Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002159.1 Hibiscus syriacus cultivar Beakdansim tig00004408_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: 68981
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:10191 original size:11 final size:11
Alignment explanation
Indices: 10175--10204 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10165 AATGATTTCC
10175 GTGAAATTATA
1 GTGAAATTATA
10186 GTGAAATTATA
1 GTGAAATTATA
*
10197 GTAAAATT
1 GTGAAATT
10205 TATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.17, T:0.37
Consensus pattern (11 bp):
GTGAAATTATA
Found at i:10244 original size:8 final size:8
Alignment explanation
Indices: 10228--10260 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
10218 TAACTAATAA
*
10228 TATTTATT
1 TATTAATT
10236 TATTAATT
1 TATTAATT
10244 TATTAATT
1 TATTAATT
10252 TATTAATT
1 TATTAATT
10260 T
1 T
10261 GGATCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTAATT
Found at i:12352 original size:36 final size:35
Alignment explanation
Indices: 12307--12431 Score: 146
Period size: 36 Copynumber: 3.6 Consensus size: 35
12297 AGCCGGGGGT
*
12307 GGTTCAGATTGTTTAGCTTTGTTCTGAGCTGCTGGC
1 GGTTGAGATTGTTTAGCTTTGTTCTGAGCTGC-GGC
* *
12343 GGTTGAGATTGTTTAGGTTTGTTCTGAGCTGCCGGA
1 GGTTGAGATTGTTTAGCTTTGTTCTGAGCTG-CGGC
* * * *
12379 GGTCGAGCTTGTTGAGGTTTGTTCTGAGC--CGGC
1 GGTTGAGATTGTTTAGCTTTGTTCTGAGCTGCGGC
*
12412 GGTTGAGCTTGTTTAGCTTT
1 GGTTGAGATTGTTTAGCTTT
12432 TCCCAAAACG
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
33 20 0.26
36 57 0.73
37 1 0.01
ACGTcount: A:0.11, C:0.14, G:0.34, T:0.40
Consensus pattern (35 bp):
GGTTGAGATTGTTTAGCTTTGTTCTGAGCTGCGGC
Found at i:13566 original size:3 final size:3
Alignment explanation
Indices: 13558--13617 Score: 113
Period size: 3 Copynumber: 20.3 Consensus size: 3
13548 TTAAATATGG
13558 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
13605 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
13618 GAAGACATGT
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:17199 original size:31 final size:30
Alignment explanation
Indices: 17159--17229 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
17149 CTTTCAAGAC
* * * **
17159 ATATAGATAGTTTACCTATGTCCTTTGGGAT
1 ATATGGATAG-TTACATATGTCCTTCGAAAT
*
17190 ATATGGATAGTTACATATGTTCTTCGAAAT
1 ATATGGATAGTTACATATGTCCTTCGAAAT
17220 ATATGGATAG
1 ATATGGATAG
17230 GTCATTCGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 25 0.74
31 9 0.26
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.39
Consensus pattern (30 bp):
ATATGGATAGTTACATATGTCCTTCGAAAT
Found at i:19312 original size:37 final size:37
Alignment explanation
Indices: 19239--19313 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
19229 GTTAGAAAAT
* *
19239 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
19276 ATTTATATATATATT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAT-T-TTCTTTAAAAAATTGAAAATCATAAA
19313 A
1 A
19314 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 16 0.48
38 15 0.45
39 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:27991 original size:20 final size:20
Alignment explanation
Indices: 27944--28061 Score: 121
Period size: 20 Copynumber: 5.9 Consensus size: 20
27934 GCGATTTTCC
* *
27944 GACTATCGCAATGCGAATAT
1 GACTATCGCAACGCGATTAT
* * *
27964 GTA-AATCGCAATGCGAGTAT
1 G-ACTATCGCAACGCGATTAT
*
27984 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTAT
* *
28004 GACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGATTAT
*
28024 GACTATCGCAACGCGATTCT
1 GACTATCGCAACGCGATTAT
* *
28044 GACTGTTGCAACGCGATT
1 GACTATCGCAACGCGATT
28062 TTCAAAGCGC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.01
20 84 0.98
21 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (20 bp):
