Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002568.1 Hibiscus syriacus cultivar Beakdansim tig00005211_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: 59464
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:309 original size:179 final size:179
Alignment explanation
Indices: 10--395 Score: 538
Period size: 179 Copynumber: 2.2 Consensus size: 179
1 CGATACTTT
*
10 AATATATTGAAAGTGTCGATAC-TT--TATAGTATCGACACATTGTGAATTTAAAAGAGAAGCAG
1 AATATATTGAAAGTGTCGATACTTTAATATAGTATCGAAACATTGTGAATTTAAAAGAGAAGCAG
* *
72 TTTTAGCGCCTATAAAGTATCGATACTTTATAACAATGTATCGATCCACAACGATATAACAAGTA
66 TTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAAAGATATAACAAGT-
* * * *
137 AAAATATGACAAAATCGGTCTCTAAAGGACAAAACC-GTATAGAGCGACCG
130 AAAATATGACAAAACCAGTCTCGAAAGGAC-AAACCGGTAAAGAGCGACCG
*
187 AATATATTGAAAGTGTCGATACTTTAATATAAGTATCGAAACTTTGTGAATTT-AAAGAGAAGCA
1 AATATATTGAAAGTGTCGATACTTTAATAT-AGTATCGAAACATTGTGAATTTAAAAGAGAAGCA
* * * *
251 GTTTTAGCGCTTAT-AAGTGTCGATACTTTATAAAAATGTATCGATCCATAAAGATATAACAGGT
65 GTTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAAAGATATAACAAGT
* * *
315 AAAATATGACAAAACCAGTCTCGAAATGACAAACCGGTAAAGCGCTACCG
130 AAAATATGACAAAACCAGTCTCGAAAGGACAAACCGGTAAAGAGCGACCG
*
365 --GATATTGAAAGTGTCGATACTTTAATA-AGTA
1 AATATATTGAAAGTGTCGATACTTTAATATAGTA
396 CGCGTATAAA
Statistics
Matches: 188, Mismatches: 16, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
174 4 0.02
176 26 0.14
177 27 0.14
178 39 0.21
179 45 0.24
180 27 0.14
181 20 0.11
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.28
Consensus pattern (179 bp):
AATATATTGAAAGTGTCGATACTTTAATATAGTATCGAAACATTGTGAATTTAAAAGAGAAGCAG
TTTTAGCGCCTATAAAGTATCGATACTTTATAAAAATGTATCGATCCACAAAGATATAACAAGTA
AAATATGACAAAACCAGTCTCGAAAGGACAAACCGGTAAAGAGCGACCG
Found at i:2187 original size:21 final size:21
Alignment explanation
Indices: 2163--2206 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2153 CAAGACATCA
2163 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
*
2184 AGAGTCGAAGAGACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2205 AG
1 AG
2207 GCATAAGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.11, G:0.34, T:0.14
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2276 original size:33 final size:33
Alignment explanation
Indices: 2239--2305 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2229 AAATAGATGG
2239 AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
*
2272 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
2305 A
1 A
2306 CTTAAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTATTGAGGGGTGA
Found at i:2511 original size:18 final size:18
Alignment explanation
Indices: 2488--2525 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
2478 AAAAAATATA
2488 AAGAAGAAAAGATGGAGG
1 AAGAAGAAAAGATGGAGG
2506 AAGAAGAAAAGATGGAGG
1 AAGAAGAAAAGATGGAGG
2524 AA
1 AA
2526 TGAGGAGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.37, T:0.05
Consensus pattern (18 bp):
AAGAAGAAAAGATGGAGG
Found at i:3890 original size:23 final size:23
Alignment explanation
Indices: 3853--3916 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
3843 CAGCTCGTAT
*
3853 AAATGCACCGAAGTGCCACATAG
1 AAATGCACCGTAGTGCCACATAG
* * *
3876 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGTAGTGCCACATAG
3899 AAATGCACCGTAGTGCCA
1 AAATGCACCGTAGTGCCA
3917 TAAGATTGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.27, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGTAGTGCCACATAG
Found at i:4611 original size:2 final size:2
Alignment explanation
Indices: 4604--4688 Score: 152
Period size: 2 Copynumber: 42.0 Consensus size: 2
4594 TACATAACCC
*
4604 AT AT AT AT AA ACT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4689 TACTTCTATT
Statistics
Matches: 80, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 79 0.99
3 1 0.01
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7511 original size:23 final size:22
Alignment explanation
Indices: 7485--7536 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 22
7475 CACCACAGCT
7485 CGTATAATTGCACCGAAGTGCC
1 CGTATAATTGCACCGAAGTGCC
* *
7507 ACGTAGAATTGCACCGTAGTGCC
1 -CGTATAATTGCACCGAAGTGCC
7530 C-TATAAT
