Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005450.1 Hibiscus syriacus cultivar Beakdansim tig00012484_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: 86092
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:1155 original size:42 final size:42
Alignment explanation
Indices: 1107--1195 Score: 111
Period size: 35 Copynumber: 2.3 Consensus size: 42
1097 ATCCGCCCTA
1107 TTTTTAAAAAATAAATAATAAACATTTAAAGTATTGGGTAAC
1 TTTTTAAAAAATAAATAATAAACATTTAAAGTATTGGGTAAC
1149 -TTTT------TAAATAATAAACATTTAAAGTATTGGGTAAC
1 TTTTTAAAAAATAAATAATAAACATTTAAAGTATTGGGTAAC
*
1184 TTGTATAAAAAA
1 TT-TTTAAAAAA
1196 AAGTATTGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 15
0.70 0.02 0.28
Matches are distributed among these distances:
35 31 0.82
36 1 0.03
37 2 0.05
41 4 0.11
ACGTcount: A:0.48, C:0.04, G:0.10, T:0.37
Consensus pattern (42 bp):
TTTTTAAAAAATAAATAATAAACATTTAAAGTATTGGGTAAC
Found at i:1158 original size:35 final size:35
Alignment explanation
Indices: 1118--1185 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
1108 TTTTAAAAAA
1118 TAAATAATAAACATTTAAAGTATTGGGTAACTTTT
1 TAAATAATAAACATTTAAAGTATTGGGTAACTTTT
1153 TAAATAATAAACATTTAAAGTATTGGGTAACTT
1 TAAATAATAAACATTTAAAGTATTGGGTAACTT
1186 GTATAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (35 bp):
TAAATAATAAACATTTAAAGTATTGGGTAACTTTT
Found at i:34255 original size:204 final size:204
Alignment explanation
Indices: 34003--34399 Score: 501
Period size: 204 Copynumber: 1.9 Consensus size: 204
33993 TTTTATGGTG
** * *
34003 ACATGTCAACACCACCGTTTTTTTACAACCAGTATCAAAATGGAACCAAAATGTAATATTAGGT-
1 ACATGTCAACACCACCGTTTTTTTACAACCAGTATCAAAACAGAACCAAAACGTAATATTA-ATA
* * * * *
34067 ATGATTTTGAAAAACAAAATAGTTTAGTGATCGTAATGGAACCAAGGAAAT-GGCAAGCAACCAA
65 ATGATTTTGAAAAACAAAATAG-TAAGTGATCATAATGAAACAAAGAAAATAGGCAAGCAACCAA
* *
34131 AAACACAGTTAACCCTATTTAAAGACTGAACCCATCAACTCTCAAGTGATTCTTGTTTTCATTCT
129 AAACACAGTTAACCCTATTTAAAGACAGAACCCATCAACTCTCAAGTGATTCTCGTTTTCATTCT
34196 ACCTTATGATA
194 ACCTTATGATA
* * ** *
34207 ACATGTCATCATCACCGTTTTTTTTTAACGAGTATCAAAACAGAACCAAAACGTAATATTAATAA
1 ACATGTCAACACCACCGTTTTTTTACAACCAGTATCAAAACAGAACCAAAACGTAATATTAATAA
* ** ** * *
34272 TGATTTTGAAAAATAAAATAGTAAGTGATCATAATGAAACAAAGAAAATAGGTGAGTGACTAAAT
66 TGATTTTGAAAAACAAAATAGTAAGTGATCATAATGAAACAAAGAAAATAGGCAAGCAACCAAAA
* * ** * *
34337 ACATAGTTAATCCTATTTAAAGACAGGCCCCATCAACTCTCAGGTGATTCTCGTTTTCCTTCT
131 ACACAGTTAACCCTATTTAAAGACAGAACCCATCAACTCTCAAGTGATTCTCGTTTTCATTCT
34400 TTTTTTCATG
Statistics
Matches: 162, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
203 24 0.15
204 138 0.85
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (204 bp):
ACATGTCAACACCACCGTTTTTTTACAACCAGTATCAAAACAGAACCAAAACGTAATATTAATAA
TGATTTTGAAAAACAAAATAGTAAGTGATCATAATGAAACAAAGAAAATAGGCAAGCAACCAAAA
ACACAGTTAACCCTATTTAAAGACAGAACCCATCAACTCTCAAGTGATTCTCGTTTTCATTCTAC
CTTATGATA
Found at i:36488 original size:6 final size:6
Alignment explanation
Indices: 36476--36507 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
36466 TCGACACAGA
*
36476 GAGAGG GAAAGG GAGAGG GAGAGG GAGAGG GA
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GA
36508 AGAGAGGTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:46293 original size:95 final size:95
Alignment explanation
Indices: 46121--46294 Score: 269
Period size: 95 Copynumber: 1.8 Consensus size: 95
46111 GAATGTAGGG
* * *
