Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold102
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1727112
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 166202 characters in sequence are not A, C, G, or T
File 6 of 5
Found at i:1518835 original size:36 final size:36
Alignment explanation
Indices: 1518795--1519418 Score: 809
Period size: 36 Copynumber: 17.4 Consensus size: 36
1518785 GCTTAGTGTA
*
1518795 AGGGGAAAAACATATCAACCAGTGAGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1518831 AGGGGAAAACCATATAAACCAGTGGGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1518867 AGGGGAAAACCATATCAAGCAGTGGGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1518903 AGGGGAAAACCATATCAAGCAGTGGGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* * *
1518939 AGGGGAAAACCATGTCAACCGGTTAGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1518975 AGGGGGAAAACCTGTATCAACCAGTGAGTGTATAACGT
1 A-GGGGAAAACC-ATATCAACCAGTGAGTGTATAATGT
* * *
1519013 AGGGGGAAACCAT-TGAAAACCAGTGGGTGTATAATGT
1 AGGGGAAAACCATAT--CAACCAGTGAGTGTATAATGT
*
1519050 AGGGGAAAACCATTTCAACCAGTGAGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* **
1519086 AGGGAAAAACCATATCAATTAGTGAGTG--TAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
1519120 AGGGGGAAAACCATATCAACCAGTGAGTGT-T--TGGT
1 A-GGGGAAAACCATATCAACCAGTGAGTGTATAAT-GT
* *
1519155 AGGGGAGTAACCTTATCAACCAGTGAGTGTATAATGT
1 AGGGGA-AAACCATATCAACCAGTGAGTGTATAATGT
1519192 AGGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
1 A-GGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1519229 AGGGGAAAACCATATAAACCAGTGGGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1519265 AGGGGAAAACCATATCAAGCAGTGGGTGTATAA--T
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* * *
1519299 --GGGAAAACCTGTATCAACCAATGAGTGTATAACGT
1 AGGGGAAAACC-ATATCAACCAGTGAGTGTATAATGT
* *
1519334 AGGGGAAAACCATATAAACCAGTGGGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
*
1519370 AGGGGAAAACCATTTCAACCAGTGAGTGTATAATGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
*
1519406 AGGGAAAAACCAT
1 AGGGGAAAACCAT
1519419 NGTAGGGAAA
Statistics
Matches: 519, Mismatches: 51, Indels: 36
0.86 0.08 0.06
Matches are distributed among these distances:
32 9 0.02
33 18 0.03
34 14 0.03
35 50 0.10
36 310 0.60
37 90 0.17
38 28 0.05
ACGTcount: A:0.37, C:0.13, G:0.28, T:0.23
Consensus pattern (36 bp):
AGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
Found at i:1519296 original size:109 final size:108
Alignment explanation
Indices: 1518795--1519693 Score: 959
Period size: 109 Copynumber: 8.2 Consensus size: 108
1518785 GCTTAGTGTA
* * *
1518795 AGGGGAAAAACATATCAACCAGTGAGTGTATAATGTAGGGGAAAACCATATAAACCAGTGGGTGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGTAGGGGAAAACCATATCAACCAGTGAGTGT
* *
1518860 ATAATGTAGGGGAAAACCATATCAAGCAGTGGGTGTATAATGT
66 ATAATGTAGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* * * * *
1518903 AGGGGAAAACCATATCAAGCAGTGGGTGTATAATGTAGGGGAAAACCATGTCAACCGGTTAGTGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGTAGGGGAAAACCATATCAACCAGTGAGTGT
* *
1518968 ATAATGTAGGGGGAAAACCTGTATCAACCAGTGAGTGTATAACGT
66 ATAATGTA-GGGGAAAACC-ATATCAACCAGTGAGTGTATAATGT
* * * *
1519013 AGGGGGAAACCAT-TGAAAACCAGTGGGTGTATAATGTAGGGGAAAACCATTTCAACCAGTGAGT
1 AGGGGAAAACCATAT--CAACCAGTGAGTGTATAATGTAGGGGAAAACCATATCAACCAGTGAGT
* **
1519077 GTATAATGTAGGGAAAAACCATATCAATTAGTGAGTG--TAATGT
64 GTATAATGTAGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* *
1519120 AGGGGGAAAACCATATCAACCAGTGAGTGT-T--TGGTAGGGGAGTAACCTTATCAACCAGTGAG
1 A-GGGGAAAACCATATCAACCAGTGAGTGTATAAT-GTAGGGGA-AAACCATATCAACCAGTGAG
1519182 TGTATAATGTAGGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
63 TGTATAATGTA-GGGGAAAACCATATCAACCAGTGAGTGTATAATGT
* * * *
1519229 AGGGGAAAACCATATAAACCAGTGGGTGTATAATGTAGGGGAAAACCATATCAAGCAGTGGGTGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGTAGGGGAAAACCATATCAACCAGTGAGTGT
* * *
1519294 ATAA--T--GGGAAAACCTGTATCAACCAATGAGTGTATAACGT
66 ATAATGTAGGGGAAAACC-ATATCAACCAGTGAGTGTATAATGT
* * *
1519334 AGGGGAAAACCATATAAACCAGTGGGTGTATAATGTAGGGGAAAACCATTTCAACCAGTGAGTGT
1 AGGGGAAAACCATATCAACCAGTGAGTGTATAATGTAGGGGAAAACCATATCAACCAGTGAGTGT
* * * * * *
1519399 ATAATGTAGGGAAAAACCATNGTAGGGAAAAACCATATCAATTAGTGAGTGTAATGT
66 ATAATGTAGGGGAAAACCA---T--------ATCA-ACCAGTGAGT--GTATAATGT
* *
1519456 AGGGGGAAAACCATATCAACCGGTGAGTGTATAATGTTTGGGGGAAAACCATATCAACCAGTGAG
1 AGG-GGAAAACCATATCAACCAGTGAGTGTATAATG--TAGGGGAAAACCATATCAACCAGTGAG
* *
1519521 TGT-T--TGGTAGGGGAGTAACCTTATCAACCAGTGAGTGTATAAT-T
63 TGTATAAT-GTAGGGGA-AAACCATATCAACCAGTGAGTGTATAATGT
* *
1519565 AGGGGGAAAACCATATCAACCGGTGAGTGTATAATGTTGGGGGGAAAACCATATCAACCAGTGA-
1 A-GGGGAAAACCATATCAACCAGTGAGTGTATAATG-T-AGGGGAAAACCATATCAACCAGTGAG
* * *
1519629 -GT-TAATGTTGGGGGAGTAACCTTATCAACCAGTGAGTGTATAATGT
63 TGTATAATG-TAGGGGA-AAACCATATCAACCAGTGAGTGTATAATGT
1519675 AGGGGGAAAACCATATCAA
1 A-GGGGAAAACCATATCAA
1519694 AGAGTAAATG
Statistics
Matches: 682, Mismatches: 65, Indels: 86
0.82 0.08 0.10
Matches are distributed among these distances:
104 10 0.01
105 96 0.14
106 29 0.04
107 47 0.07
108 105 0.15
109 160 0.23
110 78 0.11
111 55 0.08
112 7 0.01
113 3 0.00
119 3 0.00
120 8 0.01
121 1 0.00
122 11 0.02
123 36 0.05
124 5 0.01
125 28 0.04
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (108 bp):
AGGGGAAAACCATATCAACCAGTGAGTGTATAATGTAGGGGAAAACCATATCAACCAGTGAGTGT
ATAATGTAGGGGAAAACCATATCAACCAGTGAGTGTATAATGT
Found at i:1519425 original size:16 final size:15
Alignment explanation
Indices: 1519402--1519434 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
1519392 TGAGTGTATA
1519402 ATGTAGGGAAAAACC
1 ATGTAGGGAAAAACC
1519417 ATNGTAGGGAAAAACC
1 AT-GTAGGGAAAAACC
1519433 AT
1 AT
1519435 ATCAATTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.45, C:0.12, G:0.24, T:0.15
Consensus pattern (15 bp):
ATGTAGGGAAAAACC
Found at i:1519431 original size:52 final size:50
Alignment explanation
Indices: 1519366--1519469 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 50
1519356 TGGGTGTATA
* *
1519366 ATGTAGGGGAAAACCATTTCAACCAGTGAGTGTATAATGTA-GGGAAAAACC
1 ATGTAGGGAAAAACCATATCAACCAGTGAGTG--TAATGTAGGGGAAAAACC
** *
1519417 ATNGTAGGGAAAAACCATATCAATTAGTGAGTGTAATGTAGGGGGAAAACC
1 AT-GTAGGGAAAAACCATATCAACCAGTGAGTGTAATGTAGGGGAAAAACC
1519468 AT
1 AT
1519470 ATCAACCGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
50 7 0.15
51 13 0.28
52 26 0.57
ACGTcount: A:0.39, C:0.12, G:0.26, T:0.22
Consensus pattern (50 bp):
ATGTAGGGAAAAACCATATCAACCAGTGAGTGTAATGTAGGGGAAAAACC
Found at i:1519468 original size:35 final size:36
Alignment explanation
Indices: 1519427--1519693 Score: 296
Period size: 38 Copynumber: 7.4 Consensus size: 36
1519417 ATNGTAGGGA
**
1519427 AAAACCATATCAATTAGTGAGTG-TAATGTAGGGGG
1 AAAACCATATCAACCAGTGAGTGATAATGTAGGGGG
* *
1519462 AAAACCATATCAACCGGTGAGTGTATAATGTTTGGGGG
1 AAAACCATATCAACCAGTGAGTG-ATAATG-TAGGGGG
*
1519500 AAAACCATATCAACCAGTGAGTG-T-TTGGTA-GGGG
1 AAAACCATATCAACCAGTGAGTGATAAT-GTAGGGGG
* *
1519534 AGTAACCTTATCAACCAGTGAGTGTATAAT-TAGGGGG
1 A-AAACCATATCAACCAGTGAGTG-ATAATGTAGGGGG
* *
1519571 AAAACCATATCAACCGGTGAGTGTATAATGTTGGGGGG
1 AAAACCATATCAACCAGTGAGTG-ATAATG-TAGGGGG
*
1519609 AAAACCATATCAACCAGTGAGT--TAATGTTGGGGG
1 AAAACCATATCAACCAGTGAGTGATAATGTAGGGGG
* *
1519643 AGTAACCTTATCAACCAGTGAGTGTATAATGTAGGGGG
1 A-AAACCATATCAACCAGTGAGTG-ATAATGTAGGGGG
1519681 AAAACCATATCAA
1 AAAACCATATCAA
1519694 AGAGTAAATG
Statistics
Matches: 196, Mismatches: 21, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
34 12 0.06
35 66 0.34
36 29 0.15
37 21 0.11
38 68 0.35
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.25
Consensus pattern (36 bp):
AAAACCATATCAACCAGTGAGTGATAATGTAGGGGG
Found at i:1519482 original size:87 final size:86
Alignment explanation
Indices: 1519332--1519492 Score: 225
Period size: 87 Copynumber: 1.8 Consensus size: 86
1519322 AGTGTATAAC
* * *
1519332 GTAGGGGAAAACCATATAAACCAGTGGGTGTATAATGTAGGGGAAAACCATTTCAACCAGTGAGT
1 GTAGGGAAAAACCATATAAACCAGTGAGTG-ATAATGTAGGGGAAAACCATATCAACCAGTGAGT
1519397 GTATAATGTAGGGAAAAACCAT
65 GTATAATGTAGGGAAAAACCAT
