Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 69 of 240
Found at i:22226288 original size:16 final size:16
Alignment explanation
Indices: 22226264--22226315 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
22226254 GATTTGCTAT
22226264 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
22226280 TACAGCTCTAATCCAA
1 TACACCTCTAATCCAA
22226296 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
22226312 TACA
1 TACA
22226316 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.02, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:22227668 original size:19 final size:20
Alignment explanation
Indices: 22227623--22227675 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 20
22227613 ACCTTCAAGA
*
22227623 ATATGCAATCTTAGATATCAT
1 ATATGCAATCTTAGATAT-AG
22227644 ATATGCAATCTTAGATAT-G
1 ATATGCAATCTTAGATATAG
22227663 ATATGCAATCTTA
1 ATATGCAATCTTA
22227676 AAAGATATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (20 bp):
ATATGCAATCTTAGATATAG
Found at i:22227703 original size:22 final size:22
Alignment explanation
Indices: 22227623--22227686 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 22
22227613 ACCTTCAAGA
* *
22227623 ATATGCAATCTT-AGATATCAT-
1 ATATGCAATCTTAAAAGAT-ATG
22227644 ATATGCAATCTT---AGATATG
1 ATATGCAATCTTAAAAGATATG
22227663 ATATGCAATCTTAAAAGATATG
1 ATATGCAATCTTAAAAGATATG
22227685 AT
1 AT
22227687 TTTGTAATCT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 2 0.05
19 15 0.39
21 12 0.32
22 9 0.24
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (22 bp):
ATATGCAATCTTAAAAGATATG
Found at i:22227947 original size:23 final size:23
Alignment explanation
Indices: 22227903--22227947 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
22227893 TCTTATTTTG
* *
22227903 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
22227926 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
22227948 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:22228315 original size:37 final size:37
Alignment explanation
Indices: 22228239--22228315 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
22228229 CATACATACG
*
22228239 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
22228277 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
22228314 TT
1 TT
22228316 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:22228434 original size:23 final size:22
Alignment explanation
Indices: 22228405--22228448 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
22228395 ATAATTCACA
* *
22228405 TACATATATATTTTTCTTATATG
1 TACATATACATATTT-TTATATG
22228428 TACATATACATATTTTTATAT
1 TACATATACATATTTTTATAT
22228449 TTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.34, C:0.09, G:0.02, T:0.55
Consensus pattern (22 bp):
TACATATACATATTTTTATATG
Found at i:22228633 original size:3 final size:3
Alignment explanation
Indices: 22228625--22228702 Score: 111
Period size: 3 Copynumber: 26.0 Consensus size: 3
22228615 TTATCTTTTC
* * * * *
22228625 ATT ATT ATT ATT ATT ATT AGT ATT AGT ATT AGT ATT AGT ATT AGT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22228673 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22228703 GTTGTTGTTG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:22229928 original size:18 final size:17
Alignment explanation
Indices: 22229895--22229933 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
22229885 TTGTATAAAT
22229895 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
22229913 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
22229930 TGTG
1 TGTG
22229934 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:22230225 original size:45 final size:45
Alignment explanation
Indices: 22230161--22230249 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
22230151 TGTTATTGAT
* *
22230161 CAGTGGTAGCTTCGGCTACATGTCAGTGGTAGCTTTGGCTACATC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
22230206 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACAT
22230250 ACGAGTGTGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.30
Consensus pattern (45 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATC
Found at i:22230250 original size:23 final size:23
Alignment explanation
Indices: 22230159--22230250 Score: 150
Period size: 23 Copynumber: 4.0 Consensus size: 23
22230149 AGTGTTATTG
22230159 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
22230182 GTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
22230205 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
22230227 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
22230250 A
1 A
22230251 CGAGTGTGGC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 20 0.32
23 43 0.68
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:22237596 original size:45 final size:46
Alignment explanation
Indices: 22237532--22237627 Score: 167
Period size: 45 Copynumber: 2.1 Consensus size: 46
22237522 TGTTATTGAT
* *
22237532 CAGTGGTAGCTTCGGCTACATGTCAGTGGTAGCTTTGGCTACAT-C
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATAC
22237577 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATAC
1 CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATAC
22237623 CAGTG
1 CAGTG
22237628 TGGCACTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 42 0.88
46 6 0.12
ACGTcount: A:0.20, C:0.23, G:0.28, T:0.29
Consensus pattern (46 bp):
CAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTACATAC
Found at i:22237621 original size:23 final size:23
Alignment explanation
Indices: 22237530--22237627 Score: 153
Period size: 23 Copynumber: 4.3 Consensus size: 23
22237520 AGTGTTATTG
22237530 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
22237553 GTCAGTGGTAGCTTTGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
22237576 -CCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
22237598 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
22237621 ACCAGTG
1 ATCAGTG
22237628 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
22 20 0.29
23 48 0.71
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:22243326 original size:18 final size:18
Alignment explanation
Indices: 22243303--22243339 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
22243293 TAACAAAGTT
22243303 AACCTAATATGAGTATCA
1 AACCTAATATGAGTATCA
22243321 AACCTAATATGAGTATCA
1 AACCTAATATGAGTATCA
22243339 A
1 A
22243340 TACTACTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (18 bp):
AACCTAATATGAGTATCA
Found at i:22248158 original size:15 final size:15
Alignment explanation
Indices: 22248138--22248167 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22248128 TTCAAATTGT
22248138 TTGTTGAAGCTTCCA
1 TTGTTGAAGCTTCCA
*
22248153 TTGTTGAAGGTTCCA
1 TTGTTGAAGCTTCCA
22248168 GAAAACATTT
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:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (15 bp):
TTGTTGAAGCTTCCA
Found at i:22248480 original size:15 final size:13
Alignment explanation
Indices: 22248454--22248479 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22248444 TCAGGTTAGG
22248454 AGTGAGAGATATA
1 AGTGAGAGATATA
22248467 AGTGAGAGATATA
1 AGTGAGAGATATA
22248480 TGAATAATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (13 bp):
AGTGAGAGATATA
Found at i:22251047 original size:20 final size:20
Alignment explanation
Indices: 22250998--22251047 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
22250988 ACAATTTAAA
22250998 ATGTAAAAATTTATTAATAT
1 ATGTAAAAATTTATTAATAT
* * *
22251018 GTATATAAATTTATTAATAT
1 ATGTAAAAATTTATTAATAT
22251038 ATGTAAAAAT
1 ATGTAAAAAT
22251048 AACTTTTCCG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTAAAAATTTATTAATAT
Found at i:22253386 original size:30 final size:30
Alignment explanation
Indices: 22253297--22253389 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
22253287 CTGGACGAGT
* * *
22253297 AACCTCGATATAATGTCAGCTTGTGTGAGT
1 AACCTTGATATAATGTTAGCTTGTGTGAGC
*
22253327 AA-CTTCATTATAATGTTAGCTTGTGTGAGC
1 AACCTTGA-TATAATGTTAGCTTGTGTGAGC
* *
22253357 AACCTTGATATACTGTTAACTTGTGTGAGC
1 AACCTTGATATAATGTTAGCTTGTGTGAGC
22253387 AAC
1 AAC
22253390 TTATTCCCGT
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.06
30 47 0.87
31 4 0.07
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (30 bp):
AACCTTGATATAATGTTAGCTTGTGTGAGC
Found at i:22254628 original size:21 final size:21
Alignment explanation
Indices: 22254604--22254759 Score: 93
Period size: 21 Copynumber: 7.4 Consensus size: 21
22254594 TTTTACTTTT
*
22254604 TGTTTAGCTTTTTCGAGCTTC
1 TGTTTAGCTCTTTCGAGCTTC
22254625 TGTTTAGCTCTTTCGAGCTTC
1 TGTTTAGCTCTTTCGAGCTTC
* * * *
