Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 17
Found at i:243 original size:52 final size:52
Alignment explanation
Indices: 181--300 Score: 240
Period size: 52 Copynumber: 2.3 Consensus size: 52
171 CAAAAGGTGG
181 TCTCTCGATGCTCTTATATTGACAAGACATGTTTTACCAAAACCCCAGGCAA
1 TCTCTCGATGCTCTTATATTGACAAGACATGTTTTACCAAAACCCCAGGCAA
233 TCTCTCGATGCTCTTATATTGACAAGACATGTTTTACCAAAACCCCAGGCAA
1 TCTCTCGATGCTCTTATATTGACAAGACATGTTTTACCAAAACCCCAGGCAA
285 TCTCTCGATGCTCTTA
1 TCTCTCGATGCTCTTA
301 CAGTGTCAAG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (52 bp):
TCTCTCGATGCTCTTATATTGACAAGACATGTTTTACCAAAACCCCAGGCAA
Found at i:3375 original size:2 final size:2
Alignment explanation
Indices: 3368--3450 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
3358 ATGGTAGTTC
3368 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3410 AT AT AT AT AT AT AT AT 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
3451 AAACAACTAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5247 original size:42 final size:42
Alignment explanation
Indices: 5200--5292 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
5190 TAACCAAATC
5200 TCAAATTTCTCAAAACCCTAACTATGATCAAATGTTATTTCA
1 TCAAATTTCTCAAAACCCTAACTATGATCAAATGTTATTTCA
* *
5242 TCAAATTTCTCAAAACCCTAAGTATGGTCAAATGTTATTTCA
1 TCAAATTTCTCAAAACCCTAACTATGATCAAATGTTATTTCA
*
5284 TCCAATTTC
1 TCAAATTTC
5293 AAGTAGTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (42 bp):
TCAAATTTCTCAAAACCCTAACTATGATCAAATGTTATTTCA
Found at i:7240 original size:23 final size:23
Alignment explanation
Indices: 7210--7259 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
7200 ATTCTGGTTG
* *
7210 TATCAAACAAGGGTTTATGTTAT
1 TATCAAACAAGAGTTTATGTTAA
7233 TATCAAACAAGAGTTTATGTTAA
1 TATCAAACAAGAGTTTATGTTAA
7256 TATC
1 TATC
7260 TTGTTTAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (23 bp):
TATCAAACAAGAGTTTATGTTAA
Found at i:9230 original size:22 final size:24
Alignment explanation
Indices: 9196--9240 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
9186 ATGTATACTT
*
9196 TTAAAATCCAA-TTAAT-TAATAC
1 TTAAAATACAATTTAATATAATAC
*
9218 TTAAAATATAATTTAATATAATA
1 TTAAAATACAATTTAATATAATA
9241 ATATTTATTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (24 bp):
TTAAAATACAATTTAATATAATAC
Found at i:17056 original size:31 final size:32
Alignment explanation
Indices: 16990--17058 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
16980 CCTTGAAACA
* * *
16990 AAAC-AAACCATTTTTGAGTCTGTTTCTTTTG
1 AAACAAAACCATCTCTGAGTCTGTTTCCTTTG
17021 AAACAAAACCATCTCTGAGTC-GTTTCCCTTT-
1 AAACAAAACCATCTCTGAGTCTGTTT-CCTTTG
17052 AAACAAA
1 AAACAAA
17059 TTTAGTCTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 15 0.45
32 18 0.55
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (32 bp):
AAACAAAACCATCTCTGAGTCTGTTTCCTTTG
Found at i:17682 original size:3 final size:3
Alignment explanation
Indices: 17669--17725 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
17659 CTACCAAAAA
*
17669 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17716 TAT TAT TAT T
1 TAT TAT TAT T
17726 TATTTACATA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:19219 original size:30 final size:30
Alignment explanation
Indices: 19184--19350 Score: 126
Period size: 29 Copynumber: 5.6 Consensus size: 30
19174 TTAGTACCAT
* * *
19184 TTTTAGTCCCTTAAATTTTTATTTTTATTA
1 TTTTAGTCCTTTAAGTTTTTATTTTTACTA
* * * * *
19214 TTTTAGTCCTTTAAATGTTTGTATTTGCTA
1 TTTTAGTCCTTTAAGTTTTTATTTTTACTA
* * * *
19244 -TTTAGACCCTTAAGTTTTGACTTTTACTA
1 TTTTAGTCCTTTAAGTTTTTATTTTTACTA
*
19273 ATTTAGTCCTTTAAGTTTTGT-TTTTT-CTA
1 TTTTAGTCCTTTAAGTTTT-TATTTTTACTA
* *
19302 TTTTGGTCCTTTAAGTTTCTATTTTT-CTCCA
1 TTTTAGTCCTTTAAGTTTTTATTTTTACT--A
*
19333 TTTTGGTCCTTGTAAGTT
1 TTTTAGTCCTT-TAAGTT
19351 CAAATACTTA
Statistics
Matches: 109, Mismatches: 22, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
28 1 0.01
29 46 0.42
30 44 0.40
31 12 0.11
32 6 0.06
ACGTcount: A:0.19, C:0.13, G:0.11, T:0.57
Consensus pattern (30 bp):
TTTTAGTCCTTTAAGTTTTTATTTTTACTA
Found at i:19319 original size:59 final size:59
Alignment explanation
Indices: 19185--19304 Score: 152
Period size: 59 Copynumber: 2.1 Consensus size: 59
19175 TAGTACCATT
* * * * * *
19185 TTTAGTCCCTTAAATTTTTATTTTTATTATTTTAGTCCTTTAAATGTTTGTATTTGCTA
1 TTTAGACCCTTAAGTTTTGACTTTTACTAATTTAGTCCTTTAAATGTTTGTATTTGCTA
* * *
19244 TTTAGACCCTTAAGTTTTGACTTTTACTAATTTAGTCCTTTAAGT-TTTGTTTTTTCTA
1 TTTAGACCCTTAAGTTTTGACTTTTACTAATTTAGTCCTTTAAATGTTTGTATTTGCTA
19302 TTT
1 TTT
19305 TGGTCCTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
58 14 0.27
59 38 0.73
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (59 bp):
TTTAGACCCTTAAGTTTTGACTTTTACTAATTTAGTCCTTTAAATGTTTGTATTTGCTA
Found at i:19339 original size:31 final size:29
Alignment explanation
Indices: 19278--19350 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 29
19268 TACTAATTTA
* *
19278 GTCCTTTAAGTTTTGTTTTTTCTATTTTG
1 GTCCTTTAAGTTTTATTTTTTCCATTTTG
19307 GTCCTTTAAGTTTCTATTTTTCTCCATTTTG
1 GTCCTTTAAGTTT-TATTTTT-TCCATTTTG
19338 GTCCTTGTAAGTT
1 GTCCTT-TAAGTT
19351 CAAATACTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 13 0.33
30 6 0.15
31 14 0.36
32 6 0.15
ACGTcount: A:0.12, C:0.15, G:0.14, T:0.59
Consensus pattern (29 bp):
GTCCTTTAAGTTTTATTTTTTCCATTTTG
Found at i:20441 original size:25 final size:24
Alignment explanation
Indices: 20413--20476 Score: 76
Period size: 25 Copynumber: 2.6 Consensus size: 24
20403 TTTCCGCTTG
20413 ATTTTCGACTGAATTTGTGTGTAAA
1 ATTTTCGA-TGAATTTGTGTGTAAA
* **
20438 ATTTTTGATTGAATTTGTGTGTAGG
1 ATTTTCGA-TGAATTTGTGTGTAAA
20463 ATTTTC-ATGAATTT
1 ATTTTCGATGAATTT
20477 TATTATGTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 7 0.21
24 1 0.03
25 26 0.76
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (24 bp):
ATTTTCGATGAATTTGTGTGTAAA
Found at i:27173 original size:65 final size:62
Alignment explanation
Indices: 27054--27263 Score: 190
Period size: 65 Copynumber: 3.3 Consensus size: 62
27044 TTTTTCAGAG
* * * * * *
27054 TGATGCACCGATGCACTAATCCATGCATCGATGCAC-CATGAATTAAATTGAACATCGAATGCAT
1 TGATGCATCGATGCAC-AA-CCATGCACCGATGCACTCAGGCATT--TTTAAACATCGAATGCAT
27118 T
62 T
* ** *
27119 TCATGCATCGATGCACATACCATGCACCGATTTACTGAGG-ATTTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGCATTTT-T--AAACATCGAATGCAT
27183 T
62 T
* * * *
27184 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTTAAACATCGAATGCACT
1 TGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGC-ATTTTTAAACATCGAATGCATT
27248 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
27264 TCTTAGTGAA
Statistics
Matches: 120, Mismatches: 17, Indels: 18
0.77 0.11 0.12
Matches are distributed among these distances:
62 1 0.01
63 2 0.02
64 47 0.39
65 62 0.52
66 3 0.03
67 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (62 bp):
TGATGCATCGATGCACAACCATGCACCGATGCACTCAGGCATTTTTAAACATCGAATGCATT
Found at i:42463 original size:28 final size:27
Alignment explanation
Indices: 42432--42499 Score: 95
Period size: 26 Copynumber: 2.5 Consensus size: 27
42422 TACCCAATGT
42432 TGATACTTTTTGATAAAAGGTTTATATA
1 TGATA-TTTTTGATAAAAGGTTTATATA
*
42460 TGATA-TTTT-ACTAAAAGGTTTATATT
1 TGATATTTTTGA-TAAAAGGTTTATATA
42486 TGATATTTTTGATA
1 TGATATTTTTGATA
42500 TGTTAGTATA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
25 1 0.03
26 23 0.64
27 6 0.17
28 6 0.17
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (27 bp):
TGATATTTTTGATAAAAGGTTTATATA
Found at i:43071 original size:3 final size:3
Alignment explanation
Indices: 43065--43148 Score: 127
Period size: 3 Copynumber: 28.0 Consensus size: 3
43055 CATTTGGGTT
*
43065 TTA TTA TTA TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
43109 TTTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43149 CAGACCCAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 8
0.88 0.02 0.09
Matches are distributed among these distances:
2 4 0.05
3 65 0.87
4 6 0.08
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43186 original size:29 final size:27
Alignment explanation
Indices: 43146--43200 Score: 65
Period size: 29 Copynumber: 2.0 Consensus size: 27
43136 ATTATTATTA
43146 TTACAGACCCAAAAAAGACTGGCCCAG
1 TTACAGACCCAAAAAAGACTGGCCCAG
***
43173 TTACAAGAGCCCAACCCAGACTGGCCCA
1 TTAC-AGA-CCCAAAAAAGACTGGCCCA
43201 ATAGAAACCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
28 3 0.13
29 16 0.70
ACGTcount: A:0.36, C:0.35, G:0.18, T:0.11
Consensus pattern (27 bp):
TTACAGACCCAAAAAAGACTGGCCCAG
Found at i:44418 original size:3 final size:3
Alignment explanation
Indices: 44410--44456 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
44400 AATATATTTA
44410 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
44457 ATAGTCATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:44659 original size:18 final size:17
Alignment explanation
Indices: 44632--44665 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
44622 TTTTAGAGAA
44632 ATTTTTTATTAATATTT
1 ATTTTTTATTAATATTT
44649 ATTTATTTATTAATATT
1 ATTT-TTTATTAATATT
44666 AAGAAAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTTTATTAATATTT
Found at i:45298 original size:21 final size:20
Alignment explanation
Indices: 45262--45303 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
45252 TTTATAATTC
*
45262 TTTTCTTTCAAAATTTTTTA
1 TTTTCTTTCAAAATTTATTA
45282 TTTT-TTTCATAATATTTATTA
1 TTTTCTTTCA-AA-ATTTATTA