* ** *
1519419 NGTAGGGAAAAACCATATCAATTAGTGAGTG-TAATGTAGGGGGAAAACCATATCAACCGGTGAG
1 -GTAGGGAAAAACCATATAAACCAGTGAGTGATAATGTA-GGGGAAAACCATATCAACCAGTGAG
1519483 TGTATAATGT
64 TGTATAATGT
1519493 TTGGGGGAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
86 7 0.11
87 33 0.51
88 25 0.38
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (86 bp):
GTAGGGAAAAACCATATAAACCAGTGAGTGATAATGTAGGGGAAAACCATATCAACCAGTGAGTG
TATAATGTAGGGAAAAACCAT
Found at i:1519546 original size:73 final size:73
Alignment explanation
Indices: 1519427--1519693 Score: 307
Period size: 73 Copynumber: 3.7 Consensus size: 73
1519417 ATNGTAGGGA
** * *
1519427 AAAACCATATCAATTAGTGAGTGTAATGTAGGGGGAAAACCATATCAACCGGTGAGTGTATAATG
1 AAAACCATATCAACCAGTGAGTGTATTGTAGGGGGAAAACCATATCAACCAGTGAGTGTATAATG
1519492 TTTGGGGG
66 TTTGGGGG
* *
1519500 AAAACCATATCAACCAGTGAGTGT-TTGGTA-GGGGAGTAACCTTATCAACCAGTGAGTGTATAA
1 AAAACCATATCAACCAGTGAGTGTATT-GTAGGGGGA-AAACCATATCAACCAGTGAGTGTATAA
*
1519563 --TTAGGGGG
64 TGTTTGGGGG
* *
1519571 AAAACCATATCAACCGGTGAGTGTATAATGTTGGGGGGAAAACCATATCAACCAGTGA--GT-TA
1 AAAACCATATCAACCAGTGAGTGTAT--TG-TAGGGGGAAAACCATATCAACCAGTGAGTGTATA
1519633 ATG-TTGGGGG
63 ATGTTTGGGGG
* *
1519643 AGTAACCTTATCAACCAGTGAGTGTATAATGTAGGGGGAAAACCATATCAA
1 A-AAACCATATCAACCAGTGAGTGTAT--TGTAGGGGGAAAACCATATCAA
1519694 AGAGTAAATG
Statistics
Matches: 168, Mismatches: 16, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
71 33 0.20
72 35 0.21
73 76 0.45
74 19 0.11
75 5 0.03
ACGTcount: A:0.34, C:0.13, G:0.27, T:0.25
Consensus pattern (73 bp):
AAAACCATATCAACCAGTGAGTGTATTGTAGGGGGAAAACCATATCAACCAGTGAGTGTATAATG
TTTGGGGG
Found at i:1532898 original size:18 final size:18
Alignment explanation
Indices: 1532885--1532935 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1532875 CTCTTGACCT
1532885 ACTTCTGGACCTTGAACG
1 ACTTCTGGACCTTGAACG
* *
1532903 ACCTT-TTGACCTTGATCG
1 A-CTTCTGGACCTTGAACG
1532921 ACTTCTGGACCTTGA
1 ACTTCTGGACCTTGA
1532936 GTCAGATCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.11
18 22 0.79
19 3 0.11
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (18 bp):
ACTTCTGGACCTTGAACG
Found at i:1532935 original size:36 final size:30
Alignment explanation
Indices: 1532850--1532914 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
1532840 TCCTGACCGC
1532850 GACCTACTTCTGGACCTTGAACGACCTCTT
1 GACCTACTTCTGGACCTTGAACGACCTCTT
*
1532880 GACCTACTTCTGGACCTTGAACGACCTTTT
1 GACCTACTTCTGGACCTTGAACGACCTCTT
1532910 GACCT
1 GACCT
1532915 TGATCGACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.31
Consensus pattern (30 bp):
GACCTACTTCTGGACCTTGAACGACCTCTT
Found at i:1536996 original size:63 final size:63
Alignment explanation
Indices: 1536897--1537090 Score: 343
Period size: 63 Copynumber: 3.1 Consensus size: 63
1536887 AGGTAAAATG
*
1536897 CCTGTTTAGGAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
1 CCTGTTTATGAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
1536960 CCTGTTTATGAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
1 CCTGTTTATGAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
** *
1537023 CCTGTACATACAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
1 CCTGTTTAT-GAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
1537087 CCTG
1 CCTG
1537091 GCTGTCAGCG
Statistics
Matches: 126, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 69 0.55
64 57 0.45
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (63 bp):
CCTGTTTATGAGATATCTCTGATGGAGGTAAGTATAGATATTGATGTACACATACAGTGCTCC
Found at i:1539700 original size:41 final size:42
Alignment explanation
Indices: 1539634--1539864 Score: 333
Period size: 42 Copynumber: 5.5 Consensus size: 42
1539624 CGTTACTACT
*
1539634 CCAATCACAATGTCGTATCTCTCTAAACTCTAAAAATAGTAA
1 CCAATCACAATGTTGTATCTCTCTAAACTCTAAAAATAGTAA
*
1539676 CCAATCAC-ACGTTGTATCTCTCTAAACTCTAAAAATAGTAA
1 CCAATCACAATGTTGTATCTCTCTAAACTCTAAAAATAGTAA
* * *
1539717 CCAATCAC-ACGTTGTATCTCTCTTAACTCTAAAAATAGTAG
1 CCAATCACAATGTTGTATCTCTCTAAACTCTAAAAATAGTAA
* * *
1539758 CCAATCACAATGTTGTATCTCTATAAACTCTCAAAATAGTAG
1 CCAATCACAATGTTGTATCTCTCTAAACTCTAAAAATAGTAA
* * *
1539800 CCAATCACAATGTTGTTTCTCTCTAACCTCTAAAAATAGTAT
1 CCAATCACAATGTTGTATCTCTCTAAACTCTAAAAATAGTAA
1539842 CCAAT-ATCAATGTTGTATCTCTC
1 CCAATCA-CAATGTTGTATCTCTC
1539865 CCCCCCCCCC
Statistics
Matches: 173, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
41 79 0.46
42 94 0.54
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (42 bp):
CCAATCACAATGTTGTATCTCTCTAAACTCTAAAAATAGTAA
Found at i:1541225 original size:14 final size:14
Alignment explanation
Indices: 1541206--1541238 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1541196 TTGTCTGAGA
1541206 GTCCACTAACTGTG
1 GTCCACTAACTGTG
*
1541220 GTCCACTGACTGTG
1 GTCCACTAACTGTG
1541234 GTCCA
1 GTCCA
1541239 TCTTCATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.27
Consensus pattern (14 bp):
GTCCACTAACTGTG
Found at i:1541279 original size:15 final size:15
Alignment explanation
Indices: 1541259--1541294 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1541249 TTGCTATCTT
1541259 AGTCCACTGTCTGTG
1 AGTCCACTGTCTGTG
*
1541274 AGTCCACTGTTTGTG
1 AGTCCACTGTCTGTG
1541289 AGTCCA
1 AGTCCA
1541295 ATGATCGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (15 bp):
AGTCCACTGTCTGTG
Found at i:1541344 original size:76 final size:76
Alignment explanation
Indices: 1541220--1541568 Score: 413
Period size: 76 Copynumber: 4.8 Consensus size: 76
1541210 ACTAACTGTG
* * * *
1541220 GTCCACTGACTGTGGTCCATC-T--TCAT-A--ATTTGCTATCTTAGTCCACTGTCTGTGAGTCC
1 GTCCAATGACTGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTCACTGTCTCTGAGTCC
* *
1541279 -ACTGTTTGTGA
66 AAC-GTCTGAGA
*
1541290 GTCCAATGA-TCGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTTACTGTCTCTGAGTC
1 GTCCAATGACT-GTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTCACTGTCTCTGAGTC
*
1541354 CAACATCTGAGA
65 CAACGTCTGAGA
*
1541366 GTCCACA-GACTGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTTACTGTCTCTGAGTC
1 GTCCA-ATGACTGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTCACTGTCTCTGAGTC
1541430 CAACGTCTGAGA
65 CAACGTCTGAGA
* * *
1541442 GTCCACTGACTGTGGT-C--CATCATCATCATC--TT-CTATCTTAGTCCACTGTCTGTGAGTCC
1 GTCCAATGACTGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTCACTGTCTCTGAGTCC
** * *
1541501 ATTGTTTGTGA
66 AACGTCTGAGA
*
1541512 GTCCAATGACTGTGGTCCATCATCATCATCATCATTTGCTATCTTAGTTCACTGTCT
1 GTCCAATGACTGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTCACTGTCT
1541569 ATGATTCAGT
Statistics
Matches: 243, Mismatches: 19, Indels: 28
0.84 0.07 0.10
Matches are distributed among these distances:
69 1 0.00
70 64 0.26
71 4 0.02
73 30 0.12
74 1 0.00
75 3 0.01
76 136 0.56
77 4 0.02
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (76 bp):
GTCCAATGACTGTGGTCCATCATCATCATCATCATTTCCTATCTTAGTTCACTGTCTCTGAGTCC
AACGTCTGAGA
Found at i:1541498 original size:146 final size:150
Alignment explanation
Indices: 1541190--1541568 Score: 428
Period size: 146 Copynumber: 2.6 Consensus size: 150
1541180 ACTGTCTCCG
* * * *
1541190 AGTCCATTGTCTGAGAGTCC-ACTAACTGTG-GTCCACTGACTGTGGTCCATC-T--TCAT-A--
1 AGTCCACTGTCTGTGAGTCCAAC-ATCTGTGAGTCCACAGACTGTGGTCCATCATCATCATCATC
* * * *
1541247 ATTTGCTATCTTAGTCCACTGTCTGTGAGTCCACTGTTTGTGAGTCCAATGATCGTGGTCCATCA
65 ATTTGCTATCTTAGTTCACTGTCTCTGAGTCCACTGTCTGAGAGTCCAATGATCGTGGTCCA-CA
1541312 TCATCATCATCATTTCCTATCTT
129 TCATCATCATCA-TTCCTATCTT
** * *
1541335 AGTTTACTGTCTCTGAGTCCAACATCTGAGAGTCCACAGACTGTGGTCCATCATCATCATCATCA
1 AGTCCACTGTCTGTGAGTCCAACATCTGTGAGTCCACAGACTGTGGTCCATCATCATCATCATCA
* * *
1541400 TTTCCTATCTTAGTTTACTGTCTCTGAGTCCAAC-GTCTGAGAGTCCACTGA-CTGTGGT-C-CA
66 TTTGCTATCTTAGTTCACTGTCTCTGAGTCC-ACTGTCTGAGAGTCCAATGATC-GTGGTCCACA
1541461 TCATCATCATC-TT-CTATCTT
129 TCATCATCATCATTCCTATCTT
*** *
1541481 AGTCCACTGTCTGTGAGTCCATTGTTTGTGAGTCCA-ATGACTGTGGTCCATCATCATCATCATC
1 AGTCCACTGTCTGTGAGTCCAACATCTGTGAGTCCACA-GACTGTGGTCCATCATCATCATCATC
1541545 ATTTGCTATCTTAGTTCACTGTCT
65 ATTTGCTATCTTAGTTCACTGTCT
1541569 ATGATTCAGT
Statistics
Matches: 198, Mismatches: 25, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
