Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014947.1 Kokia drynarioides strain JFW-HI SEQ_129990, 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: 115107
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 402 characters in sequence are not A, C, G, or T
Found at i:8431 original size:23 final size:22
Alignment explanation
Indices: 8391--8440 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
8381 CATCAACCAA
*
8391 AAAAAAAACGTAAACTAT-AAC
1 AAAAAAAACGAAAACTATGAAC
*
8412 AGAAAAAAATGAAAATCTATGAAC
1 A-AAAAAAACGAAAA-CTATGAAC
8436 AAAAA
1 AAAAA
8441 TAGGAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 11 0.46
23 8 0.33
24 4 0.17
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAAAAAACGAAAACTATGAAC
Found at i:11659 original size:21 final size:21
Alignment explanation
Indices: 11613--11655 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
11603 AAAAATCTTT
*
11613 ATATTTTTAATATGGATGAAA
1 ATATTTTAAATATGGATGAAA
*
11634 ATATTTTAAATAT-TATGAAA
1 ATATTTTAAATATGGATGAAA
11654 AT
1 AT
11656 TATTACTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (21 bp):
ATATTTTAAATATGGATGAAA
Found at i:12192 original size:81 final size:81
Alignment explanation
Indices: 12104--12269 Score: 287
Period size: 81 Copynumber: 2.0 Consensus size: 81
12094 TGACCTCCCT
* *
12104 AAAATAGTAAATTTTTAATTTAGATTTTTTATGATTTATAAAATTTTAAATTAATAATAGTAAAT
1 AAAATAGTAAATTTTTAATTTAGATCTTTTATGATTTATAAAATTTTAAATTAATAATAATAAAT
12169 TTGTATTTTAGCCCCC
66 TTGTATTTTAGCCCCC
* *
12185 AAAATAGTAAATTTTTGATTTAGGTCTTTTATGATTTATAAAATTTTAAATTAATAATAATAAAT
1 AAAATAGTAAATTTTTAATTTAGATCTTTTATGATTTATAAAATTTTAAATTAATAATAATAAAT
*
12250 TTGTATTTTAGCCCCG
66 TTGTATTTTAGCCCCC
12266 AAAA
1 AAAA
12270 GTAATAAAAA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 80 1.00
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.45
Consensus pattern (81 bp):
AAAATAGTAAATTTTTAATTTAGATCTTTTATGATTTATAAAATTTTAAATTAATAATAATAAAT
TTGTATTTTAGCCCCC
Found at i:12305 original size:81 final size:81
Alignment explanation
Indices: 12139--12307 Score: 232
Period size: 81 Copynumber: 2.1 Consensus size: 81
12129 TTTTTATGAT
* * **
12139 TTATAAAATTTTAAATTAATAATAGTAAATTTGTATTTTAGCCCCCAAAATAGTAAATTTTTGAT
1 TTATAAAATTTTAAATTAATAATAATAAATTTGTATTTTAGCCCCCAAAATAATAAAAATTTGAT
* * ** *
12204 TTAGGTCTTTTATGAT
66 TTAGATCATTTAAAAA
*
12220 TTATAAAATTTTAAATTAATAATAATAAATTTGTATTTTAGCCCCGAAAAGTAATAAAAATTTGA
1 TTATAAAATTTTAAATTAATAATAATAAATTTGTATTTTAGCCCCCAAAA-TAATAAAAATTTGA
12285 TTTA-ATCATTTAAAAA
65 TTTAGATCATTTAAAAA
12301 TTATAAA
1 TTATAAA
12308 GATAGAGATT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
81 62 0.81
82 15 0.19
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.43
Consensus pattern (81 bp):
TTATAAAATTTTAAATTAATAATAATAAATTTGTATTTTAGCCCCCAAAATAATAAAAATTTGAT
TTAGATCATTTAAAAA
Found at i:15526 original size:23 final size:22
Alignment explanation
Indices: 15486--15535 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
15476 CATCAACCAA
*
15486 AAAAAAAACGTAAACTAT-AAC
1 AAAAAAAACGAAAACTATGAAC
*
15507 AGAAAAAAATGAAAATCTATGAAC
1 A-AAAAAAACGAAAA-CTATGAAC
15531 AAAAA
1 AAAAA
15536 TAGGAAGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.04
22 11 0.46
23 8 0.33
24 4 0.17
