Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014175.1 Kokia drynarioides strain JFW-HI SEQ_129208, 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: 43503
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:6948 original size:21 final size:21
Alignment explanation
Indices: 6922--6962 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6912 GATAGTTATA
*
6922 ATCATCTGATCATAAATGAAT
1 ATCATCTAATCATAAATGAAT
6943 ATCATCTAATCATAAATGAA
1 ATCATCTAATCATAAATGAA
6963 GAGTATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (21 bp):
ATCATCTAATCATAAATGAAT
Found at i:11231 original size:46 final size:47
Alignment explanation
Indices: 11163--11264 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 47
11153 GTTCGTGCTC
* * *
11163 GTTCGTTTATCGTTCACAAACATGTTCGTTTAT-CGTTTGTGAATAT
1 GTTCGTTTAACGTTCACAAACATGTTCGTTTATACGTTCGTGAACAT
** *
11209 GTTCGTTTAACGTTCATGAACATGTTCGTTTATATGTTCGTGAACAT
1 GTTCGTTTAACGTTCACAAACATGTTCGTTTATACGTTCGTGAACAT
11256 GTTCGTTTA
1 GTTCGTTTA
11265 TATGTTCGTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
46 30 0.61
47 19 0.39
ACGTcount: A:0.22, C:0.15, G:0.19, T:0.45
Consensus pattern (47 bp):
GTTCGTTTAACGTTCACAAACATGTTCGTTTATACGTTCGTGAACAT
Found at i:11245 original size:12 final size:12
Alignment explanation
Indices: 11230--11276 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
11220 GTTCATGAAC
11230 ATGTTCGTTTAT
1 ATGTTCGTTTAT
** *
11242 ATGTTCGTGAAC
1 ATGTTCGTTTAT
11254 ATGTTCGTTTAT
1 ATGTTCGTTTAT
11266 ATGTTCGTTTA
1 ATGTTCGTTTA
11277 ACGTTTGCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (12 bp):
ATGTTCGTTTAT
Found at i:11252 original size:24 final size:24
Alignment explanation
Indices: 11163--11273 Score: 129
Period size: 23 Copynumber: 4.8 Consensus size: 24
11153 GTTCGTGCTC
***
11163 GTTCGTTTAT-CGTTCACAAACAT
1 GTTCGTTTATACGTTCGTGAACAT
* *
11186 GTTCGTTTAT-CGTTTGTGAATAT
1 GTTCGTTTATACGTTCGTGAACAT
*
11209 GTTCGTTTA-ACGTTCATGAACAT
1 GTTCGTTTATACGTTCGTGAACAT
*
11232 GTTCGTTTATATGTTCGTGAACAT
1 GTTCGTTTATACGTTCGTGAACAT
*
11256 GTTCGTTTATATGTTCGT
1 GTTCGTTTATACGTTCGT
11274 TTAACGTTTG
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
23 46 0.61
24 30 0.39
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (24 bp):
GTTCGTTTATACGTTCGTGAACAT
Found at i:11271 original size:59 final size:59
Alignment explanation
Indices: 11205--11324 Score: 186
Period size: 59 Copynumber: 2.0 Consensus size: 59
11195 TCGTTTGTGA
* * *
11205 ATATGTTCGTTTAACGTTCATGAACATGTTCGTTTATATGTTCGTGAACATGTTCGTTT
1 ATATGTTCGTTTAACGTTCACGAACATGTTCGTTTATATGTTCGCGAACATGTTCGATT
** *
11264 ATATGTTCGTTTAACGTTTGCGAACATGTTCGTTTATGTGTTCGCGAACATGTTCGATT
1 ATATGTTCGTTTAACGTTCACGAACATGTTCGTTTATATGTTCGCGAACATGTTCGATT
11323 AT
1 AT
11325 GTTAACTATC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.44
Consensus pattern (59 bp):
ATATGTTCGTTTAACGTTCACGAACATGTTCGTTTATATGTTCGCGAACATGTTCGATT
