Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008648.1 Kokia drynarioides strain JFW-HI SEQ_123329, 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: 99090
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:7673 original size:19 final size:21
Alignment explanation
Indices: 7637--7676 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
7627 TGGAAAATAA
*
7637 TAAAATAAATAACTCTTAATT
1 TAAAATAAATAACACTTAATT
7658 TAAAA-AAATAA-ACTTAATT
1 TAAAATAAATAACACTTAATT
7677 ATCTAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 6 0.33
21 5 0.28
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATAAATAACACTTAATT
Found at i:7721 original size:14 final size:14
Alignment explanation
Indices: 7702--7732 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
7692 AAAATGAATG
7702 TGTTAGCAGTAAGT
1 TGTTAGCAGTAAGT
7716 TGTTAGCAGTAAGT
1 TGTTAGCAGTAAGT
7730 TGT
1 TGT
7733 GTAAGTCAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.39
Consensus pattern (14 bp):
TGTTAGCAGTAAGT
Found at i:7767 original size:15 final size:16
Alignment explanation
Indices: 7739--7768 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7729 TTGTGTAAGT
7739 CAGTTAGTACAGTTAG
1 CAGTTAGTACAGTTAG
7755 CAGTTAG-ACAGTTA
1 CAGTTAGTACAGTTA
7769 TGTCAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.13, G:0.23, T:0.30
Consensus pattern (16 bp):
CAGTTAGTACAGTTAG
Found at i:7777 original size:9 final size:8
Alignment explanation
Indices: 7736--7777 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
7726 AAGTTGTGTA
7736 AGTCAGTT
1 AGTCAGTT
7744 AGTACAGTT
1 AGT-CAGTT
7753 AG-CAGTT
1 AGTCAGTT
*
7760 AGACAGTT
1 AGTCAGTT
7768 ATGTCAGTT
1 A-GTCAGTT
7777 A
1 A
7778 ACATTTGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
7 7 0.23
8 9 0.30
9 14 0.47
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (8 bp):
AGTCAGTT
Found at i:13982 original size:28 final size:29
Alignment explanation
Indices: 13937--13994 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
13927 TTGAAATCTG
* *
13937 AAAATAAAAAGATTAAAATTCTAAAAATA
1 AAAATAAAAAGATAAAAATTATAAAAATA
* *
13966 AAAATAAAAATA-AAAAATTATAAATATA
1 AAAATAAAAAGATAAAAATTATAAAAATA
13994 A
1 A
13995 CTAAAATCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (29 bp):
AAAATAAAAAGATAAAAATTATAAAAATA
Found at i:14302 original size:14 final size:14
Alignment explanation
Indices: 14285--14318 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
14275 ATATAATATC
14285 AAAATAATAACAAT
1 AAAATAATAACAAT
*
14299 AAAATAGTAACAAT
1 AAAATAATAACAAT
*
14313 ATAATA
1 AAAATA
14319 TTAAAATTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAATAATAACAAT
Found at i:14315 original size:36 final size:36
Alignment explanation
Indices: 14256--14325 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
14246 ATAACAAAAT
**
14256 TAACAATAAAATAAAAATTATATAATATCAAAATAA
1 TAACAATAAAATAAAAACAATATAATATCAAAATAA
** *
14292 TAACAATAAAATAGTAACAATATAATATTAAAAT
1 TAACAATAAAATAAAAACAATATAATATCAAAAT
14326 TACAGCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (36 bp):
TAACAATAAAATAAAAACAATATAATATCAAAATAA
