Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001222.1 Hibiscus syriacus cultivar Beakdansim tig00002411_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: 78657
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Found at i:8008 original size:128 final size:128
Alignment explanation
Indices: 7833--8106 Score: 363
Period size: 128 Copynumber: 2.1 Consensus size: 128
7823 AATCAAATAC
* * * * **
7833 GTTCCTGTTTTATGTTCGGAGATGCGGCCGTGCTGAAATTCCTAGAGCCTTGTCGTCTTACAGTT
1 GTTCCTGTTTTGTTTTCCGAGATGCGGCCGTGCTGAAATTCCTAGAGCCTTATCGTCCGACAGTT
** * * *
7898 CATGTATATACTATTCTGATGTTTACATTAAACACTCTGTGTATGCTTGTAAGTATC-AACTGT
66 CATGTATATACTATTCCAATATTTACATTAAACACTCTGTGTACGCTTATAAGTATCAAAC-GT
* **
7961 GTTCCTGTTTTGTTTTCCGAGATGTGGCCGTGCTGAAATTGCC-AGAGCCTTATCGTCCGATTGT
1 GTTCCTGTTTTGTTTTCCGAGATGCGGCCGTGCTGAAATT-CCTAGAGCCTTATCGTCCGACAGT
* * *
8025 TCATGTATATGCTATTCCAATATTTACATTAAACACTGTGTGTGCGCTTATAAGTATCAAACGT
65 TCATGTATATACTATTCCAATATTTACATTAAACACTCTGTGTACGCTTATAAGTATCAAACGT
8089 GTTCCTGTTTTGTTTTCC
1 GTTCCTGTTTTGTTTTCC
8107 AAGACGTAGC
Statistics
Matches: 127, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
128 122 0.96
129 5 0.04
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (128 bp):
GTTCCTGTTTTGTTTTCCGAGATGCGGCCGTGCTGAAATTCCTAGAGCCTTATCGTCCGACAGTT
CATGTATATACTATTCCAATATTTACATTAAACACTCTGTGTACGCTTATAAGTATCAAACGT
Found at i:9995 original size:18 final size:17
Alignment explanation
Indices: 9956--9989 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
9946 TAATTTTTTA
9956 AAAATAAATATCATTAGT
1 AAAATAAATA-CATTAGT
9974 AAAATAAATA-ATTAGT
1 AAAATAAATACATTAGT
9990 TGAAAAAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.59, C:0.03, G:0.06, T:0.32
Consensus pattern (17 bp):
AAAATAAATACATTAGT
Found at i:10971 original size:2 final size:2
Alignment explanation
Indices: 10964--10996 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
10954 AATCAAACTC
10964 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 A
10997 ACCTAAACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:14004 original size:50 final size:50
Alignment explanation
Indices: 13890--14009 Score: 152
Period size: 51 Copynumber: 2.4 Consensus size: 50
13880 AGTAGTGCGC
* ** * *
13890 CCCCTACACCGCGCTATACGATGATTTGGTGCCACGTGGGGTATAGCGTG
1 CCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTATAGCGGG
*
13940 CTCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACGT-GGGTATAGCGCGG
1 C-CCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTATAGCG-GG
*
13991 CCCCTGCAACGCGCTATAC
1 CCCCTGCACCGCGCTATAC
14010 ATGTATATCT
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
50 28 0.46
51 33 0.54
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.20
Consensus pattern (50 bp):
CCCCTGCACCGCGCTATACGATGAGCTGGCGCCACGTGGGGTATAGCGGG
Found at i:14149 original size:20 final size:19
Alignment explanation
Indices: 14119--14156 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
14109 CTTTTATCAC
*
14119 AATTTTCTCAAATTCTCTA
1 AATTTTCTCAAATACTCTA
14138 AATTTCTCTCAAATACTCT
1 AATTT-TCTCAAATACTCT
14157 CTTTTTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTTTCTCAAATACTCTA
Found at i:14211 original size:17 final size:16
