Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000247.1 Hibiscus syriacus cultivar Beakdansim tig00000440_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: 65210
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3698 original size:179 final size:176
Alignment explanation
Indices: 3353--3818 Score: 548
Period size: 179 Copynumber: 2.6 Consensus size: 176
3343 GATCCAAATT
* * * * **
3353 AAAAATGTATCGATCCACAAAGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGA-ATAACAGGTAAAAATATGATAAAA-CAGTATCAAAATGATA
* * * *
3418 AAACCGGTTAAAGCAGTACCGAATATATTTAAAGTGTCGGTAC-TTTATAAGGATCGACACTCGT
64 AAACCGGTAAAAGC--TACCGGATATATTAAAAGTGTCGATACTTTTATAAGGATCGACACTCGT
* *
3482 TAATTTAAAAGAGAAGCAGTTTTTTAGCGCCTATAAAGTGTCGATACTTTCA
127 GAATTTAAAAGAGAAGCAG-TTTTTAACGCCTATAAAGTGTCGATACTTT-A
* * *
3534 AAAAATATATCGATCAACAACG-ATAACAGGTAAAAATATGATAAAACTGCTATCAAAATGATGA
1 AAAAATGTATCGATCAACAACGAATAACAGGTAAAAATATGATAAAACAG-TATCAAAATGATAA
* * * *
3598 AACCGATAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTTATATAAGGATCGACACTTTGT
65 AACCGGTAAAA-GCTACCGGATATATTAAAAGTGTCGATACTTT-TATAAGGATCGACAC-TCGT
*
3663 GAATTTAAAAGAGAAGCAG-TTTTAATGCCTATAAAGTGTCGATACTTTA
127 GAATTTAAAAGAGAAGCAGTTTTTAACGCCTATAAAGTGTCGATACTTTA
* * *
3712 AAAAATGTATTGATCAAACAACGATATAACAGGTAAAAATAT-A-AAACCGGTATCAAAATGATA
1 AAAAATGTATCGATC-AACAACGA-ATAACAGGTAAAAATATGATAAAACAGTATCAAAATGATA
* *
3775 AAACCGGTAAAATGATACTGGATATA-TAAAAGTGTCGATACTTT
64 AAACCGGTAAAA-GCTACCGGATATATTAAAAGTGTCGATACTTT
3819 CGTAAGTACG
Statistics
Matches: 247, Mismatches: 30, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
177 16 0.06
178 73 0.30
179 83 0.34
180 18 0.07
181 57 0.23
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (176 bp):
AAAAATGTATCGATCAACAACGAATAACAGGTAAAAATATGATAAAACAGTATCAAAATGATAAA
ACCGGTAAAAGCTACCGGATATATTAAAAGTGTCGATACTTTTATAAGGATCGACACTCGTGAAT
TTAAAAGAGAAGCAGTTTTTAACGCCTATAAAGTGTCGATACTTTA
Found at i:3768 original size:178 final size:178
Alignment explanation
Indices: 3353--3818 Score: 570
Period size: 178 Copynumber: 2.6 Consensus size: 178
3343 GATCCAAATT
* * * * **
3353 AAAAATGTATCGATCCACAAAGATATAACAGGTAAAACTATGACAAAACCAGTATTGAAATGATA
1 AAAAATGTATCGATCAACAACGATATAACAGGTAAAA-TATGATAAAACCGGTATCAAAATGATA
* * * *
3418 AAACCGGTTAAAGCAGTACCGAATATATTTAAAGTGTCGGTAC-TTTATAAGGATCGACACTCGT
65 AAACCGGTAAAAGC--TACCGGATATATTAAAAGTGTCGATACTTTTATAAGGATCGACACTCGT
* *
3482 TAATTTAAAAGAGAAGCAGTTTTTTAGCGCCTATAAAGTGTCGATACTTTCA
128 GAATTTAAAAGAGAAGCAG-TTTTTAACGCCTATAAAGTGTCGATACTTTCA
* * * *
3534 AAAAATATATCGATCAACAACG--ATAACAGGTAAAAATATGATAAAACTGCTATCAAAATGATG
1 AAAAATGTATCGATCAACAACGATATAACAGGT-AAAATATGATAAAACCGGTATCAAAATGATA
* * * *
3597 AAACCGATAAAACGCTACCGGATATATTGAAAGTGTCGAAACTTTATATAAGGATCGACACTTTG
65 AAACCGGTAAAA-GCTACCGGATATATTAAAAGTGTCGATACTTT-TATAAGGATCGACAC-TCG
*
3662 TGAATTTAAAAGAGAAGCAG-TTTTAATGCCTATAAAGTGTCGATACTTT-A
127 TGAATTTAAAAGAGAAGCAGTTTTTAACGCCTATAAAGTGTCGATACTTTCA
*
3712 AAAAATGTATTGATCAAACAACGATATAACAGGTAAAA-AT-ATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATC-AACAACGATATAACAGGTAAAATATGATAAAACCGGTATCAAAATGATA
* *
3775 AAACCGGTAAAATGATACTGGATATA-TAAAAGTGTCGATACTTT
65 AAACCGGTAAAA-GCTACCGGATATATTAAAAGTGTCGATACTTT
3819 CGTAAGTACG
Statistics
Matches: 246, Mismatches: 31, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
177 16 0.07
178 79 0.32
179 77 0.31
180 25 0.10
181 49 0.20
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (178 bp):
AAAAATGTATCGATCAACAACGATATAACAGGTAAAATATGATAAAACCGGTATCAAAATGATAA
AACCGGTAAAAGCTACCGGATATATTAAAAGTGTCGATACTTTTATAAGGATCGACACTCGTGAA
TTTAAAAGAGAAGCAGTTTTTAACGCCTATAAAGTGTCGATACTTTCA
Found at i:3788 original size:17 final size:19
Alignment explanation
Indices: 3747--3791 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
3737 ATAACAGGTA
3747 AAAAT-ATAAAACCGGTATC
1 AAAATGATAAAACCGG-ATC
3766 AAAATGATAAAACCGG-T-
1 AAAATGATAAAACCGGATC
3783 AAAATGATA
1 AAAATGATA
3792 CTGGATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 1 0.04
19 5 0.20
20 10 0.40
ACGTcount: A:0.56, C:0.11, G:0.13, T:0.20
Consensus pattern (19 bp):
AAAATGATAAAACCGGATC
Found at i:5582 original size:19 final size:22
Alignment explanation
Indices: 5534--5588 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
5524 CTTTTTGTGT
5534 TTTTATATAAAATGATAGTATAA
1 TTTTATATAAAA-GATAGTATAA
5557 TTATTATATAAAA-ATA-TA-AA
1 TT-TTATATAAAAGATAGTATAA
5577 TTTTATTATAAA
1 TTTTA-TATAAA
