Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014845.1 Kokia drynarioides strain JFW-HI SEQ_129888, 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: 47364
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Warning! 117 characters in sequence are not A, C, G, or T
Found at i:89 original size:24 final size:23
Alignment explanation
Indices: 49--106 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
39 TATATATTCT
*
49 AATTAA-ATTTTATAAATAATTAA
1 AATTAATA-TTTAGAAATAATTAA
* *
72 TATTAATTATTTAGAAATATTTAA
1 AATTAA-TATTTAGAAATAATTAA
96 AATTAATATTT
1 AATTAATATTT
107 CATATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.34
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAGAAATAATTAA
Found at i:12810 original size:26 final size:27
Alignment explanation
Indices: 12781--12832 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
12771 TTATAGATTT
*
12781 AATTGTAGTTTTTAATTCT-TTAAAAA
1 AATTGTAGTTCTTAATTCTATTAAAAA
*
12807 AATTGTAGTTCTTAATTTTATTAAAA
1 AATTGTAGTTCTTAATTCTATTAAAA
12833 TTAATAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 17 0.74
27 6 0.26
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (27 bp):
AATTGTAGTTCTTAATTCTATTAAAAA
Found at i:18343 original size:91 final size:91
Alignment explanation
Indices: 18222--18400 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 91
18212 AAATACCTTA
* *
18222 TAAAAATAATTATGATATCCATATTATTATCTAAACTCTTAACTCAATCGCGGTTGACTAAATTG
1 TAAAAATAATTATGATATCCATATTATTATCTAAACTCTTAACTCAATCGCAGTTAACTAAATTG
18287 AAAAATTATTAAATTATCCTTACTTG
66 AAAAATTATTAAATTATCCTTACTTG
* ** *
18313 TAAAAATAATTATGATATCCATATTGTTATCTAAACTCTTAACTCGGTTGCAGTTAACTAAATTG
1 TAAAAATAATTATGATATCCATATTATTATCTAAACTCTTAACTCAATCGCAGTTAACTAAATTG
18378 AAAAATTATTAAATTATCCTTAC
66 AAAAATTATTAAATTATCCTTAC
18401 ATATTTGAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.39
Consensus pattern (91 bp):
TAAAAATAATTATGATATCCATATTATTATCTAAACTCTTAACTCAATCGCAGTTAACTAAATTG
AAAAATTATTAAATTATCCTTACTTG
Found at i:19496 original size:272 final size:272
Alignment explanation
Indices: 19009--19557 Score: 1008
Period size: 272 Copynumber: 2.0 Consensus size: 272
18999 CAAAATTGTA
*
19009 AAAAAGATGAAAAAAAACCTTAGAAGATGAACTCGATGCTGCGTTTGAAGGACAAGCGTTGATTA
1 AAAAAGATGAAAAAAAACCTTAGAAGATGAACTCGATGCCGCGTTTGAAGGACAAGCGTTGATTA
*
19074 CAGTAATCGTTAATAGCAATAGTAAAAGAAACTTCTTTTTCACTACTTAACAAATTGAATTTGAC
66 CAGTAATCGTTAATAGCAATAGTAAAAGAAACTTCTTTTTCACTAATTAACAAATTGAATTTGAC
*
19139 CTAAATTCATATTTAATGTTAAATTAAAAAGTGACCAACAAGATGGAGCTTATTCTTTAGCGTGT
131 CTAAATTCATATTTAATGTTAAATTAAAAAGTGACCAACAAGATGGAGCTTATTCTTTAGCGTAT
*
19204 ACAACATGTGTTTGTTATTCCTCCGTCCCCCAGATTGTATGGTCTCATTAATTGAATGAATTAAT
196 ACAACATGTGTTTATTATTCCTCCGTCCCCCAGATTGTATGGTCTCATTAATTGAATGAATTAAT
19269 GAATTTCCCTTT
261 GAATTTCCCTTT
19281 AAAAAGATGAAAAAAAACCTTAGAAGATGAACTCGATGCCGCGTTTGAAGGACAAGCGTTGATTA
1 AAAAAGATGAAAAAAAACCTTAGAAGATGAACTCGATGCCGCGTTTGAAGGACAAGCGTTGATTA
* * *