45303 T
1 T
45304 ATATTCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 5 0.26
20 6 0.32
21 8 0.42
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCTTTCAAAATTTATTA
Found at i:54641 original size:19 final size:20
Alignment explanation
Indices: 54583--54644 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 20
54573 TTTTTTAAAT
54583 AGTGAATAGTACCCATGAAC
1 AGTGAATAGTACCCATGAAC
* * * **
54603 AGTGAACAATAACGGT-AAC
1 AGTGAATAGTACCCATGAAC
54622 AGTG-ATAGTACCCATGAAC
1 AGTGAATAGTACCCATGAAC
54641 AGTG
1 AGTG
54645 GGGGAATCGG
Statistics
Matches: 31, Mismatches: 10, Indels: 3
0.70 0.23 0.07
Matches are distributed among these distances:
18 6 0.19
19 14 0.45
20 11 0.35
ACGTcount: A:0.40, C:0.18, G:0.23, T:0.19
Consensus pattern (20 bp):
AGTGAATAGTACCCATGAAC
Found at i:55330 original size:33 final size:33
Alignment explanation
Indices: 55293--55360 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
55283 CACCGTAGTG
55293 CTAATCCGTATGACACATAAGGTCGTGTCCACC
1 CTAATCCGTATGACACATAAGGTCGTGTCCACC
* *
55326 CTAATCCGTATGACACATAAGGTTGTGTCTACC
1 CTAATCCGTATGACACATAAGGTCGTGTCCACC
55359 CT
1 CT
55361 TTGTACTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (33 bp):
CTAATCCGTATGACACATAAGGTCGTGTCCACC
Found at i:58931 original size:37 final size:37
Alignment explanation
Indices: 58878--58982 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
58868 CCTTTTCGTC
58878 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
58915 TTGCTAGGATTCAAACTCCCAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
58952 CTACTATTATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
58983 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:59728 original size:22 final size:20
Alignment explanation
Indices: 59703--59770 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
59693 TATACATACA
*
59703 TTTTTATATTTTTATATATAT
1 TTTTTTTATTTTTAT-TATAT
59724 TTTTTCTTA-TTTTATTTATACT
1 TTTTT-TTATTTTTA-TTATA-T
* *
59746 ATTTATTTATTTTCATTATAT
1 -TTTTTTTATTTTTATTATAT
59767 TTTT
1 TTTT
59771 AGTTTCTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 11
0.72 0.08 0.21
Matches are distributed among these distances:
20 3 0.08
21 15 0.39
22 12 0.32
23 8 0.21
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTTTATTTTTATTATAT
Found at i:59767 original size:28 final size:27
Alignment explanation
Indices: 59706--59768 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 27
59696 ACATACATTT
* *
59706 TTATATTTTTATATATATTTTTTCTTA
1 TTATATTTATATATATATTTTTTCTCA
* *
59733 TTTTATTTATACTATTTATTTATTT-TCA
1 TTATATTTATA-TATATATTT-TTTCTCA
59761 TTATATTT
1 TTATATTT
59769 TTAGTTTCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 9 0.31
28 17 0.59
29 3 0.10
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (27 bp):
TTATATTTATATATATATTTTTTCTCA
Found at i:59883 original size:20 final size:19
Alignment explanation
Indices: 59856--59912 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
59846 TTTTATCTTC
59856 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
* *
59875 ATTTCATTTTTTTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
59896 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
59913 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
19 12 0.39
20 14 0.45
21 5 0.16
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:62551 original size:15 final size:15
Alignment explanation
Indices: 62528--62557 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62518 AAGTCAAGGA
*
62528 TAACTCCTGAGAATC
1 TAACACCTGAGAATC
62543 TAACACCTGAGAATC
1 TAACACCTGAGAATC
62558 CAAATGGCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (15 bp):
TAACACCTGAGAATC
Found at i:64225 original size:16 final size:15
Alignment explanation
Indices: 64204--64256 Score: 74
Period size: 16 Copynumber: 3.5 Consensus size: 15
64194 AAAGGGCAAA
64204 AACAAAAAAGAAAAG
1 AACAAAAAAGAAAAG
64219 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAAGAA-AAG
64235 AACAAAAAA-AAAAG
1 AACAAAAAAGAAAAG
64249 AACAAAAA
1 AACAAAAA
64257 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.06
14 10 0.29
15 9 0.26
16 12 0.34
17 2 0.06
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAAAG
Found at i:64235 original size:19 final size:19
Alignment explanation
Indices: 64200--64270 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
64190 ACAAAAAGGG
*
64200 CAAAAACAAAA-AAGAAAA
1 CAAAAAAAAAAGAAGAAAA
* **
64218 GAAGCAAAAAAGAAGAAAA
1 CAAAAAAAAAAGAAGAAAA
*
64237 CAAAAAAAAAAGAACAAAAA
1 CAAAAAAAAAAGAA-GAAAA
64257 TCAAAAAGAAAAAG
1 -CAAAAA-AAAAAG
64271 GGACAAAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 7 0.17
19 18 0.44
20 4 0.10
21 6 0.15
22 6 0.15
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.01
Consensus pattern (19 bp):
CAAAAAAAAAAGAAGAAAA
Found at i:64262 original size:16 final size:14
Alignment explanation
Indices: 64204--64266 Score: 65
Period size: 16 Copynumber: 4.1 Consensus size: 14
64194 AAAGGGCAAA
64204 AACAAAAAAGAAAAG
1 AACAAAAAA-AAAAG
64219 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAA-AA-AAG
64235 AACAAAAAAAAAAG
1 AACAAAAAAAAAAG
64249 AACAAAAATCAAAAAG
1 AACAAAAA--AAAAAG
64265 AA
1 AA
64267 AAAGGGACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.05
14 10 0.23
15 9 0.21
16 20 0.47
17 2 0.05
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.02
Consensus pattern (14 bp):
AACAAAAAAAAAAG
Found at i:64824 original size:22 final size:22
Alignment explanation
Indices: 64796--64850 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
64786 ACTACCTCAT
64796 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
64818 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
64840 CAAACCTTTGA
1 CAAACCTTTGA
64851 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:65937 original size:106 final size:106
Alignment explanation
Indices: 65809--67084 Score: 1962
Period size: 106 Copynumber: 12.0 Consensus size: 106
65799 ATATCGTGCC
* * *
65809 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
* * *
65873 CAAATTCATAGCCAATTTCAACTTCACAGTGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
65915 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
65980 AATTTCAGAGCCAATTTTAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
66021 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTATCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
66086 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
66127 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
66192 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
66233 ACTCCAGACAACGCAAGATCAACTTCACGACGAAGGGACCGCTGATTGTCAAAAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
66298 AGTTTTAGAGCCAATTTCAACTTCACAACGAAGGATATGGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66339 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
66404 AATTTCAGAGCCAATTTCAACTTCAAAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** * *
66445 ACTTGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
66510 AATTTCGGAGCCGATTTCAACTTCACAGTGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
66551 ACTCCATACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTTAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
66616 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
66657 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
66722 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
66763 ACTCCAGACAACGCAAGTTCAACTTCACGACTAAGGGACCGTTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
66828 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
66869 ACTCGAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
66934 AATTTCGGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
66975 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTAGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
67040 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
67081 ACTC
1 ACTC
67085 AGAACAATGC
Statistics
Matches: 1076, Mismatches: 92, Indels: 4
0.92 0.08 0.00
Matches are distributed among these distances:
106 1074 1.00
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.22
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:67924 original size:37 final size:37
Alignment explanation
Indices: 67833--67912 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
67823 CCTTTTCGTC
67833 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
* * *
67870 TTGCTAGGATTCAAACTCCTAAAAGTAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
67907 CTACTA
1 CTACTA
67913 TTATTTAAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAGTAGGATAGAATT
Found at i:68340 original size:23 final size:23
Alignment explanation
Indices: 68312--68358 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
68302 TATATGTATA
68312 TATTTAATTAT-ATTTTATTT-ATT
1 TATTT-ATTATAATTTT-TTTCATT
68335 TATTTATTATAATTTTTTTCATT
1 TATTTATTATAATTTTTTTCATT
68358 T
1 T
68359 TTCTTTACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTATTATAATTTTTTTCATT
Found at i:68481 original size:2 final size:2
Alignment explanation
Indices: 68474--68530 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
68464 TTTTCCTAAC
68474 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
68516 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
68531 TACTTTATTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:68586 original size:29 final size:28