GACTATCGCAACGCGATTAT
Found at i:29711 original size:12 final size:12
Alignment explanation
Indices: 29692--29735 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
29682 TCAACGATCG
29692 GGTCGGGTCAAC
1 GGTCGGGTCAAC
* *
29704 GGTTGGGTC--G
1 GGTCGGGTCAAC
29714 GGTCGGGTCAAC
1 GGTCGGGTCAAC
29726 GGTCGGGTCA
1 GGTCGGGTCA
29736 GGTCAGACCG
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
10 8 0.31
12 18 0.69
ACGTcount: A:0.11, C:0.20, G:0.48, T:0.20
Consensus pattern (12 bp):
GGTCGGGTCAAC
Found at i:29716 original size:22 final size:22
Alignment explanation
Indices: 29689--29739 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
29679 CGGTCAACGA
*
29689 TCGGGTCGGGTCAACGGTTGGG
1 TCGGGTCGGGTCAACGGTCGGG
29711 TCGGGTCGGGTCAACGGTCGGG
1 TCGGGTCGGGTCAACGGTCGGG
*
29733 TCAGGTC
1 TCGGGTC
29740 AGACCGGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.10, C:0.22, G:0.47, T:0.22
Consensus pattern (22 bp):
TCGGGTCGGGTCAACGGTCGGG
Found at i:29729 original size:17 final size:17
Alignment explanation
Indices: 29680--29740 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 17
29670 AACGGTTAAC
*
29680 GGTCAACGATCGGGTCG
1 GGTCAACGGTCGGGTCG
29697 GGTCAACGGTTGGGTCGGGTCG
1 GGTCAAC-----GGTCGGGTCG
*
29719 GGTCAACGGTCGGGTCA
1 GGTCAACGGTCGGGTCG
29736 GGTCA
1 GGTCA
29741 GACCGGTCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 21 0.57
22 16 0.43
ACGTcount: A:0.15, C:0.21, G:0.44, T:0.20
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:29760 original size:19 final size:19
Alignment explanation
Indices: 29738--29835 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 19
29728 TCGGGTCAGG
29738 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
29757 TCAGACCGGTCAAACCAGT
1 TCAGACCGGTCAAACCGGT
* *
29776 TC-GAACCGGTTGAAACC-GA
1 TCAG-ACCGG-TCAAACCGGT
*
29795 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
29815 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
29835 T
1 T
29836 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 3 0.05
19 37 0.57
20 16 0.25
21 9 0.14
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:29784 original size:29 final size:29
Alignment explanation
Indices: 29742--29834 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
29732 GTCAGGTCAG
* *
29742 ACCGGTCA-AACCGGTTCAGACCGGTCAA
1 ACCGGTCAGAACCGGTTCAAACCGATCAA
* *
29770 ACCAGTTC-GAACCGGTTGAAACCGATCAA
1 ACC-GGTCAGAACCGGTTCAAACCGATCAA
* * *
29799 ACCGGTCAGAACCGGTTGAAAACCGGTTAA
1 ACCGGTCAGAACCGGTT-CAAACCGATCAA
29829 ACCGGT
1 ACCGGT
29835 TTCCAGCAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
28 6 0.11
29 32 0.60
30 15 0.28
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (29 bp):
ACCGGTCAGAACCGGTTCAAACCGATCAA
Found at i:29792 original size:10 final size:10
Alignment explanation
Indices: 29742--29835 Score: 81
Period size: 9 Copynumber: 9.7 Consensus size: 10
29732 GTCAGGTCAG
29742 ACCGG-TCAA
1 ACCGGTTCAA
*
29751 ACCGGTTCAG
1 ACCGGTTCAA
29761 ACCGG-TCAA
1 ACCGGTTCAA
* *
29770 ACCAGTTCGA
1 ACCGGTTCAA
*
29780 ACCGGTTGAA
1 ACCGGTTCAA
*
29790 ACC-GATCAA
1 ACCGGTTCAA
29799 ACCGG-TCAGA
1 ACCGGTTCA-A
*
29809 ACCGGTTGAAA
1 ACCGGTT-CAA
29820 ACCGGTT-AA
1 ACCGGTTCAA
29829 ACCGGTT
1 ACCGGTT
29836 TCCAGCAGCC
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
9 31 0.45
10 28 0.41
11 9 0.13
12 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.24, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:29833 original size:20 final size:21
Alignment explanation
Indices: 29797--29835 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
29787 GAAACCGATC
29797 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
29818 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
