Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005372.1 Hibiscus syriacus cultivar Beakdansim tig00012216_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: 106940
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2855 original size:29 final size:29
Alignment explanation
Indices: 2813--2903 Score: 164
Period size: 29 Copynumber: 3.1 Consensus size: 29
2803 TTCTACAGTA
2813 ACCTTGGAGGTCGCCATGGCATCCGGGCG
1 ACCTTGGAGGTCGCCATGGCATCCGGGCG
2842 ACCTTGGAGGTCGCCATGGCATCCGGGCG
1 ACCTTGGAGGTCGCCATGGCATCCGGGCG
* *
2871 ACCTTGGAGGTTGCCATGGCATCCGAGCG
1 ACCTTGGAGGTCGCCATGGCATCCGGGCG
2900 ACCT
1 ACCT
2904 GTGTGGTATT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 60 1.00
ACGTcount: A:0.15, C:0.31, G:0.35, T:0.19
Consensus pattern (29 bp):
ACCTTGGAGGTCGCCATGGCATCCGGGCG
Found at i:2979 original size:20 final size:20
Alignment explanation
Indices: 2954--3026 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
2944 GTATTGGAGC
2954 ATGCATGGGGGAGTTGTGGG
1 ATGCATGGGGGAGTTGTGGG
**
2974 ATGCATGCTGTGCATGG-GACGTGGG
1 ATGCATG--G-G---GGAGTTGTGGG
2999 AATGCATGGGGGAGTTGTGGG
1 -ATGCATGGGGGAGTTGTGGG
3020 ATGCATG
1 ATGCATG
3027 CTGTGCATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 16
0.67 0.07 0.26
Matches are distributed among these distances:
20 16 0.39
21 6 0.15
22 1 0.02
23 2 0.05
24 1 0.02
25 6 0.15
26 9 0.22
ACGTcount: A:0.18, C:0.10, G:0.48, T:0.25
Consensus pattern (20 bp):
ATGCATGGGGGAGTTGTGGG
Found at i:3004 original size:46 final size:46
Alignment explanation
Indices: 2954--3046 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
2944 GTATTGGAGC
2954 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
1 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
3000 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
1 ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
3046 A
1 A
3047 CTGTGCATGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.18, C:0.11, G:0.47, T:0.24
Consensus pattern (46 bp):
ATGCATGGGGGAGTTGTGGGATGCATGCTGTGCATGGGACGTGGGA
Found at i:3579 original size:21 final size:21
Alignment explanation
Indices: 3554--3597 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3544 AATCTAGTTA
3554 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
3575 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
3596 AT
1 AT
3598 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:3607 original size:28 final size:30
Alignment explanation
Indices: 3574--3636 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
3564 TAGTATAAAT
*
3574 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
3602 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
3632 TATTA
1 TATTA
3637 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:4185 original size:20 final size:21
Alignment explanation
Indices: 4141--4185 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
4131 AAATATCGTG
**
4141 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
4162 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
4182 TTTA
1 TTTA
4186 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:4475 original size:26 final size:25
Alignment explanation
Indices: 4446--4504 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
4436 AAATCATATT
*
4446 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
4472 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
4498 ATTATTA
1 ATTATTA
4505 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:7412 original size:26 final size:26
Alignment explanation
Indices: 7383--7561 Score: 162
Period size: 26 Copynumber: 7.2 Consensus size: 26
7373 TTTGATGATT
7383 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
7409 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
*
7435 TAATAATGATTT-AGTAATAATCATTA
1 TAGTAATGATTTGA-TAATAATCATTA
** *
7461 TAAAAATGA-TT--TAATAATGATT-
1 TAGTAATGATTTGATAATAATCATTA
* * * *
7483 TA--AAT-ATTTAATGATTTGATGATT-
1 TAGTAATGATTTGAT-A-ATAATCATTA
7507 TAGTAATGATTTGATAATAATCATTA
1 TAGTAATGATTTGATAATAATCATTA
* * *
7533 TAATAATGATTTTATAATAATTATT-
1 TAGTAATGATTTGATAATAATCATTA
7558 TAGT
1 TAGT
7562 TATTATTTAG
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.01
20 5 0.04
22 3 0.02
23 11 0.08
24 9 0.07
25 12 0.09
26 83 0.64
27 6 0.05
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (26 bp):
TAGTAATGATTTGATAATAATCATTA
Found at i:7519 original size:124 final size:123
Alignment explanation
Indices: 7328--7597 Score: 445
Period size: 124 Copynumber: 2.2 Consensus size: 123
7318 ATGTATTTAT
7328 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
*
7393 TTGATAATAATCATTATAGTAATGATTTGATAATAATCATTATAATAATGATTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATT-TAATAATGATTTAGTAA
