Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000120.1 Hibiscus syriacus cultivar Beakdansim tig00000217_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: 78955
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:877 original size:109 final size:109
Alignment explanation
Indices: 681--1051 Score: 383
Period size: 109 Copynumber: 3.4 Consensus size: 109
671 CCATATCCAT
* * * * **
681 GACAATAATAATTTCAAATGGCATAGAACTTTAACTATTCACATTCTTTTTTCCAGTAAAATGTC
1 GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATT-TTTTTT-CAGTGAAACATC
* * * * **
746 ACATCAGATTAAAACTTTAATTATAGTGAAAGGGAAATCATATTGAG
64 ACCTCAAATCAGAACTTTAATTATAGTGAAAGAAAAATCATATT-AG
* ***
793 GATAATAATAATTT-AAATGACAGAGAATTTTAACTATTCGTGTTTTTTTTCTAGTGAAACATCA
1 GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATTTTTTTTC-AGTGAAACATCA
* *
857 CCTCAAATCAGAAC-TTAATTATAGT-AGAAGAAAAATCATACTCAT
65 CCTCAAATCAGAACTTTAATTATAGTGA-AAGAAAAATCATA-TTAG
* * ** **
902 AACAATAATAATTTCAAAT-AAAGAGAATTTTAACTATTCACATCCTTTTTCAACGAAACATCAC
1 GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATTTTTTTTCAGTGAAACATCAC
* *
966 CTCAAATCAGAACTTTCATTATAGTGAAAGAAAAATCAGATCTAG
66 CTCAAATCAGAACTTTAATTATAGTGAAAGAAAAATCATAT-TAG
* *
1011 GACAATAATAATTTCAAATGAC-GTAAAATCTTAACTATTCA
1 GACAATAATAATTTCAAATGACAG-AGAATTTTAACTATTCA
1052 TGTCCTTGTT
Statistics
Matches: 214, Mismatches: 36, Indels: 20
0.79 0.13 0.07
Matches are distributed among these distances:
108 26 0.12
109 104 0.49
110 47 0.22
111 24 0.11
112 13 0.06
ACGTcount: A:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (109 bp):
GACAATAATAATTTCAAATGACAGAGAATTTTAACTATTCACATTTTTTTTCAGTGAAACATCAC
CTCAAATCAGAACTTTAATTATAGTGAAAGAAAAATCATATTAG
Found at i:1345 original size:14 final size:13
Alignment explanation
Indices: 1298--1345 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1288 TATGTCATGT
*
1298 TTTTTTAATTTTA
1 TTTTTTATTTTTA
*
1311 TTTATTTATTATTA
1 TTT-TTTATTTTTA
1325 TTATTTTATTTTTAA
1 TT-TTTTATTTTT-A
1340 TTTTTT
1 TTTTTT
1346 GAAATGAGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 3 0.10
14 22 0.76
15 4 0.14
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTATTTTTA
Found at i:5231 original size:19 final size:19
Alignment explanation
Indices: 5206--5257 Score: 79
Period size: 19 Copynumber: 2.7 Consensus size: 19
5196 CACACAATAT
5206 CGGTACTATT-ATACAGTA
1 CGGTACTATTCATACAGTA
5224 CTGGTACTATTCATACAGTA
1 C-GGTACTATTCATACAGTA
*
5244 CAGTACTATTCATA
1 CGGTACTATTCATA
5258 AAAACATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
18 1 0.03
19 21 0.68
20 9 0.29
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (19 bp):
CGGTACTATTCATACAGTA
Found at i:5508 original size:20 final size:20
Alignment explanation
Indices: 5465--5508 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
5455 ATATTTAATG
5465 AAAAGATATCAATTGTTAAC
1 AAAAGATATCAATTGTTAAC
*
5485 AAAAGGATATGAATTGTTAA-
1 AAAA-GATATCAATTGTTAAC
5505 AAAA
1 AAAA
5509 TACAAATTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.27
Consensus pattern (20 bp):
AAAAGATATCAATTGTTAAC
Found at i:8934 original size:30 final size:30
Alignment explanation
Indices: 8900--8966 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
8890 GGTATTAAAT
* *
8900 GAACACGTTGAACAATAAATAAACGAAAAC
1 GAACACGTTCAAAAATAAATAAACGAAAAC
* * *
8930 GAACACCTTCAAAAATAAATAAACTAACAC
1 GAACACGTTCAAAAATAAATAAACGAAAAC
8960 GAACACG
1 GAACACG
8967 AAATAAACAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.55, C:0.21, G:0.10, T:0.13
Consensus pattern (30 bp):
GAACACGTTCAAAAATAAATAAACGAAAAC
Found at i:12743 original size:25 final size:25
Alignment explanation
Indices: 12726--12776 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
12716 TTATCTTGAT
*
12726 TCGAGTTTTAATTTTTTATTTCGAG
1 TCGAGCTTTAATTTTTTATTTCGAG
