Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004056.1 Hibiscus syriacus cultivar Beakdansim tig00008873_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: 62068
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:56 original size:30 final size:28
Alignment explanation
Indices: 22--89 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 28
12 GGTGGAGGTC
22 TTGGAGGTGGTGCTGGTGCAGGAGGTGGTT
1 TTGGAGGTGGTGCTGGTGCAGGAGG-GG-T
* * *
52 TTGGAGGAGGTGCTGGTGCTGGTGGGGT
1 TTGGAGGTGGTGCTGGTGCAGGAGGGGT
80 TTGGAGGTGG
1 TTGGAGGTGG
90 CGGCGGAGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 10 0.29
29 2 0.06
30 22 0.65
ACGTcount: A:0.09, C:0.06, G:0.56, T:0.29
Consensus pattern (28 bp):
TTGGAGGTGGTGCTGGTGCAGGAGGGGT
Found at i:134 original size:30 final size:30
Alignment explanation
Indices: 99--435 Score: 211
Period size: 30 Copynumber: 11.3 Consensus size: 30
89 GCGGCGGAGC
* *
99 TGGTGGTGG-GTTGGTAAGGGTGGAGGCCT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
** * * **
128 TGGGTGG-GGAATAAGAAAAGGTGGCGGAGT
1 T-GGTGGTGGAATTGGAAAGGGTGGAGGCCT
* *
158 TGGTGGTGGCATTGG-AAGGGAGGAGGCCT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * * * * *
187 TGGAGGTGGTATAGGAAAAGGTGGTGGACT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * * * *
217 GGGTGGTGGCATTGGAAAGGGCGGGGGGCT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * *
247 TGGT-GCGGAGTTGGCAAGGGTGGAGGCCT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * *
276 TGGTGGTGGGCATTGGTAAGGGTGG-GGACT
1 TGGTGGT-GGAATTGGAAAGGGTGGAGGCCT
*
306 TGGTGGTGGAATTGGCAAGGGTGGAGGCCT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * * * * * *
336 TGGAGGGGGTATAGGAAAAGGTGGTGGAC-
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * * *
365 TGGTGGCGGCATTGGTAAGGGTGG-GGACT
1 TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
* * *
394 AGGTGTGGGGAATTGGCAAGGGTGGAGGCCT
1 TGGTG-GTGGAATTGGAAAGGGTGGAGGCCT
425 TGGTGGGTGGA
1 TGGT-GGTGGA
436 CATGGCGGTG
Statistics
Matches: 229, Mismatches: 68, Indels: 20
0.72 0.21 0.06
Matches are distributed among these distances:
28 4 0.02
29 88 0.38
30 111 0.48
31 25 0.11
32 1 0.00
ACGTcount: A:0.18, C:0.08, G:0.53, T:0.22
Consensus pattern (30 bp):
TGGTGGTGGAATTGGAAAGGGTGGAGGCCT
Found at i:162 original size:59 final size:59
Alignment explanation
Indices: 91--233 Score: 173
Period size: 59 Copynumber: 2.4 Consensus size: 59
81 TGGAGGTGGC
* * *
91 GGCGGAGCTGGTGGTGG-GTTGGTAAGGGTGGAGGCCTTGG-GTGGGGAATAAGAAAAGGT
1 GGCGGAGTTGGTGGTGGCATTGG-AAGGGAGGAGGCCTTGGAG-GGGGAATAAGAAAAGGT
* * *
150 GGCGGAGTTGGTGGTGGCATTGGAAGGGAGGAGGCCTTGGAGGTGGTATAGGAAAAGGT
1 GGCGGAGTTGGTGGTGGCATTGGAAGGGAGGAGGCCTTGGAGGGGGAATAAGAAAAGGT
* * *
209 GGTGGACTGGGTGGTGGCATTGGAA
1 GGCGGAGTTGGTGGTGGCATTGGAA
234 AGGGCGGGGG
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
59 68 0.93
60 5 0.07
ACGTcount: A:0.20, C:0.07, G:0.52, T:0.21
Consensus pattern (59 bp):
GGCGGAGTTGGTGGTGGCATTGGAAGGGAGGAGGCCTTGGAGGGGGAATAAGAAAAGGT
