Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008276.1 Hibiscus syriacus cultivar Beakdansim tig00110934_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: 133379
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1062 original size:12 final size:12
Alignment explanation
Indices: 1047--1091 Score: 63
Period size: 12 Copynumber: 3.6 Consensus size: 12
1037 CGGTTTTTTT
*
1047 ACCGGATAAAAA
1 ACCGGTTAAAAA
1059 ACCGGTTTGAAAAA
1 ACCGG-TT-AAAAA
1073 ACCGGTTAAAAA
1 ACCGGTTAAAAA
1085 ACCGGTT
1 ACCGGTT
1092 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 17 0.57
13 3 0.10
14 10 0.33
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:1073 original size:14 final size:13
Alignment explanation
Indices: 1053--1092 Score: 64
Period size: 12 Copynumber: 3.1 Consensus size: 13
1043 TTTTACCGGA
1053 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1066 TGAAAAAACCGG-T
1 T-AAAAAACCGGTT
1079 TAAAAAACCGGTT
1 TAAAAAACCGGTT
1092 T
1 T
1093 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 10 0.40
13 5 0.20
14 10 0.40
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.23
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:3379 original size:21 final size:21
Alignment explanation
Indices: 3355--3394 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3345 TTTATTTTAT
3355 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
3376 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
3395 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:3442 original size:33 final size:33
Alignment explanation
Indices: 3389--3487 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
3379 TTTGTTTCAA
3389 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3421 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
3454 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
3487 T
1 T
3488 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:3516 original size:13 final size:13
Alignment explanation
Indices: 3473--3528 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
3463 TTGGAAGTAT
3473 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
3486 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
3500 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
3513 TTAAGTATTTGAA
1 TTAAGTATTTCAA
3526 TTA
1 TTA
3529 TCGAACTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 22 0.63
14 7 0.20
15 3 0.09
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:3945 original size:15 final size:15
Alignment explanation
Indices: 3920--3975 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
3910 ATCTGGAATA
*
3920 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
3935 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
3950 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
3967 TTAAAACCG
1 TTAAAACCG
3976 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 21 0.62
17 13 0.38
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.43
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:3984 original size:21 final size:18
Alignment explanation
Indices: 3939--3972 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3929 GTTTTTTTAT
3939 AACCGG-TTTTTTAAAAA
1 AACCGGTTTTTTTAAAAA
3956 AACCGGTTTTTTTAAAA
1 AACCGGTTTTTTTAAAA
3973 CCGAAACCGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (18 bp):
AACCGGTTTTTTTAAAAA
Found at i:5172 original size:23 final size:23
Alignment explanation
Indices: 5127--5172 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5117 ACAATGATTT
5127 TTTAATAAAAAATAATTTCTAAA
1 TTTAATAAAAAATAATTTCTAAA
*
5150 TTTAATATTAAAATAATTT-TAAA
1 TTTAATA-AAAAATAATTTCTAAA
5173 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTAATAAAAAATAATTTCTAAA
Found at i:12147 original size:85 final size:85
Alignment explanation
Indices: 12004--12173 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 85
11994 GTATTGGAAT
*
12004 TTGTACAAGGTAAGAAGATGAACTTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
1 TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
12069 CCCAAGAATTGAGACTTTTA
66 CCCAAGAATTGAGACTTTTA
*
12089 TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGGGCTGATGTATTAATAGATAATGGATGGT
