.462 11.13 0.00 0.00 1.98
4696 8856 4.946157 GGACCATGTTCATGTCATTTCTCT 59.054 41.667 11.13 0.00 0.00 3.10
4706 8866 2.680312 ACTCGAGGACCATGTTCATG 57.320 50.000 18.41 5.88 0.00 3.07
4748 8908 2.497675 TCTGTTATGGCCTCACTCTCAC 59.502 50.000 3.32 0.00 0.00 3.51
4749 8909 2.820178 TCTGTTATGGCCTCACTCTCA 58.180 47.619 3.32 0.00 0.00 3.27
4777 8937 1.282875 TGTGACTCGAGACGCACAG 59.717 57.895 23.74 0.00 36.44 3.66
4782 8942 2.401017 TCAAACTGTGACTCGAGACG 57.599 50.000 21.68 6.96 0.00 4.18
4804 8965 7.106239 TGCTCTTAAGAATTAAAGTGGAGGAG 58.894 38.462 6.63 0.00 40.54 3.69
4817 8978 7.500141 ACAACCAAATGTTTGCTCTTAAGAAT 58.500 30.769 6.63 0.00 36.86 2.40
4823 8984 4.685924 CAGACAACCAAATGTTTGCTCTT 58.314 39.130 0.00 0.00 36.86 2.85
4829 8990 2.540769 CGACGCAGACAACCAAATGTTT 60.541 45.455 0.00 0.00 34.00 2.83
4830 8991 1.002900 CGACGCAGACAACCAAATGTT 60.003 47.619 0.00 0.00 37.80 2.71
4831 8992 0.586319 CGACGCAGACAACCAAATGT 59.414 50.000 0.00 0.00 35.90 2.71
4832 8993 0.586319 ACGACGCAGACAACCAAATG 59.414 50.000 0.00 0.00 0.00 2.32
4833 8994 1.305201 AACGACGCAGACAACCAAAT 58.695 45.000 0.00 0.00 0.00 2.32
4873 9034 3.620966 GCTCAACCAGGCTCAACTAAGAT 60.621 47.826 0.00 0.00 0.00 2.40
4877 9038 1.055849 TGCTCAACCAGGCTCAACTA 58.944 50.000 0.00 0.00 0.00 2.24
4883 9044 0.828762 TGCATTTGCTCAACCAGGCT 60.829 50.000 3.94 0.00 42.66 4.58
4884 9045 0.033781 TTGCATTTGCTCAACCAGGC 59.966 50.000 3.94 0.00 42.66 4.85
4885 9046 2.137523 GTTTGCATTTGCTCAACCAGG 58.862 47.619 3.94 0.00 42.66 4.45
4912 9073 1.796459 CGAATGATGCGCAGATGATGA 59.204 47.619 18.32 0.00 0.00 2.92
4913 9074 1.136057 CCGAATGATGCGCAGATGATG 60.136 52.381 18.32 4.24 0.00 3.07
4914 9075 1.154197 CCGAATGATGCGCAGATGAT 58.846 50.000 18.32 0.00 0.00 2.45
4915 9076 0.179076 ACCGAATGATGCGCAGATGA 60.179 50.000 18.32 0.00 0.00 2.92
4916 9077 0.659427 AACCGAATGATGCGCAGATG 59.341 50.000 18.32 1.88 0.00 2.90
4919 9080 1.584483 GCAACCGAATGATGCGCAG 60.584 57.895 18.32 1.98 0.00 5.18
4920 9081 1.655885 ATGCAACCGAATGATGCGCA 61.656 50.000 14.96 14.96 42.91 6.09
4921 9082 1.064621 ATGCAACCGAATGATGCGC 59.935 52.632 0.00 0.00 42.91 6.09
4923 9084 0.179132 TGCATGCAACCGAATGATGC 60.179 50.000 20.30 0.00 39.90 3.91
4924 9085 2.502213 ATGCATGCAACCGAATGATG 57.498 45.000 26.68 0.00 0.00 3.07
4927 9088 1.269206 GGGTATGCATGCAACCGAATG 60.269 52.381 29.38 0.00 33.89 2.67
4928 9089 1.032014 GGGTATGCATGCAACCGAAT 58.968 50.000 29.38 16.69 33.89 3.34
