Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011493.1 Kokia drynarioides strain JFW-HI SEQ_126478, 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: 72908
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Warning! 71 characters in sequence are not A, C, G, or T
Found at i:872 original size:26 final size:26
Alignment explanation
Indices: 843--894 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
833 AAAAGTAAAC
843 TATGTCTAATGAGTTAAACGTAACAT
1 TATGTCTAATGAGTTAAACGTAACAT
* *
869 TATGTCTGATGTGTTAAACGTAACAT
1 TATGTCTAATGAGTTAAACGTAACAT
895 GGCATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.37
Consensus pattern (26 bp):
TATGTCTAATGAGTTAAACGTAACAT
Found at i:6248 original size:22 final size:22
Alignment explanation
Indices: 6223--6272 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
6213 AAAATAGAAG
6223 AAATAAAATTAAAAAAAAAAGA
1 AAATAAAATTAAAAAAAAAAGA
* * *
6245 AAATATAATTAAAAGAAATAGA
1 AAATAAAATTAAAAAAAAAAGA
6267 AAATAA
1 AAATAA
6273 GGAAGTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (22 bp):
AAATAAAATTAAAAAAAAAAGA
Found at i:8705 original size:22 final size:21
Alignment explanation
Indices: 8646--8710 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 21
8636 TTTCCTAGAC
*
8646 AAAATAAATAAAATAAATAA-AT
1 AAAATAAA-AAAA-AAATAATAA
*
8668 AAAATAAGATAGAAAAATAATAA
1 AAAATAA-A-AAAAAAATAATAA
8691 AAAATAAAAATAAAAATAAT
1 AAAATAAAAA-AAAAATAAT
8711 TGGGTTGTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.03
22 23 0.62
23 13 0.35
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (21 bp):
AAAATAAAAAAAAAATAATAA
Found at i:8706 original size:13 final size:13
Alignment explanation
Indices: 8647--8704 Score: 64
Period size: 13 Copynumber: 4.2 Consensus size: 13
8637 TTCCTAGACA
8647 AAATAAATAAAAT
1 AAATAAATAAAAT
8660 AAATAAATAAAAT
1 AAATAAATAAAAT
*
8673 AAGATAGAAAAATAAT
1 AA-ATA-AATAA-AAT
8689 AAA-AAATAAAAAT
1 AAATAAAT-AAAAT
8702 AAA
1 AAA
8705 AATAATTGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
13 23 0.59
14 6 0.15
15 5 0.13
16 5 0.13
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:14335 original size:21 final size:21
Alignment explanation
Indices: 14311--14356 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
14301 CGATCTGAGG
*
14311 AAAAATAGAAGAAACAAAATT
1 AAAAATAAAAGAAACAAAATT
* *
14332 AAAAATAAAAGAAATATAATT
1 AAAAATAAAAGAAACAAAATT
14353 AAAA
1 AAAA
14357 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAGAAACAAAATT
Found at i:14365 original size:21 final size:20
Alignment explanation
Indices: 14311--14370 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
14301 CGATCTGAGG
* *
14311 AAAAATAGAAGAAACAAAATT
1 AAAAATAAAAGAAA-ATAATT
14332 AAAAATAAAAGAAATATAATT
1 AAAAATAAAAGAAA-ATAATT
*
14353 AAAAGA-AATAGAAAATAA
1 AAAA-ATAAAAGAAAATAA
14371 GGAAGTCGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.12
