Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003581.1 Hibiscus syriacus cultivar Beakdansim tig00007557_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: 65832
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:152 original size:53 final size:53
Alignment explanation
Indices: 1--206 Score: 172
Period size: 54 Copynumber: 3.9 Consensus size: 53
* * * * * *
1 CCCCTGAAAATCAGGCTTAGCTCCTTTAAAAATCCATTTGTAAACATCAAGAAA
1 CCCCTAAAAATCAGGTTTATCTCCTTTAAAAATTCATTTGAAAACATTAAG-AA
* *
55 CCCCCTAAAAATCTA-GTTTAGT-TCCTCT-AAAATTCATTTAAAAACATTAAGAA
1 -CCCCTAAAAATC-AGGTTTA-TCTCCTTTAAAAATTCATTTGAAAACATTAAGAA
* *
108 -CTCTTAAAATCAGGTTTATACTCCTTTAAAAATTCATTTGAAAACATTAAGAAA
1 CCCCTAAAAATCAGGTTTAT-CTCCTTTAAAAATTCATTTGAAAACATTAAG-AA
* * * * * *
162 CCCCT-GAAATCAGGCTTAGCTTCTTT-CAAATTCATTTGAAGACAT
1 CCCCTAAAAATCAGGTTTATCTCCTTTAAAAATTCATTTGAAAACAT
207 CATATTGTTT
Statistics
Matches: 124, Mismatches: 19, Indels: 19
0.77 0.12 0.12
Matches are distributed among these distances:
50 2 0.02
51 14 0.11
52 22 0.18
53 30 0.24
54 32 0.26
55 23 0.19
56 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (53 bp):
CCCCTAAAAATCAGGTTTATCTCCTTTAAAAATTCATTTGAAAACATTAAGAA
Found at i:2228 original size:16 final size:16
Alignment explanation
Indices: 2207--2239 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2197 ACTTGATATG
*
2207 TTTTCTTTTTCCCTTT
1 TTTTCTTATTCCCTTT
2223 TTTTCTTATTCCCTTT
1 TTTTCTTATTCCCTTT
2239 T
1 T
2240 CTTGCTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTCTTATTCCCTTT
Found at i:3722 original size:20 final size:20
Alignment explanation
Indices: 3694--3745 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
3684 ATGAAGTGTG
*
3694 AATGCAAAGATGCGAACACA
1 AATGTAAAGATGCGAACACA
**
3714 AATGTAAAGATGCGAACGTA
1 AATGTAAAGATGCGAACACA
*
3734 AATATAAAGATG
1 AATGTAAAGATG
3746 TGAATGCGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.17
Consensus pattern (20 bp):
AATGTAAAGATGCGAACACA
Found at i:10665 original size:19 final size:19
Alignment explanation
Indices: 10638--10682 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
10628 TAAATATTCT
* *
10638 TGATTTTTATAGTAAACTG
1 TGATATTTATAGTAAACTA
10657 TGATATTTATAGTAAACTA
1 TGATATTTATAGTAAACTA
10676 TGATATT
1 TGATATT
10683 GATTATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (19 bp):
TGATATTTATAGTAAACTA
Found at i:12948 original size:45 final size:45
Alignment explanation
Indices: 12897--12990 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
12887 TTTTAATTAG
* *
12897 AATTTGTGTTATATGTTAAATGAAGTTAAGTTGTGTTTTGGTATT
1 AATTTGTGCTATATGTTAAATGAAATTAAGTTGTGTTTTGGTATT
* *
12942 AATTTGTGCTATTTGTTGAATGAAATTAAGTTGTGTTTTGGTATT
1 AATTTGTGCTATATGTTAAATGAAATTAAGTTGTGTTTTGGTATT
12987 AATT
1 AATT
12991 AAGTGTCGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.27, C:0.01, G:0.21, T:0.51
Consensus pattern (45 bp):
AATTTGTGCTATATGTTAAATGAAATTAAGTTGTGTTTTGGTATT
Found at i:13311 original size:40 final size:39
Alignment explanation
Indices: 13184--13316 Score: 103
Period size: 40 Copynumber: 3.3 Consensus size: 39
13174 TGCATCAGCA
* *
13184 AACAAACCGCTAAAGAGGATTAAACTATTGAAAGATCATC
1 AACAAACCACAAAAGAGGATT-AACTATTGAAAGATCATC
* * * * *
13224 AACAAACCATAAATTAGAGTGAATGAC-A-TGAAATAACTATTC
1 AACAAACCACAAA--AGAG-GATTAACTATTGAAAGATC-A-TC
*
13266 -A-AAACCGCAAAAGAGGATTAAGCTATTGAAAGATCATC
1 AACAAACCACAAAAGAGGATTAA-CTATTGAAAGATCATC
13304 AACAAACCACAAA
1 AACAAACCACAAA
13317 TCAGAGTGAA
Statistics
Matches: 69, Mismatches: 14, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
37 4 0.06
38 7 0.10
39 3 0.04
40 41 0.59
41 3 0.04
42 8 0.12
43 3 0.04
ACGTcount: A:0.50, C:0.17, G:0.14, T:0.19
Consensus pattern (39 bp):
AACAAACCACAAAAGAGGATTAACTATTGAAAGATCATC
Found at i:13356 original size:80 final size:80
Alignment explanation
Indices: 13187--13346 Score: 275
Period size: 80 Copynumber: 2.0 Consensus size: 80
13177 ATCAGCAAAC
* * *
13187 AAACCGCTAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCATAAATTAGAGTGAATGACA
1 AAACCGCAAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
13252 TGAAATAACTATTCA
66 TGAAATAACTATTCA
* *
13267 AAACCGCAAAAGAGGATTAAGCTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACC
1 AAACCGCAAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
13332 TGAAATAACTATTCA
66 TGAAATAACTATTCA
13347 TAAATGCAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.21
