Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008205.1 Hibiscus syriacus cultivar Beakdansim tig00110827_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: 89261
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8145 original size:41 final size:41
Alignment explanation
Indices: 8085--8163 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
8075 ATAAATTGTA
* *
8085 AAATAGAAATACACATTCATTTATAGGTTGAGTTGTGAGAT
1 AAATAGAAATACACATTCATTTATAAGTTGAGTCGTGAGAT
* *
8126 AAATAGAAGTACACTTTCATTTATAAGTTGAGTCGTGA
1 AAATAGAAATACACATTCATTTATAAGTTGAGTCGTGA
8164 TCTTAGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (41 bp):
AAATAGAAATACACATTCATTTATAAGTTGAGTCGTGAGAT
Found at i:10107 original size:35 final size:34
Alignment explanation
Indices: 10022--10108 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
10012 AATATAATTT
*
10022 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
10056 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
10094 T-AATA-AACAAAATTA
1 TAAATACAACAAAATTA
10109 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:20229 original size:49 final size:48
Alignment explanation
Indices: 20156--20250 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 48
20146 GTAGGATACA
*
20156 AGGATCAATCAAGTTTTGAATTAATCATAAGGCTCAAAAAAGAAGATTG
1 AGGATCAATCAAGGTTTGAATTAATCATAAGGCTC-AAAAAGAAGATTG
* *
20205 AGGATCAATCAAGGTTTGATTTAATCATAAGTCTCAAAAAGAAGAT
1 AGGATCAATCAAGGTTTGAATTAATCATAAGGCTCAAAAAGAAGAT
20251 CGAAATTGAG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
48 11 0.26
49 32 0.74
ACGTcount: A:0.44, C:0.11, G:0.18, T:0.27
Consensus pattern (48 bp):
AGGATCAATCAAGGTTTGAATTAATCATAAGGCTCAAAAAGAAGATTG
Found at i:28568 original size:20 final size:20
Alignment explanation
Indices: 28543--28596 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
28533 CGATTTTAGA
28543 AAATCGCAATGCGAATTTGT
1 AAATCGCAATGCGAATTTGT
28563 AAATCGCAATGCGAATTTGT
1 AAATCGCAATGCGAATTTGT
*
28583 AAATCGCAACGCGA
1 AAATCGCAATGCGA
28597 TTCTGATTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (20 bp):
AAATCGCAATGCGAATTTGT
Found at i:31755 original size:18 final size:17
Alignment explanation
Indices: 31732--31765 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
31722 AGAAAAAGGC
31732 AATCAAAATCGCAATCAA
1 AATCAAAATC-CAATCAA
31750 AATCAAAATCCAATCA
1 AATCAAAATCCAATCA
31766 CAACTGGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.56, C:0.24, G:0.03, T:0.18
Consensus pattern (17 bp):
AATCAAAATCCAATCAA
Found at i:32075 original size:140 final size:140
Alignment explanation
Indices: 31822--32104 Score: 512
Period size: 140 Copynumber: 2.0 Consensus size: 140
31812 GCAAACGTTG
* *
31822 TATTATGTGTATTTTATGTGTAATCTTTTAATATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
*
31887 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
66 TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
31952 CGAATTTGAC
131 CGAATTTGAC
31962 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
1 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
* * *
32027 TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACATATTCATTTGACTATCGCAACG
66 TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
32092 CGAATTTGAC
131 CGAATTTGAC
32102 TAT
1 TAT
32105 CGCAACGCGA
Statistics
Matches: 137, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 137 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (140 bp):
TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGACATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATCTATTCAGTTGTTATCACTTATTACACATTCATTTGAATATCACAACG
CGAATTTGAC
Found at i:32100 original size:20 final size:20
Alignment explanation
Indices: 32075--32171 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
32065 TTACATATTC
32075 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
32095 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
32115 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* *
32135 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
