Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010756.1 Kokia drynarioides strain JFW-HI SEQ_125714, 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: 71879
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 159 characters in sequence are not A, C, G, or T
Found at i:1615 original size:29 final size:28
Alignment explanation
Indices: 1579--1896 Score: 188
Period size: 29 Copynumber: 10.9 Consensus size: 28
1569 GTCCCTGAAC
1579 CTTCCAAAAATTACTGTTTTACCTCCGAA
1 CTTCCAAAAATTACTGTTTTACC-CCGAA
** *
1608 -TTCCCAAAAATCCCAT-TTTGACCCCGAA
1 CTT-CCAAAAATTAC-TGTTTTACCCCGAA
*
1636 CCTTCCAAAAATTA-TCGTTTTACCCCCAA
1 -CTTCCAAAAATTACT-GTTTTACCCCGAA
* **
1665 ATTCCAAAAATCCCAT-TTTTGACCCCGAA
1 CTTCCAAAAATTAC-TGTTTT-ACCCCGAA
1694 CCTTCC-AAAATTACTGTTTTACCCCCGAA
1 -CTTCCAAAAATTACTGTTTTA-CCCCGAA
** * *
1723 -TTCCCAAAAATCCCCATTTTTTACCTCGAA
1 CTT-CCAAAAAT-TAC-TGTTTTACCCCGAA
*
1753 GCTTCCAAAAATTACCGTTTTACCCCCGAA
1 -CTTCCAAAAATTACTGTTTTA-CCCCGAA
** *
1783 -TTCCCAAAAATCCCCATTTTTTACCCCGAA
1 CTT-CCAAAAAT-TAC-TGTTTTACCCCGAA
1813 GCTTCCAAAAATTA-TCGTTTTACCCTCGAA
1 -CTTCCAAAAATTACT-GTTTTACCC-CGAA
**
1843 -TTCCTAAAAATCCCAT-TTTTGACCCCGAA
1 CTTCC-AAAAATTAC-TGTTTT-ACCCCGAA
*
1872 GCTTCCAAAAATTACCGTTTTACCC
1 -CTTCCAAAAATTACTGTTTTACCC
1897 TCGAGTTGCT
Statistics
Matches: 221, Mismatches: 35, Indels: 66
0.69 0.11 0.20
Matches are distributed among these distances:
27 3 0.01
28 32 0.14
29 101 0.46
30 49 0.22
31 32 0.14
32 4 0.02
ACGTcount: A:0.31, C:0.32, G:0.07, T:0.31
Consensus pattern (28 bp):
CTTCCAAAAATTACTGTTTTACCCCGAA
Found at i:1891 original size:59 final size:59
Alignment explanation
Indices: 1579--1920 Score: 483
Period size: 60 Copynumber: 5.8 Consensus size: 59
1569 GTCCCTGAAC
* * *
1579 CTTCCAAAAATTACTGTTTTACCTCCGAATTCCCAAAAATCCCA-TTTTGACCCCGAAC
1 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
* * *
1637 CTTCCAAAAATTATCGTTTTACCCCCAAATT-CCAAAAATCCCATTTTTGACCCCGAAC
1 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
* * *
1695 CTTCC-AAAATTACTGTTTTACCCCCGAATTCCCAAAAATCCCCATTTTTTACCTCGAAG
1 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAAT-CCCATTTTTGACCCCGAAG
*
1754 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCCATTTTTTACCCCGAAG
1 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAAT-CCCATTTTTGACCCCGAAG
* * *
1814 CTTCCAAAAATTATCGTTTTACCCTCGAATTCCTAAAAATCCCATTTTTGACCCCGAAG
1 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
* * * * *
1873 CTTCCAAAAATTACCGTTTTACCCTCGAGTTGCTAAAAATCCTATTTT
1 CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTT
1921 CGATTGCGAA
Statistics
Matches: 260, Mismatches: 20, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
57 34 0.13
58 54 0.21
59 83 0.32
60 89 0.34
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.31
Consensus pattern (59 bp):
CTTCCAAAAATTACCGTTTTACCCCCGAATTCCCAAAAATCCCATTTTTGACCCCGAAG
Found at i:4009 original size:20 final size:20
Alignment explanation
Indices: 3970--4023 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
3960 AGTCTTCAAG
* *
3970 GTATCGGTAGAACTGTAGTT
1 GTATCGGTAGAAGTGAAGTT
3990 GTATCGGTAGAAGTGAAGTT
1 GTATCGGTAGAAGTGAAGTT
*
4010 TTA-CTGGTAGAAGT
1 GTATC-GGTAGAAGT
4024 CTTACTGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.28, C:0.07, G:0.31, T:0.33
Consensus pattern (20 bp):
GTATCGGTAGAAGTGAAGTT
Found at i:8151 original size:20 final size:17
