Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002571.1 Hibiscus syriacus cultivar Beakdansim tig00005214_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: 81277
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:3667 original size:76 final size:75
Alignment explanation
Indices: 3577--3724 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
3567 TAAACTCAAA
3577 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
3641 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
3653 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
3718 TTAATTA
66 TTAATTA
3725 GGATTTAAGA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 24 0.36
76 43 0.64
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:12015 original size:67 final size:72
Alignment explanation
Indices: 11859--12053 Score: 206
Period size: 67 Copynumber: 2.7 Consensus size: 72
11849 AACATTATAT
** * * *
11859 TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTATTTAAGTTTTACGATATTATTTT
1 TTTATCTAGGTATTTTAGTTTAAATA-G-TTTTAGTATTTTAATTAGGATTTACGATATTA--TT
11924 TATATTTTATC
62 TATATTTTATC
**
11935 TTTATCTTTGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAGGATTTA-GA-A-TA-TTAT
1 TTTATCTAGGTATTTTAGTTTAAATA-GTTTTAGTATTTTAATTAGGATTTACGATATTATTTAT
11996 ATTATTAT-
65 ATT-TTATC
*
12004 TTT-T-TAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTTATCTAGGTATTTTAGTTTAAATAGTTTT-AGTATTTTAATTAGGATTTA
12054 AGATGTTTTA
Statistics
Matches: 110, Mismatches: 7, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
66 5 0.05
67 37 0.34
68 1 0.01
69 10 0.09
70 4 0.04
72 2 0.02
73 1 0.01
74 2 0.02
75 21 0.19
76 27 0.25
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (72 bp):
TTTATCTAGGTATTTTAGTTTAAATAGTTTTAGTATTTTAATTAGGATTTACGATATTATTTATA
TTTTATC
Found at i:14942 original size:12 final size:12
Alignment explanation
Indices: 14925--14952 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
14915 TGCGGTTGCG
14925 AACGTTACGTAA
1 AACGTTACGTAA
14937 AACGTTACGTAA
1 AACGTTACGTAA
14949 AACG
1 AACG
14953 CAACGGCTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (12 bp):
AACGTTACGTAA
Found at i:18842 original size:2 final size:2
Alignment explanation
Indices: 18835--18859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18825 AACATGAACG
18835 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 A
18860 CCTCATTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:19154 original size:18 final size:17
Alignment explanation
Indices: 19131--19164 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
19121 ATTTTACTAT
19131 TAAAAATATTAAATATTG
1 TAAAAATA-TAAATATTG
19149 TAAAAATATAAATATT
1 TAAAAATATAAATATT
19165 ACATTAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAATATAAATATTG
Found at i:20808 original size:15 final size:15
Alignment explanation
Indices: 20783--20834 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
20773 AATGCTCAAG
*
20783 TTATCTCGTCTACT-
1 TTATCTGGTCTACTA
20797 TCTATCTGGTCTACTA
1 T-TATCTGGTCTACTA
* * *
20813 TTATTTGGTCTATTG
1 TTATCTGGTCTACTA
20828 TTATCTG
1 TTATCTG
20835 TTTCATTGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
14 1 0.03
15 29 0.94
16 1 0.03
ACGTcount: A:0.15, C:0.19, G:0.13, T:0.52
Consensus pattern (15 bp):
TTATCTGGTCTACTA
Found at i:20857 original size:15 final size:15
Alignment explanation
Indices: 20799--20953 Score: 116
Period size: 15 Copynumber: 10.4 Consensus size: 15
20789 CGTCTACTTC
* *
20799 TATCTGGTCTACTAT
1 TATCTGGTCTATTGT
*
20814 TATTTGGTCTATTGT
1 TATCTGGTCTATTGT
*
20829 TATCT-GTTTCATTGT
1 TATCTGGTCT-ATTGT
*
20844 TATCTGGTATATTGT