ACGTcount: A:0.68, C:0.10, G:0.08, T:0.14
Consensus pattern (22 bp):
AAAAAAAACGAAAACTATGAAC
Found at i:25759 original size:2 final size:2
Alignment explanation
Indices: 25752--25781 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
25742 GTTAGTTGTA
*
25752 AT AT AT AT AT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25782 TTAATAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27684 original size:27 final size:25
Alignment explanation
Indices: 27654--27703 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
27644 TTTACGTTGG
*
27654 TCACCCCATTATGAAATTTTTTTTTTA
1 TCACCCAATTATG--ATTTTTTTTTTA
*
27681 TCACCTAATTATGATTTTTTTTT
1 TCACCCAATTATGATTTTTTTTT
27704 GAAAAATTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
27 11 0.52
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (25 bp):
TCACCCAATTATGATTTTTTTTTTA
Found at i:28706 original size:16 final size:16
Alignment explanation
Indices: 28685--28718 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
28675 AAACATATTT
*
28685 AATAACAATTATTTAA
1 AATAACAAATATTTAA
28701 AATAACAAATATTTAA
1 AATAACAAATATTTAA
28717 AA
1 AA
28719 CCATAGGATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (16 bp):
AATAACAAATATTTAA
Found at i:30227 original size:28 final size:29
Alignment explanation
Indices: 30195--30258 Score: 96
Period size: 28 Copynumber: 2.2 Consensus size: 29
30185 AGTCTTTATA
30195 TATTTTGTATATTTAA-AATTTAATC-TTT
1 TATTTT-TATATTTAAGAATTTAATCTTTT
*
30223 TATTTTTATTTTTAAGAATTTAATCTTTT
1 TATTTTTATATTTAAGAATTTAATCTTTT
30252 TATTTTT
1 TATTTTT
30259 TAAATTTATA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
27 8 0.24
28 15 0.45
29 10 0.30
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (29 bp):
TATTTTTATATTTAAGAATTTAATCTTTT
Found at i:33655 original size:15 final size:16
Alignment explanation
Indices: 33635--33668 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
33625 GGTCCTATCC
*
33635 TTTTTATTGACAA-AT
1 TTTTTATCGACAATAT
33650 TTTTTATCGACAATAT
1 TTTTTATCGACAATAT
33666 TTT
1 TTT
33669 AAATACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.56
Consensus pattern (16 bp):
TTTTTATCGACAATAT
Found at i:33903 original size:29 final size:29
Alignment explanation
Indices: 33849--33906 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
33839 TTTAAAAAGT
* *
33849 ATTTTTTAAGAATTTTATAAGTTTTTATA
1 ATTTTTTAAGAATTTTAAAAATTTTTATA
33878 ATTTTTTAA-AATTTTAAAAATGTTTTATA
1 ATTTTTTAAGAATTTTAAAAAT-TTTTATA
33907 TTTATTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (29 bp):
ATTTTTTAAGAATTTTAAAAATTTTTATA
Found at i:33982 original size:27 final size:28
Alignment explanation
Indices: 33936--33999 Score: 71
Period size: 26 Copynumber: 2.3 Consensus size: 28
33926 ATTTAAGAAT
33936 TTTTTATAAGCTCTTACAATATTTATAAA
1 TTTTTATAAGCTCTTACAAT-TTTATAAA
*
33965 TTTATTATAAG-T-TT-CAATTTTCTAATA
1 TTT-TTATAAGCTCTTACAATTTTATAA-A
33992 TTTTTATA
1 TTTTTATA
34000 TTTTAATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 11 0.34
27 8 0.25
28 2 0.06
29 4 0.12
30 7 0.22
ACGTcount: A:0.34, C:0.08, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTTTATAAGCTCTTACAATTTTATAAA
Found at i:48791 original size:3 final size:3
Alignment explanation
