Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013176.1 Kokia drynarioides strain JFW-HI SEQ_128195, 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: 106579
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 45 characters in sequence are not A, C, G, or T
Found at i:4858 original size:17 final size:17
Alignment explanation
Indices: 4836--4870 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4826 TTTTAAAATA
4836 TTAAAAA-AATTATATTT
1 TTAAAAATAATTA-ATTT
4853 TTAAAAATAATTAATTT
1 TTAAAAATAATTAATTT
4870 T
1 T
4871 CGCTGATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAAAATAATTAATTT
Found at i:5524 original size:18 final size:18
Alignment explanation
Indices: 5501--5542 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
5491 AATTTTTAAT
5501 TTTTTAAAATTTATTAGA
1 TTTTTAAAATTTATTAGA
* * *
5519 TTTTTATATTTTATTATA
1 TTTTTAAAATTTATTAGA
5537 TTTTTA
1 TTTTTA
5543 TAAGTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTAAAATTTATTAGA
Found at i:5543 original size:18 final size:18
Alignment explanation
Indices: 5510--5544 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5500 TTTTTTAAAA
5510 TTTATTAGATTTTTATAT
1 TTTATTAGATTTTTATAT
*
5528 TTTATTATATTTTTATA
1 TTTATTAGATTTTTATA
5545 AGTTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTATTAGATTTTTATAT
Found at i:5789 original size:9 final size:9
Alignment explanation
Indices: 5777--5922 Score: 61
Period size: 9 Copynumber: 16.0 Consensus size: 9
5767 TTTTTGTTAT
5777 TTTTTATAA
1 TTTTTATAA
5786 TTTTTATAA
1 TTTTTATAA
*
5795 GTTTATATCAA
1 -TTTTTAT-AA
* * *
5806 TCTTAATAC
1 TTTTTATAA
5815 TTTTTAT--
1 TTTTTATAA
*
5822 TTTTATAGAA
1 TTTT-TATAA
*
5832 TTTTAATACA
1 TTTTTATA-A
5842 -TTTTATAA
1 TTTTTATAA
** *
5850 AATTTAAATA
1 TTTTTATA-A
5860 TTTTTATTAA
1 TTTTTA-TAA
5870 TTTTTTATAA
1 -TTTTTATAA
*
5880 TTTATTAGAA
1 TTT-TTATAA
5890 -TTTTATAA
1 TTTTTATAA
*
5898 --TTTATCA
1 TTTTTATAA
**
5905 TGCTTATAA
1 TTTTTATAA
5914 TTTTTATAA
1 TTTTTATAA
5923 GATTATATAA
Statistics
Matches: 101, Mismatches: 23, Indels: 26
0.67 0.15 0.17
Matches are distributed among these distances:
7 10 0.10
8 8 0.08
9 45 0.45
10 29 0.29
11 9 0.09
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:5864 original size:19 final size:19
Alignment explanation
Indices: 5819--5866 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
5809 TAATACTTTT
* *
5819 TATTTTTATAGAATTTTAA
1 TATTTTTATAAAATTTAAA
*
5838 TACATTTTATAAAATTTAAA
1 TA-TTTTTATAAAATTTAAA
5858 TATTTTTAT
1 TATTTTTAT
5867 TAATTTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
TATTTTTATAAAATTTAAA
Found at i:5864 original size:45 final size:45
Alignment explanation
Indices: 5762--5867 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 45
5752 TAAATCCAAA
* * * *
5762 TTAAATTTTTGTTATTTTTTATAATTTTTATAAGTTTATATCAATC
1 TTAAATATTT-TTATTTTTTAGAATTTTAATAAGTTTATATAAATC
*
5808 TT-AATACTTTTTATTTTTATAGAATTTTAATACATTTTATA-AAAT-
1 TTAAATA-TTTTTATTTTT-TAGAATTTTAATA-AGTTTATATAAATC
5853 TTAAATATTTTTATT
1 TTAAATATTTTTATT
5868 AATTTTTTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
45 21 0.41
46 23 0.45
47 7 0.14
ACGTcount: A:0.34, C:0.04, G:0.03, T:0.59
Consensus pattern (45 bp):
TTAAATATTTTTATTTTTTAGAATTTTAATAAGTTTATATAAATC
Found at i:6844 original size:12 final size:12
Alignment explanation
Indices: 6827--6873 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
6817 ATCATTAATA
