Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009003.1 Hibiscus syriacus cultivar Beakdansim tig00112386_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: 71150
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:7701 original size:37 final size:36
Alignment explanation
Indices: 7626--7701 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
7616 TTTTTATATT
*
7626 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
7662 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
7699 TTT
1 TTT
7702 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:7882 original size:20 final size:20
Alignment explanation
Indices: 7846--7883 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7836 ATCCTATTCC
**
7846 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
7866 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
7884 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:9091 original size:23 final size:22
Alignment explanation
Indices: 9065--9131 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 22
9055 CCACAGCTCA
9065 TATAATTGCACCGAAGTGCCACG
1 TATAATTGCACCG-AGTGCCACG
*
9088 TATAATTGCACCCGAGTGCCGCG
1 TATAATTGCA-CCGAGTGCCACG
* *
9111 TAGAATTACACCGTAGTGCCA
1 TATAATTGCACCG-AGTGCCA
9132 TATAATAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.08
23 32 0.84
24 3 0.08
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.22
Consensus pattern (22 bp):
TATAATTGCACCGAGTGCCACG
Found at i:9318 original size:103 final size:103
Alignment explanation
Indices: 9147--9364 Score: 391
Period size: 103 Copynumber: 2.1 Consensus size: 103
9137 TAATGTCCAT
* *
9147 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
*
9212 GACTTCACACATGTTCCAAATAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
9250 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
9315 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
9353 AAGGACCACATA
1 AAGGACCACATA
9365 GACCCTCGAC
Statistics
Matches: 110, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATATGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:9852 original size:107 final size:107
Alignment explanation
Indices: 9732--9947 Score: 432
Period size: 107 Copynumber: 2.0 Consensus size: 107
9722 CCTATCATTT
9732 TATTATCTTTATTATTATTCTTATCCTCACCATTAATCCATTTTACTTACCATATTCATATCAAT
1 TATTATCTTTATTATTATTCTTATCCTCACCATTAATCCATTTTACTTACCATATTCATATCAAT
9797 AACACATATACTCATGCACACATATAAATCATAACCAATACA
66 AACACATATACTCATGCACACATATAAATCATAACCAATACA
9839 TATTATCTTTATTATTATTCTTATCCTCACCATTAATCCATTTTACTTACCATATTCATATCAAT
1 TATTATCTTTATTATTATTCTTATCCTCACCATTAATCCATTTTACTTACCATATTCATATCAAT
9904 AACACATATACTCATGCACACATATAAATCATAACCAATACA
66 AACACATATACTCATGCACACATATAAATCATAACCAATACA
9946 TA
1 TA
9948 CTTCTATGAA
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
107 109 1.00
ACGTcount: A:0.38, C:0.23, G:0.01, T:0.38
Consensus pattern (107 bp):
TATTATCTTTATTATTATTCTTATCCTCACCATTAATCCATTTTACTTACCATATTCATATCAAT
AACACATATACTCATGCACACATATAAATCATAACCAATACA
Found at i:10329 original size:64 final size:64