145 21 0.11
146 105 0.53
147 3 0.02
149 17 0.09
150 1 0.01
151 2 0.01
152 47 0.24
153 2 0.01
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (150 bp):
AGTCCACTGTCTGTGAGTCCAACATCTGTGAGTCCACAGACTGTGGTCCATCATCATCATCATCA
TTTGCTATCTTAGTTCACTGTCTCTGAGTCCACTGTCTGAGAGTCCAATGATCGTGGTCCACATC
ATCATCATCATTCCTATCTT
Found at i:1541501 original size:15 final size:15
Alignment explanation
Indices: 1541481--1541530 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
1541471 CTTCTATCTT
*
1541481 AGTCCACTGTCTGTG
1 AGTCCAATGTCTGTG
* *
1541496 AGTCCATTGTTTGTG
1 AGTCCAATGTCTGTG
*
1541511 AGTCCAATGACTGTG
1 AGTCCAATGTCTGTG
1541526 -GTCCA
1 AGTCCA
1541531 TCATCATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 5 0.17
15 25 0.83
ACGTcount: A:0.18, C:0.22, G:0.26, T:0.34
Consensus pattern (15 bp):
AGTCCAATGTCTGTG
Found at i:1578446 original size:12 final size:12
Alignment explanation
Indices: 1578429--1578453 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1578419 AATGTCTCAG
1578429 ATGTCAGAGACA
1 ATGTCAGAGACA
1578441 ATGTCAGAGACA
1 ATGTCAGAGACA
1578453 A
1 A
1578454 ACATATTACT
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:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (12 bp):
ATGTCAGAGACA
Found at i:1592727 original size:47 final size:47
Alignment explanation
Indices: 1592673--1592770 Score: 187
Period size: 47 Copynumber: 2.1 Consensus size: 47
1592663 CAGCATTTAG
1592673 TTCATACCGACGATGCTTTATCAATGATTATACATAAGTATTGCCAA
1 TTCATACCGACGATGCTTTATCAATGATTATACATAAGTATTGCCAA
*
1592720 TTCATACCGACGATGCTTTATCAATGATTATACCTAAGTATTGCCAA
1 TTCATACCGACGATGCTTTATCAATGATTATACATAAGTATTGCCAA
1592767 TTCA
1 TTCA
1592771 AGGACATGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (47 bp):
TTCATACCGACGATGCTTTATCAATGATTATACATAAGTATTGCCAA
Found at i:1595916 original size:2 final size:2
Alignment explanation
Indices: 1595909--1595940 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1595899 AGCAAAATAT
1595909 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1595941 ATGGGCCGAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1602495 original size:6 final size:5
Alignment explanation
Indices: 1602462--1602511 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
1602452 TTTGCGGGGT
* *
1602462 TTTTG -TTTG -TTTG TTTTG TTTTG TTTTGG TTTTGG TTTTT TTTTT TTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTT-G TTTT-G TTTTG TTTTG TTTTG
1602512 CTATATTGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 8 0.20
5 22 0.54
6 11 0.27
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
TTTTG
Found at i:1602886 original size:2 final size:2
Alignment explanation
Indices: 1602881--1602928 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1602871 TTATATATAT
1602881 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1602923 GA GA GA
1 GA GA GA
1602929 ATCCGGAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1618167 original size:22 final size:22
Alignment explanation
Indices: 1618151--1618194 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1618141 GATAATTTTT
1618151 AGGTTCATACAGAATAAAAATA
1 AGGTTCATACAGAATAAAAATA
*
1618173 AGGTTCATACAGAATTAAAATA
1 AGGTTCATACAGAATAAAAATA
1618195 CACGTACAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (22 bp):
AGGTTCATACAGAATAAAAATA
Found at i:1619844 original size:93 final size:94
Alignment explanation
Indices: 1619737--1619920 Score: 291
Period size: 93 Copynumber: 2.0 Consensus size: 94
1619727 CATAGCTCTG
*
1619737 AAATAAATAAATGACCTGT-ATGAAAAGTTACAGGTAGAGCAGTGAGGCTCGTTACCTGGACAGT
1 AAATAAAT-AATGACCTGTGA-GAAAAGTTACAGGTAGAGCAGTGAGACTCGTTACCTGGACAGT
**
1619801 ATGATTGGTACATTGGGGTTGTTTGTGAGAT
64 ATGAGCGGTACATTGGGGTTGTTTGTGAGAT
* *
1619832 AAATAAAT-ATGACCTGTGAGAATAGTTACAGGTAGAGCAGTGAGACTTGTTACCTGGACAGTAT
1 AAATAAATAATGACCTGTGAGAAAAGTTACAGGTAGAGCAGTGAGACTCGTTACCTGGACAGTAT
1619896 GAGCGGTACATTGGGGTTGTTTGTG
66 GAGCGGTACATTGGGGTTGTTTGTG
1619921 CCGGGCCCGG
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
93 74 0.89
94 1 0.01
95 8 0.10
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.29
Consensus pattern (94 bp):
AAATAAATAATGACCTGTGAGAAAAGTTACAGGTAGAGCAGTGAGACTCGTTACCTGGACAGTAT
GAGCGGTACATTGGGGTTGTTTGTGAGAT
Found at i:1643280 original size:25 final size:25
Alignment explanation
Indices: 1643246--1643865 Score: 864
Period size: 25 Copynumber: 24.4 Consensus size: 25
1643236 CTTGGTAGAC
1643246 ATAACGAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
1643271 ATAACGAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
1643296 ATAACGAAGTGTGTCCGATTGTCCCA
1 ATAACGAAGTGT-TCCGATTGTCCCA
*
1643322 ATAACGAAGTGTTCTGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* *
1643347 ATAACGAAGTGTTACGATTGTCCCT
1 ATAACGAAGTGTTCCGATTGTCCCA
*
1643372 ATAACGAAGTGTTCCGATTGTCCCT
1 ATAACGAAGTGTTCCGATTGTCCCA
* *
1643397 ATAACGAAGTGTTTCAATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
*
1643422 ATAACGAAGTGTTCCGATAGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
*
1643447 ATAACGAAGTGTTCTGATTGTCCCAA
1 ATAACGAAGTGTTCCGATTGTCCC-A
* * *
1643473 TATTAACGAAATGTTCTGATTGTCCCT
1 -A-TAACGAAGTGTTCCGATTGTCCCA
1643500 ATAACGAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* * *
1643525 ATAACGCAGTATTTCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
1643550 ATAACGAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* *
1643575 ATTACAAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
**
1643600 ATAACGAAGTGTTCCGATTGTTAACATTTTA
1 ATAACGAAGTGTTCCGATTG-T--C---CCA
1643631 ATAACGAAGTG-TCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* * *
1643655 ATAACGCAGTATTTCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
1643680 ATAACGAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
*
1643705 ATAACGAAGTGTTCCAATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* *
1643730 ATAACGAAGTGTTCCGATTGTTCTA
1 ATAACGAAGTGTTCCGATTGTCCCA
1643755 ATAACGAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* * *
1643780 ATAACGAAGTATTCCGATTGTTCTA
1 ATAACGAAGTGTTCCGATTGTCCCA
*
1643805 ATAACTAAGTGTTCCGATTGTCCCA
1 ATAACGAAGTGTTCCGATTGTCCCA
* *
1643830 ATAACGAAGTGTTCTGATTGTCCAA
1 ATAACGAAGTGTTCCGATTGTCCCA
*
1643855 ATAATGAAGTG
1 ATAACGAAGTG
1643866 ATTTAGCTTC
Statistics
Matches: 529, Mismatches: 55, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.02
25 445 0.84
26 28 0.05
27 2 0.00
28 23 0.04
29 1 0.00
30 8 0.02
31 12 0.02
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (25 bp):
ATAACGAAGTGTTCCGATTGTCCCA
Found at i:1644740 original size:2 final size:2
Alignment explanation
Indices: 1644733--1644790 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1644723 CTTGACAAAA
*
1644733 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
*
1644775 AG GG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG
1644791 GGTGGGTGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1645269 original size:32 final size:32
Alignment explanation
Indices: 1645233--1645347 Score: 194
Period size: 32 Copynumber: 3.6 Consensus size: 32
1645223 CATGTTGCTC
* *
1645233 TTGGTTCGTCCGTCCGTCTATCCATTAGTCTG
1 TTGGTCCGTCCGTCTGTCTATCCATTAGTCTG
* *
1645265 TTGGTCCGTCCGTCTGTCTTTCCATTAGTCAG
1 TTGGTCCGTCCGTCTGTCTATCCATTAGTCTG
1645297 TTGGTCCGTCCGTCTGTCTATCCATTAGTCTG
1 TTGGTCCGTCCGTCTGTCTATCCATTAGTCTG
1645329 TTGGTCCGTCCGTCTGTCT
1 TTGGTCCGTCCGTCTGTCT
1645348 TTCCGTCTGA
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 77 1.00
ACGTcount: A:0.08, C:0.29, G:0.23, T:0.41
Consensus pattern (32 bp):
TTGGTCCGTCCGTCTGTCTATCCATTAGTCTG
Found at i:1645281 original size:16 final size:16
Alignment explanation
Indices: 1645260--1645345 Score: 59
Period size: 16 Copynumber: 5.4 Consensus size: 16
1645250 CTATCCATTA
1645260 GTCTGTTGGTCCGTCC
1 GTCTGTTGGTCCGTCC
* * **
1645276 GTCTGTCT-TTCCATTA
1 GTCTGT-TGGTCCGTCC
*
1645292 GTCAGTTGGTCCGTCC
1 GTCTGTTGGTCCGTCC
* * **
1645308 GTCTGTCT-ATCCATTA
1 GTCTGT-TGGTCCGTCC
1645324 GTCTGTTGGTCCGTCC
1 GTCTGTTGGTCCGTCC
1645340 GTCTGT
1 GTCTGT
1645346 CTTTCCGTCT
Statistics
Matches: 48, Mismatches: 18, Indels: 8
