Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007885.1 Hibiscus syriacus cultivar Beakdansim tig00110265_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: 75520
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4213 original size:27 final size:26
Alignment explanation
Indices: 4166--4236 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
4156 ATCAGTGCAT
**
4166 CAAGTGCATTCGATGTTTCAAAAT-AGC
1 CAAGTGCA-TCGATGCATC-AAATGAGC
*
4193 CAGAGTGCATCGATGCATCAAATGATC
1 CA-AGTGCATCGATGCATCAAATGAGC
*
4220 TAAGTGCATCGATGCAT
1 CAAGTGCATCGATGCAT
4237 GGTATGTGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 19 0.50
27 13 0.34
28 6 0.16
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (26 bp):
CAAGTGCATCGATGCATCAAATGAGC
Found at i:4877 original size:30 final size:30
Alignment explanation
Indices: 4841--4902 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
4831 GGGTCAAGAA
* **
4841 TTAGGGACTACGAGTTTGGAAATTGGGAAT
1 TTAGGGACTACAAGTCAGGAAATTGGGAAT
* *
4871 TTAGGGATTGCAAGTCAGGAAATTGGGAAT
1 TTAGGGACTACAAGTCAGGAAATTGGGAAT
4901 TT
1 TT
4903 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.31
Consensus pattern (30 bp):
TTAGGGACTACAAGTCAGGAAATTGGGAAT
Found at i:6009 original size:19 final size:20
Alignment explanation
Indices: 5969--6011 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
5959 AGATCGAAAT
*
5969 AATAATTTAAAGATACATACA
1 AATAATTAAAAGATA-ATACA
5990 AATAATTAAAAGAT-ATACA
1 AATAATTAAAAGATAATACA
6009 AAT
1 AAT
6012 TAACGTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (20 bp):
AATAATTAAAAGATAATACA
Found at i:6427 original size:14 final size:13
Alignment explanation
Indices: 6396--6425 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
6386 TTTTTAAAAT
6396 AAAATATTATTTA
1 AAAATATTATTTA
6409 AAAATATTATTTA
1 AAAATATTATTTA
6422 AAAA
1 AAAA
6426 ATCTAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATATTATTTA
Found at i:7560 original size:2 final size:2
Alignment explanation
Indices: 7549--7621 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
7539 TGCATGTGTG
* *
7549 TA TA TG TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
7591 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 T
7622 CTTAGTTGTG
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10231 original size:36 final size:32
Alignment explanation
Indices: 10164--10236 Score: 103
Period size: 31 Copynumber: 2.3 Consensus size: 32
10154 ATTTGATGAG
*
10164 TGGCATGTGCTATGTCACTTGAAGTGATGGCA
1 TGGCATGTGCTATGTCACTCGAAGTGATGGCA
* * *
10196 TGGCATGTGCT-TGTCACTCGAAGTGAAGACG
1 TGGCATGTGCTATGTCACTCGAAGTGATGGCA
10227 TGGCATGTGC
1 TGGCATGTGC
10237 CACATCACCC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
31 26 0.70
32 11 0.30
ACGTcount: A:0.21, C:0.18, G:0.33, T:0.29
Consensus pattern (32 bp):
TGGCATGTGCTATGTCACTCGAAGTGATGGCA
Found at i:16639 original size:21 final size:21
Alignment explanation
Indices: 16610--16651 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16600 CCTAATATTG
*
16610 CAATGTCAAAATTAGGTGCAA
1 CAATATCAAAATTAGGTGCAA
16631 CAATATCAAAATTAGGTGCAA
1 CAATATCAAAATTAGGTGCAA
16652 TAATGTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.14, G:0.17, T:0.24
Consensus pattern (21 bp):
CAATATCAAAATTAGGTGCAA
Found at i:25973 original size:24 final size:23
Alignment explanation
Indices: 25944--26065 Score: 127
Period size: 24 Copynumber: 5.0 Consensus size: 23
25934 AAAAATTCAA
25944 GAGCTCGATTGAAGCTCGAGACTC
1 GAGCTCGATTGAAGCTCGA-ACTC
*
25968 GAGCTCGATTGAAGCTCGAGGCTC
1 GAGCTCGATTGAAGCTCGA-ACTC
** *
25992 GAGCTCGATTGAAGCTCGATTTT
1 GAGCTCGATTGAAGCTCGAACTC
*
26015 GAGCTCGATTCAAGCTCGATTCAAGCTC
1 GAGCTCGATTGAAGCTCG----AA-CTC
*
26043 GAGCTCGATTCAAGCTCGAACTC
1 GAGCTCGATTGAAGCTCGAACTC
26066 AAACTCGAAT
Statistics
Matches: 85, Mismatches: 8, Indels: 11
0.82 0.08 0.11
Matches are distributed among these distances:
23 21 0.25
24 44 0.52
27 1 0.01
28 19 0.22
ACGTcount: A:0.24, C:0.25, G:0.26, T:0.25
Consensus pattern (23 bp):
GAGCTCGATTGAAGCTCGAACTC
Found at i:26049 original size:17 final size:17
Alignment explanation
Indices: 26027--26061 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
26017 GCTCGATTCA
26027 AGCTCGATTCAAGCTCG
1 AGCTCGATTCAAGCTCG
26044 AGCTCGATTCAAGCTCG
1 AGCTCGATTCAAGCTCG
26061 A
1 A
26062 ACTCAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (17 bp):
AGCTCGATTCAAGCTCG
Found at i:26061 original size:11 final size:11
