Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006317.1 Hibiscus syriacus cultivar Beakdansim tig00015095_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: 69847
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--94 Score: 154
Period size: 31 Copynumber: 3.0 Consensus size: 31
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
32 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
63 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
94 G
1 G
95 GTCCTTCGGA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 59 0.98
32 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1171 original size:24 final size:22
Alignment explanation
Indices: 1130--1207 Score: 69
Period size: 24 Copynumber: 3.7 Consensus size: 22
1120 GAATGCAATT
1130 AGTGCATCGATG--CA-TAAGG
1 AGTGCATCGATGCACAGTAAGG
1149 AGTGCATCGATGCACATGTTAAGG
1 AGTGCATCGATGCACA-G-TAAGG
*
1173 -GATGCATCGATACACAGT-A-G
1 AG-TGCATCGATGCACAGTAAGG
*
1193 AATGCATCGATGCAC
1 AGTGCATCGATGCAC
1208 TTCAAGGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.24
20 13 0.27
21 3 0.06
22 1 0.02
23 2 0.04
24 18 0.37
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.22
Consensus pattern (22 bp):
AGTGCATCGATGCACAGTAAGG
Found at i:2042 original size:21 final size:21
Alignment explanation
Indices: 2004--2044 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1994 ATATAAGACA
*
2004 AGTTATATGCTAAAGTTATAG
1 AGTTATATGCAAAAGTTATAG
2025 AGTTATATG-AAAAGGTTATA
1 AGTTATATGCAAAA-GTTATA
2045 AGGAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.37
Consensus pattern (21 bp):
AGTTATATGCAAAAGTTATAG
Found at i:2741 original size:18 final size:19
Alignment explanation
Indices: 2697--2746 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
2687 GAGGGATTAT
2697 CAGTGGTCCTTCGGGATAAA
1 CAGTGGTCCTTCGGGA-AAA
*
2717 CAGTGGTCCTTCGGG-ACA
1 CAGTGGTCCTTCGGGAAAA
*
2735 TAGTGGTCCTTC
1 CAGTGGTCCTTC
2747 AGAACAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.46
20 15 0.54
ACGTcount: A:0.18, C:0.24, G:0.30, T:0.28
Consensus pattern (19 bp):
CAGTGGTCCTTCGGGAAAA
Found at i:7507 original size:23 final size:23
Alignment explanation
Indices: 7480--7539 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
7470 GTTGGTTGGA
* *
7480 AACATTAAATGAATATATTTGTT
1 AACATTAAATGAATATATTCGTG
*
7503 AACATTAAACGAATATATTCGTG
1 AACATTAAATGAATATATTCGTG
**
7526 AATGTTAAATGAAT
1 AACATTAAATGAAT
7540 CGAACACAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (23 bp):
AACATTAAATGAATATATTCGTG
Found at i:10075 original size:12 final size:13
Alignment explanation
Indices: 10060--10091 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
10050 TCATAGGTTC
10060 ATTTATTAA-TAT
1 ATTTATTAAGTAT
10072 ATTTA-TAAGTAT
1 ATTTATTAAGTAT
10084 ATTTATTA
1 ATTTATTA
10092 GGTTACCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 3 0.17
12 13 0.72
13 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (13 bp):
ATTTATTAAGTAT
Found at i:11299 original size:21 final size:21
Alignment explanation
Indices: 11257--11299 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
11247 TTTCTGGGTT
* * *
11257 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
11278 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
11299 A
1 A
11300 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:12023 original size:149 final size:149
Alignment explanation
Indices: 11843--12146 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
11833 GGATAGAGGG
11843 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
11908 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTA
11973 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
11992 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
12057 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTA
12122 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
12141 TCTACG
1 TCTACG
12147 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATAGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:18258 original size:21 final size:21
Alignment explanation
Indices: 18216--18258 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
18206 TTTCTGGGTT
* * *
18216 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
18237 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
18258 A
1 A
18259 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:18325 original size:68 final size:68
Alignment explanation
Indices: 18238--18390 Score: 288
Period size: 68 Copynumber: 2.2 Consensus size: 68
18228 ACCCATTCAA
*
18238 GGGGAACCGATACCCCCTCAACGAATATGAATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
18303 GGG
66 GGG
18306 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
18371 GGG
66 GGG
*
18374 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
18391 ATGAGAAAAA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
68 83 1.00
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:19060 original size:149 final size:149
Alignment explanation
Indices: 18869--19172 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
18859 GGGTAGAGGG
18869 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
18934 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
18999 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
19018 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
19083 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTTTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
19148 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
19167 TCTACG
1 TCTACG
19173 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:20709 original size:14 final size:15
Alignment explanation
Indices: 20689--20730 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
20679 TATCATCAGT
*
20689 TAAAATATATTTGTC
1 TAAAATATATTTATC
* *
20704 -AAAATATCTTAATC
1 TAAAATATATTTATC
20718 TAAAATATATTTA
1 TAAAATATATTTA
20731 AATATTTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (15 bp):
TAAAATATATTTATC
Found at i:20831 original size:23 final size:23
Alignment explanation
Indices: 20805--20848 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
20795 TTTAAAAGTA
*
20805 TCTTAACTTAAATTATATTTTAT
1 TCTTAACTTAAAATATATTTTAT
*
20828 TCTTAAGTTAAAATATATTTT
1 TCTTAACTTAAAATATATTTT
20849 GAAGTTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (23 bp):
TCTTAACTTAAAATATATTTTAT
Found at i:20902 original size:31 final size:31
Alignment explanation
Indices: 20865--20939 Score: 93
Period size: 31 Copynumber: 2.4 Consensus size: 31
20855 AAGATGTTTT
20865 AATATATTTTTAAAAATTAAGA-TAATAATCAA
1 AATATATTTTTAAAAATTAA-ATTAATAAT-AA
*
20897 ATATATATTTTT--ATATTAAATTAATAATAA
1 A-ATATATTTTTAAAAATTAAATTAATAATAA
20927 AATATATTTTTAA
1 AATATATTTTTAA
20940 GTGACGATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
29 10 0.26
30 4 0.11
31 13 0.34
32 1 0.03
33 10 0.26
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (31 bp):
AATATATTTTTAAAAATTAAATTAATAATAA
Found at i:20987 original size:15 final size:16
Alignment explanation
Indices: 20961--20990 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
20951 AATAAAATAT
20961 TTAAATATATTTTAAG
1 TTAAATATATTTTAAG
20977 TTAAA-ATATTTTAA
1 TTAAATATATTTTAA
