Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003701.1 Kokia drynarioides strain JFW-HI SEQ_116638, 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: 16738
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Found at i:1730 original size:97 final size:97
Alignment explanation
Indices: 1564--1757 Score: 345
Period size: 97 Copynumber: 2.0 Consensus size: 97
1554 AACCTTGAAA
* * *
1564 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGTGCCTAGTAAGTTAAGGTACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATTATGCCTAGTAAGTTAAGGCACAAATTTTCA
1629 AAACCC-AAGATAAAGGAATATTGCCTCGATTT
66 AAACCCGAA-ATAAAGGAATATTGCCTCGATTT
1661 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATTATGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATTATGCCTAGTAAGTTAAGGCACAAATTTTCA
1726 AAACCCGAAATAAAGGAATATTGCCTCGATTT
66 AAACCCGAAATAAAGGAATATTGCCTCGATTT
1758 TAAATATTTT
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 91 0.98
98 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTGAAGAAAAATTATGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCCGAAATAAAGGAATATTGCCTCGATTT
Found at i:2113 original size:29 final size:27
Alignment explanation
Indices: 2066--2461 Score: 215
Period size: 29 Copynumber: 13.9 Consensus size: 27
2056 AAAGTTTTAG
* *
2066 GGGTAAAAATGTCATTTTGGGATAGTTT
1 GGGTAAAAATGTGATTTTTGGA-AGTTT
2094 GGGTAAAAATGTGATTTTTGAGAAGTTT
1 GGGTAAAAATGTGATTTTTG-GAAGTTT
* *
2122 AGGGAAAAAATGTGATTTTTGAAAGTTT
1 -GGGTAAAAATGTGATTTTTGGAAGTTT
* * *
2150 GGGGGCAAAAATGTAATTTTTGGAAGATTGG
1 --GGGTAAAAATGTGATTTTTGGAAG-TT-T
* * *
2181 GGGTAAAATTATGATTTTTGGAAGTTC
1 GGGTAAAAATGTGATTTTTGGAAGTTT
* *
2208 GAGAG-AAAAATGTGATTTTTGAAAGTTCG
1 G-G-GTAAAAATGTGATTTTTGGAAGTT-T
* * *
2237 GGAGCAAAAATGTAATTTTTGGAAGTTCGG
1 GG-GTAAAAATGTGATTTTTGGAAGTT--T
* * *
2267 GGGTAAAAATATGATTTTTAGAAGTTCCA
1 GGGTAAAAATGTGATTTTTGGAAGTT--T
* * *
2296 GGGTAAAAATGTAATTTTTGAAAGTTCAA
1 GGGTAAAAATGTGATTTTTGGAAGTT--T
* * * *
2325 GGGAAAAAATGTAATTTTAGGAAGTTC
1 GGGTAAAAATGTGATTTTTGGAAGTTT
* *
2352 GAAGG-AAAAATGTAATTATTGAGAAGTTT
1 G--GGTAAAAATGTGATTTTTG-GAAGTTT
* * * *
2381 GGGGTAAAAATATAATTTTCGGAAGTTCGA
1 -GGGTAAAAATGTGATTTTTGGAAGTT--T
* * *
2411 GGGAAAAAATATAATTTTTGAGAAGTTT
1 GGGTAAAAATGTGATTTTTG-GAAGTTT
*
2439 GAGGGTTAAAATGT-A-TTTTGGAA
1 --GGGTAAAAATGTGATTTTTGGAA
2462 ATGTTTAAGG
Statistics
Matches: 299, Mismatches: 49, Indels: 41
0.77 0.13 0.11
Matches are distributed among these distances:
27 5 0.02
28 81 0.27
29 192 0.64
30 21 0.07
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (27 bp):
GGGTAAAAATGTGATTTTTGGAAGTTT
Found at i:2163 original size:86 final size:86
Alignment explanation
Indices: 2041--2437 Score: 367
Period size: 86 Copynumber: 4.6 Consensus size: 86
2031 ATTTAAGGTT
