Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 77 of 128
Found at i:25250298 original size:16 final size:18
Alignment explanation
Indices: 25250279--25250324 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 18
25250269 CTTGTCAGCA
25250279 ATATTTTTTT-ATTT-TT
1 ATATTTTTTTAATTTATT
25250295 ATATTTTTTTAATTTATT
1 ATATTTTTTTAATTTATT
25250313 ATTATATTTTTT
1 A-TAT-TTTTTT
25250325 TGAAATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 10 0.38
17 4 0.15
18 3 0.12
19 3 0.12
20 6 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (18 bp):
ATATTTTTTTAATTTATT
Found at i:25250312 original size:21 final size:22
Alignment explanation
Indices: 25250286--25250343 Score: 82
Period size: 21 Copynumber: 2.7 Consensus size: 22
25250276 GCAATATTTT
25250286 TTTATTTTTATATTTTTTT-AA
1 TTTATTTTTATATTTTTTTGAA
*
25250307 TTTATTATTATATTTTTTTGAA
1 TTTATTTTTATATTTTTTTGAA
* *
25250329 ATTATTTATATATTT
1 TTTATTTTTATATTT
25250344 GTATATTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTATTTTTATATTTTTTTGAA
Found at i:25250333 original size:22 final size:20
Alignment explanation
Indices: 25250291--25250343 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 20
25250281 ATTTTTTTAT
*
25250291 TTTTATATTTTTTTAATTTA
1 TTTTATATTTTTTTAAATTA
25250311 TTATTATATTTTTTTGAAATTA
1 TT-TTATATTTTTTT-AAATTA
25250333 TTTATATATTT
1 TTT-TATATTT
25250344 GTATATTTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTATATTTTTTTAAATTA
Found at i:25268514 original size:17 final size:17
Alignment explanation
Indices: 25268487--25268519 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
25268477 TCACTACATT
25268487 TTTATTTCACATATTCAC
1 TTTATTTCACA-ATTCAC
25268505 TTTA-TTCACAATTCA
1 TTTATTTCACAATTCA
25268520 TAAAAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.30, C:0.21, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTATTTCACAATTCAC
Found at i:25272121 original size:22 final size:20
Alignment explanation
Indices: 25272075--25272121 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
25272065 NNNNNNNNNA
25272075 TTTT-ATAATTTTTAAATAT
1 TTTTAATAATTTTTAAATAT
* *
25272094 TATTAATATATTTTTTAATAAT
1 TTTTAATA-ATTTTTAAAT-AT
25272116 TTTTAA
1 TTTTAA
25272122 ATTTTATATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 3 0.14
20 3 0.14
21 9 0.41
22 7 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAATAATTTTTAAATAT
Found at i:25272467 original size:46 final size:46
Alignment explanation
Indices: 25272414--25272508 Score: 190
Period size: 46 Copynumber: 2.1 Consensus size: 46
25272404 GTTGGATAAG
25272414 AAAACACAATATTTTGAAATGATGGATAACATTAATTTAATTATCT
1 AAAACACAATATTTTGAAATGATGGATAACATTAATTTAATTATCT
25272460 AAAACACAATATTTTGAAATGATGGATAACATTAATTTAATTATCT
1 AAAACACAATATTTTGAAATGATGGATAACATTAATTTAATTATCT
25272506 AAA
1 AAA
25272509 TGCAAATGAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (46 bp):
AAAACACAATATTTTGAAATGATGGATAACATTAATTTAATTATCT
Found at i:25272490 original size:25 final size:25
Alignment explanation
Indices: 25272416--25272490 Score: 68
Period size: 23 Copynumber: 3.2 Consensus size: 25
25272406 TGGATAAGAA
25272416 AACACAATATTTTGAAATGATGGAT
1 AACACAATATTTTGAAATGATGGAT
* * * ** *
25272441 -A-ACATTAATTT--AATTATCTAA
1 AACACAATATTTTGAAATGATGGAT
25272462 AACACAATATTTTGAAATGATGGAT
1 AACACAATATTTTGAAATGATGGAT
25272487 AACA
1 AACA
25272491 TTAATTTAAT
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
23 16 0.47
24 1 0.03
25 10 0.29
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.33
Consensus pattern (25 bp):
AACACAATATTTTGAAATGATGGAT
Found at i:25276302 original size:26 final size:26
Alignment explanation
Indices: 25276273--25276334 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
25276263 TACCTACAGT
*
25276273 AGTTTCAGAATATCCTA-ACATATATC
1 AGTTTCAGAATATCATAGA-ATATATC
* *
25276299 AGTTTCAGAATATCATAGAATGTTTC
1 AGTTTCAGAATATCATAGAATATATC
25276325 AGTTTCAGAA
1 AGTTTCAGAA
25276335 CACTTACAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
26 31 0.97
27 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (26 bp):
AGTTTCAGAATATCATAGAATATATC
Found at i:25282561 original size:23 final size:23
Alignment explanation
Indices: 25282534--25282615 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
25282524 TGGTAGGAGC
*
25282534 TTATTGGCACTTTGGTGTGATTG
1 TTATTGGCACTTCGGTGTGATTG
* *
25282557 TTATTGACACTTCAGTGTGATTG
1 TTATTGGCACTTCGGTGTGATTG
* * *
25282580 TTATTGGCACATCGGTTTAATTG
1 TTATTGGCACTTCGGTGTGATTG
25282603 TTATTGGCACTTC
1 TTATTGGCACTTC
25282616 AATGCAATTG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.45
Consensus pattern (23 bp):
TTATTGGCACTTCGGTGTGATTG
Found at i:25282624 original size:23 final size:23
Alignment explanation
Indices: 25282553--25282653 Score: 69
Period size: 23 Copynumber: 4.4 Consensus size: 23
25282543 CTTTGGTGTG
* * **
25282553 ATTGTTATTGACACTTCAGTGTG
1 ATTGTTATTGGCACTTCAATGCA
* ** **
25282576 ATTGTTATTGGCACATCGGTTTA
1 ATTGTTATTGGCACTTCAATGCA
25282599 ATTGTTATTGGCACTTCAATGCA
1 ATTGTTATTGGCACTTCAATGCA
* * * *
25282622 ATTGATACTAGCACTATC-ATGCG
1 ATTGTTATTGGCACT-TCAATGCA
25282645 ATTGTTATT
1 ATTGTTATT
25282654 ATGGAGTGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 59 0.97
24 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (23 bp):
ATTGTTATTGGCACTTCAATGCA
Found at i:25290909 original size:22 final size:20
Alignment explanation
Indices: 25290869--25290909 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
25290859 CATATGTTTG
*
25290869 AATGTGTTTAAATATGCTTA
1 AATGTGTTTAAACATGCTTA
25290889 AATGATGTTTAGAACATGCTT
1 AATG-TGTTTA-AACATGCTT
25290910 TTAGTGTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 6 0.33
22 8 0.44
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.41
Consensus pattern (20 bp):
AATGTGTTTAAACATGCTTA
Found at i:25291551 original size:81 final size:81
Alignment explanation
Indices: 25291430--25291680 Score: 288
Period size: 81 Copynumber: 3.1 Consensus size: 81
25291420 TTCTGCCTTC
* * * * * * *
25291430 GGCACTCCTTCTTCCACCCCTGCCTTTGGCACTCCTTCTTCCACCCCGGCCTTTGGAACTACTCC
1 GGCACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCC
* *
25291495 TTCCACTCCGGCTTTT
66 TTCGACACCGGCTTTT
** * ** *
25291511 GGGGCTCCTTCTTCCACACCGGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGTCACTCCTTC
1 GGCACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCC
*
25291576 TTCGACACCGGCCTTT
66 TTCGACACCGGCTTTT
* * * **
25291592 GGCACTCCGTCTTCGACACCTGCGTTTGGGGCTCCGTCTTCGACACCGGCGTTTGGAACTCCGTC
1 GGCACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCC-TC
25291657 C-TCGACACCGGCTTTT
65 CTTCGACACCGGCTTTT
*
25291673 GGAACTCC
1 GGCACTCC
25291681 ATCAACGCCG
Statistics
Matches: 140, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
81 138 0.99
82 2 0.01
ACGTcount: A:0.11, C:0.39, G:0.20, T:0.29
Consensus pattern (81 bp):
GGCACTCCTTCTTCCACACCTGCATTTGGCACTCCGTCTTCGACACCGGCGTTTGGAACTCCTCC
TTCGACACCGGCTTTT
Found at i:25291619 original size:27 final size:27
Alignment explanation
Indices: 25291424--25291680 Score: 228
Period size: 27 Copynumber: 9.5 Consensus size: 27
25291414 TTCCACTTCT
* * * * *
25291424 GCCTTCGGCACTCCTTCTTCCACCCCT
1 GCCTTTGGCACTCCGTCTTCGACACCG
* * *
25291451 GCCTTTGGCACTCCTTCTTCCACCCCG
1 GCCTTTGGCACTCCGTCTTCGACACCG
* * * *
25291478 GCCTTTGGAACTAC-TCCTTCCACTCCG
1 GCCTTTGGCACTCCGT-CTTCGACACCG
* ** * *
25291505 GCTTTTGGGGCTCCTTCTTCCACACCG
1 GCCTTTGGCACTCCGTCTTCGACACCG
*
25291532 GCATTTGGCACTCCGTCTTCGACACCG
1 GCCTTTGGCACTCCGTCTTCGACACCG
* * *
25291559 GCGTTTGTCACTCCTTCTTCGACACCG
1 GCCTTTGGCACTCCGTCTTCGACACCG
*
25291586 GCCTTTGGCACTCCGTCTTCGACACCT
1 GCCTTTGGCACTCCGTCTTCGACACCG
* **
25291613 GCGTTTGGGGCTCCGTCTTCGACACCG
1 GCCTTTGGCACTCCGTCTTCGACACCG
* * *
25291640 GCGTTTGGAACTCCGTCCTCGACACCG
1 GCCTTTGGCACTCCGTCTTCGACACCG
* *
25291667 GCTTTTGGAACTCC
1 GCCTTTGGCACTCC
25291681 ATCAACGCCG
Statistics
Matches: 198, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 196 0.99
28 1 0.01
ACGTcount: A:0.11, C:0.40, G:0.20, T:0.29
Consensus pattern (27 bp):
GCCTTTGGCACTCCGTCTTCGACACCG
Found at i:25300708 original size:3 final size:3
Alignment explanation
Indices: 25300700--25300794 Score: 91
Period size: 3 Copynumber: 31.7 Consensus size: 3
25300690 TAAAACAATT
* *
25300700 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * ** * * *
25300748 TAA TGA TGA TGA TGA TGG TAT TAA TAA TAA TAA CAA TAA TAA AAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
25300795 TTAAAATTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:25304786 original size:15 final size:14
Alignment explanation
Indices: 25304744--25304786 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
25304734 AAAATAAATT
* *
25304744 TATTTTTTAAAAAT
1 TATTTTTTATAAAC
25304758 TATTTTTTATAAAC
1 TATTTTTTATAAAC
25304772 TATTTTTTATGAAAC
1 TATTTTTTAT-AAAC
25304787 AAACGTGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 22 0.85
15 4 0.15
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (14 bp):
TATTTTTTATAAAC
Found at i:25305937 original size:21 final size:21
Alignment explanation
Indices: 25305911--25305974 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
25305901 TTTGGGTAGA
*
25305911 TCAGCTCTTTTGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
* *
25305932 TTAGCTCTTGTGAGCTTCTGT
1 TCAGCTCTTATGAGCTTCTGT
*
25305953 TCAGCTCTTATGAGCTTTTGT
1 TCAGCTCTTATGAGCTTCTGT
25305974 T
1 T
25305975 GACGATGTAC
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (21 bp):
TCAGCTCTTATGAGCTTCTGT
Found at i:25306540 original size:21 final size:21
Alignment explanation
Indices: 25306501--25306540 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
25306491 GAGCAAATTG
* *
25306501 CTTATGTAATGTATGAATATA
1 CTTATGTAATGGATAAATATA
*
25306522 CTTATGTCATGGATAAATA
1 CTTATGTAATGGATAAATA
25306541 CACTGAATTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (21 bp):
CTTATGTAATGGATAAATATA
Found at i:25308623 original size:20 final size:21
Alignment explanation
Indices: 25308591--25308648 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 21
25308581 AAAAATATAA
*
25308591 ATTTTGGAATTTTTAT-AAA-T
1 ATTTT-GAATTTTTTTAAAATT
25308611 ATTTT-AATTTTTTTAAAATT
1 ATTTTGAATTTTTTTAAAATT
*
25308631 ATTTTGAATTTTCTTAAA
1 ATTTTGAATTTTTTTAAA
25308649 TTTTTGTTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 8 0.24
19 3 0.09
20 11 0.33
21 11 0.33
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTGAATTTTTTTAAAATT
Found at i:25308658 original size:21 final size:21
Alignment explanation
Indices: 25308610--25308648 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
25308600 TTTTTATAAA
*
25308610 TATTTT-AATTTTTTTAAAAT
1 TATTTTGAATTTTCTTAAAAT
25308630 TATTTTGAATTTTCTTAAA
1 TATTTTGAATTTTCTTAAA
25308649 TTTTTGTTGA
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:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATTTTGAATTTTCTTAAAAT
Found at i:25311763 original size:33 final size:33
Alignment explanation
Indices: 25311721--25311788 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
25311711 CTCATTTCCA
25311721 TTGCATCCCATCTCCTCCAGGCTAATGTTTGAG
1 TTGCATCCCATCTCCTCCAGGCTAATGTTTGAG
25311754 TTGCATCCCATCTCCTCCAGGCTAATGTTTGAG
1 TTGCATCCCATCTCCTCCAGGCTAATGTTTGAG
25311787 TT
1 TT
25311789 TCACATGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.18, C:0.29, G:0.18, T:0.35
Consensus pattern (33 bp):
TTGCATCCCATCTCCTCCAGGCTAATGTTTGAG
Found at i:25316861 original size:30 final size:30
Alignment explanation
Indices: 25316818--25316875 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
25316808 TTTCGTTTAC
25316818 ATAACAAACAAATTTACTTTTATGACTCAT
1 ATAACAAACAAATTTACTTTTATGACTCAT
* * * *
25316848 ATAATAAATAAATTTATTTTTTTGACTC
