Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009460.1 Hibiscus syriacus cultivar Beakdansim tig00113722_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: 2853300
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 14 of 14
Found at i:2757475 original size:127 final size:129
Alignment explanation
Indices: 2757301--2757593 Score: 479
Period size: 127 Copynumber: 2.3 Consensus size: 129
2757291 CAACTACAAT
**
2757301 AATAAATCAATCCATATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
1 AATAAATCAATCCATATACTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
2757366 -AATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAA
66 AAATT-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAA
*
2757430 AATAAATCAATCCATA-ACTACAAT-AATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
1 AATAAATCAATCCATATACTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
*
2757493 AAATTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
66 AAATTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAA
* *
2757557 AATAAATCAAT-CATAT-TTAAAAATAAATCAATTCATA
1 AATAAATCAATCCATATACT-AAAATAAATCAATCCATA
2757594 CTAATAATTA
Statistics
Matches: 153, Mismatches: 7, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
126 5 0.03
127 112 0.73
128 20 0.13
129 16 0.10
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (129 bp):
AATAAATCAATCCATATACTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAAT
AAATTTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAA
Found at i:2757487 original size:22 final size:22
Alignment explanation
Indices: 2757301--2757360 Score: 120
Period size: 22 Copynumber: 2.7 Consensus size: 22
2757291 CAACTACAAT
2757301 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
2757323 AATAAATCAATCCATATTTTAA
1 AATAAATCAATCCATATTTTAA
2757345 AATAAATCAATCCATA
1 AATAAATCAATCCATA
2757361 CTAATAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATCAATCCATATTTTAA
Found at i:2757496 original size:22 final size:21
Alignment explanation
Indices: 2757429--2757496 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
2757419 AAATTAGTTA
2757429 AAATAAATCAATCCATAACTA-
1 AAATAAATCAATCCAT-ACTAT
* * *
2757450 CAAT-AATCAATCCATATTTT
1 AAATAAATCAATCCATACTAT
2757470 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACT-AT
2757493 AAAT
1 AAAT
2757497 TTTTAAAATA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
19 2 0.05
20 11 0.30
21 6 0.16
22 17 0.46
23 1 0.03
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAATCAATCCATACTAT
Found at i:2757517 original size:53 final size:52
Alignment explanation
Indices: 2757454--2757634 Score: 269
Period size: 53 Copynumber: 3.5 Consensus size: 52
2757444 TAACTACAAT
2757454 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTTTTAAAATA
1 AATCAAT-CATATTTTAAAATAAATCAATCCATACTAATAAATTTTTAAAATA
2757507 AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATA
1 AATCAAT-CATATTTTAAAATAAATCAATCCATACTAATAAATT-TTTAAAATA
* * *
2757561 AATCAATCATATTTAAAAATAAATCAATTCATACTAATAATTATTTTAAAAT-
1 AATCAATCATATTTTAAAATAAATCAATCCATACTAATAAAT-TTTTAAAATA
*
2757613 AATCAAT--TATTTTAATATAAAT
1 AATCAATCATATTTTAAAATAAAT
2757635 TTATTTTAAA
Statistics
Matches: 121, Mismatches: 5, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
50 13 0.11
52 7 0.06
53 84 0.69
54 17 0.14
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (52 bp):
