Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014804.1 Kokia drynarioides strain JFW-HI SEQ_129846, 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: 321267
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 207 characters in sequence are not A, C, G, or T
Found at i:17933 original size:38 final size:38
Alignment explanation
Indices: 17879--17952 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
17869 ACATTTCTAA
* *
17879 ACATCGTCATGCAGTGAAAATTTTTGGCGCAATTCTGG
1 ACATCGTCATGCAGTGAAAATTATGGGCGCAATTCTGG
* *
17917 ACATCGTCATGTAGTGACAATTATGGGCGCAATTCT
1 ACATCGTCATGCAGTGAAAATTATGGGCGCAATTCT
17953 ATACAGACTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (38 bp):
ACATCGTCATGCAGTGAAAATTATGGGCGCAATTCTGG
Found at i:28139 original size:24 final size:24
Alignment explanation
Indices: 28112--28157 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
28102 AAAAATAAAG
28112 TAGATTTAGATAAATTCACTTTGA
1 TAGATTTAGATAAATTCACTTTGA
28136 TAGATTTAGATAAATTCACTTT
1 TAGATTTAGATAAATTCACTTT
28158 TTGACCCAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (24 bp):
TAGATTTAGATAAATTCACTTTGA
Found at i:34746 original size:30 final size:30
Alignment explanation
Indices: 34712--34786 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
34702 ATAATTCCCA
*
34712 ATATCTCATTCAGGAACTTGAGAAGACTTG
1 ATATCTCATTCAGGAACTTGAGAAGACTCG
* * *
34742 ATATCTCATTTAGGAGCTTGGGAAGACTCG
1 ATATCTCATTCAGGAACTTGAGAAGACTCG
* *
34772 GTATCTCGTTCAGGA
1 ATATCTCATTCAGGA
34787 TCTTCAGATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (30 bp):
ATATCTCATTCAGGAACTTGAGAAGACTCG
Found at i:34835 original size:66 final size:66
Alignment explanation
Indices: 34729--34899 Score: 200
Period size: 66 Copynumber: 2.6 Consensus size: 66
34719 ATTCAGGAAC
* * * * * * * * * *
34729 TTGAGAAGACTTGATATCTCATTTAGGAGCTTGGGAAGACTCGGTATCTCGTTCAGGATCTTCAG
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTAGGAAGACTCGATATCGCGCTCAAGAGCTTCAA
34794 A
66 A
* *
34795 TTGAGAAGACCTGATATCTCGTTCAGGAG-TGTAGGAAGACTCGATATCGCGCTCAAGCGCTTGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCT-TAGGAAGACTCGATATCGCGCTCAAGAGCTTCA
34859 AA
65 AA
* *
34861 TTGAGAAGACCTGATATCTCGTTCAAGAGCTTGGGAAGA
1 TTGAGAAGACCTGATATCTCGTTCAGGAGCTTAGGAAGA
34900 TTCAATATTT
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
65 1 0.01
66 87 0.98
67 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (66 bp):
TTGAGAAGACCTGATATCTCGTTCAGGAGCTTAGGAAGACTCGATATCGCGCTCAAGAGCTTCAA
A
Found at i:43567 original size:166 final size:166
Alignment explanation
Indices: 43293--43616 Score: 612
Period size: 166 Copynumber: 2.0 Consensus size: 166
43283 TACAGTTCGC
* *
43293 TGACCACTGTAGCTATGCTACTGCCATGCTCATCTCGTTGTTGTATCTTGGGAGACAGTCGACCA
1 TGACCACTGCAGCTATGCTACTGCCATGCTCATCTCATTGTTGTATCTTGGGAGACAGTCGACCA
*
43358 ACATTTTTCCAGCACCAAAGGAGCGGCCAAATCTATTTTAAGGAAATTATGAAAATAAACCTCAA
66 ACATTTTTCCAACACCAAAGGAGCGGCCAAATCTATTTTAAGGAAATTATGAAAATAAACCTCAA
43423 CTACCTATGAGTACAAAATTTCAATACTCATCTCGT
131 CTACCTATGAGTACAAAATTTCAATACTCATCTCGT
43459 TGACCACTGCAGCTATGCTACTGCCATGCTCATCTCATTGTTGTATCTTGGGAGACAGTCGACCA
1 TGACCACTGCAGCTATGCTACTGCCATGCTCATCTCATTGTTGTATCTTGGGAGACAGTCGACCA
*
43524 ACATTTTTCCAACACCAAAGGAGCGGCCAAATCTGTTTTAAGGAAATTATGAAAATAAACCTCAA
66 ACATTTTTCCAACACCAAAGGAGCGGCCAAATCTATTTTAAGGAAATTATGAAAATAAACCTCAA
43589 CTACCTATGAGTACAAAATTTCAATACT
131 CTACCTATGAGTACAAAATTTCAATACT
43617 GTTTATTTTC
Statistics
Matches: 154, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
166 154 1.00
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.28
Consensus pattern (166 bp):
TGACCACTGCAGCTATGCTACTGCCATGCTCATCTCATTGTTGTATCTTGGGAGACAGTCGACCA
ACATTTTTCCAACACCAAAGGAGCGGCCAAATCTATTTTAAGGAAATTATGAAAATAAACCTCAA
CTACCTATGAGTACAAAATTTCAATACTCATCTCGT
Found at i:43918 original size:79 final size:79
Alignment explanation
Indices: 43808--44399 Score: 574
Period size: 79 Copynumber: 7.5 Consensus size: 79
43798 GTTTGTAAAT
* * * * * * * *
43808 AGAAATTAATTGAATAATTTTATTTCGGGA-TTTATTCCTTACATTCAATAGAATTTATTCGAGT
1 AGAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCTTACGTTCAACAAAATTTATTCGAGT
* * *
43872 TTTTGTTTTCAAAC
66 TTCTATTTCCAAAC
* * ***
43886 AAAAATTAAATTGAACAATTCTGTTTCAGGATTTTATTCCTGGTGTTCAACAAAATTTATTCGAG
