Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 54 of 150
Found at i:16354793 original size:44 final size:44
Alignment explanation
Indices: 16354745--16354842 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
16354735 CTTATCCCTT
* * *
16354745 TGAAGTTGCAGTGGGGCAGGTTGAAGATA-TAATTCCTATCTCCC
1 TGAAGTTGCAGTGGAGCAGGCTAAAGATATTAA-TCCTATCTCCC
* *
16354789 TGAAGTTACAGTGGAGCAGGCTAAAGCTATTAATCCTATCTCCC
1 TGAAGTTGCAGTGGAGCAGGCTAAAGATATTAATCCTATCTCCC
*
16354833 TAAAGTTGCA
1 TGAAGTTGCA
16354843 TTGAAGCGGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
44 43 0.93
45 3 0.07
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (44 bp):
TGAAGTTGCAGTGGAGCAGGCTAAAGATATTAATCCTATCTCCC
Found at i:16354858 original size:44 final size:44
Alignment explanation
Indices: 16354778--16354871 Score: 109
Period size: 44 Copynumber: 2.1 Consensus size: 44
16354768 AAGATATAAT
* * * *
16354778 TCCTATCTCCCTGAAGTTACAGTGGAGCAGGCTAAAGCTATTAA
1 TCCTATCTCCCTAAAGTTACAGTGAAGCAGGCTAAAGCGATGAA
* * *
16354822 TCCTATCTCCCTAAAGTTGCATTGAAGC-GGATTAAAGCGATGAA
1 TCCTATCTCCCTAAAGTTACAGTGAAGCAGG-CTAAAGCGATGAA
16354866 TCCTAT
1 TCCTAT
16354872 ACCTTTGAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
43 2 0.05
44 40 0.95
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (44 bp):
TCCTATCTCCCTAAAGTTACAGTGAAGCAGGCTAAAGCGATGAA
Found at i:16355042 original size:45 final size:45
Alignment explanation
Indices: 16354958--16355068 Score: 118
Period size: 45 Copynumber: 2.5 Consensus size: 45
16354948 TTAAAGCAAT
* *
16354958 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACATCA
1 AAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAAACATCA
* ** *
16355003 AAGTCTTATTTCCCTGGCGTTGCAATGGAGCAGGCTAAAACCA-CA
1 AAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAAA-CATCA
** *
16355048 AA-TCTCGTCTCCCAGAAGTTG
1 AAGTCTTATCTCCCTGAAGTTG
16355069 TGACAGAGTA
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
44 13 0.25
45 38 0.72
46 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (45 bp):
AAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAAACATCA
Found at i:16360237 original size:3 final size:3
Alignment explanation
Indices: 16360229--16360278 Score: 84
Period size: 3 Copynumber: 16.7 Consensus size: 3
16360219 TAATCCCCTT
16360229 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC ATTC TTC TT-
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC
16360274 TTC TT
1 TTC TT
16360279 TCATCAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:16360321 original size:2 final size:2
Alignment explanation
Indices: 16360314--16360339 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16360304 TGATTCCTCA
16360314 AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC
16360340 TTGAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:16361489 original size:2 final size:2
Alignment explanation
Indices: 16361482--16361516 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
16361472 TAAAGTTTTA
*
16361482 AT AT AT AT -T AT AT AC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16361517 TTGGTAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16362773 original size:30 final size:30
Alignment explanation
Indices: 16362739--16362831 Score: 168
Period size: 30 Copynumber: 3.1 Consensus size: 30
16362729 ACTTATTTTA
*
16362739 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
16362769 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
16362799 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
16362829 TTG
1 TTG
16362832 CTTGTTAAGT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 61 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:16371373 original size:33 final size:33
Alignment explanation
Indices: 16371329--16371399 Score: 99
Period size: 33 Copynumber: 2.2 Consensus size: 33
16371319 CATGATGGAG
* *
16371329 GACTGTTGTGGGGCAGGTG-AGGAGGACATATGT
1 GACTGTAGTGGGACAGGTGAAGGA-GACATATGT
*
16371362 GACTGTAGTGGGACAGGTGAAGGAGACCTATGT
1 GACTGTAGTGGGACAGGTGAAGGAGACATATGT
16371395 GACTG
1 GACTG
16371400 AGATACAGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 30 0.88
34 4 0.12
ACGTcount: A:0.24, C:0.11, G:0.42, T:0.23
Consensus pattern (33 bp):
GACTGTAGTGGGACAGGTGAAGGAGACATATGT
Found at i:16371622 original size:22 final size:22
Alignment explanation
Indices: 16371583--16371660 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
16371573 TACTTTTGTA
** *
16371583 TAAGCTCTCATGTTTAACGAAC
1 TAAGCTCTCATGGCTAACGTAC
* *
16371605 TAAACCCTCATGGCTAACGTAC
1 TAAGCTCTCATGGCTAACGTAC
16371627 TAAGCTCTCATGGCTAACGTAC
1 TAAGCTCTCATGGCTAACGTAC
16371649 TAAGCTCTCATG
1 TAAGCTCTCATG
16371661 TTTGATGGTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (22 bp):
TAAGCTCTCATGGCTAACGTAC
Found at i:16380757 original size:30 final size:30
Alignment explanation
Indices: 16380700--16380761 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
16380690 GCTTTTTGAA
* *
16380700 AATATTTACAAAAAGAGGCATCTAATTTTT
1 AATATTTACAAAAAGAGGCACCAAATTTTT
16380730 AATATTTACAAAAAGA-GCAACCAAATTTTT
1 AATATTTACAAAAAGAGGC-ACCAAATTTTT
16380760 AA
1 AA
16380762 AAATAATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAGAGGCACCAAATTTTT
Found at i:16389701 original size:29 final size:27
Alignment explanation
Indices: 16389661--16389714 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
16389651 AAAAGCCCTT
16389661 TTTTTTAAATTTACCGAAATAGGCCGG
1 TTTTTTAAATTTACCGAAATAGGCCGG
* *
16389688 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAA--ATTTACCGAAATAGGCC
16389715 ATTTTCCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
29 15 0.65
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.41
Consensus pattern (27 bp):
TTTTTTAAATTTACCGAAATAGGCCGG
Found at i:16391718 original size:22 final size:22
Alignment explanation
Indices: 16391689--16391842 Score: 227
Period size: 22 Copynumber: 7.0 Consensus size: 22
16391679 ATTTTATTGA
16391689 TAAACATGAGAGCTTAGTACGT
1 TAAACATGAGAGCTTAGTACGT
*
16391711 GAAACATGAGAGCTTAGTACGT
1 TAAACATGAGAGCTTAGTACGT
**
16391733 TAGCCATGAGAGCTTAGTACGT
1 TAAACATGAGAGCTTAGTACGT
** * * *
16391755 TAGCCATGAGGGTTTAGTTCGT
1 TAAACATGAGAGCTTAGTACGT
16391777 TAAACATGAGAGCTTAGTACGT
1 TAAACATGAGAGCTTAGTACGT
16391799 TAAACATGAGAGCTTAGTACGT
1 TAAACATGAGAGCTTAGTACGT
*
16391821 GAAACATGAGAGCTTAGTACGT
1 TAAACATGAGAGCTTAGTACGT
16391843 ACTATCAACA
Statistics
Matches: 119, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
TAAACATGAGAGCTTAGTACGT
Found at i:16394093 original size:18 final size:18
Alignment explanation
Indices: 16394070--16394118 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
16394060 TCAATTAATC
*
16394070 TAATTTTATTTATATTTT
1 TAATTTTATTTAAATTTT
16394088 TAATTTTA--TAAATTTT
1 TAATTTTATTTAAATTTT
16394104 TAATATTTTATTTAA
1 T-A-ATTTTATTTAA
16394119 TCGAATCGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 8 0.31
17 1 0.04
18 14 0.54
20 3 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTTATTTAAATTTT
Found at i:16398034 original size:23 final size:22
Alignment explanation
Indices: 16397991--16398034 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
16397981 TTCTAAGTTG
16397991 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
16398014 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
16398035 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:16398147 original size:45 final size:45
Alignment explanation
Indices: 16398081--16398172 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
16398071 CAGATACTCA
* *
16398081 GTGGATTCAGCACATAACAACCACCTTATTAATCAATGATGTCCG
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCG
* *
16398126 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCG
1 GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCG
16398171 GT
1 GT
16398173 TCACATAGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAACAACCACCTTACTAATCAATGATGTCCG
Found at i:16398241 original size:51 final size:52
Alignment explanation
Indices: 16398178--16398313 Score: 199
Period size: 50 Copynumber: 2.7 Consensus size: 52
16398168 TCGGTTCACA
*
16398178 TAGTAGCCTGCACATTGTACTACACATGTGACCATTACCA-TCC-GATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCAG-TACACG
* * *
16398229 TAGTAGCATGCACATAGTACTACACATGCGACC--TATCATTCCAGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCAGTACACG
16398279 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
16398314 CACTTTCACT
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
49 4 0.05
50 40 0.53
51 31 0.41
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (52 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCCAGTACACG
Found at i:16400262 original size:25 final size:25
Alignment explanation
Indices: 16400234--16400306 Score: 146
Period size: 25 Copynumber: 2.9 Consensus size: 25
16400224 GGACAGGATT
16400234 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
16400259 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
16400284 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
16400307 TGAGCTAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:16402210 original size:43 final size:43
Alignment explanation
Indices: 16401919--16402230 Score: 247
Period size: 43 Copynumber: 7.3 Consensus size: 43
16401909 CTAATGAATG
* * ** * *
16401919 CGCCGCTAAAGACCTTGATCTTTAGCGGCG-TTTTTGGGAGAAG
1 CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTT-CCATAAA
* *
16401962 CGCCGCTAAAGACCCTGATCTTTAGCGGCGC-TTCTCTC-TCAAA
1 CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTTC-CAT-AAA
* * * *
16402005 CGCCACTAAAGACCCTTATCTTTAGCGGCGCTTCTCCCAAAAA
1 CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTTCCATAAA
* ** * * * *
16402048 CGCCACTAAAGATCAGGGTCTTTAGCAGCGC-TTTCCCCTCAAA
1 CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTTCCAT-AAA
* * ** *
16402091 CGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCACAAA
1 CGCCACTAA-AGACCCTGATCTTTAGCGGCGCTTTTTCCATAAA
** * *
16402134 CGCCACTAAAGACTATGATATTTAGTGGCGCTTTTTCCATAAA
1 CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTTCCATAAA
* * ** *
16402177 CGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAA
1 CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTTCCATAAA
16402220 CGCCACTAAAG
1 CGCCACTAAAG
16402231 GCCAACACCT
Statistics
Matches: 209, Mismatches: 51, Indels: 18
0.75 0.18 0.06
Matches are distributed among these distances:
42 7 0.03
43 194 0.93
44 8 0.04
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (43 bp):
CGCCACTAAAGACCCTGATCTTTAGCGGCGCTTTTTCCATAAA
Found at i:16402221 original size:129 final size:127
Alignment explanation
Indices: 16401919--16402230 Score: 297
Period size: 129 Copynumber: 2.4 Consensus size: 127
16401909 CTAATGAATG
* ** * * *
16401919 CGCCGCTAAAGACCTTGATCTTTAGCGGCGTTTTTGGGAGAAGCGCCGCTAAAGACCCTGATCTT
1 CGCCGCTAAAGACCTT-ATCTTTAGCGGCG-CTTTGCCAAAAACGCCGCTAAAGACCCTGATCTA
* * * *
16401984 TAGCGGCGCTTCTCTCTCAAACGCCACTAAAGACCCTTATCTTTAGCGGCGCTTCTCCCAAAAA
64 TAGCGGCGCTTCTCTCACAAACGCCACTAAAGACCATGATATTTAGCGGCGCTTCTCCCAAAAA
* **** * * **
16402048 CGCCACTAAAGATCAGGGTCTTTAGCAGCGCTTTCCCCTCAAACGCCGC-AATAGACCCTGATCT
1 CGCCGCTAAAGA-CCTTATCTTTAGCGGCGCTTT-GCCAAAAACGCCGCTAA-AGACCCTGATCT
* * * * *
16402112 ATAGCGGCGCTT-TGAC-CACAAACGCCACTAAAGACTATGATATTTAGTGGCGCTTTTTCCATA
63 ATAGCGGCGCTTCT--CTCACAAACGCCACTAAAGACCATGATATTTAGCGGCGCTTCTCCCAAA
16402175 AA
126 AA
*
16402177 CGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAG
1 CGCCGCTAAAGA-CCTTATCTTTAGCGGCGCTTTG-CCAAAAACGCCGCTAAAG
16402231 GCCAACACCT
Statistics
Matches: 142, Mismatches: 34, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
128 6 0.04
129 132 0.93
130 4 0.03
ACGTcount: A:0.26, C:0.30, G:0.20, T:0.24
Consensus pattern (127 bp):
CGCCGCTAAAGACCTTATCTTTAGCGGCGCTTTGCCAAAAACGCCGCTAAAGACCCTGATCTATA
GCGGCGCTTCTCTCACAAACGCCACTAAAGACCATGATATTTAGCGGCGCTTCTCCCAAAAA