** * * * * * *
2041 AAAATGTAATTTTAAAAAGTTTTAGGGGTAAAAATGTCATTTTGGGATAGTT-TGGGTAAAAATG
1 AAAATGTAATTTTTGAAAG-TTCAGGGGCAAAAATGTAATTTTTGGA-AGTTGGGGGTAAAAATA
2105 TGATTTTTGAGAAGTTTAGGGAA
64 TGATTTTTGAGAAGTTTAGGGAA
* ** *
2128 AAAATGTGATTTTTGAAAGTTTGGGGGCAAAAATGTAATTTTTGGAAGATTGGGGGTAAAATTAT
1 AAAATGTAATTTTTGAAAGTTCAGGGGCAAAAATGTAATTTTTGGAAG-TTGGGGGTAAAAATAT
* *
2193 GATTTTTG-GAAG-TTCGAGAGA
65 GATTTTTGAGAAGTTTAGGGA-A
*
2214 AAAATGTGATTTTTGAAAGTTC-GGGAGCAAAAATGTAATTTTTGGAAGTTCGGGGGTAAAAATA
1 AAAATGTAATTTTTGAAAGTTCAGGG-GCAAAAATGTAATTTTTGGAAGTT-GGGGGTAAAAATA
* *
2278 TGATTTTT-AGAAGTTCCAGGGTA
64 TGATTTTTGAGAAGTT-TAGGGAA
* * * ** *
2301 AAAATGTAATTTTTGAAAGTTCAAGGGAAAAAATGTAATTTTAGGAAGTTCGAAGG-AAAAATGT
1 AAAATGTAATTTTTGAAAGTTCAGGGGCAAAAATGTAATTTTTGGAAGTT-GGGGGTAAAAATAT
* * * *
2365 AATTATTGAGAAGTTTGGGGTA
65 GATTTTTGAGAAGTTTAGGGAA
* * * * *
2387 AAAATATAATTTTCGGAAGTTC-GAGGGAAAAAATATAATTTTTGAGAAGTT
1 AAAATGTAATTTTTGAAAGTTCAG-GGGCAAAAATGTAATTTTTG-GAAGTT
2438 TGAGGGTTAA
Statistics
Matches: 263, Mismatches: 35, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
85 12 0.05
86 151 0.57
87 96 0.37
88 4 0.02
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.34
Consensus pattern (86 bp):
AAAATGTAATTTTTGAAAGTTCAGGGGCAAAAATGTAATTTTTGGAAGTTGGGGGTAAAAATATG
ATTTTTGAGAAGTTTAGGGAA
Found at i:2170 original size:58 final size:58
Alignment explanation
Indices: 2094--2457 Score: 298
Period size: 58 Copynumber: 6.3 Consensus size: 58
2084 GGGATAGTTT
* * * *
2094 GGGTAAAAATGTGATTTTTGAGAAGTTTAGGGAAAAAATGTGATTTTTGAAAGTTTGG
1 GGGTAAAAATGTAATTTTTGAGAAGTTGAGGGAAAAAATGTAATTTTTGAAAGTTTGA
* * * * * * * *
2152 GGGCAAAAATGTAATTTTTG-GAAGATTGGGGGTAAAATTATGATTTTTGGAAGTTCGA
1 GGGTAAAAATGTAATTTTTGAGAAG-TTGAGGGAAAAAATGTAATTTTTGAAAGTTTGA
* * * * * *
2210 GAG-AAAAATGTGATTTTTGA-AAGTTCG-GGAGCAAAAATGTAATTTTTGGAAGTTCGG
1 GGGTAAAAATGTAATTTTTGAGAAGTT-GAGG-GAAAAAATGTAATTTTTGAAAGTTTGA
* * * * **
2267 GGGTAAAAATATGATTTTT-AGAAGTTCCAGGGTAAAAATGTAATTTTTGAAAGTTCAA
1 GGGTAAAAATGTAATTTTTGAGAAGTT-GAGGGAAAAAATGTAATTTTTGAAAGTTTGA
* * * *
2325 GGGAAAAAATGTAATTTTAG-GAAGTTCGAAGG-AAAAATGTAATTATTGAGAAGTTTG-
1 GGGTAAAAATGTAATTTTTGAGAAGTT-GAGGGAAAAAATGTAATTTTTGA-AAGTTTGA
* * *
2382 GGGTAAAAATATAATTTTCG-GAAGTTCGAGGGAAAAAATATAATTTTTGAGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGAGAAGTT-GAGGGAAAAAATGTAATTTTTGA-AAGTTTGA
*
2441 GGGTTAAAATGT-ATTTT
1 GGGTAAAAATGTAATTTT
2458 GGAAATGTTT
Statistics
Matches: 254, Mismatches: 41, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
56 4 0.02
57 92 0.36
58 146 0.57
59 12 0.05
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTGAGGGAAAAAATGTAATTTTTGAAAGTTTGA
Found at i:2186 original size:115 final size:112
Alignment explanation
Indices: 2065--2437 Score: 312