0.65 0.24 0.11
Matches are distributed among these distances:
15 2 0.04
16 44 0.92
17 2 0.04
ACGTcount: A:0.07, C:0.28, G:0.24, T:0.41
Consensus pattern (16 bp):
GTCTGTTGGTCCGTCC
Found at i:1645352 original size:16 final size:16
Alignment explanation
Indices: 1645268--1645354 Score: 52
Period size: 16 Copynumber: 5.4 Consensus size: 16
1645258 TAGTCTGTTG
1645268 GTCCGTCCGTCTGTCT
1 GTCCGTCCGTCTGTCT
* * ** *
1645284 TTCCATTAGTCAGT-T
1 GTCCGTCCGTCTGTCT
1645299 GGTCCGTCCGTCTGTCT
1 -GTCCGTCCGTCTGTCT
* * **
1645316 ATCCATTAGTCTGT-T
1 GTCCGTCCGTCTGTCT
1645331 GGTCCGTCCGTCTGTCT
1 -GTCCGTCCGTCTGTCT
*
1645348 TTCCGTC
1 GTCCGTC
1645355 TGAGGGTCCG
Statistics
Matches: 48, Mismatches: 19, Indels: 8
0.64 0.25 0.11
Matches are distributed among these distances:
15 2 0.04
16 44 0.92
17 2 0.04
ACGTcount: A:0.07, C:0.31, G:0.22, T:0.40
Consensus pattern (16 bp):
GTCCGTCCGTCTGTCT
Found at i:1645355 original size:28 final size:29
Alignment explanation
Indices: 1645259--1645365 Score: 117
Period size: 32 Copynumber: 3.5 Consensus size: 29
1645249 TCTATCCATT
1645259 AGTCTGTTGGTCCGTCCGTCTGTCTTTCC
1 AGTCTGTTGGTCCGTCCGTCTGTCTTTCC
* *
1645288 ATTAGTCAGTTGGTCCGTCCGTCTGTCTATCC
1 ---AGTCTGTTGGTCCGTCCGTCTGTCTTTCC
1645320 ATTAGTCTGTTGGTCCGTCCGTCTGTCTTTCC
1 ---AGTCTGTTGGTCCGTCCGTCTGTCTTTCC
**
1645352 -GTCTGAGGGTCCGT
1 AGTCTGTTGGTCCGT
1645366 TCGTGTATGT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
28 12 0.17
32 57 0.83
ACGTcount: A:0.07, C:0.28, G:0.25, T:0.39
Consensus pattern (29 bp):
AGTCTGTTGGTCCGTCCGTCTGTCTTTCC
Found at i:1646152 original size:151 final size:148
Alignment explanation
Indices: 1645873--1646169 Score: 416
Period size: 151 Copynumber: 2.0 Consensus size: 148
1645863 TATACATGCC
* *
1645873 CAAAAATCTTATTTCAGCAATTCAAGTGTATATAAAAAATTGCATACTCTAGTATGAGCATAAAT
1 CAAAAATCTTATTTCAGCAATTCAAGTGTATAGAAAAAATTGCATACTCTAGAATGAGCATAAAT
* * *
1645938 GCCCGGTTAGGTATCCTAATTTTATGCGAGAAAGCTTGTCAAAGTAGAAGCAAATCAATAACAAA
66 GCCCGGTAAGGTATCCTAATTCTAAGCGAGAAAGCTTGTCAAAGTAGAAGCAAATCAATAACAAA
1646003 TTCTTTCAAAAAAGTTATT
131 TTCTTT-AAAAAAGTTATT
** * **
1646022 CAAAAATTCTTATTTCAGCAATTCAAGTGTATAGAGGAAATTTCATACTCTAGAATCTTGCATAA
1 CAAAAA-TCTTATTTCAGCAATTCAAGTGTATAGAAAAAATTGCATACTCTAGAAT-GAGCATAA
* * * *
1646087 ATGCCTGGTAAGGTA-CTCTAATTCTAAGCGAGAAAGCTTGTCAAGGTAGTAGTAAATCAATAAC
64 ATGCCCGGTAAGGTATC-CTAATTCTAAGCGAGAAAGCTTGTCAAAGTAGAAGCAAATCAATAAC
*
1646151 AAATTCTTTGAAAAAGTTA
128 AAATTCTTTAAAAAAGTTA
1646170 GGAACGTGCG
Statistics
Matches: 130, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
149 6 0.05
150 54 0.42
151 70 0.54
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (148 bp):
CAAAAATCTTATTTCAGCAATTCAAGTGTATAGAAAAAATTGCATACTCTAGAATGAGCATAAAT
GCCCGGTAAGGTATCCTAATTCTAAGCGAGAAAGCTTGTCAAAGTAGAAGCAAATCAATAACAAA
TTCTTTAAAAAAGTTATT
Found at i:1651878 original size:2 final size:2
Alignment explanation
Indices: 1651871--1651916 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1651861 AATGCTTTTT
1651871 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1651913 AG AG
1 AG AG
1651917 TTATATTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1655026 original size:11 final size:11
Alignment explanation
Indices: 1655007--1655039 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1654997 GACCAACAAA
1655007 TACACTGTATG
1 TACACTGTATG
*
1655018 TACATTGTATG
1 TACACTGTATG
1655029 TACACTGTATG
1 TACACTGTATG
1655040 CAGGGATGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (11 bp):
TACACTGTATG
Found at i:1656285 original size:13 final size:13
Alignment explanation
Indices: 1656267--1656291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1656257 AATTACACTC
1656267 AATTACCATTACA
1 AATTACCATTACA
1656280 AATTACCATTAC
1 AATTACCATTAC
1656292 CCCATCCCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AATTACCATTACA
Found at i:1656320 original size:11 final size:11
Alignment explanation
Indices: 1656304--1656643 Score: 419
Period size: 11 Copynumber: 30.9 Consensus size: 11
1656294 CATCCCTGAC
1656304 TGTATGTACAT
1 TGTATGTACAT
* *
1656315 TGTATGTGCAC
1 TGTATGTACAT
*
1656326 TGTATGTATAT
1 TGTATGTACAT
*
1656337 TGTATGTACAC
1 TGTATGTACAT
*
1656348 TGTATGTACAC
1 TGTATGTACAT
*
1656359 TGTATGTACAC
1 TGTATGTACAT
*
1656370 TGTATGTATAT
1 TGTATGTACAT
1656381 TGTATGTACAT
1 TGTATGTACAT
1656392 TGTATGTACAT
1 TGTATGTACAT
1656403 TGTATGTACAT
1 TGTATGTACAT
* *
1656414 TGTATTTATAT
1 TGTATGTACAT
*
1656425 TGTATGTACAC
1 TGTATGTACAT
*
1656436 TGTATGTATAT
1 TGTATGTACAT
*
1656447 TGTATGTAGAT
1 TGTATGTACAT
*
1656458 TGTATGTATAT
1 TGTATGTACAT
1656469 TGTATGTACAT
1 TGTATGTACAT
* *
1656480 TGTATTTATAT
1 TGTATGTACAT
*
1656491 TGTATGTACAC
1 TGTATGTACAT
*
1656502 TGTATGTATAT
1 TGTATGTACAT
*
1656513 TGTATGTATAT
1 TGTATGTACAT
1656524 TGTATGTACAT
1 TGTATGTACAT
* *
1656535 TGTATTTATAT
1 TGTATGTACAT
1656546 TGTATGTACAT
1 TGTATGTACAT
*
1656557 TGTATGTATAT
1 TGTATGTACAT
1656568 TGTATGTACAT
1 TGTATGTACAT
* *
1656579 TGTATTTATAT
1 TGTATGTACAT
*
1656590 TGTATGTACAC
1 TGTATGTACAT
*
1656601 TGTATGTGCAT
1 TGTATGTACAT
* *
1656612 TGTAAGTACAA
1 TGTATGTACAT
* *
1656623 TCTATGTACAC
1 TGTATGTACAT
1656634 TGTATGTACA
1 TGTATGTACA
1656644 GTAGTCAGTC
Statistics
Matches: 281, Mismatches: 48, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 281 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (11 bp):
TGTATGTACAT
Found at i:1658451 original size:2 final size:2
Alignment explanation
Indices: 1658444--1658490 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1658434 ACAAAGTATG
1658444 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1658486 GA GA G
1 GA GA G
1658491 CGCTTTTTTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1664858 original size:180 final size:180
Alignment explanation
Indices: 1664556--1665144 Score: 1133
Period size: 180 Copynumber: 3.3 Consensus size: 180
1664546 ACCCTACATG
*
1664556 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1664621 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
1664686 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
1664736 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1664801 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
* * * *
1664866 CTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGATACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
1664916 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1664981 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
1665046 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
1665096 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTT
1 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTT
1665145 NNNNNNNNNN
Statistics
Matches: 400, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
180 400 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (180 bp):
TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTTCCC
Found at i:1666678 original size:39 final size:39
Alignment explanation
Indices: 1666607--1666681 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
1666597 TCAATGAAGT
* ** *
1666607 AGAAATTTCGAATGTTGCTGTTTAGCTGTTTATATCGGC
1 AGAAATTTCGAATGTTGCCGTTTAAATATTTATATCGGC
1666646 AGAAATTTCGAATGTTGCCGTTTAAATATTTATATC
1 AGAAATTTCGAATGTTGCCGTTTAAATATTTATATC
1666682 ACCAGTGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (39 bp):
AGAAATTTCGAATGTTGCCGTTTAAATATTTATATCGGC
Found at i:1666818 original size:39 final size:38
Alignment explanation
Indices: 1666774--1668126 Score: 1726
Period size: 39 Copynumber: 34.7 Consensus size: 38
1666764 GAATTCTATG
1666774 TTAGCAATGA-ACTCAAGTGTTGCTGTCTATATCATGATA
1 TTAGCAATGATAC-CAA-TGTTGCTGTCTATATCATGATA
* * *
1666813 TTAGCAATGATACCGGATGTTGCTGTCTTTATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1666852 TTAGCAATGATACCGGATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
1666891 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
1666930 -TATGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1 TTA-GCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1666969 TAAGCAATGATGCCGAATGTTGC--TCTCTATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