Found at i:297 original size:60 final size:59
Alignment explanation
Indices: 157--388 Score: 191
Period size: 59 Copynumber: 3.9 Consensus size: 59
147 GGTGGCGGAG
* * * * * * * * * *
157 TTGGTGGTGGCATTGG-AAGGGAGGAGGCCTTGGAGGTGGTATAGGAAAAGGTGGTGGAC
1 TTGGTGGTGGCATTGGAAAGGG-GGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGCC
* * *
216 TGGGTGGTGGCATTGGAAAGGGCGGGGGGCTTGGT-GCGGAGTTGGCAAGGGTGGAGGCC
1 TTGGTGGTGGCATTGGAAAGGG-GGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGCC
* * *
275 TTGGTGGTGGGCATTGGTAAGGGTGGGGACTTGGTGGTGGAATTGGCAAGGGTGGAGGCC
1 TTGGTGGT-GGCATTGGAAAGGGGGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGCC
* * * * * * * *
335 TTGGAGGGGGTATAGGAAAAGGTGGTGGAC-TGGTGGCGGCATTGGTAAGGGTGG
1 TTGGTGGTGGCATTGG-AAAGGGGGGGGACTTGGTGGCGGAATTGGCAAGGGTGG
389 GGACTAGGTG
Statistics
Matches: 139, Mismatches: 30, Indels: 8
0.79 0.17 0.05
Matches are distributed among these distances:
59 75 0.54
60 64 0.46
ACGTcount: A:0.18, C:0.08, G:0.52, T:0.22
Consensus pattern (59 bp):
TTGGTGGTGGCATTGGAAAGGGGGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGCC
Found at i:338 original size:89 final size:86
Alignment explanation
Indices: 161--431 Score: 267
Period size: 89 Copynumber: 3.1 Consensus size: 86
151 GCGGAGTTGG
* * * * * * * *
161 TGGTGGCA-TTGGAAGGGAGGAGGCCTTGGAGGTGGTATAGGAAAAGGTGGTGGACTGGGTGGTG
1 TGGTGGGAGTTGGAAGGGTGGAGGCCTTGGTGGTGGCATTGGTAAGGGTGG-GGACTAGGTGGTG
* * * * *
225 GCATTGGAAAGGGCGGGGGGCT
65 GAATTGGCAAGGGTGGAGGCCT
*
247 TGGTGCGGAGTTGGCAAGGGTGGAGGCCTTGGTGGTGGGCATTGGTAAGGGTGGGGACTTGGTGG
1 TGGTG-GGAGTTGG-AAGGGTGGAGGCCTTGGTGGT-GGCATTGGTAAGGGTGGGGACTAGGTGG
312 TGGAATTGGCAAGGGTGGAGGCCT
63 TGGAATTGGCAAGGGTGGAGGCCT
* * * * * *
336 TGGAGGGGGTATAGGAAAAGGTGGTGGAC-TGGTGGCGGCATTGGTAAGGGTGGGGACTAGGTGT
1 TGGTGGGAGT-T-GG-AAGGGTGGAGGCCTTGGTGGTGGCATTGGTAAGGGTGGGGACTAGGTG-
*
400 GGGGAATTGGCAAGGGTGGAGGCCT
62 GTGGAATTGGCAAGGGTGGAGGCCT
425 TGGTGGG
1 TGGTGGG
432 TGGACATGGC
Statistics
Matches: 155, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
86 5 0.03
87 2 0.01
88 34 0.22
89 89 0.57
90 25 0.16
ACGTcount: A:0.18, C:0.08, G:0.52, T:0.21
Consensus pattern (86 bp):
TGGTGGGAGTTGGAAGGGTGGAGGCCTTGGTGGTGGCATTGGTAAGGGTGGGGACTAGGTGGTGG
AATTGGCAAGGGTGGAGGCCT
Found at i:364 original size:149 final size:150
Alignment explanation
Indices: 108--430 Score: 424
Period size: 149 Copynumber: 2.2 Consensus size: 150
98 CTGGTGGTGG
* * *
108 GTTGGTAAGGGTGGAGGCCTT-G-GGTGGGGAATAAGAAAAGGTGGCGGAGTTGGTGGTGGCATT
1 GTTGGCAAGGGTGGAGGCCTTGGTGGTGGGGAATAAGAAAAGGTGGCGGACTTGGTGGTGGAATT
* *
171 GGAAGGGAGGAGGCCTTGGAGGTGGTATAGGAAAAGGTGGTGGACTGGGTGGTGGCATTGGAAAG
66 GGAAGGGAGGAGGCCTTGGAGGGGGTATAGGAAAAGGTGGTGGACT-GGTGGCGGCATTGGAAAG
* *
236 GGCGGGGGGCT-TG-GTGCGGA
130 GG-GGGGGACTAGGTGTGCGGA
* ** * *
256 GTTGGCAAGGGTGGAGGCCTTGGTGGT-GGGCATTGGTAAGGGTGG-GGACTTGGTGGTGGAATT
1 GTTGGCAAGGGTGGAGGCCTTGGTGGTGGGGAATAAGAAAAGGTGGCGGACTTGGTGGTGGAATT
* *
319 GGCAAGGGTGGAGGCCTTGGAGGGGGTATAGGAAAAGGTGGTGGACTGGTGGCGGCATTGGTAAG
