Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007270.1 Hibiscus syriacus cultivar Beakdansim tig00019276_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: 120299
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:13592 original size:2 final size:2
Alignment explanation
Indices: 13585--13609 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13575 ACATCCATAA
13585 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13610 ATTTAAACTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17833 original size:455 final size:455
Alignment explanation
Indices: 16982--17894 Score: 1799
Period size: 455 Copynumber: 2.0 Consensus size: 455
16972 CCCATGCCCG
16982 AAAACGAGCTGCTTATGGATACTTATGCAAATAGTTGGAACGATGATCATGTAGTCGATTCAGAA
1 AAAACGAGCTGCTTATGGATACTTATGCAAATAGTTGGAACGATGATCATGTAGTCGATTCAGAA
17047 CAACACTCTGGAAGTCTGGAAGCACACGATGATACTGTCAGCCAACCTACTAATGAATCCGCTGC
66 CAACACTCTGGAAGTCTGGAAGCACACGATGATACTGTCAGCCAACCTACTAATGAATCCGCTGC
*
17112 AAATCAACATGCTGATGATGAAGTCAGTGAGCATAATGTGCAGCCTATAGTACCTCGTGGCAACA
131 AAATCAACATGCTGATGATGAAGTCAGTGAGCATAATGTGCAGCCTATAGTACCTCGTAGCAACA
17177 CTCATTCCATGCTAACTCGGAGTAAGTGTGGTGTGTACAAACCCAAAGCATACATAGGGTATGTC
196 CTCATTCCATGCTAACTCGGAGTAAGTGTGGTGTGTACAAACCCAAAGCATACATAGGGTATGTC
17242 CTGGATTATGTTCCATGCACAGTGCATGAAGCGCTTCAAGTCTCAGAATGGAAGACAGCTGTATA
261 CTGGATTATGTTCCATGCACAGTGCATGAAGCGCTTCAAGTCTCAGAATGGAAGACAGCTGTATA
17307 TGAAGAATATAATACATTGCAACGTAATGAAACTTGAGATTTAGTCAAGTTACCAGAAGGAAGAA
326 TGAAGAATATAATACATTGCAACGTAATGAAACTTGAGATTTAGTCAAGTTACCAGAAGGAAGAA
17372 AAGTGGTTGGATGTAAGTGGCTGTTCAAGCTCAAGAAGAACCCCGATGGTTCAGTTCATCGTTAC
391 AAGTGGTTGGATGTAAGTGGCTGTTCAAGCTCAAGAAGAACCCCGATGGTTCAGTTCATCGTTAC
17437 AAAACGAGCTGCTTATGGATACTTATGCAAATAGTTGGAACGATGATCATGTAGTCGATTCAGAA
1 AAAACGAGCTGCTTATGGATACTTATGCAAATAGTTGGAACGATGATCATGTAGTCGATTCAGAA
17502 CAACACTCTGGAAGTCTGGAAGCACACGATGATACTGTCAGCCAACCTACTAATGAATCCGCTGC
66 CAACACTCTGGAAGTCTGGAAGCACACGATGATACTGTCAGCCAACCTACTAATGAATCCGCTGC
17567 AAATCAACATGCTGATGATGAAGTCAGTGAGCATAATGTGCAGCCTATAGTACCTCGTAGCAACA
131 AAATCAACATGCTGATGATGAAGTCAGTGAGCATAATGTGCAGCCTATAGTACCTCGTAGCAACA
17632 CTCATTCCATGCTAACTCGGAGTAAGTGTGGTGTGTACAAACCCAAAGCATACATAGGGTATGTC
196 CTCATTCCATGCTAACTCGGAGTAAGTGTGGTGTGTACAAACCCAAAGCATACATAGGGTATGTC
17697 CTGGATTATGTTCCATGCACAGTGCATGAAGCGCTTCAAGTCTCAGAATGGAAGACAGCTGTATA
261 CTGGATTATGTTCCATGCACAGTGCATGAAGCGCTTCAAGTCTCAGAATGGAAGACAGCTGTATA
*
17762 TGAAGAATATAATGCATTGCAACGTAATGAAACTTGAGATTTAGTCAAGTTACCAGAAGGAAGAA
326 TGAAGAATATAATACATTGCAACGTAATGAAACTTGAGATTTAGTCAAGTTACCAGAAGGAAGAA
*
17827 AAGTGGTTGGATGTAAGTGGCTGTTCAAGCTCAAGAAGAACCCCGATGGTTCAGTTTATCGTTAC
391 AAGTGGTTGGATGTAAGTGGCTGTTCAAGCTCAAGAAGAACCCCGATGGTTCAGTTCATCGTTAC
17892 AAA
1 AAA
17895 GCACTTCTGG
Statistics
Matches: 455, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
455 455 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (455 bp):
AAAACGAGCTGCTTATGGATACTTATGCAAATAGTTGGAACGATGATCATGTAGTCGATTCAGAA
CAACACTCTGGAAGTCTGGAAGCACACGATGATACTGTCAGCCAACCTACTAATGAATCCGCTGC
AAATCAACATGCTGATGATGAAGTCAGTGAGCATAATGTGCAGCCTATAGTACCTCGTAGCAACA
