Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005101.1 Hibiscus syriacus cultivar Beakdansim tig00011468_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: 119937
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4165 original size:18 final size:19
Alignment explanation
Indices: 4138--4175 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
4128 TACAAGTTTA
4138 AAAAATATAGTTACAATAC
1 AAAAATATAGTTACAATAC
4157 AAAAA-ATAGTTACAATAC
1 AAAAATATAGTTACAATAC
4175 A
1 A
4176 TAATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATATAGTTACAATAC
Found at i:5761 original size:23 final size:23
Alignment explanation
Indices: 5735--5801 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
5725 CCACAGCTCA
5735 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCGAAGTGCCACG
* *
5758 TATAATTGCACCGGAGTGCCGCG
1 TATAATTGCACCGAAGTGCCACG
* *
5781 TAGAATTGCACCGTAGTGCCA
1 TATAATTGCACCGAAGTGCCA
5802 TATAATAATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
TATAATTGCACCGAAGTGCCACG
Found at i:6008 original size:101 final size:98
Alignment explanation
Indices: 5817--6028 Score: 320
Period size: 97 Copynumber: 2.1 Consensus size: 98
5807 TAATGTCCAT
* * *
5817 AAGGACCACATATCATTCTTTAAGAATCATATATATACTAGAGATCAAGTATGTGTCTCCAGACT
1 AAGGACCACATATCATTCCTTAAGAATCATATATATACAAGAGATCAAGTATGCGTCTCCAGACT
5882 TCACACATGTTCCAAAGAATAC-ATATGTCCCG
66 TCACACATGTTCCAAAGAATACAATATGTCCCG
*
5914 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAG-GATCAAGTATGCGTCTCACC
1 AAGGACCACATATCATTCCTTAAGAATCATAT--ATAT-ACAAGAGATCAAGTATGCGTCT--CC
5978 AGACTTCACACATGTTCCAAAGAATACATATATGTCCCG
61 AGACTTCACACATGTTCCAAAGAATACA-ATATGTCCCG
6017 AAGGACCACATA
1 AAGGACCACATA
6029 GACCCTCGAC
Statistics
Matches: 104, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
97 31 0.30
99 19 0.18
100 3 0.03
101 29 0.28
103 22 0.21
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (98 bp):
AAGGACCACATATCATTCCTTAAGAATCATATATATACAAGAGATCAAGTATGCGTCTCCAGACT
TCACACATGTTCCAAAGAATACAATATGTCCCG
Found at i:7268 original size:32 final size:30
Alignment explanation
Indices: 7232--7295 Score: 101
Period size: 32 Copynumber: 2.1 Consensus size: 30
7222 TTGGTTAGAA
*
7232 GAAAGGAGTTTGTTGTGTAAGAGATTGAAGAT
1 GAAAGGAGTGTGTTGTGTAAGAGA-TGAA-AT
7264 GAAAGGAGTGTGTTGTGTAAGAGATGAAAT
1 GAAAGGAGTGTGTTGTGTAAGAGATGAAAT
7294 GA
1 GA
7296 GTGTGTTATG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 4 0.13
31 4 0.13
32 23 0.74
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.28
Consensus pattern (30 bp):
GAAAGGAGTGTGTTGTGTAAGAGATGAAAT
Found at i:7288 original size:25 final size:25
Alignment explanation
Indices: 7260--7307 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
7250 AAGAGATTGA
*
7260 AGATGAAAGGAGTGTGTTGTGTAAG
1 AGATGAAAGGAGTGTGTTATGTAAG
*
7285 AGATGAAATGAGTGTGTTATGTA
1 AGATGAAAGGAGTGTGTTATGTA
7308 CGAGTTCCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.31
Consensus pattern (25 bp):
AGATGAAAGGAGTGTGTTATGTAAG
Found at i:9419 original size:6 final size:6
Alignment explanation
Indices: 9403--9432 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
9393 ATCAAATTAA
9403 AAAACTT AAAATT AAAATT AAAATT AAAAT
1 AAAA-TT AAAATT AAAATT AAAATT AAAAT
9433 AATTAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.83
7 4 0.17
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:9791 original size:2 final size:2
Alignment explanation
Indices: 9779--9827 Score: 77
Period size: 2 Copynumber: 26.0 Consensus size: 2
9769 GATTCAAATT
9779 TA TA T- 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 TA
9819 TA TA -A TA TA
1 TA TA TA TA TA
9828 AACGTACCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.07
2 41 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10604 original size:2 final size:2
