Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002041.1 Kokia drynarioides strain JFW-HI SEQ_113928, 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: 34285
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:1887 original size:29 final size:29
Alignment explanation
Indices: 1844--1936 Score: 107
Period size: 30 Copynumber: 3.1 Consensus size: 29
1834 TAAAACCGAC
1844 CAAATTTGAATTTTTGGAAAGTTTAGGGGT
1 CAAATTTGAATTTTTGGAAA-TTTAGGGGT
*
1874 CAAATTT-AATTTTTTGGAAAATTTGGGGGT
1 CAAATTTGAA-TTTTTGG-AAATTTAGGGGT
* * * *
1904 CAATTTTGAAATTTTGGAAAATTCGGGGT
1 CAAATTTGAATTTTTGGAAATTTAGGGGT
1933 CAAA
1 CAAA
1937 AAACAATTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
29 15 0.28
30 34 0.63
31 5 0.09
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (29 bp):
CAAATTTGAATTTTTGGAAATTTAGGGGT
Found at i:2068 original size:30 final size:29
Alignment explanation
Indices: 2032--2094 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
2022 TAAAACCGAC
*
2032 CAAATTTGAATTTTTGGAAAATTTGGGGGT
1 CAAATTTGAAATTTTGGAAAATTT-GGGGT
2062 CAAATTTGAAATTTTGGAAAATTTGGGGT
1 CAAATTTGAAATTTTGGAAAATTTGGGGT
2091 CAAA
1 CAAA
2095 AAACAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 9 0.28
30 23 0.72
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (29 bp):
CAAATTTGAAATTTTGGAAAATTTGGGGT
Found at i:2614 original size:30 final size:30
Alignment explanation
Indices: 2578--2642 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
2568 ACTTATTTTA
* * *
2578 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
2608 TTGTTAAATTTGTTATTATTTTAAAGACAT
1 TTGTTAAATTTGTTATTATTTTAAAGACAT
2638 TTGTT
1 TTGTT
2643 TGTTAAGTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.26, C:0.03, G:0.14, T:0.57
Consensus pattern (30 bp):
TTGTTAAATTTGTTATTATTTTAAAGACAT
Found at i:3905 original size:15 final size:16
Alignment explanation
Indices: 3885--3918 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3875 TATATTTATA
*
3885 AAATAAAAA-ACAAAT
1 AAATAAAAATAAAAAT
3900 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
3916 AAA
1 AAA
3919 AACAAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:4650 original size:40 final size:40
Alignment explanation
Indices: 4567--4935 Score: 258
Period size: 40 Copynumber: 9.3 Consensus size: 40
4557 ATAGCTTTAG
** * * **
4567 GGGTAAAAGATTAAATTGT-TTCAATCTG-CCTCATGGTCG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAGTTA
* ** *
4606 GGGTAAGAGATCAGATGGTCTTCAATTTGCCCTCTAGTTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* **
4646 GGGTAAAAGATTGGAT--TACTTCAATCTGCCC-CATGGTCG
1 GGGTAAAAGATTGGATGGT-CTTCAATCTGCCCTC-TAGTTA
* * * *
4685 GGGTAAGAGA-TCGATTGGTCTTCAATCTACCCTCTAATTA
1 GGGTAAAAGATTGGA-TGGTCTTCAATCTGCCCTCTAGTTA
* *
4725 GGGTAAAAGATTGGATTG-CTTCAATCTG-CCTC-ACGGTTG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTA--GTTA
*
4764 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
* * * * * **
4804 AGTTAAAAGATTGGATTG-CTTCAATCT-ACCTCATGGTCG
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTC-TAGTTA
* * * * *
4843 GGGTAAGAGATTGGATGATTTTCAATCTG-CCTTTTGATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAG-TTA
* * * *
4883 GAGTAAAAGATTAGATGGTCTTCAATCTGCCCTATAATTA
1 GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
4923 GGGTAAAAGATTG
1 GGGTAAAAGATTG
4936 TGTTGAAGCC
Statistics
