Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003842.1 Hibiscus syriacus cultivar Beakdansim tig00008234_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: 87883
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:10422 original size:13 final size:13
Alignment explanation
Indices: 10404--10428 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10394 GTTACTGAGA
10404 TTAAGACAATAAG
1 TTAAGACAATAAG
10417 TTAAGACAATAA
1 TTAAGACAATAA
10429 AATAAGGATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
TTAAGACAATAAG
Found at i:16797 original size:12 final size:11
Alignment explanation
Indices: 16763--16801 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
16753 TGTGTGTGCC
16763 TTTTTCTTTTA
1 TTTTTCTTTTA
16774 TTTCTT-TTTTA
1 TTT-TTCTTTTA
16785 TTTTTCCTTTTA
1 TTTTT-CTTTTA
16797 TTTTT
1 TTTTT
16802 GATGAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 2 0.08
11 11 0.44
12 12 0.48
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTCTTTTA
Found at i:20464 original size:18 final size:18
Alignment explanation
Indices: 20412--20465 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
20402 TTCGAGTCAA
* *
20412 AGTCAACGGGTCGGGTGG
1 AGTCAACGGTTCGGGTTG
* *
20430 GGTCAACGGTTTGGGTTG
1 AGTCAACGGTTCGGGTTG
*
20448 AGTCAACGGTTCAGGTTG
1 AGTCAACGGTTCGGGTTG
20466 GGTTGGGTCG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.17, C:0.15, G:0.43, T:0.26
Consensus pattern (18 bp):
AGTCAACGGTTCGGGTTG
Found at i:21487 original size:36 final size:35
Alignment explanation
Indices: 21440--21548 Score: 96
Period size: 36 Copynumber: 3.1 Consensus size: 35
21430 CAAAACTCAA
* *
21440 TTGAATTGAAAGTGAGGATGCTTCGTTTCGTTCTTC
1 TTGAATCGAAAGTGACGATGCTTC-TTTCGTTCTTC
* * *
21476 TTGAATCGAAAGTGTCGATGCTTCCTTCTGTTC-AC
1 TTGAATCGAAAGTGACGATGCTTCTTTC-GTTCTTC
* * *
21511 TTAAAGCGAAAGTG-CTGATGCTTCCTTTCATTCTTC
1 TTGAATCGAAAGTGAC-GATGCTT-CTTTCGTTCTTC
21547 TT
1 TT
21549 ATTCACCTTC
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
34 1 0.02
35 26 0.44
36 32 0.54
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (35 bp):
TTGAATCGAAAGTGACGATGCTTCTTTCGTTCTTC
Found at i:23257 original size:19 final size:19
Alignment explanation
Indices: 23209--23257 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
23199 TAACTAATCG
* *
23209 TTAACAACCATAACTACTG
1 TTAACAACCTTAACTACTA
* *
23228 TTAACAGCCTTAACTGCTA
1 TTAACAACCTTAACTACTA
23247 TTAACAACCTT
1 TTAACAACCTT
23258 TTAGACCCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.31
Consensus pattern (19 bp):
TTAACAACCTTAACTACTA
Found at i:27307 original size:18 final size:18
Alignment explanation
Indices: 27284--27323 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
27274 TTTCGATATT
27284 GTTTAATTGATCTAATCA
1 GTTTAATTGATCTAATCA
27302 GTTTAATTGATCTAATCA
1 GTTTAATTGATCTAATCA
27320 GTTT
1 GTTT
27324 TGATAATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (18 bp):
GTTTAATTGATCTAATCA
Found at i:30537 original size:20 final size:21
Alignment explanation
Indices: 30512--30552 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
30502 GTTGTGGTCG
30512 TTTCTAGCCG-TTGGGGATGA
1 TTTCTAGCCGTTTGGGGATGA
30532 TTTCTAGCCGTTTGGGGATGA
1 TTTCTAGCCGTTTGGGGATGA
30553 AATCTCTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.15, C:0.15, G:0.34, T:0.37
Consensus pattern (21 bp):
TTTCTAGCCGTTTGGGGATGA
Found at i:41034 original size:20 final size:20
Alignment explanation
Indices: 40985--41040 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 20
40975 ATACTAAAAG
*
40985 GGGTATCGATACCATAGCAT
