Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006769.1 Hibiscus syriacus cultivar Beakdansim tig00017105_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: 141894
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:694 original size:17 final size:18
Alignment explanation
Indices: 657--694 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
647 ATCTTCATTT
657 AAATCATGTATTTCATCAA
1 AAATCATGTATTT-ATCAA
676 AAATCATGTATTT-TCAA
1 AAATCATGTATTTATCAA
693 AA
1 AA
695 GGGTTTCAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (18 bp):
AAATCATGTATTTATCAA
Found at i:6250 original size:35 final size:37
Alignment explanation
Indices: 6204--6283 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
6194 TTTGTGAATT
*
6204 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
* *
6239 TGGTGATGATATATGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
6276 TGGGGATG
1 TGGTGATG
6284 GTAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:11481 original size:35 final size:37
Alignment explanation
Indices: 11435--11514 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
11425 TTTGAGAATT
*
11435 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
11470 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
11507 TGGGGATG
1 TGGTGATG
11515 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 4 0.10
37 15 0.38
ACGTcount: A:0.28, C:0.04, G:0.39, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:11898 original size:19 final size:20
Alignment explanation
Indices: 11851--11901 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
11841 GAAATCCCTT
**
11851 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
11871 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
11890 TGAAGATACATG
1 TGAAAATACATG
11902 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:13440 original size:19 final size:20
Alignment explanation
Indices: 13390--13451 Score: 90
Period size: 19 Copynumber: 3.0 Consensus size: 20
13380 ACCATCTATA
13390 TCCTTTATTTATTTCATTTCAT
1 TCCTTT-TTT-TTTCATTTCAT
*
13412 TCCTTTTTTTTTCATTTGAT
1 TCCTTTTTTTTTCATTTCAT
13432 TCC-TTTTTTTTCATTTCAT
1 TCCTTTTTTTTTCATTTCAT
13451 T
1 T
13452 AATCTTCCTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 16 0.42
20 13 0.34
21 3 0.08
22 6 0.16
ACGTcount: A:0.13, C:0.18, G:0.02, T:0.68
Consensus pattern (20 bp):
TCCTTTTTTTTTCATTTCAT
Found at i:13750 original size:25 final size:26
Alignment explanation
Indices: 13702--13771 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
13692 ATTAGAGTGC
* *
13702 AAAAAGAAAGAAAAAGACAAAAA-GA
1 AAAAAGAAAAAAAAATACAAAAAGGA
* *
13727 AAAAAGAAAAAAAAATTCAGAAAGGA
1 AAAAAGAAAAAAAAATACAAAAAGGA
13753 AGAAAAGAAAATAAAAATA
1 A-AAAAGAAAA-AAAAATA
13772 AAAGACAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.51
26 3 0.08
27 9 0.24
28 6 0.16
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (26 bp):
AAAAAGAAAAAAAAATACAAAAAGGA
Found at i:14777 original size:22 final size:22
Alignment explanation
Indices: 14735--14778 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
14725 AAAACACCTT
* *
14735 AAAGAAGAACATTGAAGCAATG
1 AAAGAACAACATTAAAGCAATG
14757 AAAGAACAAC-TTAAAGACAATG
1 AAAGAACAACATTAAAG-CAATG
14779 CAACTGAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.57, C:0.11, G:0.18, T:0.14
Consensus pattern (22 bp):
AAAGAACAACATTAAAGCAATG
Found at i:19558 original size:24 final size:25
Alignment explanation
Indices: 19531--19583 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
19521 TTTTTTGAAA
19531 TTTTGGCTTTTTGGCTTTTTTT-TT
1 TTTTGGCTTTTTGGCTTTTTTTGTT
* *
19555 TTTTTGTTTTTTGGCTTTTTTTGTT
1 TTTTGGCTTTTTGGCTTTTTTTGTT
19580 TTTT
1 TTTT
19584 TGAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.00, C:0.06, G:0.15, T:0.79
Consensus pattern (25 bp):
TTTTGGCTTTTTGGCTTTTTTTGTT
Found at i:19581 original size:8 final size:8
Alignment explanation
Indices: 19546--19585 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
19536 GCTTTTTGGC
19546 TTTTTTT-
1 TTTTTTTG
19553 TTTTTTTG
1 TTTTTTTG
*
19561 TTTTTTGG
1 TTTTTTTG
19569 CTTTTTTTG
1 -TTTTTTTG
19578 TTTTTTTG
1 TTTTTTTG
19586 AAAAAAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (8 bp):
TTTTTTTG
