Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006353.1 Hibiscus syriacus cultivar Beakdansim tig00015203_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: 83318
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:50 original size:23 final size:24
Alignment explanation
Indices: 1--53 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
* *
1 GTAGAAATGTCCCGAAATGACCAC
1 GTAGAAATATCCCGAAAGGACCAC
* *
25 GTAGAATTATCCCG-AAGGACCGC
1 GTAGAAATATCCCGAAAGGACCAC
48 GTAGAA
1 GTAGAA
54 CCCTCGACTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.17
Consensus pattern (24 bp):
GTAGAAATATCCCGAAAGGACCAC
Found at i:146 original size:12 final size:14
Alignment explanation
Indices: 125--209 Score: 72
Period size: 12 Copynumber: 6.1 Consensus size: 14
115 ACATTTTTAC
125 CATT-TCACATAG-
1 CATTATCACATAGA
137 C-TTATCACATAGA
1 CATTATCACATAGA
*
150 CATGTATTCATATAGA
1 CAT-TA-TCACATAGA
*
166 CCATTTTCACATAG-
1 -CATTATCACATAGA
180 C-TTATCACATAGA
1 CATTATCACATAGA
193 CATGTATTCACATAGA
1 CAT-TA-TCACATAGA
209 C
1 C
210 CATTTCATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
11 2 0.03
12 19 0.32
13 3 0.05
14 2 0.03
15 11 0.19
16 19 0.32
17 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (14 bp):
CATTATCACATAGA
Found at i:166 original size:16 final size:15
Alignment explanation
Indices: 128--209 Score: 79
Period size: 16 Copynumber: 5.7 Consensus size: 15
118 TTTTTACCAT
128 TTCACATAG-C-TTA
1 TTCACATAGACATTA
141 -TCACATAGACATGTA
1 TTCACATAGACAT-TA
*
156 TTCATATAGACCATT-
1 TTCACATAGA-CATTA
171 TTCACATAG-C-TTA
1 TTCACATAGACATTA
184 -TCACATAGACATGTA
1 TTCACATAGACAT-TA
199 TTCACATAGAC
1 TTCACATAGAC
210 CATTTCATTA
Statistics
Matches: 57, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
12 18 0.32
13 3 0.05
14 2 0.04
15 12 0.21
16 19 0.33
17 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (15 bp):
TTCACATAGACATTA
Found at i:178 original size:43 final size:43
Alignment explanation
Indices: 123--214 Score: 168
Period size: 43 Copynumber: 2.2 Consensus size: 43
113 TTACATTTTT
*
123 ACCA-TTTCACATAGCTTATCACATAGACATGTATTCATATAG
1 ACCATTTTCACATAGCTTATCACATAGACATGTATTCACATAG
165 ACCATTTTCACATAGCTTATCACATAGACATGTATTCACATAG
1 ACCATTTTCACATAGCTTATCACATAGACATGTATTCACATAG
208 ACCATTT
1 ACCATTT
215 CATTATCACA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 4 0.08
43 44 0.92
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.34
Consensus pattern (43 bp):
ACCATTTTCACATAGCTTATCACATAGACATGTATTCACATAG
Found at i:1377 original size:3 final size:3
Alignment explanation
Indices: 1369--1418 Score: 77
Period size: 3 Copynumber: 17.0 Consensus size: 3
1359 ACCAAGCACT
1369 AGA AGA AGA AG- AGA AGA AGA AGA AGA AGA AGA A-A AGAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA
1413 AGA AGA
1 AGA AGA
1419 GACTAAGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2346 original size:100 final size:101
Alignment explanation
Indices: 2175--2359 Score: 230
Period size: 100 Copynumber: 1.8 Consensus size: 101
2165 TTGAATTCCT
* * ** * * *
2175 TCCCCTTGAACTTGAAGGCGTCATGTCATACGGGTTTTGAACTGAGTGTTGTGTCGTAAGTATCT
1 TCCCCTGGAACTTGAAGGCATCATGTCATACGGGTACTGAACAGAGTGTTGTGTCGTAAGCATAT
*
2240 CCACATTGAGGTCGAAGAAACTCGCAGTTGAATGTC
66 CCACATTGAGGTCAAAGAAACTCGCAGTTGAATGTC
* * * *
2276 TCCCCTGGAACTTGAAGGCATCGTGTCA-ATGGGTACTGAACAGATTGTTGTGTCG-AGGGCATA
1 TCCCCTGGAACTTGAAGGCATCATGTCATACGGGTACTGAACAGAGTGTTGTGTCGTA-AGCATA
*
2339 TCCACATTTAGGTCAAAGAAA
65 TCCACATTGAGGTCAAAGAAA
2360 TTGGTAGATG
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
99 1 0.01
100 44 0.63
101 25 0.36
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (101 bp):
TCCCCTGGAACTTGAAGGCATCATGTCATACGGGTACTGAACAGAGTGTTGTGTCGTAAGCATAT
CCACATTGAGGTCAAAGAAACTCGCAGTTGAATGTC
Found at i:4173 original size:18 final size:19
Alignment explanation
Indices: 4150--4186 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4140 CAATAATTTT
4150 TTAAAAA-ATATAAAAATA
1 TTAAAAATATATAAAAATA
4168 TTAAAAATTATATAAAAAT
1 TTAAAAA-TATATAAAAAT
4187 TTATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TTAAAAATATATAAAAATA
Found at i:5255 original size:2 final size:2
Alignment explanation
Indices: 5248--5279 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5238 ATCACATGTA
5248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5280 TATTAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8523 original size:24 final size:23
Alignment explanation
Indices: 8464--8547 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 23
8454 ACAACTCATA
8464 TTTCATTATTCTTCTTATTTTTAAAGT
1 TTTCATT-TTCTT-TTA-TTTT-AAGT
* *
8491 TCTTTATTTTCTTTTCTTTTCAAGT
1 T-TTCATTTTCTTTTATTTT-AAGT
*
8516 TTTCATTTTTATTTTATTTTAAGT
1 TTTCA-TTTTCTTTTATTTTAAGT
8540 TTT-ATTTT
1 TTTCATTTT
