Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002911.1 Hibiscus syriacus cultivar Beakdansim tig00006018_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: 121235
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5123 original size:96 final size:98
Alignment explanation
Indices: 4959--5156 Score: 337
Period size: 96 Copynumber: 2.0 Consensus size: 98
4949 ATTGTCCTTT
4959 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTGCCATTAAAAACTAGTAG
1 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTGCCATTAAAAACTAGTAG
*
5024 TTTATCGACT-C-CTTTTTTTGTAAGAATTGTA
66 TTTATCGACTACTCTTTTTTTGTAAGAAGTGTA
**
5055 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTGCTGTTAAAAACTAGTAG
1 TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTGCCATTAAAAACTAGTAG
* *
5120 TTTATTGACTACTTTTTTTTTGTAAGAAGTGTA
66 TTTATCGACTACTCTTTTTTTGTAAGAAGTGTA
5153 TAAC
1 TAAC
5157 CTACTCTTAA
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 72 0.76
97 1 0.01
98 22 0.23
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (98 bp):
TAACATAAAAAGATTACTGCTACGACTGTTAGTCACCATAGTTTTTTGCCATTAAAAACTAGTAG
TTTATCGACTACTCTTTTTTTGTAAGAAGTGTA
Found at i:7675 original size:17 final size:17
Alignment explanation
Indices: 7653--7692 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
7643 CTCTTTTCGA
7653 TTTCAAGAATTTCATTC
1 TTTCAAGAATTTCATTC
**
7670 TTTCAATCATTTCATTC
1 TTTCAAGAATTTCATTC
7687 TTTCAA
1 TTTCAA
7693 TCATTTCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.28, C:0.20, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTCAAGAATTTCATTC
Found at i:7693 original size:17 final size:17
Alignment explanation
Indices: 7661--7699 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
7651 GATTTCAAGA
7661 ATTTCATTCTTTCAATC
1 ATTTCATTCTTTCAATC
7678 ATTTCATTCTTTCAATC
1 ATTTCATTCTTTCAATC
7695 ATTTC
1 ATTTC
7700 TAGTCATTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTCATTCTTTCAATC
Found at i:12572 original size:2 final size:2
Alignment explanation
Indices: 12565--12593 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
12555 TTAATACCAT
12565 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12594 ATTGGAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18741 original size:23 final size:23
Alignment explanation
Indices: 18715--18794 Score: 151
Period size: 23 Copynumber: 3.5 Consensus size: 23
18705 ATTTTCATTT
18715 GTTAAAGCCAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
18738 GTTAAAGCCAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
*
18761 GTTAAAGCTAATGAGATTGGAGC
1 GTTAAAGCCAATGAGATTGGAGC
18784 GTTAAAGCCAA
1 GTTAAAGCCAA
18795 CACCTTTCAT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.23
Consensus pattern (23 bp):
GTTAAAGCCAATGAGATTGGAGC
Found at i:19942 original size:24 final size:24
Alignment explanation
Indices: 19900--19964 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
19890 ACGTTCATGA
*
19900 ATGTTCGTTCAT-TTATGTTC-ATTT
1 ATGTTCGTTTATGTT-TGTTCGA-TT
*
19924 ATTTTCGTTTATGTTTGTTCGATT
1 ATGTTCGTTTATGTTTGTTCGATT
19948 ATGTTCGTTTATGTTTG
1 ATGTTCGTTTATGTTTG
19965 AACAGATGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 33 0.92
25 3 0.08
ACGTcount: A:0.14, C:0.09, G:0.17, T:0.60
Consensus pattern (24 bp):
ATGTTCGTTTATGTTTGTTCGATT
Found at i:29658 original size:3 final size:3
Alignment explanation
Indices: 29650--29782 Score: 187
Period size: 3 Copynumber: 44.7 Consensus size: 3
29640 TTTTTATCCA
* * *
29650 TAT TAT TAT TAT TAT TAA TAA TAT TAT TAT TAT CA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
29697 TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
29745 TAT TAT TAT TAT TAT TAT TAT TTT TTT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
29783 AATATATTAA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
2 1 0.01
3 116 0.99
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:42598 original size:10 final size:10
Alignment explanation
Indices: 42583--42621 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
42573 ATGCTTGAAG
42583 AAAAGAAAGA
1 AAAAGAAAGA
42593 AAAAGAAAGA
1 AAAAGAAAGA
*
42603 AAAAAAATAGA
1 AAAAGAA-AGA
42614 AAAAGAAA
1 AAAAGAAA
42622 AAAGGGGTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAGAAAGA
Found at i:42600 original size:15 final size:15
Alignment explanation
Indices: 42580--42624 Score: 56
Period size: 14 Copynumber: 2.9 Consensus size: 15
42570 ATTATGCTTG
*
42580 AAGAAAAGAAAGAAA
1 AAGAAAAGAAAAAAA