7452 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
1 TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
* * * * *
7517 TTGATAATAATCATTATAATAATGATTTTATAATAATTATTTAGTTATTATTTAGTAA
66 TTGATAATAATCATTATAATAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
* *
7575 TTAT--TTATAATAATGATTTAATA
1 TAATCATTATAAAAATGATTTAATA
7598 CTAATGATTT
Statistics
Matches: 138, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
121 18 0.13
123 17 0.12
124 103 0.75
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (123 bp):
TAATCATTATAAAAATGATTTAATAATGATTTAAATATTTAATGATTTGATGATTTAGTAATGAT
TTGATAATAATCATTATAATAATGATTTGATAATAATCATTTAATAATGATTTAGTAA
Found at i:7604 original size:14 final size:14
Alignment explanation
Indices: 7386--7613 Score: 105
Period size: 14 Copynumber: 17.1 Consensus size: 14
7376 GATGATTTAG
*
7386 TAATGATTTGATAA
1 TAATGATTTAATAA
* *
7400 TAATCA-TT-ATAG
1 TAATGATTTAATAA
*
7412 TAATGATTTGATAA
1 TAATGATTTAATAA
*
7426 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
7438 TAATGATTTAGTAA
1 TAATGATTTAATAA
*
7452 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
7464 AAATGA-TT--TAA
1 TAATGATTTAATAA
*
7475 TAATGATTTAAATATT
1 TAATGATTT-AATA-A
*
7491 TAATGATTTGATGATTTAG
1 TAATGATTT-A--A--TAA
*
7510 TAATGATTTGATAA
1 TAATGATTTAATAA
*
7524 TAATCA-TT-ATAA
1 TAATGATTTAATAA
*
7536 TAATGATTTTATAA
1 TAATGATTTAATAA
* *
7550 TAATTATTTAGT--
1 TAATGATTTAATAA
* *
7562 T-ATTATTTAGTAA
1 TAATGATTTAATAA
7575 T--T-ATTT-ATAA
1 TAATGATTTAATAA
*
7585 TAATGATTTAATAC
1 TAATGATTTAATAA
7599 TAATGATTTAATAA
1 TAATGATTTAATAA
7613 T
1 T
7614 TATTACTAAT
Statistics
Matches: 168, Mismatches: 25, Indels: 42
0.71 0.11 0.18
Matches are distributed among these distances:
10 4 0.02
11 22 0.13
12 40 0.24
13 19 0.11
14 58 0.35
15 2 0.01
16 11 0.07
18 1 0.01
19 9 0.05
20 2 0.01
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.46
Consensus pattern (14 bp):
TAATGATTTAATAA
Found at i:7636 original size:38 final size:38
Alignment explanation
Indices: 7566--7639 Score: 96
Period size: 38 Copynumber: 1.9 Consensus size: 38
7556 TTTAGTTATT
* **
7566 ATTTAGTAATTATTTATAATAATGATTTAATACTAATG
1 ATTTAATAATTATTTATAATAATGATAGAATACTAATG
*
7604 ATTTAATAATTA-TTACTAATAATTATAGAATACTAA
1 ATTTAATAATTATTTA-TAATAATGATAGAATACTAA
7640 CAAATGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 3 0.10
38 28 0.90
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (38 bp):
ATTTAATAATTATTTATAATAATGATAGAATACTAATG
Found at i:7846 original size:17 final size:17
Alignment explanation
Indices: 7821--7854 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7811 ACTAAATATT
*
7821 TAATTATTTGATACTAA
1 TAATGATTTGATACTAA
7838 TAATGATTTGATACTAA
1 TAATGATTTGATACTAA
7855 AAATCATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (17 bp):
TAATGATTTGATACTAA
Found at i:7846 original size:25 final size:23
Alignment explanation
Indices: 7767--7846 Score: 67
Period size: 24 Copynumber: 3.3 Consensus size: 23
7757 GATTTATTGT
7767 TAATATTTAATTATTTGATAC--
1 TAATATTTAATTATTTGATACTA
* *
7788 TAATGATTTAAAATAGTTGATTTACTA
1 TAAT-ATTT-AATTATTTGA--TACTA
7815 -AATATTTAATTATTTGATACTAA
1 TAATATTTAATTATTTGATACT-A
7838 TAATGATTT
1 TAAT-ATTT
7847 GATACTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
21 4 0.09
22 8 0.17
23 9 0.20
24 11 0.24
25 11 0.24
26 3 0.07
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (23 bp):
TAATATTTAATTATTTGATACTA
Found at i:10026 original size:15 final size:14
Alignment explanation
Indices: 10003--10033 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
9993 TACAACACTA
10003 AACTTTAATATAAT
1 AACTTTAATATAAT
10017 AACTTATAATATAAT
1 AACTT-TAATATAAT
10032 AA
1 AA
10034 ACTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (14 bp):
AACTTTAATATAAT
Found at i:10041 original size:16 final size:16
Alignment explanation
Indices: 10008--10054 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
9998 CACTAAACTT
*
10008 TAATATAAT-AACTTA
1 TAATATAATAAACTAA
10023 TAATATAATAAACTAA
1 TAATATAATAAACTAA
*
10039 TAA-ACTAACAAACTAA
1 TAATA-TAATAAACTAA
10055 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATATAATAAACTAA
Found at i:10175 original size:32 final size:34
Alignment explanation
Indices: 10095--10176 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
10085 CTAAACCCTT
*
10095 AAAC-AACTAATAAAATATTCTTTTATATAACTA
1 AAACTAACTAATAAACTATTCTTTTATATAACTA
10128 AAACTAACTAATAAACTATT-TTTTCATTATAA-T-
1 AAACTAACTAATAAACTATTCTTTT-A-TATAACTA
*
10161 ATACT-ACTAATAAACT
1 AAACTAACTAATAAACT
10177 TACTAACTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
32 11 0.25
33 12 0.27
34 16 0.36
35 5 0.11
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (34 bp):
AAACTAACTAATAAACTATTCTTTTATATAACTA