22254646 TATTAAACTCTTAT-GAGTTTC
1 TGTTTAGCTCTT-TCGAGCTTC
* * *
22254667 TGTTCAACTCTTAT-GAGTTTC
1 TGTTTAGCTCTT-TCGAGCTTC
* * *
22254688 TATTCAGCTCTTACGAGCTTC
1 TGTTTAGCTCTTTCGAGCTTC
* * * *
22254709 TATTCAACTCTTAT-GAGTTTC
1 TGTTTAGCTCTT-TCGAGCTTC
** *
22254730 TGTCAAGCTCTTACGAGCTTC
1 TGTTTAGCTCTTTCGAGCTTC
*
22254751 TATTTAGCT
1 TGTTTAGCT
22254760 TTCGAGTTTG
Statistics
Matches: 108, Mismatches: 23, Indels: 8
0.78 0.17 0.06
Matches are distributed among these distances:
21 107 0.99
22 1 0.01
ACGTcount: A:0.19, C:0.21, G:0.15, T:0.46
Consensus pattern (21 bp):
TGTTTAGCTCTTTCGAGCTTC
Found at i:22254689 original size:42 final size:42
Alignment explanation
Indices: 22254617--22254754 Score: 152
Period size: 42 Copynumber: 3.3 Consensus size: 42
22254607 TTAGCTTTTT
* * * *
22254617 CGAGCTTCTGTTTAGCTCTT-TCGAGCTTCTATTAAACTCTTA
1 CGAGCTTCTATTCAACTCTTAT-GAGTTTCTATTAAACTCTTA
* * * * *
22254659 TGAGTTTCTGTTCAACTCTTATGAGTTTCTATTCAGCTCTTA
1 CGAGCTTCTATTCAACTCTTATGAGTTTCTATTAAACTCTTA
* * *
22254701 CGAGCTTCTATTCAACTCTTATGAGTTTCTGTCAAGCTCTTA
1 CGAGCTTCTATTCAACTCTTATGAGTTTCTATTAAACTCTTA
22254743 CGAGCTTCTATT
1 CGAGCTTCTATT
22254755 TAGCTTTCGA
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 81 0.99
43 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.43
Consensus pattern (42 bp):
CGAGCTTCTATTCAACTCTTATGAGTTTCTATTAAACTCTTA
Found at i:22254708 original size:63 final size:63
Alignment explanation
Indices: 22254617--22254759 Score: 207
Period size: 63 Copynumber: 2.3 Consensus size: 63
22254607 TTAGCTTTTT
* * *
22254617 CGAGCTTCTGTTTAGCTCTTTCGAGCTTCTATTAAACTCTTATGAGTTTCTGTTCAA-CTCTTA
1 CGAGCTTCTATTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTCTG-TCAAGCTCTTA
* * *
22254680 TGAGTTTCTATTCAGCTCTTACGAGCTTCTATTCAACTCTTATGAGTTTCTGTCAAGCTCTTA
1 CGAGCTTCTATTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTCTGTCAAGCTCTTA
*
22254743 CGAGCTTCTATTTAGCT
1 CGAGCTTCTATTCAGCT
22254760 TTCGAGTTTG
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
62 4 0.06
63 66 0.94
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (63 bp):
CGAGCTTCTATTCAGCTCTTACGAGCTTCTATTAAACTCTTATGAGTTTCTGTCAAGCTCTTA
Found at i:22254923 original size:21 final size:21
Alignment explanation
Indices: 22254897--22254939 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
22254887 TACTTTTTTC
22254897 TTAGCT-TTTACGAGCTTCTGT
1 TTAGCTCTTT-CGAGCTTCTGT
22254918 TTAGCTCTTTCGAGCTTCTGT
1 TTAGCTCTTTCGAGCTTCTGT
22254939 T
1 T
22254940 CAACGAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.12, C:0.21, G:0.19, T:0.49
Consensus pattern (21 bp):
TTAGCTCTTTCGAGCTTCTGT
Found at i:22254948 original size:15 final size:15
Alignment explanation
Indices: 22254928--22254956 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
22254918 TTAGCTCTTT
22254928 CGAGCTTCTGTTCAA
1 CGAGCTTCTGTTCAA
22254943 CGAGCTTCTGTTCA
1 CGAGCTTCTGTTCA
22254957 GCTCTTAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.28, G:0.21, T:0.34
Consensus pattern (15 bp):
CGAGCTTCTGTTCAA
Found at i:22254973 original size:36 final size:36
Alignment explanation
Indices: 22254906--22254975 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
22254896 CTTAGCTTTT
* *
22254906 ACGAGCTTCTGTTTAGCTCTTTCGAGCTTCTGTTCA
1 ACGAGCTTCTGTTCAGCTCTTACGAGCTTCTGTTCA
* *
22254942 ACGAGCTTCTGTTCAGCTCTTAGGAGTTTCTGTT
1 ACGAGCTTCTGTTCAGCTCTTACGAGCTTCTGTT
22254976 AAGCTCTTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.41
Consensus pattern (36 bp):
ACGAGCTTCTGTTCAGCTCTTACGAGCTTCTGTTCA
Found at i:22255001 original size:21 final size:21
Alignment explanation
Indices: 22254942--22255009 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
22254932 CTTCTGTTCA
* *
22254942 ACGAGCTTCTGTTCAGCTCTT
1 ACGAGCTTTTGTTAAGCTCTT
*
22254963 AGGAG-TTTCTGTTAAGCTCTT
1 ACGAGCTTT-TGTTAAGCTCTT
* *
22254984 ACGAGCTTTTATTTAGCT-TT
1 ACGAGCTTTTGTTAAGCTCTT
22255004 -CGAGCT
1 ACGAGCT
22255010 CCTGTTCACG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 6 0.15
20 4 0.10
21 26 0.67
22 3 0.08
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.41
Consensus pattern (21 bp):
ACGAGCTTTTGTTAAGCTCTT
Found at i:22255830 original size:17 final size:16
Alignment explanation
Indices: 22255808--22255839 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
22255798 TTTCCAGATT
22255808 ATTGGAAGCTTGATCGG
1 ATTGGAAGCTT-ATCGG
22255825 ATTGGAAGCTTATCG
1 ATTGGAAGCTTATCG
22255840 AAGATATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.25, C:0.12, G:0.31, T:0.31
Consensus pattern (16 bp):
ATTGGAAGCTTATCGG
Found at i:22270630 original size:14 final size:14
Alignment explanation
Indices: 22270611--22270637 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22270601 ATAATTTGTC
22270611 GTTGTTGCCTTACT
1 GTTGTTGCCTTACT
22270625 GTTGTTGCCTTAC
1 GTTGTTGCCTTAC
22270638 AGTTCCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (14 bp):
GTTGTTGCCTTACT
Found at i:22275853 original size:17 final size:18
Alignment explanation
Indices: 22275818--22275853 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
22275808 AAATAATTTT
22275818 TTTAAAAATATAATATATA
1 TTTAAAAATAT-ATATATA
22275837 TTTAAAAATAT-TATATA
1 TTTAAAAATATATATATA
22275854 CTTTTGGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAAATATATATATA
Found at i:22277234 original size:20 final size:20
Alignment explanation
Indices: 22277209--22277247 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
22277199 CCATTTCTTC
22277209 CCCCTCACAGCGCCACGTTG
1 CCCCTCACAGCGCCACGTTG
22277229 CCCCTCACAGCGCCACGTT
1 CCCCTCACAGCGCCACGTT
22277248 TCTAAAACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.51, G:0.18, T:0.15
Consensus pattern (20 bp):
CCCCTCACAGCGCCACGTTG
Found at i:22280032 original size:15 final size:15
Alignment explanation
Indices: 22280012--22280042 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
22280002 GTCATGTAAG
22280012 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
22280027 TGAAAGGTCAAGAGT
1 TGAAAGGTCAAGAGT
22280042 T
1 T
22280043 ATATTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.32, T:0.23
Consensus pattern (15 bp):
TGAAAGGTCAAGAGT
Found at i:22280233 original size:17 final size:17
Alignment explanation
Indices: 22280200--22280238 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
22280190 TAAGCTTTTG
22280200 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
22280217 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
22280234 ATTTT
1 ATTTT
22280239 TCCACAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:22281005 original size:15 final size:15
Alignment explanation
Indices: 22280981--22281010 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22280971 TGGAGATCGA
*
22280981 GGAAATGGTCGTGGT
1 GGAAAAGGTCGTGGT
22280996 GGAAAAGGTCGTGGT
1 GGAAAAGGTCGTGGT
22281011 CAAGAAGGGA
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:0.23, C:0.07, G:0.47, T:0.23
Consensus pattern (15 bp):
GGAAAAGGTCGTGGT
Found at i:22284396 original size:15 final size:15
Alignment explanation
Indices: 22284372--22284402 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
22284362 GTCATGTAAG
*
22284372 TGAAAGGTCAAGAGT
1 TGAAAAGTCAAGAGT
22284387 TGAAAAGTCAAGAGT
1 TGAAAAGTCAAGAGT
22284402 T
1 T
22284403 ATATTGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (15 bp):
TGAAAAGTCAAGAGT
Found at i:22284593 original size:17 final size:17
Alignment explanation
Indices: 22284560--22284598 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
22284550 TAAGCTTTTG
22284560 ATTTTATATGAGAGAAC
1 ATTTTATATGAGAGAAC
*
22284577 AATTTTATAT-TGAGAAC
1 -ATTTTATATGAGAGAAC
22284594 ATTTT
1 ATTTT
22284599 TCCACAGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 5 0.25
17 6 0.30
18 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.13, T:0.44
Consensus pattern (17 bp):
ATTTTATATGAGAGAAC
Found at i:22289333 original size:21 final size:21
Alignment explanation
Indices: 22289309--22289348 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22289299 AAGTTATCTG
*
22289309 GATTTCTATAGGAAAAACTTA
1 GATTTCTACAGGAAAAACTTA
* *
22289330 GATTTTTGCAGGAAAAACT
1 GATTTCTACAGGAAAAACT
22289349 ATTTTATCTA
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:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
GATTTCTACAGGAAAAACTTA
Found at i:22295796 original size:33 final size:33
Alignment explanation
Indices: 22295759--22295823 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
22295749 GATTGACGTT
*
22295759 GGGATAAGAAAGAGTCGATATCCCGACGTCACG
1 GGGATAAGAAAGAGTCGATATCCCAACGTCACG
22295792 GGGATAAGAAAGAGTCGATATCCCAACGTCAC
