Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005207.1 Hibiscus syriacus cultivar Beakdansim tig00011775_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: 86184
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:2756 original size:2 final size:2
Alignment explanation
Indices: 2749--2775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2739 CTTAACCAGC
2749 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 T
2776 TGAATCCGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4102 original size:17 final size:17
Alignment explanation
Indices: 4059--4110 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
4049 TATACAGTAG
*
4059 AAACTCTTTAAATTAAT
1 AAACTCTCTAAATTAAT
**
4076 --ACTCGGTAAATTAAT
1 AAACTCTCTAAATTAAT
*
4091 AAACTCTCTAAAATAAT
1 AAACTCTCTAAATTAAT
4108 AAA
1 AAA
4111 TTTGTCCGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (17 bp):
AAACTCTCTAAATTAAT
Found at i:7290 original size:35 final size:35
Alignment explanation
Indices: 7247--7344 Score: 196
Period size: 35 Copynumber: 2.8 Consensus size: 35
7237 AAATAATATA
7247 TTTTTTCAAAGAAATTATATTATTATTTCTATTAT
1 TTTTTTCAAAGAAATTATATTATTATTTCTATTAT
7282 TTTTTTCAAAGAAATTATATTATTATTTCTATTAT
1 TTTTTTCAAAGAAATTATATTATTATTTCTATTAT
7317 TTTTTTCAAAGAAATTATATTATTATTT
1 TTTTTTCAAAGAAATTATATTATTATTT
7345 ATGGGTCGGA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 63 1.00
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (35 bp):
TTTTTTCAAAGAAATTATATTATTATTTCTATTAT
Found at i:19879 original size:7 final size:7
Alignment explanation
Indices: 19867--19894 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
19857 TTATTTATTT
19867 CATTCTC
1 CATTCTC
19874 CATTCTC
1 CATTCTC
19881 CATTCTC
1 CATTCTC
19888 CATTCTC
1 CATTCTC
19895 ATGAATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.43, G:0.00, T:0.43
Consensus pattern (7 bp):
CATTCTC
Found at i:22993 original size:2 final size:2
Alignment explanation
Indices: 22986--23013 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22976 ACTGAATTAT
22986 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
23014 GAGAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23018 original size:2 final size:2
Alignment explanation
Indices: 23013--23061 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
23003 ATATATATAT
* * *
23013 AG AG AG AG AG AG AG AG AG A- AG -G AG GG AG GG AG AG AG AG GG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
23053 AG AG AG AG A
1 AG AG AG AG A
23062 AAGACCCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25351 original size:29 final size:28
Alignment explanation
Indices: 25243--25352 Score: 96
Period size: 29 Copynumber: 3.8 Consensus size: 28
25233 TATAAATAAA
* *
25243 ATAATTTTGAAAAATTTAAATATTATTTT
1 ATAATTTT-TAAAATTTTAATATTATTTT
* * * *
25272 ATAATAGTTCAATAAATTTAATAATTACTTT
1 ATAAT-TTTTAA-AATTTTAAT-ATTATTTT
*
25303 ATAATTTCTTAAAA-TGTAATGATTATTTT
1 ATAATTT-TTAAAATTTTAAT-ATTATTTT
25332 ATAATTTTTAAAATTTTAATA
1 ATAATTTTTAAAATTTTAATA
25353 ACAAAAAATC
Statistics
Matches: 65, Mismatches: 11, Indels: 11
0.75 0.13 0.13
Matches are distributed among these distances:
28 7 0.11
29 31 0.48
30 12 0.18
31 15 0.23
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.50
Consensus pattern (28 bp):
ATAATTTTTAAAATTTTAATATTATTTT
Found at i:28968 original size:30 final size:30
Alignment explanation
Indices: 28902--29115 Score: 277
Period size: 30 Copynumber: 7.4 Consensus size: 30
28892 TGGTTACGAA
*
28902 GCTGCTGCTGCCGCCGCTGAAGTTCAA---
1 GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
*
28929 GCTGATGCTGCCGTCGCTGAAGTTCAAGCT
1 GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
*
28959 GCTGCTGCTGCTGTCGCTGAAGTTCAAGCT
1 GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
*
28989 GCTGCTGCTGCTGTCGCTGAAGTTCAAGCT
1 GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
* *
29019 GCTGCTGCCGCTGTCGCTGAAGTTCAAGCT
1 GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
* *
29049 GCTGCTGCCGCTGTCGCTGAAGTTCAAGCT
