Multiple sequence alignment - TraesCS5A01G379800

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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 TraesCS5A01G379800 chr5A 100.000 3127 0 0 1 3127 577707317 577710443 0.000000e+00 5775
1 TraesCS5A01G379800 chr5B 86.678 1734 128 61 583 2284 562225330 562226992 0.000000e+00 1827
2 TraesCS5A01G379800 chr5B 85.089 617 45 19 5 590 562222888 562223488 1.250000e-163 586
3 TraesCS5A01G379800 chr5B 89.819 442 40 3 2664 3101 562227521 562227961 2.110000e-156 562
4 TraesCS5A01G379800 chr5B 91.304 253 14 1 2359 2603 562227013 562227265 3.860000e-89 339
5 TraesCS5A01G379800 chr5D 88.748 1102 74 28 616 1695 458679569 458680642 0.000000e+00 1303
6 TraesCS5A01G379800 chr5D 91.682 541 31 9 1790 2318 458680726 458681264 0.000000e+00 737
7 TraesCS5A01G379800 chr5D 86.020 608 42 15 13 583 458678972 458679573 2.060000e-171 612
8 TraesCS5A01G379800 chr5D 90.441 272 21 2 2347 2614 458681258 458681528 1.380000e-93 353
9 TraesCS5A01G379800 chr5D 93.548 93 6 0 3009 3101 303723499 303723407 4.210000e-29 139
10 TraesCS5A01G379800 chr4A 83.442 308 27 5 185 480 197980801 197980506 6.650000e-67 265
11 TraesCS5A01G379800 chr6D 89.076 119 5 5 3009 3127 319733780 319733670 1.170000e-29 141
12 TraesCS5A01G379800 chr3A 93.548 93 6 0 3009 3101 737144380 737144288 4.210000e-29 139
13 TraesCS5A01G379800 chr3A 87.805 123 7 5 3005 3127 444086441 444086327 1.510000e-28 137
14 TraesCS5A01G379800 chr2D 92.708 96 7 0 3006 3101 228419227 228419322 4.210000e-29 139
15 TraesCS5A01G379800 chr2D 93.548 93 6 0 3009 3101 379052586 379052494 4.210000e-29 139
16 TraesCS5A01G379800 chr4D 92.632 95 7 0 3006 3100 449041738 449041832 1.510000e-28 137
17 TraesCS5A01G379800 chr1B 90.909 99 9 0 3003 3101 388906116 388906214 1.960000e-27 134
18 TraesCS5A01G379800 chr7A 80.000 200 23 4 3 186 578250512 578250314 7.040000e-27 132


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 TraesCS5A01G379800 chr5A 577707317 577710443 3126 False 5775.00 5775 100.00000 1 3127 1 chr5A.!!$F1 3126
1 TraesCS5A01G379800 chr5B 562222888 562227961 5073 False 828.50 1827 88.22250 5 3101 4 chr5B.!!$F1 3096
2 TraesCS5A01G379800 chr5D 458678972 458681528 2556 False 751.25 1303 89.22275 13 2614 4 chr5D.!!$F1 2601

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
581 647 0.031585 TCGCGCCATATGACCACTAC 59.968 55.0 3.65 0.0 0.0 2.73 F
584 650 0.032130 CGCCATATGACCACTACGCT 59.968 55.0 3.65 0.0 0.0 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 3679 0.037326 AGCGAACGCCAGATGAAGAA 60.037 50.0 15.44 0.0 43.17 2.52 R
2344 4358 0.098905 CGAGAGTCGCTCCGAAATGA 59.901 55.0 0.00 0.0 40.70 2.57 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
21 22 1.685302 CATTTGGACGGACAAAAGCG 58.315 50.000 10.18 0.00 42.91 4.68
31 32 1.982073 GACAAAAGCGCCCGATGGAG 61.982 60.000 2.29 0.00 34.00 3.86
95 98 2.430080 GAACGAGCACACACTTGCCG 62.430 60.000 0.00 0.00 44.14 5.69
114 117 3.736740 GCCGGAAAAACTTCAAGCTTGAA 60.737 43.478 33.65 33.65 44.31 2.69
128 131 4.414337 AGCTTGAAACTTGAGAGTCTGT 57.586 40.909 0.00 0.00 34.21 3.41
129 132 4.125703 AGCTTGAAACTTGAGAGTCTGTG 58.874 43.478 0.00 0.00 34.21 3.66
242 263 3.431725 CCAAGGAAGGAACGCGCC 61.432 66.667 5.73 0.00 0.00 6.53
395 425 2.975536 CCAGGTTTAGACGGGCGA 59.024 61.111 0.00 0.00 0.00 5.54
426 456 1.722082 GCCCGGCGAAAGATCTTTC 59.278 57.895 30.38 30.38 43.98 2.62
427 457 0.744771 GCCCGGCGAAAGATCTTTCT 60.745 55.000 34.15 12.38 44.93 2.52
428 458 1.009829 CCCGGCGAAAGATCTTTCTG 58.990 55.000 34.15 28.60 44.93 3.02
429 459 0.375106 CCGGCGAAAGATCTTTCTGC 59.625 55.000 33.20 33.20 44.93 4.26
432 462 0.735471 GCGAAAGATCTTTCTGCCCC 59.265 55.000 34.15 18.99 44.93 5.80
433 463 1.009829 CGAAAGATCTTTCTGCCCCG 58.990 55.000 34.15 22.44 44.93 5.73
434 464 1.383523 GAAAGATCTTTCTGCCCCGG 58.616 55.000 32.00 0.00 44.03 5.73
474 525 1.581934 CACGAAGTTGCAGGTTCAGA 58.418 50.000 9.92 0.00 41.61 3.27
570 636 2.048597 TGTCGTTTCTCGCGCCAT 60.049 55.556 0.00 0.00 39.67 4.40
581 647 0.031585 TCGCGCCATATGACCACTAC 59.968 55.000 3.65 0.00 0.00 2.73
584 650 0.032130 CGCCATATGACCACTACGCT 59.968 55.000 3.65 0.00 0.00 5.07
592 2506 1.337447 TGACCACTACGCTGCTTAACC 60.337 52.381 0.00 0.00 0.00 2.85
612 2526 2.095567 CCAGGCATCGTTTCAGAGTTTG 60.096 50.000 0.00 0.00 0.00 2.93
613 2527 2.549754 CAGGCATCGTTTCAGAGTTTGT 59.450 45.455 0.00 0.00 0.00 2.83
614 2528 3.745975 CAGGCATCGTTTCAGAGTTTGTA 59.254 43.478 0.00 0.00 0.00 2.41
688 2610 0.782384 GCACTAACACGTCAACGGAG 59.218 55.000 7.53 1.87 44.95 4.63
884 2841 4.267536 CACATGTTCCATGTCATTCCTCT 58.732 43.478 6.88 0.00 0.00 3.69
885 2842 4.095932 CACATGTTCCATGTCATTCCTCTG 59.904 45.833 6.88 0.00 0.00 3.35
1068 3031 3.241530 AAGGACAGCCGTCTGCCA 61.242 61.111 9.09 0.00 44.10 4.92
1077 3040 2.579787 CGTCTGCCATCGTCGTCC 60.580 66.667 0.00 0.00 0.00 4.79
1078 3041 2.202756 GTCTGCCATCGTCGTCCC 60.203 66.667 0.00 0.00 0.00 4.46
1079 3042 3.458163 TCTGCCATCGTCGTCCCC 61.458 66.667 0.00 0.00 0.00 4.81
1080 3043 4.873129 CTGCCATCGTCGTCCCCG 62.873 72.222 0.00 0.00 0.00 5.73
