Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D07
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: 56457815
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1765025 characters in sequence are not A, C, G, or T
File 59 of 189
Found at i:16703177 original size:76 final size:76
Alignment explanation
Indices: 16703051--16703203 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
16703041 AAAATATAAT
* *
16703051 AATAATCATATTTTTCCTTGTCGGATTTGTGGTCCCGAAACCACTGTTCCGAGTAGACCTAGAAT
1 AATAATCATATTTTTCCTTGTCGGATTTGTGGTCCCGAAACCACTGTTCCGACTAGACCCAGAAT
16703116 TGGGCTGTTAC
66 TGGGCTGTTAC
*
16703127 AATAATCATATTTTTCCTTGTCGGATTTGTGGTCCTGAAACCACTGTTCCGACTAGACCCAGAAT
1 AATAATCATATTTTTCCTTGTCGGATTTGTGGTCCCGAAACCACTGTTCCGACTAGACCCAGAAT
16703192 TGGGCTGTTAC
66 TGGGCTGTTAC
16703203 A
1 A
16703204 GCATTGATTC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (76 bp):
AATAATCATATTTTTCCTTGTCGGATTTGTGGTCCCGAAACCACTGTTCCGACTAGACCCAGAAT
TGGGCTGTTAC
Found at i:16707865 original size:20 final size:21
Alignment explanation
Indices: 16707821--16707865 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
16707811 TTAAAATACT
* *
16707821 TTTAAAATAAATTTTTTTATT
1 TTTAAAATAAATTTTTTAATG
16707842 TTTAAAAT-AATTTTTTAATG
1 TTTAAAATAAATTTTTTAATG
16707862 TTTA
1 TTTA
16707866 TTTTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTAAAATAAATTTTTTAATG
Found at i:16718716 original size:44 final size:44
Alignment explanation
Indices: 16718647--16718881 Score: 154
Period size: 44 Copynumber: 5.3 Consensus size: 44
16718637 TGAATATTAT
* * *
16718647 CTCCTTGAAGTTGCAGTGGAACAGATTGAAGCCACTAGTCTTAC
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTAC
* * ** * *
16718691 CTCTCTGAAGTTGCAGTGGAGCAGATTAAAGATATCAAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAATCTTAC
* * * *
16718736 CTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTCACTAAACATATC
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTA-C
* * * * * *
16718781 C-CCCTAAAGTTGCAGTGGGGTA-AGTTGAAACCA--AGTCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGCCACTAATCTTAC
* * * * ** * *
16718822 CTCTCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATCTTAT
1 CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCA-CTAATCTTAC
*
16718867 TTCCCTGAAGTTGCA
1 CTCCCTGAAGTTGCA
16718882 ATAGAACAGA
Statistics
Matches: 144, Mismatches: 39, Indels: 15
0.73 0.20 0.08
Matches are distributed among these distances:
41 1 0.01
42 26 0.18
43 2 0.01
44 60 0.42
45 55 0.38
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (44 bp):
CTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACTAATCTTAC
Found at i:16718749 original size:45 final size:43
Alignment explanation
Indices: 16718643--16719196 Score: 208
Period size: 45 Copynumber: 12.6 Consensus size: 43
16718633 ATGGTGAATA
* * ** * *
16718643 TTATCTCCTTGAAGTTGCAGTGGAACAGATTGAAGCCACTAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGATACAAATC
* *
16718687 TTACCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGATATCAAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGATA-CAAATC
*
16718732 TTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAG-TCACTAAA-C
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAGAT-AC-AAATC
* * * * * * *
16718776 ATATCCCCCTAAAGTTGCAGTGGGGTA-AGTTGAA-A-CCAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TT-AAGATACAAATC
* * * * *
16718818 TTATCTCTCTAAAGTTACAGTGGAGCAGACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAGATA-CAAATC
* * * * * *
16718863 TTATTTCCCTGAAGTTGCAATAGAACAGATTAAAACTATAAATTACCGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT--AA-GATACA--A---ATC
* * ** *
16718914 TTATCTCGCTGAAGTTGCAGTAGAGCA-A--ATCATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGATA-CAAATC
* * * * *
16718955 TTATCTCTCTGAAGTTGTAGTGGAGCAG-TTTA-A-ACCAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGATACAAATC
* * * * * *
16718995 TTCTCTCTCTGAATTTGCAGTGGAGTAGACTGAAGATAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAGATA-CAAATC
* * *
16719040 TTATTTCCCTGAAGTTGCAGTGGAACA-ATTTCAAGCTATAAATTACCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TT-AAG------A-TACAAATC
* ** * * *
16719091 TTATCTCGCTGAAGTTATAGTAGAGCATATT---ATAGCAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGATA-CAAATC
* * *
16719132 TTATCTCCTTGAAGTTGCAGTGGAGCAG-TTTA-A-ACCAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGATACAAATC
16719172 TTATCTCCCTGAAGTTGCAGTGGAG
1 TTATCTCCCTGAAGTTGCAGTGGAG
16719197 TTGACTGAAG
Statistics
Matches: 380, Mismatches: 91, Indels: 82
0.69 0.16 0.15
Matches are distributed among these distances:
40 59 0.16
41 57 0.15
42 29 0.08
43 5 0.01
44 67 0.18
45 96 0.25
46 4 0.01
47 3 0.01
48 1 0.00
50 1 0.00
51 55 0.14
52 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (43 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAGATACAAATC
Found at i:16718988 original size:92 final size:91
Alignment explanation
Indices: 16718870--16719165 Score: 229
Period size: 92 Copynumber: 3.3 Consensus size: 91
16718860 ATCTTATTTC
* * * *
16718870 CCTGAAGTTGCAATAGAACAGATTAAAACTATAAATTACCGATCTTATCTCGCTGAAGTTGCAGT
1 CCTGAAGTTGCAGTGGAGCAGTTTAAAACTATAAATTACCGATCTTATCTCGCTGAAGTTGCAGT
16718935 AGAGCAAATCATAGCAAACCTTATCT
66 AGAGCAAATCATAGCAAACCTTATCT
* * * * *
16718961 CTCTGAAGTTGTAGTGGAGCAGTTT-AAAC---------CAG-TCTTCTCTCTCTGAATTTGCAG
1 C-CTGAAGTTGCAGTGGAGCAGTTTAAAACTATAAATTACCGATCTTATCTCGCTGAAGTTGCAG
* * * * *
16719015 TGGAGTAGACTGAA-GATAGCGAATCTTATTT
65 T--AG-AG-C-AAATCATAGCAAACCTTATCT
* * * * * **
16719046 CCCTGAAGTTGCAGTGGAACAATTTCAAGCTATAAATTACCAATCTTATCTCGCTGAAGTTATAG
1 -CCTGAAGTTGCAGTGGAGCAGTTTAAAACTATAAATTACCGATCTTATCTCGCTGAAGTTGCAG
* *
16719111 TAGAGCATATTATAGCAAACCTTATCT
65 TAGAGCAAATCATAGCAAACCTTATCT
16719138 CCTTGAAGTTGCAGTGGAGCAGTTTAAA
1 CC-TGAAGTTGCAGTGGAGCAGTTTAAA
16719166 CCAATCTTAT
Statistics
Matches: 151, Mismatches: 34, Indels: 39
0.67 0.15 0.17
Matches are distributed among these distances:
81 20 0.13
82 2 0.01
83 2 0.01
84 2 0.01
85 34 0.23
86 6 0.04
91 8 0.05
92 54 0.36
93 2 0.01
94 2 0.01
95 1 0.01
96 18 0.12
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (91 bp):
CCTGAAGTTGCAGTGGAGCAGTTTAAAACTATAAATTACCGATCTTATCTCGCTGAAGTTGCAGT
AGAGCAAATCATAGCAAACCTTATCT
Found at i:16719028 original size:177 final size:177
Alignment explanation
Indices: 16718787--16719206 Score: 601
Period size: 177 Copynumber: 2.4 Consensus size: 177
16718777 TATCCCCCTA
* * * * * *
16718787 AAGTTGCAGTGGGGTAAGTTGAAACCAAGTCTTATCTCTCTAAAGTTACAGTGGAGCAGACTGAA
1 AAGTTGCAGTGGAG-CAGTTTAAACC-AGTCTTATCTCTCTGAAGTTGCAGTGGAGTAGACTGAA
*
16718852 GATAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAGA-TTAAAACTATAAATTACCGATCTT
64 GATAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACA-ATTTAAAACTATAAATTACCAATCTT
*
16718916 ATCTCGCTGAAGTTGCAGTAGAGCAAATCATAGCAAACCTTATCT-CTCTG
128 ATCTCGCTGAAGTTACAGTAGAGCAAATCATAGCAAACCTTATCTCCT-TG
* * *
16718966 AAGTTGTAGTGGAGCAGTTTAAACCAGTCTTCTCTCTCTGAATTTGCAGTGGAGTAGACTGAAGA
1 AAGTTGCAGTGGAGCAGTTTAAACCAGTCTTATCTCTCTGAAGTTGCAGTGGAGTAGACTGAAGA
* * * *
16719031 TAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAATTTCAAGCTATAAATTACCAATCTTATC
66 TAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAATTTAAAACTATAAATTACCAATCTTATC
* * *
16719096 TCGCTGAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTCCTTG
131 TCGCTGAAGTTACAGTAGAGCAAATCATAGCAAACCTTATCTCCTTG
* * *
16719143 AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGTTGACTGAAG
1 AAGTTGCAGTGGAGCAGTTTAAACCAGTCTTATCTCTCTGAAGTTGCAGTGGAGTAGACTGAAG
16719207 CTGAATCCTA
Statistics
Matches: 215, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
176 1 0.00
177 191 0.89
178 11 0.05
179 12 0.06
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (177 bp):
AAGTTGCAGTGGAGCAGTTTAAACCAGTCTTATCTCTCTGAAGTTGCAGTGGAGTAGACTGAAGA
TAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAATTTAAAACTATAAATTACCAATCTTATC
TCGCTGAAGTTACAGTAGAGCAAATCATAGCAAACCTTATCTCCTTG
Found at i:16719185 original size:40 final size:41
Alignment explanation
Indices: 16719084--16719196 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 41
16719074 GCTATAAATT
* ** *
16719084 ACCAATCTTATCTCGCTGAAGTTATAGTAGAGCATATTATA
1 ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTATA
* * * *
16719125 GCAAACCTTATCTCCTTGAAGTTGCAGTGGAGCAGT-TTA-A
1 ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCA-TATTATA
16719165 ACCAATCTTATCTCCCTGAAGTTGCAGTGGAG
1 ACCAATCTTATCTCCCTGAAGTTGCAGTGGAG
16719197 TTGACTGAAG
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
40 29 0.49
41 29 0.49
42 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (41 bp):
ACCAATCTTATCTCCCTGAAGTTGCAGTGGAGCATATTATA
Found at i:16719304 original size:177 final size:175
Alignment explanation
Indices: 16718787--16719290 Score: 466
Period size: 177 Copynumber: 2.9 Consensus size: 175
16718777 TATCCCCCTA
* * * * * * *
16718787 AAGTTGCAGTGGGGTAAGTTGAAACCAAGTCTTATCTCTCTAAAGTTACAGTGGAGCAGACTGAA
1 AAGTTGCAGTGGAG-CAGTTTAAACCAA-TCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAA
* * * * * * *
16718852 GATAGCGAATCTTATTTCCCTGAAGTTGCAATAGAACAGA-TTAAAACTATAAATTACCGATCTT
64 GATA--GAATCCTATTACCCTGAAGTTGCAGTGGAACA-ATTTAAAGCTATAAATTAACAATCTT
* * * ** * *
16718916 ATCTCGCTGAAGTTGCAGTAGAGCAAATCATAGCAAACCTTATCTCTCTG
126 ACCTCCCTAAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTCTCTG
* * * * *
16718966 AAGTTGTAGTGGAGCAGTTTAAACCAGTCTTCTCTCTCTGAATTTGCAGTGGAGTAGACTGAAGA
1 AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGA
* * * * *
16719031 TAGCGAATCTTATTTCCCTGAAGTTGCAGTGGAACAATTTCAAGCTATAAATTACCAATCTTATC
66 TA--GAATCCTATTACCCTGAAGTTGCAGTGGAACAATTTAAAGCTATAAATTAACAATCTTACC
* *
16719096 TCGCTGAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTC-CTTG
