Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001182.1 Kokia drynarioides strain JFW-HI SEQ_112516, 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: 45406
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5383 original size:66 final size:66
Alignment explanation
Indices: 5289--5413 Score: 189
Period size: 66 Copynumber: 1.9 Consensus size: 66
5279 CTTAAAGCGG
* *
5289 AGGTAGCAACGAGAGAAGTAGAGACTCAAAGAAAATATGATGAACTTCAGCTACAACTTGAAGCC
1 AGGTAGCAACGAGAGAAGTAGAGACTCAAAGAAAATATGACGAACTACAGCTACAACTTGAAGCC
5354 A
66 A
* * *
5355 AGGTAGCAGCGA-AGGAAGTAGAGTCTCAAAGAAAGTATGACGAACTACAGCTACAACTT
1 AGGTAGCAACGAGA-GAAGTAGAGACTCAAAGAAAATATGACGAACTACAGCTACAACTT
5414 CAAAATATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
65 1 0.02
66 52 0.98
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (66 bp):
AGGTAGCAACGAGAGAAGTAGAGACTCAAAGAAAATATGACGAACTACAGCTACAACTTGAAGCC
A
Found at i:6215 original size:24 final size:22
Alignment explanation
Indices: 6188--6239 Score: 59
Period size: 24 Copynumber: 2.3 Consensus size: 22
6178 AAAAAATTCA
6188 AAAAAAAAACTAAAACTAGTAAAT
1 AAAAAAAAACTAAAACT-G-AAAT
** *
6212 AAAAATTAAGTAAAACTGAAAT
1 AAAAAAAAACTAAAACTGAAAT
6234 AAAAAA
1 AAAAAA
6240 TATATAAGCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 9 0.38
23 1 0.04
24 14 0.58
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAAAAAACTAAAACTGAAAT
Found at i:6394 original size:20 final size:20
Alignment explanation
Indices: 6346--6394 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
6336 GTAAAAAAAG
6346 AAGAAGTAAAAAACCTTATAA
1 AAGAA-TAAAAAACCTTATAA
*
6367 AATAAATAAAAAACCATTA-AA
1 AA-GAATAAAAAACC-TTATAA
6388 AAGAATA
1 AAGAATA
6395 GCTAAAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.18
Consensus pattern (20 bp):
AAGAATAAAAAACCTTATAA
Found at i:8347 original size:36 final size:36
Alignment explanation
Indices: 8300--8404 Score: 192
Period size: 36 Copynumber: 2.9 Consensus size: 36
8290 GTTGTATATA
*
8300 CAAGAAGTGGTAACTGCACTCTAACAACGTACTGTT
1 CAAGAAGTGGTAACTACACTCTAACAACGTACTGTT
8336 CAAGAAGTGGTAACTACACTCTAACAACGTACTGTT
1 CAAGAAGTGGTAACTACACTCTAACAACGTACTGTT
*
8372 CAAGAAGTGGTAACTACACTCTAACAACATACT
1 CAAGAAGTGGTAACTACACTCTAACAACGTACT
8405 ATTAATTCAA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.24
Consensus pattern (36 bp):
CAAGAAGTGGTAACTACACTCTAACAACGTACTGTT
Found at i:12084 original size:28 final size:28
Alignment explanation
Indices: 12052--12150 Score: 85
Period size: 28 Copynumber: 3.5 Consensus size: 28
12042 AAATAGTCCA
12052 AAAATTACATTTTTACCTCGAACTTTTC
1 AAAATTACATTTTTACCTCGAACTTTTC
* * ** *
12080 AAAATTCCATTCTTGACC-CTTATTTTTCC
1 AAAATTACATT-TTTACCTCGAACTTTT-C
* *
12109 AAAATTACA-TTTTACCCTCGAACTTCTA
1 AAAATTACATTTTTA-CCTCGAACTTTTC
*
12137 AAAATTCCATTTTT
1 AAAATTACATTTTT
12151 GACCCTGATT
Statistics
Matches: 53, Mismatches: 13, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
27 3 0.06
28 27 0.51
29 23 0.43
