Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001239.1 Hibiscus syriacus cultivar Beakdansim tig00002438_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: 52149
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:39 original size:19 final size:19
Alignment explanation
Indices: 1--56 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
*
1 AAAATCGCAACGCGGAAATA
1 AAAATCACAACGC-GAAATA
**
21 ACTATCACAACGCGAAATA
1 AAAATCACAACGCGAAATA
*
40 AAAATCGCAACGCGAAA
1 AAAATCACAACGCGAAA
57 CCAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (19 bp):
AAAATCACAACGCGAAATA
Found at i:62 original size:19 final size:18
Alignment explanation
Indices: 1--67 Score: 62
Period size: 19 Copynumber: 3.5 Consensus size: 18
1 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAA-A
** *
21 ACTATCACAACGCGAAATA
1 AAAATCGCAACGCGAAA-A
*
40 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAA-A
59 AAAATCGCA
1 AAAATCGCA
68 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 29 0.74
20 10 0.26
ACGTcount: A:0.49, C:0.25, G:0.15, T:0.10
Consensus pattern (18 bp):
AAAATCGCAACGCGAAAA
Found at i:85 original size:19 final size:19
Alignment explanation
Indices: 63--188 Score: 83
Period size: 19 Copynumber: 7.1 Consensus size: 19
53 GAAACCAAAA
*
63 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
82 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
96 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
115 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
129 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
148 CCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
167 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
187 TC
1 TC
189 AACCAAAAGA
Statistics
Matches: 82, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
14 20 0.24
16 4 0.05
17 5 0.06
19 37 0.45
20 16 0.20
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:104 original size:14 final size:14
Alignment explanation
Indices: 85--140 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
75 TTTCATTTCG
85 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
99 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
118 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
132 CGTTGCGAT
1 CGTTGCGAT
141 AGTCATTCCG
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:114 original size:33 final size:33
Alignment explanation
Indices: 68--163 Score: 165
Period size: 33 Copynumber: 2.9 Consensus size: 33
58 CAAAATCGCA
**
68 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
101 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
*
134 TTGCGATAGTCATTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCGCGTTGCGATTCTC
164 ATTATCTCGT
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.11, C:0.25, G:0.23, T:0.41
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:2028 original size:92 final size:88
Alignment explanation
Indices: 1855--2035 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 88
1845 TAGATTGCTT
1855 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATGTTTATTAACACTGTGAAGTTAGTATTGT
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATGTTTATTAACACTGTGAAGTTAGTATTGT
1920 CTTTTGTTTTGTCTTTTGGTTGA
66 CTTTTGTTTTGTCTTTTGGTTGA
* *
1943 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAATGTGTATTCTTTAACACTGTGAAGTTAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAA--TGT-TT-ATTAACACTGTGAAGTTAGTA
2008 TTTGTC-TTTGTTTTGTCTTTTGGTTGA
62 -TTGTCTTTTGTTTTGTCTTTTGGTTGA
2035 A
1 A
2036 AGTTTGAAAT
Statistics
Matches: 86, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
88 34 0.40
90 3 0.03
91 2 0.02
92 42 0.49
93 5 0.06
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (88 bp):
AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATGTTTATTAACACTGTGAAGTTAGTATTGT
CTTTTGTTTTGTCTTTTGGTTGA
Found at i:3980 original size:12 final size:12
Alignment explanation
Indices: 3959--3990 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3949 TGCCGGATGG
3959 GGAA-GGATATA
1 GGAACGGATATA
3970 GGAACGGATATA
1 GGAACGGATATA
3982 GGAACGGAT
1 GGAACGGAT
3991 GTCGCCGGAG