1 CGTATAAT
7537 AATGTCCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 5 0.19
22 1 0.04
23 20 0.77
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
CGTATAATTGCACCGAAGTGCC
Found at i:7793 original size:146 final size:146
Alignment explanation
Indices: 7508--7805 Score: 467
Period size: 146 Copynumber: 2.0 Consensus size: 146
7498 CGAAGTGCCA
*
7508 CGTAGAATTGCACCGTAGTGCCCTATAATAATGTCCATAAGGACCATATCATTCCTTAAGAATCA
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCATATCATTCCTTAAGAATCA
* * * * * *
7573 TATACATATACTAGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATATAT
66 TATACATATACTAGGACCAAGTATGTGCCTCACAAGACCTCACAAATGTTCCACAGAATATACAT
7638 ATATCCCGAAGGACCG
131 ATATCCCGAAGGACCG
7654 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGA-C-CATATCATTCCTTAAGAAT
*
7719 CATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGACCTCATAAATGTTCCA-AGAATATA
64 CATATACATATACT-AGGACCAAGTATGTGCCTCACAAGACCTCACAAATGTTCCACAGAATATA
*
7782 CATATGT-CCGAAGGACCG
128 CATATATCCCGAAGGACCG
7800 CGTAGA
1 CGTAGA
7806 CCCTCGACTC
Statistics
Matches: 140, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
146 59 0.42
147 14 0.10
148 50 0.36
149 17 0.12
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.27
Consensus pattern (146 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCATATCATTCCTTAAGAATCA
TATACATATACTAGGACCAAGTATGTGCCTCACAAGACCTCACAAATGTTCCACAGAATATACAT
ATATCCCGAAGGACCG
Found at i:10091 original size:14 final size:14
Alignment explanation
Indices: 10072--10108 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
10062 AATTTTCACT
10072 GAACATATCAATAA
1 GAACATATCAATAA
10086 GAACATATCAATAA
1 GAACATATCAATAA
10100 GAACATATC
1 GAACATATC
10109 TTCTAATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.54, C:0.16, G:0.08, T:0.22
Consensus pattern (14 bp):
GAACATATCAATAA
Found at i:12818 original size:147 final size:146
Alignment explanation
Indices: 12535--12832 Score: 456
Period size: 147 Copynumber: 2.0 Consensus size: 146
12525 GAAGTGCCAT
*
12535 GTAGAATTGCACCGTATGCCCTATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCA
1 GTAGAATTGCACCGTATGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCA
* * * * * *
12600 TATACATATACTAGGGATCAAGTATATGTCTTACAAGACTTCACACATGTTCCACAGAATATATA
66 TATACATATACTAAGGACCAAGTATATGCCTCACAAGACTTCACAAATGTTCCAAAGAATATATA
12665 TATCCCGAAGGACCGC
131 TATCCCGAAGGACCGC
*
12681 GTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGATCACATATCATTCCTTAAGAATC
1 GTAGAATTGCACCGTA-TGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATC
* *
12746 ATATACATATACTAAGGACCAAGTATGTGCCTCA-AAGAC-TCATAAATGTTCCAAAGAATATAC
65 ATATACATATACTAAGGACCAAGTATATGCCTCACAAGACTTCACAAATGTTCCAAAGAATAT--
*
12809 ATATGTCCCGAAGGACCGC
128 ATATATCCCGAAGGACCGC
12828 GTAGA
1 GTAGA
12833 CCCTCGACTC
Statistics
Matches: 138, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
145 19 0.14
146 21 0.15
147 98 0.71
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (146 bp):
GTAGAATTGCACCGTATGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAATCA
TATACATATACTAAGGACCAAGTATATGCCTCACAAGACTTCACAAATGTTCCAAAGAATATATA
TATCCCGAAGGACCGC
Found at i:18484 original size:23 final size:23
Alignment explanation
Indices: 18447--18506 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
18437 CAGCTCATAT
**
18447 AAATGCACCCAAGTGCCACGTAG
1 AAATGCACCGTAGTGCCACGTAG
* * *
18470 AATTGCACCGTAGTGTCGCGTAG
1 AAATGCACCGTAGTGCCACGTAG
18493 AAATGCACCGTAGT
1 AAATGCACCGTAGT
18507 TCCATATAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.20
Consensus pattern (23 bp):
AAATGCACCGTAGTGCCACGTAG
Found at i:19266 original size:2 final size:2
Alignment explanation
Indices: 19259--19306 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
19249 ACTTATAAAC
* *
19259 AT AT AT AT AT AT AT AA AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19301 AT AT AT
1 AT AT AT
19307 TACTTCTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:19267 original size:18 final size:18
Alignment explanation
Indices: 19252--19306 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
19242 ATATTATACT
19252 TATAAACATATATATATA
1 TATAAACATATATATATA
19270 TATAAACATATATATATA
