Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006022.1 Hibiscus syriacus cultivar Beakdansim tig00014210_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: 138792
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:3247 original size:21 final size:21
Alignment explanation
Indices: 3221--3262 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3211 GCCCAGAATG
*
3221 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
*
3242 GGGAATTGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
3263 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:3428 original size:34 final size:34
Alignment explanation
Indices: 3390--3456 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
3380 AATATGTACC
*
3390 CGGGGAATCGATA-CCCTTGGGGGGAATCAGTTCT
1 CGGGGAATCGATACCCCCT-GGGGGAATCAGTTCT
*
3424 CGGGGAATCGATACCCCCTGGGGGAATCTGTTC
1 CGGGGAATCGATACCCCCTGGGGGAATCAGTTC
3457 CCCCTGGGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 26 0.87
35 4 0.13
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.22
Consensus pattern (34 bp):
CGGGGAATCGATACCCCCTGGGGGAATCAGTTCT
Found at i:3449 original size:19 final size:19
Alignment explanation
Indices: 3425--3485 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 19
3415 ATCAGTTCTC
3425 GGGGAATC-GATACCCCCTG
1 GGGGAATCTG-TACCCCCTG
*
3444 GGGGAATCTGTTCCCCCTGGGG
1 GGGGAATCTGTACCCCCT---G
3466 GGGGAATCTGTACCCCCTG
1 GGGGAATCTGTACCCCCTG
3485 G
1 G
3486 ACAATCTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
19 17 0.47
20 1 0.03
22 18 0.50
ACGTcount: A:0.15, C:0.30, G:0.36, T:0.20
Consensus pattern (19 bp):
GGGGAATCTGTACCCCCTG
Found at i:3471 original size:22 final size:22
Alignment explanation
Indices: 3443--3485 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
3433 GATACCCCCT
*
3443 GGGGGAATCTGTTCCCCCTGGG
1 GGGGGAATCTGTACCCCCTGGG
3465 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
3486 ACAATCTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.28, G:0.40, T:0.21
Consensus pattern (22 bp):
GGGGGAATCTGTACCCCCTGGG
Found at i:6834 original size:21 final size:21
Alignment explanation
Indices: 6808--6849 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
6798 CCAGAATGGG
*
6808 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
6829 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
6850 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:6991 original size:15 final size:15
Alignment explanation
Indices: 6963--7026 Score: 58
Period size: 15 Copynumber: 4.0 Consensus size: 15
6953 AACCATGCAG
6963 GGGGAATCTG-TACCC
1 GGGGAATC-GATACCC
6978 GGGGAATCGATACCTC
1 GGGGAATCGATACC-C
* *
6994 TGGGGGGAATCTATTCCC
1 ---GGGGAATCGATACCC
7012 GGGGAATCGATACCC
1 GGGGAATCGATACCC
7027 CCTGGGGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 1 0.03
15 25 0.62
16 1 0.03
18 1 0.03
19 12 0.30
ACGTcount: A:0.22, C:0.25, G:0.33, T:0.20
Consensus pattern (15 bp):
GGGGAATCGATACCC
Found at i:7037 original size:20 final size:20
Alignment explanation
Indices: 7012--7071 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
7002 ATCTATTCCC
7012 GGGGAATC-GATACCCCCTGG
1 GGGGAATCTG-TACCCCCTGG
*
7032 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCTGTACCCCCTGG
7052 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
7072 ACAATCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 36 0.97
21 1 0.03
ACGTcount: A:0.15, C:0.30, G:0.35, T:0.20
Consensus pattern (20 bp):
GGGGAATCTGTACCCCCTGG
Found at i:7039 original size:35 final size:34
Alignment explanation
Indices: 6962--7046 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
6952 AAACCATGCA
* *
6962 GGGGGAATCTGTACCCGGGGAATCGATACCTCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
*
6996 GGGGGAATCTATTCCCGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCCGGGGAATCGATA-CCCCTG
7031 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
7047 CCTGGGGGGA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 26 0.57
35 20 0.43
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (34 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCTG
Found at i:8672 original size:23 final size:23
Alignment explanation
Indices: 8646--8693 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
8636 ACCTTTTCGG
*
8646 TGAAATGAATTAACTATTTTTCA
1 TGAAAAGAATTAACTATTTTTCA
* *
8669 TGAAAAGACTTAATTATTTTTCA
1 TGAAAAGAATTAACTATTTTTCA
8692 TG
1 TG
8694 GATAGATGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (23 bp):
TGAAAAGAATTAACTATTTTTCA
Found at i:9065 original size:37 final size:37
Alignment explanation
Indices: 9013--9116 Score: 145
Period size: 37 Copynumber: 2.8 Consensus size: 37
9003 CTTTTCGTCA
*
9013 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
9050 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
** * *
9087 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
9117 CCACAAGCAT
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:9838 original size:22 final size:22
Alignment explanation
Indices: 9813--9858 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
9803 TTTTATTATA
9813 TTATACATACATTTTTATATTT
1 TTATACATACATTTTTATATTT
* * *
9835 TTATATATATATTTTTTTATTT
1 TTATACATACATTTTTATATTT
9857 TT
1 TT
9859 TTACTATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATACATACATTTTTATATTT
Found at i:9858 original size:23 final size:24
Alignment explanation
Indices: 9824--9876 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
9814 TATACATACA
9824 TTTTTATATTTTTATA-TATATATT
1 TTTTTATATTTTT-TACTATATATT
*
9848 TTTTTAT-TTTTTTACTATTTATT
1 TTTTTATATTTTTTACTATATATT
9871 TATTTT
1 T-TTTT
9877 CATTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 2 0.08
23 13 0.50
24 11 0.42
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTATATTTTTTACTATATATT
Found at i:9885 original size:19 final size:18
Alignment explanation
Indices: 9749--9886 Score: 67
Period size: 19 Copynumber: 7.6 Consensus size: 18
9739 TTTTAGTTAA
9749 TATTATATGTATATTTATTTT
1 TATTATAT-T-TATTTA-TTT
9770 TCATT-TATTTA-TTATTAT
1 T-ATTATATTTATTTATT-T
*
9788 TATTACTATTTA-GTATTT
1 TATTA-TATTTATTTATTT
** *
9806 TATTATATTATACATACATT
1 TATTATATT-TATTTA-TTT
*
9826 T-TTATA-TT-TTTA-TA
1 TATTATATTTATTTATTT
*
9840 TA-TATATTTTTTTATTT
1 TATTATATTTATTTATTT
*
9857 TTTTACTATTTATTTATTT
1 TATTA-TATTTATTTATTT
9876 TCATTATATTT
1 T-ATTATATTT
9887 TTAGTTTCTT
Statistics
Matches: 93, Mismatches: 10, Indels: 30
0.70 0.08 0.23
Matches are distributed among these distances:
14 6 0.06
15 2 0.02
16 6 0.06
17 12 0.13
18 16 0.17
19 37 0.40
20 7 0.08
21 4 0.04
22 3 0.03
ACGTcount: A:0.28, C:0.04, G:0.01, T:0.66
Consensus pattern (18 bp):
TATTATATTTATTTATTT
Found at i:10000 original size:20 final size:19
Alignment explanation
Indices: 9973--10028 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
9963 TTTTATCTTC
9973 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
9992 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
10012 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
10029 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:14346 original size:16 final size:15
Alignment explanation
Indices: 14325--14378 Score: 67
Period size: 15 Copynumber: 3.5 Consensus size: 15
14315 AAAGGTCAAA
14325 AACAAAAAAGAAAAG
1 AACAAAAAAGAAAAG
14340 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAAGAA-AAG
14356 AACAAAAAA-AGAAAG
1 AACAAAAAAGA-AAAG
14371 AACAAAAA
1 AACAAAAA
14379 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.09
15 18 0.51
16 12 0.34
17 2 0.06
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAAAG
Found at i:16116 original size:106 final size:106
Alignment explanation
Indices: 15993--16945 Score: 1375
Period size: 106 Copynumber: 9.0 Consensus size: 106
15983 GTGCCACTTG
* * * *
