Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005761.1 Hibiscus syriacus cultivar Beakdansim tig00013488_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: 118407
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1636 original size:170 final size:172
Alignment explanation
Indices: 1344--1662 Score: 529
Period size: 170 Copynumber: 1.9 Consensus size: 172
1334 AACCGAATTA
*
1344 AATATTTTTTAATTAAAAAAAACAGTTTCTAATTAATTTAAATAATATATAATTATAAAATAAAA
1 AATATTTTTTAATT-AAAAAAACAGTTACTAATTAATTTAAATAATATATAATTATAAAATAAAA
* *
1409 TTTTATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATT
65 TTTTATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATT
*
1474 AATTGGGTTTTAAATGGTTGGGCTGAGCCCATTTATATAAAAT
130 AATTGAGTTTTAAATGGTTGGGCTGAGCCCATTTATATAAAAT
*
1517 AATATTTTTTAATT-AAAAAATAGTTAC-AATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTTAATTAAAAAAACAGTTACTAATTAATTTAAATAATATATAATTATAAAAT-AAAA
*
1580 TTTATATAA-TTTTTTAATT-ATTAATATTTATTTAGGTTTAAAAATTATTAGATCTTAAATTAT
65 TTT-TATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTAT
1643 TAATTGAGTTTTAAATGGTT
129 TAATTGAGTTTTAAATGGTT
1663 TGGACCGAGT
Statistics
Matches: 138, Mismatches: 6, Indels: 7
0.91 0.04 0.05
Matches are distributed among these distances:
170 91 0.66
171 28 0.20
172 5 0.04
173 14 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (172 bp):
AATATTTTTTAATTAAAAAAACAGTTACTAATTAATTTAAATAATATATAATTATAAAATAAAAT
TTTATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTAGATCTTAAATTATTA
ATTGAGTTTTAAATGGTTGGGCTGAGCCCATTTATATAAAAT
Found at i:5665 original size:99 final size:99
Alignment explanation
Indices: 5490--5681 Score: 332
Period size: 99 Copynumber: 1.9 Consensus size: 99
5480 ACAATATGAC
*
5490 AAAAAAGGTTAAAATATCAATGGAAAAGAGATGAACTACTTCCACACATGAACACCTTGCAGAAA
1 AAAAAAGGTTAAAATATCAATGGAAAAGAGATGAACTACTTCCACACATAAACACCTTGCAGAAA
*
5555 CCTAATGAAATATGAAACCAGTAAAAAGTATGGT
66 CCTAATAAAATATGAAACCAGTAAAAAGTATGGT
*
5589 AAAAAAGGTTAAAATATCGATGGAAAAGAGATGAACTA-TATCCACACATAAACACCTTGCAGAA
1 AAAAAAGGTTAAAATATCAATGGAAAAGAGATGAACTACT-TCCACACATAAACACCTTGCAGAA
*
5653 ACCTAATAAAATATGAGACCAGTAAAAAG
65 ACCTAATAAAATATGAAACCAGTAAAAAG
5682 AAAATGTTCA
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
98 1 0.01
99 87 0.99
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (99 bp):
AAAAAAGGTTAAAATATCAATGGAAAAGAGATGAACTACTTCCACACATAAACACCTTGCAGAAA
CCTAATAAAATATGAAACCAGTAAAAAGTATGGT
Found at i:7808 original size:21 final size:21
Alignment explanation
Indices: 7783--7838 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
7773 TATATTACCA
*
7783 TTTATAAAATTTAATGATCAT
1 TTTATAACATTTAATGATCAT
7804 TTTATAACATTTAATGATCAT
1 TTTATAACATTTAATGATCAT
7825 TTTATAACATTTAA
1 TTTATAACATTTAA
7839 AAGATCGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (21 bp):
TTTATAACATTTAATGATCAT
Found at i:14296 original size:21 final size:21
Alignment explanation
Indices: 14257--14296 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
14247 CATAGATTGA
*
14257 CAAAAAGTTTGAGGATTTAAT
1 CAAAAAGTTTGAAGATTTAAT
* *
14278 CAAAATGTTTGAAGTTTTA
1 CAAAAAGTTTGAAGATTTA
14297 GAATCAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (21 bp):
CAAAAAGTTTGAAGATTTAAT
Found at i:22357 original size:33 final size:33
Alignment explanation
Indices: 22320--22384 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
22310 TTTAATCTCA
*
22320 GGTGACTAGTTTGTGTACTTCAATGGTTTTAGG
1 GGTGACTAGTTTGTGTACTTCAATAGTTTTAGG
* *
22353 GGTGACTAGTTTGTGTATTTCGATAGTTTTAG
1 GGTGACTAGTTTGTGTACTTCAATAGTTTTAG
22385 TAAGAATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.18, C:0.08, G:0.29, T:0.45
Consensus pattern (33 bp):
GGTGACTAGTTTGTGTACTTCAATAGTTTTAGG
Found at i:23013 original size:50 final size:50
Alignment explanation
Indices: 22958--23057 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
22948 AAGTCTTCTA
22958 ATCTTTTAATAAAGATGATTGACCTTTTTCATATGCTATTATAACACGTT
1 ATCTTTTAATAAAGATGATTGACCTTTTTCATATGCTATTATAACACGTT
23008 ATCTTTTAATAAAGATGATTGACCTTTTTCATATGCTATTATAACACGTT
1 ATCTTTTAATAAAGATGATTGACCTTTTTCATATGCTATTATAACACGTT