1 TATAAACATATATATATA
* *
19288 TATATATATATATATATA
1 TATAAACATATATATATA
19306 T
1 T
19307 TACTTCTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAAACATATATATATA
Found at i:20310 original size:34 final size:32
Alignment explanation
Indices: 20248--20317 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
20238 ACCTTACAAC
* *
20248 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
*
20280 TCCCTAGCTTTTACACGGGATAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
20314 TCCC
1 TCCC
20318 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Found at i:20781 original size:21 final size:21
Alignment explanation
Indices: 20737--20812 Score: 127
Period size: 21 Copynumber: 3.7 Consensus size: 21
20727 AGTGTTTGAG
*
20737 TGCATGGATGCACTGCA-TGA
1 TGCATGGATGCACTGCAGGGA
20757 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
20778 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
20799 TGCATGGATGCACT
1 TGCATGGATGCACT
20813 TTGACACCCT
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
20 17 0.32
21 36 0.68
ACGTcount: A:0.22, C:0.20, G:0.36, T:0.22
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:20913 original size:29 final size:29
Alignment explanation
Indices: 20892--20949 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
20882 AAACTTTGAA
20892 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
20921 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
20950 TGTTATATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:20939 original size:30 final size:30
Alignment explanation
Indices: 20892--20952 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 30
20882 AAACTTTGAA
20892 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
20921 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
20952 T
1 T
20953 TATATCAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.37
30 11 0.37
31 8 0.27
ACGTcount: A:0.43, C:0.16, G:0.07, T:0.34
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:23030 original size:34 final size:32
Alignment explanation
Indices: 22968--23037 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
22958 ACCTTACAAC
* * *
22968 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACATT
*
23000 TCCCTAGCTTTTACACGGGATAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACATT
23034 TCCC
1 TCCC
23038 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACATT
Found at i:23502 original size:21 final size:21
Alignment explanation
Indices: 23458--23533 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
23448 GGTGTTTGAG
*
23458 TGCATGGATGCACTGCA-TGA
1 TGCATGGATGCACTGCAGGGA
*
23478 TGCATGGATACACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
23499 TGCATGGATGCACTGCAGGGG
1 TGCATGGATGCACTGCAGGGA
23520 TGCATGGATGCACT
1 TGCATGGATGCACT
23534 TTGACACCCT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 16 0.31
21 35 0.69
ACGTcount: A:0.24, C:0.20, G:0.34, T:0.22
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:23634 original size:29 final size:29
Alignment explanation
Indices: 23602--23664 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
23592 GAAACCTTTT
23602 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
23632 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
23662 AAA
1 AAA
23665 CCATTTTGCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:23681 original size:34 final size:29
Alignment explanation
Indices: 23613--23672 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
23603 AAACTTTGAA
*
23613 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
23642 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
23673 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:25723 original size:19 final size:19
Alignment explanation
Indices: 25699--25747 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
25689 AATGTAGAGT
25699 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
25718 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
25737 TAATTTTGTAT
1 TAATTTTGTAT
25748 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:26454 original size:200 final size:199
Alignment explanation
Indices: 26100--26823 Score: 1038