Alignment explanation
Indices: 14169--14214 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 16
14159 TTTTAAGGTA
14169 TATTTA-TAATATTTT
1 TATTTATTAATATTTT
*
14184 TA-CTATT-ATATTTT
1 TATTTATTAATATTTT
14198 TAATTTATTAATATTTT
1 T-ATTTATTAATATTTT
14215 ACTAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 10 0.40
15 4 0.16
16 4 0.16
17 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTATTAATATTTT
Found at i:16235 original size:3 final size:3
Alignment explanation
Indices: 16227--16269 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
16217 ACTTGCGCAA
* *
16227 GAC GAC GAC GAC GAC GAC GAC GAC GAT GAC GAC GAC GAT GAC G
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC G
16270 GTGATGATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.28, G:0.35, T:0.05
Consensus pattern (3 bp):
GAC
Found at i:20149 original size:51 final size:50
Alignment explanation
Indices: 20031--20154 Score: 169
Period size: 50 Copynumber: 2.5 Consensus size: 50
20021 TTATACAAAA
20031 CGCGGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGT
1 CGCGGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGT
* ** * *
20081 CGCGGTACATGCCCCGCGTTATATAAAATTATGTCGGGAGTAAAGGTATAG-
1 CGCGGTACCTGATCCGCGCTATATAAAATTATGTC-AGAGTAAAGGTAT-GT
*
20132 CGCGGTTCCTGATCCGCGCTATA
1 CGCGGTACCTGATCCGCGCTATA
20155 CCCCTACGTG
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 31 0.50
51 30 0.48
52 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.27
Consensus pattern (50 bp):
CGCGGTACCTGATCCGCGCTATATAAAATTATGTCAGAGTAAAGGTATGT
Found at i:20244 original size:50 final size:51
Alignment explanation
Indices: 20166--20284 Score: 143
Period size: 51 Copynumber: 2.4 Consensus size: 51
20156 CCCTACGTGG
* **
20166 CGTATAGCGCGCTGCAGGGGCCGCGCTATACC-CACGTGGCGCCAGCTCAC
1 CGTATAGCGCGGTGCAGGGGCCGCGCTATACCACACGTGGCGCCAAATCAC
* * * * *
20216 CGTATAGCGCGGTTCAGAGGG-CGGGCTATACCACTCGTGGCGTCAAATCAT
1 CGTATAGCGCGGTGCAG-GGGCCGCGCTATACCACACGTGGCGCCAAATCAC
20267 CGTATAGCGCGGTGCAGG
1 CGTATAGCGCGGTGCAGG
20285 AGGCGAGCTT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
50 26 0.45
51 32 0.55
ACGTcount: A:0.18, C:0.30, G:0.34, T:0.18
Consensus pattern (51 bp):
CGTATAGCGCGGTGCAGGGGCCGCGCTATACCACACGTGGCGCCAAATCAC
Found at i:25756 original size:23 final size:23
Alignment explanation
Indices: 25729--25859 Score: 113
Period size: 23 Copynumber: 5.7 Consensus size: 23
25719 TAATTTGTCT
* * *
25729 TCGAGCTTGAATTGAGTTTAAAA
1 TCGAGCTTAAATCGAGCTTAAAA
* *
25752 TCGAGCTCAAAATCGAGCTCAAAA
1 TCGAGCT-TAAATCGAGCTTAAAA
25776 TCGAGCTTAAATCGAGCTT-AAA
1 TCGAGCTTAAATCGAGCTTAAAA
* *
25798 TCGAGCTCAAAATCGAGCTT-GAA
1 TCGAGCT-TAAATCGAGCTTAAAA
* *
25821 TCGAGTTTAAAATCGAGCTCAAAA
1 TCGAGCTT-AAATCGAGCTTAAAA
* * *
25845 TTGAGTTTCAATCGA
1 TCGAGCTTAAATCGA
25860 TTTCGAGTCT
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
22 10 0.11
23 52 0.58
24 27 0.30
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.27
Consensus pattern (23 bp):
TCGAGCTTAAATCGAGCTTAAAA
Found at i:25765 original size:12 final size:12
Alignment explanation
Indices: 25748--25845 Score: 121
Period size: 12 Copynumber: 8.4 Consensus size: 12
25738 AATTGAGTTT
25748 AAAATCGAGCTC
