Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006726.1 Hibiscus syriacus cultivar Beakdansim tig00016850_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: 122775
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:8548 original size:39 final size:37
Alignment explanation
Indices: 8501--8580 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 37
8491 ATATCTAAAG
8501 TTTAGTTTTTATTTCATTTTAATACTAATCGTTAAAAA
1 TTTAGTTTTTATTTCATTTTAATAC-AATCGTTAAAAA
* * *
8539 CTTTAGTTTTTGTTTCATTTTAGTACAATCGTTCAAAA
1 -TTTAGTTTTTATTTCATTTTAATACAATCGTTAAAAA
8577 TTTA
1 TTTA
8581 ACATTAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 4 0.11
38 11 0.29
39 23 0.61
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (37 bp):
TTTAGTTTTTATTTCATTTTAATACAATCGTTAAAAA
Found at i:10309 original size:3 final size:3
Alignment explanation
Indices: 10301--10325 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
10291 AAGGTAAAAG
10301 TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC T
10326 TTTTCTCAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:10314 original size:71 final size:70
Alignment explanation
Indices: 10198--10338 Score: 221
Period size: 71 Copynumber: 2.0 Consensus size: 70
10188 CGAAACCGAT
*
10198 GAATATGAGTAGCTGATTGGGGAAGGTAAAAGGACTCCTCCTCCTCCTCTTCCT-CTATATTTCT
1 GAATATGAGTAGCTGATTGGGGAAGGTAAAAGGACTCCTCCTCCTCCTCCTCCTCCT-T-TTTCT
10262 CAAGCAC
64 CAAGCAC
* **
10269 GAATATGAGTAGTTGATTGGGGAAGGTAAAAGTCCTCCTCCTCCTCCTCCTCCTCCTTTTTCTCA
1 GAATATGAGTAGCTGATTGGGGAAGGTAAAAGGACTCCTCCTCCTCCTCCTCCTCCTTTTTCTCA
10334 AGCAC
66 AGCAC
10339 TTTCTTTCAT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 12 0.18
71 51 0.78
72 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.30
Consensus pattern (70 bp):
GAATATGAGTAGCTGATTGGGGAAGGTAAAAGGACTCCTCCTCCTCCTCCTCCTCCTTTTTCTCA
AGCAC
Found at i:10751 original size:2 final size:2
Alignment explanation
Indices: 10738--10771 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
10728 TTCATATGGG
* *
10738 AT AT AC AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10772 CATGCAAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:11153 original size:15 final size:15
Alignment explanation
Indices: 11135--11190 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
11125 TAACCGGTTT
11135 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
11150 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
* *
11167 CAGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
11182 CGATTTTAA
1 CGGTTTTAA
11191 TATTCCAGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
15 19 0.59
17 13 0.41
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:11606 original size:13 final size:13
Alignment explanation
Indices: 11584--11639 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
11574 TCAAGTTCGA
*
11584 TAATTCAAATACT
1 TAATTGAAATACT
11597 TAATTGAAATACT
1 TAATTGAAATACT
* *
11610 TAATT-AACTCAACA
1 TAATTGAAAT--ACT
11624 TAATTGAAATACT
1 TAATTGAAATACT
11637 TAA
1 TAA
11640 ATACTTCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 22 0.63
14 7 0.20
15 3 0.09
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.36
Consensus pattern (13 bp):
TAATTGAAATACT
Found at i:11721 original size:32 final size:33
Alignment explanation
Indices: 11625--11723 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
11615 AACTCAACAT
* * *
11625 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
11658 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
11691 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
11723 A
1 A
11724 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:11742 original size:21 final size:21
Alignment explanation
Indices: 11718--11757 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
11708 ACTTCAAGTT
11718 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
11739 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
11758 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:14065 original size:12 final size:12
Alignment explanation
Indices: 14048--14093 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
14038 TTCGGATAAA
14048 AACCGGTTTTTT
1 AACCGGTTTTTT
14060 AACCGGTTTTTTT
1 AACCGG-TTTTTT
14073 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
14087 ATCCGGT
1 AACCGGT
14094 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:14078 original size:15 final size:14
