Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001228.1 Hibiscus syriacus cultivar Beakdansim tig00002417_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: 111923
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:7114 original size:3 final size:3
Alignment explanation
Indices: 7106--7131 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
7096 TGTTTTGTTT
7106 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
7132 GGGCTTGGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:8050 original size:24 final size:24
Alignment explanation
Indices: 7993--8066 Score: 98
Period size: 23 Copynumber: 3.2 Consensus size: 24
7983 CGAACGGATG
* *
7993 TAAACGAACATAAATGAACAC-AA
1 TAAACGAACGTAAAAGAACACAAA
8016 TAAACGAACGTAAAAGAACACAAA
1 TAAACGAACGTAAAAGAACACAAA
* *
8040 TGAACGAACGTAAACGAACAC-AA
1 TAAACGAACGTAAAAGAACACAAA
8063 TAAA
1 TAAA
8067 ATAACATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 24 0.53
24 21 0.47
ACGTcount: A:0.59, C:0.18, G:0.12, T:0.11
Consensus pattern (24 bp):
TAAACGAACGTAAAAGAACACAAA
Found at i:9157 original size:20 final size:20
Alignment explanation
Indices: 9107--9157 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
9097 TTTTCCCAAT
*
9107 TCACAATGCGAATAAGTAAA
1 TCACAATGCGAATAAGGAAA
* **
9127 TCACAACGCGAATTGGGAAA
1 TCACAATGCGAATAAGGAAA
*
9147 TCGCAATGCGA
1 TCACAATGCGA
9158 TACTTACTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.18
Consensus pattern (20 bp):
TCACAATGCGAATAAGGAAA
Found at i:9192 original size:21 final size:19
Alignment explanation
Indices: 9145--9240 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 19
9135 CGAATTGGGA
*
9145 AATCGCAATGCGATACTTAC
1 AATCGCAATGCGATA-ATAC
*
9165 TATCGCAATGCGATAATAC
1 AATCGCAATGCGATAATAC
* * *
9184 AAAATCGCAACGAGATACTGAC
1 --AATCGCAATGCGATAAT-AC
** *
9206 TTTCGCAACGCGATAATAC
1 AATCGCAATGCGATAATAC
9225 ATAATCGCAATGCGAT
1 --AATCGCAATGCGAT
9241 TTTCAAAGCG
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 24 0.41
22 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.23
Consensus pattern (19 bp):
AATCGCAATGCGATAATAC
Found at i:9192 original size:41 final size:41
Alignment explanation
Indices: 9144--9240 Score: 140
Period size: 41 Copynumber: 2.4 Consensus size: 41
9134 GCGAATTGGG
* *
9144 AAATCGCAATGCGATACTTACTATCGCAATGCGATAATACA
1 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
* * *
9185 AAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACA
1 AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
*
9226 TAATCGCAATGCGAT
1 AAATCGCAATGCGAT
9241 TTTCAAAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (41 bp):
AAATCGCAATGCGATACTGACTATCGCAACGCGATAATACA
Found at i:9435 original size:22 final size:22
Alignment explanation
Indices: 9407--9450 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9397 CACTCTCTCA
9407 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
9429 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
9451 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:9751 original size:20 final size:20
Alignment explanation
Indices: 9712--9770 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
9702 GCGATTCTCT
**
9712 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
9732 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * **
9752 TGTTGTGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
9771 AGAAACTATT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:9961 original size:25 final size:24
Alignment explanation
Indices: 9907--9961 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
9897 TGTTTATTAT
* *
9907 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
9931 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
9957 TGTTT
1 TGTTT
9962 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:11651 original size:19 final size:20
Alignment explanation
Indices: 11597--11642 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
11587 TAGTTTACTT
* *
11597 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
11617 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
11637 TCGCAA
1 TCGCAA
11643 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:11658 original size:19 final size:19
Alignment explanation
Indices: 11636--11718 Score: 104
Period size: 19 Copynumber: 4.6 Consensus size: 19
11626 GGAAATGGCT
*
11636 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
11655 ATCGCAA--CG-AA--AAA
1 ATCGCAATGCGAAATGAAA
*
11669 ATCGCAATTCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
11688 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
11707 ATCGCAATGCGA
1 ATCGCAATGCGA
11719 TTTGTGTTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.18
16 4 0.07
17 3 0.05
19 38 0.69
ACGTcount: A:0.47, C:0.18, G:0.19, T:0.16
