Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011189.1 Kokia drynarioides strain JFW-HI SEQ_126165, 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: 134491
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:1151 original size:4 final size:4
Alignment explanation
Indices: 1131--1213 Score: 96
Period size: 4 Copynumber: 20.2 Consensus size: 4
1121 AACACATTGC
* * * *
1131 CTTT CTTT CCTT C-TT CTTT CTTT CCTCT CCTT CTTC CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT -CTTT CTTT CTTT CTTT CTTT CTTT
1179 CTTT CCTTT CTTT CTTT CTTT CCTTT CTTT CTTT C
1 CTTT -CTTT CTTT CTTT CTTT -CTTT CTTT CTTT C
1214 CCGTTTATTT
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
3 3 0.04
4 54 0.79
5 11 0.16
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (4 bp):
CTTT
Found at i:1165 original size:17 final size:17
Alignment explanation
Indices: 1131--1213 Score: 72
Period size: 17 Copynumber: 5.3 Consensus size: 17
1121 AACACATTGC
1131 CTTTCTTTCCT-T-CTT
1 CTTTCTTTCCTCTCCTT
1146 CTTTCTTTCCTCTCCTT
1 CTTTCTTTCCTCTCCTT
*
1163 C-TTCCTT--TCT--TT
1 CTTTCTTTCCTCTCCTT
* *
1175 CTTTCTTTCCTTTCTTT
1 CTTTCTTTCCTCTCCTT
* *
1192 CTTTCTTTCCTTTCTTT
1 CTTTCTTTCCTCTCCTT
1209 CTTTC
1 CTTTC
1214 CCGTTTATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 12
0.79 0.04 0.16
Matches are distributed among these distances:
12 3 0.05
13 5 0.09
14 3 0.05
15 13 0.22
16 6 0.10
17 28 0.48
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (17 bp):
CTTTCTTTCCTCTCCTT
Found at i:1189 original size:13 final size:13
Alignment explanation
Indices: 1131--1214 Score: 90
Period size: 13 Copynumber: 6.8 Consensus size: 13
1121 AACACATTGC
1131 CTTTCTTTCCTTCTT
1 CTTTCTTTCC-T-TT
*
1146 CTTTCTTTCCTCT
1 CTTTCTTTCCTTT
*
1159 CCTTC-TTCCTTT
1 CTTTCTTTCCTTT
1171 CTTTCTTT-CTTT
1 CTTTCTTTCCTTT
1183 C---CTTT-CTTT
1 CTTTCTTTCCTTT
1192 CTTTCTTTCCTTT
1 CTTTCTTTCCTTT
1205 CTTTCTTTCC
1 CTTTCTTTCC
1215 CGTTTATTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
9 9 0.15
12 19 0.32
13 21 0.35
14 1 0.02
15 10 0.17
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTCTTTCCTTT
Found at i:3817 original size:3 final size:3
Alignment explanation
Indices: 3811--3838 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3801 TAATAATAAC
3811 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3839 CGAATCTAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:14681 original size:20 final size:20
Alignment explanation
Indices: 14642--14678 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
14632 TTATTATACG
*
14642 TATTAAATTAAATATTAATT
1 TATTAAAATAAATATTAATT
14662 TATTAAAATAAAT-TTAA
1 TATTAAAATAAATATTAA
14679 ATTAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTAAAATAAATATTAATT
Found at i:16205 original size:6 final size:7
Alignment explanation
Indices: 16188--16213 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16178 CTTACAAACT
16188 AAAAAAG
1 AAAAAAG
16195 AAAAAAG
1 AAAAAAG
16202 AAAAAAG
1 AAAAAAG
16209 AAAAA
1 AAAAA
16214 TAAAGTCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:21704 original size:63 final size:63
Alignment explanation
Indices: 21605--21731 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
21595 CCCGTGAGCA
21605 CTTAACAAAAGTGCGATATTACGTGTCCAGTTATGATTGGGGCGTTTATCAAACAACTTTCGT
1 CTTAACAAAAGTGCGATATTACGTGTCCAGTTATGATTGGGGCGTTTATCAAACAACTTTCGT
21668 CTTAACAAAAGTGCGATATTACGTGTCCAGTTATGATTGGGGCGTTTATCAAACAACTTTCGT
1 CTTAACAAAAGTGCGATATTACGTGTCCAGTTATGATTGGGGCGTTTATCAAACAACTTTCGT
21731 C
1 C
21732 CAAATCTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
CTTAACAAAAGTGCGATATTACGTGTCCAGTTATGATTGGGGCGTTTATCAAACAACTTTCGT
Found at i:21870 original size:16 final size:15
Alignment explanation