1 ATAACAAACAAATTTACTTTTATGACTC
25316876 GTACTTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.03, T:0.43
Consensus pattern (30 bp):
ATAACAAACAAATTTACTTTTATGACTCAT
Found at i:25320591 original size:36 final size:35
Alignment explanation
Indices: 25320551--25320668 Score: 191
Period size: 36 Copynumber: 3.3 Consensus size: 35
25320541 ACTGCCACCA
25320551 CCAGCTCCACTTATTCCAAACCCATTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCC-TTTCAGCCTCCT
25320587 CCAGCTCCACTTATTCCAAATCCCTTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAA-CCCTTTCAGCCTCCT
*
25320623 CCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCT
1 CCAGCTCCACTTATTCCAAACCC-TTTCAGCCTCCT
*
25320659 CCAGCACCAC
1 CCAGCTCCAC
25320669 CGGCTCCACT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
35 3 0.04
36 71 0.92
37 3 0.04
ACGTcount: A:0.20, C:0.46, G:0.06, T:0.28
Consensus pattern (35 bp):
CCAGCTCCACTTATTCCAAACCCTTTCAGCCTCCT
Found at i:25320802 original size:45 final size:45
Alignment explanation
Indices: 25320620--25320807 Score: 259
Period size: 45 Copynumber: 4.2 Consensus size: 45
25320610 CTTTCAGCCT
* * *
25320620 CCTCCAGCTCCTCTTATTCCAAACCCTTTTCAGCCTCCTCCAGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* * *
25320665 CCACCGGCTCCACTTATTCCAAACCCTTTTCAGCCTCCTCCCGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* *
25320710 CCACCGGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
* * * * *
25320755 CCTCCAGCTCCATTTATCCCGAACCCCTTCCAGCCTCCTCCGGCA
1 CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
25320800 CCTCCAGC
1 CCTCCAGC
25320808 ACCTCCAGCA
Statistics
Matches: 131, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 131 1.00
ACGTcount: A:0.17, C:0.50, G:0.09, T:0.24
Consensus pattern (45 bp):
CCTCCAGCTCCACTTATTCCAAACCCTTTCCAGCCTCCTCCCGCA
Found at i:25321333 original size:3 final size:3
Alignment explanation
Indices: 25321325--25321357 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
25321315 ACGACTCCAG
25321325 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
25321358 TTTTGAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:25329805 original size:13 final size:13
Alignment explanation
Indices: 25329787--25329828 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
25329777 ATATGACGTG
25329787 ATTTTTTTGGTTC
1 ATTTTTTTGGTTC
* *
25329800 ATTTTTTT-ATGC
1 ATTTTTTTGGTTC
25329812 ACTTTTTTTGGTTC
1 A-TTTTTTTGGTTC
25329826 ATT
1 ATT
25329829 AATGTGACGT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
12 3 0.13
13 17 0.74
14 3 0.13
ACGTcount: A:0.12, C:0.10, G:0.12, T:0.67
Consensus pattern (13 bp):
ATTTTTTTGGTTC
Found at i:25333853 original size:41 final size:41
Alignment explanation
Indices: 25333808--25333932 Score: 124
Period size: 41 Copynumber: 3.3 Consensus size: 41
25333798 CTAGGCCCGG
25333808 GCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCAT
1 GCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCAT
***** **
25333849 GCCCGGCCCGG---GAAA-AAAATTC-ATAA----GCCCGG
1 GCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCAT
25333881 GCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCAT
1 GCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCAT
25333922 GCCCGGCCCGG
1 GCCCGGCCCGG
25333933 GAAAAAAATT
Statistics
Matches: 61, Mismatches: 14, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
32 15 0.25
35 4 0.07
36 6 0.10
37 6 0.10
38 4 0.07
41 26 0.43
ACGTcount: A:0.21, C:0.35, G:0.27, T:0.17
Consensus pattern (41 bp):
GCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCAT
Found at i:25333887 original size:73 final size:73
Alignment explanation
Indices: 25333802--25333959 Score: 316
Period size: 73 Copynumber: 2.2 Consensus size: 73
25333792 CGGGTCCTAG
25333802 GCCCGGGCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCATGCCCGGCCCGGGAAAAAA
1 GCCCGGGCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCATGCCCGGCCCGGGAAAAAA
25333867 ATTCATAA
66 ATTCATAA
25333875 GCCCGGGCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCATGCCCGGCCCGGGAAAAAA
1 GCCCGGGCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCATGCCCGGCCCGGGAAAAAA
25333940 ATTCATAA
66 ATTCATAA
25333948 GCCCGGGCCCGG
1 GCCCGGGCCCGG
25333960 GCTTATGAAT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 85 1.00
ACGTcount: A:0.23, C:0.34, G:0.28, T:0.15
Consensus pattern (73 bp):
GCCCGGGCCCGGCCCGGCCCGAAATATGGGCCTATAATTTTGCCCATGCCCGGCCCGGGAAAAAA
ATTCATAA
Found at i:25341674 original size:12 final size:13
Alignment explanation
Indices: 25341649--25341677 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25341639 ACAAATCCAT
25341649 AATATACAAAACA
1 AATATACAAAACA
25341662 AATATAC-AAACA
1 AATATACAAAACA
25341674 AATA
1 AATA
25341678 ATATTAAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (13 bp):
AATATACAAAACA
Found at i:25343536 original size:99 final size:98
Alignment explanation
Indices: 25343364--25344068 Score: 853
Period size: 99 Copynumber: 7.1 Consensus size: 98
25343354 CTTCTGTCTG
* * * * *
25343364 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGTTCCAATGCACCGCT
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
25343429 AGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCT
66 AGG-AAGTAAGATTCGCCGTTGTGGCTTCAATCT
** * * * * *
25343463 TTTAATTGCAATGTCAAGG-AGATAAGATTCGTTGTTATAACTTTAATCTGTTCCACTGCACCGC
1 TTTAATTGCAATGTCGGGGAAG-CAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* *
25343527 CAGAGAAGTAAGATTCGCCGTTGTGGCCTCAATTT
65 CAG-GAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* *
25343562 TTTAATTG-TATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAACCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCG-C
* *
25343626 CTA-AAAGTAAGATTCACCGTTGTGGCCTT-AATCT
65 C-AGGAAGTAAGATTCGCCGTTGTGG-CTTCAATCT
* *
25343660 TTTAATTGCAATATCGGGGAAGCAAGATTTGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
*
25343725 TGGAAAGTAAGATTCGCCGTTGTGGCCTT-AATCT
66 AGG-AAGTAAGATTCGCCGTTGTGG-CTTCAATCT
* * *
25343759 TTTAATTGCAATATCGGGGAAGCAAGATTTGCTGTTGTAGCTTCAATTTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
** *
25343824 AGGGAAGTAAGATTCATCGTTGTGGCTTAAATCT
66 A-GGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* * * *
25343858 ATTTAACTACAATGTCGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCAC
1 -TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGC
** *
25343923 TTGGGAAGTAAGATTCGCCGTTGTGGCTTTAATCT
65 -CAGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
* *** * * * *
25343958 TTTAATTACAATGTCGGGGAAATGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACAGCT
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* * *
25344023 TGGAAAGTAAGATTTGTCGTTGTGGCTTCAATCTT
66 AGG-AAGTAAGATTCGCCGTTGTGGCTTCAATC-T
25344058 TTTAATTGCAA
1 TTTAATTGCAA
25344069 ACTATGGTTT
Statistics
Matches: 529, Mismatches: 62, Indels: 29
0.85 0.10 0.05
Matches are distributed among these distances:
98 84 0.16
99 344 0.65
100 101 0.19
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (98 bp):
TTTAATTGCAATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
AGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
Found at i:25343697 original size:49 final size:49
Alignment explanation
Indices: 25343644--25343796 Score: 164
Period size: 49 Copynumber: 3.1 Consensus size: 49
25343634 AAGATTCACC
25343644 GTTGTGGCCTTAATCTTTTAATTGCAATATCGGGGAAGCAAGATTTGCT
1 GTTGTGGCCTTAATCTTTTAATTGCAATATCGGGGAAGCAAGATTTGCT
* ** * **** * * * * *
25343693 GTTGTAG-CTTCAATCTGTTCCACTGCACCGCCTGGAAAGTAAGATTCGCC
1 GTTGTGGCCTT-AATCT-TTTAATTGCAATATCGGGGAAGCAAGATTTGCT
25343743 GTTGTGGCCTTAATCTTTTAATTGCAATATCGGGGAAGCAAGATTTGCT
1 GTTGTGGCCTTAATCTTTTAATTGCAATATCGGGGAAGCAAGATTTGCT
25343792 GTTGT
1 GTTGT
25343797 AGCTTCAATT
Statistics
Matches: 75, Mismatches: 26, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
48 3 0.04
49 37 0.49
50 32 0.43
51 3 0.04
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (49 bp):
GTTGTGGCCTTAATCTTTTAATTGCAATATCGGGGAAGCAAGATTTGCT
Found at i:25343747 original size:50 final size:50
Alignment explanation
Indices: 25343378--25344056 Score: 331
Period size: 50 Copynumber: 13.7 Consensus size: 50
25343368 ATTGCAATGT
* * * * *
25343378 CGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGTTCCAATGCACCGC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
** * ** * **
25343428 TAGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTAATTGCAATGTC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG-C
** * ** * * *
25343478 AAGGAGA-TAAGATTCGTTGTTATAACTTTAATCTGTTCCACTGCACCGC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * * ** * * * *
25343527 C-AGAGAAGTAAGATTCGCCGTTGTGGCCTCAAT-TTTTTAATTGTA-TGT
1 CGGGA-AAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * *
25343575 CGGGGAAGCAAGATTCGCTGTTGTAGCTTCAACCTGTTCCACTGCACCGC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
*** * * ** * ****
25343625 CCTAAAAGTAAGATTCACCGTTGTGGCCTT-AATCT-TTTAATTGCAATAT
1 CGGGAAAGTAAGATTCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACCGC
* * * *
25343674 CGGGGAAGCAAGATTTGCTGTTGTAGCTTCAATCTGTTCCACTGCACCGC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * ** * ****
25343724 CTGGAAAGTAAGATTCGCCGTTGTGGCCTT-AATCT-TTTAATTGCAATAT
1 CGGGAAAGTAAGATTCGCCGTTGTAG-CTTCAATCTGTTCCACTGCACCGC
* * * * *
25343773 CGGGGAAGCAAGATTTGCTGTTGTAGCTTCAATTTGTTCCACTGCACCGC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
** * * * ** * ** *
25343823 CAGGG-AAGTAAGATTCATCGTTGTGGCTTAAATCTATTTAACTACAATGT
1 C-GGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * *
25343873 CGGGGAAGCAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCAC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
* * * ** * * **
25343923 TTGGG-AAGTAAGATTCGCCGTTGTGGCTTTAATCT-TTTAATTACAATGTC
1 -CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCG-C
* * * *
25343973 GGGGAAA-TGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACAGC
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
** * * *
25344022 TTGGAAAGTAAGATTTGTCGTTGTGGCTTCAATCT
1 CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCT
25344057 TTTTAATTGC
Statistics
Matches: 437, Mismatches: 172, Indels: 40
0.67 0.27 0.06
Matches are distributed among these distances:
48 33 0.08
49 147 0.34
50 245 0.56
51 12 0.03
ACGTcount: A:0.25, C:0.21, G:0.23, T:0.32
Consensus pattern (50 bp):
CGGGAAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGCACCGC
Found at i:25343957 original size:199 final size:198
Alignment explanation
Indices: 25343364--25344068 Score: 912
Period size: 199 Copynumber: 3.6 Consensus size: 198
25343354 CTTCTGTCTG
* * *
25343364 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTCGTAGCTTCAATCTGTTCCAATGCACCGCT
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* ** *
25343429 AGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTAATTGCAATGTCAAGG-AGATAAGATTC
66 AGGAAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAG-CAAGATTC
* * * * * * *
25343493 GTTGTTATAACTTTAATCTGTTCCACTGCACCGCCAGAGAAGTAAGATTCGCCGTTGTGGCCTCA
130 GCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTGGCCTTA
*
25343558 ATTT
195 ATCT
* * * *
25343562 TTTAATTG-TATGTCGGGGAAGCAAGATTCGCTGTTGTAGCTTCAACCTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
*** * *
25343626 CTAAAAGTAAGATTCACCGTTGTGGCCTT-AATCTTTTAATTGCAATATCGGGGAAGCAAGATTT
66 AGGAAAGTAAGATTCACCGTTGTGG-CTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTC
*
25343690 GCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGAAAGTAAGATTCGCCGTTGTGGCCTTA
130 GCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTGGCCTTA
25343755 ATCT
195 ATCT
* ** * *
25343759 TTTAATTGCAATATCGGGGAAGCAAGATTTGCTGTTGTAGCTTCAATTTGTTCCACTGCACCGCC
