Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002403.1 Hibiscus syriacus cultivar Beakdansim tig00004914_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: 75673
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8228 original size:176 final size:177
Alignment explanation
Indices: 7906--8262 Score: 457
Period size: 176 Copynumber: 2.0 Consensus size: 177
7896 AAGAGGCGAA
*
7906 AATAAATTATCAATATAAAATATAAATAAAATATTTAAAATATACGAGAATTTAAAATTTTCAGG
1 AATAAATTATCAATATAAAATATAAATAAAATATTTAAAATATACAAGAATTTAAAATTTTCAGG
* * *
7971 ATGATGATTGCCCTACCTCTTCAATCCATCCCTGTCTACCATCAAATGATCTAGTAGGATGATAC
66 AGGACGATTGCCCTACCTCTTCAATCCATCCCTGTCTACCATCAAATGATCTAATAGGATGATAC
* * ** * *
8036 TTCATATCCTTTTAAGTAATTTTAGATGTTTGTAATGTCTATCCCAT
131 CTCATATCCATTTAAGTAAGGTTAGATGTTCGCAATGTCTATCCCAT
* * * *
8083 AATAAATTATCAAT-TAAAATATAAATGAAGTATTTAAGATATACAAGAATTTAAAATTTTCATG
1 AATAAATTATCAATATAAAATATAAATAAAATATTTAAAATATACAAGAATTTAAAATTTTCAGG
* * ** * ** * *
8147 AGGACGATTGCTCTCATCTCTTCGGTCTATCTTTGTCTATCATCACATGATCTAATAGGATGATA
66 AGGACGATTGCCCT-ACCTCTTCAATCCATCCCTGTCTACCATCAAATGATCTAATAGGATGATA
* * *
8212 CCTCATAT-CATTTAAGTAGGGTTAGATGTTCGCGATGTCTATCTCAT
130 CCTCATATCCATTTAAGTAAGGTTAGATGTTCGCAATGTCTATCCCAT
8259 AATA
1 AATA
8263 GACATCTACA
Statistics
Matches: 153, Mismatches: 26, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
176 91 0.59
177 62 0.41
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (177 bp):
AATAAATTATCAATATAAAATATAAATAAAATATTTAAAATATACAAGAATTTAAAATTTTCAGG
AGGACGATTGCCCTACCTCTTCAATCCATCCCTGTCTACCATCAAATGATCTAATAGGATGATAC
CTCATATCCATTTAAGTAAGGTTAGATGTTCGCAATGTCTATCCCAT
Found at i:9122 original size:13 final size:13
Alignment explanation
Indices: 9093--9130 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
9083 GTTAATAATT
9093 ATAATTATTATAAA
1 ATAATTATTA-AAA
*
9107 ATAAATATTAAAA
1 ATAATTATTAAAA
9120 ATAATTATTAA
1 ATAATTATTAA
9131 TTGAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATAATTATTAAAA
Found at i:12082 original size:3 final size:3
Alignment explanation
Indices: 12074--12114 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
12064 TTCTCTCTTA
12074 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12115 ATCCCTTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:30119 original size:2 final size:2
Alignment explanation
Indices: 30112--30151 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
30102 AAAAGAAAAT
30112 TA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30152 CAGATACACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:34151 original size:18 final size:17
Alignment explanation
Indices: 34106--34153 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
34096 AAAAATAAAA
* *
34106 AAAAAAAATAAACGAGT
1 AAAAAAAATAAACAAGG
*
34123 AAATAATAATAAACAAGG
1 AAA-AAAAATAAACAAGG
34141 AATAAAAAATAAA
1 AA-AAAAAATAAA
34154 ATACTACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 21 0.84
19 1 0.04
ACGTcount: A:0.73, C:0.04, G:0.08, T:0.15
Consensus pattern (17 bp):
AAAAAAAATAAACAAGG
Found at i:34243 original size:34 final size:34
Alignment explanation
Indices: 34164--34577 Score: 142
Period size: 35 Copynumber: 11.9 Consensus size: 34
34154 ATACTACATA
34164 TAAAAATGTTTTAAAA-C---TA-TATAT-ATTT
1 TAAAAATGTTTTAAAACCATATATTATATAATTT
* * *
34192 CAAAAATATTTTCAAAACCATATACTATATAATTT
1 TAAAAATGTTTT-AAAACCATATATTATATAATTT
*
34227 TAAAAATGTTTTAAAA-C-TATATGT-TATAGTTT
1 TAAAAATGTTTTAAAACCATATAT-TATATAATTT
* * *
34259 TCAAAAACGTTTTAAAA-C-TACATTATAT-GTTT
1 T-AAAAATGTTTTAAAACCATATATTATATAATTT
* *** * *
34291 CAAAAAAAATTT-CAACCATATATTATATAAATT
1 TAAAAATGTTTTAAAACCATATATTATATAATTT
* * *
