Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010203.1 Kokia drynarioides strain JFW-HI SEQ_125020, 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: 47198
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Warning! 32 characters in sequence are not A, C, G, or T
Found at i:357 original size:88 final size:89
Alignment explanation
Indices: 1--733 Score: 1088
Period size: 86 Copynumber: 8.5 Consensus size: 89
*
1 GTCAAATCAACACATTATTTGATAAAAATTAT-A-AT-ATAATAATAATAATTTTTATTTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
* *
63 TATAAAATTAATAAATAATGTACT
66 TTTAAAATTAATAAATAATGTATT
*
87 GTCAAATCAACACATTATTTGATAAAAATTAT-A-AT-ATAATAATAATAATTTTTA--T--ATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
145 --TAAAATTAATAAATAATGTATT
66 TTTAAAATTAATAAATAATGTATT
*
167 GTCAAATCAACACATTATTTGATAAAAATT-TTA-AT-ATAATAATAATAATTTTTATTTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
229 TTTAAAATTAATAAATAATGTATT
66 TTTAAAATTAATAAATAATGTATT
*
253 ATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTA-TTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
317 TTTAAAATTAATAAATAATGTATT
66 TTTAAAATTAATAAATAATGTATT
*
341 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAGTAATAATAATTTTTATTTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
406 TTT-AAATTAATAAATAATGTATT
66 TTTAAAATTAATAAATAATGTATT
* * *
429 CTCAAATCAACACAGTATTTGATAAAAATTGTAATATAATAGTAATAATAATTTTTATTTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
494 TTTAAAATTAATAAATAATGTATT
66 TTTAAAATTAATAAATAATGTATT
518 GTCAAATCAACACATTATTTGATAAAAATTGT-A-AT-ATAATAATAATAATTTTTATTTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
* *
580 TATAAAATTAATAAATAATATATT
66 TTTAAAATTAATAAATAATGTATT
*
604 GTCAAATCAACACATTATTTGATAAAAATTG-----TAAT-ATAATAATAATTTGTACTTTAAAT
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTA-TTTAAAT
* *
663 A-TGAAAATTTGATAAATAATGTATT
65 ATTTAAAA-TTAATAAATAATGTATT
* * * *
688 GTCAAATTAACACAATATTTTATATAAATTGTAATATAATAATAAT
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAAT
734 CTTTTTATTT
Statistics
Matches: 605, Mismatches: 21, Indels: 38
0.91 0.03 0.06
Matches are distributed among these distances:
79 1 0.00
80 73 0.12
82 4 0.01
83 20 0.03
84 56 0.09
86 184 0.30
87 4 0.01
88 175 0.29
89 83 0.14
90 5 0.01
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (89 bp):
GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAATA
TTTAAAATTAATAAATAATGTATT
Found at i:633 original size:351 final size:336
Alignment explanation
Indices: 1--761 Score: 1143
Period size: 351 Copynumber: 2.2 Consensus size: 336
*
1 GTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATAATTTTTATTTAAATATAT
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATAT
* * *
66 AAAATTAATAAATAATGTACTGTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATA
66 TAAATTAATAAATAATGTACTCTCAAATCAACACAGTATTTGATAAAAATTATAATATAATAATA
