Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001638.1 Hibiscus syriacus cultivar Beakdansim tig00003277_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: 106078
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1715 original size:20 final size:20
Alignment explanation
Indices: 1675--1741 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 20
1665 GAAACTTAAA
1675 ATCGCAACGCA-AAATGACT
1 ATCGCAACGCAGAAATGACT
*
1694 ATCGCAACGCAGAAATGGCT
1 ATCGCAACGCAGAAATGACT
* **
1714 ATCGCAATGC-GAAATGAAA
1 ATCGCAACGCAGAAATGACT
1733 ATCGCAACG
1 ATCGCAACG
1742 AAAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCAGAAATGACT
Found at i:1749 original size:14 final size:14
Alignment explanation
Indices: 1730--1787 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1720 ATGCGAAATG
1730 AAAATCGCAACGAA
1 AAAATCGCAACGAA
1744 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
*
1760 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAA
1776 AAAATCGCAACG
1 AAAATCGCAACG
1788 CGAAACACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:1772 original size:32 final size:33
Alignment explanation
Indices: 1714--1792 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
1704 AGAAATGGCT
1714 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
1747 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
1779 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
1793 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 28 0.64
33 16 0.36
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:1879 original size:14 final size:14
Alignment explanation
Indices: 1816--1879 Score: 74
Period size: 14 Copynumber: 4.3 Consensus size: 14
1806 GCGATTTTCA
*
1816 TTTTGCGTTGCGAT
1 TTTTTCGTTGCGAT
*
1830 TTTGTCGTTGCGAT
1 TTTTTCGTTGCGAT
1844 TTCATTTCGCATTGCGAT
1 TT--TTTCG--TTGCGAT
1862 TTTTTCGTTGCGAT
1 TTTTTCGTTGCGAT
1876 TTTT
1 TTTT
1880 ATTTCGCATT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
14 25 0.58
16 9 0.21
18 9 0.21
ACGTcount: A:0.09, C:0.16, G:0.22, T:0.53
Consensus pattern (14 bp):
TTTTTCGTTGCGAT
Found at i:1889 original size:33 final size:33
Alignment explanation
Indices: 1804--1894 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 33
1794 ACAAATCGCA
* *
1804 TTGCGATTTTCATTTTGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1837 TTGCGA-TTTCATTTCGCATTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
1869 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
1895 AGCCATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.12, C:0.16, G:0.21, T:0.51
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:1913 original size:20 final size:20
Alignment explanation
Indices: 1888--1933 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
1878 TTATTTCGCA
1888 TTGCGATAGC-CATTTCCGCG
1 TTGCGATA-CTCATTTCCGCG
* *
1908 TTGCGATACTCATTTTCGTG
1 TTGCGATACTCATTTCCGCG
1928 TTGCGA
1 TTGCGA
1934 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (20 bp):
TTGCGATACTCATTTCCGCG
Found at i:2024 original size:16 final size:16
Alignment explanation
Indices: 1990--2030 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1980 TTACTTCAAC
1990 CAAAAGACAAAAACAAA
1 CAAAA-ACAAAAACAAA
* *
2007 CAAAAACAAATACTAA
1 CAAAAACAAAAACAAA
2023 CAAAAACA
1 CAAAAACA
2031 GTTTAGCGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.73, C:0.20, G:0.02, T:0.05
Consensus pattern (16 bp):
CAAAAACAAAAACAAA
Found at i:2438 original size:18 final size:18
Alignment explanation
Indices: 2412--2451 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2402 GTCGATCAGA
* *
2412 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
2430 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
2448 TGAT
1 TGAT
2452 GGCTGCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:3836 original size:20 final size:20
Alignment explanation
Indices: 3779--3836 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
3769 AATAGTTTCT
* *
3779 GAAAATGA-AATCGCAACAC
1 GAAAATGACTATCGCAACGC
3798 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
3818 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
3837 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:4416 original size:20 final size:20
Alignment explanation
Indices: 4310--4424 Score: 90
Period size: 20 Copynumber: 5.7 Consensus size: 20
4300 CGCTTTGAAA
*
4310 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
4331 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
4351 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
4371 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
