Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001653.1 Hibiscus syriacus cultivar Beakdansim tig00003308_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: 66976
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:4186 original size:14 final size:14
Alignment explanation
Indices: 4167--4197 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4157 CTTTCTTACA
4167 AAGATGAAAAAGAC
1 AAGATGAAAAAGAC
*
4181 AAGATGAAGAAGAC
1 AAGATGAAAAAGAC
4195 AAG
1 AAG
4198 GAGTGGTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.26, T:0.06
Consensus pattern (14 bp):
AAGATGAAAAAGAC
Found at i:4745 original size:2 final size:2
Alignment explanation
Indices: 4738--4770 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4728 CCAAAAACCT
4738 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 T
4771 GTAAGAGATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17779 original size:20 final size:21
Alignment explanation
Indices: 17749--17824 Score: 75
Period size: 20 Copynumber: 3.6 Consensus size: 21
17739 CTTCATAGTA
*
17749 GTATCGGTACTACCTTGAT-G
1 GTATCGATACTACCTTGATAG
* *
17769 GTATTGATACTACTCTTGCCTAG
1 GTATCGATACTAC-CTTG-ATAG
* *
17792 GTATCGATACTA-CATGATGG
1 GTATCGATACTACCTTGATAG
17812 GTATCGATACTAC
1 GTATCGATACTAC
17825 ATGAAGTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 25 0.56
21 7 0.16
22 1 0.02
23 12 0.27
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (21 bp):
GTATCGATACTACCTTGATAG
Found at i:17825 original size:20 final size:20
Alignment explanation
Indices: 17791--17828 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
17781 CTCTTGCCTA
17791 GGTATCGATACTACATGATG
1 GGTATCGATACTACATGATG
17811 GGTATCGATACTACATGA
1 GGTATCGATACTACATGA
17829 AGTAGTATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
GGTATCGATACTACATGATG
Found at i:17838 original size:21 final size:20
Alignment explanation
Indices: 17792--17843 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
17782 TCTTGCCTAG
* *
17792 GTATCGATACTACATGATGG
1 GTATCGATACTACATGAAGA
17812 GTATCGATACTACATGAAGTA
1 GTATCGATACTACATGAAG-A
*
17833 GTATCGGTACT
1 GTATCGATACT
17844 TCTTAGTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.64
21 10 0.36
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACATGAAGA
Found at i:18082 original size:21 final size:19
Alignment explanation
Indices: 18056--18103 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
18046 AAATGTTTAA
* *
18056 TGAAAAAGATACCGATTGT
1 TGAAAAAAATACCAATTGT
18075 TGACAAAATAATACCAATTGT
1 TGA-AAAA-AATACCAATTGT
18096 TGAAAAAA
1 TGAAAAAA
18104 TATGAAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (19 bp):
TGAAAAAAATACCAATTGT
Found at i:18104 original size:21 final size:21
Alignment explanation
Indices: 18064--18105 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18054 AATGAAAAAG
* *
18064 ATACCGATTGTTGACAAAATA
1 ATACCAATTGTTGAAAAAATA
18085 ATACCAATTGTTGAAAAAATA
1 ATACCAATTGTTGAAAAAATA
18106 TGAAAATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.12, G:0.12, T:0.29
Consensus pattern (21 bp):
ATACCAATTGTTGAAAAAATA
Found at i:19235 original size:19 final size:20
Alignment explanation
Indices: 19206--19243 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
19196 CAAAATTTCA
19206 TTTTGATTTTCAAAATCGAC
1 TTTTGATTTTCAAAATCGAC
19226 TTTT-ATTTTCAAAATCGA
1 TTTTGATTTTCAAAATCGA
19244 TTTATCTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTTGATTTTCAAAATCGAC
Found at i:20809 original size:33 final size:32
Alignment explanation
Indices: 20756--20820 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
20746 CTTTACAAAC
20756 TCCCTAGTTTTACACGGGCTAAACTAGAACCAT
1 TCCCTAGTTTTACAC-GGCTAAACTAGAACCAT
*
20789 TCCCTAGCTTTTAGCA-GGCTAAGCTAGAACCA
1 TCCCTAG-TTTTA-CACGGCTAAACTAGAACCA
20821 AAATATTTAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 22 0.76
34 5 0.17
35 2 0.07
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (32 bp):