Alignment explanation
Indices: 25945--26044 Score: 74
Period size: 11 Copynumber: 8.6 Consensus size: 11
25935 AAAATTCAAG
*
25945 AGCTCGATTGA
1 AGCTCGATTCA
* *
25956 AGCTCGAGACTCG
1 AGCTC--GATTCA
*
25969 AGCTCGATTGA
1 AGCTCGATTCA
* *
25980 AGCTCGAGGCTCG
1 AGCTCGA--TTCA
*
25993 AGCTCGATTGA
1 AGCTCGATTCA
**
26004 AGCTCGATTTTG
1 AGCTCGA-TTCA
26016 AGCTCGATTCA
1 AGCTCGATTCA
26027 AGCTCGATTCA
1 AGCTCGATTCA
26038 AGCTCGA
1 AGCTCGA
26045 GCTCGATTCA
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
11 43 0.63
12 9 0.13
13 16 0.24
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.25
Consensus pattern (11 bp):
AGCTCGATTCA
Found at i:26369 original size:21 final size:21
Alignment explanation
Indices: 26344--26395 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
26334 TGGCATAACT
26344 TAAACCCTAACACATAAACCC
1 TAAACCCTAACACATAAACCC
* *
26365 TAAACCTTAACACATAAACTC
1 TAAACCCTAACACATAAACCC
*
26386 TAAACTCTAA
1 TAAACCCTAA
26396 ACCTTAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.31, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCCTAACACATAAACCC
Found at i:26370 original size:7 final size:7
Alignment explanation
Indices: 26344--26447 Score: 61
Period size: 7 Copynumber: 14.9 Consensus size: 7
26334 TGGCATAACT
26344 TAAACCC
1 TAAACCC
*
26351 T-AACACA
1 TAAAC-CC
26358 TAAACCC
1 TAAACCC
26365 TAAA-CC
1 TAAACCC
* *
26371 TTAACACA
1 TAAAC-CC
*
26379 TAAACTC
1 TAAACCC
*
26386 TAAACTC
1 TAAACCC
*
26393 TAAACCT
1 TAAACCC
*
26400 TAAATCC
1 TAAACCC
* *
26407 T-ATCACA
1 TAAAC-CC
*
26414 TAAACTC
1 TAAACCC
*
26421 TAAATCC
1 TAAACCC
26428 TAAACCC
1 TAAACCC
26435 TAAACCC
1 TAAACCC
26442 TAAACC
1 TAAACC
26448 TTATCACATA
Statistics
Matches: 71, Mismatches: 20, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
6 9 0.13
7 52 0.73
8 10 0.14
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:26397 original size:35 final size:34
Alignment explanation
Indices: 26358--26440 Score: 114
Period size: 35 Copynumber: 2.4 Consensus size: 34
26348 CCCTAACACA
26358 TAAACCCTAAACCTTAACACATAAACTCTAAA-CTC
1 TAAACCCTAAACC-TAACACATAAACTCTAAATC-C
* *
26393 TAAACCTTAAATCCTATCACATAAACTCTAAATCC
1 TAAACCCTAAA-CCTAACACATAAACTCTAAATCC
26428 TAAACCCTAAACC
1 TAAACCCTAAACC
26441 CTAAACCTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
34 2 0.05
35 38 0.88
36 3 0.07
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (34 bp):
TAAACCCTAAACCTAACACATAAACTCTAAATCC
Found at i:26417 original size:28 final size:26
Alignment explanation
Indices: 26342--26433 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 26
26332 CATGGCATAA
*
26342 CTTAAACCCTAACACATAAACCCTAAAC
1 CTTAAA-CCT-ACACATAAACTCTAAAC
* * *
26370 CTTAACACATAAACTCTAAACTCTAAAC
1 CTTAA-ACCTACAC-ATAAACTCTAAAC
26398 CTTAAATCCTATCACATAAACTCTAAATC
1 CTTAAA-CCTA-CACATAAACTCTAAA-C
26427 C-TAAACC
1 CTTAAACC
26434 CTAAACCCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
27 6 0.12
28 41 0.79
29 5 0.10
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.24
Consensus pattern (26 bp):
CTTAAACCTACACATAAACTCTAAAC
Found at i:26614 original size:25 final size:24
Alignment explanation
Indices: 26574--26622 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
26564 TAGTTATTAC
26574 AAATATTTTCATTAGA-AATATATT
1 AAATATTTTCATTAGAGAA-ATATT
26598 AAATATTTGTCATTAGAGAAATATT
1 AAATATTT-TCATTAGAGAAATATT
26623 TTTTTTATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.35
25 13 0.57
26 2 0.09
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (24 bp):
AAATATTTTCATTAGAGAAATATT
Found at i:27193 original size:2 final size:2
Alignment explanation
Indices: 27186--27243 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
27176 CTATTTATTT
27186 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27228 TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA T
27244 TTTAGTTTAA
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27493 original size:2 final size:2
Alignment explanation
Indices: 27486--27526 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
27476 ATTATACATT
27486 TA TA TA TA TA 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 TA TA T
27527 TTCATTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29179 original size:22 final size:21
Alignment explanation
Indices: 29154--29194 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
29144 TATAAAAAAT
29154 TATTTTTATTAAATATTTTTGC
1 TATTTTTATTAAAT-TTTTTGC
*
