Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 122 of 290
Found at i:41493518 original size:23 final size:23
Alignment explanation
Indices: 41493486--41493531 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41493476 CAAAGAACCA
* *
41493486 TATCGGGAAGCTCACGAAGAGCC
1 TATCGAGAAGCTCAAGAAGAGCC
*
41493509 TATCGAGAAGCTCAATAAGAGCC
1 TATCGAGAAGCTCAAGAAGAGCC
41493532 ATGTAACTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.35, C:0.24, G:0.26, T:0.15
Consensus pattern (23 bp):
TATCGAGAAGCTCAAGAAGAGCC
Found at i:41493643 original size:26 final size:25
Alignment explanation
Indices: 41493587--41493656 Score: 63
Period size: 27 Copynumber: 2.7 Consensus size: 25
41493577 GAGCACTATC
*
41493587 GGGAAGCTCACAAAGAGTCAATTTAAT
1 GGGAAGCTCA-TAAGAG-CAATTTAAT
*
41493614 GGGAAGCTCATGAAGAGCCATTT-AT
1 GGGAAGCTCAT-AAGAGCAATTTAAT
41493639 AGGGATA-CTCATAAGAGC
1 -GGGA-AGCTCATAAGAGC
41493657 TAAGGTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 8 0.21
26 14 0.37
27 16 0.42
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (25 bp):
GGGAAGCTCATAAGAGCAATTTAAT
Found at i:41494929 original size:5 final size:5
Alignment explanation
Indices: 41494896--41494955 Score: 52
Period size: 5 Copynumber: 11.8 Consensus size: 5
41494886 TTTTATTAAA
* * *
41494896 TATAT TATTT TATTAT TGTAT TAATAT TACAT TATAT TATA- T-TAT TATAT
1 TATAT TATAT TA-TAT TATAT T-ATAT TATAT TATAT TATAT TATAT TATAT
41494946 TATAT CTATA
1 TATAT -TATA
41494956 AAACAAAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
3 2 0.05
4 2 0.05
5 29 0.66
6 11 0.25
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:41497939 original size:24 final size:25
Alignment explanation
Indices: 41497811--41498002 Score: 109
Period size: 24 Copynumber: 7.9 Consensus size: 25
41497801 TATTTTTAAA
*
41497811 CGGGAAGCTCA-TACAGAGCCTTCTAAT
1 CGGGAAGCTCACTA-AGAGCC--ATAAT
*
41497838 -GGGAAGCTCA-TACAGAGCCAT-TT
1 CGGGAAGCTCACTA-AGAGCCATAAT
* *
41497861 CGGGAAGCCCACAAAGAG-CAT-AT
1 CGGGAAGCTCACTAAGAGCCATAAT
* * ** * * *
41497884 CAGGAAGCTTA-TCCGGGCTATATAA
1 CGGGAAGCTCACTAAGAGCCATA-AT
*
41497909 CGGGAAGCTCA-TAAGAGCCATAAC
1 CGGGAAGCTCACTAAGAGCCATAAT
* * *
41497933 CGGGAAGTTCACAAAGAACCAT-AT
1 CGGGAAGCTCACTAAGAGCCATAAT
*
41497957 CGGGAAGCTCACGAAGAGCC-T-AT
1 CGGGAAGCTCACTAAGAGCCATAAT
*
41497980 CGGGAAGCTCAATAAGAGCCATA
1 CGGGAAGCTCACTAAGAGCCATA
41498003 TAACAGGAAA
Statistics
Matches: 127, Mismatches: 30, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
22 2 0.02
23 36 0.28
24 44 0.35
25 26 0.20
26 19 0.15
ACGTcount: A:0.35, C:0.23, G:0.25, T:0.17
Consensus pattern (25 bp):
CGGGAAGCTCACTAAGAGCCATAAT
Found at i:41497964 original size:96 final size:97
Alignment explanation
Indices: 41497809--41497988 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 97
41497799 CCTATTTTTA
* * * * * *
41497809 AACGGGAAGCTCATACAGAGCCTTCTAATGGGAAGCTCATACAGAGCCATTTCGGGAAGCCCACA
1 AACGGGAAGCTCATACAGAGCC-TATAACGGGAAGCTCACAAAGAACCATATCGGGAAGCCCACA
41497874 AAGAGCATATCAGGAAGCTTATCCGGGCTATAT
65 AAGAGCATATCAGGAAGCTTATCCGGGCTATAT
* * *
41497907 AACGGGAAGCTCATA-AGAGCC-ATAACCGGGAAGTTCACAAAGAACCATATCGGGAAGCTCACG
1 AACGGGAAGCTCATACAGAGCCTATAA-CGGGAAGCTCACAAAGAACCATATCGGGAAGCCCACA
* *
41497970 AAGAGCCTATCGGGAAGCT
65 AAGAGCATATCAGGAAGCT
41497989 CAATAAGAGC
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
95 3 0.04
96 46 0.66
97 6 0.09
98 15 0.21
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (97 bp):
AACGGGAAGCTCATACAGAGCCTATAACGGGAAGCTCACAAAGAACCATATCGGGAAGCCCACAA
AGAGCATATCAGGAAGCTTATCCGGGCTATAT
Found at i:41497984 original size:23 final size:24
Alignment explanation
Indices: 41497838--41498003 Score: 126
Period size: 24 Copynumber: 7.0 Consensus size: 24
41497828 GCCTTCTAAT
*
41497838 GGGAAGCTCA-TACAGAGCCATTTC
1 GGGAAGCTCACTA-AGAGCCATATC
* *
41497862 GGGAAGCCCACAAAGAG-CATATC
1 GGGAAGCTCACTAAGAGCCATATC
* * ** * *
41497885 AGGAAGCTTA-TCCGGGCTATATAAC
1 GGGAAGCTCACTAAGAGCCATAT--C
*
41497910 GGGAAGCTCA-TAAGAGCCATAACC
1 GGGAAGCTCACTAAGAGCCAT-ATC
* * *
41497934 GGGAAGTTCACAAAGAACCATATC
1 GGGAAGCTCACTAAGAGCCATATC
*
41497958 GGGAAGCTCACGAAGAGCC-TATC
1 GGGAAGCTCACTAAGAGCCATATC
*
41497981 GGGAAGCTCAATAAGAGCCATAT
1 GGGAAGCTCACTAAGAGCCATAT
41498004 AACAGGAAAT
Statistics
Matches: 108, Mismatches: 27, Indels: 14
0.72 0.18 0.09
Matches are distributed among these distances:
22 2 0.02
23 37 0.34
24 44 0.41
25 24 0.22
26 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.25, T:0.16
Consensus pattern (24 bp):
GGGAAGCTCACTAAGAGCCATATC
Found at i:41504237 original size:3 final size:3
Alignment explanation
Indices: 41504231--41504260 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
41504221 TCAACAACAA
*
41504231 CAG CAG CAG CAG CAG CAG CAG CAG CTG CAG
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG
41504261 ATGCCTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.33, T:0.03
Consensus pattern (3 bp):
CAG
Found at i:41505460 original size:16 final size:16
Alignment explanation
Indices: 41505439--41505506 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
41505429 TTTGGTTCGC
41505439 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
41505455 TGTATTGGATTAGAGA
1 TGTATTGGATTAGAGG
41505471 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41505487 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41505503 TGTA
1 TGTA
41505507 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41505763 original size:18 final size:17
Alignment explanation
Indices: 41505742--41505776 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41505732 TTATTATTAA
*
41505742 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41505760 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41505777 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41505883 original size:18 final size:17
Alignment explanation
Indices: 41505862--41505896 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41505852 TTATTATTAA
*
41505862 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41505880 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41505897 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41505938 original size:120 final size:120
Alignment explanation
Indices: 41505725--41506227 Score: 997
Period size: 120 Copynumber: 4.2 Consensus size: 120
41505715 ATCATATTTA
41505725 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
41505790 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
41505845 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
41505910 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
41505965 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
41506030 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
41506085 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
41506150 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
41506205 AACATAATAATTATTAAATATAT
1 AACATAATTATTATTAAATATAT
41506228 AACTTGAAAA
Statistics
Matches: 382, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 382 1.00
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:41506003 original size:18 final size:17
Alignment explanation
Indices: 41505982--41506016 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41505972 TTATTATTAA
*
41505982 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41506000 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41506017 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41506123 original size:18 final size:17
Alignment explanation
Indices: 41506102--41506136 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41506092 TTATTATTAA
*
41506102 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
41506120 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
41506137 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:41511736 original size:27 final size:26
Alignment explanation
Indices: 41511676--41511737 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
41511666 ATTTTATTTT
41511676 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
41511702 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATAATT-AATA-TTAAG
41511730 ATTTTATT
1 ATTTTATT
41511738 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:41515381 original size:6 final size:6
Alignment explanation
Indices: 41515370--41515454 Score: 88
Period size: 6 Copynumber: 14.3 Consensus size: 6
41515360 CAGCCCAATC
** *
41515370 TTTATT TTTATT TTTATT TTTATT TATTATT TTCCTT TCT-TT TTTATT
1 TTTATT TTTATT TTTATT TTTATT T-TTATT TTTATT TTTATT TTTATT
41515418 TATTATT TATTA-T TTTA-T TTTATT TTTA-T TTTATT TT
1 T-TTATT T-TTATT TTTATT TTTATT TTTATT TTTATT TT
41515455 AGTTAAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
5 17 0.25
6 36 0.52
7 16 0.23
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:41515444 original size:31 final size:29
Alignment explanation
Indices: 41515370--41515453 Score: 107
Period size: 30 Copynumber: 2.8 Consensus size: 29
41515360 CAGCCCAATC
41515370 TTTATTTTTATTTTTATTTTTATTTATTAT
1 TTTATTTTT-TTTTTATTTTTATTTATTAT
* *
41515400 TTTCCTTTCTTTTTTATTTATTATTTATTAT
1 TTT-ATTTTTTTTTTATTT-TTATTTATTAT
*
41515431 TTTATTTTATTTTTA-TTTTATTT
1 TTTATTTTTTTTTTATTTTTATTT
41515454 TAGTTAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
28 6 0.13
29 2 0.04
30 21 0.45
31 18 0.38
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.79
Consensus pattern (29 bp):
TTTATTTTTTTTTTATTTTTATTTATTAT
Found at i:41516810 original size:1 final size:1
Alignment explanation
Indices: 41516804--41516856 Score: 52
Period size: 1 Copynumber: 53.0 Consensus size: 1
41516794 AATAAAATTT
* * * * * *
41516804 AAAAAAAAAAGAAAAAAAGAAAAAAAAAGAAAAAAAAAAGAAGAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
41516857 TAAGTACTAA
Statistics
Matches: 40, Mismatches: 12, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (1 bp):
A
Found at i:41516818 original size:11 final size:11
Alignment explanation
Indices: 41516804--41516855 Score: 63
Period size: 10 Copynumber: 4.7 Consensus size: 11
41516794 AATAAAATTT
41516804 AAAAAAAA-AA
1 AAAAAAAAGAA
*
41516814 GAAAAAAAG-A
1 AAAAAAAAGAA
41516824 AAAAAAAAGAA
1 AAAAAAAAGAA
41516835 AAAAAAAAGAA
1 AAAAAAAAGAA
41516846 GAAGAAAAAA
1 -AA-AAAAAA
41516856 ATAAGTACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
10 16 0.44
11 12 0.33
12 2 0.06
13 6 0.17
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:41516828 original size:17 final size:17
Alignment explanation
