Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005459.1 Hibiscus syriacus cultivar Beakdansim tig00012501_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: 136884
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:328 original size:70 final size:70
Alignment explanation
Indices: 215--354 Score: 271
Period size: 70 Copynumber: 2.0 Consensus size: 70
205 AAAATGGTCC
215 CATGATTATGGATATTTGTTTTATTGCGTCAATCATCTATTAAATTATGAGGATTATTTTGTGAC
1 CATGATTATGGATATTTGTTTTATTGCGTCAATCATCTATTAAATTATGAGGATTATTTTGTGAC
280 TTTTA
66 TTTTA
*
285 CATGATTATGGATATTTGTTTTATTGCGTCAATCATCTATTAAATTATGATGATTATTTTGTGAC
1 CATGATTATGGATATTTGTTTTATTGCGTCAATCATCTATTAAATTATGAGGATTATTTTGTGAC
350 TTTTA
66 TTTTA
355 ATAGTTGATG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.27, C:0.09, G:0.15, T:0.49
Consensus pattern (70 bp):
CATGATTATGGATATTTGTTTTATTGCGTCAATCATCTATTAAATTATGAGGATTATTTTGTGAC
TTTTA
Found at i:1430 original size:2 final size:2
Alignment explanation
Indices: 1423--1451 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1413 TCAGTAATTA
1423 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1452 TAGCGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:8325 original size:13 final size:14
Alignment explanation
Indices: 8298--8337 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
8288 AATATGAAAC
8298 TCTAAACATTAAAT
1 TCTAAACATTAAAT
8312 TCTAAACA-TAAAT
1 TCTAAACATTAAAT
* *
8325 TATAAACGTTAAA
1 TCTAAACATTAAA
8338 AATAATGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.33
Consensus pattern (14 bp):
TCTAAACATTAAAT
Found at i:12618 original size:12 final size:12
Alignment explanation
Indices: 12601--12625 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12591 TCATTGGGAA
12601 AGCTGAGGGTTG
1 AGCTGAGGGTTG
12613 AGCTGAGGGTTG
1 AGCTGAGGGTTG
12625 A
1 A
12626 ACTTGAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.48, T:0.24
Consensus pattern (12 bp):
AGCTGAGGGTTG
Found at i:13199 original size:10 final size:10
Alignment explanation
Indices: 13184--13231 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
13174 TGATTCATTT
13184 TGCCCTCGGA
1 TGCCCTCGGA
*
13194 TGCCCTCGCA
1 TGCCCTCGGA
13204 TAGCTCGCTCGGA
1 T-GC-C-CTCGGA
*
13217 TGGCCTCGGA
1 TGCCCTCGGA
13227 TGCCC
1 TGCCC
13232 AGCGTGTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 20 0.65
11 3 0.10
12 2 0.06
13 6 0.19
ACGTcount: A:0.10, C:0.40, G:0.29, T:0.21
Consensus pattern (10 bp):
TGCCCTCGGA
Found at i:13307 original size:29 final size:29
Alignment explanation
Indices: 13270--13327 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
13260 AATCTCTCTC
*
13270 ATAGCTCGCCGGGAAGACATGGCGACCTA
1 ATAGCTCGCCCGGAAGACATGGCGACCTA
* * *
13299 ATAGGTCGCCCGGATGGCATGGCGACCTA
1 ATAGCTCGCCCGGAAGACATGGCGACCTA
13328 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.33, T:0.16
Consensus pattern (29 bp):
ATAGCTCGCCCGGAAGACATGGCGACCTA
Found at i:18221 original size:4 final size:4
Alignment explanation
Indices: 18212--18251 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
18202 ATATGGACAT
*
18212 ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
18252 GTGTGCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:29981 original size:25 final size:26
Alignment explanation
Indices: 29938--29986 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
29928 GATTTTATTT
* **
29938 TATTTTATTTTCTGGAAAT-TATTGA
1 TATTTTATTTTATAAAAATCTATTGA
29963 TATTTTATTTTATAAAAATCTATT
1 TATTTTATTTTATAAAAATCTATT
29987 TTTCCTAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (26 bp):
TATTTTATTTTATAAAAATCTATTGA
Found at i:30647 original size:21 final size:23
Alignment explanation
Indices: 30604--30647 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
30594 TTGAGATGGA
*
30604 TGGGTGTTGGAATTAAGGGATTT
1 TGGGTGTTGAAATTAAGGGATTT