21 29 0.85
22 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (20 bp):
AAAAATAAAAGAAAATAATT
Found at i:18936 original size:6 final size:6
Alignment explanation
Indices: 18888--18921 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
18878 AATTATCAAT
18888 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCT
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCT
18922 TCATATCTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (6 bp):
CTCTCC
Found at i:22401 original size:36 final size:35
Alignment explanation
Indices: 22349--22462 Score: 147
Period size: 36 Copynumber: 3.2 Consensus size: 35
22339 AATATAATTA
22349 GTCACATGGCATGAAGAACATACCCACATATTTTCT
1 GTCACAT-GCATGAAGAACATACCCACATATTTTCT
* * *
22385 GTCACATGACACGAAGAATATACCCACATATTTTTT
1 GTCACATG-CATGAAGAACATACCCACATATTTTCT
* *
22421 GTCACATTGCATGAAGAACATACCCACAAATTTACT
1 GTCACA-TGCATGAAGAACATACCCACATATTTTCT
*
22457 TTCACA
1 GTCACA
22463 ACAAACATCA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
35 1 0.01
36 64 0.96
37 2 0.03
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (35 bp):
GTCACATGCATGAAGAACATACCCACATATTTTCT
Found at i:22558 original size:23 final size:23
Alignment explanation
Indices: 22532--22656 Score: 133
Period size: 23 Copynumber: 5.4 Consensus size: 23
22522 ATCTTAATTC
* * * *
22532 TTTAAGCAAAAATTAAATTTATA
1 TTTAAGCATAAATCACATTAATA
* *
22555 TTTAAACATAAATCACACTAATA
1 TTTAAGCATAAATCACATTAATA
22578 TTTAAGCATAAATCACATTAATA
1 TTTAAGCATAAATCACATTAATA
* * *
22601 TTTGAGCACAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
** *
22624 TTTAATAATAAATCATATTAATA
1 TTTAAGCATAAATCACATTAATA
*
22647 TTTCAGCATA
1 TTTAAGCATA
22657 GATATAAGAA
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (23 bp):
TTTAAGCATAAATCACATTAATA
Found at i:24618 original size:315 final size:315
Alignment explanation
Indices: 24040--24664 Score: 1020
Period size: 315 Copynumber: 2.0 Consensus size: 315
24030 TTTACATGAA
* * *
24040 CTATTCTATGATAACTTTGATAATAGTTTCCTCTATTCACTATGACACTCTCGTCTAAAGATCTC
1 CTATTCTATGATAACTTTGATAATAGTTTCCTCTATTCACTACGACACTCTCGTCTAAACAACTC
24105 ATAATCATTTTACCTAGTTTAATAGCTATATTGAAAATTTTCACTTTCTAGCTAAACCACTCAAA
66 ATAATCATTTTACCTAGTTTAATAGCTATATTGAAAATTTTCACTTTCTAGCTAAACCACTCAAA
**
24170 ATTTACTAAGGCGTTGAACCTAATTCTACCAATAAAAGAAGTGATTACAAGGAAAAAATACCTGC
131 ATTTACTAAGGCGTTGAACCTAATTCTACCAATAAAAGAAGTGATTACAAGGAAAAAATACCCAC
** * *
24235 AATCTTGTCAATCGAATCTCTTCAACTTGAGTAGCAACAATATGAGCAATGACTCGCTGCCCAAC
196 AATCTCATCAATCGAATCTCGTCAACTTGAGTAGCAACAATATGAGCAATGACTCGCTGCCAAAC
24300 CGGTCTCCAAATACCTTTACCTCGACCACGAGCTCTAGCGAGCGTAGAAATAAGT
261 CGGTCTCCAAATACCTTTACCTCGACCACGAGCTCTAGCGAGCGTAGAAATAAGT
24355 CTATTCTATGATAACTTTGATAATAGTTTCCTCTATTCACTACGACACTCTCGTCTAAACAACTC
1 CTATTCTATGATAACTTTGATAATAGTTTCCTCTATTCACTACGACACTCTCGTCTAAACAACTC
* * *