1152 3130 2.281484 GACACCAAGGCGAGGCAA 60.281 61.111 0.00 0.00 0.00 4.52
1211 3189 4.421515 CACCCTGGGAGCAGCCAG 62.422 72.222 22.23 0.00 38.95 4.85
1233 3211 1.371183 CAGCACCACGGAGGAGAAA 59.629 57.895 2.94 0.00 41.22 2.52
1238 3216 1.129058 ACCACGGAGGAGAAACAACT 58.871 50.000 2.94 0.00 41.22 3.16
1297 3275 2.598099 TGGCGTACGAGGTCACCA 60.598 61.111 21.65 12.79 0.00 4.17
1325 3303 3.706373 GCTCAGGCAGTTCGGGGA 61.706 66.667 0.00 0.00 38.54 4.81
1458 3436 2.504367 CTCGGTTCAGTCCCATGTTTT 58.496 47.619 0.00 0.00 0.00 2.43
1471 3449 5.064834 GTCCCATGTTTTCTCGAGGTAATTC 59.935 44.000 13.56 5.14 0.00 2.17
1472 3450 4.335594 CCCATGTTTTCTCGAGGTAATTCC 59.664 45.833 13.56 0.54 0.00 3.01
1473 3451 4.034048 CCATGTTTTCTCGAGGTAATTCCG 59.966 45.833 13.56 0.00 41.99 4.30
1474 3452 4.524316 TGTTTTCTCGAGGTAATTCCGA 57.476 40.909 13.56 0.00 41.99 4.55
1475 3453 4.240096 TGTTTTCTCGAGGTAATTCCGAC 58.760 43.478 13.56 3.34 41.99 4.79
1478 3456 4.524316 TTCTCGAGGTAATTCCGACAAA 57.476 40.909 13.56 0.00 41.99 2.83
1479 3457 4.730949 TCTCGAGGTAATTCCGACAAAT 57.269 40.909 13.56 0.00 41.99 2.32
1481 3459 4.158949 TCTCGAGGTAATTCCGACAAATGA 59.841 41.667 13.56 0.00 41.99 2.57
1482 3460 4.178540 TCGAGGTAATTCCGACAAATGAC 58.821 43.478 0.00 0.00 41.99 3.06
1483 3461 3.308866 CGAGGTAATTCCGACAAATGACC 59.691 47.826 4.36 4.36 39.60 4.02
1487 3465 4.461431 GGTAATTCCGACAAATGACCCTTT 59.539 41.667 0.00 0.00 34.99 3.11
1489 3467 6.320418 GGTAATTCCGACAAATGACCCTTTAT 59.680 38.462 0.00 0.00 34.99 1.40
1490 3468 5.835113 ATTCCGACAAATGACCCTTTATG 57.165 39.130 0.00 0.00 0.00 1.90
1491 3469 4.295141 TCCGACAAATGACCCTTTATGT 57.705 40.909 0.00 0.00 0.00 2.29
1492 3470 4.258543 TCCGACAAATGACCCTTTATGTC 58.741 43.478 0.00 0.00 35.13 3.06
1493 3471 4.006989 CCGACAAATGACCCTTTATGTCA 58.993 43.478 0.00 0.00 45.98 3.58
1494 3472 4.142687 CCGACAAATGACCCTTTATGTCAC 60.143 45.833 0.00 0.00 44.85 3.67
1495 3473 4.695455 CGACAAATGACCCTTTATGTCACT 59.305 41.667 0.00 0.00 44.85 3.41
1496 3474 5.163854 CGACAAATGACCCTTTATGTCACTC 60.164 44.000 0.00 0.00 44.85 3.51
1497 3475 5.630121 ACAAATGACCCTTTATGTCACTCA 58.370 37.500 0.00 0.00 44.85 3.41
1498 3476 5.473504 ACAAATGACCCTTTATGTCACTCAC 59.526 40.000 0.00 0.00 44.85 3.51
1500 3478 4.974645 TGACCCTTTATGTCACTCACTT 57.025 40.909 0.00 0.00 37.80 3.16
1504 3482 4.593206 ACCCTTTATGTCACTCACTTCTCA 59.407 41.667 0.00 0.00 0.00 3.27
1507 3485 6.314896 CCCTTTATGTCACTCACTTCTCAATC 59.685 42.308 0.00 0.00 0.00 2.67
1525 3503 8.862325 TCTCAATCAAGTGTAACCATTTATGT 57.138 30.769 0.00 0.00 37.80 2.29
1526 3504 8.729756 TCTCAATCAAGTGTAACCATTTATGTG 58.270 33.333 0.00 0.00 37.80 3.21
1527 3505 8.628630 TCAATCAAGTGTAACCATTTATGTGA 57.371 30.769 0.00 0.00 37.80 3.58
1528 3506 9.241919 TCAATCAAGTGTAACCATTTATGTGAT 57.758 29.630 0.00 0.00 37.80 3.06
1529 3507 9.292846 CAATCAAGTGTAACCATTTATGTGATG 57.707 33.333 0.00 0.00 37.80 3.07
1530 3508 6.851609 TCAAGTGTAACCATTTATGTGATGC 58.148 36.000 0.00 0.00 37.80 3.91
1531 3509 6.432472 TCAAGTGTAACCATTTATGTGATGCA 59.568 34.615 0.00 0.00 37.80 3.96
1532 3510 6.832520 AGTGTAACCATTTATGTGATGCAA 57.167 33.333 0.00 0.00 37.80 4.08
1533 3511 7.225784 AGTGTAACCATTTATGTGATGCAAA 57.774 32.000 0.00 0.00 37.80 3.68
1534 3512 7.839907 AGTGTAACCATTTATGTGATGCAAAT 58.160 30.769 0.00 0.00 37.80 2.32
1535 3513 8.965819 AGTGTAACCATTTATGTGATGCAAATA 58.034 29.630 0.00 0.00 37.80 1.40
1536 3514 9.019764 GTGTAACCATTTATGTGATGCAAATAC 57.980 33.333 0.00 0.00 0.00 1.89
1537 3515 8.965819 TGTAACCATTTATGTGATGCAAATACT 58.034 29.630 0.00 0.00 0.00 2.12
1541 3519 7.975616 ACCATTTATGTGATGCAAATACTGTTC 59.024 33.333 0.00 0.00 0.00 3.18
1542 3520 7.166307 CCATTTATGTGATGCAAATACTGTTCG 59.834 37.037 0.00 0.00 0.00 3.95
1549 3527 6.467047 GTGATGCAAATACTGTTCGAAATCAG 59.533 38.462 12.78 12.78 37.65 2.90
1551 3529 5.000591 TGCAAATACTGTTCGAAATCAGGA 58.999 37.500 17.22 11.05 36.17 3.86
1553 3531 5.550981 CAAATACTGTTCGAAATCAGGACG 58.449 41.667 17.22 1.61 36.17 4.79
1556 3534 1.993370 CTGTTCGAAATCAGGACGTCC 59.007 52.381 27.67 27.67 0.00 4.79
1575 3556 5.357032 ACGTCCAAGACTGATCAAACTTTTT 59.643 36.000 10.19 0.00 0.00 1.94
1599 3580 1.831736 GTGACTGTATAGGGCTGTGGT 59.168 52.381 0.00 0.00 0.00 4.16
1606 3587 4.776349 TGTATAGGGCTGTGGTATTGTTG 58.224 43.478 0.00 0.00 0.00 3.33
1608 3589 2.675658 AGGGCTGTGGTATTGTTGTT 57.324 45.000 0.00 0.00 0.00 2.83
1609 3590 2.238521 AGGGCTGTGGTATTGTTGTTG 58.761 47.619 0.00 0.00 0.00 3.33
1619 3600 5.007332 GTGGTATTGTTGTTGAGTCGTTCTT 59.993 40.000 0.00 0.00 0.00 2.52
1632 3613 1.067974 TCGTTCTTCTTGCAGTTCCGA 59.932 47.619 0.00 0.00 0.00 4.55
1641 3622 2.109126 GCAGTTCCGAGCCATGTCC 61.109 63.158 0.00 0.00 0.00 4.02
1647 3628 2.659063 CCGAGCCATGTCCCAGACA 61.659 63.158 0.00 0.00 46.90 3.41
1648 3629 1.153489 CGAGCCATGTCCCAGACAG 60.153 63.158 3.56 0.00 46.04 3.51
1655 3636 2.366916 CCATGTCCCAGACAGTAGATCC 59.633 54.545 3.56 0.00 46.04 3.36
1656 3637 2.919772 TGTCCCAGACAGTAGATCCA 57.080 50.000 0.00 0.00 37.67 3.41
1695 3676 3.132111 TGCTCATCGAAGCATTAGGTACA 59.868 43.478 7.71 0.00 47.00 2.90