Alignment explanation
Indices: 68519--68598 Score: 67
Period size: 29 Copynumber: 2.8 Consensus size: 28
68509 ATATATATAT
* *
68519 ATATATATAT-ATTACTTTATTTTATTTT
1 ATAT-TATATGATTACTTTATTTTAGTTA
* *
68547 ATATTTCTATGATTACTATTTTTTTAGTTA
1 ATA-TTATATGATTACT-TTATTTTAGTTA
68577 ATATTATATG-TATA-TTTATTTT
1 ATATTATATGAT-TACTTTATTTT
68599 TGATTTATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 9
0.74 0.11 0.16
Matches are distributed among these distances:
27 6 0.14
28 9 0.21
29 15 0.36
30 12 0.29
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.62
Consensus pattern (28 bp):
ATATTATATGATTACTTTATTTTAGTTA
Found at i:68667 original size:22 final size:22
Alignment explanation
Indices: 68632--68686 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
68622 CTATTTAGTA
*
68632 TTTTATTA-TATTATACATACAT
1 TTTTATTATTTTTATACATA-AT
* *
68654 TTTTA-TATTTTTATATATATT
1 TTTTATTATTTTTATACATAAT
68675 TTTTATTATTTT
1 TTTTATTATTTT
68687 ATTTATACTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 8 0.29
22 20 0.71
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTTATTATTTTTATACATAAT
Found at i:68679 original size:21 final size:21
Alignment explanation
Indices: 68653--68720 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
68643 TATACATACA
68653 TTTTTATATTTTTATATATAT
1 TTTTTATATTTTTATATATAT
*
68674 TTTTTATTATTTTATTTATACTAT
1 TTTTTA-TATTTT-TATATA-TAT
* *
68698 TTATT-TATTTTCAT-TATAT
1 TTTTTATATTTTTATATATAT
68717 TTTT
1 TTTT
68721 AGTTTCTTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 6 0.15
20 2 0.05
21 7 0.18
22 12 0.31
23 5 0.13
24 7 0.18
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTTATATTTTTATATATAT
Found at i:68716 original size:43 final size:43
Alignment explanation
Indices: 68632--68720 Score: 110
Period size: 43 Copynumber: 2.1 Consensus size: 43
68622 CTATTTAGTA
*
68632 TTTTATTATATTATACATACATTTTTATATTTTTATATATATT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
* **
68675 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATT
68718 TTT
1 TTT
68721 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
43 26 0.65
44 12 0.30
45 2 0.05
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.67
Consensus pattern (43 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
Found at i:68832 original size:20 final size:19
Alignment explanation
Indices: 68805--68860 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
68795 TTTTATCTTC
68805 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
68824 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
68844 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
68861 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:76966 original size:18 final size:18
Alignment explanation
Indices: 76943--76980 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
76933 CAAGTTTATC
76943 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
76961 TTTTCGAAATTCAATTTA
1 TTTTCGAAATTCAATTTA
76979 TT
1 TT
76981 CTTTTATATA
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:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (18 bp):
TTTTCGAAATTCAATTTA
Found at i:78116 original size:19 final size:19
Alignment explanation
Indices: 78094--78138 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
78084 GTTCATAATG
* *
78094 AGAAGAATTCATCTGAAGA
1 AGAAGAACTCATCTAAAGA
78113 AGAAGAACTCATCTAAAGA
1 AGAAGAACTCATCTAAAGA
78132 AGAAGAA
1 AGAAGAA
78139 GAAGTTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.53, C:0.11, G:0.20, T:0.16
Consensus pattern (19 bp):
AGAAGAACTCATCTAAAGA
Found at i:78288 original size:20 final size:20
Alignment explanation
Indices: 78226--78289 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
78216 TCCAGAGAAA
78226 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* **
78246 -ATC-TGAA-GAGGAAGAACAA
1 GTTCAT-AATGA-GAAGAACTT
78265 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
78285 GTTCA
1 GTTCA
78290 ACCTTTTGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:78411 original size:20 final size:20
Alignment explanation
Indices: 78349--78412 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
78339 TCCAGAGAAA
78349 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* ***
78369 -ATC-TGAA-GAGGAAGAAGAA
1 GTTCAT-AATGA-GAAGAACTT
78388 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
78408 GTTCA
1 GTTCA
78413 ACCTTTTGCA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
18 3 0.10
19 10 0.32
20 15 0.48
21 3 0.10
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:78523 original size:122 final size:122
Alignment explanation
Indices: 78113--78784 Score: 933
Period size: 123 Copynumber: 5.5 Consensus size: 122
78103 CATCTGAAGA
* * * * *
78113 AGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTAAACGTTTTGCTA
1 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTA
* * *
78178 GACTCTATCACAGAAGGAGATAGATCAGTATACACT-TTTCCAGAGAAAGTTCATAATG
66 GACTCTATCACAGAAGGAGATAGATCAGCAT-CAATATTTCCAGA-AGAGTTCATAATG
* *
78236 AGAAGAACTTATCTGAAGAGGAAGAACAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTA
1 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTA
* * * *
78301 GACTCTATCATAGAAGGAGATATATCAGCCTACAAT-TTTCCAGAGAAAGTTCATAATG
66 GACTCTATCACAGAAGGAGATAGATCAGCAT-CAATATTTCCAGA-AGAGTTCATAATG
*
78359 AGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-A
1 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTA
* * * *
78423 TGACTCTATCACAGAATGAGATAGATCAACATCAATATTTCTAGAAGTGTTCATAATG
66 -GACTCTATCACAGAAGGAGATAGATCAGCATCAATATTTCCAGAAGAGTTCATAATG
* *
78481 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGTATTTGTTCAACCTTTTGC-A
1 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTA
** * *
78545 TGACTCTATCACAGAAGGAGATAGATCAATATCAACATTTCCAGAAGTGTTCATAATG
66 -GACTCTATCACAGAAGGAGATAGATCAGCATCAATATTTCCAGAAGAGTTCATAATG
78603 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTATTT-CT
1 AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT-TTTGCT
* * * *
78667 CGACGCTATCACAGAAAGAGATAGATCAGCATCAATATTTCCAGAAAGAGTTCATAATA
65 AGACTCTATCACAGAAGGAGATAGATCAGCATCAATATTTCCAG-AAGAGTTCATAATG
** *
78726 AGAAGAACTCATCTGAAGAAGG-AGAAGAAGAACATAATGAGAAGAATTTGTTCAACCTT
1 AGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
78785 GCCTTAATTC
Statistics
Matches: 502, Mismatches: 41, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
122 227 0.45
123 272 0.54
124 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (122 bp):
AGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTA
GACTCTATCACAGAAGGAGATAGATCAGCATCAATATTTCCAGAAGAGTTCATAATG
Found at i:79185 original size:3 final size:3
Alignment explanation
Indices: 79179--79251 Score: 123
Period size: 3 Copynumber: 25.0 Consensus size: 3
79169 TTTATTTTTT
*
79179 TTA TTA TTA TTA TT- TTA -TA TTA TTA TTA TTA TTA TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
79225 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
79252 CAGGCCCAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:80795 original size:16 final size:18
Alignment explanation
Indices: 80774--80812 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
80764 ATAAATATCT
80774 TATTTATAAAAA-T-ATA
1 TATTTATAAAAATTAATA
80790 TATTTATAAAAATTAATA
1 TATTTATAAAAATTAATA
80808 TATTT
1 TATTT
80813 TCTTGGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.57
17 1 0.05
18 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTATAAAAATTAATA
Found at i:82739 original size:3 final size:3
Alignment explanation
Indices: 82731--82811 Score: 137
Period size: 3 Copynumber: 27.3 Consensus size: 3
82721 TCAAAATTAT
82731 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
82779 AT- ATA ATT TTA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
82812 GCCCTTGAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:99108 original size:40 final size:40
Alignment explanation
Indices: 99037--99130 Score: 127
Period size: 40 Copynumber: 2.3 Consensus size: 40
99027 TATTGCATGT
* *
99037 TTTATTCATTGTTATTAATTATTACCTTTTTTTCTATAGTC
1 TTTATT-ATTCTTATTAATTATTACCCTTTTTTCTATAGTC
*
99078 TTTATTATTCTTA-TATATTATTACCCTTTTTTCTATAGTT
1 TTTATTATTCTTATTA-ATTATTACCCTTTTTTCTATAGTC
*
99118 TTTATTCTTCTTA
1 TTTATTATTCTTA
99131 CATTTTACTA
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
39 2 0.04
40 40 0.83
41 6 0.12
ACGTcount: A:0.21, C:0.13, G:0.03, T:0.63
Consensus pattern (40 bp):
TTTATTATTCTTATTAATTATTACCCTTTTTTCTATAGTC
Found at i:116665 original size:24 final size:24
Alignment explanation
Indices: 116620--116668 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
116610 AAATATTCTT
*
116620 TTTTATTTCTTCATTTTTCTTTTC
1 TTTTATTTCTTCATTTTACTTTTC
*
116644 TTTTATTTCTT-GTTTTAACTTTTC
1 TTTTATTTCTTCATTTT-ACTTTTC
116668 T
1 T
116669 CTCTCCACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTATTTCTTCATTTTACTTTTC
Found at i:121412 original size:51 final size:51
Alignment explanation
Indices: 121339--121441 Score: 181
Period size: 51 Copynumber: 2.0 Consensus size: 51
121329 TTAAACCCTC
121339 ACTAAACCCATTTTGGGATTCTATACTTAAACCTTGAAAT-TTAGGGCTTAA
1 ACTAAACCCATTTTGGGATTCTATACTTAAACCTTGAAATATTA-GGCTTAA
*
121390 ACTAAACCCATTTTTGGATTCTATACTTAAACCTTGAAATATTAGGCTTAA
1 ACTAAACCCATTTTGGGATTCTATACTTAAACCTTGAAATATTAGGCTTAA
121441 A
1 A
121442 TTGAACCTCT
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 47 0.94