Indices: 41516804--41516856 Score: 79
Period size: 18 Copynumber: 3.1 Consensus size: 17
41516794 AATAAAATTT
41516804 AAAAAAAAAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
41516821 AGAAAAAAAAAGAAAAAA
1 A-AAAAAAAAAGAAAAAA
* *
41516839 AAAAGAAGAAGAAAAAA
1 AAAAAAAAAAGAAAAAA
41516856 A
1 A
41516857 TAAGTACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGAAAAAA
Found at i:41517461 original size:27 final size:26
Alignment explanation
Indices: 41517401--41517462 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 26
41517391 AAGAGATTTT
41517401 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
41517427 ATAATTATTAGGATTATTCAA-ATTTAGG
1 AT-TTTATTAGGATAATT-AATA-TTAAG
41517455 ATTTTATT
1 ATTTTATT
41517463 TTAATTATCT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 2 0.07
27 19 0.66
28 8 0.28
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:41525542 original size:43 final size:43
Alignment explanation
Indices: 41525452--41525572 Score: 129
Period size: 43 Copynumber: 2.8 Consensus size: 43
41525442 ATCGAGATGT
* * * * * *
41525452 GATTACATGTAAGACCATGTTTGAGACATTGGAATTGTATTGT
1 GATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTAATGC
*
41525495 GATTATGTGTAAGACCATGTTTGGGACATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTTTGGGACATTGGCATCG-TAATGC
* *
41525538 GATTACGTGTAAGA-CATTGTCTGGGACAATGGCAT
1 GATTACGTGTAAGACCA-TGTTTGGGACATTGGCAT
41525573 TGATATGTGA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 2 0.03
43 61 0.92
44 3 0.05
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.34
Consensus pattern (43 bp):
GATTACGTGTAAGACCATGTTTGGGACATTGGCATCGTAATGC
Found at i:41526936 original size:28 final size:28
Alignment explanation
Indices: 41526902--41526983 Score: 137
Period size: 28 Copynumber: 2.9 Consensus size: 28
41526892 GCCCTGTTTT
41526902 CACACGGCCTGTGACACGGGCGTGTTCC
1 CACACGGCCTGTGACACGGGCGTGTTCC
*
41526930 CACACGGCCTGTGACACGGGCATGTTCC
1 CACACGGCCTGTGACACGGGCGTGTTCC
*
41526958 CACACGGCCTGTTCACACGGGCGTGT
1 CACACGGCCTG-TGACACGGGCGTGT
41526984 GACCCTGTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
28 38 0.76
29 12 0.24
ACGTcount: A:0.16, C:0.35, G:0.30, T:0.18
Consensus pattern (28 bp):
CACACGGCCTGTGACACGGGCGTGTTCC
Found at i:41526976 original size:13 final size:13
Alignment explanation
Indices: 41526900--41526977 Score: 52
Period size: 13 Copynumber: 5.7 Consensus size: 13
41526890 ATGCCCTGTT
41526900 TTCACACGGCCTG
1 TTCACACGGCCTG
* *
41526913 -TGACACGGGCGTG
1 TTCACAC-GGCCTG
41526926 TTCCCACACGGCCTG
1 TT--CACACGGCCTG
* *
41526941 -TGACACGGGCATG
1 TTCACAC-GGCCTG
41526954 TTCCCACACGGCCTG
1 TT--CACACGGCCTG
41526969 TTCACACGG
1 TTCACACGG
41526978 GCGTGTGACC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
12 9 0.18
13 17 0.35
14 3 0.06
15 12 0.24
16 8 0.16
ACGTcount: A:0.17, C:0.36, G:0.28, T:0.19
Consensus pattern (13 bp):
TTCACACGGCCTG
Found at i:41527039 original size:31 final size:32
Alignment explanation
Indices: 41526980--41527043 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
41526970 TCACACGGGC
41526980 GTGTGACCCTGTAATGCAAGAAAATTTTTTTA
1 GTGTGACCCTGTAATGCAAGAAAATTTTTTTA
* *
41527012 GTGTGACCCTTTAATGCAAGAAATTTTTTTTA
1 GTGTGACCCTGTAATGCAAGAAAATTTTTTTA
41527044 TGTTTTCCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (32 bp):
GTGTGACCCTGTAATGCAAGAAAATTTTTTTA
Found at i:41528617 original size:17 final size:18
Alignment explanation
Indices: 41528585--41528618 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41528575 TAATAATTAA
*
41528585 ATAAATAATTTTAAAATC
1 ATAAATAATTTAAAAATC
41528603 ATAAA-AATTTAAAAAT
1 ATAAATAATTTAAAAAT
41528619 TGGTTCAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
ATAAATAATTTAAAAATC
Found at i:41532736 original size:78 final size:78
Alignment explanation
Indices: 41532567--41533162 Score: 797
Period size: 78 Copynumber: 7.7 Consensus size: 78
41532557 AAATACTTAA
* * * * * *
41532567 AAGGTCAAATATTATAATATATTTCTTCTAATCTCGACA-TTCCCCACAAGTTAATTGGATCCTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
*
41532631 ATATAAATTACTT
66 ATATCAATTACTT
* * * * * * *
41532644 AAGGTCAAATATTACAACATATTTCTTTTAATCTCGATACTCTCTCATAAGCTAACTGGATCTTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
*
41532709 ATATCAATTAATT
66 ATATCAATTACTT
*
41532722 GAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
41532787 ATATCAATTACTT
66 ATATCAATTACTT
* * **
41532800 AAGGTCAAAGATTACAACAAATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTAGATCCCA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
41532865 ATATCAATTACTT
66 ATATCAATTACTT
* * * * *
41532878 AAGGTCAAAGATTTCAACATATTTCTTTTAATCTCGACACTCCCCCATAAGCTAACTGGACCTTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
41532943 ATATCAATTACTT
66 ATATCAATTACTT
* ** * *
41532956 AAGGTCAAAGATTACAACATATTTC-TCTTAGTCTCGACTTTACCCCACAAGTTAACTGGATTTT
1 AAGGTCAAAGATTACAACATATTTCTTC-TAATCTCGACACTCCCCCACAAGTTAACTGGATCTT
*
41533020 AATATCAATTACCT
65 AATATCAATTACTT
* * * * *
41533034 AAGGTCAAAGATTACAACATATTTCTTCTAATATCGACACT-TCCC-CATGTTAACTAGATCCTA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
*
41533097 ATATCAATTAGTT
66 ATATCAATTACTT
*
41533110 AAGGTCAAAGATTACAACATATTTCTT-TCAATCTCAACACTCCCCCACAAGTT
1 AAGGTCAAAGATTACAACATATTTCTTCT-AATCTCGACACTCCCCCACAAGTT
41533163 GATGCGTAGA
Statistics
Matches: 451, Mismatches: 62, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
75 1 0.00
76 62 0.14
77 42 0.09
78 344 0.76
79 2 0.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.34
Consensus pattern (78 bp):
AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTGGATCTTA
ATATCAATTACTT
Found at i:41532975 original size:234 final size:233
Alignment explanation
Indices: 41532567--41533156 Score: 887
Period size: 234 Copynumber: 2.5 Consensus size: 233
41532557 AAATACTTAA
* * * * * *
41532567 AAGGTCAAATATTATAATATATTTCTTCTAATCTCGACATTCCCCACAAGTTAATTGGATCCTAA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCACAAGTTAACTAGATCCTAA
* * * * *
41532632 TATAAATTACTTAAGGTCAAATATTACAACATATTTCTTTTAATCTCGATACTCTCTCATAAGCT
66 TATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCATAAGCT
* *
41532697 AACTGGATCTTAATATCAATTAATTGAGGTCAAAGATTACAACATATTTCT-TCTAATCTCGACA
131 AACTGGACCTTAATATCAATTAATTAAGGTCAAAGATTACAACATATTTCTCT-TAATCTCGACA
* *
41532761 CTCCCCCACAAGTTAACTGGATCTTAATATCAATTACTT
195 CTACCCCACAAGTTAACTGGATCTTAATATCAATTACCT
* *
41532800 AAGGTCAAAGATTACAACAAATTTCTTCTAATCTCGACACTCCCCCACAAGTTAACTAGATCCCA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACT-CCCCACAAGTTAACTAGATCCTA
*
41532865 ATATCAATTACTTAAGGTCAAAGATTTCAACATATTTCTTTTAATCTCGACACTCCCCCATAAGC
65 ATATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCATAAGC
* * *
41532930 TAACTGGACCTTAATATCAATTACTTAAGGTCAAAGATTACAACATATTTCTCTTAGTCTCGACT
130 TAACTGGACCTTAATATCAATTAATTAAGGTCAAAGATTACAACATATTTCTCTTAATCTCGACA
* *
41532995 TTACCCCACAAGTTAACTGGATTTTAATATCAATTACCT
195 CTACCCCACAAGTTAACTGGATCTTAATATCAATTACCT
* * *
41533034 AAGGTCAAAGATTACAACATATTTCTTCTAATATCGACACTTCCC-CATGTTAACTAGATCCTAA
1 AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCACAAGTTAACTAGATCCTAA
* * *
41533098 TATCAATTAGTTAAGGTCAAAGATTACAACATATTTCTTTCAATCTCAACACTCCCCCA
66 TATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCA
41533157 CAAGTTGATG
Statistics
Matches: 323, Mismatches: 32, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
232 72 0.22
233 39 0.12
234 211 0.65
235 1 0.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.34
Consensus pattern (233 bp):
AAGGTCAAAGATTACAACATATTTCTTCTAATCTCGACACTCCCCACAAGTTAACTAGATCCTAA
TATCAATTACTTAAGGTCAAAGATTACAACATATTTCTTTTAATCTCGACACTCCCCCATAAGCT
AACTGGACCTTAATATCAATTAATTAAGGTCAAAGATTACAACATATTTCTCTTAATCTCGACAC
TACCCCACAAGTTAACTGGATCTTAATATCAATTACCT
Found at i:41533964 original size:40 final size:41
Alignment explanation
Indices: 41533878--41533984 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 41
41533868 CCTTTAGTGG
*
41533878 CTTTAGCGGCGCTTTTTTAAAAACGCCGCTAAAGATCAAGT
1 CTTTAGCAGCGCTTTTTTAAAAACGCCGCTAAAGATCAAGT
* * * * *
41533919 -ATTAGCAGCGCTTTTTTAAAAGCGCCGCTAATGTTCGA-T
1 CTTTAGCAGCGCTTTTTTAAAAACGCCGCTAAAGATCAAGT
41533958 CTTTAGC-G-GCATTTTTTGAAAAACGCC
1 CTTTAGCAGCGC-TTTTTT-AAAAACGCC
41533985 ACAAAAAATT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
38 2 0.04
39 8 0.15
40 45 0.82
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (41 bp):
CTTTAGCAGCGCTTTTTTAAAAACGCCGCTAAAGATCAAGT
Found at i:41534217 original size:22 final size:22
Alignment explanation
Indices: 41534158--41534217 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 22
41534148 GTTTACAATA
* *
41534158 TATGG-TTAAGGGTTTAATGTT
1 TATGGATTATGGGTTTAAGGTT
***
41534179 TAT-GAGTTATTATTTTAAGGTT
1 TATGGA-TTATGGGTTTAAGGTT
41534201 TATGGATTATGGGTTTA
1 TATGGATTATGGGTTTA
41534218 GAGATTATAG
Statistics
Matches: 28, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
20 1 0.04
21 3 0.11
22 22 0.79
23 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (22 bp):
TATGGATTATGGGTTTAAGGTT
Found at i:41534308 original size:36 final size:36
Alignment explanation
Indices: 41534240--41534308 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
41534230 CAAGGGTGGT
* *
41534240 TTAAGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGG
1 TTAAGGGTTGGGGTTTAAGGTTCAAGTGTTAGGGGG
* *
41534276 TTAAGGGTTAGGGGTTT-AGGTTCATGTTTTAGG
1 TTAAGGGTT-GGGGTTTAAGGTTCAAGTGTTAGG
41534309 ATTTACAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 22 0.79
37 6 0.21
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (36 bp):
TTAAGGGTTGGGGTTTAAGGTTCAAGTGTTAGGGGG
Found at i:41534606 original size:308 final size:308
Alignment explanation
Indices: 41534055--41535206 Score: 2053
Period size: 308 Copynumber: 3.8 Consensus size: 308
41534045 TGACTAATTG
* *
41534055 TTTTTAATTTATATGTTAAATATTTTCTTATATAATTGTAAAAGAGATAGTATTAATTTTAAAAT
1 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
* * * *
41534120 ATTGAATTAATTATCATTATAGTTTAGGGTTTA-CA---A---TATATGG-TTAAGGGTTTAATG
66 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAA-AGTTTAAAG
*
41534177 TTTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTT
130 TGTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTT
41534242 AAGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTA
195 AAGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTA
41534307 GGATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