19346 CAGTAGTCGTTAATAGCAATGGTAAAAGAAACTTCTTTTTCACTAATTGACAAATTGAATTTGAC
66 CAGTAATCGTTAATAGCAATAGTAAAAGAAACTTCTTTTTCACTAATTAACAAATTGAATTTGAC
*
19411 CTAAATTCATATTTAATGTTAAATTAAAAAGTGACCAACAAGATGGAGCTTATTCTTTTGCGTAT
131 CTAAATTCATATTTAATGTTAAATTAAAAAGTGACCAACAAGATGGAGCTTATTCTTTAGCGTAT
*
19476 ACAACATGTGTTTATTATTCCTCCGTCCCCTAGATTGTATGGTCTCATTAATTGAATGAATTAAT
196 ACAACATGTGTTTATTATTCCTCCGTCCCCCAGATTGTATGGTCTCATTAATTGAATGAATTAAT
*
19541 GGATTTCCCTTT
261 GAATTTCCCTTT
19553 AAAAA
1 AAAAA
19558 ACGTGGCCAA
Statistics
Matches: 267, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
272 267 1.00
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (272 bp):
AAAAAGATGAAAAAAAACCTTAGAAGATGAACTCGATGCCGCGTTTGAAGGACAAGCGTTGATTA
CAGTAATCGTTAATAGCAATAGTAAAAGAAACTTCTTTTTCACTAATTAACAAATTGAATTTGAC
CTAAATTCATATTTAATGTTAAATTAAAAAGTGACCAACAAGATGGAGCTTATTCTTTAGCGTAT
ACAACATGTGTTTATTATTCCTCCGTCCCCCAGATTGTATGGTCTCATTAATTGAATGAATTAAT
GAATTTCCCTTT
Found at i:20892 original size:2 final size:2
Alignment explanation
Indices: 20885--20917 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
20875 ATCTCAGTCT
20885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20918 TCCTTGAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:23760 original size:6 final size:6
Alignment explanation
Indices: 23751--23790 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
23741 GTAGTACCAT
23751 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATT
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATT
23791 GCCTCCATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (6 bp):
TATTAG
Found at i:25785 original size:18 final size:18
Alignment explanation
Indices: 25762--25810 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
25752 TTTCATTTCA
*
25762 TTAAATTAATATAAAATT
1 TTAAATTAATATAAAACT
*
25780 TTAAATTTAT-TAAAACT
1 TTAAATTAATATAAAACT
* *
25797 ATAAATAAATATAA
1 TTAAATTAATATAA
25811 CAAAAAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAATTAATATAAAACT
Found at i:26143 original size:14 final size:14
Alignment explanation
Indices: 26108--26151 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
26098 AATTATAAAA
26108 AATTATAATAAATTT
1 AATT-TAATAAATTT
* *
26123 -TTTTAATTAATTT
1 AATTTAATAAATTT
26136 AATTTAATAAATTT
1 AATTTAATAAATTT
26150 AA
1 AA
26152 AAACGTATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTTAATAAATTT
Found at i:30878 original size:22 final size:21
Alignment explanation
Indices: 30848--30893 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
30838 TCAGACATTC
30848 GGGGGTAAAAATGGTAATTTTT
1 GGGGGTAAAAATGG-AATTTTT
* *
30870 GGGGTTAAAAATGGGATTTTT
1 GGGGGTAAAAATGGAATTTTT
30891 GGG
1 GGG
30894 AGTTCGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
GGGGGTAAAAATGGAATTTTT
Found at i:30879 original size:21 final size:21
Alignment explanation
Indices: 30849--30893 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
30839 CAGACATTCG