15993 AGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
16058 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * *
16099 AGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
16164 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * * *
16205 AGACAACGAAAGTTCAACTTCACGATGAAGGGATCGTTGGTTGTCAATAAACAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
16270 CAGAGCCAATTTCAAGTTCACAACGAAGGATATTGGACTCA
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
16311 AGACAACGCTAGTTCAACTTCATGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* **
16376 CAGAGCCAATTTTAACTTCACAGTGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* ** * *
16417 AGACAATGCAAGTTCAACTTCATAACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* ** *
16482 CGGAGATAATTTCAACTTCACAGCGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * *
16523 AGACAATGCAAGTTCAACTTCACGAGGAAGGGACCGCTGGTTGTTAACAAACAACTTCTCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
16588 TAGAGCCAATTTCAACTTCAGAACGAAGGATATTGGACTCC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
16629 AGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * * *
16694 CAGAGCCAATTTCAACTTCACAGCAAAGGATATTGTACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * *
16735 AGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTAGTTGTCTACAAATAATTTCCCAATTT
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * * *
16800 CGGAGCCAATTTCAACTTCGCAACAAAGGATATTGGACTCG
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
* * * * *
16841 AGACAACACAAGTTCAACTTCACGACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTC
1 AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
16906 CAAAGCCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
16946 AGAACAATGC
Statistics
Matches: 760, Mismatches: 87, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
106 760 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
Found at i:17790 original size:37 final size:37
Alignment explanation
Indices: 17695--17773 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
17685 CTTTTCGTCA
* *
17695 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTT
1 TACTAGGATTCAAACACCTAAAAATAGGATAGAATTC
* *
17732 TGCTAGGATTCAAACACCTAAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACACCTAAAAATAGGATAGAATTC
17769 TACTA
1 TACTA
17774 TTATTTAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (37 bp):
TACTAGGATTCAAACACCTAAAAATAGGATAGAATTC
Found at i:18244 original size:23 final size:24
Alignment explanation
Indices: 18216--18263 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
18206 TATATGTATA
18216 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTTATTTCATT
*
18239 TATTTATTATAATTTTTTTTCATT
1 TATTTATTATAATTTTATTTCATT
18263 T
1 T
18264 TTCTTTACGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 5 0.23
23 13 0.59
24 4 0.18
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (24 bp):
TATTTATTATAATTTTATTTCATT
Found at i:18514 original size:48 final size:46
Alignment explanation
Indices: 18462--18565 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 46
18452 ATTTATTTTT
*
18462 CATTTATTTATTATTATTACTATTTAGTATTTTATTATATTATACATA
1 CATTTATTTATTATTATTA-TATATA-TATTTTATTATATTATACATA
* * * **
18510 CA-TT-TTTA-TATTTTTATATATATTTTTTATTATTTTATTTATA
1 CATTTATTTATTATTATTATATATATATTTTATTATATTATACATA
18553 CTATTTATTTATT
1 C-ATTTATTTATT
18566 TTCATTGTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
43 18 0.39
44 6 0.13
45 9 0.20
46 8 0.17
47 3 0.07
48 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.64
Consensus pattern (46 bp):
CATTTATTTATTATTATTATATATATATTTTATTATATTATACATA
Found at i:18526 original size:22 final size:22
Alignment explanation
Indices: 18491--18545 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
18481 CTATTTAGTA
*
18491 TTTTATTA-TATTATACATACAT
1 TTTTATTATTTTTATACATA-AT
* *
18513 TTTTA-TATTTTTATATATATT
1 TTTTATTATTTTTATACATAAT
18534 TTTTATTATTTT
1 TTTTATTATTTT
18546 ATTTATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTATTTTTATACATAAT
Found at i:18538 original size:21 final size:23
Alignment explanation
Indices: 18491--18564 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 23
18481 CTATTTAGTA
* *
18491 TTTTATTATATTATACATAC-A-T
1 TTTTA-TATTTTATATATACTATT
18513 TTTTATATTTT-TATATA-TATT
1 TTTTATATTTTATATATACTATT
*
18534 TTTTATTATTTTATTTATACTATT
1 TTTTA-TATTTTATATATACTATT
18558 TATTTAT
1 T-TTTAT
18565 TTTCATTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
20 6 0.14
21 11 0.26
22 11 0.26
23 5 0.12
24 6 0.14
25 4 0.09
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTTATATTTTATATATACTATT
Found at i:18577 original size:43 final size:43
Alignment explanation
Indices: 18491--18579 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
18481 CTATTTAGTA
*
18491 TTTTATTATATTATACATACATTTTTATATTTTTATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
* ** *
18534 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TGTATT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATT
18577 TTT
1 TTT
18580 AGTTTCTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
43 25 0.64
44 12 0.31
45 2 0.05
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (43 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
Found at i:18691 original size:20 final size:19
Alignment explanation
Indices: 18664--18719 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
18654 TTTTATCTTC
18664 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
18683 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
18703 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
18720 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:24112 original size:24 final size:24
Alignment explanation
Indices: 24090--24140 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
24080 AGATCGAGCT
* *
24090 GAGTCGATTTACCCGAA-CTGAGCC
1 GAGTCAATTAACCC-AAGCTGAGCC
*
24114 GAGTCAATTAACCCAAGCTGAGTC
1 GAGTCAATTAACCCAAGCTGAGCC
24138 GAG
1 GAG
24141 CTGAGCTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 2 0.09
24 21 0.91
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.20
Consensus pattern (24 bp):
GAGTCAATTAACCCAAGCTGAGCC
Found at i:28613 original size:15 final size:15
Alignment explanation
Indices: 28574--28614 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
28564 AAGAATCAAA
*
28574 ATGTTCAAAATGCCC
1 ATGTTCGAAATGCCC
28589 ATGTTCGAAATGCCC
1 ATGTTCGAAATGCCC
* *
28604 TTGTTTGAAAT
1 ATGTTCGAAAT
28615 TACTATTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (15 bp):
ATGTTCGAAATGCCC
Found at i:33979 original size:118 final size:117
Alignment explanation
Indices: 33771--34021 Score: 335
Period size: 118 Copynumber: 2.1 Consensus size: 117
33761 TGGGCTTTTA
* * * * * *
33771 AGTGTATAGATTTCCGTATGGAGTACTAAATGTGCTAAATGATGAGGAGATCATATTGAAAATAT
1 AGTGTATAGATTTCCATATGGAGTACTAAATATGCTAAATGATAAGGAAATCATACTGAAAAAAT
33836 GGATTTCCAAATAAGGAATTTTATGTGCTAAAAATGGTAA-GGAAGTCATACTG
66 GGATTTCCAAATAAGGAATTTTATGTGCT-AAAATGGTAAGGGAA-TCATACTG
* * *
33889 AGTGTATAGATTTCCATATGGAGCT-CTGAGTATGCTAAATGATAATGAAATCATACTGAAAAAA
1 AGTGTATAGATTTCCATATGGAG-TACTAAATATGCTAAATGATAAGGAAATCATACTGAAAAAA
* * * *
33953 TGGATTTCCAGATAGGGCATTTTATGTGCTAAAATGGTAAGGGAATCATATTG
65 TGGATTTCCAAATAAGGAATTTTATGTGCTAAAATGGTAAGGGAATCATACTG
*
34006 AGTGTATGGATTTCCA
1 AGTGTATAGATTTCCA
34022 GATAAAGCAC
Statistics
Matches: 117, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
117 32 0.27
118 84 0.72
119 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.32
Consensus pattern (117 bp):
AGTGTATAGATTTCCATATGGAGTACTAAATATGCTAAATGATAAGGAAATCATACTGAAAAAAT
GGATTTCCAAATAAGGAATTTTATGTGCTAAAATGGTAAGGGAATCATACTG
Found at i:33983 original size:58 final size:58
Alignment explanation
Indices: 33800--34021 Score: 169
