Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013779.1 Kokia drynarioides strain JFW-HI SEQ_128807, 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: 168081
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Warning! 56 characters in sequence are not A, C, G, or T
Found at i:2310 original size:28 final size:27
Alignment explanation
Indices: 2260--2312 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
2250 GATGAAGAGA
*
2260 AAGAAGAAGGAAAGGAAGAAGAACAAT
1 AAGAAGAAGGAAAGAAAGAAGAACAAT
*
2287 AAGAGGAAGGAAAAGAAAGAAGAACA
1 AAGAAGAAGG-AAAGAAAGAAGAACA
2313 GAAGAACCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.64, C:0.04, G:0.30, T:0.02
Consensus pattern (27 bp):
AAGAAGAAGGAAAGAAAGAAGAACAAT
Found at i:2317 original size:27 final size:27
Alignment explanation
Indices: 2260--2318 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
2250 GATGAAGAGA
* *
2260 AAGAAGAAGGAAAGGAAGAAGAACAAT
1 AAGAAGAAGGAAAGAAAGAAGAACAAG
*
2287 AAGAGGAAGGAAAAGAAAGAAGAAC-AG
1 AAGAAGAAGG-AAAGAAAGAAGAACAAG
2314 AAGAA
1 AAGAA
2319 CCTATTATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.64, C:0.03, G:0.31, T:0.02
Consensus pattern (27 bp):
AAGAAGAAGGAAAGAAAGAAGAACAAG
Found at i:15464 original size:31 final size:31
Alignment explanation
Indices: 15429--15489 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
15419 GTTTTCCGAG
15429 TAAGCTTTCTCCTTTTTTGCTTTTTGGTGAT
1 TAAGCTTTCTCCTTTTTTGCTTTTTGGTGAT
15460 TAAGCTTTCTCCTTTTTTGCTTTTTGGTGA
1 TAAGCTTTCTCCTTTTTTGCTTTTTGGTGA
15490 CTTGGTGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.57
Consensus pattern (31 bp):
TAAGCTTTCTCCTTTTTTGCTTTTTGGTGAT
Found at i:24340 original size:37 final size:37
Alignment explanation
Indices: 24263--24341 Score: 90
Period size: 37 Copynumber: 2.1 Consensus size: 37
24253 AAAATTGCGT
** * *
24263 CCAAACATGTCGTTGCATGAACACTTCTAGATTGTGC
1 CCAAACATGTCGCCGCATCAACACTTCTAGATTCTGC
24300 CCAAACATGTCGCCGCATCAACA-TCTCTAGATTACT-C
1 CCAAACATGTCGCCGCATCAACACT-TCTAGATT-CTGC
24337 CCAAA
1 CCAAA
24342 AACTATCACC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 1 0.03
37 34 0.94
38 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (37 bp):
CCAAACATGTCGCCGCATCAACACTTCTAGATTCTGC
Found at i:24406 original size:37 final size:38
Alignment explanation
Indices: 24365--24437 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
24355 TGAGCACTTC
24365 CAAATTGCA-CCAAAACTGTCGCCGCATAAATATTCTT
1 CAAATTGCATCCAAAACTGTCGCCGCATAAATATTCTT
* ** *
24402 CAAATTGCATCCAGAACTGTCGTTGCATAAGTATTC
1 CAAATTGCATCCAAAACTGTCGCCGCATAAATATTC
24438 AATTGCACCC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 9 0.29
38 22 0.71
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.29
Consensus pattern (38 bp):
CAAATTGCATCCAAAACTGTCGCCGCATAAATATTCTT
Found at i:28823 original size:37 final size:37
Alignment explanation
Indices: 28772--28900 Score: 177
Period size: 37 Copynumber: 3.5 Consensus size: 37
28762 ACAATTTTAA
28772 TCTAGAATTGTGCCCAAACATGTCGCTGCATGAGCACT
1 TCTAG-ATTGTGCCCAAACATGTCGCTGCATGAGCACT
* * * *
28810 TCTAGATTGTGCCCAAACATGTCACCGGATGAGCAAT
1 TCTAGATTGTGCCCAAACATGTCGCTGCATGAGCACT
* *
28847 TCTAGATTGTGCCCAAACATGTTGTTGCATGAGCACT
1 TCTAGATTGTGCCCAAACATGTCGCTGCATGAGCACT
* *
28884 TCTAAATTGCGCCCAAA
1 TCTAGATTGTGCCCAAA
28901 AATTGTCTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
37 74 0.94
38 5 0.06
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (37 bp):