Found at i:11295 original size:35 final size:36
Alignment explanation
Indices: 11230--11307 Score: 113
Period size: 35 Copynumber: 2.2 Consensus size: 36
11220 GTTCATGAAC
* *
11230 ATGTTCGTTTATATGTTCGTGAACATGTTCGTTTAT
1 ATGTTCGTTTATACGTTCGCGAACATGTTCGTTTAT
*
11266 ATGTTCGTTTA-ACGTTTGCGAACATGTTCGTTTAT
1 ATGTTCGTTTATACGTTCGCGAACATGTTCGTTTAT
*
11301 GTGTTCG
1 ATGTTCG
11308 CGAACATGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
35 27 0.71
36 11 0.29
ACGTcount: A:0.18, C:0.13, G:0.22, T:0.47
Consensus pattern (36 bp):
ATGTTCGTTTATACGTTCGCGAACATGTTCGTTTAT
Found at i:11315 original size:24 final size:22
Alignment explanation
Indices: 11266--11327 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 22
11256 GTTCGTTTAT
*
11266 ATGTTCGTTTAACGTTTGCGAAC
1 ATGTTCGTTT-ATGTTTGCGAAC
11289 ATGTTCGTTTATGTGTTCGCGAAC
1 ATGTTCGTTTATGT-TT-GCGAAC
*
11313 ATGTTCGATTATGTT
1 ATGTTCGTTTATGTT
11328 AACTATCCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 3 0.09
23 13 0.37
24 19 0.54
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.44
Consensus pattern (22 bp):
ATGTTCGTTTATGTTTGCGAAC
Found at i:12597 original size:20 final size:17
Alignment explanation
Indices: 12572--12610 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
12562 ATCATGTATG
12572 AAATTAAATAACATAAATGA
1 AAATTAAA-AA-AT-AATGA
12592 AAATTAAAAAATAATGA
1 AAATTAAAAAATAATGA
12609 AA
1 AA
12611 TAAAACTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 2 0.11
19 2 0.11
20 8 0.42
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAATAATGA
Found at i:15679 original size:12 final size:12
Alignment explanation
Indices: 15656--15736 Score: 64
Period size: 11 Copynumber: 7.0 Consensus size: 12
15646 GATGGGTCTA
*
15656 ATAAATGAGCTT
1 ATAAACGAGCTT
*
15668 ATAAACGGGCTT
1 ATAAACGAGCTT
15680 -TAGAA-GAGCTT
1 ATA-AACGAGCTT
15691 ATAAACGAGCTCT
1 ATAAACGAGCT-T
*
15704 AT--ACGAGCTA
1 ATAAACGAGCTT
* *
15714 ATAAACGAAC-C
1 ATAAACGAGCTT
15725 ATAAACGAGCTT
1 ATAAACGAGCTT
15737 GTTCGTGAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
10 2 0.04
11 25 0.46
12 24 0.44
13 3 0.06
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:15692 original size:23 final size:23
Alignment explanation
Indices: 15662--15721 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
15652 TCTAATAAAT
* *
15662 GAGCTTATAAACGGGCTTTAGAA
1 GAGCTTATAAACGAGCTCTAGAA
* *
15685 GAGCTTATAAACGAGCTCTATAC
1 GAGCTTATAAACGAGCTCTAGAA
*
15708 GAGCTAATAAACGA
1 GAGCTTATAAACGA
15722 ACCATAAACG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (23 bp):
GAGCTTATAAACGAGCTCTAGAA
Found at i:17187 original size:17 final size:16
Alignment explanation
Indices: 17161--17194 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17151 TGAATTTATA
17161 ATTAATTTATTGGGTT
1 ATTAATTTATTGGGTT
*
17177 ATTAGATTTATTTGGTT
1 ATTA-ATTTATTGGGTT
17194 A
1 A
17195 ATATAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (16 bp):