Indices: 21849--21878 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
21839 TTTGAAATTT
21849 AATTTTTTATATTTTA
1 AATTTTTT-TATTTTA
21865 AATTTTTTTATTTT
1 AATTTTTTTATTTT
21879 GTTTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
AATTTTTTTATTTTA
Found at i:21960 original size:34 final size:34
Alignment explanation
Indices: 21921--21994 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
21911 ATTATTTTAC
* *
21921 TAAATTTAAGTTTATTA-TAATATTAATTTTTAAT
1 TAAATTCAAATTTATTACT-ATATTAATTTTTAAT
*
21955 TAAATTCAAATTTATTACTATATTATTTTTTAAT
1 TAAATTCAAATTTATTACTATATTAATTTTTAAT
21989 TAAATT
1 TAAATT
21995 ATTATTAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 35 0.97
35 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (34 bp):
TAAATTCAAATTTATTACTATATTAATTTTTAAT
Found at i:23009 original size:6 final size:6
Alignment explanation
Indices: 22998--23049 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
22988 TTGCTATGGT
* * * *
22998 AATCCG AATCCG AATCTG AATTCG AATTCG AATCCG AATCCG AATCTG
1 AATCCG AATCCG AATCCG AATCCG AATCCG AATCCG AATCCG AATCCG
23046 AATC
1 AATC
23050 TTCATTTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (6 bp):
AATCCG
Found at i:32587 original size:2 final size:2
Alignment explanation
Indices: 32582--32613 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
32572 ACACACACAC
32582 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
32614 TACCAGTTGA
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:35573 original size:30 final size:30
Alignment explanation
Indices: 35539--35638 Score: 92
Period size: 30 Copynumber: 3.2 Consensus size: 30
35529 TAGTTACATC
35539 TAAATTTTGAAATATAAAAAATAAAAGAAT
1 TAAATTTTGAAATATAAAAAATAAAAGAAT
* * * ** ** *
35569 TAAATTCCTGACGATACAAATACAAGGATTGAAC
1 TAAATT-TTGA-AATATAAA-A-AATAAAAGAAT
35603 TAAATTTTGAAATATAAAAAATAAAAGAAT
1 TAAATTTTGAAATATAAAAAATAAAAGAAT
35633 TAAATT
1 TAAATT
35639 CCTGACGATA
Statistics
Matches: 50, Mismatches: 16, Indels: 8
0.68 0.22 0.11
Matches are distributed among these distances:
30 18 0.36
31 4 0.08
32 12 0.24
33 4 0.08
34 12 0.24
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (30 bp):
TAAATTTTGAAATATAAAAAATAAAAGAAT
Found at i:35607 original size:34 final size:34
Alignment explanation
Indices: 35569--35664 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 34
35559 ATAAAAGAAT
35569 TAAATTCCTGACGATACAAATACAAGGATTGAAC
1 TAAATTCCTGACGATACAAATACAAGGATTGAAC
* * * ** ** *
35603 TAAATT-TTGA-AATATAAA-A-AATAAAAGAAT
1 TAAATTCCTGACGATACAAATACAAGGATTGAAC
35633 TAAATTCCTGACGATACAAATACAAGGATTGA
1 TAAATTCCTGACGATACAAATACAAGGATTGA
35665 GCTCTTGGTC
Statistics
Matches: 43, Mismatches: 15, Indels: 8
0.65 0.23 0.12
Matches are distributed among these distances:
30 12 0.28
31 4 0.09
32 12 0.28
33 4 0.09
34 11 0.26
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.26
Consensus pattern (34 bp):
TAAATTCCTGACGATACAAATACAAGGATTGAAC
Found at i:35639 original size:64 final size:64
Alignment explanation
Indices: 35538--35664 Score: 254
Period size: 64 Copynumber: 2.0 Consensus size: 64
35528 ATAGTTACAT
35538 CTAAATTTTGAAATATAAAAAATAAAAGAATTAAATTCCTGACGATACAAATACAAGGATTGAA
1 CTAAATTTTGAAATATAAAAAATAAAAGAATTAAATTCCTGACGATACAAATACAAGGATTGAA
35602 CTAAATTTTGAAATATAAAAAATAAAAGAATTAAATTCCTGACGATACAAATACAAGGATTGA
1 CTAAATTTTGAAATATAAAAAATAAAAGAATTAAATTCCTGACGATACAAATACAAGGATTGA
35665 GCTCTTGGTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (64 bp):
CTAAATTTTGAAATATAAAAAATAAAAGAATTAAATTCCTGACGATACAAATACAAGGATTGAA
Found at i:38910 original size:4 final size:4
Alignment explanation
Indices: 38901--38936 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
38891 AGGAATCTCT
38901 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
