Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008541.1 Hibiscus syriacus cultivar Beakdansim tig00111430_pilon, whole genome shotgun sequence
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: 269401
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1018 original size:10 final size:9
Alignment explanation
Indices: 1003--1048 Score: 51
Period size: 10 Copynumber: 5.0 Consensus size: 9
993 TGTTAAACTG
1003 TAAAATGAAA
1 TAAAAT-AAA
1013 TAAAATGAAA
1 TAAAAT-AAA
1023 T--AATAAA
1 TAAAATAAA
1030 TATAAATAAA
1 TA-AAATAAA
1040 TAAAATAAA
1 TAAAATAAA
1049 AAGAAAATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 4 0.12
8 3 0.09
9 7 0.21
10 19 0.58
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (9 bp):
TAAAATAAA
Found at i:1029 original size:13 final size:13
Alignment explanation
Indices: 1005--1048 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
995 TTAAACTGTA
1005 AAATGAAATAAAAT
1 AAAT-AAATAAAAT
1019 GAAAT-AATAAATAT
1 -AAATAAATAAA-AT
1033 AAATAAATAAAAT
1 AAATAAATAAAAT
1046 AAA
1 AAA
1049 AAGAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 15 0.56
14 8 0.30
15 4 0.15
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:1915 original size:5 final size:5
Alignment explanation
Indices: 1905--2143 Score: 124
Period size: 5 Copynumber: 46.6 Consensus size: 5
1895 ATAAATAAAA
1905 ATAAT ATAAT ATATAT ATAAT ATAAT ACTAAT AT-AT A-ATAT ATAACT
1 ATAAT ATAAT ATA-AT ATAAT ATAAT A-TAAT ATAAT ATA-AT ATAA-T
*
1952 ATATAT ATTAT ATATAT AATAAT ATAACT ATATTAT ATAA- ATAAT A-AAT
1 ATA-AT ATAAT ATA-AT -ATAAT ATAA-T ATA--AT ATAAT ATAAT ATAAT
* * *
2001 AT-AT ATAAT AT-AT A-AAT ATAAT ATAAT ATTAT ATTAT ATAAT ATATAA
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT
* * * *
2049 ATAGA- ATAGT ATAAT AT-AT AATACT ATAAT ATAA- AGACT AT-AT AATAAT
1 ATA-AT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT
** * *
2098 AGCAT ATACTAT ATAA- ATACT ATAAT ATACAAT ATAAA ATAAT ATA
1 ATAAT ATA--AT ATAAT ATAAT ATAAT AT--AAT ATAAT ATAAT ATA
2144 GAATATAGCA
Statistics
Matches: 183, Mismatches: 22, Indels: 58
0.70 0.08 0.22
Matches are distributed among these distances:
4 29 0.16
5 101 0.55
6 34 0.19
7 18 0.10
8 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:1920 original size:2 final size:2
Alignment explanation
Indices: 1908--2081 Score: 104
Period size: 2 Copynumber: 95.5 Consensus size: 2
1898 AATAAAAATA
1908 AT AT A- AT AT AT AT AT A- AT AT A- AT ACT A- AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
1946 AT A- ACT AT AT AT AT -T AT AT AT AT A- AT A- AT AT A- ACT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
1985 -T AT AT AA AT A- AT AA AT AT AT AT A- AT AT AT AA AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
2023 AT A- AT AT -T AT AT -T AT AT A- AT AT AT AA AT AG A- AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
2061 A- AT AT AT A- AT ACT AT A- AT AT A
1 AT AT AT AT AT AT A-T AT AT AT AT A
2082 AAGACTATAT
Statistics
Matches: 136, Mismatches: 9, Indels: 54
0.68 0.05 0.27
Matches are distributed among these distances:
1 22 0.16
2 106 0.78
3 8 0.06
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (2 bp):
AT
Found at i:2080 original size:13 final size:12
Alignment explanation
Indices: 1908--2150 Score: 143
Period size: 13 Copynumber: 19.8 Consensus size: 12
1898 AATAAAAATA
1908 ATATAATAT-AT
1 ATATAATATAAT
1919 ATATAATATAAT
1 ATATAATATAAT
1931 ACTA-ATATATAAT
1 A-TATA-ATATAAT
1944 ATATAACTATATAT
1 ATATAA-TATA-AT
1958 ATTATATATATAAT
1 A-TATA-ATATAAT
*
1972 AATATAACTATATT
1 -ATATAA-TATAAT
1986 ATATAA-ATAAT
1 ATATAATATAAT
*
1997 AAATATATATAAT
1 ATATA-ATATAAT
2010 ATATAA-AT-AT
1 ATATAATATAAT
2020 AATATAATAT--T
1 -ATATAATATAAT
*
2031 ATATTATATAAT
1 ATATAATATAAT
*
2043 ATATAAATAGAAT
1 ATAT-AATATAAT
2056 AGTATAATAT-AT
1 A-TATAATATAAT
*
2068 A-ATACTATAAT
1 ATATAATATAAT
*
2079 ATA-AAGACT-AT
1 ATATAATA-TAAT
**
2090 ATAATAATAGCAT
1 AT-ATAATATAAT
2103 ATACT-ATATAAAT
1 ATA-TAATAT-AAT
2116 ACTATAATATACA-
1 A-TATAATATA-AT
*
2129 ATATAAAATAAT
1 ATATAATATAAT
*
2141 ATAGAATATA
1 ATATAATATA
2151 GCATATATTA
Statistics
Matches: 184, Mismatches: 18, Indels: 59
0.70 0.07 0.23
Matches are distributed among these distances:
10 16 0.09
11 36 0.20
12 42 0.23
13 56 0.30
14 24 0.13
15 9 0.05
16 1 0.01
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:2151 original size:7 final size:7
Alignment explanation
Indices: 1908--2143 Score: 166
Period size: 7 Copynumber: 32.7 Consensus size: 7
1898 AATAAAAATA
1908 ATATAAT
1 ATATAAT
1915 ATATATAT
1 ATATA-AT
1923 AATATAAT
1 -ATATAAT
*
1931 A-CTAAT
1 ATATAAT
1937 ATATAAT
1 ATATAAT
1944 ATATAACT
1 ATATAA-T
1952 ATAT-AT
1 ATATAAT
1958 AT-TATAT
1 ATATA-AT
1965 ATATAAT
1 ATATAAT
1972 AATATAACT
1 -ATATAA-T
*
1981 ATATTAT
1 ATATAAT
1988 ATA-AAT
1 ATATAAT
*
1994 AATAAATAT
1 -ATATA-AT
2003 ATATAAT
1 ATATAAT
2010 ATATAA-
1 ATATAAT
2016 ATAT-A-
1 ATATAAT
2021 ATATAAT
1 ATATAAT
*
2028 ATTATATT
1 A-TATAAT
2036 ATATAAT
1 ATATAAT
2043 ATATAA-
1 ATATAAT
*
2049 ATAGAAT
1 ATATAAT
2056 AGTATAAT
1 A-TATAAT
2064 ATATAAT
1 ATATAAT
2071 ACTATAAT
1 A-TATAAT
*
2079 ATAAAGACT
1 ATATA-A-T
2088 ATATAAT
1 ATATAAT
**
2095 A-ATAGC
1 ATATAAT
*
2101 ATATACT
1 ATATAAT
2108 ATATAAAT
1 ATAT-AAT
2116 ACTATAAT
1 A-TATAAT
*
2124 ATACAAT
1 ATATAAT
*
2131 ATAAAAT
1 ATATAAT
2138 AATATA
1 -ATATA
2144 GAATATAGCA
Statistics
Matches: 186, Mismatches: 19, Indels: 47
0.74 0.08 0.19
Matches are distributed among these distances:
5 6 0.03
6 24 0.13
7 81 0.44
8 59 0.32
9 16 0.09
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (7 bp):
ATATAAT
Found at i:3120 original size:23 final size:22
Alignment explanation
Indices: 3094--3166 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
3084 AACATGCCAC
3094 AAAGGCAGAGATAAATGTGTCGT
1 AAAGGCAGAGATAAAT-TGTCGT
* * **
3117 AAAGGCAAAGA-ACA-TGTCAC
1 AAAGGCAGAGATAAATTGTCGT
*
3137 AAAGACAGAGATAAATATGTCGT
1 AAAGGCAGAGATAAAT-TGTCGT
3160 AAAGGCA
1 AAAGGCA
3167 AAGAATATGT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
20 13 0.35
21 2 0.05
22 2 0.05
23 20 0.54
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.16
Consensus pattern (22 bp):
AAAGGCAGAGATAAATTGTCGT
Found at i:3138 original size:43 final size:43
Alignment explanation
Indices: 3084--3186 Score: 170
Period size: 43 Copynumber: 2.4 Consensus size: 43
3074 GGTAGAGAAA
* * *
3084 AACATGCCACAAAGGCAGAGATAAATGTGTCGTAAAGGCAAAG
1 AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
3127 AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
1 AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
*
3170 AATATGTCACAAAGACA
1 AACATGTCACAAAGACA
3187 TAACTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 56 1.00
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.16
Consensus pattern (43 bp):
AACATGTCACAAAGACAGAGATAAATATGTCGTAAAGGCAAAG
Found at i:3140 original size:20 final size:20
Alignment explanation
Indices: 3117--3183 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
3107 AATGTGTCGT
*
3117 AAAGGCAAAGAACATGTCAC
1 AAAGGCAAAGAATATGTCAC
* * **
3137 AAAGACAGAGATAAATATGTCGT
1 AAAGGCA-A-A-GAATATGTCAC
3160 AAAGGCAAAGAATATGTCAC
1 AAAGGCAAAGAATATGTCAC
3180 AAAG
1 AAAG
3184 ACATAACTAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 2 0.06
23 13 0.37
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (20 bp):
AAAGGCAAAGAATATGTCAC
Found at i:9725 original size:3 final size:3
Alignment explanation
Indices: 9717--9771 Score: 67
Period size: 3 Copynumber: 17.3 Consensus size: 3
9707 CGGGTCTTTT
9717 TTA TTA TTA TTTA TATA TT- TATA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA -TTA T-TA TTA T-TA TTA TTA TTA TTA TTA TTA -TTA TTA
9765 TTA TTA T
1 TTA TTA T
9772 GTTTATTAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 1 0.02
3 36 0.77
4 10 0.21
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:9783 original size:13 final size:13
Alignment explanation
Indices: 9717--9779 Score: 62
Period size: 12 Copynumber: 5.0 Consensus size: 13
9707 CGGGTCTTTT
9717 TTAT-TATTATTTA
1 TTATGTATTA-TTA
*
9730 TATATTTA-TATTA
1 T-TATGTATTATTA
9743 TTAT-TATTATTA
1 TTATGTATTATTA
*
9755 TTATTTATTATTA
1 TTATGTATTATTA
9768 TTATGT-TTATTA
1 TTATGTATTATTA
9780 ATTACATATT
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
11 2 0.04
12 18 0.40
13 18 0.40
14 5 0.11
15 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATGTATTATTA
Found at i:11355 original size:22 final size:22
Alignment explanation
Indices: 11330--11373 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
11320 TCAAACGGTG
*
11330 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
11352 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
11374 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:12824 original size:33 final size:33
Alignment explanation
Indices: 12745--12816 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
12735 TGGGTAGATT
12745 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
1 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
12778 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
1 GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
12811 GCATGT
1 GCATGT
12817 TTGGGTAGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (33 bp):
GCATGTCCGGGTAGGATTGTTATTTAATTGAAA
Found at i:16505 original size:4 final size:4
Alignment explanation
Indices: 16496--16543 Score: 82
Period size: 4 Copynumber: 12.5 Consensus size: 4
16486 CGAGAAAAGT
16496 ATAC ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
16542 AT
1 AT
16544 GATACATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
4 40 0.95
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:16524 original size:22 final size:22
Alignment explanation
Indices: 16496--16538 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
16486 CGAGAAAAGT
16496 ATACATACATACATACATACAC
1 ATACATACATACATACATACAC
16518 ATACATACATACATACATACA
1 ATACATACATACATACATACA
16539 TACATGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (22 bp):
ATACATACATACATACATACAC