Alignment explanation
Indices: 10597--10644 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
10587 GAAAATTATG
10597 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
10639 TA TA TA
1 TA TA TA
10645 GAGAGAGAGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10649 original size:2 final size:2
Alignment explanation
Indices: 10644--10687 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
10634 ATATATATAT
10644 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
10686 AG
1 AG
10688 CAGTATCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:10751 original size:2 final size:2
Alignment explanation
Indices: 10746--10775 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
10736 CTTTTTTTCT
10746 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10776 AGCAAATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13526 original size:29 final size:28
Alignment explanation
Indices: 13494--13588 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
13484 AATTGGTCTA
*
13494 TAAACTTTTGAATATTCTAATTTCATCCT
1 TAAACTTTTGAACATTCTAATTT-ATCCT
* *
13523 TAAAC-TATGATACCCATTCTAAATTAGTCCT
1 TAAACTTTTGA-A--CATTCTAATTTA-TCCT
* *
13554 TAAACTTTTGAACATTCCAATTTTATTCT
1 TAAACTTTTGAACATTCTAA-TTTATCCT
13583 TAAACT
1 TAAACT
13589 ATGACCCTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 12
0.74 0.10 0.17
Matches are distributed among these distances:
28 4 0.08
29 22 0.42
30 4 0.08
31 19 0.36
32 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (28 bp):
TAAACTTTTGAACATTCTAATTTATCCT
Found at i:13542 original size:60 final size:60
Alignment explanation
Indices: 13478--13640 Score: 172
Period size: 60 Copynumber: 2.7 Consensus size: 60
13468 TATGACTTTA
* * *
13478 ATTCTAAATTGGT-CTATAAACTTTTGAATATTCTAATTTCATCCTTAAACTATGATACCC
1 ATTCTAAATTAGTCCT-TAAACTTTTGAACATTCCAATTTCATCCTTAAACTATGATACCC
* *
13538 ATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTTATTCTTAAACTATG--ACCC
1 ATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCTTAAACTATGATACCC
* * * * *
13596 TTATTCTAAATGAGTCCCTAAA-TGCTTAAACCTTCCAATTTCATC
1 --ATTCTAAATTAGTCCTTAAACT-TTTGAACATTCCAATTTCATC
13641 ATCAAATTCA
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
58 4 0.05
59 1 0.01
60 80 0.92
61 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.06, T:0.40
Consensus pattern (60 bp):
ATTCTAAATTAGTCCTTAAACTTTTGAACATTCCAATTTCATCCTTAAACTATGATACCC
Found at i:13543 original size:31 final size:27
Alignment explanation
Indices: 13502--13592 Score: 74
Period size: 31 Copynumber: 3.1 Consensus size: 27
13492 TATAAACTTT
*
13502 TGAATATTCTAATTTCATCCTTAAACTA
1 TGAACATTCTAATTT-ATCCTTAAACTA
* *
13530 TGATACCCATTCTAAATTAGTCCTTAAACTTT
1 TGA-A--CATTCTAATTTA-TCCTTAAAC-TA
* *
13562 TGAACATTCCAATTTTATTCTTAAACTA
1 TGAACATTCTAA-TTTATCCTTAAACTA
13590 TGA
1 TGA
13593 CCCTTATTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
28 7 0.14
29 16 0.32
30 4 0.08
31 19 0.38
32 4 0.08
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (27 bp):
TGAACATTCTAATTTATCCTTAAACTA
Found at i:14072 original size:38 final size:35
Alignment explanation
Indices: 13997--14072 Score: 89
Period size: 38 Copynumber: 2.1 Consensus size: 35
13987 TAATTTTATA
* *
13997 ATTTTTAAATTGATATTTTAATTTTTATTCATATT
1 ATTTTTAAATTAATATTTTAATTTTTAATCATATT
* *
14032 ATTTATTAAATTTAATATCTTTTATTTTTAATCATTTT
1 ATTT-TTAAA-TTAATAT-TTTAATTTTTAATCATATT
14070 ATT
1 ATT
14073 AATTTTACCG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
35 4 0.12
36 5 0.15
37 6 0.18
38 19 0.56
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (35 bp):
ATTTTTAAATTAATATTTTAATTTTTAATCATATT
Found at i:14946 original size:24 final size:25
Alignment explanation
Indices: 14919--14974 Score: 87
Period size: 24 Copynumber: 2.2 Consensus size: 25
14909 ATTAATATAA
