Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009155.1 Hibiscus syriacus cultivar Beakdansim tig00112681_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: 133936
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4203 original size:14 final size:14
Alignment explanation
Indices: 4169--4222 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
4159 TTGTGCAATA
* *
4169 CAAATGCAAAGATG
1 CAAATGTAAATATG
4183 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
4198 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
4212 TAAATGTAAAT
1 CAAATGTAAAT
4223 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:10537 original size:20 final size:20
Alignment explanation
Indices: 10512--10572 Score: 97
Period size: 19 Copynumber: 3.1 Consensus size: 20
10502 AAATTGGCAT
* *
10512 GGGGGTATCGGTACCATCTG
1 GGGGGTACCAGTACCATCTG
10532 GGGGGTACCAGTACCATCT-
1 GGGGGTACCAGTACCATCTG
10551 GGGGGTACCAGTACCATCTG
1 GGGGGTACCAGTACCATCTG
10571 GG
1 GG
10573 CAATCTGGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
19 19 0.50
20 19 0.50
ACGTcount: A:0.18, C:0.23, G:0.38, T:0.21
Consensus pattern (20 bp):
GGGGGTACCAGTACCATCTG
Found at i:13158 original size:21 final size:23
Alignment explanation
Indices: 13132--13191 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 23
13122 AAATCTCGAT
*
13132 GGGGGTATCGGTACCC-TC-ATG
1 GGGGGTATCGGTACCCATCAAAG
13153 GGGGGTATCGGTACCCATTCAAAG
1 GGGGGTATCGGTACCCA-TCAAAG
*
13177 GGGGGTATCGATACC
1 GGGGGTATCGGTACC
13192 TAGCGCGCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 16 0.47
23 2 0.06
24 16 0.47
ACGTcount: A:0.20, C:0.22, G:0.37, T:0.22
Consensus pattern (23 bp):
GGGGGTATCGGTACCCATCAAAG
Found at i:21332 original size:22 final size:21
Alignment explanation
Indices: 21292--21355 Score: 62
Period size: 22 Copynumber: 3.1 Consensus size: 21
21282 AAAAATGGTC
*
21292 TCGGTACCGTA-T-TAGAGTA
1 TCGGTACCATAGTATAGAGTA
21311 TCGGTACCATAGTATAGTAGTA
1 TCGGTACCATAGTATAG-AGTA
* * *
21333 TCGATACCATGGTAT-GGGTA
1 TCGGTACCATAGTATAGAGTA
21353 TCG
1 TCG
21356 ATACTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 10 0.26
20 7 0.18
21 4 0.11
22 17 0.45
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (21 bp):
TCGGTACCATAGTATAGAGTA
Found at i:21769 original size:54 final size:54
Alignment explanation
Indices: 21687--22238 Score: 809
Period size: 54 Copynumber: 10.1 Consensus size: 54
21677 CCCAAATAGT
* *
21687 CACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
21741 CACTAAGTGTGAAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGG
* * * *
21799 CACTAAGTGTACAATTTACGAAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* * **
21853 CAATAAGTGTGCAATTCACGGAATTCACCATATGCCGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
*
21907 CACTAAGTGTGCAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCAG
1 CACTAAGTGTGCAATTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGG
*
21965 CACTAAGTTTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
22019 CACTAAGTGTGC-ATTCACGTAATTCATCATATGTTGATGAATAACAGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
22072 CACTAAGTGTGCACTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
22126 CACTAAGTGTACAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
** * *
22180 CACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAATAACCGTATGGG
1 CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
22234 CACTA
1 CACTA
22239 TTGGTGCATT
Statistics
Matches: 451, Mismatches: 38, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
53 51 0.11
54 302 0.67
58 98 0.22
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
CACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
Found at i:21860 original size:112 final size:108
Alignment explanation
Indices: 21687--22228 Score: 825
Period size: 112 Copynumber: 5.0 Consensus size: 108
21677 CCCAAATAGT
*
21687 CACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
*
21752 AAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGA
66 CAATTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGA
* * * *
21799 CACTAAGTGTACAATTTACGAAATTCATCATATGTTGATGAATAACCGTTTCGACAATAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
* ** *
21864 CAATTCACGGAATTCACCATATGCCGATGAATAACCGTTTCGG
66 CAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
* *
21907 CACTAAGTGTGCAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCAGCACTAAG
1 CACTAAGTGTGCAATTCACGAAATTCATC----ATATGTTGATGAATAACCGTTTCGGCACTAAG
* *
21972 TTTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
62 TGTGCAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
* *
22019 CACTAAGTGTGC-ATTCACGTAATTCATCATATGTTGATGAATAACAGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
*
22083 CACTTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
66 CAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
*
22126 CACTAAGTGTACAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
**
22191 CAATTCACAAAATTCATCATATGTTGATGAATAACCGT
66 CAATTCACGGAATTCATCATATGTTGATGAATAACCGT
22229 ATGGGCACTA
Statistics
Matches: 393, Mismatches: 32, Indels: 14
0.90 0.07 0.03
Matches are distributed among these distances:
107 85 0.22
108 133 0.34
111 15 0.04
112 160 0.41
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (108 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
CAATTCACGGAATTCATCATATGTTGATGAATAACCGTTTCGA
Found at i:21971 original size:166 final size:166
Alignment explanation
Indices: 21687--22238 Score: 891
Period size: 166 Copynumber: 3.4 Consensus size: 166
21677 CCCAAATAGT
*
21687 CACTAAGTGTGCAATTCACGAAATTCATCATTTGTTGATGAATAACCGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
* *
21752 AAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTACAATTTA
66 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTACAATTCA
*
21817 CGAAATTCATCATATGTTGATGAATAACCGTTTCGA
131 CGAAATTCATCATATGTTGATGAATAACCGTTTCGG
* * * **
21853 CAATAAGTGTGCAATTCACGGAATTCACCATATGCCGATGAATAACCGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
* *
21918 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTC-AGCACTAAGTTTGCAATTC
66 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGA-CACTAAGTGTACAATTC
*
21982 ACGGAATTCATCATATGTTGATGAATAACCGTTTCGG
130 ACGAAATTCATCATATGTTGATGAATAACCGTTTCGG
* *
22019 CACTAAGTGTGC-ATTCACGTAATTCATCATATGTTGATGAATAACAGTTTCGGCACTAAGTGTG
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
*
22083 CACTTCACGGAATTCATC----ATATGTTGATGAATAACCGTTTCGACACTAAGTGTACAATTCA
66 CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTACAATTCA
22144 CGAAATTCATCATATGTTGATGAATAACCGTTTCGG
131 CGAAATTCATCATATGTTGATGAATAACCGTTTCGG
* * *
22180 CACTAAGTGTGCAATTCACAAAATTCATCATATGTTGATGAATAACCGTATGGGCACTA
1 CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTA
22239 TTGGTGCATT
Statistics
Matches: 356, Mismatches: 27, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
161 86 0.24
162 42 0.12
165 65 0.18
166 163 0.46
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (166 bp):
CACTAAGTGTGCAATTCACGAAATTCATCATATGTTGATGAATAACCGTTTCGGCACTAAGTGTG
CAATTCACGGAATTCATCATATATATGTTGATGAATAACCGTTTCGACACTAAGTGTACAATTCA
CGAAATTCATCATATGTTGATGAATAACCGTTTCGG
Found at i:23663 original size:23 final size:23
Alignment explanation
Indices: 23623--23670 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
23613 TTTTTATATA
*
23623 TATTATAATATTACATATTTAAT
1 TATTATAATATTACATATTAAAT
*
23646 TATTAATAAT-TTATATATTAAAT
1 TATT-ATAATATTACATATTAAAT
23669 TA
1 TA
23671 AAATAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TATTATAATATTACATATTAAAT
Found at i:25563 original size:36 final size:36
Alignment explanation
Indices: 25523--25637 Score: 101
Period size: 36 Copynumber: 3.1 Consensus size: 36
25513 GACCAACAGC
25523 ATCAACTACATTTTCAACAACCCTCTCAGCAGCACA
1 ATCAACTACATTTTCAACAACCCTCTCAGCAGCACA
* ** * *
25559 ATCAACAACACCCTT-ACCAGCACCCTCATCAAG-ACCACCA
1 ATCAACTACA-TTTTCAACA--ACCCTC-TC-AGCAGCA-CA
*
25599 AT-AACTACATTTTCAGCAACCCTCTCAGCAGCACA
1 ATCAACTACATTTTCAACAACCCTCTCAGCAGCACA
25634 ATCA
1 ATCA
25638 CTAGCACAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 18
0.68 0.11 0.20
Matches are distributed among these distances:
35 6 0.10
36 18 0.30
37 8 0.13
38 8 0.13
39 14 0.23
40 6 0.10
ACGTcount: A:0.37, C:0.38, G:0.06, T:0.19
Consensus pattern (36 bp):
ATCAACTACATTTTCAACAACCCTCTCAGCAGCACA
Found at i:25655 original size:12 final size:12
Alignment explanation
Indices: 25627--25692 Score: 62
Period size: 12 Copynumber: 5.5 Consensus size: 12
25617 ACCCTCTCAG
25627 CAGCACAATC-A
1 CAGCACAATCAA
25638 CTAGCACAATCAA
1 C-AGCACAATCAA
**
25651 CAGCACCCTCAA
1 CAGCACAATCAA
* *
25663 CAGTACAATCAG
1 CAGCACAATCAA
* *
25675 CAGCACACTCAT
1 CAGCACAATCAA
25687 CAGCAC
1 CAGCAC
25693 CCTCACCAGT
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
11 1 0.02
12 41 0.93
13 2 0.05
ACGTcount: A:0.39, C:0.38, G:0.11, T:0.12
Consensus pattern (12 bp):
CAGCACAATCAA
Found at i:25655 original size:75 final size:77
Alignment explanation
Indices: 25506--25661 Score: 210
Period size: 75 Copynumber: 2.0 Consensus size: 77
25496 ATCTCCAATA
*
25506 TCATCAAGACCAACAGCATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAACAACACC
1 TCATCAAGACCAACA-CATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAACAACACA
* * *
25571 CTTACCAGCACCC
65 ATCAACAGCACCC
* * *
25584 TCATCAAGACCACCA-AT-AACTACATTTTCAGCAACCCTCTCAGCAGCACAATC-ACTAGCACA
1 TCATCAAGACCAACACATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAAC-AACACA
25646 ATCAACAGCACCC
65 ATCAACAGCACCC
25659 TCA
1 TCA
25662 ACAGTACAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 2 0.03
75 52 0.74
76 2 0.03
78 14 0.20
ACGTcount: A:0.37, C:0.38, G:0.07, T:0.17
Consensus pattern (77 bp):
TCATCAAGACCAACACATCAACTACATTTTCAACAACCCTCTCAGCAGCACAATCAACAACACAA
TCAACAGCACCC
Found at i:25697 original size:12 final size:12
Alignment explanation
Indices: 25651--25733 Score: 76
Period size: 12 Copynumber: 6.9 Consensus size: 12
25641 GCACAATCAA
*
25651 CAGCACCCTCAA
1 CAGCACCCTCAC
* ** *
25663 CAGTACAATCAG
1 CAGCACCCTCAC
* *
25675 CAGCACACTCAT
1 CAGCACCCTCAC
25687 CAGCACCCTCAC
1 CAGCACCCTCAC
*
25699 CAGTACCCTCAC
1 CAGCACCCTCAC
*
25711 CAGCACCCTCAT
1 CAGCACCCTCAC
*
25723 CAACACCCTCA
1 CAGCACCCTCA
25734 GCGGCAGTTA
Statistics
Matches: 58, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 58 1.00
ACGTcount: A:0.31, C:0.47, G:0.08, T:0.13
Consensus pattern (12 bp):
CAGCACCCTCAC
Found at i:25715 original size:36 final size:36
Alignment explanation
Indices: 25622--25733 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 36
25612 CAGCAACCCT
* * * * *
25622 CTCAGCAGCACAATCACTAGCACAATCAACAGCACC
1 CTCAACAGTACAATCACCAGCACACTCATCAGCACC
*
25658 CTCAACAGTACAATCAGCAGCACACTCATCAGCACC
1 CTCAACAGTACAATCACCAGCACACTCATCAGCACC
* ** * *
25694 CTCACCAGTACCCTCACCAGCACCCTCATCAACACC
1 CTCAACAGTACAATCACCAGCACACTCATCAGCACC
25730 CTCA
1 CTCA
25734 GCGGCAGTTA
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.34, C:0.44, G:0.09, T:0.13
Consensus pattern (36 bp):
CTCAACAGTACAATCACCAGCACACTCATCAGCACC
Found at i:32858 original size:2 final size:2
Alignment explanation
Indices: 32851--32879 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
32841 ATTTAATTAG
32851 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32880 GTAACATCTC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:34281 original size:21 final size:21
Alignment explanation
Indices: 34255--34303 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
34245 GGGTCTGTCA
* *
34255 ATGTGGTCGTTC-GAGACAACT
1 ATGTGGTCCTTCGGA-ACAAAT
