Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004723.1 Hibiscus syriacus cultivar Beakdansim tig00010649_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: 70501
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:14094 original size:64 final size:64
Alignment explanation
Indices: 14037--14244 Score: 217
Period size: 64 Copynumber: 3.2 Consensus size: 64
14027 GATGCATTGA
**
14037 TAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTC-ATGCATCGATGCATA
1 TAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAA-TCGATGCATCGATGCATA
14099 AG
63 AG
* *
14101 TAGTGCATCGATGCATCCCATTAATAATGAAACATCGAATGCAATCGGTGCATCGATGCATAAG
1 TAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGATGCATCGATGCATAAG
* ** * * ** ** * *
14165 GAGTGCATCGATGCATCCCAGCAATAATACTAA-ATCGAATACCTTTTATGCACCGATGCATCAG
1 TAGTGCATCGATGCATCCCATTAATAATA-AAACATCGAATGCAATCGATGCATCGATGCATAAG
14229 TAGTGCATCGATGCAT
1 TAGTGCATCGATGCAT
14245 ACCTTCATTA
Statistics
Matches: 122, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
63 2 0.02
64 112 0.92
65 8 0.07
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (64 bp):
TAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCGATGCATCGATGCATAAG
Found at i:14780 original size:16 final size:16
Alignment explanation
Indices: 14759--14843 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
14749 TCGAGGGTTT
14759 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
14775 ACATATG---AATAGTTT
1 ACATATGTTTAA-AG-GC
14790 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
* ***
14806 ACATATG--AACAATTT
1 ACATATGTTTA-AAGGC
14821 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
14837 ACATATG
1 ACATATG
14844 AACAGTTTAC
Statistics
Matches: 49, Mismatches: 12, Indels: 16
0.64 0.16 0.21
Matches are distributed among these distances:
13 2 0.04
14 3 0.06
15 16 0.33
16 23 0.47
17 3 0.06
18 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:14793 original size:31 final size:31
Alignment explanation
Indices: 14755--15009 Score: 420
Period size: 31 Copynumber: 8.2 Consensus size: 31
14745 AGAGTCGAGG
*
14755 GTTTACATATGTTTAAAGGCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
14786 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
14817 ATTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* *
14848 GTTTACATATGTTTAAAGGCATATATATAAACA
1 GTTTACATATGTTTAAAGGC--ACATATGAACA
*
14881 GTTTACATATGTTTAAAGGCACATATAAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
14912 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
* * *
14943 GTTTATATATGTTTAAAGTCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
14974 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
15005 GTTTA
1 GTTTA
15010 TATTGTGACC
Statistics
Matches: 209, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
31 180 0.86
33 29 0.14
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.35
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:14938 original size:126 final size:126
Alignment explanation
Indices: 14755--14999 Score: 427
Period size: 126 Copynumber: 1.9 Consensus size: 126
14745 AGAGTCGAGG
* *
14755 GTTTACATATGTTTAAAGGCACATATGAATAGTTTACATATGTTTAAAGGCACATATGAACAATT
1 GTTTACATATGTTTAAAGGCACATATAAACAGTTTACATATGTTTAAAGGCACATATGAACAATT
*
14820 TACATATGTTTAAAGGCACATATGAACAGTTTACATATGTTTAAAGGCATATATATAAACA
66 TACATATGTTTAAAGGCACATATGAACAGTTTACATATGTTTAAAGGCACATATATAAACA
*
14881 GTTTACATATGTTTAAAGGCACATATAAACAGTTTACATATGTTTAAAGGCACATATGAACAGTT
1 GTTTACATATGTTTAAAGGCACATATAAACAGTTTACATATGTTTAAAGGCACATATGAACAATT
* * *
14946 TATATATGTTTAAAGTCACATATGAATAGTTTACATATGTTTAAAGGCACATAT
