Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014877.1 Kokia drynarioides strain JFW-HI SEQ_129920, 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: 205558
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 65 characters in sequence are not A, C, G, or T
Found at i:3129 original size:24 final size:21
Alignment explanation
Indices: 3043--3131 Score: 81
Period size: 21 Copynumber: 4.1 Consensus size: 21
3033 CTCACAAAGA
* *
3043 AAAAAG-GAAATGAGTTAGAC
1 AAAAAGAGAAATAACTTAGAC
* *
3063 AAAAAGAGAAACAACTTGGAC
1 AAAAAGAGAAATAACTTAGAC
* *
3084 AAAAAGAGAAGTAACTTTGAC
1 AAAAAGAGAAATAACTTAGAC
*
3105 AAAAAGAAACGAAATGACTTAGAC
1 AAAAAG--A-GAAATAACTTAGAC
3129 AAA
1 AAA
3132 TCTTTTTTGT
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
20 6 0.11
21 34 0.62
23 1 0.02
24 14 0.25
ACGTcount: A:0.57, C:0.10, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAAAGAGAAATAACTTAGAC
Found at i:5982 original size:31 final size:30
Alignment explanation
Indices: 5947--6032 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
5937 ACTTGGGAGG
5947 TCCCTATATTATAAAAATTGGATCAAATTAA
1 TCCCTATATTATAAAAA-TGGATCAAATTAA
* * * *
5978 TCCCTCTATTAT-TAAATGAATCAATTTAA
1 TCCCTATATTATAAAAATGGATCAAATTAA
* *
6007 TCCATATACTATTAAAAA-GGATCAAA
1 TCCCTATATTA-TAAAAATGGATCAAA
6033 GAAGGTTAAA
Statistics
Matches: 43, Mismatches: 10, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 19 0.44
30 10 0.23
31 14 0.33
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (30 bp):
TCCCTATATTATAAAAATGGATCAAATTAA
Found at i:11049 original size:27 final size:27
Alignment explanation
Indices: 11016--11067 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
11006 CCTTTGCATG
*
11016 TATACTCATTGATTATTATAAATATAT
1 TATACTCATTGATTATCATAAATATAT
11043 TATACTCATTGATTATCATAAATAT
1 TATACTCATTGATTATCATAAATAT
11068 TATAAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (27 bp):
TATACTCATTGATTATCATAAATATAT
Found at i:14615 original size:21 final size:20
Alignment explanation
Indices: 14565--14615 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
14555 TAATATATAT
14565 TTTTAAAAAGAATATAAAAC
1 TTTTAAAAAGAATATAAAAC
*
14585 TTTTCCAAAAATATATAATAAAA-
1 TTTT--AAAAAGA-AT-ATAAAAC
14608 TTTTAAAA
1 TTTTAAAA
14616 TGGTAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 6 0.23
23 6 0.23
24 6 0.23
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
TTTTAAAAAGAATATAAAAC
Found at i:19136 original size:33 final size:33
Alignment explanation
Indices: 19098--19162 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
19088 CTTATTAAAT
19098 AGTGAATTCAAATTGAGATAAAAAGTTTTGAGA
1 AGTGAATTCAAATTGAGATAAAAAGTTTTGAGA
19131 AGTGAATTCAAATTGAGATAAAAAGTTTTGAG
1 AGTGAATTCAAATTGAGATAAAAAGTTTTGAG
19163 TGGGAAAAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.31
Consensus pattern (33 bp):
AGTGAATTCAAATTGAGATAAAAAGTTTTGAGA
Found at i:31434 original size:29 final size:30
Alignment explanation
Indices: 31365--31434 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
31355 ATATCAAAAC
*
31365 CATACATGAACTTTGATTTAATGTGCAATTT
1 CATACATGAACTTTAATTTAATGT-CAATTT
* *** *
31396 TATTGGTGAACTTTAATTTGATGT-AATTT
1 CATACATGAACTTTAATTTAATGTCAATTT
31425 CATACATGAA
1 CATACATGAA
31435 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
29 11 0.38
31 18 0.62
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (30 bp):
CATACATGAACTTTAATTTAATGTCAATTT
Found at i:32557 original size:26 final size:26
Alignment explanation
Indices: 32526--32576 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
32516 ATATTTTTCA