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* * * * *
25343824 AGGGAAGTAAGATTCATCGTTGTGGCTTAAATCTATTTAACTACAATGTCGGGGAAGCAAGATTC
66 AGGAAAGTAAGATTCACCGTTGTGGCTTCAATCT-TTTAATTGCAATGTCGGGGAAGCAAGATTC
* * * *
25343889 GCCGTTGTAGCTTCAATCTGTTCCACTGCACCACTTGGGAAGTAAGATTCGCCGTTGTGGCTTTA
130 GCTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTGGCCTTA
25343954 ATCT
195 ATCT
* *** * *
25343958 TTTAATTACAATGTCGGGGAAATGAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACAGCT
1 TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
* ***
25344023 TGGAAAGTAAGATTTGTCGTTGTGGCTTCAATCTTTTTAATTGCAA
66 AGGAAAGTAAGATTCACCGTTGTGGCTTCAATC-TTTTAATTGCAA
25344069 ACTATGGTTT
Statistics
Matches: 439, Mismatches: 62, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
197 168 0.38
198 89 0.20
199 181 0.41
200 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (198 bp):
TTTAATTGCAATGTCGGGGAAGCAAGATTCACCGTTGTAGCTTCAATCTGTTCCACTGCACCGCC
AGGAAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
CTGTTGTAGCTTCAATCTGTTCCACTGCACCGCCTGGGAAGTAAGATTCGCCGTTGTGGCCTTAA
TCT
Found at i:25354259 original size:24 final size:24
Alignment explanation
Indices: 25354232--25354281 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
25354222 AAGATCAGAT
25354232 CTCGCAGATTTTCCAAGGTATGTA
1 CTCGCAGATTTTCCAAGGTATGTA
25354256 CTCGCAGATTTTCCAAGGTATGTA
1 CTCGCAGATTTTCCAAGGTATGTA
25354280 CT
1 CT
25354282 TGTTGTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (24 bp):
CTCGCAGATTTTCCAAGGTATGTA
Found at i:25356473 original size:3 final size:3
Alignment explanation
Indices: 25356459--25356547 Score: 62
Period size: 3 Copynumber: 30.7 Consensus size: 3
25356449 AATGAGTAAC
* **
25356459 TAA TAA TGA TAA TAA TTAA TAA TAA T-A TAA TAA TAA TAA TGG TAA
1 TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
25356504 AAA TAA -AA -AA TAA TAA T-A TGAG TAA TAA TAA -AA CAA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
25356546 TA
1 TA
25356548 GGTGTAACAA
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
2 10 0.15
3 53 0.79
4 4 0.06
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:25356491 original size:11 final size:11
Alignment explanation
Indices: 25356467--25356496 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
25356457 ACTAATAATG
25356467 ATAATAAT-TA
1 ATAATAATATA
25356477 ATAATAATATA
1 ATAATAATATA
25356488 ATAATAATA
1 ATAATAATA
25356497 ATGGTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.42
11 11 0.58
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAATAATATA
Found at i:25356519 original size:25 final size:27
Alignment explanation
Indices: 25356460--25356547 Score: 83
Period size: 25 Copynumber: 3.4 Consensus size: 27
25356450 ATGAGTAACT
* * * * * *
25356460 AATAATGATAATAATTAATAATAATAT
1 AATAATAATAATGAGTAAAAATAAAAC
25356487 AATAATAATAATG-GTAAAAATAAAA-
1 AATAATAATAATGAGTAAAAATAAAAC
*
25356512 AATAATAAT-ATGAGTAATAATAAAAC
1 AATAATAATAATGAGTAAAAATAAAAC
*
25356538 AATAGTAATA
1 AATAATAATA
25356548 GGTGTAACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.06
25 20 0.39
26 17 0.33
27 11 0.22
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (27 bp):
AATAATAATAATGAGTAAAAATAAAAC
Found at i:25356554 original size:26 final size:25
Alignment explanation
Indices: 25356487--25356560 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 25
25356477 ATAATAATAT
*
25356487 AATAATAATAATG-GTAAAAATAAAA
1 AATAATAAT-AGGAGTAAAAATAAAA
* *
25356512 AATAATAATATGAGTAATAATAAAA
1 AATAATAATAGGAGTAAAAATAAAA
* * *
25356537 CAATAGTAATAGGTGTAACAATAA
1 -AATAATAATAGGAGTAAAAATAA
25356561 TGATTAAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
24 3 0.07
25 20 0.48
26 19 0.45
ACGTcount: A:0.61, C:0.03, G:0.11, T:0.26
Consensus pattern (25 bp):
AATAATAATAGGAGTAAAAATAAAA
Found at i:25357814 original size:22 final size:23
Alignment explanation
Indices: 25357771--25357815 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
25357761 TTATTTAGGT
***
25357771 AAAATTTAAAAACATTTTAATAA
1 AAAATTTAAAAACATCCAAATAA
25357794 AAAATTTAAAAA-ATCCAAATAA
1 AAAATTTAAAAACATCCAAATAA
25357816 CCCATAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATTTAAAAACATCCAAATAA
Found at i:25361299 original size:106 final size:106
Alignment explanation
Indices: 25361044--25361386 Score: 523
Period size: 104 Copynumber: 3.2 Consensus size: 106
25361034 AAGAAAAAGG
25361044 AAAAAAAAATTTGGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTACTTT
1 AAAAAAAAATTT-GGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTACTTT
25361109 TTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGT-
65 TTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTA
* *
25361150 -AAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGACACACAACAGTAA-AAAAAAATTACTTTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTAC-TTT
*
25361213 TTTTTCGTGTTAAAATTAGGTATCAGTATACGAAAAAAAGTA
65 TTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTA
***
25361255 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAATTTTTTTACTT
1 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAA--AAATTACTT
* *
25361320 TTTTTTCGTGTTAAAATCAGATATCAGTATATG-AAAAAAGTAA
64 TTTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGT-A
*
25361363 AAAAAAAAATTTTAGGTGCTGGCC
1 AAAAAAAAA-TTTGGGTGCTGGCC
25361387 CAGTAATAAA
Statistics
Matches: 217, Mismatches: 12, Indels: 13
0.90 0.05 0.05
Matches are distributed among these distances:
103 11 0.05
104 78 0.36
105 11 0.05
106 46 0.21
107 12 0.06
108 42 0.19
109 17 0.08
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (106 bp):
AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTACTTTT
TTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTA
Found at i:25362486 original size:111 final size:109
Alignment explanation
Indices: 25362201--25362855 Score: 782
Period size: 111 Copynumber: 6.0 Consensus size: 109
25362191 CGAAAAAGGG
* * * *
25362201 AAAAAAAATTTTGGGTGTTAGCTTGTCAATGGCCAGCACCCAACAGTAATAAAAAAATTTTAC-T
1 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTTTACTT
* * **
25362265 TTTTTTCGTATTAAAATCAGGTATCAGTATAGGAAAAAAAGT-A
66 TTTTTTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
* ****
25362308 AAAAAAAA-TTTGGGTGCTGGCCTGTCATTGGCCGGCACCCAACAGTAAT-AATTTTTTTTACTT
1 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTTTACTT
25362371 TTTTTCTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
66 TTTTT-TCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
* *
25362416 AAAAACAAATTTTTGGGTGTTAGCCTGTCAATGGCCGGCACCCAACAGTAATTAAAAAAATTTTA
1 AAAAA-AAA-TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAA-TAAAAAAATTTTA
* * * *
25362481 CTTTTTTTT-GTGTTAAAATCATGTATCAGTATAC--GAAAAAG-GA
63 CTTTTTTTTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
*
25362524 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCAGGCACCCAACAG---T-AAAAAATTTTACTT
1 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTTTAC-T
25362585 TTTTTTTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
65 TTTTTTTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
* * * *
25362630 AAAAAAAATTTTTTTTTGGGTGCTGGCCTGTTAATGGCCGACACCAAACAATAATAAAAAAAATT
1 AAAAAAAA-----TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAAT-AAAAAAA-T
* *
25362695 TTTACTTTTTTTTCGTGTTCAAATTAGGTATCAGTATAC-GAAAAAAGTAA
59 TTTACTTTTTTTTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
* *
25362745 AAAAAAAATTTTTTTAGGTGCTGGCCTGTCAATGGCTGGCACCCAACAGTAA-AAAAAAA-TTTA
1 AAAAAAAA---TTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTTTA
** *
25362808 CTTTTTTTTATTGTTAAAATTAGGTATCAATATACGAAAAAAAAGTAA
63 CTTTTTTTTCGTGTTAAAATTAGGTATCAGTATAC-AAAAAAAAGTAA
25362856 TGACCAGCAC
Statistics
Matches: 473, Mismatches: 49, Indels: 48
0.83 0.09 0.08
Matches are distributed among these distances:
101 12 0.03
102 9 0.02
103 23 0.05
105 14 0.03
106 86 0.18
107 44 0.09
108 12 0.03
109 44 0.09
111 110 0.23
112 2 0.00
113 53 0.11
114 1 0.00
115 18 0.04
116 39 0.08
117 6 0.01
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (109 bp):
AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGGCACCCAACAGTAATAAAAAAATTTTACTT
TTTTTTCGTGTTAAAATTAGGTATCAGTATACAAAAAAAAGTAA
Found at i:25362637 original size:217 final size:216
Alignment explanation
Indices: 25362201--25362855 Score: 856
Period size: 217 Copynumber: 3.0 Consensus size: 216
25362191 CGAAAAAGGG
* *
25362201 AAAAAAAA-TTTTGGGTGTTAGCTTGTCAATGGCCAGCACCCAACAGTAA-TAAAAAAATTTTAC
1 AAAAAAAATTTTTGGGTGTTAGCCTGTCAATGGCCGGCACCCAACAGTAATTAAAAAAATTTTAC
* * * *
25362264 TTTTTTTCGTATTAAAATCAGGTATCAGTATAGGAAAAAAAGTAAAAAAAAA-TTTGGGTGCTGG
66 TTTTTTTTGTGTTAAAATCAGGTATCAGTATACG-AAAAAAGAAAAAAAAAATTTTGGGTGCTGG
* * ** *
25362328 CCTGTCATTGGCCGGCACCCAACAGTAATAATTTTTTTTACTTTTTTTCTCGTGTTAAAATTAGG
130 CCTGTCAATGGCAGGCACCCAACAGTAA-AA--AATTTTACTTTTTTTTTCGTGTTAAAATTAGG
25362393 TATCAGTATACAAAAAAAAGT-AAA
192 TATCAGTATACAAAAAAAAGTAAAA
*
25362417 AAAACAAATTTTTGGGTGTTAGCCTGTCAATGGCCGGCACCCAACAGTAATTAAAAAAATTTTAC
1 AAAAAAAATTTTTGGGTGTTAGCCTGTCAATGGCCGGCACCCAACAGTAATTAAAAAAATTTTAC
* *
25362482 TTTTTTTTGTGTTAAAATCATGTATCAGTATACG-AAAAAGGAAAAAAAAATTTTGGGTGCTGGC
66 TTTTTTTTGTGTTAAAATCAGGTATCAGTATACGAAAAAAGAAAAAAAAAATTTTGGGTGCTGGC
25362546 CTGTCAATGGCAGGCACCCAACAGTAAAAAATTTTACTTTTTTTTTCGTGTTAAAATTAGGTATC
131 CTGTCAATGGCAGGCACCCAACAGTAAAAAATTTTACTTTTTTTTTCGTGTTAAAATTAGGTATC
25362611 AGTATACAAAAAAAAGTAAAA
196 AGTATACAAAAAAAAGTAAAA
** * * * * * * *
25362632 AAAAAATTTTTTTTTGGGTGCTGGCCTGTTAATGGCCGACACCAAACAATAATAAAAAAAATTTT
1 AAAAAA--AATTTTTGGGTGTTAGCCTGTCAATGGCCGGCACCCAACAGTAATTAAAAAAA-TTT
* * *
25362697 TACTTTTTTTTCGTGTTCAAATTAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATTTTTTTAG
63 TACTTTTTTTT-GTGTTAAAATCAGGTATCAGTATACGAAAAAAG-AAAAAAAAAA---TTTTGG
* *
25362762 GTGCTGGCCTGTCAATGGCTGGCACCCAACAGTAAAAAAAAATTTACTTTTTTTTAT--TGTTAA
123 GTGCTGGCCTGTCAATGGCAGGCACCCAACAGT--AAAAAATTTTACTTTTTTTT-TCGTGTTAA
*
25362825 AATTAGGTATCAATATACGAAAAAAAAGTAA
185 AATTAGGTATCAGTATAC-AAAAAAAAGTAA
25362856 TGACCAGCAC
Statistics
Matches: 391, Mismatches: 31, Indels: 24
0.88 0.07 0.05
Matches are distributed among these distances:
214 50 0.13
215 8 0.02
216 24 0.06
217 121 0.31
218 58 0.15
219 23 0.06
220 6 0.02
221 9 0.02
224 37 0.09
225 23 0.06
226 31 0.08
227 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (216 bp):
AAAAAAAATTTTTGGGTGTTAGCCTGTCAATGGCCGGCACCCAACAGTAATTAAAAAAATTTTAC
TTTTTTTTGTGTTAAAATCAGGTATCAGTATACGAAAAAAGAAAAAAAAAATTTTGGGTGCTGGC
CTGTCAATGGCAGGCACCCAACAGTAAAAAATTTTACTTTTTTTTTCGTGTTAAAATTAGGTATC
AGTATACAAAAAAAAGTAAAA
Found at i:25362919 original size:83 final size:79
Alignment explanation
Indices: 25362783--25362932 Score: 201
Period size: 83 Copynumber: 1.8 Consensus size: 79
25362773 TCAATGGCTG
* * * *
25362783 GCACCCAACAGTAAAAAAAAATTTACTTTTTTTTATTGTTAAAATTAGGTATCAATATACGAAAA
1 GCACCCAACAGTAAAAAAAAATTTACTTTTTTTTAGTGTTAAAATCAAGTATCAATACACGAAAA
25362848 AAAAGTAATGACCA
66 AAAAGTAATGACCA
* * *
25362862 GCACCCAACAGTAATAAAAAAAATTTTCTACTTTTTTTCGTGTTCAAATCAAGTATCAATACACG
1 GCACCCAACAGT-A-AAAAAAAATTTACT--TTTTTTTAGTGTTAAAATCAAGTATCAATACACG
25362927 AAAAAA
62 AAAAAA
25362933 GTAAAAAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
79 12 0.20
80 1 0.02
81 13 0.22
83 34 0.57
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (79 bp):
GCACCCAACAGTAAAAAAAAATTTACTTTTTTTTAGTGTTAAAATCAAGTATCAATACACGAAAA
AAAAGTAATGACCA
Found at i:25363201 original size:109 final size:109
Alignment explanation
Indices: 25363014--25363239 Score: 355
Period size: 109 Copynumber: 2.1 Consensus size: 109
25363004 GAAAAAAGAA
* *
25363014 TTTTTTTTACTTTTTTTGTATACTGATACCTGATTTTAACACGAAAAAAAAAGTAAAATTTTTTT
1 TTTTTTTTACTTTTTTTCTATACTGATACCTAATTTTAACACG-AAAAAAAAGTAAAATTTTTTT
*
