Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008652.1 Hibiscus syriacus cultivar Beakdansim tig00111642_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: 93609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2258 original size:20 final size:20
Alignment explanation
Indices: 2233--2280 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2223 ATAATACAAA
2233 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCAATTCTGACT
*
2253 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCAATTCTGACT
2273 ATCGCAAC
1 ATCGCAAC
2281 ACTGAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCAATTCTGACT
Found at i:2450 original size:17 final size:17
Alignment explanation
Indices: 2428--2460 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
2418 TATCCGTTCT
2428 TATCCAACGACATCCTA
1 TATCCAACGACATCCTA
2445 TATCCAACGACATCCT
1 TATCCAACGACATCCT
2461 TCCCCATCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.24
Consensus pattern (17 bp):
TATCCAACGACATCCTA
Found at i:5271 original size:18 final size:18
Alignment explanation
Indices: 5239--5273 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5229 AGCAAAAGGC
*
5239 AATCAAAATAGCAATCAA
1 AATCAAAATACCAATCAA
*
5257 AATCAAAATCCCAATCA
1 AATCAAAATACCAATCA
5274 CAACCAGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATACCAATCAA
Found at i:5469 original size:20 final size:20
Alignment explanation
Indices: 5444--5584 Score: 143
Period size: 20 Copynumber: 7.4 Consensus size: 20
5434 TTAGACATTC
* * *
5444 ATTTGAATATCTCAATGCGA
1 ATTTGACTATCGCAACGCGA
5464 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
5484 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
5504 ATTTGATTATCACAACGGGA
1 ATTTGACTATCGCAACGCGA
*
5524 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
5544 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
5558 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
5578 A-TTGACT
1 ATTTGACT
5585 TTTGTAACAC
Statistics
Matches: 100, Mismatches: 15, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
14 10 0.10
16 1 0.01
18 1 0.01
19 5 0.05
20 83 0.83
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:5625 original size:20 final size:20
Alignment explanation
Indices: 5597--5641 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5587 TGTAACACGA
* *
5597 TTTGACTTTTGCGTTGCGAT
1 TTTGACTTTCGCATTGCGAT
*
5617 TTTGGCTTTCGCATTGCGAT
1 TTTGACTTTCGCATTGCGAT
5637 TTTGA
1 TTTGA
5642 GTTTAGCGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTTGACTTTCGCATTGCGAT
Found at i:7234 original size:42 final size:42
Alignment explanation
Indices: 7175--7297 Score: 151
Period size: 42 Copynumber: 2.9 Consensus size: 42
7165 GTGAATCGGG
* *
7175 CTCTTGAATGGTAGGAGGGACCTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
* ** *
7217 CTCTTGAACGGTGGGAGGGGA-CTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTAGGA-GGGACCTCTTGAACGATGACAGGGGC
*
7259 CTCTTGAACGATAGGAGAGG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTAGGAG-GGACCTCTTGAACGATGACAGG
7298 TGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 1 0.01
42 62 0.93
43 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
CTCTTGAACGGTAGGAGGGACCTCTTGAACGATGACAGGGGC
Found at i:7235 original size:21 final size:21
Alignment explanation
Indices: 7175--7289 Score: 88
Period size: 21 Copynumber: 5.5 Consensus size: 21
7165 GTGAATCGGG
* * *
7175 CTCTTGAATGGTAGGAGGGAC
1 CTCTTGAACGGTGGGAGGGGC
* * **
7196 CTCTTCAACGATGACAGGGGC
1 CTCTTGAACGGTGGGAGGGGC
*
7217 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGC
* **
7238 CTCTTG-AGGGATGATAGGGGC
1 CTCTTGAACGG-TGGGAGGGGC
* * *
7259 CTCTTGAACGATAGGAGAGGC
1 CTCTTGAACGGTGGGAGGGGC
7280 CTCTTGAACG
1 CTCTTGAACG
7290 ATGACAGGTG
Statistics
Matches: 70, Mismatches: 22, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
20 3 0.04
21 65 0.93
22 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGC
Found at i:7799 original size:20 final size:20
Alignment explanation
Indices: 7774--7816 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
7764 ATAGTTTCTG
7774 AAACTTAAAATCGCAACACA
1 AAACTTAAAATCGCAACACA
*
7794 AAACTTAAAATCGCAACGCA
1 AAACTTAAAATCGCAACACA
7814 AAA
1 AAA
7817 TGACTATCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.56, C:0.23, G:0.07, T:0.14