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.42
Consensus pattern (28 bp):
AAAATTACATTTTTACCTCGAACTTTTC
Found at i:12121 original size:57 final size:57
Alignment explanation
Indices: 12052--12183 Score: 176
Period size: 57 Copynumber: 2.3 Consensus size: 57
12042 AAATAGTCCA
* * * *
12052 AAAATTACATTTTTA-CCTCGAACTTTTCAAAATTCCATTCTTGACCCTTATTTTTCC
1 AAAATTACA-TTTTACCCTCGAACTTCTAAAAATTCCATTCTTGACCCTGATTCTTCC
*
12109 AAAATTACATTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCTGATTCTTCC
1 AAAATTACATTTTACCCTCGAACTTCTAAAAATTCCATTCTTGACCCTGATTCTTCC
*
12166 AAAAAGTACCATTTTACC
1 -AAAATTA-CATTTTACC
12184 ACTGGCGTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
56 5 0.08
57 46 0.70
58 6 0.09
59 9 0.14
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.39
Consensus pattern (57 bp):
AAAATTACATTTTACCCTCGAACTTCTAAAAATTCCATTCTTGACCCTGATTCTTCC
Found at i:12162 original size:27 final size:29
Alignment explanation
Indices: 12050--12180 Score: 69
Period size: 28 Copynumber: 4.5 Consensus size: 29
12040 CTAAATAGTC
* *
12050 CAAAAATTACATTTTT-A-CCTCGAACTTTT
1 CAAAAATTCCATTTTTGACCCT-G-ACTTCT
* * * *
12079 C-AAAATTCCATTCTTGACCCTTATTTTT
1 CAAAAATTCCATTTTTGACCCTGACTTCT
* *
12107 CCAAAATTACA-TTTT-ACCCTCGAACTTCT
1 CAAAAATTCCATTTTTGACCCT-G-ACTTCT
12136 -AAAAATTCCATTTTTGACCCTGA-TTCTT
1 CAAAAATTCCATTTTTGACCCTGACTTC-T
*
12164 CCAAAAAGTACCATTTT
1 -CAAAAA-TTCCATTTT
12181 ACCACTGGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
27 8 0.10
28 31 0.39
29 19 0.24
30 13 0.16
31 8 0.10
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (29 bp):
CAAAAATTCCATTTTTGACCCTGACTTCT
Found at i:12170 original size:30 final size:30
Alignment explanation
Indices: 12080--12180 Score: 93
Period size: 29 Copynumber: 3.4 Consensus size: 30
12070 CGAACTTTTC
* * *
12080 AAAATTCCATTCTTGACCCTTATTTTTCC-
1 AAAATTCCATTTTTGACCCTGATTCTTCCA
* * *
12109 AAAATTACA-TTTT-ACCCTCGA-ACTTCTA
1 AAAATTCCATTTTTGACCCT-GATTCTTCCA
12137 AAAATTCCATTTTTGACCCTGATTCTTCCA
1 AAAATTCCATTTTTGACCCTGATTCTTCCA
*
12167 AAAAGTACCATTTT
1 AAAA-TTCCATTTT
12181 ACCACTGGCG
Statistics
Matches: 56, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
27 8 0.14
28 12 0.21
29 14 0.25
30 14 0.25
31 8 0.14
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (30 bp):
AAAATTCCATTTTTGACCCTGATTCTTCCA
Found at i:12209 original size:57 final size:56
Alignment explanation
Indices: 12052--12212 Score: 168
Period size: 57 Copynumber: 2.8 Consensus size: 56
12042 AAATAGTCCA
* * * *
12052 AAAATTACATTTTTA-CCTCGAACTTTTCAAAATTCCATTCTTGACCCTTATTTTTCC
1 AAAAGTACA-TTTTACCCTCGAACTTTTAAAAATTCCATT-TTGACCCTGATTCTTCC
* *
12109 AAAATTACATTTTACCCTCGAACTTCTAAAAATTCCATTTTTGACCCTGATTCTTCC
1 AAAAGTACATTTTACCCTCGAACTTTTAAAAATTCCA-TTTTGACCCTGATTCTTCC
*
12166 AAAAAGTACCATTTTACCACT-G-GCGTTTTAAAAATTCCA-TTTGACCC
1 -AAAAGTA-CATTTTACC-CTCGAAC-TTTTAAAAATTCCATTTTGACCC
12213 CCAACTTTCC
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
