Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015128.1 Kokia drynarioides strain JFW-HI SEQ_130172, 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: 82894
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:5366 original size:14 final size:14
Alignment explanation
Indices: 5346--5377 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
5336 AGGTTCTGGC
5346 CTTTTTTTTTTT-T
1 CTTTTTTTTTTTAT
5359 CTTTTTTTTTTTAT
1 CTTTTTTTTTTTAT
5373 CTTTT
1 CTTTT
5378 AGAGTGTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (14 bp):
CTTTTTTTTTTTAT
Found at i:8403 original size:6 final size:6
Alignment explanation
Indices: 8392--8426 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
8382 TCGCGTTGCG
8392 TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TGTCT
1 TGTCTC TGTCTC TGTCTC TGTCTC TGTCTC TGTCT
8427 TCCCTCTTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.17, T:0.51
Consensus pattern (6 bp):
TGTCTC
Found at i:12016 original size:96 final size:96
Alignment explanation
Indices: 11839--12024 Score: 311
Period size: 96 Copynumber: 1.9 Consensus size: 96
11829 TCAAGTGTAG
*
11839 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATGGTCCAAC
1 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATAGTCCAAC
* * *
11904 CTGGCCGACTGGGAAGTTACATTCCTGATAA
66 CAGGCCGACAGCGAAGTTACATTCCTGATAA
11935 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATAGTCCAAC
1 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATAGTCCAA-
*
12000 CCAGG-CGACAGCGAAGTTATATTCC
65 CCAGGCCGACAGCGAAGTTACATTCC
12025 CGAAAATCTT
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
96 80 0.95
97 4 0.05
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (96 bp):
TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATAGTCCAAC
CAGGCCGACAGCGAAGTTACATTCCTGATAA
Found at i:15642 original size:2 final size:2
Alignment explanation
Indices: 15635--15670 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
15625 AGGTAAGTTA
15635 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
15671 GCATGCTGTG
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:21110 original size:56 final size:53
Alignment explanation
Indices: 21027--21132 Score: 126
Period size: 56 Copynumber: 1.9 Consensus size: 53
21017 AATTTTTTGC
*
21027 TGGTGTTGGTCATGCATTGACGTACACCAACATTTTTTTATCAGATAAAAAAAATT
1 TGGTGTTGGTCATGCATTGACGTACACC--CA-CTTTTTATCAGATAAAAAAAATT
* *
21083 TGGTGTTGGTCATTGCA-TGGC-TGACACCCACTTTTTATTAGATAAAAAAA
1 TGGTGTTGGTCA-TGCATTGACGT-ACACCCACTTTTTATCAGATAAAAAAA
21133 TCAAATTTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
53 18 0.40
54 2 0.04
55 1 0.02
56 20 0.44
57 4 0.09
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (53 bp):
TGGTGTTGGTCATGCATTGACGTACACCCACTTTTTATCAGATAAAAAAAATT
Found at i:21553 original size:11 final size:12
Alignment explanation
Indices: 21513--21560 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
21503 TATTTGTGTA
21513 AAAATTAATTTG
1 AAAATTAATTTG
*
21525 AAAATTAAATTG
1 AAAATTAATTTG
21537 AGTTGAAATTAATTTG
1 A----AAATTAATTTG
21553 AAAATTAA
1 AAAATTAA
21561 GGTACATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 19 0.63
16 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:21889 original size:94 final size:93
Alignment explanation
Indices: 21655--21952 Score: 490
Period size: 93 Copynumber: 3.2 Consensus size: 93
21645 TTTAAATTAC
* *
21655 ATTTAAAATTATTTAAATAAAAAACTATTATTATTTTACAATTTTTATCAAATAATGTATTGATT
1 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
21720 TGACAATACATTATTTACCAAATTTAAT
66 TGACAATACATTATTTACCAAATTTAAT
* * *
21748 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATTTGTTAATA
1 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
*
21813 TGACAATACATTATTTGCCAAATTTTAAT
66 TGACAATACATTATTTACCAAA-TTTAAT
* *