129 TCCCTAAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTCTC-TG
* *
16719143 AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGTTGACTGAAGC
1 AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGA
* * * **
16719208 T-GAATCCTA-TACCTCTGAAGTTGTAGTAGG-TCAGA-TTAAATCTA-CCA-TAACAAGTCTTA
66 TAGAATCCTATTACC-CTGAAGTTGCAGT-GGAACA-ATTTAAAGCTATAAATTAACAA-TCTTA
* *
16719267 CCTCCCTAAAGTTGTAGTGGAGCA
127 CCTCCCTAAAGTTATAGTAGAGCA
16719291 GACTGTATAT
Statistics
Matches: 279, Mismatches: 40, Indels: 18
0.83 0.12 0.05
Matches are distributed among these distances:
172 5 0.02
173 28 0.10
174 28 0.10
175 3 0.01
176 2 0.01
177 191 0.68
178 10 0.04
179 12 0.04
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (175 bp):
AAGTTGCAGTGGAGCAGTTTAAACCAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTGAAGA
TAGAATCCTATTACCCTGAAGTTGCAGTGGAACAATTTAAAGCTATAAATTAACAATCTTACCTC
CCTAAAGTTATAGTAGAGCATATTATAGCAAACCTTATCTCTCTG
Found at i:16719982 original size:18 final size:18
Alignment explanation
Indices: 16719961--16720010 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
16719951 AAACCACACG
16719961 CAACAAAAAA-AACAAAAA
1 CAACAAAAAATAAC-AAAA
*
16719979 CAACAAACAAATAGCAAAA
1 CAACAAA-AAATAACAAAA
*
16719998 CGACAAAAAATAA
1 CAACAAAAAATAA
16720011 TGATTAAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
19 13 0.48
20 2 0.07
ACGTcount: A:0.74, C:0.18, G:0.04, T:0.04
Consensus pattern (18 bp):
CAACAAAAAATAACAAAA
Found at i:16724688 original size:31 final size:31
Alignment explanation
Indices: 16724653--16724734 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
16724643 CCCGAATAAT
*
16724653 AAATATTTTTATTTTTTTATTTTTAATTTTA
1 AAATATTTTTAATTTTTTATTTTTAATTTTA
* * **
16724684 AAATACTTTTAAAATAATT-TTTTTAATTTTA
1 AAATA-TTTTTAATTTTTTATTTTTAATTTTA
16724715 AAATATTTTTAAATTTTTTA
1 AAATATTTTT-AATTTTTTA
16724735 AAATACTTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
30 4 0.10
31 27 0.69
32 8 0.21
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (31 bp):
AAATATTTTTAATTTTTTATTTTTAATTTTA
Found at i:16724695 original size:11 final size:11
Alignment explanation
Indices: 16724676--16724744 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 11
16724666 TTTTTATTTT
16724676 TAATTTTAAAA
1 TAATTTTAAAA
*
16724687 TACTTTTAAAA
1 TAATTTTAAAA
**
16724698 TAATTTT--TT
1 TAATTTTAAAA
16724707 TAATTTTAAAA
1 TAATTTTAAAA
*
16724718 T-ATTTTTAAA
1 TAATTTTAAAA
*
16724728 T-TTTTTAAAA
1 TAATTTTAAAA
*
16724738 TACTTTT
1 TAATTTT
16724745 TTATTTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 7 0.16
10 17 0.38
11 21 0.47
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:16724715 original size:20 final size:21
Alignment explanation
Indices: 16724690--16724792 Score: 69
Period size: 20 Copynumber: 5.2 Consensus size: 21
16724680 TTTAAAATAC
*
16724690 TTTTAAAATAATTTTTTTAA-
1 TTTTAAAATAATTTTTTAAAT
16724710 TTTTAAAAT-A-TTTTTAAATT
1 TTTTAAAATAATTTTTTAAA-T
*
16724730 TTTTAAAATACTTTTTT--AT
1 TTTTAAAATAATTTTTTAAAT
** **
16724749 TTTT--TTTAATTTTAAAATAT
1 TTTTAAAATAATTTTTTAA-AT
*
16724769 TTTTAAAATACTTTTTT-AAT
1 TTTTAAAATAATTTTTTAAAT
16724789 TTTT
1 TTTT
16724793 GTTTTAATTT
Statistics
Matches: 62, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
17 6 0.10
18 7 0.11
19 6 0.10
20 31 0.50
21 1 0.02
22 11 0.18
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAAAATAATTTTTTAAAT
Found at i:16743443 original size:6 final size:6
Alignment explanation
Indices: 16743432--16743464 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
16743422 CCTTTCCGTT
16743432 CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTT
1 CTTTAC CTTTAC CTTTAC CTTTAC CTTTAC CTT
16743465 GTGCCCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.15, C:0.33, G:0.00, T:0.52
Consensus pattern (6 bp):
CTTTAC
Found at i:16753405 original size:3 final size:3
Alignment explanation
Indices: 16753397--16753425 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
16753387 AATAATTATT
16753397 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
16753426 TTATTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:16754115 original size:8 final size:8
Alignment explanation
Indices: 16754102--16754130 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
16754092 TGTATTTTTC
16754102 AATATTTA
1 AATATTTA
16754110 AATATTTA
1 AATATTTA
16754118 AATATTT-
1 AATATTTA
16754125 AATATT
1 AATATT
16754131 ATAATTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
AATATTTA
Found at i:16755447 original size:20 final size:19
Alignment explanation
Indices: 16755422--16755477 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
16755412 ATTCTTAATA
16755422 AATTTTAAATAATTATCTAT
1 AATTTTAAATAATTAT-TAT
**
16755442 AATTTTGTATAATT-TTAT
1 AATTTTAAATAATTATTAT
*
16755460 AATTATTTAATAATTATT
1 AATT-TTAAATAATTATT
16755478 TAAGAAACAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 7 0.23
19 9 0.30
20 14 0.47
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTTTAAATAATTATTAT
Found at i:16755639 original size:51 final size:53
Alignment explanation
Indices: 16755578--16755677 Score: 168
Period size: 53 Copynumber: 1.9 Consensus size: 53
16755568 AAAATAATAA
*
16755578 TTCTTATAAATTTT-AGT-TTTTTAAATAATTTTCTATAATGTTTTTAATCAT
1 TTCTTATAAATTTTAAGTATTTTTAAACAATTTTCTATAATGTTTTTAATCAT
*
16755629 TTCTTATAAATTTTAATTATTTTTAAACAATTTTCTATAATGTTTTTAA
1 TTCTTATAAATTTTAAGTATTTTTAAACAATTTTCTATAATGTTTTTAA
16755678 AAACCATGTC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
51 14 0.31
52 2 0.04
53 29 0.64
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (53 bp):
TTCTTATAAATTTTAAGTATTTTTAAACAATTTTCTATAATGTTTTTAATCAT
Found at i:16755660 original size:20 final size:20
Alignment explanation
Indices: 16755619--16755662 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
16755609 TCTATAATGT
*
16755619 TTTTAATCATTTCTTATAAA
1 TTTTAATCATTTCTTAAAAA
*
16755639 TTTTAATTATTT-TTAAACAA
1 TTTTAATCATTTCTTAAA-AA
16755659 TTTT
1 TTTT
16755663 CTATAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTAATCATTTCTTAAAAA
Found at i:16756796 original size:17 final size:17
Alignment explanation
Indices: 16756774--16756806 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
16756764 ATTCTATCTT
16756774 ATTTTTATT-TTATTTAG
1 ATTTTT-TTATTATTTAG
16756791 ATTTTTTTATTATTTA
1 ATTTTTTTATTATTTA
16756807 ATTAAGTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (17 bp):
ATTTTTTTATTATTTAG
Found at i:16763122 original size:25 final size:25
Alignment explanation
Indices: 16763094--16763222 Score: 126
Period size: 25 Copynumber: 5.4 Consensus size: 25
16763084 GAACTTTAGC
** * *
16763094 GTGCTCTCAAATTAGTAGCACATCA
1 GTGCTCTCTGATTACTAGCACGTCA
**
16763119 GTGCTCTCTGATTACTAGCACGTTG
1 GTGCTCTCTGATTACTAGCACGTCA
16763144 GTGCTCTCTGATTACTAGCACGTCA
1 GTGCTCTCTGATTACTAGCACGTCA
* *
16763169 GTGCTCTCTG-TT--TAGCACATCT
1 GTGCTCTCTGATTACTAGCACGTCA
* *
16763191 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTACTAGCACGTCA
16763213 GTGCTCTCTG
1 GTGCTCTCTG
16763223 TTCATTAGTG
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
21 1 0.01
22 35 0.39
24 2 0.02
25 52 0.58
ACGTcount: A:0.19, C:0.26, G:0.20, T:0.36
Consensus pattern (25 bp):
GTGCTCTCTGATTACTAGCACGTCA
Found at i:16771084 original size:14 final size:14
Alignment explanation
Indices: 16771052--16771086 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16771042 GAGTTTAGAC
16771052 TAAAAAAATCAAAA
1 TAAAAAAATCAAAA
* *
16771066 AAAAAAAATCAAAG
1 TAAAAAAATCAAAA
16771080 TAAAAAA
1 TAAAAAA
16771087 TAGGAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.80, C:0.06, G:0.03, T:0.11
Consensus pattern (14 bp):
TAAAAAAATCAAAA
Found at i:16771099 original size:15 final size:15
Alignment explanation
Indices: 16771090--16771123 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
16771080 TAAAAAATAG
16771090 GAGAAAAAAAAAGAA
1 GAGAAAAAAAAAGAA
16771105 GAGAAAAAGAAAA-AA
1 GAGAAAAA-AAAAGAA
16771120 GAGA
1 GAGA
16771124 GGTCAAGGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
GAGAAAAAAAAAGAA
Found at i:16771963 original size:16 final size:17
Alignment explanation
Indices: 16771942--16771977 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
16771932 AAAATGAATG
16771942 AAAAAATGAAAAA-TAA
1 AAAAAATGAAAAAGTAA
16771958 AAAAAATGAAAAAGTAA
1 AAAAAATGAAAAAGTAA
16771975 AAA
1 AAA
16771978 TGGAGAGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.11
Consensus pattern (17 bp):
AAAAAATGAAAAAGTAA
Found at i:16773340 original size:88 final size:88
Alignment explanation
Indices: 16773181--16773949 Score: 1151
Period size: 88 Copynumber: 8.7 Consensus size: 88
16773171 AACAGATCAG
* * * * *
16773181 TGAAGACAACAGATCTTGTCTTCTTGCATTGACAGCGAAGCAGGTCGAAGAAAAAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16773246 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * *
16773269 TAAAGGCAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACATAGACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16773334 CTCTCGGTTGTGATGAAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * *
16773357 TGAAGACAAAAGATCTTACCTTCCTGTATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16773422 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* ** * *
16773445 TGAAGATAAAAGATCTTGCCTTCCTATATTGATAGCGAAGCAGATCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16773510 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
16773533 TGAAGACAAAAGATCTTGCCTTCCTGTATTGACAGCGGAGTAGGTTGAAGACACAAACCTTACCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16773598 CTCTCGGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
*
16773621 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCAAAGCAGGTCGAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16773686 CTCTCAGTTGTGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* ** * * *