Period size: 58 Copynumber: 3.8 Consensus size: 58
33790 GGAGTACTAA
* * * * *
33800 ATGTGCTAAATGATGAGGAGATCATATTGAAAATATGGATTTCCAAATAAGGAATTTT
1 ATGTGCTAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAAATAGGGCATTTT
* * *** * * * *
33858 ATGTGCTAAAAATGGTAAGGAAGTCATACTGAGTGTATAGATTTCCATAT-GGAGC-TCTG
1 ATGTGCT--AAATGATAAGGAAATCATACTGAAAATATGGATTTCCAAATAGG-GCATTTT
* * * *
33917 AGTATGCTAAATGATAATGAAATCATACTGAAAAAATGGATTTCCAGATAGGGCATTTT
1 A-TGTGCTAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAAATAGGGCATTTT
* * * ***
33976 ATGTGCTAAAATGGTAAGGGAATCATATTGAGTGTATGGATTTCCA
1 ATGTGCT-AAATGATAAGGAAATCATACTGAAAATATGGATTTCCA
34022 GATAAAGCAC
Statistics
Matches: 122, Mismatches: 35, Indels: 13
0.72 0.21 0.08
Matches are distributed among these distances:
58 46 0.38
59 39 0.32
60 37 0.30
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (58 bp):
ATGTGCTAAATGATAAGGAAATCATACTGAAAATATGGATTTCCAAATAGGGCATTTT
Found at i:34051 original size:118 final size:118
Alignment explanation
Indices: 33803--34061 Score: 306
Period size: 118 Copynumber: 2.2 Consensus size: 118
33793 GTACTAAATG
* * * * *
33803 TGCTAAATGATGAGGAGATCATATTGAAAATATGGATTTCCAAATAAGGAATTTTATGTGCTAAA
1 TGCTAAAAGATAAGGAAATCATACTGAAAAAATGGATTTCCAAATAAGGAATTTTATGTGCTAAA
* ** * * *
33868 AATGGTAAGGAAGTCATACTGAGTGTATAGATTTCCATATGGAGCTCTGAGTA
66 AATGGTAAGGAAGTCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGGA
* * * * *
33921 TGCTAAATGATAATGAAATCATACTGAAAAAATGGATTTCCAGATAGGGCATTTTATGTGCT-AA
1 TGCTAAAAGATAAGGAAATCATACTGAAAAAATGGATTTCCAAATAAGGAATTTTATGTGCTAAA
* * *
33985 AATGGTAAGGGAA-TCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAGGG
66 AATGGTAA-GGAAGTCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGGA
*
34038 TGGTACAAAGATAAGGAAATCATA
1 TGCTA-AAAGATAAGGAAATCATA
34062 TTAATGGTAT
Statistics
Matches: 119, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
117 45 0.38
118 74 0.62
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (118 bp):
TGCTAAAAGATAAGGAAATCATACTGAAAAAATGGATTTCCAAATAAGGAATTTTATGTGCTAAA
AATGGTAAGGAAGTCATACTGAGTGTATAGATTTCCAGATAAAGCACTAAGGA
Found at i:34086 original size:118 final size:117
Alignment explanation
Indices: 33803--34131 Score: 293
Period size: 118 Copynumber: 2.8 Consensus size: 117
33793 GTACTAAATG
* * * * * * *
33803 TGCTAAATGATGAGGAGATCATATTGAAAATATGGATTTCCAAATAAGGAATTTTATGTGCTAAA
1 TGCTAAAAGATAAGGAAATCATACTGAAAATATGGATTTTCAAATAGGGCATTTTATGTGCT-AA
* * * ** * * *
33868 AATGGTAA-GGAAGTCATACTGAGTGTATAGATTTCCATATGGAGCTCTGAGTA
65 AATGGTAAGGGAA-TCATAATGAGTGTATGGATTTCCAGATAAAGCACTAAGGA
* * * * *
33921 TGCTAAATGATAATGAAATCATACTGAAAAAATGGATTTCCAGATAGGGCATTTTATGTGCTAAA
1 TGCTAAAAGATAAGGAAATCATACTGAAAATATGGATTTTCAAATAGGGCATTTTATGTGCTAAA
* *
33986 ATGGTAAGGGAATCATATTGAGTGTATGGATTTCCAGATAAAGCACTAAGGG
66 ATGGTAAGGGAATCATAATGAGTGTATGGATTTCCAGATAAAGCACTAAGGA
* * ** * * ** *
34038 TGGTACAAAGATAAGGAAATCATA-TTAATGGTATGGATTTTCGAATAGGGCACTTCGTGTCCTA
1 TGCTA-AAAGATAAGGAAATCATACTGAA-AATATGGATTTTCAAATAGGGCATTTTATGTGCTA
** * *
34102 AAATGAAAAGGGAAGCATAATAAGTGTATG
64 AAATGGTAAGGGAATCATAATGAGTGTATG
34132 ATCTTTTAGA
Statistics
Matches: 172, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
117 48 0.28
118 124 0.72
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.29
Consensus pattern (117 bp):
TGCTAAAAGATAAGGAAATCATACTGAAAATATGGATTTTCAAATAGGGCATTTTATGTGCTAAA
ATGGTAAGGGAATCATAATGAGTGTATGGATTTCCAGATAAAGCACTAAGGA
Found at i:37545 original size:38 final size:37
Alignment explanation
Indices: 37494--37714 Score: 193
Period size: 37 Copynumber: 5.9 Consensus size: 37
37484 ATATAGTTTT
*
37494 AAATAGTTTTGAAAATGTATAATATATAGTTTTTCAAA
1 AAATAGTTTTGAAAACGTATAATATATAGTTTTT-AAA
37532 AAATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
1 AAATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
* * *
37569 AAA-CGATTTTGAAAACATATAATATAT-GATTTTTTAA
1 AAATAG-TTTTGAAAACGTATAATATATAG-TTTTTAAA
* * * * *
37606 AAATGGTGTTGAAAACGTCTAATATATATTTTTTTAA
1 AAATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
* *
37643 AAA-CGATTTCTG-AAACATATAATATA-A-TTTTTGAAA
1 AAATAG-TTT-TGAAAACGTATAATATATAGTTTTT-AAA
* * ** *
37679 ACATATTTTTGAAAATATAGTATTATATAGTTTTTA
1 AAATAGTTTTGAAAACGTA-TAATATATAGTTTTTA
37715 TTATTATGTT
Statistics
Matches: 152, Mismatches: 19, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
35 7 0.05
36 17 0.11
37 85 0.56
38 38 0.25
39 5 0.03
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (37 bp):
AAATAGTTTTGAAAACGTATAATATATAGTTTTTAAA
Found at i:37639 original size:74 final size:75
Alignment explanation
Indices: 37500--37714 Score: 233
Period size: 74 Copynumber: 2.9 Consensus size: 75
37490 TTTTAAATAG
** *
37500 TTTTGAAAATGTATAATATATAGTTTTTCAAAAAATAGTTTTGAAAACGTATAATATATAGTTTT
1 TTTTGAAAACATATAATATATAGTTTTTCAAAAAATAGTGTTGAAAACGTATAATATATAGTTTT
37565 TAAAAAACGA
66 TAAAAAACGA
* * * *
37575 TTTTGAAAACATATAATATAT-GATTTTT-TAAAAATGGTGTTGAAAACGTCTAATATATATTTT
1 TTTTGAAAACATATAATATATAG-TTTTTCAAAAAATAGTGTTGAAAACGTATAATATATAGTTT
*
37638 TTTAAAAACGA
65 TTAAAAAACGA
* * * * ** *
37649 TTTCTG-AAACATATAATATA-A-TTTTTGAAAACATATTTTTGAAAATATAGTATTATATAGTT
1 TTT-TGAAAACATATAATATATAGTTTTTCAAAAAATAGTGTTGAAAACGTA-TAATATATAGTT
37711 TTTA
64 TTTA
37715 TTATTATGTT
Statistics
Matches: 116, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
72 5 0.04
73 14 0.12
74 71 0.61
75 26 0.22
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.43
Consensus pattern (75 bp):
TTTTGAAAACATATAATATATAGTTTTTCAAAAAATAGTGTTGAAAACGTATAATATATAGTTTT
TAAAAAACGA
Found at i:37774 original size:14 final size:14
Alignment explanation
Indices: 37742--37774 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
37732 TATTTAATAT
*
37742 ATTTATTTATTTTG
1 ATTTTTTTATTTTG
37756 A-TTTTTTATTTTG
1 ATTTTTTTATTTTG
37769 ATTTTT
1 ATTTTT
37775 ATTTTATTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (14 bp):
ATTTTTTTATTTTG
Found at i:37775 original size:12 final size:13
Alignment explanation
Indices: 37742--37779 Score: 60
Period size: 12 Copynumber: 2.9 Consensus size: 13
37732 TATTTAATAT
37742 ATTTATTTATTTTG
1 ATTT-TTTATTTTG
37756 ATTTTTTATTTTG
1 ATTTTTTATTTTG
37769 A-TTTTTATTTT
1 ATTTTTTATTTT
37780 ATTACTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.42
13 10 0.42
14 4 0.17
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (13 bp):
ATTTTTTATTTTG
Found at i:39665 original size:23 final size:23
Alignment explanation
Indices: 39639--39708 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
39629 AGTCGAGGGT
*
39639 TCTATGCGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
* *
39662 TCTATGTGGTCCTTCAGGACAAT
1 TCTATGTGGTCCTTCGGGACAAA
* *
39685 TTTACGTGGTCCTTCGGGACAAA
1 TCTATGTGGTCCTTCGGGACAAA
39708 T
1 T
39709 TCTACATTGT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.23, G:0.24, T:0.31
Consensus pattern (23 bp):
TCTATGTGGTCCTTCGGGACAAA
Found at i:50344 original size:14 final size:14
Alignment explanation
Indices: 50321--50352 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
50311 TGGGATGTAA
50321 AATA-AATAATAAT
1 AATATAATAATAAT
50334 AATATAATAATAAT
1 AATATAATAATAAT
50348 AATAT
1 AATAT
50353 TGGGATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AATATAATAATAAT
Found at i:52209 original size:16 final size:16
Alignment explanation
Indices: 52190--52245 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
52180 TAAAATATAT
*
52190 TAATAAGATTATTAAA
1 TAATAATATTATTAAA
* *
52206 TAATAATAATATT-AT
1 TAATAATATTATTAAA
52221 TAAATAATATTATTAAA
1 T-AATAATATTATTAAA
52238 TAATAATA
1 TAATAATA
52246 ATGTTAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TAATAATATTATTAAA
Found at i:52226 original size:13 final size:13
Alignment explanation
Indices: 52210--52242 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
