Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005686.1 Hibiscus syriacus cultivar Beakdansim tig00013298_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 73998
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:253 original size:21 final size:21
Alignment explanation
Indices: 229--269 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
219 AACTAGCATT
229 GCCAA-TTCGCAACTCGAATTC
1 GCCAATTTCGCAACTC-AATTC
250 GCCAATTTCGCAACTCAATT
1 GCCAATTTCGCAACTCAATT
270 ACCGATAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.27
Consensus pattern (21 bp):
GCCAATTTCGCAACTCAATTC
Found at i:391 original size:20 final size:20
Alignment explanation
Indices: 366--457 Score: 89
Period size: 20 Copynumber: 4.5 Consensus size: 20
356 CGAATTCGAA
* *
366 TTGCGAATTTGAAAACTGAG
1 TTGCGAATTTGGAAACTGTG
*
386 TTGCGAATTTGGGAAATTCGTG
1 TTGCGAATTT-GGAAACT-GTG
408 TTGCGAA-TTGGAAACTGTG
1 TTGCGAATTTGGAAACTGTG
* **
427 TTGCGAAATTGG-AGTTCGTG
1 TTGCGAATTTGGAAACT-GTG
447 TTGCGAATTTG
1 TTGCGAATTTG
458 ATATCGCGTT
Statistics
Matches: 61, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.20
20 33 0.54
21 7 0.11
22 9 0.15
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (20 bp):
TTGCGAATTTGGAAACTGTG
Found at i:472 original size:39 final size:41
Alignment explanation
Indices: 340--458 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 41
330 TATCGATAAT
* **
340 TGAGTTGCAAAATTGGCG-AATTCGAATTGCGAATTTGAAAAC
1 TGAGTTGCGAAATTGG-GAAATTCGTGTTGCGAATTTG-AAAC
* *
382 TGAGTTGCGAATTTGGGAAATTCGTGTTGCGAATTGGAAAC
1 TGAGTTGCGAAATTGGGAAATTCGTGTTGCGAATTTGAAAC
* *
423 TGTGTTGCGAAATT-GG-AGTTCGTGTTGCGAATTTGA
1 TGAGTTGCGAAATTGGGAAATTCGTGTTGCGAATTTGA
459 TATCGCGTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
39 18 0.27
40 2 0.03
41 17 0.25
42 30 0.45
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.33
Consensus pattern (41 bp):
TGAGTTGCGAAATTGGGAAATTCGTGTTGCGAATTTGAAAC
Found at i:2009 original size:22 final size:22
Alignment explanation
Indices: 1976--2017 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1966 CCACTCACCT
1976 TCGTTGGCCCCCGTGCCGTCCG
1 TCGTTGGCCCCCGTGCCGTCCG
1998 TCGTT-GCACCCCGTGCCGTC
1 TCGTTGGC-CCCCGTGCCGTC
2018 GCCGTCTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.02, C:0.45, G:0.29, T:0.24
Consensus pattern (22 bp):
TCGTTGGCCCCCGTGCCGTCCG
Found at i:2913 original size:3 final size:3
Alignment explanation
Indices: 2905--2940 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
2895 TGTATATATA
*
2905 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2941 TATTTAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:3353 original size:41 final size:43
Alignment explanation
Indices: 3296--3475 Score: 201
Period size: 42 Copynumber: 4.3 Consensus size: 43
3286 AGGTCGTATG
* *
3296 GATGGTCCGAAGGACTTA-TCATCTTGCTCGAAAGACTTA-TA
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
* * *
3337 GATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACTA
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
* * **
3380 -ATGGCCTG-AGGAATTAAGCATCATGCTCGAAAGACTTACT-
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
* * * *
3420 GATGGCCTGAATGACTTACTCATCATGCTCGGAAGACTTA-TT
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
3462 GATGGCCCGAAGGA
1 GATGGCCCGAAGGA
3476 TTTATGCTGA
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
41 52 0.45
42 62 0.53
43 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (43 bp):
GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
Found at i:3459 original size:83 final size:83
Alignment explanation
Indices: 3315--3468 Score: 229
Period size: 83 Copynumber: 1.9 Consensus size: 83
3305 AAGGACTTAT
