Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006149.1 Hibiscus syriacus cultivar Beakdansim tig00014608_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: 60335
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.33
Found at i:5045 original size:23 final size:23
Alignment explanation
Indices: 5019--5068 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5009 AACATCTCTA
*
5019 TTCATAAAAAATAGTTAAGTCTT
1 TTCATAAAAAATAGTTAAGTCAT
* *
5042 TTCATGAAAAATAGTTAATTCAT
1 TTCATAAAAAATAGTTAAGTCAT
5065 TTCA
1 TTCA
5069 CCCAAAAGTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (23 bp):
TTCATAAAAAATAGTTAAGTCAT
Found at i:5075 original size:24 final size:23
Alignment explanation
Indices: 5025--5075 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5015 TCTATTCATA
* **
5025 AAAAATAGTTAAGTCTTTTCATG
1 AAAAATAGTTAAGTCATTTCACC
*
5048 AAAAATAGTTAATTCATTTCACC
1 AAAAATAGTTAAGTCATTTCACC
*
5071 CAAAA
1 AAAAA
5076 GTCAAGTCTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAAATAGTTAAGTCATTTCACC
Found at i:10731 original size:142 final size:142
Alignment explanation
Indices: 10486--10765 Score: 470
Period size: 142 Copynumber: 2.0 Consensus size: 142
10476 TCGCAATGCG
* *
10486 ATCTCTAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTGCGATTTT
1 ATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTACGATTTT
* * * *
10551 CCAAATTTGCGTCATGATTTTAGAAAATCACAATGCGAATATGTAAATCGCAACGCGATTCTGAC
66 CCAAATTCGCGTCACGATTTTAGAAAATCACAATGCGAATATGTAAATCACAACGCGATTATGAC
10616 TATCGCAACGTA
131 TATCGCAACGTA
10628 ATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTACGATTTT
1 ATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTACGATTTT
** **
10693 CCAAATTCGCGTTGCGATTTTAGAAAATTGCAATGCGAATATGTAAATCACAACGCGATTATGAC
66 CCAAATTCGCGTCACGATTTTAGAAAATCACAATGCGAATATGTAAATCACAACGCGATTATGAC
10758 TATCGCAA
131 TATCGCAA
10766 TGCGATAATA
Statistics
Matches: 128, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
142 128 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.31
Consensus pattern (142 bp):
ATCTCCAGTATCGCAAATCAGTTTCCAGATTCGCAACGCGATTTTGACTATCGCATTACGATTTT
CCAAATTCGCGTCACGATTTTAGAAAATCACAATGCGAATATGTAAATCACAACGCGATTATGAC
TATCGCAACGTA
Found at i:10770 original size:20 final size:20
Alignment explanation
Indices: 10743--10812 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
10733 ATGTAAATCA
10743 CAACGCGATTATGACTATCG
1 CAACGCGATTATGACTATCG
* * *
10763 CAATGCGATAAT-ACAAAATCG
1 CAACGCGATTATGAC--TATCG
*
10784 CAACGCGATTCTGACTATCG
1 CAACGCGATTATGACTATCG
*
10804 CAACCCGAT
1 CAACGCGAT
10813 AATACATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 2 0.05
20 22 0.56
21 13 0.33
22 2 0.05
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.21
Consensus pattern (20 bp):
CAACGCGATTATGACTATCG
Found at i:10782 original size:41 final size:41
Alignment explanation
Indices: 10737--10833 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 41
10727 GCGAATATGT
* **
10737 AAATCACAACGCGATTATGACTATCGCAATGCGATAATACA
1 AAATCGCAACGCGATTATGACTATCGCAACCCGATAATACA
*
10778 AAATCGCAACGCGATTCTGACTATCGCAACCCGATAATACA
1 AAATCGCAACGCGATTATGACTATCGCAACCCGATAATACA
* *
10819 TAATCGCAACACGAT
1 AAATCGCAACGCGAT
10834 AATACAGAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.21
Consensus pattern (41 bp):
AAATCGCAACGCGATTATGACTATCGCAACCCGATAATACA
Found at i:10784 original size:21 final size:20
Alignment explanation
Indices: 10737--10854 Score: 87