56 5 0.05
57 52 0.57
58 9 0.10
59 23 0.25
60 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.06, T:0.39
Consensus pattern (56 bp):
AAAAGTACATTTTACCCTCGAACTTTTAAAAATTCCATTTTGACCCTGATTCTTCC
Found at i:18951 original size:21 final size:21
Alignment explanation
Indices: 18925--18968 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
18915 AGAGGCGGTG
18925 GAATGCTCCTTTCGATCGTTA
1 GAATGCTCCTTTCGATCGTTA
*
18946 GAATGCTCCTTTCGATTGTTA
1 GAATGCTCCTTTCGATCGTTA
18967 GA
1 GA
18969 GTTTGTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (21 bp):
GAATGCTCCTTTCGATCGTTA
Found at i:24012 original size:49 final size:49
Alignment explanation
Indices: 23959--24107 Score: 142
Period size: 49 Copynumber: 3.1 Consensus size: 49
23949 AGCGAATCCA
* * *
23959 GTATCGTAAAGACACAAAGGGAAGGGTTTAAATCGCAATGGCAAACCTT
1 GTATCGTAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTT
* * * * * * * * *
24008 GTATC-TCAGAGACATGAAA-GGAATGATCTAAGCCGCAACGGCGGATC-A
1 GTATCGT-AAAGACA-CAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTT
*
24056 GTACCGTAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTT
1 GTATCGTAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTT
24105 GTA
1 GTA
24108 CCTCAGAAAC
Statistics
Matches: 73, Mismatches: 22, Indels: 10
0.70 0.21 0.10
Matches are distributed among these distances:
47 3 0.04
48 33 0.45
49 34 0.47
50 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (49 bp):
GTATCGTAAAGACACAAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTT
Found at i:24092 original size:97 final size:98
Alignment explanation
Indices: 23921--24590 Score: 612
Period size: 98 Copynumber: 6.9 Consensus size: 98
23911 ATACCATAAA
* * * ** *
23921 ACATGAAGGGAAAGATTTAAGCTGCAACAGCGAATCCAGTATCGTAAAGACACAAAGGGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
* * * *
23986 TTAAATCGCAATGGCAAACCTTGTATCTCAGAG
66 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAG
* * * * ** *
24019 ACATGAAAGGAATGATCTAAGCCGCAACGGCGGAT-CAGTACCGTAAAGACACAAAGGGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
*
24083 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAA
66 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAG
* * * * * * *
24116 ACATAAAGGGAAAAATCTAAGCCGCAACGGCGGATCTAGTACCACGAAGACAC-AAGGAAAAGGT
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
* *
24180 TTAAGTCGCAACGACGAACCCTGTACCTCAGATG
66 TTAAGTCGCAACGGCGAACCTTGTACCTCAGA-G
* * * * * *
24214 -CA-GAA---AAGGA---AA-C-ACAACGACGAATCCAGTACCACAACA-AAATAAAGGGAAAGA
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAA-AGACACAAAGGGAAAGG
*
24268 TTTAAGTCGCAACGACGAACCTTGTACCT-AGAAG
65 TTTAAGTCGCAACGGCGAACCTTGTACCTCAG-AG
* * * * *** *
24302 ACATGAAGGGAAACATTTAAGCTGCAATGGTGAATCCAGTACCACAAAGACATGGAGGGAAGGGT
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
**
24367 TTAAGTCGCAACGGTAAACCTTGTACCTCAGAG
66 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAG
* * * * * ****