Found at i:10293 original size:46 final size:48
Alignment explanation
Indices: 10216--10307 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
10206 CAACAAACAA
*
10216 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATT-AATAATTTTTTTT
*
10265 ATATAAC-TAACTA-TTAAC-AAAACAAACTAATTAATTATTTTTT
1 ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTT
10308 AACTATATAA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 10 0.24
46 13 0.32
47 5 0.12
48 6 0.15
49 7 0.17
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (48 bp):
ATATAACTTAACTATTTAACTAAAACAAACTAATTAATAATTTTTTTT
Found at i:10318 original size:47 final size:48
Alignment explanation
Indices: 10216--10320 Score: 135
Period size: 47 Copynumber: 2.2 Consensus size: 48
10206 CAACAAACAA
* *
10216 ATATAACTTAACTATTTAACTAACACAAACTAATTAAATAATTTTTTTT
1 ATATAAC-TAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
*
10265 ATATAACTAACTA-TTAAC-AAAACAAACTAATT-AATTATTTTTTAACT
1 ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTT--CT
10312 ATATAACTA
1 ATATAACTA
10321 TCAAACATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
45 10 0.20
46 13 0.25
47 15 0.29
48 6 0.12
49 7 0.14
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (48 bp):
ATATAACTAACTATTTAACTAAAACAAACTAATTAAATAATTTTTTCT
Found at i:10376 original size:41 final size:40
Alignment explanation
Indices: 10288--10376 Score: 90
Period size: 41 Copynumber: 2.2 Consensus size: 40
10278 TTAACAAAAC
* *
10288 AAACTAATTAATTATTTTTTAACTATATAACTATCAAACAT
1 AAACTAATTAAATAATTTTTAACTATATAACTAT-AAACAT
* * * *
10329 ATACTAATTAAATAATTTTTAATTTATGTATACTAT-AACTT
1 AAACTAATTAAATAATTTTTAA-CTATATA-ACTATAAACAT
10370 AAACTAA
1 AAACTAA
10377 CAATCATATA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
41 29 0.74
42 5 0.13
43 5 0.13
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (40 bp):
AAACTAATTAAATAATTTTTAACTATATAACTATAAACAT
Found at i:10935 original size:29 final size:29
Alignment explanation
Indices: 10893--11055 Score: 292
Period size: 29 Copynumber: 5.6 Consensus size: 29
10883 AGGACTACAT
10893 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
10922 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
10951 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
10980 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
11009 GGGACTACATGGCGACCTACAAGGTCGCC
1 GGGACTACATGGCGACCTACAAGGTCGCC
* *
11038 TAGG-CTGCATGGCGACCT
1 -GGGACTACATGGCGACCT
11056 CTCTATTGGC
Statistics
Matches: 131, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
29 129 0.98
30 2 0.02
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (29 bp):
GGGACTACATGGCGACCTACAAGGTCGCC
Found at i:11106 original size:28 final size:28
Alignment explanation
Indices: 11074--11130 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
11064 GCTCGTATGA
* * *
11074 CTCGTCTAAGCCTGCATGGCGACCTCTC
1 CTCGTATAAGACTGCATGACGACCTCTC
*
11102 CTCGTATAAGACTGTATGACGACCTCTC
1 CTCGTATAAGACTGCATGACGACCTCTC
11130 C
1 C
11131 ATTGGCTCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.19, C:0.35, G:0.19, T:0.26
Consensus pattern (28 bp):
CTCGTATAAGACTGCATGACGACCTCTC
Found at i:11163 original size:21 final size:21
Alignment explanation
Indices: 11138--11185 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
11128 TCCATTGGCT
*
11138 CGTATGGCTCGTATGTCACCC
1 CGTATGGCTCGTATGCCACCC
11159 CGTATGGCTCGTATGCCACCC
1 CGTATGGCTCGTATGCCACCC
11180 CGTATG
1 CGTATG
11186 TCACCTGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.33, G:0.25, T:0.27
Consensus pattern (21 bp):
CGTATGGCTCGTATGCCACCC
Found at i:11742 original size:18 final size:17
Alignment explanation
Indices: 11719--11752 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
11709 CCGCTACTAG
11719 TGAACCGATCAGAACCGT
1 TGAACCGATCA-AACCGT
*
11737 TGAACCGTTCAAACCG
1 TGAACCGATCAAACCG
11753 GACCGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (17 bp):
TGAACCGATCAAACCGT
Found at i:21261 original size:13 final size:14
Alignment explanation
Indices: 21236--21264 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21226 ATCTTGAAAT
21236 AAAATACATTTTTA
1 AAAATACATTTTTA
21250 AAAATACATTTTTA
1 AAAATACATTTTTA
21264 A
1 A
21265 TCAGAACATA
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:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATACATTTTTA
Found at i:24214 original size:2 final size:2
Alignment explanation
Indices: 24207--24232 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24197 TTAAAATAGA
24207 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
24233 GTGTGTATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36956 original size:3 final size:3
Alignment explanation