Alignment explanation
Indices: 8104--8161 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 17
8094 GAGAAAGTAC
8104 AAATAAAAAACATTAGG
1 AAATAAAAAACATTAGG
*
8121 AAGTAACAAAACATATGAGG
1 AAATAA-AAAACAT-T-AGG
* *
8141 AAATATAAAAAAATTATG
1 AAATA-AAAAACATTAGG
8159 AAA
1 AAA
8162 GATACCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
17 5 0.15
18 12 0.36
19 2 0.06
20 13 0.39
21 1 0.03
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (17 bp):
AAATAAAAAACATTAGG
Found at i:8936 original size:20 final size:20
Alignment explanation
Indices: 8773--8929 Score: 107
Period size: 20 Copynumber: 7.8 Consensus size: 20
8763 GTACCAAACT
* *
8773 AAAATTATGATATAATATCA
1 AAAATTATGAGAAAATATCA
* * * *
8793 AGAATTATAAGAAAGTACCA
1 AAAATTATGAGAAAATATCA
* * *
8813 AAAACTACGAGTAAATATCA
1 AAAATTATGAGAAAATATCA
* * * * *
8833 AGATTTATGAGGAAGTACCA
1 AAAATTATGAGAAAATATCA
* ****
8853 AAACTTATGAGGGTGTATCA
1 AAAATTATGAGAAAATATCA
* *
8873 AGAATTATGAGAAAGTATCA
1 AAAATTATGAGAAAATATCA
* *
8893 AAAAATACGAGAAAATATCA
1 AAAATTATGAGAAAATATCA
8913 AAAATTATGAGAAAATA
1 AAAATTATGAGAAAATA
8930 CGAAAAAAAT
Statistics
Matches: 101, Mismatches: 36, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 101 1.00
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.24
Consensus pattern (20 bp):
AAAATTATGAGAAAATATCA
Found at i:8937 original size:40 final size:40
Alignment explanation
Indices: 8786--8937 Score: 160
Period size: 40 Copynumber: 3.8 Consensus size: 40
8776 ATTATGATAT
* * *
8786 AATATCAAGAATTATAAGAAAGTACCAAAAACTACGAGTA
1 AATATCAAGAATTATGAGAAAGTACCAAAAAATACGAGAA
* * ** * **
8826 AATATCAAGATTTATGAGGAAGTACCAAAACTTATGAGGG
1 AATATCAAGAATTATGAGAAAGTACCAAAAAATACGAGAA
** *
8866 TGTATCAAGAATTATGAGAAAGTATCAAAAAATACGAGAA
1 AATATCAAGAATTATGAGAAAGTACCAAAAAATACGAGAA
* * *
8906 AATATCAAAAATTATGAGAAAATACGAAAAAA
1 AATATCAAGAATTATGAGAAAGTACCAAAAAA
8938 ATATGAGGAA
Statistics
Matches: 88, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 88 1.00
ACGTcount: A:0.53, C:0.09, G:0.16, T:0.22
Consensus pattern (40 bp):
AATATCAAGAATTATGAGAAAGTACCAAAAAATACGAGAA
Found at i:9102 original size:137 final size:139
Alignment explanation
Indices: 8844--9113 Score: 293
Period size: 137 Copynumber: 1.9 Consensus size: 139
8834 GATTTATGAG
* * * * * ** *
8844 GAAGTACCAAAACTTATGAGGGTGTATCAAGAATTATGAGAAAGTATCAAAAAATACGAGAAAAT
1 GAAGTACCAAAACATATGAAGGTGCACCAAAAATTATGAGAAAGTAAAAAAAAATACAAGAAAAT
* * * *
8909 ATCAAAAATTATGAGAAAATACGAAAAAAATATGAGGAATTTCCAAAACTTAGATGTA-TA-AAA
66 ATCAAAAATTATGAGAAAATAC-AAAAAAATATGAGAAATCTACAAAACCTAGATGTATTATAAA
8972 AATTATGAAA
130 AATTATGAAA
*
8982 GAAGTACCAAAA-ATATGAAGGTGCACCAAAAATTATGA-AAATGTAAAAAAAAATTACAAGAGA
1 GAAGTACCAAAACATATGAAGGTGCACCAAAAATTATGAGAAA-GTAAAAAAAAA-TACAAGAAA
* * *
9045 ATAT-AAAAATTATGAGAAAGTATC-AAAAATTATGAGAAAATACTATAAAACCT-GATGTATTA
64 ATATCAAAAATTATGAGAAAATA-CAAAAAAATATGAG-AAAT-CTACAAAACCTAGATGTATTA
9107 TAAAAAT
126 TAAAAAT
9114 AAAAAAAAAG
Statistics
Matches: 109, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
136 14 0.13
137 56 0.51
138 33 0.30
139 6 0.06
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.23
Consensus pattern (139 bp):
GAAGTACCAAAACATATGAAGGTGCACCAAAAATTATGAGAAAGTAAAAAAAAATACAAGAAAAT
ATCAAAAATTATGAGAAAATACAAAAAAATATGAGAAATCTACAAAACCTAGATGTATTATAAAA
ATTATGAAA
Found at i:9217 original size:20 final size:19
