Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004575.1 Hibiscus syriacus cultivar Beakdansim tig00010189_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: 93027
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:7475 original size:17 final size:18
Alignment explanation
Indices: 7445--7482 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
7435 TTTATTTTAT
*
7445 TTTTAAATATATTTTAAA
1 TTTTAAAGATATTTTAAA
*
7463 TTTTAAAGA-ATTTTGAA
1 TTTTAAAGATATTTTAAA
7480 TTT
1 TTT
7483 CTTACATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (18 bp):
TTTTAAAGATATTTTAAA
Found at i:8094 original size:2 final size:2
Alignment explanation
Indices: 7997--8075 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
7987 ACTTTAAATT
7997 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8039 TA TA TA 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 T
8076 TTGGTTTGTA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10130 original size:31 final size:31
Alignment explanation
Indices: 10095--10204 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 31
10085 TTAGGTTCAT
10095 AAGGAATTACCAGTCAGTGTTGAACCTATAC
1 AAGGAATTACCAGTCAGTGTTGAACCTATAC
* * *
10126 AAGGAATTACCA-ACA-TCGATTGAACCTGCTAGAG
1 AAGGAATTACCAGTCAGT-G-TTGAA-C--CTATAC
* *
10160 ATAGGAATTACCAGTCAGTGTTAAACCAATAC
1 A-AGGAATTACCAGTCAGTGTTGAACCTATAC
10192 AAGGAATTACCAG
1 AAGGAATTACCAG
10205 CAGCGACTGA
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
29 1 0.02
30 3 0.05
31 29 0.46
32 5 0.08
34 6 0.10
35 15 0.24
36 3 0.05
37 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (31 bp):
AAGGAATTACCAGTCAGTGTTGAACCTATAC
Found at i:27516 original size:18 final size:20
Alignment explanation
Indices: 27459--27516 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
27449 CACGGAATGT
* *
27459 AAGATTACTAGTGGGAATAA
1 AAGATTACCAATGGGAATAA
*
27479 AAGATTACCAATGAGAATAA
1 AAGATTACCAATGGGAATAA
*
27499 AATATTACC-A-GGGAATAA
1 AAGATTACCAATGGGAATAA
27517 GATTACTGGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
18 7 0.21
19 1 0.03
20 25 0.76
ACGTcount: A:0.50, C:0.09, G:0.19, T:0.22
Consensus pattern (20 bp):
AAGATTACCAATGGGAATAA
Found at i:27647 original size:26 final size:26
Alignment explanation
Indices: 27611--27670 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
27601 TATTAGAATG
27611 TATATTTTATCAAATTGTCCTTGTTC
1 TATATTTTATCAAATTGTCCTTGTTC
27637 TATATTTTATCAAATTGTCCTTGTTC
1 TATATTTTATCAAATTGTCCTTGTTC
27663 TATATTTT
1 TATATTTT
27671 TTAACAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.57
Consensus pattern (26 bp):
TATATTTTATCAAATTGTCCTTGTTC
Found at i:27720 original size:14 final size:15
Alignment explanation
Indices: 27688--27719 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
27678 GTGAAATTCT
27688 AAATATTTAAATAAA
1 AAATATTTAAATAAA
*
27703 AAATATTTATATAAA
1 AAATATTTAAATAAA
27718 AA
1 AA
27720 TTCTCTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATTTAAATAAA
Found at i:30133 original size:12 final size:12
Alignment explanation
Indices: 30116--30140 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30106 TAGAGTTGAT
30116 AAGTTGAATTTG
1 AAGTTGAATTTG
30128 AAGTTGAATTTG
1 AAGTTGAATTTG
30140 A
1 A