4392 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
4412 ATCGCATTGCGAT
1 ATCGCATTGCGAT
4425 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.06
20 47 0.61
21 23 0.30
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:4443 original size:41 final size:41
Alignment explanation
Indices: 4351--4445 Score: 111
Period size: 41 Copynumber: 2.3 Consensus size: 41
4341 GAAAGTCAGA
* * * ** *
4351 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
*
4392 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CCAAT
4434 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4446 TTACTTATTC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:4848 original size:21 final size:21
Alignment explanation
Indices: 4823--4863 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4813 AAATAAGTCA
4823 AAAAATATATAAAATCATTAAT
1 AAAAA-ATATAAAATCATTAAT
* *
4845 AAAAAATTTAAAATTATTA
1 AAAAAATATAAAATCATTA
4864 TTTAAGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAAAATATAAAATCATTAAT
Found at i:4878 original size:27 final size:27
Alignment explanation
Indices: 4844--4909 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
4834 AAATCATTAA
*
4844 TAAAAAATTTAAAATTATTATTTAAGT
1 TAAAAAATTTAAAATTATTATTGAAGT
4871 TAAAAAATTTAAAATTATTATTGAAGT
1 TAAAAAATTTAAAATTATTATTGAAGT
*
4898 TAAAAAAATTAA
1 TAAAAAATTTAA
4910 TTATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (27 bp):
TAAAAAATTTAAAATTATTATTGAAGT
Found at i:4967 original size:2 final size:2
Alignment explanation
Indices: 4955--5007 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
4945 ATTTTAAATA
4955 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4996 AT AT AT AT AT AT
1 AT AT AT AT AT AT
5008 GAAATTATCA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12772 original size:43 final size:43
Alignment explanation
Indices: 12639--13173 Score: 305
Period size: 43 Copynumber: 12.6 Consensus size: 43
12629 AAAAATGATT
** * *
12639 AAATTAGGAACTTAAATTATTAAA-GTAAAAAATTG-GATTG-AA
1 AAATTAGGGGCTTCAATTA-TAAAGGT-AAAAAGTGAGATTGAAA
* *
12681 AAATTAGGGGCTTTAA-T-T-AAGGTGAAAAAATGAGAATT-AAA
1 AAATTAGGGGCTTCAATTATAAAGGT-AAAAAGTGAG-ATTGAAA
* *
12722 AAATTAGGGGTTTCAATTATAAAGGTAGAAAGTGAGATTGAAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGAAA
* * *
12765 AAATTAGGGACATCAATTATAAAGGTAAAAAGTGGGATTGAAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGAAA
* * * * * *
12808 AATTTAAGAGCCTCAATTATAAAGATAAAAAATGAGATT-AAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGAAA
* * * * * * * **
12850 AAA-CAGAGACTTTAATTATAAAGGTAGAAAGAGAAACAGAAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGAAA
* * * * * *
12892 AAAATATGAGCATCAATTATAAATGTAAAAAGTGTGATTGAATA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGAA-A
* * *
12936 AAATTAGGGGCCTCAATTAT-ACGCGTAAAAAGTGATATT-ATAA
1 AAATTAGGGGCTTCAATTATAAAG-GTAAAAAGTGAGATTGA-AA
* * ** * * *
12979 AAATAAGAGGCTTCAATTATAAAATTAGAAAGTGACATAGGAAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGAT-TGAAA
* *
13023 AAA-TAGGGG-TCTCAATTATAAAGTTAAAAATTGA-ATTTGAAA
1 AAATTAGGGGCT-TCAATTATAAAGGTAAAAAGTGAGA-TTGAAA
* * * * *
13065 AAATTA-GAGCCTGAATTATAAATGTAAAAAGT-AGAACTGAAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAG-ATTGAAA
**** * * *
13107 AAATTAGATATTTTAATTATAAAGGTAAAAAATAAGATT-ATAA
1 AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGA-AA
* *
13150 AAATTAGAAGCCTT-AATTATAAAG
1 AAATTAG-GGGCTTCAATTATAAAG
13174 AAAAAATAAA
Statistics
Matches: 374, Mismatches: 93, Indels: 51
0.72 0.18 0.10
Matches are distributed among these distances:
38 2 0.01
39 10 0.03
40 1 0.00
41 42 0.11
42 68 0.18
43 203 0.54
44 47 0.13
45 1 0.00
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.27
Consensus pattern (43 bp):
AAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGAGATTGAAA
Found at i:12909 original size:84 final size:85
Alignment explanation
Indices: 12734--12939 Score: 200
Period size: 84 Copynumber: 2.4 Consensus size: 85
12724 ATTAGGGGTT
* * * * *
12734 TCAATTATAAAGGTAGAAAGTGAGATTGAAAAAATTAGGGACATCAATTATAAAGGTAAAAAGTG
1 TCAATTATAAA-GTAAAAAATGAGATTGAAAAAATCAGAGACATCAATTATAAAGGTAAAAAGAG
** ** ** *
12799 GGATTGAAAAATTTAAGAGCC
65 AAACAGAAAAAAATAAGAGCA
* * *
12820 TCAATTATAAAGATAAAAAATGAGATT-AAAAAA-CAGAGACTTTAATTATAAAGGTAGAAAGAG
1 TCAATTATAAAG-TAAAAAATGAGATTGAAAAAATCAGAGACATCAATTATAAAGGTAAAAAGAG
*
12883 AAACAGAAAAAAATATGAGCA
65 AAACAGAAAAAAATAAGAGCA
* *
12904 TCAATTATAAATGTAAAAAGTGTGATTGAATAAAAT
1 TCAATTATAAA-GTAAAAAATGAGATTGAA-AAAAT
12940 TAGGGGCCTC
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
84 60 0.62
85 10 0.10
86 27 0.28
ACGTcount: A:0.52, C:0.05, G:0.18, T:0.24
