Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009216.1 Hibiscus syriacus cultivar Beakdansim tig00112804_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: 66994
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3823 original size:14 final size:14
Alignment explanation
Indices: 3800--3838 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
3790 TTAGCTTCTG
3800 CAAGTTCTTTGGAT
1 CAAGTTCTTTGGAT
*
3814 CAATTTCTTTGGAT
1 CAAGTTCTTTGGAT
3828 CAAGTTCTTTG
1 CAAGTTCTTTG
3839 TTCCTCAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (14 bp):
CAAGTTCTTTGGAT
Found at i:11093 original size:21 final size:22
Alignment explanation
Indices: 11060--11107 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 22
11050 TTTATATCCG
*
11060 ATTCTTTAAATTTTCTCT-AATT
1 ATTCTTTAAATTTT-TATGAATT
*
11082 ATTCTTT-GATTTTTATGAATT
1 ATTCTTTAAATTTTTATGAATT
11103 ATTCT
1 ATTCT
11108 AATGTTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 14 0.61
22 7 0.30
ACGTcount: A:0.25, C:0.10, G:0.04, T:0.60
Consensus pattern (22 bp):
ATTCTTTAAATTTTTATGAATT
Found at i:15836 original size:258 final size:260
Alignment explanation
Indices: 15358--15836 Score: 671
Period size: 258 Copynumber: 1.9 Consensus size: 260
15348 CTTAATCAGC
* * * *
15358 TCGATCTCCCACATTGTCTTTTCATCCGAGAAGCTTCTTTGTTCTTTCTCTCTCTCTAGGCTCAT
1 TCGATCTCCCACATTATCTTTTCATCCAAGAAGATTCTTTGTTCTTTCTCTCTCTCTAGACTCAT
* *
15423 TAACCGAATTTCCTCTCTCAACAACCCAGCCTCAGTTAGGAGCCTCCTCAATCACGCTTCCATGA
66 TAACCGAATTTCCTCTCACAACAACCCAGCCTCAGTCAGGAGCCTCCTCAATCACGCTTCCATGA
* * *
15488 TCAACCCATCATCCAAATTCGGCCTTAAGGTGTTGTCATTAATCCTTCCCAACCTCTGAATCTCG
131 TCAACCAATCATCCAAATTCAGCCTTAAGGTGTTGTCATTAATCCTTCCCAACCTCTGAACCTCG
* *
15553 TATCCTAGCGTAAATGCAGGCTCCATTATTTTTATGAATTATTCTAATGTTACTAATTTGTCTCT
196 TAGCCTAGCGTAAATACAGGCTCCATTATTTTTATGAATTATTCTAATGTTACTAATTTGTCTCT
15618 TCGATCTCCCACATTATCTTTTCATCCAAGAAGATTCTTTGTTC-TT-TCTCTCTCTAGACTCAT
1 TCGATCTCCCACATTATCTTTTCATCCAAGAAGATTCTTTGTTCTTTCTCTCTCTCTAGACTCAT
* * * *
15681 TAACTGAATTTCCTCTCACAACAACTCAGCCTCAGTCGGGAGCCTCCTCAATCGCGCTTCCAT-A
66 TAACCGAATTTCCTCTCACAACAACCCAGCCTCAGTCAGGAGCCTCCTCAATCACGCTTCCATGA
* ** * **
15745 GTTAGTCAATCCTCCAAATTCAGCCTTGGGGTGTTGTCATTAATCC-TCCTCAACCTC-GAAACC
131 -TCAACCAATCATCCAAATTCAGCCTTAAGGTGTTGTCATTAATCCTTCC-CAACCTCTG-AACC
* * * *
15808 TCGTAGGCTGGTGTAAATACATGCTCCAT
193 TCGTAGCCTAGCGTAAATACAGGCTCCAT
15837 CATCTTGAAG
Statistics
Matches: 191, Mismatches: 25, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
257 5 0.03
258 143 0.75
259 2 0.01
260 41 0.21
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (260 bp):
TCGATCTCCCACATTATCTTTTCATCCAAGAAGATTCTTTGTTCTTTCTCTCTCTCTAGACTCAT
TAACCGAATTTCCTCTCACAACAACCCAGCCTCAGTCAGGAGCCTCCTCAATCACGCTTCCATGA
TCAACCAATCATCCAAATTCAGCCTTAAGGTGTTGTCATTAATCCTTCCCAACCTCTGAACCTCG
TAGCCTAGCGTAAATACAGGCTCCATTATTTTTATGAATTATTCTAATGTTACTAATTTGTCTCT
Found at i:20203 original size:31 final size:31
Alignment explanation
Indices: 20168--20228 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
20158 TTATGGTTAC
20168 TTATGTTA-CTATTTTATTAAGTTTAGATCAT
1 TTATGTTATC-ATTTTATTAAGTTTAGATCAT
* *
20199 TTATGTTATCGTTTTATTAAGTTTTGATCA
1 TTATGTTATCATTTTATTAAGTTTAGATCA
20229 CTTAAATGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (31 bp):
TTATGTTATCATTTTATTAAGTTTAGATCAT