1 AAAATCGAGCTC
25760 AAAATCGAGCTC
1 AAAATCGAGCTC
25772 AAAATCGAGCT-
1 AAAATCGAGCTC
*
25783 TAAATCGAGCT-
1 AAAATCGAGCTC
*
25794 TAAATCGAGCTC
1 AAAATCGAGCTC
25806 AAAATCGAGCT-
1 AAAATCGAGCTC
** * *
25817 TGAATCGAGTTT
1 AAAATCGAGCTC
25829 AAAATCGAGCTC
1 AAAATCGAGCTC
25841 AAAAT
1 AAAAT
25846 TGAGTTTCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
11 29 0.39
12 46 0.61
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.22
Consensus pattern (12 bp):
AAAATCGAGCTC
Found at i:25789 original size:11 final size:11
Alignment explanation
Indices: 25729--25839 Score: 105
Period size: 12 Copynumber: 9.6 Consensus size: 11
25719 TAATTTGTCT
*
25729 TCGAGCTTGAA
1 TCGAGCTTAAA
* *
25740 TTGAGTTTAAAA
1 TCGAGCTT-AAA
*
25752 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
25764 TCGAGCTCAAAA
1 TCGAGCT-TAAA
25776 TCGAGCTTAAA
1 TCGAGCTTAAA
25787 TCGAGCTTAAA
1 TCGAGCTTAAA
*
25798 TCGAGCTCAAAA
1 TCGAGCT-TAAA
*
25810 TCGAGCTTGAA
1 TCGAGCTTAAA
*
25821 TCGAGTTTAAAA
1 TCGAGCTT-AAA
25833 TCGAGCT
1 TCGAGCT
25840 CAAAATTGAG
Statistics
Matches: 83, Mismatches: 13, Indels: 7
0.81 0.13 0.07
Matches are distributed among these distances:
11 36 0.43
12 47 0.57
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (11 bp):
TCGAGCTTAAA
Found at i:25804 original size:34 final size:34
Alignment explanation
Indices: 25749--25859 Score: 150
Period size: 35 Copynumber: 3.2 Consensus size: 34
25739 ATTGAGTTTA
25749 AAATCGAGCTCAAAATCGAGCTCAAAATCGAGCTT
1 AAATCGAGCT-AAAATCGAGCTCAAAATCGAGCTT
*
25784 AAATCGAGCTTAAATCGAGCTCAAAATCGAGCTT
1 AAATCGAGCTAAAATCGAGCTCAAAATCGAGCTT
* * * *
25818 GAATCGAGTTTAAAATCGAGCTCAAAATTGAGTTT
1 AAATCGAG-CTAAAATCGAGCTCAAAATCGAGCTT
*
25853 CAATCGA
1 AAATCGA
25860 TTTCGAGTCT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 30 0.44
35 38 0.56
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (34 bp):
AAATCGAGCTAAAATCGAGCTCAAAATCGAGCTT
Found at i:36199 original size:2 final size:2
Alignment explanation
Indices: 36192--36217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36182 GTCCTTCGGG
36192 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
36218 TCTGTGGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36320 original size:164 final size:163
Alignment explanation
Indices: 36045--36343 Score: 553
Period size: 164 Copynumber: 1.8 Consensus size: 163
36035 CCTTCGGGAC
* * *
36045 ATATGTATATTCTTTGGAACATGTGTGAGGTCTTGAAAGACACATACTTGATCCTTAGTATATGT
1 ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCTTAGTATATGT
36110 ATATGATTCTTAAGGAATTCTAAGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATT
66 ATATGATTCTTAAGGAATTCTAAGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATT
36175 CTACGTGGTCCTTCGGGATATATATATATATAT
131 CTACGTGGTCCTTCGGGATATATATATATATAT
36208 ATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACATACTTGATCCTTAGTATATG
1 ATATATATATTCTGTGGAACATGTGTGAAGTCTT-GAAAGACACATACTTGATCCTTAGTATATG
*
36273 TATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
65 TATATGATTCTTAAGGAATTCTAAGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAAT
36338 TCTACG
130 TCTACG
36344 CGGCACTTCG
Statistics
Matches: 131, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
