Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 62 of 91
Found at i:22322286 original size:29 final size:30
Alignment explanation
Indices: 22322230--22322286 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
22322220 ATTGTTCTCA
* *
22322230 AAGGAGAATGCAATCTTGTAGGAGTTTTTC
1 AAGGAGAATGCAAGCTTGTAGGACTTTTTC
22322260 AAGGA-AATGCGAAGCTTGTAGG-CTTTT
1 AAGGAGAATGC-AAGCTTGTAGGACTTTT
22322287 CCACTTCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.30, C:0.11, G:0.28, T:0.32
Consensus pattern (30 bp):
AAGGAGAATGCAAGCTTGTAGGACTTTTTC
Found at i:22325539 original size:20 final size:21
Alignment explanation
Indices: 22325510--22325548 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
22325500 ATAGATCACC
22325510 TATTTATAAATA-AAAATTAA
1 TATTTATAAATATAAAATTAA
*
22325530 TATTTTTAAATATAAAATT
1 TATTTATAAATATAAAATT
22325549 TGAAGTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTATAAATATAAAATTAA
Found at i:22329798 original size:42 final size:42
Alignment explanation
Indices: 22329752--22329856 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
22329742 TGTGCGAGTA
* *
22329752 GGAGTGCACATAAGCCGTTGCTGACCCGACTATGTACGAATG
1 GGAGTGTACATAAGCCGTTGCTGACCCGACTATATACGAATG
* * * * *
22329794 GGAGTGTACATAAGCCATTACTGACCCGGCTATATGCGAGTG
1 GGAGTGTACATAAGCCGTTGCTGACCCGACTATATACGAATG
* *
22329836 GGAGTATGCATAAGCCGTTGC
1 GGAGTGTACATAAGCCGTTGC
22329857 ATATGAGATG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.23
Consensus pattern (42 bp):
GGAGTGTACATAAGCCGTTGCTGACCCGACTATATACGAATG
Found at i:22339550 original size:20 final size:20
Alignment explanation
Indices: 22339525--22339570 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
22339515 TTTTGACCCC
*
22339525 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTCGAGTATA
* *
22339545 ATTTGATTTATTCGAGTATG
1 ATTTGACTTATTCGAGTATA
22339565 ATTTGA
1 ATTTGA
22339571 GGTTTAGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.04, G:0.20, T:0.48
Consensus pattern (20 bp):
ATTTGACTTATTCGAGTATA
Found at i:22342838 original size:13 final size:13
Alignment explanation
Indices: 22342822--22342863 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
22342812 TTTATTATAC
22342822 TATTTAATTATTT
1 TATTTAATTATTT
*
22342835 TATTTATTTATTT
1 TATTTAATTATTT
22342848 TGA-TTAATT-TTT
1 T-ATTTAATTATTT
22342860 TATT
1 TATT
22342864 ATATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 1 0.04
12 5 0.20
13 18 0.72
14 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (13 bp):
TATTTAATTATTT
Found at i:22342854 original size:26 final size:26
Alignment explanation
Indices: 22342825--22342874 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
22342815 ATTATACTAT
*
22342825 TTAATTATTTTATT-TATTTATTTTGA
1 TTAATT-TTTTATTATATATATTTTGA
22342851 TTAATTTTTTATTATATATATTTT
1 TTAATTTTTTATTATATATATTTT
22342875 TATTTAGGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTAATTTTTTATTATATATATTTTGA
Found at i:22345016 original size:33 final size:34
Alignment explanation
Indices: 22344974--22345038 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
22344964 GAATTCTGAG
*
22344974 ATATTAACAAAACACAGATTTTTCTTT-ATTTAA
1 ATATTAACAAAACACACATTTTTCTTTCATTTAA
* *
22345007 ATATTAACAAAACATACATTTTTGTTTCATTT
1 ATATTAACAAAACACACATTTTTCTTTCATTT
22345039 CAAAATTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (34 bp):
ATATTAACAAAACACACATTTTTCTTTCATTTAA
Found at i:22352253 original size:2 final size:2
Alignment explanation
Indices: 22352240--22352279 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
22352230 TTAGAAATTC
*
22352240 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22352280 TACACTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22369511 original size:20 final size:20
Alignment explanation
Indices: 22369473--22369511 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
22369463 GGACATTGCC
* * *
22369473 CCAAAACCAAAACAGAAACT
1 CCAAAACAAAAAAAAAAACT
22369493 CCAAAACAAAAAAAAAAAC
1 CCAAAACAAAAAAAAAAAC
22369512 ACTTGAAACA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.26, G:0.03, T:0.03
Consensus pattern (20 bp):
CCAAAACAAAAAAAAAAACT
Found at i:22371003 original size:22 final size:22
Alignment explanation
Indices: 22370956--22371003 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
22370946 ATGAAATTAT
*
22370956 AAAATATTTAAATAATAAAAAT
1 AAAATATTTAAATAATAAAAAG
22370978 AAAAT-TTTAAAATAA-AACAAAG
1 AAAATATTT-AAATAATAA-AAAG
22371000 AAAA
1 AAAA
22371004 AAATATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.25
Consensus pattern (22 bp):
AAAATATTTAAATAATAAAAAG
Found at i:22374605 original size:29 final size:31
Alignment explanation
Indices: 22374550--22374628 Score: 92
Period size: 29 Copynumber: 2.6 Consensus size: 31
22374540 AAGTACAAAA
*
22374550 AATTTAATTACATTTTTAT-TCTGTTATTGT
1 AATTTAATTAAATTTTTATATCTGTTATTGT
* *
22374580 -ATTTAATTAAATTTTTATAT-TTTTATTTT
1 AATTTAATTAAATTTTTATATCTGTTATTGT
* *
22374609 AAATTAAATAAATTTTTATA
1 AATTTAATTAAATTTTTATA
22374629 ATTAACCGTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 24 0.57
30 18 0.43
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (31 bp):
AATTTAATTAAATTTTTATATCTGTTATTGT
Found at i:22378681 original size:6 final size:6
Alignment explanation
Indices: 22378667--22378698 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
22378657 TTTCTCCCCA
*
22378667 TTTCAT TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
22378699 GTAGAGAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:22387993 original size:7 final size:7
Alignment explanation
Indices: 22387981--22388007 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
22387971 TAAAAATGCC
22387981 AAAAGAT
1 AAAAGAT
22387988 AAAAGAT
1 AAAAGAT
22387995 AAAAGAT
1 AAAAGAT
22388002 AAAAGA
1 AAAAGA
22388008 AATTAACGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
AAAAGAT
Found at i:22390736 original size:27 final size:27
Alignment explanation
Indices: 22390706--22390771 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 27
22390696 AGGAGGTGGC
*
22390706 GGTGGAGGTGGTGCTCCACCTACAGGA
1 GGTGGAGGTGGTGCTCCACCTAAAGGA
* *
22390733 GGTGGA---GGAGCTCCACGTAAAGGA
1 GGTGGAGGTGGTGCTCCACCTAAAGGA
*
22390757 GGTGGGGGTGGTGCT
1 GGTGGAGGTGGTGCT
22390772 GGTGTGCCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
24 20 0.65
27 11 0.35
ACGTcount: A:0.18, C:0.17, G:0.47, T:0.18
Consensus pattern (27 bp):
GGTGGAGGTGGTGCTCCACCTAAAGGA
Found at i:22391045 original size:3 final size:3
Alignment explanation
Indices: 22391037--22391063 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
22391027 CTAGTAAGCA
22391037 GTG GTG GTG GTG GTG GTG GTG GTG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG
22391064 CAGGTGGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GTG
Found at i:22391118 original size:42 final size:41
Alignment explanation
Indices: 22391054--22391133 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 41
22391044 TGGTGGTGGT
* *
22391054 GGTGGTGGTGCAGGTGGAGATGG-AGCTCCACGCAATGGAGGG
1 GGTGGGGGTGCAGGGGGAGATGGCA-CTCCACG-AATGGAGGG
* *
22391096 GGTGGGGGTGGAGGGGGCGATGGCACTCCACGAATGGA
1 GGTGGGGGTGCAGGGGGAGATGGCACTCCACGAATGGA
22391134 AGACGAAGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 6 0.18
42 26 0.79
43 1 0.03
ACGTcount: A:0.19, C:0.15, G:0.51, T:0.15
Consensus pattern (41 bp):
GGTGGGGGTGCAGGGGGAGATGGCACTCCACGAATGGAGGG
Found at i:22391248 original size:15 final size:15
Alignment explanation
Indices: 22391228--22391261 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
22391218 ACTGACAGGA
* *
22391228 GGAGGAGGGGGTGGT
1 GGAGGAGGAGGAGGT
22391243 GGAGGAGGAGGAGGT
1 GGAGGAGGAGGAGGT
22391258 GGAG
1 GGAG
22391262 AACATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.71, T:0.09
Consensus pattern (15 bp):
GGAGGAGGAGGAGGT
Found at i:22391248 original size:18 final size:18
Alignment explanation
Indices: 22391225--22391259 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
22391215 TGCACTGACA
*
22391225 GGAGGAGGAGGGGGTGGT
1 GGAGGAGGAGGAGGTGGT
22391243 GGAGGAGGAGGAGGTGG
1 GGAGGAGGAGGAGGTGG
22391260 AGAACATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.71, T:0.09
Consensus pattern (18 bp):
GGAGGAGGAGGAGGTGGT
Found at i:22391456 original size:6 final size:6
Alignment explanation
Indices: 22391437--22391466 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
22391427 CTGCTCTGTA
*
22391437 AGGTGG AGGGGG AGGTGG AGGTGG AGGTGG
1 AGGTGG AGGTGG AGGTGG AGGTGG AGGTGG
22391467 CGCTGCAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.17, C:0.00, G:0.70, T:0.13
Consensus pattern (6 bp):
