Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
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: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 109 of 120
Found at i:31804737 original size:38 final size:39
Alignment explanation
Indices: 31804685--31804783 Score: 164
Period size: 39 Copynumber: 2.6 Consensus size: 39
31804675 AGTTAATATG
*
31804685 TAAGTAATGTATTATGTAAGTTTATAT-AAAAAAAAGTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAAGTA
* *
31804723 TAAGTTATGAATTATGTAAGTTTATATAAAAAAAAATTA
1 TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAAGTA
31804762 TAAGTTATGTATTATGTAAGTT
1 TAAGTTATGTATTATGTAAGTT
31804784 AAAAGTAATG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
38 25 0.45
39 31 0.55
ACGTcount: A:0.46, C:0.00, G:0.13, T:0.40
Consensus pattern (39 bp):
TAAGTTATGTATTATGTAAGTTTATATAAAAAAAAAGTA
Found at i:31804789 original size:23 final size:23
Alignment explanation
Indices: 31804763--31804806 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
31804753 AAAAAATTAT
*
31804763 AAGTTATGTATTATGTAAGTTAA
1 AAGTAATGTATTATGTAAGTTAA
31804786 AAGTAATGTATTATGTAAGTT
1 AAGTAATGTATTATGTAAGTT
31804807 TACATATAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (23 bp):
AAGTAATGTATTATGTAAGTTAA
Found at i:31804841 original size:36 final size:36
Alignment explanation
Indices: 31804800--31804904 Score: 86
Period size: 36 Copynumber: 3.2 Consensus size: 36
31804790 AATGTATTAT
31804800 GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
1 GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
* ** * *
31804836 GTAAGTAATGTATTTAAGT-AACATACTT-AA----A
1 GTAAGT-TTACATATAAGTAAACTTACTTAAATTTTA
31804867 -T---TTTACATATAAGTAAACTTACTTAAATTTTA
1 GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
31804899 GTAAGT
1 GTAAGT
31804905 AATGTATTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 22
0.60 0.12 0.28
Matches are distributed among these distances:
26 8 0.17
27 9 0.19
28 2 0.04
30 1 0.02
31 1 0.02
32 1 0.02
33 1 0.02
35 2 0.04
36 15 0.31
37 8 0.17
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (36 bp):
GTAAGTTTACATATAAGTAAACTTACTTAAATTTTA
Found at i:31804873 original size:63 final size:63
Alignment explanation
Indices: 31804805--31804923 Score: 238
Period size: 63 Copynumber: 1.9 Consensus size: 63
31804795 ATTATGTAAG
31804805 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAAT
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAAT
31804868 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATA
1 TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATA
31804924 TTCAAGTAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (63 bp):
TTTACATATAAGTAAACTTACTTAAATTTTAGTAAGTAATGTATTTAAGTAACATACTTAAAT
Found at i:31804918 original size:13 final size:13
Alignment explanation
Indices: 31804900--31804951 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
31804890 TAAATTTTAG
*
31804900 TAAGTAATGTATT
1 TAAGTAATATATT
*
31804913 TAAGTAACATATT
1 TAAGTAATATATT
* *
31804926 CAAGTAATAAATT
1 TAAGTAATATATT
31804939 TAA-TATATATATT
1 TAAGTA-ATATATT
31804952 AGTAATAAGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
12 2 0.06
13 29 0.94
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (13 bp):
TAAGTAATATATT
Found at i:31807674 original size:365 final size:363
Alignment explanation
Indices: 31806998--31807710 Score: 1004
Period size: 365 Copynumber: 2.0 Consensus size: 363
31806988 TAAGTCAGAG
*
31806998 TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCGTTTTAT
1 TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTAT
* * *
31807063 AAAAATACAAGAAAACCTGGCGTTTTCCCAAACACGCCACAATCAATATATTATCGAACCGGCGT
66 AAAAATACAAGAAAACCTGGCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGACGC
** * *
31807128 CGTTTTCAGTAAATTTTATACATCTTTGCGGCGTTTTTAATAAAACGCCACTAAAAGATTCCATC
131 CGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAAGAATCCATC
* * * *
31807193 CTTCAACTAAAACAGCGTCGTTTTCGCAGAGTTCAAATATTATTTACGGCTCTTTAAGGAAAAAC
196 CTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCGCTTTAAGGAAAAAC
* *
31807258 GCCACAAGATAAATTTATCCCCTCAGTCGAAACGACGACGTATCGGTAAATGCAAT-AAATATTC
261 GCCACAAGATAAACTTATCCCCTCAATCGAAACGACGACGTATCGGTAAATGCAATAAAAT-TTC
*
31807322 GTGGCGCTTTTTATAAAAACGCCGGTAATGTCAGACTTT
325 GTGGCGCTTTTTAGAAAAACGCCGGTAATGTCAGACTTT
** *
31807361 TTGCGGCG-TTTAATTGGAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCGCCATTTTAT
1 TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTAT
* * * *
31807425 AAAAATATAAGGAAACGTTCTGGCGTTTTCCCAAAAACGCCACAATTAATATATTATCGAATCGA
66 AAAAATACAAGAAAAC---CTGGCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGA
*
31807490 CGCCGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAATAATCC
128 CGCCGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAAGAATCC
* * * * ** *
31807555 ATCCTTCAACTTAAACGGCGCCGTTTTGGCAAAGTTTAAA-AGTTATTTACAGCGCTTTTCGGTA
193 ATCCTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATA-TTATTTACAGCGCTTTAAGGAA
* * *
31807619 AAACGCCACAA-CTGAAACTTATTCCCT-AATCCGAAACGACGCCGTATCGGTAAATGCAATAAA
257 AAACGCCACAAGAT-AAACTTATCCCCTCAAT-CGAAACGACGACGTATCGGTAAATGCAATAAA
* * *
31807682 ATTTTGTGGCGTTTTTTAGCAAAACGCCG
320 ATTTCGTGGCGCTTTTTAGAAAAACGCCG
31807711 CTAAATCTTA
Statistics
Matches: 307, Mismatches: 36, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
362 66 0.21
363 8 0.03
364 4 0.01
365 225 0.73
366 4 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.28
Consensus pattern (363 bp):
TTGCGGCGTTTTAATTAAAAACGCCACTAAAATTTCAAGTACAGAAAGAAACGGCACCATTTTAT
AAAAATACAAGAAAACCTGGCGTTTTCCCAAAAACGCCACAATCAATATATTATCGAACCGACGC
CGTTTTCAGTAAATTTTATACATCCCTGCGGCGTTTATAATAAAACGCCACTAAAAGAATCCATC
CTTCAACTAAAACAGCGCCGTTTTCGCAAAGTTCAAATATTATTTACAGCGCTTTAAGGAAAAAC
GCCACAAGATAAACTTATCCCCTCAATCGAAACGACGACGTATCGGTAAATGCAATAAAATTTCG
TGGCGCTTTTTAGAAAAACGCCGGTAATGTCAGACTTT
Found at i:31807780 original size:24 final size:24
Alignment explanation
Indices: 31807753--31807833 Score: 92
Period size: 24 Copynumber: 3.2 Consensus size: 24
31807743 TGTATCATTC
31807753 ATTTAAATAATTAATTACCTATCT
1 ATTTAAATAATTAATTACCTATCT
*
31807777 ATTTAAACAATTAATTACCTA-CAAATT
1 ATTTAAATAATTAATTACCTATC----T
*
31807804 AATTTAAATAATTAATTACCTATTT
1 -ATTTAAATAATTAATTACCTATCT
31807829 ATTTA
1 ATTTA
31807834 TTTATTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.02
24 25 0.52
25 1 0.02
27 1 0.02
28 20 0.42
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAAATAATTAATTACCTATCT
Found at i:31807831 original size:4 final size:4
Alignment explanation
Indices: 31807824--31807848 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
31807814 ATTAATTACC
31807824 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
31807849 TTCTTCCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:31807836 original size:28 final size:26
Alignment explanation
Indices: 31807753--31807837 Score: 84
Period size: 28 Copynumber: 3.2 Consensus size: 26
31807743 TGTATCATTC
*
31807753 ATTTAAATAATTAATTACC--TATCT
1 ATTTAAATAATTAATTACCTATATTT
* * *
31807777 ATTTAAACAATTAATTACCTACAAATTA
1 ATTTAAATAATTAATTACCT--ATATTT
31807805 ATTTAAATAATTAATTACCTATTTATTT
1 ATTTAAATAATTAATTACCTA--TATTT
31807833 ATTTA
1 ATTTA
31807838 TTTATTTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
24 18 0.38
26 1 0.02
28 29 0.60
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTAAATAATTAATTACCTATATTT
Found at i:31808214 original size:7 final size:7
Alignment explanation
Indices: 31808202--31808250 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
31808192 ATGACCGTTG
31808202 AAACCCT
1 AAACCCT
31808209 AAACCCT
1 AAACCCT
31808216 AAACCCT
1 AAACCCT
*
31808223 AAACCCC
1 AAACCCT
31808230 AAATCCCT
1 AAA-CCCT
*
31808238 AACCCCT
1 AAACCCT
31808245 AAACCC
1 AAACCC
31808251 GATCTTGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
7 32 0.86
8 5 0.14
ACGTcount: A:0.41, C:0.47, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCCT
Found at i:31808239 original size:22 final size:21
Alignment explanation
Indices: 31808202--31808250 Score: 71
Period size: 22 Copynumber: 2.3 Consensus size: 21
31808192 ATGACCGTTG
*
31808202 AAACCCTAAACCCTAAACCCT
1 AAACCCCAAACCCTAAACCCT
*
31808223 AAACCCCAAATCCCTAACCCCT
1 AAACCCCAAA-CCCTAAACCCT
31808245 AAACCC
1 AAACCC
31808251 GATCTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.41, C:0.47, G:0.00, T:0.12
Consensus pattern (21 bp):
AAACCCCAAACCCTAAACCCT
Found at i:31808411 original size:12 final size:12
Alignment explanation
Indices: 31808394--31808418 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31808384 CTCTTAACAT
31808394 CTAACCCCTAAC
1 CTAACCCCTAAC
31808406 CTAACCCCTAAC
1 CTAACCCCTAAC
31808418 C
1 C
31808419 CCTGACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAACCCCTAAC
Found at i:31808490 original size:14 final size:14