AATCAATCATATTTTAAAATAAATCAATCCATACTAATAAATTTTTAAAATA
Found at i:2757524 original size:22 final size:22
Alignment explanation
Indices: 2757497--2757540 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2757487 ACTAATAAAT
2757497 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2757519 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
2757541 CTAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:2757529 original size:74 final size:75
Alignment explanation
Indices: 2757214--2757540 Score: 385
Period size: 75 Copynumber: 4.3 Consensus size: 75
2757204 ACTAATAAAT
* *
2757214 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATTCATACTAATAAATTATTTAAAATA
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAAAATA
2757279 AATCAATCCA
66 AATCAATCCA
** ** * **
2757289 TACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCCATA-TTTTAAAATAAAT-
1 T---A-TTTAA-AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTA
* ** *
2757352 CAATCCATACTAAT-AA
61 AAATAAAT-C-AATCCA
2757368 TTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAAAAT
1 -TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAAAAT
2757433 AAATCAATCCA
65 AAATCAATCCA
** * *
2757444 TAACTACAAT-AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATT-TTTAAAATA
1 TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAAAATA
2757507 AATCAATCCA
66 AATCAATCCA
2757517 TATTTTAAAATAAATCAATCCATA
1 TA-TTTAAAATAAATCAATCCATA
2757541 CTAATAAATT
Statistics
Matches: 209, Mismatches: 30, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
73 20 0.10
74 49 0.23
75 61 0.29
76 13 0.06
77 6 0.03
78 6 0.03
79 13 0.06
80 41 0.20
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (75 bp):
TATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAGTTAAAATA
AATCAATCCA
Found at i:2757549 original size:22 final size:22
Alignment explanation
Indices: 2757500--2757548 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
2757490 AATAAATTTT
**
2757500 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
2757522 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2757545 TAAA
1 TAAA
2757549 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2757575 original size:20 final size:22
Alignment explanation
Indices: 2757550--2757593 Score: 74
Period size: 21 Copynumber: 2.1 Consensus size: 22
2757540 ACTAATAAAT
2757550 TATTT-AAAATAAATCAA-TCA
1 TATTTAAAAATAAATCAATTCA
2757570 TATTTAAAAATAAATCAATTCA
1 TATTTAAAAATAAATCAATTCA
2757592 TA
1 TA
2757594 CTAATAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
TATTTAAAAATAAATCAATTCA
Found at i:2757653 original size:15 final size:14
Alignment explanation
Indices: 2757617--2757725 Score: 137
Period size: 15 Copynumber: 7.2 Consensus size: 14
2757607 TAAAATAATC
2757617 AATTATTTTAATATA
1 AATTATTTTAA-ATA
2757632 AATTTATTTTAAAGTA
1 AA-TTATTTTAAA-TA
2757648 AATTATTTTATAATA
1 AATTATTTTA-AATA
2757663 AATTATTTTAAAATA
1 AATTATTTT-AAATA
*
2757678 AACTATTTTATAATA
1 AATTATTTTA-AATA
2757693 AATTATTTTAAAATA
1 AATTATTTT-AAATA
2757708 AATTATTTTGAAATA
1 AATTATTTT-AAATA
2757723 AAT
1 AAT
2757726 AACATTATTA
Statistics
Matches: 85, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
14 1 0.01
15 67 0.79
16 17 0.20
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (14 bp):
AATTATTTTAAATA
Found at i:2757671 original size:30 final size:30
Alignment explanation
Indices: 2757595--2757725 Score: 169
Period size: 30 Copynumber: 4.3 Consensus size: 30
