Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001727.1 Hibiscus syriacus cultivar Beakdansim tig00003491_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: 83694
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:498 original size:54 final size:54
Alignment explanation
Indices: 415--535 Score: 179
Period size: 54 Copynumber: 2.2 Consensus size: 54
405 ACCTCAAAGG
415 GGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATTAACACAA
1 GGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATTAACACAA
* * * * * *
469 GGGTATCGGTACCCGTTGGGCATTTTGTTTTTCTCGGAGTCAAAATTGACATAG
1 GGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATTAACACAA
*
523 GGGTATCGATACC
1 GGGTATCGGTACC
536 TCCCTATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 60 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (54 bp):
GGGTATCGGTACCCATTGGGCATTCTGTTTTTCTCGGAGCCAAAATTAACACAA
Found at i:2114 original size:31 final size:31
Alignment explanation
Indices: 2076--2150 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
2066 TTCACCTTGT
*
2076 ACTTTAGATAAAATATTGATTTAATCCTTAA
1 ACTTTAGATAAAATATTGATTTAACCCTTAA
* *
2107 ATTTTAGATAAAATATTGTTTTAACCCTTAA
1 ACTTTAGATAAAATATTGATTTAACCCTTAA
*
2138 ACTTTAGAAAAAA
1 ACTTTAGATAAAA
2151 CCAATTTGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.44, C:0.09, G:0.07, T:0.40
Consensus pattern (31 bp):
ACTTTAGATAAAATATTGATTTAACCCTTAA
Found at i:3089 original size:12 final size:12
Alignment explanation
Indices: 3069--3104 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3059 ATTTATCGGT
3069 CGGGTATCGGGC
1 CGGGTATCGGGC
*
3081 CGTGTATCGGGC
1 CGGGTATCGGGC
3093 CGGGTAATCGGG
1 CGGGT-ATCGGG
3105 TAATCGGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 15 0.71
13 6 0.29
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.19
Consensus pattern (12 bp):
CGGGTATCGGGC
Found at i:3799 original size:30 final size:31
Alignment explanation
Indices: 3764--3823 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
3754 CGGGTCAATG
*
3764 TCGGATCGGTTG-GTTTCGGGTCGGATCAAA
1 TCGGATCAGTTGAGTTTCGGGTCGGATCAAA
* *
3794 TCGGATCAGTTGATTTTTGGGTCGGATCAA
1 TCGGATCAGTTGAGTTTCGGGTCGGATCAA
3824 CGTCAGATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (31 bp):
TCGGATCAGTTGAGTTTCGGGTCGGATCAAA
Found at i:8852 original size:23 final size:23
Alignment explanation
Indices: 8822--8871 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
8812 TGCCCGGGAG
*
8822 TCGTGTCTTGCGCCGATATCCTC
1 TCGTGTCTTGCGCCAATATCCTC
8845 TCGTGTCTTGCGCCAATATCCTC
1 TCGTGTCTTGCGCCAATATCCTC
8868 TCGT
1 TCGT
8872 TGGTCGCGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.34, G:0.20, T:0.36
Consensus pattern (23 bp):
TCGTGTCTTGCGCCAATATCCTC
Found at i:10217 original size:188 final size:188
Alignment explanation
Indices: 9887--10240 Score: 453
Period size: 188 Copynumber: 1.9 Consensus size: 188
9877 TTTGAAATAT
* * * *
9887 TCAAAAGATAAAACTCTTTTTACCATTTAAACTTATATATGTATTATTATAATTTAAAATATACA
1 TCAAAAGATAAAACTCTTTTTACCATTCAAACTTAGACATATATTATTATAATTTAAAATATACA
* * ** *
9952 AAAGTATAATTACCTTTAATATTCAAAGTTAAAATGGTAACAAATACCTTTTTAAGTAGACATAT
66 AAAGTATAATTAACTTTAATATTCAAAATTAAAATAATAACAAATACCTTTTTAAATAGACATAT
* * *
10017 TCAAAGAGTAATTATCTTATTAATATTTAAAATAAATAATATATTTAATTTACAATTG
131 TAAAAGAGTAATTATCCTATTAATATTCAAAATAAATAATATATTTAATTTACAATTG
** * * *
10075 TCAAAAGATAAATTTC-TTTTACTATTCAAACTTAGACATATATTATTTTAATTTGAAATATACA
1 TCAAAAGATAAAACTCTTTTTACCATTCAAACTTAGACATATATTATTATAATTTAAAATATACA
* ** * *
10139 AAAGTATATAATTATATTTTAATATTCAAAATTAAAA-AATAACAAATGTCTTTTTAAATTGACT
66 AAAG--TATAATTA-ACTTTAATATTCAAAATTAAAATAATAACAAATACCTTTTTAAATAGACA
*
10203 TA-TAAAAGAGTAATTATCCTATTAATATTCAAATTAAA
128 TATTAAAAGAGTAATTATCCTATTAATATTCAAAATAAA
10241 AATTATCTTT
Statistics
Matches: 140, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
187 45 0.32
188 46 0.33
189 30 0.21
190 19 0.14
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (188 bp):
TCAAAAGATAAAACTCTTTTTACCATTCAAACTTAGACATATATTATTATAATTTAAAATATACA