6827 AATAAACGAGTC
1 AATAAACGAGTC
6839 AATAAACGAG-C
1 AATAAACGAGTC
* *
6850 TTATAAACGAGCC
1 -AATAAACGAGTC
6863 AATAAACGAGT
1 AATAAACGAGT
6874 TTGCTCGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 1 0.03
12 28 0.93
13 1 0.03
ACGTcount: A:0.49, C:0.17, G:0.17, T:0.17
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:10426 original size:15 final size:15
Alignment explanation
Indices: 10403--10433 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10393 GAGAAAAATC
10403 TTTAATTTTTTATTT
1 TTTAATTTTTTATTT
*
10418 TTTATTTTTTTATTT
1 TTTAATTTTTTATTT
10433 T
1 T
10434 CTCTTGTACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTAATTTTTTATTT
Found at i:11177 original size:20 final size:21
Alignment explanation
Indices: 11154--11192 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11144 TTATTAACCT
11154 TGAA-ATATTTTATTTTTTCC
1 TGAATATATTTTATTTTTTCC
* *
11174 TGAATTTTTTTTATTTTTT
1 TGAATATATTTTATTTTTT
11193 TAAATCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (21 bp):
TGAATATATTTTATTTTTTCC
Found at i:12426 original size:18 final size:19
Alignment explanation
Indices: 12386--12428 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
12376 AAATTTTAGA
12386 ATTTTTCTTAATTTTTGCT
1 ATTTTTCTTAATTTTTGCT
*
12405 ATTTTT-TTTATTTTT-CT
1 ATTTTTCTTAATTTTTGCT
12422 CATTTTT
1 -ATTTTT
12429 GATTTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 2 0.09
18 14 0.64
19 6 0.27
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.74
Consensus pattern (19 bp):
ATTTTTCTTAATTTTTGCT
Found at i:12441 original size:27 final size:27
Alignment explanation
Indices: 12386--12444 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 27
12376 AAATTTTAGA
12386 ATTTTTCTTAATTTTTGCTATTTTTTTT
1 ATTTTTCTTAATTTTTGC-ATTTTTTTT
*
12414 ATTTTTC-TCATTTTTG-ATTTTTAATTT
1 ATTTTTCTTAATTTTTGCATTTTT--TTT
12441 ATTT
1 ATTT
12445 CAGCATACCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
25 6 0.21
27 15 0.54
28 7 0.25
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (27 bp):
ATTTTTCTTAATTTTTGCATTTTTTTT
Found at i:18933 original size:24 final size:26
Alignment explanation
Indices: 18885--18934 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
18875 TTCTTGATTG
*
18885 CATATTTACTAATTTTAAAAGTAATTA
1 CATATTTACTAA-TTTAAAAATAATTA
18912 CATATTTACT-A-TTAAAAATAATT
1 CATATTTACTAATTTAAAAATAATT
18935 TAATATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 11 0.50
26 1 0.05
27 10 0.45
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (26 bp):
CATATTTACTAATTTAAAAATAATTA
Found at i:26280 original size:3 final size:3
Alignment explanation
Indices: 26274--26315 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
26264 ACTCTTCCAA
*
26274 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
26316 CAAACAGCTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:27198 original size:13 final size:13
Alignment explanation
Indices: 27176--27209 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
27166 GATTGATATT
*
27176 TTAATATTTATAA
1 TTAATTTTTATAA
27189 TTAATTTTTATAA
1 TTAATTTTTATAA
27202 TATAATTT
1 T-TAATTT
27210 CAATAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTAATTTTTATAA
Found at i:29797 original size:16 final size:17
Alignment explanation
Indices: 29773--29829 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 17
29763 AATATTTATA
29773 TTTGAATTAAATTAGAT
1 TTTGAATTAAATTAGAT
*
29790 TTTG-ATTAAAAT-G--