Matches: 252, Mismatches: 59, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
37 1 0.00
38 13 0.05
39 94 0.37
40 126 0.50
41 17 0.07
42 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (40 bp):
GGGTAAAAGATTGGATGGTCTTCAATCTGCCCTCTAGTTA
Found at i:4681 original size:79 final size:79
Alignment explanation
Indices: 4567--4913 Score: 444
Period size: 79 Copynumber: 4.4 Consensus size: 79
4557 ATAGCTTTAG
** * *
4567 GGGTAAAAGATTAAATTGTTTCAATCTGCCTCATGGTCGGGGTAAGAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* *
4632 TTGCCCTCTAGTTA
66 CTGCCCTCTAATTA
* *
4646 GGGTAAAAGATTGGATTACTTCAATCTGCCCCATGGTCGGGGTAAGAGATC-GATTGGTCTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGA-TGGTCTTCAA
*
4710 TCTACCCTCTAATTA
65 TCTGCCCTCTAATTA
* * * *
4725 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCACGGTTGGGGTAAAAGATTGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
4790 CTGCCCTCTAATTA
66 CTGCCCTCTAATTA
* * * * * *
4804 AGTTAAAAGATTGGATTGCTTCAATCTACCTCATGGTCGGGGTAAGAGATTGGATGATTTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* * *
4869 CTGCCTTTTGATTA
66 CTGCCCTCTAATTA
* * *
4883 GAGTAAAAGATTAGATGGTCTTCAATCTGCC
1 GGGTAAAAGATTGGATTG-CTTCAATCTGCC
4914 CTATAATTAG
Statistics
Matches: 233, Mismatches: 32, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
78 2 0.01
79 218 0.94
80 13 0.06
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.33
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
CTGCCCTCTAATTA
Found at i:5010 original size:10 final size:10
Alignment explanation
Indices: 4981--5014 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
4971 GATCAAGCCT
4981 TTGGTTTTAAA
1 TTGG-TTTAAA
4992 TTAGGTTTAAA
1 TT-GGTTTAAA
5003 TTGGTTTAAA
1 TTGGTTTAAA
5013 TT
1 TT
5015 TATCTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.45
11 10 0.45
12 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.53
Consensus pattern (10 bp):
TTGGTTTAAA
Found at i:5073 original size:16 final size:16
Alignment explanation
Indices: 5020--5074 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
5010 AAATTTATCT
* *
5020 TTTAAATTTAAATTTGC
1 TTTAAATTTGAA-TTGA
*
5037 TTTAAATTTGAATTTA
1 TTTAAATTTGAATTGA
*
5053 ATTAAATTTGAATTGA
1 TTTAAATTTGAATTGA
5069 TTTAAA
1 TTTAAA
5075 ACTTAATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 21 0.66
17 11 0.34
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (16 bp):
TTTAAATTTGAATTGA
Found at i:5775 original size:6 final size:6
Alignment explanation
Indices: 5764--5842 Score: 61
Period size: 6 Copynumber: 12.2 Consensus size: 6
5754 TATGAATATC
* * *
5764 ATTAAT ATTAAT ATTAAT -TATAAT ATTAAT AGTAAT AATAAT AATAAAT
1 ATTAAT ATTAAT ATTAAT AT-TAAT ATTAAT ATTAAT ATTAAT -ATTAAT
5813 ATCGTAAT AATGATAAT ATTAAT ATTAAT A
1 AT--TAAT -AT--TAAT ATTAAT ATTAAT A
5843 AAAAAGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
5 1 0.02
6 43 0.72
7 5 0.08
8 5 0.08
9 6 0.10
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (6 bp):
ATTAAT
Found at i:5789 original size:18 final size:18
Alignment explanation
Indices: 5766--5841 Score: 71
Period size: 18 Copynumber: 3.9 Consensus size: 18
5756 TGAATATCAT
5766 TAATATTAATATTAATTA
1 TAATATTAATATTAATTA
* *
5784 TAATATTAATAGTAATAA
1 TAATATTAATATTAATTA
*
5802 TAATAATAAATATCGTAATAATGA
1 TAAT-ATTAATAT--TAAT--T-A
5826 TAATATTAATATTAAT
1 TAATATTAATATTAAT