163 31 0.24
164 100 0.76
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (163 bp):
ATATATATATTCTGTGGAACATGTGTGAAGTCTTGAAAGACACATACTTGATCCTTAGTATATGT
ATATGATTCTTAAGGAATTCTAAGTGGTCCTTATGGACATCATTATATGGCACTACGGTGCAATT
CTACGTGGTCCTTCGGGATATATATATATATAT
Found at i:36355 original size:23 final size:23
Alignment explanation
Indices: 36322--36366 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
36312 ATCATTATAT
*
36322 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
36345 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
36367 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:42492 original size:20 final size:20
Alignment explanation
Indices: 42467--42504 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42457 GAATGCTAGA
*
42467 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
42487 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
42505 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:43164 original size:149 final size:150
Alignment explanation
Indices: 42977--43292 Score: 566
Period size: 150 Copynumber: 2.1 Consensus size: 150
42967 GGGTAGAGGG
* *
42977 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGT-AAGGTCTT-GAAAGACAC
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAA-GTCTTGGAAAGACAC
43040 ATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCAT
65 ATACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCAT
43105 TATATGGCACTACGGTGCAAT
130 TATATGGCACTACGGTGCAAT
*
43126 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
43191 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
43256 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
43276 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
43293 TGCAATTATA
Statistics
Matches: 161, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
149 49 0.30
150 112 0.70
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:43293 original size:23 final size:23
Alignment explanation
Indices: 43260--43304 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
43250 ATCATTATAT
*
43260 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
43283 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
43305 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:50164 original size:288 final size:288
Alignment explanation
Indices: 49648--50170 Score: 1046
Period size: 288 Copynumber: 1.8 Consensus size: 288
49638 GCTTGATTAG
49648 GGATGGCAGTGGGTTGGTGCTTGGGTCATTTTCAGAGAAGGTAGGGGGAGGTCCTCCTTTACTCG
1 GGATGGCAGTGGGTTGGTGCTTGGGTCATTTTCAGAGAAGGTAGGGGGAGGTCCTCCTTTACTCG
49713 CTGAGCTTTTGGCTATCAATAGAGGGTTGATTCTTATTGAGGAAGTTGAAGTTGATTTCTGTCCA
66 CTGAGCTTTTGGCTATCAATAGAGGGTTGATTCTTATTGAGGAAGTTGAAGTTGATTTCTGTCCA
49778 AATCAAAGGATCATTTTGGAATGGGACTCTTCTAATGCTCTGAAGTGGATTAATAATCCGAATCT
131 AATCAAAGGATCATTTTGGAATGGGACTCTTCTAATGCTCTGAAGTGGATTAATAATCCGAATCT
49843 TAGTACTACTTTGTTTCAATCCTTGGTAACGGATATAGCTTCTACTGTGGAGAGGAAGGGTATTA
196 TAGTACTACTTTGTTTCAATCCTTGGTAACGGATATAGCTTCTACTGTGGAGAGGAAGGGTATTA
49908 TCACAAGGCTATAATCCTCTAACATTTT
261 TCACAAGGCTATAATCCTCTAACATTTT
49936 GGATGGCAGTGGGTTGGTGCTTGGGTCATTTTCAGAGAAGGTAGGGGGAGGTCCTCCTTTACTCG
1 GGATGGCAGTGGGTTGGTGCTTGGGTCATTTTCAGAGAAGGTAGGGGGAGGTCCTCCTTTACTCG
