Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A04
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: 82679320
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4050000 characters in sequence are not A, C, G, or T
File 50 of 255
Found at i:14145508 original size:10 final size:10
Alignment explanation
Indices: 14145492--14145549 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
14145482 CAACTCCGAC
14145492 CAGCTCAATT
1 CAGCTCAATT
* *
14145502 GAGCTCATTT
1 CAGCTCAATT
14145512 CAGCTCAA-T
1 CAGCTCAATT
14145521 CGAGCTCAATT
1 C-AGCTCAATT
*
14145532 TAGCTACAATT
1 CAGCT-CAATT
14145543 CAGCTCA
1 CAGCTCA
14145550 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:14145515 original size:20 final size:20
Alignment explanation
Indices: 14145492--14145552 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
14145482 CAACTCCGAC
14145492 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
14145512 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
14145533 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
14145553 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:14149910 original size:13 final size:13
Alignment explanation
Indices: 14149892--14149916 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14149882 TGGTCATCAT
14149892 GGTGTGAACACAA
1 GGTGTGAACACAA
14149905 GGTGTGAACACA
1 GGTGTGAACACA
14149917 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:14154156 original size:15 final size:14
Alignment explanation
Indices: 14154138--14154188 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 14
14154128 TTTAACTTGA
14154138 TTTTTTTTGCTCACC
1 TTTTTTTTGCTCA-C
14154153 TTTTTTTTTGCTCGA-
1 -TTTTTTTTGCTC-AC
14154168 TTTTTTTT--TCAC
1 TTTTTTTTGCTCAC
14154180 TTTTTTTTG
1 TTTTTTTTG
14154189 AATTTTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
11 1 0.03
12 10 0.31
14 8 0.25
16 12 0.38
17 1 0.03
ACGTcount: A:0.06, C:0.16, G:0.08, T:0.71
Consensus pattern (14 bp):
TTTTTTTTGCTCAC
Found at i:14154158 original size:30 final size:27
Alignment explanation
Indices: 14154116--14154187 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 27
14154106 CTCGCAAAAC
*
14154116 TTTTCACTTTTTTTTAACTTGATTTTT
1 TTTTCACTTTTTTTTAACTCGATTTTT
**
14154143 TTTGCTCACCTTTTTTTTTGCTCGATTTTT
1 TTT--TCA-CTTTTTTTTAACTCGATTTTT
14154173 TTTTCACTTTTTTTT
1 TTTTCACTTTTTTTT
14154188 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 12 0.31
28 3 0.08
29 3 0.08
30 21 0.54
ACGTcount: A:0.10, C:0.15, G:0.06, T:0.69
Consensus pattern (27 bp):
TTTTCACTTTTTTTTAACTCGATTTTT
Found at i:14154230 original size:10 final size:11
Alignment explanation
Indices: 14154169--14154236 Score: 57
Period size: 12 Copynumber: 5.8 Consensus size: 11
14154159 TTTGCTCGAT
* *
14154169 TTTTTTTTCAC
1 TTTTTTTTGAA
14154180 TTTTTTTTGAA
1 TTTTTTTTGAA
*
14154191 TTTTTTTTCAATCAA
1 -TTTTTTT---TGAA
14154206 TTTTTTTTCGAA
1 TTTTTTTT-GAA
14154218 TTTTTTTTG-A
1 TTTTTTTTGAA
14154228 TTTTTTTTG
1 TTTTTTTTG
14154237 TTACTCCAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
10 10 0.21
11 11 0.23
12 17 0.35
14 7 0.15
15 3 0.06
ACGTcount: A:0.15, C:0.07, G:0.06, T:0.72
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:14155300 original size:13 final size:13
Alignment explanation
Indices: 14155282--14155306 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14155272 TGGTCATCAT
14155282 GGTGTGAACACAA
1 GGTGTGAACACAA
14155295 GGTGTGAACACA
1 GGTGTGAACACA
14155307 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:14157113 original size:6 final size:6
Alignment explanation
Indices: 14157102--14157127 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
14157092 AGTTGTAAAG
14157102 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
14157128 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:14160910 original size:6 final size:6
Alignment explanation
Indices: 14160899--14160924 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
14160889 AGTTGTAAAG
14160899 TTTTAT TTTTAT TTTTAT TTTTAT TT
1 TTTTAT TTTTAT TTTTAT TTTTAT TT
14160925 ATTTATTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:14161966 original size:20 final size:20
Alignment explanation
Indices: 14161943--14161996 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14161933 AGTTTTTCCT
*
14161943 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14161963 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14161983 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14161997 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14161977 original size:30 final size:30
Alignment explanation
Indices: 14161942--14162016 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
14161932 TAGTTTTTCC
14161942 TAGCTCGATTT-AGCTCACA-TGAGCTTAATT
1 TAGCTCG-TTTGAGCTCA-ATTGAGCTTAATT
* *
14161972 TAGCTCGTTTGAGCTCAATTTAGCTTACTT
1 TAGCTCGTTTGAGCTCAATTGAGCTTAATT
14162002 TAGCTCGTTTGAGCT
1 TAGCTCGTTTGAGCT
14162017 TGGCTTAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (30 bp):
TAGCTCGTTTGAGCTCAATTGAGCTTAATT
Found at i:14162006 original size:20 final size:20
Alignment explanation
Indices: 14161942--14162007 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
14161932 TAGTTTTTCC
* * *
14161942 TAGCTCGATTTAGCTCACAT
1 TAGCTCAATTTAGCTTACTT
* *
14161962 GAGCTTAATTTAGC-T-CGTT
1 TAGCTCAATTTAGCTTAC-TT
14161981 TGAGCTCAATTTAGCTTACTT
1 T-AGCTCAATTTAGCTTACTT
14162002 TAGCTC
1 TAGCTC
14162008 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
TAGCTCAATTTAGCTTACTT
Found at i:14163663 original size:13 final size:13
Alignment explanation
Indices: 14163607--14163667 Score: 61
Period size: 14 Copynumber: 4.6 Consensus size: 13
14163597 AAAAAAAATC
14163607 AAAAAAAAATTCGA
1 AAAAAAAAATT-GA
14163621 AAAAAAAAATTGA
1 AAAAAAAAATTGA
** *
14163634 TTGAAAAAAATT-C
1 -AAAAAAAAATTGA
*
14163647 AAAAAAAAAGTGA
1 AAAAAAAAATTGA
14163660 AAAAAAAA
1 AAAAAAAA
14163668 TCGAGCAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
12 8 0.21
13 10 0.26
14 20 0.53
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAAAAATTGA
Found at i:14163676 original size:27 final size:27
Alignment explanation
Indices: 14163646--14163717 Score: 83
Period size: 27 Copynumber: 2.6 Consensus size: 27
14163636 GAAAAAAATT
*
14163646 CAAAAAAAAAGTGAAAAAAAAATCGAG
1 CAAAAAAAAAGTGAAAAAAAAATCAAG
*
14163673 CAAAAAAAAAGGTGACCAAAAAAATCAAG
1 CAAAAAAAAA-GTGA-AAAAAAAATCAAG
**
14163702 -TTAAAAAAAGTGAAAA
1 CAAAAAAAAAGTGAAAA
14163718 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
26 2 0.05
27 14 0.37
28 11 0.29
29 11 0.29
ACGTcount: A:0.68, C:0.08, G:0.14, T:0.10
Consensus pattern (27 bp):
CAAAAAAAAAGTGAAAAAAAAATCAAG
Found at i:14163680 original size:39 final size:39
Alignment explanation
Indices: 14163597--14163682 Score: 95
Period size: 38 Copynumber: 2.2 Consensus size: 39
14163587 TTGGAGTAAC
* * **
14163597 AAAAAAAATCAAAAAAAAATTCGAAAAAAAAAATTGATTG
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAAATCGA-CA
*
14163637 AAAAAAATTCAAAAAAAAAGT-G-AAAAAAAAATCGAGCA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAAATCGA-CA
14163675 AAAAAAAA
1 AAAAAAAA
14163683 GGTGACCAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 19 0.49
39 1 0.03
40 19 0.49
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.13
Consensus pattern (39 bp):
AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAAATCGACA
Found at i:14163707 original size:29 final size:28
Alignment explanation
Indices: 14163647--14163717 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
14163637 AAAAAAATTC
*
14163647 AAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCA
* *
14163675 AAAAAAAAGGTGACCAAAAAAATCAAG--