Period size: 115 Copynumber: 3.2 Consensus size: 112
2055 AAAAGTTTTA
* *
2065 GGGGTAAAAATGTCATTTTGGGATAGTTTGGGTAAAAATGTGATTTTTGAGAAGTTTAGGGAAAA
1 GGGGTAAAAATGTAATTTT-GGA-AGTTAGGG-AAAAATGTGATTTTTGAGAAGTTTAGGGAAAA
* * * *
2130 AATGTGATTTTTGAAAGTTTGGGGGCAAAAATGTAATTTTTGGAAGATT-G
63 AATGTAATTTTTGAAAGTTTGGGGGTAAAAATATAATTTTTGGAAG-TTCC
* * *
2180 GGGGTAAAATTATG-ATTTTTGGAAGTTCGAGAGAAAAATGTGATTTTTGA-AAG-TTCGGGAGC
1 GGGGTAAAA--ATGTAATTTTGGAAGTT--AGGGAAAAATGTGATTTTTGAGAAGTTTAGGGA--
* * * *
2242 AAAAATGTAATTTTTGGAAGTTCGGGGGTAAAAATATGATTTTTAGAAGTTCC
60 AAAAATGTAATTTTTGAAAGTTTGGGGGTAAAAATATAATTTTTGGAAGTTCC
* * * * * *
2295 AGGGTAAAAATGTAATTTTTGAAAGTTCAAGGGAAAAAATGTAATTTTAG-GAAGTTCGAAGG-A
1 GGGGTAAAAATGTAA-TTTTGGAAGTT--AGGG-AAAAATGTGATTTTTGAGAAGTT-TAGGGAA
* *
2358 AAAATGTAATTATTGAGAAGTTT-GGGGTAAAAATATAATTTTCGGAAGTT-C
61 AAAATGTAATTTTTGA-AAGTTTGGGGGTAAAAATATAATTTTTGGAAGTTCC
* *
2409 GAGGGAAAAAATATAATTTTTGAGAAGTT
1 G-GGGTAAAAATGTAA-TTTTG-GAAGTT
2438 TGAGGGTTAA
Statistics
Matches: 209, Mismatches: 33, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
113 9 0.04
114 11 0.05
115 150 0.72
116 33 0.16
117 4 0.02
118 2 0.01
ACGTcount: A:0.37, C:0.03, G:0.27, T:0.34
Consensus pattern (112 bp):
GGGGTAAAAATGTAATTTTGGAAGTTAGGGAAAAATGTGATTTTTGAGAAGTTTAGGGAAAAAAT
GTAATTTTTGAAAGTTTGGGGGTAAAAATATAATTTTTGGAAGTTCC
Found at i:2457 original size:115 final size:115
Alignment explanation
Indices: 2127--2461 Score: 360
Period size: 115 Copynumber: 2.9 Consensus size: 115
2117 AGTTTAGGGA
* * * * *
2127 AAAAATGTGATTTTTGA-AAGTTTGGGGGCAAAAATGTAATTTTTGGAAGATT-GGGGGTAAAAT
1 AAAAATGTAATTTTTGAGAAGTTT-GGGGTAAAAATATAATTTTTGGAAG-TTCGAGGGTAAAAA
* * * * *
2190 TATGATTTTTG-GAAGTTCGAGAGAAAAATGTGATTTTTGAAAGTTCGGGAGC
64 TATAATTTTTGAGAAGTTCGAGGGAAAAATGT-AATTTTGGAAGTTCGGAAGC
* * * *
2242 AAAAATGTAATTTTTG-GAAGTTCGGGGGTAAAAATATGATTTTTAGAAGTTCCAGGGTAAAAAT
1 AAAAATGTAATTTTTGAGAAGTT-TGGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAAT
* * *
2306 GTAATTTTTGA-AAGTTCAAGGGAAAAAATGTAATTTTAGGAAGTTC-GAAGG
65 ATAATTTTTGAGAAGTTCGAGGG-AAAAATGTAATTTT-GGAAGTTCGGAAGC
* * *
2357 AAAAATGTAATTATTGAGAAGTTTGGGGTAAAAATATAATTTTCGGAAGTTCGAGGGAAAAAATA
1 AAAAATGTAATTTTTGAGAAGTTTGGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAATA
* *
2422 TAATTTTTGAGAAGTTTGAGGGTTAAAATGT-ATTTTGGAA
66 TAATTTTTGAGAAGTTCGAGGG-AAAAATGTAATTTTGGAA
2462 ATGTTTAAGG
Statistics
Matches: 183, Mismatches: 29, Indels: 17
0.80 0.13 0.07
Matches are distributed among these distances:
114 6 0.03
115 140 0.77
116 37 0.20
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (115 bp):
AAAAATGTAATTTTTGAGAAGTTTGGGGTAAAAATATAATTTTTGGAAGTTCGAGGGTAAAAATA
TAATTTTTGAGAAGTTCGAGGGAAAAATGTAATTTTGGAAGTTCGGAAGC
Found at i:2490 original size:30 final size:29