*
3315 CATCTTGCTCGAAAGACTTATAGATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACTA
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACTA
3380 ATGGCCTGAGGAATTAAG
66 ATGGCCTGAGGAATTAAG
* * * * *
3398 CATCATGCTCGAAAGACTTACT-GATGGCCTGAATGACTTACTCATCATGCTCGGAAGACTTATT
1 CATCATGCTCGAAAGACTTA-TAGATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACT
*
3462 GATGGCC
65 AATGGCC
3469 CGAAGGATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
83 62 0.98
84 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (83 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACTA
ATGGCCTGAGGAATTAAG
Found at i:3581 original size:59 final size:59
Alignment explanation
Indices: 3511--3636 Score: 207
Period size: 59 Copynumber: 2.1 Consensus size: 59
3501 ATCAATTAAT
* *
3511 AGGAAATGTTAACCCCTCTGGTGGGGTGTTGATGATTCGAAGTGTTTTGAATCGAGAAA
1 AGGAAATGTTAACCCCTCTGGTGGGGCGTTGATGATTCGAAGTGTTGTGAATCGAGAAA
* * *
3570 AGGAAATGTTAACCCCTCTGGTGGGGCGTTGTTTATTCGAAGTGTTGTGAATCGAGCAA
1 AGGAAATGTTAACCCCTCTGGTGGGGCGTTGATGATTCGAAGTGTTGTGAATCGAGAAA
3629 AGGAAATG
1 AGGAAATG
3637 ATGAAAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (59 bp):
AGGAAATGTTAACCCCTCTGGTGGGGCGTTGATGATTCGAAGTGTTGTGAATCGAGAAA
Found at i:3815 original size:143 final size:143
Alignment explanation
Indices: 3543--3866 Score: 468
Period size: 143 Copynumber: 2.3 Consensus size: 143
3533 GGGGTGTTGA
* * * *
3543 TGATTCGAAGTGTTTTGAATCGAGAAAAGGAAATGTTAACCCCTCTGGTGGGGCGTTGTTTATTC
1 TGATTCGAAGTG-TTTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTC
* * * * *
3608 GAAGTGTTGTGAATCGAGCAAAGGAAATGATGAAAATAACCTGTCCGAAGGTATTATGGATGGCC
65 AAAGTGTTGTAAATCGAGCAAAGGAAATGATGAAAACAACATGCCCGAAGGTATTATGGATGGCC
*
3673 CGAAGGACTTAAGT
130 CGAAGGACTTAAGC
* *
3687 TGATTCGAAGTGCTTGAATTGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCA
1 TGATTCGAAGTGTTTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCA
* * * *
3752 AAGTGTTGTAAATCGAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCC
66 AAGTGTTGTAAATCGAGCAAAGGAAATGATGAAAACAACATGCCCGAAGGTATTATGGATGGCCC
*
3817 GAATGACTTAAGC
131 GAAGGACTTAAGC
*
3830 TGATTCGAAGTGTTGTGAATCAAGCAAATGAAATGTT
1 TGATTCGAAGTGTT-TGAATCGAGCAAATGAAATGTT
3867 GGAAACATCT
Statistics
Matches: 159, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
143 127 0.80
144 32 0.20
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (143 bp):
TGATTCGAAGTGTTTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCA
AAGTGTTGTAAATCGAGCAAAGGAAATGATGAAAACAACATGCCCGAAGGTATTATGGATGGCCC
GAAGGACTTAAGC
Found at i:3859 original size:85 final size:85
Alignment explanation
Indices: 3743--3914 Score: 272
Period size: 85 Copynumber: 2.0 Consensus size: 85
3733 GTGGGGCGTT
*
3743 GCTGATTCAAAGTGTTGTAAATCGAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
1 GCTGATTCAAAGTGTTGTAAATCAAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
* *
3808 GGATGGCCCGAATGACTTAA
66 GGATGGCCCAAAGGACTTAA
* * * *
3828 GCTGATTCGAAGTGTTGTGAATCAAGCAAATGAAATGTTGGAAACATCTTGCCCGAAGGTCTTAT
1 GCTGATTCAAAGTGTTGTAAATCAAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
*
3893 GGATGGCCTAAAGGACTTAA
66 GGATGGCCCAAAGGACTTAA
3913 GC
1 GC
3915 ATCATGCTGG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (85 bp):
GCTGATTCAAAGTGTTGTAAATCAAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
GGATGGCCCAAAGGACTTAA
Found at i:5403 original size:14 final size:14
Alignment explanation
Indices: 5386--5459 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
5376 TGACTTGGGT
5386 AGGTAATGTGTTTC
1 AGGTAATGTGTTTC
* **
5400 AGGTTAATTTGGGT-
1 AGG-TAATGTGTTTC
5414 AGGTAATGTGTTTC
1 AGGTAATGTGTTTC
* ***
5428 AGGTTAATTTG-GGG
1 AGG-TAATGTGTTTC