66 TACATATGTTTAAAGGCACATATGAACAGTTTACATATGTTTAAAGGCACATAT
15000 GAACAGTTTA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 112 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (126 bp):
GTTTACATATGTTTAAAGGCACATATAAACAGTTTACATATGTTTAAAGGCACATATGAACAATT
TACATATGTTTAAAGGCACATATGAACAGTTTACATATGTTTAAAGGCACATATATAAACA
Found at i:18130 original size:64 final size:64
Alignment explanation
Indices: 18062--18235 Score: 203
Period size: 64 Copynumber: 2.7 Consensus size: 64
18052 TTATTTGAAT
* * **
18062 GTGCACCGATGCAT-TGATAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAAT
1 GTGCATCGATGCATAAG-TAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGCAA-
18124 TC-
62 TCG
* *
18126 GTGCATCGATGCATAAGTAGTGCATCGATACATCCCATTAATAATGAAACATCGAATGCAATCG
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
* **
18190 GTGCATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATA
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATA
18236 CTAAATCGAA
Statistics
Matches: 95, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
63 2 0.02
64 86 0.91
65 7 0.07
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (64 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCAATCG
Found at i:18821 original size:16 final size:16
Alignment explanation
Indices: 18800--18883 Score: 54
Period size: 16 Copynumber: 5.4 Consensus size: 16
18790 TCGAGGGTTT
18800 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
18816 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
18831 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
**
18847 ACATATG---AACAGTTT
1 ACATATGTTTAA-AG-GC
18862 ACATATGTTTAAAGGC
1 ACATATGTTTAAAGGC
18878 ACATAT
1 ACATAT
18884 AAACAGTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
13 4 0.08
14 4 0.08
15 14 0.28
16 20 0.40
17 4 0.08
18 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.32
Consensus pattern (16 bp):
ACATATGTTTAAAGGC
Found at i:18834 original size:31 final size:31
Alignment explanation
Indices: 18796--18986 Score: 355
Period size: 31 Copynumber: 6.2 Consensus size: 31
18786 AGAGTCGAGG
18796 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
18827 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
18858 GTTTACATATGTTTAAAGGCACATATAAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
18889 GTTTACATATGTTTAAAGGCACATATGAATA
1 GTTTACATATGTTTAAAGGCACATATGAACA
*
18920 GTTTATATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
18951 GTTTACATATGTTTAAAGGCACATATGAACA
1 GTTTACATATGTTTAAAGGCACATATGAACA
18982 GTTTA
1 GTTTA
18987 TATTGTGACC
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 154 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.34
Consensus pattern (31 bp):
GTTTACATATGTTTAAAGGCACATATGAACA
Found at i:23081 original size:15 final size:15
Alignment explanation
Indices: 23057--23086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23047 GTTGTACGAC
*
23057 AACTTGATTTAAGAT
1 AACTTAATTTAAGAT
23072 AACTTAATTTAAGAT
1 AACTTAATTTAAGAT
23087 TAAAGAACGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (15 bp):
AACTTAATTTAAGAT
Found at i:23791 original size:15 final size:15
Alignment explanation
Indices: 23771--23821 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
23761 TTCTAGAAAA
23771 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
23786 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
*
23801 TGAATTACTGCAATT
1 TGAATTACTGGAATT
23816 TGAATT
1 TGAATT
23822 CTGAAAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.37, C:0.08, G:0.18, T:0.37
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:23800 original size:30 final size:29