*
32155 ATTTGACTATCTCAACG
1 ATTTGACTATCGCAACG
32172 AGAAAATCGC
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:33812 original size:21 final size:21
Alignment explanation
Indices: 33781--33886 Score: 81
Period size: 21 Copynumber: 5.0 Consensus size: 21
33771 TGAATGGTGG
*
33781 GAGGACCTCTTCAACGATGACA
1 GAGG-CCTCTTGAACGATGACA
* **
33803 GGGGCCTCTTGAACGATGGGA
1 GAGGCCTCTTGAACGATGACA
* * ** *
33824 GGGGACTCTTGAGGGATGATA
1 GAGGCCTCTTGAACGATGACA
*
33845 GAGGACTCTT-AACGAT-AGCA
1 GAGGCCTCTTGAACGATGA-CA
*
33865 GAGGCCTCTTAAACGATGACA
1 GAGGCCTCTTGAACGATGACA
33886 G
1 G
33887 TTGAGTCGGC
Statistics
Matches: 67, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.01
20 14 0.21
21 48 0.72
22 4 0.06
ACGTcount: A:0.28, C:0.20, G:0.32, T:0.20
Consensus pattern (21 bp):
GAGGCCTCTTGAACGATGACA
Found at i:34417 original size:20 final size:20
Alignment explanation
Indices: 34394--34461 Score: 84
Period size: 20 Copynumber: 3.4 Consensus size: 20
34384 GAAACTTAAA
*
34394 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
34414 ATCGTAACGC-AGAAATGACT
1 ATCGCAACGCGA-AAATGACT
**
34434 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
34454 ATCGCAAC
1 ATCGCAAC
34462 AAGATAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 1 0.02
20 39 0.95
21 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:34529 original size:19 final size:19
Alignment explanation
Indices: 34467--34520 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
34457 GCAACAAGAT
* **
34467 AATCGCAATGCGAAATAAA
1 AATCGCAACGCGAAACCAA
34486 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
*
34505 AATCGCAACGTGAAAC
1 AATCGCAACGCGAAAC
34521 TAAATTCGCG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:34550 original size:20 final size:20
Alignment explanation
Indices: 34525--34562 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
34515 TGAAACTAAA
34525 TTCGCGTTGCAATTTTCATT
1 TTCGCGTTGCAATTTTCATT
*
34545 TTCGCGTTGCGATTTTCA
1 TTCGCGTTGCAATTTTCA
34563 CGTTGCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.47
Consensus pattern (20 bp):
TTCGCGTTGCAATTTTCATT
Found at i:34561 original size:14 final size:14
Alignment explanation
Indices: 34542--34574 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
34532 TGCAATTTTC
*
34542 ATTTTCGCGTTGCG
1 ATTTTCACGTTGCG
34556 ATTTTCACGTTGCG
1 ATTTTCACGTTGCG
34570 ATTTT
1 ATTTT
34575 ATTTCGCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.48
Consensus pattern (14 bp):
ATTTTCACGTTGCG
Found at i:34629 original size:20 final size:19
Alignment explanation
Indices: 34575--34649 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 19
34565 TTGCGATTTT
*
34575 ATTTCGCATTGCGATAGTC
1 ATTTCGCGTTGCGATAGTC
* * *
34594 AAATTCGTGTTACGATAGTC
1 -ATTTCGCGTTGCGATAGTC
34614 ATTTCCGCGTTGCGATAGTC
1 ATTT-CGCGTTGCGATAGTC
34634 ATTTTCGCGTTGCGAT
1 A-TTTCGCGTTGCGAT
34650 TTTAAGTTTC
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 3 0.07
20 40 0.87
21 3 0.07
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (19 bp):
ATTTCGCGTTGCGATAGTC
Found at i:34666 original size:40 final size:38
Alignment explanation
Indices: 34556--34668 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 38
34546 TCGCGTTGCG
* *
34556 ATTTTCACGTTGCGATTTTATTTCGCATTGCGATAGTC
1 ATTTTCGCGTTGCGATTTTATTTCGCGTTGCGATAGTC
** * * * *
34594 AAATTCGTGTTACGATAGTCATTTCCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGAT-TTTATTT-CGCGTTGCGATAGTC
*
34634 ATTTTCGCGTTGCGATTTTAAGTTTCGTGTTGCGA
1 ATTTTCGCGTTGCGATTTT-A-TTTCGCGTTGCGA
34669 CTATTCTTCT
Statistics
Matches: 56, Mismatches: 15, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
38 11 0.20
39 6 0.11
40 36 0.64
41 3 0.05
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.42
Consensus pattern (38 bp):
ATTTTCGCGTTGCGATTTTATTTCGCGTTGCGATAGTC
Found at i:36582 original size:20 final size:20
Alignment explanation
Indices: 36559--36624 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
36549 TCTGAAACTT
*