1 GGGATAAGAAAGAGTCGATATCCCAACGTCAC
22295824 AATGAGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.22, G:0.28, T:0.15
Consensus pattern (33 bp):
GGGATAAGAAAGAGTCGATATCCCAACGTCACG
Found at i:22300168 original size:39 final size:39
Alignment explanation
Indices: 22300114--22300255 Score: 178
Period size: 39 Copynumber: 3.7 Consensus size: 39
22300104 TAATGTTCGT
*
22300114 TTGAGCA-ACTTTCAGTACAATCAGTGGGTATGGCTCGA
1 TTGAGCATACTTTCAGTAGAATCAGTGGGTATGGCTCGA
* * * *
22300152 TTAAGCATACTTTCAGTAGAATTAGTGAGTATGGCTTGA
1 TTGAGCATACTTTCAGTAGAATCAGTGGGTATGGCTCGA
* * * * *
22300191 TTGAGCATACTTTCCGTAGAATCGGTAGGTATGACCCGA
1 TTGAGCATACTTTCAGTAGAATCAGTGGGTATGGCTCGA
*
22300230 TTGAGCATACTTTTAGTAGAATCAGT
1 TTGAGCATACTTTCAGTAGAATCAGT
22300256 ATCCCATTTT
Statistics
Matches: 86, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
38 6 0.07
39 80 0.93
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (39 bp):
TTGAGCATACTTTCAGTAGAATCAGTGGGTATGGCTCGA
Found at i:22302681 original size:31 final size:28
Alignment explanation
Indices: 22302641--22302712 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 28
22302631 ACAATATCTT
*
22302641 ATAATAAAATAAAAGGATCTATATAATAAGA
1 ATAAAAAAATAAAAGG--CTA-ATAATAAGA
* *
22302672 TTAAAAAAATAAAAGGCTAATAATAATA
1 ATAAAAAAATAAAAGGCTAATAATAAGA
22302700 ATAAAAATAATAA
1 ATAAAAA-AATAA
22302713 TAATGACCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 14 0.39
29 8 0.22
31 14 0.39
ACGTcount: A:0.65, C:0.03, G:0.07, T:0.25
Consensus pattern (28 bp):
ATAAAAAAATAAAAGGCTAATAATAAGA
Found at i:22302695 original size:3 final size:3
Alignment explanation
Indices: 22302689--22302740 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
22302679 AATAAAAGGC
* * * *
22302689 TAA TAA TAA TAA TAA AAA TAA TAA TAA TGAC CAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
*
22302735 CAA TAA
1 TAA TAA
22302741 ATTAATTAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
3 37 0.97
4 1 0.03
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (3 bp):
TAA
Found at i:22302730 original size:16 final size:15
Alignment explanation
Indices: 22302690--22302741 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
22302680 ATAAAAGGCT
* *
22302690 AATAATAATAATAAA
1 AATAAAAATAATAAC
* *
22302705 AATAATAATAATGACC
1 AATAAAAATAAT-AAC
22302721 AATAAAAATAATAAC
1 AATAAAAATAATAAC
22302736 AATAAA
1 AATAAA
22302742 TTAATTAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (15 bp):
AATAAAAATAATAAC
Found at i:22305698 original size:21 final size:20
Alignment explanation
Indices: 22305672--22305788 Score: 94
Period size: 21 Copynumber: 5.6 Consensus size: 20
22305662 TTACAAAAAA
*
22305672 AATCAATTCAAACAAAGATAC
1 AATCAATTTAAACAAAGA-AC
22305693 AATCAATTTAAACACATAG-AC
1 AATCAATTTAAACA-A-AGAAC
*
22305714 AATCGATTTAAACATAAGAAC
1 AATCAATTTAAACA-AAGAAC
*
22305735 AGTCAATTTAAACATATAG-AC
1 AATCAATTTAAACA-A-AGAAC
* * *
22305756 AATCGATTTAAAAATAAGAGC
1 AATCAATTTAAACA-AAGAAC
*
22305777 AATCGATTTAAA
1 AATCAATTTAAA
22305789 AGAAGTTGTA
Statistics
Matches: 82, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
20 4 0.05
21 73 0.89
22 3 0.04
23 2 0.02
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.25
Consensus pattern (20 bp):
AATCAATTTAAACAAAGAAC
Found at i:22305742 original size:42 final size:42
Alignment explanation
Indices: 22305672--22305788 Score: 155
Period size: 42 Copynumber: 2.8 Consensus size: 42
22305662 TTACAAAAAA
* *
22305672 AATCAATTCAAACA-AAGATACAATCAATTTAAACACATAGAC
1 AATCGATTTAAACATAAGA-ACAATCAATTTAAACACATAGAC
* *
22305714 AATCGATTTAAACATAAGAACAGTCAATTTAAACATATAGAC
1 AATCGATTTAAACATAAGAACAATCAATTTAAACACATAGAC
* * *
22305756 AATCGATTTAAAAATAAGAGCAATCGATTTAAA
1 AATCGATTTAAACATAAGAACAATCAATTTAAA
22305789 AGAAGTTGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.25
Consensus pattern (42 bp):
AATCGATTTAAACATAAGAACAATCAATTTAAACACATAGAC
Found at i:22305789 original size:21 final size:20
Alignment explanation
Indices: 22305691--22305789 Score: 101
Period size: 21 Copynumber: 4.8 Consensus size: 20
22305681 AAACAAAGAT
*
22305691 ACAATCAATTTAAACACAT-AG
1 ACAATCGATTTAAA-A-ATAAG
*
22305712 ACAATCGATTTAAACATAAG
1 ACAATCGATTTAAAAATAAG
* * *
22305732 AACAGTCAATTTAAACATATAG
1 -ACAATCGATTTAAAAATA-AG
22305754 ACAATCGATTTAAAAATAAG
1 ACAATCGATTTAAAAATAAG
22305774 AGCAATCGATTTAAAA
1 A-CAATCGATTTAAAA
22305790 GAAGTTGTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
19 2 0.03
20 5 0.07
21 58 0.87
22 2 0.03
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (20 bp):
ACAATCGATTTAAAAATAAG
Found at i:22308785 original size:23 final size:22
Alignment explanation
Indices: 22308735--22308789 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
22308725 GTTCATAAAC
22308735 AAGCTCATTT-ATATTCATTTA
1 AAGCTCATTTAATATTCATTTA
*
22308756 AAACTCATTTAATAAATT-ATTTA
1 AAGCTCATTTAAT--ATTCATTTA
22308779 AAGCTCATTTA
1 AAGCTCATTTA
22308790 TTGTTTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 15 0.52
24 3 0.10
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.44
Consensus pattern (22 bp):
AAGCTCATTTAATATTCATTTA
Found at i:22311397 original size:7 final size:7
Alignment explanation
Indices: 22311385--22311418 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
22311375 AAAAGAAAAA
22311385 TAAATAT
1 TAAATAT
22311392 TAAATAT
1 TAAATAT
22311399 TAAATAT
1 TAAATAT
22311406 TAAATAT
1 TAAATAT
22311413 TCAAAT
1 T-AAAT
22311419 TACATAATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 22 0.85
8 4 0.15
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (7 bp):
TAAATAT
Found at i:22312641 original size:89 final size:87
Alignment explanation
Indices: 22312471--22312700 Score: 241
Period size: 89 Copynumber: 2.6 Consensus size: 87
22312461 CTTGAGGGTA
* * * *
22312471 CAAAAA-ACCCTTAAACTTTTTCAAAAAAAGCAATTAAGCCCCTCTTTTTTTGCATTCAATTGAG
1 CAAAAAGACCCTCAAACCTTTTAAAAAAAAGCAATTAAGCCCCTCTTTTTTTGCACTCAATTGAG
*
22312535 CACTTAAACTTTTAAAATGCAT
66 CACTTAAACTTTCAAAATGCAT
*
22312557 CAAAAAGACCCTCAAACCTTTTAAAAAAAAGTAATT-AGTCCCCTGCTTTTTTTTGCACTCAATT
1 CAAAAAGACCCTCAAACCTTTTAAAAAAAAGCAATTAAG-CCCCT-C-TTTTTTTGCACTCAATT
* *
22312621 -AGGTACTTGAACTTTCAAAATGCAT
63 GA-GCACTTAAACTTTCAAAATGCAT
* * * *
22312646 CAAAAAGACCATGAAACTTTTTTTTCAAAAAAAAAACAATTAAGCCCCTGCTTTT
1 CAAAAAGACCCTCAAAC---CTTTT--AAAAAAAAGCAATTAAGCCCCT-CTTTT
22312701 ATTAAATATT
Statistics
Matches: 120, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
86 8 0.07
87 30 0.25
88 2 0.02
89 51 0.43
92 4 0.03
93 4 0.03
94 19 0.16
95 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (87 bp):
CAAAAAGACCCTCAAACCTTTTAAAAAAAAGCAATTAAGCCCCTCTTTTTTTGCACTCAATTGAG
CACTTAAACTTTCAAAATGCAT
Found at i:22312754 original size:46 final size:48
Alignment explanation
Indices: 22312699--22312810 Score: 124
Period size: 46 Copynumber: 2.4 Consensus size: 48
22312689 GCCCCTGCTT
22312699 TTATTAAATATTAGAAAAAAATT-ATAAAAAATTAAAATCAAT-AAAAG
1 TTATTAAATATTAGAAAAAAATTAATAAAAAATTAAAAT-AATAAAAAG
** ** * *
22312746 TTA-TAAATATTA-TTAAATTTTAATAAAAAATTAAAATATTAAAAAT
1 TTATTAAATATTAGAAAAAAATTAATAAAAAATTAAAATAATAAAAAG
*
22312792 TTATTAAAAATTAGAAAAA
1 TTATTAAATATTAGAAAAA
22312811 TATAAAAATA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
45 7 0.13
46 31 0.60
47 11 0.21
48 3 0.06
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.35
Consensus pattern (48 bp):
TTATTAAATATTAGAAAAAAATTAATAAAAAATTAAAATAATAAAAAG
Found at i:22312786 original size:8 final size:8
Alignment explanation
Indices: 22312769--22312835 Score: 53
Period size: 9 Copynumber: 7.6 Consensus size: 8
22312759 TAAATTTTAA
22312769 TAAAAAAT
1 TAAAAAAT
*
22312777 TAAAATAT
1 TAAAAAAT
*
22312785 TAAAAATT
1 TAAAAAAT
22312793 TATTAAAAAT
1 TA--AAAAAT
22312803 TAGAAAAAT
1 TA-AAAAAT
*
22312812 ATAAAAATAG
1 -TAAAAA-AT
22312822 TAAAAAAT
1 TAAAAAAT
22312830 CTAAAA
1 -TAAAA
22312836 CATCTAGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
8 16 0.34
9 21 0.45
10 10 0.21
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (8 bp):
TAAAAAAT
Found at i:22312792 original size:28 final size:28
Alignment explanation
Indices: 22312741--22312819 Score: 72
Period size: 26 Copynumber: 2.8 Consensus size: 28
22312731 TAAAATCAAT
* * *
22312741 AAAAGTTATAAATATTATTAAATTTTAATA
1 AAAAATTAGAAATATTA-AAAATTTT-ATA
*
22312771 AAAAATTA-AAATATTAAAAA-TTTATT
1 AAAAATTAGAAATATTAAAAATTTTATA
*
22312797 AAAAATTAGAAAAATATAAAAAT
1 AAAAATTAGAAATAT-TAAAAAT
22312820 AGTAAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 10 0.24
27 8 0.19
28 9 0.21
29 8 0.19
30 7 0.17
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (28 bp):
