Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000694.1 Hibiscus syriacus cultivar Beakdansim tig00001351_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: 102063
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8555 original size:17 final size:16
Alignment explanation
Indices: 8513--8555 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
8503 ATGAGGCTTC
8513 AAAGAAAAGAAGAAGA
1 AAAGAAAAGAAGAAGA
* *
8529 ATAGAGAAAGAAGGAGA
1 AAAGA-AAAGAAGAAGA
8546 AGAAGAAAAG
1 A-AAGAAAAG
8556 GATGTTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (16 bp):
AAAGAAAAGAAGAAGA
Found at i:10079 original size:50 final size:49
Alignment explanation
Indices: 10004--10100 Score: 133
Period size: 50 Copynumber: 2.0 Consensus size: 49
9994 TAAAAATACA
* *
10004 ATTTTCTAGAAAAATGATCGATCCCTTTG-AGAAAAGGATCGATCCCTTGC
1 ATTTTCCAGAAAAAGGATCGATCCCTTTGCA-AAAA-GATCGATCCCTTGC
* *
10054 ATTTTCCATAAAAAGGATTGATCCCTTTGCAAAAAGATCGATCCCTT
1 ATTTTCCAGAAAAAGGATCGATCCCTTTGCAAAAAGATCGATCCCTT
10101 TTTGTGAATG
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
49 12 0.29
50 29 0.69
51 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (49 bp):
ATTTTCCAGAAAAAGGATCGATCCCTTTGCAAAAAGATCGATCCCTTGC
Found at i:10096 original size:20 final size:21
Alignment explanation
Indices: 10063--10101 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
10053 CATTTTCCAT
*
10063 AAAAAGGATTGATCCCTTTGC
1 AAAAAGGATCGATCCCTTTGC
10084 AAAAA-GATCGATCCCTTT
1 AAAAAGGATCGATCCCTTT
10102 TTGTGAATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAAAGGATCGATCCCTTTGC
Found at i:10948 original size:54 final size:54
Alignment explanation
Indices: 10890--11166 Score: 369
Period size: 54 Copynumber: 5.1 Consensus size: 54
10880 AATGCACCCG
* * * * * * * *
10890 TAGTGCCCATACGGTCATTCATAAACATATTACGAATTTCGTGGTTTGCACACA
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* * *
10944 TAGTGCCGAAACGATTATTCATTAACCTATGATGAATTTCGT-ACTTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGA-TTTGCACACT
*
10998 TAGTGCTGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* *
11052 TAGTACCGAAACAGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
* * *
11106 TAGTACCAAAACGGTTATTCATCAACATATGATGAA-TTCTATGATTTGCACACT
1 TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTC-GTGATTTGCACACT
11160 TAGTGCC
1 TAGTGCC
11167 TATTTGGTAA
Statistics
Matches: 199, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
53 3 0.02
54 195 0.98
55 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (54 bp):
TAGTGCCGAAACGGTTATTCATCAACATATGATGAATTTCGTGATTTGCACACT
Found at i:11242 original size:15 final size:15
Alignment explanation
Indices: 11222--11250 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
11212 ACTAGTATAA
11222 CATATAGTTACACAC
1 CATATAGTTACACAC
11237 CATATAGTTACACA
1 CATATAGTTACACA
11251 ATTAAATGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.24, G:0.07, T:0.28
Consensus pattern (15 bp):
CATATAGTTACACAC
Found at i:11625 original size:20 final size:20
Alignment explanation
Indices: 11600--11650 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11590 GATCCATGGC
*
11600 ATCGATACCATCCTCATAGT
1 ATCGATACCACCCTCATAGT
* *
11620 ATCGATACTC-CCCTCTTGGT
1 ATCGATAC-CACCCTCATAGT
11640 ATCGATACCAC
1 ATCGATACCAC
11651 TTGAATCGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.25, C:0.33, G:0.12, T:0.29
Consensus pattern (20 bp):
ATCGATACCACCCTCATAGT
Found at i:14579 original size:17 final size:17
Alignment explanation
Indices: 14552--14592 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
14542 CTTTAAATTA
*
14552 TTTATTTAATTATTTTCT
1 TTTA-TTAATTATTGTCT
*
14570 TTTATTAATTCTTGTCT
1 TTTATTAATTATTGTCT
14587 TTTATT
1 TTTATT
14593 TTAAAAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTATTAATTATTGTCT
Found at i:19556 original size:24 final size:24