Alignment explanation
Indices: 23761--23837 Score: 118
Period size: 30 Copynumber: 2.6 Consensus size: 29
23751 GTAATTGATT
* *
23761 TTCTAGAAAATGAATTACTGGAATTTGAA
1 TTCTGGAAAATGAATTACTGCAATTTGAA
23790 TTACTGGAAAATGAATTACTGCAATTTGAA
1 TT-CTGGAAAATGAATTACTGCAATTTGAA
*
23820 TTCTGAAAAATGAATTAC
1 TTCTGGAAAATGAATTAC
23838 ATTTCTGGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 17 0.39
30 27 0.61
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.34
Consensus pattern (29 bp):
TTCTGGAAAATGAATTACTGCAATTTGAA
Found at i:24038 original size:22 final size:22
Alignment explanation
Indices: 23992--24073 Score: 64
Period size: 21 Copynumber: 3.8 Consensus size: 22
23982 ATACAATAAA
*
23992 TAATATTATTTATTATAAAACT
1 TAATATTATTTATTATAAAAAT
*
24014 TAATATTA-TTATTTTAAAATAT
1 TAATATTATTTATTATAAAA-AT
* * **
24036 TAAAATAATTTATT-T-ATTAT
1 TAATATTATTTATTATAAAAAT
24056 TAAATATTATTT-TTATAA
1 T-AATATTATTTATTATAA
24074 TTTTATTAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
20 5 0.11
21 20 0.43
22 17 0.36
23 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (22 bp):
TAATATTATTTATTATAAAAAT
Found at i:24217 original size:23 final size:23
Alignment explanation
Indices: 24168--24218 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
24158 GTGTTATATT
**
24168 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
24191 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
24214 ATATT
1 ATATT
24219 ATTAGATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:24371 original size:59 final size:61
Alignment explanation
Indices: 24206--24380 Score: 149
Period size: 59 Copynumber: 3.0 Consensus size: 61
24196 TTAAATATCT
* *
24206 TTATTAAAATATTATTAGATTATTATA-T-TAATATTAAAAATATAA-ATA-ATATTATTCA
1 TTATTAAAATATAATT-GATTATTTTATTATAATATTAAAAATATAATATATATATTATTCA
* * * *
24264 TTATTACATATATAA-AGA--A-TTTATTAT-ATATTTATTAAAATAAAAATATATATCTTA-T-
1 TTATTA-AAATATAATTGATTATTTTATTATAATA-TTA--AAAAT-ATAATATATATATTATTC
24322 A
61 A
*
24323 TTATTATAATATAATTGATTATTTTATTATAATATTAAAAATATAATAT-TATATTATT
1 TTATTAAAATATAATTGATTATTTTATTATAATATTAAAAATATAATATATATATTATT
24381 AAAAATATTA
Statistics
Matches: 91, Mismatches: 11, Indels: 29
0.69 0.08 0.22
Matches are distributed among these distances:
54 3 0.03
55 5 0.05
56 4 0.04
57 2 0.02
58 23 0.25
59 25 0.27
60 9 0.10
61 6 0.07
62 11 0.12
63 3 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (61 bp):
TTATTAAAATATAATTGATTATTTTATTATAATATTAAAAATATAATATATATATTATTCA
Found at i:24375 original size:22 final size:23
Alignment explanation
Indices: 24347--24393 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
24337 TTGATTATTT
24347 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
*
24369 TATTATATTATTAAAAATATTAA
1 TATTATAATATTAAAAATATTAA
24392 TA
1 TA
24394 AATATATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:24392 original size:23 final size:24
Alignment explanation
Indices: 24348--24425 Score: 90
Period size: 23 Copynumber: 3.3 Consensus size: 24
24338 TGATTATTTT
*
24348 ATTATAATATTAAAAATA-TAAT-
1 ATTATATTATTAAAAATATTAATA
24370 ATTATATTATTAAAAATATTAATA
1 ATTATATTATTAAAAATATTAATA
* * *
24394 AATATATT-TTAAATATTTTAATA
1 ATTATATTATTAAAAATATTAATA
24417 ATTAATATT
1 ATT-ATATT
24426 TTGATGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
22 17 0.35
23 19 0.40
24 12 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATATTATTAAAAATATTAATA
Found at i:24401 original size:21 final size:22
Alignment explanation
Indices: 24354--24410 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
24344 TTTTATTATA
*