30627 TGGGT-TTGAAATTAA-GGATTT
1 TGGGTGTTGAAATTAAGGGATTT
30648 GAGTTTAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 9 0.45
23 5 0.25
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (23 bp):
TGGGTGTTGAAATTAAGGGATTT
Found at i:30660 original size:21 final size:22
Alignment explanation
Indices: 30610--30660 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
30600 TGGATGGGTG
*
30610 TTGGAATTAAGGGATTTTGGGT
1 TTGGAATTAAGGGATTTTGAGT
*
30632 TTGAAATTAA-GGA-TTTGAGT
1 TTGGAATTAAGGGATTTTGAGT
30652 TTAGGAATT
1 TT-GGAATT
30661 TTGGGAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 8 0.32
21 8 0.32
22 9 0.36
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (22 bp):
TTGGAATTAAGGGATTTTGAGT
Found at i:30937 original size:2 final size:2
Alignment explanation
Indices: 30930--30967 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
30920 GAAAATACAA
30930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30968 CGATTTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34647 original size:5 final size:5
Alignment explanation
Indices: 34637--34666 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
34627 AGGGACTGAC
34637 CGGAA CGGAA CGGAA CGGAA CGGAA CGGAA
1 CGGAA CGGAA CGGAA CGGAA CGGAA CGGAA
34667 GGGGAACGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
CGGAA
Found at i:36623 original size:13 final size:13
Alignment explanation
Indices: 36605--36632 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36595 CTTTTTTCTA
36605 TTAATATTTATAT
1 TTAATATTTATAT
36618 TTAATATTTATAT
1 TTAATATTTATAT
36631 TT
1 TT
36633 CAAACACATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTAATATTTATAT
Found at i:42087 original size:2 final size:2
Alignment explanation
Indices: 42082--42122 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
42072 TAAAAATTCA
42082 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42123 GTAGTTATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44871 original size:2 final size:2
Alignment explanation
Indices: 44813--44852 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44803 CTTAAAATGT
44813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
44853 CTGATATCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44909 original size:16 final size:17
Alignment explanation
Indices: 44888--44921 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
44878 TAGGTTAAAG
44888 AAATTA-AAAATATTTT
1 AAATTATAAAATATTTT
*
44904 AAATTATATAATATTTT
1 AAATTATAAAATATTTT
44921 A
1 A
44922 GGTTGTAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTATAAAATATTTT
Found at i:44952 original size:38 final size:40
Alignment explanation
Indices: 44908--45000 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 40
44898 TATTTTAAAT
* * * *
44908 TATATAATATTTTAGGTTGTAACT-AAAGA-GTCATCAAA
1 TATATAACATTTTAGGTTGCAAATCAAAAATGTCATCAAA
* * *
44946 TATATAACCTTTTAAGTTGCAAATCAAAAATGTTATCAAA
1 TATATAACATTTTAGGTTGCAAATCAAAAATGTCATCAAA
44986 TATATAACATTTTAG
1 TATATAACATTTTAG
45001 ATTGAGTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
38 19 0.43
39 4 0.09
40 21 0.48
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (40 bp):
TATATAACATTTTAGGTTGCAAATCAAAAATGTCATCAAA
Found at i:45201 original size:19 final size:20
Alignment explanation
Indices: 45165--45202 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
45155 ACTTTATATT
**
45165 ATTAAAAATATTGTAAATAA
1 ATTAAAAATATTAAAAATAA
45185 ATTAAAAA-ATTAAAAATA
1 ATTAAAAATATTAAAAATA
45203 TTATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
ATTAAAAATATTAAAAATAA
Found at i:45230 original size:33 final size:33
Alignment explanation
Indices: 45144--45240 Score: 96
Period size: 33 Copynumber: 3.1 Consensus size: 33
45134 GATACTTATC
*
45144 ATTTTATAATCACTTTATATTATT-AAAA-A-T
1 ATTTTATAATCAATTTATATTATTAAAAATATT