24420 ATAATCATTTTTCCTAGTTTAATAGTGTATATTG-AAATTTTCCACTTTCTAGCTAAATCACTCA
66 ATAATCATTTTACCTAGTTTAATAG-CTATATTGAAAATTTT-CACTTTCTAGCTAAACCACTCA
* *
24484 AAATTTACTAAGGCGTTGAACCTAATTCTACCAATAAAAGAAGTGATTATAAGGCAAAAATACCC
129 AAATTTACTAAGGCGTTGAACCTAATTCTACCAATAAAAGAAGTGATTACAAGGAAAAAATACCC
* * * *
24549 ACAAT-TCATCAATCGAATCTCGTCAACTTGAGTAGCAGCAGTATGAGTAATGATTCGCTGCCAA
194 ACAATCTCATCAATCGAATCTCGTCAACTTGAGTAGCAACAATATGAGCAATGACTCGCTGCCAA
* * * *
24613 ACCGGTCTCCAATTACCTTTACCTTGACCACGAGCTCTAGCGGGCTTAGAAA
259 ACCGGTCTCCAAATACCTTTACCTCGACCACGAGCTCTAGCGAGCGTAGAAA
24665 CATGTGTTGA
Statistics
Matches: 286, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
315 192 0.67
316 94 0.33
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.31
Consensus pattern (315 bp):
CTATTCTATGATAACTTTGATAATAGTTTCCTCTATTCACTACGACACTCTCGTCTAAACAACTC
ATAATCATTTTACCTAGTTTAATAGCTATATTGAAAATTTTCACTTTCTAGCTAAACCACTCAAA
ATTTACTAAGGCGTTGAACCTAATTCTACCAATAAAAGAAGTGATTACAAGGAAAAAATACCCAC
AATCTCATCAATCGAATCTCGTCAACTTGAGTAGCAACAATATGAGCAATGACTCGCTGCCAAAC
CGGTCTCCAAATACCTTTACCTCGACCACGAGCTCTAGCGAGCGTAGAAATAAGT
Found at i:25869 original size:18 final size:18
Alignment explanation
Indices: 25843--25877 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25833 ACATGCATAG
*
25843 CAATCAAACAAACATCAA
1 CAATCAAACAAAAATCAA
*
25861 CAATTAAACAAAAATCA
1 CAATCAAACAAAAATCA
25878 GTATATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (18 bp):
CAATCAAACAAAAATCAA
Found at i:26957 original size:18 final size:20
Alignment explanation
Indices: 26920--26957 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
26910 AACAATGGAC
26920 TCATAGAGTCGAAACATATA
1 TCATAGAGTCGAAACATATA
*
26940 TCATAG-GT-GAAGCATATA
1 TCATAGAGTCGAAACATATA
26958 GCTAATACTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 2 0.12
20 6 0.35
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.26
Consensus pattern (20 bp):
TCATAGAGTCGAAACATATA
Found at i:27320 original size:20 final size:20
Alignment explanation
Indices: 27278--27320 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
27268 ATAGCATATG
*
27278 TCACAACATCTCATGTTTGT
1 TCACAACATCACATGTTTGT
*
27298 TCACAATATCACAT-TTTGAT
1 TCACAACATCACATGTTTG-T
27318 TCA
1 TCA
27321 TTAAGCACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (20 bp):
TCACAACATCACATGTTTGT
Found at i:27355 original size:23 final size:23
Alignment explanation
Indices: 27321--27442 Score: 127
Period size: 23 Copynumber: 5.3 Consensus size: 23
27311 TTTTGATTCA
* * *
27321 TTAAGCACAAATTAAATTAATAT
1 TTAAGCATAAATCACATTAATAT
*
27344 TTAAGCATAAATTACATTAATAT
1 TTAAGCATAAATCACATTAATAT
27367 TTAAGCATAAATCACATTAATAT
1 TTAAGCATAAATCACATTAATAT
* * * *
27390 TTGAGGACAAATCAGATTAATAT
1 TTAAGCATAAATCACATTAATAT
* * ** *
27413 ATGATAATAAATCATATTAATAT
1 TTAAGCATAAATCACATTAATAT
27436 TTAAGCA
1 TTAAGCA
27443 CAGATATAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.35