5589 TGCAGGTTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 3 0.10
20 10 0.33
21 2 0.07
22 3 0.10
23 2 0.07
24 10 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (22 bp):
TTTTATATAAAAGATAGTATAA
Found at i:5890 original size:15 final size:15
Alignment explanation
Indices: 5870--5902 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5860 TGGTTGTATT
*
5870 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
5885 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
5900 GGG
1 GGG
5903 AAAATAGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.09, G:0.64, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:6011 original size:21 final size:21
Alignment explanation
Indices: 5985--6025 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5975 AAGACAATCA
5985 AGAGTCAAAGAGAAACTTGAT
1 AGAGTCAAAGAGAAACTTGAT
* * *
6006 AGAGTCGAAGATACACTTGA
1 AGAGTCAAAGAGAAACTTGA
6026 AAAGGCATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.12, G:0.24, T:0.20
Consensus pattern (21 bp):
AGAGTCAAAGAGAAACTTGAT
Found at i:9590 original size:182 final size:182
Alignment explanation
Indices: 8992--10686 Score: 2921
Period size: 182 Copynumber: 9.4 Consensus size: 182
8982 TTTTACCTTT
* *
8992 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
9057 AACAATATAACAGGCAAAAATATGATAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
9122 TGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
9174 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
9238 AACAATATAACATGTAAAAATATGAC-AAACCGGTCTCGAAATGAC-AAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
9301 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
9351 -TTAATAAGAGAAGAAGTTATAGCACCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * *
9415 TAACAATATAACATGTAAAAATATGACAAAACCGGTCACGAAATCACAAAACAGGTAAAGCGCTA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
9480 CCGGTTATGTTGAAAGTATCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
9533 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
9598 AACAATATAATAGGTAAAAATATGACAAAACCGGTCTTGAAATGACAAAACATGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
9663 CGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAACGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
9715 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGACCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
9780 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
9845 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
9897 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
9961 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
10026 CGGTTATGTTGAAAATATCGATAA-TT-TTATAAGTATCG--ACTTTT-GAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
10073 ATTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
10138 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
10203 CTGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
130 CCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
10256 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
10321 AACAATATAACAGGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
10386 CGGTTATTTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
*
10438 TTTAAAAGAGAAGAAGTTATAGCACCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
10503 AACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACAAAGCAGGTAAAGTGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
10568 CGGATATGTTGAAAGTGTAGATAATTTATTATAAGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* *
10620 -TTAATAAGATAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATTGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
10684 TAA
65 TAA
10687 GTAAAAATAT
Statistics
Matches: 1437, Mismatches: 61, Indels: 30
0.94 0.04 0.02
Matches are distributed among these distances:
176 11 0.01
177 32 0.02
178 210 0.15
179 86 0.06
180 90 0.06
181 211 0.15
182 786 0.55
183 11 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (182 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:10070 original size:541 final size:546
Alignment explanation
Indices: 8992--10686 Score: 2950
Period size: 541 Copynumber: 3.1 Consensus size: 546
8982 TTTTACCTTT
* *
8992 TTTAA-AAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* *
9056 TAACAATATAACAGGCAAAAATATGATAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
66 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
9121 CTGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAA
131 CTGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
9186 G-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
196 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
*
9250 TGTAAAAATATGAC-AAACCGGTCTCGAAATGAC-AAACAGGTAAAGCGCTACCGGTTATGTTGA
261 GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
9313 AAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA-TTAATAAGAGAAGAAGTTATAGCA
326 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAA-AAGAGAAGAAGTTATAGCA
*
9375 CCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATG
390 CCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATG
* *
9440 ACAAAACCGGTCACGAAATCACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAA
455 ACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAA
9505 TTTATTATAAGTATCGACACTTTTGGAA
520 TTTATTATAAGTATCGA-ACTTTTGGAA
*
9533 TTTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATATTTTATAAAAATGTATCGATCCA
1 TTTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
* * *
9597 TAACAATATAATAGGTAAAAATATGACAAAACCGGTCTTGAAATGACAAAACATGTAAAGCGCTA
66 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
* * *
9662 CCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAACGACACTTTTGGAATTTAAAAGAGAA
131 CTGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
*
9727 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGACCCATAACAATATAACA
196 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
9792 GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
261 GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
* *
9857 AAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG-AGTTATAGCGC
326 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCAC
9921 CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
391 CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
* *
9986 CAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTACCGGTTATGTTGAAAATATCGATAA-
456 CAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAAT
10050 TT-TTATAAGTATCG-ACTTTT-GAA
521 TTATTATAAGTATCGAACTTTTGGAA
* *
10073 ATTAATAAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
10138 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
66 TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
10203 CTGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
131 CTGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
10268 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
196 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
* *
10333 GGTAATAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATTTTGA
261 GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
10398 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCAC
326 AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCAC
*
10463 CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGA
391 CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
* * * * * *
10528 CAAAACCGATCTCGAAATGACAAAGCAGGTAAAGTGCTACCGGATATGTTGAAAGTGTAGATAAT
456 CAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAAT
10593 TTATTATAAGTATCGACACTTTTGGAA
521 TTATTATAAGTATCGA-ACTTTTGGAA
* *
10620 -TTAATAAGATAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATTGATCCA
1 TTTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
10684 TAA
66 TAA
10687 GTAAAAATAT
Statistics
Matches: 1093, Mismatches: 48, Indels: 21
0.94 0.04 0.02
Matches are distributed among these distances:
540 7 0.01
541 548 0.50
542 205 0.19
543 33 0.03
544 71 0.06
545 134 0.12
546 88 0.08
547 7 0.01
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (546 bp):
TTTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
TAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
CTGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAA
GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACA
GGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGA
AAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCAC
CAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGA
CAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAAT
TTATTATAAGTATCGAACTTTTGGAA
Found at i:10380 original size:723 final size:723
Alignment explanation
Indices: 8992--10686 Score: 3045
Period size: 723 Copynumber: 2.3 Consensus size: 723
8982 TTTTACCTTT
* *
8992 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
9057 AACAATATAACAGGCAAAAATATGATAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