8548 TAAACATGCT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.08
23 1 0.02
24 10 0.20
25 21 0.43
26 2 0.04
27 6 0.12
28 5 0.10
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTCATTTTCTTTTATTTTAAGT
Found at i:8548 original size:24 final size:25
Alignment explanation
Indices: 8497--8549 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
8487 AAGTTCTTTA
* *
8497 TTTTCTTTTCTTTTCAAGTTTTCAT
1 TTTTATTTTATTTTCAAGTTTTCAT
8522 TTTTATTTTATTTT-AAGTTTT-AT
1 TTTTATTTTATTTTCAAGTTTTCAT
8545 TTTTA
1 TTTTA
8550 AACATGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 7 0.27
24 7 0.27
25 12 0.46
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTTATTTTATTTTCAAGTTTTCAT
Found at i:8550 original size:13 final size:13
Alignment explanation
Indices: 8502--8550 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
8492 CTTTATTTTC
* *
8502 TTTTCTTTTCAAG
1 TTTTATTTTTAAG
8515 TTTTCATTTTT-A-
1 TTTT-ATTTTTAAG
8527 TTTTA-TTTTAAG
1 TTTTATTTTTAAG
8539 TTTTATTTTTAA
1 TTTTATTTTTAA
8551 ACATGCTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 11 0.37
14 4 0.13
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.69
Consensus pattern (13 bp):
TTTTATTTTTAAG
Found at i:9160 original size:17 final size:17
Alignment explanation
Indices: 9138--9180 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
9128 TTTTCTTTAT
9138 TTTTTACT-TTAAATCAC
1 TTTTTACTATTAAATC-C
* *
9155 TTTTTATTATTTAATCC
1 TTTTTACTATTAAATCC
9172 TTTTTACTA
1 TTTTTACTA
9181 AACCCTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.26, C:0.14, G:0.00, T:0.60
Consensus pattern (17 bp):
TTTTTACTATTAAATCC
Found at i:12903 original size:24 final size:24
Alignment explanation
Indices: 12871--12923 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
12861 TTGGTAAAGT
12871 TGAAAGATTTGGTAAAGTTAGTGG
1 TGAAAGATTTGGTAAAGTTAGTGG
12895 TGAAAGATTTGGTAAAGTTAGTGG
1 TGAAAGATTTGGTAAAGTTAGTGG
12919 TGAAA
1 TGAAA
12924 TTTGCAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (24 bp):
TGAAAGATTTGGTAAAGTTAGTGG
Found at i:12933 original size:22 final size:24
Alignment explanation
Indices: 12871--12934 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 24
12861 TTGGTAAAGT
**
12871 TGAAAGATTTGGTAAAGTTAGTGG
1 TGAAAGATTTGCAAAAGTTAGTGG
**
12895 TGAAAGATTTGGTAAAGTTAGTGG
1 TGAAAGATTTGCAAAAGTTAGTGG
12919 TG-AA-ATTTGCAAAAGT
1 TGAAAGATTTGCAAAAGT
12935 GTAATGTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.26
23 2 0.05
24 26 0.68
ACGTcount: A:0.36, C:0.02, G:0.30, T:0.33
Consensus pattern (24 bp):
TGAAAGATTTGCAAAAGTTAGTGG
Found at i:15140 original size:48 final size:48
Alignment explanation
Indices: 15069--15168 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
15059 CTCATCACTC
15069 CCGAGTAGGGTTGTAAAAAGTTGACCTAG-CCTGCAAAATTGACTAAAA
1 CCGAGTAGGGTTGTAAAAAGTTGACC-AGACCTGCAAAATTGACTAAAA
*
15117 CCGAGTAGGGTTGTAAAAAGTTGACCCGACCTGCAAAATTGACTAAAA
1 CCGAGTAGGGTTGTAAAAAGTTGACCAGACCTGCAAAATTGACTAAAA
15165 CCGA
1 CCGA
15169 CTAGAGTCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (48 bp):
CCGAGTAGGGTTGTAAAAAGTTGACCAGACCTGCAAAATTGACTAAAA
Found at i:15443 original size:16 final size:16
Alignment explanation
Indices: 15396--15448 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
15386 GGTATTACCC
15396 GACCTATTTTTAACCT
1 GACCTATTTTTAACCT
* ** **
15412 GACCTGTGATGGACCT
1 GACCTATTTTTAACCT
15428 GACCTATTTTTAACCT
1 GACCTATTTTTAACCT
15444 GACCT
1 GACCT
15449 GTAAATGATC
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (16 bp):
GACCTATTTTTAACCT
Found at i:15477 original size:16 final size:16
Alignment explanation
Indices: 15408--15477 Score: 59
Period size: 16 Copynumber: 4.4 Consensus size: 16
15398 CCTATTTTTA
* *
15408 ACCTGACCTGTGATGG
1 ACCTGACCTGTTATTG
* * *
15424 ACCTGACCTATTTTTA
1 ACCTGACCTGTTATTG
* *
15440 ACCTGACCTGTAAATG
1 ACCTGACCTGTTATTG
* *
15456 ATCTGACTTGTTATTG
1 ACCTGACCTGTTATTG
15472 ACCTGA
1 ACCTGA
15478 TCTGATATTT
Statistics
Matches: 39, Mismatches: 15, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (16 bp):
ACCTGACCTGTTATTG
Found at i:15522 original size:17 final size:16
Alignment explanation
Indices: 15458--15523 Score: 62
Period size: 16 Copynumber: 4.1 Consensus size: 16
15448 TGTAAATGAT
* *
15458 CTGACTTGTTATTGAC
1 CTGACTTGATATTTAC
*
15474 CTGA-TCTGATATTTAT
1 CTGACT-TGATATTTAC
*
15490 CTGACTTGACATTTAC
1 CTGACTTGATATTTAC
*
15506 CTGACTTATATATTTAC
1 CTGACTT-GATATTTAC
15523 C
1 C
15524 ATGGACGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
15 1 0.03
16 30 0.75
17 9 0.22
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (16 bp):
CTGACTTGATATTTAC
Found at i:16062 original size:12 final size:11
Alignment explanation
Indices: 16036--16075 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
16026 GATAATGATA
*
16036 ATTTAAATAAC
1 ATTTGAATAAC