Consensus pattern (23 bp):
TTAAGCATAAATCACATTAATAT
Found at i:38277 original size:41 final size:41
Alignment explanation
Indices: 38220--38315 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
38210 GAATTTTATT
* *
38220 TTAACAAGAATTCTAGTCACCCAATTCTAACAATCTCCACC
1 TTAACAAGAATTCTAGTCACCCAATTCCAACAATCTCCACA
*
38261 TTAACAAGAATTCTAGTCACTCAATTCCAACAATCTCCACA
1 TTAACAAGAATTCTAGTCACCCAATTCCAACAATCTCCACA
* *
38302 TTGACAATAATTCT
1 TTAACAAGAATTCT
38316 CTACAAACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.38, C:0.28, G:0.05, T:0.29
Consensus pattern (41 bp):
TTAACAAGAATTCTAGTCACCCAATTCCAACAATCTCCACA
Found at i:42428 original size:47 final size:48
Alignment explanation
Indices: 42327--42454 Score: 172
Period size: 47 Copynumber: 2.7 Consensus size: 48
42317 AGTTTCCATT
** *
42327 ATATATATTTTTC-TAGTCATT-ATCTAATCTCTTACCCTCCCACTCTCC
1 ATATATATTAATCATAGTC-TTCATCTAATCTC-TACACTCCCACTCTCC
*
42375 ATATATATTAATCATAGTCTTCATCTAATCTC-ACACTCTCACTCTCC
1 ATATATATTAATCATAGTCTTCATCTAATCTCTACACTCCCACTCTCC
*
42422 ATATATATTAATCATAGTCTTCTTCTAATCTCT
1 ATATATATTAATCATAGTCTTCATCTAATCTCT
42455 CATTCTCCAT
Statistics
Matches: 72, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
47 44 0.61
48 13 0.18
49 15 0.21
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.43
Consensus pattern (48 bp):
ATATATATTAATCATAGTCTTCATCTAATCTCTACACTCCCACTCTCC
Found at i:42456 original size:41 final size:43
Alignment explanation
Indices: 42367--42474 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 43
42357 CTTACCCTCC
42367 CACTCTCCATATATATTAATCATAGTCTTCATCTAATCTCACACTCT
1 CACTCTCCATATATATTAATCATAGTCTTCATCTAA-CT---ACTCT
*
42414 CACTCTCCATATATATTAATCATAGTCTTCTTCTAA-T-CTCT
1 CACTCTCCATATATATTAATCATAGTCTTCATCTAACTACTCT
*
42455 CATTCTCCATATATATTAAT
1 CACTCTCCATATATATTAAT
42475 TATTTGGATT
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
41 23 0.39
45 1 0.02
47 35 0.59
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.42
Consensus pattern (43 bp):
CACTCTCCATATATATTAATCATAGTCTTCATCTAACTACTCT
Found at i:43745 original size:41 final size:42
Alignment explanation
Indices: 43666--43763 Score: 135
Period size: 41 Copynumber: 2.3 Consensus size: 42
43656 CTAATCTTTC
* * *
43666 ACTCTCTGACTCTCCATATATATATTAGTCATAATCTTCATCT
1 ACTCTCTCACTCTCCA-ACATATATTAATCATAATCTTCATCT
*
43709 ACTCTCTCACTCTCC-ACATATATTAATCATAGTCTTCATCT
1 ACTCTCTCACTCTCCAACATATATTAATCATAATCTTCATCT
*
43750 AATCTCTCACTCTC
1 ACTCTCTCACTCTC
43764 TTGCTATCAC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 36 0.72
43 14 0.28
ACGTcount: A:0.27, C:0.31, G:0.03, T:0.40
Consensus pattern (42 bp):
ACTCTCTCACTCTCCAACATATATTAATCATAATCTTCATCT
Found at i:52377 original size:8 final size:8
Alignment explanation
Indices: 52364--52426 Score: 51
Period size: 8 Copynumber: 8.1 Consensus size: 8
52354 TAATCTCCCA