Found at i:28132 original size:28 final size:26
Alignment explanation
Indices: 28080--28148 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
28070 TCCGACCTGA
28080 ATATA-TTATATTATAAAAAATATTAT
1 ATATATTTATATT-TAAAAAATATTAT
*
28106 AT-TAATTGTATATTTAAATAATAATTAT
1 ATAT-ATT-TATATTTAAAAAAT-ATTAT
28134 ATATATTTATATTTA
1 ATATATTTATATTTA
28149 TATTAAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
25 1 0.03
26 3 0.08
27 16 0.43
28 16 0.43
29 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (26 bp):
ATATATTTATATTTAAAAAATATTAT
Found at i:29020 original size:2 final size:2
Alignment explanation
Indices: 29008--29037 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
28998 GAAGGGGAAG
*
29008 GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
29038 TCTTCAGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:30280 original size:35 final size:35
Alignment explanation
Indices: 30234--30301 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
30224 ATTTTGCTGT
30234 AATTTTTGTTTCGGTTTATGCATTCAGATTTGGTA
1 AATTTTTGTTTCGGTTTATGCATTCAGATTTGGTA
* **
30269 AATTTTTGTTTCTGTTTATGCATTTGGATTTGG
1 AATTTTTGTTTCGGTTTATGCATTCAGATTTGG
30302 AAACGGGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.18, C:0.07, G:0.21, T:0.54
Consensus pattern (35 bp):
AATTTTTGTTTCGGTTTATGCATTCAGATTTGGTA
Found at i:33737 original size:59 final size:57
Alignment explanation
Indices: 33636--33752 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 57
33626 CAATTATGGT
* *
33636 ATCATTCGTGATGAGGATTGCTATATAAGGACTTGGATTTAAACCCAATGCGGCACA
1 ATCATTCGTGATAAGGATTGCTATAAAAGGACTTGGATTTAAACCCAATGCGGCACA
* * *
33693 ATCATT-GTGATAAGGATTGCTACATAAAGAGGACTTTGATTTAAACCCGATGTGGCACA
1 ATCATTCGTGATAAGGATTGCT--ATAAA-AGGACTTGGATTTAAACCCAATGCGGCACA
33752 A
1 A
33753 CTTTGACTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
56 14 0.27
57 6 0.12
58 4 0.08
59 28 0.54
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (57 bp):
ATCATTCGTGATAAGGATTGCTATAAAAGGACTTGGATTTAAACCCAATGCGGCACA
Found at i:35111 original size:66 final size:66
Alignment explanation
Indices: 35005--35160 Score: 249
Period size: 66 Copynumber: 2.4 Consensus size: 66
34995 AAACAGGCGG
* * *
35005 TTTTCATAGGCGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCGTTACCTTTTCTTAACATGGG
1 TTTTCAGAGGCGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTAACATGGG
35070 A
66 A
*
35071 TTTTCAGAGGCGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTATCTCTTCTTAACATGGG
1 TTTTCAGAGGCGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTAACATGGG
*
35136 G
66 A
* *
35137 TTTTCAGAGGTGGTTTCGTCCATG
1 TTTTCAGAGGCGGTTTCCTCCATG
35161 TCCTCCATGA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 83 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.34
Consensus pattern (66 bp):
TTTTCAGAGGCGGTTTCCTCCATGAGAGGCCAGTAAAAACCTTCATTACCTCTTCTTAACATGGG
A
Found at i:36389 original size:16 final size:16
Alignment explanation
Indices: 36368--36401 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
36358 ATTTTGATGT
36368 TTTGACTCGTTTCAAC