Indices: 36950--37011 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
36940 ATAATATATT
* *
36950 TAA TAA TAA T-A TAA T-A TATA TAA T-A TAA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
36993 TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA T
37012 TTAAGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
2 6 0.13
3 38 0.81
4 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:36965 original size:20 final size:21
Alignment explanation
Indices: 36938--37015 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 21
36928 TTTGGGCTTG
36938 TAATAATATATTTAATAATAA
1 TAATAATATATTTAATAATAA
*
36959 T-ATAATATATATAAT-ATAA
1 TAATAATATATTTAATAATAA
36978 TAATAATAT-TTATAATAATTTTAA
1 TAATAATATATT-TAATAA---TAA
37002 TAATAATA-ATTTAA
1 TAATAATATATTTAA
37016 GTAAAATGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
19 6 0.12
20 24 0.50
21 2 0.04
23 3 0.06
24 13 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAATATATTTAATAATAA
Found at i:36970 original size:9 final size:9
Alignment explanation
Indices: 36940--36994 Score: 56
Period size: 9 Copynumber: 5.7 Consensus size: 9
36930 TGGGCTTGTA
36940 ATAATATAT
1 ATAATATAT
*
36949 TTAATAATAAT
1 ATAAT-AT-AT
36960 ATAATATAT
1 ATAATATAT
36969 ATAATATAAT
1 ATAATAT-AT
*
36979 AATAATATTT
1 -ATAATATAT
36989 ATAATA
1 ATAATA
36995 ATTTTAATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
9 19 0.49
10 7 0.18
11 13 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATAATATAT
Found at i:37007 original size:12 final size:12
Alignment explanation
Indices: 36938--37008 Score: 58
Period size: 12 Copynumber: 5.8 Consensus size: 12
36928 TTTGGGCTTG
36938 TAATAAT-ATATT
1 TAATAATAAT-TT
*
36950 TAATAATAA-TA
1 TAATAATAATTT
* *
36961 TAATATATATAATA
1 TAATA-ATA-ATTT
36975 TAATAATAATATT
1 TAATAATAAT-TT
36988 T-ATAATAATTT
1 TAATAATAATTT
36999 TAATAATAAT
1 TAATAATAAT
37009 AATTTAAGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
11 9 0.18
12 27 0.54
13 7 0.14
14 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:37278 original size:75 final size:75
Alignment explanation
Indices: 37189--38083 Score: 1646
Period size: 75 Copynumber: 11.9 Consensus size: 75
37179 TTGAAGGGTT
37189 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37254 ACCCGAAGGC
66 ACCCGAAGGC
* *
37264 TTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGGAAATATCATGCACTGCAGGACTTACAGAT
1 TTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
37329 GACCCGAAGGC
65 GACCCGAAGGC
37340 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37405 ACCCGAAGGC
66 ACCCGAAGGC
37415 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
37480 GACCCGAAGGC
65 GACCCGAAGGC
*
37491 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
37556 GACCCGAAGGC
65 GACCCGAAGGC
*
37567 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37632 ACCCGAAGGC
66 ACCCGAAGGC
37642 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37707 ACCCGAAGGC
66 ACCCGAAGGC
37717 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
37782 GACCCGAAGGC
65 GACCCGAAGGC
* * *
37793 TTGAAAACATCGAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGAACTGCAGAACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37858 ACCCGAAGGC
66 ACCCGAAGGC
*
37868 TTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37933 ACCCGAAGGC
66 ACCCGAAGGC
*
37943 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTGCAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
38008 GACCCAAAGGC
65 GACCCGAAGGC
*
38019 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
38084 TGGGAAATAG
Statistics
Matches: 796, Mismatches: 20, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
75 426 0.54
76 370 0.46
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (75 bp):
TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
ACCCGAAGGC
Found at i:37463 original size:151 final size:150
Alignment explanation
Indices: 37189--38083 Score: 1646
Period size: 151 Copynumber: 5.9 Consensus size: 150
37179 TTGAAGGGTT
37189 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
* *
37254 ACCCGAAGGCTTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGGAAATATCATGCACTGCAGG
66 ACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGCAGG
37319 ACTTACAGATGACCCGAAGGC
130 ACTTACAGATGACCCGAAGGC
37340 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37405 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
37470 ACTTACAGATGACCCGAAGGC
130 ACTTACAGATGACCCGAAGGC
*
37491 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
37556 GACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAAG
65 GACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
37621 ACTTACAGATGACCCGAAGGC
130 ACTTACAGATGACCCGAAGGC