Found at i:24373 original size:65 final size:63
Alignment explanation
Indices: 24303--24423 Score: 154
Period size: 65 Copynumber: 1.9 Consensus size: 63
24293 TGGAAGACTT
*
24303 AGTGCATCGGTACACTAGG-GGTGCATCGATGCATAAAATACATTCAATGTTTCAAATAAGCCTG
1 AGTGCATCGATACA-T-GGCGGTGCATCGATGCATAAAATACATTCAATG-TTCAAATAAGCCTG
24367 G
63 G
* * * *
24368 AGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAAT
1 AGTGCATCGATACATGG-CGGTGCATCGATGCATAAAATACATTCAATGTTCAAAT
24424 TATTTAGGAG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
63 2 0.04
64 8 0.16
65 39 0.80
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (63 bp):
AGTGCATCGATACATGGCGGTGCATCGATGCATAAAATACATTCAATGTTCAAATAAGCCTGG
Found at i:24455 original size:64 final size:65
Alignment explanation
Indices: 24323--24478 Score: 183
Period size: 64 Copynumber: 2.4 Consensus size: 65
24313 TACACTAGGG
* * *
24323 GTGCATCGATGCATAAAATACATTCAATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGCTCT
* **
24388 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGAGTGCATCGATGCATGC-C
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCT-GGAGTGCATCGATGCATGCTC
24450 TT
65 -T
* * * *
24452 GTGCAGCGGTACACAAAATGCATTCGA
1 GTGCATCGATGCATAAAATGCATTCGA
24479 AATTCAATTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 2 0.03
64 50 0.63
65 27 0.34
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAATAAGCCTGGAGTGCATCGATGCATGCTCT
Found at i:24485 original size:64 final size:64
Alignment explanation
Indices: 24366--24491 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
24356 AAATAAGCCT
* * * * **
24366 GGAGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTA
1 GGAGTGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTTA
* *
24430 GGAGTGCATCGATGCATGC-CTTGTGCAGCGGTACACAAAATGCATTCGAAATTCAATTTATT
1 GGAGTGCATCGATGCATGCTC-TGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATT
24492 CAAGGGCGCA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 1 0.02
64 52 0.98
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
GGAGTGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTTA
Found at i:24503 original size:64 final size:64
Alignment explanation
Indices: 24366--24510 Score: 150
Period size: 64 Copynumber: 2.3 Consensus size: 64
24356 AAATAAGCCT
* * * * * ** *
24366 GGAGTGCATCGATGCATGGTCTGTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTA
1 GGAGCGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTAA
* * *
24430 GGAGTGCATCGATGCATGC-CTTGTGCAGCGGTACACAAAATGCATTCGAAATTCAATTTATTCA
1 GGAGCGCATCGATGCATGCTC-TGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATT-A
24494 A
64 A
*
24495 GG-GCGCATCAATGCAT
1 GGAGCGCATCGATGCAT
24511 TATATAGTGC
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 1 0.01
64 64 0.94
65 3 0.04
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (64 bp):
GGAGCGCATCGATGCATGCTCTGTGCAGCGATACACAAAATGCATTCGAAATTCAAATTATTAA
Found at i:26035 original size:21 final size:21
Alignment explanation
Indices: 26009--26049 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
25999 ATTAGCGATG
26009 GTTTCCGAATTGATGAAAATA
1 GTTTCCGAATTGATGAAAATA
26030 GTTTCCGAATTGATGAAAAT
1 GTTTCCGAATTGATGAAAAT
26050 GACTTCTCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.34
Consensus pattern (21 bp):
GTTTCCGAATTGATGAAAATA