1 AGAAATT-AATTAAACAATTCTGTTTCAGGATTTTATTCCTTACGTTCAACAAAATTTATTCGAG
**
43951 TTTCTATTTCCAAGT
65 TTTCTATTTCCAAAC
* * * * * *
43966 AGAAATTAATTGAATAATTCTGTTTTAGGATTTTATTCC-TACCATTCAACAGAATTTA-TCTAA
1 AGAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCTTA-CGTTCAACAAAATTTATTC-GA
*
44029 GTTTCTGTTTCCAAAC
64 GTTTCTATTTCCAAAC
* * * *
44045 AAAAATTAAATTAAACAATTCTATTTCAAGATTTTATTCC-TATCGCT-AACAAAATTTATTCGA
1 AGAAATT-AATTAAACAATTCTGTTTCAGGATTTTATTCCTTA-CGTTCAACAAAATTTATTCGA
* *
44108 GTTTCTATTTTCAAAT
64 GTTTCTATTTCCAAAC
* * * * *
44124 AGAAATTAATTAAATAATTATGTTTTAGGATTTTATTCCTGT-CGTTTAACAGAATTTATTCGAG
1 AGAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCT-TACGTTCAACAAAATTTATTCGAG
* * *
44188 TTTTTATTTTCGAAC
65 TTTCTATTTCCAAAC
* * * * *
44203 AGGAATTAATTGAACAATTCTG-TTCTAGGATTTTATTCATGT-TGTTCAACAAAATTTATTTGA
1 AGAAATTAATTAAACAATTCTGTTTC-AGGATTTTATTCCT-TACGTTCAACAAAATTTATTCGA
*
44266 GTTTCTGTTTCCAAAC
64 GTTTCTATTTCCAAAC
* * * *
44282 AGAAATTAAATTAAACAATTATGTTTTAGGATTTTATTCCTTTCGTTCAATAAAATTTATTCGAG
1 AGAAATT-AATTAAACAATTCTGTTTCAGGATTTTATTCCTTACGTTCAACAAAATTTATTCGAG
44347 TTTCTATTTCCAAA-
65 TTTCTATTTCCAAAC
**
44361 A-AAAAAAATTAAACAATTCTGTTTCAGGATTTTATTCCT
1 AGAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCT
44400 ATTGTTTCAG
Statistics
Matches: 421, Mismatches: 80, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
77 31 0.07
78 43 0.10
79 210 0.50
80 135 0.32
81 2 0.00
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (79 bp):
AGAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCTTACGTTCAACAAAATTTATTCGAGT
TTCTATTTCCAAAC
Found at i:44140 original size:158 final size:158
Alignment explanation
Indices: 43804--44401 Score: 710
Period size: 158 Copynumber: 3.8 Consensus size: 158
43794 TTCTGTTTGT
* * * ** *
43804 AAATAGAAATTAATTGAATAATTTTATTTCGGGA-TTTATTCCT-TACATTCAATAGAATTTATT
1 AAATAGAAATTAATTAAATAATTATGTTTTAGGATTTTATTCCTAT-CATTCAACAGAATTTATT
* * * * *
43867 CGAGTTTTTGTTTTCAAACAAAAATTAAATTGAACAATTCTGTTTCAGGATTTTATTCCTGGTGT
65 CGAGTTTCTATTTCCAAACAAAAATTAAATTAAACAATTCTGTTTCAGGATTTTATTCCT-ATGT
43932 TCAACAAAATTTATTCGAGTTTCTATTTCC
129 TCAACAAAATTTATTCGAGTTTCTATTTCC
* * * *
43962 AAGTAGAAATTAATTGAATAATTCTGTTTTAGGATTTTATTCCTACCATTCAACAGAATTTA-TC
1 AAATAGAAATTAATTAAATAATTATGTTTTAGGATTTTATTCCTATCATTCAACAGAATTTATTC
* * * * *
44026 TAAGTTTCTGTTTCCAAACAAAAATTAAATTAAACAATTCTATTTCAAGATTTTATTCCTATCGC
66 -GAGTTTCTATTTCCAAACAAAAATTAAATTAAACAATTCTGTTTCAGGATTTTATTCCTAT-GT
*
44091 T-AACAAAATTTATTCGAGTTTCTATTTTC
129 TCAACAAAATTTATTCGAGTTTCTATTTCC
* * *
44120 AAATAGAAATTAATTAAATAATTATGTTTTAGGATTTTATTCCTGTCGTTTAACAGAATTTATTC
1 AAATAGAAATTAATTAAATAATTATGTTTTAGGATTTTATTCCTATCATTCAACAGAATTTATTC
* * * ** * * *
44185 GAGTTTTTATTTTCGAACAGGAATT-AATTGAACAATTCTG-TTCTAGGATTTTATTCATGTTGT
66 GAGTTTCTATTTCCAAACAAAAATTAAATTAAACAATTCTGTTTC-AGGATTTTATTCCT-ATGT
* *
44248 TCAACAAAATTTATTTGAGTTTCTGTTTCC
129 TCAACAAAATTTATTCGAGTTTCTATTTCC
* * * * * *
44278 AAACAGAAATTAAATTAAACAATTATGTTTTAGGATTTTATTCCTTTCGTTCAATAAAATTTATT
1 AAATAGAAATT-AATTAAATAATTATGTTTTAGGATTTTATTCCTATCATTCAACAGAATTTATT
44343 CGAGTTTCTATTTCCAAA-AAAAA--AAATTAAACAATTCTGTTTCAGGATTTTATTCCTAT
65 CGAGTTTCTATTTCCAAACAAAAATTAAATTAAACAATTCTGTTTCAGGATTTTATTCCTAT
44402 TGTTTCAGGA
Statistics
Matches: 376, Mismatches: 53, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
156 4 0.01
157 54 0.14
158 174 0.46
159 144 0.38
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (158 bp):
AAATAGAAATTAATTAAATAATTATGTTTTAGGATTTTATTCCTATCATTCAACAGAATTTATTC
GAGTTTCTATTTCCAAACAAAAATTAAATTAAACAATTCTGTTTCAGGATTTTATTCCTATGTTC
AACAAAATTTATTCGAGTTTCTATTTCC
Found at i:44212 original size:237 final size:236
Alignment explanation
Indices: 43859--44399 Score: 701
Period size: 237 Copynumber: 2.3 Consensus size: 236
43849 CATTCAATAG
* * *
43859 AATTTATTCGAGTTTTTGTTTTCAAACAAAAATTAAATTGAACAATTCTGTTTCAGGATTTTATT
1 AATTTATTCGAGTTTCTATTTTC-AA-AAAAATT-AATTAAACAATTCTGTTTCAGGATTTTATT
* *
43924 CCTGGTGTTCAACAAAATTTATTCGAGTTTCTATTTCCAAGTAGAAATTAATTGAATAATTCTGT
63 CCTGGTGTTCAACAAAATTTATTCGAGTTTCTATTTCCAAGCAGAAATTAATTGAACAATTCTGT
* * *
43989 TTTAGGATTTTATTCCTACCATTCAACAGAATTTATCTAAGTTTCTGTTTCCAAACAAAAATTAA
128 TCTAGGATTTTATTCATACCATTCAACAAAATTTATCTAAGTTTCTGTTTCCAAACAAAAATTAA
