Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005192.1 Hibiscus syriacus cultivar Beakdansim tig00011731_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: 95424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1386 original size:10 final size:10
Alignment explanation
Indices: 1373--1403 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1363 CTTTATAAAG
*
1373 GAAAATAATT
1 GAAAAGAATT
1383 GAAAAGAATT
1 GAAAAGAATT
1393 GAAAAGAATT
1 GAAAAGAATT
1403 G
1 G
1404 TAAATTAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (10 bp):
GAAAAGAATT
Found at i:5242 original size:36 final size:36
Alignment explanation
Indices: 5141--5243 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
5131 ATTTATTTAT
* * * *
5141 TATCAGCTTTGATACATTCGTGTATTAATATTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
5177 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
1 TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
5213 TATCAACTTTGGTACATTCGTGTATCAATGT
1 TATCAACTTTGGTACATTCGTGTATCAATGT
5244 CTAGCACCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 63 1.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.43
Consensus pattern (36 bp):
TATCAACTTTGGTACATTCGTGTATCAATGTTATCA
Found at i:11210 original size:24 final size:24
Alignment explanation
Indices: 11178--11225 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
11168 AAACAACATC
*
11178 CGCAACATAAAACATTATTACTTT
1 CGCAACATAAAACATAATTACTTT
11202 CGCAACATAAAACATAATTACTTT
1 CGCAACATAAAACATAATTACTTT
11226 TAAAAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.04, T:0.31
Consensus pattern (24 bp):
CGCAACATAAAACATAATTACTTT
Found at i:13600 original size:7 final size:7
Alignment explanation
Indices: 13588--13614 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13578 ACATGATTCA
13588 ATGCACC
1 ATGCACC
13595 ATGCACC
1 ATGCACC
13602 ATGCACC
1 ATGCACC
13609 ATGCAC
1 ATGCAC
13615 ACATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGCACC
Found at i:22562 original size:2 final size:2
Alignment explanation
Indices: 22555--22594 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
22545 TAGATATAAA
22555 AT AT AT AT CAT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22595 TAAATTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22572 original size:14 final size:13
Alignment explanation
Indices: 22548--22593 Score: 65
Period size: 14 Copynumber: 3.4 Consensus size: 13
22538 ATTAAAATAG
*
22548 ATATAAAATATAT
1 ATATAATATATAT
22561 ATCATAATATATAT
1 AT-ATAATATATAT
22575 ATATATATATATAT
1 ATATA-ATATATAT
22589 ATATA
1 ATATA
22594 TTAAATTCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 5 0.17
14 25 0.83
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:28773 original size:2 final size:2
Alignment explanation
Indices: 28762--28797 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
28752 GCATAATTAG
28762 TA TA -A 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
28798 TTCGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31530 original size:39 final size:38
Alignment explanation
Indices: 31472--31545 Score: 130
Period size: 39 Copynumber: 1.9 Consensus size: 38
31462 AGTTACTCAT
*
31472 CAATTCAGTATGAATGATACCTGTGATAAGAGGAGATA
1 CAATTCAGTATGAAAGATACCTGTGATAAGAGGAGATA
31510 CAATTCATGTATGAAAGATACCTGTGATAAGAGGAG