Consensus pattern (85 bp):
TCAATTATAAAGTAAAAAATGAGATTGAAAAAATCAGAGACATCAATTATAAAGGTAAAAAGAGA
AACAGAAAAAAATAAGAGCA
Found at i:13203 original size:40 final size:40
Alignment explanation
Indices: 13119--13239 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 40
13109 ATTAGATATT
*
13119 TTAATTATAAAGGTAAAAAATAAGATTATAAAAATT-AGAAGCC
1 TTAATTATAAA-G-AAAAAATAAGATTA-AAAAATTAAG-GGCC
*
13162 TTAATTATAAAGAAAAAATAAAATTAAAAAATTAAGGGCC
1 TTAATTATAAAGAAAAAATAAGATTAAAAAATTAAGGGCC
** * * * *
13202 TTGCTTGTGAAAGTAAAAATATGATTGAAAAATTAAGG
1 TTAATTAT-AAAGAAAAAATAAGATTAAAAAATTAAGG
13240 ACCTGATAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 15 0.22
41 40 0.60
42 1 0.01
43 11 0.16
ACGTcount: A:0.54, C:0.04, G:0.14, T:0.28
Consensus pattern (40 bp):
TTAATTATAAAGAAAAAATAAGATTAAAAAATTAAGGGCC
Found at i:13533 original size:14 final size:13
Alignment explanation
Indices: 13514--13565 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 13
13504 TAACTAGTAA
13514 TATTTTTATAATCT
1 TATTTTTATAAT-T
*
13528 TATTTTTAATAA-A
1 TATTTTT-ATAATT
13541 TATTTTTATAATTT
1 TATTTTTATAA-TT
13555 TATTTTT-TAAT
1 TATTTTTATAAT
13566 AAATATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
12 5 0.15
13 10 0.30
14 14 0.42
15 4 0.12
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TATTTTTATAATT
Found at i:13544 original size:13 final size:13
Alignment explanation
Indices: 13528--13576 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 13
13518 TTTATAATCT
13528 TATTTTTAATAAA
1 TATTTTTAATAAA
*
13541 TATTTTT-ATAATTT
1 TATTTTTAATAA--A
13555 TATTTTTTAATAAA
1 TA-TTTTTAATAAA
13569 TATTTTTA
1 TATTTTTA
13577 TACAACACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 4 0.13
13 13 0.43
14 4 0.13
15 5 0.17
16 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TATTTTTAATAAA
Found at i:13544 original size:27 final size:28
Alignment explanation
Indices: 13512--13578 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
13502 TTTAACTAGT
13512 AATATTTTTATAATCTTA-TTTTTAATA
1 AATATTTTTATAATCTTATTTTTTAATA
*
13539 AATATTTTTATAATTTTATTTTTTAATA
1 AATATTTTTATAATCTTATTTTTTAATA
13567 AATATTTTTATA
1 AATATTTTTATA
13579 CAACACCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 17 0.45
28 21 0.55
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
AATATTTTTATAATCTTATTTTTTAATA
Found at i:13572 original size:14 final size:14
Alignment explanation
Indices: 13530--13575 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
13520 TATAATCTTA
13530 TTTTTAATAAATAT
1 TTTTTAATAAATAT
**
13544 TTTTATAAT-TTTAT
1 TTTT-TAATAAATAT
13558 TTTTTAATAAATAT
1 TTTTTAATAAATAT
13572 TTTT
1 TTTT
13576 ATACAACACC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 4 0.15
14 18 0.69
15 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTAATAAATAT
Found at i:19213 original size:32 final size:32
Alignment explanation
Indices: 19172--19237 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
19162 TGGTTTCATC
19172 AACCATCTCCTGCCTGCTTTTTATATTTAATA
1 AACCATCTCCTGCCTGCTTTTTATATTTAATA
* *
19204 AACCATCTCCTTCCTGTTTTTTATATTTAATA
1 AACCATCTCCTGCCTGCTTTTTATATTTAATA
19236 AA
1 AA
19238 AAAATTGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.27, C:0.23, G:0.05, T:0.45
Consensus pattern (32 bp):
AACCATCTCCTGCCTGCTTTTTATATTTAATA
Found at i:19459 original size:2 final size:2
Alignment explanation
Indices: 19452--19499 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
19442 GAATAATTAA
19452 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19494 AT AT AT
1 AT AT AT
19500 GCAATGTCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40421 original size:25 final size:24
Alignment explanation
Indices: 40372--40421 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
40362 TAAGGGTTTG
* * *
40372 TTTAATTTTTAAAAATATAATTAT
1 TTTAAATTTTAAAAATAAAAATAT
40396 TTTAAATTTTAAAATATAAAAATAT
1 TTTAAATTTTAAAA-ATAAAAATAT
40421 T
1 T
40422 AAGTTAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAAATTTTAAAAATAAAAATAT
Found at i:40423 original size:23 final size:24
Alignment explanation
Indices: 40373--40423 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
40363 AAGGGTTTGT
* ** *
40373 TTAATTTTTAAAAATATAATTATT
1 TTAAATTTTAAAAATATAAAAATA
40397 TTAAATTTT-AAAATATAAAAATA
1 TTAAATTTTAAAAATATAAAAATA
40420 TTAA
1 TTAA
40424 GTTAAATACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAAATTTTAAAAATATAAAAATA
Found at i:50553 original size:1 final size:1
Alignment explanation
Indices: 50494--50545 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
50484 TTTTGTTTTC
* * *** *
