Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009413.1 Hibiscus syriacus cultivar Beakdansim tig00113360_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: 57630
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:4414 original size:19 final size:17
Alignment explanation
Indices: 4390--4433 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
4380 TAATGGGTGT
4390 ATCGATGCACTCCCTATGC
1 ATCGATGCACT-CCT-TGC
*
4409 ATCGATGTACTCCTTGC
1 ATCGATGCACTCCTTGC
4426 ATTCGATG
1 A-TCGATG
4434 TTCATTTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.39
19 10 0.43
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (17 bp):
ATCGATGCACTCCTTGC
Found at i:4433 original size:18 final size:19
Alignment explanation
Indices: 4390--4434 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
4380 TAATGGGTGT
*
4390 ATCGATGCACTCCCTATGC
1 ATCGATGTACTCCCTATGC
4409 ATCGATGTACT-CCT-TGC
1 ATCGATGTACTCCCTATGC
4426 ATTCGATGT
1 A-TCGATGT
4435 TCATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 4 0.17
18 10 0.42
19 10 0.42
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (19 bp):
ATCGATGTACTCCCTATGC
Found at i:7866 original size:2 final size:2
Alignment explanation
Indices: 7861--7910 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
7851 AGAGTAGTAA
7861 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7903 AT AT AT AT
1 AT AT AT AT
7911 CTAATTCATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8938 original size:20 final size:20
Alignment explanation
Indices: 8872--8986 Score: 125
Period size: 18 Copynumber: 6.0 Consensus size: 20
8862 TCGAGGGATT
*
8872 ATCAGTGGTCATTCGGGACA
1 ATCAGTGGTCCTTCGGGACA
* *
8892 AACATTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
* *
8911 AT-AGTGGTTCTTCGGAACA
1 ATCAGTGGTCCTTCGGGACA
8930 ATCAGTGGTCCTTCGGGAC-
1 ATCAGTGGTCCTTCGGGACA
*
8949 AT-AGTGGTCCTTTGGGAC-
1 ATCAGTGGTCCTTCGGGACA
*
8967 AT-AGTGGTCCTTTGGGACA
1 ATCAGTGGTCCTTCGGGACA
8986 A
1 A
8987 ATATTCAGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
18 46 0.56
19 6 0.07
20 30 0.37
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.29
Consensus pattern (20 bp):
ATCAGTGGTCCTTCGGGACA
Found at i:8939 original size:38 final size:38
Alignment explanation
Indices: 8875--8985 Score: 138
Period size: 38 Copynumber: 3.0 Consensus size: 38
8865 AGGGATTATC
* *
8875 AGTGG-TCATTCGGGACAAACATTGGTCCTTCGGGACAT
1 AGTGGTTC-TTCGGGACAATCAGTGGTCCTTCGGGACAT
*
8913 AGTGGTTCTTCGGAACAATCAGTGGTCCTTCGGGACAT
1 AGTGGTTCTTCGGGACAATCAGTGGTCCTTCGGGACAT
* * *
8951 AGTGGTCCTTTGGGAC-AT-AGTGGTCCTTTGGGACA
1 AGTGGTTCTTCGGGACAATCAGTGGTCCTTCGGGACA
8986 AATATTCAGT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 16 0.25
37 2 0.03
38 45 0.69
39 2 0.03
ACGTcount: A:0.21, C:0.20, G:0.31, T:0.29
Consensus pattern (38 bp):
AGTGGTTCTTCGGGACAATCAGTGGTCCTTCGGGACAT
Found at i:9370 original size:4 final size:4
Alignment explanation
Indices: 9353--9440 Score: 131
Period size: 4 Copynumber: 21.8 Consensus size: 4
9343 TAATGACATA
* * *
9353 TATG TATA TATG TATG TATG TATA TATG TATG TATG TATG TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
9401 TATG TATG TATG TATG TATG TATA TATG TATG TAGTG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TA-TG TAT
9441 TTGTTACATG
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
4 71 0.95
5 4 0.05
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:10152 original size:35 final size:36