TCTAGATTGTGCCCAAACATGTCGCTGCATGAGCACT
Found at i:28937 original size:74 final size:73
Alignment explanation
Indices: 28777--28950 Score: 188
Period size: 74 Copynumber: 2.3 Consensus size: 73
28767 TTTAATCTAG
* * * * **
28777 AATTGTGCCCAAACATGTCGCTGCATGAGCACTTCTAGATTGTGCCCAAACATGTCACCGGATGA
1 AATTGT-CCCAAACATGTCGTTGCATGAGCACTTCTAAATTGCGCCCAAAAATGTCACCACATGA
* *
28842 GCAATTCTA
65 CCAATTCCA
* * *
28851 GATTGTGCCCAAACATGTTGTTGCATGAGCACTTCTAAATTGCGCCCAAAAATTGTCTCCACATG
1 AATTGT-CCCAAACATGTCGTTGCATGAGCACTTCTAAATTGCGCCCAAAAA-TGTCACCACATG
*
28916 ACCACTTCCA
64 ACCAATTCCA
*
28926 AATTGCTCCAAAAC-TGTCGTTGCAT
1 AATTG-TCCCAAACATGTCGTTGCAT
28951 AAATATTCTT
Statistics
Matches: 83, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
74 56 0.67
75 26 0.31
76 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (73 bp):
AATTGTCCCAAACATGTCGTTGCATGAGCACTTCTAAATTGCGCCCAAAAATGTCACCACATGAC
CAATTCCA
Found at i:30769 original size:17 final size:17
Alignment explanation
Indices: 30744--30777 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30734 CTATCATAGG
*
30744 AGGAGGTGGAGGCCTTA
1 AGGAAGTGGAGGCCTTA
30761 AGGAAGTGGAGGCCTTA
1 AGGAAGTGGAGGCCTTA
30778 CTAGAGGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.12, G:0.44, T:0.18
Consensus pattern (17 bp):
AGGAAGTGGAGGCCTTA
Found at i:31216 original size:21 final size:21
Alignment explanation
Indices: 31166--31224 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
31156 AGTAGTGCAG
*
31166 ACTTCTACTGATACAAGTGAT
1 ACTTCTACCGATACAAGTGAT
*
31187 AGTTCTACCGATACAAGTGAT
1 ACTTCTACCGATACAAGTGAT
* * *
31208 TCTTTTACCGAAACAAG
1 ACTTCTACCGATACAAG
31225 ACTTACTTCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAT
Found at i:36162 original size:16 final size:16
Alignment explanation
Indices: 36141--36171 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36131 ATAGTGTGAA
36141 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
36157 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
36172 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:37102 original size:37 final size:37
Alignment explanation
Indices: 37032--37102 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
37022 GCAACGACAT
* *
37032 TCCTGGGTGCAATTGAAGAATACCTATGTAGCGATAG
1 TCCTGGATGCAATTGAAGAATACCTATGCAGCGATAG
**
37069 TCCTGGATGCAATTGAAGAATATTTATGCAGCGA
1 TCCTGGATGCAATTGAAGAATACCTATGCAGCGA
37103 CTGTCTTGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (37 bp):
TCCTGGATGCAATTGAAGAATACCTATGCAGCGATAG
Found at i:37170 original size:37 final size:37
Alignment explanation
Indices: 37129--37215 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
37119 TCGGAAATAT
* *
37129 TCATGCAACGACAGTTTTGGGTGCAATCTGGAAGTGC
1 TCATGCAACGACAGTTTTGAGTGCAATCTAGAAGTGC
** *
37166 TCATGCGGC-AGTAGTTTTGAGTGCAATCTAGAAGTGC
1 TCATGCAACGA-CAGTTTTGAGTGCAATCTAGAAGTGC
* *
37203 TCATTCAATGACA
1 TCATGCAACGACA
37216 TTAGTAGTAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
36 1 0.03
37 36 0.95
38 1 0.03
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (37 bp):
TCATGCAACGACAGTTTTGAGTGCAATCTAGAAGTGC
Found at i:47242 original size:30 final size:28
Alignment explanation
Indices: 47180--47245 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
47170 AAAAAAAAAC
* * *
47180 TCAAATATCAATATAAAAAAACTCATATA
1 TCAAAT-TAAATATAAAAAAACACAAATA
47209 TCAAATTAAATATTAAAACAAACACAAATA
1 TCAAATTAAATA-TAAAA-AAACACAAATA
47239 TCAAATT
1 TCAAATT
