Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012949.1 Kokia drynarioides strain JFW-HI SEQ_127967, 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: 130852
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 67 characters in sequence are not A, C, G, or T
Found at i:12 original size:2 final size:2
Alignment explanation
Indices: 7--39 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1 AAAAAA
7 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40 AAAGTTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:207 original size:16 final size:18
Alignment explanation
Indices: 186--223 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
176 CAAATAATTA
186 TTAAAG-TTTTTAT-TTT
1 TTAAAGATTTTTATATTT
*
202 TTAAAGATTTTTTTATTT
1 TTAAAGATTTTTATATTT
220 TTAA
1 TTAA
224 TATTTGCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 6 0.32
18 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
TTAAAGATTTTTATATTT
Found at i:581 original size:44 final size:44
Alignment explanation
Indices: 518--603 Score: 154
Period size: 44 Copynumber: 2.0 Consensus size: 44
508 AATTAACACG
*
518 GCGGATTCCGATTTTAAATTTTCGTTTTTGGTATTTGAAAGACT
1 GCGGATCCCGATTTTAAATTTTCGTTTTTGGTATTTGAAAGACT
*
562 GCGGATCCCGATTTTAAATTTTCTTTTTTGGTATTTGAAAGA
1 GCGGATCCCGATTTTAAATTTTCGTTTTTGGTATTTGAAAGA
604 TTTTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (44 bp):
GCGGATCCCGATTTTAAATTTTCGTTTTTGGTATTTGAAAGACT
Found at i:1213 original size:2 final size:2
Alignment explanation
Indices: 1206--1231 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1196 TCGTCGGTAC
1206 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1232 ATCCTTTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1303 original size:18 final size:18
Alignment explanation
Indices: 1282--1318 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1272 AGTCTTTTTT
1282 TTTAGCTTTACCTTTGGC
1 TTTAGCTTTACCTTTGGC
*
1300 TTTAGCTTTAGCTTTGGC
1 TTTAGCTTTACCTTTGGC
1318 T
1 T
1319 CTTTCTCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.19, G:0.19, T:0.51
Consensus pattern (18 bp):
TTTAGCTTTACCTTTGGC
Found at i:8017 original size:25 final size:25
Alignment explanation
Indices: 7983--8035 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
7973 TCCATCAGCT
7983 CTAACAAGCGTTCAAAAAGAATTAA
1 CTAACAAGCGTTCAAAAAGAATTAA
8008 CTAACAAGCGTTCAAAAAGAATTAA
1 CTAACAAGCGTTCAAAAAGAATTAA
8033 CTA
1 CTA
8036 TTTTCGAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.51, C:0.17, G:0.11, T:0.21
Consensus pattern (25 bp):
CTAACAAGCGTTCAAAAAGAATTAA
Found at i:9236 original size:60 final size:60
Alignment explanation
Indices: 9130--9244 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
9120 ATCTTATTAT
* *
9130 TAAGAGTATTTACTATTGTAAGTGTAATTTAAATTGAAGTCGCGTCAATTATGTTATGAG
1 TAAGAGTATTTACTATTGTAAGTGTAATTTAAATTGAAGTCACGTCAATCATGTTATGAG
* * * * *
9190 TAAGAGTGTTTATTATTTTAAGTGTGATTTAAGTTTGAA-TCACGTCAATCATGTT
1 TAAGAGTATTTACTATTGTAAGTGTAATTTAA-ATTGAAGTCACGTCAATCATGTT
9245 TTTATTAATG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
60 42 0.89
61 5 0.11
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.43
Consensus pattern (60 bp):
TAAGAGTATTTACTATTGTAAGTGTAATTTAAATTGAAGTCACGTCAATCATGTTATGAG
Found at i:20341 original size:5 final size:5
Alignment explanation
Indices: 20331--20357 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20321 TTAGTATCTT
20331 AAGAA AAGAA AAGAA AAGAA AAGAA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AA
20358 AAGGTCTAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:21241 original size:48 final size:46
Alignment explanation
Indices: 21167--21267 Score: 121
Period size: 48 Copynumber: 2.2 Consensus size: 46
21157 TATTAACTTG
21167 CAAACACTAGTGGTTTATCCACAAATTTACTAGCAGCATACTATTCTA
1 CAAACACTAGTGGTTTATCCACAAATTTACTAGCAGCATAC-A-TCTA
** * * * * *
21215 CAAACACTAGTGGTTTATTGATAAATTTGCTGGCAGCTTTCATCTA
1 CAAACACTAGTGGTTTATCCACAAATTTACTAGCAGCATACATCTA
21261 CAAACAC
1 CAAACAC
21268 ATTTTGTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
46 11 0.24
47 1 0.02
48 34 0.74
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (46 bp):
CAAACACTAGTGGTTTATCCACAAATTTACTAGCAGCATACATCTA
Found at i:24621 original size:16 final size:15
Alignment explanation
Indices: 24596--24629 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
24586 TTTAGAATTT
24596 TTTAAGAATTTTTATA
1 TTTAAGAATTTTTA-A
*
24612 TTTAATAATTTTTAA
1 TTTAAGAATTTTTAA
24627 TTT
1 TTT
24630 TTTTATAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTAAGAATTTTTAA
Found at i:34274 original size:23 final size:23
Alignment explanation
Indices: 34229--34274 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
34219 GAATTCTTAT
**
34229 TAAAATAAAATAAAGTGTTAAAA
1 TAAAATAAAATAAAGTGCCAAAA
34252 TAAAATAAAAGTAAAGT-CCAAAA
1 TAAAATAAAA-TAAAGTGCCAAAA
34275 AGAACTAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.65, C:0.04, G:0.09, T:0.22
Consensus pattern (23 bp):
TAAAATAAAATAAAGTGCCAAAA
Found at i:39841 original size:16 final size:16
Alignment explanation
Indices: 39808--39841 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
39798 TGATGGGACA
*
39808 GTACAAGTTTATTCCT
1 GTACAAGTTTATGCCT
*
39824 GTACAAGTTTATGGCT
1 GTACAAGTTTATGCCT
39840 GT
1 GT
39842 CTTCGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (16 bp):
GTACAAGTTTATGCCT
Found at i:43241 original size:40 final size:40
Alignment explanation
Indices: 43195--43332 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
43185 TAGCAATGTG
* * *
43195 GTGTTTATAGTGTCATTGGCAGTTCAGTTATGATATCGCA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTTATGATATCGCA
43235 GTGTTTACAGTGTCACTGCCAGTTCAGTGTA-GCAT-T-GCA
1 GTGTTTACAGTGTCACTGCCAGTTCAGT-TATG-ATATCGCA
* * * **
43274 ATGTTTACAGTGTCACTGCCAGTTCAGTTGTAATATCATA