Found at i:16402244 original size:86 final size:87
Alignment explanation
Indices: 16401919--16402255 Score: 312
Period size: 86 Copynumber: 3.9 Consensus size: 87
16401909 CTAATGAATG
* ** * * * **
16401919 CGCCGCTAAAGA-CCTTGATCTTTAGCGGCGTTTTTG-GGAGAAGCGCCGCTAAAGACCCTGATC
1 CGCCGCTAAAGACCCTT-ATCTTTAGCGGCG-CTTTGACCAAAAACGCCACTAAAGACCAAGATC
* *
16401982 TTTAGCGGCGC-TTCTCTC-TCAAA
64 TTTAGTGGCGCTTTTTC-CATCAAA
* * * * *
16402005 CGCCACTAAAGACCCTTATCTTTAGCGGCGCTTCT-CCCAAAAACGCCACTAAAGATCAGGGTCT
1 CGCCGCTAAAGACCCTTATCTTTAGCGGCGCTT-TGACCAAAAACGCCACTAAAGACCAAGATCT
** * *
16402069 TTAGCAGCGC-TTTCCCCTCAAA
65 TTAGTGGCGCTTTTTCCATCAAA
* * * * * *
16402091 CGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCACTAAAGACTATGATAT
1 CGCCGCTAA-AGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCAAGATCT
16402155 TTAGTGGCGCTTTTTCCAT-AAA
65 TTAGTGGCGCTTTTTCCATCAAA
* * *
16402177 CGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGGCCAACACCTT
1 CGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCAAGATCTT
*
16402242 TAGTGGCGTTTTTT
66 TAGTGGCGCTTTTT
16402256 TAAAAAGCGC
Statistics
Matches: 205, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
85 6 0.03
86 187 0.91
87 12 0.06
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (87 bp):
CGCCGCTAAAGACCCTTATCTTTAGCGGCGCTTTGACCAAAAACGCCACTAAAGACCAAGATCTT
TAGTGGCGCTTTTTCCATCAAA
Found at i:16402623 original size:21 final size:21
Alignment explanation
Indices: 16402581--16402672 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
16402571 TTTGACGCTG
**
16402581 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
16402602 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * *
16402623 CTGTACTTCTCC-CGCTGCCGC
1 CTCTGCTTC-CCTCGCTGCAGC
* * *
16402644 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
16402665 ATCTGCTT
1 CTCTGCTT
16402673 TAAGCTGCTG
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.95
22 2 0.03
ACGTcount: A:0.04, C:0.43, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:16402720 original size:66 final size:66
Alignment explanation
Indices: 16402643--16402789 Score: 199
Period size: 66 Copynumber: 2.2 Consensus size: 66
16402633 CCCGCTGCCG
* * *
16402643 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTG-TAGCTAGAGTTCTTCATATCTTT-GTT
16402706 GAA
64 GAA
* * * *
16402709 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTAGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGA
16402774 A
66 A
16402775 CCTCAGCTTCTCTCG
1 CCTCAGCTTCTCTCG
16402790 ATGTTGCCTC
Statistics
Matches: 72, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.13, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGCTGCCGCATCTGCTTTAAGCTGTAGCTAGAGTTCTTCATATCTTTGTTGA
A
Found at i:16402805 original size:66 final size:66
Alignment explanation
Indices: 16402643--16402812 Score: 191
Period size: 66 Copynumber: 2.6 Consensus size: 66
16402633 CCCGCTGCCG
* * * * * * *
16402643 CCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATACTTTCGTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTG-TAGCTAGAGTTCTTCATACTTTCGTTG
16402707 AA
65 AA
* * * *
16402709 CCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGTAGCTAGAGTTCTTCATATCTTT-TTTG
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTAGAGTTCTTCATA-CTTTCGTTG
16402773 AA
65 AA
* *
16402775 CCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
16402813 GTAATTTGCT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
65 1 0.01
66 85 0.94
67 4 0.04
ACGTcount: A:0.13, C:0.28, G:0.18, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTAGCTAGAGTTCTTCATACTTTCGTTGA
A
Found at i:16408263 original size:16 final size:16
Alignment explanation
Indices: 16408242--16408275 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
16408232 ACTAAGCTAC
16408242 GTAAGTTATGTATTAT
1 GTAAGTTATGTATTAT
*
16408258 GTAAGTTATTTATTAT
1 GTAAGTTATGTATTAT
16408274 GT
1 GT
16408276 CGAATTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (16 bp):
GTAAGTTATGTATTAT
Found at i:16408284 original size:26 final size:25
Alignment explanation
Indices: 16408253--16408309 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
16408243 TAAGTTATGT
* *
16408253 ATTATGTAAGTTATTTATTATGTCGA
1 ATTATGTAAGTTATGTATTA-GTCAA
*
16408279 ATTATGTAAGTTGTGTATTAGTCAA
1 ATTATGTAAGTTATGTATTAGTCAA
16408304 ATTATG
1 ATTATG
16408310 CTATGTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 10 0.36
26 18 0.64
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.47
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTAGTCAA
Found at i:16408323 original size:9 final size:9
Alignment explanation
Indices: 16408311--16408603 Score: 82
Period size: 9 Copynumber: 34.7 Consensus size: 9
16408301 CAAATTATGC
16408311 TATGTAAGT
1 TATGTAAGT
*
16408320 TATGTATGT
1 TATGTAAGT
** *
16408329 CGTATAAGT
1 TATGTAAGT
16408338 TATGTAAG-
1 TATGTAAGT
16408346 T-TGTAAGT
1 TATGTAAGT
16408354 TATGTAAGT
1 TATGTAAGT
*
16408363 TAT-TTA-T
1 TATGTAAGT
* *
16408370 TATGAAAAT
1 TATGTAAGT
*
16408379 TAAGTAAGT
1 TATGTAAGT
*
16408388 TATGTAATT
1 TATGTAAGT
*
16408397 TACG-AA-T
1 TATGTAAGT
* **
16408404 AAT-TAAAA
1 TATGTAAGT
*
16408412 AATTGTAAGT
1 TA-TGTAAGT
16408422 TATGTAAG-
1 TATGTAAGT
16408430 T-TGTAAGT
1 TATGTAAGT
*
16408438 TATGTATA-A
1 TATGTA-AGT
16408447 TAT-TAA-T
1 TATGTAAGT
**
16408454 TAACTAAGT
1 TATGTAAGT
*
16408463 TATGTAATT
1 TATGTAAGT
*
16408472 TATGTATAATAT
1 TATG--TAA-GT
16408484 TAAT-TAA-T
1 T-ATGTAAGT
16408492 TAAT-TAAGT
1 T-ATGTAAGT
*
16408501 TATGTAATT
1 TATGTAAGT
16408510 TATGT-A--
1 TATGTAAGT
*
16408516 TAT-TAACT
1 TATGTAAGT
*
16408524 AAT-TAAGT
1 TATGTAAGT
*
16408532 TATGTAATT
1 TATGTAAGT
16408541 TATG-AA-T
1 TATGTAAGT
* **
16408548 AAT-TAAAAA
1 TATGT-AAGT
*
16408557 AATGTAAGT
1 TATGTAAGT
16408566 TATGTAAGT
1 TATGTAAGT
16408575 TATGTAAG-
1 TATGTAAGT
16408583 T-TGTAAG-
1 TATGTAAGT
16408590 T-TGTAAGT
1 TATGTAAGT
16408598 TATGTA
1 TATGTA
16408604 TAATATTNNN
Statistics
Matches: 215, Mismatches: 40, Indels: 58
0.69 0.13 0.19
Matches are distributed among these distances:
5 1 0.00
6 4 0.02
7 39 0.18
8 41 0.19
9 114 0.53
10 9 0.04
11 3 0.01
12 2 0.01
13 2 0.01
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:16408354 original size:16 final size:16
Alignment explanation
Indices: 16408313--16408443 Score: 70
Period size: 16 Copynumber: 7.8 Consensus size: 16
16408303 AATTATGCTA
*
16408313 TGTAAGTTATGTATGT
1 TGTAAGTTATGTAAGT
*
16408329 CGTATAAGTTATGTAAGT
1 --TGTAAGTTATGTAAGT
16408347 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
* * * *
16408363 TATTTA-TTATGAAAAT
1 T-GTAAGTTATGTAAGT
*
16408379 TAAGTAAGTTATGTAATT
1 T--GTAAGTTATGTAAGT
** *
16408397 TACGAATAA-TTA-AAAAAT
1 T--G--TAAGTTATGTAAGT
16408415 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16408431 TGTAAGTTATGTA
1 TGTAAGTTATGTA
16408444 TAATATTAAT
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
14 3 0.03
15 3 0.03
16 42 0.48
17 5 0.06
18 29 0.33
19 3 0.03
20 3 0.03
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:16408420 original size:34 final size:34
Alignment explanation
Indices: 16408382--16408578 Score: 132
Period size: 34 Copynumber: 5.6 Consensus size: 34
16408372 TGAAAATTAA
*
16408382 GTAAGTTATGTAATTTACGAATAATTAAAAAATT
1 GTAAGTTATGTAATTTATGAATAATTAAAAAATT
* * *
16408416 GTAAGTTATGTAAGTTGT-AAGTTATGTATAATATTAATT
1 GTAAGTTATGTAATTTATGAA-TAAT-TA-AA-A--AATT
* * **
16408455 AACTAAGTTATGTAATTTATGTATAATATTAATTAATT
1 --GTAAGTTATGTAATTTATGAAT-A-ATTAAAAAATT
* * **
16408493 AATTAAGTTATGTAATTTATGTAT-ATTAACTAA-T
1 --GTAAGTTATGTAATTTATGAATAATTAAAAAATT
*
16408527 -TAAGTTATGTAATTTATGAATAATTAAAAAAAT
1 GTAAGTTATGTAATTTATGAATAATTAAAAAATT
*
16408560 GTAAGTTATGTAAGTTATG
1 GTAAGTTATGTAATTTATG
16408579 TAAGTTGTAA
Statistics
Matches: 132, Mismatches: 17, Indels: 28
0.75 0.10 0.16
Matches are distributed among these distances:
31 20 0.15
32 7 0.05
33 3 0.02
34 36 0.27
35 10 0.08
36 2 0.02
37 1 0.01
38 27 0.20
39 4 0.03
41 17 0.13
42 3 0.02
43 2 0.02
ACGTcount: A:0.42, C:0.02, G:0.13, T:0.44
Consensus pattern (34 bp):
GTAAGTTATGTAATTTATGAATAATTAAAAAATT
Found at i:16408527 original size:31 final size:32
Alignment explanation
Indices: 16408431--16408580 Score: 140
Period size: 34 Copynumber: 4.4 Consensus size: 32
16408421 TTATGTAAGT
* * *
16408431 TGTAAGTTATGTATAATATTAATTAACTAAGTTA
1 TGTAATTTATGTAT-A-ATTAAATAATTAAGTTA
16408465 TGTAATTTATGTATAATATTAATTAATTAATTAAGTTA
1 TGTAATTTATGTAT-A-ATT-A--AA-TAATTAAGTTA
*
16408503 TGTAATTTATGTAT-ATTAACTAATTAAGTTA
1 TGTAATTTATGTATAATTAAATAATTAAGTTA
* *
16408534 TGTAATTTATGAATAATTAAAAAAATGTAAGTTA
1 TGTAATTTATGTATAATT-AAATAAT-TAAGTTA
*
16408568 TGTAAGTTATGTA
1 TGTAATTTATGTA
16408581 AGTTGTAAGT
Statistics
Matches: 100, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
31 24 0.24
32 4 0.04
33 5 0.05
34 38 0.38
35 4 0.04
37 1 0.01
38 24 0.24
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (32 bp):
TGTAATTTATGTATAATTAAATAATTAAGTTA
Found at i:16408911 original size:31 final size:33
Alignment explanation
Indices: 16408849--16408924 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 33
16408839 NNNNNNTCAG
16408849 TTATGTATAATATTAATTAACTAAGTTATGTAAT
1 TTATGTATAATATTAATTAACT-AGTTATGTAAT
16408883 TTATGTATAATATTAATGT-A-T-GTTATGTAAT
1 TTATGTATAATATTAAT-TAACTAGTTATGTAAT
*
16408914 TTATGAATAAT
1 TTATGTATAAT
16408925 TAAAAAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
31 20 0.50
33 1 0.03
34 18 0.45
35 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.11, T:0.49
Consensus pattern (33 bp):
TTATGTATAATATTAATTAACTAGTTATGTAAT
Found at i:16408954 original size:16 final size:16
Alignment explanation
Indices: 16408932--16408984 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
16408922 AATTAAAAAA
16408932 ATGTAAGTTATGTAAG-T
1 ATGTAAG-T-TGTAAGTT
16408949 -TGTAAGTTGTAAGTT
1 ATGTAAGTTGTAAGTT
*
16408964 ATGTAAGTTGTCAGTT
1 ATGTAAGTTGTAAGTT
16408980 ATGTA
1 ATGTA
16408985 TAATATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
14 6 0.18
15 2 0.06
16 25 0.76
ACGTcount: A:0.30, C:0.02, G:0.25, T:0.43
Consensus pattern (16 bp):
ATGTAAGTTGTAAGTT
Found at i:16408962 original size:23 final size:23
Alignment explanation
Indices: 16408933--16408979 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
16408923 ATTAAAAAAA
16408933 TGTAAGTTATGTAAGTTGTAAGT
1 TGTAAGTTATGTAAGTTGTAAGT
*
16408956 TGTAAGTTATGTAAGTTGTCAGT
1 TGTAAGTTATGTAAGTTGTAAGT
16408979 T
1 T
16408980 ATGTATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.02, G:0.26, T:0.45
Consensus pattern (23 bp):
TGTAAGTTATGTAAGTTGTAAGT
Found at i:16414107 original size:41 final size:41
Alignment explanation
Indices: 16414060--16414444 Score: 467
Period size: 41 Copynumber: 9.4 Consensus size: 41
16414050 GCGCTTCGGT
* * * * *
16414060 AAAAACGCCGCTAAAGGT-CAATACATTAGCGGCGCTTAGAT
1 AAAAACGCCGCTAAAGATCCGA-GCATTAGCGGCGCCTAGAC
* * * * * **
16414101 ACAAACGCCGCTGAAGA-CAAGAGAATTAGTGGCG-CTCAGTT
1 AAAAACGCCGCTAAAGATC-CGAGCATTAGCGGCGCCT-AGAC
* * *
16414142 AAAAACGCCGCTAAAGATCCGAGTATTACCGGCGCCT-GTAT
1 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTAG-AC
*
16414183 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCATAGAC
1 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTAGAC
*
16414224 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTACAC
1 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTAGAC
*
16414265 GAAAACGCCGCTAAAGA-CTCGAGCATTAGCGGCGCCTAGAC
1 AAAAACGCCGCTAAAGATC-CGAGCATTAGCGGCGCCTAGAC
* *
16414306 AAAAACGCTGCTAAAGATCCGAGCATTAGCGGCGCCTACAC
1 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTAGAC
*
16414347 AAAAACGCCGCTAAAGA-CTCGAGCATTAGCGGCCCCTAGAC
1 AAAAACGCCGCTAAAGATC-CGAGCATTAGCGGCGCCTAGAC
* *
16414388 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCTTACAC
1 AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTAGAC
16414429 AAAAACGCCGCTAAAG
1 AAAAACGCCGCTAAAG
16414445 GTTTAAAAAA
Statistics
Matches: 299, Mismatches: 34, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
40 4 0.01
41 288 0.96
42 7 0.02
ACGTcount: A:0.35, C:0.28, G:0.23, T:0.15
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGATCCGAGCATTAGCGGCGCCTAGAC
Found at i:16414739 original size:27 final size:25
Alignment explanation
Indices: 16414669--16414739 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
16414659 GGTGTAGTGG
*
16414669 ATTATTTTAACTTGCTTTATAGACT
1 ATTATTTTAAGTTGCTTTATAGACT
* *
16414694 ATTATTTTAAGTTACTTTATATGTCAT
1 ATTATTTTAAGTTGCTTTATA-GAC-T
* *
16414721 TTTATTTTAAGTTGTTTTA
1 ATTATTTTAAGTTGCTTTA
16414740 CATATTACTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 19 0.50
26 2 0.05
27 17 0.45
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (25 bp):
ATTATTTTAAGTTGCTTTATAGACT
Found at i:16422125 original size:15 final size:14
Alignment explanation
Indices: 16422104--16422146 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
16422094 TTAAATTAAA
16422104 ATAATTTTATTTTT
1 ATAATTTTATTTTT
*
16422118 ATTAATTTAAATTTTT
1 A-TAATTT-TATTTTT
*
16422134 AAAATTTTATTTT
1 ATAATTTTATTTT
16422147 GGTGAGAGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 6 0.25
15 11 0.46
16 7 0.29
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
ATAATTTTATTTTT
Found at i:16428275 original size:12 final size:12
Alignment explanation
Indices: 16428258--16428282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16428248 CTTTGAAATC
16428258 TTTAAAAATTAT
1 TTTAAAAATTAT
16428270 TTTAAAAATTAT
1 TTTAAAAATTAT
16428282 T
1 T
16428283 AAAATTACTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTAAAAATTAT
Found at i:16428353 original size:22 final size:22
Alignment explanation
Indices: 16428322--16428363 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16428312 AAATTTATAA
* *
16428322 ATTTATAAAAATTACAAAATTT
1 ATTTAAAAAAATTAAAAAATTT
*
16428344 ATTTAAAAAATTTAAAAAAT
1 ATTTAAAAAAATTAAAAAAT
16428364 ATTAAAATGA
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:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTAAAAAAATTAAAAAATTT
Found at i:16428527 original size:27 final size:29
Alignment explanation
Indices: 16428491--16428553 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 29
16428481 TTTTATAAAA
16428491 TTTTAATAAAATTTA-TTTCTTTTTA-AT
1 TTTTAATAAAATTTAGTTTCTTTTTATAT
* * *
16428518 TTTTAGTAAATTTTAGTTTTTTTTTTATAT
1 TTTTAATAAAATTTAG-TTTCTTTTTATAT
16428548 TTTTAA
1 TTTTAA
16428554 AATGTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 13 0.45
29 9 0.31
30 7 0.24
ACGTcount: A:0.29, C:0.02, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTAATAAAATTTAGTTTCTTTTTATAT
Found at i:16428551 original size:20 final size:20
Alignment explanation
Indices: 16428528--16428580 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
16428518 TTTTAGTAAA
*
16428528 TTTTAGTTTTTTTTTTATAT
1 TTTTAATTTTTTTTTTATAT
** *
16428548 TTTTAAAATGTTTTTTATAT
1 TTTTAATTTTTTTTTTATAT
16428568 TTTGTAATTTTTT
1 TTT-TAATTTTTT
16428581 AAAATAATTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (20 bp):
TTTTAATTTTTTTTTTATAT
Found at i:16428632 original size:29 final size:30
Alignment explanation
Indices: 16428540--16428635 Score: 89
Period size: 29 Copynumber: 3.4 Consensus size: 30
16428530 TTAGTTTTTT
* *
16428540 TTTTAT-A-TTTTTAAAATGTTTTTTAT-A
1 TTTTATAATTTTTTAAAATATTTTATATAA
* *
16428567 TTTTGTAATTTTTTAAAATAATTTCA-ATAA
1 TTTTATAATTTTTTAAAAT-ATTTTATATAA
*
16428597 -TTT-TAATTTTTTTAAAT-TTTTATATAA
1 TTTTATAATTTTTTAAAATATTTTATATAA
16428624 TTTTATAATTTT
1 TTTTATAATTTT
16428636 ATTTTATAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
26 4 0.07
27 9 0.16
28 17 0.30
29 22 0.39
30 4 0.07
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (30 bp):
TTTTATAATTTTTTAAAATATTTTATATAA
Found at i:16428649 original size:24 final size:23
Alignment explanation
Indices: 16428614--16428659 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
16428604 TTTTTTAAAT
*
16428614 TTTTATATAATTTTATAATTTTA
1 TTTTATACAATTTTATAATTTTA
*
16428637 TTTTATAACAATTTTTTAATTTT
1 TTTTAT-ACAATTTTATAATTTT
16428660 TTAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (23 bp):
TTTTATACAATTTTATAATTTTA
Found at i:16428671 original size:32 final size:30
Alignment explanation
Indices: 16428605--16428680 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
16428595 AATTTTAATT
* * *
16428605 TTTTTAAATTTTTATATAATTTTATAATTTTA
1 TTTTTAAAATTTT-T-TAATTTTATAAATATA
*
16428637 TTTTATAACAATTTTTTAATTTTTTAAATATA
1 TTTT-TAA-AATTTTTTAATTTTATAAATATA
16428669 TTTTTAAAATTT
1 TTTTTAAAATTT
16428681 ATAAGTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
30 5 0.13
31 3 0.08
32 21 0.55
33 4 0.11
34 5 0.13
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTAAAATTTTTTAATTTTATAAATATA
Found at i:16429856 original size:42 final size:41
Alignment explanation
Indices: 16429792--16430117 Score: 276
Period size: 41 Copynumber: 7.8 Consensus size: 41
16429782 CAGACAAAAA
* * *
16429792 CGCCGCTAAAGACCATGTTCTTTAGCGGTGTTTTTTCTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTT-TTAAG
16429834 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAA-
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT-TAAG
* ***
16429875 ----GC--AAGAACATGGTCTTTAGCGGTGTTTTTGTTTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTT-TTTTAAG
*** *
16429912 CTAAGC--AAGAACATGGTCTTTAGCGGTGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTT-TAAG
16429952 CGCCGCTAAAGAACATGGTCTTTAGCGGCG-TTTTTTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTAAG
* **
16429992 CGCTGCTAAAGAACATTATCTTTAGCGGCGTTTAGCGGTATTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTA---GCG----GC-G--TTTTTTT-TAAG
*
16430044 CGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTTTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTAAG
* **
16430085 CGCTGCTAAAGAACATTATCTTTAGCGGCGTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTT
16430118 AGCGGCACTT
Statistics
Matches: 237, Mismatches: 24, Indels: 47
0.77 0.08 0.15
Matches are distributed among these distances:
35 21 0.09
36 5 0.02
37 5 0.02
39 3 0.01
40 33 0.14
41 64 0.27
42 64 0.27
43 3 0.01
45 2 0.01
47 2 0.01
48 1 0.00
49 3 0.01
51 6 0.03
52 25 0.11
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (41 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTAAG
Found at i:16430052 original size:52 final size:51
Alignment explanation
Indices: 16429972--16430129 Score: 185
Period size: 51 Copynumber: 3.3 Consensus size: 51
16429962 GAACATGGTC
*
16429972 TTTAGCGGC-GTTTTTTTAAGCGCTGCTAAAGAACATTATCTTTAGCGGCG
1 TTTAGCGGCATTTTTTTTAAGCGCTGCTAAAGAACATTATCTTTAGCGGCG
* * *
16430022 TTTAGCGGTATTTTTTTCTAAGCGCCGCTAAAGAAC---A----T-G-GTC-
1 TTTAGCGGCATTTTTTT-TAAGCGCTGCTAAAGAACATTATCTTTAGCGGCG
16430064 TTTAGCGGCATTTTTTTTAAGCGCTGCTAAAGAACATTATCTTTAGCGGCG
1 TTTAGCGGCATTTTTTTTAAGCGCTGCTAAAGAACATTATCTTTAGCGGCG
*
16430115 TTTAGCGGCACTTTT
1 TTTAGCGGCATTTTT
16430130 ATACAAAAAC
Statistics
Matches: 88, Mismatches: 8, Indels: 23
0.74 0.07 0.19
Matches are distributed among these distances:
41 17 0.19
42 16 0.18
43 2 0.02
44 2 0.02
45 1 0.01
48 1 0.01
49 2 0.02
50 10 0.11
51 20 0.23
52 17 0.19
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (51 bp):
TTTAGCGGCATTTTTTTTAAGCGCTGCTAAAGAACATTATCTTTAGCGGCG
Found at i:16430103 original size:93 final size:92
Alignment explanation
Indices: 16429930--16430122 Score: 359
Period size: 92 Copynumber: 2.1 Consensus size: 92
16429920 GAACATGGTC
*
16429930 TTTAGCGGTGTTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTAAGCGC
1 TTTAGCGGTATTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTAAGCGC
16429995 TGCTAAAGAACATTATCTTTAGCGGCG
66 TGCTAAAGAACATTATCTTTAGCGGCG
*
16430022 TTTAGCGGTATTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCATTTTTTTTAAGCG
1 TTTAGCGGTATTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGC-GTTTTTTTAAGCG
16430087 CTGCTAAAGAACATTATCTTTAGCGGCG
65 CTGCTAAAGAACATTATCTTTAGCGGCG
16430115 TTTAGCGG
1 TTTAGCGG
16430123 CACTTTTATA
Statistics
Matches: 98, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 50 0.51
93 48 0.49
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.36
Consensus pattern (92 bp):
TTTAGCGGTATTTTTTTCTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTAAGCGC
TGCTAAAGAACATTATCTTTAGCGGCG
Found at i:16430471 original size:21 final size:21
Alignment explanation
Indices: 16430445--16430515 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
16430435 TTTTTCTCTG
*
16430445 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
16430466 CTCTGCTTCCCTCGCTGTAGC
1 CTCTGCTTCCCTCGCTGCAGC
*
16430487 CACTGCTTCCCTCGCTGTC-GC
1 CTCTGCTTCCCTCGCTG-CAGC
16430508 CTCTGCTT
1 CTCTGCTT
16430516 TAAGTTGTAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.04, C:0.44, G:0.18, T:0.34
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:16434015 original size:9 final size:9
Alignment explanation
Indices: 16433998--16434255 Score: 171
Period size: 9 Copynumber: 27.4 Consensus size: 9
16433988 AAAACGCCAG
*
16433998 TTATTTAAT
1 TTATGTAAT
16434007 TTATGTAAT
1 TTATGTAAT
*
16434016 TTATGTAAG
1 TTATGTAAT
16434025 TTATGTAAGAT
1 TTATGT-A-AT
*
16434036 ATTATGTTA-
1 -TTATGTAAT
*
16434045 TTATGTAAG
1 TTATGTAAT
*
16434054 TTATGCAAGTT
1 TTATGTAA--T
*
16434065 TATATATAAGCT
1 T-TATGTAA--T
*
16434077 TGTA-GATAAC
1 T-TATG-TAAT
16434087 TTATGTAAGT
1 TTATGTAA-T
16434097 TAATATGTAAGT
1 T--TATGTAA-T
*
16434109 TT-TTTAAT
1 TTATGTAAT
*
16434117 TTATGTAAG
1 TTATGTAAT
*
16434126 TTATGTAAG
1 TTATGTAAT
*
16434135 TTATGTAAG
1 TTATGTAAT
*
16434144 TTATTTAAT
1 TTATGTAAT
*
16434153 TTATGTAAG
1 TTATGTAAT
*
16434162 TTATTTAAT
1 TTATGTAAT
16434171 TTATGTAAT
1 TTATGTAAT
*
16434180 TTATGTAAG
1 TTATGTAAT
*
16434189 TTATGTAAG
1 TTATGTAAT
*
16434198 TTATTTAAT
1 TTATGTAAT
*
16434207 TTATGTAAG
1 TTATGTAAT
*
16434216 TTATGTAAG
1 TTATGTAAT
*
16434225 TTATTTAAT
1 TTATGTAAT
*
16434234 TTATGTAAG
1 TTATGTAAT
*
16434243 TTATGTAAG
1 TTATGTAAT
16434252 TTAT
1 TTAT
16434256 TATGTTACTG
Statistics
Matches: 203, Mismatches: 33, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
8 10 0.05
9 156 0.77
10 6 0.03
11 2 0.01
12 29 0.14
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (9 bp):
TTATGTAAT
Found at i:16434028 original size:18 final size:18
Alignment explanation
Indices: 16434007--16434255 Score: 214
Period size: 18 Copynumber: 13.2 Consensus size: 18
16433997 GTTATTTAAT
16434007 TTATGTAATTTATGTAAG
1 TTATGTAATTTATGTAAG
*
16434025 TTATGTAAGATATTATGTTA-
1 TTATGT-A-AT-TTATGTAAG
* *
16434045 TTATGTAAGTTATGCAAG
1 TTATGTAATTTATGTAAG
* *
16434063 TTTATATATAAGCTTGTA-GATAAC
1 --T-TATGTAA--TT-TATG-TAAG
16434087 TTATGTAAGTTAATATGTAAG
1 TTATGTAA-TT--TATGTAAG
* *
16434108 TTTTTTAATTTATGTAAG
1 TTATGTAATTTATGTAAG
*
16434126 TTATGTAAGTTATGTAAG
1 TTATGTAATTTATGTAAG
*
16434144 TTATTTAATTTATGTAAG
1 TTATGTAATTTATGTAAG
* *
16434162 TTATTTAATTTATGTAAT
1 TTATGTAATTTATGTAAG
*
16434180 TTATGTAAGTTATGTAAG
1 TTATGTAATTTATGTAAG
*
16434198 TTATTTAATTTATGTAAG
1 TTATGTAATTTATGTAAG
* * *
16434216 TTATGTAAGTTATTTAAT
1 TTATGTAATTTATGTAAG
*
16434234 TTATGTAAGTTATGTAAG
1 TTATGTAATTTATGTAAG
16434252 TTAT
1 TTAT
16434256 TATGTTACTG
Statistics
Matches: 187, Mismatches: 31, Indels: 26
0.77 0.13 0.11
Matches are distributed among these distances:
17 6 0.03
18 128 0.68
19 2 0.01
20 13 0.07
21 30 0.16
22 2 0.01
23 2 0.01
24 4 0.02
ACGTcount: A:0.34, C:0.01, G:0.15, T:0.50
Consensus pattern (18 bp):
TTATGTAATTTATGTAAG
Found at i:16434147 original size:27 final size:27
Alignment explanation
Indices: 16433996--16434282 Score: 227
Period size: 27 Copynumber: 10.1 Consensus size: 27
16433986 TTAAAACGCC
* * *
16433996 AGTTATTTAATTTATGTAATTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
*
16434023 AGTTATGTAAGATATTATGTTA-TTATGTA
1 AGTTATGTAAG---TTATGTAAGTTATGTA
* * *
16434052 AGTTATGCAAGTTTATATATAAGCTTGTAGATA
1 AGTTATGTAAG--T-TATGTAAG-TTAT-G-TA
* * *
16434085 ACTTATGTAAGTTAATATGTAAGTTTTTTA
1 AGTTATGTAAG-T--TATGTAAGTTATGTA
*
16434115 ATTTATGTAAGTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* * *
16434142 AGTTATTTAATTTATGTAAGTTATTTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16434169 ATTTATGTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16434196 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16434223 AGTTATTTAATTTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGTAAGTTATGTA
* *
16434250 AGTTAT-TATGTTACTGAGTAAGTTATGCA
1 AGTTATGTAAGTTA-T--GTAAGTTATGTA
16434279 AGTT
1 AGTT
16434283 TATATATAAG
Statistics
Matches: 220, Mismatches: 28, Indels: 22
0.81 0.10 0.08
Matches are distributed among these distances:
26 5 0.02
27 128 0.58
28 2 0.01
29 38 0.17
30 19 0.09
31 3 0.01
32 6 0.03
33 19 0.09
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (27 bp):
AGTTATGTAAGTTATGTAAGTTATGTA
Found at i:16436595 original size:25 final size:26
Alignment explanation
Indices: 16436536--16436609 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 26
16436526 TGGGGATTTC
*
16436536 GGGAAATG-AA-ATTGGGGAAATTGG
1 GGGAAATGAAATATTGGGGAAATTGA
* *
16436560 GGGAAA-AAAATATTTGGGAAATT-A
1 GGGAAATGAAATATTGGGGAAATTGA
16436584 GGGAAATG-AA-ATTGGGGAAATCTGA
1 GGGAAATGAAATATTGGGGAAAT-TGA
16436609 G
1 G
16436610 TGGGGGGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
23 10 0.25
24 17 0.43
25 13 0.32
ACGTcount: A:0.42, C:0.01, G:0.35, T:0.22
Consensus pattern (26 bp):
GGGAAATGAAATATTGGGGAAATTGA
Found at i:16436791 original size:37 final size:38
Alignment explanation
Indices: 16436750--16436828 Score: 99
Period size: 40 Copynumber: 2.1 Consensus size: 38
16436740 AGCAAACACT
** *
16436750 TAAAACATA-T-TTGCGGCGTTTATTGACAAAACGCCAC
1 TAAAACATACTATTGCGGCGTTTAACGA-AAAACACCAC
16436787 TAAAACATACCTATTGCGGCGTTTAACGAAAAACACCAC
1 TAAAACATA-CTATTGCGGCGTTTAACGAAAAACACCAC
16436826 TAA
1 TAA
16436829 TAACGCAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 9 0.25
39 13 0.36
40 14 0.39
ACGTcount: A:0.39, C:0.23, G:0.14, T:0.24
Consensus pattern (38 bp):
TAAAACATACTATTGCGGCGTTTAACGAAAAACACCAC
Found at i:16436874 original size:116 final size:113
Alignment explanation
Indices: 16436722--16437020 Score: 327
Period size: 116 Copynumber: 2.6 Consensus size: 113
16436712 AAAATGGCAG
* * *
16436722 ATAAATACGACACCGTTTAGCAAACACTTAAAACATATTTGCGGCGTTTATTGACAAAACGCCAC
1 ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATTGA-AAAACGCCAC
** **
16436787 TAAAA-CATACCTATTGCGGCGTTTAACGA-AAAACACCACTAATAACGCAAA
65 TAAAACCA-AAATATTGCGGCGCATAA-GAGAAAACACCACTAA-AACGC-AA
* * * *
16436838 ATAAAAACGACTGCGTTTAGCAAATACTTAATACATAACTGCGGCGTTTATCAT-AAAAACGCCA
1 ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTAT--TGAAAAACGCCA
* * *
16436902 CAAAAACCAAAATTTTGCGGCGCATAAGAGAAAACGCCACTAAAACGCAA
64 CTAAAACCAAAATATTGCGGCGCATAAGAGAAAACACCACTAAAACGCAA
* * * * *
16436952 TTTAAAATGACAGTGTTTAGCAAAGACTTAAAACATAATTGCGGCGTTTA-TGAAGAAACGCCAC
1 ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATTGAA-AAACGCCAC
16437016 TAAAA
65 TAAAA
16437021 TGGAAACTAA
Statistics
Matches: 154, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
111 1 0.01
112 2 0.01
113 13 0.08
114 44 0.29
115 7 0.05
116 83 0.54
117 3 0.02
118 1 0.01
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (113 bp):
ATAAAAACGACAGCGTTTAGCAAACACTTAAAACATAATTGCGGCGTTTATTGAAAAACGCCACT
AAAACCAAAATATTGCGGCGCATAAGAGAAAACACCACTAAAACGCAA
Found at i:16437344 original size:49 final size:49
Alignment explanation
Indices: 16437283--16437447 Score: 120
Period size: 49 Copynumber: 3.3 Consensus size: 49
16437273 AATATAAAAT
16437283 TTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATGCCCGTA
1 TTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATGCCCGTA
* * * * * * *****
16437332 TTAATCCCTAAACTC-TAAGCTACTAGCTAAACCC-TAAACCTTAAAAT-ATAAAA
1 TTAAACCCTAAAC-CATATGC-CCT--CTTAACCCATATACCCT---ATGCCCGTA
*
16437385 TTTAAACCCTAAACCATATGCCTTCTTAACCCATATACCCTATGCCCGTA
1 -TTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATGCCCGTA
*
16437435 TTAATCCCTAAAC
1 TTAAACCCTAAAC
16437448 TCTAAGCTAC
Statistics
Matches: 81, Mismatches: 24, Indels: 22
0.64 0.19 0.17
Matches are distributed among these distances:
49 30 0.37
50 4 0.05
51 13 0.16
52 13 0.16
53 3 0.04
54 18 0.22
ACGTcount: A:0.36, C:0.32, G:0.05, T:0.28
Consensus pattern (49 bp):
TTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATGCCCGTA
Found at i:16437377 original size:103 final size:103
Alignment explanation
Indices: 16437261--16437479 Score: 402
Period size: 103 Copynumber: 2.1 Consensus size: 103
16437251 TTACCATAAT
16437261 CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATG
1 CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATG
16437326 CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
66 CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
* *
16437364 CCTAAACCTTAAAATATAAAATTTAAACCCTAAACCATATGCCTTCTTAACCCATATACCCTATG
1 CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATG
16437429 CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
66 CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
* *
16437467 TCTAAACTCTAAA
1 CCTAAACCCTAAA
16437480 CAATAAACAA
Statistics
Matches: 111, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.27
Consensus pattern (103 bp):
CCTAAACCCTAAAATATAAAATTTAAACCCTAAACCATATGCCCTCTTAACCCATATACCCTATG
CCCGTATTAATCCCTAAACTCTAAGCTACTAGCTAAAC
Found at i:16437471 original size:7 final size:7
Alignment explanation
Indices: 16437461--16437558 Score: 58
Period size: 7 Copynumber: 14.0 Consensus size: 7
16437451 AAGCTACTAG
16437461 CTAAACT
1 CTAAACT
16437468 CTAAACT
1 CTAAACT
*
16437475 CTAAACA
1 CTAAACT
* *
16437482 ATAAACA
1 CTAAACT
*
16437489 ATAAAC-
1 CTAAACT
*
16437495 CTTAAACC
1 C-TAAACT
*
16437503 CTAAACC
1 CTAAACT
* *
16437510 CTACACC
1 CTAAACT
16437517 CTAAAC-
1 CTAAACT
16437523 CATAAACT
1 C-TAAACT
16437531 CTAAACT
1 CTAAACT
* *
16437538 CTTAACA
1 CTAAACT
16437545 CTAAA-T
1 CTAAACT
16437551 CATAAACT
1 C-TAAACT
16437559 GTATACTTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
6 2 0.03
7 71 0.93
8 3 0.04
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
CTAAACT
Found at i:16437548 original size:28 final size:27
Alignment explanation
Indices: 16437461--16437558 Score: 81
Period size: 28 Copynumber: 3.5 Consensus size: 27
16437451 AAGCTACTAG
* *
16437461 CTAAACTC-TAAACTCTAAACAATAAACA
1 CTAAAC-CATAAACTCTAAAC-CTTAACA
* * * * *
16437489 ATAAACCTTAAACCCTAAACCCTACACC
1 CTAAACCATAAACTCTAAACCTTA-ACA
16437517 CTAAACCATAAACTCTAAACTCTTAACA
1 CTAAACCATAAACTCTAAAC-CTTAACA
*
16437545 CTAAATCATAAACT
1 CTAAACCATAAACT
16437559 GTATACTTAA
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
27 2 0.04
28 50 0.91
29 3 0.05
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (27 bp):
CTAAACCATAAACTCTAAACCTTAACA
Found at i:16437663 original size:15 final size:15
Alignment explanation
Indices: 16437639--16437684 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
16437629 CTAAGACGAT
*
16437639 AACC-TAAACCCCTA
1 AACCTTAAACCTCTA
*
16437653 AACCTTAAACCTTTA
1 AACCTTAAACCTCTA
*
16437668 AACGTTAAACCTCTA
1 AACCTTAAACCTCTA
16437683 AA
1 AA
16437685 GCATATACCC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.43, C:0.30, G:0.02, T:0.24
Consensus pattern (15 bp):
AACCTTAAACCTCTA
Found at i:16437792 original size:22 final size:21
Alignment explanation
Indices: 16437727--16437794 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 21
16437717 CTTGATTAAA
*
16437727 CCCTAAACCATAAGCCATTAAC
1 CCCTAAACCATAAGCC-CTAAC
* * *
16437749 CCATAGACCCTAAGCCCATAAC
1 CCCTAAACCATAAGCCC-TAAC
16437771 CCCTAAACCATAAGCTCCTAAC
1 CCCTAAACCATAAGC-CCTAAC
16437793 CC
1 CC
16437795 TTACACACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 35 0.95
23 2 0.05
ACGTcount: A:0.37, C:0.41, G:0.06, T:0.16
Consensus pattern (21 bp):
CCCTAAACCATAAGCCCTAAC
Found at i:16437983 original size:12 final size:12
Alignment explanation
Indices: 16437966--16437996 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
16437956 AATTTTTTTC
16437966 ATTTTAACAAAT
1 ATTTTAACAAAT
16437978 ATTTTAACAAAT
1 ATTTTAACAAAT
16437990 ATTTTAA
1 ATTTTAA
16437997 ACTATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTTTAACAAAT
Found at i:16438314 original size:73 final size:73
Alignment explanation
Indices: 16438122--16438439 Score: 336
Period size: 72 Copynumber: 4.4 Consensus size: 73
16438112 CTGAGCATTA
* * ** * * ** *
16438122 GCGGTGCTTTCCTAAAAACGCCGCTGTATCCACGAAAGCTCAAAAATCGACATCGTTTCGTTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGACATCGTTGGGCTTAG
*
16438187 G-TTTTTA
66 GTTTTTTT
* * * * *
16438194 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTCGTTGGGTTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGACATCGTTGGGCTTAG
16438259 GTTTTTTT
66 GTTTTTTT
** * * * * *
16438267 GCGGCGCTTTCTTAAAAATGCCACTATATCCACGAAAGCTCAAAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGACATCGTTGGGCTTAG
16438332 GTTTTTTT
66 GTTTTTTT
* * * *
16438340 GCGGCGCTTTCCC-AAAACGCCGCTAAATCC-CTAAAAGCTCAGAAAACGGCGTCGTTGGACTTA
1 GCGGCGCTTTCCCAAAAACGCCGCTAAATCCAC-AAAAGCTCAAAAAACGACATCGTTGGGCTTA
*
16438403 GGTTTGTTT
65 GGTTTTTTT
* * *
16438412 GCGGCGCTTTCTCAGAAACGCTGCTAAA
1 GCGGCGCTTTCCCAAAAACGCCGCTAAA
16438440 GCCCTGATCT
Statistics
Matches: 205, Mismatches: 38, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
71 1 0.00
72 115 0.56
73 89 0.43
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTCCCAAAAACGCCGCTAAATCCACAAAAGCTCAAAAAACGACATCGTTGGGCTTAG
GTTTTTTT
Found at i:16438393 original size:145 final size:145
Alignment explanation
Indices: 16438122--16438432 Score: 435
Period size: 145 Copynumber: 2.1 Consensus size: 145
16438112 CTGAGCATTA
* * * * * * *
16438122 GCGGTGCTTTCCTAAAAACGCCGCTGTATCCACGAAAGCTCAAAAATCGACATCGTTTCGTTTAG
1 GCGGCGCTTTCTTAAAAACGCCACTATATCCACGAAAGCTCAAAAAACGACATCGTTGCGCTTAG
16438187 GTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTCGTTG
66 GTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTCGTTG
** *
16438252 GGTTTAGGTTTTTTT
131 GACTTAGGTTTGTTT
* * *
16438267 GCGGCGCTTTCTTAAAAATGCCACTATATCCACGAAAGCTCAAAAAACGGCATCGTTGGGCTTAG
1 GCGGCGCTTTCTTAAAAACGCCACTATATCCACGAAAGCTCAAAAAACGACATCGTTGCGCTTAG
* * * *
16438332 GTTTTTTTGCGGCGCTTTCCC-AAAACGCCGCTAAATCCCTAAAAGCTCAGAAAACGGCGTCGTT
66 G-TTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTCGTT
16438396 GGACTTAGGTTTGTTT
130 GGACTTAGGTTTGTTT
* *
16438412 GCGGCGCTTTCTCAGAAACGC
1 GCGGCGCTTTCTTAAAAACGC
16438433 TGCTAAAGCC
Statistics
Matches: 145, Mismatches: 20, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
145 127 0.88
146 18 0.12
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (145 bp):
GCGGCGCTTTCTTAAAAACGCCACTATATCCACGAAAGCTCAAAAAACGACATCGTTGCGCTTAG
GTTTTTAGCGGCGCTTTCCCAAAAACGCCGCTAAATCCCCAAAAGATCAGAAAACGACGTCGTTG
GACTTAGGTTTGTTT
Found at i:16438921 original size:30 final size:27
Alignment explanation
Indices: 16438879--16438938 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
16438869 TCTGTTAAAA
* *
16438879 TATTATAGAAGAATTTACTGATAAAATTT
1 TATTATAAAAGAAGTTAC-GA-AAAATTT
*
16438908 TATTGATAAAAGAAGTTACGAAGAATTT
1 TATT-ATAAAAGAAGTTACGAAAAATTT
16438936 TAT
1 TAT
16438939 AATATTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.33
29 6 0.22
30 12 0.44
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (27 bp):
TATTATAAAAGAAGTTACGAAAAATTT
Found at i:16440340 original size:24 final size:23
Alignment explanation
Indices: 16440308--16440354 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
