Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009017.1 Hibiscus syriacus cultivar Beakdansim tig00112407_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: 1192163
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 6
Found at i:1144203 original size:23 final size:23
Alignment explanation
Indices: 1144177--1144264 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
1144167 AGCTCATATA
*
1144177 AATTACACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1144200 AATTTGTC-CCGAAG-GACCGCGTAG
1 AA-TTG-CACCGAAGTG-CCACGTAG
*
1144224 AAATGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
1144247 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
1144265 TATAAGATTG
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
22 1 0.02
23 34 0.63
24 18 0.33
25 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.25, T:0.18
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:1150789 original size:23 final size:23
Alignment explanation
Indices: 1150752--1150808 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
1150742 AGAATTTGTC
* *
1150752 CCGAAGGGCCGCGTAGAAATGCA
1 CCGAAGTGCCACGTAGAAATGCA
*
1150775 CCGAAGTGCCACGTAGAATTGCA
1 CCGAAGTGCCACGTAGAAATGCA
*
1150798 CCGTAGTGCCA
1 CCGAAGTGCCA
1150809 TATAAGATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.14
Consensus pattern (23 bp):
CCGAAGTGCCACGTAGAAATGCA
Found at i:1151868 original size:35 final size:36
Alignment explanation
Indices: 1151822--1151892 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
1151812 TTTTATTTAG
1151822 GGGGAATCGATACCCCCCA-GGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1151857 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
1151893 CCTGCACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.20, C:0.31, G:0.32, T:0.17
Consensus pattern (36 bp):
GGGGAATCGATACCCCCCAGGGGGGAATCTGTTCCC
Found at i:1153745 original size:15 final size:16
Alignment explanation
Indices: 1153727--1153760 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1153717 AAATTTCCAT
1153727 AAAATAT-ATTTAAAA
1 AAAATATGATTTAAAA
*
1153742 AAAATATGCTTTAAAA
1 AAAATATGATTTAAAA
1153758 AAA
1 AAA
1153761 TTAAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (16 bp):
AAAATATGATTTAAAA
Found at i:1154826 original size:32 final size:32
Alignment explanation
Indices: 1154788--1154863 Score: 116
Period size: 32 Copynumber: 2.4 Consensus size: 32
1154778 AGTAACTTTA
*
1154788 GAAGACTCCAAGTTAACATGGAGACTTTAGTT
1 GAAGACTCCAAGTTAACATGAAGACTTTAGTT
* *
1154820 GAAGACTCCAAGTTAACGTGAAGTCTTTAGTT
1 GAAGACTCCAAGTTAACATGAAGACTTTAGTT
*
1154852 GAAGAATCCAAG
1 GAAGACTCCAAG
1154864 ATTACTATGC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (32 bp):
GAAGACTCCAAGTTAACATGAAGACTTTAGTT
Found at i:1160383 original size:18 final size:15
Alignment explanation
Indices: 1160350--1160381 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1160340 AAAATAGATT
1160350 TTATTATTATTTTTG
1 TTATTATTATTTTTG
*
1160365 TTATTATTAATTTTG
1 TTATTATTATTTTTG
1160380 TT
1 TT
1160382 GTCTGCTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.72
Consensus pattern (15 bp):
TTATTATTATTTTTG
Found at i:1161361 original size:23 final size:22
Alignment explanation
Indices: 1161323--1161384 Score: 85
Period size: 23 Copynumber: 2.9 Consensus size: 22
1161313 CAGATAATTT
1161323 AAAA-AAATAT-TA-TTTTAAA
1 AAAATAAATATATACTTTTAAA
*
1161342 AAAATAAATAATATATTTTTAAA
1 AAAATAAAT-ATATACTTTTAAA
1161365 AAAATAAATATATACTTTTA
1 AAAATAAATATATACTTTTA
