Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 5 of 343
Found at i:1721436 original size:39 final size:39
Alignment explanation
Indices: 1721401--1721513 Score: 181
Period size: 39 Copynumber: 2.9 Consensus size: 39
1721391 TGAAGCAAAT
* *
1721401 AAGTGCTGAACGGAAGCCCGAAGGCTAATTAAAGCACAC
1 AAGTGCTAAACGGAAGCCCGAAGGCTAACTAAAGCACAC
*
1721440 AAGTGCTAAACGGAAGCCCGAAGGCTAACTGAAGCACAC
1 AAGTGCTAAACGGAAGCCCGAAGGCTAACTAAAGCACAC
* *
1721479 AAGTGCTAAACAGAAGCCCGAAGGCTAACTGAAGC
1 AAGTGCTAAACGGAAGCCCGAAGGCTAACTAAAGC
1721514 TCATCAGAGC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.12
Consensus pattern (39 bp):
AAGTGCTAAACGGAAGCCCGAAGGCTAACTAAAGCACAC
Found at i:1721495 original size:21 final size:21
Alignment explanation
Indices: 1721432--1721495 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1721422 AGGCTAATTA
*
1721432 AAGCACACAAGTGCTAAACGG
1 AAGCACACAAGTGCTAAACAG
*
1721453 AAGC-C-CGAAG-GCT-AACTG
1 AAGCACAC-AAGTGCTAAACAG
1721471 AAGCACACAAGTGCTAAACAG
1 AAGCACACAAGTGCTAAACAG
1721492 AAGC
1 AAGC
1721496 CCGAAGGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
18 8 0.22
19 8 0.22
20 8 0.22
21 12 0.33
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.09
Consensus pattern (21 bp):
AAGCACACAAGTGCTAAACAG
Found at i:1721593 original size:21 final size:19
Alignment explanation
Indices: 1721551--1721594 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1721541 AGGGTTAACT
* *
1721551 GAAACTCATATGAGTTAAC
1 GAAACTCATAAGAGTAAAC
1721570 GAAAGCTCATAAGAGCTAAAC
1 GAAA-CTCATAAGAG-TAAAC
1721591 GAAA
1 GAAA
1721595 AGCAAACACG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 4 0.19
20 9 0.43
21 8 0.38
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (19 bp):
GAAACTCATAAGAGTAAAC
Found at i:1727090 original size:19 final size:18
Alignment explanation
Indices: 1727068--1727110 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
1727058 TGTAAATTTT
1727068 ATGAATTATATAATTTA-TG
1 ATGAA-TATAT-ATTTATTG
1727087 ATGAA-ATATATTTATTG
1 ATGAATATATATTTATTG
1727104 ATGAATA
1 ATGAATA
1727111 GAGAATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 11 0.50
18 1 0.05
19 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
ATGAATATATATTTATTG
Found at i:1727243 original size:37 final size:37
Alignment explanation
Indices: 1727193--1727277 Score: 143
Period size: 37 Copynumber: 2.3 Consensus size: 37
1727183 ATCAGTGACA
1727193 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
* *
1727230 AGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
*
1727267 AGTGACAAGTG
1 AGTGATAAGTG
1727278 ATAAATGTGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (37 bp):
AGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATC
Found at i:1729087 original size:28 final size:28
Alignment explanation
Indices: 1728958--1729088 Score: 133
Period size: 28 Copynumber: 4.8 Consensus size: 28
1728948 CGCATACTCG
* * * **
1728958 ATGTCTCGGACATTAAGTGCCACCATCA
1 ATGTCTCGCACACTAAGTGTCATAATCA
1728986 ATGTCTCGCACA--AAGTG-CGATAATCA
1 ATGTCTCGCACACTAAGTGTC-ATAATCA
* * *
1729012 ATGTCTCACATACTAAGTGCCATAATCA
1 ATGTCTCGCACACTAAGTGTCATAATCA
* *
1729040 AAGTCTCGCACACTAAGTGTCATAAACA
1 ATGTCTCGCACACTAAGTGTCATAATCA
*
1729068 ATGTCTCGCACGCTAAGTGTC
1 ATGTCTCGCACACTAAGTGTC
1729089 GTACATAGCC
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
25 1 0.01
26 20 0.23
28 65 0.75
29 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (28 bp):
ATGTCTCGCACACTAAGTGTCATAATCA
Found at i:1734961 original size:27 final size:27
Alignment explanation
Indices: 1734930--1735055 Score: 111
Period size: 27 Copynumber: 4.7 Consensus size: 27
1734920 TGGTGGCTAC
1734930 GCCACAATTATCTGATCTGATGGCTCT
1 GCCACAATTATCTGATCTGATGGCTCT
*
1734957 GCCACACA-TATCTG-TCCT-AGTGGCTAT
1 GCCACA-ATTATCTGAT-CTGA-TGGCTCT
*
1734984 GCCACAATTATCTGATCTGGTGGCTCT
1 GCCACAATTATCTGATCTGATGGCTCT
* *
1735011 GCCAC-ATATATCTGTTCTGGT-GCTCT
1 GCCACAAT-TATCTGATCTGATGGCTCT
**
1735037 ATCACAA-TATCTGTATCTG
1 GCCACAATTATCTG-ATCTG
1735056 GTGACTTCGT
Statistics
Matches: 83, Mismatches: 7, Indels: 19
0.76 0.06 0.17
Matches are distributed among these distances:
25 6 0.07
26 17 0.20
27 58 0.70
28 2 0.02
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.34
Consensus pattern (27 bp):
GCCACAATTATCTGATCTGATGGCTCT
Found at i:1734998 original size:54 final size:54
Alignment explanation
Indices: 1734916--1735025 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
1734906 TAGAGGAAGC
*
1734916 GTCCTGGTGGCTACGCCACAATTATCTGATCTGATGGCTCTGCCACACATATCT
1 GTCCTAGTGGCTACGCCACAATTATCTGATCTGATGGCTCTGCCACACATATCT
* * *
1734970 GTCCTAGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTAGTGGCTACGCCACAATTATCTGATCTGATGGCTCTGCCACACATATCT
1735024 GT
1 GT
1735026 TCTGGTGCTC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (54 bp):
GTCCTAGTGGCTACGCCACAATTATCTGATCTGATGGCTCTGCCACACATATCT
Found at i:1735068 original size:27 final size:26
Alignment explanation
Indices: 1734932--1735073 Score: 96
Period size: 27 Copynumber: 5.3 Consensus size: 26
1734922 GTGGCTACGC
* *
1734932 CACAATTATCTG-ATCTGATGGCTCTGC
1 CACAA-TATCTGTATCTGGT-GCTCTGT
* * * *
1734959 CACACATATCTGT-CCTAGTGGCTATGC
1 CACA-ATATCTGTATCTGGT-GCTCTGT
*
1734986 CACAATTATCTG-ATCTGGTGGCTCTGC
1 CACAA-TATCTGTATCTGGT-GCTCTGT
*
1735013 CACATATATCTGT-TCTGGTGCTCTAT
1 CACA-ATATCTGTATCTGGTGCTCTGT
1735039 CACAATATCTGTATCTGGTGACT-TCGT
1 CACAATATCTGTATCTGGTG-CTCT-GT
1735066 CACAATAT
1 CACAATAT
1735074 TTGGCAGCCT
Statistics
Matches: 96, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
25 8 0.08
26 18 0.19
27 68 0.71
28 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.35
Consensus pattern (26 bp):
CACAATATCTGTATCTGGTGCTCTGT
Found at i:1736941 original size:63 final size:63
Alignment explanation
Indices: 1736839--1736966 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
1736829 TTCCCTAGAG
* *
1736839 ATCTGATGGAGTTACCGTTCGGAGAGTTTGATCTTATTTTGGGAATGGACTGGCTTGTTAAGC
1 ATCTGATGGAGTTACCGTTCAGAGAGTTTGATCTCATTTTGGGAATGGACTGGCTTGTTAAGC
1736902 ATCTGATGGAGTTACCGTTCAGAGAGTTTGATCTCATTTTGGGAATGGACTGGCTTGTTAAGC
1 ATCTGATGGAGTTACCGTTCAGAGAGTTTGATCTCATTTTGGGAATGGACTGGCTTGTTAAGC
1736965 AT
1 AT
1736967 AAGGCGACCC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.22, C:0.13, G:0.29, T:0.36
Consensus pattern (63 bp):
ATCTGATGGAGTTACCGTTCAGAGAGTTTGATCTCATTTTGGGAATGGACTGGCTTGTTAAGC
Found at i:1742052 original size:27 final size:27
Alignment explanation
Indices: 1742021--1742161 Score: 164
Period size: 27 Copynumber: 5.2 Consensus size: 27
1742011 AGGAAGTGTC
* *
1742021 CTGGTGGCTATACCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
1742048 CTGGTGGCTCTGCCAC-ATATATCTG-T
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
*
1742074 CCTGGTGGCTATGCCACAATTATCTGAT
1 -CTGGTGGCTCTGCCACAATTATCTGAT
*
1742102 CTGGTGGCTCTGCCAC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* *
1742129 CTCGTGGCTCTGCCACAA-TATCTATAT
1 CTGGTGGCTCTGCCACAATTATCT-GAT
1742156 CTGGTG
1 CTGGTG
1742162 ACTTCGTCAC
Statistics
Matches: 98, Mismatches: 9, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
26 10 0.10
27 84 0.86
28 4 0.04
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:1742099 original size:54 final size:54
Alignment explanation
Indices: 1742017--1742161 Score: 229
Period size: 54 Copynumber: 2.7 Consensus size: 54
1742007 ATGGAGGAAG
*
1742017 TGTCCTGGTGGCTATACCACAATTATCTGATCTGGTGGCTCTGCCACATATATC
1 TGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATC
1742071 TGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATC
1 TGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATC
* * * *
1742125 TGTTCTCGTGGCTCTGCCACAA-TATCTATATCTGGTG
1 TGTCCTGGTGGCTATGCCACAATTATCT-GATCTGGTG
1742162 ACTTCGTCAC
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
53 5 0.06
54 80 0.94
ACGTcount: A:0.19, C:0.26, G:0.21, T:0.34
Consensus pattern (54 bp):
TGTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATC
Found at i:1742173 original size:81 final size:80
Alignment explanation
Indices: 1742021--1742179 Score: 189
Period size: 81 Copynumber: 2.0 Consensus size: 80
1742011 AGGAAGTGTC
* * *
1742021 CTGGTGGCTATACCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTGGTGGCTAT
1 CTGGTGGCTATACCACAATTATCTGATCTCGTGGCTCTGCCACATATATCTATCCTGGTGACTAT