34276 ATGTGGTCCTTCGGAACAAAT
1 ATGTGGTCCTTCGGAACAAAT
34297 ATGTGGT
1 ATGTGGT
34304 ACTCGGTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.31
Consensus pattern (21 bp):
ATGTGGTCCTTCGGAACAAAT
Found at i:34324 original size:22 final size:22
Alignment explanation
Indices: 34272--34352 Score: 85
Period size: 22 Copynumber: 3.7 Consensus size: 22
34262 CGTTCGAGAC
* **
34272 AACTATGTGGTCCTTCGGAACA
1 AACTATGTGGTACTTCGGTGCA
34294 AA-TATGTGGTAC-TCGGTGCA
1 AACTATGTGGTACTTCGGTGCA
* *
34314 ACCCTATGTGGCACTTCGGTGCA
1 A-ACTATGTGGTACTTCGGTGCA
*
34337 AACTATGTGGTCCTTC
1 AACTATGTGGTACTTC
34353 ACGACAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.15
21 9 0.19
22 23 0.48
23 9 0.19
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (22 bp):
AACTATGTGGTACTTCGGTGCA
Found at i:34382 original size:21 final size:21
Alignment explanation
Indices: 34318--34383 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
34308 GGTGCAACCC
* *
34318 TATGTGGCACTTCGGTGCAAAC
1 TATGTGGCACTTC-GTACAAAT
34340 TATGTGGTC-CTTC--ACGACAAT
1 TATGTGG-CACTTCGTAC-A-AAT
34361 TATGTGGCACTTCGTACAAAT
1 TATGTGGCACTTCGTACAAAT
34382 TA
1 TA
34384 CAAGATGTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 18 0.50
22 12 0.33
23 3 0.08
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
TATGTGGCACTTCGTACAAAT
Found at i:37170 original size:19 final size:21
Alignment explanation
Indices: 37136--37175 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
37126 AAAACCAACA
37136 AAATCAATTCTTTTATTGTTT
1 AAATCAATTCTTTTATTGTTT
37157 AAAT-AATT-TTTTATTGTTT
1 AAATCAATTCTTTTATTGTTT
37176 GACTGGCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 4 0.21
21 4 0.21
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
AAATCAATTCTTTTATTGTTT
Found at i:37511 original size:32 final size:31
Alignment explanation
Indices: 37438--37513 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
37428 TAATATTTAG
* * *
37438 TTTTTGTTTCATTTTAGTATTCATTGTTTAC
1 TTTTTGTTTCATTTTAGTATCCACTGTTAAC
*
37469 TTTTTGTTTCATTTTAGTATCCCGCTGTTAAC
1 TTTTTGTTTCATTTTAGTAT-CCACTGTTAAC
*
37501 TTTTTATTTCATT
1 TTTTTGTTTCATT
37514 CTAATACCTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
31 20 0.51
32 19 0.49
ACGTcount: A:0.16, C:0.13, G:0.09, T:0.62
Consensus pattern (31 bp):
TTTTTGTTTCATTTTAGTATCCACTGTTAAC
Found at i:39831 original size:73 final size:72
Alignment explanation
Indices: 39636--39881 Score: 368
Period size: 72 Copynumber: 3.4 Consensus size: 72
39626 CAACATATCT
* *
39636 GGTAGGTAGTTTAATGTAATAGGTAGTGCCTATTTTTTTTTACCGTTTACATTATTAGCAACCTT
1 GGTAGGTATTTTAATGTAATAGGTAGTACCTA--TTTTTTTACCGTTTACATTATTAGCAACCTT
*
39701 CAAAAAAACT
64 -AAAAAAACC
*
39711 GGTAGGTATTTTAATGTAATAGGTAATA-CTATTTTTTTACCGTTTACATTATTAGCAACCTTAA
1 GGTAGGTATTTTAATGTAATAGGTAGTACCTATTTTTTTACCGTTTACATTATTAGCAACCTT-A
39775 AAAAAACC
65 AAAAAACC
* * *
39783 GGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTATCGTTTACATTATTAACAACCTTAA
1 GGTAGGTATTTTAATGTAATAGGTAGTACCTATTTTTTTACCGTTTACATTATTAGCAACCTTAA
*
39848 AAAAATC
66 AAAAACC
*
39855 GGTAGGTATTTTAATGTAATGGGTAGT
1 GGTAGGTATTTTAATGTAATAGGTAGT
39882 TTAAATTTTG
Statistics
Matches: 158, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
72 98 0.62
73 32 0.20
74 3 0.02
75 25 0.16
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (72 bp):
GGTAGGTATTTTAATGTAATAGGTAGTACCTATTTTTTTACCGTTTACATTATTAGCAACCTTAA
AAAAACC
Found at i:40111 original size:23 final size:23
Alignment explanation
Indices: 40085--40135 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
40075 TAAGTAATTA
**
40085 ACCTATTTTATTATATAAGCGCT
1 ACCTATTACATTATATAAGCGCT
* *
40108 ACCTATTACGTTATATAAGTGCT
1 ACCTATTACATTATATAAGCGCT
40131 ACCTA
1 ACCTA
40136 ATATGTTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCGCT
Found at i:40121 original size:135 final size:135
Alignment explanation
Indices: 39928--40535 Score: 633
Period size: 135 Copynumber: 4.3 Consensus size: 135
39918 ATCATAATTG
* * * * *
39928 ATAACAAATTAAGTAATTAATTACCTAGTTTGTTACATAAGCGCTACATAATATGTTATTATGTT
1 ATAACAAATTAAGTAATT-A--ACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCT
* * * * *
39993 TGATAATGTTTTCATTAATTAACCGGTTATATTATCATTGGTAACATTTTAAGTGTTTACCTAAT
63 TGATAATGTTTCCAGTAAATAACCGGTTATATTATCCTTGGTAACATTTTAAGCGTTTACCTAAT
40058 ATGTTGTA
128 ATGTTGTA
* *
40066 ATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGTGCT
1 ATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATATGTTAT-T-A-TGCT
* ** * ** *
40131 ACCTAAT-ATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACCGGTTATGTTATCCTTGGTAA
63 ---TGATAATG---TT-T-CCAG-TAA-ATAACC-G--GTT-A-----TA--TTATCCTTGGTAA
*
40195 CATTTTAGGCGTTTACCTAATATGTTGTA
107 CATTTTAAGCGTTTACCTAATATGTTGTA
* * * * *
40224 CTAACAAATTAAATAATTAACTTATTTTATTATATAAGCACTACCTAATATGTTATTGTGCTTGA
1 ATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCTTGA
* * *
40289 TAATATTTCCAGTAAATAACCGGTTATGTTATCCTTGGTAACATTTTAGGCGTTTACCTAATATG
66 TAATGTTTCCAGTAAATAACCGGTTATATTATCCTTGGTAACATTTTAAGCGTTTACCTAATATG
40354 TTGTA
131 TTGTA
*** *
40359 ATAACAAATTAAGTAATTAACCTATTACGTTATATAAGCGCTACCTAATATGTTATTGTGCTTGA
1 ATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCTTGA
* * *
40424 TAATGTTTCCAGTAAATAACCGGTTATGTTATCCTTGGTAAAATTTTAGGCGTTTACCTAATATG
66 TAATGTTTCCAGTAAATAACCGGTTATATTATCCTTGGTAACATTTTAAGCGTTTACCTAATATG
40489 TTGTA
131 TTGTA
* *
40494 ATAACAAATTAAGTAATTAACCTACTTTATTATATAAACGCT
1 ATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCT
40536 TATTGTGCTT
Statistics
Matches: 396, Mismatches: 49, Indels: 53
0.80 0.10 0.11
Matches are distributed among these distances:
135 236 0.60
136 1 0.00
137 3 0.01
138 21 0.05
140 3 0.01
141 3 0.01
142 1 0.00
143 4 0.01
144 1 0.00
145 1 0.00
146 6 0.02
147 6 0.02
148 3 0.01
149 1 0.00