ATTAATTTATTGGGTT
Found at i:17361 original size:18 final size:19
Alignment explanation
Indices: 17325--17362 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
17315 AAGTGATAAT
17325 GTCACCTAACTACATTAGTA
1 GTCACCTAACTA-ATTAGTA
17345 GTCACCTAACT-ATTAGTA
1 GTCACCTAACTAATTAGTA
17363 AATTTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (19 bp):
GTCACCTAACTAATTAGTA
Found at i:18470 original size:101 final size:99
Alignment explanation
Indices: 18311--19400 Score: 776
Period size: 101 Copynumber: 10.8 Consensus size: 99
18301 TTTGACGATT
* * * * *
18311 ATATAAACCTTCCATCATAATTTGAGGAAGATAAGTGAACTATACACGATCTACACGTGACTTTT
1 ATATAAGCCTCCCATCATAA-TTGAGGGAGACAAGTGAACTATACAAGATCTACACGTGACTTTT
18376 ACATGCTACACACTTGTCCCATGAGATTTGAGGGGC
65 ACATGCTACACACTTGTCCCATGAGATTTGA-GGGC
* * * * *
18412 ATATAAGCCTCCAATTATAATTGGGGGAGACAAGTGGACTATACAAGATCTACAACGTGACTATT
1 ATATAAGCCTCCCATCATAATTGAGGGAGACAAGTGAACTATACAAGATCTAC-ACGTGACTTTT
* * * **
18477 AAATGCCACACACTTGTCCTATGAGATTTGATGGTT
65 ACATGCTACACACTTGTCCCATGAGATTTGA-GGGC
* * * * * * *
18513 ATATAAGCCTTCCATCATAGCTTGAGGGAGACAAATGAATTATACATGA-CTTACACGTGGCCTT
1 ATATAAGCCTCCCATCATA-ATTGAGGGAGACAAGTGAACTATACAAGATC-TACACGTGACTTT
* * ** * *
18577 TACATGCT-CTGCACTTGTCCTACAAGACTTGATGGC
64 TACATGCTAC-ACACTTGTCCCATGAGATTTGAGGGC
* *
18613 TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACA-ATCTACATGTGATTT
1 -ATATAAGCCTCCCATCATAA-TTGAGGGAGACAAGTGAACTATACA-AGATCTACACGTGACTT
*
18677 TTACATGCTACACATTTGTCCCATGAGATTTGAGGGGC
63 TTACATGCTACACACTTGTCCCATGAGATTTGA-GGGC
* * * * *
18715 ATATAAGCCTCCTATCATAATTAGAGGGAGACAAGT-AGACAATACACGATATGCACGTGACTTT
1 ATATAAGCCTCCCATCATAATT-GAGGGAGACAAGTGA-ACTATACAAGATCTACACGTGACTTT
* * * * * * * * *
18779 TAAATCCCACACATTTATCCTACGAAATTTGATGGC
64 TACATGCTACACACTTGTCCCATGAGATTTGAGGGC
* * * * * *
18815 TATATAAGCCTCCCATCATACCTTGAGGGAGACAAATGAACTATACAAGA-CTTATATGTGGCCT
1 -ATATAAGCCTCCCATCATA-ATTGAGGGAGACAAGTGAACTATACAAGATC-TACACGTGACTT
* * ** * *
18879 TTACATGCT-CTAAACTTGTCCTACAAGACTTGATGGC
63 TTACATGCTAC-ACACTTGTCCCATGAGATTTGAGGGC
*
18916 TATATAAGCCTCCCATC---A-TGAGGGAGACAAGTGAACTATACACA-ATCTACACGTGACCTT
1 -ATATAAGCCTCCCATCATAATTGAGGGAGACAAGTGAACTATACA-AGATCTACACGTGACTTT
** *
18976 TACATGCTATGCACTTGTCCCATGAGATCTGAGGGGC
64 TACATGCTACACACTTGTCCCATGAGATTTGA-GGGC
* * *
19013 ATATAAGCCTCCCATCATAATTGGGGGGAGACAAGTGGACTAT-CTACA-ATATACACGTGACTT
1 ATATAAGCCTCCCATCATAATT-GAGGGAGACAAGTGAACTATAC-A-AGATCTACACGTGACTT
* * * **
19076 TTAAATGCCACACACTTGTCCTATGAGATTTGATGGTT
63 TTACATGCTACACACTTGTCCCATGAGATTTGA-GGGC
* * * * * * * *
19114 ATATAAACCTCTCGTCATAACTTAAGGGAAACAAGTGAACTATACATGA-CTTACACGTGGCCTT
1 ATATAAGCCTCCCATCATAA-TTGAGGGAGACAAGTGAACTATACAAGATC-TACACGTGACTTT
* * ** * *
19178 TACATGCTCCACACTTATCCCACAAAACTTT-ATGGC
64 TACATGCTACACACTTGTCCCATGAGA-TTTGAGGGC
* * * * *
19214 TATATAATCCTCCCATTATAACTTAAGGGAGACAAGGGAACTATACACA-ATCCACACGTGACCT