Consensus pattern (80 bp):
AAACCGCAAAAGAGGATTAAACTATTGAAAGATCATCAACAAACCACAAATCAGAGTGAATGACA
TGAAATAACTATTCA
Found at i:20997 original size:21 final size:21
Alignment explanation
Indices: 20946--20998 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
20936 ATTATTACTA
20946 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
20967 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
20988 TCGCAATGCGA
1 TCGCAATGCGA
20999 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:21013 original size:20 final size:21
Alignment explanation
Indices: 20988--21039 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
20978 TTTTCCCAAT
*
20988 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
21008 TCGCAATTCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
21029 TCGCAATGCGA
1 TCGCAATGCGA
21040 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:21053 original size:20 final size:20
Alignment explanation
Indices: 21028--21077 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
21018 AATTTGGAAA
21028 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
21048 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
21068 ATCGCAATGC
1 ATCGCAATGC
21078 AATTTTCCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:21103 original size:21 final size:21
Alignment explanation
Indices: 21069--21141 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
21059 ATACTGACTA
* *
21069 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* *
21090 TCGCATTGCGA-TTT-ATGTAT
1 TCGCAATGCGATTTTCAT-AAT
**
21110 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
21131 TCGCAATGCGA
1 TCGCAATGCGA
21142 ATGTAAATCG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
19 1 0.02
20 15 0.37
21 23 0.56
22 2 0.05
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:21178 original size:21 final size:21
Alignment explanation
Indices: 21154--21217 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
21144 GTAAATCGCG
21154 ATTAAGTAAATCGCAATGCGA
1 ATTAAGTAAATCGCAATGCGA
* *
21175 ATTAGGAAAATCGCAATGC-A
1 ATTAAGTAAATCGCAATGCGA
* *
21195 AATATGTAAATCGCAATGCGA
1 ATTAAGTAAATCGCAATGCGA
21216 AT
1 AT
21218 CTGACTATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.23
Consensus pattern (21 bp):
ATTAAGTAAATCGCAATGCGA
Found at i:21207 original size:20 final size:21
Alignment explanation
Indices: 21159--21216 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
21149 TCGCGATTAA
*
21159 GTAAATCGCAATGCGAATTAG
1 GTAAATCGCAATGCGAAATAG
* *
21180 GAAAATCGCAATGC-AAATAT
1 GTAAATCGCAATGCGAAATAG
21200 GTAAATCGCAATGCGAA
1 GTAAATCGCAATGCGAA
21217 TCTGACTATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.21
Consensus pattern (21 bp):
GTAAATCGCAATGCGAAATAG
Found at i:21800 original size:19 final size:20
Alignment explanation
Indices: 21758--21812 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 20
21748 TAGTTTCGAG
21758 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
**
21778 AATGACTATCGCAACGC-GA
1 AATGAAAATCGCAACGCGGA
21797 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
21813 AGATAATCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:21860 original size:19 final size:19
Alignment explanation
Indices: 21838--21929 Score: 104
Period size: 19 Copynumber: 5.1 Consensus size: 19
21828 GAAACCAAAA
*
21838 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
21857 TCGCGTTGCG--TTTC---
1 TCGCGTTGCGATTTTCATT
*
21871 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
21890 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
21909 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
21929 T
1 T
21930 TAACCAAAAG
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
17 4 0.07
19 26 0.43
20 17 0.28
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:23813 original size:94 final size:94
Alignment explanation
Indices: 23623--23927 Score: 503
Period size: 94 Copynumber: 3.3 Consensus size: 94
23613 TAGATTGCTT
* *
23623 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
23684 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
23713 AGTAAATTTATTCGGTTGCTTCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
23778 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
23807 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
23872 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