5842 AAAAAAGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
18 20 0.43
19 6 0.13
21 8 0.17
23 7 0.15
24 5 0.11
ACGTcount: A:0.53, C:0.01, G:0.04, T:0.42
Consensus pattern (18 bp):
TAATATTAATATTAATTA
Found at i:6724 original size:29 final size:28
Alignment explanation
Indices: 6685--6943 Score: 157
Period size: 29 Copynumber: 8.9 Consensus size: 28
6675 AAACTATACA
* *
6685 AAAATTACATTTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTA-CCCCGAACTTTCC
** **
6714 AAAATTCCATTTTTGACCTTGATTTTTCC
1 AAAATTCCATTTTT-ACCCCGAACTTTCC
* *
6743 AAAAATTACATTTTTATCCTCGAACTTTCC
1 -AAAATTCCATTTTTA-CCCCGAACTTTCC
* * **
6773 AAAATTTCATTTTTGATCCCGATTTTTCC
1 AAAATTCCATTTTT-ACCCCGAACTTTCC
*
6802 AAAATGACCA-TTTTACCCCCGAAC-TTCC
1 AAAAT-TCCATTTTTA-CCCCGAACTTTCC
* * **
6830 AAAATTCTATTTTTGACCTCGATTTTTCC
1 AAAATTCCATTTTT-ACCCCGAACTTTCC
*
6859 AAAAATTACATTTTTACTCCCGAACTTTCC
1 -AAAATTCCATTTTTAC-CCCGAACTTTCC
* * * **
6889 AAAAATCCAATTTTGACCTCGATTTTTCC
1 AAAATTCC-ATTTTTACCCCGAACTTTCC
*
6918 AAAAGTGACCA--TTTACCCCGAACTTT
1 AAAA-T-TCCATTTTTACCCCGAACTTT
6944 TGGAATTTCA
Statistics
Matches: 174, Mismatches: 42, Indels: 29
0.71 0.17 0.12
Matches are distributed among these distances:
27 2 0.01
28 30 0.17
29 84 0.48
30 56 0.32
31 2 0.01
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (28 bp):
AAAATTCCATTTTTACCCCGAACTTTCC
Found at i:6775 original size:59 final size:59
Alignment explanation
Indices: 6683--7000 Score: 375
Period size: 59 Copynumber: 5.5 Consensus size: 59
6673 CTAAACTATA
* *
6683 CAAAAATTACATTTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTTGATTTTTC
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTC
* * *
6742 CAAAAATTACATTTTTATCCTCGAACTTTCCAAAATTTCATTTTTGATCC-CGATTTTTC
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGA-CCTCGATTTTTC
* *
6801 C-AAAATGACCA-TTTTACCCCCGAAC-TTCCAAAATTCTATTTTTGACCTCGATTTTTC
1 CAAAAATTA-CATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTC
* * *
6858 CAAAAATTACATTTTTACTCCCGAACTTTCCAAAAATCCAATTTTGACCTCGATTTTTC
1 CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTC
* * *** * *
6917 CAAAAGTGACCA--TTTA-CCCCGAACTTT-TGGAATTTCATTTTTGACCTTGATTTTTC
1 CAAAAATTA-CATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTC
*
6973 TAAAAATTAC-TATTTTACCCCCGAACTT
1 CAAAAATTACAT-TTTTACCCCCGAACTT
7001 CAAAAAAAAA
Statistics
Matches: 220, Mismatches: 28, Indels: 23
0.81 0.10 0.08
Matches are distributed among these distances:
55 1 0.00
56 30 0.14
57 44 0.20
58 51 0.23
59 90 0.41
60 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.40
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTTTC
Found at i:6890 original size:116 final size:117
Alignment explanation
Indices: 6695--7000 Score: 410
Period size: 116 Copynumber: 2.6 Consensus size: 117
6685 AAAATTACAT
* *
6695 TTTTACCCCCAAACTTTCCAAAATTCCATTTTTGACCTTGATTTTTCCAAAAATTACATTTTTA-
1 TTTTACCCCCGAAC-TTCCAAAATTCTATTTTTGACCTTGATTTTTCCAAAAATTACATTTTTAC
* * *
6759 TCCTCGAACTTTCCAAAATTTCATTTTTGATCC-CGATTTTTCCAAAA-TGACCA
65 TCC-CGAACTTTCCAAAAATCCAATTTTGA-CCTCGATTTTTCCAAAAGTGACCA
*
6812 TTTTACCCCCGAACTTCCAAAATTCTATTTTTGACCTCGATTTTTCCAAAAATTACATTTTTACT
1 TTTTACCCCCGAACTTCCAAAATTCTATTTTTGACCTTGATTTTTCCAAAAATTACATTTTTACT
6877 CCCGAACTTTCCAAAAATCCAATTTTGACCTCGATTTTTCCAAAAGTGACCA
66 CCCGAACTTTCCAAAAATCCAATTTTGACCTCGATTTTTCCAAAAGTGACCA
**** *
6929 -TTTA-CCCCGAACTTTTGGAATT-TCATTTTTGACCTTGATTTTTCTAAAAATTAC-TATTTTA