Alignment explanation
Indices: 19528--19604 Score: 90
Period size: 24 Copynumber: 3.3 Consensus size: 24
19518 TGTTAAATAT
19528 TTTTAAAAGATGAGATAAATTTCA
1 TTTTAAAAGATGAGATAAATTTCA
* **
19552 TTTTAAAGGATGTCA-AAA--T-A
1 TTTTAAAAGATGAGATAAATTTCA
19572 TTTCTAAAAGATGAGATAAATTTCA
1 TTT-TAAAAGATGAGATAAATTTCA
19597 TTTTAAAA
1 TTTTAAAA
19605 CATGTAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
20 4 0.10
21 10 0.24
22 3 0.07
23 3 0.07
24 18 0.43
25 4 0.10
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (24 bp):
TTTTAAAAGATGAGATAAATTTCA
Found at i:19648 original size:2 final size:2
Alignment explanation
Indices: 19641--19708 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
19631 ATTTTTGTTC
19641 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
19683 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
19709 GAACAAAAAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23934 original size:12 final size:11
Alignment explanation
Indices: 23916--23945 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
23906 TGGATGATCG
23916 AATTTTTTTAA
1 AATTTTTTTAA
23927 ATATTTTTTTAA
1 A-ATTTTTTTAA
23939 AATTTTT
1 AATTTTT
23946 AAATGAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTTTAA
Found at i:24069 original size:19 final size:19
Alignment explanation
Indices: 24045--24085 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
24035 TGGATAATTT
24045 AATTTGAGAGGAGAGAAAA
1 AATTTGAGAGGAGAGAAAA
24064 AATTTGAGAGGAGAGAAAA
1 AATTTGAGAGGAGAGAAAA
24083 AAT
1 AAT
24086 AATAATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.17
Consensus pattern (19 bp):
AATTTGAGAGGAGAGAAAA
Found at i:28757 original size:16 final size:17
Alignment explanation
Indices: 28736--28769 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
28726 TAATTATGAT
28736 TATTTTAAAT-ATTAAA
1 TATTTTAAATAATTAAA
28752 TATTTTAAATAATTAAA
1 TATTTTAAATAATTAAA
28769 T
1 T
28770 TTTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATTTTAAATAATTAAA
Found at i:31025 original size:147 final size:147
Alignment explanation
Indices: 30758--31055 Score: 560
Period size: 147 Copynumber: 2.0 Consensus size: 147
30748 TCCCACTAAT
*
30758 CATAAAAGAATGCTAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATGTATCATAT
1 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATGTATCATAT
*
30823 AAAAATTTTGTCAAAATTTAAGGGCATCAGTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
66 AAAAATTTTGTCAAAATTTAAGGGCATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
30888 AGTATGTGTGTATTGTC
131 AGTATGTGTGTATTGTC
30905 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATGTATCATAT
1 CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATGTATCATAT
* *
30970 AAAAATTTTGTCAAAATTTAAGGGTATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGTA
66 AAAAATTTTGTCAAAATTTAAGGGCATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
31035 AGTATGTGTGTATTGTC
131 AGTATGTGTGTATTGTC
31052 CATA
1 CATA
31056 TTTCACATAA
Statistics
Matches: 147, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (147 bp):
CATAAAAGAATGCCAAAAGAAAGTATAAAGAGAAATTGAATATTTTGGAAATACATGTATCATAT
AAAAATTTTGTCAAAATTTAAGGGCATCACTGTACCTAATAAAATTCGAGTAGTTACATTTTGCA
AGTATGTGTGTATTGTC
Found at i:33655 original size:12 final size:12
Alignment explanation
Indices: 33635--33674 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
33625 TTACGAATAA
33635 ACTCATTTATTG
1 ACTCATTTATTG
*
33647 ACTCGTTTATT-
1 ACTCATTTATTG
33658 AGCTCATTTATTG
1 A-CTCATTTATTG
33671 ACTC
1 ACTC
33675 GCTTATAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 1 0.04
12 22 0.92
13 1 0.04
ACGTcount: A:0.23, C:0.20, G:0.10, T:0.47
Consensus pattern (12 bp):
ACTCATTTATTG
Found at i:33691 original size:24 final size:24
Alignment explanation
Indices: 33631--33683 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