Alignment explanation
Indices: 10257--10413 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 64
10247 TTCCCTATCG
* * * **
10257 GTGCATCGATGCACTACCTGTGCATCGGTGCATAAAATACATTCGATGTTTGTT-TATTACTAG-
1 GTGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTT-TTAGATTAAAAGA
* * * * **
10320 GATGCATCGATGCA-TGCCTTATGCATCGATGCACCAATTGTATTCGATGTTTTTAGATTAAAAG
1 G-TGCATCGATGCACTACC-TGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAAG
10384 A
64 A
*
10385 GTGCATCGATGCACTACTTGTGCATCGAT
1 GTGCATCGATGCACTACCTGTGCATCGAT
10414 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
63 6 0.08
64 66 0.88
65 3 0.04
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCTGTGCATCGATGCACAAAATACATTCGATGTTTTTAGATTAAAAGA
Found at i:14667 original size:586 final size:586
Alignment explanation
Indices: 13555--14692 Score: 2051
Period size: 586 Copynumber: 1.9 Consensus size: 586
13545 AATGTATAAT
*
13555 AAGTGCTGGAGGGTATTTCGACTGTAAAGCCTCCTGTCGCTGTATTTGATGAGGGAATTGCTAAA
1 AAGTGCTGGAGGGTATTTCGACTGTAAAGCCTCATGTCGCTGTATTTGATGAGGGAATTGCTAAA
* * *
13620 TGGGATTGTGCTGTGGTTGGGTAGTTCATTGGAGATGCTCCCAACTTTGGCTCTATGCAGCGTAT
66 TGGGATTGTGCTGTGGTTGGGCAGTTCATTGGAGACGCTCCCAACTTTGGCTCTATACAGCGTAT
13685 TGCTGAGATTCTTTGGGGGAAAGCTTCTCATGTTAAGGTAAGCTTGGCTGGGCACAACCTCTATG
131 TGCTGAGATTCTTTGGGGGAAAGCTTCTCATGTTAAGGTAAGCTTGGCTGGGCACAACCTCTATG
*
13750 TTTTTTCATTCTCTAATTCGGATTTGAGAGACTGGGTGCTTGAGAATGGCCCTTGGCACATTCAA
196 TTTTTTCATTCACTAATTCGGATTTGAGAGACTGGGTGCTTGAGAATGGCCCTTGGCACATTCAA
13815 AACAAGCCTCTTGTGTTAAGAAAATAGGAACCGAGCTTGAGGAAACTTGATTTTGATCTAAAACG
261 AACAAGCCTCTTGTGTTAAGAAAATAGGAACCGAGCTTGAGGAAACTTGATTTTGATCTAAAACG
* * * * *
13880 CATGCCTGTCTGGGTTCAATTATACAATGTTCCTTTGGAGTTTTTTTCTCGAATATGTCTTAGCT
326 CATACATGTCTGGGTTCAATTATAAAATGTTCCTTTGGAGCTTTTTTCTCGAATAGGTCTTAGCT
* * *
13945 ATATAGCTAGTGCTGTGGGTAATCCATTGTGTGTGGATATTGTTACTGCTTCAAAGGAGAAACTC
391 ATATAGCTAGTGCTGTGGGTAATCCATTGTATATGGATATTATTACTGCTTCAAAGGAGAAACTC
*
14010 GAATTTGCCAAAGTTTGTGTTGAGGTTGAAGCTGGGGCAGTGATCCTTAAGGTGATCCATATAGT
456 GAATTTGCCAAAGTTTGTGTTGAGGTTGAAGCTGGGGCAGTGATCCCTAAGGTGATCCATATAGT
*
14075 CTTAAGGGATGGCTCTATTGCAAAAATTAGGGATGAAGGAGCAATCCCTAGAGTTATTTCTGCCT
521 CTTAAGGGATGGCTCTATTACAAAAATTAGGGATGAAGGAGCAATCCCTAGAGTTATTTCTGCCT
14140 G
586 G
*
14141 AAGTGCTGGAGGGTATTTCGACTGTAAAGCCTCATGTCGCTGTATTTGATGAGGGAATTGCTGAA
1 AAGTGCTGGAGGGTATTTCGACTGTAAAGCCTCATGTCGCTGTATTTGATGAGGGAATTGCTAAA
14206 TGGGATTGTGCTGTGGTTGGGCAGTTCATTGGAGACGCTCCCAACTTTGGCTCTATACAGCGTAT
66 TGGGATTGTGCTGTGGTTGGGCAGTTCATTGGAGACGCTCCCAACTTTGGCTCTATACAGCGTAT
*
14271 TGCTGAGATTCTTTGGGGGAAAGCTTCTCATGTTAAGGTAAGCTTGGCTGGGCATAACCTCTATG
131 TGCTGAGATTCTTTGGGGGAAAGCTTCTCATGTTAAGGTAAGCTTGGCTGGGCACAACCTCTATG
14336 TTTTTTCATTCACTAATTCGGATTTGAGAGACTGGGTGCTTGAGAATGGCCCTTGGCACATTCAA
196 TTTTTTCATTCACTAATTCGGATTTGAGAGACTGGGTGCTTGAGAATGGCCCTTGGCACATTCAA
*
14401 AACAAGCCTCTTGTGTTAAGAAAATGGGAACCGAGCTTGAGGAAACTTGATTTTGATCTAAAACG
261 AACAAGCCTCTTGTGTTAAGAAAATAGGAACCGAGCTTGAGGAAACTTGATTTTGATCTAAAACG
* *