34324 TCAAAATGATTTTAAAACTATTTATTATATAAGTTT
1 TAAAAATG-TTTTAAAACCATATATTATATAA-TTT
* * *
34360 TCAAAATGGTTTTAAAAAC-TATATAATATATATGGTT
1 TAAAAAT-GTTTTAAAACCATATATTATATA-AT--TT
* * * * *
34397 TCAAAAATATCTTCAAAAACTATATAATATATATGTTT
1 T-AAAAATGT-TT-TAAAACCATATATTATATA-ATTT
* * *
34435 TCAAAAAAATGTTTTCAAAA-C-TATAATACATATGTTT
1 T---AAAAATGTTTT-AAAACCATATATTATATA-ATTT
**
34472 TCAAAAATGATTTTAAAAATTATATATTATATATATTT
1 T-AAAAATG-TTTT-AAAACCATATATTATATA-ATTT
* * * *
34510 TCTAAAATGTTTTTTTTAAACTATATATTATATAGTTT
1 T-AAAAATG---TTTTAAAACCATATATTATATAATTT
* * *
34548 TAAAAACT-ATTAAAAACTATATATTATATA
1 TAAAAA-TGTTTTAAAACCATATATTATATA
34578 CGTAGTTTCA
Statistics
Matches: 296, Mismatches: 57, Indels: 60
0.72 0.14 0.15
Matches are distributed among these distances:
28 10 0.03
29 4 0.01
30 3 0.01
31 9 0.03
32 26 0.09
33 32 0.11
34 31 0.10
35 46 0.16
36 26 0.09
37 25 0.08
38 36 0.12
39 26 0.09
40 22 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (34 bp):
TAAAAATGTTTTAAAACCATATATTATATAATTT
Found at i:34298 original size:33 final size:33
Alignment explanation
Indices: 34219--34296 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 33
34209 CCATATACTA
* * *
34219 TATAATTTT-AAAAATGTTTTAAAACTATATGT
1 TATAGTTTTCAAAAACGTTTTAAAACTACATGT
34251 TATAGTTTTCAAAAACGTTTTAAAACTACA--T
1 TATAGTTTTCAAAAACGTTTTAAAACTACATGT
34282 TATA-TGTTTCAAAAA
1 TATAGT-TTTCAAAAA
34297 AAATTTCAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.02
31 14 0.34
32 8 0.20
33 18 0.44
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (33 bp):
TATAGTTTTCAAAAACGTTTTAAAACTACATGT
Found at i:34390 original size:37 final size:38
Alignment explanation
Indices: 34189--34577 Score: 257
Period size: 38 Copynumber: 10.9 Consensus size: 38
34179 ACTATATATA
* * *
34189 TTTCAAAAAT-ATTTTCAAAACCATATACTATATAA-T
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
*
34225 TTT-AAAAATG-TTTT-AAAACTATAT-GT-TAT-AGT
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
* *
34257 TTTCAAAAACG-TTTT-AAAAC--TACATTATAT--G-
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
* * * * *
34288 TTTCAAAAA-AAATTT--CAACCATATATTATATAA-A
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
*
34322 TTTC-AAAATGATTTT-AAAACTATTTATTATATAAGT
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
* * * *
34358 TTTC-AAAATGGTTTTAAAAACTATATAATATATATGG
1 TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
* * *
34395 TTTCAAAAAT-ATCTTCAAAAACTATATAATATATATGT
1 TTTCAAAAATGAT-TTTAAAAACTATATATTATATAAGT
* * *
34433 TTTCAAAAAAATG-TTTTCAAAACTATA-A-TACATATGT
1 TTTC--AAAAATGATTTTAAAAACTATATATTATATAAGT
*
34470 TTTCAAAAATGATTTTAAAAATTATATATTATATATA-T
1 TTTCAAAAATGATTTTAAAAACTATATATTATATA-AGT
* * **
34508 TTTCTAAAATGTTTTTTTTAAACTATATATTATAT-AGT
1 TTTCAAAAATG-ATTTTAAAAACTATATATTATATAAGT
34546 TTT-AAAAACT-A--TTAAAAACTATATATTATATA
1 TTTCAAAAA-TGATTTTAAAAACTATATATTATATA
34578 CGTAGTTTCA
Statistics
Matches: 286, Mismatches: 39, Indels: 57
0.75 0.10 0.15
Matches are distributed among these distances:
30 3 0.01
31 15 0.05
32 18 0.06
33 23 0.08
34 35 0.12
35 32 0.11
36 29 0.10
37 40 0.14
38 54 0.19
39 30 0.10
40 7 0.02
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (38 bp):
TTTCAAAAATGATTTTAAAAACTATATATTATATAAGT
Found at i:34435 original size:75 final size:74
Alignment explanation
Indices: 34322--34577 Score: 240
Period size: 75 Copynumber: 3.4 Consensus size: 74
34312 ATTATATAAA
* * *
34322 TTTC-AAAATGATTTTAAAACTATTTATTATATAAGTTTTC-AAAATGGTTTTAAAAACTATATA
1 TTTCAAAAAT-ATTTAAAAACTATATATTATATATGTTTTCAAAAATGGTTTTAAAAACTATATA
34385 ATATATATGG
65 ATATATATGG
* *
34395 TTTCAAAAATATCTTCAAAAACTATATAATATATATGTTTTCAAAAAAAT-GTTTTCAAAAC--T