24400 ACAAGAAGGGAAAGATCTAAGTTGCAACGGCGGATCCAATACCACGAAGATTTGAAGGGAAAGGT
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
* *
24465 TTAAGTCGCAACGACGAACCTTGTACCTCAGAA
66 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAG
* * ** * * ** * *
24498 ACATGAAGGGAGAGATTTAAGCTATAATGGTGAATCCAGTACCATTAGGGCACAAAGGGAAAGGT
1 ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
* *
24563 TTAAGTCGCAATGGCAAACCTTGTACCT
66 TTAAGTCGCAACGGCGAACCTTGTACCT
24591 TAAAAACATA
Statistics
Matches: 465, Mismatches: 90, Indels: 34
0.79 0.15 0.06
Matches are distributed among these distances:
88 24 0.05
89 41 0.09
90 5 0.01
93 6 0.01
96 4 0.01
97 130 0.28
98 253 0.54
99 2 0.00
ACGTcount: A:0.38, C:0.20, G:0.25, T:0.17
Consensus pattern (98 bp):
ACATGAAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACAAAGACACAAAGGGAAAGGT
TTAAGTCGCAACGGCGAACCTTGTACCTCAGAG
Found at i:24124 original size:49 final size:49
Alignment explanation
Indices: 23974--24602 Score: 223
Period size: 49 Copynumber: 13.1 Consensus size: 49
23964 GTAAAGACAC
* * * * * *
23974 AAAGGGAAGGGTTTAAATCGCAATGGCAAACCTTGTATCTCAGAGACAT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
* * * * * * * *
24023 GAAA-GGAATGATCTAAGCCGCAACGGCGGATC-AGTACCGT-A-AAGACAC
1 -AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACC-TCAGAA-ACAT
*
24071 AAAGGGAAGGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
** * * * * * *
24120 AAAGGGAAAAATCTAAGCCGCAACGGCGGATCTAGTACCAC-GAAGACA-
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACAT
* * * *
24168 CAAGGAAAAGGTTTAAGTCGCAACGACGAACCCTGTACCTCAG----AT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
** * * * * * * *
24213 GCA-GAAAAGG---AA-ACACAACGACGAATCC-AGTACCACA-ACAAAAT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTCAGA-AACAT
* *
24257 AAAGGGAAAGATTTAAGTCGCAACGACGAACCTTGTACCT-AGAAGACAT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAA-ACAT
* ** * * * *
24306 GAAGGGAAACATTTAAG-CTGCAATGGTGAATCC-AGTACCACA-AAGACAT
1 AAAGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCTTGTACCTCAGAA-ACAT
** * ** *
24355 GGAGGGAAGGGTTTAAGTCGCAACGGTAAACCTTGTACCTCAGAGACA-
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
* * * * ** * **
24403 AGAAGGGAAAGATCTAAGTTGCAACGGCGGATCC-AATACCAC-GAAGATTT
1 A-AAGGGAAAGGTTTAAGTCGCAACGGC-GAACCTTGTACCTCAGAA-ACAT
* *
24453 GAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCTCAGAAACAT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
* * * ** * * * * ** *
24502 GAAGGGAGAGATTTAAG-CTATAATGGTGAATCC-AGTACCATTAG-GGCAC
1 AAAGGGAAAGGTTTAAGTC-GCAACGGCGAA-CCTTGTACC-TCAGAAACAT
* * * *
24551 AAAGGGAAAGGTTTAAGTCGCAATGGCAAACCTTGTACCTTAAAAACAT
1 AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
24600 AAA
1 AAA
24603 AGATCGAACC
Statistics
Matches: 415, Mismatches: 123, Indels: 83
0.67 0.20 0.13
Matches are distributed among these distances:
40 18 0.04
41 4 0.01
44 11 0.03
45 6 0.01
47 4 0.01
48 84 0.20
49 266 0.64