1 GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
29079 GCTGCTG-T--CGT---TGAAGTTCCAA-CT
1 GCTGCTGCTGCCGTCGCTGAAGTT-CAAGCT
29103 GCTGCTGCTGCCG
1 GCTGCTGCTGCCG
29116 CTGATGTTCC
Statistics
Matches: 173, Mismatches: 7, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.09
25 4 0.02
27 29 0.17
30 124 0.72
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.28
Consensus pattern (30 bp):
GCTGCTGCTGCCGTCGCTGAAGTTCAAGCT
Found at i:28998 original size:90 final size:90
Alignment explanation
Indices: 28902--29085 Score: 311
Period size: 90 Copynumber: 2.1 Consensus size: 90
28892 TGGTTACGAA
*
28902 GCTGCTGCTGCCGCCGCTGAAGTTCAAGCTGATGCTG-C-C-GTCGCTGAAGTTCAAGCTGCTGC
1 GCTGCTGCTGCTGCCGCTGAAGTTCAAGCTGATGCTGCCGCTGTCGCTGAAGTTCAAGCTGCTGC
*
28964 TGCTGCTGTCGCTGAAGTTCAAGCT
66 TGCCGCTGTCGCTGAAGTTCAAGCT
* *
28989 GCTGCTGCTGCTGTCGCTGAAGTTCAAGCTGCTGCTGCCGCTGTCGCTGAAGTTCAAGCTGCTGC
1 GCTGCTGCTGCTGCCGCTGAAGTTCAAGCTGATGCTGCCGCTGTCGCTGAAGTTCAAGCTGCTGC
29054 TGCCGCTGTCGCTGAAGTTCAAGCT
66 TGCCGCTGTCGCTGAAGTTCAAGCT
29079 GCTGCTG
1 GCTGCTG
29086 TCGTTGAAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
87 34 0.38
88 1 0.01
89 1 0.01
90 54 0.60
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.27
Consensus pattern (90 bp):
GCTGCTGCTGCTGCCGCTGAAGTTCAAGCTGATGCTGCCGCTGTCGCTGAAGTTCAAGCTGCTGC
TGCCGCTGTCGCTGAAGTTCAAGCT
Found at i:29132 original size:51 final size:51
Alignment explanation
Indices: 29023--29184 Score: 181
Period size: 51 Copynumber: 3.2 Consensus size: 51
29013 CAAGCTGCTG
* *
29023 CTGCCGCTGTCGCTGAAGTT-CAAGCTGCTGCTGCCGCTGTCGCTGAAGTT-CAA
1 CTGCCGCTGTCGCTGAAGTTCCAA-CTGCTGCT---GCTGCCGCTGATGTTCCAA
* *
29076 GCTGCTGCTGTCGTTGAAGTTCCAACTGCTGCTGCTGCCGCTGATGTTCCAA
1 -CTGCCGCTGTCGCTGAAGTTCCAACTGCTGCTGCTGCCGCTGATGTTCCAA
* * *
29128 CTGCTGCTGCCGCTGATGTTCCAA---CTGCTGCTGCCGCTGATGTTCCAA
1 CTGCCGCTGTCGCTGAAGTTCCAACTGCTGCTGCTGCCGCTGATGTTCCAA
29176 CTGCCGCTG
1 CTGCCGCTG
29185 CTGTTCAAAT
Statistics
Matches: 98, Mismatches: 8, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
48 32 0.33
51 34 0.35
52 3 0.03
54 26 0.27
55 3 0.03
ACGTcount: A:0.13, C:0.31, G:0.27, T:0.28
Consensus pattern (51 bp):
CTGCCGCTGTCGCTGAAGTTCCAACTGCTGCTGCTGCCGCTGATGTTCCAA
Found at i:29135 original size:30 final size:27
Alignment explanation
Indices: 28900--29161 Score: 254
Period size: 30 Copynumber: 9.5 Consensus size: 27
28890 GATGGTTACG
* *
28900 AAGCTGCTGCTGCCGCCGCTGAAGTTC
1 AAGCTGCTGCTGCTGTCGCTGAAGTTC
* *
28927 AAGCTGATGCTGCCGTCGCTGAAGTTC
1 AAGCTGCTGCTGCTGTCGCTGAAGTTC
28954 AAGCTGCTGCTGCTGCTGTCGCTGAAGTTC
1 AA---GCTGCTGCTGCTGTCGCTGAAGTTC
28984 AAGCTGCTGCTGCTGCTGTCGCTGAAGTTC
1 AA---GCTGCTGCTGCTGTCGCTGAAGTTC
29014 AAGCTGCTGCTGCCGCTGTCGCTGAAGTTC
1 AAGCTGCTGCT---GCTGTCGCTGAAGTTC
29044 AAGCTGCTGCTGCCGCTGTCGCTGAAGTTC
1 AAGCTGCTGCT---GCTGTCGCTGAAGTTC
*
29074 AA---GCTGCTGCTGTCGTTGAAGTTCC
1 AAGCTGCTGCTGCTGTCGCTGAAGTT-C
* *
29099 AA-CTGCTGCTGCTGCCGCTGATGTTCC
1 AAGCTGCTGCTGCTGTCGCTGAAGTT-C
*
29126 AA-CTGCTGCTGC---CGCTGATGTTCC
1 AAGCTGCTGCTGCTGTCGCTGAAGTT-C
29150 AA-CTGCTGCTGC
1 AAGCTGCTGCTGC
29162 CGCTGATGTT
Statistics
Matches: 218, Mismatches: 8, Indels: 21
0.88 0.03 0.09
Matches are distributed among these distances:
24 38 0.17
25 3 0.01
27 74 0.34
30 103 0.47
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.28
Consensus pattern (27 bp):
AAGCTGCTGCTGCTGTCGCTGAAGTTC
Found at i:29187 original size:27 final size:24
Alignment explanation
Indices: 29053--29185 Score: 160
Period size: 24 Copynumber: 5.4 Consensus size: 24
29043 CAAGCTGCTG
* * *
29053 CTGCCGCTGTCGCTGAAGTT-CAA
1 CTGCTGCTGCCGCTGATGTTCCAA
* * *
29076 GCTGCTGCTGTCGTTGAAGTTCCAA
1 -CTGCTGCTGCCGCTGATGTTCCAA
29101 CTGCTGCTGCTGCCGCTGATGTTCCAA
1 ---CTGCTGCTGCCGCTGATGTTCCAA
29128 CTGCTGCTGCCGCTGATGTTCCAA
1 CTGCTGCTGCCGCTGATGTTCCAA
29152 CTGCTGCTGCCGCTGATGTTCCAA
1 CTGCTGCTGCCGCTGATGTTCCAA
*
29176 CTGCCGCTGC
1 CTGCTGCTGC
29186 TGTTCAAATT
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
24 75 0.75
25 3 0.03
27 22 0.22
ACGTcount: A:0.13, C:0.32, G:0.26, T:0.29
Consensus pattern (24 bp):