38937 CTTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:40572 original size:52 final size:53
Alignment explanation
Indices: 40469--40578 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 53
40459 TTTATGATAC
*
40469 ATGTAATGTTTTGAATGAAGATGCTATACTTTTATAATATAGATTGAGAATAT
1 ATGTAATGTTTTGAATGAAGATGCTAGACTTTTATAATATAGATTGAGAATAT
40522 ATGTAATGTTTTGAATGAAGATGCT-GACTTTTATAATATAGATTGAGAATAT
1 ATGTAATGTTTTGAATGAAGATGCTAGACTTTTATAATATAGATTGAGAATAT
40574 ATGTA
1 ATGTA
40579 TTAAGATTAA
Statistics
Matches: 56, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 31 0.55
53 25 0.45
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (53 bp):
ATGTAATGTTTTGAATGAAGATGCTAGACTTTTATAATATAGATTGAGAATAT
Found at i:63274 original size:19 final size:19
Alignment explanation
Indices: 63239--63276 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
63229 GGCGTAGTTT
*
63239 AAAATGAAAATTTTAAAGA
1 AAAATGAAAATTGTAAAGA
63258 AAAAT-AAATATTGTAAAGA
1 AAAATGAAA-ATTGTAAAGA
63277 TAATGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (19 bp):
AAAATGAAAATTGTAAAGA
Found at i:64542 original size:22 final size:21
Alignment explanation
Indices: 64517--64572 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
64507 ATTCTTATAC
64517 TTTTATTTTTAAGAATTT-AATA
1 TTTTATTTTTAA-AATTTCAA-A
64539 TTTTAACTTTTT-AAATTTCAAA
1 TTTT-A-TTTTTAAAATTTCAAA
*
64561 TTTTAATTTTAA
1 TTTTATTTTTAA
64573 TTATTAACCT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
20 4 0.14
21 2 0.07
22 14 0.48
23 4 0.14
24 5 0.17
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTTTTAAAATTTCAAA
Found at i:64684 original size:19 final size:17
Alignment explanation
Indices: 64662--64706 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
64652 TTTAATTTTT
64662 TAAAATTATAATAATAAGA
1 TAAAATTA-AATAATAA-A
64681 TAAAATTCAAATAATAAA
1 TAAAATT-AAATAATAAA
*
64699 TACAATTA
1 TAAAATTA
64707 GTGCGACTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.29
19 15 0.62
20 1 0.04
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAATTAAATAATAAA
Found at i:65289 original size:122 final size:123
Alignment explanation
Indices: 65153--65680 Score: 713
Period size: 122 Copynumber: 4.3 Consensus size: 123
65143 AACCCTTTTT
* * * * * * * *
65153 TCAGAAAAAAAAAATTAAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA-CCCCTTTTTTCAG
1 TCAGATAAAAAAATTTCAAATTTTTTGGTGTTGGTCATGCAATGACCGACACCCCCTATTCTCGG
* * *
65217 AAAAAAAAATTTCAAAATTTTTTGGTGTTCTCCATGCAATGGCCAACACCCCCTGTTC
66 ATAAAAAAATTTCAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCCTGTTC
* * * *
65275 TTAGATAAAAAAAATTCAAA-TTTTTGGTGTTGGTCATGCAATGACTGACACCCCCTGTTCTCGG
1 TCAGATAAAAAAATTTCAAATTTTTTGGTGTTGGTCATGCAATGACCGACACCCCCTATTCTCGG
* *
65339 ATAAAAAATTTTCAAAATTTTTTGGTATTGTCCATGCAATGGCCGACACCCCCTGTTC
66 ATAAAAAAATTTCAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCCTGTTC
* *
65397 TTAGATAAAAAAATTTCAAA-TTTTTGGTGTTGGCCATGCAATGACCGACACCCCCTATTCTCGG
1 TCAGATAAAAAAATTTCAAATTTTTTGGTGTTGGTCATGCAATGACCGACACCCCCTATTCTCGG
** * * *
65461 ATAAAAAAATTTCAATTTTTTTTTGTGTTGGT-CATGCAATGGTCGACACCCCTTGTTC
66 ATAAAAAAATTTCAAAATTTTTTGGTGTT-GTCCATGCAATGGCCGACACCCCCTGTTC
* * * *
65519 TCGGATAAAAAAATTTCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTCTATTCTCGG
1 TCAGATAAAAAAATTTCAAATTTTTTGGTGTTGGTCATGCAATGACCGACACCCCCTATTCTCGG
* * * *
65584 ATAAAAAAATTTCAAATTTTTTTGGTGTTGGCTATGCATTGGCCGACACCCCCTGTTC
66 ATAAAAAAATTTCAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCCTGTTC
*
65642 TCGGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCAT
1 TCAGATAAAAAAATTTC-AAATTTTTTGGTGTTGGTCAT
65681 TTTCTCGGAT
Statistics
Matches: 364, Mismatches: 37, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