1 TTTGAATTAAATTAGAT
*
29803 TTTGAATTAAATGAGAT
1 TTTGAATTAAATTAGAT
29820 TTTG-ATTAAA
1 TTTGAATTAAA
29830 AATACGATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
13 4 0.12
14 6 0.18
15 2 0.06
16 13 0.39
17 8 0.24
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.46
Consensus pattern (17 bp):
TTTGAATTAAATTAGAT
Found at i:29807 original size:30 final size:30
Alignment explanation
Indices: 29773--29830 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
29763 AATATTTATA
*
29773 TTTGAATTAAATTAGATTTTGATTAAAATG
1 TTTGAATTAAATGAGATTTTGATTAAAATG
29803 TTTGAATTAAATGAGATTTTGATTAAAA
1 TTTGAATTAAATGAGATTTTGATTAAAA
29831 ATACGATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (30 bp):
TTTGAATTAAATGAGATTTTGATTAAAATG
Found at i:38141 original size:16 final size:15
Alignment explanation
Indices: 38120--38172 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
38110 TTAAATTTTA
38120 AAAAATTCAAAAATAT
1 AAAAATTCAAAAA-AT
38136 AAAAATTCAAAAAATT
1 AAAAATTCAAAAAA-T
*
38152 AAAATTATTAAAAAAAT
1 AAAA--ATTCAAAAAAT
38169 AAAA
1 AAAA
38173 TTTATTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
15 1 0.03
16 18 0.55
17 5 0.15
18 9 0.27
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAAATTCAAAAAAT
Found at i:38155 original size:8 final size:8
Alignment explanation
Indices: 38117--38172 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
38107 TAATTAAATT
38117 TTAAAAAA
1 TTAAAAAA
*
38125 TTCAAAAA
1 TTAAAAAA
38133 -TATAAAAA
1 TTA-AAAAA
38141 TTCAAAAAA
1 TT-AAAAAA
*
38150 TTAAAATTA
1 TTAAAA-AA
38159 TTAAAAAA
1 TTAAAAAA
*
38167 ATAAAA
1 TTAAAA
38173 TTTATTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 1 0.03
8 22 0.56
9 15 0.38
10 1 0.03
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.27
Consensus pattern (8 bp):
TTAAAAAA
Found at i:38202 original size:24 final size:25
Alignment explanation
Indices: 38160--38210 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
38150 TTAAAATTAT
*
38160 TAAAAAAATAAAATTTATT-TAATAA
1 TAAAAAAATAAAATATATTAT-ATAA
*
38185 TAAAAATATAAAA-ATATTATATAA
1 TAAAAAAATAAAATATATTATATAA
38209 TA
1 TA
38211 TTTAGAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAAAAATAAAATATATTATATAA
Found at i:39076 original size:35 final size:35
Alignment explanation
Indices: 39037--39114 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
39027 TTTAAATTTA
39037 AGAAGAAAAAGA-ACTAAATTCTTAAAAATAAAAAT
1 AGAAGAAAAAGATA-TAAATTCTTAAAAATAAAAAT
* *
39072 AGAAGTAAAAGATATAAATTCTTAAAAATAAAAGT
1 AGAAGAAAAAGATATAAATTCTTAAAAATAAAAAT
39107 AGAAGAAA
1 AGAAGAAA
39115 TAAATTTGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.64, C:0.04, G:0.12, T:0.21
Consensus pattern (35 bp):
AGAAGAAAAAGATATAAATTCTTAAAAATAAAAAT
Found at i:39101 original size:29 final size:29
Alignment explanation
Indices: 39065--39120 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
39055 TTCTTAAAAA
* *
39065 TAAAAATAGAAGTAAAAGATATAAATTCT
1 TAAAAATAAAAGTAAAAGAAATAAATTCT
*
39094 TAAAAATAAAAGTAGAAGAAATAAATT
1 TAAAAATAAAAGTAAAAGAAATAAATT
39121 TGAAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.11, T:0.25
Consensus pattern (29 bp):
TAAAAATAAAAGTAAAAGAAATAAATTCT
Found at i:44006 original size:30 final size:30
Alignment explanation
Indices: 43952--44068 Score: 110
Period size: 32 Copynumber: 3.8 Consensus size: 30
43942 AAAGGGATCC
** *
43952 AATTTTTTTTTCAGTTTTTAAAGGGCTTAAA
