Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000387.1 Hibiscus syriacus cultivar Beakdansim tig00000711_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: 78417
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Found at i:94 original size:24 final size:24
Alignment explanation
Indices: 67--120 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
57 ATTATAAGAT
*
67 TAGATTTTATCACATCTCAATCAA
1 TAGATTTTATCACATCTCAATAAA
91 TAGATTTTATCACATCTCAATAAA
1 TAGATTTTATCACATCTCAATAAA
115 TAGATT
1 TAGATT
121 AATGTCAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (24 bp):
TAGATTTTATCACATCTCAATAAA
Found at i:96 original size:29 final size:26
Alignment explanation
Indices: 60--120 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 26
50 GTTTAAGATT
60 ATAAGATTAGATTTTATCACATCTCA
1 ATAAGATTAGATTTTATCACATCTCA
*
86 ATCA-A-TAGATTTTATCACATCTCA
1 ATAAGATTAGATTTTATCACATCTCA
110 ATAA-A-TAGATT
1 ATAAGATTAGATT
121 AATGTCAAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 29 0.88
25 1 0.03
26 3 0.09
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.38
Consensus pattern (26 bp):
ATAAGATTAGATTTTATCACATCTCA
Found at i:4108 original size:20 final size:20
Alignment explanation
Indices: 4083--4149 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
4073 TGACACTTTA
4083 ATTTTATGGTTTGTTTATGG
1 ATTTTATGGTTTGTTTATGG
*
4103 ATTTTATTGTTTTAGATTTA--G
1 ATTTTA-TGGTTT-G-TTTATGG
*
4124 -TATTATGGTTTGTTTATGG
1 ATTTTATGGTTTGTTTATGG
4143 ATTTTAT
1 ATTTTAT
4150 TATTCTAGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
17 4 0.11
18 1 0.03
19 6 0.16
20 15 0.41
21 6 0.16
22 1 0.03
23 4 0.11
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (20 bp):
ATTTTATGGTTTGTTTATGG
Found at i:4175 original size:40 final size:40
Alignment explanation
Indices: 4079--4249 Score: 162
Period size: 40 Copynumber: 4.4 Consensus size: 40
4069 GATTTGACAC
* * *
4079 TTTAATTTTATGGTTTGTTTATGGATTTTATTGTTTTAGA
1 TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAGA
*
4119 TTTAGTATTATGGTTTGTTTATGGATTTTATTATTCTAG-
1 TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAGA
* * ** *
4158 TGTTAATATTGTAGTTTGAATATTGAGA-TTTA--A--C-A-T
1 T-TTAATATTATGGTTTGTTTA-TG-GATTTTATTATTCTAGA
4194 TTTAATATTATGGTTTGTTTATGGATTTT-TTATTCTAGA
1 TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAGA
*
4233 TTTAATATTGTGGTTTG
1 TTTAATATTATGGTTTG
4250 AGTATTGAGA
Statistics
Matches: 105, Mismatches: 15, Indels: 23
0.73 0.10 0.16
Matches are distributed among these distances:
33 2 0.02
34 5 0.05
35 17 0.16
36 2 0.02
37 2 0.02
38 1 0.01
39 18 0.17
40 50 0.48
41 6 0.06
42 2 0.02
ACGTcount: A:0.23, C:0.02, G:0.18, T:0.57
Consensus pattern (40 bp):
TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAGA
Found at i:4281 original size:75 final size:75
Alignment explanation
Indices: 4119--4262 Score: 238
Period size: 74 Copynumber: 1.9 Consensus size: 75
4109 TTGTTTTAGA
*
4119 TTTAGTATTATGGTTTGTTTATGGATTTTATTATTCTAGTGTTAATATTGTAGTTTGAATATTGA
1 TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAGTGTTAATATTGTAGTTTGAATATTGA
4184 GATTTAACAT
