Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01000997.1 Kokia drynarioides strain JFW-HI SEQ_112199, 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: 92702
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 116 characters in sequence are not A, C, G, or T
Found at i:2650 original size:20 final size:20
Alignment explanation
Indices: 2625--2662 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2615 CAAATGATTA
2625 AGAAAATATGAACAGATACT
1 AGAAAATATGAACAGATACT
*
2645 AGAAAATATGAACGGATA
1 AGAAAATATGAACAGATA
2663 TTATTATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.08, G:0.18, T:0.18
Consensus pattern (20 bp):
AGAAAATATGAACAGATACT
Found at i:5186 original size:17 final size:17
Alignment explanation
Indices: 5153--5186 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5143 AATTTTACAT
* *
5153 ATTAAAAAATAATATGA
1 ATTAAAAAAGAACATGA
5170 ATTAAAAAAGAACATGA
1 ATTAAAAAAGAACATGA
5187 CATTTGACTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (17 bp):
ATTAAAAAAGAACATGA
Found at i:9030 original size:22 final size:22
Alignment explanation
Indices: 8994--9048 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
8984 AATGAACCGA
*
8994 CCTCCATTACCCTGCCTTAACCT
1 CCTCC-TTGCCCTGCCTTAACCT
* *
9017 CCTCCTTGCCCTGCCTTATCTT
1 CCTCCTTGCCCTGCCTTAACCT
9039 CCTCCCTTGC
1 CCT-CCTTGC
9049 TGTATCTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 17 0.61
23 11 0.39
ACGTcount: A:0.09, C:0.49, G:0.07, T:0.35
Consensus pattern (22 bp):
CCTCCTTGCCCTGCCTTAACCT
Found at i:29355 original size:24 final size:24
Alignment explanation
Indices: 29327--29386 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
29317 AGAAATAATC
*
29327 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAATTAAACTCTATTTAATTG
* *
29351 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTATTTAATTG
29375 TTTCAA-TAAACT
1 TTTCAATTAAACT
29387 TTGTCTTAGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 6 0.18
24 27 0.82
ACGTcount: A:0.30, C:0.13, G:0.07, T:0.50
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTAATTG
Found at i:34289 original size:30 final size:31
Alignment explanation
Indices: 34225--34296 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 31
34215 ACAACAAGAG
* *
34225 GACTATTTTGTCACTTTTCCATAACTTTAGT
1 GACTGTTTTGTCACTTTTCCATAACTTGAGT
*
34256 GACTGTTTTGTCACATTTT-CA-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCCATAACTTGAGT
34286 GACTGTTTTGT
1 GACTGTTTTGT
34297 TAAATGTAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 18 0.49
31 15 0.41
32 4 0.11
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.47
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCCATAACTTGAGT
Found at i:34421 original size:30 final size:30
Alignment explanation
Indices: 34387--34445 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
34377 GACGAAAAAG
34387 GACTGTTTTGTCACATTTTCAAAGTTGAGA
1 GACTGTTTTGTCACATTTTCAAAGTTGAGA
34417 GACTGTTTTGTCACATTTTCAAAGTTGAG
1 GACTGTTTTGTCACATTTTCAAAGTTGAG
34446 GGATTGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (30 bp):
GACTGTTTTGTCACATTTTCAAAGTTGAGA
Found at i:38388 original size:24 final size:24
Alignment explanation
Indices: 38361--38411 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