1 -ATATAAGCCTCCCATCATAA-TTGAGGGAGACAAGTGAACTATACA-AGATCTACACGTGA-CT
* * * * * *
19278 TCTACATGCTCCACACTTGCCCCACT-AAATTTGAAAGTC
62 TTTACATGCTACACACTTGTCCCA-TGAGATTTG-AGGGC
* *** * * * * * *
19317 ATATAAGACTTTTA-CTATAATTGAAGGGAGACAAGTGAACAACACACGATTTACATGTGACATT
1 ATATAAGCCTCCCATC-ATAATTG-AGGGAGACAAGTGAACTATACAAGATCTACACGTGACTTT
* * *
19381 TGCACGCCACACACTTGTCC
64 TACATGCTACACACTTGTCC
19401 TACGAAATTT
Statistics
Matches: 772, Mismatches: 174, Indels: 86
0.75 0.17 0.08
Matches are distributed among these distances:
96 73 0.09
97 5 0.01
99 1 0.00
100 40 0.05
101 543 0.70
102 107 0.14
103 3 0.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (99 bp):
ATATAAGCCTCCCATCATAATTGAGGGAGACAAGTGAACTATACAAGATCTACACGTGACTTTTA
CATGCTACACACTTGTCCCATGAGATTTGAGGGC
Found at i:18620 original size:202 final size:199
Alignment explanation
Indices: 18297--19275 Score: 871
Period size: 202 Copynumber: 4.9 Consensus size: 199
18287 TCTATATTAC
* * * * * *
18297 GAGATTTGACGATTATATAAACCTTCCATCATAATTTGAGGAAGATAAGTGAACTATACACGATC
1 GAGATTTGATGGTTATATAAGCC-TCCATCAT-ACTTGAGGGAGACAAGTGAACTATACACGATC
* * ** * * *
18362 TACACGTGACTTTTACATGCTACACACTTGTCCCATGAGATTTGAGGGGC-ATATAAGCCTCCAA
64 TACACGTGACCTTTACATGCTCCACACTTGTCCCACAAGACTTGA-TGGCTATATAAGCCTCCCA
* * *
18426 TTATAATTGGGGGAGACAAGTGGACTATACA-AGATCTACAACGTGACTATTAAATGCCACACAC
128 TCATAATTGAGGGAGACAAGTGGACTATACACA-ATCTAC-ACGTGACTTTTAAATGCCACACAC
18490 TTGTCCTAT
191 TTGTCCTAT
* * *
18499 GAGATTTGATGGTTATATAAGCCTTCCATCATAGCTTGAGGGAGACAAATGAATTATACATGA-C
1 GAGATTTGATGGTTATATAAGCC-TCCATCATA-CTTGAGGGAGACAAGTGAACTATACACGATC
* ** *
18563 TTACACGTGGCCTTTACATGCTCTGCACTTGTCCTACAAGACTTGATGGCTATATAAGCCTCCCA
64 -TACACGTGACCTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTATATAAGCCTCCCA
* * * * * *
18628 TCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACATGTGATTTTTACATGCTACACATT
128 TCATAA-TTGAGGGAGACAAGTGGACTATACACAATCTACACGTGACTTTTAAATGCCACACACT
*
18693 TGTCCCAT
192 TGTCCTAT
* ** * *
18701 GAGATTTGAGGGGCATATAAGCCTCCTATCATAATTAGAGGGAGACAAGT-AGACAATACACGAT
1 GAGATTTGATGGTTATATAAGCCTCC-ATCATACTT-GAGGGAGACAAGTGA-ACTATACACGAT
* * * * * * *
18765 ATGCACGTGACTTTTAAAT-C-CCACACATTTATCCTACGAA-ATTTGATGGCTATATAAGCCTC
63 CTACACGTGACCTTTACATGCTCCACAC--TTGTCCCAC-AAGACTTGATGGCTATATAAGCCTC
* * * * * * * *
18827 CCATCATACCTTGAGGGAGACAAATGAACTATACA-AGA-CTTATATGTGGCCTTTACATGCTCT
125 CCATCATA-ATTGAGGGAGACAAGTGGACTATACACA-ATC-TACACGTGACTTTTAAATGC-C-
*
18890 A-A-ACTTGTCCTAC
185 ACACACTTGTCCTAT
* * * * *
18903 AAGACTTGATGGCTATATAAGCCTCC--CAT-CATGAGGGAGACAAGTGAACTATACACAATCTA
1 GAGATTTGATGGTTATATAAGCCTCCATCATACTTGAGGGAGACAAGTGAACTATACACGATCTA
*** ** *
18965 CACGTGACCTTTACATGCTATGCACTTGTCCCATGAGA-TCTGAGGGGC-ATATAAGCCTCCCAT
66 CACGTGACCTTTACATGCTCCACACTTGTCCCACAAGACT-TGA-TGGCTATATAAGCCTCCCAT
* *
19028 CATAATTGGGGGGAGACAAGTGGACTAT-CTACAATATACACGTGACTTTTAAATGCCACACACT