Found at i:27209 original size:12 final size:12
Alignment explanation
Indices: 27192--27217 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
27182 CACCTATGTT
27192 AGAATGCAAATG
1 AGAATGCAAATG
27204 AGAATGCAAATG
1 AGAATGCAAATG
27216 AG
1 AG
27218 CTAACTATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.08, G:0.27, T:0.15
Consensus pattern (12 bp):
AGAATGCAAATG
Found at i:33311 original size:16 final size:16
Alignment explanation
Indices: 33284--33339 Score: 71
Period size: 16 Copynumber: 3.5 Consensus size: 16
33274 AATTGGAGTG
33284 CAAAAAGAAAGAAAAGA
1 CAAAAAG-AAGAAAAGA
33301 CAAAAAGAAGAAAAGA
1 CAAAAAGAAGAAAAGA
33317 -AGAAAAGAAGAAAA-A
1 CA-AAAAGAAGAAAAGA
*
33332 GAAAAAGA
1 CAAAAAGA
33340 TTTCAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
15 8 0.22
16 22 0.59
17 7 0.19
ACGTcount: A:0.77, C:0.04, G:0.20, T:0.00
Consensus pattern (16 bp):
CAAAAAGAAGAAAAGA
Found at i:33314 original size:25 final size:25
Alignment explanation
Indices: 33286--33334 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
33276 TTGGAGTGCA
33286 AAAAGAAAGAAAAG-ACAAAAAGAAG
1 AAAAG-AAGAAAAGAACAAAAAGAAG
*
33311 AAAAGAAGAAAAGAAGAAAAAGAA
1 AAAAGAAGAAAAGAACAAAAAGAA
33335 AAAGATTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAAGAAGAAAAGAACAAAAAGAAG
Found at i:43684 original size:28 final size:28
Alignment explanation
Indices: 43644--43712 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
43634 TTGGAGTGCA
*
43644 AAAAG-AAAGAAAAAGACA-AAAAGAA-
1 AAAAGAAAATAAAAAGACAGAAAAGAAG
**
43669 AAAAGAAGAATAAAAATTCAGAAAAGAAG
1 AAAAGAA-AATAAAAAGACAGAAAAGAAG
43698 AAAAGAAAATAAAAA
1 AAAAGAAAATAAAAA
43713 TAAAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 5 0.14
26 1 0.03
27 9 0.24
28 15 0.41
29 7 0.19
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (28 bp):
AAAAGAAAATAAAAAGACAGAAAAGAAG
Found at i:57594 original size:18 final size:18
Alignment explanation
Indices: 57571--57611 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
57561 AATTGGAGTG
57571 CAAAAAGAAAGAAA-AAGA
1 CAAAAAGAAA-AAAGAAGA
57589 CAAAAAGAAAAAAGAAGA
1 CAAAAAGAAAAAAGAAGA
57607 -AAAAA
1 CAAAAA
57612 ATCAGAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (18 bp):
CAAAAAGAAAAAAGAAGA
Found at i:57654 original size:16 final size:16
Alignment explanation
Indices: 57573--57646 Score: 55
Period size: 18 Copynumber: 4.4 Consensus size: 16
57563 TTGGAGTGCA
57573 AAAAG-AAAGAAAAAG
1 AAAAGAAAAGAAAAAG
*
57588 ACAAAAAGAAAA-AAGAAG
1 ---AAAAGAAAAGAAAAAG
57606 AAAA-AAATCAGAAATGAAG
1 AAAAGAAA--AGAAA--AAG
57625 AAAAGAAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
57641 AAAAGA
1 AAAAGA
57647 CAAAAAAACC
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
14 3 0.06
15 4 0.09
16 10 0.21
17 2 0.04
18 15 0.32
19 10 0.21
20 3 0.06
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:58948 original size:24 final size:24
Alignment explanation
Indices: 58900--58953 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
58890 AAAATAATGG
**
58900 CTTTTGAAAAACCAAAAGATGTGA
1 CTTTTGAAAAACCAAAAGACATGA
* *
58924 CTTTTGAATAACCAAAAGCCATGA
1 CTTTTGAAAAACCAAAAGACATGA
58948 CTTTTG
1 CTTTTG
58954 GTGATTCACA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.30
Consensus pattern (24 bp):
CTTTTGAAAAACCAAAAGACATGA
Found at i:62082 original size:36 final size:36
Alignment explanation
Indices: 62042--62182 Score: 183
Period size: 36 Copynumber: 3.9 Consensus size: 36
62032 AACACCATCT
* * *
62042 TCCATCTCCATTATCACGCCTATATTATCACCATAG
1 TCCATCACCATTATCACACCTATATCATCACCATAG
*
62078 TCCATCACCATTATCACACCTTTATCATCACCATAG
1 TCCATCACCATTATCACACCTATATCATCACCATAG
* * * *
62114 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACACCTATATCATCACCATAG
* * *
62150 TCCACCACCATTATCACACCCATATTATCACCA
1 TCCATCACCATTATCACACCTATATCATCACCA
62183 ACTTATAAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 90 1.00
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACACCTATATCATCACCATAG
Found at i:62102 original size:11 final size:12
Alignment explanation
Indices: 62080--62129 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
62070 CACCATAGTC
62080 CATCACCATTAT
1 CATCACCATTAT
*
62092 CA-CACCTTTAT
1 CATCACCATTAT
