Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006467.1 Hibiscus syriacus cultivar Beakdansim tig00015668_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: 80463
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:1669 original size:21 final size:20
Alignment explanation
Indices: 1631--1684 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1621 TACTCATGCA
1631 ATGAGTATCGATA-ATGTAGG
1 ATGA-TATCGATACATGTAGG
*
1651 TATGATATCGATACTTGTAGG
1 -ATGATATCGATACATGTAGG
* *
1672 GTGGTATCGATAC
1 ATGATATCGATAC
1685 CGAGCTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (20 bp):
ATGATATCGATACATGTAGG
Found at i:1800 original size:3 final size:3
Alignment explanation
Indices: 1794--1866 Score: 85
Period size: 3 Copynumber: 24.3 Consensus size: 3
1784 AATAATAATA
* * * *
1794 ATT ATT ATC ATT ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1842 AAT ATT A-T ATAT ATT ATT ATT ATT A
1 ATT ATT ATT AT-T ATT ATT ATT ATT A
1867 AATAAAAAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:1846 original size:18 final size:18
Alignment explanation
Indices: 1776--1849 Score: 80
Period size: 18 Copynumber: 4.1 Consensus size: 18
1766 TCATTTTTAA
*
1776 ATTATTA-TAATAATAATA
1 ATTATTATTAATAAT-ATT
* * *
1794 ATTATTATCATTATTATT
1 ATTATTATTAATAATATT
1812 ATTATTATT-ATAAATATT
1 ATTATTATTAAT-AATATT
1830 ATTATTATTAATAATATT
1 ATTATTATTAATAATATT
1848 AT
1 AT
1850 ATATATTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
17 1 0.02
18 39 0.85
19 6 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTATTATTAATAATATT
Found at i:1865 original size:18 final size:18
Alignment explanation
Indices: 1776--1866 Score: 72
Period size: 18 Copynumber: 5.4 Consensus size: 18
1766 TCATTTTTAA
* *
1776 ATTATTATAATA-ATAATA
1 ATTATTATTATATAT-ATT
*
1794 ATTATTATCAT-TATTATT
1 ATTATTATTATATA-TATT
*
1812 ATTATTATTATAAATATT
1 ATTATTATTATATATATT
1830 ATTATTATTA-ATA-A-T
1 ATTATTATTATATATATT
1845 ATTA-TA-TATAT-TATT
1 ATTATTATTATATATATT
1860 ATTATTA
1 ATTATTA
1867 AATAAAAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
13 2 0.03
14 5 0.08
15 10 0.16
16 3 0.05
17 2 0.03
18 37 0.61
19 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (18 bp):
ATTATTATTATATATATT
Found at i:1878 original size:27 final size:27
Alignment explanation
Indices: 1776--1879 Score: 88
Period size: 27 Copynumber: 3.9 Consensus size: 27
1766 TCATTTTTAA
*
1776 ATTATTA-TAATAATAATAAT-TATTATC
1 ATTATTATTAATAATAA-AATATA-TATT
* * ** *
1803 ATTATTATTATTATTATTATAAATATT
1 ATTATTATTAATAATAAAATATATATT
**
1830 ATTATTATTAATAATATTATATATATT
1 ATTATTATTAATAATAAAATATATATT
1857 ATTATTATTAAATAA-AAAATATA
1 ATTATTATT-AATAATAAAATATA
1880 GACCCATTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
27 51 0.81
28 12 0.19
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
ATTATTATTAATAATAAAATATATATT
Found at i:7648 original size:21 final size:21
Alignment explanation
Indices: 7622--7666 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
7612 CAATTAAAAA
* *
7622 TCAAGGAGCTTTACTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
*
7643 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
7664 TCA
1 TCA
7667 TAGCTCGTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:12214 original size:19 final size:21
Alignment explanation
Indices: 12177--12219 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
12167 TAACTTTTTC
12177 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
12197 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
12217 TTT
1 TTT
12220 ACCTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:12225 original size:19 final size:20
Alignment explanation
Indices: 12176--12225 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
12166 TTAACTTTTT
*
12176 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
12196 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
12215 CTTTTACCTTT
1 CTTTTACCTTT
12226 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:16077 original size:17 final size:16
Alignment explanation
Indices: 16046--16079 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
16036 CACGTGAGGA
16046 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
16062 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
16079 T
1 T
16080 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:16747 original size:76 final size:75
Alignment explanation
Indices: 16571--16819 Score: 363
Period size: 75 Copynumber: 3.3 Consensus size: 75
16561 CTTAGCAAGA