32526 ATTTTCAAAAAATAAAAATAAAAATT
1 ATTTTCAAAAAATAAAAATAAAAATT
* *
32552 ATTTTCTAAAAATGAAAATAAAAAT
1 ATTTTCAAAAAATAAAAATAAAAAT
32577 AGAAAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (26 bp):
ATTTTCAAAAAATAAAAATAAAAATT
Found at i:37929 original size:82 final size:82
Alignment explanation
Indices: 37828--37988 Score: 304
Period size: 82 Copynumber: 2.0 Consensus size: 82
37818 TTTTATAATG
*
37828 AACACCTCTAATCAAAACTAATTCAATTCAGTGGTCGAGGGTTTGATTTTCGCTCTGAGTATGGA
1 AACACCTCTAATCAAAACTAATTCAATTCAGTGGTCGAGGGTTTGATCTTCGCTCTGAGTATGGA
37893 ACAGTTTTAAAATTCGT
66 ACAGTTTTAAAATTCGT
*
37910 AACACCTCTAATCAAAACTAATTCAATTCAGTGGTCGAGGGTTTGATCTTCGTTCTGAGTATGGA
1 AACACCTCTAATCAAAACTAATTCAATTCAGTGGTCGAGGGTTTGATCTTCGCTCTGAGTATGGA
37975 ACAGTTTTAAAATT
66 ACAGTTTTAAAATT
37989 TGTGGTCAGC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 77 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (82 bp):
AACACCTCTAATCAAAACTAATTCAATTCAGTGGTCGAGGGTTTGATCTTCGCTCTGAGTATGGA
ACAGTTTTAAAATTCGT
Found at i:49482 original size:49 final size:49
Alignment explanation
Indices: 49417--49534 Score: 202
Period size: 49 Copynumber: 2.4 Consensus size: 49
49407 ACATGAATAT
49417 AATTTCTACACCATAAAATATATATTTGAATATGTAAGGATATGTCAACA
1 AATTTCTACACCATAAAATATATATTTGAATATGTAAGGATATGTCAA-A
*
49467 AATTT-TACACCATAAAATATATATTTGAATATGTAAGGTTATGTCAAA
1 AATTTCTACACCATAAAATATATATTTGAATATGTAAGGATATGTCAAA
49515 AATTTCTACACCATAGAAAT
1 AATTTCTACACCATA-AAAT
49535 GTGTTAATTC
Statistics
Matches: 65, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
48 6 0.09
49 50 0.77
50 9 0.14
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (49 bp):
AATTTCTACACCATAAAATATATATTTGAATATGTAAGGATATGTCAAA
Found at i:53774 original size:27 final size:27
Alignment explanation
Indices: 53731--53784 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
53721 CCGAATAATG
**
53731 AATTTAGGGTTTGAGA-TTTGAAGTTTA
1 AATTTAGGGTTCAAGATTTTG-AGTTTA
53758 AATTTAGGGTTCAAGATTTTGAGTTTA
1 AATTTAGGGTTCAAGATTTTGAGTTTA
53785 GAGTTTCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.83
28 4 0.17
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (27 bp):
AATTTAGGGTTCAAGATTTTGAGTTTA
Found at i:53885 original size:21 final size:21
Alignment explanation
Indices: 53861--53909 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
53851 AAAAAATTAC
53861 AAAAATATAATTAAATAAT-TG
1 AAAAATATAA-TAAATAATGTG
*
53882 AAAAGATATCATAAATAATGTG
1 AAAA-ATATAATAAATAATGTG
53904 ATAAAA
1 A-AAAA
53910 AAATTCATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
21 12 0.50
22 9 0.38
23 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.29
Consensus pattern (21 bp):
AAAAATATAATAAATAATGTG
Found at i:54441 original size:51 final size:51
Alignment explanation
Indices: 54372--54471 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
54362 AAGAAAATTT
* *
54372 GAATTTGAATTTTGCTATTTAGAGAAGACTTTGAAAATGAGAAATGCATAG
1 GAATTTGAATTTTCCTATTTAGAGAAAACTTTGAAAATGAGAAATGCATAG
* *
54423 GAATTTGATTTTTCCTATTTTGAGAAAACTTTGAAAATGAGAAATGCAT
1 GAATTTGAATTTTCCTATTTAGAGAAAACTTTGAAAATGAGAAATGCAT
54472 CTTCATTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (51 bp):
GAATTTGAATTTTCCTATTTAGAGAAAACTTTGAAAATGAGAAATGCATAG
Found at i:56075 original size:16 final size:16
Alignment explanation
Indices: 56037--56079 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
56027 GAGTTCAAAT
* *
56037 CATTTCGAATTCTGAT
1 CATTTCAAATTCTGAC
* *
56053 CACTTCAAATTCTGGC
1 CATTTCAAATTCTGAC
56069 CATTTCAAATT
1 CATTTCAAATT
56080 ATTTGTTCAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (16 bp):