1742086 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * * *
1742102 CTGGTGGCTCTGCCAC-ATATATCTGTTCTCGTGGCTCTGCCACA-ATATCTATATCTGGTGACT
1 CTGGTGGCTATACCACAAT-TATCTGATCTCGTGGCTCTGCCACATATATCTAT-CCTGGTGACT
*
1742165 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
1742180 GCAGCCTCGC
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
80 16 0.24
81 51 0.76
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (80 bp):
CTGGTGGCTATACCACAATTATCTGATCTCGTGGCTCTGCCACATATATCTATCCTGGTGACTAT
GCCACAATATCTGAT
Found at i:1743403 original size:23 final size:25
Alignment explanation
Indices: 1743377--1743423 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
1743367 TATCATTCAT
*
1743377 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
1743400 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
1743424 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:1743742 original size:46 final size:45
Alignment explanation
Indices: 1743682--1743944 Score: 328
Period size: 46 Copynumber: 5.9 Consensus size: 45
1743672 TTTGACGTGA
* * * * *
1743682 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
** * * *
1743728 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
1743774 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
1743820 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATC--GT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
1743864 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
1743902 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCA
1743945 AGAGCACACT
Statistics
Matches: 194, Mismatches: 12, Indels: 22
0.85 0.05 0.10
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 30 0.15
39 1 0.01
40 3 0.02
42 3 0.02
43 1 0.01
44 30 0.15
45 5 0.03
46 119 0.61
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:1743913 original size:38 final size:39
Alignment explanation
Indices: 1743813--1743935 Score: 185
Period size: 38 Copynumber: 3.1 Consensus size: 39
1743803 CACATTTCAT
1743813 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
*
1743852 ATTTCATATCGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 A--TC--A-GGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1743896 A-CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1 ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
1743934 AT
1 AT
1743936 TTCATATCAA
Statistics
Matches: 76, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
38 35 0.46
39 2 0.03
41 3 0.04
43 1 0.01
44 35 0.46
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCAGGTTGCCATGGTATCTTTCAACCATGGTCTTACAC
Found at i:1748275 original size:25 final size:25
Alignment explanation
Indices: 1748241--1748292 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1748231 ATTTTACATC
1748241 ACTTGAAAGATTTAAAGAAATAATT
1 ACTTGAAAGATTTAAAGAAATAATT
1748266 ACTTGAAAGATTTAAAGAAATAATT
1 ACTTGAAAGATTTAAAGAAATAATT
1748291 AC
1 AC
1748293 ACAAGTGGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.31
Consensus pattern (25 bp):
ACTTGAAAGATTTAAAGAAATAATT
Found at i:1757872 original size:22 final size:23
Alignment explanation
Indices: 1757847--1757889 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1757837 ACTTAAATTT
1757847 TTAAATT-TAAAAAATAAAAAAA
1 TTAAATTCTAAAAAATAAAAAAA
*
1757869 TTAAATTCTTAAAAATAAAAA
1 TTAAATTCTAAAAAATAAAAA
1757890 TATAAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TTAAATTCTAAAAAATAAAAAAA
Found at i:1757873 original size:30 final size:31
Alignment explanation
Indices: 1757834--1757897 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
1757824 TGTTAACAAT
* * **
1757834 AAAACTTAAATTTTTAAATTTAAAAA-ATAA
1 AAAAATTAAATTCTTAAAAATAAAAATATAA
1757864 AAAAATTAAATTCTTAAAAATAAAAATATAA
1 AAAAATTAAATTCTTAAAAATAAAAATATAA
1757895 AAA
1 AAA
1757898 CAAAAATGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (31 bp):
AAAAATTAAATTCTTAAAAATAAAAATATAA
Found at i:1762747 original size:21 final size:22
Alignment explanation
Indices: 1762718--1762764 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1762708 CAGAAGGAGT
*
1762718 GAGTAGTACTTCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1762740 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCGCAGCAGGTG
1762761 GAGT
1 GAGT
1762765 TTGAGCAGAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.19, G:0.38, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCGCAGCAGGTG
Found at i:1768266 original size:15 final size:15
Alignment explanation
Indices: 1768246--1768277 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1768236 TTAGACGAAA
1768246 ATTTTAATAGCAATG
1 ATTTTAATAGCAATG
*
1768261 ATTTTAATAGTAATG
1 ATTTTAATAGCAATG
1768276 AT
1 AT
1768278 GGGTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.03, G:0.12, T:0.44
Consensus pattern (15 bp):
ATTTTAATAGCAATG
Found at i:1774159 original size:40 final size:39
Alignment explanation
Indices: 1774078--1774166 Score: 99
Period size: 40 Copynumber: 2.3 Consensus size: 39
1774068 GCCAATACAT
* * **
1774078 TTGGTTCGTTGGACAACTTCATAGCATTACAGCCATTCA
1 TTGGTTCATTGGACAACTTCATAGCATAACAGCCAGCCA
*
1774117 TTGGTTCCATTGGACAACTTCCATCGCATAACAG-CAGCCA
1 TTGGTT-CATTGGACAACTT-CATAGCATAACAGCCAGCCA
*
1774157 TTGCTTCATT
1 TTGGTTCATT
1774167 TGTTTCAGCA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
39 10 0.24
40 21 0.50
41 11 0.26
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.33
Consensus pattern (39 bp):
TTGGTTCATTGGACAACTTCATAGCATAACAGCCAGCCA
Found at i:1777044 original size:39 final size:39
Alignment explanation
Indices: 1776991--1777069 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1776981 CAAGATGAAG
1776991 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1777030 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1 TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
1777069 T
1 T
1777070 ATAAAATTCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (39 bp):
TTTTTAAGTTCAAAAACAAGACCTTAAAGTTCCATATCT
Found at i:1782494 original size:36 final size:36
Alignment explanation
Indices: 1782454--1782555 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 36
1782444 GCTTGACATC
1782454 TATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1 TATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
* * * * *
1782490 TA-TTT-A-AATA-TAA-GAAAG--GCTTGACATC--
1 TATTTTGATAAGATTAATAAAAGAAGTTTCAC-GCGA
1782518 TATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1 TATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1782554 TA
1 TA
1782556 AACATGTCAT
Statistics
Matches: 46, Mismatches: 10, Indels: 20
0.61 0.13 0.26
Matches are distributed among these distances:
28 2 0.04
29 8 0.17
30 2 0.04
31 7 0.15
32 6 0.13
33 7 0.15
34 2 0.04
35 8 0.17
36 4 0.09
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (36 bp):
TATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
Found at i:1782500 original size:64 final size:64
Alignment explanation
Indices: 1782426--1782555 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
1782416 AATCTCATGT
1782426 TATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1 TATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1782490 TATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1 TATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
1782554 TA
1 TA
1782556 AACATGTCAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.33
Consensus pattern (64 bp):
TATTTAAATATAAGAAAGGCTTGACATCTATTTTGATAAGATTAATAAAAGAAGTTTCACGCGA
Found at i:1783829 original size:19 final size:19
Alignment explanation
Indices: 1783805--1783846 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1783795 AATTATATTT
1783805 TAATTTTTAAAAATGATAA
1 TAATTTTTAAAAATGATAA
1783824 TAATTTTTAAAAATGATAA
1 TAATTTTTAAAAATGATAA
1783843 -AATT
1 TAATT
1783847 ATGATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (19 bp):
TAATTTTTAAAAATGATAA
Found at i:1793105 original size:22 final size:22
Alignment explanation
Indices: 1793080--1793121 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1793070 ATTTAAAAAA
* *
1793080 AAAATTTAAATCAATTAAACCG
1 AAAATTGAAATAAATTAAACCG
*
1793102 AAAATTGATATAAATTAAAC
1 AAAATTGAAATAAATTAAAC
1793122 TAAAAACTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.29
Consensus pattern (22 bp):
AAAATTGAAATAAATTAAACCG
Found at i:1793917 original size:17 final size:18