1 AATTTTTTTTTCAACTTTTAAGGGGC-TAAA
* * *
43983 AATTATTTTTTCAGCTTTTAAGGGGTCCAAAA
1 AATTTTTTTTTCAACTTTTAAGGGG--CTAAA
* **
44015 AATTGTTTTACCAACTTTTAAGGGGCT-AA
1 AATTTTTTTTTCAACTTTTAAGGGGCTAAA
44044 AATTTTTTTTTCTAACTTTTAAGGG
1 AATTTTTTTTTC-AACTTTTAAGGG
44069 ATCCAAAATT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
29 11 0.15
30 13 0.18
31 22 0.31
32 24 0.34
33 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.46
Consensus pattern (30 bp):
AATTTTTTTTTCAACTTTTAAGGGGCTAAA
Found at i:44077 original size:31 final size:30
Alignment explanation
Indices: 43943--44078 Score: 98
Period size: 31 Copynumber: 4.5 Consensus size: 30
43933 TCAAGGCTGA
**
43943 AAGGGATCC--AATTTTTTTTTCAGTTTTT
1 AAGGGATCCAAAATTTTTTTTTCAACTTTT
* ** * *
43971 AAAGGGCTTAAAAATTATTTTTTCAGCTTTT
1 -AAGGGATCCAAAATTTTTTTTTCAACTTTT
* * **
44002 AAGGGGTCCAAAAAATTGTTTTACCAACTTTT
1 AAGGGATCC--AAAATTTTTTTTTCAACTTTT
* *
44034 AAGGG-GCTAAAATTTTTTTTTCTAACTTTT
1 AAGGGATCCAAAATTTTTTTTTC-AACTTTT
44064 AAGGGATCCAAAATT
1 AAGGGATCCAAAATT
44079 CAATTTATTA
Statistics
Matches: 82, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
29 17 0.21
30 18 0.22
31 25 0.30
32 22 0.27
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.43
Consensus pattern (30 bp):
AAGGGATCCAAAATTTTTTTTTCAACTTTT
Found at i:50501 original size:14 final size:16
Alignment explanation
Indices: 50482--50513 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
50472 AACTTTGAAA
50482 ATTGAATA-ATC-CGT
1 ATTGAATATATCTCGT
50496 ATTGAATATATCTCGT
1 ATTGAATATATCTCGT
50512 AT
1 AT
50514 CCAACAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (16 bp):
ATTGAATATATCTCGT
Found at i:66757 original size:60 final size:58
Alignment explanation
Indices: 66653--66838 Score: 169
Period size: 60 Copynumber: 3.1 Consensus size: 58
66643 TAAATTTAGA
* * * * * *
66653 TACCAAATTGAATCTAAAAAAAGCTTAGGTATCAAATTAGGAAAAAATG-CTAAGTTCAGG
1 TACCAAATTGAGTC--AAAAAAGTTTAGGTACCAAATCAAGAAAAAATGTC-AAGTTCAAG
* * *
66713 TACCGAATTGGGTCCAACAAAAGTTTAGGTACCAAATCAAGAAAAAGTGTCAAGTTCAAG
1 TACCAAATTGAGT-CAA-AAAAGTTTAGGTACCAAATCAAGAAAAAATGTCAAGTTCAAG
* * * * * *
66773 TACCAAATTGAGTTAAAAAAGTTTAGGTACTAAATTTAA-AAAAAATATCAAATTTAAG
1 TACCAAATTGAGTCAAAAAAGTTTAGGTACCAAA-TCAAGAAAAAATGTCAAGTTCAAG
66831 TACCAAAT
1 TACCAAAT
66839 ATTATATTAA
Statistics
Matches: 104, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
58 40 0.38
59 7 0.07
60 55 0.53
61 2 0.02
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (58 bp):
TACCAAATTGAGTCAAAAAAGTTTAGGTACCAAATCAAGAAAAAATGTCAAGTTCAAG
Found at i:69659 original size:40 final size:40
Alignment explanation
Indices: 69604--69684 Score: 153
Period size: 40 Copynumber: 2.0 Consensus size: 40
69594 GAACACTCTT
*
69604 TTGAAGTTTGAACAATCAAAAGAAAATAAAATAAGTGTCC
1 TTGAAGTTTGAACAATCAAAAGAAAATAAAATAAGAGTCC
69644 TTGAAGTTTGAACAATCAAAAGAAAATAAAATAAGAGTCC
1 TTGAAGTTTGAACAATCAAAAGAAAATAAAATAAGAGTCC
69684 T
1 T
69685 CATACATTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.25
Consensus pattern (40 bp):
TTGAAGTTTGAACAATCAAAAGAAAATAAAATAAGAGTCC
Found at i:71976 original size:31 final size:31
Alignment explanation
Indices: 71938--71998 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
71928 GGAAACATAT
71938 AAGCAATTTAAAACTTTTTGCAAATTCAGAC
1 AAGCAATTTAAAACTTTTTGCAAATTCAGAC
71969 AAGCAATTTAAAACTTTTTGCAAATTCAGA
1 AAGCAATTTAAAACTTTTTGCAAATTCAGA
71999 AATTACCTGA
