Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009271.1 Kokia drynarioides strain JFW-HI SEQ_123976, 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: 79748
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:3004 original size:15 final size:15
Alignment explanation
Indices: 2969--3011 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2959 AGAGGAACAA
*
2969 AGAGAAAAGAA-AGC
1 AGAGAAAAGAAGAAC
2983 AGAAGAAAAGAAGAAC
1 AG-AGAAAAGAAGAAC
*
2999 AGAGAAACGAAGA
1 AGAGAAAAGAAGA
3012 TGGGAATAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 2 0.08
15 19 0.76
16 4 0.16
ACGTcount: A:0.65, C:0.07, G:0.28, T:0.00
Consensus pattern (15 bp):
AGAGAAAAGAAGAAC
Found at i:19180 original size:2 final size:2
Alignment explanation
Indices: 19173--19199 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19163 CTTTATCACG
19173 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 A
19200 CACATCTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22797 original size:22 final size:22
Alignment explanation
Indices: 22772--22814 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
22762 TTCCACTGTT
22772 TTGCTA-TCATTTTACTATTATG
1 TTGCTACT-ATTTTACTATTATG
*
22794 TTGCTACTATTTTATTATTAT
1 TTGCTACTATTTTACTATTAT
22815 TATTTGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.23, C:0.12, G:0.07, T:0.58
Consensus pattern (22 bp):
TTGCTACTATTTTACTATTATG
Found at i:23337 original size:24 final size:20
Alignment explanation
Indices: 23298--23364 Score: 64
Period size: 23 Copynumber: 3.1 Consensus size: 20
23288 AATAACATTT
*
23298 AAACAACCAAAATAACAATCA
1 AAACAACCAAAATAAC-AGCA
23319 AAACAACAGCAAAAGTAACAGCA
1 AAACAAC--CAAAA-TAACAGCA
*
23342 AAACAACCACAAA-AACAACA
1 AAACAACCA-AAATAACAGCA
23362 AAA
1 AAA
23365 ATAGCAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 9 0.22
21 9 0.22
22 3 0.08
23 15 0.38
24 4 0.10
ACGTcount: A:0.67, C:0.24, G:0.04, T:0.04
Consensus pattern (20 bp):
AAACAACCAAAATAACAGCA
Found at i:23361 original size:23 final size:22
Alignment explanation
Indices: 23298--23388 Score: 64
Period size: 21 Copynumber: 4.1 Consensus size: 22
23288 AATAACATTT
*
23298 AAACAACCA-AAATAACAA-TCA
1 AAACAACCACAAA-AACAACACA
**
23319 AAACAA-CAGCAAAAGTAACAGCA
1 AAACAACCA-CAAAAACAACA-CA
23342 AAACAACCACAAAAACAACA-A
1 AAACAACCACAAAAACAACACA
* * *
23363 AAATAGCAACAAAAACAACAACA
1 AAACAACCACAAAAACAAC-ACA
23386 AAA
1 AAA
23389 ATAATAGCAA
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
20 2 0.04
21 26 0.47
22 4 0.07
23 21 0.38
24 2 0.04
ACGTcount: A:0.68, C:0.23, G:0.04, T:0.04
Consensus pattern (22 bp):
AAACAACCACAAAAACAACACA
Found at i:23372 original size:24 final size:24
Alignment explanation
Indices: 23355--23448 Score: 98
Period size: 24 Copynumber: 3.9 Consensus size: 24
23345 CAACCACAAA
23355 AACAACAAAAATAGCAACAAAAAC
1 AACAACAAAAATAGCAACAAAAAC
** * *
23379 AACAACAAAAATAATAGCAAAAAT
1 AACAACAAAAATAGCAACAAAAAC
* * *
23403 AACAATAAAAATAGCAATAAAAAT
1 AACAACAAAAATAGCAACAAAAAC
* * *
23427 AACAGCAAAAACAGCACCAAAA
1 AACAACAAAAATAGCAACAAAA
23449 CAGTAAAAAG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.09
Consensus pattern (24 bp):
AACAACAAAAATAGCAACAAAAAC
Found at i:23380 original size:27 final size:27
Alignment explanation
Indices: 23350--23407 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
23340 CAAAACAACC
23350 ACAAAAACAACAAA-AATAGCAACAAA-A
1 ACAAAAACAA-AAATAATAGCAA-AAATA
*
23377 ACAACAACAAAAATAATAGCAAAAATA
1 ACAAAAACAAAAATAATAGCAAAAATA
23404 ACAA
1 ACAA
23408 TAAAAATAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.72, C:0.17, G:0.03, T:0.07
Consensus pattern (27 bp):