AGGTGG
Found at i:22398597 original size:19 final size:19
Alignment explanation
Indices: 22398573--22398622 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
22398563 TATCAACAAA
**
22398573 CCGAGGGTTTCTTGATTGG
1 CCGAGGGTTTCTTGACCGG
22398592 CCGAGGGTTTCTTGACCGG
1 CCGAGGGTTTCTTGACCGG
22398611 CCGAGGGTTTCT
1 CCGAGGGTTTCT
22398623 CACCAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.10, C:0.22, G:0.36, T:0.32
Consensus pattern (19 bp):
CCGAGGGTTTCTTGACCGG
Found at i:22399057 original size:2 final size:2
Alignment explanation
Indices: 22399052--22399104 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
22399042 TGTGTGTGTG
22399052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22399094 TA TA TA TA TA T
1 TA TA TA TA TA T
22399105 CAATCATCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22399226 original size:9 final size:9
Alignment explanation
Indices: 22399212--22399237 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
22399202 GAAGCACCCA
22399212 ATGCATATC
1 ATGCATATC
22399221 ATGCATATC
1 ATGCATATC
22399230 ATGCATAT
1 ATGCATAT
22399238 TATCATATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (9 bp):
ATGCATATC
Found at i:22407826 original size:23 final size:21
Alignment explanation
Indices: 22407800--22407853 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
22407790 ATTATTAATT
22407800 ATAAAAATTT-ATCTCAAATAAAA
1 ATAAAAATTTGAT-T-AAAT-AAA
22407823 ATAAAAGAGTTTGATTAAATAAA
1 ATAAAA-A-TTTGATTAAATAAA
22407846 ATAAAAAT
1 ATAAAAAT
22407854 ATAAAATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
21 1 0.04
22 1 0.04
23 15 0.54
24 5 0.18
25 4 0.14
26 2 0.07
ACGTcount: A:0.61, C:0.04, G:0.06, T:0.30
Consensus pattern (21 bp):
ATAAAAATTTGATTAAATAAA
Found at i:22424150 original size:16 final size:16
Alignment explanation
Indices: 22424058--22424150 Score: 62
Period size: 16 Copynumber: 5.5 Consensus size: 16
22424048 TTAAAATTTT
* *
22424058 TTTAAATAATTTTAAA
1 TTTAAATTATTTTGAA
* *
22424074 TTCAAATCATTTTGAA
1 TTTAAATTATTTTGAA
*
22424090 TTTAAATCATTCAAATTTGATA
1 TTT-AA--ATT--ATTTTGA-A
22424112 TTTAAATTA-TTTGAA
1 TTTAAATTATTTTGAA
**
22424127 TTCGAATTATTTTGAA
1 TTTAAATTATTTTGAA
22424143 TTTAAATT
1 TTTAAATT
22424151 GTTAAAAATT
Statistics
Matches: 60, Mismatches: 10, Indels: 14
0.71 0.12 0.17
Matches are distributed among these distances:
15 8 0.13
16 32 0.53
17 3 0.05
19 5 0.08
21 8 0.13
22 4 0.07
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (16 bp):
TTTAAATTATTTTGAA
Found at i:22431566 original size:21 final size:22
Alignment explanation
Indices: 22431537--22431579 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
22431527 TAACTAGTTA
22431537 AGAAGAGAAAAACA-CAAAAAAG
1 AGAAGAGAAAAA-AGCAAAAAAG
22431559 AGAA-AGAAAAAAGCAAAAAAG
1 AGAAGAGAAAAAAGCAAAAAAG
22431580 GAGCAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 1 0.05
21 15 0.75
22 4 0.20
ACGTcount: A:0.74, C:0.07, G:0.19, T:0.00
Consensus pattern (22 bp):
AGAAGAGAAAAAAGCAAAAAAG
Found at i:22438313 original size:59 final size:58
Alignment explanation
Indices: 22438242--22438363 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 58
22438232 ATGTTTGGTA
* * * *
22438242 TTAATTTAGACAAGAAAATATGTTTGTCTT-AATTTAAGGCAAGA-AAAATATTTTTTGCC
1 TTAATCTAGACAAGAAAACATATTTGT-TTCAATTT-AGACAAGATAAAATA-TTTTTGCC
*
22438301 TTAATCTAGACAAGAAAACATATTTGTTTCAATTTAGACAAGATAAAATATTTTTGTC
1 TTAATCTAGACAAGAAAACATATTTGTTTCAATTTAGACAAGATAAAATATTTTTGCC
22438359 TTAAT
1 TTAAT
22438364 TAAAGATAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
58 21 0.38
59 35 0.62
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (58 bp):
TTAATCTAGACAAGAAAACATATTTGTTTCAATTTAGACAAGATAAAATATTTTTGCC
Found at i:22438324 original size:31 final size:30
Alignment explanation
Indices: 22438212--22438364 Score: 117
Period size: 28 Copynumber: 5.2 Consensus size: 30
22438202 CATGTTATGT
* * *
22438212 CTTAATTTAGACAAG--AAATCATGTTTGGT
1 CTTAATTTAGACAAGAAAAAT-ATTTTTTGC
* * *
22438241 ATTAATTTAGACAAG-AAAATA-TGTTTGT
1 CTTAATTTAGACAAGAAAAATATTTTTTGC
*
22438269 CTTAATTTAAGGCAAGAAAAATATTTTTTGC
1 CTTAATTT-AGACAAGAAAAATATTTTTTGC
*
22438300 CTTAATCTAGACAAGAAAACATATTTGTTT--
1 CTTAATTTAGACAAGAAAA-ATATTT-TTTGC
*
22438330 C--AATTTAGACAAGATAAAATA-TTTTTGT
1 CTTAATTTAGACAAGA-AAAATATTTTTTGC
22438358 CTTAATT
1 CTTAATT
22438365 AAAGATAAGA
Statistics
Matches: 102, Mismatches: 11, Indels: 21
0.76 0.08 0.16
Matches are distributed among these distances:
26 3 0.03
27 2 0.02
28 27 0.26
29 24 0.24
30 25 0.25
31 18 0.18
32 3 0.03
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (30 bp):
CTTAATTTAGACAAGAAAAATATTTTTTGC
Found at i:22438338 original size:28 final size:28
Alignment explanation
Indices: 22438174--22438364 Score: 181
Period size: 29 Copynumber: 6.6 Consensus size: 28
22438164 AGACAACTTT
*
22438174 AACATGTTTGTCTTAATTTAGATAAG--
1 AACATGTTTGTCTTAATTTAGACAAGAA
22438200 AACATGTTATGTCTTAATTTAGACAAGAA
1 AACATGTT-TGTCTTAATTTAGACAAGAA
* *
22438229 ATCATGTTTGGTATTAATTTAGACAAGAA
1 AACATGTTT-GTCTTAATTTAGACAAGAA
* *
22438258 AATATGTTTGTCTTAATTTAAGGCAAGAAA
1 AACATGTTTGTCTTAATTT-AGACAAG-AA
* * * *
22438288 AATATTTTTTGCCTTAATCTAGACAAGAA
1 AACA-TGTTTGTCTTAATTTAGACAAGAA
*
22438317 AACATATTTGT-TTCAATTTAGACAAGATAA
1 AACATGTTTGTCTT-AATTTAGACAAG--AA
* *
22438347 AATATTTTTGTCTTAATT
1 AACATGTTTGTCTTAATT
22438365 AAAGATAAGA
Statistics
Matches: 137, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
26 8 0.06
27 19 0.14
28 26 0.19
29 43 0.31
30 27 0.20
31 14 0.10
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (28 bp):
AACATGTTTGTCTTAATTTAGACAAGAA
Found at i:22439950 original size:15 final size:16
Alignment explanation
Indices: 22439923--22439952 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
22439913 TCGTTTGCAT
22439923 GTTCCCTGGCAATTCA
1 GTTCCCTGGCAATTCA
22439939 GTTCCC-GGCAATTC
1 GTTCCCTGGCAATTC
22439953 CAGGTACTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.33, G:0.20, T:0.30
Consensus pattern (16 bp):
GTTCCCTGGCAATTCA
Found at i:22444291 original size:1 final size:1
Alignment explanation
Indices: 22444285--22444309 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22444275 AAGCCAAACC
22444285 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
22444310 GAAACCACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22445889 original size:28 final size:28
Alignment explanation
Indices: 22445856--22445911 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
22445846 ACATTACAAT
*
22445856 GCATGAAATTAAAAATGTATAATTATGA
1 GCATGAAATTAAAAATATATAATTATGA
*
22445884 GCATGAAATTAGAAATATATAATTATGA
1 GCATGAAATTAAAAATATATAATTATGA
22445912 AATAGCAGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.50, C:0.04, G:0.14, T:0.32
Consensus pattern (28 bp):
GCATGAAATTAAAAATATATAATTATGA
Found at i:22458560 original size:35 final size:35
Alignment explanation
Indices: 22458513--22458620 Score: 135
Period size: 35 Copynumber: 3.1 Consensus size: 35
22458503 AACCTGAACG
* * *
22458513 AGTGAAGTGTTACTTCACGCAAAATAATTAGAATA
1 AGTGAAGCGTTACTTCACGCAGAATAACTAGAATA
* *
22458548 AGTGAAGCGTTACTTCACGCAGAACAACTAGAACA
1 AGTGAAGCGTTACTTCACGCAGAATAACTAGAATA
** * *
22458583 AGTGAAGCACTACTTAATGCAGAATAACTAGAATA
1 AGTGAAGCGTTACTTCACGCAGAATAACTAGAATA
22458618 AGT
1 AGT
22458621 AGAACACTAC
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 62 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (35 bp):
AGTGAAGCGTTACTTCACGCAGAATAACTAGAATA
Found at i:22458629 original size:35 final size:35
Alignment explanation
Indices: 22458523--22458631 Score: 121
Period size: 35 Copynumber: 3.1 Consensus size: 35
22458513 AGTGAAGTGT
* * * **
22458523 TACTTCACGCAAAATAATTAGAATAAGTGAAGCGT
1 TACTTAACGCAGAATAACTAGAATAAGTGAAGCAC
* * *
22458558 TACTTCACGCAGAACAACTAGAACAAGTGAAGCAC
1 TACTTAACGCAGAATAACTAGAATAAGTGAAGCAC
*
22458593 TACTTAATGCAGAATAACTAGAATAAGTAGAA-CAC
1 TACTTAACGCAGAATAACTAGAATAAGT-GAAGCAC
22458628 TACT
1 TACT
22458632 CCATATGGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 60 0.95
36 3 0.05
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (35 bp):
TACTTAACGCAGAATAACTAGAATAAGTGAAGCAC
Found at i:22458647 original size:35 final size:34
Alignment explanation
Indices: 22458568--22458667 Score: 98
Period size: 35 Copynumber: 2.9 Consensus size: 34
22458558 TACTTCACGC
*
22458568 AGAACAACTAGAACAAGT-GAAGCACTACTTAATG
1 AGAACAACTAGAACAAGTAGAA-CACTACTCAATG
* *
22458602 CAGAATAACTAGAATAAGTAGAACACTACTCCATATG
1 -AGAACAACTAGAACAAGTAGAACACTACT-CA-ATG
22458639 -GAACAACTA-ATACAAGTAGAACAACTACT
1 AGAACAACTAGA-ACAAGTAGAAC-ACTACT