150 4 0.01
151 1 0.00
152 3 0.01
153 2 0.01
155 4 0.01
156 2 0.01
157 1 0.00
158 89 0.22
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.41
Consensus pattern (135 bp):
ATAACAAATTAAGTAATTAACCTATTTTATTATATAAGCGCTACCTAATATGTTATTATGCTTGA
TAATGTTTCCAGTAAATAACCGGTTATATTATCCTTGGTAACATTTTAAGCGTTTACCTAATATG
TTGTA
Found at i:40143 original size:23 final size:23
Alignment explanation
Indices: 40095--40144 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
40085 ACCTATTTTA
*
40095 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
* *
40118 TTATATAAGTGCTACCTAATATG
1 TTATATAAGCGCTACCTAATACG
40141 TTAT
1 TTAT
40145 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:40241 original size:158 final size:158
Alignment explanation
Indices: 39959--40279 Score: 489
Period size: 158 Copynumber: 2.0 Consensus size: 158
39949 TACCTAGTTT
* * * *
39959 GTTACATAAGCGCTACATAATATGTTATTATGTTTGATAATGTTTTCATTAATTAACCGGTTATA
1 GTTATATAAGCGCTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATA
* *
40024 TTATCATTGGTAACATTTTAAGTGTTTACCTAATATGTTGTAATAACAAATTAAGTAATTAACCT
66 TTATCATTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAACAAATTAAATAATTAACCT
* *
40089 ATTTTATTATATAAGCGCTACCTATTAC
131 ATTTTATTATATAAGCACTACCTAATAC
* * * *
40117 GTTATATAAGTGCTACCTAATATGTTATTGTGCTTGATAATGTTTCCAGTAATTAACCGGTTATG
1 GTTATATAAGCGCTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATA
* * * *
40182 TTATCCTTGGTAACATTTTAGGCGTTTACCTAATATGTTGTACTAACAAATTAAATAATTAACTT
66 TTATCATTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAACAAATTAAATAATTAACCT
*
40247 ATTTTATTATATAAGCACTACCTAATAT
131 ATTTTATTATATAAGCACTACCTAATAC
40275 GTTAT
1 GTTAT
40280 TGTGCTTGAT
Statistics
Matches: 146, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 146 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.42
Consensus pattern (158 bp):
GTTATATAAGCGCTACATAATATGTTATTATGCTTGATAATGTTTCCAGTAATTAACCGGTTATA
TTATCATTGGTAACATTTTAAGCGTTTACCTAATATGTTGTAATAACAAATTAAATAATTAACCT
ATTTTATTATATAAGCACTACCTAATAC
Found at i:41479 original size:24 final size:24
Alignment explanation
Indices: 41447--41506 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
41437 TAAAATGATA
* *
41447 AACGAACATAAATGAACACAAATG
1 AACGAACATAAACGAACACAAACG
* *
41471 AATGAACATAAACGAACATAAACG
1 AACGAACATAAACGAACACAAACG
41495 AACGAACATAAA
1 AACGAACATAAA
41507 ATTAATTAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.60, C:0.17, G:0.12, T:0.12
Consensus pattern (24 bp):
AACGAACATAAACGAACACAAACG
Found at i:45321 original size:29 final size:30
Alignment explanation
Indices: 45267--45356 Score: 98
Period size: 29 Copynumber: 3.0 Consensus size: 30
45257 TTTAAGTTTT
*
45267 AAAC-ATTATAAAATGATCATT-AATTTATC
1 AAACTATTACAAAAT-ATCATTAAATTTATC
45296 AAAACTATTACAAAAT-T-ATTAAATTTTATC
1 -AAACTATTACAAAATATCATTAAA-TTTATC
*
45326 AAACTGTTACAAAATAGTCATTAAATTTATC
1 AAACTATTACAAAATA-TCATTAAATTTATC
45357 TATCTTTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
28 3 0.06
29 17 0.33
30 10 0.19
31 16 0.31
32 6 0.12
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (30 bp):
AAACTATTACAAAATATCATTAAATTTATC
Found at i:52516 original size:27 final size:27
Alignment explanation
Indices: 52485--52549 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
52475 ATAATGGCTT
*
52485 TGAATCATTCATAATGTACTTTGATGC
1 TGAATCATTCAGAATGTACTTTGATGC
52512 TGAATCATTCAGAATGTACTTTGATGC
1 TGAATCATTCAGAATGTACTTTGATGC
52539 TGAATCATTCA
1 TGAATCATTCA
52550 ACATTGTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (27 bp):
TGAATCATTCAGAATGTACTTTGATGC
Found at i:52663 original size:22 final size:22
Alignment explanation
Indices: 52614--52655 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
52604 CACGCTAAAT
52614 GCTGAACGGTTCAGCATTCAAC
1 GCTGAACGGTTCAGCATTCAAC
*
52636 GCTGAACGGTTCAGCGTTCA
1 GCTGAACGGTTCAGCATTCA
52656 GCGTTGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
GCTGAACGGTTCAGCATTCAAC
Found at i:53885 original size:20 final size:20
Alignment explanation
Indices: 53840--53886 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
53830 AATGTCTAAG
*
53840 AGTT-CATTTAGGACCATAT
1 AGTTGCATTTAGAACCATAT
* * *
53859 AGATGCATTTAGAAGCATTT
1 AGTTGCATTTAGAACCATAT
53879 AGTTGCAT
1 AGTTGCAT
53887 GTGGTGAAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 3 0.14
20 19 0.86
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (20 bp):
AGTTGCATTTAGAACCATAT
Found at i:70812 original size:33 final size:33
Alignment explanation
Indices: 70736--70818 Score: 89
Period size: 33 Copynumber: 2.5 Consensus size: 33
70726 ATATACACAT
* *
70736 TTATTTTTATTTTTTATGTTTACTATTATTTTA
1 TTATTTTTATTTTTTATGTATACTATTATTATA
*
70769 TTATTATTATTTTCTTATGTATA-TA-TATATATA
1 TTATTTTTATTTT-TTATGTATACTATTAT-TATA
* *
70802 TTCTTTTTATTTATTAT
1 TTATTTTTATTTTTTAT
70819 TTTGTCTTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
32 7 0.17
33 27 0.64
34 8 0.19
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (33 bp):
TTATTTTTATTTTTTATGTATACTATTATTATA
Found at i:71012 original size:85 final size:85
Alignment explanation
Indices: 70922--71094 Score: 346
Period size: 85 Copynumber: 2.0 Consensus size: 85
70912 TTCCTTATTT
70922 TATTAACTATGATAACTTATCATGTATATATATACATTATTGATATTTATTATTATTTTTTTGTA
1 TATTAACTATGATAACTTATCATGTATATATATACATTATTGATATTTATTATTATTTTTTTGTA
70987 CGTTTCATTTCCATTTTGTC
66 CGTTTCATTTCCATTTTGTC
71007 TATTAACTATGATAACTTATCATGTATATATATACATTATTGATATTTATTATTATTTTTTTGTA
1 TATTAACTATGATAACTTATCATGTATATATATACATTATTGATATTTATTATTATTTTTTTGTA
71072 CGTTTCATTTCCATTTTGTC
66 CGTTTCATTTCCATTTTGTC
71092 TAT
1 TAT
71095 GTTTTTATTC
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 88 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.54
Consensus pattern (85 bp):