CTGCTGCTGCCGCTGATGTTCCAA
Found at i:36606 original size:24 final size:24
Alignment explanation
Indices: 36579--36631 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
36569 ATAAAATTGA
* *
36579 TTTAATTTTAAT-TTAATTAATATT
1 TTTAATTATAATATT-ATTAACATT
*
36603 TTTAATTATAATATTTTTAACATT
1 TTTAATTATAATATTATTAACATT
36627 TTTAA
1 TTTAA
36632 CATTTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTAATTATAATATTATTAACATT
Found at i:36607 original size:9 final size:9
Alignment explanation
Indices: 36595--36657 Score: 53
Period size: 9 Copynumber: 7.4 Consensus size: 9
36585 TTTAATTTAA
36595 TTAATATTT
1 TTAATATTT
36604 TT-A-A-TT
1 TTAATATTT
*
36610 ATAATATTT
1 TTAATATTT
*
36619 TTAACATTT
1 TTAATATTT
*
36628 TTAACATTT
1 TTAATATTT
* *
36637 TTATTTTTT
1 TTAATATTT
36646 TTAAT-TTT
1 TTAATATTT
36654 TTAA
1 TTAA
36658 GATGTTAGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
6 3 0.07
7 2 0.05
8 9 0.20
9 30 0.68
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (9 bp):
TTAATATTT
Found at i:46392 original size:46 final size:46
Alignment explanation
Indices: 46339--46429 Score: 182
Period size: 46 Copynumber: 2.0 Consensus size: 46
46329 ATTTTTTTTA
46339 TGGATAAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAAG
1 TGGATAAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAAG
46385 TGGATAAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAA
1 TGGATAAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAA
46430 AGTTCAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.08, T:0.42
Consensus pattern (46 bp):
TGGATAAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAAG
Found at i:46446 original size:46 final size:45
Alignment explanation
Indices: 46344--46446 Score: 136
Period size: 46 Copynumber: 2.2 Consensus size: 45
46334 TTTTATGGAT
** *
46344 AAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAAGTGGAT
1 AAAT-ATTCAACTATCTTCTCACTCTTATTTTAGTACTAAGTCAAA
46390 AAATCATTCAACTATCTTCTCACTCTTATTTTAGTACTAAAGTTCAAA
1 AAAT-ATTCAACTATCTTCTCACTCTTATTTTAGTACT-AAG-TCAAA
46438 AAAT-TTCAA
1 AAATATTCAA
46447 TTTAACTACT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
46 43 0.83
47 3 0.06
48 6 0.12
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.40
Consensus pattern (45 bp):
AAATATTCAACTATCTTCTCACTCTTATTTTAGTACTAAGTCAAA
Found at i:53073 original size:12 final size:12
Alignment explanation
Indices: 53056--53082 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
53046 AAATAGAACG
53056 TTTTCTGGGATA
1 TTTTCTGGGATA
53068 TTTTCTGGGATA
1 TTTTCTGGGATA
53080 TTT
1 TTT
53083 GGATCGTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.07, G:0.22, T:0.56
Consensus pattern (12 bp):
TTTTCTGGGATA
Found at i:53962 original size:86 final size:86
Alignment explanation
Indices: 53769--54011 Score: 399
Period size: 84 Copynumber: 2.9 Consensus size: 86
53759 TATGTTATAT
* *
53769 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATATAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
53834 AGCGC-T-TATAATAAATAGG
66 AGCGCTTATATAATAAATAGG
53853 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATAT-ATGTAATAGAT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
53917 AGCGCTTATATAATAAAATAGG
66 AGCGCTTATATAAT-AAATAGG
* *
53939 TATTTAACGGGAAATATTATCAAGTAC---AACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
54001 AGCGCTTATAT
66 AGCGCTTATAT
54012 TGACCTATTT
Statistics
Matches: 151, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
83 37 0.25
84 74 0.49
85 6 0.04
86 34 0.23
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (86 bp):
TATTTAACGGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
AGCGCTTATATAATAAATAGG
Found at i:57730 original size:120 final size:120
Alignment explanation
Indices: 57513--57759 Score: 431
Period size: 120 Copynumber: 2.1 Consensus size: 120
57503 TTTTTCTTCC
* *
57513 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATATGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
57578 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