Found at i:17075 original size:37 final size:35
Alignment explanation
Indices: 17024--17121 Score: 108
Period size: 37 Copynumber: 2.8 Consensus size: 35
17014 TCGTTTCCTC
* *
17024 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAATTTTGTCTCGCTTGAGACAATATCT-T
* ** *
17060 AAAAAAAAAATTTTGTCTCATTTGAGACTATATCTT
1 -AAAAACAAATTTTGTCTCGCTTGAGACAATATCTT
*
17096 -AAAGCAAATTTTGTCTCGCTTGAGAC
1 AAAAACAAATTTTGTCTCGCTTGAGAC
17122 TCATTTTCTC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
34 22 0.43
36 1 0.02
37 28 0.55
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (35 bp):
AAAAACAAATTTTGTCTCGCTTGAGACAATATCTT
Found at i:17413 original size:29 final size:29
Alignment explanation
Indices: 17376--17612 Score: 172
Period size: 29 Copynumber: 8.2 Consensus size: 29
17366 TCTTGAAAAA
17376 TTTGAGTTTGTTCCTTTTGAATAAAAATC
1 TTTGAGTTTGTTCCTTTTGAATAAAAATC
* *
17405 TTGGAGTTTGTTCCTTTTGAATAAATATC
1 TTTGAGTTTGTTCCTTTTGAATAAAAATC
*
17434 TTTGAG-TTGTTTCTTTTG---AAAAATC
1 TTTGAGTTTGTTCCTTTTGAATAAAAATC
* * ** *
17459 TTTGAGTCTATTTATTTTGAA-ACAAAGTTTTGTCTC
1 TTTGAGTTTGTTCCTTTTGAATA-AAA-------ATC
*** * *
17495 TCTTGAGACAGTTTCTCTTG-A-AAAAATC
1 T-TTGAGTTTGTTCCTTTTGAATAAAAATC
17523 TTTGAGTTTGTTCCTTTTGAATAAAAATC
1 TTTGAGTTTGTTCCTTTTGAATAAAAATC
* *
17552 TTGGAGTTTGTTCCTTTTGAATAAATATC
1 TTTGAGTTTGTTCCTTTTGAATAAAAATC
*
17581 TTTGAG-TTGTTTCTTTTG---AAAAATC
1 TTTGAGTTTGTTCCTTTTGAATAAAAATC
17606 TTTGAGT
1 TTTGAGT
17613 CTATTTATTT
Statistics
Matches: 168, Mismatches: 25, Indels: 33
0.74 0.11 0.15
Matches are distributed among these distances:
25 24 0.14
26 9 0.05
27 13 0.08
28 27 0.16
29 74 0.44
35 3 0.02
36 5 0.03
37 13 0.08
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.48
Consensus pattern (29 bp):
TTTGAGTTTGTTCCTTTTGAATAAAAATC
Found at i:17606 original size:147 final size:146
Alignment explanation
Indices: 17342--17673 Score: 609
Period size: 147 Copynumber: 2.3 Consensus size: 146
17332 AAAACGATTT
17342 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAA--TTTGAGTTTGTTCCTTTTGAATAAAAATC
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATC
17405 TTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTAT
66 TTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTAT
17470 TTATTTTGAAACAAAG
131 TTATTTTGAAACAAAG
17486 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTG-AAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
17551 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
65 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
17616 TTTATTTTGAAACAAAG
130 TTTATTTTGAAACAAAG
* *
17633 TTTTGTCTCTCTTGAGACA-ATT-TCGTGAAAAATCTTTGAGT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAATCTTTGAGT
17674 CTGAAACAAA
Statistics
Matches: 183, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
144 43 0.23
145 9 0.05
146 2 0.01
147 129 0.70
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.47
Consensus pattern (146 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATC
TTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTAT
TTATTTTGAAACAAAG
Found at i:17624 original size:54 final size:54
Alignment explanation
Indices: 17512--17627 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 54
17502 ACAGTTTCTC
* * *
17512 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTTGTTCCTTTTG-A-AAAAATCTTGGAGTCTATTCATT
* * *
17568 TTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
17622 TTGAAA
1 TTGAAA
17628 CAAAGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
53 1 0.02
54 23 0.44
56 5 0.10
57 14 0.27
58 9 0.17
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (54 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
Found at i:17752 original size:28 final size:28
Alignment explanation
Indices: 17713--17781 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
17703 AATTTTGTGA
*
17713 AAAAAAATCTTTGAGATTGTTTCTTTTG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
*
17741 AAAAAAATCTTTGAGTTTGTTTCTTTGG
1 AAAAAAATCTTTGAGATTGTTTCTTTGG
17769 AAACAAAAT-TTTG
1 AAA-AAAATCTTTG
17782 TCTCTCTTAA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.43
Consensus pattern (28 bp):
AAAAAAATCTTTGAGATTGTTTCTTTGG
Found at i:17810 original size:37 final size:37
Alignment explanation
Indices: 17759--17885 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 37
17749 CTTTGAGTTT
17759 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
** * * * *
17796 GTTTCTTTTAAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
17826 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
17863 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
17886 AATCTGTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 21 0.31
31 3 0.04
36 8 0.12
37 36 0.53
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.45
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:17818 original size:67 final size:65
Alignment explanation
Indices: 17726--17950 Score: 285
Period size: 67 Copynumber: 3.4 Consensus size: 65
17716 AAAATCTTTG
*
17726 AGATTGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
*
17791 AGATAGTTTCTTTTAAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTT-GAA-AAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
17856 TA
64 TA
* * * * *
17858 AGATAATTTCTTTTGAAAAAAATCTTTGAATCTGTTTCTCTT--AAA-ATGAATTTTGTATCTCT
1 AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCT-TTGGAAACA-AAATTTTGTCTCTCT
*
17920 TG
64 TA
* * **
17922 AGACAGTTTCTCTTGAAGTAAATCTTTGA
1 AGATAGTTTCTTTTGAAAAAAATCTTTGA
17951 ATATGTTCAT
Statistics
Matches: 142, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
63 1 0.01
64 41 0.29
65 33 0.23
66 6 0.04
67 61 0.43
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (65 bp):
AGATAGTTTCTTTTGAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTA
Found at i:18228 original size:63 final size:63
Alignment explanation
Indices: 18119--18242 Score: 178
Period size: 63 Copynumber: 2.0 Consensus size: 63
18109 GATGTGATCC
* *
18119 ATCTTTGAGTCTGTTTCTTTTGAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAAA
* * **
18182 ATCTTTGAGTTTGTTTCCTTTGAAGCAAAATTTTGTCTC-TCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAA-CAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAA
18243 TACCCACATT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 41 0.76
64 13 0.24
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.44
Consensus pattern (63 bp):
ATCTTTGAGTCTGTTTCCTTTGAACAAAATTTTATCTCTTAAAGACAACTTCTTTTGAAAAAA
Found at i:18287 original size:40 final size:40
Alignment explanation
Indices: 18224--18303 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
18214 TTGTCTCTCG
18224 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
1 AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
* * *
18264 AGACAATTTCTTTT-AAAACTACCCACCTTTGAGATTGTTT
1 AGACAACTTCTTTTGAAAA-TACCCACATTTGAGATCGTTT
18304 TTATTAAAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 4 0.11
40 32 0.89
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (40 bp):
AGACAACTTCTTTTGAAAATACCCACATTTGAGATCGTTT
Found at i:18380 original size:31 final size:30
Alignment explanation
Indices: 18345--18405 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
18335 GTTTCTCTAG
*
18345 AAATACAAA-ATCTTTGAGTTTGTTTCACTTT
1 AAATA-AAACATCTTTGAG-TCGTTTCACTTT
*
18376 AAATAAAACCATTTTTGAGTCGTTTCACTT
1 AAATAAAA-CATCTTTGAGTCGTTTCACTT
18406 GAAACATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
30 3 0.12
31 15 0.58
32 8 0.31
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (30 bp):
AAATAAAACATCTTTGAGTCGTTTCACTTT
Found at i:18726 original size:36 final size:34
Alignment explanation
Indices: 18675--18770 Score: 95
Period size: 36 Copynumber: 2.7 Consensus size: 34
18665 TTTGAGAAAA
* * * *
18675 ATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTACC
1 ATCTTTGAATCTGTTTCTTT-GAAACAAAA-TAAAC
*
18711 ATCTTTGAATCTGTTTCCCTTGAAACAAAATAAAC
1 ATCTTTGAATCTGTTT-CTTTGAAACAAAATAAAC
18746 ATCTTTGAGATC-GTTTCTCTTGAAA
1 ATCTTTGA-ATCTGTTTCT-TTGAAA
18771 TGAATTTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
34 1 0.02
35 21 0.41
36 26 0.51
37 3 0.06
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (34 bp):
ATCTTTGAATCTGTTTCTTTGAAACAAAATAAAC
Found at i:18762 original size:35 final size:36
Alignment explanation
Indices: 18696--18770 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
18686 TGTTTCTTTG
* *
18696 GAAACAAAATTTACCATCTTTGAATCTGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
*
18732 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCTGTTTCCCTT
18767 GAAA
1 GAAA
18771 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.35
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCTGTTTCCCTT
Found at i:19175 original size:40 final size:41
Alignment explanation
Indices: 19120--19349 Score: 150
Period size: 40 Copynumber: 5.4 Consensus size: 41
19110 TGGCCAGTAG
* * *
19120 TCCTCATCACATAGGAACCGTGTCATCCCCT-GACCAGATC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGACC
* * * *
19160 TCCTCATCATGTAGGAGCCATGTCA-ACCATAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAG---ACCAGACC
* * *
19202 GTCCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATCCAGAAC
1 -TCCTCATCACGTAGGAGCCGTGTCAT---CC--CCT--AGA-CCAGACC
* * *
19252 TCTTCATCACGTATGAGCAGTGTCATCCCCT-GACCAGACC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGACC
19292 TCCTCATCACGTAGGAGCCGTGTCAT--CCTAGATAACCAG-CC
1 TCCTCATCACGTAGGAGCCGTGTCATCCCCTAG---ACCAGACC
19333 GTCCTCATCACGTAGGA
1 -TCCTCATCACGTAGGA
19350 ATCGTGTTAT
Statistics
Matches: 147, Mismatches: 23, Indels: 38
0.71 0.11 0.18
Matches are distributed among these distances:
38 3 0.02
39 4 0.03
40 51 0.35
41 4 0.03
42 22 0.15
43 26 0.18
44 3 0.02
46 2 0.01
47 1 0.01
48 1 0.01
49 27 0.18
50 1 0.01
51 2 0.01
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (41 bp):
TCCTCATCACGTAGGAGCCGTGTCATCCCCTAGACCAGACC
Found at i:19427 original size:131 final size:131
Alignment explanation
Indices: 19139--19447 Score: 453