CTCATTCCATGCTAACTCGGAGTAAGTGTGGTGTGTACAAACCCAAAGCATACATAGGGTATGTC
CTGGATTATGTTCCATGCACAGTGCATGAAGCGCTTCAAGTCTCAGAATGGAAGACAGCTGTATA
TGAAGAATATAATACATTGCAACGTAATGAAACTTGAGATTTAGTCAAGTTACCAGAAGGAAGAA
AAGTGGTTGGATGTAAGTGGCTGTTCAAGCTCAAGAAGAACCCCGATGGTTCAGTTCATCGTTAC
Found at i:21217 original size:24 final size:25
Alignment explanation
Indices: 21171--21217 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
21161 TGATAGTCCT
**
21171 ATTTTTTAACTCGAAGTTGAGTTGA
1 ATTTTTTAACTCGAAGTCAAGTTGA
*
21196 ATTTTTTTACTCG-AGTCAAGTT
1 ATTTTTTAACTCGAAGTCAAGTT
21218 TAGAAAATCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.47
Consensus pattern (25 bp):
ATTTTTTAACTCGAAGTCAAGTTGA
Found at i:25698 original size:19 final size:18
Alignment explanation
Indices: 25661--25720 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
25651 ACTTTCACAT
25661 TTCAGAA-TTCATTCTCAGA
1 TTCAGAACTT-ATTC-CAGA
25680 TTCAGAACTTACTTCCAGA
1 TTCAGAACTTA-TTCCAGA
* * *
25699 CTCATAACTTATTCTAGA
1 TTCAGAACTTATTCCAGA
25717 TTCA
1 TTCA
25721 TAATTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 9 0.26
19 21 0.60
20 5 0.14
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (18 bp):
TTCAGAACTTATTCCAGA
Found at i:25723 original size:18 final size:18
Alignment explanation
Indices: 25671--25723 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
25661 TTCAGAATTC
*
25671 ATTCTCAGATTCAGAACTT
1 ATTCT-AGATTCATAACTT
* *
25690 ACTTCCAGACTCATAACTT
1 A-TTCTAGATTCATAACTT
25709 ATTCTAGATTCATAA
1 ATTCTAGATTCATAA
25724 TTTAATTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.43
19 13 0.46
20 3 0.11
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.36
Consensus pattern (18 bp):
ATTCTAGATTCATAACTT
Found at i:29020 original size:2 final size:2
Alignment explanation
Indices: 29015--29053 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29005 TAAAAAAGTA
29015 AT AT AT AT AT AT AT AT AT AT AT 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 AT AT AT AT A
29054 ATGATAGGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30730 original size:16 final size:16
Alignment explanation
Indices: 30709--30753 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
30699 TTAGAGTCTC
30709 TGAATTATTCAGCATT
1 TGAATTATTCAGCATT
*
30725 TGAATTATTCAGTATT
1 TGAATTATTCAGCATT
*
30741 TGAATCATTCAGC
1 TGAATTATTCAGC
30754 GCTTAATCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (16 bp):
TGAATTATTCAGCATT
Found at i:35353 original size:24 final size:24
Alignment explanation
Indices: 35322--35374 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
35312 CTCATTGACC
* *
35322 ATTGTCATTGACCCAAAAATATCT
1 ATTGTCATCGACCCAAAAATATCG
*
35346 ATTGTCATCGACCCGAAAATATCG
1 ATTGTCATCGACCCAAAAATATCG
35370 ATTGT
1 ATTGT
35375 AATTAAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.32
Consensus pattern (24 bp):
ATTGTCATCGACCCAAAAATATCG
Found at i:50962 original size:19 final size:19
Alignment explanation
Indices: 50935--50973 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
50925 ACTAGGGTAT
50935 AAATCCATA-ATCAAAATCA
1 AAATCCATATATC-AAATCA