14466 CATACATGTCTGGGTTCAATTATAAAATGTTCCTTTGGAGCTTTTTTCTTGAGTAGGTCTTAGCT
326 CATACATGTCTGGGTTCAATTATAAAATGTTCCTTTGGAGCTTTTTTCTCGAATAGGTCTTAGCT
* * *
14531 ATATAGCTAGTGTTGTGGGTAATCCATTGTATATGGATATTATTACTGCTTCAAATGAGAGACTC
391 ATATAGCTAGTGCTGTGGGTAATCCATTGTATATGGATATTATTACTGCTTCAAAGGAGAAACTC
* *
14596 GAATTTGCCAAAGTTTGTGTTGAGGTTGAAGCTGGGGCAGTGATCCCTGAGGTGATCCATGTAGT
456 GAATTTGCCAAAGTTTGTGTTGAGGTTGAAGCTGGGGCAGTGATCCCTAAGGTGATCCATATAGT
14661 CTTAAGGGATGGCTCTATTACAAAAATTAGGG
521 CTTAAGGGATGGCTCTATTACAAAAATTAGGG
14693 TGTATGCTCC
Statistics
Matches: 527, Mismatches: 25, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
586 527 1.00
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.33
Consensus pattern (586 bp):
AAGTGCTGGAGGGTATTTCGACTGTAAAGCCTCATGTCGCTGTATTTGATGAGGGAATTGCTAAA
TGGGATTGTGCTGTGGTTGGGCAGTTCATTGGAGACGCTCCCAACTTTGGCTCTATACAGCGTAT
TGCTGAGATTCTTTGGGGGAAAGCTTCTCATGTTAAGGTAAGCTTGGCTGGGCACAACCTCTATG
TTTTTTCATTCACTAATTCGGATTTGAGAGACTGGGTGCTTGAGAATGGCCCTTGGCACATTCAA
AACAAGCCTCTTGTGTTAAGAAAATAGGAACCGAGCTTGAGGAAACTTGATTTTGATCTAAAACG
CATACATGTCTGGGTTCAATTATAAAATGTTCCTTTGGAGCTTTTTTCTCGAATAGGTCTTAGCT
ATATAGCTAGTGCTGTGGGTAATCCATTGTATATGGATATTATTACTGCTTCAAAGGAGAAACTC
GAATTTGCCAAAGTTTGTGTTGAGGTTGAAGCTGGGGCAGTGATCCCTAAGGTGATCCATATAGT
CTTAAGGGATGGCTCTATTACAAAAATTAGGGATGAAGGAGCAATCCCTAGAGTTATTTCTGCCT
G
Found at i:22246 original size:12 final size:12
Alignment explanation
Indices: 22229--22256 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
22219 CCGTTTAGCA
22229 TAAACAGTTATT
1 TAAACAGTTATT
22241 TAAACAGTTATT
1 TAAACAGTTATT
22253 TAAA
1 TAAA
22257 TACCCGCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (12 bp):
TAAACAGTTATT
Found at i:24864 original size:2 final size:2
Alignment explanation
Indices: 24857--24884 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
24847 TAGCTGAAGG
24857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
24885 GAAACTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25526 original size:22 final size:24
Alignment explanation
Indices: 25496--25540 Score: 76
Period size: 22 Copynumber: 2.0 Consensus size: 24
25486 GTTATAATTA
25496 ATTTATTTTATAAATATA-AAATG
1 ATTTATTTTATAAATATATAAATG
25519 ATTT-TTTTATAAATATATAAAT
1 ATTTATTTTATAAATATATAAAT
25541 AAAGTAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (24 bp):
ATTTATTTTATAAATATATAAATG
Found at i:25747 original size:137 final size:141
Alignment explanation
Indices: 25588--25842 Score: 394
Period size: 140 Copynumber: 1.8 Consensus size: 141
25578 TATAAATATA
*
25588 AAATGAGAAAAATTGAGTGTTATAAATATATAAATAAAGAAGACAATTAATTTAG-A-AA-TAAC
1 AAATGAGAAAAATTGAGTGTTATAAATATATAAATAAAAAAGACAATTAATTTAGTATAATTAAC
* *
25650 TTTGTCACTAATGTATATACATACATCAAAAATAAAGAAGACACA-ATTTTATAAATAAAGAGAT
66 TTCGTCACTAATGTATATACATACATAAAAAATAAAGAAGACA-ATATTTTATAAATAAAGAGAT
25714 CATATGAAAGGT
130 CATATGAAAGGT
*
25726 AAATGAGAAAAA-TGAGTGTTATAAATATATAAATAAAAAAGACAATTACTTTAGTATAATTAAC
1 AAATGAGAAAAATTGAGTGTTATAAATATATAAATAAAAAAGACAATTAATTTAGTATAATTAAC
* * * *