16440298 AAGGGGTTAC
*
16440308 AAGGAGATGAAAGGTGAAGAGTT
1 AAGGAGATGAAAGGTGAAAAGTT
*
16440331 AAGGAAGATGATAGGTGAAAAGTT
1 AAGG-AGATGAAAGGTGAAAAGTT
16440355 GATTATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (23 bp):
AAGGAGATGAAAGGTGAAAAGTT
Found at i:16456489 original size:47 final size:47
Alignment explanation
Indices: 16456420--16456513 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
16456410 CATTCTACGG
* *
16456420 TTCCCTCCAAAACATTTTTCTTTTTCCTCTTTCATTCCACAAAACTT
1 TTCCCTCCAAAAAAATTTTCTTTTTCCTCTTTCATTCCACAAAACTT
* *
16456467 TTCCCTCCAAAAAAATTTTCTTTTTCCTCTTTTATTGCACAAAACTT
1 TTCCCTCCAAAAAAATTTTCTTTTTCCTCTTTCATTCCACAAAACTT
16456514 ATTCTGTAAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.26, C:0.29, G:0.01, T:0.45
Consensus pattern (47 bp):
TTCCCTCCAAAAAAATTTTCTTTTTCCTCTTTCATTCCACAAAACTT
Found at i:16478387 original size:34 final size:33
Alignment explanation
Indices: 16478294--16478398 Score: 138
Period size: 34 Copynumber: 3.1 Consensus size: 33
16478284 GTTCTTTTTT
* * *
16478294 AAAAATTAATTAAATTAGGGTTTAGGGGTTTAA
1 AAAAATTAATTAAATTTGGGTTTAGTGTTTTAA
16478327 AATAAATTAATTAAATTTGGGTTTAGTGTTTTAA
1 AA-AAATTAATTAAATTTGGGTTTAGTGTTTTAA
* * *
16478361 AGAAAACTAATTAAATTTGGGTTTAGTTTTTTTA
1 A-AAAATTAATTAAATTTGGGTTTAGTGTTTTAA
16478395 AAAA
1 AAAA
16478399 TAATATTGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
33 5 0.08
34 58 0.91
35 1 0.02
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.42
Consensus pattern (33 bp):
AAAAATTAATTAAATTTGGGTTTAGTGTTTTAA
Found at i:16478918 original size:127 final size:127
Alignment explanation
Indices: 16478467--16478980 Score: 759
Period size: 126 Copynumber: 4.1 Consensus size: 127
16478457 TTTTTTATTG
* **
16478467 CAGTAGTTCCTG-AAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTAAAAAATGCTTC
1 CAGTAGTTCCTGAAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
* * ** * *
16478531 AAGCAGGATGCACTGTCAGTAAAATTACTGAAAAAATCTCTTACGTGAACACTCTTTTTCTA
66 AAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
* * *
16478593 CAGTAGTT-CTTAAAAATATAATTTTAAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
1 CAGTAGTTCCTGAAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
* *
16478657 AAGCAGGATGCACTGTCAGCAAAATTGA-TGAAAAAAGCTCTCATGTGGACGCTCTTTTTCTA
66 AAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
16478719 CAGTAGTTCCT-AAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
1 CAGTAGTTCCTGAAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
* * *
16478783 AAGAAGGATGCACTATCAGCAAAATTGA-TGAAAAAAGCTCCCACGTGGACTCTCTTTTTCTA
66 AAGCAGGATGCACTGTCAGCAAAATT-ACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
* * *
16478845 CAGTAGTTCCTGAAAAAAATAATTTTGAGAAGACGTTTCTGAACAAATAGTGTCAAAAACGCTTC
1 CAGTAGTTCCTGAAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
* * *
16478910 AAGTAGGATGCATTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTTTTTTTCTA
66 AAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
*
16478972 TAGTAGTTC
1 CAGTAGTTC
16478981 ATGTTTGGCC
Statistics
Matches: 355, Mismatches: 28, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
125 2 0.01
126 237 0.67
127 116 0.33
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (127 bp):
CAGTAGTTCCTGAAAAAAATAATTTTGAGAAGACGATTCTAAACAAATAGTGTCAAAAACACTTC
AAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTA
Found at i:16482562 original size:20 final size:18
Alignment explanation
Indices: 16482522--16482556 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
16482512 AAAAAGGAAA
*
16482522 CATATAAGGGTTAGGATG
1 CATATAAGGGCTAGGATG
16482540 CATATAAGGGCTAGGAT
1 CATATAAGGGCTAGGAT
16482557 ATGCATCAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.09, G:0.31, T:0.26
Consensus pattern (18 bp):
CATATAAGGGCTAGGATG
Found at i:16484351 original size:30 final size:30
Alignment explanation
Indices: 16484317--16484385 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
16484307 ATTAATTAAA
16484317 GAGAGTTTTGAGAAATTTAAAAAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAAAGAAATTT
* * *
16484347 GAGAGCTTTGAGAAATTTAGAGAGAAATTT
1 GAGAGTTTTGAGAAATTTAAAAAGAAATTT
16484377 GAGAGTTTT
1 GAGAGTTTT
16484386 TTGATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (30 bp):
GAGAGTTTTGAGAAATTTAAAAAGAAATTT
Found at i:16486922 original size:51 final size:51
Alignment explanation
Indices: 16486864--16487203 Score: 347
Period size: 51 Copynumber: 6.7 Consensus size: 51
16486854 TTATCATTCA
*
16486864 ATACACGTAGTAGCCTTTACATAGTACTACACACGTGATCAAGTTTTTACG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACG
* *
16486915 GTTCACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACG
* * * **
16486966 GTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACTAAAACTTTT-CG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGA-TCAAGTTTTTACG
* * * *
16487017 ATACAC--A-TAGCCTTCACTTAGTACTACACATGTGA-CCA-TCATTTATCG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTTA-CG
* * * * *
16487065 ATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATC-AAGTTTTTACG
* * * * * *
16487116 ATAGACATTGTAGCCTTCACTTAGTACTAGACATGTGA-CAA-TTATTTATCG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTT-TTTA-CG
*
16487167 ATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 ATACACGTAGTAGCCTTCACATAGTACTACACACGTG
16487204 TTCATCGATA
Statistics
Matches: 237, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
46 4 0.02
48 34 0.14
49 5 0.02
50 2 0.01
51 181 0.76
52 8 0.03
53 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (51 bp):
ATACACGTAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTTACG
Found at i:16487174 original size:102 final size:101
Alignment explanation
Indices: 16486864--16487203 Score: 420
Period size: 102 Copynumber: 3.4 Consensus size: 101
16486854 TTATCATTCA
* * * * * * *
16486864 ATACACGTAGTAGCCTTTACATAGTACTACACACGTGATC-AAGTTTTTACGGTTCACGTAGTAG
1 ATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGATACACAT-GTAG
* *
16486928 CCTTCACATAGTACTACACACGTGATCAAGTT-TTTA-CG
64 CCTTCACTTAGTACTACACATGTGA-CAA-TTATTTATCG
* * * * *
16486966 GTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACTAAAACTTTTCGATACACA--TAGCC
1 ATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGATACACATGTAGCC
* *
16487029 TTCACTTAGTACTACACATGTGACCATCATTTATCG
66 TTCACTTAGTACTACACATGTGACAATTATTTATCG
* * *
16487065 ATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGATAGACATTGTAGC
1 ATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGATACACA-TGTAGC
*
16487130 CTTCACTTAGTACTAGACATGTGACAATTATTTATCG
65 CTTCACTTAGTACTACACATGTGACAATTATTTATCG
16487167 ATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 ATACACGTAGTAGCCTTCACACAGTACTACACACGTG
16487204 TTCATCGATA
Statistics
Matches: 208, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
97 1 0.00
98 6 0.03
99 80 0.38
102 115 0.55
103 6 0.03
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.29
Consensus pattern (101 bp):
ATACACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGATACACATGTAGCC
TTCACTTAGTACTACACATGTGACAATTATTTATCG
Found at i:16492005 original size:2 final size:2
Alignment explanation
Indices: 16491998--16492038 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
16491988 TTCTGTTTTA
16491998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16492039 NNNNNNNNNN
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16493697 original size:8 final size:9
Alignment explanation
Indices: 16493674--16493714 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
16493664 AACCATTCCA
16493674 ATAAATAATT
1 ATAAA-AATT
16493684 -TAAAAATT
1 ATAAAAATT
*
16493692 ATAAAAATA
1 ATAAAAATT
16493701 ATAAAAATT
1 ATAAAAATT
16493710 -TAAAA
1 ATAAAA
16493715 TCCAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 9 0.32
9 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:16498385 original size:63 final size:63
Alignment explanation
Indices: 16498286--16498461 Score: 192
Period size: 63 Copynumber: 2.8 Consensus size: 63
16498276 CTAACCTAGT
* * * ** * * *
16498286 TTATTTGACACAAGCATCACATCACACACAATCATTCCCCGTATCAACAC-TTACAGCTCTAGC
1 TTATTTTACACAAGCACCACAACATGCACAATCATTCCCCGCATCAACACATT-CAGCACCAGC
* * ** * *
16498349 TTATTTTACATAAGCACCACAACATGTACAATCATTCCATGCATTAACACATTCAGCACCAGT
1 TTATTTTACACAAGCACCACAACATGCACAATCATTCCCCGCATCAACACATTCAGCACCAGC
**
16498412 TTATTTTACACAAGCACCACAACATGCACAATCATTCCCTACATCAACAC
1 TTATTTTACACAAGCACCACAACATGCACAATCATTCCCCGCATCAACAC
16498462 CTTCTCTAGG
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
63 91 0.98
64 2 0.02
ACGTcount: A:0.36, C:0.31, G:0.07, T:0.26
Consensus pattern (63 bp):
TTATTTTACACAAGCACCACAACATGCACAATCATTCCCCGCATCAACACATTCAGCACCAGC
Found at i:16500250 original size:6 final size:7
Alignment explanation
Indices: 16500230--16500259 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
16500220 CAACCGTAAG
16500230 AAGAAAA
1 AAGAAAA
16500237 AAGAAAA
1 AAGAAAA
16500244 AAGAAAA
1 AAGAAAA
16500251 AAGAAAA
1 AAGAAAA
16500258 AA
1 AA
16500260 TAATTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:16505739 original size:24 final size:22
Alignment explanation
Indices: 16505712--16505756 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
16505702 ACAGTTCAAA
16505712 ATTTTTCTTTCCATTTATTAAAAG
1 ATTTTTC--TCCATTTATTAAAAG
*
16505736 ATTTTTCTGCATTTATTAAAA
1 ATTTTTCTCCATTTATTAAAA
16505757 CTATGTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.31, C:0.11, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTTCTCCATTTATTAAAAG
Found at i:16506365 original size:42 final size:42
Alignment explanation
Indices: 16506318--16506412 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 42
16506308 TAAAAATATC
* * * *
16506318 AAGGAAACAACATGGGAAAGCAACATCCATG-TCTAGACAAAA
1 AAGGAAGCAACATGGGAAAACAACATACAGGTTC-AGACAAAA
*
16506360 AAGGAAGCAACTTGGGAAAACAACATACAGGTTCAGACAAAA
1 AAGGAAGCAACATGGGAAAACAACATACAGGTTCAGACAAAA
16506402 AAGGAAGCAAC
1 AAGGAAGCAAC
16506413 GTAGAAGCAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.11
Consensus pattern (42 bp):
AAGGAAGCAACATGGGAAAACAACATACAGGTTCAGACAAAA
Found at i:16506702 original size:31 final size:31
Alignment explanation
Indices: 16506657--16506728 Score: 128
Period size: 31 Copynumber: 2.4 Consensus size: 31
16506647 ACATTTTCCT
*
16506657 TATTA-CTAGTTTTACTTTGTAAATTTGTAA
1 TATTATCTACTTTTACTTTGTAAATTTGTAA
16506687 TATTATCTACTTTTACTTTGTAAATTTGTAA
1 TATTATCTACTTTTACTTTGTAAATTTGTAA
16506718 TATTATCTACT
1 TATTATCTACT
16506729 GTTTTCCGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 5 0.12
31 35 0.88
ACGTcount: A:0.29, C:0.10, G:0.07, T:0.54
Consensus pattern (31 bp):
TATTATCTACTTTTACTTTGTAAATTTGTAA
Found at i:16517690 original size:215 final size:215
Alignment explanation
Indices: 16517319--16517756 Score: 840
Period size: 215 Copynumber: 2.0 Consensus size: 215
16517309 AGAAAATATA
16517319 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCGTTTGAAAAAATTACAAGTGTA
1 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCGTTTGAAAAAATTACAAGTGTA
*
16517384 CTTAGACGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGTG
66 CTTAGAAGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGTG
*
16517449 GATGAGTCATGTTTTGTATTCCTATCCTCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
131 GATGAGTCATGTTTTGCATTCCTATCCTCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
16517514 GTCTTGGTAAAACAAATCCC
196 GTCTTGGTAAAACAAATCCC
16517534 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCGTTTGAAAAAATTACAAGTGTA
1 CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCGTTTGAAAAAATTACAAGTGTA
*
16517599 CTTAGAAGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTTCCCTAGTGAAGTG
66 CTTAGAAGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGTG
*
16517664 GATGAGTCATGTTTTGCATTCCTATCCTCTCCACATGTTTCCCTGAAAACTCTATAGTTAGTAAA