22458668 TCGAATAGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
34 1 0.02
35 41 0.75
36 10 0.18
37 3 0.05
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (34 bp):
AGAACAACTAGAACAAGTAGAACACTACTCAATG
Found at i:22458920 original size:30 final size:30
Alignment explanation
Indices: 22458884--22458969 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
22458874 GTACAACTTC
* **
22458884 TTCTCTTGTACCTCTTCTTGTATAGTTTTT
1 TTCTCTTGTACCTATTCACGTATAGTTTTT
**
22458914 TTCTCTTGTACCTATTCACGTATAGTTTCC
1 TTCTCTTGTACCTATTCACGTATAGTTTTT
* * *
22458944 TCCCCTT-TACCTATTCACGTACAGTT
1 TTCTCTTGTACCTATTCACGTATAGTT
22458970 CTTCTCTATC
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 18 0.38
30 30 0.62
ACGTcount: A:0.15, C:0.27, G:0.09, T:0.49
Consensus pattern (30 bp):
TTCTCTTGTACCTATTCACGTATAGTTTTT
Found at i:22460671 original size:26 final size:27
Alignment explanation
Indices: 22460628--22460679 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
22460618 GGTTGAATTG
*
22460628 ATCTCCTTCATATCAAGTT-AGAGTTA
1 ATCTCCTTCATATAAAGTTGAGAGTTA
* *
22460654 ATCTCCTTGATGTAAAGTTGAGAGTT
1 ATCTCCTTCATATAAAGTTGAGAGTT
22460680 CCCTTTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.38
Consensus pattern (27 bp):
ATCTCCTTCATATAAAGTTGAGAGTTA
Found at i:22463819 original size:27 final size:26
Alignment explanation
Indices: 22463789--22463864 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 26
22463779 ATTTATGTAT
22463789 TTATCAAAAAAAAATAAATTTAATTAA
1 TTAT-AAAAAAAAATAAATTTAATTAA
22463816 TTATAAAAATTAAATAAATAAATTTAATTAA
1 TTAT--AAA--AAA-AAATAAATTTAATTAA
*
22463847 TTATAAAAATAAATAAAT
1 TTATAAAAAAAAATAAAT
22463865 AAAATTTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
26 8 0.19
27 6 0.14
28 3 0.07
29 3 0.07
30 3 0.07
31 20 0.47
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (26 bp):
TTATAAAAAAAAATAAATTTAATTAA
Found at i:22463838 original size:31 final size:30
Alignment explanation
Indices: 22463800--22463873 Score: 130
Period size: 31 Copynumber: 2.4 Consensus size: 30
22463790 TATCAAAAAA
22463800 AAATAAATTTAATTAATTATAAAAATTAAAT
1 AAATAAATTTAATTAATTATAAAAA-TAAAT
22463831 AAATAAATTTAATTAATTATAAAAATAAAT
1 AAATAAATTTAATTAATTATAAAAATAAAT
22463861 AAATAAAATTTAA
1 AAAT-AAATTTAA
22463874 AAAGCTCGCG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 9 0.21
31 33 0.79
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATAAATTTAATTAATTATAAAAATAAAT
Found at i:22463839 original size:22 final size:21
Alignment explanation
Indices: 22463814--22463876 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
22463804 AAATTTAATT
22463814 AATTATAAAAATTAAATAAATA
1 AATTATAAAAATTAAA-AAATA
*
22463836 AATT-TAATTAATTATAAAAATA
1 AATTATAA-AAATTA-AAAAATA
* *
22463858 AATAAATAAAATTTAAAAA
1 AAT-TATAAAAATTAAAAA
22463877 GCTCGCGACA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
21 3 0.09
22 21 0.64
23 6 0.18
24 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTATAAAAATTAAAAAATA
Found at i:22463856 original size:18 final size:18
Alignment explanation
Indices: 22463804--22463856 Score: 62
Period size: 14 Copynumber: 3.2 Consensus size: 18
22463794 AAAAAAAAAT
22463804 AAATTTAATTAATTATAA
1 AAATTTAATTAATTATAA
*
22463822 AAA-TTAAATAA--AT--
1 AAATTTAATTAATTATAA
22463835 AAATTTAATTAATTATAA
1 AAATTTAATTAATTATAA
22463853 AAAT
1 AAAT
22463857 AAATAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 10
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.11
14 7 0.25
15 2 0.07
16 2 0.07
17 7 0.25
18 7 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTTAATTAATTATAA
Found at i:22464047 original size:2 final size:2
Alignment explanation
Indices: 22464040--22464086 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
22464030 AAAGTCAAGT
22464040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
22464082 TA TA T
1 TA TA T
22464087 TTTAAAAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22464280 original size:26 final size:27
Alignment explanation
Indices: 22464251--22464306 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
22464241 TATTCTAATA
*
22464251 TTTCTCTCTAGCCTTTTAT-TTGC-TTC
1 TTTCACTCTAG-CTTTTATCTTGCTTTC
* *
22464277 TTTCACTTTAGCTTTTTTCTTGCTTTC
1 TTTCACTCTAGCTTTTATCTTGCTTTC
22464304 TTT
1 TTT
22464307 ATTCTAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
25 6 0.24
26 13 0.52
27 6 0.24
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.62
Consensus pattern (27 bp):
TTTCACTCTAGCTTTTATCTTGCTTTC
Found at i:22464994 original size:96 final size:95
Alignment explanation
Indices: 22464776--22464966 Score: 258
Period size: 96 Copynumber: 2.0 Consensus size: 95
22464766 GAAATTCAAC
* *
22464776 TGATTGAAAAAAAAAATTAAAAAAATTACAAGAAAAAGAAAAATTTACTTACTTGAAAAGATTCG
1 TGATTG-AAAAAAAAATGAAAAAAATTACAAGAAAAAGAAAAACTTACTTACTTGAAAAGATTCG
* *
22464841 TAAAAGAATCGATTTTCTCTAAAATTTGTAT
65 CAAAAGAATCGATTTACTCTAAAATTTGTAT
* *
22464872 TGATTGAAAAAAAAAATTAAAAAAATTACAA-AAAGAAGAAAAACTTACTTGCTTGAAAAGATTC
1 TGATTG-AAAAAAAAATGAAAAAAATTACAAGAAA-AAGAAAAACTTACTTACTTGAAAAGATTC
* * *
22464936 GCAAAAGAATTGACTTTACTTTGAAATTTGT
64 GCAAAAGAATCGA-TTTACTCTAAAATTTGT
22464967 TTTGCTTTGA
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
95 3 0.03
96 69 0.80
97 14 0.16
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (95 bp):
TGATTGAAAAAAAAATGAAAAAAATTACAAGAAAAAGAAAAACTTACTTACTTGAAAAGATTCGC
AAAAGAATCGATTTACTCTAAAATTTGTAT
Found at i:22467987 original size:19 final size:19
Alignment explanation
Indices: 22467950--22467987 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
22467940 ACTTCTAAAC
* *
22467950 CTCAAATCATATTTTAATA
1 CTCAAATCATACTTCAATA
22467969 CTCAAATCATACTTCAATA
1 CTCAAATCATACTTCAATA
22467988 AGTCAAATGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCAAATCATACTTCAATA
Found at i:22468378 original size:35 final size:35
Alignment explanation
Indices: 22468319--22468450 Score: 101
Period size: 35 Copynumber: 3.7 Consensus size: 35
22468309 GTTTGACAAT
* * **
22468319 AACTAAAACAAGTAAAACGTTACTTCACGCAGAAC
1 AACTACAACAAGTAGAACACTACTTCACGCAGAAC
* * *
22468354 AACTACAACAAGT-GAAGCACTACTTAATGCAGAAT
1 AACTACAACAAGTAGAA-CACTACTTCACGCAGAAC
* * *
22468389 AACTAGAATAAGTAGAATACTACTTCA--CATGAAAC
1 AACTACAACAAGTAGAACACTACTTCACGCA-G-AAC
22468424 AACTA-ATACAAGTAGAACAACTACTTC
1 AACTACA-ACAAGTAGAAC-ACTACTTC
22468451 GAATAGAATA
Statistics
Matches: 77, Mismatches: 14, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
33 2 0.03
34 4 0.05
35 60 0.78
36 11 0.14
ACGTcount: A:0.48, C:0.20, G:0.11, T:0.20
Consensus pattern (35 bp):
AACTACAACAAGTAGAACACTACTTCACGCAGAAC
Found at i:22468677 original size:29 final size:29
Alignment explanation
Indices: 22468645--22468710 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
22468635 GTTCTCGTAT
22468645 ACCTATTCTTCTACAGCTTCTTCTCTTGC
1 ACCTATTCTTCTACAGCTTCTTCTCTTGC
* * * * * *
22468674 ACCTGTTCTTGTATAGTTTCTTTTCTTGT
1 ACCTATTCTTCTACAGCTTCTTCTCTTGC
22468703 ACCTATTC
1 ACCTATTC
22468711 ACGTATAGCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.14, C:0.27, G:0.09, T:0.50
Consensus pattern (29 bp):
ACCTATTCTTCTACAGCTTCTTCTCTTGC
Found at i:22469669 original size:2 final size:2
Alignment explanation
Indices: 22469662--22469690 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
22469652 TGTCACAAGA
22469662 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
22469691 AATATTATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:22474340 original size:78 final size:78
Alignment explanation
Indices: 22474208--22474414 Score: 263
Period size: 78 Copynumber: 2.7 Consensus size: 78
22474198 AAGGCAGGAG
* * * * * **
22474208 CATGTGGCATTCTTATTATGCATTAAGATATAATGATGTCAATATATAAGTACCATCAAGGTCCA
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGTCAATATGTAAATACCAGCAAGAACCA
*
22474273 TGTGATCAGTGGA
66 TGTGATAAGTGGA
22474286 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGTCAATATGTAAATACCAGCAAGAACCA
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGTCAATATGTAAATACCAGCAAGAACCA
* *
22474351 TTTGGTAAGTGGA
66 TGTGATAAGTGGA
* * * * *
22474364 CATTTGGCATTCATATTATATATGAAGGTATAATGGTG-CTAATATGTAAAT
1 CATGTGGCATTCTTATTATACATTAAGGTATAATGATGTC-AATATGTAAAT
22474415 TTAATATCTT
Statistics
Matches: 113, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
77 1 0.01
78 112 0.99
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (78 bp):
CATGTGGCATTCTTATTATACATTAAGGTATAATGATGTCAATATGTAAATACCAGCAAGAACCA
TGTGATAAGTGGA
Found at i:22477091 original size:19 final size:19
Alignment explanation
Indices: 22477064--22477100 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22477054 CCATTTGACT