9122 TGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
9187 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
196 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
*
9252 TAAAAATATGACAAACCGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGT
261 TAAAAATATGACAAACCGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGTTGAAAAT
* *
9317 GTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAGAAGTTATAGCACCAATAA
326 ATCGATAATTTATTATAAGTATCGACTTTTGAAATTAATAAGAGAAGAAGTTATAGCACCAATAA
9382 CGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAC
391 CGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAC
9447 CGGTCACGAAATCACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAATTTATTA
456 CGGTCACGAAATCACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAATTTATTA
*
9512 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATATTT
521 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTT
* *
9577 TATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTCTTGAAATG
586 TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATG
*
9642 ACAAAACATGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAACGACAC
651 ACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAACGACAC
9707 TTTTGGAA
716 TTTTGGAA
*
9715 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGACCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
9780 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
9845 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
9910 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
196 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
*
9975 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACATGTAAAGCGCTACCGGTTATGTTGAAA
261 TAAAAATATGAC-AAACCGGTCTCGAAATGAC-AAACAGGTAAAGCGCTACCGGTTATGTTGAAA
*
10040 ATATCGATAA-TT-TTATAAGTATCGACTTTTGAAATTAATAAGAGAAGAAGTTATAGCGCCAAT
324 ATATCGATAATTTATTATAAGTATCGACTTTTGAAATTAATAAGAGAAGAAGTTATAGCACCAAT
10103 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
389 AACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAA
* * * *
10168 ACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACTGGTTATGTTGAAAGTGTCGATAATTTAT
454 ACCGGTCACGAAATCACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAATTTAT
10233 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAC
519 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATAC
*
10298 TTTATAAAAATGTATCGATCCATAACAATATAACAGGTAATAATATGACAAAACCGGTCTCGAAA
584 TTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAA
* * *
10363 TGACAAAACAGGTAAAGCGCTACCGGTTATTTTGAAAGTGTCGATAATTTATTATAAGTATCGAC
649 TGACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAACGAC
10428 ACTTTTGGAA
714 ACTTTTGGAA
*
10438 TTTAAAAGAGAAGAAGTTATAGCACCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
10503 AACAATATAACAGGTAAAAATATGACAAAACCGATCTCGAAATGACAAAGCAGGTAAAGTGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* * * *
10568 CGGATATGTTGAAAGTGTAGATAATTTATTATAAGTATCGACACTTTTGGAA-TTAATAAGATAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAA-AAGAGAA
*
10632 GAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATTGATCCATAA
195 G-AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAA
10687 GTAAAAATAT
Statistics
Matches: 935, Mismatches: 33, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
722 4 0.00
723 819 0.88
724 73 0.08
725 39 0.04
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.28
Consensus pattern (723 bp):
TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATACGTATCGACACTTTTGGAATTTAAAAGAGAAG
AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATG
TAAAAATATGACAAACCGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGTTGAAAAT
ATCGATAATTTATTATAAGTATCGACTTTTGAAATTAATAAGAGAAGAAGTTATAGCACCAATAA
CGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAAC
CGGTCACGAAATCACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTATCGATAATTTATTA
TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTT
TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATG
ACAAAACAGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATAATTTATTATAAGTAACGACAC
TTTTGGAA
Found at i:10964 original size:87 final size:87
Alignment explanation
Indices: 10859--11021 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
10849 AAATAGGTCA
*
10859 ATATAAGCGCTACCTATTACATTATATAAGCGCTATCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
10924 CCAGTTAAATACCTATTTTATT
66 CCAGTTAAATACCTATTTTATT
* * *