38351 AATTTGACTC
* * *
38361 AAACAACTAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTATAACTG
38385 AAACAAATAAACAGAGTATAACTG
1 AAACAAATAAACAGAGTATAACTG
38409 AAA
1 AAA
38412 GATTATGTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.12, T:0.20
Consensus pattern (24 bp):
AAACAAATAAACAGAGTATAACTG
Found at i:40379 original size:24 final size:24
Alignment explanation
Indices: 40352--40398 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
40342 AATTTGACTC
*
40352 AAACAACTAAACAGAGTTCAATTG
1 AAACAAATAAACAGAGTTCAATTG
*
40376 AAACAAATAAACAGAGTTTAATT
1 AAACAAATAAACAGAGTTCAATT
40399 AAAAGATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.53, C:0.13, G:0.11, T:0.23
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTCAATTG
Found at i:41136 original size:12 final size:11
Alignment explanation
Indices: 41119--41160 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
41109 GAACAAAATA
41119 AAAAAATGAAT
1 AAAAAATGAAT
41130 GAAAAAATTGAA-
1 -AAAAAA-TGAAT
41142 AAAAAATAGAAT
1 AAAAAAT-GAAT
41154 AAAAAAT
1 AAAAAAT
41161 TTCGGGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 1 0.04
11 9 0.33
12 13 0.48
13 4 0.15
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.17
Consensus pattern (11 bp):
AAAAAATGAAT
Found at i:41148 original size:23 final size:23
Alignment explanation
Indices: 41118--41161 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
41108 TGAACAAAAT
41118 AAAAAAAT-GAATGAAAAAATTGA
1 AAAAAAATAGAAT-AAAAAATTGA
41141 AAAAAAATAGAATAAAAAATT
1 AAAAAAATAGAATAAAAAATT
41162 TCGGGCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (23 bp):
AAAAAAATAGAATAAAAAATTGA
Found at i:50038 original size:2 final size:2
Alignment explanation
Indices: 50031--50059 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
50021 CGTTACCACC
50031 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
50060 ACTCAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:51725 original size:19 final size:20
Alignment explanation
Indices: 51696--51735 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
51686 TTATATATTG
*
51696 TTTATAATTTAATTTACATT
1 TTTATAATTTAATTAACATT
*
51716 TTTA-AATTTACTTAACATT
1 TTTATAATTTAATTAACATT
51735 T
1 T
51736 AAAATTCAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.57
Consensus pattern (20 bp):
TTTATAATTTAATTAACATT
Found at i:54187 original size:21 final size:21
Alignment explanation
Indices: 54161--54203 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
54151 CCGCTCCAGA
54161 AGGGAAAAAGTGTTGAAACCT
1 AGGGAAAAAGTGTTGAAACCT
54182 AGGGAAAAAGTGTTGAAACCT
1 AGGGAAAAAGTGTTGAAACCT
54203 A
1 A
54204 ACTTGGCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (21 bp):
AGGGAAAAAGTGTTGAAACCT
Found at i:76204 original size:24 final size:25
Alignment explanation
Indices: 76160--76207 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
76150 CGAGTAAAAA
76160 ACCATAGGTCTGAAACAAAAAAAGT
1 ACCATAGGTCTGAAACAAAAAAAGT
*
76185 ACCATAGTTCTGAAACAAAAAAA
1 ACCATAGGTCTGAAACAAAAAAA
76208 ACTACTGTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.17, G:0.12, T:0.17
Consensus pattern (25 bp):
ACCATAGGTCTGAAACAAAAAAAGT
Found at i:77637 original size:15 final size:16
Alignment explanation
