Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012592.1 Kokia drynarioides strain JFW-HI SEQ_127601, 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: 244298
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 107 characters in sequence are not A, C, G, or T
Found at i:282 original size:16 final size:15
Alignment explanation
Indices: 263--296 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
253 ATTATATTAA
263 TATTTAATAATTCTTT
1 TATTTAATAATT-TTT
279 TATTTAATAATTTTT
1 TATTTAATAATTTTT
294 TAT
1 TAT
297 ATAGTCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.33
16 12 0.67
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TATTTAATAATTTTT
Found at i:1539 original size:16 final size:17
Alignment explanation
Indices: 1518--1551 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1508 TGTATTTAAA
*
1518 TATTT-AAATTTCATTT
1 TATTTAAAATTTAATTT
1534 TATTTAAAATTTAATTT
1 TATTTAAAATTTAATTT
1551 T
1 T
1552 TTTTCATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTTAAAATTTAATTT
Found at i:5060 original size:22 final size:22
Alignment explanation
Indices: 5035--5078 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5025 AGCCAGCTGG
5035 AAAGTCTCGATCAAATGGCTAT
1 AAAGTCTCGATCAAATGGCTAT
5057 AAAGTCTCGATCAAATGGCTAT
1 AAAGTCTCGATCAAATGGCTAT
5079 GTGACATGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.27
Consensus pattern (22 bp):
AAAGTCTCGATCAAATGGCTAT
Found at i:9939 original size:5 final size:5
Alignment explanation
Indices: 9924--9952 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
9914 GTCAAAAATT
9924 GAAAA -AAAA GAAAA GAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
9953 CCCTAGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:15895 original size:30 final size:32
Alignment explanation
Indices: 15832--15891 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 32
15822 AAGGCTATAA
*
15832 TAGAATCTCCTCTCTAGTTTTTATGACTTAAC
1 TAGAATCTCATCTCTAGTTTTTATGACTTAAC
*
15864 TAGAA-CTCATCT-TAGTTTTTGTGA-TTAA
1 TAGAATCTCATCTCTAGTTTTTATGACTTAA
15892 ACTAAAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 11 0.42
31 6 0.23
32 5 0.19
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.45
Consensus pattern (32 bp):
TAGAATCTCATCTCTAGTTTTTATGACTTAAC
Found at i:21110 original size:17 final size:15
Alignment explanation
Indices: 21078--21123 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
21068 ACTATAAAAA
*
21078 TAATTATTTTTA-TT
1 TAATTATTTATATTT
21092 TAATTTATATTATATTT
1 TAA-TTAT-TTATATTT
21109 TAATTATTTATATTT
1 TAATTATTTATATTT
21124 GAAATATACG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 3 0.11
15 12 0.43
16 8 0.29
17 5 0.18
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTATTTATATTT
Found at i:21117 original size:20 final size:20
Alignment explanation
Indices: 21080--21122 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
21070 TATAAAAATA
*
21080 ATTATTTTTATTTAATTTAT
1 ATTATTTTTAATTAATTTAT
21100 ATTATATTTTAATT-ATTTAT
1 ATTAT-TTTTAATTAATTTAT
21120 ATT
1 ATT
21123 TGAAATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTATTTTTAATTAATTTAT
Found at i:23812 original size:284 final size:284
Alignment explanation
Indices: 23302--23870 Score: 1129
Period size: 284 Copynumber: 2.0 Consensus size: 284
23292 CTCTTAATTG
23302 AGCTAATTCAGTCCTGAAATAGTTTAATTTAATGGGTTTTTAATAGGATGGCCATGAATGGAGCT
1 AGCTAATTCAGTCCTGAAATAGTTTAATTTAATGGGTTTTTAATAGGATGGCCATGAATGGAGCT
23367 TGAATTGGGTAAATTTTGAGAAAAAAGAAAGCTTGATGATGTGTTTTGGTTAAATTTTGGGGCAG
66 TGAATTGGGTAAATTTTGAGAAAAAAGAAAGCTTGATGATGTGTTTTGGTTAAATTTTGGGGCAG
23432 GACCAATTAGGTGATGTATTGCATTGGATTCGACAAGTTGTAGCTCTTTTATGTGGTTTATTATG