21842 ATTTAAAATTATTTAAATAAAAAACTACTT-TTATATTATAATTTTTATTAAATAATGTGTTGAT
1 ATTTAAAATTATTTAAATAAAAAACTA-TTATTATATTACAATTTTTATCAAATAATGTGTTGAT
*
21906 TTGACAATACATTATTTACCAAACTTAAT
65 TTGACAATACATTATTTACCAAATTTAAT
21935 ATTTAAAATTATTTAAAT
1 ATTTAAAATTATTTAAAT
21953 CAATACAAAT
Statistics
Matches: 190, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
93 104 0.55
94 84 0.44
95 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (93 bp):
ATTTAAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATGTGTTGATT
TGACAATACATTATTTACCAAATTTAAT
Found at i:22935 original size:61 final size:60
Alignment explanation
Indices: 22867--23023 Score: 233
Period size: 61 Copynumber: 2.6 Consensus size: 60
22857 TGGCCATCCA
* * *
22867 AAAAAAATTGAATTTTTTTATCAGATAAAAAAGTGGTGTCGATCATGCAATGGCCAACACC
1 AAAAAAATTG-ATTTATTTATCAAATAAAAAAGTGGTGTCGACCATGCAATGGCCAACACC
* *
22928 AAAAAAATTGGATTTATTTATCAAATAAAAAAATGGTGTCGGCCATGCAATGGCCAACACC
1 AAAAAAATT-GATTTATTTATCAAATAAAAAAGTGGTGTCGACCATGCAATGGCCAACACC
* *
22989 AAAAAAATTGATTTATTTATCATATAAAAAGGTGG
1 AAAAAAATTGATTTATTTATCAAATAAAAAAGTGG
23024 CCAAAATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
60 23 0.26
61 63 0.72
62 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (60 bp):
AAAAAAATTGATTTATTTATCAAATAAAAAAGTGGTGTCGACCATGCAATGGCCAACACC
Found at i:23142 original size:60 final size:58
Alignment explanation
Indices: 23032--23372 Score: 265
Period size: 59 Copynumber: 5.9 Consensus size: 58
23022 GGCCAAAATT
* * * *
23032 TTGATTTTTTTATCAGA-AAAAAGG-GATGTCAACCATACAATGTCCAACACCAAAAAA
1 TTGA-TTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACCAAAAAA
* * * *
23089 TTGGATTTATTTATAAGATAAAAAGGTGGTGTCGGCCATGCAATGGCCTACACCAAAAAAAA
1 TT-GATTT-TTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACC--AAAAAA
* * * * *
23151 AT-ATTTTTTATCTGACAAAAAGGCGGTGTCGACCATGCAATGACCCACACCAAAAAA
1 TTGATTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACCAAAAAA
* * *
23208 TTGATTTTTTTTCAGATAAAAAAGGTAGTGTCGACCAATGC-ATTACCAACA--AAAAAA
1 TTGATTTTTTATCAGAT-AAAAAGGTGGTGTCGACC-ATGCAATGACCAACACCAAAAAA
* * ** * *
23265 -T-ATTTTTTATCTG-CAAAAAGG-GGTGTCGGTCATGCAAT-AGTCAACACTAAAAAAA
1 TTGATTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGA-CCAACAC-CAAAAAA
* * * * *
23320 TTGATTTTTTATCAAATAAAAATGTGGTGTAGACCAATGC-GTGGCCAACACCA
1 TTGATTTTTTATCAGATAAAAAGGTGGTGTCGACC-ATGCAATGACCAACACCA
23373 GGGACAAAAA
Statistics
Matches: 223, Mismatches: 41, Indels: 39
0.74 0.14 0.13
Matches are distributed among these distances:
51 5 0.02
52 14 0.06
53 7 0.03
55 16 0.07
56 2 0.01
57 28 0.13
58 28 0.13
59 83 0.37
60 33 0.15
62 7 0.03
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (58 bp):
TTGATTTTTTATCAGATAAAAAGGTGGTGTCGACCATGCAATGACCAACACCAAAAAA
Found at i:23317 original size:111 final size:112
Alignment explanation
Indices: 23037--23359 Score: 304
Period size: 111 Copynumber: 2.8 Consensus size: 112
23027 AAATTTTGAT
* * * * *
23037 TTTTTTATCAGA-AAAAAGG-GATGTCAACCATACAATGTCCAACACC-AAAAAATTGGATTTAT
1 TTTTTTATCTGACAAAAAGGCGGTGTCGACCATGCAATGACCAACACCAAAAAAATT-GATTT-T
* * *
23099 TTAT-AAGATAAAAAGGTGGTGTCGGCC-ATGCAATGGCCTACACCAAAAAAAAATA
64 TTATCAA-ATAAAAAGGTAGTGTAGACCAATGC-AT----T--ACCAAAAAAAAATA
*
23154 TTTTTTATCTGACAAAAAGGCGGTGTCGACCATGCAATGACCCACACC-AAAAAATTGATTTTTT
1 TTTTTTATCTGACAAAAAGGCGGTGTCGACCATGCAATGACCAACACCAAAAAAATTGATTTTTT
* * *
23218 TTCAGATAAAAAAGGTAGTGTCGACCAATGCATTACCAACAAAAAAATA
66 ATCAAAT-AAAAAGGTAGTGTAGACCAATGCATTACCAA-AAAAAAATA
** * *
23267 TTTTTTATCTG-CAAAAAGG-GGTGTCGGTCATGCAAT-AGTCAACACTAAAAAAATTGATTTTT
1 TTTTTTATCTGACAAAAAGGCGGTGTCGACCATGCAATGA-CCAACACCAAAAAAATTGATTTTT
* *
23329 TATCAAATAAAAATGTGGTGTAGACCAATGC
65 TATCAAATAAAAAGGTAGTGTAGACCAATGC
23360 GTGGCCAACA
Statistics
Matches: 178, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
