Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005185.1 Hibiscus syriacus cultivar Beakdansim tig00011710_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: 88700
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:5011 original size:25 final size:26
Alignment explanation
Indices: 4983--5067 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 26
4973 ATATATTTTA
*
4983 AATA-AAAATATTTTTAAATTATGTT
1 AATATAAAATATTTTTAAATTAAGTT
* *
5008 AATAATAAAATATATTT--AGTAAGTT
1 AAT-ATAAAATATTTTTAAATTAAGTT
5033 AATATAAAA-ATATTTTAAATTAA--T
1 AATATAAAATAT-TTTTAAATTAAGTT
5057 ATATATAAAAT
1 A-ATATAAAAT
5068 TATATTAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 2 0.04
24 11 0.23
25 20 0.42
26 5 0.10
27 10 0.21
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AATATAAAATATTTTTAAATTAAGTT
Found at i:5057 original size:21 final size:23
Alignment explanation
Indices: 5006--5059 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 23
4996 TTAAATTATG
*
5006 TTAATAATAAAATATATTTAGTAAG
1 TTAAT-ATAAAATATATTTA-TAAA
5031 TTAATATAAAA-ATATTT-TAAA
1 TTAATATAAAATATATTTATAAA
5052 TTAATATA
1 TTAATATA
5060 TATAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.39
23 6 0.21
24 6 0.21
25 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAATATAAAATATATTTATAAA
Found at i:5075 original size:25 final size:26
Alignment explanation
Indices: 5034--5082 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
5024 TAGTAAGTTA
*
5034 ATATAAAAATATTTTAAAT-TAATAT
1 ATATAAAAATATATTAAATATAATAT
*
5059 ATATAAAATTATATTAAATATAAT
1 ATATAAAAATATATTAAATATAAT
5083 CTAGGTCACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATAAAAATATATTAAATATAATAT
Found at i:17483 original size:20 final size:17
Alignment explanation
Indices: 17458--17506 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 17
17448 TTTTTGCCTC
17458 GAGTATCGATACCCAAGAAG
1 GAGTATCGATACCC---AAG
*
17478 GAGTATTGATACCCAAG
1 GAGTATCGATACCCAAG
17495 GAGTATCGATAC
1 GAGTATCGATAC
17507 TCTAGAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 14 0.52
20 13 0.48
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.20
Consensus pattern (17 bp):
GAGTATCGATACCCAAG
Found at i:19615 original size:11 final size:11
Alignment explanation
Indices: 19591--19632 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
19581 TCAACAAATC
*
19591 AAATCAAATCA
1 AAATCAAATAA
19602 AAATCAAATAAA
1 AAATCAAAT-AA
19614 AAAT-ATAATAA
1 AAATCA-AATAA
19625 AAATCAAA
1 AAATCAAA
19633 CCCAAGTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (11 bp):
AAATCAAATAA
Found at i:23120 original size:18 final size:18
Alignment explanation
Indices: 23097--23149 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
23087 CCACTATGAA
23097 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
*
23115 ATGTCCCGAAGGGCCACT
1 ATGTCCCGAAGGACCACT
*
23133 ATGTCCCAAAGGACCAC
1 ATGTCCCGAAGGACCAC
23150 GTAGAACCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.28, C:0.34, G:0.23, T:0.15
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:31101 original size:15 final size:15
Alignment explanation
Indices: 31081--31110 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31071 ATGCCTACAA
31081 TAAATAAAGAAAAAC
1 TAAATAAAGAAAAAC
*
31096 TAAATAAAGCAAAAC
1 TAAATAAAGAAAAAC
31111 GGATAATGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.10, G:0.07, T:0.13
Consensus pattern (15 bp):
TAAATAAAGAAAAAC