*
44054 ATTAAACAATTCTATTTCAAGATTTTATTCCTATCGCT-AACAA
193 ATTAAACAATTATATTTCAAGATTTTATTCCTATCGCTCAACAA
* * *
44097 AATTTATTCGAGTTTCTATTTTCAAATAGAAATTAATTAAATAATTATGTTTTAGGATTTTATTC
1 AATTTATTCGAGTTTCTATTTTCAAA-A-AAATTAATTAAACAATTCTGTTTCAGGATTTTATTC
* * * * *
44162 CT-GTCGTTTAACAGAATTTATTCGAGTTTTTATTTTCGAA-CAGGAATTAATTGAACAATTCTG
64 CTGGT-GTTCAACAAAATTTATTCGAGTTTCTA-TTTCCAAGCAGAAATTAATTGAACAATTCTG
**** * * *
44225 TTCTAGGATTTTATTCATGTTGTTCAACAAAATTTATTTGAGTTTCTGTTTCCAAACAGAAATTA
127 TTCTAGGATTTTATTCATACCATTCAACAAAATTTATCTAAGTTTCTGTTTCCAAACAAAAATTA
* * * * * *
44290 AATTAAACAATTATGTTTTAGGATTTTATTCCTTTCGTTCAATAA
192 AATTAAACAATTATATTTCAAGATTTTATTCCTATCGCTCAACAA
* **
44335 AATTTATTCGAGTTTCTATTTCCAAAAAAAAAAATTAAACAATTCTGTTTCAGGATTTTATTCCT
1 AATTTATTCGAGTTTCTATTTTCAAAAAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCT
44400 ATTGTTTCAG
Statistics
Matches: 262, Mismatches: 36, Indels: 12
0.85 0.12 0.04
Matches are distributed among these distances:
236 36 0.14
237 165 0.63
238 61 0.23
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (236 bp):
AATTTATTCGAGTTTCTATTTTCAAAAAAATTAATTAAACAATTCTGTTTCAGGATTTTATTCCT
GGTGTTCAACAAAATTTATTCGAGTTTCTATTTCCAAGCAGAAATTAATTGAACAATTCTGTTCT
AGGATTTTATTCATACCATTCAACAAAATTTATCTAAGTTTCTGTTTCCAAACAAAAATTAAATT
AAACAATTATATTTCAAGATTTTATTCCTATCGCTCAACAA
Found at i:44408 original size:22 final size:22
Alignment explanation
Indices: 44380--44422 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
44370 TAAACAATTC
44380 TGTTTCAGGATTTTATTCCTAT
1 TGTTTCAGGATTTTATTCCTAT
44402 TGTTTCAGGATTTTATTCCTA
1 TGTTTCAGGATTTTATTCCTA
44423 CCGTTCAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (22 bp):
TGTTTCAGGATTTTATTCCTAT
Found at i:66247 original size:35 final size:35
Alignment explanation
Indices: 66208--66280 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
66198 GAGCCCAACT
* * *
66208 CTAGTTGGATATACCAACAA-TTATTGTGCCCAGCA
1 CTAGTTGAATAAACCAACAACTT-GTGTGCCCAGCA
* *
66243 CTAGTTGAATAAACCGACAACTTGTGTGCCCATCA
1 CTAGTTGAATAAACCAACAACTTGTGTGCCCAGCA
66278 CTA
1 CTA
66281 ATTAGATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 30 0.94
36 2 0.06
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (35 bp):
CTAGTTGAATAAACCAACAACTTGTGTGCCCAGCA
Found at i:66521 original size:2 final size:2
Alignment explanation
Indices: 66514--66540 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66504 TAATATCATC
66514 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 A
66541 ATTGGATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:71693 original size:38 final size:38
Alignment explanation
Indices: 71641--71757 Score: 148
Period size: 38 Copynumber: 3.1 Consensus size: 38
71631 GAACTTGGAG
* *
71641 TTCCAAAGCATTTTCCCATAGTACGAGAAGGTTAAAAC
1 TTCCAAAGCGTTTTCCCGTAGTACGAGAAGGTTAAAAC
*
71679 TTCCAAAGCGTTTTCTCGTAGTAC-AGGAAGGTTCAAAA-
1 TTCCAAAGCGTTTTCCCGTAGTACGA-GAAGGTT-AAAAC
* * *
71717 TTCCAAAGTGTTTTCCCGTAGTATGAGAAGGTTCAAAC
1 TTCCAAAGCGTTTTCCCGTAGTACGAGAAGGTTAAAAC
71755 TTC
1 TTC
71758 TTATTTAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
37 4 0.06
38 59 0.87
39 5 0.07
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (38 bp):
TTCCAAAGCGTTTTCCCGTAGTACGAGAAGGTTAAAAC
Found at i:73529 original size:16 final size:16
Alignment explanation
Indices: 73508--73538 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
73498 ATAATGTGAA
73508 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
73524 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
73539 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:75012 original size:17 final size:18
Alignment explanation
Indices: 74990--75029 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
74980 TACACATATA
74990 TTTTTC-TTCTTTTCCTT
1 TTTTTCTTTCTTTTCCTT
*
75007 TTTTTCTTTCTTTTTCTT
1 TTTTTCTTTCTTTTCCTT
75025 TTTTT
1 TTTTT
75030 TATGTGACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTCTTTCTTTTCCTT
Found at i:75616 original size:17 final size:17
Alignment explanation
Indices: 75590--75623 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
75580 ACAAATATAT
75590 ATGTAAATGCAATGACA
1 ATGTAAATGCAATGACA
* *
75607 ATGTAGATGCAGTGACA
1 ATGTAAATGCAATGACA
75624 GTAAAAATGC