Alignment explanation
Indices: 1793885--1793921 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
1793875 GTCAAGCTAG
1793885 TTTTATCTTCTAAATATAA
1 TTTTATCTTCTAAATA-AA
1793904 TTTTAT-TT-TAAATAAA
1 TTTTATCTTCTAAATAAA
1793920 TT
1 TT
1793922 AAATAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.22
17 6 0.33
18 2 0.11
19 6 0.33
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATCTTCTAAATAAA
Found at i:1796952 original size:24 final size:22
Alignment explanation
Indices: 1796924--1796969 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
1796914 AGATTATTTC
*
1796924 ATTTTAAACCTTTACATATTTTAT
1 ATTTTAAA-CTTTA-ATATATTAT
1796948 ATTTTAAACTTTAATATATTAT
1 ATTTTAAACTTTAATATATTAT
1796970 GCAGCTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 8 0.38
23 5 0.24
24 8 0.38
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTAAACTTTAATATATTAT
Found at i:1798719 original size:23 final size:23
Alignment explanation
Indices: 1798692--1798738 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1798682 TTTATCGAAA
1798692 AGTTTATAAGCATTTAAGACAAT
1 AGTTTATAAGCATTTAAGACAAT
1798715 AGTTTATAAGCATTTAAGACAAT
1 AGTTTATAAGCATTTAAGACAAT
1798738 A
1 A
1798739 ATAAATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.09, G:0.13, T:0.34
Consensus pattern (23 bp):
AGTTTATAAGCATTTAAGACAAT
Found at i:1798802 original size:38 final size:38
Alignment explanation
Indices: 1798749--1798827 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
1798739 ATAAATGAAT
*
1798749 AGTTGAAGAATGACCAAAACATGCCTAACGTCATGATG
1 AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGATG
*
1798787 AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGGTG
1 AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGATG
1798825 AGT
1 AGT
1798828 AGGTAGGGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.38, C:0.18, G:0.24, T:0.20
Consensus pattern (38 bp):
AGTTGAAGAAGGACCAAAACATGCCTAACGTCATGATG
Found at i:1802933 original size:27 final size:27
Alignment explanation
Indices: 1802895--1802949 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1802885 AAAAGGGATG
1802895 AATGACTAGTGTACCTAAGTTTCTTGT
1 AATGACTAGTGTACCTAAGTTTCTTGT
*
1802922 AATGACTAGTGTACGTAAGTTTCTTGT
1 AATGACTAGTGTACCTAAGTTTCTTGT
1802949 A
1 A
1802950 TGTAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (27 bp):
AATGACTAGTGTACCTAAGTTTCTTGT
Found at i:1806486 original size:30 final size:30
Alignment explanation
Indices: 1806452--1806513 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1806442 CGAGCAGTAT
1806452 GTGCCAATTTTCACCTCTAATATCTACCGA
1 GTGCCAATTTTCACCTCTAATATCTACCGA
1806482 GTGCCAATTTTCACCTCTAATATCTACCGA
1 GTGCCAATTTTCACCTCTAATATCTACCGA
1806512 GT
1 GT
1806514 CGTCAGCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.34
Consensus pattern (30 bp):
GTGCCAATTTTCACCTCTAATATCTACCGA
Found at i:1819147 original size:30 final size:31
Alignment explanation
Indices: 1819113--1819183 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
1819103 AAAACTTAGC
1819113 AGCTCAGTGACTTAAACAAAAACTTTT-AAT
1 AGCTCAGTGACTTAAACAAAAACTTTTAAAT
* ** *
1819143 AGCTCAATGACTTAAATGAAAATTTTTAAAT
1 AGCTCAGTGACTTAAACAAAAACTTTTAAAT
*
1819174 AGTTCAGTGA
1 AGCTCAGTGA
1819184 TCATTTTGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
30 23 0.68
31 11 0.32
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
AGCTCAGTGACTTAAACAAAAACTTTTAAAT
Found at i:1822069 original size:48 final size:48
Alignment explanation
Indices: 1821951--1822071 Score: 190
Period size: 48 Copynumber: 2.5 Consensus size: 48
1821941 AGCCGTAACA
* *
1821951 GCTGAACCCATAAAGCAGGAGGTTACTAATACTCCATCAGTCTCGAAG
1 GCTGAATCCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
*
1821999 GCTGAATTCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
1 GCTGAATCCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
*
1822047 GCTGAATCCATTAAGC-GAGATGTTA
1 GCTGAATCCATAAAGCAG-GATGTTA
1822072 ATACTACTGC
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
47 1 0.01
48 66 0.99
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (48 bp):
GCTGAATCCATAAAGCAGGATGTTACTAATACTCCATCAGTCTCGAAG
Found at i:1824991 original size:18 final size:18
Alignment explanation
Indices: 1824968--1825004 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
1824958 TATGTATACG
1824968 AATGCAGTCAAGAGCCTT
1 AATGCAGTCAAGAGCCTT
1824986 AATGCAGTCAAGAGCCTT
1 AATGCAGTCAAGAGCCTT
1825004 A
1 A
1825005 GTCCCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.22, T:0.22
Consensus pattern (18 bp):
AATGCAGTCAAGAGCCTT
Found at i:1829700 original size:8 final size:8
Alignment explanation
Indices: 1829687--1829715 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
1829677 TATAAACTTT
1829687 AAATCTTA
1 AAATCTTA
1829695 AAATCTTA
1 AAATCTTA
1829703 AAATCTTA
1 AAATCTTA
1829711 AAATC
1 AAATC
1829716 AAGAAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATCTTA
Found at i:1831566 original size:16 final size:17
Alignment explanation
Indices: 1831545--1831585 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
1831535 AAGATAAATT
1831545 TTTTAAATTT-AACTC-A
1 TTTTAAATTTGAA-TCAA
1831561 TTTTAAATTTGAATCAA
1 TTTTAAATTTGAATCAA
1831578 TTTTAAAT
1 TTTTAAAT
1831586 ATCATTCGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (17 bp):
TTTTAAATTTGAATCAA
Found at i:1831893 original size:13 final size:13
Alignment explanation
Indices: 1831875--1831927 Score: 81
Period size: 13 Copynumber: 4.1 Consensus size: 13
1831865 AGTTTGGCAA
1831875 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
1831888 TGCTTTTCAAAAG
1 TGCTTTTGAAAAG
1831901 TGC-TTTGAAAAAG
1 TGCTTTTG-AAAAG
1831914 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
1831927 T
1 T
1831928 TTAGTTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 3 0.08
13 29 0.81
14 4 0.11
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1835723 original size:29 final size:28
Alignment explanation
Indices: 1835668--1835723 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1835658 AAAATTTAAG
*
1835668 ATTTAATCCTTTATTTTAATTATATATA
1 ATTTAATCCTTTATTTTAATAATATATA
* *
1835696 ATTTGATCCTTTATTTTTATAATGATAT
1 ATTTAATCCTTTATTTTAATAAT-ATAT
1835724 TAGTTAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (28 bp):
ATTTAATCCTTTATTTTAATAATATATA
Found at i:1844170 original size:16 final size:16
Alignment explanation
Indices: 1844151--1844185 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1844141 GTTTCATGTT
* *
1844151 TTTCTAGTTTAGATTA
1 TTTCGAGTTTAAATTA
1844167 TTTCGAGTTTAAATTA
1 TTTCGAGTTTAAATTA
1844183 TTT
1 TTT
1844186 TAAATTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.57
Consensus pattern (16 bp):
TTTCGAGTTTAAATTA
Found at i:1847956 original size:7 final size:7
Alignment explanation
Indices: 1847944--1847971 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1847934 GAATAGGGCA
1847944 GCAACAG
1 GCAACAG
1847951 GCAACAG
1 GCAACAG
1847958 GCAACAG
1 GCAACAG
1847965 GCAACAG
1 GCAACAG
1847972 AATCAGACCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.29, G:0.29, T:0.00
Consensus pattern (7 bp):
GCAACAG
Found at i:1852118 original size:16 final size:16
Alignment explanation
Indices: 1852099--1852131 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1852089 AATAATTAGT
1852099 AATATAAAACAGTAGG
1 AATATAAAACAGTAGG
1852115 AATATAAAACAGTAGG
1 AATATAAAACAGTAGG
1852131 A
1 A
1852132 TCGAATCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.18, T:0.18
Consensus pattern (16 bp):
AATATAAAACAGTAGG
Found at i:1852702 original size:13 final size:13
Alignment explanation
Indices: 1852684--1852725 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
1852674 AAATTTTTTT
1852684 TAAATATTATCAC
1 TAAATATTATCAC
1852697 TAAATA--ATC-C
1 TAAATATTATCAC
1852707 TAAATATTATCAC
1 TAAATATTATCAC
1852720 TAAATA
1 TAAATA
1852726 ATTTAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 7 0.27
11 3 0.12
12 3 0.12
13 13 0.50
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:1852712 original size:23 final size:23
Alignment explanation
Indices: 1852684--1852727 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1852674 AAATTTTTTT
1852684 TAAATATTATCACTAAATAATCC
1 TAAATATTATCACTAAATAATCC
1852707 TAAATATTATCACTAAATAAT
1 TAAATATTATCACTAAATAAT
