Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007740.1 Hibiscus syriacus cultivar Beakdansim tig00110001_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: 287134
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:254912 original size:14 final size:13
Alignment explanation
Indices: 254893--254941 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 13
254883 ATTTTTAAAT
254893 TTTTTATAATTTAA
1 TTTTTAT-ATTTAA
* *
254907 TTTTTATTTTTAG
1 TTTTTATATTTAA
*
254920 TATTTTATATTTAT
1 T-TTTTATATTTAA
254934 TTTTTATA
1 TTTTTATA
254942 ATTTTTATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TTTTTATATTTAA
Found at i:254946 original size:21 final size:21
Alignment explanation
Indices: 254891--254946 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
254881 GTATTTTTAA
* *
254891 ATTTTTTATAATTTAATTTTT
1 ATTTTTTATAATTTTATATTT
254912 A-TTTTTAGT-ATTTTATATTT
1 ATTTTTTA-TAATTTTATATTT
254932 ATTTTTTATAATTTT
1 ATTTTTTATAATTTT
254947 TATGGTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTTTATAATTTTATATTT
Found at i:255541 original size:31 final size:31
Alignment explanation
Indices: 255505--255564 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
255495 AACTTAAAAG
* *
255505 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
255536 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
255565 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:256086 original size:21 final size:19
Alignment explanation
Indices: 256024--256091 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 19
256014 TATTTAAACT
*
256024 TATATCAAAATAATTAAAATA
1 TATAT-AAAATAATT-TAATA
*
256045 AATATAAAAT--TTTAATAA
1 TATATAAAATAATTTAAT-A
256063 TATATAAAATAATTT-ATA
1 TATATAAAATAATTTAATA
256081 TGATATAAAAT
1 T-ATATAAAAT
256092 TAAATATCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
17 3 0.08
18 14 0.35
19 11 0.28
20 8 0.20
21 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (19 bp):
TATATAAAATAATTTAATA
Found at i:256124 original size:14 final size:14
Alignment explanation
Indices: 256107--256155 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
256097 ATCTATAATA
256107 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
256121 TAATATT---TAAT
1 TAATATTAAAAAAT
*
256132 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
256145 TAATATTAAAA
1 TAATATTAAAA
256156 TTAAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 6 0.22
13 6 0.22
14 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:256125 original size:28 final size:24
Alignment explanation
Indices: 256087--256151 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 24
256077 TATATGATAT
256087 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATAT-T-TAAT-TAAT-TTAA
*
256116 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
256140 AAAATTAATATT
1 AAAATTAATATT
256152 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 16 0.46
25 3 0.09
26 4 0.11
27 1 0.03
28 5 0.14
29 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:256197 original size:12 final size:12
Alignment explanation
Indices: 256140--256200 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
256130 ATTTATTTAA
256140 AAAATT-AATATT
1 AAAATTAAATA-T
256152 AAAATTAAA-AT
1 AAAATTAAATAT
*
256163 CAAA-TATAATAT
1 AAAATTA-AATAT
*
256175 AATA-T-AATAT
1 AAAATTAAATAT
256185 AAAATTAAATAT
1 AAAATTAAATAT
256197 AAAA
1 AAAA
256201 CCTCTTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
10 10 0.25
11 7 0.17
12 21 0.52
13 2 0.05
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:257937 original size:4 final size:4
Alignment explanation
Indices: 257928--257958 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
257918 GTTAGATGAA
257928 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
257959 AGAGGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:258221 original size:20 final size:16
Alignment explanation
Indices: 258181--258215 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