** *
16571 AGCAAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAG
1 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
16636 CGTTTGTATC
66 CGTTTGTATC
* * * **
16646 AGCAAATGCTGGGGCATGCTGAAAGCCTATTTCAATCAGAAATTGGAATATTGAAACAATTTTGA
1 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGC-ATTTTGA
*
16711 AAGTTTGTATC
65 ACGTTTGTATC
* *
16722 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATTTTGACGCATTTTGAA
1 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
**
16787 CGTTCATATC
66 CGTTTGTATC
*
16797 AGAAAATACTAGGGCATGCTGAA
1 AGCAAATACTAGGGCATGCTGAA
16820 GGCCTATATC
Statistics
Matches: 155, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
75 89 0.57
76 66 0.43
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (75 bp):
AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
CGTTTGTATC
Found at i:17164 original size:54 final size:54
Alignment explanation
Indices: 17005--17167 Score: 168
Period size: 54 Copynumber: 3.0 Consensus size: 54
16995 CATTGACTAG
* * * *
17005 AAATCTGTG-CAGAAGTCACATGAAATGATGAATGTGTTGTCAAATGCTTTACGA
1 AAATCTG-GCCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGCTTTACAA
* * * *
17059 ACATCTGGCCAGAAGCCACAAGAAAGGATGAATGTGTTATTAAAAGCTTTACAA
1 AAATCTGGCCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGCTTTACAA
* * * * * *
17113 AAAT-TCGGGCATAAGCCACGAGAAAGGATGAATGTATTGTCACATGTTTTACAA
1 AAATCT-GGCCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGCTTTACAA
17167 A
1 A
17168 CCAGTGATTA
Statistics
Matches: 89, Mismatches: 18, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
53 2 0.02
54 87 0.98
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (54 bp):
AAATCTGGCCAGAAGCCACAAGAAAGGATGAATGTGTTGTCAAATGCTTTACAA
Found at i:17539 original size:22 final size:22
Alignment explanation
Indices: 17514--17568 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
17504 ATATCTATAT
*
17514 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
*
17536 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
17558 TTTTCAAAGAT
1 TCTTCAAAGAT
17569 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:18305 original size:45 final size:45
Alignment explanation
Indices: 18256--18370 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
18246 GGGAGCTTTT
* * * *
18256 TGATGTTTTCAAAACCTTTGGGAAATTTATAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGAAATCTATAAGCCCTACAATGCA
** *
18301 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAATGCA
1 TGATGTTTTCAAAACCTTCGGGAAATCTATAAGCCCTACAATGCA
* *
18346 GGATGTTGTCAAAAAGCCTTCGGGA
1 TGATGTTTTC-AAAA-CCTTCGGGA
18371 GCTTTTTGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 46 0.79
46 4 0.07
47 8 0.14
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGAAATCTATAAGCCCTACAATGCA
Found at i:18417 original size:121 final size:121
Alignment explanation
Indices: 18203--18566 Score: 548
Period size: 121 Copynumber: 3.0 Consensus size: 121
18193 CTATTTCCCA
* *
18203 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCATAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
** * *
18268 AACCTTTGGGAAATTTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
66 AACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
18324 CATCTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
18389 AACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
66 AACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
18445 CATTTGTAAGCCCTACAATGCATGATGTTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * * * * * *
18510 AGCCTTCGAGTCATCTGTAAGGCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGG
66 AACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
18567 AGTTTTTTGA
Statistics
Matches: 221, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
121 210 0.95
122 4 0.02
123 7 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (121 bp):
CATCTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:18426 original size:45 final size:45
Alignment explanation
Indices: 18377--18490 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
18367 GGGAGCTTTT
* ** * *
18377 TGATGTTTTTAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA
*
18422 TGATGTTTTCAAAACCTTCAGGTCATTTGTAAGCCCTACAATGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA
*
18467 TGATGTTGTCAAAAAGCCTTCAGG
1 TGATGTTTTC-AAAA-CCTTCAGG
18491 AGCTTTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 48 0.80
46 4 0.07
47 8 0.13
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA
Found at i:18502 original size:76 final size:75
Alignment explanation
Indices: 18422--18632 Score: 314
Period size: 76 Copynumber: 2.8 Consensus size: 75
18412 CTTCAGTGCA
* *
18422 TGATGTTTTCAAAACCTTCAGGTCATTTGTAAGCCCTACAATGCATGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTC-GGTCATCTGTAAGCCCTACAGTGCATGATGTTGTCAAAAAGCCTT
18487 CAGGAGCTTTT
65 CAGGAGCTTTT
* * *
18498 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAGGCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCG-GTCATCTGTAAGCCCTACAGTGCATGATGTTGTCAAAAAGCCTT
* *
18563 CGGGAGTTTTT
65 CAGGAGCTTTT
* *
18574 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
1 TGATGTTTTCAAAACCTTC-GGTCATCTGTAAGCCCTACAGTGCATGATGTTGTCAAAA
18633 CCTTCGGGTC
Statistics
Matches: 121, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
75 1 0.01
76 119 0.98
77 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (75 bp):
TGATGTTTTCAAAACCTTCGGTCATCTGTAAGCCCTACAGTGCATGATGTTGTCAAAAAGCCTTC
AGGAGCTTTT
Found at i:18545 original size:197 final size:197
Alignment explanation
Indices: 18301--18761 Score: 725
Period size: 197 Copynumber: 2.4 Consensus size: 197
18291 CTTCAGTGCA
* *
18301 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
* *
18366 CGGGAGCTTTTTGATGTTTTTAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
*
18431 CAAAACCTTCAGGTCATTTGTAAGCCCTACAATGCATG-ATGTTGTCAAAAAGCCTTC-AGGAGC
131 CAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA-GAATGTTGTCAAAAAGCCTTCGA-GAGC
18494 TTTT
194 TTTT
* *
18498 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAGGCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
*
18563 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
66 CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
* * *
18628 CAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGTAGAATGTTGTCAAAAAGCCTTCGAGAGCTT
131 CAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTT
18693 TT
196 TT
* * * *
18695 TGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCCTTCAGTGCATGATGTTTTC-AAAA-CCT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTG-TAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCT
18757 TCGGG
65 TCGGG
18762 TCATCTGTAA
Statistics
Matches: 244, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
195 8 0.03
196 5 0.02
197 227 0.93
198 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (197 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
CGGGAGCTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
CAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTT
TT
Found at i:18623 original size:121 final size:121
Alignment explanation
Indices: 18498--18918 Score: 709
Period size: 121 Copynumber: 3.5 Consensus size: 121
18488 AGGAGCTTTT
* * *
18498 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAGGCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
18563 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
18619 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGTAGAATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
* * * *
18684 CGAGAGCTTTTTGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCCTTCAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTG-TAAGCCCTTCAGTGCA
*
18740 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
18805 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
18861 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAA
18919 GCCTTCAGGT
Statistics
Matches: 278, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
120 3 0.01
121 272 0.98
122 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:18635 original size:242 final size:242
Alignment explanation
Indices: 18377--19007 Score: 814
Period size: 242 Copynumber: 2.6 Consensus size: 242
18367 GGGAGCTTTT
* * *
18377 TGATGTTTTTAAAACCTTTGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCA
18442 GGTCATTTGTAAGCCCTACAATGCATGATGTTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTT
66 GGTCATTTGTAAGCCCTACAATGCATGATGTTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTT
* * * *
18507 CAAAGCCTTCGAGTCATCTGTAAGGCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGTTT
131 CAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTTCGGGAGTTT
18572 TTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
196 TTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
18619 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGTA-GAATGTTGTCAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATG-ATGTTTTC-AAAA-CCT