131 ATAATTTTTATATATAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAAT
131 ATAATTTTTATATATAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAAT
* * *
196 TTTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTATTATCAAATC
196 TGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATATATTATCAAATC
** *
261 AACACATTATTTGATAAAAATTGTAATATAATAATAATAATAAT-TTTTATTAAATATTTAAAA-
261 AACACATTATTTGATAAAAATTGTAATATAATAATAAT--T--TGTACT-TTAAATA-TGAAAAT
324 TTAATAAATAATGTATT
320 TTAATAAATAATGTATT
341 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAGTAATAATAATTTTTATTTAAATA
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATAT-A-A-TAATAATAATTTTTATTTAAATA
* *
406 T-TTAAATTAATAAATAATGTATTCTCAAATCAACACAGTATTTGATAAAAATTGTAATATAATA
63 TATTAAATTAATAAATAATGTACTCTCAAATCAACACAGTATTTGATAAAAATTATAATAT-A-A
470 GTAATAATAATTTTTATTTAAATATTTAAAATTAATAAATAATGTATTGTCAAATCAACACATTA
126 -TAATAATAATTTTTA--T--ATA--TAAAATTAATAAATAATGTATTGTCAAATCAACACATTA
535 TTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATA
184 TTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATA
*
600 TATTGTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTGTACTTTAAATAT
249 TATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTGTACTTTAAATAT
*
665 GAAAATTTGATAAATAATGTATT
314 GAAAATTTAATAAATAATGTATT
* * * * * *
688 GTCAAATTAACACAATATTTTATATAAATTGTAATATAATAATAAT-CTTTTTATTTAAATTATG
1 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAA-TATA
752 TTAAATTAAT
65 TTAAATTAAT
762 TTTAAATGTA
Statistics
Matches: 386, Mismatches: 19, Indels: 27
0.89 0.04 0.06
Matches are distributed among these distances:
340 36 0.09
341 1 0.00
342 55 0.14
343 37 0.10
344 11 0.03
345 26 0.07
346 6 0.02
347 58 0.15
348 2 0.01
349 4 0.01
351 150 0.39
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (336 bp):
GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATAT
TAAATTAATAAATAATGTACTCTCAAATCAACACAGTATTTGATAAAAATTATAATATAATAATA
ATAATTTTTATATATAAAATTAATAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAAT
TGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAATAATATATTATCAAATC
AACACATTATTTGATAAAAATTGTAATATAATAATAATTTGTACTTTAAATATGAAAATTTAATA
AATAATGTATT
Found at i:879 original size:12 final size:12
Alignment explanation
Indices: 862--909 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
852 AAACATGTTT
862 ATTAATTTCCAA
1 ATTAATTTCCAA
874 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
890 ATTAATTTTCAA
1 ATTAATTTCCAA
902 ATTAATTT
1 ATTAATTT
910 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:908 original size:16 final size:16
Alignment explanation
Indices: 872--906 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
862 ATTAATTTCC
*
872 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
888 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
905 AA
1 AA
907 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:919 original size:28 final size:28