30849 GGGGT-AAAAATGGTAATTTTT
1 GGGGTAAAAAATGG-AATTTTT
* *
30870 GGGGTTAAAAATGGGATTTTT
1 GGGGTAAAAAATGGAATTTTT
30891 GGG
1 GGG
30894 AGTTCGGGGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.36, T:0.36
Consensus pattern (21 bp):
GGGGTAAAAAATGGAATTTTT
Found at i:30880 original size:51 final size:50
Alignment explanation
Indices: 30821--30921 Score: 132
Period size: 51 Copynumber: 2.0 Consensus size: 50
30811 AGAGTTTCGA
30821 GGTTAAAAAT-GGAGTCTTCAGACATTCGGGGGTAAAAATGGTAATTTTTGG
1 GGTTAAAAATGGGAGTCTTCAGA-ATTCGGGGGT-AAAATGGTAATTTTTGG
* * ** *
30872 GGTTAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGG
1 GGTTAAAAATGGGAGTCTTCAGAATTCGGGGGTAAAATGGTAATTTTTGG
30922 AAGTTTTGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
50 17 0.39
51 19 0.43
52 8 0.18
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.34
Consensus pattern (50 bp):
GGTTAAAAATGGGAGTCTTCAGAATTCGGGGGTAAAATGGTAATTTTTGG
Found at i:30917 original size:29 final size:28
Alignment explanation
Indices: 30867--31221 Score: 232
Period size: 29 Copynumber: 12.1 Consensus size: 28
30857 AATGGTAATT
* * *
30867 TTTGGGGTTAAAAATGGGATTTTTGGGAG
1 TTTGGGGGT-AAAATGGAATTTTTGGAAG
*
30896 TTCGGGGGTAAAATGGTAATTTTTGGAAG
1 TTTGGGGGTAAAATGG-AATTTTTGGAAG
* *
30925 TTTTGGGGTCAAAAATGGGATTTTTGGAAG
1 TTTGGGGGT--AAAATGGAATTTTTGGAAG
* * *
30955 TTCGAGGGTAAAATGGTAATTTTAGGAAG
1 TTTGGGGGTAAAATGG-AATTTTTGGAAG
* * *
30984 TTTTTGGGTTAAAAATGGGA-TTTTGGAAG
1 -TTTGGGGGT-AAAATGGAATTTTTGGAAG
*** *
31013 TTCATGGGTAAAATGGTGATTTTTGGAAG
1 TTTGGGGGTAAAATGG-AATTTTTGGAAG
31042 TTTTGGGGGTCAAAAAT-GAGATTTTTGGAAG
1 -TTTGGGGGT--AAAATGGA-ATTTTTGGAAG
* *
31073 TTTAGAGGTAAAATGGTAA-TTTTGGAAG
1 TTTGGGGGTAAAATGG-AATTTTTGGAAG
* *
31101 TTTTGGGGTTAAAAAT-GAGATTTTTAGAAG
1 -TTTGGGGGT-AAAATGGA-ATTTTTGGAAG
* *
31131 TTTAGGGGTAAAATGGTAATTTTTTGAAG
1 TTTGGGGGTAAAATGG-AATTTTTGGAAG
* *** * *
31160 TATAAAGGTCAAAAATGGGATTTTTGGATG
1 TTTGGGGGT--AAAATGGAATTTTTGGAAG
* *
31190 TTCGGGGGTAAAATGATAATTTTTGGAAG
1 TTTGGGGGTAAAATG-GAATTTTTGGAAG
31219 TTT
1 TTT
31222 TGTGGTTAAA
Statistics
Matches: 253, Mismatches: 50, Indels: 46
0.72 0.14 0.13
Matches are distributed among these distances:
27 7 0.03
28 47 0.19
29 97 0.38
30 64 0.25
31 33 0.13
32 5 0.02
ACGTcount: A:0.30, C:0.02, G:0.31, T:0.37
Consensus pattern (28 bp):
TTTGGGGGTAAAATGGAATTTTTGGAAG
Found at i:30933 original size:59 final size:59
Alignment explanation
Indices: 30866--31271 Score: 501
Period size: 59 Copynumber: 6.9 Consensus size: 59
30856 AAATGGTAAT
*
30866 TTTTGGGGTTAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
* * *
30925 TTTTGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTAGGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
* ** *
30984 TTTTTGGGTTAAAAATGGGA-TTTTGGAAGTTCATGGGTAAAATGGTGATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
* * ** *
31042 TTTTGGGGGTCAAAAATGAGATTTTTGGAAGTTTAGAGGTAAAATGGTAA-TTTTGGAAG
1 TTTT-GGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
