Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014894.1 Kokia drynarioides strain JFW-HI SEQ_129937, 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: 206476
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 29 characters in sequence are not A, C, G, or T
Found at i:5782 original size:6 final size:6
Alignment explanation
Indices: 5771--5799 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
5761 CTATTCTGAT
5771 TATTAC TATTAC TATTAC TATTAC TATTA
1 TATTAC TATTAC TATTAC TATTAC TATTA
5800 TCTACCACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (6 bp):
TATTAC
Found at i:15315 original size:5 final size:5
Alignment explanation
Indices: 15305--15329 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
15295 GAAACTTAAC
15305 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
15330 TTATGGCTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:24557 original size:15 final size:14
Alignment explanation
Indices: 24528--24566 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
24518 AAAAAAAAGC
*
24528 AATTAAA-ATAAAT
1 AATTAAATAAAAAT
24541 AATTAAGATAAAAAT
1 AATTAA-ATAAAAAT
24556 AATTAAATAAA
1 AATTAAATAAA
24567 TCAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 6 0.26
15 11 0.48
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (14 bp):
AATTAAATAAAAAT
Found at i:27621 original size:56 final size:55
Alignment explanation
Indices: 27559--27669 Score: 152
Period size: 56 Copynumber: 2.0 Consensus size: 55
27549 CACTTGATAA
27559 ATAATATAAATATACAACTAAT-GAAACTAATAACTCGTACATATTAAAATAAAAAT
1 ATAATATAAATATACAACTAATGGAAAC-AATAACTCGTACATATT-AAATAAAAAT
** * * *
27615 ATAATATAAATATACAGTTAATGGAGACAATAACTCGTGCATGTTAAATAAAAAT
1 ATAATATAAATATACAACTAATGGAAACAATAACTCGTACATATTAAATAAAAAT
27670 GTTAAAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
55 10 0.20
56 35 0.71
57 4 0.08
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.29
Consensus pattern (55 bp):
ATAATATAAATATACAACTAATGGAAACAATAACTCGTACATATTAAATAAAAAT
Found at i:33615 original size:16 final size:16
Alignment explanation
Indices: 33588--33627 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
33578 GTACAAGGCA
33588 AATATAATTTGTAATAT
1 AATAT-ATTTGTAATAT
33605 AATATATTTGTAATAT
1 AATATATTTGTAATAT
33621 -ATATATT
1 AATATATT
33628 ATTTTCCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 7 0.30
16 11 0.48
17 5 0.22
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (16 bp):
AATATATTTGTAATAT
Found at i:39427 original size:179 final size:180
Alignment explanation
Indices: 39127--39489 Score: 613
Period size: 179 Copynumber: 2.0 Consensus size: 180
39117 TGATCAATAA
* *
39127 AATGGCATTCAAGATGATCTTATGGCTTTGCCTTTCTTAATGCTACCAATTGTAGTTAATGTCTT
1 AATGGCATTCAAGATGATCTTATGGCTTTCCCTTTCTTAATGCTACCAATTGTAGTTAATATCTT
** *
39192 TGTGGTTTCCTGCATTTTTATATTTTACTCCAAAAACTGTCAGGATTTGAATGCCAACAAGTGAA
66 TGTGGTTTCCTGCATTTTTATATTGAACTCCAAAAACTGTCAGAATTTGAATGCCAACAAGTGAA
*
39257 GTGGATTGAAAGTTCTTTAGTAATACTTGATGTAAGA-TTTTTACTGTAC
131 GTGGATTGAAAGTTCTTTAGTAATACTTGATGTAAGATTTTTTACAGTAC
* *
39306 AATGGCATTCAAGATGATCTTCTGGCTTTCCCTTTCTTACTGCTACCAATTG-AGGTTAATATCT
1 AATGGCATTCAAGATGATCTTATGGCTTTCCCTTTCTTAATGCTACCAATTGTA-GTTAATATCT
*
39370 TTGTGGTTTCCTGCATTTTTATATTGAACTCCAAAAACTGTCAGAATTTGAATGCCAACCAGTGA