50001 CTGAGCTTTTGGCTATCAATAGAGGGTTGATTCTTATTGAGGAAGTTGAAGTTGATTTCTGTCCA
66 CTGAGCTTTTGGCTATCAATAGAGGGTTGATTCTTATTGAGGAAGTTGAAGTTGATTTCTGTCCA
50066 AATCAAAGGATCATTTTGGAATGGGACTCTTCTAATGCTCTGAAGTGGATTAATAATCCGAATCT
131 AATCAAAGGATCATTTTGGAATGGGACTCTTCTAATGCTCTGAAGTGGATTAATAATCCGAATCT
50131 TAGTACTACTTTGTTTCAATCCTTGGTAACGGATATAGCT
196 TAGTACTACTTTGTTTCAATCCTTGGTAACGGATATAGCT
50171 AATTGGGAAG
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
288 235 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.34
Consensus pattern (288 bp):
GGATGGCAGTGGGTTGGTGCTTGGGTCATTTTCAGAGAAGGTAGGGGGAGGTCCTCCTTTACTCG
CTGAGCTTTTGGCTATCAATAGAGGGTTGATTCTTATTGAGGAAGTTGAAGTTGATTTCTGTCCA
AATCAAAGGATCATTTTGGAATGGGACTCTTCTAATGCTCTGAAGTGGATTAATAATCCGAATCT
TAGTACTACTTTGTTTCAATCCTTGGTAACGGATATAGCTTCTACTGTGGAGAGGAAGGGTATTA
TCACAAGGCTATAATCCTCTAACATTTT
Found at i:51533 original size:22 final size:22
Alignment explanation
Indices: 51516--51582 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
51506 CTCGTATAAA
51516 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
51538 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
51560 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
51582 T
1 T
51583 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:51843 original size:30 final size:31
Alignment explanation
Indices: 51802--51860 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
51792 TAGACATAGT
*
51802 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
51832 ATTTACATACCTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
51861 GAACTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:51917 original size:29 final size:29
Alignment explanation
Indices: 51875--51946 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
51865 TTTTCTGCAT
**
51875 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
51904 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
51933 ATTCATGTCATGTA
1 ATTCATGTCATGTA
51947 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:52398 original size:67 final size:68
Alignment explanation
Indices: 52249--52401 Score: 220
Period size: 68 Copynumber: 2.2 Consensus size: 68
52239 TTTTTCTCAT
* * *
52249 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT-CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
52314 ATGA
65 ATGA
* * *
52318 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
52381 TTGA
66 -TGA
52385 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
52402 TTGAATGGGT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
66 1 0.01
67 22 0.29
68 42 0.55
69 12 0.16
ACGTcount: A:0.18, C:0.28, G:0.27, T:0.27
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
TGA
Found at i:52418 original size:67 final size:67
Alignment explanation
Indices: 52249--52423 Score: 203
Period size: 68 Copynumber: 2.6 Consensus size: 67
52239 TTTTTCTCAT
* *
52249 GGGGGAATCGGTTCCCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACG
1 GGGGGTATCGGTT--CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACG
52314 ATGA
64 ATGA
* * * *
52318 GGGGGTATCGGTTCCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-A
1 GGGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