1667006 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* *
1667045 TAAGCAATGATACCAAATGTTGCTGTCAATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1667084 CTAGCAATGATACCAGATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACCA-ATGTTGCTGTCTATATCATGATA
** * *
1667123 CAAGCAATGATACCGAATGTTGCTGTCTAGATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667162 TTAGCAATGATACCGGATGTTGCTCTCTATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
** *
1667201 TTAGCAATGATACGGGATGGTGCTGTCTATATCATGATA
1 TTAGCAATGATAC-CAATGTTGCTGTCTATATCATGATA
1667240 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* *
1667279 TTAGCAATGATACCGGATGTTGCTCTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1667318 TTAGCAATGATACCGAATGTTGCTGTCTATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
1667357 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * * *
1667396 TTAGCAATGATACCGGATGTTGCTGTCTTTAACCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1667435 TTAGCAATGATACCGAATGTTGCTCTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1667474 TTAGCAATGATACCAAATGTTGCTGTCTATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* *
1667513 TTAGCAATGATAACTAATGTTGCTGTCTATATCCTGATA
1 TTAGCAATGAT-ACCAATGTTGCTGTCTATATCATGATA
* *
1667552 TTAGCAATGATACCGGATGTTGCTGTCTATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667591 TTAGCAATGATACCGGATGTTGCTCTCTATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
** * *
1667630 TTAGCAATGATACCGAATGTAACTGTCTATAACCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1667669 TTAGCAATGATACCGAATGTTGCTGTCTATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667708 TTAGCAATGATACCGGATGTTGCTGTCTATAACCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667747 TTAGCAATGATACCGAATGATGCTGTCAATATCCTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667786 TTAGCAATGATACCGAATGTTGTTGTCTTTATCTTGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667825 TTAGCAATGATACCGGATGTTGCTCTCTGTATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
*
1667864 TTAGCAATGATACCGGATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * *
1667903 TTAGCAACGATACTGAATGTTGCTGTCTATATCCTGATA
1 TTAGCAATGATAC-CAATGTTGCTGTCTATATCATGATA
*
1667942 TTAGCAATGATACCAGATGTTGCTGTCTAT-TACCTGATA
1 TTAGCAATGATACCA-ATGTTGCTGTCTATAT-CATGATA
*
1667981 TTAGCAATGATACCGAATGTTGCTGCCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* * * * *
1668020 TTAACAATTATAACGAATATTGCTATCTATATCATGATA
1 TTAGCAATGAT-ACCAATGTTGCTGTCTATATCATGATA
*
1668059 TAAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1 TTAGCAATGATACC-AATGTTGCTGTCTATATCATGATA
* *
1668098 TTAGCAATGATACCGGATGTTGCAGTCTA
1 TTAGCAATGATACC-AATGTTGCTGTCTA
1668127 GATTATTATT
Statistics
Matches: 1191, Mismatches: 104, Indels: 38
0.89 0.08 0.03
Matches are distributed among these distances:
37 34 0.03
38 9 0.01
39 1137 0.95
40 11 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (38 bp):
TTAGCAATGATACCAATGTTGCTGTCTATATCATGATA
Found at i:1666874 original size:78 final size:78
Alignment explanation
Indices: 1666791--1668126 Score: 1969
Period size: 78 Copynumber: 17.2 Consensus size: 78
1666781 TGAACTCAAG
* * *
1666791 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGGATGTTGCTGTCTTTATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1666856 CAATGATACCGGA
66 CAATGATACCGGA
1666869 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA-TAT
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTA-
*
1666933 GCAATGATACCGAA
65 GCAATGATACCGGA
* * *
1666947 TGTTGCTGTCTATATCATGATATAAGCAATGATGCCGAATGTTGC--TCTCTATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667010 CAATGATACCGAA
66 CAATGATACCGGA
* * * *
1667023 TGTTGCTGTCTATATCATGATATAAGCAATGATACCAAATGTTGCTGTCAATATCATGATACTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667088 CAATGATACCAGA
66 CAATGATACCGGA
** * *
1667101 TGTTGCTGTCTATATCATGATACAAGCAATGATACCGAATGTTGCTGTCTAGATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1667166 CAATGATACCGGA
66 CAATGATACCGGA
* * * * *
1667179 TGTTGCTCTCTATATCCTGATATTAGCAATGATACGGGATGGTGCTGTCTATATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667244 CAATGATACCGAA
66 CAATGATACCGGA
* *
1667257 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGGATGTTGCTCTCTATATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667322 CAATGATACCGAA
66 CAATGATACCGGA
*
1667335 TGTTGCTGTCTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1667400 CAATGATACCGGA
66 CAATGATACCGGA
* * * *
1667413 TGTTGCTGTCTTTAACCTGATATTAGCAATGATACCGAATGTTGCTCTCTATATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
**
1667478 CAATGATACCAAA
66 CAATGATACCGGA
* * * *
1667491 TGTTGCTGTCTATATCCTGATATTAGCAATGATAACTAATGTTGCTGTCTATATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1667556 CAATGATACCGGA
66 CAATGATACCGGA
* * * *
1667569 TGTTGCTGTCTATATCCTGATATTAGCAATGATACCGGATGTTGCTCTCTATATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667634 CAATGATACCGAA
66 CAATGATACCGGA
** * * *
1667647 TGTAACTGTCTATAACCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1667712 CAATGATACCGGA
66 CAATGATACCGGA
* * * * *
1667725 TGTTGCTGTCTATAACCTGATATTAGCAATGATACCGAATGATGCTGTCAATATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667790 CAATGATACCGAA
66 CAATGATACCGGA
* * * * * *
1667803 TGTTGTTGTCTTTATCTTGATATTAGCAATGATACCGGATGTTGCTCTCTGTATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1667868 CAATGATACCGGA
66 CAATGATACCGGA
* * *
1667881 TGTTGCTGTCTATATCATGATATTAGCAACGATACTGAATGTTGCTGTCTATATCCTGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
*
1667946 CAATGATACCAGA
66 CAATGATACCGGA
* *
1667959 TGTTGCTGTCTAT-TACCTGATATTAGCAATGATACCGAATGTTGCTGCCTATATCATGATATTA
1 TGTTGCTGTCTATAT-CATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTA
* * * *
1668023 ACAATTATAACGAA
65 GCAATGATACCGGA
* * *
1668037 TATTGCTATCTATATCATGATATAAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1 TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
1668102 CAATGATACCGGA
66 CAATGATACCGGA
*
1668115 TGTTGCAGTCTA
1 TGTTGCTGTCTA
1668127 GATTATTATT
Statistics
Matches: 1140, Mismatches: 112, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
76 70 0.06
77 5 0.00
78 1064 0.93
79 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (78 bp):
TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAG
CAATGATACCGGA
Found at i:1666927 original size:117 final size:117
Alignment explanation
Indices: 1666774--1668126 Score: 1975
Period size: 117 Copynumber: 11.6 Consensus size: 117
1666764 GAATTCTATG
*
1666774 TTAGCAATGA-ACTC-AAGTGTTGCTGTCTATATCATGATATTAGCAATGATACCGGATGTTGCT
1 TTAGCAATGATAC-CGAA-TGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCT
* *
1666837 GTCTTTATCCTGATATTAGCAATGATACCGGATGTTGCTGTCTATATCATGATA
64 GTCTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
1666891 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA-TATGCAATGATACCGAATGTTGCTG
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTA-GCAATGATACCGAATGTTGCTG
* * * *
1666955 TCTATATCATGATATAAGCAATGATGCCGAATGTTGC--TCTCTATCATGATA
65 TCTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* *
1667006 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATAAGCAATGATACCAAATGTTGCTGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* * *
1667071 CAATATCATGATACTAGCAATGATACC-AGATGTTGCTGTCTATATCATGATA
66 CTATATCCTGATATTAGCAATGATACCGA-ATGTTGCTGTCTATATCATGATA
** * * * *
1667123 CAAGCAATGATACCGAATGTTGCTGTCTAGATCCTGATATTAGCAATGATACCGGATGTTGCTCT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* * *
1667188 CTATATCCTGATATTAGCAATGATACGGGATGGTGCTGTCTATATCATGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* *
1667240 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGGATGTTGCTCT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* *
1667305 CTATATCATGATATTAGCAATGATACCGAATGTTGCTGTCTATATCCTGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
*
1667357 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGGATGTTGCTGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* * *