1 GTGTTTACAGTGTCACTGCCAGTTCAGTTATGATATCGCA
* *
43314 GTGTTTACATTGTCCCTGC
1 GTGTTTACAGTGTCACTGC
43333 TAGTACAATA
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
38 3 0.04
39 31 0.38
40 44 0.54
41 4 0.05
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (40 bp):
GTGTTTACAGTGTCACTGCCAGTTCAGTTATGATATCGCA
Found at i:43264 original size:17 final size:17
Alignment explanation
Indices: 43242--43301 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 17
43232 GCAGTGTTTA
43242 CAGTGTCACTGCCAGTT
1 CAGTGTCACTGCCAGTT
* *
43259 CAGTGTAGCATTGCAATGTTT
1 CAGTGT--CACTGCCA-G-TT
43280 ACAGTGTCACTGCCAGTT
1 -CAGTGTCACTGCCAGTT
43298 CAGT
1 CAGT
43302 TGTAATATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 10 0.29
18 2 0.06
19 7 0.21
20 7 0.21
21 2 0.06
22 6 0.18
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.32
Consensus pattern (17 bp):
CAGTGTCACTGCCAGTT
Found at i:43267 original size:79 final size:79
Alignment explanation
Indices: 43155--43332 Score: 194
Period size: 79 Copynumber: 2.3 Consensus size: 79
43145 GTAGCCTAGT
*** *** * * *
43155 AGTGTTTACAGTGTCACTATTAGCTCAATGTAGCAATGTGGTGTTTATAGTGTCATTGGCAGTTC
1 AGTGTTTACAGTGTCACTGCCAGCTCAATGTAGCAATGCAATGTTTACAGTGTCACTGCCAGTTC
* *
43220 AGTTATGATATCGC
66 AGTTATAATATCAC
* * *
43234 AGTGTTTACAGTGTCACTGCCAGTTCAGTGTAGCATTGCAATGTTTACAGTGTCACTGCCAGTTC
1 AGTGTTTACAGTGTCACTGCCAGCTCAATGTAGCAATGCAATGTTTACAGTGTCACTGCCAGTTC
* *
43299 AGTTGTAATATCAT
66 AGTTATAATATCAC
* *
43313 AGTGTTTACATTGTCCCTGC
1 AGTGTTTACAGTGTCACTGC
43333 TAGTACAATA
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.37
Consensus pattern (79 bp):
AGTGTTTACAGTGTCACTGCCAGCTCAATGTAGCAATGCAATGTTTACAGTGTCACTGCCAGTTC
AGTTATAATATCAC
Found at i:43289 original size:39 final size:40
Alignment explanation
Indices: 43196--43302 Score: 139
Period size: 39 Copynumber: 2.7 Consensus size: 40
43186 AGCAATGTGG
* * * *
43196 TGTTTATAGTGTCATTGGCAGTTCAGTTATGATATCGCAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTTATGATATCGCAA
43236 TGTTTACAGTGTCACTGCCAGTTCAGTGTA-GCAT-T-GCAA
1 TGTTTACAGTGTCACTGCCAGTTCAGT-TATG-ATATCGCAA
43275 TGTTTACAGTGTCACTGCCAGTTCAGTT
1 TGTTTACAGTGTCACTGCCAGTTCAGTT
43303 GTAATATCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 30 0.49
40 26 0.43
41 4 0.07
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (40 bp):
TGTTTACAGTGTCACTGCCAGTTCAGTTATGATATCGCAA
Found at i:45386 original size:19 final size:20
Alignment explanation
Indices: 45362--45399 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
45352 AATAAATATA
*
45362 AATAAAAAATATT-TAAATT
1 AATAAAAAAAATTATAAATT
45381 AATAAAAAAAATTATAAAT
1 AATAAAAAAAATTATAAAT
45400 CTTTCTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AATAAAAAAAATTATAAATT
Found at i:45780 original size:43 final size:44
Alignment explanation
Indices: 45720--45836 Score: 134
Period size: 43 Copynumber: 2.7 Consensus size: 44
45710 ATTTTAATTT
*
45720 TTTATATA-TTTATATATTTTTTATAAATTTAT-GAATTATATA
1 TTTATAAATTTTATATATTTTTTATAAATTTATAGAATTATATA
* *
45762 -TTATAAAGTTTTATATATTTTTTAAAAATATTATAGAATTTTATA
1 TTTATAAA-TTTTATATATTTTTTATAAAT-TTATAGAATTATATA
* * *
45807 TTTTTTAATTGTATATA-TTTTTATAAATTT
1 TTTATAAATTTTATATATTTTTTATAAATTT
45837 TTCAAAATAA
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
41 6 0.10
43 21 0.33
44 14 0.22
45 17 0.27
46 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (44 bp):
TTTATAAATTTTATATATTTTTTATAAATTTATAGAATTATATA
Found at i:45787 original size:19 final size:19
Alignment explanation
Indices: 45728--45788 Score: 50
Period size: 19 Copynumber: 2.9 Consensus size: 19
45718 TTTTTATATA
45728 TTTATATATTTTTTATAAAT
1 TTTATATATTTTTTA-AAAT
* * *
45748 TTATGAATTATATATTATAAAGT
1 TT-T--A-TATATTTTTTAAAAT
45771 TTTATATATTTTTTAAAA
1 TTTATATATTTTTTAAAA
45789 ATATTATAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
19 11 0.35
20 3 0.10
21 1 0.03
22 1 0.03
23 6 0.19
24 9 0.29
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTTATATATTTTTTAAAAT
Found at i:45822 original size:45 final size:43
Alignment explanation
Indices: 45709--45833 Score: 137
Period size: 45 Copynumber: 2.8 Consensus size: 43
45699 AAATTCTTTT
*
45709 AATTTTA-ATTTTTTATATATTTATATATTTTTTATAAATTTATG
1 AATTTTATATTTTTTA-AT-TTTATATATTTTTTAAAAATTTATG
* * *
45753 AATTATATA-TTATAAAGTTTTATATATTTTTTAAAAATATTATAG
1 AATTTTATATTTTTTAA-TTTTATATATTTTTTAAAAAT-TTAT-G
*
45798 AATTTTATATTTTTTAATTGTATATATTTTTATAAA
1 AATTTTATATTTTTTAATTTTATATATTTTT-TAAA
45834 TTTTTCAAAA
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
43 20 0.30
44 15 0.22
45 23 0.34
46 9 0.13
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (43 bp):
AATTTTATATTTTTTAATTTTATATATTTTTTAAAAATTTATG
Found at i:46171 original size:47 final size:48
Alignment explanation
Indices: 46120--46241 Score: 142
Period size: 48 Copynumber: 2.6 Consensus size: 48
46110 TTACCAACTA
*
46120 GGTAAAAAAAATAGAT-A-CC-AACTAGATACAAATAGACAAGTTCAAGG
1 GGTAAAAAAAATA-ATAACCCTAA-TAAATACAAATAGACAAGTTCAAGG
* * *
46167 GGTAAAATATATATTAACCCTAATAAATACAAATAGACAAGTTCAAGG
1 GGTAAAAAAAATAATAACCCTAATAAATACAAATAGACAAGTTCAAGG
* * *
46215 GGTAAAATATATATTAACCCTAATAAA
1 GGTAAAAAAAATAATAACCCTAATAAA
46242 AATAAGGCAA
Statistics
Matches: 68, Mismatches: 4, Indels: 5
0.88 0.05 0.06
Matches are distributed among these distances:
46 1 0.01
47 12 0.18
48 53 0.78
49 2 0.03
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.23
Consensus pattern (48 bp):
GGTAAAAAAAATAATAACCCTAATAAATACAAATAGACAAGTTCAAGG
Found at i:46199 original size:48 final size:48
Alignment explanation
Indices: 46145--46241 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
46135 TACCAACTAG
46145 ATACAAATAGACAAGTTCAAGGGGTAAAATATATATTAACCCTAATAA
1 ATACAAATAGACAAGTTCAAGGGGTAAAATATATATTAACCCTAATAA
46193 ATACAAATAGACAAGTTCAAGGGGTAAAATATATATTAACCCTAATAA
1 ATACAAATAGACAAGTTCAAGGGGTAAAATATATATTAACCCTAATAA