Period size: 200 Copynumber: 3.6 Consensus size: 199
26090 TAAGAAGATA
* * *
26100 TGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCTATAATTATAATATAATAG
1 TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAG
26165 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTA
66 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTA
* * *
26230 TTGACACTTTTGAAATTGGTGTCGATACTTTTTATCCAGAATGAATGCCCAAAATGGTGAAAGCA
131 TCGACAC-TTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
26295 TAAAG
195 TAAAG
*
26300 TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAACGTAATAG
1 TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAG
* ** * * * * *
26365 GTAAATTTACAATGTAACTGGTATAACTATACCGATTTTATGAGAGAATAGGTCTACATAATGTA
66 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTA
* * * * * * * *
26430 TCAACACTTCTGGAATTTGTGTCGATA-TTGTTTGTCCGGAAGGAATGCCCAAAAGGGTGCACCC
131 TCGACACTT-TGAAATTGGTGTCGATACTT-TTTGTCCAGAATGAATGCCCAAAATGGTGAACGC
26494 ATAAAG
194 ATAAAG
* * * * * * *
26500 TATCGATACATTTTTTAAAAGTGTCGATCCTAGAGACATCGAAACCCATAATTAAAATGTAATAG
1 TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAG
* * *
26565 GTAATTTTGTAATGTAACCGATATAAATATATCGGTTTTATGTGAGAATAGGTCTACATAATGTA
66 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTA
26630 TCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
131 TCGACAC-TTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCA
26695 TAAAG
195 TAAAG
* * * * *
26700 TGTCGAAACATTTTTAAAAAGTGTCGATCCAAGAGACATCG-AACCCATAATTATAATGTAATAG
1 TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAG
* *
26764 ATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGTGAGAATAGGTCTACATA
66 GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATA
26824 CCAGAAACAT
Statistics
Matches: 462, Mismatches: 58, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
199 81 0.18
200 377 0.82
201 4 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (199 bp):
TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATAG
GTAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTA
TCGACACTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCAT
AAAG
Found at i:26907 original size:96 final size:95
Alignment explanation
Indices: 26735--26915 Score: 265
Period size: 96 Copynumber: 1.9 Consensus size: 95
26725 GATCCAAGAG
* * *
26735 ACATCGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACTGGT
1 ACATCGAACCCATAATTATAATGTAATAGATAATTTTGCAATATAACCAGTATAAATATACCGGT
*
26800 TTTATGTGAGAATAGGTCTACATACCAGAA
66 TTTATGAGAGAATAGGTCTACATACCAGAA
* * * *
26830 ACATCGAAACCCATGATTATAATTTAATAGGTAATGTTT-CAATGTAACCAGTATAAATATACCG
1 ACATCG-AACCCATAATTATAATGTAATAGATAAT-TTTGCAATATAACCAGTATAAATATACCG
26894 GTTTTATGAGAGAATAGGTCTA
64 GTTTTATGAGAGAATAGGTCTA
26916 GAAAATGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
95 6 0.08
96 67 0.88
97 3 0.04
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (95 bp):
ACATCGAACCCATAATTATAATGTAATAGATAATTTTGCAATATAACCAGTATAAATATACCGGT
TTTATGAGAGAATAGGTCTACATACCAGAA
Found at i:30002 original size:18 final size:18
Alignment explanation
Indices: 29981--30017 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
29971 GTAATTGGAG
29981 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
29999 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
30017 T
1 T
30018 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:30024 original size:24 final size:24
Alignment explanation
Indices: 29973--30025 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
29963 TTTCATATGT
* * *
29973 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
29997 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
30021 AATTT
1 AATTT
30026 CGACTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:30774 original size:200 final size:199
Alignment explanation
Indices: 30251--31022 Score: 855
Period size: 200 Copynumber: 3.9 Consensus size: 199
30241 CTTAAAGTTT
* * * *
30251 CACATAAAGTGTCGATACATTTATAAAAAAAGTATCGATCCAAAAAGCAACTAAACCGAAAATTA
1 CACATAAAGTGTCGATACATTT-T-TAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTA
* * * *
30316 TAATGTAATAGGTAAATTTACAATATGACCGGTATAAATATACCGATTTTATGAGCAAATATGTC
64 TAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTC
* * * *** *
30381 AGCATAAAGTATCGACACCTTTTAAATTTGTG-CTGATACTTTTTGTCCGAGCCT--TTGCTC-A
129 AACATAATGTATCGACA-CTTTTAAATTTGTGTC-GATACATTTTGTCC-ATAATGAATGC-CAA
30442 ACGAGCT-T-CA
190 ACG-G-TGTGCA
** * * *
30452 TGCATAAAAGTGTCGATACA--TTTAAAATTA-TATCGATCCAAAAAACATCAAAACTGAATATT
1 CACAT-AAAGTGTCGATACATTTTTAAAA--AGTATCGATCCAAAAAACATCGAAACCGAAAATT
* * * * **
30514 ATAATATAATAGGTAAATATACAATGTAACCGATATAAATATACATGTTTTATGAGAAAATAGGT
63 ATAATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGT
* * * *
30579 -ATACATAATGTATTGACAATGTTTTAATTTGTGTTGATACATTTTGTCCATAATGAATGCCAAA
128 CA-ACATAATGTATCGACACT-TTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAA
30643 CGGTGTGCA
191 CGGTGTGCA
* *
30652 CACATAAAGTGTCGATACATTTTTAAAAAGTATCGATCTC-AAAAACATCGAAACCGATAATTAC
1 CACATAAAGTGTCGATACATTTTTAAAAAGTATCGATC-CAAAAAACATCGAAACCGAAAATTAT
* * * * * * *
30716 AATGTAATATGTAAATTTACAATGTAATCGGTATAAGTATACCGGTTTTTTAAGAAAATAGGTGA
65 AATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCA
* * *
30781 ACATAATGTATCGACACTTTTTAGATTTGTGTCAATACATTTTGTCCATAATGAATGCAAAACGG
130 ACATAATGTATCGACAC-TTTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACGG
*
30846 GGTGCA
194 TGTGCA
* ** * *
30852 CGCATAAAGTGTCGATACATTCATAAAAAATATCGATCCAAAAAACATCGAAACTGAAAATTATA
1 CACATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATA
* * *
30917 ATGTAATAGGTAAATTTACAATATAATCGGTATAAATATACCGGTTTTATGAGAAAATAAGTTAA
66 ATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAA
* *
30982 CATAGTGTATCGACACTTTTAAATTTGTGTCGATACGTTTT
131 CATAATGTATCGACACTTTTAAATTTGTGTCGATACATTTT
31023 AAAATTACGT
Statistics
Matches: 481, Mismatches: 72, Indels: 38
0.81 0.12 0.06
Matches are distributed among these distances:
198 9 0.02
199 161 0.33
200 284 0.59
201 13 0.03
202 14 0.03
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (199 bp):
CACATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCGAAAATTATA
ATGTAATAGGTAAATTTACAATATAACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTCAA
CATAATGTATCGACACTTTTAAATTTGTGTCGATACATTTTGTCCATAATGAATGCCAAACGGTG
TGCA
Found at i:33853 original size:21 final size:21
Alignment explanation
Indices: 33829--33870 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
33819 ATTTGAATAT
**
33829 TATGAAGGGGTATTGATTCCC
1 TATGAAGGGGTACCGATTCCC
33850 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
33871 CCCATTCTGG
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:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:33932 original size:21 final size:21
Alignment explanation
Indices: 33899--33938 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
33889 TTTTTGCAGA
*
33899 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
33921 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
33939 AGATATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:34192 original size:34 final size:32
Alignment explanation
Indices: 34153--34222 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
34143 TTTTGTAAAG
*
34153 GGGAAAGGTTCTAGCTAATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTAATCCCG-G-AAAAACTA
* *
34187 GGGAAAGGTTCTAGTTTATCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
34219 GGGA
1 GGGA
34223 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.33, C:0.16, G:0.29, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTAATCCCGGAAAAACTA
Found at i:35932 original size:200 final size:196
Alignment explanation
Indices: 35575--36097 Score: 667
Period size: 200 Copynumber: 2.6 Consensus size: 196
35565 TGTCCAGAAT
* *
35575 ATAAAGTTTTGATACATTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGAT-CCAA-AACATCGAAACCGATAATTATAATG
* * *
35640 TAATAGGTAAATTTACAATGTAACTGATATAAATATACCGGTTTTATAAGAAAATATGTCAGCAC
64 TAATAGGTAAATTTACAATGT-ACCGATATAAATATACCGGTTTTATAAGAAAATAGGTCAGAAC
* * *
35705 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGTCAAACGAGGTG
128 AAAGTATCAACACTATTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCAAACGAGGTG
35770 CACAC
192 CACAC
* * *
35775 ATAAAGTGTCGATACATTTATTAAAAGTATCAATCTCACAAACATCGAAACTGATAATTACAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGATC-CA-AAACATCGAAACCGATAATTATAATG