Alignment explanation
Indices: 14047--14086 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
14037 TTTCGGATAA
14047 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
14060 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
14073 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
14087 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:14215 original size:28 final size:26
Alignment explanation
Indices: 14175--14232 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
14165 AAAAAATCAG
*
14175 TTTTTCCCAAATCCGAT-TTCAGATATT
1 TTTTTCCAAAATCCGATATTC-GA-ATT
*
14202 TTTTTCGCAAAATCGGATATTCGAATT
1 TTTTTC-CAAAATCCGATATTCGAATT
14229 TTTT
1 TTTT
14233 GTACACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 13 0.48
28 11 0.41
29 3 0.11
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (26 bp):
TTTTTCCAAAATCCGATATTCGAATT
Found at i:15540 original size:3 final size:3
Alignment explanation
Indices: 15532--15581 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
15522 TCGGGTTTTA
* *
15532 ATT ATT ATT ATT ATT ATT AGTT ATT GTT -TT ATT A-T AAT ATT ATT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT
*
15576 AAT ATT
1 ATT ATT
15582 TACATTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:15796 original size:12 final size:12
Alignment explanation
Indices: 15779--15803 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15769 GTTTTAATAT
15779 AAAAAGCAAATC
1 AAAAAGCAAATC
15791 AAAAAGCAAATC
1 AAAAAGCAAATC
15803 A
1 A
15804 TTGAATCCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.16, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAAAGCAAATC
Found at i:16859 original size:29 final size:29
Alignment explanation
Indices: 16817--16880 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
16807 ATTGAACCAA
*
16817 AATTTATTTGAAAATTATTAACCAAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
*
16846 AATTAATTTGAAAATTATTAACCGAACCG
1 AATTAATTTGAAAATTATTAACCAAACCG
16875 AATTAA
1 AATTAA
16881 CCAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.33
Consensus pattern (29 bp):
AATTAATTTGAAAATTATTAACCAAACCG
Found at i:16943 original size:137 final size:138
Alignment explanation
Indices: 16568--16984 Score: 601
Period size: 139 Copynumber: 3.0 Consensus size: 138
16558 ATCGAATCAA
* *
16568 AATTTATTTGAAAATTATTAACCGAACCGAATTAA-CAGATTTTTTTGAAAATT-TTAACCGAAT
1 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCA-ATTTTTTT--AAATTATTAATCGAAT
* *
16631 TAATCGAAGTAAAAATTCAGTTAATTCAGTTCGGTTCATCGAACCAAAATTTATTTGAAAATTAT
63 TAATCGAAGCAAAAATTCAGTTAATTCAGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTAT
**
16696 TAACCAAACTA
128 TAACCAAACCG
* * *
16707 AAATAATTTAAAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCAAATTA
1 AATTAATTT-GAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAATTA
* *
16772 ATCGAAGCAAAAATT-AGGTTAATTCAACTT-GGTTAATTGAACCAAAATTTATTTGAAAATTAT
65 ATCGAAGCAAAAATTCA-GTTAATTC-AGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTAT
16835 TAACCAAACCG
128 TAACCAAACCG
*
16846 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTT-AATTATTAATTGAATTAA
1 AATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAATTAA
* *
16910 TCGAAGCAAAAATTCAATTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA
66 TCGAAGCAAAAATTCAGTTAATTCAGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA
* *
16975 TCGAACCG
131 CCAAACCG
16983 AA
1 AA
16985 CAAATTTTGT
Statistics
Matches: 250, Mismatches: 21, Indels: 16
0.87 0.07 0.06
Matches are distributed among these distances:
136 2 0.01
137 80 0.32
138 43 0.17
139 87 0.35
140 36 0.14
141 2 0.01
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.35
Consensus pattern (138 bp):
AATTAATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAATTAA
TCGAAGCAAAAATTCAGTTAATTCAGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA
CCAAACCG
Found at i:16991 original size:137 final size:137
Alignment explanation
Indices: 16573--16991 Score: 571
Period size: 137 Copynumber: 3.0 Consensus size: 137
16563 ATCAAAATTT
*
16573 ATTTGAAAATTATTAACCGAACCGAATTAA-CAGATTTTTTTGAAAATT-TTAACCGAATTAATC
1 ATTTGAAAATTATTAACCGAACCGAATTAACCA-ATTTTTTT--AAATTATTAATCGAATTAATC
* *
16636 GAAGTAAAAATTCAGTTAATTCAGTTCGGTTCATCGAACCAAAATTTATTTGAAAATTATTAACC
63 GAAGCAAAAATTCAGTTAATTCAGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA-C