42595 AAG-AAAGAAAAAAA
1 AAGAAAAGAAAAAAA
42609 ATAGAAAAAGAAAAAA
1 A-AG-AAAAGAAAAAA
42625 GGGGTCAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 11 0.42
15 5 0.19
17 10 0.38
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAGAAAAGAAAAAAA
Found at i:43635 original size:52 final size:52
Alignment explanation
Indices: 43575--43677 Score: 188
Period size: 52 Copynumber: 2.0 Consensus size: 52
43565 ATGGAAAAGC
* *
43575 ATCAGAACATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTG
1 ATCAGAACATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTTG
43627 ATCAGAACATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTT
1 ATCAGAACATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTT
43678 TGGCAGAACC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (52 bp):
ATCAGAACATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTTG
Found at i:43820 original size:52 final size:52
Alignment explanation
Indices: 43718--43821 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
43708 GAATTTGCCA
* * *
43718 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAAC
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTTGAGCAGAAC
43770 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTTTG-GCAGAAC
1 ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGG-TTGAGCAGAAC
43822 CAATCATTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 45 0.94
53 3 0.06
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTATTCTTTGAGTTATCGGATCTGGTTGAGCAGAAC
Found at i:43825 original size:135 final size:135
Alignment explanation
Indices: 43583--43956 Score: 671
Period size: 135 Copynumber: 2.8 Consensus size: 135
43573 GCATCAGAAC
43583 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAACATAGCATCTTCTG
43648 GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTAAATTTAGAAGATGAATT
66 GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTAAATTTAGAAGATGAATT
43713 TGCCA
131 TGCCA
43718 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAACATAGCATCTTCTG
* *
43783 GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAATT
66 GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTAAATTTAGAAGATGAATT
*
43848 TGTCA
131 TGCCA
43853 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAACATAGCATCTTCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAACATAGCATCTTCT
* *
43917 GGAAGTGTTCTTTGAGTTATCCGATCTGG-TTGGACAGAAC
65 GGAAGTATTCTTTGAGTTATCGGATCTGGTTTGG-CAGAAC
43957 ATAGCATCTT
Statistics
Matches: 232, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
134 4 0.02
135 226 0.97
136 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (135 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGATCAGAACATAGCATCTTCTG
GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTAAATTTAGAAGATGAATT
TGCCA
Found at i:43911 original size:187 final size:187
Alignment explanation
Indices: 43718--44077 Score: 650
Period size: 187 Copynumber: 1.9 Consensus size: 187
43708 GAATTTGCCA
*
43718 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAACATAGCATCTTCT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGGA-CAGAACATAGCATCTTCT
*
43782 GGAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTGAATTTGGAAGATGAAT
65 GGAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAAT
*
43847 TTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
130 TTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
43905 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGGACAGAACATAGCATCTTCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGGACAGAACATAGCATCTTCTG
* *
43970 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATT
66 GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATT
*
44035 TGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATC
131 TGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
44078 CGAAGAAGTA
Statistics
Matches: 166, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
187 164 0.99
188 2 0.01
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (187 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGGACAGAACATAGCATCTTCTG
GAAGTATTCTTTGAGTTATCGGATCTGGTTTGGCAGAACCAATCATTGAATTTAGAAGATGAATT
TGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:43915 original size:52 final size:52
Alignment explanation
Indices: 43853--44008 Score: 287
Period size: 52 Copynumber: 3.0 Consensus size: 52
43843 GAATTTGTCA
43853 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