1161385 TAATATTATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 2 0.05
22 12 0.32
23 16 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATAAATATATACTTTTAAA
Found at i:1166166 original size:21 final size:21
Alignment explanation
Indices: 1166140--1166182 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1166130 GGGCTTCGTC
1166140 AATGAGATCCGCTCTCCCCTT
1 AATGAGATCCGCTCTCCCCTT
*
1166161 AATGAGATCCGCTCTCCTCTT
1 AATGAGATCCGCTCTCCCCTT
1166182 A
1 A
1166183 CTTGTTCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.35, G:0.14, T:0.30
Consensus pattern (21 bp):
AATGAGATCCGCTCTCCCCTT
Found at i:1169214 original size:184 final size:184
Alignment explanation
Indices: 1168823--1169213 Score: 581
Period size: 184 Copynumber: 2.1 Consensus size: 184
1168813 AACCGAAATT
* * * *
1168823 AAATTTTAAATATATTATATATAATATATGGGCTTAGCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
*
1168888 TTTAAGATTCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
* * *
1168953 TATTTTATAATTATATATTTAAATTAATTGTAAACTGTTTTTTTTTAATTAAAA
131 TATTTTATAATTATATATTTAAATTAATTATAAAATGTTTTTTTTGAATTAAAA
*
1169007 AAATATTAAATATATTATATATAACATGTGGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
* * **
1169072 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTATATAATTTTTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAA--AATT
1169137 TTTATTTTATAATTATATATTATTTAAATTAATTATAAAATG-TTTTTTTGAATT-AAA
129 TTTATTTTATAA-T-TATA-TATTTAAATTAATTATAAAATGTTTTTTTTGAATTAAAA
* *
1169194 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
1169214 AATTCGAAAT
Statistics
Matches: 187, Mismatches: 15, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
184 116 0.62
186 22 0.12
187 14 0.07
188 15 0.08
189 20 0.11
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGGGCTAAGCCCAAACCATTTAAAACACAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTATATAAAATTTT
TATTTTATAATTATATATTTAAATTAATTATAAAATGTTTTTTTTGAATTAAAA
Found at i:1172887 original size:22 final size:22
Alignment explanation
Indices: 1172841--1172888 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1172831 ACATACATGC
*
1172841 ATTTGCATTTTATTTGTGTTAT
1 ATTTGCATTTTATTTGTATTAT
1172863 ATTTGCATTATTATATT-TATT-T
1 ATTTGCATT-TTAT-TTGTATTAT
1172885 ATTT
1 ATTT
1172889 AGCCTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 14 0.61
23 7 0.30
24 2 0.09
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (22 bp):
ATTTGCATTTTATTTGTATTAT
Found at i:1181046 original size:43 final size:42
Alignment explanation
Indices: 1180936--1181049 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 42
1180926 ATATCTTTAA
* **
1180936 AGATAGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCAT
1 AGATA-CCAGACGTCCTCATCACGAAGGAACAACATCATCCAT
* * * *
1180979 CGAT--CAGAAC-TCCTCATCATGAAGGAGCAACATCATCCTT
1 AGATACCAG-ACGTCCTCATCACGAAGGAACAACATCATCCAT
1181019 AGATAACCAGACGTCCTCATCACGAAGGAAC
1 AGAT-ACCAGACGTCCTCATCACGAAGGAAC
1181050 CGTGTTATCT
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
40 30 0.54
41 2 0.04
42 2 0.04
43 22 0.39
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (42 bp):
AGATACCAGACGTCCTCATCACGAAGGAACAACATCATCCAT
Found at i:1181121 original size:137 final size:137
Alignment explanation
Indices: 1180870--1181459 Score: 925
Period size: 137 Copynumber: 4.3 Consensus size: 137
1180860 TATTTTAGGA
*
1180870 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* * * *
1180935 AAGATAGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCATG
66 AAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATACATCGATCAGAACTCCTCATCACG
1181000 AAGGAGC
131 AAGGAGC
1181007 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* ** *
1181072 AAGATGGCCAGACGCCCTCATCACGAAGGAACAATGTCATATGTTGATCA-ACACTCCTCATCAC
66 AAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATACATCGATCAGA-ACTCCTCATCAC
*
1181136 GAATGAGC
130 GAAGGAGC
* * * *
1181144 AACATCGTCCTTAAATAACCAGACGTCCTCATCATGAAGGAA-CGTGTTATCTCAAATTTCTTTA
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* * *
1181208 AAGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
66 AAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATACATCGATCAGAACTCCTCATCACG
*
1181273 AAGAAGC
131 AAGGAGC
*
1181280 AACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
* * *
1181345 AAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCAT-CAATTGATCAGAACTCCTCATCAC
66 AAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATAC-ATCGATCAGAACTCCTCATCAC
1181409 GAAGGAGC
130 GAAGGAGC
* *
1181417 AACATCATCCTTAGATAATCAGACGCCCTCATCACGAAGGAAC
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAAC
1181460 AATGTCATCC
Statistics
Matches: 412, Mismatches: 37, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
136 122 0.30
137 290 0.70
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (137 bp):
AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
AAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATACATCGATCAGAACTCCTCATCACG
AAGGAGC
Found at i:1181403 original size:273 final size:274
Alignment explanation
Indices: 1180870--1181459 Score: 997
Period size: 273 Copynumber: 2.2 Consensus size: 274
1180860 TATTTTAGGA
1180870 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTA
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTA
* *
1180935 AAGATAGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCATG
66 AAGATAGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
* *
1181000 AAGGAGCAACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAAT
131 AAGAAGCAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAAT
* * *
1181065 ATCTTTAAAGATGGCCAGACGCCCTCATCACGAAGGAACAATGTCATATGTTGATCAACACTCCT
196 ATCTTTAAAGATGGCCAGACGCCCTCATCAAGAAGGAACAATGCCATATATTGATCAACACTCCT
*
1181130 CATCACGAATGAGC
261 CATCACGAAGGAGC
* * * *
1181144 AACATCGTCCTTAAATAACCAGACGTCCTCATCATGAAGGAAC-GTGTTATCTCAAATTTCTTTA
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTA
*
1181208 AAGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
66 AAGATAGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
1181273 AAGAAGCAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAAT
131 AAGAAGCAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAAT
*
1181338 ATCTTTAAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCA-ATTGATCAGA-ACTC
196 ATCTTTAAAGATGGCCAGACGCCCTCATCAAGAAGGAACAATGCCAT-ATATTGATCA-ACACTC
1181401 CTCATCACGAAGGAGC
259 CTCATCACGAAGGAGC
* *
1181417 AACATCATCCTTAGATAATCAGACGCCCTCATCACGAAGGAAC
1 AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAAC
1181460 AATGTCATCC
Statistics
Matches: 295, Mismatches: 19, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
273 253 0.86
274 42 0.14
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (274 bp):
AACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACTGTGTTATCTCAAATATCTTTA
AAGATAGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
AAGAAGCAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAAT
ATCTTTAAAGATGGCCAGACGCCCTCATCAAGAAGGAACAATGCCATATATTGATCAACACTCCT
CATCACGAAGGAGC
Found at i:1181414 original size:40 final size:40
Alignment explanation
Indices: 1181359--1181497 Score: 147
Period size: 40 Copynumber: 3.4 Consensus size: 40
1181349 TGGCCAGACG
* *
1181359 TCCTCATCAAGAAGGAACAATGCCATCAATTGATCAGAAC
1 TCCTCATCACGAAGGAACAATGTCATCAATTGATCAGAAC
* ** *
1181399 TCCTCATCACGAAGGAGCAACATCATCCTTAGA-TAATCAG-AC
1 TCCTCATCACGAAGGAACAATGTCAT-C--A-ATTGATCAGAAC
* *
1181441 GCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAAC
1 -TCCTCATCACGAAGGAACAATGTCATCAATTGATCAGAAC
1181482 TCCTCATCACGAAGGA
1 TCCTCATCACGAAGGA
1181498 GTAACATCAT
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
39 1 0.01
40 42 0.53
41 3 0.04
42 3 0.04
43 29 0.37
44 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (40 bp):
TCCTCATCACGAAGGAACAATGTCATCAATTGATCAGAAC
Found at i:1181447 original size:43 final size:43
Alignment explanation
Indices: 1181391--1181540 Score: 168
Period size: 43 Copynumber: 3.6 Consensus size: 43
1181381 CCATCAATTG
1181391 ATCAGAAC-TCCTCATCACGAAGGAGCAACATCATCCTTAGATA
1 ATCAG-ACGTCCTCATCACGAAGGAGCAACATCATCCTTAGATA
* * **
1181434 ATCAGACGCCCTCATCACGAAGGAACAATGTCATCCATT-G---
1 ATCAGACGTCCTCATCACGAAGGAGCAACATCATCC-TTAGATA
*
1181474 ATCAGAAC-TCCTCATCACGAAGGAGTAACATCATCCTTAGATA
1 ATCAG-ACGTCCTCATCACGAAGGAGCAACATCATCCTTAGATA
* *
1181517 ACCAGACGTCATCATCACGAAGGA
1 ATCAGACGTCCTCATCACGAAGGA
1181541 ACCGTGTTAT
Statistics
Matches: 88, Mismatches: 11, Indels: 16
0.77 0.10 0.14
Matches are distributed among these distances:
39 2 0.02
40 29 0.33
41 2 0.02
42 4 0.05
43 49 0.56
44 2 0.02
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.20
Consensus pattern (43 bp):
ATCAGACGTCCTCATCACGAAGGAGCAACATCATCCTTAGATA
Found at i:1181487 original size:220 final size:220
Alignment explanation
Indices: 1181216--1181679 Score: 775
Period size: 220 Copynumber: 2.1 Consensus size: 220
1181206 TAAAGATGGA
*
1181216 CAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGAAGCA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGAAGCA
1181281 ACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
66 ACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
*
1181346 AGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATCAGAACTCCTCATCACGA
131 AGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATCGATCAGAACTCCTCATCACGA
*
1181411 AGGAGCAACATCATCCTTAGATAAT
196 AGGAGCAACATCATCCTTAGATAAC
* * * *
1181436 CAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGTA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGAAGCA
1181501 ACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
66 ACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
** * * * * *
1181566 AGATGGTTAGACGTCTTCATCACGAAGGAATAATGTCATCCATCGATCAGAACTCCTCATCACGA
131 AGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATCGATCAGAACTCCTCATCACGA
*
1181631 AGGGGCAACATCATCCTTAGATAAC
196 AGGAGCAACATCATCCTTAGATAAC
* *
1181656 CAGACATCCTTATCACGAAGGAAC
1 CAGACGTCCTCATCACGAAGGAAC
1181680 CGTGTTATCT
Statistics
Matches: 226, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
220 226 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.22
Consensus pattern (220 bp):
CAGACGTCCTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGAAGCA
ACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
AGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATCGATCAGAACTCCTCATCACGA
AGGAGCAACATCATCCTTAGATAAC
Found at i:1181492 original size:83 final size:83