52364 CCCTCTCT
1 CCCTCTCT
52372 CCCTCT-T
1 CCCTCTCT
52379 -CCTCTGC-
1 CCCTCT-CT
*
52386 CACTCTCT
1 CCCTCTCT
* *
52394 CCATCCCT
1 CCCTCTCT
52402 CCCTCTCT
1 CCCTCTCT
*
52410 CTCTCTCT
1 CCCTCTCT
*
52418 CTCTCTCT
1 CCCTCTCT
52426 C
1 C
52427 TCCCCTTCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
6 5 0.11
7 2 0.05
8 37 0.84
ACGTcount: A:0.03, C:0.57, G:0.02, T:0.38
Consensus pattern (8 bp):
CCCTCTCT
Found at i:52409 original size:2 final size:2
Alignment explanation
Indices: 52404--52428 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52394 CCATCCCTCC
52404 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
52429 CCCTTCACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:55264 original size:57 final size:57
Alignment explanation
Indices: 55199--55308 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 57
55189 TTGTCTGGAC
* * *
55199 TTCATCTAATCTTTCGCTCTCCCATTCTCTCACTCTCCATATATATTAATCATAGTT
1 TTCATCTAATCTATCACTCTCCCAGTCTCTCACTCTCCATATATATTAATCATAGTT
* * *
55256 TTCATCTAATCTATCACTCTCTCAGTGTCTCACTTTCCATATATATTAATCAT
1 TTCATCTAATCTATCACTCTCCCAGTCTCTCACTCTCCATATATATTAATCAT
55309 TTGGCTTTTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.04, T:0.44
Consensus pattern (57 bp):
TTCATCTAATCTATCACTCTCCCAGTCTCTCACTCTCCATATATATTAATCATAGTT
Found at i:58848 original size:49 final size:49
Alignment explanation
Indices: 58787--58953 Score: 156
Period size: 50 Copynumber: 3.3 Consensus size: 49
58777 TAAATATAAA
* * * *
58787 ATATTTACGTAAAATATAATATCTGAACAAACAATATAAATAAATATTT
1 ATATTTATGTAAAACATAATATCTGAAAAAAAAATATAAATAAATATTT
* *
58836 ATATTTATGTAAAACACCAA-ATCTGAATAAAAAAATTTAAATAAATATTT
1 ATATTTATGTAAAACA-TAATATCTGAA-AAAAAAATATAAATAAATATTT
* * * * *
58886 ATATTTATATAAAACGTCATATATGAATAAAAAATAATTCAAATAAATATTT
1 ATATTTATGTAAAACATAATATCTGAAAAAAAAAT-A-T-AAATAAATATTT
* **
58938 ATTTTTAAATAAAACA
1 ATATTTATGTAAAACA
58954 CCATATCTAA
Statistics
Matches: 96, Mismatches: 16, Indels: 9
0.79 0.13 0.07
Matches are distributed among these distances:
49 29 0.30
50 41 0.43
51 1 0.01
52 25 0.26
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (49 bp):
ATATTTATGTAAAACATAATATCTGAAAAAAAAATATAAATAAATATTT
Found at i:58879 original size:50 final size:50
Alignment explanation
Indices: 58805--58982 Score: 196
Period size: 50 Copynumber: 3.5 Consensus size: 50
58795 GTAAAATATA
* * * *
58805 ATATCTGAA-CAAACAATATAAATAAATATTTATATTTATGTAAAACACC
1 ATATCTGAATAAAAAAATTTAAATAAATATTTATATTTATATAAAACACC
* **
58854 AAATCTGAATAAAAAAATTTAAATAAATATTTATATTTATATAAAACGTC
1 ATATCTGAATAAAAAAATTTAAATAAATATTTATATTTATATAAAACACC
* * * *
58904 ATATATGAATAAAAAATAATTCAAATAAATATTTATTTTTAAATAAAACACC
1 ATATCTGAAT-AAAAA-AATTTAAATAAATATTTATATTTATATAAAACACC
* * * *
58956 ATATCTAAACAAAACAATTTAGATAAA
1 ATATCTGAATAAAAAAATTTAAATAAA
58983 CAAGTTTTGA
Statistics
Matches: 106, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 8 0.08