121 27 0.07
122 207 0.57
123 110 0.30
124 20 0.05
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (123 bp):
TCAGATAAAAAAATTTCAAATTTTTTGGTGTTGGTCATGCAATGACCGACACCCCCTATTCTCGG
ATAAAAAAATTTCAAAATTTTTTGGTGTTGTCCATGCAATGGCCGACACCCCCTGTTC
Found at i:65676 original size:62 final size:62
Alignment explanation
Indices: 65159--65676 Score: 681
Period size: 62 Copynumber: 8.5 Consensus size: 62
65149 TTTTTCAGAA
* * * * * * *
65159 AAAAAAAATT-AAAATTTTTTTGTGTTGGTCATGCAATGGCCGACA-CCCCTTTTTTCAGAA
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
** * **
65219 AAAAAAATTTCAAAATTTTTTGGTGTTCTCCATGCAATGGCCAACACCCCCTGTTCTTAGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
* * * *
65281 AAAAAAAATTC-AAA-TTTTTGGTGTTGGTCATGCAATGACTGACACCCCCTGTTCTCGGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
* * * **
65341 AAAAAATTTTCAAAATTTTTTGGTATTGTCCATGCAATGGCCGACACCCCCTGTTCTTAGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
* *
65403 AAAAAAATTTC-AAA-TTTTTGGTGTTGGCCATGCAATGACCGACACCCCCTATTCTCGGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
** * * * *
65463 AAAAAAATTTCAATTTTTTTTTGTGTTGGTCATGCAATGGTCGACACCCCTTGTTCTCGGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
* *
65525 AAAAAAATTTC-AAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCTCTATTCTCGGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
* * *
65586 AAAAAAATTTCAAATTTTTTTGGTGTTGGCTATGCATTGGCCGACACCCCCTGTTCTCGGAT
1 AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
65648 AAAAAAATTTCAAAATTTTTTGGTGTTGG
1 AAAAAAATTTCAAAATTTTTTGGTGTTGG
65677 TCATTTTCTC
Statistics
Matches: 394, Mismatches: 57, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
60 107 0.27
61 93 0.24
62 194 0.49
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (62 bp):
AAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCCTGTTCTCGGAT
Found at i:65723 original size:43 final size:43
Alignment explanation
Indices: 65639--65723 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
65629 ACACCCCCTG
* *
65639 TTCTCGGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATT
1 TTCTCGGATAAAAAAATTTCAAAATTTTTTGGTATTAGTCATT
* ** *
65682 TTCTCGGATAAAAAAATTTTAATTTTTTTTTGTATTAGTCAT
1 TTCTCGGATAAAAAAATTTCAAAATTTTTTGGTATTAGTCAT
65724 GAAATGGCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (43 bp):
TTCTCGGATAAAAAAATTTCAAAATTTTTTGGTATTAGTCATT
Found at i:65772 original size:105 final size:105
Alignment explanation
Indices: 65577--65779 Score: 266
Period size: 105 Copynumber: 1.9 Consensus size: 105
65567 ACACCCTCTA
* * * *
65577 TTCTCGGATAAAAAAATTTCAAATTTTTTTGGTGTTGGCTATGCATTGGCCGACACCCCCTGTTC
1 TTCTCGGATAAAAAAATTTCAAATTTTTTTGGTATTGGCTATGAAATGGCCAACACCCCCTGTTC
*
65642 TCGGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATT
66 TCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATT
* * * * * *
65682 TTCTCGGATAAAAAAATTTTAATTTTTTTTTGTATTAG-TCATGAAATGGCTAACACCCTCT-TT
1 TTCTCGGATAAAAAAATTTCAAATTTTTTTGGTATTGGCT-ATGAAATGGCCAACACCCCCTGTT
* *
65745 TTCAGATAAAAAAATTTCAAATTTTTTTGGTGTTG
65 CTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTG
65780 ACCATGCAAT
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
104 35 0.42
105 49 0.58
ACGTcount: A:0.29, C:0.14, G:0.15, T:0.42
Consensus pattern (105 bp):
TTCTCGGATAAAAAAATTTCAAATTTTTTTGGTATTGGCTATGAAATGGCCAACACCCCCTGTTC
TCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGTCATT
Found at i:66518 original size:25 final size:28
Alignment explanation
Indices: 66473--66523 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 28
66463 TATTTTATCG
*
66473 TATTAATATAATTTTGATTATTAAAAAT
1 TATTAATATAATTTTGATTATGAAAAAT
66501 TATTAA-AT-ATTTTG-TTATGAAAA
1 TATTAATATAATTTTGATTATGAAAA