50494 AAAAAAAAAAAACAAAAAAAAAACAAAAAAGGCAAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
50546 GTCAAAAAGC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.88, C:0.08, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:50560 original size:22 final size:22
Alignment explanation
Indices: 50507--50553 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
50497 AAAAAAAAAC
50507 AAAAAAAAAACAAAAAAGGCAA
1 AAAAAAAAAACAAAAAAGGCAA
*
50529 AAAAAAAAAACAAAAAAGTCAA
1 AAAAAAAAAACAAAAAAGGCAA
50551 AAA
1 AAA
50554 GCCAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.83, C:0.09, G:0.06, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAACAAAAAAGGCAA
Found at i:65793 original size:18 final size:18
Alignment explanation
Indices: 65767--65801 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
65757 ACTTAGAATT
65767 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
* *
65785 TGTCTCGAATGACCACT
1 TGTCCCGAAGGACCACT
65802 CCTTAAGAAC
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:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:70623 original size:20 final size:20
Alignment explanation
Indices: 70600--70654 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
70590 ACCACGTGAA
70600 CAGTATCGATACTGTTTATG
1 CAGTATCGATACTGTTTATG
*
70620 CAGTATCAATACTGTTTATG
1 CAGTATCGATACTGTTTATG
*
70640 CAGTATCGCTACTGT
1 CAGTATCGATACTGT
70655 AAGACCTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (20 bp):
CAGTATCGATACTGTTTATG
Found at i:71959 original size:20 final size:20
Alignment explanation
Indices: 71922--71960 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
71912 CTCTAAATCA
* * *
71922 TTTTTCAAACTTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
71942 TTTTTCAAAATCTAATTTT
1 TTTTTCAAAATCTAATTTT
71961 ACTTTCAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:73211 original size:21 final size:22
Alignment explanation
Indices: 73185--73225 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
73175 CCAAAATAAG
* *
73185 GAGTATTGGTACTT-CTTTAAT
1 GAGTATCGATACTTCCTTTAAT
73206 GAGTATCGATACTTCCTTTA
1 GAGTATCGATACTTCCTTTA
73226 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (22 bp):
GAGTATCGATACTTCCTTTAAT
Found at i:75723 original size:20 final size:20
Alignment explanation
Indices: 75676--75728 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
75666 TTGAGTCTCC
*
75676 ATTAACCTTTAACTGCCACT
1 ATTAACCTTTAATTGCCACT
*
75696 ATTGACCTTTAATTGCCA-T
1 ATTAACCTTTAATTGCCACT
*
75715 CGTTAACCTTTAAT
1 -ATTAACCTTTAAT
75729 CGTCGTAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.28, C:0.25, G:0.08, T:0.40
Consensus pattern (20 bp):
ATTAACCTTTAATTGCCACT
Found at i:79492 original size:6 final size:6
Alignment explanation
Indices: 79474--79522 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
79464 ATAAGTATTT
* * * *
79474 CCACGA GCCTCGA CCTCGA CCACGA CCACGA CCACAA CCATGA CCACGA
1 CCACGA -CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA CCACGA
79523 GTTGAGCCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
6 31 0.86
7 5 0.14
ACGTcount: A:0.31, C:0.47, G:0.16, T:0.06
Consensus pattern (6 bp):
CCACGA
Found at i:86211 original size:27 final size:27
Alignment explanation
Indices: 86164--86216 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
86154 ATCAATTTTA
86164 TGAAAAATATAAATTTAAGAAGTAAAT
1 TGAAAAATATAAATTTAAGAAGTAAAT
86191 TGAACAAATATGAAA-TT-AGAAGTAAA
1 TGAA-AAATAT-AAATTTAAGAAGTAAA
86217 CAATTAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 8 0.33
29 3 0.12
ACGTcount: A:0.58, C:0.02, G:0.13, T:0.26
Consensus pattern (27 bp):
TGAAAAATATAAATTTAAGAAGTAAAT
Found at i:86549 original size:2 final size:2
Alignment explanation
Indices: 86544--87279 Score: 312
Period size: 2 Copynumber: 368.5 Consensus size: 2
86534 AAATATTGAA
* * *
86544 AT AT AT AT AA ACT AT AT AGT TT AT AT AT AA ACT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT
* * * * * *
86587 -T AT AT AT AT AT AA ACT AG AT AG AG AA ACT AT AT AGT TT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT AT AT
* * *
86629 TT AT AT -T AT -T AT AT ACT AT AT AT AA ACT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT
* * *
86671 AT AA ACT AT AT ACT AT AT AT AA ACT AT AT AT AT AT -T AT GT AT
1 AT AT A-T AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
* * * * * *
86713 AA ACT AT AT ACC AT GT AT AA ACT AT AG AGT TT AT AT AT GA- AT -T
1 AT A-T AT AT A-T AT AT AT AT A-T AT AT A-T AT AT AT AT -AT AT AT
* * * *
86756 AT AT AT AA AC A- AT AT AGT TT AT -T A- AT AT AA AT -T AT AT AGT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T
