Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007247.1 Hibiscus syriacus cultivar Beakdansim tig00019201_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: 53529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5747 original size:31 final size:31
Alignment explanation
Indices: 5712--5810 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
5702 TTTTAAAACC
* *
5712 GTACCTAATGTTTACTTTTTGTTTAATTTTA
1 GTACCCAATGTTAACTTTTTGTTTAATTTTA
* * *
5743 GTACCCATTGTTAACTTTTTGTTTCATTTTG
1 GTACCCAATGTTAACTTTTTGTTTAATTTTA
** * * *
5774 GTATCCCGCTATTAATTTTTTGTTTTATTTTA
1 GTA-CCCAATGTTAACTTTTTGTTTAATTTTA
5806 GTACC
1 GTACC
5811 TAAATTTTAA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 31 0.55
32 25 0.45
ACGTcount: A:0.19, C:0.14, G:0.11, T:0.56
Consensus pattern (31 bp):
GTACCCAATGTTAACTTTTTGTTTAATTTTA
Found at i:5804 original size:32 final size:31
Alignment explanation
Indices: 5725--5810 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 31
5715 CCTAATGTTT
* *
5725 ACTTTTTGTTTAATTTTAGTACCCATTGTTA
1 ACTTTTTGTTTAATTTTAGTACCCACTATTA
* * *
5756 ACTTTTTGTTTCATTTTGGTATCCCGCTATTA
1 ACTTTTTGTTTAATTTTAGTA-CCCACTATTA
* *
5788 ATTTTTTGTTTTATTTTAGTACC
1 ACTTTTTGTTTAATTTTAGTACC
5811 TAAATTTTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
31 21 0.46
32 25 0.54
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (31 bp):
ACTTTTTGTTTAATTTTAGTACCCACTATTA
Found at i:5906 original size:31 final size:32
Alignment explanation
Indices: 5871--5931 Score: 81
Period size: 31 Copynumber: 1.9 Consensus size: 32
5861 TATGATTTTG
*
5871 AAAATTCAA-AGTTTAAGTACTAAA-ATGTAAT
1 AAAATT-AATAGTTTAAGTAATAAATATGTAAT
*
5902 AAAATTAATAGTTTAGGTAATAAATATGTA
1 AAAATTAATAGTTTAAGTAATAAATATGTA
5932 CTTTACCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.08
31 19 0.73
32 5 0.19
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (32 bp):
AAAATTAATAGTTTAAGTAATAAATATGTAAT
Found at i:13664 original size:14 final size:14
Alignment explanation
Indices: 13645--13676 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
13635 GAAACAAATT
13645 CAAAGTCTAAAAAC
1 CAAAGTCTAAAAAC
13659 CAAAGTCTAAAAAC
1 CAAAGTCTAAAAAC
13673 CAAA
1 CAAA
13677 AATAACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.22, G:0.06, T:0.12
Consensus pattern (14 bp):
CAAAGTCTAAAAAC
Found at i:15847 original size:14 final size:14
Alignment explanation
Indices: 15809--15847 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
15799 AAATAATAGA
*
15809 TTTAAGATTTATGG
1 TTTAAGATTTAAGG
* *
15823 TTGAAGTTTTAAGG
1 TTTAAGATTTAAGG
15837 TTTAAGATTTA
1 TTTAAGATTTA
15848 GGATTTGAGG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (14 bp):
TTTAAGATTTAAGG
Found at i:16738 original size:30 final size:30
Alignment explanation
Indices: 16699--16796 Score: 124
Period size: 30 Copynumber: 3.3 Consensus size: 30
16689 GTTATAATCT
* *
16699 CATGTAGATGTCAGAACAGGAAATTTATCC
1 CATGCAGATGTCAGAACAGGGAATTTATCC
* * *
16729 CATGCAGATGTCAGAACGGGGGATTTATCT
1 CATGCAGATGTCAGAACAGGGAATTTATCC
* **
16759 CATACAGATGTCAGAACAGGGAATAAATCC
1 CATGCAGATGTCAGAACAGGGAATTTATCC
16789 CATGCAGA
1 CATGCAGA
16797 ATCAGGACGG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (30 bp):
CATGCAGATGTCAGAACAGGGAATTTATCC
Found at i:16811 original size:29 final size:29
Alignment explanation
Indices: 16769--16838 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
16759 CATACAGATG
*
16769 TCAGAACAGGGAATAAATCCCATGCAGAA
1 TCAGGACAGGGAATAAATCCCATGCAGAA
* *
16798 TCAGGACGGGGAATAAATCTCATGCAGAA
1 TCAGGACAGGGAATAAATCCCATGCAGAA
16827 TCAGGACAGGGA
1 TCAGGACAGGGA
16839 TTATGCTCTC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.40, C:0.19, G:0.27, T:0.14
Consensus pattern (29 bp):
TCAGGACAGGGAATAAATCCCATGCAGAA
Found at i:17921 original size:23 final size:23
Alignment explanation
Indices: 17889--17938 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
17879 GGTTATCTAA
17889 GATTACCGGGGGGAATGAAATGT
1 GATTACCGGGGGGAATGAAATGT
* *
17912 GATTATCGGGGGGAATGGAATGT
1 GATTACCGGGGGGAATGAAATGT
17935 GATT
1 GATT