Alignment explanation
Indices: 31808425--31808499 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
31808415 AACCCCTGAC
* *
31808425 CCTTAACCCATAAA
1 CCTTAATCCATAAT
*
31808439 CCTTAAATCACATTAAC
1 CCTT-AATC-CA-TAAT
* *
31808456 CCTTAAACCAGAAT
1 CCTTAATCCATAAT
*
31808470 CCCTAATCCATAAT
1 CCTTAATCCATAAT
31808484 CCTTAATTCCATAAT
1 CCTTAA-TCCATAAT
31808499 C
1 C
31808500 TATAAAACTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 22 0.46
15 14 0.29
16 5 0.10
17 7 0.15
ACGTcount: A:0.39, C:0.32, G:0.01, T:0.28
Consensus pattern (14 bp):
CCTTAATCCATAAT
Found at i:31809250 original size:113 final size:112
Alignment explanation
Indices: 31808998--31809376 Score: 510
Period size: 113 Copynumber: 3.3 Consensus size: 112
31808988 AAAACTTTAA
* * *
31808998 GAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCACTTTGGAAAAAACGTCGCTAAAGCCATGGG
1 GAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCCTGGG
*
31809063 TATTAGCGTCGCTTTCCAAAAAACGCCGTTAAGTCCCCGAAAGCTCAG
66 TATTAGCGTCGC-TTCCAAAAAACGCCGCTAAGTCCCCGAAAGCTCAG
31809111 GAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGGAAAAAAACGCCGCTAAAGCCCTGG
1 GAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGG-AAAAAACGCCGCTAAAGCCCTGG
*
31809176 GTATTAGCGTCGCTTCCTGAAAAACGCCGCT-AGATCCCCGAAAGCTCAG
65 GTATTAGCGTCGCTTCC-AAAAAACGCCGCTAAG-TCCCCGAAAGCTCAG
* * *** *
31809225 GAAACGGCGTCGTTGGGCTCAGTTTTTTTTGTGGCGCTTTGTTGAAAACGCTGCTAAAG-CCTGG
1 GAAACGGCGTCGTTGGGCTTAG-GTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCCTGG
* * * * *
31809289 GTTTTAGCGTCGCTTCAAAAAAAACGCCGCTAATTCCGCTAAAGCTCAG
65 GTATTAGCGTCGCTTC-CAAAAAACGCCGCTAAGTCCCCGAAAGCTCAG
* * * *
31809338 AAAACGGCATCGTTGGGATTAGGTATTTTGTGGCGCTTT
1 GAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTT
31809377 TTCGAAAACG
Statistics
Matches: 237, Mismatches: 23, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
112 15 0.06
113 109 0.46
114 96 0.41
115 17 0.07
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (112 bp):
GAAACGGCGTCGTTGGGCTTAGGTTTTTTGTGGCGCTTTGGAAAAAACGCCGCTAAAGCCCTGGG
TATTAGCGTCGCTTCCAAAAAACGCCGCTAAGTCCCCGAAAGCTCAG
Found at i:31819751 original size:45 final size:45
Alignment explanation
Indices: 31819700--31819830 Score: 152
Period size: 45 Copynumber: 3.1 Consensus size: 45
31819690 CCATAATCCC
31819700 TTTATTATAGTAAAATATCTTTTTACTTGTAGTTTTCTATCCACT
1 TTTATTATAGTAAAATATCTTTTTACTTGTAGTTTTCTATCCACT
** * * *
31819745 TTTATTATAGTAAAATTATCTTAAT-C-T-AAATATTC-A--C-C-
1 TTTATTATAGTAAAA-TATCTTTTTACTTGTAGTTTTCTATCCACT
31819783 TTTATTATAGTAAAATATCTTTTTACTTGTAGTTTTCTATCCACT
1 TTTATTATAGTAAAATATCTTTTTACTTGTAGTTTTCTATCCACT
31819828 TTT
1 TTT
31819831 GAAGAGTTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 18
0.71 0.11 0.19
Matches are distributed among these distances:
37 7 0.10
38 16 0.24
39 2 0.03
40 6 0.09
41 1 0.01
42 1 0.01
43 6 0.09
44 2 0.03
45 19 0.28
46 7 0.10
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (45 bp):
TTTATTATAGTAAAATATCTTTTTACTTGTAGTTTTCTATCCACT
Found at i:31826738 original size:13 final size:12
Alignment explanation
Indices: 31826716--31826774 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
31826706 AAAATAAAAT
31826716 CAATAATAATAA
1 CAATAATAATAA
31826728 CAATGAATAATAA
1 CAAT-AATAATAA
* *
31826741 CAACAATAACAA
1 CAATAATAATAA
*
31826753 TAATAA-AATAAA
1 CAATAATAAT-AA
31826765 CACATAATAA
1 CA-ATAATAA
31826775 GACAATATCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
11 2 0.05
12 18 0.49
13 15 0.41
14 2 0.05
ACGTcount: A:0.66, C:0.12, G:0.02, T:0.20
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:31826771 original size:22 final size:22
Alignment explanation
Indices: 31826723--31826771 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
31826713 AATCAATAAT
*
31826723 AATAACAATGAATAATAACAAC
1 AATAACAATGAATAATAAAAAC
31826745 AATAACAAT-AATAA-AATAAAC
1 AATAACAATGAATAATAA-AAAC
31826766 ACATAA
1 A-ATAA
31826772 TAAGACAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 2 0.08
21 9 0.38
22 13 0.54
ACGTcount: A:0.67, C:0.12, G:0.02, T:0.18
Consensus pattern (22 bp):
AATAACAATGAATAATAAAAAC
Found at i:31826914 original size:9 final size:9
Alignment explanation
Indices: 31826900--31826933 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
31826890 GTAGTAACAA
31826900 TAATAATGG
1 TAATAATGG
*
31826909 TAATAATAG
1 TAATAATGG
*
31826918 TAATAATGA
1 TAATAATGG
31826927 TAATAAT
1 TAATAAT
31826934 ATATAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (9 bp):
TAATAATGG
Found at i:31826923 original size:18 final size:18
Alignment explanation
Indices: 31826900--31826934 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31826890 GTAGTAACAA
*
31826900 TAATAATGGTAATAATAG
1 TAATAATGATAATAATAG
31826918 TAATAATGATAATAATA
1 TAATAATGATAATAATA
31826935 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.34
Consensus pattern (18 bp):
TAATAATGATAATAATAG
Found at i:31829127 original size:20 final size:21
Alignment explanation
Indices: 31829091--31829134 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
31829081 TAGTCGACAC
31829091 TTTTTTAATTTTGATTTTA-A
1 TTTTTTAATTTTGATTTTATA
*
31829111 TTTTTT-ATTATTTATTTTATA
1 TTTTTTAATT-TTGATTTTATA
31829132 TTT
1 TTT
31829135 GTTGATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 3 0.14
20 14 0.67
21 4 0.19
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTTTAATTTTGATTTTATA
Found at i:31829293 original size:22 final size:22
Alignment explanation
Indices: 31829236--31829293 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
31829226 ATGATGGATT
* *
31829236 ATATTTGTAAATTTAATTGAAGA
1 ATATTT-TATATTTAATTGAAAA
31829259 ATA-TTT-TATTTAATT-AATAA
1 ATATTTTATATTTAATTGAA-AA
31829279 ATATTTTATATTTAA
1 ATATTTTATATTTAA
31829294 AATTAATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 4 0.13
22 9 0.30
23 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATTTTATATTTAATTGAAAA
Found at i:31829297 original size:24 final size:24
Alignment explanation
Indices: 31829270--31829338 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
31829260 TATTTTATTT
31829270 AATTAATAAATATTTTATATTTAA
1 AATTAATAAATATTTTATATTTAA
**
31829294 AATTAATCTA-ATTTTATTATTTAA
1 AATTAATAAATATTTTA-TATTTAA
* **
31829318 TATTTGTAAATATTTCTATAT
1 AATTAATAAATATTT-TATAT
31829339 ATATATATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.17
24 20 0.57
25 7 0.20
26 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTAATAAATATTTTATATTTAA
Found at i:31831030 original size:16 final size:16
Alignment explanation
Indices: 31831009--31831061 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
31830999 TTGATTCACT
31831009 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
* *
31831025 GTAATGGAATAAATGC
1 GTAATGGAATAGAGGC
*
31831041 GTAATAGAATAGAGGC
1 GTAATGGAATAGAGGC
31831057 GTAAT
1 GTAAT
31831062 AGGTAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.42, C:0.06, G:0.30, T:0.23
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:31831385 original size:15 final size:16
Alignment explanation
Indices: 31831365--31831394 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31831355 AAACATAATT
31831365 TAATAAA-ATTCTTAA
1 TAATAAATATTCTTAA
31831380 TAATAAATATTCTTA
1 TAATAAATATTCTTA
31831395 TATGAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATAAATATTCTTAA
Found at i:31833211 original size:24 final size:27
Alignment explanation
Indices: 31833160--31833212 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
31833150 TATGTGTAAT
*
31833160 ATTATTAAAATAATATTTTTTATTTTA
1 ATTATTAAAATAATATTTTTTATATTA
*
31833187 ATTATTTAAA-AATA-TTTTTA-ATTA
1 ATTATTAAAATAATATTTTTTATATTA
31833211 AT
1 AT
31833213 GTGGTGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.21
25 6 0.25
26 4 0.17
27 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATTATTAAAATAATATTTTTTATATTA
Found at i:31838278 original size:14 final size:14
Alignment explanation
Indices: 31838259--31838286 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
31838249 GGGATGGGTT
31838259 GAATTTTGTTAAAA
1 GAATTTTGTTAAAA
31838273 GAATTTTGTTAAAA
1 GAATTTTGTTAAAA
31838287 TAATATATAT
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:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (14 bp):
GAATTTTGTTAAAA
Found at i:31843084 original size:3 final size:3
Alignment explanation
Indices: 31843076--31843134 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
31843066 TAATATATGT
* *
31843076 ATA ATA ATA ATA ATA AT- ATA AT- ATA ATA ATA ATAA ATG CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
*
31843120 ATA AT- ATA GTA ATA A
1 ATA ATA ATA ATA ATA A
31843135 ACAATTTAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 6 0.13
3 37 0.80
4 3 0.07
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31843103 original size:16 final size:17
Alignment explanation