33621 ATGTTTACGA
* *
33631 ATAAACTCATTTATTGACTCGTTT
1 ATAAGCTCATTTATTGACTCGCTT
*
33655 ATTAGCTCATTTATTGACTCGCTT
1 ATAAGCTCATTTATTGACTCGCTT
33679 ATAAG
1 ATAAG
33684 TTTGTTTACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (24 bp):
ATAAGCTCATTTATTGACTCGCTT
Found at i:33728 original size:36 final size:36
Alignment explanation
Indices: 33658--33728 Score: 88
Period size: 36 Copynumber: 2.0 Consensus size: 36
33648 CTCGTTTATT
* * **
33658 AGCTCATTTATTGACTCGCTTATAAGTTTGTTTACG
1 AGCTCATTTATCGACTCACTTATAAGTTCATTTACG
* *
33694 AGCTCATTTATCGACTCATTTATAGGTTCATTTAC
1 AGCTCATTTATCGACTCACTTATAAGTTCATTTAC
33729 TCGGTTGACT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.44
Consensus pattern (36 bp):
AGCTCATTTATCGACTCACTTATAAGTTCATTTACG
Found at i:33748 original size:29 final size:29
Alignment explanation
Indices: 33706--33763 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
33696 CTCATTTATC
33706 GACTCATTTATAGGTTCATTTACTCGGTT
1 GACTCATTTATAGGTTCATTTACTCGGTT
33735 GACTCATTTATAGGTTCATTTACTCGGTT
1 GACTCATTTATAGGTTCATTTACTCGGTT
33764 CTCTATGTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (29 bp):
GACTCATTTATAGGTTCATTTACTCGGTT
Found at i:34044 original size:30 final size:29
Alignment explanation
Indices: 33984--34044 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 29
33974 AAACACAAAT
33984 TAAACATGAATACCTTCAAAAAAATTTAAA
1 TAAACATGAATACCTTCAAAAAAA-TTAAA
34014 TAAACATGAATACCTTCAGAAATAAA-TAAA
1 TAAACATGAATACCTTCA-AAA-AAATTAAA
34044 T
1 T
34045 GAATATAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 23 0.79
31 3 0.10
32 3 0.10
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (29 bp):
TAAACATGAATACCTTCAAAAAAATTAAA
Found at i:43807 original size:20 final size:21
Alignment explanation
Indices: 43769--43809 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
43759 CTTTATTTTA
43769 TTTATTTATTTTCATTTGATT
1 TTTATTTATTTTCATTTGATT
43790 TTTATTT-TTTAT-ATTTGATT
1 TTTATTTATTT-TCATTTGATT
43810 AAATGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.20, C:0.02, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTATTTATTTTCATTTGATT
Found at i:48008 original size:23 final size:23
Alignment explanation
Indices: 47982--48026 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
47972 CACCACAGCT
*
47982 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
48005 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
48027 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:48193 original size:150 final size:149
Alignment explanation
Indices: 47994--48309 Score: 553
Period size: 150 Copynumber: 2.1 Consensus size: 149
47984 TATAAATGCA
*
47994 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* *
48058 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTT-CAAGACTTCACACATGT
* *
48123 TCCACAGAATATATATATATC
129 TCCAAAGAATATACATATATC
48144 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
48209 TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
*
48274 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
48293 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
48310 CCCTCTACCC
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
149 53 0.33
150 106 0.67
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:48821 original size:19 final size:20
Alignment explanation
Indices: 48784--48821 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48774 TTTTTTCTCA
*
48784 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
48804 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
48822 TCTAGCATAC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:54961 original size:23 final size:23
Alignment explanation
Indices: 54935--54979 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
54925 CACCACAGCT
*