52200 ATTAAATAAT
52210 AATAATATTATTA
1 AATAATATTATTA
52223 AATAATATTATTA
1 AATAATATTATTA
52236 AATAATA
1 AATAATA
52243 ATAATGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATAATATTATTA
Found at i:52227 original size:32 final size:30
Alignment explanation
Indices: 52175--52247 Score: 103
Period size: 32 Copynumber: 2.4 Consensus size: 30
52165 AAATACATGT
*
52175 AATACTAA-AATATATTAATAAGATTATTA
1 AATAATAATAATATATTAATAAGATTATTA
*
52204 AATAATAATAATATTATTAAATAATATTATTA
1 AATAATAATAATA-TATT-AATAAGATTATTA
52236 AATAATAATAAT
1 AATAATAATAAT
52248 GTTAAATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 7 0.18
30 4 0.10
31 4 0.10
32 24 0.62
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (30 bp):
AATAATAATAATATATTAATAAGATTATTA
Found at i:52247 original size:19 final size:19
Alignment explanation
Indices: 52190--52229 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
52180 TAAAATATAT
52190 TAATAAGATTATTAAATAA
1 TAATAAGATTATTAAATAA
*
52209 TAATAATATTATTAAATAA
1 TAATAAGATTATTAAATAA
52228 TA
1 TA
52230 TTATTAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (19 bp):
TAATAAGATTATTAAATAA
Found at i:52252 original size:16 final size:16
Alignment explanation
Indices: 52199--52254 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
52189 TTAATAAGAT
52199 TATTAAATAATAATAA
1 TATTAAATAATAATAA
* *
52215 TATT-ATTAAATAATAT
1 TATTAAAT-AATAATAA
52231 TATTAAATAATAATAA
1 TATTAAATAATAATAA
*
52247 TGTTAAAT
1 TATTAAAT
52255 TTGAACCCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 2 0.06
16 29 0.88
17 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TATTAAATAATAATAA
Found at i:56914 original size:17 final size:16
Alignment explanation
Indices: 56889--56929 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 16
56879 ATAACACTTG
*
56889 AAAAAAAAATTAAAAT
1 AAAAAAAAAATAAAAT
56905 AAAAATAAAAATAAAAT
1 AAAAA-AAAAATAAAAT
56922 AAAGAAAA
1 AAA-AAAA
56930 TTCAACAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 2 0.09
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (16 bp):
AAAAAAAAAATAAAAT
Found at i:57782 original size:15 final size:15
Alignment explanation
Indices: 57764--57797 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
57754 TTTTTTGAAA
57764 TTTTGGCTTTTTTGT
1 TTTTGGCTTTTTTGT
**
57779 TTTTGTTTTTTTTGT
1 TTTTGGCTTTTTTGT
57794 TTTT
1 TTTT
57798 TGCCTCTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.03, G:0.15, T:0.82
Consensus pattern (15 bp):
TTTTGGCTTTTTTGT
Found at i:58238 original size:137 final size:137
Alignment explanation
Indices: 57992--58265 Score: 539
Period size: 137 Copynumber: 2.0 Consensus size: 137
57982 CAACTCTGAT
57992 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
58057 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
58122 GTTTAGG
131 GTTTAGG
*
58129 ACCAATTGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
58194 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
58259 GTTTAGG
131 GTTTAGG
58266 GTTTCTTTTA
Statistics
Matches: 136, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 136 1.00
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (137 bp):
ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
GTTTAGG
Found at i:62973 original size:137 final size:137
Alignment explanation
Indices: 62727--63000 Score: 521
Period size: 137 Copynumber: 2.0 Consensus size: 137
62717 CAACTCTGAT
62727 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
62792 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAATCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAATCGCTAGGATT
62857 GTTTAGG
131 GTTTAGG
*
62864 ACCAATTGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
* *
62929 AAGCTCTAGACTGGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAATCGCTAGGATT
62994 GTTTAGG
131 GTTTAGG
63001 GTTTCTTTTA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 134 1.00
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (137 bp):
ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAATCGCTAGGATT
GTTTAGG
Found at i:67303 original size:5 final size:6
Alignment explanation
Indices: 67252--67305 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
67242 AATTTTGGCT
* *
67252 TTTTTG TTTTTG TTTTT- TTTTTG TTTTTTG CCTCTT- TTTTTG TTTTTG
1 TTTTTG TTTTTG TTTTTG TTTTTG -TTTTTG -TTTTTG TTTTTG TTTTTG
67300 TTTTTG
1 TTTTTG
67306 AAAAAAATAG
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
5 8 0.20
6 23 0.57
7 9 0.22
ACGTcount: A:0.00, C:0.06, G:0.13, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:67722 original size:137 final size:137
Alignment explanation
Indices: 67476--67749 Score: 530
Period size: 137 Copynumber: 2.0 Consensus size: 137
67466 CAACTCTGAT
67476 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
67541 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
67606 GTTTAGG
131 GTTTAGG
* *
67613 ACCAATTGATAGGGAAGTGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
1 ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
67678 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
66 AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
67743 GTTTAGG
131 GTTTAGG
67750 GTTTCTTTTA
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.24
Consensus pattern (137 bp):
ACCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGA
AAGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATT
GTTTAGG
Found at i:72464 original size:137 final size:137
Alignment explanation
Indices: 72218--72490 Score: 537
Period size: 137 Copynumber: 2.0 Consensus size: 137
72208 AACTCTGATT
72218 CCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
1 CCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
72283 AGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTG
66 AGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTG
72348 TTTAGGA
131 TTTAGGA
*
72355 CCAATTGATAGGGAAGCGGTGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
1 CCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
72420 AGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTG
66 AGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTG
72485 TTTAGG
131 TTTAGG
72491 GTTTCTTTTA
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.23
Consensus pattern (137 bp):
CCAATTGATAGGGAAGCGATGGCGGATTGATGAACGTTGCTCTTGTTGAAGAATCAAACCTAGAA
AGCTCTAGACTCGATGAAGAACAAAGGTGATGAATATGGGAAGGTGGCGGCAGTCGCTAGGATTG
TTTAGGA
Found at i:78482 original size:16 final size:16
Alignment explanation
Indices: 78461--78500 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
78451 TTTGAGTGTA
78461 CTTTGCTTCACTTATT
1 CTTTGCTTCACTTATT
78477 CTTTGCTTCACTTATT
1 CTTTGCTTCACTTATT
78493 CTTTGCTT
1 CTTTGCTT
78501 TTAATTATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.25, G:0.07, T:0.57
Consensus pattern (16 bp):
CTTTGCTTCACTTATT
Found at i:78510 original size:17 final size:16
Alignment explanation
Indices: 78461--78513 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
78451 TTTGAGTGTA
*
78461 CTTTGCTTCACTTATT
1 CTTTGCTTCAATTATT
*
78477 CTTTGCTTCACTTATT
1 CTTTGCTTCAATTATT
*
78493 CTTTGCTTTTAATTATT
1 CTTTGC-TTCAATTATT
78510 CTTT
1 CTTT
78514 TTCTTTTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
16 22 0.65
17 12 0.35
ACGTcount: A:0.13, C:0.21, G:0.06, T:0.60
Consensus pattern (16 bp):
CTTTGCTTCAATTATT
Found at i:80682 original size:18 final size:18
Alignment explanation
Indices: 80659--80705 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
80649 TACTAAAATG
80659 GTATCGATACCGAAGTAT
1 GTATCGATACCGAAGTAT
80677 GTATCGATACCGAAGTAT
1 GTATCGATACCGAAGTAT
80695 GTATCGATACC
1 GTATCGATACC
80706 ATAGAAGAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (18 bp):
GTATCGATACCGAAGTAT
Found at i:81376 original size:24 final size:24
Alignment explanation