1 TTTTACCCCCGAACTTCCAAAATTCT-ATTTTTGACCTTGATTTTTCCAAAAATTACAT-TTTTA
*
6990 CCCCCGAACTT
64 CTCCCGAACTT
7001 CAAAAAAAAA
Statistics
Matches: 171, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
114 2 0.01
115 59 0.35
116 88 0.51
117 22 0.13
ACGTcount: A:0.28, C:0.25, G:0.07, T:0.40
Consensus pattern (117 bp):
TTTTACCCCCGAACTTCCAAAATTCTATTTTTGACCTTGATTTTTCCAAAAATTACATTTTTACT
CCCGAACTTTCCAAAAATCCAATTTTGACCTCGATTTTTCCAAAAGTGACCA
Found at i:14111 original size:40 final size:40
Alignment explanation
Indices: 14067--14168 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 40
14057 AAACGTCATT
* *** *
14067 AGGTAAATCAATAGCGACGTTTTTTTATAAACGCTGCAAA
1 AGGTAAAGCAATAGCGACGTTTTCCCATAAACGCCGCAAA
* *
14107 AGGTAAAGCAATAG-AAGCGTTTTCCCATAAATGCCGCAAA
1 AGGTAAAGCAATAGCGA-CGTTTTCCCATAAACGCCGCAAA
*
14147 AGGTAAAGCAATAGCGGCGTTT
1 AGGTAAAGCAATAGCGACGTTT
14169 ATGGGAAAAT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
39 1 0.02
40 50 0.98
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (40 bp):
AGGTAAAGCAATAGCGACGTTTTCCCATAAACGCCGCAAA
Found at i:14179 original size:40 final size:39
Alignment explanation
Indices: 14102--14234 Score: 122
Period size: 40 Copynumber: 3.3 Consensus size: 39
14092 TATAAACGCT
** ***
14102 GCAAAAGGTAAAGCAATAGAAGCGTTTTCCCATAAATGCC
1 GCAAAAGGTAAAGCAATAGCGGCGTTTTGGGA-AAATGCC
14142 GCAAAAGGTAAAGCAATAGCGGCGTTTATGGGAAAATGCC
1 GCAAAAGGTAAAGCAATAGCGGCGTTT-TGGGAAAATGCC
* * * *
14182 GCATAAGATAAAGAACAATAGCGACGTTTTTGGGAAAACGCC
1 GCAAAAGGTAAAG--CAATAGCGGCG-TTTTGGGAAAATGCC
* *
14224 ACGAAAGGTAA
1 GCAAAAGGTAA
14235 TAAAACTTAA
Statistics
Matches: 76, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 43 0.57
41 2 0.03
42 28 0.37
43 3 0.04
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.18
Consensus pattern (39 bp):
GCAAAAGGTAAAGCAATAGCGGCGTTTTGGGAAAATGCC
Found at i:14216 original size:42 final size:40
Alignment explanation
Indices: 14135--14219 Score: 116
Period size: 42 Copynumber: 2.1 Consensus size: 40
14125 GTTTTCCCAT
* *
14135 AAATGCCGCAAAAGGTAAAGCAATAGCGGCGTTTATGGGA
1 AAATGCCGCAAAAGATAAAGCAATAGCGACGTTTATGGGA
* *
14175 AAATGCCGCATAAGATAAAGAACAATAGCGACGTTTTTGGGA
1 AAATGCCGCAAAAGATAAAG--CAATAGCGACGTTTATGGGA
14217 AAA
1 AAA
14220 CGCCACGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 18 0.46
42 21 0.54
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19
Consensus pattern (40 bp):
AAATGCCGCAAAAGATAAAGCAATAGCGACGTTTATGGGA
Found at i:16046 original size:29 final size:30
Alignment explanation
Indices: 15978--16115 Score: 160
Period size: 29 Copynumber: 4.7 Consensus size: 30
15968 CCTATTTTAT
*
15978 TCAAATATCACATTTTGACACCCTCAGACTTTC
1 TCAAA-ATCACATTTTGAC-CCCT-AAACTTTC
*
16011 TCAAAATCACATTTTGACCTCTAAACTTT-
1 TCAAAATCACATTTTGACCCCTAAACTTTC
* *
16040 TTAAAATCATATTTTGACCCCT-AACTTTC
1 TCAAAATCACATTTTGACCCCTAAACTTTC
*
16069 TAAAAATCACATTTTGA-CCCTAAAC-TTC
1 TCAAAATCACATTTTGACCCCTAAACTTTC
*
16097 -CAAAATTACATTTTGACCC
1 TCAAAATCACATTTTGACCC
16116 AAATTCTTGA
Statistics
Matches: 93, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
27 14 0.15
28 15 0.16
29 37 0.40
30 6 0.06
31 3 0.03
32 13 0.14
33 5 0.05
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (30 bp):
TCAAAATCACATTTTGACCCCTAAACTTTC
Found at i:16076 original size:58 final size:60
Alignment explanation