50 22 0.05
ACGTcount: A:0.39, C:0.20, G:0.24, T:0.17
Consensus pattern (49 bp):
AAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACAT
Found at i:25298 original size:17 final size:16
Alignment explanation
Indices: 25262--25353 Score: 87
Period size: 17 Copynumber: 5.6 Consensus size: 16
25252 AGAACTCATT
* *
25262 TTTAATTTTTAATTTA
1 TTTAAATTTGAATTTA
25278 TTTAAATTTGAATTTA
1 TTTAAATTTGAATTTA
25294 CTTTAAATTTGAATTTA
1 -TTTAAATTTGAATTTA
* * *
25311 TTTTGAGTTTGGATTTAA
1 -TTTAAATTTGAATTT-A
*
25329 TTTTAAATTTAAATTTA
1 -TTTAAATTTGAATTTA
25346 -TTAAATTT
1 TTTAAATTT
25354 AAACTTTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
15 8 0.12
16 14 0.22
17 29 0.45
18 13 0.20
ACGTcount: A:0.34, C:0.01, G:0.07, T:0.59
Consensus pattern (16 bp):
TTTAAATTTGAATTTA
Found at i:25303 original size:34 final size:34
Alignment explanation
Indices: 25262--25362 Score: 98
Period size: 33 Copynumber: 3.0 Consensus size: 34
25252 AGAACTCATT
* *
25262 TTTAATTTTTAATTTATTTAAATTTGAATTT-AC
1 TTTAAATTTAAATTTATTTAAATTTGAATTTAAC
* * * * *
25295 TTTAAATTTGAATTTATTTTGAGTTTGGATTTAAT
1 TTTAAATTTAAATTTA-TTTAAATTTGAATTTAAC
*
25330 TTTAAATTTAAATTTA-TTAAATTTAAACTTTAA
1 TTTAAATTTAAATTTATTTAAATTTGAA-TTTAA
25363 AAAGTCCAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
33 21 0.39
34 17 0.31
35 16 0.30
ACGTcount: A:0.36, C:0.02, G:0.06, T:0.56
Consensus pattern (34 bp):
TTTAAATTTAAATTTATTTAAATTTGAATTTAAC
Found at i:25351 original size:15 final size:16
Alignment explanation
Indices: 25331--25361 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
25321 GGATTTAATT
25331 TTAAATTTAAA-TTTA
1 TTAAATTTAAACTTTA
25346 TTAAATTTAAACTTTA
1 TTAAATTTAAACTTTA
25362 AAAAGTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAATTTAAACTTTA
Found at i:26029 original size:3 final size:3
Alignment explanation
Indices: 26021--26054 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
26011 TTAAATGAGT
26021 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
26055 TATTATTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:26059 original size:3 final size:3
Alignment explanation
Indices: 26053--26091 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
26043 AATAATAATA
26053 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
26092 TTAGTAAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27345 original size:29 final size:29
Alignment explanation
Indices: 27312--27680 Score: 149
Period size: 29 Copynumber: 12.6 Consensus size: 29
27302 CCCTAAATAG
*
27312 TCCAAAAATTACATTTTTACCCTCGAACT
1 TCCAAAAATTACATTTTTACCCTCGAATT
* * *
27341 TCCAAAAATTCCATTTTAACCC-CGATTTT
1 TCCAAAAATTACATTTTTACCCTCGA-ATT
* *
27370 TCCAAAAATTACATTTTTTACCTTAGAACTT
1 TCCAAAAATTACA-TTTTTACCCTCGAA-TT
* * * * * *
27401 TCCATAACTCA-ATTCTTGA-CCACGATTTT
1 TCCAAAAATTACATT-TTTACCCTCGA-ATT
* **
27430 TCC-AAGATTACATTTTTACCCCTAAAATT
1 TCCAAAAATTACATTTTTA-CCCTCGAATT
* *
27459 TCC-AAAATT-CTATTTTTAACCTCGATTTTTT