Indices: 31843075--31843134 Score: 79
Period size: 16 Copynumber: 3.6 Consensus size: 17
31843065 ATAATATATG
31843075 TATAATAATAATAATAA
1 TATAATAATAATAATAA
31843092 TATAAT-ATAATAATAA
1 TATAATAATAATAATAA
**
31843108 TA-AATGCTAATAATAA
1 TATAATAATAATAATAA
*
31843124 TATAGTAATAA
1 TATAATAATAA
31843135 ACAATTTAAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 3 0.08
16 23 0.62
17 11 0.30
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (17 bp):
TATAATAATAATAATAA
Found at i:31843120 original size:19 final size:20
Alignment explanation
Indices: 31843076--31843125 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
31843066 TAATATATGT
31843076 ATAATAATAATAATAATATA
1 ATAATAATAATAATAATATA
*
31843096 AT-ATAATAATAATAA-ATG
1 ATAATAATAATAATAATATA
*
31843114 CTAATAATAATA
1 ATAATAATAATA
31843126 TAGTAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 3 0.11
19 22 0.81
20 2 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
ATAATAATAATAATAATATA
Found at i:31847805 original size:18 final size:18
Alignment explanation
Indices: 31847790--31847825 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31847780 TACCCTTCTT
31847790 CTCCCCTTTCCCCTTCCC
1 CTCCCCTTTCCCCTTCCC
*
31847808 CTTCCCTTTCCCCTTCCC
1 CTCCCCTTTCCCCTTCCC
31847826 TTTGGGTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (18 bp):
CTCCCCTTTCCCCTTCCC
Found at i:31847818 original size:12 final size:12
Alignment explanation
Indices: 31847791--31847828 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
31847781 ACCCTTCTTC
*
31847791 TCCCCTTTCCCCT
1 TCCCC-TTCCCTT
31847804 TCCCCTTCCCTT
1 TCCCCTTCCCTT
31847816 TCCCCTTCCCTT
1 TCCCCTTCCCTT
31847828 T
1 T
31847829 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 19 0.79
13 5 0.21
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (12 bp):
TCCCCTTCCCTT
Found at i:31847827 original size:5 final size:6
Alignment explanation
Indices: 31847791--31847825 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
31847781 ACCCTTCTTC
*
31847791 TCCCCTT TCCCCT TCCCCT TCCCTT TCCCCT TCCC
1 TCCCC-T TCCCCT TCCCCT TCCCCT TCCCCT TCCC
31847826 TTTGGGTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (6 bp):
TCCCCT
Found at i:31851236 original size:12 final size:12
Alignment explanation
Indices: 31851206--31851238 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
31851196 ATGCAACAGG
31851206 AAACCAGCA-GC
1 AAACCAGCATGC
31851217 AAACCAGCATGC
1 AAACCAGCATGC
*
31851229 AGACCAGCAT
1 AAACCAGCAT
31851239 CCAAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:31852223 original size:21 final size:21
Alignment explanation
Indices: 31852199--31852251 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31852189 CGCTGTTTTT
*
31852199 AATCTCACTGCTACAATATCG
1 AATCTCACTGCTACAATAACG
* * * *
31852220 AATCTTACCGCTACAGTAACT
1 AATCTCACTGCTACAATAACG
31852241 AATCTCACTGC
1 AATCTCACTGC
31852252 CACCGCTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.30, G:0.09, T:0.28
Consensus pattern (21 bp):
AATCTCACTGCTACAATAACG
Found at i:31853868 original size:18 final size:16
Alignment explanation
Indices: 31853838--31853884 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
31853828 GTTGATATAT
31853838 ATATATAAAATTTAAC
1 ATATATAAAATTTAAC
*
31853854 ATATATAAATCATTTAAA
1 ATATATAAA--ATTTAAC
*
31853872 AAATA-AAAATTTA
1 ATATATAAAATTTA
31853885 TTAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 3 0.11
18 10 0.37
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
ATATATAAAATTTAAC
Found at i:31857635 original size:3 final size:3
Alignment explanation
Indices: 31857627--31857669 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
31857617 TCGTTTACTC
31857627 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
31857670 ACAAGTATTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:31858661 original size:109 final size:108
Alignment explanation
Indices: 31858447--31858875 Score: 540
Period size: 111 Copynumber: 3.9 Consensus size: 108
31858437 AAAATTCAAG
* *
31858447 AGGATATTTGGCTATTTGGTTAAACGAG-AAATCGAAACCCAGCACATTAGGGCATG-TTCCTCG
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
* *
31858510 AATTTCCAAACGCAAAATATAGTCTTACTTT-GAAAATTTTTTTGAA
66 AATTTCCAAACGCAAAATATTGCCTTA-TTTAG-AAA--TTTTTGAA
31858556 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
*
31858621 GAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATTTTTGAA
65 GAATTTCCAAACGCAAAATATTGCCTTATTTAGAAATTTTTGAA
* * * * * * *
31858665 AGTATATTTGGCTATTTAGTTGAACGAGAAAGTCGAAACCTAGCACATTAGGCCACATTTTCTCG
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
* *
31858730 AATTTCCAAACGCAAAATATTACCTTACTTTGAGAAATTTTTAAA
66 AATTTCCAAACGCAAAATATTGCCTTA-TTT-AGAAATTTTTGAA
* ** * * ** **
31858775 AGGATACTCAGTTATTTGGTTGAACGAGAAAAATCGAAACCCAGTACATTACAGCACGTTTTTTC
1 AGGATATTTGGCTATTTGGTTGAACGAG-AAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* *
31858840 GAATTTCCAAACGCTAAATATTGCCTCATTTAGAAA
65 GAATTTCCAAACGCAAAATATTGCCTTATTTAGAAA
31858876 AACTTTCCTT
Statistics
Matches: 282, Mismatches: 31, Indels: 14
0.86 0.09 0.04
Matches are distributed among these distances:
108 58 0.21
109 69 0.24
110 36 0.13
111 86 0.30
112 33 0.12
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (108 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCG
AATTTCCAAACGCAAAATATTGCCTTATTTAGAAATTTTTGAA
Found at i:31858834 original size:219 final size:217
Alignment explanation
Indices: 31858450--31858875 Score: 606
Period size: 219 Copynumber: 1.9 Consensus size: 217
31858440 ATTCAAGAGG
* *
31858450 ATATTTGGCTATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGGCATGTTCCTCGAATTT
1 ATATTTGGCTATTTAGTTAAACGAGAAATCGAAACCCAGCACATTAGGACATGTTCCTCGAATTT
* * * **
31858515 CCAAACGCAAAATATAGTCTTACTTTGAAAATTTTTTTGAAAGGATATTTGGCTATTTGGTTGAA
66 CCAAACGCAAAATATAGCCTTACTTTGAAAA-TTTTTTAAAAGGATACTCAGCTATTTGGTTGAA
**
31858580 CGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTCGAATTTCCAAACGCAAAATATTGC
130 CGAGAAAAATCGAAACCCAGCACATTACAGCACGTTTCCTCGAATTTCCAAACGCAAAATATTGC
* *
31858645 CTTATTTTGAAATTTTTGAAAGT
195 CTCATTTAGAAATTTTTGAAAGT
* * *
31858668 ATATTTGGCTATTTAGTTGAACGAGAAAGTCGAAACCTAGCACATTAGGCCACAT-TTTCTCGAA
1 ATATTTGGCTATTTAGTTAAACGAGAAA-TCGAAACCCAGCACATTAGG--ACATGTTCCTCGAA
*
31858732 TTTCCAAACGCAAAATATTA-CCTTACTTTGAGAAA-TTTTTAAAAGGATACTCAGTTATTTGGT
63 TTTCCAAACGCAAAATA-TAGCCTTACTTTGA-AAATTTTTTAAAAGGATACTCAGCTATTTGGT
* ** *
31858795 TGAACGAGAAAAATCGAAACCCAGTACATTACAGCACGTTTTTTCGAATTTCCAAACGCTAAATA
126 TGAACGAGAAAAATCGAAACCCAGCACATTACAGCACGTTTCCTCGAATTTCCAAACGCAAAATA
31858860 TTGCCTCATTTAGAAA
191 TTGCCTCATTTAGAAA
31858876 AACTTTCCTT
Statistics
Matches: 184, Mismatches: 19, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
218 26 0.14
219 115 0.62
220 35 0.19
221 8 0.04
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (217 bp):
ATATTTGGCTATTTAGTTAAACGAGAAATCGAAACCCAGCACATTAGGACATGTTCCTCGAATTT
CCAAACGCAAAATATAGCCTTACTTTGAAAATTTTTTAAAAGGATACTCAGCTATTTGGTTGAAC
GAGAAAAATCGAAACCCAGCACATTACAGCACGTTTCCTCGAATTTCCAAACGCAAAATATTGCC
TCATTTAGAAATTTTTGAAAGT
Found at i:31858926 original size:21 final size:20
Alignment explanation
Indices: 31858902--31858946 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
31858892 GTATGGTGTT
31858902 AATATACATAATG-GAATAATA
1 AATAT-CATAATGTGAATAA-A
*
31858923 AATATGATAATGTGAATAAA
1 AATATCATAATGTGAATAAA
31858943 AATA
1 AATA
31858947 ATATGAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (20 bp):
AATATCATAATGTGAATAAA
Found at i:31858934 original size:20 final size:20
Alignment explanation
Indices: 31858909--31858946 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31858899 GTTAATATAC
31858909 ATAATG-GAATAATAAATATG
1 ATAATGTGAATAA-AAATATG
31858929 ATAATGTGAATAAAAATA
1 ATAATGTGAATAAAAATA
31858947 ATATGAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (20 bp):
ATAATGTGAATAAAAATATG
Found at i:31859006 original size:4 final size:4
Alignment explanation
Indices: 31858997--31859062 Score: 57
Period size: 4 Copynumber: 17.0 Consensus size: 4
31858987 TACCATAACA
* * *
31858997 AAAT AAAT AAAT AAAT AAAT AAAT AAACT AAA- ACAT -AA- AAAT GAAC
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT AAAT AAAT AAAT AAAT
* *
31859043 ATAT AAAT AAAT ACAT AAAT
1 AAAT AAAT AAAT AAAT AAAT
31859063 GAACATAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
3 5 0.10
4 39 0.81
5 4 0.08
ACGTcount: A:0.70, C:0.06, G:0.02, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:31859048 original size:26 final size:24
Alignment explanation
Indices: 31858999--31859080 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
31858989 CCATAACAAA
*
31858999 ATAAATAAATAAATAAAT-AA-AT
1 ATAAATAAATACATAAATGAACAT
*
31859021 A-AACTAAA-ACATAAAAATGAACAT
1 ATAAATAAATACAT--AAATGAACAT
31859045 ATAAATAAATACATAAATGAACAT
1 ATAAATAAATACATAAATGAACAT
*
