Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004009.1 Hibiscus syriacus cultivar Beakdansim tig00008741_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: 48011
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:112 original size:66 final size:65
Alignment explanation
Indices: 1--142 Score: 180
Period size: 66 Copynumber: 2.2 Consensus size: 65
* * *
1 TCCTCTCATGCCTTAATGCATCATTCATGCATTTCATTTATGGCATCCTTTCATTGCCT-TAATA
1 TCCTTTCATGCCTGAATACATCATTCATGCATTTCATTTATGGCATCCTTTCA-T-CCTGTAATA
65 CA
64 CA
* * *
67 TCCTTTCATGCCTGAATACATCCTTTCATGCATTT-TTTTATGGCATCCTTTCATCCTGTAATGC
1 TCCTTTCATGCCTGAATACAT-CATTCATGCATTTCATTTATGGCATCCTTTCATCCTGTAATAC
131 A
65 A
*
132 TTCTTTCATGC
1 TCCTTTCATGC
143 ATTTCATTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
64 3 0.04
65 17 0.25
66 35 0.52
67 12 0.18
ACGTcount: A:0.20, C:0.27, G:0.10, T:0.43
Consensus pattern (65 bp):
TCCTTTCATGCCTGAATACATCATTCATGCATTTCATTTATGGCATCCTTTCATCCTGTAATACA
Found at i:119 original size:25 final size:25
Alignment explanation
Indices: 85--245 Score: 93
Period size: 25 Copynumber: 7.0 Consensus size: 25
75 TGCCTGAATA
85 CATCCTTTCATGCATTTTTTTATGG
1 CATCCTTTCATGCATTTTTTTATGG
* * *
110 CATCCTTTCAT-C---CTGTAAT-G
1 CATCCTTTCATGCATTTTTTTATGG
* **
130 CATTCTTTCATGCATTTCATTATGG
1 CATCCTTTCATGCATTTTTTTATGG
* *
155 CATCCTTTCATGC----CTTAAT-G
1 CATCCTTTCATGCATTTTTTTATGG
*
175 CATCC-TTCATGTATTTCTTTTATGG
1 CATCCTTTCATGCATTT-TTTTATGG
* *
200 CATCCTTTCATGC----CTTAAT-G
1 CATCCTTTCATGCATTTTTTTATGG
220 CATCCTTTCATGCATTTCTTTTATGG
1 CATCCTTTCATGCATTT-TTTTATGG
246 ATTCATTTTA
Statistics
Matches: 99, Mismatches: 19, Indels: 35
0.65 0.12 0.23
Matches are distributed among these distances:
19 6 0.06
20 31 0.31
21 13 0.13
24 8 0.08
25 34 0.34
26 7 0.07
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (25 bp):
CATCCTTTCATGCATTTTTTTATGG
Found at i:120 original size:45 final size:46
Alignment explanation
Indices: 65--245 Score: 271
Period size: 45 Copynumber: 4.0 Consensus size: 46
55 TGCCTTAATA
*
65 CATCCTTTCATGCCTGAATACATCCTTTCATGCATTT-TTTTATGG
1 CATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGG
* *
110 CATCCTTTCAT-CCTGTAATGCATTCTTTCATGCATTTC-ATTATGG
1 CATCCTTTCATGCCTG-AATGCATCCTTTCATGCATTTCTTTTATGG
* *
155 CATCCTTTCATGCCTTAATGCATCC-TTCATGTATTTCTTTTATGG
1 CATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGG
*
200 CATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCTTTTATGG
1 CATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGG
246 ATTCATTTTA
Statistics
Matches: 123, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
44 15 0.12
45 86 0.70
46 22 0.18
ACGTcount: A:0.19, C:0.25, G:0.11, T:0.45
Consensus pattern (46 bp):
CATCCTTTCATGCCTGAATGCATCCTTTCATGCATTTCTTTTATGG
Found at i:179 original size:20 final size:20
Alignment explanation
Indices: 43--232 Score: 123
Period size: 20 Copynumber: 8.7 Consensus size: 20
33 TTCATTTATG
43 GCATCCTTTCATTGCCTTAAT
1 GCATCCTTTCA-TGCCTTAAT
* *
64 ACATCCTTTCATGCCTGAAT
1 GCATCCTTTCATGCCTTAAT
* * *
84 ACATCCTTTCATGCATTTTTTTAT
1 GCATCCTTTCATGC----CTTAAT
108 GGCATCCTTTCAT-CCTGTAAT
1 -GCATCCTTTCATGCCT-TAAT
* *
129 GCATTCTTTCATGCATTTCATTAT
1 GCATCCTTTCATGC-CTT-A--AT
153 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* *
174 GCATCC-TTCATGTATTTCTTTTAT
1 GCATCCTTTCATG-----CCTTAAT
198 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
219 GCATCCTTTCATGC
1 GCATCCTTTCATGC
233 ATTTCTTTTA
Statistics
Matches: 134, Mismatches: 16, Indels: 39
0.71 0.08 0.21
Matches are distributed among these distances:
19 6 0.04
20 54 0.40
21 22 0.16
22 2 0.01
23 1 0.01
24 13 0.10
25 30 0.22
26 6 0.04
ACGTcount: A:0.19, C:0.26, G:0.11, T:0.44