* * * *
35840 TGATAGGTAAATTTACAATGTACCCGACAGAAATATACCGGTTTTATGAGAAAATAGGTCTA-AA
64 TAATAGGTAAATTTACAATGTA-CCGATATAAATATACCGGTTTTATAAGAAAATAGGTC-AGAA
* * * * *
35904 TAATGTATCAACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTG
127 CAAAGTATCAACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTG
**
35969 CATGC
192 CACAC
* * *
35974 ATAAAGTGTCGATACATTTA--AAATTGTATCGATCAAAAAAAATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATTAAA-AGTATCGATC-CAAAACATCGAAACCGATAATTATAATG
* *
36037 TAATAGGTAAATTTGCAATGTTACCGATATAAATATACCGG-TTTACTTAGAAAATAGGTCA
64 TAATAGGTAAATTTACAATG-TACCGATATAAATATACCGGTTTTA-TAAGAAAATAGGTCA
36098 ATATAAGCGT
Statistics
Matches: 282, Mismatches: 34, Indels: 18
0.84 0.10 0.05
Matches are distributed among these distances:
196 5 0.02
197 73 0.26
198 11 0.04
199 47 0.17
200 144 0.51
201 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.32
Consensus pattern (196 bp):
ATAAAGTGTCGATACATTTATTAAAAGTATCGATCCAAAACATCGAAACCGATAATTATAATGTA
ATAGGTAAATTTACAATGTACCGATATAAATATACCGGTTTTATAAGAAAATAGGTCAGAACAAA
GTATCAACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGGTGCACA
C
Found at i:36232 original size:23 final size:23
Alignment explanation
Indices: 36182--36226 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
36172 TGCCTATTTT
*
36182 ATTATATAAGAGCTACCTATTAC
1 ATTATATAAGAGCTACCTAATAC
*
36205 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGAGCTACCTAATA
36227 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGAGCTACCTAATAC
Found at i:37449 original size:200 final size:196
Alignment explanation
Indices: 37092--37613 Score: 647
Period size: 200 Copynumber: 2.6 Consensus size: 196
37082 TGTCCAGAAT
* * * *
37092 ATAAAGTTTTGATATATTTATTAAAAGTATCGATCCCAATAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGAT-ACAA-AACATCGAAACCGATAATTATAATG
* *
37157 TAATAGGTAAATTTACAATGTAACTGATATAAATATACCGGTTTTATAAGAAAATAGGTCAGCAC
64 TAATAGGTAAATTTACAATGT-ACCGATATAAATATACCGGTTTTATAAGAAAATAGGTCAGAAC
* * * *
37222 AAAGTATCGACACTATTTAAATTTGTGTCGATACTTTTTGTCCATAATGAATGTCAAACGAGGTG
128 AAAGTATCAACACTATTTAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCAAACGAGATG
37287 CACAC
192 CACAC
* * *
37292 ATAAAGTGTCGATACATTTATTAAAAGTATCAATATCACAAACATCGAAACTGATAATTACAATG
1 ATAAAGTGTCGATACATTTATTAAAAGTATCGATA-CA-AAACATCGAAACCGATAATTATAATG
* * * *
37357 TGATAGGTAAATTTACAATGTACCCGACAGAAATATACCGGTTTTATGAGAAAATAGGTCTA-AA
64 TAATAGGTAAATTTACAATGTA-CCGATATAAATATACCGGTTTTATAAGAAAATAGGTC-AGAA
* * * * *
37421 TAATGTATCAACACTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGATG
127 CAAAGTATCAACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGATG
**
37486 CATGC
192 CACAC
* * * *
37491 ATAAAGTGTCGATACATTTA--AAATTGTATCGATAAAAAAAATCGAATCCGATAATTATAATGT
1 ATAAAGTGTCGATACATTTATTAAA-AGTATCGATACAAAACATCGAAACCGATAATTATAATGT
* *
37554 AATAGGTAAATTTGCAATGTTACCGATATAAATATACCGG-TTTACTTAGAAAATAGGTCA
65 AATAGGTAAATTTACAATG-TACCGATATAAATATACCGGTTTTA-TAAGAAAATAGGTCA
37614 ATATAAGCGT
Statistics
Matches: 279, Mismatches: 36, Indels: 19
0.84 0.11 0.06
Matches are distributed among these distances:
195 5 0.02
196 69 0.25
197 6 0.02
198 8 0.03
199 45 0.16
200 144 0.52
201 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (196 bp):
ATAAAGTGTCGATACATTTATTAAAAGTATCGATACAAAACATCGAAACCGATAATTATAATGTA
ATAGGTAAATTTACAATGTACCGATATAAATATACCGGTTTTATAAGAAAATAGGTCAGAACAAA
GTATCAACACTATTTAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCAAACGAGATGCACA
C
Found at i:37748 original size:23 final size:23
Alignment explanation
Indices: 37698--37742 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
37688 TGCCTATTTT
* *
37698 ATTATATAAGAGCTACTTATTAC
1 ATTATATAAGAGCTACCTAATAC
*
37721 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGAGCTACCTAATA
37743 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGAGCTACCTAATAC
Found at i:39400 original size:19 final size:19
Alignment explanation
Indices: 39373--39426 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
39363 ATGTGTTTTA
* *
39373 TTTATTATTATTATTTTGT
1 TTTATTATTATTATTATAT
*
39392 TTTAATATTATTATTATAT
1 TTTATTATTATTATTATAT
*
39411 TATATTATTATTATTA
1 TTTATTATTATTATTA