Alignment explanation
Indices: 10109--10239 Score: 162
Period size: 35 Copynumber: 3.7 Consensus size: 36
10099 GCCTTAGATC
* *
10109 TATAAGGAATTACCAGC-TGATCGGTACTGAACCTA
1 TATAAGGAATTACCAACTTGATCAGTACTGAACCTA
* *
10144 TATAAGGAATTACCAAC-CGATCAGTGCTGAACCTGA
1 TATAAGGAATTACCAACTTGATCAGTACTGAACCT-A
10180 -ATAAGGAATTACCAACTTGATCAG-AGCTGAACCTA
1 TATAAGGAATTACCAACTTGATCAGTA-CTGAACCTA
* *
10215 TATAAGGAATTACTAGCTTGATCAG
1 TATAAGGAATTACCAACTTGATCAG
10240 AGCTAAACCT
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
35 47 0.56
36 37 0.44
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (36 bp):
TATAAGGAATTACCAACTTGATCAGTACTGAACCTA
Found at i:10209 original size:36 final size:35
Alignment explanation
Indices: 10109--10250 Score: 171
Period size: 36 Copynumber: 4.0 Consensus size: 35
10099 GCCTTAGATC
* *
10109 TATAAGGAATTACCAGCTGATCGGTA-CTGAACCTA
1 TATAAGGAATTACCAACTGATCAG-AGCTGAACCTA
* *
10144 TATAAGGAATTACCAACCGATCAGTGCTGAACCTGA
1 TATAAGGAATTACCAACTGATCAGAGCTGAACCT-A
10180 -ATAAGGAATTACCAACTTGATCAGAGCTGAACCTA
1 TATAAGGAATTACCAAC-TGATCAGAGCTGAACCTA
* * *
10215 TATAAGGAATTACTAGCTTGATCAGAGCTAAACCTA
1 TATAAGGAATTACCAAC-TGATCAGAGCTGAACCTA
10251 CAGAGAATTC
Statistics
Matches: 94, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
35 46 0.49
36 48 0.51
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (35 bp):
TATAAGGAATTACCAACTGATCAGAGCTGAACCTA
Found at i:11963 original size:23 final size:23
Alignment explanation
Indices: 11936--11995 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
11926 CAAAGTCAAC
*
11936 GGTCAACAGTTAACTATAGTCAT
1 GGTCAACAGTCAACTATAGTCAT
11959 GGTCAACAGTCAACTATAGTCAT
1 GGTCAACAGTCAACTATAGTCAT
*
11982 AGTCAACAGTCAAC
1 GGTCAACAGTCAAC
11996 GGGTCAAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.25
Consensus pattern (23 bp):
GGTCAACAGTCAACTATAGTCAT
Found at i:12008 original size:14 final size:15
Alignment explanation
Indices: 11983--12013 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
11973 TATAGTCATA
11983 GTCAACAGTCAACGG
1 GTCAACAGTCAACGG
11998 GTCAA-AGTCAACGG
1 GTCAACAGTCAACGG
12012 GT
1 GT
12014 TGACTCAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.32, C:0.23, G:0.29, T:0.16
Consensus pattern (15 bp):
GTCAACAGTCAACGG
Found at i:12029 original size:14 final size:15
Alignment explanation
Indices: 12007--12048 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
11997 GGTCAAAGTC
*
12007 AACGGGTTGACTCAG
1 AACGAGTTGACTCAG
12022 -ACGAGTTGACTC-G
1 AACGAGTTGACTCAG
12035 AACGAGTTGACTCA
1 AACGAGTTGACTCA
12049 ACATGACCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 1 0.04
14 23 0.96
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (15 bp):
AACGAGTTGACTCAG
Found at i:13128 original size:29 final size:29
Alignment explanation
Indices: 13053--13119 Score: 134
Period size: 29 Copynumber: 2.3 Consensus size: 29
13043 TTACATACGT
13053 GGATACTTTAATCATTTCTTCAATCATAA
1 GGATACTTTAATCATTTCTTCAATCATAA
13082 GGATACTTTAATCATTTCTTCAATCATAA
1 GGATACTTTAATCATTTCTTCAATCATAA
13111 GGATACTTT
1 GGATACTTT
13120 TGTCTTTTCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (29 bp):
GGATACTTTAATCATTTCTTCAATCATAA
Found at i:20661 original size:2 final size:2
Alignment explanation
Indices: 20654--20698 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
20644 CATAATTCGA
20654 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20695 AT AT