Found at i:27136 original size:22 final size:22
Alignment explanation
Indices: 27089--27190 Score: 104
Period size: 22 Copynumber: 4.7 Consensus size: 22
27079 AAAACCTGAT
* *
27089 GAGTGTATCGATGCACA-GC-A
1 GAGTGCATCGATGCACATTCAA
27109 GAGTGCATCGATGCACATTCAA
1 GAGTGCATCGATGCACATTCAA
* *
27131 GAGTGCATCGGTGCACCTTCAA
1 GAGTGCATCGATGCACATTCAA
* *
27153 G-GTGTATCGATGCATATTCAA
1 GAGTGCATCGATGCACATTCAA
27174 -AGGATGCATCGATGCAC
1 GA-G-TGCATCGATGCAC
27191 TATCTAGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
20 16 0.24
21 17 0.25
22 23 0.34
23 11 0.16
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (22 bp):
GAGTGCATCGATGCACATTCAA
Found at i:42656 original size:64 final size:64
Alignment explanation
Indices: 42520--42707 Score: 200
Period size: 64 Copynumber: 2.9 Consensus size: 64
42510 TACACTAGGG
* * ** * **
42520 GTGCATCGATGCATAAAATACATTCGATGTTTCAAATAAGCCT-GGAGTGCATCAATGCATGGTT
1 GTGCATCGATGCATAAAATGCATTCGATG-TTCAAATTA-TTTAGGAGTGCATCGATGCATGCCT
42584 T
64 T
42585 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATGCCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATGCCTT
* * * * ** * *
42649 GTTCATCGGTACACAAAATGCATTCGAAATTCAATTTATTCAAGG-GTGCATCGATGCAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATT-TAGGAGTGCATCGATGCAT
42708 TATATAGTGC
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
63 1 0.01
64 74 0.70
65 31 0.29
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTCAAATTATTTAGGAGTGCATCGATGCATGCCTT
Found at i:48072 original size:28 final size:28
Alignment explanation
Indices: 48027--48148 Score: 165
Period size: 28 Copynumber: 4.4 Consensus size: 28
48017 ATAATAGTTT
*
48027 TGAATCATTCAA-AATGTACTTTAATGC
1 TGAATCATTCAACAATGTATTTTAATGC
* * *
48054 TAAATAATTCAACAATGTATTTTAATGT
1 TGAATCATTCAACAATGTATTTTAATGC
* *
48082 TGAATCATTCAACAGTGTATTTTAATGT
1 TGAATCATTCAACAATGTATTTTAATGC
* *
48110 TGAATCATTTAACAGTGTATTTTAATGC
1 TGAATCATTCAACAATGTATTTTAATGC
48138 TGAATCATTCA
1 TGAATCATTCA
48149 GTGTACTTTT
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 10 0.12
28 74 0.88
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (28 bp):
TGAATCATTCAACAATGTATTTTAATGC
Found at i:48162 original size:25 final size:27
Alignment explanation
Indices: 48027--48164 Score: 120
Period size: 28 Copynumber: 5.1 Consensus size: 27
48017 ATAATAGTTT
* * * *
48027 TGAATCATTCAAAATGTACTTTAATGC
1 TGAATCATTTACAGTGTATTTTAATGC
* * * * *
48054 TAAATAATTCAACAATGTATTTTAATGT
1 TGAATCATT-TACAGTGTATTTTAATGC
* *
48082 TGAATCATTCAACAGTGTATTTTAATGT
1 TGAATCATT-TACAGTGTATTTTAATGC
48110 TGAATCATTTAACAGTGTATTTTAATGC
1 TGAATCATTT-ACAGTGTATTTTAATGC
48138 TGAATCA-TT-CAGTGTACTTTT-ATGC
1 TGAATCATTTACAGTGTA-TTTTAATGC
48163 TG
1 TG
48165 CAGTATTTTG
Statistics
Matches: 97, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
25 13 0.13
26 4 0.04
27 9 0.09
28 71 0.73
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (27 bp):
TGAATCATTTACAGTGTATTTTAATGC
Found at i:49030 original size:18 final size:21
Alignment explanation
Indices: 48984--49024 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
48974 GAAATTAATA
48984 ATAAATAAATTATTTTCAATTT
1 ATAAATAAATTA-TTTCAATTT
49006 ATAAATAAATTA-TTCAATT
1 ATAAATAAATTATTTCAATT
49025 AAAATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAATAAATTATTTCAATTT
Found at i:49552 original size:37 final size:37
Alignment explanation
Indices: 49504--49601 Score: 178
Period size: 37 Copynumber: 2.6 Consensus size: 37
49494 TTCGGGTCGA
* *
49504 GTTTTTTAGAGTAGAAGTTTGGGTCAGATCTAGTCAG
1 GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
49541 GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
1 GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
49578 GTTTTTCAGAGTAGAAGTTCGGGT
1 GTTTTTCAGAGTAGAAGTTCGGGT
49602 TGAGTTCGGG
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.23, C:0.10, G:0.31, T:0.36
Consensus pattern (37 bp):
GTTTTTCAGAGTAGAAGTTCGGGTCAGATCTAGTCAG
Found at i:53829 original size:19 final size:19
Alignment explanation
Indices: 53805--53855 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
53795 GCTGCTGGAA
*
53805 AACCGGTTTGACCAGTTTG
1 AACCGGTTTGACCAGTCTG
*
53824 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCAGTCTG
*
53843 AACCGGGTTGACC
1 AACCGGTTTGACC
53856 CGACCCGACC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.20, C:0.25, G:0.29, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCAGTCTG
Found at i:53834 original size:10 final size:10
Alignment explanation
Indices: 53805--53853 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
53795 GCTGCTGGAA
53805 AACCGGTTTG
1 AACCGGTTTG
*
53815 -ACCAGTTTG
1 AACCGGTTTG
53824 AACCGGTTTG
1 AACCGGTTTG
*
53834 -ACCGGTCTG
1 AACCGGTTTG
*
53843 AACCGGGTTG
1 AACCGGTTTG
53853 A
1 A
53854 CCCGACCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:53871 original size:17 final size:17
Alignment explanation
Indices: 53849--53889 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
53839 TCTGAACCGG
53849 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
53866 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
53883 ATTGACC
1 GTTGACC
53890 GTTGACCGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.44, G:0.22, T:0.15
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:53889 original size:7 final size:7
Alignment explanation
Indices: 53879--53922 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
53869 GACCCGACCC
*
53879 GACCATT
1 GACCGTT
53886 GACCGTT
1 GACCGTT
53893 GACCG-T
1 GACCGTT
53899 GACCGTT
1 GACCGTT
53906 GACCGTT
1 GACCGTT
*
53913 GACCATT
1 GACCGTT
53920 GAC
1 GAC
53923 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.20, C:0.30, G:0.25, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:53907 original size:20 final size:20
Alignment explanation
Indices: 53879--53916 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
53869 GACCCGACCC
53879 GACCATTGACCGTTGACCGT
1 GACCATTGACCGTTGACCGT
*
53899 GACCGTTGACCGTTGACC
1 GACCATTGACCGTTGACC
53917 ATTGACTTTC
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:0.18, C:0.32, G:0.26, T:0.24
Consensus pattern (20 bp):
GACCATTGACCGTTGACCGT
Found at i:61112 original size:20 final size:19
Alignment explanation
Indices: 61087--61175 Score: 74
Period size: 19 Copynumber: 4.6 Consensus size: 19
61077 GCTGCTGGAA
* *
61087 AACCGGTTTGAGCAGTTTTG
1 AACCGGTTTGA-CAGGTTCG
*
61107 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACAGGTTCG
*
61126 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACAGGTTC-G
* *
61145 AACCAGTTTGACCGG-TCTG
1 AACCGGTTTGACAGGTTC-G
*
61164 AACCGGGTTGAC
1 AACCGGTTTGAC