65 TTGTGGTTTCCTGCATTTTTATATTGAACTCCAAAAACTGTCAGAATTTGAATGCCAACAAGTGA
*
39435 AGTGGATTGAAAGTTCTTTAGTAATACTTGATGTAGGATTTTTTACAGTAC
130 AGTGGATTGAAAGTTCTTTAGTAATACTTGATGTAAGATTTTTTACAGTAC
39486 AATG
1 AATG
39490 TATGATTTTG
Statistics
Matches: 172, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
178 1 0.01
179 156 0.91
180 15 0.09
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (180 bp):
AATGGCATTCAAGATGATCTTATGGCTTTCCCTTTCTTAATGCTACCAATTGTAGTTAATATCTT
TGTGGTTTCCTGCATTTTTATATTGAACTCCAAAAACTGTCAGAATTTGAATGCCAACAAGTGAA
GTGGATTGAAAGTTCTTTAGTAATACTTGATGTAAGATTTTTTACAGTAC
Found at i:40748 original size:22 final size:22
Alignment explanation
Indices: 40733--40786 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
40723 AATCAATGTA
**
40733 AATGAGCTAATTAATCCCTAAT
1 AATGAGCTAATTAATCAATAAT
**
40755 AATGAGCTAATTAATCCCTAAT
1 AATGAGCTAATTAATCAATAAT
40777 AATGAGCTAA
1 AATGAGCTAA
40787 CTATTTGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.30
Consensus pattern (22 bp):
AATGAGCTAATTAATCAATAAT
Found at i:60852 original size:41 final size:41
Alignment explanation
Indices: 60791--60872 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
60781 AAATTTATAT
*
60791 GTACTATGAATAGGGAATGGAGTGATTGAATTATTCACTTC
1 GTACTATAAATAGGGAATGGAGTGATTGAATTATTCACTTC
60832 GTACTATAAATATGGG-ATGGAGTGATTGAATTATTCACTTC
1 GTACTATAAATA-GGGAATGGAGTGATTGAATTATTCACTTC
60873 CAAATCATTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
41 36 0.92
42 3 0.08
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (41 bp):
GTACTATAAATAGGGAATGGAGTGATTGAATTATTCACTTC
Found at i:62918 original size:12 final size:12
Alignment explanation
Indices: 62901--62931 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
62891 TTATTCACAA
*
62901 GCACCACATTAT
1 GCACCACACTAT
62913 GCACCACACTAT
1 GCACCACACTAT
62925 GCACCAC
1 GCACCAC
62932 CGTAGCACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.32, C:0.42, G:0.10, T:0.16
Consensus pattern (12 bp):
GCACCACACTAT
Found at i:69250 original size:30 final size:31
Alignment explanation
Indices: 69192--69251 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
69182 AATAATAAAA
*
69192 ATAAAATTATACTTTAATCTCCTTAAAAATG
1 ATAAAATTATAATTTAATCTCCTTAAAAATG
* *
69223 ATAAAATTTTAATTTAATC-CTTTAAAAAT
1 ATAAAATTATAATTTAATCTCCTTAAAAAT
69252 ATTACTATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 9 0.35
31 17 0.65
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (31 bp):
ATAAAATTATAATTTAATCTCCTTAAAAATG
Found at i:71874 original size:54 final size:54
Alignment explanation
Indices: 71804--71924 Score: 147
Period size: 54 Copynumber: 2.2 Consensus size: 54
71794 GTCCCCAGAT
* * *
71804 CGTGTAGCTCATTGACTTGAG-TCACACGC-CAATGTCACAGACCGTGTGCCAGGC
1 CGTGTAACTCACTGACTTGAGCT-ACACGCTC-ATGTCACAGACCGTATGCCAGGC
* * * *
71858 CGTGTAACTCACTGACTTGAGCTACATGCTCGTGTCACAGACCTTATGCCAGGT
1 CGTGTAACTCACTGACTTGAGCTACACGCTCATGTCACAGACCGTATGCCAGGC
71912 CGTGTAACTCACT
1 CGTGTAACTCACT
71925 AATTTAGGTC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
54 56 0.97
55 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.23, T:0.26
Consensus pattern (54 bp):
CGTGTAACTCACTGACTTGAGCTACACGCTCATGTCACAGACCGTATGCCAGGC
Found at i:77960 original size:44 final size:44