24354 ATATTAAAAATA-TAATATTAT
1 ATATTAAAAATATTAATATAAT
24375 ATTATTAAAAATATTAATA-AAT
1 A-TATTAAAAATATTAATATAAT
**
24397 ATATTTTAAATATT
1 ATATTAAAAATATT
24411 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 12 0.39
22 14 0.45
23 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATATTAAAAATATTAATATAAT
Found at i:24711 original size:42 final size:42
Alignment explanation
Indices: 24633--24712 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
24623 CAAACACTGG
*
24633 AAAATATTTTCCAAAAAACGAATTACGTGAAACAAACACGAA
1 AAAATATTTTCCAAAAAACGAATTACATGAAACAAACACGAA
**
24675 AAAATATTTTCCGGAAAACGAATTACAT-AAAGCAAACA
1 AAAATATTTTCCAAAAAACGAATTACATGAAA-CAAACA
24713 TGATATTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 3 0.09
42 31 0.91
ACGTcount: A:0.54, C:0.16, G:0.10, T:0.20
Consensus pattern (42 bp):
AAAATATTTTCCAAAAAACGAATTACATGAAACAAACACGAA
Found at i:24939 original size:19 final size:19
Alignment explanation
Indices: 24903--24946 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
24893 ATAATGAGTG
*
24903 ATATTAATTTATATATTTA
1 ATATTAATTAATATATTTA
24922 ATATTAATATAATA-ATTTA
1 ATATTAAT-TAATATATTTA
*
24941 GTATTA
1 ATATTA
24947 TGTTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATATTAATTAATATATTTA
Found at i:24965 original size:30 final size:27
Alignment explanation
Indices: 24907--24968 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 27
24897 TGAGTGATAT
*
24907 TAATTTATATATTTAATATTAATATAA
1 TAATTTATATATTTAATATAAATATAA
24934 TAATTTAGTATTATGTTAATA-AAATACTAA
1 TAATTTA-TA-TAT-TTAATATAAATA-TAA
24964 TAATT
1 TAATT
24969 AAAATTAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 2 0.07
29 7 0.23
30 14 0.47
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (27 bp):
TAATTTATATATTTAATATAAATATAA
Found at i:25251 original size:21 final size:21
Alignment explanation
Indices: 25227--25268 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25217 ATGTAATTCG
*
25227 TTTTACATAAAATAATTTTCA
1 TTTTACATAAAACAATTTTCA
* *
25248 TTTTACGTAAAACAGTTTTCA
1 TTTTACATAAAACAATTTTCA
25269 AATAATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTTACATAAAACAATTTTCA
Found at i:38166 original size:2 final size:2
Alignment explanation
Indices: 38155--38410 Score: 138
Period size: 2 Copynumber: 127.0 Consensus size: 2
38145 TAAAAACAAT
* *
38155 TA TA -A TA TA TA TA TA TA -A TA TA -A TA TA AA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * *
38196 TA TT TA TA TA CTA TA TA TA AA CTA TA TA GTT TA T- TA -A TA TA
1 TA TA TA TA TA -TA TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA
* * *
38237 TA TA TA TA TA TA TA -A TA TA -A TT TA T- TA CTA TA AA CTA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA
* * * * * *
38278 AA CTA TT TA TA TA AA CTA TA TA CA CTA TA TG TA TA AA CTA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA TA TA
* * * *
38322 TG TG TA AA CTA TA TA TA TA TA TA T- TA TA TA TA TA T- TA TA TG
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
38363 TA TA AA CCA 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
38406 T- TA TA
1 TA TA TA
38411 GTTCATTAAT
Statistics
Matches: 193, Mismatches: 37, Indels: 48
0.69 0.13 0.17
Matches are distributed among these distances:
1 11 0.06
2 167 0.87
3 15 0.08
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
TA
Found at i:38480 original size:31 final size:31
Alignment explanation
Indices: 38394--38495 Score: 101
Period size: 31 Copynumber: 3.5 Consensus size: 31
38384 TATATATATA
38394 TATATATATATATTATAGTTCATTAATAT-AA-
1 TATATATAT-TA-TATAGTTCATTAATATAAAC
* *
38425 -AT-TAT-GTAT-TAGTTTATTAATATAAAC