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:0.43, C:0.15, G:0.10, T:0.33
Consensus pattern (31 bp):
AAGCAATTTAAAACTTTTTGCAAATTCAGAC
Found at i:77391 original size:2 final size:2
Alignment explanation
Indices: 77384--77419 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
77374 ACTACTTAAA
77384 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
77420 TTGACCAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:79792 original size:20 final size:20
Alignment explanation
Indices: 79769--79811 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
79759 TTTAAGAAAG
* *
79769 TTTTAAATAATTTTATGTTT
1 TTTTAAAGAATTTTAGGTTT
**
79789 TTTTTTAGAATTTTAGGTTT
1 TTTTAAAGAATTTTAGGTTT
79809 TTT
1 TTT
79812 GGATTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.67
Consensus pattern (20 bp):
TTTTAAAGAATTTTAGGTTT
Found at i:80553 original size:19 final size:19
Alignment explanation
Indices: 80526--80562 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
80516 GGGGTTTCTA
* *
80526 GATTTTTAATTATTTTTTG
1 GATTATTAATGATTTTTTG
80545 GATTATTAATGATTTTTT
1 GATTATTAATGATTTTTT
80563 TAAAAATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.65
Consensus pattern (19 bp):
GATTATTAATGATTTTTTG
Found at i:83402 original size:2 final size:2
Alignment explanation
Indices: 83395--83427 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
83385 ATAAAGTAAG
83395 TA TA TA 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
83428 CCATATCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:83534 original size:14 final size:15
Alignment explanation
Indices: 83497--83539 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
83487 CAGGATCAAC
83497 AAATTGATAAAGAAA
1 AAATTGATAAAGAAA
**
83512 TTATT-ATAAA-AAA
1 AAATTGATAAAGAAA
83525 AAATTGATAAAGAAA
1 AAATTGATAAAGAAA
83540 TACTTCGCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (15 bp):
AAATTGATAAAGAAA
Found at i:84833 original size:78 final size:78
Alignment explanation
Indices: 84698--84854 Score: 269
Period size: 78 Copynumber: 2.0 Consensus size: 78
84688 TAATTATATT
* **
84698 ACTTGTAAAACCGTTGATTGAGTTGGTAATACGAATTAAGTAAACACCAAATCAATTAGAAAACT
1 ACTTGTAAAACCGTTGATTGAGTTGATAATACGAATTAAGTAAACACCAAATCAATTAGAAAAAG
84763 ATTAAAAAAATAA
66 ATTAAAAAAATAA
* *
84776 ACTTGTAAAACCGTTGATTGAGTTGATAATACGAATTAAGTAAACACCTAATTAATTAGAAAAAG
1 ACTTGTAAAACCGTTGATTGAGTTGATAATACGAATTAAGTAAACACCAAATCAATTAGAAAAAG
84841 ATTAAAAAAATAA
66 ATTAAAAAAATAA
84854 A
1 A
84855 ACTTTTAAGA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 74 1.00
ACGTcount: A:0.50, C:0.10, G:0.13, T:0.27
Consensus pattern (78 bp):
ACTTGTAAAACCGTTGATTGAGTTGATAATACGAATTAAGTAAACACCAAATCAATTAGAAAAAG
ATTAAAAAAATAA
Found at i:87588 original size:21 final size:21
Alignment explanation
Indices: 87563--87606 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
87553 CCTTAATGTC
* *
87563 TTTTTAGTCATCTATTATAAT
1 TTTTTAGCCATCTACTATAAT
*
87584 TTTTTAGCCATCTACTGTAAT
1 TTTTTAGCCATCTACTATAAT
87605 TT
1 TT
87607 GTTATTGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTTAGCCATCTACTATAAT
Found at i:89076 original size:4 final size:4
Alignment explanation
Indices: 89069--89094 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
89059 TATAGTTAGT
89069 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
89095 AATAAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:98537 original size:3 final size:3