1 TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
12154 CCCAAGAATTGAGACTTTTA
66 CCCAAGAATTGAGACTTTTA
12174 GATTTACTTT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.34
Consensus pattern (85 bp):
TTGTACAAGGTAAGAAGATGAACGTTTAATTGTATGAGCTGATGTATTAATAGATAATGGATGGT
CCCAAGAATTGAGACTTTTA
Found at i:14533 original size:22 final size:22
Alignment explanation
Indices: 14508--14557 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
14498 AATGGAACGA
* *
14508 TTCAGCGCCGAATGTTGAACCG
1 TTCAACGCCGAATGCTGAACCG
**
14530 TTCAACGTTGAATGCTGAACCG
1 TTCAACGCCGAATGCTGAACCG
14552 TTCAAC
1 TTCAAC
14558 ATTCAGCGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (22 bp):
TTCAACGCCGAATGCTGAACCG
Found at i:14854 original size:17 final size:17
Alignment explanation
Indices: 14832--14865 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
14822 TTCATACAGA
14832 GCCATTGAATCATTCAG
1 GCCATTGAATCATTCAG
14849 GCCATTGAATCATTCAG
1 GCCATTGAATCATTCAG
14866 TGCTTAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (17 bp):
GCCATTGAATCATTCAG
Found at i:25650 original size:20 final size:20
Alignment explanation
Indices: 25625--25666 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
25615 CGTGAAGTGA
25625 AACAAGCCCAAGAAATAAGG
1 AACAAGCCCAAGAAATAAGG
25645 AACAAGCCCAAGAAATAAGG
1 AACAAGCCCAAGAAATAAGG
25665 AA
1 AA
25667 TAAACTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.57, C:0.19, G:0.19, T:0.05
Consensus pattern (20 bp):
AACAAGCCCAAGAAATAAGG
Found at i:28675 original size:2 final size:2
Alignment explanation
Indices: 28668--28698 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
28658 ACCATAAACT
28668 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 T
28699 TATGGACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30998 original size:29 final size:29
Alignment explanation
Indices: 30966--31035 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 29
30956 GTAATTAATA
**
30966 TAATTAATAATATAATATTATTATTATTT
1 TAATTAATAATATAATAAAATTATTATTT
* * *
30995 TAATAAATAAT-TTATAAAATTTTTATTT
1 TAATTAATAATATAATAAAATTATTATTT
31023 TAA-TAA-AATATAA
1 TAATTAATAATATAA
31036 GTCTTAACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
26 3 0.09
27 4 0.12
28 16 0.48
29 10 0.30
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (29 bp):
TAATTAATAATATAATAAAATTATTATTT
Found at i:31027 original size:45 final size:45
Alignment explanation
Indices: 30921--31028 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 45
30911 TTAATAGTAT
* * *
30921 AATTTTTAATTATAATAACATTCTTATTTTAATAAGTAATTAATAT
1 AATTTTT-ATTATAATAACATTATTATTTTAATAAATAATTAATAA
** * ** *
30967 AATTAATAATATAATATTATTATTATTTTAATAAATAATTTATAA
1 AATTTTTATTATAATAACATTATTATTTTAATAAATAATTAATAA
*
31012 AATTTTTATTTTAATAA
1 AATTTTTATTATAATAA
31029 AATATAAGTC
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
45 43 0.90
46 5 0.10
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (45 bp):
AATTTTTATTATAATAACATTATTATTTTAATAAATAATTAATAA
Found at i:31289 original size:14 final size:14
Alignment explanation
Indices: 31270--31308 Score: 62
Period size: 14 Copynumber: 2.8 Consensus size: 14
31260 CAGGAAATGT
31270 AATTCATTTTACTA-
1 AATTCATTTT-CTAG
31284 AATTCATTTTCTAG
1 AATTCATTTTCTAG
31298 AATTCATTTTC
1 AATTCATTTTC
31309 CGTGAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.31, C:0.15, G:0.03, T:0.51
Consensus pattern (14 bp):
AATTCATTTTCTAG
Found at i:35800 original size:26 final size:24
Alignment explanation
Indices: 35738--35800 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
35728 CATTTTAATC
35738 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
35762 AAAATATAT-TTATTAATAT-TTCT
1 AAAATATATATTATTAAAATATT-T
35785 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
35801 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:35802 original size:22 final size:23
Alignment explanation
Indices: 35772--35818 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
35762 AAAATATATT
35772 TATTAATATTTCTAATAATATAA
1 TATTAATATTTCTAATAATATAA
* *
35795 TATT-ATATTTTTAATATTATAA
1 TATTAATATTTCTAATAATATAA
35817 TA
1 TA