1 TCCAAAAATTAC-ATTTTTACCCTCGA---ATT
* *
27490 TCCAAACATTACCA-TTTTACCC-CAAATT
1 TCCAAAAATTA-CATTTTTACCCTCGAATT
* * *
27518 TTCAAAAATTCCATTTTTAACCC-CGATTT
1 TCCAAAAATTACATTTTT-ACCCTCGAATT
* *
27547 TCCAAAAATTACCA-TTTTACCCTCAAACT
1 TCCAAAAATTA-CATTTTTACCCTCGAATT
* * *
27576 TCGAGAAATT-CAATTTTTAACCCT-GATTCT
1 TCCAAAAATTAC-ATTTTT-ACCCTCGAAT-T
*
27606 TCC-AAAAGTACCA-TTTTACCCTCGAAGTT
1 TCCAAAAATTA-CATTTTTACCCTCGAA-TT
* * * *
27635 T-TAAAAATTCCATTTTGACCC-CCAACTT
1 TCCAAAAATTACATTTTTACCCTCGAA-TT
*
27663 TCCCAAAATTACCATTTT
1 TCCAAAAATTA-CATTTT
27681 GTCCCCAAGT
Statistics
Matches: 245, Mismatches: 63, Indels: 63
0.66 0.17 0.17
Matches are distributed among these distances:
27 3 0.01
28 46 0.19
29 130 0.53
30 32 0.13
31 20 0.08
32 12 0.05
33 1 0.00
34 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.04, T:0.38
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCTCGAATT
Found at i:27492 original size:60 final size:58
Alignment explanation
Indices: 27312--27612 Score: 270
Period size: 58 Copynumber: 5.1 Consensus size: 58
27302 CCCTAAATAG
** *
27312 TCCAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTAACCCCGATTTT
1 TCCAAAAATTACATTTTTACCCTAAAATTTCC-AAAATTCCATTTTTAACCCCGATTTT
* * * * * * * *
27370 TCCAAAAATTACATTTTTTACCTTAGAACTTTCCATAACTCAATTCTTGACCACGATTTT
1 TCCAAAAATTACA-TTTTTACCCTA-AAATTTCCAAAATTCCATTTTTAACCCCGATTTT
* * *
27430 TCC-AAGATTACATTTTTACCCCTAAAATTTCCAAAATTCTATTTTTAACCTCGATTTTTT
1 TCCAAAAATTACATTTTTA-CCCTAAAATTTCCAAAATTCCATTTTTAACCCCGA--TTTT
* * * *
27490 TCCAAACATTACCA-TTTTACCCCAAATTTTCAAAAATTCCATTTTTAACCCCGA-TTT
1 TCCAAAAATTA-CATTTTTACCCTAAAATTTCCAAAATTCCATTTTTAACCCCGATTTT
* * * * * *
27547 TCCAAAAATTACCA-TTTTACCCTCAAACTTCGAGAAATTCAATTTTTAACCCTGATTCT
1 TCCAAAAATTA-CATTTTTACCCTAAAATTTCCA-AAATTCCATTTTTAACCCCGATTTT
27606 TCCAAAA
1 TCCAAAA
27613 GTACCATTTT
Statistics
Matches: 198, Mismatches: 35, Indels: 19
0.79 0.14 0.08
Matches are distributed among these distances:
57 30 0.15
58 61 0.31
59 36 0.18
60 58 0.29
61 11 0.06
62 2 0.01
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.38
Consensus pattern (58 bp):
TCCAAAAATTACATTTTTACCCTAAAATTTCCAAAATTCCATTTTTAACCCCGATTTT
Found at i:27618 original size:58 final size:57
Alignment explanation
Indices: 27316--27680 Score: 207
Period size: 58 Copynumber: 6.2 Consensus size: 57
27306 AAATAGTCCA
* * *
27316 AAAATTA-CATTTTTACCCTCGAA-CTTCCAAAAATTCCA-TTTTAACCCCGATTTTTCC
1 AAAATTACCA-TTTTACCCTCAAATCTT-CAAAAATTCAATTTTTAACCCTGA-TTTTCC
* * * * * *
27373 AAAAATTA-CATTTTTTA-CCTTAGAA-CTTTCCATAACTCAATTCTTGACCAC-GATTTTTCC
1 -AAAATTACCA--TTTTACCCTCA-AATC-TTCAAAAATTCAATTTTTAACC-CTGA-TTTTCC
* * * *
27433 AAGATTA-CATTTTTACCCCTAAAAT-TTCCAAAATTCTATTTTTAA-CCTCGATTTTTTTCC
1 AAAATTACCA-TTTTA-CCCTCAAATCTTCAAAAATTCAATTTTTAACCCT-GA---TTTTCC
* * *
27493 AAACATTACCATTTTACCC-CAAATTTTCAAAAATTCCATTTTTAACCCCGATTTTCC
1 AAA-ATTACCATTTTACCCTCAAATCTTCAAAAATTCAATTTTTAACCCTGATTTTCC
*