25790 TTCGTCACTAATGTATATGCGTATATAAAAAATAAAGTAGACAATATTTTATA
66 TTCGTCACTAATGTATATACATACATAAAAAATAAAGAAGACAATATTTTATA
25843 TGAAAGGTAA
Statistics
Matches: 105, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
137 40 0.38
138 13 0.12
139 3 0.03
140 49 0.47
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (141 bp):
AAATGAGAAAAATTGAGTGTTATAAATATATAAATAAAAAAGACAATTAATTTAGTATAATTAAC
TTCGTCACTAATGTATATACATACATAAAAAATAAAGAAGACAATATTTTATAAATAAAGAGATC
ATATGAAAGGT
Found at i:34399 original size:88 final size:90
Alignment explanation
Indices: 34234--34405 Score: 271
Period size: 88 Copynumber: 1.9 Consensus size: 90
34224 GTGTTTCTGC
* *
34234 TTACCATATTGCTCCCTCCATTATGAAAAATTTGTTGTCCTTTTTATGATGTTTCATTCCCCTGT
1 TTACCATATTGCTCCCCCCATTATGAAAAATTTGTTGTCCTTTTTATGATGTTCCATTCCCCTGT
34299 TATATAAAAGAAGACACCTTTTTGT
66 TATATAAAAGAAGACACCTTTTTGT
*
34324 TTACCAT-TGTGCTCCCCCCATTATGAAAAA-TTGTTGTCC-TTTTATGATGTTCCATTGCCCTG
1 TTACCATAT-TGCTCCCCCCATTATGAAAAATTTGTTGTCCTTTTTATGATGTTCCATTCCCCTG
34386 TTACT-TAAAAGAAGACACCT
65 TTA-TATAAAAGAAGACACCT
34406 CAATGCCTCC
Statistics
Matches: 77, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
88 39 0.51
89 11 0.14
90 27 0.35
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (90 bp):
TTACCATATTGCTCCCCCCATTATGAAAAATTTGTTGTCCTTTTTATGATGTTCCATTCCCCTGT
TATATAAAAGAAGACACCTTTTTGT
Found at i:48286 original size:34 final size:34
Alignment explanation
Indices: 48240--48372 Score: 185
Period size: 34 Copynumber: 3.9 Consensus size: 34
48230 GGAGGGTTAT
* * *
48240 AGTGTAATGTGTATCTTATGTATTTCAGGATTAG
1 AGTGCAATGTGTATCTTATGTAATTCAGGTTTAG
* *
48274 AGAGTAATGTGTATCTTATGTAATTCAGGTTTAG
1 AGTGCAATGTGTATCTTATGTAATTCAGGTTTAG
* *
48308 AGTGCATTTTGTATCTTATGTAATTCAGGTTTAG
1 AGTGCAATGTGTATCTTATGTAATTCAGGTTTAG
* *
48342 AGTGCATTTTGTATCTTATGTAATTCAGGTT
1 AGTGCAATGTGTATCTTATGTAATTCAGGTT
48373 AATTAATAAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 92 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.45
Consensus pattern (34 bp):
AGTGCAATGTGTATCTTATGTAATTCAGGTTTAG
Found at i:54949 original size:20 final size:20
Alignment explanation
Indices: 54909--54949 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54899 GGCTTGTGTA
*
54909 TTTTAATTTTATTATGATAT
1 TTTTAATTTTATAATGATAT
* *
54929 TTTTTATTTTATAATGTTAT
1 TTTTAATTTTATAATGATAT
54949 T
1 T
54950 AGTTATTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTAATTTTATAATGATAT
Found at i:60146 original size:30 final size:30
Alignment explanation
Indices: 60075--60296 Score: 209
Period size: 30 Copynumber: 7.4 Consensus size: 30
60065 AGAAAACTTG
* * * *
60075 ATACTTTAATTTACGAGAAGGGGA-GGAAG
1 ATACTTCAATTGACGAGAAGGGGATGAAAA
* *
60104 ATCCCTTCAATTGACAAGAAGGGGATGAAAA
1 AT-ACTTCAATTGACGAGAAGGGGATGAAAA
* * *
60135 ATACTTTAATTGGCGAG-AGAGGATGAAAA
1 ATACTTCAATTGACGAGAAGGGGATGAAAA
* * *
60164 ATACTTTAATTGATGAGACGGGGA-GAAAAA
1 ATACTTCAATTGACGAGAAGGGGATG-AAAA
* ** *
60194 ATACTTCAGTTGACGAGAAAAGGATGAAGA
1 ATACTTCAATTGACGAGAAGGGGATGAAAA
*
60224 ATACTTCAATTGACTAGAAGGGGA-GAGAAA
1 ATACTTCAATTGACGAGAAGGGGATGA-AAA