Consensus pattern (20 bp):
AAACTTAAAATCGCAACACA
Found at i:7873 original size:33 final size:33
Alignment explanation
Indices: 7830--7904 Score: 96
Period size: 33 Copynumber: 2.3 Consensus size: 33
7820 CTATCGTTCG
* * * *
7830 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTCT
1 CGTTGCGATTTTGATTTCGCATTGCGATTATCC
* *
7863 CGTTGTGATTTTTATTTCGCATTGCGATTATCC
1 CGTTGCGATTTTGATTTCGCATTGCGATTATCC
7896 CGTTGCGAT
1 CGTTGCGAT
7905 AGTCATTTCC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTGATTTCGCATTGCGATTATCC
Found at i:7913 original size:33 final size:33
Alignment explanation
Indices: 7844--7924 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 33
7834 GCGATTTTGG
* * * ** *
7844 TTTCGCGTTGCGATTTTCTCGTTGTGATTTTTA
1 TTTCGCGTTGCGATTATCCCGTTGCGATAGTCA
*
7877 TTTCGCATTGCGATTATCCCGTTGCGATAGTCA
1 TTTCGCGTTGCGATTATCCCGTTGCGATAGTCA
7910 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
7925 AATCATTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
33 29 0.74
34 10 0.26
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.44
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCCCGTTGCGATAGTCA
Found at i:7921 original size:20 final size:20
Alignment explanation
Indices: 7896--7944 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
7886 GCGATTATCC
*
7896 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAATCATTTCCG
*
7916 CGTTGCGATAATCATTTTCG
1 CGTTGCGATAATCATTTCCG
7936 CGTTGCGAT
1 CGTTGCGAT
7945 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAATCATTTCCG
Found at i:8218 original size:14 final size:14
Alignment explanation
Indices: 8199--8225 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8189 AGTATGAACC
8199 TCGTTGCGATTTTG
1 TCGTTGCGATTTTG
8213 TCGTTGCGATTTT
1 TCGTTGCGATTTT
8226 CATTTCGCGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.26, T:0.52
Consensus pattern (14 bp):
TCGTTGCGATTTTG
Found at i:8815 original size:20 final size:20
Alignment explanation
Indices: 8785--8856 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
8775 ATTTTGTATT
* *
8785 ATCGCGTTGCGATAGTCAGA
1 ATCGCGCTGCGATAGTCAAA
* *
8805 ATCGTGCTGCGATAGTCATA
1 ATCGCGCTGCGATAGTCAAA
* *
8825 ATGGCGTTGCGATAGTCAAA
1 ATCGCGCTGCGATAGTCAAA
*
8845 ATCGCGTTGCGA
1 ATCGCGCTGCGA
8857 ATCTGGAAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
ATCGCGCTGCGATAGTCAAA
Found at i:8906 original size:19 final size:19
Alignment explanation
Indices: 8882--8918 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8872 TGCGATACTG
*
8882 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
8901 GAGATCGCATTTCGATTT
1 GAGATCGCATTGCGATTT
8919 TGCTGGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:10547 original size:18 final size:18
Alignment explanation
Indices: 10524--10559 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
10514 ATATAAAAAA
10524 TATCTAATCTTATTTAAT
1 TATCTAATCTTATTTAAT
10542 TATCTAATCTTATTTAAT
1 TATCTAATCTTATTTAAT
10560 ATAAACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.56
Consensus pattern (18 bp):
TATCTAATCTTATTTAAT
Found at i:11733 original size:22 final size:22
Alignment explanation
Indices: 11689--11733 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
11679 AACACTCAAA
*
11689 TAAAAAATTGGTCAACAATCTC
1 TAAAAAATTGGTCAACAAACTC
*
11711 TAAAAAATGTGGTTAA-AAACTC
1 TAAAAAAT-TGGTCAACAAACTC
11733 T
1 T
11734 TCTCTATGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (22 bp):
TAAAAAATTGGTCAACAAACTC
Found at i:14338 original size:2 final size:2
Alignment explanation
Indices: 14331--14368 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14321 AATTATTGGC
14331 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
14369 AATTTGAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:22307 original size:23 final size:22
Alignment explanation
Indices: 22276--22319 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
22266 TGTTCGAGTT
*
22276 TATTTCACACATATATATAAATA
1 TATTCCACACATATAT-TAAATA
*
22299 TATTCCACATATATATTAAAT
1 TATTCCACACATATATTAAAT
22320 TAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (22 bp):
TATTCCACACATATATTAAATA
Found at i:22618 original size:21 final size:20
Alignment explanation