TCCCTAGTTTTACACGGCTAAACTAGAACCAT
Found at i:21097 original size:19 final size:19
Alignment explanation
Indices: 21073--21109 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
21063 ACTTTGCACT
*
21073 ATGGTATCGATATCCTTTC
1 ATGGTATCGATACCCTTTC
21092 ATGGTATCGATACCCTTT
1 ATGGTATCGATACCCTTT
21110 TTGCATTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.41
Consensus pattern (19 bp):
ATGGTATCGATACCCTTTC
Found at i:23661 original size:2 final size:2
Alignment explanation
Indices: 23648--23751 Score: 63
Period size: 2 Copynumber: 53.5 Consensus size: 2
23638 AGTGAAAGAA
* * *
23648 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * * *
23690 AA AT A- AA AT A- AG AT A- AA AT CA- AG AG AG AG AA 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
23729 AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
23752 GGATAAATAA
Statistics
Matches: 84, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
1 4 0.05
2 79 0.94
3 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (2 bp):
AT
Found at i:23804 original size:2 final size:2
Alignment explanation
Indices: 23797--23823 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23787 GAATAAAATA
23797 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 A
23824 AAAAAAAAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25625 original size:106 final size:106
Alignment explanation
Indices: 25493--25765 Score: 417
Period size: 106 Copynumber: 2.6 Consensus size: 106
25483 GACCCCTTCT
* * * * * *
25493 GAGTTCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
*
25558 CCAGCCGTCCTTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
*
25599 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
*
25664 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
* * *
25705 GAGTCCAATATCCTTCGCTGTGAAGTAGAAATTGACTCTAAAACT-GGAAA--GTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACA
25766 GACACTCCTT
Statistics
Matches: 154, Mismatches: 13, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
103 11 0.07
105 5 0.03
106 138 0.90
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
Found at i:26019 original size:106 final size:106
Alignment explanation
Indices: 25887--26098 Score: 334
Period size: 106 Copynumber: 2.0 Consensus size: 106
25877 GACCCCTTCC
* * * *
25887 GAGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCATCCGCCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
*
25952 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAACCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTT
* * *
25993 GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGGTTTGTTGACAA
1 GAGTCCAATATCATCCGCCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
**
26058 CCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTT
66 CCAACCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTT
26099 AAATGGCGCG
Statistics
Matches: 96, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 96 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCATCCGCCGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTTGTTGACAA
CCAACCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTT
Found at i:26043 original size:394 final size:394
Alignment explanation
Indices: 25310--26097 Score: 1396
Period size: 394 Copynumber: 2.0 Consensus size: 394
25300 TGCATTGTTA
* *
25310 CGAGGCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAAACTGGAAAGTGTGTTGACAGAC
1 CGAGGCCAATATCCTTCGCTGTGAAGTAGAAATTGACTCTAAAACTGGAAAGTGTGTTGACAGAC
* * * * *
25375 ACTCCTTATTTGATTTGAATATCCTTCGTCGTGTAGTTGAAATCCACTCTAAAGATAGGTGTTGC
66 ACTCCTTATTTGAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAGATGCTGC
* * * *
25440 TTGTGTGCACGATTCTCTTCGTCGTGAAGTTGAAACCGCGGGTGACCCCTTCTGAGTTCAATATC
131 TTGTATGCACGATTCCCTTCGTCGTGAAGTTGAAACCGCGGGTGACCCCTTCCGAGTCCAATATC
* *
25505 CTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAACCAGCCGTCCTT
196 CTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAACCAACCGTCCCT
*
25570 TCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGC
261 TCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGC
*
25635 TCTGAAATTGGGAAATGGTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTT
326 TCTGAAATTGGGAAATGGTTTGTTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTT
25700 GTCT
391 GTCT
* *
25704 CGAGTCCAATATCCTTCGCTGTGAAGTAGAAATTGACTCTAAAACTGGAAAGTTTGTTGACAGAC
1 CGAGGCCAATATCCTTCGCTGTGAAGTAGAAATTGACTCTAAAACTGGAAAGTGTGTTGACAGAC
*
25769 ACTCCTTCTTTGAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAGATGCTGC
66 ACTCCTTATTTGAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAGATGCTGC
*
25834 TTGTATGCACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGGTGACCCCTTCCGAGTCCAATATC
131 TTGTATGCACGATTCCCTTCGTCGTGAAGTTGAAACCGCGGGTGACCCCTTCCGAGTCCAATATC
25899 CTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAACCAACCGTCCCT
196 CTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAACCAACCGTCCCT
*
25964 TCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGC
261 TCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGC
26029 TCTGAAATTGGGAAATGGTTTGTTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTT
326 TCTGAAATTGGGAAATGGTTTGTTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTT
26094 GTCT
391 GTCT
26098 TAAATGGCGC
Statistics
Matches: 374, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
394 374 1.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (394 bp):
CGAGGCCAATATCCTTCGCTGTGAAGTAGAAATTGACTCTAAAACTGGAAAGTGTGTTGACAGAC
ACTCCTTATTTGAGTTGAATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGATAGATGCTGC
TTGTATGCACGATTCCCTTCGTCGTGAAGTTGAAACCGCGGGTGACCCCTTCCGAGTCCAATATC
CTCCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTGTTGACAACCAACCGTCCCT
TCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGC
TCTGAAATTGGGAAATGGTTTGTTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTT
GTCT
Found at i:26876 original size:37 final size:37
Alignment explanation
Indices: 26794--26878 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
26784 GTTTCATGAG
* * * * **
26794 AAACGGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
26831 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
26867 GAAATTGTCTCA
1 -AAACTGTCTCA
26879 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:27083 original size:36 final size:36
Alignment explanation
Indices: 27036--27137 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
27026 AAAGGTTTTT
* **
27036 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTG
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
*
27072 TTTCAAGGGAAACTGTCTCAAGAGACACAAAATTCA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
27108 TTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAA
27138 TGGTGAGCAC
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 61 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.23
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTCA
Found at i:27230 original size:34 final size:34
Alignment explanation
Indices: 27192--27304 Score: 226
Period size: 34 Copynumber: 3.3 Consensus size: 34
27182 GCCCCTTCAC
27192 CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
1 CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
27226 CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
1 CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
27260 CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
1 CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
27294 CGTGAAGTTGA
1 CGTGAAGTTGA
27305 AATCCAACTT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 79 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (34 bp):
CGTGAAGTTGAGCCAGGAATTGGATATCCTTCGT
Found at i:27715 original size:18 final size:18
Alignment explanation
Indices: 27692--27727 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
27682 TGTTGAATCC
