Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005038.1 Kokia drynarioides strain JFW-HI SEQ_118807, 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: 58626
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Warning! 20 characters in sequence are not A, C, G, or T
Found at i:2653 original size:19 final size:19
Alignment explanation
Indices: 2615--2653 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2605 GCAAATGACA
*
2615 ATTTTAACTCTTATAAAAT
1 ATTTTAACTCTTAGAAAAT
* *
2634 ATTTTATCTCTTAGATAAT
1 ATTTTAACTCTTAGAAAAT
2653 A
1 A
2654 AAATATGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTTTAACTCTTAGAAAAT
Found at i:3495 original size:13 final size:13
Alignment explanation
Indices: 3454--3516 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
3444 CTTAAATTAA
*
3454 ACTTTTTAAAAAT
1 ACTTTTTAAAAAC
* * *
3467 ACTTCTCAAAATC
1 ACTTTTTAAAAAC
* *
3480 ACTTTTTCACAAC
1 ACTTTTTAAAAAC
3493 ACTTTTTAAAAAC
1 ACTTTTTAAAAAC
*
3506 ACTTTTCAAAA
1 ACTTTTTAAAA
3517 GTAATACTAA
Statistics
Matches: 38, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (13 bp):
ACTTTTTAAAAAC
Found at i:3799 original size:9 final size:9
Alignment explanation
Indices: 3787--3839 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
3777 CATTAAACAC
3787 TTTAAAATT
1 TTTAAAATT
3796 TTTAAAATT
1 TTTAAAATT
*
3805 TTTAATTACACT
1 TTTAA--A-ATT
*
3817 TCTAAAATT
1 TTTAAAATT
*
3826 TTTAAAAAT
1 TTTAAAATT
3835 TTTAA
1 TTTAA
3840 TTAAACGCTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 28 0.78
10 1 0.03
11 1 0.03
12 6 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (9 bp):
TTTAAAATT
Found at i:3939 original size:30 final size:29
Alignment explanation
Indices: 3761--3938 Score: 130
Period size: 30 Copynumber: 5.8 Consensus size: 29
3751 CAAACCTCAT
* * *
3761 AATTTTGAAAATTTATCATTAAACACTTTAA
1 AATTTTTAAAATTT-T-ATTAAACTCTCTAA
*
3792 AATTTTTAAAATTTTTAATTACACT-TCTAA
1 AATTTTTAAAA-TTTT-ATTAAACTCTCTAA
*
3822 AATTTTTAAAAATTTTAATTAAACGCTCTAAA
1 AATTTTT-AAAATTTT-ATTAAACTCTCT-AA
* *
3854 AATTTTAAAAACTTTTATTAAAC-CAC-AA
1 AATTTTTAAAA-TTTTATTAAACTCTCTAA
* *
3882 AAGTTTTTAGAAATTCTCATTAGACTC-CTAA
1 AA-TTTTTA-AAATT-TTATTAAACTCTCTAA
3913 AATTTTTGAAAATTTTAGTTAAACTC
1 AATTTTT-AAAATTTTA-TTAAACTC
3939 CCATAACTTA
Statistics
Matches: 121, Mismatches: 14, Indels: 25
0.76 0.09 0.16
Matches are distributed among these distances:
28 4 0.03
29 9 0.07
30 52 0.43
31 41 0.34
32 15 0.12
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (29 bp):
AATTTTTAAAATTTTATTAAACTCTCTAA
Found at i:5343 original size:31 final size:31
Alignment explanation
Indices: 5272--5345 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
5262 GATTTAATGT
* *
5272 AATTATATATATGAAATTTTAATTATGGTTC
1 AATTATACATATAAAATTTTAATTATGGTTC
* * * *