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:11770 original size:19 final size:19
Alignment explanation
Indices: 11746--11804 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
11736 AATTTTGTCG
11746 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
11765 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
11779 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
11798 TTGCGAT
1 TTGCGAT
11805 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 13 0.39
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:11784 original size:14 final size:14
Alignment explanation
Indices: 11730--11788 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
11720 TTGTGTTTCG
*
11730 CGTTGCAATTTTGT
1 CGTTGCGATTTTGT
*
11744 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
11761 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
11777 CGTTGCGATTTT
1 CGTTGCGATTTT
11789 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
14 17 0.46
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:11802 original size:33 final size:33
Alignment explanation
Indices: 11725--11804 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
11715 GCGATTTGTG
* *
11725 TTTCGCGTTGCAATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
11758 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
11791 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
11805 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:11823 original size:20 final size:19
Alignment explanation
Indices: 11789--11839 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
11779 TTGCGATTTT
*
11789 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
11808 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
11828 CATTTTCGCGTT
1 CA-TTTCGCGTT
11840 ACAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 5 0.18
20 20 0.71
21 3 0.11
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:12242 original size:21 final size:20
Alignment explanation
Indices: 12216--12285 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
12206 CTATCATCCC
12216 TCAAGAGTCCCCTCCAATCGT
1 TCAAGAGTCCCCTCC-ATCGT
* * **
12237 TCAAGAGGCCCCTATCATCCC
1 TCAAGAGTCCCCT-CCATCGT
* *
12258 TCAAGAGTCCCCCCCCACCGT
1 TCAAGAGT-CCCCTCCATCGT
12279 TCAAGAG
1 TCAAGAG
12286 GCCACTGTCA
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
21 32 0.86
22 5 0.14
ACGTcount: A:0.24, C:0.41, G:0.16, T:0.19
Consensus pattern (20 bp):
TCAAGAGTCCCCTCCATCGT
Found at i:12264 original size:42 final size:42
Alignment explanation
Indices: 12205--12297 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
12195 GCCCGATTCA
* *
12205 CCTATCATCCCTCAAGAGTCCCCTCCAATCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCC
*
12247 CCTATCATCCCTCAAGAGTCCCCCCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCC
* *
12289 ACTGTCATC
1 CCTATCATC
12298 GTTGAAGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.43, G:0.14, T:0.20
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCCCCCCAACCGTTCAAGAGGCC
Found at i:13741 original size:14 final size:14
Alignment explanation
Indices: 13707--13745 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
13697 TTGATTGTTT
13707 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
13721 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
13735 TGTTGATTTGT
1 AATTGATTTGT
13746 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:13891 original size:14 final size:14
Alignment explanation
Indices: 13872--13925 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
13862 GAAACTGACT
13872 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
13886 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
13905 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
13919 ATCGCAA
1 ATCGCAA
13926 TGTGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:13918 original size:19 final size:19
Alignment explanation
Indices: 13882--13918 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13872 ATCGCAACGA
* *
13882 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
13901 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
13919 ATCGCAATGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:13974 original size:20 final size:20
Alignment explanation
Indices: 13949--14044 Score: 97
Period size: 20 Copynumber: 4.8 Consensus size: 20
13939 TCGCATTGCG
*
13949 ATTTTCTAGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
***
13969 ATTTTC-ACGTTGCGATTTTTC
1 ATTTTCGA-GTTGCGA-TAGCC
*
13990 A-TTTCGAATTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
14009 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGAGTTGCGATAGCC
*
14029 ATTTTCGTGTTGCGAT
1 ATTTTCGAGTTGCGAT
14045 TTCCCCGATG
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
19 4 0.06
20 54 0.87
21 4 0.06
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (20 bp):