1852728 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAATATTATCACTAAATAATCC
Found at i:1855072 original size:17 final size:17
Alignment explanation
Indices: 1855052--1855086 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1855042 AGTTTTGGTT
1855052 AAAATAGAA-AAATAAAA
1 AAAATAGAAGAAA-AAAA
1855069 AAAATAGAAGAAAAAAA
1 AAAATAGAAGAAAAAAA
1855086 A
1 A
1855087 TATATAGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.82
18 3 0.18
ACGTcount: A:0.83, C:0.00, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAGAAGAAAAAAA
Found at i:1855253 original size:16 final size:16
Alignment explanation
Indices: 1855232--1855264 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1855222 TAATATCAAC
1855232 TCAATTTTAGAGATTT
1 TCAATTTTAGAGATTT
1855248 TCAATTTTAGAGATTT
1 TCAATTTTAGAGATTT
1855264 T
1 T
1855265 AAGTATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.12, T:0.52
Consensus pattern (16 bp):
TCAATTTTAGAGATTT
Found at i:1860859 original size:31 final size:31
Alignment explanation
Indices: 1860819--1860877 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
1860809 AAATAGTCAT
*
1860819 TGAATTATTT-AAAAGTTTCCATTTAAGTTAC
1 TGAAATATTTGAAAA-TTTCCATTTAAGTTAC
**
1860850 TGAAATATTTGAAAATTTTTATTTAAGT
1 TGAAATATTTGAAAATTTCCATTTAAGT
1860878 CACTAGGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.47
Consensus pattern (31 bp):
TGAAATATTTGAAAATTTCCATTTAAGTTAC
Found at i:1862805 original size:12 final size:12
Alignment explanation
Indices: 1862788--1862817 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
1862778 CCGTATTCGA
1862788 TAAATTAATTAT
1 TAAATTAATTAT
1862800 TAAATTAATTAT
1 TAAATTAATTAT
1862812 TAAATT
1 TAAATT
1862818 CAATACTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAATTAATTAT
Found at i:1865496 original size:31 final size:31
Alignment explanation
Indices: 1865461--1865525 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1865451 TTAACAATCT
1865461 AATGACTTAAATAAAAAGTTTT-GAATAGTTC
1 AATGACTTAAATAAAAA-TTTTCGAATAGTTC
* *
1865492 AATGACTTGAATGAAAATTTTCGAATAGTTC
1 AATGACTTAAATAAAAATTTTCGAATAGTTC
1865523 AAT
1 AAT
1865526 TATTATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (31 bp):
AATGACTTAAATAAAAATTTTCGAATAGTTC
Found at i:1871279 original size:19 final size:20
Alignment explanation
Indices: 1871247--1871284 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1871237 AATATTTTAA
*
1871247 TTTAAATATATAAATTATAT
1 TTTAAATATATAAAATATAT
1871267 TTTAAATAT-TAAAATATA
1 TTTAAATATATAAAATATA
1871285 ACTGTTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATATATAAAATATAT
Found at i:1871300 original size:22 final size:21
Alignment explanation
Indices: 1871270--1871326 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
1871260 ATTATATTTT
1871270 AAATATTAAAATATAACTGTTAC
1 AAAT-TTAAAATATAA-TGTTAC
*
1871293 AAATTTAAATATATAATGTTAT
1 AAATTTAAA-ATATAATGTTAC
*
1871315 ATATTTAAAATA
1 AAATTTAAAATA
1871327 AATCTTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (21 bp):
AAATTTAAAATATAATGTTAC
Found at i:1876749 original size:29 final size:30
Alignment explanation
Indices: 1876717--1876779 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 30
1876707 TTAAGTTTTG
** *
1876717 AATTTGATTATTATTCTCAC-TTGGGTCTA
1 AATTTGACAATTATTCTCACATTGGGTATA
1876746 AA-TTGACAATTATTCTCACATTGGGTATA
1 AATTTGACAATTATTCTCACATTGGGTATA
1876775 AATTT
1 AATTT
1876780 TTTGGTCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 15 0.52
29 12 0.41
30 2 0.07
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.44
Consensus pattern (30 bp):
AATTTGACAATTATTCTCACATTGGGTATA
Found at i:1880645 original size:50 final size:50
Alignment explanation
Indices: 1880577--1880678 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
1880567 TACAGAAAGA
1880577 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1880627 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1 TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
1880677 TA
1 TA
1880679 GAAGCTGATC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.19
Consensus pattern (50 bp):
TAATCAATGGAGGGAAATTAAAGACACTGAGAAACAAACCTGTTACAGGG
Found at i:1882004 original size:51 final size:51
Alignment explanation
Indices: 1881944--1882045 Score: 204
Period size: 51 Copynumber: 2.0 Consensus size: 51
1881934 CCCTATATGC
1881944 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1881995 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1 ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
1882046 TTGGTACTCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.47, C:0.06, G:0.25, T:0.22
Consensus pattern (51 bp):
ATGGGATAGAAATCAACTAAAGGATATGTGGCAGAAATGGAAAATAAGATT
Found at i:1882030 original size:25 final size:25
Alignment explanation
Indices: 1881951--1882032 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
1881941 TGCATGGGAT
1881951 AGAAATCAACTAAAGGATATGTGGC
1 AGAAATCAACTAAAGGATATGTGGC
* * *
1881976 AGAAATGGAA--AATAAGATTATG-GGAT
1 AGAAAT-CAACTAA-AGGA-TATGTGG-C
1882002 AGAAATCAACTAAAGGATATGTGGC
1 AGAAATCAACTAAAGGATATGTGGC
1882027 AGAAAT
1 AGAAAT
1882033 GGAAAATAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
24 2 0.05
25 23 0.52
26 17 0.39
27 2 0.05
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.21
Consensus pattern (25 bp):
AGAAATCAACTAAAGGATATGTGGC
Found at i:1886496 original size:25 final size:26
Alignment explanation
Indices: 1886461--1886510 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1886451 GCGTTTTCAT
* *
1886461 TATTTTTATATTCAAAACA-ATTTTC
1 TATTTTCATATACAAAACATATTTTC
1886486 TATTTTCATATACAAAACATATTTT
1 TATTTTCATATACAAAACATATTTT
1886511 TTCAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTTTCATATACAAAACATATTTTC
Found at i:1889615 original size:20 final size:20
Alignment explanation
Indices: 1889590--1889640 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1889580 CTAAAAATAT
1889590 ATATTAATAATTAAGTAATC
1 ATATTAATAATTAAGTAATC
1889610 ATATTAATAATTAAGTAATC
1 ATATTAATAATTAAGTAATC
*
1889630 AT-TTTATAATT
1 ATATTAATAATT
1889641 TTTACAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 8 0.27
20 22 0.73
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (20 bp):
ATATTAATAATTAAGTAATC
Found at i:1889942 original size:15 final size:16
Alignment explanation
Indices: 1889922--1889951 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1889912 AAAATTTAAT
1889922 TAATATTA-TTAAATA
1 TAATATTATTTAAATA
1889937 TAATATTATTTAAAT
1 TAATATTATTTAAAT
1889952 TAGATTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAATATTATTTAAATA
Found at i:1895520 original size:16 final size:16
Alignment explanation
Indices: 1895499--1895529 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1895489 TTTGAGTCAT
1895499 TTTTGAATTTAAGTTG
1 TTTTGAATTTAAGTTG
1895515 TTTTGAATTTAAGTT
1 TTTTGAATTTAAGTT
1895530 TGAAGGTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (16 bp):
TTTTGAATTTAAGTTG
Found at i:1901873 original size:20 final size:20
Alignment explanation
Indices: 1901848--1901919 Score: 69
Period size: 20 Copynumber: 3.7 Consensus size: 20
1901838 TTGTATGATA
1901848 AATTTTATAATTTTTTTACG
1 AATTTTATAATTTTTTTACG
*
1901868 AATTTTAT-ATTTCTTTAC-
1 AATTTTATAATTTTTTTACG
* *
1901886 -ATTTTTTAATTTTCTTACG
1 AATTTTATAATTTTTTTACG
* *
1901905 ACTTTATAAAATTTT
1 AATTT-TATAATTTT
1901920 ATAAATTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
17 6 0.15
18 8 0.20
19 9 0.22
20 11 0.27
21 7 0.17
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (20 bp):
AATTTTATAATTTTTTTACG
Found at i:1901884 original size:19 final size:20
Alignment explanation
Indices: 1901848--1901897 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1901838 TTGTATGATA
*
1901848 AATTTTATAATTTTTTTACG
1 AATTTTATAATTTCTTTACG
1901868 AATTTTAT-ATTTCTTTAC-
1 AATTTTATAATTTCTTTACG
*
1901886 -ATTTTTTAATTT
1 AATTTTATAATTT
1901898 TCTTACGACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 6 0.22
18 4 0.15
19 9 0.33
20 8 0.30
ACGTcount: A:0.28, C:0.06, G:0.02, T:0.64
Consensus pattern (20 bp):
AATTTTATAATTTCTTTACG
Found at i:1901929 original size:37 final size:36
Alignment explanation
Indices: 1901845--1901929 Score: 82
Period size: 37 Copynumber: 2.3 Consensus size: 36
1901835 TTTTTGTATG
* *
1901845 ATAAATTTTATAATTTTTTTACGAATTTTATATTTCT
