Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008886.1 Hibiscus syriacus cultivar Beakdansim tig00112133_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: 72976
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4280 original size:12 final size:12
Alignment explanation
Indices: 4263--4287 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4253 AAGAATTGAT
4263 AAGTTTAATTTG
1 AAGTTTAATTTG
4275 AAGTTTAATTTG
1 AAGTTTAATTTG
4287 A
1 A
4288 CTTGTCATAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
AAGTTTAATTTG
Found at i:5318 original size:38 final size:37
Alignment explanation
Indices: 5267--5353 Score: 122
Period size: 38 Copynumber: 2.4 Consensus size: 37
5257 TTGAGGGACT
* *
5267 ATCAGGGGTCCTTCGAGACATAGTGGTTCTTCGGAAC
1 ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAAC
* *
5304 AATCAGTGGTCCTTCGGGACATAGTGGTCCTTCGGGAC
1 -ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAAC
5342 AT-AGTGGTCCTT
1 ATCAGTGGTCCTT
5354 AGGGAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 10 0.22
37 2 0.04
38 33 0.73
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.29
Consensus pattern (37 bp):
ATCAGTGGTCCTTCGAGACATAGTGGTCCTTCGGAAC
Found at i:5331 original size:18 final size:18
Alignment explanation
Indices: 5273--5358 Score: 118
Period size: 18 Copynumber: 4.7 Consensus size: 18
5263 GACTATCAGG
*
5273 GGTCCTTCGAGACATAGT
1 GGTCCTTCGGGACATAGT
* *
5291 GGTTCTTCGGAACAATCAGT
1 GGTCCTTCGGGAC-AT-AGT
5311 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
5329 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
5347 GGTCCTTAGGGA
1 GGTCCTTCGGGA
5359 AAAATATTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
18 42 0.70
19 4 0.07
20 14 0.23
ACGTcount: A:0.20, C:0.21, G:0.31, T:0.28
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:6824 original size:20 final size:22
Alignment explanation
Indices: 6779--6836 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
6769 GCATAAGGAG
6779 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
6803 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
6823 TGTATCGATGCACT
1 TGCATCGATGCACT
6837 TCAAAGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:8274 original size:21 final size:21
Alignment explanation
Indices: 8250--8314 Score: 130
Period size: 21 Copynumber: 3.1 Consensus size: 21
8240 GTCAAGGGAT
8250 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
8271 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
8292 TATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA
8313 TA
1 TA
8315 GTGGTCATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (21 bp):
TATCAGTGGTCCTTCGGGACA
Found at i:8341 original size:42 final size:41
Alignment explanation
Indices: 8250--8328 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 41
8240 GTCAAGGGAT
* *
8250 TATCAGTGGTCCTTCGGGACATATCAGTGGTCCTTCGGGACA
1 TATCAGTGGTCCTTCGGGACA-ATCAGTGGTCATTCGGGAAA
8292 TATCAGTGGTCCTTCGGGAC-AT-AGTGGTCATTCGGGA
1 TATCAGTGGTCCTTCGGGACAATCAGTGGTCATTCGGGA
8329 TAAATATTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
39 14 0.39
40 2 0.06
42 20 0.56
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (41 bp):
TATCAGTGGTCCTTCGGGACAATCAGTGGTCATTCGGGAAA
Found at i:9670 original size:2 final size:2
Alignment explanation
Indices: 9663--9688 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9653 TTATCCTTGC