ACAAAAACAAAAATAATAGCAAAAATA
Found at i:23400 original size:36 final size:36
Alignment explanation
Indices: 23379--23448 Score: 68
Period size: 36 Copynumber: 1.9 Consensus size: 36
23369 CAACAAAAAC
* * * *
23379 AACAACAAAAATAATAGCAAAAATAACAATAAAAAT
1 AACAACAAAAATAACAGCAAAAATAGCAACAAAAAC
* * * *
23415 AGCAATAAAAATAACAGCAAAAACAGCACCAAAA
1 AACAACAAAAATAACAGCAAAAATAGCAACAAAA
23449 CAGTAAAAAG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.69, C:0.16, G:0.06, T:0.10
Consensus pattern (36 bp):
AACAACAAAAATAACAGCAAAAATAGCAACAAAAAC
Found at i:23437 original size:12 final size:12
Alignment explanation
Indices: 23299--23437 Score: 99
Period size: 12 Copynumber: 11.9 Consensus size: 12
23289 ATAACATTTA
*
23299 AACAACCAAAAT
1 AACAACAAAAAT
*
23311 AACAATC-AAAAC
1 AACAA-CAAAAAT
* *
23323 AACAGCAAAAGT
1 AACAACAAAAAT
* *
23335 AACAGC-AAAAC
1 AACAACAAAAAT
*
23346 AAC--CACAAA-
1 AACAACAAAAAT
23355 AACAACAAAAAT
1 AACAACAAAAAT
* *
23367 AGCAACAAAAAC
1 AACAACAAAAAT
23379 AACAACAAAAAT
1 AACAACAAAAAT
* *
23391 AATAGCAAAAAT
1 AACAACAAAAAT
*
23403 AACAATAAAAAT
1 AACAACAAAAAT
* *
23415 AGCAATAAAAAT
1 AACAACAAAAAT
*
23427 AACAGCAAAAA
1 AACAACAAAAA
23438 CAGCACCAAA
Statistics
Matches: 100, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 12 0.12
12 80 0.80
13 1 0.01
ACGTcount: A:0.68, C:0.19, G:0.05, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:23498 original size:21 final size:20
Alignment explanation
Indices: 23467--23548 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
23457 AGAAAGCACC
*
23467 AAAAAAGCATCAAAACAGTA
1 AAAAAAACATCAAAACAGTA
* *
23487 AAAAATAACATCAAAATAGCAA
1 AAAAA-AACATCAAAACAG-TA
*
23509 AAAAAAAGTAGTCAAAACAGTA
1 AAAAAAA-CA-TCAAAACAGTA
* *
23531 AAAAAATCACCAAAACAG
1 AAAAAAACATCAAAACAG
23549 CAATATAATT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
20 13 0.27
21 14 0.29
22 14 0.29
23 8 0.16
ACGTcount: A:0.66, C:0.15, G:0.09, T:0.11
Consensus pattern (20 bp):
AAAAAAACATCAAAACAGTA
Found at i:23534 original size:43 final size:43
Alignment explanation
Indices: 23467--23551 Score: 111
Period size: 43 Copynumber: 2.0 Consensus size: 43
23457 AGAAAGCACC
* *
23467 AAAAAAGCATCAAAACAGTAAAAAATAA-CATCAAAATAGCAAA
1 AAAAAAGCATCAAAACAGTAAAAAA-AATCACCAAAACAGCAAA
*
23510 AAAAAAGTAGTCAAAACAGT-AAAAAAATCACCAAAACAGCAA
1 AAAAAAGCA-TCAAAACAGTAAAAAAAATCACCAAAACAGCAA
23552 TATAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
42 2 0.05
43 25 0.68
44 10 0.27
ACGTcount: A:0.66, C:0.15, G:0.08, T:0.11
Consensus pattern (43 bp):
AAAAAAGCATCAAAACAGTAAAAAAAATCACCAAAACAGCAAA
Found at i:32111 original size:33 final size:33
Alignment explanation
Indices: 32045--32111 Score: 77
Period size: 33 Copynumber: 2.0 Consensus size: 33
32035 TATCTAAGTA
*
32045 TAAAAACTTTTTTAGATGTATTTTCAATTTGTT
1 TAAAAACTTTTTTAGATGTATTTTCAATGTGTT
32078 TAAAAACATTTATTATA-ATGT-TTTT-AATGTGTT
1 TAAAAAC-TTT-TT-TAGATGTATTTTCAATGTGTT
32111 T
1 T
32112 GATGTATTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
33 15 0.50
34 7 0.23
35 6 0.20
36 2 0.07
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (33 bp):
TAAAAACTTTTTTAGATGTATTTTCAATGTGTT
Found at i:32949 original size:3 final size:3
Alignment explanation
Indices: 32941--32970 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
32931 GGAAGAACAA
32941 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
32971 AAAACTGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TAG
Found at i:33835 original size:27 final size:27
Alignment explanation
Indices: 33780--33835 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
33770 TATAATATTA
* **