35819 AATAATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAATATTTCTAATAATATAA
Found at i:35811 original size:31 final size:31
Alignment explanation
Indices: 35766--35882 Score: 91
Period size: 30 Copynumber: 3.8 Consensus size: 31
35756 ATATTTAAAA
*
35766 TATATTTATTAATATTTCTAATAATATAAT-AT
1 TATATTTATTAATA-TTATAATAA-ATAATAAT
35798 TATATTT-TTAATATTATAATAAATAATCAAT
1 TATATTTATTAATATTATAATAAATAAT-AAT
* * * * *
35829 TATA-TTA-TAATAATATAAGATATTATATT
1 TATATTTATTAATATTATAATAAATAATAAT
* *
35858 TTTATTTTAATAATA-TATAATAAAT
1 TATA-TTTATTAATATTATAATAAAT
35883 TATTAGTAAA
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
29 10 0.14
30 25 0.36
31 23 0.33
32 12 0.17
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (31 bp):
TATATTTATTAATATTATAATAAATAATAAT
Found at i:35871 original size:54 final size:52
Alignment explanation
Indices: 35784--35885 Score: 143
Period size: 54 Copynumber: 1.9 Consensus size: 52
35774 TTAATATTTC
*
35784 TAATAATATAATATTATATTTTTAATATTATAATAAATAATCAATTATATTA
1 TAATAATATAATATTATATTTTTAATATTATAATAAATAATAAATTATATTA
* *
35836 TAATAATATAAGATATTATATTTTT-ATTTTAATAATATATAATAAATTAT
1 TAATAATAT-A-ATATTATATTTTTAATATT-ATAATAAATAATAAATTAT
35886 TAGTAAAATT
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
52 9 0.20
53 5 0.11
54 30 0.68
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (52 bp):
TAATAATATAATATTATATTTTTAATATTATAATAAATAATAAATTATATTA
Found at i:35959 original size:19 final size:18
Alignment explanation
Indices: 35935--36003 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 18
35925 TATTATTTAA
35935 ATTATTAATAATGAATAAT
1 ATTATTAATAAT-AATAAT
* *
35954 ATTATTTAT-ATATTTAAT
1 ATTATTAATAATA-ATAAT
35972 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAA--TAATAAT
35994 ATT-TTAATAA
1 ATTATTAATAA
36004 AGATATTTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
17 1 0.03
18 9 0.22
19 16 0.40
20 4 0.10
21 1 0.03
22 7 0.17
23 2 0.05
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
ATTATTAATAATAATAAT
Found at i:36024 original size:23 final size:23
Alignment explanation
Indices: 35998--36042 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
35988 AATAATATTT
35998 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* *
36021 TAATTAAGATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
36043 ATATAATATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:39846 original size:29 final size:29
Alignment explanation
Indices: 39811--39892 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
39801 AAACTAAATT
*
39811 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
39840 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
39869 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
39893 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:44605 original size:29 final size:29
Alignment explanation
Indices: 44570--44651 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
44560 AAACTAAATT
*
44570 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
44599 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
44628 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
44652 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:48449 original size:22 final size:22
Alignment explanation
Indices: 48424--48467 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
48414 TATGTTATCA
48424 TATATTTACTCCAAAATTATAT
1 TATATTTACTCCAAAATTATAT
48446 TATATTTACTCCAAAATTATAT
1 TATATTTACTCCAAAATTATAT
48468 AAGTTTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATTTACTCCAAAATTATAT
Found at i:57818 original size:15 final size:16
Alignment explanation
Indices: 57798--57833 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
57788 ATTCAAAGCC
57798 ATAATATA-TTTGCTT
1 ATAATATAGTTTGCTT
*
57813 ATAATATAGTTTTCTT
1 ATAATATAGTTTGCTT
57829 ATAAT
1 ATAAT
57834 TTTTTATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (16 bp):
ATAATATAGTTTGCTT
Found at i:58733 original size:2 final size:2
Alignment explanation
Indices: 58728--58759 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
58718 ACACACACAC
58728 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