62103 CATCACCA-TAGT
1 CATCACCATTA-T
*
62115 CCATCTCCATTAT
1 -CATCACCATTAT
62128 CA
1 CA
62130 CGCCTATATC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
11 12 0.39
12 9 0.29
13 8 0.26
14 2 0.06
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.32
Consensus pattern (12 bp):
CATCACCATTAT
Found at i:62180 original size:72 final size:72
Alignment explanation
Indices: 62042--62182 Score: 219
Period size: 72 Copynumber: 2.0 Consensus size: 72
62032 AACACCATCT
* * **
62042 TCCATCTCCATTATCACGCCTATATTATCACCATAGTCCATCACCATTATCACACCTTTATCATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACACCCATATCATC
62107 ACCATAG
66 ACCATAG
* * *
62114 TCCATCTCCATTATCACGCCTATATCGTCACCATATTCCACCACCATTATCACACCCATATTATC
1 TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACACCCATATCATC
62179 ACCA
66 ACCA
62183 ACTTATAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.29, C:0.37, G:0.04, T:0.30
Consensus pattern (72 bp):
TCCATCTCCATTATCACGCCTATATCATCACCATAGTCCACCACCATTATCACACCCATATCATC
ACCATAG
Found at i:62595 original size:24 final size:24
Alignment explanation
Indices: 62555--62601 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
62545 AAAGTGCTAC
62555 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
62580 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
62602 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:65600 original size:17 final size:17
Alignment explanation
Indices: 65578--65616 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
65568 AGTAGGCTGC
65578 CATGTGCATCATTCAAG
1 CATGTGCATCATTCAAG
65595 CATGTGCATCATTCAAG
1 CATGTGCATCATTCAAG
65612 CATGT
1 CATGT
65617 TCATTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (17 bp):
CATGTGCATCATTCAAG
Found at i:66051 original size:36 final size:36
Alignment explanation
Indices: 66011--66151 Score: 201
Period size: 36 Copynumber: 3.9 Consensus size: 36
66001 AACACCATCT
*
66011 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
66047 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
66083 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * * *
66119 TCCACCACCATTATCACACCCATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
66152 ACTTATAAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 93 1.00
ACGTcount: A:0.28, C:0.38, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:67554 original size:6 final size:6
Alignment explanation
Indices: 67532--67608 Score: 50
Period size: 6 Copynumber: 12.2 Consensus size: 6
67522 GTGTAAAAAG
* * *
67532 AAAGAA AAAGAGTA AAAGAAA AAAGAA TAAGAA AAATTAGA AAAGAA GAAA-AG
1 AAAGAA AAAGA--A AAAG-AA AAAGAA AAAGAA AAA-GA-A AAAGAA -AAAGAA
*
67585 AAAGAA AAAG-A AAATAA AAAGAA A
1 AAAGAA AAAGAA AAAGAA AAAGAA A
67609 GACAAAACAA
Statistics
Matches: 55, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
5 7 0.13
6 28 0.51
7 10 0.18
8 9 0.16
9 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:67567 original size:27 final size:24
Alignment explanation
Indices: 67526--67615 Score: 87
Period size: 27 Copynumber: 3.6 Consensus size: 24
67516 ATTGGAGTGT
67526 AAAAAGAAAGAAAAAGAGTAAAAGA
1 AAAAAGAAAGAAAAAGAG-AAAAGA
*
67551 AAAAAGAATAAGAAAAATTAGAAAAGA
1 AAAAAG-A-AAGAAAAA-GAGAAAAGA
*
67578 AGAAAAGAAAG-AAAA-AGAAAA-T
1 A-AAAAGAAAGAAAAAGAGAAAAGA
67600 AAAAAGAAAGACAAAA
1 AAAAAGAAAGA-AAAA
67616 CAAGCCAAGG
Statistics
Matches: 57, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
21 9 0.16
22 1 0.02
23 10 0.18
25 10 0.18
26 4 0.07
27 16 0.28
28 7 0.12
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.06
Consensus pattern (24 bp):
AAAAAGAAAGAAAAAGAGAAAAGA
Found at i:67605 original size:11 final size:11
Alignment explanation
Indices: 67526--67608 Score: 53
Period size: 11 Copynumber: 6.8 Consensus size: 11
67516 ATTGGAGTGT
67526 AAAAAG-AAAG
1 AAAAAGAAAAG
67536 AAAAAGAGTAAAAG
1 -AAAA-AG-AAAAG
67550 AAAAAAGAATAAG
1 -AAAAAGAA-AAG
67563 AAAAATTAGAAAAG
1 -AAAA--AGAAAAG
67577 AAGAAA-AGAAAG
1 AA-AAAGA-AAAG
*
67589 AAAAAGAAAAT
1 AAAAAGAAAAG
67600 AAAAAGAAA
1 AAAAAGAAA
67609 GACAAAACAA
Statistics
Matches: 62, Mismatches: 1, Indels: 18
0.77 0.01 0.22
Matches are distributed among these distances:
11 20 0.32
12 12 0.19
13 12 0.19
14 14 0.23