Alignment explanation
Indices: 9172--9217 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
9162 CACGAGGAAG
9172 TAAAAAAAAATTATGAGAA
1 TAAAAAAAAATTATGAGAA
* * *
9191 TATAAAAAAATATATGATAT
1 TAAAAAAAAAT-TATGAGAA
9211 TAAAAAA
1 TAAAAAA
9218 TATGAAAAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (19 bp):
TAAAAAAAAATTATGAGAA
Found at i:9307 original size:20 final size:20
Alignment explanation
Indices: 9284--9330 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
9274 GATCAGAATG
9284 TACCAAAACA-TACGAGAAAA
1 TACCAAAA-ATTACGAGAAAA
* *
9304 TACCAAAAATTATGAGAGAA
1 TACCAAAAATTACGAGAAAA
9324 TACCAAA
1 TACCAAA
9331 TAGCATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.57, C:0.17, G:0.11, T:0.15
Consensus pattern (20 bp):
TACCAAAAATTACGAGAAAA
Found at i:9694 original size:26 final size:27
Alignment explanation
Indices: 9664--9716 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
9654 TTAAATTATC
*
9664 AATAAGTAAA-GGTTATTATAAGATTT
1 AATAAGGAAATGGTTATTATAAGATTT
* *
9690 AATAAGGAAATGTTTATTATAGGATTT
1 AATAAGGAAATGGTTATTATAAGATTT
9717 TTTTTAAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 9 0.39
27 14 0.61
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (27 bp):
AATAAGGAAATGGTTATTATAAGATTT
Found at i:18199 original size:29 final size:30
Alignment explanation
Indices: 18167--18234 Score: 79
Period size: 28 Copynumber: 2.3 Consensus size: 30
18157 AATTTTTTAA
18167 TTCTTTTTTAATTT-TCGTATCTTTTC-C-CT
1 TTCTTTTTT-ATTTCTC-TATCTTTTCTCTCT
*
18196 TTCTTTTTTCTTTCTCTATCTTTTCTCTCT
1 TTCTTTTTTATTTCTCTATCTTTTCTCTCT
*
18226 TTTTTTTTT
1 TTCTTTTTT
18235 TTTATAATAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 12 0.35
29 12 0.35
30 10 0.29
ACGTcount: A:0.06, C:0.21, G:0.01, T:0.72
Consensus pattern (30 bp):
TTCTTTTTTATTTCTCTATCTTTTCTCTCT
Found at i:21725 original size:20 final size:21
Alignment explanation
Indices: 21693--21735 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
21683 ACACAATAAA
21693 AAATTTCAAATTA-AAAAATT
1 AAATTTCAAATTATAAAAATT
*
21713 AAATTT-AATATTATTAAAATT
1 AAATTTCAA-ATTATAAAAATT
21734 AA
1 AA
21736 TGAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 2 0.10
20 10 0.50
21 8 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATTTCAAATTATAAAAATT
Found at i:23750 original size:37 final size:37
Alignment explanation
Indices: 23694--23844 Score: 216
Period size: 37 Copynumber: 4.1 Consensus size: 37
23684 TCAAACGACA
* * *
23694 TTAAAGTATCTCATAGGGTTCTCATTTTGATGAAAGG
1 TTAAAGTATCTCGTGGGGTTCTCGTTTTGATGAAAGG
*
23731 TTAAAGTATCTCGTGGGGTTCTTGTTTTGATGAAAGG
1 TTAAAGTATCTCGTGGGGTTCTCGTTTTGATGAAAGG
* *
23768 TTAAAGTATCTTGTGGGGTTCTCGTTTAGATGAAAGG
1 TTAAAGTATCTCGTGGGGTTCTCGTTTTGATGAAAGG
* *
23805 TTAATGTATCTTGTGGGGTTCTCG-TTTGATGAAA-G
1 TTAAAGTATCTCGTGGGGTTCTCGTTTTGATGAAAGG
23840 TTAAA
1 TTAAA
23845 AGGATTGACA
Statistics
Matches: 104, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
35 5 0.05
36 9 0.09
37 90 0.87
ACGTcount: A:0.25, C:0.09, G:0.26, T:0.40
Consensus pattern (37 bp):
TTAAAGTATCTCGTGGGGTTCTCGTTTTGATGAAAGG
Found at i:25227 original size:14 final size:13
Alignment explanation
Indices: 25199--25233 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
25189 AAATATGTTC
25199 CTTTCTTTTTTTT
1 CTTTCTTTTTTTT
*
25212 CTTTTTTTTTTCTT
1 CTTTCTTTTTT-TT
25226 CTTTCTTT
1 CTTTCTTT