Period size: 131 Copynumber: 2.3 Consensus size: 131
19129 CATAGGAACC
19139 GTGTCATCCCCTGACCAGATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
1 GTGTCATCCCCTGACCA-ATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
*
19204 CCTCATCACGTAGGAACCGTGTTATCGCCCTACCTAAAGATCCAGAACTCTTCATCACGTATGAG
65 CCTCATCACGTAGGAACCGTGTTATCACCCTACCTAAAGATCCAGAACTCTTCATCACGTATGAG
19269 CA
130 CA
* * * *
19271 GTGTCATCCCCTGACCAGACCTCCTCATCACGTAGGAGCCGTGTCATCC-TAGATAACCAGCCGT
1 GTGTCATCCCCTGACCA-ATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGT
* *
19335 CCTCATCACGTAGGAATCGTGTTATCACTCCT-CCTAAAGATGACCAGAACTCTTCATCATGTAT
65 CCTCATCACGTAGGAACCGTGTTATCAC-CCTACCTAAAGAT--CCAGAACTCTTCATCACGTAT
19399 GAGCA
127 GAGCA
* * * *
19404 GTGTCATCCCTTGACC-ATTTCCTCATCATGTAGGAACCTTGTCA
1 GTGTCATCCCCTGACCAATCTCCTCATCATGTAGGAGCCATGTCA
19448 CTTTTAGACG
Statistics
Matches: 161, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
131 73 0.45
132 48 0.30
133 40 0.25
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (131 bp):
GTGTCATCCCCTGACCAATCTCCTCATCATGTAGGAGCCATGTCAACCATAGATAACCAGCCGTC
CTCATCACGTAGGAACCGTGTTATCACCCTACCTAAAGATCCAGAACTCTTCATCACGTATGAGC
A
Found at i:19650 original size:3 final size:3
Alignment explanation
Indices: 19642--19705 Score: 85
Period size: 3 Copynumber: 20.3 Consensus size: 3
19632 CGGGTCTTTT
19642 TTA TTA TTA TT- TATA TATA TTTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA T-TA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
19689 TTA TTTA TTA TTA TTA T
1 TTA -TTA TTA TTA TTA T
19706 GTTTATTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.02
3 46 0.81
4 9 0.16
5 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:23388 original size:2 final size:2
Alignment explanation
Indices: 23381--23434 Score: 90
Period size: 2 Copynumber: 26.0 Consensus size: 2
23371 TCTCAAAATA
23381 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
23424 AT AT AT CAT AT
1 AT AT AT -AT AT
23435 GAGATTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 46 0.92
3 4 0.08
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:27964 original size:19 final size:19
Alignment explanation
Indices: 27922--27965 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
27912 TATTTGAATA
* *
27922 ATTAAATCGAATATAATAT
1 ATTAAATCAAATATAAAAT
*
27941 TTTAAATCAAATATAAAAT
1 ATTAAATCAAATATAAAAT
27960 ATTAAA
1 ATTAAA
27966 ATTACTTAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (19 bp):
ATTAAATCAAATATAAAAT
Found at i:33584 original size:13 final size:13
Alignment explanation
Indices: 33566--33592 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
33556 TCGAATATAA
33566 AATCTTAAAATTC
1 AATCTTAAAATTC
33579 AATCTTAAAATTC
1 AATCTTAAAATTC
33592 A
1 A
33593 TTAACACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
AATCTTAAAATTC
Found at i:42366 original size:43 final size:44
Alignment explanation
Indices: 42276--42377 Score: 116
Period size: 43 Copynumber: 2.3 Consensus size: 44
42266 TGCAACCCAA
* ** * * **
42276 TAGTATCGATACTGGCCAAGGGGTATCGGTACTACTTTTTAGTG
1 TAGTATCGATACCGGCCAAGGGGTATCAATACTACTATGTAAAG
*
42320 TAGTATCGATACCGTCC-AGGGGTATCAATACTACTATGTAAAG
1 TAGTATCGATACCGGCCAAGGGGTATCAATACTACTATGTAAAG
*
42363 TAGTATCGGTACCGG
1 TAGTATCGATACCGG
42378 TCATGGTATC
Statistics
Matches: 48, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
43 33 0.69
44 15 0.31
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (44 bp):
TAGTATCGATACCGGCCAAGGGGTATCAATACTACTATGTAAAG
Found at i:52083 original size:2 final size:2
Alignment explanation
Indices: 52076--52108 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
52066 AAAATTATAT
*
52076 TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
52109 ATATATTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:56651 original size:2 final size:2
Alignment explanation
Indices: 56644--56672 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
56634 GTCTTTAAAT
56644 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56673 TATGCAAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60236 original size:19 final size:17
Alignment explanation
Indices: 60194--60230 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
60184 ATTCCTGATA
60194 ATTAATATATATTTAAC
1 ATTAATATATATTTAAC
60211 ATTAATATATATTTAA-
1 ATTAATATATATTTAAC
60227 ATTA
1 ATTA
60231 TGAATAATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAATATATATTTAAC
Found at i:61006 original size:5 final size:5
Alignment explanation
Indices: 60964--61005 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
60954 GTAACGCCAC
* *
60964 TACCA TACCA TACCA TACCA TACCA TACCA TAACA TAACA TA
1 TACCA TACCA TACCA TACCA TACCA TACCA TACCA TACCA TA
61006 ATAAGAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (5 bp):
TACCA
Found at i:64106 original size:12 final size:12
Alignment explanation
Indices: 64089--64121 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
64079 CTCAGTCAAT
64089 GAAAGGAAATAG
1 GAAAGGAAATAG
64101 GAAAGGAAATAG
1 GAAAGGAAATAG
64113 GAAAGGAAA
1 GAAAGGAAA
64122 GTCTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.61, C:0.00, G:0.33, T:0.06
Consensus pattern (12 bp):
GAAAGGAAATAG
Found at i:69982 original size:13 final size:13
Alignment explanation
Indices: 69964--70003 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
69954 TTACAGACGC
69964 GCATATGAAGACT
1 GCATATGAAGACT
69977 GCATATGAAGACT
1 GCATATGAAGACT
69990 GCATATGAAGACT
1 GCATATGAAGACT
70003 G
1 G
70004 TACAACTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:72518 original size:85 final size:85
Alignment explanation
Indices: 72375--72544 Score: 331
Period size: 85 Copynumber: 2.0 Consensus size: 85
72365 CCATAAGCTT
*
72375 CTATTAATATTTTATTTTCATCCATGATCTTTAAAAATTGTACTAGCCATGTATAACCCCCATTT
1 CTATTAATATTTTATTTTCATCCATGATCTTTAAAAATTGTACTAGCCATCTATAACCCCCATTT
72440 ATAACACCTCTTACTCGGAC
66 ATAACACCTCTTACTCGGAC
72460 CTATTAATATTTTATTTTCATCCATGATCTTTAAAAATTGTACTAGCCATCTATAACCCCCATTT
1 CTATTAATATTTTATTTTCATCCATGATCTTTAAAAATTGTACTAGCCATCTATAACCCCCATTT
72525 ATAACACCTCTTACTCGGAC
66 ATAACACCTCTTACTCGGAC
72545 TGTTAGTGAT
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (85 bp):
CTATTAATATTTTATTTTCATCCATGATCTTTAAAAATTGTACTAGCCATCTATAACCCCCATTT
ATAACACCTCTTACTCGGAC
Found at i:75057 original size:108 final size:108
Alignment explanation
Indices: 74868--75079 Score: 424
Period size: 108 Copynumber: 2.0 Consensus size: 108
74858 CAACTAAATA
74868 ACAAGTACCGAGTGCAAAACTGAGTTTATAACTCGGTAAATTAATTCTACGATTCCAGTTCATCG
1 ACAAGTACCGAGTGCAAAACTGAGTTTATAACTCGGTAAATTAATTCTACGATTCCAGTTCATCG
74933 TACAAACTACAACCACTTTCGTAGTTATGATTCATTGAATAAT
66 TACAAACTACAACCACTTTCGTAGTTATGATTCATTGAATAAT
74976 ACAAGTACCGAGTGCAAAACTGAGTTTATAACTCGGTAAATTAATTCTACGATTCCAGTTCATCG
1 ACAAGTACCGAGTGCAAAACTGAGTTTATAACTCGGTAAATTAATTCTACGATTCCAGTTCATCG
75041 TACAAACTACAACCACTTTCGTAGTTATGATTCATTGAA
66 TACAAACTACAACCACTTTCGTAGTTATGATTCATTGAA
75080 CTACATCAAC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 104 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (108 bp):
ACAAGTACCGAGTGCAAAACTGAGTTTATAACTCGGTAAATTAATTCTACGATTCCAGTTCATCG
TACAAACTACAACCACTTTCGTAGTTATGATTCATTGAATAAT
Found at i:78200 original size:20 final size:22
Alignment explanation
Indices: 78171--78250 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 22
78161 CCCGTGGGGG
* *
78171 GGGGGTATCGATTCCC-T-ACA
1 GGGGGAATCGATTCCCATCAAA
78191 GGGGGAATCGATTCCCATTCAAA
1 GGGGGAATCGATTCCCA-TCAAA
* *
78214 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCATCAAA
*
78237 -GGGGTATCGATTCC
1 GGGGGAATCGATTCC
78251 TCCCGTCAGA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 15 0.30
21 2 0.04
22 11 0.22
23 19 0.38
24 3 0.06
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.24
Consensus pattern (22 bp):
GGGGGAATCGATTCCCATCAAA
Found at i:78245 original size:22 final size:23
Alignment explanation
Indices: 78190--78250 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
78180 GATTCCCTAC
78190 AGGGGGAATCGATTCCCATTCAA
1 AGGGGGAATCGATTCCCATTCAA
* *
78213 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCATTCAA
*
78236 A-GGGGTATCGATTCC
1 AGGGGGAATCGATTCC
78251 TCCCGTCAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 12 0.35
23 22 0.65
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGATTCCCATTCAA
Found at i:83907 original size:21 final size:21
Alignment explanation
Indices: 83855--83909 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
83845 TGGAGCGTGG
*
83855 GGGAATCGGTACCCCCTCATA
1 GGGAATCGGTTCCCCCTCATA
*
83876 AGGAATCGGTTCCCCCTCATA
1 GGGAATCGGTTCCCCCTCATA
83897 GGGAATCGGTTCC
1 GGGAATCGGTTCC
83910 TGTAGTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.22, C:0.31, G:0.25, T:0.22
Consensus pattern (21 bp):
GGGAATCGGTTCCCCCTCATA
Found at i:85105 original size:181 final size:181
Alignment explanation
Indices: 84801--85162 Score: 537
Period size: 181 Copynumber: 2.0 Consensus size: 181
84791 TTGAAAAATT
* ** * * *
84801 TCAAAACTCTTTGCTTTAGTTATAAGATCCAAAAAATAGGGGAGAGGGTTTGTGCCATCTGGGCA
1 TCAAAACTCTCTGCTTTAGACACAAGATCCAAAAAATAGGAGAGAGGGTATGTGCCATCTGGGCA
* * ** *
84866 GTGGAGAAGCTGGAGAAATCAGGACCGAGACCACGTAAGAACCAATAGACTTTGTCAGTTCCATT
66 GTAGAGAAGCTGGAGAAATCAGGACCGAAACCACACAAGAACCAATAGACTTTGTCAGTTCCATC
*
84931 AACCGGACGACCGATTACATGTAGTTGGTCACACAAAGTTTTGAAGACACG
131 AACCGGACGACCGATTACATGTAGTTGATCACACAAAGTTTTGAAGACACG
*
84982 TCAAAACTCTCTGCTTTAGACACAAGAT-CAGAAAAATAGGAGATAGGGTATGTGCCATCTGGGC
1 TCAAAACTCTCTGCTTTAGACACAAGATCCA-AAAAATAGGAGAGAGGGTATGTGCCATCTGGGC
* * *
85046 AGTAGAGAAGCTGGATAAATCGGGACCGAAACCACACAAGAACCAATGGACTTTGTCAGTTCCAT
65 AGTAGAGAAGCTGGAGAAATCAGGACCGAAACCACACAAGAACCAATAGACTTTGTCAGTTCCAT
* * *
85111 CAACTGGACGACCGATTGCATGTAGTTGATCACACAAAGTTTTGAAGGCACG
130 CAACCGGACGACCGATTACATGTAGTTGATCACACAAAGTTTTGAAGACACG
85163 AGCATAGGCA
Statistics
Matches: 161, Mismatches: 19, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
180 2 0.01
181 159 0.99
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (181 bp):