30141 CTTGTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:30444 original size:21 final size:22
Alignment explanation
Indices: 30404--30447 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
30394 CAGATAGTAC
30404 AGGGGGTACAGATTCTCCCCTA
1 AGGGGGTACAGATTCTCCCCTA
30426 AGGGGGTATC-GATTC-CCCCTA
1 AGGGGGTA-CAGATTCTCCCCTA
30447 A
1 A
30448 ATGAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.33
22 13 0.62
23 1 0.05
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (22 bp):
AGGGGGTACAGATTCTCCCCTA
Found at i:30786 original size:2 final size:2
Alignment explanation
Indices: 30781--30854 Score: 148
Period size: 2 Copynumber: 37.0 Consensus size: 2
30771 GGGTTGTGTG
30781 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
30823 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
30855 GTGCTTACAA
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31140 original size:12 final size:12
Alignment explanation
Indices: 31123--31147 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31113 ACTGGTGATG
31123 ATAAGAATAATA
1 ATAAGAATAATA
31135 ATAAGAATAATA
1 ATAAGAATAATA
31147 A
1 A
31148 AACGATATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (12 bp):
ATAAGAATAATA
Found at i:32132 original size:31 final size:31
Alignment explanation
Indices: 32011--32138 Score: 123
Period size: 31 Copynumber: 4.1 Consensus size: 31
32001 AGAGTCGAGG
32011 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
32042 GAATTACCTATG-TCTTTCGGGACATATTGACA
1 G-TTTACCTATGTTC-TACGGAACATATGGACA
* * * *
32074 ATATACCTATGTTCTAAGGAATATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
32105 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
32136 GTT
1 GTT
32139 GCTGAGGTTC
Statistics
Matches: 74, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
31 49 0.66
32 25 0.34
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:32981 original size:22 final size:22
Alignment explanation
Indices: 32956--33002 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
32946 ACATTCAGGG
*
32956 TACTGTAAACGGTATTGTTCAT
1 TACTGTAAACGGTACTGTTCAT
**
32978 TACTGTTCACGGTACTGTTCAT
1 TACTGTAAACGGTACTGTTCAT
33000 TAC
1 TAC
33003 AGTTCATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (22 bp):
TACTGTAAACGGTACTGTTCAT
Found at i:33007 original size:22 final size:22
Alignment explanation
Indices: 32964--33008 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
32954 GGTACTGTAA
* *
32964 ACGGTATTGTTCATTACTGTTC
1 ACGGTACTGTTCATTACAGTTC
32986 ACGGTACTGTTCATTACAGTTC
1 ACGGTACTGTTCATTACAGTTC
33008 A
1 A
33009 TATGATATTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.18, T:0.40
Consensus pattern (22 bp):
ACGGTACTGTTCATTACAGTTC
Found at i:33046 original size:19 final size:20
Alignment explanation
Indices: 32999--33050 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
32989 GTACTGTTCA
* **
32999 TTACAGTTCATATGATATTG
1 TTACTGTTCATACCATATTG
33019 TTCACTGTTCATACCATATT-
1 TT-ACTGTTCATACCATATTG
33039 TTACTGTTCATA
1 TTACTGTTCATA
33051 AAATGTATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.36
20 4 0.14
21 14 0.50
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (20 bp):
TTACTGTTCATACCATATTG
Found at i:34471 original size:12 final size:12
Alignment explanation