5303 AAATGTACATATAAAATTTTAATTTTGATTTC
1 AATTATACATATAAAATTTTAATTATG-GTTC
5335 -ATTATACATAT
1 AATTATACATAT
5346 TTAAAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
31 31 0.91
32 3 0.09
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (31 bp):
AATTATACATATAAAATTTTAATTATGGTTC
Found at i:16709 original size:12 final size:11
Alignment explanation
Indices: 16692--16742 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
16682 TTTTATAGAT
16692 AAATAAACAAA
1 AAATAAACAAA
*
16703 CAAATAAATAAA
1 -AAATAAACAAA
*
16715 AAATAAA-AAT
1 AAATAAACAAA
16725 AAA-AAACAAA
1 AAATAAACAAA
*
16735 ATATAAAC
1 AAATAAAC
16743 CCAATTCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 3 0.09
10 9 0.27
11 11 0.33
12 10 0.30
ACGTcount: A:0.78, C:0.08, G:0.00, T:0.14
Consensus pattern (11 bp):
AAATAAACAAA
Found at i:16711 original size:16 final size:16
Alignment explanation
Indices: 16690--16735 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
16680 TATTTTATAG
*
16690 ATAAATAAACAAACAA
1 ATAAATAAACAAAAAA
*
16706 ATAAATAAAAAATAAAA
1 ATAAATAAACAA-AAAA
16723 ATAAA-AAACAAAA
1 ATAAATAAACAAAA
16736 TATAAACCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 2 0.08
16 16 0.62
17 8 0.31
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.13
Consensus pattern (16 bp):
ATAAATAAACAAAAAA
Found at i:16726 original size:13 final size:13
Alignment explanation
Indices: 16692--16741 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
16682 TTTTATAGAT
16692 AAATAAACAAACAAA
1 AAATAAA-AAAC-AA
*
16707 TAAATAAAAAATAA
1 -AAATAAAAAACAA
16721 AAATAAAAAACAA
1 AAATAAAAAACAA
16734 AATATAAA
1 AA-ATAAA
16742 CCCAATTCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 14 0.45
14 7 0.23
15 3 0.10
16 7 0.23
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (13 bp):
AAATAAAAAACAA
Found at i:17961 original size:29 final size:29
Alignment explanation
Indices: 17929--18139 Score: 144
Period size: 29 Copynumber: 7.2 Consensus size: 29
17919 TAAAAATTTG
17929 AATTTGACCCCTAAACTTTT-TAAAATTCA
1 AATTTGACCCCTAAA-TTTTCTAAAATTCA
*
17958 AATTTGACCCTCT-CATTTTCTAAAAATTCA
1 AATTTGACCC-CTAAATTTTCT-AAAATTCA
** * * * * *
17988 AAAATAACCAC-GAATTTTCCAAAAACTCA
1 AATTTGACCCCTAAATTTT-CTAAAATTCA
* *
18017 AATTTGACCCTTAAAATTTCTAGAAATTCA
1 AATTTGACCCCTAAATTTTCTA-AAATTCA
* *
18047 AATTTGACCCC-AAATTTTCCAAAATTTCT
1 AATTTGACCCCTAAATTTTCTAAAA-TTCA
* * * *
18076 AATTT-AACCCTAAACTTTCCAAATATTCC
1 AATTTGACCCCTAAATTTTCTAAA-ATTCA
* * *
18105 GATTTGGCCCCTAAAGTTTTCAAAAATTCA
1 AATTTGACCCCTAAA-TTTTCTAAAATTCA
18135 AATTT
1 AATTT
18140 AACCTGATTT
Statistics
Matches: 139, Mismatches: 31, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
28 11 0.08
29 67 0.48
30 54 0.39
31 7 0.05
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (29 bp):