5442 AGGTAATGTGTTTC
1 AGGTAATGTGTTTC
5456 AGGT
1 AGGT
5460 TAGCTTCTTG
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
13 13 0.31
14 16 0.38
15 13 0.31
ACGTcount: A:0.22, C:0.04, G:0.34, T:0.41
Consensus pattern (14 bp):
AGGTAATGTGTTTC
Found at i:5420 original size:28 final size:28
Alignment explanation
Indices: 5380--5461 Score: 155
Period size: 28 Copynumber: 2.9 Consensus size: 28
5370 TTAGGCTGAC
5380 TTGGGTAGGTAATGTGTTTCAGGTTAAT
1 TTGGGTAGGTAATGTGTTTCAGGTTAAT
5408 TTGGGTAGGTAATGTGTTTCAGGTTAAT
1 TTGGGTAGGTAATGTGTTTCAGGTTAAT
*
5436 TTGGGGAGGTAATGTGTTTCAGGTTA
1 TTGGGTAGGTAATGTGTTTCAGGTTA
5462 GCTTCTTGCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (28 bp):
TTGGGTAGGTAATGTGTTTCAGGTTAAT
Found at i:6124 original size:8 final size:8
Alignment explanation
Indices: 6113--6168 Score: 62
Period size: 8 Copynumber: 7.1 Consensus size: 8
6103 CTCTTCTTTC
6113 TTTTTCTT
1 TTTTTCTT
6121 TTTTTCTT
1 TTTTTCTT
6129 TTTTT-TCT
1 TTTTTCT-T
*
6137 TTTTT-TA
1 TTTTTCTT
6144 TTTTTCTT
1 TTTTTCTT
*
6152 TTTTTATT
1 TTTTTCTT
*
6160 TCTTTCTT
1 TTTTTCTT
6168 T
1 T
6169 CTATATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
7 6 0.15
8 35 0.85
ACGTcount: A:0.04, C:0.11, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:6127 original size:18 final size:18
Alignment explanation
Indices: 6086--6168 Score: 91
Period size: 18 Copynumber: 4.7 Consensus size: 18
6076 ATTTGATCAA
* *
6086 TTTTCTTTCTCTTTCTTC
1 TTTTCTTTCTTTTTCTTT
*
6104 TCTTCTTTCTTTTTCTTT
1 TTTTCTTTCTTTTTCTTT
6122 TTTTCTTT-TTTTTCTTT
1 TTTTCTTTCTTTTTCTTT
*
6139 TTTTATTT-TTCTTT-TTT
1 TTTTCTTTCTT-TTTCTTT
6156 TATTTCTTTCTTT
1 T-TTTCTTTCTTT
6169 CTATATTTTT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
17 22 0.39
18 32 0.57
19 2 0.04
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTTCTTTTTCTTT
Found at i:6135 original size:23 final size:23
Alignment explanation
Indices: 6086--6156 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
6076 ATTTGATCAA
* * *
6086 TTTTCTTTCTC-TTTCTTCTCTT
1 TTTTCTTTTTCTTTTTTTCTTTT
*
6108 CTTTCTTTTTCTTTTTTTCTTTT
1 TTTTCTTTTTCTTTTTTTCTTTT
6131 TTTTCTTTTT-TTATTTTTCTTTT
1 TTTTCTTTTTCTT-TTTTTCTTTT
6154 TTT
1 TTT
6157 ATTTCTTTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
22 11 0.26
23 31 0.74
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTCTTTTTCTTTTTTTCTTTT
Found at i:6154 original size:30 final size:31
Alignment explanation
Indices: 6113--6178 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
6103 CTCTTCTTTC
* * *
6113 TTTTTCTTTTTTTCT-TTTTTTTCTTTTTTTA
1 TTTTTCTTTTTTT-TATTTCTTTCTTTCTATA
6144 TTTTTC-TTTTTTTATTTCTTTCTTTCTATA
1 TTTTTCTTTTTTTTATTTCTTTCTTTCTATA
6174 TTTTT
1 TTTTT
6179 ATGTCTCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 1 0.03
30 24 0.77
31 6 0.19
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (31 bp):
TTTTTCTTTTTTTTATTTCTTTCTTTCTATA
Found at i:6453 original size:2 final size:2
Alignment explanation
Indices: 6446--6478 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6436 ACAACAATGG
6446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6479 AATAAAACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7413 original size:2 final size:2
Alignment explanation
Indices: 7408--7434 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7398 TTTTTTATCT
7408 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7435 TTTCATTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9236 original size:3 final size:3
Alignment explanation
Indices: 9223--9266 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
9213 TCTAGAGTTC
*
9223 TCT TAT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