29176 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
29195 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGC
Found at i:29951 original size:20 final size:21
Alignment explanation
Indices: 29926--29977 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
29916 TTTTACCAAT
*
29926 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
29946 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
29967 TCGCAATGCGA
1 TCGCAATGCGA
29978 TACTTACTAT
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:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:29991 original size:20 final size:20
Alignment explanation
Indices: 29966--30077 Score: 111
Period size: 20 Copynumber: 5.7 Consensus size: 20
29956 AATTGGGAAA
*
29966 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
29986 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
30007 ATCGCAA--CGATACTTACT
1 ATCGCAACGCGATACTTACT
*
30025 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
30045 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
30065 TTCGCAACGCGAT
1 ATCGCAACGCGAT
30078 TTACATAGCG
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
18 8 0.10
19 6 0.08
20 55 0.71
21 8 0.10
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:30695 original size:19 final size:19
Alignment explanation
Indices: 30668--30852 Score: 165
Period size: 19 Copynumber: 10.1 Consensus size: 19
30658 CGAAACCAAA
*
30668 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
30687 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
30706 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
30725 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
30745 TCGCATTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
30761 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
30778 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
30792 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
30811 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
30831 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
30851 TC
1 TC
30853 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 17, Indels: 26
0.76 0.09 0.15
Matches are distributed among these distances:
14 19 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:30745 original size:39 final size:38
Alignment explanation
Indices: 30668--30852 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
30658 CGAAACCAAA
30668 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
30706 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
30745 TCGCATTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
30778 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * *
30811 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
30851 TC
1 TC
30853 AACCAAAAGA
Statistics
Matches: 122, Mismatches: 15, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
31 3 0.02
33 37 0.30
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:30829 original size:20 final size:20
Alignment explanation
Indices: 30795--30852 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
30785 GCGATTCTCT
**
30795 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
30815 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
30835 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
30853 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:32900 original size:42 final size:42
Alignment explanation
Indices: 32840--32962 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
32830 GCCCGACTCG
* * *
32840 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
32882 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
32924 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
32963 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:32920 original size:21 final size:21
Alignment explanation
Indices: 32896--32962 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
32886 TCATTCCTCG
32896 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
32917 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
32938 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
32959 AGAG
1 AGAG
32963 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:34337 original size:14 final size:14
Alignment explanation
Indices: 34318--34353 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34308 ATTGTTTAAT
34318 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
34332 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