16773709 TGAAGATAAGTGATCTTGCCTTCCTGCATTGATAGCGAAGCAAGTCAAAGACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16773774 CTCTCGGTTGTGATAGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * * *
16773797 TGAAGATAAAAGATCTTGCCTTCCTACATTGTCAGCAAAGCAGGTCGAAGACACAAACCTTGCTT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
*
16773862 CTCTCGGTTATGATGGAGCTGGT
66 CTCTCGGTTGTGATGGAGCTGGT
* * * *
16773885 TGAAGACAATAGATCTTGCCTTCCTGCATTGACAGTGAAGTAGGTCGAAAACACAAACCTTGCCT
1 TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
16773950 TCTTGTACTG
Statistics
Matches: 616, Mismatches: 65, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 616 1.00
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (88 bp):
TGAAGACAAAAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGACACAAACCTTGCCT
CTCTCGGTTGTGATGGAGCTGGT
Found at i:16774043 original size:46 final size:46
Alignment explanation
Indices: 16773976--16774135 Score: 230
Period size: 46 Copynumber: 3.5 Consensus size: 46
16773966 GAGCAGACTA
* * *
16773976 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGCAGAGGAGATCG
1 AAGATAGTAAATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCG
*
16774022 AAGATAGTAAATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATTG
1 AAGATAGTAAATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCG
* * * *
16774068 AAGATAGTAGATCTTGTCTTTCTGTATTTGGCAGCGGAGTAGATCA
1 AAGATAGTAAATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCG
* *
16774114 AAGATGGTAAATCTTATCTTCC
1 AAGATAGTAAATCTTGTCTTCC
16774136 CATTACAGTG
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 101 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.33
Consensus pattern (46 bp):
AAGATAGTAAATCTTGTCTTCCTGTATTTGGCAGCGGAGGAGATCG
Found at i:16774275 original size:132 final size:132
Alignment explanation
Indices: 16774103--16774378 Score: 408
Period size: 132 Copynumber: 2.1 Consensus size: 132
16774093 ATTTGGCAGC
* * *
16774103 GGAGTAGATCAAAGATGGTAAATCTTATCTTCCCATTACAGTGGAGAAGCGGATTTAAGCCATTA
1 GGAGCAGATCAAAGATGGTAAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* * ** ** *
16774168 GTCTTATCACCTTAAGCAGTAGTGGAGTAGGTTGAAGGTTGCAGATTCTGTCACCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGACTACAGATTCTGTCACCCTAAGCAGTA
16774233 GT
131 GT
* * *
16774235 GGAGCAGATCGAAGATGGTGAATCTTATCTTTCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
1 GGAGCAGATCAAAGATGGTAAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
* * *
16774300 GTCCTATCACCCTAAGCAGTAGTGGGGTAGGTCAAAGACTATAGATTCTGTCCCCCTAAGCAGTA
66 GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGACTACAGATTCTGTCACCCTAAGCAGTA
16774365 GT
131 GT
16774367 GGAGCAGATCAA
1 GGAGCAGATCAA
16774379 CAATAACGAA
Statistics
Matches: 127, Mismatches: 17, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
132 127 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (132 bp):
GGAGCAGATCAAAGATGGTAAATCTTATCTTCCCAATACAGTGGAGAAGCAGATTTAAGCCATTA
GTCCTATCACCCTAAGCAGTAGTGGAGTAGGTCAAAGACTACAGATTCTGTCACCCTAAGCAGTA
GT
Found at i:16781718 original size:44 final size:46
Alignment explanation
Indices: 16781657--16781749 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 46
16781647 TACAACATCT
** * *
16781657 ATTCCATTCAATTAAACACA-AGAA-TATTG-TTACAGCTCTATTCC
1 ATTCCATTCAACCAAACA-ATAGAATTACTGATTACAGATCTATTCC
*
16781701 ATTCCATTCAACCAAACAATTGAATTACTGATTACAGATCTATTCC
1 ATTCCATTCAACCAAACAATAGAATTACTGATTACAGATCTATTCC
16781747 ATT
1 ATT
16781750 ACAACTCTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 19 0.46
45 4 0.10
46 17 0.41
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.34
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAATAGAATTACTGATTACAGATCTATTCC
Found at i:16781752 original size:16 final size:16
Alignment explanation
Indices: 16781739--16781781 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
16781729 TGATTACAGA
16781739 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
16781755 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
*
16781771 CCTATTCCATT
1 TCTATTCCATT
16781782 CCCCCAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (16 bp):
TCTATTCCATTACAAC
Found at i:16783314 original size:2 final size:2
Alignment explanation
Indices: 16783307--16783331 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16783297 GGTTAGATTT
16783307 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
16783332 ATTGAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16784327 original size:18 final size:20
Alignment explanation
Indices: 16784311--16784350 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
16784301 ATACACATAT
16784311 ACATTTGTTTGCACATATCTC
1 ACATTTGTTTGCACATA-CTC
*
16784332 AGATTTGTTTGCACATACT
1 ACATTTGTTTGCACATACT
16784351 TTTGTGAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (20 bp):
ACATTTGTTTGCACATACTC
Found at i:16785657 original size:29 final size:29
Alignment explanation
Indices: 16785620--16785677 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
16785610 GAAAATATTG
* *
16785620 GAAGAAAAATTCTAGGAGAATTAGAAAAT
1 GAAGAAAAATCCTAGCAGAATTAGAAAAT
* **
16785649 GAAGTAAAATCCTAGCCTAATTAGAAAAT
1 GAAGAAAAATCCTAGCAGAATTAGAAAAT
16785678 TGGTTTAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (29 bp):
GAAGAAAAATCCTAGCAGAATTAGAAAAT
Found at i:16788194 original size:37 final size:37
Alignment explanation
Indices: 16788152--16788222 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
16788142 AGTATTACTT
16788152 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
16788189 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
16788223 AAAAAATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:16788234 original size:19 final size:19
Alignment explanation
Indices: 16788158--16788226 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
16788148 ACTTAATAGT
16788158 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
16788177 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
16788195 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
16788214 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
16788227 AATGAGTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:16788376 original size:27 final size:26
Alignment explanation
Indices: 16788299--16788384 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
16788289 ATTTTTTTCC
* *
16788299 TTTGGCACCATGGTGCTGCCAA-TGA
1 TTTGGCACCATGGTGCCGCCAATTTA
*
16788324 CTTTGGCACCAATGGTGCCACCAATTTA
1 -TTTGGCACC-ATGGTGCCGCCAATTTA
*
16788352 TTTGGCACCTTTGGTGCCGCCAATTTA
1 TTTGGCACC-ATGGTGCCGCCAATTTA
*
16788379 ATTGGC
1 TTTGGC
16788385 TGGTGTCAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
26 9 0.18
27 40 0.78
28 2 0.04
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (26 bp):
TTTGGCACCATGGTGCCGCCAATTTA
Found at i:16788456 original size:27 final size:28
Alignment explanation
Indices: 16788426--16788523 Score: 155
Period size: 28 Copynumber: 3.5 Consensus size: 28
16788416 TTTTTTTGAT
16788426 ATATTTTGGTAAATAAAAAAAAAGTT-TA
1 ATATTTTGGTAAAT-AAAAAAAAGTTATA
16788454 TATATTTTGGTAAAT-AAAAAAAGTTATA
1 -ATATTTTGGTAAATAAAAAAAAGTTATA
*
16788482 ATATTTTGGTAAATAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
16788510 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
16788524 TTTTATTTTT
Statistics
Matches: 66, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
27 24 0.36
28 28 0.42
29 14 0.21
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:16788456 original size:29 final size:28
Alignment explanation
Indices: 16788424--16788523 Score: 152
Period size: 27 Copynumber: 3.6 Consensus size: 28
16788414 TTTTTTTTTG
16788424 ATATATTTTGGTAAATAAAAAAAAAGTTT
1 ATATATTTTGGTAAAT-AAAAAAAAGTTT
16788453 ATATATTTTGGTAAAT-AAAAAAAG-TT
1 ATATATTTTGGTAAATAAAAAAAAGTTT
16788479 ATAATATTTTGGTAAATAAAAAAAAGTTGT
1 AT-ATATTTTGGTAAATAAAAAAAAGTT-T
16788509 A-ATATTTTGGTAAAT
1 ATATATTTTGGTAAAT
16788524 TTTTATTTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 9
0.88 0.00 0.12
Matches are distributed among these distances:
26 4 0.06
27 22 0.33
28 22 0.33
29 17 0.25
30 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (28 bp):
ATATATTTTGGTAAATAAAAAAAAGTTT
Found at i:16790291 original size:43 final size:43
Alignment explanation
Indices: 16790243--16790343 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
16790233 TTTTTATGAC
*
16790243 CTTTAGTGGCGTTTTTACCAAAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTACCAAAAACGCCGCTAAAGGTCATGTT
* *** *
16790286 CTTTAGCGGCGTTTCTGGTAAAAGCGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGTTTTTACCAAAAACGCCGCTAAAGGTCATGTT
16790329 CTTTAGCGGCGTTTT
1 CTTTAGCGGCGTTTT
16790344 GTCTCATAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (43 bp):
CTTTAGCGGCGTTTTTACCAAAAACGCCGCTAAAGGTCATGTT
Found at i:16790477 original size:21 final size:21
Alignment explanation
Indices: 16790434--16790478 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
16790424 TTTAGCGGCA
* **
16790434 CTAAAAAGCGCCGCTAATGGC
1 CTAAAAAACGCCGCTAAAAGC
*
16790455 CTAAAAAACGCTGCTAAAAGC
1 CTAAAAAACGCCGCTAAAAGC
16790476 CTA
1 CTA
16790479 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
CTAAAAAACGCCGCTAAAAGC
Found at i:16796914 original size:21 final size:21
Alignment explanation
Indices: 16796888--16796927 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
16796878 AATCACTTTG
16796888 AAACACTTTTATCTTACAATT
1 AAACACTTTTATCTTACAATT
16796909 AAACACTTTTATCTTACAA
1 AAACACTTTTATCTTACAA
16796928 CATGTGGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (21 bp):
AAACACTTTTATCTTACAATT
Found at i:16797509 original size:14 final size:14
Alignment explanation
Indices: 16797490--16797517 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16797480 GAGAAAAACA
16797490 ACCTCCACGACCTC
1 ACCTCCACGACCTC
16797504 ACCTCCACGACCTC
1 ACCTCCACGACCTC