1 ATAAATTTT-TAATTTTCTTACGAATTTTAAATTTCT
* * *
1901882 TTACATTTTTTAATTTTCTTACGACTTTATAAAATTT-T
1 ATA-AATTTTTAATTTTCTTACGAATTT-T-AAATTTCT
1901920 ATAAATTTTT
1 ATAAATTTTT
1901930 CTATATTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
37 24 0.63
38 9 0.24
39 5 0.13
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (36 bp):
ATAAATTTTTAATTTTCTTACGAATTTTAAATTTCT
Found at i:1901968 original size:18 final size:17
Alignment explanation
Indices: 1901947--1902065 Score: 71
Period size: 19 Copynumber: 6.6 Consensus size: 17
1901937 TTCTATATAC
*
1901947 TATAATTTTTATGGTTTT
1 TATAATTTTTAT-ATTTT
** *
1901965 TATAAAAATTTACATTTTTT
1 TAT-AATTTTTATA-TTT-T
1901985 TATATATTTTTTATGATTTT
1 TATA-AT-TTTTAT-ATTTT
*
1902005 TATAATTTTAAT-TTTT
1 TATAATTTTTATATTTT
*
1902021 TA-AATTTTTATAACTTT
1 TATAATTTTTAT-ATTTT
*
1902038 TATTAATTTTTATTTTTT
1 TA-TAATTTTTATATTTT
*
1902056 TATCATTTTT
1 TATAATTTTT
1902066 TACTACATGT
Statistics
Matches: 78, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
15 8 0.10
16 6 0.08
17 12 0.15
18 13 0.17
19 21 0.27
20 10 0.13
21 7 0.09
22 1 0.01
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (17 bp):
TATAATTTTTATATTTT
Found at i:1902038 original size:10 final size:9
Alignment explanation
Indices: 1901981--1902065 Score: 70
Period size: 8 Copynumber: 9.6 Consensus size: 9
1901971 AATTTACATT
1901981 TTTTTATATA
1 TTTTTATA-A
*
1901991 TTTTTTATGA
1 -TTTTTATAA
1902001 TTTTTATAA
1 TTTTTATAA
*
1902010 -TTTTA-AT
1 TTTTTATAA
1902017 TTTTTA-AA
1 TTTTTATAA
1902025 TTTTTATAA
1 TTTTTATAA
*
1902034 CTTTTATTAA
1 TTTTTA-TAA
*
1902044 TTTTTAT-T
1 TTTTTATAA
*
1902052 TTTTTATCA
1 TTTTTATAA
1902061 TTTTT
1 TTTTT
1902066 TACTACATGT
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
7 1 0.02
8 24 0.39
9 21 0.34
10 9 0.15
11 7 0.11
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (9 bp):
TTTTTATAA
Found at i:1902045 original size:34 final size:33
Alignment explanation
Indices: 1901992--1902055 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 33
1901982 TTTTATATAT
* *
1901992 TTTTTATGATTTTTATAATTTTAATTTTTTAAA
1 TTTTTATAACTTTTATAATTTTAATTTTTTAAA
*
1902025 TTTTTATAACTTTTATTAATTTTTATTTTTT
1 TTTTTATAACTTTTA-TAATTTTAATTTTTT
1902056 TATCATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (33 bp):
TTTTTATAACTTTTATAATTTTAATTTTTTAAA
Found at i:1906625 original size:26 final size:26
Alignment explanation
Indices: 1906596--1906648 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1906586 TACATCAATT
1906596 AAAATTAAAATTTAAATCTAAAAATA
1 AAAATTAAAATTTAAATCTAAAAATA
* *
1906622 AAAATTTAAGTTTAAATCTAAAAATA
1 AAAATTAAAATTTAAATCTAAAAATA
1906648 A
1 A
1906649 CGTCCATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (26 bp):
AAAATTAAAATTTAAATCTAAAAATA
Found at i:1912742 original size:21 final size:21
Alignment explanation
Indices: 1912716--1912756 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1912706 CAGACGAGCA
* *
1912716 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1912737 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1912757 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1930135 original size:6 final size:6
Alignment explanation
Indices: 1930124--1930157 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1930114 TTGGGAAACA
* *
1930124 AAATTT AAATTT AAATAT AAATTT AAATAT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
1930158 ATTTAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:1930144 original size:12 final size:12
Alignment explanation
Indices: 1930124--1930187 Score: 65
Period size: 12 Copynumber: 5.0 Consensus size: 12
1930114 TTGGGAAACA
*
1930124 AAATTTAAATTT
1 AAATATAAATTT
1930136 AAATATAAATTT
1 AAATATAAATTT
1930148 AAATATAAATATTT
1 AAATAT-AA-ATTT
*
1930162 AAAATATATATTT
1 -AAATATAAATTT
*
1930175 ATATATCAAATTT
1 AAATAT-AAATTT
1930188 TATTTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
12 22 0.50
13 11 0.25
14 5 0.11
15 6 0.14
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATATAAATTT
Found at i:1930147 original size:18 final size:18
Alignment explanation
Indices: 1930124--1930159 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1930114 TTGGGAAACA
*
1930124 AAATTTAAATTTAAATAT
1 AAATTTAAATATAAATAT
1930142 AAATTTAAATATAAATAT
1 AAATTTAAATATAAATAT
1930160 TTAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTTAAATATAAATAT
Found at i:1930174 original size:27 final size:28
Alignment explanation
Indices: 1930132--1930189 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
1930122 CAAAATTTAA
1930132 ATTT-AAATATAAATTTAAATAT-AAAT
1 ATTTAAAATATAAATTTAAATATCAAAT
* *
1930158 ATTTAAAATATATATTTATATATCAAAT
1 ATTTAAAATATAAATTTAAATATCAAAT
1930186 -TTTA
1 ATTTA
1930190 TTTTTAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 4 0.14
27 20 0.71
28 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTAAAATATAAATTTAAATATCAAAT
Found at i:1930931 original size:10 final size:10
Alignment explanation
Indices: 1930916--1930949 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1930906 TGAATTTTTT
*
1930916 TCGAATCGAA
1 TCGAATCGAG
1930926 TCGAATCGAG
1 TCGAATCGAG
*
1930936 TCAAATCGAG
1 TCGAATCGAG
1930946 TCGA
1 TCGA
1930950 GTTAACGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.21
Consensus pattern (10 bp):
TCGAATCGAG
Found at i:1931543 original size:7 final size:7
Alignment explanation
Indices: 1931518--1931554 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1931508 AATAGATAAA
1931518 AATTATT
1 AATTATT
1931525 -ATTATT
1 AATTATT
1931531 -ATTATT
1 AATTATT
1931537 AATTATT
1 AATTATT
1931544 AATTATT
1 AATTATT
1931551 AATT
1 AATT
1931555 TTACTTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 12 0.41
7 17 0.59
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
AATTATT
Found at i:1939704 original size:7 final size:6
Alignment explanation
Indices: 1939677--1939702 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1939667 TATTATCACC
1939677 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
1939703 ATCTTGTGCT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AATAAA
Found at i:1949205 original size:15 final size:16
Alignment explanation
Indices: 1949185--1949223 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1949175 GTTTCGTTTG
1949185 TTTTTTATAT-TAATT
1 TTTTTTATATATAATT
* *
1949200 TTTTTTACATATATTT
1 TTTTTTATATATAATT
1949216 TTTTTTAT
1 TTTTTTAT
1949224 CTGAATGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATATATAATT
Found at i:1949756 original size:19 final size:19
Alignment explanation
Indices: 1949715--1949756 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1949705 TATTAATCTT
* * *
1949715 TTTTCGATTTTTTTTTATT
1 TTTTAGATTTTTTTTGATA
1949734 TTTTAGATTTTTTTTGATA
1 TTTTAGATTTTTTTTGATA
1949753 TTTT
1 TTTT
1949757 TATTTTGTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (19 bp):
TTTTAGATTTTTTTTGATA
Found at i:1951819 original size:23 final size:23
Alignment explanation
Indices: 1951783--1951826 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1951773 TTCAAATTTT
*
1951783 AAAAATTAAAAAATATAAAAAGA
1 AAAAATTAAAAAATAAAAAAAGA
**
1951806 AAAAATTACCAAATAAAAAAA
1 AAAAATTAAAAAATAAAAAAA
1951827 ATCCATTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAATTAAAAAATAAAAAAAGA
Found at i:1959398 original size:30 final size:29
Alignment explanation
Indices: 1959341--1959398 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
1959331 ATTTTGACCA
* * *
1959341 TTTTAAAATGATAAAATTTTAATTTAATT
1 TTTTAAAATGATAAAAATATAAATTAATT
*
1959370 TTTTAAAAATTATAAAAATATAAATTAAT
1 TTTT-AAAATGATAAAAATATAAATTAAT
1959399 ATAATGATGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 4 0.17
30 20 0.83
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TTTTAAAATGATAAAAATATAAATTAATT
Found at i:1960544 original size:137 final size:133
Alignment explanation
Indices: 1960268--1960609 Score: 410
Period size: 131 Copynumber: 2.6 Consensus size: 133
1960258 ATGCACAATC
* ** * *
1960268 AAACAAGTTGTTGTTGAACATTAAAATATTAGCAACAACTTTAAAATGTTG--GTATGTAATTTA
1 AAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAACCTTAAAATGTTGTTATATGTAATTTA
* * * * * * *
1960331 GTTTCATGCTTATTCGTTGCAATGACCCGATTTGTTGTTGCAAATTCTTGATAAAATTTGTAACA
66 ATTTTATGCTTATTCATTGCAATGACACGATTCGTTGTTGCAAATCCTTAATAAAATTTGTAACA
1960396 ACA
131 ACA
* *