9663 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
9689 CTTGTTGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9982 original size:20 final size:20
Alignment explanation
Indices: 9959--10008 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
9949 AAAAACACAT
9959 AAAAAGAAAAAAAAGAAAAA
1 AAAAAGAAAAAAAAGAAAAA
** *
9979 AAAAAGAAACGAAAGAAAGA
1 AAAAAGAAAAAAAAGAAAAA
*
9999 AGAAAGAAAA
1 AAAAAGAAAA
10009 TAGATCCAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAAAGAAAAA
Found at i:12002 original size:52 final size:52
Alignment explanation
Indices: 11940--12136 Score: 243
Period size: 52 Copynumber: 3.7 Consensus size: 52
11930 AATTTTTAAA
*
11940 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCGAATAAGTTTTT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATAAGTTTTT
* * *
11992 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTCCAATGAA-TTTTT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG-T--TTTCAAAT-AAGTTTTT
* * * * *
12047 AAAAGAAGCTAAGCCTAATTTTTAGGGATTTATTGATGTTTTTAAATGAGTTTTT
1 ---AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATAAGTTTTT
12102 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG
12137 ATAACTAAAA
Statistics
Matches: 123, Mismatches: 14, Indels: 16
0.80 0.09 0.10
Matches are distributed among these distances:
52 65 0.53
53 1 0.01
54 1 0.01
55 23 0.19
56 2 0.02
57 1 0.01
58 30 0.24
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.42
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCAAATAAGTTTTT
Found at i:12107 original size:110 final size:110
Alignment explanation
Indices: 11930--12138 Score: 346
Period size: 110 Copynumber: 1.9 Consensus size: 110
11920 TTTTCAAAAT
* * *
11930 AATTTTTAAAAGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTTCGAATAAGTTTTTAGA
1 AATTTTTAAAAGAAACTAAGCCTAATTTTTAGGGATTTATTGATGTTTTCAAATAAGTTTTTAGA
*
11995 AACTAAGCCTGATTTTCAGGGGTTTCTTGATGATGATTTCCAATG
66 AACTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTTCCAATG
* * *
12040 AATTTTTAAAAGAAGCTAAGCCTAATTTTTAGGGATTTATTGATGTTTTTAAATGAGTTTTTAGA
1 AATTTTTAAAAGAAACTAAGCCTAATTTTTAGGGATTTATTGATGTTTTCAAATAAGTTTTTAGA
*
12105 AACTAAGCCTAATTTTTAGGGGTTTCTTGATGAT
66 AACTAAGCCTAATTTTCAGGGGTTTCTTGATGAT
12139 AACTAAAACG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 91 1.00
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (110 bp):
AATTTTTAAAAGAAACTAAGCCTAATTTTTAGGGATTTATTGATGTTTTCAAATAAGTTTTTAGA
AACTAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTTCCAATG
Found at i:12262 original size:42 final size:41
Alignment explanation
Indices: 12216--12301 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
12206 GGGCCATCAG
* * *
12216 TAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATCTA
1 TAAGTCTTTCGAGCAAGATG-ATAAATCCTTCAGGTCATCCA
* *
12258 TAAGTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATCCA
1 TAAGTCTTTCGAGCAAGATGATAAATCCTTCAGGTCATCCA
12299 TAA
1 TAA
12302 TACCTTCGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 20 0.51
42 19 0.49
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (41 bp):
TAAGTCTTTCGAGCAAGATGATAAATCCTTCAGGTCATCCA
Found at i:12426 original size:59 final size:60
Alignment explanation
Indices: 12327--12482 Score: 188
Period size: 59 Copynumber: 2.6 Consensus size: 60
12317 TGTTTTCAAC
* * * *