1697 3678 4.151335 GCTCATCGAAGCATTAGGTACATG 59.849 45.833 4.21 0.00 42.05 3.21
1698 3679 5.276461 TCATCGAAGCATTAGGTACATGT 57.724 39.130 2.69 2.69 0.00 3.21
1701 3682 5.339008 TCGAAGCATTAGGTACATGTTCT 57.661 39.130 2.30 5.11 0.00 3.01
1704 3685 5.580691 CGAAGCATTAGGTACATGTTCTTCA 59.419 40.000 2.30 0.00 0.00 3.02
1706 3687 7.517417 CGAAGCATTAGGTACATGTTCTTCATC 60.517 40.741 2.30 0.00 34.09 2.92
1708 3689 6.765036 AGCATTAGGTACATGTTCTTCATCTG 59.235 38.462 2.30 0.00 34.09 2.90
1709 3690 6.017605 GCATTAGGTACATGTTCTTCATCTGG 60.018 42.308 2.30 0.00 34.09 3.86
1711 3708 2.609459 GGTACATGTTCTTCATCTGGCG 59.391 50.000 2.30 0.00 34.09 5.69
1717 3714 0.037326 TTCTTCATCTGGCGTTCGCT 60.037 50.000 16.40 0.00 0.00 4.93
1722 3719 0.179215 CATCTGGCGTTCGCTTCAAC 60.179 55.000 16.40 0.73 0.00 3.18
1723 3720 0.602638 ATCTGGCGTTCGCTTCAACA 60.603 50.000 16.40 5.22 0.00 3.33
1724 3726 0.602638 TCTGGCGTTCGCTTCAACAT 60.603 50.000 16.40 0.00 0.00 2.71
1728 3730 0.790866 GCGTTCGCTTCAACATGAGC 60.791 55.000 9.99 0.00 0.00 4.26
1729 3731 0.792640 CGTTCGCTTCAACATGAGCT 59.207 50.000 0.00 0.00 0.00 4.09
1731 3733 2.349817 CGTTCGCTTCAACATGAGCTTT 60.350 45.455 0.00 0.00 0.00 3.51
1732 3734 2.975410 TCGCTTCAACATGAGCTTTG 57.025 45.000 0.00 0.00 0.00 2.77
1733 3735 1.069022 TCGCTTCAACATGAGCTTTGC 60.069 47.619 0.00 0.00 0.00 3.68
1736 3738 0.667453 TTCAACATGAGCTTTGCGCA 59.333 45.000 5.66 5.66 43.16 6.09
1740 3742 0.318955 ACATGAGCTTTGCGCAAACC 60.319 50.000 30.63 24.19 42.18 3.27
1747 3749 2.161609 AGCTTTGCGCAAACCATAGTAC 59.838 45.455 30.63 9.49 42.61 2.73
1749 3751 3.727970 GCTTTGCGCAAACCATAGTACTC 60.728 47.826 30.63 5.06 38.92 2.59
1751 3753 1.276705 TGCGCAAACCATAGTACTCCA 59.723 47.619 8.16 0.00 0.00 3.86
1753 3755 2.287915 GCGCAAACCATAGTACTCCATG 59.712 50.000 0.30 0.00 0.00 3.66
1756 3758 5.113383 CGCAAACCATAGTACTCCATGTTA 58.887 41.667 0.00 0.00 0.00 2.41
1757 3759 5.006358 CGCAAACCATAGTACTCCATGTTAC 59.994 44.000 0.00 0.00 0.00 2.50
1759 3761 7.270047 GCAAACCATAGTACTCCATGTTACTA 58.730 38.462 0.00 7.98 0.00 1.82
1760 3762 7.767198 GCAAACCATAGTACTCCATGTTACTAA 59.233 37.037 0.00 0.00 0.00 2.24
1761 3763 9.095065 CAAACCATAGTACTCCATGTTACTAAC 57.905 37.037 0.00 0.00 0.00 2.34
1762 3764 8.605325 AACCATAGTACTCCATGTTACTAACT 57.395 34.615 0.00 0.93 0.00 2.24
1763 3765 8.605325 ACCATAGTACTCCATGTTACTAACTT 57.395 34.615 0.00 0.00 0.00 2.66
1764 3766 8.475639 ACCATAGTACTCCATGTTACTAACTTG 58.524 37.037 0.00 7.54 36.58 3.16
1785 3787 4.918588 TGGGGACAAACTAATTCCTCTTC 58.081 43.478 0.00 0.00 37.44 2.87
1786 3788 4.601857 TGGGGACAAACTAATTCCTCTTCT 59.398 41.667 0.00 0.00 37.44 2.85
1787 3789 5.074515 TGGGGACAAACTAATTCCTCTTCTT 59.925 40.000 0.00 0.00 37.44 2.52
1788 3790 5.648526 GGGGACAAACTAATTCCTCTTCTTC 59.351 44.000 0.00 0.00 0.00 2.87
1811 3813 2.027745 AGACATGTTTCTGATCGGCACT 60.028 45.455 0.00 0.00 0.00 4.40
1814 3816 0.035317 TGTTTCTGATCGGCACTGCT 59.965 50.000 0.00 0.00 0.00 4.24
1826 3828 1.502163 GCACTGCTCTGCTCACGTTT 61.502 55.000 0.00 0.00 34.06 3.60
1828 3830 1.206072 CTGCTCTGCTCACGTTTGC 59.794 57.895 2.88 2.88 0.00 3.68
2022 4024 2.678580 TCACCGGCCTCGACATGA 60.679 61.111 0.00 0.00 39.00 3.07
2077 4079 1.739562 GCGTCTTCCTGCTGTCCAG 60.740 63.158 0.00 0.00 41.41 3.86
2187 4201 7.547119 GTTTGTTCTTTCATTTCAAGTTAGCG 58.453 34.615 0.00 0.00 0.00 4.26
2232 4246 9.143155 ACTAATAGAAAAACCAAAACCTGTGAT 57.857 29.630 0.00 0.00 0.00 3.06
2258 4272 3.430333 TGTGCCTTTTTCGTCTTTTCC 57.570 42.857 0.00 0.00 0.00 3.13
2267 4281 1.048601 TCGTCTTTTCCCTCACTGCT 58.951 50.000 0.00 0.00 0.00 4.24
2313 4327 8.838452 CTTGAGAGCAATGTCAATAAAGATTC 57.162 34.615 0.00 0.00 32.33 2.52
2314 4328 8.571461 TTGAGAGCAATGTCAATAAAGATTCT 57.429 30.769 0.00 0.00 0.00 2.40
2315 4329 8.206325 TGAGAGCAATGTCAATAAAGATTCTC 57.794 34.615 0.00 0.00 0.00 2.87
2316 4330 7.010830 TGAGAGCAATGTCAATAAAGATTCTCG 59.989 37.037 0.00 0.00 0.00 4.04
2317 4331 6.259608 AGAGCAATGTCAATAAAGATTCTCGG 59.740 38.462 0.00 0.00 0.00 4.63
2318 4332 5.297776 AGCAATGTCAATAAAGATTCTCGGG 59.702 40.000 0.00 0.00 0.00 5.14
2319 4333 5.506317 GCAATGTCAATAAAGATTCTCGGGG 60.506 44.000 0.00 0.00 0.00 5.73
2320 4334 4.837093 TGTCAATAAAGATTCTCGGGGT 57.163 40.909 0.00 0.00 0.00 4.95
2321 4335 5.943349 TGTCAATAAAGATTCTCGGGGTA 57.057 39.130 0.00 0.00 0.00 3.69
2322 4336 5.914033 TGTCAATAAAGATTCTCGGGGTAG 58.086 41.667 0.00 0.00 0.00 3.18
2323 4337 5.163343 TGTCAATAAAGATTCTCGGGGTAGG 60.163 44.000 0.00 0.00 0.00 3.18
2324 4338 5.070047 GTCAATAAAGATTCTCGGGGTAGGA 59.930 44.000 0.00 0.00 0.00 2.94
2325 4339 5.664006 TCAATAAAGATTCTCGGGGTAGGAA 59.336 40.000 0.00 0.00 0.00 3.36
2326 4340 5.810080 ATAAAGATTCTCGGGGTAGGAAG 57.190 43.478 0.00 0.00 0.00 3.46
2327 4341 3.399952 AAGATTCTCGGGGTAGGAAGA 57.600 47.619 0.00 0.00 0.00 2.87
2328 4342 3.399952 AGATTCTCGGGGTAGGAAGAA 57.600 47.619 0.00 0.00 0.00 2.52
2329 4343 3.721021 AGATTCTCGGGGTAGGAAGAAA 58.279 45.455 0.00 0.00 0.00 2.52
2330 4344 4.101856 AGATTCTCGGGGTAGGAAGAAAA 58.898 43.478 0.00 0.00 0.00 2.29
2331 4345 3.975168 TTCTCGGGGTAGGAAGAAAAG 57.025 47.619 0.00 0.00 0.00 2.27
