Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000679.1 Hibiscus syriacus cultivar Beakdansim tig00001317_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: 132061
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:964 original size:21 final size:19
Alignment explanation
Indices: 927--965 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
917 CGTAAATTCC
*
927 TGAAACAAAATAAAATAAA
1 TGAAAAAAAATAAAATAAA
946 TGAAAAAAGAATACAAATAA
1 TGAAAAAA-AATA-AAATAA
966 TAGCGAGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 4 0.24
21 6 0.35
ACGTcount: A:0.72, C:0.05, G:0.08, T:0.15
Consensus pattern (19 bp):
TGAAAAAAAATAAAATAAA
Found at i:10856 original size:15 final size:15
Alignment explanation
Indices: 10825--10874 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
10815 AGTTTTCATC
* *
10825 TAATAAAAAATATAT
1 TAATAAAAATTAAAT
10840 TAATAAAAATTAAAT
1 TAATAAAAATTAAAT
* *
10855 TATTATAAAATTAAAA
1 TAATA-AAAATTAAAT
10871 TAAT
1 TAAT
10875 TATTCAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAAAAATTAAAT
Found at i:10871 original size:17 final size:18
Alignment explanation
Indices: 10831--10877 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
10821 CATCTAATAA
10831 AAAATATATTAATAAAAATT
1 AAAAT-TATT-ATAAAAATT
10851 -AAATTATTAT-AAAATT
1 AAAATTATTATAAAAATT
*
10867 AAAATAATTAT
1 AAAATTATTAT
10878 TCAATTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 4 0.16
19 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTATTATAAAAATT
Found at i:11649 original size:36 final size:36
Alignment explanation
Indices: 11609--11723 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
11599 TTAATTAATT
*
11609 ATTTATTGATTTGAAAATTTTATATATTAATAAACA
1 ATTTATTGATTTGAAAATTTTATATATTATTAAACA
11645 ATTTATTGATTTGAAAATTTTATATATTATTAAACA
1 ATTTATTGATTTGAAAATTTTATATATTATTAAACA
11681 GA-TTATTGATTTGAAAATTTTATATATTATTAAACA
1 -ATTTATTGATTTGAAAATTTTATATATTATTAAACA
*
11717 ATGTATT
1 ATTTATT
11724 TTATCAATTA
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
35 1 0.01
36 73 0.97
37 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.49
Consensus pattern (36 bp):
ATTTATTGATTTGAAAATTTTATATATTATTAAACA
Found at i:14258 original size:15 final size:15
Alignment explanation
Indices: 14240--14270 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
14230 GAATTGAGTA
*
14240 CTGCATAAGTGAGAG
1 CTGCAGAAGTGAGAG
14255 CTGCAGAAGTGAGAG
1 CTGCAGAAGTGAGAG
14270 C
1 C
14271 GACCCTCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (15 bp):
CTGCAGAAGTGAGAG
Found at i:15505 original size:3 final size:3
Alignment explanation
Indices: 15497--15551 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
15487 GAGATGATAT
* * * *
15497 ATA ATA ATA ATA ATA ACA A-A CAAA ATT ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA
15542 ATA ATA ATA A
1 ATA ATA ATA A
15552 AGAATAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.95
4 1 0.02
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20910 original size:28 final size:28
Alignment explanation
Indices: 20879--20954 Score: 75
Period size: 28 Copynumber: 2.6 Consensus size: 28
20869 TATGAGGATT
*
20879 AAATAAAATTTAATATTTTAATATGT-TC
1 AAATAAAATTTAATATTTTAA-AAGTATC
*
20907 AAATAATAA-TTAATTTTTTAAAAGTAATC
1 AAATAA-AATTTAATATTTTAAAAGT-ATC
*
20936 AAATAAAGGTTTAATATTT
1 AAATAAA-ATTTAATATTT
20955 ATATATATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.08
28 18 0.46
29 10 0.26
30 8 0.21
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (28 bp):
AAATAAAATTTAATATTTTAAAAGTATC
Found at i:28372 original size:2 final size:2
Alignment explanation
Indices: 28365--28396 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28355 ATTTTAGTTA
28365 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
28397 TATTAGAGTG
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:30155 original size:2 final size:2
Alignment explanation
Indices: 30150--30179 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
30140 AGAAAAAATA
*
30150 AT AT AT AA 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