* * * **
45174 ATTGTA-AAT-AAATTAAAAAATTAAAAATATT
1 ATTTTATAATCAATTTATATTATTAAAAATATT
*
45205 ATTTTATAATCATTTTATATTATTAAAAATATT
1 ATTTTATAATCAATTTATATTATTAAAAATATT
45238 ATT
1 ATT
45241 AATAAATTAA
Statistics
Matches: 50, Mismatches: 12, Indels: 7
0.72 0.17 0.10
Matches are distributed among these distances:
28 8 0.16
29 7 0.14
30 6 0.12
31 6 0.12
32 3 0.06
33 20 0.40
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (33 bp):
ATTTTATAATCAATTTATATTATTAAAAATATT
Found at i:51710 original size:16 final size:16
Alignment explanation
Indices: 51689--51719 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
51679 CGAACATAAA
51689 CGAACATAAACGAACG
1 CGAACATAAACGAACG
51705 CGAACATAAACGAAC
1 CGAACATAAACGAAC
51720 AAATTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.16, T:0.06
Consensus pattern (16 bp):
CGAACATAAACGAACG
Found at i:51720 original size:10 final size:10
Alignment explanation
Indices: 51674--51703 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
51664 CATTTAATAA
51674 ATAAACGAAC
1 ATAAACGAAC
51684 ATAAACGAAC
1 ATAAACGAAC
51694 ATAAACGAAC
1 ATAAACGAAC
51704 GCGAACATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.20, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:51801 original size:10 final size:10
Alignment explanation
Indices: 51786--51828 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
51776 CATTTAATAA
51786 ATAAACGAAC
1 ATAAACGAAC
51796 ATAAACGAAC
1 ATAAACGAAC
51806 ----ACGAAC
1 ATAAACGAAC
51812 ATAAACGAAC
1 ATAAACGAAC
51822 ATAAACG
1 ATAAACG
51829 TTGGAGACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
6 6 0.21
10 23 0.79
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:51811 original size:16 final size:16
Alignment explanation
Indices: 51790--51822 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
51780 TAATAAATAA
51790 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51806 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
51822 A
1 A
51823 TAAACGTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:52591 original size:24 final size:24
Alignment explanation
Indices: 52564--52625 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
52554 ATAAATGAAT
* **
52564 GAACATAAACGAATATAATTAAAC
1 GAACATAAACGAACATAACCAAAC
52588 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCAAAC
*
52612 GAACATAACCGAAC
1 GAACATAAACGAAC
52626 GTTCACGAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (24 bp):
GAACATAAACGAACATAACCAAAC
Found at i:52620 original size:14 final size:14
Alignment explanation
Indices: 52594--52626 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
52584 AAACGAACAT
52594 AAACGAACATAACC
1 AAACGAACATAACC
52608 AAACGAACATAACC
1 AAACGAACATAACC
*
52622 GAACG
1 AAACG
52627 TTCACGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:56756 original size:2 final size:2
Alignment explanation
Indices: 56746--56781 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
56736 TATTTTTTAA
56746 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56782 ATCATTTTCT
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64003 original size:38 final size:38
Alignment explanation
Indices: 63952--64028 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
63942 AAAGAGAAAC
63952 AAACATCTGCATCTCACGGCTATATATCCAATAGCCCT
1 AAACATCTGCATCTCACGGCTATATATCCAATAGCCCT
*
63990 AAACATCTTCATCTCACGGCTATATATCCAATAGCCCT
1 AAACATCTGCATCTCACGGCTATATATCCAATAGCCCT
64028 A
1 A
64029 TTTTGTGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.27
Consensus pattern (38 bp):
AAACATCTGCATCTCACGGCTATATATCCAATAGCCCT
Found at i:66956 original size:2 final size:2
Alignment explanation
Indices: 66949--66997 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
66939 ATGTTCTACC
66949 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
