Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004142.1 Hibiscus syriacus cultivar Beakdansim tig00009056_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: 137872
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4219 original size:19 final size:19
Alignment explanation
Indices: 4183--4221 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4173 AGGTAATAAT
4183 ATAAGTAATGAAATAAATA
1 ATAAGTAATGAAATAAATA
4202 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAT-AAATA
4221 A
1 A
4222 ATAAAAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.64, C:0.00, G:0.13, T:0.23
Consensus pattern (19 bp):
ATAAGTAATGAAATAAATA
Found at i:9452 original size:5 final size:5
Alignment explanation
Indices: 9442--9496 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
9432 GAACTTCTCT
9442 TTTTC TTTTC TTTTC TTCTT- TTCTTC TTTTC TTCTT- TTTGTC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC TT-TTC TTTTC TT-TTC TTT-TC TTTTC
9489 -TTTC TTTT
1 TTTTC TTTT
9497 TGTACTCCAA
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
4 5 0.11
5 30 0.68
6 9 0.20
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:9460 original size:8 final size:8
Alignment explanation
Indices: 9449--9496 Score: 71
Period size: 8 Copynumber: 5.9 Consensus size: 8
9439 TCTTTTTCTT
9449 TTCTTTTC
1 TTCTTTTC
9457 TTCTTTTC
1 TTCTTTTC
9465 TTCTTTTC
1 TTCTTTTC
9473 TTCTTTT-
1 TTCTTTTC
9480 TGTCTTTTC
1 T-TCTTTTC
9489 TTTCTTTT
1 -TTCTTTT
9497 TGTACTCCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
7 1 0.03
8 29 0.78
9 6 0.16
10 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:14906 original size:14 final size:14
Alignment explanation
Indices: 14889--14923 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
14879 TTTATTTCTT
14889 TTCTTTTCT-TTTTC
1 TTCTTTT-TGTTTTC
14903 TTCTTTTTGTTTTC
1 TTCTTTTTGTTTTC
14917 TTCTTTT
1 TTCTTTT
14924 GGAGTGCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 1 0.05
14 19 0.95
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.80
Consensus pattern (14 bp):
TTCTTTTTGTTTTC
Found at i:17801 original size:23 final size:23
Alignment explanation
Indices: 17775--17819 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
17765 CGAAGAGATG
*
17775 TTCATCAAAATCAGAA-TGACCAC
1 TTCAGCAAAATCA-AAGTGACCAC
*
17798 TTCAGCAACATCAAAGTGACCA
1 TTCAGCAAAATCAAAGTGACCA
17820 TTCTTCCATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (23 bp):
TTCAGCAAAATCAAAGTGACCAC
Found at i:34452 original size:23 final size:25
Alignment explanation
Indices: 34426--34477 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
34416 GGATAATTCA
*
34426 ATGGTTAA-GGAATGGTGAT-GAAT
1 ATGGTTAATGGAATGGTGATAGAAG
*
34449 ATGG-TAATGGGATGGTGATAGAAG
1 ATGGTTAATGGAATGGTGATAGAAG
34473 ATGGT
1 ATGGT
34478 GATGTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
22 3 0.12
23 14 0.58
24 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.29
Consensus pattern (25 bp):
ATGGTTAATGGAATGGTGATAGAAG
Found at i:34892 original size:19 final size:20
Alignment explanation
Indices: 34854--34896 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
34844 GAAACCACTT
*
34854 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
34874 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
34893 TGAA
1 TGAA
34897 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:37455 original size:32 final size:32
Alignment explanation
Indices: 37394--37455 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 32
37384 GCAAAATTAA
*
37394 AAGAAAGAAATGATGAAAATGGAATATGGAGG
1 AAGAAAGAAATGATGAAAAAGGAATATGGAGG
37426 AAGAAAGGAAATGAT-AAGAAAGGAA-ATGGA
1 AAGAAA-GAAATGATGAA-AAAGGAATATGGA
37456 TAGAAATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.56, C:0.00, G:0.31, T:0.13