54935 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
54958 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
54980 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:55168 original size:147 final size:148
Alignment explanation
Indices: 54947--55259 Score: 542
Period size: 147 Copynumber: 2.1 Consensus size: 148
54937 TATAAATGCA
*
54947 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATATAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* *
55011 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCCAAGACTTCACACATGT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTT-CAAGACTTCACACATGT
*
55076 TCCACAGAATAT-ATATATC
129 TCCAAAGAATATAATATATC
55095 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAT-ATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
55159 TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
55224 CAAAGAATATACATATATC
131 CAAAGAATATA-ATATATC
55243 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
55260 CCCTCTACCC
Statistics
Matches: 158, Mismatches: 4, Indels: 6
0.94 0.02 0.04
Matches are distributed among these distances:
146 28 0.18
147 71 0.45
148 59 0.37
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (148 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGCATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATAATATATC
Found at i:57162 original size:24 final size:24
Alignment explanation
Indices: 57114--57162 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57104 GTCAATCTTC
* * **
57114 GGAGGTAATGTCTAAAGCAGTTAT
1 GGAGGTAATGTATAAAACAACTAT
57138 GGAGGTAATGTATAAAACAACTAT
1 GGAGGTAATGTATAAAACAACTAT
57162 G
1 G
57163 AAGTAAGTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.08, G:0.27, T:0.27
Consensus pattern (24 bp):
GGAGGTAATGTATAAAACAACTAT
Found at i:58198 original size:15 final size:15
Alignment explanation
Indices: 58178--58208 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
58168 TTTTCATGAT
58178 GCTGTTACTAGTCAG
1 GCTGTTACTAGTCAG
58193 GCTGTTACTAGTCAG
1 GCTGTTACTAGTCAG
58208 G
1 G
58209 AAAACGACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.29, T:0.32
Consensus pattern (15 bp):
GCTGTTACTAGTCAG
Found at i:63293 original size:10 final size:9
Alignment explanation
Indices: 63262--63294 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
63252 AAGTCCATTA
63262 TTTTTCTCT
1 TTTTTCTCT
63271 TTTTT-TCT
1 TTTTTCTCT
*
63279 TTTTCCTCT
1 TTTTTCTCT
63288 TTTTTCT
1 TTTTTCT
63295 AACACAGCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTCT
Found at i:65505 original size:96 final size:96
Alignment explanation
Indices: 65330--65507 Score: 268
Period size: 96 Copynumber: 1.9 Consensus size: 96
65320 CGACTCAACT
* *
65330 TTGAAAACTAATGAACTAAAAATTATCAAACTCAACTCGAACTCAAAATAAAATATTAAAACTTG
1 TTGAAAACTAATAAACTAAAAATTATCAAACTCAACTCGAACTCAAAATAAAATATTAAAAATTG
*
65395 AAACGAACTCGAAAAGGCTCAAACTTGAAAC
66 AAACAAACTCGAAAAGGCTCAAACTTGAAAC
* **
65426 TTGAAAACTCATAAACTAAAAATTATCAAACTCAGTTCGAACTCAAAATAAAATATTAAAAATT-
1 TTGAAAACTAATAAACTAAAAATTATCAAACTCAACTCGAACTCAAAATAAAATATTAAAAATTG
* *
65490 AACTCAAACTTGAAAAGG
66 AA-ACAAACTCGAAAAGG
65508 TTCGAACTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 2 0.03
96 71 0.97
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (96 bp):
TTGAAAACTAATAAACTAAAAATTATCAAACTCAACTCGAACTCAAAATAAAATATTAAAAATTG
AAACAAACTCGAAAAGGCTCAAACTTGAAAC
Found at i:65598 original size:11 final size:12
Alignment explanation
Indices: 65576--65613 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
65566 GCTCGATTCA
65576 AGCTCGATTTTG
1 AGCTCGATTTTG
*
65588 AGCTCTA-TTTG
1 AGCTCGATTTTG
65599 AGCTCGATTTTG
1 AGCTCGATTTTG
65611 AGC
1 AGC
65614 GTGAGGCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.39
Consensus pattern (12 bp):
AGCTCGATTTTG
Found at i:69544 original size:26 final size:25