AAAGTATAATTAACTTTAATATTCAAAATTAAAATAATAACAAATACCTTTTTAAATAGACATAT
TAAAAGAGTAATTATCCTATTAATATTCAAAATAAATAATATATTTAATTTACAATTG
Found at i:10552 original size:11 final size:11
Alignment explanation
Indices: 10536--10560 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
10526 AGGAAATGCG
10536 GGTTAATATAC
1 GGTTAATATAC
10547 GGTTAATATAC
1 GGTTAATATAC
10558 GGT
1 GGT
10561 ATTATCGGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.08, G:0.24, T:0.36
Consensus pattern (11 bp):
GGTTAATATAC
Found at i:16047 original size:63 final size:64
Alignment explanation
Indices: 15940--16080 Score: 194
Period size: 63 Copynumber: 2.2 Consensus size: 64
15930 GTGTTGCCAA
* * * *
15940 TAAAATTTAAATTTAGATTTTTTTTCATTTAAATATACAAAAATTAATATACATATCAAATAAAC
1 TAAAA-TTAAAGTTAAATCTTTTTTCATTTAAATATACAAAAATTAATATACATATCAAAGAAAC
* * *
16005 TAAAATTAAAGTTAAATCTTTTTTCATTT-AATATATAAAAATTAATATACATCTCAAAGGAAC
1 TAAAATTAAAGTTAAATCTTTTTTCATTTAAATATACAAAAATTAATATACATATCAAAGAAAC
*
16068 TAAAATTGAAGTT
1 TAAAATTAAAGTT
16081 TAGATTTTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 42 0.62
64 21 0.31
65 5 0.07
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (64 bp):
TAAAATTAAAGTTAAATCTTTTTTCATTTAAATATACAAAAATTAATATACATATCAAAGAAAC
Found at i:16631 original size:17 final size:17
Alignment explanation
Indices: 16597--16630 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
16587 TTATATTTAA
16597 TAAGAGGTTATTCATTT
1 TAAGAGGTTATTCATTT
16614 TAAGA-GTTATTCATTT
1 TAAGAGGTTATTCATTT
16630 T
1 T
16631 TGTAACACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.29, C:0.06, G:0.15, T:0.50
Consensus pattern (17 bp):
TAAGAGGTTATTCATTT
Found at i:33259 original size:23 final size:25
Alignment explanation
Indices: 33233--33285 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
33223 TCTGATAATT
* *
33233 TTAAAAAT-TTTATTTTGAAAAA-C
1 TTAAAAATATATATTTTAAAAAACC
33256 TTAAAAATATATATTTTAAAAAACC
1 TTAAAAATATATATTTTAAAAAACC
33281 TTAAA
1 TTAAA
33286 GTTTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 8 0.31
24 12 0.46
25 6 0.23
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
TTAAAAATATATATTTTAAAAAACC
Found at i:34283 original size:24 final size:22
Alignment explanation
Indices: 34256--34306 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
34246 GGTATGTCAC
34256 ATTTTCATATATCTTTTATGACAT
1 ATTTTC-T-TATCTTTTATGACAT
* *
34280 ATTTTCTTATGTTTTTTGACAT
1 ATTTTCTTATCTTTTATGACAT
34302 ATTTT
1 ATTTT
34307 TCGGTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 18 0.72
23 1 0.04
24 6 0.24
ACGTcount: A:0.24, C:0.10, G:0.06, T:0.61
Consensus pattern (22 bp):
ATTTTCTTATCTTTTATGACAT
Found at i:34353 original size:19 final size:20
Alignment explanation
Indices: 34294--34347 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
34284 TCTTATGTTT
34294 TTTGACATATTTTTCGGTTA
1 TTTGACATATTTTTCGGTTA
* *
34314 TTTGACATGTTTTCCGGTTA
1 TTTGACATATTTTTCGGTTA
34334 TTTGACAT-TTTTTC
1 TTTGACATATTTTTC
34348 ATTTATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.56
Consensus pattern (20 bp):
TTTGACATATTTTTCGGTTA
Found at i:38351 original size:20 final size:20
Alignment explanation
Indices: 38310--38353 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
38300 TTGGATTTGT
**
38310 AACGCGAAATGGAAAATTGC
1 AACGCGAAATGGAAAAACGC
38330 AACGCGAAATGGAAAAACGC
1 AACGCGAAATGGAAAAACGC
38350 AACG
1 AACG
38354 TTATTTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.18, G:0.25, T:0.09
Consensus pattern (20 bp):
AACGCGAAATGGAAAAACGC
Found at i:38681 original size:2 final size:2
Alignment explanation
Indices: 38674--38722 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
38664 ACAATTTCTT
38674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
38716 TA TA TA T
1 TA TA TA T
38723 GAATCATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45022 original size:12 final size:13
Alignment explanation
Indices: 45005--45033 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