25363079 TATTACTGTTGGGTGCCGGCCATTGACAGGCCAACACCCAAATTT
65 TATTACTGTTGGGTGCCGGCCATTGACAGGCCAACACCCAAAATT
* * *
25363124 TTTTTTTTACTTTTTTTCCTATATTGGTACCTAATTTTAACACG-AAAAAAAGTAAATTTTTTTT
1 TTTTTTTTACTTTTTTT-CTATACTGATACCTAATTTTAACACGAAAAAAAAGTAAAATTTTTTT
* *
25363188 TATTACTGTTGGGTGCCGGCCATTGACAGGCCAGCATCCAAAATT
65 TATTACTGTTGGGTGCCGGCCATTGACAGGCCAACACCCAAAATT
25363233 TTTTTTT
1 TTTTTTT
25363240 CCTTTTTCTT
Statistics
Matches: 107, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
109 68 0.64
110 17 0.16
111 22 0.21
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (109 bp):
TTTTTTTTACTTTTTTTCTATACTGATACCTAATTTTAACACGAAAAAAAAGTAAAATTTTTTTT
ATTACTGTTGGGTGCCGGCCATTGACAGGCCAACACCCAAAATT
Found at i:25363253 original size:16 final size:16
Alignment explanation
Indices: 25363232--25363263 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25363222 CATCCAAAAT
*
25363232 TTTTTTTTCCTTTTTC
1 TTTTTTCTCCTTTTTC
25363248 TTTTTTCTCCTTTTTC
1 TTTTTTCTCCTTTTTC
25363264 GTATATCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTCTCCTTTTTC
Found at i:25363878 original size:44 final size:45
Alignment explanation
Indices: 25363825--25363913 Score: 153
Period size: 44 Copynumber: 2.0 Consensus size: 45
25363815 TGCTTTCAAA
*
25363825 GCCCTGAAACCAATTCGACTAGTCATTAGATACGGCTTTT-TTTT
1 GCCCTGAAACCAATTCGAATAGTCATTAGATACGGCTTTTATTTT
*
25363869 GCCCTGAAACCAATTCGAATAGTCATTAGATTCGGCTTTTATTTT
1 GCCCTGAAACCAATTCGAATAGTCATTAGATACGGCTTTTATTTT
25363914 ACTTTTTAAC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 38 0.90
45 4 0.10
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (45 bp):
GCCCTGAAACCAATTCGAATAGTCATTAGATACGGCTTTTATTTT
Found at i:25365041 original size:112 final size:111
Alignment explanation
Indices: 25364788--25365168 Score: 535
Period size: 108 Copynumber: 3.5 Consensus size: 111
25364778 ATTTTACTTT
* *
25364788 TTTTTTTTCGTGTTAAAATTAGGTATCAGTATACGAAAAAAAATAATAAAAAAAATTTTTTAGGT
1 TTTTTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTAA-AAAAAAAA-TTTTT-GGT
* * *
25364853 GCTGGCCTGTCAATGGCCGGCATCCAACAGTAATAAAAA-AA--TTTAC
63 GTTGGCCTGTCAATGGCCGGCACCCAACAGTAAAAAAAATAATTTTTAC
* * *
25364899 TTTTTTTTCGTGTTAAAATTAGGTATCAGTATATGAAAAAAAGTAAAAAAAAAAATTTTGGTGTT
1 TTTTTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAAATTTTTGGTGTT
* * *
25364964 GGCCTGTTAATGGTCGGCACCCAACGGTAAAAAAAATAATTTTTAAC
66 GGCCTGTCAATGGCCGGCACCCAACAGTAAAAAAAATAATTTTT-AC
25365011 TTTTTTTTCGTGTTAAAATCAGGTATCAGTATACG-AAAAAAGTAAAAAAAAAATTTTTGGATGT
1 TTTTTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAAATTTTTGG-TGT
* *
25365075 TGGCCTGTCAATGGCCGGCACCCAACAGT-AATAAAAT-TTTTTTAC
65 TGGCCTGTCAATGGCCGGCACCCAACAGTAAAAAAAATAATTTTTAC
*
25365120 -TTTTTTTCGTGTTAAAATCAAGTATCAGTATAC-AAAAAAAGTAAAAAAA
1 TTTTTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTAAAAAAA
25365169 TTTCCTTTTT
Statistics
Matches: 246, Mismatches: 18, Indels: 15
0.88 0.06 0.05
Matches are distributed among these distances:
108 83 0.34
109 8 0.03
110 13 0.05
111 78 0.32
112 64 0.26
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (111 bp):
TTTTTTTTCGTGTTAAAATCAGGTATCAGTATACGAAAAAAAGTAAAAAAAAAATTTTTGGTGTT
GGCCTGTCAATGGCCGGCACCCAACAGTAAAAAAAATAATTTTTAC
Found at i:25375756 original size:17 final size:19
Alignment explanation
Indices: 25375734--25375768 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
25375724 TTTAAGTAAA
25375734 AATATTG-AAG-AATTTCG
1 AATATTGTAAGAAATTTCG
25375751 AATATTGTAAGAAATTTC
1 AATATTGTAAGAAATTTC
25375769 AAGAGCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (19 bp):
AATATTGTAAGAAATTTCG
Found at i:25376967 original size:17 final size:19
Alignment explanation
Indices: 25376945--25376979 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
25376935 TTTAAGTAAA
25376945 AATATTG-AAG-AATTTCG
1 AATATTGTAAGAAATTTCG
25376962 AATATTGTAAGAAATTTC
1 AATATTGTAAGAAATTTC
25376980 AAGAGCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (19 bp):
AATATTGTAAGAAATTTCG
Found at i:25381880 original size:18 final size:18
Alignment explanation
Indices: 25381847--25381899 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
25381837 ATTCAACTAA
*
25381847 ACCCAATCCAAACCCAAAT
1 ACCCAA-CCCAACCCAAAT
** *
25381866 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAAT
25381884 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
25381900 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAAT
Found at i:25382031 original size:9 final size:9
Alignment explanation
Indices: 25382019--25382077 Score: 91
Period size: 9 Copynumber: 6.6 Consensus size: 9
25382009 TCAATTAAGT
25382019 TAATTCGGG
1 TAATTCGGG
25382028 TAATTCGGG
1 TAATTCGGG
25382037 TAATTCGGG
1 TAATTCGGG
25382046 TAATTCGGG
1 TAATTCGGG
* *
25382055 TCATTCGGT
1 TAATTCGGG
*
25382064 TAATTCGGT
1 TAATTCGGG
25382073 TAATT
1 TAATT
25382078 TTTAACCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 47 1.00
ACGTcount: A:0.22, C:0.12, G:0.27, T:0.39
Consensus pattern (9 bp):
TAATTCGGG
Found at i:25382151 original size:14 final size:14
Alignment explanation
Indices: 25382119--25382161 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
25382109 GTTAATTCGG
**
25382119 TTAACCGACCAAA-
1 TTAACCGAAAAAAT
25382132 TTAACCGAAAAAAT
1 TTAACCGAAAAAAT
25382146 TTAACCGAAAAAAT
1 TTAACCGAAAAAAT
25382160 TT
1 TT
25382162 TGGTTCGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.51, C:0.19, G:0.07, T:0.23
Consensus pattern (14 bp):
TTAACCGAAAAAAT
Found at i:25390929 original size:33 final size:33
Alignment explanation
Indices: 25390876--25390945 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
25390866 ATTGTTTAAA
* *
25390876 TATGATTTGAACATGCTTTTGAGTATGTTTAGG
1 TATGATTTGAACATACTTTTGAGAATGTTTAGG
* * *
25390909 TATGATTTGAACATATTTTTGGGAATGTTTTGG
1 TATGATTTGAACATACTTTTGAGAATGTTTAGG
25390942 TATG
1 TATG
25390946 GTTGATAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.47
Consensus pattern (33 bp):
TATGATTTGAACATACTTTTGAGAATGTTTAGG
Found at i:25403846 original size:42 final size:42
Alignment explanation
Indices: 25403782--25403864 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
25403772 CCATAGTCGT
*
25403782 TACTCAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
1 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
25403824 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAG
1 TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAG
25403865 ATGGCTGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (42 bp):
TACTAAATTTATTTGAGAATATCAACTATGGCACTAGGCAGC
Found at i:25418277 original size:29 final size:29
Alignment explanation
Indices: 25418215--25418313 Score: 150
Period size: 28 Copynumber: 3.5 Consensus size: 29
25418205 AAAAATAAAA
*
25418215 ATTTACCAAAACATTACAAC-TTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
25418243 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTTT
*
25418272 ATTTACCAAAATATATA-AA-TATTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTTT
25418300 ATTTACCAAAATAT
1 ATTTACCAAAATAT
25418314 ATCAAAAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
28 41 0.61
29 24 0.36
30 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTACCAAAATATTACAACTTTTTTTTT
Found at i:25418384 original size:27 final size:27
Alignment explanation
Indices: 25418346--25418429 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
25418336 CCTGATCACC
25418346 CCAATGCCATTGGCGGCACCAAAGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
*
25418373 CCAATGCCATTGGCGGCACCAATGGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
* *
25418400 CCAATGCCATTGGCGGTACC-AATGTG
1 CCAATGCCATTGGCGGCACCAAAGGTG
25418426 CCAA
1 CCAA
25418430 AGGACTAAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
26 8 0.15
27 45 0.85
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (27 bp):
CCAATGCCATTGGCGGCACCAAAGGTG
Found at i:25419405 original size:27 final size:26
Alignment explanation
Indices: 25419367--25419423 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
25419357 TTTTAGTCCT
25419367 TTGGCACATTGGTGCCACCAATGGCA
1 TTGGCACATTGGTGCCACCAATGGCA
* *
25419393 TTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCACCAATGGCA
25419420 TTGG
1 TTGG
25419424 GGTGATCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.26
Consensus pattern (26 bp):
TTGGCACATTGGTGCCACCAATGGCA
Found at i:25419544 original size:29 final size:29
Alignment explanation
Indices: 25419467--25419567 Score: 161
Period size: 29 Copynumber: 3.5 Consensus size: 29
25419457 TTTTTTTTAT
25419467 ATATTTTGGTAAAT-AAAAAAAAGTT-TA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
*
25419494 TATATTTTGATAAATAATAAAAAAAGTTGTA
1 -ATATTTTGGTAAATAA-AAAAAAAGTTGTA
25419525 ATATTTTGGTAAATAAAAAAAAAGTTGTA
1 ATATTTTGGTAAATAAAAAAAAAGTTGTA
25419554 ATATTTTGGTAAAT
1 ATATTTTGGTAAAT
25419568 TTTTATTTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
28 13 0.19
29 28 0.41
30 25 0.37
31 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.39
Consensus pattern (29 bp):
ATATTTTGGTAAATAAAAAAAAAGTTGTA
Found at i:25424238 original size:2 final size:2
Alignment explanation
Indices: 25424231--25424255 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
25424221 AGACTAAATC
25424231 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
25424256 TTTAAATAAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25425522 original size:74 final size:75
Alignment explanation
Indices: 25425400--25425550 Score: 295
Period size: 74 Copynumber: 2.0 Consensus size: 75
25425390 AAATTTATCG
25425400 AAATAGGCCTGGTATTTTATTATTTACCGGAATGGGCCATTTTCCCCAAAATCGTGTCCACGTCA
1 AAATAGGCCTGGTATTTTATTATTTACCGGAATGGGCCATTTTCCCCAAAATCGTGTCCACGTCA
25425465 GTGCGATGTC
66 GTGCGATGTC
25425475 AAATAGGCCT-GTATTTTATTATTTACCGGAATGGGCCATTTTCCCCAAAATCGTGTCCACGTCA
1 AAATAGGCCTGGTATTTTATTATTTACCGGAATGGGCCATTTTCCCCAAAATCGTGTCCACGTCA
25425539 GTGCGATGTC
66 GTGCGATGTC
25425549 AA
1 AA
25425551 GGGACGTGTC
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
74 66 0.87
75 10 0.13
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (75 bp):
AAATAGGCCTGGTATTTTATTATTTACCGGAATGGGCCATTTTCCCCAAAATCGTGTCCACGTCA
GTGCGATGTC
Found at i:25426352 original size:88 final size:88
Alignment explanation
Indices: 25425631--25426334 Score: 1043
Period size: 88 Copynumber: 7.9 Consensus size: 88
25425621 AAATACCGGC
* *
25425631 CCTTATCTCCCTGAGAAGAAGTGGAGTAGGTTGAAGATAGCAGATCAGATTTTGTCTTCCTGTAC
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATC-----TTGTCTTCCTGTAC
* **
25425696 TGGCAGCAAAGTAGATCGAAGATACTAG
61 TGGCAGCGAAGTAGATCGAAGACCCTAG
25425724 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
* *
25425789 GAGAAGTAGATCGAACACCCTAG
66 GCGAAGTAGATCGAAGACCCTAG
*
25425812 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATATTGTCTTCCTGTACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
*
25425877 GAGAAGTAGATCGAAGACCCTAG
66 GCGAAGTAGATCGAAGACCCTAG
* *
25425900 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGAAAACAGATCTTGTCTTCCTGTACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
* *
25425965 GAGAAGTAAATCGAAGACCCTAG
66 GCGAAGTAGATCGAAGACCCTAG
* * * *
25425988 CCTTATCTCTCTAAGAAGCAGTAGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTAGTA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
**
25426053 GCGAAGTAGATCGAAGATACTAG
66 GCGAAGTAGATCGAAGACCCTAG
* *
25426076 CCTTATCTCTCTGAGAAGCAGTGGAGTAGATTGAAGATAGCAGATCTTGTCTTCCTATACTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
* * *
25426141 GTGAAGTAGATCGAAAACCCTAA
66 GCGAAGTAGATCGAAGACCCTAG
* * *
25426164 CCTTATCTCTCTGAGTAGCAGTGAAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTATTGGCA
1 CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
*
25426229 GCGAAGTAGGTCGAAGACTCC-AG