1960399 AAATAAGTTGTTGTTAAATGTTAAAATATTAACAACAACCTTAAAATGTTGTTATATGTAATTTA
1 AAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAACCTTAAAATGTTGTTATATGTAATTTA
*
1960464 ATTTTATGCTTATTCATTGCAATGACACGATCCGTACGTTGTTGCAAATCCTTAATCAAATTTGT
66 ATTTTATGCTTATTCATTGCAATGACACGAT---T-CGTTGTTGCAAATCCTTAATAAAATTTGT
1960529 AACAACA
127 AACAACA
* * * *
1960536 AAACAA---GTTGTTAAATGTTAAAATATTAGCAAAAATCTTAAAATGTCGTTACA--TAATTTA
1 AAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAACCTTAAAATGTTGTTATATGTAATTTA
* *
1960596 ATTTTTTACTTATT
66 ATTTTATGCTTATT
1960610 GACAACAGTA
Statistics
Matches: 182, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
131 45 0.25
132 19 0.10
133 38 0.21
134 42 0.23
136 1 0.01
137 37 0.20
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.39
Consensus pattern (133 bp):
AAACAAGTTGTTGTTAAATGTTAAAATATTAGCAACAACCTTAAAATGTTGTTATATGTAATTTA
ATTTTATGCTTATTCATTGCAATGACACGATTCGTTGTTGCAAATCCTTAATAAAATTTGTAACA
ACA
Found at i:1961239 original size:178 final size:178
Alignment explanation
Indices: 1960971--1961328 Score: 716
Period size: 178 Copynumber: 2.0 Consensus size: 178
1960961 GGATTTCATC
1960971 CTTTTTTTCCCAACTTCCATTCATCGATTGCTTCTCTTCAAGAATCATCCTTAATTTAGAATCAA
1 CTTTTTTTCCCAACTTCCATTCATCGATTGCTTCTCTTCAAGAATCATCCTTAATTTAGAATCAA
1961036 TTGGAATATCGGTTTGGAGAAATATATTAGATTGATTAATCTAAGAATTGATACAAGTCGATTAA
66 TTGGAATATCGGTTTGGAGAAATATATTAGATTGATTAATCTAAGAATTGATACAAGTCGATTAA
1961101 ATTAGACTAAAAACTAATTGAATGAATCAAACCAATTAAACTAACAAA
131 ATTAGACTAAAAACTAATTGAATGAATCAAACCAATTAAACTAACAAA
1961149 CTTTTTTTCCCAACTTCCATTCATCGATTGCTTCTCTTCAAGAATCATCCTTAATTTAGAATCAA
1 CTTTTTTTCCCAACTTCCATTCATCGATTGCTTCTCTTCAAGAATCATCCTTAATTTAGAATCAA
1961214 TTGGAATATCGGTTTGGAGAAATATATTAGATTGATTAATCTAAGAATTGATACAAGTCGATTAA
66 TTGGAATATCGGTTTGGAGAAATATATTAGATTGATTAATCTAAGAATTGATACAAGTCGATTAA
1961279 ATTAGACTAAAAACTAATTGAATGAATCAAACCAATTAAACTAACAAA
131 ATTAGACTAAAAACTAATTGAATGAATCAAACCAATTAAACTAACAAA
1961327 CT
1 CT
1961329 GATGATCTAA
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
178 180 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (178 bp):
CTTTTTTTCCCAACTTCCATTCATCGATTGCTTCTCTTCAAGAATCATCCTTAATTTAGAATCAA
TTGGAATATCGGTTTGGAGAAATATATTAGATTGATTAATCTAAGAATTGATACAAGTCGATTAA
ATTAGACTAAAAACTAATTGAATGAATCAAACCAATTAAACTAACAAA
Found at i:1966026 original size:16 final size:15
Alignment explanation
Indices: 1966007--1966036 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1965997 TTCAACTAAT
1966007 TTTTGAGTTGGAATTA
1 TTTTGAGTT-GAATTA
1966023 TTTTGAGTTGAATT
1 TTTTGAGTTGAATT
1966037 TGGATTGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.53
Consensus pattern (15 bp):
TTTTGAGTTGAATTA
Found at i:1968226 original size:16 final size:16
Alignment explanation
Indices: 1968205--1968236 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1968195 TTTTAAGTGG
1968205 GATTATTTTAGATTCA
1 GATTATTTTAGATTCA
1968221 GATTATTTTAGATTCA
1 GATTATTTTAGATTCA
1968237 ATCAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
GATTATTTTAGATTCA
Found at i:1980699 original size:11 final size:11
Alignment explanation
Indices: 1980683--1980709 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1980673 TAGAAATTAG
1980683 TTTGTGAAACT
1 TTTGTGAAACT
1980694 TTTGTGAAACT
1 TTTGTGAAACT
1980705 TTTGT
1 TTTGT
1980710 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:1982240 original size:93 final size:92
Alignment explanation
Indices: 1982108--1982302 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
1982098 TTGATTTTAG
* *
1982108 TAAATTCATATAAGAACATTTTATTATTAAGAATTTTATGAAATTATATATCACTA-TATAATTA
1 TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTA-AATTA
* *
1982172 TATTTAAT-ATTAATTATTTTAAATTGTA
65 TATGTAATAATT-ATTATTTTAAATTATA
* *
1982200 TAAATTCATATAAGAAAATTTTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTA
1 TAAATTCATATAAGAAAA-TTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTA
1982265 TATGTAATAATTATTATTTTAAATTATA
65 TATGTAATAATTATTATTTTAAATTATA
*
1982293 CAAATTCATA
1 TAAATTCATA
1982303 AACTATAATC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 17 0.18
93 71 0.76
94 5 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (92 bp):
TAAATTCATATAAGAAAATTTTATTATCAAGAATTTTATGAAATTATATATCACTATTAAATTAT
ATGTAATAATTATTATTTTAAATTATA
Found at i:1982360 original size:17 final size:17
Alignment explanation
Indices: 1982335--1982368 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1982325 ATAATTTTAA
*
1982335 ATTTTATTAAATCATAT
1 ATTTAATTAAATCATAT
1982352 ATTTAATTAAATCATAT
1 ATTTAATTAAATCATAT
1982369 TTAATATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTAATTAAATCATAT
Found at i:1982370 original size:15 final size:16
Alignment explanation
Indices: 1982335--1982373 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
1982325 ATAATTTTAA
*
1982335 ATTTTATTAAATCATAT
1 ATTTAATTAAATCA-AT
1982352 ATTTAATTAAATC-AT
1 ATTTAATTAAATCAAT
1982367 ATTTAAT
1 ATTTAAT
1982374 ATTAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
17 12 0.57
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTAAATCAAT
Found at i:1982377 original size:17 final size:18
Alignment explanation
Indices: 1982339--1982378 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1982329 TTTTAAATTT
*
1982339 TATTAAATCATATATTTA
1 TATTAAATCATATATTAA
1982357 -ATTAAATCATAT-TTAA
1 TATTAAATCATATATTAA
1982373 TATTAA
1 TATTAA
1982379 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTAAATCATATATTAA
Found at i:1982493 original size:15 final size:15
Alignment explanation
Indices: 1982458--1982592 Score: 70
Period size: 15 Copynumber: 8.9 Consensus size: 15
1982448 TTAAGAATTT
*
1982458 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1982472 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1982486 TATTTAATAATAAT-
1 TATTTAATTATAATA
1982500 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
1982514 T-TTTACAGTATCATA
1 TATTTA-ATTATAATA
*
1982529 TATTATGATTTGAGTAAATTCA
1 TATT-T-AATT-A-T-AA-T-A
*
1982551 TATTAAATTAT-ATA
1 TATTTAATTATAATA
1982565 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
1982579 TATTTAATAATAAT
1 TATTTAATTATAAT
1982593 TATGTTTAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 33
0.68 0.08 0.24
Matches are distributed among these distances:
12 3 0.03
13 21 0.23
14 17 0.18
15 32 0.34
16 3 0.03
17 2 0.02
18 3 0.03
19 2 0.02
20 4 0.04
21 1 0.01
22 5 0.05
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:1982500 original size:120 final size:119
Alignment explanation
Indices: 1982334--1982552 Score: 345
Period size: 120 Copynumber: 1.8 Consensus size: 119
1982324 AATAATTTTA
* *
1982334 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATATTAATTAT-TTGAAATTT-TCTTT
1 AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTT--AATTTATATTT
*
1982397 TATAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
64 TACAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
*
1982453 AATTTTATTAAATTATATATTTTAATTATAAT-ATATTTAATAATAATTATGTTAATTTATATTT
1 AATTTTATTAAATCATATA-TTTAATTA-AATCATATTTAATAATAATTATGTTAATTTATATTT
1982517 TACAGTATCATATATTATGATTTGAGTAAATTCATA
64 TACAGTATCATATATTATGATTTGAGTAAATTCATA
1982553 TTAAATTATA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
119 23 0.25
120 64 0.70
121 5 0.05
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (119 bp):
AATTTTATTAAATCATATATTTAATTAAATCATATTTAATAATAATTATGTTAATTTATATTTTA
CAGTATCATATATTATGATTTGAGTAAATTCATAGAAGAATTTTATTTATTAAG
Found at i:1982581 original size:16 final size:16
Alignment explanation
Indices: 1982560--1982601 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1982550 ATATTAAATT
*
1982560 ATATATTTTAATTATA
1 ATATATTTTAATAATA
1982576 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
1982591 AT-TATGTTTAA
1 ATATAT-TTTAA
1982602 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:1982709 original size:154 final size:156
Alignment explanation
Indices: 1982551--1982848 Score: 537
Period size: 154 Copynumber: 1.9 Consensus size: 156
1982541 AGTAAATTCA
*
1982551 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1982616 TTTATTATTGAT-AT-TAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
66 TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
1982679 AAATTTATGCTAATTATTAAGAATTT
131 AAATTTATGCTAATTATTAAGAATTT
