Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold202
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: 972956
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 36649 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:902526 original size:17 final size:17
Alignment explanation
Indices: 902506--902538 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
902496 ATTTAATATA
902506 TATATTTGATTAAAAAG
1 TATATTTGATTAAAAAG
902523 TATATTTGATTAAAAA
1 TATATTTGATTAAAAA
902539 TAAAATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (17 bp):
TATATTTGATTAAAAAG
Found at i:904880 original size:44 final size:44
Alignment explanation
Indices: 904817--904907 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
904807 GTAGGTAAAA
904817 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
** *
904861 TAATATTAAAATAACCTACACTTTTTAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
904905 TAA
1 TAA
904908 AAATAGAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
Found at i:904934 original size:25 final size:25
Alignment explanation
Indices: 904886--904934 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
904876 CTACACTTTT
* *
904886 TAGAGTTTAAGTGGGAAACTAAAAA
1 TAGAGTTTAACTGGGAAACGAAAAA
904911 TAGAGTTTAACTGGGAGAA-GAAAA
1 TAGAGTTTAACTGGGA-AACGAAAA
904935 GCCGAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.47, C:0.04, G:0.27, T:0.22
Consensus pattern (25 bp):
TAGAGTTTAACTGGGAAACGAAAAA
Found at i:905728 original size:44 final size:44
Alignment explanation
Indices: 905665--905986 Score: 228
Period size: 44 Copynumber: 7.4 Consensus size: 44
905655 CCACAAATCC
* *
905665 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAGATCT
* * * * * * *
905709 TATCTCTCTGAAGTTGTAGTAGAGTAGA-T--CG-CATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAAT-AGATCT
* * * * *** * *
905750 TATTTCCCTGAGGTTCCAGCGGAGCAGACCGAAG-AAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-TAGATCT
* * * **
905794 TATCTCCCTGAGGTTGCAGTGGAGTAGATTGAAGCCGATA-ATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAATAGATCT
* * * * * *
905838 TATCTCCTTGAGGTTGCAGTGGAGCAAATTGAAGCCAATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAATAGATCT
* * *
905882 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAGATCT
**
905926 TATCTCCCTGAAGTTGCAGTGGAGTGGATTGAAA-TAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTAATAGATCT
*
905970 TATCTCTCTGAAGTTGC
1 TATCTCCCTGAAGTTGC
905987 GCAGAGTAGA
Statistics
Matches: 223, Mismatches: 46, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
40 2 0.01
41 26 0.12
43 5 0.02
44 185 0.83
45 4 0.02
46 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAGATCT
Found at i:906843 original size:4 final size:4
Alignment explanation
Indices: 906834--906859 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
906824 CCATTTTTGG
906834 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
906860 GTGCGTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:912017 original size:6 final size:6
Alignment explanation
Indices: 911970--912041 Score: 63
Period size: 6 Copynumber: 11.7 Consensus size: 6
911960 AGTGAAGAAA
* * * *
911970 AAAATA AAAATC AAAATC AAAAGC AAAAGC AAAAATAA AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC -AAAAT-C AAAATC AAAATC
* * *
912020 AAAGTC AAAGTC AAAGTC AAAA
1 AAAATC AAAATC AAAATC AAAA
912042 AATGAAAAAG
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
6 48 0.84
7 9 0.16
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:914455 original size:129 final size:129
Alignment explanation
Indices: 914220--914711 Score: 675
Period size: 129 Copynumber: 3.8 Consensus size: 129
914210 ATCAATGAAT
* * *
914220 ATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCAAAGACGACGAATCTTATCTTCAA-
1 ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
* * *
914284 TAGCAAGGAAGCAGATTTAAGCCAAAAGTCTTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
66 T-GTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* *
914349 ATTACAAATCTTGTCTCCCTAAATAGTAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
1 ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
* *
914414 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCTCTGGTCAGTAGTGGAATAGGTTGGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * * * * *
914478 ATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCAAATCTTATCTTCAAG
1 ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
* * *
914543 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTAGCCAGCCGTGGAATAGGTTGGGAA