* * ** * * * * * ** * *
18683 TCGAGAG-C-TTTTTGATG-TTTTCAAAGCCT-TTG-GGTCATCTGTTAACCCTTCA-GTGC---
63 TC-AG-GTCATTTGT-AAGCCCTACAATGCATGATGTTGTCA----AAAAGCCTTCAGGAGCTTT
*
18739 ATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCT
121 TTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCT
18804 TCGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
186 TCGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
18861 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAGCCTTCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCA
** * * * * *
18926 GGTCATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
66 GGTCATTTGTAAGCCCTACAATGCATGATGTTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTT
18991 CAAAACCTTCGGGTCAT
131 CAAAACCTTCGGGTCAT
19008 TCATAAGACC
Statistics
Matches: 321, Mismatches: 48, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
238 8 0.02
239 7 0.02
240 12 0.04
241 6 0.02
242 248 0.77
243 7 0.02
244 16 0.05
245 8 0.02
246 9 0.03
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (242 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCA
GGTCATTTGTAAGCCCTACAATGCATGATGTTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTT
CAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTTCGGGAGTTT
TTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:18677 original size:45 final size:45
Alignment explanation
Indices: 18574--18661 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
18564 GGGAGTTTTT
*
18574 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
18619 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTG
18662 TAGAATGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Found at i:18748 original size:45 final size:45
Alignment explanation
Indices: 18695--18808 Score: 140
Period size: 45 Copynumber: 2.5 Consensus size: 45
18685 GAGAGCTTTT
* * *
18695 TGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTG-TAAGCCCTACAGTGCA
18740 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
* * *
18785 GGATATTGTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
18809 AGTTTTTTGA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
44 3 0.05
45 45 0.75
46 4 0.07
47 8 0.13
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Found at i:18796 original size:318 final size:317
Alignment explanation
Indices: 18203--18882 Score: 1094
Period size: 318 Copynumber: 2.1 Consensus size: 317
18193 CTATTTCCCA
18203 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCATAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCA-AAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
18268 AACCTTTGGGAAATTTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
65 AACCTTCGGGAAATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
* * *
18333 GCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAAAACCTTTGG
130 GCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAACCTTTGG
*
18398 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATTTGTAAGCCCTACAA
195 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAA
* * *
18463 TGCATGATGTTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAGCCTTCGAGT
260 TGCAGGATATTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTCGAGT
* *
18521 CATCTGTAAGGCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
** *
18586 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
65 AACCTTCGGGAAATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
* * *
18651 GCCCTACAGTGTAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAGCCTTTGG
130 GCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAACCTTTGG
*
18716 GTCATCTGTTAA-CCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACA
195 GTCATCTG-TAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACA
* * * *
18780 GTGCAGGATATTGTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGT
259 ATGCAGGATATTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTCGAGT
* * *
18839 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAGCCTTCGGG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAGCCTTCGGG
18883 TCATCTGTAA
Statistics
Matches: 334, Mismatches: 26, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
316 12 0.04
318 318 0.95
319 4 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (317 bp):
CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
ACCTTCGGGAAATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
CCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAACCTTTGGG
TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAAT
GCAGGATATTGTCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAAACCTTCGAGT
Found at i:18820 original size:76 final size:74
Alignment explanation
Indices: 18740--18882 Score: 232
Period size: 76 Copynumber: 1.9 Consensus size: 74
18730 CTTCAGTGCA
18740 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTC--AAAGCCTT
18805 CGGGAGTTTTT
64 CGGGAGTTTTT
* * * *
18816 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAGCCTTCG
18881 GG
66 GG
18883 TCATCTGTAA
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
74 12 0.19
76 51 0.81
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (74 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAGCCTTCG
GGAGTTTTT
Found at i:18865 original size:45 final size:45
Alignment explanation
Indices: 18816--18974 Score: 246
Period size: 45 Copynumber: 3.5 Consensus size: 45
18806 GGGAGTTTTT
*
18816 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
18861 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
* * *
18906 TGATGTTTTCAAAGCCTTCAGGTCATCCGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
18951 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
18975 AACTTTTTGA
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 95 0.90
46 3 0.03
47 7 0.07
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Found at i:18867 original size:166 final size:166
Alignment explanation
Indices: 18695--19007 Score: 529
Period size: 166 Copynumber: 1.9 Consensus size: 166
18685 GAGAGCTTTT
* *
18695 TGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCCTTCAGTGCATGATGTTTTCAAAACCTTC
1 TGATGTTTTCAAAGCCTTCGGGTCATCTG-TAAGCCCTACAGTGCATGATGTTTTCAAAACCTTC
* * **
18759 GGGTCATCTGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTTCGGGAGTTTTTTGATGTTT
65 AGGTCATCCGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTTCGGGAACTTTTTGATGTTT
18824 TCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
130 TCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
18861 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAGCCTTCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCA
* *
18926 GGTCATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
66 GGTCATCCGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
18991 CAAAACCTTCGGGTCAT
131 CAAAACCTTCGGGTCAT
19008 TCATAAGACC
Statistics
Matches: 137, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
165 3 0.02
166 134 0.98
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (166 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCA
GGTCATCCGTAAGCCCTACAGTGCAGGATATTGTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:19182 original size:3 final size:3
Alignment explanation
Indices: 19164--19250 Score: 86
Period size: 3 Copynumber: 28.3 Consensus size: 3
19154 TCCTTTTTAA
* * * *
19164 ATT ATT ATA ATA ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
19212 ATT ATT AAT ATT AAT ATT A-T ATAT ATAT ATAT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T AT-T AT-T ATT ATT A
19251 AATAAAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
2 2 0.03
3 59 0.82
4 11 0.15
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:21802 original size:111 final size:111
Alignment explanation
Indices: 21671--21892 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
21661 TGTAACTTTG
* **
21671 CATTTTAGTCATTGAAATCAAATTTTGAATCTTTTAATTTGATTTTTGAAGTTTGGTTTATTATA
1 CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
21736 ATTTAGTCACTGACATAATTATATATATTTATGGTAAAATATGTAT
66 ATTTAGTCACTGACATAATTATATATATTTATGGTAAAATATGTAT
21782 CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
1 CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
*
21847 ATTTAGTCTCTGACATAATTATATATATTTATGGTAAAATATGTAT
66 ATTTAGTCACTGACATAATTATATATATTTATGGTAAAATATGTAT
21893 TTAGTCCTTA
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.33, C:0.07, G:0.11, T:0.48
Consensus pattern (111 bp):
CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
ATTTAGTCACTGACATAATTATATATATTTATGGTAAAATATGTAT
Found at i:22671 original size:22 final size:22
Alignment explanation
Indices: 22644--22688 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
22634 AATCGACAAA
*
22644 GACCAATTTTGGACGTTGTGAG
1 GACCAATTTTGGACATTGTGAG
*
22666 GACCAATTTTGGGCATTGTGAG
1 GACCAATTTTGGACATTGTGAG
22688 G
1 G
22689 GTGATAATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.22, C:0.13, G:0.33, T:0.31
Consensus pattern (22 bp):
GACCAATTTTGGACATTGTGAG