14919 ATTTTATTAAATTATTC-AAAATAT
1 ATTTTATTAAATTATTCTAAAATAT
*
14943 ATTTTATTAAATTATTCTTATAATAT
1 ATTTTATTAAATTATTC-TAAAATAT
14969 ATTTTA
1 ATTTTA
14975 AAAAATTAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 17 0.59
26 12 0.41
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTTTATTAAATTATTCTAAAATAT
Found at i:15355 original size:23 final size:23
Alignment explanation
Indices: 15306--15356 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
15296 TATATTTTCA
*
15306 ATATTATAATAAAATAATCAATT
1 ATATTATAATAAAATAATCAATC
*
15329 ATATTATAATAATATAAT-ATATC
1 ATATTATAATAAAATAATCA-ATC
15352 ATATT
1 ATATT
15357 TTTATTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (23 bp):
ATATTATAATAAAATAATCAATC
Found at i:15783 original size:23 final size:25
Alignment explanation
Indices: 15757--15848 Score: 61
Period size: 24 Copynumber: 3.8 Consensus size: 25
15747 TTAACTAAAA
*
15757 AATATAGAAATAATA-T-TTTTAAT
1 AATATAAAAATAATATTATTTTAAT
15780 AATA-AATAAATAA-ATTATTTTAAT
1 AATATAA-AAATAATATTATTTTAAT
* * *
15804 ATTTTAAAAATAATA--ATATTAAT
1 AATATAAAAATAATATTATTTTAAT
** *
15827 TTTATGATAAATAATATTATTT
1 AATAT-AAAAATAATATTATTT
15849 ATTGTATTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
22 2 0.04
23 21 0.40
24 24 0.45
25 3 0.06
26 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (25 bp):
AATATAAAAATAATATTATTTTAAT
Found at i:15794 original size:27 final size:27
Alignment explanation
Indices: 15740--15802 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
15730 GTACTAATAT
*
15740 TAATATTTTAACTAAAAAATATAGAAA
1 TAATATTTTAACTAAAAAATAAAGAAA
* *
15767 TAATATTTTTAA-TAATAAATAAATAAA
1 TAATA-TTTTAACTAAAAAATAAAGAAA
15794 T--TATTTTAA
1 TAATATTTTAA
15803 TATTTTAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 6 0.19
25 2 0.06
27 18 0.56
28 6 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (27 bp):
TAATATTTTAACTAAAAAATAAAGAAA
Found at i:15958 original size:14 final size:14
Alignment explanation
Indices: 15941--15969 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15931 CTATAAAACG
15941 TTTTTCAGAAAATA
1 TTTTTCAGAAAATA
15955 TTTTTCAGAAAATA
1 TTTTTCAGAAAATA
15969 T
1 T
15970 AATTCATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (14 bp):
TTTTTCAGAAAATA
Found at i:20646 original size:12 final size:12
Alignment explanation
Indices: 20629--20676 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
20619 TTTCGATAAA
20629 AAAATAATATTT
1 AAAATAATATTT
20641 AAAATAATACTTT
1 AAAATAATA-TTT
20654 ACTAAA-AATATTT
1 A--AAATAATATTT
20667 AAAAT-ATATT
1 AAAATAATATT
20677 AATATTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 8 0.25
12 9 0.28
13 8 0.25
14 4 0.12
15 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATAATATTT
Found at i:26648 original size:29 final size:29
Alignment explanation
Indices: 26606--26664 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
26596 ATTTTCACCT
26606 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
26635 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
26664 A
1 A
26665 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:31331 original size:29 final size:29
Alignment explanation
Indices: 31289--31347 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
31279 ATTTTCACCT
31289 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
31318 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
31347 A
1 A
31348 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:33845 original size:23 final size:23
Alignment explanation
Indices: 33819--33882 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
33809 CAGCTCATAT
*
33819 AATTACACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
33842 AATTGCACC-AGAGAGCCTCGTAG
1 AATTGCACCGA-AGTGCCACGTAG
* *
33865 AATTGCACTGTAGTGCCA
1 AATTGCACCGAAGTGCCA