Found at i:31659 original size:19 final size:19
Alignment explanation
Indices: 31635--31676 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
31625 AGTTCCACAG
31635 GTAGGTGCCATTCTTTACC
1 GTAGGTGCCATTCTTTACC
31654 GTAGGTGCCATTCTTTACC
1 GTAGGTGCCATTCTTTACC
31673 GTAG
1 GTAG
31677 ACAAGTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
GTAGGTGCCATTCTTTACC
Found at i:39837 original size:21 final size:21
Alignment explanation
Indices: 39813--39865 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
39803 GTCTAAAGAA
39813 GCATGTATTATAGAATCTGGT
1 GCATGTATTATAGAATCTGGT
39834 GCATGTATTATAGAATCTGGT
1 GCATGTATTATAGAATCTGGT
39855 GCATGTATTAT
1 GCATGTATTAT
39866 TTCCCCATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.23, T:0.40
Consensus pattern (21 bp):
GCATGTATTATAGAATCTGGT
Found at i:51057 original size:2 final size:2
Alignment explanation
Indices: 51050--51074 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
51040 TTTCGTAAAT
51050 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 T
51075 GTGATTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:56734 original size:16 final size:16
Alignment explanation
Indices: 56713--56762 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
56703 TGGTATTATC
56713 TGACATGTTATCAACT
1 TGACATGTTATCAACT
56729 TGACATGTTATCAACT
1 TGACATGTTATCAACT
*
56745 TGACATGTTATGAACT
1 TGACATGTTATCAACT
56761 TG
1 TG
56763 GCCTGTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (16 bp):
TGACATGTTATCAACT
Found at i:56777 original size:32 final size:32
Alignment explanation
Indices: 56713--56782 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
56703 TGGTATTATC
*
56713 TGACATGTTATCAACTTGACATGTTATCAACT
1 TGACATGTTATCAACTTGACATGTAATCAACT
* * * *
56745 TGACATGTTATGAACTTGGCCTGTAATTAACT
1 TGACATGTTATCAACTTGACATGTAATCAACT
*
56777 TTACAT
1 TGACAT
56783 TTAAATGATC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (32 bp):
TGACATGTTATCAACTTGACATGTAATCAACT
Found at i:57444 original size:2 final size:2
Alignment explanation
Indices: 57437--57581 Score: 90
Period size: 2 Copynumber: 74.0 Consensus size: 2
57427 CTTTCACTTT
*
57437 TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA TA TA GTT 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
* * * * *
57478 CT- TA TA CT- TA TA CTT TA TA CA TA TA TA TA TA TG TA CA CA TA
1 -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
57519 TA TA TA TA TA TG TA CA TG TA TA TA T- TA TA TA T- TA TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
57559 TA TA CT- TT TA TA TA TA TA T- TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA
57582 CATAAGTAGA
Statistics
Matches: 111, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
1 8 0.07
2 98 0.88
3 5 0.05
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57777 original size:2 final size:2
Alignment explanation
Indices: 57770--57840 Score: 65
Period size: 2 Copynumber: 36.5 Consensus size: 2
57760 TTTCAAAATA
* * ** *
57770 AT AT AT AT TT AT AT AC AT AT GC AT AT -T AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
57811 AC AT AT GT AT AT -T AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57841 CATAACGGAT
Statistics
Matches: 53, Mismatches: 14, Indels: 4
0.75 0.20 0.06
Matches are distributed among these distances:
1 2 0.04
2 51 0.96
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57807 original size:27 final size:27
Alignment explanation