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:6717 original size:71 final size:71
Alignment explanation
Indices: 6640--6775 Score: 227
Period size: 71 Copynumber: 1.9 Consensus size: 71
6630 TTCATTTTCA
*
6640 TTTATGGCATCCTCTCATGCCTTAATGCATCTTTTCATGCATTTCATTTATGGCATCCTTTCATG
1 TTTATGGCATCCTCTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
6705 TATTTT
66 TATTTT
* * * *
6711 TTTATGGCATCTTTTTATGTCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
1 TTTATGGCATCCTCTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
6776 CCTTAATGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.49
Consensus pattern (71 bp):
TTTATGGCATCCTCTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATG
TATTTT
Found at i:6720 original size:25 final size:26
Alignment explanation
Indices: 6635--6855 Score: 132
Period size: 26 Copynumber: 9.5 Consensus size: 26
6625 TTAATTTCAT
*
6635 TTTCATTTATGGCATCCTCTCATGC-
1 TTTCATTTATGGCATCCTTTCATGCA
* *
6660 ---C-TTAAT-GCATCTTTTCATGCA
1 TTTCATTTATGGCATCCTTTCATGCA
*
6681 TTTCATTTATGGCATCCTTTCATGTA
1 TTTCATTTATGGCATCCTTTCATGCA
* *
6707 TTT-TTTTATGGCAT-CTTT--T-TA
1 TTTCATTTATGGCATCCTTTCATGCA
* *
6728 TGTC-TTAAT-GCATCCTTTCATGCA
1 TTTCATTTATGGCATCCTTTCATGCA
6752 TTTCATTTATGGCATCCTTTCATGC-
1 TTTCATTTATGGCATCCTTTCATGCA
* * * *
6777 ---C-TTAAT-GCATCCTTTTATTCT
1 TTTCATTTATGGCATCCTTTCATGCA
*
6798 TTTCATTTATGGCATCATTTCATGC-
1 TTTCATTTATGGCATCCTTTCATGCA
*
6823 ---C-TTAAT-GCATCCTTTCATGCA
1 TTTCATTTATGGCATCCTTTCATGCA
*
6844 TTTCTTTTATGG
1 TTTCATTTATGG
6856 ATTCGTTTTA
Statistics
Matches: 149, Mismatches: 22, Indels: 49
0.68 0.10 0.22
Matches are distributed among these distances:
20 41 0.28
21 24 0.16
22 4 0.03
23 1 0.01
24 11 0.07
25 26 0.17
26 42 0.28
ACGTcount: A:0.19, C:0.22, G:0.11, T:0.49
Consensus pattern (26 bp):
TTTCATTTATGGCATCCTTTCATGCA
Found at i:6781 original size:46 final size:46
Alignment explanation
Indices: 6692--6855 Score: 231
Period size: 46 Copynumber: 3.6 Consensus size: 46
6682 TTCATTTATG
* * * * *
6692 GCATCCTTTCATGTATTT-TTTTATGGCATCTTTTTATGTCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
*
6737 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
* * *
6783 GCATCCTTTTATTCTTTTCATTTATGGCATCATTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
*
6829 GCATCCTTTCATGCATTTCTTTTATGG
1 GCATCCTTTCATGCATTTCATTTATGG
6856 ATTCGTTTTA
Statistics
Matches: 105, Mismatches: 13, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
45 17 0.16
46 88 0.84
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.49
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTCATTTATGGCATCATTTCATGCCTTAAT
Found at i:6788 original size:20 final size:20
Alignment explanation
Indices: 6717--6842 Score: 72
Period size: 20 Copynumber: 5.7 Consensus size: 20
6707 TTTTTTTATG
* * *
6717 GCATCTTTTTATGTCTTAAT
1 GCATCCTTTCATGCCTTAAT
*
6737 GCATCCTTTCATGCATTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
6762 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
* * *
6783 GCATCCTTTTATTCTTTTCATTTAT
1 GCATCCTTTCATGC----C-TTAAT
*
6808 GGCATCATTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
6829 GCATCCTTTCATGC
1 GCATCCTTTCATGC
6843 ATTTCTTTTA
Statistics
Matches: 81, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
20 36 0.44
21 8 0.10
22 2 0.02
24 2 0.02
25 8 0.10
26 25 0.31
ACGTcount: A:0.19, C:0.24, G:0.10, T:0.47
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:7374 original size:17 final size:18
Alignment explanation
Indices: 7337--7374 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7327 TACTACTCTA
*
7337 TGGTACCGATACTCCTTT
1 TGGTACCGATACTCATTT
*
7355 TGGTATCGATAC-CATTT
