Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000205.1 Hibiscus syriacus cultivar Beakdansim tig00000365_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: 60243
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Found at i:6958 original size:74 final size:74
Alignment explanation
Indices: 6837--6991 Score: 238
Period size: 74 Copynumber: 2.1 Consensus size: 74
6827 ATGGGTGCAG
* * * * *
6837 ATGACACGCATTTGCCTGTCATTGAAGCCACCGACGTAAATCTCAGATAACACGCAATTACGTGT
1 ATGACATGCATTTGCCTATCATTAAAGCCACCAACATAAATCTCAGATAACACGCAATTACGTGT
6902 CATAAATCT
66 CATAAATCT
* * *
6911 ATGACATGCATTTGCCTATCATTAAATCCACCAACATAAATCTCAGATGACACGCAATTGCGTGT
1 ATGACATGCATTTGCCTATCATTAAAGCCACCAACATAAATCTCAGATAACACGCAATTACGTGT
6976 CATAAATCT
66 CATAAATCT
6985 ATGACAT
1 ATGACAT
6992 TTATGACACG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.34, C:0.25, G:0.14, T:0.27
Consensus pattern (74 bp):
ATGACATGCATTTGCCTATCATTAAAGCCACCAACATAAATCTCAGATAACACGCAATTACGTGT
CATAAATCT
Found at i:7025 original size:13 final size:14
Alignment explanation
Indices: 6989--7027 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
6979 AAATCTATGA
*
6989 CATTTATGACACGT
1 CATTTATGACGCGT
7003 -ATTTATGACGC-T
1 CATTTATGACGCGT
7015 CATTTATGACGCG
1 CATTTATGACGCG
7028 CGTTGAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 1 0.05
13 21 0.95
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.36
Consensus pattern (14 bp):
CATTTATGACGCGT
Found at i:7192 original size:2 final size:2
Alignment explanation
Indices: 7185--7225 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
7175 TTTCGTAAAT
7185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7226 TGTAGATTGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13711 original size:30 final size:30
Alignment explanation
Indices: 13675--13764 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 30
13665 AAATATATAT
13675 AACTTTTCAAAATTATATTTTTAGTCCCTA
1 AACTTTTCAAAATTATATTTTTAGTCCCTA
* *
13705 AACTTTTTC-AAATTTTATTCTTTAG-CCATA
1 AAC-TTTTCAAAATTATATT-TTTAGTCCCTA
* *
13735 AAC-TTTCAAAACATATATTTTT-GTCACTA
1 AACTTTTCAAAA-TTATATTTTTAGTCCCTA
13764 A
1 A
13765 CAAAAATTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
28 5 0.10
29 10 0.20
30 24 0.49
31 10 0.20
ACGTcount: A:0.34, C:0.17, G:0.03, T:0.46
Consensus pattern (30 bp):
AACTTTTCAAAATTATATTTTTAGTCCCTA
Found at i:23528 original size:8 final size:8
Alignment explanation
Indices: 23515--23550 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
23505 AGATCCTCCC
23515 ATATGTAT
1 ATATGTAT
23523 ATATGTAT
1 ATATGTAT
23531 ATATGTAT
1 ATATGTAT
23539 ATATGTAT
1 ATATGTAT
23547 ATAT
1 ATAT
23551 ATCTTATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:27035 original size:7 final size:7
Alignment explanation
Indices: 27018--27253 Score: 238
Period size: 7 Copynumber: 33.3 Consensus size: 7
27008 AAAAAATAAA
27018 AAGAAATA
1 AAGAAA-A
27026 AA-AAGAA
1 AAGAA-AA
*
27033 AA-AAAG
1 AAGAAAA
*
27039 AAGAAAG
1 AAGAAAA
27046 AAGAAAA
1 AAGAAAA
*
27053 ATGAAAA
1 AAGAAAA
*
27060 ATGAAATA
1 AAGAAA-A
*
27068 ATGAAATA
1 AAGAAA-A
*
27076 ATG-AAA
1 AAGAAAA
27082 AAGAAAA
1 AAGAAAA
27089 AA-AAAGA
1 AAGAAA-A
27096 AA-AAAA
1 AAGAAAA
27102 AGAGAAAAA
1 A-AG-AAAA
27111 AATGAAAA
1 AA-GAAAA
27119 ATGATGAAAA
1 A--A-GAAAA
*
27129 AGGAAAA
1 AAGAAAA
27136 AA-AAAA
1 AAGAAAA
27142 AAGAAAA
1 AAGAAAA
27149 AA-AAGAA
1 AAGAA-AA
27156 AAGAAAA
1 AAGAAAA
27163 AAGAAAA
1 AAGAAAA
27170 AAGAAAA
1 AAGAAAA
27177 AAGAAAA
1 AAGAAAA
27184 AAGAAAA
1 AAGAAAA
27191 AAGAAAA
