Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001009.1 Hibiscus syriacus cultivar Beakdansim tig00002013_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: 165066
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:888 original size:65 final size:65
Alignment explanation
Indices: 807--935 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
797 TGGCTCACGA
* *
807 AAAGAAAAAACCACTCGATGATCAGGTTACACCGGTAATTGATAATAGCAATGACAGGAGCAACG
1 AAAGAAAAAACCACTCGATGATCAGGTTACACCGGTAATCGATAATAGCAATGACAAGAGCAACG
872 AAAG-AAAAACCAACTCGATGATCAGGTTACACCGGTAATCGATAATAGCAATGACAAGAGCAAC
1 AAAGAAAAAACC-ACTCGATGATCAGGTTACACCGGTAATCGATAATAGCAATGACAAGAGCAAC
936 AACGTTCAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 7 0.11
65 54 0.89
ACGTcount: A:0.44, C:0.19, G:0.20, T:0.16
Consensus pattern (65 bp):
AAAGAAAAAACCACTCGATGATCAGGTTACACCGGTAATCGATAATAGCAATGACAAGAGCAACG
Found at i:1438 original size:180 final size:173
Alignment explanation
Indices: 1045--1482 Score: 573
Period size: 180 Copynumber: 2.5 Consensus size: 173
1035 CTTAAGTACG
* * * * * * *
1045 CAAGAAAACAGGGGGAATACTGAAGACAGTCAGTTGGTTGAGTCCAAGAAGGATAAGAAGCAATT
1 CAAGAAAACAAGGGGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATT
* * *
1110 GGA-TCTG-AGCTGGACAGACAAACACAGTGATGGTGAGAATTTAGCCGAGAGGATAGGGGACTC
66 GGATTCTGAAGGTGGACAGACAAACACAATGATGATGAGAATTTAGCCGAGAGGATAGGGGACTC
* * * *
1173 AAATGTGAATAGGGCTAAAGATGGTGGCACTGGCAACTTCACA
131 AAACGTGAATAGGACTAAAGATGGTGGCACTGACAACTACACA
*
1216 CAAG-AAACAAGGGAAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATT
1 CAAGAAAACAAGGGGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATT
*
1280 GGATTCTGAAGGTGGACAGACAAACACAATGGTGATGAGAATTTA-CTCAAGGATGCAAGGATAG
66 GGATTCTGAAGGTGGACAGACAAACACAATGATGATGAGAATTTAGC-C---GA-G--AGGATAG
* * *
1344 GGGATTCGAACGTGAGT-GTGACTAAAGATGGTGGCACTGACAACTCAACACA
124 GGGACTCAAACGTGAATAG-GACTAAAGATGGTGGCACTGACAACT--ACACA
1396 CAAGAAAACAAGGGGAACACTGAAG-GAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATT
1 CAAGAAAACAAGGGGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATT
1460 GGATTCTGAAGGTGGACAGACAA
66 GGATTCTGAAGGTGGACAGACAA
1483 CAACAGTGGC
Statistics
Matches: 234, Mismatches: 20, Indels: 17
0.86 0.07 0.06
Matches are distributed among these distances:
170 55 0.24
171 9 0.04
172 33 0.14
175 2 0.01
176 1 0.00
177 1 0.00
178 44 0.19
180 70 0.30
181 19 0.08
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.17
Consensus pattern (173 bp):
CAAGAAAACAAGGGGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATT
GGATTCTGAAGGTGGACAGACAAACACAATGATGATGAGAATTTAGCCGAGAGGATAGGGGACTC
AAACGTGAATAGGACTAAAGATGGTGGCACTGACAACTACACA
Found at i:1639 original size:168 final size:176
Alignment explanation
Indices: 1058--1657 Score: 516
Period size: 180 Copynumber: 3.5 Consensus size: 176
1048 GAAAACAGGG
* * * * * * *
1058 GGAATACTGAAGACAGTCAGTTGGTTGAGTCCAAGAAGGATAAGAAGCAATTGGA-TCTG-AGCT
1 GGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAGGT
** * *
1121 GGACAGACAAACAC-AGTGATGGTGAGAATTTAGC-C---G-AG--AGGATAGGGGACTCAAATG
66 GGACAGACAAACACAAG-G-TGACGAGAATTTA-CTCAAGGAAGCAAGGATAAGGGACTCAAACG
* ** * * * *
1178 TGAATAGGGCTAAAGATGGTGGCACTGGCAACT--TCACACAAG-AAACAA
128 TGAGTCTGACTAAAGATGATGGCACT--AAACTAAACACACAAGAAAACAA
1226 GGGAAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAG
1 -GG-AACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAG
* * * * *
1291 GTGGACAGACAAACACAATGGTGATGAGAATTTACTCAAGGATGCAAGGATAGGGGATTCGAACG
64 GTGGACAGACAAACACAA-GGTGACGAGAATTTACTCAAGGAAGCAAGGATAAGGGACTCAAACG
* * *
1356 TGAGTGTGACTAAAGATGGTGGCACTGACAACTCAACACACAAGAAAACAA
128 TGAGTCTGACTAAAGATGATGGCACT-A-AACTAAACACACAAGAAAACAA
1407 GGGGAACACTGAAG-GAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAG
1 --GGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAG
*
1471 GTGGACAGAC-AACA-ACA-GTGGCGAGAATTTA-TCCAAGGAAG-ACAGGA-AAGGGACTCAAA
64 GTGGACAGACAAACACA-AGGTGACGAGAATTTACT-CAAGGAAGCA-AGGATAAGGGACTCAAA
* *
1530 TGTGAGTCT-AGCT-AAGATGATGGCACT-AACTTAAATACAC-AGAAAACAA
126 CGTGAGTCTGA-CTAAAGATGATGGCACTAAAC-TAAACACACAAGAAAACAA
* * * * * * *
1579 -GATCACTGAAGAGAGTAA-TTGGACGAGTCTAAG-AAGATGAGAAGCAGTTGGATACTGAAGGT
1 GGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAGGT
*
1641 GGACAGATAAACGACAA
66 GGACAGACAAAC-ACAA
1658 TAGTGAAAAA
Statistics
Matches: 368, Mismatches: 37, Indels: 51
0.81 0.08 0.11
Matches are distributed among these distances:
168 33 0.09
169 27 0.07
170 55 0.15
171 6 0.02
172 42 0.11
173 9 0.02
174 1 0.00
175 15 0.04
176 21 0.06
177 24 0.07
178 43 0.12
179 5 0.01
180 68 0.18
181 16 0.04
182 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.29, T:0.17
Consensus pattern (176 bp):
GGAACACTGAAGAGAGTAAGTCGGATGAGTCCAAGAAAGATAAGAAGCAATTGGATTCTGAAGGT
GGACAGACAAACACAAGGTGACGAGAATTTACTCAAGGAAGCAAGGATAAGGGACTCAAACGTGA
GTCTGACTAAAGATGATGGCACTAAACTAAACACACAAGAAAACAA
Found at i:4057 original size:17 final size:17
Alignment explanation
Indices: 4035--4068 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4025 GATCCACTAA
4035 AAGTTCCAATTTTTTTT
1 AAGTTCCAATTTTTTTT
**
4052 AAGTTCTGATTTTTTTT
1 AAGTTCCAATTTTTTTT
4069 TTTGTTCCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (17 bp):
AAGTTCCAATTTTTTTT
Found at i:45181 original size:29 final size:29
Alignment explanation
Indices: 45117--45184 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
45107 TATGCTTGTT
* * *
45117 TTCCAGTTTAGTGGCTAAAGTTTATTTTA
1 TTCCAGTTTGGTGCCTAAAGTTTATTTCA
* *
45146 TTTCAGTTTGGTGCCTAAAGTTTATTTCG
1 TTCCAGTTTGGTGCCTAAAGTTTATTTCA
45175 TTCCAGTTTG
1 TTCCAGTTTG
45185 ATGTCAAACG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (29 bp):
TTCCAGTTTGGTGCCTAAAGTTTATTTCA
Found at i:45843 original size:29 final size:30
Alignment explanation
Indices: 45789--45849 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
45779 CATTTTAAAT
*
45789 AACAAAATAAAACATTAAACACTAAACTAA
1 AACAAAATAAAACATTAAACAATAAACTAA
* *
45819 AACAAAAT-AAACATTAGATAATAAACTAA
1 AACAAAATAAAACATTAAACAATAAACTAA
45848 AA
1 AA
45850 AATAGGTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.67, C:0.13, G:0.02, T:0.18
Consensus pattern (30 bp):
AACAAAATAAAACATTAAACAATAAACTAA
Found at i:55808 original size:13 final size:13
Alignment explanation
Indices: 55790--55815 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55780 GTGATTACAG
55790 TAAAGAGCACTGA
1 TAAAGAGCACTGA
55803 TAAAGAGCACTGA
1 TAAAGAGCACTGA
55816 GAGCCAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (13 bp):
TAAAGAGCACTGA
Found at i:73257 original size:32 final size:32
Alignment explanation
Indices: 73216--73282 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
73206 AGGGTTTCAC
**
73216 TAAGAACATTTATATTTGTAATGTCAACAGAT