Indices: 77614--77660 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
77604 GTGAGATATT
*
77614 CAGATTTGGGATATCC
1 CAGAATTGGGATATCC
77630 CA-AATTGGGATATACC
1 CAGAATTGGGATAT-CC
*
77646 TAGAA-TGGGATATCC
1 CAGAATTGGGATATCC
77661 TTCATTGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 12 0.44
16 13 0.48
17 2 0.07
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (16 bp):
CAGAATTGGGATATCC
Found at i:77655 original size:31 final size:31
Alignment explanation
Indices: 77620--77692 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
77610 TATTCAGATT
77620 TGGGATATCCCAAATTGGGATATACCTAGAA
1 TGGGATATCCCAAATTGGGATATACCTAGAA
*** *** *
77651 TGGGATATCCTTCATTGGGATATGGGTGGAA
1 TGGGATATCCCAAATTGGGATATACCTAGAA
77682 TGGGATATCCC
1 TGGGATATCCC
77693 TCCACGAAAT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (31 bp):
TGGGATATCCCAAATTGGGATATACCTAGAA
Found at i:77671 original size:15 final size:15
Alignment explanation
Indices: 77619--77673 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
77609 ATATTCAGAT
*
77619 TTGGGATATCCCAAA
1 TTGGGATATCCTAAA
77634 TTGGGATATACCTAGAA
1 TTGGGATAT-CCTA-AA
**
77651 -TGGGATATCCTTCA
1 TTGGGATATCCTAAA
77665 TTGGGATAT
1 TTGGGATAT
77674 GGGTGGAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 1 0.03
15 20 0.59
16 11 0.32
17 2 0.06
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.33
Consensus pattern (15 bp):
TTGGGATATCCTAAA
Found at i:78736 original size:140 final size:140
Alignment explanation
Indices: 78538--79207 Score: 710
Period size: 140 Copynumber: 4.9 Consensus size: 140
78528 AACACTTAGG
* * * * * * *
78538 AAAGTGTCGGCATAGTTTTAGTCAAAACCAACTCTTATTTAAGT-GTCGTCTTAAGCATGCATAT
1 AAAGTGTCGACATAGTGTTGGACAAAACCAACTCTTATTTAA-TCGTTGCCTTAGGCATGCATAT
** * * * *
78602 TTCAACTCTTATACAAAGAGTTGGCCAAATCGTATGCCGGCAAGTCTATCTCAACACTTAGGAAA
65 CCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAA
*
78667 GTGTCAACCCA
130 GTGTCGACCCA
*
78678 AAAGTGTCGACATAGTGTTGGACAAAACCGACTCTTATTTAATCGTTGCCTTAGGCATGCATATC
1 AAAGTGTCGACATAGTGTTGGACAAAACCAACTCTTATTTAATCGTTGCCTTAGGCATGCATATC
* * * *
78743 CCAACCCTTATACAAAGAATTGGCCAAAGCATATGTCAGCAACTCTATCCCAACACTTAGGAAA-
66 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAG
78807 -GT-------
131 TGTCGACCCA
**
78809 ---GT-T-GACATAGTGTTGGACAAAGTCAACTCTTATTTGAAT-GTTGCCTTAGGCATGCATAT
1 AAAGTGTCGACATAGTGTTGGACAAAACCAACTCTTATTT-AATCGTTGCCTTAGGCATGCATAT
* * *
78868 CCCAAACCTTATACAAAGAGTTGGCCAAAGCATATGTCGACAAGTCTATCCCAACACTTAGGAAA
65 CCCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAA
*
78933 GTGTCGACCAA
130 GTGTCGACCCA
* * ** * * * *
78944 AAAGTGTCGCCATAATGTTGGACAAAGTCGACTCTTATTTAAGCATTGCCTTAGACATGCATATC
1 AAAGTGTCGACATAGTGTTGGACAAAACCAACTCTTATTTAATCGTTGCCTTAGGCATGCATATC
* * ** *
79009 CCATCCCTTGTATA-AAAGAGTTGGCAAAAGCGTATGTTAGCAAGTCTATCCCCACACTTAGGAA
66 CCAACCC-T-TATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAA
*
79073 AGTGTCGCCCCA
129 AGTGTCGACCCA
** * * * * * *
79085 AAAGTGTCGGGATAGTGCTGGA-TAAAGCAACTCTTATTTAAGCGTTGTCTTAGACATGCATATC
1 AAAGTGTCGACATAGTGTTGGACAAAACCAACTCTTATTTAATCGTTGCCTTAGGCATGCATATC
* * * * *
79149 CCAACCCTTATACACAGAGTTGACAAAAGCGTATGTTGGCAAGTCTATCTCAACACTTA
66 CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTA
79208 AAAAATTGTC
Statistics