1 AAGAAAA
27198 AAGAAAA
1 AAGAAAA
27205 AAGAAAA
1 AAGAAAA
27212 AAGAAAA
1 AAGAAAA
27219 AAGAAAA
1 AAGAAAA
27226 AAGAAAA
1 AAGAAAA
27233 AAG-AAA
1 AAGAAAA
27239 AA-AAAA
1 AAGAAAA
27245 AAGAAAA
1 AAGAAAA
27252 AA
1 AA
27254 ATAGATAAAA
Statistics
Matches: 206, Mismatches: 6, Indels: 33
0.84 0.02 0.13
Matches are distributed among these distances:
6 29 0.14
7 140 0.68
8 23 0.11
9 6 0.03
10 8 0.04
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.04
Consensus pattern (7 bp):
AAGAAAA
Found at i:27136 original size:1 final size:1
Alignment explanation
Indices: 27132--27254 Score: 111
Period size: 1 Copynumber: 123.0 Consensus size: 1
27122 ATGAAAAAGG
* * * * * * * *
27132 AAAAAAAAAAAAGAAAAAAAAGAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * * * *
27197 AAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAGAAAAAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
27255 TAGATAAAAG
Statistics
Matches: 92, Mismatches: 30, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 92 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:27263 original size:10 final size:10
Alignment explanation
Indices: 27010--27254 Score: 164
Period size: 10 Copynumber: 23.7 Consensus size: 10
27000 TCGCCTGAAA
27010 AAAATAAAAAG
1 AAAA-AAAAAG
*
27021 AAATAAAAAG
1 AAAAAAAAAG
27031 AAAAAAAGAAG
1 AAAAAAA-AAG
27042 AAAGAAGAAAA-
1 AAA-AA-AAAAG
** *
27053 ATGAAAAATG
1 AAAAAAAAAG
* *
27063 AAATAATGAAAT
1 AAA-AA-AAAAG
**
27075 AATGAAAAAG
1 AAAAAAAAAG
27085 AAAAAAAAAG
1 AAAAAAAAAG
27095 -AAAAAAAAG
1 AAAAAAAAAG
*
27104 AGAAAAAAATG
1 A-AAAAAAAAG
** *
27115 AAAAATGATG
1 AAAAAAAAAG
*
27125 AAAAAGGAAA-
1 AAAAA-AAAAG
27135 AAAAAAAAAG
1 AAAAAAAAAG
27145 -AAAAAAAAG
1 AAAAAAAAAG
27154 AAAAGAAAAAAG
1 -AAA-AAAAAAG
27166 AAAAAAGAAA-
1 AAAAAA-AAAG
27176 AAAGAAAAAAG
1 AAA-AAAAAAG
27187 AAAAAAGAAA-
1 AAAAAA-AAAG
27197 AAAGAAAAAAG
1 AAA-AAAAAAG
27208 AAAAAAGAAA-
1 AAAAAA-AAAG
27218 AAAGAAAAAAG
1 AAA-AAAAAAG
*
27229 AAAAAAGAA-
1 AAAAAAAAAG
27238 AAAAAAAAAG
1 AAAAAAAAAG
27248 AAAAAAA
1 AAAAAAA
27255 TAGATAAAAG
Statistics
Matches: 186, Mismatches: 25, Indels: 47
0.72 0.10 0.18
Matches are distributed among these distances:
9 32 0.17
10 82 0.44
11 55 0.30
12 15 0.08
13 2 0.01
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:28584 original size:37 final size:37
Alignment explanation
Indices: 28538--28610 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
28528 TCGAAACAGG
* *
28538 TCAATCTTAAGCTTTCACGAAAGAGTAGTGAAGCAAT
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAT
*
28575 TCAAACTTAAGCCTTCACGGAAGAGTAGTGAAGCAA
1 TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAA
28611 ACTCATTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (37 bp):
TCAAACTTAAGCCTTCACGAAAGAGTAGTGAAGCAAT
Found at i:28695 original size:55 final size:55
Alignment explanation
Indices: 28627--28870 Score: 219
Period size: 55 Copynumber: 4.4 Consensus size: 55
28617 TTTATGAAGA
***
28627 TCGAGTTCTATACTCTCTGAAGGAATAAAGAGCAGATTTGTTTGT-TGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAAAGAGCAGACCCGTTT-TATGAAGATTGT
* * * *
28682 TTGAGTTCTATACTCTCTGATGGAATAGAGAGCGGACCCGTTTTATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAAAGAGCAGACCCGTTTTATGAAGATTGT
* * ** * * *
28737 TCGAGTTCTATACTCCCTGAACGAATAGGGAACGGACCC-ATTTATTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAAAGAGCAGACCCGTTTTA-TGAAGATTGT
* * ** ***
28792 TCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACATATTTTATGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAAAGAGCAGACCCGTTTTATGAAGATTGT