52 3 0.06
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (51 bp):
ACTAAACCCATTTTGGGATTCTATACTTAAACCTTGAAATATTAGGCTTAA
Found at i:128736 original size:39 final size:39
Alignment explanation
Indices: 128682--128767 Score: 136
Period size: 39 Copynumber: 2.2 Consensus size: 39
128672 AGGATACCTA
* *
128682 GTGCATATGGTGGACACAACCTTATGTGTAACCACTTCG
1 GTGCATATGGTGGACACAACCTTATGTGTAACCAATACG
* *
128721 GTGCATTTGGTGGACACAACTTTATGTGTAACCAATACG
1 GTGCATATGGTGGACACAACCTTATGTGTAACCAATACG
128760 GTGCATAT
1 GTGCATAT
128768 ATTTGACTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (39 bp):
GTGCATATGGTGGACACAACCTTATGTGTAACCAATACG
Found at i:138134 original size:2 final size:2
Alignment explanation
Indices: 138127--138182 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
138117 AGAATATGAA
138127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
138169 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
138183 CTTATATGGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:142835 original size:8 final size:8
Alignment explanation
Indices: 142824--142874 Score: 56
Period size: 8 Copynumber: 6.6 Consensus size: 8
142814 AAAAAAGAGG
142824 AAAAAGAT
1 AAAAAGAT
142832 AAAAAGAT
1 AAAAAGAT
142840 -AAAA-A-
1 AAAAAGAT
142845 AAAAAG-T
1 AAAAAGAT
142852 GGAAAAAGAT
1 --AAAAAGAT
142862 AAAAAGAT
1 AAAAAGAT
142870 AAAAA
1 AAAAA
142875 AAAGTGAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
6 5 0.14
7 4 0.11
8 21 0.57
9 6 0.16
10 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (8 bp):
AAAAAGAT
Found at i:142849 original size:30 final size:30
Alignment explanation
Indices: 142813--142877 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
142803 GAAATAGAGG
142813 AAAAAAAGAGGAAAAAGATAAAAAGATAAA
1 AAAAAAAGAGGAAAAAGATAAAAAGATAAA
*
142843 AAAAAAAGTGGAAAAAGATAAAAAGATAAA
1 AAAAAAAGAGGAAAAAGATAAAAAGATAAA
142873 AAAAA
1 AAAAA
142878 GTGAAAAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (30 bp):
AAAAAAAGAGGAAAAAGATAAAAAGATAAA
Found at i:143409 original size:21 final size:20
Alignment explanation
Indices: 143385--143423 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
143375 ACTATTGTGA
143385 GAAAGAAAAGAAGAAAAAGCG
1 GAAAGAAAAGAA-AAAAAGCG
*
143406 GAAAGAAAAGTAAAAAAG
1 GAAAGAAAAGAAAAAAAG
143424 AAGAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (20 bp):
GAAAGAAAAGAAAAAAAGCG
Found at i:144527 original size:3 final size:3
Alignment explanation
Indices: 144519--144543 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
144509 AGGTAATGTC
144519 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
144544 AGTCCTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:144647 original size:19 final size:18
Alignment explanation
Indices: 144607--144649 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
144597 TATTGAATAT
144607 ATATTATAATCATACTAC
1 ATATTATAATCATACTAC
* *
144625 ATATTATAAGTCATATTAG
1 ATATTATAA-TCATACTAC
144644 ATATTA
1 ATATTA
144650 AACCCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.42
Consensus pattern (18 bp):
ATATTATAATCATACTAC
Found at i:144856 original size:13 final size:13
Alignment explanation
Indices: 144840--144864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
144830 TTTGAAAATA
144840 TTTTTTGTTTTTG
1 TTTTTTGTTTTTG
144853 TTTTTTGTTTTT
1 TTTTTTGTTTTT
144865 ATTTCTAGAA
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:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTTGTTTTTG
Found at i:151666 original size:4 final size:4
Alignment explanation
Indices: 151657--151763 Score: 65
Period size: 4 Copynumber: 25.5 Consensus size: 4
151647 TTCATATCCC
* * * * *
151657 AATA AATA AATA AATT CA-A AATA AATA AATA ATTTAA AATA AATT ATTA
1 AATA AATA AATA AATA AATA AATA AATA AATA A-AT-A AATA AATA AATA
* * *
151706 CAA-A AATA AATA AATT ATTCAA AATA AATA AATA ATTTA AAGTA AATA
1 -AATA AATA AATA AATA AAT--A AATA AATA AATA A-ATA AA-TA AATA
151754 AATA AATA AA
1 AATA AATA AA
151764 AATTATCTCC
Statistics
Matches: 78, Mismatches: 16, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
3 3 0.04
4 61 0.78
5 10 0.13
6 4 0.05
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (4 bp):
AATA
Found at i:151695 original size:18 final size:18
Alignment explanation
Indices: 151657--151758 Score: 113
Period size: 18 Copynumber: 5.7 Consensus size: 18
151647 TTCATATCCC
151657 AATAAATAAATAAATTCAA
1 AATAAATAAAT-AATTCAA
*
151676 AATAAATAAATAATTTAA
1 AATAAATAAATAATTCAA
151694 AATAAAT---T-ATTACAAA
1 AATAAATAAATAATT-C-AA
*
151710 AATAAATAAATTATTCAA
1 AATAAATAAATAATTCAA
*
151728 AATAAATAAATAATTTAA
1 AATAAATAAATAATTCAA
*
151746 AGTAAATAAATAA
1 AATAAATAAATAA
151759 ATAAAAATTA
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
14 3 0.04
15 1 0.01
16 9 0.12
18 43 0.60
19 13 0.18
20 3 0.04
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (18 bp):
AATAAATAAATAATTCAA
Found at i:151737 original size:22 final size:21
Alignment explanation
Indices: 151693--151760 Score: 81
Period size: 20 Copynumber: 3.4 Consensus size: 21
151683 AAATAATTTA
*
151693 AAATAAATTATTACAA-AAAT
1 AAATAAATTATTAAAATAAAT
151713 AAATAAATTATTCAAAATAAAT
1 AAATAAATTATT-AAAATAAAT
*
151735 AAAT-AA-T-TTAAAGTAAAT
1 AAATAAATTATTAAAATAAAT
151753 AAATAAAT
1 AAATAAAT
151761 AAAAATTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 12 0.29
19 4 0.10
20 13 0.31
21 5 0.12
22 8 0.19
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.31
Consensus pattern (21 bp):
AAATAAATTATTAAAATAAAT
Found at i:152590 original size:37 final size:36
Alignment explanation
Indices: 152515--152591 Score: 102
Period size: 36 Copynumber: 2.1 Consensus size: 36
152505 TTTTTATATT
*
152515 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
152551 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
152588 TTTA
1 TTTA
152592 TAATATTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
36 26 0.72
37 10 0.28
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:152611 original size:18 final size:18
Alignment explanation
Indices: 152567--152614 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
152557 TTTTTAAAGA
*
152567 AAATATATAAATATTTTAC
1 AAATATAT-AATATTATAC
*
152586 -AATTTATAATATTATAC
1 AAATATATAATATTATAC
152603 AAATATATAATA
1 AAATATATAATA
152615 AGGACAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATAATATTATAC
Found at i:154396 original size:54 final size:54
Alignment explanation
Indices: 154182--154396 Score: 394
Period size: 54 Copynumber: 4.0 Consensus size: 54
154172 CTAAGTACCA
* *
154182 AAATTGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGTCG
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCG
**
154236 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCTA
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCG
154290 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCG
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCG
154344 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCC
1 AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCC
154397 AATAGTACAC
Statistics
Matches: 155, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 155 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (54 bp):
AAATGGTAATTCACAAACTCATTATGAATTCCATGGATTGCACACATAGTGCCG
Found at i:164329 original size:186 final size:185
Alignment explanation
Indices: 164097--164464 Score: 648
Period size: 186 Copynumber: 2.0 Consensus size: 185
164087 AAATTAAATG
* *
164097 TTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTA
1 TTTTTAATTAAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTA
* *
164162 GATAAAT-TTTTTAATTAATTAATATTGATTTAGGTTTAAAATTTATTGGATCTTAAATTATTAA
66 GAT-AATGTTTTTAAATAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
* *
164226 TTGGGTTTTAAATGGTTTGGGCTTAGCCCATATGTTATATATAATATATTTAATAC
130 TTGGGTTTTAAATGGTTTGGCCTGAGCCCATATGTTATATATAATATATTTAATAC
164282 TTTTTAATTAAAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
1 TTTTTAATTAAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTT
*
164347 ATATAATGTTTTTAAATAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
65 AGATAATGTTTTTAAATAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
164412 TTGGGTTTTAAATGGTTTGGCCTGAGCCCATATGTTATATATAATATATTTAA
130 TTGGGTTTTAAATGGTTTGGCCTGAGCCCATATGTTATATATAATATATTTAA
164465 AATTTAATTT
Statistics
Matches: 174, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
185 19 0.11
186 155 0.89
ACGTcount: A:0.41, C:0.04, G:0.10, T:0.45
Consensus pattern (185 bp):
TTTTTAATTAAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTTA
GATAATGTTTTTAAATAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
TGGGTTTTAAATGGTTTGGCCTGAGCCCATATGTTATATATAATATATTTAATAC
Found at i:173357 original size:21 final size:20
Alignment explanation
Indices: 173329--173367 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
173319 ACCATTGGGC
173329 AGAGGGGTTTCAAAACCTAT
1 AGAGGGGTTTCAAAACCTAT
*
173349 AGAGTGGGTTTCGAAACCT
1 AGAG-GGGTTTCAAAACCT
173368 TAAGTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (20 bp):
AGAGGGGTTTCAAAACCTAT
Found at i:178026 original size:14 final size:14
Alignment explanation
Indices: 177993--178026 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
177983 TGATTATAAG
*
177993 ATAATATTTATTTT
1 ATAATATTTATTAT
*
178007 AAAATATTTATTAT
1 ATAATATTTATTAT
178021 ATAATA
1 ATAATA