ATTTTCGAGTTGCGATAGCC
Found at i:14035 original size:40 final size:41
Alignment explanation
Indices: 13949--14044 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 41
13939 TCGCATTGCG
* ***
13949 ATTTTCTAGTTGCGATAGCCATTTTCACGTTGCGATTTTTC
1 ATTTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCC
* *
13990 A-TTTCGAATTGCGATAGCCATTTTCGCGTTGCGA-TAGCC
1 ATTTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCC
*
14029 ATTTTCGTGTTGCGAT
1 ATTTTCGAGTTGCGAT
14045 TTCCCCGATG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
39 3 0.07
40 42 0.91
41 1 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.42
Consensus pattern (41 bp):
ATTTTCGAGTTGCGATAGCCATTTTCACGTTGCGATTAGCC
Found at i:14283 original size:20 final size:20
Alignment explanation
Indices: 14258--14307 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
14248 TTGAAGATGA
14258 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
*** *
14278 TTGCGAAAGTCAGAATCTTG
1 TTGCGATTTTCAGAATCTCG
14298 TTGCGATTTT
1 TTGCGATTTT
14308 GTATTATCTC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:14601 original size:12 final size:12
Alignment explanation
Indices: 14584--14615 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
14574 CTCCGGCGAC
14584 ATCCGTTCCTAT
1 ATCCGTTCCTAT
14596 ATCCGTTCCTAT
1 ATCCGTTCCTAT
14608 ATCC-TTCC
1 ATCCGTTCC
14616 CCATCCGGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.16, C:0.38, G:0.06, T:0.41
Consensus pattern (12 bp):
ATCCGTTCCTAT
Found at i:15199 original size:24 final size:24
Alignment explanation
Indices: 15172--15225 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
15162 GTATTCGAAA
*
15172 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
15196 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
15220 TTTGAT
1 TTTGAT
15226 GATGTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:15417 original size:12 final size:12
Alignment explanation
Indices: 15400--15436 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
15390 ATATAATCCT
15400 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15412 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15424 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15436 G
1 G
15437 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:16314 original size:21 final size:21
Alignment explanation
Indices: 16248--16314 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
16238 GTGAATCGGG
*
16248 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
16268 CCTCTTCAACGATGAAAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
16290 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
16311 CTCT
1 CTCT
16315 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:16333 original size:42 final size:41
Alignment explanation
Indices: 16248--16370 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 41
16238 GTGAATCGGG
* * * * *
16248 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGAAAGTGGC
1 CTCTTGAAAGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
*
16290 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAAAGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
16332 CTCTTCAAAGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAAAGGTGGGAGGGGACTCTCGA-GGATGATAGG
16371 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.16, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAAAGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:16767 original size:91 final size:93
Alignment explanation
Indices: 16588--16772 Score: 306
Period size: 91 Copynumber: 2.0 Consensus size: 93
16578 ATTTCAAACT
16588 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
16653 AGAATTGGCAGCAACCGAATAAATTTAC
66 AGAATTGGCAGCAACCGAATAAATTTAC
*
16681 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAA-ACA-A-TTTA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
*
16742 GCAGTATTGGCAGCAACCGAATAAATTTAC
64 GCAGAATTGGCAGCAACCGAATAAATTTAC
16772 T
1 T
16773 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 34 0.39
92 1 0.01
93 22 0.25
94 4 0.05
95 27 0.31
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
AGAATTGGCAGCAACCGAATAAATTTAC
Found at i:18486 original size:20 final size:19
Alignment explanation
Indices: 18455--18576 Score: 84
Period size: 20 Copynumber: 6.8 Consensus size: 19
18445 TCTTTTGGTT
18455 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
18474 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
18495 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
18514 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
18528 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
18547 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
18561 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
18577 TGCGATTTTG
