Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008404.1 Hibiscus syriacus cultivar Beakdansim tig00111173_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: 108213
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1957 original size:24 final size:24
Alignment explanation
Indices: 1924--1996 Score: 101
Period size: 24 Copynumber: 3.0 Consensus size: 24
1914 TGTAGTTCCC
*
1924 CAGAATTACATCCATAAGGACTTA
1 CAGAACTACATCCATAAGGACTTA
**
1948 CAGAACTACATCCATATTGACTTA
1 CAGAACTACATCCATAAGGACTTA
* *
1972 CATAACTACATCTATAAGGACTTA
1 CAGAACTACATCCATAAGGACTTA
1996 C
1 C
1997 TCTAGACTTA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (24 bp):
CAGAACTACATCCATAAGGACTTA
Found at i:5075 original size:2 final size:2
Alignment explanation
Indices: 5068--5107 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5058 GAAACTTCTA
5068 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
5108 GTTTATGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20890 original size:12 final size:11
Alignment explanation
Indices: 20867--20896 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
20857 AAGCTACTTT
20867 GAAAGAGAAGA
1 GAAAGAGAAGA
20878 GAAAGAGAGAGA
1 GAAAGAGA-AGA
20890 GAAAGAG
1 GAAAGAG
20897 CCCACACCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.44
12 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (11 bp):
GAAAGAGAAGA
Found at i:22334 original size:23 final size:23
Alignment explanation
Indices: 22308--22372 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
22298 ATTCAATTTA
22308 TTTAATGTTCGCCAATATGTTCG
1 TTTAATGTTCGCCAATATGTTCG
* * ** *
22331 TTTAACGTTTGCGGACATGTTCG
1 TTTAATGTTCGCCAATATGTTCG
*
22354 TTTATATGCTCGCCAATAT
1 TTTA-ATGTTCGCCAATAT
22373 ATTGGAGAAA
Statistics
Matches: 30, Mismatches: 11, Indels: 1
0.71 0.26 0.02
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.22, C:0.18, G:0.18, T:0.42
Consensus pattern (23 bp):
TTTAATGTTCGCCAATATGTTCG
Found at i:25317 original size:23 final size:23
Alignment explanation
Indices: 25253--25348 Score: 81
Period size: 23 Copynumber: 4.3 Consensus size: 23
25243 CACCGAAGTG
* * *
25253 CCACATAG-AATGTCTCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* *
25275 CCACATAG--ATGTCCCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* *
25296 CCGCGTAGAAATGTCCTAAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
* * *
25319 CTACGTAGAATTGTCCCGAAGGA
1 CCACGTAGAAATGTCCCAAAGGA
25342 CCACGTA
1 CCACGTA
25349 AAACCCTCGA
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.30
22 8 0.13
23 35 0.57
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (23 bp):
CCACGTAGAAATGTCCCAAAGGA
Found at i:25464 original size:15 final size:15
Alignment explanation
Indices: 25444--25482 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
25434 TTTCAATTAT
*
25444 TCACATAGTTCCGTA
1 TCACATAGTTCCATA
*
25459 TCACATAG-ACCATA
1 TCACATAGTTCCATA
25473 TCACATAGTT
1 TCACATAGTT
25483 TATATCATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (15 bp):
TCACATAGTTCCATA
Found at i:27923 original size:15 final size:14
Alignment explanation
Indices: 27901--27947 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
27891 AAAGTGATTT
27901 TTTATTATAATATA
1 TTTATTATAATATA
*
27915 TTATATTATACTATA
1 TT-TATTATAATATA
*
27930 TTTATT-T-ATTTA
1 TTTATTATAATATA
27942 TTTATT
1 TTTATT
27948 TATTTGCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 9 0.31
13 1 0.03
14 6 0.21
15 13 0.45
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTATTATAATATA
Found at i:27937 original size:4 final size:4
Alignment explanation
Indices: 27928--27952 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
27918 TATTATACTA
27928 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
27953 GCTTCTTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:37054 original size:21 final size:18
Alignment explanation
Indices: 37012--37054 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 18