1 AAAAAAAAAGTGA-AAAAAAAATCAAGCA
**
14163702 TTAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
14163718 GTCTTGCGAG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
26 2 0.06
27 10 0.29
28 12 0.34
29 11 0.31
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:14164770 original size:17 final size:18
Alignment explanation
Indices: 14164738--14164771 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14164728 AAAAGAGAGT
*
14164738 GAGATTGAAGGAAGAAAC
1 GAGAGTGAAGGAAGAAAC
14164756 GAGAGTGAA-GAAGAAA
1 GAGAGTGAAGGAAGAAA
14164772 GGAGTGTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.53, C:0.03, G:0.35, T:0.09
Consensus pattern (18 bp):
GAGAGTGAAGGAAGAAAC
Found at i:14166059 original size:20 final size:20
Alignment explanation
Indices: 14166036--14166089 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14166026 AGTTTTTCCT
*
14166036 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14166056 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14166076 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14166090 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14166070 original size:30 final size:30
Alignment explanation
Indices: 14166035--14166109 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
14166025 TAGTTTTTCC
14166035 TAGCTCGATTT-AGCTCACA-TGAGCTTAATT
1 TAGCTCG-TTTGAGCTCA-ATTGAGCTTAATT
* *
14166065 TAGCTCGTTTGAGCTCAATTTAGCTTACTT
1 TAGCTCGTTTGAGCTCAATTGAGCTTAATT
14166095 TAGCTCGTTTGAGCT
1 TAGCTCGTTTGAGCT
14166110 TGGCTTAAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 37 0.90
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (30 bp):
TAGCTCGTTTGAGCTCAATTGAGCTTAATT
Found at i:14166099 original size:20 final size:20
Alignment explanation
Indices: 14166035--14166100 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
14166025 TAGTTTTTCC
* * *
14166035 TAGCTCGATTTAGCTCACAT
1 TAGCTCAATTTAGCTTACTT
* *
14166055 GAGCTTAATTTAGC-T-CGTT
1 TAGCTCAATTTAGCTTAC-TT
14166074 TGAGCTCAATTTAGCTTACTT
1 T-AGCTCAATTTAGCTTACTT
14166095 TAGCTC
1 TAGCTC
14166101 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.21, G:0.17, T:0.39
Consensus pattern (20 bp):
TAGCTCAATTTAGCTTACTT
Found at i:14176201 original size:26 final size:27
Alignment explanation
Indices: 14176172--14176231 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
14176162 CCACATATAT
*
14176172 ATATCTGT-TCTGGTGGCCTAGCCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
* * *
14176198 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGTATCTGGTGACCTAGCCACA
14176225 ATATCTG
1 ATATCTG
14176232 GCAGCTCGCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (27 bp):
ATATCTGTATCTGGTGACCTAGCCACA
Found at i:14178107 original size:35 final size:35
Alignment explanation
Indices: 14178042--14178221 Score: 182
Period size: 35 Copynumber: 5.1 Consensus size: 35
14178032 TACTTACTTG
* *
14178042 TATGGCCGAATACT-CAAGGTTCATTATATCATCACA
1 TATGGCCAAATA-TACAA-GTTCAATATATCATCACA
* *
14178078 TATGGCCAAATATACAAGTACAATATATCATCATA
1 TATGGCCAAATATACAAGTTCAATATATCATCACA
* * * *
14178113 TATGACCAAATATACAAGCTCAATAAAACATCACA
1 TATGGCCAAATATACAAGTTCAATATATCATCACA
* * * * * *
14178148 TGTAGTCAAATATTCAAGTTTAATATAACATCACA
1 TATGGCCAAATATACAAGTTCAATATATCATCACA
* * *
14178183 TGTGGCCAAATATACAAGTTCAACATGTCATCACA
1 TATGGCCAAATATACAAGTTCAATATATCATCACA
14178218 TATG
1 TATG
14178222 TACATACCTA
Statistics
Matches: 117, Mismatches: 26, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
35 103 0.88
36 14 0.12
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (35 bp):
TATGGCCAAATATACAAGTTCAATATATCATCACA
Found at i:14183330 original size:27 final size:27
Alignment explanation
Indices: 14183213--14183347 Score: 144
Period size: 27 Copynumber: 5.0 Consensus size: 27
14183203 CAAAATTATT
* * *
14183213 GAAATACCCCTATAGGGTAGAATTACT
1 GAAATACCCTTGTAGGGTAGAATTACC
* * *
14183240 GAAATACCCCTATAAGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* * * *
14183267 GAAATACACTTGTAAGGTAGAAATACT
1 GAAATACCCTTGTAGGGTAGAATTACC
14183294 GAAATACCCTTGTAGGGTAGAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
* ** *
14183321 GAGATACCCTTGGGGGGTAAAATTACC
1 GAAATACCCTTGTAGGGTAGAATTACC
14183348 ATTTTGCCCC
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (27 bp):
GAAATACCCTTGTAGGGTAGAATTACC
Found at i:14183887 original size:22 final size:22
Alignment explanation
Indices: 14183843--14183907 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
14183833 GCCAATTATT
* * * *
14183843 CTGATTATGGCTTTGCGCAAAC
1 CTGAATATGGCTCTGTGCCAAC
14183865 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-ATATGGCTCTGTGCCAAC
* *
14183887 CTGATTATGGCTGTGTGCCAA
1 CTGAATATGGCTCTGTGCCAA
14183908 ACGTACTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.31
Consensus pattern (22 bp):
CTGAATATGGCTCTGTGCCAAC
Found at i:14184061 original size:216 final size:217
Alignment explanation
Indices: 14183682--14184075 Score: 490
Period size: 216 Copynumber: 1.8 Consensus size: 217
14183672 TATCGAAGAT
* * *
14183682 TGTGTGCCAAACATATTTGCCTAAGGCTATGTGCCAATATATGATTATTGACGAATCTGTGTCGA
1 TGTGTGCCAAACATACTTGCCTAAGGATATGTGCCAATATATGATTAATGACGAATCTGTGTCGA
* * * * *
14183747 TCATATTTACTCAAGGCCTTGTGCCGACTATATTACCGTCGCTGCTGGCTATGTGCCTAACATGA
66 TCACATTTACTCAAGGACTTGTGCCGACTATATTACCGTAGCTGATGGCTATGTGCCTAACATAA
*
14183812 TACAACTACCAATGGCTTAAAGCCAATTATTCTGATT-A-TGGCTTTGCGCAAACCTACATATGG
131 TACAACTACCAATGGCTTAAAGCCAAGTATTCTG-TTAAGTGGCTTTGCGCAAACCTACATATGG
14183875 CTCTGTGCCAACCTGATTATGGC
195 CTCTGTGCCAACCTGATTATGGC
* * * *
14183898 TGTGTGCCAAACGTACTTGCCTAAGGATATGTGCCAATATATGGTTAATGATGACTCTGTGTCGA
1 TGTGTGCCAAACATACTTGCCTAAGGATATGTGCCAATATATGATTAATGACGAATCTGTGTCGA
* ** * *
14183963 TCACATTTAC-CTAGGACTGTGTGCCGGTTATGTTACTC-TAGTTGATGGCTATGTGCCTAACAT
66 TCACATTTACTCAAGGACT-TGTGCCGACTATATTAC-CGTAGCTGATGGCTATGTGCCTAACAT
* ** * * *** *
14184026 AATGCAGTTATCGATGGCTTTGTGCCACGTATTCTGTTAAGTGGCTTTGC
129 AATACAACTACCAATGGCTTAAAGCCAAGTATTCTGTTAAGTGGCTTTGC
14184076 CACATTATCT
Statistics
Matches: 147, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
215 8 0.05
216 129 0.88
217 10 0.07
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.34
Consensus pattern (217 bp):
TGTGTGCCAAACATACTTGCCTAAGGATATGTGCCAATATATGATTAATGACGAATCTGTGTCGA
TCACATTTACTCAAGGACTTGTGCCGACTATATTACCGTAGCTGATGGCTATGTGCCTAACATAA
TACAACTACCAATGGCTTAAAGCCAAGTATTCTGTTAAGTGGCTTTGCGCAAACCTACATATGGC
TCTGTGCCAACCTGATTATGGC
Found at i:14184096 original size:27 final size:27
Alignment explanation
Indices: 14184066--14184147 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
14184056 ATTCTGTTAA
* * *
14184066 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGTCACAATATCTGTTTCTG
* *
14184093 GTGGCTATGTAACAAATATCTGTATCTG
1 GTGGCTATGTCAC-AATATCTGTTTCTG
* *
14184121 GTGACTCTGTCACAATATCTG-TTCTG
1 GTGGCTATGTCACAATATCTGTTTCTG
14184147 G
1 G
14184148 CAGCCATGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
26 5 0.11
27 18 0.40
28 22 0.49
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (27 bp):
GTGGCTATGTCACAATATCTGTTTCTG
Found at i:14184274 original size:6 final size:6
Alignment explanation
Indices: 14184265--14184364 Score: 62
Period size: 6 Copynumber: 16.3 Consensus size: 6
14184255 TTGCATTCAC
* * * *
14184265 ATTCTG ATTCTG ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTA ATTCTA
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * *
14184314 ATTCTG -TCACCTG ATTCTG GTTCTG ATTCTC ATTTTG ATTCT- AGTTCTG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG
14184363 AT
1 AT
14184365 AATGTTTCTT
Statistics
Matches: 72, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