Alignment explanation
Indices: 2417--2495 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 29
2407 TCGAGGGAAA
* * *
2417 AAATATAATTTTT-GAGAAGTTTGAGGGTT
1 AAATATGATTTTTGGA-AAGTTTAAGGGTC
2446 AAA-ATG-TATTTTGGAAATGTTTAAGGGTC
1 AAATATGAT-TTTTGGAAA-GTTTAAGGGTC
2475 AAATATGATTTTTGGAAAGTT
1 AAATATGATTTTTGGAAAGTT
2496 CAGGGACTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
27 1 0.02
28 8 0.19
29 20 0.48
30 12 0.29
31 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (29 bp):
AAATATGATTTTTGGAAAGTTTAAGGGTC
Found at i:2501 original size:87 final size:84
Alignment explanation
Indices: 2094--2501 Score: 294
Period size: 86 Copynumber: 4.7 Consensus size: 84
2084 GGGATAGTTT
* * * *** *
2094 GGGTAAAAATGTGATTTTTGAGAAGTTTAGGGAAAAAATGTGATTTTTGAAAGTTTGGGGGCAAA
1 GGGTAAAAATGT-AATTTTGAGAAGTTTAGGG--TAAATATGATTTTTGAAAGTTCAAGGGAAAA
*
2159 AATGTAATTTTTGGAAGATT-GG
63 AATGTAATTTTTGGAAG-TTCGA
* * ** *
2181 GGGTAAAATTATG-ATTTTTG-GAAGTTCGAGAGAAAAATGTGATTTTTGAAAGTTC--GGGAGC
1 GGGTAAAA--ATGTAATTTTGAGAAGTT-TAG-GGTAAATATGATTTTTGAAAGTTCAAGGGA--
*
2242 AAAAATGTAATTTTTGGAAGTTCGG
60 AAAAATGTAATTTTTGGAAGTTCGA
* * * * *
2267 GGGTAAAAATATGATTTTTAGAAGTTCCAGGGTAAAAATGTAATTTTTGAAAGTTCAAGGGAAAA
1 GGGTAAAAATGTAATTTTGAGAAGTT-TAGGGTAAATATG--ATTTTTGAAAGTTCAAGGGAAAA
*
2332 AATGTAATTTTAGGAAGTTCGA
63 AATGTAATTTTTGGAAGTTCGA
* * * * * *
2354 AGG-AAAAATGTAATTATTGAGAAGTTTGGGGTAAAAATATAATTTTCGGAAGTTCGAGGGAAAA
1 GGGTAAAAATGTAATT-TTGAGAAGTTTAGGGT--AAATATGATTTTTGAAAGTTCAAGGGAAAA
* *
2418 AATATAATTTTTGAGAAGTTTGA
63 AATGTAATTTTTG-GAAGTTCGA
*
2441 GGGTTAAAATGT-ATTTTG-GAAATGTTTAAGGGTCAAATATGATTTTTGGAAAGTTC-AGGGA
1 GGGTAAAAATGTAATTTTGAG-AA-GTTT-AGGGT-AAATATGATTTTT-GAAAGTTCAAGGGA
2502 CTTTTTGGGC
Statistics
Matches: 263, Mismatches: 36, Indels: 44
0.77 0.10 0.13
Matches are distributed among these distances:
84 5 0.02
85 13 0.05
86 116 0.44
87 98 0.37
88 24 0.09
89 7 0.03
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (84 bp):
GGGTAAAAATGTAATTTTGAGAAGTTTAGGGTAAATATGATTTTTGAAAGTTCAAGGGAAAAAAT
GTAATTTTTGGAAGTTCGA
Found at i:3337 original size:17 final size:18
Alignment explanation
Indices: 3313--3404 Score: 79
Period size: 17 Copynumber: 5.4 Consensus size: 18
3303 GGACATTATC
*
3313 AATTTAAATTT-AGAATA
1 AATTTAAATTTAAAAATA
*
3330 ATTTTAAATTTAAAAATA
1 AATTTAAATTTAAAAATA
* *
3348 AATTTAAACTT---ATTA
1 AATTTAAATTTAAAAATA
* *
3363 AATTTAACTTT-AAAACA
1 AATTTAAATTTAAAAATA
*
3380 AATTTAAACTT-AAAATA
1 AATTTAAATTTAAAAATA
3397 AATTTAAA
1 AATTTAAA
3405 ATAACTTTAA
Statistics
Matches: 60, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
15 12 0.20
17 34 0.57
18 14 0.23
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (18 bp):
AATTTAAATTTAAAAATA
Found at i:3403 original size:28 final size:28