44995 CGAAGACGAT
45005 GTTGCAGTT-GCA
1 GTTGCAGTTGGCA
45017 GTTGCAGTTGGCA
1 GTTGCAGTTGGCA
45030 GTTG
1 GTTG
45034 GTAAATTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.14, C:0.14, G:0.38, T:0.34
Consensus pattern (13 bp):
GTTGCAGTTGGCA
Found at i:55420 original size:2 final size:2
Alignment explanation
Indices: 55413--55451 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55403 GCTTTATTCC
55413 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 A
55452 ATTTAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:55957 original size:60 final size:59
Alignment explanation
Indices: 55832--55981 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 59
55822 AGTTTGGGGT
** *
55832 CCAATTTAGAAA-G-AGTGTCATAGTTTATGGATAAAATTAAATATTCAAAAGTTTAAGGA
1 CCAATTTA-AAATGAAG-GTCATAGTTTGGGGATAAAATTAAATATTCAAAAGTTTAAAGA
** * * *
55891 TTAATTTGAAATGGAA-GTCATAGTTTGGGGATGAAATTAGAATATTCAAAAGTTTAAATA
1 CCAATTTAAAAT-GAAGGTCATAGTTTGGGGATAAAATTA-AATATTCAAAAGTTTAAAGA
*
55951 CCAATTTAAAATGAAGGTTATAGTTTGGGGA
1 CCAATTTAAAATGAAGGTCATAGTTTGGGGA
55982 CATACGATGC
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
58 3 0.04
59 28 0.38
60 42 0.57
61 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.33
Consensus pattern (59 bp):
CCAATTTAAAATGAAGGTCATAGTTTGGGGATAAAATTAAATATTCAAAAGTTTAAAGA
Found at i:60899 original size:21 final size:21
Alignment explanation
Indices: 60873--61090 Score: 197
Period size: 21 Copynumber: 10.6 Consensus size: 21
60863 GTTTCCAGAT
60873 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
60894 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
* *
60915 TTGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
*
60936 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
60957 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
60977 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
**
60998 TTCGC-AT--TTACTTCGACTA
1 -TCGCAATGCGAACTTCGACTA
*
61017 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
61038 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
*
61058 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTCGACTA
61079 TCGCAATGCGAA
1 TCGCAATGCGAA
61091 TATGTAAATC
Statistics
Matches: 163, Mismatches: 19, Indels: 31
0.77 0.09 0.15
Matches are distributed among these distances:
18 5 0.03
19 9 0.06
20 33 0.20
21 112 0.69
22 4 0.02
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:60997 original size:41 final size:41
Alignment explanation
Indices: 60935--61114 Score: 183
Period size: 41 Copynumber: 4.4 Consensus size: 41
60925 AACTTCGACT
* *
60935 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
** * *
60976 ATCGCAATGCGATAGTCGACTATTCGC-AT-TTACT-TCG-ACT
1 ATCGCAATGCGATAGTCGACTA-TCGCAATGCGAATAT-GTA-A
* *
61016 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
61057 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
* *
61098 ATCACATTGCGATAGTC
1 ATCGCAATGCGATAGTC
61115 CAAGTTCGCA
Statistics
Matches: 113, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
39 7 0.06
40 23 0.20
41 75 0.66
42 8 0.07
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:61025 original size:81 final size:80
Alignment explanation
Indices: 60926--61083 Score: 307
Period size: 81 Copynumber: 2.0 Consensus size: 80
60916 TGCAACGCGA
60926 ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
60991 TCGACTATTCGCATTT
66 TCGACTA-TCGCATTT
61007 ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
1 ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
61072 TCGACTATCGCA
66 TCGACTATCGCA
61084 ATGCGAATAT
Statistics
Matches: 77, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
80 5 0.06
81 72 0.94
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (80 bp):
ACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAG
TCGACTATCGCATTT
Found at i:61062 original size:20 final size:20
Alignment explanation
Indices: 61037--61100 Score: 78
Period size: 20 Copynumber: 3.1 Consensus size: 20
