Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000664.1 Hibiscus syriacus cultivar Beakdansim tig00001293_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: 78286
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6886 original size:15 final size:15
Alignment explanation
Indices: 6866--6908 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
6856 ATTCATATTT
6866 ATTTATTTATTTAAA
1 ATTTATTTATTTAAA
*
6881 ATTTATTTATTT-AT
1 ATTTATTTATTTAAA
*
6895 ATTTATTCATTTAA
1 ATTTATTTATTTAA
6909 TTTTATAGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTATTTATTTAAA
Found at i:6913 original size:14 final size:14
Alignment explanation
Indices: 6867--6914 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
6857 TTCATATTTA
*
6867 TTTATTTATTTAAAA
1 TTTATTTATTT-AAT
6882 TTTATTTATTT-AT
1 TTTATTTATTTAAT
*
6895 ATTTATTCATTTAAT
1 -TTTATTTATTTAAT
6910 TTTAT
1 TTTAT
6915 AGATAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 1 0.03
14 15 0.52
15 13 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTATTTAAT
Found at i:7142 original size:43 final size:44
Alignment explanation
Indices: 7079--7165 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 44
7069 CTCCAATCCA
7079 AGGTTCACGCCTGATCACGATCAGT-AGGGCATTAGACTTCACT
1 AGGTTCACGCCTGATCACGATCAGTAAGGGCATTAGACTTCACT
* *
7122 AGGTTTACGCCTGATTACGATCAGTAAGGGCATTAGACTTCACT
1 AGGTTCACGCCTGATCACGATCAGTAAGGGCATTAGACTTCACT
7166 TGAAATTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 23 0.56
44 18 0.44
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (44 bp):
AGGTTCACGCCTGATCACGATCAGTAAGGGCATTAGACTTCACT
Found at i:10646 original size:20 final size:20
Alignment explanation
Indices: 10621--10658 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
10611 CTGATAGTCC
10621 TTGTCTTTATTCTGTATATT
1 TTGTCTTTATTCTGTATATT
10641 TTGTCTTTATTCTGTATA
1 TTGTCTTTATTCTGTATA
10659 ATGCAACAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.63
Consensus pattern (20 bp):
TTGTCTTTATTCTGTATATT
Found at i:14003 original size:74 final size:74
Alignment explanation
Indices: 13904--14046 Score: 232
Period size: 74 Copynumber: 1.9 Consensus size: 74
13894 AAACTAACGA
* * * *
13904 AAGTTAACGTTTTAGTAACTACATCTTAATTAAAACAAAACAAAAGTGACTACGAATTAACGTTT
1 AAGTTAACGTTTCAGTAACCACATCTTAATTAAAACAAAACAAAAATAACTACGAATTAACGTTT
13969 TTGAATCGG
66 TTGAATCGG
* *
13978 AAGTTAACGTTTCAGTGACCACATCTTAATTAAAACAAAATAAAAATAACTACGAATTAACGTTT
1 AAGTTAACGTTTCAGTAACCACATCTTAATTAAAACAAAACAAAAATAACTACGAATTAACGTTT
14043 TTGA
66 TTGA
14047 TTTGATAGAC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
74 63 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (74 bp):
AAGTTAACGTTTCAGTAACCACATCTTAATTAAAACAAAACAAAAATAACTACGAATTAACGTTT
TTGAATCGG
Found at i:15250 original size:29 final size:29
Alignment explanation
Indices: 15207--15299 Score: 80
Period size: 29 Copynumber: 3.1 Consensus size: 29
15197 ATACATAATG
*
15207 AATAGTTGTGTGACTATTTTGTAACTTTT
1 AATAGTTGAGTGACTATTTTGTAACTTTT
* **** *
15236 AATAGTTGAGAGACTCAACAAAGTAACTATCT
1 AATAGTTGAGTGACT--ATTTTGTAACT-TTT
*
15268 -ATAGTTGAGTGACTATTTTGTAATTTTT
1 AATAGTTGAGTGACTATTTTGTAACTTTT
15296 AATA
1 AATA
15300 ATTAAGGACG
Statistics
Matches: 46, Mismatches: 14, Indels: 8
0.68 0.21 0.12
Matches are distributed among these distances:
28 2 0.04
29 22 0.48
31 20 0.43
32 2 0.04
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (29 bp):
AATAGTTGAGTGACTATTTTGTAACTTTT
Found at i:22903 original size:184 final size:184
Alignment explanation
Indices: 22589--22976 Score: 638
Period size: 184 Copynumber: 2.1 Consensus size: 184
22579 ATTAAATTTT
*
22589 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACTCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAATCATTTAAAACTCAATTAATAA
*
22654 TTTAAGATCCAATAACTTTTAAACCTAAATCTATATTAATTAATTAAAAAAATTATATAAAATTT
66 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
*
22719 TAATTTTATAATTATATATTATTTAAATTAATTGTAAACTGTTTTTTT-AATTAA
131 T-ATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAA
*
22773 AAATATTATATATATTATATATAACATATGAGCTCAACCCAAA-CTATTTAAAACTCAATTAATA