260 GGATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
41534356 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
1 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
41534421 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
66 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
41534486 GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTTA
131 GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTTA
41534551 AGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTAG
196 AGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTAG
41534616 GATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
261 GATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
41534664 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
1 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
41534729 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
66 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
41534794 GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTTA
131 GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTTA
41534859 AGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTAG
196 AGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTAG
41534924 GATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
261 GATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
41534972 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
1 TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
41535037 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
66 ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
* *
41535102 GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTATG-GATTATGGTT-TA---TGGTTT
131 GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTA-GAGATTATAGTTCAAGGGTGGTTT
* * * * * *
41535162 AAGGGTTGGGGTTTAAGGCTTAGGGGTTA-AGGGTTAAGTGTTAGG
195 AAGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGG
41535207 TTTACTTAAG
Statistics
Matches: 827, Mismatches: 15, Indels: 16
0.96 0.02 0.02
Matches are distributed among these distances:
301 95 0.11
302 1 0.00
303 14 0.02
304 31 0.04
305 1 0.00
307 1 0.00
308 679 0.82
309 5 0.01
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.45
Consensus pattern (308 bp):
TTTTTAATTTATATGATAAATATTTTCTTATATAATTATAAAAGAGATAGTATTAATTTTAAAAT
ATTGAATTAATTATCATTATAGTTCAGGGTTTATGATTTAGGGTATATGGTTTAAAGTTTAAAGT
GTATGAGTTATTATTTTAAGGTTTATGGATTATGGGTTTAGAGATTATAGTTCAAGGGTGGTTTA
AGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGGTTAAGGGTTAGGGGTTTAGGTTCATGTTTTAG
GATTTACAGTTTAGGGATTAGGAGTTTAGGGTTTAGATTAATTAGTGT
Found at i:41534616 original size:36 final size:36
Alignment explanation
Indices: 41534548--41534616 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
41534538 CAAGGGTGGT
* *
41534548 TTAAGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGG
1 TTAAGGGTTGGGGTTTAAGGTTCAAGTGTTAGGGGG
* *
41534584 TTAAGGGTTAGGGGTTT-AGGTTCATGTTTTAGG
1 TTAAGGGTT-GGGGTTTAAGGTTCAAGTGTTAGG
41534617 ATTTACAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 22 0.79
37 6 0.21
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (36 bp):
TTAAGGGTTGGGGTTTAAGGTTCAAGTGTTAGGGGG
Found at i:41534924 original size:36 final size:36
Alignment explanation
Indices: 41534856--41534924 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
41534846 CAAGGGTGGT
* *
41534856 TTAAGGGTTGTGGTTTAAGGTTTAAGTGTTAGGGGG
1 TTAAGGGTTGGGGTTTAAGGTTCAAGTGTTAGGGGG
* *
41534892 TTAAGGGTTAGGGGTTT-AGGTTCATGTTTTAGG
1 TTAAGGGTT-GGGGTTTAAGGTTCAAGTGTTAGG
41534925 ATTTACAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
36 22 0.79
37 6 0.21
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (36 bp):
TTAAGGGTTGGGGTTTAAGGTTCAAGTGTTAGGGGG
Found at i:41535139 original size:15 final size:15
Alignment explanation
Indices: 41535121--41535168 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
41535111 ATTATTTTAA
41535121 GGTTTATGGATTATG
1 GGTTTATGGATTATG
41535136 GGTTTATGGATTAT-
1 GGTTTATGGATTATG
* *
41535150 GGTTTATGGTTTAAG
1 GGTTTATGGATTATG
41535165 GGTT
1 GGTT
41535169 GGGGTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 12 0.40
15 18 0.60
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (15 bp):
GGTTTATGGATTATG
Found at i:41535141 original size:22 final size:21
Alignment explanation
Indices: 41535116--41535165 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
41535106 GAGTTATTAT
*
41535116 TTTAAGGTTTATGGATTATGGG
1 TTTAAGGATTATGGATTAT-GG
* *
41535138 TTTATGGATTATGGTTTATGG
1 TTTAAGGATTATGGATTATGG
41535159 TTTAAGG
1 TTTAAGG
41535166 GTTGGGGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (21 bp):
TTTAAGGATTATGGATTATGG
Found at i:41535159 original size:7 final size:7
Alignment explanation
Indices: 41535116--41535162 Score: 58
Period size: 7 Copynumber: 6.6 Consensus size: 7
41535106 GAGTTATTAT
*
41535116 TTTAAGG
1 TTTATGG
41535123 TTTATGG
1 TTTATGG
*
41535130 ATTATGGG
1 TTTAT-GG
41535138 TTTATGG
1 TTTATGG
*
41535145 ATTATGG
1 TTTATGG
41535152 TTTATGG
1 TTTATGG
41535159 TTTA
1 TTTA
41535163 AGGGTTGGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
7 28 0.82
8 6 0.18
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (7 bp):
TTTATGG
Found at i:41535174 original size:14 final size:15
Alignment explanation
Indices: 41535157--41535197 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
41535147 TATGGTTTAT
41535157 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
41535171 GGTTTAAGGCTTAGG
1 GGTTTAAGGGTTAGG
41535186 GG-TTAAGGGTTA
1 GGTTTAAGGGTTA
41535198 AGTGTTAGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 20 0.83
15 4 0.17
ACGTcount: A:0.20, C:0.02, G:0.44, T:0.34
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:41535188 original size:21 final size:21
Alignment explanation
Indices: 41535150--41535189 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41535140 TATGGATTAT
* *
41535150 GGTTTATGGTTTAAGGGTTGG
1 GGTTTAAGGCTTAAGGGTTGG
*
41535171 GGTTTAAGGCTTAGGGGTT
1 GGTTTAAGGCTTAAGGGTT
41535190 AAGGGTTAAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.15, C:0.03, G:0.42, T:0.40
Consensus pattern (21 bp):
GGTTTAAGGCTTAAGGGTTGG
Found at i:41545357 original size:60 final size:60
Alignment explanation
Indices: 41545264--41545376 Score: 208
Period size: 60 Copynumber: 1.9 Consensus size: 60
41545254 ACTGGAAATG
*
41545264 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCTAAAGCCTGTGA
1 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGCCTGTGA
*
41545324 TATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAG
1 TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAG
41545377 TCCCGCAGGC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.22, C:0.25, G:0.30, T:0.23
Consensus pattern (60 bp):
TATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGGAAATGTATCCGGGCCAAAGCCTGTGA
Found at i:41545378 original size:39 final size:39
Alignment explanation
Indices: 41545324--41545434 Score: 186
Period size: 39 Copynumber: 2.8 Consensus size: 39
41545314 AAGCCTGTGA
41545324 TATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATG
1 TATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATG
* *
41545363 TATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGGAAATG
1 TATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATG
* *
41545402 TATCCGGGTTAAAGTCTCGCAGGCTTTGTGCTG
1 TATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTG
41545435 ATAATATAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 66 1.00
ACGTcount: A:0.19, C:0.24, G:0.31, T:0.26
Consensus pattern (39 bp):
TATCCGGGCTAAAGTCTCGCAGGCTTCGTGCTGGAAATG
Found at i:41548408 original size:30 final size:30
Alignment explanation
Indices: 41548363--41548422 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
41548353 CAATAGATGA
*
41548363 CACACGACTATGTCACCAAG-CTGTGTGTCT
1 CACACGACTAAGTCA-CAAGCCTGTGTGTCT
* *
41548393 CACACGGCTAAGTCACACGCCTGTGTGTCT
1 CACACGACTAAGTCACAAGCCTGTGTGTCT
41548423 GGTCGTGTGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 3 0.12
30 23 0.88
ACGTcount: A:0.22, C:0.32, G:0.22, T:0.25
Consensus pattern (30 bp):
CACACGACTAAGTCACAAGCCTGTGTGTCT
Found at i:41559406 original size:27 final size:22
Alignment explanation
Indices: 41559352--41559396 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
41559342 GAATGAGATT
*
41559352 ATTAAAGGAAAGCATTCTGATA
1 ATTAAAGGAAAGCATCCTGATA
41559374 ATTAAAGGAAAGCATCCTGATA
1 ATTAAAGGAAAGCATCCTGATA
41559396 A
1 A
41559397 ACTTAGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.47, C:0.11, G:0.18, T:0.24
Consensus pattern (22 bp):
ATTAAAGGAAAGCATCCTGATA
Found at i:41565021 original size:3 final size:3
Alignment explanation
Indices: 41565013--41565038 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41565003 TTTTATTTAT
41565013 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
41565039 TTTAACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:41567270 original size:23 final size:25
Alignment explanation
Indices: 41567244--41567291 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
41567234 GTCTTGATTC
41567244 TTAAAAA-ATTAAAA-TTAATTTTT
1 TTAAAAATATTAAAAGTTAATTTTT
* *
41567267 TTAAAAATTTTAAAAGTTTATTTTT
1 TTAAAAATATTAAAAGTTAATTTTT
41567292 CAATTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTAAAAATATTAAAAGTTAATTTTT
Found at i:41567417 original size:20 final size:20
Alignment explanation
Indices: 41567394--41567444 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
41567384 AAATTTATTT
* *
41567394 AATAAAATAATGATTTTATA
1 AATAAAATAATAATCTTATA
41567414 AATAAAATAATAATCTTATA
1 AATAAAATAATAATCTTATA
*
41567434 AACAAAATAAT
1 AATAAAATAAT
41567445 TCAAGAGGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (20 bp):
AATAAAATAATAATCTTATA
Found at i:41573809 original size:43 final size:44
Alignment explanation
Indices: 41573748--41573840 Score: 145
Period size: 43 Copynumber: 2.2 Consensus size: 44
41573738 TCCGAATTGG
41573748 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
* * *
41573791 GAAAATAGTTCCTTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
41573835 -AAAATA
1 GAAAATA
41573841 TTTCTAGAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 45 0.98
44 1 0.02
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (44 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:41578549 original size:43 final size:44
Alignment explanation
Indices: 41578488--41578584 Score: 146
Period size: 43 Copynumber: 2.3 Consensus size: 44