9267 CTTCAGGCGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:13683 original size:21 final size:21
Alignment explanation
Indices: 13643--13683 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13633 TGACAGATGA
*
13643 ATTGTCATGTCAATATCGTGG
1 ATTGTCATGTCAATACCGTGG
*
13664 ATTGTCATGTCAGTACCGTG
1 ATTGTCATGTCAATACCGTG
13684 AAGTACCACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (21 bp):
ATTGTCATGTCAATACCGTGG
Found at i:15660 original size:9 final size:9
Alignment explanation
Indices: 15648--15793 Score: 94
Period size: 9 Copynumber: 15.3 Consensus size: 9
15638 AGTCGGATCG
*
15648 GGTCAGACC
1 GGTCAAACC
15657 GGTCAAACC
1 GGTCAAACC
* *
15666 GGTTCAGATC
1 GG-TCAAACC
15676 GGTCAAACC
1 GGTCAAACC
15685 GGTCGAAACC
1 GGTC-AAACC
15695 GGTCAAACC
1 GGTCAAACC
15704 GGTCAAACC
1 GGTCAAACC
* * *
15713 GGTTTAGATC
1 GG-TCAAACC
* *
15723 AGTCAAACT
1 GGTCAAACC
*
15732 GGTTCGAACC
1 GG-TCAAACC
*
15742 GATCGAAACC
1 GGTC-AAACC
*
15752 GGTCAAATC
1 GGTCAAACC
*
15761 GATCAGAACC
1 GGTCA-AACC
* *
15771 GATTGAAAACC
1 G-GT-CAAACC
15782 GGTCAAACC
1 GGTCAAACC
15791 GGT
1 GGT
15794 TTCCAGCCCT
Statistics
Matches: 103, Mismatches: 26, Indels: 16
0.71 0.18 0.11
Matches are distributed among these distances:
9 57 0.55
10 39 0.38
11 6 0.06
12 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:15678 original size:19 final size:19
Alignment explanation
Indices: 15650--15715 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
15640 TCGGATCGGG
15650 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
15669 TCAGATCGGTCAAACCGG-
1 TCAGACCGGTCAAACCGGT
*
15687 TCGAAACCGGTCAAACCGG-
1 TC-AGACCGGTCAAACCGGT
*
15706 TCAAACCGGT
1 TCAGACCGGT
15716 TTAGATCAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
18 10 0.23
19 33 0.77
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:15680 original size:28 final size:28
Alignment explanation
Indices: 15643--15715 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
15633 GGGTCAGTCG
*
15643 GATCGGGTCAGACCGGTC-AAACCGGTTCA
1 GATC-GGTCAAACCGGTCGAAACCGG-TCA
15672 GATCGGTCAAACCGGTCGAAACCGGTCA
1 GATCGGTCAAACCGGTCGAAACCGGTCA
* *
15700 AACCGGTCAAACCGGT
1 GATCGGTCAAACCGGT
15716 TTAGATCAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 29 0.73
29 11 0.28
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.15
Consensus pattern (28 bp):
GATCGGTCAAACCGGTCGAAACCGGTCA
Found at i:15705 original size:47 final size:47
Alignment explanation
Indices: 15648--15758 Score: 152
Period size: 47 Copynumber: 2.3 Consensus size: 47
15638 AGTCGGATCG
* *
15648 GGTCAGACCGGTCAAACCGGTTCAGATCGGTCAAACCGG-TCGAAACC
1 GGTCAAACCGGTCAAACCGGTTCAGATCAGTCAAACCGGTTCG-AACC
* *
15695 GGTCAAACCGGTCAAACCGGTTTAGATCAGTCAAACTGGTTCGAACC
1 GGTCAAACCGGTCAAACCGGTTCAGATCAGTCAAACCGGTTCGAACC
*
15742 GATCGAAACCGGTCAAA
1 GGTC-AAACCGGTCAAA
15759 TCGATCAGAA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
47 42 0.74
48 15 0.26
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (47 bp):
GGTCAAACCGGTCAAACCGGTTCAGATCAGTCAAACCGGTTCGAACC
Found at i:15756 original size:29 final size:31
Alignment explanation
Indices: 15724--15794 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 31
15714 GTTTAGATCA
15724 GTCAAACTGGTTC-GAACCGATCG-AAACCG
1 GTCAAACTGGTTCAGAACCGATCGAAAACCG
* * *
15753 GTCAAA-TCGATCAGAACCGATTGAAAACCG
1 GTCAAACTGGTTCAGAACCGATCGAAAACCG
*
15783 GTCAAACCGGTT
1 GTCAAACTGGTT
15795 TCCAGCCCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 4 0.12
29 15 0.45
30 12 0.36
31 2 0.06
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (31 bp):
GTCAAACTGGTTCAGAACCGATCGAAAACCG
Found at i:22930 original size:14 final size:14
Alignment explanation