16797518 TTCCATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.57, G:0.07, T:0.14
Consensus pattern (14 bp):
ACCTCCACGACCTC
Found at i:16804783 original size:109 final size:109
Alignment explanation
Indices: 16804625--16805011 Score: 567
Period size: 109 Copynumber: 3.6 Consensus size: 109
16804615 TGGTCAAATC
* * *
16804625 GAAAAATCGAAACCCAGCGCATTAGGGCACGTTTCCTTAAATTTCCAAACGCAAAATATTATCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
*
16804690 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAATGA
66 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
* * *
16804734 GAAAAATCGACACCCAGCGCATTAGGGCACGTTTCCTTAAATTTCCAAACGCAAAATATTATTTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
*
16804799 ACTTCGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
66 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
* * * * * * *
16804843 GAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAACGCAAAACACTGTCTT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
* *
16804908 ATTTTGAAATTTTTAAAAGGATATTAAGCCATTTGGTTGAACGA
66 ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
* * * * * *
16804952 GAAAAATCGACACCCAGCACCTTAGGGCATGTTTTCTCGAATTTCCAAAAGCTAAATATT
1 GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATT
16805012 GCCTCATTTA
Statistics
Matches: 257, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
109 257 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (109 bp):
GAAAAATCGACACCCAGCACATTAGGGCACGTTTCCTCAAATTTCCAAACGCAAAATATTATCTT
ACTTTGAAATTTTTAAAAGGATATTTAGCCATTTGGTTGAACGA
Found at i:16811427 original size:34 final size:33
Alignment explanation
Indices: 16811358--16811448 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 33
16811348 GACTTGTTGC
* *
16811358 TATGTAAACCCCCATGTTATATAGTATGACGTAG
1 TATGTAAA-CCCCATGTTATGTAGTATCACGTAG
*
16811392 TATGTAAACCCCTATGTTATGTAGTA-CATCTTAG
1 TATGTAAACCCC-ATGTTATGTAGTATCA-CGTAG
* *
16811426 TATATGAACCCACATGTTATGTA
1 TATGTAAACCC-CATGTTATGTA
16811449 CTTTGTGAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
33 5 0.10
34 43 0.88
35 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (33 bp):
TATGTAAACCCCATGTTATGTAGTATCACGTAG
Found at i:16811616 original size:15 final size:15
Alignment explanation
Indices: 16811461--16811668 Score: 109
Period size: 15 Copynumber: 14.1 Consensus size: 15
16811451 TTGTGAATTA
*
16811461 ATATGTTTGAACCCT
1 ATATGTGTGAACCCT
* *
16811476 ATATGT-TCAAACCTT
1 ATATGTGT-GAACCCT
* *
16811491 GTATGTGTAAACCCT
1 ATATGTGTGAACCCT
* *** *
16811506 ACATGTACAAATCCT
1 ATATGTGTGAACCCT
*
16811521 ATATGTGTGAACCTT
1 ATATGTGTGAACCCT
* *
16811536 ACATGTGAGAA-CCT
1 ATATGTGTGAACCCT
* * *
16811550 ATAAGTCTGAACACT
1 ATATGTGTGAACCCT
*** **
16811565 ATATG-CCCATTCCT
1 ATATGTGTGAACCCT
* * * *
16811579 GTATGTGCGAAACCA
1 ATATGTGTGAACCCT
16811594 ATATGTGTGAACCCT
1 ATATGTGTGAACCCT
16811609 ATATGTGTGAA-CCT
1 ATATGTGTGAACCCT
* *
16811623 GTATGTGTGAACCAT
1 ATATGTGTGAACCCT
* * *
16811638 GTATGCGCGAACCCT
1 ATATGTGTGAACCCT
16811653 ATATGTGTGAACCCT
1 ATATGTGTGAACCCT
16811668 A
1 A
16811669 CATGCGAACC
Statistics
Matches: 141, Mismatches: 47, Indels: 10
0.71 0.24 0.05
Matches are distributed among these distances:
14 31 0.22
15 109 0.77
16 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (15 bp):
ATATGTGTGAACCCT
Found at i:16811624 original size:44 final size:44
Alignment explanation
Indices: 16811576--16811665 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
16811566 TATGCCCATT
* *
16811576 CCTGTATGTGCGAAACCA-ATATGTGTGAACCCTATATGTGTGAA
1 CCTGTATGTGCG-AACCATATATGCGCGAACCCTATATGTGTGAA
* *
16811620 CCTGTATGTGTGAACCATGTATGCGCGAACCCTATATGTGTGAA
1 CCTGTATGTGCGAACCATATATGCGCGAACCCTATATGTGTGAA
16811664 CC
1 CC
16811666 CTACATGCGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 5 0.12
44 36 0.88
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (44 bp):
CCTGTATGTGCGAACCATATATGCGCGAACCCTATATGTGTGAA
Found at i:16813884 original size:17 final size:17
Alignment explanation
Indices: 16813864--16813905 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
16813854 TATAAAAGCC
16813864 TATAATATTTTAAAATA
1 TATAATATTTTAAAATA
* * *
16813881 TATAAAAATTTACAATA
1 TATAATATTTTAAAATA
16813898 TATAATAT
1 TATAATAT
16813906 ATAAAAATTG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAATATTTTAAAATA
Found at i:16814223 original size:16 final size:18
Alignment explanation
Indices: 16814192--16814224 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
16814182 TAAATATGAG
16814192 CAAACTGTTATCTAGATT
1 CAAACTGTTATCTAGATT
16814210 CAAA-TGTT-TCTAGAT
1 CAAACTGTTATCTAGAT
16814225 AATCATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (18 bp):
CAAACTGTTATCTAGATT
Found at i:16817862 original size:103 final size:104
Alignment explanation
Indices: 16817683--16817947 Score: 408
Period size: 103 Copynumber: 2.6 Consensus size: 104
16817673 AACCGTTATT
* * * * *
16817683 GGTGGATCTCGCACTTAGCACCACCACTTAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
** *
16817748 ATCAGCACATAGCAACCCCCTTT-TTATTTCAGAGATAC
66 ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
16817786 GGTGGATATCGCACTTAGCACCACCAATGAA-CTGGGGAATCAGCACTTAGCAACCCCTCGGGGG
1 GGTGGATATCGCACTTAGCACCACCAATGAATC-GGGGAATCAGCACTTAGCAACCCCTCGGGGG
16817850 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
65 AATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
* **
16817890 GGTGGATATCGCACATAGCACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCT
16817948 TTATGTACAA
Statistics
Matches: 148, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
102 1 0.01
103 81 0.55
104 65 0.44
105 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (104 bp):
GGTGGATATCGCACTTAGCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTCGGGGGA
ATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATAC
Found at i:16818309 original size:30 final size:29
Alignment explanation
Indices: 16818275--16818339 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
16818265 TAATCCACCA
16818275 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
16818305 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
16818335 CCCAA
1 CCCAA
16818340 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:16818313 original size:31 final size:30
Alignment explanation
Indices: 16818282--16818339 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
16818272 CCACCCAACT
16818282 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
16818312 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
16818340 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:16820275 original size:24 final size:24
Alignment explanation
Indices: 16820244--16820397 Score: 123
Period size: 24 Copynumber: 6.3 Consensus size: 24
16820234 AGCCATGTAA
16820244 CGGGAAGCTCGTAAGAGCCATAAT
1 CGGGAAGCTCGTAAGAGCCATAAT
*
16820268 CGGGAAGCTCGTAAAAGCCATAAT
1 CGGGAAGCTCGTAAGAGCCATAAT
* **
16820292 CGGGAAGCTCATGTGAGCCA-ATAT
1 CGGGAAGCTCGTAAGAGCCATA-AT
* ** * *
16820316 CGAGAAGCTCCAAAGAGCCTTTTAT
1 CGGGAAGCTCGTAAGAGCC-ATAAT
* *
16820341 CGGGAAGCTCCG-GAGAGCCAATTAT
1 CGGGAAGCT-CGTAAGAGCC-ATAAT
* * * *
16820366 CGGGAAGCTCATATGAGCAATAAA
1 CGGGAAGCTCGTAAGAGCCATAAT
16820390 CGGGAAGC
1 CGGGAAGC
16820398 GCAAGAGAGC
Statistics
Matches: 102, Mismatches: 23, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
23 1 0.01
24 67 0.66
25 33 0.32
26 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (24 bp):
CGGGAAGCTCGTAAGAGCCATAAT
Found at i:16820310 original size:48 final size:49
Alignment explanation
Indices: 16820244--16820424 Score: 129
Period size: 49 Copynumber: 3.7 Consensus size: 49
16820234 AGCCATGTAA
* * *
16820244 CGGGAAGCTCGTAAGAGCCATAATCGGGAAGCTCGTAAA-AGCC-ATAAT
1 CGGGAAGCTCATGAGAGCCATAATCGGGAAGCTC-CAAAGAGCCTATAAT
* * * *
16820292 CGGGAAGCTCATGTGAGCCA-ATATCGAGAAGCTCCAAAGAGCCTTTTAT
1 CGGGAAGCTCATGAGAGCCATA-ATCGGGAAGCTCCAAAGAGCCTATAAT
** * * * *
16820341 CGGGAAGCTCCGGAGAGCCAATTATCGGGAAGCT-CATATGAG-CAATAAA
1 CGGGAAGCTCATGAGAGCC-ATAATCGGGAAGCTCCA-AAGAGCCTATAAT
* * * *
16820390 CGGGAAGCGCAAGAGAGCTATTAATCGGGATGCTC
1 CGGGAAGCTCATGAGAGCCA-TAATCGGGAAGCTC
16820425 ATGAGAGCTA
Statistics
Matches: 102, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
47 4 0.04
48 33 0.32
49 50 0.49
50 15 0.15
ACGTcount: A:0.33, C:0.21, G:0.28, T:0.18
Consensus pattern (49 bp):
CGGGAAGCTCATGAGAGCCATAATCGGGAAGCTCCAAAGAGCCTATAAT
Found at i:16820431 original size:74 final size:73
Alignment explanation
Indices: 16820241--16820432 Score: 176
Period size: 74 Copynumber: 2.6 Consensus size: 73
16820231 TCGAGCCATG
* ** * * * * *
16820241 TAACGGGAAGCTCGTAAGAGCC-ATAATCGGGAAGCTCGTAAAAGCCATAATCGGGAAGCTCATG
1 TAACGAGAAGCTCCAAAGAGCCTTTAATCGGGAAGCTCATGAGAGCCATAATCGGGAAGCTCATA
16820305 TGAGCCAA
66 TGAGCCAA
* * ** *
16820313 TATCGAGAAGCTCCAAAGAGCCTTTTATCGGGAAGCTCCGGAGAGCCAATTATCGGGAAGCTCAT
1 TAACGAGAAGCTCCAAAGAGCCTTTAATCGGGAAGCTCATGAGAGCC-ATAATCGGGAAGCTCAT
16820378 ATGAG-CAA
65 ATGAGCCAA
* * *
16820386 TAAACGGGAAGC-GCAAGAGAG-CTATTAATCGGGATGCTCATGAGAGC
1 T-AACGAGAAGCTCCAA-AGAGCCT-TTAATCGGGAAGCTCATGAGAGC
16820433 TAAATAACGG
Statistics
Matches: 96, Mismatches: 19, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
72 18 0.19
73 27 0.28
74 51 0.53
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.18
Consensus pattern (73 bp):
TAACGAGAAGCTCCAAAGAGCCTTTAATCGGGAAGCTCATGAGAGCCATAATCGGGAAGCTCATA
TGAGCCAA
Found at i:16821379 original size:19 final size:19
Alignment explanation
Indices: 16821355--16821391 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16821345 TAATATTTTG
16821355 TTTTATTCTATTTATCTTC
1 TTTTATTCTATTTATCTTC
* *
16821374 TTTTATTTTTTTTATCTT
1 TTTTATTCTATTTATCTT
16821392 TCCAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTATTCTATTTATCTTC
Found at i:16822876 original size:3 final size:3
Alignment explanation