*
16701 AAA-CTAAAATA
127 AAACCGAAAA-A
* *
16712 ATTTAAAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCAAATTAATCGA
1 ATTT-GAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAATTAATCGA
* *
16777 AGCAAAAATT-AGGTTAATTCAACTT-GGTTAATTGAACCAAAATTTATTTGAAAATTATTAACC
65 AGCAAAAATTCA-GTTAATTC-AGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA-C
**
16840 AAACCGAATTA
127 AAACCGAAAAA
*
16851 ATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTT-AATTATTAATTGAATTAATCGAA
1 ATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAATTAATCGAA
* * *
16915 GCAAAAATTCAATTAATTCGGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAATCGAA
66 GCAAAAATTCAGTTAATTCAGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAA-CAAA
*
16980 CCGAACAA
130 CCGAAAAA
16988 ATTT
1 ATTT
16992 TGTTTAATTC
Statistics
Matches: 251, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
136 2 0.01
137 85 0.34
138 43 0.17
139 80 0.32
140 39 0.16
141 2 0.01
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (137 bp):
ATTTGAAAATTATTAACCGAACCGAATTAACCAATTTTTTTAAATTATTAATCGAATTAATCGAA
GCAAAAATTCAGTTAATTCAGTTCGGTTAATCGAACCAAAATTTATTTGAAAATTATTAACAAAC
CGAAAAA
Found at i:17575 original size:29 final size:29
Alignment explanation
Indices: 17534--17599 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
17524 TGAATCAATT
17534 AAAAAGTTTGGTGGTATGATTGAGACAAA
1 AAAAAGTTTGGTGGTATGATTGAGACAAA
17563 AAAAAGTTTGGTGGTATGATTGAGACAAA
1 AAAAAGTTTGGTGGTATGATTGAGACAAA
17592 AAAAAGTT
1 AAAAAGTT
17600 CAATGGTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.27
Consensus pattern (29 bp):
AAAAAGTTTGGTGGTATGATTGAGACAAA
Found at i:17606 original size:29 final size:29
Alignment explanation
Indices: 17545--17606 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
17535 AAAAGTTTGG
***
17545 TGGTATGATTGAGACAAAAAAAAGTTTGG
1 TGGTATGATTGAGACAAAAAAAAGTTCAA
17574 TGGTATGATTGAGACAAAAAAAAGTTCAA
1 TGGTATGATTGAGACAAAAAAAAGTTCAA
17603 TGGT
1 TGGT
17607 CAAATTGATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.05, G:0.26, T:0.27
Consensus pattern (29 bp):
TGGTATGATTGAGACAAAAAAAAGTTCAA
Found at i:17613 original size:29 final size:29
Alignment explanation
Indices: 17545--17614 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
17535 AAAAGTTTGG
* ***
17545 TGGTATGATTGAGACAAAAAAAAGTTTGG
1 TGGTATAATTGAGACAAAAAAAAGTTCAA
*
17574 TGGTATGATTGAGACAAAAAAAAGTTCAA
1 TGGTATAATTGAGACAAAAAAAAGTTCAA
17603 TGGTCA-AATTGA
1 TGGT-ATAATTGA
17615 TTATTAACTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.43, C:0.06, G:0.24, T:0.27
Consensus pattern (29 bp):
TGGTATAATTGAGACAAAAAAAAGTTCAA
Found at i:39785 original size:17 final size:17
Alignment explanation
Indices: 39763--39803 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39753 CTTAAATTCT
*
39763 TCATTAATTCTTTAAAA
1 TCATTAACTCTTTAAAA
*
39780 TCATTAACTCTTTATAA
1 TCATTAACTCTTTAAAA
*
39797 TCCTTAA
1 TCATTAA
39804 AACATAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.37, C:0.17, G:0.00, T:0.46
Consensus pattern (17 bp):
TCATTAACTCTTTAAAA
Found at i:45758 original size:29 final size:29
Alignment explanation
Indices: 45716--45775 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
45706 CACATATACT
45716 AAGCTTGGGATTTGATTTTTAGGCCCTCC
1 AAGCTTGGGATTTGATTTTTAGGCCCTCC
45745 AAGCTTGGGATTTGATTTTTAGGCCCTCC
1 AAGCTTGGGATTTGATTTTTAGGCCCTCC
45774 AA
1 AA
45776 TTAATTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (29 bp):
AAGCTTGGGATTTGATTTTTAGGCCCTCC
Found at i:54925 original size:14 final size:13
Alignment explanation
Indices: 54898--54951 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
54888 AGTTATGGAT
54898 TTTTTTTTAAAAAAA
1 TTTTTTTT--AAAAA
*
54913 TTATTTTTTAAAAT
1 TT-TTTTTTAAAAA
*
54927 TTTTATTTTAAATA
1 TTTT-TTTTAAAAA
54941 TTTTTTTTAAA
1 TTTTTTTTAAA
54952 TTATTAGAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.26
14 17 0.50
15 2 0.06
16 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTTTTTAAAAA
Found at i:54956 original size:14 final size:14
Alignment explanation
Indices: 54910--54956 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
54900 TTTTTTAAAA
*
54910 AAATTA-TTTTTTA
1 AAATTATTTTTTTT
*
54923 AAATT-TTTATTTT
1 AAATTATTTTTTTT
54936 AAA-TATTTTTTTT
1 AAATTATTTTTTTT
54949 AAATTATT
1 AAATTATT
54957 AGAACGCAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 1 0.04