33883 TATAATAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.20
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:34069 original size:103 final size:103
Alignment explanation
Indices: 33890--34115 Score: 407
Period size: 103 Copynumber: 2.2 Consensus size: 103
33880 CCATATAATA
*
33890 ATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATAATAGGGATCAAGTATGTG
1 ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATAATAGGGATCAAGTATGTG
33955 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
*
33993 ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTG
1 ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATAATAGGGATCAAGTATGTG
34058 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
66 TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
* * *
34096 ATATCCCGAAAGACCACATA
1 ATGTCCCTAAGGACCACATA
34116 GACCCTCTAC
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 118 1.00
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (103 bp):
ATGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATAATAGGGATCAAGTATGTG
TCTCACCAGACTTCACACATGTTCCAAAGAATACATAT
Found at i:35215 original size:11 final size:11
Alignment explanation
Indices: 35199--35226 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
35189 GATGGAGAAG
35199 AAGAAGTGAAT
1 AAGAAGTGAAT
35210 AAGAAGTGAAT
1 AAGAAGTGAAT
35221 AAGAAG
1 AAGAAG
35227 AGAAATCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (11 bp):
AAGAAGTGAAT
Found at i:35639 original size:76 final size:76
Alignment explanation
Indices: 35552--35702 Score: 275
Period size: 76 Copynumber: 2.0 Consensus size: 76
35542 TCTATATGAT
*
35552 AAGAAGAGAGACTAAAGCATTTACAGAAAGACAAATAATGTGGATGAGATACTATGTTCAAAGCC
1 AAGAAGAGAGACTAAAGCATTTACAGAAAGACAAATAATGTGGATGAGAGACTATGTTCAAAGCC
*
35617 GTAATCTGACA
66 GCAATCTGACA
*
35628 AAGAAGAGAGACTAAAGCATTTGCAGAAAGACAAATAATGTGGATGAGAGACTATGTTCAAAGCC
1 AAGAAGAGAGACTAAAGCATTTACAGAAAGACAAATAATGTGGATGAGAGACTATGTTCAAAGCC
35693 GCAATCTGAC
66 GCAATCTGAC
35703 CCTTTGATAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 72 1.00
ACGTcount: A:0.44, C:0.14, G:0.23, T:0.20
Consensus pattern (76 bp):
AAGAAGAGAGACTAAAGCATTTACAGAAAGACAAATAATGTGGATGAGAGACTATGTTCAAAGCC
GCAATCTGACA
Found at i:36117 original size:15 final size:15
Alignment explanation
Indices: 36097--36131 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
36087 TGGAAGATCT
*
36097 GATTGTGAAACTTCG
1 GATTGTGAAAATTCG
36112 GATTGTGAAAATTCG
1 GATTGTGAAAATTCG
36127 GATTG
1 GATTG
36132 AAGAAGGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.09, G:0.29, T:0.34
Consensus pattern (15 bp):
GATTGTGAAAATTCG
Found at i:40114 original size:23 final size:23
Alignment explanation
Indices: 40084--40130 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
40074 CATCTCTATT
* *
40084 ATGAAAAATAGTTAAGTCTTTTC
1 ATGAAAAATAATTAAGTCATTTC
*
40107 ATGAAAAATAATTAATTCATTTC
1 ATGAAAAATAATTAAGTCATTTC
40130 A
1 A
40131 CCCAAAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.38
Consensus pattern (23 bp):
ATGAAAAATAATTAAGTCATTTC
Found at i:43668 original size:60 final size:60
Alignment explanation
Indices: 43543--43684 Score: 135
Period size: 60 Copynumber: 2.4 Consensus size: 60
43533 TGATTTATTT
* * * * * * *
43543 TAAATTAATCTTTAAAATTTTTAAATATTTTAATTTCATCCCTAAATTATGACTATTATTT
1 TAAATTAGTC-TTCAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACTATCATTC
* *
43604 TAAATTAGTCTTCAAACTTTTAAATA-TTTCATGTTCATCCCCAAACTATTATCT-TCATTC
1 TAAATTAGTCTTCAAACTTTTAAATATTTTAAT-TTCATCCCCAAACTATGA-CTATCATTC
* **
43664 TAAATCAGTCCCCAAACTTTT
1 TAAATTAGTCTTCAAACTTTT
43685 TGGACATTTC
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
59 5 0.07
60 51 0.76
61 11 0.16
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.45
Consensus pattern (60 bp):