22477064 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
*
22477083 TATTGGAGTATGATTTGA
1 TATTAGAGTATGATTTGA
22477101 AGTTTAGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:22486291 original size:19 final size:20
Alignment explanation
Indices: 22486263--22486307 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
22486253 TAAAAGTTAC
*
22486263 TTTTACTATGTGAGAT-TTT
1 TTTTAATATGTGAGATGTTT
*
22486282 TTTTAATATGTTAGATGTTT
1 TTTTAATATGTGAGATGTTT
22486302 TTTTAA
1 TTTTAA
22486308 GATATTGATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.60
Consensus pattern (20 bp):
TTTTAATATGTGAGATGTTT
Found at i:22487783 original size:20 final size:20
Alignment explanation
Indices: 22487760--22487802 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
22487750 AAAAAATGTA
22487760 TTAATTAATCAAAATATT-AT
1 TTAATTAAT-AAAATATTAAT
*
22487780 TTAATTAATAAATTATTAAT
1 TTAATTAATAAAATATTAAT
22487800 TTA
1 TTA
22487803 TACATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTAATTAATAAAATATTAAT
Found at i:22489375 original size:22 final size:21
Alignment explanation
Indices: 22489347--22489402 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
22489337 TTTAGGGTTA
*
22489347 AACTTATAATACA-CATATATTT
1 AACTTATAATA-AGCAT-TACTT
*
22489369 AATTTATATATAAGCATTACTT
1 AACTTATA-ATAAGCATTACTT
22489391 AACTTATAATAA
1 AACTTATAATAA
22489403 ACTTCAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 4 0.14
22 19 0.66
23 6 0.21
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.41
Consensus pattern (21 bp):
AACTTATAATAAGCATTACTT
Found at i:22490167 original size:2 final size:2
Alignment explanation
Indices: 22490160--22490196 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22490150 NNNNNNNAAT
22490160 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22490197 CACCTTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22491268 original size:10 final size:9
Alignment explanation
Indices: 22491251--22491278 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
22491241 TTATTATATT
22491251 TTAAAAAAA
1 TTAAAAAAA
22491260 TTAAAAAAA
1 TTAAAAAAA
22491269 TTAAAAAAA
1 TTAAAAAAA
22491278 T
1 T
22491279 AAGGAGCACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:22491459 original size:31 final size:32
Alignment explanation
Indices: 22491397--22491460 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
22491387 TTTTTTTTTC
* *
22491397 TAATTAATAAAAAATAAAAAATTATATAATTA
1 TAATTAATAAAAAATAAAAAATGATAAAATTA
* **
22491429 TAATT-ATAAAAATTAATCAATGATAAAATTA
1 TAATTAATAAAAAATAAAAAATGATAAAATTA
22491460 T
1 T
22491461 TTTTCTATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 22 0.81
32 5 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (32 bp):
TAATTAATAAAAAATAAAAAATGATAAAATTA
Found at i:22493838 original size:10 final size:10
Alignment explanation
Indices: 22493823--22493850 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
22493813 TTGAAAACTC
22493823 AATTAAAAAA
1 AATTAAAAAA
22493833 AATTAAAAAA
1 AATTAAAAAA
22493843 AATTAAAA
1 AATTAAAA
22493851 CATCTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
AATTAAAAAA
Found at i:22504695 original size:3 final size:3
Alignment explanation
Indices: 22504689--22504762 Score: 59
Period size: 3 Copynumber: 25.7 Consensus size: 3
22504679 TTTTTGTCAT
* * *
22504689 TTA TTA TTA TT- TAA TTA TTA TTA TTA TT- TTA TT- TTT TTA TTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
22504734 -TA TTT TCTA TT- TTA TTTA TTA TTA TTA TT
1 TTA TTA T-TA TTA TTA -TTA TTA TTA TTA TT
22504763 TTTTCATACT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
2 8 0.14
3 44 0.77
4 5 0.09
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:22504707 original size:8 final size:8
Alignment explanation
Indices: 22504692--22504764 Score: 56
Period size: 8 Copynumber: 8.2 Consensus size: 8
22504682 TTGTCATTTA
22504692 TTATTATT
1 TTATTATT
*
22504700 TAATTATT
1 TTATTATT
22504708 ATTATTATT
1 -TTATTATT
*
22504717 TTATTTTT
1 TTATTATT
22504725 TTATTATCAT
1 TTATTAT--T
*
22504735 ATTTTCTATT
1 -TTAT-TATT
22504745 TTATTTATT
1 TTA-TTATT
22504754 ATTATTATT
1 -TTATTATT
22504763 TT
1 TT
22504765 TTCATACTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
8 22 0.42
9 18 0.35
10 6 0.12
11 3 0.06
12 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (8 bp):
TTATTATT
Found at i:22504737 original size:27 final size:30
Alignment explanation
Indices: 22504687--22504761 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 30
22504677 TTTTTTTGTC
*
22504687 ATTTATTATTATTTAATTATTATTAT-TATTTT
1 ATTTATTATTA-TT-ATCA-TATTATCTATTTT
*
22504719 ATTT-TT-TTATTATCATATTTTCTATTTT
1 ATTTATTATTATTATCATATTATCTATTTT
22504747 ATTTATTATTATTAT
1 ATTTATTATTATTAT
22504762 TTTTTCATAC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
27 5 0.13
28 13 0.34
29 4 0.11
30 10 0.26
31 2 0.05
32 4 0.11
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (30 bp):
ATTTATTATTATTATCATATTATCTATTTT
Found at i:22505049 original size:10 final size:10
Alignment explanation
Indices: 22505036--22505064 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
22505026 ATGATTATCA
22505036 TTTTTTATTT
1 TTTTTTATTT
22505046 TTTTTTA-TT
1 TTTTTTATTT
22505055 TTTTTTATTT
1 TTTTTTATTT
22505065 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTATTT
Found at i:22505530 original size:10 final size:10
Alignment explanation
Indices: 22505515--22505543 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
22505505 TATATATATA
22505515 TATTATTTTT
1 TATTATTTTT
22505525 TATTATTTTT
1 TATTATTTTT
22505535 TATT-TTTTT
1 TATTATTTTT
22505544 ACTCTTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TATTATTTTT
Found at i:22505543 original size:18 final size:18
Alignment explanation
Indices: 22505515--22505558 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
22505505 TATATATATA
*
22505515 TATTA-TTTTTTATTATT
1 TATTATTTTTTTACTATT
* *
22505532 TTTTATTTTTTTACTCTT
1 TATTATTTTTTTACTATT
22505550 TATTATTTT
1 TATTATTTT
22505559 CATATTCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTATTTTTTTACTATT
Found at i:22506805 original size:1 final size:1
Alignment explanation
Indices: 22506801--22506907 Score: 79
Period size: 1 Copynumber: 107.0 Consensus size: 1
22506791 GTTTTTCTCC
* * * * * * * *
22506801 TTTTTTTTGTTTTGTTTTTTTTTTATTTTTTTGTTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * * *
22506866 GTTTTTTTCCTTCTTTTTGTTTTTTTGTTTTGTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
22506908 GTCGTTTAAA
Statistics
Matches: 80, Mismatches: 26, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 80 1.00
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:22506832 original size:19 final size:18
Alignment explanation
Indices: 22506801--22506907 Score: 108
Period size: 19 Copynumber: 5.6 Consensus size: 18
22506791 GTTTTTCTCC
*
22506801 TTTTTTTTGTTTTGTTTT
1 TTTTTTTTTTTTTGTTTT
22506819 TTTTTTATTTTTTTGTTTT
1 TTTTTT-TTTTTTTGTTTT
22506838 TTTTGTTTTTTTTTGTTTT
1 TTTT-TTTTTTTTTGTTTT
*
22506857 TTGTTTTTGGTTTTTT-TCCTTC
1 TT-TTTTT--TTTTTTGT--TTT
*
22506879 TTTTTGTTTTTTTGTTTT
1 TTTTTTTTTTTTTGTTTT
22506897 GTTTTTTTTTT
1 -TTTTTTTTTT
22506908 GTCGTTTAAA
Statistics
Matches: 75, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
18 8 0.11
19 47 0.63
20 6 0.08
21 10 0.13
22 4 0.05
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (18 bp):
TTTTTTTTTTTTTGTTTT
Found at i:22506851 original size:32 final size:31
Alignment explanation
Indices: 22506801--22506905 Score: 120
Period size: 33 Copynumber: 3.3 Consensus size: 31
22506791 GTTTTTCTCC
22506801 TTTTTTTTGTTTTGTTTTTTTTTTATTTTTTTG
1 TTTTTTTTGTTTT-TTTTTTTTTT-TTTTTTTG
*
22506834 TTTTTTTTGTTTTTTTTTGTTTTTTGTTTTTGG
1 TTTTTTTTGTTTTTTTTT-TTTTTT-TTTTTTG
** * * *
22506867 TTTTTTTCCTTCTTTTTGTTTTTTTGTTTTG
1 TTTTTTTTGTTTTTTTTTTTTTTTTTTTTTG
22506898 TTTTTTTT
1 TTTTTTTT
22506906 TTGTCGTTTA
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
31 12 0.19
32 12 0.19
33 38 0.61
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (31 bp):
TTTTTTTTGTTTTTTTTTTTTTTTTTTTTTG
Found at i:22506889 original size:50 final size:50
Alignment explanation
Indices: 22506801--22506909 Score: 143
Period size: 50 Copynumber: 2.2 Consensus size: 50
22506791 GTTTTTCTCC
* * *
22506801 TTTTTTTTG-TTTTGTTTTTTTTTTATTTTTTTGTTTTTTTTGTTTTTTT
1 TTTTTTTTGTTTTTGTGTTTTTTTCATTTTTTTGTTTTTTTTGTTTTGTT
*
22506850 TTGTTTTTTGTTTTTG-GTTTTTTTCCTTCTTTTTG-TTTTTTTGTTTTGTT
1 TT-TTTTTTGTTTTTGTGTTTTTTTCATT-TTTTTGTTTTTTTTGTTTTGTT
22506900 TTTTTTTTGT
1 TTTTTTTTGT
22506910 CGTTTAAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