*
16047 ATTTGATATAAA
1 ATTTGA-ATAAC
16059 ATTTGAATAAC
1 ATTTGAATAAC
16070 ATTTGA
1 ATTTGA
16076 GTTAATTCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.40
Consensus pattern (11 bp):
ATTTGAATAAC
Found at i:16835 original size:20 final size:20
Alignment explanation
Indices: 16802--16840 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
16792 AATATTAATA
16802 TAATTAATATTACTTTATAT
1 TAATTAATATTACTTTATAT
16822 TAATATAATA-TACTTTATA
1 TAAT-TAATATTACTTTATA
16841 ATTTGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATTAATATTACTTTATAT
Found at i:16899 original size:24 final size:25
Alignment explanation
Indices: 16854--16900 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
16844 TGTAATTAAT
**
16854 ATTAATATAAAATATAGTCTATAAA
1 ATTAATATAAAATATAAACTATAAA
*
16879 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
16901 TTTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAA
Found at i:16930 original size:66 final size:64
Alignment explanation
Indices: 16859--17005 Score: 174
Period size: 66 Copynumber: 2.2 Consensus size: 64
16849 TTAATATTAA
* *
16859 TATAAAATATAGTCT-ATAAAATTAATATTAATATAAACTATATTTTATAAATTATATAGCATAG
1 TATAAAATATAGT-TAATAAAATTAATATTAATAT--ACTATAGTTTATAAACTATATAGCATAG
16923 TT
63 TT
* *
16925 TATAAACTATAGTTAATAAAATTAATATTAATATAGTATAGTTTATAAACTATATA-CTATA-TT
1 TATAAAATATAGTTAATAAAATTAATATTAATATACTATAGTTTATAAACTATATAGC-ATAGTT
*
16988 AATATAAATTATAGTTAA
1 --TATAAAATATAGTTAA
17006 GTTAATTAAC
Statistics
Matches: 72, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
63 3 0.04
64 22 0.31
65 16 0.22
66 31 0.43
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (64 bp):
TATAAAATATAGTTAATAAAATTAATATTAATATACTATAGTTTATAAACTATATAGCATAGTT
Found at i:16936 original size:14 final size:14
Alignment explanation
Indices: 16919--16978 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
16909 ATTATATAGC
*
16919 ATAGTTTATAAACT
1 ATAGTTAATAAACT
*
16933 ATAGTTAATAAAATT
1 ATAGTTAAT-AAACT
* *
16948 AATA-TTAATATAGT
1 -ATAGTTAATAAACT
*
16962 ATAGTTTATAAACT
1 ATAGTTAATAAACT
16976 ATA
1 ATA
16979 TACTATATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 21 0.58
15 9 0.25
16 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (14 bp):
ATAGTTAATAAACT
Found at i:17014 original size:65 final size:64
Alignment explanation
Indices: 16775--17005 Score: 197
Period size: 65 Copynumber: 3.6 Consensus size: 64
16765 ATTTATATTA
* * * * * *
16775 ATAAACTATTTA-TA-ATTAATATTAATATAATTAATATTACTTTATATTAATATAATATACTTT
1 ATAAACTATATACTATATTAATATAAATATAGTTAATA-AAATTAATATTAATATAATATACTTT
** * *
16838 ATAATTTGTA-ATTAATATTAATATAAAATATAGTCT-ATAAAATTAATATTAATATAAACTATA
1 ATAAACTATATACT-ATATTAATAT-AAATATAGT-TAATAAAATTAATATTAATAT-AA-TATA
*
16901 TTTT
61 CTTT
* * *
16905 ATAAATTATATAGC-ATAGTT--TATAAACTATAGTTAATAAAATTAATATTAATATAGTATAGT
1 ATAAACTATATA-CTATA-TTAATATAAA-TATAGTTAATAAAATTAATATTAATATAATATACT
16967 TT
63 TT
16969 ATAAACTATATACTATATTAATATAAATTATAGTTAA
1 ATAAACTATATACTATATTAATATAAA-TATAGTTAA
17006 GTTAATTAAC
Statistics
Matches: 136, Mismatches: 17, Indels: 28
0.75 0.09 0.15
Matches are distributed among these distances:
62 1 0.01
63 10 0.07
64 22 0.16
65 41 0.30
66 40 0.29
67 19 0.14
68 3 0.02
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (64 bp):
ATAAACTATATACTATATTAATATAAATATAGTTAATAAAATTAATATTAATATAATATACTTT
Found at i:17072 original size:21 final size:21
Alignment explanation
Indices: 17043--17095 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
17033 AGTACATTAA
* *
17043 TATAAACTATAGTTTATAAAT
1 TATAAACTATAGGTTATAAAG
*
17064 TATATACTATAGGTTATAAAG
1 TATAAACTATAGGTTATAAAG
17085 TATAAACTATA
1 TATAAACTATA
17096 TAGTACACTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.40
Consensus pattern (21 bp):
TATAAACTATAGGTTATAAAG
Found at i:17131 original size:21 final size:20
Alignment explanation
Indices: 17041--17131 Score: 76
Period size: 21 Copynumber: 4.3 Consensus size: 20
17031 ATAGTACATT
17041 AATATAAACTATAGTTTATA
1 AATATAAACTATAGTTTATA
* *
17061 AATTATATACTATAGGTTATA
1 AA-TATAAACTATAGTTTATA
* *
17082 AAGTATAAACTATA-TAGTACA
1 AA-TATAAACTATAGT-TTATA
*
17103 CTAATATAAACTATTGTTTATA
1 --AATATAAACTATAGTTTATA
17125 AACTATA
1 AA-TATA
17132 GGTTACATAT
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
20 4 0.07
21 35 0.64
22 13 0.24
23 3 0.05
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (20 bp):
AATATAAACTATAGTTTATA
Found at i:17177 original size:2 final size:2
Alignment explanation
Indices: 17170--17261 Score: 96
Period size: 2 Copynumber: 45.0 Consensus size: 2
17160 AAATAGATTG
* **
17170 TA TA TA TA CA TA TA CTA TA GG T- 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
* * *
17212 TA TA TA TA TA TA TA TA TA TA TA TA TA CTA TA GA TA GTT TA TA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA
17256 TA TA TA
1 TA TA TA
17262 GTTTACATGT
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
1 1 0.01
2 69 0.92
3 5 0.07
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.46
Consensus pattern (2 bp):
TA
Found at i:17189 original size:24 final size:23
Alignment explanation
Indices: 17138--17235 Score: 103
Period size: 24 Copynumber: 4.3 Consensus size: 23
17128 TATAGGTTAC
17138 ATATATAG-TT-TATATA-ACAT
1 ATATATAGATTATATATATACAT
* *
17158 ATAAATAGATTGTATATATACAT
1 ATATATAGATTATATATATACAT
* *
17181 ATACTATAGGTTATATATATATAT
1 ATA-TATAGATTATATATATACAT
* *
17205 ATATATATATATATATATATATAT
1 ATATATAGAT-TATATATATACAT
17229 ATATATA
1 ATATATA
17236 TACTATAGAT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
20 7 0.11
21 2 0.03
22 6 0.09
23 12 0.18
24 39 0.59
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (23 bp):
ATATATAGATTATATATATACAT
Found at i:17360 original size:16 final size:16
Alignment explanation
Indices: 17339--17369 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17329 TACATATATA
17339 ATTTATATAAACTATT
1 ATTTATATAAACTATT
17355 ATTTATATAAACTAT
1 ATTTATATAAACTAT
17370 ATATGAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTATATAAACTATT
Found at i:17415 original size:7 final size:7
Alignment explanation
Indices: 17403--17442 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
17393 TACATATATA
17403 GTTTAGG
1 GTTTAGG
17410 GTTTAGG
1 GTTTAGG
* *
17417 GTCTAAG
1 GTTTAGG
*
17424 GTTTAGA
1 GTTTAGG
17431 GTTTAGG
1 GTTTAGG
17438 GTTTA
1 GTTTA
17443 TAATTTAAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.20, C:0.03, G:0.35, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:17557 original size:2 final size:2
Alignment explanation
Indices: 17550--17636 Score: 165
Period size: 2 Copynumber: 43.0 Consensus size: 2
17540 CTTTATAGTT
17550 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CTA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA
17635 TA
1 TA
17637 CATAGTTTAT
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 82 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:17709 original size:21 final size:21
Alignment explanation
Indices: 17685--17745 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
17675 AGTTTAGGGG
*
17685 TTAGGGTTTAGAGTTTAAGCT
1 TTAGGGTTTAGAGTTTAAGAT
* * ***
17706 TTAGTGTTTAGGGTTCCTGAT
1 TTAGGGTTTAGAGTTTAAGAT
17727 TTAGGGTTTAGAGTTTAAG
1 TTAGGGTTTAGAGTTTAAG
17746 TTTTCTATAA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTAAGAT
Found at i:17743 original size:14 final size:14
Alignment explanation
Indices: 17685--17743 Score: 59
Period size: 14 Copynumber: 4.2 Consensus size: 14
17675 AGTTTAGGGG
17685 TTAGGGTTTAGAGT
1 TTAGGGTTTAGAGT
* * *
17699 TTAAGCTTTAGTGT
1 TTAGGGTTTAGAGT
17713 TTAGGGTTCCT-GA-T
1 TTAGGGTT--TAGAGT
17727 TTAGGGTTTAGAGT
1 TTAGGGTTTAGAGT
17741 TTA
1 TTA
17744 AGTTTTCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
12 1 0.03
13 2 0.06
14 30 0.86
15 1 0.03
16 1 0.03
ACGTcount: A:0.20, C:0.05, G:0.29, T:0.46
Consensus pattern (14 bp):
TTAGGGTTTAGAGT
Found at i:17898 original size:45 final size:44
Alignment explanation
Indices: 17799--17898 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 44
17789 ATAGTATTTC
*
17799 TATAATATATATATAGATTACTTATATTAGTTATGCATACACAA
1 TATAATATATATATAGATTACTTATATTAGTTATACATACACAA
* *
17843 TATATTTATATATATAGATTACTTATATTAGTTATACATACATATA
1 TATA-ATATATATATAGATTACTTATATTAGTTATACATACACA-A
*
17889 TATACTATAT
1 TATAATATAT
17899 TAATATAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
44 4 0.08
45 41 0.82
46 5 0.10
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (44 bp):
TATAATATATATATAGATTACTTATATTAGTTATACATACACAA
Found at i:17936 original size:81 final size:81
Alignment explanation
Indices: 17842--18038 Score: 238
Period size: 81 Copynumber: 2.4 Consensus size: 81
17832 TGCATACACA
* *
17842 ATATATTTATATATA-TAGATTACTTATATTAG-TTATACATACATATATATACTATATTAATAT
1 ATATATTT-TATATAGTAGA-TACATATA-TAGTTTATACATACATATATACACTATATTAATAT
17905 AAATTATAATTTATAAACT
63 AAATTATAATTTATAAACT
** * *
17924 ATATATTTTATATAGTTTATACATATATAGTTTATATATATATATATACACTATATTAATATAAA
1 ATATATTTTATATAGTAGATACATATATAGTTTATACATACATATATACACTATATTAATATAAA
*
17989 TTATAGTTTATAAACT
66 TTATAATTTATAAACT
** * *
18005 ATATACTTTT-TATAGTTTATGCATGTATAGTTTA
1 ATATA-TTTTATATAGTAGATACATATATAGTTTA
18039 CATGCATAGT
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
80 3 0.03
81 86 0.83
82 14 0.14
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (81 bp):
ATATATTTTATATAGTAGATACATATATAGTTTATACATACATATATACACTATATTAATATAAA
TTATAATTTATAAACT
Found at i:17962 original size:13 final size:13
Alignment explanation
Indices: 17932--18087 Score: 54
Period size: 15 Copynumber: 11.5 Consensus size: 13