1 TATCTGGTCTATTGT
* *
20859 TATTTGGTCTACTGT
1 TATCTGGTCTATTGT
** * *
20874 TATCTATTTTGTTGT
1 TATCTGGTCTATTGT
* * *
20889 TATCCGATC-ACTGT
1 TATCTGGTCTATTGT
* *
20903 TATATGTTCTATTGT
1 TATCTGGTCTATTGT
20918 TATCTGGTCTATTGT
1 TATCTGGTCTATTGT
* * *
20933 TATTTGGTCTACTAT
1 TATCTGGTCTATTGT
20948 TATCTG
1 TATCTG
20954 TTCTGTTGTG
Statistics
Matches: 106, Mismatches: 31, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
14 12 0.11
15 91 0.86
16 3 0.03
ACGTcount: A:0.17, C:0.13, G:0.16, T:0.54
Consensus pattern (15 bp):
TATCTGGTCTATTGT
Found at i:23167 original size:34 final size:35
Alignment explanation
Indices: 23116--23192 Score: 120
Period size: 34 Copynumber: 2.2 Consensus size: 35
23106 ATTAATGTTA
*
23116 GTCTAGATTTTGTGTATGCATCTTATAGATATTATT
1 GTCTAGA-TTTGTGTATGCATCTTATAGATACTATT
23152 GTCTAGA-TTGTGTATGCATCTTATAGATACTATT
1 GTCTAGATTTGTGTATGCATCTTATAGATACTATT
*
23186 GTTTAGA
1 GTCTAGA
23193 AGTAAGATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 32 0.82
36 7 0.18
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (35 bp):
GTCTAGATTTGTGTATGCATCTTATAGATACTATT
Found at i:23251 original size:36 final size:35
Alignment explanation
Indices: 23204--23273 Score: 122
Period size: 36 Copynumber: 2.0 Consensus size: 35
23194 GTAAGATTGC
23204 ATTGATAATTAATATTATTATAAAATCATTTTTATA
1 ATTGATAATTAATATTATTAT-AAATCATTTTTATA
*
23240 ATTGATAATTAATATTATTATAAATTATTTTTAT
1 ATTGATAATTAATATTATTATAAATCATTTTTAT
23274 TTGAAGGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 12 0.36
36 21 0.64
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
ATTGATAATTAATATTATTATAAATCATTTTTATA
Found at i:23518 original size:2 final size:2
Alignment explanation
Indices: 23511--23540 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
23501 TGATGAAATA
23511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
23541 GAATTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29937 original size:44 final size:44
Alignment explanation
Indices: 29802--29970 Score: 243
Period size: 44 Copynumber: 3.9 Consensus size: 44
29792 TGAAGTACGA
*
29802 GAAA-GAAAATTTAGCACATACTCAACCTAAATCCAAAAACAAT
1 GAAATGAAACTTTAGCACATACTCAACCTAAATCCAAAAACAAT
* * * *
29845 GAAATGACACTTTAGCGCATACTC-ACGTAGATCCAAAAACAAT
1 GAAATGAAACTTTAGCACATACTCAACCTAAATCCAAAAACAAT
* *
29888 GAAATGAAACTTTAGCACTTACTCAACCTAAATCCGAAAACAAT
1 GAAATGAAACTTTAGCACATACTCAACCTAAATCCAAAAACAAT
**
29932 GAAATGAAACTTTAGCACATACTTTACCTAAATCCAAAA
1 GAAATGAAACTTTAGCACATACTCAACCTAAATCCAAAA
29971 TCGAAACAAG
Statistics
Matches: 109, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
43 42 0.39
44 67 0.61
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.22
Consensus pattern (44 bp):
GAAATGAAACTTTAGCACATACTCAACCTAAATCCAAAAACAAT
Found at i:32308 original size:157 final size:159
Alignment explanation
Indices: 32013--32327 Score: 553
Period size: 157 Copynumber: 2.0 Consensus size: 159
32003 ATATCGCGAG
* *
32013 TCATTTTGTCAATACGTTAACAATTTATTTAATTTGTATTAGTTTTATTATTGTGTTATGTTAAT
1 TCATTTTGTCAATACGGTAACAATTTATTTAATTTGCATTAGTTTTATTATTGTGTTATGTTAAT
32078 TATTGCAAATATTTTATTTATTTATTTATTTAGTATTAGTTTATATTTTAATTTGTATACTATTT
66 TATTGCAAATA--TTATTTATTTATTTATTTAGTATTAGTTTATATTTTAATTTGTATACTATTT
*
32143 ATTTAATTAAGAGAATGATCGTATATTAGAC
129 ATTTAATTAAGAAAATGATCGTATATTAGAC
*
32174 TCATTTTGTCGATACGGTAACAATTTATTTAATTTGCATTAGTTTTATTATTGTGTTATGTTAAT
1 TCATTTTGTCAATACGGTAACAATTTATTTAATTTGCATTAGTTTTATTATTGTGTTATGTTAAT
*
32239 TATTGCGAATA-T-TTTATTTATTTATTTAGTATTAGTTTATATTTTAATTTGTATACTATTTAT
66 TATTGCAAATATTATTTATTTATTTATTTAGTATTAGTTTATATTTTAATTTGTATACTATTTAT