1 CAATTCA-GTATGAAAGATACCTGTGATAAGAGGAG
31546 TATCTGGATC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
38 7 0.21
39 27 0.79
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (38 bp):
CAATTCAGTATGAAAGATACCTGTGATAAGAGGAGATA
Found at i:41015 original size:18 final size:18
Alignment explanation
Indices: 40994--41032 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
40984 AAATCTCTAC
40994 TTTTAAATAAAAATAATA
1 TTTTAAATAAAAATAATA
* * *
41012 TTTTTAATAAATATATTA
1 TTTTAAATAAAAATAATA
41030 TTT
1 TTT
41033 CGGGTTGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAATAAAAATAATA
Found at i:46905 original size:35 final size:36
Alignment explanation
Indices: 46866--46940 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
46856 AAACGGGAAC
*
46866 GGGAAAAATCGTTTATGTTAAACGGGGA-CGGGATG
1 GGGAAAAACCGTTTATGTTAAACGGGGATCGGGATG
*
46901 GGGAAAAACCGTTTATGTTAAACGGGGATGGGGATG
1 GGGAAAAACCGTTTATGTTAAACGGGGATCGGGATG
46937 GGGA
1 GGGA
46941 TGAGTTTAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 27 0.73
36 10 0.27
ACGTcount: A:0.31, C:0.08, G:0.40, T:0.21
Consensus pattern (36 bp):
GGGAAAAACCGTTTATGTTAAACGGGGATCGGGATG
Found at i:47017 original size:2 final size:2
Alignment explanation
Indices: 47010--47036 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
47000 AAATAATTAT
47010 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 T
47037 TAATAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:47790 original size:15 final size:15
Alignment explanation
Indices: 47770--47799 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
47760 TGTGAACCAA
47770 ACGCACCCTGAGGGG
1 ACGCACCCTGAGGGG
47785 ACGCACCCTGAGGGG
1 ACGCACCCTGAGGGG
47800 GTGTTTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.33, G:0.40, T:0.07
Consensus pattern (15 bp):
ACGCACCCTGAGGGG
Found at i:53841 original size:17 final size:17
Alignment explanation
Indices: 53814--53852 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
53804 AATTTACAAT
53814 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
53830 TAATTATAAATAATATC
1 TAATTATAAATAATATC
53847 TAATTA
1 TAATTA
53853 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:54065 original size:21 final size:20
Alignment explanation
Indices: 54041--54095 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
54031 TAACCGTTCC
54041 CCGACAGAATTAATTCGGTGG
1 CCGAC-GAATTAATTCGGTGG
54062 CCGACCGAATTAATTCGGTGG
1 CCGA-CGAATTAATTCGGTGG
54083 CCGATCGAATTAA
1 CCGA-CGAATTAA
54096 CCGAACTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 31 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (20 bp):
CCGACGAATTAATTCGGTGG
Found at i:54507 original size:29 final size:29
Alignment explanation
Indices: 54465--54523 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
54455 ATTTTCACCT
*
54465 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
54494 AACTAAATTGATGTAAGCAATAACATCAA
1 AACTAAATTGATGTAAGCAATAACATCAA
54523 A
1 A
54524 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATAACATCAA
Found at i:59190 original size:24 final size:24
Alignment explanation
Indices: 59157--59238 Score: 94
Period size: 24 Copynumber: 3.2 Consensus size: 24
59147 TCACCTAATT
59157 AAATT-GATGTAAGCAATGACATC
1 AAATTAGATGTAAGCAATGACATC
59180 AAATTAGATGTAAGCAATGACATC
1 AAATTAGATGTAAGCAATGACATC
* *
59204 AAAACTAAATTGATGTAAGTAATGACATC