66524 TGTTAAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
26 6 0.27
27 2 0.09
28 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (28 bp):
TATTAATATAATTTTGATTATGAAAAAT
Found at i:69557 original size:12 final size:12
Alignment explanation
Indices: 69540--69574 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
69530 AATATTTGTG
69540 TAAAAATTAATC
1 TAAAAATTAATC
*
69552 TAAAAATTAATT
1 TAAAAATTAATC
*
69564 TGAAAATTAAT
1 TAAAAATTAAT
69575 GAACATGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (12 bp):
TAAAAATTAATC
Found at i:69902 original size:86 final size:86
Alignment explanation
Indices: 69675--70073 Score: 583
Period size: 86 Copynumber: 4.6 Consensus size: 86
69665 TACATTTAAA
** ** * *
69675 ATTAA-TTTAACATTATTTAAATAAAAAAGATTATTATTATATTACAATTGATATAAAATATTGT
1 ATTAATTTTAA-A-TATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGT
*
69739 GTTAATTTAACAATACATTATTT
64 GTTGATTTAACAATACATTATTT
* * *
69762 ATCAAAATTTT-CATATTTAAAGTACAAATTATTATTA--A-ATTACAATTTTTATCAAATAATG
1 AT--TAATTTTAAATATTTAAA-TAAAAATTATTATTATTATATTACAATTTTTATCAAATAATG
*
69823 TGTTGATTTGACAATACATTATTT
63 TGTTGATTTAACAATACATTATTT
69847 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
* *
69912 TGTTTTGACAATACATTATTT
66 TGATTTAACAATACATTATTT
69933 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
*
69998 TGATTTAATAATACATTATTT
66 TGATTTAACAATACATTATTT
*
70019 ATTAATTTTAAATATTTAAATAAAAATTATTATTATCATATTACAATTTTTATCA
1 ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCA
70074 TATTTTAAAT
Statistics
Matches: 285, Mismatches: 19, Indels: 17
0.89 0.06 0.05
Matches are distributed among these distances:
83 20 0.07
84 9 0.03
85 44 0.15
86 184 0.65
87 10 0.04
88 13 0.05
89 2 0.01
90 3 0.01
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (86 bp):
ATTAATTTTAAATATTTAAATAAAAATTATTATTATTATATTACAATTTTTATCAAATAATGTGT
TGATTTAACAATACATTATTT
Found at i:70198 original size:22 final size:21
Alignment explanation
Indices: 70167--70226 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 21
70157 ATTGGAACAC
*
70167 CCAAT-TTCCAGCTCACTTAAA
1 CCAATATTCCAGCTCAC-AAAA
70188 CCAATATTCCAGCTCAGCAAAA
1 CCAATATTCCAGCTCA-CAAAA
70210 CCGAA-ATTCCAGCTCAC
1 CC-AATATTCCAGCTCAC
70227 CAACACCTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
21 6 0.17
22 26 0.74
23 3 0.09
ACGTcount: A:0.35, C:0.35, G:0.08, T:0.22
Consensus pattern (21 bp):
CCAATATTCCAGCTCACAAAA
Found at i:72551 original size:30 final size:30
Alignment explanation
Indices: 72517--72586 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
72507 TCCTTTTACT
** * *
72517 TTTTAAATTTAATTTGTAATTTTGTTTTTA
1 TTTTAAATTTAATTTGTAATTTCCTGTATA
*
72547 TTTTAAATTTAATTTTTAATTTCCTGTATA
1 TTTTAAATTTAATTTGTAATTTCCTGTATA
72577 TTTTAAATTT
1 TTTTAAATTT
72587 TTTTCTATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (30 bp):
TTTTAAATTTAATTTGTAATTTCCTGTATA
Found at i:72604 original size:28 final size:29
Alignment explanation
Indices: 72517--72621 Score: 88
Period size: 30 Copynumber: 3.6 Consensus size: 29
72507 TCCTTTTACT
* ** * *
72517 TTTTAAATTTAATTTGTAATTTTGTTTTTA
1 TTTTAAATTT-ATTTTTAATTTCCTGTATA
72547 TTTTAAATTTAATTTTTAATTTCCTGTATA
1 TTTTAAATTT-ATTTTTAATTTCCTGTATA
*
72577 TTTTAAATTT-TTTTCT-ATTTCTTGTATA
1 TTTTAAATTTATTTT-TAATTTCCTGTATA
* *
72605 TTCTAATTATTATTTTT
1 TTTTAAAT-TTATTTTT
72622 TTTAAATTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
28 21 0.33
29 4 0.06
30 39 0.61
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.66
Consensus pattern (29 bp):
TTTTAAATTTATTTTTAATTTCCTGTATA
Found at i:73569 original size:61 final size:60
Alignment explanation
Indices: 73418--73588 Score: 204
Period size: 60 Copynumber: 2.8 Consensus size: 60
73408 AGGAGAAGTT
* * * * * *