Alignment explanation
Indices: 862--919 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
852 AAACATGTTT
**
862 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
890 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
918 AT
1 AT
920 ATTATTTGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:4879 original size:61 final size:61
Alignment explanation
Indices: 4765--5143 Score: 239
Period size: 61 Copynumber: 6.3 Consensus size: 61
4755 TTTTTTCTCA
* * * * * * *
4765 AAAAAGGGATGTCGACCATTGCATGGTCAACACTAAAAAAATTTGCAA-TTTTTTATCCGAT
1 AAAAGGGGGTGTCGACCATTGCATAGCCAACACAAAAAAAATTTG-AATTTTTTTATTCGAG
* * * * ***
4826 AATAGGGGGTGTCGGCCATTGCATAGCCAGCACAAAAAAAATTTGAATTTTTTTTTTCTCT
1 AAAAGGGGGTGTCGACCATTGCATAGCCAACACAAAAAAAATTTGAATTTTTTTATTCGAG
* ** *
4887 AAAAGGGGGTGTCAACCA-TGCA-ATGACCAACAC-CCAAAAATGT-AATTTTTTTTATTCGAG
1 AAAAGGGGGTGTCGACCATTGCATA-G-CCAACACAAAAAAAATTTGAA-TTTTTTTATTCGAG
* * * * * * *
4947 AACAA-GGGGTGTCGGCCATTTCATGGCCAACACAAAAAAAGTTTGAAATATTTT-CTCGAG
1 AA-AAGGGGGTGTCGACCATTGCATAGCCAACACAAAAAAAATTTGAATTTTTTTATTCGAG
* ** *
5007 AAAAGGGGGTGTCGACCCA-TGCAATGGCCAACAC-CCAAAAATAT-AA-TTTTTT-TTCGAG
1 AAAAGGGGGTGTCGA-CCATTGC-ATAGCCAACACAAAAAAAATTTGAATTTTTTTATTCGAG
* * * * * * *
5065 AAAAGAGGGTGTTTG-CCATTTG-ATGGCCAACACTAAAAAATTTTAAATTTTTTT-CTCGAG
1 AAAAGGGGGTG-TCGACCA-TTGCATAGCCAACACAAAAAAAATTTGAATTTTTTTATTCGAG
*
5125 AAAAGGGGGTGTCGGCCAT
1 AAAAGGGGGTGTCGACCAT
5144 GTAATGGCCA
Statistics
Matches: 248, Mismatches: 51, Indels: 40
0.73 0.15 0.12
Matches are distributed among these distances:
57 14 0.06
58 26 0.10
59 16 0.06
60 92 0.37
61 98 0.40
62 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.28
Consensus pattern (61 bp):
AAAAGGGGGTGTCGACCATTGCATAGCCAACACAAAAAAAATTTGAATTTTTTTATTCGAG
Found at i:4964 original size:121 final size:119
Alignment explanation
Indices: 4813--5266 Score: 463
Period size: 118 Copynumber: 3.8 Consensus size: 119
4803 AAATTTGCAA
* * * * *
4813 TTTTTTATCCGATAATAGGGGGTGTCGGCCATTGCATAGCCAGCACAAAAAAAATTTGAATTTTT
1 TTTTTTATCCGAGAACAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAA-TTTT
* *** *
4878 TTTTTCTCTAAAAGGGGGTGTCAACCATGCAATGACCAACACCCAAAAATGTAATT
65 TTTCTCGAGAAAAGGGGGTGTCAACCATGCAATGGCCAACACCCAAAAATGTAA-T
* * * * *
4934 TTTTTTATTCGAGAACAAGGGGTGTCGGCCATTTCATGGCCAACACAAAAAAAGTTTGAAATATT
1 TTTTTTATCCGAGAACAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAATTTTT
* *
4999 TTCTCGAGAAAAGGGGGTGTCGACCCATGCAATGGCCAACACCCAAAAATATAAT
66 TTCTCGAGAAAAGGGGGTGTC-AACCATGCAATGGCCAACACCCAAAAATGTAAT
** * * *
5054 TTTTTT-T-CGAGAA-AAGAGGGTGTTTGCCATTTG-ATGGCCAACACTAAAAAATTTTAAATTT
1 TTTTTTATCCGAGAACAAG-GGGTGTCGGCCA-TTGCATGGCCAACACAAAAAAAATTTGAATTT
** * *
5115 TTTTCTCGAGAAAAGGGGGTGTCGGCCATGTAATGGCCAACACCCAAAAATGCAAAT
64 TTTTCTCGAGAAAAGGGGGTGTCAACCATGCAATGGCCAACACCCAAAAATG-TAAT
* * * * * **