23901 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
23928 GAAACTATTC
Statistics
Matches: 202, Mismatches: 8, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
90 34 0.17
92 3 0.01
93 22 0.11
94 143 0.71
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:24397 original size:42 final size:42
Alignment explanation
Indices: 24350--24438 Score: 101
Period size: 42 Copynumber: 2.1 Consensus size: 42
24340 CCTATCGTTG
* *
24350 AAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTTCCACCATTC
1 AAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCACCATTC
* * *
24392 AAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCACCATTC
1 AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
24434 AAGAG
1 AAGAG
24439 CCCGATTCAC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 4 0.10
42 34 0.85
43 2 0.05
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (42 bp):
AAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCACCATTC
Found at i:24437 original size:21 final size:20
Alignment explanation
Indices: 24378--24438 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
24368 CTCGAGAGTC
*
24378 CCCTTCCACCATTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
** * * *
24398 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCATTCAAGAGG
24419 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
24439 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 10, Indels: 3
0.69 0.24 0.07
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.25, C:0.36, G:0.18, T:0.21
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:25943 original size:19 final size:18
Alignment explanation
Indices: 25921--26000 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 18
25911 AAAAATGACT
25921 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
* *
25940 ATCGTAA-CG--A-GAGA
1 ATCGCAAGCGAAATGAAA
25954 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
25973 ATCGCAA-CG-AA--AAA
1 ATCGCAAGCGAAATGAAA
25987 ATCGCAACGCGAAA
1 ATCGCAA-GCGAAA
26001 CTAAATTCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
14 19 0.39
15 1 0.02
16 6 0.12
17 6 0.12
18 1 0.02
19 16 0.33
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.11
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:25966 original size:33 final size:33
Alignment explanation
Indices: 25921--26000 Score: 124
Period size: 33 Copynumber: 2.4 Consensus size: 33
25911 AAAAATGACT
* * * *
25921 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
25954 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
25987 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
26001 CTAAATTCGC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.47, C:0.20, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAAAAA
Found at i:26061 original size:34 final size:33
Alignment explanation
Indices: 26010--26104 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 33
26000 ACTAAATTCG
26010 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
*
26043 CGTTGCGATTTTTCATTTCG-TATTGCGATTCTCT
1 CGTTGCGA-TTTTCATTTCGCT-TTGCGATTCCCT
*
26077 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCTTTGCGAT
26105 AGTAATTTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 27 0.47
34 30 0.53
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
Found at i:28439 original size:12 final size:12
Alignment explanation
Indices: 28422--28446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28412 TCTTCGGGGA
28422 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28434 CTTTTTCTTCTT
1 CTTTTTCTTCTT
28446 C
1 C
28447 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:28655 original size:24 final size:24
Alignment explanation
Indices: 28621--28674 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28611 CTGAAACATC
*
28621 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
28645 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
28669 ATCAAA
1 ATCAAA
28675 TTTCAAATAC
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:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:29440 original size:20 final size:20
Alignment explanation
Indices: 29419--29533 Score: 185
Period size: 20 Copynumber: 5.8 Consensus size: 20
29409 TGTATTATCT
* *
29419 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
29439 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