46241 A
1 A
46242 AATAAGGCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.51, C:0.12, G:0.12, T:0.25
Consensus pattern (48 bp):
ATACAAATAGACAAGTTCAAGGGGTAAAATATATATTAACCCTAATAA
Found at i:66957 original size:24 final size:24
Alignment explanation
Indices: 66930--66979 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
66920 GTTTGACTCG
* *
66930 AACAAATAAACAGAGTTTAATTGA
1 AACAAATAAACAGAGCTTAACTGA
66954 AACAAATAAACAGAGCTTAACTGA
1 AACAAATAAACAGAGCTTAACTGA
66978 AA
1 AA
66980 GATTATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.12, T:0.20
Consensus pattern (24 bp):
AACAAATAAACAGAGCTTAACTGA
Found at i:68631 original size:18 final size:18
Alignment explanation
Indices: 68610--68648 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
68600 AAAGGCTGCA
*
68610 AATAATAAAAATAATATT
1 AATAATAAAAACAATATT
*
68628 AATAATAAAAACAATTTT
1 AATAATAAAAACAATATT
68646 AAT
1 AAT
68649 GGACAGGTCG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAATAAAAACAATATT
Found at i:71834 original size:47 final size:47
Alignment explanation
Indices: 71765--71858 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
71755 TTTACCTTTT
* *
71765 GATAACGTACACAAACTTTACACACATAACGCTCGAAACTCGGAACC
1 GATAACGTACACAAACCTTACACACATAACGCTCGAAACTCGAAACC
*
71812 GATAACGTACACAAACCTTACACACATAATGCTCGAAACTCGAAACC
1 GATAACGTACACAAACCTTACACACATAACGCTCGAAACTCGAAACC
71859 CCTAAAATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.41, C:0.30, G:0.12, T:0.17
Consensus pattern (47 bp):
GATAACGTACACAAACCTTACACACATAACGCTCGAAACTCGAAACC
Found at i:71840 original size:24 final size:24
Alignment explanation
Indices: 71766--71840 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
71756 TTACCTTTTG
*
71766 ATAACGTACACAAACTTTACACAC
1 ATAACGTACACAAACCTTACACAC
* **
71790 ATAACGCT-C-GAAACTCGGA-AC-C
1 ATAACG-TACACAAAC-CTTACACAC
71812 GATAACGTACACAAACCTTACACAC
1 -ATAACGTACACAAACCTTACACAC
71837 ATAA
1 ATAA
71841 TGCTCGAAAC
Statistics
Matches: 37, Mismatches: 7, Indels: 14
0.64 0.12 0.24
Matches are distributed among these distances:
22 2 0.05
23 15 0.41
24 18 0.49
25 2 0.05
ACGTcount: A:0.44, C:0.29, G:0.09, T:0.17
Consensus pattern (24 bp):
ATAACGTACACAAACCTTACACAC
Found at i:76070 original size:21 final size:21
Alignment explanation
Indices: 76044--76085 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
76034 CCATGGAGAT
76044 AATTTTTCGACTTGATTGAAC
1 AATTTTTCGACTTGATTGAAC
76065 AATTTTTCGACTTGATTGAAC
1 AATTTTTCGACTTGATTGAAC
76086 TTTATTCCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
AATTTTTCGACTTGATTGAAC
Found at i:80932 original size:26 final size:24
Alignment explanation
Indices: 80895--80946 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
80885 AAAGCGAATG
*
80895 TTTTTTTCTAAATTTCAAAAATATAC
1 TTTTTTTCTAAA--TAAAAAATATAC
80921 TTTTTTAT-TAAATAAAAAATATAC
1 TTTTTT-TCTAAATAAAAAATATAC
80945 TT
1 TT
80947 ATGTTTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 13 0.54
26 10 0.42
27 1 0.04
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTTTTCTAAATAAAAAATATAC
Found at i:83946 original size:44 final size:43
Alignment explanation
Indices: 83853--83953 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 43
83843 ACTTTAGTTA
*
83853 TCCGATGATGCACTATGCGTACCAATACAATTACTTCGACTTG
1 TCCGATGATGCACTATGCGTACCAATACAATTACTTCGACTAG
* * * *
83896 TCCGATGATGCACTAATGTGTGCCAATATAATTGCTTCGGTA-TAG
1 TCCGATGATGCACT-ATGCGTACCAATACAATTACTTC-G-ACTAG
83941 T-CGATGATGCACT
1 TCCGATGATGCACT
83954 TACGTGCCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
43 14 0.28
44 31 0.62
45 4 0.08
46 1 0.02
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.32
Consensus pattern (43 bp):
TCCGATGATGCACTATGCGTACCAATACAATTACTTCGACTAG
Found at i:84351 original size:3 final size:3
Alignment explanation
Indices: 84337--84368 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
84327 TTGTATAAGC
*
84337 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
84369 TTCCATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:87725 original size:18 final size:19
Alignment explanation
Indices: 87704--87740 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
87694 TTTTAAAAAA
87704 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
87722 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
87741 ACTTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:93869 original size:24 final size:24
Alignment explanation
Indices: 93833--94067 Score: 263
Period size: 24 Copynumber: 9.8 Consensus size: 24
93823 TTTTTATCTG
* *
93833 AGTGGTTGACGAGCATAAACGTAT
1 AGTGGCTGACGAGCATAAACGTAC
* * * *
93857 AGTAGTTGACGAGAATTAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
*
93881 AGTGGCTGATGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
* ** *
93905 AGTGGTTGATAAGCATAAACATAC
1 AGTGGCTGACGAGCATAAACGTAC
93929 AGTGGCTGACGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
93953 AGTGGCTGACGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
* ** * * *
93977 AGCGATTGACAAGCATAAAAGTAT
1 AGTGGCTGACGAGCATAAACGTAC
* *
94001 AGTGACTGACGAGCATAAACGTAT
1 AGTGGCTGACGAGCATAAACGTAC
*
94025 AGTGGTTGACGAGCATAAACGTAC
1 AGTGGCTGACGAGCATAAACGTAC
* * *
94049 ATTAGCTGACGAGCGTAAA
1 AGTGGCTGACGAGCATAAA
94068 TGTGCTAAAC
Statistics
Matches: 178, Mismatches: 33, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 178 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (24 bp):
AGTGGCTGACGAGCATAAACGTAC
Found at i:93950 original size:72 final size:72
Alignment explanation
Indices: 93833--94049 Score: 292
Period size: 72 Copynumber: 3.0 Consensus size: 72
93823 TTTTTATCTG
* * * * * * *
93833 AGTGGTTGACGAGCATAAACGTATAGTAGTTGACGAGAATTAACGTACAGTGGCTGATGAGCATA
1 AGTGGTTGACAAGCATAAACATATAGTGGCTGACGAGCATAAACGTACAGTGGCTGACGAGCATA
93898 AACGTAC
66 AACGTAC
* *