61027 AACTTGGACT
61037 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
61057 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
61078 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
61098 ATC
1 ATC
61101 ACATTGCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 15 0.41
21 12 0.32
22 3 0.08
23 2 0.05
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:61127 original size:21 final size:21
Alignment explanation
Indices: 61102--61159 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
61092 ATGTAAATCA
61102 CATTGCGATAGTCCAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
61123 CATTGCGATAGTCGAAGTTCG
1 CATTGCGATAGTCCAAGTTCG
*
61144 CGTTGCGATAGTCCAA
1 CATTGCGATAGTCCAA
61160 ATGCGATAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (21 bp):
CATTGCGATAGTCCAAGTTCG
Found at i:61304 original size:6 final size:6
Alignment explanation
Indices: 61293--61335 Score: 72
Period size: 6 Copynumber: 7.5 Consensus size: 6
61283 GACACGTATT
61293 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
61336 CGAGATGGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.27
6 27 0.73
ACGTcount: A:0.30, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:61967 original size:21 final size:21
Alignment explanation
Indices: 61942--62065 Score: 121
Period size: 21 Copynumber: 5.8 Consensus size: 21
61932 ATTTTGGACT
61942 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
61963 ATCGCAACGTGAACTTGGACT--
1 ATCGCAAC--GAACTTGGAATAA
*
61984 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
62005 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAACTTGGAATAA
62026 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
62047 ATCGTAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
62066 CTATCGCAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
19 19 0.23
21 36 0.43
23 29 0.35
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:61994 original size:42 final size:42
Alignment explanation
Indices: 61935--62074 Score: 244
Period size: 42 Copynumber: 3.3 Consensus size: 42
61925 CGTTGCGATT
*
61935 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGTGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
61977 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* *
62019 TTCGACTATCGCAACGAACTTGGAATAAATCGTAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
62061 TTGGACTATCGCAA
1 TTGGACTATCGCAA
62075 TGCGAATATG
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:62071 original size:21 final size:20
Alignment explanation
Indices: 61935--62080 Score: 118
Period size: 21 Copynumber: 7.0 Consensus size: 20
61925 CGTTGCGATT
61935 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
61954 TTGGAATAAATCGCAACGTGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
61977 TTGGACTATCGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
61996 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
62019 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
* *
62038 TTGGAATAAATCGTAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
62061 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
62081 TATGTAAATC
Statistics
Matches: 100, Mismatches: 15, Indels: 22
0.73 0.11 0.16
Matches are distributed among these distances:
19 25 0.25
21 45 0.45
23 30 0.30
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:72098 original size:146 final size:146
Alignment explanation
Indices: 71948--72511 Score: 889
Period size: 146 Copynumber: 3.9 Consensus size: 146
71938 ACTCTGTAAT
* * *
71948 GTTCAAACGACATATCCCTAATAGGAAGACGATCGAACGATATGATATCTTCTAATCTCCATGCA
1 GTTCAAACGACATATCCCTAATAGGAAGACGGTCGAACGATATGACATCTTCTAATCTTCATGCA
*
72013 TAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCATTGTACCAAAGATAATTTATATGTA
66 TAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGATAATTTATATGTA
* *
72078 CAGAGGGTTGTACACC
131 CGGAGGGTTCTACACC
* * * *
72094 GTTCAAACGACATATCCTTAATAGAAAGACGGTCGAACAATATGGA-ATTTTCTAATCTTCATGC