27550 AAAAATTACCATTTTACCCTCAAA-CTTCGAGAAATTCAATTTTTAACCCTGATTCTTCC
1 -AAAATTACCATTTTACCCTCAAATCTTC-AAAAATTCAATTTTTAACCCTGATT-TTCC
* * * * * * ** *
27609 AAAAGTACCATTTTACCCTCGAAGT-TTTAAAAATTCCATTTTGACCCCCAACTTTCCC
1 AAAATTACCATTTTACCCTC-AAATCTTCAAAAATTCAATTTTTAACCCTGA-TTTTCC
27667 AAAATTACCATTTT
1 AAAATTACCATTTT
27681 GTCCCCAAGT
Statistics
Matches: 249, Mismatches: 35, Indels: 46
0.75 0.11 0.14
Matches are distributed among these distances:
56 1 0.00
57 25 0.10
58 116 0.47
59 40 0.16
60 53 0.21
61 12 0.05
62 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.38
Consensus pattern (57 bp):
AAAATTACCATTTTACCCTCAAATCTTCAAAAATTCAATTTTTAACCCTGATTTTCC
Found at i:27686 original size:29 final size:29
Alignment explanation
Indices: 27638--27754 Score: 107
Period size: 28 Copynumber: 4.1 Consensus size: 29
27628 CGAAGTTTTA
* **
27638 AAAATT-CCATTTTGACCCCCAACTTTCCC
1 AAAATTACCATTTTGACCCCCAA-GTGACC
*
27667 AAAATTACCATTTTG-TCCCCAAGTGACC
1 AAAATTACCATTTTGACCCCCAAGTGACC
* ***
27695 AAAATTACCATTTTG-CTCTTGAGTGACC
1 AAAATTACCATTTTGACCCCCAAGTGACC
* *
27723 AAAATTACCATTTTG-CCCTCAAGTGTCC
1 AAAATTACCATTTTGACCCCCAAGTGACC
27751 AAAA
1 AAAA
27755 ATCACATTTT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
28 54 0.73
29 12 0.16
30 8 0.11
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.31
Consensus pattern (29 bp):
AAAATTACCATTTTGACCCCCAAGTGACC
Found at i:27764 original size:28 final size:28
Alignment explanation
Indices: 27665--27754 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
27655 CCCAACTTTC
27665 CCAAAATTACCATTTTGTCCC-CAAGTGA
1 CCAAAATTACCATTTTG-CCCTCAAGTGA
* **
27693 CCAAAATTACCATTTTGCTCTTGAGTGA
1 CCAAAATTACCATTTTGCCCTCAAGTGA
*
27721 CCAAAATTACCATTTTGCCCTCAAGTGT
1 CCAAAATTACCATTTTGCCCTCAAGTGA
27749 CCAAAA
1 CCAAAA
27755 ATCACATTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 2 0.04
28 52 0.96
ACGTcount: A:0.32, C:0.27, G:0.11, T:0.30
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCTCAAGTGA
Found at i:39916 original size:34 final size:34
Alignment explanation
Indices: 39870--39984 Score: 203
Period size: 34 Copynumber: 3.4 Consensus size: 34
39860 ACATCAGCAC
*
39870 CCACCATCTGCCACCACCACCAGCAACTAGCACCA
1 CCACCA-CTGCCACCACCACTAGCAACTAGCACCA
39905 CCACCACTGCCACCACCACTAGCAACTAGCACCA
1 CCACCACTGCCACCACCACTAGCAACTAGCACCA
*
39939 CCACCACTGCCACCACCACTAGCAACTTGCACCA
1 CCACCACTGCCACCACCACTAGCAACTAGCACCA
39973 CCACCACTGCCA
1 CCACCACTGCCA
39985 TCTGCAAGGG
Statistics
Matches: 78, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
34 72 0.92
35 6 0.08
ACGTcount: A:0.30, C:0.51, G:0.09, T:0.10
Consensus pattern (34 bp):
CCACCACTGCCACCACCACTAGCAACTAGCACCA
Found at i:39919 original size:12 final size:12
Alignment explanation
Indices: 39902--39958 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 12
39892 GCAACTAGCA
39902 CCACCACCACTG
1 CCACCACCACTG
39914 CCACCACCACTAG
1 CCACCACCACT-G
* * *
39927 CAACTAGCA---
1 CCACCACCACTG
39936 CCACCACCACTG