TAAATTAGTCTTCAAACTTTTAAATATTTTAATTTCATCCCCAAACTATGACTATCATTC
Found at i:43931 original size:60 final size:60
Alignment explanation
Indices: 43832--43981 Score: 153
Period size: 60 Copynumber: 2.5 Consensus size: 60
43822 GATGAATTTG
* * ** * * *
43832 GGGATGAAATTGGAATATACAAAAGTTT-GGGAATCATTTAGAACGAGAGCTAGAGTTT-
1 GGGATGAAATTGAAATGTTGAAAAGTTTAAGGAATAATTTAGAACGAAAGCTAGAGTTTA
* * * * *
43890 GAGGATGAAATT-AGAATGTTTAAAATTTTAAGGAATAATTTAGAATGAAAGTTATAGTTTA
1 G-GGATGAAATTGA-AATGTTGAAAAGTTTAAGGAATAATTTAGAACGAAAGCTAGAGTTTA
43951 GGGATGAAATTGAAATGTTGAAAAGTTTAAG
1 GGGATGAAATTGAAATGTTGAAAAGTTTAAG
43982 AACCGGTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
58 1 0.01
59 21 0.28
60 50 0.68
61 2 0.03
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (60 bp):
GGGATGAAATTGAAATGTTGAAAAGTTTAAGGAATAATTTAGAACGAAAGCTAGAGTTTA
Found at i:52076 original size:3 final size:3
Alignment explanation
Indices: 52068--52100 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
52058 GGGCGCCAAC
52068 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
52101 CTTGGTGCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:55774 original size:2 final size:2
Alignment explanation
Indices: 55767--55799 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
55757 CCAAACTACC
55767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55800 GAAAATTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:60690 original size:59 final size:60
Alignment explanation
Indices: 60588--60733 Score: 165
Period size: 59 Copynumber: 2.5 Consensus size: 60
60578 TCTGGATAAA
* * *
60588 TTTGGAGATGAAATCAGAATATCTAGAAGTGTAGGTACCAATTTAGAATGAGATTCATAG
1 TTTGGAGATGAAATCAGAATATCTAAAAGTGTAGGTACCAATTTAAAATGAGAGTCATAG
* * *
60648 TTTGG-GATGAAATTAGAATAT-TCAAAAGTTTAAGG-ACTAATTTAAAATGAGAGTCATAG
1 TTTGGAGATGAAATCAGAATATCT-AAAAGTGT-AGGTACCAATTTAAAATGAGAGTCATAG
* * *
60707 TTTGAAGATGTAATCGGAATA-CTAAAA
1 TTTGGAGATGAAATCAGAATATCTAAAA
60734 AGTTCAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 50 0.69
60 21 0.29
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (60 bp):
TTTGGAGATGAAATCAGAATATCTAAAAGTGTAGGTACCAATTTAAAATGAGAGTCATAG
Found at i:60750 original size:60 final size:59
Alignment explanation
Indices: 60627--60765 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 59
60617 TGTAGGTACC
* * * * * * * **
60627 AATTTAGAATGAGATTCATAGTTTGGGATGAAATTAGAATATTCAAAAGTTTAAGGACT
1 AATTTAAAATGAGAGTCATAGTTTGAGATGAAATCAGAATACTAAAAAGTTCAAAAACT
* *
60686 AATTTAAAATGAGAGTCATAGTTTGAAGATGTAATCGGAATACTAAAAAGTTCAAAAACT
1 AATTTAAAATGAGAGTCATAGTTTG-AGATGAAATCAGAATACTAAAAAGTTCAAAAACT
60746 AATTTAAAATGA-ATGTCATA
1 AATTTAAAATGAGA-GTCATA
60766 ATTTAGGGAT
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
59 24 0.36
60 43 0.64
ACGTcount: A:0.45, C:0.06, G:0.17, T:0.32
Consensus pattern (59 bp):
AATTTAAAATGAGAGTCATAGTTTGAGATGAAATCAGAATACTAAAAAGTTCAAAAACT
Found at i:65466 original size:12 final size:12
Alignment explanation
Indices: 65451--65516 Score: 80
Period size: 12 Copynumber: 5.6 Consensus size: 12
65441 GTTATTTAAA
65451 CGGGTATTGGGC
1 CGGGTATTGGGC
*
65463 CGGGTATTGGGT
1 CGGGTATTGGGC
*
65475 CGGGTATTGGGT
1 CGGGTATTGGGC
*
65487 C-AGTATTGGGC
1 CGGGTATTGGGC
* *
65498 CGGGAATCGGGC
1 CGGGTATTGGGC
65510 CGGGTAT
1 CGGGTAT
65517 ATATATATAT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
11 9 0.20
12 37 0.80
ACGTcount: A:0.12, C:0.15, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:65574 original size:24 final size:25
Alignment explanation
Indices: 65518--65574 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
65508 GCCGGGTATA
65518 TATATATATTTAAATTAAATATTTAT
1 TATAT-TATTTAAATTAAATATTTAT
*
65544 T-TTTTATTTAAATT-AA-ATTTAT
1 TATATTATTTAAATTAAATATTTAT
65566 TAATATTAT
1 T-ATATTAT
65575 ATATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 7 0.26