66 GATTTAACAT
* *
4194 TTTAATATTATGGTTTGTTTATGGATTTT-TTATTCTAGAT-TTAATATTGTGGTTTGAGTATTG
1 TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAG-TGTTAATATTGTAGTTTGAATATTG
4257 AGATTT
65 AGATTT
4263 GTTTATGGTT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
74 36 0.55
75 29 0.45
ACGTcount: A:0.25, C:0.02, G:0.18, T:0.55
Consensus pattern (75 bp):
TTTAATATTATGGTTTGTTTATGGATTTTATTATTCTAGTGTTAATATTGTAGTTTGAATATTGA
GATTTAACAT
Found at i:12756 original size:75 final size:75
Alignment explanation
Indices: 12628--12841 Score: 242
Period size: 75 Copynumber: 2.9 Consensus size: 75
12618 TTTGGTTTAA
* * *
12628 TATTTTTCTAGACTTAATATTATGGTTTGAGTCTTAAGATTTGACAGTTTAATATTATGATTTTT
1 TATTATTCTAGACTTAATATTATGGTTTGAATCTTAAGATTTGACAGTTTAATATTATGATTTGT
12693 TTATGGATTT
66 TTATGGATTT
* * *
12703 TATTATTCTAGAGTTAATATTATGGTTTGAATCTTGAA-ATTTGACATTTTAATATTGTGATTTG
1 TATTATTCTAGACTTAATATTATGGTTTGAATCTT-AAGATTTGACAGTTTAATATTATGATTTG
12767 TTTATGGATTT
65 TTTATGGATTT
* * * * * * * * *
12778 TACTGTTCTAAACTTAGTATTGTTGTTTGAGTATTAATATTTGAC--TTT-AT-TTATGATTT-T
1 TATTATTCTAGACTTAATATTATGGTTTGAATCTTAAGATTTGACAGTTTAATATTATGATTTGT
12838 TTAT
66 TTAT
12842 ATATATTTAT
Statistics
Matches: 121, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
70 5 0.04
71 8 0.07
72 2 0.02
73 3 0.02
74 2 0.02
75 99 0.82
76 2 0.02
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (75 bp):
TATTATTCTAGACTTAATATTATGGTTTGAATCTTAAGATTTGACAGTTTAATATTATGATTTGT
TTATGGATTT
Found at i:36724 original size:16 final size:15
Alignment explanation
Indices: 36695--36725 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
36685 TTCATTTCAA
36695 AATTTTATAAAATAT
1 AATTTTATAAAATAT
36710 AATTTTATAAAA-AT
1 AATTTTATAAAATAT
36724 AA
1 AA
36726 CTTAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTTATAAAATAT
Found at i:39919 original size:2 final size:2
Alignment explanation
Indices: 39914--39963 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
39904 TTATAACATA
39914 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
39956 AT AT AT AT
1 AT AT AT AT
39964 GGAGAGATAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41668 original size:20 final size:20
Alignment explanation
Indices: 41643--41696 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
41633 TCCTTTGATC
41643 AAAGGATCGATCCCCTTAAG
1 AAAGGATCGATCCCCTTAAG
41663 AAAGGATCGATCCCCTTAAG
1 AAAGGATCGATCCCCTTAAG
41683 AAAGGATCGATCCC
1 AAAGGATCGATCCC
41697 TTGCATTCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAAGGATCGATCCCCTTAAG
Found at i:44056 original size:18 final size:19
Alignment explanation
Indices: 44035--44070 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44025 TCCTTTAGCT
*
44035 GTGCTTGTTCCTC-TGCTC
1 GTGCTTGTCCCTCGTGCTC
44053 GTGCTTGTCCCTCGTGCT
1 GTGCTTGTCCCTCGTGCT
44071 GTTCTGGTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42
Consensus pattern (19 bp):
GTGCTTGTCCCTCGTGCTC
Found at i:45273 original size:10 final size:10
Alignment explanation
Indices: 45248--45282 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
45238 TAAATTTTTT
*
45248 GAATTTCGAA