17939 CCCCCGTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.28, C:0.06, G:0.40, T:0.26
Consensus pattern (23 bp):
GATTACCGGGGGGAATGAAATGT
Found at i:19295 original size:10 final size:10
Alignment explanation
Indices: 19250--19336 Score: 57
Period size: 10 Copynumber: 8.1 Consensus size: 10
19240 CCAACACGTT
19250 GGGCATCCGA
1 GGGCATCCGA
*
19260 GGCCATCCGAA
1 GGGCATCCG-A
* *
19271 CGAGCTATGCGA
1 -GGGC-ATCCGA
19283 GGGCATCCGA
1 GGGCATCCGA
*
19293 GGGCAACCGA
1 GGGCATCCGA
*
19303 GCGAGCTATGCGA
1 G-G-GC-ATCCGA
*
19316 GGGAATCCGA
1 GGGCATCCGA
*
19326 GGGCAGCCGA
1 GGGCATCCGA
19336 G
1 G
19337 CGAGGCTAGG
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
10 37 0.64
11 6 0.10
12 6 0.10
13 9 0.16
ACGTcount: A:0.24, C:0.28, G:0.39, T:0.09
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:19328 original size:33 final size:33
Alignment explanation
Indices: 19254--19340 Score: 129
Period size: 33 Copynumber: 2.6 Consensus size: 33
19244 CACGTTGGGC
* * * *
19254 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
19287 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
*
19320 ATCCGAGGGCAGCCGAGCGAG
1 ATCCGAGGGCAACCGAGCGAG
19341 GCTAGGTCGC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.25, C:0.28, G:0.38, T:0.09
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCGAGGGA
Found at i:30251 original size:35 final size:35
Alignment explanation
Indices: 30212--30307 Score: 147
Period size: 35 Copynumber: 2.7 Consensus size: 35
30202 AAAATAGTCA
*
30212 TCAATTACATCCTAAACCCCAAATTCTAAAATTCT
1 TCAATTACATCCTAAACCCCAAATTCTAAAATACT
* *
30247 TCAATTACATTCTAAACCTCAAATTCTAAAATACT
1 TCAATTACATCCTAAACCCCAAATTCTAAAATACT
* *
30282 TCAATTACATGCTCAACCCCAAATTC
1 TCAATTACATCCTAAACCCCAAATTC
30308 ATAATTCATT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.40, C:0.28, G:0.01, T:0.31
Consensus pattern (35 bp):
TCAATTACATCCTAAACCCCAAATTCTAAAATACT
Found at i:31108 original size:35 final size:35
Alignment explanation
Indices: 31062--31157 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 35
31052 AATGGATTAT
***
31062 GAATTTGAGGTTGGGCATATAATTGAAGTATTTTG
1 GAATTTGAGGTTGAAAATATAATTGAAGTATTTTG
* *
31097 GAATTTGAGGTTTAAAATGTAATTGAAGTATTTTG
1 GAATTTGAGGTTGAAAATATAATTGAAGTATTTTG
* * * * *
31132 AAATTTGGGGTTTAAGATGTAATTGA
1 GAATTTGAGGTTGAAAATATAATTGA
31158 TGATTGTGTT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.32, C:0.01, G:0.26, T:0.41
Consensus pattern (35 bp):
GAATTTGAGGTTGAAAATATAATTGAAGTATTTTG
Found at i:33928 original size:29 final size:29
Alignment explanation
Indices: 33894--33949 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
33884 TCCCAACACA
*
33894 TAGGTCGCCATTCCCTCCGGGCAACCTTG
1 TAGGTCGCCATGCCCTCCGGGCAACCTTG
* *
33923 TAGGTCGTCATGCCCTCCGGGCGACCT
1 TAGGTCGCCATGCCCTCCGGGCAACCT
33950 ATCCTCGCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.12, C:0.38, G:0.27, T:0.23
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCAACCTTG
Found at i:34026 original size:33 final size:33
Alignment explanation
Indices: 33965--34027 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
33955 CGCTCGGCTT
* * *
33965 CCCTCTCATAGCTCGCTCGGTTGCCCTCGGATG
1 CCCTCGCATAGCTCGCTCAGATGCCCTCGGATG
* *
33998 CCCTCGCATAGCTCGTTCAGATGGCCTCGG
1 CCCTCGCATAGCTCGCTCAGATGCCCTCGG
34028 TTGGATGGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.11, C:0.38, G:0.25, T:0.25
Consensus pattern (33 bp):
CCCTCGCATAGCTCGCTCAGATGCCCTCGGATG
Found at i:34034 original size:14 final size:14
Alignment explanation
Indices: 34017--34073 Score: 51
Period size: 14 Copynumber: 3.6 Consensus size: 14
34007 AGCTCGTTCA
34017 GATGGCCTCGGTTG
1 GATGGCCTCGGTTG
34031 GATGGCCTCGGATGCTCTCG
1 GATGGCCTC-G--G-T-T-G
*
34051 GATGGCCTCGGTCG
1 GATGGCCTCGGTTG
34065 GATGGCCTC
1 GATGGCCTC
34074 AGATGCCCAG
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
14 19 0.53
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 2 0.06
20 10 0.28
ACGTcount: A:0.09, C:0.28, G:0.39, T:0.25
Consensus pattern (14 bp):
GATGGCCTCGGTTG
Found at i:35706 original size:15 final size:15
Alignment explanation