66 GG-AAGGGAGGAGGCCTTGGAGGGGGTATAGGAAAAGGTGGTGGACTGGTGGCGGCATTGGAAAG
* *
384 GGTGGGGACTAGGTGTGGGGA
130 GGGGGGGACTAGGTGTGCGGA
*
405 ATTGGCAAGGGTGGAGGCCTTGGTGG
1 GTTGGCAAGGGTGGAGGCCTTGGTGG
431 GTGGACATGG
Statistics
Matches: 153, Mismatches: 17, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
147 6 0.04
148 57 0.37
149 87 0.57
150 3 0.02
ACGTcount: A:0.19, C:0.08, G:0.52, T:0.21
Consensus pattern (150 bp):
GTTGGCAAGGGTGGAGGCCTTGGTGGTGGGGAATAAGAAAAGGTGGCGGACTTGGTGGTGGAATT
GGAAGGGAGGAGGCCTTGGAGGGGGTATAGGAAAAGGTGGTGGACTGGTGGCGGCATTGGAAAGG
GGGGGGACTAGGTGTGCGGA
Found at i:418 original size:59 final size:59
Alignment explanation
Indices: 227--430 Score: 171
Period size: 59 Copynumber: 3.4 Consensus size: 59
217 GGGTGGTGGC
* * * * * * *
227 ATTGGAAAGGGCGGGGGGCTTGGT-GCGGAGTTGGCAAGGGTGGAGGCCTTGGTGGTGGGC
1 ATTGGAAAGGG-TGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGACTAGGAGG-GGGA
* * * * *
287 ATTGGTAAGGGTGGGGACTTGGTGGTGGAATTGGCAAGGGTGGAGGCCTTGGAGGGGGT
1 ATTGGAAAGGGTGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGACTAGGAGGGGGA
* * * * *
346 ATAGGAAAAGGTGGTGGAC-TGGTGGCGGCATTGGTAAGGGTGG-GGACTAGGTGTGGGGA
1 ATTGGAAAGGGTGG-GGACTTGGTGGCGGAATTGGCAAGGGTGGAGGACTAGGAG-GGGGA
* *
405 ATTGGCAAGGGTGGAGGCCTTGGTGG
1 ATTGGAAAGGGTGG-GGACTTGGTGG
431 GTGGACATGG
Statistics
Matches: 118, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
58 7 0.06
59 63 0.53
60 48 0.41
ACGTcount: A:0.17, C:0.09, G:0.52, T:0.22
Consensus pattern (59 bp):
ATTGGAAAGGGTGGGGACTTGGTGGCGGAATTGGCAAGGGTGGAGGACTAGGAGGGGGA
Found at i:463 original size:42 final size:43
Alignment explanation
Indices: 411--518 Score: 132
Period size: 42 Copynumber: 2.6 Consensus size: 43
401 GGGAATTGGC
* *
411 AAGGGTGGAGGCCTTGGTGGGTGGACATGGCGGTGGCATTGGG
1 AAGGGAGGAGGCCTTGGTGGGTGGACATGGCGGTGGCATCGGG
* * * *
454 AA-GGAGGAGGCCTTGGTGGG-GGCCTTGGTGGTGGCATCGGT
1 AAGGGAGGAGGCCTTGGTGGGTGGACATGGCGGTGGCATCGGG
*
495 AAGGGCGGAGGCCTTGGT-GGTGGA
1 AAGGGAGGAGGCCTTGGTGGGTGGA
519 ACAGGAAAAG
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 20 0.36
42 33 0.60
43 2 0.04
ACGTcount: A:0.14, C:0.13, G:0.53, T:0.20
Consensus pattern (43 bp):
AAGGGAGGAGGCCTTGGTGGGTGGACATGGCGGTGGCATCGGG
Found at i:662 original size:31 final size:30
Alignment explanation
Indices: 619--676 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
609 GGAGCTGGTA
*
619 GTGGACTTGGAGGTGGTGCAGGTGGGGGTG
1 GTGGACTTGGAGGTGGTGCAGGAGGGGGTG
*
649 GTGGATTTGGGAGGTGGTGCAGGAGGGG
1 GTGGACTT-GGAGGTGGTGCAGGAGGGG
677 AGGTGGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.12, C:0.05, G:0.60, T:0.22
Consensus pattern (30 bp):
GTGGACTTGGAGGTGGTGCAGGAGGGGGTG
Found at i:682 original size:30 final size:30
Alignment explanation
Indices: 619--682 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
609 GGAGCTGGTA
* *
619 GTGGACTTGGAGGTGGTGCAGGTGGGGGTG
1 GTGGACTTGGAGGTGGTGCAGGTAGGGGAG
*
649 GTGGATTTGGGAGGTGGTGCAGG-AGGGGAG
1 GTGGACTT-GGAGGTGGTGCAGGTAGGGGAG
679 GTGG
1 GTGG