15 4 0.06
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:67615 original size:11 final size:10
Alignment explanation
Indices: 67526--67615 Score: 52
Period size: 10 Copynumber: 9.5 Consensus size: 10
67516 ATTGGAGTGT
67526 AAAAAGAAAG
1 AAAAAGAAAG
67536 AAAAAG--AG
1 AAAAAGAAAG
*
67544 TAAAAGAAA-
1 AAAAAGAAAG
*
67553 AAAGAA-TAAG
1 AAA-AAGAAAG
**
67563 AAAAA-TTAG
1 AAAAAGAAAG
67572 -AAAAG-AAG
1 AAAAAGAAAG
67580 -AAAAGAAAG
1 AAAAAGAAAG
*
67589 AAAAAGAAAAT
1 AAAAAG-AAAG
67600 AAAAAGAAAG
1 AAAAAGAAAG
67610 ACAAAA
1 A-AAAA
67616 CAAGCCAAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 17
0.73 0.08 0.19
Matches are distributed among these distances:
8 18 0.28
9 12 0.19
10 21 0.33
11 13 0.20
ACGTcount: A:0.77, C:0.01, G:0.17, T:0.06
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:68921 original size:24 final size:23
Alignment explanation
Indices: 68860--68923 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
68850 AGATGATTAA
*
68860 AAAATCATGGCTTTTGAAAAACC
1 AAAAGCATGGCTTTTGAAAAACC
*
68883 AAAAG-ATGTGACTTTTGAAGAACC
1 AAAAGCATG-G-CTTTTGAAAAACC
*
68907 AATAGCCATGGCTTTTG
1 AAAAG-CATGGCTTTTG
68924 GTGATTCACA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 3 0.09
23 5 0.15
24 22 0.65
25 1 0.03
26 3 0.09
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.28
Consensus pattern (23 bp):
AAAAGCATGGCTTTTGAAAAACC
Found at i:71025 original size:13 final size:11
Alignment explanation
Indices: 70984--71068 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
70974 ACAATCTGTC
70984 CATCACCATTAT
1 CATCACCA-TAT
*
70996 CA-CGCCTATAT
1 CATCACC-ATAT
71007 CATCACCATAGT
1 CATCACCATA-T
71019 CCATCACCATTAT
1 -CATCACCA-TAT
*
71032 CA-CGCCTATAT
1 CATCACC-ATAT
71043 CATCACCATATT
1 CATCACCATA-T
71055 CCATCACCATAT
1 -CATCACCATAT
71067 CA
1 CA
71069 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:71028 original size:36 final size:36
Alignment explanation
Indices: 70981--71085 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
70971 GATACAATCT
70981 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
71017 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
71053 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
71086 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:75195 original size:19 final size:20
Alignment explanation
Indices: 75171--75221 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
75161 CGGCCAAGAG
* *
75171 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
75190 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
75210 CATGTATTTTCA
1 CATGTATTTTCA
75222 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:79240 original size:19 final size:20
Alignment explanation
Indices: 79216--79266 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
79206 CGGCCAAGAG
* *
79216 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
79235 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
79255 CATGTATTTTCA
1 CATGTATTTTCA
79267 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:83280 original size:19 final size:20
Alignment explanation
Indices: 83256--83306 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
83246 CGGCCAAGAG
* *
83256 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
83275 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
83295 CATGTATTTTCA
1 CATGTATTTTCA
83307 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:85271 original size:13 final size:12
Alignment explanation
Indices: 85253--85324 Score: 60
Period size: 13 Copynumber: 5.8 Consensus size: 12
85243 TATAGGCGTG
85253 ATATGGTGATGGA
1 ATATGGTGAT-GA
85266 ATATGGTGATG-
1 ATATGGTGATGA
*
85277 ATATAGGCG-TG-
1 ATAT-GGTGATGA
*
85288 AGATGGTGATGGA
1 ATATGGTGAT-GA
85301 ATATGGTGATGA
1 ATATGGTGATGA
85313 TATATGCGTGAT
1 -ATATG-GTGAT
85325 AATGGTGATG
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
10 3 0.06
11 10 0.20
12 7 0.14
13 24 0.49
14 5 0.10
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (12 bp):
ATATGGTGATGA
Found at i:85281 original size:35 final size:35
Alignment explanation
Indices: 85234--85336 Score: 170
Period size: 35 Copynumber: 2.9 Consensus size: 35
85224 ATTTAGAAGT
*