36559 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
36579 AAAACCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
*
36598 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
36617 AAAATCGC
1 AAAATCGC
36625 GTTGCAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.50, C:0.24, G:0.17, T:0.09
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:37041 original size:22 final size:22
Alignment explanation
Indices: 37014--37064 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
37004 GATGGAGATA
37014 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
37036 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
37058 GATGGAT
1 GACGGAT
37065 GTCGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.45, T:0.24
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:37296 original size:21 final size:21
Alignment explanation
Indices: 37272--37312 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
37262 ATTTACATAT
*
37272 TCGCATTGCGAATTTGGAAAA
1 TCGCATTGCGAATCTGGAAAA
*
37293 TCGCGTTGCGAATCTGGAAA
1 TCGCATTGCGAATCTGGAAA
37313 CTGATTTGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (21 bp):
TCGCATTGCGAATCTGGAAAA
Found at i:42367 original size:20 final size:20
Alignment explanation
Indices: 42309--42368 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
42299 CTCAAAAATA
42309 TAAT-ATATTAATATTTTATTT
1 TAATAATATTAATATTTTA--T
* **
42330 TAA-AA-ATAAATAAATTAT
1 TAATAATATTAATATTTTAT
42348 TAATAATATTAATATTTTAT
1 TAATAATATTAATATTTTAT
42368 T
1 T
42369 GATTTGCCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
18 4 0.13
19 2 0.07
20 20 0.67
21 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATAATATTAATATTTTAT
Found at i:43598 original size:14 final size:14
Alignment explanation
Indices: 43574--43601 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
43564 TTTTCAGAAT
43574 CTGTTTTTAATAAA
1 CTGTTTTTAATAAA
43588 CTGTTTTTAATAAA
1 CTGTTTTTAATAAA
43602 AAGCATACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.50
Consensus pattern (14 bp):
CTGTTTTTAATAAA
Found at i:47205 original size:49 final size:49
Alignment explanation
Indices: 47133--47229 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
47123 CTATACCACG
* *
47133 CTATATGCTGATATGGCGTCACGTGGGATAAGACGCG-CCCTGCACCGCA
1 CTATATGCTGACATGGCATCACGT-GGATAAGACGCGCCCCTGCACCGCA
47182 CTATATGCTGACATGG-ATACACGTGGATAAGACGCGCCCCTGCACCGC
1 CTATATGCTGACATGGCAT-CACGTGGATAAGACGCGCCCCTGCACCGC
47230 GCCTTACACC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
48 13 0.30
49 31 0.70
ACGTcount: A:0.24, C:0.30, G:0.27, T:0.20
Consensus pattern (49 bp):
CTATATGCTGACATGGCATCACGTGGATAAGACGCGCCCCTGCACCGCA
Found at i:49055 original size:9 final size:9
Alignment explanation
Indices: 49041--49074 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
49031 TAAATAAAAT
49041 ATTAAATAA
1 ATTAAATAA
49050 ATTAAAT-A
1 ATTAAATAA
*
49058 CTTAAATAA
1 ATTAAATAA
49067 ATTAAATA
1 ATTAAATA
49075 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
ATTAAATAA
Found at i:49062 original size:17 final size:17
Alignment explanation
Indices: 49030--49075 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
49020 TAAAAAAATT
*
49030 ATAAATAAAATA-TTAA
1 ATAAATTAAATACTTAA
49046 ATAAATTAAATACTTAA
1 ATAAATTAAATACTTAA
49063 ATAAATTAAATAC
1 ATAAATTAAATAC
49076 AAAATATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (17 bp):
ATAAATTAAATACTTAA
Found at i:50314 original size:29 final size:29
Alignment explanation
Indices: 50280--50338 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
50270 CCTAAATTAA
50280 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
50309 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
50338 T
1 T
50339 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:54960 original size:29 final size:29
Alignment explanation
Indices: 54926--54984 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
54916 CCTAAATTAA
54926 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
