Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012987.1 Kokia drynarioides strain JFW-HI SEQ_128005, 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: 58744
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:359 original size:14 final size:14
Alignment explanation
Indices: 344--380 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
334 TTAAACCCTA
344 AAACC-TAAATTAT
1 AAACCTTAAATTAT
357 AAACCTTAAATT-T
1 AAACCTTAAATTAT
370 GAAACCTTAAA
1 -AAACCTTAAA
381 CCGTAAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (14 bp):
AAACCTTAAATTAT
Found at i:1746 original size:4 final size:4
Alignment explanation
Indices: 1737--1778 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
1727 AACACATTAC
*
1737 CTTT CTTT CTTT C-TT CTTT CTTT CCTGTC CTTT CTTT CTTT C
1 CTTT CTTT CTTT CTTT CTTT CTTT -CT-TT CTTT CTTT CTTT C
1779 CCGTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 3 0.09
4 25 0.76
5 4 0.12
6 1 0.03
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.67
Consensus pattern (4 bp):
CTTT
Found at i:1986 original size:13 final size:13
Alignment explanation
Indices: 1968--1999 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1958 TGGGTGTCAG
1968 GTATTTTTTTGTC
1 GTATTTTTTTGTC
1981 GTA--TTTTTGTC
1 GTATTTTTTTGTC
1992 GTATTTTT
1 GTATTTTT
2000 CTGAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 11 0.65
13 6 0.35
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (13 bp):
GTATTTTTTTGTC
Found at i:1998 original size:10 final size:11
Alignment explanation
Indices: 1973--1999 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1963 GTCAGGTATT
1973 TTTTTGTCGTA
1 TTTTTGTCGTA
1984 TTTTTGTCGTA
1 TTTTTGTCGTA
1995 TTTTT
1 TTTTT
2000 CTGAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.70
Consensus pattern (11 bp):
TTTTTGTCGTA
Found at i:2096 original size:9 final size:10
Alignment explanation
Indices: 2076--2100 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2066 TGAAATATAT
2076 AAAAATTAAA
1 AAAAATTAAA
2086 AAAAATTAAA
1 AAAAATTAAA
2096 AAAAA
1 AAAAA
2101 CATGTGTCAA
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAATTAAA
Found at i:6501 original size:3 final size:3
Alignment explanation
Indices: 6493--6517 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
6483 AATCATTTAT
6493 TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA T
6518 AAAACCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:8092 original size:30 final size:29
Alignment explanation
Indices: 8036--8094 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
8026 AATCTCACAA
*
8036 AATTTTTTAAAAATTTGATTAGAACTCCT
1 AATTTTTTAAAAATTTCATTAGAACTCCT
8065 AATTTTTTAAAAATTTCTCATTA-AACTCCT
1 AATTTTTTAAAAA-TT-TCATTAGAACTCCT
8095 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 13 0.48
30 9 0.33
31 5 0.19
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (29 bp):
AATTTTTTAAAAATTTCATTAGAACTCCT
Found at i:8720 original size:13 final size:13
Alignment explanation
Indices: 8685--8714 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
8675 GTTCAACCTA
8685 TTTAA-ATAAAAT
1 TTTAACATAAAAT
8697 TTTAACATAAAAT
1 TTTAACATAAAAT
8710 TTTAA
1 TTTAA
8715 TTTAAATCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTAACATAAAAT
Found at i:11671 original size:31 final size:31