110 1 0.01
111 40 0.22
112 34 0.19
113 20 0.11
114 1 0.01
117 17 0.10
118 31 0.17
119 34 0.19
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (112 bp):
TTTTTTATCTGACAAAAAGGCGGTGTCGACCATGCAATGACCAACACCAAAAAAATTGATTTTTT
ATCAAATAAAAAGGTAGTGTAGACCAATGCATTACCAAAAAAAAATA
Found at i:30300 original size:2 final size:2
Alignment explanation
Indices: 30293--30324 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
30283 GTTGACTGAC
30293 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
30325 GAAATTACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:31818 original size:20 final size:20
Alignment explanation
Indices: 31777--31823 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
31767 AGTATTGTGC
* *
31777 TAATAATTTTTTATAGTAAT
1 TAATAATTTTTTAAAATAAT
31797 TAAT-ATTTTTTAAAATATAT
1 TAATAATTTTTTAAAATA-AT
31817 TATATAA
1 TA-ATAA
31824 ATATATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 11 0.50
20 8 0.36
21 2 0.09
22 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAATAATTTTTTAAAATAAT
Found at i:36134 original size:25 final size:26
Alignment explanation
Indices: 36105--36162 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
36095 GCTTACTGTT
36105 CAGCACTGTGTGTGCTTCTGTTAC-C
1 CAGCACTGTGTGTGCTTCTGTTACTC
* * *
36130 CAGCATTGTGTGTGCTTTTGTTTCTC
1 CAGCACTGTGTGTGCTTCTGTTACTC
36156 CAGCACT
1 CAGCACT
36163 TATGTACCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.12, C:0.26, G:0.22, T:0.40
Consensus pattern (26 bp):
CAGCACTGTGTGTGCTTCTGTTACTC
Found at i:48266 original size:15 final size:14
Alignment explanation
Indices: 48222--48267 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
48212 TTTGTTATTC
48222 ACATATTTTGGTTA
1 ACATATTTTGGTTA
48236 ACATATTTTGGTTTA
1 ACATATTTTGG-TTA
**
48251 AGGTTATTTTGGTTA
1 A-CATATTTTGGTTA
48266 AC
1 AC
48268 GTAATCGTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 11 0.41
15 8 0.30
16 8 0.30
ACGTcount: A:0.26, C:0.07, G:0.17, T:0.50
Consensus pattern (14 bp):
ACATATTTTGGTTA
Found at i:62179 original size:7 final size:7
Alignment explanation
Indices: 62167--62202 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
62157 GACGTGCATC
62167 GCCGAAA
1 GCCGAAA
62174 GCCGAAA
1 GCCGAAA
62181 GCCGAAA
1 GCCGAAA
62188 GCCGAAA
1 GCCGAAA
62195 GCCGAAA
1 GCCGAAA
62202 G
1 G
62203 ACAGTCTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.42, C:0.28, G:0.31, T:0.00
Consensus pattern (7 bp):
GCCGAAA
Found at i:63686 original size:27 final size:27
Alignment explanation
Indices: 63631--63685 Score: 87
Period size: 25 Copynumber: 2.1 Consensus size: 27
63621 TAACAGAGGT
63631 ACATAAGTGCTGGGGAAACAGAAGCAC
1 ACATAAGTGCTGGGGAAACAGAAGCAC
*
63658 ACAT-AGTGCT-GGGTAACAGAAGCAC
1 ACATAAGTGCTGGGGAAACAGAAGCAC
63683 ACA
1 ACA
63686 CGATGCTGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 17 0.63
26 6 0.22
27 4 0.15
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.13
Consensus pattern (27 bp):
ACATAAGTGCTGGGGAAACAGAAGCAC
Found at i:63700 original size:22 final size:22
Alignment explanation
Indices: 63672--63746 Score: 116
Period size: 22 Copynumber: 3.4 Consensus size: 22
63662 AGTGCTGGGT
63672 AACAGAAGCACACACGATGCTG
1 AACAGAAGCACACACGATGCTG
* *
63694 AACAGAAGCATACACGGTGCTG
1 AACAGAAGCACACACGATGCTG
63716 AACAGAAGCACACAC-AGTGCTG
1 AACAGAAGCACACACGA-TGCTG
63738 AACAGAAGC
1 AACAGAAGC
63747 GCGCTAGCGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.41, C:0.25, G:0.24, T:0.09
Consensus pattern (22 bp):
AACAGAAGCACACACGATGCTG
Found at i:68090 original size:13 final size:13
Alignment explanation
Indices: 68074--68117 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
68064 ATTTCAATTT
68074 TATTTTAATAAT-A
1 TATTTTAA-AATAA
68087 TATTTTAAAAATAA
1 TATTTT-AAAATAA
*
68101 TAATTTAAAATAA
1 TATTTTAAAATAA
68114 TATT
1 TATT