37002 ATCAGTACAT
*
37012 CCATAATTTCACAAAATA
1 CCATAATTTCAAAAAATA
37030 CCATAATTTCATAAAGAATTA
1 CCATAATTTCA-AAA-AA-TA
37051 CCAT
1 CCAT
37055 CTTTCCGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.52
19 2 0.10
20 2 0.10
21 6 0.29
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.30
Consensus pattern (18 bp):
CCATAATTTCAAAAAATA
Found at i:44446 original size:17 final size:18
Alignment explanation
Indices: 44413--44446 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44403 CTGCTACTAG
44413 TGAATCGATCAGAACCGT
1 TGAATCGATCAGAACCGT
*
44431 TGAATCGTTC-GAACCG
1 TGAATCGATCAGAACCG
44447 AACCGACTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.24
Consensus pattern (18 bp):
TGAATCGATCAGAACCGT
Found at i:44687 original size:17 final size:16
Alignment explanation
Indices: 44656--44686 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
44646 AATATTGAAA
*
44656 CTTGAACTCAAAAAAG
1 CTTGAACTAAAAAAAG
44672 CTTGAACTAAAAAAA
1 CTTGAACTAAAAAAA
44687 ATTTAGAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTAAAAAAAG
Found at i:45366 original size:6 final size:6
Alignment explanation
Indices: 45355--45393 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
45345 CACGTATTAT
45355 CACGAC CACGAC CACGAC CAC--C CACGAC CACGAC CACGA
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGA
45394 GACGAGACAG
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.13
6 27 0.87
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:45379 original size:16 final size:16
Alignment explanation
Indices: 45360--45391 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
45350 ATTATCACGA
45360 CCACGACCACGACCAC
1 CCACGACCACGACCAC
45376 CCACGACCACGACCAC
1 CCACGACCACGACCAC
45392 GAGACGAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.56, G:0.12, T:0.00
Consensus pattern (16 bp):
CCACGACCACGACCAC
Found at i:53265 original size:25 final size:26
Alignment explanation
Indices: 53237--53286 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
53227 ATCAAAAATA
53237 TTAC-CAAAAAATATAATATTTTAGG
1 TTACACAAAAAATATAATATTTTAGG
* *
53262 TTACAATAAAAAATATTATATTTTA
1 TTAC-ACAAAAAATATAATATTTTA
53287 TAATAGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
27 17 0.81
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (26 bp):
TTACACAAAAAATATAATATTTTAGG
Found at i:53813 original size:21 final size:21
Alignment explanation
Indices: 53762--53821 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
53752 ATCAATTATC
* *
53762 TAAATTATCACATCAATATTA
1 TAAATTATCATATCAATACTA
* *
53783 TTAATCATCATATCAACT-CTA
1 TAAATTATCATATCAA-TACTA
53804 TAAATTATCATATCAATA
1 TAAATTATCATATCAATA
53822 TCGTAACGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTATCATATCAATACTA
Found at i:54048 original size:20 final size:21
Alignment explanation
Indices: 54023--54076 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
54013 GACCAACAAA
54023 TTCGCAACGCGAA-ATCCAAT
1 TTCGCAACGCGAATATCCAAT
* *
54043 TTCGCAAC-CCAATTTCCAAT
1 TTCGCAACGCGAATATCCAAT
54063 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
54077 TTGTAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.31, C:0.31, G:0.13, T:0.24
Consensus pattern (21 bp):
TTCGCAACGCGAATATCCAAT
Found at i:54109 original size:20 final size:20
Alignment explanation
Indices: 54086--54128 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
54076 TTTGTAAATC
54086 GCAACACAGA-AGTCAAATTT
1 GCAACAC-GATAGTCAAATTT
*
54106 GCAACGCGATAGTCAAATTT
1 GCAACACGATAGTCAAATTT
54126 GCA
1 GCA
54129 TCGAGAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
GCAACACGATAGTCAAATTT
Found at i:54139 original size:20 final size:20
Alignment explanation
Indices: 54095--54143 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
54085 CGCAACACAG
*
54095 AAGTCAAATTTGCAACGCGA
1 AAGTCAAATTTGCAACGAGA
* *
54115 TAGTCAAATTTGCATCGAGA
1 AAGTCAAATTTGCAACGAGA