*
50954 AAATTCATATATCAAATCA
1 AAATCCATATATCAAATCA
50973 A
1 A
50974 CATTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATCCATATATCAAATCA
Found at i:53894 original size:21 final size:19
Alignment explanation
Indices: 53849--53897 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
53839 TTTTCAGCCG
53849 TTTGTAACTCATAATTACT
1 TTTGTAACTCATAATTACT
*
53868 TCTGTAACTCATGTAATTA-T
1 TTTGTAACTCA--TAATTACT
53888 ATTTGTAACT
1 -TTTGTAACT
53898 GGCATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.40
20 1 0.04
21 14 0.56
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (19 bp):
TTTGTAACTCATAATTACT
Found at i:56141 original size:2 final size:2
Alignment explanation
Indices: 56134--56168 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56124 CCGTTTTGGT
56134 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56169 GAGTTAGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:58647 original size:44 final size:44
Alignment explanation
Indices: 58593--58676 Score: 132
Period size: 44 Copynumber: 1.9 Consensus size: 44
58583 ATCTGACATG
* *
58593 TCTGCGAACCAAACAGAATATGAAATTGGATTCCAATTCCATTT
1 TCTGCCAACCAAACAAAATATGAAATTGGATTCCAATTCCATTT
* *
58637 TCTGCCAACCAAACAAAATATGGATTTGGATTCCAATTCC
1 TCTGCCAACCAAACAAAATATGAAATTGGATTCCAATTCC
58677 TGACAGATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.29
Consensus pattern (44 bp):
TCTGCCAACCAAACAAAATATGAAATTGGATTCCAATTCCATTT
Found at i:58687 original size:17 final size:18
Alignment explanation
Indices: 58665--58711 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
58655 TATGGATTTG
*
58665 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
58682 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
58700 GATTCTAATTCC
1 GATTCCAATTCC
58712 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:59582 original size:21 final size:19
Alignment explanation
Indices: 59537--59585 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
59527 TTTTCAGCCG
59537 TTTGTAACTCATAATTACT
1 TTTGTAACTCATAATTACT
*
59556 TCTGTAACTCATGTAATTA-T
1 TTTGTAACTCA--TAATTACT
59576 ATTTGTAACT
1 -TTTGTAACT
59586 GGCATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 10 0.40
20 1 0.04
21 14 0.56
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (19 bp):
TTTGTAACTCATAATTACT
Found at i:61879 original size:2 final size:2
Alignment explanation
Indices: 61872--61908 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
61862 CCGTTTTGGT
61872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61909 GAGTTAGGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:66948 original size:21 final size:21
Alignment explanation
Indices: 66900--66954 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
66890 AAATTTATGT
*
66900 TTTTTTAAAA-TATATATATA
1 TTTTTTAAAATTATATATAAA
* *
66920 TATATTTAAAATTTTATATAAA
1 T-TTTTTAAAATTATATATAAA
66942 TTTTTTAAAATTA
1 TTTTTTAAAATTA
66955 CCAGGTGTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.04
21 18 0.64
22 9 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTTAAAATTATATATAAA
Found at i:72523 original size:16 final size:16