AAAAATTAGAAATATTAAAAATTTTATA
Found at i:22312818 original size:17 final size:17
Alignment explanation
Indices: 22312796--22312856 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
22312786 AAAAATTTAT
22312796 TAAAAATTAGAAAAATA
1 TAAAAATTAGAAAAATA
*
22312813 TAAAAA-TAGTAAAAAATC
1 TAAAAATTAG--AAAAATA
*
22312831 TAAAACATCTAGAAATATA
1 TAAAA-AT-TAGAAAAATA
*
22312850 AAAAAAT
1 TAAAAAT
22312857 ATAAAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
16 3 0.09
17 6 0.17
18 13 0.37
19 10 0.29
21 3 0.09
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (17 bp):
TAAAAATTAGAAAAATA
Found at i:22312819 original size:37 final size:39
Alignment explanation
Indices: 22312770--22312868 Score: 95
Period size: 37 Copynumber: 2.7 Consensus size: 39
22312760 AAATTTTAAT
*
22312770 AAAAA-ATTAAAATATTAAAAATTTAT-TAAAA-AT-TAG
1 AAAAATATAAAAATA-TAAAAATTTATCTAAAACATCTAG
22312806 AAAAATATAAAAATAGTAAAAA---ATCTAAAACATCTAG
1 AAAAATATAAAAATA-TAAAAATTTATCTAAAACATCTAG
* * *
22312843 AAATATAAAAAAATATAAAATTTTAT
1 AAAAATATAAAAATATAAAAATTTAT
22312869 AATGTCGTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
34 2 0.04
35 5 0.10
36 12 0.24
37 30 0.59
39 2 0.04
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (39 bp):
AAAAATATAAAAATATAAAAATTTATCTAAAACATCTAG
Found at i:22312827 original size:27 final size:26
Alignment explanation
Indices: 22312768--22312854 Score: 72
Period size: 27 Copynumber: 3.3 Consensus size: 26
22312758 TTAAATTTTA
*
22312768 ATAAAAAAT-TAAAATAT-TAAAAATTT
1 ATAAAAAATCTAAAAAATATAAAAA--T
*
22312794 ATTAAAAAT-TAGAAAAATATAAAAAT
1 ATAAAAAATCTA-AAAAATATAAAAAT
* * *
22312820 AGTAAAAAATCTAAAACATCTAGAAAT
1 A-TAAAAAATCTAAAAAATATAAAAAT
22312847 ATAAAAAA
1 ATAAAAAA
22312855 ATATAAAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
26 19 0.37
27 24 0.47
28 8 0.16
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (26 bp):
ATAAAAAATCTAAAAAATATAAAAAT
Found at i:22313123 original size:10 final size:10
Alignment explanation
Indices: 22313108--22313141 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
22313098 AAAAAATTCT
22313108 ATTTTTAATA
1 ATTTTTAATA
22313118 ATTTTT-A-A
1 ATTTTTAATA
22313126 ATTTTTAATA
1 ATTTTTAATA
22313136 ATTTTT
1 ATTTTT
22313142 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 7 0.32
9 2 0.09
10 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:22313339 original size:89 final size:90
Alignment explanation
Indices: 22313185--22313386 Score: 286
Period size: 89 Copynumber: 2.3 Consensus size: 90
22313175 TTTTAATAAG
* *
22313185 AGCAAGGGCTTAATTGC--TTTTTTGAAAAATTTTGATGGTCTTTTTGATGCATTTTGAAAGTTC
1 AGCAAGGGCTTAATTGCTTTTTTTTGAAAAAGTTTGATGGGCTTTTTGATGCATTTTGAAAGTTC
22313248 AAGCACCCAATTGAGTGAAAAAAAA
66 AAGCACCCAATTGAGTGAAAAAAAA
* *
22313273 A-CAGGGGCTTAATTGCTTTTTTTTGAAGAAGTTTGA-GGGCGTTTTTGATGCATTTTGAAAGTT
1 AGCAAGGGCTTAATTGCTTTTTTTTGAAAAAGTTTGATGGGC-TTTTTGATGCATTTTGAAAGTT
** *
22313336 CAAGTGCTCAATTGAGTGAAAAAAAA
65 CAAGCACCCAATTGAGTGAAAAAAAA
* *
22313362 AGGAAGGACTTAATTGCTTTTTTTT
1 AGCAAGGGCTTAATTGCTTTTTTTT
22313387 TAAGTTTGAG
Statistics
Matches: 100, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
87 14 0.14
88 4 0.04
89 62 0.62
90 20 0.20
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (90 bp):
AGCAAGGGCTTAATTGCTTTTTTTTGAAAAAGTTTGATGGGCTTTTTGATGCATTTTGAAAGTTC
AAGCACCCAATTGAGTGAAAAAAAA
Found at i:22315536 original size:27 final size:28
Alignment explanation
Indices: 22315483--22315536 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
22315473 ATCAAACAAC
22315483 CACACGGCCGTGTAGGACACCGTGTGTGG
1 CACACGGCCGTGTA-GACACCGTGTGTGG
22315512 CACACGGCCGTGT-GACAGCC-TGTGT
1 CACACGGCCGTGTAGACA-CCGTGTGT
22315537 CCTAGGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.38
28 2 0.08
29 13 0.54
ACGTcount: A:0.17, C:0.30, G:0.35, T:0.19
Consensus pattern (28 bp):
CACACGGCCGTGTAGACACCGTGTGTGG
Found at i:22316686 original size:26 final size:26
Alignment explanation
Indices: 22316654--22316781 Score: 111
Period size: 26 Copynumber: 4.9 Consensus size: 26
22316644 TAGTACCTGA
* *
22316654 TAAATAATCACTGGCTCAAAGCCTAC
1 TAAATAAACACTGGCTCAAGGCCTAC
* * *
22316680 TAAATAAACACCGGCTCAATG-CTTC
1 TAAATAAACACTGGCTCAAGGCCTAC
* * *
22316705 ATAAATAACCACTAGCTCAAGGCCTGC
1 -TAAATAAACACTGGCTCAAGGCCTAC
22316732 TAAATAAACA-TCGGCTCAAGGCC-AGC
1 TAAATAAACACT-GGCTCAAGGCCTA-C
*
22316758 TAAATAACCA-TCGGCTCAAGGCCT
1 TAAATAAACACT-GGCTCAAGGCCT
22316782 CCTTTTCCAA
Statistics
Matches: 84, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
25 4 0.05
26 77 0.92
27 3 0.04
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (26 bp):
TAAATAAACACTGGCTCAAGGCCTAC
Found at i:22316762 original size:52 final size:51
Alignment explanation
Indices: 22316653--22316781 Score: 154
Period size: 52 Copynumber: 2.5 Consensus size: 51
22316643 ATAGTACCTG
* * *
22316653 ATAAATAATCACTGGCTCAAAGCCTACTAAATAAACACCGGCTCAATGCTTC
1 ATAAATAACCACTGGCTCAAGGCCTACTAAATAAACACCGGCTCAAGGC-TC
* * *
22316705 ATAAATAACCACTAGCTCAAGGCCTGCTAAATAAACATCGGCTCAAGGC-C
1 ATAAATAACCACTGGCTCAAGGCCTACTAAATAAACACCGGCTCAAGGCTC
22316755 AGCTAAATAACCA-TCGGCTCAAGGCCT
1 A--TAAATAACCACT-GGCTCAAGGCCT
22316782 CCTTTTCCAA
Statistics
Matches: 67, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
50 2 0.03
51 1 0.01
52 64 0.96
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (51 bp):
ATAAATAACCACTGGCTCAAGGCCTACTAAATAAACACCGGCTCAAGGCTC
Found at i:22318848 original size:16 final size:16
Alignment explanation
Indices: 22318827--22318865 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
22318817 ATACAATTTT
22318827 TTTATTTTATATATAA
1 TTTATTTTATATATAA
* *
22318843 TTTATTCTATATGTAA
1 TTTATTTTATATATAA
22318859 TTT-TTTT
1 TTTATTTT
22318866 TGTACATACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 3 0.15
16 17 0.85
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTATTTTATATATAA
Found at i:22330806 original size:10 final size:11
Alignment explanation
Indices: 22330784--22330810 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
22330774 AAGACGAAAC
22330784 AAAACTTCAAA
1 AAAACTTCAAA
22330795 AAAACTTCAAA
1 AAAACTTCAAA
22330806 AAAAC
1 AAAAC
22330811 AAACACAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.19, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAACTTCAAA
Found at i:22356855 original size:33 final size:33
Alignment explanation
Indices: 22356797--22356873 Score: 95
Period size: 33 Copynumber: 2.3 Consensus size: 33
22356787 TATATATATG
* *
22356797 TGTAAGACCATAACTAGGCTTTGGCA-TTCTGA
1 TGTAAGACCATAACTAGGCTTTGGCACTACGGA
*
22356829 TGATAAGACCATAACT-GGGTTATGGCACTACGGA
1 TG-TAAGACCATAACTAGGCTT-TGGCACTACGGA
22356863 TGTAAGACCAT
1 TGTAAGACCAT
22356874 GGCAGGGCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 6 0.15
33 27 0.69
34 6 0.15
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (33 bp):
TGTAAGACCATAACTAGGCTTTGGCACTACGGA
Found at i:22366114 original size:3 final size:3
Alignment explanation
Indices: 22366106--22366148 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
22366096 TTTGGTTGCT
22366106 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
22366149 GTATTTCTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:22369980 original size:9 final size:9
Alignment explanation
Indices: 22369955--22369992 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
22369945 TTGAGTTTTC
*
22369955 TAATTCAAA
1 TAATTCGAA
*
22369964 TAACTCGAA
1 TAATTCGAA
22369973 TAATTCGAA
1 TAATTCGAA
22369982 TAATTCGAA
1 TAATTCGAA
22369991 TA
1 TA
22369993 TCAAACTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (9 bp):
TAATTCGAA
Found at i:22372199 original size:27 final size:26
Alignment explanation
Indices: 22372087--22372210 Score: 81
Period size: 27 Copynumber: 4.6 Consensus size: 26
22372077 TATCTTGATA
22372087 AACTACCTCATTTTTATTGTCCC-GG
1 AACTACCTCATTTTTATTGTCCCAGG
* ** * *
22372112 TACACTATCTTGTTTTTGTTGTCCTAGCG
1 -A-ACTACCTCATTTTTATTGTCCCAG-G
* * *
22372141 AACTACC-CAATATTTATTATCCCAGT
1 AACTACCTC-ATTTTTATTGTCCCAGG
*
22372167 AGACTACCTCGTTTTTATTGTCCCAAGG
1 A-ACTACCTCATTTTTATTGTCCC-AGG
* *
22372195 AACTATCTCATGTTTA
1 AACTACCTCATTTTTA
22372211 CTATCCTGGC
Statistics
Matches: 71, Mismatches: 20, Indels: 13
0.68 0.19 0.12
Matches are distributed among these distances:
26 2 0.03
27 62 0.87
28 6 0.08
29 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.12, T:0.40
Consensus pattern (26 bp):
AACTACCTCATTTTTATTGTCCCAGG
Found at i:22372315 original size:67 final size:68
Alignment explanation
Indices: 22372232--22372406 Score: 239
Period size: 67 Copynumber: 2.6 Consensus size: 68