178027 ATAAAATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
ATAATATTTATTAT
Found at i:179004 original size:60 final size:60
Alignment explanation
Indices: 178935--179064 Score: 233
Period size: 60 Copynumber: 2.2 Consensus size: 60
178925 AGGAGATGAA
*
178935 GGTAGCTGAGGACTTGGTAGCCAAGCTAAGGACTAAAGGCAATTGCAGTGTAGCTCAGAT
1 GGTAGCTGAGGACTTGGTAGCCAAGCTAAGGACTAAAGGCAATTGAAGTGTAGCTCAGAT
*
178995 GTTAGCTGAGGACTTGGTAGCCAAGCTAAGGACTAAAGGCAATTGAAGTGTAGCTCAGAT
1 GGTAGCTGAGGACTTGGTAGCCAAGCTAAGGACTAAAGGCAATTGAAGTGTAGCTCAGAT
*
179055 GGTAGTTGAG
1 GGTAGCTGAG
179065 TAGCTGGAGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (60 bp):
GGTAGCTGAGGACTTGGTAGCCAAGCTAAGGACTAAAGGCAATTGAAGTGTAGCTCAGAT
Found at i:180130 original size:29 final size:29
Alignment explanation
Indices: 180088--180148 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
180078 AGTCCATTAT
180088 TCTTTTACTCAACAATGTTTAACCCTTCA
1 TCTTTTACTCAACAATGTTTAACCCTTCA
* * *
180117 TCTTTTACTCAACAGTGTTTAATCGTTCA
1 TCTTTTACTCAACAATGTTTAACCCTTCA
180146 TCT
1 TCT
180149 AGCATAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.44
Consensus pattern (29 bp):
TCTTTTACTCAACAATGTTTAACCCTTCA
Found at i:180263 original size:81 final size:77
Alignment explanation
Indices: 180116--180281 Score: 233
Period size: 81 Copynumber: 2.1 Consensus size: 77
180106 TTAACCCTTC
* *
180116 ATCTTTTACTCAACAGTGTTTAATCGTTCATCTAGCATAATTGACACCTTTCTGCCAATTGCACA
1 ATCTTTTACTCAACAGTATTTAACCGTTCATCTAGCATAATTGACACCTTTCTGCCAATTGCACA
180181 GTTAGGACATTA
66 GTTAGGACATTA
* * * *
180193 TTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGGCATAATTGACACCTTTCTTCCATTTG
1 ATCTTTTACTCAACAGTATTTAACCGTTCATCT-A---GCATAATTGACACCTTTCTGCCAATTG
*
180258 CACAGTTAGGCCATTA
62 CACAGTTAGGACATTA
180274 ATCTTTTA
1 ATCTTTTA
180282 TTTTGGACTA
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
77 29 0.38
78 1 0.01
81 47 0.61
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.39
Consensus pattern (77 bp):
ATCTTTTACTCAACAGTATTTAACCGTTCATCTAGCATAATTGACACCTTTCTGCCAATTGCACA
GTTAGGACATTA
Found at i:180496 original size:55 final size:55
Alignment explanation
Indices: 180428--180820 Score: 554
Period size: 55 Copynumber: 7.1 Consensus size: 55
180418 GATGCGCACG
*
180428 TAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
*
180483 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* ** ** * * * *
180538 TAATGTTTGTACTATTATTCATGAACTTATGATAAATTCCGTGAATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * *
180593 TAGTGCCTGTACGGTTATTCATTAACTCATGATGAATTTCGTGGATTTGCACATA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * ** *
180648 TAGTGCATGTACAGTTATTCATCAACTCATGATGAATTATGTGGTTTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* *
180703 TAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
* * *
180758 TAGTGCCAGTGCGGTTATTCATCAACTCATGATGAATTCAGTGGATTTGCACACA
1 TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
180813 TAGTGCCT
1 TAGTGCCT
180821 ATTTGGTAAT
Statistics
Matches: 297, Mismatches: 40, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
55 295 0.99
56 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (55 bp):
TAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATTTGCACACA
Found at i:192274 original size:17 final size:15
Alignment explanation
Indices: 192247--192293 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
192237 TGTAAGTTAC
*
192247 TAATATATATATAGT
1 TAATATATATATATT
*
192262 TAATATATGTATATT
1 TAATATATATATATT
*
192277 TAATATACATATGATT
1 TAATATATATAT-ATT
192293 T
1 T
192294 TAATTATCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (15 bp):
TAATATATATATATT
Found at i:193269 original size:16 final size:16
Alignment explanation
Indices: 193250--193284 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
193240 TGACCCCTTC
193250 ATAAGCAACATAGAAT
1 ATAAGCAACATAGAAT
193266 ATAAGCAACATAGAAT
1 ATAAGCAACATAGAAT
193282 ATA
1 ATA
193285 GGCCCACGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.20
Consensus pattern (16 bp):
ATAAGCAACATAGAAT
Found at i:206383 original size:90 final size:89
Alignment explanation
Indices: 206228--206402 Score: 314
Period size: 90 Copynumber: 2.0 Consensus size: 89
206218 TAACACACCC
*
206228 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATATT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
*
206293 TAATTAATTGAAATTTAATAATTT
66 TAATTAATTGAAATTAAATAATTT
*
206317 TTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATAT
206382 TTAATTAATTGAAATTAAATA
65 TTAATTAATTGAAATTAAATA
206403 TCTGGGATTA
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
89 32 0.39
90 50 0.61
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (89 bp):
TTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATT
TAATTAATTGAAATTAAATAATTT
Found at i:207966 original size:60 final size:61
Alignment explanation
Indices: 207843--207967 Score: 157
Period size: 61 Copynumber: 2.1 Consensus size: 61
207833 TATAATTCGT
*
207843 TTTCATATTTATTTCCTTTTAGAAACTTTCAAAACTTTCACATTTATTTATCATATTTGAC
1 TTTCATATTTATTTCCTTTTAGAAACTTTCAAAACTTTCACATTCATTTATCATATTTGAC
* * ** *
207904 TTTCATA-TTCTTTCCTTTTAGATACTTTTCTTAACTTTCACATTCACTTT-TTATATTT-AC
1 TTTCATATTTATTTCCTTTTAGAAAC-TTTCAAAACTTTCACATTCA-TTTATCATATTTGAC
207964 TTTC
1 TTTC
207968 TTAGCCCAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
60 22 0.39
61 31 0.55
62 3 0.05
ACGTcount: A:0.25, C:0.18, G:0.02, T:0.54
Consensus pattern (61 bp):
TTTCATATTTATTTCCTTTTAGAAACTTTCAAAACTTTCACATTCATTTATCATATTTGAC
Found at i:216596 original size:23 final size:23
Alignment explanation
Indices: 216570--216622 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
216560 GTATTTAGTA
216570 TTTCATCCCAAAGGCATTTTACC
1 TTTCATCCCAAAGGCATTTTACC
*
216593 TTTCATCCCAAAGGCATTTTTCC
1 TTTCATCCCAAAGGCATTTTACC
216616 TTTCATC
1 TTTCATC
216623 TAACTTGCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.23, C:0.30, G:0.08, T:0.40
Consensus pattern (23 bp):
TTTCATCCCAAAGGCATTTTACC
Found at i:217051 original size:243 final size:243
Alignment explanation
Indices: 216614--217084 Score: 685
Period size: 243 Copynumber: 1.9 Consensus size: 243
216604 AGGCATTTTT
* * * * * *
216614 CCTTTCATCTAACTTGCATTATTGGCACATTTCTACCAAATGTATAGTTAAGCATTTAATCTTTT
1 CCTTTCATCTAACTTGCATGATTGACACATTTCTACCAAATGCACAGCTAAGAATTTAATCTTTT
* * *
216679 ACTCAAAGGTATTTAACCTTTCATCTAATTGGCATGATTGATATATTTCTATCAAATGCACAACT
66 ACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACT
* * *
216744 AGGCATTTAATCCTTTACTCAAAGGTATTTAACCTTTCATTTAACAGGCATGATTGACACCTTTC
131 AGGCATTTAATCCTTTACTCAAAGGTATTTAACCTTTCATCTAACAGGCATAATAGACACCTTTC
* * *
216809 TAACAAATTCATAGTTA-GACATTTAATCTTTTACTCAAAGGTATTTAA
196 TAACAAATACACAGCTAGGA-ATTTAATCTTTTACTCAAAGGTATTTAA
* **
216857 CCTTTCATCTAACTTGCATGATTGACACATTTTTGTCAAATGCACAGCTAAGAATTTAATCTTTT
1 CCTTTCATCTAACTTGCATGATTGACACATTTCTACCAAATGCACAGCTAAGAATTTAATCTTTT
* *
216922 ACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGCACAACT
66 ACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACT
* * *
216987 AGGCATTTAAT-CTTATACTCAAAGGTATTTAACCTTTCATCTAACTGTCATAATAGAGACCTTT
131 AGGCATTTAATCCTT-TACTCAAAGGTATTTAACCTTTCATCTAACAGGCATAATAGACACCTTT
**
217051 CTGTCAAATACACAGCTAGGAATTTAATCTTTTA
195 CTAACAAATACACAGCTAGGAATTTAATCTTTTA
217085 TTTTAAAATA
Statistics
Matches: 201, Mismatches: 25, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
242 3 0.01
243 196 0.98
244 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (243 bp):
CCTTTCATCTAACTTGCATGATTGACACATTTCTACCAAATGCACAGCTAAGAATTTAATCTTTT
ACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTATCAAATGCACAACT
AGGCATTTAATCCTTTACTCAAAGGTATTTAACCTTTCATCTAACAGGCATAATAGACACCTTTC
TAACAAATACACAGCTAGGAATTTAATCTTTTACTCAAAGGTATTTAA
Found at i:217097 original size:81 final size:81
Alignment explanation
Indices: 216614--217084 Score: 584
Period size: 81 Copynumber: 5.8 Consensus size: 81
216604 AGGCATTTTT
* * * ** * * * * *
216614 CCTTTCATCTAACTTGCATTATTGGCACATTTCTACCAAATGTATAGTTAAGCATTTAATCTTTT
1 CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGAATTTAATCTTTT
216679 ACTCAAAGGTATTTAA
66 ACTCAAAGGTATTTAA
* * * * * * *
216695 CCTTTCATCTAATTGGCATGATTGATATATTTCTATCAAATGCACAACTAGGCATTTAATCCTTT
1 CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGAATTTAATCTTTT
216760 ACTCAAAGGTATTTAA
66 ACTCAAAGGTATTTAA
* * * ** * * *
216776 CCTTTCATTTAACAGGCATGATTGACACCTTTCTAACAAATTCATAGTTA-GACATTTAATCTTT
1 CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGA-ATTTAATCTTT
216840 TACTCAAAGGTATTTAA
65 TACTCAAAGGTATTTAA
* * *
216857 CCTTTCATCTAACTTGCATGATTGACACATTTTTGTCAAATGCACAGCTAAGAATTTAATCTTTT
1 CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGAATTTAATCTTTT
216922 ACTCAAAGGTATTTAA
66 ACTCAAAGGTATTTAA
* * * *
216938 CCTTTCATCTAACTGGCATGATTGACACATTTTTGTCAAATGCACAACTAGGCATTTAATCTTAT
1 CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGAATTTAATCTTTT
217003 ACTCAAAGGTATTTAA
66 ACTCAAAGGTATTTAA
* * * * * *
217019 CCTTTCATCTAACTGTCATAATAGAGACCTTTCTGTCAAATACACAGCTAGGAATTTAATCTTTT
1 CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGAATTTAATCTTTT
217084 A
66 A
217085 TTTTAAAATA
Statistics
Matches: 337, Mismatches: 51, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
80 1 0.00
81 334 0.99
82 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (81 bp):
CCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGAATTTAATCTTTT
ACTCAAAGGTATTTAA
Found at i:222391 original size:49 final size:49
Alignment explanation
Indices: 222337--222430 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
222327 CTTTAACTAA
* * * *
222337 CTTGCATTAGTGGAACCTTTCTACCAGAAATGCACCGTTAGGTATCTAT
1 CTTGCATTAATGGAACCTTTCTACCAAAAAAGCACAGTTAGGTATCTAT
*
222386 CTTGCATTAATGGCACCTTTCTACCAAAAAAGCACAGTTAGGTAT
1 CTTGCATTAATGGAACCTTTCTACCAAAAAAGCACAGTTAGGTAT
222431 TTAGTCTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (49 bp):
CTTGCATTAATGGAACCTTTCTACCAAAAAAGCACAGTTAGGTATCTAT
Found at i:222572 original size:81 final size:81
Alignment explanation
Indices: 222445--222926 Score: 662
Period size: 81 Copynumber: 6.0 Consensus size: 81
222435 TCTTTCATCC
* * * * * * * *
222445 CAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTTTTCTGCCAAATGTACAATTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
* *
222510 CATTTAATATTTTATT
66 CATTTAATCTTTTACT
* * * * *
222526 CAAGGGTATTTAACCTTTCATCTAACTGGCACGATTGACACATTTCTATTAAATGAACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
*
222591 AATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* *
222607 CAAAGGTATTTAACCTTTCATCT-ACTGGCATGATTGATACATTTATGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
*
222671 CATTTAATCTTTTTCT
66 CATTTAATCTTTTACT
* * * * * * *
222687 CAAAGATATTCAACCTTTCATCTAACTGGCATGATTAACACCTTTCTGTCAAACGCACAGCTAGA
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
222752 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* * * *
222768 CAAATGTATTTAACCTTTCATCAAACTGGCATGATTGACACA-TTCTGCCAAATGCACATCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
222832 CATTTAATCTTTTACT
66 CATTTAATCTTTTACT
* *
222848 CAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTATGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
222913 CATTTAATCTTTTA
66 CATTTAATCTTTTA
222927 TTTTAAAATA
Statistics
Matches: 349, Mismatches: 50, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
80 143 0.41
81 206 0.59
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAACTAGG
CATTTAATCTTTTACT
Found at i:222759 original size:161 final size:161
Alignment explanation
Indices: 222445--222926 Score: 646
Period size: 161 Copynumber: 3.0 Consensus size: 161
222435 TCTTTCATCC
* * * * * * *
222445 CAAAGGCATTTAACCTTTCATCTAACTTGCATTATTGGCACTTTTCTGCCAAATGTACAATTAGG
1 CAAAGGTATTTAACCTTTCATCT-ACTGGCATGATTGACACATTTCTGCCAAATGCACAACTAGG
* * * *
222510 CATTTAATATTTTAT-TCAAGGGTATTTAACCTTTCATCTAACTGGCACGATTGACACATTTCTA
65 CATTTAATCTTTT-TCTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTG
* *
222574 TTAAATGAACAACTAGGA-ATTTAATCTTTTACT
129 TCAAATGCACAACTA-GACATTTAATCTTTTACT
* * *
222607 CAAAGGTATTTAACCTTTCATCTACTGGCATGATTGATACATTTATGTCAAATGCACAACTAGGC
1 CAAAGGTATTTAACCTTTCATCTACTGGCATGATTGACACATTTCTGCCAAATGCACAACTAGGC
* * * *
222672 ATTTAATCTTTTTCTCAAAGATATTCAACCTTTCATCTAACTGGCATGATTAACACCTTTCTGTC
66 ATTTAATCTTTTTCTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTC
* *
222737 AAACGCACAGCTAGACATTTAATCTTTTACT
131 AAATGCACAACTAGACATTTAATCTTTTACT
* * *
222768 CAAATGTATTTAACCTTTCATCAAACTGGCATGATTGACACA-TTCTGCCAAATGCACATCTAGG
1 CAAAGGTATTTAACCTTTCATC-TACTGGCATGATTGACACATTTCTGCCAAATGCACAACTAGG
* * *
222832 CATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATTTATGT
65 CATTTAATCTTTTTCTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGT
*
222897 CAAATGCACAACTAGGCATTTAATCTTTTA
130 CAAATGCACAACTAGACATTTAATCTTTTA
222927 TTTTAAAATA
Statistics
Matches: 279, Mismatches: 38, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
160 3 0.01
161 237 0.85
162 39 0.14
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.37
Consensus pattern (161 bp):
CAAAGGTATTTAACCTTTCATCTACTGGCATGATTGACACATTTCTGCCAAATGCACAACTAGGC
ATTTAATCTTTTTCTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTC
AAATGCACAACTAGACATTTAATCTTTTACT
Found at i:222882 original size:242 final size:242
Alignment explanation
Indices: 222456--222925 Score: 699
Period size: 242 Copynumber: 1.9 Consensus size: 242
222446 AAAGGCATTT
* * ** * * * * *
222456 AACCTTTCATCTAACTTGCATTATTGGCACTTTTCTGCCAAATGTACAATTAGGCATTTAATATT
1 AACCTTTCATCTAACTGGCATGATTAACACCTTTCTGCCAAACGCACAACTAGACATTTAATATT
* * * **
222521 TTATTCAAGGGTATTTAACCTTTCATCTAACTGGCACGATTGACACATTTCTATTAAATGAACAA
66 TTACTCAAAGGTATTTAACCTTTCATCAAACTGGCACGATTGACACATTTCTACCAAATGAACAA
* *
222586 CTAGGAATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTACTGGCATGATTGATACATTT
131 CTAGGAATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTACTAGCATGATTGACACATTT
222651 ATGTCAAATGCACAACTAGGCATTTAATCTTTTTCTCAAAGATATTC
196 ATGTCAAATGCACAACTAGGCATTTAATCTTTTTCTCAAAGATATTC
* * *
222698 AACCTTTCATCTAACTGGCATGATTAACACCTTTCTGTCAAACGCACAGCTAGACATTTAATCTT
1 AACCTTTCATCTAACTGGCATGATTAACACCTTTCTGCCAAACGCACAACTAGACATTTAATATT
* * * * *
222763 TTACTCAAATGTATTTAACCTTTCATCAAACTGGCATGATTGACACA-TTCTGCCAAATGCACAT
66 TTACTCAAAGGTATTTAACCTTTCATCAAACTGGCACGATTGACACATTTCTACCAAATGAACAA
*
222827 CTAGGCATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTAGCATGATTGACACATT
131 CTAGGAATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCT-ACTAGCATGATTGACACATT
222892 TATGTCAAATGCACAACTAGGCATTTAATCTTTT
195 TATGTCAAATGCACAACTAGGCATTTAATCTTTT
222926 ATTTTAAAAT
Statistics
Matches: 202, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
241 55 0.27
242 147 0.73
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.37
Consensus pattern (242 bp):
AACCTTTCATCTAACTGGCATGATTAACACCTTTCTGCCAAACGCACAACTAGACATTTAATATT
TTACTCAAAGGTATTTAACCTTTCATCAAACTGGCACGATTGACACATTTCTACCAAATGAACAA
CTAGGAATTTAATCTTTTACTCAAAGGTATTTAACCTTTCATCTACTAGCATGATTGACACATTT
ATGTCAAATGCACAACTAGGCATTTAATCTTTTTCTCAAAGATATTC
Found at i:223448 original size:94 final size:95
Alignment explanation
Indices: 223341--223513 Score: 231
Period size: 94 Copynumber: 1.8 Consensus size: 95
223331 TACCCCTACC
* * *
223341 ATGGTATCGATACTCCCTTTCAGTATCGATACCATTTCTACATTCTAG-ATCATTGGTATCAATA
1 ATGGTATCGATACTCCATTACAGTATCGATACCATTTCTACATTCTAGAATCAATGGTATCAATA
* *
223405 CCTTTCTCTTAGTAATAATACTTCTATATT
66 CCTTCCTCATAGTAATAATACTTCTATATT
* * * * * **
223435 ATGGTATCGATACTCTATTAGAGTATCGATACCATTTTTGCATTCTGGAATCAATGGTATCGTTA
1 ATGGTATCGATACTCCATTACAGTATCGATACCATTTCTACATTCTAGAATCAATGGTATCAATA
223500 CCTTCCTCATAGTA
66 CCTTCCTCATAGTA
223514 TCGATGCCCA
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
94 41 0.62
95 25 0.38
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (95 bp):
ATGGTATCGATACTCCATTACAGTATCGATACCATTTCTACATTCTAGAATCAATGGTATCAATA
CCTTCCTCATAGTAATAATACTTCTATATT
Found at i:228642 original size:21 final size:19
Alignment explanation
Indices: 228604--228649 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
228594 AATTAATTCT
228604 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
228624 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
228645 A-TAAT
1 ACTAAT
228650 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:238742 original size:21 final size:19
Alignment explanation
Indices: 238704--238749 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
238694 AATTAATCCT
238704 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
238724 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
238745 A-TAAT
1 ACTAAT
238750 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:242791 original size:32 final size:32
Alignment explanation
Indices: 242754--242818 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
242744 AGAATCTGAT
242754 TTCAATAAAACCCCACTCTCAAGAGTAAACTA
1 TTCAATAAAACCCCACTCTCAAGAGTAAACTA
242786 TTCAATAAAACCCCACTCTCAAGAGTAAACTA
1 TTCAATAAAACCCCACTCTCAAGAGTAAACTA
242818 T
1 T
242819 CTATTTATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.28, G:0.06, T:0.23
Consensus pattern (32 bp):
TTCAATAAAACCCCACTCTCAAGAGTAAACTA
Found at i:254424 original size:15 final size:15
Alignment explanation
Indices: 254404--254439 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
254394 TTAACCATAT
254404 TTAATACCAACTATA
1 TTAATACCAACTATA
254419 TTAATACCAACTATA
1 TTAATACCAACTATA
254434 TTAATA
1 TTAATA
254440 ATTTGCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATACCAACTATA
Found at i:255018 original size:67 final size:67
Alignment explanation
Indices: 254898--255026 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 67
254888 CTGCTTGCAT
* * *
254898 ATAAGGTTGTGCCCACCATATGCATTAAGTGTCCTTACACACTACAGTGCTATCCCGAGTATGAC
1 ATAAGGTCGTGCCCACCACATGCAATAAGTGTCCTTACACACTACAGTGCTATCCCGAGTATGAC
254963 AC
66 AC
* * * * *
254965 ATAAGGTCGTGTCCACCACCTGCAATAAGTGTCCTTACATACTATAGTTCTATCCCGAGTAT
1 ATAAGGTCGTGCCCACCACATGCAATAAGTGTCCTTACACACTACAGTGCTATCCCGAGTAT
255027 ACAGCCTACT
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.29
Consensus pattern (67 bp):
ATAAGGTCGTGCCCACCACATGCAATAAGTGTCCTTACACACTACAGTGCTATCCCGAGTATGAC
AC
Found at i:257892 original size:8 final size:8
Alignment explanation
Indices: 257879--257908 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
257869 TATACATTTC
257879 AAATTTTA
1 AAATTTTA
257887 AAATTTTA
1 AAATTTTA
257895 AAATTTTA
1 AAATTTTA
257903 AGAATT
1 A-AATT
257909 AAGATTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (8 bp):
AAATTTTA
Found at i:267437 original size:18 final size:18
Alignment explanation
Indices: 267314--267430 Score: 207
Period size: 18 Copynumber: 6.5 Consensus size: 18
267304 GAGGGATTAT