Consensus pattern (32 bp):
AAGAAAGAAATGATGAAAAAGGAATATGGAGG
Found at i:38046 original size:19 final size:20
Alignment explanation
Indices: 38008--38050 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
37998 GAAACCCCTT
*
38008 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
38028 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
38047 TGAA
1 TGAA
38051 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:45305 original size:85 final size:85
Alignment explanation
Indices: 45155--45324 Score: 306
Period size: 85 Copynumber: 2.0 Consensus size: 85
45145 GAGTTATTAC
45155 TTCTTCCTTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAAATTGGCA
1 TTCTTCCTTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAAATTGGCA
45220 TCGAATCTGAAACATTAAAG
66 TCGAATCTGAAACATTAAAG
*
45240 TTCTTCCTTTGATGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTC-AAAAAAATTCGGC
1 TTCTTCCTTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAAATT-GGC
*
45304 ATCGAGTCTGAAACATTAAAG
65 ATCGAATCTGAAACATTAAAG
45325 GGAGTAACAT
Statistics
Matches: 82, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
84 9 0.11
85 73 0.89
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (85 bp):
TTCTTCCTTTGACGTGATCCTTGTGATGCATGTATCATCCTCCCTTTCTTCAAAAAAAATTGGCA
TCGAATCTGAAACATTAAAG
Found at i:50901 original size:33 final size:33
Alignment explanation
Indices: 50859--50927 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
50849 GTTGATGAAT
*
50859 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
50892 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
50925 GAA
1 GAA
50928 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:50932 original size:13 final size:12
Alignment explanation
Indices: 50913--51009 Score: 62
Period size: 13 Copynumber: 8.0 Consensus size: 12
50903 TTATTGGCGT
50913 GATATGGTGATG
1 GATATGGTGATG
50925 GAATATGGTGAT-
1 G-ATATGGTGATG
*
50937 GATATAGGCG-T-
1 GATAT-GGTGATG
50948 GATAATGGTGATG
1 GAT-ATGGTGATG
50961 GACTATGGTGAT-
1 GA-TATGGTGATG
*
50973 GATATAGGCG-T-
1 GATAT-GGTGATG
*
50984 GATAATGGAGATG
1 GAT-ATGGTGATG
50997 GATTATGGTGATG
1 GA-TATGGTGATG
51010 AAAATAGTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 21
0.73 0.05 0.22
Matches are distributed among these distances:
11 21 0.30
12 16 0.23
13 30 0.43
14 2 0.03
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.31
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:50968 original size:36 final size:36
Alignment explanation
Indices: 50898--51010 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
50888 AATGGAAGGA
* *
50898 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
50933 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* *
50969 TGATGATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
51005 TGATGA
1 TGATGA
51011 AAATAGTATC
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 16 0.22
36 56 0.78
ACGTcount: A:0.27, C:0.04, G:0.36, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:54978 original size:35 final size:36
Alignment explanation
Indices: 54903--54978 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
54893 ATACTATTTT
* * *
54903 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
*
54939 CATCACCATATTCCATCACCA-TATCACGCCAATAA
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
54974 CATCA
1 CATCA
54979 TCCTTCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 17 0.47
36 19 0.53
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (36 bp):
CATCACCATAATCCATCACCATTATCACGCCAATAA
Found at i:54993 original size:33 final size:33
Alignment explanation
Indices: 54949--55017 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
54939 CATCACCATA
*
54949 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