5 3 0.04
6 61 0.85
7 6 0.08
8 2 0.03
ACGTcount: A:0.19, C:0.20, G:0.13, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:14184355 original size:37 final size:37
Alignment explanation
Indices: 14184265--14184355 Score: 128
Period size: 37 Copynumber: 2.5 Consensus size: 37
14184255 TTGCATTCAC
*
14184265 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTG
1 ATTCTAATTCTGATTCTGTCACCTAATTCTGATTCTG
* * *
14184302 ATTCTAATTCTAATTCTGTCACCTGATTCTGGTTCTG
1 ATTCTAATTCTGATTCTGTCACCTAATTCTGATTCTG
* *
14184339 ATTCTCATTTTGATTCT
1 ATTCTAATTCTGATTCT
14184356 AGTTCTGATA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (37 bp):
ATTCTAATTCTGATTCTGTCACCTAATTCTGATTCTG
Found at i:14186048 original size:20 final size:20
Alignment explanation
Indices: 14186025--14186078 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14186015 AGTTTTTCCC
*
14186025 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14186045 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14186065 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14186079 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14186060 original size:30 final size:30
Alignment explanation
Indices: 14186025--14186098 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
14186015 AGTTTTTCCC
14186025 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
14186055 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
14186085 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
14186099 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:14186088 original size:20 final size:20
Alignment explanation
Indices: 14186025--14186089 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
14186015 AGTTTTTCCC
* * * *
14186025 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
14186045 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
14186064 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
14186085 AGCTC
1 AGCTC
14186090 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:14191755 original size:12 final size:12
Alignment explanation
Indices: 14191738--14191762 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14191728 TTTCACTCTT
14191738 CTCTTTTTCAAA
1 CTCTTTTTCAAA
14191750 CTCTTTTTCAAA
1 CTCTTTTTCAAA
14191762 C
1 C
14191763 CCTCTCTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:14192805 original size:12 final size:14
Alignment explanation
Indices: 14192777--14192810 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
14192767 TTCAATCAAT
14192777 TTTTTTTTTTCGAA
1 TTTTTTTTTTCGAA
14192791 TTTTTTTTTT-G-A
1 TTTTTTTTTTCGAA
14192803 TTTTTTTT
1 TTTTTTTT
14192811 GTTACCCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 1 0.05
14 10 0.50
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (14 bp):
TTTTTTTTTTCGAA
Found at i:14192893 original size:12 final size:12
Alignment explanation
Indices: 14192876--14192905 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
14192866 TACAACTCAA
14192876 TTTTTTTGA-TT
1 TTTTTTTGACTT
14192887 TTTTTTTGACTT
1 TTTTTTTGACTT
14192899 TTTTTTT
1 TTTTTTT
14192906 TACATTACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.07, C:0.03, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTGACTT
Found at i:14197112 original size:20 final size:20
Alignment explanation
Indices: 14197089--14197142 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
14197079 AGTTTTTCCC
*
14197089 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
14197109 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
14197129 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
14197143 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:14197124 original size:30 final size:30
Alignment explanation
Indices: 14197089--14197162 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
14197079 AGTTTTTCCC
14197089 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
14197119 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
14197149 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
14197163 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:14197152 original size:20 final size:20
Alignment explanation
Indices: 14197089--14197153 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
14197079 AGTTTTTCCC
* * * *
14197089 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
14197109 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
14197128 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
14197149 AGCTC
1 AGCTC
14197154 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:14202907 original size:11 final size:10
Alignment explanation
Indices: 14202882--14202942 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
14202872 ACCAATAGAA
14202882 TAAA-TGAGC
1 TAAATTGAGC
*
14202891 TGAATTGTAGC
1 TAAATTG-AGC
14202902 TAAATTGAGC
1 TAAATTGAGC
**
14202912 TCGATTGAGC
1 TAAATTGAGC
14202922 TGAAA-TGAGC
1 T-AAATTGAGC
*
14202932 TCAATTGAGC
1 TAAATTGAGC
14202942 T
1 T
14202943 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:14202943 original size:20 final size:20
Alignment explanation
Indices: 14202883--14202943 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
14202873 CCAATAGAAT
*
14202883 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
14202903 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
14202924 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
14202944 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:14204837 original size:22 final size:22
Alignment explanation
Indices: 14204809--14204852 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
14204799 TTTTGAACCA
*
14204809 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCATACCAAATCCC
*
14204831 TTACCATTTCATACCAATTCCC
1 TTACCATTTCATACCAAATCCC
14204853 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.34
Consensus pattern (22 bp):
TTACCATTTCATACCAAATCCC
Found at i:14208516 original size:33 final size:33
Alignment explanation
Indices: 14208478--14208540 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
14208468 GATTACTCAC
14208478 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
14208511 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
14208541 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:14208567 original size:21 final size:21
Alignment explanation
Indices: 14208538--14208593 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
14208528 CAAGCTCTCT
*
14208538 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
14208559 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
14208580 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
14208594 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:14208586 original size:14 final size:14
Alignment explanation
Indices: 14208537--14208593 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
14208527 TCAAGCTCTC
14208537 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
14208550 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
14208564 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
14208578 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
14208592 TT
1 TT
14208594 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:14208643 original size:11 final size:11
Alignment explanation
Indices: 14208629--14208657 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
14208619 TTTGCAATTT
14208629 TTTTCTTTTTG
1 TTTTCTTTTTG
14208640 TTTTC-TTTTG
1 TTTTCTTTTTG
14208650 TTTTCTTT
1 TTTTCTTT
14208658 CAATTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTCTTTTTG
Found at i:14208648 original size:16 final size:16
Alignment explanation
Indices: 14208602--14208653 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