50 52 0.49
51 9 0.08
52 37 0.35
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.33
Consensus pattern (50 bp):
ATATCTGAATAAAAAAATTTAAATAAATATTTATATTTATATAAAACACC
Found at i:62463 original size:24 final size:24
Alignment explanation
Indices: 62435--62497 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
62425 TAGACTAATA
62435 AGAGTTTAACTT-AAACAAATAAAT
1 AGAGTTTAA-TTGAAACAAATAAAT
62459 AGAGTTTAATTGAAACAAATAAAT
1 AGAGTTTAATTGAAACAAATAAAT
**
62483 ATTGTTTAATTGAAA
1 AGAGTTTAATTGAAA
62498 GATTATTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 2 0.06
24 34 0.94
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (24 bp):
AGAGTTTAATTGAAACAAATAAAT
Found at i:63048 original size:246 final size:246
Alignment explanation
Indices: 62582--63064 Score: 610
Period size: 246 Copynumber: 2.0 Consensus size: 246
62572 TGACAGGAAT
* * * * * *
62582 AAATCTCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATGAGAATAGAATAAAATC
1 AAATCCCGAAACAGAATTATTCAATTAATCCTTGTTTGAAAACAAAATCAAAATAGAATAAAATA
* * * * *
62647 TGTTGAACAACGGGAATAATCTCGAAACAGAATTTTTCTATTAATTATTGTTTGGAAACAAAATC
66 TGTTGAACAACGAGAATAATCTCAAAACAGAATTATTCAATTAATTATTGTTTGGAAACAAAACC
** * * *
62712 GTAATAGAATAAAATTTGTTGTACGACAGGAATAAATCCCAAAACAAAATTATTCAACTAATCGT
131 AAAATAAAATAAAATTTGTTGAACGACAGGAATAAATCCCAAAACAAAATTATTAAACTAATCGT
* *
62777 TGTTTGGAAACAAAATTAAAATAGAATAAAATCTCTTGAACGGAAGGAAAA
196 TGTTTAGAAACAAAATCAAAATAGAATAAAATCTCTTGAACGGAAGGAAAA
* * *
62828 AAATCCCGAAATAGAATTCTTCAGTTAATCCTTGTTTGAAAACAAAATCAAAATAGAATAAAATA
1 AAATCCCGAAACAGAATTATTCAATTAATCCTTGTTTGAAAACAAAATCAAAATAGAATAAAATA
* * *
62893 TGTTGAACGACGAGAATAATTCTCAAAACAGAATTATTCAATTAATTCTTGTTTGGAACCAAAAC
66 TGTTGAACAACGAGAATAA-TCTCAAAACAGAATTATTCAATTAATTATTGTTTGGAAACAAAAC
*** *** * * * *
62958 CAAAATAAAATAAAATTTGTTGAACGGTGGGAATAAATCTTTAAATAGATTTATTAAATTAATTC
130 CAAAATAAAATAAAATTTGTTGAACGACAGGAATAAATCCCAAAACAAAATTATTAAACTAA-TC
* *
63023 -TT-TTTAGAAACAAAATCATAATAGAATAAAATCTGTTGAACG
194 GTTGTTTAGAAACAAAATCAAAATAGAATAAAATCTCTTGAACG
63065 ATGGGAATAA
Statistics
Matches: 199, Mismatches: 36, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
246 109 0.55
247 88 0.44
248 2 0.01
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (246 bp):
AAATCCCGAAACAGAATTATTCAATTAATCCTTGTTTGAAAACAAAATCAAAATAGAATAAAATA
TGTTGAACAACGAGAATAATCTCAAAACAGAATTATTCAATTAATTATTGTTTGGAAACAAAACC
AAAATAAAATAAAATTTGTTGAACGACAGGAATAAATCCCAAAACAAAATTATTAAACTAATCGT
TGTTTAGAAACAAAATCAAAATAGAATAAAATCTCTTGAACGGAAGGAAAA
Found at i:63109 original size:81 final size:81
Alignment explanation
Indices: 62567--63098 Score: 548
Period size: 82 Copynumber: 6.5 Consensus size: 81
62557 ATCAATTCTA
* * *
62567 TTGAATGACAGGAATAAATCTCGAAACAGAATTATTCAATTAATTCTTGTTTGGAAACAAAATGA
1 TTGAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAA-TCTTGTTTGGAAACAAAATCA