54982 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
55015 TTC
1 TTC
55018 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:57634 original size:11 final size:11
Alignment explanation
Indices: 57612--57646 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
57602 CAAAAGCAAC
57612 AAAAAGAA-AA
1 AAAAAGAAGAA
57622 AAAAAGAAGAA
1 AAAAAGAAGAA
57633 AAAAAGAGAGAA
1 AAAAAGA-AGAA
57645 AA
1 AA
57647 GACTCCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 8 0.35
11 9 0.39
12 6 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:61608 original size:35 final size:36
Alignment explanation
Indices: 61533--61608 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
61523 ATACTATTTT
* * *
61533 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
*
61569 CATCACCATATTCCATCACCA-TATCACGCCAATAA
1 CATCACCATAATCCATCACCATTATCACGCCAATAA
61604 CATCA
1 CATCA
61609 TCCTTCCATT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 17 0.47
36 19 0.53
ACGTcount: A:0.34, C:0.37, G:0.03, T:0.26
Consensus pattern (36 bp):
CATCACCATAATCCATCACCATTATCACGCCAATAA
Found at i:61623 original size:33 final size:33
Alignment explanation
Indices: 61579--61647 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
61569 CATCACCATA
*
61579 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
61612 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
61645 TTC
1 TTC
61648 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:64261 original size:2 final size:2
Alignment explanation
Indices: 64254--64278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
64244 TGGTAGCAGA
64254 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 A
64279 ATGGTGATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78929 original size:45 final size:45
Alignment explanation
Indices: 78879--78982 Score: 181
Period size: 45 Copynumber: 2.3 Consensus size: 45
78869 TTATGGACGA
*
78879 GCATTCACTTTCATAACAGCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
78924 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
* *
78969 ACATTAACATTCAT
1 GCATTCACATTCAT
78983 GTCAGCATAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (45 bp):
GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
Found at i:78962 original size:22 final size:22
Alignment explanation
Indices: 78892--78962 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
78882 TTCACTTTCA
78892 TAACAGCATGTTATCATTTTGT
1 TAACAGCATGTTATCATTTTGT
* * * ** **
78914 TAAC-TCACGTGCATTCACATTCA
1 TAACAGCATGT-TA-TCATTTTGT
78937 TAACAGCATGTTATCATTTTGT
1 TAACAGCATGTTATCATTTTGT
78959 TAAC
1 TAAC
78963 TCACGTACAT
Statistics
Matches: 32, Mismatches: 14, Indels: 6
0.62 0.27 0.12
Matches are distributed among these distances:
21 4 0.12
22 14 0.44
23 10 0.31
24 4 0.12
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (22 bp):
TAACAGCATGTTATCATTTTGT
Found at i:79559 original size:35 final size:35
Alignment explanation
Indices: 79475--79576 Score: 152
Period size: 34 Copynumber: 2.9 Consensus size: 35
79465 ATGGTAAGGG
*
79475 AATGGTGATGATATAGGCGTGAAATGGTGATAGAA
1 AATGGTGATGATATAGGCGTGAAATGGTGATGGAA
* * *
79510 GAT-GTGATGATATAGGCATGCAATGGTGATGGAA
1 AATGGTGATGATATAGGCGTGAAATGGTGATGGAA
79544 AATGGTGATGATATAGGCGTGAAAATGGTGATG
1 AATGGTGATGATATAGGCGTG-AAATGGTGATG
79577 AACAGATAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
34 30 0.52
35 18 0.31
36 10 0.17
ACGTcount: A:0.34, C:0.04, G:0.35, T:0.26
Consensus pattern (35 bp):
AATGGTGATGATATAGGCGTGAAATGGTGATGGAA
Found at i:83401 original size:35 final size:35
Alignment explanation
Indices: 83362--83471 Score: 88
Period size: 35 Copynumber: 3.1 Consensus size: 35
83352 TGATTTAATA
83362 GTGAATAGATGGTAAGGAATGGTGATGATATAGGC