Indices: 57770--57844 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
57760 TTTCAAAATA
57770 ATATATATTTATATACATATGCATATT
1 ATATATATTTATATACATATGCATATT
*
57797 ATATATATTTATATACATATGTATATT
1 ATATATATTTATATACATATGCATATT
57824 ATATATATATATATATACATA
1 ATATATAT-T-TATATACATA
57845 ACGGATGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 34 0.76
28 1 0.02
29 10 0.22
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (27 bp):
ATATATATTTATATACATATGCATATT
Found at i:59905 original size:116 final size:117
Alignment explanation
Indices: 59700--59974 Score: 372
Period size: 116 Copynumber: 2.4 Consensus size: 117
59690 TGGCACTTTG
* * * * * * ** * * *
59700 TGTGCTAGAATGATAAGGAAATCATACTGAGTGTTTGGATTTCCATATGGAGCACTGAGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTTCCAGATAAACCACTAAGGGTGCT
* * *
59765 AAATGATAAGGAAATCATTTTGAAATTATGGATTTCCAGATAGGGCATATTA
66 AAATGATAAGGAAATCATATTGAAAATATAGATTTCCAGATAGGGCATATTA
*
59817 TGTGCTAAAATGGTAAGGAAATCATACT-ATTGTATGGGTTTCCAGATAAACCACTAAGGGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTTCCAGATAAACCACTAAGGGTGCT
*
59881 AAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATAGGGCATATTA
66 AAATGATAAGGAAATCATATTGAAAATATAGATTTCCAGATAGGGCATATTA
** *
59933 TGTGCTAAAATGGTAATAAAATCATACTAATGGTATGGATTT
1 TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTT
59975 TCGAATAGGG
Statistics
Matches: 138, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
116 101 0.73
117 37 0.27
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTTCCAGATAAACCACTAAGGGTGCT
AAATGATAAGGAAATCATATTGAAAATATAGATTTCCAGATAGGGCATATTA
Found at i:59974 original size:59 final size:60
Alignment explanation
Indices: 59691--60047 Score: 219
Period size: 59 Copynumber: 6.1 Consensus size: 60
59681 ATTACCGAAT
* * * * * *
59691 GGCACT-TTGTGTGCTAGAATGATAAGGAAATCATACTGAGT-GTTTGGATTTCCATAT-G
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACT-AATAGTATGGATTTCCAGATAG
* * ** *
59749 GAGCACTGA--GTGTGCT-AAATGATAAGGAAATCATTTTGAA-ATTATGGATTTCCAGATAG
1 G-GCACT-ATTATGTGCTAAAATGGTAAGGAAATCATACT-AATAGTATGGATTTCCAGATAG
* * *
59808 GGCA-TATTATGTGCTAAAATGGTAAGGAAATCATACT-ATTGTATGGGTTTCCAGATAA
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAATAGTATGGATTTCCAGATAG
** * * * * * *
59866 ACCACTA--AGGGTGCT-AAATGATAAGGAAATCATATTGAA-AATATAGATTTCCATATAG
1 GGCACTATTA-TGTGCTAAAATGGTAAGGAAATCATACT-AATAGTATGGATTTCCAGATAG
** * *
59924 GGCA-TATTATGTGCTAAAATGGTAATAAAATCATACTAATGGTATGGATTTTC-GAATAG
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAATAGTATGGATTTCCAG-ATAG
* ** * *
59983 GGCACT-TTGTGTGCTAAAATGAAAAGGGAAGCATACTAAGT-GTAT-GATTTTCCAGATAG
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAA-TAGTATGGA-TTTCCAGATAG
*
60042 AGCACT
1 GGCACT
60048 GATAGTGCTA
Statistics
Matches: 230, Mismatches: 47, Indels: 43
0.72 0.15 0.13
Matches are distributed among these distances:
56 1 0.00
57 24 0.10
58 89 0.39
59 113 0.49
60 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.31
Consensus pattern (60 bp):
GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAATAGTATGGATTTCCAGATAG
Found at i:61474 original size:23 final size:23
Alignment explanation
Indices: 61427--61476 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
61417 AATAACATAT
**
61427 TAGGTAGAGCTTATATAATGTAA
1 TAGGTAGAGCTTATATAATAAAA
*
61450 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGAGCTTATATAATAAAA
61473 TAGG
1 TAGG
61477 CATTTAACCG