1667422 CTTTAACCTGATATTAGCAATGATACCGAATGTTGCTCTCTATATCATGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* * * *
1667474 TTAGCAATGATACCAAATGTTGCTGTCTATATCCTGATATTAGCAATGATAACTAATGTTGCTGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* *
1667539 CTATATCCTGATATTAGCAATGATACCGGATGTTGCTGTCTATATCCTGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* * * **
1667591 TTAGCAATGATACCGGATGTTGCTCTCTATATCCTGATATTAGCAATGATACCGAATGTAACTGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* *
1667656 CTATAACCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCCTGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* * * *
1667708 TTAGCAATGATACCGGATGTTGCTGTCTATAACCTGATATTAGCAATGATACCGAATGATGCTGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* * * *
1667773 CAATATCCTGATATTAGCAATGATACCGAATGTTGTTGTCTTTATCTTGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* * * *
1667825 TTAGCAATGATACCGGATGTTGCTCTCTGTATCATGATATTAGCAATGATACCGGATGTTGCTGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
* * * *
1667890 CTATATCATGATATTAGCAACGATACTGAATGTTGCTGTCTATATCCTGATA
66 CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
*
1667942 TTAGCAATGATACC-AGATGTTGCTGTCTAT-TACCTGATATTAGCAATGATACCGAATGTTGCT
1 TTAGCAATGATACCGA-ATGTTGCTGTCTATAT-CATGATATTAGCAATGATACCGAATGTTGCT
* * * * * * *
1668005 GCCTATATCATGATATTAACAATTATAACGAATATTGCTATCTATATCATGATA
64 GTCTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
* * *
1668059 TAAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGGATGTTGCAGT
1 TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
1668124 CTA
66 CTA
1668127 GATTATTATT
Statistics
Matches: 1120, Mismatches: 104, Indels: 24
0.90 0.08 0.02
Matches are distributed among these distances:
114 1 0.00
115 104 0.09
116 4 0.00
117 1005 0.90
118 6 0.01
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (117 bp):
TTAGCAATGATACCGAATGTTGCTGTCTATATCATGATATTAGCAATGATACCGAATGTTGCTGT
CTATATCCTGATATTAGCAATGATACCGAATGTTGCTGTCTATATCATGATA
Found at i:1668808 original size:56 final size:56
Alignment explanation
Indices: 1668678--1668908 Score: 372
Period size: 56 Copynumber: 4.1 Consensus size: 56
1668668 CTTCACCATT
* *
1668678 TTTTTCTTTGACTCTGATAACTTCACTACCTGTAGGTAGGAGCAAGATATCTGCGGG
1 TTTTTCTTTGACTCTGATAACCTCACTACATGTAGGTAGGAGC-AGATATCTGCGGG
* *
1668735 TTTTTCTTTGACTCTGATAACTTCACTACATGTAGGTAGGAGCAGATATCTGTGGG
1 TTTTTCTTTGACTCTGATAACCTCACTACATGTAGGTAGGAGCAGATATCTGCGGG
* * *
1668791 TTTTTCTTTGACTCTGATATCCTCACCACATGTAGGTAGGAGCAGATATCTGTGGG
1 TTTTTCTTTGACTCTGATAACCTCACTACATGTAGGTAGGAGCAGATATCTGCGGG
* *
1668847 TTTTTCTTTGACTCTGATAACCTCACTACCTATAGGTAGGAGCAGATATCTGCGGG
1 TTTTTCTTTGACTCTGATAACCTCACTACATGTAGGTAGGAGCAGATATCTGCGGG
1668903 TTTTTC
1 TTTTTC
1668909 GGAGCTGACC
Statistics
Matches: 164, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
56 122 0.74
57 42 0.26
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (56 bp):
TTTTTCTTTGACTCTGATAACCTCACTACATGTAGGTAGGAGCAGATATCTGCGGG
Found at i:1669139 original size:16 final size:16
Alignment explanation
Indices: 1669115--1669184 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
1669105 TGATGTAATA
1669115 ATAATTTTTGGAAATG
1 ATAATTTTTGGAAATG
* *
1669131 ATAACTTTTGGAACTG
1 ATAATTTTTGGAAATG
* *
1669147 GTAATTCTTGGAAATG
1 ATAATTTTTGGAAATG
*
1669163 ATAATTTTTGGAAATT
1 ATAATTTTTGGAAATG
1669179 ATAATT
1 ATAATT
1669185 CTTCAGGACC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (16 bp):
ATAATTTTTGGAAATG
Found at i:1673696 original size:107 final size:107
Alignment explanation
Indices: 1673510--1673724 Score: 394
Period size: 107 Copynumber: 2.0 Consensus size: 107
1673500 AAATCATTCT
* *
1673510 TTTTGGGAGTTGATTTTAATCAACTCCCCTATGCGATTCCTTTGGCAAACCGGAAGTAAAACAGT
1 TTTTGGGAGTTGATTTTAAACAACTCCCCTATGCGATTACTTTGGCAAACCGGAAGTAAAACAGT
1673575 GTTTGAACCTAAGCACAACTCATCGCCGCCGACAAAACGTAG
66 GTTTGAACCTAAGCACAACTCATCGCCGCCGACAAAACGTAG
1673617 TTTTGGGAGTTGATTTTAAACAACTCCCCTATGCGATTACTTTGGCAAACCGGAAGTAAAACAGT
1 TTTTGGGAGTTGATTTTAAACAACTCCCCTATGCGATTACTTTGGCAAACCGGAAGTAAAACAGT
* *
1673682 GTTTGGACCTAAGCACAACTCATCGCCGCCGACATAACGTAG
66 GTTTGAACCTAAGCACAACTCATCGCCGCCGACAAAACGTAG
1673724 T
1 T
1673725 ACTTGAATAT
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.27
Consensus pattern (107 bp):
TTTTGGGAGTTGATTTTAAACAACTCCCCTATGCGATTACTTTGGCAAACCGGAAGTAAAACAGT
GTTTGAACCTAAGCACAACTCATCGCCGCCGACAAAACGTAG
Found at i:1675418 original size:2 final size:2
Alignment explanation
Indices: 1675411--1675457 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1675401 GGGAAGGGGT
1675411 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1675453 TC TC T
1 TC TC T
1675458 TATCAAAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1679160 original size:51 final size:51
Alignment explanation
Indices: 1679100--1679571 Score: 597
Period size: 51 Copynumber: 9.0 Consensus size: 51
1679090 TACGACGTTC
1679100 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
* * *
1679151 ACAATCTGTATGGACACAGTGAGAGTATGGTCGCAAATAGGTGAGTACAGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
* * *
1679202 ATAATCAGTATGGGCACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
* *
1679253 ACAATCTGTATGGACACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
1679304 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
* * * ** * *
1679355 ACAATCTGTATGGTCACCAATAGGTGAGTACAGT-A-CAATCATGGTCGCCAATAGGTGAGT
1 ACAATCTGTATGGGCA-CAGT--GAGAGTATGGTCACCAAT-A-GGT-G--AGTA---CAGT
*
1679415 ACAGTACAATCTGTATGGGCACAGTGAGAGTGTGGTCACCAATAGGTGAGTACAGT
1 -----ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
* **
1679471 ACAATCAGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
**
1679522 ACAATCTGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAG
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAG
1679572 AAACACTAAG
Statistics
Matches: 371, Mismatches: 32, Indels: 36
0.85 0.07 0.08
Matches are distributed among these distances:
51 303 0.82
52 7 0.02
53 2 0.01
54 11 0.03
55 1 0.00
56 3 0.01
57 3 0.01
59 3 0.01
60 3 0.01
61 1 0.00
62 10 0.03
63 2 0.01
64 7 0.02
65 15 0.04
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (51 bp):
ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGT
Found at i:1679239 original size:102 final size:102
Alignment explanation
Indices: 1679100--1679571 Score: 701
Period size: 102 Copynumber: 4.5 Consensus size: 102
1679090 TACGACGTTC
1679100 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGA
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGA
*
1679165 CACAGTGAGAGTATGGTCGCAAATAGGTGAGTACAGT
66 CACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
* * *
1679202 ATAATCAGTATGGGCACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGA
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGA
1679267 CACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
66 CACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
1679304 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGT
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGG-
*
1679369 CACCAATAGGTGAGTACAGTACAATCATGGTCGCCAATAGGTGAGTACAGT
65 -A-C-ACA-GTGAG---AG-----T-ATGGTCGCCAATAGGTGAGTACAGT
* * *
1679420 ACAATCTGTATGGGCACAGTGAGAGTGTGGTCACCAATAGGTGAGTACAGTACAATCAGTATGGG
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGA
** *
1679485 CACAGTGAGAACATGGTCACCAATAGGTGAGTACAGT
66 CACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
**
1679522 ACAATCTGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAG
1 ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAG
1679572 AAACACTAAG
Statistics
Matches: 338, Mismatches: 18, Indels: 28
0.88 0.05 0.07
Matches are distributed among these distances:
102 230 0.68
104 1 0.00
105 1 0.00
106 2 0.01
107 5 0.01
108 1 0.00
110 2 0.01
111 5 0.01
112 2 0.01
113 1 0.00
115 1 0.00
116 87 0.26
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (102 bp):
ACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGA
CACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGT
Found at i:1679366 original size:34 final size:34
Alignment explanation