13 23 0.82
14 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
AAATTATTTTTTTT
Found at i:58712 original size:74 final size:74
Alignment explanation
Indices: 58609--58753 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 74
58599 ATATTTTAAG
* * *
58609 TATTTGAATATGAGATCTCAAGTATTAATAATAATTCTTTTACTATAAAGATCAGAGATTTAAAT
1 TATTTGAATATGAGATATCAAGTAATAATAATAATTATTTTACTATAAAGATCAGAGATTTAAAT
58674 AACGGTAGA
66 AACGGTAGA
* * *
58683 TATTTGAATATGGGATATCAGAG-AATAATAATAATTATTTTACTATGAAGATCATAGATTTAAA
1 TATTTGAATATGAGATATCA-AGTAATAATAATAATTATTTTACTATAAAGATCAGAGATTTAAA
*
58747 TAGCGGT
65 TAACGGT
58754 CTGTGATATA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
74 61 0.97
75 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (74 bp):
TATTTGAATATGAGATATCAAGTAATAATAATAATTATTTTACTATAAAGATCAGAGATTTAAAT
AACGGTAGA
Found at i:60223 original size:13 final size:14
Alignment explanation
Indices: 60197--60226 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
60187 GTAAAATTAT
60197 CCGACCCAGTTGAC
1 CCGACCCAGTTGAC
60211 CCGACCC-GTTGAC
1 CCGACCCAGTTGAC
60224 CCG
1 CCG
60227 GATATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (14 bp):
CCGACCCAGTTGAC
Found at i:60587 original size:17 final size:17
Alignment explanation
Indices: 60565--60616 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
60555 AACCGGGTAT
60565 CGGATACCCGTAAAATC
1 CGGATACCCGTAAAATC
**
60582 CGGATACCCG-ATTA-C
1 CGGATACCCGTAAAATC
*
60597 CGGGTACCCGTAAAATC
1 CGGATACCCGTAAAATC
60614 CGG
1 CGG
60617 GTTGAGACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 10 0.36
16 4 0.14
17 14 0.50
ACGTcount: A:0.29, C:0.31, G:0.23, T:0.17
Consensus pattern (17 bp):
CGGATACCCGTAAAATC
Found at i:68192 original size:229 final size:227
Alignment explanation
Indices: 67787--68235 Score: 792
Period size: 229 Copynumber: 2.0 Consensus size: 227
67777 GTAAATTATC
* * *
67787 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
67852 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
67917 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
67982 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
68015 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
68080 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAAT-ATAAT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAT-AT
* *
68144 TTTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAAT
129 TTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAT
68209 TGAAACATAAATTACATAACTTTAAAA
194 TGAAACATAAATTACATAACTTTAAAA
68236 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 8, Indels: 4
0.95 0.04 0.02
Matches are distributed among these distances:
228 42 0.20
229 169 0.80
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:68324 original size:20 final size:19
Alignment explanation
Indices: 68301--68346 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 19
68291 CGATATACCA
68301 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
68321 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
68341 GGTAAA
1 GGTAAA
68347 TTTAAAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.54, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:68491 original size:20 final size:19
Alignment explanation
Indices: 68468--68514 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
68458 CGATATAACA
68468 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
68488 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
68508 GGTAAAA
1 GGTAAAA
68515 TGATACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:68516 original size:17 final size:18
Alignment explanation
Indices: 68472--68519 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
68462 ATAACAGGTA
68472 AAAATATGATAAAACCGGT
1 AAAA-ATGATAAAACCGGT
68491 AACAAAATGATAAAACCGGT
1 -A-AAAATGATAAAACCGGT
68511 -AAAATGATA
1 AAAAATGATA
68520 CCGGATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 9 0.33
20 15 0.56
21 3 0.11
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.19
Consensus pattern (18 bp):
AAAAATGATAAAACCGGT
Found at i:70791 original size:21 final size:21
Alignment explanation
Indices: 70744--70808 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
70734 AAGACAATCA
* *
70744 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
70766 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