27692 CCAAAGATGCCCCAATAT
1 CCAAAGATGCCCCAATAT
27710 CCAAAGATGCCCCAATAT
1 CCAAAGATGCCCCAATAT
27728 TTGATGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.33, G:0.11, T:0.17
Consensus pattern (18 bp):
CCAAAGATGCCCCAATAT
Found at i:28809 original size:15 final size:16
Alignment explanation
Indices: 28791--28852 Score: 72
Period size: 16 Copynumber: 3.7 Consensus size: 16
28781 TTCCTTTTGA
28791 TTTTGCTTCTTTTCTT
1 TTTTGCTTCTTTTCTT
*
28807 TTTTGTTCTTGTTTTTTCTT
1 TTTTG--C-T-TCTTTTCTT
28827 TTTTGCTTCTTTTCTT
1 TTTTGCTTCTTTTCTT
28843 TTTTG-TTCTT
1 TTTTGCTTCTT
28853 GATTGAATCT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 5 0.12
16 18 0.45
17 1 0.03
18 2 0.05
19 1 0.03
20 13 0.32
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (16 bp):
TTTTGCTTCTTTTCTT
Found at i:28844 original size:21 final size:21
Alignment explanation
Indices: 28797--28844 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
28787 TTGATTTTGC
28797 TTCTTTTCTTTTTTGTTCTTG
1 TTCTTTTCTTTTTTGTTCTTG
28818 TT-TTTTCTTTTTTGCTTCTT-
1 TTCTTTTCTTTTTTG-TTCTTG
28838 TTCTTTT
1 TTCTTTT
28845 TTGTTCTTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (21 bp):
TTCTTTTCTTTTTTGTTCTTG
Found at i:30798 original size:17 final size:15
Alignment explanation
Indices: 30768--30801 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
30758 TACAAATAAT
30768 GAAAATAAAAGAAAA
1 GAAAATAAAAGAAAA
30783 GAAAATATAAATGAAAA
1 GAAAATA-AAA-GAAAA
30800 GA
1 GA
30802 GTTAGTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
GAAAATAAAAGAAAA
Found at i:32117 original size:2 final size:2
Alignment explanation
Indices: 32110--32141 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32100 GAATAAAACA
32110 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
32142 TAAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33424 original size:60 final size:59
Alignment explanation
Indices: 33302--33451 Score: 151
Period size: 60 Copynumber: 2.5 Consensus size: 59
33292 AATTTAATCC
* * * * * * *
33302 TCAAAAGTTTAAAGACCAATTTAAAATAAGGATCATAATTTAAGGATAAAATTAGAATAT
1 TCAAAAGTTAAAAGACTAATTTAAAATAA-AAACATAATTTAAGGATAAAATAAAAACAT
*
33362 TCAAAAGTTCAAAGACTAATTTAAAATAAAAACAATAATTTGAA-GATAAAATAAAAACAT
1 TCAAAAGTTAAAAGACTAATTTAAAATAAAAAC-ATAATTT-AAGGATAAAATAAAAACAT
* * *
33422 TCATAAATTTAAAAG-CTAGTTTAACATAAA
1 TCA-AAAGTTAAAAGACTAATTTAAAATAAA
33452 TGTGTAATAT
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 63 0.83
61 11 0.14
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.29
Consensus pattern (59 bp):
TCAAAAGTTAAAAGACTAATTTAAAATAAAAACATAATTTAAGGATAAAATAAAAACAT
Found at i:36301 original size:61 final size:61
Alignment explanation
Indices: 36206--36322 Score: 216
Period size: 61 Copynumber: 1.9 Consensus size: 61
36196 ACATTCTATC
* *
36206 CTAATTACATTTTTAATGAAGAGAATTGGGTATTGTTTGTAGGCACAGAAATTCATATGTT
1 CTAATTACATTTTTAAAGAAGAGAATTGGGTATTGTTTGTAGACACAGAAATTCATATGTT
36267 CTAATTACATTTTTAAAGAAGAGAATTGGGTATTGTTTGTAGACACAGAAATTCAT
1 CTAATTACATTTTTAAAGAAGAGAATTGGGTATTGTTTGTAGACACAGAAATTCAT
36323 CTATTTCACA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (61 bp):
CTAATTACATTTTTAAAGAAGAGAATTGGGTATTGTTTGTAGACACAGAAATTCATATGTT
Found at i:36776 original size:21 final size:21
Alignment explanation
Indices: 36751--37017 Score: 371
Period size: 21 Copynumber: 12.9 Consensus size: 21
36741 ATTTTCGCAA
* *
36751 CGCGTTGTGATTTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAC
* *
36772 CGCGTTGCGAATTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAC
* *
36793 CGCGTTGCGAATTTGGAGAAT
1 CGCGTTGCGATTTTGGAGAAC
36814 CGCGTTGCGATTTTGGAGAAC
1 CGCGTTGCGATTTTGGAGAAC
*
36835 CGCGTTGCGAATTT-GAGAAC
1 CGCGTTGCGATTTTGGAGAAC
*
36855 CGCGTTGCGATTTTTGAGAAC
1 CGCGTTGCGATTTTGGAGAAC
* *
36876 CGCATTGCGATTTTTGAGAAC
1 CGCGTTGCGATTTTGGAGAAC
36897 CGCGTTGCGATTTT-GAGAAC
1 CGCGTTGCGATTTTGGAGAAC
36917 CGCGTTGCGATTTT-GAGAAC
1 CGCGTTGCGATTTTGGAGAAC
*
36937 CGCGTTGTGATTTT-GAGAAC