1 GAATTTCAAA
45258 -AATTTCAAA
1 GAATTTCAAA
45267 GAATTTCAAA
1 GAATTTCAAA
45277 GAATTT
1 GAATTT
45283 TGTGTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (10 bp):
GAATTTCAAA
Found at i:52393 original size:197 final size:197
Alignment explanation
Indices: 52041--52438 Score: 586
Period size: 197 Copynumber: 2.0 Consensus size: 197
52031 CACATTGAAG
* * *
52041 ATTCATAATCTGTCAACAAGCCACCATATTTAATGAAGCAAATTATACCTATTGGAAGAATAAGA
1 ATTCACAATCGGTCAACAAGCCACCATATTTAATGAAGCAAATTATACCTATTAGAAGAAT-A-A
* *
52106 TAATGATGCTCTTCATTCAAGAAAATGATATAGGAGCTTGAAACTCTATAATGCAAGGTCACTCT
64 TAATGATGCTCTTCATTCAAGAAAATGATATAGGAACTAGAAACTCTATAATGCAAGGTCACTCT
* * ** *
52171 ACTCTAACCAATGAGATGGAAGATTGGAGTGAAAAAGAAAAGAAGAAGTTCCAACAAAATGTCAA
129 AATCCAACCAATGAGATAAAAGATTGGAGTGAAAAAGAAAAGAAAAAGTTCCAACAAAATGTCAA
52236 GGCC
194 GGCC
52240 ATTCACAATCGGTCAACAAGCCACCATATTTTAAT-AGAG-AAGATTATACCTATTAGAAGAAT-
1 ATTCACAATCGGTCAACAAGCCACCATA-TTTAATGA-AGCAA-ATTATACCTATTAGAAGAATA
* * * *
52302 ATGATGATGCTCTTCATTCAAGAAAATGATCTAGGAACTAGGAACTCTATAATGCAGGGTCACTC
63 ATAATGATGCTCTTCATTCAAGAAAATGATATAGGAACTAGAAACTCTATAATGCAAGGTCACTC
* *
52367 TAATCCAACCAATGAGATAAAAGATTGGAGTGAAGAAGAAAATAAAAAGTTCCAACAAAATGTCA
128 TAATCCAACCAATGAGATAAAAGATTGGAGTGAAAAAGAAAAGAAAAAGTTCCAACAAAATGTCA
52432 AGGCC
193 AGGCC
52437 AT
1 AT
52439 GCATATTCTA
Statistics
Matches: 180, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
197 124 0.69
199 29 0.16
200 27 0.15
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (197 bp):
ATTCACAATCGGTCAACAAGCCACCATATTTAATGAAGCAAATTATACCTATTAGAAGAATAATA
ATGATGCTCTTCATTCAAGAAAATGATATAGGAACTAGAAACTCTATAATGCAAGGTCACTCTAA
TCCAACCAATGAGATAAAAGATTGGAGTGAAAAAGAAAAGAAAAAGTTCCAACAAAATGTCAAGG
CC
Found at i:55164 original size:23 final size:23
Alignment explanation
Indices: 55133--55242 Score: 113
Period size: 23 Copynumber: 4.9 Consensus size: 23
55123 TGCCTCATAA
*
55133 TTGTCCCGAAGGACCACATAGGT
1 TTGTACCGAAGGACCACATAGGT
55156 TTGTACCGAAGTG-CCACATAGGT
1 TTGTACCGAAG-GACCACATAGGT
*
55179 TTGCACCGAAGTG-CCACATA--T
1 TTGTACCGAAG-GACCACATAGGT
* *
55200 TTGTCCCGAAGGACCACATATGT
1 TTGTACCGAAGGACCACATAGGT
*
55223 TTGCACCGAA-GAGCCACATA
1 TTGTACCGAAGGA-CCACATA
55243 AACCCTCGAC
Statistics
Matches: 76, Mismatches: 6, Indels: 10
0.83 0.07 0.11
Matches are distributed among these distances:
20 1 0.01
21 17 0.22
22 2 0.03
23 55 0.72
24 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
TTGTACCGAAGGACCACATAGGT
Found at i:55203 original size:44 final size:44
Alignment explanation
Indices: 55138--55242 Score: 133
Period size: 44 Copynumber: 2.3 Consensus size: 44
55128 CATAATTGTC
55138 CCGAAGGACCACATAGGTTTGTACCGAAGTG-CCACATAGGTTTGCA
1 CCGAAGG-CCACATA-GTTTGTACCGAAG-GACCACATAGGTTTGCA
* *
55184 CCGAAGTGCCACATA-TTTGTCCCGAAGGACCACATATGTTTGCA
1 CCGAAG-GCCACATAGTTTGTACCGAAGGACCACATAGGTTTGCA
55228 CCGAAGAGCCACATA
1 CCGAAG-GCCACATA
55243 AACCCTCGAC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
43 1 0.02
44 39 0.72
46 13 0.24
47 1 0.02
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.21
Consensus pattern (44 bp):
CCGAAGGCCACATAGTTTGTACCGAAGGACCACATAGGTTTGCA