30180 CGAAAACAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:32521 original size:31 final size:31
Alignment explanation
Indices: 32482--32556 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 31
32472 AAAATGGTAA
32482 AAAAACAGAAACTTTAAAAGG-C-TAAAAGAGC
1 AAAAACAGAAACTTT-AAAGGACAT-AAAGAGC
* *
32513 TAAAACAGAAA-TTTAAAGGACATAAATAGC
1 AAAAACAGAAACTTTAAAGGACATAAAGAGC
32543 AAAAACAGAAACTT
1 AAAAACAGAAACTT
32557 AAGTGACTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 5 0.13
30 20 0.53
31 13 0.34
ACGTcount: A:0.59, C:0.12, G:0.13, T:0.16
Consensus pattern (31 bp):
AAAAACAGAAACTTTAAAGGACATAAAGAGC
Found at i:32569 original size:30 final size:29
Alignment explanation
Indices: 32482--32586 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 29
32472 AAAATGGTAA
* *
32482 AAAAACAGAAACTTTAAAAGG-CTAAAAGAGC
1 AAAAACAGAAAC-TT--AAGGACTTAAATAGC
* * *
32513 TAAAACAGAAATTTAAAGGACATAAATAGC
1 AAAAACAGAAACTT-AAGGACTTAAATAGC
*
32543 AAAAACAGAAACTTAAGTGACTTAAATA-A
1 AAAAACAGAAACTTAAG-GACTTAAATAGC
32572 AATAAAC-GAAACTTA
1 AA-AAACAGAAACTTA
32587 GTTTGGTTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
29 18 0.29
30 34 0.55
31 10 0.16
ACGTcount: A:0.58, C:0.11, G:0.12, T:0.18
Consensus pattern (29 bp):
AAAAACAGAAACTTAAGGACTTAAATAGC
Found at i:34336 original size:13 final size:13
Alignment explanation
Indices: 34314--34356 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
34304 GTCACAACCC
34314 GACCCGACCCGTT
1 GACCCGACCCGTT
*
34327 GACTCGACCCGTT
1 GACCCGACCCGTT
34340 GACCCGACCCGTT
1 GACCCGACCCGTT
34353 GACC
1 GACC
34357 GTTGACCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.16, C:0.44, G:0.23, T:0.16
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:34360 original size:7 final size:7
Alignment explanation
Indices: 34348--34386 Score: 69
Period size: 7 Copynumber: 5.4 Consensus size: 7
34338 TTGACCCGAC
34348 CCGTTGA
1 CCGTTGA
34355 CCGTTGA
1 CCGTTGA
34362 CCGTTGA
1 CCGTTGA
34369 CACGTTGA
1 C-CGTTGA
34377 CCGTTGA
1 CCGTTGA
34384 CCG
1 CCG
34387 GAGTTGACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 24 0.77
8 7 0.23
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (7 bp):
CCGTTGA
Found at i:34374 original size:15 final size:14
Alignment explanation
Indices: 34348--34386 Score: 69
Period size: 15 Copynumber: 2.7 Consensus size: 14
34338 TTGACCCGAC
34348 CCGTTGACCGTTGA
1 CCGTTGACCGTTGA
34362 CCGTTGACACGTTGA
1 CCGTTGAC-CGTTGA
34377 CCGTTGACCG
1 CCGTTGACCG
34387 GAGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.15, C:0.31, G:0.28, T:0.26
Consensus pattern (14 bp):
CCGTTGACCGTTGA
Found at i:36864 original size:23 final size:24
Alignment explanation
Indices: 36817--36907 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
36807 TCCGACTTGA
* * *
36817 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
36841 ATTCTGATCTGATA-TTGACATGG
1 ATTCTGATCTGATACTTGACCTGG
*
36864 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATCTGATACTTGACCTGG
*
36888 ATTCTGATATGATACTTGAC
1 ATTCTGATCTGATACTTGAC
36908 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACCTGG
Found at i:36877 original size:47 final size:48
Alignment explanation
Indices: 36817--36907 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
36807 TCCGACTTGA
* * *
36817 ATTCTGTTATGATACCTGACCTGGATTCTGATCTGATA-TTGACATGG
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
*
36864 ATTCTGATCTGATACATGACCTGGATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGAC
36908 TTGAATTATG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.37
Consensus pattern (48 bp):
ATTCTGATATGATACATGACCTGGATTCTGATATGATACTTGACATGG
Found at i:38006 original size:19 final size:18
Alignment explanation
Indices: 37959--38007 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
37949 TTATTGCTTC
37959 ATCTGTTTTATAT-ATTT
1 ATCTGTTTTATATAATTT
*
37976 -TCATG-TTGATATAATATT
1 ATC-TGTTTTATATAAT-TT
37994 ATCTGTTTTATATA
1 ATCTGTTTTATATA
38008 TCACATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
16 8 0.32
17 4 0.16
18 4 0.16
19 9 0.36