Indices: 22594--22640 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
22584 GATTTATTTT
*
22594 AATAATTTAATATATATGTGA
1 AATAATTT-ATACATATGTGA
*
22615 AATATATTTATACATGTGTGA
1 AATA-ATTTATACATATGTGA
22636 AATAA
1 AATAA
22641 ACTCAAACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (20 bp):
AATAATTTATACATATGTGA
Found at i:27351 original size:167 final size:167
Alignment explanation
Indices: 27075--27393 Score: 466
Period size: 167 Copynumber: 1.9 Consensus size: 167
27065 GTGTTGCATA
* ** * *
27075 GAATTCGAATCAAACTCTAACAACATAGACAAGAGGTTATGAATGATGACCTCATGTTAAGGAGG
1 GAATTCGAATCAAACTCTAAAAACATAGACAAGAAATTATGAATGATAACCTAATGTTAAGGAGG
*
27140 AGAATAAGCAAAAGCACGGTTGAGAAGGAAGGGCTTTTCATGGTTATT-TT-TTTAGTTTGCAGT
66 AGAATAAGCAAAAGCACGGCTGAGAAGGAAGGGCTTTTCATGGTT-TTGTTGTTTAGTTTGCA-T
27203 TATTGGTATATACTCTAGTTTCAGAACTCGTGTCGGATC
129 TATTGGTATATACTCTAGTTTCAGAACTCGTGTCGGATC
* * *
27242 GAATTCGAATCAAACTCTAAAAACATAGATAAGAAATTATGAATGATAATCTAATGTTAAGGATG
1 GAATTCGAATCAAACTCTAAAAACATAGACAAGAAATTATGAATGATAACCTAATGTTAAGGAGG
27307 AGAATAAGCAAAAGCACGGCTGA-AATGG-AGGGACTTTTCATGGTTTTGTTGTTTAGTTTGCAT
66 AGAATAAGCAAAAGCACGGCTGAGAA-GGAAGGG-CTTTTCATGGTTTTGTTGTTTAGTTTGCAT
* * *
27370 TGTTGGTCTGTACTCTAGTTTCAG
129 TATTGGTATATACTCTAGTTTCAG
27394 GTAGTGTAGA
Statistics
Matches: 136, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
166 8 0.06
167 117 0.86
168 11 0.08
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.32
Consensus pattern (167 bp):
GAATTCGAATCAAACTCTAAAAACATAGACAAGAAATTATGAATGATAACCTAATGTTAAGGAGG
AGAATAAGCAAAAGCACGGCTGAGAAGGAAGGGCTTTTCATGGTTTTGTTGTTTAGTTTGCATTA
TTGGTATATACTCTAGTTTCAGAACTCGTGTCGGATC
Found at i:34894 original size:32 final size:32
Alignment explanation
Indices: 34851--35112 Score: 301
Period size: 32 Copynumber: 8.2 Consensus size: 32
34841 TAGCACAATG
* * *
34851 GTGTCCGTGTTGCATTCAGATAATGCACAATA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * * *
34883 GTATCAATGTTGTATTTAGATAATGCATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * *
34915 GAGTCATTGTTGCATTCAGATAATACATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * **
34947 GTGTCAGTGTTGCATTCATATAATGCACAACA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
*
34979 GTGTCAGTGTTGCA-TCTAGATAATGCACAGTA
1 GTGTCAGTGTTGCATTC-AGATAATGCATAGTA
*
35011 GTGTCAGTGTTGCATTCAGATAATGCATAATA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * * *
35043 ATGTCAGTGTCGCATTTAGATAATACATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
* * *
35075 GTGTCAGTGTCGCATTTAGATAATACATAGTA
1 GTGTCAGTGTTGCATTCAGATAATGCATAGTA
35107 GTGTCA
1 GTGTCA
35113 CATTTAGATA
Statistics
Matches: 197, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
31 2 0.01
32 193 0.98
33 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (32 bp):
GTGTCAGTGTTGCATTCAGATAATGCATAGTA
Found at i:35022 original size:96 final size:96
Alignment explanation
Indices: 34851--35112 Score: 344
Period size: 96 Copynumber: 2.7 Consensus size: 96
34841 TAGCACAATG
* * * *
34851 GTGTCCGTGTTGCATTCAGATAATGCACAATAGTATCAATGTTGTATTTAGATAATGCATAGTAG
1 GTGTCAGTGTTGCATTCAGATAATGCACAATAGTGTCAGTGTTGCATTTAGATAATGCATAGTAG
* * *
34916 AGTCATTGTTGCATTCAGATAATACATAGTA
66 TGTCAGTGTTGCATTCAGATAATACATAATA
* * * *
34947 GTGTCAGTGTTGCATTCATATAATGCACAACAGTGTCAGTGTTGCATCTAGATAATGCACAGTAG
1 GTGTCAGTGTTGCATTCAGATAATGCACAATAGTGTCAGTGTTGCATTTAGATAATGCATAGTAG
*
35012 TGTCAGTGTTGCATTCAGATAATGCATAATA
66 TGTCAGTGTTGCATTCAGATAATACATAATA
* * * * * * * *
35043 ATGTCAGTGTCGCATTTAGATAATACATAGTAGTGTCAGTGTCGCATTTAGATAATACATAGTAG
1 GTGTCAGTGTTGCATTCAGATAATGCACAATAGTGTCAGTGTTGCATTTAGATAATGCATAGTAG
35108 TGTCA
66 TGTCA
35113 CATTTAGATA
Statistics
Matches: 142, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
96 142 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (96 bp):
GTGTCAGTGTTGCATTCAGATAATGCACAATAGTGTCAGTGTTGCATTTAGATAATGCATAGTAG
TGTCAGTGTTGCATTCAGATAATACATAATA
Found at i:41810 original size:20 final size:20
Alignment explanation
Indices: 41773--41809 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41763 TTTTGGTGCA
*
41773 GAGGGAATCGATATCCCCAT
1 GAGGGAACCGATATCCCCAT
41793 GAGGGAACCGAT-TCCCC
1 GAGGGAACCGATATCCCC
41810 CCACAGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATATCCCCAT
Found at i:43824 original size:17 final size:17