47246 TAAAAAATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 5 0.16
29 11 0.34
30 16 0.50
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (28 bp):
TCAAATTAAATATAAAAAAACACAAATA
Found at i:47267 original size:51 final size:52
Alignment explanation
Indices: 47171--47279 Score: 141
Period size: 51 Copynumber: 2.1 Consensus size: 52
47161 TGACAAAAAA
* * * *
47171 AAAAAAAACTCAAATATCAATATAAAAAAACTCATATATCAAATTAAATATT
1 AAAACAAACACAAATATCAATATAAAAAAACTCAAATATCAAATTAAACATT
* *
47223 AAAACAAACACAAATATCAA-ATTTAAAAAA-TTAAATATCAAATTAAACATT
1 AAAACAAACACAAATATCAATA-TAAAAAAACTCAAATATCAAATTAAACATT
47274 AAAACA
1 AAAACA
47280 TATCAAATAG
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
51 25 0.50
52 25 0.50
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.25
Consensus pattern (52 bp):
AAAACAAACACAAATATCAATATAAAAAAACTCAAATATCAAATTAAACATT
Found at i:48467 original size:29 final size:29
Alignment explanation
Indices: 48435--48520 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 29
48425 ATTTAATGTG
*
48435 TAATTATATACTTG-AACTTTTATTTGGT
1 TAATTATATACTTGAAACTTTAATTTGGT
* * *
48463 ATAATTATACACGTGAAACTCTAATTGTGGT
1 -TAATTATATACTTGAAACTTTAATT-TGGT
*
48494 TCAAATATATACTTGAAACTTTAATTT
1 T-AATTATATACTTGAAACTTTAATTT
48521 TGATTTAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 12 0.26
30 10 0.22
31 24 0.52
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (29 bp):
TAATTATATACTTGAAACTTTAATTTGGT
Found at i:51074 original size:25 final size:26
Alignment explanation
Indices: 51046--51102 Score: 84
Period size: 24 Copynumber: 2.3 Consensus size: 26
51036 TTCTATCACC
51046 GAAAACAAGT-TTGAAATCTTTGC-A
1 GAAAACAAGTCTTGAAATCTTTGCAA
*
51070 GGAAA-AAGTCTTGAAATCTTTGCAA
1 GAAAACAAGTCTTGAAATCTTTGCAA
51095 GAAAACAA
1 GAAAACAA
51103 AGAAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 4 0.14
24 17 0.61
25 5 0.18
26 2 0.07
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.25
Consensus pattern (26 bp):
GAAAACAAGTCTTGAAATCTTTGCAA
Found at i:52306 original size:16 final size:15
Alignment explanation
Indices: 52278--52324 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
52268 AATATTGAAC
52278 TAAAATACAATAAAAA
1 TAAAATAC-ATAAAAA
52294 TAAAATAACATAACACAA
1 TAAAAT-ACATAA-A-AA
52312 -AAAATACATAAAA
1 TAAAATACATAAAA
52325 TTATACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 1 0.04
15 1 0.04
16 16 0.57
17 8 0.29
18 2 0.07
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAATACATAAAAA
Found at i:58421 original size:6 final size:6
Alignment explanation
Indices: 58396--58434 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
58386 ACAATTCATA
* * *
58396 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
58435 ATTTTGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (6 bp):
TCACTT
Found at i:61445 original size:12 final size:12
Alignment explanation
Indices: 61414--61449 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
61404 TGTAAAAAAA
*
61414 TAAAATATTTATG
1 TAAAA-ATTGATG
61427 TAAAAATTGATG
1 TAAAAATTGATG
61439 TAAAAATTGAT
1 TAAAAATTGAT
61450 ATCAAAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 17 0.77
13 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (12 bp):
TAAAAATTGATG
Found at i:63074 original size:20 final size:21
Alignment explanation
Indices: 63035--63135 Score: 61
Period size: 20 Copynumber: 4.9 Consensus size: 21
63025 GTTTGAAACA
*
63035 ATTTTAAAATCAAGTTAAAAT-T
1 ATTTT-AAA-CAAGTCAAAATCT