31859069 AAAAATACAATA
1 ATAAATA-AATA
31859081 AAGGAAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
20 3 0.06
21 6 0.12
22 5 0.10
23 2 0.04
24 19 0.39
25 10 0.20
26 4 0.08
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.22
Consensus pattern (24 bp):
ATAAATAAATACATAAATGAACAT
Found at i:31859074 original size:12 final size:12
Alignment explanation
Indices: 31859028--31859074 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
31859018 AATAAACTAA
31859028 AACATAAAAATG
1 AACATAAAAATG
*
31859040 AACATATAAAT-
1 AACATAAAAATG
31859051 AA-ATACATAAATG
1 AACATA-A-AAATG
31859064 AACATAAAAAT
1 AACATAAAAAT
31859075 ACAATAAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 3 0.10
11 2 0.07
12 18 0.62
13 3 0.10
14 3 0.10
ACGTcount: A:0.66, C:0.09, G:0.04, T:0.21
Consensus pattern (12 bp):
AACATAAAAATG
Found at i:31859338 original size:2 final size:2
Alignment explanation
Indices: 31859331--31859371 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
31859321 AACAATGTGC
*
31859331 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31859372 CTTATACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:31859593 original size:3 final size:3
Alignment explanation
Indices: 31859578--31859659 Score: 64
Period size: 3 Copynumber: 28.7 Consensus size: 3
31859568 AAAAGGTATT
* * ** *
31859578 TAA TAA TAT TAA TAA TGA TGC TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
31859626 TTT TAA TAA TAA T-A TGA -AA TAA TAA -AA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
31859660 GCATATATTA
Statistics
Matches: 64, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 7 0.11
3 57 0.89
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31859745 original size:6 final size:5
Alignment explanation
Indices: 31859699--31859744 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
31859689 ATATAAAGAT
*
31859699 AAATGA AAATA TAAATA AAACAA AAATA AAATA AAATA AAATA AAA
1 AAAT-A AAATA -AAATA AAA-TA AAATA AAATA AAATA AAATA AAA
31859745 ACGCAAGGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 23 0.64
6 13 0.36
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (5 bp):
AAATA
Found at i:31860722 original size:13 final size:11
Alignment explanation
Indices: 31860690--31860714 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31860680 GAAAATTTTG
31860690 TTGTTTCTGAT
1 TTGTTTCTGAT
31860701 TTGTTTCTGAT
1 TTGTTTCTGAT
31860712 TTG
1 TTG
31860715 AGTTTCTGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (11 bp):
TTGTTTCTGAT
Found at i:31861373 original size:13 final size:12
Alignment explanation
Indices: 31861351--31861398 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
31861341 AAAATAAAAT
31861351 CAATAATAATAA
1 CAATAATAATAA
31861363 CAATGAATAATAA
1 CAAT-AATAATAA
* *
31861376 CAACAATAAAAA
1 CAATAATAATAA
*
31861388 TAATAA-AATAA
1 CAATAATAATAA
31861399 ACACATAACA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
11 4 0.13
12 15 0.50
13 11 0.37
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (12 bp):
CAATAATAATAA
Found at i:31861550 original size:12 final size:12
Alignment explanation
Indices: 31861532--31861566 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
31861522 AGTTGTAGTA
31861532 ATAATAATAATG
1 ATAATAATAATG
*
31861544 GTAATAATAATG
1 ATAATAATAATG
31861556 ATAATAATAAT
1 ATAATAATAAT
31861567 ATATAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (12 bp):
ATAATAATAATG
Found at i:31861589 original size:3 final size:3
Alignment explanation
Indices: 31861530--31861572 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
31861520 AAAGTTGTAG
** *
31861530 TAA TAA TAA TAA TGG TAA TAA TAA TGA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
31861573 AAAAACGACA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31863987 original size:24 final size:24
Alignment explanation
Indices: 31863957--31864025 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
31863947 TATTTTATTT
31863957 AATTAATAAATATTTTATATTTAA
1 AATTAATAAATATTTTATATTTAA
**
31863981 AATTAATCTA-ATTTTATTATTTAA
1 AATTAATAAATATTTTA-TATTTAA
* **
31864005 TATTTGTAAATATTTCTATAT
1 AATTAATAAATATTT-TATAT
31864026 ACATATATCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
23 6 0.17
24 20 0.57
25 7 0.20
26 2 0.06
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (24 bp):
AATTAATAAATATTTTATATTTAA
Found at i:31872678 original size:40 final size:40
Alignment explanation
Indices: 31872634--31872743 Score: 159
Period size: 40 Copynumber: 2.8 Consensus size: 40
31872624 AAAAAGCGTC
*
31872634 CTAAAGATCGAGCATTAGCGGCGCTTTTTGGAAAACGCCG
1 CTAAAGATCGAGCATTAGTGGCGCTTTTTGGAAAACGCCG
* *
31872674 CTAAAGATCGAGTATTAGTGGCGCTTTATGGAAAACGCCG
1 CTAAAGATCGAGCATTAGTGGCGCTTTTTGGAAAACGCCG
* * *
31872714 CTAAAAAT-AAGCATTAGTGGCGTTTTTTGG
1 CTAAAGATCGAGCATTAGTGGCGCTTTTTGG
31872744 GAAGTGCCGC
Statistics
Matches: 62, Mismatches: 8, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
39 18 0.29
40 44 0.71
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.27
Consensus pattern (40 bp):
CTAAAGATCGAGCATTAGTGGCGCTTTTTGGAAAACGCCG
Found at i:31873111 original size:29 final size:29
Alignment explanation
Indices: 31873074--31873202 Score: 113
Period size: 29 Copynumber: 4.5 Consensus size: 29
31873064 GTGTTACCAT
* *
31873074 TTTAAGGTTTATGGATTATGGGTTTAGGG
1 TTTATGGTTTATGGGTTATGGGTTTAGGG
* * * *
31873103 GTTATGGTTTATGGTTTAAGGG-CTAGGG
1 TTTATGGTTTATGGGTTATGGGTTTAGGG
* * *
31873131 TTTAAGGTTTA-GAGGTTATGTGTTAAGGG
1 TTTATGGTTTATG-GGTTATGGGTTTAGGG
*
31873160 TTTATGGTTT-TAGGGTTTTAGGGTTTA-GG
1 TTTATGGTTTAT-GGGTTAT-GGGTTTAGGG
31873189 TTTATGGTTTATGG
1 TTTATGGTTTATGG
31873203 TTTAGATTAA
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
27 1 0.01
28 20 0.26
29 50 0.64
30 7 0.09
ACGTcount: A:0.19, C:0.01, G:0.35, T:0.46
Consensus pattern (29 bp):
TTTATGGTTTATGGGTTATGGGTTTAGGG
Found at i:31873113 original size:14 final size:14
Alignment explanation
Indices: 31873074--31873206 Score: 99
Period size: 14 Copynumber: 9.3 Consensus size: 14
31873064 GTGTTACCAT
* *
31873074 TTTAAGGTTTATGG
1 TTTATGGTTTAGGG
*
31873088 ATTATGGGTTTAGGG
1 TTTAT-GGTTTAGGG
* *
31873103 GTTATGGTTTATGG
1 TTTATGGTTTAGGG
* **
31873117 TTTAAGGGCTAGGG
1 TTTATGGTTTAGGG
*
31873131 TTTAAGGTTTAGAGG
1 TTTATGGTTTAG-GG
*
31873146 -TTATGTGTTAAGGG
1 TTTATG-GTTTAGGG
31873160 TTTATGGTTTTAGGG
1 TTTATGG-TTTAGGG
*
31873175 TTTTAGGGTTTA-GG
1 -TTTATGGTTTAGGG
*
31873189 TTTATGGTTTATGG
1 TTTATGGTTTAGGG
31873203 TTTA
1 TTTA
31873207 GATTAACTAT
Statistics
Matches: 95, Mismatches: 17, Indels: 14
0.75 0.13 0.11
Matches are distributed among these distances:
13 10 0.11
14 45 0.47
15 34 0.36
16 6 0.06
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.47
Consensus pattern (14 bp):
TTTATGGTTTAGGG
Found at i:31873116 original size:7 final size:7
Alignment explanation
Indices: 31873074--31873206 Score: 81
Period size: 7 Copynumber: 18.6 Consensus size: 7
31873064 GTGTTACCAT
*
31873074 TTTAAGG
1 TTTATGG
31873081 TTTATGG
1 TTTATGG
*
31873088 ATTATGGG
1 TTTAT-GG
*
31873096 TTTAGGG
1 TTTATGG
*
31873103 GTTATGG
1 TTTATGG
31873110 TTTATGG
1 TTTATGG
*
31873117 TTTAAGG
1 TTTATGG
** *
31873124 GCTAGGG
1 TTTATGG
*
31873131 TTTAAGG
1 TTTATGG
31873138 TTTA-GAG
1 TTTATG-G
*
31873145 GTTATGTG
1 TTTATG-G
* *
31873153 TTAAGGG
1 TTTATGG
31873160 TTTATGG
1 TTTATGG
*
31873167 TTTTAGGG
1 -TTTATGG
*
31873175 TTTTAGGG
1 -TTTATGG
31873183 TTTA-GG
1 TTTATGG
31873189 TTTATGG
1 TTTATGG
31873196 TTTATGG
1 TTTATGG
31873203 TTTA
1 TTTA
31873207 GATTAACTAT
Statistics
Matches: 99, Mismatches: 22, Indels: 10
0.76 0.17 0.08
Matches are distributed among these distances:
6 7 0.07
7 68 0.69
8 24 0.24
ACGTcount: A:0.19, C:0.01, G:0.34, T:0.47
Consensus pattern (7 bp):
TTTATGG
Found at i:31873778 original size:10 final size:12
Alignment explanation
Indices: 31873750--31873782 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31873740 CGTGATTTAA
31873750 AATTTTAAAATG
1 AATTTTAAAATG
31873762 AATTTTAAAA-G
1 AATTTTAAAATG
31873773 -ATTTTAAAAT
1 AATTTTAAAAT
31873783 TTTTTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 9 0.45
11 1 0.05
12 10 0.50
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (12 bp):
AATTTTAAAATG
Found at i:31876720 original size:43 final size:43
Alignment explanation
Indices: 31876670--31876917 Score: 327
Period size: 43 Copynumber: 5.8 Consensus size: 43
31876660 AGATTATGTT
* ** * *
31876670 TTTAGCGGCGTTTTTGCTAGAAGCGCCGCTAAAGGTCATGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* ** * * *
31876713 TATAGCGGCGTTTGTGATAAAAGTGCCACTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
31876756 TTTAGCGGCATTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
31876799 TTTAGCGGCGTTTGTAGGAAAAGCGCCGCTAAAGGTC-TGAGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTG-GTC
* * *