*
57633 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
* * * *
57698 CATAAAACCGGTATATTTATACCGGTTTTATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
57753 ATTCTGG
1 ATTCTGG
57760 GTTCCGATGT
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (120 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:57895 original size:303 final size:303
Alignment explanation
Indices: 57348--57938 Score: 1047
Period size: 303 Copynumber: 2.0 Consensus size: 303
57338 TTAAAATTAG
* * *
57348 CGACACAATATTTAAAAGTGTCGATATAGGTTTTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
57413 ATACCAGTTATATTATAAAATTATCTATTACATTATAATTCTGGGTGCCGATGTGTAAATGTCGA
66 ATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTGCCGATGTGTAAATGTCGA
* *
57478 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATCGACACAATTTTCTTCCATTCCGGACATAAAGTACCGACACAATATT
*
57543 AAAAAGTGTCGACATATGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
57608 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
261 TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
57651 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* * *
57716 ATACCGGTTTTATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGA
66 ATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTGCCGATGTGTAAATGTCGA
*
57781 CACTTTTTGACAAGGTATCGACACAATTTTCTTCCATTCCGGACATAAAGTACTGACACAATATT
131 CACTTTTTGACAAGGTATCGACACAATTTTCTTCCATTCCGGACATAAAGTACCGACACAATATT
* * *
57846 AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCGGTTATA
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
*
57911 TTACAAAATTATCTATTACATTATAATT
261 TTACAAAATTATCTAGTACATTATAATT
57939 TTGGGTTCCG
Statistics
Matches: 273, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
303 273 1.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (303 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTGCCGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATCGACACAATTTTCTTCCATTCCGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
TTACAAAATTATCTAGTACATTATAATTCTGGACATAAAGTAC
Found at i:57946 original size:183 final size:183
Alignment explanation
Indices: 57633--58220 Score: 993
Period size: 183 Copynumber: 3.2 Consensus size: 183
57623 GTACATTATA
*
57633 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
57698 CATAAAACCGGTATATTTATACCGGTTTTATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
*
57763 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACAATTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
* *
57816 ATTCCGGACATAAAGTACTGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
*
57881 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTTTGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
* *
57946 CCGATGTGTAAATGTCGATACTTTTTGACAAGGTATCAACACATTTTTCTTCC
131 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
*
57999 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTATCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
58064 CATAAAACCAGTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGTT
66 CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
* * *
58129 CCGATGTTTTTTCAA--TCGACAC-TTTTGAAAAGGTATCGACACATTTTTCTTCC
131 CCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
58182 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
58221 GAAAACTTTG
Statistics
Matches: 382, Mismatches: 20, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
183 372 0.97
184 6 0.02
186 4 0.01
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (183 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTT
CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
Found at i:60175 original size:23 final size:23
Alignment explanation
Indices: 60149--60209 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
60139 CTCATATAAA
*
60149 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
***
60172 TGCACCGTAGTGCCGTGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
60195 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