10946 ATATAAGCGTTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
*
11011 CCGGTTAAATA
66 CCAGTTAAATA
11022 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
CCAGTTAAATACCTATTTTATT
Found at i:10993 original size:23 final size:23
Alignment explanation
Indices: 10943--10987 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
10933 TACCTATTTT
* *
10943 ATTATATAAGCGTTATCTATTAC
1 ATTATATAAGCGTTACCTAATAC
10966 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGTTACCTAATA
10988 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATATAAGCGTTACCTAATAC
Found at i:11845 original size:33 final size:33
Alignment explanation
Indices: 11798--11868 Score: 108
Period size: 33 Copynumber: 2.2 Consensus size: 33
11788 ACAAAGTTTA
* *
11798 CGAT-AATTGAAATACTTAAATACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
11830 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
1 CGATAAATTCAAATACTTAAAAACTTCCAAGTT
*
11863 CAATAA
1 CGATAA
11869 TTGAAACGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (33 bp):
CGATAAATTCAAATACTTAAAAACTTCCAAGTT
Found at i:11890 original size:21 final size:21
Alignment explanation
Indices: 11865--11904 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11855 TCCAAGTTCA
*
11865 ATAATTGAAACGAAGTTTACG
1 ATAATTGAAACAAAGTTTACG
11886 ATAATTGAAACAAAGTTTA
1 ATAATTGAAACAAAGTTTA
11905 AAATAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
ATAATTGAAACAAAGTTTACG
Found at i:11910 original size:21 final size:21
Alignment explanation
Indices: 11864--11910 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
11854 TTCCAAGTTC
* *
11864 AATAATTGAAACGAAGTTTAC
1 AATAATTGAAACAAAGTTTAA
*
11885 GATAATTGAAACAAAGTTTAA
1 AATAATTGAAACAAAGTTTAA
11906 AATAA
1 AATAA
11911 ACTACATCGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.53, C:0.06, G:0.13, T:0.28
Consensus pattern (21 bp):
AATAATTGAAACAAAGTTTAA
Found at i:15995 original size:21 final size:21
Alignment explanation
Indices: 15969--16020 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
15959 TCTTTTCCAG
15969 AAATCAACAAGTCACCAACAT
1 AAATCAACAAGTCACCAACAT
*
15990 AAATCAACAAGTCATCAACAT
1 AAATCAACAAGTCACCAACAT
16011 AAATCAACAA
1 AAATCAACAA
16021 AACTACAATC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.56, C:0.25, G:0.04, T:0.15
Consensus pattern (21 bp):
AAATCAACAAGTCACCAACAT
Found at i:18779 original size:18 final size:18
Alignment explanation
Indices: 18756--18790 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18746 TAGCATTATC
*
18756 ATTTATATTATTATCATT
1 ATTTATATCATTATCATT
18774 ATTTATATCATTATCAT
1 ATTTATATCATTATCAT
18791 CAAATTATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTTATATCATTATCATT
Found at i:19076 original size:23 final size:23
Alignment explanation
Indices: 19050--19131 Score: 128
Period size: 23 Copynumber: 3.6 Consensus size: 23
19040 CTCGTATAAA
* *
19050 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
19073 TGCACTGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
19096 TGCACCGTAGTGCCACGTAGAAT
1 TGCACCGTAGTGCCACGTAGAAT
*
19119 TACACCGTAGTGC
1 TGCACCGTAGTGC
19132 TATATAATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.26, C:0.26, G:0.27, T:0.22
Consensus pattern (23 bp):
TGCACCGTAGTGCCACGTAGAAT
Found at i:20025 original size:24 final size:23
Alignment explanation
Indices: 19998--20055 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 23
19988 TCAATTTACT
19998 TAATTCAATTTCATATAACTCCTA
1 TAATTCAATTTCATATAACT-CTA
*
20022 TAATGT--TTTTCATATAACTCTA
1 TAAT-TCAATTTCATATAACTCTA
20044 T-ATTCAAGTTTC
1 TAATTCAA-TTTC
20056 CTAATTGATA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
20 1 0.04
21 2 0.07
22 4 0.14
23 16 0.57
24 4 0.14
25 1 0.04
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (23 bp):
TAATTCAATTTCATATAACTCTA
Found at i:40657 original size:20 final size:20
Alignment explanation
Indices: 40629--40878 Score: 219
Period size: 20 Copynumber: 12.7 Consensus size: 20
40619 AAAATCCGTA
* *
40629 AAATTGCAACGCGTATCCGT
1 AAATCGCAACGCGTATACGT
*
40649 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATACGT
*
40669 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATACGT
* *
40690 AAATCGCAACGCCTATATGT
1 AAATCGCAACGCGTATACGT
* *
40710 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGTATACGT
*
40730 AAATCG--A--C-AATACGT
1 AAATCGCAACGCGTATACGT
*
40745 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATACGT
* *
40766 AAATCGCAACGCCTATATGT