22372222 GACTCTCTAT
* *
22372232 GTTG-CCATAGTCGAGCTATGGTCTTACACATCATACCCCATGTTTAATGTCCTGACGAACTCTA
1 GTTGTCCATAGTCGAGCTATGGTCTTACACCTCATACCCCATGTTTAATGTCCTGACAAACTCTA
22372296 TTG
66 TTG
* * * **
22372299 GTT-TCCATAGTTGAGCTATGGTCTTACACCTCAAACCCCATGTTTAGTGTCCTGGTAAACTCTA
1 GTTGTCCATAGTCGAGCTATGGTCTTACACCTCATACCCCATGTTTAATGTCCTGACAAACTCTA
22372363 TTG
66 TTG
* * *
22372366 GTTGT-CATAGCCGAACTATGGTCTCACACCTCATACCCCAT
1 GTTGTCCATAGTCGAGCTATGGTCTTACACCTCATACCCCAT
22372407 TATAGCCCAT
Statistics
Matches: 94, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
67 93 0.99
68 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (68 bp):
GTTGTCCATAGTCGAGCTATGGTCTTACACCTCATACCCCATGTTTAATGTCCTGACAAACTCTA
TTG
Found at i:22378777 original size:26 final size:27
Alignment explanation
Indices: 22378748--22378810 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
22378738 TAGGGTTTTT
22378748 CCATACTTACCATTC-TTTAGAATTAA
1 CCATACTTACCATTCTTTTAGAATTAA
* * * * *
22378774 CCATTCATATCATTCTTTTAGAGTTCA
1 CCATACTTACCATTCTTTTAGAATTAA
22378801 CCATACTTAC
1 CCATACTTAC
22378811 TATTTCTCTA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (27 bp):
CCATACTTACCATTCTTTTAGAATTAA
Found at i:22379006 original size:28 final size:28
Alignment explanation
Indices: 22378915--22379016 Score: 96
Period size: 28 Copynumber: 3.6 Consensus size: 28
22378905 CTATAGATCG
* **
22378915 CCACAAAGGCTTTTATTTTCATAGATTT
1 CCACAAAGGCGTCCATTTTCATAGATTT
* * * *
22378943 CCATAAAAGCGTCTATTTTTATAGATTT
1 CCACAAAGGCGTCCATTTTCATAGATTT
* * * *
22378971 CTATAAAGGCGTCCATTTTCATATATTA
1 CCACAAAGGCGTCCATTTTCATAGATTT
*
22378999 CCACAAAGGCATCCATTT
1 CCACAAAGGCGTCCATTT
22379017 CTATACGTTT
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (28 bp):
CCACAAAGGCGTCCATTTTCATAGATTT
Found at i:22380893 original size:10 final size:10
Alignment explanation
Indices: 22380878--22380912 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
22380868 AAGGTAATCC
22380878 TATTTCCCCT
1 TATTTCCCCT
22380888 TATTTCCCCT
1 TATTTCCCCT
* *
22380898 TTTTTCCCAT
1 TATTTCCCCT
22380908 TATTT
1 TATTT
22380913 TCTTACTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.11, C:0.31, G:0.00, T:0.57
Consensus pattern (10 bp):
TATTTCCCCT
Found at i:22397568 original size:13 final size:13
Alignment explanation
Indices: 22397550--22397583 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
22397540 TACATACCTA
*
22397550 TTCATATAAACAT
1 TTCATATAAACAC
22397563 TTCATAT-AACAC
1 TTCATATAAACAC
22397575 TTCATATAA
1 TTCATATAA
22397584 TTATTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.18, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCATATAAACAC
Found at i:22397662 original size:13 final size:13
Alignment explanation
Indices: 22397642--22397750 Score: 92
Period size: 13 Copynumber: 8.3 Consensus size: 13
22397632 GTATAACTGA
22397642 TTCATATAACCAT
1 TTCATATAACCAT
* * *
22397655 TTCGTATATCTAT
1 TTCATATAACCAT
*
22397668 TTCTATATAACCAA
1 TTC-ATATAACCAT
* *
22397682 TTCTTATAATCAT
1 TTCATATAACCAT
* *
22397695 TTCACATAACCAA
1 TTCATATAACCAT
* *
22397708 TTCGTATAACCAA
1 TTCATATAACCAT
22397721 TTCATATAACCAT
1 TTCATATAACCAT
** *
22397734 TTTGTATAGCCAT
1 TTCATATAACCAT
22397747 TTCA
1 TTCA
22397751 AAGTGTTAAC
Statistics
Matches: 72, Mismatches: 23, Indels: 2
0.74 0.24 0.02
Matches are distributed among these distances:
13 63 0.88
14 9 0.12
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:22397708 original size:26 final size:26
Alignment explanation
Indices: 22397642--22397750 Score: 112
Period size: 26 Copynumber: 4.2 Consensus size: 26
22397632 GTATAACTGA
*
22397642 TTCATATAACCATTTCGTAT-ATCTAT
1 TTCATATAACCAATTCGTATAATC-AT
*
22397668 TTCTATATAACCAATTCTTATAATCAT
1 TTC-ATATAACCAATTCGTATAATCAT
* * *
22397695 TTCACATAACCAATTCGTATAACCAA
1 TTCATATAACCAATTCGTATAATCAT
* * **
22397721 TTCATATAACCATTTTGTATAGCCAT
1 TTCATATAACCAATTCGTATAATCAT
22397747 TTCA
1 TTCA
22397751 AAGTGTTAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 47 0.67
27 20 0.29
28 3 0.04
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (26 bp):
TTCATATAACCAATTCGTATAATCAT
Found at i:22404486 original size:18 final size:20
Alignment explanation
Indices: 22404442--22404491 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 20
22404432 ATGAAAAATC
*
22404442 AACTGAAAATAAATCGTAAG
1 AACTGAAAATAAAACGTAAG
22404462 AAC--AAAATAAAAC-TAA-
1 AACTGAAAATAAAACGTAAG
22404478 AACTGAAAACTAAA
1 AACTGAAAA-TAAA
22404492 CTGAAAGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.12
17 3 0.12
18 13 0.50
19 4 0.15
20 3 0.12
ACGTcount: A:0.64, C:0.12, G:0.08, T:0.16
Consensus pattern (20 bp):
AACTGAAAATAAAACGTAAG
Found at i:22408074 original size:24 final size:23
Alignment explanation
Indices: 22408018--22408176 Score: 116
Period size: 23 Copynumber: 7.0 Consensus size: 23
22408008 TATACATAAA
* *
22408018 AATAGTATATGATAGATAT-AAAT
1 AATAGTA-ATGATAAATTTAAAAT
*
22408041 AAT-G-ATATGATAAGTTTAAAAT
1 AATAGTA-ATGATAAATTTAAAAT
* *
22408063 TATAGTACATGATAAATTTCAAAT
1 AATAGTA-ATGATAAATTTAAAAT
* *
22408087 TAT-GATATATGATAAACTT-AAAT
1 AATAG-TA-ATGATAAATTTAAAAT
*
22408110 AATATTAATGAT-AATTTAAAAT
1 AATAGTAATGATAAATTTAAAAT
* *
22408132 AATAGTATATTATATA-TTAAAAT
1 AATAGTA-ATGATAAATTTAAAAT
*
22408155 AATACTAATGATAAATTTAAAA
1 AATAGTAATGATAAATTTAAAA
22408177 CAATGTTAAG
Statistics
Matches: 109, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
21 14 0.13
22 28 0.26
23 36 0.33
24 31 0.28
ACGTcount: A:0.52, C:0.03, G:0.08, T:0.38
Consensus pattern (23 bp):
AATAGTAATGATAAATTTAAAAT
Found at i:22408203 original size:47 final size:45
Alignment explanation
Indices: 22408106--22408208 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 45
22408096 TGATAAACTT
* * *
22408106 AAATAATATTAATGATAATTTAAAATAATAGTATATTATATATTA
1 AAATAATACTAATGATAATTTAAAACAATAGTATATTAGATATTA
22408151 AAATAATACTAATGATAAATTTAAAACAAT-GT-TAAGCTTAGATATTA
1 AAATAATACTAATGAT-AATTTAAAACAATAGTAT-A--TTAGATATTA
22408198 AAATAATACTA
1 AAATAATACTA
22408209 GATTTTAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
44 1 0.02
45 18 0.35
46 12 0.24
47 20 0.39
ACGTcount: A:0.53, C:0.04, G:0.06, T:0.37
Consensus pattern (45 bp):
AAATAATACTAATGATAATTTAAAACAATAGTATATTAGATATTA
Found at i:22408216 original size:18 final size:17
Alignment explanation
Indices: 22408189--22408222 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
22408179 ATGTTAAGCT
22408189 TAGATATTAAAATAATAC
1 TAGATATTAAAA-AATAC
*
22408207 TAGATTTTAAAAAATA
1 TAGATATTAAAAAATA
22408223 TGCCAAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (17 bp):
TAGATATTAAAAAATAC
Found at i:22419157 original size:31 final size:30
Alignment explanation
Indices: 22419117--22419178 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 30
22419107 TCATACACAT
*
22419117 TAAATTTTTATTTTGATTCAAATATATATA
1 TAAATTTTTATTTTAATTCAAATATATATA
**
22419147 TAAATCTTTTATTTTAATTCAGTTATATATA
1 TAAAT-TTTTATTTTAATTCAAATATATATA
22419178 T
1 T
22419179 TATAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (30 bp):
TAAATTTTTATTTTAATTCAAATATATATA
Found at i:22423935 original size:35 final size:35
Alignment explanation
Indices: 22423896--22423977 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
22423886 GGATAAATTG
* ** * *
22423896 TCTACTGGCTCTATGGAGTGACATCATGTAAATGA
1 TCTACTGGCTCTACGGAGCAACACCATGAAAATGA
* *
22423931 TCTACTAGCTCTACGGAGCAACACCATGAAAATGG
1 TCTACTGGCTCTACGGAGCAACACCATGAAAATGA
*
22423966 TCTACTGACTCT
1 TCTACTGGCTCT
22423978 TCAGAGTCAA
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (35 bp):
TCTACTGGCTCTACGGAGCAACACCATGAAAATGA
Found at i:22425327 original size:18 final size:16
Alignment explanation
Indices: 22425294--22425342 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
22425284 TACAAATAAT
*
22425294 TAATTTAATTATAAAAG
1 TAATTTAATTA-AAAAA
22425311 TAATTTATATTAAAAAA
1 TAATTTA-ATTAAAAAA
22425328 TAATTTAA-TAAAAAA
1 TAATTTAATTAAAAAA
22425343 ACTAAAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
15 7 0.23
16 1 0.03
17 18 0.60
18 4 0.13
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TAATTTAATTAAAAAA
Found at i:22425463 original size:22 final size:22
Alignment explanation
Indices: 22425428--22425480 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
22425418 TTAATTGTTC
* **
22425428 ATCCC-AATCGTTCGTCCCTAA
1 ATCCCTAATCATTCGTCCAAAA
22425449 ATCCCTAATCATTCGTCCAAAA
1 ATCCCTAATCATTCGTCCAAAA
*
22425471 ATCTCTAATC
1 ATCCCTAATC
22425481 GCAAATACCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.30, C:0.34, G:0.06, T:0.30
Consensus pattern (22 bp):