31876842 TTTAACGACGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
31876885 TTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAA
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAA
31876918 AGCCGGTTTT
Statistics
Matches: 179, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
42 2 0.01
43 175 0.98
44 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:31877214 original size:7 final size:7
Alignment explanation
Indices: 31877202--31877232 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
31877192 ATCATTACTT
31877202 AATATTC
1 AATATTC
31877209 AATATTC
1 AATATTC
31877216 AATATTC
1 AATATTC
31877223 AATATTC
1 AATATTC
31877230 AAT
1 AAT
31877233 TGATCATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.13, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:31890722 original size:32 final size:32
Alignment explanation
Indices: 31890681--31890757 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
31890671 GACACGACCG
* * *
31890681 TGTGGGCCACACGGGCTAGGTCAAGT-TGGGCA
1 TGTGGGCCACACAGGCAAGGCCAA-TCTGGGCA
* *
31890713 TGTGCGCCACACAGGCAAGGCCAATCTGGGCG
1 TGTGGGCCACACAGGCAAGGCCAATCTGGGCA
31890745 TGTGGGCCACACA
1 TGTGGGCCACACA
31890758 TGCGTATGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.03
32 37 0.97
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.16
Consensus pattern (32 bp):
TGTGGGCCACACAGGCAAGGCCAATCTGGGCA
Found at i:31893066 original size:18 final size:18
Alignment explanation
Indices: 31893043--31893080 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
31893033 ATCCCAATGA
31893043 TCGCCAGCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
31893061 TCGCCAGCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
31893079 TC
1 TC
31893081 ACCACCAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.45, G:0.11, T:0.34
Consensus pattern (18 bp):
TCGCCAGCACCTTCTTCT
Found at i:31893873 original size:3 final size:3
Alignment explanation
Indices: 31893865--31893893 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31893855 TCTTAATACT
31893865 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
31893894 TAATAATAAT
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:31893984 original size:19 final size:21
Alignment explanation
Indices: 31893960--31893998 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
31893950 AGTAAAACAA
*
31893960 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
31893979 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
31893999 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:31894204 original size:27 final size:26
Alignment explanation
Indices: 31894131--31894196 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
31894121 AATACGAGTA
*
31894131 GTGCCGCCAATCAATACGGCACCATTG
1 GTGCCGCCAATCAAT-TGGCACCATTG
**
31894158 GTGCCGCCAATGGTATTGGCACCATTG
1 GTGCCGCCAAT-CAATTGGCACCATTG
31894185 GTGCCGCCAATC
1 GTGCCGCCAATC
31894197 CCATTGGCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.21, C:0.32, G:0.26, T:0.21
Consensus pattern (26 bp):
GTGCCGCCAATCAATTGGCACCATTG
Found at i:31895388 original size:17 final size:17
Alignment explanation
Indices: 31895354--31895388 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31895344 AATTTTAAAA
*
31895354 TATTTTTAAAATACTTT
1 TATTTTTAAAATAATTT
*
31895371 TATTTTTAAATTAATTT
1 TATTTTTAAAATAATTT
31895388 T
1 T
31895389 TTGGTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTAAAATAATTT
Found at i:31900681 original size:2 final size:2
Alignment explanation
Indices: 31900674--31900707 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
31900664 TCTATCTATC
31900674 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
31900708 TTATGCTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31901856 original size:23 final size:23
Alignment explanation
Indices: 31901795--31901883 Score: 114
Period size: 23 Copynumber: 4.0 Consensus size: 23
31901785 ACCTGATCAG
31901795 TATACGACACAT-AAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
** *
31901817 -A-ACGAC-CACGAGGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
31901837 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
31901860 GATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
31901883 T
1 T
31901884 CGGCAAGGCC
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.04
20 14 0.25
21 2 0.04
22 5 0.09
23 33 0.59
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:31902830 original size:22 final size:22
Alignment explanation
Indices: 31902805--31902852 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31902795 TCTTCCCCTG
*
31902805 TTTTC-GTCTCTTTCTCTGTTTC
1 TTTTCTGT-TCTTCCTCTGTTTC
*
31902827 TTTTCTGTTCTTCCTTTGTTTC
1 TTTTCTGTTCTTCCTCTGTTTC
31902849 TTTT
1 TTTT
31902853 TTCTTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (22 bp):
TTTTCTGTTCTTCCTCTGTTTC
Found at i:31902906 original size:3 final size:3
Alignment explanation
Indices: 31902898--31902980 Score: 132
Period size: 3 Copynumber: 27.7 Consensus size: 3
31902888 ATGCATTAGT
31902898 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
31902946 TAA TAA TAA TATA TTA TAA TAA TCA T-A TAA TAA TA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
31902981 TTTTATTCAC
Statistics
Matches: 75, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
2 2 0.03
3 71 0.95
4 2 0.03
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:31903152 original size:30 final size:27
Alignment explanation
Indices: 31903111--31903175 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 27
31903101 TTTCCTATAA
*
31903111 TATATTATTTTAATTTTAATTAATATAATT
1 TATAATATTTTAA-TTTAA-TAATAT-ATT
*
31903141 TATAATATTTTAATTTAATAATATTTT
1 TATAATATTTTAATTTAATAATATATT
31903168 TATAATAT
1 TATAATAT
31903176 AAATCAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 10 0.30
28 6 0.18
29 5 0.15
30 12 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATAATATTTTAATTTAATAATATATT
Found at i:31903158 original size:25 final size:26
Alignment explanation
Indices: 31903123--31903175 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
31903113 TATTATTTTA
31903123 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
31903147 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
31903174 AT
1 AT
31903176 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:31903161 original size:16 final size:16
Alignment explanation
Indices: 31903116--31903167 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
31903106 TATAATATAT
31903116 TATTTTAATTTTAATTAA
1 TATTTTAA-TTTAA-TAA
31903134 TA---TAATTT-ATAA
1 TATTTTAATTTAATAA
31903146 TATTTTAATTTAATAA
1 TATTTTAATTTAATAA
31903162 TATTTT
1 TATTTT
31903168 TATAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 3 0.10
15 9 0.30
16 10 0.33
18 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTAATTTAATAA
Found at i:31904244 original size:19 final size:20
Alignment explanation
Indices: 31904217--31904259 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31904207 ATTTCATATA
*
31904217 TAAATTAATA-AATATTTTT
1 TAAAATAATATAATATTTTT
*
31904236 TAAAATAATATAATTTTTTT
1 TAAAATAATATAATATTTTT
31904256 TAAA
1 TAAA
31904260 TTTCATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAAATAATATAATATTTTT
Found at i:31904260 original size:19 final size:19
Alignment explanation
Indices: 31904217--31904260 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
31904207 ATTTCATATA
31904217 TAAATTAATAAATATTTTTT
1 TAAA-TAATAAATATTTTTT
*
31904237 AAAATAATATAAT-TTTTTT
1 TAAATAATA-AATATTTTTT
31904256 TAAAT
1 TAAAT
31904261 TTCATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATAATAAATATTTTTT
Found at i:31906758 original size:2 final size:2
Alignment explanation
Indices: 31906751--31906784 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
31906741 CATGTCTGTC
31906751 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
31906785 TTATGCTCAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31907459 original size:90 final size:93
Alignment explanation
Indices: 31907238--31907461 Score: 269
Period size: 96 Copynumber: 2.4 Consensus size: 93
31907228 CTTTCTGATT
* * * *
31907238 AATTTTAG-TTTTATACATTATGAATTGGTTCAATTTAATTCCTTTAATTTGAAGTTTTAAAATT
1 AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAATTCCTTTAATTGGAAGTTTTAAAATT
* * *
31907302 GTAATCTTGGTATTTGTATTTTAATTTGGTT
66 GTAATCTT-GTA--TATATTTTAATTTAGTC
* * *
31907333 AATTTTAATTCTTATACTTTTCGAATTGGTTAAATTTAATT-CTTGTAATTGGAAGTTTTAAAAT
1 AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAATTCCTT-TAATTGGAAGTTTTAAAAT
*
31907397 TGTAGTC-T-TA-ATATTTTAATTTAGTC
65 TGTAATCTTGTATATATTTTAATTTAGTC
*
31907423 AATTTTAGTTTTTATACTTTTTGAATTAGTTAAATTTAA
1 AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAA
31907462 ACCTAAACAA
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
90 48 0.43
93 2 0.02
95 11 0.10
96 51 0.46