Indices: 35686--35716 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35676 AGTTGCTAGC
35686 GGTGATTATTCAATT
1 GGTGATTATTCAATT
35701 GGTGATTATTCAATT
1 GGTGATTATTCAATT
35716 G
1 G
35717 AGACGAGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.23, T:0.45
Consensus pattern (15 bp):
GGTGATTATTCAATT
Found at i:42405 original size:29 final size:29
Alignment explanation
Indices: 42315--42398 Score: 150
Period size: 29 Copynumber: 2.9 Consensus size: 29
42305 TGATCGCCAT
*
42315 AGGTCGCCATGCGATCCAGGCGACCTTGG
1 AGGTCGCCATGCAATCCAGGCGACCTTGG
42344 AGGTCGCCATGCAATCCAGGCGACCTTGG
1 AGGTCGCCATGCAATCCAGGCGACCTTGG
*
42373 AGGTCGCCATGCAATCCGGGCGACCT
1 AGGTCGCCATGCAATCCAGGCGACCT
42399 CCAAGGTATA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.19, C:0.32, G:0.32, T:0.17
Consensus pattern (29 bp):
AGGTCGCCATGCAATCCAGGCGACCTTGG
Found at i:42486 original size:20 final size:20
Alignment explanation
Indices: 42437--42477 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
42427 ATCATGGGCC
42437 GTGGGAATGCATGGGGGAGG
1 GTGGGAATGCATGGGGGAGG
42457 GTGGGAATGCATGGGGGAGG
1 GTGGGAATGCATGGGGGAGG
42477 G
1 G
42478 GATGCATGCT
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:0.20, C:0.05, G:0.61, T:0.15
Consensus pattern (20 bp):
GTGGGAATGCATGGGGGAGG
Found at i:43020 original size:21 final size:21
Alignment explanation
Indices: 42995--43038 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
42985 AATCTAGTTA
42995 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
43016 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
43037 AT
1 AT
43039 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:43048 original size:28 final size:30
Alignment explanation
Indices: 43015--43077 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
43005 TAGTATAAAT
*
43015 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
43043 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
43073 TATTA
1 TATTA
43078 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:43587 original size:15 final size:16
Alignment explanation
Indices: 43567--43596 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43557 TTCCGTTATA
43567 AAAAATATT-GTGTTT
1 AAAAATATTAGTGTTT
43582 AAAAATATTAGTGTT
1 AAAAATATTAGTGTT
43597 GTTTTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (16 bp):
AAAAATATTAGTGTTT
Found at i:43910 original size:26 final size:25
Alignment explanation
Indices: 43881--43939 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
43871 AAATCATATT
*
43881 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
43907 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
43933 ATTATTA
1 ATTATTA
43940 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:45471 original size:47 final size:47
Alignment explanation
Indices: 45368--45458 Score: 134
Period size: 45 Copynumber: 2.0 Consensus size: 47
45358 CAACAAACAA
45368 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
1 ATATAAC-TAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
* *
45416 ATATAACTAACTA-TTAAC-AATACAAACTAATT-AATTATTTTTT
1 ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTT
45459 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
44 10 0.24
45 13 0.32
46 5 0.12
47 6 0.15
48 7 0.17
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (47 bp):
ATATAACTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTT
Found at i:45527 original size:41 final size:40
Alignment explanation
Indices: 45389--45527 Score: 111
Period size: 41 Copynumber: 3.3 Consensus size: 40
45379 CTATTTAACT
* * *
45389 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATT
1 AACATAAACTAATTAAAT-ATTTTTTAACTAT-A-TAACTATA
*
45431 AACAATACAAACTAATTAATTATTTTTTAACTATATAACTATCA
1 AAC-AT--AAACTAATTAAATATTTTTTAACTATATAACTAT-A
* * *
45475 AACATATACTAATTAAATATTTTTTAATTTATGTATACTAT-
1 AACATAAACTAATTAAATATTTTTTAA-CTATATA-ACTATA
*
45516 AACTTAAACTAA
1 AACATAAACTAA
45528 CAATCATATA
Statistics
Matches: 80, Mismatches: 10, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
41 30 0.38
42 8 0.10
43 15 0.19
44 12 0.15
45 15 0.19