1 AT AT
20699 TATCTAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22020 original size:79 final size:79
Alignment explanation
Indices: 21932--22082 Score: 266
Period size: 79 Copynumber: 1.9 Consensus size: 79
21922 ACGCTAGAAA
21932 AAGTTTAATAGTTTTTATATGGTTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
1 AAGTTTAATAGTTTTTATATGGTTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
21997 TTATTTTCGTTAAG
66 TTATTTTCGTTAAG
* * * *
22011 AAGTTTAATAGTTTTTATATGGTTTGTTAATGTCATGTTAAATTAATTGTTCAAAGTAAGAGAAT
1 AAGTTTAATAGTTTTTATATGGTTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
22076 TTATTTT
66 TTATTTT
22083 TTAGTTTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.46
Consensus pattern (79 bp):
AAGTTTAATAGTTTTTATATGGTTTATGAATGACATGTTAAATTAATTGTTCAAAATAAGAGAAT
TTATTTTCGTTAAG
Found at i:24185 original size:10 final size:10
Alignment explanation
Indices: 24150--24185 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
24140 TAAATATATT
*
24150 AAAATATAAC
1 AAAAAATAAC
*
24160 TAAAAATAAC
1 AAAAAATAAC
24170 AAAAAATAAC
1 AAAAAATAAC
24180 AAAAAA
1 AAAAAA
24186 CGAAACAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (10 bp):
AAAAAATAAC
Found at i:24917 original size:2 final size:2
Alignment explanation
Indices: 24912--25007 Score: 192
Period size: 2 Copynumber: 48.0 Consensus size: 2
24902 AATAACTTTA
24912 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24996 AT AT AT AT AT AT
1 AT AT AT AT AT AT
25008 CCAAATATTA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 94 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27057 original size:143 final size:138
Alignment explanation
Indices: 26767--27048 Score: 431
Period size: 143 Copynumber: 2.0 Consensus size: 138
26757 CAAAGCCTGC
*
26767 AACTTTTCCTCTAAGTCGTCCAAAGCTTATTTTTTTCATGGGGACCCCCAACTGCTGATATCATT
1 AACTTTTCCTCTAAGTCATCCAAAGCTTATTTTTTTCATGGGGACCCCCAACTGCTGATATCATT
*
26832 TCCCTCAAACTCGGCCAAATTGTCGAGATATTGTTGTGGGAAAAAATTCCCGAGATAAGACATAT
66 TCCCTCAAACTCGGCCAAATTGTCGAGATATTGTTGTGGGAAAAAATTCCAGAGATAAGACATAT
**
26897 CAGGGATT
131 CAGAAATT
*
26905 GCAACTTTTCCTCTAAGTCATCCAAAAGCTTATTTTTTTTTCATGGGGGCCCCCAACTGCTGATA
1 --AACTTTTCCTCTAAGTCATCC-AAAGCTTA--TTTTTTTCATGGGGACCCCCAACTGCTGATA
26970 TCATTTCCCTCAAACTCGGCCAAATTGTCGAGATATTGTTGTGGGGGGAAAAAAATTCCAGAGAT
61 TCATTTCCCTCAAACTCGGCCAAATTGTCGAGATATTGTTGT---GGG-AAAAAATTCCAGAGAT
27035 AAGACATATC-GAAA
122 AAGACATATCAGAAA
27049 ATTATTTTCT
Statistics
Matches: 130, Mismatches: 5, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
140 20 0.15
141 8 0.06
143 72 0.55
146 5 0.04
147 25 0.19
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (138 bp):
AACTTTTCCTCTAAGTCATCCAAAGCTTATTTTTTTCATGGGGACCCCCAACTGCTGATATCATT
TCCCTCAAACTCGGCCAAATTGTCGAGATATTGTTGTGGGAAAAAATTCCAGAGATAAGACATAT
CAGAAATT
Found at i:31670 original size:10 final size:10
Alignment explanation
Indices: 31631--31680 Score: 55
Period size: 10 Copynumber: 5.0 Consensus size: 10
31621 TTCATCACAC
31631 CAAATTCTCT
1 CAAATTCTCT
*
31641 CAATTTCTCT
1 CAAATTCTCT
*
31651 CAACTTCTCT
1 CAAATTCTCT
*
31661 CAAATACTCT
1 CAAATTCTCT
* *
31671 TATATTCTCT
1 CAAATTCTCT
31681 GTTTAAGGTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:31729 original size:9 final size:9
Alignment explanation
Indices: 31717--31750 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
31707 TAATATTTTG
31717 TATTTAATT
