Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004489.1 Kokia drynarioides strain JFW-HI SEQ_117918, 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: 47191
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:910 original size:23 final size:23
Alignment explanation
Indices: 880--933 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
870 ACGCTAGCAC
880 GCTTACTGTTCAGCACTGTGTGA
1 GCTTACTGTTCAGCACTGTGTGA
* *
903 GCTTACTGTTTAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGTGA
926 GCTTACTG
1 GCTTACTG
934 GATTGCACTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.15, C:0.20, G:0.26, T:0.39
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGTGA
Found at i:941 original size:23 final size:23
Alignment explanation
Indices: 880--953 Score: 89
Period size: 23 Copynumber: 3.2 Consensus size: 23
870 ACGCTAGCAC
*
880 GCTTACTG-TTCAGCACTGTGTGA
1 GCTTACTGATT-AGCACTGTGTGT
*
903 GCTTACTGTTTAGCACTGTGTGT
1 GCTTACTGATTAGCACTGTGTGT
*
926 GCTTACTGGATT-GCACTATGTGT
1 GCTTACT-GATTAGCACTGTGTGT
949 GCTTA
1 GCTTA
954 TTGTTTCCCC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
23 41 0.89
24 5 0.11
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (23 bp):
GCTTACTGATTAGCACTGTGTGT
Found at i:953 original size:46 final size:46
Alignment explanation
Indices: 892--982 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 46
882 TTACTGTTCA
*
892 GCACTGTGTGAGCTTACTGTTT-AGCACTGTGTGTGCTTACTGGATT
1 GCACTATGTGAGCTTACTGTTTCAGCACT-TGTGTGCTTACTGGATT
* *
938 GCACTATGTGTGCTTATTGTTTCCCCAGCACTTGTGTGCTTACTG
1 GCACTATGTGAGCTTACTGTTT---CAGCACTTGTGTGCTTACTG
983 TTAAGTACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
46 19 0.50
49 13 0.34
50 6 0.16
ACGTcount: A:0.14, C:0.21, G:0.25, T:0.40
Consensus pattern (46 bp):
GCACTATGTGAGCTTACTGTTTCAGCACTTGTGTGCTTACTGGATT
Found at i:2607 original size:8 final size:8
Alignment explanation
Indices: 2579--2646 Score: 64
Period size: 8 Copynumber: 8.0 Consensus size: 8
2569 GGCAACCCAA
2579 TTATTTTT
1 TTATTTTT
*
2587 ATTTTTATTT
1 -TTATT-TTT
2597 TTATTTTT
1 TTATTTTT
2605 TTATTTTT
1 TTATTTTT
*
2613 CTATCTTATT
1 TTAT-TT-TT
*
2623 TTATTTAT
1 TTATTTTT
*
2631 TTATTTAT
1 TTATTTTT
2639 TTATTTTT
1 TTATTTTT
2647 GTCCAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
8 30 0.60
9 12 0.24
10 8 0.16
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (8 bp):
TTATTTTT
Found at i:2612 original size:6 final size:6
Alignment explanation
Indices: 2579--2604 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2569 GGCAACCCAA
2579 TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TT
2605 TTATTTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTATTT
Found at i:2631 original size:4 final size:4
Alignment explanation
Indices: 2596--2644 Score: 55
Period size: 4 Copynumber: 11.8 Consensus size: 4
2586 TATTTTTATT
*
2596 TTTA TTTT TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA TTTA TTT
2645 TTGTCCAGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
3 2 0.05
4 29 0.74
5 6 0.15
6 2 0.05
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:4216 original size:19 final size:19
Alignment explanation
Indices: 4194--4238 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4184 TTATATTAGG
4194 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
4213 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
4232 ATTTAAT
1 ATTTAAT
4239 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:5064 original size:15 final size:16
Alignment explanation
Indices: 5046--5075 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5036 CTTCCCTATT
5046 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
5061 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
5076 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:5068 original size:22 final size:22
Alignment explanation
Indices: 5041--5095 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5031 TTCGACTTCC