43905 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
43957 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
44009 CAATCATTGA
Statistics
Matches: 101, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
52 97 0.96
53 4 0.04
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:44838 original size:119 final size:114
Alignment explanation
Indices: 44633--45307 Score: 1018
Period size: 114 Copynumber: 5.9 Consensus size: 114
44623 TAGCAAAAAT
* * * *
44633 TTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTG
1 TTGAATTCATCAATTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTG
44697 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
44746 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATC-AATTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAA--C-TC
*
44811 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
61 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * *
44865 TTAAATTAATCACTTGATGGATCATTCTTTTCCAGAGAAG-GTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCAATTGATGGATCA-TCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCT
*
44929 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
44979 TTGAATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTC
1 TTGAATTCATC-AATTGATGGATCATCATTTCCAGA-GAAGAGTTCATAATGAGAAGAA--C-TC
*
45044 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGT
61 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
45098 TTAAATTAATCACTTGATGGATCATTCTTTTTCAGAGAAG-GTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCAATTGATGGATCA-TCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCT
45162 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * *
45212 TTGAATTCATCATTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCAATTGATGGATCATCATTTCCAGAG-AAGAGTTCATAATGAGAAGAACTCATCT
*
45275 GAAGAAGGAAGAAAAAGTTCATAATGAGAAGAA
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
45308 CTCATCAAGA
Statistics
Matches: 515, Mismatches: 31, Indels: 32
0.89 0.05 0.06
Matches are distributed among these distances:
112 1 0.00
113 74 0.14
114 170 0.33
115 21 0.04
116 35 0.07
117 34 0.07
118 34 0.07
119 146 0.28
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (114 bp):
TTGAATTCATCAATTGATGGATCATCATTTCCAGAGAAGAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:45064 original size:233 final size:233
Alignment explanation
Indices: 44641--45307 Score: 1195
Period size: 233 Copynumber: 2.9 Consensus size: 233
44631 ATTTGAATCC
* * *
44641 ATCATTTGGTGGATCA-TCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
44705 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATC
44770 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
131 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
44835 ATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTA
196 ATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTA
44873 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
44938 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATC
45003 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
131 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
45068 ATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTA
196 ATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTA
*
45106 ATCACTTGATGGATCATTCTTTTTCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
45171 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATC-ATTTGATGGATC
66 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATC
* * * *
45235 AACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAAAAGTTC
131 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
45295 ATAATGAGAAGAA
196 ATAATGAGAAGAA
45308 CTCATCAAGA
Statistics
Matches: 423, Mismatches: 11, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
227 38 0.09
228 1 0.00
230 18 0.04
231 3 0.01
232 34 0.08
233 329 0.78
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (233 bp):
ATCACTTGATGGATCATTCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTGAATTCATCAAATTGATGGATC
ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAATTTGTTCAACCTTTTGTTTAAATTA
Found at i:45563 original size:3 final size:3
Alignment explanation
Indices: 45555--45684 Score: 190
Period size: 3 Copynumber: 43.7 Consensus size: 3
45545 TTTTTATCCA
* *
45555 TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
45602 TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
45650 TAT TAT TAT TAT TAT TAT TTT TTT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