Statistics
Matches: 80, Mismatches: 11, Indels: 24
0.70 0.10 0.21
Matches are distributed among these distances:
14 20 0.25
16 4 0.05
17 4 0.05
19 21 0.26
20 29 0.36
21 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:18523 original size:14 final size:14
Alignment explanation
Indices: 18504--18559 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
18494 GGAAATGACT
18504 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
18518 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
18535 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
18551 ATCGCAACG
1 ATCGCAACG
18560 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 16 0.46
16 6 0.17
17 6 0.17
19 7 0.20
ACGTcount: A:0.39, C:0.25, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:18537 original size:33 final size:33
Alignment explanation
Indices: 18480--18576 Score: 167
Period size: 33 Copynumber: 2.9 Consensus size: 33
18470 ACGAGATAAT
18480 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
18514 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
18547 GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGACTATCGCAA
18577 TGCGATTTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:18610 original size:19 final size:19
Alignment explanation
Indices: 18577--18643 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
18567 AAAATCGCAA
**
18577 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
18596 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
* **
18615 TGTGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
18635 TGCGATTTT
1 TGCGATTTT
18644 CATTCTCGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 28 0.72
20 11 0.28
ACGTcount: A:0.10, C:0.15, G:0.25, T:0.49
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:19183 original size:20 final size:20
Alignment explanation
Indices: 19158--19309 Score: 78
Period size: 20 Copynumber: 7.5 Consensus size: 20
19148 GCTATGTAAA
19158 TCGCATTGCGATAGTAAG-AT
1 TCGCATTGCGAT-GTAAGTAT
* *
19178 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
* ***
19198 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATGTAAGT-AT
* *
19219 TCGCATTGCGAT-TTACTAAT
1 TCGCATTGCGATGTAAGT-AT
* * *
19239 TCGCGTTGCGAT-TTACTAAT
1 TCGCATTGCGATGTAAGT-AT
* * *
19259 TCGCGTTGCGAT-TTACTAAT
1 TCGCATTGCGATGTAAGT-AT
* * *
19279 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATGTAAGTAT
19299 TCGCATTGCGA
1 TCGCATTGCGA
19310 ATTATGAAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
19 3 0.03
20 100 0.84
21 16 0.13
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
TCGCATTGCGATGTAAGTAT
Found at i:19228 original size:41 final size:42
Alignment explanation
Indices: 19176--19409 Score: 207
Period size: 41 Copynumber: 5.7 Consensus size: 42
19166 CGATAGTAAG
19176 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCTA
* *
19217 ATTCGCATTGCGATTTAC-TAATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCTA
* * * *
19257 ATTCGCGTTGCGATTTAC-TAATTCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCTA
* * * * ** * * *
19297 ATTCGCATTGCGAATTATGAAAATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCTA
* * * *
19338 AATCGCATTGCGA-ATA-GTCAGTATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTTACGT-AAT-TCGCATTGCGATTTTCCTA
*
19380 ATTCGCATTGCGATTTAC-TTATTCGCATTG
1 ATTCGCATTGCGATTTACGTAATTCGCATTG
19410 AGAATTGGGA
Statistics
Matches: 154, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
39 1 0.01
40 62 0.40
41 72 0.47
42 16 0.10
43 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (42 bp):
ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCTA
Found at i:19350 original size:20 final size:21
Alignment explanation
Indices: 19176--19409 Score: 216
Period size: 20 Copynumber: 11.5 Consensus size: 21
19166 CGATAGTAAG
19176 ATTCGCATTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* *
19196 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTA
19217 ATTCGCATTGCGATTTAC-TA
1 ATTCGCATTGCGATTTACGTA
*
19237 ATTCGCGTTGCGATTTAC-TA
1 ATTCGCATTGCGATTTACGTA
*
19257 ATTCGCGTTGCGATTTAC-TA
1 ATTCGCATTGCGATTTACGTA
*
19277 ATTCGCGTTGCGATTTACGT-
1 ATTCGCATTGCGATTTACGTA
* * *
19297 ATTCGCATTGCGAATTATGAA
1 ATTCGCATTGCGATTTACGTA
* ** *
19318 AATCGCAACGCGA-ATACGTA
1 ATTCGCATTGCGATTTACGTA
* *
19338 AATCGCATTGCGA-ATA-GTCA
1 ATTCGCATTGCGATTTACGT-A
* * **
19358 GTATCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTACGTA
*
19380 ATTCGCATTGCGATTTAC-TT
1 ATTCGCATTGCGATTTACGTA
19400 ATTCGCATTG
1 ATTCGCATTG
19410 AGAATTGGGA
Statistics
Matches: 181, Mismatches: 26, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 122 0.67
21 54 0.30
22 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (21 bp):
ATTCGCATTGCGATTTACGTA
Found at i:19415 original size:103 final size:102
Alignment explanation