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:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
ATGTAAATGCAATGACA
Found at i:77191 original size:16 final size:15
Alignment explanation
Indices: 77158--77191 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
77148 AGTCTTAGCA
*
77158 AAATATTGTATCAGC
1 AAATATTGTATCACC
77173 AAATATTGTATCATCC
1 AAATATTGTATCA-CC
77189 AAA
1 AAA
77192 ATTCCCCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (15 bp):
AAATATTGTATCACC
Found at i:77781 original size:16 final size:16
Alignment explanation
Indices: 77760--77790 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77750 ATAATGTGAA
77760 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
77776 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
77791 GGATCCACAA
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:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:87009 original size:33 final size:33
Alignment explanation
Indices: 86967--87033 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
86957 GTTCTATTCT
86967 ATGCATGGGATAACGTCGAAGCAAAGTCTTGTA
1 ATGCATGGGATAACGTCGAAGCAAAGTCTTGTA
*
87000 ATGCATGGGATAACGTCGATGCAAAGTCTTGTA
1 ATGCATGGGATAACGTCGAAGCAAAGTCTTGTA
87033 A
1 A
87034 CGCTCCCATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (33 bp):
ATGCATGGGATAACGTCGAAGCAAAGTCTTGTA
Found at i:102222 original size:19 final size:20
Alignment explanation
Indices: 102175--102225 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
102165 TAAGATTGAG
*
102175 AGGATTTTTTTATTCAGAGA
1 AGGAATTTTTTATTCAGAGA
* *
102195 AGGATTTTTTTGTTCAGAG-
1 AGGAATTTTTTATTCAGAGA
*
102214 GGGAATTTTTTA
1 AGGAATTTTTTA
102226 ATGAGATTGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.25, C:0.04, G:0.24, T:0.47
Consensus pattern (20 bp):
AGGAATTTTTTATTCAGAGA
Found at i:102224 original size:20 final size:20
Alignment explanation
Indices: 102175--102213 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
102165 TAAGATTGAG
102175 AGGATTTTTTTATTCAGAGA
1 AGGATTTTTTTATTCAGAGA
*
102195 AGGATTTTTTTGTTCAGAG
1 AGGATTTTTTTATTCAGAG
102214 GGGAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.23, T:0.46
Consensus pattern (20 bp):
AGGATTTTTTTATTCAGAGA
Found at i:102512 original size:20 final size:20
Alignment explanation
Indices: 102464--102512 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
102454 GTTCGTATTT
*
102464 TTTATTATTTTTCATATTTAG
1 TTTATTA-TTTTCATATTTAA
*
102485 TTGT-TTATTTTGATATTTAA
1 TT-TATTATTTTCATATTTAA
102505 TTTATTAT
1 TTTATTAT
102513 CTTGTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 17 0.71
21 5 0.21
22 1 0.04
ACGTcount: A:0.24, C:0.02, G:0.06, T:0.67
Consensus pattern (20 bp):
TTTATTATTTTCATATTTAA
Found at i:115826 original size:18 final size:18
Alignment explanation
Indices: 115805--115839 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
115795 TTTAACATCT
115805 CTTTTTGCTTCAACATTA
1 CTTTTTGCTTCAACATTA
*
115823 CTTTTTGCTTCAGCATT
1 CTTTTTGCTTCAACATT
115840 CAACTCTAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.23, G:0.09, T:0.51
Consensus pattern (18 bp):
CTTTTTGCTTCAACATTA
Found at i:120122 original size:11 final size:11
Alignment explanation
Indices: 120106--120130 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
120096 CTTTCATTGA
120106 TCAAAACCTTG
1 TCAAAACCTTG
120117 TCAAAACCTTG
1 TCAAAACCTTG
120128 TCA
1 TCA
120131 TCAGACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (11 bp):
TCAAAACCTTG
Found at i:122017 original size:11 final size:11
Alignment explanation
Indices: 122001--122025 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
121991 CATACTAGTT
122001 TTTATAAAAGA
1 TTTATAAAAGA
122012 TTTATAAAAGA
1 TTTATAAAAGA
122023 TTT
1 TTT
122026 TCGAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTATAAAAGA
Found at i:126851 original size:18 final size:18
Alignment explanation
Indices: 126828--126863 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
126818 AAAAATTGTG
126828 GGCACATTTTTCTTGAAA
1 GGCACATTTTTCTTGAAA
*
126846 GGCACATTTTTGTTGAAA
1 GGCACATTTTTCTTGAAA
126864 TTTTGCTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (18 bp):
GGCACATTTTTCTTGAAA
Found at i:126955 original size:42 final size:42
Alignment explanation