66 GCGAAGTAGATCGAAGAC-CCTAG
* * *
25426252 CCTTATCTC-CTTGAGAAGTAATGGAGTAGGTTGAAGATAGCAGATCTTGTCTTTCTGTACTGGC
1 CCTTATCTCTC-TGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGC
*
25426316 AGCGAAGCAGATCGAAGAC
65 AGCGAAGTAGATCGAAGAC
25426335 ACCAGTCTTA
Statistics
Matches: 558, Mismatches: 51, Indels: 9
0.90 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 511 0.92
89 2 0.00
93 44 0.08
ACGTcount: A:0.29, C:0.19, G:0.26, T:0.27
Consensus pattern (88 bp):
CCTTATCTCTCTGAGAAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTGTCTTCCTGTACTGGCA
GCGAAGTAGATCGAAGACCCTAG
Found at i:25437896 original size:15 final size:15
Alignment explanation
Indices: 25437878--25437910 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25437868 AACAATTATG
25437878 TTTCTTCTTCTTCCT
1 TTTCTTCTTCTTCCT
*
25437893 TTTCTTTTTCTTCCT
1 TTTCTTCTTCTTCCT
25437908 TTT
1 TTT
25437911 GTAGTTACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTCTTCTTCTTCCT
Found at i:25442803 original size:101 final size:101
Alignment explanation
Indices: 25442628--25442816 Score: 369
Period size: 101 Copynumber: 1.9 Consensus size: 101
25442618 AGATTGCATT
*
25442628 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATTGGCCATGAGAATTGCTATGCCAATCTTC
1 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
25442693 GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
66 GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
25442729 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
1 GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
25442794 GGCTGTTTAAATTCCATAATGTT
66 GGCTGTTTAAATTCCATAATGTT
25442817 TAAATCACCC
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (101 bp):
GTTTGAATTCCTTTAATCATGATTTCTGAAGTTGATAGGCCATGAGAATTGCTATGCCAATCTTC
GGCTGTTTAAATTCCATAATGTTATTTAACATTTAA
Found at i:25443085 original size:24 final size:23
Alignment explanation
Indices: 25443041--25443085 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
25443031 GGTACTGTAG
*
25443041 TTCATTTCATGTTATTTTGGTAT
1 TTCATTTCATGTTATTATGGTAT
* *
25443064 TTCATATTCTTGTTCTTATGGT
1 TTCAT-TTCATGTTATTATGGT
25443086 CAATTTCAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.16, C:0.11, G:0.13, T:0.60
Consensus pattern (23 bp):
TTCATTTCATGTTATTATGGTAT
Found at i:25444727 original size:21 final size:21
Alignment explanation
Indices: 25444663--25444735 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
25444653 ATTTTGATTT
*
25444663 TGAATGATTGAATTTAGAAAA
1 TGAAAGATTGAATTTAGAAAA
** * ***
25444684 TGGGAGAGTG-ATTT-GATTG
1 TGAAAGATTGAATTTAGAAAA
25444703 TGAAAGATTGAATTTAGAAAA
1 TGAAAGATTGAATTTAGAAAA
25444724 TGAAAGATTGAA
1 TGAAAGATTGAA
25444736 CGTGCAAGTA
Statistics
Matches: 37, Mismatches: 13, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
19 9 0.24
20 8 0.22
21 20 0.54
ACGTcount: A:0.42, C:0.00, G:0.26, T:0.32
Consensus pattern (21 bp):
TGAAAGATTGAATTTAGAAAA
Found at i:25454346 original size:17 final size:18
Alignment explanation
Indices: 25454324--25454365 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
25454314 GACATATTAC
25454324 CCCTAATTTCTAATT-GG
1 CCCTAATTTCTAATTAGG
25454341 CCCTAATTTCTAATTAGG
1 CCCTAATTTCTAATTAGG
*
25454359 CCTTAAT
1 CCCTAAT
25454366 CAATTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.40
Consensus pattern (18 bp):
CCCTAATTTCTAATTAGG
Found at i:25460969 original size:21 final size:21
Alignment explanation
Indices: 25460944--25460986 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
25460934 GATCTTGATA
25460944 GTCGAATATTAAGTTGATTAT
1 GTCGAATATTAAGTTGATTAT
25460965 GTCGAATATTAAGTTGATTAT
1 GTCGAATATTAAGTTGATTAT
25460986 G
1 G
25460987 CTTATGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.42
Consensus pattern (21 bp):
GTCGAATATTAAGTTGATTAT
Found at i:25461921 original size:21 final size:21
Alignment explanation
Indices: 25461895--25461934 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
25461885 GAACAAAAAT
25461895 GACATGTTTAATAGGTTTCAG
1 GACATGTTTAATAGGTTTCAG
25461916 GACATGTTTAATAGGTTTC
1 GACATGTTTAATAGGTTTC
25461935 TAGGTAAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (21 bp):
GACATGTTTAATAGGTTTCAG
Found at i:25462809 original size:4 final size:4
Alignment explanation
Indices: 25462802--25462862 Score: 113
Period size: 4 Copynumber: 15.2 Consensus size: 4
25462792 CAATAAATAA
25462802 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
25462850 ACAC ATAC ATAC A
1 ATAC ATAC ATAC A
25462863 GTTCCCTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 55 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ATAC
Found at i:25464753 original size:43 final size:42
Alignment explanation
Indices: 25464690--25464811 Score: 104
Period size: 42 Copynumber: 2.9 Consensus size: 42
25464680 AAAAAGCTCG
* * *
25464690 TACGATGCCAAC-GTCACAGACGTGGTCTTACATGTAATGAAA
1 TACGATGCC-ACTGTCCCAGACGTGGTCTTACAAGTAATCAAA
* * *
25464732 TATCGATGCCACTGTCCCAGACAG-GATCTTTCAAGTAATCATA
1 TA-CGATGCCACTGTCCCAGAC-GTGGTCTTACAAGTAATCAAA
* * * * *
25464775 TACAATGCCAATGTCCCAAACATGGTCTTACACGTAA
1 TACGATGCCACTGTCCCAGACGTGGTCTTACAAGTAA
25464812 ATCACATATC
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
42 31 0.49
43 31 0.49
44 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
TACGATGCCACTGTCCCAGACGTGGTCTTACAAGTAATCAAA
Found at i:25476402 original size:27 final size:28
Alignment explanation
Indices: 25476357--25476411 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
25476347 AAATAAATAC
* *
25476357 TAATAATTTTATTTGAATATA-ATTAAA
1 TAATAATTTTATTTAAATAAATATTAAA
25476384 TAATAA-TTTATTATAAATAAATATTAAA
1 TAATAATTTTATT-TAAATAAATATTAAA
25476412 ATCCTAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.25
27 12 0.50
28 6 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TAATAATTTTATTTAAATAAATATTAAA
Found at i:25476457 original size:21 final size:21
Alignment explanation
Indices: 25476407--25476459 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
25476397 TAAATAAATA
*
25476407 TTAAAATCCTAAACCTTGAAC
1 TTAAAATCCTAAACCCTGAAC
* * *
25476428 TCAATATCCTAAACCCTGAGC
1 TTAAAATCCTAAACCCTGAAC
25476449 TTAAAATCCTA
1 TTAAAATCCTA
25476460 GATTTGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.26, G:0.06, T:0.28
Consensus pattern (21 bp):
TTAAAATCCTAAACCCTGAAC
Found at i:25486251 original size:30 final size:30
Alignment explanation
Indices: 25486217--25486274 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
25486207 AGAGCACTAA
25486217 TTATTTTATTTATATTTTTATTTAAGCTTT
1 TTATTTTATTTATATTTTTATTTAAGCTTT
25486247 TTATTTTATTTATATTTTTATTTAAGCT
1 TTATTTTATTTATATTTTTATTTAAGCT
25486275 CTTGAGTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (30 bp):
TTATTTTATTTATATTTTTATTTAAGCTTT
Found at i:25486270 original size:12 final size:12
Alignment explanation
Indices: 25486220--25486269 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
25486210 GCACTAATTA
25486220 TTTTATTTATAT
1 TTTTATTTATAT
25486232 TTTTATTTA-AGCT
1 TTTTATTTATA--T
25486245 TTTTATTT-TAT
1 TTTTATTTATAT
* *
25486256 TTATATTTTTAT
1 TTTTATTTATAT
25486268 TT
1 TT
25486270 AAGCTCTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
11 9 0.27
12 14 0.42
13 10 0.30
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (12 bp):
TTTTATTTATAT
Found at i:25494944 original size:16 final size:16
Alignment explanation
Indices: 25494925--25494958 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
25494915 TTTTTTTTGG
25494925 TTGTTTTGCTGTCATT
1 TTGTTTTGCTGTCATT
* *
25494941 TTGTTTTGTTGTTATT
1 TTGTTTTGCTGTCATT
25494957 TT
1 TT
25494959 ATTGTCATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.18, T:0.71
Consensus pattern (16 bp):
TTGTTTTGCTGTCATT
Found at i:25496343 original size:19 final size:19
Alignment explanation
Indices: 25496319--25496366 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
25496309 TTTTTCAAAT
25496319 AATTATAAAATATTAAAAA
1 AATTATAAAATATTAAAAA
* *
25496338 AATTATTAAGA-ATTATAAA
1 AATTA-TAAAATATTAAAAA
25496357 AATT-TAAAAT
1 AATTATAAAAT
25496367 TAATCTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 4 0.17
19 16 0.67
20 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (19 bp):
AATTATAAAATATTAAAAA
Found at i:25500369 original size:18 final size:18
Alignment explanation
Indices: 25500328--25500369 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
25500318 CTTCGGAAGC
* *
25500328 TTCTTCTTCTCCTTCGGA
1 TTCTTCTTCGCCTTCAGA
*
25500346 TGCTTCTTCGCCTTCAGA
1 TTCTTCTTCGCCTTCAGA
25500364 TTCTTC
1 TTCTTC
25500370 GTCTTCTTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.07, C:0.33, G:0.12, T:0.48
Consensus pattern (18 bp):
TTCTTCTTCGCCTTCAGA
Found at i:25504558 original size:43 final size:41
Alignment explanation
Indices: 25504485--25504649 Score: 131
Period size: 43 Copynumber: 3.9 Consensus size: 41
25504475 AGCACCGCAT
* * *
25504485 TGCATCATCAGATAAATCGAAGGAAATATACTGACACACATAG
1 TGCATCATCAGATAAA-CCAAAG-ATTATACTGACACACATAG
* *
25504528 TGCATCATCAGATAAACCAAAGTAGTTATAC---CGCGCATAG
1 TGCATCATCAGATAAACCAAAG-A-TTATACTGACACACATAG
* * *
25504568 TGCATCATCGGATAAACCGAAAGATGAATACTGACACACATAA
1 TGCATCATCAGATAAACC-AAAGAT-TATACTGACACACATAG
* *
25504611 TGCATCATC-GAATAAACCGAAGGATGAATACTGACACAC
1 TGCATCATCAG-ATAAACC-AAAGAT-TATACTGACACAC
25504650 TATACTGACA
Statistics
Matches: 103, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
39 1 0.01
40 29 0.28
41 4 0.04
42 6 0.06
43 63 0.61
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (41 bp):
TGCATCATCAGATAAACCAAAGATTATACTGACACACATAG
Found at i:25504656 original size:13 final size:13
Alignment explanation
Indices: 25504638--25504662 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
25504628 CGAAGGATGA
25504638 ATACTGACACACT
1 ATACTGACACACT
25504651 ATACTGACACAC
1 ATACTGACACAC
25504663 ATAGTGCATC
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:0.40, C:0.32, G:0.08, T:0.20
Consensus pattern (13 bp):
ATACTGACACACT
Found at i:25504682 original size:56 final size:56
Alignment explanation
Indices: 25504595--25504705 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
25504585 CGAAAGATGA
*
25504595 ATACTGACACACATAATGCATCATCGAATAAACCGAAGGA-TGAATACTGACACACT
1 ATACTGACACACATAATGCATCATCGAATAAACCGAAGCAGT-AATACTGACACACT
* * * *
25504651 ATACTGACACACATAGTGCATCATCGGATAAATCGAAGCAGTTATACTGACACAC
1 ATACTGACACACATAATGCATCATCGAATAAACCGAAGCAGTAATACTGACACAC
25504706 ATCATTGGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
56 48 0.98
57 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (56 bp):
ATACTGACACACATAATGCATCATCGAATAAACCGAAGCAGTAATACTGACACACT
Found at i:25508179 original size:107 final size:107
Alignment explanation
Indices: 25507992--25508192 Score: 307
Period size: 107 Copynumber: 1.9 Consensus size: 107
25507982 AGGATATTTA
* *
25507992 GCTATTTGGTTAAACGAGAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTCCAAACG
1 GCTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTCCAAACG
*
25508057 CAAAATATTATCTTACTTT-G-AAATTTTAAAAGGACACTTG
66 CAAAATATTACCTTACTTTGGAAAATTTTAAAAGGACACTTG
* * *
25508097 GCTATTTGGTCAAACGAAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTCGAATTTTCAAA
1 GCTATTTGGTCAAACG-AAAAATCGAAACCCAACACATTAGGGCACG-TTCCTCGAATTTCCAAA
*
25508162 CGCAAAATATTGCCTTACTTTGGAAAATTTT
64 CGCAAAATATTACCTTACTTTGGAAAATTTT
25508193 CCTTTTTGAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
105 15 0.18
106 28 0.33
107 34 0.40
108 1 0.01
109 7 0.08
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.29
Consensus pattern (107 bp):
GCTATTTGGTCAAACGAAAAATCGAAACCCAACACATTAGGGCACGTTCCTCGAATTTCCAAACG
CAAAATATTACCTTACTTTGGAAAATTTTAAAAGGACACTTG
Found at i:25508434 original size:21 final size:20
Alignment explanation