TATTAACTATGATAACTTATCATGTATATATATACATTATTGATATTTATTATTATTTTTTTGTA
CGTTTCATTTCCATTTTGTC
Found at i:71161 original size:31 final size:30
Alignment explanation
Indices: 71111--71170 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
71101 ATTCTTGCTT
*
71111 TATTTTTGTTTTCTCCTTATGTT-TTTTTTA
1 TATTTTTATTTTCTCCTTAT-TTATTTTTTA
*
71141 TATTTTTAATTTTTTCCTTATTTATTTTTT
1 TATTTTT-ATTTTCTCCTTATTTATTTTTT
71171 CGTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.75
Consensus pattern (30 bp):
TATTTTTATTTTCTCCTTATTTATTTTTTA
Found at i:71226 original size:18 final size:17
Alignment explanation
Indices: 71189--71236 Score: 60
Period size: 18 Copynumber: 2.8 Consensus size: 17
71179 TTAATGTTTG
* *
71189 TTTGTTTTATCATTTTA
1 TTTGTTTTATTATGTTA
71206 TTTGTTTTCATTATGTTA
1 TTTGTTTT-ATTATGTTA
*
71224 TTTATTTTATTAT
1 TTTGTTTTATTAT
71237 CATTTTCATC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.71
Consensus pattern (17 bp):
TTTGTTTTATTATGTTA
Found at i:73360 original size:12 final size:12
Alignment explanation
Indices: 73343--73368 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
73333 CTTGGAATTT
73343 GGGGTGCAGTTG
1 GGGGTGCAGTTG
73355 GGGGTGCAGTTG
1 GGGGTGCAGTTG
73367 GG
1 GG
73369 TATACTCCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.62, T:0.23
Consensus pattern (12 bp):
GGGGTGCAGTTG
Found at i:82073 original size:92 final size:91
Alignment explanation
Indices: 81892--82063 Score: 218
Period size: 92 Copynumber: 1.9 Consensus size: 91
81882 CCTAGAACAC
* *
81892 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATATGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTACATATGGATCATTTAGGCACCAAGATG
** * *
81957 AAGAGTTCTCTCCCTATTTAGCCAAG
66 AAGACATCTATCCCTATTCAGCCAAG
** * * *
81983 CCATGTGTTTTGCATGTGATCAGCCCCCCATGTGCCTTACATATGGTTCATTTAGGCACCAAGAT
1 CCATGTGCCTTGCATATGACCAG-CCCCCATGTGCCTTACATATGGATCATTTAGGCACCAAGAT
82048 GAATGACCATCTATCC
65 GAA-GA-CATCTATCC
82064 ATTCGGCCAA
Statistics
Matches: 68, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
91 19 0.28
92 41 0.60
93 2 0.03
94 6 0.09
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTACATATGGATCATTTAGGCACCAAGATG
AAGACATCTATCCCTATTCAGCCAAG
Found at i:82878 original size:23 final size:22
Alignment explanation
Indices: 82851--82903 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
82841 AAAATTCAGC
82851 AAAGAAAACAAAAGCACTTAAA
1 AAAGAAAACAAAAGCACTTAAA
*** *
82873 AGAAGAAATTGAAAGCACTTGAA
1 A-AAGAAAACAAAAGCACTTAAA
82896 AAAGAAAA
1 AAAGAAAA
82904 AGAAAGAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.64, C:0.09, G:0.15, T:0.11
Consensus pattern (22 bp):
AAAGAAAACAAAAGCACTTAAA
Found at i:86157 original size:12 final size:12
Alignment explanation
Indices: 86140--86166 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
86130 TAAATTAGTT
86140 AAATTAGTGAAC
1 AAATTAGTGAAC
86152 AAATTAGTGAAC
1 AAATTAGTGAAC
86164 AAA
1 AAA
86167 GATGGAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (12 bp):
AAATTAGTGAAC
Found at i:88814 original size:2 final size:2
Alignment explanation
Indices: 88797--88857 Score: 58
Period size: 2 Copynumber: 32.0 Consensus size: 2
88787 CCTCTAATGT
* * *
88797 TA TA T- TA TA CA TA TA TA TG T- TT TA TCA TA T- TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA
88836 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
88858 ATTTATTTGT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
1 4 0.08
2 44 0.88
3 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:91399 original size:65 final size:66
Alignment explanation
Indices: 91265--91425 Score: 224
Period size: 65 Copynumber: 2.5 Consensus size: 66
91255 GTGCACTAAG
*
91265 TGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
91329 A
66 A
* * *
91330 -GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-TCATTAGTGCATCGATGCTTGG
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATAGCCA-GAGTGCATCGATGCATGG
91392 -TA
64 CTA
*
91394 TGTGCATCGATGCATGAAATGCATTCGATGTT
1 TGTGCATCGATGCATCAAATGCATTCGATGTT
91426 CAACTTATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
64 32 0.37
65 52 0.60
66 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (66 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATGCATGGCT
A
Found at i:91464 original size:65 final size:62
Alignment explanation
Indices: 91265--91475 Score: 203
Period size: 65 Copynumber: 3.3 Consensus size: 62
91255 GTGCACTAAG
* * **
91265 TGTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATCAAATGCATTCGATGTTTC-AATTAATCATG-GTGCATCGATGCATGG-T
* * * *
91329 AGTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAATCATTAGTGCATCGATGCTTGGT
1 TGTGCATCGATGCATCAAATGCATTCGATG-TTTCAAT-TAATCA-TGGTGCATCGATGCATGGT
* *
91393 ATGTGCATCGATGCATGAAATGCATTCGATG-TTCAACTTATTTCATGGTGCATCGATGCATGGA
1 -TGTGCATCGATGCATCAAATGCATTCGATGTTTCAA-TTA-ATCATGGTGCATCGATGCATGG-
91457 T
62 T
*
91458 TGGTGCATCGGTGCATCA
1 T-GTGCATCGATGCATCA
91476 CTATGAAAAA
Statistics
Matches: 121, Mismatches: 16, Indels: 19
0.78 0.10 0.12
Matches are distributed among these distances:
63 4 0.03
64 51 0.42
65 66 0.55
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (62 bp):
TGTGCATCGATGCATCAAATGCATTCGATGTTTCAATTAATCATGGTGCATCGATGCATGGT
Found at i:92907 original size:56 final size:56
Alignment explanation
Indices: 92821--92932 Score: 224
Period size: 56 Copynumber: 2.0 Consensus size: 56
92811 GATTGAAAAG
92821 AATTTATGTACCTAGAGTACAATTCAACTCTACGACGCTCAGGCATGTTAAAACAA
1 AATTTATGTACCTAGAGTACAATTCAACTCTACGACGCTCAGGCATGTTAAAACAA
92877 AATTTATGTACCTAGAGTACAATTCAACTCTACGACGCTCAGGCATGTTAAAACAA
1 AATTTATGTACCTAGAGTACAATTCAACTCTACGACGCTCAGGCATGTTAAAACAA
92933 GATCCTAGTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (56 bp):
AATTTATGTACCTAGAGTACAATTCAACTCTACGACGCTCAGGCATGTTAAAACAA
Found at i:93256 original size:13 final size:13