*
62632 GAATAGAATAAAATCTG
65 AAATAGAATAAAATCTG
* * * * *
62649 TTGAACAACGGGAAT-AATCTCGAAACAGAATTTTTCTATTAATTATTGTTTGGAAACAAAATCG
1 TTGAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAA-TCTTGTTTGGAAACAAAATCA
* *
62713 TAATAGAATAAAATTTG
65 AAATAGAATAAAATCTG
* * * * * * *
62730 TTGTACGACAGGAATAAATCCCAAAACAAAATTATTCAACTAATCGTTGTTTGGAAACAAAATTA
1 TTGAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAATC-TTGTTTGGAAACAAAATCA
*
62795 AAATAGAATAAAATCTC
65 AAATAGAATAAAATCTG
* * * * * * * *
62812 TTGAACGGAAGGAAAAAAATCCCGAAATAGAATTCTTCAGTTAATCCTTGTTTGAAAACAAAATC
1 TTGAAC-GACGGGAATAAATCTCGAAACAGAATTATTCAATTAAT-CTTGTTTGGAAACAAAATC
*
62877 AAAATAGAATAAAATATG
64 AAAATAGAATAAAATCTG
* * * * *
62895 TTGAACGACGAGAATAATTCTCAAAACAGAATTATTCAATTAATTCTTGTTTGGAACCAAAACCA
1 TTGAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAA-TCTTGTTTGGAAACAAAATCA
* *
62960 AAATAAAATAAAATTTG
65 AAATAGAATAAAATCTG
** ** * * * *
62977 TTGAACGGTGGGAATAAATCTTTAAATAGATTTATTAAATTAATTCTT-TTTAGAAACAAAATCA
1 TTGAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAA-TCTTGTTTGGAAACAAAATCA
*
63041 TAATAGAATAAAATCTG
65 AAATAGAATAAAATCTG
* * *
63058 TTGAACGATGGGAATAATTCTCGGAACA-AATTTATTCAATT
1 TTGAACGACGGGAATAAATCTCGAAACAGAA-TTATTCAATT
63099 TTAATTTTTT
Statistics
Matches: 366, Mismatches: 78, Indels: 13
0.80 0.17 0.03
Matches are distributed among these distances:
80 1 0.00
81 130 0.36
82 167 0.46
83 67 0.18
84 1 0.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (81 bp):
TTGAACGACGGGAATAAATCTCGAAACAGAATTATTCAATTAATCTTGTTTGGAAACAAAATCAA
AATAGAATAAAATCTG
Found at i:63642 original size:50 final size:50
Alignment explanation
Indices: 63570--63745 Score: 203
Period size: 50 Copynumber: 3.5 Consensus size: 50
63560 AAAATACAAG
* * *
63570 ATCTG-AAAAAATAATATAAATAAATATTTATATTTATGTAAAACACTAA
1 ATCTGAAAAAAACAATTTAAATAAATATTTATATTTATATAAAACACTAA
*
63619 ATCTGAACAAAAA-AATTTAAATAAATATTTATATTTATATAAAACACTAG
1 ATCTGAA-AAAAACAATTTAAATAAATATTTATATTTATATAAAACACTAA
** * * *
63669 ATCCAAACAAAAAACAATTTAAATAAATATTTATTTTTATATAAAACACCAG
1 AT-CTGA-AAAAAACAATTTAAATAAATATTTATATTTATATAAAACACTAA
* * *
63721 ATTTGAAAAAAATAATTTAGATAAA
1 ATCTGAAAAAAACAATTTAAATAAA
63746 CAAGATCTGA
Statistics
Matches: 110, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
49 5 0.05
50 54 0.49
51 13 0.12
52 38 0.35
ACGTcount: A:0.55, C:0.08, G:0.04, T:0.33
Consensus pattern (50 bp):
ATCTGAAAAAAACAATTTAAATAAATATTTATATTTATATAAAACACTAA
Found at i:63708 original size:52 final size:51
Alignment explanation
Indices: 63575--63722 Score: 208
Period size: 50 Copynumber: 2.9 Consensus size: 51
63565 ACAAGATCTG
* * * **
63575 AAAAAATAATATAAATAAATATTTATATTTATGTAAAACACTAAATCTGAAC
1 AAAAAA-AATTTAAATAAATATTTATATTTATATAAAACACTAGATCCAAAC
63627 -AAAAAAATTTAAATAAATATTTATATTTATATAAAACACTAGATCCAAAC
1 AAAAAAAATTTAAATAAATATTTATATTTATATAAAACACTAGATCCAAAC