5172 TTTTTTATCCAAAAACTAGGGGTGTCGGCCATTTG-ATGGCTAACAC-AAAAAAATTTAAAAATT
1 TTTTTTATCCGAGAACAAGGGGTGTCGGCCA-TTGCATGGCCAACACAAAAAAAATTTGAATTTT
** * *
5235 TTTCTTAAG-AAAGGGGGTGTCGACAATGCAAT
65 TTTCTCGAGAAAAGGGGGTGTCAACCATGCAAT
5267 AATTAACACC
Statistics
Matches: 282, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
117 28 0.10
118 91 0.32
119 25 0.09
120 55 0.20
121 83 0.29
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (119 bp):
TTTTTTATCCGAGAACAAGGGGTGTCGGCCATTGCATGGCCAACACAAAAAAAATTTGAATTTTT
TTCTCGAGAAAAGGGGGTGTCAACCATGCAATGGCCAACACCCAAAAATGTAAT
Found at i:5096 original size:118 final size:115
Alignment explanation
Indices: 4887--5313 Score: 459
Period size: 118 Copynumber: 3.6 Consensus size: 115
4877 TTTTTTCTCT
* *
4887 AAAAGGGGGTGTCAACCATGCAATGACCAACACCCAAAAATGTAATTTTTTTTATTCGAGAACAA
1 AAAAGGGGGTGTCGACCATGCAATGACCAACACCCAAAAATATAA--TTTTTT-TTCGAGAA-AA
*
4952 G-GGGTGTCGGCCATTTCATGGCCAACACAAAAAAAGTTTGAAATATTTTCTCGAG
62 GAGGGTGTCGGCCATTTGATGGCCAACACAAAAAAA-TTT-AAATATTTTCTCGAG
*
5007 AAAAGGGGGTGTCGACCCATGCAATGGCCAACACCCAAAAATATAATTTTTTTTCGAGAAAAGAG
1 AAAAGGGGGTGTCGA-CCATGCAATGACCAACACCCAAAAATATAATTTTTTTTCGAGAAAAGAG
** * *
5072 GGTGTTTGCCATTTGATGGCCAACACTAAAAAATTTTAAATTTTTTTCTCGAG
65 GGTGTCGGCCATTTGATGGCCAACAC-AAAAAAATTTAAA-TATTTTCTCGAG
* * * *
5125 AAAAGGGGGTGTCGGCCATGTAATGGCCAACACCCAAAAATGCA-AATTTTTTTATCCA-AAAAC
1 AAAAGGGGGTGTCGACCATGCAATGACCAACACCCAAAAAT--ATAATTTTTTT-TCGAGAAAA-
* * * **
5188 TAGGGGTGTCGGCCATTTGATGGCTAACACAAAAAAATTTAAAAATTTTTCTTAAG
62 GA-GGGTGTCGGCCATTTGATGGCCAACACAAAAAAATTTAAATA-TTTTCTCGAG
* * ** * * *
5244 -AAAGGGGGTGTCGACAATGCAATAATTAACACCCAAAAAAACAATTTTTTTTCAAGAAAAG-GG
1 AAAAGGGGGTGTCGACCATGCAATGACCAACACCCAAAAATATAATTTTTTTTCGAGAAAAGAGG
5307 AGTGTCG
66 -GTGTCG
5314 ACCACAAAAA
Statistics
Matches: 264, Mismatches: 30, Indels: 31
0.81 0.09 0.10
Matches are distributed among these distances:
114 2 0.01
115 6 0.02
116 4 0.02
117 44 0.17
118 105 0.40
119 37 0.14
120 38 0.14
121 28 0.11
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (115 bp):
AAAAGGGGGTGTCGACCATGCAATGACCAACACCCAAAAATATAATTTTTTTTCGAGAAAAGAGG
GTGTCGGCCATTTGATGGCCAACACAAAAAAATTTAAATATTTTCTCGAG
Found at i:5237 original size:60 final size:61
Alignment explanation
Indices: 4726--5237 Score: 234
Period size: 60 Copynumber: 8.5 Consensus size: 61
4716 AGAACAAGCA
* * * * * *
4726 ATGGCCGACACCAAAAAATTTTGAAAATTTTTTTTCTC-A-AAAAAGGGATGTCGACCA-TTG
1 ATGGCCAACA-CAAAAAAATTT-AAAAATTTTTATCTCGAGAAAAAGGGGTGTCGGCCATTTG
* ** * * * *
4786 CATGGTCAACACTAAAAAAATTTGCAATTTTTTATC-CGATAATAGGGGGTGTCGGCCA-TTG
1 -ATGGCCAACAC-AAAAAAATTTAAAAATTTTTATCTCGAGAAAAAGGGGTGTCGGCCATTTG
* * *** * * * ** ***
4847 CATAGCCAGCACAAAAAAAATTTGAATTTTTTTTTTCTC--TAAAAGGGGGTGTCAACCATGCA
1 -ATGGCCAACAC-AAAAAAATTT-AAAAATTTTTATCTCGAGAAAAAGGGGTGTCGGCCATTTG
* ** * *** * *
4909 ATGACCAACACCCAAAAATGTAATTTTTTTTAT-TCGAGAACAAGGGGTGTCGGCCATTTC
1 ATGGCCAACACAAAAAAATTTAAAAATTTTTATCTCGAGAAAAAGGGGTGTCGGCCATTTG