39427 AATAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTATTATTATTATAT
Found at i:39403 original size:22 final size:22
Alignment explanation
Indices: 39366--39426 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
39356 TTATTTCATG
*
39366 TGTTTTATTTATTATTATTATTT
1 TGTTTTA-TTATTATTATTATAT
*
39389 TGTTTTAATATTATTATTATAT
1 TGTTTTATTATTATTATTATAT
* *
39411 TATATTATTATTATTA
1 TGTTTTATTATTATTA
39427 AATAAATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (22 bp):
TGTTTTATTATTATTATTATAT
Found at i:39446 original size:3 final size:3
Alignment explanation
Indices: 39374--39426 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
39364 TGTGTTTTAT
* *
39374 TTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39418 TTA TTA TTA
1 TTA TTA TTA
39427 AATAAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 8 0.18
3 36 0.82
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:39912 original size:16 final size:16
Alignment explanation
Indices: 39891--39921 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39881 AACCTGCAAA
*
39891 AACAAAAAAAGGAGAC
1 AACAAAAAAAAGAGAC
39907 AACAAAAAAAAGAGA
1 AACAAAAAAAAGAGA
39922 ATAGAGAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.10, G:0.16, T:0.00
Consensus pattern (16 bp):
AACAAAAAAAAGAGAC
Found at i:41111 original size:117 final size:118
Alignment explanation
Indices: 40968--41201 Score: 278
Period size: 119 Copynumber: 2.0 Consensus size: 118
40958 TTTAATCCTA
* ** * * *
40968 TTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAATTAGATGTCCAT
1 TTTTAATATTTATTTATTTTTCAATATCAAAGAAAAGAACAGTCTTAAAACAACTAGAAGT-CAT
* *
41031 TTTT-TGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATTAATTG
65 TTTTCTGATATTTCTAAATAAATAAATATCCTA-TTTATAAATATATATAAATTG
* * * * *
41084 TTTTAATTATTTATTTATTTTTTAATATCAAAGAAAAGAACTGTCTTAAGACACCTAGAAGTCTT
1 TTTTAA-TATTTATTTATTTTTCAATATCAAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCAT
**
41149 TTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
65 TTTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATT
41202 AATATTTTTT
Statistics
Matches: 98, Mismatches: 15, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
116 6 0.06
117 20 0.20
118 18 0.18
119 54 0.55
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (118 bp):
TTTTAATATTTATTTATTTTTCAATATCAAAGAAAAGAACAGTCTTAAAACAACTAGAAGTCATT
TTTCTGATATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATTG
Found at i:43473 original size:14 final size:14
Alignment explanation
Indices: 43435--43473 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
43425 ATTTTAAATA
*
43435 ATTTACATTTACAT
1 ATTTACATTTGCAT
43449 -TTTAACATTTGCAT
1 ATTT-ACATTTGCAT
43463 ATTTACATTTG
1 ATTTACATTTG
43474 GAATCTTTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 3 0.14
14 16 0.73
15 3 0.14
ACGTcount: A:0.31, C:0.13, G:0.05, T:0.51
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:43563 original size:12 final size:13
Alignment explanation
Indices: 43546--43574 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
43536 ACATTCACAT
43546 ATTTACATTT-GC
1 ATTTACATTTAGC
43558 ATTTACATTTAGC
1 ATTTACATTTAGC
43571 ATTT
1 ATTT
43575 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTACATTTAGC
Found at i:45586 original size:16 final size:16
Alignment explanation
Indices: 45564--45603 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
45554 GAAAGAAGAA
45564 GAAAAAAAATAAAAA-
1 GAAAAAAAATAAAAAG
*
45579 TAAAAAAAATAAAAAG
1 GAAAAAAAATAAAAAG
45595 GAAAAAAAA
1 GAAAAAAAA
45604 GGAAAAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (16 bp):
GAAAAAAAATAAAAAG
Found at i:51351 original size:77 final size:73
Alignment explanation
Indices: 51270--51434 Score: 231
Period size: 77 Copynumber: 2.2 Consensus size: 73
51260 TCCAACATCC
* *
51270 GTAAGCCCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACCC
1 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGA--TCTT--AAACCC
51335 TCAGGGTCATAT
62 TCAGGGTCATAT
* * * *
51347 GTAAGACCTACAATGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAAGCCTCAG
1 GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACCCTCAG
*
51412 GGTCATCT
66 GGTCATAT
51420 GTAAGCCCTACAGTG