93905 AGTGGTTGATAAGCATAAACATACAGTGGCTGACGAGCATAAACGTACAGTGGCTGACGAGCATA
1 AGTGGTTGACAAGCATAAACATATAGTGGCTGACGAGCATAAACGTACAGTGGCTGACGAGCATA
93970 AACGTAC
66 AACGTAC
* * * * *
93977 AGCGATTGACAAGCATAAA-AGTATAGTGACTGACGAGCATAAACGTATAGTGGTTGACGAGCAT
1 AGTGGTTGACAAGCATAAACA-TATAGTGGCTGACGAGCATAAACGTACAGTGGCTGACGAGCAT
94041 AAACGTAC
65 AAACGTAC
94049 A
1 A
94050 TTAGCTGACG
Statistics
Matches: 128, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
71 1 0.01
72 127 0.99
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (72 bp):
AGTGGTTGACAAGCATAAACATATAGTGGCTGACGAGCATAAACGTACAGTGGCTGACGAGCATA
AACGTAC
Found at i:95221 original size:70 final size:70
Alignment explanation
Indices: 95093--95272 Score: 245
Period size: 70 Copynumber: 2.6 Consensus size: 70
95083 TGGGTATTTG
* * *
95093 CTACTGACTTGAGTTATTTCGGTAGAACTCAATA-AGGTATCGATAGAAGTACAAGGTATTAGAG
1 CTACTGACTTGAATTATTTCGGTAG-AGTCATTAGA-GTATCGATAGAAGTACAAGGTATTAGAG
*
95157 ACCTTTA
64 ACCTTGA
* * *
95164 CTACTGACTTGAATTATTTCGGAAGAGTCATTAGAGTATCGATAGAGGTACAGGGTATTAGAGAC
1 CTACTGACTTGAATTATTTCGGTAGAGTCATTAGAGTATCGATAGAAGTACAAGGTATTAGAGAC
95229 CTTGA
66 CTTGA
* * *
95234 CTACTGCCTTTAATTGTTTCGGTAGAGTCATTAGAGTAT
1 CTACTGACTTGAATTATTTCGGTAGAGTCATTAGAGTAT
95273 TAGTAGTACT
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
70 73 0.75
71 24 0.25
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.33
Consensus pattern (70 bp):
CTACTGACTTGAATTATTTCGGTAGAGTCATTAGAGTATCGATAGAAGTACAAGGTATTAGAGAC
CTTGA
Found at i:95757 original size:73 final size:73
Alignment explanation
Indices: 95638--95853 Score: 378
Period size: 73 Copynumber: 3.0 Consensus size: 73
95628 TTTAAGTAAA
* *
95638 TTAATTAAAATGGATTCAATGTCGTTATTAAGTTATTCGAATCTTTGTATCATCTAATATAAACA
1 TTAATTAAAATGGATTCAATGTTGTTATTAAGTTATTCGGATCTTTGTATCATCTAATATAAACA
95703 AAATGAAG
66 AAATGAAG
* *
95711 TTAATAAAAATGGATTCAATGTTATTATTAAGTTATTCGGATCTTTGTATCATCTAATATAAACA
1 TTAATTAAAATGGATTCAATGTTGTTATTAAGTTATTCGGATCTTTGTATCATCTAATATAAACA
95776 AAATGAAG
66 AAATGAAG
* *
95784 TTAATTAAAATGGATTCAATGTTGTTATTAAATTATTCGGATCTTTGTATCATTTAATATAAACA
1 TTAATTAAAATGGATTCAATGTTGTTATTAAGTTATTCGGATCTTTGTATCATCTAATATAAACA
95849 AAATG
66 AAATG
95854 GACATTTGAT
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 135 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (73 bp):
TTAATTAAAATGGATTCAATGTTGTTATTAAGTTATTCGGATCTTTGTATCATCTAATATAAACA
AAATGAAG
Found at i:97417 original size:24 final size:24
Alignment explanation
Indices: 97390--97564 Score: 96
Period size: 24 Copynumber: 7.4 Consensus size: 24
97380 GTGTTTATGT
97390 TCGTCAGCTTGCACACGTTTACGC
1 TCGTCAGCTTGCACACGTTTACGC
* * **
97414 TCGTCAACTTATTCATGCGTTT--GC
1 TCGTCAGC-T-TGCACACGTTTACGC
* *** *
97438 TCGTCAGCTTATTCATGTGTTTACAC
1 TCGTCAGC-T-TGCACACGTTTACGC
* * *
97464 TCGTCAGTTTACACATGTTTACGC
1 TCGTCAGCTTGCACACGTTTACGC
97488 TCGTCAGCTTGCACACAGTTTACG-
1 TCGTCAGCTTGCACAC-GTTTACGC
* ** *
97512 -C-TCA--TT-TATGCGTTTAAGC
1 TCGTCAGCTTGCACACGTTTACGC
97531 TCGTCAGCTTGCACACGTTTACGC
1 TCGTCAGCTTGCACACGTTTACGC
*
97555 TCGTTAGCTT
1 TCGTCAGCTT
97565 ATTTATGCAT
Statistics
Matches: 116, Mismatches: 24, Indels: 22
0.72 0.15 0.14
Matches are distributed among these distances:
18 6 0.05
19 2 0.02
20 3 0.03
21 3 0.03
22 3 0.03
23 3 0.03
24 71 0.61
25 9 0.08
26 16 0.14
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (24 bp):
TCGTCAGCTTGCACACGTTTACGC
Found at i:97425 original size:50 final size:50
Alignment explanation
Indices: 97366--97670 Score: 229
Period size: 50 Copynumber: 6.3 Consensus size: 50
97356 GTTTATACTT
* * *
97366 GTCAGCTTATTTATGTGTTTATGTTCGTCAGCTTGCACACGTTTACGCTC
1 GTCAACTTATTTATGCGTTTATGCTCGTCAGCTTGCACACGTTTACGCTC
* * *** *
97416 GTCAACTTATTCATGCG-TT-TGCTCGTCAGCTTATTCATGTGTTTACACTC
1 GTCAACTTATTTATGCGTTTATGCTCGTCAGC-T-TGCACACGTTTACGCTC
** *** *
97466 GTCAGTTTACACAT--GTTTACGCTCGTCAGCTTGCACACAGTTTACG--C
1 GTCAACTTATTTATGCGTTTATGCTCGTCAGCTTGCACAC-GTTTACGCTC
*
97513 -T---C--ATTTATGCGTTTAAGCTCGTCAGCTTGCACACGTTTACGCTC
1 GTCAACTTATTTATGCGTTTATGCTCGTCAGCTTGCACACGTTTACGCTC
* * * * * * * *
97557 GTTAGCTTATTTATGCATTTACGCTTGCCAGCTTGCACATGTTTACGTTC
1 GTCAACTTATTTATGCGTTTATGCTCGTCAGCTTGCACACGTTTACGCTC
* * ** * *
97607 GTCAACTTATTTATGCATTAATGCTCACCAGCTTACATACGTTTACGCTC
1 GTCAACTTATTTATGCGTTTATGCTCGTCAGCTTGCACACGTTTACGCTC
97657 GTCAACTTATTTAT
1 GTCAACTTATTTAT
97671 ACTTTGTATA
Statistics
Matches: 200, Mismatches: 40, Indels: 30
0.74 0.15 0.11
Matches are distributed among these distances:
41 3 0.01
42 7 0.04
43 23 0.12
44 1 0.00
45 1 0.00
46 1 0.00
47 1 0.00
48 15 0.08
49 12 0.06
50 136 0.68
ACGTcount: A:0.20, C:0.24, G:0.17, T:0.39
Consensus pattern (50 bp):
GTCAACTTATTTATGCGTTTATGCTCGTCAGCTTGCACACGTTTACGCTC
Found at i:100053 original size:2 final size:2
Alignment explanation
Indices: 100046--100087 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
100036 TAAATAGACA
100046 AT AT AT AT AT 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 AT AT AT AT AT
100088 TAAGATTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:102875 original size:24 final size:25
Alignment explanation
Indices: 102830--102876 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
102820 TATATGGAAC
*
102830 TTATAACTTATTTTAATGAATATGG
1 TTATAACTTATTTTAATCAATATGG
*
102855 TTATAATTTA-TTTAATCAATAT
1 TTATAACTTATTTTAATCAATAT
102877 TTTAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (25 bp):
TTATAACTTATTTTAATCAATATGG
Found at i:109695 original size:11 final size:12
Alignment explanation
Indices: 109653--109692 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 12
109643 CAAAATTTCA
109653 AAAATAT-AATT
1 AAAATATAAATT
109664 AAAATTAATAAATT
1 AAAA-T-ATAAATT
109678 AAAATATAAATT
1 AAAATATAAATT
109690 AAA
1 AAA
109693 TATTTGCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.15
12 11 0.42
