Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002527.1 Hibiscus syriacus cultivar Beakdansim tig00005140_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: 64545
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:815 original size:24 final size:20
Alignment explanation
Indices: 788--845 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
778 GCATGGGTAG
788 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
812 TGCATCGATACACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
832 TGTATCGATGCACT
1 TGCATCGATGCACT
846 TCAAGGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:1180 original size:19 final size:21
Alignment explanation
Indices: 1142--1186 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
1132 GAGCATATGG
*
1142 TTGATATGTTACTGTGTGTTA
1 TTGATATGTTACTATGTGTTA
1163 TTGAT-TGTTAC-ATGTGTTA
1 TTGATATGTTACTATGTGTTA
1182 -TGATA
1 TTGATA
1187 GGTATGAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.18
19 7 0.32
20 6 0.27
21 5 0.23
ACGTcount: A:0.22, C:0.04, G:0.22, T:0.51
Consensus pattern (21 bp):
TTGATATGTTACTATGTGTTA
Found at i:1327 original size:11 final size:13
Alignment explanation
Indices: 1303--1334 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
1293 TGAAGAATGT
1303 ATATATGATAGAG
1 ATATATGATAGAG
1316 AT-TATG-TAGAG
1 ATATATGATAGAG
1327 ATATATGA
1 ATATATGA
1335 GAAGAGGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.41
12 8 0.47
13 2 0.12
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.34
Consensus pattern (13 bp):
ATATATGATAGAG
Found at i:1771 original size:32 final size:31
Alignment explanation
Indices: 1729--1837 Score: 116
Period size: 31 Copynumber: 3.5 Consensus size: 31
1719 AGAGTCAAGG
1729 GTTTACCTATGTTCTACGGAACATATGGAA-A
1 GTTTACCTATGTTCTACGGAACATAT-GAACA
*
1760 GTTTTACCTATG-TCTTTC-GAGACATATGAACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGAACA
* * *
1792 GTATACCTATGTTCTAAGGAACATATAAACA
1 GTTTACCTATGTTCTACGGAACATATGAACA
*
1823 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
1838 TCGGGACCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
31 41 0.63
32 24 0.37
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGAACA
Found at i:7031 original size:2 final size:2
Alignment explanation
Indices: 7024--7058 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
7014 CATGAGTTAG
7024 AT 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 AT A
7059 GGAATTTGTA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7788 original size:22 final size:22
Alignment explanation
Indices: 7762--7883 Score: 199
Period size: 22 Copynumber: 5.5 Consensus size: 22
7752 GGGTATATTA
*
7762 GTCCTTCGAGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
7784 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
7806 GTCCTTCGGGACGTATCCAGTG
1 GTCCTTCGGGACGTATCCAGTG
* *
7828 GTCTTTCGGGACGTATCCAATG
1 GTCCTTCGGGACGTATCCAGTG
* *
7850 GTCATTCGGGACGTATCTAGTG
1 GTCCTTCGGGACGTATCCAGTG
7872 GTCCTTCGGGAC
1 GTCCTTCGGGAC
7884 ATAATAGTCC
Statistics
Matches: 93, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 93 1.00
ACGTcount: A:0.16, C:0.25, G:0.30, T:0.29
Consensus pattern (22 bp):
GTCCTTCGGGACGTATCCAGTG
Found at i:7895 original size:18 final size:17
Alignment explanation
Indices: 7872--7906 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
7862 GTATCTAGTG
7872 GTCCTTCGGGACATAATA
1 GTCCTTCGGGACA-AATA
*
7890 GTCCTTTGGGACAAATA
1 GTCCTTCGGGACAAATA
7907 CTGAACAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (17 bp):
GTCCTTCGGGACAAATA
Found at i:9666 original size:32 final size:31
Alignment explanation
Indices: 9624--9732 Score: 96
Period size: 31 Copynumber: 3.5 Consensus size: 31
9614 AGAGTCGAGG
9624 GTTTACCTATGTTCTACGGAACATATGGAAA
1 GTTTACCTATGTTCTACGGAACATATGGAAA
* *
9655 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGAAA
* * * * * *
9687 GTATATCTATGTTATAAGGAACATATAGATA
1 GTTTACCTATGTTCTACGGAACATATGGAAA
*
9718 GTTTACCTAGGTTCT
1 GTTTACCTATGTTCT
9733 TCGAGACCTA
Statistics
Matches: 60, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
31 34 0.57
32 26 0.43
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGAAA
Found at i:9745 original size:62 final size:63
Alignment explanation
Indices: 9630--9750 Score: 165
Period size: 62 Copynumber: 1.9 Consensus size: 63
9620 GAGGGTTTAC
* * * *
9630 CTATGTTCTACGGAACATATGGAAAGTTTTACCTATGTCTTTCGAGACATATGGACAGTATAT
1 CTATGTTATAAGGAACATATAGAAAGTTTTACCTAGGTCTTTCGAGACATATGGACAGTATAT