1 TGGTACCGATACTCATTT
7372 TGG
1 TGG
7375 CATTCTGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (18 bp):
TGGTACCGATACTCATTT
Found at i:9903 original size:16 final size:17
Alignment explanation
Indices: 9882--9916 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
9872 CTGATTTCTA
9882 TTATACAATATATA-TT
1 TTATACAATATATAGTT
9898 TTATACAATATATAGTT
1 TTATACAATATATAGTT
9915 TT
1 TT
9917 GAAAACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (17 bp):
TTATACAATATATAGTT
Found at i:9930 original size:23 final size:22
Alignment explanation
Indices: 9904--10012 Score: 64
Period size: 25 Copynumber: 4.8 Consensus size: 22
9894 TATTTTATAC
9904 AATATATAGTTTTGAAAACATAT
1 AATATATAGTTTTGAAAA-ATAT
**
9927 -A-ATATAGTTTTTTAAAATAT
1 AATATATAGTTTTGAAAAATAT
* *
9947 --TATATAGTTTTTCAAGAAGTAT
1 AATATATAG-TTTTGAA-AAATAT
*
9969 ATATATATAATTTTGAAACATATAT
1 A-ATATATAGTTTTGAAA-A-ATAT
* *
9994 AATGTATAATTTTTGAAAA
1 AATATAT-AGTTTTGAAAA
10013 CTTAGTTTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
20 10 0.15
21 18 0.27
22 6 0.09
23 1 0.01
24 13 0.19
25 19 0.28
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (22 bp):
AATATATAGTTTTGAAAAATAT
Found at i:9932 original size:21 final size:21
Alignment explanation
Indices: 9907--9992 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
9897 TTTATACAAT
9907 ATATAGTTTTGAAAACATATA
1 ATATAGTTTTGAAAACATATA
** *
9928 ATATAGTTTTTTAAA-ATATT
1 ATATAGTTTTGAAAACATATA
* *
9948 ATATAGTTTTTCAAGAAGTATATA
1 ATATAG-TTTTGAA-AA-CATATA
*
9972 TATATAATTTTG-AAACATATA
1 -ATATAGTTTTGAAAACATATA
9993 TAATGTATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
20 10 0.20
21 23 0.45
22 4 0.08
23 1 0.02
24 8 0.16
25 5 0.10
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (21 bp):
ATATAGTTTTGAAAACATATA
Found at i:9951 original size:20 final size:21
Alignment explanation
Indices: 9906--9958 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
9896 TTTTATACAA
*
9906 TATATAGTTTTGAAAACATAT
1 TATATAGTTTTTAAAACATAT
* *
9927 AATATAGTTTTTTAAA-ATAT
1 TATATAGTTTTTAAAACATAT
9947 TATATAGTTTTT
1 TATATAGTTTTT
9959 CAAGAAGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.51
Consensus pattern (21 bp):
TATATAGTTTTTAAAACATAT
Found at i:9969 original size:19 final size:20
Alignment explanation
Indices: 9906--9971 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
9896 TTTTATACAA
**
9906 TATATAGTTTTGAAAACATA-
1 TATATAGTTTTTCAAA-ATAG
* *
9926 TAATATAGTTTTTTAAAATAT
1 T-ATATAGTTTTTCAAAATAG
*
9947 TATATAGTTTTTCAAGA-AG
1 TATATAGTTTTTCAAAATAG
9966 TATATA
1 TATATA
9972 TATATAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 7 0.18
20 18 0.46
21 14 0.36
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (20 bp):
TATATAGTTTTTCAAAATAG
Found at i:10001 original size:24 final size:24
Alignment explanation
Indices: 9966--10011 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
9956 TTTCAAGAAG
9966 TATATATATATAA-TTTTGAAACA
1 TATATATATATAATTTTTGAAACA
*
9989 TATATAATGTATAATTTTTGAAA
1 TATAT-ATATATAATTTTTGAAA
10012 ACTTAGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (24 bp):
TATATATATATAATTTTTGAAACA
Found at i:10074 original size:18 final size:19
Alignment explanation
Indices: 10040--10082 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
10030 TAATATATAT
10040 TATATAGTTTTTGAAAATA
1 TATATAGTTTTTGAAAATA
10059 TATATAGTTTTT-AAAATA
1 TATATAGTTTTTGAAAATA
10077 TATATA
1 TATATA
10083 ATATGTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
TATATAGTTTTTGAAAATA
Found at i:10081 original size:22 final size:21
Alignment explanation
Indices: 10031--10091 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 21
10021 CTGAAAATAT
*