Indices: 22913--22939 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22903 GGTCAACGGC
22913 CGGGTCGGGTCAGT
1 CGGGTCGGGTCAGT
22927 CGGGTCGGGTCAG
1 CGGGTCGGGTCAG
22940 ACCGGTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (14 bp):
CGGGTCGGGTCAGT
Found at i:22972 original size:29 final size:31
Alignment explanation
Indices: 22940--23014 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 31
22930 GTCGGGTCAG
*
22940 ACCGGTCAAACCGGTTC-GAACCGGTCG-AA
1 ACCGGTCAAACCGGTTCAGAACCGATCGAAA
* *
22969 ACCGGTCAAACC-GATCAGAACCGATTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGATCGAAA
*
22999 ACTGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
23015 TCCAGCCCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 3 0.08
29 20 0.53
30 13 0.34
31 2 0.05
ACGTcount: A:0.32, C:0.28, G:0.24, T:0.16
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGATCGAAA
Found at i:22975 original size:10 final size:9
Alignment explanation
Indices: 22934--22991 Score: 62
Period size: 9 Copynumber: 6.1 Consensus size: 9
22924 AGTCGGGTCG
*
22934 GGTCAGACC
1 GGTCAAACC
22943 GGTCAAACC
1 GGTCAAACC
*
22952 GGTTCGAACC
1 GG-TCAAACC
22962 GGTCGAAACC
1 GGTC-AAACC
22972 GGTCAAACC
1 GGTCAAACC
*
22981 GATCAGAACC
1 GGTCA-AACC
22991 G
1 G
22992 ATTGAAAACT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 21 0.50
10 21 0.50
ACGTcount: A:0.29, C:0.31, G:0.28, T:0.12
Consensus pattern (9 bp):
GGTCAAACC
Found at i:24247 original size:23 final size:23
Alignment explanation
Indices: 24211--24257 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
24201 TAATTTATGT
*
24211 AAAAAATAAGTATTTAA-ATTTA
1 AAAAAATAAGTATTAAATATTTA
*
24233 AAAAAATAATTTATTAAATATTTA
1 AAAAAATAA-GTATTAAATATTTA
24257 A
1 A
24258 TTATGTACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAAATAAGTATTAAATATTTA
Found at i:33782 original size:11 final size:11
Alignment explanation
Indices: 33766--33791 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33756 ATAAAAAAAT
33766 AAAAGACAATA
1 AAAAGACAATA
33777 AAAAGACAATA
1 AAAAGACAATA
33788 AAAA
1 AAAA
33792 ATACCAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.08, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAGACAATA
Found at i:34012 original size:2 final size:2
Alignment explanation
Indices: 34007--34045 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
33997 ATTTTTTAGG
34007 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34046 TACATAATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36179 original size:21 final size:21
Alignment explanation
Indices: 36150--36191 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
36140 ATTGCTAACA
*
36150 TTACTCTCAATATCGATATTG
1 TTACCCTCAATATCGATATTG
*
36171 TTACCCTCAGTATCGATATTG
1 TTACCCTCAATATCGATATTG
36192 CTCCTTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (21 bp):
TTACCCTCAATATCGATATTG
Found at i:36511 original size:23 final size:23
Alignment explanation
Indices: 36485--36538 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
36475 GTTATAAATT
36485 TGAATACAATAATAAAGGTCCTA
1 TGAATACAATAATAAAGGTCCTA
36508 TGAATACAATAATAAAGGTCCTA
1 TGAATACAATAATAAAGGTCCTA
36531 TGAATACA
1 TGAATACA
36539 TATGCCCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (23 bp):
TGAATACAATAATAAAGGTCCTA
Found at i:40942 original size:24 final size:24
Alignment explanation
Indices: 40893--40945 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
40883 TAAGTGAACC
*
40893 ATGTG-TTTATATGTATATGGGAT
1 ATGTGATTTATATGTATATGAGAT
*
40916 ATGTGATTTATATG-ATGATGAGCT
1 ATGTGATTTATATGTAT-ATGAGAT
40940 ATGTGA
1 ATGTGA
40946 AAGAACTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.43
Consensus pattern (24 bp):