52381 TTGA
65 -TGA
* *
52385 GGGGGTATCGGTT-CCCCTTGAATGGGTATCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTG--GGGGTATCGATTCCCCT
52424 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
65 6 0.06
66 1 0.01
67 33 0.35
68 42 0.45
69 12 0.13
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:58485 original size:22 final size:22
Alignment explanation
Indices: 58468--58534 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
58458 CTCGTATAAA
58468 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
58490 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
58512 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
58534 T
1 T
58535 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:58795 original size:30 final size:31
Alignment explanation
Indices: 58754--58812 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
58744 TAGACATAGT
*
58754 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
58784 ATTTACATACCTTTATCACATAGTGCATA
1 ATTTACATACCTTTAACACATAGTGCATA
58813 GAACTTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.36
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:58869 original size:29 final size:29
Alignment explanation
Indices: 58827--58898 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
58817 TTTTCTGCAT
**
58827 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
58856 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
58885 ATTCATGTCATGTA
1 ATTCATGTCATGTA
58899 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:59352 original size:67 final size:68
Alignment explanation
Indices: 59217--59355 Score: 210
Period size: 68 Copynumber: 2.1 Consensus size: 68
59207 ATCGGTTCCC
* *
59217 CCCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCG
1 CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCG
59282 GTT
66 GTT
* * *
59285 CCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-ATTGAGGGGGTATC
1 CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA-TGAGGGGGTATC
59348 GGTT
65 GGTT
59352 CCCC
1 CCCC
59356 TTGAATGGGT
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 1 0.02
67 22 0.34
68 42 0.65
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.27
Consensus pattern (68 bp):
CCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCG
GTT
Found at i:59367 original size:67 final size:67
Alignment explanation
Indices: 59218--59377 Score: 200
Period size: 68 Copynumber: 2.4 Consensus size: 67
59208 TCGGTTCCCC
* *
59218 CCCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCGG
1 CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
59283 TT
66 TT
* * *
59285 CCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTC-ATTGAGGGGGTATC
1 -CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA-TGAGGGGGTATC
59348 GGTT
64 GGTT
* *
59352 -CCCCTTGAATGGGTACCGATTCCCCT
1 CCCCCCTG--GGGGTACCGATTCCCCT
59378 AACCCAGAAA
Statistics
Matches: 82, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
65 6 0.07
66 1 0.01
67 34 0.41
68 41 0.50
ACGTcount: A:0.18, C:0.29, G:0.25, T:0.28
Consensus pattern (67 bp):
CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATGAGGGGGTATCGG
TT
Found at i:66202 original size:14 final size:14