33780 AATTTAGTTTTTAATTTTTTTTTTGTT
1 AATTTAGTTTTTAATTATTTTTTAATT
33807 AATTTAGTTTTTTAA-TATTTTTTAATT
1 AATTTAG-TTTTTAATTATTTTTTAATT
33834 AA
1 AA
33836 ATTTGACTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (27 bp):
AATTTAGTTTTTAATTATTTTTTAATT
Found at i:33838 original size:28 final size:26
Alignment explanation
Indices: 33776--33839 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 26
33766 TTGGTATAAT
*
33776 ATTAAATTTAGTTTTTAATTTTTTTT
1 ATTAAATTTAGTTTTTAATTTTTTTA
* *
33802 TTGTTAATTTAGTTTTTTAATATTTTTTA
1 AT-TAAATTTAG-TTTTTAAT-TTTTTTA
33831 ATTAAATTT
1 ATTAAATTT
33840 GACTATCAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
26 1 0.03
27 8 0.27
28 14 0.47
29 7 0.23
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (26 bp):
ATTAAATTTAGTTTTTAATTTTTTTA
Found at i:34539 original size:20 final size:20
Alignment explanation
Indices: 34514--34553 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
34504 TTGTATTTTT
*
34514 TGACC-AATGATTTTGGACAG
1 TGACCAAAT-ATTTTAGACAG
34534 TGACCAAATATTTTAGACAG
1 TGACCAAATATTTTAGACAG
34554 ACACGGCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (20 bp):
TGACCAAATATTTTAGACAG
Found at i:40282 original size:12 final size:12
Alignment explanation
Indices: 40261--40293 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
40251 ATTAATTGAA
40261 TAATATTTAATAT
1 TAATATTTAAT-T
40274 TAA-ATTTAATT
1 TAATATTTAATT
40285 TAATATTTA
1 TAATATTTA
40294 TCTTGATGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.21
12 12 0.63
13 3 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATATTTAATT
Found at i:41710 original size:21 final size:20
Alignment explanation
Indices: 41668--41712 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
41658 ATGAAATTTA
* * *
41668 CTCTCCTTTTTTGCTTCTCT
1 CTCTCCCTTTTAGATTCTCT
41688 CTCTCCCTTTTAGATTCTC-
1 CTCTCCCTTTTAGATTCTCT
41707 CTCTCC
1 CTCTCC
41713 TCAAACCCTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.04, C:0.40, G:0.04, T:0.51
Consensus pattern (20 bp):
CTCTCCCTTTTAGATTCTCT
Found at i:41941 original size:6 final size:6
Alignment explanation
Indices: 41930--41957 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41920 GATGCTACTT
41930 CTTCAG CTTCAG CTTCAG CTTCAG CTTC
1 CTTCAG CTTCAG CTTCAG CTTCAG CTTC
41958 TCCGGAAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (6 bp):
CTTCAG
Found at i:49545 original size:20 final size:20
Alignment explanation
Indices: 49522--49572 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
49512 AAATATTAAA
49522 AAAATATTTTTTA-TATATTT
1 AAAATATTTTTTAGTA-ATTT
*
49542 AAAATA-ATTTTAGTAATTT
1 AAAATATTTTTTAGTAATTT
*
49561 ATAAT-TTTTTTA
1 AAAATATTTTTTA
49573 AGATAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
AAAATATTTTTTAGTAATTT
Found at i:52268 original size:114 final size:114
Alignment explanation
Indices: 52135--52363 Score: 440
Period size: 114 Copynumber: 2.0 Consensus size: 114
52125 TTAAATAATA
*
52135 TTCAAATTAGTAGTATATTTTAATAATTAAAAGAGTATATATATTTTTTATATTAAAATAGAAAG
1 TTCAAATTAGTAGTATATTTTAATAATTAAAAGAGTATATATAGTTTTTATATTAAAATAGAAAG
52200 TATATATAAAGGTAAGAAATCCAGAAGATTTGACTTCAGAAGCAGAACG
66 TATATATAAAGGTAAGAAATCCAGAAGATTTGACTTCAGAAGCAGAACG
*
52249 TTCAAATTAGTAGTATATTTTAATAATTAAAAGAGTCTATATAGTTTTTATATTAAAATAGAAAG
1 TTCAAATTAGTAGTATATTTTAATAATTAAAAGAGTATATATAGTTTTTATATTAAAATAGAAAG
52314 TATATATAAAGGTAAGAAATCCAGAAGATTTGACTTCAGAAGCAGAACG
66 TATATATAAAGGTAAGAAATCCAGAAGATTTGACTTCAGAAGCAGAACG
52363 T
1 T
52364 CATCAAATGA
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 113 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCAAATTAGTAGTATATTTTAATAATTAAAAGAGTATATATAGTTTTTATATTAAAATAGAAAG