Alignment explanation
Indices: 11636--11718 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
11626 AAAGCACAGC
* *
11636 CAAAAGCGCTTCCACGTGTGCA-CTTTTTTGG
1 CAAAAGCGCTTCCACGTGGGCATC-ATTTTGG
11667 CAAAAGCGCTTCCACGTGGGCATCATTTTGG
1 CAAAAGCGCTTCCACGTGGGCATCATTTTGG
11698 CAAAAAG-GC-TCCTACGTGGGC
1 C-AAAAGCGCTTCC-ACGTGGGC
11719 GCGCTTTTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
30 3 0.06
31 38 0.81
32 6 0.13
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (31 bp):
CAAAAGCGCTTCCACGTGGGCATCATTTTGG
Found at i:12255 original size:5 final size:5
Alignment explanation
Indices: 12245--12269 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12235 TCCACACCCA
12245 TCTCT TCTCT TCTCT TCTCT TCTCT
1 TCTCT TCTCT TCTCT TCTCT TCTCT
12270 AGATTGATAT
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:0.40, G:0.00, T:0.60
Consensus pattern (5 bp):
TCTCT
Found at i:15597 original size:16 final size:16
Alignment explanation
Indices: 15576--15608 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
15566 GTGATCATTG
15576 GGTGATTGTTATCAAA
1 GGTGATTGTTATCAAA
15592 GGTGATTGTTATCAAA
1 GGTGATTGTTATCAAA
15608 G
1 G
15609 AAAACCAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (16 bp):
GGTGATTGTTATCAAA
Found at i:19404 original size:33 final size:33
Alignment explanation
Indices: 19362--19427 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
19352 TCTTTGAAGC
19362 TGATTTTGAACAATGGTTTATGGGAAATCTGCA
1 TGATTTTGAACAATGGTTTATGGGAAATCTGCA
19395 TGATTTTGAACAATGGTTTATGGGAAATCTGCA
1 TGATTTTGAACAATGGTTTATGGGAAATCTGCA
19428 GAGGCAGCGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.09, G:0.24, T:0.36
Consensus pattern (33 bp):
TGATTTTGAACAATGGTTTATGGGAAATCTGCA
Found at i:22157 original size:42 final size:42
Alignment explanation
Indices: 22110--22194 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
22100 GGATGCTTTC
22110 GAATTGGTTAAATGTGGTTTAAAAGGATTGTTTGTTGCCTAA
1 GAATTGGTTAAATGTGGTTTAAAAGGATTGTTTGTTGCCTAA
22152 GAATTGGTTAAATGTGGTTTAAAAGGATTGTTTGTTGCCTAA
1 GAATTGGTTAAATGTGGTTTAAAAGGATTGTTTGTTGCCTAA
22194 G
1 G
22195 TGAACTAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.05, G:0.27, T:0.40
Consensus pattern (42 bp):
GAATTGGTTAAATGTGGTTTAAAAGGATTGTTTGTTGCCTAA
Found at i:24921 original size:10 final size:11
Alignment explanation
Indices: 24896--24922 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
24886 TTTTTTACAA
24896 AAAAATATGAG
1 AAAAATATGAG
24907 AAAAATATGAG
1 AAAAATATGAG
24918 AAAAA
1 AAAAA
24923 AATACCTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (11 bp):
AAAAATATGAG
Found at i:24923 original size:13 final size:13
Alignment explanation
Indices: 24894--24926 Score: 52
Period size: 11 Copynumber: 2.7 Consensus size: 13
24884 GTTTTTTTAC
24894 AAAAAAATATGAG
1 AAAAAAATATGAG
24907 --AAAAATATGAG
1 AAAAAAATATGAG
24918 AAAAAAATA
1 AAAAAAATA
24927 CCTGACATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
11 11 0.61
13 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (13 bp):
AAAAAAATATGAG
Found at i:25154 original size:4 final size:4
Alignment explanation
Indices: 25145--25235 Score: 94
Period size: 4 Copynumber: 22.2 Consensus size: 4
25135 AGATAGGGGG
*
25145 GAAA GAAA GAAAA GAGA GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA
* * * * *
25195 GAAA GGAA TAAG GAGA GAAAA GAAA G-AA GAAA GAAA TAAA G
1 GAAA GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA G
25236 GTAATGTGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
3 3 0.04
4 57 0.80
5 11 0.15
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:25169 original size:21 final size:21
Alignment explanation
Indices: 25145--25198 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
25135 AGATAGGGGG
*
25145 GAAAGAAAGAAAAGAGAGAAA
1 GAAAGAAAGAAAAGAAAGAAA
25166 GAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAAGAAAAGAAAGAAA
25187 GAAAGAAAGAAA
1 GAAAGAAAGAAA
25199 GGAATAAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (21 bp):
GAAAGAAAGAAAAGAAAGAAA
Found at i:25173 original size:25 final size:24
Alignment explanation
Indices: 25145--25226 Score: 94
Period size: 25 Copynumber: 3.3 Consensus size: 24
25135 AGATAGGGGG
25145 GAAAGAAAGAAAAGAGAGAAAGAAA
1 GAAAGAAA-AAAAGAGAGAAAGAAA
*
25170 GAAAGAAAAGAAAGAAAGAAAGAAA
1 GAAAGAAAA-AAAGAGAGAAAGAAA
* * *
25195 GAAAGGAATAAGGAGAGAAAAGAAA
1 GAAAGAAAAAAAGAGAG-AAAGAAA
25220 G-AAGAAA
1 GAAAGAAA
25227 GAAATAAAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
24 12 0.24
25 37 0.76
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (24 bp):
GAAAGAAAAAAAGAGAGAAAGAAA
Found at i:29001 original size:14 final size:14
Alignment explanation
Indices: 28984--29051 Score: 79
Period size: 14 Copynumber: 4.9 Consensus size: 14
28974 GGTGTTTACG
*
28984 GTTTAGAGTTTTAA
1 GTTTAGGGTTTTAA
*
28998 GTTTAGTGTTTATAA
1 GTTTAGGGTTT-TAA
29013 -TTTAGGGTTTTAA
1 GTTTAGGGTTTTAA
29026 GTTTAGGGTTTATAA
1 GTTTAGGGTTT-TAA
29041 -TTTA-GGTTTTA
1 GTTTAGGGTTTTA
29052 GGGTTTAATG
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.04
13 8 0.16
14 33 0.67
15 6 0.12
ACGTcount: A:0.25, C:0.00, G:0.22, T:0.53
Consensus pattern (14 bp):
GTTTAGGGTTTTAA
Found at i:29007 original size:28 final size:28
Alignment explanation
Indices: 28975--29051 Score: 93
Period size: 28 Copynumber: 2.8 Consensus size: 28
28965 AATCAATTTG
**
28975 GTGTTTACGGTTTAGAGTTTTAAGTTTA
1 GTGTTTACAATTTAGAGTTTTAAGTTTA
* *
29003 GTGTTTATAATTTAGGGTTTTAAGTTTA
1 GTGTTTACAATTTAGAGTTTTAAGTTTA
* *
29031 GGGTTTATAATTTAG-GTTTTA
1 GTGTTTACAATTTAGAGTTTTA
29052 GGGTTTAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 6 0.14
28 38 0.86
ACGTcount: A:0.23, C:0.01, G:0.23, T:0.52
Consensus pattern (28 bp):
GTGTTTACAATTTAGAGTTTTAAGTTTA
Found at i:29424 original size:45 final size:45
Alignment explanation
Indices: 29302--29430 Score: 168
Period size: 45 Copynumber: 2.9 Consensus size: 45
29292 TAGAGTATCA
* * * **
29302 CGGTGGCTCGTCAAACTCAGCCTGATATTCTTCCCTTGAGTATTG
1 CGGTGGCTCGTCAAACTAAGGCTGATATCCTTGACTTGAGTATTG
* * * *
29347 TGGTGGTTCGTCAAATTGAGGCTGATATCCTTGACTTGAGTATTG
1 CGGTGGCTCGTCAAACTAAGGCTGATATCCTTGACTTGAGTATTG
*
29392 CGGTGGCTCGTCAAACTAAGGCTGATATCCTTGGCTTGA
1 CGGTGGCTCGTCAAACTAAGGCTGATATCCTTGACTTGA
29431 TGAGCTATGC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.19, C:0.21, G:0.26, T:0.33
Consensus pattern (45 bp):
CGGTGGCTCGTCAAACTAAGGCTGATATCCTTGACTTGAGTATTG
Found at i:31383 original size:16 final size:16
Alignment explanation
Indices: 31362--31410 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
31352 TGATGGAGAT