12327 ATTTTCTTTGCTCGATTCACGACATTTCAAATCAACAATGCACCACCAGA-GGGGTTAAA
1 ATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAATGCACCACCAGAGGGGGTTAAA
* * * * *
12386 ATTTCCTTTGCTCGATTCACAACACTTCAAATCAGTAATGCCCCTCCATAGGGGGTTAAC
1 ATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAATGCACCACCAGAGGGGGTTAAA
* * *
12446 ATTTCCCATGGCTCGATTCACAACACTTCGAATCAGC
1 ATTT-CCTTTGCTCGATTCACAACACTTCAAATCAGC
12483 TTAAGTCCTT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 42 0.51
60 12 0.15
61 28 0.34
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.29
Consensus pattern (60 bp):
ATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAATGCACCACCAGAGGGGGTTAAA
Found at i:12735 original size:59 final size:59
Alignment explanation
Indices: 12621--12736 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
12611 CAATATTTCC
* * * *
12621 TTTGCTCGATTCACAACACTTCAAATCAACAACGCCCCACCAGAGGGGTTCACATTTTA
1 TTTGCTCAATTCACAACACTTCAAATCAACAACACACCACCAGAGGGGATCACATTTTA
* *
12680 TTTGCTCAATTCACAACACTTCAAATCAGCAACACATCACTC-GA-GGGATCAACATTT
1 TTTGCTCAATTCACAACACTTCAAATCAACAACACACCAC-CAGAGGGGATC-ACATTT
12737 CCAGTGGAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 5 0.10
59 43 0.88
60 1 0.02
ACGTcount: A:0.33, C:0.29, G:0.12, T:0.26
Consensus pattern (59 bp):
TTTGCTCAATTCACAACACTTCAAATCAACAACACACCACCAGAGGGGATCACATTTTA
Found at i:24192 original size:46 final size:46
Alignment explanation
Indices: 24125--24248 Score: 158
Period size: 46 Copynumber: 2.7 Consensus size: 46
24115 CTCTCAGTTG
* *
24125 TTTAGAAGGTTGGAGAGCATGGGGAATGTTGGTCCTCAAACTACTA
1 TTTAGAAGGTTGGAAAGCATGGGGAATGTTGATCCTCAAACTACTA
* * * * *
24171 TTTAGAAGGTTGAAAAGCATGGGGAATATTGATCCTCAAGCTGCTG
1 TTTAGAAGGTTGGAAAGCATGGGGAATGTTGATCCTCAAACTACTA
* * *
24217 TTTAGAAGTTTGGAAATCATTGGGAATGTTGA
1 TTTAGAAGGTTGGAAAGCATGGGGAATGTTGA
24249 GACTTTATAG
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 66 1.00
ACGTcount: A:0.30, C:0.10, G:0.29, T:0.31
Consensus pattern (46 bp):
TTTAGAAGGTTGGAAAGCATGGGGAATGTTGATCCTCAAACTACTA
Found at i:27476 original size:42 final size:43
Alignment explanation
Indices: 27429--27542 Score: 117
Period size: 43 Copynumber: 2.7 Consensus size: 43
27419 TGACAACATA
* *
27429 TAGCGGCGATT-G-TTAACAAATGCCGCAAAAGGTATTGATATT
1 TAGCGGCGATTGGCATAA-AAACGCCGCAAAAGGTATTGATATT
* * *
27471 TAGCGGCGTTTGGCATAAAAACGCCGCAATAGGTGTTGATATT
1 TAGCGGCGATTGGCATAAAAACGCCGCAAAAGGTATTGATATT
* * *
27514 TAACGGC-ATTTGGCAGACAAACGCCGCAA
1 TAGCGGCGA-TTGGCATAAAAACGCCGCAA
27543 TAGTCGTTGA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 10 0.17
43 47 0.78
44 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (43 bp):
TAGCGGCGATTGGCATAAAAACGCCGCAAAAGGTATTGATATT
Found at i:27510 original size:43 final size:43
Alignment explanation
Indices: 27450--27567 Score: 157
Period size: 43 Copynumber: 2.7 Consensus size: 43
27440 GTTAACAAAT
* * * *
27450 GCCGCAAAAGGTATTGATATTTAGCGGCGTTTGGCATAAAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAAAAAC
* *
27493 GCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAGACAAAC
1 GCCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAAAAAC
*
27536 GCCGCAATA-GTCGTTGATGTTTAGCGGCATTT
1 GCCGCAATAGGT-GTTGATATTTAGCGGCATTT
27568 TCTTCACAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
42 2 0.03
43 64 0.97
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