Indices: 126896--126978 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
126886 AAGAAATAAG
126896 TAAAATTCAAAGTTGTGGATGTAATTGCATTTCCATTTCACT
1 TAAAATTCAAAGTTGTGGATGTAATTGCATTTCCATTTCACT
126938 TAAAATTCAAAGTTGTGGATGTAATTGCATTTCCATTTCAC
1 TAAAATTCAAAGTTGTGGATGTAATTGCATTTCCATTTCAC
126979 AATATCCCTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (42 bp):
TAAAATTCAAAGTTGTGGATGTAATTGCATTTCCATTTCACT
Found at i:129462 original size:19 final size:20
Alignment explanation
Indices: 129416--129462 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
129406 TTCTGTAAAG
**
129416 AAATTAAAACGAAACAAGTA
1 AAATTAAAACGAAACAAAAA
* *
129436 AAAGTAAAAC-AAATAAAAA
1 AAATTAAAACGAAACAAAAA
129455 AAATTAAA
1 AAATTAAA
129463 TATGCATCGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.15
Consensus pattern (20 bp):
AAATTAAAACGAAACAAAAA
Found at i:146131 original size:3 final size:3
Alignment explanation
Indices: 146125--146180 Score: 64
Period size: 3 Copynumber: 18.7 Consensus size: 3
146115 GTATTGTAGT
146125 AGA AGA AGA AGCA AG- AGA AGA AGA GAGA A-A AGA AG- AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA -AGA AGA AGA AGA AGA A-GA AGA
146170 AGA AGA AGA AG
1 AGA AGA AGA AG
146181 GAATTGCCCC
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.13
3 32 0.68
4 9 0.19
ACGTcount: A:0.62, C:0.02, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:155549 original size:14 final size:16
Alignment explanation
Indices: 155518--155556 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
155508 TAAAAAAATA
155518 TTTTCTTTTTACAGA-T
1 TTTTC-TTTTACAGATT
155534 TTTTCTTTTA-AGATT
1 TTTTCTTTTACAGATT
155549 TTTTCTTT
1 TTTTCTTT
155557 CTTTTTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 14 0.64
16 5 0.23
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTTCTTTTACAGATT
Found at i:158538 original size:40 final size:40
Alignment explanation
Indices: 158483--158563 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
158473 CTTTCTAACC
158483 ACACCTACCAAATATCCATAGCTCTCATACAAGTCCCTAT
1 ACACCTACCAAATATCCATAGCTCTCATACAAGTCCCTAT
* *
158523 ACACCTATCGAATATCCATAGCTCTCATACAAGTCCCTAT
1 ACACCTACCAAATATCCATAGCTCTCATACAAGTCCCTAT
158563 A
1 A
158564 ATTTAATTTC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.35, C:0.33, G:0.06, T:0.26
Consensus pattern (40 bp):
ACACCTACCAAATATCCATAGCTCTCATACAAGTCCCTAT
Found at i:173219 original size:17 final size:17
Alignment explanation
Indices: 173199--173241 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
173189 CAATGAACTA
* *
173199 ACAAGTAAACTGCAACG
1 ACAACTAAAATGCAACG
*
173216 ACAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
173233 ACAATTAAA
1 ACAACTAAA
173242 TAAGATGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:187555 original size:15 final size:15
Alignment explanation
Indices: 187535--187564 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
187525 GCTAAATGAT
*
187535 AACATGGTGATTGAA
1 AACATGATGATTGAA
187550 AACATGATGATTGAA
1 AACATGATGATTGAA
187565 GCATGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (15 bp):
AACATGATGATTGAA
Found at i:194973 original size:9 final size:10
Alignment explanation
Indices: 194952--194976 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
194942 GTGACCTCTA
194952 TTTTCAAATT
1 TTTTCAAATT
194962 TTTTCAAATT
1 TTTTCAAATT
194972 TTTTC
1 TTTTC
194977 GTTTTCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTCAAATT
Found at i:195530 original size:23 final size:22
Alignment explanation
Indices: 195483--195530 Score: 53
Period size: 21 Copynumber: 2.1 Consensus size: 22
195473 GCAAATGATT
* *
195483 TTAAATTTATTTTTAAAAATTA
1 TTAAAATTATTTTTAAAAATAA
195505 TTAAAATTA-TTTTAAAATCATAA
1 TTAAAATTATTTTTAAAA--ATAA
195528 TTA
1 TTA
195531 TTATCATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
22 8 0.36
23 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAAATTATTTTTAAAAATAA
Found at i:195633 original size:22 final size:22
Alignment explanation
Indices: 195590--195633 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
195580 ATTATTAAAA
*
195590 TCATCATCATCATCACCGTTCC
1 TCATCATCATCATCACCATTCC
*
195612 TCATCATCGTCATC-CTCATTCC
1 TCATCATCATCATCAC-CATTCC
195634 CCTTCAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.20, C:0.41, G:0.05, T:0.34