131 GACCAATTAGGTGATGTATTGCATTGGATTCGACAAGTTGTAGCTCTTTTATGTGGTTTATTATG
23497 GGGTGCAATCCCTGTTGTCGGAGGCATTTGGATCTTCATGTAAGTTCACATATTCATGTTACATG
196 GGGTGCAATCCCTGTTGTCGGAGGCATTTGGATCTTCATGTAAGTTCACATATTCATGTTACATG
23562 CATTTTTTGAATTGCAGTGTTCCA
261 CATTTTTTGAATTGCAGTGTTCCA
23586 AGCTAATTCAGTCCTGAAATAGTTTAATTTAATGGGTTTTTAATAGGATGGCCATGAATGGAGCT
1 AGCTAATTCAGTCCTGAAATAGTTTAATTTAATGGGTTTTTAATAGGATGGCCATGAATGGAGCT
*
23651 TGAATTGGGTAAATTTTGAGAAAAAAGAAAGCTTGATGATGTGTTTTGGTTGAATTTTGGGGCAG
66 TGAATTGGGTAAATTTTGAGAAAAAAGAAAGCTTGATGATGTGTTTTGGTTAAATTTTGGGGCAG
23716 GACCAATTAGGTGATGTATTGCATTGGATTCGACAAGTTGTAGCTCTTTTATGTGGTTTATTATG
131 GACCAATTAGGTGATGTATTGCATTGGATTCGACAAGTTGTAGCTCTTTTATGTGGTTTATTATG
23781 GGGTGCAATCCCTGTTGTCGGAGGCATTTGGATCTTCATGTAAGTTCACATATTCATGTTACATG
196 GGGTGCAATCCCTGTTGTCGGAGGCATTTGGATCTTCATGTAAGTTCACATATTCATGTTACATG
23846 CATTTTTTGAATTGCAGTGTTCCA
261 CATTTTTTGAATTGCAGTGTTCCA
23870 A
1 A
23871 ACTTGTCTGG
Statistics
Matches: 284, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 284 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.38
Consensus pattern (284 bp):
AGCTAATTCAGTCCTGAAATAGTTTAATTTAATGGGTTTTTAATAGGATGGCCATGAATGGAGCT
TGAATTGGGTAAATTTTGAGAAAAAAGAAAGCTTGATGATGTGTTTTGGTTAAATTTTGGGGCAG
GACCAATTAGGTGATGTATTGCATTGGATTCGACAAGTTGTAGCTCTTTTATGTGGTTTATTATG
GGGTGCAATCCCTGTTGTCGGAGGCATTTGGATCTTCATGTAAGTTCACATATTCATGTTACATG
CATTTTTTGAATTGCAGTGTTCCA
Found at i:32785 original size:23 final size:22
Alignment explanation
Indices: 32743--32789 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
32733 TACAGTGAGT
* *
32743 AAAAAATTAATGTAATAAATCTA
1 AAAAAATTAATATAAAAAAT-TA
*
32766 AAAAAATTCATATAAAAAATTA
1 AAAAAATTAATATAAAAAATTA
32788 AA
1 AA
32790 TATGATGCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (22 bp):
AAAAAATTAATATAAAAAATTA
Found at i:34138 original size:36 final size:36
Alignment explanation
Indices: 34088--34164 Score: 118
Period size: 36 Copynumber: 2.1 Consensus size: 36
34078 GAAGGAATGA
*
34088 TTCATGCATCGATGGATTGAAACTCATTAAATTAAT
1 TTCATGCATAGATGGATTGAAACTCATTAAATTAAT
* * *
34124 TTCATGCATAGATGGGTTGAAATTCATTGAATTAAT
1 TTCATGCATAGATGGATTGAAACTCATTAAATTAAT
34160 TTCAT
1 TTCAT
34165 CAAAGGATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.39
Consensus pattern (36 bp):
TTCATGCATAGATGGATTGAAACTCATTAAATTAAT
Found at i:40660 original size:5 final size:5
Alignment explanation
Indices: 40653--40701 Score: 89
Period size: 5 Copynumber: 9.8 Consensus size: 5
40643 GTCGCTCTCT
*
40653 CTTCT CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTC
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTCC CTTC
40702 TTCCCTACAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (5 bp):
CTTCC
Found at i:43358 original size:24 final size:25
Alignment explanation
Indices: 43331--43378 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
43321 AAGTATATTA
*
43331 TTTTTAT-AATATATATACCATAAC
1 TTTTTATAAATAAATATACCATAAC
*
43355 TTTTTATAAATAAATATATCATAA
1 TTTTTATAAATAAATATACCATAA
43379 ACACTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTTATAAATAAATATACCATAAC
Found at i:57961 original size:18 final size:17
Alignment explanation
Indices: 57938--58013 Score: 73
Period size: 20 Copynumber: 4.2 Consensus size: 17
57928 ATTCCAAAAG
57938 TAATATTATTTTAATAGT
1 TAATATTATTTTAATA-T
*
57956 TAATATTAAATTTAAT-T
1 TAATATT-ATTTTAATAT
57973 TAATACTTATTTTAATAT
1 TAATA-TTATTTTAATAT
*
57991 TAAAATGATTATCTTAATAT
1 T--AAT-ATTATTTTAATAT
58011 TAA
1 TAA
58014 ATTTAATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
17 13 0.27
18 13 0.27
19 7 0.14
20 15 0.31
21 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
TAATATTATTTTAATAT