73418 GGTGTCGGCCATTACATGGCTAACAC-AAAAAAATT--TAATTTTTTACCAAATAAAAAAGAG
1 GGTGTCGACCATTGCATGGCCAACACAAAAAAAATTGAAAATTTTTTATC---TGAAAAAGAG
73478 GGTGTCGACCATTGCATGGCCAACACAAAAAAAATTGAAAATTTTTTATCTGAAAAAGAG
1 GGTGTCGACCATTGCATGGCCAACACAAAAAAAATTGAAAATTTTTTATCTGAAAAAGAG
* * *
73538 GGTGTCGACCATTGCATGGCCAATACCAAAAAAATTTGAAATTTTTTTATC
1 GGTGTCGACCATTGCATGGCCAACA-CAAAAAAAATTGAAAATTTTTTATC
73589 CGAGAACAAG
Statistics
Matches: 98, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
60 56 0.57
61 32 0.33
63 10 0.10
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (60 bp):
GGTGTCGACCATTGCATGGCCAACACAAAAAAAATTGAAAATTTTTTATCTGAAAAAGAG
Found at i:73605 original size:47 final size:47
Alignment explanation
Indices: 73551--73641 Score: 155
Period size: 47 Copynumber: 1.9 Consensus size: 47
73541 GTCGACCATT
* * *
73551 GCATGGCCAATACCAAAAAAATTTGAAATTTTTTTATCCGAGAACAA
1 GCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCCAAGAACAA
73598 GCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCCAAGAA
1 GCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCCAAGAA
73642 TAGGGGGTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (47 bp):
GCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCCAAGAACAA
Found at i:73677 original size:107 final size:106
Alignment explanation
Indices: 73491--73700 Score: 300
Period size: 108 Copynumber: 2.0 Consensus size: 106
73481 GTCGACCATT
*
73491 GCATGGCCAACACAAAAAAAATTGAAAATTTTTTATCTGAAAAAGAGGGTGTCGACCATTGCATG
1 GCATGGCCAACACAAAAAAAATTGAAAATTTTTTATCTCAAAAAGAGGGTGTCGACCATTGCATG
* * *
73556 GCCAATACCAAAAAAATTTGAAATTTTTTTATCCGAGAACAA
66 ACCAACACCAAAAAAA-ATGAAATTTTTTTATCCGAGAACAA
* *
73598 GCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATC-CAAGAATAGGGGGTGTCGACCATTGC
1 GCATGGCCAACA-CAAAAAAAATTGAAAATTTTTTATCTCAA-AA-AGAGGGTGTCGACCATTGC
*
73662 ATGACCAACA-C-AAAAAAATGCAATTTTTTTATCCGAGAA
63 ATGACCAACACCAAAAAAAATGAAATTTTTTTATCCGAGAA
73701 AAATAGGGGT
Statistics
Matches: 93, Mismatches: 7, Indels: 7
0.87 0.07 0.07
Matches are distributed among these distances:
106 20 0.22
107 20 0.22
108 27 0.29
109 26 0.28
ACGTcount: A:0.41, C:0.17, G:0.16, T:0.26
Consensus pattern (106 bp):
GCATGGCCAACACAAAAAAAATTGAAAATTTTTTATCTCAAAAAGAGGGTGTCGACCATTGCATG
ACCAACACCAAAAAAAATGAAATTTTTTTATCCGAGAACAA
Found at i:73720 original size:61 final size:59
Alignment explanation
Indices: 73598--73741 Score: 173
Period size: 61 Copynumber: 2.4 Consensus size: 59
73588 CCGAGAACAA
* *
73598 GCATGGCCAACACCAAAAAAATTTGAAAATTTTTTATCCAAGAATAGGGGGTGTCGACCATT
1 GCATGACCAACA-CAAAAAAA--TGAAAATTTTTTATCCAAAAATAGGGGGTGTCGACCATT
* * *
73660 GCATGACCAACACAAAAAAATGCAATTTTTTTATCCGAGAAAAATA-GGGGTGTCGGCCATT
1 GCATGACCAACACAAAAAAATGAAAATTTTTTATCC---AAAAATAGGGGGTGTCGACCATT
*
73721 GTATGACCAACACAAAAAAAT
1 GCATGACCAACACAAAAAAAT
73742 TGTATTTTTT
Statistics
Matches: 73, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
59 14 0.19
61 42 0.58
62 17 0.23
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (59 bp):
GCATGACCAACACAAAAAAATGAAAATTTTTTATCCAAAAATAGGGGGTGTCGACCATT
Found at i:96281 original size:27 final size:27
Alignment explanation
Indices: 96251--96312 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
96241 TAAATTAATA
96251 AAAATAAAAATTTTAATTT-AATTAT-TT
1 AAAATAAAAA-TTTAATTTAAATT-TCTT
* *
96278 AAAAGTTACAATTTAATTTAAATTTCTT
1 AAAA-TAAAAATTTAATTTAAATTTCTT
96306 AAAATAA
1 AAAATAA
96313 TTTTTTGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 15 0.52
28 14 0.48
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAATAAAAATTTAATTTAAATTTCTT
Found at i:96724 original size:15 final size:16
Alignment explanation
Indices: 96695--96724 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
96685 TAAGTTCAAC
96695 ATATTTTATACAATTA