41578478 TCCTAATTGG
*
41578488 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
* *
41578531 GAAAATAGTTTCCTTATTCTAGTAAACTACTAAAAGATAAAATA
1 GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
41578575 -AAAATA-TTTC
1 GAAAATAGTTTC
41578585 TAAAATATGA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 4 0.08
43 45 0.90
44 1 0.02
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.31
Consensus pattern (44 bp):
GAAAATAGTTTCCTTATTCTAATAAACTACTAAAACATAAAATA
Found at i:41578756 original size:64 final size:64
Alignment explanation
Indices: 41578655--41579464 Score: 1516
Period size: 64 Copynumber: 12.7 Consensus size: 64
41578645 TATATACATA
41578655 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41578719 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41578783 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41578847 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41578911 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41578975 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41579039 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41579103 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41579167 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41579231 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
41579295 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
** ** * * *
41579359 TTTCAACAATACACACATACACACATACATATACATATATATGTAAAT-T-TAAAATATATACAT
1 TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGT-ATGTGTGTA-TT
*
41579422 A
64 G
41579423 TTTCAACAATACACACATACACACATACATATACATATATAT
1 TTTCAACAATACACACATACACACATACATATACATATATAT
41579465 TACATTATTG
Statistics
Matches: 736, Mismatches: 8, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
62 1 0.00
63 6 0.01
64 729 0.99
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (64 bp):
TTTCAACAATACACACATACACACATACATATACATATATATGTATGTGTGTATGTGTGTATTG
Found at i:41579645 original size:20 final size:19
Alignment explanation
Indices: 41579612--41579650 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
41579602 AAAATTACAA
*
41579612 TAAAAAAAGGAGAAAATAAT
1 TAAAAAAAGAAG-AAATAAT
*
41579632 TAAAAGAAGAAGAAATAAT
1 TAAAAAAAGAAGAAATAAT
41579651 AGAATAGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (19 bp):
TAAAAAAAGAAGAAATAAT
Found at i:41597441 original size:40 final size:40
Alignment explanation
Indices: 41597397--41597472 Score: 125
Period size: 40 Copynumber: 1.9 Consensus size: 40
41597387 GTACCTTATG
* *
41597397 GTGTGTAGGGTTAGATGGGTTGATTTTATCCCCATACTTA
1 GTGTGTAGGGCTAGATGGGTCGATTTTATCCCCATACTTA
*
41597437 GTGTGTAGGGCTGGATGGGTCGATTTTATCCCCATA
1 GTGTGTAGGGCTAGATGGGTCGATTTTATCCCCATA
41597473 TGGTATGTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.18, C:0.14, G:0.30, T:0.37
Consensus pattern (40 bp):
GTGTGTAGGGCTAGATGGGTCGATTTTATCCCCATACTTA
Found at i:41606192 original size:35 final size:34
Alignment explanation
Indices: 41606153--41606235 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
41606143 GAGCCCAATT
* *
41606153 CTAGTTGGATAAACCAATGATATCTGTGCCCAGCG
1 CTAGTCGGATAAACCAATGA-ATCTGTGCCCAGCA
* * *
41606188 CTAGTCGGATAAACCGATGAATGTGTGCCTAGCA
1 CTAGTCGGATAAACCAATGAATCTGTGCCCAGCA
*
41606222 CTAGTCAGATAAAC
1 CTAGTCGGATAAAC
41606236 TGACGAAAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
34 24 0.57
35 18 0.43
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (34 bp):
CTAGTCGGATAAACCAATGAATCTGTGCCCAGCA
Found at i:41606292 original size:143 final size:143
Alignment explanation
Indices: 41606042--41606337 Score: 432
Period size: 143 Copynumber: 2.1 Consensus size: 143
41606032 CTTGTGCCTG
* *
41606042 GCGCTAGTCGGATAAACCGACAAATGTGTGCCCAGCACTAGTCAAATAAACTGACGAAGGTTGCG
1 GCGCTAGTCGGATAAACCGACAAATGTGTGCCCAGCACTAGTCAAATAAACTGACGAAAGTTGCA
* * * *
41606107 CCCAGAGCTAGCTGGATAAACCGACAAATAATTAGTGAGCCCAATTCTAGTTGGATAAACCAATG
66 CCCAGAGCTAGATGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAACG
**
41606172 ATATCTGTGCCCA
131 ATATCTGCACCCA
** * *
41606185 GCGCTAGTCGGATAAACCGATGAATGTGTGCCTAGCACTAGTCAGATAAACTGACGAAAGTTGCA
1 GCGCTAGTCGGATAAACCGACAAATGTGTGCCCAGCACTAGTCAAATAAACTGACGAAAGTTGCA
* *
41606250 CCCA-ACGCTAGATGAATAAACCGACAAATAATTAGTGAGCCCAGCTCTAGTTGTATAAACCAAC
66 CCCAGA-GCTAGATGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAAC
*
41606314 GATATTTGCACCCA
130 GATATCTGCACCCA
*
41606328 ACGCTAGTCG
1 GCGCTAGTCG
41606338 AATGAATCGA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
142 1 0.01
143 135 0.99
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.21
Consensus pattern (143 bp):
GCGCTAGTCGGATAAACCGACAAATGTGTGCCCAGCACTAGTCAAATAAACTGACGAAAGTTGCA
CCCAGAGCTAGATGAATAAACCGACAAATAATTAGTGAGCCCAACTCTAGTTGGATAAACCAACG
ATATCTGCACCCA
Found at i:41606323 original size:74 final size:72
Alignment explanation
Indices: 41606113--41606335 Score: 197
Period size: 74 Copynumber: 3.1 Consensus size: 72
41606103 TGCGCCCAGA
** * *
41606113 GCTAGCTGGATAAACCGACAAATAATTAGTGAGCCCAATTCTAGTTGGATAAACCAATGATATCT
1 GCTAG-TGGATAAACCGACAAATAATTAGTGAGCCCAGCTCTAGTT-GATAAACCAACGATATTT
** *
41606178 GTGCCCAGC
64 GCACCCAAC
* * * * ** * *
41606187 GCTAGTCGGATAAACCG----ATGAA-T-GTGTGCCTAGCACTAGTCAGATAAACTGACGAAAGT
1 GCTAGT-GGATAAACCGACAAAT-AATTAGTGAGCCCAGCTCTAGT-TGATAAACCAACGATATT
41606246 TGCACCCAAC
63 TGCACCCAAC
*
41606256 GCTAGATGAATAAACCGACAAATAATTAGTGAGCCCAGCTCTAGTTGTATAAACCAACGATATTT
1 GCTAG-TGGATAAACCGACAAATAATTAGTGAGCCCAGCTCTAGTTG-ATAAACCAACGATATTT
41606321 GCACCCAAC
64 GCACCCAAC
41606330 GCTAGT
1 GCTAGT
41606336 CGAATGAATC
Statistics
Matches: 114, Mismatches: 24, Indels: 23
0.71 0.15 0.14
Matches are distributed among these distances:
69 44 0.39
70 4 0.04
71 2 0.02
72 2 0.02
73 6 0.05
74 56 0.49
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (72 bp):
GCTAGTGGATAAACCGACAAATAATTAGTGAGCCCAGCTCTAGTTGATAAACCAACGATATTTGC
ACCCAAC
Found at i:41609804 original size:17 final size:17
Alignment explanation
Indices: 41609782--41609814 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41609772 GCCCATACAA
41609782 AAACCAAAAAACAAAAT
1 AAACCAAAAAACAAAAT
*
41609799 AAACCAAAATACAAAA
1 AAACCAAAAAACAAAA
41609815 ACCAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.18, G:0.00, T:0.06
Consensus pattern (17 bp):
AAACCAAAAAACAAAAT
Found at i:41609822 original size:14 final size:14
Alignment explanation
Indices: 41609776--41609822 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 14
41609766 GCCCTGGCCC
41609776 ATACAAAAACCAAA
1 ATACAAAAACCAAA
*
41609790 AAACAAAATAAACCAAA
1 ATAC--AA-AAACCAAA
41609807 ATACAAAAACCAAA
1 ATACAAAAACCAAA
41609821 AT
1 AT
41609823 TAAAGTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
14 13 0.46
15 2 0.07
16 2 0.07
17 11 0.39
ACGTcount: A:0.72, C:0.19, G:0.00, T:0.09
Consensus pattern (14 bp):
ATACAAAAACCAAA
Found at i:41612190 original size:26 final size:24
Alignment explanation
Indices: 41612148--41612198 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 24
41612138 AGTGTACGAG
41612148 TTTTTGAAAGTCAAAAGTCGATCGTA
1 TTTTTGAAAGTCAAAAG--GATCGTA
*
41612174 TTTTTGAAGGT-ATAAAGGATCGTA
1 TTTTTGAAAGTCA-AAAGGATCGTA
41612198 T
1 T
41612199 CCAATCATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 8 0.35
25 1 0.04
26 14 0.61
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (24 bp):
TTTTTGAAAGTCAAAAGGATCGTA
Found at i:41614486 original size:14 final size:14
Alignment explanation
Indices: 41614467--41614496 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41614457 TTATATCGAG
41614467 ACCAATCCAAATCA
1 ACCAATCCAAATCA
*
41614481 ACCAATCCAATTCA
1 ACCAATCCAAATCA
41614495 AC
1 AC
41614497 ATATTTTCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (14 bp):
ACCAATCCAAATCA
Found at i:41619633 original size:16 final size:16
Alignment explanation
Indices: 41619614--41619656 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 16
41619604 ATAAAAATAA
41619614 AAAAAGAGAAAGAAAT
1 AAAAAGAGAAAGAAAT
41619630 AAAAAGAG--A-AAAT
1 AAAAAGAGAAAGAAAT
41619643 AAAAA-AGAAAGAAA
1 AAAAAGAGAAAGAAA
41619657 GAAAGAATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 2 0.08
13 9 0.38
14 2 0.08
15 3 0.12
16 8 0.33
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (16 bp):
AAAAAGAGAAAGAAAT
Found at i:41619649 original size:14 final size:14
Alignment explanation
Indices: 41619598--41619650 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
41619588 CTTGAGAACT
*
41619598 TAAAAAATA-AAAA
1 TAAAAAAGAGAAAA
41619611 TAAAAAAAGAGAAAGA
1 T-AAAAAAGAGAAA-A
*
41619627 AATAAAAAGAGAAAA
1 TA-AAAAAGAGAAAA
41619642 TAAAAAAGA
1 TAAAAAAGA
41619651 AAGAAAGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 14 0.42
15 6 0.18
16 12 0.36
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.09
Consensus pattern (14 bp):
TAAAAAAGAGAAAA
Found at i:41620754 original size:17 final size:16
Alignment explanation
Indices: 41620721--41620750 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41620711 GCATTTAAAA
41620721 AAAAAAGAGATCATTC
1 AAAAAAGAGATCATTC
41620737 AAAAAA-AGATCATT
1 AAAAAAGAGATCATT
41620751 TTCATTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.20
Consensus pattern (16 bp):
AAAAAAGAGATCATTC
Found at i:41620878 original size:64 final size:64
Alignment explanation
Indices: 41620776--41620983 Score: 353
Period size: 64 Copynumber: 3.2 Consensus size: 64
41620766 TTCATAACAC
*
41620776 GTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACACCAGCATCACATCTA
1 GTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACATCTA
* * * *
41620840 ATTAGGAGTATTTGATTCATTTTGATCATAGCATCCTAATTATTTGACATAAGCATCACATCTA
1 GTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACATCTA
*
41620904 GTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTAACATCAGCATCACATCTA
1 GTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACATCTA
*
41620968 GTTAGGAGTATTTGAT
1 GTTAGGAGCATTTGAT
41620984 CGTAGCATCC
Statistics
Matches: 133, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 133 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (64 bp):
GTTAGGAGCATTTGATTCATTTCGATCATAGCATCCTAATTATTTGACATCAGCATCACATCTA
Found at i:41621385 original size:44 final size:44
Alignment explanation
Indices: 41621337--41621528 Score: 114
Period size: 44 Copynumber: 4.3 Consensus size: 44
41621327 GCAGGTTGGC
41621337 GATTGTAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAA
1 GATTGTAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAA
* * * * **
41621381 GATTGAATA-TCTTATCTCCATGTACCGGTA--ATGG-AGCAGATTTTA
1 GATTG--TAGTCTTATCTTCTTG-A--GGTAGCAAGGAAGCAGACTGAA
* **
41621426 GCCATTG-A-CCTTATC-TCTCTGAGGTAGCAA-GAGAGCAGGTTGAA
1 G--ATTGTAGTCTTATCTTCT-TGAGGTAGCAAGGA-AGCAGACTGAA
* *
41621470 GA-TGATAGTCTTATCCTCTTGAGGCAGCAAGGAAGCAGACTGAA
1 GATTG-TAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAA
*
41621514 GATTGCAGGTCTTAT
1 GATTGTA-GTCTTAT
41621529 TTCCCTAAGC
Statistics
Matches: 111, Mismatches: 18, Indels: 37
0.67 0.11 0.22
Matches are distributed among these distances:
41 6 0.05
42 2 0.02
43 4 0.04
44 51 0.46
45 34 0.31
46 6 0.05
47 4 0.04
48 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
GATTGTAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAA
Found at i:41621517 original size:133 final size:133
Alignment explanation
Indices: 41621256--41621518 Score: 395
Period size: 133 Copynumber: 2.0 Consensus size: 133
41621246 AAGATGGCGA
*
41621256 ATCTTATCTCCATGTATCGGCAATGGAGCAGATTTTAGCCACCAGCCTTACCTCTCTGAAGTAGC
1 ATCTTATCTCCATGTACCGGCAATGGAGCAGATTTTAGCCACCAGCCTTACCTCTCTGAAGTAGC
* ** * *
41621321 AAGGGAGCAGGTTGGCGATTGTAGTCTTATCTTCTTGAGGTAGCAAGGAAGCAGACTGAAGATTG
66 AAGAGAGCAGGTTGAAGATTGTAGTCTTATCCTCTTGAGGCAGCAAGGAAGCAGACTGAAGATTG
41621386 AAT
131 AAT
* ** * *
41621389 ATCTTATCTCCATGTACCGGTAATGGAGCAGATTTTAGCCA-TTGACCTTATCTCTCTGAGGTAG
1 ATCTTATCTCCATGTACCGGCAATGGAGCAGATTTTAGCCACCAG-CCTTACCTCTCTGAAGTAG
41621453 CAAGAGAGCAGGTTGAAGA-TGATAGTCTTATCCTCTTGAGGCAGCAAGGAAGCAGACTGAAGAT
65 CAAGAGAGCAGGTTGAAGATTG-TAGTCTTATCCTCTTGAGGCAGCAAGGAAGCAGACTGAAGAT
41621517 TG
129 TG
41621519 CAGGTCTTAT
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
132 3 0.03
133 114 0.97
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (133 bp):
ATCTTATCTCCATGTACCGGCAATGGAGCAGATTTTAGCCACCAGCCTTACCTCTCTGAAGTAGC
AAGAGAGCAGGTTGAAGATTGTAGTCTTATCCTCTTGAGGCAGCAAGGAAGCAGACTGAAGATTG
AAT
Found at i:41621798 original size:44 final size:44
Alignment explanation
Indices: 41621750--41621982 Score: 157
Period size: 44 Copynumber: 5.2 Consensus size: 44
41621740 AGCCCCAAGC
* *
41621750 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTGAAGATTGAAGT
1 CTTATCTCTCTGAGGTAGCAAGAGAGCAGATTAAAGATTGAAGT
* * * * *
41621794 CTTATCGTC-CTGAGGTAGCAAG-GAAGCAGACTGAATATTGGAGG
1 CTTATC-TCTCTGAGGTAGCAAGAG-AGCAGATTAAAGATTGAAGT
** * * * * * * ** *
41621838 CAAATCTTATCTCCATGTATCGACAATAGAGCATATTTAAGCCTGAAGC
1 CTTATC-TCTCT-GAGGTA--G-CAAGAGAGCAGATTAAAGATTGAAGT
*
41621887 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTAAAGATTG-AGT
1 CTTATCTCTCTGAGGTAGCAAGAGAGCAGATTAAAGATTGAAGT
* * * * *
41621930 CTTATCTTTCTGAAGTAGTAAGAAAGCAGACTAAAGATTGAAGAT
1 CTTATCTCTCTGAGGTAGCAAGAGAGCAGATTAAAGATTGAAG-T
41621975 CTTATCTC
1 CTTATCTC
41621983 CCCTAAGCAG
Statistics
Matches: 140, Mismatches: 39, Indels: 19
0.71 0.20 0.10
Matches are distributed among these distances:
43 37 0.26
44 57 0.41
45 13 0.09
46 4 0.03
47 4 0.03
48 5 0.04
49 19 0.14
50 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (44 bp):
CTTATCTCTCTGAGGTAGCAAGAGAGCAGATTAAAGATTGAAGT
Found at i:41621855 original size:137 final size:135
Alignment explanation
Indices: 41621563--41621969 Score: 462
Period size: 137 Copynumber: 3.0 Consensus size: 135
41621553 CCAAAGACGA
* * * *
41621563 CAAATCTTATCTCCATGTACCGGCAATAGAGTAGATTTAAGTCCCC-AGCCTTATCTCTCTGAAG
1 CAAATCTTATCTCCATGTATCGACAATAGAGCAGATTTAAG-CCCCAAGCCTTATCTCTCTGAGG
* * * * * * ** * * *
41621627 TTGC-AGTGGGGTAGGCTCG-ATATACAAGTCTCTATCTCCCTGAGGTTGTAGTGGAGCAGACTG
65 TAGCAAG-AGAGCAGG-TTGAAGATTGAAGTCT-TATCT-CCTGAGGTAGAAG-GAAGCAGACTG
41621690 AAGATTGGAGG
125 AAGATTGGAGG
* *
41621701 CAAATCTTATCTTCATGTATCGACAATGGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGT
1 CAAATCTTATCTCCATGTATCGACAATAGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGT
*
41621766 AGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCGTCCTGAGGTAGCAAGGAAGCAGACTGAATA
66 AGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATC-TCCTGAGGTAG-AAGGAAGCAGACTGAAGA
41621831 TTGGAGG
129 TTGGAGG
* **
41621838 CAAATCTTATCTCCATGTATCGACAATAGAGCATATTTAAGCCTGAAGCCTTATCTCTCTGAGGT
1 CAAATCTTATCTCCATGTATCGACAATAGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGT
* * * * *
41621903 AGCAAGAGAGCAGGTTAAAGATTG-AGTCTTATCTTTCTGAAGTAGTAAGAAAGCAGACTAAAGA
66 AGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATC-TCCTGAGGTAG-AAGGAAGCAGACTGAAGA
41621967 TTG
129 TTG
41621970 AAGATCTTAT
Statistics
Matches: 233, Mismatches: 31, Indels: 12
0.84 0.11 0.04
Matches are distributed among these distances:
136 36 0.15
137 122 0.52
138 73 0.31
139 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (135 bp):
CAAATCTTATCTCCATGTATCGACAATAGAGCAGATTTAAGCCCCAAGCCTTATCTCTCTGAGGT
AGCAAGAGAGCAGGTTGAAGATTGAAGTCTTATCTCCTGAGGTAGAAGGAAGCAGACTGAAGATT
GGAGG
Found at i:41621958 original size:43 final size:45
Alignment explanation
Indices: 41621887--41621982 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 45
41621877 AGCCTGAAGC
* * **
41621887 CTTATCTCTCTGAGGTAGCAAGAGAGCAGGTTAAAGATTG-AG-T
1 CTTATCTCTCTGAAGTAGCAAGAAAGCAGACTAAAGATTGAAGAT
* *
41621930 CTTATCTTTCTGAAGTAGTAAGAAAGCAGACTAAAGATTGAAGAT
1 CTTATCTCTCTGAAGTAGCAAGAAAGCAGACTAAAGATTGAAGAT
41621975 CTTATCTC
1 CTTATCTC
41621983 CCCTAAGCAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 34 0.77
44 2 0.05
45 8 0.18
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (45 bp):
CTTATCTCTCTGAAGTAGCAAGAAAGCAGACTAAAGATTGAAGAT
Found at i:41622033 original size:177 final size:178
Alignment explanation
Indices: 41621838--41622232 Score: 442
Period size: 177 Copynumber: 2.2 Consensus size: 178
41621828 ATATTGGAGG
* ** *
41621838 CAAATCTTATCTCCATGTATCGA-CAATAGAGCATATTTAAGCCTGAAGCCTTATCTCTCTGAGG
1 CAAATCTTATCTCCATGTATCGAGCAATAGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAAG
* **
41621902 TAGCAAGAGAGCAGGTTAAAGA-TTGAGTCTTATCTTTCTGAAGTAGTAAGAAAGCAGACTAAAG
66 TAGCAAGAGAGCAGGTTAAAGATTTGAGTCTTATCTTCCTGAAGTACCAAGAAAGCAGACTAAAG
* * * **
41621966 ATTGAAGATCTTATCTCCCCT-AAGCAGTAGTGGAGCAGATCGA-AGATGG
131 ACTAAAGATC-TAT-TCCCCTAAAGCAGTAGCGGAGCAGATCGAGA-ATAA
* * * * *
41622015 CGAATCTTATCTCCATGTA-CTAGCAATGGAGCAGATTTTAGCCACTAGCCTTATCTCTCTGAAG
1 CAAATCTTATCTCCATGTATCGAGCAATAGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAAG
*** * * * * *
41622079 TAGCAAGAGAGCAGGTTGGCGATTTTAGTCTTATCTTCCTGAGGTACCAAGGAAGTAGACTGAAG
66 TAGCAAGAGAGCAGGTTAAAGATTTGAGTCTTATCTTCCTGAAGTACCAAGAAAGCAGACTAAAG
* * *
41622144 ACTAAAGATCTATTTCCCTAAAGCAGTTGCGGAGCAGATTGAGAATAA
131 ACTAAAGATCTATTCCCCTAAAGCAGTAGCGGAGCAGATCGAGAATAA
* * *
41622192 CAAATCTTATCTCCATGTATTG-GCAATGGAACAGATTTAAG
1 CAAATCTTATCTCCATGTATCGAGCAATAGAGCAGATTTAAG
41622233 TCACTAGTCC
Statistics
Matches: 180, Mismatches: 33, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
176 7 0.04
177 130 0.72
178 43 0.24
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (178 bp):
CAAATCTTATCTCCATGTATCGAGCAATAGAGCAGATTTAAGCCACAAGCCTTATCTCTCTGAAG
TAGCAAGAGAGCAGGTTAAAGATTTGAGTCTTATCTTCCTGAAGTACCAAGAAAGCAGACTAAAG
ACTAAAGATCTATTCCCCTAAAGCAGTAGCGGAGCAGATCGAGAATAA
Found at i:41626053 original size:11 final size:12
Alignment explanation
Indices: 41626036--41626068 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
41626026 CAAAACTACC
41626036 CAAACCCAATTA
1 CAAACCCAATTA
41626048 -AAACCCAATTA
1 CAAACCCAATTA
41626059 CAAAGCCCAA
1 CAAA-CCCAA
41626069 AACAAATCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 11 0.58
12 3 0.16
13 5 0.26
ACGTcount: A:0.52, C:0.33, G:0.03, T:0.12
Consensus pattern (12 bp):
CAAACCCAATTA
Found at i:41627364 original size:24 final size:26
Alignment explanation
Indices: 41627337--41627387 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
41627327 TATTTTAAAC
41627337 TATTATCCATTTTAAA-T-TTATATA
1 TATTATCCATTTTAAAGTATTATATA
**
41627361 TATTATTTATTTTAAAGTATTATATA
1 TATTATCCATTTTAAAGTATTATATA
41627387 T
1 T
41627388 TATTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 1 0.04
26 8 0.35
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.57
Consensus pattern (26 bp):
TATTATCCATTTTAAAGTATTATATA
Found at i:41627551 original size:26 final size:24
Alignment explanation
Indices: 41627515--41627617 Score: 104
Period size: 26 Copynumber: 4.2 Consensus size: 24
41627505 AAGTATCTTA
41627515 TATATTATTTATTTGAAATTGCTTT
1 TATATTATTTATTTGAAATTG-TTT
*
41627540 GTATATTATTTA-TTGTAATTTGTTT
1 -TATATTATTTATTTG-AAATTGTTT
*
41627565 TACATATTATTTATTTTAAATTGTTT
1 T--ATATTATTTATTTGAAATTGTTT
*
41627591 TATATTATTTACTTCG-AATT-TTT
1 TATATTATTTA-TTTGAAATTGTTT
41627614 TATA
1 TATA
41627618 ACTTATTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.10
24 15 0.22
25 8 0.12
26 35 0.52
27 2 0.03
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (24 bp):
TATATTATTTATTTGAAATTGTTT
Found at i:41627600 original size:24 final size:24
Alignment explanation
Indices: 41627345--41627601 Score: 117
Period size: 26 Copynumber: 10.0 Consensus size: 24
41627335 ACTATTATCC
*
41627345 ATTTTAAATT-TATATATATTATTT
1 ATTTTAAATTGT-TTTATATTATTT
* * *
41627369 ATTTTAAAGTATTATATATTATTT
1 ATTTTAAATTGTTTTATATTATTT
*
41627393 ATTTTGAATTACTT-TTTTATATATCTTTT
1 ATTTT-AA--A-TTGTTTTATAT-T-ATTT
* *
41627422 ATTTTTAAACTGCTTTGTATATTATTC
1 A-TTTTAAATTG-TTT-TATATTATTT
* *
41627449 ATTTTAAATTTCTTTTTACATATTATAT
1 ATTTTAAA-TT-GTTTT--ATATTATTT
* * * * *
41627477 ATCTTAAACTCTTTCATA-T-GTT
1 ATTTTAAATTGTTTTATATTATTT
* * * *
41627499 GTTTAAAAGTATCTTATATATTATTT
1 ATTTTAAA-T-TGTTTTATATTATTT
*
41627525 ATTTGAAATTGCTTTGTATATTATTT
1 ATTTTAAATTG-TTT-TATATTATTT
* *
41627551 ATTGTAATTTGTTTTACATATTATTT
1 ATTTTAAATTGTTTT--ATATTATTT
41627577 ATTTTAAATTGTTTTATATTATTT
1 ATTTTAAATTGTTTTATATTATTT
41627601 A
1 A
41627602 CTTCGAATTT
Statistics
Matches: 177, Mismatches: 33, Indels: 46
0.69 0.13 0.18
Matches are distributed among these distances:
22 6 0.03
23 1 0.01
24 48 0.27
25 10 0.06
26 60 0.34
27 17 0.10
28 20 0.11
29 11 0.06
30 4 0.02
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (24 bp):
ATTTTAAATTGTTTTATATTATTT
Found at i:41629382 original size:28 final size:28
Alignment explanation
Indices: 41629301--41629401 Score: 121
Period size: 28 Copynumber: 3.6 Consensus size: 28
41629291 GTCAAAATCG
* * * *
41629301 TAAAATCTAAAAAATAGAGGCAAAATTG
1 TAAAATCTAAAAAACAGTGGCAAAACTA
* * *
41629329 TAAAATCTGAAAAATAGTGGAAAAACTA
1 TAAAATCTAAAAAACAGTGGCAAAACTA
41629357 TAAAATCTAAAAAACAGTGGCAAAACTA
1 TAAAATCTAAAAAACAGTGGCAAAACTA
* *