32302 TTAATTAAGAAAATGATCGTATATTA
131 TTAATTAAGAAAATGATCGTATATTA
32328 ATGTTAAGTT
Statistics
Matches: 149, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
157 76 0.51
158 1 0.01
161 72 0.48
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.54
Consensus pattern (159 bp):
TCATTTTGTCAATACGGTAACAATTTATTTAATTTGCATTAGTTTTATTATTGTGTTATGTTAAT
TATTGCAAATATTATTTATTTATTTATTTAGTATTAGTTTATATTTTAATTTGTATACTATTTAT
TTAATTAAGAAAATGATCGTATATTAGAC
Found at i:33056 original size:21 final size:21
Alignment explanation
Indices: 33021--33060 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
33011 TACTGAGTTC
33021 ATATATAAATAATTTTTTAGT
1 ATATATAAATAATTTTTTAGT
33042 ATATAATAAAT-ATTTTTTA
1 ATAT-ATAAATAATTTTTTA
33061 CACTGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
ATATATAAATAATTTTTTAGT
Found at i:42556 original size:20 final size:20
Alignment explanation
Indices: 42518--42557 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42508 AGTAATTAGT
* **
42518 AAAATTAATATTTTTGATAA
1 AAAAATAATATTTAAGATAA
42538 AAAAATAATATTTAAGATAA
1 AAAAATAATATTTAAGATAA
42558 CGTTTTATCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAAATAATATTTAAGATAA
Found at i:45155 original size:21 final size:21
Alignment explanation
Indices: 45130--45173 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
45120 CAGGCTGTCC
45130 GATGTGCAGAAAGATCTCATG
1 GATGTGCAGAAAGATCTCATG
45151 GATGTGCAGAAAGATCTCATG
1 GATGTGCAGAAAGATCTCATG
45172 GA
1 GA
45174 AAGGGAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.23
Consensus pattern (21 bp):
GATGTGCAGAAAGATCTCATG
Found at i:55944 original size:25 final size:25
Alignment explanation
Indices: 55910--55965 Score: 112
Period size: 25 Copynumber: 2.2 Consensus size: 25
55900 AGAGCGACTG
55910 AATATATTGAAAGTGTCGATACTTT
1 AATATATTGAAAGTGTCGATACTTT
55935 AATATATTGAAAGTGTCGATACTTT
1 AATATATTGAAAGTGTCGATACTTT
55960 AATATA
1 AATATA
55966 AGTATCGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (25 bp):
AATATATTGAAAGTGTCGATACTTT
Found at i:56084 original size:207 final size:207
Alignment explanation
Indices: 55729--56147 Score: 757
Period size: 207 Copynumber: 2.0 Consensus size: 207
55719 GCGGTACCAG
* *
55729 ATATATTGAAAGTGTCGATACTTTAATATGAGTATCAACACTTTGTGAATTTAAAAGAGAAGAAG
1 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCAACACATTGTGAATTTAAAAGAGAAGAAG
*
55794 TTTTAGCGCCTATAAAGTATTAATACTTTATAACAATGTATCGATCCACAACAATATAACAAGTA
66 TTTTAGCGCCTATAAAGTATCAATACTTTATAACAATGTATCGATCCACAACAATATAACAAGTA
* *
55859 AAAATATGACAAAATCGGTCTCTAAAGGACATAACCGGTATAGAGCGACTGAATATATTGAAAGT
131 AAAATATGACAAAATCGGTCTCTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGT
55924 GTCGATACTTTA
196 GTCGATACTTTA
* *
55936 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCAG
1 ATATATTGAAAGTGTCGATACTTTAATATAAGTATCAACACATTGTGAATTTAAAAGAGAAGAAG
* *
56001 TTTTAGCGCCTATAAAGTATCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTA
66 TTTTAGCGCCTATAAAGTATCAATACTTTATAACAATGTATCGATCCACAACAATATAACAAGTA
56066 AAAATATGACAAAATCGGTCTCTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGT
131 AAAATATGACAAAATCGGTCTCTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGT
56131 GTCGATACTTTA
196 GTCGATACTTTA
56143 ATATA
1 ATATA
56148 AGTATCGAAA
Statistics
Matches: 203, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
207 203 1.00
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (207 bp):
ATATATTGAAAGTGTCGATACTTTAATATAAGTATCAACACATTGTGAATTTAAAAGAGAAGAAG
TTTTAGCGCCTATAAAGTATCAATACTTTATAACAATGTATCGATCCACAACAATATAACAAGTA
AAAATATGACAAAATCGGTCTCTAAAGGACAAAACCGGTATAGAGCGACCGAATATATTGAAAGT