1 GTTCAAACGACATATCCCTAATAGGAAGACGGTCGAACGATAT-GACATCTTCTAATCTTCATGC
* * *
72158 ATAACTATAGTCAACTTTACTCCAAATATGTTCATCATCTACTGTACCAAAGATAATTTATATGT
65 ATAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGATAATTTATATGT
72223 ACGGAGGGTTCTACACC
130 ACGGAGGGTTCTACACC
* * *
72240 GTTTAAACGACATATCCCTAATAGGAAGA-GGTCGAAGGATATGACAACTTCTAATCTTCATGCA
1 GTTCAAACGACATATCCCTAATAGGAAGACGGTCGAACGATATGACATCTTCTAATCTTCATGCA
* *
72304 TAGCTATGGTCAACTTTACTCCAAATATGGTCATCATCCATTGTACCAAAGATAATTTATATGTA
66 TAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGATAATTTATATGTA
* * *
72369 CGGAGAGCTCTTCACC
131 CGGAGGGTTCTACACC
* * *
72385 ATTCAAAAGACATATCCCTAATAGGAAGACGGTCGAACGATATGGCATCTTCTAATCTTCATGCA
1 GTTCAAACGACATATCCCTAATAGGAAGACGGTCGAACGATATGACATCTTCTAATCTTCATGCA
72450 TAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGATAATTTATAT
66 TAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGATAATTTATAT
72512 CAATTGTTAT
Statistics
Matches: 380, Mismatches: 35, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
144 2 0.01
145 127 0.33
146 249 0.66
147 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (146 bp):
GTTCAAACGACATATCCCTAATAGGAAGACGGTCGAACGATATGACATCTTCTAATCTTCATGCA
TAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGATAATTTATATGTA
CGGAGGGTTCTACACC
Found at i:72399 original size:291 final size:292
Alignment explanation
Indices: 71952--72511 Score: 924
Period size: 291 Copynumber: 1.9 Consensus size: 292
71942 TGTAATGTTC
* *
71952 AAACGACATATCCCTAATAGGAAGACGATCGAACGATATGATATCTTCTAATCTCCATGCATAGC
1 AAACGACATATCCCTAATAGGAAGACGATCGAACGATATGACAACTTCTAATCTCCATGCATAGC
*
72017 TATGGTCAACTTTACTCCAAATATGTTCATCATCCATTGTACCAAAGATAATTTATATGTACAGA
66 TATGGTCAACTTTACTCCAAATATGGTCATCATCCATTGTACCAAAGATAATTTATATGTACAGA
* * * * * * *
72082 GGGTTGTACACCGTTCAAACGACATATCCTTAATAGAAAGACGGTCGAACAATATGGAATTTTCT
131 GAGCTCTACACCATTCAAAAGACATATCCCTAATAGAAAGACGGTCGAACAATATGGAATCTTCT
*
72147 AATCTTCATGCATAACTATAGTCAACTTTACTCCAAATATGTTCATCATCTACTGTACCAAAGAT
196 AATCTTCATGCATAACTATAGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGAT
72212 AATTTATATGTACGGAGGGTTCTACACCGTTT
261 AATTTATATGTACGGAGGGTTCTACACCGTTT
* * *
72244 AAACGACATATCCCTAATAGGAAGA-GGTCGAAGGATATGACAACTTCTAATCTTCATGCATAGC
1 AAACGACATATCCCTAATAGGAAGACGATCGAACGATATGACAACTTCTAATCTCCATGCATAGC
*
72308 TATGGTCAACTTTACTCCAAATATGGTCATCATCCATTGTACCAAAGATAATTTATATGTACGGA
66 TATGGTCAACTTTACTCCAAATATGGTCATCATCCATTGTACCAAAGATAATTTATATGTACAGA
* * * *
72373 GAGCTCTTCACCATTCAAAAGACATATCCCTAATAGGAAGACGGTCGAACGATATGGCATCTTCT
131 GAGCTCTACACCATTCAAAAGACATATCCCTAATAGAAAGACGGTCGAACAATATGGAATCTTCT
* *
72438 AATCTTCATGCATAGCTATGGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGAT
196 AATCTTCATGCATAACTATAGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGAT
72503 AATTTATAT
261 AATTTATAT
72512 CAATTGTTAT
Statistics
Matches: 247, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
291 222 0.90
292 25 0.10
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (292 bp):
AAACGACATATCCCTAATAGGAAGACGATCGAACGATATGACAACTTCTAATCTCCATGCATAGC
TATGGTCAACTTTACTCCAAATATGGTCATCATCCATTGTACCAAAGATAATTTATATGTACAGA
GAGCTCTACACCATTCAAAAGACATATCCCTAATAGAAAGACGGTCGAACAATATGGAATCTTCT
AATCTTCATGCATAACTATAGTCAACTTTACTCCAAATATGTTCATCATCCACTGTACCAAAGAT
AATTTATATGTACGGAGGGTTCTACACCGTTT
Found at i:76594 original size:52 final size:52
Alignment explanation
Indices: 76535--76661 Score: 134
Period size: 52 Copynumber: 2.4 Consensus size: 52
76525 TGATTACGGG
76535 TTATTTTA-TAAAGTCTTAT-AATTATTAAAAATTATAAAATAATTATTTAATA
1 TTATTTTATTAAA-T-TTATCAATTATTAAAAATTATAAAATAATTATTTAATA
* * * * *
76587 TTATTTTATTGAATTTTTCAATTATTAAAAGTTATAAAATGATTATTGAAATA
1 TTATTTTATTAAATTTATCAATTATTAAAAATTATAAAATAATTATT-TAATA
76640 TTTATATGTT-TTAAATTTATCA
1 -TTAT-T-TTATTAAATTTATCA
76662 TTTTTCATTA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
51 3 0.05
52 35 0.56
53 7 0.11
54 4 0.06
55 11 0.18
56 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (52 bp):