1 AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAATC-ATTTAAAACTCAATTAATA
* * *
22837 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAATTTATCTGAAATT
65 ATTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATT
*
22902 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTTTTTTTTTGAATTAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAA
* * *
22957 AAACATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
22977 AATTAGAAAA
Statistics
Matches: 190, Mismatches: 12, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
183 53 0.28
184 137 0.72
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.43
Consensus pattern (184 bp):
AAATATTAAATATATTATATATAACATATGAGCTCAACCCAAATCATTTAAAACTCAATTAATAA
TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTTGAATTAA
Found at i:28484 original size:29 final size:29
Alignment explanation
Indices: 28424--28491 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
28414 CTAATTTTTA
*
28424 TTTA-TATATTTTATAGTATTATTAGTTTT
1 TTTATTAT-TTTTATAGTATTATTAGTTAT
* *
28453 TTTTTTATTTTTATATGTGTTATTAG-TAT
1 TTTATTATTTTTATA-GTATTATTAGTTAT
28482 TTTATTATTT
1 TTTATTATTT
28492 ATTTTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 21 0.64
30 12 0.36
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (29 bp):
TTTATTATTTTTATAGTATTATTAGTTAT
Found at i:28494 original size:33 final size:30
Alignment explanation
Indices: 28418--28496 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 30
28408 TTAATTCTAA
*
28418 TTTTTATTTATATATTTTATAGTATTATTAG
1 TTTTTATTTTTAT-TTTTATAGTATTATTAG
*
28449 TTTTT-TTTTTATTTTTATATGTGTTATTAG
1 TTTTTATTTTTATTTTTATA-GTATTATTAG
28479 TATTTTATTATTTATTTT
1 T-TTTTATT-TTTATTTT
28497 ATTTATTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
29 7 0.17
30 16 0.38
31 9 0.21
32 2 0.05
33 8 0.19
ACGTcount: A:0.23, C:0.00, G:0.06, T:0.71
Consensus pattern (30 bp):
TTTTTATTTTTATTTTTATAGTATTATTAG
Found at i:28496 original size:12 final size:13
Alignment explanation
Indices: 28479--28507 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28469 GTGTTATTAG
28479 TATTTTA-TTATT
1 TATTTTATTTATT
28491 TATTTTATTTATT
1 TATTTTATTTATT
28504 TATT
1 TATT
28508 ATATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:28497 original size:38 final size:36
Alignment explanation
Indices: 28419--28512 Score: 102
Period size: 38 Copynumber: 2.6 Consensus size: 36
28409 TAATTCTAAT
*
28419 TTTTATTTATATATTTTATAGTATTATTAGTTTTTT
1 TTTTATTTATATATTTTATAGTATTATTAGTTTTTA
*
28455 TTTTATTTTTATATGTGTTATTAGTATT-TTA-TTATTTA
1 TTTTATTTATATAT-T-TTA-TAGTATTATTAGTT-TTTA
* *
28493 TTTTATTTATTTATTATATA
1 TTTTATTTATATATTTTATA
28513 TATCTATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
35 2 0.04
36 15 0.31
37 4 0.08
38 21 0.43
39 7 0.14
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (36 bp):
TTTTATTTATATATTTTATAGTATTATTAGTTTTTA
Found at i:28800 original size:28 final size:29
Alignment explanation
Indices: 28749--28805 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
28739 AATGTTGGTC
*
28749 ATGTCGTTTGTTTTTTGTCCTTATTTTAT
1 ATGTCGTTAGTTTTTTGTCCTTATTTTAT
* *
28778 ATGTTGTTAGTTTTTT-TCTTTATTTTAT
1 ATGTCGTTAGTTTTTTGTCCTTATTTTAT
28806 TTTCTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.68
Consensus pattern (29 bp):
ATGTCGTTAGTTTTTTGTCCTTATTTTAT
Found at i:28826 original size:11 final size:11
Alignment explanation
Indices: 28810--28840 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
28800 TTTTATTTTC
28810 TTATTTTCAAT
1 TTATTTTCAAT
28821 TTATTTTCAAT
1 TTATTTTCAAT
28832 TTATTTTCA
1 TTATTTTCA
28841 TCACCTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATTTTCAAT
Found at i:40452 original size:105 final size:105
Alignment explanation
Indices: 40259--40824 Score: 900
Period size: 105 Copynumber: 5.5 Consensus size: 105
40249 ATTCAAGTCA
*
40259 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAA
40323 TTTCAACTTCACAACG-AAGAATATTGGACTCCAGACAACGC
65 TTTCAACTTCACAACGAAAG-ATATTGGACTCCAGACAACGC
* * *
40364 AAGTTCAACTTCACGATGAAGGGACTGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAA
* *
40428 TTTCAACTTCACAGCGAAAGATATTGGACTCGAGACAACGC