* * * * ***
4969 ATGGCCAACACAAAAAAAGTTT-GAAATATTT-TCTCGAGAAAAGGGGGTGTCGACCCATGCA
1 ATGGCCAACACAAAAAAA-TTTAAAAATTTTTATCTCGAGAAAAAGGGGTGTCG-GCCATTTG
** * * **
5030 ATGGCCAACACCCAAAAA--T-ATAATTTTT-TTTCGAG-AAAAGAGGGTGTTTGCCATTTG
1 ATGGCCAACACAAAAAAATTTAAAAATTTTTATCTCGAGAAAAAG-GGGTGTCGGCCATTTG
* * * * * *
5087 ATGGCCAACACTAAAAAATTT-TAAATTTTTTTCTCGAGAAAAGGGGGTGTCGGCCATGTA
1 ATGGCCAACACAAAAAAATTTAAAAATTTTTATCTCGAGAAAAAGGGGTGTCGGCCATTTG
** ** **
5147 ATGGCCAACACCCAAAAATGCAAATTTTTTTATC-C-A-AAAACTAGGGGTGTCGGCCATTTG
1 ATGGCCAACACAAAAAAATTTAAAAATTTTTATCTCGAGAAAA--AGGGGTGTCGGCCATTTG
*
5207 ATGGCTAACACAAAAAAATTTAAAAATTTTT
1 ATGGCCAACACAAAAAAATTTAAAAATTTTT
5238 CTTAAGAAAG
Statistics
Matches: 336, Mismatches: 96, Indels: 39
0.71 0.20 0.08
Matches are distributed among these distances:
57 24 0.07
58 25 0.07
59 22 0.07
60 145 0.43
61 111 0.33
62 8 0.02
63 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (61 bp):
ATGGCCAACACAAAAAAATTTAAAAATTTTTATCTCGAGAAAAAGGGGTGTCGGCCATTTG
Found at i:5416 original size:48 final size:52
Alignment explanation
Indices: 5363--5490 Score: 141
Period size: 48 Copynumber: 2.6 Consensus size: 52
5353 CAGCCATTTG
* * *
5363 ATGGCCAAAACCAAAAAAATTTTGAAATTTTTTTTTC-TCAAAA-T-GTG-C
1 ATGGCCGACACCAAAAAAATTTTGAAATTTTTTTTTCTTAAAAAGTGGTGTC
*
5411 ATGGCCGACACC-CAAAAA---TGAAA-TTTTTTTTCTTAAAAAGTGGGTGTC
1 ATGGCCGACACCAAAAAAATTTTGAAATTTTTTTTTCTTAAAAAGT-GGTGTC
5459 ATGGCCGACA-CAAAAAAATTTTGAAATTTTTT
1 ATGGCCGACACCAAAAAAATTTTGAAATTTTTT
5491 ATCTGACAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 16
0.76 0.06 0.19
Matches are distributed among these distances:
43 9 0.14
44 10 0.15
45 1 0.02
47 9 0.14
48 26 0.40
51 5 0.08
52 5 0.08
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.34
Consensus pattern (52 bp):
ATGGCCGACACCAAAAAAATTTTGAAATTTTTTTTTCTTAAAAAGTGGTGTC
Found at i:9469 original size:27 final size:27
Alignment explanation
Indices: 9439--9490 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
9429 TATTAGGATT
*
9439 AAATTGGAAAGATATGAAAGTATGAGC
1 AAATTGGAAAAATATGAAAGTATGAGC
9466 AAATTGGAAAAATATGAAAGTATGA
1 AAATTGGAAAAATATGAAAGTATGA
9491 AGATTACATT
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:0.52, C:0.02, G:0.23, T:0.23
Consensus pattern (27 bp):
AAATTGGAAAAATATGAAAGTATGAGC
Found at i:12868 original size:9 final size:9
Alignment explanation
Indices: 12851--12974 Score: 58
Period size: 10 Copynumber: 13.4 Consensus size: 9
12841 ATGTGATTCA
12851 AAAAATTAT
1 AAAAATTAT
*
12860 AAAAGTTATT
1 AAAAATTA-T
*
12870 GAAAA-TAT
1 AAAAATTAT
*
12878 AAAAATTAA
1 AAAAATTAT
*
12887 AAATAATTGT
1 AAA-AATTAT
12897 AAATAATTAT
1 AAA-AATTAT
12907 AAAAAATTA-
1 -AAAAATTAT
* *
12916 AATAATTTT
1 AAAAATTAT
* *
12925 AATAATGATT
1 AAAAATTA-T
*
12935 TAAAATTAT
1 AAAAATTAT
*
12944 AATAA-TAT
1 AAAAATTAT
*
12952 AGAAAAATAT
1 A-AAAATTAT
12962 AAAATATTA-
1 AAAA-ATTAT