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.53
Consensus pattern (93 bp):
AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAATTCCTTTAATTGGAAGTTTTAAAATT
GTAATCTTGTATATATTTTAATTTAGTC
Found at i:31909789 original size:27 final size:30
Alignment explanation
Indices: 31909745--31909801 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
31909735 ATAATCATAA
*
31909745 TTTAATTCACTTTTATTCAAT-TC-ATATT
1 TTTAATTCACTTTAATTCAATATCGATATT
31909773 TTTAATTCA-TTTAATTCAATATCGATATT
1 TTTAATTCACTTTAATTCAATATCGATATT
31909802 CACCTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 11 0.42
29 5 0.19
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTAATTCACTTTAATTCAATATCGATATT
Found at i:31910551 original size:13 final size:13
Alignment explanation
Indices: 31910533--31910573 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
31910523 CTCAATTTTC
31910533 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
31910546 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
* *
31910559 TC-CTTCTTTCCT
1 TCTTTTCTTTCTT
31910571 TCT
1 TCT
31910574 CTGTTTCGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:31910786 original size:3 final size:3
Alignment explanation
Indices: 31910778--31910851 Score: 54
Period size: 3 Copynumber: 26.0 Consensus size: 3
31910768 TATTTAAAAT
31910778 ATA ATA AT- ATA ATA AT- ATA ATA AT- ATA ATA AT- ATA AT- ATA ATTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* *
31910822 AT- ATA ATTT ACA AT- ATA ATAA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA AT-A ATA ATA ATA
31910852 TACTTCAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
2 14 0.25
3 35 0.61
4 8 0.14
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:31910788 original size:8 final size:8
Alignment explanation
Indices: 31910775--31910853 Score: 92
Period size: 8 Copynumber: 9.8 Consensus size: 8
31910765 GTTTATTTAA
31910775 AATATAAT
1 AATATAAT
31910783 AATATAAT
1 AATATAAT
31910791 AATATAAT
1 AATATAAT
31910799 AATATAAT
1 AATATAAT
31910807 AATATAAT
1 AATATAAT
*
31910815 -ATA-ATT
1 AATATAAT
31910821 AATATAATTT
1 AATATAA--T
31910831 ACAATATAAT
1 --AATATAAT
31910841 AA-ATAAT
1 AATATAAT
31910848 AATATA
1 AATATA
31910854 CTTCAAAAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
6 2 0.03
7 13 0.21
8 38 0.61
10 2 0.03
12 7 0.11
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (8 bp):
AATATAAT
Found at i:31910789 original size:5 final size:5
Alignment explanation
Indices: 31910775--31910853 Score: 58
Period size: 5 Copynumber: 15.2 Consensus size: 5
31910765 GTTTATTTAA
31910775 AATAT AATA- ATATAAT AATAT AATA- ATATAAT AATAT AATAT AAT-T
1 AATAT AATAT A-AT-AT AATAT AATAT A-AT-AT AATAT AATAT AATAT
*
31910821 AATAT AATTTAC AATAT AATA- AATAAT AATAT A
1 AATAT AA--TAT AATAT AATAT AAT-AT AATAT A
31910854 CTTCAAAAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
4 9 0.15
5 37 0.61
6 9 0.15
7 6 0.10
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (5 bp):
AATAT
Found at i:31910805 original size:21 final size:21
Alignment explanation
Indices: 31910781--31910848 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
31910771 TTAAAATATA
31910781 ATAATATAATAATATAATAAT
1 ATAATATAATAATATAATAAT
31910802 ATAATA-ATATAATATAATTAAT
1 ATAATATA-ATAATATAA-TAAT
* *
31910824 ATAAT-TTACAATATAATAA-
1 ATAATATAATAATATAATAAT
31910843 ATAATA
1 ATAATA
31910849 ATATACTTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
19 5 0.12
20 4 0.10
21 23 0.56
22 9 0.22
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATATAATAATATAATAAT
Found at i:31912446 original size:12 final size:12
Alignment explanation
Indices: 31912425--31912461 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
31912415 ATTCCAAAGA
*
31912425 TGAAAGCTTGAT
1 TGAAAACTTGAT
31912437 TGAAAACTTGAT
1 TGAAAACTTGAT
*
31912449 TAAAAACTTGAT
1 TGAAAACTTGAT
31912461 T
1 T
31912462 ATTAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (12 bp):
TGAAAACTTGAT
Found at i:31915126 original size:19 final size:21
Alignment explanation
Indices: 31915102--31915140 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
31915092 TTTTAAAGTA
31915102 ATATTGATAA-AA-TTAAAAC
1 ATATTGATAATAATTTAAAAC
31915121 ATATTGATAATAATTTAAAA
1 ATATTGATAATAATTTAAAA
31915141 AAATAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
ATATTGATAATAATTTAAAAC
Found at i:31917507 original size:31 final size:29
Alignment explanation
Indices: 31917469--31917545 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
31917459 CTAACGGCTC
* *
31917469 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
31917500 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
31917529 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
31917546 CTGAGCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:31923012 original size:22 final size:23
Alignment explanation
Indices: 31922970--31923017 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
31922960 TTTCTAAATT
31922970 TAGATAGAATACTCTAAAAAACTG
1 TAGATAGAATACTCT-AAAAACTG
31922994 TAGATAGAACT-CTCT-AAAACTG
1 TAGATAGAA-TACTCTAAAAACTG
31923016 TA
1 TA
31923018 CTAAGTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.39
24 13 0.57
25 1 0.04
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (23 bp):
TAGATAGAATACTCTAAAAACTG
Found at i:31931882 original size:40 final size:40
Alignment explanation
Indices: 31931820--31931900 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
31931810 ATTTTTTCAA
* *
31931820 GTATATTTTAATTTTGGCAACTTTGACAACCGTACACTCC
1 GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
*
31931860 GTATGTTTTAATTTTGGAAACTTTGACAACAGTACACTCC
1 GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
31931900 G
1 G
31931901 CAATGAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (40 bp):
GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
Found at i:31933810 original size:108 final size:110
Alignment explanation
Indices: 31933543--31933852 Score: 453
Period size: 108 Copynumber: 2.8 Consensus size: 110
31933533 GAAATTCAAG
* * *
31933543 AGGATATTTTGCTATTTGGTTAAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* **
31933608 GAATTTCCCAAATGCAAAACATTGCCTTATTTCGAATTTTTTTAAA
66 GAATTT-CCAAACGCAAAACATTGCCTTATTTCGAATAATTTTAAA
* * * *
31933654 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAACACCTTAGGGCATGTTTCCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* * *
31933719 GAATTTTCAAACGCAAAACATTGCCTTATTT-TAA-AATTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTCGAATAATTTTAAA
*
31933762 AGGATATTTAGCTATTTTGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
31933827 GAATTTCCAAACGCTAAATATTGCCT
66 GAATTTCCAAACGCAAAACATTGCCT
31933853 CAATTAGAAA
Statistics
Matches: 178, Mismatches: 21, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
108 89 0.50
109 2 0.01
110 23 0.13
111 64 0.36
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (110 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTCGAATAATTTTAAA
Found at i:31934491 original size:3 final size:3
Alignment explanation
Indices: 31934475--31934535 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
31934465 AAAATAAAAT
* * * * *
31934475 TAA TAA TAGT TAA TAA TAG TAA TAA TAA TGA TAA TAA CAC TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31934521 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
31934536 ACTAAATAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 45 0.96
4 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31938487 original size:41 final size:41
Alignment explanation
Indices: 31938430--31938512 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
31938420 CTACATAGAG
*
31938430 AGCCATGCTTGTTGACACGGGATACATGGTATAAAATCGCC
1 AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
31938471 AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
1 AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
31938512 A
1 A
31938513 TGGGAGTGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (41 bp):
AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
Found at i:31947409 original size:17 final size:17
Alignment explanation
Indices: 31947387--31947420 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
31947377 CAATTTTGAC
31947387 TATATAAAATCTAAAAT
1 TATATAAAATCTAAAAT
*
31947404 TATATAACATCTAAAAT
1 TATATAAAATCTAAAAT
31947421 ATACATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
TATATAAAATCTAAAAT
Found at i:31950504 original size:8 final size:7
Alignment explanation
Indices: 31950477--31950503 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
31950467 CTTTATACTA
31950477 AAAAAAT
1 AAAAAAT
31950484 AAAAAAT
1 AAAAAAT
31950491 AAAAAAT
1 AAAAAAT
31950498 AAAAAA
1 AAAAAA
31950504 ACCTTAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:31956799 original size:25 final size:25
Alignment explanation
