Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005337.1 Hibiscus syriacus cultivar Beakdansim tig00012085_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: 69362
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6578 original size:33 final size:34
Alignment explanation
Indices: 6533--6603 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
6523 CCTTTACAGC
6533 TCCCTAGTTTTTCAA-TGACTAA-ACTAGAACCAA
1 TCCCTAGTTTTTCAATTGACTAAGA-TAGAACCAA
*
6566 TCCCTA-TCTTTTCAATTGGCTAAGATAGAACCAA
1 TCCCTAGT-TTTTCAATTGACTAAGATAGAACCAA
6600 TCCC
1 TCCC
6604 CTTTACAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
32 1 0.03
33 13 0.38
34 19 0.56
35 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.31
Consensus pattern (34 bp):
TCCCTAGTTTTTCAATTGACTAAGATAGAACCAA
Found at i:9638 original size:15 final size:15
Alignment explanation
Indices: 9618--9648 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
9608 ATTGACCGGT
*
9618 TGTGAATCTTGAATG
1 TGTGAATCTTCAATG
9633 TGTGAATCTTCAATG
1 TGTGAATCTTCAATG
9648 T
1 T
9649 AATAGACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.42
Consensus pattern (15 bp):
TGTGAATCTTCAATG
Found at i:12951 original size:53 final size:53
Alignment explanation
Indices: 12851--13160 Score: 365
Period size: 53 Copynumber: 5.8 Consensus size: 53
12841 TTCAAATGAT
* * **** *
12851 GGGTTCGCTCCCTCTTG-TTCAGGGATTAAAGAACTTGAACAATCTTCTAAAAAT
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGT--AGAACTCGAACAATCTTCTGCCTAC
* * * * *
12905 GGGTTCACTCCCTATTGATTCAGGGAGTAGAACTCGAATAATCTTCTGCTTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * *
12958 GGGTTCGTTCCCTCTTGCTTCAGGGGGTAGAACTCGAACAATCTTCTGCCCAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* * * *
13011 GGGTTCACTCCCTCTTGCTTTAGGGAGTAGAACTCGAATAATCTTCTGTCTAC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
13064 GGGTT-GCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCTAT
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
* *
13116 AGGTTTGCTCCCTCTTAG-TTCAGGGAGTAGAACTCGAACAATCTT
1 GGGTTCGCTCCCTCTT-GCTTCAGGGAGTAGAACTCGAACAATCTT
13161 TTGGTGTGAT
Statistics
Matches: 220, Mismatches: 33, Indels: 7
0.85 0.13 0.03
Matches are distributed among these distances:
52 45 0.20
53 150 0.68
54 16 0.07
55 9 0.04
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (53 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTAC
Found at i:13129 original size:105 final size:105
Alignment explanation
Indices: 12851--13160 Score: 392
Period size: 105 Copynumber: 2.9 Consensus size: 105
12841 TTCAAATGAT
* * ***
12851 GGGTTCGCTCCCTCTTG-TTCAGGGATTAAAGAACTTGAACAATCTTCTAAAAATGGGTTCACTC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGT-AA-AACTCGAACAATCTTCTGCCAATGGGTTCACTC
*
12915 CCTATTGATTCAGGGAGTAGAACTCGAATAATCTTCTGCTTAC
64 CCTCTTG-TTCAGGGAGTAGAACTCGAATAATCTTCTGCTTAC
* * * * *
12958 GGGTTCGTTCCCTCTTGCTTCAGGGGGTAGAACTCGAACAATCTTCTGCCCACGGGTTCACTCCC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCAATGGGTTCACTCCC
*
13023 TCTTGCTTTAGGGAGTAGAACTCGAATAATCTTCTG-TCTAC
66 TCTTG-TTCAGGGAGTAGAACTCGAATAATCTTCTGCT-TAC
* * **
13064 GGGTT-GCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCTATAGGTTTGCTCCC
1 GGGTTCGCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCAATGGGTTCACTCCC
*
13128 TCTTAGTTCAGGGAGTAGAACTCGAACAATCTT
66 TCTT-GTTCAGGGAGTAGAACTCGAATAATCTT
13161 TTGGTGTGAT
Statistics
Matches: 177, Mismatches: 23, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
105 81 0.46
106 71 0.40
107 17 0.10
108 8 0.05
ACGTcount: A:0.23, C:0.25, G:0.21, T:0.31
Consensus pattern (105 bp):