Indices: 1679328--1679432 Score: 180
Period size: 34 Copynumber: 3.2 Consensus size: 34
1679318 CACAGTGAGA
1679328 GTATGGTCACCAATAGGTGAGTACAGTACAATCT
1 GTATGGTCACCAATAGGTGAGTACAGTACAATCT
1679362 GTATGGTCACCAATAGGTGAGTACAGTACAATC-
1 GTATGGTCACCAATAGGTGAGTACAGTACAATCT
*
1679395 --ATGGTCGCCAATAGGTGAGTACAGTACAATCT
1 GTATGGTCACCAATAGGTGAGTACAGTACAATCT
1679427 GTATGG
1 GTATGG
1679433 GCACAGTGAG
Statistics
Matches: 67, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
31 30 0.45
34 37 0.55
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (34 bp):
GTATGGTCACCAATAGGTGAGTACAGTACAATCT
Found at i:1679422 original size:167 final size:167
Alignment explanation
Indices: 1679228--1679534 Score: 560
Period size: 167 Copynumber: 1.8 Consensus size: 167
1679218 CAGTGAGAGT
*
1679228 ATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGACACAGTGAGAGTATGGTCGCCAATAG
1 ATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGACACAGTGAGAGTATGGTCACCAATAG
* **
1679293 GTGAGTACAGTACAATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACA
66 GTGAGTACAGTACAATCAGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
1679358 ATCTGTATGGTCACCAATAGGTGAGTACAGTACAATC
131 ATCTGTATGGTCACCAATAGGTGAGTACAGTACAATC
* *
1679395 ATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGGCACAGTGAGAGTGTGGTCACCAATAG
1 ATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGACACAGTGAGAGTATGGTCACCAATAG
1679460 GTGAGTACAGTACAATCAGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
66 GTGAGTACAGTACAATCAGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
1679525 ATCTGTATGG
131 ATCTGTATGG
1679535 GCACAGTGAG
Statistics
Matches: 134, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
167 134 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (167 bp):
ATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGACACAGTGAGAGTATGGTCACCAATAG
GTGAGTACAGTACAATCAGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
ATCTGTATGGTCACCAATAGGTGAGTACAGTACAATC
Found at i:1679555 original size:218 final size:218
Alignment explanation
Indices: 1679177--1679571 Score: 682
Period size: 218 Copynumber: 1.8 Consensus size: 218
1679167 CAGTGAGAGT
* *
1679177 ATGGTCGCAAATAGGTGAGTACAGTATAATCAGTATGGGCACAGTGAGAGTATGGTCGCCAATAG
1 ATGGTCGCAAATAGGTGAGTACAGTACAATCAGTATGGGCACAGTGAGAGTATGGTCACCAATAG
* ** *
1679242 GTGAGTACAGTACAATCTGTATGGACACAGTGAGAGTATGGTCGCCAATAGGTGAGTACAGTACA
66 GTGAGTACAGTACAATCAGTATGGACACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
**
1679307 ATCTGTATGGGCACAGTGAGAGTATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGTCAC
131 ATCTGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGTCAC
1679372 CAATAGGTGAGTACAGTACAATC
196 CAATAGGTGAGTACAGTACAATC
* * *
1679395 ATGGTCGCCAATAGGTGAGTACAGTACAATCTGTATGGGCACAGTGAGAGTGTGGTCACCAATAG
1 ATGGTCGCAAATAGGTGAGTACAGTACAATCAGTATGGGCACAGTGAGAGTATGGTCACCAATAG
*
1679460 GTGAGTACAGTACAATCAGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
66 GTGAGTACAGTACAATCAGTATGGACACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
1679525 ATCTGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAG
131 ATCTGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAG
1679572 AAACACTAAG
Statistics
Matches: 165, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
218 165 1.00
ACGTcount: A:0.32, C:0.16, G:0.29, T:0.23
Consensus pattern (218 bp):
ATGGTCGCAAATAGGTGAGTACAGTACAATCAGTATGGGCACAGTGAGAGTATGGTCACCAATAG
GTGAGTACAGTACAATCAGTATGGACACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACA
ATCTGTATGGGCACAGTGAGAACATGGTCACCAATAGGTGAGTACAGTACAATCTGTATGGTCAC
CAATAGGTGAGTACAGTACAATC
Found at i:1683944 original size:2 final size:2
Alignment explanation
Indices: 1683939--1683982 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1683929 AGATTATGAA
1683939 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1683981 TC
1 TC
1683983 ATATCAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1687125 original size:13 final size:13
Alignment explanation
Indices: 1687107--1687131 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1687097 TTAATGCAGA
1687107 TTAATGCAAATTC
1 TTAATGCAAATTC
1687120 TTAATGCAAATT
1 TTAATGCAAATT
1687132 ATTCTATATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (13 bp):
TTAATGCAAATTC
Found at i:1687998 original size:43 final size:43
Alignment explanation
Indices: 1687940--1688063 Score: 124
Period size: 43 Copynumber: 2.9 Consensus size: 43
1687930 GTTAACATAA
* * * * *
1687940 TACAAATGTAGCCATACTTTATCAAATAACTTTGTAACAAAAAG
1 TACAAAAGTAACCATACTTCATCAAATAGCTATGTAAC-AAAAG
** * * * *
1687984 TACATTA-TAACCATACCTCATTAAATAGCTGTGTAACAAACG
1 TACAAAAGTAACCATACTTCATCAAATAGCTATGTAACAAAAG
*
1688026 TACAAAAGTAGCCATACTTCATCAAATAGCTATGTAAC
1 TACAAAAGTAACCATACTTCATCAAATAGCTATGTAAC
1688064 TTAAGTTCAC
Statistics
Matches: 63, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
42 9 0.14
43 50 0.79
44 4 0.06
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.28
Consensus pattern (43 bp):
TACAAAAGTAACCATACTTCATCAAATAGCTATGTAACAAAAG
Found at i:1688098 original size:42 final size:42
Alignment explanation
Indices: 1688039--1688158 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 42
1688029 AAAAGTAGCC
* *
1688039 ATACTTCATCAAATAGCTATGTAACTTAAGTTCACTGTAGTA
1 ATACTTCATCAAATAGCTCTGTAACTTAAGTACACTGTAGTA
* * * *
1688081 ATATTTCATCAAATAGCTCTGTGA-TCAAAGTACACTGTAGTC
1 ATACTTCATCAAATAGCTCTGTAACT-TAAGTACACTGTAGTA
* *
1688123 ATACTTCATCAATTAGCTCTGAAACTTAAGTA-ACTG
1 ATACTTCATCAAATAGCTCTGTAACTTAAGTACACTG
1688159 AAGCCGTGCT
Statistics
Matches: 65, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
41 5 0.08
42 59 0.91
43 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.34
Consensus pattern (42 bp):
ATACTTCATCAAATAGCTCTGTAACTTAAGTACACTGTAGTA
Found at i:1688199 original size:29 final size:29
Alignment explanation
Indices: 1688167--1688228 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
1688157 TGAAGCCGTG
*
1688167 CTTCGTAACTAATGTAAACTGTAACCATA
1 CTTCGTAACTAAAGTAAACTGTAACCATA
* *
1688196 CTTCGTAACTAAAGTACATTGTAACCATA
1 CTTCGTAACTAAAGTAAACTGTAACCATA
1688225 CTTC
1 CTTC
1688229 ATCAAATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (29 bp):
CTTCGTAACTAAAGTAAACTGTAACCATA
Found at i:1688681 original size:2 final size:2
Alignment explanation
Indices: 1688674--1688718 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1688664 AATTTCTGAT
1688674 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1688716 TG T
1 TG T
1688719 CGATTACTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1690180 original size:2 final size:2
Alignment explanation
Indices: 1690175--1690212 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1690165 GATCTCTCGA
1690175 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1690213 ATTAGCGAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1690498 original size:24 final size:24
Alignment explanation
Indices: 1690466--1690539 Score: 139
Period size: 24 Copynumber: 3.1 Consensus size: 24
1690456 AATCATAAAG
1690466 TTCCCATGAGAAGTGAAATATCAA
1 TTCCCATGAGAAGTGAAATATCAA
*
1690490 TTCCCATGAGAAGTTAAATATCAA
1 TTCCCATGAGAAGTGAAATATCAA
1690514 TTCCCATGAGAAGTGAAATATCAA
1 TTCCCATGAGAAGTGAAATATCAA
1690538 TT
1 TT
1690540 TTTTGTTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (24 bp):
TTCCCATGAGAAGTGAAATATCAA
Found at i:1694820 original size:2 final size:2
Alignment explanation
Indices: 1694807--1694839 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1694797 CGTTCTTCGC
*
1694807 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1694840 TTACTCATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1696223 original size:2 final size:2
Alignment explanation
Indices: 1696216--1696270 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1696206 TTGGACTTTC
1696216 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1696258 AG AG AG AG AG AG A
1 AG AG AG AG AG AG A
1696271 TTCCTTTGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1696648 original size:49 final size:49
Alignment explanation
Indices: 1696595--1696723 Score: 181