1 -AAA-T---TAGATGTAAGCAATGACATC
59233 AAATTA
1 AAATTA
59239 ATTTAGGTGT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
23 5 0.10
24 19 0.38
25 3 0.06
26 1 0.02
27 1 0.02
28 3 0.06
29 18 0.36
ACGTcount: A:0.48, C:0.11, G:0.15, T:0.27
Consensus pattern (24 bp):
AAATTAGATGTAAGCAATGACATC
Found at i:59227 original size:29 final size:28
Alignment explanation
Indices: 59156--59235 Score: 105
Period size: 29 Copynumber: 3.0 Consensus size: 28
59146 TTCACCTAAT
59156 TAAATTGATGTAAGCAATGACATC-AAA
1 TAAATTGATGTAAGCAATGACATCAAAA
*
59183 T---TAGATGTAAGCAATGACATCAAAA
1 TAAATTGATGTAAGCAATGACATCAAAA
*
59208 CTAAATTGATGTAAGTAATGACATCAAA
1 -TAAATTGATGTAAGCAATGACATCAAA
59236 TTAATTTAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
24 19 0.42
25 3 0.07
26 1 0.02
27 1 0.02
29 21 0.47
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.26
Consensus pattern (28 bp):
TAAATTGATGTAAGCAATGACATCAAAA
Found at i:61976 original size:21 final size:21
Alignment explanation
Indices: 61952--61996 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
61942 TTTAAAAATA
*
61952 AAAACT-AAAAGTTTAGGTACT
1 AAAACTGAAAA-TTTAGATACT
*
61973 AAAACTGATAATTTAGATACT
1 AAAACTGAAAATTTAGATACT
61994 AAA
1 AAA
61997 CTCGTAACGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.51, C:0.09, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAACTGAAAATTTAGATACT
Found at i:66918 original size:38 final size:38
Alignment explanation
Indices: 66867--66942 Score: 127
Period size: 38 Copynumber: 2.0 Consensus size: 38
66857 CATTGGAAAG
*
66867 AAAGAAGCATAGAATGACATCCTA-TATCAGGTTCGAAT
1 AAAGAAGCATAGAATGACAT-CGAGTATCAGGTTCGAAT
66905 AAAGAAGCATAGAATGACATCGAGTATCAGGTTCGAAT
1 AAAGAAGCATAGAATGACATCGAGTATCAGGTTCGAAT
66943 GATCTAGGAC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
37 2 0.06
38 34 0.94
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.22
Consensus pattern (38 bp):
AAAGAAGCATAGAATGACATCGAGTATCAGGTTCGAAT
Found at i:71810 original size:37 final size:37
Alignment explanation
Indices: 71740--71811 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 37
71730 GAAAAATATT
* *
71740 TATATATTTTCTTTAAAAAATTTAAATTCATAAAATG
1 TATATATTTTCTTTAAAAAATTGAAAATCATAAAATG
* *
71777 TATATAATTTTTTTTACAAAATTGAAAAT-ATAAAA
1 TATAT-ATTTTCTTTAAAAAATTGAAAATCATAAAA
71812 AGGTTTAATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 11 0.37
38 19 0.63
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATATTTTCTTTAAAAAATTGAAAATCATAAAATG
Found at i:72289 original size:21 final size:19
Alignment explanation
Indices: 72251--72289 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
72241 CTTCTTTTCA
72251 TCTTTATTTTTACTTTAAG
1 TCTTTATTTTTACTTTAAG
*
72270 TCTTTACTTATTTTCTTTAA
1 TCTTTA-TT-TTTACTTTAA
72290 AAAATGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 2 0.12
21 9 0.53
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.64
Consensus pattern (19 bp):
TCTTTATTTTTACTTTAAG
Found at i:74130 original size:17 final size:18
Alignment explanation
Indices: 74098--74132 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
74088 GTGAAAAAGA
*
74098 TTATTACTATGTAATAAT
1 TTATTACTAAGTAATAAT
74116 TTATTAC-AAGTAATAAT
1 TTATTACTAAGTAATAAT
74133 ATTTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.46
Consensus pattern (18 bp):
TTATTACTAAGTAATAAT