TCAAAACTCTCTGCTTTAGACACAAGATCCAAAAAATAGGAGAGAGGGTATGTGCCATCTGGGCA
GTAGAGAAGCTGGAGAAATCAGGACCGAAACCACACAAGAACCAATAGACTTTGTCAGTTCCATC
AACCGGACGACCGATTACATGTAGTTGATCACACAAAGTTTTGAAGACACG
Found at i:89946 original size:14 final size:14
Alignment explanation
Indices: 89927--90003 Score: 54
Period size: 14 Copynumber: 5.6 Consensus size: 14
89917 ATAGGAGCTA
89927 AAAAAAAGAAATAG
1 AAAAAAAGAAATAG
* *
89941 AAAAAAACAAA-AC
1 AAAAAAAGAAATAG
* *
89954 AAGAAAAAAAAAT-T
1 AA-AAAAAGAAATAG
*
89968 AAAAAAA-TAATAG
1 AAAAAAAGAAATAG
89981 AAAAAAAAGAAA-AG
1 -AAAAAAAGAAATAG
*
89995 TAAAAAAGA
1 AAAAAAAGA
90004 GAAAAAAATG
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
12 3 0.06
13 16 0.32
14 29 0.58
15 2 0.04
ACGTcount: A:0.81, C:0.03, G:0.09, T:0.08
Consensus pattern (14 bp):
AAAAAAAGAAATAG
Found at i:89971 original size:27 final size:28
Alignment explanation
Indices: 89926--90001 Score: 84
Period size: 27 Copynumber: 2.8 Consensus size: 28
89916 CATAGGAGCT
89926 AAAAAAAAGAAATAG-AAAAAAACAAAAC
1 AAAAAAAAGAAA-AGTAAAAAAACAAAAC
* * * * *
89954 AAGAAAAA-AAAATTAAAAAAATAATAG
1 AAAAAAAAGAAAAGTAAAAAAACAAAAC
89981 AAAAAAAAGAAAAGTAAAAAA
1 AAAAAAAAGAAAAGTAAAAAA
90002 GAGAAAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.82, C:0.03, G:0.08, T:0.08
Consensus pattern (28 bp):
AAAAAAAAGAAAAGTAAAAAAACAAAAC
Found at i:94038 original size:46 final size:46
Alignment explanation
Indices: 93897--94348 Score: 679
Period size: 46 Copynumber: 9.9 Consensus size: 46
93887 GTAAGCATGC
* * * * *
93897 AAATAAGCTTACGAGCTTATGGA-AT-AGTGGCATGCATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
* *
93941 AAATAAGCTTACGAGCTTATGGAATTAAAT-GTAAGTATATTGTTA
1 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
*
93986 AAATAAGCTTACGAGTTTATGGAGTTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
94032 AAATAAGCTTACGAGCTTATGG-GATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAG-TTAAATGGTAAGTATATTGGTA
* *
94078 AAATAGGCTTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
94124 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
94170 AAATAAGCTTACGAGCTTATGG-GATTAAAT-GTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAG-TTAAATGGTAAGTATATTGGTA
94215 AAATAAGCTTACGAGCTTATGG-GATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAG-TTAAATGGTAAGTATATTGGTA
*
94261 AAATAAGCTTACTAGCTTAT-GAGATTAAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAG-TTAAATGGTAAGTATATTGGTA
* * *
94307 AAATAAGCTTACGAGCTTATGG-GATAAATGGAAATTATATTG
1 AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTG
94349 ATAAGAAATT
Statistics
Matches: 380, Mismatches: 19, Indels: 17
0.91 0.05 0.04
Matches are distributed among these distances:
44 23 0.06
45 104 0.27
46 252 0.66
47 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (46 bp):
AAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTATATTGGTA
Found at i:94091 original size:137 final size:138
Alignment explanation
Indices: 93897--94348 Score: 745
Period size: 137 Copynumber: 3.3 Consensus size: 138
93887 GTAAGCATGC
* * * * *
93897 AAATAAGCTTACGAGCTTAT-GGAAT-AGTGGCATGCATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
93960 TGGAATTAAAT-GTAAGTATATTGTTAAAATAAGCTTACGAGTTTATGGAGTTAAATGGTAAGTA
66 TGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTA
94024 TATTGGTA
131 TATTGGTA
*
94032 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAGGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
94097 TGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTA
66 TGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTA
94162 TATTGGTA
131 TATTGGTA
94170 AAATAAGCTTACGAGCTTATGGGATTAAAT-GTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
* *
94234 TGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACTAGCTTAT-GAGATTAAATGGTAAGT
66 TGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAG-TTAAATGGTAAGT
94298 ATATTGGTA
130 ATATTGGTA
* *
94307 AAATAAGCTTACGAGCTTATGGGA-TAAATGGAAATTATATTG
1 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTG
94349 ATAAGAAATT
Statistics
Matches: 299, Mismatches: 13, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
135 20 0.07
136 12 0.04
137 178 0.60
138 89 0.30
ACGTcount: A:0.38, C:0.07, G:0.23, T:0.33
Consensus pattern (138 bp):
AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTA
TGGAATTAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAGTTAAATGGTAAGTA
TATTGGTA
Found at i:95593 original size:34 final size:32
Alignment explanation
Indices: 95540--95609 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
95530 CCTTACAAAC
*
95540 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
95572 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
95606 TCCC
1 TCCC
95610 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:95850 original size:20 final size:22
Alignment explanation
Indices: 95825--95864 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
95815 TGTTGTTTAT
95825 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
95845 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
95865 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:95916 original size:21 final size:21
Alignment explanation
Indices: 95892--95934 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
95882 CCCAGAATAG
*
95892 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
95913 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
95934 A
1 A
95935 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:96066 original size:15 final size:15
Alignment explanation
Indices: 96046--96075 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
96036 ACCCCCTGGG
96046 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
96061 GGGGTATCTGTACCC
1 GGGGTATCTGTACCC
96076 CCTGGGGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (15 bp):
GGGGTATCTGTACCC
Found at i:96085 original size:21 final size:21
Alignment explanation
Indices: 96024--96103 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
96014 AAAACCTGCA
*
96024 GGGGGTATATGTACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
96045 GGGGGTATCTGTA--CCC---
1 GGGGGTATCTGTACCCCCTGG
96061 -GGGGTATCTGTACCCCCTGGG
1 GGGGGTATCTGTACCCCCT-GG
* *
96082 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
96103 G
1 G
96104 CAATCTTGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
15 12 0.24
17 3 0.06
19 3 0.06
21 15 0.31
22 16 0.33
ACGTcount: A:0.14, C:0.26, G:0.38, T:0.23
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:96097 original size:37 final size:36
Alignment explanation
Indices: 96025--96097 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
96015 AAACCTGCAG
* *
96025 GGGGTATATGTACCCCCTGGGGGGGTATCTGTACCC
1 GGGGTATATGTACCCCCTGGGGGGGAATCTATACCC
*
96061 GGGGTATCTGTACCCCCTGGGGGGGGAATCTATACCC
1 GGGGTATATGTACCCCCT-GGGGGGGAATCTATACCC
96098 CCTGGGCAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 17 0.52
37 16 0.48
ACGTcount: A:0.15, C:0.26, G:0.36, T:0.23
Consensus pattern (36 bp):
GGGGTATATGTACCCCCTGGGGGGGAATCTATACCC
Found at i:96225 original size:29 final size:31
Alignment explanation
Indices: 96193--96252 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
96183 AAACTTTGAA
96193 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
96222 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
96253 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:97574 original size:39 final size:38
Alignment explanation
Indices: 97531--97621 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 38
97521 ATGTACATTT
97531 ATATAAAGTTGACCAAAATTT-TCATTC-AAAATTGACAAA
1 ATATAAAGTT-ACC-AAATTTAT-ATTCAAAAATTGACAAA
*
97570 ATATATGAAGTTACCATATTTATATTCAAAAATTGACAAA
1 ATATA--AAGTTACCAAATTTATATTCAAAAATTGACAAA
97610 ATACATAAAGTT
1 AT--ATAAAGTT
97622 TAACTAAAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
39 14 0.31
40 23 0.51
41 5 0.11
42 3 0.07
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (38 bp):
ATATAAAGTTACCAAATTTATATTCAAAAATTGACAAA
Found at i:97783 original size:30 final size:30
Alignment explanation
Indices: 97749--97825 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 30
97739 GTGGTGGTGA
*
97749 TGCCTATTGTGTTGCTGACTGTTATGTTGC
1 TGCCTATTGTGTTGCTGACTCTTATGTTGC
* * * * *
97779 TGCCTGTTGTGTTGGTGCCTCTTCTGTTGG
1 TGCCTATTGTGTTGCTGACTCTTATGTTGC
*
97809 TGTCTATTGTGTTGCTG
1 TGCCTATTGTGTTGCTG
97826 TTTTCTGTTG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.05, C:0.17, G:0.30, T:0.48
Consensus pattern (30 bp):
TGCCTATTGTGTTGCTGACTCTTATGTTGC
Found at i:97797 original size:15 final size:15
Alignment explanation
Indices: 97749--97825 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
97739 GTGGTGGTGA
97749 TGCCTATTGTGTTGC
1 TGCCTATTGTGTTGC
* * *
97764 TGACTGTTATGTTGC
1 TGCCTATTGTGTTGC
* *
97779 TGCCTGTTGTGTTGG
1 TGCCTATTGTGTTGC
* * *
97794 TGCCTCTTCTGTTGG
1 TGCCTATTGTGTTGC
*
97809 TGTCTATTGTGTTGC
1 TGCCTATTGTGTTGC
97824 TG
1 TG
97826 TTTTCTGTTG
Statistics
Matches: 50, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.05, C:0.17, G:0.30, T:0.48
Consensus pattern (15 bp):
TGCCTATTGTGTTGC
Found at i:117110 original size:15 final size:15
Alignment explanation
Indices: 117090--117124 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
117080 ATAGTTTATG
*
117090 TTATATAGTAGCGTA
1 TTATATAGTAGCATA
*
117105 TTATATAGTTGCATA
1 TTATATAGTAGCATA
117120 TTATA
1 TTATA
117125 AATAGTAGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.14, T:0.46
Consensus pattern (15 bp):
TTATATAGTAGCATA
Found at i:117149 original size:14 final size:15
Alignment explanation
Indices: 117130--117160 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
117120 TTATAAATAG
117130 TAGTCCATGTTA-AA
1 TAGTCCATGTTAGAA
117144 TAGTCCATGTTAGAA
1 TAGTCCATGTTAGAA
117159 TA
1 TA
117161 TTAGCCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (15 bp):
TAGTCCATGTTAGAA
Found at i:117240 original size:32 final size:32
Alignment explanation
Indices: 117204--117278 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