Indices: 16822868--16822898 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
16822858 CACATAGATA
16822868 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16822899 GTATAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16824333 original size:21 final size:19
Alignment explanation
Indices: 16824291--16824333 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
16824281 TAAAATGTTA
**
16824291 CTTAAATTATATTAGTTTT
1 CTTAAATTATATTAACTTT
16824310 CTTAAATTGATATTTAACTTT
1 CTTAAATT-ATA-TTAACTTT
16824331 CTT
1 CTT
16824334 TTATCAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 8 0.40
20 3 0.15
21 9 0.45
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (19 bp):
CTTAAATTATATTAACTTT
Found at i:16825536 original size:18 final size:21
Alignment explanation
Indices: 16825500--16825551 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 21
16825490 AATTTTGGTC
16825500 AATTTATTATATTTAAATTTA
1 AATTTATTATATTTAAATTTA
* *
16825521 AATTTATT-T-TTTAATTTTT
1 AATTTATTATATTTAAATTTA
16825540 AATTT-TTA-ATTT
1 AATTTATTATATTT
16825552 TTAATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
18 2 0.07
19 16 0.59
20 1 0.04
21 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTTATTATATTTAAATTTA
Found at i:16825588 original size:8 final size:7
Alignment explanation
Indices: 16825523--16825586 Score: 74
Period size: 7 Copynumber: 8.6 Consensus size: 7
16825513 TAAATTTAAA
*
16825523 TTTATTT
1 TTTAATT
16825530 TTTAATT
1 TTTAATT
16825537 TTTAATT
1 TTTAATT
16825544 TTTAATT
1 TTTAATT
16825551 TTTAATT
1 TTTAATT
16825558 TTTAATAT
1 TTTAAT-T
*
16825566 AATATAATT
1 --TTTAATT
16825575 TTTATATT
1 TTTA-ATT
16825583 TTTA
1 TTTA
16825587 TAATGTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
7 36 0.72
8 8 0.16
9 1 0.02
10 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:16825697 original size:22 final size:23
Alignment explanation
Indices: 16825672--16825714 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
16825662 AAAGTGAATT
16825672 TTTAAATT-TAAAAAATAAAAAA
1 TTTAAATTCTAAAAAATAAAAAA
*
16825694 TTTAAATTCTCAAAAATAAAA
1 TTTAAATTCTAAAAAATAAAA
16825715 GTAGAGACTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (23 bp):
TTTAAATTCTAAAAAATAAAAAA
Found at i:16828857 original size:25 final size:22
Alignment explanation
Indices: 16828841--16828903 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 22
16828831 TCTCCGATTA
16828841 TTAGCACATTAGTGCTCTCCGT
1 TTAGCACATTAGTGCTCTCCGT
* * *
16828863 TTATCACATTCGTGCTCTCTGT
1 TTAGCACATTAGTGCTCTCCGT
* **
16828885 ATAGCATTTTAGTGCTCTC
1 TTAGCACATTAGTGCTCTC
16828904 TATTCAATAG
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.17, C:0.25, G:0.16, T:0.41
Consensus pattern (22 bp):
TTAGCACATTAGTGCTCTCCGT
Found at i:16829119 original size:16 final size:16
Alignment explanation
Indices: 16829100--16829132 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16829090 GTGTCTAAAT
16829100 ATGTATTAATTGAGTA
1 ATGTATTAATTGAGTA
16829116 ATGTATTAATTGAGTA
1 ATGTATTAATTGAGTA
16829132 A
1 A
16829133 GTTTAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGTATTAATTGAGTA
Found at i:16837250 original size:25 final size:24
Alignment explanation
Indices: 16837174--16837250 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 24
16837164 GAACACACGA
* *
16837174 TGGCTCTCACGAGCTTCTCGTTATT
1 TGGCTCTCATGAGCTTCT-GATATT
* * *
16837199 TAGCTCTTATGAGCATTCTAATATT
1 TGGCTCTCATGAGC-TTCTGATATT
16837224 TGGCTCTCATGAGCTTCCTGATATT
1 TGGCTCTCATGAGCTT-CTGATATT
16837249 TG
1 TG
16837251 ACTCGTATAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
24 2 0.05
25 36 0.86
26 4 0.10
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.42
Consensus pattern (24 bp):
TGGCTCTCATGAGCTTCTGATATT
Found at i:16837312 original size:25 final size:25
Alignment explanation
Indices: 16837252--16837312 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
16837242 TGATATTTGA
* **
16837252 CTCGTATAAGCTTCCCGTTGTATGT
1 CTCGTATGAGCTTCCCGTTACATGT
* *
16837277 CTCGGAAGAGCTTCCCGTTAACATG-
1 CTCGTATGAGCTTCCCGTT-ACATGT
16837302 CTCGTATGAGC
1 CTCGTATGAGC
16837313 ACATATGTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 25 0.89
26 3 0.11
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (25 bp):
CTCGTATGAGCTTCCCGTTACATGT
Found at i:16838543 original size:30 final size:31
Alignment explanation
Indices: 16838499--16838557 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
16838489 TTCGAGCTTT
16838499 GGGACAAAAGTATAAATATGCAAAAGTTTAG
1 GGGACAAAAGTATAAATATGCAAAAGTTTAG
* * * *
16838530 GGGA-AAAATTATAATTTTGCCAAAGTTT
1 GGGACAAAAGTATAAATATGCAAAAGTTT
16838558 GAGTCAAGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (31 bp):
GGGACAAAAGTATAAATATGCAAAAGTTTAG
Found at i:16839039 original size:50 final size:52
Alignment explanation
Indices: 16838902--16839039 Score: 138
Period size: 50 Copynumber: 2.6 Consensus size: 52
16838892 GAGATCCCAT
* *
16838902 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTTCCAT
1 GTAAGACCATGTCTGGGACATGGCATTGGCA-CA-TGAG--TATGAAAGGTTCCAC
* * * *
16838958 GTAAGACCATGTTTGGAACGTGGCGTTGGCAC-TGAG-ATGAAAGG-TCCACC
1 GTAAGACCATGTCTGGGACATGGCATTGGCACATGAGTATGAAAGGTTCCA-C
* *
16839008 GTAAGACCATGTCTGGGACATAGCATGGGCAC
1 GTAAGACCATGTCTGGGACATGGCATTGGCAC
16839040 CGATATGAGA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
49 4 0.06
50 33 0.48
53 4 0.06
55 1 0.01
56 27 0.39
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (52 bp):
GTAAGACCATGTCTGGGACATGGCATTGGCACATGAGTATGAAAGGTTCCAC
Found at i:16849516 original size:24 final size:25
Alignment explanation
Indices: 16849475--16849522 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
16849465 ATAATAATCT
*
16849475 TAATATTTTATTAAAAAA-ATATAC
1 TAATATTTTAATAAAAAATATATAC
**
16849499 TAATATTTTAATGGAAAATATATA
1 TAATATTTTAATAAAAAATATATA
16849523 TTACAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (25 bp):
TAATATTTTAATAAAAAATATATAC
Found at i:16849516 original size:25 final size:24
Alignment explanation
Indices: 16849475--16849522 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
16849465 ATAATAATCT
*
16849475 TAATATTTTATTAAAAAAATATAC
1 TAATATTTTATGAAAAAAATATAC
* *
16849499 TAATATTTTAATGGAAAATATATA
1 TAATATTTT-ATGAAAAAAATATA
16849523 TTACAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (24 bp):
TAATATTTTATGAAAAAAATATAC
Found at i:16850693 original size:17 final size:19
Alignment explanation
Indices: 16850671--16850705 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
16850661 TTATAACACT
16850671 TTCTTT-CAAC-TTTTTTG
1 TTCTTTACAACGTTTTTTG
16850688 TTCTTTACAACGTTTTTT
1 TTCTTTACAACGTTTTTT
16850706 TTTTTTGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.14, C:0.17, G:0.06, T:0.63
Consensus pattern (19 bp):
TTCTTTACAACGTTTTTTG
Found at i:16850703 original size:18 final size:17
Alignment explanation
Indices: 16850671--16850704 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16850661 TTATAACACT
*
16850671 TTCTTTCAACTTTTTTG
1 TTCTTTCAACGTTTTTG
16850688 TTCTTTACAACGTTTTT
1 TTCTTT-CAACGTTTTT
16850705 TTTTTTTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.18, G:0.06, T:0.62
Consensus pattern (17 bp):
TTCTTTCAACGTTTTTG
Found at i:16851617 original size:21 final size:21
Alignment explanation
Indices: 16851582--16851622 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16851572 ACCCCAAACC
*
16851582 TCAAGGTTCAAGGTTTAAAGT
1 TCAAGGTTCAAGGTTCAAAGT
**
16851603 TCAAGGTTCGGGGTTCAAAG
1 TCAAGGTTCAAGGTTCAAAG
16851623 CAAAATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (21 bp):
TCAAGGTTCAAGGTTCAAAGT
Found at i:16854872 original size:16 final size:16
Alignment explanation
Indices: 16854847--16854880 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
16854837 TCACTTTCTC
*
16854847 AAATATTAATTAAATA
1 AAATAATAATTAAATA
*
16854863 AAATAATAATTTAATA
1 AAATAATAATTAAATA
16854879 AA
1 AA
16854881 GAATGTTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATAATAATTAAATA
Found at i:16861119 original size:6 final size:6
Alignment explanation
Indices: 16861097--16861149 Score: 79
Period size: 6 Copynumber: 8.5 Consensus size: 6
16861087 AGAAGGAAGT
*
16861097 TAATGG TATTGG TTAATGG TAATGG TAATGG TAATGG TAATGG TAAATGG
1 TAATGG TAATGG -TAATGG TAATGG TAATGG TAATGG TAATGG T-AATGG
16861147 TAA
1 TAA
16861150 ATGGGGGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
6 32 0.74
7 11 0.26
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (6 bp):
TAATGG
Found at i:16865566 original size:13 final size:13
Alignment explanation
Indices: 16865548--16865573 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16865538 GGGTAGATAC
16865548 ATATATGTTTGGT
1 ATATATGTTTGGT
16865561 ATATATGTTTGGT
1 ATATATGTTTGGT
16865574 GAATACTCAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
ATATATGTTTGGT
Found at i:16866186 original size:27 final size:27
Alignment explanation
Indices: 16866151--16866247 Score: 113
Period size: 27 Copynumber: 3.6 Consensus size: 27
16866141 ATATAATCAA
16866151 AGTACGCCACAAAGGCAATCCATACAG
1 AGTACGCCACAAAGGCAATCCATACAG
* * * * *
16866178 AGCATGCCACAAAGGCTATCTATAGAG
1 AGTACGCCACAAAGGCAATCCATACAG
* * * *
16866205 GGTACGCCACAAAGGCGATTCATTCAG
1 AGTACGCCACAAAGGCAATCCATACAG
16866232 AGTACGCCACAAAGGC
1 AGTACGCCACAAAGGC
16866248 TTACAGGATG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (27 bp):
AGTACGCCACAAAGGCAATCCATACAG
Found at i:16873594 original size:17 final size:18
Alignment explanation
Indices: 16873574--16873607 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16873564 ACATTTTTTG
16873574 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
16873591 TATATAATATTATTTTA
1 TATATAACATTATTTTA
16873608 AGTGTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Found at i:16878670 original size:9 final size:9
Alignment explanation