1 TATTTAATT
*
31726 TATTTAA-G
1 TATTTAATT
31734 TATTTAATT
1 TATTTAATT
31743 TATTTAAT
1 TATTTAAT
31751 ATTTTACTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (9 bp):
TATTTAATT
Found at i:31756 original size:17 final size:17
Alignment explanation
Indices: 31716--31754 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
31706 TTAATATTTT
31716 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
31733 GTATTTAATTTATTTAA
1 GTATTTAATTTATTTAA
31750 -TATTT
1 GTATTT
31755 TACTTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
GTATTTAATTTATTTAA
Found at i:31761 original size:16 final size:16
Alignment explanation
Indices: 31717--31766 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 16
31707 TAATATTTTG
*
31717 TATTTAATTTATTTAA
1 TATTTAACTTATTTAA
*
31733 GTATTTAATTTATTTAA
1 -TATTTAACTTATTTAA
* *
31750 TATTTTACTTATATAA
1 TATTTAACTTATTTAA
31766 T
1 T
31767 TGTTTTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 14 0.47
17 16 0.53
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTAACTTATTTAA
Found at i:35219 original size:20 final size:20
Alignment explanation
Indices: 35194--35234 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
35184 CGTTACACAG
*
35194 GGGGAATTGGTATCCC-CTGA
1 GGGGAATCGGT-TCCCTCTGA
35214 GGGGAATCGGTTCCCTCTGA
1 GGGGAATCGGTTCCCTCTGA
35234 G
1 G
35235 CATTCTGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.17, C:0.22, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGAATCGGTTCCCTCTGA
Found at i:35630 original size:13 final size:14
Alignment explanation
Indices: 35612--35643 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
35602 GATTTTCTAA
35612 TTGAAAATAAA-TT
1 TTGAAAATAAAGTT
35625 TTG-AAATAAAGTT
1 TTGAAAATAAAGTT
35638 TTGAAA
1 TTGAAA
35644 TTACTCCCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 8 0.47
14 2 0.12
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (14 bp):
TTGAAAATAAAGTT
Found at i:35633 original size:12 final size:13
Alignment explanation
Indices: 35616--35644 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
35606 TTCTAATTGA
35616 AAATAAA-TTTTG
1 AAATAAAGTTTTG
35628 AAATAAAGTTTTG
1 AAATAAAGTTTTG
35641 AAAT
1 AAAT
35645 TACTCCCCCT
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:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (13 bp):
AAATAAAGTTTTG
Found at i:35673 original size:21 final size:21
Alignment explanation
Indices: 35647--35697 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
35637 TTTGAAATTA
35647 CTCCCCCTTACTTTAACACTT
1 CTCCCCCTTACTTTAACACTT
* *
35668 CTCCCCCTAATTTTAACACTT
1 CTCCCCCTTACTTTAACACTT
35689 CTCCCCCTT
1 CTCCCCCTT
35698 TTTGTTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.45, G:0.00, T:0.37
Consensus pattern (21 bp):
CTCCCCCTTACTTTAACACTT
Found at i:35718 original size:14 final size:14
Alignment explanation
Indices: 35699--35726 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35689 CTCCCCCTTT
35699 TTGTTAAATCAAAA
1 TTGTTAAATCAAAA
35713 TTGTTAAATCAAAA
1 TTGTTAAATCAAAA
35727 AGACTCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.36
Consensus pattern (14 bp):
TTGTTAAATCAAAA
Found at i:37901 original size:22 final size:22
Alignment explanation
Indices: 37860--37934 Score: 98
Period size: 23 Copynumber: 3.4 Consensus size: 22
37850 CGTGGGTGGT
37860 ATCGATT-CCCTCCAAGGGGGA
1 ATCGATTCCCCTCCAAGGGGGA
*
37881 ATCGATTCCCCTTCAAAGGGGGA