Found at i:57977 original size:17 final size:18
Alignment explanation
Indices: 57938--58025 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 18
57928 ATTCCAAAAG
*
57938 TAATA-TTATTTTAATAGT
1 TAATATTTAATTTAATA-T
*
57956 TAATATTAAATTTAAT-T
1 TAATATTTAATTTAATAT
* *
57973 TAATACTTATTTTAATAT
1 TAATATTTAATTTAATAT
*
57991 TAAAATGATT-ATCTTAATAT
1 TAATAT--TTAAT-TTAATAT
58011 TAA-ATTTAATTTAAT
1 TAATATTTAATTTAAT
58026 GTTTATCTAC
Statistics
Matches: 56, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
17 21 0.38
18 12 0.21
19 11 0.20
20 12 0.21
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATATTTAATTTAATAT
Found at i:58075 original size:62 final size:59
Alignment explanation
Indices: 58004--58120 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 59
57994 AATGATTATC
* * * *
58004 TTAATATTAAATTTAATTTAATGTTTATCTACAAGATAAATATTCTATTATTTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATCT--AA-ATAAATATTATATTAATTTAATAAGAT
*
58066 TTAATATTAAATTTAATCTAATATTTATCTTAATAAATATTATATTAATTTAATA
1 TTAATATTAAATTTAATCTAATATTTATCTAAATAAATATTATATTAATTTAATA
58121 TTTAAAGAGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 21 0.42
60 1 0.02
62 28 0.56
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTAAATAAATATTATATTAATTTAATAAGAT
Found at i:85475 original size:43 final size:45
Alignment explanation
Indices: 85377--85475 Score: 107
Period size: 45 Copynumber: 2.2 Consensus size: 45
85367 TACTTTATTC
* * *
85377 AAATATAATTTCGTTCTTAAAAAAAAAACTTATAAACTAAATCCA
1 AAATATATTTTCCTTCTTAAAAAAAAAACTTATAAACTAAATCAA
* *
85422 AAATCA-ATTTTCTCTTCTT-AAAAAAAAAC-TGTAAATTAAAT-AA
1 AAAT-ATATTTTC-CTTCTTAAAAAAAAAACTTATAAACTAAATCAA
85465 AAATATATTTT
1 AAATATATTTT
85476 TTAAAAATTA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
42 1 0.02
43 10 0.22
44 10 0.22
45 19 0.41
46 6 0.13
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (45 bp):
AAATATATTTTCCTTCTTAAAAAAAAAACTTATAAACTAAATCAA
Found at i:86119 original size:20 final size:19
Alignment explanation
Indices: 86067--86119 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
86057 TAAAAATCTT
*
86067 AAAAATTATAAAACTTATA
1 AAAAACTATAAAACTTATA
*
86086 AAAAACTTAGAAAACTTA-A
1 AAAAAC-TATAAAACTTATA
86105 ATTAAAACTATAAAA
1 A--AAAACTATAAAA
86120 GAAAGAATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 7 0.25
20 16 0.57
21 5 0.18
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAACTATAAAACTTATA
Found at i:93369 original size:2 final size:2
Alignment explanation
Indices: 93362--93389 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93352 AGGTTCATAA
93362 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
93390 TTGTTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:97053 original size:42 final size:42
Alignment explanation
Indices: 96994--97078 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
96984 TTTCCTATTT
*
96994 ATGTATTATAATATGAAGAGTTGAATCTTCTTATATATATAG
1 ATGTATTAGAATATGAAGAGTTGAATCTTCTTATATATATAG
97036 ATGTATTAGAATATGAAGAGTTGAATCTTCTTATATATATAG
1 ATGTATTAGAATATGAAGAGTTGAATCTTCTTATATATATAG
97078 A
1 A
97079 AGAGTATGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (42 bp):
ATGTATTAGAATATGAAGAGTTGAATCTTCTTATATATATAG
Found at i:100955 original size:37 final size:37
Alignment explanation
Indices: 100905--100977 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
100895 TATTATTTGG
*
100905 TTATCGTTGAAAAATGCAACCGACTTCTAACTTTAGC
1 TTATCATTGAAAAATGCAACCGACTTCTAACTTTAGC
*
100942 TTATCATTGAAAAATGCAATCGACTTCTAACTTTAG
1 TTATCATTGAAAAATGCAACCGACTTCTAACTTTAG
100978 TTGGTGTTAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (37 bp):
TTATCATTGAAAAATGCAACCGACTTCTAACTTTAGC