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:0.40, C:0.06, G:0.22, T:0.32
Consensus pattern (23 bp):
TAGGTAGAGCTTATATAATAAAA
Found at i:61913 original size:198 final size:201
Alignment explanation
Indices: 61505--62182 Score: 647
Period size: 198 Copynumber: 3.4 Consensus size: 201
61495 ATACCAGTAG
* * * *
61505 CATTGCAAATTTACCTATTGCATTATAATTATTGGTTTCGTTGTTTTTTGG-ATCGATACAATTT
1 CATTGTAAATTTACCTATTACATTATAATT-TTCGTTTCGATG-TTTTTGGAATCGATACAATTT
* *
61569 TAAATGTATCGACACTTTATGCTTGCACTTCGTTGGGCATTCCTAATTCATTCTGGAAAAAAGTA
64 TAAATGTATCGACACTTTATGCTTGCACCTCGTTGGGCA-T-C-AATTCATTATGGAAAAAAGTA
* *
61634 TCGACACAAACTATAAAGGTGTCGATACATTATTTAGACATATTTTCTCATAAAACCGATATATT
126 TCGACACAAACTACAAAGGTGTCGATACATTATTTAGACATATTTTCTCATAAAACCGATAAATT
*
61699 TATACCGGATA
191 TAAACCGGATA
* * *
61710 CATTGTAAATTTACCTATAACATTGTAATTTTCGTTTCGATGTTTTTGGAATCGATATAATTTTA
1 CATTGTAAATTTACCTATTACATTATAATTTTCGTTTCGATGTTTTTGGAATCGATACAATTTTA
* * *
61775 AATGTATCGACACGTTATTCTTGCACCTCGTT-GG-A-C-ATTCATTATGGACAAAATGTATCGA
66 AATGTATCGACACTTTATGCTTGCACCTCGTTGGGCATCAATTCATTATGGA-AAAAAGTATCGA
* * *
61836 CACAAATTACACAA-GTGTCGATACTTTATTCT-GACCTATTTTCTCATAAAACC-AGTAAATTT
130 CACAAACTACA-AAGGTGTCGATACATTATT-TAGACATATTTTCTCATAAAACCGA-TAAATTT
*
61898 AAACCGGTTA
192 AAACCGGATA
* * *
61908 CATTGTAAATTGACCTATTACATTATAATTATCGGTTTCGATGTTTTTGTAATCGATACAATTTT
1 CATTGTAAATTTACCTATTACATTATAATTTTC-GTTTCGATGTTTTTGGAATCGATACAATTTT
* * * * *
61973 AAATGTATCGACACTTTATGCGTG-AACTTGTTTGTGC-T---TTC-TTTTGGAAAAAA-TATCG
65 AAATGTATCGACACTTTATGCTTGCACCTCG-TTGGGCATCAATTCATTATGGAAAAAAGTATCG
* * * * * * * * *
62031 ACACAAACTTA-AAAAGTGTCGATACTTTATGTT-GACATGTTTTATAAT-TAACCAATATATGT
129 ACACAAAC-TACAAAGGTGTCGATACATTAT-TTAGACATATTTTCTCATAAAACCGATAAATTT
* * *
62093 ATACTGGTTA
192 AAACCGGATA
* ** * ** ** *
62103 CATTGTTAATTTAAATATTACATTATAATTATTTGTTTTAATGTTTTTGGGGTCGATAC-TTTTT
1 CATTGTAAATTTACCTATTACATTATAATT-TTCGTTTCGATGTTTTTGGAATCGATACAATTTT
62167 GAAAATGTATCGACAC
65 --AAATGTATCGACAC
62183 ATATTCTTAC
Statistics
Matches: 401, Mismatches: 55, Indels: 43
0.80 0.11 0.09
Matches are distributed among these distances:
194 4 0.01
195 65 0.16
196 56 0.14
197 19 0.05
198 108 0.27
199 59 0.15
200 1 0.00
202 1 0.00
203 9 0.02
204 53 0.13
205 26 0.06
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.40
Consensus pattern (201 bp):
CATTGTAAATTTACCTATTACATTATAATTTTCGTTTCGATGTTTTTGGAATCGATACAATTTTA
AATGTATCGACACTTTATGCTTGCACCTCGTTGGGCATCAATTCATTATGGAAAAAAGTATCGAC
ACAAACTACAAAGGTGTCGATACATTATTTAGACATATTTTCTCATAAAACCGATAAATTTAAAC
CGGATA
Found at i:64985 original size:199 final size:197
Alignment explanation
Indices: 64585--65342 Score: 1083
Period size: 199 Copynumber: 3.8 Consensus size: 197
64575 AGACATTTGG
* * *
64585 TTATAATTATGTTTTTTGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTT-
1 TTATAATTATGTTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTA
* * * * * *
64649 GTGCACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTCGA
65 GTGCACTTGG-TTTTGAAATACATTCTGGACAAAAA-GTATCGACACTTG-TTTATTTGTGTCAA
** * * * * *
64714 TACTTCATGTATACCTGTTTTCTCATAAACCGATACATTTAGACTGGTTACATTGTTAATTTACC
127 TACTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACA-TGATAATTTACC
64779 TATTACA
191 TATTACA
64786 TTATAATTATAG-TTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA
1 TTATAATTAT-GTTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA
* *