34346 TGATTTGT
1 TGATTTGT
34354 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:34579 original size:33 final size:32
Alignment explanation
Indices: 34537--34663 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
34527 ATTAAATTCG
34537 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
34570 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
34603 CGTTACGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
34636 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
34664 AGTAATTTCC
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:34626 original size:66 final size:66
Alignment explanation
Indices: 34530--34662 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
34520 ACGCGAAATT
* *
34530 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
34595 G
66 G
*
34596 AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
34661 G
66 G
34662 A
1 A
34663 TAGTAATTTC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTACGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:36967 original size:12 final size:12
Alignment explanation
Indices: 36950--36974 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36940 TCTTCGGGGA
36950 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36962 CTTTTTCTTCTT
1 CTTTTTCTTCTT
36974 C
1 C
36975 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:37183 original size:24 final size:24
Alignment explanation
Indices: 37149--37202 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37139 CTGAAACATC
* *
37149 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
37173 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
37197 ATCAAA
1 ATCAAA
37203 TTTCGAATAC
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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:38288 original size:20 final size:20
Alignment explanation
Indices: 38263--38318 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
38253 CCATTTGACT
38263 ATCGCAACGCGAAAATGGCC
1 ATCGCAACGCGAAAATGGCC
**
38283 ATCGCAACGCGAAAATGGTT
1 ATCGCAACGCGAAAATGGCC
*
38303 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
38319 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCC
Found at i:38361 original size:14 final size:14
Alignment explanation
Indices: 38342--38398 Score: 53
Period size: 14 Copynumber: 3.8 Consensus size: 14
38332 GAAAATCGCA
38342 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
38356 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
*
38373 CATTGCG-GTTTCTCG
1 --TTGCGATTTTCTCG
38388 TTGCGATTTTC
1 TTGCGATTTTC
38399 ATTTCGCATT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
13 5 0.14
14 15 0.43
15 3 0.09
17 3 0.09
18 4 0.11
19 5 0.14
ACGTcount: A:0.09, C:0.21, G:0.21, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:38378 original size:19 final size:19
Alignment explanation
Indices: 38337--38451 Score: 126
Period size: 19 Copynumber: 6.6 Consensus size: 19
38327 GAAATGAAAA
38337 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
38353 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
38370 TCGCATTGCG-GTTTC---
1 TCGCATTGCGATTTTCATT
38385 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38402 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
38421 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTTTCATT
*
38440 TCGCGTTGCGAT
1 TCGCATTGCGAT
38452 AGTCTGTTTT
Statistics
Matches: 84, Mismatches: 4, Indels: 19
0.79 0.04 0.18
Matches are distributed among these distances:
13 5 0.06
14 15 0.18
15 3 0.04
16 3 0.04
17 6 0.07
18 4 0.05
19 48 0.57
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:38390 original size:32 final size:33
Alignment explanation
Indices: 38337--38450 Score: 140
Period size: 32 Copynumber: 3.3 Consensus size: 33
38327 GAAATGAAAA
*
38337 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAGTTTCTCGTTGCGATTTTCATT
38370 TCGCATTGCG-GTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAGTTTCTCGTTGCGATTTTCATT
* *
38402 TCGCATTGCGATTTTCATTTCGCATTGCGATTTCCATT
1 TCGCATTGCGAGTTTC---TCG--TTGCGATTTTCATT
*
38440 TCGCGTTGCGA
1 TCGCATTGCGA
38451 TAGTCTGTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
32 31 0.44
33 14 0.20
36 3 0.04
38 23 0.32
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TCGCATTGCGAGTTTCTCGTTGCGATTTTCATT
Found at i:40473 original size:20 final size:19
Alignment explanation
Indices: 40438--40504 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