65 TTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGC
* *
40469 AAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
40534 TTC-A----A-AACGAAAGATATTGGACTCCAGACAACGC
66 TTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGC
* *
40568 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
*
40633 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
66 TTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGC
* *
40673 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
*
40738 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
66 TTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGC
*
40778 AAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAA-ATTTC
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTC
40825 CCAGTTTAAA
Statistics
Matches: 436, Mismatches: 17, Indels: 17
0.93 0.04 0.04
Matches are distributed among these distances:
99 92 0.21
100 2 0.00
104 7 0.02
105 330 0.76
106 5 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
TTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGC
Found at i:40615 original size:204 final size:207
Alignment explanation
Indices: 40259--40824 Score: 867
Period size: 204 Copynumber: 2.7 Consensus size: 207
40249 ATTCAAGTCA
*
40259 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAA
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAA
*
40323 TTTCAACTTCACAACG-AAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGG
65 TTTCAA---CACAACGAAAG-ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * *
40387 ACTGCTGGTTGTCAACAAACATTTCT-CAGATTCAGAGTCAATTTCAACTTCACAGCGAAAGATA
126 ACCGCTGGTTGTCAACAAACATTTCTCCA-ATTCAGAGCCAATTTCAACTTCACAACGAAAGATA
*
40451 TTGGACTCGAGACAACGC
190 TTGGACTCCAGACAACGC
* *
40469 AAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCACCAAACATTTCTCCAATTCAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
40534 TTC-A-A-AACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
66 TTCAACACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
* * *
40596 TGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGGAC
131 TGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGAC
40661 TCCAGACAACGC
196 TCCAGACAACGC
* *
40673 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAAT
1 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
*
40738 TTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
66 TTCAA---CACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGAC
*
40803 CGTTGGTTGTCAACAAA-ATTTC
128 CGCTGGTTGTCAACAAACATTTC
40825 CCAGTTTAAA
Statistics
Matches: 330, Mismatches: 17, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
204 184 0.56
205 7 0.02
209 7 0.02
210 130 0.39
211 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (207 bp):
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAAT
TTCAACACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGC
TGGTTGTCAACAAACATTTCTCCAATTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGGAC
TCCAGACAACGC
Found at i:40949 original size:164 final size:168
Alignment explanation
Indices: 40672--40992 Score: 420
Period size: 164 Copynumber: 1.9 Consensus size: 168
40662 CCAGACAACG
* * *
40672 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAACATTTCTCCAATTTAGAGCCAA
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAA-TT--A-CCAA
* *
40737 TTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGA
62 TTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGA
* **
40802 CCGTTGGTTGTCAAC-AA-AATTTCCCAGTTTAAAGACAGCA
127 CCGCTGACTGTCAACAAACAATTTCCCAGTTTAAAGACAGCA
*
40842 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTC-CCAA-T-CCAATTT
1 CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAAC-ATTTCTCCAATTACCAATTT
* * * * *
40904 CAACTTCACAGA-AAATGATATTGGACTCGAGACAGCTCAAGTTCAACTTCACAACGAAGGGGCC
65 CAACTTCACA-ACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACC
40968 GCTGACTGTCAACAAACAATTTCCC
129 GCTGACTGTCAACAAACAATTTCCC
40993 GAGCCAATTT
Statistics
Matches: 133, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
164 72 0.54
165 3 0.02
166 8 0.06
168 1 0.01
170 44 0.33
171 5 0.04