Indices: 31956770--31956854 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
31956760 GCCAATATTT
*
31956770 GGAAGCTCCGGATAGCCATTAATCG
1 GGAAGCTCCGGAAAGCCATTAATCG
* ** **
31956795 GGAAGTTCATGAAAGAGAATTTAATCG
1 GGAAGCTCCGGAAAG-CCA-TTAATCG
*
31956822 GGAAGCTTC-GAAGAGCCATTAATCG
1 GGAAGCTCCGGAA-AGCCATTAATCG
31956847 GGAAGCTC
1 GGAAGCTC
31956855 ATGAAAGAGC
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
25 25 0.56
26 5 0.11
27 15 0.33
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (25 bp):
GGAAGCTCCGGAAAGCCATTAATCG
Found at i:31956819 original size:27 final size:27
Alignment explanation
Indices: 31956788--31956873 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
31956778 CGGATAGCCA
*
31956788 TTAATCGGGAAGTTCATGAAAGAGAAT
1 TTAATCGGGAAGTTCATGAAAGAGCAT
31956815 TTAATCGGGAAGCTTC--G-AAGAGCCA-
1 TTAATCGGGAAG-TTCATGAAAGAG-CAT
*
31956840 TTAATCGGGAAGCTCATGAAAGAGCAT
1 TTAATCGGGAAGTTCATGAAAGAGCAT
31956867 TTAATCG
1 TTAATCG
31956874 AAAAGCCTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
24 2 0.04
25 17 0.33
26 5 0.10
27 24 0.47
28 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (27 bp):
TTAATCGGGAAGTTCATGAAAGAGCAT
Found at i:31956841 original size:52 final size:52
Alignment explanation
Indices: 31956783--31956944 Score: 211
Period size: 52 Copynumber: 3.1 Consensus size: 52
31956773 AGCTCCGGAT
* * *
31956783 AGCCATTAATCGGGAAGTTCATGAAAGAGAATTTAATCGGGAAGCTTCGAAG
1 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAGCTTCGAAG
* *
31956835 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGAAAAGCCTT-GGAG
1 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAG-CTTCGAAG
* * * *
31956887 AGCCATTAATCGAGAAGCTCA-CAAAGAGCCTTTAATCGGAAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAGCT-TCGAAG
31956939 AGCCAT
1 AGCCAT
31956945 ATATCAGGAT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
50 2 0.02
51 19 0.20
52 72 0.75
53 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (52 bp):
AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAGCTTCGAAG
Found at i:31956914 original size:26 final size:26
Alignment explanation
Indices: 31956783--31956944 Score: 116
Period size: 26 Copynumber: 6.2 Consensus size: 26
31956773 AGCTCCGGAT
* *
31956783 AGCCATTAATCGGGAAGTTCATGAAAG
1 AGCCATTAATCGGGAAGCTCA-CAAAG
* * *
31956810 AG-AATTTAATCGGGAAGCT-TCGAAG
1 AGCCA-TTAATCGGGAAGCTCACAAAG
*
31956835 AGCCATTAATCGGGAAGCTCATGAAAG
1 AGCCATTAATCGGGAAGCTCA-CAAAG
** ****
31956862 AG-CATTTAATCGAAAAGC-CTTGGAG
1 AGCCA-TTAATCGGGAAGCTCACAAAG
*
31956887 AGCCATTAATCGAGAAGCTCACAAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
* * *
31956913 AGCCTTTAATCGGAAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
31956939 AGCCAT
1 AGCCAT
31956945 ATATCAGGAT
Statistics
Matches: 103, Mismatches: 25, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
25 35 0.34
26 37 0.36
27 31 0.30
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (26 bp):
AGCCATTAATCGGGAAGCTCACAAAG
Found at i:31959026 original size:2 final size:2
Alignment explanation
Indices: 31959019--31959043 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31959009 TCTTAAATTC
31959019 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31959044 CTAATTTAAT
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31959060 original size:12 final size:12
Alignment explanation
Indices: 31959045--31959070 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
31959035 ATATATATAC
31959045 TAATTTAATTCA
1 TAATTTAATTCA
31959057 TAATTTAATTCA
1 TAATTTAATTCA
31959069 TA
1 TA
31959071 CATTCTTTCT
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:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTTAATTCA
Found at i:31959557 original size:24 final size:23
Alignment explanation
Indices: 31959526--31959572 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
31959516 TATTCACACA
31959526 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
*
31959549 TATTACTTACCTTACTTTAAATGT
1 TATT-CTTACCTTAATTTAAATGT
31959573 CTCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:31960281 original size:29 final size:29
Alignment explanation
Indices: 31960224--31960280 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
31960214 TTTTCTTCCC
31960224 CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
1 CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
*
31960253 CTGTTCTTC-TTTTGTT-TCTTTTTCTTTT
1 CTGTT-TTCGTTTTGTTCTCTGTTTCTTTT
31960281 TATTTACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.42
29 12 0.46
30 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.72
Consensus pattern (29 bp):
CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
Found at i:31963293 original size:29 final size:29
Alignment explanation
Indices: 31963254--31963336 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 29
31963244 ATAATTCGTA
*
31963254 AAAAAGATATAAAAATGTAATTTTATAGT
1 AAAAAGTTATAAAAATGTAATTTTATAGT
*
31963283 AAAAAGTTATAAAAATGT-AGTTT-TA-T
1 AAAAAGTTATAAAAATGTAATTTTATAGT
31963309 AAAAAGTTATAAAAATGTAATTTTATAG
1 AAAAAGTTATAAAAATGTAATTTTATAG
31963337 ATATGCATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 19 0.40
27 6 0.12
28 6 0.12
29 17 0.35
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (29 bp):
AAAAAGTTATAAAAATGTAATTTTATAGT
Found at i:31965757 original size:30 final size:29
Alignment explanation
Indices: 31965721--31965780 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
31965711 ATAATTTGTG
*
31965721 AAAATTGAATC-AAATCAAATTTTCATGTAT
1 AAAATTGAA-CAAAATCAAAGTTT-ATGTAT
*
31965751 AAAATTGCACAAAATCAAAGTTTATGTAT
1 AAAATTGAACAAAATCAAAGTTTATGTAT
31965780 A
1 A
31965781 GTTTTGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAGTTTATGTAT
Found at i:31966171 original size:3 final size:3
Alignment explanation
Indices: 31966165--31966243 Score: 56
Period size: 3 Copynumber: 25.3 Consensus size: 3
31966155 ATTATTTCAC
* * *
31966165 TAT TAT TAT CAT TAT TAT ATAG TAT TAT TAAT TGAAT TGT TAT TATT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT T--AT TAT TAT TA-T
31966212 TAT TAT TA- TATT TAT TA- TAT TAT TA- TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
31966244 GTCATTTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 6 0.10
3 42 0.68
4 10 0.16
5 4 0.06
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:31966229 original size:22 final size:22
Alignment explanation
Indices: 31966204--31966270 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 22
31966194 AATTGAATTG
31966204 TTATTATTTATTATTATATTTA
1 TTATTATTTATTATTATATTTA
31966226 TTA-TA-TTATTA-TATTATTGTCA
1 TTATTATTTATTATTA-TATT-T-A
31966248 TT-TTATTTCATTATT-TATGTTA
1 TTATTATTT-ATTATTATAT-TTA
31966270 T
1 T
31966271 CATTTTGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
19 2 0.05
20 10 0.27
21 3 0.08
22 10 0.27
23 6 0.16
24 5 0.14
25 1 0.03
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (22 bp):
TTATTATTTATTATTATATTTA
Found at i:31966234 original size:8 final size:8
Alignment explanation
Indices: 31966205--31966243 Score: 62
Period size: 8 Copynumber: 4.9 Consensus size: 8
31966195 ATTGAATTGT
31966205 TATTATT-
1 TATTATTA
31966212 TATTATTA
1 TATTATTA
31966220 TATTTATTA
1 TA-TTATTA
31966229 TATTATTA
1 TATTATTA
31966237 TATTATT
1 TATTATT
31966244 GTCATTTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.23
8 15 0.50
9 8 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTATTA
Found at i:31966234 original size:17 final size:16
Alignment explanation
Indices: 31966207--31966240 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
31966197 TGAATTGTTA
31966207 TTATTTATTATTATAT
1 TTATTTATTATTATAT
31966223 TTATTATATTATTATAT
1 TTATT-TATTATTATAT
31966240 T
1 T
31966241 ATTGTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTATTATTATAT
Found at i:31966260 original size:27 final size:27
Alignment explanation
Indices: 31966204--31966262 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
31966194 AATTGAATTG
*
31966204 TTATTATTTATTATTATATTTATTATA
1 TTATTATTTATTATCATATTTATTATA
*
31966231 TTATTATATTATTGTCAT-TTTATT-TCA
1 TTATTAT-TTATTATCATATTTATTAT-A
31966258 TTATT
1 TTATT
31966263 TATGTTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 19 0.68
28 8 0.29
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (27 bp):
TTATTATTTATTATCATATTTATTATA
Found at i:31966262 original size:47 final size:47
Alignment explanation
Indices: 31966156--31966262 Score: 107
Period size: 47 Copynumber: 2.3 Consensus size: 47
31966146 CATTTTTATA
*
31966156 TTATTTCACTATTATTATCATTATTATATAGTATTATTAATTGAATTG
1 TTATTTCATTATTATTATCATTATTATATA-TATTATTAATTGAATTG
* *
31966204 TTA-TT-ATTTATTATTAT-ATTTATTATAT-TATTATATTATTGTCATT-
1 TTATTTCA-TTATTATTATCA-TTATTATATATATTAT-TAATTG-AATTG
31966250 TTATTTCATTATT
1 TTATTTCATTATT
31966263 TATGTTATCA
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