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:0.41, C:0.06, G:0.38, T:0.16
Consensus pattern (12 bp):
GGAACGGATATA
Found at i:4214 original size:20 final size:20
Alignment explanation
Indices: 4189--4233 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
4179 TTCCTAATTT
*
4189 GCAATGCGAATAAGTAAATC
1 GCAATGCGAATAAGAAAATC
**
4209 GCAATGCGAATTTGAAAATC
1 GCAATGCGAATAAGAAAATC
4229 GCAAT
1 GCAAT
4234 CGATACTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (20 bp):
GCAATGCGAATAAGAAAATC
Found at i:4306 original size:18 final size:19
Alignment explanation
Indices: 4262--4308 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
4252 GAGATAATAC
4262 AAAATCGCAACAGATTCTG
1 AAAATCGCAACAGATTCTG
***
4281 ACTTTCGCAA-AGATTCTG
1 AAAATCGCAACAGATTCTG
4299 AAAATCGCAA
1 AAAATCGCAA
4309 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 15 0.68
19 7 0.32
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.23
Consensus pattern (19 bp):
AAAATCGCAACAGATTCTG
Found at i:4545 original size:20 final size:20
Alignment explanation
Indices: 4520--4605 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
4510 CATCGGGGAA
4520 ATCGCAACACGAAAATGGCT
1 ATCGCAACACGAAAATGGCT
*
4540 ATCGCAACGCGAAAATGGCT
1 ATCGCAACACGAAAATGGCT
** ***
4560 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACACGAAAATG-GCT
4580 ATCGC-A-ACGAAAATGGCT
1 ATCGCAACACGAAAATGGCT
4598 ATCGCAAC
1 ATCGCAAC
4606 TAGAAAATCG
Statistics
Matches: 52, Mismatches: 10, Indels: 8
0.74 0.14 0.11
Matches are distributed among these distances:
18 7 0.13
19 12 0.23
20 33 0.63
ACGTcount: A:0.41, C:0.23, G:0.20, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGGCT
Found at i:4656 original size:14 final size:14
Alignment explanation
Indices: 4637--4690 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
4627 GAAAATCACA
4637 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
4651 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
4668 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
4684 TTGCGAT
1 TTGCGAT
4691 AGTCAGTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:4656 original size:33 final size:33
Alignment explanation
Indices: 4619--4689 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
4609 AAAATCGCAA
4619 TGCGAAATGAAAATCACATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCACATTGCGATTTTCTCGT
** ** ** *
4652 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCACATTGCGATTTTCTCGT
4685 TGCGA
1 TGCGA
4690 TAGTCAGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCACATTGCGATTTTCTCGT
Found at i:6285 original size:41 final size:42
Alignment explanation
Indices: 6231--6322 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
6221 CCTCTTCAAC
* * *
6231 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
*
6272 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
6314 GATGATAGG
1 GATGATAGG
6323 TGAATCGGGC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 20 0.43
42 26 0.57
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGATAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:6287 original size:21 final size:21
Alignment explanation
Indices: 6258--6322 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
6248 GAACGGTGGG
6258 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
* ** *
6279 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGATA
6300 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGATA
6321 GG
1 GG
6323 TGAATCGGGC
Statistics
Matches: 34, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.88
22 2 0.06
ACGTcount: A:0.22, C:0.12, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGATA
Found at i:6717 original size:19 final size:19
Alignment explanation
Indices: 6682--6742 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
6672 CTTAAAATGT
6682 AACGCGAAAATGACTATCGC
1 AACGCG-AAATGACTATCGC
*
6702 AACGCGAAATGGCTATCGC
1 AACGCGAAATGACTATCGC
* *
6721 AATGCGAAATGA-AATCGC
1 AACGCGAAATGACTATCGC
6739 AACG
1 AACG
6743 ACAAAATCGC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
18 8 0.22
19 22 0.61
20 6 0.17
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.15
Consensus pattern (19 bp):