* * *
86796 TT AT AC AT AT AT -T AT AT AT AA AT -T AT AT AT GA- AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
* * * * * *
86835 TT AA AT AT AT AC AT CT -T AT AT TT AT AT AT GT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
86874 AT ACT AT GT AT AA AT -T AT AT AGT TT AT AT AGT TT AA AT AT AA
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT
* * *
86916 AGT AT AT A- AGT AT AT GT AA ACT AT AA AT -T AT AT AT AT AT AT
1 A-T AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
86957 AT A- AT AT AT A- AT AT AT A- AT AT A- AT AT AT AA AGT AT A- AGT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
* *
86996 AT AT -T AT A- AT AA AGT AT AT AT AT AT AT AT AT AA AGT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
87038 AT A- AT A- AA AT AT AT AT AT AT A- AT -T AGT AT AT AA AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* *
87077 AT AT A- AT AT AA AGT AT A- AT AT AT AT AA AT AT AT AGT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
87119 AT A- AA AT AT A- AGT AT AT A- AT AT AT AT AT AT AT AT AT AA AGT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* *
87160 AT A- AT AT AT AA AG ACT AT A- AGT AT AT A- AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
87201 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AGT AT -T AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* *
87242 AGT AT AT AT AT AT AA AGT AT AT AC ACT AT AT AT AT AT A
1 A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT A
87280 AAGTATTAAG
Statistics
Matches: 548, Mismatches: 105, Indels: 162
0.67 0.13 0.20
Matches are distributed among these distances:
1 41 0.07
2 463 0.84
3 44 0.08
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:86840 original size:53 final size:52
Alignment explanation
Indices: 86728--86845 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 52
86718 ATATACCATG
* * **
86728 TATAAACTATAGAGTTTATATATGAATTATATATAAACAATATAGTTTATTAA
1 TATAAA-TATATAGTTTATACATGAATTATATATAAACAATATAGTGAATTAA
**
86781 TATAAATTATATAGTTTATACAT-ATATTATATATAAATTATATA-TGAATTATA
1 TATAAA-TATATAGTTTATACATGA-ATTATATATAAACAATATAGTGAATTA-A
*
86834 TTTAAATATATA
1 TATAAATATATA
86846 CATCTTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
52 12 0.22
53 43 0.78
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (52 bp):
TATAAATATATAGTTTATACATGAATTATATATAAACAATATAGTGAATTAA
Found at i:87291 original size:31 final size:30
Alignment explanation
Indices: 87208--87409 Score: 105
Period size: 31 Copynumber: 6.9 Consensus size: 30
87198 TATATATATA
*
87208 TATATATATA-TATATATATATA-TA-TAAG
1 TATATA-ATAGTATATATATAAAGTATTAAG
*
87236 TAT-TAA-AGTATATATATATAAAGTATATACAC
1 TATATAATAG--TATATATATAAAGTAT-TA-AG
* * *
87268 TATAT-ATA-TATAAAGTATTAAGTATAAAG
1 TATATAATAGTATATA-TATAAAGTATTAAG
87297 TAT-TAA-AGTATACCTATATAAAGTATTAAAG
1 TATATAATAGTATA--TATATAAAGTATT-AAG
*
87328 TAT-TAA-AGTATA-ATATAAAGTATTAAA
1 TATATAATAGTATATATATAAAGTATTAAG
*
87355 TATA-AAGTA-TAAATATATATAAAGTATTAAA
1 TATATAA-TAGT--ATATATATAAAGTATTAAG
87386 TATATAATA-TA-AGTAT-TAAAGTAT
1 TATATAATAGTATA-TATATAAAGTAT
87410 ATAAATAGAA
Statistics
Matches: 141, Mismatches: 10, Indels: 46
0.72 0.05 0.23
Matches are distributed among these distances:
25 1 0.01
26 1 0.01
27 9 0.06
28 38 0.27
29 16 0.11
30 18 0.13
31 49 0.35
32 7 0.05
33 2 0.01
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (30 bp):
TATATAATAGTATATATATAAAGTATTAAG
Found at i:87305 original size:8 final size:8
Alignment explanation
Indices: 87278--87414 Score: 90
Period size: 8 Copynumber: 18.5 Consensus size: 8
87268 TATATATATA
87278 TAAAGTAT
1 TAAAGTAT
87286 T-AAGTA-
1 TAAAGTAT
87292 TAAAGTAT
1 TAAAGTAT
87300 TAAAGTA-
1 TAAAGTAT
**
87307 T-ACCTAT
1 TAAAGTAT
87314 ATAAAGTAT
1 -TAAAGTAT
87323 TAAAGTAT
1 TAAAGTAT
87331 TAAAGTA-
1 TAAAGTAT
87338 T-AA-TA-
1 TAAAGTAT
87343 TAAAGTAT
1 TAAAGTAT
87351 TAAA-TA-
1 TAAAGTAT
87357 TAAAGTA-
1 TAAAGTAT
*
87364 TAAATATAT
1 TAAA-GTAT
87373 ATAAAGTAT
1 -TAAAGTAT
87382 TAAA-TA-
1 TAAAGTAT
87388 TATAA-TA-
1 TA-AAGTAT
87395 T-AAGTAT
1 TAAAGTAT
87402 TAAAGTAT
1 TAAAGTAT
87410 ATAAA
1 -TAAA
87415 TAGAATTATA
Statistics
Matches: 106, Mismatches: 6, Indels: 33
0.73 0.04 0.23
Matches are distributed among these distances:
5 5 0.05
6 16 0.15
7 30 0.28
8 40 0.38
9 11 0.10
10 4 0.04
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (8 bp):
TAAAGTAT
Found at i:87354 original size:51 final size:52
Alignment explanation
Indices: 87323--87428 Score: 144
Period size: 51 Copynumber: 2.0 Consensus size: 52
87313 TATAAAGTAT
87323 TAAAGTATTAAAGTATAATATAAAGTATTAAA-TATAAAGTATAAATATATA