37642 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37707 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCGAAGGC-TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
37772 ACTTACAGATGACCCGAAGGC
130 ACTTACAGATGACCCGAAGGC
* * *
37793 TTGAAAACATCGAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGAACTGCAGAACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
*
37858 ACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGCAGGA
66 ACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGA
37923 CTTACAGATGACCCGAAGGC
131 CTTACAGATGACCCGAAGGC
*
37943 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTGCAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
* *
38008 GACCCAAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGG
65 GACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
38073 ACTTACAGATG
130 ACTTACAGATG
38084 TGGGAAATAG
Statistics
Matches: 723, Mismatches: 17, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
150 148 0.20
151 474 0.66
152 101 0.14
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (150 bp):
TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
ACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGA
CTTACAGATGACCCGAAGGC
Found at i:37756 original size:226 final size:226
Alignment explanation
Indices: 37189--38083 Score: 1650
Period size: 226 Copynumber: 4.0 Consensus size: 226
37179 TTGAAGGGTT
37189 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
* *
37254 ACCCGAAGGC-TTGAAAACATCAAAAAACTCCCGAAGGCTTTTTTGGAAATATCATGCACTGCAG
66 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGC-TTTTTGGAAACATCATGCACTGCAG
37318 GACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
130 GACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
*
37383 TGCACTGCAGGACTTACAGATGACCCGAAGGC
195 TGCACTGCAAGACTTACAGATGACCCGAAGGC
37415 TTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
1 -TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGAT
*
37480 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTACAG
65 GACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAG
37545 GACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
130 GACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCA
37610 TGCACTGCAAGACTTACAGATGACCCGAAGGC
195 TGCACTGCAAGACTTACAGATGACCCGAAGGC
37642 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
37707 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
66 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
*
37772 ACTTACAGATGACCCGAAGGCTTGAAAACATCGAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
131 ACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
*
37837 GAACTGC-AGAACTTACAGATGACCCGAAGGC
196 GCACTGCAAG-ACTTACAGATGACCCGAAGGC
*
37868 TTGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
*
37933 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTAGAAACATCATGCACTGCAGG
66 ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
*
37998 ACTTACAGATGACCCAAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
131 ACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
* *
38063 GCACTGTAGGACTTACAGATG
196 GCACTGCAAGACTTACAGATG
38084 TGGGAAATAG
Statistics
Matches: 651, Mismatches: 14, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
225 2 0.00
226 427 0.66
227 195 0.30
228 27 0.04
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (226 bp):
TTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATG
ACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGG
ACTTACAGATGACCCGAAGGCTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCAT
GCACTGCAAGACTTACAGATGACCCGAAGGC
Found at i:38289 original size:166 final size:166
Alignment explanation
Indices: 38100--38406 Score: 535
Period size: 167 Copynumber: 1.8 Consensus size: 166
38090 ATAGTTTATC
* **
38100 AAAAAACTAAGGAAATCGTTTTCTTACTTTTCAACAATTTCATTTTTAGAAAAGATTGAATGAGA
1 AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCA-TTTTAGAAAAGATAAAATGAGA
38165 AACTATGAAAATCGTTTTCTCATTA-TTTTTAAAAATAACATGTTGATTGGGTAACATGCCCCAA
65 AACTATGAAAATCGTTTTCTCATTAGTTTTTAAAAATAACATGTTGATTGGGTAACATGCCCCAA
38229 TCTCAAGATAAGGTTGTTGGAAATAGTTTACTAAGTA
130 TCTCAAGATAAGGTTGTTGGAAATAGTTTACTAAGTA
38266 AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
1 AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
* **
38331 ACTATGAAAATCGTTTTTTCATTATGTTTTTTGAAATAACATGTTGATTGGGTAACATGCCCCAA
66 ACTATGAAAATCGTTTTCTCATTA-GTTTTTAAAAATAACATGTTGATTGGGTAACATGCCCCAA
38396 TCTCAAGATAA
130 TCTCAAGATAA
38407 TGCTCATTTT
Statistics
Matches: 133, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
165 44 0.33
166 41 0.31
167 48 0.36
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (166 bp):
AAAAAACTAAGAAAATCGTTTTCTTACTTTTCAACAATTTCATTTTAGAAAAGATAAAATGAGAA