Indices: 19259--19474 Score: 292
Period size: 103 Copynumber: 2.1 Consensus size: 102
19249 ATTTACTAAT
* * * *
19259 TCGCGTTGCGATTTACTAATTCGCGTTGCGATTTACGTATTCGCATTGCGAATTATGAAAATCGC
1 TCGCGTTGCGATTTACAAATTCGCATTGCGATTTACGTATTCGCATTGAGAATTAGGAAAATCGC
*
19324 AACGCG-AATACGTAAATCGCATTGCGAATAGTCAGT-A
66 AACGCGAAATACGAAAATCGCATTGCG-ATAGTCA-TAA
* * * *
19361 TCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTATTCGCATTGAGAATTGGGAAAATCG
1 TCGCGTTGCGA-TTTACAAATTCGCATTGCGATTTACGTATTCGCATTGAGAATTAGGAAAATCG
**
19426 CAACGCGAAATTGGAAAATCGCATTGCGATAGTCATAA
65 CAACGCGAAATACGAAAATCGCATTGCGATAGTCATAA
19464 TCGCGTTGCGA
1 TCGCGTTGCGA
19475 ATCTGGAAAC
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
102 11 0.11
103 71 0.72
104 17 0.17
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (102 bp):
TCGCGTTGCGATTTACAAATTCGCATTGCGATTTACGTATTCGCATTGAGAATTAGGAAAATCGC
AACGCGAAATACGAAAATCGCATTGCGATAGTCATAA
Found at i:19454 original size:21 final size:22
Alignment explanation
Indices: 19402--19454 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
19392 ATTTACTTAT
*
19402 TCGCATTGAG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
19423 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
19444 TCGCATTGCGA
1 TCGCATTGCGA
19455 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.36, C:0.17, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:22213 original size:8 final size:9
Alignment explanation
Indices: 22187--22224 Score: 53
Period size: 8 Copynumber: 4.3 Consensus size: 9
22177 TTCATACGTG
22187 TATAAATAT
1 TATAAATAT
22196 TATTAAATAT
1 TA-TAAATAT
22206 TA-AAATA-
1 TATAAATAT
22213 TATAAATAT
1 TATAAATAT
22222 TAT
1 TAT
22225 CTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
7 2 0.08
8 10 0.38
9 5 0.19
10 9 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TATAAATAT
Found at i:29375 original size:35 final size:34
Alignment explanation
Indices: 29329--29440 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 34
29319 AAAACAATTC
* *
29329 TCAATTTCATTCTAAACCACAAATTCCAAAGTATT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
29364 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* ** *
29399 TCAATTACATTCTAAAACCCAAATTATAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
29434 TCAATTT
1 TCAATTT
29441 TTGTCTTTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 1 0.01
35 61 0.90
36 6 0.09
ACGTcount: A:0.43, C:0.21, G:0.01, T:0.35
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:30368 original size:35 final size:34
Alignment explanation
Indices: 30320--30431 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
30310 ATTCCTCCTT
*
30320 AAATTGAAATGTTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTGTTTTAGAATTTGGG-TTTAGAATG
*
30355 TAATTGAATTGTTTTAGAATTTAGGGTTTAGAATG
1 AAATTGAATTGTTTTAGAATTT-GGGTTTAGAATG
* *
30390 AAATTGAATTATTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTGTTTTAGAATTT-GGGTTTAGAATG
30425 AAATTGA
1 AAATTGA
30432 GGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.34, C:0.00, G:0.23, T:0.43
Consensus pattern (34 bp):
AAATTGAATTGTTTTAGAATTTGGGTTTAGAATG
Found at i:36509 original size:16 final size:15
Alignment explanation
Indices: 36487--36551 Score: 64
Period size: 14 Copynumber: 4.3 Consensus size: 15
36477 AAAATTATTT
36487 AAAAT-TTAAATATA
1 AAAATATTAAATATA
*
36501 AAAATATTTAGATATTCA
1 AAAATA-TTAAATA-T-A
36519 AAAA-ATTAAATAT-
1 AAAATATTAAATATA
*
36532 AAAATATTAAAAATA
1 AAAATATTAAATATA
36547 AAAAT
1 AAAAT
36552 TAAATTACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
13 4 0.10
14 13 0.31
15 6 0.14
16 12 0.29
17 2 0.05
18 5 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAATATTAAATATA
Found at i:39407 original size:20 final size:20
Alignment explanation
Indices: 39367--39406 Score: 57
Period size: 18 Copynumber: 2.0 Consensus size: 20
39357 AAATTCATTT
39367 AGATTATAAAAAACAAAAAA
1 AGATTATAAAAAACAAAAAA
39387 AGA-T-TAAAAAACATAAAAA
1 AGATTATAAAAAACA-AAAAA
39406 A
1 A
39407 ATATTCAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 9 0.47
19 7 0.37
20 3 0.16
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (20 bp):
AGATTATAAAAAACAAAAAA
Found at i:41402 original size:18 final size:19
Alignment explanation
Indices: 41379--41415 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
41369 CCGGTAATCC
41379 TATTCCC-TGATAATCTTT
1 TATTCCCATGATAATCTTT
41397 TATTCCCATTGATAATCTT
1 TATTCCCA-TGATAATCTT
41416 ACATTCTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.24, C:0.22, G:0.05, T:0.49
Consensus pattern (19 bp):
TATTCCCATGATAATCTTT
Found at i:45021 original size:24 final size:23
Alignment explanation
Indices: 44977--45021 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
44967 AAATAAGAAA
*
44977 AAATAATTATTACATAAAATTTT