1 ATATTTTATACAATTA
96711 ATATTTTA-ACAATT
1 ATATTTTATACAATT
96725 CAACAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (16 bp):
ATATTTTATACAATTA
Found at i:105475 original size:23 final size:19
Alignment explanation
Indices: 105449--105500 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 19
105439 TATAATTATG
105449 AATAATATTAATCATTGTAATAT
1 AATAATATTAAT--TTG-AA-AT
105472 AATAAT-TTAATTTGAAAT
1 AATAATATTAATTTGAAAT
105490 AA-AATATTAAT
1 AATAATATTAAT
105501 AAAAATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.11
18 9 0.32
19 2 0.07
20 3 0.11
22 5 0.18
23 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.42
Consensus pattern (19 bp):
AATAATATTAATTTGAAAT
Found at i:112374 original size:20 final size:19
Alignment explanation
Indices: 112331--112376 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
112321 ATCAAAGTTT
*
112331 TATTTTAATATAATATTTA
1 TATTTTAATATAATATGTA
* *
112350 CATTTTAATTATATTATGTA
1 TATTTTAA-TATAATATGTA
112370 TATTTTA
1 TATTTTA
112377 TTACTTCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTTAATATAATATGTA
Found at i:117275 original size:7 final size:6
Alignment explanation
Indices: 117243--117302 Score: 70
Period size: 6 Copynumber: 10.3 Consensus size: 6
117233 AATTAGTATA
* * *
117243 TTTATT TTCATA TTTATT TTTATT TTTAGT TTTA-T TTTA-T TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
117289 TTTAAT TTTATT TT
1 TTTATT TTTATT TT
117303 AATTATGCGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
5 10 0.22
6 36 0.78
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:117278 original size:22 final size:22
Alignment explanation
Indices: 117246--117303 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 22
117236 TAGTATATTT
117246 ATTTTCATATTTATTTTTATTTTTA
1 ATTTT-AT-TTTA-TTTTATTTTTA
*
117271 GTTTTATTTTATTTTATTTTTA
1 ATTTTATTTTATTTTATTTTTA
117293 ATTTTATTTTA
1 ATTTTATTTTA
117304 ATTATGCGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
22 21 0.68
23 4 0.13
24 2 0.06
25 4 0.13
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (22 bp):
ATTTTATTTTATTTTATTTTTA
Found at i:117952 original size:8 final size:8
Alignment explanation
Indices: 117936--118003 Score: 61
Period size: 8 Copynumber: 8.9 Consensus size: 8
117926 TATTGTTTAG
117936 AAAAA-AA
1 AAAAAGAA
117943 AAAAAGAA
1 AAAAAGAA
117951 AAAAAG-A
1 AAAAAGAA
**
117958 AAAAAGTC
1 AAAAAGAA
*
117966 GAAAAGAA
1 AAAAAGAA
** *
117974 AAATTGAG
1 AAAAAGAA
117982 AAAAA-AA
1 AAAAAGAA
117989 AAAAAGAA
1 AAAAAGAA
117997 AAAAAGA
1 AAAAAGA
118004 GACAAAAGTG
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
7 18 0.38
8 29 0.62
ACGTcount: A:0.81, C:0.01, G:0.13, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:118005 original size:23 final size:23
Alignment explanation
Indices: 117934--118010 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
117924 TTTATTGTTT
117934 AGAAAAAAAAAAAAGAAAAAAAG
1 AGAAAAAAAAAAAAGAAAAAAAG
*** **
117957 A-AAAAAGTCGAAAAGAAAAATTG
1 AGAAAAA-AAAAAAAGAAAAAAAG
117980 AGAAAAAAAAAAAAGAAAAAAAG
1 AGAAAAAAAAAAAAGAAAAAAAG
*
118003 AGACAAAA
1 AGAAAAAA
118011 GTGTGTTTGA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
22 5 0.12
23 31 0.76
24 5 0.12
ACGTcount: A:0.79, C:0.03, G:0.14, T:0.04
Consensus pattern (23 bp):
AGAAAAAAAAAAAAGAAAAAAAG
Found at i:119066 original size:23 final size:25
Alignment explanation
Indices: 119039--119084 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
119029 CTAATTAGGG
119039 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
119062 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
119085 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:120246 original size:71 final size:71
Alignment explanation
Indices: 120171--120320 Score: 277