ACTATGAAAATCGTTTTCTCATTAGTTTTTAAAAATAACATGTTGATTGGGTAACATGCCCCAAT
CTCAAGATAAGGTTGTTGGAAATAGTTTACTAAGTA
Found at i:38946 original size:22 final size:22
Alignment explanation
Indices: 38921--38975 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
38911 CATAAAGCTT
38921 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
38943 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
38965 TCATCTTTGAA
1 TCATCTTTGAA
38976 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:41636 original size:115 final size:115
Alignment explanation
Indices: 41469--42038 Score: 948
Period size: 115 Copynumber: 5.0 Consensus size: 115
41459 ATCATGCAGC
* * * * * *
41469 TCATCTTTTAATTCCAATGATTGG-TTCTGTGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
41533 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGA-ACAAAT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGA-AAAT
41583 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
41648 ACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTTTACTATGAGCAAAT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
*
41698 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACTAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
41763 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
41813 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
41878 ACACTTACAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
41928 TCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * ** ** *
41992 ACACCTCCAGAATATATTATTGGGGATCCTTATTTCTACTACGAGAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAA
42039 TATGGCACTT
Statistics
Matches: 431, Mismatches: 23, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
114 101 0.23
115 330 0.77
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (115 bp):
TCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGAAAAT
Found at i:48535 original size:13 final size:12
Alignment explanation
Indices: 48517--48546 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
48507 TTAATTCTTG
48517 AATAAAATAAATA
1 AATAAAATAAA-A
48530 AATAAAATAAAA
1 AATAAAATAAAA
48542 AATAA
1 AATAA
48547 TAAGTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AATAAAATAAAA
Found at i:48548 original size:19 final size:18
Alignment explanation
Indices: 48520--48561 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
48510 ATTCTTGAAT
48520 AAAATAAATAAATAAAATAA
1 AAAATAAATAAAT--AATAA
*
48540 AAAAT-AATAAGTAATAA
1 AAAATAAATAAATAATAA
48557 AAAAT
1 AAAAT
48562 TTGAAAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (18 bp):
AAAATAAATAAATAATAA
Found at i:50832 original size:3 final size:3
Alignment explanation
Indices: 50826--50902 Score: 79
Period size: 3 Copynumber: 26.3 Consensus size: 3
50816 ATAATATATT
* * *
50826 TAA TAA TAA T-A TAA T-A TATA TAA T-A TTA TAA TAA TAT TTA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
**
50869 TAA TAA TAA TAA TAA TAA TTT TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
50903 TTAAGTAAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 6 0.10
3 52 0.85
4 3 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:50834 original size:15 final size:14
Alignment explanation
Indices: 50814--50906 Score: 87
Period size: 15 Copynumber: 7.0 Consensus size: 14
50804 TTTGGGCTTG
50814 TAATAATATATTTAA
1 TAATAATA-ATTTAA
50829 TAATAAT-A--TAA
1 TAATAATAATTTAA
50840 T-ATATATAATATT-A
1 TAATA-ATAAT-TTAA
50854 TAATAAT-ATTT-A
1 TAATAATAATTTAA
50866 TAATAATAA--TAA
1 TAATAATAATTTAA
50878 TAATAATAATTTTAA
1 TAATAATAA-TTTAA
50893 TAATAATAATTTAA
1 TAATAATAATTTAA
50907 GTAAAATGAA
Statistics
Matches: 67, Mismatches: 0, Indels: 23
0.74 0.00 0.26
Matches are distributed among these distances:
10 3 0.04
11 7 0.10
12 21 0.31
13 4 0.06
14 9 0.13
15 23 0.34
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TAATAATAATTTAA
Found at i:50898 original size:12 final size:12
Alignment explanation
Indices: 50814--50899 Score: 68
Period size: 12 Copynumber: 6.8 Consensus size: 12
50804 TTTGGGCTTG
50814 TAATAAT-ATATT
1 TAATAATAAT-TT
*
50826 TAATAATAATAT
1 TAATAATAATTT
*
50838 AATATATATAATATT
1 TA-ATA-ATAAT-TT
50853 ATAATAAT-ATTT
1 -TAATAATAATTT
**
50865 ATAATAATAATAA
1 -TAATAATAATTT
50878 TAATAATAATTT
1 TAATAATAATTT
50890 TAATAATAAT
1 TAATAATAAT
50900 AATTTAAGTA
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
12 39 0.65
13 9 0.15
14 7 0.12
15 4 0.07
16 1 0.02
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:51933 original size:35 final size:35
Alignment explanation
Indices: 51867--51945 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
51857 AACATAATCC
*
51867 TCAATTTAATTCTAAACCCTAAATTTCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTTCAAAATAAT
**
51902 TCAA-TTATATTCTAAACCCCAAA-TTCTAAAATTCT
1 TCAATTTA-ATTCTAAACCCCAAATTTC-AAAATAAT
51937 TCAATTTAA
1 TCAATTTAA
51946 GGTTTAGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
34 6 0.16
35 29 0.76
36 3 0.08
ACGTcount: A:0.43, C:0.19, G:0.00, T:0.38
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTTCAAAATAAT
Found at i:52781 original size:322 final size:321
Alignment explanation
Indices: 52197--52838 Score: 1185
Period size: 322 Copynumber: 2.0 Consensus size: 321
52187 GTGAGGGGAG
52197 AGGCTAAGAAATAAAAGCAATCGGTGCTGCGTTTCAGCAATCTTCCTCCATTTTTTCTTTGTAAA
1 AGGCTAAGAAATAAAAGCAATCGGTGCTGCGTTTCAGCAATCTTCCTCCATTTTTTCTTTGTAAA
52262 TAAAAAGTTGAAAGACAGAGTACTGCTTGGGTTTACACTTTTACATGGCGAAAAACTAAAGAACA
66 TAAAAAGTTGAAAGACAGAGTACTGCTTGGGTTTACACTTTTACATGGCGAAAAACTAAAGAACA
* *
52327 AAAACCAAACGAGAGTGCATGTGAGCAAAAAAAGACAGAGAGGTGAAGGCGTTGTTTGGGATTTC
131 AAAACAAAACGAGAGTGCATGTGAGCAAAAAAAGACAAAGAGGTGAAGGCGTTGTTTGGGATTTC
*
52392 ATTATATTTGATCATCTTTTGGAAAATCCTTAACCACAAGGATTAAACGAAGAAATTATTATATG
196 ATTATATTTGATCATCTTTTGAAAAATCCTTAACCACAAGGATTAAACGAAGAAATTATTATATG
* * *
52457 TCATTTTTACAAAATAATTTTAGTTTTGCTGGTGACTTTCGACAATGATACTTAGTTCATA
261 TCATTTATACAAAATAATTTCAATTTTGCTGGTGACTTTCGACAATGATACTTAGTTCATA
* *
52518 AGGCTAAGAAATAAACGCAATCGGTGTTGCGTTTCAGCAATTCTTCCTCCATTTTTTCTTTGTAA
1 AGGCTAAGAAATAAAAGCAATCGGTGCTGCGTTTCAGCAA-TCTTCCTCCATTTTTTCTTTGTAA
*
52583 ATAAAAAGTTGAAAGACAGAGTACTGCTTGGGTTTACACTTTTACATGGCGGAAAACTAAAGAAC
65 ATAAAAAGTTGAAAGACAGAGTACTGCTTGGGTTTACACTTTTACATGGCGAAAAACTAAAGAAC
*
52648 AAAAACAAAACGAGAGTGCATGTGAGCGAAAAAAGACAAAGAGGTGAAGGCGTTGTTTGGGATTT
130 AAAAACAAAACGAGAGTGCATGTGAGCAAAAAAAGACAAAGAGGTGAAGGCGTTGTTTGGGATTT
52713 CATTATATTTGATCATCTTTTGAAAAATCCTTAACCACAAGGATTAAACGAAGAAATTATTATAT
195 CATTATATTTGATCATCTTTTGAAAAATCCTTAACCACAAGGATTAAACGAAGAAATTATTATAT
52778 GTCATTTATACAAAATAATTTCAATTTTGCTGGTGACTTTCGACAATGATACTTAGTTCAT
260 GTCATTTATACAAAATAATTTCAATTTTGCTGGTGACTTTCGACAATGATACTTAGTTCAT
52839 CTTAGTAGTA
Statistics
Matches: 310, Mismatches: 10, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
321 38 0.12
322 272 0.88
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (321 bp):
AGGCTAAGAAATAAAAGCAATCGGTGCTGCGTTTCAGCAATCTTCCTCCATTTTTTCTTTGTAAA
TAAAAAGTTGAAAGACAGAGTACTGCTTGGGTTTACACTTTTACATGGCGAAAAACTAAAGAACA
AAAACAAAACGAGAGTGCATGTGAGCAAAAAAAGACAAAGAGGTGAAGGCGTTGTTTGGGATTTC
ATTATATTTGATCATCTTTTGAAAAATCCTTAACCACAAGGATTAAACGAAGAAATTATTATATG
TCATTTATACAAAATAATTTCAATTTTGCTGGTGACTTTCGACAATGATACTTAGTTCATA
Found at i:54708 original size:32 final size:32
Alignment explanation
Indices: 54687--54778 Score: 91
Period size: 32 Copynumber: 2.9 Consensus size: 32
54677 CCTACACCGA
54687 AAATC-AACCGATCTGATATTGACCCGACCCG
1 AAATCTAACCGATCTGATATTGACCCGACCCG
* * * *
54718 AAATCTAACCGATCTGGTATTAACTCGACCCAAA
1 AAATCTAACCGATCTGATATTGACCCGACCC--G
*
54752 AAATC-AACCGAT-TTAGTATTGACCCGA
1 AAATCTAACCGATCTGA-TATTGACCCGA
54779 TCTGATATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
31 5 0.10
32 23 0.47
33 16 0.33
34 5 0.10
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (32 bp):
AAATCTAACCGATCTGATATTGACCCGACCCG
Found at i:55894 original size:20 final size:20
Alignment explanation
Indices: 55857--55895 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55847 ACTGCCGATA
* * *
55857 TTCTTTATTGTCTTTTTATT
1 TTCTATATTGTATATTTATT
55877 TTCTATATTGTATATTTAT
1 TTCTATATTGTATATTTAT
55896 ATTTTTTTAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.05, T:0.69
Consensus pattern (20 bp):
TTCTATATTGTATATTTATT
Found at i:58645 original size:16 final size:16
Alignment explanation
Indices: 58624--58655 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
58614 TTTATTTGTC
58624 TAAATGTCATGAAAAG
1 TAAATGTCATGAAAAG
*
58640 TAAATGTCATGGAAAG
1 TAAATGTCATGAAAAG
58656 ATTGACTGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.22, T:0.25
Consensus pattern (16 bp):
TAAATGTCATGAAAAG
Found at i:60571 original size:13 final size:13
Alignment explanation
Indices: 60550--60583 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
60540 AAAGTTTTAA
60550 TGAATTTGGAAGC
1 TGAATTTGGAAGC
*
60563 TGGATTTGGAAGC
1 TGAATTTGGAAGC
60576 TGAATTTG
1 TGAATTTG
60584 ACTTGCCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.32, T:0.35
Consensus pattern (13 bp):
TGAATTTGGAAGC
Found at i:61822 original size:18 final size:18
Alignment explanation
Indices: 61799--61840 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
61789 GGTTCTACGC
*
61799 GGTCCTTCGGGATATAAT
1 GGTCCTTCGGGACATAAT
*
61817 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAAT
61835 GGTCCT
1 GGTCCT
61841 ACGAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (18 bp):
GGTCCTTCGGGACATAAT
Found at i:67434 original size:38 final size:37