58760 TTGAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59862 original size:19 final size:19
Alignment explanation
Indices: 59846--59883 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
59836 TTTAATATGC
59846 ATAT-ATAAGTATAATATA
1 ATATGATAAGTATAATATA
*
59864 ATATGATATGTATAATATA
1 ATATGATAAGTATAATATA
59883 A
1 A
59884 AAATATGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (19 bp):
ATATGATAAGTATAATATA
Found at i:59882 original size:24 final size:24
Alignment explanation
Indices: 59822--59891 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
59812 TATAAATACA
* *
59822 ATGTATAAAATATATTTAATATGCAT
1 ATGTATAATATA-ATATAATATG-AT
59848 A--TATAAGTATAATATAATATGAT
1 ATGTATAA-TATAATATAATATGAT
59871 ATGTATAATATAA-A-AATATGA
1 ATGTATAATATAATATAATATGA
59892 GGGTGACTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 7 0.18
23 4 0.10
24 19 0.49
25 8 0.21
26 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (24 bp):
ATGTATAATATAATATAATATGAT
Found at i:60387 original size:43 final size:42
Alignment explanation
Indices: 60339--60424 Score: 102
Period size: 43 Copynumber: 2.0 Consensus size: 42
60329 AATGAATAAC
* *
60339 TTAGGGACAAAAATTATAAAAGTAAGAA-GTGAGGTTGAAAAAA
1 TTAGGGACAAAAATTATAAAA-TAA-AATGTGAGATTAAAAAAA
***
60382 TTAGGGACCTCAATTATAAAATAAAATGTGAGATTAAAAAAA
1 TTAGGGACAAAAATTATAAAATAAAATGTGAGATTAAAAAAA
60424 T
1 T
60425 CAAGAGCCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.05
42 17 0.46
43 18 0.49
ACGTcount: A:0.52, C:0.05, G:0.19, T:0.24
Consensus pattern (42 bp):
TTAGGGACAAAAATTATAAAATAAAATGTGAGATTAAAAAAA
Found at i:60469 original size:21 final size:21
Alignment explanation
Indices: 60436--60508 Score: 51
Period size: 21 Copynumber: 3.5 Consensus size: 21
60426 AAGAGCCTCG
* *
60436 ATTATAAAGATAGAAAGTGAT
1 ATTAAAAAAATAGAAAGTGAT
* *
60457 ATTAAAAAAATAG-GAGCCTCA-
1 ATTAAAAAAATAGAAAG--TGAT
* * *
60478 ATTATAAAGATAAAAAGTGAT
1 ATTAAAAAAATAGAAAGTGAT
60499 ATTAAAAAAA
1 ATTAAAAAAA
60509 ATTAAATCCT
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
20 4 0.11
21 29 0.78
22 4 0.11
ACGTcount: A:0.58, C:0.04, G:0.14, T:0.25
Consensus pattern (21 bp):
ATTAAAAAAATAGAAAGTGAT
Found at i:60509 original size:43 final size:41
Alignment explanation
Indices: 60350--60508 Score: 176
Period size: 42 Copynumber: 3.8 Consensus size: 41
60340 TAGGGACAAA
* * *
60350 AATTATAAAAGTAAGAAGTGAGGTTGAAAAAATTAGG-GACCTC
1 AATTATAAAA-TAAAAAGTGAGATT-AAAAAAATAGGAG-CCTC
* *
60393 AATTATAAAATAAAATGTGAGATTAAAAAAATCAAGAGCCTC
1 AATTATAAAATAAAAAGTGAGATTAAAAAAAT-AGGAGCCTC
* * *
60435 GATTATAAAGATAGAAAGTGATATTAAAAAAATAGGAGCCTC
1 AATTATAAA-ATAAAAAGTGAGATTAAAAAAATAGGAGCCTC
*
60477 AATTATAAAGATAAAAAGTGATATTAAAAAAA
1 AATTATAAA-ATAAAAAGTGAGATTAAAAAAA
60509 ATTAAATCCT
Statistics
Matches: 101, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 7 0.07
42 63 0.62
43 31 0.31
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.24
Consensus pattern (41 bp):
AATTATAAAATAAAAAGTGAGATTAAAAAAATAGGAGCCTC
Found at i:61066 original size:6 final size:6
Alignment explanation
Indices: 61055--61079 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
61045 TTTGAATATA
61055 TAAAAT TAAAAT TAAAAT TAAAAT T
1 TAAAAT TAAAAT TAAAAT TAAAAT T
61080 TTACTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TAAAAT
Found at i:61068 original size:26 final size:26
Alignment explanation
Indices: 61008--61068 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 26
60998 TAAAATAATT
*
61008 TTAAAATAATATTTTTGAATATATAATA
1 TTAAAAT--TATTTTTGAATATATAAAA
*
61036 TT--TATTATTTTTGAATATATAAAA
1 TTAAAATTATTTTTGAATATATAAAA
61060 TTAAAATTA
1 TTAAAATTA
61069 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 20 0.71
26 6 0.21
28 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (26 bp):
TTAAAATTATTTTTGAATATATAAAA
Found at i:68146 original size:2 final size:2
Alignment explanation
Indices: 68139--68164 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
68129 TATGTATCAC
68139 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
68165 GTTAGCAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68857 original size:63 final size:63
Alignment explanation
Indices: 68766--68943 Score: 250
