Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004870.1 Kokia drynarioides strain JFW-HI SEQ_118540, 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: 119711
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Warning! 26 characters in sequence are not A, C, G, or T
Found at i:5701 original size:17 final size:17
Alignment explanation
Indices: 5679--5711 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5669 CCAACCACAT
5679 AAAGAACCAAAATCAAA
1 AAAGAACCAAAATCAAA
5696 AAAGAACCAAAATCAA
1 AAAGAACCAAAATCAA
5712 TCACAACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.18, G:0.06, T:0.06
Consensus pattern (17 bp):
AAAGAACCAAAATCAAA
Found at i:9437 original size:16 final size:14
Alignment explanation
Indices: 9405--9449 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
9395 TTTGGATAAT
9405 TTAT-AATTTT-T-
1 TTATAAATTTTATA
9416 TTATAAATGTTATATA
1 TTATAAAT-TT-TATA
9432 TTATAAATTTTATA
1 TTATAAATTTTATA
9446 TTAT
1 TTAT
9450 CTTTTACTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 4 0.14
12 3 0.10
13 2 0.07
14 9 0.31
15 3 0.10
16 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (14 bp):
TTATAAATTTTATA
Found at i:29517 original size:23 final size:23
Alignment explanation
Indices: 29474--29518 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
29464 AGAAGAGAGT
* **
29474 TTTTATAAAATTTAATTTCTTTG
1 TTTTATAAAAATTAAACTCTTTG
29497 TTTTATAAAAATTAAACTCTTT
1 TTTTATAAAAATTAAACTCTTT
29519 TATGAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTTATAAAAATTAAACTCTTTG
Found at i:40548 original size:6 final size:6
Alignment explanation
Indices: 40537--40563 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40527 TGCGTAGTCA
40537 TGATTT TGATTT TGATTT TGATTT TGA
1 TGATTT TGATTT TGATTT TGATTT TGA
40564 GAATAGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.63
Consensus pattern (6 bp):
TGATTT
Found at i:44108 original size:17 final size:18
Alignment explanation
Indices: 44082--44116 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
44072 TAATTCAACA
*
44082 TTCTCTATTTTAT-TTTT
1 TTCTCCATTTTATATTTT
44099 TTCTCCATTTTATATTTT
1 TTCTCCATTTTATATTTT
44117 ATTACTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (18 bp):
TTCTCCATTTTATATTTT
Found at i:44663 original size:15 final size:17
Alignment explanation
Indices: 44642--44682 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
44632 TTAATCCTTA
44642 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
44658 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
44674 AAAATTATA
1 AAAATTATA
44683 TTTTTACTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:45360 original size:5 final size:5
Alignment explanation
Indices: 45350--45378 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
45340 TAATTGCTTT
45350 TTTAA TTTAA TTTAA TTTAA TTT-A TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
45379 GTTTTGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTTAA
Found at i:49227 original size:16 final size:15
Alignment explanation
Indices: 49202--49231 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
49192 GTAATAAATA
49202 TAAATAAAAAATATT
1 TAAATAAAAAATATT
49217 TAAATTAAAAAATAT
1 TAAA-TAAAAAATAT
49232 ATTTTTTCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAATAAAAAATATT
Found at i:50367 original size:24 final size:23
Alignment explanation
Indices: 50324--50381 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
50314 TATATATTTT
50324 AATTAGAT-TTTAAAAATAATTAA
1 AATTA-ATATTTAAAAATAATTAA
* *
50347 TATTAATTATTTAAAATTAATTAA
1 AATTAA-TATTTAAAAATAATTAA
50371 AATTAATATTT
1 AATTAATATTT