1 AAATCGCAACGCGTATACGT
* *
40786 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGTATACGT
* * *
40806 AAATCACAATGCGTATCCGT
1 AAATCGCAACGCGTATACGT
*
40826 AAATCGCAACGAC-AATACGT
1 AAATCGCAACG-CGTATACGT
* *
40846 AAA-CTGCAACACGTATCCGT
1 AAATC-GCAACGCGTATACGT
40866 AAATCGCAACGCG
1 AAATCGCAACGCG
40879 CTTTTTAAAG
Statistics
Matches: 182, Mismatches: 35, Indels: 26
0.75 0.14 0.11
Matches are distributed among these distances:
15 7 0.04
16 6 0.03
18 2 0.01
19 2 0.01
20 141 0.77
21 24 0.13
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATACGT
Found at i:40748 original size:76 final size:76
Alignment explanation
Indices: 40658--40820 Score: 310
Period size: 76 Copynumber: 2.2 Consensus size: 76
40648 TAAATCGCAA
40658 CGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCCTATATGTAAATCGCAACGAG
1 CGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCCTATATGTAAATCGCAACGAG
40723 AATACGTAAAT
66 AATACGTAAAT
40734 CGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCCTATATGTAAATCGCAACGAG
1 CGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCCTATATGTAAATCGCAACGAG
40799 AATACGTAAAT
66 AATACGTAAAT
*
40810 C-ACAATGCGTA
1 CGACAATACGTA
40821 TCCGTAAATC
Statistics
Matches: 86, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
75 9 0.10
76 77 0.90
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (76 bp):
CGACAATACGTAAAATCGCAACGCGTATCCGTAAATCGCAACGCCTATATGTAAATCGCAACGAG
AATACGTAAAT
Found at i:41462 original size:20 final size:20
Alignment explanation
Indices: 41437--41526 Score: 70
Period size: 20 Copynumber: 4.8 Consensus size: 20
41427 TTCTAAACTT
*
41437 AAAATCGCAACATGAAAATG
1 AAAATCGCAACACGAAAATG
41457 AAAATCGCAACACGAAAAT-
1 AAAATCGCAACACGAAAATG
*
41476 AACTATCGC-A-ACG---A-G
1 AA-AATCGCAACACGAAAATG
* *
41491 AGAATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
*
41510 AAAATCGCAACGCGAAA
1 AAAATCGCAACACGAAA
41527 CCAAAATCGC
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
14 5 0.09
15 3 0.05
16 2 0.04
18 4 0.07
19 17 0.30
20 25 0.45
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:41517 original size:19 final size:19
Alignment explanation
Indices: 41493--41537 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
41483 GCAACGAGAG
**
41493 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAACCAA
41512 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
41531 AATCGCA
1 AATCGCA
41538 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:41574 original size:14 final size:14
Alignment explanation
Indices: 41555--41592 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
41545 TTTCATTTCG
41555 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41569 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
41583 CGTTGCGATT
1 CGTTGCGATT
41593 TTCATTTCGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.08, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:41625 original size:20 final size:19
Alignment explanation
Indices: 41583--41659 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
41573 GCGATTCTCT
*
41583 CGTTGCGATTTTCATTTCG
1 CGTTGCGATGTTCATTTCG
41602 CGTTGCGATAGTT-ATTTCCG
1 CGTTGCGAT-GTTCATTT-CG
* *
41622 CGTTGCGATTTTCATTCTCT
1 CGTTGCGATGTTCATT-TCG
*
41642 CGTTGCGATTTTCATTTC
1 CGTTGCGATGTTCATTTC
41660 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
19 17 0.33
20 33 0.65
21 1 0.02
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (19 bp):
CGTTGCGATGTTCATTTCG
Found at i:43698 original size:21 final size:21
Alignment explanation
Indices: 43674--43740 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
43664 TCATTCCACG
43674 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
43695 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
43716 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
43737 AGAG
1 AGAG
43741 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:45104 original size:14 final size:14
Alignment explanation
Indices: 45085--45120 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
45075 ATTGTTTAAT
45085 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
45099 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
45113 TGATTTGT
1 TGATTTGT
45121 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:45257 original size:19 final size:19
Alignment explanation
Indices: 45222--45327 Score: 123
Period size: 19 Copynumber: 5.7 Consensus size: 19
45212 AAAACAGACT
*