61176 CCGACCCGAC
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
18 2 0.03
19 49 0.79
20 11 0.18
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACAGGTTCG
Found at i:61116 original size:10 final size:10
Alignment explanation
Indices: 61087--61174 Score: 83
Period size: 10 Copynumber: 9.1 Consensus size: 10
61077 GCTGCTGGAA
61087 AACCGGTTTG
1 AACCGGTTTG
* * *
61097 AGCAGTTTTG
1 AACCGGTTTG
61107 AACCGGTTTG
1 AACCGGTTTG
*
61117 -ACCGGTTCG
1 AACCGGTTTG
61126 AACCGGTTTG
1 AACCGGTTTG
*
61136 -ACCGGTCTG
1 AACCGGTTTG
*
61145 AACCAGTTTG
1 AACCGGTTTG
*
61155 -ACCGGTCTG
1 AACCGGTTTG
*
61164 AACCGGGTTG
1 AACCGGTTTG
61174 A
1 A
61175 CCCGACCCGA
Statistics
Matches: 60, Mismatches: 15, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
9 23 0.38
10 37 0.62
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:61130 original size:19 final size:19
Alignment explanation
Indices: 61105--61176 Score: 110
Period size: 19 Copynumber: 3.8 Consensus size: 19
61095 TGAGCAGTTT
61105 TGAACCGGTTTGACCGGT-
1 TGAACCGGTTTGACCGGTC
61123 TCGAACCGGTTTGACCGGTC
1 T-GAACCGGTTTGACCGGTC
*
61143 TGAACCAGTTTGACCGGTC
1 TGAACCGGTTTGACCGGTC
*
61162 TGAACCGGGTTGACC
1 TGAACCGGTTTGACC
61177 CGACCCGACT
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
18 1 0.02
19 47 0.96
20 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (19 bp):
TGAACCGGTTTGACCGGTC
Found at i:61154 original size:38 final size:38
Alignment explanation
Indices: 61087--61176 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 38
61077 GCTGCTGGAA
* * * *
61087 AACCGGTTTGAGCAGTTTTGAACCGGTTTGACCGGT-TCG
1 AACCGGTTTGA-CCGGTCTGAACCAGTTTGACCGGTCT-G
61126 AACCGGTTTGACCGGTCTGAACCAGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTGAACCAGTTTGACCGGTCTG
*
61164 AACCGGGTTGACC
1 AACCGGTTTGACC
61177 CGACCCGACT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
38 33 0.73
39 12 0.27
ACGTcount: A:0.19, C:0.24, G:0.30, T:0.27
Consensus pattern (38 bp):
AACCGGTTTGACCGGTCTGAACCAGTTTGACCGGTCTG
Found at i:61192 original size:17 final size:17
Alignment explanation
Indices: 61170--61227 Score: 98
Period size: 17 Copynumber: 3.4 Consensus size: 17
61160 TCTGAACCGG
*
61170 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
61187 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
*
61204 GTTGACCCGACCCGTCC
1 GTTGACCCGACCCGACC
61221 GTTGACC
1 GTTGACC
61228 GTTAACCGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:61229 original size:7 final size:7
Alignment explanation
Indices: 61219--61253 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
61209 CCCGACCCGT
61219 CCGTTGA
1 CCGTTGA
*
61226 CCGTTAA
1 CCGTTGA
61233 CCG-TGA
1 CCGTTGA
61239 CCGTTGA
1 CCGTTGA
61246 CCGTTGA
1 CCGTTGA
61253 C
1 C
61254 TTTCTTTGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.20
7 20 0.80
ACGTcount: A:0.17, C:0.31, G:0.26, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:62954 original size:21 final size:21
Alignment explanation
Indices: 62928--62972 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
62918 CAATAAAAAA
* *
62928 TCAAGGAGCTTTACTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
*
62949 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
62970 TCA
1 TCA
62973 TAGCTCATCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Done.