12751 TCGAGCTTTAATTTTTTATTTCGAG
1 TCGAGCTTTAATTTTTTATTTCGAG
12776 T
1 T
12777 TTGAATCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.55
Consensus pattern (25 bp):
TCGAGCTTTAATTTTTTATTTCGAG
Found at i:16335 original size:23 final size:22
Alignment explanation
Indices: 16288--16336 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
16278 TTTCATATGT
* *
16288 AATATATATTATTAAAAATAAA
1 AATATATATTATAAAAAAGAAA
16310 AATATA-ATTATAATAAAAGAAGA
1 AATATATATTATAA-AAAAGAA-A
16333 AATA
1 AATA
16337 GTGGGAGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (22 bp):
AATATATATTATAAAAAAGAAA
Found at i:17071 original size:31 final size:31
Alignment explanation
Indices: 17002--17086 Score: 136
Period size: 30 Copynumber: 2.8 Consensus size: 31
16992 AATGATTTTG
* * *
17002 AAAAATGAAAGTTTAGGTACTAAAACAGATC
1 AAAACTGATAGTTTAGGTACTAAAACAAATC
17033 -AAACTGATAGTTTAGGTACTAAAACAAATC
1 AAAACTGATAGTTTAGGTACTAAAACAAATC
17063 AAAACTGATAGTTTAGGTACTAAA
1 AAAACTGATAGTTTAGGTACTAAA
17087 TGCATATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
30 27 0.54
31 23 0.46
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.26
Consensus pattern (31 bp):
AAAACTGATAGTTTAGGTACTAAAACAAATC
Found at i:18331 original size:130 final size:130
Alignment explanation
Indices: 18190--18436 Score: 413
Period size: 130 Copynumber: 1.9 Consensus size: 130
18180 ATTTATATAA
*
18190 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGT
1 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT
* * *
18255 TAGCACATGATCATGACACATGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTT
66 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTT
18320 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT
1 TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT
* ** * *
18385 TAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCTCCTAATTA
66 TAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
18437 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (130 bp):
TCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGT
TAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTT
Found at i:18467 original size:130 final size:129
Alignment explanation
Indices: 18203--18467 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
18193 ATTTGGTCCT
* *
18203 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * * **** *
18268 TGACACATGTCATTGGTGACACGTGTTACCACCTAATTATTTATATATGCTTTCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTTACAAAGAAGT-CA
18333 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
* ** * *
18398 TGATATGTGTTATTGGTGACACATGTCACCTCCTAATTAGAAGAAAATTAAG-TTACAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTTACAAAGAAGT
18462 -A
128 CA
18463 AAATT
1 AAATT
18468 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 10 0.09
133 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAATCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTTACAAAGAAGTCA
Found at i:18794 original size:28 final size:27
Alignment explanation
Indices: 18763--18825 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
18753 AGTTGATACA
*
18763 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
18791 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
18819 ATATTTT
1 ATATTTT
18826 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:19085 original size:21 final size:21
Alignment explanation
Indices: 19061--19103 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
19051 TATTACCTTA
19061 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
19082 AATTGAAGTATTTTAGAATTT
1 AATTGAAGTATTTTAGAATTT
19103 A
1 A
19104 GGGTTTAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
AATTGAAGTATTTTAGAATTT
Found at i:19121 original size:35 final size:35
Alignment explanation