Found at i:74293 original size:3 final size:3
Alignment explanation
Indices: 74285--74319 Score: 61
Period size: 3 Copynumber: 11.3 Consensus size: 3
74275 ATTCTAAATT
74285 TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T
74320 GAGTTCAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:74374 original size:24 final size:24
Alignment explanation
Indices: 74347--74400 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
74337 ATGTTACTAA
* *
74347 ATTTTAGTAGTTAAAATTATTTAT-
1 ATTTTAATA-TTAAAATTATTAATC
*
74371 ATTTTAATATTTAAATTATTAATC
1 ATTTTAATATTAAAATTATTAATC
74395 ATTTTA
1 ATTTTA
74401 TAATTTTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTTAATATTAAAATTATTAATC
Found at i:74627 original size:20 final size:21
Alignment explanation
Indices: 74591--74639 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
74581 AATCATTTAA
*
74591 AAATATA-AAATTGATATATT
1 AAATATATTAATTGATATATT
*
74611 AATTATATTAATT-ATATATT
1 AAATATATTAATTGATATATT
74631 AAATATATT
1 AAATATATT
74640 TTTTCTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATATTAATTGATATATT
Found at i:76767 original size:83 final size:84
Alignment explanation
Indices: 76628--76791 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 84
76618 GGCAAGCAAA
*
76628 TTCAATCGGTGGCCCTCAATCTGTTTCTCCGGCACTTATGCGATCAAATTCTGCTA-TTTGGGAT
1 TTCAATCGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
*
76692 CTCAGGGTGGTTCAATACC
66 CTCAAGGTGGTTCAATACC
* * *
76711 TTCAATTGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCGAGTTCTGCTATTTTGGGAT
1 TTCAATCGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
76776 CTCAAGGTGGTTCAAT
66 CTCAAGGTGGTTCAAT
76792 GCCTCCACAG
Statistics
Matches: 75, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
83 52 0.69
84 23 0.31
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (84 bp):
TTCAATCGGTGGCCCTCAATCTGGTTCTCCGGCACTTATGCGATCAAATTCTGCTATTTTGGGAT
CTCAAGGTGGTTCAATACC
Found at i:78361 original size:33 final size:33
Alignment explanation
Indices: 78324--78389 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
78314 CTATATAATC
* * *
78324 TCAAGTGGACGGTTTTGTATAGTTGGTTTTGGG
1 TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
78357 TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
1 TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
78390 ATATGATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.18, C:0.06, G:0.36, T:0.39
Consensus pattern (33 bp):
TCAAGTGGACGGTTTTGGAAAGTTGATTTTGGG
Found at i:85611 original size:38 final size:38
Alignment explanation
Indices: 85563--85671 Score: 164
Period size: 38 Copynumber: 2.9 Consensus size: 38
85553 CTCCAATGAT
*
85563 TAAAATGAGTGCTATTTTCTCTTGAGGTTTCGGATGGC
1 TAAAAGGAGTGCTATTTTCTCTTGAGGTTTCGGATGGC
* * *
85601 TAAAAGGAGTGTTATTCTCTCTTGAGGTTTCGGATGGT
1 TAAAAGGAGTGCTATTTTCTCTTGAGGTTTCGGATGGC
* *
85639 TAAATGGAGTGCTATTTTCTCTTGAAGTTTCGG
1 TAAAAGGAGTGCTATTTTCTCTTGAGGTTTCGG
85672 GTGAGAACAG
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 63 1.00
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (38 bp):
TAAAAGGAGTGCTATTTTCTCTTGAGGTTTCGGATGGC
Found at i:86715 original size:61 final size:62
Alignment explanation
Indices: 86607--86816 Score: 215
Period size: 61 Copynumber: 3.5 Consensus size: 62
86597 ATATTTCCTC
* *
86607 TGATCAATT-TTTTGTCCATCTATATTTATTAT-GAAAGTCGTTAAATTTTTAGTGAATCTA