Indices: 81300--81403 Score: 115
Period size: 23 Copynumber: 4.4 Consensus size: 24
81290 GAGTCGAGGG
* *
81300 TTCTACGCGGTCCTTCGAGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
81324 -TCTATGTGGTCCTTCGGGA-TAA
1 TTCTACGTGGTCCTTCGGGACAAA
* *
81346 TTTTACGTGGTCCTTTGGGACAAA
1 TTCTACGTGGTCCTTCGGGACAAA
81370 TTCTACGTGGTCCTTCGAGG-CAAA
1 TTCTACGTGGTCCTTCG-GGACAAA
*
81394 TTCTATGTGG
1 TTCTACGTGG
81404 CACTTCAATG
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.03
23 32 0.48
24 30 0.45
25 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (24 bp):
TTCTACGTGGTCCTTCGGGACAAA
Found at i:81409 original size:24 final size:24
Alignment explanation
Indices: 81308--81424 Score: 73
Period size: 24 Copynumber: 5.0 Consensus size: 24
81298 GGTTCTACGC
* *
81308 GGTCCTTCGAGACAAA-TCTATGT
1 GGTCCTTCAAGGCAAATTCTATGT
* * *
81331 GGTCCTTC--GGGATAATTTTACGT
1 GGTCCTTCAAGGCA-AATTCTATGT
** *
81354 GGTCCTT-TGGGACAAATTCTACGT
1 GGTCCTTCAAGG-CAAATTCTATGT
*
81378 GGTCCTTCGAGGCAAATTCTATGT
1 GGTCCTTCAAGGCAAATTCTATGT
* *
81402 GG-CACTTCAATGCAAATTATATG
1 GGTC-CTTCAAGGCAAATTCTATG
81425 AGCAGTGGTG
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
21 2 0.03
22 2 0.03
23 21 0.28
24 47 0.63
25 3 0.04
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (24 bp):
GGTCCTTCAAGGCAAATTCTATGT
Found at i:86629 original size:75 final size:79
Alignment explanation
Indices: 86482--86667 Score: 224
Period size: 75 Copynumber: 2.4 Consensus size: 79
86472 TACATATAGC
* * *
86482 ATATATAATATATAGTGTTGAAAGCATTTTTTTCGAATATATATATATATAATATAGTTTTGGGA
1 ATATATAATATATAGTTTTGAAAACA-TTTTTTCGAATATATATATATATAATATAGTTTT-GAA
***
86547 ATTTTTTTTG-AAAAT
64 AACATTTTTGAAAAAT
*
86562 ATATATAATATATTGTTTTGAAAACA-TTTTT-GAA-A-ATATATATAGT-ATATAGTTTTGAAA
1 ATATATAATATATAGTTTTGAAAACATTTTTTCGAATATATATATATA-TAATATAGTTTTGAAA
86622 ACATTTTTGAAAAAT
65 ACATTTTTGAAAAAT
*
86637 ATATATAATATATAGTTTTG-AAATATTTTTT
1 ATATATAATATATAGTTTTGAAAACATTTTTT
86668 TAAAACGTAT
Statistics
Matches: 94, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
74 13 0.14
75 48 0.51
76 2 0.02
77 3 0.03
78 5 0.05
80 23 0.24
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.47
Consensus pattern (79 bp):
ATATATAATATATAGTTTTGAAAACATTTTTTCGAATATATATATATATAATATAGTTTTGAAAA
CATTTTTGAAAAAT
Found at i:86667 original size:38 final size:37
Alignment explanation
Indices: 86482--86672 Score: 204
Period size: 37 Copynumber: 5.0 Consensus size: 37
86472 TACATATAGC
* * *
86482 ATATATAATATATAGTGTTGAAAGCATTTTTTTCGAATAT
1 ATATATAATATATAGTTTTGAAA--ACTTTTTT-GAAAAT
* **
86522 ATATATATATAATATAGTTTTGGGAATTTTTTTTGAAAAT
1 ATATATA-AT-ATATAGTTTT-GAAAACTTTTTTGAAAAT
* *
86562 ATATATAATATATTGTTTTGAAAACATTTTTGAAAAT
1 ATATATAATATATAGTTTTGAAAACTTTTTTGAAAAT
* *
86599 ATATATAGTATATAGTTTTGAAAACATTTTTGAAAAAT
1 ATATATAATATATAGTTTTGAAAACTTTTTTG-AAAAT
*
86637 ATATATAATATATAGTTTTGAAATA-TTTTTTTAAAA
1 ATATATAATATATAGTTTTGAAA-ACTTTTTTGAAAA
86673 CGTATAATAT
Statistics
Matches: 132, Mismatches: 14, Indels: 13
0.83 0.09 0.08
Matches are distributed among these distances:
37 48 0.36
38 41 0.31
39 3 0.02
40 19 0.14
41 9 0.07
42 9 0.07
43 3 0.02
ACGTcount: A:0.41, C:0.02, G:0.10, T:0.47
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAAAACTTTTTTGAAAAT
Found at i:86782 original size:2 final size:2
Alignment explanation
Indices: 86775--86805 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
86765 TACATTGTAT
*
86775 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
86806 TTGTTCACGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:89174 original size:15 final size:15
Alignment explanation
Indices: 89154--89185 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
89144 TCACACTTAC
*
89154 TTTTTTTCTTTTATT
1 TTTTTTTCTTTCATT
89169 TTTTTTTCTTTCATT
1 TTTTTTTCTTTCATT
89184 TT
1 TT
89186 AATTTTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTTTCTTTCATT
Found at i:89191 original size:20 final size:18
Alignment explanation
Indices: 89154--89192 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
89144 TCACACTTAC
*
89154 TTTTTTTCTTTTATTTTT
1 TTTTTTTCTTTTAATTTT
89172 TTTTCTTTCATTTTAATTTT
1 TTTT-TTTC-TTTTAATTTT
89192 T
1 T
89193 ATCATTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.10, C:0.08, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTCTTTTAATTTT
Found at i:95739 original size:39 final size:37
Alignment explanation
Indices: 95671--95808 Score: 168
Period size: 39 Copynumber: 3.6 Consensus size: 37
95661 TACATATAGA
** *
95671 ATATATAATATATAGTGCTGAAAGCAATTTGTTTCAAAAAT
1 ATATATAATATATAGTTTTG--AGAAATTT-TTT-AAAAAT
*
95712 ATATATAATATATAGTTTTGAGAAATTTTTTGAAAAT
1 ATATATAATATATAGTTTTGAGAAATTTTTTAAAAAT
* *
95749 ATATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
1 ATATATAATATATAGTTTTGAGAA-ATTTTTTAAAA-AT
95788 ATATATAATATATAGTTTTGA
1 ATATATAATATATAGTTTTGA
95809 AAACGTATAA
Statistics
Matches: 88, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
37 28 0.32
38 12 0.14
39 30 0.34
41 18 0.20
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (37 bp):
ATATATAATATATAGTTTTGAGAAATTTTTTAAAAAT
Found at i:95809 original size:39 final size:38
Alignment explanation
Indices: 95671--95812 Score: 180
Period size: 37 Copynumber: 3.7 Consensus size: 38
95661 TACATATAGA
** * *
95671 ATATATAATATATAGTGCTGAAAGCAATTTGTTTCAAAAAT
1 ATATATAATATATAGTTTTGAAAAC-A-TT-TTTGAAAAAT
*
95712 ATATATAATATATAGTTTTGAGAAA-TTTTTTG-AAAAT
1 ATATATAATATATAGTTTTGA-AAACATTTTTGAAAAAT
95749 ATATATAATATATAGTTTTGAAAACATTTTTGAAAATAT
1 ATATATAATATATAGTTTTGAAAACATTTTTGAAAA-AT
95788 ATATATAATATATAGTTTTGAAAAC
1 ATATATAATATATAGTTTTGAAAAC
95813 GTATAATATA
Statistics
Matches: 91, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
36 3 0.03
37 32 0.35
38 6 0.07
39 29 0.32
41 19 0.21
42 2 0.02
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.42
Consensus pattern (38 bp):
ATATATAATATATAGTTTTGAAAACATTTTTGAAAAAT
Found at i:95821 original size:23 final size:23
Alignment explanation
Indices: 95791--95834 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
95781 AAAATATATA
95791 TATAATATATAGTTTTGAAAACG
1 TATAATATATAGTTTTGAAAACG
*
95814 TATAATATATGGTTTTGAAAA
1 TATAATATATAGTTTTGAAAA
95835 TGTTTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.41
Consensus pattern (23 bp):
TATAATATATAGTTTTGAAAACG
Found at i:95822 original size:62 final size:58
Alignment explanation
Indices: 95752--95870 Score: 168
Period size: 58 Copynumber: 2.0 Consensus size: 58
95742 TGAAAATATA
*
95752 TATAATATATAGTTTTGAAAACAT-TTTTGAAAATATATATATAATATATAGTTTTGAAAACG
1 TATAATATATAGTTTTG-AAA-ATGTTTT--AAA-ACATATATAATATATAGTTTTGAAAACG
*
95814 TATAATATATGGTTTTGAAAATGTTTTAAAACATATATAATATATAGTTTTGAAAAC
1 TATAATATATAGTTTTGAAAATGTTTTAAAACATATATAATATATAGTTTTGAAAAC
95871 ATTTTTTAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
58 26 0.48
59 3 0.06
60 2 0.04
61 7 0.13
62 16 0.30
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (58 bp):
TATAATATATAGTTTTGAAAATGTTTTAAAACATATATAATATATAGTTTTGAAAACG
Found at i:95857 original size:35 final size:36
Alignment explanation
Indices: 95814--95971 Score: 175
Period size: 36 Copynumber: 4.4 Consensus size: 36
95804 TTTGAAAACG
95814 TATAATATATGGTTTTG-AAA-ATGTTTTAAAACATA
1 TATAATATATGGTTTTGAAAACATGTTTTAAAA-ATA
* * *
95849 TATAATATATAGTTTTGAAAACATTTTTTAAAACT-
1 TATAATATATGGTTTTGAAAACATGTTTTAAAAATA
* *
95884 TATAATATATGATTTTGAAAAC--GTTTTAAAAATGTG
1 TATAATATATGGTTTTGAAAACATGTTTTAAAAA--TA
* *
95920 TATAATATATAGTTTTGAAAACATTTTTTGAAAAA-A
1 TATAATATATGGTTTTGAAAACATGTTTT-AAAAATA
95956 TATAATATATGGTTTT
1 TATAATATATGGTTTT
95972 ATTTTTTAAA
Statistics
Matches: 103, Mismatches: 12, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
33 8 0.08
35 37 0.36
36 39 0.38
37 10 0.10
38 4 0.04
39 5 0.05
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (36 bp):