1 TAAAGTATTAAAGTATAATATAAAGTATTAAAGTATAAAGTATAAATATATA
* * * *
87374 TAAAGTATTAAATATATAATAT-AAGTATTAAAGTATATAAATAGAATTATATA
1 TAAAGTATTAAA-GTATAATATAAAGTATTAAAGTATA-AAGTATAAATATATA
87427 TA
1 TA
87429 TTAAATTATA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
51 22 0.46
52 12 0.25
53 14 0.29
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (52 bp):
TAAAGTATTAAAGTATAATATAAAGTATTAAAGTATAAAGTATAAATATATA
Found at i:88218 original size:17 final size:17
Alignment explanation
Indices: 88196--88229 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
88186 AGTATTTAAC
88196 ATGCAATGCAACATGAA
1 ATGCAATGCAACATGAA
*
88213 ATGCAATTCAACATGAA
1 ATGCAATGCAACATGAA
88230 TTAATATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.21
Consensus pattern (17 bp):
ATGCAATGCAACATGAA
Found at i:88252 original size:14 final size:14
Alignment explanation
Indices: 88233--88262 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
88223 ACATGAATTA
*
88233 ATATGGAATGTCAC
1 ATATGGAATGCCAC
88247 ATATGGAATGCCAC
1 ATATGGAATGCCAC
88261 AT
1 AT
88263 GAATTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (14 bp):
ATATGGAATGCCAC
Found at i:88446 original size:14 final size:14
Alignment explanation
Indices: 88429--88469 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
88419 TAATATACAA
*
88429 ACTATACTATATGT
1 ACTATACTATATAT
88443 ACTA-ACTATATAT
1 ACTATACTATATAT
88456 -CTTATACTATATAT
1 AC-TATACTATATAT
88470 TACAAACCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 1 0.04
13 10 0.42
14 13 0.54
ACGTcount: A:0.39, C:0.15, G:0.02, T:0.44
Consensus pattern (14 bp):
ACTATACTATATAT
Found at i:89654 original size:15 final size:16
Alignment explanation
Indices: 89634--89664 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
89624 TTGCACTCTG
89634 GATGC-AAAAATTAAA
1 GATGCAAAAAATTAAA
89649 GATGCAAAAAATTAAA
1 GATGCAAAAAATTAAA
89665 TAAAATGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.61, C:0.06, G:0.13, T:0.19
Consensus pattern (16 bp):
GATGCAAAAAATTAAA
Found at i:95654 original size:26 final size:26
Alignment explanation
Indices: 95605--95655 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
95595 CTTACGGGAT
****
95605 ATAAATGATCAATATTTTTTTATTAA
1 ATAAATGATCAATATTAAAATATTAA
95631 ATAAATGATCAATATTAAAATATTA
1 ATAAATGATCAATATTAAAATATTA
95656 TTTTATTAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (26 bp):
ATAAATGATCAATATTAAAATATTAA
Found at i:96880 original size:467 final size:466
Alignment explanation
Indices: 95605--96982 Score: 2193
Period size: 467 Copynumber: 3.0 Consensus size: 466
95595 CTTACGGGAT
95605 ATAAATGATCAATATTTTTTT-ATTAAATAAATGATCAATATTAAAATATTATTTTATTAGT-AA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
* * *
95668 TAAAAA---TA-T-CT---T-A---T-CGCGCATGTCACACATCGCAACACACCGAAATATACTG
66 TAAAAATCTTATTAATGGATGAGTTTACGTGCATGTCACAC--CGCAACACACCGAAACATACTG
*
95720 TTAATTAAATATTAGAAAGGTAAATTATACATTTAGTACTTATACTATTATTTTTATTTTGTTTT
129 TTAATTAAATATTAGAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTT
95785 ACTACCTAAA-TTCTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTT
194 ACTACCTAAACTT-TATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTT
*
95849 TTTTAATTTCACATCATCTTTTTATTTTTCCATCAGTATTTTAATTAATTTTATTCAACCAATTA
258 TTTTAATTTCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAATTA
* *
95914 AATGATGACATGTGTCA-CAACTAT-GGGTTAAAAT-AAAGAAAATATTTTTTTAGCATGAACCG
323 AATGATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACCG
* * * *
95976 TACATAAATCTCTTACATGAAATGCAAGGCACTCAACCATTGAGTTAAGCTAATTATTTGTTAAT
388 TACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAAT
96041 TTCATCATATTAAA
453 TTCATCATATTAAA
*
96055 AT-AATGATCAATATTTTTTTGATTAAATAAATGATTAATATTAAAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
*
96119 TAAAAATATCTTATCAATGGATGAGTTTACGGTGCATGT-------C-ACACACCGAAACATACT
66 T-AAAA-ATCTTATTAATGGATGAGTTTAC-GTGCATGTCACACCGCAACACACCGAAACATACT
*
96176 GTTAATTAAATATTAGTAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTT
128 GTTAATTAAATATTAGAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTT
*
96241 TACTATCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTT
193 TACTACCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAA---
*
96306 TTTTTTTAATTTTCACATCATCTTTTTATTTCTCCATCAATATTTTAATTAATTTTATTCAACCA
255 TTTTTTTAA-TTTCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCA
* *
96371 ATTAAATGATGACATGTGCCACCAACTATGGGGATAAAATAAAATAAAATATTTTCTTAGCATGA
319 ATTAAATGATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGA
*