70786 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
70807 AG
1 AG
70809 GAATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:70884 original size:33 final size:33
Alignment explanation
Indices: 70842--70907 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
70832 AAATAGATGG
*
70842 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
70875 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
70908 TATTAAGATG
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:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:71422 original size:23 final size:23
Alignment explanation
Indices: 71391--71454 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
71381 ATAGGTAAAC
*
71391 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGCCCTT
* * **
71414 ATATAATGTAATAGATATCGTTT
1 ATATAATGTAATAGGTAGCCCTT
71437 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
71455 TGGTTATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCCCTT
Found at i:71461 original size:23 final size:23
Alignment explanation
Indices: 71391--71463 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
71381 ATAGGTAAAC
* **
71391 ATATGATGTAATAGGTAGCCCTT
1 ATATAATGTAATAGGTAGTGCTT
* *
71414 ATATAATGTAATAGATA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
71437 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
71460 ATAT
1 ATAT
71464 TGTAAAGTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
23 40 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:72987 original size:2 final size:2
Alignment explanation
Indices: 72978--73008 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
72968 TGGTTTATTA
72978 AT AT -T 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
73009 TCATATGCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:75719 original size:19 final size:19
Alignment explanation
Indices: 75698--75733 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
75688 AATATATTTA
75698 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
75716 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
75734 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:76294 original size:13 final size:13
Alignment explanation
Indices: 76276--76304 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
76266 CCACCGTACT
76276 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
76289 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
76302 CCG
1 CCG
76305 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:77018 original size:3 final size:3
Alignment explanation
Indices: 77010--77124 Score: 171
Period size: 3 Copynumber: 38.7 Consensus size: 3
77000 TTATTTATTA
*
77010 AAT AAT AAT AAT AAT AAT -AT ATAT ATT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* *
77054 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
77102 AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
77125 AATGGATAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
2 4 0.04
3 94 0.93
4 3 0.03
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:77665 original size:113 final size:113
Alignment explanation
Indices: 77418--78433 Score: 1757
Period size: 113 Copynumber: 9.0 Consensus size: 113
77408 GATATCAAAC
** *
77418 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * * * ***
77483 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
* *
77532 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
77597 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAAGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
*
77645 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
77710 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
77758 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
77823 ATGAACTTTCTCTGG-AAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
77870 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
77935 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
77983 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
78048 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
*
78096 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
78161 ATGAACTTTCTCTGGAAATGTTGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
*
78209 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
78274 ATGAACTTTCTCT-GAAAGAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAA-AGATGATCCACCAAATGATGGATTCAGGTA