40428 GAAACTTAAA
40438 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
40457 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
40477 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
40496 ATCGCAACG
1 ATCGCAACG
40505 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:40512 original size:14 final size:14
Alignment explanation
Indices: 40493--40550 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
40483 ATGCGAAATG
40493 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
40507 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
40523 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
40539 AAAATCGCAACG
1 AAAATCGCAACG
40551 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:40535 original size:32 final size:33
Alignment explanation
Indices: 40477--40555 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
40467 GGAAATGGCT
*
40477 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
40510 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
40542 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
40556 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:40584 original size:19 final size:18
Alignment explanation
Indices: 40562--40657 Score: 73
Period size: 14 Copynumber: 5.7 Consensus size: 18
40552 GAAACACAAA
40562 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
40581 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
*
40597 T--CTTTGCGATTTCATT
1 TCGCATTGCGATTTCATT
* *
40613 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
40629 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
40646 TCGCATTGCGAT
1 TCGCATTGCGAT
40658 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
14 16 0.26
15 3 0.05
16 8 0.13
17 4 0.07
18 14 0.23
19 16 0.26
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:40648 original size:33 final size:33
Alignment explanation
Indices: 40567--40657 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
40557 ACAAATCGCA
*
40567 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCT
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
40600 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
40632 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
40658 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:40676 original size:20 final size:19
Alignment explanation
Indices: 40642--40695 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
40632 TTGCGATTTT
*
40642 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
40661 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
40681 CATTTCGTGTTGCGA
1 CATTTCGCGTTGCGA
40696 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:40694 original size:19 final size:19
Alignment explanation
Indices: 40630--40695 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
40620 GCGATTTTGT
**
40630 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
40649 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
40669 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
40688 TGTTGCGA
1 CGTTGCGA
40696 AAGTAAACTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.15, C:0.23, G:0.24, T:0.38
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:41196 original size:18 final size:18
Alignment explanation
Indices: 41173--41212 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41163 TCAGATAATG
* *
41173 GCTCTGGGTGGGGTGATA
1 GCTCTGGGAGAGGTGATA
*
41191 GCTCTGGGAGAGGTGATG
1 GCTCTGGGAGAGGTGATA
41209 GCTC
1 GCTC
41213 CCGAAGTGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.47, T:0.25
Consensus pattern (18 bp):
GCTCTGGGAGAGGTGATA
Found at i:42556 original size:20 final size:20
Alignment explanation
Indices: 42531--42568 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42521 AATAGTTTCT
42531 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
42551 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
42569 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:42857 original size:22 final size:22
Alignment explanation
Indices: 42832--42875 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
42822 GATTTAGATA
42832 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
42854 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
42876 TGAGAGAGTG
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:43134 original size:41 final size:41
Alignment explanation
Indices: 43082--43159 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