2332 4346 2.185387 TCTCGGGGTAGGAAGAAAAGG 58.815 52.381 0.00 0.00 0.00 3.11
2333 4347 1.907255 CTCGGGGTAGGAAGAAAAGGT 59.093 52.381 0.00 0.00 0.00 3.50
2334 4348 3.102204 CTCGGGGTAGGAAGAAAAGGTA 58.898 50.000 0.00 0.00 0.00 3.08
2335 4349 2.833943 TCGGGGTAGGAAGAAAAGGTAC 59.166 50.000 0.00 0.00 0.00 3.34
2337 4351 3.369157 CGGGGTAGGAAGAAAAGGTACTG 60.369 52.174 0.00 0.00 40.86 2.74
2338 4352 3.607741 GGGTAGGAAGAAAAGGTACTGC 58.392 50.000 0.00 0.00 40.86 4.40
2339 4353 3.008704 GGGTAGGAAGAAAAGGTACTGCA 59.991 47.826 0.00 0.00 40.86 4.41
2340 4354 4.506095 GGGTAGGAAGAAAAGGTACTGCAA 60.506 45.833 0.00 0.00 40.86 4.08
2341 4355 5.067954 GGTAGGAAGAAAAGGTACTGCAAA 58.932 41.667 0.00 0.00 40.86 3.68
2342 4356 5.533528 GGTAGGAAGAAAAGGTACTGCAAAA 59.466 40.000 0.00 0.00 40.86 2.44
2343 4357 6.040054 GGTAGGAAGAAAAGGTACTGCAAAAA 59.960 38.462 0.00 0.00 40.86 1.94
2344 4358 6.731292 AGGAAGAAAAGGTACTGCAAAAAT 57.269 33.333 0.00 0.00 40.86 1.82
2345 4359 6.749139 AGGAAGAAAAGGTACTGCAAAAATC 58.251 36.000 0.00 0.00 40.86 2.17
2365 4383 1.063616 CATTTCGGAGCGACTCTCGTA 59.936 52.381 6.78 1.74 42.81 3.43
2423 4441 0.534203 TTCACCTTCACGTTGCCTCC 60.534 55.000 0.00 0.00 0.00 4.30
2431 4449 0.596082 CACGTTGCCTCCCGAAATTT 59.404 50.000 0.00 0.00 0.00 1.82
2590 4616 4.451150 TCGCACTGCCGCTTAGGG 62.451 66.667 0.00 0.00 41.48 3.53
2603 4629 0.326618 CTTAGGGGAGGGAAGAGGCA 60.327 60.000 0.00 0.00 0.00 4.75
2629 4862 2.856346 GCGCGCGACATCGTAACAT 61.856 57.895 37.18 0.00 42.22 2.71
2630 4863 1.195985 CGCGCGACATCGTAACATC 59.804 57.895 28.94 0.00 42.22 3.06
2639 4872 0.539986 ATCGTAACATCGGCCAACCT 59.460 50.000 2.24 0.00 0.00 3.50
2649 4882 1.223763 GGCCAACCTAGCTACCCAC 59.776 63.158 0.00 0.00 0.00 4.61
2652 4885 1.518572 CAACCTAGCTACCCACGCG 60.519 63.158 3.53 3.53 0.00 6.01
2653 4886 1.679977 AACCTAGCTACCCACGCGA 60.680 57.895 15.93 0.00 0.00 5.87
2654 4887 1.252904 AACCTAGCTACCCACGCGAA 61.253 55.000 15.93 0.00 0.00 4.70
2655 4888 1.065928 CCTAGCTACCCACGCGAAG 59.934 63.158 15.93 4.40 0.00 3.79
2656 4889 1.381928 CCTAGCTACCCACGCGAAGA 61.382 60.000 15.93 0.00 0.00 2.87
2657 4890 0.248539 CTAGCTACCCACGCGAAGAC 60.249 60.000 15.93 0.00 0.00 3.01
2658 4891 0.961857 TAGCTACCCACGCGAAGACA 60.962 55.000 15.93 0.00 0.00 3.41
2659 4892 2.092882 GCTACCCACGCGAAGACAC 61.093 63.158 15.93 0.00 0.00 3.67
2660 4893 1.287815 CTACCCACGCGAAGACACA 59.712 57.895 15.93 0.00 0.00 3.72
2661 4894 1.007038 TACCCACGCGAAGACACAC 60.007 57.895 15.93 0.00 0.00 3.82
2662 4895 1.736365 TACCCACGCGAAGACACACA 61.736 55.000 15.93 0.00 0.00 3.72
2663 4896 2.594962 CCCACGCGAAGACACACAC 61.595 63.158 15.93 0.00 0.00 3.82
2664 4897 1.591594 CCACGCGAAGACACACACT 60.592 57.895 15.93 0.00 0.00 3.55
2665 4898 0.318360 CCACGCGAAGACACACACTA 60.318 55.000 15.93 0.00 0.00 2.74
2670 4903 2.729360 CGCGAAGACACACACTATTGAA 59.271 45.455 0.00 0.00 0.00 2.69
2681 4914 7.141363 ACACACACTATTGAAAAGAAAGCATC 58.859 34.615 0.00 0.00 0.00 3.91
2693 4926 4.913335 AGAAAGCATCGTCGAGGTTATA 57.087 40.909 8.86 0.00 0.00 0.98
2720 4953 4.357325 ACCAGTATTGTCATCACTCCTCT 58.643 43.478 0.00 0.00 0.00 3.69
2723 4956 2.306341 ATTGTCATCACTCCTCTGCG 57.694 50.000 0.00 0.00 0.00 5.18
2763 4996 1.206578 CATTGACGACCACCAACGC 59.793 57.895 0.00 0.00 0.00 4.84
2775 5008 0.606401 ACCAACGCAACCCTCATCAG 60.606 55.000 0.00 0.00 0.00 2.90
2781 5014 1.731720 GCAACCCTCATCAGACAGTC 58.268 55.000 0.00 0.00 0.00 3.51
2782 5015 1.277557 GCAACCCTCATCAGACAGTCT 59.722 52.381 0.00 0.00 0.00 3.24
2788 5021 2.428890 CCTCATCAGACAGTCTACCACC 59.571 54.545 1.67 0.00 0.00 4.61
2816 5052 1.203523 GCGATGAGACACCTGAGACTT 59.796 52.381 0.00 0.00 0.00 3.01
2843 5079 3.648339 TGAACCTTGCATGAGAAAAGC 57.352 42.857 0.00 0.00 0.00 3.51
2861 5097 1.893808 CGTTGAGCCAGCACCAACT 60.894 57.895 18.83 0.00 38.32 3.16
2863 5099 1.160137 GTTGAGCCAGCACCAACTAG 58.840 55.000 15.89 0.00 37.69 2.57
2880 5116 2.196997 TAGGCCCTGCAAGCGAACAT 62.197 55.000 0.00 0.00 0.00 2.71
2881 5117 2.486966 GCCCTGCAAGCGAACATC 59.513 61.111 0.00 0.00 0.00 3.06
2888 5124 1.280982 GCAAGCGAACATCGATCTCA 58.719 50.000 3.61 0.00 43.74 3.27
2901 5137 1.506493 GATCTCATGCCATCGTCACC 58.494 55.000 0.00 0.00 0.00 4.02
2902 5138 0.249615 ATCTCATGCCATCGTCACCG 60.250 55.000 0.00 0.00 0.00 4.94
2922 5158 2.501223 CTAACGCACCTCCTCCGCAA 62.501 60.000 0.00 0.00 0.00 4.85
2941 5178 0.389948 ACTCCGATCCACAAAGACGC 60.390 55.000 0.00 0.00 0.00 5.19
2951 5188 1.291877 ACAAAGACGCGATGAGGCAC 61.292 55.000 15.93 0.00 0.00 5.01
2961 5198 0.820871 GATGAGGCACGAGAACTCCT 59.179 55.000 0.00 0.00 0.00 3.69
2962 5199 0.820871 ATGAGGCACGAGAACTCCTC 59.179 55.000 0.00 0.00 44.04 3.71
2997 5234 0.178909 TACCGACTACCAAACCCCCA 60.179 55.000 0.00 0.00 0.00 4.96
3007 5244 0.827507 CAAACCCCCACCTCAACTGG 60.828 60.000 0.00 0.00 0.00 4.00
3035 5272 1.156736 CCACAACCATCGACAAGTCC 58.843 55.000 0.00 0.00 0.00 3.85
3040 5277 0.036306 ACCATCGACAAGTCCCCAAC 59.964 55.000 0.00 0.00 0.00 3.77
3070 5307 0.924090 CCTATCACAAGAAGTCGCGC 59.076 55.000 0.00 0.00 0.00 6.86
3090 5327 4.250464 CGCCAAACTAATAAGTGACCAGA 58.750 43.478 0.00 0.00 35.62 3.86