17922 CTATATATTT
17932 TATATAGTTTATACA
1 TATATAGTTTAT--A
17947 TATATAGTTTATA
1 TATATAGTTTATA
*
17960 TATATA-TATATA
1 TATATAGTTTATA
*
17972 CACTATA-TTAATATA
1 TA-TATAGTT--TATA
*
17987 AATTATAGTTTATAAA
1 TA-TATAGTTTAT--A
*
18003 CTATATA-CTT-T-
1 -TATATAGTTTATA
18014 T-TATAGTTTATGCA
1 TATATAGTTTAT--A
* *
18028 TGTATAGTTTACA
1 TATATAGTTTATA
**
18041 TGCATAGTTTATA
1 TATATAGTTTATA
18054 TATATAGTTCATATA
1 TATATAGTT--TATA
* * *
18069 AACATAATTTATA
1 TATATAGTTTATA
18082 TATATA
1 TATATA
18088 TAGCTTATAA
Statistics
Matches: 108, Mismatches: 18, Indels: 32
0.68 0.11 0.20
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 1 0.01
12 6 0.06
13 39 0.36
14 5 0.05
15 42 0.39
16 7 0.06
17 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.47
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:17969 original size:17 final size:15
Alignment explanation
Indices: 17932--17967 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17922 CTATATATTT
17932 TATATAGTTTATACA
1 TATATAGTTTATACA
*
17947 TATATAGTTTATATA
1 TATATAGTTTATACA
17962 TATATA
1 TATATA
17968 TATACACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:18035 original size:15 final size:14
Alignment explanation
Indices: 18015--18062 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
18005 ATATACTTTT
18015 TATAGTTTATGCATG
1 TATAGTTTAT-CATG
18030 TATAGTTTA-CATG
1 TATAGTTTATCATG
* *
18043 CATAGTTTAT-ATA
1 TATAGTTTATCATG
18056 TATAGTT
1 TATAGTT
18063 CATATAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 20 0.69
15 9 0.31
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (14 bp):
TATAGTTTATCATG
Found at i:18080 original size:81 final size:81
Alignment explanation
Indices: 17866--18089 Score: 262
Period size: 81 Copynumber: 2.8 Consensus size: 81
17856 ATAGATTACT
17866 TATATTAGTTATACATAC--ATATATATACTATATTAATATAAATTATAATTTATAAACTATATA
1 TATA-TAGTT-TACATACATATATATATACTATATTAATATAAATTATAATTTATAAACTATATA
17929 TTTTATATAGTTTATACA
64 TTTTATATAGTTTATACA
* * * *
17947 TATATAGTTTATATATATATATATACACTATATTAATATAAATTATAGTTTATAAACTATATACT
1 TATATAGTTTACATACATATATATATACTATATTAATATAAATTATAATTTATAAACTATATA-T
*
18012 TTT-TATAGTTTATGCA
65 TTTATATAGTTTATACA
* * * * * *
18028 TGTATAGTTTACATGCATAGTTTATATA-TATAGTTCATATAAA-CATAATTTATATA-TATATA
1 TATATAGTTTACATACATA-TATATATACTATA-TTAATATAAATTATAATTTATAAACTATATA
18090 GCTTATAATA
Statistics
Matches: 123, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
79 5 0.04
80 11 0.09
81 88 0.72
82 19 0.15
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (81 bp):
TATATAGTTTACATACATATATATATACTATATTAATATAAATTATAATTTATAAACTATATATT
TTATATAGTTTATACA
Found at i:18095 original size:15 final size:15
Alignment explanation
Indices: 18050--18136 Score: 66
Period size: 15 Copynumber: 5.4 Consensus size: 15
18040 ATGCATAGTT
*
18050 TATATATATAGTTCA
1 TATATATATAGTTTA
* * *
18065 TATAAACATAATTTA
1 TATATATATAGTTTA
*
18080 TATATATATAGCTTA
1 TATATATATAGTTTA
18095 TAATAATTATATAGTTTA
1 T-AT-A-TATATAGTTTA
*
18113 TAATATAAATGTAGTTTA
1 T-ATAT--ATATAGTTTA
18131 TATATA
1 TATATA
18137 AACTTATATT
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
15 24 0.42
16 3 0.05
17 6 0.11
18 24 0.42
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (15 bp):
TATATATATAGTTTA
Found at i:18148 original size:17 final size:16
Alignment explanation
Indices: 18110--18162 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
18100 ATTATATAGT
18110 TTATAATATAAATGTAGT-
1 TTAT-ATATAAAT-TA-TA
18128 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
18145 TTATATATATATTATA
1 TTATATATAAATTATA
18161 TT
1 TT
18163 TTTTTCAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
16 8 0.25
17 19 0.59
18 5 0.16
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:21149 original size:11 final size:11
Alignment explanation
Indices: 21133--21158 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21123 TAAAAGTATG
21133 ATTTATGTCTT
1 ATTTATGTCTT
21144 ATTTATGTCTT
1 ATTTATGTCTT
21155 ATTT
1 ATTT
21159 CCATAATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.08, G:0.08, T:0.65
Consensus pattern (11 bp):
ATTTATGTCTT
Found at i:47488 original size:20 final size:20
Alignment explanation
Indices: 47458--47508 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
47448 CCACCAACTT
47458 CCTTCAAACTTTCAATTGAGC
1 CCTT-AAACTTTCAATTGAGC
*
47479 CCTTAAACTTTCAATTGAGT
1 CCTTAAACTTTCAATTGAGC
47499 CCTTAAACTT
1 CCTTAAACTT
47509 ATAAACTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (20 bp):
CCTTAAACTTTCAATTGAGC
Found at i:52037 original size:2 final size:2
Alignment explanation
Indices: 52030--52055 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52020 TTTATATTTA
52030 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