54135 AAGTCAAAT
1 AAGTCAAAT
54144 GTTTTTACGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.24
Consensus pattern (20 bp):
AAGTCAAATTTGCAACGAGA
Found at i:54653 original size:20 final size:19
Alignment explanation
Indices: 54618--54671 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
54608 AAAATCGCAC
54618 GTGATTTTAGTTTCGCGTT
1 GTGATTTTAGTTTCGCGTT
*
54637 GTGATTTTCATTTTCGCGTT
1 GTGATTTT-AGTTTCGCGTT
* *
54657 GCGAATTTAAGTTTC
1 GTG-ATTTTAGTTTC
54672 AGAAACTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.15, C:0.13, G:0.22, T:0.50
Consensus pattern (19 bp):
GTGATTTTAGTTTCGCGTT
Found at i:57406 original size:20 final size:21
Alignment explanation
Indices: 57381--57432 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
57371 ATTTCTCAAT
*
57381 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
57401 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
57422 TCGCAATGCGA
1 TCGCAATGCGA
57433 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:57445 original size:41 final size:39
Alignment explanation
Indices: 57400--57493 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 39
57390 GAATAAGTAA
* * *
57400 ATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATAT--AAAATCGCAACGCGATACTGACT
57441 ATCGCAACGCGATAATATAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCG--AATATAAAATCGCAACGCGATACTGACT
*
57482 TTCGCAACGCGA
1 ATCGCAACGCGA
57494 TACTGATTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 1 0.02
41 42 0.89
43 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (39 bp):
ATCGCAACGCGAATATAAAATCGCAACGCGATACTGACT
Found at i:57446 original size:20 final size:20
Alignment explanation
Indices: 57421--57499 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
57411 AATTTGGAAA
*
57421 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * **
57441 ATCGCAACGCGATAATATAAA
1 ATCGCAACGCGATACT-GACT
57462 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
57482 TTCGCAACGCGATACTGA
1 ATCGCAACGCGATACTGA
57500 TTCAATAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 32 0.67
21 16 0.33
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:57494 original size:41 final size:41
Alignment explanation
Indices: 57418--57495 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
57408 GCGAATTTGG
*
57418 AAAATCGCAATGCGATACTGACTATCGCAACGCGATAATAT
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAT
*
57459 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATA
1 AAAATCGCAACGCGATACTGACTATCGCAACGCGATA
57496 CTGATTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGCGATAATAT
Found at i:74099 original size:21 final size:21
Alignment explanation
Indices: 74073--74209 Score: 79
Period size: 21 Copynumber: 6.7 Consensus size: 21
74063 GCAACACATG
74073 TTCCAAAATCGCAATGCGATT
1 TTCCAAAATCGCAATGCGATT
* * *
74094 TTCCAAATTCGCAACGCGAAT
1 TTCCAAAATCGCAATGCGATT
*
74115 AT--ATAAATCGCAA--CGATAAT
1 TTCCA-AAATCGCAATGCGAT--T
* ** * *
74135 AT-GTAAATCACAATGCGGTT
1 TTCCAAAATCGCAATGCGATT
* *
74155 TTCCAAAATCGCAACGCCATT
1 TTCCAAAATCGCAATGCGATT
* *
74176 TTCCAAATTCGCAATGAGATT
1 TTCCAAAATCGCAATGCGATT
*
74197 TT-CAAATTCGCAA
1 TTCCAAAATCGCAA
74210 CGCTAATTAC
Statistics
Matches: 89, Mismatches: 20, Indels: 15
0.72 0.16 0.12
Matches are distributed among these distances:
18 3 0.03
19 1 0.01
20 32 0.36
21 50 0.56
22 3 0.03
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCCAAAATCGCAATGCGATT
Found at i:74266 original size:20 final size:20
Alignment explanation
Indices: 74241--74289 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
74231 AACAGTACTA
74241 TCGCAACGCGATTTACAAAT
1 TCGCAACGCGATTTACAAAT
* *
74261 TCGCAACGAGATTTTCAAAT
1 TCGCAACGCGATTTACAAAT
74281 TCGCAACGC
1 TCGCAACGC
74290 TAATTACCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGATTTACAAAT
Found at i:74272 original size:77 final size:77
Alignment explanation
Indices: 74179--74422 Score: 434