1 TGATCAATTCTTTTGTCGATCTCTATTTATTATAGAAAGTCGTTAAATTTTTAGTGAATCTA
* * *
86667 TGATCTATTCTTTTATCGATCTCTATTTATTATAG-AAG-CTGTTGAATTTTTAGTGAATCTA
1 TGATCAATTCTTTTGTCGATCTCTATTTATTATAGAAAGTC-GTTAAATTTTTAGTGAATCTA
* * * * *
86728 TGATGAATTCTTTTGTCGATTTCTATTTATTATA-AAA-TGGTTGAA---TTATTGAATCTA
1 TGATCAATTCTTTTGTCGATCTCTATTTATTATAGAAAGTCGTTAAATTTTTAGTGAATCTA
* * * *
86785 TGAT-AATTATTTTGTCGTTTTCGATTTATTAT
1 TGATCAATTCTTTTGTCGATCTCTATTTATTAT
86817 TATACGGTTG
Statistics
Matches: 131, Mismatches: 14, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
56 25 0.19
57 15 0.11
60 15 0.11
61 75 0.57
62 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.13, T:0.50
Consensus pattern (62 bp):
TGATCAATTCTTTTGTCGATCTCTATTTATTATAGAAAGTCGTTAAATTTTTAGTGAATCTA
Found at i:86826 original size:56 final size:60
Alignment explanation
Indices: 86657--86872 Score: 197
Period size: 61 Copynumber: 3.6 Consensus size: 60
86647 TTAAATTTTT
* * * * * * * * * *
86657 AGTGAATCTATGATCTATTCTTTTATCGATCTCTATTTATTATAGAAGCTGTTGAATTTTT
1 AGTGAATCTATGATCAATTCTTTTGTCGTTTTCGATTTATTATA-AAACGGTTGTATATTC
* * * *
86718 AGTGAATCTATGATGAATTCTTTTGTCGATTTCTATTTATTATAAAATGGTTG-A-ATT-
1 AGTGAATCTATGATCAATTCTTTTGTCGTTTTCGATTTATTATAAAACGGTTGTATATTC
* * * * *
86775 ATTGAATCTATGAT-AATTATTTTGTCGTTTTCGATTTATTATTATACGGTTGTATTTTC
1 AGTGAATCTATGATCAATTCTTTTGTCGTTTTCGATTTATTATAAAACGGTTGTATATTC
* * *
86834 AGTGAATATATGATCATTTCTTTTGTCGTTTTTGATTTA
1 AGTGAATCTATGATCAATTCTTTTGTCGTTTTCGATTTA
86873 ATATCAATCA
Statistics
Matches: 130, Mismatches: 21, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
56 32 0.25
57 14 0.11
58 4 0.03
59 13 0.10
60 27 0.21
61 40 0.31
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (60 bp):
AGTGAATCTATGATCAATTCTTTTGTCGTTTTCGATTTATTATAAAACGGTTGTATATTC
Found at i:89529 original size:2 final size:2
Alignment explanation
Indices: 89522--89565 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
89512 TGTGAAAAGA
89522 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
89564 AT
1 AT
89566 CTTATATGGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:91411 original size:153 final size:147
Alignment explanation
Indices: 91123--91412 Score: 386
Period size: 153 Copynumber: 1.9 Consensus size: 147
91113 TCACTGAAAC
*
91123 AGTAAAACTTGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
1 AGTAAAACTGGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
* ** * *
91188 TCATCTGAACTTTGCAAGTACAATAACCCTTTTCCCATGGGATTTTGTTCTTTTAAAGGTGTATT
66 TCATCTGAACTTTGCAAGTACAATAACCCTTTTCCCAAGGGATTTTGTTCTCGTAAAGGTATAGT
*
91253 TAAAACTAGAAAAAAAA
131 GAAAACTAGAAAAAAAA
* *
91270 AGTAAAACTGGTATGTCAGATTTGATATGGGTGCTTT-TTTTTGCTATCTATAAATACAATGCTA
1 AGTAAAACTGGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
* * *
91334 TCATCTGGCATTTGAACTTTGCAAGTATAATAACTC-TTTCCTCAAGGGATTTTGTTGTCGTAAA
66 TCA--T--C---TGAACTTTGCAAGTACAATAACCCTTTTCC-CAAGGGATTTTGTTCTCGTAAA
91398 GGTATAGTGAAAACT
123 GGTATAGTGAAAACT
91413 TGCTTGTATC
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
146 29 0.24
147 35 0.28
148 1 0.01
150 1 0.01
152 5 0.04
153 52 0.42
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (147 bp):
AGTAAAACTGGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
TCATCTGAACTTTGCAAGTACAATAACCCTTTTCCCAAGGGATTTTGTTCTCGTAAAGGTATAGT
GAAAACTAGAAAAAAAA
Done.