Found at i:55219 original size:67 final size:67
Alignment explanation
Indices: 55111--55242 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
55101 CAATTCGTAA
* * *
55111 TTTGCACAGAAGTGCCTCATAATTGTCCCGAAGGACCACATAGGTTTGTACCGAAGTGCCACATA
1 TTTGCACAGAAGTGCCACATAATTGTCCCGAAGGACCACATAGGTTTGCACCGAAGAGCCACATA
55176 GG
66 GG
* * *
55178 TTTGCACCGAAGTGCCACATATTTGTCCCGAAGGACCACATATGTTTGCACCGAAGAGCCACATA
1 TTTGCACAGAAGTGCCACATAATTGTCCCGAAGGACCACATAGGTTTGCACCGAAGAGCCACATA
55243 AACCCTCGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.23
Consensus pattern (67 bp):
TTTGCACAGAAGTGCCACATAATTGTCCCGAAGGACCACATAGGTTTGCACCGAAGAGCCACATA
GG
Found at i:55329 original size:13 final size:15
Alignment explanation
Indices: 55301--55332 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
55291 TACTTTGGGC
55301 TATTAATCACATCAT
1 TATTAATCACATCAT
55316 TATT-ATCA-ATCAT
1 TATTAATCACATCAT
55329 TATT
1 TATT
55333 CGAAGTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 4 0.24
15 4 0.24
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAATCACATCAT
Found at i:55907 original size:54 final size:55
Alignment explanation
Indices: 55800--55925 Score: 141
Period size: 54 Copynumber: 2.3 Consensus size: 55
55790 TATACTTTCC
* * * * *
55800 TTCAAGGGTATCAATACCTCCTCATGGTACCGATGTCGATATAGAATTCGATG-T
1 TTCAAGGGTATCGATACCTCCGCAAGGTACCGATCTCAATATAGAATTCGATGTT
* * * *
55854 TTCAAGGGCATCGATACCTCCGCAAGGTACCGATACT-AATATGGTATTTGATGTT
1 TTCAAGGGTATCGATACCTCCGCAAGGTACCGAT-CTCAATATAGAATTCGATGTT
55909 TTC-AGGGTATCGATACC
1 TTCAAGGGTATCGATACC
55926 ATCCTTCAGG
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
54 55 0.92
55 5 0.08
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (55 bp):
TTCAAGGGTATCGATACCTCCGCAAGGTACCGATCTCAATATAGAATTCGATGTT
Found at i:55934 original size:21 final size:20
Alignment explanation
Indices: 55909--55991 Score: 64
Period size: 20 Copynumber: 4.1 Consensus size: 20
55899 ATTTGATGTT
55909 TTCAGGGTATCGATACCATCC
1 TTCA-GGTATCGATACCATCC
* * *
55930 TTCAGGTATAGATACTACCC
1 TTCAGGTATCGATACCATCC
*
55950 TT-ACGTATCGATACC-T-C
1 TTCAGGTATCGATACCATCC
*
55967 TTCAACAGGTATCGATACTATCC
1 TT---CAGGTATCGATACCATCC
55990 TT
1 TT
55992 ACAAAATACT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
17 3 0.06
19 10 0.21
20 15 0.32
21 15 0.32
22 1 0.02
23 3 0.06
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.33
Consensus pattern (20 bp):
TTCAGGTATCGATACCATCC
Found at i:62107 original size:21 final size:21
Alignment explanation
Indices: 62081--62161 Score: 76
Period size: 21 Copynumber: 3.8 Consensus size: 21
62071 GTAATTTGCA
*
62081 CCGAAGTACCACATAATTATC
1 CCGAAGGACCACATAATTATC
* *
62102 TCGAAGGACCACATAGGTT-TGC
1 CCGAAGGACCACATA-ATTAT-C
62124 ACCGAAGTG-CCACATAATTATC
1 -CCGAAG-GACCACATAATTATC
*
62146 CCAAAGGACCACATAA
1 CCGAAGGACCACATAA
62162 ACCCTAGACT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 27 0.56
22 6 0.12
23 13 0.27
24 1 0.02
ACGTcount: A:0.37, C:0.27, G:0.16, T:0.20
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:62128 original size:44 final size:44