96436 ACCGTACATAAATCTCTTACATCAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGT
384 ACCGTACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGT
96501 TAATTTCATCATATTAAA
449 TAATTTCATCATATTAAA
* *
96519 ATAAATTATGAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
1 ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
96584 TAAAAATCTTATTAATGGATGAGTTTACAGTGCATGTCACACCGCAACACACCGAAACATACTGT
66 TAAAAATCTTATTAATGGATGAGTTTAC-GTGCATGTCACACCGCAACACACCGAAACATACTGT
* * *
96649 TAATTAAATATTAAAAAGATAAATTATACATTTAGTAATTATACTATCATTTTTATTTTGTTTTA
130 TAATTAAATATTAGAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTA
*
96714 CTACCTAAACTTTATTTTTAACGCCA-TAACGACAATGATGATGTTTCATGGCATGTCAATTTTT
195 CTACCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTTTT
*
96778 TTAATTTCCACATCATCTTTTTATTTCTCCATTAGTATTTTAATTAATTTTATTCAACCAATTAA
260 TTAATTT-CACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAATTAA
96843 ATGATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACCGT
324 ATGATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACCGT
* *
96908 ACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAATTAAGATAGTCATTTGTTAATT
389 ACATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAATT
96973 TCATCATATT
454 TCATCATATT
96983 TTTTATTTAA
Statistics
Matches: 855, Mismatches: 37, Indels: 55
0.90 0.04 0.06
Matches are distributed among these distances:
449 18 0.02
450 41 0.05
451 3 0.00
452 4 0.00
453 1 0.00
456 2 0.00
457 137 0.16
458 4 0.00
460 9 0.01
461 74 0.09
462 8 0.01
463 39 0.05
464 106 0.12
465 61 0.07
466 4 0.00
467 206 0.24
470 33 0.04
471 105 0.12
ACGTcount: A:0.37, C:0.13, G:0.10, T:0.40
Consensus pattern (466 bp):
ATAAATGATCAATATTTTTTTGATTAAATAAATGATCAATATTAAAATATTATTTTATTAGTAAA
TAAAAATCTTATTAATGGATGAGTTTACGTGCATGTCACACCGCAACACACCGAAACATACTGTT
AATTAAATATTAGAAAGGTAAATTATACATTTAGTACTTATACTATCATTTTTATTTTGTTTTAC
TACCTAAACTTTATTTTTAACGCCATTAACGACAATGATGATGTTTCATGACATGTCAATTTTTT
TAATTTCACATCATCTTTTTATTTCTCCATCAGTATTTTAATTAATTTTATTCAACCAATTAAAT
GATGACATGTGTCACCAACTATGGGGATAAAATAAAAGAAAATATTTTCTTAGCATGAACCGTAC
ATAAATCTCTTACATGAAATGCAAGGCACTCGATCATTGAGTTAAGCTAGTCATTTGTTAATTTC
ATCATATTAAA
Found at i:97312 original size:23 final size:24
Alignment explanation
Indices: 97286--97336 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
97276 AATATTTTAA
97286 CATATTTATTTATTT-TTAAAAAT
1 CATATTTATTTATTTATTAAAAAT
*
97309 CATA-TTATTTATTTATTTAAAAT
1 CATATTTATTTATTTATTAAAAAT
*
97332 AATAT
1 CATAT
97337 CATTTTTTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
CATATTTATTTATTTATTAAAAAT
Found at i:97341 original size:23 final size:23
Alignment explanation
Indices: 97293--97345 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
97283 TAACATATTT
* *
97293 ATTTATTT-TTAAAAATCATATT
1 ATTTATTTATTAAAAATAATATC
*
97315 ATTTATTTATTTAAAATAATATC
1 ATTTATTTATTAAAAATAATATC
97338 ATTT-TTTA
1 ATTTATTTA
97346 GATCATCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTATTTATTAAAAATAATATC
Found at i:97652 original size:21 final size:23
Alignment explanation
Indices: 97607--97654 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 23
97597 TATATTAACT
* *
97607 TATTCTAAAAAGTATATTTATAA
1 TATTATAAAAAGTATATTTAAAA
97630 TATTATAAAAA-TAT-TTTAAAA
1 TATTATAAAAAGTATATTTAAAA
97651 TATT
1 TATT
97655 TATTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 10 0.43
22 3 0.13
23 10 0.43
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
TATTATAAAAAGTATATTTAAAA
Found at i:97664 original size:18 final size:20
Alignment explanation
Indices: 97641--97685 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
97631 ATTATAAAAA
97641 TATTTTAAAAT-AT-TTATT
1 TATTTTAAAATCATATTATT
97659 TATTTTTTAAAATCATATTATT
1 TA--TTTTAAAATCATATTATT
97681 TATTT
1 TATTT
97686 ATTTGAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 2 0.09
20 12 0.52
21 2 0.09
22 7 0.30
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TATTTTAAAATCATATTATT
Found at i:97694 original size:23 final size:22
Alignment explanation
Indices: 97643--97704 Score: 83
Period size: 23 Copynumber: 2.9 Consensus size: 22
97633 TATAAAAATA
97643 TTTTAAAAT-AT-TTATTTATT
1 TTTTAAAATAATATTATTTATT
*
97663 TTTTAAAATCATATTATTTATT
1 TTTTAAAATAATATTATTTATT
*
97685 TATTTGAAATAATATTATTT
1 T-TTTAAAATAATATTATTT
97705 TTAAATCATC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 9 0.24
21 2 0.05
22 10 0.27
23 16 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTAAAATAATATTATTTATT
Found at i:98092 original size:23 final size:23
Alignment explanation
Indices: 98065--98136 Score: 121
Period size: 23 Copynumber: 3.2 Consensus size: 23