129 CATAATT-GAGGGAGACAAGTGGACTATAC-ACAATCTACACGTGACTTTTAAATGCCACACACT
19092 TGTCCTAT
192 TGTCCTAT
* * * * *
19100 GAGATTTGATGGTTATATAAACCTCTCGTCATAACTTAAGGGAAACAAGTGAACTATACATGA-C
1 GAGATTTGATGGTTATATAAGCCTC-CATCAT-ACTTGAGGGAGACAAGTGAACTATACACGATC
* * * * *
19164 TTACACGTGGCCTTTACATGCTCCACACTTATCCCACAAAACTTTATGGCTATATAATCCTCCCA
64 -TACACGTGACCTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTATATAAGCCTCCCA
* * *
19229 TTATAACTTAAGGGAGACAAG-GGAACTATACACAATCCACACGTGAC
128 TCATAA-TTGAGGGAGACAAGTGG-ACTATACACAATCTACACGTGAC
19276 CTTCTACATG
Statistics
Matches: 623, Mismatches: 114, Indels: 80
0.76 0.14 0.10
Matches are distributed among these distances:
195 1 0.00
196 7 0.01
197 132 0.21
198 8 0.01
199 6 0.01
200 7 0.01
201 20 0.03
202 404 0.65
203 36 0.06
204 2 0.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (199 bp):
GAGATTTGATGGTTATATAAGCCTCCATCATACTTGAGGGAGACAAGTGAACTATACACGATCTA
CACGTGACCTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTATATAAGCCTCCCATCA
TAATTGAGGGAGACAAGTGGACTATACACAATCTACACGTGACTTTTAAATGCCACACACTTGTC
CTAT
Found at i:18821 original size:303 final size:302
Alignment explanation
Indices: 18310--19441 Score: 1373
Period size: 303 Copynumber: 3.7 Consensus size: 302
18300 ATTTGACGAT
* * * * * *
18310 TATATAAACCTTCCATCATAATTTGAGGAAGATAAGTGAACTATACACGATCTACACGTGACTTT
1 TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACACGTGACTTT
* * *
18375 TACATGCTACACACTTGTCCCATGAGATTTGAGGGGCATATAAGCCTCCAATTATAATTGGGGGA
66 TACATGCTACACACTTGTCCCATGAGATTTGAGGGGCATATAAGCCTCCTATCATAATTGAGGGA
* * * * * * *
18440 GACAAGTGGACTATACAAGATCTACAACGTGACTATTAAATGCCACACACTTGTCCTATGAGATT
131 GACAAGTGGACAATACACGATATAC-ACGTGACTTTTAAATCCCACACACTTGTCCTACGAAATT
* * * * *
18505 TGATGGTTATATAAGCCTTCCATCATAGCTTGAGGGAGACAAATGAATTATACATGACTTACACG
195 TGATGGCTATATAAACCTCCCATCATAACTTGAGGGAGACAAATGAACTATACATGACTTACACG
*
18570 TGGCCTTTACATGCTCTGCACTTGTCCTACAAGACTTGATGGC
260 TGGCCTTTACATGCTCTACACTTGTCCTACAAGACTTGATGGC
* *
18613 TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACATGTGATTTT
1 TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACACGTGACTTT
*
18678 TACATGCTACACATTTGTCCCATGAGATTTGAGGGGCATATAAGCCTCCTATCATAATTAGAGGG
66 TACATGCTACACACTTGTCCCATGAGATTTGAGGGGCATATAAGCCTCCTATCATAATT-GAGGG
* * * *
18743 AGACAAGTAGACAATACACGATATGCACGTGACTTTTAAATCCCACACATTTATCCTACGAAATT
130 AGACAAGTGGACAATACACGATATACACGTGACTTTTAAATCCCACACACTTGTCCTACGAAATT
* * * * *
18808 TGATGGCTATATAAGCCTCCCATCATACCTTGAGGGAGACAAATGAACTATACAAGACTTATATG
195 TGATGGCTATATAAACCTCCCATCATAACTTGAGGGAGACAAATGAACTATACATGACTTACACG
*
18873 TGGCCTTTACATGCTCTAAACTTGTCCTACAAGACTTGATGGC
260 TGGCCTTTACATGCTCTACACTTGTCCTACAAGACTTGATGGC
*
18916 TATATAAGCCTCCCATC---A--TGAGGGAGACAAGTGAACTATACACAATCTACACGTGACCTT
1 TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACACGTGACTTT
** * * *
18976 TACATGCTATGCACTTGTCCCATGAGATCTGAGGGGCATATAAGCCTCCCATCATAATTGGGGGG
66 TACATGCTACACACTTGTCCCATGAGATTTGAGGGGCATATAAGCCTCCTATCATAATT-GAGGG
* * * * *
19041 AGACAAGTGGACTAT-CTACAATATACACGTGACTTTTAAATGCCACACACTTGTCCTATGAGAT
130 AGACAAGTGGACAATAC-ACGATATACACGTGACTTTTAAATCCCACACACTTGTCCTACGAAAT
* * * * * *
19105 TTGATGGTTATATAAACCTCTCGTCATAACTTAAGGGAAACAAGTGAACTATACATGACTTACAC
194 TTGATGGCTATATAAACCTCCCATCATAACTTGAGGGAGACAAATGAACTATACATGACTTACAC
* * * * *
19170 GTGGCCTTTACATGCTCCACACTTATCCCACAAAACTTTATGGC
259 GTGGCCTTTACATGCTCTACACTTGTCCTACAAGACTTGATGGC
* * * * *
19214 TATATAATCCTCCCATTATAACTTAAGGGAGACAAGGGAACTATACACAATCCACACGTGACCTT
1 TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACACGTGA-CTT
* * * * ** * * **
19279 CTACATGCTCCACACTTGCCCCACT-AAATTTGAAAGTCATATAAGACTTTTA-CTATAATTGAA
65 TTACATGCTACACACTTGTCCCA-TGAGATTTGAGGGGCATATAAGCCTCCTATC-ATAATTG-A
* * * * * **
19342 GGGAGACAAGTGAACAACACACGATTTACATGTGACATTTGCA-CGCCACACACTTGTCCTACGA
127 GGGAGACAAGTGGACAATACACGATATACACGTGACTTTTAAATC-CCACACACTTGTCCTACGA
* * *
19406 AATTTGATGACTACATAAACCTCCCATTCTTAACTT
191 AATTTGATGGCTATATAAACCTCCCA-TCATAACTT
19442 AAAGATAAAA
Statistics
Matches: 708, Mismatches: 107, Indels: 26
0.84 0.13 0.03
Matches are distributed among these distances:
297 1 0.00
298 257 0.36
300 1 0.00
301 1 0.00
303 299 0.42
304 139 0.20
305 10 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (302 bp):
TATATAAGCCTCCCATCATAACTTGAGGGAGACAAGTGAACTATACACAATCTACACGTGACTTT
TACATGCTACACACTTGTCCCATGAGATTTGAGGGGCATATAAGCCTCCTATCATAATTGAGGGA
GACAAGTGGACAATACACGATATACACGTGACTTTTAAATCCCACACACTTGTCCTACGAAATTT
GATGGCTATATAAACCTCCCATCATAACTTGAGGGAGACAAATGAACTATACATGACTTACACGT
GGCCTTTACATGCTCTACACTTGTCCTACAAGACTTGATGGC
Found at i:19751 original size:18 final size:18
Alignment explanation
Indices: 19725--19762 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
19715 TTCATTAAAC
*
19725 TTTAGAATTTT-ACGATAA
1 TTTAAAATTTTCAC-ATAA
19743 TTTAAAATTTTCACATAA
1 TTTAAAATTTTCACATAA
19761 TT
1 TT
19763 ATATATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.47
Consensus pattern (18 bp):
TTTAAAATTTTCACATAA
Found at i:32063 original size:19 final size:19
Alignment explanation
Indices: 32039--32085 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
32029 TTTGAATTTT
32039 AATTTTCAAAAAATTAGCA
1 AATTTTCAAAAAATTAGCA
32058 AATTTTCAAAAAATTAGCA
1 AATTTTCAAAAAATTAGCA
32077 AATTTTCAA
1 AATTTTCAA
32086 TTGAATCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (19 bp):
AATTTTCAAAAAATTAGCA
Found at i:33376 original size:16 final size:16
Alignment explanation
Indices: 33357--33400 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
33347 TCTTTTTTTG
33357 TTGAATCATTTTAAGT
1 TTGAATCATTTTAAGT
* **
33373 TTGAATAATTTCGAGT
1 TTGAATCATTTTAAGT
*
33389 TTCAATCATTTT
1 TTGAATCATTTT
33401 GGATTATTTG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (16 bp):
TTGAATCATTTTAAGT
Done.