* *
9693 CTATGTTATAAGGAACATATAGATAG-TTTACCTAGGT-TCTTCGAGACCTATGGACAGT
1 CTATGTTATAAGGAACATATAGAAAGTTTTACCTAGGTCT-TTCGAGACATATGGACAGT
9751 TGCCGAGGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
61 1 0.02
62 28 0.55
63 22 0.43
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (63 bp):
CTATGTTATAAGGAACATATAGAAAGTTTTACCTAGGTCTTTCGAGACATATGGACAGTATAT
Found at i:13129 original size:24 final size:26
Alignment explanation
Indices: 13076--13127 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
13066 ATAATGAAAT
13076 AAATAAATAGTATAAATAAAATAATA
1 AAATAAATAGTATAAATAAAATAATA
*
13102 AAATAAA-A-TATATATAAAAT-ATA
1 AAATAAATAGTATAAATAAAATAATA
13125 AAA
1 AAA
13128 ATGTATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 1 0.04
26 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (26 bp):
AAATAAATAGTATAAATAAAATAATA
Found at i:13150 original size:21 final size:21
Alignment explanation
Indices: 13096--13151 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 21
13086 TATAAATAAA
*
13096 ATAATAAAATAAAATATATAT
1 ATAATATAATAAAATATATAT
* * *
13117 AAAATAT-A-AAAATGTATGT
1 ATAATATAATAAAATATATAT
13136 ATAATATAATAAAATA
1 ATAATATAATAAAATA
13152 CTAAATAGTA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
19 15 0.56
20 2 0.07
21 10 0.37
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (21 bp):
ATAATATAATAAAATATATAT
Found at i:13876 original size:37 final size:37
Alignment explanation
Indices: 13835--13919 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
13825 GGATCCTATC
* *
13835 TTTAGGAGTTTAAATAATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
* ** *
13872 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCATATT
1 TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
13909 TTTAGGAGTTT
1 TTTAGGAGTTT
13920 GAATCCTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTAGGAGTTTAAATAATAGCAAAACTCTATCATATT
Found at i:14865 original size:106 final size:106
Alignment explanation
Indices: 14681--15955 Score: 1985
Period size: 106 Copynumber: 12.0 Consensus size: 106
14671 GAATTGTTCC
* * * * * *
14681 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATTGTTTGGTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
14746 CCAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
14787 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
14852 CCAGCGGTTCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
14893 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
14958 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
14999 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
15064 CCAACAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
15105 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCCGAAATGGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
15170 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * * *
15211 GAGTCCAATATTTTTCGTTGTGAAATTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGAAAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
15276 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
15317 GAGTCCAATATTTTTCGTTGTGAAATTCAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
15382 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
15423 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
15488 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCTTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
15529 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
15594 CCAGCGGTCCCTTCGTCATGAAGTTGAATTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
15635 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
15700 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
15741 GAGTCCAATATCCTTCGTTGTGAAGTT-AAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
15805 CTAGCAGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
15846 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATTTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** ** * *
15911 CCAGCCATCCCTTCGTTTTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
15952 GAGT
1 GAGT
15956 GACACGATAT
Statistics
Matches: 1086, Mismatches: 82, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
105 96 0.09
106 990 0.91
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:16945 original size:22 final size:22
Alignment explanation
Indices: 16915--16970 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
16905 TTGTGTTTAG