45222 ATCGCAACGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
45242 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
45261 ATCGCACTGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
45280 ATCGCAA--CG-AGTG--A
1 ATCGCAATGCGAAATGAAA
45294 ATCGCAATGCGAAAATGAAA
1 ATCGCAATGCG-AAATGAAA
*
45314 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
45328 CTAATTTCGC
Statistics
Matches: 74, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
14 8 0.11
16 5 0.07
17 2 0.03
18 3 0.04
19 36 0.49
20 20 0.27
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:45353 original size:19 final size:19
Alignment explanation
Indices: 45331--45498 Score: 97
Period size: 19 Copynumber: 9.8 Consensus size: 19
45321 CGCGAAACTA
*
45331 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
45350 ATTTTCGCATTACGA--TTC
1 A-TTTCGCATTGCGATTTTC
* *
45368 A---CTCATTGTGATTTTC
1 ATTTCGCATTGCGATTTTC
45384 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
45401 -TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
45417 ATTTCGCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
*
45434 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
45450 ATTTCTCATTGCGA--TTC
1 ATTTCGCATTGCGATTTTC
* *
45467 -TCTCG--TTACGATTTTC
1 ATTTCGCATTGCGATTTTC
*
45483 ATTTCGCATTGTGATT
1 ATTTCGCATTGCGATT
45499 CTCTCGTTGC
Statistics
Matches: 110, Mismatches: 18, Indels: 42
0.65 0.11 0.25
Matches are distributed among these distances:
14 24 0.22
16 24 0.22
17 20 0.18
18 4 0.04
19 27 0.25
20 11 0.10
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:45399 original size:33 final size:33
Alignment explanation
Indices: 45337--45531 Score: 273
Period size: 33 Copynumber: 5.8 Consensus size: 33
45327 ACTAATTTCG
* *
45337 CGTTGCGATTTTCATTTTCGCATTACGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* *
45371 CATTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
45404 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
45437 CGTTGCGATTTTCATTTCTCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
45470 CGTTACGATTTTCATTTCGCATTGTGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
45503 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
45532 AGTCAATTCC
Statistics
Matches: 143, Mismatches: 17, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
33 122 0.85
34 21 0.15
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:45411 original size:14 final size:14
Alignment explanation
Indices: 45392--45511 Score: 51
Period size: 14 Copynumber: 7.5 Consensus size: 14
45382 TCATTTCGCA
45392 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
45406 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
45423 CATTGCGATTCACTCG
1 --TTGCGATTCTCTCG
*
45439 TTGCGATTTTCATTTCTCA
1 TTGCGA--TTC---TCTCG
45458 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
* *
45472 TTACGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
45489 CATTGTGATTCTCTCG
1 --TTGCGATTCTCTCG
45505 TTGCGAT
1 TTGCGAT
45512 AGTCATTTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 30
0.65 0.10 0.25
Matches are distributed among these distances:
14 27 0.34
16 16 0.20
17 17 0.22
19 19 0.24
ACGTcount: A:0.13, C:0.23, G:0.17, T:0.46
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:45528 original size:20 final size:20
Alignment explanation
Indices: 45503--45557 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
45493 GTGATTCTCT
*
45503 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
45523 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
45543 CATTGCGATAGTCAA
1 CGTTGCGATAGTCAA
45558 ATGAATGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:47960 original size:24 final size:24
Alignment explanation
Indices: 47926--47979 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
47916 TCTGAAAATC
47926 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
47950 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
47974 ATCAAA
1 ATCAAA
47980 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:47993 original size:24 final size:24
Alignment explanation
Indices: 47926--47993 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
47916 TCTGAAAATC
* * *
47926 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
47950 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
47974 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
47994 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:48885 original size:40 final size:40
Alignment explanation