Consensus pattern (22 bp):
TCATCATCATCATCACCATTCC
Found at i:199433 original size:31 final size:31
Alignment explanation
Indices: 199398--199461 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
199388 AGAAAAAAAT
199398 AAGTAAAATAAATAAAGAACATAATTTATGC
1 AAGTAAAATAAATAAAGAACATAATTTATGC
199429 AAGTAAAATAAATAAAGAACATAATTTATGC
1 AAGTAAAATAAATAAAGAACATAATTTATGC
199460 AA
1 AA
199462 AAATATTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.59, C:0.06, G:0.09, T:0.25
Consensus pattern (31 bp):
AAGTAAAATAAATAAAGAACATAATTTATGC
Found at i:204637 original size:13 final size:13
Alignment explanation
Indices: 204606--204640 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
204596 AAAGGAGAAG
*
204606 AAAAAGGAAAAGA
1 AAAAAGAAAAAGA
204619 ATAAAAGAAAAAGA
1 A-AAAAGAAAAAGA
204633 AAAAAGAA
1 AAAAAGAA
204641 GAGAAGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:204637 original size:21 final size:20
Alignment explanation
Indices: 204603--204649 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
204593 GAGAAAGGAG
* *
204603 AAGAAAAAGGAAAAGAATAA
1 AAGAAAAAGAAAAAGAAGAA
*
204623 AAGAAAAAGAAAAAAGAAGAG
1 AAGAAAAAG-AAAAAGAAGAA
204644 AAGAAA
1 AAGAAA
204650 TGGAGATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (20 bp):
AAGAAAAAGAAAAAGAAGAA
Found at i:213752 original size:58 final size:58
Alignment explanation
Indices: 213594--213759 Score: 214
Period size: 58 Copynumber: 2.9 Consensus size: 58
213584 ATATTATATA
*
213594 TTATGATTTTTATT-AATTCATATTTTAATAATAATTATATTAAAA-ATTAATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAATA-TAATTAAATTAT
* * * *
213653 ATATTA-TTTTACTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
213710 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
213760 AACAATAATC
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
57 38 0.41
58 46 0.49
59 9 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:213940 original size:16 final size:16
Alignment explanation
Indices: 213916--213969 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
213906 TGAATTACTG
*
213916 ATTACAGCCTTATTCC
1 ATTACAGCCATATTCC
*
213932 ATTATAGCCATATTCC
1 ATTACAGCCATATTCC
*
213948 ATTACAGCTC-TATTCT
1 ATTACAGC-CATATTCC
213964 ATTACA
1 ATTACA
213970 ACGAACCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 32 0.97
17 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACAGCCATATTCC
Found at i:221643 original size:15 final size:12
Alignment explanation
Indices: 221612--221650 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
221602 CGACAGACTC
221612 TTCTTCTTCCTT
1 TTCTTCTTCCTT
221624 TTCTTCTTCCTT
1 TTCTTCTTCCTT
221636 TCCCTCTTCTTCCTT
1 T---TCTTCTTCCTT
221651 GTATTGATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 13 0.54
15 11 0.46
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCTTCTTCCTT
Found at i:236252 original size:17 final size:18
Alignment explanation
Indices: 236228--236269 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
236218 CTCTAACTTA
*
236228 TCCTTCTCCTCTTCA-CT
1 TCCTTCTCCCCTTCATCT
*
236245 TTCTTCTCCCCTTCATCT
1 TCCTTCTCCCCTTCATCT
236263 TCCTTCT
1 TCCTTCT
236270 TATCATGTTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 13 0.62
18 8 0.38
ACGTcount: A:0.05, C:0.45, G:0.00, T:0.50
Consensus pattern (18 bp):
TCCTTCTCCCCTTCATCT
Found at i:256107 original size:19 final size:19
Alignment explanation
Indices: 256083--256148 Score: 96
Period size: 19 Copynumber: 3.5 Consensus size: 19
256073 AACACATTTT
** *
256083 ATATTCACATCTATTTCAC
1 ATATTCACATAAATGTCAC
256102 ATATTCACATAAATGTCAC
1 ATATTCACATAAATGTCAC
256121 ATATTCACATAAATGTCAC
1 ATATTCACATAAATGTCAC
*
256140 ATGTTCACA
1 ATATTCACA
256149 AATTCCATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.35
Consensus pattern (19 bp):
ATATTCACATAAATGTCAC
Found at i:256120 original size:11 final size:11
Alignment explanation
Indices: 256106--256141 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
256096 TTTCACATAT
256106 TCACATAAATG
1 TCACATAAATG
256117 TCACAT--AT-
1 TCACATAAATG
256125 TCACATAAATG
1 TCACATAAATG
256136 TCACAT
1 TCACAT
256142 GTTCACAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.27
9 2 0.09
10 2 0.09
11 12 0.55
ACGTcount: A:0.42, C:0.22, G:0.06, T:0.31