98055 TTGATGTATG
98065 ATTTTAGAATTTAAAATTTTAAA
1 ATTTTAGAATTTAAAATTTTAAA
98088 ATTTTAGAATTTAAAATTTTAAA
1 ATTTTAGAATTTAAAATTTTAAA
*
98111 ATTTTAGAATTT--AATTTTATA
1 ATTTTAGAATTTAAAATTTTAAA
98132 ATTTT
1 ATTTT
98137 GGATTTATTG
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 13 0.27
23 35 0.73
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTTTAGAATTTAAAATTTTAAA
Found at i:98124 original size:15 final size:16
Alignment explanation
Indices: 98065--98122 Score: 75
Period size: 15 Copynumber: 3.8 Consensus size: 16
98055 TTGATGTATG
*
98065 ATTTTAGAA-TTTAAA
1 ATTTTAAAATTTTAAA
*
98080 ATTTTAAAATTTTAGA
1 ATTTTAAAATTTTAAA
98096 A-TTTAAAATTTTAAA
1 ATTTTAAAATTTTAAA
*
98111 ATTTTAGAATTT
1 ATTTTAAAATTT
98123 AATTTTATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
15 22 0.59
16 15 0.41
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
ATTTTAAAATTTTAAA
Found at i:98136 original size:8 final size:8
Alignment explanation
Indices: 98065--98122 Score: 75
Period size: 8 Copynumber: 7.5 Consensus size: 8
98055 TTGATGTATG
*
98065 ATTTTAGA
1 ATTTTAAA
98073 A-TTTAAA
1 ATTTTAAA
98080 ATTTTAAA
1 ATTTTAAA
*
98088 ATTTTAGA
1 ATTTTAAA
98096 A-TTTAAA
1 ATTTTAAA
98103 ATTTTAAA
1 ATTTTAAA
*
98111 ATTTTAGA
1 ATTTTAAA
98119 ATTT
1 ATTT
98123 AATTTTATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
7 12 0.27
8 32 0.73
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (8 bp):
ATTTTAAA
Found at i:98809 original size:30 final size:30
Alignment explanation
Indices: 98773--98911 Score: 138
Period size: 30 Copynumber: 4.6 Consensus size: 30
98763 ACCCTTATAC
* *
98773 AATAACATAAAATATAATATCA-GAAATTAA
1 AATAACATAAAATACAATACCATG-AATTAA
* *
98803 AATAACATTAAATACAAAACCATGAATTAA
1 AATAACATAAAATACAATACCATGAATTAA
* * *
98833 AATACCAGAAAATATAATACCA-GAAATTAA
1 AATAACATAAAATACAATACCATG-AATTAA
** *
98863 AATAATGTAAAATACAAAACCATGAATTAA
1 AATAACATAAAATACAATACCATGAATTAA
* *
98893 AATACCAGAAAATACAATA
1 AATAACATAAAATACAATA
98912 GTAGAAAATA
Statistics
Matches: 86, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
29 1 0.01
30 83 0.97
31 2 0.02
ACGTcount: A:0.61, C:0.12, G:0.05, T:0.22
Consensus pattern (30 bp):
AATAACATAAAATACAATACCATGAATTAA
Found at i:98857 original size:60 final size:60
Alignment explanation
Indices: 98781--98911 Score: 217
Period size: 60 Copynumber: 2.2 Consensus size: 60
98771 ACAATAACAT
* *
98781 AAAATATAATATCAGAAATTAAAATAACATTAAATACAAAACCATGAATTAAAATACCAG
1 AAAATATAATACCAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
**
98841 AAAATATAATACCAGAAATTAAAATAATGTAAAATACAAAACCATGAATTAAAATACCAG
1 AAAATATAATACCAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
*
98901 AAAATACAATA
1 AAAATATAATA
98912 GTAGAAAATA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.22
Consensus pattern (60 bp):
AAAATATAATACCAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
Found at i:98911 original size:15 final size:15
Alignment explanation
Indices: 98769--98926 Score: 72
Period size: 15 Copynumber: 10.5 Consensus size: 15
98759 GAAGACCCTT
* *
98769 ATACAATAACATAAA
1 ATACAATACCAGAAA
* *
98784 ATATAATATCAGAAA
1 ATACAATACCAGAAA
* * * **
98799 TTAAAATAACATTAA
1 ATACAATACCAGAAA
*
98814 ATACAAAACCATG-AA
1 ATACAATACCA-GAAA
* *
98829 TTAAAATACCAGAAA
1 ATACAATACCAGAAA
*
98844 ATATAATACCAGAAA
1 ATACAATACCAGAAA
* *
98859 TTAAAATA--ATGTAAA
1 ATACAATACCA-G-AAA
*
98874 ATACAAAACCATG-AA
1 ATACAATACCA-GAAA
* *
98889 TTAAAATACCAGAAA
1 ATACAATACCAGAAA
**
98904 ATACAATAGTAGAAA
1 ATACAATACCAGAAA
98919 ATACAATA
1 ATACAATA
98927 TCATATAATA
Statistics
Matches: 106, Mismatches: 30, Indels: 14
0.71 0.20 0.09
Matches are distributed among these distances:
13 1 0.01
14 3 0.03
15 99 0.93
17 3 0.03
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.22
Consensus pattern (15 bp):
ATACAATACCAGAAA
Found at i:98918 original size:60 final size:59
Alignment explanation
Indices: 98781--98936 Score: 204
Period size: 60 Copynumber: 2.6 Consensus size: 59
98771 ACAATAACAT
*
98781 AAAATATAATATCAGAAATTAAAATAACATTAAATACAAAACCATGAATTAAAATACCAG
1 AAAATATAATAT-AGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
* **
98841 AAAATATAATACCAGAAATTAAAATAATGTAAAATACAAAACCATGAATTAAAATACCAG
1 AAAATATAATA-TAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
* * * * *
98901 AAAATACAATAGTAGAAAATACAATATCATATAATA
1 AAAATATAATA-TAGAAATTAAAATAACATAAAATA
98937 AAACTATATA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
60 82 1.00
ACGTcount: A:0.60, C:0.11, G:0.06, T:0.23
Consensus pattern (59 bp):
AAAATATAATATAGAAATTAAAATAACATAAAATACAAAACCATGAATTAAAATACCAG
Done.