43072 CGAAAGTCAG
* * *
43082 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
*
43123 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
43160 CCCAATTCGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTAT
Found at i:43156 original size:20 final size:20
Alignment explanation
Indices: 43063--43156 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
43053 GATTGTGTAA
* *
43063 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTAAGT
*
43083 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
* * *
43103 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTAAGT
*
43124 ATCGCATTGCGATAGTAAGT
1 ATCGCGTTGCGATAGTAAGT
*
43144 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
43157 TTTCCCAATT
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 45 0.73
21 12 0.19
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTAAGT
Found at i:43175 original size:41 final size:41
Alignment explanation
Indices: 43082--43177 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
43072 CGAAAGTCAG
* * * ** *
43082 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
*
43123 TATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
43165 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
43178 TTTCCCAATT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 44 0.96
42 2 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:43196 original size:62 final size:62
Alignment explanation
Indices: 43125--43258 Score: 191
Period size: 62 Copynumber: 2.2 Consensus size: 62
43115 TTTTGTATTA
43125 TCGCATTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
1 TCGCATTGCGAT-GTAAGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
* * ** **
43187 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTT-CTTAT
1 TCGCATTGCGATGTAAGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
43248 TCGCATTGCGA
1 TCGCATTGCGA
43259 ATTGGGAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
61 17 0.27
62 47 0.73
ACGTcount: A:0.18, C:0.24, G:0.19, T:0.39
Consensus pattern (62 bp):
TCGCATTGCGATGTAAGTATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAAT
Found at i:43209 original size:41 final size:41
Alignment explanation
Indices: 43164--43258 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
43154 GATTTTCCCA
*
43164 ATTCGCGTTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
1 ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
*
43205 ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCTT
1 ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
43246 ATTCGCATTGCGA
1 ATTCGCATTGCGA
43259 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.16, C:0.24, G:0.19, T:0.41
Consensus pattern (41 bp):
ATTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTT
Found at i:43210 original size:20 final size:21
Alignment explanation
Indices: 43145--43243 Score: 146
Period size: 21 Copynumber: 4.8 Consensus size: 21
43135 ATAGTAAGTA
*
43145 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
43166 TCGCGTTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
* **
43187 TCGCGTTGCGA-TTTACTTAT
1 TCGCGTTGCGATTTTCCCAAT
*
43207 TCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATTTTCCCAAT
43228 TCGCGTTGCGATTTTC
1 TCGCGTTGCGATTTTC
43244 TTATTCGCAT
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 16 0.24
21 52 0.76
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCCAAT
Found at i:43273 original size:62 final size:62
Alignment explanation
Indices: 43144--43273 Score: 163
Period size: 62 Copynumber: 2.1 Consensus size: 62
43134 GATAGTAAGT
* * **
43144 ATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAATTCGCGTTGCGATTTACTTA
1 ATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAATTCGCATTGCGATTGACAAA
* ** **
43206 TTCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTT-CTTATTCGCATTGCGAATTGGGAAA
1 ATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAATTCGCATTGCG-ATTGACAAA
43268 ATCGCA
1 ATCGCA
43274 ACGATACTGT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 12 0.21
62 45 0.79
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (62 bp):
ATCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTTCCCAATTCGCATTGCGATTGACAAA
Found at i:45646 original size:23 final size:25
Alignment explanation
Indices: 45615--45661 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
45605 GCGGTAATGG
*
45615 CTTTGACTT-AAAAT-TTCAAAAAC
1 CTTTCACTTCAAAATATTCAAAAAC