Alignment explanation
Indices: 77911--77995 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
77901 TTTAACTTTC
* * * * *
77911 AACTTTTACATATTATATCAATTT-AGTTATAATTTTAAAAAATT
1 AACTTTCACAAATGATATCAATTTGA-TCATAATTCTAAAAAATT
*
77955 AACTTTCACAAATGATCTCAATTTGATCATAATTCTAAAAA
1 AACTTTCACAAATGATATCAATTTGATCATAATTCTAAAAA
77996 TTCAAGAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 33 0.97
45 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.41
Consensus pattern (44 bp):
AACTTTCACAAATGATATCAATTTGATCATAATTCTAAAAAATT
Found at i:78115 original size:24 final size:26
Alignment explanation
Indices: 78087--78143 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
78077 GTTGACAAGA
*
78087 AATAATATACACA-ATTTAAAAATAT
1 AATAATATAAACATATTTAAAAATAT
* * *
78112 -ATAAAATAAATATTTTTAAAAATAT
1 AATAATATAAACATATTTAAAAATAT
78137 AATAATA
1 AATAATA
78144 AATTTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
24 9 0.36
25 11 0.44
26 5 0.20
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (26 bp):
AATAATATAAACATATTTAAAAATAT
Found at i:78385 original size:28 final size:29
Alignment explanation
Indices: 78348--78410 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
78338 ATTTATAAAG
78348 ATTTATACTATTA-AAATAATA-A-AAATATA
1 ATTT-TACTATTATAAA-AATATACAAAT-TA
78377 ATTTTACTATTATAAAAATATACAAATTA
1 ATTTTACTATTATAAAAATATACAAATTA
78406 ATTTT
1 ATTTT
78411 GATACTTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
28 12 0.39
29 15 0.48
30 4 0.13
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (29 bp):
ATTTTACTATTATAAAAATATACAAATTA
Found at i:78827 original size:31 final size:29
Alignment explanation
Indices: 78792--78859 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
78782 ATATTAATAC
*
78792 AAAATTTAAATTTATTATTATAATTTTTTT
1 AAAATTTAAATTTATTATTAT-ATATTTTT
* *
78822 GAAAATATT-TATTTATTTTTATATATTTTT
1 -AAAAT-TTAAATTTATTATTATATATTTTT
78852 AAAATTTA
1 AAAATTTA
78860 TTATTATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 2 0.06
29 5 0.16
30 7 0.22
31 16 0.50
32 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (29 bp):
AAAATTTAAATTTATTATTATATATTTTT
Found at i:78860 original size:54 final size:54
Alignment explanation
Indices: 78799--78903 Score: 167
Period size: 54 Copynumber: 1.9 Consensus size: 54
78789 TACAAAATTT
* **
78799 AAATTTATTATTATA-ATTTTTTTGAAAATATTTATTTATTTTTATATATTTTTA
1 AAATTTATTATTATATA-TTTTATGAAAATATTTAGGTATTTTTATATATTTTTA
78853 AAATTTATTATTATATATTTTATGAAAATATTTAGGTATTTTTATATATTT
1 AAATTTATTATTATATATTTTATGAAAATATTTAGGTATTTTTATATATTT
78904 CTTTGAATTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
54 46 0.98
55 1 0.02
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (54 bp):
AAATTTATTATTATATATTTTATGAAAATATTTAGGTATTTTTATATATTTTTA
Found at i:81854 original size:15 final size:15
Alignment explanation
Indices: 81834--81869 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
81824 AGCAACAAAC
**
81834 GCAGCAACTGCAGCA
1 GCAGCAACACCAGCA
81849 GCAGCAACACCAGCA
1 GCAGCAACACCAGCA
81864 GCAGCA
1 GCAGCA
81870 GCAGCAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.36, G:0.25, T:0.03
Consensus pattern (15 bp):
GCAGCAACACCAGCA
Found at i:85785 original size:6 final size:6
Alignment explanation
Indices: 85783--85823 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