29836 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:37019 original size:17 final size:17
Alignment explanation
Indices: 36997--37034 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
36987 ACGGTCAACT
36997 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
37014 GTCAACGGTCGGGTCGG
1 GTCAACGGTCGGGTCGG
37031 GTCA
1 GTCA
37035 GACCGGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGG
Found at i:37054 original size:19 final size:20
Alignment explanation
Indices: 37032--37099 Score: 81
Period size: 19 Copynumber: 3.5 Consensus size: 20
37022 TCGGGTCGGG
37032 TCAG-ACCGGTCAAACCGGT
1 TCAGAACCGGTCAAACCGGT
*
37051 TCAG-ACCGGTCAAATCGGT
1 TCAGAACCGGTCAAACCGGT
*
37070 TC-GAACCGGTTGAAACCGG-
1 TCAGAACCGG-TCAAACCGGT
37089 TCAGAACCGGT
1 TCAGAACCGGT
37100 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
18 1 0.02
19 28 0.65
20 14 0.33
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (20 bp):
TCAGAACCGGTCAAACCGGT
Found at i:37087 original size:29 final size:30
Alignment explanation
Indices: 37030--37100 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 30
37020 GGTCGGGTCG
* *
37030 GGTCAG-ACCGG-TCAAACCGGTTCAGACC
1 GGTCAGAACCGGTTCGAACCGGTTCAAACC
* *
37058 GGTCA-AATCGGTTCGAACCGGTTGAAACC
1 GGTCAGAACCGGTTCGAACCGGTTCAAACC
37087 GGTCAGAACCGGTT
1 GGTCAGAACCGGTT
37101 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 9 0.26
29 19 0.54
30 7 0.20
ACGTcount: A:0.25, C:0.27, G:0.30, T:0.18
Consensus pattern (30 bp):
GGTCAGAACCGGTTCGAACCGGTTCAAACC
Found at i:37951 original size:22 final size:22
Alignment explanation
Indices: 37926--37968 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
37916 GGCGACATCC
37926 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
37948 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
37969 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:40313 original size:20 final size:20
Alignment explanation
Indices: 40288--40328 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
40278 TAGTTTACTT
40288 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
40308 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
40328 T
1 T
40329 AAAATCGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.17
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:40375 original size:20 final size:20
Alignment explanation
Indices: 40350--40405 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
40340 GCGATTCTCT
40350 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
40370 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
40390 CATTGCGATAGTCATT
1 CGTTGCGATAGTCATT
40406 CGTGTTACGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:40997 original size:21 final size:20
Alignment explanation
Indices: 40906--41004 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
40896 GACTCACCTG
40906 TCATCGTTCAAGAGG-CCTCC
1 TCATCGTTCAAGAGGCCCT-C
* *
40926 CCTATCGTTCAAGAGGCCCTTA
1 TC-ATCGTTCAAGAGGCCC-TC
** *
40948 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAG-GCCCTC
* * *
40969 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCC-CTC
*
40990 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
41005 TCCATCCCAA
Statistics
Matches: 58, Mismatches: 16, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
20 3 0.05
21 48 0.83
22 6 0.10
23 1 0.02
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.23
Consensus pattern (20 bp):
TCATCGTTCAAGAGGCCCTC
Found at i:41003 original size:42 final size:41
Alignment explanation
Indices: 40902--41004 Score: 109
Period size: 42 Copynumber: 2.5 Consensus size: 41
40892 GCCCGACTCA
* *
40902 CCTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGC
1 CCTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGC
* ** *