2757585 CAATTCATAC
2757595 TAAT-AATTATTTTAAAATAATCAATTATTTTA
1 TAATAAATTATTTTAAAAT-A--AATTATTTTA
*
2757627 -ATATAAATTTATTTTAAAGTAAATTATTTTA
1 TA-ATAAA-TTATTTTAAAATAAATTATTTTA
*
2757658 TAATAAATTATTTTAAAATAAACTATTTTA
1 TAATAAATTATTTTAAAATAAATTATTTTA
2757688 TAATAAATTATTTTAAAATAAATTATTTTGA
1 TAATAAATTATTTTAAAATAAATTATTTT-A
2757719 -AATAAAT
1 TAATAAAT
2757726 AACATTATTA
Statistics
Matches: 90, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
30 56 0.62
31 17 0.19
32 3 0.03
33 3 0.03
34 11 0.12
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TAATAAATTATTTTAAAATAAATTATTTTA
Found at i:2757700 original size:45 final size:46
Alignment explanation
Indices: 2757611--2757725 Score: 162
Period size: 45 Copynumber: 2.5 Consensus size: 46
2757601 TTATTTTAAA
* * *
2757611 ATAATCAATTATTTTAATATAAATTTATTTTAAAGTAAATTATTTT
1 ATAATAAATTATTTTAAAATAAATCTATTTTAAAGTAAATTATTTT
2757657 ATAATAAATTATTTTAAAATAAA-CTATTTTATAA-TAAATTATTTT
1 ATAATAAATTATTTTAAAATAAATCTATTTTA-AAGTAAATTATTTT
* *
2757702 AAAATAAATTATTTTGAAATAAAT
1 ATAATAAATTATTTTAAAATAAAT
2757726 AACATTATTA
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
45 39 0.63
46 23 0.37
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (46 bp):
ATAATAAATTATTTTAAAATAAATCTATTTTAAAGTAAATTATTTT
Found at i:2764432 original size:16 final size:17
Alignment explanation
Indices: 2764413--2764444 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2764403 ATTAAATCGT
2764413 TTTG-TTATTACAAATG
1 TTTGTTTATTACAAATG
2764429 TTTGTTTATTACAAAT
1 TTTGTTTATTACAAAT
2764445 ATCATGCCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (17 bp):
TTTGTTTATTACAAATG
Found at i:2765942 original size:20 final size:21
Alignment explanation
Indices: 2765903--2765975 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
2765893 GGAAGCAAAG
* *
2765903 AGAGAAACAACGAAAGCACAT
1 AGAGAAACAACGACAGCACAA
*
2765924 AGAGAAAC-ACGACATCACAA
1 AGAGAAACAACGACAGCACAA
*
2765944 AGAGAAGCAACGACAGCACAA
1 AGAGAAACAACGACAGCACAA
*
2765965 AGAGAAGCAAC
1 AGAGAAACAAC
2765976 ATATAAGAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.55, C:0.22, G:0.21, T:0.03
Consensus pattern (21 bp):
AGAGAAACAACGACAGCACAA
Found at i:2766474 original size:42 final size:43
Alignment explanation
Indices: 2766399--2766500 Score: 127
Period size: 42 Copynumber: 2.4 Consensus size: 43
2766389 TTTGTATCCT
* *
2766399 AAAAACGTCGTTATATACCAGACCTTTTACGGCATTTATAT-G
1 AAAAACGCCGTTATATACCACACCTTTTACGGCATTTATATCG
*
2766441 AAAAACGCCGTTATATATCACA-CTTTTAGCGGCATTTATATCCG
1 AAAAACGCCGTTATATACCACACCTTTTA-CGGCATTTATAT-CG
* *
2766485 ACAAACGCCGCTATAT
1 AAAAACGCCGTTATAT
2766501 CCCAAAGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
41 6 0.12
42 31 0.60
44 15 0.29
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (43 bp):
AAAAACGCCGTTATATACCACACCTTTTACGGCATTTATATCG
Found at i:2766714 original size:42 final size:42
Alignment explanation
Indices: 2766667--2766844 Score: 221
Period size: 42 Copynumber: 4.2 Consensus size: 42
2766657 AAAACATCGT
* *
2766667 TAAATCTCAACACCTATTGTGGCGTTTGTGGGAAAATGCCGC
1 TAAATCTCAACACCTATTGTGGCATTTGTGGGAAAACGCCGC
* ** *
2766709 TAAATCTCAACACCTATTGCGATATTTGTGGAAAAACGCCGC
1 TAAATCTCAACACCTATTGTGGCATTTGTGGGAAAACGCCGC
* *
2766751 TAAATCACAACATCTATTGTGGCATTTGTGGGACAAACGCCGC
1 TAAATCTCAACACCTATTGTGGCATTTGTGGGA-AAACGCCGC
* * * *
2766794 TAAATCTCAACACCTACTGTGGCGTTTGTTGGACAAACGCCAC