TATAATATATGGTTTTGAAAACATGTTTTAAAAATA
Found at i:95892 original size:70 final size:70
Alignment explanation
Indices: 95803--95971 Score: 241
Period size: 70 Copynumber: 2.4 Consensus size: 70
95793 TAATATATAG
* * *
95803 TTTTGAAAACGTATAATATATGGTTTTGAAAATGTTTTAAAACA-TATATAATATATAGTTTTGA
1 TTTTTAAAACATATAATATATGGTTTTGAAAACGTTTTAAAA-AGTATATAATATATAGTTTTGA
95867 AAACAT
65 AAACAT
* * *
95873 TTTTTAAAACTTATAATATATGATTTTGAAAACGTTTTAAAAATGTGTATAATATATAGTTTTGA
1 TTTTTAAAACATATAATATATGGTTTTGAAAACGTTTTAAAAA-GTATATAATATATAGTTTTGA
95938 AAACAT
65 AAACAT
*
95944 TTTTTGAAAAAATATAATATATGGTTTT
1 TTTTT-AAAACATATAATATATGGTTTT
95972 ATTTTTTAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
69 1 0.01
70 38 0.43
71 30 0.34
72 19 0.22
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.44
Consensus pattern (70 bp):
TTTTTAAAACATATAATATATGGTTTTGAAAACGTTTTAAAAAGTATATAATATATAGTTTTGAA
AACAT
Found at i:96093 original size:2 final size:2
Alignment explanation
Indices: 96073--96114 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
96063 TAACATTATT
* *
96073 TA TA TT TA TT TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
96114 T
1 T
96115 CTTTGTTCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:97338 original size:26 final size:24
Alignment explanation
Indices: 97296--97360 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
97286 TTTAATTTAA
* *
97296 TTTTTTAAATCTTTCTTAAAGGCAT
1 TTTTTTATATTTTTCTTAAAGGC-T
**
97321 TTTTTTATATTTTCTCTTTTAGGCT
1 TTTTTTATATTTT-TCTTAAAGGCT
97346 TTTTCTTATATTTTT
1 TTTT-TTATATTTTT
97361 GTATTTCTCT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 17 0.50
26 17 0.50
ACGTcount: A:0.18, C:0.11, G:0.06, T:0.65
Consensus pattern (24 bp):
TTTTTTATATTTTTCTTAAAGGCT
Found at i:100857 original size:267 final size:267
Alignment explanation
Indices: 100381--100952 Score: 657
Period size: 267 Copynumber: 2.1 Consensus size: 267
100371 CATATAAAAC
* *
100381 GTTGATTCATTTCACTGTTCTTCAGGGAAGATTGAATGGAAGTAGACTTGTTCCGCTGTCACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATGGAAGTAGACTTGTTCCACTGTCACTCA
* * * *
100446 TGGAATATCAAATCTTGAAAAAGATGGATCTGTTCTGCCTCTTCTCGAGGGAAAATAAAATATGG
66 TGGAATATCAAATATTGAAAAAGAAGGATATGTTC-GCCTCTTCTCGAGGGAAAATAAAATATGA
* *
100511 GGACATTGATTCATTTAACTGTTCCTCAGGAAAGATTGAATCAAGATAGACTTGTTCCACTGTCA
130 GGACATGGATTCATTTAACTGTTCCTCAGGAAAGATTGAATCAAGATAGACTTGTTCCACTATCA
* * *
100576 CTCATGGAATATCAAATATTGAAAGAGATGGATCCATTCCACTTTTGCTTGAAGGAAAATTAGAT
195 CTCAGGGAATATCAAATATTGAAAGAGAGGGATACATTCCACTTTTGCTTGAAGGAAAATTAGAT
*
100641 CTGGGGAT
260 CTAGGGAT
* * * * *
100649 GTTGATTAATTCCATTGTTCTTTAGGGAAGATTGAATTGAGGTAGA-TCTGTTCCACTGTCAAC-
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATGGAAGTAGACT-TGTTCCACTGTC-ACT
* * * * * * *
100712 CATGGAATATCAAATATTGAAAGAGAAGGATATGTTC-CATTTTTCTTGAGGGAAAATCAGATCT
64 CATGGAATATCAAATATTGAAAAAGAAGGATATGTTCGC-CTCTTCTCGAGGGAAAATAAAATAT
* ** ** * * * * *
100776 GATGATGTGGATTCATTTAGTTGTTCTTTAGGGAAGATTGAATCGACG-TATACTTGTTCCACTA
128 GAGGACATGGATTCATTTAACTGTTCCTCAGGAAAGATTGAATC-AAGATAGACTTGTTCCACTA
* * ** * * * *
100840 TCACTTAGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGCTTTTTCTTGAGGGAAATTTA
192 TCACTCAGGGAATATCAAATATTGAAAGAGAGGGATACATTCCACTTTTGCTTGAAGGAAAATTA
*
100905 GATTTAGGGAT
257 GATCTAGGGAT
* * *
100916 TTTGATTCATTCCACTATTCTTCAGAGAAGATTGAAT
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAAT
100953 CGAGTTCGAT
Statistics
Matches: 251, Mismatches: 49, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
266 1 0.00
267 162 0.65
268 86 0.34
269 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (267 bp):
GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATGGAAGTAGACTTGTTCCACTGTCACTCA
TGGAATATCAAATATTGAAAAAGAAGGATATGTTCGCCTCTTCTCGAGGGAAAATAAAATATGAG
GACATGGATTCATTTAACTGTTCCTCAGGAAAGATTGAATCAAGATAGACTTGTTCCACTATCAC
TCAGGGAATATCAAATATTGAAAGAGAGGGATACATTCCACTTTTGCTTGAAGGAAAATTAGATC
TAGGGAT
Found at i:100954 original size:134 final size:134
Alignment explanation
Indices: 100381--100955 Score: 611
Period size: 134 Copynumber: 4.3 Consensus size: 134
100371 CATATAAAAC
* * *
100381 GTTGATTCATTTCACTGTTCTTCAGGGAAGATTGAATGGAAGTAGACTTGTTCCGCTGTCACTCA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAAGTAGACTTGTTCCACTGTCACTCA
* * * * * * * * * *
100446 TGGAATATCAAATCTTGAAAAAGATGGATCTGTTCTGCCTCTTCTCGAGGGAAAATAAAATATGG
66 TGGAATATCAAATATTGAAAGAGATGGATATGTTCCGCTTTTTCTTGAGGGAAAATTAGATCTGG
*
100511 GGAC
131 GGAT
* ** * *
100515 ATTGATTCATTTAACTGTTCCTCAGGAAAGATTGAATC-AAGATAGACTTGTTCCACTGTCACTC
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAAG-TAGACTTGTTCCACTGTCACTC
*** * * *
100579 ATGGAATATCAAATATTGAAAGAGATGGATCCATTCCACTTTTGCTTGAAGGAAAATTAGATCTG
65 ATGGAATATCAAATATTGAAAGAGATGGATATGTTCCGCTTTTTCTTGAGGGAAAATTAGATCTG
100644 GGGAT
130 GGGAT
* * * * *
100649 GTTGATTAATTCCATTGTTCTTTAGGGAAGATTGAATTGAGGTAGA-TCTGTTCCACTGTCAAC-
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAAGTAGACT-TGTTCCACTGTC-ACT
* * *
100712 CATGGAATATCAAATATTGAAAGAGAAGGATATGTTCC-ATTTTTCTTGAGGGAAAATCAGATCT
64 CATGGAATATCAAATATTGAAAGAGATGGATATGTTCCGCTTTTTCTTGAGGGAAAATTAGATCT
**
100776 GATGAT
129 GGGGAT
* * * * * * * *
100782 GTGGATTCATT-TAGTTGTTCTTTAGGGAAGATTGAATCGACGTATACTTGTTCCACTATCACTT
1 GTTGATTCATTCCA-CTGTTCTTCAGGGAAGATTGAATCGAAGTAGACTTGTTCCACTGTCACTC
* * * * * *
100846 AGGGAATATCAAATCTTGAAAGAGAGGGATATGTTCCGCTTTTTCTTGAGGGAAATTTAGATTTA
65 ATGGAATATCAAATATTGAAAGAGATGGATATGTTCCGCTTTTTCTTGAGGGAAAATTAGATCTG
100911 GGGAT
130 GGGAT
* * *
100916 TTTGATTCATTCCACTATTCTTCAGAGAAGATTGAATCGA
1 GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGA
100956 GTTCGATTTG
Statistics
Matches: 366, Mismatches: 66, Indels: 18
0.81 0.15 0.04
Matches are distributed among these distances:
132 3 0.01
133 113 0.31
134 245 0.67
135 5 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (134 bp):
GTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAAGTAGACTTGTTCCACTGTCACTCA
TGGAATATCAAATATTGAAAGAGATGGATATGTTCCGCTTTTTCTTGAGGGAAAATTAGATCTGG
GGAT
Found at i:101691 original size:233 final size:232
Alignment explanation
Indices: 101249--102472 Score: 1344
Period size: 233 Copynumber: 5.3 Consensus size: 232
101239 TTAGAAATTG
* * *
101249 TTTT-TTACTTTTCAAAATTTTCAAATTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCAAAT
1 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTTC-AA-
** * *
101313 AAAACATGTGAAAACATCCAGCCCGAAGGTCTTATGAATGGCCC-AAAGGACTTATGATCTTGCT
64 AAAACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAA-GACTTATCATCTTGCT
* * * *
101377 CGAAAGGCTTATAGATGACTCGAAGGATTTAAGCATCATTCTCGAAAGACTTACTGATGGCCTGA
128 CGAAAGACTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAAACTTACTGATGGCC-GA
* * *
101442 AGGACCTACAAATTTTGGAAATAGTTTGCTAGGTAAAAAAC
192 AGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAAAAAC
* * *
101483 TTTTCTTACTTTTAAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTTCGAGA
1 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTTCAAAA
* * * * * *
101548 GACATGTGAAAACATCCTTCCCAAAGGTCTTGTGGATGGCCTGAAAGACTCATCATCTTGATCGA
66 AACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGA
* * * * * *
101613 AACACTTACAGATGACACAAATGATTTAAGCATCATGCTCGAAAAACTAACTAATGGCCGAAAGG
131 AAGACTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAAACTTACTGATGGCCG-AAGG
* * * *
101678 GCTTACTAATTTTGGAAATAGTTTTCTAGGTAAGAAAC
195 ACTTACCAATTTTGGAAATAGTTTACTAGGTAAAAAAC
* * **
101716 TTTTCTTACTTTTCAAAAATTTCAAGTTTCATATTTAAATGAGAAACTTTTCTTATTTTTTTAAA
1 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTTCAAAA
* * * * * *
101781 AACATGTGAAAACATCCTGT-CTGAAGGTCTTGTGAATGGCCCGAAGGACTTATTATCTTGCTCA
66 AACATGTGAAAACATCCT-TCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCG
* * *