14208592 TTCTCTCACT
14208602 TTTTTGATTTCTTTTC
1 TTTTTGATTTCTTTTC
14208618 -TTTTGCAATTT-TTTTC
1 TTTTTG--ATTTCTTTTC
* *
14208634 TTTTTGTTTTCTTTTG
1 TTTTTGATTTCTTTTC
14208650 TTTT
1 TTTT
14208654 CTTTCAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
15 8 0.27
16 13 0.43
17 9 0.30
ACGTcount: A:0.06, C:0.10, G:0.08, T:0.77
Consensus pattern (16 bp):
TTTTTGATTTCTTTTC
Found at i:14209741 original size:12 final size:12
Alignment explanation
Indices: 14209737--14209761 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14209727 TTTTTTTCAA
14209737 TTTTTTTGAATT
1 TTTTTTTGAATT
14209749 TTTTTTTGAATT
1 TTTTTTTGAATT
14209761 T
1 T
14209762 CTTCTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:14209858 original size:12 final size:12
Alignment explanation
Indices: 14209843--14209874 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
14209833 CCAACTCAAA
14209843 TTTTTTTTTGA-
1 TTTTTTTTTGAC
14209854 TTTTTTTTTGAC
1 TTTTTTTTTGAC
14209866 TTTTTTTTT
1 TTTTTTTTT
14209875 CGTTACGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.06, C:0.03, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTGAC
Found at i:14212931 original size:21 final size:22
Alignment explanation
Indices: 14212905--14212948 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
14212895 AAACGAGCTC
14212905 GTTGAGCTAAGTTGAG-TTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
* *
14212926 GTTGAGCTGATTTGAGCTTGAA
1 GTTGAGCTAAGTTGAGCTTGAA
14212948 G
1 G
14212949 GAGTATGCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.25, C:0.07, G:0.34, T:0.34
Consensus pattern (22 bp):
GTTGAGCTAAGTTGAGCTTGAA
Found at i:14219631 original size:20 final size:20
Alignment explanation
Indices: 14219585--14219631 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14219575 AGCTCGTTTC
*
14219585 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14219605 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14219625 CAGCTCA
1 CAGCTCA
14219632 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14224036 original size:20 final size:20
Alignment explanation
Indices: 14223991--14224036 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
14223981 GCTCGTTTCT
*
14223991 AGCTCACTCGAGCTCAAGTC
1 AGCTCACTCAAGCTCAAGTC
* * *
14224011 AACTCACTCAAGCTTAATTC
1 AGCTCACTCAAGCTCAAGTC
14224031 AGCTCA
1 AGCTCA
14224037 ATCTTAACCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.33, G:0.13, T:0.24
Consensus pattern (20 bp):
AGCTCACTCAAGCTCAAGTC
Found at i:14228630 original size:30 final size:30
Alignment explanation
Indices: 14228596--14228692 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
14228586 AGCTCACTCC
14228596 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
14228626 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
14228656 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
14228686 TAGCTCA
1 TAGCTCA
14228693 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:14230449 original size:13 final size:13
Alignment explanation
Indices: 14230430--14230463 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
14230420 AAGAAATTTA
*
14230430 GAAAAAAAAATTC
1 GAAAAAAAAAATC
14230443 -AAAAAAAAAATC
1 GAAAAAAAAAATC
14230455 GAAAAAAAA
1 GAAAAAAAA
14230464 GGAAAAAAAA
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:0.79, C:0.06, G:0.06, T:0.09
Consensus pattern (13 bp):
GAAAAAAAAAATC
Found at i:14232959 original size:37 final size:37
Alignment explanation
Indices: 14232908--14232978 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
14232898 CATTCTTGTA
14232908 AAGAGAAAACAAAGAAAA-GAAAAGAAAAAGAAAAAGC
1 AAGAGAAAACAAAGAAAATG-AAAGAAAAAGAAAAAGC
*
14232945 AAGAGAAGAA-AAAGAAAATGAAATAAAAAGAAAA
1 AAGAGAA-AACAAAGAAAATGAAAGAAAAAGAAAA
14232979 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (37 bp):
AAGAGAAAACAAAGAAAATGAAAGAAAAAGAAAAAGC
Found at i:14232978 original size:6 final size:6
Alignment explanation
Indices: 14232918--14232967 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
14232908 AAGAGAAAAC
*
14232918 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAGAA AATGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
14232967 A
1 A
14232968 TAAAAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
5 9 0.22
6 22 0.55
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.20, T:0.02
Consensus pattern (6 bp):
AAAGAA
Found at i:14235261 original size:30 final size:30
Alignment explanation
Indices: 14235227--14235323 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
14235217 AGCTCACTCC
14235227 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
14235257 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
14235287 CAGCTCAACTTTAGCTCACGAGCTAAAACT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
14235317 TAGCTCA
1 TAGCTCA
14235324 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:14237075 original size:15 final size:16
Alignment explanation
Indices: 14237049--14237090 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
14237039 CTTGTCAATC
14237049 TCTTTT-TTTTTCT-T
1 TCTTTTATTTTTCTCT
14237063 T-TTCTTATTTTTCTCT
1 TCTT-TTATTTTTCTCT
14237079 TCTTTTATTTTT
1 TCTTTTATTTTT
14237091 TTACAACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 2 0.08
14 3 0.12
15 7 0.29
16 10 0.42
17 2 0.08
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTATTTTTCTCT
Found at i:14241750 original size:24 final size:25
Alignment explanation
Indices: 14241697--14241750 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
14241687 CAAATTCTTT
* *
14241697 TTTTTTCATTTTCATCACTCGTTTC
1 TTTTTTCATTTTAATCACTCGTCTC
14241722 -TTTTTC-TTTTGAATCACTC-TCTC
1 TTTTTTCATTTT-AATCACTCGTCTC
14241745 TTTTTT
1 TTTTTT
14241751 TATCACTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 7 0.28
24 18 0.72
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (25 bp):
TTTTTTCATTTTAATCACTCGTCTC
Found at i:14246990 original size:20 final size:19
Alignment explanation
Indices: 14246967--14247031 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
14246957 AAGCTCAAAC
14246967 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
14246987 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
14247007 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
14247027 GAGCT
1 GAGCT
14247032 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:14253595 original size:20 final size:20
Alignment explanation
Indices: 14253549--14253595 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14253539 AGCTCGTTTC
*
14253549 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14253569 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14253589 CAGCTCA
1 CAGCTCA
14253596 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14255140 original size:9 final size:9
Alignment explanation
Indices: 14255126--14255160 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
14255116 AGAAGTGAAC
14255126 AAAAAAAG-
1 AAAAAAAGA
14255134 AAAAAAAGTA
1 AAAAAAAG-A
14255144 AAAAAAAGA
1 AAAAAAAGA
14255153 AAAAAAAG
1 AAAAAAAG
14255161 TGAAAAGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.86, C:0.00, G:0.11, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:14255159 original size:19 final size:19
Alignment explanation
Indices: 14255112--14255166 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 19
14255102 AAATTCGAAA
14255112 AAAAAGAAGTGAACAAAAAAAG
1 AAAAA-AAGTG-A-AAAAAAAG
14255134 AAAAAAAGT-AAAAAAAAG
1 AAAAAAAGTGAAAAAAAAG
14255152 AAAAAAAAGTGAAAA
1 -AAAAAAAGTGAAAA
14255167 GTCTTGTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.26
19 10 0.32
20 4 0.13
21 4 0.13
22 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.15, T:0.05