Indices: 34454--34478 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
34444 TAGAGTTGAT
34454 AAGTTGAATTTG
1 AAGTTGAATTTG
34466 AAGTTGAATTTG
1 AAGTTGAATTTG
34478 A
1 A
34479 CTTGTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:34767 original size:22 final size:22
Alignment explanation
Indices: 34742--34786 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
34732 TAGATTGTGC
34742 AGGGGGTATAGATTCCCCCCTA
1 AGGGGGTATAGATTCCCCCCTA
*
34764 AGGGGGTATCGATTCCCCCCTA
1 AGGGGGTATAGATTCCCCCCTA
34786 A
1 A
34787 ATGAAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.22, C:0.29, G:0.27, T:0.22
Consensus pattern (22 bp):
AGGGGGTATAGATTCCCCCCTA
Found at i:35957 original size:20 final size:18
Alignment explanation
Indices: 35929--35972 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
35919 TGTAATATCA
*
35929 ATGTTATATGAAATGTGACT
1 ATGTGATATG-AATGTGA-T
35949 ATGTGATATGAATGTGAT
1 ATGTGATATGAATGTGAT
35967 ATGTGA
1 ATGTGA
35973 ACATAAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.30
19 7 0.30
20 9 0.39
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (18 bp):
ATGTGATATGAATGTGAT
Found at i:36146 original size:153 final size:153
Alignment explanation
Indices: 35974--36283 Score: 611
Period size: 153 Copynumber: 2.0 Consensus size: 153
35964 GATATGTGAA
35974 CATAAGTGACTAATTGACATGAGCTATGTAACTATATGAAAGCAAGAACATGTGACATGAAATAC
1 CATAAGTGACTAATTGACATGAGCTATGTAACTATATGAAAGCAAGAACATGTGACATGAAATAC
36039 ATGATAAGAAGATATAATACTATGTAAGGGTATTACATGATATGAAATTAAAGAGTAATGAGTTA
66 ATGATAAGAAGATATAATACTATGTAAGGGTATTACATGATATGAAATTAAAGAGTAATGAGTTA
36104 TATGTATATGAGATATATGTTTT
131 TATGTATATGAGATATATGTTTT
36127 CATAAGTGACTAATTGACATGAGCTATGTAACTATATGAAAGCAAGAACATGTGACATGAAATAC
1 CATAAGTGACTAATTGACATGAGCTATGTAACTATATGAAAGCAAGAACATGTGACATGAAATAC
36192 ATGATAAGAAGATATAATACTATGTAAGGGTATTACATGATATGAAATTAAAGAGTAATGAGTTA
66 ATGATAAGAAGATATAATACTATGTAAGGGTATTACATGATATGAAATTAAAGAGTAATGAGTTA
*
36257 TATGTATATGAGATATTTGTTTT
131 TATGTATATGAGATATATGTTTT
36280 CATA
1 CATA
36284 TACATGTGGT
Statistics
Matches: 156, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 156 1.00
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (153 bp):
CATAAGTGACTAATTGACATGAGCTATGTAACTATATGAAAGCAAGAACATGTGACATGAAATAC
ATGATAAGAAGATATAATACTATGTAAGGGTATTACATGATATGAAATTAAAGAGTAATGAGTTA
TATGTATATGAGATATATGTTTT
Found at i:37371 original size:22 final size:23
Alignment explanation
Indices: 37341--37397 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
37331 TTAACATTCG
* *
37341 GGTACTGTTCATTATTGTTC-AC
1 GGTATTGTTCATTACTGTTCAAC
*
37363 GGTATTGTTCATTACTGTTCATAT
1 GGTATTGTTCATTACTGTTCA-AC
37387 GGTATTGTTCA
1 GGTATTGTTCA
37398 ATGTTCATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 18 0.60
24 12 0.40
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.47
Consensus pattern (23 bp):
GGTATTGTTCATTACTGTTCAAC
Found at i:37404 original size:21 final size:21
Alignment explanation
Indices: 37361--37425 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 21
37351 ATTATTGTTC
37361 ACGGTATTGTTCATTACTGTTCAT
1 ACGGTATTGTTCA--A-TGTTCAT
*
37385 ATGGTATTGTTCAATGTTCAT
1 ACGGTATTGTTCAATGTTCAT
*
37406 ACCGTATT-TT-AATGTTCAT
1 ACGGTATTGTTCAATGTTCAT
37425 A
1 A