Indices: 16878658--16878701 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
16878648 CTCAAAAGAA
16878658 AAAAAAATC
1 AAAAAAATC
16878667 AAAAAAATC
1 AAAAAAATC
16878676 --AAAAAT-
1 AAAAAAATC
*
16878682 -AAAAAATA
1 AAAAAAATC
16878690 AAAAAAATC
1 AAAAAAATC
16878699 AAA
1 AAA
16878702 GTCAAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
7 12 0.39
9 19 0.61
ACGTcount: A:0.82, C:0.07, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:16880880 original size:48 final size:48
Alignment explanation
Indices: 16880816--16880967 Score: 153
Period size: 48 Copynumber: 3.1 Consensus size: 48
16880806 AAGAATCTTA
*
16880816 CTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCG
1 CTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCG
* ** * * * * *** *
16880864 CTTCCCCGAC-ATTGCAGTTAAAAAGGTTAAAGCTACAACAACGAATCTTA
1 CTTCCCAGACGA-TGCAGTGGAACAGATTAAAGCCACATCGGTGAATC--G
*
16880914 CTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCG
1 CTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCG
16880962 CTTCCC
1 CTTCCC
16880968 TTACACTGCA
Statistics
Matches: 76, Mismatches: 24, Indels: 8
0.70 0.22 0.07
Matches are distributed among these distances:
47 1 0.01
48 40 0.53
50 34 0.45
51 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (48 bp):
CTTCCCAGACGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCG
Found at i:16880978 original size:98 final size:98
Alignment explanation
Indices: 16880808--16881151 Score: 535
Period size: 98 Copynumber: 3.5 Consensus size: 98
16880798 GTGAAATCAA
*
16880808 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCGA
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCAA
16880873 CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
66 CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
**
16880906 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCTTA
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCAA
* *
16880971 CACTGCAGTTAAAAAGGTTAAAGCTACAACAGC
66 CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
* * * * * *
16881004 AAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTAAAGCCATATCAGTGAATCTTGCTTCCCC
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATC--GCTTCCCC
**
16881069 AACATTGCAGTTAAAATCGTTAAAGCTACAACAAC
64 AACATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
* *
16881104 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCG
1 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
16881152 TGGAACAAAT
Statistics
Matches: 224, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
98 143 0.64
100 81 0.36
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (98 bp):
GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGTGAATCGCTTCCCCAA
CATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
Found at i:16880992 original size:48 final size:47
Alignment explanation
Indices: 16880842--16880994 Score: 135
Period size: 48 Copynumber: 3.1 Consensus size: 47
16880832 GTGGAACAGA
*
16880842 TTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAGG
1 TTAAAGCCACATCGGTGAATCGCTTCCCAGACA-TGCAGTTAAAAAGG
* * *** * * ** * *
16880890 TTAAAGCTACAACAACGAATCTTACTTCCCAGGCGATGCAGTGGAACAGA
1 TTAAAGCCACATCGGTGAATC--GCTTCCCAGAC-ATGCAGTTAAAAAGG
**
16880940 TTAAAGCCACATCGGTGAATCGCTTCCCTTACACTGCAGTTAAAAAGG
1 TTAAAGCCACATCGGTGAATCGCTTCCCAGACA-TGCAGTTAAAAAGG
16880988 TTAAAGC
1 TTAAAGC
16880995 TACAACAGCA
Statistics
Matches: 76, Mismatches: 25, Indels: 8
0.70 0.23 0.07
Matches are distributed among these distances:
47 1 0.01
48 40 0.53
50 34 0.45
51 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (47 bp):
TTAAAGCCACATCGGTGAATCGCTTCCCAGACATGCAGTTAAAAAGG
Found at i:16881142 original size:50 final size:50
Alignment explanation
Indices: 16880808--16881148 Score: 214
Period size: 50 Copynumber: 6.9 Consensus size: 50
16880798 GTGAAATCAA
* * * *
16880808 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAGC
* * * ** * * * *
16880858 GAATC--GCTTCCCCGAC-ATTGCAGTTAAAAAGGTTAAAGCTACAACAAC
1 GAATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTAAAGCCACAACAGC
* * * *
16880906 GAATCTTACTTCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCGGT
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAGC
* ** ** * * *
16880956 GAATC--GCTTCCCTTAC-ACTGCAGTTAAAAAGGTTAAAGCTACAACAGC
1 GAATCTTACTTCCCTGGCGA-TGCAGTGGAACAGATTAAAGCCACAACAGC
* * * * * *
16881004 AAATCTTACTTCCCTGGCGGTGCAATGGAACAGATTAAAGCCATATCAGT
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAGC
* *** * * * *
16881054 GAATCTTGCTTCCCCAAC-ATTGCAGT-TAAAATCG-TTAAAGCTACAACAAC
1 GAATCTTACTTCCCTGGCGA-TGCAGTGGAACA--GATTAAAGCCACAACAGC
*
16881104 GAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACA
1 GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACA
16881149 TCGTGGAACA
Statistics
Matches: 205, Mismatches: 72, Indels: 28
0.67 0.24 0.09
Matches are distributed among these distances:
47 2 0.01
48 67 0.33
49 4 0.02
50 127 0.62
51 5 0.02
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
GAATCTTACTTCCCTGGCGATGCAGTGGAACAGATTAAAGCCACAACAGC
Found at i:16881158 original size:23 final size:23
Alignment explanation
Indices: 16881128--16881174 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16881118 TGGCGGTGCA
*
16881128 GTGGAACAGATTAAAGCCACATC
1 GTGGAACAAATTAAAGCCACATC
16881151 GTGGAACAAATTAAAGCCACATC
1 GTGGAACAAATTAAAGCCACATC
16881174 G
1 G
16881175 GTGAATCGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (23 bp):
GTGGAACAAATTAAAGCCACATC
Found at i:16881227 original size:48 final size:47
Alignment explanation
Indices: 16881160--16881327 Score: 140
Period size: 48 Copynumber: 3.5 Consensus size: 47
16881150 CGTGGAACAA
* *
16881160 ATTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAG
1 ATTAAAGCCACAACAGTGAATCGCTTCCCCGACA-TGCAGTTAAAAAG
* * * ** *
16881208 ATTAAAGCTACAACAGTGAATC-TTACTCCCCAGGCGATGCAGTGGAACAG
1 ATTAAAGCCACAACAGTGAATCGCT--TCCCC-GAC-ATGCAGTTAAAAAG
* * * * * *
16881258 ATTAAAGCCACATCGGTAAATCGCTTCTCTGACACTGCAATTAAAAAG
1 ATTAAAGCCACAACAGTGAATCGCTTCCCCGACA-TGCAGTTAAAAAG
*
16881306 ATTAAAGCTACAACAGTGAATC
1 ATTAAAGCCACAACAGTGAATC
16881328 TTACTTCTCA
Statistics
Matches: 90, Mismatches: 24, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
47 2 0.02
48 48 0.53
49 8 0.09
50 30 0.33
51 2 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (47 bp):
ATTAAAGCCACAACAGTGAATCGCTTCCCCGACATGCAGTTAAAAAG
Found at i:16881249 original size:121 final size:122
Alignment explanation
Indices: 16881029--16881272 Score: 366
Period size: 121 Copynumber: 2.0 Consensus size: 122
16881019 GGCGGTGCAA
* * *
16881029 TGGAACAGATTAAAGCCATATCAGTGAATCTTGCTTCCCCAACATTGCAGTTAAAATCGTTAAAG
1 TGGAACAAATTAAAGCCACATCAGTGAATC-TGCTTCCCCAACATTGCAGTTAAAATAGTTAAAG
* * *
16881094 CTACAACAACGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTAAAGCCACATCG
65 CTACAACAACGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
* *
16881152 TGGAACAAATTAAAGCCACATCGGTGAATC-GCTTCCCCGACATTGCAGTTAAAA-AGATTAAAG
1 TGGAACAAATTAAAGCCACATCAGTGAATCTGCTTCCCCAACATTGCAGTTAAAATAG-TTAAAG
**
16881215 CTACAACAGTGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
65 CTACAACAACGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
16881273 GTAAATCGCT
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
120 1 0.01
121 82 0.75
123 27 0.25
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (122 bp):
TGGAACAAATTAAAGCCACATCAGTGAATCTGCTTCCCCAACATTGCAGTTAAAATAGTTAAAGC
TACAACAACGAATCTTACTCCCCAGGCGATGCAGTGGAACAGATTAAAGCCACATCG
Found at i:16881263 original size:50 final size:50
Alignment explanation
Indices: 16881206--16881379 Score: 165
Period size: 50 Copynumber: 3.5 Consensus size: 50
16881196 GCAGTTAAAA
* *
16881206 AGATTAAAGCTACAACAGTGAATCTTACTCCCCAGGCGATGCAGTGGAAC
1 AGATTAAAGCTACAACAGTGAATCTTACTTCTCAGGCGATGCAGTGGAAC
* * * * * * * * ** *
16881256 AGATTAAAGCCACATCGGTAAATC--GCTTCTCTGAC-ACTGCAATTAAAA
1 AGATTAAAGCTACAACAGTGAATCTTACTTCTCAGGCGA-TGCAGTGGAAC
* *
16881304 AGATTAAAGCTACAACAGTGAATCTTACTTCTCAGGCGGTGTAGTGGAAC
1 AGATTAAAGCTACAACAGTGAATCTTACTTCTCAGGCGATGCAGTGGAAC
* *
16881354 AGATTGAAGCTACAACTGTGAATCTT
1 AGATTAAAGCTACAACAGTGAATCTT
16881380 TCTTTGTCGA
Statistics
Matches: 92, Mismatches: 28, Indels: 8
0.72 0.22 0.06
Matches are distributed among these distances:
47 1 0.01
48 33 0.36
50 58 0.63
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (50 bp):
AGATTAAAGCTACAACAGTGAATCTTACTTCTCAGGCGATGCAGTGGAAC
Found at i:16881320 original size:98 final size:98
Alignment explanation
Indices: 16881151--16881363 Score: 327
Period size: 98 Copynumber: 2.2 Consensus size: 98
16881141 AAGCCACATC
* * * *
16881151 GTGGAACAAATTAAAGCCACATCGGTGAATCGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
1 GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACACTGCAATTAAAAAGATTAAAGC
16881216 TACAACAGTGAATCTTACTCCCCAGGCGATGCA
66 TACAACAGTGAATCTTACTCCCCAGGCGATGCA
* *
16881249 GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCTCTGACACTGCAATTAAAAAGATTAAAGC
1 GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACACTGCAATTAAAAAGATTAAAGC
* * * *
16881314 TACAACAGTGAATCTTACTTCTCAGGCGGTGTA
66 TACAACAGTGAATCTTACTCCCCAGGCGATGCA
*
16881347 GTGGAACAGATTGAAGC
1 GTGGAACAGATTAAAGC
16881364 TACAACTGTG
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 104 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.23
Consensus pattern (98 bp):
GTGGAACAGATTAAAGCCACATCGGTAAATCGCTTCCCCGACACTGCAATTAAAAAGATTAAAGC
TACAACAGTGAATCTTACTCCCCAGGCGATGCA
Found at i:16881814 original size:23 final size:23
Alignment explanation
Indices: 16881769--16881816 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
16881759 AATAAAATAC
*
16881769 CCTAACCCGAAATACTAACTAAA
1 CCTAACCCGAAATACCAACTAAA
* * *
16881792 CCTAACCCGAATTACCCATTAAA
1 CCTAACCCGAAATACCAACTAAA
16881815 CC
1 CC