1 TAAATCTCAACACCTATTGTGGCATTTGTGGGA-AAACGCCGC
*
2766837 TATATCTC
1 TAAATCTC
2766845 GTTACTTATT
Statistics
Matches: 116, Mismatches: 19, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
42 63 0.54
43 53 0.46
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (42 bp):
TAAATCTCAACACCTATTGTGGCATTTGTGGGAAAACGCCGC
Found at i:2767797 original size:2 final size:2
Alignment explanation
Indices: 2767790--2767845 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
2767780 TTACTTGTTA
2767790 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
2767832 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
2767846 CATAAGGATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2771162 original size:2 final size:2
Alignment explanation
Indices: 2771157--2771203 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
2771147 AGATTTTAAC
2771157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
2771200 AT AT
1 AT AT
2771204 TACGCATTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2778093 original size:8 final size:8
Alignment explanation
Indices: 2778073--2778102 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
2778063 GTTGAGTTGC
2778073 AATTTTGAA
1 AATTTT-AA
2778082 AATTTTAA
1 AATTTTAA
2778090 AATTTTAA
1 AATTTTAA
2778098 AATTT
1 AATTT
2778103 GACTAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 15 0.71
9 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (8 bp):
AATTTTAA
Found at i:2780082 original size:24 final size:24
Alignment explanation
Indices: 2780042--2780089 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
2780032 TAATGCCATT
2780042 TTTTTAATCAAATAATTATATTAA
1 TTTTTAATCAAATAATTATATTAA
*
2780066 TTTTTAATTTAAA-AATTATATTAA
1 TTTTTAA-TCAAATAATTATATTAA
2780090 AAAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.82
25 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTTAATCAAATAATTATATTAA
Found at i:2799877 original size:16 final size:16
Alignment explanation
Indices: 2799853--2799885 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2799843 TATCGCCGAC
*
2799853 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2799869 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2799885 C
1 C
2799886 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:2801155 original size:7 final size:7
Alignment explanation
Indices: 2801140--2801310 Score: 123
Period size: 7 Copynumber: 24.6 Consensus size: 7
2801130 TTAAACCCTT
*
2801140 AACCCTA
1 AACCATA
*
2801147 AACTATA
1 AACCATA
*
2801154 AACTATA
1 AACCATA
2801161 AACCATA
1 AACCATA
2801168 AACCATA
1 AACCATA
*
2801175 AACCTTA
1 AACCATA
* *
2801182 CACCCTA
1 AACCATA
2801189 AACCATA
1 AACCATA
*
2801196 AACTATA
1 AACCATA
*
2801203 AACCCTA
1 AACCATA
2801210 AACCATA
1 AACCATA
2801217 AA-CATTA
1 AACCA-TA
2801224 AACCATA
1 AACCATA
*
2801231 AACTATA
1 AACCATA
*
2801238 AACTATA
1 AACCATA
*
2801245 AACCCTA
1 AACCATA
* *
2801252 TACCTTA
1 AACCATA
* *
2801259 TACCTTA
1 AACCATA
2801266 AACC-TA
1 AACCATA
* *
2801272 TACCTTA
1 AACCATA
* *
2801279 TACCTTA
1 AACCATA
*
2801286 AACCCTA
1 AACCATA
2801293 AA-CACTA
1 AACCA-TA
2801300 AACCATA
1 AACCATA
2801307 AACC
1 AACC
2801311 CTATCACATA
Statistics
Matches: 137, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
6 8 0.06
7 125 0.91
8 4 0.03
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (7 bp):
AACCATA
Found at i:2801249 original size:42 final size:42