* * ** *
31101 TTTTGGGGTTAAAAATGAGATTTTTAGAAGTTTAGGGGTAAAATGGTAATTTTTTGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
* *** * * *
31160 TATAAAGGTCAAAAATGGGATTTTTGGATGTTCGGGGGTAAAATGATAATTTTTGGAAG
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
* *** * **
31219 TTTTGTGGTTAAAAATTTTATTTTTGGAAATTCGAAGGTAAAATGGTAATTTT
1 TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTT
31272 CGTATAGTTT
Statistics
Matches: 298, Mismatches: 46, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
58 80 0.27
59 194 0.65
60 24 0.08
ACGTcount: A:0.31, C:0.02, G:0.29, T:0.38
Consensus pattern (59 bp):
TTTTGGGGTTAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTGGAAG
Found at i:33003 original size:14 final size:15
Alignment explanation
Indices: 32984--33020 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
32974 GGCTTTAGGT
32984 AATTTGGGTT-TAT-
1 AATTTGGGTTATATG
32997 AAGTTTGGGTTATATG
1 AA-TTTGGGTTATATG
33013 AATTTGGG
1 AATTTGGG
33021 CCCCATTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 8 0.38
15 9 0.43
16 2 0.10
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (15 bp):
AATTTGGGTTATATG
Found at i:33086 original size:6 final size:6
Alignment explanation
Indices: 33077--33179 Score: 92
Period size: 6 Copynumber: 17.8 Consensus size: 6
33067 AATTTTGAAG
* * * *
33077 TTAAAT TTAAA- TTATAT TTAAAT TTAAGA- TTAATT TTGAAG TTAAAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT
*
33124 TTAAA- TTATAT TTAAAT TTAAGA- TT-AAT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT
*
33169 TCAAAT TTAAA
1 TTAAAT TTAAA
33180 ATAAATTAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 16
0.73 0.11 0.15
Matches are distributed among these distances:
4 1 0.01
5 15 0.19
6 59 0.77
7 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.48
Consensus pattern (6 bp):
TTAAAT
Found at i:33099 original size:17 final size:17
Alignment explanation
Indices: 33077--33164 Score: 88
Period size: 17 Copynumber: 4.8 Consensus size: 17
33067 AATTTTGAAG
33077 TTAAATTTAAATTATAT
1 TTAAATTTAAATTATAT
*
33094 TTAAATTTAAGATTAATTTTGAAG
1 TTAAATTTAA-ATT-A---T--AT
33118 TTAAATTTAAATTATAT
1 TTAAATTTAAATTATAT
33135 TTAAATTTAAGATTA-AT
1 TTAAATTTAA-ATTATAT
33152 TTAAATTTAAATT
1 TTAAATTTAAATT
33165 TAAATCAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
16 3 0.05
17 33 0.54
18 7 0.11
19 2 0.03
22 2 0.03
23 3 0.05
24 11 0.18
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTAAATTTAAATTATAT
Found at i:33110 original size:41 final size:41
Alignment explanation
Indices: 33065--33179 Score: 187
Period size: 41 Copynumber: 2.8 Consensus size: 41
33055 TTTGAACTTT
33065 TTAATTTTGAAGTTAAATTTAAATTATATTTAAATTTAAGA
1 TTAATTTTGAAGTTAAATTTAAATTATATTTAAATTTAAGA
33106 TTAATTTTGAAGTTAAATTTAAATTATATTTAAATTTAAGA
1 TTAATTTTGAAGTTAAATTTAAATTATATTTAAATTTAAGA
* * * *
33147 TTAA-TTTAAATTTAAATTTAAATCAAATTTAAA
1 TTAATTTTGAAGTTAAATTTAAATTATATTTAAA