GTCGATACTTTA
Found at i:56242 original size:182 final size:182
Alignment explanation
Indices: 55935--56327 Score: 651
Period size: 182 Copynumber: 2.2 Consensus size: 182
55925 TCGATACTTT
*
55935 AATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACATTGTGAATTTAAAAGAGAAGCA
1 AATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAAACATTGTGAATTTAAAAGAGAAGCA
* *
56000 GTTTTAGCGCCTATAAAGTATCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGT
66 GTTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAAAGATATAACAAGT
* * *
56065 AAAAATATGACAAAATCGGTCTCTAAAGGACAAAACCGGTATAGAGCGACCG
131 AAAAATATGACAAAACCGGTCTCGAAAGGACAAAACCGGTAAAGAGCGACCG
*
56117 AATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAAACTTTGTGAATTTAAAAGAGAAGCA
1 AATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAAACATTGTGAATTTAAAAGAGAAGCA
* * * *
56182 GTTTTAGCGCTTATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAAGATATAACATGT
66 GTTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAAAGATATAACAAGT
* * *
56247 AAAAATATGACAAAACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACCG
131 AAAAATATGACAAAACCGGTCTCGAAAGGACAAAACCGGTAAAGAGCGACCG
*
56299 GATATATTGAAAGTGTCGATACTTTAATA
1 AATATATTGAAAGTGTCGATACTTTAATA
56328 AGTACGCGTA
Statistics
Matches: 196, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
182 196 1.00
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (182 bp):
AATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAAACATTGTGAATTTAAAAGAGAAGCA
GTTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAAAGATATAACAAGT
AAAAATATGACAAAACCGGTCTCGAAAGGACAAAACCGGTAAAGAGCGACCG
Found at i:58164 original size:21 final size:21
Alignment explanation
Indices: 58140--58183 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
58130 AAGACAATCA
58140 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
58161 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
58182 AG
1 AG
58184 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:58253 original size:33 final size:33
Alignment explanation
Indices: 58216--58282 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
58206 AAATAGATGG
58216 AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
*
58249 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
58282 A
1 A
58283 CTTAAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
Found at i:58490 original size:18 final size:18
Alignment explanation
Indices: 58467--58504 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
58457 AAAAAATATA
58467 AAGAAGAAAAGATGGAGG
1 AAGAAGAAAAGATGGAGG
58485 AAGAAGAAAAGATGGAGG
1 AAGAAGAAAAGATGGAGG
58503 AA
1 AA
58505 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAGATGGAGG
Found at i:59901 original size:23 final size:23
Alignment explanation
Indices: 59864--59927 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
59854 CAGCTCGTAT
*
59864 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGTAGTGCCACATAG
* * *
59887 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGTAGTGCCACATAG
59910 AAATGCACCGTAGTGCCA
1 AAATGCACCGTAGTGCCA
59928 TATAAGATTG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGTAGTGCCACATAG
Found at i:60710 original size:2 final size:2
Alignment explanation
Indices: 60624--60691 Score: 120
Period size: 2 Copynumber: 34.0 Consensus size: 2
60614 TACATAACCC
60624 AT AT -T AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60666 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
60692 CTATTATTTA
Statistics
Matches: 64, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.02
2 61 0.95
3 2 0.03