*
267314 CAGTGGTCTTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
267332 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
267350 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
267368 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
267386 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
267404 CAGTGGTCCTTCGGGATA
1 CAGTGGTCCTTCGGGACA
267422 CAGTGGTCC
1 CAGTGGTCC
267431 AATGGGACAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 95 1.00
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:269787 original size:2 final size:2
Alignment explanation
Indices: 269780--269817 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
269770 AGTAAGAAAG
269780 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
269818 GAGTATCGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270855 original size:18 final size:18
Alignment explanation
Indices: 270731--270845 Score: 185
Period size: 18 Copynumber: 6.4 Consensus size: 18
270721 AGGGATTATC
*
270731 AGTGGTCCTTCGGGTCAT
1 AGTGGTCCTTCGGGACAT
*
270749 AGTGGTTCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
270767 AGTGGTCCTTCGGGACAC
1 AGTGGTCCTTCGGGACAT
270785 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
270803 AGTGGTCCTTCGGGACAC
1 AGTGGTCCTTCGGGACAT
*
270821 AGTGGTCCTTCGTGACAT
1 AGTGGTCCTTCGGGACAT
270839 AGTGGTC
1 AGTGGTC
270846 ATACAGGACA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 89 1.00
ACGTcount: A:0.16, C:0.23, G:0.33, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:286523 original size:34 final size:34
Alignment explanation
Indices: 286474--286542 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 34
286464 TATATCGGTT
286474 TAAAGCTTTTAGGTGTGACAAGAGATATTTCTAA
1 TAAAGCTTTTAGGTGTGACAAGAGATATTTCTAA
*
286508 TAAAGCATTTT-GGTGTTACAAGAGATATTTCTAA
1 TAAAGC-TTTTAGGTGTGACAAGAGATATTTCTAA
286542 T
1 T
286543 CTTTTAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
34 29 0.88
35 4 0.12
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (34 bp):
TAAAGCTTTTAGGTGTGACAAGAGATATTTCTAA
Found at i:292610 original size:20 final size:21
Alignment explanation
Indices: 292566--292618 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 21
292556 AAAATGTCTT
* *
292566 AGTATCGATACTAACCCTTTG
1 AGTATCGATACTAACACTCTG
292587 AGTATCGATACTAA-ACTCTG
1 AGTATCGATACTAACACTCTG
292607 AGTATCGATACT
1 AGTATCGATACT
292619 CCTTAAATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTAACACTCTG
Found at i:301656 original size:76 final size:78
Alignment explanation
Indices: 301522--301665 Score: 188
Period size: 77 Copynumber: 1.9 Consensus size: 78
301512 TTAAGCATTA
*
301522 AAAGAATGTAATTTAGATTACAACTCTTTTAATTGATATATAATTCGGAATAATTAAATAAT-TT
1 AAAGAATGTAATTTAGATTACAAATCTTTTAATTGATATATAATTCGGAATAATTAAATAATATT
301586 TTAAATAAAAATT
66 TTAAATAAAAATT
* * * * *
301599 AAAGATTGTCATTTAGATTATAAATC-TTTAA-TGTATATTTAATT-TGAATTAATTAAATAATA
1 AAAGAATGTAATTTAGATTACAAATCTTTTAATTG-ATATATAATTCGGAA-TAATTAAATAATA
301661 TTTTA
64 TTTTA
301666 TTTATTAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
75 5 0.09
76 26 0.45
77 27 0.47
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (78 bp):
AAAGAATGTAATTTAGATTACAAATCTTTTAATTGATATATAATTCGGAATAATTAAATAATATT
TTAAATAAAAATT
Found at i:305766 original size:178 final size:177
Alignment explanation
Indices: 305402--305847 Score: 431
Period size: 178 Copynumber: 2.5 Consensus size: 177
305392 AATTGAAGGC
* * ** * * *
305402 ATATAGTGACTACTTTTGTAACTAA-AAGTTTTAGTAACTATGACAAAAAAGTTGTCACAACAAA
1 ATATAGTGACAAATTTTGTAAC-AATAAGTGATAATAATTATTACAAAAAA-TTGTCACAACAAA
* * ***
305466 TAATGAGATT-TAGATTTGTTGTGACAAATTTTGTTTGTAATTATATATTTTAATTATAGTGACA
64 TAATGAGATTCAAG-TTT-TTGTGAAAAAAAATGTTTGTAATTATATATTTTAATTATAGTGACA
* * *
305530 AAATGTATAGTCACAAATGATTATCTCCAATTTTTGGTACAAAAACAAAATC
127 AAATATATAGCCACAAATGATTATCTCCAATTTTT-GTACAAAAACAAAATA
** * *
305582 ATATAGTGACATGTTTTGTAACAATAAGCT-ATAATTATTGTTACAAAAAATTGTCACAACAAAT
1 ATATAGTGACAAATTTTGTAACAATAAG-TGATAATAATTATTACAAAAAATTGTCACAACAAAT
** *
305646 AATGAGATTCAAGTTTTTAGT-AAAAAAAATGTTTGTCGTTATATGTTTTAATTATAGTGACAAA
65 AATGAGATTCAAGTTTTT-GTGAAAAAAAATGTTTGTAATTATATATTTTAATTATAGTGACAAA
* * *
305710 ATATATTGCCATAAA-GATT-TCCCTCCATATTTATT-TGCAAAAA-AAAAGTA
129 ATATATAGCCACAAATGATTAT--CTCCA-ATTT-TTGTACAAAAACAAAA-TA
* * *
305760 ATATAGTGACAAATTTTGTAACTATAAGTGTTAATAATTATTACAAAAAACATTGTCACAAAAAA
1 ATATAGTGACAAATTTTGTAACAATAAGTGATAATAATTATTAC-AAAAA-ATTGTCACAACAAA
* * *
305825 TAATTATATTCATGTTTTTGTGA
64 TAATGAGATTCAAGTTTTTGTGA
305848 CAAATTATAT
Statistics
Matches: 220, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
176 1 0.00
177 9 0.04
178 98 0.45
179 41 0.19
180 70 0.32
181 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (177 bp):
ATATAGTGACAAATTTTGTAACAATAAGTGATAATAATTATTACAAAAAATTGTCACAACAAATA
ATGAGATTCAAGTTTTTGTGAAAAAAAATGTTTGTAATTATATATTTTAATTATAGTGACAAAAT
ATATAGCCACAAATGATTATCTCCAATTTTTGTACAAAAACAAAATA
Found at i:307127 original size:21 final size:18
Alignment explanation
Indices: 307092--307136 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
307082 TCTTCGTAAT
307092 GATACCTCTATTGGGAGTATC
1 GATA-CTCTATT-GG-GTATC
307113 GATACTCTATCTGGGTATC
1 GATACTCTAT-TGGGTATC
307132 GATAC
1 GATAC
307137 AACCATTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.43
20 8 0.35
21 5 0.22
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (18 bp):
GATACTCTATTGGGTATC
Found at i:324920 original size:2 final size:2
Alignment explanation
Indices: 324913--324967 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
324903 GGGGTCACAA
324913 AT AT AT AT AT AT A- AT AT AT AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324953 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
324968 ACTAACCAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 2 0.04
2 49 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:331018 original size:24 final size:22
Alignment explanation
Indices: 330983--331027 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
330973 ATTCATGTGA
330983 TTTAAATAACTACAT-GATCATT
1 TTTAAATAACTAC-TGGATCATT
331005 TTTACAATATACTACTGGATCAT
1 TTTA-AATA-ACTACTGGATCAT
331028 GATTTTGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAAATAACTACTGGATCATT
Found at i:341926 original size:22 final size:23
Alignment explanation
Indices: 341884--341927 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
341874 TTGAGCCTCC
*
341884 TTACATCCAATGGCCTAGATTAT
1 TTACATCCAACGGCCTAGATTAT
*
341907 TTACAT-CAACGGTCTAGATTA
1 TTACATCCAACGGCCTAGATTA
341928 AAAGTATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (23 bp):
TTACATCCAACGGCCTAGATTAT
Found at i:342174 original size:3 final size:3
Alignment explanation
Indices: 342168--342237 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
342158 TAAATATCAA
342168 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
342216 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
342238 TACTCCACAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:342565 original size:27 final size:26
Alignment explanation
Indices: 342497--342578 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 26
342487 ATTTATATCA
*
342497 ATATTATTATTAAAATATTATATCTA-T
1 ATATT-TTATTAAAATATTAAAT-TATT
*
342524 A-ATTTTATAAAAAAATATTAAGATTATT
1 ATATTTTAT--TAAAATATTAA-ATTATT
342552 ATATTTTATTAAAATA--AAATTATT
1 ATATTTTATTAAAATATTAAATTATT
342576 ATA
1 ATA
342579 AATCATATTA
Statistics
Matches: 47, Mismatches: 3, Indels: 13
0.75 0.05 0.21
Matches are distributed among these distances:
24 9 0.19
25 6 0.13
26 3 0.06
27 18 0.38
28 4 0.09
29 7 0.15
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (26 bp):
ATATTTTATTAAAATATTAAATTATT
Found at i:342750 original size:14 final size:15
Alignment explanation
Indices: 342721--342753 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
342711 AGTATATTTT
342721 AAATATTTAATTATG
1 AAATATTTAATTATG
*
342736 AAATATTT-TTTATG
1 AAATATTTAATTATG
342750 AAAT
1 AAAT
342754 TAATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (15 bp):
AAATATTTAATTATG
Found at i:344931 original size:3 final size:3
Alignment explanation
Indices: 344925--345022 Score: 196
Period size: 3 Copynumber: 32.7 Consensus size: 3
344915 GTTTTTTTTT
344925 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
344973 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
345021 TT
1 TT
345023 GTTGTTGCAG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:346093 original size:15 final size:15
Alignment explanation
Indices: 346056--346106 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
346046 AATATTAATT
346056 TTTATTTTTATATAA
1 TTTATTTTTATATAA
* * *
346071 ATTA-TTTTCTATAC
1 TTTATTTTTATATAA
346085 TTTATTTTTTAATATAA
1 TTTA-TTTTT-ATATAA
346102 TTTAT
1 TTTAT
346107 AAATGCATGT
Statistics
Matches: 27, Mismatches: 6, Indels: 5
0.71 0.16 0.13
Matches are distributed among these distances:
14 11 0.41
15 3 0.11
16 5 0.19
17 8 0.30
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTATTTTTATATAA
Found at i:354282 original size:20 final size:19
Alignment explanation
Indices: 354257--354298 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
354247 CATCCTGATC
354257 AAAATGAACGAAATGTAAAT
1 AAAATGAAC-AAATGTAAAT
**
354277 AAAATGGTCAAATGTAAAT
1 AAAATGAACAAATGTAAAT
354296 AAA
1 AAA
354299 CAAAATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (19 bp):