Alignment explanation
Indices: 69515--69596 Score: 61
Period size: 25 Copynumber: 3.4 Consensus size: 25
69505 GTATGAATTG
69515 GCATAAAAGGTGCCACTAATGAAAAT
1 GCAT-AAAGGTGCCACTAATGAAAAT
* *
69541 GCATAACGGTG-CA-TTATCG-----
1 GCATAAAGGTGCCACTAAT-GAAAAT
*
69560 GCATAAAAGATGCCACTAATGAAAAT
1 GCAT-AAAGGTGCCACTAATGAAAAT
69586 GCATAAAGGTG
1 GCATAAAGGTG
69597 TATTATCGGC
Statistics
Matches: 41, Mismatches: 6, Indels: 19
0.62 0.09 0.29
Matches are distributed among these distances:
19 4 0.10
20 5 0.12
21 3 0.07
22 3 0.07
23 3 0.07
24 3 0.07
25 12 0.29
26 8 0.20
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.21
Consensus pattern (25 bp):
GCATAAAGGTGCCACTAATGAAAAT
Found at i:69563 original size:45 final size:45
Alignment explanation
Indices: 69514--69666 Score: 252
Period size: 45 Copynumber: 3.4 Consensus size: 45
69504 TGTATGAATT
69514 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
* * *
69559 GGCATAAAAGATGCCACTAATGAAAATGCATAAAGGTGTATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
* * *
69604 GGCATAAAAGGTTCCACTAATAAAAATGCATAACGATGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
69649 GGCATAAAAGGTGCCACT
1 GGCATAAAAGGTGCCACT
69667 CATGGTATTC
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (45 bp):
GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
Found at i:76559 original size:44 final size:45
Alignment explanation
Indices: 76511--76615 Score: 176
Period size: 44 Copynumber: 2.4 Consensus size: 45
76501 TGTATGAATT
76511 GGCATAAAAGGTGCCACTAATGAAAATGCAT-ACGGTGCATTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
** *
76555 GGCATAAAATATGCCACTAATGAAAATGCATAACGGTGCTTTATC
1 GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
76600 GGCATAAAAGGTGCCA
1 GGCATAAAAGGTGCCA
76616 TTCATGGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 29 0.53
45 26 0.47
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (45 bp):
GGCATAAAAGGTGCCACTAATGAAAATGCATAACGGTGCATTATC
Found at i:80426 original size:18 final size:18
Alignment explanation
Indices: 80403--80440 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
80393 GATTGGGGTC
*
80403 GTTGACGGCTGAAGACTG
1 GTTGACGGCTAAAGACTG
*
80421 GTTGACGGTTAAAGACTG
1 GTTGACGGCTAAAGACTG
80439 GT
1 GT
80441 AGTCGAAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (18 bp):
GTTGACGGCTAAAGACTG
Found at i:84576 original size:14 final size:14
Alignment explanation
Indices: 84557--84622 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 14
84547 GAGTCAACGG
84557 GTTGACTCAGACGA
1 GTTGACTCAGACGA
84571 GTTGACTCAGACGA
1 GTTGACTCAGACGA
* *
84585 ATTAACTC-GATCGA
1 GTTGACTCAGA-CGA
** * *
84599 GTTGAAGCAGTCAA
1 GTTGACTCAGACGA
84613 GTTGACTCAG
1 GTTGACTCAG
84623 TCGGGTAAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
13 2 0.05
14 37 0.93
15 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGACGA
Found at i:97983 original size:27 final size:27
Alignment explanation
Indices: 97945--97996 Score: 63
Period size: 27 Copynumber: 1.9 Consensus size: 27
97935 TTAAATTTTT
97945 GGTCAAAGTCAATGG-TAAAAGTCAACG
1 GGTCAAAGTCAA-GGATAAAAGTCAACG
*
97972 GGTC-AAGTTCAAGGATCAAAGTCAA
1 GGTCAAAG-TCAAGGATAAAAGTCAA
97997 TGAGTTGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.19
Consensus pattern (27 bp):
GGTCAAAGTCAAGGATAAAAGTCAACG
Found at i:102012 original size:20 final size:18
Alignment explanation
Indices: 101962--102013 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
101952 ATATAAGTTT
101962 ATTATAT-ATATAGTATA
1 ATTATATAATATAGTATA
*
101979 ATTATGATATATATATTATTA
1 ATTAT-ATA-ATATAGTA-TA
102000 ATCTATATAATATA
1 AT-TATATAATATA
102014 AGATAGTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 5 0.17
18 2 0.07
20 12 0.41
21 7 0.24
22 3 0.10
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (18 bp):
ATTATATAATATAGTATA
Done.