1 GTGAATAGATGGTAAGGAATGGTGATGATATAGGC
* *
83397 GTG-A-A-ATGGTGATAGAAGATGGTGATGATATAGGA
1 GTGAATAGATGGT-A-AGGA-ATGGTGATGATATAGGC
* *
83432 ATGCAATGGTGATGG-AA-GAA-GGTGATGATATAGGC
1 GTG-AAT--AGATGGTAAGGAATGGTGATGATATAGGC
83467 GTGAA
1 GTGAA
83472 AATGGTGATG
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
32 5 0.08
33 2 0.03
34 6 0.10
35 37 0.63
36 1 0.02
37 2 0.03
38 1 0.02
39 1 0.02
41 4 0.07
ACGTcount: A:0.35, C:0.03, G:0.37, T:0.25
Consensus pattern (35 bp):
GTGAATAGATGGTAAGGAATGGTGATGATATAGGC
Found at i:85383 original size:19 final size:20
Alignment explanation
Indices: 85336--85386 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
85326 GAAATCCCTT
**
85336 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
85356 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
85375 TGAAGATACATG
1 TGAAAATACATG
85387 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:89358 original size:19 final size:20
Alignment explanation
Indices: 89311--89361 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
89301 GAAATCCCTT
**
89311 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
89331 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
89350 TGAAGATACATG
1 TGAAAATACATG
89362 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:96335 original size:13 final size:13
Alignment explanation
Indices: 96319--96378 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
96309 TTTTTGGCTC
96319 TTTTTTTG-TTTT
1 TTTTTTTGTTTTT
**
96331 TTTTTTTGCCTTT
1 TTTTTTTGTTTTT
96344 TTTTTTTGTCTTTT
1 TTTTTTTGT-TTTT
*
96358 TTGTTTTT-TTTTG
1 TT-TTTTTGTTTTT
96371 TTTTTTTG
1 TTTTTTTG
96379 AGAAAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 13 0.32
13 16 0.40
14 6 0.15
15 5 0.12
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTT
Found at i:96364 original size:19 final size:18
Alignment explanation
Indices: 96342--96378 Score: 65
Period size: 19 Copynumber: 2.0 Consensus size: 18
96332 TTTTTTGCCT
96342 TTTTTTTTTGTCTTTTTTG
1 TTTTTTTTTGT-TTTTTTG
96361 TTTTTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTTTTTG
96379 AGAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.00, C:0.03, G:0.11, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTGTTTTTTTG
Found at i:111093 original size:24 final size:21
Alignment explanation
Indices: 111059--111101 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
111049 TCCACAAGAT
*
111059 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
111081 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
111102 ATAATGAGCC
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:114058 original size:15 final size:15
Alignment explanation
Indices: 114038--114070 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
114028 GGACTCCAAT
*
114038 GCTAGCTTTAGGTCA
1 GCTAGCTTTAAGTCA
114053 GCTAGCTTTAAGTCA
1 GCTAGCTTTAAGTCA
114068 GCT
1 GCT
114071 CCCATCATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.33
Consensus pattern (15 bp):
GCTAGCTTTAAGTCA
Found at i:119604 original size:45 final size:45
Alignment explanation
Indices: 119554--119657 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
119544 TTATGGACGA
* *
119554 GCATTCACTTTCATAACAGCATGTTATCATTTTGTTAACTCAAGT
1 GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
* *
119599 GCATTCACATTCATAACAACCTGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
*
119644 ACATTCACATTCAT
1 GCATTCACATTCAT
119658 GTCAGCATAC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (45 bp):
GCATTCACATTCATAACAACATGTTATCATTTTGTTAACTCAAGT
Found at i:122583 original size:11 final size:11
Alignment explanation
Indices: 122569--122620 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
122559 TTTGTTTTTC
*
122569 AAAAAAAA-TA
1 AAAAAAAACAA