Consensus pattern (19 bp):
AAAAAAAGTGAAAAAAAAG
Found at i:14257841 original size:20 final size:20
Alignment explanation
Indices: 14257795--14257841 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
14257785 AGCTCGTTTC
*
14257795 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
14257815 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14257835 CAGCTCA
1 CAGCTCA
14257842 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14263313 original size:21 final size:22
Alignment explanation
Indices: 14263287--14263329 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
14263277 AACGAGCTCA
14263287 TTGAGCTAAGTTGAG-TTGAAG
1 TTGAGCTAAGTTGAGCTTGAAG
* *
14263308 TTGAGCTGATTTGAGCTTGAAG
1 TTGAGCTAAGTTGAGCTTGAAG
14263330 GAGTATGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.26, C:0.07, G:0.33, T:0.35
Consensus pattern (22 bp):
TTGAGCTAAGTTGAGCTTGAAG
Found at i:14270039 original size:16 final size:15
Alignment explanation
Indices: 14270019--14270060 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
14270009 AAAAAAAATC
14270019 GAAAAAAAAAATTAATT
1 GAAAAAAAAAATT--TT
*
14270036 -AAAAAAAATATTTT
1 GAAAAAAAAAATTTT
14270050 GAAAAAAAAAA
1 GAAAAAAAAAA
14270061 ATTGCATACG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 9 0.41
16 11 0.50
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (15 bp):
GAAAAAAAAAATTTT
Found at i:14270869 original size:15 final size:15
Alignment explanation
Indices: 14270837--14270870 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
14270827 GTTCAACGAA
*
14270837 GAGGCCAACGCAACC
1 GAGGCCAACGAAACC
*
14270852 GAGGCCAACGAAATC
1 GAGGCCAACGAAACC
14270867 GAGG
1 GAGG
14270871 GAGGTTCGAT
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:0.35, C:0.29, G:0.32, T:0.03
Consensus pattern (15 bp):
GAGGCCAACGAAACC
Found at i:14279096 original size:27 final size:27
Alignment explanation
Indices: 14279060--14279113 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
14279050 CACGTTTAAT
*
14279060 ATATTCTTTCCCATATCTTGTACTCTA
1 ATATTCTTTCCCATATATTGTACTCTA
14279087 ATATTCTTTCCCATATATTGTACTCTA
1 ATATTCTTTCCCATATATTGTACTCTA
14279114 TCATCAGACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATTCTTTCCCATATATTGTACTCTA
Found at i:14279278 original size:42 final size:43
Alignment explanation
Indices: 14279173--14279314 Score: 132
Period size: 43 Copynumber: 3.3 Consensus size: 43
14279163 TCGACTCTCG
* **
14279173 GACATGGTCTTACATGTAATTCAGTATCGATGCCTCTGTCCCA
1 GACATGGTCTTACATGTAAATCAGTATCGATGCCGATGTCCCA
* * *
14279216 GACAGGGTCTTACACG-AAATCAG-ATGTGATGCCGATGTCCC-
1 GACATGGTCTTACATGTAAATCAGTAT-CGATGCCGATGTCCCA
* *
14279257 GACATGGTCTTACATGTAAATCTCA-AATCGAGGCCTG-TGTCCCA
1 GACATGGTCTTACATGTAAA--TCAGTATCGATGCC-GATGTCCCA
*
14279301 GACACGGTCTTACA
1 GACATGGTCTTACA
14279315 CGATATCCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
41 16 0.20
42 21 0.26
43 25 0.31
44 19 0.23
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (43 bp):
GACATGGTCTTACATGTAAATCAGTATCGATGCCGATGTCCCA
Found at i:14279327 original size:43 final size:42
Alignment explanation
Indices: 14279198--14279332 Score: 132
Period size: 43 Copynumber: 3.2 Consensus size: 42
14279188 GTAATTCAGT
* * *
14279198 ATCGATGCCTCTGTCCCAGACAGGGTCTTACACGAAAT-CAG
1 ATCGATGCCTGTGTCCCAGACACGGTCTTACACGAAATCCAA
* * *
14279239 ATGTGATGCC-GATGTCCC-GACATGGTCTTACATGTAAATCTCAA
1 AT-CGATGCCTG-TGTCCCAGACACGGTCTTACACG-AAATC-CAA
* *
14279283 ATCGAGGCCTGTGTCCCAGACACGGTCTTACACGATATCCCAA
1 ATCGATGCCTGTGTCCCAGACACGGTCTTACACGAAAT-CCAA
14279326 ATCGATG
1 ATCGATG
14279333 TCAACGTTCC
Statistics
Matches: 75, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
41 16 0.21
42 16 0.21
43 23 0.31
44 20 0.27
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (42 bp):
ATCGATGCCTGTGTCCCAGACACGGTCTTACACGAAATCCAA
Found at i:14280232 original size:21 final size:20
Alignment explanation
Indices: 14280193--14280245 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
14280183 ATCAGCTCAC
*
14280193 TTGAGCTCGATTTATCTCGT
1 TTGAGCTCGATTTAGCTCGT
*
14280213 TTGAGCTTGAATTTAGCTCGT
1 TTGAGCTCG-ATTTAGCTCGT
*
14280234 TTCAGCTC-ATTT
1 TTGAGCTCGATTT
14280246 CTTTTACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 8 0.29
21 16 0.57
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (20 bp):
TTGAGCTCGATTTAGCTCGT
Found at i:14280478 original size:13 final size:13
Alignment explanation
Indices: 14280460--14280494 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
14280450 ATTATATGAA
*
14280460 TAATTATTTTATT
1 TAATTATGTTATT
14280473 TAATTATGTTATT
1 TAATTATGTTATT
14280486 TAATTATGT
1 TAATTATGT
14280495 AGGTTAGCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (13 bp):
TAATTATGTTATT
Found at i:14285010 original size:43 final size:43
Alignment explanation
Indices: 14284962--14285047 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
14284952 GGCAAGAAGA
14284962 AGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAAAACAAC
1 AGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAAAACAAC
14285005 AGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAAAACAAC
1 AGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAAAACAAC
14285048 TTCTAAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.21
Consensus pattern (43 bp):
AGGTTGAAGATGGCTCCCACAATCAAAAGATTGTTAAAACAAC
Found at i:14286538 original size:20 final size:20
Alignment explanation
Indices: 14286492--14286538 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
14286482 AGCTTGTTTC
*
14286492 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
14286512 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
14286532 CAGCTCA
1 CAGCTCA
14286539 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:14288418 original size:12 final size:12
Alignment explanation
Indices: 14288401--14288472 Score: 54
Period size: 12 Copynumber: 5.6 Consensus size: 12
14288391 TTGGAGTAAC
14288401 AAAAAAAATCAA
1 AAAAAAAATCAA
*
14288413 AAAAAAATTCGAA
1 AAAAAAAATC-AA
*
14288426 AAAAAAATTGATTGAA
1 AAAAAAA---A-TCAA
*
14288442 AAAAAAATTCAA
1 AAAAAAAATCAA
* *
14288454 AAAAAAAGTGAA
1 AAAAAAAATCAA
14288466 AAAAAAA
1 AAAAAAA
14288473 TCGAGCAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
12 29 0.60
13 9 0.19
16 9 0.19
17 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:14288484 original size:40 final size:40
Alignment explanation
Indices: 14288401--14288488 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
14288391 TTGGAGTAAC
* *
14288401 AAAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTG-AA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGA--GCAA
*
14288442 AAAAAAATTCAAAAAAAAAGT-GAAAAAAAAATCGAGCAA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCAA
14288481 AAAAAAAA
1 AAAAAAAA
14288489 GGTGACCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 9 0.21
40 13 0.31
41 19 0.45
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.12
Consensus pattern (40 bp):
AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGAGCAA
Found at i:14288514 original size:30 final size:28
Alignment explanation
Indices: 14288452--14288524 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
14288442 AAAAAAATTC
*
14288452 AAAAAAAAAGTGAAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAAATCAAGCA
* *
14288480 AAAAAAAAAGGTGACCAAAAAAATCAAG-T
1 AAAAAAAAA-GTGA-AAAAAAAATCAAGCA
*
14288509 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
14288525 GTCTTGCGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 2 0.05
28 13 0.34
29 12 0.32
30 11 0.29
ACGTcount: A:0.70, C:0.07, G:0.14, T:0.10
Consensus pattern (28 bp):
AAAAAAAAAGTGAAAAAAAAATCAAGCA