5041 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
5063 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
*
5085 CTGTTTT-TTTT
1 CTATTTTCTTTT
5096 CCTTAGATCG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 7 0.23
22 23 0.77
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.73
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:5952 original size:17 final size:18
Alignment explanation
Indices: 5930--5968 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
5920 GTTATAATAA
5930 ATTTAA-AAAATTACAAT
1 ATTTAAGAAAATTACAAT
5947 ATTTAAGTAAAATTACAAT
1 ATTTAAG-AAAATTACAAT
5966 ATT
1 ATT
5969 ATATTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTTAAGAAAATTACAAT
Found at i:5985 original size:16 final size:17
Alignment explanation
Indices: 5964--6001 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
5954 TAAAATTACA
*
5964 ATATT-ATATTAATTAT
1 ATATTAATAATAATTAT
5980 ATATTAAATAATAATTAT
1 ATATT-AATAATAATTAT
5998 ATAT
1 ATAT
6002 ATTTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
18 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAATAATAATTAT
Found at i:6430 original size:10 final size:10
Alignment explanation
Indices: 6404--6436 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
6394 ACAGACACAT
6404 ATTAAATATG
1 ATTAAATATG
*
6414 A-TAAATATA
1 ATTAAATATG
6423 ATTAAATATG
1 ATTAAATATG
6433 ATTA
1 ATTA
6437 TCTTGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (10 bp):
ATTAAATATG
Found at i:9106 original size:7 final size:7
Alignment explanation
Indices: 9094--9129 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
9084 GGTGAAGCAG
9094 TTCGACA
1 TTCGACA
9101 TTCGACA
1 TTCGACA
9108 TTCGACA
1 TTCGACA
9115 TTCGACA
1 TTCGACA
9122 TTCGACA
1 TTCGACA
9129 T
1 T
9130 ATTCCTAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (7 bp):
TTCGACA
Found at i:9490 original size:32 final size:33
Alignment explanation
Indices: 9444--9517 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 33
9434 GTCAAAGTTG
* ** *
9444 TTTATTTTATTAATTTTGTTTTGATT-AAATTT
1 TTTATTTTACTAATTTCATTTTGATTAAAATTA
*
9476 TTTATTTTCCTAATTTCATTTTGATTAAAATTA
1 TTTATTTTACTAATTTCATTTTGATTAAAATTA
9509 TTTATTTTA
1 TTTATTTTA
9518 AGTAAATAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
32 22 0.63
33 13 0.37
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.65
Consensus pattern (33 bp):
TTTATTTTACTAATTTCATTTTGATTAAAATTA
Found at i:11334 original size:36 final size:35
Alignment explanation
Indices: 11288--11357 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 35
11278 CAAGTTAAAC
* *
11288 GAACGTGTTCATCGAAC-ATATTCATGAATATATAAT
1 GAACATGTTCAT-AAACAATATTCATGAATA-ATAAT
11324 GAACATGTTCATAAACAATATTCATGAATAATAA
1 GAACATGTTCATAAACAATATTCATGAATAATAA
11358 ACAAATAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
35 7 0.23
36 24 0.77
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (35 bp):
GAACATGTTCATAAACAATATTCATGAATAATAAT
Found at i:11418 original size:2 final size:2
Alignment explanation
Indices: 11372--11399 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
11362 ATAAATAAAC
11372 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11400 TGAATATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17064 original size:18 final size:18
Alignment explanation
Indices: 17041--17085 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
17031 TTAACTTGAA
17041 GTTCGAATCATATGGACT
1 GTTCGAATCATATGGACT
17059 GTTCGAATCATATGGACT
1 GTTCGAATCATATGGACT
17077 GTTCGAATC
1 GTTCGAATC
17086 CTTGATATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (18 bp):
GTTCGAATCATATGGACT
Found at i:21318 original size:20 final size:19
Alignment explanation
Indices: 21293--21366 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 19
21283 AAAAAAAATC
21293 TAGTAAGCTTTATGAAAGCT
1 TAGTAAG-TTTATGAAAGCT
* *
21313 TAGTAAGTTTATATAAAACT
1 TAGTAAGTTTAT-GAAAGCT
*
21333 AAGTATTCA-TCTTATGAAAGCT