50382 CATATATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 1 0.03
23 10 0.33
24 19 0.63
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTAATATTTAAAAATAATTAA
Found at i:52878 original size:3 final size:3
Alignment explanation
Indices: 52870--52903 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
52860 GCATTTCTCC
52870 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
52904 TTTTTTAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:55957 original size:30 final size:31
Alignment explanation
Indices: 55923--55984 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
55913 AATAATAATA
* *
55923 ATTT-AGTCATTAAATTATTCGAAAA-TTTTT
1 ATTTAAGTCACTAAACTATTC-AAAAGTTTTT
55953 ATTTAAGTCACTAAACTATTCAAAAGTTTTT
1 ATTTAAGTCACTAAACTATTCAAAAGTTTTT
55984 A
1 A
55985 AATTATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 8 0.29
31 20 0.71
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (31 bp):
ATTTAAGTCACTAAACTATTCAAAAGTTTTT
Found at i:56965 original size:21 final size:21
Alignment explanation
Indices: 56935--56974 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
56925 CAATCTATGG
56935 AATAGAAAAACAACCGATTGA
1 AATAGAAAAACAACCGATTGA
*
56956 AATAGGAAAACAACCGATT
1 AATAGAAAAACAACCGATT
56975 CAAGAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.15, G:0.15, T:0.15
Consensus pattern (21 bp):
AATAGAAAAACAACCGATTGA
Found at i:57013 original size:168 final size:169
Alignment explanation
Indices: 56811--57160 Score: 490
Period size: 168 Copynumber: 2.1 Consensus size: 169
56801 TTGGATTTTT
*
56811 TAAAATAATTAATAATTTAATCTAAGCTTTTTTAATGTAAAACTTTGACTTTCATCCTTCTGAAA
1 TAAAATAATT--TAATTTAATCTAAGCTTTTTTAATGTAAAACTTTGACTTTCATCCCTCTGAAA
* * * * *
56876 TTTTATTGAGATACCATTCG-GTTTCGAAATAATCAATTAAAAAAAGAAACAATCTA-TGGAAT-
64 TTTTATTGAGATACCA-TCGAGTATCAAAATAAGCAATTAAAAAAAGAAACAATCAATTGAAATA
*
56938 AGAAAAACAACCGATTGAAATAGGAAAACAACCGATTCAAGAG
128 AGAAAAA-AACCAATTGAAATAGGAAAACAACCGATTCAAGAG
* *
56981 TAAAATAATTTATTTTAATCTAAGCTTTTTTAATGTAAAACTTTGGCTTTCATCCCTCTGAAATT
1 TAAAATAATTTAATTTAATCTAAGCTTTTTTAATGTAAAACTTTGACTTTCATCCCTCTGAAATT
* * * ** *
57046 TTGTTGAGGTATCATCGAGTATCAAAATAAGCAATTAAAGTAAGAAACAATCAATTGAAATAAGG
66 TTATTGAGATACCATCGAGTATCAAAATAAGCAATTAAAAAAAGAAACAATCAATTGAAATAAGA
* *
57111 AAAAAATCAATTGAAATAGGAAAACAATCGATTCAAGAG
131 AAAAAACCAATTGAAATAGGAAAACAACCGATTCAAGAG
57150 TAAAATAATTT
1 TAAAATAATTT
57161 CTTCATCGAT
Statistics
Matches: 160, Mismatches: 17, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
167 3 0.02
168 93 0.58
169 48 0.30
170 16 0.10
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (169 bp):
TAAAATAATTTAATTTAATCTAAGCTTTTTTAATGTAAAACTTTGACTTTCATCCCTCTGAAATT
TTATTGAGATACCATCGAGTATCAAAATAAGCAATTAAAAAAAGAAACAATCAATTGAAATAAGA
AAAAAACCAATTGAAATAGGAAAACAACCGATTCAAGAG
Found at i:57118 original size:21 final size:21
Alignment explanation
Indices: 57077--57139 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
57067 TCAAAATAAG
*
57077 CAATT-AAAGTAA-GAAACAAT
1 CAATTGAAA-TAAGGAAAAAAT
57097 CAATTGAAATAAGGAAAAAAT
1 CAATTGAAATAAGGAAAAAAT
57118 CAATTGAAAT-AGGAAAACAAT
1 CAATTGAAATAAGGAAAA-AAT
57139 C
1 C
57140 GATTCAAGAG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
20 15 0.38
21 24 0.62
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.19
Consensus pattern (21 bp):
CAATTGAAATAAGGAAAAAAT
Found at i:58515 original size:20 final size:20
Alignment explanation
Indices: 58490--58543 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
58480 TCAGATATCA
*
58490 AAACAATCGATTAAAAGAAG
1 AAACAATCAATTAAAAGAAG
*
58510 AAACAATCAATTAAAATAAG
1 AAACAATCAATTAAAAGAAG