ATCCCTAATCATTCGTCCAAAA
Found at i:22441109 original size:64 final size:63
Alignment explanation
Indices: 22441029--22441158 Score: 170
Period size: 64 Copynumber: 2.0 Consensus size: 63
22441019 ACGAGCATCC
* * * * * * *
22441029 TGATCGGTATTGATCCTGCATGTGTTGCGGAAATACCGCAGCTCTTTGTGAGCGTCCTGTTATA
1 TGATCAGTATTGATCCTACATGTATTGCAGAAATACCGCAGCTC-TTATGAGCGTCCCGATATA
* *
22441093 TGATCAGTATTGATCCTACATGTATTGCAGACATACCGTAGCTCTTATGAGCGTCCCGATATA
1 TGATCAGTATTGATCCTACATGTATTGCAGAAATACCGCAGCTCTTATGAGCGTCCCGATATA
22441156 TGA
1 TGA
22441159 CTCTTCATGA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
63 19 0.33
64 38 0.67
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (63 bp):
TGATCAGTATTGATCCTACATGTATTGCAGAAATACCGCAGCTCTTATGAGCGTCCCGATATA
Found at i:22441889 original size:24 final size:24
Alignment explanation
Indices: 22441857--22441914 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
22441847 TCAGTTCATT
22441857 TTGGTATAATTAGTAAAATTTCCC
1 TTGGTATAATTAGTAAAATTTCCC
22441881 TTGGTATAATTAGTAAAATTTCCC
1 TTGGTATAATTAGTAAAATTTCCC
22441905 TTGGTATAAT
1 TTGGTATAAT
22441915 GGCATGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (24 bp):
TTGGTATAATTAGTAAAATTTCCC
Found at i:22444916 original size:19 final size:17
Alignment explanation
Indices: 22444877--22444925 Score: 66
Period size: 16 Copynumber: 2.9 Consensus size: 17
22444867 ATAAATTTAA
22444877 AAATAATTATAAAAAAT
1 AAATAATTATAAAAAAT
22444894 -AATAATTATATTAAAAAT
1 AAATAATTATA--AAAAAT
22444912 AAATAA-TATAAAAA
1 AAATAATTATAAAAA
22444926 CATTCAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.48
18 10 0.34
19 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAATTATAAAAAAT
Found at i:22445514 original size:19 final size:20
Alignment explanation
Indices: 22445490--22445530 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
22445480 TTAAATTTTG
22445490 AATTCTAAAAAAT-AAATTA
1 AATTCTAAAAAATAAAATTA
* *
22445509 AATTCTTACAAATAAAATTA
1 AATTCTAAAAAATAAAATTA
22445529 AA
1 AA
22445531 AGGACTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AATTCTAAAAAATAAAATTA
Found at i:22452502 original size:10 final size:10
Alignment explanation
Indices: 22452487--22452520 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
22452477 CCTGTCCATG
22452487 GGCCTGGCCC
1 GGCCTGGCCC
22452497 GGCCTGGCCC
1 GGCCTGGCCC
22452507 GGCCTGGCCC
1 GGCCTGGCCC
22452517 GGCC
1 GGCC
22452521 CGAATATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.41, T:0.09
Consensus pattern (10 bp):
GGCCTGGCCC
Found at i:22452554 original size:13 final size:13
Alignment explanation
Indices: 22452538--22452565 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
22452528 AATAAATATA
22452538 TATTTTTTATTTT
1 TATTTTTTATTTT
22452551 TATTTTTTATTTT
1 TATTTTTTATTTT
22452564 TA
1 TA
22452566 AAATACTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:22452624 original size:27 final size:27
Alignment explanation
Indices: 22452572--22452626 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
22452562 TTTAAAATAC
* *
22452572 TTTTAAAATATTTTTTTATTTTTTTAT
1 TTTTAAAATATTTTTTTATATGTTTAT
22452599 TTTTAAAATAATTTTTTTA-ATGTTTAT
1 TTTTAAAAT-ATTTTTTTATATGTTTAT
22452626 T
1 T
22452627 AAAAAATAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTTAAAATATTTTTTTATATGTTTAT
Found at i:22460534 original size:19 final size:18
Alignment explanation
Indices: 22460522--22460564 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
22460512 AAAAAAACTC
22460522 TTTAAAAATAAAATAAAT
1 TTTAAAAATAAAATAAAT
*
22460540 TTTAAAAA-AATA-AAAT
1 TTTAAAAATAAAATAAAT
22460556 TTCTAAAAA
1 TT-TAAAAA
22460565 GTTATGCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 6 0.26
17 9 0.39
18 8 0.35
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAAAAATAAAATAAAT
Found at i:22460551 original size:15 final size:17
Alignment explanation
Indices: 22460531--22460564 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
22460521 CTTTAAAAAT
22460531 AAAAT-AAATTT-TAAA
1 AAAATAAAATTTCTAAA
22460546 AAAATAAAATTTCTAAA
1 AAAATAAAATTTCTAAA
22460563 AA
1 AA
22460565 GTTATGCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 6 0.35
17 6 0.35
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAATAAAATTTCTAAA
Found at i:22463445 original size:93 final size:93
Alignment explanation
Indices: 22463286--22463472 Score: 374
Period size: 93 Copynumber: 2.0 Consensus size: 93
22463276 AACCACGGGA
22463286 CCGTAGTCCGCTAAAAATTTTCACTATGTAAAGGAACTTGTTACACAGTAGACATGTACCTCGTA
1 CCGTAGTCCGCTAAAAATTTTCACTATGTAAAGGAACTTGTTACACAGTAGACATGTACCTCGTA
22463351 TGACCAACTTCAATAACTAACAGTAGTT
66 TGACCAACTTCAATAACTAACAGTAGTT
22463379 CCGTAGTCCGCTAAAAATTTTCACTATGTAAAGGAACTTGTTACACAGTAGACATGTACCTCGTA
1 CCGTAGTCCGCTAAAAATTTTCACTATGTAAAGGAACTTGTTACACAGTAGACATGTACCTCGTA
22463444 TGACCAACTTCAATAACTAACAGTAGTT
66 TGACCAACTTCAATAACTAACAGTAGTT
22463472 C
1 C
22463473 TTCAACACTA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 94 1.00
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (93 bp):
CCGTAGTCCGCTAAAAATTTTCACTATGTAAAGGAACTTGTTACACAGTAGACATGTACCTCGTA
TGACCAACTTCAATAACTAACAGTAGTT
Found at i:22466901 original size:86 final size:85
Alignment explanation
Indices: 22466765--22466959 Score: 245
Period size: 86 Copynumber: 2.3 Consensus size: 85
22466755 AATTTTTTCA
* * * * * *
22466765 AAAAAAAATAATCAAG-TCTTTTTTTT-TACTCATTTGGATATTTGAACTTTCAAAATGCATCAA
1 AAAAAAAACAATTAAGCCCTTTTTTTTGCACTCAATTGGATATTTGAACTTTCAAAATGCATAAA
**
22466828 AAAA-A-TTTCAAACCTTTT
66 AAAAGACCCTCAAACCTTTT
*
22466846 CAAAAAAAACAATTAAGCCCCTATTTTTTTGCACTCAATTGGGTATTTGAACTTTCAAAATGCAT
1 -AAAAAAAACAATTAAG-CCCT-TTTTTTTGCACTCAATTGGATATTTGAACTTTCAAAATGCAT
22466911 AAAAAAAGACCCTCAAACCTTTT
63 AAAAAAAGACCCTCAAACCTTTT
*
22466934 TAAAAAAACAATTAAGCCCTTTTTTT
1 AAAAAAAACAATTAAGCCCTTTTTTT
22466960 ATGAAAAATT
Statistics
Matches: 97, Mismatches: 10, Indels: 9
0.84 0.09 0.08
Matches are distributed among these distances:
82 14 0.14
84 2 0.02
85 13 0.13
86 41 0.42
87 16 0.16
88 11 0.11
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.35
Consensus pattern (85 bp):
AAAAAAAACAATTAAGCCCTTTTTTTTGCACTCAATTGGATATTTGAACTTTCAAAATGCATAAA
AAAAGACCCTCAAACCTTTT
Found at i:22467090 original size:9 final size:10
Alignment explanation
Indices: 22467058--22467101 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
22467048 CAAAATTAGG
*
22467058 AAAAATGTTA
1 AAAAATATTA
22467068 AAAAATATT-
1 AAAAATATTA
22467077 AAAAAT-TTA
1 AAAAATATTA
*
22467086 AAAAATATAA
1 AAAAATATTA
22467096 AAAAAT
1 AAAAAT
22467102 TGCAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 2 0.07
9 12 0.40
10 16 0.53
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAATATTA
Found at i:22467099 original size:18 final size:19
Alignment explanation
Indices: 22467058--22467099 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
22467048 CAAAATTAGG
*
22467058 AAAAATGTTAAAAAATATT
1 AAAAATGTTAAAAAATATA
22467077 AAAAAT-TTAAAAAATATA
1 AAAAATGTTAAAAAATATA
22467095 AAAAA
1 AAAAA
22467100 ATTGCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAATGTTAAAAAATATA
Found at i:22468060 original size:45 final size:44
Alignment explanation
Indices: 22467995--22468103 Score: 130
Period size: 45 Copynumber: 2.5 Consensus size: 44
22467985 CTAAGGGCAC
* * *
22467995 GTTTGGTTCACTGTATTGGAATAGAGGCGTAATAGTAAATCAAT-T
1 GTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGT-AATC-ATGT
* * *
22468040 GTTTGGTTGAATGTAATGGAATAGAGGCGTAATTGTATTCTTGT
1 GTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCATGT
*
22468084 GTTTGGTTGAATGGAATGGA
1 GTTTGGTTGAATGTAATGGA
22468104 GGTGTAATAG
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
43 1 0.02
44 23 0.41
45 32 0.57
ACGTcount: A:0.28, C:0.06, G:0.29, T:0.38
Consensus pattern (44 bp):
GTTTGGTTGAATGTAATGGAATAGAGGCGTAATAGTAATCATGT
Found at i:22468102 original size:44 final size:45
Alignment explanation
Indices: 22468011--22468103 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 45
22468001 TTCACTGTAT
*
22468011 TGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGTAA
1 TGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGGAA
* * *
22468056 TGGAATAGAGGCGTAATTGT-ATTC-TTGTGTTTGGTTGAATGGAA
1 TGGAATAGAGGCGTAATAGTAAATCAAT-TGTTTGGTTGAATGGAA
22468100 TGGA
1 TGGA
22468104 GGTGTAATAG
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.53
45 19 0.44
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.35
Consensus pattern (45 bp):
TGGAATAGAGGCGTAATAGTAAATCAATTGTTTGGTTGAATGGAA
Found at i:22468281 original size:18 final size:17
Alignment explanation