Alignment explanation
Indices: 1181352--1181542 Score: 319
Period size: 83 Copynumber: 2.3 Consensus size: 83
1181342 TTAAAGATGG
*
1181352 CCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATCAGAACTCCTCATCACGAAGGAGC
1 CCAGACGTCCTCATCACGAAGGAACAATGCCATCAATTGATCAGAACTCCTCATCACGAAGGAGC
1181417 AACATCATCCTTAGATAA
66 AACATCATCCTTAGATAA
* * * * *
1181435 TCAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGT
1 CCAGACGTCCTCATCACGAAGGAACAATGCCATCAATTGATCAGAACTCCTCATCACGAAGGAGC
1181500 AACATCATCCTTAGATAA
66 AACATCATCCTTAGATAA
*
1181518 CCAGACGTCATCATCACGAAGGAAC
1 CCAGACGTCCTCATCACGAAGGAAC
1181543 CGTGTTATCT
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
83 99 1.00
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.19
Consensus pattern (83 bp):
CCAGACGTCCTCATCACGAAGGAACAATGCCATCAATTGATCAGAACTCCTCATCACGAAGGAGC
AACATCATCCTTAGATAA
Found at i:1181529 original size:40 final size:40
Alignment explanation
Indices: 1181402--1181530 Score: 116
Period size: 40 Copynumber: 3.1 Consensus size: 40
1181392 TCAGAACTCC
*
1181402 TCATCACGAAGGAGCAACATCATCCTTAGATAATCAGACG
1 TCATCACGAAGGAGCAACATCATCCTTAGATAACCAGACG
* ** * ** ** *
1181442 CCCTCATCACGAAGGAACAATGTCATCCATT-GATCAGAACTCC
1 ---TCATCACGAAGGAGCAACATCATCC-TTAGATAACCAGACG
*
1181485 TCATCACGAAGGAGTAACATCATCCTTAGATAACCAGACG
1 TCATCACGAAGGAGCAACATCATCCTTAGATAACCAGACG
1181525 TCATCA
1 TCATCA
1181531 TCACGAAGGA
Statistics
Matches: 65, Mismatches: 19, Indels: 7
0.71 0.21 0.08
Matches are distributed among these distances:
39 2 0.03
40 33 0.51
43 28 0.43
44 2 0.03
ACGTcount: A:0.36, C:0.28, G:0.16, T:0.21
Consensus pattern (40 bp):
TCATCACGAAGGAGCAACATCATCCTTAGATAACCAGACG
Found at i:1181647 original size:357 final size:356
Alignment explanation
Indices: 1181079--1181816 Score: 1217
Period size: 357 Copynumber: 2.1 Consensus size: 356
1181069 TTAAAGATGG
** *
1181079 CCAGACGCCCTCATCACGAAGGAACAATGTCATATGTTGATCAACACTCCTCATCACGAATGAGC
1 CCAGACGCCCTCATCACGAAGGAACAATGTCATACATTGATCAACACTCCTCATCACGAAGGAGC
* * * *
1181144 AACATCGTCCTTAAATAACCAGACGTCCTCATCATGAAGGAACGTGTTATCTCAAATTTCTTTAA
66 AACATCATCCTTAAATAACCAGACGTCATCATCACGAAGGAACGTGTTATCTCAAATATCTTTAA
1181209 AGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGA
131 AGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGA
*
1181274 AGAAGCAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATA
196 AGAAGCAACATCATCCTTAGATAACCAGACATCATCATCACGAAGGAACCGTGTTATCTCAAATA
*
1181339 TCTTTAAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATCAGAACTCCTC
261 TCTTTAAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATAAGAACTCCTC
*
1181404 ATCACGAAGGAGCAACATCATCCTTAGATAA
326 ATCACGAAGAAGCAACATCATCCTTAGATAA
* *
1181435 TCAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGA-ACTCCTCATCACGAAGGAG
1 CCAGACGCCCTCATCACGAAGGAACAATGTCATACATTGATCA-ACACTCCTCATCACGAAGGAG
* *
1181499 TAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTT
65 CAACATCATCCTTAAATAACCAGACGTCATCATCACGAAGGAA-CGTGTTATCTCAAATATCTTT
** *
1181564 AAAGATGGTTAGACGTCTTCATCACGAAGGAATAATGTCATCCATCGATCAGAACTCCTCATCAC
129 AAAGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCAC
** * *
1181629 GAAGGGGCAACATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGTTATCTCAAA
194 GAAGAAGCAACATCATCCTTAGATAACCAGACATCATCATCACGAAGGAACCGTGTTATCTCAAA
* * *
1181694 TATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATAAGAACTCC
259 TATCTTTAAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATAAGAACTCC
*
1181759 TCATCACGAAGAAGCAACATCATCCTTCGATAA
324 TCATCACGAAGAAGCAACATCATCCTTAGATAA
*
1181792 CCAGACGTCCTCATCACGAAGGAAC
1 CCAGACGCCCTCATCACGAAGGAAC
1181817 CGTGTTATCT
Statistics
Matches: 353, Mismatches: 27, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
356 95 0.27
357 258 0.73
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (356 bp):
CCAGACGCCCTCATCACGAAGGAACAATGTCATACATTGATCAACACTCCTCATCACGAAGGAGC
AACATCATCCTTAAATAACCAGACGTCATCATCACGAAGGAACGTGTTATCTCAAATATCTTTAA
AGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGA
AGAAGCAACATCATCCTTAGATAACCAGACATCATCATCACGAAGGAACCGTGTTATCTCAAATA
TCTTTAAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATAAGAACTCCTC
ATCACGAAGAAGCAACATCATCCTTAGATAA
Found at i:1181683 original size:137 final size:137
Alignment explanation
Indices: 1181436--1181953 Score: 856
Period size: 137 Copynumber: 3.8 Consensus size: 137
1181426 CTTAGATAAT
* *
1181436 CAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGTA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGCA
*
1181501 ACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
66 ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
*
1181566 AGATGGT
131 AGATGGC
* * * * *
1181573 TAGACGTCTTCATCACGAAGGAATAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGGGCA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGCA
* *
1181638 ACATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
66 ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
1181703 AGATGGC
131 AGATGGC
* *
1181710 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATAAGAACTCCTCATCACGAAGAAGCA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGCA
*
1181775 ACATCATCCTTCGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
66 ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
1181840 AGATGGC
131 AGATGGC
* * * *
1181847 CAGACATCCTCATCACGAAAGAACAATGTCATCCATTGATCAGAACTCCTCATCAAGAAGGAGAA
1 CAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGCA
* *
1181912 ACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAAC
66 ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAAC
1181954 AATGTCATCC
Statistics
Matches: 351, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
137 351 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (137 bp):
CAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGCA
ACATCATCCTTAGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAA
AGATGGC
Found at i:1181809 original size:43 final size:42
Alignment explanation
Indices: 1181709--1181812 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 42
1181699 TTAAAGATGG
**
1181709 CCAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATAA
1 CCAGACGTCCTCATCACGAA-GAACAACATCATCCATTGATAA
*
1181752 -GA-AC-TCCTCATCACGAAGAAGCAACATCATCC-TTCGATAA
1 CCAGACGTCCTCATCACGAAGAA-CAACATCATCCATT-GATAA
1181792 CCAGACGTCCTCATCACGAAG
1 CCAGACGTCCTCATCACGAAG
1181813 GAACCGTGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
39 5 0.10
40 27 0.52
41 3 0.06
42 3 0.06
43 14 0.27
ACGTcount: A:0.35, C:0.31, G:0.15, T:0.19
Consensus pattern (42 bp):
CCAGACGTCCTCATCACGAAGAACAACATCATCCATTGATAA
Found at i:1181945 original size:357 final size:347
Alignment explanation
Indices: 1181079--1182099 Score: 1065
Period size: 357 Copynumber: 2.9 Consensus size: 347
1181069 TTAAAGATGG
*** * *
1181079 CCAGACGCCCTCATCACGAAGGAACAATGTCATATGTTGATCA-ACACTCCTCATCACGAATGAG
1 CCAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGA-ACTCCTCATCACGAAAGAA