Alignment explanation
Indices: 62075--62160 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
62065 CAGCTCGTAA
* *
62075 TTTGCACCGAAGTACCACATAATTATCTCGAAGGACCACATAGG
1 TTTGCACCGAAGTACCACATAATTATCCCAAAGGACCACATAGG
*
62119 TTTGCACCGAAGTGCCACATAATTATCCCAAAGGACCACATA
1 TTTGCACCGAAGTACCACATAATTATCCCAAAGGACCACATA
62161 AACCCTAGAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.22
Consensus pattern (44 bp):
TTTGCACCGAAGTACCACATAATTATCCCAAAGGACCACATAGG
Found at i:62789 original size:54 final size:54
Alignment explanation
Indices: 62731--62849 Score: 175
Period size: 54 Copynumber: 2.2 Consensus size: 54
62721 CAAGACTATC
* *
62731 GATACCTCCTCATGGTACCGATACCGATATAGCATTCAATGTTTCAAGGGTATT
1 GATACCTCCTCAAGGTACCGACACCGATATAGCATTCAATGTTTCAAGGGTATT
* * * *
62785 GATACCTCCTCAAGGTACCGACATCGATCTAGCATTCGATGTTTTAAGGGTATT
1 GATACCTCCTCAAGGTACCGACACCGATATAGCATTCAATGTTTCAAGGGTATT
62839 GATACCATCCT
1 GATACC-TCCT
62850 TCCGGTATCG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
54 54 0.93
55 4 0.07
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (54 bp):
GATACCTCCTCAAGGTACCGACACCGATATAGCATTCAATGTTTCAAGGGTATT
Found at i:62862 original size:20 final size:20
Alignment explanation
Indices: 62833--62886 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
62823 ATGTTTTAAG
*
62833 GGTATTGATACCAT-CCTTCC
1 GGTATCGATACC-TCCCTTCC
*
62853 GGTATCGATACCTCCCTTTC
1 GGTATCGATACCTCCCTTCC
*
62873 AGTATCGATACCTC
1 GGTATCGATACCTC
62887 TTCAACAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.33
Consensus pattern (20 bp):
GGTATCGATACCTCCCTTCC
Found at i:63999 original size:2 final size:2
Alignment explanation
Indices: 63994--64018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
63984 TATATATATA
63994 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
64019 AGTTAGATGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:65621 original size:17 final size:18
Alignment explanation
Indices: 65588--65621 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
65578 TCTTCTGATA
65588 TTTAATCTCCAAGGAATC
1 TTTAATCTCCAAGGAATC
*
65606 TTTAAT-TCCAATGAAT
1 TTTAATCTCCAAGGAAT
65622 ATATTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTAATCTCCAAGGAATC
Found at i:66970 original size:34 final size:34
Alignment explanation
Indices: 66927--66995 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
66917 ATAACTTAGT
66927 TTTAATCTCATTTAAACCTTCTTTTTAGATTCCA
1 TTTAATCTCATTTAAACCTTCTTTTTAGATTCCA
66961 TTTAATCTCATTTAAACCTTCTTTTTAGATTCCA
1 TTTAATCTCATTTAAACCTTCTTTTTAGATTCCA
66995 T
1 T
66996 AATATACAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.26, C:0.20, G:0.03, T:0.51
Consensus pattern (34 bp):
TTTAATCTCATTTAAACCTTCTTTTTAGATTCCA
Found at i:72826 original size:58 final size:59
Alignment explanation
Indices: 72764--72995 Score: 163
Period size: 59 Copynumber: 3.9 Consensus size: 59
72754 GATCATACAC
* * * * *
72764 TTAGTATGCTTCCTCTT-TCATTTTAGCACACGAAGTG-CCTAT-TCGAAAATCCTTACCA
1 TTAGTATGATT-CTCTTACCATTTTAGCACACAAAATGCCCTATAT-GAAAATCCATACCA
* * *
72822 TTAGTATGATTTTGTTACCATTTTAGCACATAAAATGCCCTATATGAAAATCCATACCA