Indices: 48783--48810 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
48773 TGTGTTCAAA
48783 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
48811 TTGCAATAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:50302 original size:20 final size:20
Alignment explanation
Indices: 50277--50328 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
50267 TAAGTAAATA
50277 ATATTTTAAATTTAAATTTT-
1 ATATTTTAAATTT-AATTTTC
*
50297 ATA-TTTACAATTTATTTTTC
1 ATATTTTA-AATTTAATTTTC
*
50317 CTATTTTAAATT
1 ATATTTTAAATT
50329 GCGACTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
19 9 0.33
20 14 0.52
21 4 0.15
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATTTTAAATTTAATTTTC
Found at i:50488 original size:13 final size:13
Alignment explanation
Indices: 50470--50495 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50460 TTTCAAATCC
50470 TTTGAAGTTTGAA
1 TTTGAAGTTTGAA
50483 TTTGAAGTTTGAA
1 TTTGAAGTTTGAA
50496 AGTGTTGTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (13 bp):
TTTGAAGTTTGAA
Found at i:52503 original size:18 final size:17
Alignment explanation
Indices: 52467--52512 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
52457 TTATTTATTT
*
52467 ATTTATATTAAATTTAA
1 ATTTATATTAAATTAAA
*
52484 ATTTATCATTCAATTAAA
1 ATTTAT-ATTAAATTAAA
*
52502 ATTTATTTTAA
1 ATTTATATTAA
52513 CTTTTAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTTATATTAAATTAAA
Found at i:52960 original size:37 final size:37
Alignment explanation
Indices: 52919--52997 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 37
52909 CTAATTAAAG
*
52919 ATATATT-AAA-TATTTTTATTTCATAAA-CTAATAAAT
1 ATATATTGAAAGTATTTAT-TTTCATAAATCTAA-AAAT
*
52955 AATATATTGAAAGTATTTATTTTGATAAATCTAAAAAT
1 -ATATATTGAAAGTATTTATTTTCATAAATCTAAAAAT
52993 ATATA
1 ATATA
52998 CAAAAATTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 12 0.32
38 15 0.41
39 10 0.27
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (37 bp):
ATATATTGAAAGTATTTATTTTCATAAATCTAAAAAT
Found at i:52993 original size:38 final size:36
Alignment explanation
Indices: 52909--52997 Score: 92
Period size: 37 Copynumber: 2.4 Consensus size: 36
52899 AGATTTTAAT
* *
52909 CTAATTAAAGATATATTAAATATTTTTATTTCATAAA
1 CTAA-TAAATATATATTAAATATTTATATTTCATAAA
*
52946 CTAATAAATAATATATTGAAAGTATTTAT-TTTGATAAA
1 CTAATAAAT-ATATATT-AAA-TATTTATATTTCATAAA
52984 TCTAA-AAATATATA
1 -CTAATAAATATATA
52998 CAAAAATTCA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
36 4 0.09
37 16 0.36
38 15 0.33
39 10 0.22
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.43
Consensus pattern (36 bp):
CTAATAAATATATATTAAATATTTATATTTCATAAA
Found at i:53250 original size:24 final size:24
Alignment explanation
Indices: 53213--53261 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
53203 ATCAAAATCA
*
53213 TATTTGATTTTTATATCAAT-TTT
1 TATTTAATTTTTATATCAATGTTT
*
53236 TATTTAATTTATTATATTAATGTTT
1 TATTTAATTT-TTATATCAATGTTT
53261 T
1 T
53262 CACTCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 9 0.41
24 9 0.41
25 4 0.18
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (24 bp):
TATTTAATTTTTATATCAATGTTT
Found at i:54812 original size:7 final size:7
Alignment explanation
Indices: 54800--54826 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