Indices: 19072--19157 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
19062 ATTGAAGTAT
** * *
19072 TTTAGAATTTAATTGAAGTATTTTAGAATTTAGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
* * *
19107 TTTAGAATAAAATTGAATTACTTTGGAAATTGGGG
1 TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
*
19142 TTTAGAATGAAATTGA
1 TTTAGAATAAAATTGA
19158 TGACTGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.21, T:0.41
Consensus pattern (35 bp):
TTTAGAATAAAATTGAAGTACTTTAGAAATTAGGG
Found at i:19340 original size:29 final size:29
Alignment explanation
Indices: 19288--19345 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
19278 GCAAACGGAA
* *
19288 TAAATGTTGGGGGACTGTATTGCAAGTTT
1 TAAATGTTGGGGGACTGAAATGCAAGTTT
19317 TAAATGTTGGGGGACCT-AAATGCAAGTTT
1 TAAATGTTGGGGGA-CTGAAATGCAAGTTT
19346 CAGAAATGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.28, C:0.09, G:0.29, T:0.34
Consensus pattern (29 bp):
TAAATGTTGGGGGACTGAAATGCAAGTTT
Found at i:23745 original size:148 final size:148
Alignment explanation
Indices: 23477--23774 Score: 587
Period size: 148 Copynumber: 2.0 Consensus size: 148
23467 TTCAAGCTGC
23477 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC
1 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC
*
23542 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGTCATGTTCTAAGAAAGATAC
66 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC
23607 ACAAGCGAAGACATTTGT
131 ACAAGCGAAGACATTTGT
23625 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC
1 AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC
23690 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC
66 TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC
23755 ACAAGCGAAGACATTTGT
131 ACAAGCGAAGACATTTGT
23773 AA
1 AA
23775 AAAATCTGCT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 149 1.00
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (148 bp):
AACGAAGACTTGGGTACGACATGATATGATTAAAGGTCAAGATTAGATGGCCAAATGTCCTCTGC
TCATTTAGTAGTAATTAAACCAAAGACATTAAGTTAAAGAAATTGCCATGTTCTAAGAAAGATAC
ACAAGCGAAGACATTTGT
Found at i:30957 original size:25 final size:25
Alignment explanation
Indices: 30929--31000 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
30919 CCGGGTATCA
*
30929 GGTAATCGGGTACCCGGATTTTGCG
1 GGTAATCGGATACCCGGATTTTGCG
30954 GGT-ATCCGGATACCCGGATTTTGCG
1 GGTAAT-CGGATACCCGGATTTTGCG
*
30979 GGTATTCGGATACCCGGATTTT
1 GGTAATCGGATACCCGGATTTT
31001 TTTCTTCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.05
25 40 0.93
26 1 0.02
ACGTcount: A:0.17, C:0.21, G:0.32, T:0.31
Consensus pattern (25 bp):
GGTAATCGGATACCCGGATTTTGCG
Found at i:32261 original size:64 final size:64
Alignment explanation
Indices: 32192--32412 Score: 243
Period size: 64 Copynumber: 3.5 Consensus size: 64
32182 TTGAAGGTGT
* **
32192 ATCGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCGAATGCAATTCATG
1 ATCGATGCATAGGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCAATTCATG
32255 C
64 C
* * **
32256 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
** * * ** *
32320 ATCGATGCATAAGG-AGTGCATCGATGCATCCCAGCAATAATAATACATCGAATACCTTTTATGC
1 ATCGATGCAT-AGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
*
32384 ACCGATGCATCA-GTAGTGCATCGATGCAT
1 ATCGATGCAT-AGGTAGTGCATCGATGCAT
32413 ACCTTCATTA
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
63 1 0.01
64 127 0.95
65 6 0.04
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATTCATGC
Found at i:32738 original size:12 final size:12
Alignment explanation
Indices: 32720--32755 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
32710 TATATATGTT
32720 CATGTGATATGA
1 CATGTGATATGA
*
32732 TATGTGATATGA
1 CATGTGATATGA
32744 CATGTGATATGA
1 CATGTGATATGA
32756 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:32777 original size:23 final size:26