Matches: 452, Mismatches: 58, Indels: 41
0.82 0.11 0.07
Matches are distributed among these distances:
126 109 0.24
127 4 0.01
128 4 0.01
138 8 0.02
139 46 0.10
140 204 0.45
141 73 0.16
142 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (140 bp):
AAAGTGTCGACATAGTGTTGGACAAAACCAACTCTTATTTAATCGTTGCCTTAGGCATGCATATC
CCAACCCTTATACAAAGAGTTGGCCAAAGCGTATGTCGGCAAGTCTATCCCAACACTTAGGAAAG
TGTCGACCCA
Found at i:78903 original size:126 final size:125
Alignment explanation
Indices: 78678--79077 Score: 455
Period size: 126 Copynumber: 3.1 Consensus size: 125
78668 TGTCAACCCA
* **
78678 AAAGTGTCGACATAGTGTTGGACAAAACCGACTCTTATTTAATCGTTGCCTTAGGCATGCATATC
1 AAAGTGTTGACATAGTGTTGGACAAAGTCGACTCTTATTTAAT-GTTGCCTTAGGCATGCATATC
* *
78743 CCAACCCTTATACAAAGAATTGGCCAAAGCATATGTCAGCAACTCTATCCCAACACTTAGG
65 CCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCAGCAAGTCTATCCCAACACTTAGG
*
78804 AAAGTGTTGACATAGTGTTGGACAAAGTCAACTCTTATTTGAATGTTGCCTTAGGCATGCATATC
1 AAAGTGTTGACATAGTGTTGGACAAAGTCGACTCTTATTT-AATGTTGCCTTAGGCATGCATATC
*
78869 CCAAACCTTATACAAAGAGTTGGCCAAAGCATATGTC-GACAAGTCTATCCCAACACTTAGG
65 CCAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCAG-CAAGTCTATCCCAACACTTAGG
* *
78930 AAAGTGTCGACCAAAAAGTGTCGCCATAATGTTGGACAAAGTCGACTCTTATTTAA-GCATTGCC
1 AAA--GT----------GT-T-GACATAGTGTTGGACAAAGTCGACTCTTATTTAATG--TTGCC
* * * * *
78994 TTAGACATGCATATCCCATCCCTTGTATA-AAAGAGTTGGCAAAAGCGTATGTTAGCAAGTCTAT
50 TTAGGCATGCATATCCCAACCC-T-TATACAAAGAGTTGGCCAAAGCATATGTCAGCAAGTCTAT
*
79058 CCCCACACTTAGG
113 CCCAACACTTAGG
79071 AAAGTGT
1 AAAGTGT
79078 CGCCCCAAAA
Statistics
Matches: 236, Mismatches: 17, Indels: 39
0.81 0.06 0.13
Matches are distributed among these distances:
125 1 0.00
126 116 0.49
127 3 0.01
128 2 0.01
129 2 0.01
138 3 0.01
139 5 0.02
140 53 0.22
141 46 0.19
142 5 0.02
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (125 bp):
AAAGTGTTGACATAGTGTTGGACAAAGTCGACTCTTATTTAATGTTGCCTTAGGCATGCATATCC
CAACCCTTATACAAAGAGTTGGCCAAAGCATATGTCAGCAAGTCTATCCCAACACTTAGG
Found at i:78965 original size:266 final size:267
Alignment explanation
Indices: 78527--79079 Score: 754
Period size: 266 Copynumber: 2.1 Consensus size: 267
78517 CCCAAGTTCT
* * * *
78527 CAACACTTAGGAAAGTGTCGGCATAGTTTTAGTCAAAACCAACTCTTATTTAAGTGTCGTCTTAA
1 CAACACTTAGGAAAGTGTCGACATAGTGTTAGACAAAACCAACTCTTATTTAAGTGTCGCCTTAA
** * * * *
78592 GCATGCATATTTCAACTCTTATACAAAGAGTTGGCCAAATCGTATGCCGGCAAGTCTATCTCAAC
66 GCATGCATATCCCAACTCTTATACAAAGAGTTGGCCAAAGCATATGCCGACAAGTCTATCCCAAC
* * *
78657 ACTTAGGAAAGTGTCAACCCAAAAGTGTCGACATAGTGTTGGACAAAACCGACTCTTATTTAATC
131 ACTTAGGAAAGTGTCAACCAAAAAGTGTCGACATAATGTTGGACAAAACCGACTCTTATTTAAGC
* * *
78722 GTTGCCTTAGGCATGCATATCCCAACCC-T-TATACAAAGAATTGGCCAAAGCATATGTCAGCAA
196 ATTGCCTTAGACATGCATATCCCAACCCTTGTATA-AAAGAATTGGCAAAAGCATATGTCAGCAA
78785 CTCTATCC
260 CTCTATCC
* * ** *
78793 CAACACTTAGGAAAGTGTTGACATAGTGTTGGACAAAGTCAACTCTTATTTGAA-TGTTGCCTTA
1 CAACACTTAGGAAAGTGTCGACATAGTGTTAGACAAAACCAACTCTTATTT-AAGTGTCGCCTTA
* *
78857 GGCATGCATATCCCAAAC-CTTATACAAAGAGTTGGCCAAAGCATATGTCGACAAGTCTATCCCA
65 AGCATGCATATCCC-AACTCTTATACAAAGAGTTGGCCAAAGCATATGCCGACAAGTCTATCCCA
* * **
78921 ACACTTAGGAAAGTGTCGACCAAAAAGTGTCGCCATAATGTTGGACAAAGTCGACTCTTATTTAA
129 ACACTTAGGAAAGTGTCAACCAAAAAGTGTCGACATAATGTTGGACAAAACCGACTCTTATTTAA