Period size: 71 Copynumber: 2.1 Consensus size: 71
120161 AATTTCTAAC
120171 TTATATTAATAGGTAACTAAAATAAATTATATTAATAATTATTATCAAAATTAATCATTAAAAAT
1 TTATATTAATAGGTAACTAAAATAAATTATATTAATAATTATTATCAAAATTAATCATTAAAAAT
120236 ATTAAA
66 ATTAAA
*
120242 TTATATTAATGGGTAACTAAAATAAATTATATTAATAATTATTATCAAAATTAATCATTAAAAAT
1 TTATATTAATAGGTAACTAAAATAAATTATATTAATAATTATTATCAAAATTAATCATTAAAAAT
120307 ATTAAA
66 ATTAAA
120313 -TA-ATTAAT
1 TTATATTAAT
120321 TCAACTCGAA
Statistics
Matches: 78, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
69 6 0.08
70 2 0.03
71 70 0.90
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (71 bp):
TTATATTAATAGGTAACTAAAATAAATTATATTAATAATTATTATCAAAATTAATCATTAAAAAT
ATTAAA
Found at i:121434 original size:19 final size:21
Alignment explanation
Indices: 121396--121434 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
121386 AAAAAATAGG
*
121396 TTAATCATATTCTTTATTTTT
1 TTAATCATATTCTATATTTTT
121417 TTAATCA-A-TCTATATTTT
1 TTAATCATATTCTATATTTT
121435 ATAATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 1 0.06
21 7 0.41
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATCATATTCTATATTTTT
Found at i:121636 original size:17 final size:17
Alignment explanation
Indices: 121614--121648 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
121604 TTCATGAAGT
121614 CTAAAAAACACCATCGA
1 CTAAAAAACACCATCGA
121631 CTAAAAAACACCATCGA
1 CTAAAAAACACCATCGA
121648 C
1 C
121649 GTTGTATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.31, G:0.06, T:0.11
Consensus pattern (17 bp):
CTAAAAAACACCATCGA
Found at i:121749 original size:18 final size:19
Alignment explanation
Indices: 121723--121765 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
121713 TATTTTATTT
121723 TAAATATTT-TTATTATATA
1 TAAATATTTATTA-TATATA
*
121742 TAAA-ATTTATTATATTTA
1 TAAATATTTATTATATATA
121760 TAAATA
1 TAAATA
121766 AAATTTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAAATATTTATTATATATA
Found at i:121760 original size:22 final size:23
Alignment explanation
Indices: 121735--121777 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
121725 AATATTTTTA
*
121735 TTATATATAAAATTT-ATTATAT
1 TTATAAATAAAATTTAATTATAT
121757 TTATAAATAAAATTTAATTAT
1 TTATAAATAAAATTTAATTAT
121778 TCAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTATAAATAAAATTTAATTATAT
Found at i:127874 original size:23 final size:23
Alignment explanation
Indices: 127848--127902 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
127838 TCTTGAATGT
*
127848 TTACATCATATT-TGTGTTATAGA
1 TTACAT-ATATTATGTGTTATAAA
*
127871 TTACAATAAATTTATGTGTTATAAA
1 TTAC-ATATA-TTATGTGTTATAAA
127896 TTACATA
1 TTACATA
127903 ATATATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 6 0.22
24 7 0.26
25 14 0.52
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.45
Consensus pattern (23 bp):
TTACATATATTATGTGTTATAAA
Found at i:127913 original size:18 final size:18
Alignment explanation
Indices: 127890--127937 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
127880 ATTTATGTGT
127890 TATAAATTACATAATATA
1 TATAAATTACATAATATA
*
127908 TATAAAAATAACATAATATA
1 TAT--AAATTACATAATATA
*
127928 -AGAAATTACA
1 TATAAATTACA
127938 GACTTGTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 7 0.28
18 3 0.12
19 1 0.04
20 14 0.56
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.31
Consensus pattern (18 bp):
TATAAATTACATAATATA
Found at i:132615 original size:16 final size:16
Alignment explanation
Indices: 132591--132621 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
132581 TCAATGGAAA
132591 AAAAAAAAAAAAAAGC
1 AAAAAAAAAAAAAAGC
*
132607 AAAACAAAAAAAAAG
1 AAAAAAAAAAAAAAG
132622 ATTGAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAGC
Done.