37426 AAACGTATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 10 0.26
20 2 0.05
21 13 0.34
22 1 0.03
24 12 0.32
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (21 bp):
ACGGTATTGTTCAATGTTCAT
Found at i:38859 original size:16 final size:16
Alignment explanation
Indices: 38838--38871 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38828 ATTGTAAAGG
38838 AAGGGAGAGGAGAAGA
1 AAGGGAGAGGAGAAGA
38854 AAGGGAGAGGAGAAGA
1 AAGGGAGAGGAGAAGA
38870 AA
1 AA
38872 TCTTACAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (16 bp):
AAGGGAGAGGAGAAGA
Found at i:40598 original size:31 final size:31
Alignment explanation
Indices: 40489--40603 Score: 99
Period size: 33 Copynumber: 3.6 Consensus size: 31
40479 AATAATATAG
* **
40489 TAAAATAAGATAAAATATATACTTTGAAAAGT
1 TAAAATAAAATAAAATATATA-TTTTTAAAGT
* *
40521 TAAAATGATATATCAAA-ATATATTTTTAAAGGT
1 TAAAAT-A-AAATAAAATATATATTTTTAAA-GT
* *
40554 TTAGATAAGAATAAAATATATATTTTTAAA-T
1 TAAAATAA-AATAAAATATATATTTTTAAAGT
40585 TAAAATACAAATAAAATAT
1 TAAAATA-AAATAAAATAT
40604 TTTTAAATTA
Statistics
Matches: 67, Mismatches: 10, Indels: 13
0.74 0.11 0.14
Matches are distributed among these distances:
31 17 0.25
32 19 0.28
33 25 0.37
34 6 0.09
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAAATAAAATAAAATATATATTTTTAAAGT
Found at i:40608 original size:27 final size:27
Alignment explanation
Indices: 40573--40636 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
40563 AATAAAATAT
40573 ATATTTTTAAATTAAAATACA-AATAAA
1 ATATTTTTAAATTAAAATA-ATAATAAA
**
40600 ATATTTTTAAATTAAGTTAATAATAAA
1 ATATTTTTAAATTAAAATAATAATAAA
*
40627 ATATATTTAA
1 ATATTTTTAA
40637 TAAGTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 1 0.03
27 32 0.97
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
ATATTTTTAAATTAAAATAATAATAAA
Found at i:40652 original size:25 final size:27
Alignment explanation
Indices: 40594--40657 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
40584 TTAAAATACA
*
40594 AATAAAATATTTTTAAATTAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
40621 AATAAAATATATTT-AA-TAAGTTAAT
1 AATAAAATATATTTAAATTAAGTTAAT
*
40646 -GTAAAA-ATATTT
1 AATAAAATATATTT
40658 CTTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 6 0.17
24 5 0.14
25 9 0.26
26 2 0.06
27 13 0.37
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (27 bp):
AATAAAATATATTTAAATTAAGTTAAT
Found at i:42890 original size:5 final size:5
Alignment explanation
Indices: 42880--42915 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
42870 ATTTGCGCAA
*
42880 AAAAG AAAAG AAAAG AAAAA AGAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG A-AAAG AAAAG AAAAG
42916 TTTCCTCATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:42905 original size:16 final size:17
Alignment explanation
Indices: 42878--42914 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
42868 TTATTTGCGC
42878 AAAAAAGAAAAGAAAAG
1 AAAAAAGAAAAGAAAAG
42895 AAAAAAG-AAAGAAAAG
1 AAAAAAGAAAAGAAAAG
42911 AAAA
1 AAAA
42915 GTTTCCTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAGAAAAG
Found at i:43347 original size:11 final size:11
Alignment explanation
Indices: 43331--43364 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
43321 TATTTGGAGA
43331 GTACTTGTGAG
1 GTACTTGTGAG
43342 GTACTTGTGA-