Alignment explanation
Indices: 3334--3437 Score: 120
Period size: 28 Copynumber: 3.6 Consensus size: 28
3324 AGAATAATTT
3334 TAAATTTAAAAATAAATTTAAACTTATTAAA
1 TAAATTT-AAAATAAATTTAAACTTA--AAA
* *
3365 TTTAACTTTAAAACAAATTTAAACTTAAAA
1 --TAAATTTAAAATAAATTTAAACTTAAAA
* *
3395 TAAATTTAAAATAACTTTAAGCTTAAAA
1 TAAATTTAAAATAAATTTAAACTTAAAA
3423 TAAATTTAAAA-AAAT
1 TAAATTTAAAATAAAT
3438 GGGTTTAGTT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
27 3 0.05
28 35 0.55
30 3 0.05
32 17 0.27
33 6 0.09
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.37
Consensus pattern (28 bp):
TAAATTTAAAATAAATTTAAACTTAAAA
Found at i:3900 original size:39 final size:39
Alignment explanation
Indices: 3841--4604 Score: 317
Period size: 39 Copynumber: 19.7 Consensus size: 39
3831 AATGACTATA
* * * * *
3841 ATCTGCCCCATGATTGGGGTATGAGATTGGTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
3880 ATCTACCCCAGGCTCGGGGTAAAAGATCGAATG--GTTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
3917 CAATCTACACCAAGCTCGGGGTAAGAGATTTACTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * * ** *
3958 ATCTACCCCAAGCTTGGGGTAAGTGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * *
3995 CAATCTACCCCATGATCGGGGTAAGAGATTTGCTGAAGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
4036 ATTTGCCCCAGGCTCGGAGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
*** * **
4073 CAATCTGCCCCATAATCAGGGTAAGAGATTTACTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * ** * *
4114 ATTTACCCCAAGCTCGGGGTAAGAGATCGAATGGTTG-TA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-GATGATG
* * ** * *
4153 ATCTGCCCCATGATTAGGGTAAGAGATTTGCTGATGATT
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* *
4192 ATCTGCCCCAGGCTCGGGGT--GAGATTGGCTGACGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** **
4229 ATCTACCCCAGGCTTGGGGTAAGAGATCGAATGACT-ACA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGATG
* *
4268 ATCTACCCCAGGCTCGGGGTAAGAGATTAGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * *
4307 ATCTGCCCTAGGCTCAGGGTAAGAGATCAAATGGCT--TCA--
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT----TGGCTGATGATG
* * * *
4346 ATCTGCTCCACGCTCGGGGTAAGAGATTTGCTGATGGTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
** * *
4385 ATCTGCCATAGGCTCGGGGTAAGAGATTGGTTGACGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
4424 ATCTGTCCCAAGCTCAGGGTAAGAGATTGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * ** * *
4461 CAATCTGGCCCAAGCTCAAGGTAAGAGATTTGCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * ** *
4502 ATCTGCCCCAGGCTTGCGGTAAGAGATCGAATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * **
4539 CAATCTGCCCCATG-AC-GGGTAAGAGATTTACTGATGATG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * *
4578 ATCTGCCCCAAGTTCGAGGTAAGAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
4605 CGAATGGCTT
Statistics
Matches: 534, Mismatches: 155, Indels: 72
0.70 0.20 0.09
Matches are distributed among these distances:
35 4 0.01
37 71 0.13
38 5 0.01
39 433 0.81
40 3 0.01
41 14 0.03
43 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
Found at i:3960 original size:78 final size:78
Alignment explanation
Indices: 3872--4613 Score: 490
Period size: 78 Copynumber: 9.6 Consensus size: 78
3862 TGAGATTGGT
* * * * *
3872 TGATGATGATCTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCAATCTACACCAAGCTCGGG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
3937 GTAAGAGATTTAC
66 GTAAGAGATTTAC
* * * * * *
3950 TGATGGTGATCTACCCCAAGCTTGGGGTAAGTGATCGAATGGCTGCAATCTACCCCATGATCGGG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
*
4015 GTAAGAGATTTGC
66 GTAAGAGATTTAC
* * * * *
4028 TGAAGATGATTTGCCCCAGGCTCGGAGTAAGAGATCGAATGGCTGCAATCTGCCCCATA-ATCAG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCA-AGATCAG
4092 GGTAAGAGATTTAC
65 GGTAAGAGATTTAC
* * * * * * *
4106 TGATGATGATTTACCCCAAGCTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCATGATTAGG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
*
4171 GTAAGAGATTTGC
66 GTAAGAGATTTAC
* * * ** * * ** * * **
4184 TGATGATTATCTGCCCCAGGCTCGGGGT--GAGATTGGCTGACGGTGATCTACCCCAGGCTTGGG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
** *
4247 GTAAGAGATCGAA
66 GTAAGAGATTTAC
** * * * * *
4260 TGACT-ACAATCTACCCCAGGCTCGGGGTAAGAGATTAGCTG-AT-GATG--ATCTGCCCTAGGC
1 TGA-TGATGATCTACCCCAGGCTCGGGGTAAGAGA-T--C-GAATGGCTGCAATCTACCCCAAGA
** *
4320 TCAGGGTAAGAGATCAAA
61 TCAGGGTAAGAGATTTAC
* * * * * * ** *
4338 TG--GCTTCAATCTGCTCCACGCTCGGGGTAAGAGATTTGCTG-ATGG-TG--ATCTGCCATAGG
1 TGATG-AT-GATCTACCCCAGGCTCGGGGTAAGAGA--T-C-GAATGGCTGCAATCTACCCCAAG
* * ***
4397 CTCGGGGTAAGAGATTGGT
60 ATCAGGGTAAGAGATTTAC
* ** * * * ** * *
4416 TGACGATGATCTGTCCCAAGCTCAGGGTAAGAGATTGAATGGCTGCAATCTGGCCCAAGCTCAAG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
*
4481 GTAAGAGATTTGC
66 GTAAGAGATTTAC
* * * * * *
4494 TGATGGTGATCTGCCCCAGGCTTGCGGTAAGAGATCGAATGGCTGCAATCTGCCCCATGA-C-GG
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
4557 GTAAGAGATTTAC
66 GTAAGAGATTTAC
* * * *
4570 TGATGATGATCTGCCCCAAGTTCGAGGTAAGAGATCGAATGGCT
1 TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCT
4614 TTAATCTATC
Statistics
Matches: 537, Mismatches: 107, Indels: 42
0.78 0.16 0.06
Matches are distributed among these distances:
74 1 0.00
75 4 0.01
76 111 0.21
77 2 0.00
78 410 0.76
79 5 0.01
80 2 0.00
81 1 0.00
82 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (78 bp):
TGATGATGATCTACCCCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATCTACCCCAAGATCAGG
GTAAGAGATTTAC
Found at i:4257 original size:115 final size:115
Alignment explanation
Indices: 4112--4326 Score: 286
Period size: 115 Copynumber: 1.9 Consensus size: 115
4102 TTACTGATGA
* ** ** * * *
4112 TGATTTACCCCAAGCTCGGGGTAAGAGATCGAATGGTTGTAATCTGCCCCATGATTAGGGTAAGA
1 TGATCTACCCCAAGCTCGGGGTAAGAGATCGAATGACTACAATCTACCCCAGGATCAGGGTAAGA
* * *
4177 GATTTGCTGATGATTATCTGCCCCAGGCTCGGGGTGAGATTGGCTGACGG
66 GATTAGCTGATGATGATCTGCCCCAGGCTCAGGGTGAGATTGGCTGACGG
* * * *
4227 TGATCTACCCCAGGCTTGGGGTAAGAGATCGAATGACTACAATCTACCCCAGGCTCGGGGTAAGA
1 TGATCTACCCCAAGCTCGGGGTAAGAGATCGAATGACTACAATCTACCCCAGGATCAGGGTAAGA
*
4292 GATTAGCTGATGATGATCTGCCCTAGGCTCAGGGT
66 GATTAGCTGATGATGATCTGCCCCAGGCTCAGGGT
4327 AAGAGATCAA
Statistics
Matches: 84, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 84 1.00
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (115 bp):
TGATCTACCCCAAGCTCGGGGTAAGAGATCGAATGACTACAATCTACCCCAGGATCAGGGTAAGA
GATTAGCTGATGATGATCTGCCCCAGGCTCAGGGTGAGATTGGCTGACGG
Found at i:4445 original size:271 final size:269
Alignment explanation
Indices: 3896--4620 Score: 807
Period size: 271 Copynumber: 2.7 Consensus size: 269
3886 CCCAGGCTCG
* * * * * *
3896 GGGTAAAAGATCGAATGGTTGCAATCTACACCAAGCTCGGGGTAAGAGATTTACTGATGGTGATC
1 GGGTAAGAGATTGAATGGATGCAATCTGCCCCAAGCTCGGGGT-AGAGATTTGCTGATGGTGATC
* * *
3961 TACCCCAAGCTTGGGGTAAGTGATCGAATGGCTGCAATCTACCCCATGATCGGGGTAAGAGATTT
65 TACCCCAGGCTTGGGGTAAGAGATCGAATGGCTGCAATCTACCCCATG-TCGGGGTAAGAGATTA
* * * *
4026 GCTGAAGATGATTTGCCCCAGGCTCGGAGTAAGAGATCGAATGGCTGCAATCTGCCCCATAATCA
129 GCTGATGATGATCTGCCCCAGGCTCGG-GTAAGAGATCGAATGGCTTCAATCTGCCCCACAATCA
* * *
4091 GGGTAAGAGATTTACTGATGATGATTTACCCCAAGCTCGGGGTAAGAGATCGAATGGTTGTAATC
193 GGGTAAGAGATTTACTGATGATGATCTACCACAAGCTCGGGGTAAGAGATCGAATGGATG-AATC
* *
4156 TGCCCCATGATTA
257 TGCCCCAAGATCA
* * * *
4169 GGGTAAGAGATTTG-CT-GATG-ATTATCTGCCCCAGGCTCGGGGT-GAGATTGGCTGACGGTGA
1 GGGTAAGAGA-TTGAATGGATGCA--ATCTGCCCCAAGCTCGGGGTAGAGATTTGCTGATGGTGA
* * *
4230 TCTACCCCAGGCTTGGGGTAAGAGATCGAATGACTACAATCTACCCCAGGCTCGGGGTAAGAGAT
63 TCTACCCCAGGCTTGGGGTAAGAGATCGAATGGCTGCAATCTACCCCATG-TCGGGGTAAGAGAT
* * * **
4295 TAGCTGATGATGATCTGCCCTAGGCTCAGGGTAAGAGATCAAATGGCTTCAATCTGCTCCACGCT
127 TAGCTGATGATGATCTGCCCCAGGCTC-GGGTAAGAGATCGAATGGCTTCAATCTGCCCCACAAT
* * * * * * * **
4360 CGGGGTAAGAGATTTGCTGATGGTGATCTGCCATAGGCTCGGGGTAAGAGATTGGTTGACGATG-
191 CAGGGTAAGAGATTTACTGATGATGATCTACCACAAGCTCGGGGTAAGAGATCGAATG--GATGA
* *
4424 ATCTGTCCCAAGCTCA
254 ATCTGCCCCAAGATCA
* * **
4440 GGGTAAGAGATTGAATGGCTGCAATCTGGCCCAAGCTCAAGGTAAGAGATTTGCTGATGGTGATC
1 GGGTAAGAGATTGAATGGATGCAATCTGCCCCAAGCTCGGGGT-AGAGATTTGCTGATGGTGATC
* * * *
4505 TGCCCCAGGCTTGCGGTAAGAGATCGAATGGCTGCAATCTGCCCCATGAC-GGGTAAGAGATTTA