66991 TA TA TA T
1 TA TA TA T
66998 GAGTTAAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70925 original size:2 final size:2
Alignment explanation
Indices: 70918--70960 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
70908 TGACTTTAAC
70918 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
70960 A
1 A
70961 GGTAGAGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:79149 original size:25 final size:27
Alignment explanation
Indices: 79091--79149 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
79081 TTAATTATCA
79091 TAATTTATTAAATATTTTTAAGAATGT
1 TAATTTATTAAATATTTTTAAGAATGT
*
79118 TAA-TTATT-ATTATTTTTTAA-AATG-
1 TAATTTATTAAATA-TTTTTAAGAATGT
79142 TAATTTAT
1 TAATTTAT
79150 CAGGAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 3 0.10
25 11 0.38
26 12 0.41
27 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (27 bp):
TAATTTATTAAATATTTTTAAGAATGT
Found at i:81882 original size:17 final size:18
Alignment explanation
Indices: 81847--81883 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
81837 TTTATTTTAG
81847 ACAAACTTGATGAATTAA
1 ACAAACTTGATGAATTAA
81865 ACAAA-TTGATAGAA-TAA
1 ACAAACTTGAT-GAATTAA
81882 AC
1 AC
81884 TATTAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (18 bp):
ACAAACTTGATGAATTAA
Found at i:86147 original size:15 final size:14
Alignment explanation
Indices: 86117--86180 Score: 67
Period size: 15 Copynumber: 4.4 Consensus size: 14
86107 TTGTAATATT
86117 AATTATAAAT-AAA
1 AATTATAAATAAAA
86130 AATTATAACATAAAA
1 AATTATAA-ATAAAA
86145 AATTATAATATAATAA
1 AATTATAA-ATAA-AA
* * *
86161 TATTACAATTAAAA
1 AATTATAAATAAAA
86175 AATTAT
1 AATTAT
86181 GGATTTGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
13 8 0.19
14 8 0.19
15 18 0.43
16 8 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTATAAATAAAA
Found at i:86149 original size:28 final size:30
Alignment explanation
Indices: 86117--86180 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
86107 TTGTAATATT
*
86117 AATTATAA-ATAA-AA-ATTATAACATAAAA
1 AATTATAATATAATAATATTACAA-ATAAAA
*
86145 AATTATAATATAATAATATTACAATTAAAA
1 AATTATAATATAATAATATTACAAATAAAA
86175 AATTAT
1 AATTAT
86181 GGATTTGATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 8 0.26
29 4 0.13
30 13 0.42
31 6 0.19
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (30 bp):
AATTATAATATAATAATATTACAAATAAAA
Found at i:90500 original size:31 final size:30
Alignment explanation
Indices: 90465--90551 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
90455 TTGTTTTTTA
90465 AATTTTAAATAAAATATTAATTTAATTA-AT
1 AATTTTAAATAAAATATTAATTTAA-TACAT
* * * *
90495 GAATTTTAGATAAGATATTCATTTAATACCT
1 -AATTTTAAATAAAATATTAATTTAATACAT
* *
90526 AAGCTTTAAATAAAATATCAATTTAA
1 AA-TTTTAAATAAAATATTAATTTAA
90552 CTCATGATCA
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
30 4 0.09
31 41 0.91
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (30 bp):
AATTTTAAATAAAATATTAATTTAATACAT
Found at i:90814 original size:15 final size:14
Alignment explanation
Indices: 90777--90816 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
90767 ATCAAATCCC
90777 TAATTTTTTATTTA
1 TAATTTTTTATTTA
90791 TAATATTTTTATGTTA
1 TAAT-TTTTTAT-TTA
*
90807 TAGTTTTTTA
1 TAATTTTTTA
90817 CTATGTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 13 0.57
16 6 0.26
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
TAATTTTTTATTTA
Found at i:95134 original size:15 final size:16
Alignment explanation
Indices: 95102--95134 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
95092 AAAATCTTTC
95102 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
95118 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
95133 TT
1 TT
95135 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:95911 original size:16 final size:17
Alignment explanation