GGGTTCGCTCCCTCTTGCTTCAGGGAGTAAAACTCGAACAATCTTCTGCCAATGGGTTCACTCCC
TCTTGTTCAGGGAGTAGAACTCGAATAATCTTCTGCTTAC
Found at i:13689 original size:42 final size:42
Alignment explanation
Indices: 13643--14123 Score: 360
Period size: 42 Copynumber: 11.0 Consensus size: 42
13633 TAAAAAATGA
13643 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* *
13685 CCCGAATGATTTAATCATCATTCTCGAAAGACTTACTGATGA
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * * * *
13727 CCCGAAGGACTTCATCATCATGCTTGAAAGACTTACTGTTGA
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*
13769 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
** * * ** **
13811 CACTTACTG-ATGGATTTGCTTCA-CTACT-CTTCGGTGAAGGCTTACAAATTA
1 C-C---C-GAAT-GATTT-AATCATC-A-TGC-TC-G-AAAGACTTACTGATGG
*
13862 CCCGAATGATTTAATTATCATGCTCGAAAGACTTACTGATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
** * * * * *
13904 CCTAAAGGACTTCATCATTATGCTCGAAAGACTTACTGATGA
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
*
13946 CCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * * ** **
13988 CACTTACTAATGGATTTACTTCA-CTACT-CTTCGGTGAAGGCTTACAAATTA
1 C-C---CGAAT-GATTTA-ATCATC-A-TGC-TC-G-AAAGACTTACTGATGG
*
14039 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
* * * * *
14081 CCCGAAGGACTTCATCATCATGGTCGAAAGACTTATTGATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
14123 C
1 C
14124 ACTTACTGAT
Statistics
Matches: 342, Mismatches: 69, Indels: 56
0.73 0.15 0.12
Matches are distributed among these distances:
42 242 0.71
43 4 0.01
44 6 0.02
45 9 0.03
46 19 0.06
47 20 0.06
48 10 0.03
49 6 0.02
50 4 0.01
51 22 0.06
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (42 bp):
CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGG
Found at i:13817 original size:13 final size:13
Alignment explanation
Indices: 13799--13823 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13789 TGCTCGAAAG
13799 ACTTACTGATGGC
1 ACTTACTGATGGC
13812 ACTTACTGATGG
1 ACTTACTGATGG
13824 ATTTGCTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:13882 original size:93 final size:91
Alignment explanation
Indices: 13768--14081 Score: 419
Period size: 93 Copynumber: 3.5 Consensus size: 91
13758 CTTACTGTTG
13768 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTGATGGATTTGCTTC
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACT-ATGGATTT-CTTC
13833 ACTACTCTTCGGTGAAGGCTTACAAATT
64 ACTACTCTTCGGTGAAGGCTTACAAATT
* * * * * *
13861 ACCCGAATGATTTAATTATCATGCTCGAAAGACTTACTGATGGC-C-TA--AAGGACTTCATCAT
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTATGGATTTCTTCAC
* * ** *
13922 TA-TGC-TC-G-AAAGACTTACTGATG
66 TACT-CTTCGGTGAAGGCTTACAAATT
*
13945 ACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTAATGGATTTACTTC
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACT-ATGGATTT-CTTC
14010 ACTACTCTTCGGTGAAGGCTTACAAATT
64 ACTACTCTTCGGTGAAGGCTTACAAATT
14038 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
1 ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGC
14082 CCGAAGGACT
Statistics
Matches: 187, Mismatches: 23, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
84 52 0.28
85 2 0.01
86 5 0.03
87 7 0.04
88 6 0.03
89 6 0.03
90 7 0.04
91 5 0.03
92 2 0.01
93 95 0.51
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (91 bp):
ACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACTTACTATGGATTTCTTCAC
TACTCTTCGGTGAAGGCTTACAAATT
Found at i:13936 original size:22 final size:21
Alignment explanation
Indices: 13878--13980 Score: 63
Period size: 22 Copynumber: 4.9 Consensus size: 21
13868 TGATTTAATT
13878 ATCATGCTCGAAAGACTTA-C
1 ATCATGCTCGAAAGACTTATC
* *