23 2 0.07
24 15 0.56
25 2 0.07
26 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATTATTTAAATTAAATATTTAT
Found at i:67993 original size:25 final size:25
Alignment explanation
Indices: 67965--68045 Score: 146
Period size: 25 Copynumber: 3.2 Consensus size: 25
67955 TTTAGATACT
67965 TTAATTCTAAAACAT-TTGGGTGACA
1 TTAATTCTAAAACATCTT-GGTGACA
67990 TTAATTCTAAAACATCTTGGTGACA
1 TTAATTCTAAAACATCTTGGTGACA
68015 TTAATTCTAAAACATCTTGGTGACA
1 TTAATTCTAAAACATCTTGGTGACA
68040 TTAATT
1 TTAATT
68046 GCCTTCTTTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
25 53 0.96
26 2 0.04
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (25 bp):
TTAATTCTAAAACATCTTGGTGACA
Found at i:70876 original size:44 final size:45
Alignment explanation
Indices: 70782--70898 Score: 209
Period size: 44 Copynumber: 2.6 Consensus size: 45
70772 ATACCACTAG
* *
70782 TGTTATTATGGTATTGGACTCAGTTGCAAGCCCTCTTGTGAATGT
1 TGTTATTGTGGTATTGGACTCAGTTGCAAGCCCTCTTGTGAATAT
70827 TGTTATTGTGGTATTGGACTCAGTTGCAAG-CCTCTTGTGAATAT
1 TGTTATTGTGGTATTGGACTCAGTTGCAAGCCCTCTTGTGAATAT
70871 TGTTATTGTGGTATTGGACTCAGTTGCA
1 TGTTATTGTGGTATTGGACTCAGTTGCA
70899 TTCCCTTAAG
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 41 0.59
45 29 0.41
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.41
Consensus pattern (45 bp):
TGTTATTGTGGTATTGGACTCAGTTGCAAGCCCTCTTGTGAATAT
Found at i:73914 original size:27 final size:27
Alignment explanation
Indices: 73883--73950 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
73873 TTTATTTACA
*
73883 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATAGTAAC
73910 AAATCATATCTCTATAGGAATAGTAAC
1 AAATCATATCTCTATAGGAATAGTAAC
73937 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
73951 ATTCCTACAC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATAGTAAC
Found at i:77677 original size:27 final size:27
Alignment explanation
Indices: 77646--77713 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
77636 TCTATTTACA
77646 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
77673 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
77700 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
77714 ATTCTTACTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:83022 original size:23 final size:24
Alignment explanation
Indices: 82996--83042 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
82986 AATATTTTCA
* *
82996 TTGTATAACTTTTAATATG-TAAT
1 TTGTATAAATTTAAATATGCTAAT
83019 TTGTATAAATTTAAATATGCTAAT
1 TTGTATAAATTTAAATATGCTAAT
83043 AATGTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (24 bp):
TTGTATAAATTTAAATATGCTAAT
Found at i:88168 original size:6 final size:6
Alignment explanation
Indices: 88157--88184 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
88147 CCCGTGTTAG
88157 AATAGA AATAGA AATAGA AATAGA AATA
1 AATAGA AATAGA AATAGA AATAGA AATA
88185 AAAAGGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.14, T:0.18
Consensus pattern (6 bp):
AATAGA
Found at i:88998 original size:16 final size:15
Alignment explanation
Indices: 88979--89028 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
88969 TTTTTTTATG
88979 TTTTAATAACTTTTTA
1 TTTTAATAA-TTTTTA
*
88995 TTTTAATAATATTTA
1 TTTTAATAATTTTTA
*
89010 TTTTAATTATTTTT-
1 TTTTAATAATTTTTA
89024 TTTTA
1 TTTTA
89029 TTTTTATAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTAATAATTTTTA
Found at i:92980 original size:16 final size:16
Alignment explanation
Indices: 92961--92998 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
92951 GATATTTTCG
92961 GTTCAAATTACTTTTA
1 GTTCAAATTACTTTTA
*
92977 GTTCAAATTATTTTTA
1 GTTCAAATTACTTTTA
*
92993 ATTCAA
1 GTTCAA
92999 GTTAATATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (16 bp):
GTTCAAATTACTTTTA