54955 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
54984 T
1 T
54985 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:63405 original size:20 final size:21
Alignment explanation
Indices: 63380--63423 Score: 81
Period size: 20 Copynumber: 2.1 Consensus size: 21
63370 GTCAAAGAAA
63380 GTCAACGGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
63400 GTCAACGGTCAACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
63421 GTC
1 GTC
63424 GGGTCGGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:63435 original size:17 final size:17
Alignment explanation
Indices: 63413--63487 Score: 141
Period size: 17 Copynumber: 4.4 Consensus size: 17
63403 AACGGTCAAC
63413 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63430 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63447 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
63464 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
63481 GGTCAAC
1 GGTCAAC
63488 CCGGTTCAGA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 57 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:63440 original size:7 final size:7
Alignment explanation
Indices: 63380--63423 Score: 81
Period size: 7 Copynumber: 6.4 Consensus size: 7
63370 GTCAAAGAAA
63380 GTCAACG
1 GTCAACG
63387 GTCAACG
1 GTCAACG
63394 GTC-ACG
1 GTCAACG
63400 GTCAACG
1 GTCAACG
63407 GTCAACG
1 GTCAACG
63414 GTCAACG
1 GTCAACG
63421 GTC
1 GTC
63424 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:63515 original size:10 final size:10
Alignment explanation
Indices: 63483--63532 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
63473 TCGGGTCGGG
*
63483 TCAACCCGGT
1 TCAAACCGGT
*
63493 TCAGACCGG-
1 TCAAACCGGT
63502 TCAAACCGGT
1 TCAAACCGGT
*
63512 TCAAAACTGG-
1 TC-AAACCGGT
63522 TCAAACCGGT
1 TCAAACCGGT
63532 T
1 T
63533 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:63523 original size:20 final size:19
Alignment explanation
Indices: 63481--63532 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
63471 AGTCGGGTCG
* *
63481 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
63500 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
63520 GGTCAAACCGGTT
1 GGTCAAACCGGTT
63533 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:69775 original size:32 final size:31
Alignment explanation
Indices: 69732--69813 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
69722 ATAGATTTCG
* *
69732 GGGCCGTAGGGCCTACCTAAGAACACATCTTA
1 GGGCCGCAGGGCCTACCTAAGAA-ACATCTCA
** **
69764 GGGCCGCAGGGCCTACCCGAGAATGATCTCA
1 GGGCCGCAGGGCCTACCTAAGAAACATCTCA
*
69795 GGGCCGCAGAGCCTACCTA
1 GGGCCGCAGGGCCTACCTA
69814 TGAGTCACAT
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 21 0.51
32 20 0.49
ACGTcount: A:0.24, C:0.32, G:0.29, T:0.15
Consensus pattern (31 bp):
GGGCCGCAGGGCCTACCTAAGAAACATCTCA
Found at i:70703 original size:13 final size:13
Alignment explanation
Indices: 70685--70747 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
70675 AAGAAAGTCA
70685 ACGGTCAACGGTC
1 ACGGTCAACGGTC
70698 ACGGTCAACGGTC
1 ACGGTCAACGGTC
*
70711 ACGGTCAACAGTC
1 ACGGTCAACGGTC
70724 AACGGTC-A-GGTC
1 -ACGGTCAACGGTC
*
70736 -GGGTCAACGGTC
1 ACGGTCAACGGTC
70748 GGGTCGGGTC
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
10 4 0.09
11 1 0.02
12 7 0.16
13 26 0.59
14 6 0.14
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.16
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:70706 original size:20 final size:19
Alignment explanation
Indices: 70681--70747 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
70671 GTCAAAGAAA
70681 GTCAACGGTCAACGGTCACG
1 GTCAACGGTC-ACGGTCACG
*
70701 GTCAACGGTCACGGTCAACA
1 GTCAACGGTCACGGTC-ACG
*
70721 GTCAACGGTCA-GGTC-GG
1 GTCAACGGTCACGGTCACG
70738 GTCAACGGTC
1 GTCAACGGTC
70748 GGGTCGGGTC
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
17 10 0.23
19 10 0.23
20 23 0.53
ACGTcount: A:0.24, C:0.28, G:0.31, T:0.16
Consensus pattern (19 bp):
GTCAACGGTCACGGTCACG
Found at i:70743 original size:17 final size:17