131 GATGAGTCATGTTTTGCATTCCTATCCTCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
16517729 GTCTTGGTAAAACAAATCCC
196 GTCTTGGTAAAACAAATCCC
16517749 CAAAGTAT
1 CAAAGTAT
16517757 ATCCTCAGAT
Statistics
Matches: 219, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
215 219 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.33
Consensus pattern (215 bp):
CAAAGTATTAATGTAATTCATGAATAATTTTATTAACCAATCCGTTTGAAAAAATTACAAGTGTA
CTTAGAAGAAAATACTACACTTAGGGCACTATATCCAACAGTCTCCTATTTGCCCTAGTGAAGTG
GATGAGTCATGTTTTGCATTCCTATCCTCTCCACATGTTTCCCTGAAAACTCTATAGCTAGTAAA
GTCTTGGTAAAACAAATCCC
Found at i:16523167 original size:34 final size:33
Alignment explanation
Indices: 16523118--16523184 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
16523108 AATTTGTGAA
* * * *
16523118 ACTTTTGTTATTTTGATGCCTTGATGGTTGGTGT
1 ACTTTTGGTACTTTGATG-CTTCATGGTTAGTGT
16523152 ACTTTTGGTACTTTGATGCTTCATGGTTAGTGT
1 ACTTTTGGTACTTTGATGCTTCATGGTTAGTGT
16523185 TTATAAGATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.13, C:0.10, G:0.25, T:0.51
Consensus pattern (33 bp):
ACTTTTGGTACTTTGATGCTTCATGGTTAGTGT
Found at i:16526404 original size:38 final size:37
Alignment explanation
Indices: 16526346--16526430 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 37
16526336 ATAGCACCTA
* *
16526346 TTTTAATATATGTATGTATATATTATTTAGTTTAAATTGT
1 TTTTTATATATGTA-GTATATATTATTTAGTATAAA-T-T
16526386 TTTTTATATATGTA-TATATATTATTTAGTATAAATT
1 TTTTTATATATGTAGTATATATTATTTAGTATAAATT
16526422 TTTTTATAT
1 TTTTTATAT
16526431 GTTATTTCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
36 10 0.23
37 1 0.02
38 19 0.44
40 13 0.30
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (37 bp):
TTTTTATATATGTAGTATATATTATTTAGTATAAATT
Found at i:16530766 original size:6 final size:6
Alignment explanation
Indices: 16530755--16530828 Score: 73
Period size: 6 Copynumber: 12.7 Consensus size: 6
16530745 AATTCAAAAA
* *
16530755 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAGC AAAA-G AAAA--
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
** *
16530800 AAAGAAA AAAATC AAAATC AAAGTC AAAA
1 AAA-ATC AAAATC AAAATC AAAATC AAAA
16530829 AAATGAAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
4 3 0.05
5 5 0.08
6 48 0.81
7 3 0.05
ACGTcount: A:0.72, C:0.12, G:0.05, T:0.11
Consensus pattern (6 bp):
AAAATC
Found at i:16533131 original size:88 final size:87
Alignment explanation
Indices: 16532967--16533133 Score: 244
Period size: 87 Copynumber: 1.9 Consensus size: 87
16532957 ATCAGTGAAA
* * **
16532967 ATAGCAGATCTTGCCTTCCTGCATCGACGGCAAAGCAGATCGAAAATAAAGCCTTGCCTCCCTTG
1 ATAGCAGATATTGCCTTCCTGCATCGACAGCAAAGCAGATCGAAAATAAAGCCTTGCCTCCAATG
16533032 GTTGCAGTGGAGCAAGTTAAAG
66 GTTGCAGTGGAGCAAGTTAAAG
* * * * *
16533054 ATAGTAGATATTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATACTAGCCTTGCCTCCAAT
1 ATAGCAGATATTGCCTTCCTGCATCGACAGCAAAGCAGATCGAAAATA-AAGCCTTGCCTCCAAT
16533119 GGTTGCAGTGGAGCA
65 GGTTGCAGTGGAGCA
16533134 GGTTGATGGC
Statistics
Matches: 70, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
87 42 0.60
88 28 0.40
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (87 bp):
ATAGCAGATATTGCCTTCCTGCATCGACAGCAAAGCAGATCGAAAATAAAGCCTTGCCTCCAATG
GTTGCAGTGGAGCAAGTTAAAG
Found at i:16533279 original size:44 final size:44
Alignment explanation
Indices: 16533194--16533279 Score: 100
Period size: 44 Copynumber: 2.0 Consensus size: 44
16533184 CCAGTAATTC
* * * **
16533194 TATCTCCCTAGGCAGCAGTGGAATAGATTGAAAATTTCAGATCT
1 TATCTCCCTAAGCAGCAGTGGAACAGATCGAAAATGACAGATCT
* * *
16533238 TATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGACAGAT
1 TATCTCCCTAAGCAGCAGTGGAACAGATCGAAAATGACAGAT
16533280 TTTACCTCAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.26
Consensus pattern (44 bp):
TATCTCCCTAAGCAGCAGTGGAACAGATCGAAAATGACAGATCT
Found at i:16533380 original size:132 final size:132
Alignment explanation
Indices: 16533138--16533799 Score: 1067
Period size: 132 Copynumber: 5.0 Consensus size: 132
16533128 GGAGCAGGTT
* * * *
16533138 GATGGCAGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
** *
16533203 AGG-CAGCAGTGGAATAGATTGAAAATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
66 -GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
16533267 GAA
130 GAA
* * *
16533270 GATGACAGATTTTACCTCATTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
*
16533335 GGTTGGAAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
66 GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
16533400 AA
131 AA
*
16533402 GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTGCATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
16533467 GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
66 GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
16533532 AA
131 AA
* *
16533534 GATGGCGGATTTTACCTCCTTATGGTTACAGTGGAGTACATTGAAACCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* * * * *
16533599 GGTTGACAGTGAAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGAAGTAGATCG
66 GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
16533664 AA
131 AA
* * **
16533666 GATGGCGGATTTTACCTCCCTGAGGTTTTAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
16533731 GGTTGGCAGTGGAATAGATTGAA-AGTTACAGATCTTATCTGCCTAAGCAGTAGTGGAGCAGATC
66 GGTTGGCAGTGGAATAGATTGAAGA-TTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
16533795 GAA
130 GAA
16533798 GA
1 GA
16533800 CCCAAGCCTT
Statistics
Matches: 495, Mismatches: 33, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
131 3 0.01
132 492 0.99
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (132 bp):
GATGGCGGATTTTACCTCCTTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
AA
Found at i:16533786 original size:44 final size:43
Alignment explanation
Indices: 16533738--16533880 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 43
16533728 CCTGGTTGGC
*
16533738 AGTGGAATAGATTGAAAGTTACAGATCTTATCTGCCTAAGCAGT
1 AGTGGAGTAGATTGAAAGTTACAGATCTTATCT-CCTAAGCAGT
* * *** * * *
16533782 AGTGGAGCAGATCG-AAGACCCA-AGCCTTATCTCCTTGAGCAGC
1 AGTGGAGTAGATTGAAAGTTACAGA-TCTTATCTCC-TAAGCAGT
* * *
16533825 AGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGTAGT
1 AGTGGAGTAGATTGAAAGTTACAGATCTTATCT-CCTAAGCAGT
16533869 AGTGGAGTAGAT
1 AGTGGAGTAGAT
16533881 CGAAGAAACC
Statistics
Matches: 73, Mismatches: 21, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
42 3 0.04
43 29 0.40
44 38 0.52
45 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.27
Consensus pattern (43 bp):
AGTGGAGTAGATTGAAAGTTACAGATCTTATCTCCTAAGCAGT
Found at i:16533814 original size:87 final size:87
Alignment explanation
Indices: 16533721--16533968 Score: 277
Period size: 87 Copynumber: 2.8 Consensus size: 87
16533711 GCCAGTAATT
* * *
16533721 CTATCTCCCTG-GTTGGCAGTGGAATAGATTGAAAGTTACAGATCTTATCTGCCTAAGCAGTAGT
1 CTATCTCCCTGAGTT-GCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGT
*
16533785 GGAGCAGATCGAAG-ACCCAAGC
65 GGAGCAGATCGAAGAAACCAAGC
* ** * *
16533807 CTTATCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGTAGTAGT
1 C-TATCTCCCTGAGTTGCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGT
* *
16533872 GGAGTAGATCGAAGAAACCAATC
65 GGAGCAGATCGAAGAAACCAAGC
** * * **
16533895 CTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATCACAGATCTTATCTCTCTGAAGTTGTAG
1 CTATCTCCCTG-AGTTGCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCT-AAGCAGTAG
*
16533959 TAGAGCAGAT
64 TGGAGCAGAT
16533969 TGCATCTAGT
Statistics
Matches: 135, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
86 1 0.01
87 96 0.71
88 38 0.28
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (87 bp):
CTATCTCCCTGAGTTGCAGTGGAGTAGATTGAAAATTACAGATCTTATCTCCCTAAGCAGTAGTG
GAGCAGATCGAAGAAACCAAGC
Found at i:16533917 original size:44 final size:43
Alignment explanation
Indices: 16533853--16534058 Score: 132
Period size: 44 Copynumber: 4.8 Consensus size: 43
16533843 TTACAGATCT
* * *
16533853 TATCTCCCT-AAGTAGTAGTGGAGTAGATCGAAGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-GAAGAAACCAATCC
* * * *
16533896 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGAAAC-CA-ATCC
* * * * * * * * *
16533940 TATCTCTCTGAAGTTGTAGTAGAGCAGAT--TGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGAAACCAATCC
* * * *
16533981 TATCTCCCTAAAGTTACAGTGGAACAGACAGAAGAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAAGAAACCAATCC
* * * *
16534025 TATCTTCCTGAAGTTACAGTGGAGCGGATTAAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGA
16534059 TGATGGATCT
Statistics
Matches: 122, Mismatches: 34, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
41 25 0.20
42 4 0.03
43 20 0.16
44 73 0.60
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATGAAGAAACCAATCC
Found at i:16537767 original size:13 final size:13
Alignment explanation
Indices: 16537718--16537784 Score: 80
Period size: 13 Copynumber: 5.2 Consensus size: 13
16537708 CATCTATTAC
*
16537718 CATATAACCAATT
1 CATATAACCATTT
*
16537731 CATTTAACCATTT
1 CATATAACCATTT
* *
16537744 CATGTAGCCATTT
1 CATATAACCATTT
*
16537757 CATAAAACCATTT
1 CATATAACCATTT
*
16537770 CGTATAACCATTT
1 CATATAACCATTT
16537783 CA
1 CA
16537785 ACAAAACTCA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.36, C:0.24, G:0.04, T:0.36
Consensus pattern (13 bp):
CATATAACCATTT
Found at i:16538192 original size:21 final size:21
Alignment explanation
Indices: 16538168--16538237 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
16538158 CTATATAGTC
16538168 TTTCAACTATGGTCTTATTTG
1 TTTCAACTATGGTCTTATTTG
* * * *
16538189 TTTCCA-TCATGATGCTATATAGTC
1 TTTCAACT-ATGGT-CT-TAT-TTG
16538213 TTTCAACTATGGTCTTATTTG
1 TTTCAACTATGGTCTTATTTG
16538234 TTTC
1 TTTC
16538238 TGTTATGATT
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
20 1 0.03
21 14 0.39
22 5 0.14
23 5 0.14
24 10 0.28
25 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.13, T:0.50
Consensus pattern (21 bp):
TTTCAACTATGGTCTTATTTG
Found at i:16538246 original size:45 final size:45
Alignment explanation
Indices: 16538105--16538237 Score: 223
Period size: 45 Copynumber: 3.0 Consensus size: 45
16538095 CTCACTCCCT
* * *
16538105 TCATGATGCCATAGAGTC-TTCTAGCTATGGTCTTATTTGTTTCCA
1 TCATGATGCTATATAGTCTTTC-AACTATGGTCTTATTTGTTTCCA
16538150 TCATGATGCTATATAGTCTTTCAACTATGGTCTTATTTGTTTCCA
1 TCATGATGCTATATAGTCTTTCAACTATGGTCTTATTTGTTTCCA
16538195 TCATGATGCTATATAGTCTTTCAACTATGGTCTTATTTGTTTC
1 TCATGATGCTATATAGTCTTTCAACTATGGTCTTATTTGTTTC
16538238 TGTTATGATT
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
45 81 0.96
46 3 0.04
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (45 bp):
TCATGATGCTATATAGTCTTTCAACTATGGTCTTATTTGTTTCCA
Found at i:16540213 original size:29 final size:29
Alignment explanation
Indices: 16540188--16540297 Score: 143
Period size: 28 Copynumber: 3.9 Consensus size: 29
16540178 GTAAAATTTT
16540188 GGACAAAATTGTAAAATCTAAAAAATAGA
1 GGACAAAATTGTAAAATCTAAAAAATAGA
*
16540217 GG-CAAAACTGTAAAATCTAAAAAATA-A
1 GGACAAAATTGTAAAATCTAAAAAATAGA
* * * ** *
16540244 GGGCAAAATTATAAAATTTTGAAAATAGG
1 GGACAAAATTGTAAAATCTAAAAAATAGA
16540273 GGACAAAATTGTAAAATCTAAAAAA
1 GGACAAAATTGTAAAATCTAAAAAA
16540298 AAGGGAATAC
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
27 3 0.04
28 42 0.63
29 22 0.33
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (29 bp):
GGACAAAATTGTAAAATCTAAAAAATAGA
Found at i:16544308 original size:19 final size:19
Alignment explanation
Indices: 16544284--16544377 Score: 143
Period size: 19 Copynumber: 4.8 Consensus size: 19
16544274 AATTTTTGAG
16544284 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
16544303 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
16544322 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
16544341 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
**
16544362 GATATATAATCTTAGA
1 GATATGCAATCTTAGA
16544378 AGATATGATT