Alignment explanation
Indices: 93238--93262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
93228 TTAAATCAAA
93238 AAAAATCAAATTT
1 AAAAATCAAATTT
93251 AAAAATCAAATT
1 AAAAATCAAATT
93263 CAAATTTTCG
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATCAAATTT
Found at i:93811 original size:19 final size:19
Alignment explanation
Indices: 93787--93823 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
93777 AAAAATGTCA
93787 AAAATCTGTTTAAACACTC
1 AAAATCTGTTTAAACACTC
*
93806 AAAATCTGTTTATACACT
1 AAAATCTGTTTAAACACT
93824 GCATCCACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.19, G:0.05, T:0.35
Consensus pattern (19 bp):
AAAATCTGTTTAAACACTC
Found at i:94624 original size:13 final size:13
Alignment explanation
Indices: 94606--94630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
94596 ATTAAATCAA
94606 AAAAATCAAATTT
1 AAAAATCAAATTT
94619 AAAAATCAAATT
1 AAAAATCAAATT
94631 CAAATTTTCG
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:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAAATCAAATTT
Found at i:95095 original size:23 final size:22
Alignment explanation
Indices: 95067--95146 Score: 90
Period size: 23 Copynumber: 3.6 Consensus size: 22
95057 GCATGGCCTT
95067 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
95089 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
95111 GTGTATCAATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
95133 ATGCATCGATGCAC
1 GTGCATCGATGCAC
95147 TGTTAGGTGT
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 14 0.31
22 15 0.33
23 16 0.36
ACGTcount: A:0.25, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:100703 original size:18 final size:17
Alignment explanation
Indices: 100649--100697 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
100639 TTGGACCCTT
* *
100649 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
100667 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
100685 AGTGCATTCGATG
1 AGTGCA-TCGATG
100698 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:100738 original size:19 final size:19
Alignment explanation
Indices: 100714--100765 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
100704 AATAGCCACA
*
100714 GTGCATTGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
100733 GTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGGCTG
100752 GTGCATCGATGCAT
1 GTGCATCGATGCAT
100766 CAAATGCATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.17, C:0.19, G:0.35, T:0.29
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTG
Found at i:100825 original size:83 final size:83
Alignment explanation
Indices: 100669--100826 Score: 205
Period size: 83 Copynumber: 1.9 Consensus size: 83
100659 TGCACTAAGA
* * ***
100669 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCACAGTGCATTGATGCATGGCTGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
100734 TGCATCGATGCATGGCTG
66 TGCATCGATGCATGGCTG
* *
100752 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-A
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCACAGTGCATCGATGCATGGCA
100814 AATGCATTCGATG
64 AATGCA-TCGATG
100827 TTCAATTTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
82 4 0.06
83 35 0.54
84 23 0.35
85 3 0.05
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (83 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGCAAA
TGCATCGATGCATGGCTG
Found at i:101226 original size:21 final size:21
Alignment explanation
Indices: 101202--101254 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
101192 AGTACAGAGG
101202 GTATCGATACTCCTGTAGGGA
1 GTATCGATACTCCTGTAGGGA
101223 GTATCGATACTCCTGTAGGGA
1 GTATCGATACTCCTGTAGGGA
101244 GTATCGATACT
1 GTATCGATACT
101255 ACCTTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATCGATACTCCTGTAGGGA
Found at i:101709 original size:17 final size:17
Alignment explanation
Indices: 101687--101728 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
101677 AATCTCCCAT
*
101687 TTTTGATATAACAAAAC
1 TTTTGAAATAACAAAAC
101704 TTTTGAAATAACAAAAC
1 TTTTGAAATAACAAAAC
101721 TTTTGAAA
1 TTTTGAAA
101729 AATTGTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.07, T:0.36
Consensus pattern (17 bp):
TTTTGAAATAACAAAAC
Found at i:103413 original size:3 final size:3
Alignment explanation
Indices: 103405--103467 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
103395 CAAAGCCTAC
*
103405 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT GTT -TT ACTT C-T
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT -CTT CTT
* *
103449 CTT CAT CTT CTT CCT CTT C
1 CTT CTT CTT CTT CTT CTT C
103468 CTTCACCATC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
2 4 0.08
3 46 0.88
4 2 0.04
ACGTcount: A:0.03, C:0.33, G:0.02, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:104763 original size:24 final size:25
Alignment explanation
Indices: 104736--104790 Score: 103
Period size: 24 Copynumber: 2.2 Consensus size: 25
104726 AAAGGGGTAC
104736 TGATACTATTTTACATAGTAGTA-T
1 TGATACTATTTTACATAGTAGTATT
104760 TGATACTATTTTACATAGTAGTATT
1 TGATACTATTTTACATAGTAGTATT
104785 TGATAC
1 TGATAC
104791 CTTAGGCTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 23 0.77
25 7 0.23
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (25 bp):
TGATACTATTTTACATAGTAGTATT
Found at i:106143 original size:25 final size:24
Alignment explanation
Indices: 106115--106186 Score: 65
Period size: 26 Copynumber: 2.9 Consensus size: 24
106105 ATATATATTT
*
106115 TTAAATAAAAATAAAAAAATTTAAA
1 TTAAATAAAAATAAAAATATTT-AA
* *
106140 TTAAGTTAATAATAAAATATATTTAA
1 TTAA-ATAAAAATAAAA-ATATTTAA
* *
106166 -TAAATTAATATAAAAATATTT
1 TTAAATAAAAATAAAAATATTT
106187 TTAAGTTAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
23 6 0.16
24 8 0.21
25 7 0.18
26 12 0.32
27 5 0.13