31362 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
31378 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
31392 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
31407 ATTA
1 ATTA
31411 GTTAAGTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:31915 original size:20 final size:21
Alignment explanation
Indices: 31890--31932 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
31880 TACTTACTAC
31890 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
* *
31910 TACTAACTAGCAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
31931 TA
1 TA
31933 AAATAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:32105 original size:12 final size:12
Alignment explanation
Indices: 32090--32114 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32080 AAATTAAAAT
32090 ATTTTAAAATTA
1 ATTTTAAAATTA
32102 ATTTTAAAATTA
1 ATTTTAAAATTA
32114 A
1 A
32115 CCATACTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTTAAAATTA
Found at i:32310 original size:7 final size:7
Alignment explanation
Indices: 32298--32345 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
32288 TTCCTTCTCC
32298 TTCTTCT
1 TTCTTCT
32305 TTCTTCT
1 TTCTTCT
32312 TTCTTTCT
1 TTC-TTCT
32320 TTCATTCT
1 TTC-TTCT
32328 TTCTT-T
1 TTCTTCT
* *
32334 CTCTTTT
1 TTCTTCT
32341 TTCTT
1 TTCTT
32346 TTTTTTTCCT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 5 0.14
7 17 0.47
8 14 0.39
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTCT
Found at i:32315 original size:4 final size:4
Alignment explanation
Indices: 32301--32346 Score: 58
Period size: 4 Copynumber: 11.5 Consensus size: 4
32291 CTTCTCCTTC
* *
32301 TTCT TTC- TTCT TTCT TTCT TTCA TTCT TTCT TTCT CTTTT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT -TTCT TTCT TT
32347 TTTTTTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.83
5 3 0.08
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (4 bp):
TTCT
Found at i:33772 original size:17 final size:18
Alignment explanation
Indices: 33740--33774 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
33730 AATTACAAAT
*
33740 TTTAAATATAAATATATA
1 TTTAAAAATAAATATATA
33758 TTTAAAAAT-AATATATA
1 TTTAAAAATAAATATATA
33775 ATAAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAAAAATAAATATATA
Found at i:33780 original size:14 final size:14
Alignment explanation
Indices: 33747--33784 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
33737 AATTTTAAAT
*
33747 ATAAATATATATTTA
1 ATAAATA-ATATATA
33762 A-AAATAATATATA
1 ATAAATAATATATA
33775 ATAAATAATA
1 ATAAATAATA
33785 AAGCATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 7 0.33
14 13 0.62
15 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
ATAAATAATATATA
Found at i:50642 original size:17 final size:17
Alignment explanation
Indices: 50617--50668 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
50607 GTAATGAATT
*
50617 TTAAATTTTAATAGGT-
1 TTAAGTTTTAATAGGTA
* *
50633 TTGAGCTTTTAAGA-GTA
1 TTAAG-TTTTAATAGGTA
50650 TTAAGTTTTAATAGGTA
1 TTAAGTTTTAATAGGTA
50667 TT
1 TT
50669 TGATTTCTCG
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (17 bp):
TTAAGTTTTAATAGGTA
Found at i:50781 original size:22 final size:22
Alignment explanation
Indices: 50743--50791 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
50733 TCAAAACTGA
*
50743 AAACCGACCAAATAAACTAATT