41629385 TAAAATATGAAAAACAG
1 TAAAATCTAAAAAACAG
41629402 GGGACACAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.20
Consensus pattern (28 bp):
TAAAATCTAAAAAACAGTGGCAAAACTA
Found at i:41630309 original size:11 final size:12
Alignment explanation
Indices: 41630285--41630336 Score: 63
Period size: 12 Copynumber: 4.3 Consensus size: 12
41630275 TTAGCATGCT
41630285 AATTTTTATCTC
1 AATTTTTATCTC
41630297 AATTTTTAT-TC
1 AATTTTTATCTC
*
41630308 AATTTTT-TTTC
1 AATTTTTATCTC
41630319 ATAATTTTTATCTC
1 --AATTTTTATCTC
41630333 AATT
1 AATT
41630337 CATATTTGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 1 0.03
11 11 0.31
12 13 0.37
13 7 0.20
14 3 0.09
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (12 bp):
AATTTTTATCTC
Found at i:41630839 original size:30 final size:29
Alignment explanation
Indices: 41630805--41630862 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
41630795 ATTTTTAAAA
*
41630805 ATAAAAAATCAT-TAAATTTATTTAAAAATG
1 ATAAAAAAT-ATATAAATAT-TTTAAAAATG
41630835 ATAAAAAATATATAAATATTTTAAAAAT
1 ATAAAAAATATATAAATATTTTAAAAAT
41630863 TAATTAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 15 0.58
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (29 bp):
ATAAAAAATATATAAATATTTTAAAAATG
Found at i:41631768 original size:28 final size:28
Alignment explanation
Indices: 41631728--41631784 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41631718 GGTTGAAATC
*
41631728 ATAGGGGGTGATTTTACATTCCATTTTA
1 ATAGAGGGTGATTTTACATTCCATTTTA
41631756 ATAGAGGGTGATTTTACATTCCATTTTA
1 ATAGAGGGTGATTTTACATTCCATTTTA
41631784 A
1 A
41631785 CATTCTCACA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (28 bp):
ATAGAGGGTGATTTTACATTCCATTTTA
Found at i:41635685 original size:30 final size:31
Alignment explanation
Indices: 41635631--41635691 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
41635621 ATTGATCAAG
* *
41635631 TTCCATATACATGTATCATCCATTT-CATGT
1 TTCCATATACATGTAACATACATTTCCATGT
41635661 TTCCATATACCATGTAACA-ACATTTCCATGT
1 TTCCATATA-CATGTAACATACATTTCCATGT
41635692 AATTCATGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (31 bp):
TTCCATATACATGTAACATACATTTCCATGT
Found at i:41636798 original size:20 final size:20
Alignment explanation
Indices: 41636761--41636798 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41636751 TGATGAGGAG
*
41636761 CAAGAATATCAAGTTGGATT
1 CAAGAATATCAAGCTGGATT
41636781 CAAGAA-ATCGAAGCTGGA
1 CAAGAATATC-AAGCTGGA
41636799 GGAGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
CAAGAATATCAAGCTGGATT
Found at i:41638752 original size:46 final size:46
Alignment explanation
Indices: 41638696--41638923 Score: 278
Period size: 46 Copynumber: 5.0 Consensus size: 46
41638686 AGTGTGCTCT
* *
41638696 CTGATATGAAATGTGTAAGACCGTGGTTGAAAGATACCATGGCAGC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
41638742 CTGGTATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *
41638788 TTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* *** *
41638834 GTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGACAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * * * *
41638880 ATAACA-GAAAATGAGTAAGACCATAGCTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
41638924 TCATGTCAAA
Statistics
Matches: 159, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
45 1 0.01
46 158 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:41639654 original size:21 final size:21
Alignment explanation
Indices: 41639628--41639667 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41639618 ATCTATACAG
41639628 ATAAATTTAACTCAATTTAAT
1 ATAAATTTAACTCAATTTAAT
* *
41639649 ATAAATTTTATTCAATTTA
1 ATAAATTTAACTCAATTTA
41639668 GCCCAAAATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAATTTAACTCAATTTAAT
Found at i:41646264 original size:38 final size:37
Alignment explanation
Indices: 41646205--41646309 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 37
41646195 CATTTTTAAG
**
41646205 AATAT-AAAGAATATATATAAGTATGTATATGATGTA-A
1 AATATGAAA-AATATATATAAGTATGTATAAAAT-TAGA
* * *
41646242 AATATGCATAAATATATGTAAGTATATA-AAAATTATGA
1 AATATG-AAAAATATATATAAGTATGTATAAAATTA-GA
*
41646280 AATATGAAAAATATATTTAAGTATGTATAA
1 AATATGAAAAATATATATAAGTATGTATAA
41646310 GTACGTATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
36 2 0.04
37 26 0.47
38 25 0.45
39 2 0.04
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (37 bp):
AATATGAAAAATATATATAAGTATGTATAAAATTAGA
Found at i:41646652 original size:22 final size:23
Alignment explanation
Indices: 41646596--41646652 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
41646586 AGTTTAAAAT
41646596 AAAATATATAAAAGAAAGTCTTA
1 AAAATATATAAAAGAAAGTCTTA
*
41646619 AATAATA-A-AAAAGACAGT-TTA
1 AA-AATATATAAAAGAAAGTCTTA
41646640 AAAATATATAAAA
1 AAAATATATAAAA
41646653 ATAGTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
20 4 0.13
21 6 0.20
22 13 0.43
23 3 0.10
24 4 0.13
ACGTcount: A:0.65, C:0.04, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAATATATAAAAGAAAGTCTTA
Found at i:41647914 original size:44 final size:44
Alignment explanation
Indices: 41647861--41648378 Score: 172
Period size: 44 Copynumber: 11.8 Consensus size: 44
41647851 CCTTTATTTT
* * * *
41647861 AATCCACTCCACTGTAATCTCAGGCAGATAGGAT-TACTATCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-CTAGCTTC
* *
41647905 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTC
* * * *** *
41647949 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATTTTTTTTTT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATC-----TCTAGCTTC
** * * * * *** *
41647998 GGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGTATAATA
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTC
* * * * * * * * * *
41648042 AACCTAAT-TA-TGCCTAATGATTA-GGATGACATGATATC-A-TTTT
1 AATCTACTCCACTG--TAAT-CTCAGGGA-GATAAGATCTCTAGCTTC
* ** * * *
41648085 GATCCGCTCCACTGTAATCTCAGGCAGATAGGAT-TACTATCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-CTAGCTTC
* ** * *
41648129 AATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGGAATTCTCC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-CTA-GCTTC
** * * *
41648175 GGTCTACTCCACTGTAACCTCAGGGAAATAAGA-C-CT-GATGT-
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCT-TC
* * * *
41648216 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCT-T---TT-
1 AATCTACTCCACTGTAATC-TCAGGGAGATAAGATCTCTAGCTTC
** * * * ** *
41648255 AATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-TACTATATTT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCT-CTAGCTTC
* * *
41648299 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGGCTTC
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTC
* *
41648343 AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCT
1 AATCTACTCCACTGTAATCTCAGGGAGATAAGATCT
41648379 GAATTTTTTT
Statistics
Matches: 345, Mismatches: 99, Indels: 60
0.68 0.20 0.12
Matches are distributed among these distances:
38 1 0.00
39 25 0.07
40 4 0.01
41 28 0.08
42 12 0.03
43 14 0.04
44 182 0.53
45 15 0.04
46 32 0.09
49 32 0.09
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (44 bp):
AATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAGCTTC
Found at i:41658526 original size:71 final size:71
Alignment explanation
Indices: 41658434--41658572 Score: 201
Period size: 71 Copynumber: 2.0 Consensus size: 71
41658424 CTGACAGCAG
* * *
41658434 CAGTGATGTAGATTTGGAAAATCACTAAAAATAGTAGGAATGGAATTAAATAG-TGAATAAATTA
1 CAGTGACGTAGATTTGAAAAATCACTAAAAATAGTAGGAATGGAA-TAAATAGACGAATAAATTA
41658498 TGTAAAC
65 TGTAAAC
* *
41658505 CAGTGACGTGAGA-TTGAAAAATCACTAAAAATAGTAGGAGTGGAATAAATTGACGAATAAATTA
1 CAGTGACGT-AGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATAAATAGACGAATAAATTA
41658569 TGTA
65 TGTA
41658573 TTCGAAGCTC
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
70 6 0.10
71 52 0.85
72 3 0.05
ACGTcount: A:0.46, C:0.06, G:0.21, T:0.27
Consensus pattern (71 bp):
CAGTGACGTAGATTTGAAAAATCACTAAAAATAGTAGGAATGGAATAAATAGACGAATAAATTAT
GTAAAC
Found at i:41660650 original size:5 final size:5
Alignment explanation
Indices: 41660640--41660671 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
41660630 TTGTGTGTTC
41660640 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41660672 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:41660654 original size:9 final size:9
Alignment explanation
Indices: 41660640--41660670 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
41660630 TTGTGTGTTC
41660640 TTTATTTTA
1 TTTATTTTA
41660649 TTTATTTTA
1 TTTATTTTA
41660658 TTTTATTTTA
1 -TTTATTTTA
41660668 TTT
1 TTT
41660671 TTCACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:41665102 original size:5 final size:5
Alignment explanation
Indices: 41665092--41665123 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
41665082 TTGTGTGTTC
41665092 TTTAT TTTA- TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
41665124 TCACACCCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:41665106 original size:9 final size:9
Alignment explanation
Indices: 41665092--41665122 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
41665082 TTGTGTGTTC
41665092 TTTATTTTA
1 TTTATTTTA
41665101 TTTATTTTA
1 TTTATTTTA
41665110 TTTTATTTTA
1 -TTTATTTTA
41665120 TTT
1 TTT
41665123 TTCACACCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:41666127 original size:22 final size:22
Alignment explanation
Indices: 41666092--41666146 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 22
41666082 ACTTGTGTTT
41666092 ATTATGATTATTGATATG-ATGAG
1 ATTAT-ATT-TTGATATGTATGAG
*
41666115 ATTGATATTTTGATATGTATGTG
1 ATT-ATATTTTGATATGTATGAG
41666138 ATTATATTT
1 ATTATATTT
41666147 GTGTTGATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 14 0.48
23 13 0.45
24 2 0.07
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (22 bp):
ATTATATTTTGATATGTATGAG
Found at i:41666677 original size:18 final size:18
Alignment explanation
Indices: 41666654--41666691 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
41666644 GAGTTTCCTA
41666654 AAGATAAACAAA-TGAAAC
1 AAGATAAA-AAATTGAAAC
41666672 AAGATAAAAAATTGAAAC
1 AAGATAAAAAATTGAAAC
41666690 AA
1 AA
41666692 AATCTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.68, C:0.08, G:0.11, T:0.13
Consensus pattern (18 bp):
AAGATAAAAAATTGAAAC
Found at i:41668384 original size:27 final size:27
Alignment explanation
Indices: 41668353--41668530 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
41668343 TAAATTGTAC