66 TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
* * * **
914607 ATTACAAATCTTGTCTCCCGAAGA-AATAGCGGAGCAAATC-AAGGACGGTGAATCTTATCTTCA
1 ATTACAAATCTTGTCTCCCTAA-ACAGTAGCGGAGCAGATCGAA-GACGACGAATCTTATCTTCA
* * * * *
914670 AGAGTAAGAAAGTAGATTTAAGCCACAAATCCTATCTCCCTG
64 AGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTG
914712 AAGTTGTAGT
Statistics
Matches: 322, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
128 2 0.01
129 319 0.99
130 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.25
Consensus pattern (129 bp):
ATTACAAATCTTGTCTCCCTAAACAGTAGCGGAGCAGATCGAAGACGACGAATCTTATCTTCAAG
TGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAA
Found at i:914765 original size:44 final size:44
Alignment explanation
Indices: 914702--915118 Score: 254
Period size: 44 Copynumber: 9.6 Consensus size: 44
914692 CCACAAATCC
* * *
914702 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
* * * * * * *
914746 TATCTCTCTGAAGTTGTAGTAGAGTAGA-T--CGCATTAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
* * * *** * *
914787 TATTTCCCTG-AGATTACAGCGGAGCAGACCGAAG-AAGCAAATCT
1 TATCTCCCTGAAG-TTGCAGTGGAGCAGATTAAAGCAA-TAGATCT
* * *
914831 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCGATA-ATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAGATCT
* * *
914875 TATCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGCCAATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAGATCT
* * *
914919 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
* ** *
914963 TATCTCCCTAAAGTTGCAGTGGAGTGGATTGAAA-TAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCAATAGATCT
** ** * * *
915007 TATCTATCTGAAGTTGC-GCAGAGTAGA-T-CA-C-ATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT-AGATCT
* * *
915047 TATCTCCCTGAGGTTGCACTGGAGCAGACTGAGAAAGC-A-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-T--TAAAGCAATAGATCT
* *
915091 TATCCCCCTGAAGTTGCAGTGGGGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
915119 CTGACAACAG
Statistics
Matches: 293, Mismatches: 62, Indels: 36
0.75 0.16 0.09
Matches are distributed among these distances:
39 2 0.01
40 22 0.08
41 32 0.11
42 1 0.00
43 13 0.04
44 212 0.72
45 7 0.02
46 2 0.01
47 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAGATCT
Found at i:915879 original size:4 final size:4
Alignment explanation
Indices: 915870--915895 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
915860 CCATTTTTGG
915870 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
915896 GTGCGTTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:920354 original size:11 final size:11
Alignment explanation
Indices: 920334--920367 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
920324 AATTACAAAG
920334 TTTGTCATTAT
1 TTTGTCATTAT
920345 ATTT-TCATTAT
1 -TTTGTCATTAT
920356 TTTGTCATTAT
1 TTTGTCATTAT
920367 T
1 T
920368 CATCAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (11 bp):
TTTGTCATTAT
Found at i:922476 original size:44 final size:45
Alignment explanation
Indices: 922409--922495 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 45
922399 GTAGGTCAAA
922409 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTG-GAAAAT
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAAT
*
922453 TAATATTAAAATAACCTATACTAATCAGAGTTTAAGTGAGAAA
1 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAA
922496 CTAAAAATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.30
Consensus pattern (45 bp):
TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGAGAAAAT
Found at i:926322 original size:24 final size:24
Alignment explanation
Indices: 926295--926389 Score: 73
Period size: 25 Copynumber: 3.9 Consensus size: 24
926285 CAGCTCGAAA
*
926295 GAGCATCCCGTTATTAGCTCTCAT
1 GAGCATCCCGTTATTAGCTCTCAC
* *
926319 GAGCATCCCGATATTTGGCTCTCAC
1 GAGCATCCCGTTA-TTAGCTCTCAC
* * * **
926344 GAGCTTCCCATTATATGGCTCTTGC
1 GAGCATCCCGTTAT-TAGCTCTCAC
* * *
926369 AAGCTTCCCGTTAATAGCTCT
1 GAGCATCCCGTTATTAGCTCT
926390 TCGGAGCATC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
24 19 0.33
25 38 0.67
ACGTcount: A:0.20, C:0.29, G:0.18, T:0.33
Consensus pattern (24 bp):
GAGCATCCCGTTATTAGCTCTCAC
Found at i:926347 original size:25 final size:25
Alignment explanation
Indices: 926295--926365 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
926285 CAGCTCGAAA
* * *
926295 GAGCATCCCGTTA-TTAGCTCTCAT
1 GAGCATCCCGATATTTGGCTCTCAC
926319 GAGCATCCCGATATTTGGCTCTCAC
1 GAGCATCCCGATATTTGGCTCTCAC
* *
926344 GAGCTTCCC-ATTATATGGCTCT
1 GAGCATCCCGA-TATTTGGCTCT