3101 5338 3.724508 AGTGACCAGATGATCGCTAAG 57.275 47.619 0.00 0.00 33.94 2.18
3102 5339 3.291584 AGTGACCAGATGATCGCTAAGA 58.708 45.455 0.00 0.00 33.94 2.10
3103 5340 3.067461 AGTGACCAGATGATCGCTAAGAC 59.933 47.826 0.00 0.00 33.94 3.01
3104 5341 2.033424 TGACCAGATGATCGCTAAGACG 59.967 50.000 0.00 0.00 0.00 4.18
3105 5342 1.269309 ACCAGATGATCGCTAAGACGC 60.269 52.381 0.00 0.00 0.00 5.19
3106 5343 1.000827 CCAGATGATCGCTAAGACGCT 60.001 52.381 0.00 0.00 0.00 5.07
3107 5344 2.226674 CCAGATGATCGCTAAGACGCTA 59.773 50.000 0.00 0.00 0.00 4.26
3108 5345 3.304726 CCAGATGATCGCTAAGACGCTAA 60.305 47.826 0.00 0.00 0.00 3.09
3109 5346 3.666334 CAGATGATCGCTAAGACGCTAAC 59.334 47.826 0.00 0.00 0.00 2.34
3110 5347 3.566322 AGATGATCGCTAAGACGCTAACT 59.434 43.478 0.00 0.00 0.00 2.24
3111 5348 3.066369 TGATCGCTAAGACGCTAACTG 57.934 47.619 0.00 0.00 0.00 3.16
3112 5349 2.681344 TGATCGCTAAGACGCTAACTGA 59.319 45.455 0.00 0.00 0.00 3.41
3113 5350 3.128068 TGATCGCTAAGACGCTAACTGAA 59.872 43.478 0.00 0.00 0.00 3.02
3114 5351 3.132629 TCGCTAAGACGCTAACTGAAG 57.867 47.619 0.00 0.00 0.00 3.02
3115 5352 2.486982 TCGCTAAGACGCTAACTGAAGT 59.513 45.455 0.00 0.00 0.00 3.01
3116 5353 3.057736 TCGCTAAGACGCTAACTGAAGTT 60.058 43.478 0.71 0.71 41.73 2.66
3117 5354 3.673809 CGCTAAGACGCTAACTGAAGTTT 59.326 43.478 0.21 0.00 39.31 2.66
3118 5355 4.855388 CGCTAAGACGCTAACTGAAGTTTA 59.145 41.667 0.21 0.00 39.31 2.01
3119 5356 5.219987 CGCTAAGACGCTAACTGAAGTTTAC 60.220 44.000 0.21 0.00 39.31 2.01
3120 5357 5.061933 GCTAAGACGCTAACTGAAGTTTACC 59.938 44.000 0.21 0.00 39.31 2.85
3121 5358 4.868314 AGACGCTAACTGAAGTTTACCT 57.132 40.909 0.21 0.00 39.31 3.08
3122 5359 5.211174 AGACGCTAACTGAAGTTTACCTT 57.789 39.130 0.21 0.00 39.31 3.50
3123 5360 4.989168 AGACGCTAACTGAAGTTTACCTTG 59.011 41.667 0.21 0.00 39.31 3.61
3124 5361 4.700700 ACGCTAACTGAAGTTTACCTTGT 58.299 39.130 0.21 0.00 39.31 3.16
3125 5362 5.846203 ACGCTAACTGAAGTTTACCTTGTA 58.154 37.500 0.21 0.00 39.31 2.41
3126 5363 6.282930 ACGCTAACTGAAGTTTACCTTGTAA 58.717 36.000 0.21 0.00 39.31 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.000274 GCTTTTGTCCGTCCAAATGCT 60.000 47.619 19.08 0.00 45.08 3.79
1 2 1.418373 GCTTTTGTCCGTCCAAATGC 58.582 50.000 14.65 14.65 43.56 3.56
2 3 1.685302 CGCTTTTGTCCGTCCAAATG 58.315 50.000 0.00 2.70 34.50 2.32
3 4 0.039527 GCGCTTTTGTCCGTCCAAAT 60.040 50.000 0.00 0.00 34.50 2.32
95 98 6.589907 TCAAGTTTCAAGCTTGAAGTTTTTCC 59.410 34.615 33.76 19.42 46.21 3.13
114 117 0.034059 CGGGCACAGACTCTCAAGTT 59.966 55.000 0.00 0.00 35.28 2.66
190 211 4.368808 CGGGCACGTGACGCAAAG 62.369 66.667 22.23 2.14 34.81 2.77
419 449 1.147153 CCTCCGGGGCAGAAAGATC 59.853 63.158 0.00 0.00 0.00 2.75
433 463 0.960861 CAAACTTCCTTCCGGCCTCC 60.961 60.000 0.00 0.00 0.00 4.30
434 464 1.587043 GCAAACTTCCTTCCGGCCTC 61.587 60.000 0.00 0.00 0.00 4.70
474 525 1.705745 GGAGGAAGGAGGAAAGGTTGT 59.294 52.381 0.00 0.00 0.00 3.32
570 636 3.429822 GGTTAAGCAGCGTAGTGGTCATA 60.430 47.826 0.00 0.00 0.00 2.15
581 647 1.723870 GATGCCTGGTTAAGCAGCG 59.276 57.895 25.82 19.75 43.38 5.18
584 650 1.810151 GAAACGATGCCTGGTTAAGCA 59.190 47.619 7.22 7.22 44.45 3.91
592 2506 2.549754 ACAAACTCTGAAACGATGCCTG 59.450 45.455 0.00 0.00 0.00 4.85
612 2526 2.868583 TCGTGCTGGTATCTCGTAGTAC 59.131 50.000 0.00 0.00 0.00 2.73
613 2527 3.183793 TCGTGCTGGTATCTCGTAGTA 57.816 47.619 0.00 0.00 0.00 1.82
614 2528 2.034104 TCGTGCTGGTATCTCGTAGT 57.966 50.000 0.00 0.00 0.00 2.73
924 2885 6.715464 CGTTGAAGTTGAAGTATTGACTGTT 58.285 36.000 0.00 0.00 35.52 3.16
1041 3004 2.113139 CTGTCCTTGGCGGTGGTT 59.887 61.111 0.00 0.00 0.00 3.67
1152 3130 4.537433 GCGCGGCTGATCTTCCCT 62.537 66.667 8.83 0.00 0.00 4.20
1233 3211 4.974438 TCCCCCGGCAGGAGTTGT 62.974 66.667 3.68 0.00 41.02 3.32
1255 3233 0.754957 AGCAGGAGATCTACGCTGCT 60.755 55.000 19.30 17.03 42.41 4.24
1263 3241 1.049855 CCAGAGGCAGCAGGAGATCT 61.050 60.000 0.00 0.00 0.00 2.75
1297 3275 3.007920 CCTGAGCACCAGCCTCCT 61.008 66.667 1.06 0.00 43.56 3.69
1404 3382 1.878522 GCCGATGAGCGTGAACGAT 60.879 57.895 7.10 0.00 43.02 3.73
1458 3436 4.158949 TCATTTGTCGGAATTACCTCGAGA 59.841 41.667 15.71 0.00 36.31 4.04
1471 3449 4.006989 TGACATAAAGGGTCATTTGTCGG 58.993 43.478 0.00 0.00 40.16 4.79
1472 3450 4.695455 AGTGACATAAAGGGTCATTTGTCG 59.305 41.667 0.00 0.00 46.01 4.35
1473 3451 5.705441 TGAGTGACATAAAGGGTCATTTGTC 59.295 40.000 0.00 0.00 46.01 3.18
1474 3452 5.473504 GTGAGTGACATAAAGGGTCATTTGT 59.526 40.000 0.00 0.00 46.01 2.83
1475 3453 5.707298 AGTGAGTGACATAAAGGGTCATTTG 59.293 40.000 0.00 0.00 46.01 2.32
1478 3456 5.249393 AGAAGTGAGTGACATAAAGGGTCAT 59.751 40.000 0.00 0.00 46.01 3.06
1479 3457 4.593206 AGAAGTGAGTGACATAAAGGGTCA 59.407 41.667 0.00 0.00 42.62 4.02
1481 3459 4.593206 TGAGAAGTGAGTGACATAAAGGGT 59.407 41.667 0.00 0.00 0.00 4.34
1482 3460 5.152623 TGAGAAGTGAGTGACATAAAGGG 57.847 43.478 0.00 0.00 0.00 3.95
1483 3461 6.875726 TGATTGAGAAGTGAGTGACATAAAGG 59.124 38.462 0.00 0.00 0.00 3.11
1487 3465 6.997655 ACTTGATTGAGAAGTGAGTGACATA 58.002 36.000 0.00 0.00 32.30 2.29
1489 3467 5.282055 ACTTGATTGAGAAGTGAGTGACA 57.718 39.130 0.00 0.00 32.30 3.58