41668353 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41668380 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41668406 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
41668434 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41668462 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41668489 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41668516 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41668531 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41668467 original size:82 final size:81
Alignment explanation
Indices: 41668354--41668509 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
41668344 AAATTGTACA
* *
41668354 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
41668418 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
41668435 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
41668500 TGCGAGTTGA
65 TGCGAATTGA
41668510 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:41668521 original size:82 final size:81
Alignment explanation
Indices: 41668350--41668530 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
41668340 GATTAAATTG
* *
41668350 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
41668415 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
41668431 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
41668495 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
41668513 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
41668531 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:41683652 original size:43 final size:43
Alignment explanation
Indices: 41683599--41683684 Score: 136
Period size: 43 Copynumber: 2.0 Consensus size: 43
41683589 GATATATGTG
* * *
41683599 GCATCCGAGCTCGTTGATTGGTTCGAGTTCATTATGGACGCGA
1 GCATCCGAGCTCGTTGAGTGGTTCAAGTTCATAATGGACGCGA
*
41683642 GCATCCGAGCTCGTTGAGTGGTTCAAGTTCATAATGGATGCGA
1 GCATCCGAGCTCGTTGAGTGGTTCAAGTTCATAATGGACGCGA
41683685 TACATGTGAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (43 bp):
GCATCCGAGCTCGTTGAGTGGTTCAAGTTCATAATGGACGCGA
Found at i:41689978 original size:43 final size:43
Alignment explanation
Indices: 41689879--41689979 Score: 98
Period size: 43 Copynumber: 2.3 Consensus size: 43
41689869 CTAGTATAAT
*
41689879 CACACATATCATACAATGCCAACGTCCCAGACGTGGTCTTACATG
1 CACACATAT-AT-CGATGCCAACGTCCCAGACGTGGTCTTACATG
* ** * *
41689924 TAGTCACATATCGATGCC-ACTGTCCCAGACAG-GGTCTTACTTG
1 CACACATATATCGATGCCAAC-GTCCCAGAC-GTGGTCTTACATG
41689967 CACACATATATCG
1 CACACATATATCG
41689980 GAGTCACATA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
42 2 0.05
43 34 0.77
44 3 0.07
45 5 0.11
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.25
Consensus pattern (43 bp):
CACACATATATCGATGCCAACGTCCCAGACGTGGTCTTACATG
Found at i:41697790 original size:31 final size:31
Alignment explanation
Indices: 41697728--41697790 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
41697718 GGAGATGGAA
* *
41697728 AAAGTTAAAGAATGGAAGAAGAAGAAAGCTT
1 AAAGTTAAAGAACGGAAGAAGAAAAAAGCTT
*
41697759 AAAGTTGAAGAACGGAAGAA-AAAAAAGGCTT
1 AAAGTTAAAGAACGGAAGAAGAAAAAA-GCTT
41697790 A
1 A
41697791 TCTGGATGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 5 0.18
31 23 0.82
ACGTcount: A:0.56, C:0.05, G:0.25, T:0.14
Consensus pattern (31 bp):
AAAGTTAAAGAACGGAAGAAGAAAAAAGCTT
Found at i:41698351 original size:46 final size:46
Alignment explanation
Indices: 41698207--41698422 Score: 215
Period size: 46 Copynumber: 4.6 Consensus size: 46
41698197 TTTGTGGGCT
* * *
41698207 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGAGAGCC
* * * * *
41698253 AGTGTAAGACCATGTCTGGGACACGGCATCAGCAAT-GAGACAAGAGCT
1 AGTGTAAGA-CATGTCTGGGACA-TGCATCGGC-CTCGAGACGAGAGCC
41698301 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AGAGCC
* * *
41698347 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGAGAGCC
* *
41698393 AGTGTAAGACCATATCTGAGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
41698423 AAGCCAGTGT
Statistics
Matches: 143, Mismatches: 17, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
45 4 0.03
46 72 0.50
47 39 0.27
48 27 0.19
49 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAGAGCC
Found at i:41704055 original size:21 final size:20
Alignment explanation
Indices: 41704031--41704069 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41704021 GTGTAAATGT
41704031 AGTAACATAATTGTTATTTTA
1 AGTAACATAA-TGTTATTTTA
**
41704052 AGTAATTTAATGTTATTT
1 AGTAACATAATGTTATTT
41704070 ATATGATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.51
Consensus pattern (20 bp):
AGTAACATAATGTTATTTTA
Found at i:41705901 original size:215 final size:216
Alignment explanation
Indices: 41705524--41705937 Score: 695
Period size: 215 Copynumber: 1.9 Consensus size: 216
41705514 CAAAATTCTG
* *
41705524 AAAAAGAATTAGTAAATAGATATATGAGTCTAGTTTTAGGGAAAATTTACAGATTTAAATTTTGA
1 AAAAAGAATTAGTAAATAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGATTTAAATTTCGA
* * **
41705589 GTTTCATAACTCGAGATATGAATTTTTTTAGTGACTGTGACGTAGATGGGCAGTTTATTATGAAA
66 GTTTCATAACTCGAGATATGAATTTTTTTAGCGACTGTGACGCAGATGGGCAGTTTATTACCAAA
* * * *
41705654 GGTAAAATAAATTTTTTGAAATTGTTTAAGTGATAATTTAAGTCTGTTAATGCTTCGTACTCGAC
131 GGTAAAATAAATTGTCTGAAATTGTTTAAGTGATAATTTAAGTCTGTTAACGCCTCGTACTCGAC
41705719 TCCGGTGATTGTCTAGTCATT
196 TCCGGTGATTGTCTAGTCATT
* *
41705740 AAAAA-AATTAGTAAATATATATATGAGTCTAGTTTCAGGGAAAATTTACAGATTTGAATTTCGA
1 AAAAAGAATTAGTAAATAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGATTTAAATTTCGA
* *
41705804 GTTTCGTAACTCGAGATATGAATTTTTTTAGCGACTGTGACGCATATGGGCAGTTTATTACCAAA
66 GTTTCATAACTCGAGATATGAATTTTTTTAGCGACTGTGACGCAGATGGGCAGTTTATTACCAAA
41705869 GGTAAAATAAATTGTCTGAAATTGTTTAAGTGATAATTTAAGTCTGTTAACGCCTCGTACTCGAC
131 GGTAAAATAAATTGTCTGAAATTGTTTAAGTGATAATTTAAGTCTGTTAACGCCTCGTACTCGAC
41705934 TCCG
196 TCCG
41705938 TCGATGGTCT
Statistics
Matches: 184, Mismatches: 14, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
215 179 0.97
216 5 0.03
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (216 bp):
AAAAAGAATTAGTAAATAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGATTTAAATTTCGA
GTTTCATAACTCGAGATATGAATTTTTTTAGCGACTGTGACGCAGATGGGCAGTTTATTACCAAA
GGTAAAATAAATTGTCTGAAATTGTTTAAGTGATAATTTAAGTCTGTTAACGCCTCGTACTCGAC
TCCGGTGATTGTCTAGTCATT
Found at i:41715750 original size:35 final size:34
Alignment explanation
Indices: 41715704--41715773 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 34
41715694 TATTCTCCTC
41715704 ATTCCTGCTATCAATCTCATCAAAATAAGGTTTT
1 ATTCCTGCTATCAATCTCATCAAAATAAGGTTTT
41715738 NATTCCTGCTATCAATCTCATCAAAATAAGGTTTT
1 -ATTCCTGCTATCAATCTCATCAAAATAAGGTTTT
41715773 A
1 A
41715774 ATCGGGTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 1 0.03
35 34 0.97
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.37
Consensus pattern (34 bp):
ATTCCTGCTATCAATCTCATCAAAATAAGGTTTT
Found at i:41721800 original size:43 final size:43
Alignment explanation
Indices: 41721752--41721837 Score: 154
Period size: 43 Copynumber: 2.0 Consensus size: 43
41721742 GGAAATTCAT
* *
41721752 AAAAAGGTGAAATTTGCTATAAAACAGTATCATACAGCAGGAA
1 AAAAAGGTGAAATTTGCTAAAAAACAATATCATACAGCAGGAA
41721795 AAAAAGGTGAAATTTGCTAAAAAACAATATCATACAGCAGGAA
1 AAAAAGGTGAAATTTGCTAAAAAACAATATCATACAGCAGGAA
41721838 TGATGTGAGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.51, C:0.12, G:0.17, T:0.20
Consensus pattern (43 bp):
AAAAAGGTGAAATTTGCTAAAAAACAATATCATACAGCAGGAA
Found at i:41724879 original size:35 final size:35
Alignment explanation
Indices: 41724833--41724899 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
41724823 TTATGAGAGC
41724833 CAGTGTAAGACCATGTCTGGGACATGGCATCGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGAGT
*
41724868 CAGTGTAAGACCATGTTTGGGACATGGCATCG
1 CAGTGTAAGACCATGTCTGGGACATGGCATCG
41724900 GTACCTTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.24
Consensus pattern (35 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGAGT
Found at i:41728871 original size:15 final size:15
Alignment explanation
Indices: 41728851--41728884 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41728841 TTCTTTGCGC
41728851 TTCTGGTCGATAAAT
1 TTCTGGTCGATAAAT
* *
41728866 TTCTGGTTGATATAT
1 TTCTGGTCGATAAAT
41728881 TTCT
1 TTCT
41728885 TACAGAACTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.50
Consensus pattern (15 bp):
TTCTGGTCGATAAAT
Found at i:41734530 original size:26 final size:29
Alignment explanation
Indices: 41734485--41734541 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
41734475 AAAGATTGTT
*
41734485 AAAACTCTTCTAAAAGAAAACT-TAAGAG
1 AAAACTCTTCTAAAAGAAAACTCAAAGAG
41734513 AAAA-TCTTC-AAAAGAAAACTCAAAGAG
1 AAAACTCTTCTAAAAGAAAACTCAAAGAG
41734540 AA
1 AA
41734542 TTTTATTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 11 0.41
27 12 0.44
28 4 0.15
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.18
Consensus pattern (29 bp):
AAAACTCTTCTAAAAGAAAACTCAAAGAG
Found at i:41735343 original size:16 final size:17
Alignment explanation
Indices: 41735297--41735344 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
41735287 TTATTCATAC
*
41735297 TTTAATGTCACTTCACTAG
1 TTTAATGT-ACTT-ATTAG
41735316 TTTAAT-TACTTATTA-
1 TTTAATGTACTTATTAG
41735331 TTTAATGTACTTAT
1 TTTAATGTACTTAT
41735345 CACACATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 6 0.22
16 10 0.37
17 4 0.15
18 1 0.04
19 6 0.22
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (17 bp):
TTTAATGTACTTATTAG
Found at i:41741132 original size:21 final size:22
Alignment explanation
Indices: 41741082--41741139 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
41741072 GGGAAAAAAC
* *
41741082 ACATGTTAAAATGTCATTTTTAT
1 ACAT-TTAAAATTTAATTTTTAT
41741105 ACATTTAAAATTTAATTTTTAT
1 ACATTTAAAATTTAATTTTTAT
*
41741127 A-TTTTAAAATTTA
1 ACATTTAAAATTTA
41741140 TTAATATGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 11 0.34
22 17 0.53
23 4 0.12
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (22 bp):
ACATTTAAAATTTAATTTTTAT
Found at i:41747322 original size:29 final size:29
Alignment explanation
Indices: 41747288--41747346 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
41747278 GGAATAAAAT
41747288 AGGAAAGAGAGACATGTCACTAGGAACCC
1 AGGAAAGAGAGACATGTCACTAGGAACCC
*
41747317 AGGAAAGAGTGACATGTCACTAGGAACCC
1 AGGAAAGAGAGACATGTCACTAGGAACCC
41747346 A
1 A
41747347 TGTGTTTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.20, G:0.27, T:0.12
Consensus pattern (29 bp):
