Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003392.1 Hibiscus syriacus cultivar Beakdansim tig00007138_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: 89965
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:3866 original size:199 final size:196
Alignment explanation
Indices: 3336--4030 Score: 793
Period size: 198 Copynumber: 3.5 Consensus size: 196
3326 AGAAAATTAA
* * * * *
3336 ACCGGTTACATTTTAAAGTGACCTATTACATTATAA-TATGGGTTTCGATG-TTTTAGGATCGAC
1 ACCGGTTACATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGAC
* * *
3399 ACTTTTTCTAAACGTATCGACAC-TTTTCGTGAACTTGTTTGGAAAATTTATTATGGACATAAAG
66 ACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATT-TGGACATAAAG
* *
3463 TGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTAATAACCGGTATGTTT
130 TGTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTAATAAACGGTATATTT
3528 AG
195 AG
* * *
3530 ACCGGTTACATTGTTATGTTACCTATTACATTATAATTTTGTGTTTCGATGTTTTTGGGATCGAA
1 ACCGGTTACATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGAC
* * *
3595 AATTGTTATAAATGTATCGACACTTTTTCATGAACTTGTTTGGAAAATTTATATGGACATAAAGT
66 ACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTTGGACATAAAGT
*
3660 GTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTCTTTTTTAATAAATGGTATAT
131 GTCGACACAAATGTATAAAGTATCGATACATTATGTATACC--T-TTTTTTAATAAACGGTATAT
3725 TTAG
193 TTAG
*
3729 ACCGGTTACATTTTTATGTTACTTATTACATTATAATTATGTG-TTCGATGTTTTTGGGATCGAC
1 ACCGGTTACATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGAC
* **
3793 ACTTGTTATAAATGTATCGACACTTTTTTCGTGCACTTGGTTTGG-AAATACATTTGGACA-ACA
66 ACTTGTTATAAATGTATCGACAC-TTTTTCGTGAACTT-GTTTGGAAAATTTATTTGGACATA-A
* * * * * * * **
3856 TGTATCGACACAAATGAATAAAGT-GCGATACA-TATTGTAGACCTATTTTCTCATAAAACCTTT
128 AGTGTCGACACAAATGTATAAAGTATCGATACATTA-TGTATACCT-TTTTTTAAT-AAA-CGGT
* *
3919 AAATTTAA
189 ATATTTAG
* * * * * * * *
3927 ACTGGTTACATTGTAAAGTGACCTATT--ATTATAGTTACGGGTTTCGATGTTTTTTGGGATCGA
1 ACCGGTTACATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGATG-TTTTTGGGATCGA
* * * *
3990 TACTTGATATAAATGTGTCGACACATATTT-GTG-ACTTGTTT
65 CACTTGTTATAAATGTATCGACAC-TTTTTCGTGAACTTGTTT
4031 TGGTTGGAAA
Statistics
Matches: 433, Mismatches: 54, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
194 32 0.07
195 16 0.04
196 106 0.24
197 42 0.10
198 124 0.29
199 107 0.25
200 6 0.01
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (196 bp):
ACCGGTTACATTTTTATGTTACCTATTACATTATAATTATGTGTTTCGATGTTTTTGGGATCGAC
ACTTGTTATAAATGTATCGACACTTTTTCGTGAACTTGTTTGGAAAATTTATTTGGACATAAAGT
GTCGACACAAATGTATAAAGTATCGATACATTATGTATACCTTTTTTTAATAAACGGTATATTTA
G
Found at i:4100 original size:12 final size:12
Alignment explanation
Indices: 4083--4107 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4073 TAAGTGTTGA
4083 TATTTGTGAACT
1 TATTTGTGAACT
4095 TATTTGTGAACT
1 TATTTGTGAACT
4107 T
1 T
4108 GTTTTGGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.08, G:0.16, T:0.52
Consensus pattern (12 bp):
TATTTGTGAACT
Found at i:4591 original size:24 final size:24
Alignment explanation
Indices: 4540--4591 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4530 ATTTACATTT
* *
4540 AAATTCAAACTCAAATTGAAATTT
1 AAATTCAAACTCAAATTGAAAATG
*
4564 AAATTCAAACTCTAATT-ATAAATG
1 AAATTCAAACTCAAATTGA-AAATG
4588 AAAT
1 AAAT
4592 GAAAATGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.52, C:0.12, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATTCAAACTCAAATTGAAAATG
Found at i:6944 original size:15 final size:15
Alignment explanation
Indices: 6932--6960 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6922 TCAGAAGATC
6932 TGGGTTGAGAAGAGA
1 TGGGTTGAGAAGAGA
6947 TGGGTTGAGAAGAG
1 TGGGTTGAGAAGAG
6961 CCCTGATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.48, T:0.21
Consensus pattern (15 bp):
TGGGTTGAGAAGAGA
Found at i:7698 original size:200 final size:197
Alignment explanation
Indices: 7348--7849 Score: 756
Period size: 200 Copynumber: 2.6 Consensus size: 197
7338 TTGCAAAATG
*
7348 ACCTATTACATTATAATTATGGGTCTCG--ATTTTTTGGATCGATACTTTTTACAAATGTAT---
1 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
*
7408 CACATTGTGGTGACCTTGGTAAGGAAATCATT-TGGACACAAAGT-ATCGACACAATTAAAAAAG
66 CACATT-TAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTAATCGACACAATTAAAAAAG
*
7471 TGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTTTATTTAGACCGGTTAGATTGATAA
130 TGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATTGATAA
7536 TTT
195 TTT
*
7539 ACCTATTACATT-TAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAAGGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
*
7603 CACATTATAGTGACCTTGGTAAGG-AATCATTCTGGACACAAAGTACGGATCGGCACAAATTAAA