Found at i:14290136 original size:13 final size:13
Alignment explanation
Indices: 14290118--14290142 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14290108 TGGTCATCAT
14290118 GGTGTGAACACAA
1 GGTGTGAACACAA
14290131 GGTGTGAACACA
1 GGTGTGAACACA
14290143 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:14293431 original size:13 final size:13
Alignment explanation
Indices: 14293415--14293475 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
14293405 TGCTCGATTT
*
14293415 TTTTTTTCACTTA
1 TTTTTTTCAATTA
* *
14293428 TTTTTTTGAATTT
1 TTTTTTTCAATTA
*
14293441 TTTTTTTCAATCAA
1 TTTTTTTCAAT-TA
14293455 TTTTTTTTCGAATT-
1 -TTTTTTTC-AATTA
14293469 TTTTTTT
1 TTTTTTT
14293476 TGATTTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 27 0.71
15 8 0.21
16 3 0.08
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTTTTTCAATTA
Found at i:14293443 original size:12 final size:12
Alignment explanation
Indices: 14293413--14293486 Score: 51
Period size: 13 Copynumber: 5.7 Consensus size: 12
14293403 TTTGCTCGAT
* *
14293413 TTTTTTTTTCAC
1 TTTTTTTTTGAA
14293425 TTATTTTTTTGAA
1 TT-TTTTTTTGAA
*
14293438 TTTTTTTTTTCAA
1 -TTTTTTTTTGAA
14293451 TCAATTTTTTTTCGAA
1 T---TTTTTTTT-GAA
14293467 TTTTTTTTTTG-A
1 -TTTTTTTTTGAA
14293479 TTTTTTTT
1 TTTTTTTT
14293487 GTTACTCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
11 8 0.16
12 4 0.08
13 18 0.35
14 10 0.20
15 8 0.16
16 2 0.04
17 1 0.02
ACGTcount: A:0.15, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:14293444 original size:29 final size:29
Alignment explanation
Indices: 14293411--14293476 Score: 93
Period size: 26 Copynumber: 2.4 Consensus size: 29
14293401 TTTTTGCTCG
* *
14293411 ATTTTTTTTTTCACT-TA-TTTTTTT-GA
1 ATTTTTTTTTTCAATCAATTTTTTTTCGA
14293437 ATTTTTTTTTTCAATCAATTTTTTTTCGA
1 ATTTTTTTTTTCAATCAATTTTTTTTCGA
14293466 ATTTTTTTTTT
1 ATTTTTTTTTT
14293477 GATTTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 14 0.40
27 1 0.03
28 7 0.20
29 13 0.37
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.73
Consensus pattern (29 bp):
ATTTTTTTTTTCAATCAATTTTTTTTCGA
Found at i:14294550 original size:13 final size:13
Alignment explanation
Indices: 14294532--14294556 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14294522 TGGTCATCAT
14294532 GGTGTGAACACAA
1 GGTGTGAACACAA
14294545 GGTGTGAACACA
1 GGTGTGAACACA
14294557 TGATCAATAC
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:0.36, C:0.16, G:0.32, T:0.16
Consensus pattern (13 bp):
GGTGTGAACACAA
Found at i:14295441 original size:18 final size:18
Alignment explanation
Indices: 14295420--14295454 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14295410 AGAAAAGAAA
14295420 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
14295438 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
14295455 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:14298970 original size:12 final size:12
Alignment explanation
Indices: 14298953--14299023 Score: 52
Period size: 12 Copynumber: 5.5 Consensus size: 12
14298943 TTGGAGTAAC
14298953 AAAAAAAATCAA
1 AAAAAAAATCAA
*
14298965 AAAAAAATTCGAA
1 AAAAAAAATC-AA
*
14298978 AAAAAAATTGATTGAA
1 AAAAAAA---A-TCAA
*
14298994 AAAAAAATTCAA
1 AAAAAAAATCAA
* *
14299006 AAAAAAAGTGAA
1 AAAAAAAATCAA
14299018 AAAAAA
1 AAAAAA
14299024 TCGAGCAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
12 28 0.60
13 9 0.19
16 9 0.19
17 1 0.02
ACGTcount: A:0.75, C:0.04, G:0.07, T:0.14
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:14299036 original size:40 final size:40
Alignment explanation
Indices: 14298953--14299039 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 40
14298943 TTGGAGTAAC
* * **
14298953 AAAAAAAATCAAAAAAAAATTCGAAAAAAAAATTGATTGAA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGA-CAAA
*
14298994 AAAAAAATTCAAAAAAAAAGT-G-AAAAAAAATCGAGCAAA
1 AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGA-CAAA
14299033 AAAAAAA
1 AAAAAAA
14299040 GGTGACCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
39 20 0.50
40 1 0.03
41 19 0.47
ACGTcount: A:0.74, C:0.06, G:0.08, T:0.13
Consensus pattern (40 bp):
AAAAAAAATCAAAAAAAAAGTCGAAAAAAAAATCGACAAA
Found at i:14299065 original size:30 final size:27
Alignment explanation
Indices: 14299004--14299075 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 27
14298994 AAAAAAATTC
*
14299004 AAAAAAAAAGTGAAAAAAAATCGAGCA
1 AAAAAAAAAGTGAAAAAAAATCAAGCA
*
14299031 AAAAAAAAAGGTGACCAAAAAAATCAAG-T
1 AAAAAAAAA-GTGA--AAAAAAATCAAGCA
*
14299060 TAAAAAAAAGTGAAAA
1 AAAAAAAAAGTGAAAA
14299076 GTCTTGCGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 3 0.08
27 9 0.23
28 8 0.21
29 8 0.21
30 11 0.28
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.10
Consensus pattern (27 bp):
AAAAAAAAAGTGAAAAAAAATCAAGCA
Found at i:14299964 original size:18 final size:18
Alignment explanation
Indices: 14299943--14299977 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14299933 AGAAAAGAAA
14299943 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
14299961 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
14299978 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:14301652 original size:24 final size:23
Alignment explanation
Indices: 14301598--14301653 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
14301588 GGATAACTAA
* *
14301598 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
14301621 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
14301645 GAAATGGTA
1 GAAATGGTA
14301654 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:14305385 original size:15 final size:15
Alignment explanation
Indices: 14305358--14305391 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
14305348 ATCGAACCTC
14305358 CCTCGAGTTCGTTGG
1 CCTCGAGTTCGTTGG
14305373 CCTCG-GTTGCGTTGG
1 CCTCGAGTT-CGTTGG
14305388 CCTC
1 CCTC
14305392 TTCGTTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.03, C:0.32, G:0.32, T:0.32
Consensus pattern (15 bp):
CCTCGAGTTCGTTGG
Found at i:14306176 original size:16 final size:15
Alignment explanation
Indices: 14306140--14306193 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 15
14306130 CGTATGCAAT
14306140 TTTTTTTTTTCAAAA
1 TTTTTTTTTTCAAAA
*
14306155 TATTTTTTTT-AATTAA
1 TTTTTTTTTTCAA--AA
*
14306171 TTTTTTTTTTC--GA
1 TTTTTTTTTTCAAAA
14306184 TTTTTTTTTT
1 TTTTTTTTTT
14306194 GAATCTACAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
13 11 0.33
14 2 0.06
15 9 0.27
16 11 0.33
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTTTTTTCAAAA
Found at i:14306523 original size:24 final size:23
Alignment explanation
Indices: 14306469--14306524 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
14306459 GGATAACTAA
* *
14306469 GAAAGGGTATTTGGTTTTGGTAC
1 GAAATGGTATTTGGATTTGGTAC
***
14306492 GTTTTGGTATTTGGGATTTGGTAC
1 GAAATGGTATTT-GGATTTGGTAC
14306516 GAAATGGTA
1 GAAATGGTA
14306525 ATGGTTCAAA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
23 8 0.33
24 16 0.67
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (23 bp):
GAAATGGTATTTGGATTTGGTAC
Found at i:14312206 original size:48 final size:47
Alignment explanation
Indices: 14312127--14312232 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
14312117 GAGTGTCATG
*
14312127 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
14312175 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
14312223 GAAAAAGAAA
1 GAAAAAGAAA
14312233 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:14315854 original size:11 final size:10
Alignment explanation
Indices: 14315829--14315889 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
14315819 ACCAATAAAA
14315829 TAAA-TGAGC
1 TAAATTGAGC
*