1497 3475 7.823745 AAATGGTTACACTTGATTGAGAAGT 57.176 32.000 0.00 0.00 33.82 3.01
1498 3476 9.778993 CATAAATGGTTACACTTGATTGAGAAG 57.221 33.333 0.00 0.00 0.00 2.85
1500 3478 8.729756 CACATAAATGGTTACACTTGATTGAGA 58.270 33.333 0.00 0.00 0.00 3.27
1504 3482 7.975616 GCATCACATAAATGGTTACACTTGATT 59.024 33.333 0.00 0.00 0.00 2.57
1507 3485 6.619744 TGCATCACATAAATGGTTACACTTG 58.380 36.000 0.00 0.00 0.00 3.16
1514 3492 7.839907 ACAGTATTTGCATCACATAAATGGTT 58.160 30.769 0.00 0.00 0.00 3.67
1515 3493 7.408756 ACAGTATTTGCATCACATAAATGGT 57.591 32.000 0.00 0.00 0.00 3.55
1525 3503 6.403527 CCTGATTTCGAACAGTATTTGCATCA 60.404 38.462 13.04 7.93 32.93 3.07
1526 3504 5.967674 CCTGATTTCGAACAGTATTTGCATC 59.032 40.000 13.04 4.20 32.93 3.91
1527 3505 5.647658 TCCTGATTTCGAACAGTATTTGCAT 59.352 36.000 13.04 0.00 32.93 3.96
1528 3506 5.000591 TCCTGATTTCGAACAGTATTTGCA 58.999 37.500 13.04 0.00 32.93 4.08
1529 3507 5.324697 GTCCTGATTTCGAACAGTATTTGC 58.675 41.667 13.04 0.00 32.93 3.68
1530 3508 5.120208 ACGTCCTGATTTCGAACAGTATTTG 59.880 40.000 13.04 0.60 32.93 2.32
1531 3509 5.235516 ACGTCCTGATTTCGAACAGTATTT 58.764 37.500 13.04 0.00 32.93 1.40
1532 3510 4.817517 ACGTCCTGATTTCGAACAGTATT 58.182 39.130 13.04 0.00 32.93 1.89
1533 3511 4.421948 GACGTCCTGATTTCGAACAGTAT 58.578 43.478 3.51 0.00 32.93 2.12
1534 3512 3.366679 GGACGTCCTGATTTCGAACAGTA 60.367 47.826 27.64 0.00 32.93 2.74
1535 3513 2.609737 GGACGTCCTGATTTCGAACAGT 60.610 50.000 27.64 0.00 32.93 3.55
1536 3514 1.993370 GGACGTCCTGATTTCGAACAG 59.007 52.381 27.64 2.76 0.00 3.16
1537 3515 1.341852 TGGACGTCCTGATTTCGAACA 59.658 47.619 33.39 7.46 36.82 3.18
1541 3519 1.993370 GTCTTGGACGTCCTGATTTCG 59.007 52.381 33.39 14.27 36.82 3.46
1542 3520 2.996621 CAGTCTTGGACGTCCTGATTTC 59.003 50.000 33.39 18.68 37.67 2.17
1549 3527 2.737252 GTTTGATCAGTCTTGGACGTCC 59.263 50.000 28.17 28.17 37.67 4.79
1551 3529 3.753294 AGTTTGATCAGTCTTGGACGT 57.247 42.857 0.00 0.00 37.67 4.34
1575 3556 4.323417 CACAGCCCTATACAGTCACAAAA 58.677 43.478 0.00 0.00 0.00 2.44
1576 3557 3.307410 CCACAGCCCTATACAGTCACAAA 60.307 47.826 0.00 0.00 0.00 2.83
1578 3559 1.831106 CCACAGCCCTATACAGTCACA 59.169 52.381 0.00 0.00 0.00 3.58
1579 3560 1.831736 ACCACAGCCCTATACAGTCAC 59.168 52.381 0.00 0.00 0.00 3.67
1580 3561 2.247699 ACCACAGCCCTATACAGTCA 57.752 50.000 0.00 0.00 0.00 3.41
1581 3562 4.101119 ACAATACCACAGCCCTATACAGTC 59.899 45.833 0.00 0.00 0.00 3.51
1582 3563 4.037927 ACAATACCACAGCCCTATACAGT 58.962 43.478 0.00 0.00 0.00 3.55
1583 3564 4.689612 ACAATACCACAGCCCTATACAG 57.310 45.455 0.00 0.00 0.00 2.74
1584 3565 4.226394 ACAACAATACCACAGCCCTATACA 59.774 41.667 0.00 0.00 0.00 2.29
1585 3566 4.777463 ACAACAATACCACAGCCCTATAC 58.223 43.478 0.00 0.00 0.00 1.47
1587 3568 4.016444 CAACAACAATACCACAGCCCTAT 58.984 43.478 0.00 0.00 0.00 2.57
1593 3574 3.807622 ACGACTCAACAACAATACCACAG 59.192 43.478 0.00 0.00 0.00 3.66
1599 3580 6.511121 GCAAGAAGAACGACTCAACAACAATA 60.511 38.462 0.00 0.00 0.00 1.90
1606 3587 2.866762 ACTGCAAGAAGAACGACTCAAC 59.133 45.455 0.00 0.00 37.43 3.18
1608 3589 2.890808 ACTGCAAGAAGAACGACTCA 57.109 45.000 0.00 0.00 37.43 3.41
1609 3590 2.476997 GGAACTGCAAGAAGAACGACTC 59.523 50.000 0.00 0.00 37.43 3.36
1619 3600 0.674581 CATGGCTCGGAACTGCAAGA 60.675 55.000 0.00 0.00 37.43 3.02
1632 3613 1.198713 CTACTGTCTGGGACATGGCT 58.801 55.000 0.00 0.00 41.94 4.75
1641 3622 0.387202 CGGCTGGATCTACTGTCTGG 59.613 60.000 0.00 0.00 0.00 3.86
1647 3628 2.666272 TGATCTCGGCTGGATCTACT 57.334 50.000 18.84 0.00 39.95 2.57
1648 3629 2.822561 TGATGATCTCGGCTGGATCTAC 59.177 50.000 18.84 14.35 39.95 2.59
1655 3636 1.329906 GCAGTTTGATGATCTCGGCTG 59.670 52.381 0.00 0.00 0.00 4.85
1656 3637 1.209019 AGCAGTTTGATGATCTCGGCT 59.791 47.619 0.00 0.01 0.00 5.52
1695 3676 2.002586 CGAACGCCAGATGAAGAACAT 58.997 47.619 0.00 0.00 42.47 2.71
1697 3678 0.095417 GCGAACGCCAGATGAAGAAC 59.905 55.000 8.03 0.00 34.56 3.01
1698 3679 0.037326 AGCGAACGCCAGATGAAGAA 60.037 50.000 15.44 0.00 43.17 2.52
1701 3682 0.320334 TGAAGCGAACGCCAGATGAA 60.320 50.000 15.44 0.00 43.17 2.57
1704 3685 0.602638 TGTTGAAGCGAACGCCAGAT 60.603 50.000 15.44 0.15 43.17 2.90
1706 3687 0.453282 CATGTTGAAGCGAACGCCAG 60.453 55.000 15.44 0.00 43.17 4.85
1708 3689 0.179215 CTCATGTTGAAGCGAACGCC 60.179 55.000 15.44 2.23 43.17 5.68
1709 3690 0.790866 GCTCATGTTGAAGCGAACGC 60.791 55.000 11.31 11.31 42.33 4.84
1711 3708 2.975851 CAAAGCTCATGTTGAAGCGAAC 59.024 45.455 0.00 0.00 0.00 3.95
1717 3714 3.477504 GCGCAAAGCTCATGTTGAA 57.522 47.368 0.30 0.00 44.04 2.69
1728 3730 3.181510 GGAGTACTATGGTTTGCGCAAAG 60.182 47.826 34.35 24.23 0.00 2.77
1729 3731 2.745281 GGAGTACTATGGTTTGCGCAAA 59.255 45.455 30.63 30.63 0.00 3.68
1731 3733 1.276705 TGGAGTACTATGGTTTGCGCA 59.723 47.619 5.66 5.66 0.00 6.09
1732 3734 2.018542 TGGAGTACTATGGTTTGCGC 57.981 50.000 0.00 0.00 0.00 6.09
1733 3735 3.531538 ACATGGAGTACTATGGTTTGCG 58.468 45.455 9.83 0.00 38.92 4.85
1736 3738 9.043548 AGTTAGTAACATGGAGTACTATGGTTT 57.956 33.333 15.28 0.39 38.92 3.27
1749 3751 4.295141 TGTCCCCAAGTTAGTAACATGG 57.705 45.455 24.28 24.28 46.89 3.66