Period size: 49 Copynumber: 2.7 Consensus size: 49
1696585 TGTACAACGC
*
1696595 AGGACAAAAACATGACATAGTAACAAATCAGAAAGCGCCCATACAACAT
1 AGGACAAAAACATGACATAGTAACAAATCAGAAAGCACCCATACAACAT
*
1696644 AGGACAAAAACATGACATAATAACAAATCAGAAAGCACCCATACAACAT
1 AGGACAAAAACATGACATAGTAACAAATCAGAAAGCACCCATACAACAT
* * * *
1696693 --GATAAAATATAAGACATAGTAACAAAGCAGA
1 AGGACAAAA-ACATGACATAGTAACAAATCAGA
1696724 GAGTATAGAA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
47 6 0.08
48 19 0.26
49 47 0.65
ACGTcount: A:0.54, C:0.19, G:0.13, T:0.13
Consensus pattern (49 bp):
AGGACAAAAACATGACATAGTAACAAATCAGAAAGCACCCATACAACAT
Found at i:1698131 original size:17 final size:17
Alignment explanation
Indices: 1698109--1698159 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 17
1698099 CATATACATG
1698109 CATGTAAATTAAATATA
1 CATGTAAATTAAATATA
1698126 CATGTATGTAAATTAAATATA
1 C----ATGTAAATTAAATATA
*
1698147 AATGTAAATTAAA
1 CATGTAAATTAAA
1698160 ATTCAGGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 13 0.45
21 16 0.55
ACGTcount: A:0.53, C:0.04, G:0.08, T:0.35
Consensus pattern (17 bp):
CATGTAAATTAAATATA
Found at i:1698151 original size:21 final size:21
Alignment explanation
Indices: 1698100--1698152 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1698090 TCATAAATTC
*
1698100 ATATACATGCATGTAAATTAA
1 ATATACATGTATGTAAATTAA
1698121 ATATACATGTATGTAAATTAA
1 ATATACATGTATGTAAATTAA
*
1698142 ATATAAATGTA
1 ATATACATGTA
1698153 AATTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATACATGTATGTAAATTAA
Found at i:1705165 original size:16 final size:17
Alignment explanation
Indices: 1705144--1705177 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1705134 CTGATTGCAT
1705144 TACATGTA-CTAGGTTA
1 TACATGTACCTAGGTTA
1705160 TACATGTACCTAGGTTA
1 TACATGTACCTAGGTTA
1705177 T
1 T
1705178 TCACCCATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (17 bp):
TACATGTACCTAGGTTA
Found at i:1713338 original size:80 final size:80
Alignment explanation
Indices: 1713237--1713862 Score: 1089
Period size: 80 Copynumber: 7.8 Consensus size: 80
1713227 TTTGTAAAAG
1713237 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1713302 GAAATATTCGCACAA
66 GAAATATTCGCACAA
1713317 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1713382 GAAATATTCGCACAA
66 GAAATATTCGCACAA
* *
1713397 TTTATTCTAAATATAGTGCTTTTAAAAAAAAAAAAAATAATATACATGTAAATTTACATGCAGGT
1 TTTATTCTAAATATAGTGC-TTT---AAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGT
1713462 AAAAGAAATATTCGCACAA
62 AAAAGAAATATTCGCACAA
*
1713481 TTTATTCTAAATATAGTGCTTTTAAAAAAAAAAAATAGTATTCATGTAAATTTACATGCATGTAA
1 TTTATTCTAAATATAGTGC-TTT-AAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAA
1713546 AAGAAATATTCGCACAA
64 AAGAAATATTCGCACAA
1713563 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1713628 GAAATATTCGCACAA
66 GAAATATTCGCACAA
*
1713643 -TTATTTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATACATGTAAATTTACATGCAGGTAAA
1 TTTA-TTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAA
1713707 AGAAATATTCGCACAA
65 AGAAATATTCGCACAA
* *
1713723 TTTATTCTAAATATAGTGCTTTTAAAAAAAAAATAGTATTCATGTAAATTAACATGCAGGTAAAA
1 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1713788 GAAATATTCGCACAA
66 GAAATATTCGCACAA
1713803 TTTATTCTAAATATATAGTGCTTT--AAAAAAAAA-AGTATTCATGTAAATTTACATGCAGGT
1 TTTATTCT-AA-ATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGT
1713863 TCAACTAATT
Statistics
Matches: 527, Mismatches: 11, Indels: 17
0.95 0.02 0.03
Matches are distributed among these distances:
79 29 0.06
80 321 0.61
81 11 0.02
82 87 0.17
84 79 0.15
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (80 bp):
TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
GAAATATTCGCACAA
Found at i:1713365 original size:37 final size:37
Alignment explanation
Indices: 1713244--1713365 Score: 91
Period size: 37 Copynumber: 3.1 Consensus size: 37
1713234 AAGTTTATTC
1713244 TAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATG
1 TAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATG
* * ** * * * ** * *
1713281 TAAATTTACATGCAGGTAAAAGAAATATTCGCACAATTTATTC
1 TAAATATA-GTGC-TTTAAAAAAAAAAAT---AGTATTCA-TG
1713324 TAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATG
1 TAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATG
1713361 TAAAT
1 TAAAT
1713366 TTACATGCAG
Statistics
Matches: 57, Mismatches: 22, Indels: 12
0.63 0.24 0.13
Matches are distributed among these distances:
37 13 0.23
38 8 0.14
39 10 0.18
41 10 0.18
42 8 0.14
43 8 0.14
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (37 bp):
TAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATG
Found at i:1713836 original size:326 final size:323
Alignment explanation
Indices: 1713237--1713859 Score: 1098
Period size: 326 Copynumber: 1.9 Consensus size: 323
1713227 TTTGTAAAAG
1713237 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
*
1713302 GAAATATTCGCACAATTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATT
66 GAAATATTCGCACAATTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATACATGTAAATT
1713367 TACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAGTGCTTTTAAAAAAAAAAAA
131 TACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAGTGCTTTT---AAAAAAAAA
*
1713432 AATAATATACATGTAAATTTACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAG
193 AATAATATACATGTAAATTAACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAG
*
1713497 TGCTTTTAAAAAAAAAAAATAGTATTCATGTAAATTTACATGCATGTAAAAGAAATATTCGCACA
258 TGCTTTAAAAAAAAAAAAATAGTATTCATGTAAATTTACATGCATGTAAAAGAAATATTCGCACA
1713562 A
323 A
1713563 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1 TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
1713628 GAAATATTCGCACAA-TTATTTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATACATGTAAAT
66 GAAATATTCGCACAATTTA-TTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATACATGTAAAT
1713692 TTACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAGTGCTTTT-AAAAAAAAAA
130 TTACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAGTGCTTTTAAAAAAAAAAA
* *
1713756 TAGTATTCATGTAAATTAACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATATAG
195 TAATATACATGTAAATTAACATGCAGGTAAAAGAAATATTCGCACAATTTATTCT-AA-ATATAG
1713821 TGCTTT----AAAAAAAAA-AGTATTCATGTAAATTTACATGCA
258 TGCTTTAAAAAAAAAAAAATAGTATTCATGTAAATTTACATGCA
1713860 GGTTCAACTA
Statistics
Matches: 290, Mismatches: 4, Indels: 13
0.94 0.01 0.04
Matches are distributed among these distances:
319 24 0.08
320 9 0.03
322 62 0.21
323 2 0.01
324 12 0.04
325 3 0.01
326 178 0.61
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.33
Consensus pattern (323 bp):
TTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATTCATGTAAATTTACATGCAGGTAAAA
GAAATATTCGCACAATTTATTCTAAATATAGTGCTTTAAAAAAAAAAATAGTATACATGTAAATT
TACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAGTGCTTTTAAAAAAAAAAAT
AATATACATGTAAATTAACATGCAGGTAAAAGAAATATTCGCACAATTTATTCTAAATATAGTGC
TTTAAAAAAAAAAAAATAGTATTCATGTAAATTTACATGCATGTAAAAGAAATATTCGCACAA
Found at i:1713881 original size:13 final size:13
Alignment explanation
Indices: 1713863--1713892 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1713853 ACATGCAGGT
1713863 TCAACTAATTCAG
1 TCAACTAATTCAG
1713876 TCAACTAATTCAG
1 TCAACTAATTCAG
1713889 TCAA
1 TCAA
1713893 AAAACGATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (13 bp):
TCAACTAATTCAG
Found at i:1716231 original size:2 final size:2
Alignment explanation
Indices: 1716224--1716257 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
1716214 GAGGTGGCGC
1716224 AT AT AT AT AT AT AT ANT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A
1716258 CGATACTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1720786 original size:15 final size:16
Alignment explanation
Indices: 1720756--1720789 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1720746 ATTTTCTAGA
1720756 AATTCACACAATATAC
1 AATTCACACAATATAC
*
1720772 AATTCATAC-ATATAC
1 AATTCACACAATATAC
1720787 AAT
1 AAT
1720790 GTTCAAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTCACACAATATAC
Done.