AATTTGACCCCTAAATTTTCTAAAATTCA
Found at i:18063 original size:59 final size:59
Alignment explanation
Indices: 17929--18139 Score: 157
Period size: 59 Copynumber: 3.6 Consensus size: 59
17919 TAAAAATTTG
* * *
17929 AATTTGACCCCTAAACTTTT-TAAAATTCAAATTTGACCCTCT-CATTTTCTAAAAATTCA
1 AATTTGACCCCTAAACTTTTCAAAAATTCAAATTTGACCCT-TAAAATTTCT-AAAATTCA
** * * * *
17988 AAAATAACCAC-GAA-TTTTCCAAAAACTCAAATTTGACCCTTAAAATTTCTAGAAATTCA
1 AATTTGACCCCTAAACTTTT-CAAAAATTCAAATTTGACCCTTAAAATTTCTA-AAATTCA
* * * * * *
18047 AATTTGACCCC-AAA-TTTTCCAAAATTTCTAATTTAACCC-TAAACTTTCCAAATATTCC
1 AATTTGACCCCTAAACTTTT-CAAAAATTCAAATTTGACCCTTAAAATTTCTAAA-ATTCA
* * *
18105 GATTTGGCCCCTAAAGTTTTCAAAAATTCAAATTT
1 AATTTGACCCCTAAACTTTTCAAAAATTCAAATTT
18140 AACCTGATTT
Statistics
Matches: 120, Mismatches: 25, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
57 6 0.05
58 26 0.22
59 84 0.70
60 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (59 bp):
AATTTGACCCCTAAACTTTTCAAAAATTCAAATTTGACCCTTAAAATTTCTAAAATTCA
Found at i:18095 original size:88 final size:88
Alignment explanation
Indices: 17929--18139 Score: 210
Period size: 88 Copynumber: 2.4 Consensus size: 88
17919 TAAAAATTTG
* * ** *
17929 AATTTGACCCCTAAACTTTTTAAAATTCAAATTTGACCCTCTCATTTTCTAAAAATTCAAAAATA
1 AATTTGACCCCTAAAATTTCTAAAATTCAAATTTGACCCTCAAATTTTCCAAAAATTCAAAAATA
* *
17994 ACCACGAATTTTCCAAAAACTCA
66 ACCACAAACTTTCCAAAAACTCA
* * * **
18017 AATTTGACCCTTAAAATTTCTAGAAATTCAAATTTGACCC-CAAATTTTCCAAAATTTCTAATTT
1 AATTTGACCCCTAAAATTTCTA-AAATTCAAATTTGACCCTCAAATTTTCCAAAAATTCAAAAAT
* * *
18081 AACC-CTAAACTTTCCAAATATTCC
65 AACCAC-AAACTTTCCAAAAACTCA
* * * *
18105 GATTTGGCCCCTAAAGTTTTCAAAAATTCAAATTT
1 AATTTGACCCCTAAA-ATTTCTAAAATTCAAATTT
18140 AACCTGATTT
Statistics
Matches: 100, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
87 1 0.01
88 77 0.77
89 22 0.22
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (88 bp):
AATTTGACCCCTAAAATTTCTAAAATTCAAATTTGACCCTCAAATTTTCCAAAAATTCAAAAATA
ACCACAAACTTTCCAAAAACTCA
Found at i:18140 original size:59 final size:59
Alignment explanation
Indices: 18000--18143 Score: 159
Period size: 59 Copynumber: 2.4 Consensus size: 59
17990 AATAACCACG
* * *
18000 AATTTTCCAAAAACTCAAATTTGACCCTTAAAATTTCTAGAAATTCAAATTTGACCCCA
1 AATTTTCCAAAAATTCAAATTTAACCCTTAAAATTTCCAGAAATTCAAATTTGACCCCA
* * * ** *
18059 AATTTTCCAAAATTTCTAATTTAACCC-TAAACTTTCCA-AATATTCCGATTTGGCCCCTA
1 AATTTTCCAAAAATTCAAATTTAACCCTTAAAATTTCCAGAA-ATTCAAATTTGACCCC-A
18118 AAGTTTT-CAAAAATTCAAATTTAACC
1 AA-TTTTCCAAAAATTCAAATTTAACC
18144 TGATTTTAAT
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
57 2 0.03
58 22 0.31
59 43 0.61
60 4 0.06
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.35
Consensus pattern (59 bp):
AATTTTCCAAAAATTCAAATTTAACCCTTAAAATTTCCAGAAATTCAAATTTGACCCCA