1 TTAGTATGATTCTCTTACCATTTTAGCACACAAAATGCCCTATATGAAAATCCATACCA
* * ** * **
72881 TTAGTATGATT-TCCTTATCC-TTGTAGCACCCTTAGTGCTTTATAT-AGAAATCCATA-CA
1 TTAGTATGATTCT-CTTA-CCATTTTAGCACACAAAATGCCCTATATGA-AAATCCATACCA
* * ** * * *
72939 CTCAGTATGATTCCCTTAAAATTTTAGCACATAAAATGCCCTATCTGGAAATCCATA
1 -TTAGTATGATTCTCTTACCATTTTAGCACACAAAATGCCCTATATGAAAATCCATA
72996 TTTTCAATAT
Statistics
Matches: 133, Mismatches: 31, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
57 3 0.02
58 30 0.23
59 97 0.73
60 3 0.02
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (59 bp):
TTAGTATGATTCTCTTACCATTTTAGCACACAAAATGCCCTATATGAAAATCCATACCA
Found at i:72908 original size:59 final size:58
Alignment explanation
Indices: 72808--72995 Score: 166
Period size: 59 Copynumber: 3.2 Consensus size: 58
72798 GTGCCTATTC
* **
72808 GAAAATCCTTACCATTAGTATGATTTTGTTACCATTTTAGCACATAAAATGCCCTATAT
1 GAAAATCCATACCATTAGTATGATTTCCTTACC-TTTTAGCACATAAAATGCCCTATAT
* * * * **
72867 GAAAATCCATACCATTAGTATGATTTCCTTATCCTTGTAGCACCCT-TAGTGCTTTATAT
1 GAAAATCCATACCATTAGTATGATTTCCTTA-CCTTTTAGCA-CATAAAATGCCCTATAT
* * ** *
72926 -AGAAATCCATA-CACTCAGTATGATTCCCTTAAAATTTTAGCACATAAAATGCCCTATCT
1 GA-AAATCCATACCA-TTAGTATGATTTCCTT-ACCTTTTAGCACATAAAATGCCCTATAT
*
72985 GGAAATCCATA
1 GAAAATCCATA
72996 TTTTCAATAT
Statistics
Matches: 101, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
58 5 0.05
59 91 0.90
60 5 0.05
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.35
Consensus pattern (58 bp):
GAAAATCCATACCATTAGTATGATTTCCTTACCTTTTAGCACATAAAATGCCCTATAT
Found at i:72964 original size:118 final size:117
Alignment explanation
Indices: 72841--73095 Score: 296
Period size: 117 Copynumber: 2.2 Consensus size: 117
72831 TTTTGTTACC
* * *
72841 ATTTTAGCACATAAAATGCCCTATATGAAAATCCATACCATT-AGTATGATTTCCTTATCCTTGT
1 ATTTTAGCACATAAAATGCCCTATATGAAAATCCATA-CATTCAATATGATTTCATTATCATT-T
* * ** *
72905 AGCACCCTTAGTGCTTTATATAGAAATCCATACACTCAGTATGATTCCCTTAAA
64 AGCACACTCAGTGCTCCATATAGAAAACCATACACTCAGTATGATTCCCTTAAA
* * ** *
72959 ATTTTAGCACATAAAATGCCCTATCTGGAAATCCATATTTTCAATATGATTTCATTGTCATTTAG
1 ATTTTAGCACATAAAATGCCCTATATGAAAATCCATACATTCAATATGATTTCATTATCATTTAG
* * * * **
73024 CACACTCAGTGCTCCATATGGAAAACTATACACTCAGTATTATTTCCTTATC
66 CACACTCAGTGCTCCATATAGAAAACCATACACTCAGTATGATTCCCTTAAA
* *
73076 ATTTTAGCACACAAAGTGCC
1 ATTTTAGCACATAAAATGCC
73096 ATTCGGTAAT
Statistics
Matches: 115, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
117 64 0.56
118 51 0.44
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (117 bp):
ATTTTAGCACATAAAATGCCCTATATGAAAATCCATACATTCAATATGATTTCATTATCATTTAG
CACACTCAGTGCTCCATATAGAAAACCATACACTCAGTATGATTCCCTTAAA
Found at i:73532 original size:17 final size:18
Alignment explanation
Indices: 73491--73537 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
73481 TCTTAAGGGG
*
73491 GTGCATCGATACACTAACT
1 GTGCATCGATACACT-ACA
73510 GTGCATCGATACACT-CA
1 GTGCATCGATACACTACA
73527 GTGCATTCGAT
1 GTGCA-TCGAT
73538 GTTTATTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 15 0.58
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (18 bp):
GTGCATCGATACACTACA
Done.