85773 GCATATACAT
* * *
85783 ATATAC TTATAC ATATAC TTATAC ATATAG ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
85824 TGTAGAGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (6 bp):
ATATAC
Found at i:85800 original size:12 final size:12
Alignment explanation
Indices: 85783--85823 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
85773 GCATATACAT
85783 ATATACTTATAC
1 ATATACTTATAC
85795 ATATACTTATAC
1 ATATACTTATAC
**
85807 ATATAGATATAC
1 ATATACTTATAC
85819 ATATA
1 ATATA
85824 TGTAGAGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (12 bp):
ATATACTTATAC
Found at i:85953 original size:3 final size:3
Alignment explanation
Indices: 85939--85976 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
85929 CATGCAGCCA
*
85939 CAG CAA CAG CAG CAG CAG CAG CAG TCA- CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG -CAG CAG CAG CAG CA
85977 TGGTTCACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.87
4 2 0.06
ACGTcount: A:0.37, C:0.34, G:0.26, T:0.03
Consensus pattern (3 bp):
CAG
Found at i:86305 original size:80 final size:80
Alignment explanation
Indices: 86172--86335 Score: 301
Period size: 80 Copynumber: 2.0 Consensus size: 80
86162 TATAATCTTC
* *
86172 CATGTTTCATCATTGAAAAGTATGAGTACTAATGTGCAAAATTATCCGAATATGGAAAATATTAA
1 CATGTTTCATCATTGAAAAGTACGAGTACTAATGTGAAAAATTATCCGAATATGGAAAATATTAA
*
86237 TTATGGATTATTTTG
66 TTATGGATTAATTTG
86252 CATGTTTCATCATTGAAAAGTACGAGTACTAATGTGAAAAATTATCCGAATATGGAAAATATTAA
1 CATGTTTCATCATTGAAAAGTACGAGTACTAATGTGAAAAATTATCCGAATATGGAAAATATTAA
86317 TTATGGATTAATTTG
66 TTATGGATTAATTTG
86332 CATG
1 CATG
86336 AAACGGATTG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (80 bp):
CATGTTTCATCATTGAAAAGTACGAGTACTAATGTGAAAAATTATCCGAATATGGAAAATATTAA
TTATGGATTAATTTG
Found at i:88755 original size:77 final size:76
Alignment explanation
Indices: 88618--88897 Score: 314
Period size: 76 Copynumber: 3.7 Consensus size: 76
88608 CATAAAAGAG
* * * *
88618 TTTGTGCCCAACGCTAGTCGGATAAACCGACG-ATATCAATTGTGAGCCGAACTCTAGTTGGATT
1 TTTGTG-CCAGCGCTAGTCGGATAAACCGACGAATATCAAATGTGAGCCCAACTCTAGTTGGATA
**
88682 TACCAATAATAT
65 TACCAACGATAT
* *
88694 TTTGCGCACATCGCTAGTCGGATAAACCGACGAATATCAAATGTGAGCCCAACTCTAGTTGGATA
1 TTTGTGC-CAGCGCTAGTCGGATAAACCGACGAATATCAAATGTGAGCCCAACTCTAGTTGGATA
*
88759 TACCAACGATGT
65 TACCAACGATAT
* * * * * *
88771 TTTGTGCCTAGCGCCAGTCGGGTAAATCG-CGAATACCAAATGTGAGCCCAGCTCTAATTGGATA
1 TTTGTGCC-AGCGCTAGTCGGATAAACCGACGAATATCAAATGTGAGCCCAACTCTAGTTGGATA
*
88835 TATCAACGATAT
65 TACCAACGATAT
* * * *
88847 TTTGTGCCCAGCACTAATC-GAGTAAACCGACAAATATCAAATGTGAACCCA
1 TTTGTG-CCAGCGCTAGTCGGA-TAAACCGACGAATATCAAATGTGAGCCCA
88898 TCTATACTCG
Statistics
Matches: 172, Mismatches: 26, Indels: 11
0.82 0.12 0.05
Matches are distributed among these distances:
75 2 0.01
76 90 0.52
77 80 0.47
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (76 bp):
TTTGTGCCAGCGCTAGTCGGATAAACCGACGAATATCAAATGTGAGCCCAACTCTAGTTGGATAT
ACCAACGATAT
Found at i:90237 original size:19 final size:18
Alignment explanation
Indices: 90213--90255 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
90203 CTAAAAAAAT
90213 TATTTTTATCA-T-ATTAA
1 TATTTTTA-CAGTAATTAA
90230 TAATTTTTACAGTAATTAA
1 T-ATTTTTACAGTAATTAA
90249 TATTTTT
1 TATTTTT