12971 AAAA
1 AAAA
12975 TTGGATATTC
Statistics
Matches: 87, Mismatches: 19, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
8 15 0.17
9 34 0.39
10 35 0.40
11 3 0.03
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12895 original size:25 final size:27
Alignment explanation
Indices: 12851--12901 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
12841 ATGTGATTCA
*
12851 AAAAATTATAAAAGTTATTGAAAATAT
1 AAAAATTATAAAAGTAATTGAAAATAT
*
12878 AAAAATTA-AAAA-TAATTGTAAATA
1 AAAAATTATAAAAGTAATTGAAAATA
12902 ATTATAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 4 0.18
27 8 0.36
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (27 bp):
AAAAATTATAAAAGTAATTGAAAATAT
Found at i:12919 original size:28 final size:28
Alignment explanation
Indices: 12878--12977 Score: 75
Period size: 28 Copynumber: 3.6 Consensus size: 28
12868 TTGAAAATAT
12878 AAAAATTAAAAATAATTGTAAATAATTATA
1 AAAAATT--AAATAATTGTAAATAATTATA
* * *
12908 AAAAATTAAATAATT-TTAATAATGATT
1 AAAAATTAAATAATTGTAAATAATTATA
*
12935 TAAAATTATAATAATATAG-AAA-AA-TATA
1 AAAAATTA-AATAAT-T-GTAAATAATTATA
*
12963 AAATATTAAA-AATTG
1 AAAAATTAAATAATTG
12978 GATATTCATC
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
24 1 0.02
25 1 0.02
26 3 0.05
27 18 0.32
28 22 0.39
29 3 0.05
30 9 0.16
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAAATTAAATAATTGTAAATAATTATA
Found at i:13726 original size:24 final size:24
Alignment explanation
Indices: 13694--13742 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
13684 TCTAGAACCA
13694 AATCATGATGTAAGGAAAAAAGGG
1 AATCATGATGTAAGGAAAAAAGGG
13718 AATCATGATGTAAGGAAAAAAGGG
1 AATCATGATGTAAGGAAAAAAGGG
13742 A
1 A
13743 CTAAGTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.04, G:0.29, T:0.16
Consensus pattern (24 bp):
AATCATGATGTAAGGAAAAAAGGG
Found at i:14373 original size:26 final size:26
Alignment explanation
Indices: 14340--14390 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
14330 ATGAATATTT
14340 CCCCATTTTACAGTTTATACTGATTC
1 CCCCATTTTACAGTTTATACTGATTC
*
14366 CCCCATTTTACCGTTTATACTGATT
1 CCCCATTTTACAGTTTATACTGATT
14391 GAATAGGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.27, G:0.08, T:0.43
Consensus pattern (26 bp):
CCCCATTTTACAGTTTATACTGATTC
Found at i:15351 original size:106 final size:106
Alignment explanation
Indices: 15166--15378 Score: 426
Period size: 106 Copynumber: 2.0 Consensus size: 106
15156 TTTGGGAAGC
15166 ATGCTTGTGAAAAAAACTCTTATTTTTATCACCTGCTCTAAGCCAATTAGCTCTAGCCCTTTATT
1 ATGCTTGTGAAAAAAACTCTTATTTTTATCACCTGCTCTAAGCCAATTAGCTCTAGCCCTTTATT
15231 CCCAAAAAACTTCTTCTTTATCAATTTCCTAATTCAAATGT
66 CCCAAAAAACTTCTTCTTTATCAATTTCCTAATTCAAATGT
15272 ATGCTTGTGAAAAAAACTCTTATTTTTATCACCTGCTCTAAGCCAATTAGCTCTAGCCCTTTATT
1 ATGCTTGTGAAAAAAACTCTTATTTTTATCACCTGCTCTAAGCCAATTAGCTCTAGCCCTTTATT
15337 CCCAAAAAACTTCTTCTTTATCAATTTCCTAATTCAAATGT
66 CCCAAAAAACTTCTTCTTTATCAATTTCCTAATTCAAATGT