AACGCGAAATGACTATCGC
Found at i:6751 original size:14 final size:14
Alignment explanation
Indices: 6732--6821 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
6722 ATGCGAAATG
6732 AAATCGCAACGACA
1 AAATCGCAACGACA
*
6746 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
6765 AAATCGCAACGACA
1 AAATCGCAACGACA
*
6779 AAATCGCAATGCGAAA
1 AAATCGCAA--CGACA
6795 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
*
6811 AAATTGCAACG
1 AAATCGCAACG
6822 CGAAACAAAT
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 29 0.47
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:6774 original size:33 final size:32
Alignment explanation
Indices: 6716--6835 Score: 197
Period size: 32 Copynumber: 3.8 Consensus size: 32
6706 CGAAATGGCT
6716 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
6748 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
6781 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
* * *
6813 ATTGCAACGCGAAA-CAAATCGCA
1 ATCGCAATGCGAAATGAAATCGCA
6836 TTGCGATTTT
Statistics
Matches: 84, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
31 8 0.10
32 44 0.52
33 32 0.38
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:6868 original size:12 final size:13
Alignment explanation
Indices: 6853--6907 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 13
6843 TTTCATTTCG
6853 CGTTGCGA-TTTT
1 CGTTGCGATTTTT
6865 CGTTGCGATTTCATTT
1 CGTTGCGA-TT--TTT
6881 CGAATTGCGATTTTT
1 CG--TTGCGATTTTT
6896 CGTTGCGATTTT
1 CGTTGCGATTTT
6908 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
12 8 0.22
13 10 0.27
14 1 0.03
15 5 0.14
16 5 0.14
17 2 0.05
18 6 0.16
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (13 bp):
CGTTGCGATTTTT
Found at i:6874 original size:31 final size:31
Alignment explanation
Indices: 6836--6923 Score: 142
Period size: 31 Copynumber: 2.8 Consensus size: 31
6826 ACAAATCGCA
*
6836 TTGCGATTTTCATTTCGCGTTGCGATTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTCG
*
6867 TTGCGA-TTTCATTTCGAATTGCGATTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGA-TTTTCG
6898 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
6924 AGCCATTTCC
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 16 0.31
31 19 0.37
32 17 0.33
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (31 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCG
Found at i:6920 original size:19 final size:18
Alignment explanation
Indices: 6831--6923 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 18
6821 GCGAAACAAA
6831 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
*
6850 TCGCGTTGCGA--T--TT
1 TCGCATTGCGATTTCATT
6864 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
6880 TCGAATTGCGA-TT--TT
1 TCGCATTGCGATTTCATT
6895 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
6912 TCGCATTGCGAT
1 TCGCATTGCGAT
6924 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 1, Indels: 25
0.70 0.01 0.29
Matches are distributed among these distances:
12 6 0.10
13 6 0.10
14 6 0.10
15 7 0.11
16 6 0.10
17 7 0.11
18 7 0.11
19 16 0.26
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.46
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:6942 original size:20 final size:19
Alignment explanation
Indices: 6908--6962 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
6898 TTGCGATTTT
*
6908 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
6927 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
6947 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
6963 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:8807 original size:20 final size:20
Alignment explanation
Indices: 8770--8833 Score: 74
Period size: 20 Copynumber: 3.2 Consensus size: 20
8760 AATAGTTTCT
** * *
8770 GAAAATGAAAATCACAACAC
1 GAAAATGACTATCGCAACGC
8790 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
8810 GAATTTGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
8830 GAAA
1 GAAA
8834 TTAAAATCGT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.16
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:9101 original size:22 final size:22
Alignment explanation
Indices: 9074--9117 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