63057 ATTTTAAACAAGTCAAAA--T
1 ATTTTAAACAAGTCAAAATCT
**
63076 AAATTAAACCAAGTCAAAATCT
1 ATTTTAAA-CAAGTCAAAATCT
** * *
63098 -TTTT-AACACTTCAACATGT
1 ATTTTAAACAAGTCAAAATCT
63117 -TTTTCAAACAAGTCAAAAT
1 ATTTT-AAACAAGTCAAAAT
63136 AGCTTCAGGC
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
19 20 0.32
20 21 0.34
21 15 0.24
22 6 0.10
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (21 bp):
ATTTTAAACAAGTCAAAATCT
Found at i:70408 original size:15 final size:15
Alignment explanation
Indices: 70388--70420 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
70378 ATACAAATGT
70388 CACCCTTCCCCATGG
1 CACCCTTCCCCATGG
70403 CACCCTTCCCCATGG
1 CACCCTTCCCCATGG
70418 CAC
1 CAC
70421 GTACTTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.55, G:0.12, T:0.18
Consensus pattern (15 bp):
CACCCTTCCCCATGG
Found at i:80388 original size:17 final size:17
Alignment explanation
Indices: 80365--80405 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
80355 GTTAACTTGC
*
80365 TTACATTTTTATTAT-G
1 TTACATTTTAATTATCG
80381 TCTACATTTTAATTATCG
1 T-TACATTTTAATTATCG
80399 TTACATT
1 TTACATT
80406 AAATTTAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 19 0.86
18 2 0.09
ACGTcount: A:0.27, C:0.12, G:0.05, T:0.56
Consensus pattern (17 bp):
TTACATTTTAATTATCG
Found at i:83611 original size:20 final size:20
Alignment explanation
Indices: 83576--83644 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
83566 GTTTGAAACA
*
83576 ATTTTAAAATCAAGTTAAAAT
1 ATTTT-AAACCAAGTTAAAAT
83597 GATTTTAAA-CAAGTTAAAAT
1 -ATTTTAAACCAAGTTAAAAT
* * *
83617 AATTCAAACCAAGTCAAAAT
1 ATTTTAAACCAAGTTAAAAT
83637 AATTTTAA
1 -ATTTTAA
83645 CACATCAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 6 0.15
20 21 0.52
21 8 0.20
22 5 0.12
ACGTcount: A:0.52, C:0.09, G:0.06, T:0.33
Consensus pattern (20 bp):
ATTTTAAACCAAGTTAAAAT
Found at i:83751 original size:18 final size:18
Alignment explanation
Indices: 83713--83759 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
83703 ATTTTTGGCC
*
83713 AAATATCGATAATTCTTG
1 AAATATCGATAATCCTTG
83731 AAATATCGATAA-CCTTAG
1 AAATATCGATAATCCTT-G
*
83749 AAAAATCGATA
1 AAATATCGATA
83760 CCAAACTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 23 0.88
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (18 bp):
AAATATCGATAATCCTTG
Found at i:87228 original size:14 final size:15
Alignment explanation
Indices: 87203--87231 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
87193 AGTAATCACG
87203 AATAAGAATATAAAA
1 AATAAGAATATAAAA
87218 AATAA-AATATAAAA
1 AATAAGAATATAAAA
87232 TATTAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AATAAGAATATAAAA
Found at i:92986 original size:68 final size:68
Alignment explanation
Indices: 92867--93005 Score: 242
Period size: 68 Copynumber: 2.0 Consensus size: 68
92857 ATATAAAACC
*
92867 AATGCGGAAATAAAGATAAGTGACACAATGATGTCAACTCTATTAAGAGTCCTATTTCCAACACA
1 AATGCGGAAATAAAGATAAGTGACACAATAATGTCAACTCTATTAAGAGTCCTATTTCCAACACA
92932 TTG
66 TTG
* * *
92935 AATGTGGAATTAAAGATAAGTGACGCAATAATGTCAACTCTATTAAGAGTCCTATTTCCAACACA
1 AATGCGGAAATAAAGATAAGTGACACAATAATGTCAACTCTATTAAGAGTCCTATTTCCAACACA
93000 TTG
66 TTG
93003 AAT
1 AAT
93006 ACAGCACCAT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.40, C:0.17, G:0.16, T:0.28
Consensus pattern (68 bp):
AATGCGGAAATAAAGATAAGTGACACAATAATGTCAACTCTATTAAGAGTCCTATTTCCAACACA
TTG
Found at i:97007 original size:23 final size:23
Alignment explanation