20991 AAATATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATATATTTTAAG
Found at i:21085 original size:29 final size:30
Alignment explanation
Indices: 21039--21113 Score: 109
Period size: 29 Copynumber: 2.6 Consensus size: 30
21029 TATTTTTACA
* *
21039 TTAAAATAACAAT-AAATATATTTAATAAG
1 TTAAAACAAAAATAAAATATATTTAATAAG
*
21068 TTAAGA-AAAAATAAAATATATTTAATAAG
1 TTAAAACAAAAATAAAATATATTTAATAAG
21097 TTAAAACAAAAATAAAA
1 TTAAAACAAAAATAAAA
21114 GTAATTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
28 5 0.12
29 26 0.63
30 10 0.24
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (30 bp):
TTAAAACAAAAATAAAATATATTTAATAAG
Found at i:34583 original size:15 final size:15
Alignment explanation
Indices: 34562--34603 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
34552 CGTCTTGACC
34562 CTCTTTTTCATCATT
1 CTCTTTTTCATCATT
* *
34577 TTCTTTTTCCTCATT
1 CTCTTTTTCATCATT
*
34592 CTCTTTATCATC
1 CTCTTTTTCATC
34604 GCCCTCGGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.60
Consensus pattern (15 bp):
CTCTTTTTCATCATT
Found at i:34828 original size:18 final size:19
Alignment explanation
Indices: 34806--34858 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
34796 CGCCTCTTCT
*
34806 TCTTCTTCGTGTTTGCTTC
1 TCTTCTTCGTGTTTGCTCC
* *
34825 -CTTCTTCCTG-CTGCTCC
1 TCTTCTTCGTGTTTGCTCC
34842 TCTTCTTCGTGTTTGCT
1 TCTTCTTCGTGTTTGCT
34859 AGCTCCTTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 5 0.19
18 18 0.67
19 4 0.15
ACGTcount: A:0.00, C:0.32, G:0.15, T:0.53
Consensus pattern (19 bp):
TCTTCTTCGTGTTTGCTCC
Found at i:45723 original size:53 final size:54
Alignment explanation
Indices: 45610--45715 Score: 160
Period size: 53 Copynumber: 2.0 Consensus size: 54
45600 GAATCAAAAA
* * * *
45610 TATATATATATTATCAATAGTAAACACAAAGTAAATATCTAAAATGAATATATG
1 TATACATATATTATCAATAGAAAACACAAAGTAAATATCCAAAATAAATATATG
*
45664 TATACATAT-TTATCAATAGAAAATACAAAGTAAATATCCAAAATAAATATAT
1 TATACATATATTATCAATAGAAAACACAAAGTAAATATCCAAAATAAATATAT
45716 TTGTACATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 39 0.83
54 8 0.17
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (54 bp):
TATACATATATTATCAATAGAAAACACAAAGTAAATATCCAAAATAAATATATG
Found at i:48519 original size:270 final size:270
Alignment explanation
Indices: 48038--48577 Score: 1026
Period size: 270 Copynumber: 2.0 Consensus size: 270
48028 TGGGGTGCAT
48038 TAATAAACCGTTAGATGTTCAAAGGAAACAGTTGAGAGGGAGAGAGGTTAAAAGCCGCGTGTATG
1 TAATAAACCGTTAGATGTTCAAAGGAAACAGTTGAGAGGGAGAGAGGTTAAAAGCCGCGTGTATG
*
48103 ATTCTTTGCATTGCCAGAAGCAGATGAATGAGGAAGCTAAATCTGTAAAACGTTTGAAGAAAAAG
66 ATTCTTTGCATTGCCAGAAGCAGATGAATGAAGAAGCTAAATCTGTAAAACGTTTGAAGAAAAAG
*
48168 AACAGCAACAAAGACTTGCTGTTGTCCGAGGCTCCTATGTATCGAAAACCAGATGAAAAGGACTT
131 AACAGCAACAAAGACTTGCCGTTGTCCGAGGCTCCTATGTATCGAAAACCAGATGAAAAGGACTT
48233 GGTTGAGAGTCCTTCAGATAGCTTGGAGCAAGCAGTTAGCGAGAATACCAAAATTTCATCTCCCT
196 GGTTGAGAGTCCTTCAGATAGCTTGGAGCAAGCAGTTAGCGAGAATACCAAAATTTCATCTCCCT
*
48298 CTAGGTGTAA
261 CTAGGAGTAA
* * *
48308 TAATAAACCGTTAGATGTTCCAAGGAAGCAGTTGAGAGGGAGAGAGGTTAAAAGCCGCTTGTATG
1 TAATAAACCGTTAGATGTTCAAAGGAAACAGTTGAGAGGGAGAGAGGTTAAAAGCCGCGTGTATG
48373 ATTCTTTGCATTGCCAGAAGCAGATGAATGAAGAAGCTAAATCTGTAAAACGTTTGAAGAAAAAG
66 ATTCTTTGCATTGCCAGAAGCAGATGAATGAAGAAGCTAAATCTGTAAAACGTTTGAAGAAAAAG
48438 AACAGCAACAAAGACTTGCCGTTGTCCGAGGCTCCTATGTATCGAAAACCAGATGAAAAGGACTT
131 AACAGCAACAAAGACTTGCCGTTGTCCGAGGCTCCTATGTATCGAAAACCAGATGAAAAGGACTT
48503 GGTTGAGAGTCCTTCAGATAGCTTGGAGCAAGCAGTTAGCGAGAATACCAAAATTTCATCTCCCT
196 GGTTGAGAGTCCTTCAGATAGCTTGGAGCAAGCAGTTAGCGAGAATACCAAAATTTCATCTCCCT
48568 CTAGGAGTAA