45638 CTTTCACTTCAAAATAATTCAAAA
1 CTTTCACTTCAAAAT-ATTCAAAA
45662 CCCTATTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 5 0.25
26 7 0.35
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (25 bp):
CTTTCACTTCAAAATATTCAAAAAC
Found at i:46352 original size:33 final size:33
Alignment explanation
Indices: 46281--46352 Score: 76
Period size: 33 Copynumber: 2.2 Consensus size: 33
46271 GTTTCAATAT
* **
46281 TTTTGTTTTAAAAATTGTAGTTAGACTTTTAATT
1 TTTT-TTTTAAAAATTGTAATTAGACTTTTAAAA
46315 TTTTTTTTAAAAATTG-AATTA-AGCTCTTTAAAA
1 TTTTTTTTAAAAATTGTAATTAGA-CT-TTTAAAA
46348 TTTTT
1 TTTTT
46353 GAAAATTTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
31 1 0.03
32 6 0.18
33 22 0.67
34 4 0.12
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (33 bp):
TTTTTTTTAAAAATTGTAATTAGACTTTTAAAA
Found at i:54307 original size:3 final size:3
Alignment explanation
Indices: 54288--54331 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
54278 CAGTTTATTT
* *
54288 ATA ACA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
54332 TTATTTATAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:61694 original size:43 final size:43
Alignment explanation
Indices: 61627--61712 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
61617 TGACTTCGAA
** *
61627 TTTTTTGATAAGAATTTCAAGCCTCGTTAAAAACCCCCTTCTT
1 TTTTTTGATAAGAATGACAAGCCTCCTTAAAAACCCCCTTCTT
* * *
61670 TTTTTTTATAAGAATGACAGGCCTCCTTAAAAACCTCCTTCTT
1 TTTTTTGATAAGAATGACAAGCCTCCTTAAAAACCCCCTTCTT
61713 GATCAAAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (43 bp):
TTTTTTGATAAGAATGACAAGCCTCCTTAAAAACCCCCTTCTT
Found at i:66883 original size:16 final size:16
Alignment explanation
Indices: 66862--66892 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
66852 CAAGCTATAA
*
66862 TCTTAACTTAGGAAAC
1 TCTTAAATTAGGAAAC
66878 TCTTAAATTAGGAAA
1 TCTTAAATTAGGAAA
66893 GTAACTAATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (16 bp):
TCTTAAATTAGGAAAC
Found at i:71986 original size:21 final size:21
Alignment explanation
Indices: 71953--72027 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
71943 GCGAATAAGT
71953 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGGAA
* * ** *
71974 AATCGTAATGCGAA-TAAGTA
1 AATCGCAACGCGAATTGGGAA
71994 AATCGCAACGCGAATTGGGAA
1 AATCGCAACGCGAATTGGGAA
*
72015 AATCGCAATGCGA
1 AATCGCAACGCGA
72028 TACTGACTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AATCGCAACGCGAATTGGGAA
Found at i:72008 original size:41 final size:40
Alignment explanation
Indices: 71936--72027 Score: 166
Period size: 41 Copynumber: 2.3 Consensus size: 40
71926 TTTTCCCAAT
71936 TCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGAAAA
*
71976 TCGTAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGT-AATCGCAACGCGAATTGGGAAAA
72017 TCGCAATGCGA
1 TCGCAATGCGA
72028 TACTGACTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
40 16 0.33
41 33 0.67
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.18
Consensus pattern (40 bp):
TCGCAATGCGAATAAGTAATCGCAACGCGAATTGGGAAAA
Found at i:72040 original size:41 final size:41
Alignment explanation
Indices: 71954--72088 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
71944 CGAATAAGTA
* * *
71954 ATCGCAACGCGAATTGGGAAAATCGTAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
71995 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
72036 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
72077 TTCGCAACGCGA
1 ATCGCAACGCGA
72089 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:72041 original size:20 final size:20
Alignment explanation
Indices: 72016--72130 Score: 115
Period size: 20 Copynumber: 5.7 Consensus size: 20
72006 AATTGGGAAA
*
72016 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
72036 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
72057 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
72077 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
72097 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
72117 TTCGCAACGCGATA
1 ATCGCAACGCGATA
72131 ATACATAATC
Statistics
Matches: 81, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:72089 original size:41 final size:41
Alignment explanation
Indices: 72013--72150 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
72003 GCGAATTGGG
* * *
72013 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* * *
72054 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATACTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAAT-AC