33180 ATAAATTAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
40 25 0.36
41 45 0.64
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (41 bp):
TTAATTTTGAAGTTAAATTTAAATTATATTTAAATTTAAGA
Found at i:33161 original size:11 final size:11
Alignment explanation
Indices: 33080--33179 Score: 69
Period size: 11 Copynumber: 8.7 Consensus size: 11
33070 TTTGAAGTTA
33080 AATTTAAA-TT
1 AATTTAAATTT
33090 ATATTTAAATTT
1 A-ATTTAAATTT
* *
33102 AAGATTAATTTT
1 AA-TTTAAATTT
*
33114 GAAGTTAAATTT
1 -AATTTAAATTT
* *
33126 AAATTATATTT
1 AATTTAAATTT
33137 AAATTTAAGA-TT
1 -AATTTAA-ATTT
33149 AATTTAAATTT
1 AATTTAAATTT
**
33160 AAATTTAAATCA
1 -AATTTAAATTT
33172 AATTTAAA
1 AATTTAAA
33180 ATAAATTAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 15
0.74 0.10 0.15
Matches are distributed among these distances:
10 2 0.03
11 34 0.47
12 33 0.46
13 3 0.04
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:33167 original size:17 final size:17
Alignment explanation
Indices: 33080--33179 Score: 82
Period size: 17 Copynumber: 5.8 Consensus size: 17
33070 TTTGAAGTTA
*
33080 AATTTAAA-TTATATTT
1 AATTTAAATTTAAATTT
*
33096 AAATTTAAGA-TTAATTTT
1 -AATTTAA-ATTTAAATTT
*
33114 GAAGTTAAATTTAAA-TT
1 -AATTTAAATTTAAATTT
33131 ATATTTAAATTTAAGA-TT
1 A-ATTTAAATTTAA-ATTT
33149 AATTTAAATTTAAATTT
1 AATTTAAATTTAAATTT
* *
33166 AAATCAAATTTAAA
1 AATTTAAATTTAAA
33180 ATAAATTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
16 2 0.03
17 47 0.67
18 21 0.30
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (17 bp):
AATTTAAATTTAAATTT
Found at i:33175 original size:23 final size:23
Alignment explanation
Indices: 33125--33179 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
33115 AAGTTAAATT
*
33125 TAAA-TTATATTTAAATTTAAGA
1 TAAATTTAAATTTAAATTTAAGA
*
33147 TTAATTTAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAATTTAAGA
33169 TCAAATTTAAA
1 T-AAATTTAAA
33180 ATAAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 23 0.82
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTTAAGA
Found at i:33185 original size:11 final size:11
Alignment explanation
Indices: 33136--33190 Score: 51
Period size: 11 Copynumber: 5.0 Consensus size: 11
33126 AAATTATATT
*
33136 TAAATTTAAGA
1 TAAATTTAAAA
* *
33147 TTAATTTAAATT
1 TAAATTTAAA-A
33159 TAAATTT-AAA
1 TAAATTTAAAA
33169 TCAAATTTAAAA
1 T-AAATTTAAAA
33181 TAAA-TTAAAA
1 TAAATTTAAAA
33191 AAGGGCCCAG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.19
11 19 0.53
12 10 0.28
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:33823 original size:204 final size:204
Alignment explanation
Indices: 33455--34055 Score: 968
Period size: 204 Copynumber: 2.9 Consensus size: 204
33445 GCATCGTTTA
* * * * * *
33455 TTTCGATTCGCTTCTCTATATCTCATCAGGACGACGAGTTTGATTCACTTCTCAATATCTCATCA
1 TTTCAATTCGCTCCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCA
* * * * * *
33520 GGAAGATAACCTTTTATTGCTTCGACCCGCTTCTCAATGTCTTATCAGGGAGCTTGGGTTTGAAG