14315838 TGAATTGTAGC
1 TAAATTG-AGC
14315849 TAAATTGAGC
1 TAAATTGAGC
**
14315859 TCGATTGAGC
1 TAAATTGAGC
14315869 TGAAA-TGAGC
1 T-AAATTGAGC
*
14315879 TCAATTGAGC
1 TAAATTGAGC
14315889 T
1 T
14315890 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:14315890 original size:20 final size:20
Alignment explanation
Indices: 14315830--14315890 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
14315820 CCAATAAAAT
*
14315830 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
14315850 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
14315871 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
14315891 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:14317957 original size:33 final size:33
Alignment explanation
Indices: 14317919--14317981 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
14317909 GATTACTCAC
14317919 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
14317952 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
14317982 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:14318062 original size:18 final size:18
Alignment explanation
Indices: 14317996--14318134 Score: 86
Period size: 18 Copynumber: 7.7 Consensus size: 18
14317986 TCTTTTTTCG
14317996 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTCAA-TTT
* **
14318015 CTTTTCTTTATTTTCTTTTT
1 CTTTT-TCT-TTTTCAATTT
* ** *
14318035 CTCTCACTTTTTCGATTT
1 CTTTTTCTTTTTCAATTT
*
14318053 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCAATTT
* **
14318071 CTTTTTCTTCTTCGTTTT
1 CTTTTTCTTTTTCAATTT
*
14318089 CTTTTT-GTTTTC--TTT
1 CTTTTTCTTTTTCAATTT
** *
14318104 CAATTTCTTTTTCAATCT
1 CTTTTTCTTTTTCAATTT
*
14318122 CTTTTTCCTTTTC
1 CTTTTTCTTTTTC
14318135 TCGCTCAATG
Statistics
Matches: 88, Mismatches: 27, Indels: 11
0.70 0.21 0.09
Matches are distributed among these distances:
15 7 0.08
16 5 0.06
17 4 0.05
18 53 0.60
19 6 0.07
20 8 0.09
21 5 0.06
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (18 bp):
CTTTTTCTTTTTCAATTT
Found at i:14318116 original size:6 final size:6
Alignment explanation
Indices: 14317996--14318103 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
14317986 TCTTTTTTCG
* * * **
14317996 CTTTTT CTTTTT CAATTTT CTTTTCT TTATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT CTTTT-T CT-TTTT CTTTTT CTTTTT CTTTTT
** * ** * *
14318047 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTCTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
14318095 -GTTTT CTTT
1 CTTTTT CTTT
14318104 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 26, Indels: 8
0.68 0.25 0.08
Matches are distributed among these distances:
5 4 0.06
6 56 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:14318128 original size:39 final size:38
Alignment explanation
Indices: 14318001--14318133 Score: 110
Period size: 39 Copynumber: 3.3 Consensus size: 38
14317991 TTTCGCTTTT
* *
14318001 TCTTTTTCAATTTTCTTTTCTTT-ATTTTCTTTTTC-TC
1 TCTTTTTC-ATTTTTTTTTCTTTCAATTTCTTTTTCATC
* *
14318038 TCACTTTTTCGATTTCTTTTTCTTTTGCAATTTCTTTTTCTTC
1 T--CTTTTTC-ATTTTTTTTTC-TTT-CAATTTCTTTTTCATC
*
14318081 TTCGTTTTC-TTTTTGTTTTCTTTCAATTTCTTTTTCAATC
1 -TCTTTTTCATTTTT-TTTTCTTTCAATTTCTTTTTC-ATC
*
14318121 TCTTTTTCCTTTT
1 TCTTTTTCATTTT
14318134 CTCGCTCAAT
Statistics
Matches: 78, Mismatches: 8, Indels: 17
0.76 0.08 0.17
Matches are distributed among these distances:
37 1 0.01
39 36 0.46
40 16 0.21
41 5 0.06
42 17 0.22
43 2 0.03
44 1 0.01
ACGTcount: A:0.08, C:0.20, G:0.03, T:0.69
Consensus pattern (38 bp):
TCTTTTTCATTTTTTTTTCTTTCAATTTCTTTTTCATC
Found at i:14319159 original size:37 final size:35
Alignment explanation
Indices: 14319118--14319189 Score: 94
Period size: 38 Copynumber: 2.0 Consensus size: 35
14319108 GCAAGACTTT
14319118 TCACTT-TTTTTTCTT-CTTTTTTAACTCGATTTTTTTG
1 TCACTTCTTTTTT-TTCCTTTTTT---TCGATTTTTTTG
14319155 TCACTTCTTTTTTTTCCTTTTTTTCGATTTTTTTG
1 TCACTTCTTTTTTTTCCTTTTTTTCGATTTTTTTG
14319190 AAATATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
35 12 0.36
37 8 0.24
38 13 0.39
ACGTcount: A:0.08, C:0.17, G:0.06, T:0.69
Consensus pattern (35 bp):
TCACTTCTTTTTTTTCCTTTTTTTCGATTTTTTTG
Found at i:14320584 original size:11 final size:10
Alignment explanation
Indices: 14320559--14320619 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
14320549 ACCAATAAAA
14320559 TAAA-TGAGC
1 TAAATTGAGC
*
14320568 TGAATTGTAGC
1 TAAATTG-AGC
14320579 TAAATTGAGC
1 TAAATTGAGC
**
14320589 TCGATTGAGC
1 TAAATTGAGC
14320599 TGAAA-TGAGC
1 T-AAATTGAGC
*
14320609 TCAATTGAGC
1 TAAATTGAGC
14320619 T
1 T
14320620 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:14320620 original size:20 final size:20
Alignment explanation
Indices: 14320560--14320620 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
14320550 CCAATAAAAT
*
14320560 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
14320580 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
14320601 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
14320621 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:14324668 original size:23 final size:22
Alignment explanation
Indices: 14324616--14324668 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
14324606 TCCACGTCTT
*
14324616 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
14324638 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
14324661 TTTCTTTT
1 TTTCTTTT
14324669 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:14328722 original size:18 final size:18
Alignment explanation
Indices: 14328701--14328735 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14328691 TTTTTCTTTT
14328701 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
14328719 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
14328736 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:14329406 original size:12 final size:12
Alignment explanation
Indices: 14329389--14329445 Score: 71
Period size: 13 Copynumber: 4.7 Consensus size: 12
14329379 ACGGTATTGT
*
14329389 AAAAAAAATTGA
1 AAAAAAAATTCA
14329401 ACAAAAAAA-TCA
1 A-AAAAAAATTCA
*
14329413 AAAAAAAATTTGA
1 AAAAAAAA-TTCA
14329426 AAAAAAAATTCA
1 AAAAAAAATTCA
14329438 AAAAAAAA
1 AAAAAAAA
14329446 ATTGTATTCA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
11 7 0.18
12 15 0.38
13 17 0.44
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:14329408 original size:13 final size:12
Alignment explanation
Indices: 14329384--14329445 Score: 72
Period size: 12 Copynumber: 5.1 Consensus size: 12
14329374 TCATTACGGT
*
14329384 ATTGTAAAAAAA
1 ATTGAAAAAAAA
14329396 ATTGAACAAAAAA
1 ATTGAA-AAAAAA
*
14329409 A-TCAAAAAAAA
1 ATTGAAAAAAAA
14329420 ATTTGAAAAAAAA
1 A-TTGAAAAAAAA
*
14329433 ATTCAAAAAAAA
1 ATTGAAAAAAAA
14329445 A
1 A
14329446 ATTGTATTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
11 7 0.16
12 19 0.44
13 17 0.40
ACGTcount: A:0.73, C:0.05, G:0.05, T:0.18
Consensus pattern (12 bp):
ATTGAAAAAAAA
Found at i:14329425 original size:25 final size:24
Alignment explanation
Indices: 14329389--14329445 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 24
14329379 ACGGTATTGT
14329389 AAAAAAAATTGAACAAAAAAA-TCA
1 AAAAAAAATTGAA-AAAAAAATTCA
14329413 AAAAAAAATTTGAAAAAAAAATTCA
1 AAAAAAAA-TTGAAAAAAAAATTCA
14329438 AAAAAAAA
1 AAAAAAAA
14329446 ATTGTATTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 15 0.48
25 16 0.52
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (24 bp):
AAAAAAAATTGAAAAAAAAATTCA
Found at i:14334779 original size:30 final size:30
Alignment explanation
Indices: 14334745--14334841 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
14334735 TAAACTAAAA
*
14334745 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