1 TTTGACTCGTTTCAAC
*
36384 TTTGACTTGTTTCAAC
1 TTTGACTCGTTTCAAC
36400 TT
1 TT
36402 AGTACCGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.21, G:0.12, T:0.50
Consensus pattern (16 bp):
TTTGACTCGTTTCAAC
Found at i:54614 original size:22 final size:23
Alignment explanation
Indices: 54581--54642 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 23
54571 TATTATATTT
54581 TCTCATC-A-ATAATTAAAATAA
1 TCTCATCAATATAATTAAAATAA
* *
54602 TCT-TTCAATATAATT-CAATAA
1 TCTCATCAATATAATTAAAATAA
*
54623 TCTCATCAATA-ATTTAAAAT
1 TCTCATCAATATAATTAAAAT
54643 CATAATATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
20 2 0.06
21 15 0.47
22 15 0.47
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (23 bp):
TCTCATCAATATAATTAAAATAA
Found at i:57523 original size:98 final size:96
Alignment explanation
Indices: 57344--57530 Score: 241
Period size: 98 Copynumber: 1.9 Consensus size: 96
57334 GTAAAGGATG
* ** * * *
57344 TTCGCTTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGACACAAATTTTCAGAATCGA
1 TTCGCTTATTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAAATTTTCAAAACCCA
* *
57409 AGATAAGGAAACATTGCCTCGATTAAGGGTA
66 AAATAAAGAAACATTGCCTCGATTAAGGGTA
* *
57440 TTCGGTTATTTCAATTTGAAGAAAAAAATTGCACCTAGTAAGTTAAGGCACAAATTTTCAAAACC
1 TTCGCTTATTTCAATTTGAAG--AAAAATTGCACCTAGTAAGTTAAGACACAAATTTTCAAAACC
*
57505 CAAAATAAA-AGAATATTGCCTCGATT
64 CAAAATAAAGA-AACATTGCCTCGATT
57531 TTAAAGTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
96 19 0.25
97 1 0.01
98 57 0.74
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (96 bp):
TTCGCTTATTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGACACAAATTTTCAAAACCCA
AAATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:57945 original size:28 final size:29
Alignment explanation
Indices: 57890--58180 Score: 124
Period size: 29 Copynumber: 10.3 Consensus size: 29
57880 GTAAAAGGGT
* *
57890 AATTTTTTAAAGTTTCAGGGTTAAAAATGA
1 AATTTTTGAAAG-TTCAGGGGTAAAAATGA
* *
57920 AATTTTTGAAAGTTCGGGGGT-AAAATGT
1 AATTTTTGAAAGTTCAGGGGTAAAAATGA
* ** *
57948 AATTTTTGGAAGTTTTGAGGTTAAAAATG-
1 AATTTTTGAAAGTTCAG-GGGTAAAAATGA
* * *
57977 -------G-GAGTTTC-GGGATAAAAATGT
1 AATTTTTGAAAG-TTCAGGGGTAAAAATGA
* * * * *
57998 ATTTTTTGGAAGTTTTA-GGGTTAAAATGG
1 AATTTTTGAAAG-TTCAGGGGTAAAAATGA
* * *
58027 AATTTTTGGAAGTTTAGGGGTAAAAATGT
1 AATTTTTGAAAGTTCAGGGGTAAAAATGA
* ** * *
58056 ATTTTTTGAAAGTTTTGGGGTTAAAATGG
1 AATTTTTGAAAGTTCAGGGGTAAAAATGA
* *
58085 AATTTTT-AGAAGTTCAAGGGTAAAAATGC
1 AATTTTTGA-AAGTTCAGGGGTAAAAATGA
* ** *
58114 AATTTTTTAAATGTTTTGGGGTTAAAATGGA
1 AATTTTTGAAA-GTTCAGGGGTAAAAAT-GA
* * *
58145 ATTTTTTG-AAGTTCAAGGGTAAAAATGT
1 AATTTTTGAAAGTTCAGGGGTAAAAATGA
58173 AATTTTTG
1 AATTTTTG
58181 GACAATTTAG
Statistics
Matches: 200, Mismatches: 43, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
20 10 0.05
21 3 0.01
22 3 0.01
28 34 0.17
29 111 0.56
30 32 0.16
31 7 0.04
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.40
Consensus pattern (29 bp):
AATTTTTGAAAGTTCAGGGGTAAAAATGA
Found at i:57950 original size:58 final size:57
Alignment explanation
Indices: 57878--58179 Score: 259