29459 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
29479 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
29499 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
*
29519 CGTTGCGATAGTCAG
1 CGTTGCGAAAGTCAG
29534 TAAAATTCGC
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 91 1.00
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:29534 original size:20 final size:20
Alignment explanation
Indices: 29414--29592 Score: 171
Period size: 20 Copynumber: 8.7 Consensus size: 20
29404 GATTCTGTAT
*
29414 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
29434 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
29454 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
29474 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
29494 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
29514 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
29534 TAAAATTCGCATTGCGATTTTGT-AT
1 T---A-TCGCGTTGCGA--TAGTCAG
*
29559 TATTGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
29579 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
29593 TTTCCAAATT
Statistics
Matches: 138, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.02
20 109 0.79
21 9 0.07
22 1 0.01
23 1 0.01
24 10 0.07
25 2 0.01
26 3 0.02
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:29611 original size:41 final size:43
Alignment explanation
Indices: 29521--29613 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 43
29511 CAGTATCGCG
** * *
29521 TTGCGATAGTCAGTAAAATTCGCATTGCGATTTTGTATTATTGCG
1 TTGCGATAGTCAGT--AATTCGCATTGCGATTTTCAAATATTGCA
29566 TTGCGATAGTCAGT-A-TCGCATTGCGATTTTCCAAAT-TTGCA
1 TTGCGATAGTCAGTAATTCGCATTGCGATTTT-CAAATATTGCA
29607 TTGCGAT
1 TTGCGAT
29614 TTACTTATTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
41 26 0.60
42 3 0.07
45 14 0.33
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.39
Consensus pattern (43 bp):
TTGCGATAGTCAGTAATTCGCATTGCGATTTTCAAATATTGCA
Found at i:29629 original size:20 final size:21
Alignment explanation
Indices: 29581--29632 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
29571 ATAGTCAGTA
*
29581 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
* **
29602 TTGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
29622 TCGCATTGCGA
1 TCGCATTGCGA
29633 ATTGGGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:31000 original size:16 final size:17
Alignment explanation
Indices: 30977--31014 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
30967 ATTATATGGA
*
30977 TATT-TTATTCATTTAT
1 TATTATTATTCATGTAT
30993 T-TTATTATTCATGTAT
1 TATTATTATTCATGTAT
31009 TATTAT
1 TATTAT
31015 ATATGTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 2 0.11
16 13 0.68
17 4 0.21
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (17 bp):
TATTATTATTCATGTAT
Found at i:31345 original size:2 final size:2
Alignment explanation
Indices: 31340--31387 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
31330 TAATACTTTG
31340 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
31382 AT AT AT
1 AT AT AT
31388 TTTTTCCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34497 original size:9 final size:9
Alignment explanation
Indices: 34485--34540 Score: 62
Period size: 9 Copynumber: 6.3 Consensus size: 9
34475 TAAAAAGGGC
34485 AAAAAGAAA
1 AAAAAGAAA
*
34494 AAAAA-AGCA
1 AAAAAGA-AA
34503 AAAAA-AAA
1 AAAAAGAAA
*
34511 AAAAAGCAA
1 AAAAAGAAA
*
34520 AAAAAGAAC
1 AAAAAGAAA
34529 AAAAAGAAA
1 AAAAAGAAA
34538 AAA
1 AAA
34541 GAAAAAGGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
8 7 0.18
9 32 0.82
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:34505 original size:11 final size:10
Alignment explanation
Indices: 34485--34540 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 10
34475 TAAAAAGGGC
34485 AAAAAGAAAA
1 AAAAAGAAAA
34495 AAAAAGCAAAA
1 AAAAAG-AAAA
34506 AAAAA-AAAA
1 AAAAAGAAAA
*
34515 AGCAAAAAAAGAA
1 A--AAAAGAA-AA
34528 CAAAAAGAAAA
1 -AAAAAGAAAA
34539 AA
1 AA
34541 GAAAAAGGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
9 5 0.13
10 8 0.21
11 15 0.38
12 8 0.21
13 2 0.05
14 1 0.03
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:34505 original size:16 final size:16
Alignment explanation
Indices: 34483--34546 Score: 85
Period size: 16 Copynumber: 3.8 Consensus size: 16
34473 AATAAAAAGG
34483 GCAAAAAGAAAAAAAAA