Period size: 63 Copynumber: 2.8 Consensus size: 63
68756 TAGTCGGGTG
* * *
68766 ATCATTTTGTACACATGACATGTATCATATCATCACTTGTGTACATGTAGCATATGTCACGTT
1 ATCATTTTGTACACATGACATGTGTCATATCATCACTTATGTACATGTAGCATATGTCAAGTT
* * * * *
68829 ATCGTTTTGTACACACGACATGTGTCATACCATCACTTATGTACATGTAGCATGTGTCAATTT
1 ATCATTTTGTACACATGACATGTGTCATATCATCACTTATGTACATGTAGCATATGTCAAGTT
* * *
68892 ATCACTTCGTACACATGACATGTGTCACATCAT-ACTTATGTACATGTAGCAT
1 ATCATTTTGTACACATGACATGTGTCATATCATCACTTATGTACATGTAGCAT
68944 TTACCAATTC
Statistics
Matches: 101, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 19 0.19
63 82 0.81
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (63 bp):
ATCATTTTGTACACATGACATGTGTCATATCATCACTTATGTACATGTAGCATATGTCAAGTT
Found at i:68935 original size:31 final size:32
Alignment explanation
Indices: 68773--68935 Score: 108
Period size: 31 Copynumber: 5.2 Consensus size: 32
68763 GTGATCATTT
* * *
68773 TGTACACATGACATGTATCATATCATCACTTG
1 TGTACACATGACATGTGTCACATCATCACTTA
* * * * *
68805 TGT--ACATGTAGCATATGTCACGTTATC-GTTT
1 TGTACACATG-A-CATGTGTCACATCATCACTTA
* * *
68836 TGTACACACGACATGTGTCATACCATCACTTA
1 TGTACACATGACATGTGTCACATCATCACTTA
*
68868 TGT--ACATGTAGCATGTGTCA-ATTTATCACTT-
1 TGTACACATG-A-CATGTGTCACA-TCATCACTTA
*
68899 CGTACACATGACATGTGTCACATCAT-ACTTA
1 TGTACACATGACATGTGTCACATCATCACTTA
68930 TGTACA
1 TGTACA
68936 TGTAGCATTT
Statistics
Matches: 98, Mismatches: 21, Indels: 25
0.68 0.15 0.17
Matches are distributed among these distances:
30 13 0.13
31 38 0.39
32 38 0.39
33 9 0.09
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (32 bp):
TGTACACATGACATGTGTCACATCATCACTTA
Found at i:69425 original size:53 final size:52
Alignment explanation
Indices: 69347--69453 Score: 162
Period size: 53 Copynumber: 2.0 Consensus size: 52
69337 TAGACTAGAC
*
69347 TTGATACATAAATTTTCTTAAATTAATATCTAGACTTGAAATTT-TCTTAAA
1 TTGATACATAAATTTTCTTAAATTAATATATAGACTTGAAATTTCTCTTAAA
* *
69398 TTGATACATAAATCTTTTCTTAAATTAATATATGGACTTGAAATTTCTTTTAAA
1 TTGATACATAAA--TTTTCTTAAATTAATATATAGACTTGAAATTTCTCTTAAA
69452 TT
1 TT
69454 CATCCATGAT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 12 0.24
53 30 0.60
54 8 0.16
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (52 bp):
TTGATACATAAATTTTCTTAAATTAATATATAGACTTGAAATTTCTCTTAAA
Found at i:77785 original size:69 final size:69
Alignment explanation
Indices: 77702--77851 Score: 174
Period size: 69 Copynumber: 2.2 Consensus size: 69
77692 AACATCGCCG
* * * * * *
77702 CCACCTCCACCACTACCACCGCCAGCTCCATCAAAACCAAATATAGGGGTAACAGCAACAGCACC
1 CCACCACCACCACTACCACCACCAGCGCCAACAAAACCAAATATAGAGGTAACAGCAACAGAACC
*
77767 ACCT
66 ACCA
* * * * * *
77771 CCACCACCATCACTACCACCATCAGCGCCAACAGAGCCAAATATAGAGGTAGCAGCAGCAGAACC
1 CCACCACCACCACTACCACCACCAGCGCCAACAAAACCAAATATAGAGGTAACAGCAACAGAACC
*
77836 TCCA
66 ACCA
77840 CCACCACCACCA
1 CCACCACCACCA
77852 TCAGTGCAAC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.35, C:0.42, G:0.13, T:0.10
Consensus pattern (69 bp):
CCACCACCACCACTACCACCACCAGCGCCAACAAAACCAAATATAGAGGTAACAGCAACAGAACC
ACCA
Found at i:77925 original size:54 final size:55
Alignment explanation
Indices: 77785--78016 Score: 290
Period size: 54 Copynumber: 4.1 Consensus size: 55
77775 CACCATCACT
* *
77785 ACCACCATCAGCGCCAACAGAGCCAAATATAGAGGTAGCAGCAGCAGAACCTCCACCACC
1 ACCACCATCAGCTCCAACAGAGCCAAATATAGAGGTA--A-CAGCAGAACCT-C-CCTCC
* *
77845 ACCACCATCAG-TGCAACCAGAGCCAAACATAGAGGTAACAGCAGAACCT-CCTCC
1 ACCACCATCAGCTCCAA-CAGAGCCAAATATAGAGGTAACAGCAGAACCTCCCTCC
* *
77899 ACCACCATCAGCTCCAACAGGGCCAAATATAGAGGTAACAGCAGCA-CTCCCTCC
1 ACCACCATCAGCTCCAACAGAGCCAAATATAGAGGTAACAGCAGAACCTCCCTCC
* * *
77953 ACCACCAGCAGCTCCAACAGAGCCAAATATAGAGGTAACAGCAGCAGCACTTCCTCC
1 ACCACCATCAGCTCCAACAGAGCCAAATATAGAGGTAACAGCAG-AAC-CTCCCTCC
78010 ACCACCA
1 ACCACCA
78017 CCTCCTGTAG
Statistics
Matches: 153, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
53 2 0.01
54 88 0.58
55 4 0.03
57 25 0.16
58 1 0.01
59 3 0.02
60 30 0.20
ACGTcount: A:0.36, C:0.37, G:0.17, T:0.11
Consensus pattern (55 bp):
ACCACCATCAGCTCCAACAGAGCCAAATATAGAGGTAACAGCAGAACCTCCCTCC
Found at i:80006 original size:29 final size:30
Alignment explanation