117194 CAAAATAAAG
117204 GTCCATTATATTTAAAAGAGTCCATTTACATA
1 GTCCATTATATTTAAAAGAGTCCATTTACATA
**
117236 GTCCATTGCATTTAAAAGAGTCCATTTACATA
1 GTCCATTATATTTAAAAGAGTCCATTTACATA
117268 GTCCATTATAT
1 GTCCATTATAT
117279 AGGCCCAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (32 bp):
GTCCATTATATTTAAAAGAGTCCATTTACATA
Found at i:121526 original size:14 final size:14
Alignment explanation
Indices: 121509--121539 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
121499 ATAATAGGTG
121509 ATAAGTGATCTTGA
1 ATAAGTGATCTTGA
121523 ATAAGTGATCTTGA
1 ATAAGTGATCTTGA
121537 ATA
1 ATA
121540 GCTCTCGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.35
Consensus pattern (14 bp):
ATAAGTGATCTTGA
Found at i:124258 original size:209 final size:213
Alignment explanation
Indices: 123894--124321 Score: 828
Period size: 209 Copynumber: 2.0 Consensus size: 213
123884 GGTAAGAGAT
123894 ATCTTGCAAGTCTGACACAGCTCAACAACACTATTGACGTCACTTACCCAACTTCAACCTCAAGT
1 ATCTTGCAAGTCTGACACAGCTCAACAACACTATTGACGTCACTTACCCAACTTCAACCTCAAGT
123959 TCAATCATGCCCCTATTAAGTTAATTGAGACCACTGCCAGTTGTTATATCATTCATAAAATGGTA
66 TCAATCATGCCCCTATTAAGTTAATTGAGACCACTGCCAGTTGTTATATCATTCATAAAATGGTA
124024 TGACGTCAAGGGTATTTAGGGATTTTCAAGGGAACTAAACCCTATAAATTCCCACTATAATACCC
131 TGACGTCAAGGGTATTTAGGGATTTTCAAGGGAACTAAACCCTATAAATTCCCACTATAATACCC
124089 CATTATAACGCTTCATGA
196 CATTATAACGCTTCATGA
124107 ATCTTGCAAGTCTGACACAGCTC-ACAACAC-ATTGACGTCACTTACCCAACTTCAACCTC-AGT
1 ATCTTGCAAGTCTGACACAGCTCAACAACACTATTGACGTCACTTACCCAACTTCAACCTCAAGT
124169 TCAATCATG-CCCTATTAAGTTAATTGAGACCACTGCCAGTTGTTATATCATTCATAAAATGGTA
66 TCAATCATGCCCCTATTAAGTTAATTGAGACCACTGCCAGTTGTTATATCATTCATAAAATGGTA
124233 TGACGTCAAGGGTATTTAGGGATTTTCAAGGGAACTAAACCCTATAAATTCCCACTATAATACCC
131 TGACGTCAAGGGTATTTAGGGATTTTCAAGGGAACTAAACCCTATAAATTCCCACTATAATACCC
124298 CATTATAACGCTTCATGA
196 CATTATAACGCTTCATGA
124316 ATCTTG
1 ATCTTG
124322 AGAGAGGCTG
Statistics
Matches: 215, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
209 144 0.67
210 12 0.06
211 29 0.13
212 7 0.03
213 23 0.11
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.29
Consensus pattern (213 bp):
ATCTTGCAAGTCTGACACAGCTCAACAACACTATTGACGTCACTTACCCAACTTCAACCTCAAGT
TCAATCATGCCCCTATTAAGTTAATTGAGACCACTGCCAGTTGTTATATCATTCATAAAATGGTA
TGACGTCAAGGGTATTTAGGGATTTTCAAGGGAACTAAACCCTATAAATTCCCACTATAATACCC
CATTATAACGCTTCATGA
Found at i:127060 original size:53 final size:54
Alignment explanation
Indices: 126850--127065 Score: 208
Period size: 53 Copynumber: 4.1 Consensus size: 54
126840 GTTGTGCCTA
* * * * * *
126850 AGTGCCGAAATGGAAATTCATAAACTTATTAT-AATTCCATAGATTGCACACAT
1 AGTGCCGATACGGTAATTCATAAACTCATTATGAATTCCGTAGGTTGCACACAT
* * * * * *
126903 ACTGCCGATACGGTAATCCACAAACTCATTATGAATTCTGTGGGTTGGACACAT
1 AGTGCCGATACGGTAATTCATAAACTCATTATGAATTCCGTAGGTTGCACACAT
* * * *
126957 GGTGCCGATACGGTAAATACA-AAA-TTATTATGAATT-CGTGGGTTGCACACAT
1 AGTGCCGATACGGT-AATTCATAAACTCATTATGAATTCCGTAGGTTGCACACAT
* * **
127009 AGTG-CGATATGGTCATTCATAAACTCATTATGAATTATGTAGGTTGCACACAT
1 AGTGCCGATACGGTAATTCATAAACTCATTATGAATTCCGTAGGTTGCACACAT
127062 AGTG
1 AGTG
127066 TCAATAGTAC
Statistics
Matches: 133, Mismatches: 25, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
50 4 0.03
51 11 0.08
52 28 0.21
53 54 0.41
54 31 0.23
55 5 0.04
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.30
Consensus pattern (54 bp):
AGTGCCGATACGGTAATTCATAAACTCATTATGAATTCCGTAGGTTGCACACAT
Found at i:130719 original size:9 final size:9
Alignment explanation
Indices: 130705--130729 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
130695 TATCATCCTC
130705 TTTAATTTT
1 TTTAATTTT
130714 TTTAATTTT
1 TTTAATTTT
130723 TTTAATT
1 TTTAATT
130730 GATGGTATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTAATTTT
Found at i:132766 original size:2 final size:2
Alignment explanation
Indices: 132759--132790 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
132749 CTAGAGCATC
132759 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
132791 TACATGACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133286 original size:54 final size:55
Alignment explanation
Indices: 133191--133318 Score: 143
Period size: 54 Copynumber: 2.4 Consensus size: 55
133181 ATTCCGTAGA
* * ** * *
133191 TTGCACACAT-GTGCAGATACAATTATTCACAAACTTGTTATGAATTATAT-GGG
1 TTGCACACATAGTGCCGATACAATCATTCACAAACTCATTATGAACTACATGGGG
* * * *
133244 TTGCACACATAGTGCCGATACAGTCATTCATAAACTCATTATGAACTCCGTGGGG
1 TTGCACACATAGTGCCGATACAATCATTCACAAACTCATTATGAACTACATGGGG
*
133299 TTGCACACATAGTGACGATA
1 TTGCACACATAGTGCCGATA
133319 GTACACATAG
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
53 10 0.16
54 30 0.48
55 22 0.35
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (55 bp):
TTGCACACATAGTGCCGATACAATCATTCACAAACTCATTATGAACTACATGGGG
Found at i:140027 original size:45 final size:45
Alignment explanation
Indices: 139962--140239 Score: 423
Period size: 45 Copynumber: 6.2 Consensus size: 45
139952 AATGAACCTT
*
139962 TATGCATTTTCAACTATAGCATACTTTTATGTTGATAATGCACCCA
1 TATGCA-TTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * * *
140008 TGTACATTCCAACTATAGCATACTTTTTTGTTGATAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* *
140053 TATGCATTTTAACTATAGCATACTTTTCTGTTGACAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
*
140098 TATGCATTTCAACTATAGCATACTTTTCTATTGAT-ATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
* * **
140142 TATGCATTTCAACTATATCATACTTTTATGTTGATAATGCACCTG
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
*
140187 TATGCATTTCAACTATAGCATATTTTTCTGTTGATAATGCACCCA
1 TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
140232 TATGCATT
1 TATGCATT
140240 CCTTCCACAA
Statistics
Matches: 208, Mismatches: 23, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
44 41 0.20
45 163 0.78
46 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (45 bp):
TATGCATTTCAACTATAGCATACTTTTCTGTTGATAATGCACCCA
Found at i:140214 original size:134 final size:135
Alignment explanation
Indices: 139962--140239 Score: 432
Period size: 134 Copynumber: 2.1 Consensus size: 135
139952 AATGAACCTT
* *
139962 TATGCATTTTCAACTATAGCATACTTTTATGTTGATAATGCACCCATGTACATTCCAACTATAGC
1 TATGCA-TTTCAACTATAGCATACTTTTATATTGATAATGCACCCATATACATTCCAACTATAGC
* *
140027 ATACTTTTTTGTTGATAATGCACCCATATGCATTTTAACTATAGCATACTTTTCTGTTGACAATG
65 ATACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGACAATG
140092 CACCCA
130 CACCCA
* * * *
140098 TATGCATTTCAACTATAGCATACTTTTCTATTGAT-ATGCACCCATATGCATTTCAACTATATCA
1 TATGCATTTCAACTATAGCATACTTTTATATTGATAATGCACCCATATACATTCCAACTATAGCA
** * *
140162 TACTTTTATGTTGATAATGCACCTGTATGCATTTCAACTATAGCATATTTTTCTGTTGATAATGC
66 TACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGC
140227 ACCCA
131 ACCCA
140232 TATGCATT
1 TATGCATT
140240 CCTTCCACAA
Statistics
Matches: 130, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
134 97 0.75
135 27 0.21
136 6 0.05
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.40
Consensus pattern (135 bp):
TATGCATTTCAACTATAGCATACTTTTATATTGATAATGCACCCATATACATTCCAACTATAGCA
TACTTTTATGTTGATAATGCACCCATATGCATTTCAACTATAGCATACTTTTCTGTTGACAATGC
ACCCA
Found at i:141584 original size:81 final size:81
Alignment explanation
Indices: 141499--141649 Score: 275
Period size: 81 Copynumber: 1.9 Consensus size: 81
141489 AACTAATCCC
* *
141499 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTAACAA
1 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTAACAA
141564 TTGCAGAATTAGGCAG
66 TTGCAGAATTAGGCAG
*
141580 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTACCAA
1 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTAACAA
141645 TTGCA
66 TTGCA
141650 CAGTTAGACC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 67 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTAACAA
TTGCAGAATTAGGCAG
Found at i:141665 original size:81 final size:81
Alignment explanation
Indices: 141499--141671 Score: 267
Period size: 81 Copynumber: 2.1 Consensus size: 81
141489 AACTAATCCC
* *
141499 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATCTAACTGGCATAATTGGCACCTTTCTAACAA
1 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTAACAA
* *
141564 TTGCAGAATTAGGCAG
66 TTGCACAATTAGCCAG
*
141580 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTACCAA
1 TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTAACAA
*
141645 TTGCACAGTTAGACCA-
66 TTGCACAATTAG-CCAG
*
141661 TTATTATTTTA
1 TTATTCTTTTA
141672 TTTTGTACTA
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
81 82 0.98
82 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (81 bp):
TTATTCTTTTACTCAACGGTGTTTAACCGTTCATATAACTGGCATAATTGACACCTTTCTAACAA
TTGCACAATTAGCCAG
Found at i:141951 original size:55 final size:54
Alignment explanation
Indices: 141835--142149 Score: 289
Period size: 55 Copynumber: 5.8 Consensus size: 54
141825 TATAAGGTAG
* * *
141835 TTCATCAACTCATGATGAATTCTGTGG-GTTGCACACATCGTGTCTGTACGGTTAT
1 TTCATCAAATCATGATGAATTCTGTGGATTTGCACACATAGT-TCTGTACGGTT-T
* * * *
141890 TT-ATCAACTCAAGATGAATTCTGTGGATTTACACACATAGTTCATGTACGATTT
1 TTCATCAAATCATGATGAATTCTGTGGATTTGCACACATAGTTC-TGTACGGTTT
* * * * *
141944 TTCATCAAATCATGATGAATTCCGTTGATTTGCACACCTAGTGCTGGTACGGTTA
1 TTCATCAAATCATGATGAATTCTGTGGATTTGCACACATAGTTCT-GTACGGTTT
* * * * **
141999 TTAATCAAATCATGATGCATTATGTGGATTTGCACACATAGTGCCTGTACAATTAT
1 TTCATCAAATCATGATGAATTCTGTGGATTTGCACACATAGT-TCTGTACGGTT-T
** * **
142055 TT-ATCAAATCATGATGAATT-TGGTGGATTTGCACACATAGTGATGGTATGGTAA
1 TTCATCAAATCATGATGAATTCT-GTGGATTTGCACACATAGTTCT-GTACGGTTT
* * *
142109 TTCATCAACTCATGATGAATTATGTGGA-TTGCACACTTAGT
1 TTCATCAAATCATGATGAATTCTGTGGATTTGCACACATAGT
142150 GCCGAAATAG
Statistics
Matches: 216, Mismatches: 34, Indels: 21
0.80 0.13 0.08
Matches are distributed among these distances:
54 45 0.21
55 166 0.77
56 5 0.02
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (54 bp):
TTCATCAAATCATGATGAATTCTGTGGATTTGCACACATAGTTCTGTACGGTTT
Found at i:142025 original size:110 final size:111
Alignment explanation
Indices: 141835--142151 Score: 374