Alignment explanation
Indices: 66183--66215 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
66173 CAAATAGGTG
66183 CTCAGCATTTGCTT
1 CTCAGCATTTGCTT
66197 CTCAGCATTTGCTT
1 CTCAGCATTTGCTT
66211 CTCAG
1 CTCAG
66216 TTACTAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.30, G:0.15, T:0.39
Consensus pattern (14 bp):
CTCAGCATTTGCTT
Found at i:70485 original size:45 final size:43
Alignment explanation
Indices: 70436--70572 Score: 125
Period size: 45 Copynumber: 3.1 Consensus size: 43
70426 TTGTAATGAT
* *
70436 AAAAAATTGTAATTGAAAAAATTAGAGGTCTCAATTATAAAAGTA
1 AAAAAATT-TAATTGAAAAAATTAG-GGCCTTAATTATAAAAGTA
* * *
70481 AAAAAAATAAGATTGAAAAAAATAGGTGCCTTAATTATAAAAGT-
1 AAAAAATTTA-ATTGAAAAAATTAGG-GCCTTAATTATAAAAGTA
* * * *
70525 AAAAAGTACT-ATTGAAAAAATTAGGGGCCTTAGTTATAAAGGTA
1 AAAAAAT-TTAATTGAAAAAATTA-GGGCCTTAATTATAAAAGTA
70569 AAAA
1 AAAA
70573 GTGAGATTAA
Statistics
Matches: 75, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
43 27 0.36
44 13 0.17
45 35 0.47
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.26
Consensus pattern (43 bp):
AAAAAATTTAATTGAAAAAATTAGGGCCTTAATTATAAAAGTA
Found at i:70543 original size:43 final size:42
Alignment explanation
Indices: 70447--70723 Score: 236
Period size: 44 Copynumber: 6.4 Consensus size: 42
70437 AAAAATTGTA
* * * * * *
70447 ATTGAAAAAATTAGAGGTCTCAATTATAAAAGTAAAAAAAATAAG
1 ATTGAAAAAAATAG-GGCCTTAATTATAAAGGT--AAAAAGTGAG
* *
70492 ATTGAAAAAAATAGGTGCCTTAATTATAAAAGTAAAAAGT-ACT
1 ATTGAAAAAAATAGG-GCCTTAATTATAAAGGTAAAAAGTGA-G
* *
70535 ATTGAAAAAATTAGGGGCCTTAGTTATAAAGGTAAAAAGTGAG
1 ATTGAAAAAAATA-GGGCCTTAATTATAAAGGTAAAAAGTGAG
* * * *
70578 ATT-AAAAAAGCTAGGGCCTTTATTATAAAGGTAGAAAGTGAA
1 ATTGAAAAAA-ATAGGGCCTTAATTATAAAGGTAAAAAGTGAG
***
70620 ATT-AAAAAGAATTAGAGATATTAATTATAAAGGTAAAAAGTGAG
1 ATTGAAAAA-AA-TAG-GGCCTTAATTATAAAGGTAAAAAGTGAG
* * *
70664 ATTGAAAAAAATGAGAGACCTTAATTATAAAGGTAAAATGTAAG
1 ATTGAAAAAAAT-AG-GGCCTTAATTATAAAGGTAAAAAGTGAG
*
70708 ATTGAAAAAAGTAGGG
1 ATTGAAAAAAATAGGG
70724 GTCCAATTAT
Statistics
Matches: 195, Mismatches: 27, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
42 41 0.21
43 52 0.27
44 69 0.35
45 33 0.17
ACGTcount: A:0.51, C:0.04, G:0.19, T:0.26
Consensus pattern (42 bp):
ATTGAAAAAAATAGGGCCTTAATTATAAAGGTAAAAAGTGAG
Found at i:70660 original size:44 final size:42
Alignment explanation
Indices: 70511--70893 Score: 202
Period size: 43 Copynumber: 8.9 Consensus size: 42
70501 AATAGGTGCC
* * * * **
70511 TTAATTATAAAAGTAAAAAGT-ACTATTGAAAAAATTAGGGGCC
1 TTAATTATAAAGGTAAAAAGTGA-GATTAAAAAAATTA-GAGAT
* ** * *
70554 TTAGTTATAAAGGTAAAAAGTGAGATTAAAAAAGCTAGGGCCT
1 TTAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAG-AT
* *
70597 TT-ATTATAAAGGTAGAAAGTGAAATTAAAAAGAATTAGAGAT
1 TTAATTATAAAGGTAAAAAGTGAGATTAAAAA-AATTAGAGAT
* *
70639 ATTAATTATAAAGGTAAAAAGTGAGATTGAAAAAAATGAGAGACC
1 -TTAATTATAAAGGTAAAAAGTGAGATT-AAAAAAATTAGAGA-T
* * * * * *
70684 TTAATTATAAAGGTAAAATGTAAGATTGAAAAAAGTAGGGGT
1 TTAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGAT
** * * * * *
70726 CCAATTATAAAGAT-AAATGTGAGATTACAAAAATTAAGGGTT
1 TTAATTATAAAGGTAAAAAGTGAGATTAAAAAAATT-AGAGAT
* * * * *
70768 TTACTTATAAAGATAGAAAA-CGAAATTTAAAAAAATTAGAGACA