40943 CCTTATCATCCCTCAAGAGTCC-CCTCCCACCGTTCAAGAGGC
1 CC-TGTCATCGTTCAAGAGGCCTCC-CCCACCGTTCAAGAGGC
*
40985 CACTGTCATCGTTGAAGAGG
1 C-CTGTCATCGTTCAAGAGG
41005 TCCATCCCAA
Statistics
Matches: 48, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
41 4 0.08
42 43 0.90
43 1 0.02
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.23
Consensus pattern (41 bp):
CCTGTCATCGTTCAAGAGGCCTCCCCCACCGTTCAAGAGGC
Found at i:42449 original size:14 final size:14
Alignment explanation
Indices: 42415--42476 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
42405 TTGCTTGTTT
*
42415 AATTGATTTATAAA
1 AATTGATTTGTAAA
*
42429 AACTGATTTGTAAA
1 AATTGATTTGTAAA
* *
42443 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
42458 TATTGATGTGTAAA
1 AATTGATTTGTAAA
42472 TAATT
1 -AATT
42477 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.45
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:42776 original size:20 final size:20
Alignment explanation
Indices: 42673--42955 Score: 205
Period size: 20 Copynumber: 14.8 Consensus size: 20
42663 GATTTTCTCG
* *
42673 TTGCGATAGTCAAATACCCA
1 TTGCGATAGTCAAATTCGCA
* *
42693 TTGTGATAATCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
42713 TTGCGATACTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* *
42733 TTGTGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
*
42753 TTGCGATAGACAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* *
42773 TTGCGAT--T----TTTGCG
1 TTGCGATAGTCAAATTCGCA
* **
42787 TTGCGATAGTCATATTCGTG
1 TTGCGATAGTCAAATTCGCA
* **
42807 TTGCGATAGTCATATTCGTG
1 TTGCGATAGTCAAATTCGCA
*
42827 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
*
42847 TTGCGAT--T----TTTG-A
1 TTGCGATAGTCAAATTCGCA
* * * *
42860 GTTACGATAATCAAATTCACG
1 -TTGCGATAGTCAAATTCGCA
*
42881 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
* *
42901 TTGCGATATTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
* *
42921 TTGCGATATTCAAATTCGCG
1 TTGCGATAGTCAAATTCGCA
* *
42941 TTGTGATATTCAAAT
1 TTGCGATAGTCAAAT
42956 GATTGTGTAA
Statistics
Matches: 219, Mismatches: 30, Indels: 28
0.79 0.11 0.10
Matches are distributed among these distances:
14 20 0.09
16 2 0.01
18 1 0.00
20 196 0.89
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:42793 original size:34 final size:34
Alignment explanation
Indices: 42750--42887 Score: 125
Period size: 34 Copynumber: 3.9 Consensus size: 34
42740 AGTCAAATTC
*
42750 GCGTTGCGATAGACAAATTCGCATTGCGATTTTT
1 GCGTTGCGATAGACAAATTCGCGTTGCGATTTTT
* * *
42784 GCGTTGCGATAGTCATATTCGTGTTGCGATAGTCATATT
1 GCGTTGCGATAGACAAATTCGCGTTGCGAT--T--T-TT
* *
42823 CGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
1 -GCGTTGCGATAGACAAATTCGCGTTGCGATTTTT
* * *
42858 GAGTTACGATA-ATCAAATTCACGTTGCGAT
1 GCGTTGCGATAGA-CAAATTCGCGTTGCGAT
42888 AGTCAAATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
34 51 0.59
35 2 0.02
36 2 0.02
38 2 0.02
39 2 0.02
40 27 0.31
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (34 bp):
GCGTTGCGATAGACAAATTCGCGTTGCGATTTTT
Found at i:42818 original size:74 final size:74
Alignment explanation
Indices: 42713--42927 Score: 304
Period size: 74 Copynumber: 2.9 Consensus size: 74
42703 CAAATTCGCA
* * * * *
42713 TTGCGATACTCAAATTCGCATTGTGATAGTCAAATTCGCGTTGCGATAGACAAATTCGCATTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCG
*
42778 ATTTTTGCG
66 ATTTTTGAG
* * * * *
42787 TTGCGATAGTCATATTCGTGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCG
42852 ATTTTTGAG
66 ATTTTTGAG
* * *
42861 TTACGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAATTCGCGTTGCG
1 TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCG
42926 AT
66 AT
42928 ATTCAAATTC
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 123 1.00
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (74 bp):
TTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCG
ATTTTTGAG
Found at i:43279 original size:18 final size:18
Alignment explanation
Indices: 43256--43290 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43246 AAGCCGGTTG
*
43256 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
43274 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
43291 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:46476 original size:20 final size:20
Alignment explanation
Indices: 46430--46499 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
46420 AAATTCAGTG
* * *
46430 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCATAATCGCA
46450 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCATAATCGCA
* *
46470 TTGCGAT-TTACATATTCGCA
1 TTGCGATAGT-CATAATCGCA
46490 TTGCGATAGT
1 TTGCGATAGT
46500 TGAAAAATCG
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 40 0.95
21 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCATAATCGCA
Found at i:47165 original size:2 final size:2
Alignment explanation
Indices: 47160--47191 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
47150 ACAGAAAGCC
47160 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47192 GAATTTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:52224 original size:45 final size:45
Alignment explanation
Indices: 52160--52252 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
52150 AAAGAGCAAC
52160 GAGACGAATGACAAGCACCGAACTTAGCGAGTAACAAGTCAAGTT
1 GAGACGAATGACAAGCACCGAACTTAGCGAGTAACAAGTCAAGTT
52205 GAGACGAATGACAAGCACCGAACTTAGCGAGTAACAAGTCAAGTT
1 GAGACGAATGACAAGCACCGAACTTAGCGAGTAACAAGTCAAGTT
52250 GAG
1 GAG
52253 TAACAATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.15
Consensus pattern (45 bp):
GAGACGAATGACAAGCACCGAACTTAGCGAGTAACAAGTCAAGTT
Found at i:52859 original size:27 final size:27
Alignment explanation
Indices: 52813--52876 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
52803 TAAACAGTGT
52813 TGAATGATTCAACACAGAAATACATTC
1 TGAATGATTCAACACAGAAATACATTC
* * *
52840 TGAATGATTCAGCACGGAAATGCATTC
1 TGAATGATTCAACACAGAAATACATTC
*
52867 TAAATGATTC
1 TGAATGATTC
52877 GGGGCCATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (27 bp):
TGAATGATTCAACACAGAAATACATTC
Found at i:54390 original size:31 final size:31
Alignment explanation
Indices: 54353--54428 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
54343 GATAAGATAG
* * *
54353 ATGATCACATATTAATTAAATAAAAATGAAT
1 ATGATCACATATTAATAAAATAAAAATAAAA
* *
54384 GTGATCACATTTTAATAAAATAAAAATAAAA
1 ATGATCACATATTAATAAAATAAAAATAAAA
*
54415 ATGATCAAATATTA
1 ATGATCACATATTA
54429 TATTTTTTAA
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.32
Consensus pattern (31 bp):
ATGATCACATATTAATAAAATAAAAATAAAA
Found at i:58121 original size:60 final size:60
Alignment explanation
Indices: 58039--58162 Score: 214
Period size: 60 Copynumber: 2.1 Consensus size: 60
58029 GAAACTGTCA
**
58039 CTAATGAAAGAAGCAATCAACATAATAAAGTTGTTGCAGCCGAGGGCTTTGAAAT-GCCTT
1 CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTG-AATGGCCTT
58099 CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTGAATGGCCTT
1 CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTGAATGGCCTT
58159 CTAA
1 CTAA
58163 CTTGGAGTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 3 0.05
60 58 0.95
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (60 bp):
CTAATGAAAGAAGCAATCAACATAATAAAGTTACTGCAGCCGAGGGCTTTGAATGGCCTT
Found at i:68580 original size:2 final size:2
Alignment explanation
Indices: 68573--68597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
68563 GACAAGAGGT
68573 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
68598 ATCCCTATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Done.