1 AAATAATTATTACAAAAAATTTT
45000 AAATAATCTATTA-AAAAGAATT
1 AAATAAT-TATTACAAAA-AATT
45022 AATATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
AAATAATTATTACAAAAAATTTT
Found at i:50773 original size:14 final size:15
Alignment explanation
Indices: 50735--50777 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
50725 TTGGTTTTCC
50735 GGAAAATGAATTACT
1 GGAAAATGAATTACT
**
50750 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
50764 GGAAAATGAATTAC
1 GGAAAATGAATTAC
50778 ATTTATGGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.42, C:0.07, G:0.21, T:0.30
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:51112 original size:23 final size:23
Alignment explanation
Indices: 51063--51124 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
51053 GTGTTATATT
* **
51063 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAACTAAA
* *
51086 ATATTTTAAATATATTTACTAAA
1 ATATTTTAAAAATATTAACTAAA
*
51109 ATATTATTTAAAATAT
1 ATATT-TTAAAAATAT
51125 AAATAATATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 23 0.74
24 8 0.26
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
ATATTTTAAAAATATTAACTAAA
Found at i:51151 original size:27 final size:26
Alignment explanation
Indices: 51110--51263 Score: 88
Period size: 27 Copynumber: 5.8 Consensus size: 26
51100 TTTACTAAAA
*
51110 TATTATTTAAAATATAAATAATATTAT
1 TATTA-TTAATATATAAATAATATTAT
*
51137 TCATTATTAATATATAAA-AAAATTTAT
1 T-ATTATTAATATATAAATAATA-TTAT
* *
51164 TATATATTAA-A-ATAAAAAATATAAT
1 TAT-TATTAATATATAAATAATATTAT
* *
51189 ATCTTA-TATTATTATAATATAATTATTA-
1 -TATTATTAATA-TATAA-ATAA-TATTAT
*
51217 TATTATTAA-ACTAAAAAATAATATTA-
1 TATTATTAATA-T-ATAAATAATATTAT
*
51243 TATTATTATATATATTAATAA
1 TATTATTA-ATATATAAATAA
51264 ATATATTTTA
Statistics
Matches: 99, Mismatches: 14, Indels: 29
0.70 0.10 0.20
Matches are distributed among these distances:
24 2 0.02
25 11 0.11
26 30 0.30
27 39 0.39
28 13 0.13
29 4 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TATTATTAATATATAAATAATATTAT
Found at i:51199 original size:54 final size:50
Alignment explanation
Indices: 51109--51252 Score: 134
Period size: 52 Copynumber: 2.8 Consensus size: 50
51099 ATTTACTAAA
*
51109 ATATTATTTAAAATATAAATAATATTATTCATTATTAATATATAAAAAAATTTATT
1 ATATTA-TTAAAATA-AAA-AATATAATTCATTATT-AT-TATAAAAAAA-TTATT
* * *
51165 ATA-TATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTATT
1 ATATTATTAAAATAAAAAATATAAT-TCAT-TATTATTATAAAAAAATTATT
*
51216 ATATTATTAAACTAAAAAATA-ATATT-A-TATTATTATA
1 ATATTATTAAAATAAAAAATATA-ATTCATTATTATTATA
51253 TATATTAATA
Statistics
Matches: 78, Mismatches: 6, Indels: 16
0.78 0.06 0.16
Matches are distributed among these distances:
48 10 0.13
51 10 0.13
52 33 0.42
53 8 0.10
54 12 0.15
55 2 0.03
56 3 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (50 bp):
ATATTATTAAAATAAAAAATATAATTCATTATTATTATAAAAAAATTATT
Found at i:54596 original size:21 final size:20
Alignment explanation
Indices: 54555--54599 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
54545 TGATATTAGT
*
54555 TTGTCATGCAAAATTATTAG
1 TTGTCATGCAAAATTAATAG
54575 TTGTCATGCAACTAA-TAATAG
1 TTGTCATGCAA--AATTAATAG
54596 TTGT
1 TTGT
54600 ATAATGCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 9 0.41
22 2 0.09
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (20 bp):
TTGTCATGCAAAATTAATAG
Found at i:58360 original size:289 final size:286
Alignment explanation
Indices: 57844--58418 Score: 1087
Period size: 289 Copynumber: 2.0 Consensus size: 286
57834 AGAATTTAGA
57844 GAATTTCTTGAGAGTTGTTTTCTCTTTTTTATCAAAAGAGAATTATGATTGTTTCCTTGGTAGAT
1 GAATTTCTTGAGAGTTGTTTTCTCTTTTTTATCAAAAGAGAATTATGATTGTTTCCTTGGTAGAT
* *
57909 TGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTCTACCGTTGCTCGTGGTTTTTAC
66 CGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTCTACCGTTGCTCATGGTTTTTAC
57974 CCTATATTATTTAGGGGTTTTCCACATAAATTTTGTGTCTCTTTTATCTTCATTTTTATTTTTTC
131 CCTATATTATTTAGGGGTTTTCCACATAAATTTTGTGTCTCTTTTATCTTCATTTTTATTTTTTC
*
58039 AAATTATTAGTTGCGATTTTACTCTATCCGATAGCCGTCTTCCGTAACACCAGATTGATTCAAGG
196 AAATTATTAGTTGCGATTTTACTCTATCCGATAGCCGTCTTCCGCAACACCAGATTGATTCAAGG
58104 TTTTCGAAGTGATTTTTTCAAGAGGG
261 TTTTCGAAGTGATTTTTTCAAGAGGG
*
58130 GAATTTCTTGAGAGTTGTTTTCTCTTTTTTATCAAAAGAGAATTATTATTGTTTTCTCCTTGGTA
1 GAATTTCTTGAGAGTTGTTTTCTCTTTTTTATCAAAAGAGAATTATGATTG--TT-TCCTTGGTA
58195 GATCGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTCTACCGTTGCTCATGGTTTT
63 GATCGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTCTACCGTTGCTCATGGTTTT
58260 TACCCTATATTATTTAGGGGTTTTCCACATAAATTTTGTGTCTCTTTTATCTTCATTTTTATTTT
128 TACCCTATATTATTTAGGGGTTTTCCACATAAATTTTGTGTCTCTTTTATCTTCATTTTTATTTT
58325 TTCAAATTATTAGTTGCGATTTTACTCTATCCGATAGCCGTCTTCCGCAACACCAGATTGATTCA
193 TTCAAATTATTAGTTGCGATTTTACTCTATCCGATAGCCGTCTTCCGCAACACCAGATTGATTCA