1 GGGTATCGATACCATAGCAA
* *
41005 GGTAGTATCGATACCATGGTAA
1 GG--GTATCGATACCATAGCAA
41027 GGGTATCGATACCA
1 GGGTATCGATACCA
41041 GGAAACATCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 14 0.45
22 17 0.55
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (20 bp):
GGGTATCGATACCATAGCAA
Found at i:41072 original size:94 final size:95
Alignment explanation
Indices: 40911--41109 Score: 292
Period size: 94 Copynumber: 2.1 Consensus size: 95
40901 ATATCGAAGA
* * * * * *
40911 GGTAGTATCGATACCATGGTAAGGGTATCGATACCATGAATCATTGAATCTAAACTTGGTATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGCATCGA
*
40976 TACT-AAAAGGGGTATCGATACCATAGCAT
66 TACTGAAAAGGGGTATCGATACCATAACAT
41005 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGCATCGA
1 GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGCATCGA
* *
41070 TACTGAAAAGTGGTATCGGTACCATAACAT
66 TACTGAAAAGGGGTATCGATACCATAACAT
* *
41100 AGAAGTATCG
1 GGTAGTATCG
41110 TTACTAGGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
94 63 0.68
95 30 0.32
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (95 bp):
GGTAGTATCGATACCATGGTAAGGGTATCGATACCAGGAAACATCGAACCTAAAATTGGCATCGA
TACTGAAAAGGGGTATCGATACCATAACAT
Found at i:41925 original size:59 final size:59
Alignment explanation
Indices: 41454--41916 Score: 637
Period size: 59 Copynumber: 7.9 Consensus size: 59
41444 GATTACAAAA
* ** *
41454 AGGGCACTTCGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
** **
41513 AGGGCACTTCGTGTGCTAATGTGAGAAGGAATTCATGTTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * *
41572 AGGGAACTTCTTGTGCTAACCTGAGAAGGAATT--T-CTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * *
41628 AGGGCAGTTCGTGTGCTAACATGAGAAGAAATTCATACTAAGTGTTTGAATTTTCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* *
41687 AGGGCACTTCGTGTGCTAACATGAAAATGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * *
41746 AAGCCACTTCGTGTGCTAAAATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * *
41805 AGGGTACTTCGTGTGCTAACATGGGAAGGAATTCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
* * * * *
41864 GGGGCACCTT-GTGTGCTAAAATGATAAGAAATTCATCCTAAGTGTATGAATTT
1 AGGGCA-CTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTT
41917 TCGTATGGGA
Statistics
Matches: 357, Mismatches: 43, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
56 49 0.14
57 1 0.00
58 1 0.00
59 303 0.85
60 3 0.01
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.33
Consensus pattern (59 bp):
AGGGCACTTCGTGTGCTAACATGAGAAGGAATTCATACTAAGTGTATGAATTTCCATAT
Found at i:42382 original size:68 final size:68
Alignment explanation
Indices: 42273--42467 Score: 354
Period size: 68 Copynumber: 2.9 Consensus size: 68
42263 AGATTAAATA
*
42273 CCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
42338 AGG
66 AGG
* *
42341 CCTAACTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
42406 AGG
66 AGG
*
42409 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAATTAGATGAAAGGCTAAGTG
1 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTG
42468 TGATACAATT
Statistics
Matches: 121, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 121 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (68 bp):
CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
AGG
Found at i:47658 original size:68 final size:68
Alignment explanation
Indices: 47549--48101 Score: 768
Period size: 68 Copynumber: 8.1 Consensus size: 68
47539 GATCGCATCA
* ** * *
47549 AAGTGCCTTTGGGGTTTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGACAG
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
47614 ACT
66 GCT
* * * *
47617 AAGTGTCTTTGAGGCCTAGTTGTGCATTTGACAGAAAGGTGTTAATTATGTCAGTTAGATGAAAG
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
47682 GCT
66 GCT
* * *
47685 AAGTGCCTTTGAGGCCTAACTGTGCATTT-ATTAGAAGGGTGTCAATTATGCCAGTTAGATGAAA
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGA-CAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
47749 GGCT
65 GGCT
* * *
47753 AAGTGCCTTTGATGCCTAATTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGATAG
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
47818 GCT
66 GCT
* * *
47821 AAGTGCCTTTGAGGCCTAACTGAGCATTTGACAGAAAGGTGTCAATTATGCCAGATAGATGAAAG
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
47886 GCT
66 GCT
** * *
47889 AAGTGCCTTTGAGTTCTAGTTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
47954 GCT
66 GCT
* * * *
47957 AAGT-CTCTTTGAGGCCTAACTGTGCATTTGACATAAAGGTGTCAATTATGGCAATTAGATGAAA
1 AAGTGC-CTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAA
48021 GGCT
65 GGCT
* * * * *
48025 AAGTGCCTTTGAGGCCTAGTTGTGCATTTGAAAAAAATGTGTCAATCATGCCAGTTAGATGAAAG
1 AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
48090 GTT
66 GCT
*
48093 AAATGCCTT
1 AAGTGCCTT
48102 GAGTAAAAGA
Statistics
Matches: 428, Mismatches: 53, Indels: 8
0.88 0.11 0.02
Matches are distributed among these distances:
67 2 0.00
68 424 0.99
69 2 0.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.31
Consensus pattern (68 bp):
AAGTGCCTTTGAGGCCTAATTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GCT
Found at i:48181 original size:45 final size:45
Alignment explanation
Indices: 48123--48399 Score: 338
Period size: 45 Copynumber: 6.1 Consensus size: 45
48113 TAGATGTATA
* * *
48123 AAAATTTATAATGGTGTATAAAATGCATGGAAGGATGCCATAAAT
1 AAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
* * *
48168 AAAATTTATAATGGTGTATAAAAGGCATGAAAGGATGACATATAT
1 AAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
* *
48213 AAAATGTATAATAGTGTATAAAAGGCATGAAAGGATACCATAAAT
1 AAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
** **
48258 AAAATGTATAATTATGTATAAAAGGCATGAAAATATGCCATAAAT
1 AAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
* * * * *
48303 GAAATTTATAATGATGTATAAAAGACATGAAATGATGCCATAAAT
1 AAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
* * * * *
48348 AAAATGTATAATAGTATATAAAAATGCATGAACGGTTGCCATAAAT
1 AAAATGTATAATGGTGTAT-AAAAGGCATGAAAGGATGCCATAAAT
48394 GAAAAT
1 -AAAAT
48400 ACACAATGAT
Statistics
Matches: 200, Mismatches: 30, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
45 174 0.87
46 21 0.10
47 5 0.03
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (45 bp):
AAAATGTATAATGGTGTATAAAAGGCATGAAAGGATGCCATAAAT
Found at i:48368 original size:135 final size:137
Alignment explanation
Indices: 48123--48399 Score: 378
Period size: 135 Copynumber: 2.0 Consensus size: 137
48113 TAGATGTATA
* * * * * *
48123 AAAATTTATAATGGTGTATAAAATGCATGGAAGGATGCCATAAATAAAATTTATAATGGTGTATA
1 AAAATGTATAATGATGTATAAAAGGCATGAAAAGATGCCATAAATAAAATTTATAATGATGTATA
* * *
48188 AAAGGCATGAAAGGATGACATATATAAAATGTATAATAGTGTAT-AAAAGGCATGAAAGGATACC
66 AAAGACATGAAAGGATGACATAAATAAAATGTATAATAGTATATAAAAAGGCATGAAAGGATACC
48252 ATAAAT-
131 ATAAATG
* * *
48258 AAAATGTATAATTATGTATAAAAGGCATGAAAATATGCCATAAATGAAATTTATAATGATGTATA
1 AAAATGTATAATGATGTATAAAAGGCATGAAAAGATGCCATAAATAAAATTTATAATGATGTATA
* * * * * *
48323 AAAGACATGAAATGATGCCATAAATAAAATGTATAATAGTATATAAAAATGCATGAACGGTTGCC
66 AAAGACATGAAAGGATGACATAAATAAAATGTATAATAGTATATAAAAAGGCATGAAAGGATACC