1 TAAGAACATTTATATTTACAATGTCAACAGAT
73248 TAAGAACATTTATATTTACAATGTCAACAGAT
1 TAAGAACATTTATATTTACAATGTCAACAGAT
73280 TAA
1 TAA
73283 TACCATAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (32 bp):
TAAGAACATTTATATTTACAATGTCAACAGAT
Found at i:78602 original size:27 final size:27
Alignment explanation
Indices: 78565--78634 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
78555 TGACAATCAT
* *
78565 GTTTTTCAATCAAATTTAATCATCAGA
1 GTTTCTCAATCAAATATAATCATCAGA
78592 GTTTCTCAATCAAATATAATCATCAGA
1 GTTTCTCAATCAAATATAATCATCAGA
78619 GCTTTC-CAATCAAATA
1 G-TTTCTCAATCAAATA
78635 AAGGGGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.36
Consensus pattern (27 bp):
GTTTCTCAATCAAATATAATCATCAGA
Found at i:82086 original size:12 final size:11
Alignment explanation
Indices: 82064--82096 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
82054 GCCTGACAAT
82064 TAAGAGAAAAA
1 TAAGAGAAAAA
82075 TAAGAGGAAAAA
1 TAAGA-GAAAAA
82087 TAAGA-AAAAA
1 TAAGAGAAAAA
82097 GTTGCCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 5 0.24
11 5 0.24
12 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (11 bp):
TAAGAGAAAAA
Found at i:82704 original size:20 final size:20
Alignment explanation
Indices: 82679--82716 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
82669 TTTGGTTCAC
*
82679 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAGTG
82699 GGAATAAAAGATTACCAG
1 GGAATAAAAGATTACCAG
82717 GGAATAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.21
Consensus pattern (20 bp):
GGAATAAAAGATTACCAGTG
Found at i:82719 original size:18 final size:19
Alignment explanation
Indices: 82679--82722 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
82669 TTTGGTTCAC
*
82679 GGAATATAAGATTACCAGTG
1 GGAATAAAAGATTACCAG-G
82699 GGAATAAAAGATTACCA-G
1 GGAATAAAAGATTACCAGG
82717 GGAATA
1 GGAATA
82723 GGATTACTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.45, C:0.09, G:0.25, T:0.20
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGG
Found at i:87581 original size:16 final size:16
Alignment explanation
Indices: 87562--87598 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
87552 AGAGGGATTT
87562 AAATCAGACCGGCCGA
1 AAATCAGACCGGCCGA
*
87578 AAATTCGGACCGGCCGA
1 AAA-TCAGACCGGCCGA
87595 AAAT
1 AAAT
87599 ATGAGAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.38, C:0.27, G:0.24, T:0.11
Consensus pattern (16 bp):
AAATCAGACCGGCCGA
Found at i:87774 original size:2 final size:2
Alignment explanation
Indices: 87767--87807 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
87757 AGCCCAATTT
87767 TA TA TA TA TA TA TA TA T- TA TA -A TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87806 TA
1 TA
87808 ACTGTATCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 33 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:88826 original size:17 final size:17
Alignment explanation
Indices: 88804--88838 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
88794 TTTAACCCGC
88804 GACCCGTGCGGGCTTCG
1 GACCCGTGCGGGCTTCG
88821 GACCCGTGCGGGCTTCG
1 GACCCGTGCGGGCTTCG
88838 G
1 G
88839 GCCTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.06, C:0.34, G:0.43, T:0.17
Consensus pattern (17 bp):
GACCCGTGCGGGCTTCG
Found at i:96782 original size:2 final size:2
Alignment explanation
Indices: 96732--96765 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