58390 AGGTTTTCGAAGTGATTTTTTCAAGAGGG
258 AGGTTTTCGAAGTGATTTTTTCAAGAGGG
58419 TTGAGATTTG
Statistics
Matches: 282, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
286 50 0.18
288 2 0.01
289 230 0.82
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (286 bp):
GAATTTCTTGAGAGTTGTTTTCTCTTTTTTATCAAAAGAGAATTATGATTGTTTCCTTGGTAGAT
CGAGAGAAGTTGTAATTCCTATTTTCTCATAGTGAAATTCTTCTACCGTTGCTCATGGTTTTTAC
CCTATATTATTTAGGGGTTTTCCACATAAATTTTGTGTCTCTTTTATCTTCATTTTTATTTTTTC
AAATTATTAGTTGCGATTTTACTCTATCCGATAGCCGTCTTCCGCAACACCAGATTGATTCAAGG
TTTTCGAAGTGATTTTTTCAAGAGGG
Found at i:63909 original size:6 final size:6
Alignment explanation
Indices: 63900--63938 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
63890 AATATTATTA
* * *
63900 TTAATT TTAATT TTAATT TTAATT GTACTT ATAATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTA
63939 CTTGCAGCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (6 bp):
TTAATT
Found at i:71030 original size:21 final size:21
Alignment explanation
Indices: 71006--71045 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
70996 GAAGCCATTG
*
71006 ATGAAAGACTGGGACTTTCGT
1 ATGAAAGACTGGAACTTTCGT
*
71027 ATGAAAGATTGGAACTTTC
1 ATGAAAGACTGGAACTTTC
71046 AGAATTGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (21 bp):
ATGAAAGACTGGAACTTTCGT
Found at i:81693 original size:42 final size:42
Alignment explanation
Indices: 81646--81728 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
81636 TAAGTCATTC
* * * *
81646 GGGCCATCAGTATGTCTTTCGGGCATGATGTTTAAATCCTTA
1 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTA
81688 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTT
1 GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTT
81729 CGGGAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (42 bp):
GGGCCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTA
Found at i:81836 original size:80 final size:80
Alignment explanation
Indices: 81691--81901 Score: 332
Period size: 80 Copynumber: 2.6 Consensus size: 80
81681 ATCCTTAGGG
* * * * * *
81691 CCATCAATAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGAAATTTGTAAGCCTTCACGGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAACATGCACCGAAG
81756 AGTAGTGAAGCAAAC
66 AGTAGTGAAGCAAAC
*
81771 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAATATGCACCGAAG
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAACATGCACCGAAG
*
81836 AGTAGTGAAGCAAAT
66 AGTAGTGAAGCAAAC
* *
81851 CCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTA
1 CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTA
81902 CGTCTTTCGA
Statistics
Matches: 121, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 121 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (80 bp):
CCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAACATGCACCGAAG
AGTAGTGAAGCAAAC
Found at i:81920 original size:42 final size:41
Alignment explanation
Indices: 81861--81939 Score: 131
Period size: 42 Copynumber: 1.9 Consensus size: 41
81851 CCATCAGTAA
*
81861 GTCTTTCGAGCATGATGATGAAATCCTTCGGGTCATTTGTAC
1 GTCTTTCGAGCAAGATGAT-AAATCCTTCGGGTCATTTGTAC
*
81903 GTCTTTCGAGCAAGATGATAAGTCCTTCGGGTCATTT
1 GTCTTTCGAGCAAGATGATAAATCCTTCGGGTCATTT
81940 TAAGCCTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
41 17 0.49
42 18 0.51
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (41 bp):
GTCTTTCGAGCAAGATGATAAATCCTTCGGGTCATTTGTAC
Found at i:82433 original size:53 final size:53
Alignment explanation
Indices: 82315--82546 Score: 293
Period size: 53 Copynumber: 4.4 Consensus size: 53
82305 ATAATCACAC
*
82315 CAGAAGATTGTTCGAGTTCTACTCCCTGAAAGCAAGAGTGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTG-AAGCAAGAGGGAGCGAACCCGTAGG
* * *
82369 CTGAAGGTTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * * * *
82422 CGGAAGATTGTTCGAGTTCTACCCCCTAAAGCTAGAGGGGGCGAACTCGTAAG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * ***
82475 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGTGAACCCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
82528 TAGAAGATTGTTCGAGTTC
1 CAGAAGATTGTTCGAGTTC
82547 CTTAATCCCT
Statistics
Matches: 151, Mismatches: 27, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
53 125 0.83
54 26 0.17
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:82588 original size:54 final size:53
Alignment explanation
Indices: 82316--82590 Score: 153
Period size: 53 Copynumber: 5.2 Consensus size: 53
82306 TAATCACACC
* * * * * * **
82316 AGAAGATTGTTCGAGTTCTACTCCCTGAAAGCAAGAGTGAGCGAACCCGTAGGCT
1 AGAAGATTATTCGAGTTCTAATCCCTG-AAGAAATAGGGAGTGAACCCGTA-TTT
* * * * * * ***
82371 -GAAGGTTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGGC
1 AGAAGATTATTCGAGTTCTAATCCCTGAAGAAATAGGGAGTGAACCCGTATTT
* * ** * ** * * * * ***
82423 GGAAGATTGTTCGAGTTCTACCCCCTAAAGCTAGAGGGGGCGAACTCGTAAGC