Alignment explanation
Indices: 32720--32788 Score: 85
Period size: 24 Copynumber: 2.8 Consensus size: 26
32710 TATATATGTT
**
32720 CATGTGATAT--GATATGTGATATGA
1 CATGTGATATGAGATACATGATATGA
32744 CATGTGATATGAGA-ACATGATATGA
1 CATGTGATATGAGATACATGATATGA
32769 -A-GTGATATGAGATACATGAT
1 CATGTGATATGAGATACATGAT
32789 CACAAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
23 11 0.28
24 18 0.45
25 9 0.22
26 2 0.05
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.32
Consensus pattern (26 bp):
CATGTGATATGAGATACATGATATGA
Found at i:35229 original size:17 final size:17
Alignment explanation
Indices: 35204--35244 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
35194 TTTATGATTT
*
35204 TTTTATTAAATTTAAGGA
1 TTTT-TTAAATTTAAAGA
35222 TTTTTTAAATTTAAAGA
1 TTTTTTAAATTTAAAGA
35239 TTTTTT
1 TTTTTT
35245 TTGGGTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (17 bp):
TTTTTTAAATTTAAAGA
Found at i:35794 original size:9 final size:9
Alignment explanation
Indices: 35780--35805 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35770 GAAATCGGTT
35780 AATTAACCG
1 AATTAACCG
35789 AATTAACCG
1 AATTAACCG
35798 AATTAACC
1 AATTAACC
35806 TTTAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (9 bp):
AATTAACCG
Found at i:36256 original size:21 final size:20
Alignment explanation
Indices: 36222--36266 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
36212 ACCTTATAAA
**
36222 TATATTTAAATTTATTTTTT
1 TATATTTAAATTTATAATTT
36242 TATATTTATAATTTATAATTT
1 TATATTTA-AATTTATAATTT
36263 TATA
1 TATA
36267 ATTTCTTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TATATTTAAATTTATAATTT
Found at i:36277 original size:24 final size:24
Alignment explanation
Indices: 36250--36303 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
36240 TTTATATTTA
36250 TAATTTATAATTTTATAATTTCTT
1 TAATTTATAATTTTATAATTTCTT
** * *
36274 TAATTGGTTATTTTATAATTTTTT
1 TAATTTATAATTTTATAATTTCTT
36298 TAATTT
1 TAATTT
36304 TACTTAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
TAATTTATAATTTTATAATTTCTT
Found at i:55535 original size:14 final size:13
Alignment explanation
Indices: 55510--55542 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
55500 CAAGATTGAG
55510 TATTATAGAGTAA
1 TATTATAGAGTAA
55523 TATTATGAGAGTAA
1 TATTAT-AGAGTAA
55537 T-TTATA
1 TATTATA
55543 AGGTGGGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 10 0.53
14 8 0.42
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (13 bp):
TATTATAGAGTAA
Found at i:59926 original size:36 final size:34
Alignment explanation
Indices: 59872--59940 Score: 111
Period size: 36 Copynumber: 2.0 Consensus size: 34
59862 TGACTAAAAC
59872 AATTTAAAATACCACACATCCACAATTTATTTGG
1 AATTTAAAATACCACACATCCACAATTTATTTGG
*
59906 AATTTAACAGATATCACACATCCACAATTTATTTG
1 AATTTAA-A-ATACCACACATCCACAATTTATTTG
59941 AGAAGAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 7 0.22
35 1 0.03
36 24 0.75
ACGTcount: A:0.41, C:0.20, G:0.06, T:0.33
Consensus pattern (34 bp):
AATTTAAAATACCACACATCCACAATTTATTTGG
Found at i:63702 original size:12 final size:12
Alignment explanation
Indices: 63685--63716 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
63675 CAATATCTAA
63685 GACATGAAGATT
1 GACATGAAGATT
63697 GACATGAAGATT
1 GACATGAAGATT
63709 GACATGAA
1 GACATGAA
63717 ACTTCTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.25, T:0.22
Consensus pattern (12 bp):
GACATGAAGATT
Found at i:66303 original size:26 final size:26
Alignment explanation
Indices: 66263--66312 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
66253 TGACAGGTGA
* *
66263 ATTTGAGGGGTTTTTAGT-TGCCTAAC
1 ATTTGAGGAGCTTTT-GTCTGCCTAAC
66289 ATTTGAGGAGCTTTTGTCTGCCTA
1 ATTTGAGGAGCTTTTGTCTGCCTA
66313 GTATAGATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 2 0.10
26 19 0.90