64850 GTGCACTTGGTTTTGAAATACATTCTGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTT-TATTTGTGTCAATA
* * *
64915 CTTTTTGTACACATGTTTTCTCAAAAATCGGTATATTTAGACTGTTTACATGAATAATTTACCTA
129 CTTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATG-ATAATTTACCTA
64980 TTACA
193 TTACA
* *
64985 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTAT
1 TTATAATTATGTTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-
* * *
65049 GTGCACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCAATA
65 GTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTT-TATTTGTGTCAATA
* * ** *
65114 -TTTTTGTACACCTGTTTTCTCAAAAAACCGGTATATTTAGACCGGTTATATTTCTAATTTACAT
129 CTTTTTGTACACCTGTTTTCTC-AAAAACCGGTATATTTAGACTGGTTACA-TGATAATTTACCT
65178 ATTACA
192 ATTACA
*
65184 TTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
1 TTATAATTATGTTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
65249 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCAATAC
66 TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTT-ATTTGTGTCAATAC
65314 TTTTTGTACACCTGTTTTCTCAAAAACCG
130 TTTTTGTACACCTGTTTTCTCAAAAACCG
65343 ATATTAATTA
Statistics
Matches: 505, Mismatches: 41, Indels: 24
0.89 0.07 0.04
Matches are distributed among these distances:
198 29 0.06
199 359 0.71
200 50 0.10
201 66 0.13
202 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (197 bp):
TTATAATTATGTTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
TGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTATTTGTGTCAATACT
TTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATGATAATTTACCTATTA
CA
Found at i:65451 original size:160 final size:160
Alignment explanation
Indices: 65187--65502 Score: 571
Period size: 160 Copynumber: 2.0 Consensus size: 160
65177 TATTACATTA
65187 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
65252 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCAATACTT-
66 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCAATACTTG
*
65316 TTTGTACACCTGTTTTCTCAAAAACCGATAT
131 TTT-TACACATGTTTTCTCAAAAACCGATAT
*
65347 TAATTATGGTTTTCGATGTTTTTTGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
* * *
65412 ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTG
66 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCAATACTTG
65477 TTTTACACATGTTTTCTCAAAAACCG
131 TTTTACACATGTTTTCTCAAAAACCG
65503 GTATATTTAG
Statistics
Matches: 150, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
160 147 0.98
161 3 0.02
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (160 bp):
TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCAATACTTG
TTTTACACATGTTTTCTCAAAAACCGATAT
Found at i:65993 original size:18 final size:19
Alignment explanation
Indices: 65950--65994 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
65940 ATTCACATAA
*
65950 AAAATTATAAATCGTATAC
1 AAAATTAAAAATCGTATAC
*
65969 AAAATTAAAAATCTTATAC
1 AAAATTAAAAATCGTATAC
65988 -AAATTAA
1 AAAATTAA
65995 CCATGCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTAAAAATCGTATAC
Found at i:67499 original size:21 final size:18
Alignment explanation
Indices: 67461--67499 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
67451 TTCTCCTCAT
67461 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
67479 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
67497 TTC
1 TTC
67500 AAAATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:69208 original size:18 final size:18