66 GGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAG
*
33585 ATTTTGCTCGTTTTGAGCTTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACAT
131 ATTTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACAT
33650 CGCTCTTTG
196 CGCTCTTTG
* * *
33659 TTTCAATTCTCTCCTCTGTATCTCATCAGAAAGACGAATTTGGTTCACTTCTCAGTATCTCATCA
1 TTTCAATTCGCTCCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCA
33724 GGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAG
66 GGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAG
* *
33789 ATTTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTTTCATTAGGAAGATGATCACAT
131 ATTTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACAT
*
33854 CGCTGTTTG
196 CGCTCTTTG
*
33863 TTTCAATTCGCTCCTCTGTACCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCA
1 TTTCAATTCGCTCCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCA
* * *
33928 GGAAGCTATCCTTTTATTGCTTTGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTAAAG
66 GGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAG
* * *
33993 ATTTTGCTCGTTTTGAGCCTCGTCTGGGTCTTCTTCTCAGTTTCTCATCAAGAAGATGATCAC
131 ATTTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCAC
34056 GTCGTTTGTG
Statistics
Matches: 366, Mismatches: 31, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
204 366 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (204 bp):
TTTCAATTCGCTCCTCTGTATCTCATCAGGAAGACGAATTTGATTCACTTCTCAGTATCTCATCA
GGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTTGAAG
ATTTTGCTCGTTTTGAGCCTCGTTTGGGTCTTCTTCTCAGTGTCTCATCAGGAAGATGATCACAT
CGCTCTTTG
Found at i:34565 original size:23 final size:23
Alignment explanation
Indices: 34524--34568 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
34514 GAATTCTATT
* * *
34524 AAAGAGGATTAATGGAAACAATA
1 AAAGAGGATCAAAGAAAACAATA
34547 AAAGAGGATCAAAGAAAACAAT
1 AAAGAGGATCAAAGAAAACAAT
34569 CACTAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.60, C:0.07, G:0.20, T:0.13
Consensus pattern (23 bp):
AAAGAGGATCAAAGAAAACAATA
Found at i:35429 original size:20 final size:20
Alignment explanation
Indices: 35404--35453 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
35394 TCATTTTTGC
35404 CACAATCTTCTACTATCGTT
1 CACAATCTTCTACTATCGTT
35424 CACAATCTTCTACTATCGTT
1 CACAATCTTCTACTATCGTT
35444 CACAATCTTC
1 CACAATCTTC
35454 GGGCGGTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.32, G:0.04, T:0.38
Consensus pattern (20 bp):
CACAATCTTCTACTATCGTT
Found at i:45840 original size:30 final size:30
Alignment explanation
Indices: 45806--46305 Score: 371
Period size: 29 Copynumber: 17.0 Consensus size: 30
45796 CAGACATTCG
*
45806 GGGGTAAAAATGGTAATTTTTGGATGTTTT
1 GGGGTAAAAATGGTAATTTTTGGAAGTTTT
* *
45836 GGGGTCAAAAATGG-GATTTTTGGGAG-TTT
1 GGGGT-AAAAATGGTAATTTTTGGAAGTTTT
* *
45865 GAGGG-AAAAATAGTAATTTTTGGAAGTTTC
1 G-GGGTAAAAATGGTAATTTTTGGAAGTTTT
* *
45895 GGGGTTAAAAATGG-AATTTTTAGAAGTTTA
1 GGGG-TAAAAATGGTAATTTTTGGAAGTTTT
* * ***