25234 GATTTTGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
CTTTCTTTTTTTT
Found at i:25739 original size:19 final size:18
Alignment explanation
Indices: 25715--25773 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
25705 CTTTCAAAAG
*
25715 ATTTTTCCTAAATTTTTTA
1 ATTTTT-CTAAATTTATTA
**
25734 ATTTTTAAAACATTTATTA
1 ATTTTTCTAA-ATTTATTA
25753 ATTTTTCTAAATTTA-TA
1 ATTTTTCTAAATTTATTA
25770 ATTT
1 ATTT
25774 ATTATTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 21 0.62
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (18 bp):
ATTTTTCTAAATTTATTA
Found at i:34670 original size:17 final size:17
Alignment explanation
Indices: 34648--34720 Score: 85
Period size: 17 Copynumber: 4.3 Consensus size: 17
34638 CCAACAGGAT
34648 TTAAATTTATTTTAAAA
1 TTAAATTTATTTTAAAA
**
34665 TTAAATTTATTTTAAGT
1 TTAAATTTATTTTAAAA
*
34682 TTAAATTTA-CTTAAAA
1 TTAAATTTATTTTAAAA
* *
34698 TTTAAATTTATTATAAAT
1 -TTAAATTTATTTTAAAA
34716 TTAAA
1 TTAAA
34721 GTTAAAATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
16 4 0.09
17 38 0.83
18 4 0.09
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (17 bp):
TTAAATTTATTTTAAAA
Found at i:34684 original size:6 final size:6
Alignment explanation
Indices: 34646--34726 Score: 55
Period size: 6 Copynumber: 14.2 Consensus size: 6
34636 GCCCAACAGG
* * * *
34646 ATTTAA ATTT-A TTTTAA AATTAA ATTT-A TTTTAA GTTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * *
34691 CTTAAA ATTTAA ATTT-- ATTATAA ATTTAA AGTTAA A
1 ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA ATTTAA A
34727 ATCTATCTAA
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
4 3 0.05
5 12 0.21
6 39 0.68
7 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:34690 original size:34 final size:34
Alignment explanation
Indices: 34646--34720 Score: 107
Period size: 34 Copynumber: 2.2 Consensus size: 34
34636 GCCCAACAGG
* *
34646 ATTTAAATTTATTTTAAAA-TTAAATTTATTTTAA
1 ATTTAAATTTA-CTTAAAATTTAAATTTATTATAA
*
34680 GTTTAAATTTACTTAAAATTTAAATTTATTATAA
1 ATTTAAATTTACTTAAAATTTAAATTTATTATAA
34714 ATTTAAA
1 ATTTAAA
34721 GTTAAAATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 6 0.17
34 30 0.83
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (34 bp):
ATTTAAATTTACTTAAAATTTAAATTTATTATAA
Found at i:35871 original size:77 final size:77
Alignment explanation
Indices: 35744--35890 Score: 224
Period size: 77 Copynumber: 1.9 Consensus size: 77
35734 TTGAACTTAT
* * * *
35744 CGGTGATCGGAGATGGGGGCGCGTGGACGACCGGACGGTGCTATGACAGAGACGCGCAACGGCGC
1 CGGTGATCGGAGATGGGGGCGCGTGGACCACCGGACGGCGCCATGACAGAGACGAGCAACGGCGC
35809 GTGGCTACGGAC
66 GTGGCTACGGAC
* *
35821 CGGTGA-CTGGAGATGGGGGCGCGTGGACCATCGGACGGCGCCATGGCAGAGACGAGCAACGGCG
1 CGGTGATC-GGAGATGGGGGCGCGTGGACCACCGGACGGCGCCATGACAGAGACGAGCAACGGCG
35885 CGTGGC
65 CGTGGC
35891 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
76 1 0.02
77 62 0.98
ACGTcount: A:0.19, C:0.25, G:0.45, T:0.11
Consensus pattern (77 bp):
CGGTGATCGGAGATGGGGGCGCGTGGACCACCGGACGGCGCCATGACAGAGACGAGCAACGGCGC
GTGGCTACGGAC
Found at i:41095 original size:22 final size:23
Alignment explanation
Indices: 41056--41100 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
41046 CCCCAAAACT
41056 CGTAAACAAAGAACTCT-CAAAA
1 CGTAAACAAAGAACTCTCCAAAA
*
41078 CGTAAACACAA-AATTCTCCAAAA
1 CGTAAACA-AAGAACTCTCCAAAA