Period size: 21 Copynumber: 5.8 Consensus size: 20
10727 GCGAATATGT
* *
10737 AAATCACAACGCGATTATGAC
1 AAATCGCAACGCGATAAT-AC
* *
10758 -TATCGCAATGCGATAATAC
1 AAATCGCAACGCGATAATAC
**
10777 AAAATCGCAACGCGATTCTGAC
1 -AAATCGCAACGCGATAAT-AC
* *
10799 -TATCGCAACCCGATAATAC
1 AAATCGCAACGCGATAATAC
*
10818 ATAATCGCAACACGATAATAC
1 A-AATCGCAACGCGATAATAC
*
10839 AGAATCGCAATGCGAT
1 A-AATCGCAACGCGAT
10855 TTTCCAAATT
Statistics
Matches: 75, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
19 4 0.05
20 26 0.35
21 43 0.57
22 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGATAATAC
Found at i:11319 original size:19 final size:19
Alignment explanation
Indices: 11295--11403 Score: 110
Period size: 19 Copynumber: 5.4 Consensus size: 19
11285 TTATTTTGGA
11295 TTTTTCACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
11314 TTTTTCACTATCGCAACAACAC
1 TTTTTCACTATCG---CAACAC
*
11336 GTTTTTCAAACTCTCGCAACAC
1 -TTTTTC--ACTATCGCAACAC
* *
11358 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
* *
11377 ATTTTAACTATCGCAACAC
1 TTTTTCACTATCGCAACAC
11396 ATTTTTCA
1 -TTTTTCA
11404 AAATCGCGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
19 44 0.57
20 5 0.06
21 4 0.05
22 12 0.16
23 6 0.08
25 6 0.08
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (19 bp):
TTTTTCACTATCGCAACAC
Found at i:14676 original size:36 final size:37
Alignment explanation
Indices: 14636--14723 Score: 124
Period size: 37 Copynumber: 2.4 Consensus size: 37
14626 TAGAAAAAGA
* *
14636 AGAAGAAGAAGAAGAGT-AGGTTAATAGGGGTGTGAG
1 AGAAGAAGAAGAAGAGTGAGGTTAACAGGGGCGTGAG
* *
14672 AGAAGAAGAAGAATAGTGAGGTTAACGGGGGCGTGAG
1 AGAAGAAGAAGAAGAGTGAGGTTAACAGGGGCGTGAG
*
14709 AGAAGAATAAGAAGA
1 AGAAGAAGAAGAAGA
14724 AGAAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
36 16 0.36
37 29 0.64
ACGTcount: A:0.44, C:0.02, G:0.40, T:0.14
Consensus pattern (37 bp):
AGAAGAAGAAGAAGAGTGAGGTTAACAGGGGCGTGAG
Found at i:14723 original size:3 final size:3
Alignment explanation
Indices: 14709--14778 Score: 61
Period size: 3 Copynumber: 22.3 Consensus size: 3
14699 GGGGCGTGAG
* * * *
14709 AGA AGA ATA AGA AGA AGA AAA AAA AGA A-A AAA AGA AGGA AGA TAGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA -AGA
14755 AGA AGGA AGA AGA AGGA AGA AGA A
1 AGA A-GA AGA AGA A-GA AGA AGA A
14779 AAATGGGGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
2 2 0.04
3 43 0.75
4 12 0.21
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:14759 original size:10 final size:10
Alignment explanation
Indices: 14752--14778 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
14742 GAAGGAAGAT
14752 AGAAGAAGGA
1 AGAAGAAGGA
14762 AGAAGAAGGA
1 AGAAGAAGGA
14772 AGAAGAA
1 AGAAGAA
14779 AAATGGGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (10 bp):
AGAAGAAGGA
Found at i:15029 original size:18 final size:19
Alignment explanation
Indices: 15006--15045 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
14996 AAGAACTTCT
*
15006 ATAATA-TTAATTATGAAA
1 ATAATATTTAAGTATGAAA
*
15024 ATAATATTTAAGTCTGAAA
1 ATAATATTTAAGTATGAAA
15043 ATA
1 ATA
15046 TCATAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (19 bp):
ATAATATTTAAGTATGAAA
Found at i:15392 original size:22 final size:22
Alignment explanation
Indices: 15367--15409 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
15357 TTCTGTCACA
* *
15367 TTTTTATTTGTCTTTTGGTATG
1 TTTTCATTTGTCTTTTAGTATG
*
15389 TTTTCGTTTGTCTTTTAGTAT
1 TTTTCATTTGTCTTTTAGTAT
15410 ATTTCAGTCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.67