*
16915 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
16937 TTAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
16959 TCAAAGGTTTGA
1 TCAAAGGTTTGA
16971 TGGGGTAGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:17601 original size:25 final size:25
Alignment explanation
Indices: 17573--17625 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
17563 TTTTTGTCCC
*
17573 TTTTCCTTTTTGATTTTTGTTCTTTT
1 TTTTCCTTTTTGATTCTT-TTCTTTT
* *
17599 TTTTCTTTTTTGCTTCTTTTCTTTT
1 TTTTCCTTTTTGATTCTTTTCTTTT
17624 TT
1 TT
17626 GTGTTTGCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.02, C:0.13, G:0.06, T:0.79
Consensus pattern (25 bp):
TTTTCCTTTTTGATTCTTTTCTTTT
Found at i:22353 original size:26 final size:26
Alignment explanation
Indices: 22324--22402 Score: 78
Period size: 24 Copynumber: 3.2 Consensus size: 26
22314 TAATGAAAAT
*
22324 AAATAAATAGTATAAATAAAATAATA
1 AAATAAATAGTATATATAAAATAATA
22350 AAATAAA-A-TATATATATAAA-AATA
1 AAATAAATAGTATATATA-AAATAATA
* * *
22374 TAA-AAAT-GTATGTATAATATAATA
1 AAATAAATAGTATATATAAAATAATA
22398 AAATA
1 AAATA
22403 CTAAATAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
23 5 0.12
24 26 0.60
25 5 0.12
26 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
AAATAAATAGTATATATAAAATAATA
Found at i:22357 original size:13 final size:14
Alignment explanation
Indices: 22322--22370 Score: 59
Period size: 13 Copynumber: 3.7 Consensus size: 14
22312 CATAATGAAA
*
22322 ATAAAT-AAATAGT
1 ATAAATAAAATAAT
22335 ATAAATAAAATAAT
1 ATAAATAAAATAAT
22349 A-AAATAAAAT-AT
1 ATAAATAAAATAAT
*
22361 ATATATAAAA
1 ATAAATAAAA
22371 ATATAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
12 3 0.09
13 22 0.69
14 7 0.22
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (14 bp):
ATAAATAAAATAAT
Found at i:22542 original size:13 final size:13
Alignment explanation
Indices: 22524--22549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22514 TAACGTTAGG
22524 AAAATATAGTAAA
1 AAAATATAGTAAA
22537 AAAATATAGTAAA
1 AAAATATAGTAAA
22550 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:22611 original size:21 final size:21
Alignment explanation
Indices: 22570--22618 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
22560 TAGATAAAAA
* *
22570 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
22591 ATAATAATAGGAAAATAATATAAT
1 ATAATAATA-GAAAAT-ATAT-AT
22615 ATAA
1 ATAA
22619 CGTAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 4 0.17
24 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:24907 original size:14 final size:15
Alignment explanation
Indices: 24888--24916 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24878 CCCTTACTCT
24888 CAAAAA-GAAATAAA
1 CAAAAATGAAATAAA
24902 CAAAAATGAAATAAA
1 CAAAAATGAAATAAA
24917 TGTAGTAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.07, G:0.07, T:0.10
Consensus pattern (15 bp):
CAAAAATGAAATAAA
Found at i:28671 original size:145 final size:147
Alignment explanation
Indices: 28399--28687 Score: 331
Period size: 145 Copynumber: 2.0 Consensus size: 147
28389 TGAGAGACTA
* * **
28399 AATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGTAGTTTAAATTTGGTAAAAACAA
1 AATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGTAGATCAAATTTAATAAAAACAA
* * ** *
28464 ATTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATACTAATTTGAAAAAT-AAAAAAAAA
66 ACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTAAAAAAAATTGAAAAATAAAAAAAAAA
28528 -TATTATCAAAAAGAGG
131 TTATTATCAAAAAGAGG
** *
28544 AATTGAAGTTACATATTTATTCTAT--TATGTTATATTAGCATG-AGGATCAAATTTAATAAAAA
1 AATTGAAGTTACATAGGTATTCTATAGT-TG-TATATGAGCATGTA-GATCAAATTTAATAAAAA
* * * *
28606 CGAACTTAAAATAAATGATGAATTGAATAAAT-AGAAAATTAAAAAAAATT-AAAGACTAAATAA
63 CAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTAAAAAAAATTGAAA-AATAAA-AA
28669 AAAAATTTATTATCAAAAA
126 AAAAA-TTATTATCAAAAA
28688 AGATAAATTG
Statistics
Matches: 120, Mismatches: 16, Indels: 13
0.81 0.11 0.09
Matches are distributed among these distances:
143 4 0.03
144 19 0.16
145 78 0.65
146 7 0.06
148 12 0.10
ACGTcount: A:0.52, C:0.05, G:0.12, T:0.31
Consensus pattern (147 bp):
AATTGAAGTTACATAGGTATTCTATAGTTGTATATGAGCATGTAGATCAAATTTAATAAAAACAA
ACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTAAAAAAAATTGAAAAATAAAAAAAAAA
TTATTATCAAAAAGAGG
Found at i:28753 original size:149 final size:145
Alignment explanation
Indices: 28447--28754 Score: 304
Period size: 149 Copynumber: 2.1 Consensus size: 145