52056 GAAGGGTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53131 original size:25 final size:25
Alignment explanation
Indices: 53103--53156 Score: 85
Period size: 23 Copynumber: 2.2 Consensus size: 25
53093 CTAGTAACTT
*
53103 ATTCAGAGCAAAACAGTGTTGACTG
1 ATTCAGAGCAAAACAGTGCTGACTG
53128 ATTC--AGCAAAACAGTGCTGACTG
1 ATTCAGAGCAAAACAGTGCTGACTG
53151 ATTCAG
1 ATTCAG
53157 CACAGAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 22 0.85
25 4 0.15
ACGTcount: A:0.35, C:0.19, G:0.22, T:0.24
Consensus pattern (25 bp):
ATTCAGAGCAAAACAGTGCTGACTG
Found at i:53137 original size:23 final size:23
Alignment explanation
Indices: 53109--53158 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
53099 ACTTATTCAG
*
53109 AGCAAAACAGTGTTGACTGATTC
1 AGCAAAACAGTGCTGACTGATTC
53132 AGCAAAACAGTGCTGACTGATTC
1 AGCAAAACAGTGCTGACTGATTC
53155 AGCA
1 AGCA
53159 CAGAAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (23 bp):
AGCAAAACAGTGCTGACTGATTC
Found at i:54049 original size:29 final size:27
Alignment explanation
Indices: 53933--54033 Score: 125
Period size: 29 Copynumber: 3.6 Consensus size: 27
53923 TTTTCTTTTG
53933 ATTGTAATTTATAAATAGTTTTGGTATTT
1 ATTGTAATTTATAAA-AG-TTTGGTATTT
*
53962 ATTTTAATTTATAAAAG--TGGTATTT
1 ATTGTAATTTATAAAAGTTTGGTATTT
*
53987 ATTGTAAATTATAGAAAGATTTGGTATTT
1 ATTGTAATTTATA-AAAG-TTTGGTATTT
54016 ATTGTAATTTATAGAAAG
1 ATTGTAATTTATA-AAAG
54034 CTTCGCTATT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
25 19 0.30
26 4 0.06
28 2 0.03
29 39 0.61
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (27 bp):
ATTGTAATTTATAAAAGTTTGGTATTT
Found at i:58147 original size:174 final size:173
Alignment explanation
Indices: 57798--58235 Score: 513
Period size: 174 Copynumber: 2.5 Consensus size: 173
57788 ATTTTAGTGG
* * * * * *
57798 AAAGTAGTTCCTCAAC-ACTACCATGTGGTTGATAGGCCCTCAAGCTGAATGGAATCGAACTCGA
1 AAAGTAGTTCCTC-GCTGCTACCATGCGGTTGATATG-TCTCGAGCTGAATGGAATCGAACTCGA
* * * * *
57862 AAGTTTTAATTGACATATAACCCTTCTTGCCTTGAGTTATGCTATACTAAGCTAAGAGATTACCC
64 AAGTTTT-TTTGACAGATAACCCTTATCGCCTTGAGTTATGCTATACAAAGCTAAGAGATTACCC
* *
57927 CAGATCTTACTCTTGACTTAAAGACCTCGGTTTAAACTTCAACTGA
128 CAGATCTTACTATTGACTTAAAGACCTCGATTTAAACTTCAACTGA
*
57973 AAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGTCATCGAGCAGAATGGAATCGAACTCGAA
1 AAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGTC-TCGAGCTGAATGGAATCGAACTCGAA
* * * * *
58038 AGTTTTTTTGACAGATAACCCTTATCGCTTTTAGTTATGTTGA-ACAAAGCTGAGAGATTGCCCC
65 AGTTTTTTTGACAGATAACCCTTATCGCCTTGAGTTATGCT-ATACAAAGCTAAGAGATTACCCC
* * *
58102 AGATCTTCCTATTGACTTAAATACCTCGATTTAAACTTTAACTGA
129 AGATCTTACTATTGACTTAAAGACCTCGATTTAAACTTCAACTGA
* * ** * * *
58147 AAAGTAGTTCCTCGTTGTTACTGTGCGGTTGATATGCTCTTGAGCTGAATGAAATCGAGCTC-AA
1 AAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATG-TCTCGAGCTGAATGGAATCGAACTCGAA
*
58211 AGGTTTTTGTTGACAGATAGCCCTT
65 A-GTTTTT-TTGACAGATAACCCTT
58236 CTCTCTTTGA
Statistics
Matches: 226, Mismatches: 31, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
173 3 0.01
174 145 0.64
175 78 0.35
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (173 bp):
AAAGTAGTTCCTCGCTGCTACCATGCGGTTGATATGTCTCGAGCTGAATGGAATCGAACTCGAAA
GTTTTTTTGACAGATAACCCTTATCGCCTTGAGTTATGCTATACAAAGCTAAGAGATTACCCCAG
ATCTTACTATTGACTTAAAGACCTCGATTTAAACTTCAACTGA
Found at i:58320 original size:85 final size:85
Alignment explanation
Indices: 58175--58336 Score: 234
Period size: 85 Copynumber: 1.9 Consensus size: 85
58165 TACTGTGCGG
* * * * *
58175 TTGATATGCTCTTGAGCTGAATGAAATCGAGCTCAAAGGTTTTTGTTGACAGATAGCCCTTCTCT
1 TTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGGTTTTAGTTGACAGATAACCCTTCTCG
*
58240 CTTTGAGCTATATTATAAAT
66 CCTTGAGCTATATTATAAAT
* * * *
58260 TTGATATGCCCTTGAGGTGAATGGAATCGAACTCGAAGGTTTTAGTTGATAGATAACCCTTCTCG
1 TTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGGTTTTAGTTGACAGATAACCCTTCTCG
58325 CCTTGAGCTATA
66 CCTTGAGCTATA
58337 CTGTAATAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 67 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (85 bp):
TTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGGTTTTAGTTGACAGATAACCCTTCTCG
CCTTGAGCTATATTATAAAT
Found at i:60102 original size:99 final size:98
Alignment explanation
Indices: 59920--60120 Score: 269
Period size: 99 Copynumber: 2.0 Consensus size: 98
59910 GGACAGCTCA
* * * *
59920 ATATTATAATCACTTTATCAGGCTAGCTGAATCTTATCCATAAAGCCGGTGCATTTAACCAATTG
1 ATATTATAATCACTTTATCAGACTAGCTAAATATTATCCATAAAGCCGGGGCATTTAACCAATTG
* * * * *
59985 CTTTATATAGACATCTCAAGCTTTATTGTATAG
66 CTCTAGATAGACAACTCAAACTTTATTGTATAC
* * *
60018 ATATTATAATCACCTTTATCAGACTAGCTAAATATTATCCATAAAGTCGGGGCGTTTAATCAATT
1 ATATTATAATCA-CTTTATCAGACTAGCTAAATATTATCCATAAAGCCGGGGCATTTAACCAATT
60083 GCTCTAGA-AGGACAACTCAAACTTTATTGTATAC
65 GCTCTAGATA-GACAACTCAAACTTTATTGTATAC