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (18 bp):
ATCTGTTTTATATAATTT
Found at i:38225 original size:2 final size:2
Alignment explanation
Indices: 38218--38245 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
38208 ATTTGACTTT
38218 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
38246 ATCTAATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39803 original size:129 final size:129
Alignment explanation
Indices: 39647--39904 Score: 498
Period size: 129 Copynumber: 2.0 Consensus size: 129
39637 ATACAGTTGC
39647 TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTTG
1 TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTTG
*
39712 AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTTAACAAAGTAAAAGATGA
66 AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
*
39776 TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTATTATTAAATTAATCGAATAAGTTTG
1 TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTTG
39841 AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
66 AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
39905 AAACAAAAGA
Statistics
Matches: 127, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 127 1.00
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (129 bp):
TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTTG
AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
Found at i:49779 original size:15 final size:15
Alignment explanation
Indices: 49759--49789 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
49749 TCTTGGCACA
49759 CCCATTTCTTCAACT
1 CCCATTTCTTCAACT
49774 CCCATTTCTTCAACT
1 CCCATTTCTTCAACT
49789 C
1 C
49790 ATTTGATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (15 bp):
CCCATTTCTTCAACT
Found at i:54342 original size:12 final size:13
Alignment explanation
Indices: 54325--54357 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
54315 TGTATTTTAT
54325 ATTATTAAT-AAA
1 ATTATTAATAAAA
*
54337 ATTATTATTAAAA
1 ATTATTAATAAAA
54350 ATTATTAA
1 ATTATTAA
54358 AACAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATTAATAAAA
Found at i:54364 original size:25 final size:24
Alignment explanation
Indices: 54325--54372 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
54315 TGTATTTTAT
54325 ATTATTAATAAAATTATTATTAAAA
1 ATTATTAATAAAATT-TTATTAAAA
*
54350 ATTATTAA-AACAATTTTTTTAAA
1 ATTATTAATAA-AATTTTATTAAA
54373 TTTTATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTATTAATAAAATTTTATTAAAA
Found at i:56559 original size:98 final size:96
Alignment explanation
Indices: 56386--56568 Score: 312
Period size: 98 Copynumber: 1.9 Consensus size: 96
56376 AAATTATACT
* *
56386 TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTG
1 TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAAATTCTATATCGTTA
* *
56451 TCAGCTTTATTCATTTGTGTGTGATTATTTTA
66 ACAACTTTATTCA-TTGTGTGTGATTATTTTA
56483 TGATCTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAAATTCTATATCGTT
1 TGAT-TCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAAATTCTATATCGTT
56548 AACAACTTTATTCATTGTGTG
65 AACAACTTTATTCATTGTGTG
56569 ATTACTTTAG
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 11 0.14
98 70 0.86
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.48
Consensus pattern (96 bp):
TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAAATTCTATATCGTTA
ACAACTTTATTCATTGTGTGTGATTATTTTA
Found at i:62091 original size:12 final size:13
Alignment explanation
Indices: 62070--62118 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
62060 CAATGAAATT
62070 TATA-AATTATAA
1 TATATAATTATAA
62082 TA-ATAATTATAA
1 TATATAATTATAA
*
62094 TATATCATATATATA
1 TATATAAT-TATA-A
62109 TATATAATTA
1 TATATAATTA
62119 CAAATAATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
11 1 0.03
12 12 0.39
13 4 0.13
14 6 0.19
15 8 0.26
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
TATATAATTATAA
Found at i:69742 original size:32 final size:32
Alignment explanation
Indices: 69701--69766 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
69691 GTGTTTTTTT
69701 TTCTTCTTAAACTCCATTAATATCTTGATTTG