45685 AATATATTAA
Statistics
Matches: 114, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
2 1 0.01
3 113 0.99
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:47974 original size:8 final size:8
Alignment explanation
Indices: 47961--47985 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
47951 CCGCAGCTAG
47961 TGTTGTAA
1 TGTTGTAA
47969 TGTTGTAA
1 TGTTGTAA
47977 TGTTGTAA
1 TGTTGTAA
47985 T
1 T
47986 ATTGAGGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (8 bp):
TGTTGTAA
Found at i:49315 original size:16 final size:16
Alignment explanation
Indices: 49296--49326 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49286 TTATTAGCAT
49296 ATAAATTATAATAAAA
1 ATAAATTATAATAAAA
*
49312 ATAAGTTATAATAAA
1 ATAAATTATAATAAA
49327 TCATAGTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAAATTATAATAAAA
Found at i:49547 original size:2 final size:2
Alignment explanation
Indices: 49540--49619 Score: 82
Period size: 2 Copynumber: 42.0 Consensus size: 2
49530 TCATTTGTGT
49540 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA GTGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -T-A
* *
49583 TA TA TA T- TA -A TA T- TA T- TA T- TA TA AA AA 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
49620 AGCTGAAATT
Statistics
Matches: 68, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
1 6 0.09
2 59 0.87
3 2 0.03
4 1 0.01
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:52577 original size:154 final size:154
Alignment explanation
Indices: 52297--52604 Score: 589
Period size: 154 Copynumber: 2.0 Consensus size: 154
52287 TATTCACTCT
52297 TTAATACCAACAATTATTGTCCATAGATCATCTTCAGAATCATCGCTGAATAGATCTTAAGAAGA
1 TTAATACCAACAATTATTGTCCATAGATCATCTTCAGAATCATCGCTGAATAGATCTTAAGAAGA
*
52362 TGAACAAATATTCTGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
66 TGAACAAATATTCCGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
52427 TACTTAATTCGTGGTTCATTACCC
131 TACTTAATTCGTGGTTCATTACCC
* *
52451 TTAATACCAACAATTCTTGTCCATAGATCATCTTCAGAATCATTGCTGAATAGATCTTAAGAAGA
1 TTAATACCAACAATTATTGTCCATAGATCATCTTCAGAATCATCGCTGAATAGATCTTAAGAAGA
52516 TGAACAAATATTCCGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
66 TGAACAAATATTCCGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
52581 TACTTAATTCGTGGTTCATTACCC
131 TACTTAATTCGTGGTTCATTACCC
52605 ATAGGGATAA
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
154 151 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (154 bp):
TTAATACCAACAATTATTGTCCATAGATCATCTTCAGAATCATCGCTGAATAGATCTTAAGAAGA
TGAACAAATATTCCGATGGTCTTTATTTCATTTCCACATTTCAACAATATCAGGAATTGTCCATG
TACTTAATTCGTGGTTCATTACCC
Found at i:54639 original size:17 final size:18
Alignment explanation
Indices: 54617--54651 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
54607 CATGTACATA
54617 TGTGAGAAC-TTAAGGTT
1 TGTGAGAACATTAAGGTT
*
54634 TGTGAGTACATTAAGGTT
1 TGTGAGAACATTAAGGTT
54652 GTGCACTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.37
Consensus pattern (18 bp):
TGTGAGAACATTAAGGTT
Found at i:54833 original size:32 final size:32
Alignment explanation
Indices: 54730--54865 Score: 100
Period size: 31 Copynumber: 4.3 Consensus size: 32
54720 ACCTCGACAA
* * * *
54730 CTGTCCATAGGTCCC-GAAGAACCTAGGTAAAT
1 CTGTCCATATGTCCCAAAAG-ACATAGGTAATT
* ** *
54762 -TGTCCATATGTTCC-TTAGAACATAGGT-ATA
1 CTGTCCATATGTCCCAAAAG-ACATAGGTAATT
*
54792 CTGTCCATATGTCTCAAAAGACATAGGTAATT
1 CTGTCCATATGTCCCAAAAGACATAGGTAATT
* * *
54824 CTGTCCATATTTCCCGAAAGACATATGTAATT
1 CTGTCCATATGTCCCAAAAGACATAGGTAATT
* *
54856 TTGTTCATAT
1 CTGTCCATAT
54866 ATTCTGTAGA
Statistics
Matches: 83, Mismatches: 18, Indels: 6
0.78 0.17 0.06
Matches are distributed among these distances:
30 1 0.01
31 42 0.51
32 40 0.48
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (32 bp):
CTGTCCATATGTCCCAAAAGACATAGGTAATT
Found at i:55423 original size:16 final size:17
Alignment explanation
Indices: 55402--55446 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
55392 CATATCAATA
55402 ACACATATACTCAT-GC
1 ACACATATACTCATAGC
*
55418 ACACATATAAATCATAGC
1 ACACATAT-ACTCATAGC
*
55436 AAACATATACT
1 ACACATATACT
55447 TCTATGAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 8 0.33
17 7 0.29
18 9 0.38
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (17 bp):
ACACATATACTCATAGC
Found at i:61654 original size:22 final size:23
Alignment explanation