16881817 CTAGCCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.35, G:0.04, T:0.19
Consensus pattern (23 bp):
CCTAACCCGAAATACCAACTAAA
Found at i:16883078 original size:17 final size:18
Alignment explanation
Indices: 16883058--16883091 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16883048 ACATTTTTTG
16883058 TATAT-ACATTATTTTAC
1 TATATAACATTATTTTAC
*
16883075 TATATAATATTATTTTA
1 TATATAACATTATTTTA
16883092 AGTGTTAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATAACATTATTTTAC
Found at i:16904096 original size:348 final size:348
Alignment explanation
Indices: 16903460--16904507 Score: 1908
Period size: 348 Copynumber: 3.0 Consensus size: 348
16903450 GGATGAAACA
* *
16903460 CTCATTTTTAAATGATTCATATACATAGGATTTGCCTAAAGAATTTAGC-AAAAGGAGACAGTTA
1 CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
* * * * * *
16903524 CAAATCCAACTTTTATTTAAAGGGCGGATAAGTAATTCTGTGCTGGACATGAGTGAAGCTTAAAA
66 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAA
16903589 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
131 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
16903654 ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
196 ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
16903719 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
261 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
16903784 ATCCTTCAGGATCTCTCCTAGTT
326 ATCCTTCAGGATCTCTCCTAGTT
16903807 CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
1 CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
16903872 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAA
66 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAA
16903937 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
131 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
16904002 ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
196 ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
16904067 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
261 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
16904132 ATCCTTCAGGATCTCTCCTAGTT
326 ATCCTTCAGGATCTCTCCTAGTT
16904155 CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
1 CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
*
16904220 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTTATTCTGCGGTGGACATGAGTGAAACTTAAAA
66 CAAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAA
*
16904285 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCTTGGTC
131 CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
* * *
16904350 ACTACTCGCTAGAACTAAGAGTTCAGCACTC--CCAAAAAACAATAAGGCTATTGGCAAATGCCT
196 ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
*
16904413 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAG-TTTTAGAATCCCAACTGAGGCCT
261 AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
*
16904477 ATCCTTCAGGAT-TACTCCTAATT
326 ATCCTTCAGGATCT-CTCCTAGTT
*
16904500 CTAATTTT
1 CTCATTTT
16904508 GGATTGGAGA
Statistics
Matches: 683, Mismatches: 16, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
344 1 0.00
345 49 0.07
346 70 0.10
347 47 0.07
348 516 0.76
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (348 bp):
CTCATTTTTAAATGATTCACAGACATAGGATTTGCCTAAAGAATTTAGCAAAAAGGAGACAGTTA
CAAATCCAACTTTTAATTGAAGGGCAGATAAGTAATTCTGCGGTGGACATGAGTGAAACTTAAAA
CCTCATGGTCTGATTCCTACTTATTCCTTTTATATTGGAGGTTTCTGAAGCTTTGACCCATGGTC
ACTACTCGCTAGAACTAAGAGTTCAGCACTCTACCAAAAAACAACAAGGCCATTGGAAAATGCCT
AACTTCTATGGTGACAACAGACAGCCTTTTGCACTTGGAAGCTTTTAGAATCCCAACTAAGGCCT
ATCCTTCAGGATCTCTCCTAGTT
Found at i:16906277 original size:1 final size:1
Alignment explanation
Indices: 16906271--16906301 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
16906261 TTTTCTCTTC
16906271 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16906302 GCATAGGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16906279 original size:15 final size:14
Alignment explanation
Indices: 16906248--16906301 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 14
16906238 AATCAATTCC
*
16906248 TTTTCTTCTTTCATT
1 TTTTCTTCTTT-TTT
*
16906263 TTCTCTTCTTTTTT
1 TTTTCTTCTTTTTT
16906277 TTTT-TT-TTTTTT
1 TTTTCTTCTTTTTT
16906289 TTTT-TT-TTTTTT
1 TTTTCTTCTTTTTT
16906301 T
1 T
16906302 GCATAGGATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
12 19 0.53
13 2 0.06
14 5 0.14
15 10 0.28
ACGTcount: A:0.02, C:0.11, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTCTTCTTTTTT
Found at i:16907451 original size:33 final size:33
Alignment explanation
Indices: 16907410--16907473 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
16907400 ACAAGGCGCA
16907410 AAAAAAAGCGCTCA-CCCGAGTAAACCGAGGCTC
1 AAAAAAAGCGCT-AGCCCGAGTAAACCGAGGCTC
16907443 AAAAAAAGCGCTAGCCCGAGTAAACCGAGGC
1 AAAAAAAGCGCTAGCCCGAGTAAACCGAGGC
16907474 CCAAGCATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 1 0.03
33 29 0.97
ACGTcount: A:0.41, C:0.28, G:0.23, T:0.08
Consensus pattern (33 bp):
AAAAAAAGCGCTAGCCCGAGTAAACCGAGGCTC
Found at i:16913226 original size:11 final size:11
Alignment explanation
Indices: 16913210--16913254 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
16913200 TCAATTATTT
16913210 TCTCAATTTCC
1 TCTCAATTTCC
16913221 TCTCAATTTCC
1 TCTCAATTTCC
* *
16913232 TCTCAAATTGC
1 TCTCAATTTCC
16913243 TCTCAATTTCC
1 TCTCAATTTCC
16913254 T
1 T
16913255 TCCAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 30 1.00
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:16913245 original size:22 final size:22
Alignment explanation
Indices: 16913210--16913270 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
16913200 TCAATTATTT
*
16913210 TCTCAATTTCCTCTCAATTTCC
1 TCTCAAATTCCTCTCAATTTCC
*
16913232 TCTCAAATTGCTCTCAATTTCC
1 TCTCAAATTCCTCTCAATTTCC
*
16913254 T-TCCAAATTTCTCTCAA
1 TCT-CAAATTCCTCTCAA
16913271 ATCCATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.43
Consensus pattern (22 bp):
TCTCAAATTCCTCTCAATTTCC
Found at i:16913248 original size:33 final size:33
Alignment explanation
Indices: 16913210--16913272 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
16913200 TCAATTATTT
16913210 TCTCAATTTCC-TCTC-AATTTCCTCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTT-CTCTCAAATTGC
16913243 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
1 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
16913273 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.43
Consensus pattern (33 bp):
TCTCAATTTCCTTCCAAATTTCTCTCAAATTGC
Found at i:16913342 original size:51 final size:51
Alignment explanation
Indices: 16913232--16913331 Score: 155
Period size: 51 Copynumber: 2.0 Consensus size: 51
16913222 CTCAATTTCC
*
16913232 TCTCAAATTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
1 TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
** * *
16913283 TCTCAATTTGCTCTCAATTTCCTTTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTT
16913332 TTAGTTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.46
Consensus pattern (51 bp):
TCTCAATTTGCTCTCAATTTCCTTCCAAATTTCTCTCAAATCCATATTTAA
Found at i:16915147 original size:18 final size:18
Alignment explanation
Indices: 16915124--16915166 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
16915114 TGCCAGGTGC
* *
16915124 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
16915142 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
16915160 GTTTCCT
1 GTATCCT
16915167 TTTTCTAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:16916493 original size:25 final size:23
Alignment explanation
Indices: 16916436--16916493 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 23
16916426 AATTATTGAT
*
16916436 ATATTTTTGTCTGAATGTCTTAA
1 ATATTTTTGTATGAATGTCTTAA
16916459 ATATTATTTTGTATGAATGTCTTAA
1 ATA-T-TTTTGTATGAATGTCTTAA
16916484 CACTATTTTT
1 -A-TATTTTT
16916494 AACCTTACAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.10
24 1 0.03
25 22 0.73
26 2 0.07
27 2 0.07
ACGTcount: A:0.28, C:0.09, G:0.10, T:0.53
Consensus pattern (23 bp):
ATATTTTTGTATGAATGTCTTAA
Found at i:16922796 original size:110 final size:110
Alignment explanation
Indices: 16922603--16922804 Score: 334
Period size: 110 Copynumber: 1.8 Consensus size: 110
16922593 TTTTCTTAAG
* * **
16922603 TAAGCCTCTTCAAATCCTCAAGCCAACCCAGTTGGCATTCACAACACAAACTGGTATGACACAAA
1 TAAGCCTCTTCAAACCCTCAAGCCAACCCAGTTGGCATTCACAAAACAAACTGCCATGACACAAA
16922668 AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
66 AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
* *
16922713 TAAGCCTC-TCAAAACCCTCAAGCCAGCCCAGTTGGCATTCACAAAACAAACTGCCATGACACCA
1 TAAGCCTCTTC-AAACCCTCAAGCCAACCCAGTTGGCATTCACAAAACAAACTGCCATGACACAA
16922777 AAAGGTAAATTTACCTATCTTCCTGTAA
65 AAAGGTAAATTTACCTATCTTCCTGTAA
16922805 TAACTTAATT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
109 2 0.02
110 83 0.98
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.23
Consensus pattern (110 bp):
TAAGCCTCTTCAAACCCTCAAGCCAACCCAGTTGGCATTCACAAAACAAACTGCCATGACACAAA
AAGGTAAATTTACCTATCTTCCTGTAACTCAAGTCGCAGCTAAAA
Found at i:16934222 original size:17 final size:17
Alignment explanation
Indices: 16934199--16934232 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
16934189 CTAAAGCATA
16934199 AAAAAAAGAGAAAAAAAC
1 AAAAAAA-AGAAAAAAAC
16934217 AAAAAAAAGAAAAAAA
1 AAAAAAAAGAAAAAAA
16934233 ATAATTTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAC
Found at i:16934222 original size:19 final size:18
Alignment explanation
Indices: 16934198--16934233 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
16934188 CCTAAAGCAT
16934198 AAAAAAAAGAGAAAAAAAC
1 AAAAAAAAGA-AAAAAAAC
16934217 AAAAAAAAGAAAAAAAA
1 AAAAAAAAGAAAAAAAA
16934234 TAATTTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (18 bp):
AAAAAAAAGAAAAAAAAC
Found at i:16934233 original size:9 final size:9
Alignment explanation
Indices: 16934198--16934233 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