Indices: 79973--80038 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
79963 TTTTTCTCAT
* *
79973 TCAATTGAATTTTTAAA-TAAAAAATTAAA
1 TCAATTAAAATTTTAAATTAAAAAATTAAA
* *
80002 TCAATTAAAATTTTAAATTAATAAATTGAA
1 TCAATTAAAATTTTAAATTAAAAAATTAAA
*
80032 TTAATTA
1 TCAATTA
80039 CATCTTTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (30 bp):
TCAATTAAAATTTTAAATTAAAAAATTAAA
Found at i:81096 original size:31 final size:31
Alignment explanation
Indices: 81056--81130 Score: 107
Period size: 31 Copynumber: 2.5 Consensus size: 31
81046 CTGTTTTTAT
*
81056 GCAG-TTGAACAAAGTTGAGAGCACACTAGG
1 GCAGTTTGAACAAAGTTGAAAGCACACTAGG
*
81086 GCAGTTTGAACAAAGTTGAAAGCGCACTAGG
1 GCAGTTTGAACAAAGTTGAAAGCACACTAGG
* *
81117 GAAATTTGAACAAA
1 GCAGTTTGAACAAA
81131 ACTGAAGACG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 4 0.10
31 36 0.90
ACGTcount: A:0.40, C:0.15, G:0.27, T:0.19
Consensus pattern (31 bp):
GCAGTTTGAACAAAGTTGAAAGCACACTAGG
Found at i:81331 original size:16 final size:17
Alignment explanation
Indices: 81312--81359 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 17
81302 TAAAGATTTT
81312 TTTTTTAATTTTAT-GA
1 TTTTTTAATTTTATAGA
81328 TTTTTTAATAATATTATAGA
1 TTTTTTAAT--T-TTATAGA
*
81348 TGTTTTAATTTT
1 TTTTTTAATTTT
81360 TTAAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 9 0.33
17 2 0.07
18 2 0.07
19 4 0.15
20 10 0.37
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTTTAATTTTATAGA
Found at i:81339 original size:19 final size:20
Alignment explanation
Indices: 81317--81356 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
81307 ATTTTTTTTT
* *
81317 TAATTTTAT-GATTTTTTAA
1 TAATATTATAGATGTTTTAA
81336 TAATATTATAGATGTTTTAA
1 TAATATTATAGATGTTTTAA
81356 T
1 T
81357 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.57
Consensus pattern (20 bp):
TAATATTATAGATGTTTTAA
Found at i:87874 original size:16 final size:16
Alignment explanation
Indices: 87833--87877 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
87823 TTTAATTTGA
87833 AATAAATATATTAGAAT
1 AATAAA-ATATTAGAAT
*
87850 AATATAATATTA-AAT
1 AATAAAATATTAGAAT
87865 AATAGAAATATTA
1 AATA-AAATATTA
87878 TTAGCTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.28
16 13 0.52
17 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (16 bp):
AATAAAATATTAGAAT
Found at i:88837 original size:18 final size:19
Alignment explanation
Indices: 88797--88838 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
88787 TTAGTCGAGT
* *
88797 TTAAAGGTTAAATTATTTT
1 TTAAAGGTTAAATGATTTA
*
88816 TTAAA-GTTCAATGATTTA
1 TTAAAGGTTAAATGATTTA
88834 TTAAA
1 TTAAA
88839 TTTAGTGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TTAAAGGTTAAATGATTTA
Found at i:89065 original size:14 final size:14
Alignment explanation
Indices: 89032--89094 Score: 76
Period size: 14 Copynumber: 4.5 Consensus size: 14
89022 ATCTAAAATT
89032 TAAAATA-TAAAAGA
1 TAAAATATTAAAA-A
89046 TAAAATATTAAAAA
1 TAAAATATTAAAAA
89060 -ACAAATATTAAAAA
1 TA-AAATATTAAAAA
*
89074 TAAAAAATTAAAAA
1 TAAAATATTAAAAA
*
89088 TTAAATA
1 TAAAATA
89095 ATTTTTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
13 1 0.02
14 36 0.84
15 6 0.14
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (14 bp):
TAAAATATTAAAAA
Found at i:89089 original size:7 final size:7
Alignment explanation
Indices: 89026--89097 Score: 56
Period size: 7 Copynumber: 9.9 Consensus size: 7
89016 TTTTAAATCT
*
89026 AAAATTT
1 AAAATTA
89033 AAAATATA
1 AAAAT-TA
89041 AAAGA-TA
1 AAA-ATTA
89048 AAATATTA
1 AAA-ATTA
**
89056 AAAAACA
1 AAAATTA
*
89063 AATATTA
1 AAAATTA
*
89070 AAAATAA
1 AAAATTA
89077 AAAATTA
1 AAAATTA
89084 AAAATTA
1 AAAATTA
89091 AATAATT
1 AA-AATT
89098 TTTTTTTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
7 37 0.73
8 13 0.25
9 1 0.02
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:89093 original size:28 final size:30
Alignment explanation
Indices: 89020--89094 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 30
89010 AAATTATTTT
*
89020 AAATCTAAAATTTAAA-ATATAAAAGATAAA
1 AAAT-TAAAAATTAAATATATAAAAGATAAA
* **
89050 ATATTAAAAAACAAATAT-TAAAA-ATAAA
1 AAATTAAAAATTAAATATATAAAAGATAAA
89078 AAATTAAAAATTAAATA
1 AAATTAAAAATTAAATA