1 CCACCACCACTG
39948 CCACCACCACT
1 CCACCACCACT
39959 AGCAACTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 6 0.17
12 22 0.63
13 7 0.20
ACGTcount: A:0.30, C:0.54, G:0.07, T:0.09
Consensus pattern (12 bp):
CCACCACCACTG
Found at i:41508 original size:30 final size:29
Alignment explanation
Indices: 41431--41790 Score: 200
Period size: 30 Copynumber: 12.1 Consensus size: 29
41421 CCCAGTAGGT
* ** *
41431 CCCT-AAACTTTCTAGAAATCTTATTTTGA
1 CCCTCAAACTTTTTA-AAATCACATTTTAA
** *
41460 CCCT-AAACTTCTCCAAAATAACATTTTAA
1 CCCTCAAACTT-TTTAAAATCACATTTTAA
* * *
41489 CCCTCGAACTTTTATAAAATAATATTTTAA
1 CCCTCAAACTTTT-TAAAATCACATTTTAA
* *
41519 CCC-CTAACTTTCTTAAAATCATATTTTAA
1 CCCTCAAACTTT-TTAAAATCACATTTTAA
** * *
41548 CCCTCTAAACTTTCCAAAAAAT-ATATTTTGA
1 CCCTC-AAACTTT--TTAAAATCACATTTTAA
* *
41579 CCCTTAAACTACTTTAAAATCACATTTTAA
1 CCCTCAAACT-TTTTAAAATCACATTTTAA
* * * *
41609 -ACTCGAAACTTCTTTAAAATTATATTTTGA
1 CCCTC-AAACTT-TTTAAAATCACATTTTAA
*
41639 CCC-CTAAACTTTTCCAAAATCACATTTTAA
1 CCCTC-AAACTTTT-TAAAATCACATTTTAA
* * *
41669 -CCTCGAAACTTCTTTAAAATTATATTTTGA
1 CCCTC-AAACTT-TTTAAAATCACATTTTAA
*
41699 CCC-CTAAACTTTCCTAAAATCACATTTTAA
1 CCCTC-AAACTTT-TTAAAATCACATTTTAA
*
41729 -CCTCTAAACTTTCCTAAAATCACATTTTAA
1 CCCTC-AAACTTT-TTAAAATCACATTTTAA
* **
41759 -CCTTAAACTTTTCTAAAATTGCATTTTAA
1 CCCTCAAACTTTT-TAAAATCACATTTTAA
41788 CCC
1 CCC
41791 CGAATTCCTC
Statistics
Matches: 264, Mismatches: 47, Indels: 39
0.75 0.13 0.11
Matches are distributed among these distances:
29 85 0.32
30 149 0.56
31 24 0.09
32 6 0.02
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTCAAACTTTTTAAAATCACATTTTAA
Found at i:41748 original size:60 final size:60
Alignment explanation
Indices: 41433--41789 Score: 333
Period size: 60 Copynumber: 6.0 Consensus size: 60
41423 CAGTAGGTCC
*
41433 CTAAACTTT-CTAGAAATCT-TATTTTGA-CCCTAAACTTCTCC-AAAATAACATTTTAACC-
1 CTAAACTTTCCTA-AAAT-TATATTTTGACCCCTAAACTT-TCCTAAAATCACATTTTAACCT
* ** * * * *
41491 CTCGAACTTTTATAAAATAATATTTTAACCCCT-AACTTTCTTAAAATCATATTTTAACCCT
1 CT-AAACTTTCCTAAAATTATATTTTGACCCCTAAACTTTCCTAAAATCACATTTTAA-CCT
* * * *
41552 CTAAACTTTCCAAAAAATATATTTTGACCCTTAAACTACTT--TAAAATCACATTTTAAACT
1 CTAAACTTTCCTAAAATTATATTTTGACCCCTAAACT--TTCCTAAAATCACATTTTAACCT
* *
41612 CGAAAC-TTCTTTAAAATTATATTTTGACCCCTAAACTTTTCC-AAAATCACATTTTAACCT
1 CTAAACTTTC-CTAAAATTATATTTTGACCCCTAAAC-TTTCCTAAAATCACATTTTAACCT
* *
41672 CGAAAC-TTCTTTAAAATTATATTTTGACCCCTAAACTTTCCTAAAATCACATTTTAACCT
1 CTAAACTTTC-CTAAAATTATATTTTGACCCCTAAACTTTCCTAAAATCACATTTTAACCT
* * * * * **
41732 CTAAACTTTCCTAAAATCACATTTT-AACCTTAAACTTTTCTAAAATTGCATTTTAACC
1 CTAAACTTTCCTAAAATTATATTTTGACCCCTAAACTTTCCTAAAATCACATTTTAACC
41790 CCGAATTCCT
Statistics
Matches: 251, Mismatches: 32, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
58 4 0.02
59 73 0.29
60 147 0.59
61 25 0.10
63 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (60 bp):
CTAAACTTTCCTAAAATTATATTTTGACCCCTAAACTTTCCTAAAATCACATTTTAACCT
Done.