14334775 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
14334805 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
14334834 ATGAGCTA
1 -TGAGCTA
14334842 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:14337036 original size:12 final size:12
Alignment explanation
Indices: 14337021--14337051 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
14337011 TTCTTTTTGC
14337021 TTTTCAAAGGCT
1 TTTTCAAAGGCT
14337033 TTTTCAAAGGCT
1 TTTTCAAAGGCT
14337045 TTTTCAA
1 TTTTCAA
14337052 GTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:14337128 original size:6 final size:6
Alignment explanation
Indices: 14337112--14337161 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
14337102 TTTCTTTTTA
*
14337112 TTTCAT TTTCTT TTTCTT CTCTTGCTT TTTCTT TTTC-T TTTC-T TTTCTT
1 TTTCTT TTTCTT TTTCTT -T-TT-CTT TTTCTT TTTCTT TTTCTT TTTCTT
14337161 T
1 T
14337162 GTTTTCTCTT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
5 10 0.26
6 20 0.51
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:14337144 original size:37 final size:37
Alignment explanation
Indices: 14337101--14337171 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
14337091 CTTGCCTCTC
14337101 TTTTCTTTTT-ATTTCATTTTCTTT-TTCTTCTCTTGCT
1 TTTTCTTTTTCATTTC-TTTTCTTTGTT-TTCTCTTGCT
*
14337138 TTTTCTTTTTCTTTTCTTTTCTTTGTTTTCTCTT
1 TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTT
14337172 TACAAGAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
37 25 0.81
38 6 0.19
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.76
Consensus pattern (37 bp):
TTTTCTTTTTCATTTCTTTTCTTTGTTTTCTCTTGCT
Found at i:14337172 original size:16 final size:16
Alignment explanation
Indices: 14337097--14337157 Score: 63
Period size: 16 Copynumber: 3.8 Consensus size: 16
14337087 GCCTCTTGCC
*
14337097 TCTCTTTTCTTTTTAT
1 TCTCTTTTCTTTTTCT
14337113 T-TCATTTTCTTTTTCT
1 TCTC-TTTTCTTTTTCT
*
14337129 TCTC-TTGCTTTTTCTT
1 TCTCTTTTCTTTTTC-T
*
14337145 TTTCTTTTCTTTT
1 TCTCTTTTCTTTT
14337158 CTTTGTTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 11 0.30
16 17 0.46
17 9 0.24
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (16 bp):
TCTCTTTTCTTTTTCT
Found at i:14338120 original size:13 final size:12
Alignment explanation
Indices: 14338079--14338113 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
14338069 TTCAAAAAAC
14338079 AATTTTTTTTTG
1 AATTTTTTTTTG
14338091 AATTTTTTTTTG
1 AATTTTTTTTTG
14338103 AATTTTTTTTT
1 AATTTTTTTTT
14338114 CAAATTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.06, T:0.77
Consensus pattern (12 bp):
AATTTTTTTTTG
Found at i:14339852 original size:30 final size:30
Alignment explanation
Indices: 14339812--14339884 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
14339802 CGAGTTTAAA
*
14339812 CTAAA-ATGAGCTAAGTTTTAGCTCGTGAG
1 CTAAATATGAGCTAAGGTTTAGCTCGTGAG
14339841 CTAAAGT-TGAGCTAAGGTTTAGCTCGTGAG
1 CTAAA-TATGAGCTAAGGTTTAGCTCGTGAG
14339871 CTAAATATGAGCTA
1 CTAAATATGAGCTA
14339885 GGAGTGAGCT
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 6 0.15
30 34 0.85
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
CTAAATATGAGCTAAGGTTTAGCTCGTGAG
Found at i:14339895 original size:30 final size:30
Alignment explanation
Indices: 14339831--14339896 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
14339821 GCTAAGTTTT
* *
14339831 AGCTCGTGAGCTAAAGTTGAGCTAAGGTTT
1 AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
14339861 AGCTCGTGAGCTAAA-TATGAGCT-AGGAGTG
1 AGCTCGTGAGCTAAAGT-TGAGCTAAGG-GTG
14339891 AGCTCG
1 AGCTCG
14339897 GTTTAGCTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (30 bp):
AGCTCGTGAGCTAAAGTTGAGCTAAGGGTG
Found at i:14347161 original size:23 final size:22
Alignment explanation
Indices: 14347110--14347161 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
14347100 CCTCGTCTTT
*
14347110 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
14347132 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
14347155 TTCTTTT
1 TTCTTTT
14347162 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:14347176 original size:18 final size:18
Alignment explanation
Indices: 14347155--14347193 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
14347145 TTTCTTCAAC
* *
14347155 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
14347173 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
14347191 TTC
1 TTC
14347194 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:14351271 original size:20 final size:19
Alignment explanation
Indices: 14351248--14351312 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
14351238 AAGCTCAAAC
14351248 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
14351268 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
14351288 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
14351308 GAGCT
1 GAGCT
14351313 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:14352599 original size:17 final size:18
Alignment explanation
Indices: 14352577--14352610 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
14352567 ACAACACTCC
*
14352577 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
14352594 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
14352611 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:14352718 original size:15 final size:16
Alignment explanation
Indices: 14352693--14352724 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
14352683 TATCTCACAC
14352693 TCATCTTCTTTTTCTT
1 TCATCTTCTTTTTCTT
14352709 TCAT-TTCTTTTTCTT
1 TCATCTTCTTTTTCTT
14352724 T
1 T
14352725 TTCATTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.06, C:0.22, G:0.00, T:0.72
Consensus pattern (16 bp):
TCATCTTCTTTTTCTT
Found at i:14353671 original size:29 final size:27
Alignment explanation
Indices: 14353639--14353708 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 27
14353629 GCAAGACTTT
*
14353639 TCACTTTTTTTTTAACTTGATTTTTTTGG
1 TCACTTTTTTTTT-ACTCGATTTTTTT-G
* *
14353668 TCACCTTTTTTTTTGCTCGATTTTTTTT
1 TCA-CTTTTTTTTTACTCGATTTTTTTG
14353696 TCACTTTTTTTTT
1 TCACTTTTTTTTT
14353709 GAATTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 10 0.27
28 3 0.08
29 14 0.38
30 10 0.27
ACGTcount: A:0.10, C:0.14, G:0.07, T:0.69
Consensus pattern (27 bp):
TCACTTTTTTTTTACTCGATTTTTTTG
Found at i:14353703 original size:12 final size:12
Alignment explanation
Indices: 14353636--14353719 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 12
14353626 CTCGCAAGAC
14353636 TTTTCACTTTTT
1 TTTTCACTTTTT
*
14353648 TTTTAACTTGATTTT
1 TTTTCAC-T--TTTT
14353663 TTTGGTCACCTTTTT
1 TTT--TCA-CTTTTT
*
14353678 TTTTGCTCGATTTTT
1 TTTT-CAC--TTTTT
14353693 TTTTCACTTTTT
1 TTTTCACTTTTT
* *
14353705 TTTTGAATTTTT
1 TTTTCACTTTTT
14353717 TTT
1 TTT
14353720 CAATCAATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
12 24 0.42
13 3 0.05
14 3 0.05
15 23 0.40
17 3 0.05
18 1 0.02
ACGTcount: A:0.11, C:0.12, G:0.07, T:0.70
Consensus pattern (12 bp):
TTTTCACTTTTT
Found at i:14353718 original size:27 final size:27
Alignment explanation
Indices: 14353636--14353747 Score: 75
Period size: 27 Copynumber: 4.0 Consensus size: 27
14353626 CTCGCAAGAC
14353636 TTTTCACTTTTTTTTT-AACTTGATTTTTT
1 TTTTCACTTTTTTTTTGAA-TT--TTTTTT
** * **
14353665 TGGTCACCTTTTTTTTTG-CTCGATTTTT
1 TTTTCA-CTTTTTTTTTGAAT-TTTTTTT
14353693 TTTTCACTTTTTTTTTGAATTTTTTTT
1 TTTTCACTTTTTTTTTGAATTTTTTTT
*** * *
14353720 CAATCAATTTTTTTTCGAATTTTTTTT
1 TTTTCACTTTTTTTTTGAATTTTTTTT
14353747 T
1 T
14353748 GATTTTTTTT
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
27 38 0.60
28 10 0.16
29 5 0.08
30 10 0.16
ACGTcount: A:0.13, C:0.12, G:0.06, T:0.69
Consensus pattern (27 bp):
TTTTCACTTTTTTTTTGAATTTTTTTT
Done.