Alignment explanation
Indices: 43791--43824 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43781 TTGAATATTT
* *
43791 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
43808 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
43825 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:44104 original size:13 final size:13
Alignment explanation
Indices: 44086--44111 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44076 GGAGAAGTGT
44086 TAAGTGTTTTAAA
1 TAAGTGTTTTAAA
44099 TAAGTGTTTTAAA
1 TAAGTGTTTTAAA
44112 GGGAGAAGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAAGTGTTTTAAA
Found at i:45428 original size:13 final size:14
Alignment explanation
Indices: 45386--45427 Score: 56
Period size: 13 Copynumber: 3.3 Consensus size: 14
45376 TCAAAAAAAT
45386 TAAATAATTAATT-
1 TAAATAATTAATTA
45399 TAAATAA-T-ATTA
1 TAAATAATTAATTA
45411 TAAA-AATTAATTA
1 TAAATAATTAATTA
45424 TAAA
1 TAAA
45428 AGTGATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
12 6 0.23
13 15 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATAATTAATTA
Found at i:49215 original size:16 final size:17
Alignment explanation
Indices: 49191--49223 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49181 TGAGATATAA
49191 ATTTATT-AAATATTTT
1 ATTTATTAAAATATTTT
*
49207 ATTTTTTAAAATATTTT
1 ATTTATTAAAATATTTT
49224 TTATATTACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTATTAAAATATTTT
Found at i:53928 original size:6 final size:6
Alignment explanation
Indices: 53919--53949 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
53909 TATATATGTA
53919 TGTATG TGTATG TGTATG TGTATG TGTATG T
1 TGTATG TGTATG TGTATG TGTATG TGTATG T
53950 ATGTACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.32, T:0.52
Consensus pattern (6 bp):
TGTATG
Found at i:56767 original size:76 final size:76
Alignment explanation
Indices: 56641--56787 Score: 267
Period size: 76 Copynumber: 1.9 Consensus size: 76
56631 ATTTAAGACT
* *
56641 GTTGGATGAGTGAAATCAAAGGTTGAGATTAACTCCTTGTTTTTTTTCCCGAGTGATAATCTTCA
1 GTTGGATGAGTAAAATCAAAGGTTGAGATTAACTCCTTGTTTTTTTTCCCGAGTGATAATATTCA
56706 CATTTCCTACC
66 CATTTCCTACC
*
56717 GTTGGATGAGTAAAATCAAAGGTTGAGATTACCTCCTTGTTTTTTTTCCCGAGTGATAATATTCA
1 GTTGGATGAGTAAAATCAAAGGTTGAGATTAACTCCTTGTTTTTTTTCCCGAGTGATAATATTCA
56782 CATTTC
66 CATTTC
56788 ATACTTTTAA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.39
Consensus pattern (76 bp):
GTTGGATGAGTAAAATCAAAGGTTGAGATTAACTCCTTGTTTTTTTTCCCGAGTGATAATATTCA
CATTTCCTACC
Found at i:57979 original size:17 final size:17
Alignment explanation
Indices: 57928--57981 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 17
57918 AGCTAAAATT
*
57928 AATTAGTATAATTTGTTA
1 AATTAGTATAAGTTG-TA
*
57946 AGATTGAGGACTAAGTTGTA
1 A-ATT-AGTA-TAAGTTGTA
57966 AATTAGTATAAGTTGT
1 AATTAGTATAAGTTGT
57982 GATCTGAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 6 0.20
20 6 0.20
21 6 0.20
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (17 bp):
AATTAGTATAAGTTGTA
Found at i:59783 original size:19 final size:19
Alignment explanation
Indices: 59759--59802 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
59749 GGCCATTAAC
59759 GATAAATGATTGATTAATT
1 GATAAATGATTGATTAATT
* *
59778 GATAAAGGATTGATTTATT
1 GATAAATGATTGATTAATT
59797 -ATAAAT
1 GATAAAT
59803 TAATAACGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (19 bp):
GATAAATGATTGATTAATT
Found at i:59907 original size:30 final size:29
Alignment explanation
Indices: 59854--59915 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
59844 AATTTGTTAT
59854 TTCTAAAACTTCAAATTGAAAATTAAAAAC
1 TTCTAAAACTTCAAATTGAAAATT-AAAAC
** *
59884 TTCTAAAACTTCAAATTTCAAATTGAAAC
1 TTCTAAAACTTCAAATTGAAAATTAAAAC
59913 TTC
1 TTC
59916 AAGATCAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.47, C:0.16, G:0.03, T:0.34
Consensus pattern (29 bp):
TTCTAAAACTTCAAATTGAAAATTAAAAC
Found at i:63288 original size:21 final size:21
Alignment explanation
Indices: 63262--63315 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
63252 GCGTTGCATT
63262 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
63283 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
63304 TCGCGTTGCGAT
1 TCGCGTTGCGAT