66 CACATT-TAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTA---ATCGACAC-AATTAAA
* * *
7667 CAAGTGTCGATACTTTATGTACACCTGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATTG
126 AAAGTGTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATTG
7732 ATAATTT
191 ATAATTT
* *
7739 ACCTATTACATTATAATTATGGGTCTCGATGTTTTTTGAATCGATACTTTTTATAAATGTATCGA
1 ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
7804 CACATTTCCA-TG-CACTTGGTAAGGAAATCATTCTGGACACAAAGTA
66 CACATTT--AGTGAC-CTTGGTAAGGAAATCATTCTGGACACAAAGTA
7850 TACTTGGAAT
Statistics
Matches: 283, Mismatches: 12, Indels: 21
0.90 0.04 0.07
Matches are distributed among these distances:
190 15 0.05
191 12 0.04
192 30 0.11
194 7 0.02
195 34 0.12
199 7 0.02
200 89 0.31
201 67 0.24
202 22 0.08
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (197 bp):
ACCTATTACATTATAATTATGGGTCTCGATATTTTTTGGATCGATACTTTTTATAAATGTATCGA
CACATTTAGTGACCTTGGTAAGGAAATCATTCTGGACACAAAGTAATCGACACAATTAAAAAAGT
GTCGATACTTCATGTACACATGTTTTCTCATAAACCGGTATATTTAGACCGGTTAGATTGATAAT
TT
Found at i:8010 original size:18 final size:18
Alignment explanation
Indices: 7989--8034 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
7979 TTACATTCAC
* *
7989 ATACAAAATATAAATCGT
1 ATACAAAATAAAAAGCGT
*
8007 ATACAAAATTAAAAAGCTT
1 ATACAAAA-TAAAAAGCGT
8026 ATACAAAAT
1 ATACAAAAT
8035 TAACCCTACA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.26
Consensus pattern (18 bp):
ATACAAAATAAAAAGCGT
Found at i:10101 original size:179 final size:180
Alignment explanation
Indices: 9710--10180 Score: 745
Period size: 179 Copynumber: 2.6 Consensus size: 180
9700 TTAACTCCAT
*
9710 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGCT-TTTTACCGG
1 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAG-TGGTTTACCGG
* * * *
9774 TTTTATCAT-TTCGA-GACCTGTTTTGTCATATTATTACCTGTTATATTGCTATGGATCGATACA
65 TTTTATCATAAT-GACG-CC-GTTTTATCATATTTTTACCTGTTATATTGATAT-GATCGATACA
*
9837 TTTGTATAAAATATCGACACTTTTTAGGCGCTATAACTTCTTCTCTTTTAAATTA
126 TTTGTATAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
9892 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
1 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
9957 TTTATCATAATGACGCCGATTTTATCATATTTTTACCTGTTATATT-ATAT-ATCGATACATTTG
66 TTTATCATAATGACGCCG-TTTTATCATATTTTTACCTGTTATATTGATATGATCGATACATTTG
*
10020 TATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
130 TATAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
** *
10071 CAAAAGTGTTAATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGCGGTTTACCGGT
1 CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
*
10136 TTTATCATAATGACACCGGTTTTATCATATTTTTACCTGTTATAT
66 TTTATCATAATGACGCC-GTTTTATCATATTTTTACCTGTTATAT
10181 GGCTGTGGAT
Statistics
Matches: 273, Mismatches: 11, Indels: 13
0.92 0.04 0.04
Matches are distributed among these distances:
179 166 0.61
180 1 0.00
181 5 0.02
182 99 0.36
183 2 0.01
ACGTcount: A:0.29, C:0.17, G:0.13, T:0.42
Consensus pattern (180 bp):
CAAAAGTGTCGATACTTATATTAATTTATCGACACTTTCAATATATCCGGTAGTGGTTTACCGGT
TTTATCATAATGACGCCGTTTTATCATATTTTTACCTGTTATATTGATATGATCGATACATTTGT
ATAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTA
Found at i:11123 original size:44 final size:41
Alignment explanation
Indices: 11046--11127 Score: 119
Period size: 44 Copynumber: 1.9 Consensus size: 41
11036 GCAACGCGAT
* *
11046 TTTGAAAAATGTGTTGCGATAGTTAAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
11087 TTTGAAAAACGTGTTGTTGCGATAGTGAAAAAGTGTTGCGA
1 TTTGAAAAA--TG-TGTTGCGATAGTGAAAAAGTGTTGCGA
11128 TAGTGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 9 0.25
43 2 0.06
44 25 0.69
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.33
Consensus pattern (41 bp):
TTTGAAAAATGTGTTGCGATAGTGAAAAAGTGTTGCGAGAG
Found at i:11137 original size:19 final size:20
Alignment explanation
Indices: 11048--11138 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
11038 AACGCGATTT
11048 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
* *
11068 T-TAAAATGTGTTGCGAGAG
1 TGAAAAATGTGTTGCGATAG
11087 TTTGAAAAACGTGTTGTTGCGATAG
1 --TGAAAAA--TG-TGTTGCGATAG
11112 TGAAAAA-GTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
11131 TGAAAAAT
1 TGAAAAAT
11139 CCAAAATAAG
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
19 34 0.57
20 2 0.03
21 1 0.02
22 4 0.07
23 7 0.12
24 2 0.03
25 10 0.17
ACGTcount: A:0.35, C:0.05, G:0.29, T:0.31
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:11287 original size:65 final size:65
Alignment explanation
Indices: 11183--11358 Score: 289
Period size: 65 Copynumber: 2.7 Consensus size: 65
11173 CACGTGGAGT
* * *
11183 TTGAAACAATAAAGAATGTGTTACAATAGTGTATAAGATTCTCAAGCCATTTGTAAGATCTTAGC