Indices: 61613--61656 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
61603 TTTAAATTTT
*
61613 AAATATAAAAATATTCAAAAATC
1 AAATATAAAAATACTCAAAAATC
*
61636 AAATATAAAAGTACT-AAAAAT
1 AAATATAAAAATACTCAAAAAT
61657 AAAAGTCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.25
Consensus pattern (23 bp):
AAATATAAAAATACTCAAAAATC
Found at i:61759 original size:21 final size:21
Alignment explanation
Indices: 61717--61765 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
61707 TATCGAAAAA
*
61717 ATAAAATATATATCATAGATT
1 ATAAAATATATATCATAAATT
*
61738 ATAAAATATA-ACTTATAAATT
1 ATAAAATATATA-TCATAAATT
61759 ATTAAAA
1 A-TAAAA
61766 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (21 bp):
ATAAAATATATATCATAAATT
Found at i:67114 original size:5 final size:6
Alignment explanation
Indices: 67092--67133 Score: 66
Period size: 6 Copynumber: 6.7 Consensus size: 6
67082 TCGATAAAAT
67092 TTTTATA TTTTTA TTTTTA TTTTTA TTTTTA CTTTTTA TTTT
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTTTA -TTTTTA TTTT
67134 GTAGGTTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 24 0.71
7 10 0.29
ACGTcount: A:0.17, C:0.02, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTA
Found at i:69388 original size:21 final size:21
Alignment explanation
Indices: 69362--69414 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
69352 ATTCTGACTA
69362 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* *
69383 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
69404 TCGCAATGCGA
1 TCGCATTGCGA
69415 ATACGTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.26, G:0.17, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:69428 original size:41 final size:41
Alignment explanation
Indices: 69383--69478 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
69373 TTTCCCAAAT
* * *
69383 TCGCATTGCGATTTTCCTAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTTTCCAAAATCGCAATGCGAATACGTAAA
* * ** *
69424 TCGCAACGCGAATTTGGAAAATCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTTTCCAAAATCGCAATGCGAATACGTAAA
69465 TCGCAATGCGATTT
1 TCGCAATGCGATTT
69479 ACATAGCGCC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (41 bp):
TCGCAATGCGATTTTCCAAAATCGCAATGCGAATACGTAAA
Found at i:69476 original size:20 final size:20
Alignment explanation
Indices: 69404--69477 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
69394 TTTTCCTAAT
*
69404 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTACGTAAA
* ** *
69424 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCG-ATTACGTAAA
69445 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGATTACGTAAA
69465 TCGCAATGCGATT
1 TCGCAATGCGATT
69478 TACATAGCGC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGATTACGTAAA
Found at i:73148 original size:20 final size:20
Alignment explanation
Indices: 73123--73171 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
73113 GCGATTCTGT
73123 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
73143 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
73163 TGTTGCGAT
1 CGTTGCGAT
73172 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:73177 original size:20 final size:20
Alignment explanation
Indices: 73139--73193 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
73129 GATAGTCAAA
* **
73139 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
73159 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
73179 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
73194 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:73201 original size:20 final size:20
Alignment explanation
Indices: 73158--73201 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
73148 CGATAGTCAT
** *
73158 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
73178 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
73198 TTTC
1 TTTC
73202 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:75139 original size:34 final size:38
Alignment explanation
Indices: 75070--75200 Score: 144
Period size: 34 Copynumber: 3.4 Consensus size: 38
75060 AGAATAGTTT
* *
75070 ACTATCGCAATGTGAAAATGACTATCGCAACGCGAAAATG
1 ACTATCGCAA-GCGAAAATGAC-ATCGCAATGCGAAAATG
*
75110 ACTATCGCAA-CG-AGA-GA-ATCGCAATGCGAAAATG
1 ACTATCGCAAGCGAAAATGACATCGCAATGCGAAAATG
*
75144 ACTATCGTAATGCGAAAATGACTATCGCAATGCGAAAAATG
1 ACTATCGCAA-GCGAAAATGAC-ATCGCAATGCG-AAAATG
75185 ACTATCGCAATGCGAA
1 ACTATCGCAA-GCGAA
75201 TTTGACTATA
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
34 25 0.32
36 4 0.05