GCCGCAATAGGTGTTGATATTTAGCGGCATTTGGCAGAAAAAC
Found at i:27577 original size:43 final size:43
Alignment explanation
Indices: 27444--27593 Score: 142
Period size: 43 Copynumber: 3.5 Consensus size: 43
27434 GCGATTGTTA
* * * * * *
27444 ACAAATGCCGCAAAAGGTATTGATATTTAGCGGCGTTTGGCAT
1 ACAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAC
* *
27487 AAAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAG
1 ACAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAC
* * * *
27530 ACAAACGCCGCAATA-GTCGTTGATGTTTAGCGGCATTT-TCTTC
1 ACAAACGCCGCAATAGGT-GTTGATATTTAACGGCATTTGGC-AC
* *
27573 ACAAACGCCGCAGTAGATGTT
1 ACAAACGCCGCAATAGGTGTT
27594 TATTTTTACC
Statistics
Matches: 89, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
42 3 0.03
43 85 0.96
44 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
ACAAACGCCGCAATAGGTGTTGATATTTAACGGCATTTGGCAC
Found at i:27620 original size:43 final size:43
Alignment explanation
Indices: 27489--27628 Score: 106
Period size: 43 Copynumber: 3.3 Consensus size: 43
27479 TTTGGCATAA
* * * ** **
27489 AAACGCCGCAATAGGT-GTTGATATTTAACGGCATTTGGCAGAC
1 AAACGCCGCAGTA-GTCGTTGATGTTTACCGGCATTTTCCTCAC
* * *
27532 AAACGCCGCAATAGTCGTTGATGTTTAGCGGCATTTTCTTCAC
1 AAACGCCGCAGTAGTCGTTGATGTTTACCGGCATTTTCCTCAC
* * *
27575 AAACGCCGCAGTAGAT-GTTTATTTTTACCGGCGTTTTTCCT-AC
1 AAACGCCGCAGTAG-TCGTTGATGTTTACCGGC-ATTTTCCTCAC
*
27618 AAACACCGCAG
1 AAACGCCGCAG
27629 AATATGTCTT
Statistics
Matches: 80, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
42 2 0.03
43 71 0.89
44 7 0.09
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.29
Consensus pattern (43 bp):
AAACGCCGCAGTAGTCGTTGATGTTTACCGGCATTTTCCTCAC
Found at i:28056 original size:42 final size:42
Alignment explanation
Indices: 28010--28125 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
28000 TGATATATTA
* * *
28010 CTTCTCTCTGTTCTGCCGCTGCCT-CTCTCTG-TGCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG-CTGCTCT-AGCTGCTGCCGCTG
* *
28052 CTTCTCTCTCTGCTTCCGTTGCTGCTCTAGCTGCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTGCTGCTCTAGCTGCTGCCGCTG
* *
28094 CTTCTCTCTCTGCTTCCGTTGCTGCTCTAGCT
1 CTTCTCTCTCTGCTGCCGCTGCTGCTCTAGCT
28126 ACTTCCGTTT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.04
42 64 0.96
ACGTcount: A:0.02, C:0.39, G:0.20, T:0.40
Consensus pattern (42 bp):
CTTCTCTCTCTGCTGCCGCTGCTGCTCTAGCTGCTGCCGCTG
Found at i:28086 original size:33 final size:34
Alignment explanation
Indices: 28047--28154 Score: 94
Period size: 42 Copynumber: 3.0 Consensus size: 34
28037 TCTGTGCTGC
28047 CGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTA
1 CGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTA
28081 GCTGCTGCCGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTA
1 --------CGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTA
* * *
28123 -GCTACTTC-CGTTTCTGCTTCCGCTGCTGCTCT
1 CGCTGCTTCTC-TCTCTGCTTCCGTTGCTGCTCT
28155 CTCTGTTTCC
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
32 1 0.02
33 27 0.44
42 34 0.55
ACGTcount: A:0.03, C:0.38, G:0.19, T:0.40
Consensus pattern (34 bp):
CGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTA
Found at i:28116 original size:21 final size:21
Alignment explanation
Indices: 28010--28121 Score: 116
Period size: 21 Copynumber: 5.3 Consensus size: 21
28000 TGATATATTA
* *
28010 CTTCTCTCTGTTCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
* *
28031 CCTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
* *
28052 CTTCTCTCTCTGCTTCCGTTG
1 CTTCTCTCTCTGCTGCCGCTG
* **
28073 CTGCTCTAGCTGCTGCCGCTG
1 CTTCTCTCTCTGCTGCCGCTG
* *
28094 CTTCTCTCTCTGCTTCCGTTG
1 CTTCTCTCTCTGCTGCCGCTG
*
28115 CTGCTCT
1 CTTCTCT
28122 AGCTACTTCC
Statistics
Matches: 74, Mismatches: 17, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 74 1.00
ACGTcount: A:0.01, C:0.39, G:0.20, T:0.40
Consensus pattern (21 bp):
CTTCTCTCTCTGCTGCCGCTG
Found at i:28130 original size:21 final size:21
Alignment explanation
Indices: 28061--28140 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
28051 GCTTCTCTCT
28061 CTGCTTCCGTTGCTGCTCTAG
1 CTGCTTCCGTTGCTGCTCTAG
* * * **
28082 CTGCTGCCGCTGCTTCTCTCT
1 CTGCTTCCGTTGCTGCTCTAG
28103 CTGCTTCCGTTGCTGCTCTAG
1 CTGCTTCCGTTGCTGCTCTAG
* *
28124 CTACTTCCGTTTCTGCT
1 CTGCTTCCGTTGCTGCT
28141 TCCGCTGCTG
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.04, C:0.36, G:0.20, T:0.40
Consensus pattern (21 bp):
CTGCTTCCGTTGCTGCTCTAG
Found at i:28151 original size:63 final size:63
Alignment explanation
Indices: 28022--28140 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 63
28012 TCTCTCTGTT
* * ** *
28022 CTGCCGCTGCCTCTCTCTGTGCTGCCGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTAGCTG
1 CTGCCGCTGCCTCTCTCTCTGCTGCCGCTGCTGCTCTAGCTACTTCCGTTGCTGCTCTAGCTG
* * * *
28085 CTGCCGCTGCTTCTCTCTCTGCTTCCGTTGCTGCTCTAGCTACTTCCGTTTCTGCT
1 CTGCCGCTGCCTCTCTCTCTGCTGCCGCTGCTGCTCTAGCTACTTCCGTTGCTGCT
28141 TCCGCTGCTG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 47 1.00
ACGTcount: A:0.03, C:0.39, G:0.20, T:0.39
Consensus pattern (63 bp):
CTGCCGCTGCCTCTCTCTCTGCTGCCGCTGCTGCTCTAGCTACTTCCGTTGCTGCTCTAGCTG
Found at i:36966 original size:41 final size:41
Alignment explanation
Indices: 36921--37050 Score: 172
Period size: 41 Copynumber: 3.2 Consensus size: 41
36911 AATATTTTAC
36921 GGCGTTTATACAAAAAACGCCACTATTGATT-ACACTATTGT
1 GGCGTTTAT-CAAAAAACGCCACTATTGATTAACACTATTGT
* * *
36962 GGCGTTTGTTAAAAAACGCCACTATTGATTAAAACTATTGT
1 GGCGTTTATCAAAAAACGCCACTATTGATTAACACTATTGT
* * * **
37003 GGCGTTTATCTAAAAGCTCCACTATTGATTAACACTATTAC
1 GGCGTTTATCAAAAAACGCCACTATTGATTAACACTATTGT
37044 GGCGTTT
1 GGCGTTT
37051 GTGGTATAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 20 0.26
41 57 0.74
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (41 bp):
GGCGTTTATCAAAAAACGCCACTATTGATTAACACTATTGT
Found at i:44585 original size:59 final size:59
Alignment explanation
Indices: 44053--44577 Score: 863
Period size: 59 Copynumber: 8.9 Consensus size: 59
44043 TTCAATAGGT
* *
44053 AATTCATACAATTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* *
44112 AATTCATACACATAGTGTGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
*
44171 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* * *
44230 AATTCATACACTTAGTATGAGTTCTTTATAATTTTAGCACACGAAGTGCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* *
44289 AATTCATACACCTAGTATGAGTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* * * *
44348 AATTCATACACTTGGTATGATTTCCTTATCATTTTAGAACACGGAGTGCCCTATCTAGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* *
44407 AATTCATACACTTAGTATGATTTCCTTAT-ATTTTAGCACACAAAGTTCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* *