Period size: 58 Copynumber: 5.3 Consensus size: 57
57868 GAGACATCCA
** * *
57878 GGGTAAAAGGGTAATTTTTTAAAGTTTCAGGGTTAAAAATGAAATTTTTGAAAGTTCGG
1 GGGTAAAAATGTAATTTTTTAAAGTTTTAGGGTT-AAAATGAAATTTTTG-AAGTTCAG
** * *
57937 GGGT-AAAATGTAATTTTTGGAAGTTTT-GAGGTT--AA--AAA---TGGGAGTTTC-G
1 GGGTAAAAATGTAATTTTTTAAAGTTTTAG-GGTTAAAATGAAATTTTTGAAG-TTCAG
* * * *
57986 GGATAAAAATGT-ATTTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTTAG
1 GGGTAAAAATGTAATTTTTT-AAAGTTTTAGGGTTAAAATGAAATTTTT-GAAGTTCAG
* * *
58044 GGGTAAAAATGT-ATTTTTTGAAAGTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCAA
1 GGGTAAAAATGTAATTTTTT-AAAGTTTTAGGGTTAAAATGAAATTTTT-GAAGTTCAG
* * * *
58102 GGGTAAAAATGCAATTTTTTAAATGTTTTGGGGTTAAAATGGAATTTTTTGAAGTTCAA
1 GGGTAAAAATGTAATTTTTTAAA-GTTTTAGGGTTAAAAT-GAAATTTTTGAAGTTCAG
58161 GGGTAAAAATGTAATTTTT
1 GGGTAAAAATGTAATTTTT
58180 GGACAATTTA
Statistics
Matches: 203, Mismatches: 23, Indels: 34
0.78 0.09 0.13
Matches are distributed among these distances:
49 12 0.06
50 24 0.12
51 1 0.00
52 2 0.01
53 3 0.01
54 2 0.01
55 2 0.01
57 4 0.02
58 92 0.45
59 54 0.27
60 7 0.03
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.39
Consensus pattern (57 bp):
GGGTAAAAATGTAATTTTTTAAAGTTTTAGGGTTAAAATGAAATTTTTGAAGTTCAG
Found at i:58032 original size:79 final size:78
Alignment explanation
Indices: 57900--58054 Score: 195
Period size: 79 Copynumber: 2.0 Consensus size: 78
57890 AATTTTTTAA
* * * *
57900 AGTTTCAGGGTTAAAAATGAAATTTTTGAAAGTTCGGGGGTAAAATGTAATTTTTGGAAGTTTTG
1 AGTTTCAGGGATAAAAATGAAATTTTTGAAAGTTCAGGGGTAAAATGGAATTTTTGGAAGTTTAG
*
57965 AGGTTAAAAATGGG
66 -GGGTAAAAATGGG
* * * * *
57979 AGTTTC-GGGATAAAAATGTATTTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTTA
1 AGTTTCAGGGATAAAAATGAAATTTTTGAAAG-TTCAGGGGTAAAATGGAATTTTTGGAAGTTTA
58043 GGGGTAAAAATG
65 GGGGTAAAAATG
58055 TATTTTTTGA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
78 31 0.48
79 34 0.52
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (78 bp):
AGTTTCAGGGATAAAAATGAAATTTTTGAAAGTTCAGGGGTAAAATGGAATTTTTGGAAGTTTAG
GGGTAAAAATGGG
Found at i:58148 original size:59 final size:58
Alignment explanation
Indices: 57989--58179 Score: 276
Period size: 58 Copynumber: 3.3 Consensus size: 58
57979 AGTTTCGGGA
* * * * * *
57989 TAAAAATGTATTTTTTGGAAGTTTTAGGGTTAAAATGGAATTTTTGGAAGTTTAGGGG
1 TAAAAATGAATTTTTTGAAAGTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCAAGGG
*
58047 TAAAAATGTATTTTTTGAAAGTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCAAGGG
1 TAAAAATGAATTTTTTGAAAGTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCAAGGG
*
58105 TAAAAATGCAATTTTTT-AAATGTTTTGGGGTTAAAATGGAATTTTTTGAAGTTCAAGGG
1 TAAAAATG-AATTTTTTGAAA-GTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCAAGGG
58164 TAAAAATGTAATTTTT
1 TAAAAATG-AATTTTT
58180 GGACAATTTA
Statistics
Matches: 123, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
58 64 0.52
59 59 0.48
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (58 bp):
TAAAAATGAATTTTTTGAAAGTTTTGGGGTTAAAATGGAATTTTTAGAAGTTCAAGGG
Found at i:61070 original size:21 final size:21