Found at i:111782 original size:14 final size:15
Alignment explanation
Indices: 111763--111799 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
111753 AATAAGTATT
111763 AAAATTTAAAT-TAA
1 AAAATTTAAATATAA
111777 AAAA-TT-AATATAA
1 AAAATTTAAATATAA
111790 AAAATTTAAA
1 AAAATTTAAA
111800 AATTAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.15
13 9 0.45
14 6 0.30
15 2 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATTTAAATATAA
Found at i:111824 original size:20 final size:20
Alignment explanation
Indices: 111799--111837 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
111789 AAAAATTTAA
*
111799 AAATTA-AATTAAATCAAATC
1 AAATTATAATAAAAT-AAATC
111819 AAATTATAATAAAATAAAT
1 AAATTATAATAAAATAAAT
111838 AACGGAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTATAATAAAATAAATC
Found at i:112420 original size:3 final size:3
Alignment explanation
Indices: 112412--112437 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
112402 CCTAATAAAC
112412 CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CC
112438 CATTTCCGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:112608 original size:21 final size:21
Alignment explanation
Indices: 112575--112615 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
112565 TTAATATAAA
*
112575 AAATTTAAATTGAATAGAGTG
1 AAATATAAATTGAATAGAGTG
* *
112596 AAATATAATTTGAGTAGAGT
1 AAATATAAATTGAATAGAGT
112616 TGAATTGAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (21 bp):
AAATATAAATTGAATAGAGTG
Found at i:112847 original size:10 final size:10
Alignment explanation
Indices: 112829--112867 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
112819 ACTTTCTGTA
*
112829 TATATTTTTT
1 TATAATTTTT
112839 TATAATTTTT
1 TATAATTTTT
*
112849 TTTAA-TTTT
1 TATAATTTTT
112858 TATAATTTTT
1 TATAATTTTT
112868 GGATAGTTCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
9 8 0.32
10 17 0.68
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATAATTTTT
Found at i:127588 original size:5 final size:5
Alignment explanation
Indices: 127578--127603 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
127568 TCTCTCCCTG
127578 AACCA AACCA AACCA AACCA AACCA A
1 AACCA AACCA AACCA AACCA AACCA A
127604 CAATGGCTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.38, G:0.00, T:0.00
Consensus pattern (5 bp):
AACCA
Found at i:129971 original size:19 final size:16
Alignment explanation
Indices: 129938--129983 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 16
129928 ATACAACATT
*
129938 AAAAGAAAAGGAAAAA
1 AAAAAAAAAGGAAAAA
129954 GAAAGAAAAAATGGAAAAA
1 -AAA-AAAAAA-GGAAAAA
129973 AAAAAAAAAGG
1 AAAAAAAAAGG
129984 GAGAGGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 2 0.08
17 9 0.35
18 8 0.31
19 7 0.27
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAAAAAAGGAAAAA
Found at i:130721 original size:18 final size:20
Alignment explanation
Indices: 130682--130721 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
130672 CCAAAAATTA
*
130682 TTATTTTAATAACTTTTAAT
1 TTATTTTAATAACTTATAAT
130702 TTATTTTAA-AA-TTATAAT
1 TTATTTTAATAACTTATAAT
130720 TT
1 TT
130722 CTTACATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTTAATAACTTATAAT
Found at i:131232 original size:47 final size:46
Alignment explanation
Indices: 131164--131315 Score: 223
Period size: 47 Copynumber: 3.2 Consensus size: 46
131154 ATCTATCCCC
*
131164 AAACCCTAAATTTCTCTAATCCCTAATTCTTAATTTCTCCTCTCTA
1 AAACCCCAAATTTCTCTAATCCCTAATTCTTAATTTCTCCTCTCTA
* *
131210 AAACCTCCAAATTTCTCCAATCCTTAATTCTTAATTTCTCCTCTCTTA
1 AAACC-CCAAATTTCTCTAATCCCTAATTCTTAATTTCTCCTCTC-TA
* * *
131258 AAACCCCAAATTTCTATAATCCCCAATTCTTAATTTTTCCTCTCTCA
1 AAACCCCAAATTTCTCTAATCCCTAATTCTTAATTTCTCCTCTCT-A