1 TTTCAAAAATAT-TT-AAAAACTATATATTATATATGTTTTC--AAAAATGGTTTTAAAAACTAT
* *
34457 ATAATACATATGT
62 ATAATATATATGG
* * * * **
34470 TTTCAAAAATGATTTTAAAAATTATATATTATATATATTTTCTAAAATGTTTTTTTTAAACTATA
1 TTTCAAAAAT-A-TTTAAAAACTATATATTATATATGTTTTCAAAAATG-GTTTTAAAAACTATA
*
34535 T-AT-TATATAG
63 TAATATATATGG
*
34545 TTTTAAAAACTA-TTAAAAACTATATATTATATA
1 TTTCAAAAA-TATTTAAAAACTATATATTATATA
34578 CGTAGTTTCA
Statistics
Matches: 151, Mismatches: 19, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
73 31 0.21
74 7 0.05
75 88 0.58
76 6 0.04
77 14 0.09
78 5 0.03
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (74 bp):
TTTCAAAAATATTTAAAAACTATATATTATATATGTTTTCAAAAATGGTTTTAAAAACTATATAA
TATATATGG
Found at i:35940 original size:9 final size:9
Alignment explanation
Indices: 35927--35962 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
35917 CCGGTTCTTC
35927 CGATCGG-T
1 CGATCGGTT
35935 CAGATCGGTT
1 C-GATCGGTT
35945 CGATCGGTT
1 CGATCGGTT
35954 CGATCGGTT
1 CGATCGGTT
35963 GAACTAGTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 1 0.04
9 23 0.88
10 2 0.08
ACGTcount: A:0.14, C:0.22, G:0.33, T:0.31
Consensus pattern (9 bp):
CGATCGGTT
Found at i:42817 original size:60 final size:60
Alignment explanation
Indices: 42697--42839 Score: 162
Period size: 60 Copynumber: 2.4 Consensus size: 60
42687 GTATTTAAAA
* * * * * **
42697 TTTTGAATATTCTAATTTTATCATCAAACTATGATACTCGTTCTTAATTAGTCCTTAAAC
1 TTTTGAATATTCTAATTTCATCCTCAAACTATGACACTCATTCTAAATTAGTCCCCAAAC
* *
42757 TTTTGAACATTCTAATTTCATCCTCAAACTATGACCCTCATTCTAAATT-GATCCCCAAAC
1 TTTTGAATATTCTAATTTCATCCTCAAACTATGACACTCATTCTAAATTAG-TCCCCAAAC
* * *
42817 TTTTAAATTTTCCAATTTCATCC
1 TTTTGAATATTCTAATTTCATCC
42840 AAATATATAA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
59 1 0.01
60 68 0.99
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (60 bp):
TTTTGAATATTCTAATTTCATCCTCAAACTATGACACTCATTCTAAATTAGTCCCCAAAC
Found at i:44805 original size:2 final size:2
Alignment explanation
Indices: 44798--44823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44788 TCAGGTAGAC
44798 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
44824 TGATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46907 original size:24 final size:24
Alignment explanation
Indices: 46880--46925 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
46870 TTAATAATTT
46880 AAAAATA-TAAGAAATTAAAAAACC
1 AAAAATATTAAG-AATTAAAAAACC
*
46904 AAAAATATTAAGTATTAAAAAA
1 AAAAATATTAAGAATTAAAAAA
46926 TAAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAAATATTAAGAATTAAAAAACC
Found at i:46931 original size:24 final size:24
Alignment explanation
Indices: 46880--46931 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
46870 TTAATAATTT
*
46880 AAAAATATAAGAAATTAAAAAACC
1 AAAAATATAAGAAATTAAAAAACA
* *
46904 AAAAATATTAAG-TATTAAAAAATA
1 AAAAATA-TAAGAAATTAAAAAACA
46928 AAAA
1 AAAA
46932 TTGAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (24 bp):
AAAAATATAAGAAATTAAAAAACA
Found at i:55592 original size:32 final size:31
Alignment explanation
Indices: 55556--55621 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
55546 TATTTTGAAG
55556 TTGTCCCTCTCAT-TTTTATAGTTAATTATAAT
1 TTGTCCC-CT-ATCTTTTATAGTTAATTATAAT
* * *
55588 TTGTCTCCTATCTTTTATGGTTAATTATACT
1 TTGTCCCCTATCTTTTATAGTTAATTATAAT
55619 TTG
1 TTG
55622 CTCTCTCTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 2 0.07
31 22 0.73
32 6 0.20
ACGTcount: A:0.21, C:0.15, G:0.09, T:0.55
Consensus pattern (31 bp):
TTGTCCCCTATCTTTTATAGTTAATTATAAT
Found at i:61522 original size:42 final size:42
Alignment explanation
Indices: 61471--61590 Score: 181
Period size: 42 Copynumber: 2.9 Consensus size: 42