Alignment explanation
Indices: 61025--61087 Score: 81
Period size: 21 Copynumber: 2.9 Consensus size: 21
61015 AAATATTAGC
*
61025 AATAAATAGCATTAATAAGTATT
1 AATAAA-AACATTAATAA-TATT
* *
61048 AATAAAAATATTATTAATATT
1 AATAAAAACATTAATAATATT
61069 AATAAAAACATTAATAATA
1 AATAAAAACATTAATAATA
61088 ATAAAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 21 0.60
22 8 0.23
23 6 0.17
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
AATAAAAACATTAATAATATT
Found at i:62198 original size:29 final size:29
Alignment explanation
Indices: 62157--62413 Score: 236
Period size: 30 Copynumber: 8.8 Consensus size: 29
62147 AAACTGTTCG
62157 AAAATTACATTTTTACCCTCGAACTTCCA
1 AAAATTACATTTTTACCCTCGAACTTCCA
* * *
62186 AAAATTTCATTTTTGA-CCTCCAAACTTTCA
1 AAAATTACATTTTT-ACCCT-CGAACTTCCA
*
62216 AAAATTACATTTTTACCCTCGAACTTCTA
1 AAAATTACATTTTTACCCTCGAACTTCCA
* * *
62245 AAAATTCCATTTTGA-CCTCGAAACTTTCA
1 AAAATTACATTTTTACCCTCG-AACTTCCA
* * * *
62274 AAATTTACA-TATTACCCCCAAACTTCCA
1 AAAATTACATTTTTACCCTCGAACTTCCA
* * *
62302 AAAATTCCATTTTTGA-CATTGAAACTTCCA
1 AAAATTACATTTTT-ACCCTCG-AACTTCCA
62332 AAAATTACATTTTTACCCTCGAACTTCCAA
1 AAAATTACATTTTTACCCTCGAACTTCC-A
* * * *
62362 AAAATTCCATTTTTAACCTTGAAACTTTCA
1 AAAATTACATTTTTACCCTCG-AACTTCCA
**
62392 AAAATTACCCTTTTACCC-CGAA
1 AAAATTACATTTTTACCCTCGAA
62414 TGTCCCAAAA
Statistics
Matches: 180, Mismatches: 37, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
28 24 0.13
29 66 0.37
30 84 0.47
31 6 0.03
ACGTcount: A:0.36, C:0.25, G:0.04, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTTACCCTCGAACTTCCA
Found at i:62249 original size:59 final size:59
Alignment explanation
Indices: 62147--62472 Score: 369
Period size: 58 Copynumber: 5.5 Consensus size: 59
62137 GGAGGTCCTT
* * *
62147 AAACTGTTCGAAAATTACATTTTTACCCTCGAACTTCCAAAAATTTCATTTTTGACCTCC
1 AAACT-TTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
*
62207 AAACTTTCAAAAATTACATTTTTACCCTCGAACTTCTAAAAATTCCA-TTTTGACCTCG
1 AAACTTTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * * * * *
62265 AAACTTTCAAAATTTACA-TATTACCCCCAAACTTCCAAAAATTCCATTTTTGACATTG
1 AAACTTTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
62323 AAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTTAACCTTG
1 AAACTTTCAAAAATTACATTTTTACCCTCGAACTTCC-AAAAATTCCATTTTTGACCTCG
** * **
62383 AAACTTTCAAAAATTACCCTTTTACCC-CGAA-TGTCCCAAAATTCTGTTTTTGATCC-CG
1 AAACTTTCAAAAATTACATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTTGA-CCTCG
**
62441 -ATTTTTCTAAAAATTACCA-TTTTACCCTCGAA
1 AAACTTTC-AAAAATTA-CATTTTTACCCTCGAA
62473 TGTTTAAAGT
Statistics
Matches: 229, Mismatches: 29, Indels: 17
0.83 0.11 0.06
Matches are distributed among these distances:
57 29 0.13
58 83 0.36
59 68 0.30
60 49 0.21
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (59 bp):
AAACTTTCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:62455 original size:118 final size:115
Alignment explanation
Indices: 62147--62472 Score: 320
Period size: 118 Copynumber: 2.8 Consensus size: 115
62137 GGAGGTCCTT
* * * * * *
62147 AAACTGTTCGAAAATTACATTTTTACCCTCGAACTTCCAAAAATTTCATTTTTGAC-CTCCAAAC