131305 AAACCCCAAAT
1 AAACCCCAAAT
131316 CCCAAATTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
46 6 0.06
47 82 0.86
48 7 0.07
ACGTcount: A:0.30, C:0.32, G:0.00, T:0.38
Consensus pattern (46 bp):
AAACCCCAAATTTCTCTAATCCCTAATTCTTAATTTCTCCTCTCTA
Found at i:131705 original size:35 final size:35
Alignment explanation
Indices: 131664--131733 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
131654 TCGTAAGTTC
131664 CTGTATTTTAATAAAATTTTAGATTTAGTCCATGT
1 CTGTATTTTAATAAAATTTTAGATTTAGTCCATGT
*
131699 CTGTATTTTAATAAAGTTTTAGATTTAGTCCATGT
1 CTGTATTTTAATAAAATTTTAGATTTAGTCCATGT
131734 ACTTGAAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.49
Consensus pattern (35 bp):
CTGTATTTTAATAAAATTTTAGATTTAGTCCATGT
Found at i:131812 original size:39 final size:39
Alignment explanation
Indices: 131767--131846 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 39
131757 TCCTCCTACT
*
131767 TTTGTATTTGGGACAATGATTTCATCGAGAAAGTCCAGG
1 TTTGTATTTGGGACAATGATTTCATCGAGAAAATCCAGG
131806 TTTGTATTTGGGACAATGATTTCATCGAGAAAATCCAGG
1 TTTGTATTTGGGACAATGATTTCATCGAGAAAATCCAGG
131845 TT
1 TT
131847 CTACCCAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (39 bp):
TTTGTATTTGGGACAATGATTTCATCGAGAAAATCCAGG
Found at i:134553 original size:21 final size:21
Alignment explanation
Indices: 134498--134547 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
134488 CTACAACTTA
*
134498 AAGCGGAAG-CAGCAGTGAGGG
1 AAGC-GAAGACAGCAGTAAGGG
134519 AAGCGAAGACAGCAGTAAGGG
1 AAGCGAAGACAGCAGTAAGGG
134540 AAGCGAAG
1 AAGCGAAG
134548 GTAGCAACGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 4 0.15
21 23 0.85
ACGTcount: A:0.40, C:0.14, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCGAAGACAGCAGTAAGGG
Found at i:134963 original size:43 final size:44
Alignment explanation
Indices: 134859--135043 Score: 148
Period size: 43 Copynumber: 4.3 Consensus size: 44
134849 AATCTATTAA
* * *
134859 TTTTAGCAACGTTTGT-GGAAAAAGCGTCGCTAAAAACCATGTT
1 TTTTAGCGACGTTTGTGGGGAAAAGCGCCGCTAAAAACCATGTT
* * * *
134902 TTTTAGTGGCGTTTGTGGGGAAAA-CGCCGCTAAAGATCAT-TCT
1 TTTTAGCGACGTTTGTGGGGAAAAGCGCCGCTAAAAACCATGT-T
* ** ** * *
134945 TTTTAGCGACGTTTGTGGGG-ACATTGCTACTAAAGACTATGTT
1 TTTTAGCGACGTTTGTGGGGAAAAGCGCCGCTAAAAACCATGTT
* * *
134988 TTTTAGTGGCGTTTGT--GGAAAAGCGCCGCTAAATACCATGTT
1 TTTTAGCGACGTTTGTGGGGAAAAGCGCCGCTAAAAACCATGTT
* *
135030 CTATAGCGACGTTT
1 TTTTAGCGACGTTT
135044 TTCCTCATAA
Statistics
Matches: 109, Mismatches: 28, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
41 2 0.02
42 29 0.27
43 71 0.65
44 7 0.06
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (44 bp):
TTTTAGCGACGTTTGTGGGGAAAAGCGCCGCTAAAAACCATGTT
Found at i:148517 original size:2 final size:2
Alignment explanation
Indices: 148510--148542 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
148500 TCTTAACCAA
148510 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
148543 AATTAATTAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:161013 original size:42 final size:42
Alignment explanation
Indices: 160966--161057 Score: 141
Period size: 42 Copynumber: 2.2 Consensus size: 42
160956 GAAGAAACAT
* * *
160966 GCTTTGAG-TCGGTGTATTTGTATCAAGTCTTGGGCCTAGTAG
1 GCTTTGAGAT-GGTGTATTTGTATCAAGCCTTGGGCCAAGCAG
161008 GCTTTGAGATGGTGTATTTGTATCAAGCCTTGGGCCAAGCAG
1 GCTTTGAGATGGTGTATTTGTATCAAGCCTTGGGCCAAGCAG
161050 GCTTTGAG
1 GCTTTGAG
161058 CCGATGAATA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 45 0.98
43 1 0.02
ACGTcount: A:0.18, C:0.15, G:0.32, T:0.35
Consensus pattern (42 bp):
GCTTTGAGATGGTGTATTTGTATCAAGCCTTGGGCCAAGCAG
Found at i:162678 original size:20 final size:21
Alignment explanation