89095 ATTTTTTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
28 19 0.51
29 13 0.35
30 5 0.14
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (30 bp):
AAATTAAAAATTAAATATATAAAAGATAAA
Found at i:90449 original size:2 final size:2
Alignment explanation
Indices: 90438--90473 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
90428 TGTAATCTAG
90438 TA TA -A 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
90474 TTAAATAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:105354 original size:31 final size:31
Alignment explanation
Indices: 105299--105359 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
105289 TATAGTTTTC
**
105299 GAATTAAGTTTTAATTTTTTATTTTAAATTA
1 GAATTAAGTTTTAATTTTCGATTTTAAATTA
*
105330 GAATTGAA-TTTTAATTTTCGATTTTGAATT
1 GAATT-AAGTTTTAATTTTCGATTTTAAATT
105360 CCAATCTGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.56
Consensus pattern (31 bp):
GAATTAAGTTTTAATTTTCGATTTTAAATTA
Found at i:108609 original size:21 final size:21
Alignment explanation
Indices: 108585--108637 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
108575 ATCCTCCAAC
* *
108585 TCCTCTTCCTCAAGCTGCTCT
1 TCCTCTTCCTCAACCTCCTCT
* **
108606 TCCTCTTCTTCCTCCTCCTCT
1 TCCTCTTCCTCAACCTCCTCT
108627 TCCTCTTCCTC
1 TCCTCTTCCTC
108638 TTCCTCCAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.04, C:0.49, G:0.04, T:0.43
Consensus pattern (21 bp):
TCCTCTTCCTCAACCTCCTCT
Found at i:108611 original size:6 final size:6
Alignment explanation
Indices: 108612--108643 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
108602 CTCTTCCTCT
*
108612 TCTTCC TCCTCC TCTTCC TCTTCC TCTTCC TC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TC
108644 CAAATCACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (6 bp):
TCTTCC
Found at i:108627 original size:12 final size:12
Alignment explanation
Indices: 108606--108644 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
108596 AAGCTGCTCT
*
108606 TCCTCTTCTTCC
1 TCCTCCTCTTCC
108618 TCCTCCTCTTCC
1 TCCTCCTCTTCC
*
108630 TCTTCCTCTTCC
1 TCCTCCTCTTCC
108642 TCC
1 TCC
108645 AAATCACCCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (12 bp):
TCCTCCTCTTCC
Found at i:108642 original size:21 final size:21
Alignment explanation
Indices: 108602--108644 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
108592 CCTCAAGCTG
*
108602 CTCTTCCTCTTCTTCCTCCTC
1 CTCTTCCTCTTCCTCCTCCTC
*
108623 CTCTTCCTCTTCCTCTTCCTC
1 CTCTTCCTCTTCCTCCTCCTC
108644 C
1 C
108645 AAATCACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (21 bp):
CTCTTCCTCTTCCTCCTCCTC
Found at i:113162 original size:23 final size:25
Alignment explanation
Indices: 113126--113171 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
113116 AAGATTTTAT
113126 TTTAGGAAGATAAATTT-TTAAAAA
1 TTTAGGAAGATAAATTTATTAAAAA
113150 TTTAGG-AGATAAATTTATTAAA
1 TTTAGGAAGATAAATTTATTAAA
113172 TTCTAGGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (25 bp):
TTTAGGAAGATAAATTTATTAAAAA
Found at i:113178 original size:23 final size:22
Alignment explanation
Indices: 113126--113180 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 22
113116 AAGATTTTAT
113126 TTTAGGAAGATAAATTTTTAAAAA
1 TTTAGG-AGATAAATTTTT-AAAA
113150 TTTAGGAGATAAATTTATT-AAA
1 TTTAGGAGATAAATTT-TTAAAA
113172 TTCTAGGAG
1 TT-TAGGAG
113181 TAACAAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
22 5 0.17
23 16 0.55
24 8 0.28
ACGTcount: A:0.44, C:0.02, G:0.16, T:0.38
Consensus pattern (22 bp):
TTTAGGAGATAAATTTTTAAAA
Found at i:113593 original size:30 final size:30
Alignment explanation
Indices: 113557--113630 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
113547 TCTTTAAAAA
113557 TTATAAATAGGTCACTCAATAAAATTATTG
1 TTATAAATAGGTCACTCAATAAAATTATTG
113587 TTATAAATAGGTCACTCAATAAAATTATTG
1 TTATAAATAGGTCACTCAATAAAATTATTG
113617 TTATAAATAGGTCA
1 TTATAAATAGGTCA
113631 TTGTATCGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (30 bp):
TTATAAATAGGTCACTCAATAAAATTATTG
Found at i:117532 original size:28 final size:28
Alignment explanation
Indices: 117500--117555 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
117490 CCCCATCATT
* * *
117500 TATTTCAAATACTGACTTGATGACATAA