60210 TATAATAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:60404 original size:103 final size:103
Alignment explanation
Indices: 60225--60545 Score: 570
Period size: 103 Copynumber: 3.1 Consensus size: 103
60215 TAATGTCCAT
* * * *
60225 AAGGACCACATATCATTCCTTAAGAATCATATAAATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
60290 GACTTCACACATGTTCCAAAGAATACATATACGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
60328 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
* *
60393 GACTTCACACATATTCCAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
60431 AATGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
60496 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
60534 AAGGACCACATA
1 AAGGACCACATA
60546 GACCCTCGAC
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:61749 original size:21 final size:21
Alignment explanation
Indices: 61725--61769 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
61715 TTTTGTTCGT
* *
61725 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
61746 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
61767 TTG
1 TTG
61770 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:62494 original size:12 final size:12
Alignment explanation
Indices: 62473--62530 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
62463 TGTTATAGGA
* *
62473 TCATCATCATCG
1 TCATCGTCATCT
62485 TCATCGTCATCT
1 TCATCGTCATCT
62497 TCATCGTCATCT
1 TCATCGTCATCT
*
62509 TCATCGTCAGCT
1 TCATCGTCATCT
*
62521 TCATCTTCAT
1 TCATCGTCAT
62531 TGACCGCTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:62500 original size:18 final size:18
Alignment explanation
Indices: 62473--62530 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
62463 TGTTATAGGA
*
62473 TCATCATCATCGTCATCG
1 TCATCATCATCGTCATCT
*
62491 TCATCTTCATCGTCATCT
1 TCATCATCATCGTCATCT
* * *
62509 TCATCGTCAGCTTCATCT
1 TCATCATCATCGTCATCT
62527 TCAT
1 TCAT
62531 TGACCGCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.19, C:0.33, G:0.09, T:0.40
Consensus pattern (18 bp):
TCATCATCATCGTCATCT
Found at i:62530 original size:6 final size:6
Alignment explanation
Indices: 62473--62517 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
62463 TGTTATAGGA
* * *
62473 TCATCA TCATCG TCATCG TCATCT TCATCG TCATCT TCATCG TCA
1 TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCATCG TCA
62518 GCTTCATCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.20, C:0.33, G:0.09, T:0.38
Consensus pattern (6 bp):
TCATCG
Found at i:64352 original size:200 final size:200
Alignment explanation
Indices: 64028--64791 Score: 1341
Period size: 200 Copynumber: 3.8 Consensus size: 200
64018 AACATTAAAC
* * * *
64028 AGTGTCGATACA-TATTATATACCAATTCTCCCATAAAACCGGTATACTTATACCGGTTAGATTG
1 AGTGTCGATACATTATT-TAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTG
* *
64092 AAAAATTACCTAATACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
65 AAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATAT
* *
64157 GGATCGACACTTTATAGTTGCACCCTGTTTGCCATTCATTTTGGACCAAAAATATCGACACAAAC
130 GGATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAAC
64222 TACAAA
195 TACAAA
* * *
64228 AGTGTCGACACATTATTTAGACCTATTCTCTCATAAAACAGGTATACTTGTACCAGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
64293 AAAATTACCTATTACATTATACTTATGGGTTTCGATGCTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
64358 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACAAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
64423 ACAAA
196 ACAAA
64428 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
64493 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATCGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
64558 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
64623 ACAAA
196 ACAAA
* * *
64628 AGTGTTGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACTGATTAGATTGA
1 AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
*
64693 AAAATTACCTATTACATTATACTTTTGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
66 AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