10031 AATATATATTATATAGTTTTTG
1 AATATATA-TATATAGTTTTTA
10053 AA-A-ATATATATAGTTTTTA
1 AATATATATATATAGTTTTTA
10072 AA-ATATATATAATATGTTTT
1 AATATATATAT-ATA-GTTTT
10092 ATATTTTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
19 15 0.43
20 9 0.26
21 4 0.11
22 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.51
Consensus pattern (21 bp):
AATATATATATATAGTTTTTA
Found at i:10130 original size:21 final size:21
Alignment explanation
Indices: 10094--10173 Score: 56
Period size: 22 Copynumber: 3.7 Consensus size: 21
10084 TATGTTTTAT
*
10094 ATTTTTATTT-TCTTTTTTATTC
1 ATTTTTATTTAT-TTTATT-TTC
*
10116 ATTTTTATTTATTTTATTTTT
1 ATTTTTATTTATTTTATTTTC
* **
10137 GTTTTTATTTAATTCCATTTT-
1 ATTTTTATTT-ATTTTATTTTC
*
10158 ATTTTAATTTTATTTT
1 ATTTTTA-TTTATTTT
10174 CAGTCCAAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 19 0.41
22 26 0.57
23 1 0.02
ACGTcount: A:0.19, C:0.05, G:0.01, T:0.75
Consensus pattern (21 bp):
ATTTTTATTTATTTTATTTTC
Found at i:10132 original size:31 final size:30
Alignment explanation
Indices: 10088--10145 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
10078 ATATAATATG
10088 TTTTATATTTTTATTTTCT-TTTTTATTCAT
1 TTTTATATTTTTATTTT-TGTTTTTATTCAT
*
10118 TTTTATTTATTTTATTTTTGTTTTTATT
1 TTTTATAT-TTTTATTTTTGTTTTTATT
10146 TAATTCCATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.16, C:0.03, G:0.02, T:0.79
Consensus pattern (30 bp):
TTTTATATTTTTATTTTTGTTTTTATTCAT
Found at i:10172 original size:16 final size:16
Alignment explanation
Indices: 10118--10173 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
10108 TTTTATTCAT
*
10118 TTTTA-TTTATTTTAT
1 TTTTATTTTATTTTAA
*
10133 TTTTGTTTT-TATTTAA
1 TTTTATTTTAT-TTTAA
**
10149 TTCCATTTTATTTTAA
1 TTTTATTTTATTTTAA
10165 TTTTATTTT
1 TTTTATTTT
10174 CAGTCCAAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
15 5 0.16
16 25 0.81
17 1 0.03
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTTATTTTATTTTAA
Found at i:12353 original size:5 final size:5
Alignment explanation
Indices: 12345--12489 Score: 53
Period size: 5 Copynumber: 27.2 Consensus size: 5
12335 TATTATTTTA
* * * *
12345 TATTT TATTT TATTA TATTAT ATCTTT TATTT TACTT TA-TT T-TTT TCTTT
1 TATTT TATTT TATTT TATT-T -TATTT TATTT TATTT TATTT TATTT TATTT
* * * * ** *
12395 TATTG TATTT TCTTT AAAATTT AACACT T-TTT TATTT TATTT TGTTT
1 TATTT TATTT TATTT --TATTT TA-TTT TATTT TATTT TATTT TATTT
*
12442 TATCTT TATTT TCCCACTTTT TATTT TATTT TGTTT TATTTT TATTT T
1 TAT-TT TATTT T---A--TTT TATTT TATTT TATTT TA-TTT TATTT T
12490 CTCTTTTAAC
Statistics
Matches: 105, Mismatches: 20, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
4 8 0.08
5 73 0.70
6 12 0.11
7 7 0.07
8 1 0.01
10 4 0.04
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (5 bp):
TATTT
Found at i:12358 original size:20 final size:22
Alignment explanation
Indices: 12333--12378 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
12323 TTATTTATTA
12333 TTTATTAT-TT-TATATTTTAT
1 TTTATTATATTATATATTTTAT
*
12353 TTTATTATATTATATCTTTTAT
1 TTTATTATATTATATATTTTAT
12375 TTTA
1 TTTA
12379 CTTTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.35
21 2 0.09
22 13 0.57
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTATTATATTATATATTTTAT
Found at i:12363 original size:22 final size:22
Alignment explanation
Indices: 12337--12387 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
12327 TTATTATTTA
12337 TTATTTTATATTTTATTTTA-T
1 TTATTTTATATTTTATTTTACT
* *
12358 TATATTATATCTTTTATTTTACT
1 T-TATTTTATATTTTATTTTACT
12381 TTATTTT
1 TTATTTT
12388 TTTCTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 1 0.04
22 22 0.88
23 2 0.08
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.73