Found at i:29881 original size:50 final size:50
Alignment explanation
Indices: 29733--29865 Score: 140
Period size: 50 Copynumber: 2.7 Consensus size: 50
29723 GACGAGTCCT
* * ** * ** * *
29733 ATACCCCTAAAGGTGTAGAGGAACGGATTAAAGCCCCAATGGCAAATCTC
1 ATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCTGCAAAGGCGAATCTC
* * * *
29783 ATACACCTAAAGCTGTAGAGGGGTAGATTGAAGCTGTAATGGCGAATCTC
1 ATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCTGCAAAGGCGAATCTC
*
29833 ATTCACCTAAAGCTGTAGAGGGGCAGATTAAAG
1 ATACACCTAAAGCTGTAGAGGGGCAGATTAAAG
29866 TCACAAGGAT
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.21
Consensus pattern (50 bp):
ATACACCTAAAGCTGTAGAGGGGCAGATTAAAGCTGCAAAGGCGAATCTC
Found at i:30014 original size:40 final size:40
Alignment explanation
Indices: 29942--30134 Score: 223
Period size: 39 Copynumber: 4.9 Consensus size: 40
29932 CCCAACTATG
* **
29942 GGGCAGATTGAAG-CAATCCAATCTTTTACCTTAACCAGA
1 GGGCAGATTGAAGACCATCTGATCTTTTACCTTAACCAGA
* *
29981 GGGCAGATTGAAGATCATTTGATCTTTTACCTTAACCATG-
1 GGGCAGATTGAAGACCATCTGATCTTTTACCTTAACCA-GA
* * **
30021 GGGCATATTGAAG-CAATCCAATCTTTTACCTTAACCAGA
1 GGGCAGATTGAAGACCATCTGATCTTTTACCTTAACCAGA
* * * *
30060 GGGCAGATTCAAGACCATCTGATCTTTTACCCTGACCA-T
1 GGGCAGATTGAAGACCATCTGATCTTTTACCTTAACCAGA
30099 GGGCAGATTGAAGACCATCTGATCTTTTACCCTTAA
1 GGGCAGATTGAAGACCATCTGATCTTTTA-CCTTAA
30135 AGGCATAGAG
Statistics
Matches: 127, Mismatches: 22, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
38 1 0.01
39 71 0.56
40 54 0.43
41 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (40 bp):
GGGCAGATTGAAGACCATCTGATCTTTTACCTTAACCAGA
Found at i:30024 original size:79 final size:79
Alignment explanation
Indices: 29923--30134 Score: 300
Period size: 79 Copynumber: 2.7 Consensus size: 79
29913 ATAACCTCGA
* *
29923 ATCTTTTACCCCAACTATGGGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGA
1 ATCTTTTACCCTAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGA
* * *
29988 TTGAAGATCATTTG
66 TTCAAGACCATCTG
* *
30002 ATCTTTTACCTTAACCATGGGGCATATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGA
1 ATCTTTTACCCTAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGA
30067 TTCAAGACCATCTG
66 TTCAAGACCATCTG
* * **
30081 ATCTTTTACCCTGACCAT-GGGCAGATTGAAGACCATCTGATCTTTTACCCTTAA
1 ATCTTTTACCCTAACCATGGGGCAGATTGAAG-CAATCCAATCTTTTA-CCTTAA
30135 AGGCATAGAG
Statistics
Matches: 118, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
78 12 0.10
79 100 0.85
80 6 0.05
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (79 bp):
ATCTTTTACCCTAACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGA
TTCAAGACCATCTG
Found at i:30811 original size:23 final size:23
Alignment explanation
Indices: 30781--30833 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
30771 AATTCCATTT