90256 TAAAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTTTACAGTAATTAA
Found at i:101583 original size:7 final size:7
Alignment explanation
Indices: 101571--101608 Score: 51
Period size: 7 Copynumber: 5.3 Consensus size: 7
101561 GTTAAAGAAA
101571 AAGGGAG
1 AAGGGAG
101578 AAGGGAG
1 AAGGGAG
101585 AAGGGAG
1 AAGGGAG
101592 AAAGGGA-
1 -AAGGGAG
101599 AATGGGAG
1 AA-GGGAG
101607 AA
1 AA
101609 AAGAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
6 2 0.07
7 18 0.64
8 8 0.29
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (7 bp):
AAGGGAG
Found at i:101598 original size:15 final size:14
Alignment explanation
Indices: 101570--101609 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
101560 TGTTAAAGAA
101570 AAAGGGAG-AAGGG
1 AAAGGGAGAAAGGG
101583 AGAAGGGAGAAAGGG
1 A-AAGGGAGAAAGGG
101598 AAATGGGAGAAA
1 AAA-GGGAGAAA
101610 AGAAATAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.04
14 9 0.38
15 14 0.58
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (14 bp):
AAAGGGAGAAAGGG
Found at i:109680 original size:32 final size:33
Alignment explanation
Indices: 109613--109680 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
109603 ATGATGATTT
* **
109613 AATTTTTAAACATATTATATTTCAATTTTAATA
1 AATTTTTAAACATATTAAAAATCAATTTTAATA
109646 AATTTTTAAACATATTAAAAAAT-AA-TTTAATA
1 AATTTTTAAACATATT-AAAAATCAATTTTAATA
109678 AAT
1 AAT
109681 ACAATAAACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 10 0.32
33 18 0.58
34 3 0.10
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (33 bp):
AATTTTTAAACATATTAAAAATCAATTTTAATA
Found at i:110536 original size:21 final size:21
Alignment explanation
Indices: 110510--110551 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
110500 ATCACTGGAG
110510 CCTTTAGCTCTGGACAAAATT
1 CCTTTAGCTCTGGACAAAATT
*
110531 CCTTTAGCTCTGGTCAAAATT
1 CCTTTAGCTCTGGACAAAATT
110552 TTGTCAACCG
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:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (21 bp):
CCTTTAGCTCTGGACAAAATT
Found at i:113874 original size:2 final size:2
Alignment explanation
Indices: 113867--113895 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
113857 TAAATAATTA
113867 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113896 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115868 original size:2 final size:2
Alignment explanation
Indices: 115857--115888 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
115847 TTTCAGTCAT
115857 TA TA -A TA 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 TA TA TA TA T
115889 TCAAGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:116133 original size:16 final size:16
Alignment explanation
Indices: 116112--116146 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
116102 AAAAATACTG
116112 AAATATTAGAAAAAAA
1 AAATATTAGAAAAAAA
116128 AAATATTAGAAAAAAA
1 AAATATTAGAAAAAAA
116144 AAA
1 AAA
116147 AATAAACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (16 bp):
AAATATTAGAAAAAAA
Found at i:121549 original size:29 final size:29
Alignment explanation
Indices: 121516--121576 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
121506 TAAATTGTAA
*
121516 ATTTAT-TTTGAAATTAAATAATTTAGGTT
1 ATTTATATTT-AAATTAAATAATTCAGGTT
* * *
121545 ATTTATATTTAGATTAATTAATTCAGTTT