96722 TTAATTAATT
96732 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
96766 GTACTTATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:103781 original size:42 final size:42
Alignment explanation
Indices: 103719--103805 Score: 124
Period size: 42 Copynumber: 2.1 Consensus size: 42
103709 ACAATGAAAA
*
103719 TTTATAACCACAACTGTAAAACTAAGCTC-ATAATAAGAACAT
1 TTTATAACCACAACTGTAAAACTAAAC-CAATAATAAGAACAT
*
103761 TTTATAACCACAACAT-TAAAACTAAACCAATAATAAGAATAT
1 TTTATAACCACAAC-TGTAAAACTAAACCAATAATAAGAACAT
103803 TTT
1 TTT
103806 CTTATATTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
41 1 0.02
42 39 0.95
43 1 0.02
ACGTcount: A:0.49, C:0.17, G:0.05, T:0.29
Consensus pattern (42 bp):
TTTATAACCACAACTGTAAAACTAAACCAATAATAAGAACAT
Found at i:119047 original size:16 final size:15
Alignment explanation
Indices: 119028--119064 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
119018 AGTTAAAGAT
*
119028 TATTTAGTAATTAAA
1 TATTTACTAATTAAA
119043 GTATTTACTAATTAAA
1 -TATTTACTAATTAAA
119059 TATTTA
1 TATTTA
119065 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (15 bp):
TATTTACTAATTAAA
Found at i:136970 original size:24 final size:24
Alignment explanation
Indices: 136943--137058 Score: 180
Period size: 24 Copynumber: 4.8 Consensus size: 24
136933 TTCTATTTGA
*
136943 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
136967 ATTCTGATATGATA-TCTGACATGG
1 ATTCTGATATGATACT-TGACATGG
*
136991 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
*
137015 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
137039 ATTTTGATATGATACTTGAC
1 ATTCTGATATGATACTTGAC
137059 CTGAATTATG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 1 0.01
24 82 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.40
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:136996 original size:12 final size:12
Alignment explanation
Indices: 136959--137021 Score: 58
Period size: 12 Copynumber: 5.2 Consensus size: 12
136949 ATCTGATACT
136959 TGACATGGATTC
1 TGACATGGATTC
*
136971 TGATAT-GATATC
1 TGACATGGAT-TC
136983 TGACATGGATTC
1 TGACATGGATTC
* *
136995 TGATAT-GATAC
1 TGACATGGATTC
*
137006 TTGACTTGGATTC
1 -TGACATGGATTC
137019 TGA
1 TGA
137022 TCTGATACTT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
11 7 0.17
12 26 0.65
13 7 0.17
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (12 bp):
TGACATGGATTC
Found at i:139374 original size:18 final size:18
Alignment explanation
Indices: 139348--139388 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
139338 CTTGAGTATG
139348 TTTTTCTTTTTGT-ATCA
1 TTTTTCTTTTTGTCATCA
139365 TTTTTCCTTTTTGTCATCA
1 TTTTT-CTTTTTGTCATCA
139384 TTTTT
1 TTTTT
139389 AAATAAATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.23
18 8 0.36
19 9 0.41
ACGTcount: A:0.10, C:0.15, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTTTCTTTTTGTCATCA
Found at i:139797 original size:23 final size:22
Alignment explanation
Indices: 139771--139819 Score: 73
Period size: 21 Copynumber: 2.2 Consensus size: 22
139761 GTTCAATCAG
139771 AAAGTATGTACCTATTCACTTCC
1 AAAGT-TGTACCTATTCACTTCC
139794 AAAG-TGTACCTATTCACTTCC
1 AAAGTTGTACCTATTCACTTCC
*
139815 GAAGT
1 AAAGT
139820 GGTATTCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 20 0.83
23 4 0.17
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAGTTGTACCTATTCACTTCC
Found at i:139803 original size:21 final size:21
Alignment explanation
Indices: 139777--139820 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
139767 TCAGAAAGTA
139777 TGTACCTATTCACTTCCAAAG
1 TGTACCTATTCACTTCCAAAG
*
139798 TGTACCTATTCACTTCCGAAG
1 TGTACCTATTCACTTCCAAAG
139819 TG
1 TG
139821 GTATTCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (21 bp):
TGTACCTATTCACTTCCAAAG
Found at i:147125 original size:20 final size:20
Alignment explanation
Indices: 147102--147149 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
147092 TACAGAATTT
*
147102 AAGATTATTAGTAAGAATAA
1 AAGATTACTAGTAAGAATAA
* **
147122 AAGATTACTGGTGGGAATAA
1 AAGATTACTAGTAAGAATAA
147142 AAGATTAC
1 AAGATTAC
147150 CGGTGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.04, G:0.21, T:0.27
Consensus pattern (20 bp):
AAGATTACTAGTAAGAATAA
Found at i:147154 original size:20 final size:20
Alignment explanation
Indices: 147116--147169 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
147106 TTATTAGTAA
*
147116 GAATAAAAGATTACTGGTGG
1 GAATAAAAGATTACCGGTGG
147136 GAATAAAAGATTACCGGTGG
1 GAATAAAAGATTACCGGTGG
*
147156 AAATAAAAGATTAC
1 GAATAAAAGATTAC
147170 TGGGAATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.22
Consensus pattern (20 bp):
GAATAAAAGATTACCGGTGG
Found at i:152921 original size:3 final size:3
Alignment explanation
Indices: 152915--152948 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
152905 TTGTTACCTC
152915 TCT TCT TCT TCT TCT TCT TCT TCT TCTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT
152949 CTCACACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:153410 original size:3 final size:3
Alignment explanation
Indices: 153402--153440 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
153392 ATTGTTGGTT
* * *
153402 AAG AAG AAG AAG AAT AAA AAG AAG AAG ATG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
153441 GGAGTTAACG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.00, G:0.28, T:0.05
Consensus pattern (3 bp):
AAG
Found at i:155984 original size:29 final size:30
Alignment explanation
Indices: 155948--156008 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
155938 ATGCCCCTTT
* *
155948 TTCCAGTTTAGTGTCTAACGTTT-TTTTCG
1 TTCCAGTTTAGTGCCTAACGTTTCATTTCG
*
155977 TTCCAGTTTGGTGCCTAACGTTTCATTTCG
1 TTCCAGTTTAGTGCCTAACGTTTCATTTCG
156007 TT
1 TT
156009 ACTCAAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.13, C:0.20, G:0.18, T:0.49
Consensus pattern (30 bp):
TTCCAGTTTAGTGCCTAACGTTTCATTTCG
Found at i:161103 original size:23 final size:23
Alignment explanation
Indices: 161058--161104 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
161048 TGCATGTAAC
* *
161058 TGTTTATTTAGCGTTCGCGAACA
1 TGTTTATTTAACGTTCGCAAACA
* *
161081 TGTTTGTTTAACGTTCGTAAACA
1 TGTTTATTTAACGTTCGCAAACA
161104 T
1 T
161105 ATTCGTTGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (23 bp):
TGTTTATTTAACGTTCGCAAACA
Found at i:161397 original size:25 final size:26
Alignment explanation
Indices: 161362--161415 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
161352 CAAGCCATTA
*
161362 AACGAGTTTGTC-ATGAACT-TAAACG
1 AACGAGCTTGTCTATGAA-TATAAACG
*
161387 AACGAGCTTGTCTTTGAATATAAACG
1 AACGAGCTTGTCTATGAATATAAACG
161413 AAC
1 AAC
161416 CACACACACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.28
Consensus pattern (26 bp):
AACGAGCTTGTCTATGAATATAAACG
Done.