1 TATATATATTATATAGTTCATTAATATAAAC
*
38452 TATATATATTATATAGTTCATTAGTATAAAC
1 TATATATATTATATAGTTCATTAATATAAAC
*
38483 TATAT-TAATATAT
1 TATATATATTATAT
38496 GAACTATAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
25 13 0.22
26 3 0.05
27 2 0.03
28 2 0.03
29 6 0.10
30 12 0.20
31 21 0.36
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (31 bp):
TATATATATTATATAGTTCATTAATATAAAC
Found at i:38557 original size:20 final size:22
Alignment explanation
Indices: 38534--38615 Score: 80
Period size: 22 Copynumber: 3.8 Consensus size: 22
38524 CTATATGAAC
* * *
38534 TATAGTTCATTAATATTAATTA
1 TATAGTTTATTAATATAAATCA
*
38556 TATAGTTTATTGATATAAA-C-
1 TATAGTTTATTAATATAAATCA
**
38576 TATAGTTTATTAATATAAAGAA
1 TATAGTTTATTAATATAAATCA
38598 TATAGTTTA-TACATATAA
1 TATAGTTTATTA-ATATAA
38616 TATTAATTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
20 18 0.35
21 2 0.04
22 31 0.61
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (22 bp):
TATAGTTTATTAATATAAATCA
Found at i:38577 original size:42 final size:42
Alignment explanation
Indices: 38526--38607 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
38516 TGTATAAACT
* * **
38526 ATATGAACTATAGTTCATTAATATTAATTATATAGTTTATTG
1 ATATAAACTATAGTTCATTAATATAAAGAATATAGTTTATTG
*
38568 ATATAAACTATAGTTTATTAATATAAAGAATATAGTTTAT
1 ATATAAACTATAGTTCATTAATATAAAGAATATAGTTTAT
38608 ACATATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.45
Consensus pattern (42 bp):
ATATAAACTATAGTTCATTAATATAAAGAATATAGTTTATTG
Found at i:41884 original size:15 final size:15
Alignment explanation
Indices: 41864--41914 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
41854 ACTTCTGTTT
41864 ATTAATGTTTATTAA
1 ATTAATGTTTATTAA
* **
41879 ATTAATTTTTATATTT
1 ATTAATGTTTAT-TAA
*
41895 ATT-ATGTTTATTCA
1 ATTAATGTTTATTAA
41909 ATTAAT
1 ATTAAT
41915 TTTTCGATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (15 bp):
ATTAATGTTTATTAA
Found at i:41904 original size:30 final size:31
Alignment explanation
Indices: 41861--41918 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
41851 GTAACTTCTG
41861 TTTATTAATGTTTATTAAATTAATTTTTATA
1 TTTATTAATGTTTATTAAATTAATTTTTATA
*
41892 TTTATT-ATGTTTATTCAATTAATTTTT
1 TTTATTAATGTTTATTAAATTAATTTTT
41919 CGATATGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTATTAATGTTTATTAAATTAATTTTTATA
Found at i:42575 original size:14 final size:14
Alignment explanation
Indices: 42536--42575 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
42526 GATTATATTG
* *
42536 AAGATTTATAACAT
1 AAGAATTATAATAT
*
42550 AAGAATCATAATAT
1 AAGAATTATAATAT
42564 AAGAATTATAAT
1 AAGAATTATAAT
42576 TAATATCATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (14 bp):
AAGAATTATAATAT
Found at i:48470 original size:42 final size:42
Alignment explanation
Indices: 48417--48545 Score: 224
Period size: 42 Copynumber: 3.1 Consensus size: 42
48407 TAATTAACTA
48417 AAATATACATAATTGAATTTCTAATTTTAATTATAATTTTTT
1 AAATATACATAATTGAATTTCTAATTTTAATTATAATTTTTT
* *
48459 AAATATGCATAATCGAATTTCTAATTTTAATTATAATTTTTT
1 AAATATACATAATTGAATTTCTAATTTTAATTATAATTTTTT
48501 AAATATACATAATCT-AATTTCTAATTTTAATTATAATTTTTT
1 AAATATACATAAT-TGAATTTCTAATTTTAATTATAATTTTTT
48543 AAA
1 AAA
48546 GAAATACACA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 82 1.00
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.50
Consensus pattern (42 bp):
AAATATACATAATTGAATTTCTAATTTTAATTATAATTTTTT
Found at i:48576 original size:42 final size:42
Alignment explanation
Indices: 48432--48564 Score: 153
Period size: 42 Copynumber: 3.2 Consensus size: 42
48422 TACATAATTG
* * * * *
48432 AATTTCTAATTTTAATTATAATTTTTTAAATATGCATAATCG