1 TTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGCCATTTGTAAGATCTTAGC
* *
11248 TTGAAACAATAAAGAATGTGTTGCGATAGTATAAAAGATTCTCAAGCCATTTGTAAGATCTTAGT
1 TTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGCCATTTGTAAGATCTTAGC
* *
11313 TTGAAACAATAAAGAATATGTTGCGATAGTGTAAAAGATTCCCAAG
1 TTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAG
11359 TGTTGGCAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 103 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (65 bp):
TTGAAACAATAAAGAATGTGTTGCGATAGTGTAAAAGATTCTCAAGCCATTTGTAAGATCTTAGC
Found at i:11624 original size:21 final size:21
Alignment explanation
Indices: 11607--11786 Score: 224
Period size: 21 Copynumber: 8.8 Consensus size: 21
11597 AATTTGGAAA
11607 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
**
11628 ATCGCAACGCGAACTTCAACT
1 ATCGCAACGCGAACTTGGACT
11649 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
11670 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
*
11689 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
* *
11710 ATCGCAACGCCAACTTCGACT
1 ATCGCAACGCGAACTTGGACT
*
11731 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
* **
11752 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTGGACT
11771 ATCGCAACGCGAACTT
1 ATCGCAACGCGAACTT
11787 CGAACGTGAA
Statistics
Matches: 135, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
19 31 0.23
21 104 0.77
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:11732 original size:82 final size:82
Alignment explanation
Indices: 11592--11789 Score: 360
Period size: 82 Copynumber: 2.4 Consensus size: 82
11582 ATGCAATTCA
* *
11592 CAACGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGCGAACTTCAACTATCGCAAC
1 CAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCCAACTTCAACTATCGCAAC
11657 GCGAACTTGGACTATCG
66 GCGAACTTGGACTATCG
*
11674 CAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCCAACTTCGACTATCGCAAC
1 CAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCCAACTTCAACTATCGCAAC
*
11739 GTGAACTTGGACTATCG
66 GCGAACTTGGACTATCG
11756 CAACGAATTTGGAAAATCGCAACGCGAACTTCGA
1 CAACGAATTTGGAAAATCGCAACGCGAACTTCGA
11790 ACGTGAACTT
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 112 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (82 bp):
CAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCCAACTTCAACTATCGCAAC
GCGAACTTGGACTATCG
Found at i:11775 original size:61 final size:62
Alignment explanation
Indices: 11607--11872 Score: 270
Period size: 61 Copynumber: 4.5 Consensus size: 62
11597 AATTTGGAAA
* * * * *
11607 ATCGCAACGCGAACTTGGACTATCGCAACGCGAACTT-CAACTATCGCAACGCGAACTTGGACT
1 ATCGCAACGTGAACTTGGACTATCGCAAC-CGAACTTGGAA-AATCGCAACGCCAACTTCGACT
* ** * **
11670 ATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGCCAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAAC-CGAACTTGGAAAATCGCAACGCCAACTTCGACT
* *
11731 ATCGCAACGTGAACTTGGACTATCGCAA-CGAATTTGGAAAATCGCAACG-CGA-----ACT
1 ATCGCAACGTGAACTTGGACTATCGCAACCGAACTTGGAAAATCGCAACGCCAACTTCGACT
* * *
11786 -TCG-AACGTGAACTTGGACTATCGCAA-CAAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGTGAACTTGGACTATCGCAACCGAACTTGGAAAATCGCAACGCCAACTTCGACT
11845 ATCGCAACGTGAACTTGGACTATCGCAA
1 ATCGCAACGTGAACTTGGACTATCGCAA
11873 AATCGCGTTG
Statistics
Matches: 174, Mismatches: 18, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
53 43 0.25
54 4 0.02
55 3 0.02
59 3 0.02
60 5 0.03
61 92 0.53
62 1 0.01
63 23 0.13
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (62 bp):
ATCGCAACGTGAACTTGGACTATCGCAACCGAACTTGGAAAATCGCAACGCCAACTTCGACT
Found at i:11818 original size:53 final size:53
Alignment explanation
Indices: 11736--11842 Score: 205
Period size: 53 Copynumber: 2.0 Consensus size: 53
11726 CGACTATCGC
*
11736 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
1 AACGTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCG
11789 AACGTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCG
1 AACGTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCG
11842 A
1 A
11843 CTATCGCAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (53 bp):
AACGTGAACTTGGACTATCGCAACAAATTTGGAAAATCGCAACGCGAACTTCG
Found at i:11850 original size:21 final size:21
Alignment explanation
Indices: 11824--11872 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
11814 AATTTGGAAA
11824 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* *
11845 ATCGCAACGTGAACTTGGACT
1 ATCGCAACGCGAACTTCGACT
11866 ATCGCAA
1 ATCGCAA
11873 AATCGCGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:14606 original size:12 final size:12
Alignment explanation
Indices: 14589--14613 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14579 TTTTTCTTTT
14589 GAAAAAAAAAGA
1 GAAAAAAAAAGA
14601 GAAAAAAAAAGA