23058 TTTTTGAATT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (50 bp):
ATCTTTTAATAAAGATGATTGACCTTTTTCATATGCTATTATAACACGTT
Found at i:24471 original size:22 final size:22
Alignment explanation
Indices: 24446--24493 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
24436 AGTTGATGTT
*
24446 TTTTATATGCTTTTATAGTATA
1 TTTTATATGCTCTTATAGTATA
* * *
24468 TTTTATCTTCTCTTATAGTATT
1 TTTTATATGCTCTTATAGTATA
24490 TTTT
1 TTTT
24494 TCTTTTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTTATATGCTCTTATAGTATA
Found at i:31510 original size:23 final size:23
Alignment explanation
Indices: 31484--31528 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
31474 CACCACAGCT
*
31484 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
31507 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
31529 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:32590 original size:18 final size:18
Alignment explanation
Indices: 32569--32603 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
32559 TCCCATCTAG
32569 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
32587 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
32604 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:33211 original size:21 final size:21
Alignment explanation
Indices: 33187--33231 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33177 TGTTGTTCGT
* *
33187 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
33208 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
33229 TTG
1 TTG
33232 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:36056 original size:22 final size:22
Alignment explanation
Indices: 36031--36078 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
36021 AGTTGATGTT
*
36031 TTTTATATGCTTTTATAGTATA
1 TTTTATATGCTCTTATAGTATA
* * *
36053 TTTTATCTTCTCTTATAGTATT
1 TTTTATATGCTCTTATAGTATA
36075 TTTT
1 TTTT
36079 TTCCTTTTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.21, C:0.08, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTTATATGCTCTTATAGTATA
Found at i:52600 original size:37 final size:37
Alignment explanation
Indices: 52550--52625 Score: 127
Period size: 37 Copynumber: 2.1 Consensus size: 37
52540 ATTATTATTC
52550 TTAAAGGTCTCGAGTTCAAGA-ATCGTCTGCAAAAATG
1 TTAAAGGTCTCGAGTTCAA-ACATCGTCTGCAAAAATG
*
52587 TTAAAGGTCTCGAGTTCAAACATTGTCTGCAAAAATG
1 TTAAAGGTCTCGAGTTCAAACATCGTCTGCAAAAATG
52624 TT
1 TT
52626 TGAGCGTTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 1 0.03
37 36 0.97
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (37 bp):
TTAAAGGTCTCGAGTTCAAACATCGTCTGCAAAAATG
Found at i:61175 original size:18 final size:18
Alignment explanation
Indices: 61154--61189 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
61144 TTCTGGGTCC
*
61154 GGTTCTGCTTCGGGTTCT
1 GGTTCTGCTTCAGGTTCT
*
61172 GGTTCTGTTTCAGGTTCT
1 GGTTCTGCTTCAGGTTCT
61190 TGTATTAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.03, C:0.19, G:0.31, T:0.47
Consensus pattern (18 bp):
GGTTCTGCTTCAGGTTCT
Found at i:63945 original size:17 final size:17
Alignment explanation
Indices: 63915--63947 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
63905 ATGAAGCAAC
63915 TTAATAAAATAAGAAAG
1 TTAATAAAATAAGAAAG
63932 TTAATGAAAA-AAGAAA
1 TTAAT-AAAATAAGAAA
63948 AACTTTCAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (17 bp):
TTAATAAAATAAGAAAG
Found at i:77930 original size:24 final size:24
Alignment explanation
Indices: 77910--77964 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
77900 GAACGTTCGG
*
77910 TTATGTTCGTTTATATGCGTTTAA
1 TTATGTTCGTTTATATGCGTTCAA
*
77934 TTATGTTCGTTTATATGCGTTCAT
1 TTATGTTCGTTTATATGCGTTCAA
77958 TTATGTT
1 TTATGTT
77965 TAACCTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.56
Consensus pattern (24 bp):
TTATGTTCGTTTATATGCGTTCAA
Found at i:82730 original size:16 final size:16
Alignment explanation
Indices: 82711--82777 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
82701 TTTATGTTTG
82711 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
82727 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
* *
82743 TTTATGTTTGTGTTCG
1 TTTATGTTCGTGTTCA