78322 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
78387 ATGAACCTTCTCTGGTAATGTTGATCCACCAAATGATGGATTCAGGT
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
78434 CTTTGCTAAA
Statistics
Matches: 871, Mismatches: 28, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
112 116 0.13
113 690 0.79
114 65 0.07
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
Found at i:79114 original size:52 final size:52
Alignment explanation
Indices: 79049--79469 Score: 767
Period size: 52 Copynumber: 8.1 Consensus size: 52
79039 TTCTAAATCA
79049 ATGCT-TGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATG-TTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
79101 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
79153 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
79205 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
79256 ATGCTATGTTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
79307 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
79359 ATGCTATGTTCTGTTCAACCAGGTCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
79411 ATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
79463 ATGCTAT
1 ATGCTAT
79470 TGAGCACATA
Statistics
Matches: 362, Mismatches: 5, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
51 101 0.28
52 259 0.72
53 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (52 bp):
ATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:79419 original size:206 final size:207
Alignment explanation
Indices: 79065--79469 Score: 769
Period size: 206 Copynumber: 2.0 Consensus size: 207
79055 GATTCTGTCC
79065 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGAT
79130 AACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
66 AACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
79195 CTTCCAGAAGATGCTATGTTC--TTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
131 CTTCCAGAAGATGCTATGTTCTGTTC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGAT
79258 GCTATGTTCTTCT
195 GCTATGTTCTTCT
79271 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGAT
* *
79336 AACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTTCAACCAGGTCAGATAACTCAAAGAACA
66 AACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
79401 CTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
131 CTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
79466 CTAT
196 CTAT
79470 TGAGCACATA
Statistics
Matches: 195, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
206 149 0.76
207 43 0.22
208 3 0.02
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (207 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGAT
AACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATGTTCTGTTCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
CTATGTTCTTCT
Found at i:80048 original size:19 final size:20
Alignment explanation
Indices: 80026--80067 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
80016 AATAGAAAAG
*
80026 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
80045 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
80065 AAT
1 AAT
80068 TGAACTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:80441 original size:11 final size:11
Alignment explanation
Indices: 80425--80449 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
80415 TCTATATTTA
80425 TTTATTTTTTT
1 TTTATTTTTTT
80436 TTTATTTTTTT
1 TTTATTTTTTT
80447 TTT
1 TTT
80450 CTTTCTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:80441 original size:15 final size:14
Alignment explanation
Indices: 80397--80449 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
80387 TTGACCCTCC
* *
80397 TTTTTTCTTTTTTC
1 TTTTTTTTTTTTTA
* * *
80411 TTTTTCTATATTTA
1 TTTTTTTTTTTTTA
80425 TTTATTTTTTTTTTA
1 TTT-TTTTTTTTTTA
80440 TTTTTTTTTT
1 TTTTTTTTTT
80450 CTTTCTTTTC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
14 19 0.63
15 11 0.37
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTTTTTTTA
Found at i:91492 original size:18 final size:17
Alignment explanation
Indices: 91464--91497 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
91454 ATATATTTAA
91464 AAACAATAAAATAAATT
1 AAACAATAAAATAAATT
91481 AAACATATAAAATAAAT
1 AAACA-ATAAAATAAAT
91498 GACTAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.24
Consensus pattern (17 bp):
AAACAATAAAATAAATT
Found at i:92054 original size:13 final size:13