Alignment explanation
Indices: 72511--72551 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
72501 ATCTAATATC
*
72511 ATTTTTAATTAATTTA
1 ATTTTTAACTAATTTA
72527 ATTTTTAACTAATTTA
1 ATTTTTAACTAATTTA
72543 ATTTTTAAC
1 ATTTTTAAC
72552 AGATTATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTTTAACTAATTTA
Found at i:80274 original size:59 final size:60
Alignment explanation
Indices: 80211--80332 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 60
80201 AGTCCTTTAT
** * * *
80211 TATATGCTGATGCTTTGTTGAGTCTGTTAATTATGAAAAGTTATAAAATGGTCCCT-GAC
1 TATATGCTGATGCTTTGTTGAGTCCCTTAACTATGAAAAGTTACAAAATGGTCACTCGAC
* * * *
80270 TATATGGTGTTGCTTTGTTGAGTCCCTTGACTATTAAAAGTTACAAAATGGTCACTCGAC
1 TATATGCTGATGCTTTGTTGAGTCCCTTAACTATGAAAAGTTACAAAATGGTCACTCGAC
80330 TAT
1 TAT
80333 TCATATGTTC
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
59 47 0.89
60 6 0.11
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.39
Consensus pattern (60 bp):
TATATGCTGATGCTTTGTTGAGTCCCTTAACTATGAAAAGTTACAAAATGGTCACTCGAC
Found at i:81794 original size:15 final size:14
Alignment explanation
Indices: 81776--81806 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
81766 AAATTAGGGG
81776 AAAACAAAAAACAAA
1 AAAACAAAAAA-AAA
81791 AAAACAAAAAAAAA
1 AAAACAAAAAAAAA
81805 AA
1 AA
81807 GTAAAAGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACAAAAAAAAA
Found at i:83135 original size:60 final size:59
Alignment explanation
Indices: 82965--83145 Score: 163
Period size: 60 Copynumber: 3.1 Consensus size: 59
82955 CATATGTACT
* * * *
82965 CAAACTATAACCCTCATTT-TAAATTGGTCTTTAAACTTTTAAATATT--ATTTCTTCCC
1 CAAACTATGACTCTC-TTTCTAAATTGGTCCTTAAACTTTTAAATATTCAATTTCATCCC
* * * * * *
83022 CAAACTATGACTGCT-ATTCCAAATTAGTCCTTAAATTTTTTAACATTCTAATTTCATCCC
1 CAAACTATGACT-CTCTTTCTAAATTGGTCCTTAAACTTTTAAATATTC-AATTTCATCCC
* ** * *
83082 TAAACTATGACTCTCTTTCTAAATTGGTCCCCAAACTTTTGAATATTCCAATTTCAACCC
1 CAAACTATGACTCTCTTTCTAAATTGGTCCTTAAACTTTTAAATATT-CAATTTCATCCC
83142 CAAA
1 CAAA
83146 TTCACCCAAA
Statistics
Matches: 96, Mismatches: 21, Indels: 11
0.75 0.16 0.09
Matches are distributed among these distances:
56 2 0.02
57 32 0.33
58 2 0.02
59 2 0.02
60 57 0.59
61 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (59 bp):
CAAACTATGACTCTCTTTCTAAATTGGTCCTTAAACTTTTAAATATTCAATTTCATCCC
Found at i:94796 original size:182 final size:182
Alignment explanation
Indices: 94489--94828 Score: 504
Period size: 182 Copynumber: 1.9 Consensus size: 182
94479 CCTTTCAACT
* *
94489 TATTATTAATGATGCTTATACATAACATCACTTTATAATTTATATTCAATGAAAAATTATTACGT
1 TATTATTAATGATGCTTATACATAACATCACTTTATAATTTATATTCAATGAAAAATTATCACGC
* ** *
94554 CACTAAATTATATAAGATTTCGTTATTGATAATTTATATCGTCACAGAAAATACATTAAAATTAA
66 CACTAAATTATATAAAATTTAATTATTGATAATTTATATCGTCACAGAAAATACATTAAAATCAA
94619 CCTATATATGACGAAAGAGATATTGTCAAATTTTATAAATGTTACCAAATAA
131 CCTATATATGACGAAAGAGATATTGTCAAATTTTATAAATGTTACCAAATAA
* * * * * *
94671 TATTATTAATGTTGCTTATACATAACGTCACTTTATAATTTATATTCTATGACAACTTGTCACGC
1 TATTATTAATGATGCTTATACATAACATCACTTTATAATTTATATTCAATGAAAAATTATCACGC
* *