Indices: 15984--16113 Score: 178
Period size: 58 Copynumber: 2.2 Consensus size: 60
15974 TTATTCAAAT
*
15984 ATCACATTTTGACACCCTCAGACTTTCTCAAAATCACATTTTGACCTCTAAACTTTTTAAA
1 ATCACATTTTGACACCCTCAGACTTTCTAAAAATCACATTTTGACC-CTAAACTTTTTAAA
* **
16045 ATCATATTTTGAC-CCCT-A-ACTTTCTAAAAATCACATTTTGACCCTAAAC-TTCCAAA
1 ATCACATTTTGACACCCTCAGACTTTCTAAAAATCACATTTTGACCCTAAACTTTTTAAA
*
16101 ATTACATTTTGAC
1 ATCACATTTTGAC
16114 CCAAATTCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
56 16 0.25
57 6 0.10
58 24 0.38
59 1 0.02
60 4 0.06
61 12 0.19
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (60 bp):
ATCACATTTTGACACCCTCAGACTTTCTAAAAATCACATTTTGACCCTAAACTTTTTAAA
Found at i:16412 original size:29 final size:29
Alignment explanation
Indices: 16341--16526 Score: 155
Period size: 28 Copynumber: 6.3 Consensus size: 29
16331 TTATTCAAAT
*
16341 ATCACATTTTGACACCCCCAAACTTTCTCAAA
1 ATCACATTTTG--A-CCCCAAACTTTCTAAAA
*
16373 ATCACATTTTGACCTCCAAACTTT-TTAAA
1 ATCACATTTTGACC-CCAAACTTTCTAAAA
*
16402 ATCATATTTTGACCCCTAAACTTTCTAAAA
1 ATCACATTTTGACCCC-AAACTTTCTAAAA
* * *
16432 ATTACATTTTGACCCTAAAC-TTCCAAAA
1 ATCACATTTTGACCCCAAACTTTCTAAAA
* * * *
16460 ATTACATTTTGACCCTAAA-TTTTTCCAAA
1 ATCACATTTTGACCCCAAACTTTCT-AAAA
* * * *
16489 ATTACA-TTTGACCCCAAATTTTTTCAAA
1 ATCACATTTTGACCCCAAACTTTCTAAAA
*
16517 ATTACATTTT
1 ATCACATTTT
16527 TCAACCCTAT
Statistics
Matches: 136, Mismatches: 11, Indels: 17
0.83 0.07 0.10
Matches are distributed among these distances:
28 51 0.38
29 47 0.35
30 27 0.20
32 11 0.08
ACGTcount: A:0.35, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
ATCACATTTTGACCCCAAACTTTCTAAAA
Found at i:16468 original size:28 final size:28
Alignment explanation
Indices: 16370--16502 Score: 126
Period size: 29 Copynumber: 4.6 Consensus size: 28
16360 AAACTTTCTC
* * ***
16370 AAAATCACATTTTGACCTCCAAACTTTTT
1 AAAATTACATTTTGACC-CTAAACTTCCA
* * *
16399 AAAATCATATTTTGACCCCTAAACTTTCTA
1 AAAATTACATTTTGA-CCCTAAAC-TTCCA
16429 AAAATTACATTTTGACCCTAAACTTCCA
1 AAAATTACATTTTGACCCTAAACTTCCA
*
16457 AAAATTACATTTTGACCCTAAATTTTTCC-
1 AAAATTACATTTTGACCCTAAA--CTTCCA
16486 AAAATTACA-TTTGACCC
1 AAAATTACATTTTGACCC
16503 CAAATTTTTT
Statistics
Matches: 92, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
28 34 0.37
29 36 0.39
30 22 0.24
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (28 bp):
AAAATTACATTTTGACCCTAAACTTCCA
Found at i:16518 original size:57 final size:58
Alignment explanation
Indices: 16334--16526 Score: 189
Period size: 59 Copynumber: 3.3 Consensus size: 58
16324 CCCTATTTTA
* * *
16334 TTCAAATATCACATTTTGACACCCCCAAACTTTCTCAAAATCACATTTTGACCTCCAAACTTT
1 TTCAAA-ATTACATTTTG--ACCCCTAAACTTTCTCAAAATTACATTTTGACC-CCAAA-TTT
* * * * *
16397 TT-AAAATCATATTTTGACCCCTAAACTTTCTAAAAATTACATTTTGACCCTAAA-CT
1 TTCAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTTGACCCCAAATTT
* *
16453 TCCAAAAATTACATTTTGA-CCCTAAA-TTTTTCCAAAATTACA-TTTGACCCCAAATTTT
1 TTC-AAAATTACATTTTGACCCCTAAACTTTCT-CAAAATTACATTTTGACCCCAAA-TTT
16511 TTCAAAATTACATTTT
1 TTCAAAATTACATTTT
16527 TCAACCCTAT
Statistics
Matches: 111, Mismatches: 14, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
56 17 0.15
57 29 0.26
58 20 0.18
59 30 0.27
61 10 0.09
62 3 0.03
63 2 0.02
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (58 bp):
TTCAAAATTACATTTTGACCCCTAAACTTTCTCAAAATTACATTTTGACCCCAAATTT