683 TGTCGGTGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.12, C:0.05, G:0.61, T:0.22
Consensus pattern (30 bp):
GTGGACTTGGAGGTGGTGCAGGTAGGGGAG
Found at i:816 original size:30 final size:29
Alignment explanation
Indices: 782--884 Score: 136
Period size: 30 Copynumber: 3.5 Consensus size: 29
772 GTGGTGGTTT
*
782 TGGAGGCGGATTTGGTGGGGGTGCAGGAGG
1 TGGAGGTGGATTTGGTGGGGG-GCAGGAGG
812 TGGAGGTGGA-TTGGTGGGGGGCAGGAGG
1 TGGAGGTGGATTTGGTGGGGGGCAGGAGG
* * *
840 TGGAGGTGGTTTTGGTGGAGGAGCAGGCGG
1 TGGAGGTGGATTTGGTGG-GGGGCAGGAGG
*
870 TGGAGGTGGAATTGG
1 TGGAGGTGGATTTGG
885 AGGACTCCAC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 17 0.26
29 17 0.26
30 31 0.48
ACGTcount: A:0.15, C:0.05, G:0.59, T:0.21
Consensus pattern (29 bp):
TGGAGGTGGATTTGGTGGGGGGCAGGAGG
Found at i:2896 original size:24 final size:24
Alignment explanation
Indices: 2851--2897 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
2841 AACTAAGGGA
*
2851 GGTGGGTTTGGTGCCGGAGGTGGG
1 GGTGGGTTTGGTGCAGGAGGTGGG
* * *
2875 GGTGGTTTTGGTGGAGGTGGTGG
1 GGTGGGTTTGGTGCAGGAGGTGG
2898 TGCAGGAGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.04, C:0.04, G:0.62, T:0.30
Consensus pattern (24 bp):
GGTGGGTTTGGTGCAGGAGGTGGG
Found at i:2905 original size:15 final size:15
Alignment explanation
Indices: 2887--2929 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
2877 TGGTTTTGGT
2887 GGAGGTGGTGGTGCA
1 GGAGGTGGTGGTGCA
** *
2902 GGAGGTGGTTTTGGA
1 GGAGGTGGTGGTGCA
*
2917 GGAGGTGCTGGTG
1 GGAGGTGGTGGTG
2930 GTGGTGGAGG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.12, C:0.05, G:0.58, T:0.26
Consensus pattern (15 bp):
GGAGGTGGTGGTGCA
Found at i:3012 original size:30 final size:30
Alignment explanation
Indices: 2931--3013 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
2921 GTGCTGGTGG
* * *
2931 TGGTGGAGGGCTTGGAGGTGGAGTTGGAGC
1 TGGTGGAGGGTTTGGTGGTGGCGTTGGAGC
*
2961 TGGTAGAGGGTTTGGTGGTGGCGTTGGAGC
1 TGGTGGAGGGTTTGGTGGTGGCGTTGGAGC
2991 TGGTGGAGGGTTTGGTGGTGGCG
1 TGGTGGAGGGTTTGGTGGTGGCG
3014 GTGGGATTGG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.10, C:0.06, G:0.57, T:0.28
Consensus pattern (30 bp):
TGGTGGAGGGTTTGGTGGTGGCGTTGGAGC
Found at i:3083 original size:30 final size:30
Alignment explanation
Indices: 3069--3151 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
3059 GATTGGTAAG
3069 GGTGGAGGCCTTGGTGGGGGAATAGAAAAA
1 GGTGGAGGCCTTGGTGGGGGAATAGAAAAA
*
3099 GGTGGAGGCCTTGGTGGGGGAATAGGAAAA
1 GGTGGAGGCCTTGGTGGGGGAATAGAAAAA
* * * *
3129 GGTGGTGGACATGGTGGAGGAAT
1 GGTGGAGGCCTTGGTGGGGGAAT
3152 TGGCAAAGGT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.27, C:0.06, G:0.49, T:0.18
Consensus pattern (30 bp):
GGTGGAGGCCTTGGTGGGGGAATAGAAAAA
Found at i:3160 original size:30 final size:30
Alignment explanation
Indices: 3080--3167 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
3070 GTGGAGGCCT
* * * * *
3080 TGGTGGGGGAATAGAAAAAGGTGGAGGCCT
1 TGGTGGAGGAATAGGAAAAGGTGGTGGACA
*
3110 TGGTGGGGGAATAGGAAAAGGTGGTGGACA
1 TGGTGGAGGAATAGGAAAAGGTGGTGGACA
* *