Alignment explanation
Indices: 67379--67466 Score: 101
Period size: 38 Copynumber: 2.4 Consensus size: 37
67369 ATAAAAAAAA
*
67379 TTAAAAA--AAAAATTAGAATGTTA-ATATGAAATAAT
1 TTAAAAATTAAAATTTAGAATGTTAGA-ATGAAATAAT
*
67414 TTAAGAAATTAAAATTTAGAATGTTAGAGTGAAATAAT
1 TTAA-AAATTAAAATTTAGAATGTTAGAATGAAATAAT
*
67452 TTTAAAATTATAAAT
1 TTAAAAATTA-AAAT
67467 AAAAATTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
35 4 0.09
36 3 0.07
37 6 0.13
38 31 0.69
39 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (37 bp):
TTAAAAATTAAAATTTAGAATGTTAGAATGAAATAAT
Found at i:68101 original size:32 final size:32
Alignment explanation
Indices: 68051--68143 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 32
68041 CATATAATTA
* * *
68051 TTAA-TGATATGATATATATCATGTCATTACC
1 TTAAGTGATGTGATATATATCATATCATCACC
* **
68082 TTAAGTGATGTGATGTATATCATATCATCATG
1 TTAAGTGATGTGATATATATCATATCATCACC
* * *
68114 TTATGTGATGTGGTATATATCATATTATCA
1 TTAAGTGATGTGATATATATCATATCATCA
68144 ATTAAATATA
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 4 0.08
32 47 0.92
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (32 bp):
TTAAGTGATGTGATATATATCATATCATCACC
Found at i:68215 original size:59 final size:59
Alignment explanation
Indices: 68149--68262 Score: 228
Period size: 59 Copynumber: 1.9 Consensus size: 59
68139 TATCAATTAA
68149 ATATATATATATTATGCTAGTAATATACATTAACAGTTAGTTAATTAACGGTTTACATT
1 ATATATATATATTATGCTAGTAATATACATTAACAGTTAGTTAATTAACGGTTTACATT
68208 ATATATATATATTATGCTAGTAATATACATTAACAGTTAGTTAATTAACGGTTTA
1 ATATATATATATTATGCTAGTAATATACATTAACAGTTAGTTAATTAACGGTTTA
68263 TATTCAACCA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (59 bp):
ATATATATATATTATGCTAGTAATATACATTAACAGTTAGTTAATTAACGGTTTACATT
Found at i:74521 original size:21 final size:21
Alignment explanation
Indices: 74470--74521 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 21
74460 TCTTAAGGAG
* *
74470 TGGTCATTCGGGACATTTACG
1 TGGTCATTCGGGACATATACA
* * *
74491 TGATCCTTCGGGACATATATA
1 TGGTCATTCGGGACATATACA
*
74512 TGGTCGTTCG
1 TGGTCATTCG
74522 AGGCAAATTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (21 bp):
TGGTCATTCGGGACATATACA
Found at i:83477 original size:20 final size:20
Alignment explanation
Indices: 83452--83496 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
83442 ATTGAATTTG
*
83452 TTCAAAGTTTTCAAAAATAA
1 TTCAAACTTTTCAAAAATAA
83472 TTCAAACTTTTCAAAAATAA
1 TTCAAACTTTTCAAAAATAA
83492 TTCAA
1 TTCAA
83497 GCTCCATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (20 bp):
TTCAAACTTTTCAAAAATAA
Found at i:93432 original size:3 final size:3
Alignment explanation
Indices: 93424--93479 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
93414 ATTTAACACG
93424 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
93472 TTA TTA TT
1 TTA TTA TT
93480 CCGTACTAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:97900 original size:25 final size:24
Alignment explanation
Indices: 97872--97941 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 24
97862 TTAAATTCAT
* *
97872 ATATATTTATATATTAACTTTTGAA
1 ATATATTT-TATATTAACTTATAAA
*
97897 ATATTTTTTATATTAACTTATAAA
1 ATATATTTTATATTAACTTATAAA
97921 ATATATTTTATTATTAACTTA
1 ATATATTTTA-TATTAACTTA
97942 ATTTAAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 23 0.57
25 17 0.43
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.54
Consensus pattern (24 bp):
ATATATTTTATATTAACTTATAAA
Found at i:97953 original size:27 final size:25
Alignment explanation
Indices: 97872--97956 Score: 84
Period size: 25 Copynumber: 3.3 Consensus size: 25
97862 TTAAATTCAT
**
97872 ATATATTTATATATTAACTT-TTGAA
1 ATAT-TTTATATATTAACTTATAAAA
*
97897 ATATTTTTTATATTAACTTATAAAA
1 ATATTTTATATATTAACTTATAAAA
97922 TATATTTTAT-TATTAACTTAATTTAAAA
1 -ATATTTTATATATTAACTT-A--TAAAA
97950 ATATTTT
1 ATATTTT
97957 TAAATCCATT
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
24 14 0.27
25 16 0.31
26 9 0.18
27 7 0.14
28 5 0.10
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (25 bp):
ATATTTTATATATTAACTTATAAAA
Found at i:100860 original size:48 final size:49
Alignment explanation
Indices: 100777--100884 Score: 137
Period size: 48 Copynumber: 2.2 Consensus size: 49
100767 TATCAAAAGA
* * * *
100777 TTCATCTTCATCATCGTCGAGATCGTTGTCGTTAACGACGGCATCTGACCG
1 TTCATCTTCATCATCGTCGAGA--GTCGTCGTTAACAACGCCATCCGACCG
* *
100828 TTCATCTTCATCATCGTCGAG-GTCGTCGTTAACAACTCCATCCGGCCG
1 TTCATCTTCATCATCGTCGAGAGTCGTCGTTAACAACGCCATCCGACCG
100876 TTCATCTTC
1 TTCATCTTC
100885 GTCGTCACTT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
48 30 0.59
51 21 0.41
ACGTcount: A:0.19, C:0.31, G:0.19, T:0.32
Consensus pattern (49 bp):
TTCATCTTCATCATCGTCGAGAGTCGTCGTTAACAACGCCATCCGACCG
Done.