Alignment explanation
Indices: 2801131--2801313 Score: 196
Period size: 42 Copynumber: 4.4 Consensus size: 42
2801121 GTGCATAACT
*
2801131 TAAACCCTT-AACCCTAAACTATAAACTATAAACCATAAACCA
1 TAAA-CCTTAAACCCTAAACTATAAACTATAAACCCTAAACCA
* *
2801173 TAAACCTTACACCCTAAACCATAAACTATAAACCCTAAACCA
1 TAAACCTTAAACCCTAAACTATAAACTATAAACCCTAAACCA
* * * *
2801215 TAAACATTAAACCATAAACTATAAACTATAAACCCTATACCT
1 TAAACCTTAAACCCTAAACTATAAACTATAAACCCTAAACCA
* * *
2801257 TATACCTTAAA-CCTATACCT-TATACCT-TAAACCCTAAA-CA
1 TAAACCTTAAACCCTA-AACTATA-AACTATAAACCCTAAACCA
*
2801297 CTAAACCATAAACCCTA
1 -TAAACCTTAAACCCTA
2801314 TCACATAATT
Statistics
Matches: 118, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
40 1 0.01
41 28 0.24
42 89 0.75
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (42 bp):
TAAACCTTAAACCCTAAACTATAAACTATAAACCCTAAACCA
Found at i:2801273 original size:20 final size:20
Alignment explanation
Indices: 2801243--2801289 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
2801233 CTATAAACTA
2801243 TAAACCCTATACCTTATACCT
1 TAAA-CCTATACCTTATACCT
2801264 TAAACCTATACCTTATACCT
1 TAAACCTATACCTTATACCT
2801284 TAAACC
1 TAAACC
2801290 CTAAACACTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (20 bp):
TAAACCTATACCTTATACCT
Found at i:2801410 original size:14 final size:14
Alignment explanation
Indices: 2801391--2801420 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2801381 TATAATTATC
*
2801391 AATAATGTATTTTT
1 AATAATGTAATTTT
2801405 AATAATGTAATTTT
1 AATAATGTAATTTT
2801419 AA
1 AA
2801421 AAAATCTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:2801497 original size:26 final size:26
Alignment explanation
Indices: 2801475--2801529 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
2801465 GCTTTTCGAG
2801475 TCGAATATCAAGTAGCTCGTTTCGGC
1 TCGAATATCAAGTAGCTCGTTTCGGC
* ** *
2801501 TTGAATATTGAGTAGCTTGTTTCGGC
1 TCGAATATCAAGTAGCTCGTTTCGGC
2801527 TCG
1 TCG
2801530 TTAAGAAATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.36
Consensus pattern (26 bp):
TCGAATATCAAGTAGCTCGTTTCGGC
Found at i:2801935 original size:23 final size:23
Alignment explanation
Indices: 2801897--2801941 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2801887 TTTAGGAAAT
* *
2801897 AGAAGAAGAATTGTCTCGATTAC
1 AGAAGAAAAATAGTCTCGATTAC
*
2801920 AGAAGAAAAATAGTCTTGATTA
1 AGAAGAAAAATAGTCTCGATTA
2801942 GATTTTAGGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (23 bp):
AGAAGAAAAATAGTCTCGATTAC
Found at i:2802833 original size:4 final size:4
Alignment explanation
Indices: 2802808--2802873 Score: 50
Period size: 4 Copynumber: 17.2 Consensus size: 4
2802798 TATAAGTATA
* * **
2802808 ACAT ATAT ACAT GCAT -CAT ACAT ACAT -CAT TGAT -CAT ACAT A-ATT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA-T
*
2802853 ACAT ATAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT A
2802874 TGTATATATA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
3 9 0.18
4 40 0.80
5 1 0.02
ACGTcount: A:0.45, C:0.20, G:0.03, T:0.32
Consensus pattern (4 bp):
ACAT
Found at i:2802863 original size:8 final size:8
Alignment explanation
Indices: 2802771--2802894 Score: 62
Period size: 8 Copynumber: 15.0 Consensus size: 8
2802761 TTTAAAAAAA
2802771 ATATGACAT
1 ATAT-ACAT
*
2802780 ATATATAT
1 ATATACAT
*
2802788 ATATATAT
1 ATATACAT
2802796 AGTATA-AGT
1 A-TATACA-T
2802805 ATA-ACAT
1 ATATACAT
2802812 ATATACAT
1 ATATACAT
2802820 GCATCATACAT