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (24 bp):
TTAAATAAAAATAAAAATATTTAA
Found at i:106154 original size:26 final size:25
Alignment explanation
Indices: 106124--106209 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 25
106114 TTTAAATAAA
106124 AATAAAAAAATTTAAATTAAGTTAAT
1 AATAAAAAAATTT-AATTAAGTTAAT
* *
106150 AATAAAATATATTTAA-TAAATTAAT
1 AATAAAA-AAATTTAATTAAGTTAAT
*
106175 -ATAAAAATATTT--TTAAGTTAAT
1 AATAAAAAAATTTAATTAAGTTAAT
106197 ATATATAAAAAAT
1 A-ATA-AAAAAAT
106210 ATTATGAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
22 8 0.16
23 6 0.12
24 9 0.18
25 14 0.27
26 9 0.18
27 5 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (25 bp):
AATAAAAAAATTTAATTAAGTTAAT
Found at i:106189 original size:25 final size:24
Alignment explanation
Indices: 106109--106212 Score: 74
Period size: 25 Copynumber: 4.2 Consensus size: 24
106099 CATAATATAT
*
106109 ATATTTTTAAATAAA-AATAAAAA
1 ATATTTTTAAGTAAATAATAAAAA
*
106132 A-ATTTAAATTAAGTTAATAAT--AAA
1 ATATTT---TTAAGTAAATAATAAAAA
*
106156 ATATATTTAA-TAAATTAATATAAAA
1 ATATTTTTAAGTAAA-TAATA-AAAA
106181 ATATTTTTAAGTTAATATATATAAAAA
1 ATATTTTTAAG-TAA-ATA-ATAAAAA
106208 ATATT
1 ATATT
106213 ATGAATTTAA
Statistics
Matches: 63, Mismatches: 5, Indels: 22
0.70 0.06 0.24
Matches are distributed among these distances:
21 3 0.05
22 12 0.19
23 1 0.02
24 4 0.06
25 22 0.35
26 3 0.05
27 14 0.22
28 4 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATTTTTAAGTAAATAATAAAAA
Found at i:106195 original size:22 final size:24
Alignment explanation
Indices: 106139--106199 Score: 81
Period size: 22 Copynumber: 2.6 Consensus size: 24
106129 AAAAATTTAA
106139 ATTAAGTTAATAATAAAATATATTT
1 ATTAAGTTAAT-ATAAAATATATTT
* *
106164 AATAAATTAATATAAAA-ATATTT
1 ATTAAGTTAATATAAAATATATTT
106187 -TTAAGTTAATATA
1 ATTAAGTTAATATA
106200 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 11 0.34
23 6 0.19
24 6 0.19
25 9 0.28
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (24 bp):
ATTAAGTTAATATAAAATATATTT
Found at i:106222 original size:27 final size:28
Alignment explanation
Indices: 106173--106231 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 28
106163 TAATAAATTA
* *
106173 ATAT-AAAAATATTTTTAAGTTAA-TAT
1 ATATAAAAAATATTATGAAGTTAAGTAT
*
106199 ATATAAAAAATATTATGAATTTAAGTAT
1 ATATAAAAAATATTATGAAGTTAAGTAT
*
106227 TTATA
1 ATATA
106232 CGTTAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.15
27 16 0.59
28 7 0.26
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (28 bp):
ATATAAAAAATATTATGAAGTTAAGTAT
Found at i:109624 original size:14 final size:14
Alignment explanation
Indices: 109615--109681 Score: 64
Period size: 14 Copynumber: 4.6 Consensus size: 14
109605 ACTTTTTTTA
*
109615 TATTTGTTTTTATT
1 TATTTATTTTTATT
109629 TATTTATTTTTATT
1 TATTTATTTTTATT
** *
109643 TATTCCTTTTAATAT
1 TATTTATTTTTAT-T
109658 T-TTTATTTATTTATT
1 TATTTA-TT-TTTATT
109673 TATTTATTT
1 TATTTATTT
109682 ATTTTCATTG
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
14 26 0.62
15 8 0.19
16 8 0.19
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (14 bp):
TATTTATTTTTATT
Found at i:109632 original size:4 final size:4
Alignment explanation
Indices: 109623--109740 Score: 66
Period size: 4 Copynumber: 28.2 Consensus size: 4
109613 TATATTTGTT
109623 TTTA TTTA TTTA -TT- TTTA TTTA TTCCT- TTTAA TATT- TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT--TA TTT-A T-TTA TTTA TTTA
** *
109667 TTTA TTTA TTTA TTTA TTTTCA TTGC TTTA TCTTA TCTTA TTTT TTTA
1 TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA T-TTA T-TTA TTTA TTTA
* *
109715 CTTTC TTT- TTTAA ATTA TTTA TTTA T
1 -TTTA TTTA TTT-A TTTA TTTA TTTA T
109741 CTAGTTTTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 28
0.71 0.07 0.22
Matches are distributed among these distances:
3 10 0.11
4 55 0.60
5 22 0.24
6 4 0.04
ACGTcount: A:0.21, C:0.07, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:109668 original size:40 final size:38
Alignment explanation
Indices: 109609--109684 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 38
109599 TTAAACACTT
*
109609 TTTTTATATTTGTTTTTATTTATTTATTTTTATTTATTCC
1 TTTTAATATTTGTTTTTATTTATTTA--TTTATTTATTCC
109649 TTTTAATATTT-TTATTTATTTATTTATTTATTTATT
1 TTTTAATATTTGTT-TTTATTTATTTATTTATTTATT
109685 TTCATTGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
38 10 0.29
39 2 0.06
40 22 0.65
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (38 bp):
TTTTAATATTTGTTTTTATTTATTTATTTATTTATTCC
Found at i:109680 original size:22 final size:22
Alignment explanation
Indices: 109623--109681 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
109613 TATATTTGTT
109623 TTTATTTATTTATTTTTATTTA
1 TTTATTTATTTATTTTTATTTA
*
109645 TTCCT-TTTA-ATATTTTTATTTA
1 TT--TATTTATTTATTTTTATTTA
109667 TTTATTTATTTATTT
1 TTTATTTATTTATTT
109682 ATTTTCATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 1 0.03
21 4 0.13
22 21 0.68
23 4 0.13
24 1 0.03
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (22 bp):
TTTATTTATTTATTTTTATTTA
Found at i:120223 original size:20 final size:20
Alignment explanation
Indices: 120186--120224 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
120176 AAAAAAAAGA
*
120186 GAAAAAAGAACAACGAAAAT
1 GAAAAAAGAACAAAGAAAAT
120206 GAAAAAGAGAA-AAAGAAAA
1 GAAAAA-AGAACAAAGAAAA
120225 AATAATAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.74, C:0.05, G:0.18, T:0.03
Consensus pattern (20 bp):
GAAAAAAGAACAAAGAAAAT
Found at i:121147 original size:65 final size:64
Alignment explanation
Indices: 121038--121279 Score: 262
Period size: 65 Copynumber: 3.8 Consensus size: 64
121028 AAAGCGACAC
*
121038 AATTTA-CTCGAGATTGGATTTTAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGATG
1 AATTTACCT-GAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGATG
* * * *