Consensus pattern (22 bp):
TTTTCATTTGTCTTTTAGTATG
Found at i:16040 original size:33 final size:33
Alignment explanation
Indices: 15998--16063 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
15988 GATCTGCTGA
15998 GCTCATGTCTGTTTTTAATATGTAGCAAGGGTT
1 GCTCATGTCTGTTTTTAATATGTAGCAAGGGTT
16031 GCTCATGTCTGTTTTTAATATGTAGCAAGGGTT
1 GCTCATGTCTGTTTTTAATATGTAGCAAGGGTT
16064 TGTGAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.42
Consensus pattern (33 bp):
GCTCATGTCTGTTTTTAATATGTAGCAAGGGTT
Found at i:17429 original size:2 final size:2
Alignment explanation
Indices: 17422--17449 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17412 ACCTTAAATA
17422 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
17450 GTACATTTAT
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):
AT
Found at i:18951 original size:3 final size:3
Alignment explanation
Indices: 18945--18981 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
18935 AACATTATAG
18945 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18982 CAAAAGTCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20159 original size:61 final size:61
Alignment explanation
Indices: 19999--20143 Score: 238
Period size: 61 Copynumber: 2.4 Consensus size: 61
19989 AAAGACTACA
** *
19999 TTTGAAGATAACATTGTTCCTTTACGTTGAGGAAGTCTAATTGTCTGAATATAATTTGCTT
1 TTTGAAGACGACATTGTTCCTTTACGTTGAGGAAGTCTAATTGCCTGAATATAATTTGCTT
*
20060 GTTGAAGACGACATTGTTCCTTTACGTTGAGGAAGTCTAATTGCCAT-AATATAATTTGCTT
1 TTTGAAGACGACATTGTTCCTTTACGTTGAGGAAGTCTAATTGCC-TGAATATAATTTGCTT
20121 TTTGAAGACGACATTGTTCCTTT
1 TTTGAAGACGACATTGTTCCTTT
20144 GTGTTAAGGA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
61 77 0.99
62 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.19, T:0.41
Consensus pattern (61 bp):
TTTGAAGACGACATTGTTCCTTTACGTTGAGGAAGTCTAATTGCCTGAATATAATTTGCTT
Found at i:20592 original size:24 final size:24
Alignment explanation
Indices: 20558--20606 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20548 TTTTAAAATG
20558 TGAAAAAGTTTGATG-AAGAAGTTT
1 TGAAAAAGTTTGATGAAAGAA-TTT
* *
20582 TGAAAATGTTTTATGAAAGAATTT
1 TGAAAAAGTTTGATGAAAGAATTT
20606 T
1 T
20607 AAATAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.41, C:0.00, G:0.20, T:0.39
Consensus pattern (24 bp):
TGAAAAAGTTTGATGAAAGAATTT
Found at i:20614 original size:25 final size:24
Alignment explanation
Indices: 20560--20614 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
20550 TTAAAATGTG
20560 AAAAA-GTTTGATGAAGAAGTTTT
1 AAAAATGTTTGATGAAGAAGTTTT
* *
20583 GAAAATGTTTTATGAAAGAA-TTTT
1 AAAAATGTTTGATG-AAGAAGTTTT
20607 AAATAATG
1 AAA-AATG
20615 AAAGAATTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 13 0.50
25 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.36
Consensus pattern (24 bp):
AAAAATGTTTGATGAAGAAGTTTT
Found at i:20632 original size:18 final size:18
Alignment explanation
Indices: 20594--20632 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20584 AAAATGTTTT
* *
20594 ATGAAAGAATTTTAAATA
1 ATGAAAGAATTTGAAAAA
20612 ATGAAAGAATTTGAAAAA
1 ATGAAAGAATTTGAAAAA
20630 ATG
1 ATG
20633 TTTGATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.28
Consensus pattern (18 bp):
ATGAAAGAATTTGAAAAA
Found at i:22967 original size:13 final size:13
Alignment explanation
Indices: 22949--22996 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
22939 ACCCGACCCG
22949 ACCCGACCCGTTT
1 ACCCGACCCGTTT