Period size: 110 Copynumber: 2.9 Consensus size: 111
141825 TATAAGGTAG
* * ** * *
141835 TTCATCAACTCATGATGAATTCTG-TGGGTTGCACACATCGTGTCT-GTACGGTTATTTATCAAC
1 TTCATCAAATCATGATGAATTCCGTTGATTTGCACACATAGTG-CTGGTACGGTTATTAATCAAC
* * * *
141898 TCAAGATGAATTCTGTGGATTTACACACATAGTTCATGTACGATT-T
65 TCATGATGAATTATGTGGATTTACACACATAGTGCATGTACAATTAT
* *
141944 TTCATCAAATCATGATGAATTCCGTTGATTTGCACACCTAGTGCTGGTACGGTTATTAATCAAAT
1 TTCATCAAATCATGATGAATTCCGTTGATTTGCACACATAGTGCTGGTACGGTTATTAATCAACT
* * *
142009 CATGATGCATTATGTGGATTTGCACACATAGTGCCTGTACAATTAT
66 CATGATGAATTATGTGGATTTACACACATAGTGCATGTACAATTAT
** * * * * *
142055 TT-ATCAAATCATGATGAATTTGGTGGATTTGCACACATAGTGATGGTATGGTAATTCATCAACT
1 TTCATCAAATCATGATGAATTCCGTTGATTTGCACACATAGTGCTGGTACGGTTATTAATCAACT
* *
142119 CATGATGAATTATGTGGA-TTGCACACTTAGTGC
66 CATGATGAATTATGTGGATTTACACACATAGTGC
142152 CGAAATAGTT
Statistics
Matches: 179, Mismatches: 26, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
109 38 0.21
110 138 0.77
111 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (111 bp):
TTCATCAAATCATGATGAATTCCGTTGATTTGCACACATAGTGCTGGTACGGTTATTAATCAACT
CATGATGAATTATGTGGATTTACACACATAGTGCATGTACAATTAT
Found at i:142115 original size:165 final size:163
Alignment explanation
Indices: 141838--142151 Score: 389
Period size: 165 Copynumber: 1.9 Consensus size: 163
141828 AAGGTAGTTC
* * * * ** *
141838 ATCAACTCATGATGAATTCTGTGGGTTGCACACATCGTGTCTGTACGGTTATTTATCAACTCAAG
1 ATCAAATCATGATGAATTATGTGGGTTGCACACATAGTGCCTGTACAATTATTTATCAAATCAAG
** *
141903 ATGAATTCTGTGGATTTACACACATAGTTCATGTACGATTTTTCATCAAATCATGATGAATTCCG
66 ATGAATTCTGTGGATTTACACACATAGTTCATGTACGATAATTCATCAAATCATGATGAATTACG
*
141968 TTGATTTGCACACCTAGTGCTGGTACGGTTATTA
131 TGGA-TTGCACACCTAGTGCTGGTACGGTTATTA
* * *
142002 ATCAAATCATGATGCATTATGTGGATTTGCACACATAGTGCCTGTACAATTATTTATCAAATCAT
1 ATCAAATCATGATGAATTATGTGG-GTTGCACACATAGTGCCTGTACAATTATTTATCAAATCAA
* * * * *
142067 GATGAATT-TGGTGGATTTGCACACATAG-TGATGGTATGGTAATTCATCAACTCATGATGAATT
65 GATGAATTCT-GTGGATTTACACACATAGTTCAT-GTACGATAATTCATCAAATCATGATGAATT
* *
142130 ATGTGGATTGCACACTTAGTGC
128 ACGTGGATTGCACACCTAGTGC
142152 CGAAATAGTT
Statistics
Matches: 126, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
164 39 0.31
165 87 0.69
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (163 bp):
ATCAAATCATGATGAATTATGTGGGTTGCACACATAGTGCCTGTACAATTATTTATCAAATCAAG
ATGAATTCTGTGGATTTACACACATAGTTCATGTACGATAATTCATCAAATCATGATGAATTACG
TGGATTGCACACCTAGTGCTGGTACGGTTATTA
Found at i:142166 original size:54 final size:53
Alignment explanation
Indices: 141810--142330 Score: 230
Period size: 54 Copynumber: 9.6 Consensus size: 53
141800 TTTATTTAGA
* * * *
141810 TGCACACGTAGTGCCTATAAGG-TAGTTCATCAACTCATGATGAATTCTGTGGGT
1 TGCACACATAGTGCCGA-AAGGTTA-TTCATCAACTCATGATGAATTATGTGGAT
* * * * * * *
141864 TGCACACATCGTGTCTGTACGGTTATTTATCAACTCAAGATGAATTCTGTGGATT
1 TGCACACATAGTG-CCGAAAGGTTATTCATCAACTCATGATGAATTATGTGGA-T
* * * * * * * * ** *
141919 TACACACATAGTTCATGTACGATTTTTCATCAAATCATGATGAATTCCGTTGATT
1 TGCACACATAGTGC-CGAAAGGTTATTCATCAACTCATGATGAATTATGTGGA-T
* * * * * * *
141974 TGCACACCTAGTGCTGGTACGGTTATTAATCAAATCATGATGCATTATGTGGATT
1 TGCACACATAGTGC-CGAAAGGTTATTCATCAACTCATGATGAATTATGTGGA-T
* *
142029 TGCACACATAGTGCCTGTACAA--TTATTTATCAAATCATGATGAATT-TGGTGGATT
1 TGCACACATAGTGCC-G-A-AAGGTTATTCATCAACTCATGATGAATTAT-GTGGA-T
** * * *
142084 TGCACACATAGTGATGGTATGGTAATTCATCAACTCATGATGAATTATGTGGAT
1 TGCACACATAGTG-CCGAAAGGTTATTCATCAACTCATGATGAATTATGTGGAT
* * * * * * *
142138 TGCACACTTAGTGCCGAAATAGTTATTCATCCACAT-AGGATGAATTTTGTGAAA
1 TGCACACATAGTGCCGAAA-GGTTATTCATCAAC-TCATGATGAATTATGTGGAT
* * * * * ** * *
142192 TGCACACTTGGTGCAGAAACGATTATTCATCCATA-T-AGGATGAATTACATGAAA
1 TGCACACATAGTGCCGAAA-GGTTATTCAT-CA-ACTCATGATGAATTATGTGGAT
* * * * * * * *
142246 TGCACACTTAGTGACGAAACGATTATTCATCCACAT-AGGATGAATTACGTGAAA
1 TGCACACATAGTGCCGAAA-GGTTATTCATCAAC-TCATGATGAATTATGTGGAT
* *
142300 TACACACTTAGTGCCGAAACGGTTATTCATC
1 TGCACACATAGTGCCGAAA-GGTTATTCATC
142331 CAGATAAGAT
Statistics
Matches: 376, Mismatches: 73, Indels: 36
0.78 0.15 0.07
Matches are distributed among these distances:
52 1 0.00
53 4 0.01
54 193 0.51
55 175 0.47
56 2 0.01
57 1 0.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (53 bp):
TGCACACATAGTGCCGAAAGGTTATTCATCAACTCATGATGAATTATGTGGAT
Found at i:142331 original size:54 final size:54
Alignment explanation
Indices: 142138--143286 Score: 1474
Period size: 54 Copynumber: 21.3 Consensus size: 54
142128 TTATGTGGAT
** **
142138 TGCACACTTAGTGCCGAAATAGTTATTCATCCACATAGGATGAATTTTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * *
142192 TGCACACTTGGTGCAGAAACGATTATTCATCCATATAGGATGAATTACATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
142246 TGCACACTTAGTGACGAAACGATTATTCATCCACATAGGATGAATTACGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
142300 TACACACTTAGTGCCGAAACGGTTATTCATCCAGATAAGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * *
142354 TGCACACTTACTGGCTAAATGGTTATTCATCCACATAGGATAAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * *
142408 TACACACTTATTACAGAAATGGTTATTCATACACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
142462 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCTC-TGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTC-CGTGAAA
* * * * *
142516 TACACACTTAGTTCCAAAACGGTTATTCATCCACATAGGATGAATTTCGTTAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
142570 TGCACACTTTGTGCCGAAACGTTTATTCATCCACATAGGCTAAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
142624 TGCACACTTAGTGCCGAAATGGTTATTCATCCATATAGGATGATTTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* *** * * *
142678 TACATGTTTAGTGCCGAAACGGTTATTCATCCATATATGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
*
142732 TGCACGCTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * * * *
142786 TTCGCACTTAGTGTCGAAATGATTATTTATCCACATAAGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * ** *
142840 TGTATACTTAATATCGAAACAGTTATTCATCCACATAGGATGAATTCCGTGAAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTG-AAA
* * *
142895 T-CACAGTTAGTGCTGAAACGGTTATTCATCCACATAGGACGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * * *
142948 AGCACACTTAGTGCCGAAACCGTTATTTATCCACGTAGGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
143002 TGCACACTTAGTGCCGAAACGGCTATTCATCCATATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
143056 TACACACTTAGTGCCGAAACCGTTATTCATCCATATAGGATGAATTCCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * * *
143110 TGCACACTTAGTGCCGAAAAGGCTATTCATCCATATAGGATGAATTCCATGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
143164 TGCACACTTAGTGCCGAAACCGTTATTCATCCATATAGGATGAATTCTGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
* * *
143218 TGCACACTTAGTTCCGAAACGATTATTCATCCACATAGGATGAATTTCGTGAAA
1 TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
143272 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
143287 TATTTTGTAA
Statistics
Matches: 946, Mismatches: 145, Indels: 8
0.86 0.13 0.01
Matches are distributed among these distances:
53 4 0.00
54 937 0.99
55 5 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (54 bp):
TGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTCCGTGAAA
Found at i:143745 original size:74 final size:75
Alignment explanation
Indices: 143630--143768 Score: 192
Period size: 74 Copynumber: 1.9 Consensus size: 75
143620 ACCTCTATAA
* * * * *
143630 TATGGTACCGATACGCCCTTCCGATATCGATATCAAATTTAGGTTTGACGTTTCTTGGTATCGAT
1 TATGGTACCAATACGCCCTTCCGATATCGATATCAAATTTAGCTTCGACGATGCTTGGTATCGAT
143695 CCTACCATAC
66 CCTACCATAC
* *
143705 TATGGTACCAATAC-CCCTTCCGATATCGATA-CTAATTTTAGCTTCGATGATGCTTGGTATCGA
1 TATGGTACCAATACGCCCTTCCGATATCGATATC-AAATTTAGCTTCGACGATGCTTGGTATCGA
143768 T
65 T
143769 ACCCCTACCA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
73 1 0.02
74 42 0.75
75 13 0.23
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.35
Consensus pattern (75 bp):
TATGGTACCAATACGCCCTTCCGATATCGATATCAAATTTAGCTTCGACGATGCTTGGTATCGAT
CCTACCATAC
Found at i:166747 original size:16 final size:16
Alignment explanation
Indices: 166722--166753 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
166712 TCTTGTCGAA
*
166722 GTGCATGAATTATTTC
1 GTGCAAGAATTATTTC
166738 GTGCAAGAATTATTTC
1 GTGCAAGAATTATTTC
166754 CCTTGTTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (16 bp):
GTGCAAGAATTATTTC
Found at i:169261 original size:6 final size:6
Alignment explanation
Indices: 169250--169284 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
169240 AATTGGAGTG
169250 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACCAA
1 ACCAAA ACCAAA ACCAAA ACCAAA ACCAAA ACCAA
169285 TTGGAGTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.34, G:0.00, T:0.00
Consensus pattern (6 bp):
ACCAAA
Found at i:171419 original size:43 final size:43
Alignment explanation
Indices: 171247--171443 Score: 154
Period size: 43 Copynumber: 4.7 Consensus size: 43
171237 GTTTTTTCCC
* ** **
171247 CAAAAGGTTAGGTCTTTTAGCT-TCATTTT-TAACAAACGCCG
1 CAAAATGTTAGGTCTTTTAGCTGTGTTTTTGTAACAAACGCTA
* *** * * *
171288 CAAAATGTTAGG-GTTTTAGCAACG-ATTTGGAACAAACGCCA
1 CAAAATGTTAGGTCTTTTAGCTGTGTTTTTGTAACAAACGCTA
* * ** *
171329 CAAAATGCTACGTCTTTTAGC-GCATTTTAGTAACAAACGCTA
1 CAAAATGTTAGGTCTTTTAGCTGTGTTTTTGTAACAAACGCTA
* * *
171371 CAAAATGTTAGGTCTTTTAGCTGTGTTTTTGTAACAAATGTTG
1 CAAAATGTTAGGTCTTTTAGCTGTGTTTTTGTAACAAACGCTA
*
171414 CAAAATGTTAGGTCATTTAG-TGGTGTTTTT
1 CAAAATGTTAGGTCTTTTAGCT-GTGTTTTT
171444 TTAGAACAAA
Statistics
Matches: 124, Mismatches: 26, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
40 10 0.08
41 32 0.26
42 40 0.32
43 42 0.34
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.36
Consensus pattern (43 bp):
CAAAATGTTAGGTCTTTTAGCTGTGTTTTTGTAACAAACGCTA
Found at i:173961 original size:12 final size:12
Alignment explanation
Indices: 173944--173968 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
173934 ATCTTATAAA
173944 TATTTAATTATT
1 TATTTAATTATT
173956 TATTTAATTATT
1 TATTTAATTATT
173968 T
1 T