1 ATTTATATTTAAATTAAATAATTCAGGTT
121574 ATT
1 ATT
121577 ATACCGTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 24 0.89
30 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (29 bp):
ATTTATATTTAAATTAAATAATTCAGGTT
Found at i:148039 original size:20 final size:21
Alignment explanation
Indices: 148006--148045 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
147996 TTAATTAATT
*
148006 TTAAAAATTCAATTAATTTAA
1 TTAAAAAATCAATTAATTTAA
148027 TTAAAAAAT-AATTAATTTA
1 TTAAAAAATCAATTAATTTA
148046 TTTCGCAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAAAAAATCAATTAATTTAA
Found at i:163055 original size:14 final size:14
Alignment explanation
Indices: 163035--163092 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
163025 AGTTTTTCTT
*
163035 TTATTTTTTTTCAA
1 TTATTTTTTTTAAA
163049 TT-TTTTTATTTAAA
1 TTATTTTT-TTTAAA
* *
163063 TTATTTTTTTTCAC
1 TTATTTTTTTTAAA
*
163077 TTATTTATTTTAAA
1 TTATTTTTTTTAAA
163091 TT
1 TT
163093 TTCACTAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 5 0.14
14 26 0.72
15 5 0.14
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (14 bp):
TTATTTTTTTTAAA
Found at i:163067 original size:28 final size:28
Alignment explanation
Indices: 163035--163092 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
163025 AGTTTTTCTT
* *
163035 TTATTTTTTTTCAATT-TTTTTATTTAAA
1 TTATTTTTTTTCACTTATTTAT-TTTAAA
163063 TTATTTTTTTTCACTTATTTATTTTAAA
1 TTATTTTTTTTCACTTATTTATTTTAAA
163091 TT
1 TT
163093 TTCACTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (28 bp):
TTATTTTTTTTCACTTATTTATTTTAAA
Found at i:169878 original size:3 final size:3
Alignment explanation
Indices: 169870--169895 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
169860 AAGGAAGAAT
169870 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
169896 TTTGATTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:176178 original size:104 final size:104
Alignment explanation
Indices: 175998--176204 Score: 396
Period size: 104 Copynumber: 2.0 Consensus size: 104
175988 ATACTTAGAT
*
175998 AACAACACAAGCTTGAAAACCAGGTCAATGCACATAAGCACCAGCAGCAGAAGCAAAATTGAGTG
1 AACAACACAAGCTTGAAAACCAGGTCAATGCACATAAGCACCAGCAACAGAAGCAAAATTGAGTG
*
176063 TGTTCCAAGAAACTATTTAGCACAAGCCCTGAATTCATA
66 TGTTCCAAGAAACTATTTAGCAAAAGCCCTGAATTCATA
176102 AACAACACAAGCTTGAAAACCAGGTCAATGCACATAAGCACCAGCAACAGAAGCAAAATTGAGTG
1 AACAACACAAGCTTGAAAACCAGGTCAATGCACATAAGCACCAGCAACAGAAGCAAAATTGAGTG
176167 TGTTCCAAGAAACTATTTAGCAAAAGCCCTGAATTCAT
66 TGTTCCAAGAAACTATTTAGCAAAAGCCCTGAATTCAT
176205 CAAGAGAAAG
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.18
Consensus pattern (104 bp):
AACAACACAAGCTTGAAAACCAGGTCAATGCACATAAGCACCAGCAACAGAAGCAAAATTGAGTG
TGTTCCAAGAAACTATTTAGCAAAAGCCCTGAATTCATA
Found at i:184486 original size:17 final size:18
Alignment explanation
Indices: 184459--184492 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
184449 GTTTTAAAGA
184459 ATATGCCAAAATCTTCAC
1 ATATGCCAAAATCTTCAC
184477 ATAT-CCAAAATCTTCA
1 ATATGCCAAAATCTTCA
184493 TAATTGTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.29
Consensus pattern (18 bp):
ATATGCCAAAATCTTCAC
Found at i:185347 original size:82 final size:82
Alignment explanation
Indices: 185232--185395 Score: 319
Period size: 82 Copynumber: 2.0 Consensus size: 82