Consensus pattern (22 bp):
TTATTTTATATTTTATTTTACT
Found at i:12375 original size:27 final size:26
Alignment explanation
Indices: 12326--12405 Score: 87
Period size: 27 Copynumber: 3.1 Consensus size: 26
12316 ACTACTATTA
12326 TTTATTATTTATTAT-TTTATATTTTAT
1 TTTATTATTTA-TATCTTT-TATTTTAT
*
12353 TTTATTATATTATATCTTTTATTTTAC
1 TTTATTAT-TTATATCTTTTATTTTAT
*
12380 TTTATT-TTT-T-TCTTTTATTGTAT
1 TTTATTATTTATATCTTTTATTTTAT
12403 TTT
1 TTT
12406 CTTTAAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
23 14 0.29
24 1 0.02
25 2 0.04
26 1 0.02
27 24 0.50
28 6 0.12
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.74
Consensus pattern (26 bp):
TTTATTATTTATATCTTTTATTTTAT
Found at i:12395 original size:18 final size:18
Alignment explanation
Indices: 12323--12410 Score: 51
Period size: 17 Copynumber: 4.9 Consensus size: 18
12313 TTAACTACTA
12323 TTATT-TATTATTTATTATT
1 TTATTGTATT-TTT-TTATT
*
12342 TTATAT-T-TTATTTTATT
1 TTAT-TGTATTTTTTTATT
* * *
12359 ATATTATA-TCTTTTATT
1 TTATTGTATTTTTTTATT
*
12376 TTACTT-TATTTTTTTCTT
1 TTA-TTGTATTTTTTTATT
12394 TTATTGTATTTTCTTTA
1 TTATTGTATTTT-TTTA
12411 AAATTTAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 14
0.72 0.09 0.18
Matches are distributed among these distances:
16 1 0.02
17 23 0.42
18 20 0.36
19 9 0.16
20 2 0.04
ACGTcount: A:0.22, C:0.05, G:0.01, T:0.73
Consensus pattern (18 bp):
TTATTGTATTTTTTTATT
Found at i:13077 original size:18 final size:19
Alignment explanation
Indices: 13042--13079 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
13032 AATAACAAGT
*
13042 TTAAATTTTAATTTATTTA
1 TTAAATTCTAATTTATTTA
13061 TTAAATTCTAA-TTATTTA
1 TTAAATTCTAATTTATTTA
13079 T
1 T
13080 CTTTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATTCTAATTTATTTA
Found at i:18367 original size:103 final size:102
Alignment explanation
Indices: 18182--18387 Score: 349
Period size: 103 Copynumber: 2.0 Consensus size: 102
18172 ACTTCAACTC
*
18182 TTTTTTTAAGCATACTTTAAGGGGAGTCATCTCATCACACTACCATCCCACACTCTAAGTGAAAG
1 TTTTTTTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAG
18247 GAAACATACATTCCACCCCTGAGCTAGTCAAGTAGAG
66 GAAACATACATTCCACCCCTGAGCTAGTCAAGTAGAG
18284 TTTTTATTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAA
1 TTTTT-TTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAA
* * * * *
18349 GGGAGCATACCTTTCACCCCTGAGCTAGTCAGGTAGAG
65 GGAAACATACATTCCACCCCTGAGCTAGTCAAGTAGAG
18387 T
1 T
18388 CATCCCGTGA
Statistics
Matches: 97, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
102 5 0.05
103 92 0.95
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (102 bp):
TTTTTTTAAGCATACTTTAAGGGGAGTCAGCTCATCACACTACCATCCCACACTCTAAGTGAAAG
GAAACATACATTCCACCCCTGAGCTAGTCAAGTAGAG
Found at i:27313 original size:123 final size:123
Alignment explanation
Indices: 27089--27330 Score: 344
Period size: 123 Copynumber: 2.0 Consensus size: 123
27079 TTGTTAAAGT
* * *
27089 CAATGTCAACTTCACAATGAATGATATTAAACTTGAGCCAATGCAATTTTCAAGATTGGATTTCA
1 CAATGTCAACTTCACAATGAAAGATATTAAACTAGAGCCAATGCAATTTACAAGATTGGATTTCA
* *
27154 ACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAATAAATGAGCCATCCA
66 ACTTCACAACGAAGGACATCCAATTCAAAGATCAACTTCACAACAAATGAGCCATCCA
* * * *
27212 CAATTTCAACTTCAC-ATCGAAAGATATTAATCTCAGAG-CGATTCAATTTACAAGATTGGATTT
1 CAATGTCAACTTCACAAT-GAAAGATATTAAACT-AGAGCCAATGCAATTTACAAGATTGGATTT
* * *
27275 CAACTTCACAATGAAGGATATCCAATTCAAATATCAACTTCACAACAAATGAGCCA
64 CAACTTCACAACGAAGGACATCCAATTCAAAGATCAACTTCACAACAAATGAGCCA
27331 CCTATGATTT
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
122 2 0.02
123 100 0.95
124 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.27
Consensus pattern (123 bp):