46121 TAAACAAAATAAATTTTTAAAAAAAGAGGTTGATCCATTCCATTCTTATGACATGACCTAATATC
1 TAAACAAAATAAA-TATTAAAAAAAAAGGTTGATCCATTCCATGCTTATGACATGACCTAATATC
*
46186 ATTGTTCCAATTACGGGTTTATAATTATATA
65 ATTGCTCCAATTACGGGTTTATAATTATATA
*
46217 TAAACAAAATAAA-ATTAAAAAAAAAGGTGTGATCCATTCCATGCTTATGACATGACCTAGTATC
1 TAAACAAAATAAATATTAAAAAAAAAGGT-TGATCCATTCCATGCTTATGACATGACCTAATATC
*
46281 ATTGCTCTAATTAC
65 ATTGCTCCAATTAC
46295 AGATGGATCG
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
94 13 0.18
95 45 0.63
96 13 0.18
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (95 bp):
TAAACAAAATAAATATTAAAAAAAAAGGTTGATCCATTCCATGCTTATGACATGACCTAATATCA
TTGCTCCAATTACGGGTTTATAATTATATA
Found at i:46818 original size:32 final size:32
Alignment explanation
Indices: 46746--46818 Score: 83
Period size: 32 Copynumber: 2.3 Consensus size: 32
46736 TTGAGTGATG
* * ** *
46746 TGACACATGTTATGTCATCACTTTTGGTGATA
1 TGACACATGTCATGTCACCACTTTAAGTAATA
**
46778 TGGTACATGTCATGTCACCACTTTAAGTAATA
1 TGACACATGTCATGTCACCACTTTAAGTAATA
46810 TGACACATG
1 TGACACATG
46819 CCACTTCATT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (32 bp):
TGACACATGTCATGTCACCACTTTAAGTAATA
Found at i:51634 original size:23 final size:22
Alignment explanation
Indices: 51608--51659 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
51598 CAATGATTTT
*
51608 TTAAAA-TTATTCATTTATTAAAA
1 TTAAAATTTA-TC-TTTAATAAAA
*
51631 TTAAAATTTATCTTTAATATAA
1 TTAAAATTTATCTTTAATAAAA
51653 TTAAAAT
1 TTAAAAT
51660 GTTTAGTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 8 0.31
24 3 0.12
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TTAAAATTTATCTTTAATAAAA
Found at i:70505 original size:42 final size:44
Alignment explanation
Indices: 70402--70505 Score: 113
Period size: 47 Copynumber: 2.3 Consensus size: 44
70392 AGTTAGATAA
*
70402 TAAAATGACCCTTGACACGAATCACGACCATCTAAGATATATATAGTC
1 TAAAA-GACCCTTGACAAGAATCACGACCATCTAAG--A-ATATAGTC
* * *
70450 TCAATGACCCTTGACAAGAATCACGATCATCTAAG-AT-TAGTC
1 TAAAAGACCCTTGACAAGAATCACGACCATCTAAGAATATAGTC
*
70492 TAAAAGACGCTTGA
1 TAAAAGACCCTTGA
70506 ATTGGACGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 16 0.33
43 2 0.04
47 28 0.57
48 3 0.06
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.25
Consensus pattern (44 bp):
TAAAAGACCCTTGACAAGAATCACGACCATCTAAGAATATAGTC
Found at i:73217 original size:21 final size:21
Alignment explanation
Indices: 73191--73304 Score: 101
Period size: 21 Copynumber: 5.4 Consensus size: 21
73181 TTTCCAAATT
73191 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * *
73212 CGTTGCAATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
73233 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
73254 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
73275 CGTTACGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
73296 CGTTGCGAT
1 CGTTGCGAT
73305 TTATTCCAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 17 0.24
21 37 0.52
23 17 0.24
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:73228 original size:42 final size:42
Alignment explanation
Indices: 73182--73318 Score: 247
Period size: 42 Copynumber: 3.3 Consensus size: 42
73172 CAATGTGATT
*
73182 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCAATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
*
73224 TTCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
*
73266 TTCCAAATTCGTTACGATAGTCCAAGTTCGCGTTGCGATTTA