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
19 50 0.72
21 19 0.28
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:16544359 original size:40 final size:38
Alignment explanation
Indices: 16544284--16544384 Score: 143
Period size: 40 Copynumber: 2.7 Consensus size: 38
16544274 AATTTTTGAG
16544284 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
*
16544322 GATATGCAATCTTAGATATGATATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATATG--ATATGCAATCCTAGATAT
**
16544362 GATATATAATCTTAGA-A-GATATG
1 GATATGCAATCTTAGATATGATATG
16544385 ATTTTGTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
36 5 0.09
38 21 0.36
39 1 0.02
40 31 0.53
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGCAATCCTAGATAT
Found at i:16544410 original size:22 final size:23
Alignment explanation
Indices: 16544368--16544411 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
16544358 ATATGATATA
*
16544368 TAATCTTAGAAGATATGATTTTG
1 TAATCTTAGAAGATATAATTTTG
*
16544391 TAATCTTAG-AGATTTAATTTT
1 TAATCTTAGAAGATATAATTTT
16544412 AGATACCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.48
Consensus pattern (23 bp):
TAATCTTAGAAGATATAATTTTG
Found at i:16544972 original size:25 final size:25
Alignment explanation
Indices: 16544921--16544972 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16544911 AATTTTGTTA
**
16544921 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
16544946 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
16544971 AT
1 AT
16544973 ATATATGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:16545566 original size:19 final size:20
Alignment explanation
Indices: 16545525--16545566 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
16545515 ATTTCTAGGC
* *
16545525 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
16545545 CATTGT-ATATTTAATATAG
1 CATTGTAATATTTAATATAG
16545564 CAT
1 CAT
16545567 CACATCATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.33, C:0.07, G:0.10, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:16545927 original size:98 final size:98
Alignment explanation
Indices: 16545807--16546001 Score: 363
Period size: 98 Copynumber: 2.0 Consensus size: 98
16545797 CTAAAAACAA
* *
16545807 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
16545872 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
16545905 TAAAGGAAATATTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
16545970 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
16546002 ATTTTATTGT
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.37
Consensus pattern (98 bp):
TAAAGGAAATATTCCGAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:16546998 original size:10 final size:10
Alignment explanation
Indices: 16546978--16547011 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
16546968 AATTAATAAC
16546978 GATTT-TCAA
1 GATTTATCAA
16546987 GATTTATCAA
1 GATTTATCAA
16546997 GATTTATCAA
1 GATTTATCAA
16547007 GATTT
1 GATTT
16547012 CGGGAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 5 0.21
10 19 0.79
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (10 bp):
GATTTATCAA
Found at i:16547604 original size:39 final size:39
Alignment explanation
Indices: 16547555--16547645 Score: 148
Period size: 38 Copynumber: 2.3 Consensus size: 39
16547545 AATTTATTTT
* *
16547555 AAAAATTAAAAAAAAGTATTTTAAAAATATTTTAATATA
1 AAAAAATAAAAAAAAGTATTTTAAAAATATTTTAAAATA
16547594 AAAAAAT-AAAAAAAGTATTTTAAAAATATTTTAAAATA
1 AAAAAATAAAAAAAAGTATTTTAAAAATATTTTAAAATA
16547632 ATAAAAATAAAAAA
1 A-AAAAATAAAAAA
16547646 TAAAAAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
38 31 0.65
39 12 0.25
40 5 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (39 bp):
AAAAAATAAAAAAAAGTATTTTAAAAATATTTTAAAATA
Found at i:16549704 original size:40 final size:40
Alignment explanation
Indices: 16549631--16549744 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
16549621 GCTTTTTTGG
* *
16549631 AAAA-CGCCGCTAATGCTT-ATTTTTAGCGTCGTTTTC-C
1 AAAAGCGCCGCTAATGCTTGATCTTTAGCGGCGTTTTCTC
** *
16549668 ATAAAGCGCCGCTAATATTTGATCTTTAGCGGCGTTTTCTG
1 A-AAAGCGCCGCTAATGCTTGATCTTTAGCGGCGTTTTCTC
*
16549709 AAAAGCGCCGCTAATGCTCGATCTTTAG-GGCGTTTT
1 AAAAGCGCCGCTAATGCTTGATCTTTAGCGGCGTTTT
16549745 TTATCCAAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.02
38 3 0.05
39 20 0.31
40 40 0.62
41 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAAGCGCCGCTAATGCTTGATCTTTAGCGGCGTTTTCTC
Found at i:16551675 original size:21 final size:22
Alignment explanation
Indices: 16551638--16551680 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
16551628 TCTTTGCTGT
*
16551638 TAGGTTTAGGTTA-TTTTGGGC
1 TAGGGTTAGGTTATTTTTGGGC
16551659 TAGGGTTA-GTTATTTTTTGGGC
1 TAGGGTTAGGTTA-TTTTTGGGC
16551681 CTATTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.14, C:0.05, G:0.33, T:0.49
Consensus pattern (22 bp):
TAGGGTTAGGTTATTTTTGGGC
Found at i:16553404 original size:24 final size:24
Alignment explanation
Indices: 16553376--16553427 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16553366 TTCATAGGTC
* *
16553376 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
*
16553400 AAATATATTATACTAATAAATACT
1 AAATAAATTATACTAATAAATACT
16553424 AAAT
1 AAAT
16553428 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.08, G:0.04, T:0.35
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:16554233 original size:42 final size:43
Alignment explanation
Indices: 16554186--16554267 Score: 121
Period size: 43 Copynumber: 1.9 Consensus size: 43
16554176 AGACTAAGAC
*
16554186 CTTTAGCGGCGCTTTAG-TGGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCGGCGCTTTAGCTAGAAGCGCCGCTAAAGATCAGGGT
* * *
16554228 CTTTAGCGGCGTTTTTGCTAGAAGCGCCGGTAAAGATCAG
1 CTTTAGCGGCGCTTTAGCTAGAAGCGCCGCTAAAGATCAG
16554268 ACGCCGCTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 15 0.43
43 20 0.57
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTAGCTAGAAGCGCCGCTAAAGATCAGGGT
Found at i:16554323 original size:60 final size:60
Alignment explanation
Indices: 16554209--16554323 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
16554199 TTAGTGGAAG
* * * * * **
16554209 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGTTTTTGCTAGAAGCGCCGGTAAAGATCAGA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGATCAGA
*
16554269 CGCCGCTAAAGATTAGGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGA
1 CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGA
16554324 CCCTGATCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (60 bp):
CGCCGCTAAAGATCAGGGTCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGATCAGA
Found at i:16554338 original size:43 final size:43
Alignment explanation
Indices: 16554287--16554474 Score: 250
Period size: 43 Copynumber: 4.4 Consensus size: 43
16554277 AAGATTAGGG
*
16554287 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCAAAAGACCCTGA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCCTGA
* *** * * *
16554330 TCTCTAGCGGCGCTTCGACCACAAACGCCACTAAAGAACCTAA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCCTGA
* *
16554373 TCTTTAGCGGCGCTTTCCCCACAAACGCCGCTAAAGACCATGA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCCTGA
* * *
16554416 TCTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCCTGA
*
16554459 TGTTTAGCGGCGCTTT
1 TCTTTAGCGGCGCTTT
16554475 AGTGGCTTTT
Statistics
Matches: 122, Mismatches: 23, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 122 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCCTGA
Found at i:16554897 original size:42 final size:42
Alignment explanation
Indices: 16554811--16554912 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
16554801 TTTGACGCTG
*
16554811 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCTCTCGCTATAGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCTCTCGCTACAGC
* * *
16554853 CTCTGCTTCCCTCGCTGCAGCCTGTACTTCTCTCGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGCCTCTACTTCTCTCGCTACAGC
* * *
16554895 CTCTACTTCTCTTGCTGC
1 CTCTGCTTCCCTCGCTGC
16554913 CGCATCTGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (42 bp):
CTCTGCTTCCCTCGCTGCAGCCTCTACTTCTCTCGCTACAGC
Found at i:16554915 original size:21 final size:21
Alignment explanation
Indices: 16554811--16554912 Score: 123
Period size: 21 Copynumber: 4.9 Consensus size: 21
16554801 TTTGACGCTG
* *
16554811 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCTCTCGCTGCAGC
**
16554832 CTCTACTTCTCTCGCTATAGC
1 CTCTACTTCTCTCGCTGCAGC
* *
16554853 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCTCTCGCTGCAGC
* *
16554874 CTGTACTTCTCTCGCTGCCGC
1 CTCTACTTCTCTCGCTGCAGC
*
16554895 CTCTACTTCTCTTGCTGC
1 CTCTACTTCTCTCGCTGC
16554913 CGCATCTGCT
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (21 bp):
CTCTACTTCTCTCGCTGCAGC
Found at i:16554972 original size:66 final size:66
Alignment explanation
Indices: 16554894--16555040 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
16554884 CTCGCTGCCG
* * *
16554894 CCTCTACTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGTTCTTCATA-CTTTCGTT
1 CCTCAACTTCTCTCGCTGCCGCATCAGCTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
16554957 GAA
64 GAA
* ** * *
16554960 CCTCAGCTTCTCTCGCTGTTGCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAACTTCTCTCGCTGCCGCATCAGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
16555025 A
66 A
16555026 CCTCAACTTCTCTCG
1 CCTCAACTTCTCTCG
16555041 ATGTTGCCTC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
65 1 0.01
66 65 0.93
67 4 0.06
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (66 bp):
CCTCAACTTCTCTCGCTGCCGCATCAGCTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:16555046 original size:66 final size:65
Alignment explanation
Indices: 16554914--16555064 Score: 205
Period size: 66 Copynumber: 2.3 Consensus size: 65
16554904 TCTTGCTGCC
* * * *
16554914 GCATCTGCTTTAAGCTGCTGCTGGAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGCTGT
1 GCATCAGCTTTAAGTTG-TGCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGATGT
16554979 T
65 T
*
16554980 GCATCAGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-TTTGAACCTCAACTTCTCTCGATG
1 GCATCAGCTTTAAGTTGT-GCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAACTTCTCTCGATG
16555044 TT
64 TT
* *
16555046 GCCTCCGCTTTAAGTTGTG
1 GCATCAGCTTTAAGTTGTG
16555065 TAATTTGATC
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
65 2 0.03
66 70 0.92
67 4 0.05
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (65 bp):
GCATCAGCTTTAAGTTGTGCTGGAGTTCTTCATACTTTCGTTGAACCTCAACTTCTCTCGATGTT
Found at i:16560525 original size:9 final size:9
Alignment explanation
Indices: 16560508--16561341 Score: 219
Period size: 9 Copynumber: 94.3 Consensus size: 9
16560498 TAAGTATAAT
*
16560508 TAAGCTATG
1 TAAGTTATG
16560517 TAAGTTATG
1 TAAGTTATG
16560526 T-A-TTATG
1 TAAGTTATG
16560533 TAAGTTAT-
1 TAAGTTATG
*
16560541 TTA-TTATG
1 TAAGTTATG
* *
16560549 AAAATTATG
1 TAAGTTATG
*
16560558 TAAGTTGTG
1 TAAGTTATG
16560567 T-A-TTATG
1 TAAGTTATG
*
16560574 -AA--AAT-
1 TAAGTTATG
* *
16560579 TATGCTATG
1 TAAGTTATG
16560588 TAAGTTATG
1 TAAGTTATG
* *
16560597 TAAGTCATA
1 TAAGTTATG
16560606 TAAGTTATG
1 TAAGTTATG
16560615 T-A-TTATG
1 TAAGTTATG
16560622 TAAGTTATG
1 TAAGTTATG
16560631 TAAGTTAT-
1 TAAGTTATG
*
16560639 TTA-TTATG
1 TAAGTTATG
* * *
16560647 AAAATTAAG
1 TAAGTTATG
16560656 TAAGTTATG
1 TAAGTTATG
* *
16560665 TAATTTACG
1 TAAGTTATG
*
16560674 -AA-TAAT-
1 TAAGTTATG
***
16560680 TAAAAAAATG
1 T-AAGTTATG
16560690 TAAGTTATG
1 TAAGTTATG
16560699 TAAGTTAT-
1 TAAGTTATG
*
16560707 TTA-TTATG
1 TAAGTTATG
* * *
16560715 AAAATTAAG
1 TAAGTTATG
16560724 TAAGTTATG
1 TAAGTTATG
* *
16560733 TAATTTACG
1 TAAGTTATG
*
16560742 -AA-TAAT-
1 TAAGTTATG
***
16560748 TAAAAAAATG
1 T-AAGTTATG
16560758 TAAGTTATG
1 TAAGTTATG
16560767 TAAG-T-TG
1 TAAGTTATG
16560774 TAAGTTATG
1 TAAGTTATG