28847 TCGAG-TCTTATACT-TCCTGAAGGA
1 TCGAGTTC-TATACTCT-CTGAAGGA
28871 GTAGGGAGCG
Statistics
Matches: 163, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
54 7 0.04
55 152 0.93
56 4 0.02
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAAAGAGCAGACCCGTTTTATGAAGATTGT
Found at i:28876 original size:55 final size:55
Alignment explanation
Indices: 28672--28879 Score: 233
Period size: 55 Copynumber: 3.8 Consensus size: 55
28662 ATTTGTTTGT
* * ** * * * *
28672 TGAAGATTGTTTGAGT-TCTATACTCTCTGATGGAATAGAGAGCGGACCCGTTTTA
1 TGAAGATTGTTCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACATTTTA
* * *
28727 TGAAGATTGTTCGAGT-TCTATACTCCCTGAACGAATAGGGAACGGACCCA-TTTA
1 TGAAGATTGTTCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACACATTTTA
*
28781 TTGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACATATTTTA
1 -TGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACATTTTA
* * *
28837 TGAAGATTGTTCGAGTCTTATACTTCCTGAAGGAGTAGGGAGC
1 TGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGC
28880 GGGCTCGTTA
Statistics
Matches: 136, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
54 4 0.03
55 127 0.93
56 5 0.04
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (55 bp):
TGAAGATTGTTCGAGTCTTATACTCCCTGAACGAATAGGGAGCAGACACATTTTA
Found at i:28895 original size:110 final size:111
Alignment explanation
Indices: 28671--28877 Score: 276
Period size: 110 Copynumber: 1.9 Consensus size: 111
28661 GATTTGTTTG
* * ** * * *
28671 TTGAAGATTGTTTGAGT-TCTATACTCTCTGATGGAATAGAGAGCGGACCCGTTTTATGAAGATT
1 TTGAAGATTGTTCGAGTCTCTATACTCCCTGAACGAATAGAGAGCAGACACATTTTATGAAGATT
28735 GTTCGAGTTCTATACTCCCTGAACGAATAGGGAACGGACCCATTTA
66 GTTCGAGTTCTATACTCCCTGAACGAATAGGGAACGGACCCATTTA
* *
28781 TTGAAGATTGTTCGAGTCT-TATACTCCCTGAACGAATAGGGAGCAGACATATTTTATGAAGATT
1 TTGAAGATTGTTCGAGTCTCTATACTCCCTGAACGAATAGAGAGCAGACACATTTTATGAAGATT
* * *
28845 GTTCGAG-TCTTATACTTCCTGAAGGAGTAGGGA
66 GTTCGAGTTC-TATACTCCCTGAACGAATAGGGA
28878 GCGGGCTCGT
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
109 2 0.02
110 80 0.96
111 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (111 bp):
TTGAAGATTGTTCGAGTCTCTATACTCCCTGAACGAATAGAGAGCAGACACATTTTATGAAGATT
GTTCGAGTTCTATACTCCCTGAACGAATAGGGAACGGACCCATTTA
Found at i:33119 original size:15 final size:15
Alignment explanation
Indices: 33099--33128 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33089 TTGTTTTGGC
33099 CATATAGGTTATCAA
1 CATATAGGTTATCAA
*
33114 CATATAGTTTATCAA
1 CATATAGGTTATCAA
33129 GATGGAGAAT
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:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (15 bp):
CATATAGGTTATCAA
Found at i:33281 original size:23 final size:23
Alignment explanation
Indices: 33247--33292 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
33237 TTTAAAGACT
33247 TAAATTGCTAATATATCAAACTA
1 TAAATTGCTAATATATCAAACTA
*
33270 TAAATTGTTAATATATCAAACTA
1 TAAATTGCTAATATATCAAACTA
33293 CATCATCTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
TAAATTGCTAATATATCAAACTA
Found at i:38047 original size:3 final size:3
Alignment explanation
Indices: 38033--38079 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
38023 ATGTTAACGA
*
38033 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
38080 CCACTGCCTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38672 original size:3 final size:3
Alignment explanation
Indices: 38657--38747 Score: 94
Period size: 3 Copynumber: 30.0 Consensus size: 3
38647 TTTTTTTTAT