1 AAACT-TTCAAAAATTACA-TATTACCCCCAAACTTCCAAAAATTCCATTTTTGACAC-CGAAA-
* *
62211 TTTCAAAAATTACATTTTTACCCTCGAACTTCTAAAAATTCCATTTTGACCTCG
62 TTTCAAAAATTACATTTTTACCCTCGAACTTCAAAAAATTCCATTTTAACCTCG
* ** *
62265 AAACTTTCAAAATTTACATATTACCCCCAAACTTCCAAAAATTCCATTTTTGACATTGAAACTTC
1 AAACTTTCAAAAATTACATATTACCCCCAAACTTCCAAAAATTCCATTTTTGACACCGAAA-TTT
*
62330 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAAATTCCATTTTTAACCTTG
65 CAAAAATTACATTTTTACCCTCGAACTT-CAAAAAATTCCA-TTTTAACCTCG
* * * * ** **
62383 AAACTTTCAAAAATTACCCTTTTA-CCCCGAA-TGTCCCAAAATTCTGTTTTTGATC-CCGATTT
1 AAACTTTCAAAAATTA-CATATTACCCCCAAACT-TCCAAAAATTCCATTTTTGA-CACCGAAAT
62445 TTCTAAAAATTACCA-TTTTACCCTCGAA
63 TTC-AAAAATTA-CATTTTTACCCTCGAA
62473 TGTTTAAAGT
Statistics
Matches: 175, Mismatches: 25, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
116 66 0.38
117 26 0.15
118 75 0.43
119 8 0.05
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (115 bp):
AAACTTTCAAAAATTACATATTACCCCCAAACTTCCAAAAATTCCATTTTTGACACCGAAATTTC
AAAAATTACATTTTTACCCTCGAACTTCAAAAAATTCCATTTTAACCTCG
Found at i:65262 original size:3 final size:3
Alignment explanation
Indices: 65254--65285 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
65244 GTTGCCATAT
65254 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
65286 AAATAAACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:78620 original size:21 final size:22
Alignment explanation
Indices: 78579--78622 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
78569 TTAGTTTTCA
78579 AAATTTACAAAACTACAAAATT
1 AAATTTACAAAACTACAAAATT
* *
78601 AAATTTA-AAAAGTACGAAATT
1 AAATTTACAAAACTACAAAATT
78622 A
1 A
78623 TTGAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (22 bp):
AAATTTACAAAACTACAAAATT
Found at i:86176 original size:3 final size:3
Alignment explanation
Indices: 86170--86198 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
86160 AGGGGTTCCA
86170 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
86199 GATTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:88472 original size:2 final size:2
Alignment explanation
Indices: 88467--88498 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
88457 TTACTGATTA
88467 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
88499 GTTTACGTAC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90251 original size:3 final size:3
Alignment explanation
Indices: 90245--90272 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
90235 TAATTCACAA
90245 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
90273 GTTAATGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:96974 original size:20 final size:20
Alignment explanation
Indices: 96949--97011 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
96939 TGCACGTTGA
* *
96949 CAATTGGCTCTATCACAACT
1 CAATTGACTTTATCACAACT
96969 CAATTGACTTTATCACAACT
1 CAATTGACTTTATCACAACT
96989 CAATTGACTTTATCACAACT
1 CAATTGACTTTATCACAACT
97009 CAA
1 CAA
97012 GTACAACATA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.32
Consensus pattern (20 bp):
CAATTGACTTTATCACAACT
Done.