* *
63677 AAAAAACAATTTAAATAAATATTTATTTTTATATAAAACACCAGAT
1 AAAAAA-AATTTAAATAAATATTTATATTTATATAAAACACTAGAT
63723 TTGAAAAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
50 40 0.46
51 10 0.11
52 37 0.43
ACGTcount: A:0.55, C:0.09, G:0.03, T:0.33
Consensus pattern (51 bp):
AAAAAAAATTTAAATAAATATTTATATTTATATAAAACACTAGATCCAAAC
Found at i:66235 original size:4 final size:4
Alignment explanation
Indices: 66228--66256 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
66218 CCTTCTCTCG
66228 CCCT CCCT CCCT CCCT CCCT CCCT CCCT C
1 CCCT CCCT CCCT CCCT CCCT CCCT CCCT C
66257 TCACTCTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CCCT
Found at i:69443 original size:49 final size:48
Alignment explanation
Indices: 69390--69509 Score: 141
Period size: 49 Copynumber: 2.5 Consensus size: 48
69380 TGTTGTTACC
69390 AGTCTTCATCTAATCTCTCAGCCTCTCACTCTCCATATATATTAATCAT
1 AGTCTTCATCTAATCTCTCA-CCTCTCACTCTCCATATATATTAATCAT
* * * * *
69439 AGTCTTCATCGAATGTCACACTCTCTCACTCTTCATATATATTTATCAT
1 AGTCTTCATCTAATCTCTCAC-CTCTCACTCTCCATATATATTAATCAT
* * * *
69488 AATCTTCTTTTAACCTCTCACC
1 AGTCTTCATCTAATCTCTCACC
69510 CTCCATATAT
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
48 2 0.03
49 56 0.97
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.40
Consensus pattern (48 bp):
AGTCTTCATCTAATCTCTCACCTCTCACTCTCCATATATATTAATCAT
Found at i:72027 original size:18 final size:18
Alignment explanation
Indices: 72004--72040 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
71994 ACAATTCATA
72004 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
72022 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
72040 T
1 T
72041 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:72749 original size:13 final size:12
Alignment explanation
Indices: 72723--72760 Score: 58
Period size: 13 Copynumber: 3.0 Consensus size: 12
72713 AAAATTCTAG
72723 TTTCTCCTTTTTC
1 TTTC-CCTTTTTC
72736 TTTCCCTTTCTTC
1 TTTCCCTTT-TTC
72749 TTTCCCTTTTTC
1 TTTCCCTTTTTC
72761 GTTTAAACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (12 bp):
TTTCCCTTTTTC
Found at i:72811 original size:10 final size:9
Alignment explanation
Indices: 72786--72818 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
72776 CTTCTATTCC
*
72786 TTCTTTTGT
1 TTCTTTTTT
72795 TTCTTTTTT
1 TTCTTTTTT
72804 TTC-TTTTT
1 TTCTTTTTT
72812 TTCTTTT
1 TTCTTTT
72819 ATATCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:72825 original size:17 final size:18
Alignment explanation
Indices: 72787--72825 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
72777 TTCTATTCCT
* *
72787 TCTTTTGTTTCTTTTTTT
1 TCTTTTGTTTCTTTTATA
72805 TCTTTT-TTTCTTTTATA
1 TCTTTTGTTTCTTTTATA
72822 TCTT
1 TCTT
72826 ATATATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.05, C:0.13, G:0.03, T:0.79
Consensus pattern (18 bp):
TCTTTTGTTTCTTTTATA
Done.