1 GTACTTGTGAG
43352 GTACGTTGTGAG
1 GTAC-TTGTGAG
43364 G
1 G
43365 CTTTAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 16 0.76
12 1 0.05
ACGTcount: A:0.18, C:0.09, G:0.38, T:0.35
Consensus pattern (11 bp):
GTACTTGTGAG
Found at i:44569 original size:27 final size:27
Alignment explanation
Indices: 44531--44596 Score: 132
Period size: 27 Copynumber: 2.4 Consensus size: 27
44521 ATTATTTGAT
44531 GGCATACGAGGATAAGGCAAAGGATAA
1 GGCATACGAGGATAAGGCAAAGGATAA
44558 GGCATACGAGGATAAGGCAAAGGATAA
1 GGCATACGAGGATAAGGCAAAGGATAA
44585 GGCATACGAGGA
1 GGCATACGAGGA
44597 AATGTACAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.11
Consensus pattern (27 bp):
GGCATACGAGGATAAGGCAAAGGATAA
Found at i:44571 original size:15 final size:15
Alignment explanation
Indices: 44531--44596 Score: 90
Period size: 12 Copynumber: 4.8 Consensus size: 15
44521 ATTATTTGAT
44531 GGCATACGAGGATAA
1 GGCATACGAGGATAA
44546 GGCA-A--AGGATAA
1 GGCATACGAGGATAA
44558 GGCATACGAGGATAA
1 GGCATACGAGGATAA
44573 GGCA-A--AGGATAA
1 GGCATACGAGGATAA
44585 GGCATACGAGGA
1 GGCATACGAGGA
44597 AATGTACAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
12 22 0.49
13 2 0.04
14 2 0.04
15 19 0.42
ACGTcount: A:0.42, C:0.12, G:0.35, T:0.11
Consensus pattern (15 bp):
GGCATACGAGGATAA
Found at i:70227 original size:7 final size:7
Alignment explanation
Indices: 70215--70253 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
70205 GCTTTCAATT
70215 TTTCAAA
1 TTTCAAA
70222 TTTCAAA
1 TTTCAAA
70229 TTTCAAA
1 TTTCAAA
70236 TTTCAAA
1 TTTCAAA
70243 TTTCAAA
1 TTTCAAA
70250 TTTC
1 TTTC
70254 TTATTTCCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (7 bp):
TTTCAAA
Found at i:75893 original size:105 final size:105
Alignment explanation
Indices: 75711--75920 Score: 420
Period size: 105 Copynumber: 2.0 Consensus size: 105
75701 CTGTACAAGG
75711 AATGAATTTATTAAAATTCAGGAAGAAGGAAGAAAGAGTGTAAGAAACGCCTAAAAGGGAGAAGG
1 AATGAATTTATTAAAATTCAGGAAGAAGGAAGAAAGAGTGTAAGAAACGCCTAAAAGGGAGAAGG
75776 AAACAGATAATGATGCTAAGATACATCACATTTTTCTAAT
66 AAACAGATAATGATGCTAAGATACATCACATTTTTCTAAT
75816 AATGAATTTATTAAAATTCAGGAAGAAGGAAGAAAGAGTGTAAGAAACGCCTAAAAGGGAGAAGG
1 AATGAATTTATTAAAATTCAGGAAGAAGGAAGAAAGAGTGTAAGAAACGCCTAAAAGGGAGAAGG
75881 AAACAGATAATGATGCTAAGATACATCACATTTTTCTAAT
66 AAACAGATAATGATGCTAAGATACATCACATTTTTCTAAT
75921 GTATTTACTG
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 105 1.00
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.23
Consensus pattern (105 bp):
AATGAATTTATTAAAATTCAGGAAGAAGGAAGAAAGAGTGTAAGAAACGCCTAAAAGGGAGAAGG
AAACAGATAATGATGCTAAGATACATCACATTTTTCTAAT
Found at i:78828 original size:2 final size:2
Alignment explanation
Indices: 78815--78846 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
78805 AAATAAATAA
*
78815 AT AT AC 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
78847 TTACTTGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:81950 original size:55 final size:56
Alignment explanation
Indices: 81853--81979 Score: 159
Period size: 55 Copynumber: 2.3 Consensus size: 56
81843 ATAGGATCCT
* * * * *
81853 GAAATCGAATATATCTATCAGTTGTTACAATTAATAAGCAT-AAAATAGGGGCTCC
1 GAAATCGAATATATCTATCAGTTGTTACAATTAAGAAACATAAAAATAAGAGCCCC
* **