* *
38657 TTA TTCA TT- TTA TTA TTA TTA TTA ATA TTA TTA TAA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
38702 TTA TAA TAA TAA TTA TTA TTA TTA ATA TATA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
38748 CAAACAGGCC
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
2 2 0.03
3 67 0.89
4 6 0.08
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:39174 original size:17 final size:18
Alignment explanation
Indices: 39152--39187 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
39142 GAACCTGAAA
39152 AAAAAAAAAGAAG-ACAG
1 AAAAAAAAAGAAGAACAG
39169 AAAAAAAAAGAAGAACAG
1 AAAAAAAAAGAAGAACAG
39187 A
1 A
39188 GAGACAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.78, C:0.06, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAGAACAG
Found at i:40906 original size:18 final size:18
Alignment explanation
Indices: 40865--40907 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40855 AATTTTTATA
40865 TTTATTTATTATTTTCAT
1 TTTATTTATTATTTTCAT
**
40883 AATATTTA-TATGTTTCAT
1 TTTATTTATTAT-TTTCAT
40901 TTTATTT
1 TTTATTT
40908 TATTTGCAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTATTTATTATTTTCAT
Found at i:40922 original size:15 final size:13
Alignment explanation
Indices: 40902--40939 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
40892 ATGTTTCATT
40902 TTATTTTATTTGCAA
1 TTATTTTATTT-C-A
40917 TTATTTTATTTCA
1 TTATTTTATTTCA
40930 TTA-TTTATTT
1 TTATTTTATTT
40940 TTCTGTCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.30
13 4 0.17
14 1 0.04
15 11 0.48
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (13 bp):
TTATTTTATTTCA
Found at i:44184 original size:15 final size:15
Alignment explanation
Indices: 44166--44198 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
44156 TTTTTGGGAT
*
44166 CATACCTTTTGCATA
1 CATACATTTTGCATA
44181 CATACATTTTGCATA
1 CATACATTTTGCATA
44196 CAT
1 CAT
44199 TCATCATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.39
Consensus pattern (15 bp):
CATACATTTTGCATA
Found at i:52823 original size:83 final size:83
Alignment explanation
Indices: 52680--53718 Score: 1658
Period size: 83 Copynumber: 12.5 Consensus size: 83
52670 CAATGGGCTC
52680 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
* * *
52745 TGGAAGATGAATTTGCTA
66 TAGAAGATGAATGTGTTA
*
52763 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
* * *
52828 TGGAAGATGAATTTGCTA
66 TAGAAGATGAATGTGTTA
52846 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
* *
52911 TGGAAGATGAAAT-TGCTA
66 TAGAAGATG-AATGTGTTA
*
52929 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTAGTTTAGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
* *
52994 TGGAAGATGAAAT-TGCTA
66 TAGAAGATG-AATGTGTTA
*
53012 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
53077 TAGAAGATGAATGTGTTA
66 TAGAAGATGAATGTGTTA
*
53095 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
53160 TAGAAGATGAATGTGTTA
66 TAGAAGATGAATGTGTTA
* *
53178 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAGAA-CAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
* *
53242 TAGAAGATAAATGTGTTC
66 TAGAAGATGAATGTGTTA
* * * *
53260 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTAGTTTGGCAGAACAAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
53325 TAGAAGATGAATGTGTTA
66 TAGAAGATGAATGTGTTA
* * *
53343 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTTGGCAGAACAAATCATTGAATT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
* *
53408 TAGAAGATAAATGTGTTC
66 TAGAAGATGAATGTGTTA
*