15378 A
1 A
15379 ACTTGGTTTC
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (106 bp):
ATGCTTGTGAAAAAAACTCTTATTTTTATCACCTGCTCTAAGCCAATTAGCTCTAGCCCTTTATT
CCCAAAAAACTTCTTCTTTATCAATTTCCTAATTCAAATGT
Found at i:17766 original size:16 final size:16
Alignment explanation
Indices: 17741--17777 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
17731 ATTCTTAAAA
17741 AAAAACAAAGAAATAG
1 AAAAACAAAGAAATAG
*
17757 AAAAATAAAGAAATAG
1 AAAAACAAAGAAATAG
17773 AAAAA
1 AAAAA
17778 ACCTCGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (16 bp):
AAAAACAAAGAAATAG
Found at i:18250 original size:19 final size:18
Alignment explanation
Indices: 18226--18261 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
18216 TGACTTCATT
18226 ATTAATTATGATTTATTTG
1 ATTAATT-TGATTTATTTG
*
18245 ATTAATTTGTTTTATTT
1 ATTAATTTGATTTATTT
18262 CTTTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (18 bp):
ATTAATTTGATTTATTTG
Found at i:40064 original size:24 final size:24
Alignment explanation
Indices: 40037--40091 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
40027 TCTTCTAATT
* *
40037 AAACTTTGTTTATTTGTTTCAATC
1 AAACTCTGCTTATTTGTTTCAATC
*
40061 AAACTCTGCTTATTTGTTTCATTC
1 AAACTCTGCTTATTTGTTTCAATC
40085 AAACTCT
1 AAACTCT
40092 TATTAGTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.49
Consensus pattern (24 bp):
AAACTCTGCTTATTTGTTTCAATC
Found at i:40095 original size:21 final size:23
Alignment explanation
Indices: 40046--40100 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
40036 TAAACTTTGT
40046 TTATTTGTTTCAATCAAACTCTGC
1 TTATTTGTTTCAATCAAAC-CTGC
*
40070 TTATTTGTTTCATTCAAA-CT-C
1 TTATTTGTTTCAATCAAACCTGC
*
40091 TTATTAGTTT
1 TTATTTGTTT
40101 AGATTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
24 17 0.59
ACGTcount: A:0.24, C:0.16, G:0.07, T:0.53
Consensus pattern (23 bp):
TTATTTGTTTCAATCAAACCTGC
Found at i:41322 original size:39 final size:39
Alignment explanation
Indices: 41279--41354 Score: 143
Period size: 39 Copynumber: 1.9 Consensus size: 39
41269 ACTATTAAAA
*
41279 TTAGGATGCATGATGGTACGATTAGGACACTATCAAATG
1 TTAGGATGCACGATGGTACGATTAGGACACTATCAAATG
41318 TTAGGATGCACGATGGTACGATTAGGACACTATCAAA
1 TTAGGATGCACGATGGTACGATTAGGACACTATCAAA
41355 ATTAGTTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.26
Consensus pattern (39 bp):
TTAGGATGCACGATGGTACGATTAGGACACTATCAAATG
Found at i:41344 original size:21 final size:21
Alignment explanation
Indices: 41278--41344 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
41268 TACTATTAAA
*
41278 ATTAGGATGCATGATGGTACG
1 ATTAGGATGCACGATGGTACG
* *** *
41299 ATTAGGA--CACTATCAAATG
1 ATTAGGATGCACGATGGTACG
41318 -TTAGGATGCACGATGGTACG
1 ATTAGGATGCACGATGGTACG
41338 ATTAGGA
1 ATTAGGA
41345 CACTATCAAA
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 7 0.22
21 13 0.41
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (21 bp):
ATTAGGATGCACGATGGTACG
Done.