45 6 0.12
46 10 0.20
47 30 0.60
48 4 0.08
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.61
Consensus pattern (47 bp):
TTATTTCATTATTATTATCATTATTATATATATTATTAATTGAATTG
Found at i:31970222 original size:48 final size:48
Alignment explanation
Indices: 31970170--31970323 Score: 254
Period size: 48 Copynumber: 3.2 Consensus size: 48
31970160 GAAGGTATGC
* *
31970170 GGGCCATCAGCACCGACATGAGGAGGAGCGCGATAAACCAACGTAGTA
1 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
31970218 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
1 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
* * * *
31970266 GGGCCATCAGCACCGACAGGAAGAGGAGCACGAGAAACCACCGTATTA
1 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
31970314 GGGCCATCAG
1 GGGCCATCAG
31970324 GGGGGACAGA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.33, C:0.27, G:0.31, T:0.10
Consensus pattern (48 bp):
GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
Found at i:31977128 original size:21 final size:21
Alignment explanation
Indices: 31977102--31977142 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
31977092 AATATAATAG
31977102 CAAAAT-GATAGTAAACAACAA
1 CAAAATAGA-AGTAAACAACAA
31977123 CAAAATAGAAGTAAACAACA
1 CAAAATAGAAGTAAACAACA
31977143 CTGAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (21 bp):
CAAAATAGAAGTAAACAACAA
Found at i:31979634 original size:15 final size:15
Alignment explanation
Indices: 31979614--31979644 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31979604 TCGCCATTGT
31979614 TATATATTTTTAATA
1 TATATATTTTTAATA
*
31979629 TATATATTTTTTATA
1 TATATATTTTTAATA
31979644 T
1 T
31979645 GTCAACACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATATTTTTAATA
Found at i:31982037 original size:42 final size:42
Alignment explanation
Indices: 31981978--31982059 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
31981968 CATAGCGAGC
31981978 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTAGA
1 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTAGA
31982020 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTA
1 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTA
31982060 TCTGTCTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (42 bp):
TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTAGA
Found at i:31983723 original size:27 final size:27
Alignment explanation
Indices: 31983659--31983730 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
31983649 GGTGGAGGGC
* *
31983659 CTGCCACAGGCGACACCAAAGGTGTCT
1 CTGCCACAGGCGACACCAAAGGTGCCA
* * *
31983686 GTGGCAGAGGCGACACCAAAGGTGCCA
1 CTGCCACAGGCGACACCAAAGGTGCCA
*
31983713 CTGCCACAGGCGGCACCA
1 CTGCCACAGGCGACACCA
31983731 TTTCAATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (27 bp):
CTGCCACAGGCGACACCAAAGGTGCCA
Found at i:31983778 original size:9 final size:9
Alignment explanation
Indices: 31983764--31983793 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
31983754 CAGTTCAGCT
31983764 GAAGGAGAA
1 GAAGGAGAA
31983773 GAAGGAGAA
1 GAAGGAGAA
*
31983782 GAAGAAGAA
1 GAAGGAGAA
31983791 GAA
1 GAA
31983794 AAAGGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (9 bp):
GAAGGAGAA
Found at i:31983830 original size:15 final size:15
Alignment explanation
Indices: 31983810--31983862 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
31983800 GGTGCCGGAA
31983810 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
* * *
31983825 AGAGAAAGGAGAAAG
1 AAAGAAAAGAAAAAG
*
31983840 AAAGAGAAGAAAAA-
1 AAAGAAAAGAAAAAG
31983854 AATAGAAAA
1 AA-AGAAAA
31983863 AATAATGTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 2 0.07
15 27 0.93
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:31984240 original size:76 final size:77
Alignment explanation
Indices: 31984081--31984259 Score: 195
Period size: 76 Copynumber: 2.3 Consensus size: 77
31984071 AAACTAATAT
* *
31984081 TATTATTATGGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTATTTTAGTTAGTATGATTGT
1 TATTATTATTGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTATATTAGTTAGTATGATTGT
*** *
31984146 TAGTTTTTAAAT
66 TAGTTAAAAAAC
*** * *
31984158 TA-TATTATTGTTAGTTATTATTTTTAGT-AAAACCCTAATTATTACTATTAGTTAGTATTATT-
1 TATTATTATTGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTA-TATTAGTTAGTATGATTG
31984220 TTGAG-TAAAAAAC
65 TT-AGTTAAAAAAC
31984233 TATTATTATTGTGTTAGTTATTAGGAT
1 TATTATTA-T-TGTTAGTTATTAGGAT
31984260 TAGTGGTTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
75 24 0.29
76 43 0.52
77 3 0.04
78 13 0.16
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (77 bp):
TATTATTATTGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTATATTAGTTAGTATGATTGT
TAGTTAAAAAAC
Found at i:31987670 original size:8 final size:8
Alignment explanation
Indices: 31987657--31987685 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
31987647 AAAATATACT
31987657 ATTTTCTG
1 ATTTTCTG
31987665 ATTTTCTG
1 ATTTTCTG
31987673 ATTTTCTG
1 ATTTTCTG
31987681 ATTTT
1 ATTTT
31987686 ACATTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (8 bp):
ATTTTCTG
Found at i:31987740 original size:161 final size:159
Alignment explanation
Indices: 31987426--31987939 Score: 705
Period size: 161 Copynumber: 3.3 Consensus size: 159
31987416 ACTTCAAAAC
* *
31987426 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCGGATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
*
31987491 CAAAAAATATACTATTTTCT-A-----ATTTTCTAATTTTATATTATTTTAGTACATTATGTTTG
66 CAAAAAATATACTATTTTCTGATTTTTATTTTCT-ATTTTACATTATTTTAGTACATTATGTTTG
* * *
31987550 AAATGTATTAATTAATTGTGTTTTTTAAAT
130 AAATGTATTAATTTAGTGTGTGTTTTAAAT
* ***
31987580 AAATTTAGTAAAAAACCTTTATTTCGGCCATTTGTTCGTA-TTTTTTCCAAAATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
31987644 CAAAAAATATACTATTTTCTGATTTTCTGATTTTCTGATTTTACATTATTTTAGTACATTATGTT
66 CAAAAAATATACTATTTTCTGATTTT-T-ATTTTCT-ATTTTACATTATTTTAGTACATTATGTT
31987709 TGAAATGTATTAATTTAGTGTGTGTTTTAAAT
128 TGAAATGTATTAATTTAGTGTGTGTTTTAAAT
31987741 AAATTTAGTAAAAAACCCTTATTTCGGCC-TTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
*
31987805 CAAAAAATATATTATTTTC-G-TATTTTA---T-TATTTTACATTATTTTAGTACATTATGTTTG
66 CAAAAAATATACTATTTTCTGAT-TTTTATTTTCTATTTTACATTATTTTAGTACATTATGTTTG
* * *
31987864 AAATGTATTAATTTAGTATATGTTTTATAT
130 AAATGTATTAATTTAGTGTGTGTTTTAAAT
* * * * *
31987894 AAATTTACTACAAAAACCTTTATTTTGGCCCTTTATTCGTATTTTT
1 AAATTTAGTA-AAAAACCCTTATTTCGGCCATTTGTTCGTATTTTT
31987940 CTTATTTTCA
Statistics
Matches: 325, Mismatches: 23, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
153 107 0.33
154 56 0.17
155 15 0.05
158 1 0.00
159 2 0.01
160 14 0.04
161 130 0.40
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (159 bp):
AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
CAAAAAATATACTATTTTCTGATTTTTATTTTCTATTTTACATTATTTTAGTACATTATGTTTGA
AATGTATTAATTTAGTGTGTGTTTTAAAT
Found at i:31988214 original size:11 final size:11
Alignment explanation
Indices: 31988192--31988286 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 11
31988182 AAAAAATACA
31988192 TTTCCTTAT-TT
1 TTTCCTT-TCTT
31988203 TTT-CTTTCTT
1 TTTCCTTTCTT
31988213 TTTCCTTTC--
1 TTTCCTTTCTT
* *
31988222 CTCCCTCTTCTT
1 TTTCCT-TTCTT
*
31988234 TTTCTCATTTC-C
1 TTTC-C-TTTCTT
31988246 TTTCCTTTC-T
1 TTTCCTTTCTT
* *
31988256 TCTCCTTTCCT
1 TTTCCTTTCTT
31988267 TTT-CTTTCTT
1 TTTCCTTTCTT
31988277 TTT-CTTTCTT
1 TTTCCTTTCTT
31988287 CTCCTTCTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.07
10 39 0.58
11 12 0.18
12 6 0.09
13 4 0.06
14 1 0.01
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCCTTTCTT
Found at i:31988283 original size:20 final size:20
Alignment explanation
Indices: 31988206--31988301 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 20
31988196 CTTATTTTTT
*
31988206 CTTTCTTTTTCCTTTCC-TCC
1 CTTTCTTTTT-CTTTCCTTTC
31988226 CTCTTCTTTTTCTCATTTCCTTTC
1 CT-TTC-TTTT-TC-TTTCCTTTC
* * *
31988250 CTTTCTTCTCCTTTCCTTTT
1 CTTTCTTTTTCTTTCCTTTC
31988270 CTTTCTTTTTCTTT-CTTCTC
1 CTTTCTTTTTCTTTCCTT-TC
31988290 C-TTCTTTCTTCT
1 CTTTCTTT-TTCT
31988302 CCTTCAGCCG
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 9 0.15
20 28 0.45
21 4 0.06
22 8 0.13
23 9 0.15
24 4 0.06
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTTCTTTTTCTTTCCTTTC
Found at i:31988302 original size:13 final size:13
Alignment explanation
Indices: 31988250--31988306 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
31988240 ATTTCCTTTC
31988250 CTTTCTTCTCCTTT
1 CTTTCTTCTCC-TT
**
31988264 CCTTTTCTTTCTTTTT
1 -C-TTTC-TTCTCCTT
31988280 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
31988293 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
31988306 C
1 C
31988307 AGCCGAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 20 0.56
14 4 0.11
15 2 0.06
16 6 0.17
17 4 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTCTTCTCCTT
Done.