Alignment explanation
Indices: 70721--70794 Score: 121
Period size: 17 Copynumber: 4.4 Consensus size: 17
70711 ACGGTCAACA
* *
70721 GTCAACGGTCAGGTCGG
1 GTCAACAGTCGGGTCGG
*
70738 GTCAACGGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
70755 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
70772 GTCAACAGTCGGGTCGG
1 GTCAACAGTCGGGTCGG
70789 GTCAAC
1 GTCAAC
70795 CCAGTTCAGA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 55 1.00
ACGTcount: A:0.18, C:0.24, G:0.41, T:0.18
Consensus pattern (17 bp):
GTCAACAGTCGGGTCGG
Found at i:70747 original size:7 final size:7
Alignment explanation
Indices: 70681--70731 Score: 79
Period size: 7 Copynumber: 7.6 Consensus size: 7
70671 GTCAAAGAAA
70681 GTCAACG
1 GTCAACG
70688 GTCAACG
1 GTCAACG
70695 GTC-ACG
1 GTCAACG
70701 GTCAACG
1 GTCAACG
70708 GTC-ACG
1 GTCAACG
*
70714 GTCAACA
1 GTCAACG
70721 GTCAACG
1 GTCAACG
70728 GTCA
1 GTCA
70732 GGTCGGGTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 12 0.30
7 28 0.70
ACGTcount: A:0.27, C:0.29, G:0.27, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:70834 original size:20 final size:20
Alignment explanation
Indices: 70811--70848 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
70801 CAGACCGGTC
70811 AAACCGGTCAAACCGGTTCA
1 AAACCGGTCAAACCGGTTCA
*
70831 AAACTGGTCAAACCGGTT
1 AAACCGGTCAAACCGGTT
70849 TTCCAGCAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (20 bp):
AAACCGGTCAAACCGGTTCA
Found at i:70841 original size:10 final size:9
Alignment explanation
Indices: 70804--70847 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
70794 CCCAGTTCAG
70804 ACCGGTCAA
1 ACCGGTCAA
70813 ACCGGTCAA
1 ACCGGTCAA
70822 ACCGGTTCAAA
1 ACCGG-TC-AA
*
70833 ACTGGTCAA
1 ACCGGTCAA
70842 ACCGGT
1 ACCGGT
70848 TTTCCAGCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 21 0.68
10 4 0.13
11 6 0.19
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:74516 original size:23 final size:23
Alignment explanation
Indices: 74471--74523 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
74461 ACTCTTCCTC
* *
74471 TTTTTCTCGGTTTTTCTCCTTTT
1 TTTTTCTAGGTTTTTATCCTTTT
*
74494 TTTTTCTAGGTTTTTAT-GTTTT
1 TTTTTCTAGGTTTTTATCCTTTT
74516 TTTCTTCT
1 TTT-TTCT
74524 TCTTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.04, C:0.15, G:0.09, T:0.72
Consensus pattern (23 bp):
TTTTTCTAGGTTTTTATCCTTTT
Found at i:75558 original size:28 final size:27
Alignment explanation
Indices: 75526--75585 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 27
75516 TAAAAAATTT
**
75526 AAATAATTTAGGTATCTACTTTAACATA
1 AAATAATTTAAATATCTACTTTAAC-TA
* *
75554 AAATATTTTAAATATCTATTTTAACTA
1 AAATAATTTAAATATCTACTTTAACTA
75581 AAATA
1 AAATA
75586 TAATTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (27 bp):
AAATAATTTAAATATCTACTTTAACTA
Found at i:76178 original size:59 final size:60
Alignment explanation
Indices: 76109--76240 Score: 187
Period size: 59 Copynumber: 2.2 Consensus size: 60
76099 CTAACTAAAC
*
76109 TCTAAATTAGTCCTCAAACTTTTGAACATTCTATTTTCATCC-CTAACTATGACTC-TCAT
1 TCTAAATTAGTCCTCAAACTTTTGAACATTCTACTTTCATCCTCTAACTATGAC-CATCAT
* ** *
76168 TCTAAGTTAGTCCTCAAACTTTTGAATGTTCTACTTTCATCCTCTAGCTATGACCATCAT
1 TCTAAATTAGTCCTCAAACTTTTGAACATTCTACTTTCATCCTCTAACTATGACCATCAT
*
76228 TCTAAATTGGTCC
1 TCTAAATTAGTCC
76241 CAATTTTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
59 39 0.61
60 25 0.39
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (60 bp):
TCTAAATTAGTCCTCAAACTTTTGAACATTCTACTTTCATCCTCTAACTATGACCATCAT
Found at i:78532 original size:13 final size:12
Alignment explanation
Indices: 78496--78533 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
78486 ATATACATAT
78496 AATAATAAAATA
1 AATAATAAAATA
78508 AATAATAAAAATA
1 AATAAT-AAAATA
78521 AATGAATAAAATA
1 AAT-AATAAAATA
78534 TCCATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 15 0.62
14 3 0.12
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (12 bp):
AATAATAAAATA
Found at i:79971 original size:207 final size:208