68118 CTTCACATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 19 0.70
14 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTTAAAATAA
Found at i:68168 original size:15 final size:15
Alignment explanation
Indices: 68148--68204 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
68138 ATTCAATATT
68148 AATATTTTAATAATA
1 AATATTTTAATAATA
*
68163 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
*
68182 AATATATTAATAATA
1 AATATTTTAATAATA
68197 AATATTTT
1 AATATTTT
68205 GTAGTACAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:68876 original size:11 final size:11
Alignment explanation
Indices: 68846--68879 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
68836 CCTGATCAAT
68846 TTAAAAAAA-A
1 TTAAAAAAATA
*
68856 TTAATAAAATA
1 TTAAAAAAATA
68867 TTAAAAAAATA
1 TTAAAAAAATA
68878 TT
1 TT
68880 TTATATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.38
11 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TTAAAAAAATA
Found at i:68926 original size:26 final size:27
Alignment explanation
Indices: 68871--68926 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
68861 AAAATATTAA
* *
68871 AAAAATATTTTATATTAATATTTTTGT
1 AAAAATATTTTATATTAATATATATGT
*
68898 AAAAATA-TTTATATTTATATAATAT-T
1 AAAAATATTTTATATTAATAT-ATATGT
68924 AAA
1 AAA
68927 TTCGATCCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
AAAAATATTTTATATTAATATATATGT
Found at i:69644 original size:3 final size:3
Alignment explanation
Indices: 69636--69666 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
69626 CCATCTGGCC
*
69636 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
69667 TCTTTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:75056 original size:24 final size:22
Alignment explanation
Indices: 75007--75060 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
74997 ATTATTTATT
* *
75007 TATTTTAATATTAAATTATTTT
1 TATTTTAATATTAAATTATATG
*
75029 TATTTTAATATATATATGTATATG
1 TATTTTAATAT-TAAAT-TATATG
75053 TATTTTAA
1 TATTTTAA
75061 CATTTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 11 0.41
23 4 0.15
24 12 0.44
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (22 bp):
TATTTTAATATTAAATTATATG
Found at i:78275 original size:13 final size:13
Alignment explanation
Indices: 78226--78276 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
78216 TAACCCAAGA
*
78226 TTTTCAAAATCAC
1 TTTTCAAAAGCAC
*
78239 ATTTTC-AAAGAAC
1 -TTTTCAAAAGCAC
*
78252 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
78265 TTTTCAAAAGCA
1 TTTTCAAAAGCA
78277 ATATTAAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 4 0.13
13 22 0.71
14 5 0.16
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:78619 original size:24 final size:24
Alignment explanation
Indices: 78592--78637 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
78582 TGGTTTTTTC
*
78592 TTTC-ATTTTTCTATTTTTCTAACA
1 TTTCAATTTTTC-ATCTTTCTAACA
78616 TTTCAATTTTTCATCTTTCTAA
1 TTTCAATTTTTCATCTTTCTAA
78638 TTTTCTTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCAATTTTTCATCTTTCTAACA
Found at i:79430 original size:25 final size:23
Alignment explanation
Indices: 79355--79481 Score: 136
Period size: 23 Copynumber: 5.4 Consensus size: 23
79345 ACGGAACAAA
* *
79355 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
79376 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
79401 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
79424 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
79447 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
79470 AACAGAGAGCAC
1 --CAGAGAGCAC
79482 GAGACGTACT
Statistics
Matches: 92, Mismatches: 5, Indels: 14
0.83 0.05 0.13
Matches are distributed among these distances:
21 15 0.16
22 2 0.02
23 45 0.49
25 23 0.25
26 7 0.08
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Done.