22962 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
22975 ACCCGACCAGTTG
1 ACCCGACCCGTTT
22988 ACCCGACCC
1 ACCCGACCC
22997 AACCCGTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:23002 original size:31 final size:31
Alignment explanation
Indices: 22962--23021 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
22952 CGACCCGTTT
* *
22962 ACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCAACCCGTTGACCCGACCAGTTGACCCG
*
22993 ACCCAACCCGTTGACCCGACCCGTTGACC
1 ACCCAACCCGTTGACCCGACCAGTTGACC
23022 GTTGACCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCAACCCGTTGACCCGACCAGTTGACCCG
Found at i:23008 original size:13 final size:13
Alignment explanation
Indices: 22992--23021 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22982 CAGTTGACCC
22992 GACCCAACCCGTT
1 GACCCAACCCGTT
*
23005 GACCCGACCCGTT
1 GACCCAACCCGTT
23018 GACC
1 GACC
23022 GTTGACCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:25520 original size:23 final size:23
Alignment explanation
Indices: 25494--25583 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
25484 TCAAATTTGA
* *
25494 ATTCTGTTATGATATTGACCTGG
1 ATTCTGATATGATATTGACATGG
*
25517 ATTCTGATCTGATATTGACATGG
1 ATTCTGATATGATATTGACATGG
* * *
25540 ATTCTGATCTGATACATGACATGA
1 ATTCTGATATGATA-TTGACATGG
*
25564 ATTATGATATGATACTTGAC
1 ATTCTGATATGATA-TTGAC
25584 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 34 0.59
24 24 0.41
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATATTGACATGG
Found at i:25571 original size:24 final size:24
Alignment explanation
Indices: 25503--25593 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
25493 AATTCTGTTA
* * *
25503 TGATA-TTGACCTGGATTCTGATC
1 TGATACTTGACATGAATTATGATC
* *
25526 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACATGAATTATGATC
* *
25549 TGATACATGACATGAATTATGATA
1 TGATACTTGACATGAATTATGATC
*
25573 TGATACTTGACTTGAATTATG
1 TGATACTTGACATGAATTATG
25594 TTTTGATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
23 27 0.45
24 33 0.55
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGAATTATGATC
Found at i:25709 original size:35 final size:35
Alignment explanation
Indices: 25662--25736 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
25652 TGGAGGAAGA
* *
25662 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
25697 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
25732 TTACT
1 TTACT
25737 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:27730 original size:13 final size:13
Alignment explanation
Indices: 27712--27759 Score: 78
Period size: 13 Copynumber: 3.7 Consensus size: 13
27702 ACCCGACCCG
27712 ACCCGACCCGTTT
1 ACCCGACCCGTTT
27725 ACCCGACCCGTTT
1 ACCCGACCCGTTT
* *
27738 ACCCGACCAGTTG
1 ACCCGACCCGTTT
27751 ACCCGACCC
1 ACCCGACCC
27760 AACCCGTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 32 1.00
ACGTcount: A:0.19, C:0.48, G:0.17, T:0.17
Consensus pattern (13 bp):
ACCCGACCCGTTT
Found at i:27765 original size:31 final size:31
Alignment explanation
Indices: 27725--27784 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
27715 CGACCCGTTT
* *
27725 ACCCGACCCGTTTACCCGACCAGTTGACCCG
1 ACCCAACCCGTTGACCCGACCAGTTGACCCG
*
27756 ACCCAACCCGTTGACCCGACCCGTTGACC
1 ACCCAACCCGTTGACCCGACCAGTTGACC
27785 GTTGACCCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.18, T:0.15
Consensus pattern (31 bp):
ACCCAACCCGTTGACCCGACCAGTTGACCCG
Found at i:27771 original size:13 final size:13
Alignment explanation