1 GTAAGCCCTACAGTG
51435 TAAGATGATA
Statistics
Matches: 79, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
73 29 0.37
75 3 0.04
77 47 0.59
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.30
Consensus pattern (73 bp):
GTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATCTTAAACCCTCAG
GGTCATAT
Found at i:51861 original size:113 final size:113
Alignment explanation
Indices: 51497--52248 Score: 1045
Period size: 113 Copynumber: 6.7 Consensus size: 113
51487 CAATATTTCC
* *
51497 AGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-TGGAAGGAA-AAGTTCATAATTAGAAGAAC
1 AGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-GAAGAAGTTCATAATGAGAAGAAC
* * * *
51560 TTCTTCAACCTTTTGCTTTAATTCATCACCCGATGGATTAGCATTGCCAG
64 TTGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
51610 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT--G-AGAACTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* *
51672 GTTCAACCTTTTGCTTGAATTCATCACCCGATGGATTAGCATTGCCAG
66 GTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
* * * *
51720 AGAAAGTTCATAATGAGAAGAACTCATCTGAAAAAGGAAGAGGAAGTTCATAATAAGAAAAACTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
** * *
51785 GTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCATTGCCAG
66 GTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
* *
51833 -GTAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGAAGAATT
1 AG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * *
51897 TGTTCAACCTTTCGCTTGAATTCATCATTCGATGGATCAGCATTACCAG
65 TGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
* *
51946 -GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCT
1 AG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
* ** * * * *
52010 TGTTCAACCTTTTACTCAAATCCATCACTTGATGGATCAGCTTTTCCAG
65 TGTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
* * *
52059 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAAAAGAATTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * *
52124 GTTCAA-CTTTTGTTTGAATTCATCACTCGATGGATCAACTTTTCCAG
66 GTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
* *
52171 AGAAAGTTCATAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG-AGAGCTT
1 AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
*
52235 GTTCGACCTTTTGC
66 GTTCAACCTTTTGC
52249 ATGACTCTAT
Statistics
Matches: 574, Mismatches: 57, Indels: 17
0.89 0.09 0.03
Matches are distributed among these distances:
110 105 0.18
111 11 0.02
112 128 0.22
113 329 0.57
114 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTTTGCTTGAATTCATCACTCGATGGATCAGCATTGCCAG
Found at i:52667 original size:3 final size:3
Alignment explanation
Indices: 52590--52647 Score: 50
Period size: 3 Copynumber: 19.3 Consensus size: 3
52580 TTTATTTCAT
* *
52590 TTA TT- TTA TTTA TTA TTA TTA TT- TTG TT- TTA ATA TTA TTA TATA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
52634 TTA TATA TTA TTA T
1 TTA T-TA TTA TTA T
52648 AAATAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
2 6 0.13
3 32 0.68
4 9 0.19
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54298 original size:113 final size:113
Alignment explanation
Indices: 54166--54390 Score: 262
Period size: 113 Copynumber: 2.0 Consensus size: 113
54156 TTTAATCCTA
* ** *
54166 TTTTAATATGTATTTATTTTTCAATAT-TAAG-AAAGGGCGGTCTTAA-ACAACTAGATGTCCAT
1 TTTTAATATGTATTTATTTTTCAATATCGAAGAAAAGAACGGTCTTAAGACAACT-GAAGT-C-T
*
54228 TTTCTGATATTTTTAAATAAATAATATCCTATTTTATAAAT-TAT-TAATTG
63 TTTCTGATATTTCTAAATAAATAATATCCTA-TTTATAAATATATATAATTG
* * * * *
54278 TTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAACTGTCTTAAGGCACCTGAAGTCTTT
1 TTTTAA-TATGTATTTATTTTTCAATATCGAAGAAAAGAACGGTCTTAAGACAACTGAAGTCTTT
**
54343 TCTGATATTTCTAAATAAATAATATTTTATTTATAAATATATATAATT
65 TCTGATATTTCTAAATAAATAATATCCTATTTATAAATATATATAATT
54391 AATATTTTTT
Statistics
Matches: 95, Mismatches: 12, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
112 15 0.16
113 51 0.54
114 9 0.09
115 16 0.17
116 4 0.04
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.46
Consensus pattern (113 bp):
TTTTAATATGTATTTATTTTTCAATATCGAAGAAAAGAACGGTCTTAAGACAACTGAAGTCTTTT
CTGATATTTCTAAATAAATAATATCCTATTTATAAATATATATAATTG
Done.