* *
58530 AAAAAAGCAATTAA
1 AAACAATCAATTAA
58544 CCAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (20 bp):
AAACAATCAATTAAAAGAAG
Found at i:59600 original size:18 final size:19
Alignment explanation
Indices: 59577--59613 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
59567 AAGTTTTGAA
59577 AGTTTTT-CAATTTAGTCT
1 AGTTTTTACAATTTAGTCT
59595 AGTTTTTACAATTTAGTCT
1 AGTTTTTACAATTTAGTCT
59614 CTATACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.24, C:0.11, G:0.11, T:0.54
Consensus pattern (19 bp):
AGTTTTTACAATTTAGTCT
Found at i:61441 original size:5 final size:5
Alignment explanation
Indices: 61431--61467 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
61421 CCAGTCGATT
61431 GCATG GCATG GCATG GCATG GCATG GCATG GCATG GC
1 GCATG GCATG GCATG GCATG GCATG GCATG GCATG GC
61468 CCCAAGTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.19
Consensus pattern (5 bp):
GCATG
Found at i:62870 original size:14 final size:15
Alignment explanation
Indices: 62845--62877 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
62835 TCACGTGCTC
62845 TTTTCTTTTTAAATA
1 TTTTCTTTTTAAATA
62860 TTTTC-TTTTAAATA
1 TTTTCTTTTTAAATA
62874 TTTT
1 TTTT
62878 ACTATATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCTTTTTAAATA
Found at i:73163 original size:1 final size:1
Alignment explanation
Indices: 73113--73143 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
73103 GAAGATAAGG
73113 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
73144 NNNNNNNNNN
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:73164 original size:1 final size:1
Alignment explanation
Indices: 73154--73182 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
73144 NNNNNNNNNN
73154 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
73183 GAATATGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:88425 original size:18 final size:19
Alignment explanation
Indices: 88397--88432 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
88387 TTAATTTCTA
*
88397 TGCTAATATTTTATTATAT
1 TGCTAATATTTTAGTATAT
88416 TGCT-ATATTTTAGTATA
1 TGCTAATATTTTAGTATA
88433 CTTGTTACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.31, C:0.06, G:0.08, T:0.56
Consensus pattern (19 bp):
TGCTAATATTTTAGTATAT
Found at i:89629 original size:43 final size:43
Alignment explanation
Indices: 89569--89683 Score: 106
Period size: 43 Copynumber: 2.6 Consensus size: 43
89559 AATAGCATCT
** * *
89569 AAACAACAAAAATAACAATTAAAACAGTAGCAAAAATAACAAC
1 AAACAACAAAAATAACAACAAAAACAGCAACAAAAATAACAAC
* * *
89612 AAACAACATTAAA-AACAACAAAAATAGCAACAAAAATAACAGAA
1 AAACAACA-AAAATAACAACAAAAACAGCAACAAAAATAACA-AC
* *
89656 AAAAAACACGAAAATAACAACCAAAACA
1 AAACAACA--AAAATAACAACAAAAACA
89684 ATAAAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
43 31 0.55
44 11 0.20
45 3 0.05
46 11 0.20
ACGTcount: A:0.70, C:0.17, G:0.04, T:0.09
Consensus pattern (43 bp):
AAACAACAAAAATAACAACAAAAACAGCAACAAAAATAACAAC
Found at i:89660 original size:34 final size:35
Alignment explanation
Indices: 89622--89737 Score: 96
Period size: 34 Copynumber: 3.3 Consensus size: 35
89612 AAACAACATT
89622 AAAAACAACAAAAATAGCAACAAA-AATAACAGAA
1 AAAAACAACAAAAATAGCAACAAACAATAACAGAA
* * *
89656 AAAAA-ACACGAAAATAACAACCAAAACAATAA-AAAA
1 AAAAACA-ACAAAAATAGCAA-C-AAACAATAACAGAA
* * * * *
89692 AAAAAGC-ACCAAAATAGTAAAAAACAAAAACAGCA
1 AAAAA-CAACAAAAATAGCAACAAACAATAACAGAA
89727 AAAAACAACAA
1 AAAAACAACAA
89738 CAAAAACAGT
Statistics
Matches: 63, Mismatches: 11, Indels: 15
0.71 0.12 0.17
Matches are distributed among these distances:
33 1 0.02
34 25 0.40
35 11 0.17
36 21 0.33
37 5 0.08