*
122579 AAAAAACACAA
1 AAAAAAAACAA
*
122590 AAAAAAAGCAA
1 AAAAAAAACAA
122601 AAAAAAAAGCCAA
1 AAAAAAAA--CAA
122614 AAAAAAA
1 AAAAAAA
122621 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 7 0.21
11 17 0.50
13 10 0.29
ACGTcount: A:0.85, C:0.10, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:122596 original size:13 final size:13
Alignment explanation
Indices: 122578--122627 Score: 72
Period size: 12 Copynumber: 4.2 Consensus size: 13
122568 CAAAAAAAAT
122578 AAAAAAA-CACAA
1 AAAAAAAGCACAA
122590 AAAAAAAGCA-AA
1 AAAAAAAGCACAA
122602 AAAAAAAGC-CAA
1 AAAAAAAGCACAA
122614 AAAAAAAGC-CAA
1 AAAAAAAGCACAA
122626 AA
1 AA
122628 TTTCAAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 34 0.94
13 2 0.06
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (13 bp):
AAAAAAAGCACAA
Found at i:130725 original size:45 final size:45
Alignment explanation
Indices: 130667--130770 Score: 172
Period size: 45 Copynumber: 2.3 Consensus size: 45
130657 TTATGGACGA
* *
130667 GCATTCACTTTCATAACATCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
130712 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
1 GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
* *
130757 ACATTAACATTCAT
1 GCATTCACATTCAT
130771 GTCAGCATAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 55 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
GCATTCACATTCATAACAGCATGTTATCATTTTGTTAACTCACGT
Found at i:131307 original size:34 final size:35
Alignment explanation
Indices: 131261--131375 Score: 162
Period size: 34 Copynumber: 3.3 Consensus size: 35
131251 TGGTAAGGGA
131261 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
* * * *
131296 AT-GTGATGATATAGGCATGCAATGGTGATGGAAA
1 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
131330 ATGGTGATGATATAGGCGTGAAAATGGTGATCA-AAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGAT-AGAAG
131366 ATGGTGATGA
1 ATGGTGATGA
131376 ACAGATATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
34 30 0.43
35 18 0.26
36 21 0.30
ACGTcount: A:0.35, C:0.04, G:0.35, T:0.26
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
Found at i:131736 original size:19 final size:19
Alignment explanation
Indices: 131712--131752 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
131702 GAAACCCCTT
*
131712 TGAAAACACATGATTTTAA
1 TGAAAACACATAATTTTAA
*
131731 TGAAAATACATAATTTTAA
1 TGAAAACACATAATTTTAA
131750 TGA
1 TGA
131753 GATAAATGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.10, T:0.34
Consensus pattern (19 bp):
TGAAAACACATAATTTTAA
Found at i:134682 original size:12 final size:11
Alignment explanation
Indices: 134648--134694 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
134638 ACTTTCTTCA
134648 CTTTTCTTTTT
1 CTTTTCTTTTT
134659 CTTTGAAT-TTTTT
1 CTTT---TCTTTTT
134672 CTTATTCTTTTT
1 CTT-TTCTTTTT
134684 CTTTTCTTTTT
1 CTTTTCTTTTT
134695 TGCACTCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
11 13 0.42
12 8 0.26
13 8 0.26
14 2 0.06
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (11 bp):
CTTTTCTTTTT
Found at i:135167 original size:35 final size:35
Alignment explanation
Indices: 135122--135235 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
135112 TGGTAAGGGA
*
135122 ATGGTGATGATATAGGCGTGAAATGGTGATAGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
** *
135157 ATGGTGATGATATAGGAATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
* *
135192 AAGGTGATG--ATAGGCGTGAAAATGGTTATGGAAG
1 ATGGTGATGATATAGGCGTG-AAATGGTGATGGAAG
135226 ATGGTGATGA
1 ATGGTGATGA
135236 ACATATAGTA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
33 7 0.10
34 21 0.31
35 39 0.58
ACGTcount: A:0.34, C:0.03, G:0.38, T:0.25
Consensus pattern (35 bp):
ATGGTGATGATATAGGCGTGAAATGGTGATGGAAG
Done.