41101 GTTTTATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (23 bp):
CGTAAACAAAGAACTCTCCAAAA
Found at i:47230 original size:21 final size:21
Alignment explanation
Indices: 47206--47247 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
47196 TTCACCCAAA
47206 AAGAAAAAAAGAAACAAAAAG
1 AAGAAAAAAAGAAACAAAAAG
*
47227 AAGAAAAAAAGAAATAAAAAG
1 AAGAAAAAAAGAAACAAAAAG
47248 GAGAGGTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAAGAAACAAAAAG
Found at i:47235 original size:11 final size:11
Alignment explanation
Indices: 47206--47239 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
47196 TTCACCCAAA
47206 AAGAAAAAAAG
1 AAGAAAAAAAG
*
47217 AA-ACAAAAAG
1 AAGAAAAAAAG
47227 AAGAAAAAAAG
1 AAGAAAAAAAG
47238 AA
1 AA
47240 ATAAAAAGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAG
Found at i:47245 original size:11 final size:10
Alignment explanation
Indices: 47209--47247 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
47199 ACCCAAAAAG
47209 AAAAAAAGAA
1 AAAAAAAGAA
*
47219 ACAAAAAGAA
1 AAAAAAAGAA
47229 GAAAAAAAGAA
1 -AAAAAAAGAA
*
47240 ATAAAAAG
1 AAAAAAAG
47248 GAGAGGTCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 16 0.64
11 9 0.36
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:48340 original size:48 final size:47
Alignment explanation
Indices: 48288--48619 Score: 152
Period size: 49 Copynumber: 6.8 Consensus size: 47
48278 AATGAATCCA
*
48288 GTACCATGAAATGCAATGGGAAAGGTTGGGGCCGCAACGGTGAACCCG
1 GTACCATGAAATG-AATGGGAAAGGTTGAGGCCGCAACGGTGAACCCG
* * **** ****
48336 GTACCATAGAGATTTGAA-GGGAAAGGTTAAGGCCGCAACAACAAATTTA
1 GTACCAT-GA-A-ATGAATGGGAAAGGTTGAGGCCGCAACGGTGAACCCG
* * * * *
48385 GTACC-TTAAAAGAAGTGATGGGAAGGATTGAGGCCGCAATGGTGAATCCG
1 GTACCATGAAATGAA-TG--GGAAAGG-TTGAGGCCGCAACGGTGAACCCG
* * * *
48435 ATATCATGAAATGCGATGGGAAAGGTTGAGGCCGCAACGGTGAACTCG
1 GTACCATGAAATG-AATGGGAAAGGTTGAGGCCGCAACGGTGAACCCG
* * *** *
48483 GTACCATGAAGATTTGAA-CGGAAAGGTTAAGGTTACAACGGCGAACCCG
1 GTACCATGAA-A--TGAATGGGAAAGGTTGAGGCCGCAACGGTGAACCCG
* * * ***
48532 ATACCTTAGAAGACATG-ATGGG-AAGGATTGAGGTCGCAACGGTGAATTTG
1 GTACCAT-G-A-A-ATGAATGGGAAAGG-TTGAGGCCGCAACGGTGAACCCG
* * *
48582 GTACCGTGGAATGTGATGGGAAAGGTTGAGGCCGCAAC
1 GTACCATGAAATG-AATGGGAAAGGTTGAGGCCGCAAC
48620 AGCGAACTTA
Statistics
Matches: 205, Mismatches: 58, Indels: 42
0.67 0.19 0.14
Matches are distributed among these distances:
45 3 0.01
46 4 0.02
47 3 0.01
48 53 0.26
49 80 0.39
50 47 0.23
51 12 0.06
52 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.32, T:0.19
Consensus pattern (47 bp):
GTACCATGAAATGAATGGGAAAGGTTGAGGCCGCAACGGTGAACCCG
Found at i:48627 original size:147 final size:147
Alignment explanation
Indices: 48193--48692 Score: 520
Period size: 147 Copynumber: 3.4 Consensus size: 147
48183 ACCGAGGAAA
* * * *
48193 CATGGAGATTTGAAGGGAAAGGTTGAGGTTGCAACGACGAACCCGGTACCTTAAAAGACGTGATG
1 CATGAAGATTTGAAGGGAAAGGTTAAGGTTGCAACGACGAACCCGATACCTTAAAAGACATGATG
* * ** * * *
48258 GGAAGGATTGATGCCACAACAATGAATCCAGTACCATGAAATGCAATGGGAAAGGTTGGGGCCGC
66 GGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAAGGTTGAGGCCGC
*
48323 AACGGTGAACCCGGTAC
131 AACGGTGAACTCGGTAC
** * ****
48340 CAT-AGAGATTTGAAGGGAAAGGTTAAGGCCGCAACAAC-AAATTTAGTACCTTAAAAGA-AGTG
1 CATGA-AGATTTGAAGGGAAAGGTTAAGGTTGCAACGACGAACCCGA-TACCTTAAAAGACA-TG
* * *
48402 ATGGGAAGGATTGAGGCCGCAATGGTGAATCCGATATCATGAAATGCGATGGGAAAGGTTGAGGC