ACGTcount: A:0.73, C:0.16, G:0.05, T:0.05
Consensus pattern (35 bp):
AAAAACAACAAAAATAGCAACAAACAATAACAGAA
Found at i:89693 original size:24 final size:24
Alignment explanation
Indices: 89675--89729 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
89665 GAAAATAACA
89675 ACCAAAACAATAAAAAAAAAAAGC
1 ACCAAAACAATAAAAAAAAAAAGC
* *
89699 ACCAAAATAGTAAAAAACAAAAA-C
1 ACCAAAACAATAAAAAA-AAAAAGC
*
89723 AGCAAAA
1 ACCAAAA
89730 AACAACAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.73, C:0.16, G:0.05, T:0.05
Consensus pattern (24 bp):
ACCAAAACAATAAAAAAAAAAAGC
Found at i:92263 original size:19 final size:19
Alignment explanation
Indices: 92239--92282 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
92229 TTTAATTTGA
92239 ATATATA-AACTAT-ATAT-
1 ATATATATAA-TATGATATG
92256 ATATATATAATATGATATG
1 ATATATATAATATGATATG
92275 ATATATAT
1 ATATATAT
92283 TTGAAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.42
18 6 0.25
19 8 0.33
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (19 bp):
ATATATATAATATGATATG
Found at i:109338 original size:30 final size:31
Alignment explanation
Indices: 109277--109345 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
109267 AATAGAGGAT
* * * *
109277 TGTTTTGTCATTTTTTGATAATTTTAGTGAC
1 TGTTTTGTCATATTTTCATAAGTTAAGTGAC
109308 TGTTTTGTCATATTTTCA-AAGTTAAGTGAC
1 TGTTTTGTCATATTTTCATAAGTTAAGTGAC
109338 TGTTTTGT
1 TGTTTTGT
109346 TAAACGTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.53
31 16 0.47
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.55
Consensus pattern (31 bp):
TGTTTTGTCATATTTTCATAAGTTAAGTGAC
Found at i:113395 original size:21 final size:23
Alignment explanation
Indices: 113374--113419 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
113364 ATAATAATAT
113374 TTAAAAAAAG-TTATCATTTATTA
1 TTAAAAAAAGCTTATCATTTA-TA
* *
113397 TTCAGAAAAGCTTATCATTTATA
1 TTAAAAAAAGCTTATCATTTATA
113420 ATAGATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (23 bp):
TTAAAAAAAGCTTATCATTTATA
Found at i:113398 original size:24 final size:24
Alignment explanation
Indices: 113374--113418 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
113364 ATAATAATAT
113374 TTAAAAAAAG-TTATCATTTATTA
1 TTAAAAAAAGCTTATCATTTATTA
* *
113397 TTCAGAAAAGCTTATCATTTAT
1 TTAAAAAAAGCTTATCATTTAT
113419 AATAGATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (24 bp):
TTAAAAAAAGCTTATCATTTATTA
Found at i:113882 original size:13 final size:13
Alignment explanation
Indices: 113864--113897 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
113854 AACAAATATT
*
113864 ATTTAATTAATTA
1 ATTTAATTAACTA
113877 ATTTAATTAACTA
1 ATTTAATTAACTA
*
113890 AATTAATT
1 ATTTAATT
113898 TTCCAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTTAATTAACTA
Found at i:116208 original size:28 final size:27
Alignment explanation
Indices: 116143--116210 Score: 68
Period size: 28 Copynumber: 2.5 Consensus size: 27
116133 TAAAACCATG
*
116143 TTAAGATAATTATATAAAAATTTTAATA
1 TTAAAATAA-TATATAAAAATTTTAATA
* *
116171 -AAAAAAAATATAT-AAAATTATTAAATA
1 TTAAAATAATATATAAAAATT-TT-AATA
116198 TTAAAATAATATA
1 TTAAAATAATATA
116211 ATATAAATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 6 0.19
26 7 0.22
27 9 0.28
28 10 0.31
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
TTAAAATAATATATAAAAATTTTAATA
Found at i:117134 original size:3 final size:3
Alignment explanation
Indices: 117126--117150 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
117116 AATTTTAAGT
117126 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
117151 AGGAAACGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.