1982705 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
* *
1982770 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACTAAAA
66 TTTATTATTGATAAT-ATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
1982835 CAAATTTCTGCTAA
130 CAAATTTATGCTAA
1982849 GGGTATTCTA
Statistics
Matches: 137, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 76 0.55
155 2 0.01
157 59 0.43
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (156 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAAC
AAATTTATGCTAATTATTAAGAATTT
Found at i:1982729 original size:18 final size:17
Alignment explanation
Indices: 1982701--1982735 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1982691 ATTATTAAGA
*
1982701 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
1982718 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
1982736 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:1983003 original size:16 final size:16
Alignment explanation
Indices: 1982981--1983029 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
1982971 ACACAACTTT
*
1982981 TCCATTACACCTCTAT
1 TCCATTACACCTCTAA
*
1982997 TCTATTACACCTCTAA
1 TCCATTACACCTCTAA
*
1983013 TCCAATACACCTCTAA
1 TCCATTACACCTCTAA
1983029 T
1 T
1983030 TCAATACAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.31, C:0.35, G:0.00, T:0.35
Consensus pattern (16 bp):
TCCATTACACCTCTAA
Found at i:1983034 original size:16 final size:16
Alignment explanation
Indices: 1982986--1983037 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
1982976 ACTTTTCCAT
*
1982986 TACACCTCT-ATTCTAT
1 TACACCTCTAATTC-AA
*
1983002 TACACCTCTAATCCAA
1 TACACCTCTAATTCAA
1983018 TACACCTCTAATTCAA
1 TACACCTCTAATTCAA
1983034 TACA
1 TACA
1983038 GCTTAATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 29 0.91
17 3 0.09
ACGTcount: A:0.35, C:0.33, G:0.00, T:0.33
Consensus pattern (16 bp):
TACACCTCTAATTCAA
Found at i:1983622 original size:3 final size:3
Alignment explanation
Indices: 1983614--1983652 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1983604 GTAGTGATTT
1983614 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1983653 AAAGGGTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:1983780 original size:18 final size:18
Alignment explanation
Indices: 1983741--1983782 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1983731 TTCATGCTCT
*
1983741 GGTTCTGGTTCGGCTTCC
1 GGTTCTGGTTCGGCTTCA
* *
1983759 GGTTCTGGTTCTGTTTCA
1 GGTTCTGGTTCGGCTTCA
1983777 GGTTCT
1 GGTTCT
1983783 TGTATTAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.02, C:0.21, G:0.31, T:0.45
Consensus pattern (18 bp):
GGTTCTGGTTCGGCTTCA
Found at i:1992689 original size:16 final size:16
Alignment explanation
Indices: 1992668--1992703 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1992658 TTTAAAATCA
*
1992668 GAAATGATCTGAACTT
1 GAAATGATCGGAACTT
1992684 GAAATGATCGGAACTT
1 GAAATGATCGGAACTT
1992700 -AAAT
1 GAAAT
1992704 TTGTACCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (16 bp):
GAAATGATCGGAACTT
Found at i:1998269 original size:14 final size:14
Alignment explanation
Indices: 1998250--1998280 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1998240 AACTAACATG
*
1998250 TAATTTTAAAAATT
1 TAATTTTAAAAACT
1998264 TAATTTTAAAAACT
1 TAATTTTAAAAACT
1998278 TAA
1 TAA
1998281 AAGGACTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TAATTTTAAAAACT
Found at i:2001652 original size:27 final size:26
Alignment explanation
Indices: 2001621--2001672 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
2001611 GAGATTAAAA
*
2001621 AAATTTGAGATAAAACAAAAAAAAATG
1 AAATTTAAGATAAAA-AAAAAAAAATG
* *
2001648 AAATTTAAGATTAAAAAAATAAAAT
1 AAATTTAAGATAAAAAAAAAAAAAT
2001673 TTTTATCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.23
Consensus pattern (26 bp):
AAATTTAAGATAAAAAAAAAAAAATG
Found at i:2004970 original size:24 final size:24
Alignment explanation
Indices: 2004943--2004988 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2004933 TTATGTACAT
* *
2004943 GAAATTTTAATTGTGTTTCAATAC
1 GAAACTTTAATTGTATTTCAATAC
*
2004967 GAAACTTTAATTTTATTTCAAT
1 GAAACTTTAATTGTATTTCAAT
2004989 CATACACGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (24 bp):
GAAACTTTAATTGTATTTCAATAC
Found at i:2014244 original size:20 final size:20
Alignment explanation
Indices: 2014219--2014258 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2014209 AATATTTTCC
*
2014219 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
2014239 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
2014259 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:2014264 original size:34 final size:35
Alignment explanation
Indices: 2014207--2014273 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
2014197 CAAACACTAG
*
2014207 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
2014242 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2014274 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2027677 original size:18 final size:16
Alignment explanation
Indices: 2027646--2027681 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
2027636 ATCTTTCATC
2027646 AATTGTATATAATTTT
1 AATTGTATATAATTTT
2027662 AATTAGTATAATAATTTT
1 AATT-GTAT-ATAATTTT
2027680 AA
1 AA
2027682 CCTTCGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 4 0.22
18 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AATTGTATATAATTTT
Found at i:2030969 original size:33 final size:33
Alignment explanation
Indices: 2030898--2030962 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
2030888 ATAAAAACAC
* * *
2030898 CATTTCAAAATTTTTATATTAAAAGTTAGATTA
1 CATTTTAAAATTCTTATATTAAAAGTTAAATTA
*
2030931 CATTTTAAAATTCTTGTATTAAAAGTTAAATT
1 CATTTTAAAATTCTTATATTAAAAGTTAAATT
2030963 GTATTTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (33 bp):
CATTTTAAAATTCTTATATTAAAAGTTAAATTA
Found at i:2037135 original size:26 final size:27
Alignment explanation
Indices: 2037087--2037138 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
2037077 TCTTATAAAT
*
2037087 AAAATAAATTATTATTTTAATATATTA
1 AAAATAAATTATTAGTTTAATATATTA
* *
2037114 AAAATAAATTCTT-GTTTCATATATT
1 AAAATAAATTATTAGTTTAATATATT
2037139 TACGGTGGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTATTAGTTTAATATATTA
Found at i:2037302 original size:15 final size:15
Alignment explanation
Indices: 2037250--2037305 Score: 50
Period size: 15 Copynumber: 4.1 Consensus size: 15
2037240 AAATATTTTA
* *
2037250 ACATATAATTTATAC
1 ACATATAAATTATAT
*
2037265 ACATACAAA-TATAT
1 ACATATAAATTATAT
2037279 -C-T-T-AATTATAT
1 ACATATAAATTATAT
2037290 ACATATAAATTATAT
1 ACATATAAATTATAT
2037305 A
1 A
2037306 TGAATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
10 2 0.06
11 5 0.16
12 2 0.06
13 2 0.06
14 5 0.16
15 16 0.50
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (15 bp):
ACATATAAATTATAT
Found at i:2039010 original size:26 final size:27
Alignment explanation
Indices: 2038968--2039018 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
2038958 TTTTCTTTTT
*
2038968 TTTTTTTAAAATTAATACTACTAATTA
1 TTTTTTTAAAATAAATACTACTAATTA
*
2038995 TTTTTTTAAAA-AAATATTACTAAT
1 TTTTTTTAAAATAAATACTACTAAT
2039019 AAAAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTTTTTAAAATAAATACTACTAATTA
Found at i:2040606 original size:23 final size:24
Alignment explanation
Indices: 2040550--2040606 Score: 98
Period size: 25 Copynumber: 2.4 Consensus size: 24
2040540 TTCAACTTCA
2040550 ACTATTAAAATCGTTGAAATTCTC
1 ACTATTAAAATCGTTGAAATTCTC
2040574 TACTATTAAAATCGTTGAAATTCTC
1 -ACTATTAAAATCGTTGAAATTCTC
2040599 -CTATTAAA
1 ACTATTAAA
2040607 TCCATTGGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 8 0.25
25 24 0.75
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (24 bp):
ACTATTAAAATCGTTGAAATTCTC
Found at i:2048773 original size:184 final size:185
Alignment explanation
Indices: 2048502--2048848 Score: 477
Period size: 184 Copynumber: 1.9 Consensus size: 185
2048492 AATATCACAT
* * * *
2048502 GAGCCAACCTATATTATGTAACTAGTTCAAATGGCAAACCCTTTGCGGGGTTCGAACTTTGGATC
1 GAGCCAACCTACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGGTTCGAACTTTGGATC
* * * *
2048567 ATTCTTATCAAACATTAGGACAAGTTTATAC-T-TAACTACCATTGAAGTTGCA-AAACATCATT
66 ATTCTTATCAAACATAAGGACAAGCTTATACATCTAACAACCATTGAA-AT-CAGAAACATCATT