1 TAGTA---AGT-TTATGAAAGCT
21355 TAGTAAGTTTAT
1 TAGTAAGTTTAT
21367 ATAAAATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
19 10 0.24
20 17 0.40
22 10 0.24
23 5 0.12
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (19 bp):
TAGTAAGTTTATGAAAGCT
Found at i:21361 original size:42 final size:42
Alignment explanation
Indices: 21302--21385 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
21292 CTAGTAAGCT
21302 TTATGAAAGCTTAGTAAGTTTATATAAAACTAAGTATTCATC
1 TTATGAAAGCTTAGTAAGTTTATATAAAACTAAGTATTCATC
*
21344 TTATGAAAGCTTAGTAAGTTTATATAAAATTAAGTATTCATC
1 TTATGAAAGCTTAGTAAGTTTATATAAAACTAAGTATTCATC
21386 GGACAATCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (42 bp):
TTATGAAAGCTTAGTAAGTTTATATAAAACTAAGTATTCATC
Found at i:21722 original size:20 final size:19
Alignment explanation
Indices: 21608--21728 Score: 84
Period size: 20 Copynumber: 6.1 Consensus size: 19
21598 GAGCACCTAG
*
21608 GTGCTAAACAGGGTACAAAT
1 GTGC-AAACAGGGCACAAAT
* * *
21628 GTACATACAGAAGCACCAAA-
1 GTGCAAACAG-GGCA-CAAAT
*
21648 GTGCAAACAGGGCACTGAA-
1 GTGCAAACAGGGCAC-AAAT
21667 GTGCATAACAGGGCACAAAT
1 GTGCA-AACAGGGCACAAAT
* **
21687 GTGTAATTAGGGGCACAAAT
1 GTGCAAACA-GGGCACAAAT
*
21707 GTGCAAACAGAAGCACAAAT
1 GTGCAAACAG-GGCACAAAT
21727 GT
1 GT
21729 TCTATTAAGA
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
18 1 0.01
19 20 0.26
20 53 0.68
21 4 0.05
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (19 bp):
GTGCAAACAGGGCACAAAT
Found at i:25318 original size:12 final size:12
Alignment explanation
Indices: 25303--25336 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
25293 AAAAAAATGA
25303 AGAAAAGCTAAG
1 AGAAAAGCTAAG
25315 AGAAAAGCTAAG
1 AGAAAAGCTAAG
25327 -GAAAA-CTAAG
1 AGAAAAGCTAAG
25337 CCTAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 5 0.23
12 12 0.55
ACGTcount: A:0.59, C:0.09, G:0.24, T:0.09
Consensus pattern (12 bp):
AGAAAAGCTAAG
Found at i:26134 original size:18 final size:17
Alignment explanation
Indices: 26107--26140 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26097 CATTAGAGAA
*
26107 TAATGAGTTAAGAAAGT
1 TAATGAGTTAAAAAAGT
26124 TAATCGAGTTAAAAAAG
1 TAAT-GAGTTAAAAAAG
26141 GGGTAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (17 bp):
TAATGAGTTAAAAAAGT
Found at i:26871 original size:59 final size:59
Alignment explanation
Indices: 26779--26949 Score: 195
Period size: 58 Copynumber: 2.9 Consensus size: 59
26769 TTAATATAAC
* * * *
26779 ATTTGGTACCTAAACTTGAGACTTTTTT-ATAATTTGGTACCCAAACTTTTTTTAACCCA
1 ATTTGGTACCTGAACTTGACA-TTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCCA
* * **
26838 ATTTGGTATCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAAC-ATTTTGGACCCA
1 ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCCA
* * * *
26896 ATTTGGTACCTGAAATTGGCA-TTTTTCTCTAATTTGGTGCCTAAGCTTTTTTTA
1 ATTTGGTACCTGAACTTGACATTTTTTC-CTAATTTGGTACCTAAACTTTTTTTA
26950 GATTTAATTT
Statistics
Matches: 93, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
57 6 0.06
58 49 0.53
59 38 0.41
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (59 bp):
ATTTGGTACCTGAACTTGACATTTTTTCCTAATTTGGTACCTAAACTTTTTTTAACCCA
Found at i:27218 original size:89 final size:89
Alignment explanation
Indices: 27116--27299 Score: 201
Period size: 89 Copynumber: 2.1 Consensus size: 89
27106 AATTTGGGAT
* ** *
27116 CCAAATTAAGAAAAAGAGTCAAGTTC-AGGCACCAAATTGGATCCCAAAAAGTTTAAGTACCAAC
1 CCAAATTAAGAAAAAGAGTAAAGTTCGA-GCACCAAATTGGAT-AAAAAAAGTTTAAGTACCAAA
* * * *
27180 TTAA-AAAAAGTGTCAAGTTTAGGTA
64 TTAAGAAAAAATATCAAGTTCAAGTA
* *** * * *
27205 CCAAATTAGGAAAATTTGTAAAGTTCGAGTATCAAATTGGATAAAAAAAGTTTAGGTACCAAATT
1 CCAAATTAAGAAAAAGAGTAAAGTTCGAGCACCAAATTGGATAAAAAAAGTTTAAGTACCAAATT
27270 AAGAAAAAATATCAAGTTCAAGTA
66 AAGAAAAAATATCAAGTTCAAGTA
27294 CCAAAT
1 CCAAAT
27300 GTTATATTAA
Statistics
Matches: 78, Mismatches: 15, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
88 21 0.27
89 56 0.72