173969 TTTCCTTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:180946 original size:18 final size:17
Alignment explanation
Indices: 180913--180946 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
180903 TTTTGGGCTT
*
180913 ATTTTCAAATCAAAAGG
1 ATTTTCAAAACAAAAGG
180930 ATTTTCAAAAACAAAAG
1 ATTTTC-AAAACAAAAG
180947 CCAACATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (17 bp):
ATTTTCAAAACAAAAGG
Found at i:182362 original size:3 final size:3
Alignment explanation
Indices: 182343--182395 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
182333 TAAAATTAAA
* * *
182343 ATT ATT AATT -TT TTT ATT ATT ATT AAT ATAT ATT ATT AAT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
182389 ATT ATT A
1 ATT ATT A
182396 AATAAATTAC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
2 2 0.05
3 34 0.81
4 6 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:182815 original size:12 final size:14
Alignment explanation
Indices: 182786--182814 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
182776 AAAAAAACAG
182786 AAACGAGAGAAAAA
1 AAACGAGAGAAAAA
182800 AAACGA-AGAAAAA
1 AAACGAGAGAAAAA
182813 AA
1 AA
182815 CTACCAACGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.76, C:0.07, G:0.17, T:0.00
Consensus pattern (14 bp):
AAACGAGAGAAAAA
Found at i:183665 original size:22 final size:22
Alignment explanation
Indices: 183640--183686 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
183630 TATTTATTTC
*
183640 TTATTTTGTTATTACTTTT-ATA
1 TTATTTTATTATTA-TTTTCATA
183662 TTATTTTATTATTATTTTCATA
1 TTATTTTATTATTATTTTCATA
183684 TTA
1 TTA
183687 GTCACATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (22 bp):
TTATTTTATTATTATTTTCATA
Found at i:183699 original size:2 final size:2
Alignment explanation
Indices: 183692--183723 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
183682 TATTAGTCAC
183692 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
183724 TTTTAATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:189850 original size:7 final size:8
Alignment explanation
Indices: 189833--189861 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
189823 TATACATGAA
189833 AAAAAAGG
1 AAAAAAGG
189841 AAAAAA-G
1 AAAAAAGG
189848 AAAAAAGG
1 AAAAAAGG
189856 AAAAAA
1 AAAAAA
189862 ATTTGAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:189853 original size:15 final size:15
Alignment explanation
Indices: 189833--189861 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
189823 TATACATGAA
189833 AAAAAAGGAAAAAAG
1 AAAAAAGGAAAAAAG
189848 AAAAAAGGAAAAAA
1 AAAAAAGGAAAAAA
189862 ATTTGAACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGGAAAAAAG
Found at i:194551 original size:22 final size:22
Alignment explanation
Indices: 194522--194576 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
194512 ATCTACACTC
*
194522 TTCAAAGATGATAGGTTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
194544 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
194566 TTCAAAGATGA
1 TTCAAAGATGA
194577 AAGCTTTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:195364 original size:166 final size:166
Alignment explanation
Indices: 195090--195414 Score: 562
Period size: 166 Copynumber: 2.0 Consensus size: 166
195080 AGAATGAACA
* *
195090 TTATCTTGAGATTGGGTCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACAA
1 TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACAA
**
195155 TTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCC
66 TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCC
195220 TTAGTTTTTTTACTTAGTAAACTATTTCCAACATCC
131 TTAGTTTTTTTACTTAGTAAACTATTTCCAACATCC
** *
195256 TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAAATAATGAGAAAACGA
1 TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACAA
*
195320 TTTCCATAGTTTCTTATTCAATCTTTTCTAGAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
66 TTTCCATAGTTTCTCATTCAATCTTTTCTA-AAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
195385 CTTAGTTTTTTTACTTAGTAAACTATTTCC
130 CTTAGTTTTTTTACTTAGTAAACTATTTCC
195415 CATATCTGTA
Statistics
Matches: 150, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
165 45 0.30
166 105 0.70
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (166 bp):
TTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACAA
TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTCC
TTAGTTTTTTTACTTAGTAAACTATTTCCAACATCC
Found at i:195516 original size:76 final size:76
Alignment explanation
Indices: 195418--196358 Score: 1693
Period size: 76 Copynumber: 12.4 Consensus size: 76
195408 TATTTCCCAT
* *
195418 ATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
* *
195483 ACCTTATGGTC
66 GCCTTAGGGTC
195494 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
195559 GCCTTAGGGTC
66 GCCTTAGGGTC
195570 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
195635 GCCTTAGGGTC
66 GCCTTAGGGTC
* *
195646 ATCTGTAAGTCCTTCACTGCATGATGTTTCTAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
195711 GCCTTAGGGTC
66 GCCTTAGGGTC
* *
195722 ATCTGTAAGTGCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
195787 ACCTTAGGGTC
66 GCCTTAGGGTC
* *
195798 ATCTGTAAGTCCTTCAGTGCCTGATGTTTCCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
195863 GCCTTAGGGTC
66 GCCTTAGGGTC
195874 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
195939 ACCTTAGGGTC
66 GCCTTAGGGTC
* *
195950 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTTAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
196015 GCCTTAGGGTC
66 GCCTTAGGGTC
*
196026 ATCTGTAAGTCCTTCGGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
196091 GCCTTAGGGTC
66 GCCTTAGGGTC
*
196102 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
196167 GCCTTAGGGTC
66 GCCTTAGGGTC
*
196178 ATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
196243 GCCTTAGGGTC
66 GCCTTAGGGTC
*
196254 ATCTGTAAGTCCTTTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
1 ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
*
196319 ACCTTAGGGTC
66 GCCTTAGGGTC
* *
196330 ATCTGTAAGCCCTTTAGTGCATGATGTTT
1 ATCTGTAAGTCCTTCAGTGCATGATGTTT
196359 TCAATATTTC
Statistics
Matches: 834, Mismatches: 31, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 834 1.00
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (76 bp):
ATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
GCCTTAGGGTC
Found at i:196515 original size:3 final size:3
Alignment explanation
Indices: 196497--196546 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
196487 TAAAATTAAA
*
196497 ATT ATT AATT -TT -TT ATT ATT ATT AAT ATAT ATT ATT ATT ATT ATT
1 ATT ATT -ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
196542 ATT AT
1 ATT AT
196547 ATAAATAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 4 0.10
3 32 0.76
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:196533 original size:19 final size:17
Alignment explanation
Indices: 196497--196546 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 17
196487 TAAAATTAAA
*
196497 ATTATTAATTTTTTATT
1 ATTATTAATTTATTATT
*
196514 ATTATTAATATA-TATT
1 ATTATTAATTTATTATT
196530 ATTATT-A-TTATTATT
1 ATTATTAATTTATTATT
196545 AT
1 AT
196547 ATAAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 2 0.07
15 7 0.24
16 10 0.34
17 10 0.34
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTATTAATTTATTATT
Found at i:196558 original size:22 final size:25
Alignment explanation
Indices: 196509--196558 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
196499 TATTAATTTT
* *
196509 TTATTATTATTAATATATATTATTA
1 TTATTATTATTAATATATAATATAA
196534 TTATTATTATT-ATATA-AATA-AA
1 TTATTATTATTAATATATAATATAA
196556 TTA
1 TTA
196559 CAAAACTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 3 0.13
24 5 0.22
25 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTATTATTAATATATAATATAA
Found at i:197807 original size:11 final size:11
Alignment explanation
Indices: 197793--197844 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
197783 CTTTTTAATA
197793 ATTA-TTTATTT
1 ATTATTTTA-TT
*
197804 ATTATTTTGTT
1 ATTATTTTATT
197815 ATTACTTTTA-T
1 ATTA-TTTTATT
197826 ATTATTTTATT
1 ATTATTTTATT
197837 ATTATTTT
1 ATTATTTT
197845 CATATTAGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 24 0.67
12 7 0.19
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTATTTTATT
Found at i:197828 original size:22 final size:22
Alignment explanation
Indices: 197803--197851 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
197793 ATTATTTATT
*
197803 TATTATTTTGTTATTACTTTT-A
1 TATTATTTTATTATTA-TTTTCA
197825 TATTATTTTATTATTATTTTCA
1 TATTATTTTATTATTATTTTCA
197847 TATTA
1 TATTA
197852 GTCACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
TATTATTTTATTATTATTTTCA
Found at i:197839 original size:33 final size:36
Alignment explanation
Indices: 197777--197844 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 36
197767 TAAATTAATA
197777 TTATTACTTTTTAATAATTATTTATTTATTATTTTG
1 TTATTACTTTTTAATAATTATTTATTTATTATTTTG
197813 TTATTAC-TTTT-AT-ATTATTT-TATTATTATTTT
1 TTATTACTTTTTAATAATTATTTAT-TTATTATTTT
197845 CATATTAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 1 0.03
33 17 0.55
34 2 0.06
35 4 0.13
36 7 0.23
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (36 bp):
TTATTACTTTTTAATAATTATTTATTTATTATTTTG
Found at i:197850 original size:11 final size:10
Alignment explanation
Indices: 197793--197851 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 10
197783 CTTTTTAATA
*
197793 ATTATTTATTT
1 ATTATTT-TAT
*
197804 ATTATTTTGTT
1 ATTATTTT-AT
197815 ATTACTTTTAT
1 ATTA-TTTTAT
197826 ATTATTTTATT
1 ATTATTTTA-T
197837 ATTATTTTCAT
1 ATTATTTT-AT
197848 ATTA
1 ATTA
197852 GTCACATAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
10 6 0.14
11 32 0.74
12 5 0.12
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTATTTTAT
Found at i:207062 original size:324 final size:324
Alignment explanation
Indices: 206473--207127 Score: 1229
Period size: 324 Copynumber: 2.0 Consensus size: 324
206463 CCTGAGTTTC
* *