13 3 0.12
14 8 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATATAAATT
Found at i:120602 original size:10 final size:10
Alignment explanation
Indices: 120589--120646 Score: 73
Period size: 10 Copynumber: 5.7 Consensus size: 10
120579 AAAAATATAT
120589 AATTATAATA
1 AATTATAATA
120599 AATTATAATA
1 AATTATAATA
120609 AATTATAATA
1 AATTATAATA
*
120619 AATTA-AAAA
1 AATTATAATA
*
120628 TAATTATAAAA
1 -AATTATAATA
120639 AATATATA
1 AAT-TATA
120647 GAGAATTGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
9 3 0.07
10 33 0.75
11 8 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AATTATAATA
Found at i:120749 original size:10 final size:10
Alignment explanation
Indices: 120734--120829 Score: 79
Period size: 10 Copynumber: 9.6 Consensus size: 10
120724 AGCAAACAGT
120734 AAAAATTATA
1 AAAAATTATA
*
120744 AAAAATTATTT
1 AAAAATTA-TA
120755 AAAAA-TATA
1 AAAAATTATA
*
120764 AAAAATTATT
1 AAAAATTATA
* *
120774 AAAATTTACA
1 AAAAATTATA
* *
120784 AAATATTATC
1 AAAAATTATA
*
120794 AAATATTAT-
1 AAAAATTATA
*
120803 AAAAACTATA
1 AAAAATTATA
*
120813 TAAAAATTTTA
1 -AAAAATTATA
120824 AAAAAT
1 AAAAAT
120830 AAAATCAAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
9 13 0.19
10 41 0.60
11 14 0.21
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (10 bp):
AAAAATTATA
Found at i:120758 original size:20 final size:19
Alignment explanation
Indices: 120735--120829 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 19
120725 GCAAACAGTA
120735 AAAATTATAAAAAATTATTT
1 AAAATTATAAAAAATTA-TT
*
120755 AAAAATATAAAAAATTATT
1 AAAATTATAAAAAATTATT
*
120774 AAAATT-TACAAAATATTATC
1 AAAATTATA-AAAA-ATTATT
* *
120794 AAATATTATAAAAACTATATA
1 AAA-ATTATAAAAAAT-TATT
*
120815 AAAATTTTAAAAAAT
1 AAAATTATAAAAAAT
120830 AAAATCAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
18 2 0.03
19 11 0.17
20 35 0.56
21 13 0.21
22 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATTATAAAAAATTATT
Found at i:120924 original size:9 final size:9
Alignment explanation
Indices: 120901--121044 Score: 53
Period size: 9 Copynumber: 15.4 Consensus size: 9
120891 GTAGAAATTT
120901 TTTTTAATAA
1 TTTTT-ATAA
120911 TTTTTATAA
1 TTTTTATAA
120920 TTTTTTTATAA
1 --TTTTTATAA
*
120931 CTTTTATAA
1 TTTTTATAA
* *
120940 TGTTT-TGA
1 TTTTTATAA
**
120948 TTTTT-TTT
1 TTTTTATAA
*
120956 TTTTTACATA
1 TTTTTATA-A
*
120966 TTTTAATAA
1 TTTTTATAA
* *
120975 ATTTCATAA
1 TTTTTATAA
120984 TTTGTT-TATA
1 TTT-TTATA-A
* *
120994 GTTTTGTAA
1 TTTTTATAA
121003 TTTTTAAATAA
1 TTTTT--ATAA
*
121014 TTTTTATGA
1 TTTTTATAA
*
121023 -TTTTACATA
1 TTTTTATA-A
*
121032 TTTTTATGA
1 TTTTTATAA
121041 TTTT
1 TTTT
121045 AAATAATAAT
Statistics
Matches: 99, Mismatches: 24, Indels: 23
0.68 0.16 0.16
Matches are distributed among these distances:
8 17 0.17
9 43 0.43
10 22 0.22
11 17 0.17
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (9 bp):
TTTTTATAA
Found at i:120925 original size:20 final size:20
Alignment explanation
Indices: 120900--121026 Score: 69
Period size: 20 Copynumber: 6.2 Consensus size: 20
120890 TGTAGAAATT
120900 TTTTTTAATAATTTTTATAA
1 TTTTTTAATAATTTTTATAA
* *
120920 TTTTTTTATAACTTTTATAA
1 TTTTTTAATAATTTTTATAA
** ** *
120940 TGTTTTGATTTTTTTTTTTTTACA
1 T-TTTT--TAATAATTTTTATA-A
* * *
120964 TATTTTAATAAATTTCATAA
1 TTTTTTAATAATTTTTATAA
* *
120984 TTTGTTT-AT-AGTTTTGTAA
1 TTT-TTTAATAATTTTTATAA
* *
121003 TTTTTAAATAATTTTTATGA
1 TTTTTTAATAATTTTTATAA
121023 TTTT
1 TTTT
121027 ACATATTTTT
Statistics
Matches: 77, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
18 2 0.03
19 12 0.16
20 35 0.45
21 14 0.18
23 12 0.16
24 2 0.03
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (20 bp):
TTTTTTAATAATTTTTATAA
Found at i:121018 original size:64 final size:66
Alignment explanation
Indices: 120902--121035 Score: 150
Period size: 64 Copynumber: 2.1 Consensus size: 66
120892 TAGAAATTTT
* * * * **
120902 TTTTAATAATTTTTATAATTTTTTTATAACTTTTATAATGTTTTGAT-TTTTT-TTTTTTTACAT
1 TTTTAATAAATTTCATAATTTGTTTATAACTTTTATAATGTTTTAATATTTTTATGATTTTACAT
120965 A
66 A
* *
120966 TTTTAATAAATTTCATAATTTGTTTAT-AGTTTTGTAAT-TTTTAAATAATTTTTATGATTTTAC
1 TTTTAATAAATTTCATAATTTGTTTATAACTTTTATAATGTTTT-AAT-ATTTTTATGATTTTAC
121029 ATA
64 ATA
121032 TTTT
1 TTTT
121036 TATGATTTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
62 4 0.07
63 11 0.19
64 24 0.41
65 5 0.09
66 14 0.24
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.63
Consensus pattern (66 bp):
TTTTAATAAATTTCATAATTTGTTTATAACTTTTATAATGTTTTAATATTTTTATGATTTTACAT
A
Found at i:123815 original size:7 final size:7
Alignment explanation
Indices: 123803--123837 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
123793 GATGGAAACC
123803 AATTTTA
1 AATTTTA
123810 AATTTTA
1 AATTTTA
123817 AATTTTA
1 AATTTTA
123824 AATTATTTA
1 AA-T-TTTA
123833 AATTT
1 AATTT
123838 AAACTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
7 18 0.69
8 2 0.08
9 6 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AATTTTA
Found at i:123834 original size:16 final size:16
Alignment explanation
Indices: 123803--123847 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
123793 GATGGAAACC
123803 AATTTTAAA-T-TTTA
1 AATTTTAAATTATTTA
123817 AATTTTAAATTATTTA
1 AATTTTAAATTATTTA
123833 AA-TTTAAACTTATTT
1 AATTTTAAA-TTATTT
123848 TGAGTTTGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.32
15 7 0.25
16 12 0.43
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
AATTTTAAATTATTTA
Found at i:123876 original size:17 final size:17
Alignment explanation
Indices: 123811--123878 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
123801 CCAATTTTAA
123811 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
123828 A-TTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
123844 ATTTTGAGTTTGAATTT
1 ATTTTAAATTTAAATTT
*
123861 ATTTTAAAATTAAATTT
1 ATTTTAAATTTAAATTT