94736 CACTAAATTATATAAAATTTAATT-TCTGATAATTTATATTGTCAC-GAATAATTCATTAAAATC
66 CACTAAATTATATAAAATTTAATTAT-TGATAATTTATATCGTCACAGAA-AATACATTAAAATC
* *
94799 CACCTATATGTGACGAAAGAGATATTGTCA
129 AACCTATATATGACGAAAGAGATATTGTCA
94829 TTTTTTAGTG
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
181 4 0.03
182 136 0.97
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (182 bp):
TATTATTAATGATGCTTATACATAACATCACTTTATAATTTATATTCAATGAAAAATTATCACGC
CACTAAATTATATAAAATTTAATTATTGATAATTTATATCGTCACAGAAAATACATTAAAATCAA
CCTATATATGACGAAAGAGATATTGTCAAATTTTATAAATGTTACCAAATAA
Found at i:96900 original size:12 final size:12
Alignment explanation
Indices: 96883--96909 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
96873 TAGCGAAATG
96883 TTTGGTTGAACA
1 TTTGGTTGAACA
96895 TTTGGTTGAACA
1 TTTGGTTGAACA
96907 TTT
1 TTT
96910 TGTGAGAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (12 bp):
TTTGGTTGAACA
Found at i:102493 original size:69 final size:69
Alignment explanation
Indices: 102375--102503 Score: 213
Period size: 69 Copynumber: 1.9 Consensus size: 69
102365 AATAATGGAT
* * *
102375 GTAAAATTGTCAAAAATCTCACATTTTCAAGTTAATGTAAGGTTGTCTAAGAAACATGTTGTAAT
1 GTAAAATTGTCAAAAAACTCACATTTTCAAGTTAATGTAAGATTATCTAAGAAACATGTTGTAAT
102440 TGAA
66 TGAA
* *
102444 GTAAAATTGTTAAAAAACTCGCATTTTCAAGTTAATGTAAGATTATCTAAGAAACATGTT
1 GTAAAATTGTCAAAAAACTCACATTTTCAAGTTAATGTAAGATTATCTAAGAAACATGTT
102504 CTATTAAGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (69 bp):
GTAAAATTGTCAAAAAACTCACATTTTCAAGTTAATGTAAGATTATCTAAGAAACATGTTGTAAT
TGAA
Found at i:106002 original size:24 final size:24
Alignment explanation
Indices: 105975--106023 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
105965 TATCAGCTTA
105975 TGGGATACACATAATATCATGTAT
1 TGGGATACACATAATATCATGTAT
* *
105999 TGGGATACACGTGATATCATGTAT
1 TGGGATACACATAATATCATGTAT
106023 T
1 T
106024 TGTACTCTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (24 bp):
TGGGATACACATAATATCATGTAT
Found at i:108234 original size:13 final size:12
Alignment explanation
Indices: 108207--108231 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
108197 ATATTTTAAG
108207 TAATTTTTTTAT
1 TAATTTTTTTAT
108219 TAATTTTTTTAT
1 TAATTTTTTTAT
108231 T
1 T
108232 TAAATAATAA
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:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TAATTTTTTTAT
Found at i:112287 original size:12 final size:13
Alignment explanation
Indices: 112251--112289 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
112241 TATATAAAGT
112251 TATTAAATATTAAA
1 TATTAAAT-TTAAA
*
112265 TATTGAATTTAAA
1 TATTAAATTTAAA
112278 T-TTAAATTTAAA
1 TATTAAATTTAAA
112290 ATTTCTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 10 0.43
13 6 0.26
14 7 0.30
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (13 bp):
TATTAAATTTAAA
Found at i:115154 original size:89 final size:89
Alignment explanation
Indices: 115002--115168 Score: 189
Period size: 90 Copynumber: 1.9 Consensus size: 89
114992 TAAAAATTTA
**
115002 AAATTTTAAAAAATAATTAATAATTTAATTTATAAAATTTTAAAAAAAATTTAACTTATAATT-A
1 AAATTTTAAAAAATAATTAATAATTTAATTTATAAAATTTTAAAAAAAATTTAAAATATAATTAA