**
2048629 CACAGTGACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCAC
129 CACAGCAACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCAC
*
2048686 GAGCCAACCTACATTACGTAGCTAGTGCAAAAGGCAAACCCTTTG-GGGGATTCGAACTTTGGAT
1 GAGCCAACCTACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGG-TTCGAACTTTGGAT
* ** *
2048750 CGTTCTTATCAAATGTAAGGACAAGCTTATACATCTAACAATCATTGAAATCATGAAACATCATT
65 CATTCTTATCAAACATAAGGACAAGCTTATACATCTAACAACCATTGAAATCA-GAAACATCATT
* *
2048815 CACAGCAACATCAAGAATTGTTGGAATACTAATA
129 CACAGCAACATCAAGAATTGTCGAAATACTAATA
2048849 GACACTGTAC
Statistics
Matches: 141, Mismatches: 17, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
183 4 0.03
184 83 0.59
185 2 0.01
186 52 0.37
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (185 bp):
GAGCCAACCTACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGGTTCGAACTTTGGATC
ATTCTTATCAAACATAAGGACAAGCTTATACATCTAACAACCATTGAAATCAGAAACATCATTCA
CAGCAACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCAC
Found at i:2051017 original size:56 final size:58
Alignment explanation
Indices: 2050942--2051056 Score: 130
Period size: 56 Copynumber: 2.0 Consensus size: 58
2050932 CCACTTGAGG
* * * *
2050942 AAATTACATTTTATCTAAAAATGAT-AAAATTTTAATTTAACTTTTTA-AAAATT-TATA
1 AAATTACATATTATCT-AAAATAATAAAAATTATAATTTAAC-TCTTACAAAATTATATA
* *
2050999 AAATTATATATTAT-TAAAATAATAAAAATTATATTTTAACTCTTACAAAATTATATA
1 AAATTACATATTATCTAAAATAATAAAAATTATAATTTAACTCTTACAAAATTATATA
2051056 A
1 A
2051057 TTTAATTTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
55 11 0.22
56 21 0.43
57 17 0.35
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (58 bp):
AAATTACATATTATCTAAAATAATAAAAATTATAATTTAACTCTTACAAAATTATATA
Found at i:2054449 original size:51 final size:53
Alignment explanation
Indices: 2054366--2054506 Score: 137
Period size: 54 Copynumber: 2.7 Consensus size: 53
2054356 TGCAGTGGAA
* * * *
2054366 GTTGATTCCCTTCTCA-TAATTTGGTTTACAGTAATGCTG-TC-AGAAGCAGAG
1 GTTGATTCTCTTCT-AGAAATTTGGTTTCCAGTAATGCTGCACTAGAAGCAGAG
* *
2054417 GTTGATT-TCATTCTAGAAATTTGATTTCCAGTAATGGTGCCACTAGAAGCAGAG
1 GTTGATTCTC-TTCTAGAAATTTGGTTTCCAGTAATGCTG-CACTAGAAGCAGAG
* * * *
2054471 TTTGATTCTCTTCTGGAAATTCGGTTTCCAGCAATG
1 GTTGATTCTCTTCTAGAAATTTGGTTTCCAGTAATG
2054507 ATCCTCTCAG
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
50 2 0.03
51 30 0.41
53 1 0.01
54 38 0.52
55 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (53 bp):
GTTGATTCTCTTCTAGAAATTTGGTTTCCAGTAATGCTGCACTAGAAGCAGAG
Found at i:2054594 original size:54 final size:56
Alignment explanation
Indices: 2054536--2054708 Score: 148
Period size: 54 Copynumber: 3.2 Consensus size: 56
2054526 TTGATTCCTT
*
2054536 TCTA-GAAGTTTGGTTTCCAGTAATGACCTTATCAGGA-TTGGACATTAATTCCGC
1 TCTAGGAAGTTTGGTTTCCAGTAATGACCTTATCAGGAGTTGGACGTTAATTCCGC
* ** ** * * * *
2054590 TCTAGGAAG-TTGATCCCCAGTAACAAGCC-CA-CCGGAAGTGGGA-GTTGATTCC-C
1 TCTAGGAAGTTTGGTTTCCAGTAATGA-CCTTATCAGG-AGTTGGACGTTAATTCCGC
* *
2054643 TTCTA-GAAGTTTGGTTTCTAATAATGACCTTATCAGGAGTT-GACGTTAATTCCGC
1 -TCTAGGAAGTTTGGTTTCCAGTAATGACCTTATCAGGAGTTGGACGTTAATTCCGC
2054698 TCTAGGAAGTT
1 TCTAGGAAGTT
2054709 GATCGCCAGT
Statistics
Matches: 87, Mismatches: 21, Indels: 21
0.67 0.16 0.16
Matches are distributed among these distances:
53 12 0.14
54 55 0.63
55 20 0.23
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.32
Consensus pattern (56 bp):
TCTAGGAAGTTTGGTTTCCAGTAATGACCTTATCAGGAGTTGGACGTTAATTCCGC
Found at i:2054718 original size:108 final size:108
Alignment explanation
Indices: 2054525--2054758 Score: 380
Period size: 108 Copynumber: 2.2 Consensus size: 108
2054515 AGGGGTTATG
* *
2054525 GTTGATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGATTGGACATTAATTCCGC
*
2054590 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCGGAAGTGGGA
66 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
* *
2054633 GTTGATTCCCTTCTAGAAGTTTGGTTTCTAATAATGACCTTATCAGGAGTT-GACGTTAATTCCG
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGA-TTGGACATTAATTCCG
* **
2054697 CTCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGA
65 CTCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
2054741 GTTGATTCCCTTCTAGAA
1 GTTGATTCCCTTCTAGAA
2054759 ATCTGAATTC
Statistics
Matches: 117, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 115 0.98
109 2 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (108 bp):
GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGATTGGACATTAATTCCGC
TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
Found at i:2054756 original size:54 final size:54
Alignment explanation
Indices: 2054590--2054756 Score: 144
Period size: 54 Copynumber: 3.1 Consensus size: 54
2054580 TTAATTCCGC
** *
2054590 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCGGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
* ** * * * * * * *
2054644 TCTA-GAAGTTTGGTTTCTAATAATGA-CCTTATCAGGAGT-TGACGTTAATTCCGC-
1 TCTAGGAAG-TTGATCCCCAGTAATGAGCC-CACCAGAAGTGGGA-GTTGATTCC-CT
*
2054698 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
1 TCTAGGAAGTTGATCCCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
2054752 TCTAG
1 TCTAG
2054757 AAATCTGAAT
Statistics
Matches: 82, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
53 9 0.11
54 64 0.78
55 9 0.11
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.28
Consensus pattern (54 bp):
TCTAGGAAGTTGATCCCCAGTAATGAGCCCACCAGAAGTGGGAGTTGATTCCCT
Found at i:2054803 original size:108 final size:108
Alignment explanation
Indices: 2054525--2054803 Score: 282
Period size: 108 Copynumber: 2.6 Consensus size: 108
2054515 AGGGGTTATG
* * * * * *
2054525 GTTGATTCCTTTCTAGAAGTTTGGTTTCC-AGTAATGACCTTATCAGGA-TTGGACA-TTAATTC
1 GTTGATTCCCTTCTAGAAATCT-GATTCCTAATAATGACCTCATCAGGACTT-GA-AGTTAATTC
*
2054587 CGCTCTAGGAAGTTGATCCCCAGTAACAAGCCCACCGGAAGTGGGA
63 CGCTCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
* * * * * * *
2054633 GTTGATTCCCTTCTAGAAGTTTGGTTTCTAATAATGACCTTATCAGGAGTTGACGTTAATTCCGC
1 GTTGATTCCCTTCTAGAAATCTGATTCCTAATAATGACCTCATCAGGACTTGAAGTTAATTCCGC
* **
2054698 TCTAGGAAGTTGATCGCCAGTAATGAGCCCACCAGAAGTGGGA
66 TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
* * *
2054741 GTTGATTCCCTTCTAGAAATCTGAATTCCGGTAATACTTACCTCA-CA-G-CTTGAAGTTGATTC
1 GTTGATTCCCTTCTAGAAATCTG-ATTCC--TAATAATGACCTCATCAGGACTTGAAGTTAATTC
2054803 C
63 C
2054804 ATTCTAGAAA
Statistics
Matches: 146, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
107 4 0.03
108 123 0.84
109 6 0.04
110 2 0.01
111 11 0.08
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (108 bp):
GTTGATTCCCTTCTAGAAATCTGATTCCTAATAATGACCTCATCAGGACTTGAAGTTAATTCCGC
TCTAGGAAGTTGATCCCCAGTAACAAGCCCACCAGAAGTGGGA
Found at i:2063379 original size:15 final size:14
Alignment explanation
Indices: 2063352--2063408 Score: 60
Period size: 14 Copynumber: 4.0 Consensus size: 14
2063342 CAATCAAACA
*
2063352 CCAGAAAATATTTT
1 CCAGAAAACATTTT
2063366 CCAGTAAAACATTTT
1 CCAG-AAAACATTTT
*
2063381 CCAGAAATCATTTT
1 CCAGAAAACATTTT
* * *
2063395 ACGGAAAATATTTT
1 CCAGAAAACATTTT
2063409 ACCGGCAATC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 23 0.64
15 13 0.36
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (14 bp):
CCAGAAAACATTTT
Found at i:2065753 original size:18 final size:18
Alignment explanation
Indices: 2065704--2065753 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2065694 GATCTCGACC
2065704 AAATTAATTCGATTAACT
1 AAATTAATTCGATTAACT
*
2065722 AAATTCGATT-GATTAACT
1 AAATT-AATTCGATTAACT
*
2065740 GAATTAATTCGATT
1 AAATTAATTCGATT
2065754 TTACCTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (18 bp):
AAATTAATTCGATTAACT
Found at i:2071255 original size:12 final size:12
Alignment explanation
Indices: 2071238--2071274 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
2071228 GGGGAACCAT
2071238 AAAAAAAAAACA
1 AAAAAAAAAACA
2071250 AAAAAAAAAACA
1 AAAAAAAAAACA
*
2071262 AAAAAAGAAACA
1 AAAAAAAAAACA
2071274 A
1 A
2071275 TCACTAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAACA
Found at i:2071788 original size:11 final size:10
Alignment explanation
Indices: 2071772--2071797 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2071762 TCCCCCCCCC
2071772 AAAAAAAAAG
1 AAAAAAAAAG
2071782 AAAAAAAAAG
1 AAAAAAAAAG
2071792 AAAAAA
1 AAAAAA
2071798 GAAGTGATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Done.