Indices: 162634--162679 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
162624 TACAAAATAA
162634 TCAAAA-TAATTTTCAAAAAT
1 TCAAAATTAATTTTCAAAAAT
*
162654 T-AAAATTAATTTT-TAAAAT
1 TCAAAATTAATTTTCAAAAAT
162673 TCAAAAT
1 TCAAAAT
162680 ATTTATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
TCAAAATTAATTTTCAAAAAT
Found at i:162690 original size:19 final size:19
Alignment explanation
Indices: 162634--162692 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
162624 TACAAAATAA
162634 TCAAAATAATTTTCAAAAAT
1 TCAAAATAATTTT-AAAAAT
*
162654 T-AAAATTAATTTTTAAAAT
1 TCAAAA-TAATTTTAAAAAT
162673 TCAAAAT-ATTTATAAAAAT
1 TCAAAATAATTT-TAAAAAT
162692 T
1 T
162693 TTAAAATTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.12
19 18 0.53
20 12 0.35
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (19 bp):
TCAAAATAATTTTAAAAAT
Found at i:166497 original size:6 final size:6
Alignment explanation
Indices: 166486--166519 Score: 50
Period size: 6 Copynumber: 5.3 Consensus size: 6
166476 TTGAAGCCCT
166486 CCTTCC CCTTCCC CTCTTCC CCTTCC CCTTCC CC
1 CCTTCC CCTT-CC C-CTTCC CCTTCC CCTTCC CC
166520 ATCTCTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 17 0.65
7 6 0.23
8 3 0.12
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (6 bp):
CCTTCC
Found at i:166506 original size:14 final size:15
Alignment explanation
Indices: 166482--166514 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
166472 AAACTTGAAG
166482 CCCTCCTTCCCCTTC
1 CCCTCCTTCCCCTTC
166497 CCCT-CTTCCCCTTC
1 CCCTCCTTCCCCTTC
166511 CCCT
1 CCCT
166515 TCCCCATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (15 bp):
CCCTCCTTCCCCTTC
Found at i:169411 original size:2 final size:2
Alignment explanation
Indices: 169404--169428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
169394 ATTGTATAAA
169404 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 A
169429 ATACGAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:174055 original size:3 final size:3
Alignment explanation
Indices: 174047--174080 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
174037 AACTATCCAA
174047 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
174081 TAAAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:192921 original size:15 final size:15
Alignment explanation
Indices: 192903--192938 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
192893 CCTCCGTTGG
192903 CTTCTCAGCAGGCTT
1 CTTCTCAGCAGGCTT
*
192918 CTTCTCAGCGGGCTT
1 CTTCTCAGCAGGCTT
*
192933 TTTCTC
1 CTTCTC
192939 GGCTTTCGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.33, G:0.19, T:0.39
Consensus pattern (15 bp):
CTTCTCAGCAGGCTT
Found at i:196100 original size:16 final size:18
Alignment explanation
Indices: 196079--196112 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
196069 TTAAACACAA
196079 AATTAA-AC-AAATTCAT
1 AATTAACACTAAATTCAT
196095 AATTAACACTAAATTCAT
1 AATTAACACTAAATTCAT
196113 TCTCTTGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.53, C:0.15, G:0.00, T:0.32
Consensus pattern (18 bp):
AATTAACACTAAATTCAT
Found at i:202190 original size:14 final size:15
Alignment explanation
Indices: 202167--202200 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
202157 AAGAAGAGTT
202167 CAAAATAAAGAAGAA
1 CAAAATAAAGAAGAA
*
202182 CAAAA-AAAGGAGAA
1 CAAAATAAAGAAGAA
202196 CAAAA
1 CAAAA
202201 GTCAAGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.74, C:0.09, G:0.15, T:0.03
Consensus pattern (15 bp):
CAAAATAAAGAAGAA
Found at i:213358 original size:49 final size:50
Alignment explanation
Indices: 213296--213400 Score: 194
Period size: 49 Copynumber: 2.1 Consensus size: 50
213286 TTGCCATGCT
*
213296 CTTTCTTTTTATGCTTTTCTAGGTGCTTAATGAATGCAAAGTGAAACTTA