82759 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
82773 TTTAT
1 TTTAT
82778 TAAATGAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.10, C:0.09, G:0.19, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:82746 original size:32 final size:32
Alignment explanation
Indices: 82705--82769 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
82695 CCAACGTTTA
*
82705 TGTTTGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
* *
82737 TGTTCGTTTATGTTTGTGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
82769 T
1 T
82770 TTATTTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.08, C:0.09, G:0.23, T:0.60
Consensus pattern (32 bp):
TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
Found at i:82756 original size:22 final size:22
Alignment explanation
Indices: 82699--82759 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
82689 ATTGTACCAA
*
82699 CGTTTATGTTTGT-TT-ATGTT
1 CGTTTATGTTTGTGTTCGTGTT
*
82719 CGTGTTCA--TTTATGTTCGTGTT
1 CGT-TT-ATGTTTGTGTTCGTGTT
82741 CGTTTATGTTTGTGTTCGT
1 CGTTTATGTTTGTGTTCGT
82760 TTATGTTCGT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
20 8 0.25
21 6 0.19
22 18 0.56
ACGTcount: A:0.08, C:0.10, G:0.23, T:0.59
Consensus pattern (22 bp):
CGTTTATGTTTGTGTTCGTGTT
Found at i:94459 original size:31 final size:32
Alignment explanation
Indices: 94424--94491 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 32
94414 TTTTTATTAG
* *
94424 TTTAAAGATAATTTTGTAAT-AGTTTAAT-AAT
1 TTTAAACATAATTCTGTAATGA-TTTAATAAAT
*
94455 TTTAAACATAATTCTGTAATGATTTGATAAAT
1 TTTAAACATAATTCTGTAATGATTTAATAAAT
94487 TTTAA
1 TTTAA
94492 TAATCGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (32 bp):
TTTAAACATAATTCTGTAATGATTTAATAAAT
Found at i:101235 original size:21 final size:21
Alignment explanation
Indices: 101211--101254 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
101201 CAAAGAATGG
*
101211 TAAGTTGAAGTTACCAAA-ATA
1 TAAGTTCAA-TTACCAAATATA
*
101232 TAAGTTCTATTACCAAATATA
1 TAAGTTCAATTACCAAATATA
101253 TA
1 TA
101255 CTACAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.34
Consensus pattern (21 bp):
TAAGTTCAATTACCAAATATA
Found at i:101412 original size:22 final size:22
Alignment explanation
Indices: 101386--101428 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
101376 TTTAGTAAAA
*
101386 TTTTATTTAAAATATTAATTTT
1 TTTTATTAAAAATATTAATTTT
*
101408 TTTTATTAAAAATGTTAATTT
1 TTTTATTAAAAATATTAATTT
101429 CTCTATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATTAAAAATATTAATTTT
Found at i:101487 original size:25 final size:25
Alignment explanation
Indices: 101459--101518 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
101449 AAAAAATAAC
*
101459 ATTTTAGATAGCGTCTAATATTAAT
1 ATTTTAGATAGCGCCTAATATTAAT
101484 ATTTTAGATAGCGCCTAATATTAAT
1 ATTTTAGATAGCGCCTAATATTAAT
*
101509 ATTTTTGATA
1 ATTTTAGATA
101519 AAAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.12, T:0.45
Consensus pattern (25 bp):
ATTTTAGATAGCGCCTAATATTAAT
Found at i:106144 original size:19 final size:19
Alignment explanation
Indices: 106110--106146 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
106100 ATGACCAACA
*
106110 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
106129 AAATCGCAACGTGATCTC
1 AAATCGCAACGCGATCTC
106147 CAGTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:106239 original size:20 final size:21
Alignment explanation
Indices: 106214--106271 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
106204 TATTTAAATT
106214 GCAACGCGATTCTGACT-ATC
1 GCAACGCGATTCTGACTAATC
**
106234 GCAACGCGATAAT-ACATAATC
1 GCAACGCGATTCTGAC-TAATC
106255 GCAACGCGATTCTGACT
1 GCAACGCGATTCTGACT
106272 GTCACAACAC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
21 15 0.48
22 2 0.06
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (21 bp):
GCAACGCGATTCTGACTAATC
Found at i:106298 original size:41 final size:41
Alignment explanation
Indices: 106170--106300 Score: 126
Period size: 41 Copynumber: 3.2 Consensus size: 41
106160 CAGTTTCCAG
* ** *
106170 ATTCGCAACGCGATTTTGACTATCGCAA-TGTGAATATTTAA
1 ATTCGCAACGCGATTCTGACTATCGCAACACTGAAT-TTCAA
* * *
106211 ATT-GCAACGCGATTCTGACTATCGCAACGC-GATAATACATA