Indices: 25508387--25508441 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
25508377 AACATAAAGT
*
25508387 AAAAAATAATAATAACAATA
1 AAAAAATAATAAAAACAATA
**
25508407 AATAAAATAGATAAAAATTATA
1 AA-AAAATA-ATAAAAACAATA
25508429 AAAAAATACATAA
1 AAAAAATA-ATAA
25508442 GTATGTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 2 0.07
21 16 0.55
22 11 0.38
ACGTcount: A:0.73, C:0.04, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAAAATAATAAAAACAATA
Found at i:25515519 original size:101 final size:101
Alignment explanation
Indices: 25515344--25515546 Score: 343
Period size: 101 Copynumber: 2.0 Consensus size: 101
25515334 GACTTCACTT
* ** * *
25515344 CCTCTTCGTCCACTCTGTAGCGCTTGCTTTAGTCTGTCCCATTTGTCATGGTATTCATTCCACAC
1 CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTCCACAC
25515409 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
66 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
* *
25515445 CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTTCGCAC
1 CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTCCACAC
25515510 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
66 ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
25515546 C
1 C
25515547 TATTCTACTA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 95 1.00
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.32
Consensus pattern (101 bp):
CCTCTTCATCCACTCCATAGCGCTTGCTTCAGTCTGTCCCACTTGTCATGGTATTCATTCCACAC
ATAATCCAATATGAGCAAAAATCGTTTCCCAACAAA
Found at i:25522020 original size:41 final size:41
Alignment explanation
Indices: 25521958--25522045 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
25521948 AACTCGAATG
* *
25521958 TTCAGTTGTTTGGATGAAAATAGATTTTTAATTAAATAAAT
1 TTCAATTGTTGGGATGAAAATAGATTTTTAATTAAATAAAT
*
25521999 TTCAATTGTTGGGATGAAAATATATTTTTAATTAAATAAAT
1 TTCAATTGTTGGGATGAAAATAGATTTTTAATTAAATAAAT
25522040 TT-AATT
1 TTCAATT
25522046 TGGACTGCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 4 0.09
41 40 0.91
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.45
Consensus pattern (41 bp):
TTCAATTGTTGGGATGAAAATAGATTTTTAATTAAATAAAT
Found at i:25522321 original size:28 final size:28
Alignment explanation
Indices: 25522289--25522344 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
25522279 AGGAAAAAGT
25522289 AAGTAGTTTTTAAACATTTTTATATGAA
1 AAGTAGTTTTTAAACATTTTTATATGAA
25522317 AAGTAGTTTTTAAACATTTTTATATGAA
1 AAGTAGTTTTTAAACATTTTTATATGAA
25522345 TAATGTAAGN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.04, G:0.11, T:0.46
Consensus pattern (28 bp):
AAGTAGTTTTTAAACATTTTTATATGAA
Found at i:25523996 original size:23 final size:23
Alignment explanation
Indices: 25523969--25524014 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
25523959 CTAATACAAG
25523969 AATTTAACAAAAACACCCCCTCA
1 AATTTAACAAAAACACCCCCTCA
25523992 AATTTAACAAAAACACCCCCTCA
1 AATTTAACAAAAACACCCCCTCA
25524015 GATTAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.35, G:0.00, T:0.17
Consensus pattern (23 bp):
AATTTAACAAAAACACCCCCTCA
Found at i:25527053 original size:20 final size:19
Alignment explanation
Indices: 25527024--25527062 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
25527014 AATGACACGA
*
25527024 TCTATCTCATCACAGACAT
1 TCTATCTCATCAAAGACAT
25527043 TCTAGTCTCATCAAAGACAT
1 TCTA-TCTCATCAAAGACAT
25527063 CTGCCCCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (19 bp):
TCTATCTCATCAAAGACAT
Found at i:25535233 original size:111 final size:111
Alignment explanation
Indices: 25535083--25535311 Score: 440
Period size: 111 Copynumber: 2.1 Consensus size: 111
25535073 AATAAATATC
*
25535083 AAATAAGTGGAGTTTAATAAGATTTACAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
1 AAATAAGTGGAGTTTAATAAGATTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
25535148 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
66 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
*
25535194 AAATAAGTGGAGTTTAATAAGATTTAAAAAACTTTATTCTAAAATAAAATAAAAGAAGTGTAATT
1 AAATAAGTGGAGTTTAATAAGATTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
25535259 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
66 CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
25535305 AAATAAG
1 AAATAAG
25535312 GATTCGGGTC
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 116 1.00
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.42
Consensus pattern (111 bp):
AAATAAGTGGAGTTTAATAAGATTTAAAAAACCTTATTCTAAAATAAAATAAAAGAAGTGTAATT
CTATAGGGATTTTACTTTTATTTTATTTTACCACTGTATTTTATTT
Found at i:25545765 original size:17 final size:18
Alignment explanation
Indices: 25545735--25545768 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
25545725 ATTTAAATTG
25545735 CGGTCGCGGTCGCGTTTT
1 CGGTCGCGGTCGCGTTTT
25545753 CGGTCGC-GTCGCGTTT
1 CGGTCGCGGTCGCGTTT
25545769 ATCGCGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.00, C:0.29, G:0.38, T:0.32
Consensus pattern (18 bp):
CGGTCGCGGTCGCGTTTT
Found at i:25547618 original size:14 final size:14
Alignment explanation
Indices: 25547580--25547622 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
25547570 CAAAATTTAC
25547580 AATATAATTAAA-T
1 AATATAATTAAATT
25547593 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
25547608 AA-ATAATTTAATT
1 AATATAATTAAATT
25547621 AA
1 AA
25547623 CTGTTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:25548531 original size:21 final size:20
Alignment explanation
Indices: 25548473--25548532 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
25548463 TCTGATCAAT
25548473 AAATGACACATAAGTGCCTG
1 AAATGACACATAAGTGCCTG
* * *
25548493 AAACGACACACGAGGTGCCT-
1 AAATGACACA-TAAGTGCCTG
25548513 AATATGACACATAAAGTGCC
1 AA-ATGACACAT-AAGTGCC
25548533 AGATCGGCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 11 0.35
21 20 0.65
ACGTcount: A:0.40, C:0.23, G:0.20, T:0.17
Consensus pattern (20 bp):
AAATGACACATAAGTGCCTG
Found at i:25551066 original size:24 final size:24
Alignment explanation
Indices: 25551031--25551106 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
25551021 GGTACCATTT
*
25551031 CATTGGAAATTTAACTATAAAGTA
1 CATTGCAAATTTAACTATAAAGTA
* * *
25551055 CA-TGTCATATTTAACTATAAATTT
1 CATTG-CAAATTTAACTATAAAGTA
*
25551079 CATTGGAAATTTAACTATAAAGTA
1 CATTGCAAATTTAACTATAAAGTA
25551103 CATT
1 CATT
25551107 TGTATTTACT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.05
24 38 0.90
25 2 0.05
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (24 bp):
CATTGCAAATTTAACTATAAAGTA
Found at i:25551330 original size:25 final size:25
Alignment explanation
Indices: 25551298--25551352 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
25551288 TAGTGGTTAA
25551298 AATG-GACGGTGGCTGCCCCTAATT
1 AATGAGACGGTGGCTGCCCCTAATT
25551322 AATGAGACGGTGGCTGCCCCTAATT
1 AATGAGACGGTGGCTGCCCCTAATT
25551347 AATGAG
1 AATGAG
25551353 TAAAACAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 4 0.13
25 26 0.87
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (25 bp):
AATGAGACGGTGGCTGCCCCTAATT
Found at i:25558275 original size:18 final size:17
Alignment explanation
Indices: 25558247--25558281 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
25558237 ATTATTAATA
*
25558247 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
25558264 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
25558282 TTAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:25558281 original size:16 final size:16
Alignment explanation
Indices: 25558243--25558292 Score: 52
Period size: 15 Copynumber: 3.2 Consensus size: 16
25558233 ATTGATTATT
25558243 AATA-ATTTT-ATTAA
1 AATATATTTTAATTAA
25558257 ATTATATATTTTAATTAA
1 A--ATATATTTTAATTAA
*
25558275 AATATA-TTTAATAAA
1 AATATATTTTAATTAA
25558290 AAT
1 AAT
25558293 TATGTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.03
15 11 0.35
16 8 0.26
17 5 0.16
18 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATATTTTAATTAA
Found at i:25558535 original size:16 final size:16
Alignment explanation
Indices: 25558514--25558546 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25558504 TTGATTTGCT
25558514 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
25558530 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
25558546 A
1 A
25558547 ATACAGCGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:25560290 original size:11 final size:11
Alignment explanation
Indices: 25560269--25560329 Score: 54
Period size: 11 Copynumber: 5.5 Consensus size: 11
25560259 ACTAATCCTA
25560269 TCTCAAATTTCC
1 TCTC-AATTTCC
*
25560281 TCTCAATTTCT
1 TCTCAATTTCC
*
25560292 TCT-AATTTTTC
1 TCTCAA-TTTCC
*
25560303 TCTCAATTTGC
1 TCTCAATTTCC
*
25560314 TCTCAAATTCC
1 TCTCAATTTCC
25560325 T-TCAA
1 TCTCAA
25560330 AATTTCTCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
10 6 0.15
11 29 0.71
12 6 0.15
ACGTcount: A:0.23, C:0.28, G:0.02, T:0.48
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:25560367 original size:51 final size:51
Alignment explanation
Indices: 25560305--25560402 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
25560295 AATTTTTCTC
25560305 TCAATTTGCTCTCAAATTCCT-TCAAAATTTCTCTTAAATCCATATTTATTT
1 TCAATTTGCTCTCAAATTCCTCT-AAAATTTCTCTTAAATCCATATTTATTT
* * *
25560356 TCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTTAAATCCATATTT
25560403 TTAAATAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (51 bp):
TCAATTTGCTCTCAAATTCCTCTAAAATTTCTCTTAAATCCATATTTATTT
Found at i:25562821 original size:21 final size:22
Alignment explanation
Indices: 25562750--25564318 Score: 1648
Period size: 22 Copynumber: 72.0 Consensus size: 22
25562740 TTTAATTGAC
* *
25562750 AAACCTTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25562772 AAACCCTAACCCTAACCATTAACTTTA
1 AAACCCT-A----AACCCTTAACTTAA
* *
25562799 AAACTCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25562821 AAACCCTAACACTAATCCCTTAACCTAA
1 AAACCCT---A--AA-CCCTTAACTTAA
* *
25562849 AAACCCT-AACCATTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
25562870 AAACCCTAACCCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25562892 AAACCCT-AACTCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
** *
25562913 AAACCCTAAACTTTTAACCTAAA
1 AAACCCTAAACCCTTAA-CTTAA
* *
25562936 AAACCTTAAACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
25562958 AAACACT-AACCCTTAATTTCA
1 AAACCCTAAACCCTTAACTTAA
* *
25562979 AAACCCTAAACCTTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563001 AAACCCT-AACCTTTAA-TCTGA
1 AAACCCTAAACCCTTAACT-TAA
**
25563022 AAACCCT-AACCCTTAACTTTT
1 AAACCCTAAACCCTTAACTTAA
*
25563043 AAACCCTAGACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
25563064 AAACCCTTAAACCCTTAACTTAA
1 AAACCC-TAAACCCTTAACTTAA
* * *
25563087 AAACTCT-AATCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* * * *
25563108 TAACCGTAAACACTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563130 AAACCCT-AACCATTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563151 AAACCCTAGACCCTTAACATAA
1 AAACCCTAAACCCTTAACTTAA
*
25563173 AAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563195 AAACCAT-AACCCTTAAATT-A
1 AAACCCTAAACCCTTAACTTAA
*
25563215 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563237 AAACCCT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
25563258 AAACCCTAAA-CCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563279 AAACACTAGACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563301 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563323 AAACCCT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563344 AAACTCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563366 AAACCATAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
* *
25563387 AAGCCCT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