1 TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
73308 TTCCAAATTCG
1 TTCCAAATTCG
73319 CAACGACTGG
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (42 bp):
TTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTA
Found at i:74051 original size:6 final size:6
Alignment explanation
Indices: 74040--74064 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
74030 TCGTCTCGTC
74040 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
74065 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:74185 original size:21 final size:21
Alignment explanation
Indices: 74161--74211 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
74151 AATTTGGAAA
74161 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* ** *
74182 ATCGCAACACGATTTTGGACT
1 ATCGCAACGCGAACTTCGACT
74203 ATCGCAACG
1 ATCGCAACG
74212 AATTTGGAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:74238 original size:29 final size:29
Alignment explanation
Indices: 74196--74254 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
74186 CAACACGATT
74196 TTGGACTATCGCAACGAATTTGGAATAAA
1 TTGGACTATCGCAACGAATTTGGAATAAA
* *
74225 TTGGACTATGGCAACGAATTTGTAATAAA
1 TTGGACTATCGCAACGAATTTGGAATAAA
74254 T
1 T
74255 CGCAACGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (29 bp):
TTGGACTATCGCAACGAATTTGGAATAAA
Found at i:75006 original size:20 final size:20
Alignment explanation
Indices: 74981--75159 Score: 116
Period size: 20 Copynumber: 8.8 Consensus size: 20
74971 ATGCGAAACA
*
74981 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTAAG
* * *
75001 AAAATCGCAATGTTGA-AAAG
1 AAAATCGCAACG-CGATTAAG
*
75021 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TAAG
* ***
75041 AAAATCGCAACGCAATCTTCC
1 AAAATCGCAACGCGAT-TAAG
*
75062 AAGAATCGCAATGCGATTCAA-
1 AA-AATCGCAACGCGATT-AAG
* *
75083 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTAAG
*
75103 AAAATCGCAACGCGATTCCAG
1 AAAATCGCAACGCGATT-AAG
* * *
75124 -GAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTAAG
75143 AAAATCGCAACGCGATT
1 AAAATCGCAACGCGATT
75160 CCAAGAATCG
Statistics
Matches: 123, Mismatches: 25, Indels: 22
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 3 0.02
20 98 0.80
21 8 0.07
22 13 0.11
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTAAG
Found at i:75118 original size:40 final size:40
Alignment explanation
Indices: 75065--75172 Score: 180
Period size: 40 Copynumber: 2.7 Consensus size: 40
75055 ATCTTCCAAG
* *
75065 AATCGCAATGCGATTCAAAGAATCGCAACGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
* *
75105 AATCGCAACGCGATTCCAGGAATCGCAATGCGATTGAGAA
1 AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
75145 AATCGCAACGCGATTCCAAGAATCGCAA
1 AATCGCAACGCGATTCCAAGAATCGCAA
75173 AACGGCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (40 bp):
AATCGCAACGCGATTCCAAGAATCGCAACGCGATTGAGAA
Found at i:75149 original size:60 final size:61
Alignment explanation
Indices: 75039--75159 Score: 183
Period size: 60 Copynumber: 2.0 Consensus size: 61
75029 AACGGTCAAA
75039 AGAAAATCGCAACGCAATCTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
1 AGAAAATCGCAACGCAA-CTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
* * *
75101 AGAAAATCGCAACGCGA-TTCCAGGAATCGCAATGCGATTGAGAA-AATCGCAACGCGATT
1 AGAAAATCGCAACGCAACTTCCAAGAATCGCAATGCGATTCA-AAGAATCGCAACGCGATT
75160 CCAAGAATCG
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
60 37 0.67
61 2 0.04