16934188 CCTAAAGCAT
16934198 AAAAAAAAG
1 AAAAAAAAG
*
16934207 AGAAAAAAAC
1 A-AAAAAAAG
16934217 AAAAAAAAG
1 AAAAAAAAG
16934226 AAAAAAAA
1 AAAAAAAA
16934234 TAATTTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.89, C:0.03, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:16939507 original size:20 final size:20
Alignment explanation
Indices: 16939482--16939523 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
16939472 GAGAGTAAAT
16939482 GGTGAAAAGTAAAAATTTAG
1 GGTGAAAAGTAAAAATTTAG
*
16939502 GGTGAAAAGTAAAAGTTTAG
1 GGTGAAAAGTAAAAATTTAG
16939522 GG
1 GG
16939524 GAATAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (20 bp):
GGTGAAAAGTAAAAATTTAG
Found at i:16939666 original size:30 final size:31
Alignment explanation
Indices: 16939627--16939686 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
16939617 AGAGGTGGGA
* *
16939627 TGGGAAGGGAATAAAATTTTTAGGGGAAAAG
1 TGGGAAGGGAATAAAAATTTGAGGGGAAAAG
* *
16939658 TGGG-AGGGAGTAAAAATTTGGGGGGAAAA
1 TGGGAAGGGAATAAAAATTTGAGGGGAAAA
16939687 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.40, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTGAGGGGAAAAG
Found at i:16942406 original size:35 final size:34
Alignment explanation
Indices: 16942366--16942432 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
16942356 TTTTTCATAA
16942366 ATTTTAGATATAAAT-TTTATTTATGATTTTTAACT
1 ATTTTA-ATATAAATATTTATTTAT-ATTTTTAACT
* **
16942401 ATTTTAATTTATTTATTTATTTATATTTTTAA
1 ATTTTAATATAAATATTTATTTATATTTTTAA
16942433 TTACTTAGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 13 0.46
35 15 0.54
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (34 bp):
ATTTTAATATAAATATTTATTTATATTTTTAACT
Found at i:16942789 original size:46 final size:44
Alignment explanation
Indices: 16942722--16942813 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 44
16942712 GAAATAAAAC
* *
16942722 TGTAATGGACTAGAATTGTAATCAGTGATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAAT-AGT-ATT-AATGTGTTTGGTTGAA
*
16942768 TGTAATGGAATAGAACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
16942812 TG
1 TG
16942814 GAACAGATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
43 2 0.05
44 17 0.40
45 3 0.07
46 20 0.48
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.40
Consensus pattern (44 bp):
TGTAATGGAATAGAACTGTAATAGTATTAATGTGTTTGGTTGAA
Found at i:16958402 original size:20 final size:21
Alignment explanation
Indices: 16958377--16958416 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16958367 ATATTTGTTG
16958377 ATGGA-TGTAAAAGGACTTTA
1 ATGGATTGTAAAAGGACTTTA
**
16958397 ATGGATTGTTTAAGGACTTT
1 ATGGATTGTAAAAGGACTTT
16958417 TATAACTGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.38
Consensus pattern (21 bp):
ATGGATTGTAAAAGGACTTTA
Found at i:16961666 original size:58 final size:58
Alignment explanation
Indices: 16961604--16961736 Score: 178
Period size: 58 Copynumber: 2.3 Consensus size: 58
16961594 TGCTTTTTGG
* *
16961604 TGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTATCACTTTAGTGCTATTCAA
1 TGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTAGCACTTCAGTGCTATTCAA
* * * * ***
16961662 TGTGTTTTGGAGGGATTTGATCTATTGTTTTCAATTTTAGCACTTCAGTGCTCTTTGG
1 TGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTAGCACTTCAGTGCTATTCAA
16961720 TGTG-TTTGGAGGGATGT
1 TGTGTTTTGGAGGGATGT
16961737 AATTTGTTTC
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
57 12 0.18
58 53 0.82
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (58 bp):
TGTGTTTTGGAGGGATGTGATCTATTGTCTTCAAGTTTAGCACTTCAGTGCTATTCAA
Found at i:16968731 original size:18 final size:18
Alignment explanation
Indices: 16968700--16968743 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
16968690 TCGAAAAATG
* * *
16968700 CATAAAAATTAAAATAAA
1 CATAAACATAAAAACAAA
16968718 CATAAACATAAAAACAAA
1 CATAAACATAAAAACAAA
*
16968736 AATAAACA
1 CATAAACA
16968744 CACATAAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.73, C:0.11, G:0.00, T:0.16
Consensus pattern (18 bp):
CATAAACATAAAAACAAA
Found at i:16974565 original size:14 final size:14
Alignment explanation
Indices: 16974546--16974573 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
16974536 TCATCATTTA
16974546 CCTATAACCAAAAC
1 CCTATAACCAAAAC
16974560 CCTATAACCAAAAC
1 CCTATAACCAAAAC
16974574 TCATAAACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:16974694 original size:8 final size:9
Alignment explanation
Indices: 16974679--16974709 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
16974669 GAAGAGAATG
16974679 GAAAAAAAA
1 GAAAAAAAA
16974688 GAAAAAAAA
1 GAAAAAAAA
16974697 GAAAAAAAA
1 GAAAAAAAA
16974706 GAAA
1 GAAA
16974710 GAAAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:16975724 original size:20 final size:19
Alignment explanation
Indices: 16975681--16975752 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
16975671 AGAAATATAG
*
16975681 ATTTTGGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTAAAAATT
16975701 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
* *
16975720 AATTTAAATTTTAAAAAATT
1 ATTTTGAATTTT-AAAAATT
16975740 ATTTTGAATTTTA
1 ATTTTGAATTTTA
16975753 TTTTTGTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 8 0.18
19 15 0.33
20 22 0.49
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:16978236 original size:2 final size:2
Alignment explanation
Indices: 16978229--16978257 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16978219 TTAAAGCTTT
16978229 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
16978258 TTCTATTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:16979048 original size:13 final size:12
Alignment explanation
Indices: 16979030--16979059 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
16979020 ATTTATCCAA
16979030 TTTTTTTGAATAT
1 TTTTTTTG-ATAT
16979043 TTTTTTTGATAT
1 TTTTTTTGATAT
16979055 TTTTT
1 TTTTT
16979060 ATACCCGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.77
Consensus pattern (12 bp):
TTTTTTTGATAT
Found at i:16979229 original size:21 final size:21
Alignment explanation
Indices: 16979183--16979226 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
16979173 TCCAACATTT
*
16979183 ATTATTATTTAAACATTATTA
1 ATTATTATTTAAACATTAATA
16979204 ATTATTATATTAAA-A-TAATA
1 ATTATTAT-TTAAACATTAATA
16979224 ATT
1 ATT
16979227 TATCATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTATTTAAACATTAATA
Found at i:16986503 original size:3 final size:3
Alignment explanation
Indices: 16986495--16986565 Score: 133
Period size: 3 Copynumber: 23.3 Consensus size: 3
16986485 ATGTTCAACC
16986495 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16986543 TAT TAT TAT TAT TAT TAT GTAT T
1 TAT TAT TAT TAT TAT TAT -TAT T
16986566 TTCATATATT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 64 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:16993070 original size:30 final size:32
Alignment explanation
Indices: 16993008--16993070 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
16992998 TAGAAAGAAG
* **
16993008 AAGTATAAACATATTGGGTCATTTACGCAAAA
1 AAGTATAAACATATTGGGCCATTTACAAAAAA
*
16993040 AAGTA-AAA-ATATTGGGCCATTTATAAAAAA
1 AAGTATAAACATATTGGGCCATTTACAAAAAA
16993070 A
1 A
16993071 TAAAAAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 19 0.70
31 3 0.11
32 5 0.19
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.27
Consensus pattern (32 bp):
AAGTATAAACATATTGGGCCATTTACAAAAAA
Found at i:16995370 original size:24 final size:23
Alignment explanation
Indices: 16995333--16995380 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 23
16995323 TGCTCTCCCT
*
16995333 ATTTAAATCCATTAA-ATTATAAA
1 ATTTAAACCCATTAATATT-TAAA
16995356 ATTTAATACCCATTAATATTTAAA
1 ATTTAA-ACCCATTAATATTTAAA
16995380 A
1 A
16995381 CCCTGATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 6 0.27
24 13 0.59
25 3 0.14
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (23 bp):
ATTTAAACCCATTAATATTTAAA
Found at i:16996351 original size:16 final size:16
Alignment explanation
Indices: 16996330--16996360 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16996320 TTTAAGAAAA
*
16996330 ATTTAATAAACAAATG
1 ATTTAATAAAAAAATG
16996346 ATTTAATAAAAAAAT
1 ATTTAATAAAAAAAT
16996361 TCGAATAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTTAATAAAAAAATG
Found at i:16997142 original size:20 final size:20
Alignment explanation
Indices: 16997104--16997142 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16997094 ACAGAAGTGC
* **
16997104 TGGCATAATTATATTTTTAT
1 TGGCATAATAATAAGTTTAT
16997124 TGGCATAATAATAAGTTTA
1 TGGCATAATAATAAGTTTA
16997143 GCCATTTAAT
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:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (20 bp):
TGGCATAATAATAAGTTTAT
Found at i:16998329 original size:44 final size:44
Alignment explanation
Indices: 16998236--16998330 Score: 111
Period size: 44 Copynumber: 2.2 Consensus size: 44
16998226 AAAAAAATTA
* * * *
16998236 AAAATGAAATATAGAAGTAATAGATATTACATAGTTTTGTTGGT
1 AAAATGAAATAGACAAGTAATAGATATTACATACTTTGGTTGGT
* * *
16998280 TAAATGAAATAGACAAGTAATAG-TATTAGATTCTTTGGTTGGCT
1 AAAATGAAATAGACAAGTAATAGATATTACATACTTTGGTTGG-T
16998324 AAAATGA
1 AAAATGA
16998331 TGTTAACGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 15 0.36
44 27 0.64
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (44 bp):
AAAATGAAATAGACAAGTAATAGATATTACATACTTTGGTTGGT
Found at i:16998487 original size:21 final size:20
Alignment explanation
Indices: 16998463--16998501 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
16998453 AAATAAAAAA
*
16998463 TATAAGTAAACAATTTAATAT
1 TATAAGTAAA-AATATAATAT
*
16998484 TATAATTAAAAATATAAT
1 TATAAGTAAAAATATAAT
16998502 TTAGTAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (20 bp):
TATAAGTAAAAATATAATAT
Done.