1 GAAAAAAAAAGA
14613 G
1 G
14614 GTATATAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAAAAAAAAAGA
Found at i:21786 original size:14 final size:14
Alignment explanation
Indices: 21767--21814 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 14
21757 TGTGTATGTT
*
21767 TGTATCTATCTAAA
1 TGTATCTATCTATA
* * *
21781 TGTATCT-CCTGTT
1 TGTATCTATCTATA
21794 TGTATCTATCTATA
1 TGTATCTATCTATA
21808 TGTATCT
1 TGTATCT
21815 CCGTAAGCTG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (14 bp):
TGTATCTATCTATA
Found at i:21794 original size:27 final size:27
Alignment explanation
Indices: 21763--21816 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
21753 TATGTGTGTA
21763 TGTTTGTATCTATCTAAATGTATCTCC
1 TGTTTGTATCTATCTAAATGTATCTCC
*
21790 TGTTTGTATCTATCTATATGTATCTCC
1 TGTTTGTATCTATCTAAATGTATCTCC
21817 GTAAGCTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.19, G:0.11, T:0.50
Consensus pattern (27 bp):
TGTTTGTATCTATCTAAATGTATCTCC
Found at i:26899 original size:35 final size:35
Alignment explanation
Indices: 26853--26953 Score: 184
Period size: 35 Copynumber: 2.9 Consensus size: 35
26843 ATATCGAGTA
26853 ATCAATTTGTAACAAACGAACTCATAGTAATGACT
1 ATCAATTTGTAACAAACGAACTCATAGTAATGACT
*
26888 ATCAATTTGTAACAAACGAACTCATAGTAACGACT
1 ATCAATTTGTAACAAACGAACTCATAGTAATGACT
*
26923 ATCAATTTGTAACAAACGAACTCACAGTAAT
1 ATCAATTTGTAACAAACGAACTCATAGTAAT
26954 AGCTGTTAAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.27
Consensus pattern (35 bp):
ATCAATTTGTAACAAACGAACTCATAGTAATGACT
Found at i:32963 original size:31 final size:32
Alignment explanation
Indices: 32909--32971 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
32899 TTTAATATAC
* * *
32909 GGCTAAAAAAAGACGGTATCGATTTTTTTATT
1 GGCTAAAAAAAGACAGTACCGATTTTGTTATT
32941 GGCTAAAAAAA-ACAGTACCGATTTTGTTATT
1 GGCTAAAAAAAGACAGTACCGATTTTGTTATT
32972 ATTGTGCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 17 0.61
32 11 0.39
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (32 bp):
GGCTAAAAAAAGACAGTACCGATTTTGTTATT
Found at i:33396 original size:24 final size:25
Alignment explanation
Indices: 33369--33437 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
33359 AACATCAAAT
33369 ACAATAA-AATAATATTATTTATTA
1 ACAATAAGAATAATATTATTTATTA
*
33393 ACAA-AATAATAATATTATTT-TTA
1 ACAATAAGAATAATATTATTTATTA
33416 A-AATATTAGAATAAT-TTATTTA
1 ACAATA--AGAATAATATTATTTA
33438 ATATTATTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 7 0.18
24 23 0.59
25 7 0.18
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (25 bp):
ACAATAAGAATAATATTATTTATTA
Found at i:33558 original size:16 final size:16
Alignment explanation
Indices: 33506--33550 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
33496 AATTATGATT
33506 ATTATATTTTATTA-AA
1 ATTATA-TTTATTATAA
*
33522 A-TAAATTTATTATAA
1 ATTATATTTATTATAA
33537 ATTATATTTATTAT
1 ATTATATTTATTAT
33551 TTATTATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 7 0.28
15 6 0.24
16 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTATATTTATTATAA
Found at i:34117 original size:18 final size:17
Alignment explanation
Indices: 34081--34123 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
34071 TTTGCAATGT
*
34081 TTATTTTAAAAATATTA
1 TTATTTTAAAAATAATA
*
34098 TTTTTTTAATAAATAATA
1 TTATTTTAA-AAATAATA
34116 TTATTTTA
1 TTATTTTA
34124 TTGTTATCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTTTAAAAATAATA
Found at i:34680 original size:23 final size:23
Alignment explanation
Indices: 34654--34704 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
34644 TAAGTAATTA
**
34654 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
34677 ACCTATTACGTTATATAAGCGTT
1 ACCTATTACATTATATAAGCGCT
34700 ACCTA
1 ACCTA
34705 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:34712 original size:23 final size:23
Alignment explanation
Indices: 34664--34713 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
34654 ACCTATTTTA
*
34664 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
34687 TTATATAAGCGTTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
34710 TTAT
1 TTAT
34714 TGTGTTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:34827 original size:86 final size:87
Alignment explanation
Indices: 34646--34856 Score: 318
Period size: 86 Copynumber: 2.4 Consensus size: 87
34636 TAACAAATTA
* *
34646 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGTTACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGATATATAAGCGGTACCTAATATGT
* *
34711 TATTGTGTTTGATAATATTTTC
66 TATCGTGCTTGATAATATTTTC
* * * *
34733 AGTAATTAACCTATTTTATTATATAAGTGTTACCTATTAC-ATATATAAGTGGTATCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGATATATAAGCGGTACCTAATATGT
*