258171 ATTGAGAAAT
*
258181 AAAATAAAAATAATAA
1 AAAACAAAAATAATAA
258197 AAAACCAAAAATAATAA
1 AAAA-CAAAAATAATAA
258214 AA
1 AA
258216 CAAAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (16 bp):
AAAACAAAAATAATAA
Found at i:258227 original size:105 final size:105
Alignment explanation
Indices: 258104--258312 Score: 391
Period size: 105 Copynumber: 2.0 Consensus size: 105
258094 GCAATAATAA
* * *
258104 AATAAAAGAAAACAAAACAAAAGAAAAGATTAAAAAAAGAAAAAAATTTATGTAAAAATAGTAAA
1 AATAAAACAAAACAAAACAAAACAAAAGATTAAAAAAAGAAAAAAAATTATGTAAAAATAGTAAA
258169 ATATTGAGAAATAAAATAAAAATAATAAAAAACCAAAAAT
66 ATATTGAGAAATAAAATAAAAATAATAAAAAACCAAAAAT
258209 AATAAAACAAAACAAAACAAAACAAAAGATTAAAAAAAGAAAAAAAATTATGTAAAAATAGTAAA
1 AATAAAACAAAACAAAACAAAACAAAAGATTAAAAAAAGAAAAAAAATTATGTAAAAATAGTAAA
258274 ATATTGAGAAATAAAATAAAAATAATAAAAAACCAAAAA
66 ATATTGAGAAATAAAATAAAAATAATAAAAAACCAAAAA
258313 AAAAGATAAA
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (105 bp):
AATAAAACAAAACAAAACAAAACAAAAGATTAAAAAAAGAAAAAAAATTATGTAAAAATAGTAAA
ATATTGAGAAATAAAATAAAAATAATAAAAAACCAAAAAT
Found at i:259366 original size:3 final size:3
Alignment explanation
Indices: 259358--259396 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
259348 AAAAATATAT
*
259358 TAA TAA TAA TAA AAA TAA TAAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA
259397 TTATTATTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:259381 original size:19 final size:19
Alignment explanation
Indices: 259348--259396 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
259338 GAAAAAATTA
*
259348 AAAAATATATTAATAATAAT
1 AAAAATA-ATAAATAATAAT
259368 AAAAATAATAAATAATAAT
1 AAAAATAATAAATAATAAT
*
259387 AATAATAATA
1 AAAAATAATA
259397 TTATTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 20 0.74
20 7 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATAATAAATAATAAT
Found at i:259777 original size:84 final size:84
Alignment explanation
Indices: 259625--259809 Score: 235
Period size: 84 Copynumber: 2.2 Consensus size: 84
259615 AGCTGAATGA
**
259625 AATCGAACTCGTTTGGTCTTTGGTTGGCAAATAACCATTATTGACTTAAGCTATGCTGCAAATAA
1 AATCGAACTCG-AAGGTCTTTGGTTGGCAAATAACCATTATTGACTTAAGCTATGCTGCAAATAA
*
259690 TGTGCCTTGGATCTGAGCGT
65 TGTGCCTTGGAGCTGAGCGT
* * * * * * * * * *
259710 AGTCGAACTCGAAGGTCTTTGGTTGGCAAATAGCCTTTCTTGCCTTGAGTTATGTTGTAAATGAT
1 AATCGAACTCGAAGGTCTTTGGTTGGCAAATAACCATTATTGACTTAAGCTATGCTGCAAATAAT
*
259775 GTGCCTTGGAGCTGAGTGT
66 GTGCCTTGGAGCTGAGCGT
259794 AATCGAACTCGAAGGT
1 AATCGAACTCGAAGGT
259810 TTGGTATTTC
Statistics
Matches: 85, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
84 75 0.88
85 10 0.12
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (84 bp):
AATCGAACTCGAAGGTCTTTGGTTGGCAAATAACCATTATTGACTTAAGCTATGCTGCAAATAAT
GTGCCTTGGAGCTGAGCGT
Found at i:259973 original size:37 final size:36
Alignment explanation
Indices: 259923--260052 Score: 147
Period size: 37 Copynumber: 3.6 Consensus size: 36
259913 GGTTTTCAAG
*
259923 AGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCGAA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC-AA
* * ** *
259960 AGAAACTATCTCAAG-GAAGACGAAA-TTTTTTTCAA
1 AGAAACTGTCTCAAGAG-AGACAAAACTTAGTTCCAA
*
259995 GGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAA
1 AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCC-AA
*
260032 AGAAACTGTCTCAAGGGAGAC
1 AGAAACTGTCTCAAGAGAGAC
260053 GAAATTTGTT
Statistics
Matches: 75, Mismatches: 14, Indels: 8
0.77 0.14 0.08
Matches are distributed among these distances:
35 22 0.29
36 12 0.16
37 41 0.55
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (36 bp):
AGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA
Found at i:260034 original size:72 final size:72
Alignment explanation
Indices: 259915--260070 Score: 258
Period size: 72 Copynumber: 2.2 Consensus size: 72
259905 CAAAGATTGG
* *
259915 TTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTAGTTCCGAAAGAAACTATCTCAAGGAAGA