90 1 0.01
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (89 bp):
CCAAATTAAGAAAAAGAGTAAAGTTCGAGCACCAAATTGGATAAAAAAAGTTTAAGTACCAAATT
AAGAAAAAATATCAAGTTCAAGTA
Found at i:27295 original size:31 final size:31
Alignment explanation
Indices: 27164--27299 Score: 93
Period size: 31 Copynumber: 4.5 Consensus size: 31
27154 GGATCCCAAA
* * *
27164 AAGTTTAAGTACCAACTTAA-AAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAATATC
* * ** * *
27194 AAGTTTAGGTACCAAATTAGGAAAATTTGTA
1 AAGTTTAAGTACCAAATTAAGAAAAAATATC
** * * *
27225 AAGTTCGAGTATCAAATT-GGATAAAA-A--
1 AAGTTTAAGTACCAAATTAAGAAAAAATATC
*
27252 AAGTTTAGGTACCAAATTAAGAAAAAATATC
1 AAGTTTAAGTACCAAATTAAGAAAAAATATC
*
27283 AAGTTCAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
27300 GTTATATTAA
Statistics
Matches: 79, Mismatches: 22, Indels: 9
0.72 0.20 0.08
Matches are distributed among these distances:
27 14 0.18
28 6 0.08
29 1 0.01
30 22 0.28
31 36 0.46
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.27
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAATATC
Found at i:29126 original size:4 final size:4
Alignment explanation
Indices: 29119--29147 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
29109 AAAAAAAACC
29119 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
29148 AACCCTTTCA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:34290 original size:2 final size:2
Alignment explanation
Indices: 34283--34315 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34273 GTGTCCAAGA
34283 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34316 ATAAGCTTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35477 original size:26 final size:26
Alignment explanation
Indices: 35448--35505 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
35438 TATAGCTTGG
35448 TTTCTCAAAGAAATTTTTAAATTTAC
1 TTTCTCAAAGAAATTTTTAAATTTAC
****
35474 TTTCTTTTTGGAAATTTTTAAATTTAC
1 TTTC-TCAAAGAAATTTTTAAATTTAC
35501 TTTCT
1 TTTCT
35506 TTTTGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.29, C:0.10, G:0.05, T:0.55
Consensus pattern (26 bp):
TTTCTCAAAGAAATTTTTAAATTTAC
Found at i:35488 original size:27 final size:27
Alignment explanation
Indices: 35457--35517 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
35447 GTTTCTCAAA
35457 GAAATTTTTAAATTTACTTTCTTTTTG
1 GAAATTTTTAAATTTACTTTCTTTTTG
35484 GAAATTTTTAAATTTACTTTCTTTTTG
1 GAAATTTTTAAATTTACTTTCTTTTTG
*
35511 TAAATTT
1 GAAATTT
35518 ACAAAACCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.28, C:0.07, G:0.07, T:0.59
Consensus pattern (27 bp):
GAAATTTTTAAATTTACTTTCTTTTTG
Found at i:41226 original size:92 final size:92
Alignment explanation
Indices: 41068--41245 Score: 232
Period size: 92 Copynumber: 1.9 Consensus size: 92
41058 ATTTGGTACG
* ** *
41068 TGTACTTTCATAAAATATTCAATGTGATATTTATACTTTGAAAATGTTCAATGTAATACATAAAC
1 TGTACTTTCATAAAATATTCAATATGATACATATACTTTGAAAATATTCAATGTAATACATAAAC
*
41133 TATCAAAATGTGTTTTATTATCGTGCT
66 TATCAAAATGTGGTTTATTATCGTGCT
* * * ** *
41160 TGTACTTTCATAAAATTTTCAATATGGTACATGTACTTTGAAAATA-TCTAATGTGGTACATGAA
1 TGTACTTTCATAAAATATTCAATATGATACATATACTTTGAAAATATTC-AATGTAATACATAAA
*
41224 CTATCAATATGTGGTTTATTAT
65 CTATCAAAATGTGGTTTATTAT
41246 AGATTCTAAT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
91 2 0.03
92 71 0.97
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (92 bp):
TGTACTTTCATAAAATATTCAATATGATACATATACTTTGAAAATATTCAATGTAATACATAAAC
TATCAAAATGTGGTTTATTATCGTGCT
Found at i:45943 original size:30 final size:30
Alignment explanation
Indices: 45904--45965 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
45894 TATTTTATAA
*
45904 TTAAATTTGTTATTATTTTAGAGGCATTTG
1 TTAAATTTGTTATTATTTTAGAGGAATTTG
*
45934 TTAATTTTGTTATTATTTTAGAGGAATTTG
1 TTAAATTTGTTATTATTTTAGAGGAATTTG
45964 TT
1 TT
45966 TGTTAAGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.02, G:0.16, T:0.56
Consensus pattern (30 bp):
TTAAATTTGTTATTATTTTAGAGGAATTTG
Done.