* * * * * *
1181143 CAACATCGTCCTTAAATAACCAGACGTCCTCATCATGAAGGAACGTGTTATCTCAAATTTCTTTA
65 CAACATCATCCTTAGAT-A-CAGACGTCATCATCAAGAAGGAAC--G-TA---CAAATATCCTT-
* *
1181208 AAGATGGACAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
121 AAGATAGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
** * * *
1181273 AAGAAGCAACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAAT
186 AAGGGGCAACATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGTTATCTCAAAT
* * *
1181338 ATCTTTAAAGATGGCCAGACGTCCTCATCAAGAAGGAACAATGCCATCAATTGATCAGAACTCCT
251 ATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCAATTGATAAGAACTCCT
*
1181403 CATCACGAAGGAGCAACATCATCCTTAGATAA
316 CATCACGAAGAAGCAACATCATCCTTAGATAA
* * **
1181435 TCAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAGGAGT
1 CCAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAAGAAC
* *
1181500 AACATCATCCTTAGATAACCAGACGTCATCATCACGAAGGAACCGTGTTATCTCAAATATCTTTA
66 AACATCATCCTTAGAT-A-CAGACGTCATCATCAAGAAGGAA-C--G-TA---CAAATATCCTT-
* ** *
1181565 AAGATGGTTAGACGTCTTCATCACGAAGGAATAATGTCATCCATCGATCAGAACTCCTCATCACG
121 AAGATAGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACG
1181630 AAGGGGCAACATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGTTATCTCAAAT
186 AAGGGGCAACATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGTTATCTCAAAT
*
1181695 ATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATAAGAACTCCT
251 ATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCAATTGATAAGAACTCCT
*
1181760 CATCACGAAGAAGCAACATCATCCTTCGATAA
316 CATCACGAAGAAGCAACATCATCCTTAGATAA
* ** *
1181792 CCAGACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAG-ACATCC
1 CCAGACGCCCTCATCACGAAGGAACAATGTCATC-C----A---TT---GAT---CAGAAC-TCC
** *
1181856 TCATCACGAAAGAACAATGTCATCCATT-GAT-CAGAAC-TCCTCATCAAGAAGG-A-G-A-AAC
51 TCATCACGAAAGAACAACATCATCC-TTAGATACAG-ACGTCATCATCAAGAAGGAACGTACAA-
* * * *
1181914 ATCATCCTT-AGATAGCCAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTT
113 AT-ATCCTTAAGATAGCCAGACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTC
* * * * *
1181978 CTCATCACAAAGGAGTC-GCTTCATCCTTAGATAATCAGACATCCTTATCACGAAGGAACCGTGT
177 CTCATCACGAAGG-GGCAACATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGT
* ** * * * * * *
1182042 TATCACTATTTATCTCTAAAAATGACCAAATGTCCTCATCTCGAAGGAACAATGTCAT
241 TATCTC-AAATATCTTTAAAGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCAT
1182100 ACACTCGTTT
Statistics
Matches: 582, Mismatches: 60, Indels: 44
0.85 0.09 0.06
Matches are distributed among these distances:
356 95 0.16
357 374 0.64
358 48 0.08
359 5 0.01
361 1 0.00
362 1 0.00
363 1 0.00
365 2 0.00
367 1 0.00
368 19 0.03
369 2 0.00
370 2 0.00
371 29 0.05
372 2 0.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.24
Consensus pattern (347 bp):
CCAGACGCCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAACTCCTCATCACGAAAGAAC
AACATCATCCTTAGATACAGACGTCATCATCAAGAAGGAACGTACAAATATCCTTAAGATAGCCA
GACGTCTTCATCACGAAGGAACAATGTCATCCATCGATCAGAACTCCTCATCACGAAGGGGCAAC
ATCATCCTTAGATAACCAGACATCCTTATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAG
ATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCAATTGATAAGAACTCCTCATCACGAAG
AAGCAACATCATCCTTAGATAA
Found at i:1181962 original size:43 final size:40
Alignment explanation
Indices: 1181853--1181991 Score: 129
Period size: 40 Copynumber: 3.4 Consensus size: 40
1181843 TGGCCAGACA
*
1181853 TCCTCATCACGAAAGAACAATGTCATCCATTGATCAGAAC