AAAATGAACAAATGTAAAT
Found at i:356050 original size:122 final size:121
Alignment explanation
Indices: 355727--356106 Score: 395
Period size: 122 Copynumber: 3.1 Consensus size: 121
355717 TAATTTTGAG
* * * * * ** * * *
355727 GTTGAAAATGACACTACTCATTCACGTTGAAGAGATT-TGGCCACTTTTATGTAAATTGTTTGTT
1 GTTGAAGACGACACTACTCATCCATGTTAAAGAG-TTCTGGCTGCTTTCAGGTAAATTGTTTGCT
* * * *
355791 GAAGATGATGTTGTTTCTTTTCTTTTAGGAAGTCAAGTCAATCTGAAGATAATTTAGT
65 GAAGATGATGTTG-TTCTTTTCATTGAGGAAGTCAGGTCAATCTGGAGATAATTTAGT
* *
355849 GTTGAAGACGACACTACTCATCCATGTTAAAGAGTTCTGGCTGCTTTTAGGTAAATTATTTGCTG
1 GTTGAAGACGACACTACTCATCCATGTTAAAGAGTTCTGGCTGCTTTCAGGTAAATTGTTTGCTG
* * *
355914 AAGATGATGTTGTTCATTTTCATTGAGGAAATTAGGTCAATCTGGAGATAATTTTGT
66 AAGATGATGTTGTTC-TTTTCATTGAGGAAGTCAGGTCAATCTGGAGATAATTTAGT
* * * *
355971 GTTGAAGGCGATACTGCTCATCCATGTTGAAGAGTTCTGG-TCGCTTTCAGGTAAATTGTTTGCT
1 GTTGAAGACGACACTACTCATCCATGTTAAAGAGTTCTGGCT-GCTTTCAGGTAAATTGTTTGCT
* * * * ** * * * *
356035 GAAGATAACGATGTTCCTTCTGGTTGAGGAAGTCGGGTTAATCTGGAGATAATATGGT
65 GAAGATGATGTTGTT-CTTTTCATTGAGGAAGTCAGGTCAATCTGGAGATAATTTAGT
*
356093 GTTGAAAACGACAC
1 GTTGAAGACGACAC
356107 CGTTCATTCT
Statistics
Matches: 216, Mismatches: 38, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
121 6 0.03
122 209 0.97
123 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (121 bp):
GTTGAAGACGACACTACTCATCCATGTTAAAGAGTTCTGGCTGCTTTCAGGTAAATTGTTTGCTG
AAGATGATGTTGTTCTTTTCATTGAGGAAGTCAGGTCAATCTGGAGATAATTTAGT
Found at i:356497 original size:137 final size:136
Alignment explanation
Indices: 356264--356779 Score: 569
Period size: 137 Copynumber: 3.8 Consensus size: 136
356254 ATATCATGGC
* * * * *
356264 TCCTTCGCGTTGAGGAAGTGTGATTGTCTGAGGATAACACCGCTCATTCGCATTGAGGAGATCTG
1 TCCTTCGC-TTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCTTTTGCATTGAGGAGATCTG
* **
356329 GTCGGTGGACAACATTATTT-CTTCGCATTGAGGATGTCTAGATGTATTTGGATAATTTGGAGAC
65 GTCGGTGGACGACATT-TTTCCTTCATATTGAGGATGTCTAGATGTATTTGGATAATTTGGAGAC
* *
356393 AACACAGA
129 AACATAGT
* * * * *
356401 TCCTTCGCTCTGAGGAAGTCTAATTTTCTGAGGATGACACTACTCTTTTACATTGGGGAGATCTG
1 TCCTTCGCT-TGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCTTTTGCATTGAGGAGATCTG
* *
356466 GTCGGTGGACGACATTTTTCCTTCATGTTGAGGATATCTAG-TCGTATTT-GA-AGATTTGGAGA
65 GTCGGTGGACGACATTTTTCCTTCATATTGAGGATGTCTAGAT-GTATTTGGATA-ATTTGGAGA
356528 CAACATAGT
128 CAACATAGT
* * * * * * *
356537 TCTTTCGTGTTGAGGGAGTCTGGTTATCTGAAGATGACACTGCT-TATTTGCGTTGAGGAGATCT
1 TCCTTCG-CTTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCT-TTTGCATTGAGGAGATCT
* * *
356601 GGTCGGTGGACGACATTTTTCCTTCATGTTGAGGACGTCTAGAAGTATTTGGATAATTTGGAGAC
64 GGTCGGTGGACGACATTTTTCCTTCATATTGAGGATGTCTAGATGTATTTGGATAATTTGGAGAC
*
356666 AACATGGT
129 AACATAGT
* * *
356674 TCCTTCGGGTTGAGGAATTCTGATTGTCTGAGGATGACACTGCTCCTTTTTG--TTGAGGAGATA
1 TCCTTC-GCTTGAGGAAGTCTGATTGTCTGAGGATGACACTGCT-C-TTTTGCATTGAGGAGATC
* * * * *
356737 TGGTCGGTGGATGACACTGTTCCTTTATATTGAGTATGTCTAG
63 TGGTCGGTGGACGACATTTTTCCTTCATATTGAGGATGTCTAG
356780 CCGTACTTTG
Statistics
Matches: 320, Mismatches: 46, Indels: 26
0.82 0.12 0.07
Matches are distributed among these distances:
135 2 0.01
136 118 0.37
137 193 0.60
138 2 0.01
139 4 0.01
140 1 0.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (136 bp):
TCCTTCGCTTGAGGAAGTCTGATTGTCTGAGGATGACACTGCTCTTTTGCATTGAGGAGATCTGG
TCGGTGGACGACATTTTTCCTTCATATTGAGGATGTCTAGATGTATTTGGATAATTTGGAGACAA
CATAGT
Found at i:358411 original size:19 final size:19
Alignment explanation
Indices: 358384--358452 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
358374 ATCATAAAAC
*
358384 AAGAGTTCATTAGATATCA
1 AAGAATTCATTAGATATCA
358403 AAGAATTCATTAGATATCA
1 AAGAATTCATTAGATATCA
358422 AAGAATTCATTAGATATCA
1 AAGAATTCATTAGATATCA
*
358441 AAGAATTAATTA
1 AAGAATTCATTA
358453 CACTTTTAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.32
Consensus pattern (19 bp):
AAGAATTCATTAGATATCA
Found at i:359242 original size:19 final size:18
Alignment explanation
Indices: 359215--359260 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 18
359205 GAAATACTTG
359215 ATTTCTTTTCCCTTTTTCTT
1 ATTT-TTTTCCC-TTTTCTT
*
359235 ATTTTTTTCTCTTTTCTT
1 ATTTTTTTCCCTTTTCTT
359253 ATTTTTTT
1 ATTTTTTT
359261 TGTTTCTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 15 0.60
19 6 0.24
20 4 0.16
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (18 bp):
ATTTTTTTCCCTTTTCTT
Found at i:364750 original size:16 final size:16
Alignment explanation
Indices: 364726--364756 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
364716 GGGAATTTAT
364726 ATTTGATTTCGTTGTA
1 ATTTGATTTCGTTGTA
*
364742 ATTTTATTTCGTTGT
1 ATTTGATTTCGTTGT
364757 GTTTGGAAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.06, G:0.16, T:0.61
Consensus pattern (16 bp):
ATTTGATTTCGTTGTA
Found at i:367631 original size:2 final size:2
Alignment explanation
Indices: 367624--367658 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
367614 TCAATCTACA
367624 AT AT AT AT AT 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 A
367659 AATTTACGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:370722 original size:23 final size:21
Alignment explanation
Indices: 370682--370723 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
370672 ACCTAGGGGA
*
370682 GAGTATCAATACGCCATATAG
1 GAGTATCAATACGACATATAG
370703 GAGTATCAATACCGGACATAT
1 GAGTATCAATA-C-GACATAT
370724 TTTCAAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 1 0.06
23 6 0.33
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (21 bp):
GAGTATCAATACGACATATAG
Found at i:372435 original size:14 final size:14
Alignment explanation
Indices: 372381--372451 Score: 72
Period size: 14 Copynumber: 5.1 Consensus size: 14
372371 GATTTTGAGT
*
372381 TGTTGATTCTGAAC
1 TGTTGATTCTAAAC
*
372395 TGTTGACTCTGAAA-
1 TGTTGATTCT-AAAC
*
372409 TATTGATTCTAAAC
1 TGTTGATTCTAAAC
* *
372423 TGTTGATTTTAAAT
1 TGTTGATTCTAAAC
*
372437 TGTTTATTCTAAAC
1 TGTTGATTCTAAAC
372451 T
1 T
372452 ACTGATTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
13 3 0.07
14 40 0.89
15 2 0.04
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.46
Consensus pattern (14 bp):
TGTTGATTCTAAAC
Found at i:372445 original size:28 final size:28
Alignment explanation
Indices: 372369--372460 Score: 87
Period size: 28 Copynumber: 3.3 Consensus size: 28
372359 ATTTGAACGA
* * *
372369 TTGATTTTGAGTTGTTGATTCTGAACTG
1 TTGATTTTAAATTGTTGATTCTAAACTG
* * *
372397 TTGACTCTGAAA-TATTGATTCTAAACTG
1 TTGA-TTTTAAATTGTTGATTCTAAACTG
* *
372425 TTGATTTTAAATTGTTTATTCTAAACTA
1 TTGATTTTAAATTGTTGATTCTAAACTG
*
372453 CTGATTTT
1 TTGATTTT
372461 TAGGTTACTT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 5 0.10
28 42 0.84
29 3 0.06
ACGTcount: A:0.26, C:0.10, G:0.15, T:0.49
Consensus pattern (28 bp):
TTGATTTTAAATTGTTGATTCTAAACTG
Found at i:376820 original size:21 final size:20
Alignment explanation
Indices: 376778--376821 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
376768 ACCTTCTAAC
376778 ATCAATTCCATGCAATTCCA
1 ATCAATTCCATGCAATTCCA
* *
376798 ATCAATTTCATGTCAATTTCA
1 ATCAATTCCATG-CAATTCCA
376819 ATC
1 ATC
376822 CATATTCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (20 bp):
ATCAATTCCATGCAATTCCA
Found at i:377648 original size:21 final size:21
Alignment explanation
Indices: 377624--377665 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
377614 GATTCCTACT
377624 AAAACATCATTCTTGGCTGAA
1 AAAACATCATTCTTGGCTGAA
*
377645 AAAACATCATTCTTGGGTGAA
1 AAAACATCATTCTTGGCTGAA
377666 CTATTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (21 bp):
AAAACATCATTCTTGGCTGAA
Found at i:377692 original size:17 final size:18
Alignment explanation
Indices: 377651--377693 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
377641 TGAAAAAACA
*
377651 TCATTCTTGGGTGAACTAT
1 TCATT-TTGGGTGAAATAT
377670 TCATTTTGGG-GAAATAT
1 TCATTTTGGGTGAAATAT
*
377687 TTATTTT
1 TCATTTT
377694 TGGTAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 12 0.55
18 5 0.23
19 5 0.23
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.49
Consensus pattern (18 bp):
TCATTTTGGGTGAAATAT
Found at i:382745 original size:24 final size:24
Alignment explanation
Indices: 382706--382756 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
382696 ATCAGCAAAG
382706 AAATTGAAGAACTCAAAA-GAAGA
1 AAATTGAAGAACTCAAAAGGAAGA
*
382729 AAATTGCAAGCACTCAAAAGGAAGA
1 AAATTG-AAGAACTCAAAAGGAAGA
382754 AAA
1 AAA
382757 AGAAAAGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.24
24 11 0.44
25 8 0.32
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.12
Consensus pattern (24 bp):
AAATTGAAGAACTCAAAAGGAAGA
Found at i:388516 original size:6 final size:6
Alignment explanation
Indices: 388505--388538 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
388495 ATTAGGACTG
* *
388505 TATTGT TATTGT TATTGT TATTTT TATTAT TATT
1 TATTGT TATTGT TATTGT TATTGT TATTGT TATT
388539 TTCAAGCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (6 bp):
TATTGT
Found at i:398969 original size:19 final size:19
Alignment explanation
Indices: 398945--398986 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
398935 TCGTGATGAT
398945 TGCCTTGGCATAACAGACA
1 TGCCTTGGCATAACAGACA
398964 TGCCTTGGCATAACAGACA
1 TGCCTTGGCATAACAGACA
398983 TGCC
1 TGCC
398987 AGACTAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (19 bp):
TGCCTTGGCATAACAGACA
Done.