1 GCAAAAA-AAAAAAAAA
34500 GCAAAAAAAAAAAAAA
1 GCAAAAAAAAAAAAAA
34516 GCAAAAAAAGAACAAAAA
1 GCAAAAAAA-AA-AAAAA
34534 G-AAAAAAGAAAAA
1 GCAAAAAA-AAAAA
34547 GGGACAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
16 20 0.45
17 17 0.39
18 7 0.16
ACGTcount: A:0.83, C:0.06, G:0.11, T:0.00
Consensus pattern (16 bp):
GCAAAAAAAAAAAAAA
Found at i:34513 original size:25 final size:25
Alignment explanation
Indices: 34485--34546 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
34475 TAAAAAGGGC
34485 AAAAAGAAAAAAA-AAGCAAAAAAAAA
1 AAAAAGAAAAAAAGAA-C-AAAAAAAA
*
34511 AAAAAGCAAAAAAAGAAC-AAAAAGA
1 AAAAAG-AAAAAAAGAACAAAAAAAA
34536 AAAAAGAAAAA
1 AAAAAGAAAAA
34547 GGGACAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 5 0.15
25 12 0.36
26 6 0.18
27 8 0.24
28 2 0.06
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAGAAAAAAAGAACAAAAAAAA
Found at i:34555 original size:34 final size:32
Alignment explanation
Indices: 34476--34558 Score: 96
Period size: 33 Copynumber: 2.5 Consensus size: 32
34466 TAATCAGAAT
34476 AAAAAGGGCAAAAAGAAAAAAAAAGCAAAAAAA
1 AAAAAGGGCAAAAA-AAAAAAAAAGCAAAAAAA
** *
34509 AAAAAAAGCAAAAAAAGAACAAAAAG-AAAAAAG
1 AAAAAGGGCAAAAAAA-AA-AAAAAGCAAAAAAA
34542 AAAAAGGGACAAAAAAA
1 AAAAAGGG-CAAAAAAA
34559 CACATGCAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
32 2 0.05
33 26 0.62
34 14 0.33
ACGTcount: A:0.80, C:0.06, G:0.14, T:0.00
Consensus pattern (32 bp):
AAAAAGGGCAAAAAAAAAAAAAAGCAAAAAAA
Found at i:35172 original size:21 final size:22
Alignment explanation
Indices: 35146--35188 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
35136 AGCTACCCCA
35146 TCAAACC-TTGAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
*
35167 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTGAGCATCAAATG
35189 AACAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.26
Consensus pattern (22 bp):
TCAAACCATTGAGCATCAAATG
Found at i:36270 original size:36 final size:36
Alignment explanation
Indices: 36152--36275 Score: 151
Period size: 36 Copynumber: 3.4 Consensus size: 36
36142 ATTGAAAACA
* *
36152 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGATAG
* * *
36188 TTTCTCTTGGAACTAAGTTTT-GTCTCTCTTAAGATAG
1 TTTCCCTTGAAAC-AA-TTTTCGTCTCTCTTGAGATAG
* * *
36225 TTTCTCTTGAAACAATTTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGATAG
36261 TTTCCCTTGAAACAA
1 TTTCCCTTGAAACAA
36276 AACCTTTGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
35 4 0.05
36 39 0.52
37 29 0.39
38 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (36 bp):
TTTCCCTTGAAACAATTTTCGTCTCTCTTGAGATAG
Found at i:36369 original size:67 final size:68
Alignment explanation
Indices: 36251--36407 Score: 196
Period size: 68 Copynumber: 2.4 Consensus size: 68
36241 TTTCGTCTAT
* **
36251 CTTGAGACAGTTTCCCTTG-AA-ACAAAACCTTTGAATTTATTTCCCCTAAAACA-AATTTT-TT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
36312 CTCC
66 -TCC
* * *
36316 CTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTTGTT
1 CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
36381 TCC
66 TCC
* * *
36384 TTTGAGACCGTTTCTCATGAAACA
1 CTTGAGACAGTTTCTCTTGAAACA
36408 ACAGATATCT
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
65 17 0.22
66 2 0.03
67 28 0.36
68 29 0.37
69 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (68 bp):
CTTGAGACAGTTTCTCTTGAAACACAAAACCTTCAAATTTATTTCCCCTAAAACATAATTTTGTT
TCC
Found at i:37231 original size:105 final size:105
Alignment explanation
Indices: 37046--37663 Score: 975
Period size: 105 Copynumber: 6.0 Consensus size: 105
37036 GCACTCGAGG
* * * *
37046 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
*
37111 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
37152 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
37217 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
37257 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* * *
37319 ACCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
37359 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
37424 GCCAATTTCAACTTCAC-ACGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
37463 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCACAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
37528 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
*
37568 CAACGCAAGTTAAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