115066 TAAATTAGTTAAAAATTTAAAGAT
66 TAAATTAGTTAAAAATTTAAAGAT
* * * * *
115090 AAATTATTAAAATAA-AATTAATTATATTATTTTCAT-AATTTTTAATAATAATTTAAAATA-AA
1 AAATT-TTAAAA-AATAATTAATAAT-TTAATTT-ATAAAATTTTAAAAAAAATTTAAAATATAA
* *
115152 TTAATATATTATTTAAA
62 TTAATAAATTAGTTAAA
115169 TTATAATTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
88 5 0.08
89 19 0.29
90 39 0.60
91 2 0.03
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (89 bp):
AAATTTTAAAAAATAATTAATAATTTAATTTATAAAATTTTAAAAAAAATTTAAAATATAATTAA
TAAATTAGTTAAAAATTTAAAGAT
Found at i:115169 original size:21 final size:21
Alignment explanation
Indices: 115092--115169 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 21
115082 TTAAAGATAA
*
115092 ATTATTAAAATAAAATTAATTAT
1 ATTATTTAAAT-AAATTAA-TAT
** *
115115 ATTATTTTCATAATTTTTAATA-
1 ATTATTTAAATAA--ATTAATAT
*
115137 ATAATTTAAAATAAATTAATAT
1 ATTATTT-AAATAAATTAATAT
115159 ATTATTTAAAT
1 ATTATTTAAAT
115170 TATAATTTTT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
21 10 0.24
22 14 0.33
23 14 0.33
24 4 0.10
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (21 bp):
ATTATTTAAATAAATTAATAT
Found at i:115991 original size:55 final size:55
Alignment explanation
Indices: 115901--116005 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
115891 TCATAATATG
* * * *
115901 TAAGTGTGCAAAACCACATAATTCATAATATGTTTATGAATGACTGTATCAATAC
1 TAAGTGTACAAAACCACATAATTCATAATACGTTTATGAACGACCGTATCAATAC
*
115956 TAAGTGTACAAAACCACGA-AATTCATAATGCGTTTATGAACGACCGTATC
1 TAAGTGTACAAAACCAC-ATAATTCATAATACGTTTATGAACGACCGTATC
116006 GACACTACGT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
55 43 0.98
56 1 0.02
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (55 bp):
TAAGTGTACAAAACCACATAATTCATAATACGTTTATGAACGACCGTATCAATAC
Found at i:119451 original size:2 final size:2
Alignment explanation
Indices: 119444--119498 Score: 94
Period size: 2 Copynumber: 28.0 Consensus size: 2
119434 GCATGGAAGA
*
119444 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
119486 A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
119499 CTACAGTTCT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:120056 original size:27 final size:29
Alignment explanation
Indices: 120015--120069 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
120005 GAGCAAGGGT
*
120015 AGGTCGCCCGGAGTGCA-GGCGACCTACA
1 AGGTCGCCCGGAGTGCATGACGACCTACA
120043 AGGTCG-CCGGAGTGCATGACGACCTAC
1 AGGTCGCCCGGAGTGCATGACGACCTAC
120070 GGCCAACACT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.22, C:0.31, G:0.35, T:0.13
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGACGACCTACA
Found at i:120095 original size:31 final size:31
Alignment explanation
Indices: 120057--120117 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
120047 CGCCGGAGTG
120057 CATGACGACCTACGGCCAACACTGTGGATTA
1 CATGACGACCTACGGCCAACACTGTGGATTA
120088 CATGACGACCTACGGCCAACACTGTGGATT
1 CATGACGACCTACGGCCAACACTGTGGATT
120118 TCACCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.20
Consensus pattern (31 bp):
CATGACGACCTACGGCCAACACTGTGGATTA
Done.