TATATATAAAGGTAAGAAATCCAGAAGATTTGACTTCAGAAGCAGAACG
Found at i:59119 original size:28 final size:28
Alignment explanation
Indices: 59065--59117 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
59055 ACCTTAAATA
59065 TAAATGGAGTGCAGCGTTTAGCTTTTTG
1 TAAATGGAGTGCAGCGTTTAGCTTTTTG
59093 TAAATGGAGTGCA-C-TTTAGCTTTTT
1 TAAATGGAGTGCAGCGTTTAGCTTTTT
59118 TTTTTTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 11 0.44
27 1 0.04
28 13 0.52
ACGTcount: A:0.23, C:0.11, G:0.25, T:0.42
Consensus pattern (28 bp):
TAAATGGAGTGCAGCGTTTAGCTTTTTG
Found at i:59395 original size:20 final size:19
Alignment explanation
Indices: 59361--59403 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
59351 CAATATTTGG
*
59361 ATTTGAAATTTATTTTAAA
1 ATTTAAAATTTATTTTAAA
*
59380 ATTTAAAATCTTATTTTATA
1 ATTTAAAAT-TTATTTTAAA
59400 ATTT
1 ATTT
59404 GACTCCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTAAAATTTATTTTAAA
Found at i:62964 original size:23 final size:23
Alignment explanation
Indices: 62931--62983 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
62921 ACTTCAAGGG
*
62931 TTGACACCTATCATTTTCTTATA
1 TTGACACCTATCATTCTCTTATA
*
62954 TTGACATCTATCATTCTCTTATA
1 TTGACACCTATCATTCTCTTATA
62977 TTGACAC
1 TTGACAC
62984 TTGTTAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (23 bp):
TTGACACCTATCATTCTCTTATA
Found at i:73046 original size:34 final size:34
Alignment explanation
Indices: 73008--73072 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
72998 TTTTAGATTT
*
73008 TAAATTTTAA-TTCATTTTAAGTTTAAATTTAACG
1 TAAA-TTTAAGTTCATTTGAAGTTTAAATTTAACG
*
73042 TAAATTTAAGTTTATTTGAAGTTTAAATTTA
1 TAAATTTAAGTTCATTTGAAGTTTAAATTTA
73073 TTTTGAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.18
34 23 0.82
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (34 bp):
TAAATTTAAGTTCATTTGAAGTTTAAATTTAACG
Found at i:73247 original size:7 final size:7
Alignment explanation
Indices: 73212--73236 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
73202 TTCAAAACCC
73212 AATTTTA
1 AATTTTA
73219 AATTTTA
1 AATTTTA
73226 AATTTTA
1 AATTTTA
73233 AATT
1 AATT
73237 ATTTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:73259 original size:17 final size:17
Alignment explanation
Indices: 73239--73295 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
73229 TTTAAATTAT
73239 TTTAAATTTACTTTGAG-
1 TTTAAATTTA-TTTGAGA
*
73256 TTTAAATTTATTTTAGA
1 TTTAAATTTATTTGAGA
73273 TTTAAATTTATTTTG-GA
1 TTTAAATTTA-TTTGAGA
73290 TTTAAA
1 TTTAAA
73296 ATTAAAAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 5 0.14
17 28 0.78
18 3 0.08
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTGAGA
Found at i:73414 original size:16 final size:17
Alignment explanation
Indices: 73381--73421 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
73371 TTTCAATTTC
73381 ACCC-ATTACAACCCAA
1 ACCCAATTACAACCCAA
*
73397 ACCCAATTAC-ACCTAA
1 ACCCAATTACAACCCAA
*
73413 ACCTAATTA
1 ACCCAATTA
73422 TCCAACATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.44, C:0.37, G:0.00, T:0.20
Consensus pattern (17 bp):
ACCCAATTACAACCCAA
Found at i:78456 original size:39 final size:39
Alignment explanation
Indices: 78400--78479 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
78390 CCAAGAGTAA
*
78400 TAGGAATCCTTTTATAAAGGGCACATGACCACAATCTTT
1 TAGGAATCCTTTCATAAAGGGCACATGACCACAATCTTT
*
78439 TAGGAATCCTTTCATAAAGGGCACATGACCACTATCTTT
1 TAGGAATCCTTTCATAAAGGGCACATGACCACAATCTTT
78478 TA
1 TA
78480 TTTCAATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (39 bp):
TAGGAATCCTTTCATAAAGGGCACATGACCACAATCTTT
Done.