926366 TGCAAGCTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 13 0.32
25 27 0.68
ACGTcount: A:0.20, C:0.30, G:0.18, T:0.32
Consensus pattern (25 bp):
GAGCATCCCGATATTTGGCTCTCAC
Found at i:931103 original size:31 final size:33
Alignment explanation
Indices: 931036--931105 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 33
931026 CCGACGGCCC
*
931036 GCCCGAAATATGGGAGGGTTCGGGTAAAAATATAG
1 GCCCGAAATATGGGA--GTTCGGGCAAAAATATAG
*
931071 GCCCGAAATATGGGA-TT-GGGCAAAAATTTAG
1 GCCCGAAATATGGGAGTTCGGGCAAAAATATAG
931102 GCCC
1 GCCC
931106 ATTTAGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 16 0.48
32 2 0.06
35 15 0.45
ACGTcount: A:0.33, C:0.16, G:0.31, T:0.20
Consensus pattern (33 bp):
GCCCGAAATATGGGAGTTCGGGCAAAAATATAG
Found at i:932131 original size:14 final size:15
Alignment explanation
Indices: 932100--932132 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932090 GAAACAGTTT
*
932100 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932115 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932129 GAAT
1 GAAT
932133 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:932215 original size:112 final size:112
Alignment explanation
Indices: 932080--932895 Score: 1632
Period size: 112 Copynumber: 7.3 Consensus size: 112
932070 ATTACCCATT
932080 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932145 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932192 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932257 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932304 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932369 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932416 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932481 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932528 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932593 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932640 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932705 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932752 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
932817 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
66 AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
932864 CTTTTTCTTAGAAACAGTTTGAATTAAAAATG
1 CTTTTTCTTAGAAACAGTTTGAATTAAAAATG
932896 GAAATCTAAT
Statistics
Matches: 704, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 704 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.34
Consensus pattern (112 bp):
CTTTTTCTTAGAAACAGTTTGAATTAAAAATGTTAGAATTAAAAATGGAGAATATTAGAGGGTAG
AGTCAGTAGTGAGTCATGTCAATGGAGAATATTTAATACAATTCTTC
Found at i:932243 original size:14 final size:15
Alignment explanation
Indices: 932212--932244 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932202 GAAACAGTTT
*
932212 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932227 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932241 GAAT
1 GAAT
932245 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:932355 original size:14 final size:15
Alignment explanation
Indices: 932324--932356 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932314 GAAACAGTTT
*
932324 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932339 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932353 GAAT
1 GAAT
932357 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:932467 original size:14 final size:15
Alignment explanation
Indices: 932436--932468 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932426 GAAACAGTTT
*
932436 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932451 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932465 GAAT
1 GAAT
932469 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:932579 original size:14 final size:15
Alignment explanation
Indices: 932548--932580 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932538 GAAACAGTTT
*
932548 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932563 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932577 GAAT
1 GAAT
932581 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:932691 original size:14 final size:15
Alignment explanation
Indices: 932660--932692 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932650 GAAACAGTTT
*
932660 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932675 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932689 GAAT
1 GAAT
932693 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:932803 original size:14 final size:15
Alignment explanation