261 CTAGGAGTAA
48578 GATGGCCTCC
Statistics
Matches: 264, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
270 264 1.00
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.24
Consensus pattern (270 bp):
TAATAAACCGTTAGATGTTCAAAGGAAACAGTTGAGAGGGAGAGAGGTTAAAAGCCGCGTGTATG
ATTCTTTGCATTGCCAGAAGCAGATGAATGAAGAAGCTAAATCTGTAAAACGTTTGAAGAAAAAG
AACAGCAACAAAGACTTGCCGTTGTCCGAGGCTCCTATGTATCGAAAACCAGATGAAAAGGACTT
GGTTGAGAGTCCTTCAGATAGCTTGGAGCAAGCAGTTAGCGAGAATACCAAAATTTCATCTCCCT
CTAGGAGTAA
Found at i:55691 original size:15 final size:15
Alignment explanation
Indices: 55667--55696 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
55657 ATTTGTTTCT
*
55667 GCCAGTAATGCTCCA
1 GCCAGAAATGCTCCA
55682 GCCAGAAATGCTCCA
1 GCCAGAAATGCTCCA
55697 AGCTGCATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (15 bp):
GCCAGAAATGCTCCA
Found at i:68189 original size:9 final size:10
Alignment explanation
Indices: 68170--68224 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 10
68160 ATTATAATTA
68170 ATATAAA-AT
1 ATATAAATAT
68179 ATA-AAATAT
1 ATATAAATAT
*
68188 ATATATAATTT
1 ATATA-AATAT
* *
68199 ATATAAAAAA
1 ATATAAATAT
*
68209 ATATATATAT
1 ATATAAATAT
68219 ATATAA
1 ATATAA
68225 TCGAGGCGGG
Statistics
Matches: 35, Mismatches: 8, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
8 3 0.09
9 8 0.23
10 15 0.43
11 9 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATATAAATAT
Found at i:68196 original size:25 final size:23
Alignment explanation
Indices: 68168--68224 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
68158 GTATTATAAT
68168 TAATATAAAATATAAAATATATATA
1 TAATATAAAA-A-AAAATATATATA
*
68193 TAATTTATATAAAAAAATATATATA
1 TAA--TATAAAAAAAAATATATATA
68218 T-ATATAA
1 TAATATAA
68225 TCGAGGCGGG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
22 4 0.14
24 1 0.04
25 16 0.57
26 1 0.04
27 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TAATATAAAAAAAAATATATATA
Found at i:68225 original size:29 final size:29
Alignment explanation
Indices: 68162--68221 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
68152 AGGTTTGTAT
68162 TATAATTAATATAAAATATAAAATATATA
1 TATAATTAATATAAAATATAAAATATATA
* *
68191 TATAATTTATATAAAA-A-AATATATATA
1 TATAATTAATATAAAATATAAAATATATA
68218 TATA
1 TATA
68222 TAATCGAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.45
28 1 0.03
29 15 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
TATAATTAATATAAAATATAAAATATATA
Found at i:69162 original size:34 final size:34
Alignment explanation
Indices: 69113--69190 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
69103 AACACAGTCA
69113 TCAATTACATTTAAACCCCAAATTCCAAAATAAT
1 TCAATTACATTTAAACCCCAAATTCCAAAATAAT
* *
69147 TCAA-TACATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATT-TAAACCCCAAATTCCAAAATAAT
69181 TCAATTACAT
1 TCAATTACAT
69191 GCCCAAACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
33 6 0.15
34 29 0.73
35 5 0.12
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (34 bp):
TCAATTACATTTAAACCCCAAATTCCAAAATAAT
Found at i:69204 original size:35 final size:33
Alignment explanation
Indices: 69129--69206 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 33
69119 ACATTTAAAC
* *
69129 CCCAAATTCCAAAATAATTCAATACATTCTAAA
1 CCCAAATTCCAAAATAATTCAATACATCCCAAA
*
69162 CCTCAAATTCCAAAATACTTCAATTACATGCCCAAA
1 CC-CAAATTCCAAAATAATTCAA-TACAT-CCCAAA
69198 CCCAAATTC
1 CCCAAATTC
69207 ATAATCCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 2 0.05
34 19 0.49
35 12 0.31
36 6 0.15
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (33 bp):
CCCAAATTCCAAAATAATTCAATACATCCCAAA
Done.