54790 TTGTAGTGGT
54800 TGTCCAA
1 TGTCCAA
54807 TGTCCAA
1 TGTCCAA
54814 TGTCCAA
1 TGTCCAA
54821 TGTCCA
1 TGTCCA
54827 TGCCTTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (7 bp):
TGTCCAA
Found at i:61474 original size:2 final size:2
Alignment explanation
Indices: 61467--61501 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
61457 TAAGGGAGGT
61467 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
61502 TGTGTGTGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:64055 original size:27 final size:28
Alignment explanation
Indices: 64010--64066 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 28
64000 TTATTTGGTT
64010 GAAATTAAAAAAAAAAAGAAATCATTGA
1 GAAATTAAAAAAAAAAAGAAATCATTGA
64038 GAAATT-AAAAAAAAAAGAAATCATTGA
1 GAAATTAAAAAAAAAAAGAAATCATTGA
64065 GA
1 GA
64067 CTTCTCACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.18
Consensus pattern (28 bp):
GAAATTAAAAAAAAAAAGAAATCATTGA
Found at i:80919 original size:204 final size:198
Alignment explanation
Indices: 80342--80925 Score: 777
Period size: 198 Copynumber: 2.9 Consensus size: 198
80332 ACCGCGAGTC
* * * *
80342 AGTCTAGTTTCT-TTTAGAACAAATAGAGATTGATTTCAATTTTTATTTTAAAATATATGAATTT
1 AGTCTAGTTT-TGTTTAGAACAAATGGAGAATGATTT-TATTTTTATTTTAAAAGATATGAATTT
* * * *
80406 TTGAGTGTTTAAAGGTTGTAAAAATCTAGCAGCA-AAATTCTTATAAAACAGATTTAACAGT-AA
64 TTGAATGTTGAAAGGTTATAAAAATCTAGCAGCATAAATTCTTATAAAACAGATTTAGCAGTGAA
** *
80469 CTTTGAAAAATCACCAAAAATTGAACAAGATAAAATAGGAAATGAGCCTTATATTCCTATAAATT
129 -TTTGAAAAATCACCAAAAATTTCACAAGATAAAATAGGAAATGAGCCTTATATCCCTATAAATT
80534 TACAGA
193 TACAGA
* * *
80540 AGTCTAGTTTTGTTTAAAAAAAACGGA-AATTGATTTCTATTTTTATTTTAAAAGATATGAATTT
1 AGTCTAGTTTTGTTTAGAACAAATGGAGAA-TGATTT-TATTTTTATTTTAAAAGATATGAATTT
* *
80604 TTGAATGTTGAAAGATTATAAAAATCTAGCAG--TAGAATTCTTATAAAATAGATTTAGCAGTGA
64 TTGAATGTTGAAAGGTTATAAAAATCTAGCAGCATA-AATTCTTATAAAACAGATTTAGCAGTGA
* * *
80667 CTTTGAAAAATCACCAAAATTTTCACAAGATATAATAGGAAATGAGCCTTATATCCCTAT-AATT
128 ATTTGAAAAATCACCAAAAATTTCACAAGATAAAATAGGAAATGAGCCTTATATCCCTATAAATT
*
80731 GTACATA
193 -TACAGA
* * *
80738 AGTTTAGTTTTGTTTAGAACAAATGGAGAATGATTTTGATTTTGATTTTAAAAGATATAAATTTT
1 AGTCTAGTTTTGTTTAGAACAAATGGAGAATGATTTT-ATTTTTATTTTAAAAGATATGAATTTT
*
80803 TGAATGTTGAAAGGTCATAAAAATCTAGCAGCAAAATTCAAATTCTTATAAAACAGATTTAGCAG
65 TGAATGTTGAAAGGTTATAAAAATCTAGCAGC---A-T-AAATTCTTATAAAACAGATTTAGCAG
*
80868 TGAATTTGAAAAATCACCAAAAATTTCACAAGATAAAATAGGAAGTGAGCCTTATATC
125 TGAATTTGAAAAATCACCAAAAATTTCACAAGATAAAATAGGAAATGAGCCTTATATC
80926 TTTATAATCA
Statistics
Matches: 338, Mismatches: 33, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
197 8 0.02
198 247 0.73
199 3 0.01
204 79 0.23
205 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.35
Consensus pattern (198 bp):
AGTCTAGTTTTGTTTAGAACAAATGGAGAATGATTTTATTTTTATTTTAAAAGATATGAATTTTT
GAATGTTGAAAGGTTATAAAAATCTAGCAGCATAAATTCTTATAAAACAGATTTAGCAGTGAATT
TGAAAAATCACCAAAAATTTCACAAGATAAAATAGGAAATGAGCCTTATATCCCTATAAATTTAC
AGA
Found at i:81279 original size:56 final size:56
Alignment explanation
Indices: 81183--81313 Score: 183
Period size: 56 Copynumber: 2.3 Consensus size: 56
81173 CTAACCTAAT
* * * * *
81183 TAGCAGTCATGAGTGACACTC-GAGATAACACTATGGACACCCGAGATTATTTTGAC
1 TAGCAGCCATGAGTGGCGCTCGGA-ATAACACTACGAACACCCGAGATTATTTTGAC