62 16 0.29
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (61 bp):
AGAAAATCGCAACGCAACTTCCAAGAATCGCAATGCGATTCAAAGAATCGCAACGCGATTG
Found at i:75168 original size:20 final size:20
Alignment explanation
Indices: 75043--75172 Score: 129
Period size: 20 Copynumber: 6.4 Consensus size: 20
75033 GTCAAAAGAA
*
75043 AATCGCAACGCAATCTTCCAAG
1 AATCGCAACGCGA--TTCCAAG
* *
75065 AATCGCAATGCGATTCAAAG
1 AATCGCAACGCGATTCCAAG
* *
75085 AATCGCAACGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
*
75105 AATCGCAACGCGATTCCAGG
1 AATCGCAACGCGATTCCAAG
* * *
75125 AATCGCAATGCGATT-GAGAA
1 AATCGCAACGCGATTCCA-AG
75145 AATCGCAACGCGATTCCAAG
1 AATCGCAACGCGATTCCAAG
75165 AATCGCAA
1 AATCGCAA
75173 AACGGCAAAA
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
19 2 0.02
20 73 0.83
21 2 0.02
22 11 0.12
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGATTCCAAG
Found at i:75294 original size:6 final size:6
Alignment explanation
Indices: 75283--75321 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
75273 GACACGTATT
75283 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
75322 CGAGACGAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:76084 original size:6 final size:6
Alignment explanation
Indices: 76068--76105 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
76058 CGCCGTCTCG
76068 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
76106 AATACGTGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:76241 original size:20 final size:20
Alignment explanation
Indices: 76216--76447 Score: 222
Period size: 20 Copynumber: 11.4 Consensus size: 20
76206 TTTTGCCGTT
*
76216 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
**
76236 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
76256 TTGCGATTCTTGGAATCGCG
1 TTGCGATTCTTGGAATCGCG
**
76276 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
**
76296 TTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTT-GGAATCGCG
*
76316 TTGCGATTCTTTGAATCGCG
1 TTGCGATTCTTGGAATCGCG
* *
76336 TTGCGATTCTTCGAAGATCGCA
1 TTGCGATTCTT-GGA-ATCGCG
* *
76358 TTGCGATTCTTTGG-CTCGCA
1 TTGCGATTC-TTGGAATCGCG
*
76378 TTGCGATTCTTGGAATCGCA
1 TTGCGATTCTTGGAATCGCG
*
76398 TTGCGATTCTTTGG-ATCGCA
1 TTGCGATTC-TTGGAATCGCG
76418 TTGCGATTCTTGGAAGATCGCG
1 TTGCGATTCTTGG-A-ATCGCG
76440 TTGCGATT
1 TTGCGATT
76448 TTCTTTTGAC
Statistics
Matches: 185, Mismatches: 15, Indels: 22
0.83 0.07 0.10
Matches are distributed among these distances:
19 12 0.06
20 134 0.72
21 9 0.05
22 28 0.15
23 2 0.01
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTTGGAATCGCG
Found at i:76263 original size:40 final size:40
Alignment explanation
Indices: 76216--76447 Score: 263
Period size: 40 Copynumber: 5.7 Consensus size: 40
76206 TTTTGCCGTT
*
76216 TTGCGATTCTTGGAATCGCATTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTCTT-TGAATCGCG
* *
76256 TTGCGATTCTTGGAATCGCGTTGCGATT-TTCTCAATCGCG
1 TTGCGATTCTTGGAATCGCATTGCGATTCTT-TGAATCGCG
** *
76296 TTGCGATT-TTCTCAATCGCGTTGCGATTCTTTGAATCGCG
1 TTGCGATTCTT-GGAATCGCATTGCGATTCTTTGAATCGCG
* ** *
76336 TTGCGATTCTTCGAAGATCGCATTGCGATTCTTTGGCTCGCA
1 TTGCGATTCTT-GGA-ATCGCATTGCGATTCTTTGAATCGCG
* *
76378 TTGCGATTCTTGGAATCGCATTGCGATTCTTTGGATCGCA
1 TTGCGATTCTTGGAATCGCATTGCGATTCTTTGAATCGCG
*
76418 TTGCGATTCTTGGAAGATCGCGTTGCGATT
1 TTGCGATTCTTGG-A-ATCGCATTGCGATT
76448 TTCTTTTGAC
Statistics
Matches: 173, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