1 --AT-ATACAT
*
2802831 ACAT-CATT
1 ATATACA-T
2802839 GATCATACAT
1 -AT-ATACAT
2802849 A-ATTACAT
1 ATA-TACAT
2802857 ATATACAT
1 ATATACAT
*
2802865 ACATACAT
1 ATATACAT
*
2802873 ATGT--AT
1 ATATACAT
2802879 ATATACAT
1 ATATACAT
*
2802887 ATGTACAT
1 ATATACAT
2802895 CAGGGGCGGA
Statistics
Matches: 92, Mismatches: 8, Indels: 31
0.70 0.06 0.24
Matches are distributed among these distances:
6 5 0.05
7 8 0.09
8 52 0.57
9 14 0.15
10 5 0.05
11 8 0.09
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (8 bp):
ATATACAT
Found at i:2802864 original size:16 final size:16
Alignment explanation
Indices: 2802808--2802874 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 16
2802798 TATAAGTATA
*
2802808 ACATATATACATGCAT
1 ACATATATACATACAT
*
2802824 -CATACATACAT-CAT
1 ACATATATACATACAT
** *
2802838 TGAT-CATACATA-ATT
1 ACATATATACATACA-T
2802853 ACATATATACATACAT
1 ACATATATACATACAT
2802869 ACATAT
1 ACATAT
2802875 GTATATATAC
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
14 11 0.27
15 15 0.37
16 14 0.34
17 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (16 bp):
ACATATATACATACAT
Found at i:2803145 original size:2 final size:2
Alignment explanation
Indices: 2803138--2803196 Score: 54
Period size: 2 Copynumber: 31.5 Consensus size: 2
2803128 TAACGTACAT
* * *
2803138 TA TA TA TA TA TA TG TA T- TA TA -A CA TA TA TG TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
2803177 TA CA T- TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
2803197 TGTAGTTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
1 4 0.09
2 42 0.91
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2805111 original size:16 final size:16
Alignment explanation
Indices: 2805090--2805122 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2805080 TACTATTCAT
*
2805090 GTGAATAGTGAACTTC
1 GTGAATAGTGAAATTC
2805106 GTGAATAGTGAAATTC
1 GTGAATAGTGAAATTC
2805122 G
1 G
2805123 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (16 bp):
GTGAATAGTGAAATTC
Found at i:2810386 original size:14 final size:15
Alignment explanation
Indices: 2810369--2810402 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2810359 TTTATAAATA
2810369 ATTAAAAA-TATTAT
1 ATTAAAAATTATTAT
2810383 ATTAAAAATTATTAT
1 ATTAAAAATTATTAT
*
2810398 TTTAA
1 ATTAA
2810403 TACACCCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTAAAAATTATTAT
Found at i:2810648 original size:37 final size:37
Alignment explanation
Indices: 2810597--2810684 Score: 149
Period size: 37 Copynumber: 2.4 Consensus size: 37
2810587 TAAAAATTCG
*
2810597 ATGAGTTTAACGAGCAATGAGGCGAGCAACAAGCTTA
1 ATGAGCTTAACGAGCAATGAGGCGAGCAACAAGCTTA
* *
2810634 ATGAGCTTAGCGAGCAATGAGTCGAGCAACAAGCTTA
1 ATGAGCTTAACGAGCAATGAGGCGAGCAACAAGCTTA
2810671 ATGAGCTTAACGAG
1 ATGAGCTTAACGAG
2810685 AAACAAGTCG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.17, G:0.27, T:0.19
Consensus pattern (37 bp):
ATGAGCTTAACGAGCAATGAGGCGAGCAACAAGCTTA
Found at i:2810694 original size:37 final size:37
Alignment explanation
Indices: 2810619--2810699 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
2810609 AGCAATGAGG
* * **
2810619 CGAGCAACAAGCTTAATGAGCTTAGCGAGCAATGAGT
1 CGAGCAACAAGCTTAATGAGCTTAACGAGAAACAAGT
2810656 CGAGCAACAAGCTTAATGAGCTTAACGAGAAACAAGT
1 CGAGCAACAAGCTTAATGAGCTTAACGAGAAACAAGT
2810693 CGAGCAA
1 CGAGCAA
2810700 TAAATTTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.40, C:0.20, G:0.25, T:0.16