3140 TGGTGGAGGAATTGGCAAAGGTGGTGGA
1 TGGTGGAGGAATAGGAAAAGGTGGTGGA
3168 ATAGGAAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.28, C:0.05, G:0.49, T:0.18
Consensus pattern (30 bp):
TGGTGGAGGAATAGGAAAAGGTGGTGGACA
Found at i:3160 original size:60 final size:60
Alignment explanation
Indices: 3032--3400 Score: 271
Period size: 60 Copynumber: 6.4 Consensus size: 60
3022 GGTGTTGGAG
* * * * * * * * *
3032 TTGGAAAAGGAGG-GGATTTGGTGGGGGGATTGGTAAGGGTGGAGGCCTTGGTGGGGGAA
1 TTGGCAAAGGTGGAGGACTTGGTGGGGGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
* ** * * *
3091 TAGAAAAAGGTGGAGGCCTTGGTGGGGGAATAGGAAAAGGTGGTGGACATGGTGGAGGAA
1 TTGGCAAAGGTGGAGGACTTGGTGGGGGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
*
3151 TTGGC-AA-----AGG---TGGT---GGAATAGGAAAAGGTGGTGGACTTGGTGGAGGAA
1 TTGGCAAAGGTGGAGGACTTGGTGGGGGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
* * * * * * *
3199 TTGGCAAGGGTGGTGGCCTTGGTGGAGGAATTGGCAAGGGTGGTGGCCTTGGTGGAGGAA
1 TTGGCAAAGGTGGAGGACTTGGTGGGGGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
* * * * *
3259 TTGGCAAGGGTGGTGGACTTGG-GGGAGGAATTGGCAAGGGTGGTGGACTTGGGGGAGGAA
1 TTGGCAAAGGTGGAGGACTTGGTGGG-GGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
* * * * * * * * * *
3319 TTGGCAAGGGTGGTGAACATGGTGGTGGAATTGGAATAGGTGGTGGACATGGTAGTGGCA
1 TTGGCAAAGGTGGAGGACTTGGTGGGGGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
* *
3379 TTGGAAAAGGTGGAGGAATTGG
1 TTGGCAAAGGTGGAGGACTTGG
3401 CAATGGTGGT
Statistics
Matches: 251, Mismatches: 44, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
48 38 0.15
49 1 0.00
51 4 0.02
54 5 0.02
57 4 0.02
59 14 0.06
60 183 0.73
61 2 0.01
ACGTcount: A:0.24, C:0.06, G:0.49, T:0.21
Consensus pattern (60 bp):
TTGGCAAAGGTGGAGGACTTGGTGGGGGAATTGGAAAAGGTGGTGGACTTGGTGGAGGAA
Found at i:3168 original size:18 final size:18
Alignment explanation
Indices: 3141--3190 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
3131 TGGTGGACAT
* *
3141 GGTGGAGGAATTGGCAAA
1 GGTGGTGGAATTGGAAAA
*
3159 GGTGGTGGAATAGGAAAA
1 GGTGGTGGAATTGGAAAA
*
3177 GGTGGTGGACTTGG
1 GGTGGTGGAATTGG
3191 TGGAGGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.48, T:0.20
Consensus pattern (18 bp):
GGTGGTGGAATTGGAAAA
Found at i:3169 original size:78 final size:78
Alignment explanation
Indices: 3081--3244 Score: 229
Period size: 78 Copynumber: 2.1 Consensus size: 78
3071 TGGAGGCCTT
* * *
3081 GGTGGGGGAATAGAAAAAGGTGGAGGCCTTGGTGGGGGAATAGGAAAAGGTGGTGGACATGGTGG
1 GGTGGTGGAATAGAAAAAGGTGGAGGACTTGGTGGAGGAATAGGAAAAGGTGGTGGACATGGTGG
3146 AGGAATTGGCAAA
66 AGGAATTGGCAAA
* * * * * * *
3159 GGTGGTGGAATAGGAAAAGGTGGTGGACTTGGTGGAGGAATTGGCAAGGGTGGTGGCCTTGGTGG
1 GGTGGTGGAATAGAAAAAGGTGGAGGACTTGGTGGAGGAATAGGAAAAGGTGGTGGACATGGTGG
*
3224 AGGAATTGGCAAG
66 AGGAATTGGCAAA
3237 GGTGGTGG
1 GGTGGTGG
3245 CCTTGGTGGA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 75 1.00
ACGTcount: A:0.26, C:0.05, G:0.49, T:0.20
Consensus pattern (78 bp):
GGTGGTGGAATAGAAAAAGGTGGAGGACTTGGTGGAGGAATAGGAAAAGGTGGTGGACATGGTGG