Indices: 95884--95918 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
95874 TATCGCCGAC
95884 CGAAATTTCACTATTCA
1 CGAAATTTCACTATTCA
95901 CGAAA-TTCACTATTCA
1 CGAAATTTCACTATTCA
95917 CG
1 CG
95919 TGAATAGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (17 bp):
CGAAATTTCACTATTCA
Found at i:98458 original size:28 final size:27
Alignment explanation
Indices: 98427--98518 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 27
98417 TTATGACATG
98427 AATATTTTTAAATATTATTAAATATAAA
1 AATA-TTTTAAATATTATTAAATATAAA
* * *
98455 AATAATTTAAA-ATAACT-AATA-AAA
1 AATATTTTAAATATTATTAAATATAAA
* *
98479 TAATATTTT-ATTATTATTAAATTTAAA
1 -AATATTTTAAATATTATTAAATATAAA
*
98506 AATATTTAAAATA
1 AATATTTTAAATA
98519 ACTATTACTG
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
24 4 0.08
25 15 0.31
26 14 0.29
27 12 0.24
28 4 0.08
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (27 bp):
AATATTTTAAATATTATTAAATATAAA
Found at i:99013 original size:26 final size:25
Alignment explanation
Indices: 98976--99033 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
98966 GATATAATCT
* *
98976 AAAAAT-TCAATGAGTAAATTAAAAA
1 AAAAATAT-AATGAATAAAATAAAAA
*
99001 ATAAAATATAATGAATAAAATAAGAA
1 A-AAAATATAATGAATAAAATAAAAA
99027 AAAAATA
1 AAAAATA
99034 AAATTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 20 0.71
27 1 0.04
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (25 bp):
AAAAATATAATGAATAAAATAAAAA
Found at i:99500 original size:21 final size:20
Alignment explanation
Indices: 99467--99513 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
99457 CAATTATTTG
*
99467 AATAACATTTAAAAATAAAA
1 AATAATATTTAAAAATAAAA
**
99487 AATAATATATTAAATCTAAAA
1 AATAATAT-TTAAAAATAAAA
99508 AATAAT
1 AATAAT
99514 TAATAAGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
AATAATATTTAAAAATAAAA
Found at i:99679 original size:59 final size:59
Alignment explanation
Indices: 99556--99683 Score: 184
Period size: 59 Copynumber: 2.2 Consensus size: 59
99546 AGTCCAGTAT
**
99556 AGTTAATAAATTTGACCTAACTTTCTTACTTAAATTAGTTTAGTCCACAATCTAAAATT
1 AGTTAATAAATTTGACCTAACTTTCTTACTTAAATTAGTTTAGTCCACAATCTAAAACC
* * * * *
99615 AGTTAATAAATTTGACTTAACTTTCTTACTTAATTTAGTTTAGTCCATAATTTAGAACC
1 AGTTAATAAATTTGACCTAACTTTCTTACTTAAATTAGTTTAGTCCACAATCTAAAACC
*
99674 GGTTAATAAA
1 AGTTAATAAA
99684 ATTAGTTTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.41
Consensus pattern (59 bp):
AGTTAATAAATTTGACCTAACTTTCTTACTTAAATTAGTTTAGTCCACAATCTAAAACC
Found at i:104717 original size:12 final size:12
Alignment explanation
Indices: 104700--104725 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
104690 ATCTAATATC
104700 AGTAACCATTTA
1 AGTAACCATTTA
104712 AGTAACCATTTA
1 AGTAACCATTTA
104724 AG
1 AG
104726 AGTAGTTTTA
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:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (12 bp):
AGTAACCATTTA
Found at i:105660 original size:22 final size:21
Alignment explanation
Indices: 105635--105678 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
105625 AATGTAAAGT
*
105635 TATAAAAAAAGTAAAAATACAA
1 TATAAAAAAA-TAAAAAAACAA
**
105657 TATAGTAAAATAAAAAAACAA
1 TATAAAAAAATAAAAAAACAA
105678 T
1 T
105679 GAATAACGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.20
Consensus pattern (21 bp):
TATAAAAAAATAAAAAAACAA
Found at i:108121 original size:17 final size:18
Alignment explanation
Indices: 108089--108123 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
108079 TTTGTATCTG
108089 TTGGGCTGCTGGGTTGTA
1 TTGGGCTGCTGGGTTGTA
*
108107 TTGGGCTTC-GGGTTGTA
1 TTGGGCTGCTGGGTTGTA
108124 ATCTGATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.06, C:0.11, G:0.43, T:0.40
Consensus pattern (18 bp):
TTGGGCTGCTGGGTTGTA
Found at i:108216 original size:3 final size:3
Alignment explanation