123878 A
1 A
123879 AAATTAAGTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
15 6 0.15
16 9 0.22
17 26 0.63
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:123878 original size:12 final size:12
Alignment explanation
Indices: 123863--123894 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
123853 TTGAATTTAT
123863 TTTAAAATTAAA
1 TTTAAAATTAAA
*
123875 TTTAAAATTAAG
1 TTTAAAATTAAA
123887 TTTAAAAT
1 TTTAAAAT
123895 GTTCAAACAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:125546 original size:30 final size:30
Alignment explanation
Indices: 125475--125550 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
125465 AACTGTCTAG
* *
125475 AAATCATAGTTTAACCCTTAAACTTTTCCA
1 AAATCATATTTTAACCCCTAAACTTTTCCA
* * * *
125505 AAATTACATTTTGACCCCTAAACTTTTCTA
1 AAATCATATTTTAACCCCTAAACTTTTCCA
*
125535 AAGTCATATTTTAACC
1 AAATCATATTTTAACC
125551 TTCGAACTTC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (30 bp):
AAATCATATTTTAACCCCTAAACTTTTCCA
Found at i:125622 original size:28 final size:29
Alignment explanation
Indices: 125542--125811 Score: 160
Period size: 29 Copynumber: 9.2 Consensus size: 29
125532 CTAAAGTCAT
* * * *
125542 ATTTTAACCTTCGAACTTCAAAAAATCAC
1 ATTTTTACCCTCGAACTTCCAAAAATTAC
* *
125571 ATTTTGT-CTC-CGAACTTCAAAAAATTAC
1 ATTTT-TACCCTCGAACTTCCAAAAATTAC
*
125599 ATTTTTACCCTCGAACTTCCAAAAAGAAAATCAC
1 ATTTTTACCCTCGAACTTCC----A-AAAATTAC
125633 ATTTTTA-CCTCGAACTTCTCAAAAATTAC
1 ATTTTTACCCTCGAACTTC-CAAAAATTAC
* * *
125662 ATTTTTGCACTCGAACTTCCAAAAATAAC
1 ATTTTTACCCTCGAACTTCCAAAAATTAC
* ** **
125691 ATTTTTACCC-CTAAACTT-TTAAAACCAC
1 ATTTTTACCCTC-GAACTTCCAAAAATTAC
* * *
125719 ATTTTTA-CCTTGAACTTTCCTAAAATGAC
1 ATTTTTACCCTCGAAC-TTCCAAAAATTAC
** *
125748 ATTTTTACCCCTAAAACTTTCC-AAAACTAC
1 ATTTTTA-CCCTCGAAC-TTCCAAAAATTAC
* * *
125778 TTTTTTACCC-CGAACTTTCCTAAAATGAC
1 ATTTTTACCCTCGAAC-TTCCAAAAATTAC
125807 ATTTT
1 ATTTT
125812 ATCCCTAAAT
Statistics
Matches: 191, Mismatches: 33, Indels: 34
0.74 0.13 0.13
Matches are distributed among these distances:
27 6 0.03
28 48 0.25
29 76 0.40
30 23 0.12
31 11 0.06
33 12 0.06
34 15 0.08
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
ATTTTTACCCTCGAACTTCCAAAAATTAC
Found at i:125648 original size:62 final size:63
Alignment explanation
Indices: 125563--125686 Score: 182
Period size: 63 Copynumber: 2.0 Consensus size: 63
125553 CGAACTTCAA
*
125563 AAAATCACATTTTGTCTCCGAACTTC-AAAAAATTACATTTTTACCCTCGAACTTCCAAAAAG
1 AAAATCACATTTTGTCTCCGAACTTCTAAAAAATTACATTTTTACACTCGAACTTCCAAAAAG
* *
125625 AAAATCACATTTT-TAC-CTCGAACTTCTCAAAAATTACATTTTTGCACTCGAACTTCCAAAAA
1 AAAATCACATTTTGT-CTC-CGAACTTCTAAAAAATTACATTTTTACACTCGAACTTCCAAAAA
125687 TAACATTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
61 2 0.04
62 22 0.39
63 32 0.57
ACGTcount: A:0.39, C:0.24, G:0.06, T:0.31
Consensus pattern (63 bp):
AAAATCACATTTTGTCTCCGAACTTCTAAAAAATTACATTTTTACACTCGAACTTCCAAAAAG
Found at i:125649 original size:33 final size:35
Alignment explanation
Indices: 125591--125657 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
125581 CGAACTTCAA
*
125591 AAAATTACATTTTTACCCTCGAACTTC-CAAAAAG
1 AAAATCACATTTTTACCCTCGAACTTCTCAAAAAG
125625 AAAATCACATTTTTA-CCTCGAACTTCTCAAAAA
1 AAAATCACATTTTTACCCTCGAACTTCTCAAAAA
125658 TTACATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 11 0.35
34 20 0.65
ACGTcount: A:0.42, C:0.24, G:0.04, T:0.30
Consensus pattern (35 bp):
AAAATCACATTTTTACCCTCGAACTTCTCAAAAAG
Found at i:125707 original size:29 final size:30
Alignment explanation
Indices: 125499--125831 Score: 153
Period size: 29 Copynumber: 11.3 Consensus size: 30
125489 CCCTTAAACT
* * *
125499 TTTCC-AAAATTACATTTTGACCCCTAAAC
1 TTTCCAAAAATCACATTTTTACCCCTGAAC
* * * * * *
125528 TTTTCTAAAGTCATA-TTTTAACCTTCGAAC
1 TTTCCAAAAATCACATTTTTACCCCT-GAAC
* *
125558 -TTCAAAAAATCACATTTTGT-CTCC-GAAC
1 TTTCCAAAAATCACATTTT-TACCCCTGAAC
* *
125586 -TTCAAAAAATTACATTTTTA-CCCTCGAAC
1 TTTCCAAAAATCACATTTTTACCCCT-GAAC
*
125615 -TTCCAAAAAGAAAATCACATTTTTACCTC-GAAC
1 TTTCC----A-AAAATCACATTTTTACCCCTGAAC
* * *
125648 -TTCTCAAAAATTACATTTTT-GCACTCGAAC
1 TTTC-CAAAAATCACATTTTTACCCCT-GAAC
* *
125678 -TTCCAAAAATAACATTTTTACCCCTAAAC
1 TTTCCAAAAATCACATTTTTACCCCTGAAC
* * *
125707 TTT--TAAAACCACATTTTTA-CCTTGAAC
1 TTTCCAAAAATCACATTTTTACCCCTGAAC
* * *
125734 TTTCCTAAAATGACATTTTTACCCCTAAAAC
1 TTTCCAAAAATCACATTTTTACCCCT-GAAC
* *
125765 TTTCCAAAACT-ACTTTTTTACCCC-GAAC
1 TTTCCAAAAATCACATTTTTACCCCTGAAC
* * * *
125793 TTTCCTAAAATGACA-TTTTATCCCTAAATC
1 TTTCCAAAAATCACATTTTTACCCCTGAA-C
125823 TTTCCAAAA
1 TTTCCAAAA
125832 TTATATTTTA
Statistics
Matches: 232, Mismatches: 47, Indels: 49
0.71 0.14 0.15
Matches are distributed among these distances:
27 12 0.05
28 56 0.24
29 76 0.33
30 50 0.22
31 13 0.06
33 8 0.03
34 15 0.06
35 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.04, T:0.35
Consensus pattern (30 bp):
TTTCCAAAAATCACATTTTTACCCCTGAAC
Found at i:125708 original size:92 final size:91
Alignment explanation
Indices: 125542--125708 Score: 214
Period size: 92 Copynumber: 1.8 Consensus size: 91
125532 CTAAAGTCAT
* *
125542 ATTTTAACCTTCGAACTTCAAAAAATCACATTTTGTCTCCGAACTTCAAAAAATTACATTTTTAC
1 ATTTTAACCTTCGAACTTCAAAAAATCACATTTTGACTCCGAACTTCAAAAAATAACATTTTTAC
*
125607 CCTCGAACTTCCAAAAAGAAAATCAC
66 CCTCAAACTTCCAAAAAGAAAATCAC
* * * *
125633 ATTTTTACC-TCGAACTTCTCAAAAATTACATTTTTGCACT-CGAACTTCCAAAAATAACATTTT
1 ATTTTAACCTTCGAACTTC-AAAAAATCACA-TTTTG-ACTCCGAACTTCAAAAAATAACATTTT
125696 TACCC-CTAAACTT
63 TACCCTC-AAACTT
125709 TTAAAACCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
90 9 0.14
91 18 0.28
92 36 0.55
93 2 0.03
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.34
Consensus pattern (91 bp):
ATTTTAACCTTCGAACTTCAAAAAATCACATTTTGACTCCGAACTTCAAAAAATAACATTTTTAC
CCTCAAACTTCCAAAAAGAAAATCAC
Found at i:125750 original size:57 final size:58