Period size: 77 Copynumber: 3.2 Consensus size: 77
74169 CGCCATTTTC
*
74179 CAAATTCGCAATGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
1 CAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
*
74244 CAACGCGATTTA
66 CAACACGATTTA
*
74256 CAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCAATATAGGTAAACAGTACTATCG
1 CAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
74321 CAACACGATTTA
66 CAACACGATTTA
*
74333 CAAATTCGCAACGAGATTTTCAAGTTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
1 CAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
*
74398 CAACACGATTTT
66 CAACACGATTTA
*
74410 GAAATTCGCAACG
1 CAAATTCGCAACG
74423 CTAATTACCG
Statistics
Matches: 160, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 160 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (77 bp):
CAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCG
CAACACGATTTA
Found at i:74343 original size:20 final size:20
Alignment explanation
Indices: 74318--74365 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
74308 AACAGTACTA
74318 TCGCAAC-ACGATTTACAAAT
1 TCGCAACGA-GATTTACAAAT
* *
74338 TCGCAACGAGATTTTCAAGT
1 TCGCAACGAGATTTACAAAT
74358 TCGCAACG
1 TCGCAACG
74366 CTAATTACCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (20 bp):
TCGCAACGAGATTTACAAAT
Found at i:74399 original size:57 final size:57
Alignment explanation
Indices: 74338--74536 Score: 321
Period size: 57 Copynumber: 3.5 Consensus size: 57
74328 ATTTACAAAT
*
74338 TCGCAACGAGATTTTCAAGTTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
74395 TCGCAAC-ACGATTTTGAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGA-GATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* *
74452 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
1 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
74509 TCGCAACGCA-ATTTTCAAATTCGAAACG
1 TCGCAACG-AGATTTTCAAATTCGCAACG
74537 AGATTTTCAA
Statistics
Matches: 131, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
56 1 0.01
57 130 0.99
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (57 bp):
TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:74530 original size:191 final size:191
Alignment explanation
Indices: 74261--74656 Score: 666
Period size: 191 Copynumber: 2.1 Consensus size: 191
74251 ATTTACAAAT
* *
74261 TCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCAATATAGGTAAACAGTACTATCGCAACA
1 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCAATATAGGTAAACAGTACTATCGCAACA
* * *
74326 CGATTTACAAATTCGCAACGAGATTTTCAAGTTCGCAACGCTAATTACCGATATAGGTAAACAGT
66 CAATTTACAAATTCGAAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
74391 ACTATCGCAACACGATTTTGAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
131 ACTATCGCAACACGATTTTGAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
* *
74452 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
1 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCAATATAGGTAAACAGTACTATCGCAACA
* *
74517 CAATTTTCAAATTCGAAACGAGATTTTCAAATTCGCAACGCTAATTACCGATGTAGGTAAACAGT
66 CAATTTACAAATTCGAAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
** * *
74582 GTTATCGCAACGCGATTTTTAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
131 ACTATCGCAACACGATTTTGAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
*
74643 TCGTAACGCGATTT
1 TCGCAACGCGATTT
74657 TGGAAACTGT
Statistics
Matches: 191, Mismatches: 14, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
191 191 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (191 bp):
TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCAATATAGGTAAACAGTACTATCGCAACA
CAATTTACAAATTCGAAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
ACTATCGCAACACGATTTTGAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTA
Found at i:74542 original size:20 final size:20
Alignment explanation
Indices: 74519--74556 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
74509 TCGCAACGCA