60117 ATAT
1 ATAT
60121 AATATTATAA
Statistics
Matches: 89, Mismatches: 12, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
98 13 0.15
99 76 0.85
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (98 bp):
ATATTATAATCACTTTATCAGACTAGCTAAATATTATCCATAAAGCCGGGGCATTTAACCAATTG
CTCTAGATAGACAACTCAAACTTTATTGTATAC
Found at i:60584 original size:36 final size:36
Alignment explanation
Indices: 60535--60608 Score: 139
Period size: 36 Copynumber: 2.1 Consensus size: 36
60525 TTAAATATCC
60535 TTATAAAAAGAAATATGAGAAAGTTCAAAAAACAAG
1 TTATAAAAAGAAATATGAGAAAGTTCAAAAAACAAG
*
60571 TTATAAAAGGAAATATGAGAAAGTTCAAAAAACAAG
1 TTATAAAAAGAAATATGAGAAAGTTCAAAAAACAAG
60607 TT
1 TT
60609 CAAACAATAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.58, C:0.05, G:0.15, T:0.22
Consensus pattern (36 bp):
TTATAAAAAGAAATATGAGAAAGTTCAAAAAACAAG
Found at i:66551 original size:23 final size:22
Alignment explanation
Indices: 66508--66595 Score: 90
Period size: 23 Copynumber: 4.0 Consensus size: 22
66498 TAATGTCAAA
66508 AAAAGAATAAAATAAAATAAAT
1 AAAAGAATAAAATAAAATAAAT
66530 AAAAGCAA-AAAATAAAACTAAAT
1 AAAAG-AATAAAATAAAA-TAAAT
* * *
66553 AAAATAATGAAATTAAATTAAAT
1 AAAAGAAT-AAAATAAAATAAAT
* *
66576 AAAATAA-AAAATAAGATAAA
1 AAAAGAATAAAATAAAATAAA
66596 AATATAAACA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
21 10 0.18
22 16 0.29
23 23 0.41
24 7 0.12
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAGAATAAAATAAAATAAAT
Found at i:69894 original size:171 final size:173
Alignment explanation
Indices: 69636--69958 Score: 447
Period size: 172 Copynumber: 1.9 Consensus size: 173
69626 GTAGGGACTA
* * * **
69636 TTTTATAAAATTGAAAACAATTAGAGGCCCTTAGTTATAAACTTTTATCGAAAACTAAAAAATAA
1 TTTTATAAAATTGAAAAAAATTAGAGGCCCTTAGATATAAACCTGGA-CGAAAACTAAAAAATAA
* *
69701 GTCCTATAAAACAAATATATATT-CTATTATTTTAAA-AAATAATTTAATAATACAGTAATAAAC
65 GTACTATAAAACAAAAATATATTACTATTATTTTAAATAAATAATTTAATAATACAGTAATAAAC
*
69764 CATAAAAATGATTAAATTGTGAGCCCTTAGTTAAGTATGGAATC
130 CATAAAAATAATTAAATTGTGAGCCCTTAGTTAAGTATGGAATC
* *
69808 TTTTATAAAATTGAAAAAAATTAG-GGACTCTTAGATATAAACCTGGA-GAAAAACTAAGAAATA
1 TTTTATAAAATTGAAAAAAATTAGAGG-CCCTTAGATATAAACCTGGACG-AAAACTAAAAAATA
* * * * *
69871 AGTATTATAAAACAAAAATATATTACTTTTATTTTAAATAATTAATTTAATATTACATTAATAAA
64 AGTACTATAAAACAAAAATATATTACTATTATTTTAAATAAATAATTTAATAATACAGTAATAAA
*
69936 TCATAAAAATAATTAAATTGTGA
129 CCATAAAAATAATTAAATTGTGA
69959 TTTTTCAATT
Statistics
Matches: 131, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
170 1 0.01
171 36 0.27
172 50 0.38
173 44 0.34
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (173 bp):
TTTTATAAAATTGAAAAAAATTAGAGGCCCTTAGATATAAACCTGGACGAAAACTAAAAAATAAG
TACTATAAAACAAAAATATATTACTATTATTTTAAATAAATAATTTAATAATACAGTAATAAACC
ATAAAAATAATTAAATTGTGAGCCCTTAGTTAAGTATGGAATC
Found at i:71556 original size:14 final size:14
Alignment explanation
Indices: 71537--71565 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
71527 GTATTTCTAA
71537 TACATAAATATATC
1 TACATAAATATATC
71551 TACATAAATATATC
1 TACATAAATATATC
71565 T
1 T
71566 TATATTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (14 bp):
TACATAAATATATC
Found at i:71613 original size:25 final size:25
Alignment explanation
Indices: 71579--71629 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
71569 ATTATTACAT
71579 TATATATATATTACGTATCCAACTA
1 TATATATATATTACGTATCCAACTA
71604 TATATATATATTACGTATCCAACTA
1 TATATATATATTACGTATCCAACTA
71629 T
1 T
71630 CCATTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TATATATATATTACGTATCCAACTA
Found at i:72806 original size:42 final size:42
Alignment explanation
Indices: 72720--72807 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
72710 CGATTTAAAT
* * * ***
72720 TCTTCGAATAAAATTAGGGTATTACAATAAGACTATTTGTCA
1 TCTTCGAACAAAATTAGGGTAGTACAAGAAGACTATTAACCA
* *
72762 TCTTCGGACAAAATTAGGGTAGTACAAGAAGATTATTAACCA
1 TCTTCGAACAAAATTAGGGTAGTACAAGAAGACTATTAACCA
72804 TCTT
1 TCTT
72808 TATTGCCTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (42 bp):
TCTTCGAACAAAATTAGGGTAGTACAAGAAGACTATTAACCA
Found at i:74512 original size:13 final size:13
Alignment explanation
Indices: 74494--74520 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
74484 ATGAACTATG
74494 ACAAAATCTCTCT
1 ACAAAATCTCTCT
74507 ACAAAATCTCTCT
1 ACAAAATCTCTCT
74520 A
1 A
74521 AGTTAGTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.30, G:0.00, T:0.30
Consensus pattern (13 bp):
ACAAAATCTCTCT
Found at i:75797 original size:28 final size:27
Alignment explanation
Indices: 75760--75831 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
75750 TTTAATATTT
75760 AAAACTACATTTTTTAAAATCTGTAAAA
1 AAAACTACATTTTTTAAAATCTG-AAAA
*** * * *
75788 AAAACTACATTTAAAAAAATTTGACAT
1 AAAACTACATTTTTTAAAATCTGAAAA
75815 AAAACTACATTTTTTAA