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (168 bp):
CAAGTTCAACTTCACAACGAAGGGACCGCTGGCTGTCAACAAACATTTCTCCAATTACCAATTTC
AACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGC
TGACTGTCAACAAACAATTTCCCAGTTTAAAGACAGCA
Found at i:41005 original size:99 final size:99
Alignment explanation
Indices: 40834--41091 Score: 419
Period size: 99 Copynumber: 2.6 Consensus size: 99
40824 CCCAGTTTAA
*
40834 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAATCC
1 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAAGCC
*
40899 AATTTCAACTTCACAGAAAATGATATTGGACTCG
66 AATTTCAACTTCACAGAAAAGGATATTGGACTCG
* * *
40933 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAATTTCCCGAGCC
1 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAAGCC
**
40998 AATTTCAACTTCACAGCGAAGGATATTGGACTCG
66 AATTTCAACTTCACAGAAAAGGATATTGGACTCG
* * *
41032 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCA
1 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCA
41092 GTTTAAGACA
Statistics
Matches: 146, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
98 8 0.05
99 138 0.95
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.20
Consensus pattern (99 bp):
AGACAGCACAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAAGCC
AATTTCAACTTCACAGAAAAGGATATTGGACTCG
Found at i:41102 original size:263 final size:266
Alignment explanation
Indices: 40567--41309 Score: 987
Period size: 263 Copynumber: 2.7 Consensus size: 266
40557 CCAGACAACG
* * * *
40567 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCATCAAAC-ATTTCTCCAATTTAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTC-CCAA-TT--A-CCA
* *
40631 ATTTCAACTTCACA-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
61 ATTTCAACTTCACAGA-GAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGG
* * *
40695 GACCGCTGGTTGTCATCAAAC-ATTTCTCCAATTTAGAGCCAATTTCAACTTCACAACGAAGGAT
125 GGCCGCTGGTTGTCAACAAACAATTTC-CC-----AGAGCCAATTTCAACTTCACAGCGAAGGAT
* * *
40759 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAAATTT
184 ATTGGACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAATTT
40824 CCCAGTTTAAAGACAGCA
249 CCCAGTTTAAAGACAGCA
40842 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAA-T-CCAATTTC
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAATTACCAATTTC
* * * *
40905 AACTTCACAGAAAATGATATTGGACTCGAGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGC
66 AACTTCACAGAGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGGCCGC
**
40970 TGACTGTCAACAAACAATTTCCC-GAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAG
131 TGGTTGTCAACAAACAATTTCCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAG
*
41034 ACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAACAAAAATTTCCCAGTTT-AA
196 ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC-AAAATTTCCCAGTTTAAA
41098 GACAGCA
260 GACAGCA
* *
41105 CAAGTTCAACTTCACAACGAAGGGGCTGCTGGCTGTCAACAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAA-TT---A-CCA
*
41170 ATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGG
61 ATTTCAACTTCACAGAGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGG
* * *
41235 GCCGCTGGTTGTCAACAAACACTTTCCAAGTTTCAGAGTCAATTTCAACTTCACAGCAAAGGATA
126 GCCGCTGGTTGTCAACAAACAATTTCC------CAGAGCCAATTTCAACTTCACAGCGAAGGATA
*
41300 TTGGCCTCGA
185 TTGGACTCGA
41310 AGCAACATAA
Statistics
Matches: 418, Mismatches: 32, Indels: 34
0.86 0.07 0.07
Matches are distributed among these distances:
263 143 0.34
264 15 0.04
265 1 0.00
269 78 0.19
270 93 0.22
273 1 0.00
275 44 0.11
276 6 0.01
277 37 0.09
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (266 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACAATTTCCCAATTACCAATTTC
AACTTCACAGAGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACAACGAAGGGGCCGC
TGGTTGTCAACAAACAATTTCCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAG
ACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAATTTCCCAGTTTAAAG
ACAGCA
Found at i:41103 original size:164 final size:168
Alignment explanation
Indices: 40933--41289 Score: 539
Period size: 171 Copynumber: 2.1 Consensus size: 168
40923 ATTGGACTCG
*