1751 3753 5.948842 AGTTTGTCCCCAAGTTAGTAACAT 58.051 37.500 15.28 0.00 0.00 2.71
1753 3755 7.991084 ATTAGTTTGTCCCCAAGTTAGTAAC 57.009 36.000 4.78 4.78 0.00 2.50
1756 3758 6.008331 GGAATTAGTTTGTCCCCAAGTTAGT 58.992 40.000 0.00 0.00 0.00 2.24
1757 3759 6.246163 AGGAATTAGTTTGTCCCCAAGTTAG 58.754 40.000 0.00 0.00 31.25 2.34
1759 3761 5.074746 AGGAATTAGTTTGTCCCCAAGTT 57.925 39.130 0.00 0.00 31.25 2.66
1760 3762 4.354087 AGAGGAATTAGTTTGTCCCCAAGT 59.646 41.667 0.00 0.00 31.25 3.16
1761 3763 4.923415 AGAGGAATTAGTTTGTCCCCAAG 58.077 43.478 0.00 0.00 31.25 3.61
1762 3764 5.074515 AGAAGAGGAATTAGTTTGTCCCCAA 59.925 40.000 0.00 0.00 31.25 4.12
1763 3765 4.601857 AGAAGAGGAATTAGTTTGTCCCCA 59.398 41.667 0.00 0.00 31.25 4.96
1764 3766 5.180810 AGAAGAGGAATTAGTTTGTCCCC 57.819 43.478 0.00 0.00 31.25 4.81
1765 3767 5.648526 GGAAGAAGAGGAATTAGTTTGTCCC 59.351 44.000 0.00 0.00 31.25 4.46
1766 3768 6.238648 TGGAAGAAGAGGAATTAGTTTGTCC 58.761 40.000 0.00 0.00 0.00 4.02
1767 3769 7.162082 TCTGGAAGAAGAGGAATTAGTTTGTC 58.838 38.462 0.00 0.00 42.31 3.18
1768 3770 7.079451 TCTGGAAGAAGAGGAATTAGTTTGT 57.921 36.000 0.00 0.00 42.31 2.83
1784 3786 4.498241 CGATCAGAAACATGTCTGGAAGA 58.502 43.478 13.06 2.32 44.40 2.87
1785 3787 3.620374 CCGATCAGAAACATGTCTGGAAG 59.380 47.826 13.06 6.10 44.40 3.46
1786 3788 3.599343 CCGATCAGAAACATGTCTGGAA 58.401 45.455 13.06 0.00 44.40 3.53
1787 3789 2.677902 GCCGATCAGAAACATGTCTGGA 60.678 50.000 13.06 3.86 44.40 3.86
1788 3790 1.667724 GCCGATCAGAAACATGTCTGG 59.332 52.381 13.06 0.81 44.40 3.86
1811 3813 2.253758 GGCAAACGTGAGCAGAGCA 61.254 57.895 13.57 0.00 0.00 4.26
1814 3816 1.236616 CCATGGCAAACGTGAGCAGA 61.237 55.000 13.57 1.26 38.41 4.26
1826 3828 2.915079 CCGTACATCCCCATGGCA 59.085 61.111 6.09 0.00 33.82 4.92
1828 3830 0.890542 CATGCCGTACATCCCCATGG 60.891 60.000 4.14 4.14 36.64 3.66
2162 4176 7.431084 TCGCTAACTTGAAATGAAAGAACAAAC 59.569 33.333 0.00 0.00 0.00 2.93
2232 4246 1.333619 GACGAAAAAGGCACAAGAGCA 59.666 47.619 0.00 0.00 35.83 4.26
2258 4272 2.103143 CCGCTACGAGCAGTGAGG 59.897 66.667 0.00 0.00 42.58 3.86
2267 4281 4.497300 AGCTACAAATTAAACCGCTACGA 58.503 39.130 0.00 0.00 0.00 3.43
2310 4324 3.200165 CCTTTTCTTCCTACCCCGAGAAT 59.800 47.826 0.00 0.00 0.00 2.40
2311 4325 2.570302 CCTTTTCTTCCTACCCCGAGAA 59.430 50.000 0.00 0.00 0.00 2.87
2312 4326 2.185387 CCTTTTCTTCCTACCCCGAGA 58.815 52.381 0.00 0.00 0.00 4.04
2313 4327 1.907255 ACCTTTTCTTCCTACCCCGAG 59.093 52.381 0.00 0.00 0.00 4.63
2314 4328 2.034436 ACCTTTTCTTCCTACCCCGA 57.966 50.000 0.00 0.00 0.00 5.14
2315 4329 2.836372 AGTACCTTTTCTTCCTACCCCG 59.164 50.000 0.00 0.00 0.00 5.73
2316 4330 3.621709 GCAGTACCTTTTCTTCCTACCCC 60.622 52.174 0.00 0.00 0.00 4.95
2317 4331 3.008704 TGCAGTACCTTTTCTTCCTACCC 59.991 47.826 0.00 0.00 0.00 3.69
2318 4332 4.281898 TGCAGTACCTTTTCTTCCTACC 57.718 45.455 0.00 0.00 0.00 3.18
2319 4333 6.628919 TTTTGCAGTACCTTTTCTTCCTAC 57.371 37.500 0.00 0.00 0.00 3.18
2320 4334 7.504238 TGATTTTTGCAGTACCTTTTCTTCCTA 59.496 33.333 0.00 0.00 0.00 2.94
2321 4335 6.323739 TGATTTTTGCAGTACCTTTTCTTCCT 59.676 34.615 0.00 0.00 0.00 3.36
2322 4336 6.512297 TGATTTTTGCAGTACCTTTTCTTCC 58.488 36.000 0.00 0.00 0.00 3.46
2323 4337 8.593492 AATGATTTTTGCAGTACCTTTTCTTC 57.407 30.769 0.00 0.00 0.00 2.87
2324 4338 8.962884 AAATGATTTTTGCAGTACCTTTTCTT 57.037 26.923 0.00 0.00 0.00 2.52
2325 4339 7.382218 CGAAATGATTTTTGCAGTACCTTTTCT 59.618 33.333 0.00 0.00 0.00 2.52
2326 4340 7.359181 CCGAAATGATTTTTGCAGTACCTTTTC 60.359 37.037 0.00 0.00 0.00 2.29
2327 4341 6.423604 CCGAAATGATTTTTGCAGTACCTTTT 59.576 34.615 0.00 0.00 0.00 2.27
2328 4342 5.925969 CCGAAATGATTTTTGCAGTACCTTT 59.074 36.000 0.00 0.00 0.00 3.11
2329 4343 5.242838 TCCGAAATGATTTTTGCAGTACCTT 59.757 36.000 0.00 0.00 0.00 3.50
2330 4344 4.764823 TCCGAAATGATTTTTGCAGTACCT 59.235 37.500 0.00 0.00 0.00 3.08
2331 4345 5.054390 TCCGAAATGATTTTTGCAGTACC 57.946 39.130 0.00 0.00 0.00 3.34
2332 4346 4.558860 GCTCCGAAATGATTTTTGCAGTAC 59.441 41.667 0.00 0.00 0.00 2.73
2333 4347 4.671508 CGCTCCGAAATGATTTTTGCAGTA 60.672 41.667 0.00 0.00 0.00 2.74
2334 4348 3.578688 GCTCCGAAATGATTTTTGCAGT 58.421 40.909 0.00 0.00 0.00 4.40
2335 4349 2.595536 CGCTCCGAAATGATTTTTGCAG 59.404 45.455 0.00 0.00 0.00 4.41
2336 4350 2.227626 TCGCTCCGAAATGATTTTTGCA 59.772 40.909 0.00 0.00 31.06 4.08
2337 4351 2.594214 GTCGCTCCGAAATGATTTTTGC 59.406 45.455 0.00 0.00 37.72 3.68
2338 4352 4.083581 AGTCGCTCCGAAATGATTTTTG 57.916 40.909 0.00 0.00 37.72 2.44
2339 4353 4.003648 AGAGTCGCTCCGAAATGATTTTT 58.996 39.130 0.00 0.00 37.72 1.94
2340 4354 3.600388 AGAGTCGCTCCGAAATGATTTT 58.400 40.909 0.00 0.00 37.72 1.82
2341 4355 3.190874 GAGAGTCGCTCCGAAATGATTT 58.809 45.455 0.00 0.00 37.72 2.17
2342 4356 2.796383 CGAGAGTCGCTCCGAAATGATT 60.796 50.000 0.00 0.00 40.70 2.57
2343 4357 1.268794 CGAGAGTCGCTCCGAAATGAT 60.269 52.381 0.00 0.00 40.70 2.45
2344 4358 0.098905 CGAGAGTCGCTCCGAAATGA 59.901 55.000 0.00 0.00 40.70 2.57
2345 4359 0.179161 ACGAGAGTCGCTCCGAAATG 60.179 55.000 17.33 0.00 45.12 2.32