37628 TTCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTC
37664 TGAACAATGC
Statistics
Matches: 484, Mismatches: 24, Indels: 14
0.93 0.05 0.03
Matches are distributed among these distances:
100 36 0.07
101 1 0.00
102 101 0.21
103 2 0.00
104 102 0.21
105 202 0.42
106 40 0.08
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:37410 original size:207 final size:207
Alignment explanation
Indices: 37046--37662 Score: 967
Period size: 207 Copynumber: 3.0 Consensus size: 207
37036 GCACTCGAGG
* * * *
37046 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--AC-AACAACTTCTCAATTTCAG
*
37111 AGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
63 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
37176 AAGGGACCGCTGCCTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAATGAAG
128 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC-ACGAAG
37241 GATATTGGACTTCAGA
192 GATATTGGACTTCAGA
* *
37257 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT-CAACAACTTCTCAATTTCAGAAC
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGC
* *
37321 CAATTTCAACTTCACAATGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAG
66 CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
37386 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACACGAAGGATA
131 GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACACGAAGGATA
37451 TTGGACTTCAGA
196 TTGGACTTCAGA
* **
37463 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCACAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGT--ACAACAACTTCTCAATTTCAGA
*
37528 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTAAACTTCACGACGA
64 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGA
** *
37593 AGGGACCGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCAATTTCAACTTCACGACGGAGG
129 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCAC-ACGAAGG
37653 ATATTGGACT
193 ATATTGGACT
37663 CTGAACAATG
Statistics
Matches: 380, Mismatches: 22, Indels: 14
0.91 0.05 0.03
Matches are distributed among these distances:
204 21 0.06
205 17 0.04
206 63 0.17
207 139 0.37
208 3 0.01
209 101 0.27
211 36 0.09
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (207 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTACAACAACTTCTCAATTTCAGAGC
CAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAG
GGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACACGAAGGATA
TTGGACTTCAGA
Found at i:38855 original size:18 final size:17
Alignment explanation
Indices: 38816--38858 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
38806 ATTATATGGA
38816 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
38832 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
38850 TATTATTAT
1 TATTATTAT
38859 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:38910 original size:17 final size:16
Alignment explanation
Indices: 38888--38940 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
38878 AATTATTTTC
38888 ATTTATTTTTTTACTAT
1 ATTTATTTTTTTA-TAT
*
38905 ATTTATTATTATTATAT
1 ATTTATT-TTTTTATAT
* *
38922 ATATATTTCTTTA-AT
1 ATTTATTTTTTTATAT
38937 ATTT
1 ATTT
38941 TACTTATAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 4 0.13
17 16 0.53
18 5 0.17
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (16 bp):
ATTTATTTTTTTATAT
Found at i:39180 original size:2 final size:2
Alignment explanation
Indices: 39175--39216 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
39165 TAATACTTTG
*
39175 AT AT AT AT AT AT AT AT AC 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
39217 TTTTTCCTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:49316 original size:9 final size:8
Alignment explanation
Indices: 49304--49361 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 8
49294 ATATTAGTAT
49304 AATAATAA
1 AATAATAA
49312 TAATAATAA
1 -AATAATAA
49321 AATAAATAAA
1 AAT-AAT-AA
*
49331 AATTAGTAAA
1 AA-TAAT-AA
49341 AATAATAA
1 AATAATAA
*
49349 AGTAATAA
1 AATAATAA
49357 AATAA
1 AATAA
49362 AATTAAAGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 16 0.38
9 14 0.33
10 11 0.26
11 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:49355 original size:36 final size:37
Alignment explanation
Indices: 49291--49362 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 37
49281 GAAAAAAGAA
49291 AAAATATTAGTATAATAATAATAATAATAAAATAAAT
1 AAAATATTAGTATAATAATAATAATAATAAAATAAAT