Indices: 27755--27784 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
27745 CAGTTGACCC
27755 GACCCAACCCGTT
1 GACCCAACCCGTT
*
27768 GACCCGACCCGTT
1 GACCCAACCCGTT
27781 GACC
1 GACC
27785 GTTGACCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.47, G:0.20, T:0.13
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:30283 original size:23 final size:23
Alignment explanation
Indices: 30257--30346 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 23
30247 TCAAATTTGA
* *
30257 ATTCTGTTATGATATTGACCTGG
1 ATTCTGATATGATATTGACATGG
*
30280 ATTCTGATCTGATATTGACATGG
1 ATTCTGATATGATATTGACATGG
* * *
30303 ATTCTGATCTGATACATGACATGA
1 ATTCTGATATGATA-TTGACATGG
*
30327 ATTATGATATGATACTTGAC
1 ATTCTGATATGATA-TTGAC
30347 TTGAATTATG
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 34 0.59
24 24 0.41
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (23 bp):
ATTCTGATATGATATTGACATGG
Found at i:30334 original size:24 final size:24
Alignment explanation
Indices: 30266--30356 Score: 96
Period size: 24 Copynumber: 3.9 Consensus size: 24
30256 AATTCTGTTA
* * *
30266 TGATA-TTGACCTGGATTCTGATC
1 TGATACTTGACATGAATTATGATC
* *
30289 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACATGAATTATGATC
* *
30312 TGATACATGACATGAATTATGATA
1 TGATACTTGACATGAATTATGATC
*
30336 TGATACTTGACTTGAATTATG
1 TGATACTTGACATGAATTATG
30357 TTTTGATTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
23 27 0.45
24 33 0.55
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (24 bp):
TGATACTTGACATGAATTATGATC
Found at i:30471 original size:35 final size:35
Alignment explanation
Indices: 30424--30498 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
30414 TGGAGGAAGA
* *
30424 TTACTTGGAGGCTCCTTGGCTGTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
*
30459 TTACTTGCAGGCTCCTCGGCTTTGTGCTCAGGGCC
1 TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
30494 TTACT
1 TTACT
30499 GTTCGTGACG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.09, C:0.28, G:0.29, T:0.33
Consensus pattern (35 bp):
TTACTTGCAGGCTCCTCGGCTGTGTGCTCAGGGCC
Found at i:41575 original size:16 final size:16
Alignment explanation
Indices: 41554--41588 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
41544 GGGATGATTG
41554 GATTTTGATTTAATTT
1 GATTTTGATTTAATTT
41570 GATTTTGATTTAATTT
1 GATTTTGATTTAATTT
41586 GAT
1 GAT
41589 ATTGTGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (16 bp):
GATTTTGATTTAATTT
Found at i:49324 original size:29 final size:29
Alignment explanation
Indices: 49275--49331 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
49265 TCTGTACATT
*
49275 AAAGAAAGGCATCATTAGTGCAATTGATC
1 AAAGAAAGGCATCATTAGTGCAAATGATC
* * *
49304 AAAGAAATGCATCGTTGGTGCAAATGAT
1 AAAGAAAGGCATCATTAGTGCAAATGAT
49332 ATAAATACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (29 bp):
AAAGAAAGGCATCATTAGTGCAAATGATC
Found at i:55228 original size:9 final size:9
Alignment explanation
Indices: 55214--55239 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
55204 ACCTTAATTA
55214 GTTAAAGAT
1 GTTAAAGAT
55223 GTTAAAGAT
1 GTTAAAGAT
55232 GTTAAAGA
1 GTTAAAGA
55240 GATAGTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (9 bp):
GTTAAAGAT
Found at i:57716 original size:2 final size:2
Alignment explanation
Indices: 57709--57747 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
57699 TGCTACTTTA
57709 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 A
57748 CATTTATCCC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Done.