Alignment explanation
Indices: 69185--69223 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
69175 TACTGTCAAC
69185 ATTTAAAATTTATAAT-CA
1 ATTTAAAATTT-TAATCCA
*
69203 ATTTAAAGTTTTAATCCA
1 ATTTAAAATTTTAATCCA
69221 ATT
1 ATT
69224 ATCATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTAAAATTTTAATCCA
Found at i:69518 original size:19 final size:20
Alignment explanation
Indices: 69471--69519 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
69461 CATTTATACA
69471 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
69490 ACCTAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
69508 ACCTATAAATAT
1 ACCTATAAATAT
69520 TAACTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:70433 original size:165 final size:164
Alignment explanation
Indices: 70236--70560 Score: 447
Period size: 165 Copynumber: 2.0 Consensus size: 164
70226 TAACTTCTCT
* *
70236 TTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACAATTTCAATATATCCGACAACTT
1 TTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACAATTTCAACATATCCGACAACGT
* * * * *
70301 TTTTCTGGTTTTGTCATTTTTTAGA-TTAGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
66 TTTACTAGTTTTGACAATTTTGAGACTT-GTTTTATCATATTTTTACCTGTTATATTGTTATGGA
*
70365 TCGATACATTTTTCATAAAGTGTCGACACTTTTTAG
130 TCGATACATTTTT-ATAAAGTATCGACACTTTTTAG
* * ** *
70401 TTTAATTTCAGAAAGTGTCGATACTT-ATATTAAATTATCGACACTTTCAACATATCCGGTATCG
1 TTTAAATTCAGAAAGTGTCGATA-TTAATATTAAATTATCGACAATTTCAACATATCCGACAACG
* * *
70465 TTTTACTAGTTTTGACAATTTTGGGACTTGTTTTATCATATTTTTACTTGTTATATTGTTGTGGA
65 TTTTACTAGTTTTGACAATTTTGAGACTTGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
* *
70530 TCGATATATTTTTTTAAAGTATCGACACTTT
130 TCGATACATTTTTATAAAGTATCGACACTTT
70561 ATAGGCGCTA
Statistics
Matches: 140, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
164 16 0.11
165 120 0.86
166 4 0.03
ACGTcount: A:0.28, C:0.12, G:0.13, T:0.47
Consensus pattern (164 bp):
TTTAAATTCAGAAAGTGTCGATATTAATATTAAATTATCGACAATTTCAACATATCCGACAACGT
TTTACTAGTTTTGACAATTTTGAGACTTGTTTTATCATATTTTTACCTGTTATATTGTTATGGAT
CGATACATTTTTATAAAGTATCGACACTTTTTAG
Found at i:70715 original size:183 final size:183
Alignment explanation
Indices: 70401--71265 Score: 1016
Period size: 183 Copynumber: 4.8 Consensus size: 183
70391 CACTTTTTAG
* *
70401 TTTAATTTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTATCGT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
** * * * *
70466 TTTACTAGTTTTG-ACAATTTTGGGACTTGTTTTATCATATTTTTACTTGTTATATTGTTGTGGA
66 TTTACCGGTTTTGTA-AATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGA
*
70530 TCGATATATTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
130 TCGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * * *
70584 TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATTGACACTTTCAATATATCCGGTAGCGT
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
*
70649 TTTACTGGTTTTGTAAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGAT
66 TTTACCGGTTTTGTAAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGAT
* * * * * * * *
70714 CGATACATTTTCATAAAGTGTCGACACTTTTTAAGCGCAATAATTTTTTCTCT
131 CGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* *
70767 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTTAACATATTCGGTAAC-T
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
* * * * * * * *
70831 TTTTCCGGTTTTGTCATTTTTTAGACATG-TTTATCATATTTTTACCTATTATATTGGTAAGGAT
66 TTTACCGGTTTTGTAAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGAT
* * * * * * * *
70895 CGAAACATTTTCATAAAGTGTCGATATTTTTTAGGCGCTATAACTTCTTATCT
131 CGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* * *
70948 TTTAAATTCAGAAAGTGTCGATACTAATATTAAATTATCGACACTTTCAATATATCCGATAAC-T
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
* ** * * * *
71012 TTTTCCCATTTT-TTAATTTTTAGACCAGTTTTATCATATTTTTACCTGTTATATTGTTGTGGAT
66 TTTACCGGTTTTGTAAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGAT
* * *
71076 CGATAT-TTTTTTTAAAGTATCGACACTTTATATGCGTTATAA---CTTCTCT
131 CGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
* *
71125 TTTAAATTCAGAAAGTTTCGATACTTATATTAAATTATCGACAC--TCGACACATATCCGGTAGC
1 TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTC-A-ACATATCCGGTAAC
* * * * * * * * * *
71188 GTTTTACCGGTTTTGT-CATTTTGGGACCGGTTTTGTCTTATTTGTACTTATAATATTGCTATGG
64 GTTTTACCGGTTTTGTAAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGG
* *
71252 AGCGATCTATTTTT
129 ATCGATATATTTTT
71266 CATTTGTATC
Statistics
Matches: 585, Mismatches: 90, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
175 2 0.00
176 1 0.00
177 59 0.10
178 52 0.09
179 6 0.01
180 40 0.07
181 181 0.31
182 24 0.04
183 219 0.37
184 1 0.00
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (183 bp):
TTTAAATTCAGAAAGTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGGTAACGT
TTTACCGGTTTTGTAAATTTTGAGACCTGTTTTATCATATTTTTACCTGTTATATTGTTATGGAT
CGATATATTTTTATAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCT
Found at i:72135 original size:22 final size:22
Alignment explanation
Indices: 72108--72151 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
72098 TGAGACAAAC
72108 CTCTCAACCAAGTTTGCTCCGT
1 CTCTCAACCAAGTTTGCTCCGT
*
72130 CTCTCAACCAAGTTTGTTCCGT
1 CTCTCAACCAAGTTTGCTCCGT
72152 GCACAACGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.34, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTCAACCAAGTTTGCTCCGT
Found at i:76114 original size:84 final size:87
Alignment explanation
Indices: 75964--76123 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 87
75954 GGATTGACTT
*
75964 ACTTAATAATACCCCTAGTAGGCTCTTATGAAAGGATTGCAATGGGTGGAGTTAGGGTCAGGTTT
1 ACTTAATAATACCCCTAGTAGACTCTTATGAAAGGATTGCAATGGGTGGAGTTAGGGTCAGGTTT
*
76029 TTGTTCAAACCAACCCGAGCCC
66 TTGATCAAACCAACCCGAGCCC
*
76051 ACTTAATAATA-CCC-AGTAGACTCTTATGTAAGGATTG-AATGGGTTGGA-TTAGGGTC-GGAT
1 ACTTAATAATACCCCTAGTAGACTCTTATGAAAGGATTGCAATGGG-TGGAGTTAGGGTCAGG-T
76111 TTTTGATCAAACC
64 TTTTGATCAAACC
76124 GACCTAACCC
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
83 2 0.03
84 27 0.40
85 25 0.37
86 3 0.04
87 11 0.16
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (87 bp):
ACTTAATAATACCCCTAGTAGACTCTTATGAAAGGATTGCAATGGGTGGAGTTAGGGTCAGGTTT
TTGATCAAACCAACCCGAGCCC
Found at i:77071 original size:22 final size:21
Alignment explanation
Indices: 77037--77077 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
77027 ATAATTATTT
77037 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
77058 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
77078 ATTTTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:77854 original size:32 final size:30
Alignment explanation
Indices: 77812--77870 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
77802 TAATCATCTA
*
77812 ATTAAATATATCTTTTATTTTTGTTTTAAATT
1 ATTAAATATA--TTTTATTTTTATTTTAAATT
*
77844 ATTAAGTATATTTTATTTTTATTTTAA
1 ATTAAATATATTTTATTTTTATTTTAA