9064 GATGGAGATA
9074 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
9096 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
9118 TGAGAGTGAG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:10236 original size:14 final size:14
Alignment explanation
Indices: 10217--10247 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10207 TCAGTAATAT
*
10217 GTTCATTTATGTTC
1 GTTCATTTATATTC
10231 GTTCATTTATATTC
1 GTTCATTTATATTC
10245 GTT
1 GTT
10248 TATGTGCGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (14 bp):
GTTCATTTATATTC
Found at i:10257 original size:24 final size:24
Alignment explanation
Indices: 10222--10267 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
10212 AATATGTTCA
*
10222 TTTATGTTCGTTCATTTATATTCG
1 TTTATGTGCGTTCATTTATATTCG
10246 TTTATGTGCGTTCATTTATATT
1 TTTATGTGCGTTCATTTATATT
10268 TAGCCCAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.59
Consensus pattern (24 bp):
TTTATGTGCGTTCATTTATATTCG
Found at i:10466 original size:20 final size:20
Alignment explanation
Indices: 10429--10466 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10419 AAAAAATATT
*
10429 TTCATTTATGTTCGTTTACA
1 TTCATTTATGTTAGTTTACA
*
10449 TTCATTTATGTTATTTTA
1 TTCATTTATGTTAGTTTA
10467 TTGTGTTCGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.61
Consensus pattern (20 bp):
TTCATTTATGTTAGTTTACA
Found at i:18517 original size:80 final size:80
Alignment explanation
Indices: 18384--18543 Score: 311
Period size: 80 Copynumber: 2.0 Consensus size: 80
18374 CACACAAAAT
18384 TCAGCTAAACATATAACAAAACTTCAGCCTCAGAGAAAGCATTAATGGGGGTAGAAGACTTTCAC
1 TCAGCTAAACATATAACAAAACTTCAGCCTCAGAGAAAGCATTAATGGGGGTAGAAGACTTTCAC
*
18449 TGAGAAGATTTCCAC
66 TGAGAAGACTTCCAC
18464 TCAGCTAAACATATAACAAAACTTCAGCCTCAGAGAAAGCATTAATGGGGGTAGAAGACTTTCAC
1 TCAGCTAAACATATAACAAAACTTCAGCCTCAGAGAAAGCATTAATGGGGGTAGAAGACTTTCAC
18529 TGAGAAGACTTCCAC
66 TGAGAAGACTTCCAC
18544 GAATATAAGT
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (80 bp):
TCAGCTAAACATATAACAAAACTTCAGCCTCAGAGAAAGCATTAATGGGGGTAGAAGACTTTCAC
TGAGAAGACTTCCAC
Found at i:21102 original size:2 final size:2
Alignment explanation
Indices: 21097--21121 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21087 AATCTCTCCA
21097 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
21122 GCATATGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:25244 original size:35 final size:35
Alignment explanation
Indices: 25204--25283 Score: 117
Period size: 35 Copynumber: 2.3 Consensus size: 35
25194 AATAATTGTT
* *
25204 AACCAAACACGGTAATCTTACATTTCTGCTAAACC
1 AACCAAACACGGAAATCTTACATTCCTGCTAAACC
*
25239 AACCAAACTA-GGAAATCTTACATTCCTGTTAAACC
1 AACCAAAC-ACGGAAATCTTACATTCCTGCTAAACC
25274 AACCAAACAC
1 AACCAAACAC
25284 AAAATACAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
34 1 0.03
35 38 0.95
36 1 0.03
ACGTcount: A:0.41, C:0.29, G:0.07, T:0.23
Consensus pattern (35 bp):
AACCAAACACGGAAATCTTACATTCCTGCTAAACC
Found at i:25387 original size:60 final size:60
Alignment explanation
Indices: 25299--25414 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
25289 ACAACATTCC
* * *
25299 CTGGTAATCTTATATTCCCACTAGTAATCTTATATTCTCACTGATAATCTTACATTCTTA
1 CTGGTAATCTTATATTCCCACTAATAATCTTACATTCTCACTAATAATCTTACATTCTTA
* *
25359 CTGGTAATCTTATATTCCCATTAATAATCTTACATTTTCACTAATAATCTTACATT
1 CTGGTAATCTTATATTCCCACTAATAATCTTACATTCTCACTAATAATCTTACATT
25415 TTGTAAACTA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (60 bp):
CTGGTAATCTTATATTCCCACTAATAATCTTACATTCTCACTAATAATCTTACATTCTTA
Found at i:25416 original size:20 final size:20
Alignment explanation
Indices: 25303--25414 Score: 116
Period size: 20 Copynumber: 5.6 Consensus size: 20
25293 CATTCCCTGG
* * *
25303 TAATCTTATATTCCCACTAG
1 TAATCTTACATTCTCACTAA
* *
25323 TAATCTTATATTCTCACTGA
1 TAATCTTACATTCTCACTAA
* **
25343 TAATCTTACATTCTTACTGG
1 TAATCTTACATTCTCACTAA
* * *
25363 TAATCTTATATTCCCATTAA
1 TAATCTTACATTCTCACTAA
*
25383 TAATCTTACATTTTCACTAA
1 TAATCTTACATTCTCACTAA
25403 TAATCTTACATT
1 TAATCTTACATT
25415 TTGTAAACTA
Statistics
Matches: 76, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.31, C:0.21, G:0.04, T:0.45