206473 ACAAGAATCAGTTTCAGCAACACTACCTTCCCGAAAGTGAAGAACAAGATTTGCATAAATGCCTT
1 ACAAGAATCAGTTTCAGCAACACCACCTTCCCGAAAGTGAAGAACAAGATTTGCAGAAATGCCTT
* *
206538 CACTCAAGAACATTTTCTGTCGAGTTTCACAGTCTAACAAAATCTCAGTAAGAACATCAAGAGAA
66 CACTCAAGAACATCTTCTGTCGAGCTTCACAGTCTAACAAAATCTCAGTAAGAACATCAAGAGAA
206603 AAATTTTCTCGTGATGCAATTGCAATAATGGACTCAAACTCCATTGTAAGTCCAGCTAATACAAC
131 AAATTTTCTCGTGATGCAATTGCAATAATGGACTCAAACTCCATTGTAAGTCCAGCTAATACAAC
*
206668 ATTAACATGTTATTGCTCAGTAACCACACTACCTGAAGCATTCAACAAATCACATATGGATTTGA
196 ATTAACATGTTATTGCTCAATAACCACACTACCTGAAGCATTCAACAAATCACATATGGATTTGA
206733 CTTTGGCAAGATACTCCCTAATCGTCAAACCAGTCTTTCGCTGGGAATGAAGATTATGTCGAAG
261 CTTTGGCAAGATACTCCCTAATCGTCAAACCAGTCTTTCGCTGGGAATGAAGATTATGTCGAAG
*
206797 ACAAGAATCAGTTTCAGCAACACCACCTTCCCGAGAGTGAAGAACAAGATTTGCAGAAATGCCTT
1 ACAAGAATCAGTTTCAGCAACACCACCTTCCCGAAAGTGAAGAACAAGATTTGCAGAAATGCCTT
*
206862 CACTCAAGAACATCTTCTGTCGAGCTTCGCAGTCTAACAAAATCTCAGTAAGAACATCAAGAGAA
66 CACTCAAGAACATCTTCTGTCGAGCTTCACAGTCTAACAAAATCTCAGTAAGAACATCAAGAGAA
*
206927 ATATTTTCTCGTGATGCAATTGCAATAATGGACTCAAACTCCATTGTAAGTCCAGCTAATACAAC
131 AAATTTTCTCGTGATGCAATTGCAATAATGGACTCAAACTCCATTGTAAGTCCAGCTAATACAAC
206992 ATTAACATGTTATTGCTCAATAACCACACTACCTGAAGCATTCAACAAATCACATATGGATTTGA
196 ATTAACATGTTATTGCTCAATAACCACACTACCTGAAGCATTCAACAAATCACATATGGATTTGA
207057 CTTTGGCAAGATACTCCCTAATCGTCAAACCAGTCTTTCGCTGGGAATGAAGATTATGTCGAAG
261 CTTTGGCAAGATACTCCCTAATCGTCAAACCAGTCTTTCGCTGGGAATGAAGATTATGTCGAAG
*
207121 AGAAGAA
1 ACAAGAA
207128 ATCTTGGCAC
Statistics
Matches: 322, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
324 322 1.00
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.26
Consensus pattern (324 bp):
ACAAGAATCAGTTTCAGCAACACCACCTTCCCGAAAGTGAAGAACAAGATTTGCAGAAATGCCTT
CACTCAAGAACATCTTCTGTCGAGCTTCACAGTCTAACAAAATCTCAGTAAGAACATCAAGAGAA
AAATTTTCTCGTGATGCAATTGCAATAATGGACTCAAACTCCATTGTAAGTCCAGCTAATACAAC
ATTAACATGTTATTGCTCAATAACCACACTACCTGAAGCATTCAACAAATCACATATGGATTTGA
CTTTGGCAAGATACTCCCTAATCGTCAAACCAGTCTTTCGCTGGGAATGAAGATTATGTCGAAG
Found at i:210018 original size:46 final size:45
Alignment explanation
Indices: 209946--210044 Score: 146
Period size: 46 Copynumber: 2.2 Consensus size: 45
209936 ATAAAATCTT
* *
209946 TTACCATTTATCTCATAAGCTGGTAAGGTTATTTTACCAATATAC
1 TTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAATATAC
*
209991 TTACCATTTAATAC-CATAAGCTCGTAAGCTTATTTTACCAATATAT
1 TTACCATTT-AT-CTCATAAGCTCGTAAGCTTATTTTACCAATATAC
210037 TTACCATT
1 TTACCATT
210045 ATTCCGTAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
45 9 0.18
46 39 0.80
47 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.40
Consensus pattern (45 bp):
TTACCATTTATCTCATAAGCTCGTAAGCTTATTTTACCAATATAC
Found at i:210080 original size:36 final size:36
Alignment explanation
Indices: 210013--210085 Score: 121
Period size: 36 Copynumber: 2.0 Consensus size: 36
210003 ACCATAAGCT
*
210013 CGTAAGCTTATTTTACCAATATATTTACCATTATTC
1 CGTAAGCTTATTTTACCAATACATTTACCATTATTC
210049 CGTAAGCTTATTTTACCAATACACTTT-CCATTATTC
1 CGTAAGCTTATTTTACCAATACA-TTTACCATTATTC
210085 C
1 C
210086 ATAACCATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 32 0.91
37 3 0.09
ACGTcount: A:0.29, C:0.23, G:0.05, T:0.42
Consensus pattern (36 bp):
CGTAAGCTTATTTTACCAATACATTTACCATTATTC
Found at i:213303 original size:21 final size:22
Alignment explanation
Indices: 213277--213319 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
213267 AATATAAATC
* *
213277 CAAACAAATTCAAAC-ATCCAA
1 CAAACAAAGTAAAACAATCCAA
213298 CAAACAAAGTAAAACAATCCAA
1 CAAACAAAGTAAAACAATCCAA
213320 AAGCATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.60, C:0.26, G:0.02, T:0.12
Consensus pattern (22 bp):
CAAACAAAGTAAAACAATCCAA
Found at i:214234 original size:193 final size:193
Alignment explanation
Indices: 213908--214298 Score: 716
Period size: 193 Copynumber: 2.0 Consensus size: 193
213898 AAATTGATTT
213908 TTCTATTATGTTGGATACAATACATCCACTATAATCCCTAATAGAAGAGTGGAGTACCTACCTCC
1 TTCTATTATGTTGGATACAATACATCCACTATAATCCCTAATAGAAGAGTGGAGTACCTACCTCC
*
213973 GATGGTCTAAACCACCAAGAGATCATCAAATGGAGAAATCGATCGTGATGAGATCATAGAGTACT
66 GATGGTCTAAACCACCAAGAGATCATCAAATGGAGAAATCAATCGTGATGAGATCATAGAGTACT
214038 AACACTAACATTA-GAAGATAGGGATATGCCATAG-TTC-TTTTCATTGTATAGACCATTGTC
131 AACACTAACATTAGGAAGATAGGGATATGCCATAGTTTCTTTTTCATTGTATAGACCATTGTC
214098 TTCTATTATGTTGGATACAATACATCCACTATAAATCCCTAATACGAAGAGTGGAGTACCTACCT
1 TTCTATTATGTTGGATACAATACATCCACTAT-AATCCCTAATA-GAAGAGTGGAGTACCTACCT
214163 CCGGATGGTCTAAACCACCAAGAGATCATCAAATGGAGAAATCAATCGTGATGAGATCATAGAGT
64 CC-GATGGTCTAAACCACCAAGAGATCATCAAATGGAGAAATCAATCGTGATGAGATCATAGAGT
214228 ACTAACACTAACATTAGGAAGATAGGGATATGCCATAGTTTCTTTTTCATTGTATAGACCATTGT
128 ACTAACACTAACATTAGGAAGATAGGGATATGCCATAGTTTCTTTTTCATTGTATAGACCATTGT
214293 C
193 C
*
214294 ATCTA
1 TTCTA
214299 GCCCAAATTG
Statistics
Matches: 193, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
190 32 0.17
191 11 0.06
192 22 0.11
193 77 0.40
194 21 0.11
195 3 0.02
196 27 0.14
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (193 bp):
TTCTATTATGTTGGATACAATACATCCACTATAATCCCTAATAGAAGAGTGGAGTACCTACCTCC
GATGGTCTAAACCACCAAGAGATCATCAAATGGAGAAATCAATCGTGATGAGATCATAGAGTACT
AACACTAACATTAGGAAGATAGGGATATGCCATAGTTTCTTTTTCATTGTATAGACCATTGTC
Found at i:215416 original size:44 final size:44
Alignment explanation
Indices: 215322--215416 Score: 106
Period size: 44 Copynumber: 2.2 Consensus size: 44
215312 CCTTGTGCAC
* *
215322 CGATGCACATTCAAGGAGTGCATCGGTGCACTTTCATGGTGTAT
1 CGATGCACATTCAAGGAGTGCATCGATGCACTTTCATAGTGTAT
**
215366 TAATGCACATTCAAAGG-GATGCATCGATGCACTGTT-A-AGTGTAT
1 CGATGCACATTC-AAGGAG-TGCATCGATGCACT-TTCATAGTGTAT
215410 CGATGCA
1 CGATGCA
215417 TTAAGCACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
44 22 0.52
45 18 0.43
46 2 0.05
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
CGATGCACATTCAAGGAGTGCATCGATGCACTTTCATAGTGTAT
Found at i:221089 original size:19 final size:19
Alignment explanation
Indices: 221065--221115 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
221055 AATAGCTGAG
*
221065 TGCATCGATGCAT-GTCTTA
1 TGCATCGATGCATGGT-ATA
*
221084 TGCATCGATGCATGGTATG
1 TGCATCGATGCATGGTATA
221103 TGCATCGATGCAT
1 TGCATCGATGCAT
221116 AAAATGCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.93
20 2 0.07
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (19 bp):
TGCATCGATGCATGGTATA
Found at i:226904 original size:23 final size:24
Alignment explanation
Indices: 226855--226906 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
226845 CAGTTTTGAC
*
226855 TGCCACGTAGAATTTGCACCGAAG
1 TGCCACGTAGAATATGCACCGAAG
226879 TGCCACGTAGAATATGCA-CGAAG
1 TGCCACGTAGAATATGCACCGAAG
226902 TGCCA
1 TGCCA
226907 TATAGATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCGAAG
Found at i:226912 original size:23 final size:24
Alignment explanation
Indices: 226855--226912 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
226845 CAGTTTTGAC
* *
226855 TGCCACGTAGAATTTGCACCGAAG
1 TGCCACATAGAATATGCACCGAAG
*
226879 TGCCACGTAGAATATGCA-CGAAG
1 TGCCACATAGAATATGCACCGAAG
*
226902 TGCCATATAGA
1 TGCCACATAGA
226913 TTTATCCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCGAAG
Found at i:226940 original size:23 final size:23
Alignment explanation
Indices: 226909--226981 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 23
226899 AAGTGCCATA
*
226909 TAGATTTATCCCAAAGGACCACG
1 TAGAATTATCCCAAAGGACCACG
* *
226932 TAGAATTAT-CCAAAAGACCACA
1 TAGAATTATCCCAAAGGACCACG
* * * *
226954 TAGAATTATCTCGAAGTACCGCG
1 TAGAATTATCCCAAAGGACCACG
226977 TAGAA
1 TAGAA
226982 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (23 bp):
TAGAATTATCCCAAAGGACCACG
Found at i:236048 original size:30 final size:31
Alignment explanation
Indices: 236007--236064 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
235997 CAACACGTCT
236007 TTTTGTTTTTCT-TCACTTTGTATCAGTGCTC
1 TTTTGTTTTTCTCT-ACTTTGTATCAGTGCTC
236038 TTTT-TTTTTCTCTACTTTGTATCAGTG
1 TTTTGTTTTTCTCTACTTTGTATCAGTG
236065 GTATAAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.10, C:0.17, G:0.12, T:0.60
Consensus pattern (31 bp):
TTTTGTTTTTCTCTACTTTGTATCAGTGCTC
Found at i:253026 original size:27 final size:26
Alignment explanation
Indices: 252977--253027 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
252967 CAAAAAATTC
*
252977 AAACTAAAAAAAAGTAAATATAAAAT
1 AAACTAAAAAAAAGTAAAAATAAAAT
253003 AAACTAAAAGAAAAG-AGAAAATAAA
1 AAACTAAAA-AAAAGTA-AAAATAAA
253028 GTGATAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.75, C:0.04, G:0.08, T:0.14
Consensus pattern (26 bp):
AAACTAAAAAAAAGTAAAAATAAAAT
Found at i:254864 original size:16 final size:16
Alignment explanation
Indices: 254843--254874 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
254833 TCTTGTCGAA
254843 GTGCATGAATTATTTC
1 GTGCATGAATTATTTC
254859 GTGCATGAATTATTTC
1 GTGCATGAATTATTTC
254875 CCTTGTTTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (16 bp):
GTGCATGAATTATTTC
Found at i:263485 original size:7 final size:7
Alignment explanation
Indices: 263473--263500 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
263463 ATCCTACAAA
263473 ACTCATC
1 ACTCATC
263480 ACTCATC
1 ACTCATC
263487 ACTCATC
1 ACTCATC
263494 ACTCATC
1 ACTCATC
263501 TCTGCAACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (7 bp):
ACTCATC
Found at i:265277 original size:43 final size:42
Alignment explanation
Indices: 265171--265301 Score: 140
Period size: 43 Copynumber: 3.1 Consensus size: 42
265161 TAAGCAACGA
* * **
265171 TTTGGAACAAACGCCACAAAATGTTACGTCTTTTAGC-GCATT
1 TTTGTAACAAACGCTACAAAATGTTA-GTCTTTTAGCTGTGTT
* *
265213 TTAGTAACAAACGCTGCAAAATGTTAGATCTTTTAGCTGTGTT
1 TTTGTAACAAACGCTACAAAATGTTAG-TCTTTTAGCTGTGTT
* *
265256 TTTGTAACAAATGCTACAAAATGTTAGGTCATTTAG-TGGTGTT
1 TTTGTAACAAACGCTACAAAATGTTA-GTCTTTTAGCT-GTGTT
265299 TTT
1 TTT
265302 TTAGAACAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
41 1 0.01
42 32 0.43
43 41 0.55
44 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (42 bp):
TTTGTAACAAACGCTACAAAATGTTAGTCTTTTAGCTGTGTT
Done.