13898 -TGATGGC-CTAAAGGACTTCATC
1 ATCAT-GCTCGAAA-GACTT-ATC
*
13920 ATTATGCTCGAAAGACTTA-C
1 ATCATGCTCGAAAGACTTATC
* * * *
13940 -TGATGACCCGAAGGATTTAATC
1 ATCATG-CTCGAAAGACTT-ATC
13962 ATCATGCTCGAAAGACTTA
1 ATCATGCTCGAAAGACTTA
13981 CTGATGGCAC
Statistics
Matches: 61, Mismatches: 12, Indels: 19
0.66 0.13 0.21
Matches are distributed among these distances:
19 11 0.18
20 17 0.28
21 4 0.07
22 18 0.30
23 11 0.18
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (21 bp):
ATCATGCTCGAAAGACTTATC
Found at i:13981 original size:177 final size:177
Alignment explanation
Indices: 13685--14121 Score: 748
Period size: 177 Copynumber: 2.5 Consensus size: 177
13675 TTACTGATGG
* *
13685 CCCGAATGATTTAATCATCATTCTCGAAAGACTTACTGATGACCCGAAGGACTTCATCATCATGC
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
* *
13750 TTGAAAGACTTACTGTTGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACT
66 TCGAAAGACTTACTGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACT
* *
13815 TACTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTA
131 TACTAATGGATTTACTTCACTACTCTTCGGTGAAGGCTTACAAATTA
* ** *
13862 CCCGAATGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCTAAAGGACTTCATCATTATGC
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
*
13927 TCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACT
66 TCGAAAGACTTACTGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACT
13992 TACTAATGGATTTACTTCACTACTCTTCGGTGAAGGCTTACAAATTA
131 TACTAATGGATTTACTTCACTACTCTTCGGTGAAGGCTTACAAATTA
* *
14039 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGG
1 CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
*
14104 TCGAAAGACTTATTGATG
66 TCGAAAGACTTACTGATG
14122 GCACTTACTG
Statistics
Matches: 242, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
177 242 1.00
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.30
Consensus pattern (177 bp):
CCCGAATGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGC
TCGAAAGACTTACTGATGACCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCACT
TACTAATGGATTTACTTCACTACTCTTCGGTGAAGGCTTACAAATTA
Found at i:14032 original size:135 final size:134
Alignment explanation
Indices: 13904--14228 Score: 463
Period size: 135 Copynumber: 2.4 Consensus size: 134
13894 TTACTGATGG
* * * *
13904 CCTAAAGGACTTCATCATTATGCTCGAAAGACTTACTGATGACCCGAAGGATTTAATCATCATGC
1 CCTAAA-GACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAATCATCATGC
*
13969 TCGAAAGACTTACTGATGGCACTTACTAATGGATTTACTTCACTACTCTTCGGTGAAGGCTTACA
65 TCGAAAGACTTACTGATGGCACTTACTAATGGATTTACTTCACTACTCTTCGATGAAGGCTTACA
*
14034 AATTA
130 AATGA
* * * *
14039 CCCGAAAGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTCATCATCATGG
1 -CCTAAAGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAATCATCATGC
* * * **
14104 TCGAAAGACTTATTGATGGCACTTACTGATGGGTTTGTTTCACTACTCTTCGATGAAGG-TTACA
65 TCGAAAGACTTACTGATGGCACTTACTAATGGATTTACTTCACTACTCTTCGATGAAGGCTTACA
14168 AATGA
130 AATGA
* *
14173 CCTAAAAGACTTAATCATCATGCTCGAAAGCCTTACTGATGGCCCAAAGGACTTAA
1 CCT-AAAGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAA
14229 ATTTTTTACT
Statistics
Matches: 168, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
133 2 0.01
134 57 0.34
135 104 0.62
136 5 0.03
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (134 bp):
CCTAAAGACTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAATCATCATGCT
CGAAAGACTTACTGATGGCACTTACTAATGGATTTACTTCACTACTCTTCGATGAAGGCTTACAA
ATGA
Found at i:14113 original size:22 final size:21
Alignment explanation
Indices: 14041--14116 Score: 66
Period size: 22 Copynumber: 3.6 Consensus size: 21
14031 ACAAATTACC
* *