Found at i:100412 original size:16 final size:16
Alignment explanation
Indices: 100391--100439 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
100381 ATATTATATG
100391 TCTGTTCATCTATCTA
1 TCTGTTCATCTATCTA
100407 TCTGTTCATCTATCTA
1 TCTGTTCATCTATCTA
*
100423 TCTGTTTATCTATCTA
1 TCTGTTCATCTATCTA
100439 T
1 T
100440 TTATCATATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.53
Consensus pattern (16 bp):
TCTGTTCATCTATCTA
Found at i:102548 original size:39 final size:39
Alignment explanation
Indices: 102448--102558 Score: 125
Period size: 39 Copynumber: 2.8 Consensus size: 39
102438 GTATTTATAA
* ** * *
102448 TTCTCAAATTATTTCACTCTAACATTTTTAATTCCTAAT
1 TTCTTAAATTATTTCACAATAACATTATAAATTCCTAAT
* * * *
102487 TTCTTAAATT-TTGCCACCATAACATTCTAAATTCTTAAT
1 TTCTTAAATTATT-TCACAATAACATTATAAATTCCTAAT
102526 TTCTTAAATTATTTCACAATAACATTATAAATT
1 TTCTTAAATTATTTCACAATAACATTATAAATT
102559 ATTTTTAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
38 2 0.03
39 56 0.93
40 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.01, T:0.46
Consensus pattern (39 bp):
TTCTTAAATTATTTCACAATAACATTATAAATTCCTAAT
Found at i:102637 original size:19 final size:19
Alignment explanation
Indices: 102606--102657 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
102596 AATATAATTA
*
102606 TAATTTTTGTTTTAATT-TT
1 TAATTTTT-TTTTAATTATG
102625 TAATATTTTTTTTAATTATG
1 TAAT-TTTTTTTTAATTATG
102645 TAATTTTATTTTT
1 TAATTTT-TTTTT
102658 TAAACTTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TAATTTTTTTTTAATTATG
Found at i:102754 original size:14 final size:16
Alignment explanation
Indices: 102722--102754 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
102712 ATCTATATAT
102722 ATATATATTTTAAATA
1 ATATATATTTTAAATA
102738 ATATA-ATTTTAAA-A
1 ATATATATTTTAAATA
102752 ATA
1 ATA
102755 AAAAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 8 0.47
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATATATTTTAAATA
Found at i:102865 original size:16 final size:16
Alignment explanation
Indices: 102844--102895 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
102834 ACACGGGCCG
102844 AAATTTTGATACCCGA
1 AAATTTTGATACCCGA
*
102860 AAATTTTGGGTACCCG-
1 AAATTTT-GATACCCGA
* *
102876 ATATTTCGGATACCCGA
1 AAATTT-TGATACCCGA
102893 AAA
1 AAA
102896 CACGGATTCC
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (16 bp):
AAATTTTGATACCCGA
Found at i:104102 original size:29 final size:29
Alignment explanation
Indices: 104020--104091 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
104010 GCGACCTCCT
104020 AGGTCGCCATGCACTCTGGGCGACCAAGG
1 AGGTCGCCATGCACTCTGGGCGACCAAGG
*
104049 AGGTTGCCATGCACTCTGGGCGACCAAGG
1 AGGTCGCCATGCACTCTGGGCGACCAAGG
104078 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
104092 GCCCGTCGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.21, C:0.31, G:0.33, T:0.15
Consensus pattern (29 bp):
AGGTCGCCATGCACTCTGGGCGACCAAGG
Found at i:107546 original size:60 final size:60
Alignment explanation
Indices: 107433--107584 Score: 164
Period size: 60 Copynumber: 2.5 Consensus size: 60
107423 ATACATATGG
* * * * *
107433 TTTGGGATAAAAGTGAAATATTCAAAAAGTTTGAGGATCAATTTAGAATGAAAGTCATAGT
1 TTTGGGATGAAATTGAAATGTTC-AAAAGTTTGAGGATCAATTTAGAACGAAAGCCATAGT
* * *
107494 TTTGGGATGAAATTGAAATGTTCAAAAGTTTGGGGA-CTGATTTAGAACGAAAGCCATTGT
1 TTTGGGATGAAATTGAAATGTTCAAAAGTTTGAGGATC-AATTTAGAACGAAAGCCATAGT
** *
107554 TTAAGGATGAAATT-AGAATGTTTAAAAGTTT
1 TTTGGGATGAAATTGA-AATGTTCAAAAGTTT
107585 AAAAACTAAT
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.03
60 56 0.72
61 20 0.26
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (60 bp):
TTTGGGATGAAATTGAAATGTTCAAAAGTTTGAGGATCAATTTAGAACGAAAGCCATAGT
Found at i:107597 original size:60 final size:60
Alignment explanation
Indices: 107472--107600 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