* *
81239 TAGCGGCCGTGAGTGGCGCTCGGAATAACACTACGAACACCCGAGATTATTTTGAC
1 TAGCAGCCATGAGTGGCGCTCGGAATAACACTACGAACACCCGAGATTATTTTGAC
81295 TAGCAGCCATGAGTGGCGC
1 TAGCAGCCATGAGTGGCGC
81314 GGGACTATCC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
56 63 0.97
57 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (56 bp):
TAGCAGCCATGAGTGGCGCTCGGAATAACACTACGAACACCCGAGATTATTTTGAC
Found at i:81542 original size:22 final size:22
Alignment explanation
Indices: 81514--81560 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
81504 TTAGTTGTGT
81514 ACCACTGAGCCTATAAAGCTCA
1 ACCACTGAGCCTATAAAGCTCA
81536 ACCACTGAGCCTATAAAGCTCA
1 ACCACTGAGCCTATAAAGCTCA
81558 ACC
1 ACC
81561 TTCGAATGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.34, G:0.13, T:0.17
Consensus pattern (22 bp):
ACCACTGAGCCTATAAAGCTCA
Found at i:86546 original size:20 final size:20
Alignment explanation
Indices: 86501--86551 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
86491 TCAAAAAAAA
86501 AATATAATAATAATTTAAATT
1 AATATAATAAT-ATTTAAATT
*
86522 -GTATAATAATA-TTAATATT
1 AATATAATAATATTTAA-ATT
86541 AATATAA-AATA
1 AATATAATAATA
86552 AAATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 4 0.15
19 8 0.31
20 14 0.54
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATATAATAATATTTAAATT
Found at i:90416 original size:2 final size:2
Alignment explanation
Indices: 90409--90438 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
90399 TGAGAAATTA
90409 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
90439 TAACCTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:90816 original size:20 final size:20
Alignment explanation
Indices: 90774--90816 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
90764 AATCAATTGA
* *
90774 AAAATAATTAATTTTTTTAT
1 AAAATAATAAATTTATTTAT
90794 AAAATAATAAATATTATTT-T
1 AAAATAATAAAT-TTATTTAT
90814 AAA
1 AAA
90817 GTTGTTTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AAAATAATAAATTTATTTAT
Found at i:92811 original size:3 final size:3
Alignment explanation
Indices: 92803--92830 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
92793 ATATAATTTA
92803 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
92831 TTAAGGGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:92970 original size:2 final size:2
Alignment explanation
Indices: 92963--92998 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
92953 TCGAATTCTA
92963 AT AT AT AT 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 AT AT AT AT
92999 TTGTTTATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93747 original size:22 final size:22
Alignment explanation
Indices: 93705--93764 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
93695 GATCTAAGGG
*
93705 AAAATAAAAG-AAACAGAATTA
1 AAAATAAAAGAAAATAGAATTA
93726 AAAATAAAAGAAAATAGAATTA
1 AAAATAAAAGAAAATAGAATTA
*
93748 AAAGA-AATAGAAAATAG
1 AAA-ATAAAAGAAAATAG
93765 GAAAGTAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
21 10 0.29
22 24 0.69
23 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.15
Consensus pattern (22 bp):
AAAATAAAAGAAAATAGAATTA
Found at i:93755 original size:15 final size:16
Alignment explanation
Indices: 93730--93759 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