CAATGTCAACTTCACAATGAAAGATATTAAACTAGAGCCAATGCAATTTACAAGATTGGATTTCA
ACTTCACAACGAAGGACATCCAATTCAAAGATCAACTTCACAACAAATGAGCCATCCA
Found at i:27347 original size:123 final size:123
Alignment explanation
Indices: 27089--27361 Score: 343
Period size: 123 Copynumber: 2.2 Consensus size: 123
27079 TTGTTAAAGT
* * * * * * * *
27089 CAATGTCAACTTCACAATGAATGATATTAAACT-TGAGCCAATGCAATTTTCAAGATTGGATTTC
1 CAATTTCAACTTCACAACGAAAGATATTAATCTCAGAG-CGATTCAATTTACAAGATTGGATTTC
* *
27153 AACTTCACAACGAAGGACATCCAATTCAAAGCTCAACTTCACAATAAATGAGCCATCCA
65 AACTTCACAACGAAGGACATCCAATTCAAAGATCAACTTCACAACAAATGAGCCATCCA
*
27212 CAATTTCAACTTCACATCGAAAGATATTAATCTCAGAGCGATTCAATTTACAAGATTGGATTTCA
1 CAATTTCAACTTCACAACGAAAGATATTAATCTCAGAGCGATTCAATTTACAAGATTGGATTTCA
* * *
27277 ACTTCACAATGAAGGATATCCAATTCAAATATCAACTTCACAACAAATGAGCCA-CCTA
66 ACTTCACAACGAAGGACATCCAATTCAAAGATCAACTTCACAACAAATGAGCCATCC-A
** ** *
27335 TGATTTTGACTTCACAACGAAGGATAT
1 CAATTTCAACTTCACAACGAAAGATAT
27362 CATACCCAAT
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
122 2 0.02
123 123 0.96
124 3 0.02
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (123 bp):
CAATTTCAACTTCACAACGAAAGATATTAATCTCAGAGCGATTCAATTTACAAGATTGGATTTCA
ACTTCACAACGAAGGACATCCAATTCAAAGATCAACTTCACAACAAATGAGCCATCCA
Found at i:27789 original size:270 final size:270
Alignment explanation
Indices: 27308--27910 Score: 827
Period size: 270 Copynumber: 2.2 Consensus size: 270
27298 AATTCAAATA
* * *
27308 TCAACTTCACAACAAATGAGCCACCTATGATTTTGACTTCACAACGAAGGATATCATACCCAATA
1 TCAACTTCACAACAAAGGAGCCACCTACGATTTTGACTTCACAACGAAGGATATCATACCCAAAA
* * * *
27373 TATTGACCCAATTTCACAAAGAATGAGTCATCTGTAACACAACAATAAAAAACCAGTTTCATACC
66 GATTGACCCAACTTCACAAAGAAGGAATCATCTGTAACACAACAATAAAAAACCAGTTTCATACC
* ** *
27438 AAAGTCTTCAGGTCAAATTCCAGCTTCACGACGAAGTATATTAGGCTAAAAGACGATCCGAGAGT
131 AAAGCCTTCAGGTCAAATTCCAGCCCCACGACGAAGTATATTAGGCTAAAAGACGATCCGAGAGC
* * *
27503 GACTTTCCAATGCTTTGAGCCCGATTTCAACTTCACAACGAAGGATATCGTGCTCAGGATTTTTC
196 GACTTTCCAATGCTTTGAGACCGATTTAAACTTCACAACGAAGGATATCGTGCTCAGGAATTTTC
27568 AGTTCAAAGC
261 AGTTCAAAGC
** * *
27578 TCAACTTCACAATGAAGGAGCCACCTACGATTTTGACTTCACAATGAAGGATATCATATCCAAAA
1 TCAACTTCACAACAAAGGAGCCACCTACGATTTTGACTTCACAACGAAGGATATCATACCCAAAA
* *
27643 GATTGATCCAACTTCACGAAGAAGGAATCATCTGTAACA-AGACAATAAAAAACCAGTTTCATAC
66 GATTGACCCAACTTCACAAAGAAGGAATCATCTGTAACACA-ACAATAAAAAACCAGTTTCATAC
* * *
27707 CAAAGCCTTCAGGTCAAATTTCAGCCCCACGACGAAGTATATTGGGCTAAAAGATGATCC-AGGA
130 CAAAGCCTTCAGGTCAAATTCCAGCCCCACGACGAAGTATATTAGGCTAAAAGACGATCCGA-GA
* * *
27771 GCGACTTTCCAATGCTTTGAGACCGTTTTAAACTTTACAACTAAGGATATCGTGCTCAGGAATTT
194 GCGACTTTCCAATGCTTTGAGACCGATTTAAACTTCACAACGAAGGATATCGTGCTCAGGAATTT
*
27836 TCAGTTCAGAGC
259 TCAGTTCAAAGC
* * * * * ** *
27848 TCAAATTCACAACGAATGAGTCA-CTCATGATTTCAACTTCACTAA-GAAGGATATTATACCCAA
1 TCAACTTCACAACAAAGGAGCCACCT-ACGATTTTGACTTCAC-AACGAAGGATATCATACCCAA
27911 TGGTTCGACT
Statistics
Matches: 293, Mismatches: 36, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
269 4 0.01
270 287 0.98
271 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.26
Consensus pattern (270 bp):
TCAACTTCACAACAAAGGAGCCACCTACGATTTTGACTTCACAACGAAGGATATCATACCCAAAA
GATTGACCCAACTTCACAAAGAAGGAATCATCTGTAACACAACAATAAAAAACCAGTTTCATACC
AAAGCCTTCAGGTCAAATTCCAGCCCCACGACGAAGTATATTAGGCTAAAAGACGATCCGAGAGC
GACTTTCCAATGCTTTGAGACCGATTTAAACTTCACAACGAAGGATATCGTGCTCAGGAATTTTC
AGTTCAAAGC
Found at i:29049 original size:4 final size:4
Alignment explanation
Indices: 29040--29073 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
29030 TCTCTTTAGA
*
29040 TTAT TTAT TTAT TTAT TTATT TTAT TTAA TTAT T
1 TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT T