ACGTcount: A:0.18, C:0.14, G:0.26, T:0.42
Consensus pattern (26 bp):
ATTTGAGGAGCTTTTGTCTGCCTAAC
Found at i:67496 original size:20 final size:22
Alignment explanation
Indices: 67441--67504 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 22
67431 ATTTCTTAAT
*
67441 ATTAAAAATAA-ATAAATATTA
1 ATTAAAATTAATATAAATATTA
* **
67462 ATAAAAATTTCTATAAA-A-TA
1 ATTAAAATTAATATAAATATTA
67482 ATTAAAATTAATATATAAT-TTA
1 ATTAAAATTAATATA-AATATTA
67504 A
1 A
67505 GAATATGATA
Statistics
Matches: 32, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
20 14 0.44
21 10 0.31
22 8 0.25
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTAAAATTAATATAAATATTA
Found at i:67618 original size:2 final size:2
Alignment explanation
Indices: 67611--67650 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
67601 ATTTAAACAA
67611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
67651 AAATAATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:69061 original size:3 final size:3
Alignment explanation
Indices: 69055--69127 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
69045 TTTTTTTATT
* * * * *
69055 TAA TAA TAA TAA TAA TAA TCA TCA TCA TCA TAA TCA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
69103 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
69128 CCAAATGGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:69510 original size:19 final size:17
Alignment explanation
Indices: 69471--69504 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
69461 GTTGAACAAG
69471 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
69488 TTCTTCTCATTATGAAC
1 TTCTTCTCATTATGAAC
69505 ACTTCTGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.47
Consensus pattern (17 bp):
TTCTTCTCATTATGAAC
Found at i:69682 original size:124 final size:121
Alignment explanation
Indices: 69488--69868 Score: 427
Period size: 124 Copynumber: 3.2 Consensus size: 121
69478 CATTATGAAC
*
69488 TTCTTCTCATTATGAACAC-T-TCT-GAAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAC
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAATG-T-ATGCTGATCTATCTCCTTC--TGATAGAC
*
69550 TC-ATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG
62 TCGA-GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG
*
69610 TTCTTCTCATTATGAACTCTTCTCTGGAAAAGTGTATGCTGATCTATCTCCTTCTACGATAGAGT
1 TTCTTCTCATTATGAACTCTTCTCTGGAAAA-TGTATGCTGATCTATCTCCTTCT--GATAGACT
* *
69675 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCTTCAGATAAG
63 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG
* ** *
69734 TTCTTCTCATTATGAA--CTTCTTTGGAGAAAT-TGATGC--ATC-A------AGTGAT-GAATT
1 TTCTTCTCATTATGAACTCTTCTCTGGA-AAATGT-ATGCTGATCTATCTCCTTCTGATAG-ACT
* * *
69786 CGAGCCAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAG
63 CGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAG
69846 TTCTTCTCATTATGAACTCTTCT
1 TTCTTCTCATTATGAACTCTTCT
69869 GGAAATGTTG
Statistics
Matches: 232, Mismatches: 14, Indels: 34
0.83 0.05 0.12
Matches are distributed among these distances:
110 1 0.00
111 48 0.21
112 27 0.12
113 1 0.00
114 5 0.02
119 1 0.00
120 3 0.01
121 1 0.00
122 33 0.14
123 4 0.02
124 99 0.43
125 7 0.03
126 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.39
Consensus pattern (121 bp):
TTCTTCTCATTATGAACTCTTCTCTGGAAAATGTATGCTGATCTATCTCCTTCTGATAGACTCGA
GCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAG
Found at i:72222 original size:18 final size:18
Alignment explanation
Indices: 72185--72222 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
72175 TATGTGAAAG
*
72185 AATAAATTGAATTTCGAA
1 AATAAATTGAATTTCAAA
72203 AATAAATTGAATTTCAAA
1 AATAAATTGAATTTCAAA
72221 AA
1 AA
72223 GATAATCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.05, G:0.08, T:0.32
Consensus pattern (18 bp):
AATAAATTGAATTTCAAA
Done.