1 TATTTCAAACACTGACTCGACGACATAA
*
117528 TATTTCAAGCACTGACTCGACGACATAA
1 TATTTCAAACACTGACTCGACGACATAA
117556 CGTAAACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (28 bp):
TATTTCAAACACTGACTCGACGACATAA
Found at i:118619 original size:2 final size:2
Alignment explanation
Indices: 118612--118645 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
118602 AAGAGGAATT
118612 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
118646 ACTACAACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:125529 original size:29 final size:28
Alignment explanation
Indices: 125487--125546 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
125477 TTTACCTAAC
*
125487 TAAATTGATGTAAGCAATGACATCAAAAT
1 TAAATTGATGTAAGCAATAACATC-AAAT
*
125516 TAAATTGATGTAAGCAATAATATCAAAT
1 TAAATTGATGTAAGCAATAACATCAAAT
125544 TAA
1 TAA
125547 TTTAAGTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (28 bp):
TAAATTGATGTAAGCAATAACATCAAAT
Found at i:125556 original size:29 final size:29
Alignment explanation
Indices: 125487--125557 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
125477 TTTACCTAAC
* *
125487 TAAATTGATGTAAGCAATGACATCAAAAT
1 TAAATTAATGTAAGCAATAACATCAAAAT
* *
125516 TAAATTGATGTAAGCAATAATATC-AAAT
1 TAAATTAATGTAAGCAATAACATCAAAAT
*
125544 TAATTTAAGTGTAA
1 TAAATTAA-TGTAA
125558 ACTTATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
28 10 0.27
29 27 0.73
ACGTcount: A:0.48, C:0.07, G:0.13, T:0.32
Consensus pattern (29 bp):
TAAATTAATGTAAGCAATAACATCAAAAT
Found at i:133223 original size:9 final size:9
Alignment explanation
Indices: 133211--133263 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 9
133201 TTTTTTGAAA
133211 TTTTGGCTT
1 TTTTGGCTT
133220 TTTTGGCTT
1 TTTTGGCTT
*
133229 TTTTTG-TT
1 TTTTGGCTT
133237 TTTT-G--T
1 TTTTGGCTT
*
133243 TTTT-GTTT
1 TTTTGGCTT
133251 TTTTGGCTT
1 TTTTGGCTT
133260 TTTT
1 TTTT
133264 TTTGTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 6 0.15
7 1 0.03
8 11 0.28
9 21 0.54
ACGTcount: A:0.00, C:0.06, G:0.17, T:0.77
Consensus pattern (9 bp):
TTTTGGCTT
Found at i:133247 original size:13 final size:12
Alignment explanation
Indices: 133229--133276 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
133219 TTTTTGGCTT
133229 TTTTTGTTTTTTG
1 TTTTT-TTTTTTG
133242 TTTTTGTTTTTTTG
1 -TTTT-TTTTTTTG
**
133256 GCTTTTTTTTTG
1 TTTTTTTTTTTG
133268 TTTTTTTTT
1 TTTTTTTTT
133277 GTTTTGTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 15 0.52
13 2 0.07
14 11 0.38
15 1 0.03
ACGTcount: A:0.00, C:0.02, G:0.12, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTTG
Found at i:133253 original size:20 final size:21
Alignment explanation
Indices: 133227--133285 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
133217 CTTTTTTGGC
133227 TTTTTTTGTTTTTTGTTTTTG
1 TTTTTTTGTTTTTTGTTTTTG
**
133248 TTTTTTTGGCTTTT-TTTTTG
1 TTTTTTTGTTTTTTGTTTTTG
133268 TTTTTTT-TTGTTTTGTTT
1 TTTTTTTGTT-TTTTGTTT
133286 GAAAAAAAGC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.85
Consensus pattern (21 bp):
TTTTTTTGTTTTTTGTTTTTG
Found at i:133256 original size:31 final size:30
Alignment explanation
Indices: 133218--133286 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 30
133208 AAATTTTGGC
133218 TTTTTTGGCTTTTTTTGTT-TTTTGTTTTTGT
1 TTTTTTGGCTTTTTTT-TTGTTTT-TTTTTGT
133249 TTTTTTGGCTTTTTTTTTGTTTTTTTTTGT
1 TTTTTTGGCTTTTTTTTTGTTTTTTTTTGT
133279 TTTGTTTG
1 TTT-TTTG
133287 AAAAAAAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
30 12 0.33
31 24 0.67
ACGTcount: A:0.00, C:0.03, G:0.16, T:0.81
Consensus pattern (30 bp):
TTTTTTGGCTTTTTTTTTGTTTTTTTTTGT
Found at i:133271 original size:10 final size:10
Alignment explanation
Indices: 133227--133281 Score: 67
Period size: 10 Copynumber: 5.2 Consensus size: 10
133217 CTTTTTTGGC
133227 TTTTTTTGTT
1 TTTTTTTGTT
133237 TTTTGTTT-TT
1 TTTT-TTTGTT
133247 GTTTTTTTGGCTT
1 -TTTTTTT-G-TT
133260 TTTTTTTGTT
1 TTTTTTTGTT
133270 TTTTTTTGTT
1 TTTTTTTGTT
133280 TT
1 TT
133282 GTTTGAAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 23 0.57
11 8 0.20
12 7 0.17
13 2 0.05
ACGTcount: A:0.00, C:0.02, G:0.13, T:0.85
Consensus pattern (10 bp):
TTTTTTTGTT
Done.