74519 ATTTTCAAATTCGAAACGAG
1 ATTTTCAAATTCGAAACGAG
*
74539 ATTTTCAAATTCGCAACG
1 ATTTTCAAATTCGAAACG
74557 CTAATTACCG
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:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (20 bp):
ATTTTCAAATTCGAAACGAG
Found at i:74588 original size:77 final size:77
Alignment explanation
Indices: 74456--74613 Score: 244
Period size: 77 Copynumber: 2.1 Consensus size: 77
74446 GTACTATCGC
*
74456 AACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
1 AACGAGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
74521 TTTCAAATTCGA
66 TTTCAAATTCGA
* * ** *
74533 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATGTAGGTAAACAGTGTTATCGCAACGCGAT
1 AACGAGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
* *
74598 TTTTAAATTCGC
66 TTTCAAATTCGA
74610 AACG
1 AACG
74614 CTAATTACCG
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 73 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.27
Consensus pattern (77 bp):
AACGAGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACGCAAT
TTTCAAATTCGA
Found at i:74631 original size:57 final size:57
Alignment explanation
Indices: 74533--74657 Score: 196
Period size: 57 Copynumber: 2.2 Consensus size: 57
74523 TCAAATTCGA
* * **
74533 AACGAGATTTTCAAATTCGCAACGCTAATTACCGATGTAGGTAAACAGTGTTATCGC
1 AACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
* *
74590 AACGCGATTTTTAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGT
1 AACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
74647 AACGCGATTTT
1 AACGCGATTTT
74658 GGAAACTGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Consensus pattern (57 bp):
AACGCGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGC
Found at i:74657 original size:134 final size:134
Alignment explanation
Indices: 74184--74656 Score: 552
Period size: 134 Copynumber: 3.5 Consensus size: 134
74174 TTTTCCAAAT
* * *
74184 TCGCAATGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
1 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
*
74249 CGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCAATATAGGTAAACAGT
66 CGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
74314 ACTA
131 ACTA
* ** ** * * *
74318 TCGCAACACGATTTACAAATTCGCAACG--AGATTTTC-A-AGTTCG-CAAC-GCTAATTACCG-
1 TCGCAACGCGATTTACAAATTCGCAACGCTA-ATTACCGATA-TAGGTAAACAG-T-ACTATCGC
* ** * *
74376 ATATAG-G-TAAACAGTACTATCGCAAC-ACGATTTTGAAATTCGCAACGCTAATTACCGATATA
62 A-A-CGCGATTTACA--AAT-TCGCAACGA-GATTTTCAAATTCGCAACGCTAATTACCGATATA
74438 GGTAAACAGTACTA
121 GGTAAACAGTACTA
74452 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
1 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
* * * *
74517 CAATTTTCAAATTCGAAACGAGATTTTCAAATTCGCAACGCTAATTACCGATGTAGGTAAACAGT
66 CGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
**
74582 GTTA
131 ACTA
** *
74586 TCGCAACGCGATTTTTAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGTAACG
1 TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
74651 CGATTT
66 CGATTT
74657 TGGAAACTGT
Statistics
Matches: 279, Mismatches: 40, Indels: 40
0.78 0.11 0.11
Matches are distributed among these distances:
130 1 0.00
131 10 0.04
132 11 0.04
133 8 0.03
134 221 0.79
135 8 0.03
136 10 0.04
137 9 0.03
138 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (134 bp):
TCGCAACGCGATTTACAAATTCGCAACGCTAATTACCGATATAGGTAAACAGTACTATCGCAACG
CGATTTACAAATTCGCAACGAGATTTTCAAATTCGCAACGCTAATTACCGATATAGGTAAACAGT
ACTA
Found at i:74675 original size:20 final size:20
Alignment explanation
Indices: 74650--74732 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 20
74640 CTATCGTAAC
74650 GCGATTTTGGAAACTGTGTT
1 GCGATTTTGGAAACTGTGTT
** * *
74670 GCGA-TTTACAAATTCGCGTT
1 GCGATTTTGGAAACT-GTGTT
**
74690 GCGATTTTGGAAACTGTACT
1 GCGATTTTGGAAACTGTGTT
*
74710 ACGATTTT-GAAACATGTGTT
1 GCGATTTTGGAAAC-TGTGTT
74730 GCG
1 GCG
74733 GAATTAGAGT
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
19 12 0.26