2365 4383 3.541632 ACGTGGTTGATCACAAAAGAGT 58.458 40.909 0.00 0.00 37.77 3.24
2401 4419 0.316689 GGCAACGTGAAGGTGAAACG 60.317 55.000 0.00 0.00 40.93 3.60
2409 4427 0.882927 TTTCGGGAGGCAACGTGAAG 60.883 55.000 0.00 0.00 46.39 3.02
2423 4441 1.154035 GCGGCCACTGAAATTTCGG 60.154 57.895 22.79 22.79 39.48 4.30
2577 4603 3.083997 CCTCCCCTAAGCGGCAGT 61.084 66.667 1.45 0.00 0.00 4.40
2590 4616 1.298014 CACACTGCCTCTTCCCTCC 59.702 63.158 0.00 0.00 0.00 4.30
2614 4640 1.837450 CCGATGTTACGATGTCGCG 59.163 57.895 0.00 0.00 44.43 5.87
2616 4642 0.526739 TGGCCGATGTTACGATGTCG 60.527 55.000 0.00 0.11 46.33 4.35
2617 4643 1.326548 GTTGGCCGATGTTACGATGTC 59.673 52.381 0.00 0.00 35.09 3.06
2618 4644 1.365699 GTTGGCCGATGTTACGATGT 58.634 50.000 0.00 0.00 35.09 3.06
2619 4645 0.655733 GGTTGGCCGATGTTACGATG 59.344 55.000 0.00 0.00 35.09 3.84
2620 4646 0.539986 AGGTTGGCCGATGTTACGAT 59.460 50.000 0.00 0.00 40.50 3.73
2621 4647 1.135527 CTAGGTTGGCCGATGTTACGA 59.864 52.381 0.00 0.00 40.50 3.43
2622 4648 1.567504 CTAGGTTGGCCGATGTTACG 58.432 55.000 0.00 0.00 40.50 3.18
2629 4862 2.062177 GGGTAGCTAGGTTGGCCGA 61.062 63.158 0.00 0.00 40.50 5.54
2630 4863 2.363975 TGGGTAGCTAGGTTGGCCG 61.364 63.158 0.00 0.00 40.50 6.13
2639 4872 0.961857 TGTCTTCGCGTGGGTAGCTA 60.962 55.000 5.77 0.00 0.00 3.32
2649 4882 2.324860 TCAATAGTGTGTGTCTTCGCG 58.675 47.619 0.00 0.00 0.00 5.87
2652 4885 7.377131 GCTTTCTTTTCAATAGTGTGTGTCTTC 59.623 37.037 0.00 0.00 0.00 2.87
2653 4886 7.148086 TGCTTTCTTTTCAATAGTGTGTGTCTT 60.148 33.333 0.00 0.00 0.00 3.01
2654 4887 6.318648 TGCTTTCTTTTCAATAGTGTGTGTCT 59.681 34.615 0.00 0.00 0.00 3.41
2655 4888 6.494842 TGCTTTCTTTTCAATAGTGTGTGTC 58.505 36.000 0.00 0.00 0.00 3.67
2656 4889 6.449635 TGCTTTCTTTTCAATAGTGTGTGT 57.550 33.333 0.00 0.00 0.00 3.72
2657 4890 6.303970 CGATGCTTTCTTTTCAATAGTGTGTG 59.696 38.462 0.00 0.00 0.00 3.82
2658 4891 6.017109 ACGATGCTTTCTTTTCAATAGTGTGT 60.017 34.615 0.00 0.00 0.00 3.72
2659 4892 6.373779 ACGATGCTTTCTTTTCAATAGTGTG 58.626 36.000 0.00 0.00 0.00 3.82
2660 4893 6.560253 ACGATGCTTTCTTTTCAATAGTGT 57.440 33.333 0.00 0.00 0.00 3.55
2661 4894 5.729883 CGACGATGCTTTCTTTTCAATAGTG 59.270 40.000 0.00 0.00 0.00 2.74
2662 4895 5.637810 TCGACGATGCTTTCTTTTCAATAGT 59.362 36.000 0.00 0.00 0.00 2.12
2663 4896 6.094739 TCGACGATGCTTTCTTTTCAATAG 57.905 37.500 0.00 0.00 0.00 1.73
2664 4897 5.063438 CCTCGACGATGCTTTCTTTTCAATA 59.937 40.000 0.00 0.00 0.00 1.90
2665 4898 4.142816 CCTCGACGATGCTTTCTTTTCAAT 60.143 41.667 0.00 0.00 0.00 2.57
2670 4903 2.457366 ACCTCGACGATGCTTTCTTT 57.543 45.000 0.00 0.00 0.00 2.52
2693 4926 4.985538 AGTGATGACAATACTGGTTGGTT 58.014 39.130 0.00 0.00 33.40 3.67
2702 4935 3.119291 CGCAGAGGAGTGATGACAATAC 58.881 50.000 0.00 0.00 0.00 1.89
2706 4939 2.961424 TCGCAGAGGAGTGATGACA 58.039 52.632 0.00 0.00 0.00 3.58
2720 4953 1.667236 ATCGAAATTGATGGCTCGCA 58.333 45.000 0.00 0.00 0.00 5.10
2723 4956 4.040376 GCTGAAATCGAAATTGATGGCTC 58.960 43.478 0.00 0.00 0.00 4.70
2763 4996 3.118956 GGTAGACTGTCTGATGAGGGTTG 60.119 52.174 20.19 0.00 0.00 3.77
2775 5008 1.446272 GCGCAGGTGGTAGACTGTC 60.446 63.158 0.30 0.00 37.07 3.51
2788 5021 3.260483 GTCTCATCGCCAGCGCAG 61.260 66.667 11.47 0.00 39.59 5.18
2798 5031 5.592282 TCATCTAAGTCTCAGGTGTCTCATC 59.408 44.000 0.00 0.00 0.00 2.92
2801 5034 5.592282 TCATCATCTAAGTCTCAGGTGTCTC 59.408 44.000 0.00 0.00 0.00 3.36
2816 5052 5.619132 TCTCATGCAAGGTTCATCATCTA 57.381 39.130 0.00 0.00 0.00 1.98
2843 5079 0.602638 TAGTTGGTGCTGGCTCAACG 60.603 55.000 18.17 0.00 43.70 4.10
2852 5088 3.081554 CAGGGCCTAGTTGGTGCT 58.918 61.111 5.28 0.00 38.35 4.40
2861 5097 2.046314 GTTCGCTTGCAGGGCCTA 60.046 61.111 5.28 0.00 0.00 3.93
2863 5099 3.056313 GATGTTCGCTTGCAGGGCC 62.056 63.158 0.00 0.00 0.00 5.80
2880 5116 1.032014 TGACGATGGCATGAGATCGA 58.968 50.000 25.08 8.31 43.36 3.59
2881 5117 1.135046 GTGACGATGGCATGAGATCG 58.865 55.000 19.56 19.56 45.58 3.69
2902 5138 2.202756 CGGAGGAGGTGCGTTAGC 60.203 66.667 0.00 0.00 45.41 3.09
2922 5158 0.389948 GCGTCTTTGTGGATCGGAGT 60.390 55.000 0.00 0.00 0.00 3.85
2941 5178 0.526524 GGAGTTCTCGTGCCTCATCG 60.527 60.000 6.41 0.00 0.00 3.84
2972 5209 3.493873 GGGTTTGGTAGTCGGTATCATCC 60.494 52.174 0.00 0.00 0.00 3.51
3007 5244 1.523758 GATGGTTGTGGTGTCCTCAC 58.476 55.000 0.00 0.00 43.19 3.51
3040 5277 7.056635 ACTTCTTGTGATAGGACCCATAATTG 58.943 38.462 0.00 0.00 0.00 2.32
3053 5290 0.245266 TGGCGCGACTTCTTGTGATA 59.755 50.000 15.80 0.00 0.00 2.15
3056 5293 0.657368 GTTTGGCGCGACTTCTTGTG 60.657 55.000 15.80 0.00 0.00 3.33
3058 5295 1.144969 TAGTTTGGCGCGACTTCTTG 58.855 50.000 15.80 0.00 0.00 3.02
3070 5307 7.042456 CGATCATCTGGTCACTTATTAGTTTGG 60.042 40.741 0.00 0.00 30.26 3.28
3090 5327 3.315470 TCAGTTAGCGTCTTAGCGATCAT 59.685 43.478 0.00 0.00 43.00 2.45
3101 5338 4.748600 ACAAGGTAAACTTCAGTTAGCGTC 59.251 41.667 0.00 0.00 37.29 5.19
3102 5339 4.700700 ACAAGGTAAACTTCAGTTAGCGT 58.299 39.130 0.00 0.00 37.29 5.07
3103 5340 6.774354 TTACAAGGTAAACTTCAGTTAGCG 57.226 37.500 0.00 0.00 37.29 4.26


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

AutoCloner maintained by Alex Coulton.