Found at i:16631 original size:7 final size:7
Alignment explanation
Indices: 16619--16643 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16609 TGTTTTAATG
16619 TTATAAA
1 TTATAAA
16626 TTATAAA
1 TTATAAA
16633 TTATAAA
1 TTATAAA
16640 TTAT
1 TTAT
16644 TAACATGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (7 bp):
TTATAAA
Found at i:20622 original size:29 final size:30
Alignment explanation
Indices: 20586--20850 Score: 213
Period size: 30 Copynumber: 9.0 Consensus size: 30
20576 GGCAAAATCA
*
20586 TAATTTTGGAGAAG-TTGGGGGTCAAAATG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
* *
20615 TGATTTTGGAGAAGTTTAAGGGTCAAAATG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
** * *
20645 TAATTTTAAAGAAGTTTAGGGGT-TAAACG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
*
20674 TAATTTTGGAGAAGTTTAGGGGTTAAAATG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
* * * *
20704 TAATTTTAGAGAA-TTT-TGTGTAAAAATG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
* * *
20732 TAATATTTGGA-AAGTTTAGGTGTTAAAATA
1 TAAT-TTTGGAGAAGTTTAGGGGTCAAAATG
* ** * * *
20762 CAATTTTAAAAAAATTTTA-GGGTTAAAATAG
1 TAATTTT-GGAGAAGTTTAGGGGTCAAAAT-G
* * *
20793 -GATTTT-GAAAAGTTTGGGGGTCAAAATG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
* *
20821 TAATTTTGGAGAAGTTCAAGGGTCAAAATG
1 TAATTTTGGAGAAGTTTAGGGGTCAAAATG
20851 GGATTTTTAA
Statistics
Matches: 188, Mismatches: 37, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
28 23 0.12
29 66 0.35
30 93 0.49
31 6 0.03
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (30 bp):
TAATTTTGGAGAAGTTTAGGGGTCAAAATG
Found at i:20658 original size:59 final size:59
Alignment explanation
Indices: 20586--20857 Score: 196
Period size: 59 Copynumber: 4.6 Consensus size: 59
20576 GGCAAAATCA
* **
20586 TAATTTTGGAGAAGTTGGGGGTCAAAATGTGATTTTGGAGAAGTTTAAGGGTCAAAATG
1 TAATTTTAGAGAAGTTAAGGGTCAAAATGTGATTTTGGAGAAGTTTAAGGGTCAAAATG
* * * * * * *
20645 TAATTTTAAAGAAGTTTAGGGGT-TAAACGTAATTTTGGAGAAGTTTAGGGGTTAAAATG
1 TAATTTTAGAGAAG-TTAAGGGTCAAAATGTGATTTTGGAGAAGTTTAAGGGTCAAAATG
** * * * * *
20704 TAATTTTAGAGAA-TTTTGTGTAAAAATGTAATATTTGGA-AAGTTT-AGGTGTTAAAATA
1 TAATTTTAGAGAAGTTAAGGGTCAAAATGTGAT-TTTGGAGAAGTTTAAGG-GTCAAAATG
* * * * * * * **
20762 CAATTTTAAAAAAATTTTAGGGTTAAAATAG-GATTTT-GAAAAGTTTGGGGGTCAAAATG
1 TAATTTT-AGAGAAGTTAAGGGTCAAAAT-GTGATTTTGGAGAAGTTTAAGGGTCAAAATG
* *
20821 TAATTTTGGAGAAGTTCAAGGGTCAAAATGGGATTTT
1 TAATTTTAGAGAAGTT-AAGGGTCAAAATGTGATTTT
20858 TAAAGAAAAT
Statistics
Matches: 169, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
57 7 0.04
58 36 0.21
59 103 0.61
60 22 0.13
61 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (59 bp):
TAATTTTAGAGAAGTTAAGGGTCAAAATGTGATTTTGGAGAAGTTTAAGGGTCAAAATG
Found at i:20760 original size:117 final size:116
Alignment explanation
Indices: 20609--20833 Score: 269
Period size: 117 Copynumber: 1.9 Consensus size: 116
20599 GTTGGGGGTC
* ** *
20609 AAAATGTGATTTTGGAGAAGTTTAAGGGTCAAAATGTAATTTT-AAAGAAGTTTAGGGGTTAAAC
1 AAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATACAATTTTAAAAAAAGTTTA-GGGTTAAA-
* * *
20673 GTA-ATTTTGGAGAAGTTTAGGGGTTAAAATGTAATTTTAGAGAATTTTGTGTA
64 ATAGATTTT-GAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAATTTTGTGTA
* *
20726 AAAATGTAATATTTGGA-AAGTTT-AGGTGTTAAAATACAATTTTAAAAAAATTTTAGGGTTAAA
1 AAAATGTAAT-TTTGGAGAAGTTTAAGG-GTCAAAATACAATTTTAAAAAAAGTTTAGGGTTAAA