1 CGCGTTGCGATTTTGGAGAAC
*
36957 CGCGTTGCTATTTTGGAGAAC
1 CGCGTTGCGATTTTGGAGAAC
*
36978 TGCGTTGCGATTTTGGAGAAC
1 CGCGTTGCGATTTTGGAGAAC
* *
36999 TGCATTGCGATTTTGGAGA
1 CGCGTTGCGATTTTGGAGA
37018 CTGTGTTGCG
Statistics
Matches: 230, Mismatches: 14, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
20 76 0.33
21 154 0.67
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (21 bp):
CGCGTTGCGATTTTGGAGAAC
Found at i:36884 original size:62 final size:63
Alignment explanation
Indices: 36759--37017 Score: 364
Period size: 62 Copynumber: 4.2 Consensus size: 63
36749 AACGCGTTGT
* * * * *
36759 GATTTTGGAGAATCGCGTTGCGAATTTGGAGAATCGCGTTGCGAATTTGGAGAATCGCGTTGC
1 GATTTTGGAGAACCGCGTTGCGAATTTGGAGAACCGCGTTGCGATTTTGGAGAACCGCATTGC
*
36822 GATTTTGGAGAACCGCGTTGCGAATTT-GAGAACCGCGTTGCGATTTTTGAGAACCGCATTGC
1 GATTTTGGAGAACCGCGTTGCGAATTTGGAGAACCGCGTTGCGATTTTGGAGAACCGCATTGC
* * * *
36884 GATTTTTGAGAACCGCGTTGCG-ATTTTGAGAACCGCGTTGCGATTTT-GAGAACCGCGTTGT
1 GATTTTGGAGAACCGCGTTGCGAATTTGGAGAACCGCGTTGCGATTTTGGAGAACCGCATTGC
* * * *
36945 GATTTT-GAGAACCGCGTTGCTATTTTGGAGAACTGCGTTGCGATTTTGGAGAACTGCATTGC
1 GATTTTGGAGAACCGCGTTGCGAATTTGGAGAACCGCGTTGCGATTTTGGAGAACCGCATTGC
37007 GATTTTGGAGA
1 GATTTTGGAGA
37018 CTGTGTTGCG
Statistics
Matches: 176, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
60 14 0.08
61 44 0.25
62 88 0.50
63 30 0.17
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.32
Consensus pattern (63 bp):
GATTTTGGAGAACCGCGTTGCGAATTTGGAGAACCGCGTTGCGATTTTGGAGAACCGCATTGC
Found at i:37045 original size:102 final size:102
Alignment explanation
Indices: 36751--37033 Score: 307
Period size: 102 Copynumber: 2.8 Consensus size: 102
36741 ATTTTCGCAA
* * * * * * * *
36751 CGCGTTGTGATTTTGGAGAATCGCGTTGCGAATTTGGAGAATCGCGTTGCGAATTTGGAGAATCG
1 CGCGTTGCGATTTTGGAGAACCGCATTGCGATTTTGGAGAACCGCATTGCG-ATTTTGAGAACCG
***
36816 CGTTGCGATTTTGGAGAACCGCGTTGCGAATTTGAGAAC
65 CGTTGCGAAACT-GAGAACCGCGTTGCGAATTTGAGAAC
* * *
36855 CGCGTTGCGATTTTTGAGAACCGCATTGCGATTTTTGAGAACCGCGTTGCGATTTTGAGAACCGC
1 CGCGTTGCGATTTTGGAGAACCGCATTGCGATTTTGGAGAACCGCATTGCGATTTTGAGAACCGC
*** * *
36920 GTTGCGATTTTGAGAACCGCGTTGTGATTTTGAGAAC
66 GTTGCGAAACTGAGAACCGCGTTGCGAATTTGAGAAC
* * * * *
36957 CGCGTTGCTATTTTGGAGAACTGCGTTGCGATTTTGGAGAACTGCATTGCGATTTTG-GAGACTG
1 CGCGTTGCGATTTTGGAGAACCGCATTGCGATTTTGGAGAACCGCATTGCGATTTTGAGA-ACCG
*
37021 TGTTGCGAAACTG
65 CGTTGCGAAACTG
37034 TAGTTTGCGT
Statistics
Matches: 155, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
101 2 0.01
102 86 0.55
103 23 0.15
104 44 0.28
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.32
Consensus pattern (102 bp):
CGCGTTGCGATTTTGGAGAACCGCATTGCGATTTTGGAGAACCGCATTGCGATTTTGAGAACCGC
GTTGCGAAACTGAGAACCGCGTTGCGAATTTGAGAAC
Found at i:37827 original size:28 final size:28
Alignment explanation
Indices: 37742--37846 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
37732 ATTTTTTATT
* *
37742 TAAGTACTTAAAGTATTCTTTGGTCAAAA
1 TAAGTACCTAAAGTATT-TTTAGTCAAAA
* * *
37771 TAAATACCTAAATTTATATTTTTACTCAAAA
1 TAAGTACCTAAA---GTATTTTTAGTCAAAA
37802 TAAGTACCTAAAGTA-TTTTATGTCAAAA
1 TAAGTACCTAAAGTATTTTTA-GTCAAAA
* * *
37830 TAGGTATCTAAACTATT
1 TAAGTACCTAAAGTATT
37847 CAATATTTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
27 5 0.08
28 20 0.33
29 11 0.18
31 20 0.33
32 4 0.07
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (28 bp):
TAAGTACCTAAAGTATTTTTAGTCAAAA
Found at i:37956 original size:23 final size:22
Alignment explanation
Indices: 37908--37959 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
37898 AATACTTTTG
**
37908 ATACTTTGAATGAAAAACTTTAA
1 ATAC-TTGAATGAAAAAAATTAA
*
37931 ATACTTGAATGAAAATAAATTGA
1 ATACTTGAATGAAAA-AAATTAA
37954 ATACTT
1 ATACTT
37960 TAGGTATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 11 0.44
23 14 0.56
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.35
Consensus pattern (22 bp):
ATACTTGAATGAAAAAAATTAA
Found at i:38056 original size:29 final size:29