Alignment explanation
Indices: 125625--125831 Score: 215
Period size: 58 Copynumber: 3.6 Consensus size: 58
125615 TTCCAAAAAG
* * * * ** * *
125625 AAAATCACATTTTTACCTC-GAACTTCTCAAAAATTACATTTTTGCACTCGAAC-TTCCA
1 AAAATGACATTTTTACCCCTAAACTT-TCCAAAACCACATTTTTAC-CTCGAACTTTCCT
* * *
125683 AAAATAACATTTTTACCCCTAAACTTT-TAAAACCACATTTTTACCTTGAACTTTCCT
1 AAAATGACATTTTTACCCCTAAACTTTCCAAAACCACATTTTTACCTCGAACTTTCCT
* * *
125740 AAAATGACATTTTTACCCCTAAAACTTTCCAAAACTACTTTTTTACCCCGAACTTTCCT
1 AAAATGACATTTTTACCCCT-AAACTTTCCAAAACCACATTTTTACCTCGAACTTTCCT
*
125799 AAAATGACA-TTTTATCCCTAAATCTTTCCAAAA
1 AAAATGACATTTTTACCCCTAAA-CTTTCCAAAA
125832 TTATATTTTA
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
56 6 0.05
57 39 0.30
58 44 0.34
59 39 0.30
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
AAAATGACATTTTTACCCCTAAACTTTCCAAAACCACATTTTTACCTCGAACTTTCCT
Found at i:125795 original size:86 final size:86
Alignment explanation
Indices: 125625--125788 Score: 197
Period size: 86 Copynumber: 1.9 Consensus size: 86
125615 TTCCAAAAAG
* * * **
125625 AAAATCACATTTTTACCTCGAACTTCTCAAAAATTACATTTTTGCACTCGAACTTCCAAAAATAA
1 AAAACCACATTTTTACCTCGAACTTCTCAAAAATGACATTTTTCCACTAAAACTTCCAAAAATAA
125690 CATTTTTACCCCTAAACTTTT
66 CATTTTTACCCCTAAACTTTT
* * * *
125711 AAAACCACATTTTTACCTTGAACTT-TCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAAC
1 AAAACCACATTTTTACCTCGAACTTCT-CAAAAATGACATTTTT-CCACTAAAAC-TTCCAAAAA
*
125775 T-ACTTTTTTACCCC
63 TAACATTTTTACCCC
125789 GAACTTTCCT
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
85 1 0.02
86 37 0.57
87 18 0.28
88 9 0.14
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (86 bp):
AAAACCACATTTTTACCTCGAACTTCTCAAAAATGACATTTTTCCACTAAAACTTCCAAAAATAA
CATTTTTACCCCTAAACTTTT
Found at i:125818 original size:58 final size:59
Alignment explanation
Indices: 125673--125831 Score: 209
Period size: 59 Copynumber: 2.8 Consensus size: 59
125663 TTTTTGCACT
* * * *
125673 CGAAC-TTCCAAAAATAACATTTTTACCCCT-AAACTTT-TAAAACCACATTTTTACCT
1 CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACCACATTTTTACCC
* * *
125729 TGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACTACTTTTTTACCC
1 CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACCACATTTTTACCC
* *
125788 CGAACTTTCCTAAAATGACA-TTTTATCCCTAAATCTTTCCAAAA
1 CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAA
125832 TTATATTTTA
Statistics
Matches: 90, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
56 4 0.04
57 23 0.26
58 29 0.32
59 34 0.38
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (59 bp):
CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACCACATTTTTACCC
Found at i:125832 original size:29 final size:29
Alignment explanation
Indices: 125678--125851 Score: 101
Period size: 29 Copynumber: 6.0 Consensus size: 29
125668 GCACTCGAAC
* * *
125678 TTCCAAAAATAACATTTTTACCCCTAAACT
1 TTCCTAAAATGACA-TTTTATCCCTAAACT
** * *
125708 TT--TAAAACCACATTTT-TACCTTGAACT
1 TTCCTAAAATGACATTTTAT-CCCTAAACT
*
125735 TTCCTAAAATGACATTTTTACCCCTAAAACT
1 TTCCTAAAATGACA-TTTTATCCCT-AAACT
* **
125766 TTCC-AAAACT-AC-TTTTTTACCCCGAACT
1 TTCCTAAAA-TGACATTTTAT-CCCTAAACT
125794 TTCCTAAAATGACATTTTATCCCTAAATCT
1 TTCCTAAAATGACATTTTATCCCTAAA-CT
* * * *
125824 TTCC-AAAATTATATTTTAACCCCAAACT
1 TTCCTAAAATGACATTTTATCCCTAAACT
125852 CTCTGAAACT
Statistics
Matches: 110, Mismatches: 22, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
27 13 0.12
28 22 0.20
29 40 0.36
30 26 0.24
31 9 0.08
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (29 bp):
TTCCTAAAATGACATTTTATCCCTAAACT
Found at i:125846 original size:58 final size:59
Alignment explanation
Indices: 125673--125851 Score: 199
Period size: 58 Copynumber: 3.1 Consensus size: 59
125663 TTTTTGCACT
* * * * *
125673 CGAAC-TTCCAAAAATAACATTTTTACCCCT-AAACTTT-TAAAACCACATTTTT-ACCT
1 CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACTAC-TTTTTAACCC
* *
125729 TGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACTACTTTTTTACCC
1 CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACTACTTTTTAACCC
* * *
125788 CGAACTTTCCTAAAATGACA-TTTTATCCCTAAATCTTTCCAAAATTA-TATTTTAACCC
1 CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACTACT-TTTTAACCC
*
125846 CAAACT
1 CGAACT
125852 CTCTGAAACT
Statistics
Matches: 106, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
56 4 0.04
57 24 0.23
58 49 0.46
59 29 0.27
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (59 bp):
CGAACTTTCCTAAAATGACATTTTTACCCCTAAAACTTTCCAAAACTACTTTTTAACCC
Found at i:129149 original size:58 final size:59
Alignment explanation
Indices: 129035--129573 Score: 752
Period size: 58 Copynumber: 9.3 Consensus size: 59
129025 GCACGAGGGC
* * * *
129035 AAAATGGT-AGTTTTAGAAGGTTCGGAGTC-AAAATGGGAGTTTTGGAAGTTCAGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
129092 -AAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
129150 AAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
*
129209 AAAATGGTAATTTTTAGAAGGTTC-GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * ** * * * * *
129267 AAGATGATAATTTTTAGAAGGTTTAGAGT-GAAAATGAGATTTTTAGAAGTTTGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* *
129325 AAAATGGTAATTTTTAGAAGGTTCGGGCTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
129384 AAAATTGTAA-TTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
129442 AAAAATGGTACTTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGAGGGT
1 -AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
* * *
129502 AAAATGGTAA-TTTTATAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT-TGGGGT
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
129559 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
129574 GAAAAGTTTA
Statistics
Matches: 428, Mismatches: 46, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
56 7 0.02
57 34 0.08