Alignment explanation
Indices: 79666--80227 Score: 805
Period size: 207 Copynumber: 2.7 Consensus size: 208
79656 CAAGTAAGTA
* * ** * *
79666 GCATTGT-TCAGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCT-GAAT-GAAATT-TT
1 GCATTGTCT-AGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGAAGTTGTT
*
79727 GTTGACAAGCAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
65 GTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTC
* * *
79792 GTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAAGCAGCGGT-CCTTCGTC
130 GTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTGTTGAAAAGCAGCGGTCCCTTCGTC
79856 GTGAAGTTGAACTT
195 GTGAAGTTGAACTT
*
79870 GCATTGTCTGGAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGT
1 GCATTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATT-GGAAGTTGT
* * *
79934 TGTTGACAA-CAGTGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGAAGTCCAATATCCTT
64 TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTT
*
79998 CGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGAAAAGCAGCGGTCCCTTCGT
129 CGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTGTTGAAAAGCAGCGGTCCCTTCGT
80063 CGTGAAGTTGAACTT
194 CGTGAAGTTGAACTT
* * *
80078 GCGTTGTCTAAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGT
1 GCATTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTG-GAAGTTGT
*
80143 TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTCGAGTGCCACGATATC
64 TGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CCA--ATATC
* * *
80208 CTCCGTCGTGGAGTTGAAAT
126 CTTCGTTGTGAAGTTGAAAT
80228 CGCGGATGGC
Statistics
Matches: 318, Mismatches: 27, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
203 28 0.09
204 13 0.04
205 4 0.01
207 109 0.34
208 46 0.14
209 53 0.17
210 40 0.13
211 3 0.01
213 22 0.07
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (208 bp):
GCATTGTCTAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGAAGTTGTTG
TTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCG
TTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTGTTGAAAAGCAGCGGTCCCTTCGTCG
TGAAGTTGAACTT
Found at i:80101 original size:105 final size:105
Alignment explanation
Indices: 79676--80227 Score: 823
Period size: 105 Copynumber: 5.3 Consensus size: 105
79666 GCATTGTTCA
* * **
79676 GAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGAATCTG-AA-TGA-AA-TT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
79736 CAGCGGTCCCTTCTTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
79776 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
79841 CAGCGGT-CCTTCGTCGTGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
79880 GAGTCC-ATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGCGATTGGGAAGTTGTTGTTGACAA-
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
* *
79943 CAGTGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
79983 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGAAAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
80048 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
80088 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
*
80153 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
80193 GAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 GAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
80228 CGCGGATGGC
Statistics
Matches: 413, Mismatches: 28, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
100 35 0.08
101 1 0.00
102 7 0.02
103 93 0.23
104 91 0.22
105 161 0.39
106 3 0.01
108 22 0.05
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.33
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:80947 original size:63 final size:61
Alignment explanation
Indices: 80829--80982 Score: 164
Period size: 63 Copynumber: 2.4 Consensus size: 61
80819 AATATATATG
* * * **
80829 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGG--A-GAAA--ATGTTTTAAGGGAAATAAATTCAAAGA-
80894 TT
60 TT
* * *
80896 TGTGTTTCAAGAGTAATTGTCTCAAGGGAGAAAATGTTTTAGGGGAAATAAATTCAAAGATT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAATGTTTTAAGGGAAATAAATTCAAAGATT