Indices: 108208--108234 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
108198 GTAATAAATA
108208 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
108235 TATTATTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:116701 original size:35 final size:35
Alignment explanation
Indices: 116654--116739 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
116644 AAAACAGTCA
* * *
116654 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
116689 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
116724 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
116740 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:116733 original size:21 final size:21
Alignment explanation
Indices: 116708--116750 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
116698 TTCTAAACCC
116708 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
116729 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
116750 T
1 T
116751 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:116905 original size:16 final size:18
Alignment explanation
Indices: 116873--116906 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
116863 TATTAATGTA
116873 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
116891 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
116907 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:117573 original size:130 final size:130
Alignment explanation
Indices: 117370--117617 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
117360 AATTTTCTTC
* * *
117370 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
117435 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
117500 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
117565 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
117618 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:124051 original size:17 final size:17
Alignment explanation
Indices: 124029--124064 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
124019 TCGGTGATGT
124029 TATCACTGACATAATAC
1 TATCACTGACATAATAC
124046 TATCACTGACATAATAC
1 TATCACTGACATAATAC
124063 TA
1 TA
124065 GAATTTATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (17 bp):
TATCACTGACATAATAC
Found at i:124525 original size:7 final size:7
Alignment explanation
Indices: 124513--124565 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
124503 TACAAACGAA
124513 GGAATGT
1 GGAATGT
124520 GGAATGT
1 GGAATGT
124527 GGAATGT
1 GGAATGT
124534 GGAATGT
1 GGAATGT
124541 GGAATGT
1 GGAATGT
124548 GGAATGT
1 GGAATGT
124555 GGAATGT
1 GGAATGT
124562 GGAA
1 GGAA
124566 GCAACTTAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.30, C:0.00, G:0.43, T:0.26
Consensus pattern (7 bp):
GGAATGT
Found at i:131172 original size:29 final size:30
Alignment explanation
Indices: 131119--131184 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
131109 AACAGAAGCT
**
131119 CACCA-TTTCTCTTCTCCTTTCTCTATTTC
1 CACCATTTTCTCTTCTCCTTAATCTATTTC
131148 CACCATTTTCTCTTCTCC-TAATCTATTTC
1 CACCATTTTCTCTTCTCCTTAATCTATTTC
*
131177 AACC-TTTT
1 CACCATTTT
131185 AAAATCCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 4 0.12
29 17 0.52
30 12 0.36
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (30 bp):
CACCATTTTCTCTTCTCCTTAATCTATTTC
Found at i:134097 original size:2 final size:2
Alignment explanation
Indices: 134090--134115 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
134080 TCGTTTCGTT
134090 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
134116 ATGACTACGA
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:136223 original size:3 final size:3
Alignment explanation
Indices: 136215--136239 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
136205 TCTGTAGTCT
136215 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
136240 AGTCAACGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Done.