29074 ATCTTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTAT
Found at i:29063 original size:17 final size:18
Alignment explanation
Indices: 29043--29084 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
29033 CTTTAGATTA
*
29043 TTTATTTATTTATT-TAT
1 TTTATTTAATTATTATAT
*
29060 TTTATTTAATTATTATCT
1 TTTATTTAATTATTATAT
29078 TTTATTT
1 TTTATTT
29085 TAAAAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:29150 original size:22 final size:22
Alignment explanation
Indices: 29132--29175 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29122 TGCTATTATT
*
29132 TATTATTTTATCTTTTATTTTA
1 TATTATTATATCTTTTATTTTA
* *
29154 TTTTATTATATCTTTTGTTTTA
1 TATTATTATATCTTTTATTTTA
29176 CCCTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTATTATATCTTTTATTTTA
Found at i:30445 original size:11 final size:11
Alignment explanation
Indices: 30429--30463 Score: 70
Period size: 11 Copynumber: 3.2 Consensus size: 11
30419 AAGAAGGAAG
30429 AAGAATAAGAA
1 AAGAATAAGAA
30440 AAGAATAAGAA
1 AAGAATAAGAA
30451 AAGAATAAGAA
1 AAGAATAAGAA
30462 AA
1 AA
30464 AGGAGGTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (11 bp):
AAGAATAAGAA
Found at i:30449 original size:6 final size:6
Alignment explanation
Indices: 30429--30461 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
30419 AAGAAGGAAG
30429 AAGAAT AAGAA- AAGAAT AAGAA- AAGAAT AAGAA
1 AAGAAT AAGAAT AAGAAT AAGAAT AAGAAT AAGAA
30462 AAAGGAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.73, C:0.00, G:0.18, T:0.09
Consensus pattern (6 bp):
AAGAAT
Found at i:34742 original size:20 final size:20
Alignment explanation
Indices: 34717--34792 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
34707 GGTATACAAA
34717 TATTTTAAAAGAGATGGATC
1 TATTTTAAAAGAGATGGATC
** *
34737 TATTTTTCAAGGGATGGATC
1 TATTTTAAAAGAGATGGATC
** *
34757 TATTTTTCAAGGGATGGATC
1 TATTTTAAAAGAGATGGATC
34777 -ATTTCTGAAAAGAGAT
1 TATTT-T-AAAAGAGAT
34793 CGATATTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
19 4 0.08
20 38 0.79
21 6 0.12
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (20 bp):
TATTTTAAAAGAGATGGATC
Found at i:38491 original size:3 final size:3
Alignment explanation
Indices: 38483--38528 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
38473 AATGTTGTAT
38483 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
38529 TTTTTGGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39200 original size:43 final size:43
Alignment explanation
Indices: 39153--39262 Score: 148
Period size: 43 Copynumber: 2.6 Consensus size: 43
39143 GATTCCCTTT
* * **
39153 GTCGTGAAGTTGAAACCGTGGATGTGTGGGCACGATATCCTCC
1 GTCGTGGAGTTGAAATCGTGGATGCATGGGCACGATATCCTCC
* * *
39196 GTCGTGGAGTTGAAATCGTGGATCCATGGGTACGATATCCTCT
1 GTCGTGGAGTTGAAATCGTGGATGCATGGGCACGATATCCTCC
*
39239 GTCGTGGAGTTAAAATCGTGGATG
1 GTCGTGGAGTTGAAATCGTGGATG
39263 GCCTCTTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.22, C:0.17, G:0.33, T:0.28
Consensus pattern (43 bp):
GTCGTGGAGTTGAAATCGTGGATGCATGGGCACGATATCCTCC
Found at i:39555 original size:64 final size:64
Alignment explanation
Indices: 39468--39658 Score: 253
Period size: 64 Copynumber: 3.0 Consensus size: 64
39458 ATTTCATTTC
* * * *
39468 GAGTTCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAATTGTTTGTT
1 GAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTAGAAAGTTGTTTGTT
* *
39532 GAGTACAATATCCTTCGTTGTGAAGTTGAAATTGACTCTG-A--AAGTTAGAAAGTTGTTTGTT
1 GAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTAGAAAGTTGTTTGTT
* * * * * *
39593 GAGTCCAATATCTTTTGCCGTGAAGTTGAAATTGACTCTGAATGAAATTGGGAAGTTGTTTGTT
1 GAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTAGAAAGTTGTTTGTT
39657 GA
1 GA
39659 CAGACACTCA