Indices: 96963--97007 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
96953 AATTCGTCTT
* * * *
96963 ATTTATTTTTATTTTATTTCAAG
1 ATTTAATTTGATTGTATCTCAAG
96986 ATTTAATTTGATTGTATCTCAA
1 ATTTAATTTGATTGTATCTCAA
97008 TTTAAGGGAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (23 bp):
ATTTAATTTGATTGTATCTCAAG
Found at i:97798 original size:73 final size:74
Alignment explanation
Indices: 97688--97824 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 74
97678 GAAATGTTTT
* * * **
97688 GTGTAATTATACAAAACATTACGATAGTTGTAATAATTTCTATAATT-GAGT-ATGTTTTGTATA
1 GTGTAATGATACAAAACATTACAAAAGTAATAATAATTTCTATAATTCG-GTAATGTTTTGTATA
97751 ATTCTCAATA
65 ATTCTCAATA
* * *
97761 GTGTAATGATACAAAACATTGCAAAAGTAATACTAATTTGTATAATTCGGTAATGTTTTGTATA
1 GTGTAATGATACAAAACATTACAAAAGTAATAATAATTTCTATAATTCGGTAATGTTTTGTATA
97825 GTTGAAGTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
73 41 0.76
74 13 0.24
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (74 bp):
GTGTAATGATACAAAACATTACAAAAGTAATAATAATTTCTATAATTCGGTAATGTTTTGTATAA
TTCTCAATA
Found at i:102947 original size:3 final size:3
Alignment explanation
Indices: 102934--102987 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
102924 CTTTGATTTG
*
102934 AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
102982 GAT AAT
1 AAT AAT
102988 GATGATGATG
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:102992 original size:3 final size:3
Alignment explanation
Indices: 102980--103023 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
102970 AATAATAATA
* * * *
102980 ATG ATA ATG ATG ATG ATG GTG CTG ATG ATG ATG CTG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
103024 AATGTTAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:102995 original size:12 final size:12
Alignment explanation
Indices: 102980--103023 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
102970 AATAATAATA
* *
102980 ATGATAATGATG
1 ATGATGATGCTG
*
102992 ATGATGGTGCTG
1 ATGATGATGCTG
103004 ATGATGATGCTG
1 ATGATGATGCTG
103016 ATGATGAT
1 ATGATGAT
103024 AATGTTAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.34
Consensus pattern (12 bp):
ATGATGATGCTG
Found at i:103005 original size:15 final size:15
Alignment explanation
Indices: 102986--103023 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
102976 AATAATGATA
*
102986 ATGATGATGATGGTG
1 ATGATGATGATGCTG
*
103001 CTGATGATGATGCTG
1 ATGATGATGATGCTG
103016 ATGATGAT
1 ATGATGAT
103024 AATGTTAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.34, T:0.34
Consensus pattern (15 bp):
ATGATGATGATGCTG
Found at i:109621 original size:57 final size:57
Alignment explanation
Indices: 109559--109670 Score: 181
Period size: 57 Copynumber: 2.0 Consensus size: 57
109549 AATGCATGAA
* *
109559 ATGTAAAATTGATCAAGTGTAAAAGGGTAGAAAT-GATTCACTGATTCTGTAAAGTGC
1 ATGTAAAATTAATCAAGTGTAAAAGGGTAGAAATAG-TTCACTAATTCTGTAAAGTGC
*
109616 ATGTAAAATTAATCAAGTGTAAAAGGGTAGAAATAGTTCACTAATTTTGTAAAGT
1 ATGTAAAATTAATCAAGTGTAAAAGGGTAGAAATAGTTCACTAATTCTGTAAAGT
109671 TGCACTGCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
57 50 0.98
58 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.21, T:0.31
Consensus pattern (57 bp):
ATGTAAAATTAATCAAGTGTAAAAGGGTAGAAATAGTTCACTAATTCTGTAAAGTGC
Found at i:111104 original size:16 final size:17
Alignment explanation
Indices: 111083--111130 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 17
111073 TTATCAAAAA
111083 TTTCTTTCTTTTTCT-T
1 TTTCTTTCTTTTTCTAT