Alignment explanation
Indices: 37953--38057 Score: 124
Period size: 29 Copynumber: 3.6 Consensus size: 29
37943 AAATAAATTG
*
37953 AATACTTTAGGTA-TCTATTTTGACCAAAA
1 AATACTTTAGGTACT-TATTTTGATCAAAA
* * *
37982 AATACTTTAAGTACCTATATTGATCAAAA
1 AATACTTTAGGTACTTATTTTGATCAAAA
*
38011 GATAACTTT-GAGTACTTATTTTGATCAAAA
1 AAT-ACTTTAG-GTACTTATTTTGATCAAAA
38041 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
38058 AATGAAAATG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
29 38 0.60
30 25 0.40
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.38
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGATCAAAA
Found at i:40689 original size:2 final size:2
Alignment explanation
Indices: 40682--40722 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
40672 CTTATGATCG
40682 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
40723 TAATGAATAC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:44140 original size:2 final size:2
Alignment explanation
Indices: 44133--44177 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
44123 TCTTTAAGCT
44133 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
44175 TA T
1 TA T
44178 TTCTTTTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:46466 original size:21 final size:21
Alignment explanation
Indices: 46425--46466 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46415 TCCTACGATC
* *
46425 ACTTGTTTGTAATGTTTTGTT
1 ACTTGTTTGTAATATTGTGTT
46446 ACTTGTTTGTAATATTGTGTT
1 ACTTGTTTGTAATATTGTGTT
46467 GTATACACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.05, G:0.19, T:0.60
Consensus pattern (21 bp):
ACTTGTTTGTAATATTGTGTT
Found at i:56342 original size:21 final size:21
Alignment explanation
Indices: 56316--56360 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
56306 GATTTATAGG
* *
56316 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
56337 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
56358 CAA
1 CAA
56361 ACGAATAAAA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:58058 original size:23 final size:23
Alignment explanation
Indices: 58028--58087 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
58018 ATTATTATAT
58028 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
58051 GGCACTACGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
58074 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
58088 TTTATATGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:59478 original size:23 final size:23
Alignment explanation
Indices: 59452--59509 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
59442 CATTCGGGAT
*
59452 AATTCTATGTGGTTCTTCAGGAC
1 AATTCTATGTGGTCCTTCAGGAC
***
59475 AATTCTACAAGGTCCTTCAGGAC
1 AATTCTATGTGGTCCTTCAGGAC
*
59498 AAATCTATGTGG
1 AATTCTATGTGG
59510 CACTTTGTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (23 bp):
AATTCTATGTGGTCCTTCAGGAC
Found at i:59533 original size:24 final size:24
Alignment explanation
Indices: 59497--59555 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
59487 TCCTTCAGGA
* * *
59497 CAAA-TCTATGTGGCACTTTGTTG
1 CAAATTCTACGTGGCACTTCGGTG
*
59520 CATATTCTACGTGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCGGTG
59544 CAAATTCTACGT
1 CAAATTCTACGT
59556 ATCAGTTTCG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCGGTG
Found at i:66710 original size:19 final size:20
Alignment explanation
Indices: 66688--66764 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 20
66678 TTTGTGCAGA
*
66688 GGGAATCGATCCCCCATGA-
1 GGGAACCGATCCCCCATGAG
*
66707 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGA-TCCCCC-ATG-AG
*
66730 GGGAACCGATCCCCCA-CAG
1 GGGAACCGATCCCCCATGAG
*
66749 GGGAATCGATACCCCC
1 GGGAACCGAT-CCCCC
66765 CTGGGGTTCT
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 19 0.40
20 11 0.23
21 2 0.04
22 7 0.15
23 9 0.19
ACGTcount: A:0.25, C:0.35, G:0.26, T:0.14
Consensus pattern (20 bp):
GGGAACCGATCCCCCATGAG
Done.