61461 TTTCTCCGAA
* * *
61471 TTTC-CGTGTTTGTTTCACGTAATTTGTTTTTCGGAAAATGT
1 TTTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGT
*
61512 TTTCTCGTGTTTGTTTTACGTAATTCGTTTTCCGGAAAACGT
1 TTTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGT
61554 TTT-TCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTTCT-CGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
61591 TGTAATTCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 5 0.07
42 67 0.93
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.49
Consensus pattern (42 bp):
TTTCTCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAACGT
Found at i:61848 original size:43 final size:43
Alignment explanation
Indices: 61762--61853 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 43
61752 ATTTCATCAA
* *
61762 AATAT-TAATTATTAAAATATTTAAAATATATTTAATATTTAT
1 AATATATAATTATTAAAAAATTTAAAATATATTTAATATATAT
* *
61804 AATATATAATTA-TAAAAAATTATCAATTATATTATAATA-ATAT
1 AATATATAATTATTAAAAAATT-TAAAATATATT-TAATATATAT
*
61847 AAGATAT
1 AATATAT
61854 TATTTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
42 13 0.31
43 24 0.57
44 5 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (43 bp):
AATATATAATTATTAAAAAATTTAAAATATATTTAATATATAT
Found at i:61873 original size:26 final size:26
Alignment explanation
Indices: 61830--61929 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 26
61820 AAATTATCAA
61830 TTATATTATAATAATATAAGATATTATT
1 TTATATT-TAATAATATAA-ATATTATT
* *
61858 TT-TATTTAATAATATAATAAATTTTTT
1 TTATATTTAATAATATAA-ATA-TTATT
61885 TTATATTTAATAATGA-ATAATATTATT
1 TTATATTTAATAAT-ATA-AATATTATT
61912 TATATATTTCAATAATAT
1 T-TATATTT-AATAATAT
61930 TTTAGTAAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
26 13 0.22
27 15 0.25
28 24 0.40
29 8 0.13
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (26 bp):
TTATATTTAATAATATAAATATTATT
Found at i:61917 original size:28 final size:28
Alignment explanation
Indices: 61830--61928 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 28
61820 AAATTATCAA
* *
61830 TTATATTATAATAATATAA-GATATTATT
1 TTATATT-TAATAATAGAATAATATTATT
* *
61858 TT-TATTTAATAATATAATAA-ATTTTTT
1 TTATATTTAATAATAGAATAATA-TTATT
61885 TTATATTTAATAAT-GAATAATATTATT
1 TTATATTTAATAATAGAATAATATTATT
61912 TATATATTTCAATAATA
1 T-TATATTT-AATAATA
61929 TTTTAGTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
26 12 0.20
27 21 0.35
28 21 0.35
29 6 0.10
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (28 bp):
TTATATTTAATAATAGAATAATATTATT
Found at i:62168 original size:20 final size:20
Alignment explanation
Indices: 62090--62159 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
62080 TTTCCAGATG
62090 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
62110 TTTTCCAAAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
62130 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
62150 TTTTCCAGAA
1 TTTTCCAGAA
62160 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:62168 original size:40 final size:40
Alignment explanation
Indices: 62090--62168 Score: 113
Period size: 40 Copynumber: 2.0 Consensus size: 40
62080 TTTCCAGATG
* **
62090 TTTTCCAGAAATGTAATTCATTTTCCAAAAATGTAATTCA
1 TTTTACAGAAATGTAATTCATTTTCCAAAAATCAAATTCA
* *
62130 TTTTACAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTCATTTTCCAAAAATCAAATTC
62169 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTCATTTTCCAAAAATCAAATTCA
Found at i:62178 original size:15 final size:15
Alignment explanation
Indices: 62142--62221 Score: 117
Period size: 15 Copynumber: 5.4 Consensus size: 15
62132 TTACAGAAAT
**
62142 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