*
111099 TTTCTTCCTTTTTCTCAT
1 TTTCTTTCTTTTTCT-AT
*
111117 TTTGTTTCTTTTTC
1 TTTCTTTCTTTTTC
111131 AAATGACTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 14 0.52
18 13 0.48
ACGTcount: A:0.02, C:0.21, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTCTTTTTCTAT
Found at i:113097 original size:20 final size:20
Alignment explanation
Indices: 113051--113098 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
113041 TAGTGCTATG
* *
113051 TGTTGAAGGCATGATGTGAC
1 TGTTGATGGCATGATGCGAC
*
113071 TGTTGATGGCATGATGCGGC
1 TGTTGATGGCATGATGCGAC
113091 TGTTGATG
1 TGTTGATG
113099 AAATGGAACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.10, G:0.38, T:0.33
Consensus pattern (20 bp):
TGTTGATGGCATGATGCGAC
Found at i:126791 original size:23 final size:23
Alignment explanation
Indices: 126730--126796 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
126720 TTCAGTCAAA
* *
126730 GTTAATGGGTCGGGTTAGGTTCG
1 GTTAATAGGTCGGGTCAGGTTCG
* * *
126753 ATCAATAGGTCAGGTCAGGTTCG
1 GTTAATAGGTCGGGTCAGGTTCG
* *
126776 GTTAATAGGTTGGGTCGGGTT
1 GTTAATAGGTCGGGTCAGGTT
126797 TAGTCAATGG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.10, G:0.39, T:0.33
Consensus pattern (23 bp):
GTTAATAGGTCGGGTCAGGTTCG
Found at i:127878 original size:24 final size:24
Alignment explanation
Indices: 127844--127891 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
127834 TCTGAGTTTT
127844 GTATACACCATTAGGCATACTATG
1 GTATACACCATTAGGCATACTATG
*
127868 GTATACGCCATTAGGCATACTATG
1 GTATACACCATTAGGCATACTATG
127892 TGATAATGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (24 bp):
GTATACACCATTAGGCATACTATG
Found at i:129333 original size:21 final size:21
Alignment explanation
Indices: 129307--129349 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
129297 TAGTGTGTCT
129307 AGAGGTGGTCAAGTTGTTGGC
1 AGAGGTGGTCAAGTTGTTGGC
129328 AGAGGTGGTCAAGTTGTTGGC
1 AGAGGTGGTCAAGTTGTTGGC
129349 A
1 A
129350 CCATTACCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.09, G:0.42, T:0.28
Consensus pattern (21 bp):
AGAGGTGGTCAAGTTGTTGGC
Found at i:142446 original size:21 final size:23
Alignment explanation
Indices: 142422--142463 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
142412 TAAGGGTAAT
142422 TTTGTA-AAAAT-ATCAAAAAAA
1 TTTGTATAAAATGATCAAAAAAA
*
142443 TTTGTATAAAATGATTAAAAA
1 TTTGTATAAAATGATCAAAAA
142464 TTCATGTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 5 0.28
23 7 0.39
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (23 bp):
TTTGTATAAAATGATCAAAAAAA
Found at i:146210 original size:22 final size:22
Alignment explanation
Indices: 146185--146243 Score: 91
Period size: 22 Copynumber: 2.7 Consensus size: 22
146175 AAAAAAATAT
146185 TCAATTAAATTGGCACAATCAA
1 TCAATTAAATTGGCACAATCAA
**
146207 TCAATTAAATTGGTGCAATCAA
1 TCAATTAAATTGGCACAATCAA
*
146229 TCAATTATATTGGCA
1 TCAATTAAATTGGCA
146244 TATTACATCC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (22 bp):
TCAATTAAATTGGCACAATCAA
Found at i:150504 original size:2 final size:2
Alignment explanation
Indices: 150497--150521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
150487 TAGTATACTC
150497 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
150522 AAAGGATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:150602 original size:24 final size:24
Alignment explanation
Indices: 150573--150635 Score: 94
Period size: 24 Copynumber: 2.6 Consensus size: 24
150563 AAAGGGTTAC
150573 AAGAAGATGAAAGGTG-AAGAGTT-