1 TCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAAC
* ** **
1181893 TCCTCATCAAGAAGGAGA-AACATCATCC-TTAGATAGCCAGATG
1 TCCTCATCACGAAGGA-ACAATGTCATCCATT-GAT---CAGAAC
**
1181936 TCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAAC
1 TCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAAC
* *
1181976 TTCTCATCACAAAGGA
1 TCCTCATCACGAAGGA
1181992 GTCGCTTCAT
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
39 2 0.03
40 43 0.56
41 1 0.01
42 1 0.01
43 30 0.39
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (40 bp):
TCCTCATCACGAAGGAACAATGTCATCCATTGATCAGAAC
Found at i:1181984 original size:83 final size:83
Alignment explanation
Indices: 1181846--1182036 Score: 249
Period size: 83 Copynumber: 2.3 Consensus size: 83
1181836 TTAAAGATGG
* **
1181846 CCAGACATCCTCATCACGAAAGAACAATGTCATCCATTGATCAGAACTCCTCATCA-AGAAGGAG
1 CCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACA-AAGGAG
*
1181910 AAACATCATCCTTAGATAG
65 AAACATCATCCTTAGATAA
** * *
1181929 CCAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTTCTCATCACAAAGGAGT
1 CCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACAAAGGAGA
** *
1181994 CGCTTCATCCTTAGATAA
66 AACATCATCCTTAGATAA
* *
1182012 TCAGACATCCTTATCACGAAGGAAC
1 CCAGACATCCTCATCACGAAGGAAC
1182037 CGTGTTATCA
Statistics
Matches: 92, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
83 91 0.99
84 1 0.01
ACGTcount: A:0.36, C:0.28, G:0.15, T:0.21
Consensus pattern (83 bp):
CCAGACATCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTCCTCATCACAAAGGAGA
AACATCATCCTTAGATAA
Found at i:1182004 original size:220 final size:221
Alignment explanation
Indices: 1181703--1182099 Score: 546
Period size: 220 Copynumber: 1.8 Consensus size: 221
1181693 ATATCTTTAA
* ** *
1181703 AGATGGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCATTGATAAGAACTCCTCATCACGA
1 AGATAGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCACAA
* * *
1181768 AGAAGCAACATCATCCTTCGATAACCAGACGTCCTCATCACGAAGGAACCGTGTTATCTC-AAAT
66 AGAAGCAACATCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACCGTGTTATCACTAAAT
* * * *
1181832 ATCTTTAAAGATGGCCAGACATCCTCATCACGAAAGAACAATGTCATCCATTGATCAGAACTCCT
131 ATCTCTAAAAATGACCAAACATCCTCATCACGAAAGAACAATGTCATCCATTGATCAGAACTCCT
1181897 CATCAAGAAGGAGAAACATCATCCTT
196 CATCAAGAAGGAGAAACATCATCCTT
* * *
1181923 AGATAGCCAGATGTCCTCATCACGAAGGAACAATGTCATCCACCGATCAGAACTTCTCATCACAA
1 AGATAGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCACAA
* * * * * **
1181988 AGGAGTC-GCTTCATCCTTAGATAATCAGACATCCTTATCACGAAGGAACCGTGTTATCACTATT
66 AGAAG-CAACATCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACCGTGTTATCACTAAA
** * *
1182052 TATCTCTAAAAATGACCAAATGTCCTCATCTCGAAGGAACAATGTCAT
130 TATCTCTAAAAATGACCAAACATCCTCATCACGAAAGAACAATGTCAT
1182100 ACACTCGTTT
Statistics
Matches: 150, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
220 108 0.72
221 42 0.28
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (221 bp):
AGATAGCCAGACGTCCTCATCACGAAGGAACAATGTCATCCACCGATAAGAACTCCTCATCACAA
AGAAGCAACATCATCCTTAGATAACCAGACATCCTCATCACGAAGGAACCGTGTTATCACTAAAT
ATCTCTAAAAATGACCAAACATCCTCATCACGAAAGAACAATGTCATCCATTGATCAGAACTCCT
CATCAAGAAGGAGAAACATCATCCTT
Found at i:1182263 original size:3 final size:3
Alignment explanation
Indices: 1182255--1182285 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1182245 TGTCACATAC
1182255 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1182286 AATAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Done.