14041 CGAAAGATTTAATCATCATGCT
1 CGAAAGACTT-ATCATCATGGT
* *
14063 CGAAAGACTTA-C-TGATGGCC
1 CGAAAGACTTATCATCATGG-T
*
14083 CGAAGGACTTCATCATCATGGT
1 CGAAAGACTT-ATCATCATGGT
14105 CGAAAGACTTAT
1 CGAAAGACTTAT
14117 TGATGGCACT
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
19 4 0.10
20 10 0.24
21 4 0.10
22 19 0.45
23 5 0.12
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (21 bp):
CGAAAGACTTATCATCATGGT
Found at i:29964 original size:2 final size:2
Alignment explanation
Indices: 29957--29985 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29947 TCAATCTACA
29957 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 A
29986 AATAATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30203 original size:13 final size:13
Alignment explanation
Indices: 30168--30212 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
30158 CTCAATGAAC
* *
30168 GTCATAAATATGC
1 GTCATAAATGTGT
30181 GTCATAAATGTGT
1 GTCATAAATGTGT
*
30194 GTCATAAATGCGT
1 GTCATAAATGTGT
30207 GTCATA
1 GTCATA
30213 GATTTATGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (13 bp):
GTCATAAATGTGT
Found at i:30210 original size:26 final size:28
Alignment explanation
Indices: 30181--30239 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 28
30171 ATAAATATGC
* *
30181 GTCATAAATGTGTGTCATA-AA-TGCGT
1 GTCATAAATGTATGTCACACAATTGCGT
* *
30207 GTCATAGATTTATGTCACACAATTGCGT
1 GTCATAAATGTATGTCACACAATTGCGT
30235 GTCAT
1 GTCAT
30240 CTAAAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 15 0.56
27 2 0.07
28 10 0.37
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (28 bp):
GTCATAAATGTATGTCACACAATTGCGT
Found at i:33803 original size:31 final size:31
Alignment explanation
Indices: 33765--33889 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
33755 AGGGTCGAGG
*
33765 GTTTACCTATGTTCTTCGGGATATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
33796 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
33827 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
33858 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
33889 G
1 G
33890 GTCCTTCGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:38172 original size:62 final size:62
Alignment explanation
Indices: 38052--38176 Score: 189
Period size: 62 Copynumber: 2.0 Consensus size: 62
38042 AGGGTCGAGG
* * * *
38052 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGATTCTTCAGAACATATGGACT
*
38114 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGATTCTTCAGAA-CATATGGACT
38176 G
1 G
38177 GTCCTTTGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 56 0.98
63 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGATTCTTCAGAACATATGGACT
Found at i:38176 original size:31 final size:31
Alignment explanation
Indices: 38052--38161 Score: 193
Period size: 31 Copynumber: 3.5 Consensus size: 31
38042 AGGGTCGAGG
38052 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
38083 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
38114 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
38145 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
38162 AGAATCTATG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 75 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:42378 original size:31 final size:31
Alignment explanation
Indices: 42340--42464 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
42330 AGGGTCGAGG
42340 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
42371 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
42402 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
42433 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
42464 G
1 G