Consensus pattern (11 bp):
TCACATAAATG
Found at i:256557 original size:45 final size:45
Alignment explanation
Indices: 256454--256567 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
256444 GCCACCCTGT
* * * *
256454 GTTGCCCGATAATGATGGCTCGCTTATATTGAATAGGTACCCTGA
1 GTTGCCCGACAATGATGGCTCACTTATATTGAATAGCTACCCAGA
* * *
256499 GTTTCCCAACAATGATGGCTCACTTATATTGAATTGCTACCCCAG-
1 GTTGCCCGACAATGATGGCTCACTTATATTGAATAGCTA-CCCAGA
* *
256544 GTTGCCCGGCAATGATAGCTCACT
1 GTTGCCCGACAATGATGGCTCACT
256568 GATCGGCCTA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
45 53 0.93
46 4 0.07
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (45 bp):
GTTGCCCGACAATGATGGCTCACTTATATTGAATAGCTACCCAGA
Found at i:259432 original size:15 final size:15
Alignment explanation
Indices: 259412--259451 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
259402 GGCATCTATA
259412 TCCTCTTCATCCTTC
1 TCCTCTTCATCCTTC
* *
259427 TTCTCTTCCTCCTTC
1 TCCTCTTCATCCTTC
259442 TCCTCTTCAT
1 TCCTCTTCAT
259452 TTCCTTTTTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.45, G:0.00, T:0.50
Consensus pattern (15 bp):
TCCTCTTCATCCTTC
Found at i:262784 original size:22 final size:23
Alignment explanation
Indices: 262754--262797 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
262744 AGTGTTTTAT
*
262754 TATGCAAG-AATAAAATCCTAAA
1 TATGAAAGAAATAAAATCCTAAA
*
262776 TATGAAAGAAATAAACTCCTAA
1 TATGAAAGAAATAAAATCCTAA
262798 GGACCTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (23 bp):
TATGAAAGAAATAAAATCCTAAA
Found at i:264705 original size:19 final size:19
Alignment explanation
Indices: 264681--264720 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
264671 GACCCCCTTT
* *
264681 ATTAAAAGTAGCAATTAAA
1 ATTAAAAGTAACAATAAAA
*
264700 ATTAAAATTAACAATAAAA
1 ATTAAAAGTAACAATAAAA
264719 AT
1 AT
264721 GGAAAATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (19 bp):
ATTAAAAGTAACAATAAAA
Found at i:274503 original size:25 final size:24
Alignment explanation
Indices: 274466--274513 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
274456 GAAATAATTC
274466 ATGTTTAATTATTAAATATAATTTT
1 ATGTTTAATTATTAAAT-TAATTTT
*
274491 ATGTCTTAA-TATTTAATTAATTT
1 ATGT-TTAATTATTAAATTAATTT
274514 ATACATGACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (24 bp):
ATGTTTAATTATTAAATTAATTTT
Found at i:276823 original size:19 final size:19
Alignment explanation
Indices: 276799--276861 Score: 101
Period size: 19 Copynumber: 3.3 Consensus size: 19
276789 GTGACATTGC
276799 GAATATGTGAAATTGATGT
1 GAATATGTGAAATTGATGT
276818 GAATATGT-AACATTGATGT
1 GAATATGTGAA-ATTGATGT
*
276837 GAATATGTGAAATAGATGT
1 GAATATGTGAAATTGATGT
276856 GAATAT
1 GAATAT
276862 CAAATGTGTT
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
18 2 0.05
19 37 0.90
20 2 0.05
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.35
Consensus pattern (19 bp):
GAATATGTGAAATTGATGT
Found at i:279565 original size:37 final size:38
Alignment explanation
Indices: 279513--279601 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 38
279503 TTGTTATTAA
*
279513 ATTTTAATAATAATTATTATTAAATATAATTTAATCAT
1 ATTTTAATAATAATTATTATAAAATATAATTTAATCAT
* * *
279551 ATTTTAA-CATAATTATTATAAAATATAATTTAATAAC
1 ATTTTAATAATAATTATTATAAAATATAATTTAATCAT
279588 ATTCTTAAT-ATAAT
1 ATT-TTAATAATAAT
279602 ATACAACATT
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
37 29 0.64
38 16 0.36
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.47
Consensus pattern (38 bp):
ATTTTAATAATAATTATTATAAAATATAATTTAATCAT
Found at i:280582 original size:21 final size:20
Alignment explanation
Indices: 280554--280592 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
280544 TTTATGTATT
280554 GTACTAGACTACCGATACAA
1 GTACTAGACTACCGATACAA
280574 GTACATAGACTACCGATAC
1 GTAC-TAGACTACCGATAC
280593 TCCTATGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (20 bp):
GTACTAGACTACCGATACAA
Found at i:284533 original size:102 final size:101
Alignment explanation
Indices: 284361--284561 Score: 341
Period size: 102 Copynumber: 2.0 Consensus size: 101
284351 ATTATTTCAG
*
284361 TTTAGGGAACTCGATAAATTGTGCCCTAACGTACTGGATATGGTTTTCTTTAAACCTAAGTAATT
1 TTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGATATGGTTTTCTTTAAACCTAAGTAATT