1 TTCTTCTTAAACTCCATTAATATCTTGATTTG
69733 TTCTTCTTAAACTCCATTAATATCTTGATTTG
1 TTCTTCTTAAACTCCATTAATATCTTGATTTG
69765 TT
1 TT
69767 TCAACAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (32 bp):
TTCTTCTTAAACTCCATTAATATCTTGATTTG
Found at i:81904 original size:14 final size:14
Alignment explanation
Indices: 81885--81917 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
81875 GGAAGGAAAT
81885 GAAGAGAAAGAGCA
1 GAAGAGAAAGAGCA
81899 GAAGAGAAAGAGCA
1 GAAGAGAAAGAGCA
81913 GAAGA
1 GAAGA
81918 AGATAGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.36, T:0.00
Consensus pattern (14 bp):
GAAGAGAAAGAGCA
Found at i:92754 original size:22 final size:23
Alignment explanation
Indices: 92724--92784 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
92714 CTCAAACTGA
*
92724 AAATATGTCA-AAAGACAAAGAG
1 AAATGTGTCATAAAGACAAAGAG
* *
92746 AAATGTGTCATAAATACAAAGAT
1 AAATGTGTCATAAAGACAAAGAG
*
92769 AAATGTTTCATAAAGA
1 AAATGTGTCATAAAGA
92785 TAGAGTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 9 0.27
23 24 0.73
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (23 bp):
AAATGTGTCATAAAGACAAAGAG
Found at i:106258 original size:7 final size:7
Alignment explanation
Indices: 106228--106257 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
106218 TCTAAAGTTC
106228 AAATTTA
1 AAATTTA
106235 AAATTTA
1 AAATTTA
106242 AAATTTA
1 AAATTTA
106249 AAA-TTA
1 AAATTTA
106255 AAA
1 AAA
106258 AAAATTGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATTTA
Found at i:124415 original size:64 final size:65
Alignment explanation
Indices: 124347--124487 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 65
124337 GAACACTTGA
* *
124347 TGCATCGGTGCACCAAGTGTGCATCAATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAG
1 TGCATCGGTGCACCAAGTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
* **** * **
124411 TGCATCGATGCATGGCGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGGTGCACCAAGTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
124476 TGCATCGGTGCA
1 TGCATCGGTGCA
124488 TGGAATGCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
64 40 0.62
65 25 0.38
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (65 bp):
TGCATCGGTGCACCAAGTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAG
Found at i:124502 original size:64 final size:64
Alignment explanation
Indices: 124366--124503 Score: 172
Period size: 64 Copynumber: 2.2 Consensus size: 64
124356 GCACCAAGTG
* * * **
124366 TGCATCAATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCGTG
1 TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGGCGAA
** *
124430 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATCAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGGCGAA
124493 TGCATTCGATG
1 TGCA-TCGATG
124504 TTTCAATTAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
63 5 0.08
64 33 0.52
65 26 0.41
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGGCGAA
Found at i:124747 original size:20 final size:21
Alignment explanation
Indices: 124724--124763 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
124714 GAATCGAATA
124724 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
124744 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
124764 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:127875 original size:74 final size:75
Alignment explanation
Indices: 127792--127934 Score: 198
Period size: 75 Copynumber: 1.9 Consensus size: 75
127782 TTGCTCATAG
* ** * *
127792 GGAACCGATT-CCCCCTGAATGGTTTGGCTCTGAGATTTCCAGAATGCTCGGAGGGAACCGATTC
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAGGGAACCGATTC
127856 CCCCATAGGA
66 CCCCATAGGA
* * **
127866 GGAACCGATTCCCCCCTAAACAGTTTTGTTCCGAGAATTCCATTATGCTCGGAGGGAACCGATTC
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAGGGAACCGATTC
127931 CCCC
66 CCCC
127935 CTTTTTACAA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 10 0.17
75 49 0.83
ACGTcount: A:0.23, C:0.29, G:0.24, T:0.24
Consensus pattern (75 bp):
GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAGGGAACCGATTC
CCCCATAGGA
Done.