Indices: 48839--49050 Score: 266
Period size: 40 Copynumber: 5.3 Consensus size: 40
48829 GTCAGAATCT
* * *
48839 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCGTTGCGATTTACGGATACG
* * * *
48879 CATTGCGGTTTACGTATTCGCATTGCGATTTACGGATACT
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* * *
48919 CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
*
48959 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
*
48999 CGTTGCGATTTTACATATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
*
49040 CGTTACGATTT
1 CGTTGCGATTT
49051 TACAGATACT
Statistics
Matches: 154, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
39 1 0.01
40 117 0.76
41 36 0.23
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
Found at i:48907 original size:60 final size:60
Alignment explanation
Indices: 48839--49050 Score: 230
Period size: 60 Copynumber: 3.5 Consensus size: 60
48829 GTCAGAATCT
* * * *
48839 CGTTGCGATTTACAGATTCGCATTGCGATTTACGTATTCGCATTGCGGTTTACGTATTCG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCG
* * * *
48899 CATTGCGATTTACGGATACTCATTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTAC-GTATTCG
* * * * * * *
48959 CGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACATATT-G
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGA-TTTACGTATTCG
* *
49019 TCGTTGCGATTTACGGATACGCGTTACGATTT
1 -CGTTGCGATTTACGGATACGCATTGCGATTT
49051 TACAGATACT
Statistics
Matches: 127, Mismatches: 21, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
60 92 0.72
61 35 0.28
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGTATTCG
Found at i:49105 original size:20 final size:20
Alignment explanation
Indices: 48839--49130 Score: 147
Period size: 20 Copynumber: 14.5 Consensus size: 20
48829 GTCAGAATCT
* *
48839 CGTTGCGATTTACAGATTCG
1 CGTTGCGATTTTCATATTCG
* * *
48859 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTTCATATTCG
* * * *
48879 CATTGCGGTTTACGTATTCG
1 CGTTGCGATTTTCATATTCG
* * ** * *
48899 CATTGCGATTTACGGATACT
1 CGTTGCGATTTTCATATTCG
* * * *
48919 CATTGCGATTTACGTATTCT
1 CGTTGCGATTTTCATATTCG
* * *
48939 CGTTGCGATTTACAGATACG
1 CGTTGCGATTTTCATATTCG
* * *
48959 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTTCATATTCG
* ** *
48979 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTTCATATTCG
48999 CGTTGCGATTTTACATATT-G
1 CGTTGCGATTTT-CATATTCG
* ** *
49019 TCGTTGCGATTTACGGATACG
1 -CGTTGCGATTTTCATATTCG
* * * *
49040 CGTTACGATTTTACAGATACT
1 CGTTGCGATTTT-CATATTCG
** * *
49061 CGTTGCGATAGTCAGAATCG
1 CGTTGCGATTTTCATATTCG
*
49081 CGTTGCGATTTAT-ATGTTCG
1 CGTTGCGATTT-TCATATTCG
*
49101 TGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCG
49121 CGTTGCGATT
1 CGTTGCGATT
49131 ATGGAAAATC
Statistics
Matches: 218, Mismatches: 48, Indels: 12
0.78 0.17 0.04
Matches are distributed among these distances:
19 1 0.00
20 186 0.85
21 31 0.14
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCG
Found at i:49582 original size:16 final size:16
Alignment explanation
Indices: 49561--49591 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49551 ATTAAAAATA
49561 AAATAAAACAAAGTAG
1 AAATAAAACAAAGTAG
*
49577 AAATAAAACGAAGTA
1 AAATAAAACAAAGTA
49592 AAAAAATAAT
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:0.68, C:0.06, G:0.13, T:0.13
Consensus pattern (16 bp):
AAATAAAACAAAGTAG
Found at i:50263 original size:34 final size:34
Alignment explanation
Indices: 50143--50270 Score: 140
Period size: 34 Copynumber: 3.8 Consensus size: 34
50133 TTAGTTTGTG
*
50143 CAAT-AAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAAATAAAAAGTTAG-AATGTTAGTAAGAA
* *
50176 CAATAAAAATAAACAAGTCA-ATATGTTAGTATGAA
1 CAATAAAAATAAA-AAGTTAGA-ATGTTAGTAAGAA
* *
50211 CAAT-AAAAT-AAAAGTTAGAATGTTTGTAAAAA
1 CAATAAAAATAAAAAGTTAGAATGTTAGTAAGAA
*
50243 TAATAAAAATAAAAAGTTAGAATGTTAG
1 CAATAAAAATAAAAAGTTAGAATGTTAG
50271 CGATTAATGG
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
32 18 0.23
33 13 0.16
34 30 0.38
35 18 0.23
ACGTcount: A:0.55, C:0.04, G:0.13, T:0.27
Consensus pattern (34 bp):
CAATAAAAATAAAAAGTTAGAATGTTAGTAAGAA
Found at i:61695 original size:17 final size:18
Alignment explanation
Indices: 61652--61696 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
61642 TTTTAAAGTT
*
61652 TTATTAATTTTTTATATA
1 TTATTAATTTTTTATAAA
*
61670 TTTTTAATTTTTT-TAAA
1 TTATTAATTTTTTATAAA
*
61687 TTATAAATTT
1 TTATTAATTT
61697 CACATTGCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTATTAATTTTTTATAAA
Done.