CATTTCAAATTCTGAC
Found at i:71039 original size:56 final size:56
Alignment explanation
Indices: 70971--71124 Score: 184
Period size: 56 Copynumber: 2.7 Consensus size: 56
70961 ATTTTGAGTC
* * * * *
70971 TGAACTTGACAATTATTTTCACATTGGGGTTAATTTTTTTTTTTCAAGTTCATCCT
1 TGAACTTAACAATTGTTCTCACATTGGGTTTAATTTTTTTTTTTAAAGTTCATCCT
* * *
71027 TGAACTTAACAATTGTTCTCACATTTTGGTTTAA-ATTTTTTTTTAAAGTTCTTCCT
1 TGAACTTAACAATTGTTCTCACA-TTGGGTTTAATTTTTTTTTTTAAAGTTCATCCT
* *
71083 TGAACTTAGCAATTGTTCCCACATTGGAGTTTGAATTTTTTT
1 TGAACTTAACAATTGTTCTCACATTGG-GTTT-AATTTTTTT
71125 ATGGTCCAAG
Statistics
Matches: 82, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
55 3 0.04
56 64 0.78
57 10 0.12
58 5 0.06
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.49
Consensus pattern (56 bp):
TGAACTTAACAATTGTTCTCACATTGGGTTTAATTTTTTTTTTTAAAGTTCATCCT
Found at i:85318 original size:22 final size:21
Alignment explanation
Indices: 85276--85318 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
85266 ACGATAAATG
*
85276 GAGAAGAGAAGAAAATAGAGA
1 GAGAAGAAAAGAAAATAGAGA
* *
85297 GAGAAGCAAAAGATAATGGAGA
1 GAGAAG-AAAAGAAAATAGAGA
85319 ATAAAGAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.58, C:0.02, G:0.33, T:0.07
Consensus pattern (21 bp):
GAGAAGAAAAGAAAATAGAGA
Found at i:86139 original size:11 final size:11
Alignment explanation
Indices: 86123--86147 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
86113 CACTTTAAAA
86123 ATTATTAAATT
1 ATTATTAAATT
86134 ATTATTAAATT
1 ATTATTAAATT
86145 ATT
1 ATT
86148 CGAAAATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:87480 original size:30 final size:30
Alignment explanation
Indices: 87424--87480 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
87414 TATATATGAA
*
87424 ATATTTTTAATGAAATGTAATTTATTATTT
1 ATATTTTTAATGAAATATAATTTATTATTT
87454 ATATTATTTAAT-AAA-ATAATTATATTA
1 ATATT-TTTAATGAAATATAATT-TATTA
87481 CATGAAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.21
30 13 0.54
31 6 0.25
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
ATATTTTTAATGAAATATAATTTATTATTT
Found at i:90943 original size:16 final size:15
Alignment explanation
Indices: 90913--90952 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
90903 TATGTGAATT
*
90913 TAAAAATTCATTTAA
1 TAAAAATTAATTTAA
90928 TAAAATATTAATTTAA
1 TAAAA-ATTAATTTAA
90944 -AAAAATTAA
1 TAAAAATTAA
90953 AATCATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 9 0.39
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAATTAATTTAA
Found at i:91081 original size:17 final size:19
Alignment explanation
Indices: 91059--91099 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
91049 GTTTATATAT
91059 TATTATATAA-AA-ATAAA
1 TATTATATAATAACATAAA
*
91076 TATTATATAATAACATAAT
1 TATTATATAATAACATAAA
91095 TATTA
1 TATTA
91100 ATGCCATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TATTATATAATAACATAAA
Found at i:111612 original size:44 final size:44
Alignment explanation
Indices: 111549--111654 Score: 149
Period size: 44 Copynumber: 2.4 Consensus size: 44
111539 AGTGCTCAAC
* * *
111549 ACTCGTATCCGAAGCATATACTAACATAGGTATTGGTGTTTGAT
1 ACTCGTATCCGAAGCATATACTAACATAGGTATTGGCGTCTAAT
* *
111593 ACTCGTATCCGAAGCATATACTAACGTAGGTATTTGCGTCTAAT
1 ACTCGTATCCGAAGCATATACTAACATAGGTATTGGCGTCTAAT
* *
111637 GCTCGTATCCGAACCATA
1 ACTCGTATCCGAAGCATA
111655 AAAATCAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (44 bp):
ACTCGTATCCGAAGCATATACTAACATAGGTATTGGCGTCTAAT
Found at i:132485 original size:31 final size:30
Alignment explanation
Indices: 132450--132542 Score: 77