*
80958 TTGTTTCAAGGGAAACTGTCTCAAG
1 TTGTTTCAAGAGAAACTGTCTCAAG
80983 ATAGACGAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
61 21 0.28
62 3 0.04
63 24 0.32
65 3 0.04
66 1 0.01
67 1 0.01
68 22 0.29
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.32
Consensus pattern (61 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGAAAATGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:81216 original size:36 final size:37
Alignment explanation
Indices: 81084--81216 Score: 196
Period size: 37 Copynumber: 3.6 Consensus size: 37
81074 AAAACATATT
* * *
81084 CAAATATTTTGTTTCAAGGGAAATTGTCTTAAGAGAGA
1 CAAA-ATTTTATTTCAAGGGAAACTGTCTCAAGAGAGA
81122 CAAAATTTTATTTCAAGGGAAACTGTCTCAAGAGAGA
1 CAAAATTTTATTTCAAGGGAAACTGTCTCAAGAGAGA
* *
81159 CAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGA
1 CAAAATTTTATTTCAAGGGAAACTGTCTCAAGAGAGA
*
81196 CGAAA-TTTATTTCAAGGGAAA
1 CAAAATTTTATTTCAAGGGAAA
81217 TGTTTTCAAT
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
36 15 0.17
37 69 0.78
38 4 0.05
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (37 bp):
CAAAATTTTATTTCAAGGGAAACTGTCTCAAGAGAGA
Found at i:81663 original size:18 final size:18
Alignment explanation
Indices: 81636--81671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
81626 TGTTGAATCC
* *
81636 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
81654 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
81672 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:82088 original size:22 final size:22
Alignment explanation
Indices: 82063--82117 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
82053 TATTGTGTGG
82063 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
82085 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
82107 TCAAATGTTTG
1 TCAAAGGTTTG
82118 ATGGGATAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:82745 original size:13 final size:12
Alignment explanation
Indices: 82728--82780 Score: 61
Period size: 13 Copynumber: 4.2 Consensus size: 12
82718 TTTTTGTCCC
82728 TTTTTCTTTTTT
1 TTTTTCTTTTTT
* *
82740 CTTTTTGTTCTTT
1 -TTTTTCTTTTTT
*
82753 TTTTGCTTTTTT
1 TTTTTCTTTTTT
82765 TTTTTGCTTTTTT
1 TTTTT-CTTTTTT
82778 TTT
1 TTT
82781 CTTTTGCCCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
12 13 0.39
13 20 0.61
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:82747 original size:23 final size:25
Alignment explanation
Indices: 82717--82770 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
82707 TTTGCATGTG
82717 CTTTTTG-TCCCTTTTT-CTTTTTT
1 CTTTTTGTTCCCTTTTTGCTTTTTT
**
82740 CTTTTTGTTCTTTTTTTGCTTTTTT
1 CTTTTTGTTCCCTTTTTGCTTTTTT
82765 -TTTTTG
1 CTTTTTG
82771 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 7 0.26
24 13 0.48
25 7 0.26
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (25 bp):
CTTTTTGTTCCCTTTTTGCTTTTTT
Found at i:82750 original size:9 final size:8
Alignment explanation
Indices: 82728--82785 Score: 59
Period size: 8 Copynumber: 7.2 Consensus size: 8
82718 TTTTTGTCCC
82728 TTTTTC-T
1 TTTTTCTT
82735 TTTTTCTT
1 TTTTTCTT
82743 TTTGTTCTT
1 TTT-TTCTT
82752 TTTTTGCTT
1 TTTTT-CTT
82761 TTTTT-TT
1 TTTTTCTT
*
82768 TTGCTT-TT
1 TT-TTTCTT
82776 TTTTTCTT
1 TTTTTCTT
82784 TT
1 TT
82786 GCCCTTTTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
7 12 0.27
8 16 0.36
9 16 0.36
ACGTcount: A:0.00, C:0.10, G:0.05, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:82757 original size:11 final size:10
Alignment explanation
Indices: 82734--82785 Score: 54
Period size: 11 Copynumber: 5.1 Consensus size: 10
82724 TCCCTTTTTC
82734 TTTTTTC-TT
1 TTTTTTCTTT
*
82743 TTTGTTCTTT
1 TTTTTTCTTT
82753 TTTTGCTT-TTT
1 TTTT--TTCTTT
82764 TTTTTTGCTTT
1 TTTTTT-CTTT
82775 TTTTTTCTTT
1 TTTTTTCTTT
82785 T
1 T
82786 GCCCTTTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
9 8 0.22
10 10 0.28
11 16 0.44
12 2 0.06
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.85