62157 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
62171 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
62186 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
62201 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
62216 GTAATT
1 GTAATT
62222 TATTTTCTGG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.21
15 46 0.79
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:62194 original size:30 final size:30
Alignment explanation
Indices: 62142--62221 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
62132 TTACAGAAAT
62142 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
62171 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
62201 GTAATTCAAATTCCAGTAATT
1 GTAATTCATTTTCCAGTAATT
62222 TATTTTCTGG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.33
30 32 0.67
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:62216 original size:45 final size:44
Alignment explanation
Indices: 62142--62228 Score: 138
Period size: 45 Copynumber: 2.0 Consensus size: 44
62132 TTACAGAAAT
**
62142 GTAATTCATTTTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
1 GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
*
62186 GTAATTCAAATTCCAGTAATTCAAATTCCAGTAATTTATTTTC
1 GTAATTCAAATTCCAG-AATTCAAATTCCAGTAATTCATTTTC
62229 TGGAAAACCA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.36
45 25 0.64
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (44 bp):
GTAATTCAAATTCCAGAATTCAAATTCCAGTAATTCATTTTCCA
Found at i:62983 original size:6 final size:6
Alignment explanation
Indices: 62928--62971 Score: 70
Period size: 6 Copynumber: 7.3 Consensus size: 6
62918 TTCTTCTTCT
* *
62928 TCATCC TCATCC TCCTCC TCATCG TCATCC TCATCC TCATCC TC
1 TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TCATCC TC
62972 CTCATCGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.14, C:0.50, G:0.02, T:0.34
Consensus pattern (6 bp):
TCATCC
Found at i:65869 original size:22 final size:22
Alignment explanation
Indices: 65844--65901 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
65834 TCACTCTCTA
*
65844 CGACGACATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
65866 CGACGAAATCCCTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
65888 CGACGAAATCCGTC
1 CGACGAAATCCGTC
65902 TATCTCCGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.22, C:0.47, G:0.14, T:0.17
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:66301 original size:14 final size:14
Alignment explanation
Indices: 66282--66314 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
66272 TCGCAACGCA
66282 ATTTTAGTTTCGCG
1 ATTTTAGTTTCGCG
66296 ATTTTAGTTTCGCG
1 ATTTTAGTTTCGCG
66310 ATTTT
1 ATTTT
66315 CTCGTTGCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.12, G:0.18, T:0.55
Consensus pattern (14 bp):
ATTTTAGTTTCGCG
Found at i:66339 original size:19 final size:19
Alignment explanation
Indices: 66312--66366 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
66302 GTTTCGCGAT
*
66312 TTTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
**
66331 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTTTCA
*
66350 TTTCGTGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
66367 AAGTTTCAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:67688 original size:18 final size:19
Alignment explanation
Indices: 67665--67700 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
67655 CTCCACTTCG
67665 AGAGCCATCACC-TCACCC
1 AGAGCCATCACCATCACCC
67683 AGAGCCATCACCATCACC
1 AGAGCCATCACCATCACC
67701 TGATCGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.31, C:0.47, G:0.11, T:0.11
Consensus pattern (19 bp):
AGAGCCATCACCATCACCC
Found at i:67945 original size:21 final size:21