44465 AATTTATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTAGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
* *
44524 AATTCATACACTAAGTATGATTTCCTTATCATTTTAGCACAGGAAGTGCCCTAT
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTAT
44578 ATAGAAATCA
Statistics
Matches: 432, Mismatches: 33, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
58 52 0.12
59 380 0.88
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.35
Consensus pattern (59 bp):
AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACGAAGTGCCCTATCTGGA
Found at i:44860 original size:16 final size:16
Alignment explanation
Indices: 44821--44860 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
44811 ATTATACTTA
44821 AACA-ATACTCAAAAG
1 AACATATACTCAAAAG
44836 AACAAATATACTCAAAAG
1 AAC--ATATACTCAAAAG
44854 AACATAT
1 AACATAT
44861 CATTAACTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 3 0.14
16 4 0.18
17 1 0.05
18 14 0.64
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.17
Consensus pattern (16 bp):
AACATATACTCAAAAG
Found at i:45127 original size:75 final size:74
Alignment explanation
Indices: 44950--45127 Score: 195
Period size: 75 Copynumber: 2.4 Consensus size: 74
44940 ACTTCTATAC
44950 TATGGTATCGATACTCC-CTTCAGGTATCAATACCAAAAATAAGTTCGATGTTGTCTGGTATCGA
1 TATGGTATCGATACTCCTCTTCA-GTATCAATACCAAAAATAAGTTCGATGTTGTCTGGTATCGA
*
45014 TACTACCTTTA
65 TAC-ACCCTTA
* * * * * *
45025 TATGGTACCGATAC-GCTCTACCGGTATCGATACC-AAAATTAGATTCGATGTT-TCTTGGTATC
1 TATGGTATCGATACTCCTCT-TCAGTATCAATACCAAAAATAAG-TTCGATGTTGTC-TGGTATC
45087 GATAC-CCCTTA
63 GATACACCCTTA
45098 TCATGGTATCGATACTACCTCTTCAGTATC
1 T-ATGGTATCGATACT-CCTCTTCAGTATC
45128 TGATGAGTGT
Statistics
Matches: 85, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
73 6 0.07
74 22 0.26
75 52 0.61
76 5 0.06
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (74 bp):
TATGGTATCGATACTCCTCTTCAGTATCAATACCAAAAATAAGTTCGATGTTGTCTGGTATCGAT
ACACCCTTA
Found at i:53918 original size:23 final size:23
Alignment explanation
Indices: 53885--53949 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
53875 GTTTGAAAAA
53885 AAAAGAGAAAAAAACATAAAAATG-G
1 AAAA-AGAAAAAAAC--AAAAATGTG
* *
53910 -AAAATAAAACAACAAAAATGTG
1 AAAAAGAAAAAAACAAAAATGTG
53932 AAAAAGAAAAAAATCAAA
1 AAAAAGAAAAAAA-CAAA
53950 TGCATTTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 7 0.21
22 1 0.03
23 18 0.55
24 7 0.21
ACGTcount: A:0.74, C:0.06, G:0.11, T:0.09
Consensus pattern (23 bp):
AAAAAGAAAAAAACAAAAATGTG
Found at i:55005 original size:17 final size:17
Alignment explanation
Indices: 54957--55007 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
54947 TTACTAAATC
54957 TTTCTCTTTTATTTTAAT
1 TTTCT-TTTTATTTTAAT
** *
54975 TTTCAAGTTT-TTTTATT
1 TTTC-TTTTTATTTTAAT
54992 TTTCTTTTTATTTTAA
1 TTTCTTTTTATTTTAA
55008 AACTTTGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 5
0.69 0.17 0.14
Matches are distributed among these distances:
16 3 0.12
17 15 0.60
18 7 0.28
ACGTcount: A:0.18, C:0.08, G:0.02, T:0.73
Consensus pattern (17 bp):
TTTCTTTTTATTTTAAT
Found at i:57653 original size:45 final size:45
Alignment explanation
Indices: 57589--57678 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
57579 TACAACTCAA
*
57589 CATACTTATTCATTGAGTAGTCTACTCAAACTGGAATGAAATGAG
1 CATACTTATTCATTGAGTAGTCTACTCAAACTGGAACGAAATGAG
*
57634 CATACTTATTCATTGAGTAGTCTACTCGAACTGGAACGAAATGAG