30781 ACCCAAAA-CCCAAACTAAACAA
1 ACCCAAAAGCCCAAACTAAACAA
*
30803 ACCCTAAAAGCCCAACCTAAACTAA
1 ACCC-AAAAGCCCAAACTAAAC-AA
*
30828 GCCCAA
1 ACCCAA
30834 GTAGCCTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 4 0.15
24 13 0.50
25 5 0.19
ACGTcount: A:0.51, C:0.38, G:0.04, T:0.08
Consensus pattern (23 bp):
ACCCAAAAGCCCAAACTAAACAA
Found at i:31949 original size:30 final size:30
Alignment explanation
Indices: 31915--32151 Score: 203
Period size: 30 Copynumber: 8.0 Consensus size: 30
31905 TTTCAACCTA
* * *
31915 TAAACTATCCAAAAATTCGAATTTGACCCT
1 TAAACTTTCCAAAAATTCAAATTTGACCCC
** *
31945 TAAACTTT-TTAAAATTAAAATTTGACCCC
1 TAAACTTTCCAAAAATTCAAATTTGACCCC
* * *
31974 TAAATTTTCCAAAAAATCAAATTTAACCCC
1 TAAACTTTCCAAAAATTCAAATTTGACCCC
** *
32004 T-ATTTTTTCAAAAGATTCAAATTTGACCCC
1 TAAACTTTCCAAAA-ATTCAAATTTGACCCC
** * *
32034 TAAACTTTCCAAAAATTTGAATTCGACCCT
1 TAAACTTTCCAAAAATTCAAATTTGACCCC
* * *
32064 TAAATTTTCTAAAAATTCCAATTTGA-CCC
1 TAAACTTTCCAAAAATTCAAATTTGACCCC
* * * *
32093 TAAACTTTCTAAACATTTC-GATTTAACCCC
1 TAAACTTTCCAAA-AATTCAAATTTGACCCC
* *
32123 TAAAGTTTTCAAAAATTCAAATTTGACCC
1 TAAACTTTCCAAAAATTCAAATTTGACCC
32152 GATTTTAATG
Statistics
Matches: 162, Mismatches: 39, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
29 56 0.35
30 97 0.60
31 9 0.06
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.35
Consensus pattern (30 bp):
TAAACTTTCCAAAAATTCAAATTTGACCCC
Found at i:31985 original size:59 final size:60
Alignment explanation
Indices: 31915--32151 Score: 252
Period size: 59 Copynumber: 4.0 Consensus size: 60
31905 TTTCAACCTA
* * * *
31915 TAAACTATCCAAAAATTCGAATTTGACCCTTAAACTTTT-T-AAAATTAAAATTTGACCCC
1 TAAACTTTCCAAAAATTCGAATTTAACCCCTAAA-TTTTCTAAAAATTCAAATTTGACCCC
* * * **
31974 TAAATTTTCCAAAAAATCAAATTTAACCCCTATTTTTTC-AAAAGATTCAAATTTGACCCC
1 TAAACTTTCCAAAAATTCGAATTTAACCCCTAAATTTTCTAAAA-ATTCAAATTTGACCCC
* ** * *
32034 TAAACTTTCCAAAAATTTGAATTCGACCCTTAAATTTTCTAAAAATTCCAATTTGA-CCC
1 TAAACTTTCCAAAAATTCGAATTTAACCCCTAAATTTTCTAAAAATTCAAATTTGACCCC
* *
32093 TAAACTTTCTAAACATTTCG-ATTTAACCCCTAAAGTTTTC-AAAAATTCAAATTTGACCC
1 TAAACTTTCCAAA-AATTCGAATTTAACCCCTAAA-TTTTCTAAAAATTCAAATTTGACCC
32152 GATTTTAATG
Statistics
Matches: 145, Mismatches: 26, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
58 4 0.03
59 70 0.48
60 67 0.46
61 4 0.03
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.35
Consensus pattern (60 bp):
TAAACTTTCCAAAAATTCGAATTTAACCCCTAAATTTTCTAAAAATTCAAATTTGACCCC
Found at i:37839 original size:18 final size:19
Alignment explanation
Indices: 37816--37866 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
37806 GATTAATTTC
37816 TTAATTCGGGTAATTC-AG
1 TTAATTCGGGTAATTCAAG
*
37834 TTAATTC-GATAAATTCAAG
1 TTAATTCGGGT-AATTCAAG
37853 -TAATTCGGGTAATT
1 TTAATTCGGGTAATT