TTATTTTATTAAATTTATCAATTATTAAAAATTATAAAATAATTATTTAATA
Found at i:77268 original size:18 final size:19
Alignment explanation
Indices: 77245--77286 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
77235 GAGCAATCCT
77245 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
77263 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
77283 ATTC
1 ATTC
77287 TGTGAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.14
19 3 0.14
20 16 0.73
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:77415 original size:18 final size:18
Alignment explanation
Indices: 77392--77427 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
77382 GATTATTAAA
77392 AATTATA-AATAATTATTT
1 AATTATATAAT-ATTATTT
77410 AATTATATAATATTATTT
1 AATTATATAATATTATTT
77428 TATTGAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTATATAATATTATTT
Found at i:79024 original size:38 final size:39
Alignment explanation
Indices: 78981--79060 Score: 117
Period size: 38 Copynumber: 2.1 Consensus size: 39
78971 ATTAATAATA
78981 TTTTATTATTTATTAAAAAAAATATTAGTTA-ACTTATT
1 TTTTATTATTTATTAAAAAAAATATTAGTTAGACTTATT
* * * *
79019 TTTTATTATTTATTAATAAAATTATTATTTAGATTTATT
1 TTTTATTATTTATTAAAAAAAATATTAGTTAGACTTATT
79058 TTT
1 TTT
79061 GAATGAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 28 0.76
39 9 0.24
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.59
Consensus pattern (39 bp):
TTTTATTATTTATTAAAAAAAATATTAGTTAGACTTATT
Found at i:80550 original size:19 final size:19
Alignment explanation
Indices: 80526--80567 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
80516 TCTCTCGAAA
80526 TTTAAAATGTAT-TATATAT
1 TTTAAAAT-TATCTATATAT
*
80545 TTTAAAATTTTCTATATAT
1 TTTAAAATTATCTATATAT
80564 TTTA
1 TTTA
80568 TATTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.10
19 19 0.90
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTAAAATTATCTATATAT
Found at i:81228 original size:21 final size:21
Alignment explanation
Indices: 81198--81458 Score: 220
Period size: 21 Copynumber: 12.6 Consensus size: 21
81188 GATTTACATA
*
81198 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
81219 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* ** *
81240 CTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
81261 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
81280 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
81303 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
81322 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
81345 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
81364 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
*
81387 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
81406 TTCGCGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
81429 -T--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
81447 TTCGCGTTGCGA
1 TTCGCGTTGCGA
81459 ATCTGAAAAC
Statistics
Matches: 189, Mismatches: 32, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
18 7 0.04
19 41 0.22
20 8 0.04
21 100 0.53
22 1 0.01
23 32 0.17
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:81252 original size:42 final size:41
Alignment explanation
Indices: 81223--81458 Score: 395
Period size: 42 Copynumber: 5.7 Consensus size: 41
81213 TCCAAGTTCG
*
81223 CGTTGCGATAGTCGAAGCTCGCGTTGCGATT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
*
81263 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
81305 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
81347 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
*
81389 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCC-AAGT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
81430 CGTTGCGATAGTCGAAGTTCGCGTTGCGA
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA
81459 ATCTGAAAAC
Statistics
Matches: 190, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
40 28 0.15
41 34 0.18
42 128 0.67
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.34
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Done.