1 TTAATTATAAAGGTA-AAAAGTGAGA-TTAAAAAAATTAGAGA-T
* ** * * *
70812 TCAATTATAAATATTAAAAAATAAGATT-AAAAAATTAGAGACA
1 TTAATTATAAA-GGTAAAAAGTGAGATTAAAAAAATTAGAGA-T
* * * * *
70855 TCAATTATGAAGATTAAAAAATAAGATT-AAAAAATTAGA
1 TTAATTATAAAG-GTAAAAAGTGAGATTAAAAAAATTAGA
70894 TAACCTGAAC
Statistics
Matches: 272, Mismatches: 53, Indels: 30
0.77 0.15 0.08
Matches are distributed among these distances:
41 17 0.06
42 57 0.21
43 105 0.39
44 84 0.31
45 9 0.03
ACGTcount: A:0.52, C:0.04, G:0.16, T:0.27
Consensus pattern (42 bp):
TTAATTATAAAGGTAAAAAGTGAGATTAAAAAAATTAGAGAT
Found at i:70778 original size:172 final size:171
Alignment explanation
Indices: 70446--70888 Score: 438
Period size: 172 Copynumber: 2.6 Consensus size: 171
70436 AAAAAATTGT
* * * *
70446 AATTGAAAAAATTAGAGGTCTCAATTATAAAAGTAAAAAAAATAAGATTGAAAAAAATAGGTGCC
1 AATTAAAAAAATTAGAGATATCAATTATAAAAGT-AAAAAAATAAGATTGAAAAAAATAGGTACC
** * * *
70511 TTAATTATAAAAGTAAAAAGTACTATTGAAAAAATTAGGGGCCTTAGTTATAAAGGTAAAAAGTG
65 TTAATTATAAAAGTAAAAAGTAAGATTGAAAAAAGTAGGGGCC-TAATTATAAAGATAAAAAGTG
* **
70576 AGATTAAAAAAGCTAGGGCCTTTATTATAAAGGTAGAAAGTGA
129 AGATTAAAAAAGCTAGGGCCTTTATTATAAAGATAGAAAACGA
* * * *
70619 AATTAAAAAGAATTAGAGATATTAATTATAAAGGT-AAAAAGTGAGATTGAAAAAAATGAGAG-A
1 AATTAAAAA-AATTAGAGATATCAATTATAAAAGTAAAAAAATAAGATTGAAAAAAAT-AG-GTA
* * *
70682 CCTTAATTATAAAGGTAAAATGTAAGATTGAAAAAAGTAGGGGTCC-AATTATAAAGAT-AAATG
63 CCTTAATTATAAAAGTAAAAAGTAAGATTGAAAAAAGTAGGGG-CCTAATTATAAAGATAAAAAG
* *
70745 TGAGATTACAAAAA-TTAAGGG-TTTTACTTATAAAGATAGAAAACGA
127 TGAGATTA-AAAAAGCT-AGGGCCTTTA-TTATAAAGATAGAAAACGA
* * *
70791 AATTTAAAAAAATTAGAGACATCAATTATAAATA-TTAAAAAATAAGATT-AAAAAATTAGAG-A
1 AA-TTAAAAAAATTAGAGATATCAATTATAAA-AGTAAAAAAATAAGATTGAAAAAAATAG-GTA
* * * * *
70853 CATCAATTATGAAGATTAAAAAATAAGATT-AAAAAA
63 CCTTAATTAT-AAAAGTAAAAAGTAAGATTGAAAAAA
70889 TTAGATAACC
Statistics
Matches: 225, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
171 36 0.16
172 99 0.44
173 66 0.29
174 24 0.11
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (171 bp):
AATTAAAAAAATTAGAGATATCAATTATAAAAGTAAAAAAATAAGATTGAAAAAAATAGGTACCT
TAATTATAAAAGTAAAAAGTAAGATTGAAAAAAGTAGGGGCCTAATTATAAAGATAAAAAGTGAG
ATTAAAAAAGCTAGGGCCTTTATTATAAAGATAGAAAACGA
Found at i:70842 original size:13 final size:13
Alignment explanation
Indices: 70824--70894 Score: 61
Period size: 13 Copynumber: 5.2 Consensus size: 13
70814 AATTATAAAT
70824 ATTAAAAAATAAG
1 ATTAAAAAATAAG
70837 ATTAAAAAATTAGAG
1 ATTAAAAAA-TA-AG
* * **
70852 ACATCAATTATGAAG
1 A-TTAAAAAAT-AAG
70867 ATTAAAAAATAAG
1 ATTAAAAAATAAG
*
70880 ATTAAAAAATTAG
1 ATTAAAAAATAAG
70893 AT
1 AT
70895 AACCTGAACA
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
13 26 0.58
14 7 0.16
15 7 0.16
16 5 0.11
ACGTcount: A:0.61, C:0.03, G:0.10, T:0.27
Consensus pattern (13 bp):
ATTAAAAAATAAG
Found at i:78184 original size:20 final size:20
Alignment explanation
Indices: 78159--78198 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
78149 ATTTATCATG
*
78159 CTGTTGATCTAGCTTATCTT
1 CTGTTGATCTAGCTCATCTT
*
78179 CTGTTGATCTTGCTCATCTT
1 CTGTTGATCTAGCTCATCTT
78199 TAAGTCTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.23, G:0.15, T:0.50
Consensus pattern (20 bp):
CTGTTGATCTAGCTCATCTT
Done.