AGGAATTGGCAAA
Found at i:3193 original size:30 final size:30
Alignment explanation
Indices: 3159--3371 Score: 293
Period size: 30 Copynumber: 7.1 Consensus size: 30
3149 AATTGGCAAA
* * * *
3159 GGTGGTGGAATAGGAAAAGGTGGTGGACTT
1 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
*
3189 GGTGGAGGAATTGGCAAGGGTGGTGGCCTT
1 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
*
3219 GGTGGAGGAATTGGCAAGGGTGGTGGCCTT
1 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
3249 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
1 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
*
3279 GGGGGAGGAATTGGCAAGGGTGGTGGACTT
1 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
* * *
3309 GGGGGAGGAATTGGCAAGGGTGGTGAACAT
1 GGTGGAGGAATTGGCAAGGGTGGTGGACTT
* * *
3339 GGTGGTGGAATTGG-AATAGGTGGTGGACAT
1 GGTGGAGGAATTGGCAA-GGGTGGTGGACTT
3369 GGT
1 GGT
3372 AGTGGCATTG
Statistics
Matches: 169, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
29 2 0.01
30 167 0.99
ACGTcount: A:0.21, C:0.07, G:0.50, T:0.23
Consensus pattern (30 bp):
GGTGGAGGAATTGGCAAGGGTGGTGGACTT
Found at i:3212 original size:48 final size:48
Alignment explanation
Indices: 3111--3214 Score: 181
Period size: 48 Copynumber: 2.2 Consensus size: 48
3101 TGGAGGCCTT
*
3111 GGTGGGGGAATAGGAAAAGGTGGTGGACATGGTGGAGGAATTGGCAAA
1 GGTGGTGGAATAGGAAAAGGTGGTGGACATGGTGGAGGAATTGGCAAA
* *
3159 GGTGGTGGAATAGGAAAAGGTGGTGGACTTGGTGGAGGAATTGGCAAG
1 GGTGGTGGAATAGGAAAAGGTGGTGGACATGGTGGAGGAATTGGCAAA
3207 GGTGGTGG
1 GGTGGTGG
3215 CCTTGGTGGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.27, C:0.04, G:0.50, T:0.19
Consensus pattern (48 bp):
GGTGGTGGAATAGGAAAAGGTGGTGGACATGGTGGAGGAATTGGCAAA
Found at i:3410 original size:48 final size:48
Alignment explanation
Indices: 3339--3442 Score: 138
Period size: 48 Copynumber: 2.2 Consensus size: 48
3329 TGGTGAACAT
* * *
3339 GGTGGTGGAATTGGAATAGGTGGTGGACATGGTAGTGGCATTGGAAAA
1 GGTGGAGGAATTGGAATAGGTGGTGGACATGGCAGTGGCATCGGAAAA
* * *
3387 GGTGGAGGAATTGGCAAT-GGTGGTGGACATGGCGGTGGCATCGGTAAG
1 GGTGGAGGAATTGG-AATAGGTGGTGGACATGGCAGTGGCATCGGAAAA
3435 GGTGGAGG
1 GGTGGAGG
3443 CCTTGGTGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
48 46 0.94
49 3 0.06
ACGTcount: A:0.23, C:0.07, G:0.48, T:0.22
Consensus pattern (48 bp):
GGTGGAGGAATTGGAATAGGTGGTGGACATGGCAGTGGCATCGGAAAA
Found at i:3463 original size:78 final size:78
Alignment explanation
Indices: 3312--3466 Score: 186
Period size: 78 Copynumber: 2.0 Consensus size: 78
3302 TGGACTTGGG
* * *
3312 GGAGGAATTGGCAAGGGTGGTGAACATGGTGGTGGAATTGGAATAGGTGGTGGACATGGTAGTGG
1 GGAGGAATTGGCAAGGGTGGTGAACATGGCGGTGGAATCGGAATAGGTGGAGGACATGGTAGTGG
* *
3377 CATTGGAAAAGGT
66 AATCGGAAAAGGT
* * * * * * *
3390 GGAGGAATTGGCAATGGTGGTGGACATGGCGGTGGCATCGGTAA-GGGTGGAGGCCTTGGTGGTG
1 GGAGGAATTGGCAAGGGTGGTGAACATGGCGGTGGAATCGG-AATAGGTGGAGGACATGGTAGTG
3454 GAATCGGAAAAGG
65 GAATCGGAAAAGG
3467 AGGTGAGATT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
78 62 0.97
79 2 0.03