40933 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAA-TTTCC-C-GA
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCTCAGA
*
40995 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACGACGA
66 GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGA
*
41060 AGGGGCCGCTGGTTGTCAACAAA-AATTTCCCAGTTTA
131 AGGGGCCGCTGGTTGTCAACAAACAATTTCCAAGTTTA
* * *
41097 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCTGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCC----T
*
41162 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACA
62 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACA
* *
41227 ACGAAGGGGCCGCTGGTTGTCAACAAACACTTTCCAAGTTTC
127 ACGAAGGGGCCGCTGGTTGTCAACAAACAATTTCCAAGTTTA
*
41269 AG--AG-TCAATTTCAACTTCACA
1 AGACAGCTCAAGTTCAACTTCACA
41290 GCAAAGGATA
Statistics
Matches: 174, Mismatches: 11, Indels: 11
0.89 0.06 0.06
Matches are distributed among these distances:
164 51 0.29
165 4 0.02
169 15 0.09
170 3 0.02
171 88 0.51
172 13 0.07
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (168 bp):
AGACAGCTCAAGTTCAACTTCACAACGAAGGGGCCGCTGACTGTCAACAAACAACTTCCCTCAGA
GCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGA
AGGGGCCGCTGGTTGTCAACAAACAATTTCCAAGTTTA
Found at i:41114 original size:65 final size:65
Alignment explanation
Indices: 41032--41190 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
41022 ATTGGACTCG
* * * *
41032 AGACAACACAAGTTCAACTTCACGACGAAGGGGCCGCTGGTTGTCAACAAA-AATTTCCCAGTTT
1 AGACAGCACAAGTTCAACTTCAC-ACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
41096 A
65 A
*
41097 AGACAGCACAAGTTCAACTTCACAACGAAGGGGCTGCTGGCTGTCAACAAACAACTTCCCAATTT
1 AGACAGCACAAGTTCAACTTCAC-ACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTT
*
41162 C
65 A
*
41163 AG--AGC-CAATTTCAACTTCACAGCGAAGG
1 AGACAGCACAAGTTCAACTTCACA-CGAAGG
41191 ATATTGGACT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
62 1 0.01
63 20 0.24
64 3 0.04
65 47 0.56
66 13 0.15
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (65 bp):
AGACAGCACAAGTTCAACTTCACACGAAGGGGCCGCTGGCTGTCAACAAACAACTTCCCAATTTA
Found at i:41218 original size:106 final size:106
Alignment explanation
Indices: 41105--41309 Score: 340
Period size: 106 Copynumber: 1.9 Consensus size: 106
41095 TAAGACAGCA
*
41105 CAAGTTCAACTTCACAACGAAGGGGCTGCTGGCTGTCAACAAACAACTTCCCAA-TTTCAGAGCC
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAAC-ACTTCCCAAGTTTCAGAGCC
*
41169 AATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACG
65 AATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACG
* * *
41211 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGTTGTCAACAAACACTTTCCAAGTTTCAGAGTCA
1 CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACACTTCCCAAGTTTCAGAGCCA
*
41276 ATTTCAACTTCACAGCAAAGGATATTGGCCTCGA
66 ATTTCAACTTCACAGCAAAGGATATTGGACTCGA
41310 AGCAACATAA
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
105 8 0.09
106 84 0.91
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.22
Consensus pattern (106 bp):
CAAGTTCAACTTCACAACGAAGGGGCCGCTGGCTGTCAACAAACACTTCCCAAGTTTCAGAGCCA
ATTTCAACTTCACAGCAAAGGATATTGGACTCGAGACAACG
Found at i:42994 original size:12 final size:13
Alignment explanation
Indices: 42977--43005 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42967 GTGTTATTAG
42977 TATTTTA-TTATT
1 TATTTTATTTATT
42989 TATTTTATTTATT
1 TATTTTATTTATT
43002 TATT
1 TATT
43006 ATATATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTATT
Found at i:43323 original size:11 final size:11
Alignment explanation
Indices: 43307--43336 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
43297 TTTTATTTTC
43307 TTATTTTCAAT
1 TTATTTTCAAT
43318 TTATTTTCAAT
1 TTATTTTCAAT
43329 TTATTTTC
1 TTATTTTC
43337 GTCACCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (11 bp):
TTATTTTCAAT
Found at i:47296 original size:25 final size:26
Alignment explanation
Indices: 47243--47296 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
47233 AATTATATAT
* * *
47243 TAAACTTATACAATTTTAAGAGGGGA
1 TAAACTTACAAAATTTTAAGAGGGAA
*
47269 TAAACTTACAAAATTTT-AGAGGTAA
1 TAAACTTACAAAATTTTAAGAGGGAA
47294 TAA
1 TAA