Statistics
Matches: 110, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
61 52 0.47
62 1 0.01
63 1 0.01
64 56 0.51
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.37
Consensus pattern (64 bp):
GAGTACAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAATTAGAAAGTTGTTTGTT
Found at i:39616 original size:61 final size:61
Alignment explanation
Indices: 39468--39634 Score: 208
Period size: 61 Copynumber: 2.7 Consensus size: 61
39458 ATTTCATTTC
* * *
39468 GAGTTCAATATCCTTCACTGTGAAGTTGAAATTGACTCTGAATGAAACTAGAAAATTGTTTGTT
1 GAGTACAATATCCTTCGCCGTGAAGTTGAAATTGACTCTG-A--AAACTAGAAAATTGTTTGTT
** ** *
39532 GAGTACAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAAGTTAGAAAGTTGTTTGTT
1 GAGTACAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAAACTAGAAAATTGTTTGTT
* * *
39593 GAGTCCAATATCTTTTGCCGTGAAGTTGAAATTGACTCTGAA
1 GAGTACAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAA
39635 TGAAATTGGG
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
61 54 0.59
63 1 0.01
64 37 0.40
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (61 bp):
GAGTACAATATCCTTCGCCGTGAAGTTGAAATTGACTCTGAAAACTAGAAAATTGTTTGTT
Found at i:39998 original size:32 final size:32
Alignment explanation
Indices: 39923--39998 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 32
39913 TTCGTATCAG
* *
39923 GATGTTGAATCCCCAAAGATGCCCCAATATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* * * *
39955 GATGTTGAATCTCGAAAGATTCCCTAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
39987 GATGTTGAATCT
1 GATGTTGAATCT
39999 TTAATGATGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:40690 original size:27 final size:27
Alignment explanation
Indices: 40659--40720 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
40649 TATCATGCAT
40659 TAAAGATTTTAGAAAACCTTTTGCAAA
1 TAAAGATTTTAGAAAACCTTTTGCAAA
40686 TAAAGATTTTAGAAAACCTTTTGCAAA
1 TAAAGATTTTAGAAAACCTTTTGCAAA
40713 TAAAGATT
1 TAAAGATT
40721 AAACCTGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (27 bp):
TAAAGATTTTAGAAAACCTTTTGCAAA
Found at i:41094 original size:20 final size:20
Alignment explanation
Indices: 41069--41110 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
41059 GCTTATTGTC
41069 TTCATTT-TTTCTTTACTTTT
1 TTCATTTGTTT-TTTACTTTT
*
41089 TTCATTTGTTTTTTCCTTTT
1 TTCATTTGTTTTTTACTTTT
41109 TT
1 TT
41111 TGTTTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 17 0.85
21 3 0.15
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.76
Consensus pattern (20 bp):
TTCATTTGTTTTTTACTTTT
Found at i:44496 original size:30 final size:30
Alignment explanation
Indices: 44429--44516 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 30
44419 ACTCAAAAGG
** * * *
44429 CTAAAATAGCTAAAACAGATATTTAAATGA
1 CTAAAATAGAAAAAACAGAAACTTAAGTGA
44459 C-ATAAATAGAAAAAACAGAAACTTAAGTGA
1 CTA-AAATAGAAAAAACAGAAACTTAAGTGA
* *
44489 CTAAAATA-AAATAACAGAAACTAAAGTG
1 CTAAAATAGAAAAAACAGAAACTTAAGTG
44517 TCAAAATCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 19 0.39
30 29 0.59
31 1 0.02
ACGTcount: A:0.58, C:0.10, G:0.11, T:0.20
Consensus pattern (30 bp):
CTAAAATAGAAAAAACAGAAACTTAAGTGA
Found at i:44533 original size:29 final size:28
Alignment explanation
Indices: 44468--44533 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
44458 ACATAAATAG
*
44468 AAAAAACAGAAACTTAAGTGACTAAAAT
1 AAAAAACAGAAACTAAAGTGACTAAAAT
*
44496 AAAATAACAGAAACTAAAGTGTC-AAAAT
1 AAAA-AACAGAAACTAAAGTGACTAAAAT
44524 CAAGAAAACA
1 -AA-AAAACA
44534 TATATATTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 9 0.27
29 22 0.67
30 2 0.06
ACGTcount: A:0.62, C:0.12, G:0.11, T:0.15
Consensus pattern (28 bp):
AAAAAACAGAAACTAAAGTGACTAAAAT
Done.