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62952 original size:16 final size:17
Alignment explanation
Indices: 62931--62963 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
62921 TTCAAAACCG
62931 TTCAGTGCATA-ACCAA
1 TTCAGTGCATATACCAA
62947 TTCAGTGCATATACCAA
1 TTCAGTGCATATACCAA
62964 CCATTTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.27
Consensus pattern (17 bp):
TTCAGTGCATATACCAA
Found at i:63296 original size:21 final size:21
Alignment explanation
Indices: 63271--63326 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
63261 TACATATATC
* *
63271 ATCATCTATTTTCTTAGCATT
1 ATCATCTATATTATTAGCATT
* *
63292 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
63313 ATC-TCTATCATTAT
1 ATCATCTAT-ATTAT
63327 CATCAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:63331 original size:21 final size:21
Alignment explanation
Indices: 63288--63331 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
63278 ATTTTCTTAG
*
63288 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
63309 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
63330 CA
1 CA
63332 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:63531 original size:23 final size:22
Alignment explanation
Indices: 63505--63556 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
63495 CACCACAGCT
63505 CGTATAATTGCACCGAAGTGCC
1 CGTATAATTGCACCGAAGTGCC
* *
63527 ACGTAGAATTGCACCGTAGTGCC
1 -CGTATAATTGCACCGAAGTGCC
63550 C-TATAAT
1 CGTATAAT
63557 AATGTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 1 0.04
23 20 0.77
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
CGTATAATTGCACCGAAGTGCC
Found at i:63767 original size:149 final size:148
Alignment explanation
Indices: 63528--63830 Score: 498
Period size: 149 Copynumber: 2.0 Consensus size: 148
63518 CGAAGTGCCA
*
63528 CGTAGAATTGCACCGTAGTGCCCTATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
* * * * * * *
63593 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCACAAATGTTCCAAAGAATATA
*
63658 TATATATCCCGAAGGACCG
130 CATATATCCCGAAGGACCG
63677 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
*
63742 CATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCATAAATGTTCCAAAGAATATAC
66 CATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCCAAAGAATATAC
*
63807 ATATGTCCCGAAGGACCG
131 ATATATCCCGAAGGACCG
63825 CGTAGA
1 CGTAGA
63831 CCCTCGACTC
Statistics
Matches: 143, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
148 48 0.34
149 95 0.66
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (148 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCACAAATGTTCCAAAGAATATAC
ATATATCCCGAAGGACCG
Found at i:68350 original size:21 final size:21
Alignment explanation
Indices: 68325--68380 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
68315 TACATATATC
* *
68325 ATCATCTATTTTCTTAGCATT
1 ATCATCTATATTATTAGCATT
* *
68346 ATCATATATATTATTATCATT
1 ATCATCTATATTATTAGCATT
68367 ATC-TCTATCATTAT
1 ATCATCTAT-ATTAT
68381 CATCAAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (21 bp):
ATCATCTATATTATTAGCATT
Found at i:68385 original size:21 final size:21
Alignment explanation
Indices: 68342--68385 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
68332 ATTTTCTTAG
*
68342 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
68363 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
68384 CA
1 CA
68386 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:68821 original size:149 final size:148
Alignment explanation
Indices: 68583--68884 Score: 478
Period size: 149 Copynumber: 2.0 Consensus size: 148
68573 GAAGTGCCAT
*