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.41
Consensus pattern (40 bp):
AACATAAACTAATTAAATATTTTTTAACTATATAACTATA
Found at i:45813 original size:24 final size:25
Alignment explanation
Indices: 45780--45830 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
45770 TTTCTTTTAT
*
45780 AACCGGCTGCCTCAATTA-TTCACC
1 AACCGACTGCCTCAATTAGTTCACC
*
45804 AACCGACTGCCTTAATTAGTTCACC
1 AACCGACTGCCTCAATTAGTTCACC
45829 AA
1 AA
45831 TAATTGTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.25
Consensus pattern (25 bp):
AACCGACTGCCTCAATTAGTTCACC
Found at i:45971 original size:23 final size:23
Alignment explanation
Indices: 45941--45992 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
45931 ACACGTGAAG
45941 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
45964 GAATGGATGATGGGGCTGCATGT
1 GAATGGATGATGGGGCTGCATGT
45987 GAATGG
1 GAATGG
45993 GAATGGATGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.08, G:0.44, T:0.25
Consensus pattern (23 bp):
GAATGGATGATGGGGCTGCATGT
Found at i:46050 original size:29 final size:29
Alignment explanation
Indices: 46008--46117 Score: 220
Period size: 29 Copynumber: 3.8 Consensus size: 29
45998 GATGGAATGG
46008 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
46037 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
46066 CGCCGGGACTACATGGCGACCTATAAGGT
1 CGCCGGGACTACATGGCGACCTATAAGGT
46095 CGCCGGGACTACATGGCGACCTA
1 CGCCGGGACTACATGGCGACCTA
46118 CACCCTATTC
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 81 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (29 bp):
CGCCGGGACTACATGGCGACCTATAAGGT
Found at i:46177 original size:41 final size:41
Alignment explanation
Indices: 46131--46260 Score: 115
Period size: 41 Copynumber: 3.1 Consensus size: 41
46121 CCTATTCCTC
46131 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
46172 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
46214 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
46256 TGCAT
1 TGCAT
46261 CTATTCCTCT
Statistics
Matches: 65, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.05
39 3 0.05
40 1 0.02
41 27 0.42
42 2 0.03
43 22 0.34
44 1 0.02
45 3 0.05
46 3 0.05
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.24
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:46273 original size:55 final size:55
Alignment explanation
Indices: 46205--46315 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
46195 GAACGACCTC
46205 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
*
46260 TCTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
46315 T
1 T
46316 GGGGACCTCG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.15, C:0.34, G:0.22, T:0.29
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:46298 original size:139 final size:139
Alignment explanation
Indices: 46122--46538 Score: 816
Period size: 139 Copynumber: 3.0 Consensus size: 139
46112 GACCTACACC
46122 CTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
1 CTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
46187 CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCT
66 CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCT
46252 CGTATGCAT
131 CGTATGCAT
46261 CTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
1 CTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
*
46326 CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCACATGGCTCGCACTCGTATGGCT
66 CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCT
46391 CGTATGCAT
131 CGTATGCAT
*
46400 CTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
1 CTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
46465 CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCT
66 CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCT
46530 CGTATGCAT
131 CGTATGCAT
46539 GGGGAGAACC
Statistics
Matches: 275, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 275 1.00
ACGTcount: A:0.17, C:0.33, G:0.25, T:0.25
Consensus pattern (139 bp):
CTATTCCTCTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCATGGGGACCTCG
CATGGGGAGAACGACCTCTCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCT
CGTATGCAT
Found at i:46408 original size:55 final size:55
Alignment explanation
Indices: 46344--46454 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
46334 GAACGACCTC
46344 TCTATTCCACTGCATGGCCACCTCACATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCACATGGCTCGCACTCGTATGGCTCGTATGCA
*
46399 TCTATTCCACTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTATGCA
1 TCTATTCCACTGCATGGCCACCTCACATGGCTCGCACTCGTATGGCTCGTATGCA
46454 T
1 T
46455 GGGGACCTCG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.17, C:0.34, G:0.21, T:0.28
Consensus pattern (55 bp):
TCTATTCCACTGCATGGCCACCTCACATGGCTCGCACTCGTATGGCTCGTATGCA
Found at i:46463 original size:41 final size:41
Alignment explanation
Indices: 46409--46540 Score: 119
Period size: 41 Copynumber: 3.2 Consensus size: 41
46399 TCTATTCCAC
46409 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
** *** * *
46450 TGCATGGGGACCTCGCATGGGGAGAACGACCTCTCTAT---TC-CA
1 TGCATGGCCACCTCGCATGGCTCG--C-A-CTC-GTATGGCTCGTA
46492 CTGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
1 -TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
46534 TGCATGG
1 TGCATGG
46541 GGAGAACCAG
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
38 3 0.04
39 3 0.04
40 1 0.01
41 29 0.43
42 2 0.03
43 22 0.33
44 1 0.01
45 3 0.04
46 3 0.04
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (41 bp):
TGCATGGCCACCTCGCATGGCTCGCACTCGTATGGCTCGTA
Found at i:48116 original size:21 final size:20
Alignment explanation
Indices: 48092--48148 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
48082 ATTTTTTTAC
48092 AAAATAAAACTTATATTATTA
1 AAAATAAAACTTA-ATTATTA
*
48113 AAAATATTATA-TTAATTATTA
1 AAAATA--AAACTTAATTATTA
*
48134 AAAATACAAC-TAATT
1 AAAATAAAACTTAATT
48149 GGTGGGTGAG
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
19 6 0.20
21 19 0.63
22 3 0.10
23 2 0.07
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAATAAAACTTAATTATTA
Found at i:48813 original size:23 final size:23
Alignment explanation
Indices: 48760--48806 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
48750 AATACACTTA
48760 TAACTTTTGTTTTAAATAAATTG
1 TAACTTTTGTTTTAAATAAATTG
48783 TAACTTTTGTTTTAAATAAATTG
1 TAACTTTTGTTTTAAATAAATTG
48806 T
1 T
48807 TTTTTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (23 bp):
TAACTTTTGTTTTAAATAAATTG
Found at i:49616 original size:29 final size:29
Alignment explanation
Indices: 49555--49612 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
49545 TTAGGCATCG
* *
49555 TATTATTTATATCACTAAACTTTTAATTT
1 TATTAATTATAACACTAAACTTTTAATTT
49584 TATTAATTATAACACTAAA-TTTTAATTT
1 TATTAATTATAACACTAAACTTTTAATTT
49612 T
1 T
49613 TATTTCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 10 0.37
29 17 0.63
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (29 bp):
TATTAATTATAACACTAAACTTTTAATTT
Found at i:49816 original size:29 final size:29
Alignment explanation
Indices: 49748--49817 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
49738 TTTAAAGGTC
*
49748 TAGTGATATAATTGAAATGAAATCAAAGTT
1 TAGTGATATAATTGAAA-GAAATAAAAGTT
* *
49778 TAAT-ACTATAATTGATAA-AACTAAAAGTT
1 TAGTGA-TATAATTGA-AAGAAATAAAAGTT
49807 TAGTGATATAA
1 TAGTGATATAA
49818 ACAATATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
29 18 0.55
30 13 0.39
31 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.34
Consensus pattern (29 bp):
TAGTGATATAATTGAAAGAAATAAAAGTT
Found at i:50217 original size:4 final size:4
Alignment explanation
Indices: 50201--50236 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
50191 TGGGGACAAC
*
50201 CCCA CCTA CCCA CCCA CCCA CCCA CCCA CCCA CCCA
1 CCCA CCCA CCCA CCCA CCCA CCCA CCCA CCCA CCCA
50237 ACAGAGCGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.25, C:0.72, G:0.00, T:0.03
Consensus pattern (4 bp):
CCCA
Found at i:50850 original size:2 final size:2
Alignment explanation
Indices: 50843--50868 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50833 ACGTAATCTA
50843 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
50869 TAAAGTCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.