42465 GTCCTTCGGG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:45833 original size:2 final size:2
Alignment explanation
Indices: 45828--45862 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
45818 AAGAATATGA
45828 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45863 GGTTAGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:46743 original size:2 final size:2
Alignment explanation
Indices: 46736--46786 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
46726 AATTTTGCGT
46736 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA
46778 TA TA TA TA T
1 TA TA TA TA T
46787 TCATACTAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46864 original size:2 final size:2
Alignment explanation
Indices: 46857--46889 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
46847 GCTAAACTTT
46857 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 T
46890 TCATCCTAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46946 original size:104 final size:103
Alignment explanation
Indices: 46754--46958 Score: 392
Period size: 104 Copynumber: 2.0 Consensus size: 103
46744 TATATATATA
46754 TATATATATATATATATATATATATATATATATTCATACTAAAAATATTTTTTAATCTGTCAGTT
1 TATATATATATATATATATATATATATATATATTCATACTAAAAATATTTTTTAATCTGTCAGTT
46819 GTGCTGAATGAACTTTGTCAAAGTATAAGCTAAACTTT
66 GTGCTGAATGAACTTTGTCAAAGTATAAGCTAAACTTT
*
46857 TATATATATATATATATATATATATATATATATTCATCCTAAAAAATATTTTTTAATCTGTCAGT
1 TATATATATATATATATATATATATATATATATTCATACT-AAAAATATTTTTTAATCTGTCAGT
46922 TGTGCTGAATGAACTTTGTCAAAGTATAAGCTAAACT
65 TGTGCTGAATGAACTTTGTCAAAGTATAAGCTAAACT
46959 AAAGTTTAGA
Statistics
Matches: 100, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
103 39 0.39
104 61 0.61
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (103 bp):
TATATATATATATATATATATATATATATATATTCATACTAAAAATATTTTTTAATCTGTCAGTT
GTGCTGAATGAACTTTGTCAAAGTATAAGCTAAACTTT
Found at i:46986 original size:104 final size:101
Alignment explanation
Indices: 46769--46986 Score: 312
Period size: 104 Copynumber: 2.1 Consensus size: 101
46759 ATATATATAT
46769 ATATATATATATATATATTCATACTAAAAATATTTTTTAATCTGTCAGTTGTGCTGAATGAACTT
1 ATATATATATATATATATTCATACTAAAAATATTTTTTAATCTGTCAGTTGTGCTGAATGAACTT
* * * *
46834 TGTCAAAGTATAAGCTAAACTTTTATATATATATATAT
66 TGTCAAAGTATAAGCTAAAC--TTAAATATAGATAAAC
*
46872 ATATATATATATATATATTCATCCTAAAAAATATTTTTTAATCTGTCAGTTGTGCTGAATGAACT
1 ATATATATATATATATATTCATACT-AAAAATATTTTTTAATCTGTCAGTTGTGCTGAATGAACT
*
46937 TTGTCAAAGTATAAGCTAAAC-TAAAGTTTAGACTAAAC
65 TTGTCAAAGTATAAGCTAAACTTAAA-TATAGA-TAAAC
*
46975 ATGTATGATATA
1 ATATAT-ATATA
46987 AATAGATGTA
Statistics
Matches: 104, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
101 3 0.03
102 4 0.04
103 32 0.31
104 65 0.62
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (101 bp):
ATATATATATATATATATTCATACTAAAAATATTTTTTAATCTGTCAGTTGTGCTGAATGAACTT
TGTCAAAGTATAAGCTAAACTTAAATATAGATAAAC
Found at i:48434 original size:2 final size:2
Alignment explanation
Indices: 48427--48460 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
48417 GTCCCTACTT
48427 TA TA TA TA 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 TA TA TA TA
48461 GAAGTGGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:50479 original size:19 final size:17
Alignment explanation
Indices: 50455--50499 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
50445 GTCAGAACTT
*
50455 TAATAATTATTATAAATA
1 TAATAATTATGA-AAATA
50473 GTAATAATGTATGAAAATA
1 -TAATAAT-TATGAAAATA
50492 TAATAATT
1 TAATAATT
50500 TAATTAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 12 0.50
20 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