* * * *
78986 GCATTGCCTTAGACATGCATATCCCATCCCTTGTATAAAAGAGTTGGCAAAAGCGTATGTTAGCA
194 GCATTGCCTTAGACATGCATATCCCAACCCTTGTATAAAAGAATTGGCAAAAGCATATGTCAGCA
*
79051 AGTCTATCC
259 ACTCTATCC
*
79060 CCACACTTAGGAAAGTGTCG
1 CAACACTTAGGAAAGTGTCG
79080 CCCCAAAAGT
Statistics
Matches: 249, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
266 189 0.76
267 56 0.22
268 4 0.02
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (267 bp):
CAACACTTAGGAAAGTGTCGACATAGTGTTAGACAAAACCAACTCTTATTTAAGTGTCGCCTTAA
GCATGCATATCCCAACTCTTATACAAAGAGTTGGCCAAAGCATATGCCGACAAGTCTATCCCAAC
ACTTAGGAAAGTGTCAACCAAAAAGTGTCGACATAATGTTGGACAAAACCGACTCTTATTTAAGC
ATTGCCTTAGACATGCATATCCCAACCCTTGTATAAAAGAATTGGCAAAAGCATATGTCAGCAAC
TCTATCC
Found at i:80599 original size:6 final size:6
Alignment explanation
Indices: 80584--80633 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
80574 TTGATTAACT
* * *
80584 TTTTTA TTTTTC -TTTTC -TTTTC TTCTTC TTTTTC TTTTTC TTTTCC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
80630 TTTT
1 TTTT
80634 CATTTGAATT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 10 0.26
6 29 0.74
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:80616 original size:17 final size:17
Alignment explanation
Indices: 80584--80634 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
80574 TTGATTAACT
* *
80584 TTTTTATTTTTCTTTTC
1 TTTTTCTTTTCCTTTTC
*
80601 -TTTTCTTCTTCTTTTTC
1 TTTTTCTT-TTCCTTTTC
80618 TTTTTCTTTTCCTTTTC
1 TTTTTCTTTTCCTTTTC
80635 ATTTGAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.21
17 15 0.54
18 7 0.25
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTCCTTTTC
Found at i:80634 original size:6 final size:5
Alignment explanation
Indices: 80591--80634 Score: 52
Period size: 5 Copynumber: 8.0 Consensus size: 5
80581 ACTTTTTTAT
80591 TTTTC TTTTC TTTTC TTCTTC TTTTTC TTTTTC TTTTCC TTTTC
1 TTTTC TTTTC TTTTC TT-TTC -TTTTC -TTTTC TTTT-C TTTTC
80635 ATTTGAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 17 0.47
6 17 0.47
7 2 0.06
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTC
Found at i:85672 original size:16 final size:16
Alignment explanation
Indices: 85648--85681 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
85638 CTAAAAACTC
*
85648 AACAATTACTTTTTTT
1 AACAATTACTCTTTTT
*
85664 AACACTTACTCTTTTT
1 AACAATTACTCTTTTT
85680 AA
1 AA
85682 TCATGAAAAA
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:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (16 bp):
AACAATTACTCTTTTT
Found at i:88914 original size:4 final size:4
Alignment explanation
Indices: 88905--88944 Score: 80
Period size: 4 Copynumber: 10.0 Consensus size: 4
88895 AACCAAACTA
88905 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
88945 CAATTTAACA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:90978 original size:25 final size:25
Alignment explanation
Indices: 90950--91000 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
90940 TGTAATAAAG
* *
90950 ACAAAAGGACAACAGATACAAATAT
1 ACAAAAGGAAAACAAATACAAATAT
*
90975 ACAAGAGGAAAACAAATACAAATAT
1 ACAAAAGGAAAACAAATACAAATAT
91000 A
1 A
91001 TAAATCATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.14, G:0.12, T:0.12
Consensus pattern (25 bp):
ACAAAAGGAAAACAAATACAAATAT
Done.