28437 CATGTAGTTT
* * ** *
28447 AAATTTGGTAAAAACAAATTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTATACTAATTT
1 AAATTTGGTAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTAAAAAAAATT
* ** *
28512 GAAAAATAAAAAAAAATATTATCAAAAAGAGGAATTGAAGTTACATATTTATTCTATTATGTTAT
66 GAAAAATAAAAAAAAATATTATCAAAAAGAGAAATTGAAGTTACATATTTATAATATGATGTTAT
* * *
28577 ATTAGCATGAGGATC
131 ATGAACATGAGGATA
** * * *
28592 AAATTTAATAAAAACGAACTTAAAATAAATGATGAATTGAATAAAT-AGAAAATTAAAAAAAATT
1 AAATTTGGTAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTAAAAAAAATT
* *
28656 -AAAGACTAAATAAAAAAATTTATTATCAAAAAAGATAAATTGAAAG-TACAT-TTGTATAATAT
66 GAAA-AAT-AA-AAAAAAA--TATTATC-AAAAAGAGAAATTG-AAGTTACATATT-TATAATAT
*
28718 GATGATT-TATGAACATG-TGACTA
123 GATG-TTATATGAACATGAGGA-TA
28741 AAATTTGGTAAAAA
1 AAATTTGGTAAAAA
28755 GTTGATTTAA
Statistics
Matches: 131, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
143 3 0.02
144 16 0.12
145 42 0.32
146 7 0.05
148 11 0.08
149 47 0.36
150 5 0.04
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (145 bp):
AAATTTGGTAAAAACAAACTTAAAATAAAAGATGAATTGAAGAAATAAGAAAATTAAAAAAAATT
GAAAAATAAAAAAAAATATTATCAAAAAGAGAAATTGAAGTTACATATTTATAATATGATGTTAT
ATGAACATGAGGATA
Found at i:29254 original size:2 final size:2
Alignment explanation
Indices: 29249--29274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29239 TATTTTAATG
29249 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
29275 ATTTGAGACA
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):
TA
Found at i:41628 original size:17 final size:17
Alignment explanation
Indices: 41597--41642 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
41587 CAGTCAACGG
**
41597 TCGGTCAACGGTCAACA
1 TCGGTCAACAATCAACA
*
41614 TCGGTCAACAATCAACG
1 TCGGTCAACAATCAACA
*
41631 TCAGTCAACAAT
1 TCGGTCAACAAT
41643 TAACGGCTCG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.35, C:0.28, G:0.17, T:0.20
Consensus pattern (17 bp):
TCGGTCAACAATCAACA
Found at i:45452 original size:23 final size:23
Alignment explanation
Indices: 45425--45473 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
45415 TTGTGGTTGG
45425 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
45448 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
45471 TTT
1 TTT
45474 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:55667 original size:23 final size:23
Alignment explanation
Indices: 55640--55688 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
55630 AGGTGGTTGG
55640 TTTAATGG-ATATTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
55663 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
55686 TTT
1 TTT
55689 GGTTCTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:57342 original size:75 final size:74
Alignment explanation
Indices: 57219--57409 Score: 310
Period size: 75 Copynumber: 2.5 Consensus size: 74
57209 AGTTTGTCCA
*
57219 GAGGGAACCGATTCCCCCCAAGGAGGTACCGATTCCCCCTGAATGGTTTGGCTCCGAGAAATAAC
1 GAGGGAACCGATTCCCCCCAAGG-GGTACCGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAAC
57284 AGAATGCTCG
65 AGAATGCTCG
* * *
57294 GAGGGAACCGATTCCCCTCCAAGGGGTACTGATTCTCCCTGAATGGTTTGGCTCTAAGAAATAAC
1 GAGGGAACCGATTCCCC-CCAAGGGGTACCGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAAC
*
57359 AGAATGCTTG
65 AGAATGCTCG
57369 GAGGGAACCGATTCCCCCCAAGGGGGTACCGATTCCCCCTG
1 GAGGGAACCGATTCCCCCCAA-GGGGTACCGATTCCCCCTG
57410 TTCAATGGTC
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
74 4 0.04
75 97 0.91
76 6 0.06
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (74 bp):
GAGGGAACCGATTCCCCCCAAGGGGTACCGATTCCCCCTGAATGGTTTGGCTCCAAGAAATAACA
GAATGCTCG
Found at i:57642 original size:11 final size:11
Alignment explanation
Indices: 57618--57650 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
57608 AAGAAATAAC
57618 AATCAAAA-AG
1 AATCAAAAGAG
57628 AATCAAAAGAG
1 AATCAAAAGAG
57639 AATC-AAAGAG
1 AATCAAAAGAG
57649 AA
1 AA
57651 AGCATCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.67, C:0.09, G:0.15, T:0.09
Consensus pattern (11 bp):
AATCAAAAGAG
Found at i:61730 original size:16 final size:16
Alignment explanation
Indices: 61697--61730 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61687 TGCCTTCTCT
*
61697 GATACAAATTATAGAG
1 GATACAAATTAGAGAG
*
61713 GATACAAATTAGATAG
1 GATACAAATTAGAGAG
61729 GA
1 GA
61731 AAAGCACCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.21, T:0.24
Consensus pattern (16 bp):
GATACAAATTAGAGAG
Done.