34797 TATCGTGCTTGATAAT-GTTTC
66 TATCGTGCTTGATAATATTTTC
34818 TAGTAATTAACCTATTTTATTATATAAGCGCTACCTATT
1 -AGTAATTAACCTATTTTATTATATAAGCGCTACCTATT
34857 TTATTATATA
Statistics
Matches: 112, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
85 4 0.04
86 70 0.62
87 38 0.34
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (87 bp):
AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGATATATAAGCGGTACCTAATATGT
TATCGTGCTTGATAATATTTTC
Found at i:34857 original size:23 final size:23
Alignment explanation
Indices: 34827--34900 Score: 130
Period size: 23 Copynumber: 3.2 Consensus size: 23
34817 CTAGTAATTA
34827 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
34850 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
**
34873 ACCTATTACATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
34896 ACCTA
1 ACCTA
34901 ATATGTTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGCGCT
Found at i:34909 original size:23 final size:23
Alignment explanation
Indices: 34827--34909 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
34817 CTAGTAATTA
*
34827 ACCTATTTTATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
*
34850 ACCTATTTTATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
*
34873 ACCTATTACATTATATAAGCGCT
1 ACCTATTATATTATATAAGCGCT
* *
34896 ACCTAATATGTTAT
1 ACCTATTATATTAT
34910 TGTGTTTGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (23 bp):
ACCTATTATATTATATAAGCGCT
Found at i:34933 original size:110 final size:110
Alignment explanation
Indices: 34741--34996 Score: 370
Period size: 110 Copynumber: 2.3 Consensus size: 110
34731 TCAGTAATTA
* * * * *
34741 ACCTATTTTATTATATAAGTGTTACCTATTACA-TATATAAGTGGTATCTAATATGTTATCGTGC
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATCGTGC
* *
34805 TTGATAATGTTTCTAGTAATTAACCTATTTTATTATATAAGCGCT
66 TTGATAATGTTTATAGTAATTAACCTATTTTATTATATAAGCGAT
* *
34850 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATCGTGC
*
34915 TTGATAATGTTTATAGTAATTAACCTATTTTATTATATAAGTGAT
66 TTGATAATGTTTATAGTAATTAACCTATTTTATTATATAAGCGAT
** * * *
34960 ACCTATTACATTATATAAGCGGTACCTAATATATTAT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTAT
34997 TATGTTTAAT
Statistics
Matches: 131, Mismatches: 15, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
109 31 0.24
110 100 0.76
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (110 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATCGTGC
TTGATAATGTTTATAGTAATTAACCTATTTTATTATATAAGCGAT
Found at i:34941 original size:87 final size:86
Alignment explanation
Indices: 34850--35096 Score: 377
Period size: 87 Copynumber: 2.8 Consensus size: 86
34840 TATAAGCGCT
34850 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCG-TACCTAATATGTTATTGTGT
*
34915 TTGATAATGTTTATAGTAATTA
65 TTGATAATGTTTACAGTAATTA
* * * *
34937 ACCTATTTTATTATATAAGTGATACCTATTACATTATATAAGCGGTACCTAATATATTATTATGT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGC-GTACCTAATATGTTATTGTGT
* *
35002 TTAATAATGTTTCCAGTAATTA
65 TTGATAATGTTTACAGTAATTA
** *
35024 ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAATAGTACCTAATATGTTATTGTAT
1 ACCTATTTTATTATATAAGCGCTACCTATTACATTATAT-AAGCGTACCTAATATGTTATTGTGT
35089 TTGATAAT
65 TTGATAAT
35097 ATAACATAAC
Statistics
Matches: 143, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
87 140 0.98
88 3 0.02
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (86 bp):
ACCTATTTTATTATATAAGCGCTACCTATTACATTATATAAGCGTACCTAATATGTTATTGTGTT
TGATAATGTTTACAGTAATTA
Found at i:34964 original size:23 final size:23
Alignment explanation
Indices: 34937--34996 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
34927 ATAGTAATTA
* *
34937 ACCTATTTTATTATATAAGTGAT
1 ACCTATTATATTATATAAGCGAT
* *
34960 ACCTATTACATTATATAAGCGGT
1 ACCTATTATATTATATAAGCGAT
*
34983 ACCTAATATATTAT
1 ACCTATTATATTAT
34997 TATGTTTAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (23 bp):
ACCTATTATATTATATAAGCGAT
Found at i:50338 original size:14 final size:14
Alignment explanation
Indices: 50311--50354 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
50301 TTTAATATAT
50311 ATACATATAATAATA
1 ATACATA-AATAATA
50326 ATACATAAATAATA
1 ATACATAAATAATA
*
50340 A-AAATAAATGAATA
1 ATACATAAAT-AATA
50354 A
1 A
50355 AATATCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 13 0.48
15 7 0.26
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (14 bp):
ATACATAAATAATA
Found at i:50339 original size:17 final size:17
Alignment explanation
Indices: 50317--50358 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
50307 ATATATACAT
*
50317 ATAATAATAATACATAA
1 ATAATAATAATAAATAA
* *
50334 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
50351 ATAA-AATA
1 ATAATAATA