68583 GTAGAATTGCACCGTAGTGCCCTATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATC
* * * * * * * *
68648 ATATACATATACTAGGGATCAAGTATATGTCTTACAAGACTTCACACATGTTCCACAGAATATAT
66 ATATACATATACTAAGGACCAAGTATATGCCTCA-AAGACCTCACAAATGTTCCAAAGAATATAC
68713 ATATATCCCGAAGGACCGC
130 ATATATCCCGAAGGACCGC
*
68732 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGATCACATATCATTCCTTAAGAATC
1 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATC
* *
68797 ATATACATATACTAAGGACCAAGTATGTGCCTCAAAGACCTCATAAATGTTCCAAAGAATATACA
66 ATATACATATACTAAGGACCAAGTATATGCCTCAAAGACCTCACAAATGTTCCAAAGAATATACA
*
68862 TATGTCCCGAAGGACCGC
131 TATATCCCGAAGGACCGC
68880 GTAGA
1 GTAGA
68885 CCCTCGACTC
Statistics
Matches: 140, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
148 48 0.34
149 92 0.66
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (148 bp):
GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATC
ATATACATATACTAAGGACCAAGTATATGCCTCAAAGACCTCACAAATGTTCCAAAGAATATACA
TATATCCCGAAGGACCGC
Found at i:74577 original size:23 final size:23
Alignment explanation
Indices: 74540--74599 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
74530 CAGCTCATAT
**
74540 AAATGCACCCAAGTGCCACGTAG
1 AAATGCACCGTAGTGCCACGTAG
* * *
74563 AATTGCACCGTAGTGTCGCGTAG
1 AAATGCACCGTAGTGCCACGTAG
74586 AAATGCACCGTAGT
1 AAATGCACCGTAGT
74600 TCCATATAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATGCACCGTAGTGCCACGTAG
Found at i:75359 original size:2 final size:2
Alignment explanation
Indices: 75352--75394 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
75342 ACTTATAAAC
75352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75393 AT
1 AT
75395 TCTCTATTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:76396 original size:34 final size:32
Alignment explanation
Indices: 76334--76403 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
76324 ACCTTACAAC
* *
76334 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
76366 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
76400 TCCC
1 TCCC
76404 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:76868 original size:21 final size:21
Alignment explanation
Indices: 76824--76899 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
76814 AGTGTTTGAG
*
76824 TGCATGGATGCACTGCA-TGA
1 TGCATGGATGCACTGCAGGGA
76844 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
76865 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
76886 TGCATGGATGCACT
1 TGCATGGATGCACT
76900 TTGACACCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:77012 original size:29 final size:31
Alignment explanation
Indices: 76980--77040 Score: 108
Period size: 29 Copynumber: 2.0 Consensus size: 31
76970 AAACTTTGAA
76980 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
77009 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
77040 T
1 T
77041 TATATCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.37
30 11 0.37
31 8 0.27
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:79588 original size:21 final size:21
Alignment explanation
Indices: 79529--79603 Score: 109
Period size: 20 Copynumber: 3.7 Consensus size: 21
79519 GGTGTTTGAG
*
79529 TGCATGGATGCACTGCA-TGA
1 TGCATGGATGCACTGCAGGGA
*
79549 TGCATGGATACAC-GCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
79569 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
79590 TGCATGGATGCACT
1 TGCATGGATGCACT
79604 TTGACACCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 3 0.06
20 26 0.53
21 20 0.41
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.21
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Done.