39 2 0.01
40 116 0.67
41 9 0.05
42 46 0.27
ACGTcount: A:0.16, C:0.22, G:0.25, T:0.38
Consensus pattern (40 bp):
TTGCGATTCTTGGAATCGCATTGCGATTCTTTGAATCGCG
Found at i:76464 original size:82 final size:83
Alignment explanation
Indices: 76199--76528 Score: 275
Period size: 82 Copynumber: 4.1 Consensus size: 83
76189 CTGCTTTTGA
*
76199 GATTTTCTTTTG-C-CGTTTTGCGATTCTTGGAATCGCATTGCGATT-TTCTCAATCGCGTTGCG
1 GATTTTC-TTTGACGCG-TTTGCGATTCTTGGAATCGCATTGCGATTCTT-TGAATCGCGTTGCG
76261 ATTCTTGG-A-ATCGCGTTGC
63 ATTCTTGGAAGATCGCGTTGC
** ** *
76280 GATTTTC-TCAATCGCG-TTGCGATT-TTCTCAATCGCGTTGCGATTCTTTGAATCGCGTTGCGA
1 GATTTTCTTTGA-CGCGTTTGCGATTCTT-GGAATCGCATTGCGATTCTTTGAATCGCGTTGCGA
* *
76342 TTCTTCGAAGATCGCATTGC
64 TTCTTGGAAGATCGCGTTGC
* * * * *
76362 GA--TTCTTTGGCTCGCATTGCGATTCTTGGAATCGCATTGCGATTCTTTGGATCGCATTGCGAT
1 GATTTTCTTTGACGCG-TTTGCGATTCTTGGAATCGCATTGCGATTCTTTGAATCGCGTTGCGAT
76425 TCTTGGAAGATCGCGTTGC
65 TCTTGGAAGATCGCGTTGC
** *
76444 GATTTTCTTTTGAC-CG-TTGCGATTTTCTTTTCAA-CG--TTGCGATT-TTCTAAATCGCGTTG
1 GATTTTC-TTTGACGCGTTTGCGA--TTC-TTGGAATCGCATTGCGATTCTT-TGAATCGCGTTG
*
76503 CGATT-TT-G-ATATCGCGTTGC
61 CGATTCTTGGAAGATCGCGTTGC
76523 GATTTT
1 GATTTT
76529 GTTGGTCATT
Statistics
Matches: 205, Mismatches: 26, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
79 20 0.10
80 49 0.24
81 16 0.08
82 99 0.48
83 2 0.01
84 10 0.05
85 9 0.04
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.41
Consensus pattern (83 bp):
GATTTTCTTTGACGCGTTTGCGATTCTTGGAATCGCATTGCGATTCTTTGAATCGCGTTGCGATT
CTTGGAAGATCGCGTTGC
Found at i:76501 original size:20 final size:20
Alignment explanation
Indices: 76228--76528 Score: 205
Period size: 20 Copynumber: 14.9 Consensus size: 20
76218 GCGATTCTTG
*
76228 GAATCGCATTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
* *
76248 CAATCGCGTTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
76268 GAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
*
76288 CAATCGCGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
*
76308 CAATCGCGTTGCGATTCTT-T
1 GAATCGCGTTGCGATT-TTCT
76328 GAATCGCGTTGCGATTCTTC-
1 GAATCGCGTTGCGATT-TTCT
*
76348 GAAGATCGCATTGCGATTCTT-T
1 G-A-ATCGCGTTGCGATT-TTCT
** * *
76370 GGCTCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
*
76390 GAATCGCATTGCGATTCTT-T
1 GAATCGCGTTGCGATT-TTCT
* * *
76410 GGATCGCATTGCGATTCTT-G
1 GAATCGCGTTGCGATT-TTCT
76430 GAAGATCGCGTTGCGATTTTCTTTT
1 G-A-ATCGCGTTGCGATTTTC---T
76455 G-A-C-CGTTGCGATTTTCT
1 GAATCGCGTTGCGATTTTCT
** *
76472 -TTTCAACGTTGCGATTTTCT
1 GAATC-GCGTTGCGATTTTCT
*
76492 AAATCGCGTTGCGA-TTT-T
1 GAATCGCGTTGCGATTTTCT
76510 GATATCGCGTTGCGATTTT
1 GA-ATCGCGTTGCGATTTT
76529 GTTGGTCATT
Statistics
Matches: 237, Mismatches: 24, Indels: 40
0.79 0.08 0.13
Matches are distributed among these distances:
17 1 0.00
18 3 0.01
19 17 0.07
20 174 0.73
21 10 0.04
22 31 0.13
25 1 0.00
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.40
Consensus pattern (20 bp):
GAATCGCGTTGCGATTTTCT
Found at i:76826 original size:6 final size:6
Alignment explanation
Indices: 76815--76866 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
76805 TTTCCCTCAT
* *
76815 GAATAC GAATAC GAATAC GAATAC GAATAT AAATAC GAATAC GAATAC
1 GAATAC GAATAC GAATAC GAATAC GAATAC GAATAC GAATAC GAATAC
76863 GAAT
1 GAAT
76867 GCAATATCCA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.52, C:0.13, G:0.15, T:0.19
Consensus pattern (6 bp):
GAATAC
Done.