16560783 TAAGTTATG
1 TAAGTTATG
**
16560792 TATA-AAAT-
1 TA-AGTTATG
**
16560800 TAA-TTAAC
1 TAAGTTATG
16560808 TAAGTTATG
1 TAAGTTATG
*
16560817 TAATTTATG
1 TAAGTTATG
*
16560826 TATAATATTAATG
1 --TAA-GTT-ATG
16560839 TAAGTTATG
1 TAAGTTATG
*
16560848 TAATTTATG
1 TAAGTTATG
16560857 TATA-TTAAT-
1 TA-AGTT-ATG
16560866 TAAGTTATG
1 TAAGTTATG
*
16560875 TAATTTATG
1 TAAGTTATG
*
16560884 TATAATATTAATG
1 --TAA-GTT-ATG
16560897 TAAGTTATG
1 TAAGTTATG
*
16560906 TAATTTATG
1 TAAGTTATG
16560915 AATAA-TTA--
1 --TAAGTTATG
* ***
16560923 AAAAAAATG
1 TAAGTTATG
16560932 TAAGTTATG
1 TAAGTTATG
16560941 TAAG-T-TG
1 TAAGTTATG
16560948 TAAGTTATG
1 TAAGTTATG
16560957 TAAGTTATG
1 TAAGTTATG
*
16560966 TATA-ATAT-
1 TA-AGTTATG
**
16560974 TAA-TTAAC
1 TAAGTTATG
16560982 TAAGTTATG
1 TAAGTTATG
*
16560991 TAATTTATG
1 TAAGTTATG
*
16561000 TATAATATTAATG
1 --TAA-GTT-ATG
16561013 TAAGTTATG
1 TAAGTTATG
*
16561022 TAATTTATG
1 TAAGTTATG
16561031 T-A--TAT-
1 TAAGTTATG
16561036 TAA-TTAAT-
1 TAAGTT-ATG
16561044 TAAGTTATG
1 TAAGTTATG
*
16561053 TAATTTATG
1 TAAGTTATG
*
16561062 TATAATATTAATG
1 --TAA-GTT-ATG
16561075 TAAGTTATG
1 TAAGTTATG
*
16561084 TAATTTATG
1 TAAGTTATG
16561093 -AA-TTAT-
1 TAAGTTATG
*
16561099 TAA-TAAAATG
1 TAAGT--TATG
16561109 TAAGTTATG
1 TAAGTTATG
16561118 TAAG-T-TG
1 TAAGTTATG
16561125 TAAGTTATG
1 TAAGTTATG
16561134 TAAGTTATG
1 TAAGTTATG
*
16561143 TATA-ATAT-
1 TA-AGTTATG
16561151 TAA-TTAAT-
1 TAAGTT-ATG
16561159 TAAGTTATG
1 TAAGTTATG
*
16561168 TAATTTATG
1 TAAGTTATG
*
16561177 TATAATATTAATG
1 --TAA-GTT-ATG
16561190 TAAGTTATG
1 TAAGTTATG
*
16561199 TATAATATTAATG
1 --TAA-GTT-ATG
16561212 TAAGTTATG
1 TAAGTTATG
*
16561221 TAATTTATG
1 TAAGTTATG
16561230 T-A--TAT-
1 TAAGTTATG
16561235 TAA-TTAAT-
1 TAAGTT-ATG
16561243 TAAGTTATG
1 TAAGTTATG
*
16561252 TAATTTATG
1 TAAGTTATG
*
16561261 TATAATATTAATG
1 --TAA-GTT-ATG
16561274 TAAGTTATG
1 TAAGTTATG
*
16561283 TATA-ATAT-
1 TA-AGTTATG
16561291 TAA-TTCAT-
1 TAAGTT-ATG
16561299 TAAGTTATG
1 TAAGTTATG
*
16561308 TAATTTATG
1 TAAGTTATG
*
16561317 TATAATATTAATG
1 --TAA-GTT-ATG
16561330 TAAGTTATG
1 TAAGTTATG
16561339 TAA
1 TAA
16561342 TCTATGTATA
Statistics
Matches: 626, Mismatches: 100, Indels: 198
0.68 0.11 0.21
Matches are distributed among these distances:
5 2 0.00
6 13 0.02
7 70 0.11
8 79 0.13
9 339 0.54
10 31 0.05
11 52 0.08
12 16 0.03
13 24 0.04
ACGTcount: A:0.40, C:0.01, G:0.14, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:16560534 original size:16 final size:16
Alignment explanation
Indices: 16560513--16560632 Score: 96
Period size: 16 Copynumber: 7.9 Consensus size: 16
16560503 ATAATTAAGC
16560513 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
16560529 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
16560545 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
16560554 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
16560570 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
16560584 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
16560602 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
16560618 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
16560633 AGTTATTTAT
Statistics
Matches: 80, Mismatches: 13, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
9 6 0.08
10 2 0.03
12 1 0.01
14 11 0.14
15 2 0.03
16 45 0.56
17 1 0.01
18 12 0.15
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:16560555 original size:25 final size:25
Alignment explanation
Indices: 16560527--16560666 Score: 142
Period size: 25 Copynumber: 5.7 Consensus size: 25
16560517 TAAGTTATGT
*
16560527 ATTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
*
16560552 ATTATGTAAGTTGTGTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
* * *
16560577 ATTATGCTATG-TAAG--TTATGTAA
1 ATTATG-TAAGTTATGTATTATGAAA
* * * *
16560600 GTCATATAAGTTATGTATTATGTAA
1 ATTATGTAAGTTATGTATTATGAAA
* *
16560625 GTTATGTAAGTTATTTATTATGAAA
1 ATTATGTAAGTTATGTATTATGAAA
*
16560650 ATTAAGTAAGTTATGTA
1 ATTATGTAAGTTATGTA
16560667 ATTTACGAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
22 3 0.03
23 13 0.14
25 74 0.80
26 3 0.03
ACGTcount: A:0.37, C:0.01, G:0.16, T:0.45
Consensus pattern (25 bp):
ATTATGTAAGTTATGTATTATGAAA
Found at i:16560659 original size:34 final size:34
Alignment explanation
Indices: 16560553--16560735 Score: 156
Period size: 34 Copynumber: 5.2 Consensus size: 34
16560543 ATTATGAAAA
* *
16560553 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATTTATTATGAAAATTA----A-GTAAG
* * * *
16560592 TTATGTAAGTCATATAAGTTATG--TATTATGTAAG
1 TTATGTAAGTTAT-TTA-TTATGAAAATTAAGTAAG
16560626 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
* *** * * *
16560660 TTATGTAATTTACGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATTTATTATGAAAATTAA-GTAAG
16560694 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
1 TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
16560728 TTATGTAA
1 TTATGTAA
16560736 TTTACGAATA
Statistics
Matches: 114, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
32 5 0.04
33 4 0.04
34 82 0.72
35 2 0.02
39 15 0.13
40 1 0.01
41 5 0.04
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.43
Consensus pattern (34 bp):
TTATGTAAGTTATTTATTATGAAAATTAAGTAAG
Found at i:16560761 original size:34 final size:34
Alignment explanation
Indices: 16560655--16560769 Score: 151
Period size: 34 Copynumber: 3.4 Consensus size: 34
16560645 TGAAAATTAA
16560655 GTAAGTTATGTAATTTACGAATAATTAAAAAAAT
1 GTAAGTTATGTAATTTACGAATAATTAAAAAAAT
* *** * * *
16560689 GTAAGTTATGTAAGTTATTTATTATGAAAATTAA-
1 GTAAGTTATGTAATTTACGAATAATTAAAA-AAAT
16560723 GTAAGTTATGTAATTTACGAATAATTAAAAAAAT
1 GTAAGTTATGTAATTTACGAATAATTAAAAAAAT
16560757 GTAAGTTATGTAA
1 GTAAGTTATGTAA
16560770 GTTGTAAGTT
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
33 2 0.03
34 61 0.94
35 2 0.03
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (34 bp):
GTAAGTTATGTAATTTACGAATAATTAAAAAAAT
Found at i:16560777 original size:16 final size:16
Alignment explanation
Indices: 16560756--16560788 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16560746 ATTAAAAAAA
16560756 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16560772 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16560788 T
1 T
16560789 ATGTATAAAA
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:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:16560782 original size:68 final size:68
Alignment explanation
Indices: 16560619--16560772 Score: 308
Period size: 68 Copynumber: 2.3 Consensus size: 68
16560609 GTTATGTATT
16560619 ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAA
1 ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAA
16560684 AAA
66 AAA
16560687 ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAA
1 ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAA
16560752 AAA
66 AAA
16560755 ATGTAAGTTATGTAAGTT
1 ATGTAAGTTATGTAAGTT
16560773 GTAAGTTATG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 86 1.00
ACGTcount: A:0.44, C:0.01, G:0.14, T:0.40
Consensus pattern (68 bp):
ATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTACGAATAATTAAA
AAA
Found at i:16560846 original size:31 final size:31
Alignment explanation
Indices: 16560772--16561360 Score: 466
Period size: 31 Copynumber: 20.0 Consensus size: 31
16560762 TTATGTAAGT
* *
16560772 TGTAAGTTATGTAAGTTATGTATAAAATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
16560803 TTAACTAAGTTATGTAATTTATGTATAATATTAA
1 -T--GTAAGTTATGTAATTTATGTATAATATTAA
16560837 TGTAAGTTATGTAATTTATG--T-ATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
16560865 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* **
16560895 TGTAAGTTATGTAATTTATGAATAATTAAAAAAAA
1 TGTAAGTTATGTAATTTATG--T-A-TAATATTAA
* *
16560930 TGTAAGTTATGTAA-GT-TG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
16560955 TGTAAGTTATGT-A--TA-ATATTA-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
16560981 -CTAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
16561011 TGTAAGTTATGTAATTTATGTATATTAATTAA
1 TGTAAGTTATGTAATTTATGTATAAT-ATTAA
16561043 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
16561073 TGTAAGTTATGTAATTTATGAATTATTAATA-AAA
1 TGTAAGTTATGTAATTTATG---TA-TAATATTAA
* *
16561107 TGTAAGTTATGTAA-GT-TG--TAA-GTT-A
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
16561132 TGTAAGTTATGT-A--TA-ATATTA-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
16561158 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
*
16561188 TGTAAGTTATGTATAATATTAATG--TAA-GTT-A
1 TGTAAGTTATG--TAAT-TT-ATGTATAATATTAA
*
16561219 TGTAATTTATGT-A--TA--T-T-A-ATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
16561242 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* * *
16561272 TGTAAGTTATGT-A--TA-ATATTA-ATTCA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
16561298 T-TAAGTTATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATTTATGTATAATATTAA
* *
16561328 TGTAAGTTATGTAATCTATGTATATTAATTAA
1 TGTAAGTTATGTAATTTATGTATAAT-ATTAA
16561360 T
1 T
16561361 TAAATGATAT
Statistics
Matches: 457, Mismatches: 41, Indels: 118
0.74 0.07 0.19
Matches are distributed among these distances:
22 12 0.03
23 6 0.01
24 3 0.01
25 67 0.15
26 14 0.03
27 26 0.06
28 18 0.04
29 16 0.04
30 37 0.08
31 152 0.33
32 17 0.04
33 12 0.03
34 49 0.11
35 28 0.06
ACGTcount: A:0.40, C:0.01, G:0.13, T:0.47
Consensus pattern (31 bp):
TGTAAGTTATGTAATTTATGTATAATATTAA
Found at i:16560951 original size:16 final size:16
Alignment explanation
Indices: 16560930--16560962 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16560920 TTAAAAAAAA
16560930 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16560946 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16560962 T
1 T
16560963 ATGTATAATA
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:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:16561020 original size:22 final size:21
Alignment explanation
Indices: 16560986--16561292 Score: 136
Period size: 22 Copynumber: 15.1 Consensus size: 21
16560976 ATTAACTAAG
*
16560986 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
16561007 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
*
16561026 TTATGTATA-TTAAT-TAATTAA-G
1 TTATGTA-AGTT-ATGT-A-TAATA
*
16561048 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
16561069 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
16561088 TTATG-AA-TTAT-TAATAA-A
1 TTATGTAAGTTATGT-ATAATA
16561106 --ATGTAAGTTATG--T-A-A
1 TTATGTAAGTTATGTATAATA
* *
16561121 GT-TGTAAGTTATG--TAA-G
1 TTATGTAAGTTATGTATAATA
*
16561138 TTATGTATA-ATAT-TAATTAATTAA
1 TTATGTA-AGTTATGT-A-TAA-T-A
*
16561162 GTTATGTAATTTATGTATAATA
1 -TTATGTAAGTTATGTATAATA
16561184 TTAATGTAAGTTATGTATAATA
1 TT-ATGTAAGTTATGTATAATA
16561206 TTAATGTAAGTTATG--TAAT-
1 TT-ATGTAAGTTATGTATAATA
*
16561225 TTATGTATA-TTAAT-TAATTAA-G
1 TTATGTA-AGTT-ATGT-A-TAATA
*
16561247 TTATGTAATTTATGTATAATA
1 TTATGTAAGTTATGTATAATA
16561268 TTAATGTAAGTTATGTATAATA
1 TT-ATGTAAGTTATGTATAATA
16561290 TTA
1 TTA
16561293 ATTCATTAAG
Statistics
Matches: 229, Mismatches: 11, Indels: 92
0.69 0.03 0.28
Matches are distributed among these distances:
15 2 0.01
16 20 0.09
17 6 0.03
18 31 0.14
19 13 0.06
20 18 0.08
21 20 0.09
22 102 0.45
23 1 0.00
24 4 0.02
25 11 0.05
26 1 0.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (21 bp):
TTATGTAAGTTATGTATAATA
Found at i:16561128 original size:16 final size:16
Alignment explanation
Indices: 16561107--16561139 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
16561097 ATTAATAAAA
16561107 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16561123 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
16561139 T
1 T
16561140 ATGTATAATA
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:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Done.