45925 GTGGT-AAAATGGTGATTTTCAAAAGTTTT
1 GGGGTAAAAATGGTAATTTTTGGAAGTTTT
**
45954 GGGGTCAAAAAT--TAGATTTTTGGAAGTTCG
1 GGGGT-AAAAATGGTA-ATTTTTGGAAGTTTT
* *
45984 GGGGT-AAAATGGTAATTTTAGGAAGTTTC
1 GGGGTAAAAATGGTAATTTTTGGAAGTTTT
* *
46013 GAGGTAAAAAATGG-GATTTTTGGAAG-TTT
1 GGGGT-AAAAATGGTAATTTTTGGAAGTTTT
*
46042 GAGGGT-AAAATGGTAATTTGTGGAAGTTTT
1 G-GGGTAAAAATGGTAATTTTTGGAAGTTTT
**
46072 GGGGTCAAAAAT-CAAATTTTTGGAAG-TTT
1 GGGGT-AAAAATGGTAATTTTTGGAAGTTTT
* *
46101 GGGTGT-AAAATGGTGATTTTTGGAAGTTTC
1 GGG-GTAAAAATGGTAATTTTTGGAAGTTTT
* * * * **
46131 GGGATTAAAATGG-GATTTTTAGAAGTTCA
1 GGGGTAAAAATGGTAATTTTTGGAAGTTTT
*
46160 GGTG-AAAAATGGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGTAATTTTTGGAAGTTTT
* *
46189 AGGGTCAAAAATGCG--ATTTTTGGAAG-TTC
1 GGGGT-AAAAATG-GTAATTTTTGGAAGTTTT
46218 GAGGGT--AAATGGTAATTTTTGGAAGTTTT
1 G-GGGTAAAAATGGTAATTTTTGGAAGTTTT
* * * **
46247 GGGGTTAAAAAT-TTTATTTTTGGAAATTCG
1 GGGG-TAAAAATGGTAATTTTTGGAAGTTTT
*
46277 GGGGT-AAAATGGTAATTTTCGGATAGTTT
1 GGGGTAAAAATGGTAATTTTTGGA-AGTTT
46306 AGGGATCTTC
Statistics
Matches: 369, Mismatches: 65, Indels: 72
0.73 0.13 0.14
Matches are distributed among these distances:
26 1 0.00
27 5 0.01
28 57 0.15
29 131 0.36
30 131 0.36
31 43 0.12
32 1 0.00
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (30 bp):
GGGGTAAAAATGGTAATTTTTGGAAGTTTT
Found at i:45874 original size:59 final size:59
Alignment explanation
Indices: 45807--46305 Score: 540
Period size: 59 Copynumber: 8.5 Consensus size: 59
45797 AGACATTCGG
* *
45807 GGGTAAAAATGGTAATTTTTGGATGTTTTGGGGTCAAAAATGGGATTTTTGGGAGTTTGA
1 GGGT-AAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* * * * * *
45867 GGGAAAAATAGTAATTTTTGGAAGTTTCGGGGTTAAAAATGGAATTTTTAGAAGTTT-A
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* *** ** * *
45925 GTGGTAAAATGGTGATTTTCAAAAGTTTTGGGGTCAAAAATTAGATTTTTGGAAGTTCGG
1 G-GGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* * * *
45985 GGGTAAAATGGTAATTTTAGGAAGTTTCGAGGTAAAAAATGGGATTTTTGGAAGTTTGA
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* ***
46044 GGGTAAAATGGTAATTTGTGGAAGTTTTGGGGTCAAAAATCAAATTTTTGGAAGTTTG-
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* * * * * *
46102 GGTGTAAAATGGTGATTTTTGGAAGTTTCGGGAT-TAAAATGGGATTTTTAGAAG-TTCA
1 GG-GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* * * *
46160 GGTGAAAAATGGTAATTTTTGGAAGTTTTAGGGTCAAAAATGCGATTTTTGGAAGTTCGA
1 GG-GTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
* *** * * *
46220 GGGT-AAATGGTAATTTTTGGAAGTTTTGGGGTTAAAAATTTTATTTTTGGAAATTCGG
1 GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
*
46278 GGGTAAAATGGTAATTTTCGGATAGTTT
1 GGGTAAAATGGTAATTTTTGGA-AGTTT
46306 AGGGATCTTC
Statistics
Matches: 361, Mismatches: 70, Indels: 16
0.81 0.16 0.04
Matches are distributed among these distances:
57 2 0.01
58 99 0.27
59 247 0.68
60 13 0.04
ACGTcount: A:0.31, C:0.03, G:0.29, T:0.37
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTGA
Done.