53426 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAG-AGAACAAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-AGCAGAACCAATCATTGAAT
* *
53490 TTAGAAGATAAATGTGTTC
65 TTAGAAGATGAATGTGTTA
* *
53509 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGAG-AGAACAAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-AGCAGAACCAATCATTGAAT
* *
53573 TTAGAAGATAAATGTGTTC
65 TTAGAAGATGAATGTGTTA
*
53592 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG-ACCAAATCATTGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACC-AATCATTGAAT
* *
53656 GTAGAAGATGAATGTGTCA
65 TTAGAAGATGAATGTGTTA
53675 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
53719 GGTAAGAACT
Statistics
Matches: 923, Mismatches: 27, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
82 85 0.09
83 834 0.90
84 4 0.00
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAGCAGAACCAATCATTGAATT
TAGAAGATGAATGTGTTA
Found at i:54948 original size:112 final size:112
Alignment explanation
Indices: 54445--55217 Score: 1128
Period size: 112 Copynumber: 7.0 Consensus size: 112
54435 ATCAAGATTT
54445 AAATCCATCA-TTCGATGGATCAGCATTTT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCCATCACTT-GATGGATCAGC-TTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGA
* ** *
54508 AGAA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATTTTTTTCT-
64 AGAAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
54556 TAATTCATCCCTTGATGGATCAGCATTTT-CAGTTAGAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATCAGC-TTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAA
*
54620 GAA-GAAGAAAAATTCATAATGAGAAGAA-TTGTTCAACCTTTTGCTC
65 GAAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
54666 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
*
54731 AAGGAAGAAAAATTCATAAT--GAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
*
54776 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
54841 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
** *
54888 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
54953 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
** *
55000 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
55065 AA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTCTTAC-C
66 AAGGAAGAA-AAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
55111 TGAATTCATCAATTGATGGATTATCTTTTCCAG--AGAAGTTCATAATGAGAAGAACTCATCTGA
1 -AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAG-AGTTCATAATGAGAAGAACTCATCTGA
* *
55174 AGAAGGAAG--AAGTTCATAATAAGAAGAACTTGTTCAA-CTTTTGC
64 AGAAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGC
55218 ATAATTCTAT
Statistics
Matches: 621, Mismatches: 30, Indels: 25
0.92 0.04 0.04
Matches are distributed among these distances:
108 5 0.01
109 49 0.08
110 179 0.29
111 122 0.20
112 266 0.43
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (112 bp):
AAATCCATCACTTGATGGATCAGCTTTTCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:55449 original size:9 final size:8
Alignment explanation
Indices: 55426--55503 Score: 50
Period size: 9 Copynumber: 9.0 Consensus size: 8
55416 ACTAATTTTT
55426 TTTTATT-
1 TTTTATTA
55433 TATTTATTCA
1 T-TTTATT-A
55443 TTTTATTA
1 TTTTATTA
55451 TTATTATTAA
1 TT-TTATT-A
*
55461 TATTATTA
1 TTTTATTA
*
55469 TAATTATTA
1 T-TTTATTA
*
55478 TTATTATAA
1 TT-TTATTA
*
55487 TATTATTA
1 TTTTATTA
55495 TTATTATTA
1 TT-TTATTA
55504 ATATATATTA
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
7 1 0.02
8 17 0.30
9 36 0.63
10 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTTATTA
Found at i:55453 original size:3 final size:3
Alignment explanation
Indices: 55436--55526 Score: 96
Period size: 3 Copynumber: 30.0 Consensus size: 3
55426 TTTTATTTAT
* *
55436 TTA TTCA TT- TTA TTA TTA TTA TTA ATA TTA TTA TAA TTA TTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
55481 TTA -TA ATA TTA TTA TTA TTA TTA ATA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
55527 CAAACAGGCC
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
2 4 0.05
3 61 0.82
4 9 0.12
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:55964 original size:20 final size:20
Alignment explanation
Indices: 55939--55980 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
55929 ACCCGAACCT
55939 GAAAAAAAAAAAAGAAG-ACA
1 GAAAAAAAAAAAA-AAGAACA
55959 GAAAAAAAAAAAAAAGAACA
1 GAAAAAAAAAAAAAAGAACA
55979 GA
1 GA
55981 GAGACAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (20 bp):
GAAAAAAAAAAAAAAGAACA
Found at i:56936 original size:19 final size:20
Alignment explanation
Indices: 56898--56939 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
56888 TTTTTTATTT
**
56898 TATTTGTTTATATTTTTAAA
1 TATTTGTTTATATTCATAAA
56918 TATTT-TTTATATTCATAAA
1 TATTTGTTTATATTCATAAA
56937 TAT
1 TAT
56940 ATATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTGTTTATATTCATAAA
Found at i:59035 original size:65 final size:65
Alignment explanation
Indices: 58745--59007 Score: 391
Period size: 65 Copynumber: 4.0 Consensus size: 65
58735 GCTGCACCGA
* * * *
58745 TACAGATCACTCATATGACTCATGTACTTTTGTGGTGCATGAGGTGGAGTGATAATTGAGTATTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
*
58810 TACAAATCACTCATATAACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
* * * *
58875 TACAAATTACTTATATGACTCAAGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
* * ** * *
58940 TACAGATCACTCATATGACTTAAATACCTTTGTGGTTCATGAGGTGAAGTGATAATTGAATACTG
1 TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
59005 TAC
1 TAC
59008 TTCTCACTCA
Statistics
Matches: 180, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 180 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.34
Consensus pattern (65 bp):
TACAAATCACTCATATGACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
Found at i:59055 original size:130 final size:130
Alignment explanation
Indices: 58745--59056 Score: 349
Period size: 130 Copynumber: 2.4 Consensus size: 130
58735 GCTGCACCGA
* * * * * * * *
58745 TACAGATCACTCATATGACTCATGTACTTTTGTGGTGCATGAGGTGGAGTGATAATTGAGTATTG
1 TACAAATCACTCAGATGACTCAAGTACCTTTGTGGTGCATAAGATAGAGTGATAATTGAATATTG
** *
58810 TACAAATCACTCATATAACTCATGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATACTG
66 TACAAATCACTCATATAACTCAAATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAATACTG
* * * * * *
58875 TACAAATTACTTATATGACTCAAGTACCTTTGTGGTGCATGAGGTGGAGTGATAATTGAATATTG
1 TACAAATCACTCAGATGACTCAAGTACCTTTGTGGTGCATAAGATAGAGTGATAATTGAATATTG
* * * *
58940 TACAGATCACTCATATGACTTAAATACCTTTGTGGTTCATGAGGTGAAGTGATAATTGAATACTG
66 TACAAATCACTCATATAACTCAAATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAATACTG
*** ***
59005 TACTTCTCACTCACGA-GACTTGTGTACCTTTAG-GGTGCATAAGATAGAGTGA
1 TACAAATCACTCA-GATGACTCAAGTACCTTT-GTGGTGCATAAGATAGAGTGA
59057 CTATGATACA
Statistics
Matches: 155, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
130 153 0.99
131 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (130 bp):
TACAAATCACTCAGATGACTCAAGTACCTTTGTGGTGCATAAGATAGAGTGATAATTGAATATTG
TACAAATCACTCATATAACTCAAATACCTTTGTGGTGCATGAGGTGAAGTGATAATTGAATACTG
Done.