37 4 0.05
38 3 0.04
40 21 0.27
41 21 0.27
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (38 bp):
ACTATCGCAAGCGAAAATGACATCGCAATGCGAAAATG
Found at i:75209 original size:20 final size:20
Alignment explanation
Indices: 75070--75200 Score: 175
Period size: 20 Copynumber: 6.8 Consensus size: 20
75060 AGAATAGTTT
*
75070 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
*
75090 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
75110 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
75126 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
75144 ACTATCGTAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
75164 ACTATCGCAATGCGAAAAATG
1 ACTATCGCAATGCG-AAAATG
75185 ACTATCGCAATGCGAA
1 ACTATCGCAATGCGAA
75201 TTTGACTATA
Statistics
Matches: 98, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
14 7 0.07
16 4 0.04
17 4 0.04
18 4 0.04
20 59 0.60
21 20 0.20
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:75286 original size:20 final size:20
Alignment explanation
Indices: 75261--75376 Score: 111
Period size: 20 Copynumber: 6.2 Consensus size: 20
75251 GATTCTCTCG
**
75261 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
75281 TTGCGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
*
75301 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
**
75321 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
75340 TTTCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
75354 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
75374 TTG
1 TTG
75377 TGATTTTAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
17 2 0.03
18 4 0.05
19 12 0.15
20 48 0.62
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:77554 original size:34 final size:33
Alignment explanation
Indices: 77466--77561 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
77456 AAAACAGACT
** *
77466 ATCGCAATGCGGAAATGACTATCGCAACAAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
77500 ATCACAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
77533 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
77562 CGAAACTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:77592 original size:19 final size:19
Alignment explanation
Indices: 77570--77661 Score: 175
Period size: 19 Copynumber: 4.8 Consensus size: 19
77560 CGCGAAACTA
*
77570 ATTTCGCATTACGATTTTC
1 ATTTCGCATTGCGATTTTC
77589 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
77608 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
77627 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
77646 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
77662 CTCTCATTGC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
19 72 1.00
ACGTcount: A:0.17, C:0.21, G:0.15, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:77596 original size:38 final size:38
Alignment explanation
Indices: 77554--77634 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
77544 AAAATGAAAA
77554 TCGCAACGCGAAACTAATTTCGCATTACGATTTTCATT
1 TCGCAACGCGAAACTAATTTCGCATTACGATTTTCATT
** *** * *
77592 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCAACGCGAAACTAATTTCGCATTACGATTTTCATT
77630 TCGCA
1 TCGCA
77635 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.22, C:0.23, G:0.15, T:0.40
Consensus pattern (38 bp):
TCGCAACGCGAAACTAATTTCGCATTACGATTTTCATT
Found at i:77693 original size:20 final size:20
Alignment explanation
Indices: 77668--77759 Score: 150
Period size: 20 Copynumber: 4.6 Consensus size: 20
77658 GATTCTCTCA
77668 TTGCGATAGTCATTTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
77688 TTGCGATAGTCAATTCCGCG
1 TTGCGATAGTCATTTCCGCG
*
77708 TTGCGATAGTCATTTCCGTG
1 TTGCGATAGTCATTTCCGCG
77728 TTGCGATAGTCATATT-CGCG
1 TTGCGATAGTCAT-TTCCGCG
77748 TTGCGATAGTCA
1 TTGCGATAGTCA
77760 AATGAATGTC
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
20 65 0.97
21 2 0.03
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCATTTCCGCG
Found at i:80198 original size:24 final size:24
Alignment explanation
Indices: 80164--80217 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
80154 TCTAAAAAAT
80164 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
80188 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
80212 ATCAAA
1 ATCAAA
80218 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:81225 original size:20 final size:20
Alignment explanation
Indices: 81079--81225 Score: 206
Period size: 20 Copynumber: 7.3 Consensus size: 20