49 10 0.19
50 32 0.60
51 11 0.21
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (50 bp):
TTTTTTTTGTTTTTGTGTTTTTTTCATTTTTTTGTTTTTTTTGTTTTGTT
Found at i:22507602 original size:283 final size:283
Alignment explanation
Indices: 22506997--22507709 Score: 1004
Period size: 283 Copynumber: 2.5 Consensus size: 283
22506987 GAAAAATATA
* * * **
22506997 GCTCCTCGAAAATTGAGGCAACGTAACTTTAAGAAAATCTTGAAACTAATTA-CTTGAAGACTTT
1 GCTCCTCGAAAACTGAGACAACGTAAC-TTAA-AAAATCTTGAAACTAATTACCTAG-AGGTTTT
* * * * *
22507061 GGAA-ATGTACCCTGAGGTTTTAAGAGAATAATGTGCCTAGAGGTCTTGAGAATGTACCCAGAGG
63 AGAAGATGCA-CCTGAGGATTTAAGAGAATAATGTGCCTAGAGGTCTTCAGAATGTACCCGGAGG
* *
22507125 ATTTAAGAAATGTGGCTCCTCAAACACTGAGGCAACGTAACTTTAAAAAATCTTGACATTAATTA
127 ATTTAGGAAATGTGGCTCCTCAAACACTGAGGCAACGTAACTTTAAAAAATCTTGACACTAATTA
* * * *
22507190 CCCGGAGGTTTTAAAAGATGCACCCGAAGGATTTAAGAGAATAATGTGACCCGGAGGACTTTAGA
192 CCCAGAGGTTTTAAAAGATGCACCCGAAGGATTTAAAAGAATAATGTGACCCGGAGGACTTCAAA
*
22507255 ATGCACCCGGAGGATTTAGAAAATGTG
257 ATACACCCGGAGGATTTAGAAAATGTG
*
22507282 GCTCCTCGAAAACTGAGACAACGTAACTTAAAAAATCTTGAAACTAATTACCTAGAGGTTTTAAA
1 GCTCCTCGAAAACTGAGACAACGTAACTTAAAAAATCTTGAAACTAATTACCTAGAGGTTTTAGA
* *
22507347 AGATGCACCTAGAGGATTTAAGAGAATAATGTGCCTGGAGGTCTTCAGAATGTACTCGGAGGATT
66 AGATGCACCT-GAGGATTTAAGAGAATAATGTGCCTAGAGGTCTTCAGAATGTACCCGGAGGATT
* * * *
22507412 TAGGAATTGTGGCTCCTTGAAA-ATTGAGGCAATGTAACTTTAAAAAATCTTGACACTAATTACC
130 TAGGAAATGTGGCTCC-TCAAACACTGAGGCAACGTAACTTTAAAAAATCTTGACACTAATTACC
* *
22507476 CAGAGGTTTTAGAAA-ATGCACCCGGAGGATTTAAAAGAATAATGT-ACCCGGAGGTCTTCAAAA
194 CAGAGGTTTTA-AAAGATGCACCCGAAGGATTTAAAAGAATAATGTGACCCGGAGGACTTCAAAA
*
22507539 TATACCCGGAGGATTTAGAAAATGTG
258 TACACCCGGAGGATTTAGAAAATGTG
* *
22507565 GCTCCTCGAAAACTGAGACAACGTAACTTAAAAAATCTTGAAACTAATTACCCAAAGGTTTTAGA
1 GCTCCTCGAAAACTGAGACAACGTAACTTAAAAAATCTTGAAACTAATTACCTAGAGGTTTTAGA
* * * * * *
22507630 AGATGCACCCGGAGAATTTAAGAGAATAATGTACCCAAAGGTCTTCAGAATGTACCCGGAAGATT
66 AGATGCA-CCTGAGGATTTAAGAGAATAATGTGCCTAGAGGTCTTCAGAATGTACCCGGAGGATT
22507695 TAGGAAATGTGGCTC
130 TAGGAAATGTGGCTC
22507710 ATCGAAAACT
Statistics
Matches: 383, Mismatches: 39, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
283 198 0.52
284 153 0.40
285 32 0.08
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (283 bp):
GCTCCTCGAAAACTGAGACAACGTAACTTAAAAAATCTTGAAACTAATTACCTAGAGGTTTTAGA
AGATGCACCTGAGGATTTAAGAGAATAATGTGCCTAGAGGTCTTCAGAATGTACCCGGAGGATTT
AGGAAATGTGGCTCCTCAAACACTGAGGCAACGTAACTTTAAAAAATCTTGACACTAATTACCCA
GAGGTTTTAAAAGATGCACCCGAAGGATTTAAAAGAATAATGTGACCCGGAGGACTTCAAAATAC
ACCCGGAGGATTTAGAAAATGTG
Found at i:22507656 original size:141 final size:142
Alignment explanation
Indices: 22506997--22507719 Score: 927
Period size: 142 Copynumber: 5.1 Consensus size: 142
22506987 GAAAAATATA
* ** **
22506997 GCTCCTCGAAAATTGAGGCAACGTAACTTTAAGAAAATCTTGAAACTAATTA-CTTGAAGACTTT
1 GCTCCTCGAAAACTGAGGCAACGTAACTTTAA-AAAATCTTGAAACTAATTACCCAG-AGGTTTT
* * * * * ** * *
22507061 GGAA-ATGTACCCTGAGGTTTTAAGAGAATAATGTGCCTAGAGGTCTTGAGAATGTACCCAGAGG
64 AGAAGATGCACCCGGAGGATTTAAGAGAATAATGTACCCGGAGGTCTTCAGAATGTACCCGGAGG
22507125 ATTTA-AGAAATGTG
129 ATTTAGA-AAATGTG
* * *
22507139 GCTCCTC-AAACACTGAGGCAACGTAACTTTAAAAAATCTTGACATTAATTACCCGGAGGTTTTA
1 GCTCCTCGAAA-ACTGAGGCAACGTAACTTTAAAAAATCTTGAAACTAATTACCCAGAGGTTTTA
* * * * *
22507203 AAAGATGCACCCGAAGGATTTAAGAGAATAATGTGACCCGGAGGACTTTAGAATGCACCCGGAGG
65 GAAGATGCACCCGGAGGATTTAAGAGAATAATGT-ACCCGGAGGTCTTCAGAATGTACCCGGAGG
22507268 ATTTAGAAAATGTG
129 ATTTAGAAAATGTG
* * *
22507282 GCTCCTCGAAAACTGAGACAACGTAAC-TTAAAAAATCTTGAAACTAATTACCTAGAGGTTTTAA
1 GCTCCTCGAAAACTGAGGCAACGTAACTTTAAAAAATCTTGAAACTAATTACCCAGAGGTTTTAG
** * * *
22507346 AAGATGCACCTAGAGGATTTAAGAGAATAATGTGCCTGGAGGTCTTCAGAATGTACTCGGAGGAT
66 AAGATGCACCCGGAGGATTTAAGAGAATAATGTACCCGGAGGTCTTCAGAATGTACCCGGAGGAT
* *
22507411 TTAGGAATTGTG
131 TTAGAAAATGTG
* * * *
22507423 GCTCCTTGAAAATTGAGGCAATGTAACTTTAAAAAATCTTGACACTAATTACCCAGAGGTTTTAG
1 GCTCCTCGAAAACTGAGGCAACGTAACTTTAAAAAATCTTGAAACTAATTACCCAGAGGTTTTAG
* * * *
22507488 AAAATGCACCCGGAGGATTTAAAAGAATAATGTACCCGGAGGTCTTCAAAATATACCCGGAGGAT
66 AAGATGCACCCGGAGGATTTAAGAGAATAATGTACCCGGAGGTCTTCAGAATGTACCCGGAGGAT
22507553 TTAGAAAATGTG
131 TTAGAAAATGTG
* *
22507565 GCTCCTCGAAAACTGAGACAACGTAAC-TTAAAAAATCTTGAAACTAATTACCCAAAGGTTTTAG
1 GCTCCTCGAAAACTGAGGCAACGTAACTTTAAAAAATCTTGAAACTAATTACCCAGAGGTTTTAG
* ** *
22507629 AAGATGCACCCGGAGAATTTAAGAGAATAATGTACCCAAAGGTCTTCAGAATGTACCCGGAAGAT
66 AAGATGCACCCGGAGGATTTAAGAGAATAATGTACCCGGAGGTCTTCAGAATGTACCCGGAGGAT
*
22507694 TTAGGAAATGTG
131 TTAGAAAATGTG
*
22507706 GCTCATCGAAAACT
1 GCTCCTCGAAAACT
22507720 AANCCCGAAG
Statistics
Matches: 504, Mismatches: 70, Indels: 15
0.86 0.12 0.03
Matches are distributed among these distances:
141 202 0.40
142 241 0.48
143 57 0.11
144 4 0.01
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (142 bp):
GCTCCTCGAAAACTGAGGCAACGTAACTTTAAAAAATCTTGAAACTAATTACCCAGAGGTTTTAG
AAGATGCACCCGGAGGATTTAAGAGAATAATGTACCCGGAGGTCTTCAGAATGTACCCGGAGGAT
TTAGAAAATGTG
Found at i:22507739 original size:60 final size:59
Alignment explanation
Indices: 22507662--22507779 Score: 209
Period size: 60 Copynumber: 2.0 Consensus size: 59
22507652 AGAATAATGT
* *
22507662 ACCCAAAGGTCTTCAGAATGTACCCGGAAGATTTAGGAAATGTGGCTCATCGAAAACTA
1 ACCCGAAGGTCTTCAGAATGTACCCAGAAGATTTAGGAAATGTGGCTCATCGAAAACTA
22507721 ANCCCGAAGGTCTTCAGAATGTACCCAGAAGATTTAGGAAATGTGGCTCATCGAAAACT
1 A-CCCGAAGGTCTTCAGAATGTACCCAGAAGATTTAGGAAATGTGGCTCATCGAAAACT
22507780 GAGGCAACGT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
59 1 0.02
60 55 0.98
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (59 bp):
ACCCGAAGGTCTTCAGAATGTACCCAGAAGATTTAGGAAATGTGGCTCATCGAAAACTA
Found at i:22507875 original size:201 final size:200
Alignment explanation
Indices: 22507521--22507920 Score: 602
Period size: 201 Copynumber: 2.0 Consensus size: 200
22507511 AGAATAATGT
* * * *
22507521 ACCCGGAGGTCTTCAAAATATACCCGGAGGATTTAGAAAATGTGGCTCCTCGAAAACTGAGACAA
1 ACCCGAAGGTCTTCAAAATATACCCAGAAGATTTAGAAAATGTGGCTCATCGAAAACTGAGACAA
*
22507586 CGTAACTTAAAAAATCTTGAAACTAATTACCCAAAGGTTTTAGAAGATGCACCCGGAGAATTTAA
66 CGTAACTTAAAAAATCTTGAAACTAATTACCCAAAGGTTTTAGAAAATGCACCCGGAGAATTTAA
* * * *
22507651 GAGAATAATGTACCCAAAGGTCTTCAGAATGTACCCGGAAGATTTAGGAAATGTGGCTCATCGAA
131 AAGAATAATGTACCCAAAGGTCTTCAAAATATACCCGGAAGATTTAGAAAATGTGGCTCATCGAA
22507716 AACTA
196 AACTA
* * * *
22507721 ANCCCGAAGGTCTTCAGAATGTACCCAGAAGATTTAGGAAATGTGGCTCATCGAAAACTGAGGCA
1 A-CCCGAAGGTCTTCAAAATATACCCAGAAGATTTAGAAAATGTGGCTCATCGAAAACTGAGACA
* * * *
22507786 ACGTAACTTTAAAAATCTTGACACTAATTACCCAGAGGTTTTAGAAAATGCACCCGGAGGATTTA
65 ACGTAACTTAAAAAATCTTGAAACTAATTACCCAAAGGTTTTAGAAAATGCACCCGGAGAATTTA
** * *
22507851 AAAGAATAATGTACCCGGAGGTCTTCAAAATATACCCGGAGGATTTAGAAAATGTGGCTCCTCGA
130 AAAGAATAATGTACCCAAAGGTCTTCAAAATATACCCGGAAGATTTAGAAAATGTGGCTCATCGA
22507916 AAACT
195 AAACT
22507921 GAGGCAACGT
Statistics
Matches: 178, Mismatches: 21, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
200 1 0.01
201 177 0.99
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (200 bp):
ACCCGAAGGTCTTCAAAATATACCCAGAAGATTTAGAAAATGTGGCTCATCGAAAACTGAGACAA
CGTAACTTAAAAAATCTTGAAACTAATTACCCAAAGGTTTTAGAAAATGCACCCGGAGAATTTAA
AAGAATAATGTACCCAAAGGTCTTCAAAATATACCCGGAAGATTTAGAAAATGTGGCTCATCGAA
AACTA
Found at i:22509222 original size:68 final size:68
Alignment explanation
Indices: 22509113--22509248 Score: 186
Period size: 68 Copynumber: 2.0 Consensus size: 68
22509103 CATAAATTTC
* *
22509113 CATCTTCGCTCTAGACTGTCCTTTCGAGTTTTCACCATAGAGCTTCATCTTTTTCACTCACTTTT
1 CATCTTCGCTCTAGACTGTCCTTTAGAGTTTTCACCATAGAGCTTCATCTTTCTCACTCACTTTT
22509178 TTT
66 TTT
* * **
22509181 CATCTTTGCTCTAGATTG-CTCTTTAGAGTTTTCATCC-TAGAGCTTCATCTTTCTCACTTGCTT
1 CATCTTCGCTCTAGACTGTC-CTTTAGAGTTTTCA-CCATAGAGCTTCATCTTTCTCACTCACTT
22509244 TTTTT
64 TTTTT
22509249 TTTTTCTGAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
67 1 0.02
68 57 0.95
69 2 0.03
ACGTcount: A:0.15, C:0.26, G:0.11, T:0.48
Consensus pattern (68 bp):
CATCTTCGCTCTAGACTGTCCTTTAGAGTTTTCACCATAGAGCTTCATCTTTCTCACTCACTTTT
TTT
Found at i:22509648 original size:12 final size:13
Alignment explanation
Indices: 22509625--22509653 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
22509615 TTCCTTTCTT
22509625 TTTTCAATTTTCA
1 TTTTCAATTTTCA
22509638 TTTTC-ATTTTCA
1 TTTTCAATTTTCA
22509650 TTTT
1 TTTT
22509654 TTCTTCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTCAATTTTCA
Found at i:22509680 original size:19 final size:18
Alignment explanation
Indices: 22509632--22509683 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