47297 CAGTTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (26 bp):
TAAACTTACAAAATTTTAAGAGGGAA
Found at i:48086 original size:4 final size:4
Alignment explanation
Indices: 48077--48106 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
48067 TGAAAATCCT
48077 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
48107 CAGTTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:55789 original size:12 final size:12
Alignment explanation
Indices: 55751--55842 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
55741 ATTTCCTAAT
55751 TGAATTCTGTTC
1 TGAATTCTGTTC
*
55763 TG-ATAC-GTTACC
1 TGAATTCTGTT--C
55775 TGAATTCTGTTC
1 TGAATTCTGTTC
*
55787 TG-ATTCTGATC
1 TGAATTCTGTTC
*
55798 TGGATTCTGTTC
1 TGAATTCTGTTC
* *
55810 TG-ATATCTGATA
1 TGAAT-TCTGTTC
*
55822 TGAATTCTGTTT
1 TGAATTCTGTTC
*
55834 TGATTTCTG
1 TGAATTCTG
55843 ATATCTCCGT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
10 3 0.05
11 15 0.23
12 38 0.59
13 5 0.08
14 3 0.05
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:55805 original size:47 final size:48
Alignment explanation
Indices: 55737--55844 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 48
55727 AAATATTTTA
* * *
55737 TCTGATTTCCTAAT-TGAATTCTGTTCTGATA-C-GTTACCTGAATTCTGT
1 TCTGATTT-CTGATCTGGATTCTGTTCTGATATCTGATA--TGAATTCTGT
55785 TCTGA-TTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
*
55832 TTTGATTTCTGAT
1 TCTGATTTCTGAT
55845 ATCTCCGTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
46 4 0.08
47 32 0.62
48 13 0.25
49 3 0.06
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (48 bp):
TCTGATTTCTGATCTGGATTCTGTTCTGATATCTGATATGAATTCTGT
Found at i:55842 original size:24 final size:24
Alignment explanation
Indices: 55737--55846 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
55727 AAATATTTTA
*
55737 TCTGATTTCCTAAT-TGAATTCTGT
1 TCTGATTT-CTGATATGAATTCTGT
* *
55761 TCTGA-TAC-GTTACCTGAATTCTGT
1 TCTGATTTCTGATA--TGAATTCTGT
* *
55785 TCTGA-TTCTGATCTGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
55808 TCTGATATCTGATATGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
55832 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
55847 CTCCGTTTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 15 0.22
24 50 0.72
25 2 0.03
ACGTcount: A:0.20, C:0.15, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:64181 original size:111 final size:111
Alignment explanation
Indices: 63987--64208 Score: 410
Period size: 111 Copynumber: 2.0 Consensus size: 111
63977 GAAACTATCG
* *
63987 AAGAGAAATTCACTCACAAAGCAAGCACCGAAATCACTATATTCATGTTTCATTGCCATCTTCAT
1 AAGAGAAATTCACTCACAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCAT
64052 GAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
66 GAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
64098 AAGAGAAATTCACT-AGCAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCA
1 AAGAGAAATTCACTCA-CAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCA
64162 TGAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
65 TGAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
64209 TGAGTTTGGT
Statistics
Matches: 108, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
110 1 0.01
111 107 0.99
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (111 bp):
AAGAGAAATTCACTCACAAAGCAAGCACCGAAATCACTAAATTCATGCTTCATTGCCATCTTCAT
GAAGTATAATCCGTTTTCTAATTTAGATTAGACTGAGCTAAGTTGT
Found at i:72507 original size:25 final size:25
Alignment explanation
Indices: 72479--72537 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
72469 CAGAAGAATA
72479 TGCTGCTTTTATTTTGAAATATGAT
1 TGCTGCTTTTATTTTGAAATATGAT
72504 TGCTGCTTTTATTTTGAAATATGAT
1 TGCTGCTTTTATTTTGAAATATGAT
*
72529 TGCTACTTT
1 TGCTGCTTT
72538 GCATAGCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.15, T:0.53
Consensus pattern (25 bp):
TGCTGCTTTTATTTTGAAATATGAT
Found at i:75605 original size:4 final size:4
Alignment explanation
Indices: 75596--75623 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
75586 TAACAAGAAG
75596 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
75624 CCTTGTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Done.