50359 TCCATATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:51808 original size:105 final size:105
Alignment explanation
Indices: 51513--52343 Score: 1201
Period size: 105 Copynumber: 8.0 Consensus size: 105
51503 CATTGTTCCA
* * **
51513 AGTCCAATATCCTCCGTCGTGAAGTTGAAA-TGGCTCTG-GAACCGGGAAATTG-T-TTGACAA-
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTGTTGTTGACAAC
* * * *
51573 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
51614 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
*
51674 AGCGGTCCATTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
51714 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
*
51779 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
51819 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
51879 AGCGGTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
51918 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAC
*
51982 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
52023 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
52088 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
52128 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATTG-TTGTTGACAA
52193 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
52235 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAC
* * * *
52300 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
52341 AGT
1 AGT
52344 GCCACGATAT
Statistics
Matches: 668, Mismatches: 43, Indels: 33
0.90 0.06 0.04
Matches are distributed among these distances:
98 7 0.01
99 74 0.11
100 93 0.14
101 36 0.05
102 11 0.02
103 3 0.00
104 27 0.04
105 256 0.38
106 65 0.10
107 96 0.14
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:51942 original size:204 final size:206
Alignment explanation
Indices: 51513--52374 Score: 1218
Period size: 204 Copynumber: 4.2 Consensus size: 206
51503 CATTGTTCCA
* * **
51513 AGTCCAATATCCTCCGTCGTGAAGTTGAAA-TGGCTCTGGAACCGGGAAATTG-T-TTGAC-AAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAAAC
* * ** *
51574 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
** * *
51639 TGAAATTGAATCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTTGAACTT
131 TGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
51703 GCGTTGTCTGG
196 GCGTTGTCTGG
* * ** *
51714 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAAAC
*
51779 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
51844 TGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCGGTCCC-TCGTCGTGAAGTTGAACTT
131 TGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
51907 GCGTTGTCTGG
196 GCGTTGTCTGG
* *
51918 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTGTTGACAAA
51982 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
*
52047 TTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
130 TTGAAATTGGCTCTGA-ATT--GAAATT-TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
52112 AACTTGCGTTGTCTGG
191 AACTTGCGTTGTCTGG
* * *
52128 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGG-AAATTG-TTGTTGACAA
* *
52193 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
64 ACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* *
52258 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
129 GTTGAAATTGGCTCTG-AATTGA-AA--T-TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGT
* *
52323 TGAACTTGTGTTGTCTCG
189 TGAACTTGCGTTGTCTGG
* * *
52341 AGTGCCACGATATTCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTCCGTTGTGAAGTTGAAAT
52375 CGCGGATGGC
Statistics
Matches: 599, Mismatches: 40, Indels: 29
0.90 0.06 0.04
Matches are distributed among these distances:
201 27 0.05
202 18 0.03
203 5 0.01
204 169 0.28
205 104 0.17
206 1 0.00
208 5 0.01
209 20 0.03
210 73 0.12
211 6 0.01
212 94 0.16
213 53 0.09
214 4 0.01
216 20 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (206 bp):
AGTCCAATATCCTCCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAAAC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAATTGAAATTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
GCGTTGTCTGG
Found at i:52058 original size:309 final size:307
Alignment explanation
Indices: 51513--52330 Score: 1236
Period size: 309 Copynumber: 2.6 Consensus size: 307
51503 CATTGTTCCA
* * *
51513 AGTCCAATATCCTCCG-TCGTGAAGTTGAAA-TGGCTCTGGAACCGGGAAATTGTTTGACAACAG
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAA-C-TGAAATTTTTTGACAACAG
* * * *
51576 CCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTG
62 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
** *
51641 AAATTGAATCTGAA-TGAAA-TT-TTGTTGACAAGCAGCGGTCCATTCGTCGTGAAGTTGAACTT
127 AAATTGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * *
51703 GCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGT
192 GCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
51768 TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
257 TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
51819 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAATTTTGTTGACAAGCAGCG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTT-TTGACAA-CAGCG
*
51883 GTCCC-TCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTCCGTTGTGAAGTTGAA
64 GTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
51947 ATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
129 ATTGGCTCTGA-ATT-GAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
52012 GCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
192 GCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGT
* *
52077 TGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
257 TGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
*
52128 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AACT--G-AAA-T-TTT-TTGACAA
52193 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
59 -CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * *
52258 GTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
123 GTTGAAATTGGCTCTG-AATTGA-AAGTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
52323 TGAACTTG
185 TGAACTTG
52331 TGTTGTCTCG
Statistics
Matches: 470, Mismatches: 22, Indels: 28
0.90 0.04 0.05
Matches are distributed among these distances:
303 7 0.01
304 71 0.15
305 10 0.02
306 31 0.07
307 12 0.03
308 2 0.00
309 190 0.40
310 2 0.00
311 1 0.00
313 1 0.00
314 3 0.01
315 1 0.00
316 22 0.05
317 77 0.16
318 40 0.09
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (307 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTTTTTGACAACAGCGGT
CCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAAT
TGGCTCTGAATTGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCAT
TGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTT
GACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:53176 original size:22 final size:22
Alignment explanation
Indices: 53099--53169 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
53089 TTGTGTTTGG
*
53099 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
53121 TCAAAGGTTTAACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
* *
53143 TTAAAGGTTTGACATTGGATGC
1 TCAAAGGTTTGACATTTGATGC
53165 TCAAA
1 TCAAA
53170 AGATTGATGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:53846 original size:15 final size:15
Alignment explanation
Indices: 53828--53878 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
53818 TGCTCTTTTT
53828 TTTTTCTTGTTTCTC
1 TTTTTCTTGTTTCTC
*
53843 TTTTTCTTTGTTT-TT
1 TTTTTC-TTGTTTCTC
*
53858 TTTTTGCTTTTTTGCTC
1 TTTTT-CTTGTTT-CTC
53875 TTTT
1 TTTT
53879 CTTTTGTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 17 0.59
16 7 0.24
17 5 0.17
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (15 bp):
TTTTTCTTGTTTCTC
Found at i:53861 original size:31 final size:31
Alignment explanation
Indices: 53823--53882 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
53813 ATTTTTGCTC
53823 TTTTTTTTTT-CTTGTTT-CTCTTTTTCTTTG
1 TTTTTTTTTTGCTTGTTTGCTC-TTTTCTTTG
*
53853 TTTTTTTTTTGCTTTTTTGCTCTTTTCTTT
1 TTTTTTTTTTGCTTGTTTGCTCTTTTCTTT
53883 TGTTCTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 10 0.37
31 14 0.52
32 3 0.11
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (31 bp):
TTTTTTTTTTGCTTGTTTGCTCTTTTCTTTG
Found at i:57183 original size:24 final size:25
Alignment explanation
Indices: 57133--57184 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
57123 CAAGGTTTTT
* **
57133 TAAAAAAATAAAATATAATAATGAA
1 TAAAAAAACAAAATATAATAAAAAA
*
57158 TAAAAAAACGAAA-ATAATAAAAAA
1 TAAAAAAACAAAATATAATAAAAAA
57182 TAA
1 TAA
57185 TATAAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (25 bp):
TAAAAAAACAAAATATAATAAAAAA
Found at i:59673 original size:6 final size:6
Alignment explanation
Indices: 59608--59679 Score: 51
Period size: 6 Copynumber: 11.8 Consensus size: 6
59598 AATTTTCAAA
* ** *
59608 AAAATT AAAAATC AAAATT AGATTTT AAACA-T AAATATT AAAATA AAAATT
1 AAAATT -AAAATT AAAATT A-AAATT AAA-ATT AAA-ATT AAAATT AAAATT
59659 -AAATT -AAATT AAAATT AAAAT
1 AAAATT AAAATT AAAATT AAAAT
59680 ATAATTTTAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
5 10 0.19
6 29 0.56
7 13 0.25
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (6 bp):
AAAATT
Found at i:65848 original size:165 final size:165
Alignment explanation
Indices: 65577--65907 Score: 646
Period size: 165 Copynumber: 2.0 Consensus size: 165
65567 GAGTTAAATT
65577 TAGTTGACAAGTTTATAATTTACTCTAAAGATTCACACTCCTTTCTAATGGGTTTTGGGGCATTT
1 TAGTTGACAAGTTTATAATTTACTCTAAAGATTCACACTCCTTTCTAATGGGTTTTGGGGCATTT