22509622 CTTTTTTCAA
*
22509632 TTTTCATTTTCATTTTCATT
1 TTTTCATCTTCA--TTCATT
*
22509652 TTTTCTTCTTCATTCATT
1 TTTTCATCTTCATTCATT
22509670 TTTTCAATCTTCAT
1 TTTTC-ATCTTCAT
22509684 GTTGATGGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 11 0.39
19 7 0.25
20 10 0.36
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTCATCTTCATTCATT
Found at i:22512970 original size:18 final size:16
Alignment explanation
Indices: 22512945--22513006 Score: 70
Period size: 19 Copynumber: 3.6 Consensus size: 16
22512935 TTGGTGTGGG
22512945 TTTTTTTTTATATTTT
1 TTTTTTTTTATATTTT
22512961 ATTTTATTTTTATTATTATT
1 -TTTT-TTTTTA-TATT-TT
*
22512981 TTTTATTTTTTTATTTT
1 TTTT-TTTTTATATTTT
22512998 TTTTTTTTT
1 TTTTTTTTT
22513007 GAGAAATCCT
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
16 5 0.12
17 10 0.24
18 10 0.24
19 14 0.34
20 2 0.05
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTATATTTT
Found at i:22512970 original size:19 final size:18
Alignment explanation
Indices: 22512948--22513006 Score: 70
Period size: 18 Copynumber: 3.3 Consensus size: 18
22512938 GTGTGGGTTT
22512948 TTTTTTATATTTTATTTTA
1 TTTTTTATATTTT-TTTTA
22512967 -TTTTTATTATTATTTTTTA
1 TTTTTTA-TATT-TTTTTTA
22512986 TTTTTT-TATTTTTTTT-
1 TTTTTTATATTTTTTTTA
22513002 TTTTT
1 TTTTT
22513007 GAGAAATCCT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
16 5 0.14
17 6 0.16
18 10 0.27
19 9 0.24
20 7 0.19
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTTTATATTTTTTTTA
Found at i:22512973 original size:6 final size:6
Alignment explanation
Indices: 22512945--22513006 Score: 53
Period size: 6 Copynumber: 10.7 Consensus size: 6
22512935 TTGGTGTGGG
*
22512945 TTTT-T TTTTAT ATTTTA- TTTTAT TTTTAT TATTATT TTTTAT TTTT-T
1 TTTTAT TTTTAT -TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT
22512992 TATTT-T TTTT-T TTTT
1 T-TTTAT TTTTAT TTTT
22513007 GAGAAATCCT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
5 19 0.38
6 21 0.42
7 10 0.20
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:22512979 original size:24 final size:22
Alignment explanation
Indices: 22512945--22513000 Score: 67
Period size: 24 Copynumber: 2.4 Consensus size: 22
22512935 TTGGTGTGGG
22512945 TTTTTTTTTATATTTTATTTTA
1 TTTTTTTTTATATTTTATTTTA
* *
22512967 TTTTTATTATTATTTTTTATTTTT
1 TTTTT-TT-TTATATTTTATTTTA
22512991 TTATTTTTTT
1 TT-TTTTTTT
22513001 TTTTTTGAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
22 5 0.17
23 4 0.14
24 17 0.59
25 3 0.10
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTTTTATATTTTATTTTA
Found at i:22513003 original size:12 final size:12
Alignment explanation
Indices: 22512945--22513004 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
22512935 TTGGTGTGGG
*
22512945 TTTTTTTTTATA
1 TTTTTTTTTATT
*
22512957 TTTTATTTTATT
1 TTTTTTTTTATT
22512969 TTTATTATTATT-TT
1 TTT-TT-TT-TTATT
22512983 TTATTTTTTTATT
1 TT-TTTTTTTATT
22512996 TTTTTTTTT
1 TTTTTTTTT
22513005 TTGAGAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
12 22 0.55
13 7 0.17
14 8 0.20
15 3 0.08
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:22514692 original size:108 final size:108
Alignment explanation
Indices: 22514447--22514669 Score: 364
Period size: 108 Copynumber: 2.1 Consensus size: 108
22514437 AAATGAAAAG
* *
22514447 TGGAAGATTTATTCAAAATTAAAATCCCTTTTTT-C-TTTTC--TCTTTTTTGAACATAATGAAA
1 TGGAAGATCTATTCAAAATTAAAAT-CCTTTTTTCCTTTTTCTTTTTTTTTTGAACATAATGAAA
*
22514508 GAAATGAAAAACCCTTCTTATTTCTTTTTTCATTTCTATTTAAA
65 GAAATGAAAAACCCTTCTTATTTCTTTTTTCATTCCTATTTAAA
*
22514552 TGGAAGATCTNTTCAAAATTAAAATCCTTTTTTCCTTTTTCTTTTTTTTTTGAACATAATGAAAG
1 TGGAAGATCTATTCAAAATTAAAATCCTTTTTTCCTTTTTCTTTTTTTTTTGAACATAATGAAAG
*
22514617 AAATGAAAAACCCTTTTTATTTCTTTTTTCATTCCTATTTAAA
66 AAATGAAAAACCCTTCTTATTTCTTTTTTCATTCCTATTTAAA
22514660 TGGAAGATCT
1 TGGAAGATCT
22514670 TTGTTTTTCC
Statistics
Matches: 109, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
104 8 0.07
105 24 0.22
106 5 0.05
108 72 0.66
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (108 bp):
TGGAAGATCTATTCAAAATTAAAATCCTTTTTTCCTTTTTCTTTTTTTTTTGAACATAATGAAAG
AAATGAAAAACCCTTCTTATTTCTTTTTTCATTCCTATTTAAA
Found at i:22516062 original size:28 final size:30
Alignment explanation
Indices: 22516021--22516085 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
22516011 GTCTATGGGC
* *
22516021 AATTTTTCAGTTTT-T-GGGGTAAAAATGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
* *
22516049 AATTTTTGACTTTTATAGGGGCAAAAGTGT
1 AATTTTTCACTTTTATAGGGGCAAAAATGT
*
22516079 AAATTTT
1 AATTTTT
22516086 AAAAAATTAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 12 0.40
29 1 0.03
30 17 0.57
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
AATTTTTCACTTTTATAGGGGCAAAAATGT
Found at i:22519801 original size:14 final size:13
Alignment explanation
Indices: 22519759--22519810 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 13
22519749 TGAATTATTA
22519759 TTATTATTTTTA-
1 TTATTATTTTTAT
*
22519771 TCATT-TTTTTAT
1 TTATTATTTTTAT
* *
22519783 CTATTGTTATTTAT
1 TTATTATT-TTTAT
22519797 TTATTATTTTTAT
1 TTATTATTTTTAT
22519810 T
1 T
22519811 GAGTAATTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
11 6 0.19
12 7 0.22
13 8 0.25
14 11 0.34
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (13 bp):
TTATTATTTTTAT
Found at i:22526785 original size:10 final size:9
Alignment explanation
Indices: 22526770--22526794 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
22526760 TTTGGGTTGG
22526770 TTTTTTTTA
1 TTTTTTTTA
22526779 TTTTTTTTA
1 TTTTTTTTA
22526788 TTTTTTT
1 TTTTTTT
22526795 GGCTTCTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:22530029 original size:84 final size:84
Alignment explanation
Indices: 22529773--22530038 Score: 272
Period size: 84 Copynumber: 3.2 Consensus size: 84
22529763 GAATGCTCGC
* * * * *
22529773 TGACAACAGAAATGATGATAACC-AAATAGG-CGAAGTTGAGGACTGTACTCCAAGGAGACTCAA
1 TGACAACAGAAATGCTGATAACCAAAAT-GGTAG-AGGTGAGGACTATACTCCAAGGAAACTCAA
**
22529836 GTTCAGGCAAAGAGTGCTCAT
64 GTTCAGGCAAAGAGTGCTTGT
* * * *
22529857 TGACAACAGAAATGGTGATAACCAAAATGGTAGATGTGAGGAGTTTACTCCAA-GAAGACTCAAG
1 TGACAACAGAAATGCTGATAACCAAAATGGTAGAGGTGAGGACTATACTCCAAGGAA-ACTCAAG
*
22529921 TTCAGG-AGGAGAGCT-CTTGT
65 TTCAGGCA-AAGAG-TGCTTGT
** * * *
22529941 TGACAATGGAAATTCTGATAACCAAAATGGTAGAGGTGAGGACTATACCCCAAGGAAACTTAAGT
1 TGACAACAGAAATGCTGATAACCAAAATGGTAGAGGTGAGGACTATACTCCAAGGAAACTCAAGT
* *
22530006 TCAGGCCAAGAGTGCTTGG
66 TCAGGCAAAGAGTGCTTGT
*
22530025 TGACAACAAAAATG
1 TGACAACAGAAATG
22530039 GTAATATCCT
Statistics
Matches: 148, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
83 4 0.03
84 135 0.91
85 9 0.06
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.21
Consensus pattern (84 bp):
TGACAACAGAAATGCTGATAACCAAAATGGTAGAGGTGAGGACTATACTCCAAGGAAACTCAAGT
TCAGGCAAAGAGTGCTTGT
Found at i:22535808 original size:20 final size:20
Alignment explanation
Indices: 22535759--22535810 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
22535749 CAAAAACATA
*
22535759 AAAATAAACATAACTAATAT
1 AAAATAAACATTACTAATAT
*
22535779 AAAACT-AACATTATTAACT-T
1 AAAA-TAAACATTACTAA-TAT
22535799 AAAATAAACATT
1 AAAATAAACATT
22535811 TAAACATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
20 24 0.89
21 2 0.07
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAACATTACTAATAT
Found at i:22535850 original size:24 final size:25
Alignment explanation
Indices: 22535793--22535850 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
22535783 CTAACATTAT
*
22535793 TAACTTAAAA-TAAACATTTAAACA
1 TAACTTAAAACTAAACATATAAACA
*
22535817 TAAATT-AAACTAAAC-TAATAAA-A
1 TAACTTAAAACTAAACAT-ATAAACA
22535840 TAACTTAAAAC
1 TAACTTAAAAC
22535851 ACCTAAATCC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (25 bp):
TAACTTAAAACTAAACATATAAACA
Found at i:22561470 original size:20 final size:21
Alignment explanation
Indices: 22561442--22561484 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
22561432 AACACTTGTC
22561442 AAGACATGGA-TACAAGTGTT
1 AAGACATGGATTACAAGTGTT
*
22561462 AAGATATGGATTACAAGTGTT
1 AAGACATGGATTACAAGTGTT
22561483 AA
1 AA
22561485 ATGAAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (21 bp):
AAGACATGGATTACAAGTGTT
Found at i:22561885 original size:19 final size:19
Alignment explanation
Indices: 22561858--22561895 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
22561848 CCATTTGACT
*
22561858 TATTGGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
22561877 TATTAGAGTATGATTTGAG
1 TATTAGAGTATGATTTGAG
22561896 GTTTATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATGATTTGAG
Found at i:22563165 original size:13 final size:13