185222 TAGTGATTAC
185232 TATAGTGTGTCGACCTCAATTGATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGT
1 TATAGTGTGTCGACCTCAATTGATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGT
185297 TATAAAATAAAATGACA
66 TATAAAATAAAATGACA
*
185314 TATAGTGTGTTGACCTCAATTGATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGT
1 TATAGTGTGTCGACCTCAATTGATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGT
185379 TATAAAATAAAATGACA
66 TATAAAATAAAATGACA
185396 GAAAGTAAAG
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (82 bp):
TATAGTGTGTCGACCTCAATTGATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGT
TATAAAATAAAATGACA
Found at i:185431 original size:82 final size:82
Alignment explanation
Indices: 185253--185417 Score: 208
Period size: 82 Copynumber: 2.0 Consensus size: 82
185243 GACCTCAATT
* *
185253 GATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGTTATAAAATAAAATGACATATA
1 GATGACAGAAAAAAAATTAAATGAGAATCGTACTAATAACATGTTATAAAATAAAATGACAGATA
* *** * ** **
185318 GTGTGTTGACCTCAATT
66 GAGTAAAGAACAAAAAA
*
185335 GATGACTGAAAAAAAATTAAATGAGAATCGTACTAATAACATGTTATAAAATAAAATGACAGA-A
1 GATGACAGAAAAAAAATTAAATGAGAATCGTACTAATAACATGTTATAAAATAAAATGACAGATA
185399 -AGTAAAGAACAAAAAA
66 GAGTAAAGAACAAAAAA
185415 GAT
1 GAT
185418 AGGAGAGCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
80 10 0.14
81 1 0.01
82 62 0.85
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (82 bp):
GATGACAGAAAAAAAATTAAATGAGAATCGTACTAATAACATGTTATAAAATAAAATGACAGATA
GAGTAAAGAACAAAAAA
Found at i:185979 original size:19 final size:20
Alignment explanation
Indices: 185955--185992 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
185945 CAAGTAATTT
185955 TAAAATTATTT-TTAAAATA
1 TAAAATTATTTATTAAAATA
185974 TAAAATTATTTATTAAAAT
1 TAAAATTATTTATTAAAAT
185993 TATTTTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAAAATTATTTATTAAAATA
Found at i:187050 original size:24 final size:26
Alignment explanation
Indices: 187023--187076 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 26
187013 AAATTGTGGA
187023 AATTGGATATT-AAAATAA-TATAAT
1 AATTGGATATTAAAAATAATTATAAT
** *
187047 AATTTTATATTAAAAATAATTTTAAT
1 AATTGGATATTAAAAATAATTATAAT
187073 AATT
1 AATT
187077 TTAAAATCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 9 0.36
25 7 0.28
26 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (26 bp):
AATTGGATATTAAAAATAATTATAAT
Found at i:187077 original size:26 final size:24
Alignment explanation
Indices: 187029--187079 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 24
187019 TGGAAATTGG
187029 ATATTAAAATAATATAATAATTTT
1 ATATTAAAATAATATAATAATTTT
*
187053 ATATTAAAAATAATTTTAATAATTTT
1 ATATT-AAAATAA-TATAATAATTTT
187079 A
1 A
187080 AAATCATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 5 0.21
25 7 0.29
26 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
ATATTAAAATAATATAATAATTTT
Found at i:187510 original size:18 final size:19
Alignment explanation
Indices: 187473--187513 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
187463 ACATTTCATA
*
187473 AAATTATAATTTAATATTT
1 AAATCATAATTTAATATTT
*
187492 AAATCATAA-TTATTATTT
1 AAATCATAATTTAATATTT
187510 AAAT
1 AAAT
187514 TTAATTACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATCATAATTTAATATTT
Done.