25563408 AAACCTTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563430 AAACCTTTAAACCCTTAACTTAA
1 AAACC-CTAAACCCTTAACTTAA
* * *
25563453 AAACACT-AATCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
25563474 TAACCCTAAACACTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563496 AAACCCT-AACCCTTAACCTGA
1 AAACCCTAAACCCTTAACTTAA
*
25563517 AAACCCTAAA-CCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
25563538 AAACACTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563560 AAACCCTAAATCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563582 AAACCAT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563603 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563625 AAACCCT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563646 AAACCTTAAA-CCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563667 AAACACT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25563688 AAACCCTAAATCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563710 AAACCCT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
25563731 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563753 AAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
25563775 AAACCCTAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
* *
25563796 AAGCCCT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
25563817 AAACACTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563839 AAACCCT-AACCCTAACACTTAA
1 AAACCCTAAACCCTTA-ACTTAA
25563861 CTTTAAACCCTAAACCCTTTAA-TTAA
1 ----AAACCCTAAACCC-TTAACTTAA
*
25563887 AAACCCT-AACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563908 AAACCCTAAA-CCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* * *
25563929 AAACCCTAGACCCTGAACCTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563951 AAACCCTAAACTCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563973 AAATCCT-AACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25563994 AAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25564016 AAACCCT-AACCTTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* * *
25564037 AAACCCTAAA-CTTTAAGTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
25564058 AGACCCTAAACCCATAACTTAA
1 AAACCCTAAACCCTTAACTTAA
25564080 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25564102 AAACCCT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25564123 AAACACTAAAACCCTTAACCT-A
1 AAACCCT-AAACCCTTAACTTAA
* *
25564145 AAACCCTAAA-CCTTAATTTAG
1 AAACCCTAAACCCTTAACTTAA
*
25564166 AAACCCTAAAACCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25564188 AAACCAT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25564209 AAACCATAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25564231 AAACCCT-AACCTTTAACCTAA
1 AAACCCTAAACCCTTAACTTAA
* *
25564252 AAACCTTAAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
25564274 AAACCCTAGACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
*
25564296 AAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
25564318 A
1 A
25564319 CGCACAACTT
Statistics
Matches: 1303, Mismatches: 185, Indels: 118
0.81 0.12 0.07
Matches are distributed among these distances:
20 43 0.03
21 542 0.42
22 606 0.47
23 53 0.04
25 1 0.00
26 12 0.01
27 25 0.02
28 21 0.02
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:25562826 original size:43 final size:44
Alignment explanation
Indices: 25562750--25564318 Score: 1648
Period size: 43 Copynumber: 36.0 Consensus size: 44
25562740 TTTAATTGAC
* * * *
25562750 AAACCTTAAACCCTTAACCTAAAAACCCTAACCCTAACCATTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCT-A----AACCCTTAACTTAA
* * *
25562799 AAACTCTAAACCCTTAACCTAAAAACCCTAACACTAATCCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCT---A--AA-CCCTTAACTTAA
* * * *
25562849 AAACCCT-AACCATTAACTTTAAAACCCTAACCCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * ** *
25562892 AAACCCT-AACTCTTAACTTTAAAACCCTAAACTTTTAACCTAAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAA-CTTAA
* * * * *
25562936 AAACCTTAAACCCTTAAATTAAAAACACT-AACCCTTAATTTCA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
25562979 AAACCCTAAACCTTTAAATTAAAAACCCT-AACCTTTAA-TCTGA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACT-TAA
** *
25563022 AAACCCT-AACCCTTAACTTTTAAACCCTAGACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563064 AAACCCTTAAACCCTTAACTTAAAAACTCT-AATCCTTAAATTAA
1 AAACCC-TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * * * *
25563108 TAACCGTAAACACTTAACCTAAAAACCCT-AACCATTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563151 AAACCCTAGACCCTTAACATAAAAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563195 AAACCAT-AACCCTTAAATT-AAAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
25563237 AAACCCT-AACCCTTAACCTAAAAACCCTAAA-CCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563279 AAACACTAGACCCTTAACTTAAAAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
25563323 AAACCCT-AACCCTTAACCTAAAAACTCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563366 AAACCATAAACCCTTAACTT-AAAGCCCT-AACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
25563408 AAACCTTAAACCCTAAACCTAAAAACCTTTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACC-CTAAACCCTTAACTTAA
* * * * * *
25563453 AAACACT-AATCCTTAAATTAATAACCCTAAACACTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563496 AAACCCT-AACCCTTAACCTGAAAACCCTAAA-CCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
25563538 AAACACTAAACCCTTAACTTAAAAACCCTAAATCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563582 AAACCAT-AACCCTTAAATTAAAAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
25563625 AAACCCT-AACCCTTAACCTAAAAACCTTAAA-CCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25563667 AAACACT-AACCCTTAACTTAAAAACCCTAAATCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
25563710 AAACCCT-AACCCTTAACCTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
25563753 AAACCATAAACCCTTAACTTAAAAACCCTAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * * *
25563796 AAGCCCT-AACCCTTAAATTAAAAACACTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
*
25563839 AAACCCT-AACCCTAACACTTAACTTTAAACCCTAAACCCTTTAA-TTAA
1 AAACCCTAAACCCTTA-ACTTAA----AAACCCTAAACCC-TTAACTTAA
* *
25563887 AAACCCT-AACCCTTAACCTAAAAACCCTAAA-CCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
25563929 AAACCCTAGACCCTGAACCTAAAAACCCTAAACTCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
25563973 AAATCCT-AACCCTTAACTTAAAAACCCTAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * * *
25564016 AAACCCT-AACCTTTAACCTAAAAACCCTAAA-CTTTAAGTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
25564058 AGACCCTAAACCCATAACTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * *
25564102 AAACCCT-AACCCTTAAATTAAAAACACTAAAACCCTTAACCT-A
1 AAACCCTAAACCCTTAACTTAAAAACCCT-AAACCCTTAACTTAA
* * *
25564145 AAACCCTAAA-CCTTAATTTAGAAACCCTAAAACCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
25564188 AAACCAT-AACCCTTAAATTAAAAACCATAAACCCTTAACCTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* * * *
25564231 AAACCCT-AACCTTTAACCTAAAAACCTTAAACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
* *
25564274 AAACCCTAGACCCTTAACTTAAAAACCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
25564318 A
1 A
25564319 CGCACAACTT
Statistics
Matches: 1278, Mismatches: 202, Indels: 85
0.82 0.13 0.05
Matches are distributed among these distances:
41 4 0.00
42 228 0.18
43 679 0.53
44 229 0.18
45 35 0.03
46 1 0.00
47 5 0.00
48 29 0.02
49 52 0.04
50 15 0.01
51 1 0.00
ACGTcount: A:0.45, C:0.30, G:0.01, T:0.24
Consensus pattern (44 bp):
AAACCCTAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAA
Found at i:25562835 original size:28 final size:28
Alignment explanation
Indices: 25562804--25562858 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
25562794 CTTTAAAACT
25562804 CTAAACCCTTAACCTAAAAACCCTAACA
1 CTAAACCCTTAACCTAAAAACCCTAACA
*
25562832 CTAATCCCTTAACCTAAAAACCCTAAC
1 CTAAACCCTTAACCTAAAAACCCTAAC
25562859 CATTAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (28 bp):
CTAAACCCTTAACCTAAAAACCCTAACA
Found at i:25562858 original size:14 final size:15
Alignment explanation
Indices: 25562806--25562859 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 15
25562796 TTAAAACTCT
25562806 AAACCCTTAACCTAA
1 AAACCCTTAACCTAA
25562821 AAACCC-TAACACT--
1 AAACCCTTAAC-CTAA
*
25562834 AATCCCTTAACCTAA
1 AAACCCTTAACCTAA
25562849 AAACCC-TAACC
1 AAACCCTTAACC
25562860 ATTAACTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 7 0.21
14 13 0.39
15 13 0.39
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.19
Consensus pattern (15 bp):
AAACCCTTAACCTAA
Found at i:25563844 original size:15 final size:15
Alignment explanation
Indices: 25563824--25563853 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
25563814 TAAAAACACT
25563824 AAACCCTAAACCTAA
1 AAACCCTAAACCTAA
*
25563839 AAACCCTAACCCTAA
1 AAACCCTAAACCTAA
25563854 CACTTAACTT
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:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACCCTAAACCTAA
Found at i:25564145 original size:14 final size:14
Alignment explanation
Indices: 25564123--25564157 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
25564113 CTTAAATTAA
25564123 AAACACTAAAACCCT
1 AAAC-CTAAAACCCT
*
25564138 TAACCTAAAACCCT
1 AAACCTAAAACCCT
25564152 AAACCT
1 AAACCT
25564158 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.49, C:0.34, G:0.00, T:0.17
Consensus pattern (14 bp):
AAACCTAAAACCCT
Found at i:25567735 original size:251 final size:250
Alignment explanation
Indices: 25567252--25567804 Score: 734
Period size: 251 Copynumber: 2.2 Consensus size: 250
25567242 GTTACTATAA
* * * *
25567252 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGAAGCGA
1 CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATCATGCTAGAAGCCA
* * * *
25567317 TTTTATACTATTTGTTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACCAACTGTAGCAAAAG
66 TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAAGACCAACTGTAGCAAAAG
* * * *
25567382 TGCGTCCACGATGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAGCGTTGTTTT
131 CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTACTTGAAGCGTTGTTTT
* * * * *
25567447 ATACCATTTGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGTCCTACTGTAG
196 AAACCATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAG
* * * *
25567502 CAAAAGCGCGTCCACGTGGACGCGACTTCACAAATTCTTCTTATAAATCATCATGTTTG-AGCCA
1 CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATCATGCTAGAAGCCA
* *
25567566 TTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTGTAGTAA
66 --TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTT-TTCCAAGACCAACTGTAGCAA
*
25567631 AAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCACAA-AGCATCCTGCTTGAAGCGTT-
128 AAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATCCTACTTGAAGCGTTG
* * *
25567694 TTTTAAACTATTTACTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACTGTAG
192 TTTTAAACCATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAG
* ** * * * * *
25567753 CAAAAGCACGTATATGTGGGCGCAACTTCAAAAATCCTTCTGATAAATCATC
1 CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATC
25567805 CTACTTTGAT
Statistics
Matches: 263, Mismatches: 36, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
249 4 0.02
250 52 0.20
251 131 0.50
252 74 0.28
253 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (250 bp):
CAAAAGCGCGTCCACGTGGGCGCGACTTCACAAATTCTTCTCATAAATCATCATGCTAGAAGCCA
TTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTTTCCAAGACCAACTGTAGCAAAAG
CGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTACTTGAAGCGTTGTTTT
AAACCATTTACTCAGAAACGTCAACTCAAAATTATTTTTCCAGGACCTACTGTAG
Found at i:25567805 original size:125 final size:125