284426 GAATATCCTATTTAAAATTGATAAATGTTCTTTTAT
66 GAATATCCTATTTAAAATTGATAAATGTTCTTTTAT
* * *
284462 TTTAGGGAACTCGAGAAATTGTGCCCTAACGTATTAGG-TATGATTTTTCTTTGAACCTAAGTAA
1 TTTAGGGAACTCGAGAAATTGTGCCCTAACGTACT-GGATATG-GTTTTCTTTAAACCTAAGTAA
284526 TTGAATATCCTATTTAAAATTGATAAATGTTCTTTT
64 TTGAATATCCTATTTAAAATTGATAAATGTTCTTTT
284562 CGAATATTCG
Statistics
Matches: 94, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
101 37 0.39
102 57 0.61
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (101 bp):
TTTAGGGAACTCGAGAAATTGTGCCCTAACGTACTGGATATGGTTTTCTTTAAACCTAAGTAATT
GAATATCCTATTTAAAATTGATAAATGTTCTTTTAT
Found at i:287502 original size:16 final size:17
Alignment explanation
Indices: 287477--287522 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
287467 CCATCATTTT
287477 CCTATCTGTTCTT-CTTC
1 CCTAT-TGTTCTTCCTTC
287494 CCTATTGTTTCTTCCTTC
1 CCTATTG-TTCTTCCTTC
*
287512 CATATT-TTCTT
1 CCTATTGTTCTT
287523 TCCATTGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.09, C:0.30, G:0.04, T:0.57
Consensus pattern (17 bp):
CCTATTGTTCTTCCTTC
Found at i:292555 original size:22 final size:22
Alignment explanation
Indices: 292511--292556 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
292501 TGCTTTTCTT
*
292511 AAGGAAAAGATTGTAGGTGAAG
1 AAGGAAAAGATTGTAGGTAAAG
*
292533 AAGGAGAAATATTGTA-GTAAAG
1 AAGGA-AAAGATTGTAGGTAAAG
292555 AA
1 AA
292557 CATGTTGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.30, T:0.20
Consensus pattern (22 bp):
AAGGAAAAGATTGTAGGTAAAG
Found at i:296031 original size:17 final size:18
Alignment explanation
Indices: 296005--296042 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
295995 ATTAGATAAA
*
296005 TTTTAGATTT-AAATTAT
1 TTTTAAATTTGAAATTAT
*
296022 TTTTAAATTTGAATTTAT
1 TTTTAAATTTGAAATTAT
296040 TTT
1 TTT
296043 ATTTGAGTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (18 bp):
TTTTAAATTTGAAATTAT
Found at i:299259 original size:34 final size:34
Alignment explanation
Indices: 299191--299260 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
299181 TGATACTTTT
**
299191 TTTGAATTTTTTTTTACTCAATTTGATATTTAAA
1 TTTGAATTTTTTTTTACTCAATTTGATACCTAAA
*
299225 TTTGACATTTTTTTTTTCT-AATTTGATACCTAAA
1 TTTGA-ATTTTTTTTTACTCAATTTGATACCTAAA
299259 TT
1 TT
299261 CTTTTGGACC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
34 20 0.62
35 12 0.38
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.59
Consensus pattern (34 bp):
TTTGAATTTTTTTTTACTCAATTTGATACCTAAA
Found at i:303074 original size:36 final size:35
Alignment explanation
Indices: 303033--303100 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
303023 ATGTTATTTG
303033 TATATATTA-TATAAGT-TATAATATATAAAAATTAAA
1 TATATATTACTATAA-TATA-AATAT-TAAAAATTAAA
303069 TATATATTACTATAATATAAATATTAAAAATT
1 TATATATTACTATAATATAAATATTAAAAATT
303101 GTTAAGACGT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
35 8 0.27
36 15 0.50
37 7 0.23
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (35 bp):
TATATATTACTATAATATAAATATTAAAAATTAAA
Found at i:303175 original size:17 final size:16
Alignment explanation
Indices: 303135--303180 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
303125 TTAATAAATG
*
303135 AAAAATATTAAATTAA
1 AAAAATATAAAATTAA
*
303151 AAATAATATAAATATTTA
1 AAA-AATATAAA-ATTAA
303169 AAAAATATAAAA
1 AAAAATATAAAA
303181 AAATAAGACG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 15 0.58
18 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATATAAAATTAA
Found at i:312398 original size:20 final size:21
Alignment explanation
Indices: 312373--312424 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
312363 CCCCAAATAT
312373 TAAACTTCAAACTTT-AAATC
1 TAAACTTCAAACTTTGAAATC
* * *
312393 TAAAC-TCGAATTTTGAACTC
1 TAAACTTCAAACTTTGAAATC
312413 TAAA-TTCAAACT
1 TAAACTTCAAACT
312425 CGATCAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
19 7 0.28
20 18 0.72
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (21 bp):
TAAACTTCAAACTTTGAAATC
Found at i:313277 original size:2 final size:2
Alignment explanation
Indices: 313270--313294 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
313260 TTAAATTTAT
313270 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
313295 TAATTTAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.