81908 GAAATCGAATATATCTATCAGTTGTTGCCGTTAAGAAACATAAAAATAAGAGCCCC
1 GAAATCGAATATATCTATCAGTTGTTACAATTAAGAAACATAAAAATAAGAGCCCC
81964 GAAATC-ACATATATCT
1 GAAATCGA-ATATATCT
81980 CTATTTATCA
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
55 37 0.60
56 25 0.40
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.28
Consensus pattern (56 bp):
GAAATCGAATATATCTATCAGTTGTTACAATTAAGAAACATAAAAATAAGAGCCCC
Found at i:82328 original size:54 final size:54
Alignment explanation
Indices: 82239--82422 Score: 252
Period size: 54 Copynumber: 3.5 Consensus size: 54
82229 TTAATTAATA
*
82239 AGGGTCTTGAAATCGAGTATATCTATCAGTTGTTGTTATTAAGAAACATAAAAT
1 AGGGTCCTGAAATCGAGTATATCTATCAGTTGTTGTTATTAAGAAACATAAAAT
*
82293 AGGATCCTGAAATCGAGTATATCTATCAGTTGTTGTTATTAAG-AA-ATAAAAGT
1 AGGGTCCTGAAATCGAGTATATCTATCAGTTGTTGTTATTAAGAAACATAAAA-T
* * * *
82346 AGGGTCCT-AAATTGAGTATA--TATCAGTTGTTGTCATTAACAAGCATAAAAT
1 AGGGTCCTGAAATCGAGTATATCTATCAGTTGTTGTTATTAAGAAACATAAAAT
* *
82397 AGGGTCCCGAAATCGAATATATCTAT
1 AGGGTCCTGAAATCGAGTATATCTAT
82423 AAAATATGAG
Statistics
Matches: 114, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
50 18 0.16
51 9 0.08
52 33 0.29
53 10 0.09
54 44 0.39
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (54 bp):
AGGGTCCTGAAATCGAGTATATCTATCAGTTGTTGTTATTAAGAAACATAAAAT
Found at i:82634 original size:19 final size:20
Alignment explanation
Indices: 82607--82645 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
82597 ATCATCAATA
82607 AAAATTATA-AAAAAACATTT
1 AAAATTATACAAAAAA-ATTT
82627 AAAA-TATACAAAAAAATTT
1 AAAATTATACAAAAAAATTT
82646 TTTTTAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATTATACAAAAAAATTT
Found at i:85096 original size:20 final size:19
Alignment explanation
Indices: 85058--85096 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
85048 AATTAAAATC
* *
85058 ACCTAAACCATTATTTTTT
1 ACCTAAAACATTATGTTTT
85077 ACCTAAAACATTAATGTTTT
1 ACCTAAAACATT-ATGTTTT
85097 TTAACATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.18, G:0.03, T:0.44
Consensus pattern (19 bp):
ACCTAAAACATTATGTTTT
Found at i:85383 original size:3 final size:3
Alignment explanation
Indices: 85377--85412 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
85367 TTCATTTGGT
85377 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
85413 ATAAAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:87096 original size:22 final size:23
Alignment explanation
Indices: 87055--87101 Score: 87
Period size: 22 Copynumber: 2.1 Consensus size: 23
87045 ATTCTTTATT
87055 TTTAGAGAAATGTTTTATTAATA
1 TTTAGAGAAATGTTTTATTAATA
87078 TTTAGAGAAATG-TTTATTAATA
1 TTTAGAGAAATGTTTTATTAATA
87100 TT
1 TT
87102 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (23 bp):
TTTAGAGAAATGTTTTATTAATA
Found at i:87104 original size:25 final size:25
Alignment explanation
Indices: 87051--87106 Score: 75
Period size: 23 Copynumber: 2.4 Consensus size: 25
87041 ATTTATTCTT
87051 TATT-TTTAGAGAAATGTTTTATTA
1 TATTATTTAGAGAAATGTTTTATTA
87075 -A-TATTTAGAGAAATG-TTTATTAA
1 TATTATTTAGAGAAATGTTTTATT-A
87098 TATTATTTA
1 TATTATTTA
87107 TTTATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 7 0.25
23 14 0.50
24 1 0.04
25 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (25 bp):
TATTATTTAGAGAAATGTTTTATTA
Done.