101845 AAAGACTTATAGATGAC-CAAAAGGA-TTAA-CTATCATGCT--AAAAAGGCTTACTGATAGCCC
130 AAAGACTTACAGATGACTC-GAAGGATTTAAGC-ATCATGCTCGAAAAA--CTTACTGAT-GGCC
* * * *
101905 GAAGGACTTA-CAATTTTAGAAATAGTTCACTAAGTAAGAAAC
190 GAAGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAAAAAC
* * *
101947 TTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAAAC-TCTCTCATTTTTCGAA
1 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAG-AAACTTTTCTCATTTTTCAAA
*** * * * * * *
102011 AAGTTTATGAAAACAT-CTTGCCCGAAGGTCTTATGGATAGCCCGAAGGGCTTCTCATCTTACTC
65 AAACATGTGAAAACATCCTT-CCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTC
* *
102075 GAAAGACTTACAGATGGCTTGAAGGATTTAAGCATCATGCTC-AAAAGACTTACTGATGGCCCGA
129 GAAAGACTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAA-ACTTACTGATGG-CCGA
* *** *
102139 AGAACTTACCAATTTCAAAAAAAGTTTACTAGG-AAAGAAAC
192 AGGACTTACCAATTTTGGAAATAGTTTACTAGGTAAA-AAAC
* * * * *
102180 TTTTCTTACTTTTCAAAAATTCCAATTTTCAAATTTAATTGAGAAACCTTCCTCATTTTTCAAAA
1 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTTCAAAA
* * ** * * ** * *
102245 AACGTGTGAAAATATCCTTCCCGAATATGTTATAGATGGCCATAATGACTTATCATCTTGCTAGA
66 AACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGA
* * * *
102310 AAGACTTACAAATGACTTGAATGATTTAAGCATCATGCTCGAAAGAA-TTACTGATTGCCCGAAG
131 AAGACTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAA-AACTTACTGA-TGGCCGAAG
* *
102374 GACTTACCAATTTCGAAAATAGTTTACTAGGTAAGAAAA-
194 GACTTACCAATTTTGGAAATAGTTTACTAGGTAA-AAAAC
* *
102413 TTTTCTTACTTTTCAAAAATTCCAATTTTCATATTTAAATGAGAAACATTTCTCATTTTT
1 TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTT
102473 TTACTTATAA
Statistics
Matches: 840, Mismatches: 123, Indels: 55
0.83 0.12 0.05
Matches are distributed among these distances:
229 1 0.00
230 7 0.01
231 149 0.18
232 71 0.08
233 534 0.64
234 24 0.03
235 54 0.06
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (232 bp):
TTTTCTTACTTTTCAAAAATTTCAATTTTCATATTTAAATGAGAAACTTTTCTCATTTTTCAAAA
AACATGTGAAAACATCCTTCCCGAAGGTCTTATGGATGGCCCGAAAGACTTATCATCTTGCTCGA
AAGACTTACAGATGACTCGAAGGATTTAAGCATCATGCTCGAAAAACTTACTGATGGCCGAAGGA
CTTACCAATTTTGGAAATAGTTTACTAGGTAAAAAAC
Found at i:102183 original size:464 final size:464
Alignment explanation
Indices: 101249--102472 Score: 1434
Period size: 464 Copynumber: 2.6 Consensus size: 464
101239 TTAGAAATTG
* *
101249 TTTT-TTACTTTTCAAAATTTTCAAATTTCAGATTTAAATGAGAAACTTTTCTCATTTTTCAAAT
1 TTTTCTTACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACTTTTCTCATTTTT-AAA-
* * *
101313 AAAACATGTGAAAACATCCAGCCCGAAGGTCTTATGAATGGCCCAAAGGACTTATGATCTTGCTC
64 AAAACATGTGAAAACATCCTGTCCGAAGGTCTTATGAATGGCCCAAAGGACTTATCATCTTGCTC
* * * * *
101378 GAAAGGCTTATAGATGACTCGAAGGATTTAAGCATCATTCTCGAAAGACTTACTGATGGCCTGAA
129 AAAAGACTTATAGATGAC-CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAA
* * * * *
101443 GGACCTACAAATTTTGGAAATAGTTTGCTAGGTAAAAAACTTTTCTTACTTTTAAAAAATTTCAA
193 GGACTTAC-AATTTTAGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAA
* * *
101508 TTTTCATATTTAAATGAGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTTCCCAAA
257 TTTTCATATTTAAATGAGAAACATTTCTCATTTTTCGAAAGACATATGAAAACATCCTTCCCAAA
* * * *
101573 GGTCTTGTGGATGGCCTGAAAGACTCATCATCTTGATCGAAACACTTACAGATGACACAAATGAT
322 GGTCTTATGGATAGCCCGAAAGACTCATCATCTTGATCGAAACACTTACAGATGACACAAAGGAT
** * *** * *
101638 TTAAGCATCATGCTCGAAAAACTAACTAATGGCCGAAAGGGCTTACTAATTTTGGAAATAGTTTT
387 TTAAGCATCATGCTCGAAAAACTAACTAATGGCCGAAAGAACTTACCAATTTCAAAAAAAGTTTA
*
101703 CTAGGTAAGAAAC
452 CTAGGAAAGAAAC
* * * **
101716 TTTTCTTACTTTTCAAAAATTTCAAGTTTCATATTTAAATGAGAAACTTTTCTTATTTTTTTAAA
1 TTTTCTTACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACTTTTCTCATTTTTAAAAA
* * * *
101781 AACATGTGAAAACATCCTGTCTGAAGGTCTTGTGAATGGCCCGAAGGACTTATTATCTTGCTCAA
66 AACATGTGAAAACATCCTGTCCGAAGGTCTTATGAATGGCCCAAAGGACTTATCATCTTGCTCAA
* ** *
101846 AAGACTTATAGATGACCAAAAGGA-TTAA-CTATCATGCTAAAAAGGCTTACTGATAGCCCGAAG
131 AAGACTTATAGATGACC-GAAGGATTTAAGC-ATCATGCTCGAAAGACTTACTGATAGCCCGAAG
* *
101909 GACTTACAATTTTAGAAATAGTTCACTAAGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATT
194 GACTTACAATTTTAGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATT
* * ** *
101974 TTCAAATTTAAATGAGAAA-ACTCTCTCATTTTTCGAAA-AGTTTATGAAAACAT-CTTGCCCGA
259 TTCATATTTAAATGAGAAACA-TTTCTCATTTTTCGAAAGA-CATATGAAAACATCCTT-CCCAA
* * * * ***
102036 AGGTCTTATGGATAGCCCGAAGGGCTTC-TCATCTT-ACTCGAAAGACTTACAGATGGCTTGAAG
321 AGGTCTTATGGATAGCCCGAAAGAC-TCATCATCTTGA-TCGAAACACTTACAGATGACACAAAG
* *
102099 GATTTAAGCATCATGCTC-AAAAGACTTACTGATGGCCCG-AAGAACTTACCAATTTCAAAAAAA
384 GATTTAAGCATCATGCTCGAAAA-ACTAACTAATGG-CCGAAAGAACTTACCAATTTCAAAAAAA
102162 GTTTACTAGGAAAGAAAC
447 GTTTACTAGGAAAGAAAC
* * * * * *
102180 TTTTCTTACTTTTCAAAAATTCCAATTTTCAAATTTAATTGAGAAACCTTCCTCATTTTTCAAAA
1 TTTTCTTACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACTTTTCTCATTTTTAAAAA
* * ** * *
102245 AACGTGTGAAAATATCCT-TCCCGAATATGTTAT-AGATGG-CCATAATGACTTATCATCTTGCT
66 AACATGTGAAAACATCCTGT-CCGAAGGTCTTATGA-ATGGCCCA-AAGGACTTATCATCTTGCT
* * * * * *
102307 -AGAAAGACTTACAAATGACTTGAATGATTTAAGCATCATGCTCGAAAGAATTACTGATTGCCCG
128 CA-AAAGACTTATAGATGAC-CGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCG
* * *
102371 AAGGACTTACCAA-TTTCGAAAATAGTTTACTAGGTAAGAAAATTTTCTTACTTTTCAAAAATTC
191 AAGGACTTA-CAATTTTAG-AAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTT
102435 CAATTTTCATATTTAAATGAGAAACATTTCTCATTTTT
254 CAATTTTCATATTTAAATGAGAAACATTTCTCATTTTT
102473 TTACTTATAA
Statistics
Matches: 643, Mismatches: 94, Indels: 41
0.83 0.12 0.05
Matches are distributed among these distances:
463 14 0.02
464 328 0.51
465 85 0.13
466 159 0.25
467 6 0.01
468 51 0.08
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (464 bp):
TTTTCTTACTTTTCAAAAATTTCAAATTTCAAATTTAAATGAGAAACTTTTCTCATTTTTAAAAA
AACATGTGAAAACATCCTGTCCGAAGGTCTTATGAATGGCCCAAAGGACTTATCATCTTGCTCAA
AAGACTTATAGATGACCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATAGCCCGAAGGA
CTTACAATTTTAGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAATTTCAATTTT
CATATTTAAATGAGAAACATTTCTCATTTTTCGAAAGACATATGAAAACATCCTTCCCAAAGGTC
TTATGGATAGCCCGAAAGACTCATCATCTTGATCGAAACACTTACAGATGACACAAAGGATTTAA
GCATCATGCTCGAAAAACTAACTAATGGCCGAAAGAACTTACCAATTTCAAAAAAAGTTTACTAG
GAAAGAAAC
Found at i:118061 original size:23 final size:23
Alignment explanation
Indices: 118035--118078 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
118025 GCGTATAATT
* *
118035 TATCCTGAATGACCACATAGAAA
1 TATCCCGAAGGACCACATAGAAA
118058 TATCCCGAAGGACCACATAGA
1 TATCCCGAAGGACCACATAGA
118079 TTTGTCCCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (23 bp):
TATCCCGAAGGACCACATAGAAA
Found at i:118086 original size:23 final size:23
Alignment explanation
Indices: 118032--118086 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
118022 ACCGCGTATA
* *
118032 ATTTATCCTGAATGACCACATAG
1 ATTTATCCCGAAGGACCACATAG
**
118055 AAATATCCCGAAGGACCACATAG
1 ATTTATCCCGAAGGACCACATAG
*
118078 ATTTGTCCC
1 ATTTATCCC
118087 AAAAGACCGC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (23 bp):
ATTTATCCCGAAGGACCACATAG
Found at i:118094 original size:23 final size:23
Alignment explanation
Indices: 118045--118094 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
118035 TATCCTGAAT
* *
118045 GACCACATAGAAATATCCCGAAG
1 GACCACATAGAAATATCCCAAAA
** *
118068 GACCACATAGATTTGTCCCAAAA
1 GACCACATAGAAATATCCCAAAA
118091 GACC
1 GACC
118095 GCGTAGAACC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.28, G:0.16, T:0.16
Consensus pattern (23 bp):
GACCACATAGAAATATCCCAAAA
Found at i:118773 original size:20 final size:21
Alignment explanation
Indices: 118748--118797 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
118738 ATTTTTTACG
*
118748 GTATCGATAC-CTCTACATAA
1 GTATCGATACTCTCTAAATAA
* *
118768 GTATCGATACTCTTTAAATCA