48388 ATAAATG
131 ATAAATG
48395 AAAAT
1 AAAAT
48400 ACACAATGAT
Statistics
Matches: 122, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
135 95 0.78
136 22 0.18
137 5 0.04
ACGTcount: A:0.49, C:0.06, G:0.17, T:0.28
Consensus pattern (137 bp):
AAAATGTATAATGATGTATAAAAGGCATGAAAAGATGCCATAAATAAAATTTATAATGATGTATA
AAAGACATGAAAGGATGACATAAATAAAATGTATAATAGTATATAAAAAGGCATGAAAGGATACC
ATAAATG
Found at i:56456 original size:20 final size:20
Alignment explanation
Indices: 56433--56472 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
56423 GTCAATGGTC
56433 AACGAGTTGACTCAATCGAG
1 AACGAGTTGACTCAATCGAG
56453 AACGAGTTGACTCAATCGAG
1 AACGAGTTGACTCAATCGAG
56473 TTGACTCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (20 bp):
AACGAGTTGACTCAATCGAG
Found at i:59732 original size:44 final size:44
Alignment explanation
Indices: 59677--60018 Score: 400
Period size: 44 Copynumber: 8.0 Consensus size: 44
59667 ATACCATGAC
* *
59677 TGGCACCTTTCTGCCAATAATGTACTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
** *
59721 TGGCATTTTTCTGCCAATAATACACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
*
59765 TGGCACCTTTCTGCCAATAATGCACCG-TATG-AATTTCAATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTC-ATTTA
*
59808 TGGCACCTTTCTGCCAAT-A---A---TTATGCATTTTTATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * * *
59845 TAGAACCTTTCGGCCAATAATGCTCTGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* *
59889 TGCCACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTA
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* **
59933 TGGCATCGTTT-TGCCAATAATGCACTATTATGCATTTTCATTTA
1 TGGCA-CCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
* * * *
59977 TGGCGCCTTTCTGCCAATAATACATCGTTATTCA-TTTCATTT
1 TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTT
60019 GTTTTAGAGC
Statistics
Matches: 252, Mismatches: 34, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
37 24 0.10
38 5 0.02
39 1 0.00
42 6 0.02
43 39 0.15
44 173 0.69
45 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.13, T:0.42
Consensus pattern (44 bp):
TGGCACCTTTCTGCCAATAATGCACCGTTATGCATTTTCATTTA
Found at i:59853 original size:37 final size:37
Alignment explanation
Indices: 59748--59865 Score: 119
Period size: 43 Copynumber: 3.0 Consensus size: 37
59738 TAATACACCG
*
59748 TTATGCATTTTCATTTATGGCACCTTTCTGCCAATAA
1 TTATGCATTTTAATTTATGGCACCTTTCTGCCAATAA
* *
59785 TGCACCGTATGAATTTCAATTTATGGCACCTTTCTGCCAATAA
1 T------TATGCATTTTAATTTATGGCACCTTTCTGCCAATAA
* * * *
59828 TTATGCATTTTTATTTATAGAACCTTTCGGCCAATAA
1 TTATGCATTTTAATTTATGGCACCTTTCTGCCAATAA
59865 T
1 T
59866 GCTCTGTTAT
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
37 32 0.48
43 34 0.52
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (37 bp):
TTATGCATTTTAATTTATGGCACCTTTCTGCCAATAA
Found at i:59861 original size:124 final size:125
Alignment explanation
Indices: 59704--60018 Score: 350
Period size: 124 Copynumber: 2.5 Consensus size: 125
59694 TAATGTACTG
* * ** * *
59704 TTATGCATTTTCATTTATGGCATTTTTCTGCCAATAATACACCGTTATGCATTTTCATTTATGGC
1 TTATGCATTTTCATTTATAGAACCTTTCGGCCAATAATACACCGTTATGCATTTTCATTTATGCC
*
59769 ACCTTTCTGCCAATAATGCACCG-TATG-AATTTCAATTTATGGCA-CCTTTCTGCCAATAA
66 ACCTTTATGCCAATAATGCACCGTTATGCAATTTC-ATTTATGGCATCCTTT-TGCCAATAA
* * * *
59828 TTATGCATTTTTATTTATAGAACCTTTCGGCCAATAATGCTCTGTTATGCATTTTCATTTATGCC
1 TTATGCATTTTCATTTATAGAACCTTTCGGCCAATAATACACCGTTATGCATTTTCATTTATGCC
* *
59893 ACCTTTATGCCAATAATGCACCGTTATGCATTTTCATTTATGGCATCGTTTTGCCAATAATGCAC