** *
72096 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
* *
72135 ATAATCGCAATGCGAT
1 AAAATCGCAACGCGAT
72151 TTTCAAAGCG
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.39
41 44 0.56
42 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATAC
Found at i:72645 original size:20 final size:20
Alignment explanation
Indices: 72620--72657 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
72610 CGATTCTCTC
72620 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
72640 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
72658 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:73961 original size:18 final size:18
Alignment explanation
Indices: 73940--73985 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
73930 CTCCACTTCG
*
73940 AGAGCCATCACCTCGCCC
1 AGAGCCATCACCTCACCC
*
73958 AGAGCTATCACCTCACCC
1 AGAGCCATCACCTCACCC
73976 AGAGCCATCA
1 AGAGCCATCA
73986 TCTGATCGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.28, C:0.43, G:0.15, T:0.13
Consensus pattern (18 bp):
AGAGCCATCACCTCACCC
Found at i:74522 original size:14 final size:14
Alignment explanation
Indices: 74503--74560 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
74493 ATGCGAAATG
74503 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
74517 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
74533 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
74549 AAAATCGCAACG
1 AAAATCGCAACG
74561 CGAAATAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:74541 original size:18 final size:16
Alignment explanation
Indices: 74487--74581 Score: 72
Period size: 18 Copynumber: 5.7 Consensus size: 16
74477 GGAAAAGGCT
74487 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAAT--AA
*
74506 ATCGCAA-CGACA-AA
1 ATCGCAAGCGAAATAA
74520 ATCGCAACGCGAAATGAA
1 ATCGCAA-GCGAAAT-AA
*
74538 ATCGCAA-CGACA-AA
1 ATCGCAAGCGAAATAA
74552 ATCGCAACGCGAAATAAA
1 ATCGCAA-GCGAAAT-AA
74570 ATCGCAATGCGA
1 ATCGCAA-GCGA
74582 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
14 18 0.29
16 12 0.19
17 4 0.06
18 22 0.35
19 7 0.11
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (16 bp):
ATCGCAAGCGAAATAA
Found at i:74545 original size:32 final size:32
Alignment explanation
Indices: 74487--74576 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
74477 GGAAAAGGCT
*
74487 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
74520 ATCGCAACGCGAAATGAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAATCGCAACGACAAA
*
74552 ATCGCAACGCGAAATAAAATCGCAA
1 ATCGCAACGCGAAATGAAATCGCAA
74577 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 40 0.73
33 15 0.27
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (32 bp):
ATCGCAACGCGAAATGAAATCGCAACGACAAA
Found at i:74612 original size:14 final size:14
Alignment explanation
Indices: 74593--74650 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
74583 TTGTGTTTCG
74593 CGTTGCGATTTTAT
1 CGTTGCGATTTTAT
*
74607 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TAT
*
74623 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTAT
74639 CGTTGCGATTTT
1 CGTTGCGATTTT
74651 CATTTGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTAT
Found at i:74627 original size:32 final size:32
Alignment explanation
Indices: 74588--74707 Score: 127
Period size: 32 Copynumber: 3.6 Consensus size: 32
74578 GCGATTTGTG
74588 TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
*
74620 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTATCGTTGCGA-TTTCA
* *
74653 TTT-GCATTGCGATATCCTT-TCCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGAT-T--TTAT---CGTTGCGAT-TTCA
74690 TTTCGCGTTGCGATTTTA
1 TTTCGCGTTGCGATTTTA
74708 AGTTTCGTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
32 35 0.47
33 9 0.12
34 1 0.01
35 4 0.05
36 1 0.01
37 15 0.20
38 9 0.12
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTATCGTTGCGATTTCA
Found at i:74683 original size:19 final size:19
Alignment explanation
Indices: 74639--74703 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
74629 GCGATTTTGT
**
74639 CGTTGCGATTTTCATTT-G
1 CGTTGCGATAGTCATTTCG
* *
74657 CATTGCGATA-TCCTTTCCG
1 CGTTGCGATAGTCATTT-CG
74676 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
74695 CGTTGCGAT
1 CGTTGCGAT
74704 TTTAAGTTTC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 5 0.13
18 8 0.21
19 21 0.54
20 5 0.13
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Done.