107462 TTTGAGGATC
* * ** ****
107472 AATTTAGAATGAAAGTCATAGTTTTGGGATGAAATTGAAATGTTCAAAAGTTTGGGGACT
1 AATTTAGAACGAAAGCCATAGTTTAAGGATGAAATTGAAATGTTCAAAAGTTTAAAAACT
* * *
107532 GATTTAGAACGAAAGCCATTGTTTAAGGATGAAATT-AGAATGTTTAAAAGTTTAAAAACT
1 AATTTAGAACGAAAGCCATAGTTTAAGGATGAAATTGA-AATGTTCAAAAGTTTAAAAACT
107592 AATTTAGAA
1 AATTTAGAA
107601 TGAGGACCAT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (60 bp):
AATTTAGAACGAAAGCCATAGTTTAAGGATGAAATTGAAATGTTCAAAAGTTTAAAAACT
Found at i:108403 original size:16 final size:16
Alignment explanation
Indices: 108382--108428 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
108372 CATTAATCAA
108382 ATATTTTTTAAAATAT
1 ATATTTTTTAAAATAT
*
108398 ATATTTTATAAAAT-T
1 ATATTTTTTAAAATAT
*
108413 -TAGTTATTTAAAATAT
1 ATA-TTTTTTAAAATAT
108429 TTAAAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 10 0.38
16 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATATTTTTTAAAATAT
Found at i:109701 original size:6 final size:6
Alignment explanation
Indices: 109692--109720 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
109682 AACTATATGT
109692 ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATA
109721 TATTCATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:112235 original size:35 final size:35
Alignment explanation
Indices: 112192--112261 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
112182 ATCCAAGAAC
112192 AACTACGACAATTCCAAACATTAGTAGATCAAAAG
1 AACTACGACAATTCCAAACATTAGTAGATCAAAAG
112227 AACTACGACAATTCCAAACATTAGTAGATCAAAAG
1 AACTACGACAATTCCAAACATTAGTAGATCAAAAG
112262 GAGATAAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.20, G:0.11, T:0.20
Consensus pattern (35 bp):
AACTACGACAATTCCAAACATTAGTAGATCAAAAG
Found at i:114949 original size:7 final size:7
Alignment explanation
Indices: 114933--114963 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
114923 GTCAAAGAAA
*
114933 GTCAATG
1 GTCAACG
114940 GTCAACG
1 GTCAACG
114947 GTCAACG
1 GTCAACG
114954 GTCAACG
1 GTCAACG
114961 GTC
1 GTC
114964 GGGTCGGTCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (7 bp):
GTCAACG
Found at i:115015 original size:22 final size:22
Alignment explanation
Indices: 114953--115016 Score: 103
Period size: 22 Copynumber: 2.9 Consensus size: 22
114943 AACGGTCAAC
114953 GGTCAACGGTCGGGTC-GGTCG
1 GGTCAACGGTCGGGTCGGGTCG
114974 GTGTCAACGGTCGGGTCGGGTCG
1 G-GTCAACGGTCGGGTCGGGTCG
*
114997 GGTCAACAGTCGGGTCGGGT
1 GGTCAACGGTCGGGTCGGGT
115017 TAGACCGGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 1 0.03
22 33 0.82
23 6 0.15
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.20
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:115063 original size:29 final size:31
Alignment explanation
Indices: 115029--115103 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
115019 GACCGGTCAG
115029 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
115058 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
115088 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
115104 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:115100 original size:9 final size:9
Alignment explanation
Indices: 115014--115103 Score: 72
Period size: 9 Copynumber: 9.4 Consensus size: 9
115004 AGTCGGGTCG
*
115014 GGTTAGACC
1 GGTTAAACC
* *
115023 GGTCAGACC
1 GGTTAAACC
*
115032 GGTCAAACC
1 GGTTAAACC
*
115041 GGTTCGAACC
1 GGTT-AAACC
115051 GGTTGAAACC
1 GGTT-AAACC
*
115061 GGTCAAACC
1 GGTTAAACC
*
115070 GGTCAGAACC
1 GGTTA-AACC
115080 GGTTGAAAACC
1 GGTT--AAACC
115091 GGTTAAACC
1 GGTTAAACC
115100 GGTT
1 GGTT
115104 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
9 38 0.55
10 22 0.32
11 8 0.12
12 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.18
Consensus pattern (9 bp):
GGTTAAACC
Done.