Period size: 31 Copynumber: 3.2 Consensus size: 30
132440 TTAATATTTT
132450 ATTTGGTACTTGAGTTTAATTTTAGTATTCA
1 ATTTGGTACTTGAGTTT-ATTTTAGTATTCA
* * * * *
132481 ATTTGGTATTTAAG-TT-TTCT-GT-TCCT
1 ATTTGGTACTTGAGTTTATTTTAGTATTCA
* *
132507 ATTTGGTACTTGAGTTTAGCTTTAATATTCA
1 ATTTGGTACTTGAGTTTA-TTTTAGTATTCA
132538 ATTTG
1 ATTTG
132543 ATATCTGTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 10
0.67 0.18 0.15
Matches are distributed among these distances:
26 14 0.31
27 4 0.09
28 3 0.07
29 2 0.04
30 3 0.07
31 19 0.42
ACGTcount: A:0.23, C:0.09, G:0.16, T:0.53
Consensus pattern (30 bp):
ATTTGGTACTTGAGTTTATTTTAGTATTCA
Found at i:138337 original size:25 final size:24
Alignment explanation
Indices: 138269--138338 Score: 79
Period size: 25 Copynumber: 2.9 Consensus size: 24
138259 ATTAAATTTA
**
138269 AATT-TATTATATTAATTAAAAAT
1 AATTATATTATATTAAAAAAAAAT
* *
138292 AATTATATTAAATTCACAAAAAAAT
1 AATTATATTATATT-AAAAAAAAAT
138317 AATTATATTTATATTAAAAAAA
1 AATTATA-TTATATTAAAAAAA
138339 TTCCTCCCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
23 4 0.11
24 8 0.21
25 20 0.53
26 6 0.16
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTATATTATATTAAAAAAAAAT
Found at i:139829 original size:28 final size:27
Alignment explanation
Indices: 139792--139847 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 27
139782 AATTGACATT
139792 TACAATATAAATT-AATAAAATATAAAA
1 TACAATATAAATTGAAT-AAATATAAAA
139819 TACAATAATAAATTGAATAAATATAAAA
1 TACAAT-ATAAATTGAATAAATATAAAA
139847 T
1 T
139848 TCTTAGTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 6 0.22
28 18 0.67
29 3 0.11
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (27 bp):
TACAATATAAATTGAATAAATATAAAA
Found at i:156383 original size:31 final size:31
Alignment explanation
Indices: 156345--156413 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
156335 AGTTAGGTCT
156345 TGAACTTGGCAATTGCTCCCACATT-GAGGCC
1 TGAACTTGGCAATTGCTCCCACATTAGA-GCC
*
156376 TGAACTTGGCAATTGTTCCCACATTAGAGCC
1 TGAACTTGGCAATTGCTCCCACATTAGAGCC
*
156407 TAAACTT
1 TGAACTT
156414 TAGGATTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (31 bp):
TGAACTTGGCAATTGCTCCCACATTAGAGCC
Found at i:158856 original size:9 final size:9
Alignment explanation
Indices: 158842--158866 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
158832 TCATTAAATG
158842 GTTTGCATT
1 GTTTGCATT
158851 GTTTGCATT
1 GTTTGCATT
158860 GTTTGCA
1 GTTTGCA
158867 CCAATCGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.24, T:0.52
Consensus pattern (9 bp):
GTTTGCATT
Found at i:159128 original size:29 final size:30
Alignment explanation
Indices: 159090--159165 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
159080 ACAAATTTTG
* *
159090 GAATATTTCAATGACTT-ATGAAAACTTTTC
1 GAATAATTCAGTGACTTAATGAAAAC-TTTC
* *
159120 -AATAGTTCAGTGATTTAAATGAAAACTTTC
1 GAATAATTCAGTGACTT-AATGAAAACTTTC
159150 GAATAATTCAGTGACT
1 GAATAATTCAGTGACT
159166 GTTTTATAAC
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
29 13 0.34
30 4 0.11
31 21 0.55
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (30 bp):
GAATAATTCAGTGACTTAATGAAAACTTTC
Found at i:159833 original size:16 final size:17
Alignment explanation
Indices: 159812--159852 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
159802 TATGCTTTTT
159812 TATAATATATTTAT-TA
1 TATAATATATTTATGTA
* *
159828 TATAATTTTTTTATGTA
1 TATAATATATTTATGTA
159845 -ATAATATA
1 TATAATATA
159853 ATATTAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (17 bp):
TATAATATATTTATGTA
Found at i:160402 original size:2 final size:2
Alignment explanation