Alignment explanation
Indices: 98529--98570 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
98519 CTCATCGTAT
98529 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
98571 ATGTCCTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:101961 original size:58 final size:58
Alignment explanation
Indices: 101877--101994 Score: 175
Period size: 58 Copynumber: 2.0 Consensus size: 58
101867 AAGAAGTTGC
* * * *
101877 TTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTTAAAATATTTGGGTTTAGT
1 TTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
*
101935 TTATGAGTATT-TTTGAAGAATGAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
1 TTATGAGTATTATTT-AAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
101993 TT
1 TT
101995 GTTGATGAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
57 3 0.06
58 51 0.94
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.48
Consensus pattern (58 bp):
TTATGAGTATTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGGTTTAGT
Found at i:103845 original size:31 final size:30
Alignment explanation
Indices: 103791--103874 Score: 80
Period size: 30 Copynumber: 2.6 Consensus size: 30
103781 TTTTATAAAA
*
103791 TTTTAAATTAATAATGATAAAATTGTAATTTGA-C
1 TTTTAAA--AATAAT-A-AAAATT-TAATTTAATC
*
103825 TTTCTAAAAATAATAAAAATTTGATTTAATC
1 TTT-TAAAAATAATAAAAATTTAATTTAATC
*
103856 TTTTAAAAATTATAAAAAT
1 TTTTAAAAATAATAAAAAT
103875 ATAAATAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
30 21 0.47
31 10 0.22
32 1 0.02
33 6 0.13
34 3 0.07
35 4 0.09
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTTAAAAATAATAAAAATTTAATTTAATC
Found at i:105051 original size:96 final size:95
Alignment explanation
Indices: 104877--105052 Score: 221
Period size: 96 Copynumber: 1.8 Consensus size: 95
104867 AGGATATTTG
** * * * *
104877 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGGAGAT
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCCGAAAT
*
104942 AAGGAAACGTTGCCTCGATTAAGGGTATTCA
66 AAAGAAAC-TTGCCTCGATTAAGGGTATTCA
* *
104973 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGCAA-ATTTTCGAAACCCGAAA
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATA-TTTCGAAACCCGAAA
105037 TGAAAGAATA-TTGCCT
65 T-AAAGAA-ACTTGCCT
105053 TGATATTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
95 1 0.01
96 61 0.90
97 5 0.07
98 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (95 bp):
ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAATATTTCGAAACCCGAAAT
AAAGAAACTTGCCTCGATTAAGGGTATTCA
Found at i:105421 original size:59 final size:58
Alignment explanation
Indices: 105359--105707 Score: 369
Period size: 59 Copynumber: 5.9 Consensus size: 58
105349 GGAAAATTCA
* * *
105359 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATTGACCTTTTGAAAGTTTTA
1 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGA-TTTTTGAAAGTTTTG
* * * ** ** * *
105418 AGGTTAAAAATGGAATTTTTGGTGGTTTTGGGGTCAAAAATGGAATTTTTTAAAGTTTTT
1 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGT-AAAAATGG-ATTTTTGAAAGTTTTG
* * * * *
105478 CGGTTAAAAATGGGGA-TTTTAGAAGTTTGAGGGTAAAAATGGGATTTTTGGAAGTTTTG
1 AGGTCAAAAAT-GGGATTTTTAGAAGTTCGGGGGTAAAAAT-GGATTTTTGAAAGTTTTG
* * *
105537 GGGTCAAAATTGGGATTCTTTAGAAGTTTGGGGGTAAAAATGGGATTTTT-AGAAGTTTTG
1 AGGTCAAAAATGGGATT-TTTAGAAGTTCGGGGGTAAAAAT-GGATTTTTGA-AAGTTTTG
* *
105597 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTCG
1 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATG-GATTTTTGAAAGTTTTG
* * *
105656 GGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGAA
1 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGG-ATTTTTGAA
105708 TAATTTAGGG
Statistics
Matches: 245, Mismatches: 35, Indels: 20
0.82 0.12 0.07
Matches are distributed among these distances:
58 6 0.02
59 137 0.56
60 98 0.40
61 4 0.02
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.36
Consensus pattern (58 bp):
AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGATTTTTGAAAGTTTTG
Found at i:105438 original size:30 final size:30
Alignment explanation
Indices: 105364--105707 Score: 237
Period size: 30 Copynumber: 11.6 Consensus size: 30
105354 ATTCAAGGTC
* *
105364 AAAAATGGGATTTTT-AGAAG-TTCGGGGGT
1 AAAAATGGGATTTTTGA-AAGTTTTGGGGTT
* * **
105393 AAAAAT-TGACCTTTTGAAAGTTTTAAGGTT
1 AAAAATGGGA-TTTTTGAAAGTTTTGGGGTT
* *** *
105423 AAAAATGGAATTTTTGGTGGTTTTGGGGTC
1 AAAAATGGGATTTTTGAAAGTTTTGGGGTT
* * **
105453 AAAAATGGAATTTTTTAAAGTTTTTCGGTT
1 AAAAATGGGATTTTTGAAAGTTTTGGGGTT
*
105483 AAAAATGGGGATTTTAG-AAG-TTTGAGGG-T
1 AAAAAT-GGGATTTTTGAAAGTTTTG-GGGTT
* *
105512 AAAAATGGGATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGGATTTTTGAAAGTTTTGGGGTT
* *
105542 AAAATTGGGATTCTTT-AGAAG-TTTGGGGGT
1 AAAAATGGGATT-TTTGA-AAGTTTTGGGGTT
* *
105572 AAAAATGGGATTTTT-AGAAGTTTTGAGGTC
1 AAAAATGGGATTTTTGA-AAGTTTTGGGGTT
* *
105602 AAAAATGGGATTTTT-AGAAG-TTCGGGGGT
1 AAAAATGGGATTTTTGA-AAGTTTTGGGGTT
* * * *
105631 AAAAATGAGATTTTTGGAAGTTTCGGGGTC
1 AAAAATGGGATTTTTGAAAGTTTTGGGGTT
* *
105661 AAAAATGGGATTTTTGGAAG-TTCGAGGG-T
1 AAAAATGGGATTTTTGAAAGTTTTG-GGGTT
*
105690 AAAAATGGAATTTTTGAA
1 AAAAATGGGATTTTTGAA
105708 TAATTTAGGG
Statistics
Matches: 251, Mismatches: 49, Indels: 30
0.76 0.15 0.09
Matches are distributed among these distances:
28 11 0.04
29 79 0.31
30 147 0.59
31 14 0.06
ACGTcount: A:0.32, C:0.03, G:0.29, T:0.36
Consensus pattern (30 bp):
AAAAATGGGATTTTTGAAAGTTTTGGGGTT
Found at i:105500 original size:119 final size:119
Alignment explanation
Indices: 105359--105704 Score: 369
Period size: 119 Copynumber: 2.9 Consensus size: 119
105349 GGAAAATTCA
* *
105359 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAAT-TGACCTTTTGAAAGTTTTAAGGTT
1 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGA-CTTTTGAAAGTTTTAAGGTC
* ** * *
105423 AAAAATGGAATT-TTTGGTGGTTTTGGGGTCAAAAATGGAATTTTTTA-AAGTTTTT
65 AAAAATGGAATTCTTTAGAAGTTTGGGGGT-AAAAATGGAA-TTTTTAGAAGTTTTG
* * * * * * **
105478 CGGTTAAAAATGGGGA-TTTTAGAAGTTTGAGGGTAAAAATGGGATTTTTGGAAGTTTTGGGGTC
1 AGGTCAAAAAT-GGGATTTTTAGAAGTTCGGGGGTAAAAATGGGACTTTTGAAAGTTTTAAGGTC
* * *
105542 AAAATTGGGATTCTTTAGAAGTTTGGGGGTAAAAATGGGATTTTTAGAAGTTTTG
65 AAAAATGGAATTCTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTTG
* * * ***
105597 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGAGATTTTTGGAAGTTTCGGGGTCA
1 AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGACTTTTGAAAGTTTTAAGGTCA
* * * *
105662 AAAATGGGATT-TTTGGAAGTTCGAGGGTAAAAATGGAATTTTT
66 AAAATGGAATTCTTTAGAAGTTTGGGGGTAAAAATGGAATTTTT
105705 GAATAATTTA
Statistics
Matches: 193, Mismatches: 29, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
118 38 0.20
119 136 0.70
120 19 0.10
ACGTcount: A:0.31, C:0.04, G:0.29, T:0.36
Consensus pattern (119 bp):
AGGTCAAAAATGGGATTTTTAGAAGTTCGGGGGTAAAAATGGGACTTTTGAAAGTTTTAAGGTCA
AAAATGGAATTCTTTAGAAGTTTGGGGGTAAAAATGGAATTTTTAGAAGTTTTG
Done.