1 GTATCGATACTCTCTAAATAA
118789 GTATCGATA
1 GTATCGATA
118798 TTGATTATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (21 bp):
GTATCGATACTCTCTAAATAA
Found at i:123019 original size:18 final size:19
Alignment explanation
Indices: 122992--123041 Score: 50
Period size: 18 Copynumber: 2.6 Consensus size: 19
122982 GCCAAATTTT
* *
122992 GTATCCATACTCATGG-GA
1 GTATCGATACTCAGGGAGA
123010 GTATCGATACAT-AGGGTAGA
1 GTATCGATAC-TCAGGG-AGA
123030 GTATCGATACTC
1 GTATCGATACTC
123042 CTCATAGGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 12 0.46
19 2 0.08
20 12 0.46
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (19 bp):
GTATCGATACTCAGGGAGA
Found at i:128935 original size:27 final size:28
Alignment explanation
Indices: 128842--128945 Score: 97
Period size: 31 Copynumber: 3.6 Consensus size: 28
128832 TAAAAAATTG
*
128842 AATAC-TTATGGTAC-TATTTTGACCCAAAA
1 AATACTTTA-GGTACTTATTTTGA--CTAAA
* *
128871 AATGCTTTAGGTACGTATTTTGACTAAA
1 AATACTTTAGGTACTTATTTTGACTAAA
*
128899 ATTATAACTTTAGGTACTTATTTTGA-TTAA
1 A--AT-ACTTTAGGTACTTATTTTGACTAAA
128929 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
128946 AACAAAAAGA
Statistics
Matches: 65, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
27 14 0.22
28 7 0.11
29 9 0.14
30 17 0.26
31 18 0.28
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (28 bp):
AATACTTTAGGTACTTATTTTGACTAAA
Found at i:130266 original size:16 final size:15
Alignment explanation
Indices: 130247--130295 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
130237 AAAAAATATC
130247 AAATAATAAAAATAAA
1 AAATAAT-AAAATAAA
*
130263 AAATAGTAAAATAAA
1 AAATAATAAAATAAA
130278 AACA-ACATAAAATAAA
1 AA-ATA-ATAAAATAAA
130294 AA
1 AA
130296 TAAGATAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 11 0.38
16 18 0.62
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.16
Consensus pattern (15 bp):
AAATAATAAAATAAA
Found at i:130303 original size:16 final size:15
Alignment explanation
Indices: 130255--130304 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
130245 TCAAATAATA
130255 AAAATAAAAAATAG-T
1 AAAATAAAAAA-AGAT
*
130270 AAAATAAAAACAACAT
1 AAAATAAAAA-AAGAT
130286 AAAATAAAAATAAGAT
1 AAAATAAAAA-AAGAT
130302 AAA
1 AAA
130305 GAGAAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (15 bp):
AAAATAAAAAAAGAT
Found at i:130431 original size:24 final size:24
Alignment explanation
Indices: 130386--130431 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
130376 GGGACTTAAA
* * **
130386 TAAATTAAATTAAAATTCAAAAGC
1 TAAATCAAAATAAAATGAAAAAGC
130410 TAAATCAAAATAAAATGAAAAA
1 TAAATCAAAATAAAATGAAAAA
130432 TAAAGAGATT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (24 bp):
TAAATCAAAATAAAATGAAAAAGC
Found at i:130813 original size:11 final size:13
Alignment explanation
Indices: 130787--130818 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
130777 ATTTCAAGCA
130787 AAAACAGAAGAAG
1 AAAACAGAAGAAG
130800 AAAACA-AA-AAG
1 AAAACAGAAGAAG
130811 AAAACAGA
1 AAAACAGA
130819 GAAACATGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.50
12 3 0.17
13 6 0.33
ACGTcount: A:0.75, C:0.09, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAACAGAAGAAG
Found at i:132028 original size:37 final size:38
Alignment explanation
Indices: 131954--132039 Score: 122
Period size: 37 Copynumber: 2.3 Consensus size: 38
131944 TTTAAGAAAA
* *
131954 ATCTCAAGTGAGATAAATATTATGTTTCGAGTGAAACT
1 ATCTCAAGCGAGATAAATATTATGTTTCGAGTAAAACT
*
131992 ATCTCAAGCGAGATAAA-ATCT-TTTTTCGAGTAAAACT
1 ATCTCAAGCGAGATAAATAT-TATGTTTCGAGTAAAACT
132029 ATCTCAAGCGA
1 ATCTCAAGCGA
132040 TAAGTTGATC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 27 0.61
38 17 0.39
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.31
Consensus pattern (38 bp):
ATCTCAAGCGAGATAAATATTATGTTTCGAGTAAAACT
Found at i:132643 original size:109 final size:109
Alignment explanation
Indices: 132492--132910 Score: 519
Period size: 109 Copynumber: 3.8 Consensus size: 109
132482 TTTCAGTTAT
* * *
132492 CATCAAGAAACCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTTG-AATAATCATCAAGA
1 CATCAAGAAACCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATTCTTTAGAAATCATCATCAAGA
* * *
132556 AACCCCTCAAAATCAAGCTTTGTTTCTAAAAACCCATTTGAAAA
66 AACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
* * *
132600 CATCAAGAAACCCATAAAAATTAGGCTTAGTTTCTTTTAAAAATTCATT-GAAATCATCATCAAG
1 CATCAAGAAACCC-TAAAAATTAGGCTTAGCTTCTTTAAAAAATTCTTTAGAAATCATCATCAAG
* * *
132664 AAACCCCTGAATATCAAGCTTAGTTTCTTAAAAAATTCTTTTGAAAA
65 AAACCCCTGAAAATCAAGCTTAGTTTC-T-AAAAACTCATTTGAAAA
* * * *
132711 CATAAAAAAACACCT-AAAATTAGGCTTAGCTTCTCTGAAAAAATTCTTTAGAAATGATC-TCAA
1 CATCAAGAAAC-CCTAAAAATTAGGCTTAGCTTCT-TTAAAAAATTCTTTAGAAATCATCATCAA
* * *
132774 GAAAGCCCTGAAAATTAAGCTTAATTTCTAAAAACTCATTTGAAAA
64 GAAACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
* * *
132820 CATCAAGAAAACTCTAAAAA-TAGGCTTAGCTTCTTTTAAGAAATTCTTGA-AAATCATCATCAA
1 CATCAAG-AAACCCTAAAAATTAGGCTTAGCTTC-TTTAAAAAATTCTTTAGAAATCATCATCAA
*
132883 G-AACCTCTGAAAATCAAGCTTAGTTTCT
64 GAAACCCCTGAAAATCAAGCTTAGTTTCT
132911 TTAAAATTTC
Statistics
Matches: 265, Mismatches: 35, Indels: 22
0.82 0.11 0.07
Matches are distributed among these distances:
108 44 0.17
109 119 0.45
110 29 0.11
111 63 0.24
112 10 0.04
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (109 bp):
CATCAAGAAACCCTAAAAATTAGGCTTAGCTTCTTTAAAAAATTCTTTAGAAATCATCATCAAGA
AACCCCTGAAAATCAAGCTTAGTTTCTAAAAACTCATTTGAAAA
Found at i:132928 original size:219 final size:219
Alignment explanation
Indices: 132499--132929 Score: 631
Period size: 220 Copynumber: 2.0 Consensus size: 219
132489 TATCATCAAG
*
132499 AAACCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTTGAATAATCATCAAGAAACCCCTC
1 AAACCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTAGAATAATCATCAAGAAACCCCTC
**
132564 AAAATCAAGCTTTGTTTCTAAAAACCCATTTGAAAACATCAAGAAACCCATAAAAATTAGGCTTA
66 AAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAACCCATAAAAATTAGGCTTA
* *
132629 GTTTCTTTTAAAAATTCATTGAAATCATCATCAAGAAACCCCTGAATATCAAGCTTAGTTTCTTA
131 GCTTCTTTTAAAAATTCATTGAAATCATCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTA
132694 AAAAATTCTTTTGAAAACATAAAA
196 AAAAATTCTTTTGAAAACATAAAA
* * *
132718 AAACACCT-AAAATTAGGCTTAGCTTCTCTGAAAAAATTCTTTAGAAATGATC-TCAAGAAAGCC
1 AAAC-CCTAAAAATTAGGCTTAGCTTCT-TAAAAAAATTCTTTAG-AATAATCATCAAGAAACCC
* * * *
132781 CTGAAAATTAAGCTTAATTTCTAAAAACTCATTTGAAAACATCAAGAAAACTC-TAAAAA-TAGG
63 CTCAAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAG-AAACCCATAAAAATTAGG
*
132844 CTTAGCTTCTTTTAAGAAATTC-TTGAAAATCATCATCAAG-AACCTCTGAAAATCAAGCTTAGT
127 CTTAGCTTCTTTTAA-AAATTCATTG-AAATCATCATCAAGAAACCCCTGAAAATCAAGCTTAGT
* *
132907 TTCTTTAAAATTTCTTTTGAAAA
190 TTCTTAAAAAATTCTTTTGAAAA
132930 TATCTTGTAA
Statistics
Matches: 191, Mismatches: 15, Indels: 12
0.88 0.07 0.06
Matches are distributed among these distances:
219 86 0.45
220 94 0.49
221 11 0.06
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (219 bp):
AAACCCTAAAAATTAGGCTTAGCTTCTTAAAAAAATTCTTTAGAATAATCATCAAGAAACCCCTC
AAAATCAAGCTTAATTTCTAAAAACCCATTTGAAAACATCAAGAAACCCATAAAAATTAGGCTTA
GCTTCTTTTAAAAATTCATTGAAATCATCATCAAGAAACCCCTGAAAATCAAGCTTAGTTTCTTA
AAAAATTCTTTTGAAAACATAAAA
Found at i:137541 original size:14 final size:14
Alignment explanation
Indices: 137509--137574 Score: 69
Period size: 14 Copynumber: 4.4 Consensus size: 14
137499 GATTAATTTT
*
137509 AAAAAATAAAATATC
1 AAAAAATAAAATA-A
137524 AAAAAATAAAATAA
1 AAAAAATAAAATAA
**
137538 AAAACGTAAAATAA
1 AAAAAATAAAATAA
137552 AAACAATATAAAATAA
1 AAA-AA-ATAAAATAA
137568 ACAAAAA
1 A-AAAAA
137575 ATATGAGGAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
14 15 0.35
15 15 0.35
16 11 0.26
17 2 0.05
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (14 bp):
AAAAAATAAAATAA
Done.