1 AAACCGACCAAATAAACCAATT
* *
50765 AAACCGACCATGA-AAACCGATT
1 AAACCGACCA-AATAAACCAATT
50787 AAACC
1 AAACC
50792 AAAAAACCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.51, C:0.27, G:0.08, T:0.14
Consensus pattern (22 bp):
AAACCGACCAAATAAACCAATT
Found at i:53404 original size:26 final size:27
Alignment explanation
Indices: 53354--53405 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
53344 CTAAAAAAGC
*
53354 TAAAATAATTATAAATTTTTATTTATG
1 TAAAAAAATTATAAATTTTTATTTATG
53381 TAAAAAAATTA-AAATTATTT-TTTAT
1 TAAAAAAATTATAAATT-TTTATTTAT
53406 AAAAATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TAAAAAAATTATAAATTTTTATTTATG
Found at i:53648 original size:23 final size:23
Alignment explanation
Indices: 53620--53665 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
53610 ATAATTCTTA
*
53620 AATTTTAAATTTATTATTTTTAT
1 AATTTTAAATTTATTATTATTAT
* *
53643 AATTTTAATTTTTTTATTATTAT
1 AATTTTAAATTTATTATTATTAT
53666 GCAAATTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
AATTTTAAATTTATTATTATTAT
Found at i:55074 original size:10 final size:10
Alignment explanation
Indices: 55061--55087 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
55051 AATTCATAAA
55061 AAAATAATAC
1 AAAATAATAC
55071 AAAATAATAC
1 AAAATAATAC
55081 AAAATAA
1 AAAATAA
55088 AAAATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATAATAC
Found at i:58047 original size:29 final size:29
Alignment explanation
Indices: 57987--58356 Score: 260
Period size: 29 Copynumber: 12.7 Consensus size: 29
57977 TCGGGGGGCG
* * * *
57987 AAATGGCAATTTTGGGAAAATTCGGAGTTAA
1 AAATGG-AATTTTTGG-AAGTTCGGGGGTAA
*
58018 AAATGGAATTTTTAGACA-TTCGGGGGT-A
1 AAATGGAATTTTTGGA-AGTTCGGGGGTAA
* * * *
58046 AAAGGGTAA-TTTT-GAGAGTTTTGAGGTTAA
1 AAATGG-AATTTTTGGA-AG-TTCGGGGGTAA
* * *
58076 AAAT-GAAGTTTTTGGGCA-TCCGGGGGT-T
1 AAATGGAA-TTTTT-GGAAGTTCGGGGGTAA
** *
58104 AAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAATGG-AATTTTTGGAAGTTCGGGGGTAA
* * **
58134 AAATGGAATTTTTTGAAATTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTCGGGGGTAA
**
58163 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTCGGGGGT-AA
* * *
58193 AATTGAAATTTTTGGTAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCGGGGGTAA
* *
58222 AAAT-G--TTTTTGGAAGTTTGTGGGTTAA
1 AAATGGAATTTTTGGAAGTTCG-GGGGTAA
* **
58249 AAATAGAATTTTTGGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTCGGGGGTAA
*
58278 AAATGGAAATTTTTGGAAGTTTC-GAGGTCAA
1 AAATGG-AATTTTTGGAAG-TTCGGGGGT-AA
58309 AAATGGAA-TTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTCGGGGGTAA
58337 AAATGGAATTTTTGGAAGTT
1 AAATGGAATTTTTGGAAGTT
58357 TCGAGACCTC
Statistics
Matches: 272, Mismatches: 44, Indels: 48
0.75 0.12 0.13
Matches are distributed among these distances:
26 12 0.04
27 13 0.05
28 33 0.12
29 117 0.43
30 79 0.29
31 17 0.06
32 1 0.00
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.35
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTCGGGGGTAA
Found at i:58147 original size:30 final size:29
Alignment explanation
Indices: 58104--58357 Score: 291
Period size: 29 Copynumber: 8.7 Consensus size: 29
58094 TCCGGGGGTT
*
58104 AAATGGTAATTTTTGGAAGTTTTGGGGTCA
1 AAATGG-AATTTTTGGAAGTTTTGGGGTAA
* * *
58134 AAATGGAATTTTTTGAAATTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