Alignment explanation
Indices: 67921--67977 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
67911 TGGTGCATGG
*
67921 CGTGATGAGGTATCAACTCTA
1 CGTGATGAGGTAGCAACTCTA
* **
67942 CGTGGTGAGGTAGCGGCTCTA
1 CGTGATGAGGTAGCAACTCTA
67963 CGTGA-GATGGTAGCA
1 CGTGATGA-GGTAGCA
67978 TCGTTACAGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.23, C:0.18, G:0.35, T:0.25
Consensus pattern (21 bp):
CGTGATGAGGTAGCAACTCTA
Found at i:68265 original size:20 final size:19
Alignment explanation
Indices: 68242--68380 Score: 139
Period size: 20 Copynumber: 7.5 Consensus size: 19
68232 GAAACTTAAA
68242 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG-AAATGACT
*
68262 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA-ATGACT
68282 ATCGCAA--C--AA-GA-T
1 ATCGCAACGCGAAATGACT
* * *
68295 AATCGCAATGCGAAATAACA
1 -ATCGCAACGCGAAATGACT
68315 ATCGCAACGCG-AATGACT
1 ATCGCAACGCGAAATGACT
68333 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
*
68353 ATCGCAACGCGAATTGACT
1 ATCGCAACGCGAAATGACT
*
68372 ATTGCAACG
1 ATCGCAACG
68381 GGATAATCGC
Statistics
Matches: 100, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.01
14 9 0.09
16 2 0.02
18 18 0.18
19 30 0.30
20 40 0.40
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:68319 original size:19 final size:19
Alignment explanation
Indices: 68295--68380 Score: 93
Period size: 19 Copynumber: 4.5 Consensus size: 19
68285 GCAACAAGAT
* *
68295 AATCGCAATGCGAAATAAC
1 AATCGCAACGCGAAATGAC
68314 AATCGCAACGCG-AATGAC
1 AATCGCAACGCGAAATGAC
*
68332 TATCGCAACGCGGAAATGAC
1 AATCGCAACGC-GAAATGAC
* *
68352 TATCGCAACGCGAATTGAC
1 AATCGCAACGCGAAATGAC
* *
68371 TATTGCAACG
1 AATCGCAACG
68381 GGATAATCGC
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
18 15 0.25
19 28 0.47
20 17 0.28
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:68328 original size:53 final size:52
Alignment explanation
Indices: 68241--68340 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 52
68231 CGAAACTTAA
* *
68241 AATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAAGAT
1 AATCGCAACGCGAAAATAACAATCGCAACGCGAA--TGACTATCGCAACAAGAT
*
68295 AATCGCAATGCG-AAATAACAATCGCAACGCGAATGACTATCGCAAC
1 AATCGCAACGCGAAAATAACAATCGCAACGCGAATGACTATCGCAAC
68341 GCGGAAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 13 0.30
53 19 0.44
54 11 0.26
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (52 bp):
AATCGCAACGCGAAAATAACAATCGCAACGCGAATGACTATCGCAACAAGAT
Found at i:68340 original size:71 final size:72
Alignment explanation
Indices: 68219--68360 Score: 200
Period size: 71 Copynumber: 2.0 Consensus size: 72
68209 CAAAAGAAGA
*
68219 ATAATCGCAACACGAAACTTAAAATCGCAACGCGAAAATGACTATCGCAACGC-GAATTTGACTA
1 ATAATCGCAACACGAAAC-TAAAATCGCAACGCG-AAATGACTATCGCAACGCGGAA-ATGACTA
68283 TCGCAACAAG
63 TCGCAACAAG
**
68293 ATAATCGCAATGCGAAA-TAACAATCGCAACGCG-AATGACTATCGCAACGCGGAAATGACTATC
1 ATAATCGCAACACGAAACTAA-AATCGCAACGCGAAATGACTATCGCAACGCGGAAATGACTATC
68356 GCAAC
65 GCAAC
68361 GCGAATTGAC
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
71 30 0.48
72 6 0.10
73 12 0.19
74 15 0.24
ACGTcount: A:0.41, C:0.25, G:0.18, T:0.17
Consensus pattern (72 bp):
ATAATCGCAACACGAAACTAAAATCGCAACGCGAAATGACTATCGCAACGCGGAAATGACTATCG
CAACAAG
Found at i:68411 original size:91 final size:91
Alignment explanation
Indices: 68242--68419 Score: 279
Period size: 91 Copynumber: 2.0 Consensus size: 91
68232 GAAACTTAAA
68242 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAAGATAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAAGATAATCGCAATGCG
68307 AAATAACAATCGCAACGCGAATGACT
66 AAATAACAATCGCAACGCGAATGACT
* * **