65 TACCCCAGGCTTGGGGTAAGAGATCGAATGGCTGCAATCTACCCCATGTCGGGGTAAGAGA-TTA
* * *
4569 -CTGATGATGATCTGCCCCAAGTTCGAGGTAAGAGATCGAATGGCTTTAATCT
129 GCTGATGATGATCTGCCCCAGGCTCG-GGTAAGAGATCGAATGGCTTCAATCT
4621 ATCCTTTTGA
Statistics
Matches: 377, Mismatches: 62, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
270 4 0.01
271 268 0.71
272 12 0.03
273 91 0.24
274 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (269 bp):
GGGTAAGAGATTGAATGGATGCAATCTGCCCCAAGCTCGGGGTAGAGATTTGCTGATGGTGATCT
ACCCCAGGCTTGGGGTAAGAGATCGAATGGCTGCAATCTACCCCATGTCGGGGTAAGAGATTAGC
TGATGATGATCTGCCCCAGGCTCGGGTAAGAGATCGAATGGCTTCAATCTGCCCCACAATCAGGG
TAAGAGATTTACTGATGATGATCTACCACAAGCTCGGGGTAAGAGATCGAATGGATGAATCTGCC
CCAAGATCA
Found at i:16330 original size:97 final size:97
Alignment explanation
Indices: 16155--16348 Score: 316
Period size: 97 Copynumber: 2.0 Consensus size: 97
16145 AACCTTGAAA
* * *
16155 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATTACGCCTAGTAAGTTAAGGCATAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGCCACAAATTTTCA
* *
16220 AAACTCGAGATAAAAGAATATTGCCTCGATTT
66 AAACCCGAAATAAAAGAATATTGCCTCGATTT
**
16252 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGCCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGCCACAAATTTTCA
*
16317 AAACCCGAAATAAAGGAATATTGCCTCGATTT
66 AAACCCGAAATAAAAGAATATTGCCTCGATTT
16349 TAAATATTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAGTAAGTTAAGCCACAAATTTTCA
AAACCCGAAATAAAAGAATATTGCCTCGATTT
Found at i:16672 original size:30 final size:31
Alignment explanation
Indices: 16637--16737 Score: 77
Period size: 29 Copynumber: 3.4 Consensus size: 31
16627 GTTAAAACAT
16637 AATTTT-GAAAAGTTTTAGGGGTAAAAATGT-
1 AATTTTAGAAAAG-TTTAGGGGTAAAAATGTA
* * * *
16667 AATTTTAGGAGAGTTCA-GGATAAAAATGT-
1 AATTTTAGAAAAGTTTAGGGGTAAAAATGTA
* * * *
16696 GATTTTTG-GAAGTTTAGGGGCAAAAATGTA
1 AATTTTAGAAAAGTTTAGGGGTAAAAATGTA
*
16726 AATTTTGGAAAA
1 AATTTTAGAAAA
16738 T
Statistics
Matches: 53, Mismatches: 14, Indels: 7
0.72 0.19 0.09
Matches are distributed among these distances:
28 5 0.09
29 27 0.51
30 15 0.28
31 6 0.11
ACGTcount: A:0.40, C:0.02, G:0.25, T:0.34
Consensus pattern (31 bp):
AATTTTAGAAAAGTTTAGGGGTAAAAATGTA
Found at i:16720 original size:29 final size:29
Alignment explanation
Indices: 16650--16735 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
16640 TTTGAAAAGT
*
16650 TTTAGGGGTAAAAATGTAATTTTAGGAGAG
1 TTTAGGGGTAAAAATGTAATTTTTGGA-AG
* * *
16680 TTCA-GGATAAAAATGTGATTTTTGGAAG
1 TTTAGGGGTAAAAATGTAATTTTTGGAAG
* *
16708 TTTAGGGGCAAAAATGTAAATTTTGGAA
1 TTTAGGGGTAAAAATGTAATTTTTGGAA
16736 AAT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 5 0.11
29 38 0.83
30 3 0.07
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTAGGGGTAAAAATGTAATTTTTGGAAG
Done.