Alignment explanation
Indices: 25567252--25567806 Score: 668
Period size: 126 Copynumber: 4.4 Consensus size: 125
25567242 GTTACTATAA
*
25567252 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAGAAGCG-
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGT
* * * * *
25567316 ATTTTATACTATTTGTTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACCAACTGTAG
66 TTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
* * * *
25567376 CAAAAGTGCGTCCACGAT-GGCGCGATTTCACAAATTCTTCTCA-AATAGCATGCTACTTGCAGC
1 CAAAAGCGCGTCCACG-TGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTTGAAGC
* * * * * * *
25567439 GTTGTTTTATACCATTTGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGTCCTACTGTAG
64 GTT-TTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
* * * * * * *
25567502 CAAAAGCGCGTCCACGTGGACGCGACTTCACAAATTCTTCTTATAAATCATCATGTTTG-AGCCA
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAG-CG
*
25567566 TTTTTTAAACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAACTGTAG
65 TTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCAACTGTAG
* * *
25567628 TAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCACAAAGCATCCTGCTTGAAGCGT
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGT
* * *
25567693 TTTTTAAACTATTTACTCAGAAACGTCAAGTCGAAATTATTTTTCCAGGACCTACTGTAG
66 TTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
* ** * * * * * * *
25567753 CAAAAGCACGTATATGTGGGCGCAACTTCAAAAATCCTTCTGATAAATCATCCT
1 CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT
25567807 ACTTTGATTT
Statistics
Matches: 362, Mismatches: 60, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
123 2 0.01
124 54 0.15
125 98 0.27
126 204 0.56
127 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (125 bp):
CAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTTGAAGCGT
TTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAACTGTAG
Found at i:25568354 original size:45 final size:45
Alignment explanation
Indices: 25568299--25568387 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 45
25568289 ATACACAAAC
* * *
25568299 AAAGACAATAATAAGAGTACAAATAAAAATATGGGGAACAATAAT
1 AAAGACAATAATAACAATACAAATAAAAATATGGAGAACAATAAT
* * * *
25568344 AAAGAGAATAATAACAATATAAATAATAATATGGAGAATAATAA
1 AAAGACAATAATAACAATACAAATAAAAATATGGAGAACAATAA
25568388 GAGTGATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.62, C:0.04, G:0.13, T:0.20
Consensus pattern (45 bp):
AAAGACAATAATAACAATACAAATAAAAATATGGAGAACAATAAT
Found at i:25569985 original size:30 final size:29
Alignment explanation
Indices: 25569949--25570013 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 29
25569939 AAAAATTAAA
*
25569949 AAAAAAGTATTTTAAAAATATTTTAAAATT
1 AAAAAAGTATTTTAAAAA-AATTTAAAATT
25569979 AAAAAAGTATTTTAAAAAAATTTAAAATT
1 AAAAAAGTATTTTAAAAAAATTTAAAATT
25570008 AAAAAA
1 AAAAAA
25570014 ATTAAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.47
30 18 0.53
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAAAAGTATTTTAAAAAAATTTAAAATT
Found at i:25570021 original size:16 final size:16
Alignment explanation
Indices: 25569990--25570021 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25569980 AAAAAGTATT
*
25569990 TTAAAAAAATTTAAAA
1 TTAAAAAAATTAAAAA
25570006 TTAAAAAAATTAAAAA
1 TTAAAAAAATTAAAAA
25570022 AAAGTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
TTAAAAAAATTAAAAA
Found at i:25570030 original size:29 final size:30
Alignment explanation
Indices: 25569962--25570035 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
25569952 AAAGTATTTT
**
25569962 AAAAATATTTTAAAATTAAAAAAGTATTTTA
1 AAAAATATTTTAAAATTAAAAAAG-ATTAAA
25569993 AAAAA-A-TTTAAAATTAAAAAA-ATTAAA
1 AAAAATATTTTAAAATTAAAAAAGATTAAA
25570020 AAAAAGTATTTTAAAA
1 AAAAA-TATTTTAAAA
25570036 GTATTTTAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
27 9 0.24
29 16 0.42
30 8 0.21
31 5 0.13
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAAATATTTTAAAATTAAAAAAGATTAAA
Found at i:25572214 original size:20 final size:20
Alignment explanation
Indices: 25572189--25572227 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25572179 TGAGTGCAAA
*
25572189 ATTAAAAAATTTAAAAAATT
1 ATTAAAAAAGTTAAAAAATT
*
25572209 ATTAAAAAAGTTATAAAAT
1 ATTAAAAAAGTTAAAAAAT
25572228 ATATAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
ATTAAAAAAGTTAAAAAATT
Found at i:25575711 original size:9 final size:9
Alignment explanation
Indices: 25575697--25575733 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
25575687 TATAGTTTGA
25575697 TATTCGAAT
1 TATTCGAAT
25575706 TATTCGAAT
1 TATTCGAAT
*
25575715 TATTCGAGT
1 TATTCGAAT
25575724 TATTCGAAT
1 TATTCGAAT
25575733 T
1 T
25575734 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:25577394 original size:20 final size:20
Alignment explanation
Indices: 25577371--25577495 Score: 96
Period size: 20 Copynumber: 6.2 Consensus size: 20
25577361 ATTAGAAATT
25577371 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* **
25577391 TTATCTTAATATTAAACGAG
1 TTATCTTAATATTATATAAG
* * *
25577411 TTAT-GT-A-ATTAGA-AATT
1 TTATCTTAATATTATATAA-G
25577428 TTATCTTAATATTATATAAG
1 TTATCTTAATATTATATAAG
* **
25577448 TTATCTTAATATTAAACGAG
1 TTATCTTAATATTATATAAG
25577468 TTATGTACCTTAATATTATATAAG
1 TTA--T--CTTAATATTATATAAG
25577492 TTAT
1 TTAT
25577496 GAAGTGTCCC
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
16 1 0.01
17 9 0.11
18 2 0.03
19 2 0.03
20 46 0.57
21 2 0.03
22 2 0.03
24 16 0.20
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.46
Consensus pattern (20 bp):
TTATCTTAATATTATATAAG
Found at i:25577400 original size:57 final size:57
Alignment explanation
Indices: 25577339--25577474 Score: 272
Period size: 57 Copynumber: 2.4 Consensus size: 57
25577329 AAATTAGAAA
25577339 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
25577396 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
1 TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
25577453 TTAATATTAAACGAGTTATGTA
1 TTAATATTAAACGAGTTATGTA
25577475 CCTTAATATT
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 79 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (57 bp):
TTAATATTAAACGAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAGTTATC
Found at i:25577450 original size:94 final size:94
Alignment explanation
Indices: 25577237--25577451 Score: 245
Period size: 94 Copynumber: 2.3 Consensus size: 94
25577227 AAATTATGTT
** *
25577237 ATTAGAAAGGAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATTGTATAAGTTATC
1 ATTAGAAATTAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATTATATAAGTTATC
** * *
25577302 TAAAATTAGAAATTGATGTGTACTTAGAA
66 TAAAATTAGAAAGAGATATGTAATTAGAA
* **
25577331 ATTAGAAATTAATATTAAACGAGTTATGTAATT-AGAAATTTTATCTTAATATTATATAAGTTAT
1 ATTAGAAATTAATATTATATAAGTTATGTAATTCA-AAATTTTATCTTAATATTATATAAGTTAT
* * *
25577395 CTTAATATTA-AACGAGTTATGTAATTAGAA
65 C-TAAAATTAGAAAGAGATATGTAATTAGAA
** **
25577425 ATTTTATCTTAATATTATATAAGTTAT
1 ATTAGAAATTAATATTATATAAGTTAT
25577452 CTTAATATTA
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
93 1 0.01
94 91 0.92
95 7 0.07
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (94 bp):
ATTAGAAATTAATATTATATAAGTTATGTAATTCAAAATTTTATCTTAATATTATATAAGTTATC
TAAAATTAGAAAGAGATATGTAATTAGAA
Found at i:25577493 original size:24 final size:22
Alignment explanation
Indices: 25577431--25577496 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 22
25577421 AGAAATTTTA
25577431 TCTTAATATTATATAAGTTA--
1 TCTTAATATTATATAAGTTATG
* **
25577451 TCTTAATATTAAACGAGTTATG
1 TCTTAATATTATATAAGTTATG
25577473 TACCTTAATATTATATAAGTTATG
1 T--CTTAATATTATATAAGTTATG
25577497 AAGTGTCCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 17 0.47
22 1 0.03
24 18 0.50
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (22 bp):
TCTTAATATTATATAAGTTATG
Found at i:25579519 original size:147 final size:147
Alignment explanation
Indices: 25579336--25579633 Score: 524
Period size: 147 Copynumber: 2.0 Consensus size: 147
25579326 TGGCATTTTT
* * *
25579336 AAAAAATTCCACAACTTATATAGAGAAAATGGCACCGTTTATGTAAAACATAAAACATATTTGCG
1 AAAAAATGCCACAACTTATATAGAGAAAACGACACCGTTTATGTAAAACATAAAACATATTTGCG
* *
25579401 GCGCTTTAAGGAAAGCGCCACTATAGACAATGCCAAAAGACACAGTTTCTTAACTCATAATACAC
66 GCGCTTTAAGGAAAGCGCCACTACAGACAATACCAAAAGACACAGTTTCTTAACTCATAATACAC
25579466 TTTTGCGACGTTTACAA
131 TTTTGCGACGTTTACAA
25579483 AAAAAATGCCACAACTTATATAGAGAAAACGACACCGTTTATGTAAAACATAAAACATATTTGCG
1 AAAAAATGCCACAACTTATATAGAGAAAACGACACCGTTTATGTAAAACATAAAACATATTTGCG
* *
25579548 GCGCTTTAATGAAAGCGCCACTACAGACAATACCAAACGACACAGTTTCTTAACTCATAATACAC
66 GCGCTTTAAGGAAAGCGCCACTACAGACAATACCAAAAGACACAGTTTCTTAACTCATAATACAC
*
25579613 TTTTGCGGCGTTTACAA
131 TTTTGCGACGTTTACAA
25579630 AAAA
1 AAAA
25579634 GCGCCACCAA
Statistics
Matches: 143, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
147 143 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (147 bp):
AAAAAATGCCACAACTTATATAGAGAAAACGACACCGTTTATGTAAAACATAAAACATATTTGCG
GCGCTTTAAGGAAAGCGCCACTACAGACAATACCAAAAGACACAGTTTCTTAACTCATAATACAC
TTTTGCGACGTTTACAA
Found at i:25579618 original size:72 final size:71
Alignment explanation
Indices: 25579395--25579640 Score: 215
Period size: 72 Copynumber: 3.4 Consensus size: 71
25579385 ATAAAACATA
** * * *
25579395 TTTGCGGCGCTTTAAGGAAAGCGCCACTATAGACAATGCCAAAAGACACAGTTTCTTAACTCATA
1 TTTGCGGCG-TTTAAAAAAAGCGCCACTACAGACAATACCAAACGACACAGTTTCTTAACTCATA
25579460 ATACACT
65 ATACACT
* ** * ** * * ** * * **
25579467 TTTGCGACGTTTACAAAAAAAATGCCACAACTTATATAGAGAAAACGACACCGTTTATGTAAAAC
1 TTTGCGGCGTTT--AAAAAAAGCGCCACTACAGACA-ATACCAAACGACACAGTTTCT-TAACTC
*
25579532 ATAAAACA-T
62 ATAATACACT
**
25579541 ATTTGCGGCGCTTTAATGAAAGCGCCACTACAGACAATACCAAACGACACAGTTTCTTAACTCAT
1 -TTTGCGGCG-TTTAAAAAAAGCGCCACTACAGACAATACCAAACGACACAGTTTCTTAACTCAT
25579606 AATACACT
64 AATACACT
25579614 TTTGCGGCGTTTACAAAAAAGCGCCAC
1 TTTGCGGCGTTTA-AAAAAAGCGCCAC
25579641 CAAAAGCAAA
Statistics
Matches: 127, Mismatches: 39, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
71 7 0.06
72 39 0.31
73 30 0.24
74 29 0.23
75 19 0.15
76 3 0.02
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.24
Consensus pattern (71 bp):
TTTGCGGCGTTTAAAAAAAGCGCCACTACAGACAATACCAAACGACACAGTTTCTTAACTCATAA
TACACT
Found at i:25580230 original size:14 final size:14
Alignment explanation
Indices: 25580213--25580252 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
25580203 CCGTAAACCG
*
25580213 TAAACCCCAAACTA
1 TAAACCCTAAACTA
**
25580227 TAAACTATAAACTA
1 TAAACCCTAAACTA
25580241 TAAACCCTAAAC
1 TAAACCCTAAAC
25580253 CCCAAATCCT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.53, C:0.28, G:0.00, T:0.20
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:25580231 original size:7 final size:7
Alignment explanation
Indices: 25580221--25580245 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
25580211 CGTAAACCCC
25580221 AAACTAT
1 AAACTAT
25580228 AAACTAT
1 AAACTAT
25580235 AAACTAT
1 AAACTAT
25580242 AAAC
1 AAAC
25580246 CCTAAACCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (7 bp):
AAACTAT
Found at i:25580385 original size:21 final size:21
Alignment explanation
Indices: 25580367--25580442 Score: 66
Period size: 21 Copynumber: 3.6 Consensus size: 21
25580357 ACCGTAAATC
25580367 TTAAACCCTAAACCATAAACA
1 TTAAACCCTAAACCATAAACA
* *
25580388 TTAAACCCATAGACCACAAACA
1 TTAAACCC-TAAACCATAAACA
* * *
25580410 AT-AACCAC-AAAGTCATAAACT
1 TTAAACC-CTAAA-CCATAAACA
25580431 TTAAACCCTAAA
1 TTAAACCCTAAA
25580443 ACTAGCCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 9
0.71 0.14 0.15
Matches are distributed among these distances:
20 2 0.05
21 20 0.48
22 20 0.48
ACGTcount: A:0.51, C:0.28, G:0.03, T:0.18
Consensus pattern (21 bp):
TTAAACCCTAAACCATAAACA
Done.