63 ATGGGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAAGGTTGAGGC
48467 CGCAACGGTGAACTCGGTAC
128 CGCAACGGTGAACTCGGTAC
* * * *
48487 CATGAAGATTTGAACGGAAAGGTTAAGGTTACAACGGCGAACCCGATACCTTAGAAGACATGATG
1 CATGAAGATTTGAAGGGAAAGGTTAAGGTTGCAACGACGAACCCGATACCTTAAAAGACATGATG
* ** * * *
48552 GGAAGGATTGAGGTCGCAACGGTGAATTTGGTACCGTGGAATGTGATGGGAAAGGTTGAGGCCGC
66 GGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAAGGTTGAGGCCGC
* * **
48617 AACAGCGAACTTAGTAC
131 AACGGTGAACTCGGTAC
* * * * * ** * * * *
48634 CTTAAAAAATGTGAAGGGAAAGGTTGAGGTTTTAATGGCAAACCCGATACCTTAGAAGA
1 CAT-GAAGATTTGAAGGGAAAGGTTAAGGTTGCAACGACGAACCCGATACCTTAAAAGA
48693 TGTAATGGGA
Statistics
Matches: 290, Mismatches: 56, Indels: 13
0.81 0.16 0.04
Matches are distributed among these distances:
146 2 0.01
147 237 0.82
148 51 0.18
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.20
Consensus pattern (147 bp):
CATGAAGATTTGAAGGGAAAGGTTAAGGTTGCAACGACGAACCCGATACCTTAAAAGACATGATG
GGAAGGATTGAGGCCGCAACGGTGAATCCGGTACCATGAAATGCGATGGGAAAGGTTGAGGCCGC
AACGGTGAACTCGGTAC
Found at i:48634 original size:48 final size:49
Alignment explanation
Indices: 48547--48662 Score: 119
Period size: 48 Copynumber: 2.4 Consensus size: 49
48537 TTAGAAGACA
* * * * * **
48547 TGATGGG-AAGGATTGAGGTCGCAACGGTGAATTTGGTACCGT-GGAATG
1 TGATGGGAAAGG-TTGAGGCCGCAACAGCGAACTTAGTACCGTAAAAATG
*
48595 TGATGGGAAAGGTTGAGGCCGCAACAGCGAACTTAGTACCTTAAAAAATG
1 TGATGGGAAAGGTTGAGGCCGCAACAGCGAACTTAGTACCGT-AAAAATG
*
48645 TGAAGGGAAAGGTTGAGG
1 TGATGGGAAAGGTTGAGG
48663 TTTTAATGGC
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
48 31 0.55
49 4 0.07
50 21 0.38
ACGTcount: A:0.31, C:0.11, G:0.36, T:0.22
Consensus pattern (49 bp):
TGATGGGAAAGGTTGAGGCCGCAACAGCGAACTTAGTACCGTAAAAATG
Found at i:49203 original size:38 final size:39
Alignment explanation
Indices: 49072--49460 Score: 239
Period size: 38 Copynumber: 10.4 Consensus size: 39
49062 GTTACGTCAT
* * * * *
49072 CATCCAATCTCTAACCCTAATCA-GAGGGAAAATTTAAGA
1 CATCCAATCTCTTACCCTGATCATG-GGGCAGATTGAAGA
*
49111 CACACCAATCTCTTACCCTGATCATGGGGCAGATTGGAAG-
1 CA-TCCAATCTCTTACCCTGATCATGGGGCAGATT-GAAGA
*
49151 TATCCAATCTCTTACTCC-GATCATGGGGCAGATTGAAGA
1 CATCCAATCTCTTAC-CCTGATCATGGGGCAGATTGAAGA
* * *
49190 -ATCCAATCTCTTACCCTGATCTTGAGGCAAATTGAA-A
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * * ** *
49227 CACCCAATCTTTTACCCTAATCAAAGGGCAGATTAAAGA
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * * *
49266 CAT-CAATCTCTTACCTTAATTA-GAAGGCAGATTGAAGA
1 CATCCAATCTCTTACCCTGATCATG-GGGCAGATTGAAGA
* **
49304 CA-CCGATCTC--A-----ATCATGGGATAGATTGAA-A
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * * * ***
49334 CACCCAATCTTTTACCTTAATCAAAAGGCAGATTGAAG-
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * *
49372 ---GCAATCTCTTACCCCGATCATGGGGCAGATTGAACA
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
* * *
49408 CA-CCAATCTCTTACCCTAATTA-GAGGGTAGATTGAAGA
1 CATCCAATCTCTTACCCTGATCATG-GGGCAGATTGAAGA
49446 CA-CCAATCTCTTACC
1 CATCCAATCTCTTACC
49461 TTAATTAGAA
Statistics
Matches: 272, Mismatches: 54, Indels: 49
0.73 0.14 0.13
Matches are distributed among these distances:
30 3 0.01
31 18 0.07
32 1 0.00
33 1 0.00
35 26 0.10
36 1 0.00
37 4 0.01
38 153 0.56
39 33 0.12
40 28 0.10
41 4 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (39 bp):
CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAGA
Found at i:49498 original size:38 final size:38
Alignment explanation
Indices: 49398--49482 Score: 134
Period size: 38 Copynumber: 2.2 Consensus size: 38
49388 ATCATGGGGC
* * *
49398 AGATTGAACACACCAATCTCTTACCCTAATTAGAGGGT
1 AGATTGAAGACACCAATCTCTTACCCTAATTAGAAGGA
*
49436 AGATTGAAGACACCAATCTCTTACCTTAATTAGAAGGA
1 AGATTGAAGACACCAATCTCTTACCCTAATTAGAAGGA
49474 AGATTGAAG
1 AGATTGAAG
49483 CACTTAGTCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.26
Consensus pattern (38 bp):
AGATTGAAGACACCAATCTCTTACCCTAATTAGAAGGA
Found at i:53305 original size:298 final size:298
Alignment explanation
Indices: 52811--53445 Score: 1072
Period size: 298 Copynumber: 2.1 Consensus size: 298
52801 TCATATGCAC
* * *
52811 ATTTTTATTGGTTTTTTAAATAAAAAGAGTAAATTACTATTGGATAATAAAACTTATTTTAATTG
1 ATTTTTATT-GTTTTTTTAATAAAAAGATTAAATTACTATTGGATAATAAAACTTATTTTAATTA
* * * * * *
52876 CGAAAGGGCATTTCAATAGTTTTTTTAATCGAGTTGGTAAGCTGGTTGAGGGTGACACCAATTTA
65 CAAAAGGGCATTTCAATAGTTTTCTTAACCGAGTTGGTAACCCGATTGAGGGTGACACCAATTTA
* *
52941 ATAAAACCTTAATAAATAGTAAGTATATAGATATATAATTAATAAATATAATAAAATATTCATAA
130 ATAAAACCTTAATAAATAGTAAATATATAGATATACAATTAATAAATATAATAAAATATTCATAA
*
53006 TAAAAATTGAAATGCATGGAAATATTAAAATAAAGCTATAAGTGAGTACTAAATTAAAATTTTAT
195 TAAAAATTGAAATGCATGGAAATATTAAAATAAAGCTATAAGTGAGTACTAAATTAAAAGTTTAT
* *
53071 TAATGTAATTGGTTTGCATTTAAATCCCACAATATGCTT
260 TAATGTAATTGGTTTGCATTTAAATCCCACAATAGGCCT
* *
53110 ATTTTTATTGTTTTTTTAATAAAAAGATTAAATTATTATTGGATAATAAAACTTATTTTAATTAT
1 ATTTTTATTGTTTTTTTAATAAAAAGATTAAATTACTATTGGATAATAAAACTTATTTTAATTAC
53175 AAAAGGGCATTTCAATAGTTTTCTTAACCGAGTTGGTAACCCGATTGAGGGTGACACCAATTTAA
66 AAAAGGGCATTTCAATAGTTTTCTTAACCGAGTTGGTAACCCGATTGAGGGTGACACCAATTTAA
53240 TAAAACCTTAATAAATAGTAAATATATAGATATACAATTAATAAATATAATAAAATATTCATAAT
131 TAAAACCTTAATAAATAGTAAATATATAGATATACAATTAATAAATATAATAAAATATTCATAAT
*
53305 AAAAATTGAAATGCATGGAAATATTAAAATAAAGCTTTAAGTGAGTACTAAATTAAAAGTTTATT
196 AAAAATTGAAATGCATGGAAATATTAAAATAAAGCTATAAGTGAGTACTAAATTAAAAGTTTATT
53370 AATGTAATTGGTTTGCATTTAAATCCCACAATAGGCCT
261 AATGTAATTGGTTTGCATTTAAATCCCACAATAGGCCT
* *
53408 ATCTTTATTGATTTTTTTTAATAAAAAGATTAAGTTAC
1 ATTTTTATTG--TTTTTTTAATAAAAAGATTAAATTAC
53446 CCTCAAACAA
Statistics
Matches: 314, Mismatches: 20, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
298 281 0.89
299 9 0.03
300 24 0.08
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (298 bp):
ATTTTTATTGTTTTTTTAATAAAAAGATTAAATTACTATTGGATAATAAAACTTATTTTAATTAC
AAAAGGGCATTTCAATAGTTTTCTTAACCGAGTTGGTAACCCGATTGAGGGTGACACCAATTTAA
TAAAACCTTAATAAATAGTAAATATATAGATATACAATTAATAAATATAATAAAATATTCATAAT
AAAAATTGAAATGCATGGAAATATTAAAATAAAGCTATAAGTGAGTACTAAATTAAAAGTTTATT
AATGTAATTGGTTTGCATTTAAATCCCACAATAGGCCT
Found at i:55605 original size:20 final size:20
Alignment explanation
Indices: 55582--55626 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 20
55572 ATTTATTATA
55582 TAATTTTTAAATATATAATT
1 TAATTTTTAAATATATAATT
*
55602 TAA--TTTAAATATATATTT
1 TAATTTTTAAATATATAATT
*
55620 TTATTTT
1 TAATTTT
55627 AATTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 16 0.76
20 5 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTTTAAATATATAATT
Found at i:55628 original size:24 final size:24
Alignment explanation
Indices: 55600--55673 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
55590 AAATATATAA