66 ACCTTTATGCCAATAATGCACCGTTATGCAATTTCATTTATGGCATCCTTTTGCC---AAT--A-
59958 TA
125 -A
* ** * * *
59960 TTATGCATTTTCATTTATGGCGCCTTTCTGCCAATAATACATCGTTATTCA-TTTCATTT
1 TTATGCATTTTCATTTATAGAACCTTTCGGCCAATAATACACCGTTATGCATTTTCATTT
60019 GTTTTAGAGC
Statistics
Matches: 158, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
124 77 0.49
125 18 0.11
126 9 0.06
128 3 0.02
130 1 0.01
131 8 0.05
132 42 0.27
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (125 bp):
TTATGCATTTTCATTTATAGAACCTTTCGGCCAATAATACACCGTTATGCATTTTCATTTATGCC
ACCTTTATGCCAATAATGCACCGTTATGCAATTTCATTTATGGCATCCTTTTGCCAATAA
Found at i:65934 original size:16 final size:16
Alignment explanation
Indices: 65913--65944 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
65903 ATAGTTGTAT
65913 CGAATATACATAGAAA
1 CGAATATACATAGAAA
*
65929 CGAATATACTTAGAAA
1 CGAATATACATAGAAA
65945 ATCAATACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.22
Consensus pattern (16 bp):
CGAATATACATAGAAA
Found at i:65954 original size:15 final size:15
Alignment explanation
Indices: 65934--65963 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
65924 AGAAACGAAT
65934 ATACTTAGAAAATCA
1 ATACTTAGAAAATCA
65949 ATACTTAGAAAATCA
1 ATACTTAGAAAATCA
65964 TTCGTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
ATACTTAGAAAATCA
Found at i:66424 original size:16 final size:16
Alignment explanation
Indices: 66403--66435 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
66393 AATATCTAAA
*
66403 ACAAATTTAAACATCC
1 ACAAATTCAAACATCC
66419 ACAAATTCAAACATCC
1 ACAAATTCAAACATCC
66435 A
1 A
66436 TAAACATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (16 bp):
ACAAATTCAAACATCC
Found at i:68099 original size:20 final size:20
Alignment explanation
Indices: 68074--68113 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
68064 TGTTCATCCT
68074 AGAACTAATTAAAACTAGTC
1 AGAACTAATTAAAACTAGTC
68094 AGAACTAATTAAAACTAGTC
1 AGAACTAATTAAAACTAGTC
68114 CTAAAATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGAACTAATTAAAACTAGTC
Found at i:74322 original size:15 final size:15
Alignment explanation
Indices: 74302--74331 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
74292 TGTATCGAAT
74302 ATACTTAGAAAATCA
1 ATACTTAGAAAATCA
74317 ATACTTAGAAAATCA
1 ATACTTAGAAAATCA
74332 TTCGTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
ATACTTAGAAAATCA
Found at i:75251 original size:44 final size:44
Alignment explanation
Indices: 75191--75668 Score: 595
Period size: 44 Copynumber: 11.0 Consensus size: 44
75181 CCATGAGTGA
**
75191 CACCTTTCTGCCAATAATGTGTCGTTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * * * *
75235 CAACTTGCTACCAATAATGCACCATTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * *
75279 CACCTTTCTGCCAGTAACGCATCGTTATGAATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * * *
75323 AACATTTTTGCCAATAATGCATCGTTATGCATTTTCATTTATAG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * * *
75367 CACATTTCTGCCAATAATGCACCATTATGCATTTTCATTTAGGG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* *
75411 CACCTTTCTGCCAAAAAT--ATCGTTATGCATTTTCATTTATGT
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * * *
75453 CATCTTTCTG-CAAAAATGTATTGTTATGCA-TTTCATTTATGG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* *
75495 CACCTTTCTACCAATAATGCATCGTTATGCATTTTCATTTATGA
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * * *
75539 CACCTTTCTGCAAATAATGCACCATTATGCATTTTCATTTATGT
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * *
75583 CACCTTTCTACCAATAATGCGTTGTTATGCATTTTCATTTATGG