93720 GAATTAAAAA
93730 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
93746 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
93760 AATAGGAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:94546 original size:14 final size:14
Alignment explanation
Indices: 94529--94558 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
94519 TTTAAACTCT
*
94529 AAAAGATAAATATA
1 AAAAGATAAACATA
94543 AAAAGATAAACATA
1 AAAAGATAAACATA
94557 AA
1 AA
94559 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:94582 original size:19 final size:19
Alignment explanation
Indices: 94560--94602 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
94550 AAACATAAAT
94560 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
94579 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
94598 TAAAT
1 TAAAT
94603 CCTAATATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:95108 original size:16 final size:16
Alignment explanation
Indices: 95087--95117 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
95077 ATTAATACAT
*
95087 TTTATATTTGTCCAAG
1 TTTATATTAGTCCAAG
95103 TTTATATTAGTCCAA
1 TTTATATTAGTCCAA
95118 AATATGAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTATATTAGTCCAAG
Found at i:100381 original size:24 final size:24
Alignment explanation
Indices: 100340--100387 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
100330 ATTACAAGCA
*
100340 AAAAAAAAAATTAGTATTAAAAAT
1 AAAAAAAAAATCAGTATTAAAAAT
* * *
100364 AAAAATAAAATCATTATTATAAAT
1 AAAAAAAAAATCAGTATTAAAAAT
100388 TCGGGCCGGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (24 bp):
AAAAAAAAAATCAGTATTAAAAAT
Found at i:100731 original size:14 final size:15
Alignment explanation
Indices: 100712--100741 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
100702 TAATTTAAAA
100712 TTTTAA-TATAATTT
1 TTTTAATTATAATTT
100726 TTTTAATTATAATTT
1 TTTTAATTATAATTT
100741 T
1 T
100742 ACTAATCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATTATAATTT
Found at i:110772 original size:23 final size:23
Alignment explanation
Indices: 110746--110845 Score: 164
Period size: 23 Copynumber: 4.3 Consensus size: 23
110736 ACACTAGCGC
110746 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
110769 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
*
110792 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
* * *
110815 ACTCTCAGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTGTGTGT
110838 GCTCTCTG
1 GCTCTCTG
110846 TTGCCCAGCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.13, C:0.23, G:0.24, T:0.40
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTGTGTGT
Found at i:112012 original size:42 final size:44
Alignment explanation
Indices: 111966--112048 Score: 152
Period size: 42 Copynumber: 1.9 Consensus size: 44
111956 CAACAGAAGC
111966 TGAAGAATGGCTAGAAAATAATC-AA-AGTGTTTGAAGAGTAGT
1 TGAAGAATGGCTAGAAAATAATCAAAGAGTGTTTGAAGAGTAGT
112008 TGAAGAATGGCTAGAAAATAATCAAAGAGTGTTTGAAGAGT
1 TGAAGAATGGCTAGAAAATAATCAAAGAGTGTTTGAAGAGT
112049 TACAATGTAC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 23 0.59
43 2 0.05
44 14 0.36
ACGTcount: A:0.43, C:0.05, G:0.27, T:0.25
Consensus pattern (44 bp):
TGAAGAATGGCTAGAAAATAATCAAAGAGTGTTTGAAGAGTAGT
Done.