55600 TTTAATTTAAATA-TATATTTTTAT
1 TTTAATTTAAATACT-TATTTTTAT
*
55624 TTTAA-TTAATATATTCTATTTTTA-
1 TTTAATTTAA-ATACT-TATTTTTAT
55648 TTTAATTTTAAA-ACTTATTTTTAT
1 TTTAA-TTTAAATACTTATTTTTAT
55672 TT
1 TT
55674 AAACTTTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
23 12 0.28
24 17 0.40
25 10 0.23
26 4 0.09
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTAATTTAAATACTTATTTTTAT
Found at i:55635 original size:18 final size:20
Alignment explanation
Indices: 55586--55645 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 20
55576 ATTATATAAT
55586 TTTTAAATATATA-A-TTTA
1 TTTTAAATATATATATTTTA
*
55604 ATTTAAATATATAT-TTTTA
1 TTTTAAATATATATATTTTA
* *
55623 TTTTAATTA-ATATATTCTA
1 TTTTAAATATATATATTTTA
55642 TTTT
1 TTTT
55646 TATTTAATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 16 0.46
19 19 0.54
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTAAATATATATATTTTA
Found at i:58212 original size:14 final size:14
Alignment explanation
Indices: 58193--58226 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
58183 AATTTACTAG
58193 TTTAAAACATATAT
1 TTTAAAACATATAT
* *
58207 TTTAAAATATATGT
1 TTTAAAACATATAT
58221 TTTAAA
1 TTTAAA
58227 TAAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (14 bp):
TTTAAAACATATAT
Found at i:62901 original size:22 final size:24
Alignment explanation
Indices: 62871--62920 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 24
62861 GAGTTTTGCA
*
62871 TGATTTATAAAATGTG-AAATAT-
1 TGATATATAAAATGTGTAAATATG
* *
62893 TGATATATATATTGTGTAAATATG
1 TGATATATAAAATGTGTAAATATG
62917 TGAT
1 TGAT
62921 GAGCATATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 13 0.57
23 6 0.26
24 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (24 bp):
TGATATATAAAATGTGTAAATATG
Found at i:66766 original size:22 final size:23
Alignment explanation
Indices: 66741--66795 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
66731 TTTTTAATAA
66741 AATATCATAATAAA-ATTAATTT
1 AATATCATAATAAATATTAATTT
* *
66763 AATATCAT-TTAAATATTATTTT
1 AATATCATAATAAATATTAATTT
*
66785 AAT-TTATAATA
1 AATATCATAATA
66796 TCATGCTCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (23 bp):
AATATCATAATAAATATTAATTT
Found at i:70124 original size:21 final size:20
Alignment explanation
Indices: 70090--70130 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
70080 TTAAAATATT
70090 ATTTTAATAAAATAT-TTAA
1 ATTTTAATAAAATATGTTAA
70109 ATTTTACATAAAAATATGTTAA
1 ATTTTA-AT-AAAATATGTTAA
70131 TCACATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 7 0.37
22 4 0.21
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTTTAATAAAATATGTTAA
Found at i:70158 original size:18 final size:17
Alignment explanation
Indices: 70135--70182 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
70125 TGTTAATCAC
70135 ATTTTATTAAATAAAAAT
1 ATTTTA-TAAATAAAAAT
* *
70153 ATTTTAAAAAATAAAATT
1 ATTTT-ATAAATAAAAAT
70171 ATATTTATAAAT
1 AT-TTTATAAAT
70183 TTTATTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTTATAAATAAAAAT
Found at i:71646 original size:2 final size:2
Alignment explanation
Indices: 71639--71690 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
71629 TAATTACAAA
71639 AT AT AT AT AT 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 AT AT AT AT AT
71681 AT AT AT AT AT
1 AT AT AT AT AT
71691 CAACACAATC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.