Indices: 22468260--22468294 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
22468250 TTATTATTAA
*
22468260 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
22468278 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
22468295 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:22468380 original size:120 final size:120
Alignment explanation
Indices: 22468235--22468748 Score: 811
Period size: 120 Copynumber: 4.3 Consensus size: 120
22468225 ATAATTTAAT
*
22468235 TATATTTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* *
22468300 ATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
*
22468355 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* *
22468420 ATAATCAATATTCTTATATGAATTTACTAAAATTATAATATATGATACTAT-AAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
*
22468474 TATAATTTGAA-ATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTT
1 TATAATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTT
* *
22468538 AAT-ATTAAGTATTCTTATATGAATTTACTAAAATTATAATATATAAT-CGTATAAAA
65 AATAATCAA-TATTCTTATATGAATTTACTAAAATCATAATATATAATAC-TATAAAA
* * * * *
22468594 TATATTTTAACATAATTACTATTAAATACAATTTAATAAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* *
22468659 ATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
*
22468714 TATAATTTAAAATAATTATTATTAAATATAATTTT
1 TATAATTTAACATAATTATTATTAAATAT-ATTTT
22468749 TCTAAATATA
Statistics
Matches: 366, Mismatches: 20, Indels: 15
0.91 0.05 0.04
Matches are distributed among these distances:
118 5 0.01
119 109 0.30
120 244 0.67
121 8 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
TATAATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
ATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
Found at i:22468401 original size:18 final size:17
Alignment explanation
Indices: 22468378--22468414 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
22468368 AATTATTATT
22468378 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
22468394 AAATATATGATTTAATA
1 AAATATATGATTTAATA
22468411 AAAT
1 AAAT
22468415 TCTTAATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:22468520 original size:18 final size:17
Alignment explanation
Indices: 22468497--22468533 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
22468487 AATTATTATT
22468497 AAATATAT--TTTAATTA
1 AAATATATGATTTAA-TA
22468513 AAATATATGATTTAATA
1 AAATATATGATTTAATA
22468530 AAAT
1 AAAT
22468534 TCTTAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 8 0.42
17 6 0.32
18 5 0.26
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (17 bp):
AAATATATGATTTAATA
Found at i:22468671 original size:239 final size:240
Alignment explanation
Indices: 22468235--22468748 Score: 818
Period size: 239 Copynumber: 2.1 Consensus size: 240
22468225 ATAATTTAAT
* *
22468235 TATATTTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
1 TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* *
22468300 ATAATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAATTTAA
66 ATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAA
* * * * * *
22468365 CATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTAATAATCAATA
131 CATAATTACTATTAAATACAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATA
* *
22468430 TTCTTATATGAATTTACTAAAATTATAATATATGATACTAT-AAA
196 TTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
* *
22468474 TATAATTTGAAATAATTATTATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTCTTA
1 TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
* * *
22468539 AT-ATTAAGTATTCTTATATGAATTTACTAAAATTATAATATATAAT-CGTATAAAATATATTTT
66 ATAATCAA-TATTCTTATATGAATTTACTAAAATCATAATATATAATAC-TATAAAATATAATTT
*
22468602 AACATAATTACTATTAAATACAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
129 AACATAATTACTATTAAATACAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAA
22468667 TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
194 TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
22468714 TATAATTTAAAATAATTATTATTAAATATAATTTT
1 TATAATTTAAAATAATTATTATTAAATAT-ATTTT
22468749 TCTAAATATA
Statistics
Matches: 252, Mismatches: 19, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
238 5 0.02
239 211 0.84
240 31 0.12
241 5 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (240 bp):
TATAATTTAAAATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTA
ATAATCAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAATTTAA
CATAATTACTATTAAATACAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAATAAATA
TTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA
Found at i:22471402 original size:25 final size:25
Alignment explanation
Indices: 22471368--22471495 Score: 112
Period size: 25 Copynumber: 4.9 Consensus size: 25
22471358 AATAAGTGGG
*
22471368 GCCCACCGATTAGGGGTGTATTTAC
1 GCCCACCGATTAGGGGTGTATTGAC
*
22471393 GCCCACCGATTAGGGGTGTATTGGC
1 GCCCACCGATTAGGGGTGTATTGAC
** * * * * **
22471418 AAACAACGGATTAGAGGCGTAATAAGTGGG
1 -GCCCACCGATTAG-GG-GT-GT-ATTGAC
*
22471448 GCCCACCGATTAGGGGTGTATTTAC
1 GCCCACCGATTAGGGGTGTATTGAC
22471473 GCCCACCGATTAGGGGTGTATTG
1 GCCCACCGATTAGGGGTGTATTG
22471496 GCTATGCCAA
Statistics
Matches: 79, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 47 0.59
26 10 0.13
27 4 0.05
28 4 0.05
29 10 0.13
30 4 0.05
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (25 bp):
GCCCACCGATTAGGGGTGTATTGAC
Found at i:22471432 original size:80 final size:80
Alignment explanation
Indices: 22471337--22471497 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
22471327 TACATTGAAC
22471337 CAAACAACGGATTAGAGGCGTAATAAGTGGGGCCCACCGATTAGGGGTGTATTTACGCCCACCGA
1 CAAACAACGGATTAGAGGCGTAATAAGTGGGGCCCACCGATTAGGGGTGTATTTACGCCCACCGA
22471402 TTAGGGGTGTATTGG
66 TTAGGGGTGTATTGG
22471417 CAAACAACGGATTAGAGGCGTAATAAGTGGGGCCCACCGATTAGGGGTGTATTTACGCCCACCGA
1 CAAACAACGGATTAGAGGCGTAATAAGTGGGGCCCACCGATTAGGGGTGTATTTACGCCCACCGA
22471482 TTAGGGGTGTATTGG
66 TTAGGGGTGTATTGG
22471497 C
1 C
22471498 TATGCCAATA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.26, C:0.19, G:0.32, T:0.22
Consensus pattern (80 bp):
CAAACAACGGATTAGAGGCGTAATAAGTGGGGCCCACCGATTAGGGGTGTATTTACGCCCACCGA
TTAGGGGTGTATTGG
Found at i:22471672 original size:32 final size:32
Alignment explanation
Indices: 22471596--22471673 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 32
22471586 AATGATTTAC
*
22471596 TGAAAATATTTTCTGGTGTTTGGATGAATCTG
1 TGAAAATATTTTCTGCTGTTTGGATGAATCTG
*
22471628 TGTAAAATATTTTCTGCTGTTTGGCA-GATTTCT-
1 TG-AAAATATTTTCTGCTGTTTGG-ATGA-ATCTG
22471661 TGAAAATATTTTC
1 TGAAAATATTTTC
22471674 CAGAAAAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
32 13 0.32
33 24 0.59
34 4 0.10
ACGTcount: A:0.26, C:0.09, G:0.19, T:0.46
Consensus pattern (32 bp):
TGAAAATATTTTCTGCTGTTTGGATGAATCTG
Found at i:22473020 original size:35 final size:35
Alignment explanation
Indices: 22472973--22473071 Score: 162
Period size: 35 Copynumber: 2.8 Consensus size: 35
22472963 TGTCAATCAT
*
22472973 TTCAATATCCAACAAGCTTAAAACATAATAACAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAAAAA
* *
22473008 TTCAATACCCAACAAACTTAAAACATAATAAAAAA
1 TTCAATATCCAACAAGCTTAAAACATAATAAAAAA
*
22473043 TTCAATATCCAACAAGCTTAAAGCATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
22473072 CAATATCTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.54, C:0.20, G:0.03, T:0.23
Consensus pattern (35 bp):
TTCAATATCCAACAAGCTTAAAACATAATAAAAAA
Found at i:22473096 original size:27 final size:27
Alignment explanation
Indices: 22473044--22473098 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
22473034 AATAAAAAAT
*
22473044 TCAATATCCAACAAGCTTAAAGCATAA
1 TCAATATCCAACAAGATTAAAGCATAA
* *
22473071 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCCAACAAGATTAAAG-CATAA
22473098 T
1 T
22473099 ATCAAAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.49, C:0.20, G:0.05, T:0.25
Consensus pattern (27 bp):
TCAATATCCAACAAGATTAAAGCATAA
Found at i:22475065 original size:36 final size:36
Alignment explanation
Indices: 22475017--22475092 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
22475007 AATATTTAAC
*
22475017 ATAT-AAAAAATATACATTAATAGAAATTTGACTAT
1 ATATAAAAAAATATACATTAACAGAAATTTGACTAT
* *
22475052 TTATAAAAAAATATACATTAACAGAAATTTGATTAT
1 ATATAAAAAAATATACATTAACAGAAATTTGACTAT
22475088 ATATA
1 ATATA
22475093 TGAGTTAGTA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 3 0.08
36 33 0.92
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (36 bp):
ATATAAAAAAATATACATTAACAGAAATTTGACTAT
Found at i:22476719 original size:16 final size:16
Alignment explanation
Indices: 22476698--22476734 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