49328 AAAA-ATTAGTA-AA-AATAATAAAGTAATAAAATAAA
1 AAAATATTAGTATAATAATAAT-AA-TAATAAAATAAA
49363 ATTAAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
34 6 0.18
35 4 0.12
36 19 0.58
37 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (37 bp):
AAAATATTAGTATAATAATAATAATAATAAAATAAAT
Found at i:50791 original size:14 final size:14
Alignment explanation
Indices: 50772--50800 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
50762 CTGTCCCTTT
50772 TTGCACATTTTTCG
1 TTGCACATTTTTCG
50786 TTGCACATTTTTCG
1 TTGCACATTTTTCG
50800 T
1 T
50801 AGAACGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.52
Consensus pattern (14 bp):
TTGCACATTTTTCG
Found at i:51249 original size:84 final size:85
Alignment explanation
Indices: 51103--51296 Score: 257
Period size: 84 Copynumber: 2.3 Consensus size: 85
51093 AACTGAATGA
* * * * *
51103 AGTCAAACTCGAAAGGTC-TTCGTTGACAGATAACCCTTTTAGCCTTGGGTTATGCTGTAAATGA
1 AGTCGAACTC-AAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGA
* * * *
51167 TGTG-CCTTGGAGTTGAGTGT
65 TGTGCCCTCGAAGCTAAGTGT
*
51187 AGTCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
1 AGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
51252 GTGCCCTCGAAGCTAAGTGT
66 GTGCCCTCGAAGCTAAGTGT
*
51272 AGTCGAACTCGAAGGTCTTTGTGTT
1 AGTCGAACTCAAAGGTCTTT-TGTT
51297 TCAAGAAAAA
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
83 7 0.07
84 54 0.56
85 31 0.32
86 4 0.04
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (85 bp):
AGTCGAACTCAAAGGTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGAT
GTGCCCTCGAAGCTAAGTGT
Found at i:51390 original size:34 final size:34
Alignment explanation
Indices: 51289--51407 Score: 190
Period size: 33 Copynumber: 3.6 Consensus size: 34
51279 CTCGAAGGTC
*
51289 TTTGTGTTTCAAGAAAAAC-ATTTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGA-TTTCAAAGGTTTT
51323 TTT-TGTTTCAAGAGAAACGATTTCAAAGG-TTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
*
51355 TTTGTGCTTCAAGAGAAACGATTTCAAAGGTTTT
1 TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
51389 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
51408 TGTCTCCAAG
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
32 6 0.08
33 48 0.61
34 25 0.32
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:51441 original size:37 final size:36
Alignment explanation
Indices: 51393--51746 Score: 309
Period size: 37 Copynumber: 10.1 Consensus size: 36
51383 GGTTTTTTTG
*
51393 TGTTTCAAGAGAAACTGTCTCCAAG-GAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAA-TT
*
51430 TGTTTCAAGAGAAACAT-ACTCAA-AG-G------TT
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT
51458 GGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 --TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
51497 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
**
51531 TGTTTCAAGAGAATTTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * *
51568 AGTTCCAAAAGAAATTGTCTCATGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
51604 TATTTCAAG-GAACACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAGAA-AC-TGTCTCAAGAGAGACAAAATT
*
51633 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
** *
51669 TGTTTTTAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
51705 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
51742 TGTTT
1 TGTTT
51747 TGAGTAAATT
Statistics
Matches: 259, Mismatches: 29, Indels: 58
0.75 0.08 0.17
Matches are distributed among these distances:
28 4 0.02
29 16 0.06
30 24 0.09
31 3 0.01
32 3 0.01
33 2 0.01
34 29 0.11
35 6 0.02
36 84 0.32
37 85 0.33
38 1 0.00
39 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:51519 original size:67 final size:69
Alignment explanation
Indices: 51390--51581 Score: 207
Period size: 67 Copynumber: 2.8 Consensus size: 69
51380 AAAGGTTTTT
* *
51390 TTGTGTTTCAAGAGAAACTGTCTCCAAG-GAGGCAAAATTTTGTTTCAAGAGAAACATACTCAA-
1 TTGTGTTTCAAGAGAAACTGTCT-CAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAG
51453 AG-G-
65 AGAGA
* *
51456 TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-TGTCTCAA
1 TT-GTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAT-ACTCAA
51520 GAGAGACAA
64 GAGAG---A
** * * *
51529 TT-TGTTTCAAGAGAATTTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAA
1 TTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAA
51582 TTGTCTCATG
Statistics