Found at i:48204 original size:82 final size:82
Alignment explanation
Indices: 48065--48507 Score: 517
Period size: 82 Copynumber: 5.4 Consensus size: 82
48055 GATACATCAA
* * *
48065 TGAAAAGTTACTA-AAGATGATAA-GACACCACTATTTTACCCT-TTGTCTGAAAAGTTGTTTAA
1 TGAAAAGTTGC-AGAAGATGATAATG-CACCACTATTTCA-CCTGTTTTCTGAAAAGTTGTTTAA
*
48127 ATTATGCATTGAATGGTCTC
63 ATTATGCATTGAATGGACTC
* ** * * *
48147 TAAAAAGTTATAAAAGATGATAATGCACCACTATTTCACGTATTTTCTGAAAAGTTGTTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
* * *
48212 ATGCGTAGAA-CGACCTC
66 ATGCATTGAATGGA-CTC
* * *
48229 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCTG-AAAGTTGTTTAACTT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
* *
48293 ATACATTGAAT-GACCTA
66 ATGCATTGAATGGA-CTC
* * *
48310 TG-AAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGCTATTTGAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
*
48374 ATGTATTGAAT-GACCTC
66 ATGCATTGAATGGA-CTC
* * * *
48391 TGAAAAGTTGCAGAAGATGATAATGCACCATTATTTCACCTGTTTTCTAAAAAGCTATTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
48456 ATGCATTGAAT-GACATC
66 ATGCATTGAATGGAC-TC
*
48473 TGAAAAGTTGGAGAAGATGATAATGCACCACTATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATT
48508 ATTTGACCTA
Statistics
Matches: 316, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
80 44 0.14
81 60 0.19
82 211 0.67
83 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (82 bp):
TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
ATGCATTGAATGGACTC
Found at i:48359 original size:162 final size:162
Alignment explanation
Indices: 48065--48507 Score: 552
Period size: 162 Copynumber: 2.7 Consensus size: 162
48055 GATACATCAA
*
48065 TGAAAAGTTACTA-AAGATGATAA-GACACCACTATTTTACCC-TTTGTCTGAAAAGTTGTTTAA
1 TGAAAAGTTGC-AGAAGATGATAATG-CACCACTATTTTACCCGTTT-TCTG-AAAGTTGTTTAA
* * ** * *
48127 ATTATGCATTGAATGGTCTCTA-AAAAGTTATAAAAGATGATAATGCACCACTATTTCACGTATT
62 ATTATGCATTGAAT-GAC-CTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTATT
* * *
48191 TTCTGAAAAGTTGTTTAAATTATGCGTAGAACGACCTC
125 TTCTGAAAAGCTATTTAAATTATGCATAGAACGACCTC
*
48229 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCTGAAAGTTGTTTAACTTA
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCTGAAAGTTGTTTAAATTA
* *
48294 TACATTGAATGACCTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGA
66 TGCATTGAATGACCTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTATTTTCTGA
* * * *
48359 AAAGCTATTTGAATTATGTATTGAATGACCTC
131 AAAGCTATTTAAATTATGCATAGAACGACCTC
* * * * * *
48391 TGAAAAGTTGCAGAAGATGATAATGCACCATTATTTCACCTGTTTTCTAAAAAGCTATTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCT-GAAAGTTGTTTAAATT
* * *
48456 ATGCATTGAATGACATCTGAAAAGTTGGAGAAGATGATAATGCACCACTATT
65 ATGCATTGAATGACCTATG-AAAGTTGCAGAAGATGATAATGCACCACTATT
48508 ATTTGACCTA
Statistics
Matches: 245, Mismatches: 28, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
161 3 0.01
162 114 0.47
163 53 0.22
164 71 0.29
165 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (162 bp):
TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCTGAAAGTTGTTTAAATTA
TGCATTGAATGACCTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTATTTTCTGA
AAAGCTATTTAAATTATGCATAGAACGACCTC
Found at i:50323 original size:20 final size:20
Alignment explanation
Indices: 50291--50328 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
50281 TAATGGATGG
*
50291 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
50311 TTGTTTTCT-TATGATGTT
1 TTGTTTT-TGTATGATGTT
50329 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.11, C:0.03, G:0.18, T:0.68
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:50425 original size:18 final size:18
Alignment explanation
Indices: 50402--50438 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
50392 AGAGAATGAC
50402 TAAGTAGCATATCTTTAG
1 TAAGTAGCATATCTTTAG
50420 TAAGTAGCATATCTTTAG
1 TAAGTAGCATATCTTTAG
50438 T
1 T
50439 GTTCGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (18 bp):
TAAGTAGCATATCTTTAG
Found at i:51300 original size:12 final size:12
Alignment explanation
Indices: 51257--51306 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
51247 CATAACATTT
51257 TTATTTTACTTG
1 TTATTTTACTTG
51269 TTCATTTT--TTG
1 TT-ATTTTACTTG
51280 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
51294 TTATTTTCCTTG
1 TTATTTTACTTG
51306 T
1 T
51307 CTTTTTAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:53146 original size:807 final size:806
Alignment explanation