ACGTcount: A:0.25, C:0.08, G:0.46, T:0.21
Consensus pattern (78 bp):
GGAGGAATTGGCAAGGGTGGTGAACATGGCGGTGGAATCGGAATAGGTGGAGGACATGGTAGTGG
AATCGGAAAAGGT
Found at i:3484 original size:30 final size:29
Alignment explanation
Indices: 3445--3544 Score: 92
Period size: 30 Copynumber: 3.3 Consensus size: 29
3435 GGTGGAGGCC
*
3445 TTGGTGGTGGAATCGGAAAAGGAGGTGAGA
1 TTGGAGGTGGAATCGGAAAAGGAGGTG-GA
* * * *
3475 TTGGAGGTGGATTTGGAAAAGAAGGTGGGC
1 TTGGAGGTGGAATCGGAAAAGGAGGT-GGA
** * *
3505 TAAGAGGTGGAATCGGAAAGGGTGGTGGCA
1 TTGGAGGTGGAATCGGAAAAGGAGGTGG-A
3535 TTGGAGGTGG
1 TTGGAGGTGG
3545 GATTAGGAAA
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
29 2 0.04
30 50 0.94
31 1 0.02
ACGTcount: A:0.27, C:0.04, G:0.48, T:0.21
Consensus pattern (29 bp):
TTGGAGGTGGAATCGGAAAAGGAGGTGGA
Found at i:5317 original size:44 final size:44
Alignment explanation
Indices: 5267--5403 Score: 202
Period size: 44 Copynumber: 3.1 Consensus size: 44
5257 ATACGAATAT
* * *
5267 TGAATACGACCATGTCGGATACATACACATCCCACACTCGAACC
1 TGAATACGCCCTTGTCGGATACATACACATCCGACACTCGAACC
5311 TGAATACGCCCTTGTCGGATACATACACATCCGACACTCGAACC
1 TGAATACGCCCTTGTCGGATACATACACATCCGACACTCGAACC
* * * *
5355 AGAATACTCCCTTGTTGGATACATACACATACGACACTCGAACC
1 TGAATACGCCCTTGTCGGATACATACACATCCGACACTCGAACC
*
5399 CGAAT
1 TGAAT
5404 TCGCATAACA
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 85 1.00
ACGTcount: A:0.33, C:0.32, G:0.15, T:0.20
Consensus pattern (44 bp):
TGAATACGCCCTTGTCGGATACATACACATCCGACACTCGAACC
Found at i:12526 original size:42 final size:42
Alignment explanation
Indices: 12479--12561 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
12469 TATACTGACC
12479 CTATGTCCTAAACCATCTGAAACAGTTCATTTATGTATCTAG
1 CTATGTCCTAAACCATCTGAAACAGTTCATTTATGTATCTAG
12521 CTATGTCCTAAACCATCTGAAACAGTTCATTTATGTATCTA
1 CTATGTCCTAAACCATCTGAAACAGTTCATTTATGTATCTA
12562 ACGACGATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (42 bp):
CTATGTCCTAAACCATCTGAAACAGTTCATTTATGTATCTAG
Found at i:20702 original size:18 final size:18
Alignment explanation
Indices: 20676--20712 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20666 CAAAAAAATA
*
20676 TTAGTATTTAATAATTTT
1 TTAGAATTTAATAATTTT
*
20694 TTAGAATTTATTAATTTT
1 TTAGAATTTAATAATTTT
20712 T
1 T
20713 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TTAGAATTTAATAATTTT
Found at i:25412 original size:28 final size:27
Alignment explanation
Indices: 25325--25412 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 27
25315 GAATTTCTTA
** *
25325 AATTGATTTTTAAATTTTTGAATACTTT
1 AATTGATTTTTAAA-TTTTGACCATTTT
* * * *
25353 AATTTTATATTTAAATTATGACC-TTCTG
1 AA-TTGATTTTTAAATTTTGACCATT-TT
25381 AATTGATTTTTAAACTTTTGACCATTTT
1 AATTGATTTTTAAA-TTTTGACCATTTT
25409 AATT
1 AATT
25413 TCATCTTAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
27 11 0.24
28 22 0.49
29 12 0.27
ACGTcount: A:0.32, C:0.08, G:0.07, T:0.53
Consensus pattern (27 bp):
AATTGATTTTTAAATTTTGACCATTTT
Found at i:26376 original size:60 final size:60
Alignment explanation