58 213 0.50
59 130 0.30
60 44 0.10
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGT
Found at i:129325 original size:175 final size:174
Alignment explanation
Indices: 129028--129573 Score: 782
Period size: 175 Copynumber: 3.1 Consensus size: 174
129018 TTCGAATGCA
* * *
129028 CGAGGGCAAAATGGT-AGTTTTAGAAGGTTCGGAGTC-AAAATGGGAGTTTTGGAAGTTC-AGGG
1 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGG-GTCAAAAATGGGATTTTTGGAAGTTCGA-GG
*
129090 GTAAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTGGAAGTTTGGGGGTAAAAT
64 GTAAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAAT
129155 GGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
129 GGTAATTTTT-GAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
129202 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
1 CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
* ** * *
129267 AAGATGATAATTTTTAGAAGGTTTAGAGT-GAAAATGAGATTTTTAGAAGTTTGGGGGTAAAATG
66 AA-ATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATG
*
129331 GTAATTTTTAGAAGGTTCGGGCTCAAAAATGGGATTTTTGGAAGTT
130 GTAATTTTT-GAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
* * * *
129377 CGAGGGTAAAATTGTAA-TTTTAGAAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGGGGG
1 CGAGGGTAAAATGGTAATTTTTAGAAGG-TTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGG
* * * *
129441 TAAAAATGGTACTTTTTAGAAGGTTCGGGGTCAAAAATGGGATTTTTAGAAGTTCGAGGGTAAAA
65 T--AAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAA
*
129506 TGGTAATTTTAT-AAGGTTTGGGGTCAAAAATGGGATTTTTGGAAGTT
128 TGGTAATTTT-TGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
*
129553 TG-GGGTAAAATGGTAATTTTT
1 CGAGGGTAAAATGGTAATTTTT
129574 GAAAAGTTTA
Statistics
Matches: 334, Mismatches: 28, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
174 27 0.08
175 182 0.54
176 83 0.25
177 41 0.12
178 1 0.00
ACGTcount: A:0.31, C:0.04, G:0.32, T:0.34
Consensus pattern (174 bp):
CGAGGGTAAAATGGTAATTTTTAGAAGGTTCGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGT
AAATGGTAATTTTTAGAAGGTTCGGAGTCAAAAATGGGATTTTTAGAAGTTTGGGGGTAAAATGG
TAATTTTTGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTT
Found at i:129543 original size:29 final size:29
Alignment explanation
Indices: 129035--129544 Score: 160
Period size: 29 Copynumber: 17.4 Consensus size: 29
129025 GCACGAGGGC
* * *
129035 AAAATGGTAGTTTTAGAAGGTTCGGAGTC-
1 AAAATGGGA-TTTTATAAGGTTCGGGGTCA
**
129064 AAAATGGGAGTTTTGGAA-GTTCAGGGGT--
1 AAAATGGGA-TTTTATAAGGTTC-GGGGTCA
* * *
129092 -AAATGGTAATTTTTAGAAGGTTCGGAGTCA
1 AAAATGG-GA-TTTTATAAGGTTCGGGGTCA
* *
129122 AAAATGGGATTTT-TGGAAGTTTGGGGGT--
1 AAAATGGGATTTTAT--AAGGTTCGGGGTCA
*
129150 AAAATGGTAATTTT-TGGAAGGTTCGGGGTCA
1 AAAATGG-GATTTTAT--AAGGTTCGGGGTCA
129181 AAAATGGGATTTT-TGGAA-GTTCGAGGGT--
1 AAAATGGGATTTTAT--AAGGTTCG-GGGTCA
* *
129209 AAAATGGTAATTTTTAGAAGGTTC-GGGTCA
1 AAAATGG-GA-TTTTATAAGGTTCGGGGTCA
129239 AAAATGGGATTTT-TGGAA-GTTCGAGGGT--
1 AAAATGGGATTTTAT--AAGGTTCG-GGGTCA
* ** * ** * *
129267 AAGATGATAATTTTTAGAAGGTTTAGAGT-G
1 AAAATG-GGA-TTTTATAAGGTTCGGGGTCA
* * * *
129297 AAAATGAGATTTTTAGAAGTTTGGGGGT--
1 AAAATGGGA-TTTTATAAGGTTCGGGGTCA
* * *
129325 AAAATGGTAATTTTTAGAAGGTTCGGGCTCA
1 AAAATGG-GA-TTTTATAAGGTTCGGGGTCA
129356 AAAATGGGATTTT-TGGAA-GTTCGAGGGT-A
1 AAAATGGGATTTTAT--AAGGTTCG-GGGTCA
* ** * *
129385 AAATTGTAATTTTAGAAGGTTTGGGGTCA
1 AAAATGGGATTTTATAAGGTTCGGGGTCA
* *
129414 AAAATGGGATTTT-TGGAAGTTTGGGGGT-A
1 AAAATGGGATTTTAT--AAGGTTCGGGGTCA
* *
129443 AAAATGGTACTTTTTAGAAGGTTCGGGGTCA
1 AAAATGGGA--TTTTATAAGGTTCGGGGTCA
*
129474 AAAATGGGATTTT-TAGAAGTTCGAGGGT--
1 AAAATGGGATTTTATA-AGGTTCG-GGGTCA
* *
129502 AAAATGGTAATTTTATAAGGTTTGGGGTCA
1 AAAATGG-GATTTTATAAGGTTCGGGGTCA
129532 AAAATGGGATTTT
1 AAAATGGGATTTT
129545 TGGAAGTTTG
Statistics
Matches: 369, Mismatches: 64, Indels: 96
0.70 0.12 0.18
Matches are distributed among these distances:
27 6 0.02
28 71 0.19
29 165 0.45
30 94 0.25
31 33 0.09
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (29 bp):
AAAATGGGATTTTATAAGGTTCGGGGTCA
Found at i:129580 original size:29 final size:30
Alignment explanation
Indices: 129092--129582 Score: 294
Period size: 29 Copynumber: 16.8 Consensus size: 30
129082 GTTCAGGGGT
* *
129092 AAATGGTAATTTTT-AGAAGGTTCGGAGTCAA
1 AAATGGTAATTTTTGAGAA-GTTTGGGGT-AA
*
129123 AAATGG-GATTTTTG-GAAGTTTGGGGGT-A
1 AAATGGTAATTTTTGAGAAGTTT-GGGGTAA
*
129151 AAATGGTAATTTTTG-GAAGGTTCGGGGTCAA
1 AAATGGTAATTTTTGAGAA-GTTTGGGGT-AA
* *
129182 AAATGG-GATTTTTG-GAAGTTCGAGGGT-A
1 AAATGGTAATTTTTGAGAAGTTTG-GGGTAA
* *
129210 AAATGGTAATTTTT-AGAAGGTTCGGGTCAA
1 AAATGGTAATTTTTGAGAAGTTTGGGGT-AA
* *
129240 AAATGG-GATTTTTG-GAAGTTCGAGGGT-A
1 AAATGGTAATTTTTGAGAAGTTTG-GGGTAA
* * * * *
129268 AGATGATAATTTTT-AGAAGGTTTAGAGTGA
1 AAATGGTAATTTTTGAGAA-GTTTGGGGTAA
129298 AAAT-G-AGATTTTT-AGAAGTTTGGGGGT-A
1 AAATGGTA-ATTTTTGAGAAGTTT-GGGGTAA
* *
129326 AAATGGTAATTTTT-AGAAGGTTCGGGCTCAA
1 AAATGGTAATTTTTGAGAA-GTTTGGGGT-AA
* *
129357 AAATGG-GATTTTTG-GAAGTTCGAGGGT-A
1 AAATGGTAATTTTTGAGAAGTTTG-GGGTAA
*
129385 AAATTGTAA-TTTT-AGAAGGTTTGGGGTCAA
1 AAATGGTAATTTTTGAGAA-GTTTGGGGT-AA
*
129415 AAATGG-GATTTTTG-GAAGTTTGGGGGTAA
1 AAATGGTAATTTTTGAGAAGTTT-GGGGTAA
* *
129444 AAATGGTACTTTTT-AGAAGGTTCGGGGTCAA
1 AAATGGTAATTTTTGAGAA-GTTTGGGGT-AA
* *
129475 AAATGG-GATTTTT-AGAAGTTCGAGGGT-A
1 AAATGGTAATTTTTGAGAAGTTTG-GGGTAA
*
129503 AAATGGTAATTTTAT-A-AGGTTTGGGGTCAA
1 AAATGGTAATTTT-TGAGAAGTTTGGGGT-AA
*
129533 AAATGG-GATTTTTG-GAAGTTTGGGGT-A
1 AAATGGTAATTTTTGAGAAGTTTGGGGTAA
*
129560 AAATGGTAATTTTTGAAAAGTTT
1 AAATGGTAATTTTTGAGAAGTTT
129583 AGGGACCTTC
Statistics
Matches: 368, Mismatches: 45, Indels: 96
0.72 0.09 0.19
Matches are distributed among these distances:
27 7 0.02
28 69 0.19
29 144 0.39
30 117 0.32
31 31 0.08
ACGTcount: A:0.31, C:0.04, G:0.31, T:0.34
Consensus pattern (30 bp):
AAATGGTAATTTTTGAGAAGTTTGGGGTAA
Done.