22476688 CAAACAAGTT
*
22476698 TACTTAGAATTCTCAA
1 TACTTAGAATTATCAA
22476714 TACTTAGAATTATCAA
1 TACTTAGAATTATCAA
22476730 TACTT
1 TACTT
22476735 GTATATCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (16 bp):
TACTTAGAATTATCAA
Found at i:22477942 original size:30 final size:31
Alignment explanation
Indices: 22477908--22477975 Score: 77
Period size: 30 Copynumber: 2.2 Consensus size: 31
22477898 TTGCTCAAGA
* * *
22477908 GTAAATACCGA-AAATTTGAGGGGTTAA-AGT
1 GTAAATA-CGAGAAATTTGAAGGATCAATAGT
*
22477938 GTAAATATGAGAAATTTGAAGGATCAATAGT
1 GTAAATACGAGAAATTTGAAGGATCAATAGT
22477969 GTAAATA
1 GTAAATA
22477976 TTTTAAGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 2 0.06
30 20 0.62
31 10 0.31
ACGTcount: A:0.44, C:0.04, G:0.24, T:0.28
Consensus pattern (31 bp):
GTAAATACGAGAAATTTGAAGGATCAATAGT
Found at i:22478761 original size:16 final size:16
Alignment explanation
Indices: 22478740--22478774 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
22478730 GCACTAAAAT
22478740 AGTTTTGGACAGCAAC
1 AGTTTTGGACAGCAAC
22478756 AGTTTTGGACAGCAAC
1 AGTTTTGGACAGCAAC
22478772 AGT
1 AGT
22478775 AGGTTAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (16 bp):
AGTTTTGGACAGCAAC
Found at i:22479642 original size:57 final size:60
Alignment explanation
Indices: 22479530--22479665 Score: 181
Period size: 57 Copynumber: 2.3 Consensus size: 60
22479520 AATTGACGGT
*
22479530 AAAAAGGATCTAGCCCAGATGGGTGATCCTATCCTGATATAGCCCTCTCGAAGAATATGTGTG
1 AAAAAGGATCTAGCCCAGATGGGTGATCC-AT-CTGATATAGCCCTCCCGAAGAATATGTG-G
*
22479593 AAAAA-GATCTAGCCCGGATGGGTGAT-C-T-TGATATAGCCCTCCCGAAGAATATGTGG
1 AAAAAGGATCTAGCCCAGATGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
* *
22479649 AAAATGGATTTAGCCCA
1 AAAAAGGATCTAGCCCA
22479666 CACGGGTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
56 5 0.07
57 35 0.52
59 1 0.01
61 1 0.01
62 20 0.30
63 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (60 bp):
AAAAAGGATCTAGCCCAGATGGGTGATCCATCTGATATAGCCCTCCCGAAGAATATGTGG
Found at i:22479908 original size:67 final size:67
Alignment explanation
Indices: 22479800--22479930 Score: 244
Period size: 67 Copynumber: 2.0 Consensus size: 67
22479790 TTTATATTAC
22479800 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCTCTT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCTCTT
22479865 GT
66 GT
**
22479867 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGTGGGAGTGTGCTCTCT
1 AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCTCT
22479931 GAATTGGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 62 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.28
Consensus pattern (67 bp):
AGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCAGGAGTGTGCTCTCTT
GT
Found at i:22481690 original size:20 final size:21
Alignment explanation
Indices: 22481667--22481707 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
22481657 ATTGGGGGTT
22481667 TAAGGTTTTA-TTTTTTAAAG
1 TAAGGTTTTATTTTTTTAAAG
22481687 TAAGGTTTTATTTTTTTAAAG
1 TAAGGTTTTATTTTTTTAAAG
22481708 GTTTTGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (21 bp):
TAAGGTTTTATTTTTTTAAAG
Found at i:22485315 original size:25 final size:25
Alignment explanation
Indices: 22485287--22485342 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
22485277 AAGTATTATA
* *
22485287 CAGAGAATATAAATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
* **
22485312 CAGAGAGCACCGATGTGCTAATAAT
1 CAGAGAACACAAATGTGCTAATAAT
22485337 CAGAGA
1 CAGAGA
22485343 GTACGCTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (25 bp):
CAGAGAACACAAATGTGCTAATAAT
Found at i:22485381 original size:46 final size:46
Alignment explanation
Indices: 22485329--22485451 Score: 198
Period size: 46 Copynumber: 2.7 Consensus size: 46
22485319 CACCGATGTG
* *
22485329 CTAATAATCAGAGAGTACGCTAAACTCTCTTAATATCCTAATAGTT
1 CTAATAATCAGAGAGCACGCTAAACTCCCTTAATATCCTAATAGTT
*
22485375 CTAATAATCAGAGAGCATGCTAAACTCCCTTAATATCCTAATAGTT
1 CTAATAATCAGAGAGCACGCTAAACTCCCTTAATATCCTAATAGTT
22485421 C---TAATCAGAGAGCACGCTAAACTCCCTTAAT
1 CTAATAATCAGAGAGCACGCTAAACTCCCTTAAT
22485452 CTTTTCAGAG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
43 29 0.40
46 44 0.60
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (46 bp):
CTAATAATCAGAGAGCACGCTAAACTCCCTTAATATCCTAATAGTT
Found at i:22485954 original size:20 final size:20
Alignment explanation
Indices: 22485931--22485980 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
22485921 AGAATAGAGT
*
22485931 AGAGCAGAGCAGAAC-GAAAC
1 AGAGCAGAACAGAACAG-AAC
22485951 AGAGCAGAACAGAACAGAAC
1 AGAGCAGAACAGAACAGAAC
22485971 AGAGCAGAAC
1 AGAGCAGAAC
22485981 GGAATAAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.52, C:0.20, G:0.28, T:0.00
Consensus pattern (20 bp):
AGAGCAGAACAGAACAGAAC
Found at i:22485955 original size:15 final size:15
Alignment explanation
Indices: 22485935--22485980 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
22485925 TAGAGTAGAG
22485935 CAGAGCAGAAC-GAAA
1 CAGAGCAGAACAG-AA
22485950 CAGAGCAGAACAGAA
1 CAGAGCAGAACAGAA
* *
22485965 CAGAACAGAGCAGAA
1 CAGAGCAGAACAGAA
22485980 C
1 C
22485981 GGAATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 27 0.96
16 1 0.04
ACGTcount: A:0.52, C:0.22, G:0.26, T:0.00
Consensus pattern (15 bp):
CAGAGCAGAACAGAA
Found at i:22485961 original size:10 final size:10
Alignment explanation
Indices: 22485948--22485980 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
22485938 AGCAGAACGA
22485948 AACAGAGCAG
1 AACAGAGCAG
*
22485958 AACAGAACAG
1 AACAGAGCAG
22485968 AACAGAGCAG
1 AACAGAGCAG
22485978 AAC
1 AAC
22485981 GGAATAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.55, C:0.21, G:0.24, T:0.00
Consensus pattern (10 bp):
AACAGAGCAG
Found at i:22488406 original size:15 final size:15
Alignment explanation
Indices: 22488381--22488415 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
22488371 GAGTCTATTT
*
22488381 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
22488395 TAATTAATATTAAGA
1 TAATTAATATTAAGA
22488410 TAATTA
1 TAATTA
22488416 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:22495326 original size:5 final size:5
Alignment explanation
Indices: 22495316--22495343 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
22495306 AGTGAATAGA
22495316 ACAAT ACAAT ACAAT ACAAT ACAAT ACA
1 ACAAT ACAAT ACAAT ACAAT ACAAT ACA
22495344 TGTATTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.21, G:0.00, T:0.18
Consensus pattern (5 bp):
ACAAT
Found at i:22498051 original size:24 final size:24
Alignment explanation
Indices: 22498019--22498064 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
22498009 TTACAATGTC
22498019 ACTTATCTTCAGTTTGAACTTTAG
1 ACTTATCTTCAGTTTGAACTTTAG
22498043 ACTTATCTTCAGTTTGAACTTT
1 ACTTATCTTCAGTTTGAACTTT
22498065 GGACAATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.17, G:0.11, T:0.48
Consensus pattern (24 bp):
ACTTATCTTCAGTTTGAACTTTAG
Found at i:22500731 original size:17 final size:17
Alignment explanation
Indices: 22500679--22500731 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 17
22500669 TATGAAAACA
* *
22500679 TAATCTTCGAGGATATG
1 TAATCTTAGAAGATATG
*
22500696 TAATCGTAGATATGATATG
1 TAATCTTAGA-A-GATATG
22500715 TAATCTTAGAAGATATG
1 TAATCTTAGAAGATATG
22500732 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 14 0.47
18 1 0.03
19 15 0.50
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (17 bp):
TAATCTTAGAAGATATG
Found at i:22500731 original size:22 final size:21
Alignment explanation
Indices: 22500703--22500760 Score: 80
Period size: 22 Copynumber: 2.7 Consensus size: 21
22500693 ATGTAATCGT
*
22500703 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
22500724 AAGATATGATTTTGTAATCTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
22500747 AGATTTGATTTGTA
1 AGATATGATTTGTA
22500761 GATACTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 6 0.18
22 15 0.45
23 12 0.36
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.43
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Found at i:22505863 original size:22 final size:21
Alignment explanation
Indices: 22505835--22505892 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
22505825 ATGCAATCGC
*
22505835 AGATATGATATGTAATCTTAG
1 AGATATGATTTGTAATCTTAG
*
22505856 AAGATATGATTTTGTAATTTTAG
1 -AGATATGA-TTTGTAATCTTAG
*
22505879 AGATTTGATTTGTA
1 AGATATGATTTGTA
22505893 GATACCTTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 15 0.47
23 11 0.34
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (21 bp):
AGATATGATTTGTAATCTTAG
Done.