65642 TTAGTATGGACTAGGATATTGGTATCTCTCTAAAGTCCCCTAA-CTTCTAAACTTATTTAGGTCA
66 TTAGTATGGACTAGGATATTGGTATCTCTCTAAAGTCCCCTAACCTTCTAAACTTATTTAGGTCA
65706 AATTATGATTCTACGGCCCCTCAACTATGTTGTAA
131 AATTATGATTCTACGGCCCCTCAACTATGTTGTAA
65741 TAGTTGACAAGTTTATAATTTACTCTAAAGATTCACACTCCTTTTCTAATGGGTTTTGGGGCATT
1 TAGTTGACAAGTTTATAATTTACTCTAAAGATTCACACTCC-TTTCTAATGGGTTTTGGGGCATT
65806 TTTAGTATGGACTAGGATATTGGTATCTCTCTAAAGTCCCCTAACCTTCTAAACTTATTTAGGTC
65 TTTAGTATGGACTAGGATATTGGTATCTCTCTAAAGTCCCCTAACCTTCTAAACTTATTTAGGTC
65871 AAATTATGATTCTACGGCCCCTCAACTATGTTGTAA
130 AAATTATGATTCTACGGCCCCTCAACTATGTTGTAA
65907 T
1 T
65908 TCGAGATTTA
Statistics
Matches: 165, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
164 41 0.25
165 67 0.41
166 57 0.35
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (165 bp):
TAGTTGACAAGTTTATAATTTACTCTAAAGATTCACACTCCTTTCTAATGGGTTTTGGGGCATTT
TTAGTATGGACTAGGATATTGGTATCTCTCTAAAGTCCCCTAACCTTCTAAACTTATTTAGGTCA
AATTATGATTCTACGGCCCCTCAACTATGTTGTAA
Found at i:67985 original size:41 final size:41
Alignment explanation
Indices: 67894--67976 Score: 114
Period size: 41 Copynumber: 2.0 Consensus size: 41
67884 TTTTAAGCAT
* * * *
67894 AAACTC-TACTTTAGTGACCTTTTTATATAAATGCCGCTAA
1 AAACTCGTATTTTAGTGACCTTTTTATACAAACGCCACTAA
*
67934 AAACTCGTATTTTAGTGACGTTTTTATACAAACGCCACTAA
1 AAACTCGTATTTTAGTGACCTTTTTATACAAACGCCACTAA
67975 AA
1 AA
67977 TTTTGTATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 6 0.16
41 31 0.84
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (41 bp):
AAACTCGTATTTTAGTGACCTTTTTATACAAACGCCACTAA
Found at i:71645 original size:22 final size:22
Alignment explanation
Indices: 71610--71651 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
71600 TATTCATTAT
* *
71610 TAAATGATTAAAAATCTTTAAA
1 TAAATAATTAAAAATATTTAAA
*
71632 TAAATAATTTAAAATATTTA
1 TAAATAATTAAAAATATTTA
71652 TCTAGATTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (22 bp):
TAAATAATTAAAAATATTTAAA
Found at i:82446 original size:14 final size:15
Alignment explanation
Indices: 82420--82453 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
82410 GAGGATTGTG
82420 GGAACTGGGAAAGAA
1 GGAACTGGGAAAGAA
82435 GGAACT-GGAAAGAA
1 GGAACTGGGAAAGAA
82449 GGAAC
1 GGAAC
82454 AGTGTTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.47, C:0.09, G:0.38, T:0.06
Consensus pattern (15 bp):
GGAACTGGGAAAGAA
Found at i:84478 original size:59 final size:60
Alignment explanation
Indices: 84299--84480 Score: 167
Period size: 59 Copynumber: 3.0 Consensus size: 60
84289 AGTGATGTTA
* * * *
84299 TTAGTATATACGT-ATAATGTA-GGATGAAATTGAAATGTTTAAAAAGTTTGGCGGATCAAT
1 TTAGAATATACGTCATAATTTAGGGATGAAATTGAAATGTTTAAAAA-TTT-GAGGATTAAT
* * * * * * * * *
84359 TTAGAAGGA-AGGTCATAGTTTTGGGATGAAAATGAAATGTTCAAAAGTTTGAAGAATAAT
1 TTAGAA-TATACGTCATAATTTAGGGATGAAATTGAAATGTTTAAAAATTTGAGGATTAAT
*
84419 TTAGAATATA-GTCATAATTTAGGGATGAAATTAAAATGTTTAAAAATTT-AGGGATTAAT
1 TTAGAATATACGTCATAATTTAGGGATGAAATTGAAATGTTTAAAAATTTGA-GGATTAAT
84478 TTA
1 TTA
84481 AAACGAGTGT
Statistics
Matches: 95, Mismatches: 22, Indels: 11
0.74 0.17 0.09
Matches are distributed among these distances:
58 1 0.01
59 43 0.45
60 21 0.22
61 9 0.09
62 21 0.22
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (60 bp):
TTAGAATATACGTCATAATTTAGGGATGAAATTGAAATGTTTAAAAATTTGAGGATTAAT
Found at i:85746 original size:104 final size:104
Alignment explanation
Indices: 85528--85734 Score: 288
Period size: 104 Copynumber: 2.0 Consensus size: 104
85518 ACGTATATGT
* * * * * * *
85528 AAGTTGTCAGTGATTACTACTCATCACGTGACCATAGTAATAAAAGAGTATTGTTTTCCTTAGAG
1 AAGTTGTCAATAATTACTACTCATCAAGCGACCATAGTAATAAAAGAGTATTGTTCTCCTTAAAA
* * *
85593 GTCACAAGTTCAACACAGTTTTACCTGCGGGATTTGTGC
66 ATCACAAGTTCAACACAATTTTACCTGCAGGATTTGTGC
* * *
85632 AAGTTGTCAATAATTATTACTCATCAAGCGACTATAGTAATAAAATAGTATTGTTCTCCTTAAAA
1 AAGTTGTCAATAATTACTACTCATCAAGCGACCATAGTAATAAAAGAGTATTGTTCTCCTTAAAA
*
85697 ATCACAAGTTCAACACAATTTTATCTGCAGGATTTGTG
66 ATCACAAGTTCAACACAATTTTACCTGCAGGATTTGTG
85735 TGAGTTTTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
104 89 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (104 bp):
AAGTTGTCAATAATTACTACTCATCAAGCGACCATAGTAATAAAAGAGTATTGTTCTCCTTAAAA
ATCACAAGTTCAACACAATTTTACCTGCAGGATTTGTGC
Found at i:86258 original size:22 final size:21
Alignment explanation
Indices: 86233--86275 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
86223 AATCACATAT
86233 AATA-AAATTATATTCATTAATA
1 AATATAAA-TATATTCA-TAATA
*
86255 AATATAAATATTTTCATAATA
1 AATATAAATATATTCATAATA
86276 TAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 5 0.26
22 11 0.58
23 3 0.16
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
AATATAAATATATTCATAATA
Done.