Indices: 51588--53201 Score: 3030
Period size: 807 Copynumber: 2.0 Consensus size: 806
51578 ACTCATGAGG
*
51588 ATGCAGGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTCATTTCAACAACAAGGTGTGCAT
1 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTCATTTCAACAACAAGGTGTGCAT
51653 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAAATCATGCCAGGGCATGGCTTAA
66 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAAATCATGCCAGGGCATGGCTTAA
51718 TGGAGTACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATA
131 TGGAGTACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATA
51783 ATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGAAAACGCAATGAAAAG
196 ATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGAAAACGCAATGAAAAG
51848 TCTATGTATGAGTGTTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCCA
261 TCTATGTATGAGTGTTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCCA
* *
51913 CAGCTGGACTCAAGCTATGATGTTTTATAATAGAGTCAATGCATCCACGATGATGATGCTAGATG
326 CAGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGATGATGATGCTAGATG
*
51978 CCTAGAAAAATGGGACATTGCTCTATGAATCACATACAGAGGCATTCAACATTCTGGATAGGATT
391 CCTAGAAAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGATT
52043 GCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCATT
456 GCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCATT
52108 CGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAATT
521 CGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAATT
* *
52173 TGCAAAGACCAGGTGAGGGGAAATAAGTGAAGGCAACTAATTCAGCATGTTTATTATGCCATGAC
586 TGCAAAGACCAGGTGAGGGGAAATAAATGAAGGCAACTAATTCAGCATGTTTAGTATGCCATGAC
52238 AATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATTA
651 AATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATTA
* *
52303 AGGTAACAACAACCCCTATTTTAATACATATAATCCTGGATAGTGTCAGCATCCAAACTTCTCTT
716 AGGTAACAACAACCCCTACTCTAATACATATAATCCTGGATAGTGTCAGCATCCAAACTTCTCTT
52368 GGGGAAATCAATGAACCATCAATGAT
781 GGGGAAATCAATGAACCATCAATGAT
**
52394 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTCATTTTGACAACAAGGTGTGCAT
1 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTCATTTCAACAACAAGGTGTGCAT
*
52459 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAGATCATGCCAGGGCATGGCTTAA
66 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAAATCATGCCAGGGCATGGCTTAA
*
52524 TGGAGTACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGATATA
131 TGGAGTACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACAT-
*
52589 AATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGACAACGCAATGAAAA
195 AATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGAAAACGCAATGAAAA
*
52654 GTCTATGTATGAGTGTTGAAACTGAAATGAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCC
260 GTCTATGTATGAGTGTTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCC
* * *
52719 ACAGCTGGACTCAAGTTGTGATGTTTTACAATAGAGTCAATGCACCCACGATGATGATGTTAGAT
325 ACAGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGATGATGATGCTAGAT
*
52784 GCCTAGACAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGAT
390 GCCTAGAAAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGAT
52849 TGCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCAT
455 TGCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCAT
52914 TCGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAAT
520 TCGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAAT
52979 TTGCAAAGACCAGGTGAGGGGAAATAAATGAAGGCAACTAATTCAGCATGTTTAGTATGCCATGA
585 TTGCAAAGACCAGGTGAGGGGAAATAAATGAAGGCAACTAATTCAGCATGTTTAGTATGCCATGA
*
53044 CAATCACCATGAGAGTGAGTGACTTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATT
650 CAATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATT
* *
53109 GAGGTAACAATAACCCCTACTCTAATACATATAATCCTGGATAGTGTCAGCATCCAAACTTCTCT
715 AAGGTAACAACAACCCCTACTCTAATACATATAATCCTGGATAGTGTCAGCATCCAAACTTCTCT
53174 TGGGGAAATCAATGAACCATCAATGAT
780 TGGGGAAATCAATGAACCATCAATGAT
53201 A
1 A
53202 GTCAGCCCTC
Statistics
Matches: 786, Mismatches: 21, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
806 189 0.24
807 597 0.76
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (806 bp):
ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTCATTTCAACAACAAGGTGTGCAT
AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAAATCATGCCAGGGCATGGCTTAA
TGGAGTACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATA
ATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGAAAACGCAATGAAAAG
TCTATGTATGAGTGTTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCCA
CAGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGATGATGATGCTAGATG
CCTAGAAAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGATT
GCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCATT
CGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAATT
TGCAAAGACCAGGTGAGGGGAAATAAATGAAGGCAACTAATTCAGCATGTTTAGTATGCCATGAC
AATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATTA
AGGTAACAACAACCCCTACTCTAATACATATAATCCTGGATAGTGTCAGCATCCAAACTTCTCTT
GGGGAAATCAATGAACCATCAATGAT
Found at i:56908 original size:21 final size:20
Alignment explanation
Indices: 56875--56913 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56865 TCATGGATGG
*
56875 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
56895 TTGTTTTTCTTATGATGTT
1 TTGTTTTT-GTATGATGTT
56914 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:60170 original size:23 final size:22
Alignment explanation
Indices: 60144--60189 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
60134 TTCATAAAAC
*
60144 TTAAATCAACAAATTTTATAATT
1 TTAAAT-AACAAATTTTAGAATT
* *
60167 TTAAATATCTAATTTTAGAATT
1 TTAAATAACAAATTTTAGAATT
60189 T
1 T
60190 ATTATCATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATAACAAATTTTAGAATT
Found at i:63320 original size:21 final size:21
Alignment explanation
Indices: 63296--63412 Score: 121
Period size: 21 Copynumber: 5.6 Consensus size: 21
63286 GCGTTGCATT
63296 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
63317 TCGCGTTGCGAT-CTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
63337 TCGCGTTGCGATAGTCT-ACAG
1 TCGCGTTGCGATAGT-TGAAAA
* *
63358 TTGTCGTTGTGATAGTTGAAAA
1 TCG-CGTTGCGATAGTTGAAAA
63380 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
63401 TCGCGTTGCGAT
1 TCGCGTTGCGAT
63413 CGTGGTCGTG
Statistics
Matches: 76, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
20 15 0.20
21 45 0.59
22 16 0.21
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:63423 original size:6 final size:6
Alignment explanation
Indices: 63412--63438 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
63402 CGCGTTGCGA
63412 TCGTGG TCGTGG TCGTGG TCGTGG TCG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCG
63439 CGATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.48, T:0.33
Consensus pattern (6 bp):
TCGTGG
Found at i:63480 original size:20 final size:20
Alignment explanation
Indices: 63455--63502 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
63445 TCAACTATCG
63455 CAACGCGAAATGGAAAATCA
1 CAACGCGAAATGGAAAATCA
*
63475 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCA
63495 CAACGCGA
1 CAACGCGA
63503 TTTTCAACTA
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:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCA
Found at i:63531 original size:21 final size:21
Alignment explanation
Indices: 63446--63531 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 21
63436 TCGCGATTTT
*
63446 CAACTATCGCAACGCGAAATG
1 CAACAATCGCAACGCGAAATG
* *
63467 GAA-AATCACAACGCGAAATG
1 CAACAATCGCAACGCGAAATG
* ** *
63487 GAA-AATCGCAACGCGATTTT
1 CAACAATCGCAACGCGAAATG
*
63507 CAACTATCGCAACGCGAAATG
1 CAACAATCGCAACGCGAAATG
63528 CAAC
1 CAAC
63532 GCGAATTTGC
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 33 0.63
21 19 0.37
ACGTcount: A:0.41, C:0.26, G:0.19, T:0.15
Consensus pattern (21 bp):
CAACAATCGCAACGCGAAATG
Found at i:67062 original size:12 final size:12
Alignment explanation
Indices: 67045--67069 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
67035 AAATAGAAAC
67045 AACGAGCGAGCG
1 AACGAGCGAGCG
67057 AACGAGCGAGCG
1 AACGAGCGAGCG
67069 A
1 A
67070 GAGATGAAGC
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:0.36, C:0.24, G:0.40, T:0.00
Consensus pattern (12 bp):
AACGAGCGAGCG
Found at i:75066 original size:27 final size:28
Alignment explanation
Indices: 75029--75087 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
75019 AAAATTTACA
75029 AACATTCAAGTGAAATGTAATGTAGTTC
1 AACATTCAAGTGAAATGTAATGTAGTTC
75057 AACATT-AAGTGAAATGTAATGTAGTTC
1 AACATTCAAGTGAAATGTAATGTAGTTC
75084 AACA
1 AACA
75088 ACTAGAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (28 bp):
AACATTCAAGTGAAATGTAATGTAGTTC
Found at i:75647 original size:13 final size:13
Alignment explanation
Indices: 75629--75653 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
75619 AATGAATTTT
75629 AAGATTTTCTAAA
1 AAGATTTTCTAAA
75642 AAGATTTTCTAA
1 AAGATTTTCTAA
75654 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Done.