1 CTTTATTTTTATGCTTTTCTAGGTGCTTAATGAATGCAAAGTGAAACTTA
213346 -TTTATTTTTATGCTTTTCTAGGTGCTTAATGAATGCAAAGTGAAACTTA
1 CTTTATTTTTATGCTTTTCTAGGTGCTTAATGAATGCAAAGTGAAACTTA
213395 CTTTAT
1 CTTTAT
213401 AAATAAATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
49 48 0.91
50 5 0.09
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (50 bp):
CTTTATTTTTATGCTTTTCTAGGTGCTTAATGAATGCAAAGTGAAACTTA
Found at i:215609 original size:21 final size:20
Alignment explanation
Indices: 215574--215615 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
215564 AAATTATAAT
* *
215574 TTTTAAATTTATAAAAGTTA
1 TTTTAAATTAATAAAAATTA
215594 TTTTAAATTAATTAAAAATTA
1 TTTTAAATTAA-TAAAAATTA
215615 T
1 T
215616 AGTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTTAAATTAATAAAAATTA
Found at i:215823 original size:11 final size:10
Alignment explanation
Indices: 215797--215859 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 10
215787 AAAATAATTC
215797 TATTTTT-AT
1 TATTTTTAAT
*
215806 GATTTTTAAT
1 TATTTTTAAT
215816 TCATTTTTAA-
1 T-ATTTTTAAT
215826 TATTTTAATAATT
1 TATTTT--TAA-T
215839 TATTTTTAA-
1 TATTTTTAAT
*
215848 TGTTTTTAAT
1 TATTTTTAAT
215858 TA
1 TA
215860 ATTATTTCTA
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
9 19 0.44
10 4 0.09
11 14 0.33
13 6 0.14
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.65
Consensus pattern (10 bp):
TATTTTTAAT
Found at i:215921 original size:19 final size:19
Alignment explanation
Indices: 215897--215945 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
215887 AATTAATTCA
215897 TAATAATTTTTATA-AAATT
1 TAATAATTTTTA-ACAAATT
* * *
215916 TAATAAATATTAACAATTT
1 TAATAATTTTTAACAAATT
215935 TAATAATTTTT
1 TAATAATTTTT
215946 TTATAATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 1 0.04
19 23 0.96
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATAATTTTTAACAAATT
Found at i:218456 original size:21 final size:22
Alignment explanation
Indices: 218430--218476 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
218420 ATTTTGTTGA
218430 AATTTG-ATATTTAATTTCTAT
1 AATTTGAATATTTAATTTCTAT
* *
218451 AATTTGAAATATTTATTTTTTAT
1 AATTTG-AATATTTAATTTCTAT
218474 AAT
1 AAT
218477 GTTATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
23 16 0.73
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.57
Consensus pattern (22 bp):
AATTTGAATATTTAATTTCTAT
Found at i:218617 original size:13 final size:14
Alignment explanation
Indices: 218599--218628 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
218589 CTCTACTATG
218599 TTTAATA-TTTAAT
1 TTTAATATTTTAAT
218612 TTTAATATTTTAAT
1 TTTAATATTTTAAT
218626 TTT
1 TTT
218629 TAACATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATATTTTAAT
Found at i:221564 original size:40 final size:40
Alignment explanation
Indices: 221509--221589 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
221499 CACCACCACC
221509 ACCACCATCACCACTCACCTTCAGCTGATGCAATACCCTT
1 ACCACCATCACCACTCACCTTCAGCTGATGCAATACCCTT
*
221549 ACCACCATCACCACTCATCTTCAGCTGATGCAATACCCTT
1 ACCACCATCACCACTCACCTTCAGCTGATGCAATACCCTT
221589 A
1 A
221590 TCTCCCTTCT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.41, G:0.07, T:0.23
Consensus pattern (40 bp):
ACCACCATCACCACTCACCTTCAGCTGATGCAATACCCTT
Found at i:222068 original size:3 final size:3
Alignment explanation
Indices: 222060--222085 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
222050 ATATGAACTG
222060 GCA GCA GCA GCA GCA GCA GCA GCA GC
1 GCA GCA GCA GCA GCA GCA GCA GCA GC
222086 CCCAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.35, G:0.35, T:0.00
Consensus pattern (3 bp):
GCA
Found at i:222515 original size:21 final size:23