Alignment explanation
Indices: 22563147--22563171 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22563137 GGAGAAATTG
22563147 TGATTTTATAAAA
1 TGATTTTATAAAA
22563160 TGATTTTATAAA
1 TGATTTTATAAA
22563172 TTTTCTAGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:22573438 original size:48 final size:48
Alignment explanation
Indices: 22573381--22573476 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
22573371 TTTTGTAAGG
*
22573381 CTTTAAATGCACACATTAGTTTTGTTTTAGCCATGTCTTTAATTTTCT
1 CTTTAAATGCACACATTAGTTTCGTTTTAGCCATGTCTTTAATTTTCT
22573429 CTTTAAATGCACACATTAGTTTCGTTTTAGCCATGTCTTTAATTTTCT
1 CTTTAAATGCACACATTAGTTTCGTTTTAGCCATGTCTTTAATTTTCT
22573477 TTGTTATACG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (48 bp):
CTTTAAATGCACACATTAGTTTCGTTTTAGCCATGTCTTTAATTTTCT
Found at i:22595696 original size:4 final size:4
Alignment explanation
Indices: 22595687--22595721 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
22595677 TGGACATGAT
* *
22595687 ATAC ATAC ATAC ATAC ATAT ATAT ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
22595722 TATATATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.31
Consensus pattern (4 bp):
ATAC
Found at i:22595710 original size:2 final size:2
Alignment explanation
Indices: 22595703--22595741 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
22595693 ACATACATAC
* *
22595703 AT AT AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22595742 ATCATTTTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:22595714 original size:20 final size:20
Alignment explanation
Indices: 22595680--22595733 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
22595670 TTTAGCATGG
*
22595680 ACATGATATACATACATACAT
1 ACAT-ATATATATACATACAT
22595701 ACATATATATATACATACAT
1 ACATATATATATACATACAT
*
22595721 ATATATATATATA
1 ACATATATATATA
22595734 TATATATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 27 0.87
21 4 0.13
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (20 bp):
ACATATATATATACATACAT
Found at i:22595716 original size:16 final size:16
Alignment explanation
Indices: 22595695--22595741 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
22595685 ATATACATAC
22595695 ATACATACATATATAT
1 ATACATACATATATAT
22595711 ATACATACATATATAT
1 ATACATACATATATAT
* *
22595727 ATATATATATATATA
1 ATACATACATATATA
22595742 ATCATTTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (16 bp):
ATACATACATATATAT
Found at i:22619353 original size:14 final size:14
Alignment explanation
Indices: 22619334--22619378 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
22619324 TATAATGATA
22619334 AATAATATTTAATT
1 AATAATATTTAATT
*
22619348 AATAATAATTAATT
1 AATAATATTTAATT
*
22619362 -ATAAATATTTATTT
1 AAT-AATATTTAATT
22619376 AAT
1 AAT
22619379 TTAAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
13 2 0.08
14 22 0.85
15 2 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATAATATTTAATT
Found at i:22619387 original size:32 final size:32
Alignment explanation
Indices: 22619325--22619405 Score: 94
Period size: 32 Copynumber: 2.6 Consensus size: 32
22619315 ACACCTGCAT
*
22619325 ATAATGATAAATA-ATATTTAATTAATAATAA
1 ATAATTATAAATATATATTTAATTAATAATAA
* *
22619356 TTAATTATAAATATTTATTTAATTTAA-AATAA
1 ATAATTATAAATATATATTTAA-TTAATAATAA
* *
22619388 ATAAATATATATATATAT
1 ATAATTATAAATATATAT
22619406 ATATATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 11 0.27
32 26 0.63
33 4 0.10
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (32 bp):
ATAATTATAAATATATATTTAATTAATAATAA
Found at i:22622765 original size:9 final size:10
Alignment explanation
Indices: 22622732--22622770 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
22622722 TGGCCCTTAG
22622732 AAAATTATTT
1 AAAATTATTT
22622742 AATAATTAATTT
1 AA-AATT-ATTT
22622754 AAAATT-TTT
1 AAAATTATTT
22622763 AAAATTAT
1 AAAATTAT
22622771 CTTTCATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 9 0.35
10 3 0.12
11 8 0.31
12 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (10 bp):
AAAATTATTT
Found at i:22622970 original size:34 final size:32
Alignment explanation
Indices: 22622932--22623008 Score: 100
Period size: 33 Copynumber: 2.3 Consensus size: 32
22622922 TTATTATATT
*
22622932 TATAAATATTTTCATTTATTTTAATTAAAAATAA
1 TATAAATATTTTCA-TTATATTAA-TAAAAATAA
*
22622966 TATAAAATATTTTCATTATATTAATAATAATAA
1 TAT-AAATATTTTCATTATATTAATAAAAATAA
22622999 TAATAAATAT
1 T-ATAAATAT
22623009 AGCTATTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 15 0.38
34 13 0.33
35 11 0.28
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
TATAAATATTTTCATTATATTAATAAAAATAA
Found at i:22623511 original size:4 final size:4
Alignment explanation
Indices: 22623502--22623529 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
22623492 AGTTCTGCTA
22623502 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT
22623530 CAATAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:22629232 original size:29 final size:29
Alignment explanation
Indices: 22629190--22629263 Score: 130
Period size: 29 Copynumber: 2.6 Consensus size: 29
22629180 TAATTATCAC
*
22629190 TAATTTCTGGAGCAATGTTATGTGGAAAA
1 TAATTTCTGCAGCAATGTTATGTGGAAAA
22629219 TAATTTCTGCAGCAATGTTATGTGGAAAA
1 TAATTTCTGCAGCAATGTTATGTGGAAAA
*
22629248 TAATTTCTGTAGCAAT
1 TAATTTCTGCAGCAAT
22629264 TGTATAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.36
Consensus pattern (29 bp):
TAATTTCTGCAGCAATGTTATGTGGAAAA
Found at i:22659963 original size:15 final size:15
Alignment explanation
Indices: 22659943--22659984 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
22659933 TAATGTTGTA
22659943 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
22659958 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
*
22659973 A-TAATATAAAAA
1 ATTAAAATAAAAA
22659985 TTAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 9 0.38
15 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:22659970 original size:20 final size:21
Alignment explanation
Indices: 22659947--22659990 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
22659937 GTTGTAATTA
*
22659947 AAATAAAAAATATTAAAA-TA
1 AAATAAAAAATATAAAAATTA
* *
22659967 AAATATATAATATAAAAATTA
1 AAATAAAAAATATAAAAATTA
22659988 AAA
1 AAA
22659991 AATATAAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AAATAAAAAATATAAAAATTA
Found at i:22659996 original size:16 final size:17
Alignment explanation
Indices: 22659975--22660006 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22659965 TAAAATATAT
22659975 AATATAA-AAATTAAAA
1 AATATAAGAAATTAAAA
22659991 AATATAAGAAATTAAA
1 AATATAAGAAATTAAA
22660007 TTTTATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
AATATAAGAAATTAAAA
Found at i:22660073 original size:22 final size:22
Alignment explanation
Indices: 22660033--22660098 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
22660023 TAAAAGAAAT
* *
22660033 TAAAATAAAATAAATAATATAAA
1 TAAAAT-ATATAAAAAATATAAA
* *
22660056 -AAATTATATTAAAAAATAAAAA
1 TAAAATATA-TAAAAAATATAAA
22660078 TAAAATATATAAAAAATATAA
1 TAAAATATATAAAAAATATAA
22660099 GTATATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
21 2 0.06
22 26 0.74
23 7 0.20
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
TAAAATATATAAAAAATATAAA
Found at i:22660089 original size:73 final size:72
Alignment explanation
Indices: 22659950--22660088 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 72
22659940 GTAATTAAAA
* * *
22659950 TAAAAAATATTAAAATAAAATATATAATATAAAAATTAAAAAATATAAGAAATTAAATTTTATAT
1 TAAAAAATATTAAAATAAAATAAATAATATAAAAATTAAAAAAAATAAGAAATTAAA-TATATAT
22660015 AATATAGG
65 AATATAGG
*
22660023 TAAAAGAA-ATTAAAATAAAATAAATAATATAAAAAATTATATTAAAAAATAA-AAATAAAATAT
1 TAAAA-AATATTAAAATAAAATAAATAATAT-AAAAATTA-A--AAAAAATAAGAAATTAAATAT
22660086 ATA
61 ATA
22660089 AAAAATATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
73 26 0.46
74 10 0.18
75 6 0.11
76 7 0.12
77 8 0.14
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (72 bp):
TAAAAAATATTAAAATAAAATAAATAATATAAAAATTAAAAAAAATAAGAAATTAAATATATATA
ATATAGG
Found at i:22660104 original size:40 final size:40
Alignment explanation
Indices: 22660029--22660108 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
22660019 TAGGTAAAAG
* *
22660029 AAATTAAAATAAAATAAATAATATAAAAAATTATATTAAA
1 AAATAAAAATAAAATAAATAATATAAAAAAGTATATTAAA
*
22660069 AAATAAAAATAAAATATATAA-A-AAATATAAGTATATTAAA
1 AAATAAAAATAAAATAAATAATATAAA-A-AAGTATATTAAA
22660109 CTTGTATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 3 0.09
39 2 0.06
40 30 0.86
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (40 bp):