*
64758 GATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GATCGACACTTTATTGTTGCACCCTGTTTGCCAT
64792 ATTGTAGATT
Statistics
Matches: 538, Mismatches: 25, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
200 534 0.99
201 4 0.01
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (200 bp):
AGTGTCGATACATTATTTAGACCTATTCTCTCATAAAACCGGTATACTTGTACCGGTTAGATTGA
AAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATGGGATCGACACTTTTTATATATG
GATCGACACTTTATTGTTGCACCCTGTTTGCCATTCATTCTGGACCAAAAATATCGACACAAACT
ACAAA
Found at i:65036 original size:18 final size:18
Alignment explanation
Indices: 65013--65073 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
65003 TCTCATTCAT
*
65013 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
65031 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
65050 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
65069 AATTA
1 AATTA
65074 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:65049 original size:19 final size:19
Alignment explanation
Indices: 65025--65073 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
65015 TTATATTCAC
65025 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
65044 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
65063 ATACAAAATTA
1 ATACAAAATTA
65074 ACCCTACATT
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:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:66898 original size:33 final size:33
Alignment explanation
Indices: 66861--66926 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
66851 CATCTTAATA
*
66861 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
66894 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
66927 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:66985 original size:21 final size:21
Alignment explanation
Indices: 66961--67024 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
66951 CCCTTATGCA
*
66961 TCTCAAGTGTATCTTCGACTC
1 TCTCAAGTTTATCTTCGACTC
*
66982 TCTCAAGTTTCTCTTCGACTC
1 TCTCAAGTTTATCTTCGACTC
* * *
67003 TATCAAATTTTTCTTCGACTC
1 TCTCAAGTTTATCTTCGACTC
67024 T
1 T
67025 TGATTGTCCT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (21 bp):
TCTCAAGTTTATCTTCGACTC
Found at i:69297 original size:20 final size:19
Alignment explanation
Indices: 69242--69288 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
69232 TCTGGTATCG
69242 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
69261 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
69282 TTTTACC
1 TTTTACC
69289 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:69468 original size:20 final size:19
Alignment explanation
Indices: 69422--69468 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
69412 TCTGGTAACG
69422 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
69441 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
69462 TTTTACC
1 TTTTACC
69469 TGGTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:69511 original size:180 final size:182
Alignment explanation
Indices: 69209--69680 Score: 723
Period size: 180 Copynumber: 2.6 Consensus size: 182
69199 CGTACTTACG
*
69209 AAAGTATCGACACTTTCAATATATCTGGTATCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
69274 TATCATATTTTTACCTGTTATATCGTTATGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
* *
69339 AGGCGCT-AAACTGCTTTTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
69389 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
69454 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
69519 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * * * **
69571 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGATTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
69636 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
69681 AATTTGGATC
Statistics
Matches: 266, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
180 128 0.48
181 40 0.15
182 98 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCTGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATT
Done.