1 ATCGATTCCCC-TCCAAGGGGGA
* * *
37904 ATCGGTTCCCCTGCAAGGGGGT
1 ATCGATTCCCCTCCAAGGGGGA
37926 ATCGATTCC
1 ATCGATTCC
37935 TCTTGCACTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 7 0.15
22 19 0.41
23 20 0.43
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (22 bp):
ATCGATTCCCCTCCAAGGGGGA
Found at i:37903 original size:23 final size:22
Alignment explanation
Indices: 37860--37934 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
37850 CGTGGGTGGT
*
37860 ATCGATT-CCCTCCAAGGGGGA
1 ATCGATTCCCCTTCAAGGGGGA
37881 ATCGATTCCCCTTCAAAGGGGGA
1 ATCGATTCCCCTTC-AAGGGGGA
* * *
37904 ATCGGTTCCCCTGCAAGGGGGT
1 ATCGATTCCCCTTCAAGGGGGA
37926 ATCGATTCC
1 ATCGATTCC
37935 TCTTGCACTA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
21 7 0.15
22 20 0.43
23 20 0.43
ACGTcount: A:0.21, C:0.28, G:0.28, T:0.23
Consensus pattern (22 bp):
ATCGATTCCCCTTCAAGGGGGA
Found at i:38546 original size:22 final size:22
Alignment explanation
Indices: 38529--38595 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
38519 CTCGTATAAA
38529 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38551 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38573 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
38595 T
1 T
38596 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:38856 original size:30 final size:31
Alignment explanation
Indices: 38815--38874 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
38805 TAGACATAGT
*
38815 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
38845 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
38875 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:38932 original size:29 final size:29
Alignment explanation
Indices: 38890--38959 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
38880 TTCTGCATAA
**
38890 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
38919 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
38948 TCATGTCATGTA
1 TCATGTCATGTA
38960 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:39408 original size:67 final size:67
Alignment explanation
Indices: 39263--39413 Score: 196
Period size: 68 Copynumber: 2.2 Consensus size: 67
39253 TTTTCTCATG
* * *
39263 GGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTCAAGCAATCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
*
39328 GAG
65 GAA
** * * *
39331 GGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCTTGCATTCTGGAAATTCAT-TTCGTT
1 GGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
39395 GAA
65 GAA
39398 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
39414 TTGAATGGGT
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
67 30 0.41
68 43 0.59
ACGTcount: A:0.17, C:0.28, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATATACGATG
AA
Found at i:39423 original size:21 final size:21
Alignment explanation
Indices: 39393--39435 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
39383 ATTCATTTCG
* *
39393 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
39414 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
39435 T
1 T
39436 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:45488 original size:22 final size:22
Alignment explanation
Indices: 45471--45537 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
45461 CTCGTATAAA
45471 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
45493 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