TAATAATTATGAAAATA
Found at i:51440 original size:19 final size:17
Alignment explanation
Indices: 51416--51457 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
51406 AGAAAATTAA
51416 AATCTGTGAAGGAATTTGG
1 AATCTGT-AAGGAA-TTGG
*
51435 AATCTGTCAGGAATTGG
1 AATCTGTAAGGAATTGG
51452 AATCTG
1 AATCTG
51458 AATCTGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 5 0.23
19 7 0.32
ACGTcount: A:0.31, C:0.10, G:0.29, T:0.31
Consensus pattern (17 bp):
AATCTGTAAGGAATTGG
Found at i:51923 original size:18 final size:18
Alignment explanation
Indices: 51900--51946 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
51890 TGACTTAAAA
51900 AAACCCTAAACTTGAGC-C
1 AAACCCTAAACTTGA-CTC
51918 AAACCCTAAACTTGACTC
1 AAACCCTAAACTTGACTC
*
51936 GAACCCTAAAC
1 AAACCCTAAAC
51947 CCAACCCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.40, C:0.34, G:0.09, T:0.17
Consensus pattern (18 bp):
AAACCCTAAACTTGACTC
Found at i:57695 original size:53 final size:53
Alignment explanation
Indices: 57633--57735 Score: 154
Period size: 53 Copynumber: 1.9 Consensus size: 53
57623 TATGAAAATA
* * * *
57633 TCTTCAAATTTAAGAATCAAA-TTAAAAGATGTTTTCAAATTCAGAATTAAAAG
1 TCTTCAAATTAAAGAACCAAACTTAAAA-ATGTTGTCAAATCCAGAATTAAAAG
57686 TCTTCAAATTAAAGAACCAAACTTAAAAATGTTGTCAAATCCAGAATTAA
1 TCTTCAAATTAAAGAACCAAACTTAAAAATGTTGTCAAATCCAGAATTAA
57736 TGTAAATCAC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
53 39 0.87
54 6 0.13
ACGTcount: A:0.48, C:0.13, G:0.09, T:0.31
Consensus pattern (53 bp):
TCTTCAAATTAAAGAACCAAACTTAAAAATGTTGTCAAATCCAGAATTAAAAG
Found at i:58126 original size:60 final size:59
Alignment explanation
Indices: 58043--58155 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 59
58033 ATTTCTTCTC
* * ** *
58043 TAAACTATGACTTTTATTTTAAATTAGTCCTTAAACTTTTGAACATTCTAATTTTATCCA
1 TAAACTATGACTTCTATTCTAAATTAGTCCCCAAAC-TTTGAACATTCCAATTTTATCCA
* *
58103 TAAACTATGACTCTCT-TTCTAAATTATTCCCCAAACTTTGAATATTCCAATTT
1 TAAACTATGACT-TCTATTCTAAATTAGTCCCCAAACTTTGAACATTCCAATTT
58156 CATATCTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 15 0.33
60 28 0.62
61 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (59 bp):
TAAACTATGACTTCTATTCTAAATTAGTCCCCAAACTTTGAACATTCCAATTTTATCCA
Found at i:67323 original size:20 final size:20
Alignment explanation
Indices: 67298--67335 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
67288 TTTGGTTCAC
*
67298 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
67318 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
67336 GGAATAAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:67338 original size:18 final size:19
Alignment explanation
Indices: 67298--67342 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
67288 TTTGGTTCAC
*
67298 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
67318 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
67336 GGAATAA
1 GGAATAA
67343 GATTACTGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 8 0.33
20 16 0.67
ACGTcount: A:0.47, C:0.09, G:0.24, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:67520 original size:35 final size:37
Alignment explanation
Indices: 67488--67555 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 37
67478 TACAAATTGT
67488 AAAATA-TTATAT-A-TTTCTTTAAAAAATTAAATTC
1 AAAATATTTATATAATTTTCTTTAAAAAATTAAATTC
* * *
67522 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTCTTTAAAAAATTAAA
67556 AATATAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 5 0.18
35 6 0.21
36 1 0.04
37 16 0.57
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (37 bp):
AAAATATTTATATAATTTTCTTTAAAAAATTAAATTC
Done.