1 ATTCGCAACGCGATTCTGACTATCGCAACACTGA-ATTTCA-A
* *
106252 A-TCGCAACGCGATTCTGACTGTCACAACACTGAATTTCAA
1 ATTCGCAACGCGATTCTGACTATCGCAACACTGAATTTCAA
106292 ATTCGCAAC
1 ATTCGCAAC
106301 AGGTTTTAGT
Statistics
Matches: 73, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
40 30 0.41
41 41 0.56
42 2 0.03
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (41 bp):
ATTCGCAACGCGATTCTGACTATCGCAACACTGAATTTCAA
Found at i:107126 original size:24 final size:24
Alignment explanation
Indices: 107099--107152 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
107089 GTATTCGAAA
107099 TTTGATCTCAGTCAATACCCGGAC
1 TTTGATCTCAGTCAATACCCGGAC
** * *
107123 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTCAGTCAATACCCGGAC
107147 TTTGAT
1 TTTGAT
107153 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATCTCAGTCAATACCCGGAC
Found at i:108401 original size:22 final size:23
Alignment explanation
Indices: 108358--108420 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
108348 CAGCTCATAT
**
108358 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
108381 AATTGCA-CGGAGTGCCGCGTAG
1 AATTGCACCGGAGTGCCACGTAG
*
108403 AATTGCACCGTAGTGCCA
1 AATTGCACCGGAGTGCCA
108421 TATAATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (23 bp):
AATTGCACCGGAGTGCCACGTAG
Found at i:115123 original size:23 final size:22
Alignment explanation
Indices: 115092--115153 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
115082 CAGCTCATAT
*
115092 AATTACACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
115115 AATTGCACC-GGAGCCGCGTAG
1 AATTGCACCTAGTGCCACGTAG
115136 AATTGCACCTTAGTGCCA
1 AATTGCACC-TAGTGCCA
115154 TATAATAATG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
21 18 0.60
23 12 0.40
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:118098 original size:22 final size:22
Alignment explanation
Indices: 118047--118099 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 22
118037 TCTGAGAGAT
*
118047 GGAGAT-A-GACGGATTTCGTC
1 GGAGATGAGGACGAATTTCGTC
*
118067 -G-GATGGGGACGAATTTCGTC
1 GGAGATGAGGACGAATTTCGTC
118087 GGAGATGAGGACG
1 GGAGATGAGGACG
118100 GATGTCGCCG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 12 0.46
21 1 0.04
22 9 0.35
ACGTcount: A:0.25, C:0.13, G:0.42, T:0.21
Consensus pattern (22 bp):
GGAGATGAGGACGAATTTCGTC
Found at i:118322 original size:21 final size:20
Alignment explanation
Indices: 118247--118321 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
118237 CGCTTTGAAA
*
118247 ATCGCATTGCGATATTGTATT
1 ATCGCGTTGCGATA-TGTATT
**
118268 ATCGCGTTGCGATA-GTCAGA
1 ATCGCGTTGCGATATGT-ATT
118288 ATCGCGTTGCGATTATGTATT
1 ATCGCGTTGCGA-TATGTATT
*
118309 ATCACGTTGCGAT
1 ATCGCGTTGCGAT
118322 TTACATATTC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.04
20 14 0.31
21 27 0.60
22 2 0.04
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (20 bp):
ATCGCGTTGCGATATGTATT
Found at i:118359 original size:38 final size:40
Alignment explanation
Indices: 118309--118398 Score: 148
Period size: 38 Copynumber: 2.3 Consensus size: 40
118299 ATTATGTATT
118309 ATCACGTTGCGATTTACATATTCGCA-TGCGATAGT-AAA
1 ATCACGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
*
118347 ATCGCGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
1 ATCACGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
*
118387 ATCATGTTGCGA
1 ATCACGTTGCGA
118399 ATCTGGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
38 25 0.53
39 9 0.19
40 13 0.28
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (40 bp):
ATCACGTTGCGATTTACATATTCGCATTGCGATAGTCAAA
Found at i:118376 original size:20 final size:20
Alignment explanation
Indices: 118315--118379 Score: 73
Period size: 19 Copynumber: 3.4 Consensus size: 20
118305 TATTATCACG
118315 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
* * *
118335 -TGCGATAGTA-A-AATCGCG
1 TTGCGAT-TTACATATTCGCA
118353 TTGCGATTTACATATTCGCA
1 TTGCGATTTACATATTCGCA
118373 TTGCGAT
1 TTGCGAT
118380 AGTCAAAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 7 0.20
19 14 0.40
20 14 0.40
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGCGATTTACATATTCGCA
Done.