45515 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
45537 T
1 T
45538 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:45798 original size:30 final size:31
Alignment explanation
Indices: 45757--45816 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 31
45747 TAGACATAGT
*
45757 ATTTCCATACCTTTAACACATAG-GCATATC
1 ATTTACATACCTTTAACACATAGTGCATATC
*
45787 ATTTACATACCTTTATCACATAGTGCATAT
1 ATTTACATACCTTTAACACATAGTGCATAT
45817 AACTTTTCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (31 bp):
ATTTACATACCTTTAACACATAGTGCATATC
Found at i:45874 original size:29 final size:29
Alignment explanation
Indices: 45832--45901 Score: 113
Period size: 29 Copynumber: 2.4 Consensus size: 29
45822 TTCTGCATAA
**
45832 TCATGTCATGTAATACATATAATATGAAT
1 TCATGTCATGTAATACATATAATACAAAT
*
45861 TCATGTCATGTAATACATTTAATACAAAT
1 TCATGTCATGTAATACATATAATACAAAT
45890 TCATGTCATGTA
1 TCATGTCATGTA
45902 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.39
Consensus pattern (29 bp):
TCATGTCATGTAATACATATAATACAAAT
Found at i:46328 original size:67 final size:66
Alignment explanation
Indices: 46203--46353 Score: 196
Period size: 68 Copynumber: 2.3 Consensus size: 66
46193 TTTTTCTCAT
* * *
46203 GGGGGAATCGGTTCCCCCCCCTGGGGTATCGGTTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCAT-TACGA
46268 TGA
64 TGA
* * * *
46271 GGGGGTATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTC-TGCATTCTGGAAATTCATTTCGTT
1 GGGGGTATCGGTTCCCCCCCT-GGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGAT
46335 GA
65 GA
*
46337 AGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
46354 TTGAATGGGT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
66 22 0.30
67 23 0.31
68 29 0.39
ACGTcount: A:0.17, C:0.28, G:0.28, T:0.28
Consensus pattern (66 bp):
GGGGGTATCGGTTCCCCCCCTGGGGTATCGATTCCCCTCAAGCAATCTGGAAATTCATTACGATG
A
Found at i:46363 original size:21 final size:21
Alignment explanation
Indices: 46333--46375 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
46323 ATTCATTTCG
* *
46333 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
46354 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
46375 T
1 T
46376 AACCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:49791 original size:27 final size:27
Alignment explanation
Indices: 49760--49811 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
49750 ATCCAGGCGG
49760 ATTTCTCGGTCATGATCAGAGATCCGA
1 ATTTCTCGGTCATGATCAGAGATCCGA
*
49787 ATTTCTCGGTCATGGTCAGAGATCC
1 ATTTCTCGGTCATGATCAGAGATCC
49812 CATGAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (27 bp):
ATTTCTCGGTCATGATCAGAGATCCGA
Found at i:50078 original size:20 final size:20
Alignment explanation
Indices: 50041--50083 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
50031 ATTCCACCAC
*
50041 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
50061 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
50081 ATG
1 ATG
50084 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:54690 original size:27 final size:27
Alignment explanation
Indices: 54659--54713 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
54649 CTGATCCAGG
54659 CAGATTTCTCGGTCATGATCAGAGATC
1 CAGATTTCTCGGTCATGATCAGAGATC
*
54686 CAGATTTCTCGGTCATGGTCAGAGATC
1 CAGATTTCTCGGTCATGATCAGAGATC
54713 C
1 C
54714 CGTGAAAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (27 bp):
CAGATTTCTCGGTCATGATCAGAGATC
Done.