Alignment explanation
Indices: 222459--222520 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
222449 GGGGTTGAAG
*
222459 TTAAATTATAATTTTTATAATAG
1 TTAAATTATAATTTTTATAATAA
* *
222482 TAAAAATATAATTTTTA-AATAA
1 TTAAATTATAATTTTTATAATAA
222504 TTAAATTA-AATTTTTAT
1 TTAAATTATAATTTTTAT
222521 TATTTTTAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 8 0.24
22 10 0.30
23 15 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
TTAAATTATAATTTTTATAATAA
Found at i:227580 original size:17 final size:18
Alignment explanation
Indices: 227543--227580 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
227533 TGATTTTTGG
227543 ATTATAAAAATATTAAAT
1 ATTATAAAAATATTAAAT
* *
227561 ATTATTAAAAT-TTTAAT
1 ATTATAAAAATATTAAAT
227578 ATT
1 ATT
227581 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTATAAAAATATTAAAT
Found at i:228246 original size:106 final size:106
Alignment explanation
Indices: 228120--228339 Score: 404
Period size: 106 Copynumber: 2.1 Consensus size: 106
228110 TAACAAAATT
* *
228120 ATGTGGTATATGTACTTTTAATTTGTCCAATTTAATATCTGTATTTTTGTTTTGTCTGACCTTTG
1 ATGTGG-ATATGTACTTTTAATTTGTCCAATTTAATATCTGTATTTTTATTTTATCTGACCTTTG
228185 GGTACTCCGATTTAACGGTGTAAAATTTTAATTCATATTTAC
65 GGTACTCCGATTTAACGGTGTAAAATTTTAATTCATATTTAC
228227 ATGTGGATATGTACTTTTAATTTGTCCAATTTAATATCTGTATTTTTATTTTATCTGACCTTTGG
1 ATGTGGATATGTACTTTTAATTTGTCCAATTTAATATCTGTATTTTTATTTTATCTGACCTTTGG
*
228292 GTACTCCGATTTAACGGTGTAAAATTTTGATTCATATTTAC
66 GTACTCCGATTTAACGGTGTAAAATTTTAATTCATATTTAC
228333 ATGTGGA
1 ATGTGGA
228340 CCATTGATGC
Statistics
Matches: 110, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
106 104 0.95
107 6 0.05
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.48
Consensus pattern (106 bp):
ATGTGGATATGTACTTTTAATTTGTCCAATTTAATATCTGTATTTTTATTTTATCTGACCTTTGG
GTACTCCGATTTAACGGTGTAAAATTTTAATTCATATTTAC
Found at i:230027 original size:14 final size:14
Alignment explanation
Indices: 230005--230038 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
229995 TTTAATCTGA
230005 TTTTTTATTTTT-C
1 TTTTTTATTTTTAC
230018 TTTTTGTATTTTTAC
1 TTTTT-TATTTTTAC
230033 TTTTTT
1 TTTTTT
230039 TTTATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 8 0.42
15 6 0.32
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTATTTTTAC
Found at i:243874 original size:29 final size:29
Alignment explanation
Indices: 243810--243885 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
243800 TTGTATATTT
* * *
243810 AGAATTTAGTCTTTTTATTCTTATTTTTA
1 AGAATTTAATCTTTTTACTCTTATTTTCA
*
243839 AGTATTTAATCTTTTTACTCTTATTTTCA
1 AGAATTTAATCTTTTTACTCTTATTTTCA
* * *
243868 GGAATTTGATCTCTTTAC
1 AGAATTTAATCTTTTTAC
243886 ATTTTAGATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.24, C:0.12, G:0.08, T:0.57
Consensus pattern (29 bp):
AGAATTTAATCTTTTTACTCTTATTTTCA
Found at i:244200 original size:17 final size:17
Alignment explanation
Indices: 244175--244220 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
244165 CCAACAGAAT
244175 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
* **
244192 TTAATTTTATTTTAAGT
1 TTAAATTTATTTTAAAA
244209 TTAAATTTATTT
1 TTAAATTTATTT
244221 AAATTAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:244248 original size:20 final size:20
Alignment explanation
Indices: 244223--244275 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
244213 ATTTATTTAA
244223 ATTAATGTCCAATTACAAAC
1 ATTAATGTCCAATTACAAAC
*
244243 ATTAATATCCAATTACAAAC
1 ATTAATGTCCAATTACAAAC
244263 ATTAATGTCCAAT
1 ATTAATGTCCAAT
244276 ACTAAAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.45, C:0.19, G:0.04, T:0.32
Consensus pattern (20 bp):
ATTAATGTCCAATTACAAAC
Done.