* *
20789 ATAGGATTTTGAAAAGTTTGGGGGTCAAAATGTAATTTTGGAGAA
64 ATA-GATTTTGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAA
20834 GTTCAAGGGT
Statistics
Matches: 92, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
116 5 0.05
117 67 0.73
118 20 0.22
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.36
Consensus pattern (116 bp):
AAAATGTAATTTTGGAGAAGTTTAAGGGTCAAAATACAATTTTAAAAAAAGTTTAGGGTTAAAAT
AGATTTTGAAAAGTTTAGGGGTCAAAATGTAATTTTAGAGAATTTTGTGTA
Found at i:21972 original size:31 final size:32
Alignment explanation
Indices: 21937--21999 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
21927 CATCCACAGT
21937 TTATTATATATAT-ATATTAATCATATTAAAA
1 TTATTATATATATAATATTAATCATATTAAAA
21968 TTATTATATATATAATATTAATCATATTAAAA
1 TTATTATATATATAATATTAATCATATTAAAA
22000 ATAAAAACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (32 bp):
TTATTATATATATAATATTAATCATATTAAAA
Found at i:26150 original size:18 final size:18
Alignment explanation
Indices: 26127--26161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
26117 CGATCTTAAG
* *
26127 CAAAAAGAAAAAGAAAAC
1 CAAAAACAAAAACAAAAC
26145 CAAAAACAAAAACAAAA
1 CAAAAACAAAAACAAAA
26162 TGGGAAAACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.14, G:0.06, T:0.00
Consensus pattern (18 bp):
CAAAAACAAAAACAAAAC
Found at i:29435 original size:18 final size:18
Alignment explanation
Indices: 29412--29447 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
29402 TATAACATTC
29412 CTGCAACACTCAAAATTG
1 CTGCAACACTCAAAATTG
29430 CTGCAACACTCAAAATTG
1 CTGCAACACTCAAAATTG
29448 ATATCTTGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.28, G:0.11, T:0.22
Consensus pattern (18 bp):
CTGCAACACTCAAAATTG
Found at i:30769 original size:30 final size:29
Alignment explanation
Indices: 30656--30917 Score: 251
Period size: 29 Copynumber: 9.0 Consensus size: 29
30646 AATTCGAGGT
* * *
30656 TAAAAATGGGATTTTTAGAA-ATTCGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* * *
30684 TAAAAATGGAATTTTT-GAAATTTCGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* * *
30712 -ACAAAAAGGGATTTTTGGGAGTTCGGGGG
1 TA-AAAATGGGATTTTTGGAAGTTTGGGGG
* *
30741 TAAAAATGGAATTTTTGGAAGTTTCGGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
*
30770 TCAAAAATGGGATTTTTGGAAGTTTAGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGGGGG
* * **
30800 TAAAATTGGAATTTTTGGAAGTTTTAGGG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* **
30829 TCAAAAATGGGATTTTTTGAAGTTTAAGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGGGGG
* * *
30859 TAAAAATGGAATTTTTGGAAGTTTTGGCG
1 TAAAAATGGGATTTTTGGAAGTTTGGGGG
* *
30888 TCAGAAATGGGATTTTTGGAAGTTTTGGGG
1 T-AAAAATGGGATTTTTGGAAGTTTGGGGG
30918 ACCTCTAGGG
Statistics
Matches: 196, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
27 4 0.02
28 34 0.17
29 80 0.41
30 78 0.40
ACGTcount: A:0.31, C:0.03, G:0.31, T:0.35
Consensus pattern (29 bp):
TAAAAATGGGATTTTTGGAAGTTTGGGGG
Found at i:30810 original size:59 final size:59
Alignment explanation
Indices: 30648--30917 Score: 348
Period size: 59 Copynumber: 4.6 Consensus size: 59
30638 TTTCGAAAAA
* * * * * *
30648 TTCGAGGTTAAAAATGGGATTTTTAGAA-ATTCGGGGTAAAAATGGAATTTTT-GAAAT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGT
* * **
30705 TTCGGGGACAAAAA-GGGATTTTTGGGAGTTCGGGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGT
*