1 CATACTTATTCATTGAGTAGTCTACTCAAACTGGAACGAAATGAG
57679 TTGTCTTGGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (45 bp):
CATACTTATTCATTGAGTAGTCTACTCAAACTGGAACGAAATGAG
Found at i:62025 original size:59 final size:59
Alignment explanation
Indices: 61932--62111 Score: 288
Period size: 59 Copynumber: 3.1 Consensus size: 59
61922 TTCAATAGGT
* * *
61932 AATTCATACAATTAGTATGATTTCCTTATTATTTTAGCACACAAACTGCCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCTGGA
*
61991 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGTCCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCTGGA
* * * *
62050 AATACATACACTTAGTATGATTTTCTTATCATTTTAGCACACGAAGTGCTCTATCTGGA
1 AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCTGGA
62109 AAT
1 AAT
62112 CACTATACAT
Statistics
Matches: 112, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 112 1.00
ACGTcount: A:0.32, C:0.19, G:0.12, T:0.37
Consensus pattern (59 bp):
AATTCATACACTTAGTATGATTTCCTTATCATTTTAGCACACAAAGTGCCCTATCTGGA
Found at i:62539 original size:95 final size:95
Alignment explanation
Indices: 62435--62636 Score: 234
Period size: 95 Copynumber: 2.1 Consensus size: 95
62425 TACTACCCTA
* * *
62435 GTATCGATACT-TCCATAT-TATGGTA-TCGATACCCCCTTCGGGTATCAATACCAAAAACAGGT
1 GTATCGATACTATCC-T-TCTATGGTACT-GATACCCCCTACCGGTATCAATACC-AAAACAGAT
62497 TCGATGTTGCCTGATATCGACAC-CCTTAAT-ATG
62 TCGATGTTGCCTGATATCGACACTCCTT-ATCATG
* **
62530 GTATCGATACTATCCTTCTATGGTACTGATACCCCCTACCGGTATCGATACCAAAATTGATTCGA
1 GTATCGATACTATCCTTCTATGGTACTGATACCCCCTACCGGTATCAATACCAAAACAGATTCGA
* * * *
62595 TGTTTCTTGGTATCGATACTCCTTATCATG
66 TGTTGCCTGATATCGACACTCCTTATCATG
62625 GTATCGATACTA
1 GTATCGATACTA
62637 CCTCTTCGAT
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
94 28 0.30
95 60 0.65
96 4 0.04
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (95 bp):
GTATCGATACTATCCTTCTATGGTACTGATACCCCCTACCGGTATCAATACCAAAACAGATTCGA
TGTTGCCTGATATCGACACTCCTTATCATG
Found at i:63584 original size:9 final size:9
Alignment explanation
Indices: 63570--63597 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
63560 GAGAGTTAAT
63570 ACTAAAGGG
1 ACTAAAGGG
63579 ACTAAAGGG
1 ACTAAAGGG
63588 ACTAAAGGG
1 ACTAAAGGG
63597 A
1 A
63598 ATTATATCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.32, T:0.11
Consensus pattern (9 bp):
ACTAAAGGG
Found at i:65434 original size:115 final size:115
Alignment explanation
Indices: 65228--65461 Score: 407
Period size: 115 Copynumber: 2.0 Consensus size: 115
65218 CCAAGTAGTT
* *
65228 CAAAAATACTTGTTTATCATTGAACTCCCAATCATTACAAGCTAACCAGAACTCCAAAGCGCTGC
1 CAAAAATAATTGTTTATCATTGAACTCCCAATCATTACAAGCTAACCAGAACTCCAAACCGCTGC
* * *
65293 CGCAATTGACATTAACCTAACTTTTTTCAACTTCCCTAGTACATGAACTA
66 CGCAATTGACATTAACCAAACGTTTTTCAACTTCCCTAGCACATGAACTA
65343 CAAAAATAATTGTTTATCATTGAACTCCCAATCATTACAAGCTAACCAGAACTCCAAACCGCTGC
1 CAAAAATAATTGTTTATCATTGAACTCCCAATCATTACAAGCTAACCAGAACTCCAAACCGCTGC
*
65408 CGCAATTGACATTAACCAAACGTTTTTCAACTTCCCTAGCATATGAACTA
66 CGCAATTGACATTAACCAAACGTTTTTCAACTTCCCTAGCACATGAACTA
65458 -AAAA
1 CAAAA
65462 GCAAAAAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
114 4 0.04
115 109 0.96
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.27
Consensus pattern (115 bp):
CAAAAATAATTGTTTATCATTGAACTCCCAATCATTACAAGCTAACCAGAACTCCAAACCGCTGC
CGCAATTGACATTAACCAAACGTTTTTCAACTTCCCTAGCACATGAACTA
Done.