121102 TAATTTACCTGAGATTGGATTTCAACTTCACAACGAAGGACATCCAAATAAAAGCCAATTTGGTG
1 -AATTTACCTGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGATG
* * * * * * *
121167 AAGCTTACTTAAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAACCCAATTTGGTC
1 AA-TTTACCTGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGATG
* * * *
121232 AA---A-C-AATCATTGGAATTCAACTTCACAAAGAAGGATATCCAACTCAAA
1 AATTTACCTGA-GATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
121280 ACTCAACTTC
Statistics
Matches: 155, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
59 2 0.01
60 37 0.24
61 1 0.01
64 2 0.01
65 111 0.72
66 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (64 bp):
AATTTACCTGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGATG
Found at i:123059 original size:3 final size:3
Alignment explanation
Indices: 123042--123075 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
123032 TTTATTTAAA
123042 TAT TA- TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
123076 ATATATACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 25 0.86
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:123149 original size:40 final size:41
Alignment explanation
Indices: 123089--123181 Score: 100
Period size: 40 Copynumber: 2.3 Consensus size: 41
123079 TATACATATG
* * * * *
123089 TTTTTTCTTGTTTTATTTAAT-TTATTTAC-TTTATTTTTCC
1 TTTTTTCTTTTTTTAGTTAATATTATGTACATATATTTTT-A
*
123129 TTTTTTCTTTTTTTCGTTAATATTATGTACATATATTTTTA
1 TTTTTTCTTTTTTTAGTTAATATTATGTACATATATTTTTA
*
123170 TTTTTTATTTTT
1 TTTTTTCTTTTT
123182 CCCTTCTTCT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
40 18 0.41
41 18 0.41
42 8 0.18
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (41 bp):
TTTTTTCTTTTTTTAGTTAATATTATGTACATATATTTTTA
Found at i:123229 original size:29 final size:31
Alignment explanation
Indices: 123197--123266 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
123187 CTTCTCCTTA
123197 TTTTATTTAAACATTTTTTA-TATTTGT-TT
1 TTTTATTTAAACATTTTTTATTATTTGTATT
** *
123226 TTTTATTTATTCATTTTTTATTATTTTTATT
1 TTTTATTTAAACATTTTTTATTATTTGTATT
123257 TATTTATTTA
1 T-TTTATTTA
123267 CTTACTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 18 0.51
30 6 0.17
31 3 0.09
32 8 0.23
ACGTcount: A:0.23, C:0.03, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTTATTTAAACATTTTTTATTATTTGTATT
Found at i:123236 original size:4 final size:4
Alignment explanation
Indices: 123217--123360 Score: 103
Period size: 4 Copynumber: 34.5 Consensus size: 4
123207 ACATTTTTTA
* * * *
123217 TATT TGTT TTTT TATT TATT CATT T-TT TATT ATTTT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT -TATT TATT TATT TATT
* **
123265 TACT TACTT TATT TATT TATT TATT TATT TATT T-TT TCATT GCTT TATCT
1 TATT TA-TT TATT TATT TATT TATT TATT TATT TATT T-ATT TATT TAT-T
* * * *
123315 TATTT TATTT TATT TCTT TACTT TCTT TTTT TAGAT TATT TATT TA
1 TA-TT TA-TT TATT TATT TA-TT TATT TATT TA-TT TATT TATT TA
123361 CCTACTTTTT
Statistics
Matches: 111, Mismatches: 20, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
3 6 0.05
4 79 0.71
5 25 0.23
6 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:123252 original size:25 final size:25
Alignment explanation
Indices: 123223--123301 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
123213 TTTATATTTG
*
123223 TTTTTTTATTTATTCATTT-TTTAT
1 TTTTTTTATTTATTTATTTATTTAT
* * *
123247 TATTTTTATTTATTTATTTACTTAC
1 TTTTTTTATTTATTTATTTATTTAT
*
123272 TTTATTTATTTATTTATTTATTTAT
1 TTTTTTTATTTATTTATTTATTTAT
123297 TTTTT
1 TTTTT
123302 CATTGCTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
24 17 0.38
25 28 0.62
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (25 bp):
TTTTTTTATTTATTTATTTATTTAT
Found at i:123341 original size:26 final size:26
Alignment explanation
Indices: 123312--123361 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
123302 CATTGCTTTA
** *
123312 TCTTATTTTATTTTATTTCTTTACTT
1 TCTTATTTTAGATTATTTATTTACTT
*
123338 TCTTTTTTTAGATTATTTATTTAC
1 TCTTATTTTAGATTATTTATTTAC
123362 CTACTTTTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.18, C:0.10, G:0.02, T:0.70
Consensus pattern (26 bp):
TCTTATTTTAGATTATTTATTTACTT
Found at i:126595 original size:25 final size:26
Alignment explanation
Indices: 126516--126624 Score: 84
Period size: 25 Copynumber: 4.2 Consensus size: 26
126506 CATAAAATAT
* * * *
126516 ATATTTTTAAATAAAAATAAAAATCAA
1 ATATTTTT-AATTAAATTAATAATAAA
*
126543 ATATTTTTATATTAAGTTAATAATAAA
1 ATATTTTTA-ATTAAATTAATAATAAA
*
126570 ATATATTTAA-TAAATTAAT-ATAAAA
1 ATATTTTTAATTAAATTAATAAT-AAA
126595 ATATTTTTAAGTT-AA-T-ATATATAAA
1 ATATTTTTAA-TTAAATTAATA-ATAAA
126620 ATATT
1 ATATT
126625 ATGAATTTAA
Statistics
Matches: 68, Mismatches: 8, Indels: 14
0.76 0.09 0.16
Matches are distributed among these distances:
24 4 0.06
25 29 0.43
26 6 0.09
27 29 0.43
ACGTcount: A:0.54, C:0.01, G:0.02, T:0.43
Consensus pattern (26 bp):
ATATTTTTAATTAAATTAATAATAAA
Found at i:126634 original size:25 final size:26
Alignment explanation
Indices: 126587--126643 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
126577 TAATAAATTA
* *
126587 ATATA-AAAATATTTTTAAGTTAA-T
1 ATATATAAAATATTATGAAGTTAAGT
*
126611 ATATATAAAATATTATGAATTTAAGT
1 ATATATAAAATATTATGAAGTTAAGT
*
126637 ATTTATA
1 ATATATA
126644 CACTAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (26 bp):
ATATATAAAATATTATGAAGTTAAGT
Found at i:129622 original size:20 final size:20
Alignment explanation
Indices: 129594--129637 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
129584 TCTAGTTTCT
* * *
129594 TATTTTACTAGATCAACTTA
1 TATTCTACTAAATCAACTAA
129614 TATTCTACTAAATCAACTAA
1 TATTCTACTAAATCAACTAA
129634 TATT
1 TATT
129638 AATCAACTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.02, T:0.43
Consensus pattern (20 bp):
TATTCTACTAAATCAACTAA
Done.