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
* * * *
75627 CACCTTTTTACCAATAATGCACCATTATGCATTTTCATTTAT
1 CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTAT
75669 TTTAAAACAG
Statistics
Matches: 370, Mismatches: 60, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
41 7 0.02
42 48 0.13
43 27 0.07
44 288 0.78
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.41
Consensus pattern (44 bp):
CACCTTTCTGCCAATAATGCATCGTTATGCATTTTCATTTATGG
Found at i:76198 original size:18 final size:18
Alignment explanation
Indices: 76171--76228 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
76161 CCTTTCTCTT
*
76171 AGTATTGATACCCACATC
1 AGTATCGATACCCACATC
** *
76189 AGTATCGATACTAATTGTATC
1 AGTATCGATACCCA---CATC
76210 AGTATCGATACCCACATC
1 AGTATCGATACCCACATC
76228 A
1 A
76229 CTTAACCCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
18 15 0.50
21 15 0.50
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (18 bp):
AGTATCGATACCCACATC
Found at i:80396 original size:17 final size:18
Alignment explanation
Indices: 80370--80406 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
80360 ATCCCTTAAC
80370 TTTATATTTT-ACT-CAA
1 TTTATATTTTGACTACAA
80386 TTTAGTATTTTGACTACAA
1 TTTA-TATTTTGACTACAA
80405 TT
1 TT
80407 GTTTGCAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 3 0.17
19 5 0.28
ACGTcount: A:0.30, C:0.11, G:0.05, T:0.54
Consensus pattern (18 bp):
TTTATATTTTGACTACAA
Found at i:80573 original size:2 final size:2
Alignment explanation
Indices: 80566--80593 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
80556 GAAAAGAATA
80566 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
80594 CTTATATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81807 original size:8 final size:8
Alignment explanation
Indices: 81794--81847 Score: 65
Period size: 8 Copynumber: 6.6 Consensus size: 8
81784 TAAAGAGACT
81794 GAAAAAAA
1 GAAAAAAA
81802 GAAAAAAA
1 GAAAAAAA
81810 GAAAAAAAA
1 G-AAAAAAA
81819 GAAAAAAA
1 GAAAAAAA
*
81827 GAGAGAAAA
1 GA-AAAAAA
*
81836 -AAGAAAA
1 GAAAAAAA
81843 GAAAA
1 GAAAA
81848 TAAGCAGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 6 0.15
8 22 0.54
9 13 0.32
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:81809 original size:9 final size:9
Alignment explanation
Indices: 81795--81847 Score: 72
Period size: 9 Copynumber: 5.8 Consensus size: 9
81785 AAAGAGACTG
81795 AAAAAAAG-
1 AAAAAAAGA
81803 AAAAAAAGA
1 AAAAAAAGA
81812 AAAAAAAGA
1 AAAAAAAGA
81821 AAAAAAGAGA
1 AAAAAA-AGA
*
81831 GAAAAAAGA
1 AAAAAAAGA
81840 AAAGAAAA
1 AAA-AAAA
81848 TAAGCAGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
8 8 0.20
9 20 0.50
10 12 0.30
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:81817 original size:17 final size:18
Alignment explanation
Indices: 81794--81842 Score: 82
Period size: 17 Copynumber: 2.7 Consensus size: 18
81784 TAAAGAGACT
81794 GAAAAAAAGAAAAAAAGA
1 GAAAAAAAGAAAAAAAGA
81812 -AAAAAAAGAAAAAAAGA
1 GAAAAAAAGAAAAAAAGA
81829 GAGAAAAAAGAAAA
1 GA-AAAAAAGAAAA
81843 GAAAATAAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 17 0.59
18 1 0.03
19 11 0.38
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
GAAAAAAAGAAAAAAAGA
Found at i:87275 original size:17 final size:19
Alignment explanation
Indices: 87242--87280 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
87232 TTTAACAACT
87242 TATAGAACATTAAATA-TAA
1 TATAGAACA-TAAATATTAA
87261 TATAGAACA-AAATATTAA
1 TATAGAACATAAATATTAA
87279 TA
1 TA
87281 ATACAGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
TATAGAACATAAATATTAA
Done.