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:82793 original size:16 final size:16
Alignment explanation
Indices: 82758--82799 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
82748 TCTTTTTTTG
*
82758 CTTTTTTT-TTTTGCT
1 CTTTTTTTCTTTTGCC
*
82773 TTTTTTTTCTTTTGCC
1 CTTTTTTTCTTTTGCC
82789 CTTTTTATTCT
1 CTTTTT-TTCT
82800 GATTAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (16 bp):
CTTTTTTTCTTTTGCC
Found at i:82793 original size:31 final size:33
Alignment explanation
Indices: 82719--82794 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 33
82709 TGCATGTGCT
*
82719 TTTTGTCCCTTTTTCTTTTTTCTTTTTGTTCTTT
1 TTTTG-CCCTTTTTCTTTTTTCTTTTTGTTCTTC
82753 TTTTG--CTTTTT-TTTTTTGCTTTTT-TT-TTC
1 TTTTGCCCTTTTTCTTTTTT-CTTTTTGTTCTTC
82782 TTTTGCCCTTTTT
1 TTTTGCCCTTTTT
82795 ATTCTGATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
29 7 0.18
30 8 0.21
31 18 0.47
34 5 0.13
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.78
Consensus pattern (33 bp):
TTTTGCCCTTTTTCTTTTTTCTTTTTGTTCTTC
Found at i:82794 original size:18 final size:15
Alignment explanation
Indices: 82728--82787 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
82718 TTTTTGTCCC
*
82728 TTTTTCTTTTTT-CTT
1 TTTTTTTTTTTTGC-T
82743 TTTGTTCTTTTTTTGC-
1 TTT-TT-TTTTTTTGCT
82759 -TTTTTTTTTTTGCT
1 TTTTTTTTTTTTGCT
82773 TTTTTTTTCTTTTGC
1 TTTTTTTT-TTTTGC
82788 CCTTTTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.24
14 2 0.05
15 12 0.32
16 8 0.21
17 6 0.16
18 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTTGCT
Found at i:83966 original size:8 final size:8
Alignment explanation
Indices: 83950--83988 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
83940 ATTGTAGATG
83950 AAAATGCA
1 AAAATGCA
*
83958 AAAAGGCA
1 AAAATGCA
83966 AAAATGC-
1 AAAATGCA
83973 AAAATGCA
1 AAAATGCA
*
83981 AGAATGCA
1 AAAATGCA
83989 TGAAATGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (8 bp):
AAAATGCA
Found at i:83976 original size:15 final size:15
Alignment explanation
Indices: 83950--83988 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
83940 ATTGTAGATG
83950 AAAATGCAAAAAGGCA
1 AAAATGC-AAAAGGCA
*
83966 AAAATGCAAAATGCA
1 AAAATGCAAAAGGCA
*
83981 AGAATGCA
1 AAAATGCA
83989 TGAAATGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAAATGCAAAAGGCA
Found at i:85367 original size:5 final size:5
Alignment explanation
Indices: 85357--85385 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
85347 GCAAGTGATG
85357 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
85386 GAAAGATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:86512 original size:13 final size:13
Alignment explanation
Indices: 86490--86522 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
86480 GGGAAAAGGG
86490 AAAA-AAATAAAT
1 AAAATAAATAAAT
86502 AAAATAAATAAAT
1 AAAATAAATAAAT
*
86515 AAGATAAA
1 AAAATAAA
86523 GGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:87020 original size:18 final size:17
Alignment explanation
Indices: 86999--87041 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
86989 ATATATACAT
86999 ATAATAATAATAACATAA
1 ATAATAATAATAA-ATAA
* *
87017 ATAATAAAAATAAATGA
1 ATAATAATAATAAATAA
87034 ATAA-AATA
1 ATAATAATA
87042 TCCATATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 3 0.14
17 7 0.32
18 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATAA
Found at i:87038 original size:14 final size:13
Alignment explanation
Indices: 87001--87039 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
86991 ATATACATAT
87001 AATAATAATAACATA
1 AATAATAA-AA-ATA
87016 AATAATAAAAATA
1 AATAATAAAAATA
87029 AATGAATAAAA
1 AAT-AATAAAA
87040 TATCCATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (13 bp):
AATAATAAAAATA
Found at i:88188 original size:2 final size:2
Alignment explanation
Indices: 88181--88222 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
88171 CACATATGAA
88181 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
88223 TGTATTTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.