63316 TTTCCAGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:63471 original size:6 final size:6
Alignment explanation
Indices: 63460--63488 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
63450 GAAGACACGT
63460 ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
63489 CGAGACGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:64115 original size:22 final size:22
Alignment explanation
Indices: 64086--64176 Score: 91
Period size: 22 Copynumber: 4.3 Consensus size: 22
64076 AATTTGGAAA
64086 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
64108 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
64130 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
*
64149 ATCGCAACGAC-ATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
64170 ATCGCAA
1 ATCGCAA
64177 AGCGAAATGA
Statistics
Matches: 54, Mismatches: 12, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
19 13 0.24
20 3 0.06
21 11 0.20
22 27 0.50
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:64191 original size:41 final size:41
Alignment explanation
Indices: 64122--64226 Score: 110
Period size: 41 Copynumber: 2.6 Consensus size: 41
64112 CAACAACAAC
* *
64122 TGTAGACTATCGC-AA-CGAATTTGGAAAATCGCAACGAC-AT
1 TGTAGACTATCGCAAAGCGAA-ATGAAAAATCGCAACG-CGAT
*
64162 TGTAGACTATCGCAAAGCGAAATGAAAAATCGTAACGCGAT
1 TGTAGACTATCGCAAAGCGAAATGAAAAATCGCAACGCGAT
* *
64203 TTTCA-ACTATCGCAACGCGAAATG
1 TGT-AGACTATCGCAAAGCGAAATG
64227 CAACGCGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
40 14 0.25
41 37 0.66
42 5 0.09
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (41 bp):
TGTAGACTATCGCAAAGCGAAATGAAAAATCGCAACGCGAT
Found at i:64230 original size:21 final size:21
Alignment explanation
Indices: 64167--64230 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
64157 GACATTGTAG
*
64167 ACTATCGCAAAGCGAAATG-A
1 ACTATCGCAACGCGAAATGCA
** * ** *
64187 AAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
64208 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
64229 AC
1 AC
64231 GCGAATTTGC
Statistics
Matches: 30, Mismatches: 13, Indels: 1
0.68 0.30 0.02
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:77153 original size:3 final size:3
Alignment explanation
Indices: 77134--77301 Score: 211
Period size: 3 Copynumber: 56.7 Consensus size: 3
77124 TTATTTATTA
*
77134 AAT AAT -AT AAT ATAT AAT AAT -AT ATAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT
* **
77180 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GCT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
77228 AAT AAT ACT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
77275 GAT AAT AAT AAT -AT AAT -AT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
77302 AATGGATAAA
Statistics
Matches: 143, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
2 10 0.07
3 124 0.87
4 9 0.06
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:77811 original size:113 final size:112
Alignment explanation
Indices: 77591--78489 Score: 1367
Period size: 113 Copynumber: 8.0 Consensus size: 112
77581 TCAGATGATA
* * * *
77591 TCAAACAAAGGTTGAACAAGCTCTTCTTATTATGAACTTTTTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCT
* ** *
77656 TCTCATTCATGAACTTTCTTTGGCCATGTTGATCCATC-AATGATGAAT
65 TCTCATT-ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
* * *
77704 TTAAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
77769 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
65 TCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
*
77817 TCAGGCAAAGGTTGAACAAGTTC-TCTCATTATG-ACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
* ** *
77880 CTCATTCATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAAT
66 CTCATT-ATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
* * *
77928 TTAAACAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
* * *
77993 CTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
66 CTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
* *
78040 TCAGGCAAAAGGTTG-ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* *
78104 TCTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAAT
65 TCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
78152 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
* * *
78217 TCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGAT
65 TCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
* *
78265 TCAGGCAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
1 TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
* *
78329 CTCATTATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAAT
66 CTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
78376 TCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
1 TCAAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCT
*
78441 TCTCATTATGAACTTTCTCTGGTAATGATGATCCATCAAATGATGAAT
65 TCTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
78489 T
1 T
78490 TGAATCTTTG
Statistics
Matches: 714, Mismatches: 63, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
110 36 0.05
111 164 0.23
112 198 0.28
113 288 0.40
114 28 0.04
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (112 bp):
TCAAGCAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTT
CTCATTATGAACTTTCTCTGGAAATGATGATCCATCAAATGATGAAT
Found at i:78150 original size:224 final size:226
Alignment explanation
Indices: 77596--78485 Score: 1526
Period size: 224 Copynumber: 4.0 Consensus size: 226
77586 TGATATCAAA
** * *
77596 CAAAGGTTGAACAAGCTCTTCTTATTATGAACTTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAGGTTGAACAAATTCTTCTCATTATGAAC-TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* ** * *
77661 TTCATGAACTTTCTTTGGCCATGTTGATCCATCAA-TGATGAATTTAAACAAAAAGTTGAACAAG
65 TTCATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAG
77725 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
130 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
77790 GAAAAGATGATCCACCAAATGATGGATTCAGG
195 GAAAAGATGATCCACCAAATGATGGATTCAGG
*
77822 CAAAGGTTGAACAAGTTC-TCTCATTATG-ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** * *
77885 TCATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACAAAA-GTTGAACAAGT
66 TCATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAGT
77949 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
78014 AAAAGATGATCCACCAAATGATGGATTCAGG
196 AAAAGATGATCCACCAAATGATGGATTCAGG
78045 CAAAAGGTTG-ACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 C-AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
*
78109 TT-ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAG
65 TTCATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAG
78173 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
130 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
78238 GAAAAGATGATCCACCAAATGATGGATTCAGG
195 GAAAAGATGATCCACCAAATGATGGATTCAGG
78270 CAAA-GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
78334 T-ATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAGCAAAAGGTTGAACAAGT
66 TCATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAGT
78398 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* * *
78463 TAATGATGATCCATCAAATGATG
196 AAAAGATGATCCACCAAATGATG
78486 AATTTGAATC
Statistics
Matches: 645, Mismatches: 13, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
223 185 0.29
224 290 0.45
225 153 0.24
226 17 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (226 bp):
CAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TCATGAACTTTCTCTGGAAATGTTGATCCATCAAGTGATGAATTCAAACAAAAGGTTGAACAAGT
TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGATGATCCACCAAATGATGGATTCAGG
Found at i:79171 original size:52 final size:52
Alignment explanation
Indices: 79036--79803 Score: 1328
Period size: 52 Copynumber: 14.7 Consensus size: 52
79026 CACTTCTTCG
*
79036 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTC-ATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC-CAATCA
*
79088 GATCA-ATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
79139 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* * *
79191 GATCAGATAACTCAAAGAACACTTCCAGAAGATACTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
79243 GATCAGATAACTCAAAG-ACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
79294 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
79347 GATCAG-TAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
*
79399 GATCAGATAACTCAAAGAACACTTCCAGAAGGTGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* *
79451 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* *