Indices: 26289--26416 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
26279 GCATCACATG
* * *
26289 CCCTCAAAGCATGACTCTCATTTTAAATCGA-TCATTAAACTTTTAAATATTTAAATTTCAT
1 CCCT-AAAGCATGACTATCATTCTAAAT-GATTCATCAAACTTTTAAATATTTAAATTTCAT
* * * * *
26350 CCCTAAATCATGACTATCATTCTAAATTATTCCTCAAACTTTTGAATATTTCAATTTCAT
1 CCCTAAAGCATGACTATCATTCTAAATGATTCATCAAACTTTTAAATATTTAAATTTCAT
26410 CCCTAAA
1 CCCTAAA
26417 CTATGAACTT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.02
60 53 0.91
61 4 0.07
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (60 bp):
CCCTAAAGCATGACTATCATTCTAAATGATTCATCAAACTTTTAAATATTTAAATTTCAT
Found at i:49443 original size:26 final size:25
Alignment explanation
Indices: 49408--49462 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
49398 TAATTTTAAA
*
49408 AAAATTTATATAAATTTTAAAAAAT
1 AAAATTTATATAAATTTTAAAAAAG
* *
49433 AAAATTATATATATATTTTTAAAAAG
1 AAAATT-TATATAAATTTTAAAAAAG
49459 AAAA
1 AAAA
49463 CACAAATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AAAATTTATATAAATTTTAAAAAAG
Found at i:50352 original size:17 final size:17
Alignment explanation
Indices: 50330--50362 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
50320 GGTTAGGGTT
*
50330 AGGATTTTGAGGTTTTA
1 AGGATTTTGAGCTTTTA
50347 AGGATTTTGAGCTTTT
1 AGGATTTTGAGCTTTT
50363 TTGTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.27, T:0.48
Consensus pattern (17 bp):
AGGATTTTGAGCTTTTA
Found at i:55550 original size:22 final size:22
Alignment explanation
Indices: 55510--55551 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
55500 GACGGTTATC
**
55510 TTAACCCCTAAAATTTTAAACT
1 TTAACCCCTAAAACATTAAACT
*
55532 TTAACCCCTGAAACATTAAA
1 TTAACCCCTAAAACATTAAA
55552 GAAAATTACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.24, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAACCCCTAAAACATTAAACT
Found at i:57481 original size:30 final size:30
Alignment explanation
Indices: 57442--57507 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
57432 TTAGAAAATC
57442 ATTTGGAAAATCTTAAAATCCATTTAACTTA
1 ATTT-GAAAATCTTAAAATCCATTTAACTTA
57473 ATTTGAAAATCTTAAAATCCATTTAACTTA
1 ATTTGAAAATCTTAAAATCCATTTAACTTA
57503 ATTTG
1 ATTTG
57508 TTATATCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 31 0.89
31 4 0.11
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (30 bp):
ATTTGAAAATCTTAAAATCCATTTAACTTA
Found at i:59970 original size:20 final size:20
Alignment explanation
Indices: 59895--59978 Score: 71
Period size: 20 Copynumber: 4.0 Consensus size: 20
59885 AACAGAACCC
*
59895 CAGGGGGGTATCGATTCCC-
1 CAGGGGGGAATCGATTCCCT
* *
59914 CTGTGGGGGAATCGGTTCCCCTT
1 CAG-GGGGGAATCGATT-CCC-T
* *
59937 CAAAGGGGGAATCGGTTCCCT
1 C-AGGGGGGAATCGATTCCCT
*
59958 CAGGGGGGGATCGATTCCCT
1 CAGGGGGGAATCGATTCCCT
59978 C
1 C
59979 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
19 2 0.04
20 28 0.54
21 5 0.10
22 3 0.06
23 14 0.27
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (20 bp):
CAGGGGGGAATCGATTCCCT
Done.