* *
60254 ACACTTCAACTGACGAGAAGGGGATGAAAA
1 ATACTTCAATTGACGAGAAGGGGATGAAAA
*
60284 ACACTTCAATTGA
1 ATACTTCAATTGA
60297 GAAGAAGAGC
Statistics
Matches: 155, Mismatches: 31, Indels: 13
0.78 0.16 0.07
Matches are distributed among these distances:
29 31 0.20
30 116 0.75
31 8 0.05
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (30 bp):
ATACTTCAATTGACGAGAAGGGGATGAAAA
Found at i:61865 original size:16 final size:17
Alignment explanation
Indices: 61846--61911 Score: 57
Period size: 18 Copynumber: 3.9 Consensus size: 17
61836 TTTATAAGGT
61846 ATATTTATTA-TATTTA
1 ATATTTATTAGTATTTA
*
61862 ATATTTGTTAGTATTTTA
1 ATATTTATTAGTA-TTTA
* * *
61880 TTAATTATTATTTATTTA
1 ATATTTATTA-GTATTTA
61898 AT-TTT-TTAGTATTT
1 ATATTTATTAGTATTT
61912 TTTAATTATT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
15 5 0.13
16 12 0.31
17 4 0.10
18 16 0.41
19 2 0.05
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (17 bp):
ATATTTATTAGTATTTA
Found at i:61907 original size:34 final size:36
Alignment explanation
Indices: 61850--61921 Score: 114
Period size: 34 Copynumber: 2.1 Consensus size: 36
61840 TAAGGTATAT
61850 TTATTATATTTAATATTTGTTAGTATTTTATTAATTA
1 TTATTATATTTAATATTTGTTAGTATTTT-TTAATTA
61887 TTATT-TATTTAAT-TTT-TTAGTATTTTTTAATTA
1 TTATTATATTTAATATTTGTTAGTATTTTTTAATTA
61920 TT
1 TT
61922 TTTTTGCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
33 9 0.26
34 10 0.29
35 3 0.09
36 8 0.23
37 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (36 bp):
TTATTATATTTAATATTTGTTAGTATTTTTTAATTA
Found at i:61915 original size:18 final size:18
Alignment explanation
Indices: 61858--61923 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
61848 ATTTATTATA
61858 TTTAATATTTGTTAGTATTT
1 TTTAAT-TTT-TTAGTATTT
* *
61878 TATTAA-TTATTA-T-TTA
1 T-TTAATTTTTTAGTATTT
61894 TTTAATTTTTTAGTATTT
1 TTTAATTTTTTAGTATTT
61912 TTTAATTATTTT
1 TTTAATT-TTTT
61924 TTTGCAGTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 4 0.11
16 8 0.22
17 2 0.05
18 12 0.32
19 6 0.16
20 1 0.03
21 4 0.11
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTAATTTTTTAGTATTT
Found at i:61921 original size:11 final size:11
Alignment explanation
Indices: 61873--61925 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
61863 TATTTGTTAG
61873 TATTTTATTAAT
1 TATTTT-TTAAT
* *
61885 TATTATTTATT
1 TATTTTTTAAT
*
61896 TAATTTTTT-AG
1 T-ATTTTTTAAT
61907 TATTTTTTAAT
1 TATTTTTTAAT
61918 TATTTTTT
1 TATTTTTT
61926 TGCAGTTATA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
10 7 0.21
11 15 0.45
12 11 0.33
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (11 bp):
TATTTTTTAAT
Found at i:64002 original size:30 final size:28
Alignment explanation
Indices: 63897--64002 Score: 86
Period size: 30 Copynumber: 3.6 Consensus size: 28
63887 AAGTTCTCAA
* *
63897 GAAAATACTTCAACTGAGGAGAAGAGGAT
1 GAAAATACTTCAATTGAGGAGAAG-GGAG
* * * *
63926 GAAAATACTTGAATCGACGAGGAGGGGAG
1 GAAAATACTTCAATTGAGGA-GAAGGGAG
* *
63955 AGAAAACAATTCAATTGAGGAGAAGGGAAG
1 -GAAAATACTTCAATTGAGGAGAAGGG-AG
*
63985 GAAGAATACTTGAATTGA