77871 TGTAAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.64
32 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (30 bp):
ATTAAATATATTTTATTTTTATTTTAAATT
Found at i:77883 original size:29 final size:28
Alignment explanation
Indices: 77810--77915 Score: 77
Period size: 30 Copynumber: 3.6 Consensus size: 28
77800 TTTAATCATC
* * *
77810 TAATTAAATATATCTTTTATTTTTGTTT
1 TAATTAAAAATATATTTTATTTTTATTT
* *
77838 TAAATTATTAAGTATATTTTATTTTTATTT
1 T-AATTA-AAAATATATTTTATTTTTATTT
* *
77868 TAATGTAAAAATATATATTCTATCTTTATCAT
1 TAAT-TAAAAATATAT-TT-TATTTTTAT-TT
* *
77900 CACTTAAAAATATATT
1 TAATTAAAAATATATT
77916 ATTCAAAATA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
28 1 0.02
29 15 0.25
30 23 0.38
31 19 0.31
32 3 0.05
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.55
Consensus pattern (28 bp):
TAATTAAAAATATATTTTATTTTTATTT
Found at i:78011 original size:31 final size:28
Alignment explanation
Indices: 77973--78076 Score: 136
Period size: 29 Copynumber: 3.5 Consensus size: 28
77963 TTTAAAAAAG
77973 ATAAGAATTAAATATATATTTTTAATTTAAA
1 ATAAGAA-TAAA-ATATATTTTT-ATTTAAA
*
78004 ATAAGAATAAAATATATTTTTATGTAAA
1 ATAAGAATAAAATATATTTTTATTTAAA
78032 GATAAGAATAAAATATATTTTTATATTAAA
1 -ATAAGAATAAAATATATTTTTAT-TTAAA
* *
78062 TTAATAATAAAATAT
1 ATAAGAATAAAATAT
78077 TTAAACATAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
28 6 0.09
29 46 0.69
30 8 0.12
31 7 0.10
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (28 bp):
ATAAGAATAAAATATATTTTTATTTAAA
Found at i:78160 original size:30 final size:29
Alignment explanation
Indices: 78124--78209 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
78114 TTTTCAAGTG
* *
78124 ATAATAAAGATAATATATATATATCACATT
1 ATAATAAAAATAATATATATATAT-AAATT
*
78154 ATAATAAAAATAA-ATTATATTTAATAAATT
1 ATAATAAAAATAATA-TATATAT-ATAAATT
*
78184 AAAATAAAAAATAATATATATATATA
1 ATAAT-AAAAATAATATATATATATA
78210 TATATTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
29 1 0.02
30 29 0.62
31 16 0.34
32 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (29 bp):
ATAATAAAAATAATATATATATATAAATT
Found at i:82144 original size:73 final size:73
Alignment explanation
Indices: 82019--82162 Score: 234
Period size: 73 Copynumber: 2.0 Consensus size: 73
82009 TGGCGGGACC
* * * * *
82019 TCCCTCCTCGGATCAGCTGCCGGCAATGGTTTGACGGATAGCGTAGATCTGAGAAGTGTGGCCTC
1 TCCCTCCTCGGATCAGCCGCCAGCAATGATTTGACGGATAGCATAGACCTGAGAAGTGTGGCCTC
*
82084 TGCCTTGG
66 CGCCTTGG
82092 TCCCTCCTCGGATCAGCCGCCAGCAATGATTTGACGGATAGCATAGACCTGAGAAGTGTGGCCTC
1 TCCCTCCTCGGATCAGCCGCCAGCAATGATTTGACGGATAGCATAGACCTGAGAAGTGTGGCCTC
82157 CGCCTT
66 CGCCTT
82163 TGACTTAGAT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 65 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.24
Consensus pattern (73 bp):
TCCCTCCTCGGATCAGCCGCCAGCAATGATTTGACGGATAGCATAGACCTGAGAAGTGTGGCCTC
CGCCTTGG
Found at i:83596 original size:33 final size:35
Alignment explanation
Indices: 83559--83628 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 35
83549 CCAGGAGGAA
83559 AAATTAGA-GACTGATGA-GA-AGAAAAGGGGAAAC
1 AAATTAGAGGA-TGATGAGGAGAGAAAAGGGGAAAC
*
83592 AAATTAGAGGATGATGAGGAGGAGAAAGGGGGAAAC
1 AAATTAGAGGATGATGAGGA-GAGAAAAGGGGAAAC
83628 A
1 A
83629 CGGGGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
33 14 0.44
34 4 0.12
36 14 0.44
ACGTcount: A:0.49, C:0.04, G:0.36, T:0.11
Consensus pattern (35 bp):
AAATTAGAGGATGATGAGGAGAGAAAAGGGGAAAC
Done.