Consensus pattern (37 bp):
CGAGCAACAAGCTTAATGAGCTTAACGAGAAACAAGT
Found at i:2827223 original size:3 final size:3
Alignment explanation
Indices: 2827208--2827237 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
2827198 TATATGCTAC
*
2827208 TGA TGA TGG TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2827238 GAGTGAGGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:2827474 original size:42 final size:38
Alignment explanation
Indices: 2827419--2827534 Score: 106
Period size: 42 Copynumber: 2.8 Consensus size: 38
2827409 TTTTTATTTA
* *
2827419 TTTTGTTTCTTAATTTTTTTATTATTTAATTGTTCGAATTGT
1 TTTTATTTTTTAATTTTTTTATTATTTAATT-TTC---TTGT
* * * *
2827461 TTTTATTTTTTAATTTTTTTGTTGTATCATTTTCTTGT
1 TTTTATTTTTTAATTTTTTTATTATTTAATTTTCTTGT
2827499 TTTTATTTTATTTAAATTGTTTTTATTATTTAATTT
1 TTTTA-TTT-TTT-AATT-TTTTTATTATTTAATTT
2827535 CTTTAGTTGT
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
38 9 0.15
39 3 0.05
40 3 0.05
41 7 0.12
42 38 0.63
ACGTcount: A:0.19, C:0.03, G:0.07, T:0.71
Consensus pattern (38 bp):
TTTTATTTTTTAATTTTTTTATTATTTAATTTTCTTGT
Found at i:2827529 original size:18 final size:19
Alignment explanation
Indices: 2827495--2827531 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2827485 TATCATTTTC
2827495 TTGTTTTTATTTTATTTAAA
1 TTGTTTTTA-TTTATTTAAA
2827515 TTGTTTTTA-TTATTTAA
1 TTGTTTTTATTTATTTAA
2827532 TTTCTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.70
Consensus pattern (19 bp):
TTGTTTTTATTTATTTAAA
Found at i:2832453 original size:15 final size:15
Alignment explanation
Indices: 2832433--2832486 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
2832423 TCAAAGTCAA
2832433 TGAGTTGACTCTGTC
1 TGAGTTGACTCTGTC
**
2832448 TGAGTTGACTC--AA
1 TGAGTTGACTCTGTC
2832461 TGAGTTGACTCTGTC
1 TGAGTTGACTCTGTC
2832476 TGAGTTGACTC
1 TGAGTTGACTC
2832487 AATGAGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 11 0.33
15 22 0.67
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (15 bp):
TGAGTTGACTCTGTC
Found at i:2832461 original size:28 final size:28
Alignment explanation
Indices: 2832429--2832494 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
2832419 CAGGTCAAAG
2832429 TCAATGAGTTGACTCTGTCTGAGTTGAC
1 TCAATGAGTTGACTCTGTCTGAGTTGAC
2832457 TCAATGAGTTGACTCTGTCTGAGTTGAC
1 TCAATGAGTTGACTCTGTCTGAGTTGAC
2832485 TCAATGAGTT
1 TCAATGAGTT
2832495 AAAGGTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (28 bp):
TCAATGAGTTGACTCTGTCTGAGTTGAC
Found at i:2832466 original size:13 final size:13
Alignment explanation
Indices: 2832429--2832494 Score: 60
Period size: 15 Copynumber: 4.8 Consensus size: 13
2832419 CAGGTCAAAG
2832429 TCAATGAGTTGAC
1 TCAATGAGTTGAC
**
2832442 TCTGTCTGAGTTGAC
1 TC--AATGAGTTGAC
2832457 TCAATGAGTTGAC
1 TCAATGAGTTGAC
**
2832470 TCTGTCTGAGTTGAC
1 TC--AATGAGTTGAC
2832485 TCAATGAGTT
1 TCAATGAGTT
2832495 AAAGGTTCTT
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
13 19 0.46
15 22 0.54
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (13 bp):
TCAATGAGTTGAC
Found at i:2853175 original size:16 final size:16
Alignment explanation
Indices: 2853154--2853187 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2853144 TTACTATTCA
*
2853154 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
2853170 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
2853186 CG
1 CG
2853188 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Done.