85234 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
*
85269 TGGTGATGATATAGGCGTGAGATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
*
85304 TGGTGATGATATATGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGA
85337 CAGATTGTAT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 52 0.83
36 11 0.17
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATA
Found at i:89318 original size:23 final size:20
Alignment explanation
Indices: 89275--89321 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
89265 TGTAGGAGTC
*
89275 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGTTT
89295 TTTTTCTTCTTTCTTGTTGCTTT
1 TTTTTC-T-TTTCTTGTTG-TTT
89318 TTTT
1 TTTT
89322 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 9 0.39
23 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGTTT
Found at i:89730 original size:13 final size:12
Alignment explanation
Indices: 89711--89797 Score: 78
Period size: 11 Copynumber: 7.3 Consensus size: 12
89701 ATATAGGCGT
89711 GATATGGTGATG
1 GATATGGTGATG
89723 GAATATGGTGAT-
1 G-ATATGGTGATG
*
89735 GATATAGGCG-T-
1 GATAT-GGTGATG
89746 GATATGGTGATG
1 GATATGGTGATG
89758 GAATATGGTGAT-
1 G-ATATGGTGATG
89770 GATATAGGTG-T-
1 GATAT-GGTGATG
89781 GATAATGGTGATG
1 GAT-ATGGTGATG
89794 GATA
1 GATA
89798 GATTGTATCT
Statistics
Matches: 64, Mismatches: 2, Indels: 18
0.76 0.02 0.21
Matches are distributed among these distances:
10 3 0.05
11 23 0.36
12 15 0.23
13 23 0.36
ACGTcount: A:0.30, C:0.01, G:0.37, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:89740 original size:35 final size:35
Alignment explanation
Indices: 89693--89795 Score: 179
Period size: 35 Copynumber: 2.9 Consensus size: 35
89683 ATTTAGAAGT
*
89693 TGGTGATAATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
89728 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATATGGTGATGGAATA
*
89763 TGGTGATGATATAGGTGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGAT-ATGGTGATGGA
89796 TAGATTGTAT
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 54 0.83
36 11 0.17
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (35 bp):
TGGTGATGATATAGGCGTGATATGGTGATGGAATA
Found at i:89783 original size:11 final size:12
Alignment explanation
Indices: 89694--89793 Score: 72
Period size: 11 Copynumber: 8.6 Consensus size: 12
89684 TTTAGAAGTT
*
89694 GGTGATAATATA
1 GGTGATGATATA
*
89706 GGCG-TGATAT-
1 GGTGATGATATA
89716 GGTGATGGA-ATA
1 GGTGAT-GATATA
89728 TGGTGATGATATA
1 -GGTGATGATATA
*
89741 GGCG-TGATAT-
1 GGTGATGATATA
89751 GGTGATGGA-ATA
1 GGTGAT-GATATA
89763 TGGTGATGATATA
1 -GGTGATGATATA
89776 GGTG-TGATA-A
1 GGTGATGATATA
89786 TGGTGATG
1 -GGTGATG
89794 GATAGATTGT
Statistics
Matches: 71, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
10 7 0.10
11 26 0.37
12 20 0.28
13 18 0.25
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.32
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:92851 original size:24 final size:21
Alignment explanation
Indices: 92816--92858 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
92806 GGCTCATTCT
*
92816 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
92839 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
92859 ATCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:94116 original size:23 final size:24
Alignment explanation
Indices: 94074--94126 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
94064 TTTCTTTCTT
94074 TTTCTTCTTTTCGAGTGCTTTCAA
1 TTTCTTCTTTTCGAGTGCTTTCAA
* *
94098 TTTCTTCTTTT-GAGTGCTTTTAT
1 TTTCTTCTTTTCGAGTGCTTTCAA
94121 TTTCTT
1 TTTCTT
94127 TGCTGATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (24 bp):
TTTCTTCTTTTCGAGTGCTTTCAA
Found at i:95632 original size:36 final size:36
Alignment explanation
Indices: 95581--95685 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
95571 GATACAATCT
*
95581 GTCCATCACCATTATCACTCCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
*
95617 GTCTATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
* * *
95653 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACACCTATATCATCACCA
95686 ACTTATAAAT
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 20 0.32
36 43 0.68
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACACCTATATCATCACCATA
Found at i:95643 original size:11 final size:11
Alignment explanation
Indices: 95584--95668 Score: 75
Period size: 11 Copynumber: 7.2 Consensus size: 11
95574 ACAATCTGTC
95584 CATCACCATTAT
1 CATCACCA-TAT
*
95596 CACTC-CTATAT
1 CA-TCACCATAT
95607 CATCACCATAGT
1 CATCACCATA-T
95619 CTATCACCATTAT
1 C-ATCACCA-TAT
95632 CA-CACCTATAT
1 CATCACC-ATAT
95643 CATCACCATATT
1 CATCACCATA-T
95655 CCATCACCATAT
1 -CATCACCATAT
95667 CA
1 CA
95669 CGCCTATATT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
10 2 0.03
11 23 0.37
12 14 0.23
13 21 0.34
14 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.01, T:0.31
Consensus pattern (11 bp):
CATCACCATAT
Found at i:98096 original size:16 final size:16
Alignment explanation
Indices: 98075--98106 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
98065 TAGTTAGCTC
98075 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
98091 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
98107 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:101400 original size:19 final size:20
Alignment explanation
Indices: 101359--101409 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
101349 GAAACCCCTT
*
101359 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
101379 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
101398 TGAAGATACATG
1 TGAAAATACATG
101410 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:103462 original size:16 final size:16
Alignment explanation
Indices: 103441--103472 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
103431 TAGTTAGCTC
103441 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
103457 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
103473 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:106655 original size:36 final size:36
Alignment explanation
Indices: 106596--106700 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
106586 GATACAATTT
*
106596 GTCCATCACCATTATCACTCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
106632 GTCTATCACCATTATAACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
106668 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
106701 ACTTATAAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 19 0.32
36 41 0.68
ACGTcount: A:0.31, C:0.33, G:0.04, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:114963 original size:19 final size:21
Alignment explanation
Indices: 114920--114971 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
114910 GAAACCCCTT
114920 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
114941 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
114960 TGAAGATACATG
1 TGAAAATACATG
114972 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:119039 original size:19 final size:21
Alignment explanation
Indices: 118996--119047 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
118986 GAAACCCCTT
118996 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
119017 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
119036 TGAAGATACATG
1 TGAAAATACATG
119048 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:120961 original size:24 final size:21
Alignment explanation
Indices: 120927--120969 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
120917 TGCACAAGAT
*
120927 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
120949 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
120970 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:124851 original size:24 final size:21
Alignment explanation
Indices: 124817--124859 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
124807 TGCACAAGAT
*
124817 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
124839 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
124860 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:135757 original size:16 final size:15
Alignment explanation
Indices: 135719--135757 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
135709 TAAGATTAGA
135719 ATAAATAAACAAAAG
1 ATAAATAAACAAAAG
**
135734 ATAAATAAACGGAAG
1 ATAAATAAACAAAAG
135749 ATGAAATAA
1 AT-AAATAA
135758 GATAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.67, C:0.05, G:0.13, T:0.15
Consensus pattern (15 bp):
ATAAATAAACAAAAG
Done.