Indices: 932772--932804 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
932762 GAAACAGTTT
*
932772 GAATTAAAAATGTTA
1 GAATTAAAAATGTGA
932787 GAATTAAAAATG-GA
1 GAATTAAAAATGTGA
932801 GAAT
1 GAAT
932805 ATTAGAGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (15 bp):
GAATTAAAAATGTGA
Found at i:938640 original size:14 final size:14
Alignment explanation
Indices: 938621--938648 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
938611 AGCAGAAATC
938621 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
938635 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
938649 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:938646 original size:19 final size:18
Alignment explanation
Indices: 938624--938668 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
938614 AGAAATCTGG
938624 AGAAAAGAAAATG-GAGAAA
1 AGAAAAGAAAATGTGAG--A
938643 AGAAAAG-AAATGTGAGA
1 AGAAAAGAAAATGTGAGA
938660 AGAAAAGAA
1 AGAAAAGAA
938669 GCGTATCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.33
18 6 0.25
19 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.07
Consensus pattern (18 bp):
AGAAAAGAAAATGTGAGA
Found at i:942206 original size:9 final size:9
Alignment explanation
Indices: 942192--942234 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
942182 AGCAAATTAG
942192 CAATTAATA
1 CAATTAATA
942201 CAATTAATA
1 CAATTAATA
942210 CAATT-A-A
1 CAATTAATA
942217 CAATTAATA
1 CAATTAATA
942226 CAATTAATA
1 CAATTAATA
942235 ATTTGATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.19
8 2 0.06
9 24 0.75
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.33
Consensus pattern (9 bp):
CAATTAATA
Found at i:942219 original size:16 final size:16
Alignment explanation
Indices: 942200--942237 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
942190 AGCAATTAAT
942200 ACAATTAATACAATTA
1 ACAATTAATACAATTA
942216 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
942232 ATAATT
1 ACAATT
942238 TGATAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:942246 original size:25 final size:25
Alignment explanation
Indices: 942186--942234 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
942176 TGTTATAGCA
*
942186 AATTAGCAATTAATACAATTAATAC
1 AATTAACAATTAATACAATTAATAC
942211 AATTAACAATTAATACAATTAATA
1 AATTAACAATTAATACAATTAATA
942235 ATTTGATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (25 bp):
AATTAACAATTAATACAATTAATAC
Found at i:942365 original size:16 final size:17
Alignment explanation
Indices: 942346--942379 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
942336 AATTAGTTTT
942346 TAATTTT-ATTAAAAAA
1 TAATTTTAATTAAAAAA
*
942362 TAATTTTAATTTAAAAA
1 TAATTTTAATTAAAAAA
942379 T
1 T
942380 GGGTCGGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATTTTAATTAAAAAA
Found at i:942368 original size:23 final size:22
Alignment explanation
Indices: 942322--942373 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
942312 TTACTACCAA
* * *
942322 TTAATTTTAATAACAATTAGTTT
1 TTAATTTTAATAAAAAATA-ATT
*
942345 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
942367 TTAATTT
1 TTAATTT
942374 AAAAATGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 9 0.36
23 16 0.64
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:943159 original size:42 final size:42
Alignment explanation
Indices: 943066--943160 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
943056 GGCCGTGTCC
*
943066 CAGCTCGTGTCTCCGCCTGTGTAACTTACTGACTTGAGACACA
1 CAGC-CGTGTCTCCGCCCGTGTAACTTACTGACTTGAGACACA
* * * * *
943109 TAGTCGTGTCTCTGCCCGTGTAACTTACTGACTTGGGTCACA
1 CAGCCGTGTCTCCGCCCGTGTAACTTACTGACTTGAGACACA
*
943151 CGGCCGTGTC
1 CAGCCGTGTC
943161 CTAAGTCGTG
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 41 0.95
43 2 0.05
ACGTcount: A:0.17, C:0.29, G:0.24, T:0.29
Consensus pattern (42 bp):
CAGCCGTGTCTCCGCCCGTGTAACTTACTGACTTGAGACACA
Found at i:953781 original size:20 final size:20
Alignment explanation
Indices: 953746--953787 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
953736 TATTTTTATT
953746 TAAATTTAATATAAAATATA
1 TAAATTTAATATAAAATATA
953766 TAAATGTTAATA-AAAATATA
1 TAAAT-TTAATATAAAATATA
953786 TA
1 TA
953788 TTTTATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAATTTAATATAAAATATA
Found at i:956286 original size:5 final size:6
Alignment explanation
Indices: 956271--956295 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
956261 TTCAAGAATC
956271 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
956296 GGCCAATAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Done.