4930 9091 1.453015 GGGGTATGCATGCAACCGA 60.453 57.895 29.38 15.07 33.89 4.69
4931 9092 2.489275 GGGGGTATGCATGCAACCG 61.489 63.158 29.38 0.00 33.89 4.44
4938 9099 2.771321 CCAGGCTGGGGGTATGCAT 61.771 63.158 26.34 3.79 32.67 3.96
4951 9112 2.694760 CCTTTCTTCGCTGCCAGGC 61.695 63.158 3.66 3.66 0.00 4.85
4957 9118 1.229428 TGTCTTGCCTTTCTTCGCTG 58.771 50.000 0.00 0.00 0.00 5.18
4958 9119 1.808945 CATGTCTTGCCTTTCTTCGCT 59.191 47.619 0.00 0.00 0.00 4.93
4968 9129 2.865551 CAACCAAACAACATGTCTTGCC 59.134 45.455 0.00 0.00 0.00 4.52
4974 9135 1.107114 TCCGCAACCAAACAACATGT 58.893 45.000 0.00 0.00 0.00 3.21
4976 9137 1.398692 AGTCCGCAACCAAACAACAT 58.601 45.000 0.00 0.00 0.00 2.71
4977 9138 1.135257 CAAGTCCGCAACCAAACAACA 60.135 47.619 0.00 0.00 0.00 3.33
4991 9152 3.560902 GCTTTCTGCCTAAACAAGTCC 57.439 47.619 0.00 0.00 35.15 3.85
5010 9171 1.680338 ACCAAACAGTCTGACTTGGC 58.320 50.000 25.63 0.00 37.37 4.52
5011 9172 4.703897 TCTAACCAAACAGTCTGACTTGG 58.296 43.478 24.77 24.77 38.72 3.61
5012 9173 5.334414 GCATCTAACCAAACAGTCTGACTTG 60.334 44.000 7.77 9.29 0.00 3.16
5020 9181 2.031157 GCGTTGCATCTAACCAAACAGT 60.031 45.455 0.00 0.00 0.00 3.55
5021 9182 2.031245 TGCGTTGCATCTAACCAAACAG 60.031 45.455 0.00 0.00 31.71 3.16
5039 9200 5.233957 TGGAGATTATCAAACAACATGCG 57.766 39.130 0.00 0.00 0.00 4.73
5056 9217 8.815087 ATGTCTTGCATCATTCCGAATGGAGA 62.815 42.308 18.91 12.15 38.41 3.71
5061 9222 5.614308 TCTATGTCTTGCATCATTCCGAAT 58.386 37.500 0.00 0.00 38.94 3.34
5063 9224 4.670896 TCTATGTCTTGCATCATTCCGA 57.329 40.909 0.00 0.00 38.94 4.55
5064 9225 6.162079 ACTATCTATGTCTTGCATCATTCCG 58.838 40.000 0.00 0.00 38.94 4.30
5068 9229 6.212187 TGGCTACTATCTATGTCTTGCATCAT 59.788 38.462 0.00 0.00 38.94 2.45
5071 9232 5.541868 ACTGGCTACTATCTATGTCTTGCAT 59.458 40.000 0.00 0.00 41.42 3.96
5076 9259 6.607600 TGTTGAACTGGCTACTATCTATGTCT 59.392 38.462 0.00 0.00 0.00 3.41
5088 9271 2.304470 TGCCACTATGTTGAACTGGCTA 59.696 45.455 21.77 9.81 46.46 3.93
5092 9275 5.878332 TTATGTGCCACTATGTTGAACTG 57.122 39.130 0.00 0.00 0.00 3.16
5124 9307 3.608474 GCGTTGAGCGGTTTGTTTAAGAT 60.608 43.478 0.00 0.00 41.69 2.40
5139 9322 4.382754 GGTTTGCTTCATTTTAGCGTTGAG 59.617 41.667 0.00 0.00 41.54 3.02
5145 9328 2.408368 GCGTGGTTTGCTTCATTTTAGC 59.592 45.455 0.00 0.00 39.10 3.09
5165 9348 3.122111 GCGTCTAGAAAGTTCACTCTTGC 59.878 47.826 0.00 0.00 0.00 4.01
5195 9378 0.674895 AGAAGCATGACGTGGCCTTC 60.675 55.000 3.32 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.