81069 CAGAATCTCG
81079 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
81099 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
81119 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
81139 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
81159 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** * *
81179 TTGCGATTTTCCAAATTTGCG
1 TTGCGA-TTTACGTATTCGCA
81200 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
81220 TTGCGA
1 TTGCGA
81226 ATTAGGAAAA
Statistics
Matches: 111, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
19 1 0.01
20 96 0.86
21 14 0.13
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:81246 original size:21 final size:21
Alignment explanation
Indices: 81222--81267 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
81212 TATTCGCATT
81222 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
81243 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
81264 GCGA
1 GCGA
81268 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:83155 original size:20 final size:21
Alignment explanation
Indices: 83106--83154 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
83096 GGGTGTATAG
83106 ATACCCCCTGTAAGGGTACCT
1 ATACCCCCTGTAAGGGTACCT
*
83127 ATACCCCCTGTAGGGGTATCC-
1 ATACCCCCTGTAAGGGTA-CCT
83148 ATACCCC
1 ATACCCC
83155 TATGATTGCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.22
Consensus pattern (21 bp):
ATACCCCCTGTAAGGGTACCT
Found at i:83618 original size:34 final size:34
Alignment explanation
Indices: 83560--83624 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
83550 CCTTTTGTAA
*
83560 AGGGAAAGGTTCTAGCTAAGCTCATGTAAAAGCT
1 AGGGAAAGGTTCTAGCTAAGCTCATGAAAAAGCT
* * *
83594 AGGGAAAGGTTCTAGTTTATCTCATGAAAAA
1 AGGGAAAGGTTCTAGCTAAGCTCATGAAAAA
83625 CTATGGAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (34 bp):
AGGGAAAGGTTCTAGCTAAGCTCATGAAAAAGCT
Found at i:86313 original size:18 final size:18
Alignment explanation
Indices: 86290--86346 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 18
86280 TATATTTTCC
*
86290 AACAATTGGTATCTTTTT
1 AACAATTGATATCTTTTT
86308 AACAATTGATATCCTTTTGTT
1 AACAATTGATAT-C-TTT-TT
86329 AACAATTGATATCTTTTT
1 AACAATTGATATCTTTTT
86347 CATTAAACAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 13 0.37
19 4 0.11
20 4 0.11
21 14 0.40
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.49
Consensus pattern (18 bp):
AACAATTGATATCTTTTT
Found at i:103488 original size:17 final size:16
Alignment explanation
Indices: 103460--103496 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
103450 TTGTTTTAAC
103460 ATTT-TGGATGTTTGA
1 ATTTGTGGATGTTTGA
103475 ATTTGTGGATTGTTTGA
1 ATTTGTGGA-TGTTTGA
103492 ATTTG
1 ATTTG
103497 GATGCTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 4 0.20
17 12 0.60
ACGTcount: A:0.19, C:0.00, G:0.27, T:0.54
Consensus pattern (16 bp):
ATTTGTGGATGTTTGA
Found at i:105741 original size:21 final size:21
Alignment explanation
Indices: 105717--105757 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
105707 TTTGGGGAAG
105717 AAAAAATGTTA-ATTTTATTA
1 AAAAAATGTTATATTTTATTA
*
105737 AAAAAATGTTATTTTTTATTA
1 AAAAAATGTTATATTTTATTA
105758 GTTTACCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAAAAATGTTATATTTTATTA
Found at i:115912 original size:35 final size:35
Alignment explanation
Indices: 115819--115914 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
115809 AACACATTCA
* **
115819 TCAATTACATTCTAAACCCCAAAATCCAAAATTCT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
*
115854 TCAATTACATTCTAAACCTCAAATTCCAAAATAAT
1 TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
* **
115889 TCAATTACATGCCCAACCCCAAATTC
1 TCAATTACATTCTAAACCCCAAATTC
115915 ACAATCCAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.42, C:0.29, G:0.01, T:0.28
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCCAAAATAAT
Found at i:116926 original size:35 final size:36
Alignment explanation
Indices: 116859--116939 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
116849 GGGGTTGGTC
* *
116859 ATGTAATTGAAGTATTTTTGGAATTTGAGGTTTATA
1 ATGTAATTGAAGCATTTTTGGAATTTGAGGTTTAGA
116895 ATGTAATTGAAGCA-TTTTGGAATTT-AGGGTTTAGA
1 ATGTAATTGAAGCATTTTTGGAATTTGA-GGTTTAGA
*
116930 CTGTAATTGA
1 ATGTAATTGA
116940 TGATTATGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 1 0.02
35 27 0.66
36 13 0.32
ACGTcount: A:0.31, C:0.02, G:0.23, T:0.43
Consensus pattern (36 bp):
ATGTAATTGAAGCATTTTTGGAATTTGAGGTTTAGA
Done.