1 AAGAAGATGAAAGGTGAAAG-GTTG
150596 AAGGAAGATGAAAGGTGAAAGGTTG
1 AA-GAAGATGAAAGGTGAAAGGTTG
150621 AAGAAGATGAAAGGT
1 AAGAAGATGAAAGGT
150636 TGAACATCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
23 2 0.05
24 30 0.81
25 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.37, T:0.16
Consensus pattern (24 bp):
AAGAAGATGAAAGGTGAAAGGTTG
Found at i:162844 original size:6 final size:6
Alignment explanation
Indices: 162833--162878 Score: 56
Period size: 6 Copynumber: 7.7 Consensus size: 6
162823 AGGCTCCCAA
* * * *
162833 AAATGG AAATGG AAATGG AAATGA AAATGA AAATGA AAATAG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
162879 TTGCAACCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.22, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:162850 original size:12 final size:12
Alignment explanation
Indices: 162832--162878 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
162822 TAGGCTCCCA
162832 AAAATGGAAATG
1 AAAATGGAAATG
*
162844 GAAATGGAAATG
1 AAAATGGAAATG
*
162856 AAAATGAAAATG
1 AAAATGGAAATG
*
162868 AAAATAGAAAT
1 AAAATGGAAAT
162879 TTGCAACCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:163090 original size:25 final size:26
Alignment explanation
Indices: 163036--163090 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
163026 TACCAAGGAA
*
163036 AAAATTGTCAAATTTTTACTTGAAGT
1 AAAATCGTCAAATTTTTACTTGAAGT
* *
163062 -AAATCGTCAAATTTTTGC-TGGAGT
1 AAAATCGTCAAATTTTTACTTGAAGT
163086 AAAAT
1 AAAAT
163091 AGGGATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (26 bp):
AAAATCGTCAAATTTTTACTTGAAGT
Found at i:166822 original size:20 final size:18
Alignment explanation
Indices: 166781--166847 Score: 74
Period size: 15 Copynumber: 3.9 Consensus size: 18
166771 GATAAAGATA
166781 CAAGAAGAAGCAAAAAAG
1 CAAGAAGAAGCAAAAAAG
166799 -AAGAAGAAAGCAGAAAAAG
1 CAAGAAG-AAGCA-AAAAAG
166818 CAAG-AGAAG-AAAAAAG
1 CAAGAAGAAGCAAAAAAG
166834 -AA-AAGAAG-AAAAAA
1 CAAGAAGAAGCAAAAAA
166848 ACCTTGGTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 11
0.80 0.00 0.20
Matches are distributed among these distances:
15 13 0.29
16 6 0.13
17 7 0.16
18 8 0.18
19 8 0.18
20 3 0.07
ACGTcount: A:0.72, C:0.06, G:0.22, T:0.00
Consensus pattern (18 bp):
CAAGAAGAAGCAAAAAAG
Found at i:166830 original size:15 final size:14
Alignment explanation
Indices: 166782--166846 Score: 53
Period size: 14 Copynumber: 4.6 Consensus size: 14
166772 ATAAAGATAC
*
166782 AAGAAGAAGCAAAA-
1 AAGAAAAAG-AAAAG
*
166796 AAGAAGAAG-AAAG
1 AAGAAAAAGAAAAG
* *
166809 CAGAAAAAGCAAGAG
1 AAGAAAAAG-AAAAG
166824 AAGAAAAAAGAAAAG
1 AAG-AAAAAGAAAAG
166839 AAGAAAAA
1 AAGAAAAA
166847 AACCTTGGTA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
12 3 0.07
13 7 0.17
14 14 0.33
15 12 0.29
16 6 0.14
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (14 bp):
AAGAAAAAGAAAAG
Found at i:166848 original size:17 final size:18
Alignment explanation
Indices: 166782--166848 Score: 61
Period size: 17 Copynumber: 3.8 Consensus size: 18
166772 ATAAAGATAC
166782 AAGAAGAAGCAAAAAAGAA
1 AAGAAGAAG-AAAAAAGAA
* *
166801 GAAGAAAGCAG-AAAAAG-C
1 -AAG-AAGAAGAAAAAAGAA
166819 AAG-AGAAGAAAAAAGAA
1 AAGAAGAAGAAAAAAGAA
166836 AAGAAGAA-AAAAA
1 AAGAAGAAGAAAAA
166849 CCTTGGTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
15 4 0.10
16 6 0.15
17 11 0.28
18 4 0.10
19 6 0.15
20 3 0.08
21 5 0.13
ACGTcount: A:0.73, C:0.04, G:0.22, T:0.00
Consensus pattern (18 bp):
AAGAAGAAGAAAAAAGAA
Done.