20 27 0.59
21 7 0.15
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (20 bp):
GCGATTTTGGAAACTGTGTT
Found at i:76453 original size:2 final size:2
Alignment explanation
Indices: 76446--76486 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
76436 CCATAAATTA
76446 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76487 GACAAGGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77302 original size:23 final size:23
Alignment explanation
Indices: 77266--77349 Score: 132
Period size: 23 Copynumber: 3.7 Consensus size: 23
77256 TAGATGAATT
* * *
77266 GAAGAATAATAAATGGGTTTATG
1 GAAGAAAAAGAAATGAGTTTATG
*
77289 GAAGAAGAAGAAATGAGTTTATG
1 GAAGAAAAAGAAATGAGTTTATG
77312 GAAGAAAAAGAAATGAGTTTATG
1 GAAGAAAAAGAAATGAGTTTATG
77335 GAAGAAAAAGAAATG
1 GAAGAAAAAGAAATG
77350 GAAGAAGCAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.21
Consensus pattern (23 bp):
GAAGAAAAAGAAATGAGTTTATG
Found at i:77381 original size:58 final size:57
Alignment explanation
Indices: 77292--77403 Score: 172
Period size: 58 Copynumber: 1.9 Consensus size: 57
77282 GTTTATGGAA
77292 GAAGAAGAAATGAGTTTATGGAAGAAAAAG-AAATGAGTTTATGGAAGAAAAAGAAATG
1 GAAGAAGAAATGAGTTTATGGAAGAAAAAGAAAAT--GTTTATGGAAGAAAAAGAAATG
* * *
77350 GAAGAAGCAATGAGTTTATGGAAGAAGAAGAAAATGTTTATGGAAGAAGAAGAA
1 GAAGAAGAAATGAGTTTATGGAAGAAAAAGAAAATGTTTATGGAAGAAAAAGAA
77404 TGGTTCAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
57 18 0.36
58 28 0.56
59 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.29, T:0.19
Consensus pattern (57 bp):
GAAGAAGAAATGAGTTTATGGAAGAAAAAGAAAATGTTTATGGAAGAAAAAGAAATG
Found at i:78356 original size:26 final size:26
Alignment explanation
Indices: 78246--78348 Score: 197
Period size: 26 Copynumber: 4.0 Consensus size: 26
78236 ATTTTAATCA
*
78246 TTATTTATTAAATTAACATAAATAAC
1 TTATTGATTAAATTAACATAAATAAC
78272 TTATTGATTAAATTAACATAAATAAC
1 TTATTGATTAAATTAACATAAATAAC
78298 TTATTGATTAAATTAACATAAATAAC
1 TTATTGATTAAATTAACATAAATAAC
78324 TTATTGATTAAATTAACATAAATAA
1 TTATTGATTAAATTAACATAAATAA
78349 TATCTTGAAA
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.50, C:0.07, G:0.03, T:0.40
Consensus pattern (26 bp):
TTATTGATTAAATTAACATAAATAAC
Found at i:94296 original size:36 final size:36
Alignment explanation
Indices: 94222--94301 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
94212 TACCAAACCT
* **
94222 GTCCCCATCCCCGTTTAACATAAACGGTTTTTTCCC
1 GTCCCCGTCCCCGTTTAACATAAACAATTTTTTCCC
* *
94258 GTCTCCGTCCCCGTTTAGCATAAACAA-TTTTTCTCC
1 GTCCCCGTCCCCGTTTAACATAAACAATTTTTTC-CC
94294 GTCCCCGT
1 GTCCCCGT
94302 TTAATTCGAT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 6 0.16
36 31 0.84
ACGTcount: A:0.17, C:0.36, G:0.12, T:0.34
Consensus pattern (36 bp):
GTCCCCGTCCCCGTTTAACATAAACAATTTTTTCCC
Found at i:95023 original size:101 final size:101
Alignment explanation
Indices: 94848--95045 Score: 362
Period size: 101 Copynumber: 2.0 Consensus size: 101
94838 AATTGCATAA
*
94848 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATGTCA
1 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
*
94913 TGATTTTTTTATCATTTTTACAAAATTATAACATCC
66 TGATTTTTTTATCATTTTTACAAAATGATAACATCC
94949 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
1 ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
95014 T-ATATTTTTTATCATTTTTACAAAATGATAAC
66 TGAT-TTTTTTATCATTTTTACAAAATGATAAC
95046 TGGATGTTAT
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
100 2 0.02
101 92 0.98
ACGTcount: A:0.40, C:0.07, G:0.08, T:0.45
Consensus pattern (101 bp):
ATTATTAGTAAACTATGTTGAAATAATTATTCTGGTTATTAAATTTTAAAAATTATGAAATATCA
TGATTTTTTTATCATTTTTACAAAATGATAACATCC
Found at i:97428 original size:2 final size:2
Alignment explanation
Indices: 97421--97455 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
97411 ATATCGTTTA
97421 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
97456 AATACTGGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.