Consensus pattern (20 bp):
TAATCTTACATTCTCACTAA
Found at i:26072 original size:2 final size:2
Alignment explanation
Indices: 26059--26095 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
26049 TAATTAAATT
*
26059 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26096 CATAAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:31436 original size:12 final size:10
Alignment explanation
Indices: 31409--31440 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
31399 ATCATACCAT
31409 ATTCTCTCAA
1 ATTCTCTCAA
31419 ATTCTCTCAA
1 ATTCTCTCAA
*
31429 ATTATCTCAA
1 ATTCTCTCAA
31439 AT
1 AT
31441 ACTTTCTGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.34, C:0.25, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTCTCTCAA
Found at i:33232 original size:18 final size:18
Alignment explanation
Indices: 33205--33242 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
33195 ACAGCAGCCA
*
33205 CCGCAACCATTTATGATG
1 CCGCAACCATATATGATG
*
33223 CCGCAGCCATATATGATG
1 CCGCAACCATATATGATG
33241 CC
1 CC
33243 ACCGCCTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:33306 original size:33 final size:30
Alignment explanation
Indices: 33244--33310 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
33234 TATGATGCCA
33244 CCGCCTTTCCATTACCAGATGTCGCCGCCG
1 CCGCCTTTCCATTACCAGATGTCGCCGCCG
* *
33274 CCGCCTTTCCATTACTAGATGTCGTCGCCG
1 CCGCCTTTCCATTACCAGATGTCGCCGCCG
33304 CCGCCTT
1 CCGCCTT
33311 CAACTGATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.12, C:0.42, G:0.19, T:0.27
Consensus pattern (30 bp):
CCGCCTTTCCATTACCAGATGTCGCCGCCG
Found at i:33892 original size:35 final size:33
Alignment explanation
Indices: 33852--33936 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
33842 GTATTTCAGT
33852 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
33887 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
33922 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
33937 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:39811 original size:2 final size:2
Alignment explanation
Indices: 39804--39857 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
39794 AATGAATTTA
39804 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
39846 AT AT AT AT AT AT
1 AT AT AT AT AT AT
39858 TTTAACGATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41085 original size:24 final size:23
Alignment explanation
Indices: 41048--41110 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 23
41038 AATAATATAT
*
41048 ATATATATTATATTTATTTTTTATTA
1 ATATATA-T-TATTTAATTTTT-TTA
41074 ATATATATTATTTAATTTTTTTA
1 ATATATATTATTTAATTTTTTTA
41097 ATA-AT-TTA-TTAATT
1 ATATATATTATTTAATT
41111 GACTAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 6 0.17
21 3 0.08
22 2 0.06
23 6 0.17
24 11 0.31
25 1 0.03
26 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
ATATATATTATTTAATTTTTTTA
Found at i:41095 original size:26 final size:26
Alignment explanation
Indices: 41048--41101 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
41038 AATAATATAT
* *
41048 ATATATATTATATTTATTTTTTATTA
1 ATATATATTATATTAATTTTTTAATA
41074 ATATATATTAT-TTAATTTTTTTAATA
1 ATATATATTATATTAA-TTTTTTAATA
41100 AT
1 AT
41102 TTATTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 3 0.12
26 22 0.88
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATATATATTATATTAATTTTTTAATA
Found at i:43837 original size:21 final size:22
Alignment explanation
Indices: 43785--43838 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
43775 CATAATTATT
*
43785 TAAAAA-ATTAAATAAAAATAC
1 TAAAAACATTTAATAAAAATAC
*
43806 TAAAAACATTTAAT-AAAATTC
1 TAAAAACATTTAATAAAAATAC
43827 TAAAAACATTTA
1 TAAAAACATTTA
43839 GGTTGAACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAACATTTAATAAAAATAC
Found at i:51016 original size:6 final size:6
Alignment explanation
Indices: 50979--51013 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
50969 TTAAAAAGTC
*
50979 TGTAAA TGTAAA TGTAAA TGTAAA TGTAAT TGTAA
1 TGTAAA TGTAAA TGTAAA TGTAAA TGTAAA TGTAA
51014 TTGAACTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (6 bp):
TGTAAA
Done.