1 TTTTCAAG-GAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGAAGA
259980 CGAAATTT
65 CGAAATTT
* *
259988 TTTTCAAGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAC
1 TTTTCAAGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGAAGAC
260053 GAAATTT
66 GAAATTT
*
260060 GTTTCAAGGAA
1 TTTTCAAGGAA
260071 CACATATTCA
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
72 70 0.90
73 8 0.10
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.24
Consensus pattern (72 bp):
TTTTCAAGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGAAGAC
GAAATTT
Found at i:260117 original size:102 final size:100
Alignment explanation
Indices: 259984--260165 Score: 276
Period size: 101 Copynumber: 1.8 Consensus size: 100
259974 GGAAGACGAA
*
259984 ATTTTTTTCAAGGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 ATTTTTTTCAAGGAAACTGTCTCAAGAGAGACAAAA-TTAGTTCCAAAAGAAACTGTCTCAAGAG
*
260049 AGACGAAA-TTTGTTTCAAGGAACACATATTCAAAG
65 AGACAAAACTTTGTTTCAAGGAACACATATTCAAAG
* * **
260084 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
1 ATTTT-TTTCAA-GGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGA
260149 GAGACAAAACTTTGTTT
64 GAGACAAAACTTTGTTT
260166 TGAGTAAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
100 5 0.07
101 36 0.49
102 32 0.44
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (100 bp):
ATTTTTTTCAAGGAAACTGTCTCAAGAGAGACAAAATTAGTTCCAAAAGAAACTGTCTCAAGAGA
GACAAAACTTTGTTTCAAGGAACACATATTCAAAG
Found at i:260133 original size:36 final size:37
Alignment explanation
Indices: 260086--260165 Score: 153
Period size: 36 Copynumber: 2.2 Consensus size: 37
260076 ATTCAAAGAT
260086 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
260122 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
260159 TTTGTTT
1 TTTGTTT
260166 TGAGTAAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 36 0.84
37 7 0.16
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (37 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
Found at i:260524 original size:116 final size:115
Alignment explanation
Indices: 260329--260667 Score: 428
Period size: 125 Copynumber: 2.8 Consensus size: 115
260319 GCTTGTGGGA
*
260329 ACGATTCCCTTCGTCGTGAAGTTGAAACCATGGATGGCCCATTCGTTGTGAAGTTGAGCCTTGAA
1 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGA-CCTTGAA
*
260394 TTGGATGTCATTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTAAGC
65 TTGGATATCATTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTAAGC
* * * *
260445 ACGATTCCCTTCGGCGTGAAGTTGAAACCGTTGATGGCCCGTTCGTTGTGAAGTTGATCCTAGAA
1 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGA-CCTTGAA
* * *
260510 TTGGATATCCTTCGTCATGAAGTTGAAATCCAAATATTTTGATGAATGTTGCTGGTGAGC
65 TTGGATATCATTCGTCGTGAAGTTGAAATCC----A-----ATGAATGTTGCTGGTAAGC
* *
260570 ACGATTCCCTTCGTCGTGAAGTTGAAGCCGTGGATGGCCCATTCGTTGTGAAGTGTAGA-CTTGG
1 ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGT-T-GACCTTGA
* * *
260634 CTTGAATATCATTCATCGTGAAGTTGAAATCCAA
64 ATTGGATATCATTCGTCGTGAAGTTGAAATCCAA
260668 GCCTGTATTG
Statistics
Matches: 191, Mismatches: 21, Indels: 22
0.82 0.09 0.09
Matches are distributed among these distances:
116 88 0.46
120 1 0.01
121 1 0.01
125 98 0.51
126 1 0.01
127 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (115 bp):
ACGATTCCCTTCGTCGTGAAGTTGAAACCGTGGATGGCCCATTCGTTGTGAAGTTGACCTTGAAT
TGGATATCATTCGTCGTGAAGTTGAAATCCAATGAATGTTGCTGGTAAGC
Found at i:262135 original size:95 final size:96
Alignment explanation
Indices: 261925--262168 Score: 330
Period size: 95 Copynumber: 2.5 Consensus size: 96
261915 GGCTAGCTGA
* * *
261925 ATCCATAAAGCCGGGGCGTTTAACCAATTACTCTAGAGGGACAGCTCAATATCATTGTATATATA
1 ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACTC-A-AGCATTGTATATATA
*
261990 TTATAATCACCTTTATTAGGCTAGCTGAATATT
64 TTATAATCACCTTTATCAGGCTAGCTGAATATT
*** *
262023 ATCCATAAAGTTAGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGC-TT-TATTATATAT