1 AATTTATAATTTTAATTATAATTTTTTAAAGATACATAAACT
* * *
48474 AATTTCTAATTTTAATTATAATTTTTTAAATATACATAATCT
1 AATTTATAATTTTAATTATAATTTTTTAAAGATACATAAACT
*
48516 AATTTCTAATTTTAATTATAATTTTTTAAAGA-A-ATACACACT
1 AATTTATAATTTTAATTATAATTTTTTAAAGATACATA-A-ACT
48558 AATTTAT
1 AATTTAT
48565 TATTATTATT
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
40 3 0.04
41 2 0.02
42 79 0.94
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.50
Consensus pattern (42 bp):
AATTTATAATTTTAATTATAATTTTTTAAAGATACATAAACT
Found at i:48842 original size:37 final size:38
Alignment explanation
Indices: 48791--48872 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
48781 TTTTTTTGTA
* *
48791 AACCCGACCCAACCCAAAAAT-AGGTATCCTCCACCCG
1 AACCCGACCAAACCCAAAAATCAGATATCCTCCACCCG
* **
48828 AACCCGACCAAACCCGAAAATCTTATATCCTCCACCCG
1 AACCCGACCAAACCCAAAAATCAGATATCCTCCACCCG
48866 -ACCCGAC
1 AACCCGAC
48873 TTGACCTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 26 0.67
38 13 0.33
ACGTcount: A:0.34, C:0.44, G:0.10, T:0.12
Consensus pattern (38 bp):
AACCCGACCAAACCCAAAAATCAGATATCCTCCACCCG
Found at i:48892 original size:37 final size:38
Alignment explanation
Indices: 48791--48892 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 38
48781 TTTTTTTGTA
* **
48791 AACCCGACCCAACCC-AAAAATAGGTATCCTCCACCCG
1 AACCCGACCAAACCCGAAAAATATATATCCTCCACCCG
*
48828 AACCCGACCAAACCCG-AAAATCTTATATCCTCCACCCG
1 AACCCGACCAAACCCGAAAAAT-ATATATCCTCCACCCG
*** *
48866 -ACCCGACTTGACCTGAAAAATATATAT
1 AACCCGACCAAACCCGAAAAATATATAT
48893 ATTCTATCCG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
37 35 0.66
38 18 0.34
ACGTcount: A:0.36, C:0.37, G:0.10, T:0.17
Consensus pattern (38 bp):
AACCCGACCAAACCCGAAAAATATATATCCTCCACCCG
Found at i:55484 original size:20 final size:20
Alignment explanation
Indices: 55447--55485 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55437 TATAATTTTT
* * *
55447 AAAAATATTTTTATACTTTA
1 AAAAATAATTATAAACTTTA
55467 AAAAATAATTATAAACTTT
1 AAAAATAATTATAAACTTT
55486 TATATATTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATAATTATAAACTTTA
Found at i:61602 original size:23 final size:23
Alignment explanation
Indices: 61576--61620 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
61566 CCTATCAAGG
61576 ACAACGATGAAGCCGTCAAAGCA
1 ACAACGATGAAGCCGTCAAAGCA
61599 ACAACGATGAAGCCGTCAAAGC
1 ACAACGATGAAGCCGTCAAAGC
61621 CTACGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.27, G:0.22, T:0.09
Consensus pattern (23 bp):
ACAACGATGAAGCCGTCAAAGCA
Found at i:62733 original size:32 final size:31
Alignment explanation
Indices: 62692--62768 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
62682 TTTTTCATCC
* ** * *
62692 AAGTACCTAAAGTATTTTTTTTTTGTTAAAAT
1 AAGTACCTAAAGT-TATCATTTTGGTCAAAAT
62724 AAGTACCTAAAGTTATCATTTTGGTCAAAAT
1 AAGTACCTAAAGTTATCATTTTGGTCAAAAT
*
62755 AAATACCTAAAGTT
1 AAGTACCTAAAGTT
62769 TTCTTGCTTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 26 0.67
32 13 0.33
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.40
Consensus pattern (31 bp):
AAGTACCTAAAGTTATCATTTTGGTCAAAAT
Found at i:67082 original size:31 final size:30
Alignment explanation
Indices: 67044--67103 Score: 111
Period size: 31 Copynumber: 2.0 Consensus size: 30
67034 CAAAACGTCT
67044 AATTCTATGGCAAGATTTAGACTTGTTTCAC
1 AATTCTATGGCAAGATTTAGACTT-TTTCAC
67075 AATTCTATGGCAAGATTTAGACTTTTTCA
1 AATTCTATGGCAAGATTTAGACTTTTTCA
67104 ACATTTATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 5 0.17
31 24 0.83
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (30 bp):
AATTCTATGGCAAGATTTAGACTTTTTCAC
Done.