Indices: 160395--160435 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
160385 CTTAAAATTG
160395 TA TA TA TA 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 TA TA TA TA T
160436 TTCTGCATGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:163514 original size:27 final size:27
Alignment explanation
Indices: 163476--163530 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
163466 AAGTAAATAA
*
163476 TCGAATAAATCAAAAATCGATTTTAGT
1 TCGAATAAATCAAAAACCGATTTTAGT
163503 TCGAATAAATCAAAAACCGATTTTAGT
1 TCGAATAAATCAAAAACCGATTTTAGT
163530 T
1 T
163531 GTAATGTCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.33
Consensus pattern (27 bp):
TCGAATAAATCAAAAACCGATTTTAGT
Found at i:166799 original size:20 final size:19
Alignment explanation
Indices: 166774--166813 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
166764 AGGGGGAAGA
166774 AGAAGCAGACATCTGAGAAT
1 AGAAGCAGA-ATCTGAGAAT
* *
166794 AGAAGCTGAGTCTGAGAAT
1 AGAAGCAGAATCTGAGAAT
166813 A
1 A
166814 CATGCGACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.17
Consensus pattern (19 bp):
AGAAGCAGAATCTGAGAAT
Found at i:192888 original size:17 final size:17
Alignment explanation
Indices: 192864--192910 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
192854 AGTTGAATCG
192864 AATTTTTATTTTTTAAA
1 AATTTTTATTTTTTAAA
* *
192881 AGTTTTTATAATTTTAAA
1 AATTTTTAT-TTTTTAAA
192899 AATTATTTATTT
1 AATT-TTTATTT
192911 AATTGAACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 8 0.33
18 11 0.46
19 5 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
AATTTTTATTTTTTAAA
Found at i:198329 original size:78 final size:78
Alignment explanation
Indices: 198200--198357 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
198190 TGGTTCCTTT
198200 CTGAATGCTTTCTATTGAAATAAGCTGCTGCATTAACTTTGGGTGCTATAATGGGTACATGAGTT
1 CTGAATGCTTTCTATTGAAATAAGCTGCTGCATTAACTTTGGGTGCTATAATGGGTACATGAGTT
198265 GTATACACTGAAC
66 GTATACACTGAAC
198278 CTGAATGCTTTCTATTGAAATAAGCTGCTGCATTAACTTTGGGTGCTATAATGGGTACATGAGTT
1 CTGAATGCTTTCTATTGAAATAAGCTGCTGCATTAACTTTGGGTGCTATAATGGGTACATGAGTT
198343 GTATACACTGAAC
66 GTATACACTGAAC
198356 CT
1 CT
198358 CCTATATTTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (78 bp):
CTGAATGCTTTCTATTGAAATAAGCTGCTGCATTAACTTTGGGTGCTATAATGGGTACATGAGTT
GTATACACTGAAC
Found at i:200160 original size:24 final size:25
Alignment explanation
Indices: 200133--200180 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
200123 TTTGAATTAA
*
200133 ATTATTTATA-ATATTCATTTTTTT
1 ATTATTTATAGAAATTCATTTTTTT
*
200157 ATTATTTATAGAAATTTATTTTTT
1 ATTATTTATAGAAATTCATTTTTT
200181 CAGGGTTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTATTTATAGAAATTCATTTTTTT
Found at i:201550 original size:21 final size:21
Alignment explanation
Indices: 201509--201550 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 21
201499 GATTATATAT
* *
201509 ATAATTTATATTTTGAAAAAA
1 ATAATATATATTTTAAAAAAA
*
201530 ATAATATATA-TTTAAAGAAA
1 ATAATATATATTTTAAAAAAA
201550 A
1 A
201551 GTTACATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATAATATATATTTTAAAAAAA
Found at i:203668 original size:21 final size:22
Alignment explanation
Indices: 203619--203669 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
203609 GTAATATAAT
*
203619 AATAAAATGATAGCAAAACAAC
1 AATAAAATGACAGCAAAACAAC
*
203641 -ATCAAAATGACAGC-AATCAAC
1 AAT-AAAATGACAGCAAAACAAC
203662 AATAAAAT
1 AATAAAAT
203670 AGTAATGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.61, C:0.16, G:0.08, T:0.16
Consensus pattern (22 bp):
AATAAAATGACAGCAAAACAAC
Done.