1 ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCATTGTA-TATATAT
* *
262086 TATAATCGCCTTTATCAGGCTAGCTGAATCTT
65 TATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
262118 ATCCGTATAGACGGGGCGTTTAACCAATTTCTCTAGAGGGACAACTCAAGC
1 ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGC
262169 GGATTCAACT
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
94 2 0.02
95 83 0.64
96 2 0.02
97 1 0.01
98 42 0.32
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (96 bp):
ATCCATAAAGACGGGGCGTTTAACCAATTACTCTAGAGGGACAACTCAAGCATTGTATATATATT
ATAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:264734 original size:23 final size:22
Alignment explanation
Indices: 264706--264761 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
264696 AATGTTAGAT
*
264706 GAAAAATAAATAAAAGAGGAAAAA
1 GAAAAA-AAACAAAAGA-GAAAAA
*
264730 GAAAAAAAACAAATGAGAAAAA
1 GAAAAAAAACAAAAGAGAAAAA
*
264752 TAATAAAAAA
1 GAA-AAAAAA
264762 GATAAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (22 bp):
GAAAAAAAACAAAAGAGAAAAA
Found at i:266378 original size:60 final size:60
Alignment explanation
Indices: 266305--266417 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
266295 CCATAGGATA
* *
266305 TTGCTTTGTTGAGT-CTTCTAACTATTAAAAGTTGTAAAATGGTC-CCCTAACTACAGGACT
1 TTGCTTTGTTGAGTCCATC-AACTATTAAAAGTTATAAAATGGTCACCC-AACTACAGGACT
*
266365 TTGCTTTGTTGAGTCCATCGACTATTAAAAGTTATAAAATGGTCACCCAACTA
1 TTGCTTTGTTGAGTCCATCAACTATTAAAAGTTATAAAATGGTCACCCAACTA
266418 TTCATTTGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
60 42 0.88
61 6 0.12
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (60 bp):
TTGCTTTGTTGAGTCCATCAACTATTAAAAGTTATAAAATGGTCACCCAACTACAGGACT
Found at i:266760 original size:60 final size:59
Alignment explanation
Indices: 266615--266752 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
266605 AACAAAATGA
* * * * *
266615 ATAATCGAGTGACCATTTTATAACTTTTGTAGTCGAGTGACTCAACAAAGCAACATTCT
1 ATAATCGAGGGATCATTTTATAACTTTTATAGTCGAGTGACTCAACAAAACAACATCCT
* * * * *
266674 ATACTCGGGGGATCATTTTGTAACTTTTAATAGTCGAAG-GACTCAACAAAATAATATCCT
1 ATAATCGAGGGATCATTTTATAACTTTT-ATAGTCG-AGTGACTCAACAAAACAACATCCT
266734 ATAATCGAGGGATCATTTT
1 ATAATCGAGGGATCATTTT
266753 TTTACTTTAC
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 23 0.35
60 40 0.62
61 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (59 bp):
ATAATCGAGGGATCATTTTATAACTTTTATAGTCGAGTGACTCAACAAAACAACATCCT
Found at i:279682 original size:8 final size:8
Alignment explanation
Indices: 279669--279696 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
279659 GGATTCTCCC
279669 ATATGTAT
1 ATATGTAT
279677 ATATGTAT
1 ATATGTAT
279685 ATATGTAT
1 ATATGTAT
279693 ATAT
1 ATAT
279697 CTTCTTTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:284242 original size:55 final size:55
Alignment explanation
Indices: 284158--284538 Score: 514
Period size: 55 Copynumber: 6.9 Consensus size: 55
284148 AGATTTCCCA
* * *
284158 ACGATT-ATTGAAGATTGATCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGA-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
284213 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
284268 ACGACTGTTGAAGATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
284323 ACGATTGATGAAGATTATTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
284378 ACGGTTGATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * * * * *
284433 AAGAGTTGTTGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAACAAAC
1 ACGA-TTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
284489 ACGATTGATGAAGATTGTTCGAGT-TCTATACTCCCTGAAGAAAGAGGGAG
1 ACGATTGATGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAG
284539 TGAACTCGTT
Statistics
Matches: 287, Mismatches: 36, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
54 1 0.00
55 236 0.82
56 50 0.17
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.28
Consensus pattern (55 bp):
ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Done.