79504 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
*
79557 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
* *
79609 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
79662 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
79714 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
*
79766 GATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
79804 TGAGCACATA
Statistics
Matches: 688, Mismatches: 21, Indels: 14
0.95 0.03 0.02
Matches are distributed among these distances:
50 1 0.00
51 96 0.14
52 390 0.57
53 201 0.29
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (52 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
Found at i:79415 original size:105 final size:104
Alignment explanation
Indices: 79036--79803 Score: 1337
Period size: 105 Copynumber: 7.4 Consensus size: 104
79026 CACTTCTTCG
*
79036 GATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCTC-ATCAGATCA-ATAACT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTC-CAATCAGATCAGATAACT
79099 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
79139 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
* *
79204 AAAGAACACTTCCAGAAGATACTATGTTCTGTTCAACCA
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
79243 GATCAGATAACTCAAAG-ACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
*
79307 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
66 AAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
79347 GATCAG-TAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
* *
79411 CAAAGAACACTTCCAGAAGGTGCTATGTTCTGTCCAATCA
65 CAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
* *
79451 GATCAGATAACTCAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACT
1 GATCAGATAACTCAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACT
*
79516 CAAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
65 CAAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
79557 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
*
79622 AAAGAAACACTTCCAGAAGATGCTATGTTCTGTTCAACCA
66 AAAG-AACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
79662 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
*
79727 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCA
66 AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
*
79766 GATCAGATAACTCAAAGAAAACTTCCAGAAGATGCTAT
1 GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
79804 TGAGCACATA
Statistics
Matches: 639, Mismatches: 19, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
102 1 0.00
103 115 0.18
104 209 0.33
105 265 0.41
106 49 0.08
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.25
Consensus pattern (104 bp):
GATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCA
Found at i:80749 original size:1 final size:1
Alignment explanation
Indices: 80743--80785 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
80733 CCTTGACCCC
* * *
80743 TTTTTTTTCTTTTTCTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
80786 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:80756 original size:9 final size:9
Alignment explanation
Indices: 80742--80786 Score: 65
Period size: 9 Copynumber: 5.1 Consensus size: 9
80732 ACCTTGACCC
80742 CTTTTTTTT
1 CTTTTTTTT
*
80751 CTTTTTCTT
1 CTTTTTTTT
80760 CTTTTTTTT
1 CTTTTTTTT
80769 -TTTTTTTT
1 CTTTTTTTT
*
80777 TTTTTTTTT
1 CTTTTTTTT
80786 C
1 C
80787 AAGCATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
8 8 0.25
9 24 0.75
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:93337 original size:3 final size:3
Alignment explanation
Indices: 93329--93491 Score: 184
Period size: 3 Copynumber: 52.7 Consensus size: 3
93319 AATTATATTA
* *
93329 AAT AAT AAT AAT ATAT AAT AAT ATAT ATT AAT AAT AAT AAT AAAT ACT
1 AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT
**
93377 AAT AAT AAT AAT ATAT AAT AAT AAT AAT AAT GCT AAT -AT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
93422 AAT ACT AAT AAT AAT AAT ATT AAT AAT AAT AAT AAT ATT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
93470 AAT ATAT ATT AAT AAT ATAT AA
1 AAT A-AT AAT AAT AAT A-AT AA
93492 AATGGATAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.01
3 115 0.85
4 18 0.13
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (3 bp):
AAT
Done.