1 GAA-AATACTTCAATTGA
64003 CAAGAAAAAT
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
29 27 0.47
30 31 0.53
ACGTcount: A:0.44, C:0.08, G:0.30, T:0.17
Consensus pattern (28 bp):
GAAAATACTTCAATTGAGGAGAAGGGAG
Found at i:66840 original size:138 final size:137
Alignment explanation
Indices: 66609--67291 Score: 874
Period size: 138 Copynumber: 5.0 Consensus size: 137
66599 AATTCTAGCT
* * *
66609 CTTTAAGAGATGTCAAATGATTGAGGCATGGTAGTTCAACCAAATTTTCACACCCATTGAAGCAA
1 CTTTAAGAGATGTCAAATGATTGAGGCAAGGTAGTTCAACCAAATTTTCACACCCATAGCAGCAA
** * * * * * * ** *
66674 AGGCTTTGAAGGTTGATAACTCCGGATAGATTAGGAATCTTTCTTAAATTATTGCAACAAGACAG
66 AGGCTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAAAG
66739 GTCAAGG
131 GTCAAGG
* * * *
66746 CGTTTAAGAGAT-TCCAAATGATTGAGGCAAGGTAGTTCAACCAGATTTTCACACCCACAGAAGA
1 C-TTTAAGAGATGT-CAAATGATTGAGGCAAGGTAGTTCAACCAAATTTTCACACCCATAGCAGC
*
66810 AAATGCTTTGAAGGTTGATGGCTCCTGATAGATTA--GATCTTCCTTAGACTCTTGCAATGAGAA
64 AAAGGCTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAA
*
66873 AGTTCAAGG
129 AGGTCAAGG
* ** * *
66882 CTTTCAAGAAATACCAAATGATTGAGGCAAGGTA-TTCAATCAAATTTTCACACCTATAGCAGCA
1 CTTT-AAGAGATGTCAAATGATTGAGGCAAGGTAGTTCAACCAAATTTTCACACCCATAGCAGCA
* * *
66946 AAGGCTTTGAAGGTTGATGACTCCTGAAAGATTAGGGATCTTTCTTAGACTCTTGCAATGAGAAA
65 AAGGCTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAAA
67011 GGTCAAGG
130 GGTCAAGG
* * * * *
67019 CTTTGAAGGGATGTCAACTGATTGAGGCAAGGTAGTTCAATCAAATTTTCACACCTATGGCAGCA
1 CTTT-AAGAGATGTCAAATGATTGAGGCAAGGTAGTTCAACCAAATTTTCACACCCATAGCAGCA
*
67084 AAGGCTTTGAAGGTTGACGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAAA
65 AAGGCTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAAA
*
67149 GGTCAAGA
130 GGTCAAGG
* ** * * *
67157 CGTTGAAGAGATGTCAGTTGATTGAGAG-AAGATAGTTCAACCAAATTTTCACATCCATTGCAGC
1 C-TTTAAGAGATGTCAAATGATTGAG-GCAAGGTAGTTCAACCAAATTTTCACACCCATAGCAGC
* * *
67221 AAAGGGTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGTCTC-TGCAATCAGAA
64 AAAGGCTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAA
67285 AGGTCAA
129 AGGTCAA
67292 TTGACCTTAA
Statistics
Matches: 481, Mismatches: 56, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
135 58 0.12
136 55 0.11
137 82 0.17
138 283 0.59
139 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (137 bp):
CTTTAAGAGATGTCAAATGATTGAGGCAAGGTAGTTCAACCAAATTTTCACACCCATAGCAGCAA
AGGCTTTGAAGGTTGATGGCTCCTGATAGATTAGGGATCTTCCTTAGACTCTTGCAATGAGAAAG
GTCAAGG
Found at i:70401 original size:28 final size:30
Alignment explanation
Indices: 70335--70403 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
70325 ATTTAACGTC
70335 AGTGATATAATTGAAACAAAATAAAAATTT
1 AGTGATATAATTGAAACAAAATAAAAATTT
* * * * *
70365 AGCGCTATAATTGATA-AAATTAAAAGTTT
1 AGTGATATAATTGAAACAAAATAAAAATTT
70394 -GTGATATAAT
1 AGTGATATAAT
70404 GACACAATGC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
28 8 0.25
29 11 0.34
30 13 0.41
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.33
Consensus pattern (30 bp):
AGTGATATAATTGAAACAAAATAAAAATTT
Done.