68333 ATCGCAACGCGGAAATGACTATCGCAACGCGAA-TTGACTATTGCAACGGGATAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAAGATAATCGCAATGCG
*
68397 AAATGAA-AATTCGCAATGCGAAT
66 AAAT-AACAA-TCGCAACGCGAAT
68420 TTAGTTTCGC
Statistics
Matches: 80, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
90 34 0.43
91 46 0.57
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (91 bp):
ATCGCAACGCGAAAATGACTATCGCAACGCGAATTTGACTATCGCAACAAGATAATCGCAATGCG
AAATAACAATCGCAACGCGAATGACT
Found at i:68517 original size:20 final size:20
Alignment explanation
Indices: 68473--68521 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
68463 ATTGCGATCT
68473 TGTTGCGATAGTCAAATTCG
1 TGTTGCGATAGTCAAATTCG
* *
68493 CGTTGCGATAGTC-ATTTCCG
1 TGTTGCGATAGTCAAATT-CG
68513 TGTTGCGAT
1 TGTTGCGAT
68522 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
TGTTGCGATAGTCAAATTCG
Found at i:69100 original size:41 final size:42
Alignment explanation
Indices: 68994--69114 Score: 124
Period size: 41 Copynumber: 2.9 Consensus size: 42
68984 AAGCCCGACT
* *
68994 CCTGTCAT-GTTCAAGAGG-CCTCTCCTATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGGTCC-CTCCCACCGTTCAAGAGGCC
* ** *
69035 CCTATCATCCCTCAAGA-ATCCCCTCCCACCGTTCAAGAGG-C
1 CCTGTCATCGTTCAAGAGGT-CCCTCCCACCGTTCAAGAGGCC
* *
69076 CCTGTCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAG
69115 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
41 39 0.61
42 23 0.36
43 2 0.03
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTGTCATCGTTCAAGAGGTCCCTCCCACCGTTCAAGAGGCC
Found at i:69113 original size:21 final size:20
Alignment explanation
Indices: 69055--69114 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
69045 CTCAAGAATC
69055 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
69075 CCCTGTCATCGTTGAAGAGG
1 CCCTCCCACCGTTCAAGAGG
*
69095 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
69115 CCCGATTCAT
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.22, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:72982 original size:24 final size:24
Alignment explanation
Indices: 72915--72974 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
72905 CTGAAACATC
72915 ATCAAAATTCGAGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
* * *
72939 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATTCGAGTATTGACCAAG
*
72963 ATCAAATTTCGA
1 ATCAAAATTCGA
72975 ATACTGACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (24 bp):
ATCAAAATTCGAGTATTGACCAAG
Found at i:73804 original size:43 final size:43
Alignment explanation
Indices: 73755--73837 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
73745 AACTAAACCT
*
73755 GTTGCGAATT-TGAAAT-TCAGTGTTGCGATAGTCAGAATCGCGC
1 GTTGCG-ATTATGAAATATC-GCGTTGCGATAGTCAGAATCGCGC
* *
73798 GTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCG
1 GTTGCGATTATGAAATATCGCGTTGCGATAGTCAGAATCG
73838 TGTTGCGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.09
43 30 0.86
44 2 0.06
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
GTTGCGATTATGAAATATCGCGTTGCGATAGTCAGAATCGCGC
Found at i:73842 original size:20 final size:20
Alignment explanation
Indices: 73776--73925 Score: 171
Period size: 20 Copynumber: 7.4 Consensus size: 20
73766 GAAATTCAGT
73776 GTTGCGATAGTCAGAATCGCGC
1 GTTGCGATAGTCAGAAT--CGC
**
73798 GTTGCGATTATGT-ATTATCGC
1 GTTGCGA-TA-GTCAGAATCGC
*
73819 GTTGCGATAGTCAGAATCGT
1 GTTGCGATAGTCAGAATCGC
73839 GTTGCGATAGTC-GAATCGC
1 GTTGCGATAGTCAGAATCGC
** *
73858 GTTGCGATATGT-ATTATTGC
1 GTTGCGATA-GTCAGAATCGC
73878 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
73898 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
73918 ATTGCGAT
1 GTTGCGAT
73926 TACATATTCG
Statistics
Matches: 109, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