Alignment explanation
Indices: 92036--92064 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
92026 CCACCGTACT
92036 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
92049 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
92062 CCG
1 CCG
92065 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:92773 original size:3 final size:3
Alignment explanation
Indices: 92765--92884 Score: 170
Period size: 3 Copynumber: 39.7 Consensus size: 3
92755 TTATTTATTA
* *
92765 AAT AAT AAT AAT AAT AAT -AT ATAT ATT AAT AAT AAT AAT AAAT ACT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT
*
92811 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
92859 ATT AAT ATT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
92885 AATGGATAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.02
3 96 0.92
4 6 0.06
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:96066 original size:58 final size:60
Alignment explanation
Indices: 95971--96082 Score: 156
Period size: 58 Copynumber: 1.9 Consensus size: 60
95961 TATTTTGAAC
*
95971 TTTTAATAGTCGAGAGACTTAACAAAACAACATTCTATAGTTAGATGACCATTTTATAAT
1 TTTTAATAGTCGAGAGACTTAACAAAACAACATTCTATAGTTAGAGGACCATTTTATAAT
* ** * *
96031 TTTTAATAGTCGA-A-ACTTAATAAAGTAATATTCTATAGTTGGAGGACCATTT
1 TTTTAATAGTCGAGAGACTTAACAAAACAACATTCTATAGTTAGAGGACCATTT
96083 GTGTACTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
58 32 0.70
59 1 0.02
60 13 0.28
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (60 bp):
TTTTAATAGTCGAGAGACTTAACAAAACAACATTCTATAGTTAGAGGACCATTTTATAAT
Found at i:98216 original size:19 final size:19
Alignment explanation
Indices: 98192--98228 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
98182 AGAAGATAAG
98192 AAGTTTGATTTCATTTTAA
1 AAGTTTGATTTCATTTTAA
*
98211 AAGTTTGGTTTCATTTTA
1 AAGTTTGATTTCATTTTA
98229 GTTTTCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.05, G:0.14, T:0.54
Consensus pattern (19 bp):
AAGTTTGATTTCATTTTAA
Found at i:98553 original size:60 final size:60
Alignment explanation
Indices: 98434--98581 Score: 154
Period size: 60 Copynumber: 2.5 Consensus size: 60
98424 ATACGAATAG
* * * * * *
98434 TTTGGGATGAAATTCAAATGTTAAAAAATTTTGGGGCCGATTTAGAATAAAGATCATAAT
1 TTTGGGATGAAATTAAAATATTAAAAAAATTTAGGGCCGATTTAAAAGAAAGATCATAAT
* * * *
98494 TTTGGGATGAAATTGAAATATTAAAAAAATTTAGGGCTGATTTAAAAGGATAG-TTATAAT
1 TTTGGGATGAAATTAAAATATTAAAAAAATTTAGGGCCGATTTAAAA-GAAAGATCATAAT
* * * *
98554 TTAGGAATGCAATTAAAATATTTAAAAA
1 TTTGGGATGAAATTAAAATATTAAAAAA
98582 TATAACGACC
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
60 70 0.96
61 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (60 bp):
TTTGGGATGAAATTAAAATATTAAAAAAATTTAGGGCCGATTTAAAAGAAAGATCATAAT
Found at i:117677 original size:14 final size:14
Alignment explanation
Indices: 117658--117684 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
117648 AAAAACCCTC
117658 AGTTGAAATCATTA
1 AGTTGAAATCATTA
117672 AGTTGAAATCATT
1 AGTTGAAATCATT
117685 GAAGATCTCA
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:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (14 bp):
AGTTGAAATCATTA
Found at i:119611 original size:20 final size:20
Alignment explanation
Indices: 119586--119639 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 20
119576 TATTTGATTT
119586 AAATTTTATATTATTAATAA
1 AAATTTTATATTATTAATAA
119606 AAATTTTA-ATTA--AATAA
1 AAATTTTATATTATTAATAA
* *
119623 ATATTTT-TAATATTAAT
1 AAATTTTATATTATTAAT
119640 TTTTTAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
17 14 0.48
19 7 0.24
20 8 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
AAATTTTATATTATTAATAA
Found at i:119700 original size:2 final size:2
Alignment explanation
Indices: 119693--119737 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
119683 TTTTTATTAT
119693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
119735 TA T
1 TA T
119738 CATACAGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:119755 original size:26 final size:26
Alignment explanation
Indices: 119740--119792 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
119730 ATATATATCA
*
119740 TACAGCTAGCAAATATATTTTAAAAT
1 TACAGCTAGCAAATATATTATAAAAT
*
119766 TACAGCTAGCAAATATATTTTAAAAT
1 TACAGCTAGCAAATATATTATAAAAT
119792 T
1 T
119793 GGTTTGTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (26 bp):
TACAGCTAGCAAATATATTATAAAAT
Done.