1 AAAACTACATTTTTTAA
75832 TTAATCATAC
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
27 16 0.46
28 19 0.54
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.35
Consensus pattern (27 bp):
AAAACTACATTTTTTAAAATCTGAAAA
Found at i:76036 original size:13 final size:13
Alignment explanation
Indices: 76018--76042 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76008 TTCGGGTAGG
76018 CCCGGAATAGGGA
1 CCCGGAATAGGGA
76031 CCCGGAATAGGG
1 CCCGGAATAGGG
76043 CTTCGACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.28, C:0.24, G:0.40, T:0.08
Consensus pattern (13 bp):
CCCGGAATAGGGA
Found at i:76415 original size:2 final size:2
Alignment explanation
Indices: 76408--76438 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
76398 ATATTTTAAG
76408 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
76439 GCTGAGGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:76713 original size:11 final size:10
Alignment explanation
Indices: 76687--76767 Score: 61
Period size: 10 Copynumber: 8.8 Consensus size: 10
76677 AGAAAATAAC
76687 AAAATAAAGT
1 AAAATAAAGT
76697 AAAATAAAGT
1 AAAATAAAGT
76707 AAAAATAAAG-
1 -AAAATAAAGT
76717 -AAATAAAG-
1 AAAATAAAGT
76725 -AAA-AAA-T
1 AAAATAAAGT
*
76732 AAAATAATG-
1 AAAATAAAGT
*
76741 GAAATAAA-T
1 AAAATAAAGT
*
76750 AAAATAAAAT
1 AAAATAAAGT
*
76760 AAGATAAA
1 AAAATAAA
76768 AAAGGAACAA
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
7 3 0.05
8 14 0.24
9 15 0.25
10 18 0.31
11 9 0.15
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (10 bp):
AAAATAAAGT
Found at i:76720 original size:29 final size:28
Alignment explanation
Indices: 76679--76766 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
76669 AAAAAAGGAG
76679 AAAATAACA-AAATAAAGTAAAATAAAGT
1 AAAATAACAGAAATAAAGTAAAATAAA-T
76707 AAAAATAA-AGAAATAAAG--AAA-AAAT
1 -AAAATAACAGAAATAAAGTAAAATAAAT
**
76732 AAAATAATGGAAATAAA-TAAAATAAAAT
1 AAAATAACAGAAATAAAGTAAAAT-AAAT
*
76760 AAGATAA
1 AAAATAA
76767 AAAAGGAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
24 7 0.14
25 9 0.18
26 6 0.12
27 3 0.06
28 11 0.22
29 15 0.29
ACGTcount: A:0.74, C:0.01, G:0.08, T:0.17
Consensus pattern (28 bp):
AAAATAACAGAAATAAAGTAAAATAAAT
Found at i:76722 original size:19 final size:20
Alignment explanation
Indices: 76687--76734 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
76677 AGAAAATAAC
*
76687 AAAATAAAGTAAAATAAAGTA
1 AAAATAAAG-AAAATAAAGAA
76708 AAAATAAAG-AAATAAAGAA
1 AAAATAAAGAAAATAAAGAA
76727 AAAATAAA
1 AAAATAAA
76735 ATAATGGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 17 0.65
21 9 0.35
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAATAAAGAAAATAAAGAA
Found at i:76787 original size:2 final size:2
Alignment explanation
Indices: 76782--76806 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
76772 GAACAAAAAC
76782 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
76807 ATAAAATGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:78858 original size:32 final size:32
Alignment explanation
Indices: 78817--78918 Score: 138
Period size: 31 Copynumber: 3.2 Consensus size: 32
78807 GAGTCGAGGG
78817 TTTACCTATGTCTTTCGGGACATATGGACAGA
1 TTTACCTATGTCTTTCGGGACATATGGACAGA
78849 TTTACCTATGTCTTTCGGGACATATGGACAG-
1 TTTACCTATGTCTTTCGGGACATATGGACAGA
* ** *
78880 TATACCTATGT-TCTAAGGAACATATGGACA-A
1 TTTACCTATGTCT-TTCGGGACATATGGACAGA
78911 TTTACCTA
1 TTTACCTA
78919 GGTTCTTCAG
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
30 1 0.02
31 31 0.49
32 31 0.49
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTCTTTCGGGACATATGGACAGA
Found at i:78889 original size:31 final size:32
Alignment explanation
Indices: 78819--78890 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
78809 GTCGAGGGTT
*
78819 TACCTATGTCTTTCGGGACATATGGACAGATT
1 TACCTATGTCTTTCGGGACATATGGACAGATA
78851 TACCTATGTCTTTCGGGACATATGGACAG-TA
1 TACCTATGTCTTTCGGGACATATGGACAGATA
78882 TACCTATGT
1 TACCTATGT
78891 TCTAAGGAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 10 0.26
32 29 0.74
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (32 bp):
TACCTATGTCTTTCGGGACATATGGACAGATA
Found at i:78937 original size:31 final size:31
Alignment explanation
Indices: 78817--78938 Score: 117
Period size: 31 Copynumber: 3.9 Consensus size: 31
78807 GAGTCGAGGG
*
78817 TTTACCTATG-TCTTTCGGGACATATGGACAGA
1 TTTACCTATGTTC-TTCAGGACATATGGACA-A
* *
78849 TTTACCTATG-TCTTTCGGGACATATGGACAG
1 TTTACCTATGTTC-TTCAGGACATATGGACAA
* *
78880 TATACCTATGTTC-TAAGGAACATATGGACAA
1 TTTACCTATGTTCTTCAGG-ACATATGGACAA
*
78911 TTTACCTAGGTTCTTCAGGATC-TATGGA
1 TTTACCTATGTTCTTCAGGA-CATATGGA
78939 TAGTTATCGA
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
30 3 0.04
31 38 0.49
32 37 0.47
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
TTTACCTATGTTCTTCAGGACATATGGACAA
Done.