19 19 0.17
20 66 0.61
21 10 0.09
22 7 0.06
23 5 0.05
24 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:73880 original size:59 final size:60
Alignment explanation
Indices: 73774--73925 Score: 243
Period size: 59 Copynumber: 2.5 Consensus size: 60
73764 TTGAAATTCA
73774 GTGTTGCGATAGTCAGAATCGCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATC
1 GTGTTGCGATAGTCAGAAT--CGCGTTGCGA-TATGTATTATCGCGTTGCGATAGTCAGAATC
*
73837 GTGTTGCGATAGTC-GAATCGCGTTGCGATATGTATTATTGCGTTGCGATAGTCAGAATC
1 GTGTTGCGATAGTCAGAATCGCGTTGCGATATGTATTATCGCGTTGCGATAGTCAGAATC
* *
73896 GCGTTGCGATAGTCAGAATCGCATTGCGAT
1 GTGTTGCGATAGTCAGAATCGCGTTGCGAT
73926 TACATATTCG
Statistics
Matches: 85, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
59 43 0.51
60 24 0.28
62 4 0.05
63 14 0.16
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.32
Consensus pattern (60 bp):
GTGTTGCGATAGTCAGAATCGCGTTGCGATATGTATTATCGCGTTGCGATAGTCAGAATC
Found at i:73942 original size:59 final size:59
Alignment explanation
Indices: 73776--73944 Score: 216
Period size: 59 Copynumber: 2.8 Consensus size: 59
73766 GAAATTCAGT
* *
73776 GTTGCGATAGTCAGAATCGCGCGTTGCGATTATGTATTATCGCGTTGCGATAGTCAGAATCGT
1 GTTGCGATAGTCAGAAT--CGCGTTGCGATTATATA-T-TCGCGTTGCGATAGTCAGAATCGC
*
73839 GTTGCGATAGTC-GAATCGCGTTGCGATATGTATTATT-GCGTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGAT-TATA-TATTCGCGTTGCGATAGTCAGAATCGC
* * *
73898 GTTGCGATAGTCAGAATCGCATTGCGATTACATATTCGCATTGCGAT
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATATATTCGCGTTGCGAT
73945 TTTCTAAAAG
Statistics
Matches: 95, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
58 4 0.04
59 44 0.46
60 26 0.27
61 3 0.03
62 6 0.06
63 12 0.13
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (59 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTATATATTCGCGTTGCGATAGTCAGAATCGC
Found at i:74003 original size:20 final size:20
Alignment explanation
Indices: 73980--74044 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
73970 AAAAATCGCA
73980 TGCGATAGTCATAATCGCGT
1 TGCGATAGTCATAATCGCGT
*
74000 TGCGATTA-TTAT-ATCGCGT
1 TGCGA-TAGTCATAATCGCGT
* * *
74019 TGCGATAGTCAGAATCACAT
1 TGCGATAGTCATAATCGCGT
74039 TGCGAT
1 TGCGAT
74045 TTATAGATCG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 2 0.05
19 14 0.38
20 19 0.51
21 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATAGTCATAATCGCGT
Found at i:74024 original size:39 final size:40
Alignment explanation
Indices: 73776--74063 Score: 182
Period size: 39 Copynumber: 7.2 Consensus size: 40
73766 GAAATTCAGT
*
73776 GTTGCGATAGTCAGAATCGCGCGTTGCGATTATGTATTATCGC
1 GTTGCGATAGTCAGAAT--CGCGTTGCGATTATATA-TATCGC
* **
73819 GTTGCGATAGTCAGAATCGTGTTGCGA-TAGTCGA-ATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTA-TATATATCGC
** * *
73858 GTTGCGATATGT-ATTATTGCGTTGCGA-TAGTCAGA-ATCGC
1 GTTGCGATA-GTCAGAATCGCGTTGCGATTA-T-ATATATCGC
* *
73898 GTTGCGATAGTCAGAATCGCATTGCGATTACATAT-TCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATATATATCGC
* ** * * *** * *
73937 ATTGCGATTTTCTAAAAGCGCAACGCGAATT-TGAAAAATCGC
1 GTTGCGATAGTC-AGAATCGCGTTGCG-ATTAT-ATATATCGC
* *
73979 -ATGCGATAGTCATAATCGCGTTGCGATTAT-TATATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATATATATCGC
* * *
74017 GTTGCGATAGTCAGAATCACATTGCGATT-TATAGATCGC
1 GTTGCGATAGTCAGAATCGCGTTGCGATTATATATATCGC
*
74056 ATTGCGAT
1 GTTGCGAT
74064 TTTGTTGGTC
Statistics
Matches: 192, Mismatches: 40, Indels: 30
0.73 0.15 0.11
Matches are distributed among these distances:
38 7 0.04
39 87 0.45
40 51 0.27
41 26 0.14
42 4 0.02
43 17 0.09
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (40 bp):
GTTGCGATAGTCAGAATCGCGTTGCGATTATATATATCGC
Done.