58163 AAATGGAATTTTTGGAAGTTTTGGGGTCAA
1 AAATGGAATTTTTGGAAGTTTTGGGGT-AA
* * * **
58193 AATTGAAATTTTTGGTAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
*
58222 AAAT-G--TTTTTGGAAGTTTGTGGGTTAA
1 AAATGGAATTTTTGGAAGTTT-TGGGGTAA
* *
58249 AAATAGAATTTTTGGAAGTTTAGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
* *
58278 AAATGGAAATTTTTGGAAGTTTCGAGGTCAA
1 AAATGG-AATTTTTGGAAGTTTTGGGGT-AA
**
58309 AAATGGAA-TTTTGGAAGTTCGGGGGTAA
1 AAATGGAATTTTTGGAAGTTTTGGGGTAA
58337 AAATGGAATTTTTGGAAGTTT
1 AAATGGAATTTTTGGAAGTTT
58358 CGAGACCTCT
Statistics
Matches: 189, Mismatches: 27, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
26 11 0.06
27 10 0.05
28 11 0.06
29 85 0.45
30 64 0.34
31 8 0.04
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (29 bp):
AAATGGAATTTTTGGAAGTTTTGGGGTAA
Found at i:58266 original size:86 final size:88
Alignment explanation
Indices: 58104--58357 Score: 302
Period size: 86 Copynumber: 2.9 Consensus size: 88
58094 TCCGGGGGTT
* * * * * **
58104 AAATGGTAATTTTTGGAAGTTTTGGGGTC-AAAATGGAATTTTTTGAAATTTAGGGGTAAAAATG
1 AAATGGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGAA-TTTTGGAAGTTCGGGGGTAAAAATG
* *
58168 GAATTTTTGGAAGTTTTGGGGTCA
65 GAATTTTTGGAAGTTTAGGGGTAA
* * * * * *
58192 AAATTGAAATTTTTGGTAG-TTCGGGGGT-AAAAAT-G-TTTTTGGAAGTTTGTGGGTTAAAAAT
1 AAATGGAAATTTTTGGAAGTTTC-GAGGTCAAAAATGGAATTTTGGAAGTTCG-GGGGTAAAAAT
*
58253 AGAATTTTTGGAAGTTTAGGGGTAA
64 GGAATTTTTGGAAGTTTAGGGGTAA
58278 AAATGGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGG
1 AAATGGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGG
58343 AATTTTTGGAAGTTT
66 AATTTTTGGAAGTTT
58358 CGAGACCTCT
Statistics
Matches: 140, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
85 10 0.07
86 53 0.38
87 12 0.09
88 53 0.38
89 12 0.09
ACGTcount: A:0.32, C:0.02, G:0.29, T:0.37
Consensus pattern (88 bp):
AAATGGAAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTGGAAGTTCGGGGGTAAAAATGG
AATTTTTGGAAGTTTAGGGGTAA
Found at i:58361 original size:58 final size:60
Alignment explanation
Indices: 58016--58357 Score: 338
Period size: 58 Copynumber: 5.9 Consensus size: 60
58006 ATTCGGAGTT
* * *
58016 AAAAATGGAATTTTTAGACA-TTCGGGGGT-AAAAGGGTAA-TTTT-GAGAGTTTTGAGGTT
1 AAAAATGGAATTTTTGGA-AGTTCGGGGGTAAAAATGGTAATTTTTGGA-AGTTTTGAGGTC
* * * *
58074 AAAAAT-GAAGTTTTTGGGCA-TCCGGGGGT-TAAATGGTAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAA-TTTTT-GGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGAGGTC
* * ** *
58133 -AAAATGGAATTTTTTGAAATTTAGGGGTAAAAATGG-AATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGAGGTC
* * * *
58191 AAAATTGAAATTTTTGGTAGTTCGGGGGTAAAAAT-G---TTTTTGGAAGTTTGTG-GGTT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTT-TGAGGTC
* ** * *
58247 AAAAATAGAATTTTTGGAAGTTTAGGGGTAAAAATGGAAATTTTTGGAAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGAGGTC
58307 AAAAATGGAA-TTTTGGAAGTTCGGGGGTAAAAATGG-AATTTTTGGAAGTTT
1 AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTT
58358 CGAGACCTCT
Statistics
Matches: 238, Mismatches: 32, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
56 45 0.19
57 8 0.03
58 82 0.34
59 76 0.32
60 27 0.11
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (60 bp):
AAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGGTAATTTTTGGAAGTTTTGAGGTC
Done.