Matches: 107, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
66 7 0.07
67 50 0.47
68 2 0.02
69 1 0.01
71 45 0.42
73 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (69 bp):
TTGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACATACTCAAGA
GAGA
Found at i:51547 original size:15 final size:15
Alignment explanation
Indices: 51527--51557 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51517 CAAGAGAGAC
*
51527 AATTTGTTTCAAGAG
1 AATTTGTCTCAAGAG
51542 AATTTGTCTCAAGAG
1 AATTTGTCTCAAGAG
51557 A
1 A
51558 GACAAAACTT
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:0.35, C:0.10, G:0.19, T:0.35
Consensus pattern (15 bp):
AATTTGTCTCAAGAG
Found at i:51680 original size:36 final size:36
Alignment explanation
Indices: 51631--51746 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
51621 ATTCAAAGAT
51631 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
**
51667 TTTGTTTTTAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
51703 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
51739 CTTTGTTT
1 -TTTGTTT
51747 TGAGTAAATT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
36 67 0.91
37 7 0.09
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:51728 original size:174 final size:175
Alignment explanation
Indices: 51417--51741 Score: 505
Period size: 174 Copynumber: 1.9 Consensus size: 175
51407 CTGTCTCCAA
* * *
51417 GGAGGCAAAATTTTGTTTCAAGAGAAACATACTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCA
1 GGAGACAAAATTTTATTTCAAGAGAAACATACTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCA
**
51482 AGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTTGTTTCAAGAGAATTT
66 AGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTTGTTTCAAGAGAAACT
51547 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCATG
131 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCATG
* * *
51592 GGAGACAAAA-TTTATTTCAAG-GAACACATATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTC
1 GGAGACAAAATTTTATTTCAAGAGAA-ACATACTCAAAGATTGGTGTTTCAAGAGAAACTGTCTC
**
51654 AAGAGAGACAAAA-TTTGTTTTTAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAA
65 AAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATTTGTTTCAAGAGAA
51718 ACTGTCTCAAGAGAGACAAAACTT
128 ACTGTCTCAAGAGAGACAAAACTT
51742 TGTTTTGAGT
Statistics
Matches: 137, Mismatches: 10, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
172 30 0.22
173 36 0.26
174 62 0.45
175 9 0.07
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (175 bp):
GGAGACAAAATTTTATTTCAAGAGAAACATACTCAAAGATTGGTGTTTCAAGAGAAACTGTCTCA
AGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAATTTGTTTCAAGAGAAACT
GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCATG
Found at i:51762 original size:37 final size:34
Alignment explanation
Indices: 51643--51771 Score: 159
Period size: 36 Copynumber: 3.6 Consensus size: 34
51633 TGTTTCAAGG
*
51643 GAAACTGTCTCAAGAGAGACAAAATTTGTTTTTAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTG-TTTT-GA
*
51679 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTTGTTT--TGA
51715 GAAACTGTCTCAAGAGAGACAAAACTTTGTTTTGA
1 GAAACTGTCTCAAGAGAGACAAAA-TTTGTTTTGA
* *
51750 GTAAATTAGTCTCAAGCGAGAC
1 G-AAACT-GTCTCAAGAGAGAC
51772 GACCCCTTGT
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
35 6 0.07
36 57 0.69
37 20 0.24
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (34 bp):
GAAACTGTCTCAAGAGAGACAAAATTTGTTTTGA
Found at i:59992 original size:23 final size:23
Alignment explanation
Indices: 59956--60011 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
59946 CAGAGGGAAT
*
59956 CGATACCCCC-TTGAAGGAGAAC
1 CGATTCCCCCTTTGAAGGAGAAC
* *
59978 CGATTCCCCCTTTGAAGGGGAAT
1 CGATTCCCCCTTTGAAGGAGAAC
60001 CGATTCCCCCT
1 CGATTCCCCCT
60012 GTAGGGAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 9 0.30
23 21 0.70
ACGTcount: A:0.23, C:0.34, G:0.21, T:0.21
Consensus pattern (23 bp):
CGATTCCCCCTTTGAAGGAGAAC
Found at i:61615 original size:18 final size:18
Alignment explanation
Indices: 61594--61634 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
61584 AGAACAACAC
* *
61594 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
61612 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
61630 GAGGA
1 GAGGA
61635 TCAAATGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.32, T:0.00
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Done.