ATGTGATTTATATGTATATGAGAT
Found at i:41189 original size:103 final size:103
Alignment explanation
Indices: 41063--41275 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
41053 GGGTCTACGC
*
41063 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
41128 CATTGGTATATGTATATGATTCTTAATGAATGATATGT
66 CACTAGTATATGTATATGATTCTTAAGGAATGATATGT
41166 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
41231 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CACTAGTATATGTATATGATTCTTAAGGAATGATATGT
*
41269 GCTCCTT
1 GGTCCTT
41276 ATGGACATTA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
GGTCCTTCGGAACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CACTAGTATATGTATATGATTCTTAAGGAATGATATGT
Found at i:41325 original size:23 final size:23
Alignment explanation
Indices: 41292--41359 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
41282 ATTATTATAT
41292 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
41315 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
41338 GGAACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
41360 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:50090 original size:3 final size:3
Alignment explanation
Indices: 50082--50114 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
50072 ACTGAAAGTA
50082 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
50115 GGAATAGTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:50281 original size:2 final size:2
Alignment explanation
Indices: 50274--50308 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
50264 ATTTGAACTT
50274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
50309 TAATAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52948 original size:9 final size:7
Alignment explanation
Indices: 52922--52946 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52912 TTAAAATTAA
52922 AAAATAT
1 AAAATAT
52929 AAAATAT
1 AAAATAT
52936 AAAATAT
1 AAAATAT
52943 AAAA
1 AAAA
52947 AAGAAAACAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:55315 original size:16 final size:17
Alignment explanation
Indices: 55294--55325 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55284 TTAGTATAGT
55294 TTTTTAA-TTTATTTTA
1 TTTTTAAGTTTATTTTA
55310 TTTTTAAGTTTATTTT
1 TTTTTAAGTTTATTTT
55326 CATGTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TTTTTAAGTTTATTTTA
Found at i:55382 original size:39 final size:40
Alignment explanation
Indices: 55339--55418 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
55329 GTATGTTTGG
55339 TTGTTTGGTTAGTGAGAAAGTT-AA-AAACTGATAAGAAAA
1 TTGTTTGGTTAGTGAGAAAGTTGAAGAAA-TGATAAGAAAA
55378 TTGTTTGGTTAGTGAGAAAGTTGAAGAAATGATAAGAAAA
1 TTGTTTGGTTAGTGAGAAAGTTGAAGAAATGATAAGAAAA
55418 T
1 T
55419 AAGGGAACAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
39 22 0.56
40 14 0.36
41 3 0.08
ACGTcount: A:0.42, C:0.01, G:0.25, T:0.31
Consensus pattern (40 bp):
TTGTTTGGTTAGTGAGAAAGTTGAAGAAATGATAAGAAAA
Found at i:56457 original size:21 final size:21
Alignment explanation
Indices: 56415--56457 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
56405 TTTCTGGGCT
* *
56415 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
56436 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
56457 A
1 A
56458 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:57142 original size:23 final size:23
Alignment explanation
Indices: 57106--57169 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
57096 CATTATTATA
* *
57106 TGGCACTACGGTGCAATTCTACG
1 TGGCACTCCAGTGCAATTCTACG
57129 CT-GCACTCCAGTGCAATTCTACG
1 -TGGCACTCCAGTGCAATTCTACG
*
57152 TGGCACTTCAGTGCAATT
1 TGGCACTCCAGTGCAATT
57170 ATAAGAGCTG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (23 bp):