AGGAAAGAGAGACATGTCACTAGGAACCC
Found at i:41754996 original size:40 final size:40
Alignment explanation
Indices: 41754949--41755024 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
41754939 CAGCTAAGAA
***
41754949 TGGCACTTAGTGTGTGGTTTGAAATAGCTTCGGCTAAATG
1 TGGCACTTAGTGTGCAATTTGAAATAGCTTCGGCTAAATG
* *
41754989 TGGCACTTGGTGTGCAATTTGAGATAGCTTCGGCTA
1 TGGCACTTAGTGTGCAATTTGAAATAGCTTCGGCTA
41755025 TATATATATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.21, C:0.14, G:0.30, T:0.34
Consensus pattern (40 bp):
TGGCACTTAGTGTGCAATTTGAAATAGCTTCGGCTAAATG
Found at i:41755108 original size:28 final size:28
Alignment explanation
Indices: 41755039--41755109 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
41755029 TATATGTGGC
* *
41755039 ACTTAGTGTGCGAAATATTGAGAATGAC
1 ACTTAGTGTGCGAGATATTGAGAATGAA
* * *
41755067 ACTTGGTGTACGAGATATTGAGTATGAA
1 ACTTAGTGTGCGAGATATTGAGAATGAA
41755095 ACTTAGTGTGCGAGA
1 ACTTAGTGTGCGAGA
41755110 CATCGAAGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.10, G:0.28, T:0.30
Consensus pattern (28 bp):
ACTTAGTGTGCGAGATATTGAGAATGAA
Found at i:41764516 original size:56 final size:53
Alignment explanation
Indices: 41764430--41764576 Score: 143
Period size: 56 Copynumber: 2.6 Consensus size: 53
41764420 AACTTAGGAA
* * *
41764430 TAGGTTCCGGAGCTTATGCAGCCTCGTTGAGAGGCAT-GTAATTATGTGGTACACGC
1 TAGG-TCCGGAGCTTATGTAGCCCCGTTGAGAGGCATGGT-A--ATGTGATACACGC
* * *
41764486 TAGGTCCAGGAGCTTATGTAGCCCCGTTGAGAGGCGTGGTAATGTGATGCATGC
1 TAGGTCC-GGAGCTTATGTAGCCCCGTTGAGAGGCATGGTAATGTGATACACGC
* *
41764540 TAGGTCCGGGTGCTCATATGTAGCCCTGTTGAGAGGC
1 TAGGTCC-GGAGCT--TATGTAGCCCCGTTGAGAGGC
41764577 GTGCTATGTC
Statistics
Matches: 78, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
54 22 0.28
55 3 0.04
56 51 0.65
57 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.27
Consensus pattern (53 bp):
TAGGTCCGGAGCTTATGTAGCCCCGTTGAGAGGCATGGTAATGTGATACACGC
Found at i:41780577 original size:28 final size:28
Alignment explanation
Indices: 41780537--41780652 Score: 133
Period size: 28 Copynumber: 4.1 Consensus size: 28
41780527 CTTCAGCTAT
* *
41780537 GTATGGCACTTAGTGTATGAGATATCGA
1 GTATGACACTTAGTGTACGAGATATCGA
* **
41780565 GTATGGCACTTAGTGTGGGAGATATCGA
1 GTATGACACTTAGTGTACGAGATATCGA
* * *
41780593 CTATGAAACTTCGTGTACGAGATATCGA
1 GTATGACACTTAGTGTACGAGATATCGA
* * *
41780621 GTATGACATTTAGTGTGCGAGATATTGA
1 GTATGACACTTAGTGTACGAGATATCGA
41780649 GTAT
1 GTAT
41780653 TCAACTGCAT
Statistics
Matches: 74, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 74 1.00
ACGTcount: A:0.28, C:0.11, G:0.28, T:0.32
Consensus pattern (28 bp):
GTATGACACTTAGTGTACGAGATATCGA
Found at i:41780764 original size:57 final size:57
Alignment explanation
Indices: 41780676--41780788 Score: 217
Period size: 57 Copynumber: 2.0 Consensus size: 57
41780666 GTGTATGTAA
*
41780676 GAACTCTTTATGGATTGGTACAATTATGTACATGTATATTATGAGCTTAAAATCTAT
1 GAACTCTTTATGGATTGGTACAAGTATGTACATGTATATTATGAGCTTAAAATCTAT
41780733 GAACTCTTTATGGATTGGTACAAGTATGTACATGTATATTATGAGCTTAAAATCTA
1 GAACTCTTTATGGATTGGTACAAGTATGTACATGTATATTATGAGCTTAAAATCTA
41780789 AAAAGATACA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.39
Consensus pattern (57 bp):
GAACTCTTTATGGATTGGTACAAGTATGTACATGTATATTATGAGCTTAAAATCTAT
Found at i:41784042 original size:34 final size:34
Alignment explanation
Indices: 41783999--41784066 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41783989 ACACTACATG
41783999 GTCCTGAAGGTAAGCGAGGTAAGGAAATTTTAGA
1 GTCCTGAAGGTAAGCGAGGTAAGGAAATTTTAGA
41784033 GTCCTGAAGGTAAGCGAGGTAAGGAAATTTTAGA
1 GTCCTGAAGGTAAGCGAGGTAAGGAAATTTTAGA
41784067 AATCGAGTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (34 bp):
GTCCTGAAGGTAAGCGAGGTAAGGAAATTTTAGA
Found at i:41784493 original size:32 final size:32
Alignment explanation
Indices: 41784448--41784510 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
41784438 AAATCGACCC
41784448 TTATTCTTCTGCTTATCAAGGTAAGATGCTTA
1 TTATTCTTCTGCTTATCAAGGTAAGATGCTTA
*
41784480 TTATTCTTTTGCTTATCAAGGTAAGATGCTT
1 TTATTCTTCTGCTTATCAAGGTAAGATGCTT
41784511 GAAACCTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (32 bp):
TTATTCTTCTGCTTATCAAGGTAAGATGCTTA
Found at i:41804801 original size:10 final size:10
Alignment explanation
Indices: 41804786--41804814 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
41804776 GTGTGATAGG
41804786 ATCTCCAACA
1 ATCTCCAACA
41804796 ATCTCCAACA
1 ATCTCCAACA
41804806 ATCTCCAAC
1 ATCTCCAAC
41804815 TCGAGCTAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (10 bp):
ATCTCCAACA
Found at i:41805657 original size:42 final size:42
Alignment explanation
Indices: 41805558--41805750 Score: 287
Period size: 42 Copynumber: 4.6 Consensus size: 42
41805548 TACCAATTAC
* * *
41805558 ATATCCCAGATATGGTCTTACATGAAATCTCGTATCGATGCCA
1 ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATG-CA
* * *
41805601 ATAGCCCAGCTATGGTCTTACACGAAGTCTCATATCAATGCA
1 ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGCA
* **
41805643 ATATCCCAGTTATGGTCTTACACGAAGTCTCATATCGATGTT
1 ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGCA
*
41805685 ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGCC
1 ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGCA
41805727 ATATCCCAGATATGGTCTTACACG
1 ATATCCCAGATATGGTCTTACACG
41805751 TAACCTTAGT
Statistics
Matches: 136, Mismatches: 14, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
42 102 0.75
43 34 0.25
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
ATATCCCAGATATGGTCTTACACGAAGTCTCATATCGATGCA
Found at i:41808672 original size:13 final size:14
Alignment explanation
Indices: 41808639--41808676 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
41808629 TAACAATGTT
41808639 TAAAGAAAGAGATA
1 TAAAGAAAGAGATA
41808653 TAAAGAATAGAG-TA
1 TAAAGAA-AGAGATA
41808667 -AAAGAAAGAG
1 TAAAGAAAGAG
41808677 GTGCTCATGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 9 0.39
15 4 0.17
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (14 bp):
TAAAGAAAGAGATA
Found at i:41813282 original size:61 final size:60
Alignment explanation
Indices: 41813171--41813296 Score: 139
Period size: 61 Copynumber: 2.1 Consensus size: 60
41813161 CTTAAATATA
** * *
41813171 TAAAAAATTAATAAATTTAGCCCTCAATGTTTACAAAAATTATCATTTTAGTTCTAA-TT
1 TAAAAAATTAATAAATTTAGCCCTCAACATTTACAAAAATTATCAATTTAGTCCTAACTT
* * * *
41813230 CTAAAAACATTAATAAATTTGGCTCTCAACATTTAC-AGAATCTATTAATTTAGTCCTAACTT
1 -TAAAAA-ATTAATAAATTTAGCCCTCAACATTTACAAAAAT-TATCAATTTAGTCCTAACTT
41813292 TAAAA
1 TAAAA
41813297 TTTTAAAAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
60 10 0.18
61 43 0.78
62 2 0.04
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (60 bp):
TAAAAAATTAATAAATTTAGCCCTCAACATTTACAAAAATTATCAATTTAGTCCTAACTT
Found at i:41820330 original size:48 final size:47
Alignment explanation
Indices: 41820274--41820685 Score: 425
Period size: 48 Copynumber: 8.7 Consensus size: 47
41820264 CATGCGTGCT
* * *
41820274 AGTGTAAGACCATGTCTGGAACATGGCATCAGCCACATTATCAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GCCACATTATGAGAGCC
* * * * * * *
41820322 AGTGTAAGACCATGTTTGGAACATAGCATCGGCA-TTGATATGTGCGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGCCACAT--TATGAGAGCC
* *
41820370 AGTGTAAGACCATGTCTGGGACATGGCAT--CCATATTATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATCGCCACATTATGAGAGCC
41820415 AGTGTAAGACCATGTTTGGGACATGGCATCAGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GCCACATTATGAGAGCC
* * ** * ** * *
41820463 AGTGTAAGACCATGTCTGGGACATGGCATTGGTATTAAGACGAGAGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGCCA-CATTATGAGAGCC
* *
41820511 AGTATAAGACCGTGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GCCACATTATGAGAGCC
* * * * * * * * *
41820559 AATATAAGACCATGTTTGGAACATGGCATCGGCATTAATATGTGCGCT
1 AGTGTAAGACCATGTTTGGGACATGGCATCGCCA-CATTATGAGAGCC
*
41820607 AGTGTAAGACCAAGTTTGGGACATGGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACCATGTTTGGGACATGGCATC-GCCACATTATGAGAGCC
*
41820655 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTTTGGGACATGGCATCG
41820686 ACAAATTCAC
Statistics
Matches: 295, Mismatches: 59, Indels: 21
0.79 0.16 0.06
Matches are distributed among these distances:
45 35 0.12
46 3 0.01
47 10 0.03
48 242 0.82
49 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (47 bp):
AGTGTAAGACCATGTTTGGGACATGGCATCGCCACATTATGAGAGCC
Found at i:41820546 original size:96 final size:95
Alignment explanation
Indices: 41820274--41820685 Score: 476
Period size: 96 Copynumber: 4.3 Consensus size: 95
41820264 CATGCGTGCT
* ** * *
41820274 AGTGTAAGACCATGTCTGGAACATGGCATCAGCCACATT--ATCAGAGCCAGTGTAAGACCATGT
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G--GTATTAAATGAGAGCTAGTGTAAGACCATGT
* * * * * *
41820337 TTGGAACATAGCATCGG-CA-TTGATATGTGCGCT
63 TTGGGACATGGCATCGGCCACAT--TATGAGAGCC
** *
41820370 AGTGTAAGACCATGTCTGGGACATGGCATCCATATT--ATGAGAGCCAGTGTAAGACCATGTTTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTATTAAATGAGAGCTAGTGTAAGACCATGTTTG
*
41820433 GGACATGGCATCAGCCACATTATGAGAGCC
66 GGACATGGCATCGGCCACATTATGAGAGCC
* * * *
41820463 AGTGTAAGACCATGTCTGGGACATGGCATTGGTATTAAGACGAGAGCTAGTATAAGACCGTGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTATTAA-ATGAGAGCTAGTGTAAGACCATGTTT
41820528 GGGACATGGCATCGGCCACATTATGAGAGCC
65 GGGACATGGCATCGGCCACATTATGAGAGCC
* * * * * * * *
41820559 AATATAAGACCATGTTTGGAACATGGCATCGGCATTAATATGTGCGCTAGTGTAAGACCAAGTTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGTATTAA-ATGAGAGCTAGTGTAAGACCATGTTT
41820624 GGGACATGGCATCGGCCACATTATGAGAGCC
65 GGGACATGGCATCGGCCACATTATGAGAGCC
41820655 AGTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
41820686 ACAAATTCAC
Statistics
Matches: 275, Mismatches: 36, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
93 81 0.29
94 2 0.01
95 1 0.00
96 191 0.69
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.24
Consensus pattern (95 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGTATTAAATGAGAGCTAGTGTAAGACCATGTTTG
GGACATGGCATCGGCCACATTATGAGAGCC
Found at i:41821897 original size:21 final size:20
Alignment explanation
Indices: 41821871--41821910 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
41821861 GTTAAAAAGA
*
41821871 CACACGGGCGTGTGACCCTTC
1 CACACGGGCATGTG-CCCTTC
41821892 CACACGGGCATGTGCCCTT
1 CACACGGGCATGTGCCCTT
41821911 GTCTACTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.15, C:0.38, G:0.28, T:0.20
Consensus pattern (20 bp):
CACACGGGCATGTGCCCTTC
Done.