37867 TTTTATACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 2 0.07
18 22 0.79
19 4 0.14
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (19 bp):
TTAATTCGGGTAATTCAAG
Found at i:46210 original size:72 final size:72
Alignment explanation
Indices: 46100--46244 Score: 281
Period size: 72 Copynumber: 2.0 Consensus size: 72
46090 TTTATAGAGA
*
46100 TAACTAGTCATATATGTTACTTGTTGAGACTATCCCAAGATGACTCATTTGTGGTACATGGAATG
1 TAACTAGTCATATATGTTACTTGTTGAGACTATCCCAAGATGACTCATTTGTGGTACATAGAATG
46165 ATAGATG
66 ATAGATG
46172 TAACTAGTCATATATGTTACTTGTTGAGACTATCCCAAGATGACTCATTTGTGGTACATAGAATG
1 TAACTAGTCATATATGTTACTTGTTGAGACTATCCCAAGATGACTCATTTGTGGTACATAGAATG
46237 ATAGATG
66 ATAGATG
46244 T
1 T
46245 TGAGTTGATG
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
72 72 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (72 bp):
TAACTAGTCATATATGTTACTTGTTGAGACTATCCCAAGATGACTCATTTGTGGTACATAGAATG
ATAGATG
Found at i:51147 original size:18 final size:18
Alignment explanation
Indices: 51124--51166 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
51114 GTTCAAGGTG
51124 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
51142 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
51160 TAATTAA
1 TAATTAA
51167 AAATTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:54390 original size:48 final size:48
Alignment explanation
Indices: 54338--54466 Score: 213
Period size: 48 Copynumber: 2.7 Consensus size: 48
54328 TCTGCCAGCA
54338 ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
1 ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
* *
54386 ACATTTTGAGCCTACAACATTCTGGTTTTGAAACATAAGATGGTAGTC
1 ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
* * *
54434 ACATTTTGAGCATGCAAGATTCTGGTTTTGGAA
1 ACATTTTGAGCCTACAACATTCTGGTTTTGGAA
54467 TACACCAATG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (48 bp):
ACATTTTGAGCCTACAACATTCTGGTTTTGGAACACAAGATGGTAGTC
Found at i:55605 original size:15 final size:15
Alignment explanation
Indices: 55582--55616 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
55572 TTTTCAGAAT
* *
55582 GATTAGGGATTTCAC
1 GATTTGGGATTGCAC
55597 GATTTGGGATTGCAC
1 GATTTGGGATTGCAC
55612 GATTT
1 GATTT
55617 TGTTCTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (15 bp):
GATTTGGGATTGCAC
Found at i:55783 original size:16 final size:17
Alignment explanation
Indices: 55754--55795 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
55744 GGTTCGAATG
*
55754 GTTTGAGGAATTTA-AA
1 GTTTGGGGAATTTAGAA
*
55770 GTTTGGGGATTTTAGAA
1 GTTTGGGGAATTTAGAA
55787 -TTTGGGGAA
1 GTTTGGGGAA
55796 AATTATCTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 20 0.91
17 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.33, T:0.38
Consensus pattern (17 bp):
GTTTGGGGAATTTAGAA
Done.