TGGCACTCCAGTGCAATTCTACG
Found at i:58867 original size:18 final size:18
Alignment explanation
Indices: 58840--58930 Score: 96
Period size: 18 Copynumber: 4.9 Consensus size: 18
58830 ATTGAATATT
* *
58840 TGTCCCGAAGTACCACTA
1 TGTCCAGAAGGACCACTA
*
58858 TGTCCTGAAGGACCACTA
1 TGTCCAGAAGGACCACTA
58876 TGTCCAGAAGGACCACTGA
1 TGTCCAGAAGGACCACT-A
*
58895 TTGTTCCA-AAGAACCACTA
1 -TG-TCCAGAAGGACCACTA
58914 TGTCCCA-AAGGACCACT
1 TGT-CCAGAAGGACCACT
58931 GATAATCCCT
Statistics
Matches: 64, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.72
19 2 0.03
20 11 0.17
21 4 0.06
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCAGAAGGACCACTA
Found at i:59981 original size:19 final size:18
Alignment explanation
Indices: 59957--59998 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
59947 CGATGACAAG
59957 TCAAAT-TCAACCTCTGATT
1 TCAAATATCAA-CTCT-ATT
*
59976 TCAAATATGAACTCTATT
1 TCAAATATCAACTCTATT
59994 TCAAA
1 TCAAA
59999 ATCCCATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 10 0.48
20 3 0.14
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (18 bp):
TCAAATATCAACTCTATT
Found at i:65820 original size:18 final size:18
Alignment explanation
Indices: 65797--65868 Score: 92
Period size: 18 Copynumber: 3.9 Consensus size: 18
65787 ACTGAATATT
65797 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
65815 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
* *
65833 TTTGTTCCGAAGAACCACTA
1 --TGTCCCGAAGGACCACTA
65853 -GTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
65869 GATAATCTCT
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
17 14 0.30
18 17 0.37
20 15 0.33
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:65844 original size:38 final size:37
Alignment explanation
Indices: 65793--65868 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 37
65783 GGGCACTGAA
*
65793 TATTTGTCCCGAAGGACCACTATGTCCCGAAAGACCAC
1 TATTTGTCCCGAAGAACCACTA-GTCCCGAAAGACCAC
* *
65831 TATTTGTTCCGAAGAACCACTAGTCCCGAAGGACCAC
1 TATTTGTCCCGAAGAACCACTAGTCCCGAAAGACCAC
65868 T
1 T
65869 GATAATCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
37 15 0.43
38 20 0.57
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (37 bp):
TATTTGTCCCGAAGAACCACTAGTCCCGAAAGACCAC
Found at i:65849 original size:20 final size:20
Alignment explanation
Indices: 65793--65868 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
65783 GGGCACTGAA
*
65793 TATTTGTCCCGAAGGACCAC
1 TATTTGTCCCGAAGAACCAC
65813 TA--TGTCCCGAA-AGACCAC
1 TATTTGTCCCGAAGA-ACCAC
*
65831 TATTTGTTCCGAAGAACCAC
1 TATTTGTCCCGAAGAACCAC
*
65851 TA---GTCCCGAAGGACCAC
1 TATTTGTCCCGAAGAACCAC
65868 T
1 T
65869 GATAATCTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
17 14 0.29
18 16 0.33
20 17 0.35
21 1 0.02
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (20 bp):
TATTTGTCCCGAAGAACCAC
Found at i:70770 original size:23 final size:23
Alignment explanation
Indices: 70744--70835 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
70734 CACCACAGCT
* *
70744 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
70767 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
70790 CGTAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
70813 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
70836 TATAAGATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:71300 original size:2 final size:2
Alignment explanation
Indices: 71293--71346 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
71283 ATTCATCTTC
71293 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
71335 -T AT AT AT AT AT A
1 AT AT AT AT AT AT A
71347 ATTTTTCCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.