30763 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAATTGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGT
** * *
30822 TTTAGGGTCAAAAATGGGATTTTTTGAAGTTTAAGGGTAAAAATGGAATTTTTGGAAGT
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGT
* * * *
30881 TTTGGCGTCAGAAATGGGATTTTTGGAAGTTTTGGGG
1 TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGG
30918 ACCTCTAGGG
Statistics
Matches: 185, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
56 11 0.06
57 32 0.17
58 17 0.09
59 125 0.68
ACGTcount: A:0.30, C:0.04, G:0.31, T:0.35
Consensus pattern (59 bp):
TTCGGGGTCAAAAATGGGATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGT
Found at i:32684 original size:15 final size:15
Alignment explanation
Indices: 32664--32699 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
32654 TTTGGGCCGT
32664 TTTGGGTTATTT-AA
1 TTTGGGTTATTTGAA
32678 GTTTGGGTTATTTGAA
1 -TTTGGGTTATTTGAA
32694 TTTGGG
1 TTTGGG
32700 CCCCATTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.53
Consensus pattern (15 bp):
TTTGGGTTATTTGAA
Found at i:32767 original size:6 final size:6
Alignment explanation
Indices: 32745--32796 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
32735 TGTTGGACCT
* *
32745 TTTAAT TTTGAAA -TTAAA TTTAAA -TTAAA TTTAAA TTTAAA -TCAAA
1 TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
32791 TTTAAA
1 TTTAAA
32797 ATAAATTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
5 12 0.31
6 25 0.64
7 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:32771 original size:11 final size:11
Alignment explanation
Indices: 32755--32786 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
32745 TTTAATTTTG
32755 AAATTAAATTT
1 AAATTAAATTT
32766 AAATTAAATTT
1 AAATTAAATTT
32777 AAATTTAAAT
1 AAA-TTAAAT
32787 CAAATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:32780 original size:17 final size:17
Alignment explanation
Indices: 32758--32806 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
32748 AATTTTGAAA
32758 TTAAATTTAAATTAAAT
1 TTAAATTTAAATTAAAT
*
32775 TTAAATTTAAATCAAAT
1 TTAAATTTAAATTAAAT
*
32792 TTAAA-ATAAATTAAA
1 TTAAATTTAAATTAAA
32807 AAAGGCTCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 8 0.28
17 21 0.72
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
TTAAATTTAAATTAAAT
Found at i:33905 original size:30 final size:29
Alignment explanation
Indices: 33868--33951 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 29
33858 TAAAACAAAT
* * *
33868 CAAAACAAAAGTCCAAATTACAAATGGCC
1 CAAAACAAATGGCCCAATTACAAATGGCC
* *
33897 CAATAACAAATGGCCCAGTTACAGATGGCC
1 CAA-AACAAATGGCCCAATTACAAATGGCC
33927 CAAATACAAATGGCCCAATTACAAA
1 CAAA-ACAAATGGCCCAATTACAAA
33952 GTGCCCGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 4 0.09
30 42 0.91
ACGTcount: A:0.46, C:0.25, G:0.13, T:0.15
Consensus pattern (29 bp):
CAAAACAAATGGCCCAATTACAAATGGCC
Found at i:33957 original size:15 final size:15
Alignment explanation
Indices: 33883--33951 Score: 102
Period size: 15 Copynumber: 4.6 Consensus size: 15
33873 CAAAAGTCCA
33883 AATTACAAATGGCCC
1 AATTACAAATGGCCC
*
33898 AATAACAAATGGCCC
1 AATTACAAATGGCCC
* *
33913 AGTTACAGATGGCCC
1 AATTACAAATGGCCC
*
33928 AAATACAAATGGCCC
1 AATTACAAATGGCCC
33943 AATTACAAA
1 AATTACAAA
33952 GTGCCCGAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.17
Consensus pattern (15 bp):
AATTACAAATGGCCC
Done.