1 AGAAGATTATTCGAGTTCTAATCCCTGAAGAAATAGGGAGTGAACCCGTATTT
* * *
82476 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAATAGGGAGTGAACCCGTTTTT
1 AGAAGATTATTCGAGTTCTAATCCCTGAAGAAATAGGGAGTGAACCCGTATTT
*
82529 AGAAGATTGTTCGAGTTCCTTAATCCCTG-AGAAATAGGGAGT-AGACCCGTCATTT
1 AGAAGATTATTCGAGTT-C-TAATCCCTGAAGAAATAGGGAGTGA-ACCCGT-ATTT
82584 -GAAGATT
1 AGAAGATT
82591 TTTCAAGTCT
Statistics
Matches: 185, Mismatches: 30, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
52 1 0.01
53 122 0.66
54 51 0.28
55 11 0.06
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (53 bp):
AGAAGATTATTCGAGTTCTAATCCCTGAAGAAATAGGGAGTGAACCCGTATTT
Found at i:90658 original size:37 final size:36
Alignment explanation
Indices: 90595--90714 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
90585 ATCCCATTAT
* * *
90595 CATTTTTC-AACAAACATCTACTAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
90630 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
90667 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
90702 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
90715 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 35 0.46
36 8 0.11
37 33 0.43
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:90670 original size:21 final size:20
Alignment explanation
Indices: 90643--90706 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
90633 TTTTTCAAAG
90643 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
90663 AAACCATTT-TCAAA----G-
1 AAA-CATTTACCAAACTTTGA
90678 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
90698 AAATCATTT
1 AAA-CATTT
90707 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
19 1 0.03
20 10 0.29
21 10 0.29
ACGTcount: A:0.45, C:0.19, G:0.05, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:94812 original size:12 final size:12
Alignment explanation
Indices: 94795--94819 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
94785 ACTATTTACG
94795 TGAATAGTAACC
1 TGAATAGTAACC
94807 TGAATAGTAACC
1 TGAATAGTAACC
94819 T
1 T
94820 CGCAAAAAAT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (12 bp):
TGAATAGTAACC
Found at i:95264 original size:37 final size:36
Alignment explanation
Indices: 95202--95321 Score: 163
Period size: 35 Copynumber: 3.3 Consensus size: 36
95192 ATCCCATTAT
* *
95202 CATTTTTC-AACAAACATCTACCAAACTTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* *
95237 CTATTTTTCAAAGAAACATTTATCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
95274 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
95309 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
95322 TTGGTTACCA
Statistics
Matches: 75, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
35 34 0.45
36 8 0.11
37 33 0.44
ACGTcount: A:0.43, C:0.18, G:0.05, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:95277 original size:21 final size:20
Alignment explanation
Indices: 95250--95313 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
95240 TTTTTCAAAG
95250 AAACATTTATCAAACTTTGA
1 AAACATTTATCAAACTTTGA
95270 AAACCATTT-TCAAA----G-
1 AAA-CATTTATCAAACTTTGA
*
95285 AAACATTTACCAAACTTTGA
1 AAACATTTATCAAACTTTGA
95305 AAATCATTT
1 AAA-CATTT
95314 TTTCAAAGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 15
0.69 0.02 0.29
Matches are distributed among these distances:
14 5 0.14
15 7 0.20
16 1 0.03
19 1 0.03
20 11 0.31
21 10 0.29
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (20 bp):
AAACATTTATCAAACTTTGA
Found at i:105832 original size:22 final size:22
Alignment explanation
Indices: 105807--105849 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
105797 TGTATTTCTT
*
105807 ACTATTTGGGAATAACATTTAC
1 ACTATTTGGAAATAACATTTAC
105829 ACTATTTGGAAATAACATTTA
1 ACTATTTGGAAATAACATTTA
105850 TTATTTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (22 bp):
ACTATTTGGAAATAACATTTAC
Found at i:105957 original size:24 final size:23
Alignment explanation
Indices: 105922--105986 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 23
105912 AAGAATAACA
*
105922 AATTATAAAATATCTAAATTATCT
1 AATTATACAATATCTAAATTAT-T
105946 AATTATACAATATCTAAATTA-T
1 AATTATACAATATCTAAATTATT
105968 -A-TATACAATATCT-AATTAT
1 AATTATACAATATCTAAATTAT
105987 ATACATATGG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
19 5 0.13
20 12 0.31
21 1 0.03
22 1 0.03
24 20 0.51
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (23 bp):
AATTATACAATATCTAAATTATT
Found at i:111716 original size:22 final size:22
Alignment explanation
Indices: 111694--111736 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
111684 ATTATTTATT
*
111694 ATTATCTATAATTTTATCAATTA
1 ATTATCTA-AATGTTATCAATTA
*
111717 ATTATTTAAATGTTATCAAT
1 ATTATCTAAATGTTATCAAT
111737 CTAGTCATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTATCTAAATGTTATCAATTA
Done.