AAATAAAAATAAAATAAATAATATAAAAAAGTATATTAAA
Found at i:22664843 original size:2 final size:2
Alignment explanation
Indices: 22664836--22664879 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
22664826 GCAGGAAGAA
22664836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22664878 AT
1 AT
22664880 TTAGTGTCAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22671149 original size:2 final size:2
Alignment explanation
Indices: 22671142--22671169 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22671132 AAATATAAAA
22671142 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22671170 GTTCAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22678921 original size:17 final size:16
Alignment explanation
Indices: 22678885--22678927 Score: 52
Period size: 17 Copynumber: 2.7 Consensus size: 16
22678875 TTAATAATCT
22678885 AAAAATTTA-AGTGAA
1 AAAAATTTATAGTGAA
*
22678900 AAAAATTTATAGTGTTA
1 AAAAATTTATAGTG-AA
*
22678917 AAAAATATATA
1 AAAAATTTATA
22678928 TATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.38
16 4 0.17
17 11 0.46
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAAATTTATAGTGAA
Found at i:22679754 original size:34 final size:35
Alignment explanation
Indices: 22679716--22679783 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
22679706 AGTTAAAAAT
* *
22679716 TAAATCAAATAAAT-TTTAAATT-TTTGTATTATTA
1 TAAAT-AAAAAAATATTTAAATTATTTATATTATTA
22679750 TAAATAAAAAAATATTTAAATTATTTATATTATT
1 TAAATAAAAAAATATTTAAATTATTTATATTATT
22679784 TTATTCAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 7 0.23
34 13 0.43
35 10 0.33
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
TAAATAAAAAAATATTTAAATTATTTATATTATTA
Found at i:22680231 original size:32 final size:33
Alignment explanation
Indices: 22680173--22680238 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
22680163 TATTAGCATG
* *
22680173 TTAGTGTCATGTTAGTATTTTTATGTCATCATA
1 TTAGTGTCATGTGAGTATTGTTATGTCATCATA
* *
22680206 TTAGTGTTATGTGA-TATTGTTATGTCATTATA
1 TTAGTGTCATGTGAGTATTGTTATGTCATCATA
22680238 T
1 T
22680239 GCGTTTTACG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.24, C:0.06, G:0.17, T:0.53
Consensus pattern (33 bp):
TTAGTGTCATGTGAGTATTGTTATGTCATCATA
Found at i:22681860 original size:37 final size:36
Alignment explanation
Indices: 22681810--22681933 Score: 164
Period size: 37 Copynumber: 3.4 Consensus size: 36
22681800 AGGTTTGATG
22681810 AATATTAATATTTAACTTAAAATATTAAAAAAATAAA
1 AATATTAATATTTAACTTAAAATATT-AAAAAATAAA
22681847 AATATTAATATTTAACTTAAAAAATATTAAAAAATAAA
1 AATATTAATATTTAACTT--AAAATATTAAAAAATAAA
** *
22681885 AATATTAATATTTTAACTTAAAA-A--AATTAATTAA
1 AATATTAATA-TTTAACTTAAAATATTAAAAAATAAA
22681919 AATATTAATATTTAA
1 AATATTAATATTTAA
22681934 ATTATACAAC
Statistics
Matches: 81, Mismatches: 3, Indels: 10
0.86 0.03 0.11
Matches are distributed among these distances:
33 5 0.06
34 17 0.21
36 1 0.01
37 22 0.27
38 20 0.25
39 16 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (36 bp):
AATATTAATATTTAACTTAAAATATTAAAAAATAAA
Found at i:22681872 original size:22 final size:22
Alignment explanation
Indices: 22681844--22681915 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
22681834 TTAAAAAAAT
22681844 AAAAATATTAATATTTAACTTA
1 AAAAATATTAATATTTAACTTA
*
22681866 AAAAATATTAA-A---AA-AT-
1 AAAAATATTAATATTTAACTTA
22681882 AAAAATATTAATATTTTAACTTA
1 AAAAATATTAATA-TTTAACTTA
22681905 AAAAA-ATTAAT
1 AAAAATATTAAT
22681916 TAAAATATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
16 11 0.27
17 2 0.05
18 2 0.05
21 3 0.07
22 18 0.44
23 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATATTAATATTTAACTTA
Found at i:22681900 original size:39 final size:38
Alignment explanation
Indices: 22681810--22681933 Score: 172
Period size: 38 Copynumber: 3.4 Consensus size: 38
22681800 AGGTTTGATG
22681810 AATATTAATATTTAACTT--AAAATATTAAAAAAATAAA
1 AATATTAATATTTAACTTAAAAAATATT-AAAAAATAAA
22681847 AATATTAATATTTAACTTAAAAAATATTAAAAAATAAA
1 AATATTAATATTTAACTTAAAAAATATTAAAAAATAAA
*
22681885 AATATTAATATTTTAACTTAAAAAA-ATT----AATTAA
1 AATATTAATA-TTTAACTTAAAAAATATTAAAAAATAAA
22681919 AATATTAATATTTAA
1 AATATTAATATTTAA
22681934 ATTATACAAC
Statistics
Matches: 83, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 5 0.06
34 15 0.18
37 18 0.22
38 23 0.28
39 22 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (38 bp):
AATATTAATATTTAACTTAAAAAATATTAAAAAATAAA
Found at i:22681951 original size:33 final size:34
Alignment explanation
Indices: 22681883--22681958 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
22681873 TTAAAAAATA
* *
22681883 AAAATATTAATATTTTAACTTAAAAAAATTAATT
1 AAAATATTAATATTTTAAATTAAAAAAACTAATT
* *
22681917 AAAATATTAATA-TTTAAATTATACAACACT-ATT
1 AAAATATTAATATTTTAAATTA-AAAAAACTAATT
22681950 AAAAT-TTAA
1 AAAATATTAA
22681959 AAAAATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.11
33 16 0.43
34 17 0.46
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.39
Consensus pattern (34 bp):
AAAATATTAATATTTTAAATTAAAAAAACTAATT
Found at i:22682071 original size:70 final size:70
Alignment explanation
Indices: 22681997--22682138 Score: 223
Period size: 70 Copynumber: 2.0 Consensus size: 70
22681987 TAAATTTTTT
*
22681997 TATTTATAA-ATGGAATAAATCTTACTAATAATTATAATTAAAAATATTTCAATGATCATCATTT
1 TATTTATAACA-GGAATAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTT
*
22682061 GATGAA
65 AATGAA
** *
22682067 TATTTATAACAGGCTTAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCGTCATTTA
1 TATTTATAACAGGAATAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTA
22682132 ATGAA
66 ATGAA
22682137 TA
1 TA
22682139 CATATTTATA
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
70 65 0.98
71 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (70 bp):
TATTTATAACAGGAATAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCATCATTTA
ATGAA
Found at i:22694642 original size:56 final size:56
Alignment explanation
Indices: 22694483--22694702 Score: 397
Period size: 56 Copynumber: 3.9 Consensus size: 56
22694473 CGCATTCTGG
*
22694483 TGTTATGTTTAATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
1 TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
22694539 TGTTATGTTTCATCATG-TTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
1 TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
22694594 TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
1 TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
* * *
22694650 TGTCATGTTTCATCATGATTAATGTTGTTGAAGCCTCTAATTGATTAGCACTA
1 TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTA
22694703 CGCTATAGGT
Statistics
Matches: 159, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
55 55 0.35
56 104 0.65
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (56 bp):
TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
Found at i:22701420 original size:34 final size:34
Alignment explanation
Indices: 22701371--22701436 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
22701361 CTTCATGAAG
* *
22701371 GCTTTAGCTGCTGTTTCTTTAGTTTAATCTTCAA
1 GCTTAAGCTGCTGTTTCTTCAGTTTAATCTTCAA
*
22701405 GCTTAAGCTGTTGTTTCTTCAGTTTAATCTTC
1 GCTTAAGCTGCTGTTTCTTCAGTTTAATCTTC
22701437 CAGTCTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.17, C:0.18, G:0.15, T:0.50
Consensus pattern (34 bp):
GCTTAAGCTGCTGTTTCTTCAGTTTAATCTTCAA
Found at i:22705402 original size:2 final size:2
Alignment explanation
Indices: 22705395--22705433 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
22705385 AATTGAATAC
22705395 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22705434 TAATTCAAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22706794 original size:12 final size:12
Alignment explanation
Indices: 22706774--22706802 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
22706764 AGAAAATAGG
22706774 TTTTT-TTTTTT
1 TTTTTATTTTTT
22706785 TTTTTATTTTTT
1 TTTTTATTTTTT
22706797 TTTTTA
1 TTTTTA
22706803 AAAAAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (12 bp):
TTTTTATTTTTT
Found at i:22724810 original size:22 final size:22
Alignment explanation
Indices: 22724784--22724850 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 22
22724774 TTTCCTAAAT
* *
22724784 TGATTCCACTAAGTTATAAAAG
1 TGATTCAACTAAGTTATAAAAA
* *
22724806 TGATTTAACTAAGTTAGCAAAAA
1 TGATTCAACTAAGTTA-TAAAAA
22724829 TGATTCAACT-A-TTATAAAAA
1 TGATTCAACTAAGTTATAAAAA
22724849 TG
1 TG
22724851 GTTTAGGTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 7 0.18
21 3 0.08
22 15 0.39
23 13 0.34
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.33
Consensus pattern (22 bp):
TGATTCAACTAAGTTATAAAAA
Done.